Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 153 of 228
Found at i:46045370 original size:18 final size:18
Alignment explanation
Indices: 46045347--46045391 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
46045337 ATCCCAATGA
46045347 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
46045365 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
46045383 TCACCACCA
1 TCGCCACCA
46045392 ACCATGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:46046253 original size:3 final size:3
Alignment explanation
Indices: 46046245--46046273 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
46046235 TCTTAATACT
46046245 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
46046274 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:46046364 original size:19 final size:21
Alignment explanation
Indices: 46046340--46046378 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
46046330 ACTAAAACAA
*
46046340 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
46046359 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
46046379 ATCAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:46046679 original size:21 final size:20
Alignment explanation
Indices: 46046637--46046677 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
46046627 TTTTTTTGAT
46046637 ATATTTTGATAAATAAAAAA
1 ATATTTTGATAAATAAAAAA
*
46046657 ATATTTTGGTAAATAAAAAA
1 ATATTTTGATAAATAAAAAA
46046677 A
1 A
46046678 ATTATAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (20 bp):
ATATTTTGATAAATAAAAAA
Found at i:46050164 original size:28 final size:28
Alignment explanation
Indices: 46050132--46050189 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
46050122 TATGCATATC
46050132 AAAGCATTATTGTATTAGTTAGTTTTTT
1 AAAGCATTATTGTATTAGTTAGTTTTTT
46050160 AAAGCATTATTGTATTAGTTAGTTTTTT
1 AAAGCATTATTGTATTAGTTAGTTTTTT
46050188 AA
1 AA
46050190 CATTAACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (28 bp):
AAAGCATTATTGTATTAGTTAGTTTTTT
Found at i:46050473 original size:40 final size:42
Alignment explanation
Indices: 46050429--46050520 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
46050419 TTTCATAAAT
46050429 GCCGCTAAAAATC-ACT-TTTAGCCGCGTTTGT-GATAAAAGC
1 GCCGCTAAAAATCAACTGTTTAGCCGCGTTTGTGGAT-AAAGC
* * * *
46050469 GCCGCTAAAGATCATATTGTTTAGCGGCGTTTGTGGGTAAAGC
1 GCCGCTAAAAATCA-ACTGTTTAGCCGCGTTTGTGGATAAAGC
46050512 GCCGCTAAA
1 GCCGCTAAA
46050521 GGTCATGTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
40 12 0.27
42 2 0.05
43 28 0.64
44 2 0.05
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (42 bp):
GCCGCTAAAAATCAACTGTTTAGCCGCGTTTGTGGATAAAGC
Found at i:46050499 original size:43 final size:43
Alignment explanation
Indices: 46050445--46050586 Score: 178
Period size: 43 Copynumber: 3.3 Consensus size: 43
46050435 AAAAATCACT
* * * *
46050445 TTTAGCCGCGTTTGT-GATAAAAGCGCCGCTAAAGATCATATTG
1 TTTAGCGGCGTTTGTGGGT-AAAGCGCCGCTAAAGATCATGTTC
*
46050488 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
* * * *
46050531 TTTAGTGGCGTTTGTGGGTTAAGCGCCGATAAATATCATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
*
46050574 TTTAGTGGCGTTT
1 TTTAGCGGCGTTT
46050587 TATCACATTA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 86 0.98
44 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
Found at i:46050617 original size:34 final size:34
Alignment explanation
Indices: 46050574--46050680 Score: 178
Period size: 34 Copynumber: 3.1 Consensus size: 34
46050564 TATCATGTTC
*
46050574 TTTAGTGGCGTTTTATCACATTAACGCCGCAAAA
1 TTTAGTGGCGTTTTATCACATAAACGCCGCAAAA
46050608 TTTAGTGGCGTTTTATCACATAAACGCCGCAAAA
1 TTTAGTGGCGTTTTATCACATAAACGCCGCAAAA
* **
46050642 TTTAGCGGCGTTTTATCACATAAACGCTTCAAAA
1 TTTAGTGGCGTTTTATCACATAAACGCCGCAAAA
46050676 TTTAG
1 TTTAG
46050681 CATCATTGTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (34 bp):
TTTAGTGGCGTTTTATCACATAAACGCCGCAAAA
Found at i:46062507 original size:44 final size:44
Alignment explanation
Indices: 46062366--46062496 Score: 137
Period size: 43 Copynumber: 3.0 Consensus size: 44
46062356 AGCTCGTACA
* * *
46062366 ATGCCAACGTCCTAGAC-GAGGTCTTACATGT-AATCA-AATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAAATCACAA-ATCG
* * *
46062409 ATACCACTGTCCCAGACAGGGTCTTACACGTAAATCTCAAATCG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAAATCACAAATCG
*
46062453 ATGCCAATGTCCCAGAC-GTGGTCTTACACG-AAATCACATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAAATCACAAATCG
46062496 A
1 A
46062497 AATCTTATGT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
43 37 0.50
44 35 0.47
45 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAAATCACAAATCG
Found at i:46062656 original size:34 final size:35
Alignment explanation
Indices: 46062604--46062676 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
46062594 TTCCATGCTA
* ** *
46062604 AATTCAATTCGGCAATGTA-ATTATACATACATAC
1 AATTCAATTCGACAATGTACAAAATAAATACATAC
* *
46062638 AATTCAATTTGACTATGTACAAAATAAATACATAC
1 AATTCAATTCGACAATGTACAAAATAAATACATAC
46062673 AATT
1 AATT
46062677 TAACATCCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 16 0.50
35 16 0.50
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (35 bp):
AATTCAATTCGACAATGTACAAAATAAATACATAC
Found at i:46063121 original size:34 final size:35
Alignment explanation
Indices: 46063069--46063141 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
46063059 TTCCATGCTA
* ** *
46063069 AATTCAATTCGGCAATGTA-ATTATACATACATAC
1 AATTCAATTCGACAATGTACAAAATAAATACATAC
* *
46063103 AATTCAATTTGACTATGTACAAAATAAATACATAC
1 AATTCAATTCGACAATGTACAAAATAAATACATAC
46063138 AATT
1 AATT
46063142 TAACATCCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 16 0.50
35 16 0.50
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (35 bp):
AATTCAATTCGACAATGTACAAAATAAATACATAC
Found at i:46063250 original size:465 final size:465
Alignment explanation
Indices: 46062379--46063309 Score: 1844
Period size: 465 Copynumber: 2.0 Consensus size: 465
46062369 CCAACGTCCT
46062379 AGACGAGGTCTTACATGTAATCAAATATCGATACCACTGTCCCAGACAGGGTCTTACACGTAAAT
1 AGACGAGGTCTTACATGTAATCAAATATCGATACCACTGTCCCAGACAGGGTCTTACACGTAAAT
*
46062444 CTCAAATCGATGCCAATGTCCCAGACGTGGTCTTACACGAAATCACATATCGAAATCTTATGTCA
66 CTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATATCGAAATCTTATGTCA
46062509 TGACATATGTATTCTAACTATTCCTAAGGTTCGAACGGGGCTTTCGGACGTCGTATTTTGATCGA
131 TGACATATGTATTCTAACTATTCCTAAGGTTCGAACGGGGCTTTCGGACGTCGTATTTTGATCGA
46062574 TTCAAGCTCGTAACAAATCATTCCATGCTAAATTCAATTCGGCAATGTAATTATACATACATACA
196 TTCAAGCTCGTAACAAATCATTCCATGCTAAATTCAATTCGGCAATGTAATTATACATACATACA
46062639 ATTCAATTTGACTATGTACAAAATAAATACATACAATTTAACATCCTTTATTCACTTACAATCTT
261 ATTCAATTTGACTATGTACAAAATAAATACATACAATTTAACATCCTTTATTCACTTACAATCTT
46062704 ACCTCGGACGAAGACGAACGGACCGGGACGACTATTCGACAACTTTTGATTTCCTCCGATCCAAA
326 ACCTCGGACGAAGACGAACGGACCGGGACGACTATTCGACAACTTTTGATTTCCTCCGATCCAAA
46062769 TTCGATTTCTTCTTTTCTTGATCTAAATTAATACAAATTTGACTTGTTTAGTCATATATTTATTC
391 TTCGATTTCTTCTTTTCTTGATCTAAATTAATACAAATTTGACTTGTTTAGTCATATATTTATTC
46062834 AAATTCATCC
456 AAATTCATCC
46062844 AGACGAGGTCTTACATGTAATCAAATATCGATACCACTGTCCCAGACAGGGTCTTACACGTAAAT
1 AGACGAGGTCTTACATGTAATCAAATATCGATACCACTGTCCCAGACAGGGTCTTACACGTAAAT
*
46062909 CTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATATCGGAATCTTATGTCA
66 CTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATATCGAAATCTTATGTCA
46062974 TGACATATGTATTCTAACTATTCCTAAGGTTCGAACGGGGCTTTCGGACGTCGTATTTTGATCGA
131 TGACATATGTATTCTAACTATTCCTAAGGTTCGAACGGGGCTTTCGGACGTCGTATTTTGATCGA
46063039 TTCAAGCTCGTAACAAATCATTCCATGCTAAATTCAATTCGGCAATGTAATTATACATACATACA
196 TTCAAGCTCGTAACAAATCATTCCATGCTAAATTCAATTCGGCAATGTAATTATACATACATACA
46063104 ATTCAATTTGACTATGTACAAAATAAATACATACAATTTAACATCCTTTATTCACTTACAATCTT
261 ATTCAATTTGACTATGTACAAAATAAATACATACAATTTAACATCCTTTATTCACTTACAATCTT
46063169 ACCTCGGACGAAGACGAACGGACCGGGACGACTATTCGACAACTTTTGATTTCCTCCGATCCAAA
326 ACCTCGGACGAAGACGAACGGACCGGGACGACTATTCGACAACTTTTGATTTCCTCCGATCCAAA
46063234 TTCGATTTCTTCTTTTCTTGATCTAAATTAATACAAATTTGACTTGTTTAGTCATATATTTATTC
391 TTCGATTTCTTCTTTTCTTGATCTAAATTAATACAAATTTGACTTGTTTAGTCATATATTTATTC
46063299 AAATTCATCC
456 AAATTCATCC
46063309 A
1 A
46063310 AAAACACAAA
Statistics
Matches: 464, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
465 464 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (465 bp):
AGACGAGGTCTTACATGTAATCAAATATCGATACCACTGTCCCAGACAGGGTCTTACACGTAAAT
CTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATATCGAAATCTTATGTCA
TGACATATGTATTCTAACTATTCCTAAGGTTCGAACGGGGCTTTCGGACGTCGTATTTTGATCGA
TTCAAGCTCGTAACAAATCATTCCATGCTAAATTCAATTCGGCAATGTAATTATACATACATACA
ATTCAATTTGACTATGTACAAAATAAATACATACAATTTAACATCCTTTATTCACTTACAATCTT
ACCTCGGACGAAGACGAACGGACCGGGACGACTATTCGACAACTTTTGATTTCCTCCGATCCAAA
TTCGATTTCTTCTTTTCTTGATCTAAATTAATACAAATTTGACTTGTTTAGTCATATATTTATTC
AAATTCATCC
Found at i:46068072 original size:37 final size:35
Alignment explanation
Indices: 46068031--46068099 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
46068021 GATGGGTTTC
* *
46068031 TTTAGTTCTTTTATATATTTTTATAAGTTTATAAAAT
1 TTTAGTTCTTTTATACATTTATAT-A-TTTATAAAAT
46068068 TTTAGTTCTTTTATACATTTATATATTTATAA
1 TTTAGTTCTTTTATACATTTATATATTTATAA
