Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 136 of 182
Found at i:41856056 original size:24 final size:25
Alignment explanation
Indices: 41856019--41856067 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
41856009 CCAAATAATA
41856019 AAAAAAGGAAAAACAATTAAAAACAG
1 AAAAAAGG-AAAACAATTAAAAACAG
41856045 AAAAAAGG-AAACAATTAAAAACA
1 AAAAAAGGAAAACAATTAAAAACA
41856068 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 15 0.65
26 8 0.35
ACGTcount: A:0.73, C:0.08, G:0.10, T:0.08
Consensus pattern (25 bp):
AAAAAAGGAAAACAATTAAAAACAG
Found at i:41857066 original size:323 final size:323
Alignment explanation
Indices: 41856459--41857097 Score: 1014
Period size: 323 Copynumber: 2.0 Consensus size: 323
41856449 TAAAAAAACC
* * *
41856459 GAATTCGAGGATTGCGTGTCGTTATTTTCAACCACAGCAAAATTACAAGGACTTCGCATGGATCC
1 GAATTCAAGGATTGCATGTCGTTACTTTCAACCACAGCAAAATTACAAGGACTTCGCATGGATCC
* * *
41856524 TAGGCAGAATCTATATTTTATACTACTATACCCGTTCGAATGTGAACTATTTTTTGGGAAAACAA
66 CAGGCAGAATCTATATTTTATACTACTATACACGTTCGAATGTGAACTATTTTTTGCGAAAACAA
*
41856589 AAAAAAAGTTTTTTTTTTATGTATGATTTAAATTACATTTTGGTCATTGAGTTATAATTTGTTAG
131 AAAAAAAG---TTTATTTATGTATGATTTAAATTACATTTTGGTCATTGAGTTATAATTTGTTAG
* * * * * *
41856654 ATTTTGATCACTAATGTTATTAATTTATAACATTTTGGTTATTTTGTCGTTATTCGACATTAGTG
193 ACTCTGATCACTAATGTTATTAATTTATAACATTTTGGTCATTATGCCGTTATTCGACATTAGCG
*
41856719 ATGTAACAAAAGTCTAACGTGACACAAATTGTGTCTTTAAATGCTGACATATCATTATTTTCAAC
258 ATGTAACAAAAGTCTAACGTGACACAAATTGTGTCGTTAAATGCTGACATATCATTATTTTCAAC
41856784 T
323 T
* *
41856785 GAATTCAAGGATTGCATGTCGTTACTTTCAACCATAGTAAAATTACAAGGACTTCGCATGGATCC
1 GAATTCAAGGATTGCATGTCGTTACTTTCAACCACAGCAAAATTACAAGGACTTCGCATGGATCC
*
41856850 CAGGCAGAATCTATATTTTATAC-AGCTATACATGTTCGAATGTGAACTATTTTTTGCGAAAACA
66 CAGGCAGAATCTATATTTTATACTA-CTATACACGTTCGAATGTGAACTATTTTTTGCGAAAACA
*
41856914 ACAAAAAAAG-TTATTTATGTATTATTTAAATTACATTTTGGTCATTGAGTTATAATTTGTTACG
130 A-AAAAAAAGTTTATTTATGTATGATTTAAATTACATTTTGGTCATTGAGTTATAATTTGTTA-G
41856978 -CTCTGATCACTAATGTTATTAATTTATAACATTTTGGTCATTATGCCGTTATTCGACATTAGCG
193 ACTCTGATCACTAATGTTATTAATTTATAACATTTTGGTCATTATGCCGTTATTCGACATTAGCG
* * *
41857042 ATGTAACAAAAGTCTGATGTGACACAAATTGTGTCGTTAAATGCTGACATGTCATT
258 ATGTAACAAAAGTCTAACGTGACACAAATTGTGTCGTTAAATGCTGACATATCATT
41857098 CACGTCATCA
Statistics
Matches: 289, Mismatches: 21, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
323 160 0.55
324 1 0.00
325 1 0.00
326 119 0.41
327 8 0.03
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (323 bp):
GAATTCAAGGATTGCATGTCGTTACTTTCAACCACAGCAAAATTACAAGGACTTCGCATGGATCC
CAGGCAGAATCTATATTTTATACTACTATACACGTTCGAATGTGAACTATTTTTTGCGAAAACAA
AAAAAAAGTTTATTTATGTATGATTTAAATTACATTTTGGTCATTGAGTTATAATTTGTTAGACT
CTGATCACTAATGTTATTAATTTATAACATTTTGGTCATTATGCCGTTATTCGACATTAGCGATG
TAACAAAAGTCTAACGTGACACAAATTGTGTCGTTAAATGCTGACATATCATTATTTTCAACT
Found at i:41857187 original size:12 final size:13
Alignment explanation
