Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 165 of 279
Found at i:54643521 original size:17 final size:18
Alignment explanation
Indices: 54643487--54643524 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54643477 GAAATTTTTA
*
54643487 TTTTAATGTTTTAGTATT
1 TTTTAATGTATTAGTATT
*
54643505 TTTTTATGTATTA-TATT
1 TTTTAATGTATTAGTATT
54643522 TTT
1 TTT
54643525 AAATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (18 bp):
TTTTAATGTATTAGTATT
Found at i:54645136 original size:21 final size:21
Alignment explanation
Indices: 54645112--54645155 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
54645102 ATTGGGCTGT
* *
54645112 TACACTCCACCTGTTTTGGAG
1 TACACTCCACCTGCTGTGGAG
54645133 TACACTCCACCTGCTGTGGAG
1 TACACTCCACCTGCTGTGGAG
54645154 TA
1 TA
54645156 TTGCTCGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TACACTCCACCTGCTGTGGAG
Found at i:54649232 original size:30 final size:30
Alignment explanation
Indices: 54649198--54649256 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
54649188 ACTTAACAAG
* *
54649198 CAAATACGTATAAAATAATAATAAAATTAA
1 CAAATACCTATAAAATAATAACAAAATTAA
*
54649228 CAAATACCTTTAAAATAATAACAAAATTA
1 CAAATACCTATAAAATAATAACAAAATTA
54649257 GCAATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTATAAAATAATAACAAAATTAA
Found at i:54649332 original size:22 final size:22
Alignment explanation
Indices: 54649287--54649337 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
54649277 CAATATTTAA
* *
54649287 AAAATAACAATAAAATAGTTGC
1 AAAATAAAAATAAAATAGTAGC
*
54649309 AACATAAAAATAAAATTA-TAGC
1 AAAATAAAAATAAAA-TAGTAGC
54649331 AAAATAA
1 AAAATAA
54649338 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.22
Consensus pattern (22 bp):
AAAATAAAAATAAAATAGTAGC
Found at i:54649496 original size:18 final size:19
Alignment explanation
Indices: 54649460--54649500 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54649450 GCCTGATTCA
*
54649460 TTTTTTAAATAGACTTTAT
1 TTTTTTAAATAAACTTTAT
*
54649479 TTTTTTATATAAAC-TTAT
1 TTTTTTAAATAAACTTTAT
54649497 TTTT
1 TTTT
54649501 CGAACTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTTAAATAAACTTTAT
Found at i:54651555 original size:420 final size:420
Alignment explanation
Indices: 54650776--54651613 Score: 1631
Period size: 420 Copynumber: 2.0 Consensus size: 420
54650766 TGTTGCTAAT
54650776 GTATACATATTTATTTACAGGAAAGTAGCCGATGATGATGAGTCAAAGAAGAGCAGAATGGTAAG
1 GTATACATATTTATTTACAGGAAAGTAGCCGATGATGATGAGTCAAAGAAGAGCAGAATGGTAAG
54650841 TTGATTCATTTTCTTTGGTATTTATCATGGATATGCCCTTTCTACTGTCCAACCTGAAAGCAGTT
66 TTGATTCATTTTCTTTGGTATTTATCATGGATATGCCCTTTCTACTGTCCAACCTGAAAGCAGTT
54650906 CGGGTTGGAGGACTTGGACTTATAAGAAGAATGCACTTGCAAGTTTGAAATTTTAATTTGCTGCC
131 CGGGTTGGAGGACTTGGACTTATAAGAAGAATGCACTTGCAAGTTTGAAATTTTAATTTGCTGCC
54650971 TTTAGTGACCAGTTTAAGTCTTGGTAGCAATTATAATTCATGCCACGAGTCGCTGACTACCTGAA
196 TTTAGTGACCAGTTTAAGTCTTGGTAGCAATTATAATTCATGCCACGAGTCGCTGACTACCTGAA
*
54651036 ATTGTGTTCACTCTGGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAG
261 ATTGTGTTCACTCTAGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAG
* *
54651101 AGGACGGGGTAGGGGCAGAGGTAGAGGTCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTG
326 AGGACGGGGTAGGGGCAGAGGTAAAGGGCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTG
*
54651166 CTGCACATTGTGGAAAGTTTGAAGATGATC
391 CTGCACATTGTGGAAAGTTCGAAGATGATC
54651196 GTATACATATTTATTTACAGGAAAGTAGCCGATGATGATGAGTCAAAGAAGAGCAGAATGGTAAG
1 GTATACATATTTATTTACAGGAAAGTAGCCGATGATGATGAGTCAAAGAAGAGCAGAATGGTAAG
54651261 TTGATTCATTTTCTTTGGTATTTATCATGGATATGCCCTTTCTACTGTCCAACCTGAAAGCAGTT
66 TTGATTCATTTTCTTTGGTATTTATCATGGATATGCCCTTTCTACTGTCCAACCTGAAAGCAGTT
54651326 CGGGTTGGAGGACTTGGACTTATAAGAAGAATGCACTTGCAAGTTTGAAATTTTAATTTGCTGCC
131 CGGGTTGGAGGACTTGGACTTATAAGAAGAATGCACTTGCAAGTTTGAAATTTTAATTTGCTGCC
*
54651391 TTTAGTGACCAGTTTAAGTCTTGGTAGCAATTATAATTCATGCCACGAGTCGCTGACTACCTGCA
196 TTTAGTGACCAGTTTAAGTCTTGGTAGCAATTATAATTCATGCCACGAGTCGCTGACTACCTGAA
54651456 ATTGTGTTCACTCTAGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAG
261 ATTGTGTTCACTCTAGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAG
54651521 AGGACGGGGTAGGGGCAGAGGTAAAGGGCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTG
326 AGGACGGGGTAGGGGCAGAGGTAAAGGGCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTG
54651586 CTGCACATTGTGGAAAGTTCGAAGATGA
391 CTGCACATTGTGGAAAGTTCGAAGATGA
54651614 CCCCGACATT
Statistics
Matches: 413, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
420 413 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (420 bp):
GTATACATATTTATTTACAGGAAAGTAGCCGATGATGATGAGTCAAAGAAGAGCAGAATGGTAAG
TTGATTCATTTTCTTTGGTATTTATCATGGATATGCCCTTTCTACTGTCCAACCTGAAAGCAGTT
CGGGTTGGAGGACTTGGACTTATAAGAAGAATGCACTTGCAAGTTTGAAATTTTAATTTGCTGCC
TTTAGTGACCAGTTTAAGTCTTGGTAGCAATTATAATTCATGCCACGAGTCGCTGACTACCTGAA
ATTGTGTTCACTCTAGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAG
AGGACGGGGTAGGGGCAGAGGTAAAGGGCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTG
CTGCACATTGTGGAAAGTTCGAAGATGATC
Found at i:54652142 original size:373 final size:373
Alignment explanation
Indices: 54651457--54652203 Score: 1467
Period size: 373 Copynumber: 2.0 Consensus size: 373
54651447 CTACCTGCAA
54651457 TTGTGTTCACTCTAGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAGA
1 TTGTGTTCACTCTAGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAGA
54651522 GGACGGGGTAGGGGCAGAGGTAAAGGGCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTGC
66 GGACGGGGTAGGGGCAGAGGTAAAGGGCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTGC
54651587 TGCACATTGTGGAAAGTTCGAAGATGACCCCGACATTTCTTATTTTGAAGAAAAGCATGATTTAA
131 TGCACATTGTGGAAAGTTCGAAGATGACCCCGACATTTCTTATTTTGAAGAAAAGCATGATTTAA
54651652 GCTTGGAAAGGCACGTGCCTGATGATGTGGTAGAGTCTGATGAGTCAAAGAAACATAATCATGCA
196 GCTTGGAAAGGCACGTGCCTGATGATGTGGTAGAGTCTGATGAGTCAAAGAAACATAATCATGCA
54651717 GGGAAGAACATCAAAACTCCAGTTCGGAACATTGACCTCAATGCAGACTTGGATGAGAATGGGGA
261 GGGAAGAACATCAAAACTCCAGTTCGGAACATTGACCTCAATGCAGACTTGGATGAGAATGGGGA
54651782 CTTGATCACATCCATTGCTGCTGCTAGTCCAAGAACAGATGACATGCC
326 CTTGATCACATCCATTGCTGCTGCTAGTCCAAGAACAGATGACATGCC
*
54651830 TTGTGTTCACTCTGGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAGA
1 TTGTGTTCACTCTAGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAGA
* *
54651895 GGACGGGGTAGGGGCAGAGGTAGAGGTCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTGC
66 GGACGGGGTAGGGGCAGAGGTAAAGGGCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTGC
54651960 TGCACATTGTGGAAAGTTCGAAGATGACCCCGACATTTCTTATTTTGAAGAAAAGCATGATTTAA
131 TGCACATTGTGGAAAGTTCGAAGATGACCCCGACATTTCTTATTTTGAAGAAAAGCATGATTTAA
54652025 GCTTGGAAAGGCACGTGCCTGATGATGTGGTAGAGTCTGATGAGTCAAAGAAACATAATCATGCA
196 GCTTGGAAAGGCACGTGCCTGATGATGTGGTAGAGTCTGATGAGTCAAAGAAACATAATCATGCA
54652090 GGGAAGAACATCAAAACTCCAGTTCGGAACATTGACCTCAATGCAGACTTGGATGAGAATGGGGA
261 GGGAAGAACATCAAAACTCCAGTTCGGAACATTGACCTCAATGCAGACTTGGATGAGAATGGGGA
54652155 CTTGATCACATCCATTGCTGCTGCTAGTCCAAGAACAGATGACATGCC
326 CTTGATCACATCCATTGCTGCTGCTAGTCCAAGAACAGATGACATGCC
54652203 T
1 T
54652204 GAAAATAGTG
Statistics
Matches: 371, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
373 371 1.00
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (373 bp):
TTGTGTTCACTCTAGCTTTTTCTTTTTTGTAGCATGAGAGTTGCCATGTTACTAGCTCAAGCAGA
GGACGGGGTAGGGGCAGAGGTAAAGGGCAAGGTAGAGGGAGACAAACAGCAGGGAGAGAGACTGC
TGCACATTGTGGAAAGTTCGAAGATGACCCCGACATTTCTTATTTTGAAGAAAAGCATGATTTAA
GCTTGGAAAGGCACGTGCCTGATGATGTGGTAGAGTCTGATGAGTCAAAGAAACATAATCATGCA
GGGAAGAACATCAAAACTCCAGTTCGGAACATTGACCTCAATGCAGACTTGGATGAGAATGGGGA
CTTGATCACATCCATTGCTGCTGCTAGTCCAAGAACAGATGACATGCC
Found at i:54679236 original size:18 final size:18
Alignment explanation
Indices: 54679213--54679269 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
54679203 CCCAACTACT
* *
54679213 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTGCC
54679231 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
54679249 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
54679267 GTA
1 GTA
54679270 AACGGTCGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTGCC
Found at i:54690590 original size:18 final size:18
Alignment explanation
Indices: 54690567--54690604 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
54690557 CGCAGAATCC
54690567 GAAACAGAGAGCAGAAAT
1 GAAACAGAGAGCAGAAAT
54690585 GAAACAGAGAGCAGAAAT
1 GAAACAGAGAGCAGAAAT
54690603 GA
1 GA
54690605 TCAATAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.29, T:0.05
Consensus pattern (18 bp):
GAAACAGAGAGCAGAAAT
Found at i:54692217 original size:17 final size:17
Alignment explanation
Indices: 54692183--54692216 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54692173 TCCAAATACC
*
54692183 TCGATTTGGATCGATTT
1 TCGATTTGGATCAATTT
54692200 TCGATTTGG-TCAATTT
1 TCGATTTGGATCAATTT
54692216 T
1 T
54692217 TTTACTCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.18, C:0.12, G:0.21, T:0.50
Consensus pattern (17 bp):
TCGATTTGGATCAATTT
Found at i:54694023 original size:11 final size:11
Alignment explanation
Indices: 54694007--54694036 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
54693997 AAAGTACGAA
54694007 AAAATAATATT
1 AAAATAATATT
*
54694018 AAAATAATGTT
1 AAAATAATATT
54694029 AAAATAAT
1 AAAATAAT
54694037 TGAAAGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
AAAATAATATT
Found at i:54694498 original size:21 final size:21
Alignment explanation