46068100 TTTTTCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 7 0.23
36 1 0.03
37 22 0.73
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (35 bp):
TTTAGTTCTTTTATACATTTATATATTTATAAAAT
Found at i:46072978 original size:21 final size:21
Alignment explanation
Indices: 46072946--46072986 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
46072936 GAACATTTGG
46072946 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
46072967 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
46072987 CCTCAAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:46074112 original size:13 final size:13
Alignment explanation
Indices: 46074094--46074121 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
46074084 ATGCAGCAGC
46074094 CAAGGTGGCCATG
1 CAAGGTGGCCATG
46074107 CAAGGTGGCCATG
1 CAAGGTGGCCATG
46074120 CA
1 CA
46074122 GGGAACGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.25, G:0.36, T:0.14
Consensus pattern (13 bp):
CAAGGTGGCCATG
Found at i:46077261 original size:29 final size:30
Alignment explanation
Indices: 46077218--46077299 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
46077208 GAATTAGATC
46077218 AAATTAAAATTTTATATATAAAATTACACA-
1 AAATTAAAA-TTTATATATAAAATTACACAT
* * * *
46077248 AAATCAAAATTTATATATTAAATTATATATT
1 AAATTAAAATTTATATATAAAATTACACA-T
*
46077279 AAATTAAAATTTATGTATAAA
1 AAATTAAAATTTATATATAAA
46077300 TTTAATACTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 17 0.40
30 8 0.19
31 18 0.42
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (30 bp):
AAATTAAAATTTATATATAAAATTACACAT
Found at i:46077275 original size:12 final size:12
Alignment explanation
Indices: 46077258--46077284 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
46077248 AAATCAAAAT
46077258 TTATATATTAAA
1 TTATATATTAAA
46077270 TTATATATTAAA
1 TTATATATTAAA
46077282 TTA
1 TTA
46077285 AAATTTATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATATATTAAA
Found at i:46077288 original size:31 final size:29
Alignment explanation
Indices: 46077218--46077301 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
46077208 GAATTAGATC
*
46077218 AAATTAAAATTTTATATATAAAATTACACA
1 AAATTAAAA-TTTATATATTAAATTACACA
* * *
46077248 AAATCAAAATTTATATATTAAATTATATA
1 AAATTAAAATTTATATATTAAATTACACA
*
46077277 TTAAATTAAAATTTATGTA-TAAATT
1 --AAATTAAAATTTATATATTAAATT
46077302 TAATACTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.37
30 14 0.30
31 15 0.33
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (29 bp):
AAATTAAAATTTATATATTAAATTACACA
Found at i:46087489 original size:28 final size:30
Alignment explanation
Indices: 46087457--46087531 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 30
46087447 ATGCACAAGG
*
46087457 TAGCCATAGAGGCGTCCATACAA-A-TAGA
1 TAGCCATAGAGGCGTCCACACAACATTAGA
* * *
46087485 TAGCCACAAAGGCGTCCACATAACATTAGA
1 TAGCCATAGAGGCGTCCACACAACATTAGA
46087515 TAGCCAT-GAAGGCGTCC
1 TAGCCATAG-AGGCGTCC
46087532 TCATATAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 19 0.50
29 1 0.03
30 18 0.47
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.17
Consensus pattern (30 bp):
TAGCCATAGAGGCGTCCACACAACATTAGA
Found at i:46087616 original size:19 final size:19
Alignment explanation
Indices: 46087587--46087632 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
46087577 GGATATATTT
46087587 TAAAT-TTATTTAGGTAGA
1 TAAATCTTATTTAGGTAGA
46087605 TAAATCTTATTTAGGTAGA
1 TAAATCTTATTTAGGTAGA
*
46087624 TAATTCTTA
1 TAAATCTTA
46087633 GAATAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (19 bp):
TAAATCTTATTTAGGTAGA
Found at i:46095037 original size:25 final size:25
Alignment explanation
Indices: 46095012--46095135 Score: 94
Period size: 25 Copynumber: 5.0 Consensus size: 25
46095002 ATACATATAT
*
46095012 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTATGAATCGGTAA
* * *
46095037 GCTC-TCACGAGCTGTAAATCGGCAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
* * *
46095062 GCTCATACGAGTTAAGAATTGGTAA
1 GCTCATACGAGCTATGAATCGGTAA
* *
46095087 GCT-TTCACGAGCTGT-AATCGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
* *
46095111 GCTCATATGAGTTGA-GAATCGGTAA
1 GCTCATACGAGCT-ATGAATCGGTAA
46095136 TCACTAATGA
Statistics
Matches: 74, Mismatches: 19, Indels: 12
0.70 0.18 0.11
Matches are distributed among these distances:
24 18 0.24
25 55 0.74
26 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCGGTAA
Found at i:46095123 original size:49 final size:50
Alignment explanation
Indices: 46095012--46095135 Score: 169
Period size: 50 Copynumber: 2.5 Consensus size: 50
46095002 ATACATATAT
* * *
46095012 GCTCATACGAGCTATGAATCGGTATGCTCTCACGAGCTGTAAATCGGCAA
1 GCTCATACGAGTTAAGAATCGGTAAGCTCTCACGAGCTGTAAATCGGCAA
* * *
46095062 GCTCATACGAGTTAAGAATTGGTAAGCTTTCACGAGCTGT-AATCGGTAA
1 GCTCATACGAGTTAAGAATCGGTAAGCTCTCACGAGCTGTAAATCGGCAA
* *
46095111 GCTCATATGAGTTGAGAATCGGTAA
1 GCTCATACGAGTTAAGAATCGGTAA
46095136 TCACTAATGA
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 30 0.46
50 35 0.54
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (50 bp):
GCTCATACGAGTTAAGAATCGGTAAGCTCTCACGAGCTGTAAATCGGCAA
Found at i:46107261 original size:31 final size:33
Alignment explanation
Indices: 46107221--46107286 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
46107211 GGGTAAGACA
46107221 TTTTCCACAGCTCATC-TTCACTCTCTTCACCC
1 TTTTCCACAGCTCATCTTTCACTCTCTTCACCC
*
46107253 TTTT-CACAGCTCCTCTTTTCACTCTCTTCACCC
1 TTTTCCACAGCTCATC-TTTCACTCTCTTCACCC
46107286 T
1 T
46107287 AACGATTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 10 0.32
32 4 0.13
33 17 0.55
ACGTcount: A:0.14, C:0.42, G:0.03, T:0.41
Consensus pattern (33 bp):
TTTTCCACAGCTCATCTTTCACTCTCTTCACCC
Found at i:46107509 original size:11 final size:12
Alignment explanation
Indices: 46107493--46107525 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
46107483 TGAATTAGGG
46107493 CTTTTTTTT-TC
1 CTTTTTTTTCTC
46107504 CTTTTTTTTTCTC
1 C-TTTTTTTTCTC
46107517 CTTTTTTTT
1 CTTTTTTTT
46107526 GGGTTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 16 0.80
13 3 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
CTTTTTTTTCTC
Found at i:46107512 original size:13 final size:13
Alignment explanation
Indices: 46107494--46107525 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
46107484 GAATTAGGGC
46107494 TTTTTTTT-TCCT
1 TTTTTTTTCTCCT
46107506 TTTTTTTTCTCCT
1 TTTTTTTTCTCCT
46107519 TTTTTTT
1 TTTTTTT
46107526 GGGTTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTCCT
Found at i:46116974 original size:76 final size:77
Alignment explanation
Indices: 46116856--46117029 Score: 289
Period size: 76 Copynumber: 2.3 Consensus size: 77
46116846 AAAGTTTATT
**
46116856 TATTTAAATTGCAAAAAAAATTCATAAAATTGATAAATAAAATGGA-AAAAAAGTCATTACATAA
1 TATTTAAATTGCAAAAAAAACCCATAAAATTGATAAATAAAAT-GACAAAAAAGTCATTACATAA
46116920 ATACAAAGTTGAC
65 ATACAAAGTTGAC
*
46116933 TATTTAAATTG-AAAAAAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAAA
1 TATTTAAATTGCAAAAAAAACCCATAAAATTGATAAATAAAATGACAAAAAAGTCATTACATAAA
46116997 TACAAAGTTGAC
66 TACAAAGTTGAC
46117009 TATTTAAATTGCAAAATAAAA
1 TATTTAAATTGCAAAA-AAAA
46117030 AATAAAAAAA
Statistics
Matches: 91, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
75 2 0.02
76 70 0.77
77 15 0.16
78 4 0.04
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (77 bp):
TATTTAAATTGCAAAAAAAACCCATAAAATTGATAAATAAAATGACAAAAAAGTCATTACATAAA
TACAAAGTTGAC
Found at i:46117134 original size:93 final size:92
Alignment explanation
Indices: 46116944--46117124 Score: 262
Period size: 93 Copynumber: 2.0 Consensus size: 92
46116934 ATTTAAATTG
46116944 AAAAA-AAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAAATACAAAGTTGA
1 AAAAATAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACA-AAATACAAAGTTGA
46117008 CTATTTAAATTGCAAAATAAAAAATAAA
65 CTATTTAAATTGCAAAATAAAAAATAAA
* * * * **
46117036 AAAAATAAACCCATAAATTTGATAAATAAAATGATAACAAATTCATTTC-AAATATGAAGTTGAC
1 AAAAATAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACAAAATACAAAGTTGAC
*
46117100 TATTTAAATTGC-AGA-AAAAAATAAA
66 TATTTAAATTGCAAAATAAAAAATAAA
46117125 CTCATAAAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
89 10 0.12
90 2 0.02
91 25 0.31
92 5 0.06
93 39 0.48
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (92 bp):
AAAAATAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACAAAATACAAAGTTGAC
TATTTAAATTGCAAAATAAAAAATAAA
Found at i:46119645 original size:103 final size:102
Alignment explanation
Indices: 46119506--46119757 Score: 359
Period size: 103 Copynumber: 2.5 Consensus size: 102
46119496 TACATTATAT
*
46119506 AAAAATTACA-T--TAAAAATCACAAAACACTAAACTAAACACTAACAAATTATATAACCTAATC
1 AAAAATTACATTACTAAAAATCACAAAACAC-ATACTAAACACTAACAAATTATATAACCTAATC
* * * *
46119568 ATAAATTACTAATAAAATAACTATAAATTTATTTTTTT
65 ATAAAATACTAACAAAATAACTATAAAATTATTTTTTA
* *
46119606 AATAA-TACATTACTAAAATATCACAAAACACATACCTAAACACTAACAATTTATATAACCTAAT
1 AAAAATTACATTACTAAAA-ATCACAAAACACATA-CTAAACACTAACAAATTATATAACCTAAT
46119670 CATAAAATACTAACAAAATAACTATAAAATTATTTTTTA
64 CATAAAATACTAACAAAATAACTATAAAATTATTTTTTA
*
46119709 AAAAATTACATTACTAGAAAATCACAAAACCCTATACTAAACACTAACA
1 AAAAATTACATTACTA-AAAATCACAAAACAC-ATACTAAACACTAACA
46119758 GCATGTTTGG
Statistics
