Genome: /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/data/Pocillopora_meandrina_HIv1.assembly.fa
Alignments: /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/merged_alignments.bam
Location: Pocillopora_meandrina_HIv1___Sc0000024:4808666-4808760 plus
PDF file name: /home/shared/8TB_HDD_02/shedurkin/timeseries_molecular/F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/strucVis/Cluster_5627.ps.pdf
Locus Name: Cluster_5627
UUUGUACUUACCCCUGCCGUCCAGAACCCAAGAAUCUCGAAGGUUUUUAAAACCUUCAAGGUUCUGGGGUUAUACGGCUUGGGUACAAACACUCU
..(((...(((((..(((((....(((((.(((((((.((((((((...)))))))).))))))).)))))..)))))..)))))...))).... (-42.70)
.UUGUACUUACCCCUGCCGUCC......................................................................... len:21 al:3
.UUGUACUUACCCCUGCCGUCu......................................................................... len:21 al:1
..UGUACUUACCCCUGCCGUCC......................................................................... len:20 al:2
...GUACUUACCCCUGCCGUCu......................................................................... len:19 al:1
...GUACUUACCCCUGCCGUCa......................................................................... len:19 al:1
...GUACUUACCCCUGCCGUCC......................................................................... len:19 al:1
....UACUUACCCCUGCCGUCC......................................................................... len:18 al:1
........UACCCCUGCCGUCCAGAA..................................................................... len:18 al:1
....................uCAGAACCCAAGAAUCUCGAAGG.................................................... len:23 al:1
.....................CAGAACCCAAGAAUCUCGA....................................................... len:19 al:3
.....................CAGAACCCAAGAAUCUCGAAGG.................................................... len:22 al:13
.....................CAGAACCCAAGAAUCUCGAAGGU................................................... len:23 al:2
.....................CAGAACCCAAGAAUC........................................................... len:15 al:1
.....................CAGAACCCAAGAAUCUCGAAGGUU.................................................. len:24 al:3
.....................CAGcACCCAAGAAUCUCGA....................................................... len:19 al:1
.....................CAGAACCCAAGAAUCUCGAAG..................................................... len:21 al:11
.....................CAGAACCCAAGAAUCUCGAAGuUUU................................................. len:25 al:2
.....................CAGAACCCAAGAAUCUCGAu...................................................... len:20 al:2
......................AGAuCCCAAGAAUCUCGAA...................................................... len:19 al:1
......................AaAACCCAAGAAUCUCGAA...................................................... len:19 al:2
......................AGAACuCAAGAAUCUCGAAGGUU.................................................. len:23 al:1
......................AGAACCCAAGAAUCUCGA....................................................... len:18 al:2558
......................gGAACCCAAGAAUCUCGAA...................................................... len:19 al:5
......................AGAACCCAAGAAcCUCGAAGG.................................................... len:21 al:4
......................AGAACCCAAGAAcCUCGAA...................................................... len:19 al:2
......................AGAACCCAAGAAUCUCG........................................................ len:17 al:11
......................AGAACCCAAGAAgCUCGAAGG.................................................... len:21 al:1
......................AGAACCCuAGAAUCUCGAA...................................................... len:19 al:1
......................AaAACCCAAGAAUCUCGA....................................................... len:18 al:5
......................AGAACCCAAGAAUCUCGAcG..................................................... len:20 al:1
......................AGAACCCAAGAAUCUCGuAGG.................................................... len:21 al:1
......................AGAACCCAAGAAUCUC......................................................... len:16 al:11
......................AGAACCCcAGAAUCUCGA....................................................... len:18 al:3
......................AGAACCCAAGAAUCUCGAAGG.................................................... len:21 al:2542
......................AGAACCCgAGAAUCUCGAAGGUU.................................................. len:23 al:1
......................AGAACCCAAGAAUCaCGAAGG.................................................... len:21 al:1
......................AGAACCCAgGAAUCUCGA....................................................... len:18 al:7
......................AGgACCCAAGAAUCUCGAA...................................................... len:19 al:4
......................AGAACCCAAGAcUCUCGA....................................................... len:18 al:2
......................AGAuCCCAAGAAUCUCGAAGG.................................................... len:21 al:1
......................AGAACCCAAGAAUCUCGAAu..................................................... len:20 al:46
......................AGAACCCAAGAAUCUCGAAG..................................................... len:20 al:3894
......................AGAACCCAAGAAUuUCGAAG..................................................... len:20 al:11