Indices: 54694455--54694498 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
54694445 ACTTTGGACT
* **
54694455 AAAAATGAAAATAATTCCCTA
1 AAAAATGAAAATAATACAATA
*
54694476 AAAAATGAAAATAATAGAATA
1 AAAAATGAAAATAATACAATA
54694497 AA
1 AA
54694499 TTTGATAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAATGAAAATAATACAATA
Found at i:54696400 original size:26 final size:27
Alignment explanation
Indices: 54696371--54696465 Score: 79
Period size: 29 Copynumber: 3.4 Consensus size: 27
54696361 TATCAAAGAT
*
54696371 TTTATTGATTAAA-ATATATATATT-TA
1 TTTATTAATTAAATATAT-TATATTATA
*
54696397 TTTAATAATTAAATATATTATATTATA
1 TTTATTAATTAAATATATTATATTATA
* *
54696424 TTATATT-CTTATATTATTATTATATTATA
1 TT-TATTAATTA-AATA-TATTATATTATA
54696453 TTATATTATATTA
1 TT-TATTA-ATTA
54696466 TATAAAAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
26 17 0.30
27 11 0.20
28 6 0.11
29 19 0.34
31 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTATTAATTAAATATATTATATTATA
Found at i:54696420 original size:5 final size:5
Alignment explanation
Indices: 54696410--54696468 Score: 86
Period size: 5 Copynumber: 12.0 Consensus size: 5
54696400 AATAATTAAA
*
54696410 TATAT TATAT TATAT TATA- T-TCT TATAT TATTAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT
54696459 TATAT TATAT
1 TATAT TATAT
54696469 AAAAGAAACA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 41 0.84
6 5 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:54697556 original size:12 final size:12
Alignment explanation
Indices: 54697539--54697563 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54697529 GCCGACTACT
54697539 GTTACTGTTACC
1 GTTACTGTTACC
54697551 GTTACTGTTACC
1 GTTACTGTTACC
54697563 G
1 G
54697564 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:54699751 original size:5 final size:5
Alignment explanation
Indices: 54699715--54699744 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
54699705 CTTATGTTTT
54699715 ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
54699745 TAATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:54700458 original size:19 final size:19
Alignment explanation
Indices: 54700434--54700470 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54700424 TATTTCTTAT
54700434 ATTTTTTACAATGTTTTAA
1 ATTTTTTACAATGTTTTAA
* *
54700453 ATTTTTTTCAATTTTTTA
1 ATTTTTTACAATGTTTTA
54700471 TGAATAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTTTACAATGTTTTAA
Found at i:54702626 original size:11 final size:11
Alignment explanation
Indices: 54702610--54702634 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54702600 TAATATAACT
54702610 ATTATTTTATA
1 ATTATTTTATA
54702621 ATTATTTTATA
1 ATTATTTTATA
54702632 ATT
1 ATT
54702635 CGTTAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTTTATA
Found at i:54703178 original size:18 final size:19
Alignment explanation
Indices: 54703146--54703185 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
54703136 ATTACAAAAT
*
54703146 AAATTCAAAATTATTTTTA
1 AAATTCAAAATTATTTATA
54703165 AAATTCAAAA-TATTTATA
1 AAATTCAAAATTATTTATA
54703183 AAA
1 AAA
54703186 ATTTCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTCAAAATTATTTATA
Found at i:54703186 original size:19 final size:19
Alignment explanation
Indices: 54703146--54703193 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
54703136 ATTACAAAAT
*
54703146 AAATTCAAAATTATTTTTA
1 AAATTCAAAATTATTTTAA
54703165 AAATTCAAAA-TATTTATAA
1 AAATTCAAAATTATTT-TAA
54703184 AAATTTCAAA
1 AAA-TTCAAA
54703194 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 15 0.58
20 6 0.23
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTCAAAATTATTTTAA
Found at i:54703220 original size:32 final size:33
Alignment explanation
Indices: 54703182--54703246 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
54703172 AAATATTTAT
* *
54703182 AAAAATTTCAAATTTT-AAATTTTT-AAAAATA
1 AAAAAATTAAAATTTTAAAATTTTTCAAAAATA
*
54703213 AAAAAATTAAAATTTTAAAATTTTTCTAAAATA
1 AAAAAATTAAAATTTTAAAATTTTTCAAAAATA
54703246 A
1 A
54703247 TAATTTTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 14 0.48
32 8 0.28
33 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (33 bp):
AAAAAATTAAAATTTTAAAATTTTTCAAAAATA
Found at i:54704476 original size:3 final size:3
Alignment explanation
Indices: 54704470--54704503 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
54704460 TAATAATAAT
54704470 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
54704504 ATAATGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54704658 original size:15 final size:15
Alignment explanation
Indices: 54704638--54704670 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
54704628 GGCAAATATA
54704638 AATATAAATATAAAT
1 AATATAAATATAAAT
*
54704653 AATATAAATTTAAAT
1 AATATAAATATAAAT
54704668 AAT
1 AAT
54704671 TATTTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATAAATATAAAT
Found at i:54724170 original size:22 final size:22
Alignment explanation
Indices: 54724142--54724184 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
54724132 TTAGTTAAAT
54724142 ATAATTTTCTCTGTGTTGTGTC
1 ATAATTTTCTCTGTGTTGTGTC
54724164 ATAATTTTCTCTGTGTTGTGT
1 ATAATTTTCTCTGTGTTGTGT
54724185 TCCCAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.12, G:0.19, T:0.56
Consensus pattern (22 bp):
ATAATTTTCTCTGTGTTGTGTC
Found at i:54726290 original size:33 final size:33
Alignment explanation
Indices: 54726253--54726320 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
54726243 TTAAAAAGGA
54726253 ATAAATTATTACATTAATTATATTTTACCTTTT
1 ATAAATTATTACATTAATTATATTTTACCTTTT
*
54726286 ATAAATTATTACATTAATTATATTTTATCTTTT
1 ATAAATTATTACATTAATTATATTTTACCTTTT
54726319 AT
1 AT
54726321 GTTAAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (33 bp):
ATAAATTATTACATTAATTATATTTTACCTTTT
Found at i:54726306 original size:19 final size:19
Alignment explanation
Indices: 54726253--54726307 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 19
54726243 TTAAAAAGGA
54726253 ATAAATTATTACATTAATT
1 ATAAATTATTACATTAATT
*
54726272 AT--ATT-TTACCTT--TT
1 ATAAATTATTACATTAATT
54726286 ATAAATTATTACATTAATT
1 ATAAATTATTACATTAATT
54726305 ATA
1 ATA
54726308 TTTTATCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 4 0.14
16 9 0.31
17 9 0.31
19 7 0.24
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAAATTATTACATTAATT
Found at i:54730184 original size:34 final size:34
Alignment explanation
Indices: 54730145--54730213 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
54730135 GAAACATTAC
*
54730145 CATCTTGGTGCATTGATATAATCATTGATATGAT
1 CATCTTGGTACATTGATATAATCATTGATATGAT
54730179 CATCTTGGTACATTGATATAATCATTGATATGAT
1 CATCTTGGTACATTGATATAATCATTGATATGAT
54730213 C
1 C
54730214 TTTGTTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (34 bp):
CATCTTGGTACATTGATATAATCATTGATATGAT
Found at i:54734217 original size:6 final size:6
Alignment explanation
Indices: 54734208--54734241 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
54734198 CTAAATGATA
54734208 TATATG TATATG TATATG TATATG TATATG TATA
1 TATATG TATATG TATATG TATATG TATATG TATA
54734242 CATGTGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:54739102 original size:23 final size:22
Alignment explanation
Indices: 54739067--54739137 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 22
54739057 ATTTTTAATT
*
54739067 TATTTTGAA-ATATTTATTTTAA
1 TATTTTTAATATATTTATTTT-A
54739089 TATTTTTAATATATTTGATGTATTA
1 TATTTTTAATATATTT-AT-T-TTA
*
54739114 TATTTTT--TAAATTTATTTTTA
1 TATTTTTAATATATTTA-TTTTA
54739135 TAT
1 TAT
54739138 AAAAATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
21 6 0.14
22 10 0.24
23 13 0.31
24 2 0.05
25 9 0.21
26 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
TATTTTTAATATATTTATTTTA
Found at i:54743091 original size:3 final size:3
Alignment explanation
Indices: 54743083--54743146 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
54743073 GGGAGGTAAG
54743083 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
54743131 GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA G
54743147 CAGGAGGAGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:54746549 original size:25 final size:25
Alignment explanation
Indices: 54746504--54746567 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
54746494 TTTTATTTAT
* *
54746504 AAAAATAAAAATGTATGTAATAATAA
1 AAAAAT-AAAATGGATATAATAATAA
* * *
54746530 TATAATAAAATGGATATAATATTAA
1 AAAAATAAAATGGATATAATAATAA
54746555 AAAAATAAAATGG
1 AAAAATAAAATGG
54746568 GAAAAAGAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (25 bp):
AAAAATAAAATGGATATAATAATAA
Found at i:54746925 original size:20 final size:20
Alignment explanation
Indices: 54746902--54746949 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
54746892 TTTTTTCATC
* *
54746902 TTCATTTTTATTTTTTGGAT
1 TTCATTTTCATTTTTAGGAT
*
54746922 TTCATTATTCCTTTTTAGGAT
1 TTCATT-TTCATTTTTAGGAT
54746943 TTC-TTTT
1 TTCATTTT
54746950 GTTTGATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 8 0.33
21 14 0.58
ACGTcount: A:0.15, C:0.10, G:0.08, T:0.67
Consensus pattern (20 bp):
TTCATTTTCATTTTTAGGAT
Found at i:54756946 original size:20 final size:20
Alignment explanation
Indices: 54756921--54756963 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
54756911 ACAAGCAATA
54756921 TTAACAGATGGATAAAAAAT
1 TTAACAGATGGATAAAAAAT
54756941 TTAACAGATGGATAAAAAAT
1 TTAACAGATGGATAAAAAAT
54756961 TTA
1 TTA