Matches: 135, Mismatches: 9, Indels: 12
0.87 0.06 0.08
Matches are distributed among these distances:
99 4 0.03
100 5 0.04
102 7 0.05
103 79 0.59
104 34 0.25
105 6 0.04
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (102 bp):
AAAAATTACATTACTAAAAATCACAAAACACATACTAAACACTAACAAATTATATAACCTAATCA
TAAAATACTAACAAAATAACTATAAAATTATTTTTTA
Found at i:46123363 original size:17 final size:17
Alignment explanation
Indices: 46123329--46123369 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
46123319 AGAATTTCAT
**
46123329 TAAATTATATTTTTTAA
1 TAAATTATATTTAATAA
46123346 TAAATTATATTTAATAA
1 TAAATTATATTTAATAA
46123363 T-AATTAT
1 TAAATTAT
46123370 GTTAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTATATTTAATAA
Found at i:46123402 original size:119 final size:121
Alignment explanation
Indices: 46123257--46123553 Score: 503
Period size: 119 Copynumber: 2.5 Consensus size: 121
46123247 TACATTATAC
*
46123257 ATTAT-TTTTATAGCATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
46123321 AATTTCATTAAATTATAT-TTTTTAATAAATTATATTTAATAATAATTATGTT-AA
66 AATTTCATTAAATTATATATTTTTAATAAATTATATTTAATAATAATTATGTTAAA
46123375 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTTAATATTAA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-TTTAATATTAA
* *
46123440 GAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
65 GAATTTCATTAAATTATATATTTTTAATAAATTATATTTAATAATAATTATGTTAAA
* *
46123497 ATTATATTTTATAGTATTATATATTATGATTTTAGTAATTTAATATTAAGAAT-TTTA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATA-TAAGAATATTTA
46123554 TTAAATTATA
Statistics
Matches: 169, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
118 5 0.03
119 46 0.27
120 29 0.17
121 37 0.22
122 45 0.27
123 7 0.04
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (121 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
AATTTCATTAAATTATATATTTTTAATAAATTATATTTAATAATAATTATGTTAAA
Found at i:46123455 original size:17 final size:17
Alignment explanation
Indices: 46123420--46123473 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
46123410 TAAATTCATA
*
46123420 TAAGAATATT-TTAATAT
1 TAAGAATTTTATTAA-AT
46123437 TAAGAATTTTATTAAAT
1 TAAGAATTTTATTAAAT
* *
46123454 TATATATTTTTATTAAAT
1 TA-AGAATTTTATTAAAT
46123472 TA
1 TA
46123474 TATTTAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TAAGAATTTTATTAAAT
Found at i:46123542 original size:22 final size:22
Alignment explanation
Indices: 46123497--46123567 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
46123487 TTATGTTAAA
*
46123497 ATTAT-ATTTTATAGTATTATAT
1 ATTATGATTTTATAAT-TTATAT
46123519 ATTATGATTTTAGTAATTTA-AT
1 ATTATGATTTTA-TAATTTATAT
* *
46123541 ATTAAGAATTTTATTAAATTATAT
1 ATTATG-ATTTTA-TAATTTATAT
46123565 ATT
1 ATT
46123568 TTTACTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 12 0.29
23 21 0.51
24 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (22 bp):
ATTATGATTTTATAATTTATAT
Found at i:46123566 original size:24 final size:23
Alignment explanation
Indices: 46123512--46123567 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
46123502 ATTTTATAGT
*
46123512 ATTATATATTATGATTTTAGTAA
1 ATTATATATTAAGATTTTAGTAA
* *
46123535 TTTA-ATATTAAGAATTTTATTAA
1 ATTATATATTAAG-ATTTTAGTAA
46123558 ATTATATATT
1 ATTATATATT
46123568 TTTACTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 7 0.26
23 15 0.56
24 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (23 bp):
ATTATATATTAAGATTTTAGTAA
Found at i:46124089 original size:16 final size:16
Alignment explanation
Indices: 46124064--46124117 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
46124054 TTAAATTGCT
*
46124064 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
46124080 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
**
46124096 ATTACGTCTCTATTCC
1 ATTACACCTCTATTCC
46124112 ATTACA
1 ATTACA
46124118 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.24, C:0.33, G:0.04, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:46124205 original size:18 final size:19
Alignment explanation
Indices: 46124163--46124207 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
46124153 TCCCATAAAT
*
46124163 TACTAACAAAATAAATAAC
1 TACTAACAAAACAAATAAC
46124182 TA-TAACAAAACACAA-AA-
1 TACTAACAAAACA-AATAAC
46124199 TACTAACAA
1 TACTAACAA
46124208 TTTATAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 17 0.74
19 4 0.17
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (19 bp):
TACTAACAAAACAAATAAC
Found at i:46124448 original size:60 final size:60
Alignment explanation
Indices: 46124375--46124489 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 60
46124365 TAAAATAAAT
* *
46124375 ACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTACAAAC
1 ACAACAAGTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAC
46124435 ACAACAAGTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 ACAACAAGTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
46124490 TAAAAAATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (60 bp):
ACAACAAGTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAC
Found at i:46124665 original size:3 final size:3
Alignment explanation
Indices: 46124657--46124697 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
46124647 CTTTCTTTCT
* *
46124657 TTC TTC TTC TTC -TC TTC TTC TTC TTA TTC TT- TTT TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
46124698 CCTTTCTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:46124666 original size:14 final size:14
Alignment explanation
Indices: 46124645--46124710 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
46124635 CATTACCTTT
46124645 TTCTTTCTTTCTTTC
1 TTCTTTCTTTC-TTC
46124660 TTC-TTC-TTC-TC
1 TTCTTTCTTTCTTC
*
46124671 TTC-TTC-TTCTTA
1 TTCTTTCTTTCTTC
*
46124683 TTCTTTTTTTCTTC
1 TTCTTTCTTTCTTC
* *
46124697 TCCTTTCTCTCTTC
1 TTCTTTCTTTCTTC
46124711 CGGTGCACCT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
11 11 0.26
12 4 0.10
13 5 0.12
14 19 0.45
15 3 0.07
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (14 bp):
TTCTTTCTTTCTTC
Found at i:46124677 original size:17 final size:17
Alignment explanation
Indices: 46124657--46124710 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
46124647 CTTTCTTTCT
46124657 TTCTTCTTCTTCTCTTC
1 TTCTTCTTCTTCTCTTC
* * *
46124674 TTCTTCTTATTCTTTTT
1 TTCTTCTTCTTCTCTTC
*
46124691 TTCTTCTCCTT-TCTCTC
1 TTCTTCTTCTTCTCT-TC
46124708 TTC
1 TTC
46124711 CGGTGCACCT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 2 0.07
17 27 0.93
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCTTCTTCTTCTCTTC
Found at i:46125028 original size:26 final size:24
Alignment explanation
Indices: 46124999--46125049 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
46124989 TATATATTTA
46124999 AATATTTTTAATAAAAATAAAATAAT
1 AATA-TTTTAATAAAAATAAAA-AAT
* *
46125025 AATATTTTATTTAAAATAAAAAAT
1 AATATTTTAATAAAAATAAAAAAT
46125049 A
1 A
46125050 TTTTAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 15 0.65
26 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATATTTTAATAAAAATAAAAAAT
Found at i:46125039 original size:20 final size:21
Alignment explanation
Indices: 46125016--46125054 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46125006 TTAATAAAAA
*
46125016 TAAAAT-AATAATATTTTATT
1 TAAAATAAAAAATATTTTATT
46125036 TAAAATAAAAAATATTTTA
1 TAAAATAAAAAATATTTTA
46125055 ATATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATAAAAAATATTTTATT
Found at i:46125123 original size:17 final size:17
Alignment explanation
Indices: 46125101--46125137 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
46125091 GCCCCAAAAA
46125101 ATATACCATTTTCGTAT
1 ATATACCATTTTCGTAT
46125118 ATATACCATTTTCGTAT
1 ATATACCATTTTCGTAT
46125135 ATA
1 ATA
46125138 ATCCAGCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (17 bp):
ATATACCATTTTCGTAT
Found at i:46126952 original size:44 final size:44
Alignment explanation
Indices: 46126889--46126977 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
46126879 GCTTGGATAT
46126889 TTGTGTCTCTATTTATGAATCCATGTTCGGTTAATTAAGGCTAA
1 TTGTGTCTCTATTTATGAATCCATGTTCGGTTAATTAAGGCTAA
*
46126933 TTGTGTCTCTATTTATGAATCCATGTTCGGTTAATTGAGGCTAA
1 TTGTGTCTCTATTTATGAATCCATGTTCGGTTAATTAAGGCTAA
46126977 T
1 T
46126978 CTTAGTGAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (44 bp):
TTGTGTCTCTATTTATGAATCCATGTTCGGTTAATTAAGGCTAA
Found at i:46131606 original size:74 final size:74
Alignment explanation
Indices: 46131510--46131654 Score: 211
Period size: 74 Copynumber: 2.0 Consensus size: 74
46131500 AAAGTGCCAC
* *
46131510 AAAAAACCTAAGTCCAACGACGCCGTTTCCCGAGCTTTCGGGGATTTAGTAGCGTTTTTCGGAAA
1 AAAAAACCTAAGTCCAACGACGCCGTTTCCCGAGCTTTCGGGGATTTAGCAGCGTTTTTCAGAAA
46131575 GCACCGTAA
66 GCACCGTAA
* *** *
46131584 AAAAAACCTAAG-CCTAGCGACGCCGTTTTTTGAGCTTTCGGGGATTTAGCGGCGTTTTTCAGAA
1 AAAAAACCTAAGTCC-AACGACGCCGTTTCCCGAGCTTTCGGGGATTTAGCAGCGTTTTTCAGAA
46131648 AGCACCG
65 AGCACCG
46131655 CTAATGCTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
73 2 0.03
74 61 0.97
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (74 bp):
AAAAAACCTAAGTCCAACGACGCCGTTTCCCGAGCTTTCGGGGATTTAGCAGCGTTTTTCAGAAA
GCACCGTAA
Found at i:46131756 original size:114 final size:113
Alignment explanation