......................AGAACCCAcGAAUCUCGAAGG.................................................... len:21 al:1
......................AGAACCaAAGAAUCUCGA....................................................... len:18 al:1
......................AGAgCCCAAGAAUCUCGAA...................................................... len:19 al:5
......................AGAACCuAAGAAUCUCGA....................................................... len:18 al:4
......................AGAACCCAAGAAUCcCGAAGG.................................................... len:21 al:7
......................AGAACCCAuGAAUCUCGA....................................................... len:18 al:1
......................AGAACCCAAGAAUCUCGAAGGUa.................................................. len:23 al:2
......................AGAACCCAAGcAUCUCGAAG..................................................... len:20 al:1
......................uGAACCCAAGAAUCUCGAAGG.................................................... len:21 al:5
......................AGAcCCCAAGAAUCUCGAA...................................................... len:19 al:1
......................AGgACCCAAGAAUCUCGA....................................................... len:18 al:13
......................AGAACCCAAuAAUCUCGAA...................................................... len:19 al:1
......................AGAACCCAAGAgUCUCGA....................................................... len:18 al:7
......................AGAACCCgAGAAUCUCGAA...................................................... len:19 al:2
......................AGAACCCAAGAAUCUuGA....................................................... len:18 al:6
......................AGAACCCAAGAAUCUCGAgG..................................................... len:20 al:22
......................AGAACCCAAGgAUCUCGA....................................................... len:18 al:2
......................AGAACCCgAGAAUCUCGAAGGU................................................... len:22 al:1
......................AGAACCCAgGAAUCUCGAAG..................................................... len:20 al:17
......................AGAACCCAAGAAUCUCGgA...................................................... len:19 al:5
......................AGAACCCAAGAAUCUCGAgGGU................................................... len:22 al:3
......................AGAACCCAAGAAUCUCGgAGG.................................................... len:21 al:4
......................AGAgCCCAAGAAUCUCGAAGG.................................................... len:21 al:9
......................AGAACCCAuGAAUCUCGAAGG.................................................... len:21 al:1
......................AGAACCCAAGAAUuUCGAA...................................................... len:19 al:3
......................AGAACCCAAGAAUCUuGAAGG.................................................... len:21 al:3
......................AGAACCCAAGAAUCUuGAAG..................................................... len:20 al:16
......................AGAACCCAgGAAUCUCGAAGG.................................................... len:21 al:12
......................AGAACCCAAGAAUCUCGAAGa.................................................... len:21 al:212
......................AGgACCCAAGAAUCUCGAAG..................................................... len:20 al:13
......................gGAACCCAAGAAUCUCGAAGG.................................................... len:21 al:9
......................AGAACCCAAGAAUCUCGAg...................................................... len:19 al:3
......................AGAACCCAAGAAUCUCGAAGuU................................................... len:22 al:1
......................AuAACCCAAGAAUCUCGAAGG.................................................... len:21 al:1
......................AGAACCCAAGAAUCcCGAAG..................................................... len:20 al:11
......................AGAgCCCAAGAAUCUCGAAG..................................................... len:20 al:2
......................AGAuCCCAAGAAUCUCGAAG..................................................... len:20 al:1
......................AGAACCCAAGgAUCUCGAAGG.................................................... len:21 al:10
......................AGAACCCAcGAAUCUCGAAG..................................................... len:20 al:2
......................AGAACCCAAGAAUuUCGAAGG.................................................... len:21 al:4
......................AGAcCCCAAGAAUCUCGAAGG.................................................... len:21 al:2
......................AuAACCCAAGAAUCUCGA....................................................... len:18 al:2
......................AGAcCCCAAGAAUCUCGAAG..................................................... len:20 al:4
......................AGAACuCAAGAAUCUCGAA...................................................... len:19 al:1
......................cGAACCCAAGAAUCUCGAAG..................................................... len:20 al:11
......................AGAACCCAcGAAUCUCGA....................................................... len:18 al:1
......................AGAACCCAAGAAUCUCGAAGGUUa................................................. len:24 al:1
......................AGAcCCCAAGAAUCUCGA....................................................... len:18 al:1
......................AGAACCCAAGAAUCUCuAAGG.................................................... len:21 al:1