54756964 TAGGGGATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (20 bp):
TTAACAGATGGATAAAAAAT
Found at i:54763775 original size:23 final size:23
Alignment explanation
Indices: 54763736--54763781 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
54763726 TCTTTTAAAA
* *
54763736 TATTAATTTAATTAAATATTGCC
1 TATTAATTTAATAAAATAATGCC
54763759 TATTAATATTAA-AAAATAATGCC
1 TATTAAT-TTAATAAAATAATGCC
54763782 CACAACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (23 bp):
TATTAATTTAATAAAATAATGCC
Found at i:54763953 original size:28 final size:29
Alignment explanation
Indices: 54763919--54763994 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
54763909 ATTTATAATG
54763919 ATAAAAA-TTACATTTTAATC-TTAAAAATA
1 ATAAAAATTTA-A-TTTAATCTTTAAAAATA
*
54763948 ATAAAAATTTAATTTAATCTTTTAAAAATT
1 ATAAAAATTTAATTTAATC-TTTAAAAATA
* *
54763978 ATAAAAATATAAGTTAA
1 ATAAAAATTTAATTTAA
54763995 AATGGTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.17
29 8 0.20
30 26 0.63
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (29 bp):
ATAAAAATTTAATTTAATCTTTAAAAATA
Found at i:54772373 original size:22 final size:21
Alignment explanation
Indices: 54772339--54772383 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
54772329 CCTACTATTT
* *
54772339 TATTTTTTGCTATTTTCTTGG
1 TATTTTTTACTATTATCTTGG
*
54772360 TATTTTTTCACTATTATGTTGG
1 TATTTTTT-ACTATTATCTTGG
54772382 TA
1 TA
54772384 CTATTATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.16, C:0.09, G:0.13, T:0.62
Consensus pattern (21 bp):
TATTTTTTACTATTATCTTGG
Found at i:54773669 original size:31 final size:32
Alignment explanation
Indices: 54773613--54773672 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
54773603 CCAATATTTG
*
54773613 ATAAAAAAATTATATATTTTGATATTTAAAAA
1 ATAAAAAAATTATATATTTTAATATTTAAAAA
* *
54773645 ATAAAAATATTA-ATTTTTTAATATTTAA
1 ATAAAAAAATTATATATTTTAATATTTAA
54773673 TACAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (32 bp):
ATAAAAAAATTATATATTTTAATATTTAAAAA
Found at i:54775271 original size:7 final size:7
Alignment explanation
Indices: 54775254--54775286 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
54775244 TCTCTCTCTC
54775254 TTTTTTA
1 TTTTTTA
54775261 -TTTTTA
1 TTTTTTA
54775267 TTTTTTA
1 TTTTTTA
54775274 TTTTTTTA
1 -TTTTTTA
54775282 TTTTT
1 TTTTT
54775287 ATCCTGCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:54787387 original size:20 final size:21
Alignment explanation
Indices: 54787362--54787403 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
54787352 GACCTAAAAA
54787362 TAAATATTAA-TAAAT-TTATT
1 TAAATA-TAATTAAATATTATT
54787382 TAAATATAATTAAATATTATT
1 TAAATATAATTAAATATTATT
54787403 T
1 T
54787404 GTAATTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 11 0.55
21 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATATAATTAAATATTATT
Found at i:54787824 original size:21 final size:20
Alignment explanation
Indices: 54787784--54787824 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
54787774 CTACCCAAAT
* *
54787784 CCTAGCCCAATAACAGAAAC
1 CCTAGCCCAATAAAAAAAAC
54787804 CCTAGCCCAAATAAAAAAAAC
1 CCTAGCCC-AATAAAAAAAAC
54787825 AAAATGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.51, C:0.32, G:0.07, T:0.10
Consensus pattern (20 bp):
CCTAGCCCAATAAAAAAAAC
Found at i:54789391 original size:24 final size:23
Alignment explanation
Indices: 54789364--54789410 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
54789354 ACATATGCAC
54789364 ATACTTACA-TCTTTATTTTATATA
1 ATACTTACAGT-TTT-TTTTATATA
*
54789388 ATACTTATAGTTTTTTTTATATA
1 ATACTTACAGTTTTTTTTATATA
54789411 TGTATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 11 0.52
25 1 0.05
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (23 bp):
ATACTTACAGTTTTTTTTATATA
Found at i:54796297 original size:3 final size:3
Alignment explanation
Indices: 54796289--54796556 Score: 536
Period size: 3 Copynumber: 89.3 Consensus size: 3
54796279 CTTGTGACGG
54796289 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54796337 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54796385 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54796433 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54796481 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54796529 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
54796557 ATGTTTAAAA
Statistics
Matches: 265, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 265 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:54801772 original size:22 final size:24
Alignment explanation
Indices: 54801725--54801773 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
54801715 ATAATATAAA
54801725 TAATAACTAGTAAAAAAGAAAGAG
1 TAATAACTAGTAAAAAAGAAAGAG
*
54801749 TAAT-ACT-GTAATAAA-AAAGAAG
1 TAATAACTAGTAAAAAAGAAAG-AG
54801771 TAA
1 TAA
54801774 AATTTATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 12 0.52
23 3 0.13
24 4 0.17
ACGTcount: A:0.61, C:0.04, G:0.14, T:0.20
Consensus pattern (24 bp):
TAATAACTAGTAAAAAAGAAAGAG
Found at i:54820522 original size:25 final size:25
Alignment explanation
Indices: 54820494--54820558 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
54820484 TCGAGCTATA
54820494 TAACGGGAAGCTCATGTAAGCC-AT
1 TAACGGGAAGCTCATGTAAGCCAAT
** *
54820518 GTAACGGGAAGCTTTTGTGAGCCAAT
1 -TAACGGGAAGCTCATGTAAGCCAAT
*
54820544 TATCGGGAAGCTCAT
1 TAACGGGAAGCTCAT
54820559 ACGAGCCATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 31 0.94
26 2 0.06
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (25 bp):
TAACGGGAAGCTCATGTAAGCCAAT
Found at i:54820564 original size:25 final size:24
Alignment explanation
Indices: 54820536--54820731 Score: 116
Period size: 25 Copynumber: 8.0 Consensus size: 24
54820526 AAGCTTTTGT
54820536 GAGCCAATTATCGGGAAGCTCATA
1 GAGCCAATTATCGGGAAGCTCATA
* * *
54820560 CGAGCC-ATAATGGGGAAGCTCAAGA
1 -GAGCCAATTATCGGGAAGCTC-ATA
* *
54820585 GAGCCAAATT-T-GGAAAGCTCATGC
1 GAGCC-AATTATCGGGAAGCTCAT-A
*
54820609 GAGCCAA-TATCGGGAAGCTCCGTA
1 GAGCCAATTATCGGGAAGCT-CATA
*
54820633 GAGCC-ATTAATCGGAAAGCTCATTA
1 GAGCCAATT-ATCGGGAAGCTCA-TA
* *
54820658 GAGCC-ATATATCAGGATGCTCATAA
1 GAGCCAAT-TATCGGGAAGCTCAT-A
* * *
54820683 GAGCTAAATAACGGGAAGCTCATGA
1 GAGCCAATTATCGGGAAGCTCAT-A
* * * *
54820708 GAGGCAAGTATCGAGACGCTCATA
1 GAGCCAATTATCGGGAAGCTCATA
54820732 AGAGTGGTGG
Statistics
Matches: 131, Mismatches: 27, Indels: 27
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.01
23 5 0.04
24 47 0.36
25 74 0.56
26 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (24 bp):
GAGCCAATTATCGGGAAGCTCATA
Found at i:54820636 original size:48 final size:48
Alignment explanation
Indices: 54820536--54820679 Score: 125
Period size: 48 Copynumber: 2.9 Consensus size: 48
54820526 AAGCTTTTGT
* * *
54820536 GAGCCAATTATCGGGAAGCTCATACGAGCC-ATAATGGGGAAGCTCAAGA
1 GAGCC-ATAATCGGAAAGCTCATACGAGCCAAT-ATCGGGAAGCTCAAGA
* * *
54820585 GAGCCA-AATTTGGAAAGCTCATGCGAGCCAATATCGGGAAGCTC-CGTA
1 GAGCCATAA-TCGGAAAGCTCATACGAGCCAATATCGGGAAGCTCAAG-A
* *
54820633 GAGCCATTAATCGGAAAGCTCATTA-GAGCCATATATCAGGATGCTCA
1 GAGCCA-TAATCGGAAAGCTCA-TACGAGCCA-ATATCGGGAAGCTCA
54820680 TAAGAGCTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
47 2 0.03
48 36 0.47
49 24 0.31
50 15 0.19
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (48 bp):
GAGCCATAATCGGAAAGCTCATACGAGCCAATATCGGGAAGCTCAAGA
Found at i:54822959 original size:18 final size:19
Alignment explanation
Indices: 54822938--54822987 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
54822928 ATGTATTAGA
54822938 TATTAAATAA-ATATTTAT
1 TATTAAATAAGATATTTAT
54822956 TATTTTATAA-AAGATATTTAT
1 TA--TTA-AATAAGATATTTAT
54822977 TAATTAAATAA
1 T-ATTAAATAA
54822988 TTATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 10 0.38
21 11 0.42
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTAAATAAGATATTTAT
Found at i:54825564 original size:25 final size:24
Alignment explanation
Indices: 54825530--54825632 Score: 99
Period size: 22 Copynumber: 4.4 Consensus size: 24
54825520 GACCTCAGCA
*
54825530 TGCTTTCTGATTATTAGCACATTTG
1 TGCTCTCTGA-TATTAGCACATTTG
* **
54825555 TGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTGATA-TTAGCACATTTG
54825580 TGCTCTCTG--ATTAGCACATTTG
1 TGCTCTCTGATATTAGCACATTTG
*
54825602 TGCTCTCTG-TA-TAGCAC-TTCAG
1 TGCTCTCTGATATTAGCACATT-TG
54825624 TGCTCTCTG
1 TGCTCTCTG
54825633 TTCATTAGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
21 2 0.03
22 34 0.51
23 2 0.03
24 2 0.03
25 27 0.40
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.41
Consensus pattern (24 bp):
TGCTCTCTGATATTAGCACATTTG
Found at i:54825640 original size:47 final size:46
Alignment explanation
Indices: 54825542--54825632 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 46
54825532 CTTTCTGATT
54825542 ATTAGCACATTTGTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTG
1 ATTAGCACATTTGTGCTCTCTGATA-TTAGCACGTCAGTGCTCTCTG
*
54825589 ATTAGCACATTTGTGCTCTCTG-TA-TAGCACTTCAGTGCTCTCTG
1 ATTAGCACATTTGTGCTCTCTGATATTAGCACGTCAGTGCTCTCTG
54825633 TTCATTAGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
44 19 0.44
46 2 0.05
47 22 0.51
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (46 bp):
ATTAGCACATTTGTGCTCTCTGATATTAGCACGTCAGTGCTCTCTG
Found at i:54828069 original size:18 final size:19
Alignment explanation
Indices: 54828048--54828097 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
54828038 ATGTATTAGA
54828048 TATTAAATAA-ATATTTAT
1 TATTAAATAAGATATTTAT