Indices: 46131561--46132339 Score: 1065
Period size: 114 Copynumber: 6.8 Consensus size: 113
46131551 GGATTTAGTA
* * * * * *
46131561 GCGTTTTTCGGAAAGCACCGTAAAAAAAACCTAAGCCTAGCGACGCCGTTTTTTGAGCTTTCGGG
1 GCGTTTTTGGGAAAGCGCCG-CAAAAAAACCTAAGCC-AACGGCGCCGTTTTCTGAGCTTTCGGG
* * *
46131626 GATTTAGCGGCGTTTTTCAGAAAGCACCGCTAATGCTCAGGGCTTTAGCG
64 GATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCG
* * * *
46131676 GTGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCGAACGGTGCCTTTTTCTGAGCTATCGGGG
1 GCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCC-AACGGCGCCGTTTTCTGAGCTTTCGGGG
* *
46131741 ATTTAGCGGCATTTTTAAGGAAGTGCCGCTAATGCTCAGGGCTTTAGCG
65 ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCG
* * *
46131790 GCGTTTTTGGGAAAGCGCCGCAAACAAACCTAAGACCAACGACGCCGTTTTCTGAGCTTTTGGGG
1 GCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAG-CCAACGGCGCCGTTTTCTGAGCTTTCGGGG
* *
46131855 ATTTAGCGGCGTTTTTAGGGAAGCGCCCCTAATGCTCAGGGCTTTAGCG
65 ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCG
* * *
46131904 ACGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCGCCGTTTTCTGAGCTATCAGGG
1 GCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAG-CCAACGGCGCCGTTTTCTGAGCTTTCGGGG
* *
46131969 ATTTAGTGGCGTTTTTAAGGAAGCACCGCTAATGCTCAGGGCTTTAGCG
65 ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCG
* * * *
46132018 GCATTTTTGGGAAAGCGCCGCAAACAAACCTAAGACCAACGGCGCCGTTTTATAAGCTTTCGGGG
1 GCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAG-CCAACGGCGCCGTTTTCTGAGCTTTCGGGG
* * *
46132083 ATTTAGCGGCTTTTTTAGGGAAGCGCTGCTAATGCTCAGGGCTTTAGCG
65 ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCG
** *
46132132 ATGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCGCCGTTTTTTGAGCTTTCGGGG
1 GCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAG-CCAACGGCGCCGTTTTCTGAGCTTTCGGGG
* * * * * **
46132197 ATTTTGTGGCGTTTTTAAGGAAGCGTCACTAATGCTCAGGCCTTTAGTA
65 ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCG
* *
46132246 GCGTTTTTGGGAAAGCTCCGCAAAAAAACCTAAGCTCAACGGCGCCATTTTCTGAGCTTTCGGGG
1 GCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGC-CAACGGCGCCGTTTTCTGAGCTTTCGGGG
*
46132311 ATTTAGCGGCGTTTTTGAA-AAAGCGCCGC
65 ATTTAGCGGCGTTTTT-AAGGAAGCGCCGC
46132340 AAAAAAACCT
Statistics
Matches: 583, Mismatches: 78, Indels: 7
0.87 0.12 0.01
Matches are distributed among these distances:
113 1 0.00
114 561 0.96
115 21 0.04
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (113 bp):
GCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCAACGGCGCCGTTTTCTGAGCTTTCGGGGA
TTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCG
Found at i:46132359 original size:73 final size:73
Alignment explanation
Indices: 46132246--46132417 Score: 272
Period size: 73 Copynumber: 2.4 Consensus size: 73
46132236 GCCTTTAGTA
* * * *
46132246 GCGTTTTTGGGAAAGCTCCGCAAAAAAACCTAAGCTCAACGGCGCCATTTTCTGAGCTTTCGGGG
1 GCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCGCCATTTTCTGAGATTTCGGGG
46132311 ATTTAGCG
66 ATTTAGCG
* * *
46132319 GCGTTTTTGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGTCGCCGTTTTCTGAGATTTCGGGG
1 GCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCGCCATTTTCTGAGATTTCGGGG
46132384 ATTTAGCG
66 ATTTAGCG
*
46132392 GCGTTTTTGGAAAAGCGCCGCTAAAA
1 GCGTTTTTGGAAAAGCGCCGCAAAAA
46132418 TTATTTTATC
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 90 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (73 bp):
GCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCGCCATTTTCTGAGATTTCGGGG
ATTTAGCG
Found at i:46132747 original size:15 final size:15
Alignment explanation
Indices: 46132678--46132749 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
46132668 TAGGTAGTAT
*
46132678 GGGTTTAGGGATTA-
1 GGGTTTAGGGGTTAG
* *
46132692 TGGATTAGGGGTT-G
1 GGGTTTAGGGGTTAG
* * *
46132706 GGATTTAAGGTTTAG
1 GGGTTTAGGGGTTAG
* *
46132721 GGGTTAAAGGGTTAG
1 GGGTTTAGGGGTTAG
46132736 GGGTTTAGGGGTTA
1 GGGTTTAGGGGTTA
46132750 AAAGTTAGGA
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
14 18 0.42
15 25 0.58
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (15 bp):
GGGTTTAGGGGTTAG
Found at i:46132767 original size:22 final size:23
Alignment explanation
Indices: 46132719--46132769 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
46132709 TTTAAGGTTT
* ** *
46132719 AGGGGTTAAAGGGTTAGGGGTTT
1 AGGGGTTAAAGAGTTAGGAATTC
46132742 AGGGGTTAAA-AGTTAGGAATTC
1 AGGGGTTAAAGAGTTAGGAATTC
46132764 AGGGGT
1 AGGGGT
46132770 CGAGTTAGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.27, C:0.02, G:0.43, T:0.27
Consensus pattern (23 bp):
AGGGGTTAAAGAGTTAGGAATTC
Found at i:46132954 original size:15 final size:15
Alignment explanation
Indices: 46132934--46132980 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
46132924 TATTTTAAGG
*
46132934 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
46132949 TTTAGGGATTAT-GA
1 TTTAGGGATTATGGA
*
46132963 ATTAGGGATTATGG-
1 TTTAGGGATTATGGA
46132977 TTTA
1 TTTA
46132981 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:46133001 original size:21 final size:20
Alignment explanation
Indices: 46132967--46133007 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
46132957 TTATGAATTA
*
46132967 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
46132987 GGGATTTAAGGTTTAAGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
46133008 AAGGGTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:46133031 original size:14 final size:14
Alignment explanation
Indices: 46133003--46133047 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
46132993 TAAGGTTTAA
*
46133003 GGGTTAAGGGTTTAG
1 GGGTTAAGAG-TTAG
46133018 GGGTT-AGATGTTAG
1 GGGTTAAGA-GTTAG
46133032 GGGTTAAGAGTTAG
1 GGGTTAAGAGTTAG
46133046 GG
1 GG
46133048 ATTTAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGTTAAGAGTTAG
Found at i:46133057 original size:14 final size:16
Alignment explanation
Indices: 46132987--46133065 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 16
46132977 TTTAAGGGTT
46132987 GGGATTTAAG-GTTTAA
1 GGGATTTAAGAGTTT-A
*
46133003 GGG--TTAAGGGTTTA
1 GGGATTTAAGAGTTTA
*
46133017 GGG-GTT-AGA-TGTTA
1 GGGATTTAAGAGT-TTA
*
46133031 GGG-GTTAAGAG-TTA
1 GGGATTTAAGAGTTTA
46133045 GGGATTTAA-AGTTTA
1 GGGATTTAAGAGTTTA
46133060 GGGATT
1 GGGATT
46133066 CAGGGGTCGA
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
13 1 0.02
14 28 0.52
15 22 0.41
16 3 0.06
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (16 bp):
GGGATTTAAGAGTTTA
Found at i:46133989 original size:103 final size:105
Alignment explanation
Indices: 46133843--46134052 Score: 316
Period size: 103 Copynumber: 2.0 Consensus size: 105
46133833 AAAGATAAGC
*
46133843 AATAGCGGTGTTTTCTATAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAA
1 AATAGCGGCGTTTTCTATAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAA
* * *
46133908 TTTTTAGCATAATAAAACGGCGTCATTTTGTTCAAAATGA
66 TTTTTAGAATAACAAAACGGCATCATTTTGTTCAAAATGA
* *
46133948 AATAGCGGCGTTTT-TAT-TAACGCTGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAA
1 AATAGCGGCGTTTTCTATAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAA
* * * *
46134011 TTTTTAGAATAGCAAAACGGTATCGTTTTGTTCAGAATGA
66 TTTTTAGAATAACAAAACGGCATCATTTTGTTCAAAATGA
46134051 AA
1 AA
46134053 AAAATTTTAC
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 79 0.83
104 3 0.03
105 13 0.14
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (105 bp):
AATAGCGGCGTTTTCTATAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAA
TTTTTAGAATAACAAAACGGCATCATTTTGTTCAAAATGA
Found at i:46136821 original size:45 final size:45
Alignment explanation
Indices: 46136764--46136865 Score: 204
Period size: 45 Copynumber: 2.3 Consensus size: 45
46136754 GGAATGTTAA
46136764 ACCTTTATGTGGCTAATTGTTTGAGTATGCCTTATTGAGTTAATT
1 ACCTTTATGTGGCTAATTGTTTGAGTATGCCTTATTGAGTTAATT
46136809 ACCTTTATGTGGCTAATTGTTTGAGTATGCCTTATTGAGTTAATT
1 ACCTTTATGTGGCTAATTGTTTGAGTATGCCTTATTGAGTTAATT
46136854 ACCTTTATGTGG
1 ACCTTTATGTGG
46136866 TGATAGTGGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.46
Consensus pattern (45 bp):
ACCTTTATGTGGCTAATTGTTTGAGTATGCCTTATTGAGTTAATT
Found at i:46137801 original size:43 final size:43
Alignment explanation
Indices: 46137707--46137951 Score: 221
Period size: 43 Copynumber: 5.7 Consensus size: 43
46137697 CAAGAAGCGT
* * * * *
46137707 CGCTAAAGGT-TTGTTCTATAGCGGCGTTTTTGATATAAGCGC
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAGTGC
*
46137749 CGCTAAAAGGTCTTGATCTATAGCGGCGTTTGT-AAAAAAGGTGC
1 CGCT-AAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAA-GTGC
* * * *
46137793 CGCTAAAGGTCTTGATCTACAGTGGCATTTGTGGGAAAA-TCGC
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAGT-GC
* * * * *
46137836 CGTTAAAGGTCTTGAGCTATAGCGGCTTTTGTTGTAG--AAGCGT
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTG-TG-AGAAAAGTGC
* * * *
46137879 CGCTAAAGATCCTGATCTATAGCGGCGTTTGTGAGGAAAGCGC
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAGTGC
* *
46137922 CGCTAAAGGTCATGGTCTATAGCGGCGTTT
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTT
46137952 ATTTCCAAAA
Statistics
Matches: 166, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
41 2 0.01
42 7 0.04
43 124 0.75
44 32 0.19