......................AGAAuCCAAGAAUCUCGA....................................................... len:18 al:1
......................AGAACCCAuGAAUCUCGAA...................................................... len:19 al:1
......................AGAACCCAAGgAUCUCGAA...................................................... len:19 al:4
......................AGAACCCAAGAAUCgCGAA...................................................... len:19 al:1
......................AGAACCCAAGAAUCUCGAAaG.................................................... len:21 al:1
......................AGAACCCAAGAAUCUCaA....................................................... len:18 al:5
......................AGAACCCAAGAAUCUCGAu...................................................... len:19 al:51
......................AGAACCCAAGAgUCUCGAAGG.................................................... len:21 al:3
......................AGcACCCAAGAAUCUCGA....................................................... len:18 al:3
......................AGAACCCAAGAAUCUCcA....................................................... len:18 al:2
......................AGAACCCAAGAAUCUCu........................................................ len:17 al:1
......................gGAACCCAAGAAUCUCGA....................................................... len:18 al:15
......................AGAACuCAAGAAUCUCGAAG..................................................... len:20 al:4
......................AaAACCCAAGAAUCUCGAAG..................................................... len:20 al:9
......................AGAACCCcAGAAUCUCGAAGG.................................................... len:21 al:3
......................AGuACCCAAGAAUCUCGAAG..................................................... len:20 al:4
......................AGcACCCAAGAAUCUCGAAG..................................................... len:20 al:3
......................AGAACCCAAGAAUCUCGAAGu.................................................... len:21 al:69
......................AGAACCCAAGAAUCcCGA....................................................... len:18 al:7
......................AGAACCCAAGAAUCcCGAA...................................................... len:19 al:2
......................AGAACCaAAGAAUCUCGAAG..................................................... len:20 al:1
......................AGAACCCAAGAAUCUCGAcGG.................................................... len:21 al:1
......................AGAACCCAAGAAUCUCGAAGGaU.................................................. len:23 al:4
......................uGAACCCAAGAAUCUC......................................................... len:16 al:1
......................AGAACCCAAGAAUCUCGAAGGU................................................... len:22 al:120
......................AGAACCCAAGAAUuUCGA....................................................... len:18 al:5
......................AGAACCCAgGAAUCUCGAA...................................................... len:19 al:1
......................AGAACCCAAGAAUCUCGAAa..................................................... len:20 al:78
......................cGAACCCAAGAAUCUCGAA...................................................... len:19 al:3
......................AGAACCCAAGAAUCUCGg....................................................... len:18 al:8
......................AGAACCCAAaAAUCUCGAA...................................................... len:19 al:1
......................gGAACCCAAGAAUCUCGAAG..................................................... len:20 al:10
......................AGAACCCAAGAAUCUCGAgGG.................................................... len:21 al:6
......................AGAACCCgAGAAUCUCGAAGG.................................................... len:21 al:11
......................AGAACCCAAGAcUCUCGAAG..................................................... len:20 al:6
......................uGAACCCAAGAAUCUCGA....................................................... len:18 al:3
......................AGAACCCAAGAAUCUCGAAGGc................................................... len:22 al:12
......................AGAACCCAAGAAUCUCGAAGGa................................................... len:22 al:5
......................AGAAgCCAAGAAUCUCGAAGG.................................................... len:21 al:1
......................AGAACCCAAGAAUCU.......................................................... len:15 al:2
......................AGAACCaAAGAAUCUCGAAGG.................................................... len:21 al:1
......................AGgACCCAAGAAUCUCGAAGG.................................................... len:21 al:8
......................AaAACCCAAGAAUCUCGAAGGU................................................... len:22 al:1
......................AGAACCCgAGAAUCUCGA....................................................... len:18 al:4
......................AGAACCCAAGgAUCUCGAAG..................................................... len:20 al:12
......................AGAACCCAAGAAUCUCaAAG..................................................... len:20 al:2
......................AGAACCCAAGAAUCUCGAc...................................................... len:19 al:2
......................AGAAuCCAAGAAUCUCGAAG..................................................... len:20 al:2
......................AGAACCCAAGAAUCaCGAAG..................................................... len:20 al:1