54828066 TATTTTATAA-AAGATATTTAT
1 TA--TTA-AATAAGATATTTAT
54828087 TAATTAAATAA
1 T-ATTAAATAA
54828098 TTATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 10 0.38
21 11 0.42
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTAAATAAGATATTTAT
Found at i:54846400 original size:16 final size:16
Alignment explanation
Indices: 54846367--54846400 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54846357 TATTTCTGTT
* *
54846367 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
54846383 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
54846399 AA
1 AA
54846401 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:54849228 original size:21 final size:21
Alignment explanation
Indices: 54849202--54849242 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54849192 AGACGAGCAA
* *
54849202 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
54849223 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
54849243 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:54858983 original size:30 final size:30
Alignment explanation
Indices: 54858947--54859005 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
54858937 AATCCCTATT
54858947 TTCATATTTTATGTGAATTGCAAAGTTTTG
1 TTCATATTTTATGTGAATTGCAAAGTTTTG
54858977 TTCATATTTTATGTGAATTGCAAAGTTTT
1 TTCATATTTTATGTGAATTGCAAAGTTTT
54859006 ACTCTTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (30 bp):
TTCATATTTTATGTGAATTGCAAAGTTTTG
Found at i:54871516 original size:18 final size:18
Alignment explanation
Indices: 54871478--54871516 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54871468 ATCTACTTAA
*
54871478 TATTTAAATAATTTTGGT
1 TATTTAAATAATTTTGAT
* *
54871496 TATTTTAATAATTTTTAT
1 TATTTAAATAATTTTGAT
54871514 TAT
1 TAT
54871517 ATTCACTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTTAAATAATTTTGAT
Found at i:54877565 original size:16 final size:17
Alignment explanation
Indices: 54877544--54877576 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54877534 AATGTCTGGG
54877544 AAAATTA-TTAATTGAT
1 AAAATTAGTTAATTGAT
54877560 AAAATTAGTTTAATTGA
1 AAAATTAG-TTAATTGA
54877577 GGGGTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
AAAATTAGTTAATTGAT
Found at i:54880601 original size:52 final size:49
Alignment explanation
Indices: 54880544--54880753 Score: 194
Period size: 52 Copynumber: 4.2 Consensus size: 49
54880534 CGTAAAAGAT
* *
54880544 GTGATATGTGCTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAA
1 GTGATATGTGATCCCGTATAAGACCATAGCTGGGCTATGGCTTCGGTG--A
* * ** *
54880595 CGTGATACGTGTTCTTGTATAAGACCATAGCTGGGCTATGGTTTCGGTGTGA
1 -GTGATATGTGATCCCGTATAAGACCATAGCTGGGCTATGGCTTC-G-GTGA
* * * *
54880647 TGTGATAATGTGATTCCGTATAGGACCATATCTGGGATATGGC-TCGGT-A
1 -GTGAT-ATGTGATCCCGTATAAGACCATAGCTGGGCTATGGCTTCGGTGA
* * * *
54880696 -TGATATGTGAT-CCGTGTAAGACCATGGCGGGGCTATGGCTTCGGTGT
1 GTGATATGTGATCCCGTATAAGACCATAGCTGGGCTATGGCTTCGGTGA
54880743 GTGATATGTGA
1 GTGATATGTGA
54880754 CTATGTGCAA
Statistics
Matches: 129, Mismatches: 23, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
45 22 0.17
46 12 0.09
47 4 0.03
48 10 0.08
49 1 0.01
50 2 0.02
51 1 0.01
52 46 0.36
53 28 0.22
54 3 0.02
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATCCCGTATAAGACCATAGCTGGGCTATGGCTTCGGTGA
Found at i:54894716 original size:18 final size:20
Alignment explanation
Indices: 54894679--54894717 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
54894669 TTGTTATTTT
*
54894679 TACATTGTTATTATTATATA
1 TACATTGTTATTAGTATATA
54894699 TACA-TGTT-TTAGTATATA
1 TACATTGTTATTAGTATATA
54894717 T
1 T
54894718 GTATATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 4 0.22
20 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (20 bp):
TACATTGTTATTAGTATATA
Found at i:54895074 original size:21 final size:21
Alignment explanation
Indices: 54895045--54895084 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54895035 ATTCATGTAT
*
54895045 TTTATTATATATGTATATATC
1 TTTAATATATATGTATATATC
*
54895066 TTTAATATATATTTATATA
1 TTTAATATATATGTATATA
54895085 AGTATATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTAATATATATGTATATATC
Found at i:54895184 original size:24 final size:25
Alignment explanation
Indices: 54895157--54895207 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
54895147 ATGTGTGTAC
*
54895157 ATATTATGTAAATGTTTTA-ATATT
1 ATATTATATAAATGTTTTATATATT
**
54895181 ATATTATATGTATGTTTTATATATT
1 ATATTATATAAATGTTTTATATATT
54895206 AT
1 AT
54895208 GAACATGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (25 bp):
ATATTATATAAATGTTTTATATATT
Found at i:54901576 original size:39 final size:40
Alignment explanation
Indices: 54901533--54901641 Score: 107
Period size: 38 Copynumber: 2.8 Consensus size: 40
54901523 GATAGTTTGT
*
54901533 AGTAATAGTTGACACCCAGTGTCTCATCG-GCCTAGCCGA
1 AGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGCCGA
** ** * *
54901572 AGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATCCGA
1 AGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGCCGA
*
54901611 AGAAATA-TAGTGACACCCAGTGTCTCATCGA
1 AGTAATAGT--TGACACCCAGTGTCTCATCGA
54901642 CTCGAGGTCG
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
38 19 0.35
39 17 0.31
40 1 0.02
41 17 0.31
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (40 bp):
AGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGCCGA
Found at i:54913083 original size:43 final size:43
Alignment explanation
Indices: 54913036--54913171 Score: 111
Period size: 43 Copynumber: 3.2 Consensus size: 43
54913026 AGAAGCAGAT
*
54913036 CTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTACATTAACAGCGAAGCAGATCAAAAACAAAGC
* * * * * * *
54913079 CTTG-CATCC-ATCGATT-GCAGTGGAGCTAG-TTAAAGAAGCAGA-T
1 CTTGCCTTCCTA-C-ATTAACAGCGAAGC-AGATCAAA-AA-CAAAGC
*
54913122 CTTGCCTTCCTACATTAACAGCAAAGCAGATCAAAAACAAAGC
1 CTTGCCTTCCTACATTAACAGCGAAGCAGATCAAAAACAAAGC
54913165 CTTGCCT
1 CTTGCCT
54913172 CCATCGGTTG
Statistics
Matches: 67, Mismatches: 16, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
41 1 0.01
42 18 0.27
43 29 0.43
44 18 0.27
45 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (43 bp):
CTTGCCTTCCTACATTAACAGCGAAGCAGATCAAAAACAAAGC
Found at i:54913116 original size:86 final size:87
Alignment explanation
Indices: 54912857--54913199 Score: 374
Period size: 86 Copynumber: 4.0 Consensus size: 87
54912847 NNNNNNNNNN
* * * **
54912857 AGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCCATCGGTTG
* * * **
54912922 -TGATAGAGCTGGTTGAAGACAAA
66 CAG-TGGAGCTGGTTAAAGA-AGC
* * * * * * * *
54912945 AGATCTTACCTTTCTGCATTGACAGTGAAGCAGGTCGAAGATACAAACTTTGCCTCTC-TCGGTT
1 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTC-CATCGGTT
*
54913009 GTAGTGGAGCTGGTTAAAGAAGC
65 GCAGTGGAGCTGGTTAAAGAAGC
* *
54913032 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCATCCATCGATT
1 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCCATCGGTT
*
54913095 GCAGTGGAGCTAGTTAAAGAAGC
65 GCAGTGGAGCTGGTTAAAGAAGC
* *
54913118 AGATCTTGCCTTCCTACATTAACAGCAAAGCAGATC-AA-AAACAAAGCCTTGCCTCCATCGGTT
1 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCCATCGGTT
*
54913181 GCATTGGAGCTGGTTAAAG
65 GCAGTGGAGCTGGTTAAAG
54913200 GTTACAGATT
Statistics
Matches: 223, Mismatches: 27, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
85 9 0.04
86 107 0.48
87 34 0.15
88 72 0.32
89 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (87 bp):
AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCCATCGGTTG
CAGTGGAGCTGGTTAAAGAAGC
Found at i:54915245 original size:109 final size:109
Alignment explanation
Indices: 54915048--54915249 Score: 352
Period size: 109 Copynumber: 1.9 Consensus size: 109
54915038 AAATATTTCC
54915048 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
*
54915113 CTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAA
66 CTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAA
*
54915157 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
54915222 CTCGTTTAACCAAATTG-TCAAATATCCT
66 CTCGTTCAACCAAATAGCT-AAATATCCT
54915250 ATTGAATTTA
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
108 1 0.01
109 87 0.99
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (109 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAA
Found at i:54916008 original size:22 final size:22
Alignment explanation
Indices: 54915983--54916038 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
54915973 ATTTATTATT
* * *
54915983 TTTTGTTGTTGTATTGTTACAA
1 TTTTGTTATTATATTATTACAA
*
54916005 TTTTGTTATTATATTATTACTA
1 TTTTGTTATTATATTATTACAA
*
54916027 TTTTATTATTAT
1 TTTTGTTATTAT
54916039 TATTTGGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTTGTTATTATATTATTACAA
Found at i:54920403 original size:12 final size:12
Alignment explanation
Indices: 54920386--54920412 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54920376 AATTCTCACA
54920386 AATTATTAATAT
1 AATTATTAATAT
54920398 AATTATTAATAT
1 AATTATTAATAT
54920410 AAT
1 AAT
54920413 ATCATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATTAATAT
Found at i:54930517 original size:21 final size:19
Alignment explanation
Indices: 54930471--54930518 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
54930461 TTATGAAAGT
* *
54930471 AATAAAATATACAAAATAA
1 AATAAAATATAAAAAACAA
54930490 AATTAAATATATGAAAAAACAA
1 AA-TAAA-ATAT-AAAAAACAA
54930512 AATAAAA
1 AATAAAA
54930519 CGTTAACTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 2 0.08
20 5 0.21