45 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (43 bp):
CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAGTGC
Found at i:46145840 original size:18 final size:20
Alignment explanation
Indices: 46145817--46145860 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
46145807 TTTTCCAACA
*
46145817 AAATATCT-TAAAC-ATGTT
1 AAATATCTATAAACGATATT
46145835 AAATATCTATAAACGATATT
1 AAATATCTATAAACGATATT
46145855 AAATAT
1 AAATAT
46145861 TTCTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 10 0.43
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (20 bp):
AAATATCTATAAACGATATT
Found at i:46150436 original size:35 final size:36
Alignment explanation
Indices: 46150396--46150467 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
46150386 TCTAGGATCA
46150396 CATATC-TCAAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
* *
46150431 CATATCTTCAAAAGATCACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
46150467 C
1 C
46150468 TCCGGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
Found at i:46152290 original size:35 final size:36
Alignment explanation
Indices: 46152250--46152321 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
46152240 TCTAGGATCA
46152250 CATATC-TCAAAAGATCACCATCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACCATCCATATTTGCCAAG
** *
46152285 CATATCTTCAAAAGATCACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCATCCATATTTGCCAAG
46152321 C
1 C
46152322 TCCGGAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCATCCATATTTGCCAAG
Found at i:46162890 original size:30 final size:30
Alignment explanation
Indices: 46162834--46163119 Score: 224
Period size: 30 Copynumber: 9.6 Consensus size: 30
46162824 GTACATGTTT
*
46162834 TATAT-ATTGCCAAATTGATTTGTATATAGA
1 TATATCATTGCCGAATTGA-TTGTATATAGA
*
46162864 TATATTTATTGCCGAATTGATT-TATAT--A
1 TATA-TCATTGCCGAATTGATTGTATATAGA
* * *
46162892 TAT-TTATAGCCGAATTGATTCGTATATGGA
1 TATATCATTGCCGAATTGATT-GTATATAGA
* *
46162922 TATA-CATTGCTGAATTGATTTGTATATGGA
1 TATATCATTGCCGAATTGA-TTGTATATAGA
* *
46162952 TATA-CATTACCGAATTGATTTGTATATGGA
1 TATATCATTGCCGAATTGA-TTGTATATAGA
*
46162982 TATA-CATTGCCGGATTGATTTGTATAT-G-
1 TATATCATTGCCGAATTGA-TTGTATATAGA
*
46163010 TATATACATTGCCGAATTAATTTGTATATAGA
1 TATAT-CATTGCCGAATTGA-TTGTATATAGA
*
46163042 TATA-CATTACCGAATTGATTTGTATAT-G-
1 TATATCATTGCCGAATTGA-TTGTATATAGA
* *
46163070 TATATGTATTGTCGAATTGATTTGTATAT-GTA
1 TATAT-CATTGCCGAATTGA-TTGTATATAG-A
*
46163102 TATAT-ATTGCCGATTTGA
1 TATATCATTGCCGAATTGA
46163120 GCATTGGATG
Statistics
Matches: 222, Mismatches: 18, Indels: 32
0.82 0.07 0.12
Matches are distributed among these distances:
26 16 0.07
28 17 0.08
29 2 0.01
30 160 0.72
31 6 0.03
32 21 0.09
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.44
Consensus pattern (30 bp):
TATATCATTGCCGAATTGATTGTATATAGA
Found at i:46162898 original size:26 final size:26
Alignment explanation
Indices: 46162863--46162948 Score: 91
Period size: 26 Copynumber: 3.2 Consensus size: 26
46162853 TTGTATATAG
46162863 ATATATTTATTGCCGAATTGATTTAT
1 ATATATTTATTGCCGAATTGATTTAT
*
46162889 ATATATTTATAGCCGAATTGATTCGTAT
1 ATATATTTATTGCCGAATTGATT--TAT
** * *
46162917 ATGGATATACATTGCTGAATTGATTTGT
1 AT--ATATTTATTGCCGAATTGATTTAT
46162945 ATAT
1 ATAT
46162949 GGATATACAT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
26 24 0.48
28 9 0.18
30 17 0.34
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.45
Consensus pattern (26 bp):
ATATATTTATTGCCGAATTGATTTAT
Found at i:46162981 original size:60 final size:60
Alignment explanation
Indices: 46162846--46163119 Score: 315
Period size: 60 Copynumber: 4.6 Consensus size: 60
46162836 TATATTGCCA
* * **
46162846 AATTGATTTGTATATAGATATATTTATTGCCGAATTGA-TT-TATA--TATATTTA-TAGCCG
1 AATTGATTTGTATATGGATATA--CATTGCCGAATTGATTTGTATATGTATATACATTA-CCG
* * *
46162904 AATTGATTCGTATATGGATATACATTGCTGAATTGATTTGTATATGGATATACATTACCG
1 AATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATGTATATACATTACCG
* *
46162964 AATTGATTTGTATATGGATATACATTGCCGGATTGATTTGTATATGTATATACATTGCCG
1 AATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATGTATATACATTACCG
* * * ** **
46163024 AATTAATTTGTATATAGATATACATTACCGAATTGATTTGTATATGTATATGTATTGTCG
1 AATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATGTATATACATTACCG
* * *
46163084 AATTGATTTGTATATGTATATATATTGCCGATTTGA
1 AATTGATTTGTATATGGATATACATTGCCGAATTGA
46163120 GCATTGGATG
Statistics
Matches: 186, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
56 12 0.06
57 2 0.01
58 24 0.13
60 146 0.78
61 2 0.01
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (60 bp):
AATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATGTATATACATTACCG
Found at i:46163027 original size:90 final size:89
Alignment explanation
Indices: 46162834--46163119 Score: 362
Period size: 90 Copynumber: 3.2 Consensus size: 89
46162824 GTACATGTTT
* * * * *
46162834 TATATATTGCCAAATTGATTTGTATATAGATATATTTATTGCCGAATTGA-TT-TATAT-ATATT
1 TATACATTGCCGAATTGATTTGTATATAGATATA--CATTACCGAATTGATTTGTATATGATATA
* * *
46162896 TATAGCCGAATTGATTCGTATATGGA
64 TATTGCCGAATTGATTTGTATATGTA
* * *
46162922 TATACATTGCTGAATTGATTTGTATATGGATATACATTACCGAATTGATTTGTATATGGATATAC
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTACCGAATTGATTTGTATAT-GATATAT
*
46162987 ATTGCCGGATTGATTTGTATATGTA
65 ATTGCCGAATTGATTTGTATATGTA
* *
46163012 TATACATTGCCGAATTAATTTGTATATAGATATACATTACCGAATTGATTTGTATATGTATATGT
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTACCGAATTGATTTGTATATG-ATATAT
*
46163077 ATTGTCGAATTGATTTGTATATGTA
65 ATTGCCGAATTGATTTGTATATGTA
* *
46163102 TATATATTGCCGATTTGA
1 TATACATTGCCGAATTGA
46163120 GCATTGGATG
Statistics
Matches: 171, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
86 12 0.07
87 2 0.01
88 35 0.20
89 1 0.01
90 121 0.71
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.44
Consensus pattern (89 bp):
TATACATTGCCGAATTGATTTGTATATAGATATACATTACCGAATTGATTTGTATATGATATATA
TTGCCGAATTGATTTGTATATGTA
Found at i:46165447 original size:49 final size:49
Alignment explanation
Indices: 46165377--46165516 Score: 228
Period size: 49 Copynumber: 2.9 Consensus size: 49
46165367 ACTTATTTTC
* *
46165377 TCGATGCCATAGTCCAACTATGGTCTTACACGTAATCACATAACATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATA
*
46165426 -CTGATGTCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATA
1 TC-GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATA
*
46165475 TCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
46165517 TCACTTATTA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
48 1 0.01
49 82 0.98
50 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (49 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATA
Found at i:46168593 original size:18 final size:17
Alignment explanation
Indices: 46168560--46168598 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
46168550 TTTTATAAAT
46168560 TGTGAATTATGTTTGATA
1 TGTGAATTATGTTTGA-A
46168578 TGTGAATTAT-TATTGAA
1 TGTGAATTATGT-TTGAA
46168595 TGTG
1 TGTG
46168599 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (17 bp):
TGTGAATTATGTTTGAA
Found at i:46168857 original size:23 final size:23
Alignment explanation
Indices: 46168824--46168876 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
46168814 AGTGTTATTG
*
46168824 ATCAGTAGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTACGGCTACGT
*
46168847 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTACGGCTACGT
46168870 ATCAGTG
1 ATCAGTG
46168877 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACGT
Found at i:46181025 original size:23 final size:22
Alignment explanation
Indices: 46180974--46181025 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
46180964 CCTCGTCTTT
*
46180974 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
46180996 -TCATTTTCTATTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
46181019 TTCTTTT
1 TTCTTTT
46181026 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.12, C:0.21, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:46181040 original size:18 final size:18
Alignment explanation
Indices: 46181019--46181057 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
46181009 TTTCTTCAAC
*
46181019 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTTCTT
*
46181037 TTCTGTTTCACATTTCTT
1 TTCTGTTTCAAATTTCTT
46181055 TTC
1 TTC
46181058 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (18 bp):
TTCTGTTTCAAATTTCTT
Found at i:46192911 original size:31 final size:31
Alignment explanation
Indices: 46192848--46192911 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
46192838 TTTATTAATG
*
46192848 TATGAATATTATGTTTGTTAATATATGAATA
1 TATGAATATTATGTTTGATAATATATGAATA
46192879 TATGAATATTATGTTTGGAT-AT-TATGACATA
1 TATGAATATTATGTTT-GATAATATATGA-ATA
46192910 TA
1 TA
46192912 AACTAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 5 0.17
31 23 0.77
32 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.47
Consensus pattern (31 bp):
TATGAATATTATGTTTGATAATATATGAATA
Found at i:46193139 original size:21 final size:21
Alignment explanation
Indices: 46193094--46193140 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
46193084 AAATAATAAA
*
46193094 ATAG-ATTATATATTATTTTT
1 ATAGTATTATATATTATATTT
46193114 ATAGTATTATATATTATGATTT