......................AGAACCCAAGAAUCUCGAAGGUUU................................................. len:24 al:1
......................AGAACCCAAGAAUCUCGAAGGUUUU................................................ len:25 al:16
......................AGAACCCAAGAAUCUCGAAc..................................................... len:20 al:15
......................AGAACCCAAGAAUCUCGAAGGUU.................................................. len:23 al:13
......................AGAACCCuAGAAUCUCGAAGG.................................................... len:21 al:2
......................AGAACCCAAGAAcCUCGA....................................................... len:18 al:5
......................uGAACCCAAGAAUCUCGAA...................................................... len:19 al:1
......................AGAAuCCAAGAAUCUCGAA...................................................... len:19 al:1
......................cGAACCCAAGAAUCUCGA....................................................... len:18 al:1
......................AaAACCCAAGAAUCUCGAAGG.................................................... len:21 al:9
......................AGAACCCAuGAAUCUCGAAG..................................................... len:20 al:1
......................AGAACCCcAGAAUCUCGAAG..................................................... len:20 al:2
......................AGAACCCAAGAAcCUCGAAG..................................................... len:20 al:14
......................AGcACCCAAGAAUCUCGAAGG.................................................... len:21 al:1
......................uGAACCCAAGAAUCUCGAAG..................................................... len:20 al:4
......................AGAACCCAAGAAUCUCGAAGc.................................................... len:21 al:8
......................AGAACCCAAGAAUCUCGu....................................................... len:18 al:52
......................AGAACCCAAGAgUCUCGAAG..................................................... len:20 al:8
......................cGAACCCAAGAAUCUCGAAGG.................................................... len:21 al:4
......................AGAACCCAAGAAUCUCGgAG..................................................... len:20 al:10
......................AGAACCCAAGAAUCUCGAA...................................................... len:19 al:1192
......................AGAgCCCAAGAAUCUCGA....................................................... len:18 al:4
......................AGAACCCgAGAAUCUCGAAG..................................................... len:20 al:11
......................AGAACCCAAGAAUCUCGAAcG.................................................... len:21 al:1
.......................GgACCCAAGAAUCUCGAA...................................................... len:18 al:1
.......................GAACCCAAGAAUCUCGAAGa.................................................... len:20 al:4
.......................GAACCCAAGAAUCUCGAAGGaU.................................................. len:22 al:1
.......................uAACCCAAGAAUCUCGAAG..................................................... len:19 al:1
.......................GAACCCAAGAAUCUCGAu...................................................... len:18 al:3
.......................GAACCCAAGAAUCUCGAAGu.................................................... len:20 al:6
.......................aAACCCAAGAAUCUCGAAG..................................................... len:19 al:1
.......................GAACCCAAuAAUCUCGAAG..................................................... len:19 al:1
.......................aAACCCAAGAAUCUCGAAGG.................................................... len:20 al:1
.......................GAACCCAAGAAcCUCGAA...................................................... len:18 al:1
.......................GAACCCgAGAAUCUCGAAG..................................................... len:19 al:1
.......................GAACCCAAGAAUCUCGAAu..................................................... len:19 al:1
.......................GAACCCAAGAAUCUCGAA...................................................... len:18 al:18
.......................GAACCCAAGgAUCUCGAAG..................................................... len:19 al:1
.......................GAACCCAAGAAUCUCGAAGG.................................................... len:20 al:1
.......................GAACCCAAGAAUCUCGAAa..................................................... len:19 al:2
.......................GAACCCAAGAAUCUCGAAG..................................................... len:19 al:144
.......................GgACCCAAGAAUCUCGAAG..................................................... len:19 al:2
.......................GAACCCAAGAAUCUCGA....................................................... len:17 al:1
........................AACCCAAGAAUCUCGAAG..................................................... len:18 al:9
........................AACCCAAGAAUCUCGAAGu.................................................... len:19 al:1
........................AACCCAAGAAUCcCGAAG..................................................... len:18 al:1
.........................ACCCAAGAAUCUCGAAG..................................................... len:17 al:1
.........................ACCCAAGAAUCUCGAAGGUUUUUAAAACCc........................................ len:30 al:1
.........................ACCCAAGAAUCUCGAAGGUUUUUAAAACC......................................... len:29 al:1