21 8 0.33
22 9 0.38
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAATATAAAAAACAA
Found at i:54960560 original size:21 final size:21
Alignment explanation
Indices: 54960534--54960574 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54960524 AGACGAGCAA
* *
54960534 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
54960555 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
54960575 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:54969098 original size:3 final size:3
Alignment explanation
Indices: 54969090--54969126 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
54969080 AAAATTTTCT
*
54969090 TCA TCA TCA TCA TCA TTA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
54969127 ATATATTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:54973445 original size:43 final size:43
Alignment explanation
Indices: 54973384--54973470 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
54973374 TTTTTTTACG
54973384 TAAAATAAAATAAATAATTATTAATAAATTGTTATAACCATGC
1 TAAAATAAAATAAATAATTATTAATAAATTGTTATAACCATGC
54973427 TAAAATAAAATAAATAATTATTAATAAATTGTTATAACCATGC
1 TAAAATAAAATAAATAATTATTAATAAATTGTTATAACCATGC
54973470 T
1 T
54973471 TTACAATAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.36
Consensus pattern (43 bp):
TAAAATAAAATAAATAATTATTAATAAATTGTTATAACCATGC
Found at i:54975888 original size:7 final size:7
Alignment explanation
Indices: 54975876--54975901 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54975866 GATCAATGAC
54975876 AAGTGAT
1 AAGTGAT
54975883 AAGTGAT
1 AAGTGAT
54975890 AAGTGAT
1 AAGTGAT
54975897 AAGTG
1 AAGTG
54975902 GTAGTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (7 bp):
AAGTGAT
Found at i:54975916 original size:58 final size:58
Alignment explanation
Indices: 54975821--54976058 Score: 249
Period size: 58 Copynumber: 4.1 Consensus size: 58
54975811 TGAGTACTTC
* *
54975821 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAG
* * *
54975879 TGATAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTGTCTGATCAGTGACAAG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAG
* *
54975937 TG---A-T-A-AA-TGATAAGTGGTAGCTTTAGCTACACTTATCTTATCACTTATCATTTATCAA
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT--C--A--A-TGA-CAA
54975995 -
58 G
* * * *
54975995 TGACAAGTAATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACAAG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAG
54976053 TGATAA
1 TGATAA
54976059 ATGTGATCAG
Statistics
Matches: 149, Mismatches: 15, Indels: 32
0.76 0.08 0.16
Matches are distributed among these distances:
51 31 0.21
52 2 0.01
53 2 0.01
54 1 0.01
55 2 0.01
57 3 0.02
58 66 0.44
59 3 0.02
61 2 0.01
62 1 0.01
63 2 0.01
64 2 0.01
65 32 0.21
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (58 bp):
TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAG
Found at i:54975932 original size:51 final size:51
Alignment explanation
Indices: 54975877--54975979 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
54975867 ATCAATGACA
* * * *
54975877 AGTGATAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTGTCTGATC
1 AGTGACAAGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
*
54975928 AGTGACAAGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTTATC
1 AGTGACAAGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
54975979 A
1 A
54975980 CTTATCATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (51 bp):
AGTGACAAGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:54976042 original size:116 final size:109
Alignment explanation
Indices: 54975826--54976061 Score: 330
Period size: 116 Copynumber: 2.1 Consensus size: 109
54975816 ACTTCTGATC
* * * *
54975826 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGTGATAAGTGATA
1 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGTGACAAGTAATA
*
54975891 AGTGATAAGTGGTAGTTTTAGCTACACTTGTCTGATCAGTGACA
66 AGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
* *
54975935 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTTATCACTTATCATTTATCAA-TGAC
1 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGAT--C--A--A-TGA-CAAGTGAC
54975999 AAGTAATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
58 AAGTAATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
54976051 AGTGATAAATG
1 AGTGATAAATG
54976062 TGATCAGTGT
Statistics
Matches: 112, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
109 40 0.36
111 1 0.01
113 1 0.01
115 1 0.01
116 66 0.59
117 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (109 bp):
AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGTGACAAGTAATA
AGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
Found at i:54978555 original size:46 final size:46
Alignment explanation
Indices: 54978495--54978763 Score: 342
Period size: 46 Copynumber: 5.8 Consensus size: 46
54978485 TTTGACATGA
* * * **
54978495 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATTT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGT
* *
54978541 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* * ** *
54978587 TGCCATGATATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* *
54978633 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* * * *
54978679 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* *
54978725 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
54978764 ATCAGAGAGC
Statistics
Matches: 199, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 4 0.02
46 195 0.98
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
Found at i:54978652 original size:92 final size:92
Alignment explanation
Indices: 54978505--54978767 Score: 382
Period size: 92 Copynumber: 2.9 Consensus size: 92
54978495 TGCCATAGTG
* * *
54978505 TCTTTCAACTATGGTCTTACTCATTTTCTGTCATTTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
*
54978570 TTCATTTCATGTCACGCTGCCATGATA
66 TTCATTTCATATCACGCTGCCATGATA
* *
54978597 TCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
* * *
54978662 TTCATTTCATATCACGTTGTCATGGTA
66 TTCATTTCATATCACGCTGCCATGATA
* * * * *
54978689 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGATATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
**
54978754 CACATTTCATATCA
66 TTCATTTCATATCA
54978768 GAGAGCACAC
Statistics
Matches: 153, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 153 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (92 bp):
TCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
TTCATTTCATATCACGCTGCCATGATA
Found at i:54978743 original size:138 final size:138
Alignment explanation
Indices: 54978490--54978753 Score: 386
Period size: 138 Copynumber: 1.9 Consensus size: 138
54978480 TTATCTTTGA
* * * **
54978490 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATTTTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTCTATCACGTTGCCATGGTATCTT
** *
54978555 TCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATGATATCTTTCAACCATGGTCTTATTCA
66 TCAACCATGGTCTTACACATTTCATATCACGCTGCCATGATATCTTTCAACCATGGTCTTATTCA
54978620 TTTCCCGT
131 TTTCCCGT
* * * *
54978628 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCACGTTGTCATGGTATCT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTC-TATCACGTTGCCATGGTATCT
* *
54978692 TTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGATATCTTTCAACCATGGTCTTA
65 TTCAACCATGGTCTTACACATTTCATATCACGCTGCCATGATATCTTTCAACCATGGTCTTA
54978754 CACATTTCAT
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
137 4 0.04
138 107 0.96
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (138 bp):
CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTCTATCACGTTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTCATATCACGCTGCCATGATATCTTTCAACCATGGTCTTATTCA
TTTCCCGT
Found at i:54990245 original size:21 final size:21
Alignment explanation
Indices: 54990219--54990259 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54990209 ATCTGCTCAA
* *
54990219 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54990240 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54990260 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54994364 original size:19 final size:19
Alignment explanation
Indices: 54994340--54994394 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
54994330 TATCACGTTA
*
54994340 AAAAATACTTTAAAATTAT
1 AAAAATAATTTAAAATTAT
*
54994359 AAAAATATTTTAAAA--AT
1 AAAAATAATTTAAAATTAT
*
54994376 -AACATAATTTAAAATTAT
1 AAAAATAATTTAAAATTAT
54994394 A
1 A
54994395 CCATGTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 12 0.40
17 2 0.07
18 2 0.07
19 14 0.47
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATAATTTAAAATTAT
Found at i:54999233 original size:22 final size:21
Alignment explanation
Indices: 54999193--54999234 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54999183 TTTAAATTTA
* *
54999193 AAAATATTTTTATATTTTTTT
1 AAAATAATTTTATAATTTTTT
54999214 AAAATAATTTTATTAATTTTT
1 AAAATAATTTTA-TAATTTTT
54999235 AAACTTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AAAATAATTTTATAATTTTTT
Found at i:55011322 original size:25 final size:23
Alignment explanation
Indices: 55011293--55011357 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
55011283 AATAAAAAAC
*
55011293 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
55011318 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
55011339 -TTAAAACA-AAAAATAAATA
1 TTTAAAACATAAAAACAAATA
55011358 AATAATGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:55011356 original size:19 final size:20