1 ATAGTATTATATATTAT-ATTT
46193136 -TAGTA
1 ATAGTA
46193141 AATTCATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 17 0.71
22 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
ATAGTATTATATATTATATTT
Found at i:46193192 original size:16 final size:16
Alignment explanation
Indices: 46193171--46193201 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
46193161 TATTAAGAAT
46193171 TTTATTAAATTATATA
1 TTTATTAAATTATATA
46193187 TTTATTAAATTATAT
1 TTTATTAAATTATAT
46193202 TTAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATTAAATTATATA
Found at i:46193196 original size:53 final size:52
Alignment explanation
Indices: 46193126--46193241 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 52
46193116 AGTATTATAT
* *
46193126 ATTATGAT-TTTAGTAAATTCATA-TAAGAATAATTATATTAAGAATTTTATTAA
1 ATTAT-ATATTTAGTAAATT-ATATTAAGAATAATTATATTAA-AATATGATTAA
* * *
46193179 ATTATATATTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAA
1 ATTATATATTTAGTAAATTATA-TTAAGAATAATTATATTAAAATATGATTAA
*
46193232 ATTATTTATT
1 ATTATATATT
46193242 ATTTATATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
52 5 0.09
53 33 0.61
54 16 0.30
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (52 bp):
ATTATATATTTAGTAAATTATATTAAGAATAATTATATTAAAATATGATTAA
Found at i:46193447 original size:45 final size:44
Alignment explanation
Indices: 46193359--46193451 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 44
46193349 ATTACAACAT
46193359 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
46193403 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
46193448 CATT
1 CATT
46193452 ACACCTCTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:46193454 original size:16 final size:16
Alignment explanation
Indices: 46193433--46193504 Score: 99
Period size: 16 Copynumber: 4.5 Consensus size: 16
46193423 TTGAATTACT
*
46193433 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
* *
46193449 ATTACACCTCTATTTC
1 ATTACAGCTCTATTCC
*
46193465 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
46193481 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
46193497 ATTACAGC
1 ATTACAGC
46193505 GAACCAAACG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:46206793 original size:17 final size:17
Alignment explanation
Indices: 46206771--46206804 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46206761 AAAAAATAAA
*
46206771 ACTTTACAAATTGGGCC
1 ACTTTAAAAATTGGGCC
*
46206788 ACTTTAAAAATTTGGCC
1 ACTTTAAAAATTGGGCC
46206805 TGATTTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (17 bp):
ACTTTAAAAATTGGGCC
Found at i:46210229 original size:16 final size:15
Alignment explanation
Indices: 46210180--46210221 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
46210170 TAACAATCCA
*
46210180 AGTTCAAGAAAACCTG
1 AGTTCAA-AAAACCCG
46210196 AGTTCAAAAAACCCG
1 AGTTCAAAAAACCCG
46210211 AGTTCAAAAAA
1 AGTTCAAAAAA
46210222 GTCCGAGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (15 bp):
AGTTCAAAAAACCCG
Found at i:46212412 original size:17 final size:18
Alignment explanation
Indices: 46212390--46212450 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
46212380 TCATTAATGC
46212390 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
* *
46212407 ATATATTATATACTATATG
1 ATATA-TATAAACTATATA
* *
46212426 ATATGATATAACATTGTATA
1 ATAT-ATATAA-ACTATATA
46212446 ATATA
1 ATATA
46212451 GTACAAGAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 5 0.15
18 9 0.26
19 10 0.29
20 10 0.29
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:46215389 original size:25 final size:24
Alignment explanation
Indices: 46215346--46215395 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
46215336 TGAGCATTCT
**
46215346 GATATTGGCTTTCTTGAGCTACCC
1 GATATTGGCTTTCACGAGCTACCC
*
46215370 GATATATGGCTTTCACGAGCTTCCC
1 GATAT-TGGCTTTCACGAGCTACCC
46215395 G
1 G
46215396 TTAATAGCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (24 bp):
GATATTGGCTTTCACGAGCTACCC
Found at i:46215619 original size:25 final size:25
Alignment explanation
Indices: 46215517--46215626 Score: 71
Period size: 25 Copynumber: 4.4 Consensus size: 25
46215507 TTGCTCTCCG
* * **
46215517 GAGCTACCCGATAT-TGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCGGAT
* * * **
46215541 GAGCTTCCTGTTACATGACTCACAT
1 GAGCTTCCCGTTATATGGCTCGGAT
*
46215566 GAGCTTCCCGTTATATGGCTCGGAA
1 GAGCTTCCCGTTATATGGCTCGGAT
* **
46215591 GAGCTTCTCGTT-TATGTGCTCTTAT
1 GAGCTTCCCGTTATATG-GCTCGGAT
46215616 GAGCATTCCCG
1 GAGC-TTCCCG
46215627 AATATGAATT
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
24 14 0.21
25 48 0.72
26 5 0.07
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCGGAT
Found at i:46217607 original size:25 final size:25
Alignment explanation
Indices: 46217579--46217666 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 25
46217569 CAGCTCTTAT
*
46217579 GAGCGTCCCGATATATGGCTCACAC
1 GAGCTTCCCGATATATGGCTCACAC
* * *
46217604 GAGCTTCCTGAT-TAATTGCTCTC-C
1 GAGCTTCCCGATAT-ATGGCTCACAC
* *
46217628 GGAGCTACCCGATAT-TGGCTCACAT
1 -GAGCTTCCCGATATATGGCTCACAC
*
46217653 GAGCTTCCCAATAT
1 GAGCTTCCCGATAT
46217667 GAATTGACAT
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
24 20 0.42
25 27 0.56
26 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (25 bp):
GAGCTTCCCGATATATGGCTCACAC
Found at i:46218700 original size:12 final size:12
Alignment explanation
Indices: 46218691--46218723 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
46218681 TAGCACACAA
46218691 GCTGGGACACGG
1 GCTGGGACACGG
*
46218703 GTTGGGACACGG
1 GCTGGGACACGG
46218715 GCTGGGACA
1 GCTGGGACA
46218724 TGGTCGTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.48, T:0.12
Consensus pattern (12 bp):
GCTGGGACACGG
Found at i:46224306 original size:42 final size:42
Alignment explanation
Indices: 46224247--46224329 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
46224237 GACCAGAGGC
*
46224247 ATGGGCGTGTGCCCAGGCCGTGTAAGCCACACAGCCAAGGAT
1 ATGGGCGTGTGCCCAGGCCGTGTAAGCCACACAGACAAGGAT
* * *
46224289 ATGGGTGTGTGCCCAGGCCGTGTGAGCCACACGGACAAGGA
1 ATGGGCGTGTGCCCAGGCCGTGTAAGCCACACAGACAAGGA
46224330 CATCGCCATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (42 bp):
ATGGGCGTGTGCCCAGGCCGTGTAAGCCACACAGACAAGGAT
Found at i:46224979 original size:17 final size:17
Alignment explanation
Indices: 46224939--46224982 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
46224929 GGTTTAGCCT
*
46224939 ACACCCATGTGTTCCAC
1 ACACCCGTGTGTTCCAC
46224956 ACACCCGTGTGTTCCAC
1 ACACCCGTGTGTTCCAC
46224973 ACACCCGTGT
1 ACACCCGTGT
46224983 CACCTACCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (17 bp):
ACACCCGTGTGTTCCAC
Found at i:46225536 original size:19 final size:18
Alignment explanation
Indices: 46225509--46225570 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 18
46225499 ACGAAGAATG
46225509 GAAAGTAAAACGAAAATAAA
1 GAAA-TAAAA-GAAAATAAA
46225529 GAAAT-AAAGAAAGAATAAA
1 GAAATAAAAG-AA-AATAAA
46225548 GAAAT-AAAGTAAAAATAAA
1 GAAATAAAAG--AAAATAAA
46225567 GAAA
1 GAAA
46225571 GAATGGAGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.03
18 5 0.13
19 26 0.67
20 7 0.18
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.11
Consensus pattern (18 bp):
GAAATAAAAGAAAATAAA
Found at i:46225545 original size:11 final size:11
Alignment explanation
Indices: 46225526--46225574 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
46225516 AAACGAAAAT
46225526 AAAGAAATAAAG
1 AAAG-AATAAAG
46225538 AAAGAATAAAG
1 AAAGAATAAAG
46225549 --A-AATAAAG
1 AAAGAATAAAG
46225557 TAAA-AATAAAG
1 -AAAGAATAAAG
46225568 AAAGAAT
1 AAAGAAT
46225575 GGAGGAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 3 0.09
11 18 0.55
12 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.12
Consensus pattern (11 bp):
AAAGAATAAAG
Found at i:46227103 original size:80 final size:80
Alignment explanation
Indices: 46226970--46227131 Score: 218
Period size: 80 Copynumber: 2.0 Consensus size: 80
46226960 TTTTGTTTCC
* * * *
46226970 CTCAAATTACATTTTAATTACTTTTGTTTGAAATGTTACGTTTTAGCCACTTACGTTAACATGTT
1 CTCAAATTACATTTTAATCACTTATGTTTGAAATGTTACATTTTAGCCACTTACATTAACATGTT
46227035 ATAAT-ATTTTAGTCA
66 AT-ATCATTTTAGTCA
* * ** *
46227050 CTCAAATTATATTTTAGTCACTTATGTTTGAAATGTTACATTTTAGTTACTTACATTAATATGTT
1 CTCAAATTACATTTTAATCACTTATGTTTGAAATGTTACATTTTAGCCACTTACATTAACATGTT
*
46227115 GTATCATTTTAGTCA
66 ATATCATTTTAGTCA
46227130 CT
1 CT
46227132 ATGCTGTTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 2 0.03
80 69 0.97
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (80 bp):
CTCAAATTACATTTTAATCACTTATGTTTGAAATGTTACATTTTAGCCACTTACATTAACATGTT
ATATCATTTTAGTCA
Found at i:46227726 original size:14 final size:14
Alignment explanation
Indices: 46227686--46227728 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
46227676 AATAGTAAAC
46227686 AAAA-TTATTATAA
1 AAAATTTATTATAA
**
46227699 AAAATTTAAAATAA
1 AAAATTTATTATAA
*
46227713 AAAATTTCTTATAA
1 AAAATTTATTATAA
46227727 AA
1 AA
46227729 TTAAGGGGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTTATTATAA
Found at i:46235874 original size:20 final size:20
Alignment explanation
Indices: 46235832--46235872 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
46235822 TACAACACAA
*