.........................ACCCAAGAAUCUCGAAGa.................................................... len:18 al:1
..........................CCCAAGAAUCUCGAAGGU................................................... len:18 al:1
...........................CCAAGAAUCUCGAAGGUU.................................................. len:18 al:2
...........................CCAAGAAUCUCGAAGGUUUUUAAAACCUUCA..................................... len:31 al:1
...........................CCAAGAAUCUCGAAGGUc.................................................. len:18 al:1
....................................................CCUUCAgGGUUCUGGGGUUAUA..................... len:22 al:1
....................................................CCUUCAAGGUUCUGGGaUU........................ len:19 al:1
....................................................CCUUCAAGGUUCUGGGGUUAUAa.................... len:23 al:1
....................................................CCUUCgAGGUUCUGGGGUUAUA..................... len:22 al:1
....................................................CCUUCAcGGUUCUGGGGUUAUA..................... len:22 al:1
....................................................CCUUCAAGGUUCUGGGGUUAU...................... len:21 al:14
....................................................CCUUCAAGGUUCUGGGGUU........................ len:19 al:4
....................................................CCUUCAAGGUUCcGGGGUUAUA..................... len:22 al:1
....................................................CCUUCAAGGUUCUGGGGUUAUA..................... len:22 al:153
....................................................CCUUCAAGGUUCUGGGGUUAUAu.................... len:23 al:8
....................................................CCUUCgAGGUUCUGGGGUUAU...................... len:21 al:1
....................................................CCUUCAAGGUUCUGGGGUUAUu..................... len:22 al:7
....................................................CCUUCAAGGUUCUGGGGUUcUA..................... len:22 al:1
....................................................CCUUCAAGGUUCUGGGGcUAUA..................... len:22 al:1
....................................................CCUUCAAGGUUCUGaGGUUAUA..................... len:22 al:1
....................................................CCUUCAAGGUUCUGGGGcU........................ len:19 al:1
.....................................................CUUCAAGGUUCUGGGGUU........................ len:18 al:1
.....................................................CUUCAAGGUUCUGGGGUUAUAu.................... len:22 al:1
......................................................UUCAAGGUUCUGGGGUUAUAu.................... len:21 al:19
......................................................UUCAAGGUUCUGGGGUUAcA..................... len:20 al:1
......................................................UUCAAGGUUCUGGGGUUAc...................... len:19 al:1
......................................................UUCAAGGUUCUGGGGUUAUAC.................... len:21 al:2
......................................................UUCAAGGUUCUGGGGUUAUu..................... len:20 al:4
......................................................UUCgAGGUUCUGGGGUUAUA..................... len:20 al:1
......................................................UUCAAGGUUCUGGaGUUAU...................... len:19 al:1
......................................................UUCAAGGUUCUGGGGcUAUA..................... len:20 al:1
......................................................UUCAAGGUUCUGGGGUUuU...................... len:19 al:1
......................................................UUCAAGGcUCUGGGGUUAUA..................... len:20 al:1
......................................................UUCAAGGUUCUGGGGUUAUAa.................... len:21 al:1
......................................................UcCAAGGUUCUGGGGUUAUA..................... len:20 al:1
......................................................UUCAAGGUUCUGGGGUUAUA..................... len:20 al:38
......................................................UUCAAGGUUCUGGGGUUA....................... len:18 al:6
......................................................UUCAAGGUUCUGGGGUUAU...................... len:19 al:15
.......................................................UCAAGGUUCUGGGGUUAUA..................... len:19 al:25
.......................................................UCAAGGUUCUGGGGcUAUA..................... len:19 al:1
.......................................................UCAAGGUUCUGGGGUUAU...................... len:18 al:2
........................................................CAAGGUUCUGGGGUUAUA..................... len:18 al:11
........................................................CAAGGUcCUGGGGUUAUA..................... len:18 al:1
.........................................................AAGGUUCUGGGGUUAUA..................... len:17 al:2
........................................................................UACGGCUUGGGUACAAACACU.. len:21 al:1
..........................................................................CGGCUUGGGUACAAACACU.. len:19 al:2
..........................................................................CGGCUUGGGUACAAACACUCU len:21 al:9
..........................................................................CGGCUUGGGUACAAACACUC. len:20 al:2
..........................................................................CGGCUUGGGUACAAgCACUC. len:20 al:1