Alignment explanation
Indices: 55011319--55011357 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
55011309 TCAAATACAT
55011319 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
*
55011339 TTAAAACA-AAAAATAAATA
1 TTAAAACATAAAAACAAATA
55011358 AATAATGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:55012182 original size:30 final size:30
Alignment explanation
Indices: 55012148--55012206 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
55012138 CCTTAATACG
55012148 AACTTTGGAAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGAAAAATTACAC-TTTTGCCCCTA
* *
55012178 AACTTTGGCATAATTACACTTTTGCCCCT
1 AACTTTGGAAAAATTACACTTTTGCCCCT
55012207 CGGCTCAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:55013784 original size:42 final size:42
Alignment explanation
Indices: 55013698--55013810 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 42
55013688 GCACATAAGT
* * * * ** *
55013698 GCTAATCGGAAACCCGTATGGGTTAAACGGAAGCTCTTAGGA
1 GCTAAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
*
55013740 GCTGAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
* * *
55013782 GCTAAACTGAAACCCAAAAGGGTTGAACT
1 GCTAAACGGAAACCCATAAGGGTTAAACT
55013811 AAAACTCATA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (42 bp):
GCTAAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
Found at i:55013810 original size:21 final size:21
Alignment explanation
Indices: 55013748--55013815 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
55013738 GAGCTGAACG
*
55013748 GAAACCCATAAGGGTTAAACT
1 GAAACCCAAAAGGGTTAAACT
* * * *
55013769 GAAGCTCAAAAGAGCTAAACT
1 GAAACCCAAAAGGGTTAAACT
*
55013790 GAAACCCAAAAGGGTTGAACT
1 GAAACCCAAAAGGGTTAAACT
*
55013811 AAAAC
1 GAAAC
55013816 TCATATGAGT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (21 bp):
GAAACCCAAAAGGGTTAAACT
Found at i:55016155 original size:31 final size:32
Alignment explanation
Indices: 55016120--55016179 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
55016110 TAAATTGTGA
55016120 AATAAGTAAAAAGGTTACAAATGA-ATATGAT
1 AATAAGTAAAAAGGTTACAAATGAGATATGAT
55016151 AATAAGTAAAAAGGTTACAAATGAGATAT
1 AATAAGTAAAAAGGTTACAAATGAGATAT
55016180 CGGAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.25
Consensus pattern (32 bp):
AATAAGTAAAAAGGTTACAAATGAGATATGAT
Found at i:55019002 original size:23 final size:23
Alignment explanation
Indices: 55018976--55019073 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
55018966 ATAAGTGCCA
55018976 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55018999 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
55019022 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55019044 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55019067 CACTGAT
1 CACTGAT
55019074 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:55019041 original size:45 final size:45
Alignment explanation
Indices: 55018983--55019071 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
55018973 CCACACTGAT
* *
55018983 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
55019028 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
55019072 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:55026374 original size:23 final size:23
Alignment explanation
Indices: 55026348--55026445 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
55026338 ATAAGTGCCA
55026348 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55026371 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
55026394 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55026416 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55026439 CACTGAT
1 CACTGAT
55026446 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:55026413 original size:45 final size:45
Alignment explanation
Indices: 55026355--55026443 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
55026345 CCACACTGAT
* *
55026355 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
55026400 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
55026444 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:55029773 original size:50 final size:50
Alignment explanation
Indices: 55029711--55029894 Score: 214
Period size: 50 Copynumber: 3.7 Consensus size: 50
55029701 ATTATGTGTA
*
55029711 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATTATGTGATTCTATG
1 TAAGACCATAGCTGGGCTATGGCATCAATATGTGATTATGTGATTCTATG
**
55029761 TAAGACCATAGCTGGGCTATGGCATCGGTATGTGATTATGTGATCTCGTA--
1 TAAGACCATAGCTGGGCTATGGCATCAATATGTGATTATGTGAT-TC-TATG
** * * *
55029811 TAAGATGATAGCTGGGCTATGGCATCAATACGTGA-TATATGATTAC-GTG
1 TAAGACCATAGCTGGGCTATGGCATCAATATGTGATTATGTGATT-CTATG
* * *
55029860 TAAGACTATAGCTGGGTTATGGCATTAATATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCAATATGTGA
55029895 ATATATGTAA
Statistics
Matches: 116, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
48 1 0.01
49 38 0.33
50 73 0.63
51 2 0.02
52 2 0.02
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.33
Consensus pattern (50 bp):
TAAGACCATAGCTGGGCTATGGCATCAATATGTGATTATGTGATTCTATG
Found at i:55029892 original size:99 final size:100
Alignment explanation
Indices: 55029708--55029894 Score: 252
Period size: 99 Copynumber: 1.9 Consensus size: 100
55029698 GTGATTATGT
* * *
55029708 GTATAAGACCATAGCTGGGCTATGGCATCGATATGTGATTATGTGATTCTATGTAAGACCATAGC
1 GTATAAGACCATAGCTGGGCTATGGCATCAATACGTGATTATATGATTCTATGTAAGACCATAGC
**
55029773 TGGGCTATGGCATCGGTATGTGATTATGTGATCTC
66 TGGGCTATGGCATCAATATGTGATTATGTGATCTC
** * *
55029808 GTATAAGATGATAGCTGGGCTATGGCATCAATACGTGA-TATATGATTAC-GTGTAAGACTATAG
1 GTATAAGACCATAGCTGGGCTATGGCATCAATACGTGATTATATGATT-CTATGTAAGACCATAG
* *
55029871 CTGGGTTATGGCATTAATATGTGA
65 CTGGGCTATGGCATCAATATGTGA
55029895 ATATATGTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
99 40 0.53
100 35 0.47
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.33
Consensus pattern (100 bp):
GTATAAGACCATAGCTGGGCTATGGCATCAATACGTGATTATATGATTCTATGTAAGACCATAGC
TGGGCTATGGCATCAATATGTGATTATGTGATCTC
Found at i:55029905 original size:42 final size:42
Alignment explanation
Indices: 55029858--55029968 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 42
55029848 TATGATTACG
* * *
55029858 TGTAAGACTATAGCTGGGTTATGGCATTAATATGTGAATATA
1 TGTAAGACTATAGTTGGGCTATGGCATTAATATGTGAAGATA
* *
55029900 TGTAAGA-TCATAGTTGGGCTATGGCATTATTATGTGAAGATG
1 TGTAAGACT-ATAGTTGGGCTATGGCATTAATATGTGAAGATA
* *
55029942 TGTAAGACCATAGTTGGACTATGGCAT
1 TGTAAGACTATAGTTGGGCTATGGCAT
55029969 CGAGGAAACG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
41 1 0.02
42 59 0.98
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (42 bp):
TGTAAGACTATAGTTGGGCTATGGCATTAATATGTGAAGATA
Found at i:55032065 original size:18 final size:18
Alignment explanation
Indices: 55032039--55032076 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55032029 ATTCTTGGGT
* *
55032039 TTAATCGGTTTGCGGGCA
1 TTAACCGGTTTGCAGGCA
55032057 TTAACCGGTTTGCAGGCA
1 TTAACCGGTTTGCAGGCA
55032075 TT
1 TT
55032077 TGTTCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.34
Consensus pattern (18 bp):
TTAACCGGTTTGCAGGCA
Found at i:55036916 original size:5 final size:5
Alignment explanation
Indices: 55036908--55036933 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55036898 AAATTAACGT
55036908 TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA T
55036934 GTATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:55048504 original size:21 final size:21
Alignment explanation
Indices: 55048480--55048520 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55048470 AGGTGGCGGG
*
55048480 GGTGATGGAGAAGGAGGTGGT
1 GGTGAGGGAGAAGGAGGTGGT
* *
55048501 GGTGAGGGAGATGGTGGTGG
1 GGTGAGGGAGAAGGAGGTGG
55048521 GGGACTAGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.61, T:0.20
Consensus pattern (21 bp):
GGTGAGGGAGAAGGAGGTGGT
Found at i:55048567 original size:48 final size:45
Alignment explanation
Indices: 55048515--55048988 Score: 252
Period size: 48 Copynumber: 9.9 Consensus size: 45
55048505 AGGGAGATGG
*
55048515 TGGTGGGGGACTAGGAGATGGTGGAGGTACTGGAGACTTGTAGTAGTA
1 TGGTGGGGGACTAGGAGATGGTGGAGG---TGGTGACTTGTAGTAGTA
* * * *
55048563 TGGTGGTGGAGGACTAGGTGAAGGTGGTGGTGGTGATTTGTAGTAGTA
1 TGGT-G-GG-GGACTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGTA
* * *
55048611 AGGAGGAGGTG-GTGAGGGAGATGGTGGAGGTGGTGACTTGTAGTAGTA
1 TGGTGG-GG-GACT-A-GGAGATGGTGGAGGTGGTGACTTGTAGTAGTA
* * * *
55048659 TGGTGGGGGGGGACTAGGTGAGGGTGGTGGTGGTGATTTGTAGTAGTA
1 TGGT---GGGGGACTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGTA
* * ** *
55048707 AGGAGGAGGGGGTGAGGGAGACGGTGGAGGTGGTGACTTGTAGTAGTA
1 TGGTGG-GGGACT-A-GGAGATGGTGGAGGTGGTGACTTGTAGTAGTA
* * * * * *
55048755 TGGTGGTGGGGGACTAGGTGAGGGCGGGGGTGGAGACTTGTAATAGTA
1 ---TGGTGGGGGACTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGTA
* * * *
55048803 AGGAGGAGGTG-GTGAAGGAGATGGTGGAGGTGGTGAGTTGTAGTAGTATGA
1 TGGTGG-GG-GACT--AGGAGATGGTGGAGGTGGTGACTTGTAGTAG--T-A
* * * * * *
55048854 TGGTGGGGGACTAGGTGAAGGGGGTGGTGGTGATTTGTAATAGTA
1 TGGTGGGGGACTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGTA
* * * *
55048899 AGGAGGAGGTG-GTGAAGGAGATGGTGGAGGTGGAGACTTGTAGTAGTAA
1 TGGTGG-GG-GACT--AGGAGATGGTGGAGGTGGTGACTTGTAGTAGT-A
* * * * *
55048948 GGTGGTGGAGGACTAGGTGAAGGCGGCGGTGGTGACTTGTA
1 --TGGTGGGGGACTAGGAGATGGTGGAGGTGGTGACTTGTA
55048989 AGGTGGTGAA
Statistics
Matches: 318, Mismatches: 75, Indels: 66