46235832 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
46235852 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
46235871 TT
1 TT
46235873 TCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:46236055 original size:19 final size:19
Alignment explanation
Indices: 46236043--46236085 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
46236033 AATTTACAAT
46236043 AATTTCTAAAATTTCTAAA
1 AATTTCTAAAATTTCTAAA
*
46236062 AATTTTTAAAATTTCT-AA
1 AATTTCTAAAATTTCTAAA
46236080 AATTTC
1 AATTTC
46236086 GACATGGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTCTAAAATTTCTAAA
Found at i:46236057 original size:9 final size:9
Alignment explanation
Indices: 46236043--46236085 Score: 68
Period size: 9 Copynumber: 4.7 Consensus size: 9
46236033 AATTTACAAT
46236043 AATTTCTAA
1 AATTTCTAA
46236052 AATTTCTAAA
1 AATTTCT-AA
*
46236062 AATTTTTAA
1 AATTTCTAA
46236071 AATTTCTAA
1 AATTTCTAA
46236080 AATTTC
1 AATTTC
46236086 GACATGGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTTCTAA
Found at i:46236062 original size:28 final size:28
Alignment explanation
Indices: 46236031--46236085 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
46236021 CCTATTAATC
46236031 AAAATTTACAATAATTTCTAAAATTTCTA
1 AAAATTTACAA-AATTTCTAAAATTTCTA
**
46236060 AAAATTTTTAAAATTTCTAAAATTTC
1 AAAATTTACAAAATTTCTAAAATTTC
46236086 GACATGGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAATTTACAAAATTTCTAAAATTTCTA
Found at i:46236668 original size:76 final size:76
Alignment explanation
Indices: 46236542--46236685 Score: 200
Period size: 76 Copynumber: 1.9 Consensus size: 76
46236532 ATATATTTAA
* *
46236542 TAAATATTTAAGAGTCCAATTTACGGGAATAGAGTCTCAGGAATGTACTTTCCAACACCCCTGAC
1 TAAATATTTAAGAGTCCAATTTACGGGAACAGAGTCTCAGGAATGCACTTTCCAACACCCCTGAC
46236607 TATTGGGTTGT
66 TATTGGGTTGT
* * * * **
46236618 TAAATATTTACGAGTCTAATTTACGGGGACGGAGTCTC-GAGAATGCACTTTCTGACACCCCTGA
1 TAAATATTTAAGAGTCCAATTTACGGGAACAGAGTCTCAG-GAATGCACTTTCCAACACCCCTGA
46236682 CTAT
65 CTAT
46236686 CGAGTCGTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
75 1 0.02
76 58 0.98
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (76 bp):
TAAATATTTAAGAGTCCAATTTACGGGAACAGAGTCTCAGGAATGCACTTTCCAACACCCCTGAC
TATTGGGTTGT
Found at i:46243960 original size:24 final size:26
Alignment explanation
Indices: 46243926--46243977 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
46243916 GATTTCAGTC
46243926 AAAAACTCTAAA-TTTAAAAATATTA
1 AAAAACTCTAAATTTTAAAAATATTA
*
46243951 AAAAAC-CTAAATTTTAAAAATTTTA
1 AAAAACTCTAAATTTTAAAAATATTA
46243976 AA
1 AA
46243978 CCTAGAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAACTCTAAATTTTAAAAATATTA
Found at i:46248906 original size:24 final size:24
Alignment explanation
Indices: 46248891--46248942 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
46248881 AATCAAAGTC
46248891 AAATATATTATACTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
* *
46248915 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATGCT
46248939 AAAT
1 AAAT
46248943 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:46249623 original size:17 final size:18
Alignment explanation
Indices: 46249601--46249641 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
46249591 TTATTAATTG
46249601 ATATT-TTTAAATAGTAT
1 ATATTCTTTAAATAGTAT
46249618 ATATTTCTTTAAATAGTAT
1 ATA-TTCTTTAAATAGTAT
46249637 ATATT
1 ATATT
46249642 AATTCTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 4 0.18
19 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (18 bp):
ATATTCTTTAAATAGTAT
Found at i:46249785 original size:29 final size:29
Alignment explanation
Indices: 46249743--46249799 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
46249733 ATTTGAACCA
**
46249743 CAAATAAAGTTTCATGTGTACAATTGCAC
1 CAAATAAAGTTTCATGTACACAATTGCAC
46249772 CAAATTAAAG-TTCATGTACACAATTGCA
1 CAAA-TAAAGTTTCATGTACACAATTGCA
46249800 TACTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (29 bp):
CAAATAAAGTTTCATGTACACAATTGCAC
Found at i:46253256 original size:37 final size:37
Alignment explanation
Indices: 46253194--46253348 Score: 177
Period size: 37 Copynumber: 4.0 Consensus size: 37
46253184 ACGTATGATC
*
46253194 ACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGCA
1 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCA
* *
46253230 ACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCC
1 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCA
*
46253267 ACCTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTA
1 ACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC-A
*
46253311 TCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 --ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
46253349 CGAAGCTATC
Statistics
Matches: 101, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
36 9 0.09
37 51 0.50
39 2 0.02
40 4 0.04
41 1 0.01
42 1 0.01
43 3 0.03
44 2 0.02
46 28 0.28
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCA
Found at i:46253337 original size:46 final size:46
Alignment explanation
Indices: 46253270--46253488 Score: 267
Period size: 52 Copynumber: 4.5 Consensus size: 46
46253260 TGTAGCCACC
* **
46253270 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACT
1 TATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
46253316 TATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
46253362 TCTCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
46253414 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
46253466 TATCACTTTGTCACTTGATCAGA
1 TATCACTTTGTCACTTGATCAGA
46253489 AGTACTCAAA
Statistics
Matches: 158, Mismatches: 8, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
46 64 0.41
49 1 0.01
50 1 0.01
51 3 0.02
52 89 0.56
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (46 bp):
TATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:46253385 original size:52 final size:52
Alignment explanation
Indices: 46253309--46253482 Score: 276
Period size: 52 Copynumber: 3.3 Consensus size: 52
46253299 TAGCTAAAGC
* * *
46253309 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
46253362 TCTCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
46253414 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
46253466 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
46253483 ATCAGAAGTA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
52 95 0.85
53 17 0.15
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:46258814 original size:14 final size:14
Alignment explanation
Indices: 46258795--46258833 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 14
46258785 TTTCTCATAT
46258795 ATTATTTATTTTAA
1 ATTATTTATTTTAA
46258809 ATTATTT-TTTT--
1 ATTATTTATTTTAA
46258820 ATTATTTATTTTAA
1 ATTATTTATTTTAA
46258834 GTTTTCCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 7 0.32
12 4 0.18
13 4 0.18
14 7 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTATTTATTTTAA
Found at i:46258950 original size:26 final size:26
Alignment explanation
Indices: 46258767--46259164 Score: 226
Period size: 26 Copynumber: 15.1 Consensus size: 26
46258757 TGTTATTTAT
46258767 TTATTTATTTTAAACCTT-TTTCTCATATA
1 TTATTTATTTTAAA--TTGTTT-T-ATATA
* *
46258796 TTATTTATTTTAAATTATTTT-TTTA
1 TTATTTATTTTAAATTGTTTTATATA
* ** *
46258821 TTATTTATTTTAAGTT-TTCCACATA
1 TTATTTATTTTAAATTGTTTTATATA
* * * * * *
46258846 TAATGTATTTTAAACTATTTCAAACTA
1 TTATTTATTTTAAATTGTTTTATA-TA
**
46258873 TTATCCATTTTAAATT-TTTTATATA
1 TTATTTATTTTAAATTGTTTTATATA
* **
46258898 TTATTTATTTTTAAACTGTCATATATA
1 TTATTTA-TTTTAAATTGTTTTATATA
*
46258925 TTATTTATTTTGAATTGTTTTTTATATA
1 TTATTTATTTTAAATTG--TTTTATATA
* *
46258953 TATCATTTATTTTTTAAAAAACT-TTTTAGTACA
1 T-T-ATTTA--TTTT---AAATTGTTTTA-TATA
* *
46258986 TTATTTATTTTAAACTTCTTTTTACATA
1 TTATTTATTTTAAA-TT-GTTTTATATA
*
46259014 TTATTTATTTTAAA--CTTTT-TATA
1 TTATTTATTTTAAATTGTTTTATATA
* *
46259037 -TA-TTATTTTAAATTGTCTTATATG
1 TTATTTATTTTAAATTGTTTTATATA
* * *
46259061 TTATTTATTTTAAATTGCTTTGTCTA
1 TTATTTATTTTAAATTGTTTTATATA
* *
46259087 TTATTTATTTTAATTTGTTTTACATA
1 TTATTTATTTTAAATTGTTTTATATA
* *
46259113 TTAGTTACTTTAAATTG-TTT-TATA
1 TTATTTATTTTAAATTGTTTTATATA
* * * *
46259137 CTATTTACTTCAAATTGTTCTATATA
1 TTATTTATTTTAAATTGTTTTATATA
46259163 TT
1 TT
46259165 TTTTGTTTCG
Statistics
Matches: 286, Mismatches: 57, Indels: 55
0.72 0.14 0.14
Matches are distributed among these distances:
21 10 0.03
22 2 0.01
23 6 0.02
24 26 0.09
25 46 0.16
26 86 0.30
27 32 0.11
28 27 0.09
29 24 0.08
30 5 0.02
31 5 0.02
32 10 0.03
33 4 0.01
35 3 0.01
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.59
Consensus pattern (26 bp):
TTATTTATTTTAAATTGTTTTATATA
Found at i:46259044 original size:21 final size:22
Alignment explanation
Indices: 46259018--46259066 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
46259008 TACATATTAT
46259018 TTATTTTAAACTT-T-TTATATA
1 TTATTTTAAA-TTGTCTTATATA
*
46259039 TTATTTTAAATTGTCTTATATG
1 TTATTTTAAATTGTCTTATATA
46259061 TTATTT
1 TTATTT
46259067 ATTTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 12 0.48
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (22 bp):
TTATTTTAAATTGTCTTATATA
Found at i:46259151 original size:24 final size:23
Alignment explanation