0.69 0.16 0.14
Matches are distributed among these distances:
45 11 0.03
46 14 0.04
47 7 0.02
48 232 0.73
49 7 0.02
50 15 0.05
51 32 0.10
ACGTcount: A:0.21, C:0.04, G:0.51, T:0.24
Consensus pattern (45 bp):
TGGTGGGGGACTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGTA
Found at i:55048659 original size:96 final size:96
Alignment explanation
Indices: 55048527--55048989 Score: 683
Period size: 96 Copynumber: 4.8 Consensus size: 96
55048517 GTGGGGGACT
* * *
55048527 AGGAGATGGTGGAGGTACTGGAGACTTGTAGTAGTATGGTGGTGGAGGACTAGGTGAAGGTGGTG
1 AGGAGATGGTGGAGG---TGGTGACTTGTAGTAGTATGGTGGTGGGGGACTAGGTGAAGGCGGTG
*
55048592 GTGGTGATTTGTAGTAGTAAGGAGGAGGTGGTGA
63 GTGGTGATTTGTAATAGTAAGGAGGAGGTGGTGA
* * * *
55048626 GGGAGATGGTGGAGGTGGTGACTTGTAGTAGTATGGTGGGGGGGGACTAGGTGAGGGTGGTGGTG
1 AGGAGATGGTGGAGGTGGTGACTTGTAGTAGTATGGTGGTGGGGGACTAGGTGAAGGCGGTGGTG
* *
55048691 GTGATTTGTAGTAGTAAGGAGGAGGGGGTGA
66 GTGATTTGTAATAGTAAGGAGGAGGTGGTGA
* * * *
55048722 GGGAGACGGTGGAGGTGGTGACTTGTAGTAGTATGGTGGTGGGGGACTAGGTGAGGGCGGGGGTG
1 AGGAGATGGTGGAGGTGGTGACTTGTAGTAGTATGGTGGTGGGGGACTAGGTGAAGGCGGTGGTG
* *
55048787 GAGACTTGTAATAGTAAGGAGGAGGTGGTGA
66 GTGATTTGTAATAGTAAGGAGGAGGTGGTGA
* * *
55048818 AGGAGATGGTGGAGGTGGTGAGTTGTAGTAGTATGATGGTGGGGGACTAGGTGAAGGGGGTGGTG
1 AGGAGATGGTGGAGGTGGTGACTTGTAGTAGTATGGTGGTGGGGGACTAGGTGAAGGCGGTGGTG
55048883 GTGATTTGTAATAGTAAGGAGGAGGTGGTGA
66 GTGATTTGTAATAGTAAGGAGGAGGTGGTGA
* * * *
55048914 AGGAGATGGTGGAGGTGGAGACTTGTAGTAGTAAGGTGGTGGAGGACTAGGTGAAGGCGGCGGTG
1 AGGAGATGGTGGAGGTGGTGACTTGTAGTAGTATGGTGGTGGGGGACTAGGTGAAGGCGGTGGTG
*
55048979 GTGACTTGTAA
66 GTGATTTGTAA
55048990 GGTGGTGAAT
Statistics
Matches: 333, Mismatches: 31, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
96 319 0.96
99 14 0.04
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.24
Consensus pattern (96 bp):
AGGAGATGGTGGAGGTGGTGACTTGTAGTAGTATGGTGGTGGGGGACTAGGTGAAGGCGGTGGTG
GTGATTTGTAATAGTAAGGAGGAGGTGGTGA
Found at i:55048993 original size:15 final size:15
Alignment explanation
Indices: 55048975--55049004 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55048965 TGAAGGCGGC
*
55048975 GGTGGTGACTTGTAA
1 GGTGGTGAATTGTAA
55048990 GGTGGTGAATTGTAA
1 GGTGGTGAATTGTAA
55049005 TAGTAAGGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.40, T:0.33
Consensus pattern (15 bp):
GGTGGTGAATTGTAA
Found at i:55052490 original size:23 final size:23
Alignment explanation
Indices: 55052464--55052516 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
55052454 TGTTCATCGT
*
55052464 CATTGTCCCTTAATGTTTTGATC
1 CATTGCCCCTTAATGTTTTGATC
55052487 CATTGCCCCTTAATGTTTTGATC
1 CATTGCCCCTTAATGTTTTGATC
55052510 CATTGCC
1 CATTGCC
55052517 AAACACCTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.26, G:0.13, T:0.43
Consensus pattern (23 bp):
CATTGCCCCTTAATGTTTTGATC
Found at i:55062225 original size:3 final size:3
Alignment explanation
Indices: 55062210--55062243 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
55062200 TAATTAATTA
*
55062210 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
55062244 GCTTCCCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:55076677 original size:25 final size:23
Alignment explanation
Indices: 55076623--55076670 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
55076613 GGCCGATATT
55076623 AAATTAAAACTTTCCATTTTTTA
1 AAATTAAAACTTTCCATTTTTTA
* *
55076646 AACATTAAAACATTTTCTTTTTTTA
1 AA-ATTAAAAC-TTTCCATTTTTTA
55076671 CTAATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 8 0.38
25 11 0.52
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATTAAAACTTTCCATTTTTTA
Found at i:55077849 original size:24 final size:24
Alignment explanation
Indices: 55077789--55077837 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
55077779 TTCGTGTCTA
*
55077789 AGCTGAGGCTAAACTCTTAAGCTG
1 AGCTGAGGCTAAACTCCTAAGCTG
55077813 AGCTGAGGCTAAACTCCTAAGCTG
1 AGCTGAGGCTAAACTCCTAAGCTG
55077837 A
1 A
55077838 AGTTGAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (24 bp):
AGCTGAGGCTAAACTCCTAAGCTG
Found at i:55080309 original size:131 final size:132
Alignment explanation
Indices: 55079966--55080486 Score: 633
Period size: 132 Copynumber: 4.0 Consensus size: 132
55079956 ATTATTCGTT
* *
55079966 TAAAAATTCTTTAAAACGAAGGCGAGATTTGATATTTGGCAATTCGCGAAATCGTGCCCTAACGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * *
55080031 GCTGGGTTGCAATTTATCGTTTGCTCAAAATAATCGAATA-TCCCTTCAAAATTTCACTCATGTC
66 GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAA-AGTCCCTTTAGAATTTCACTCATGTC
55080095 TTC
130 TTC
* *
55080098 TAAAAATCCTTTAAAACGAAGGCGAGATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * * * *
55080163 GTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATTGAAGGTCCCTTTAGAATTTCACCCATGTCC
66 GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAAGTCCCTTTAGAATTTCACTCATGT-C
55080228 TT-
130 TTC
* *
55080230 TAAAAATTCTTT-AAACGAAAGCGATG-TTCGATATTTGGCAATTCGCGGAATCGTGCCTTAACG
1 TAAAAATTCTTTAAAACGAAGGCGA-GATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACG
* * * * * *
55080293 TGCTGGGTTGCGATTTCTCGTTTGTTCAAAATGATCGAAAGTCCCTTTTGAATTTCACTTATGTT
65 TGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAAGTCCCTTTAGAATTTCACTCATGTC
55080358 TTC
130 TTC
* * * ** * * * * * *
55080361 TAAAAACTCTTCAAAACGAGGGTAATATTCGATGTATGACAATTCGGGGAATCGTGCCCTATCGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * *
55080426 GCTGGGTTGCGATTTC-CTGTTTG-TCCAAAATGATCGAACA-TTCCTTTAGAATTTCACTCAT
66 GCTGGGTTGCAATTTCTC-GTTTGCT-CAAAATAATCGAA-AGTCCCTTTAGAATTTCACTCAT
55080487 ACTCTCTAAA
Statistics
Matches: 339, Mismatches: 41, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
130 2 0.01
131 112 0.33
132 221 0.65
133 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (132 bp):
TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAAGTCCCTTTAGAATTTCACTCATGTCT
TC
Found at i:55080474 original size:263 final size:264
Alignment explanation
Indices: 55079964--55080482 Score: 663
Period size: 263 Copynumber: 2.0 Consensus size: 264
55079954 TAATTATTCG
* *
55079964 TTTAAAAATTCTTTAAAACGAAGGCGAGATTTGATATTTGGCAATTCGCGAAATCGTGCCCTAAC
1 TTTAAAAATTCTTTAAAACGAAAGCGAGATTCGATATTTGGCAATTCGCGAAATCGTGCCCTAAC
55080029 GTGCTGGGTTGCAATTTATCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGT
66 GTGCTGGGTTGCAATTTATCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGT
* * * * *
55080094 CTTCTAAAAATCCTTTAAAACGAAGGCGAGATTTGATATTTGGCAATTCGCGGAATCGTGCCCTA
131 CTTCTAAAAATCCTTCAAAACGAAGGCAAGATTCGATATATGACAATTCGCGGAATCGTGCCCTA
* * * **
55080159 ACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATTGAAGGTCCCTTTAGAATTTCACCCAT
196 ACGTGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAACATCCCTTTAGAATTTCACCCAT
55080224 GTCC
261 GTCC
* *
55080228 TTTAAAAATTCTTT-AAACGAAAGCGATG-TTCGATATTTGGCAATTCGCGGAATCGTGCCTTAA
1 TTTAAAAATTCTTTAAAACGAAAGCGA-GATTCGATATTTGGCAATTCGCGAAATCGTGCCCTAA
* * * * *** *
55080291 CGTGCTGGGTTGCGATTTCTCGTTTGTTCAAAATGATCGAA-AGTCCCTTTTGAATTTCACTTAT
65 CGTGCTGGGTTGCAATTTATCGTTTGCTCAAAATAATCGAATA-TCCCTTCAAAATTTCACTCAT
* * * * * *
55080355 GTTTTCTAAAAA-CTCTTCAAAACGAGGGTAATATTCGATGTATGACAATTCGGGGAATCGTGCC
129 GTCTTCTAAAAATC-CTTCAAAACGAAGGCAAGATTCGATATATGACAATTCGCGGAATCGTGCC
* * * *
55080419 CTATCGTGCTGGGTTGCGATTTC-CTGTTTG-TCCAAAATGATCGAACATTCCTTTAGAATTTCA
193 CTAACGTGCTGGGTTGCAATTTCTC-GTTTGCT-CAAAATAATCGAACATCCCTTTAGAATTTCA
55080482 C
256 C
55080483 TCATACTCTC
Statistics
Matches: 218, Mismatches: 32, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
262 4 0.02
263 199 0.91
264 15 0.07
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (264 bp):
TTTAAAAATTCTTTAAAACGAAAGCGAGATTCGATATTTGGCAATTCGCGAAATCGTGCCCTAAC
GTGCTGGGTTGCAATTTATCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGT
CTTCTAAAAATCCTTCAAAACGAAGGCAAGATTCGATATATGACAATTCGCGGAATCGTGCCCTA
ACGTGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAACATCCCTTTAGAATTTCACCCAT
GTCC
Found at i:55082913 original size:14 final size:15
Alignment explanation
Indices: 55082896--55082929 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
55082886 GAAAAATAAT
55082896 AAGAAGAAT-AGGAG
1 AAGAAGAATAAGGAG
55082910 AAGAAGAATAAGGAG
1 AAGAAGAATAAGGAG
55082925 AAGAA
1 AAGAA
55082930 AATGAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.32, T:0.06
Consensus pattern (15 bp):
AAGAAGAATAAGGAG
Found at i:55084525 original size:20 final size:20
Alignment explanation
Indices: 55084451--55084585 Score: 101
Period size: 20 Copynumber: 6.8 Consensus size: 20
55084441 TTCAATGGTC
*
55084451 TTATCAAAATATT-TAAGGAT
1 TTATCAAAAT-TTCTAACGAT
* * ** *
55084471 TTACCAATACATCTAACTAT
1 TTATCAAAATTTCTAACGAT
* *
55084491 TTATCAATATATCTAACGAT
1 TTATCAAAATTTCTAACGAT
** *
55084511 TTATCAAAATTTCTATTGTT
1 TTATCAAAATTTCTAACGAT
* * *
55084531 TTACCAACATTTCTAAGGAT
1 TTATCAAAATTTCTAACGAT
* *
55084551 TTAACAAAATATCTAACGAT
1 TTATCAAAATTTCTAACGAT
*
55084571 TTATTAAAATTTCTA
1 TTATCAAAATTTCTA
55084586 TCATTTTATC
Statistics
Matches: 88, Mismatches: 26, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
19 1 0.01
20 87 0.99
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (20 bp):
TTATCAAAATTTCTAACGAT
Found at i:55084583 original size:40 final size:40
Alignment explanation
Indices: 55084451--55084585 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 40
55084441 TTCAATGGTC
* * * *
55084451 TTATCAAAATATT-TAAGGATTTACCAATACATCTAACTAT
1 TTATCAAAAT-TTCTAAGGATTTAACAAAATATCTAACGAT
* * * * * ** *
55084491 TTATCAATATATCTAACGATTTATCAAAATTTCTATTGTT
1 TTATCAAAATTTCTAAGGATTTAACAAAATATCTAACGAT
* *
55084531 TTACCAACATTTCTAAGGATTTAACAAAATATCTAACGAT
1 TTATCAAAATTTCTAAGGATTTAACAAAATATCTAACGAT
*
55084571 TTATTAAAATTTCTA
1 TTATCAAAATTTCTA
55084586 TCATTTTATC
Statistics
Matches: 71, Mismatches: 23, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
39 1 0.01
40 70 0.99
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (40 bp):
TTATCAAAATTTCTAAGGATTTAACAAAATATCTAACGAT
Found at i:55084652 original size:20 final size:20
Alignment explanation
Indices: 55084610--55084651 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
55084600 TTAAGGAGAC
*
55084610 TTTACCAAATTTCTTAATAT
1 TTTACCAAATTTCTCAATAT
55084630 TTTACCAATATTT-TCAAT-T
1 TTTACCAA-ATTTCTCAATAT
55084649 TTT
1 TTT
55084652 TCTAAACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTACCAAATTTCTCAATAT
Found at i:55084882 original size:40 final size:39
Alignment explanation
Indices: 55084834--55084910 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 39
55084824 AGGATTTCTA
*
55084834 AAGATTTACCAAAATTTCTATTG-TTTTACCAATATTTAT
1 AAGATTTACCAAAATTTCTA-AGATTTTACCAATATTTAT
55084873 AAGACTTTACCAAAATTTCTAAGATTTTACCAATATTT
1 AAGA-TTTACCAAAATTTCTAAGATTTTACCAATATTT
55084911 TCAAATTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 5 0.14
40 30 0.86
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (39 bp):
AAGATTTACCAAAATTTCTAAGATTTTACCAATATTTAT
Found at i:55084891 original size:60 final size:60
Alignment explanation
Indices: 55084765--55084910 Score: 143
Period size: 60 Copynumber: 2.4 Consensus size: 60
55084755 AGATTTACTT
* * * *
55084765 AAATATCTAATGAGTTACCAAAATTTCTATCATTTCACCAATATAACTAACAATTTATCA
1 AAATTTCTAAAGATTTACCAAAATTTCTATCATTTCACCAATATAACTAACAATTTACCA
** ** * * * *
55084825 GGATTTCTAAAGATTTACCAAAATTTCTATTGTTTTACCAATATTTA-TAAGACTTTACCA
1 AAATTTCTAAAGATTTACCAAAATTTCTATCATTTCACCAATA-TAACTAACAATTTACCA
*
55084885 AAATTTCT-AAGATTTTACCAATATTT
1 AAATTTCTAAAGA-TTTACCAAAATTT
55084911 TCAAATTTTC
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
59 4 0.06
60 63 0.91
61 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (60 bp):
AAATTTCTAAAGATTTACCAAAATTTCTATCATTTCACCAATATAACTAACAATTTACCA
Found at i:55084901 original size:20 final size:19
Alignment explanation
Indices: 55084736--55084910 Score: 107
Period size: 20 Copynumber: 8.8 Consensus size: 19
55084726 AATATTTAAC
*
55084736 GATTTACCGAAATTTCTAAA
1 GATTTACCAAAATTTCT-AA
** *
55084756 GATTTACTTAAATATCTAA
1 GATTTACCAAAATTTCTAA
* *
55084775 TGAGTTACCAAAATTTCTAT
1 -GATTTACCAAAATTTCTAA
* * **
55084795 CATTTCACCAATATAACTAA
1 GATTT-ACCAAAATTTCTAA
* * **
55084815 CAATTTATCAGGATTTCTAAA
1 -GATTTACCAAAATTTCT-AA
*
55084836 GATTTACCAAAATTTCTATT
1 GATTTACCAAAATTTCTA-A
* * *
55084856 GTTTTACCAATATTTATAA
1 GATTTACCAAAATTTCTAA
55084875 GACTTTACCAAAATTTCTAA
1 GA-TTTACCAAAATTTCTAA
*
55084895 GATTTTACCAATATTT
1 GA-TTTACCAAAATTT
55084911 TCAAATTTTC
Statistics
Matches: 115, Mismatches: 34, Indels: 12
0.71 0.21 0.07
Matches are distributed among these distances:
19 7 0.06
20 102 0.89
21 6 0.05
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (19 bp):
GATTTACCAAAATTTCTAA
Found at i:55085051 original size:36 final size:37
Alignment explanation
Indices: 55084947--55085051 Score: 104
Period size: 40 Copynumber: 2.7 Consensus size: 37
55084937 TCTTAACAAT
* * *
55084947 TACCAAAAGTTCCTCAACTTTACCAAAATATCTAACGATT
1 TACCAAAA-TTTCT-AAC-TTACCAATATATCTAACGATC
* *
55084987 TACCAATATTTTTAAGAACTTACCAATATATCTAACGATC
1 TACCAAAATTTCT---AACTTACCAATATATCTAACGATC
55085027 TACCAAAATTTCT-ACTTACCAATAT
1 TACCAAAATTTCTAACTTACCAATAT
55085052 TTCCAAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
36 12 0.22
39 3 0.05
40 37 0.67
41 3 0.05
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (37 bp):
TACCAAAATTTCTAACTTACCAATATATCTAACGATC
Found at i:55085174 original size:143 final size:144
Alignment explanation
Indices: 55084830--55085184 Score: 389
Period size: 143 Copynumber: 2.5 Consensus size: 144
55084820 TATCAGGATT
* ***
55084830 TCTAAAGATTTACCAAAATTTCTATTGTTTTACCAATATTTATAAGACTTTACCAAAATTTCTAA
1 TCTAACGATTTACCAAAATTTCTATCAATTTACCAATATTTATAAGACTTTACCAAAATTTCT-A
* * * *
55084895 GATTTTACCAATATTTTCAAATTTTCAAAACCATGTACAAAGTCTTAACAATTACCAAAAGTTCC
65 -ATCTTACCAATATTTCCAAATTTTCAAAACCA-GTACAAAGTATTAACAATTACCAAAAGTTCA
55084960 TCAACTTTACCAAAATA
128 TCAACTTTACCAAAATA
* * ** * * * *
55084977 TCTAACGATTTACCAATATTTTTAAGAACTTACCAATATATCTAACGA-TCTACCAAAATTTCT-
1 TCTAACGATTTACCAAAATTTCTATCAATTTACCAATATTTATAA-GACTTTACCAAAATTTCTA
*
55085040 A-CTTACCAATATTTCCAAATTTTCTAAACACCA-TACCAAGTATTAACAATTACC-AAAGTTTC
65 ATCTTACCAATATTTCCAAATTTTC-AAA-ACCAGTACAAAGTATTAACAATTACCAAAAG-TTC
*
55085102 TATC-ACTTTATCAAAATA
127 -ATCAACTTTACCAAAATA
** * * *
55085120 TCTAACGATTTACCAAAATTTCCGTCAATTTACCAATATTTATGAGACTTTACCAATATCTCTAA
1 TCTAACGATTTACCAAAATTTCTATCAATTTACCAATATTTATAAGACTTTACCAAAATTTCTAA
55085185 GGATTTACCA
Statistics
Matches: 171, Mismatches: 30, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
142 6 0.04
143 103 0.60
144 7 0.04
145 4 0.02
147 49 0.29
148 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (144 bp):
TCTAACGATTTACCAAAATTTCTATCAATTTACCAATATTTATAAGACTTTACCAAAATTTCTAA
TCTTACCAATATTTCCAAATTTTCAAAACCAGTACAAAGTATTAACAATTACCAAAAGTTCATCA
ACTTTACCAAAATA
Found at i:55085209 original size:60 final size:60
Alignment explanation
Indices: 55085106--55085218 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
55085096 AGTTTCTATC
* * **
55085106 ACTTTATCAAAATATCTAACGATTTACCAAAATTTCCGTCAATTTACCAATATTTATGAG
1 ACTTTACCAAAATATCTAACGATTTACCAAAATATCCAACAATTTACCAATATTTATGAG
* * * * *
55085166 ACTTTACCAATATCTCTAAGGATTTACCAAAATATCTAACAATTTACCTATAT
1 ACTTTACCAAAATATCTAACGATTTACCAAAATATCCAACAATTTACCAATAT
55085219 ATCCAATAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.36
Consensus pattern (60 bp):
ACTTTACCAAAATATCTAACGATTTACCAAAATATCCAACAATTTACCAATATTTATGAG
Found at i:55085220 original size:20 final size:20
Alignment explanation
Indices: 55084965--55085221 Score: 74
Period size: 20 Copynumber: 12.7 Consensus size: 20
55084955 GTTCCTCAAC
* *
55084965 TTTACCAAAATATCTAACGA
1 TTTACCAATATATCTAACAA
* * *
55084985 TTTACCAATATTTTTAAGAA
1 TTTACCAATATATCTAACAA
* *
55085005 CTTACCAATATATCTAACGA
1 TTTACCAATATATCTAACAA
* * *
55085025 TCTACCAAAATTTCTACTTACCAA
1 TTTACCAATATATCTA---A-CAA
* * *
55085049 TATTTCCAA-ATTTTCTAAACAC
1 T-TTACCAATA-TATCT-AACAA
** *
55085071 CATACCAA-GTAT-TAACAA
1 TTTACCAATATATCTAACAA
* * *
55085089 -TTACCAA-AGTTTCTATCAC
1 TTTACCAATA-TATCTAACAA
* * *
55085108 TTTATCAAAATATCTAACGA
1 TTTACCAATATATCTAACAA
* * ***
55085128 TTTACCAAAATTTCCGTCAA
1 TTTACCAATATATCTAACAA
* * * * *
55085148 TTTACCAATATTTATGAGAC
1 TTTACCAATATATCTAACAA
* **
55085168 TTTACCAATATCTCTAAGGA
1 TTTACCAATATATCTAACAA
*
55085188 TTTACCAAAATATCTAACAA
1 TTTACCAATATATCTAACAA
*
55085208 TTTACCTATATATC
1 TTTACCAATATATC
55085222 CAATAGTTTA
Statistics
Matches: 169, Mismatches: 57, Indels: 22
0.68 0.23 0.09
Matches are distributed among these distances:
17 6 0.04
18 6 0.04
19 5 0.03
20 127 0.75
21 6 0.04
22 2 0.01
23 2 0.01
24 4 0.02
25 10 0.06
26 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (20 bp):
TTTACCAATATATCTAACAA
Found at i:55085533 original size:20 final size:20
Alignment explanation
Indices: 55085488--55085533 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
55085478 ATGATTTACC
* *
55085488 ATTTACCAAAATTTTTAAGG
1 ATTTACCAAAATATTTAACG
* *
55085508 AATTACCAAAATATTTGACG
1 ATTTACCAAAATATTTAACG
55085528 ATTTAC
1 ATTTAC
55085534 TAATATTTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (20 bp):
ATTTACCAAAATATTTAACG
Found at i:55085601 original size:20 final size:20
Alignment explanation
Indices: 55085527--55085601 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
55085517 AATATTTGAC
* *
55085527 GATTTACTAATATTTCTATG
1 GATTTACAAATATTTCTATA
* * *
55085547 GATTTACCAATATATCTAACA
1 GATTTACAAATATTTCT-ATA
*
55085568 AATTGT-CAAA-ATTTCTATA
1 GATT-TACAAATATTTCTATA
55085587 GATTTACAAATATTT
1 GATTTACAAATATTT
55085602 ATGAGACTTC
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
18 1 0.02
19 9 0.21
20 24 0.57
21 7 0.17
22 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.43
Consensus pattern (20 bp):
GATTTACAAATATTTCTATA
Found at i:55086722 original size:17 final size:18
Alignment explanation
Indices: 55086700--55086736 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
55086690 TCGAAATTTT
*
55086700 TTATTTAAAATTTTA-AA
1 TTATTTAAAAATTTATAA
55086717 TTATTTAAAAATTTATAA
1 TTATTTAAAAATTTATAA
55086735 TT
1 TT
55086737 TATAACAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTTAAAAATTTATAA
Found at i:55088692 original size:20 final size:20
Alignment explanation
Indices: 55088667--55088706 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
55088657 ATTTGTCTTA
55088667 AAGCCTTGGAACAAGACCGT
1 AAGCCTTGGAACAAGACCGT
55088687 AAGCCTTGGAACAAGACCGT
1 AAGCCTTGGAACAAGACCGT
55088707 TATTGGTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
AAGCCTTGGAACAAGACCGT
Found at i:55096440 original size:3 final size:3
Alignment explanation
Indices: 55096434--55096461 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55096424 CAATAATAAT
55096434 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
55096462 TGATAAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Done.