Indices: 46259117--46259165 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
46259107 TACATATTAG
* *
46259117 TTACTTTAAATTGTTTTATACTAT
1 TTACTTCAAATTGTTCTATA-TAT
46259141 TTACTTCAAATTGTTCTATATAT
1 TTACTTCAAATTGTTCTATATAT
46259164 TT
1 TT
46259166 TTTGTTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (23 bp):
TTACTTCAAATTGTTCTATATAT
Found at i:46269030 original size:19 final size:20
Alignment explanation
Indices: 46268988--46269023 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
46268978 GTTTTCAAAT
46268988 AATT-ATAAAAATATATTAA
1 AATTAATAAAAATATATTAA
46269007 AATTAATAAAAA-ATATT
1 AATTAATAAAAATATATT
46269024 CGAATTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTAATAAAAATATATTAA
Found at i:46269036 original size:21 final size:21
Alignment explanation
Indices: 46268991--46269037 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
46268981 TTCAAATAAT
46268991 TATAAAAATATATTAAAATTA
1 TATAAAAATATATTAAAATTA
**
46269012 -ATAAAAA-ATATTCGAATTA
1 TATAAAAATATATTAAAATTA
46269031 CTATAAA
1 -TATAAA
46269038 TATAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.45
20 7 0.32
21 5 0.23
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
TATAAAAATATATTAAAATTA
Found at i:46269376 original size:8 final size:8
Alignment explanation
Indices: 46269358--46269391 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
46269348 TTAAGTTTAA
*
46269358 TTTTAAAT
1 TTTTATAT
46269366 TTTT-TAT
1 TTTTATAT
46269373 TTTTATAT
1 TTTTATAT
46269381 TTTTATAT
1 TTTTATAT
46269389 TTT
1 TTT
46269392 CTTATAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATAT
Found at i:46269376 original size:15 final size:15
Alignment explanation
Indices: 46269353--46269391 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
46269343 TTAAATTAAG
*
46269353 TTTAATTTTAAATTT
1 TTTATTTTTAAATTT
*
46269368 TTTATTTTTATATTT
1 TTTATTTTTAAATTT
46269383 TTATATTTT
1 TT-TATTTT
46269392 CTTATAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTTTAAATTT
Found at i:46270703 original size:27 final size:22
Alignment explanation
Indices: 46270649--46270699 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
46270639 CCATACAACC
46270649 ATACTTTAACTTCAGGATTCCT
1 ATACTTTAACTTCAGGATTCCT
46270671 ATACTTTAACTTCAGGATTCCT
1 ATACTTTAACTTCAGGATTCCT
46270693 ATCACTT
1 AT-ACTT
46270700 ACTTAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (22 bp):
ATACTTTAACTTCAGGATTCCT
Found at i:46270709 original size:27 final size:24
Alignment explanation
Indices: 46270654--46270705 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
46270644 CAACCATACT
46270654 TTAACTTCAGGATTCCTATACT--
1 TTAACTTCAGGATTCCTATACTAC
46270676 TTAACTTCAGGATTCCTATCACTTAC
1 TTAACTTCAGGATTCCTAT-AC-TAC
46270702 TTAA
1 TTAA
46270706 ACTTGTTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 19 0.73
23 2 0.08
24 1 0.04
26 4 0.15
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (24 bp):
TTAACTTCAGGATTCCTATACTAC
Found at i:46279722 original size:15 final size:14
Alignment explanation
Indices: 46279702--46279736 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
46279692 GGAAATTTTA
46279702 AAAAAAATAATATGT
1 AAAAAAATAAT-TGT
*
46279717 AAAAAAATAATTTT
1 AAAAAAATAATTGT
46279731 AAAAAA
1 AAAAAA
46279737 TGGGATGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAAAATAATTGT
Found at i:46280888 original size:55 final size:55
Alignment explanation
Indices: 46280822--46280935 Score: 219
Period size: 55 Copynumber: 2.1 Consensus size: 55
46280812 TATGCTTTAT
*
46280822 ATTATTAAAATATGAAAAATCGTTTAATTATAATATAAGGAAAGTGCCATGTGCC
1 ATTATTAAAATATGAAAAATCGTTTAAGTATAATATAAGGAAAGTGCCATGTGCC
46280877 ATTATTAAAATATGAAAAATCGTTTAAGTATAATATAAGGAAAGTGCCATGTGCC
1 ATTATTAAAATATGAAAAATCGTTTAAGTATAATATAAGGAAAGTGCCATGTGCC
46280932 ATTA
1 ATTA
46280936 AAAAAGAATG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (55 bp):
ATTATTAAAATATGAAAAATCGTTTAAGTATAATATAAGGAAAGTGCCATGTGCC
Found at i:46282641 original size:44 final size:43
Alignment explanation
Indices: 46282591--46282683 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
46282581 ATGTTGTGGA
* * * *
46282591 GTTTGTAGCTAGAAGCGTCGCAAAAGATCATGTTCTGTAGCAGC
1 GTTTGTAG-TAAAAGCGCCACAAAAGATCATGTTCTATAGCAGC
* * *
46282635 GTTTGTAGTAAAAGCGCCACTAAAGATCATGTTCTATAGCGGT
1 GTTTGTAGTAAAAGCGCCACAAAAGATCATGTTCTATAGCAGC
46282678 GTTTGT
1 GTTTGT
46282684 GGGAAAACAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 34 0.81
44 8 0.19
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (43 bp):
GTTTGTAGTAAAAGCGCCACAAAAGATCATGTTCTATAGCAGC
Found at i:46287003 original size:40 final size:42
Alignment explanation
Indices: 46286922--46287043 Score: 122
Period size: 41 Copynumber: 2.9 Consensus size: 42
46286912 ATATTCGCGA
* * * * *
46286922 CATTTATGAGAAAAACATCGCTATTTTTTTTAACCTTTTGCAG
1 CATTTATGCGAAAAATACCACTA-TTGTTTTAACCTTTTGCAG
* *
46286965 TATTTATGC-AAAAATGCCACTATTGTTTT-ACCTTTTGCAG
1 CATTTATGCGAAAAATACCACTATTGTTTTAACCTTTTGCAG
* *
46287005 CGTTTATGCGAAAAATACCGCTATTGTTATTATACCTTT
1 CATTTATGCGAAAAATACCACTATTGTT-TTA-ACCTTT
46287044 AGCGGCGTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
40 18 0.28
41 22 0.34
42 11 0.17
43 7 0.11
44 6 0.09
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (42 bp):
CATTTATGCGAAAAATACCACTATTGTTTTAACCTTTTGCAG
Found at i:46287054 original size:44 final size:40
Alignment explanation
Indices: 46286949--46287054 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 40
46286939 TCGCTATTTT
* ** *
46286949 TTTTAACCTTTTGCAGTATTTATGCAAAAATGCCACTATTG
1 TTTT-ACCTTTAGCAGCGTTTATGCAAAAATACCACTATTG
* *
46286990 TTTTACCTTTTGCAGCGTTTATGCGAAAAATACCGCTATTG
1 TTTTACCTTTAGCAGCGTTTATGC-AAAAATACCACTATTG
*
46287031 TTATTATACCTTTAGCGGCGTTTA
1 -T-TT-TACCTTTAGCAGCGTTTA
46287055 GGGAAAGCGC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
40 18 0.33
41 18 0.33
42 1 0.02
43 2 0.04
44 16 0.29
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (40 bp):
TTTTACCTTTAGCAGCGTTTATGCAAAAATACCACTATTG
Found at i:46290490 original size:18 final size:18
Alignment explanation
Indices: 46290464--46290514 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
46290454 TAAAAGTAAC
46290464 TAAAAATAAAAACAAAAA
1 TAAAAATAAAAACAAAAA
* *
46290482 TAAACATAAAAAGAAAAA
1 TAAAAATAAAAACAAAAA
* *
46290500 GAAAAA-GAAAACAAA
1 TAAAAATAAAAACAAA
46290515 TAAACTCAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.08
Consensus pattern (18 bp):
TAAAAATAAAAACAAAAA
Found at i:46291977 original size:35 final size:35
Alignment explanation
Indices: 46291915--46291991 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
46291905 CGCCGAAAAT
* *
46291915 AATAAGAAATAATAAGCAAATTAAATAA-AATAAGA
1 AATAAAAAATAATAAGCAAATGAAATAATAATAA-A
* *
46291950 AATAAAAAATGATAAGCAAA-GAGAATAATAATAAT
1 AATAAAAAATAATAAGCAAATGA-AATAATAATAAA
46291985 AATAAAA
1 AATAAAA
46291992 GAAGTAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.03
35 30 0.83
36 5 0.14
ACGTcount: A:0.69, C:0.03, G:0.09, T:0.19
Consensus pattern (35 bp):
AATAAAAAATAATAAGCAAATGAAATAATAATAAA
Found at i:46298487 original size:22 final size:25
Alignment explanation
Indices: 46298461--46298514 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
46298451 TTATAAATTC
46298461 AATTTAAAAG-ATA-TAAT-ACAAT
1 AATTTAAAAGCATATTAATAACAAT
*
46298483 AATTT-CAAGCATATTTAATAACAAT
1 AATTTAAAAGCATA-TTAATAACAAT
46298508 AATTTAA
1 AATTTAA
46298515 TTATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
24 4 0.16
25 10 0.40
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTTAAAAGCATATTAATAACAAT
Found at i:46299205 original size:31 final size:31
Alignment explanation
Indices: 46299170--46299237 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
46299160 TTACTTTGAA
46299170 AAAATGTATAATATGAAATAGAAAACAATTT
1 AAAATGTATAATATGAAATAGAAAACAATTT
46299201 AAAATGTATAATATGAAATAGAAAACAATTT
1 AAAATGTATAATATGAAATAGAAAACAATTT
46299232 AAAATG
1 AAAATG
46299238 AAAAAAAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (31 bp):
AAAATGTATAATATGAAATAGAAAACAATTT
Found at i:46305467 original size:4 final size:4
Alignment explanation
Indices: 46305458--46305482 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
46305448 TATTATTAAA
46305458 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
46305483 ATCATTGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:46305680 original size:3 final size:3
Alignment explanation
Indices: 46305672--46305732 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
46305662 TTTATATTTC
* * * * * *
46305672 TAT TAT TAT TAT TAT TAT TAT TAT CAT CAT CAT CAT CAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
46305720 TAC TAA TAT TAT T
1 TAT TAT TAT TAT T
46305733 CTTAAATTGT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (3 bp):
TAT
Found at i:46310787 original size:6 final size:6
Alignment explanation
Indices: 46310753--46310795 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
46310743 AGATTCAATC
* *
46310753 GAAAAA GAAGAA GAATAA GAGAAAA -AAAAA GAAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GA-AAAA GAAAAA GAAAAA GAAAAA G
46310796 GAGAGTCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.12
6 25 0.78
7 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (6 bp):
GAAAAA
Done.