Indices: 41857163--41857187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41857153 TTTTTACTTC
41857163 ATTTCCTTTTTTT
1 ATTTCCTTTTTTT
41857176 ATTTCCTTTTTT
1 ATTTCCTTTTTT
41857188 CCATTCTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTCCTTTTTTT
Found at i:41860993 original size:43 final size:43
Alignment explanation
Indices: 41860928--41861162 Score: 181
Period size: 43 Copynumber: 5.3 Consensus size: 43
41860918 TTTTATAAAT
*
41860928 AAACGCCGCT-TAGATCATGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * * *
41860970 AAACGCCGCTATAGGTTAGGACCTTTAGCTGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * * *
41861013 AAACGCCGCTATAGACCGCTATAGATCAGGACCTATAGCGGCAC-TTCTACAC
1 AAA-----C----G-CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * *
41861065 AAACGCCGCTATAGCTCAAGACCTTTAGCAGCACTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
*
41861108 AAACGCCGCTATAGATCAAAGACCTTTAGCGACGCTTTGATT--AC
1 AAACGCCGCTATAGATC-AAGACCTTTAGCGGCGCTTT--TTCCAC
41861152 AAACGCCGCTA
1 AAACGCCGCTA
41861163 AAAACACCGT
Statistics
Matches: 153, Mismatches: 25, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
42 35 0.23
43 52 0.34
44 30 0.20
46 1 0.01
47 1 0.01
48 1 0.01
52 9 0.06
53 24 0.16
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:41861102 original size:95 final size:95
Alignment explanation
Indices: 41860933--41861122 Score: 274
Period size: 95 Copynumber: 2.0 Consensus size: 95
41860923 TAAATAAACG
* * * * * * * *
41860933 CCGCTTAGATCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGGTTAGGACCTTTAG
1 CCGCTTAGATCAGGACCTATAGCGGCACTTTCTACACAAACGCCGCTATAGCTCAAGACCTTTAG
* *
41860998 CTGCGCTTTTCCCACAAACGCCGCTATAGA
66 CAGCACTTTTCCCACAAACGCCGCTATAGA
41861028 CCGCTATAGATCAGGACCTATAGCGGCAC-TTCTACACAAACGCCGCTATAGCTCAAGACCTTTA
1 CCGCT-TAGATCAGGACCTATAGCGGCACTTTCTACACAAACGCCGCTATAGCTCAAGACCTTTA
41861092 GCAGCACTTTTCCCACAAACGCCGCTATAGA
65 GCAGCACTTTTCCCACAAACGCCGCTATAGA
41861123 TCAAAGACCT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 64 0.76
96 20 0.24
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (95 bp):
CCGCTTAGATCAGGACCTATAGCGGCACTTTCTACACAAACGCCGCTATAGCTCAAGACCTTTAG
CAGCACTTTTCCCACAAACGCCGCTATAGA
Found at i:41861154 original size:44 final size:43
Alignment explanation
Indices: 41861028--41861162 Score: 141
Period size: 44 Copynumber: 3.1 Consensus size: 43
41861018 CCGCTATAGA
* * *
41861028 CCGCTATAGATCAGGACCTATAGCGGCACTTCT-A-CACAAACG
1 CCGCTATAGATCAAGACCTTTAGCAGCACTT-TGACCACAAACG
* **
41861070 CCGCTATAGCTCAAGACCTTTAGCAGCACTTTTCCCACAAACG
1 CCGCTATAGATCAAGACCTTTAGCAGCACTTTGACCACAAACG
* **
41861113 CCGCTATAGATCAAAGACCTTTAGC-GACGCTTTGATTACAAACG
1 CCGCTATAGATC-AAGACCTTTAGCAG-CACTTTGACCACAAACG
41861157 CCGCTA
1 CCGCTA
41861163 AAAACACCGT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.01
42 27 0.35
43 20 0.26
44 30 0.38
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (43 bp):
CCGCTATAGATCAAGACCTTTAGCAGCACTTTGACCACAAACG
Found at i:41861514 original size:3 final size:3
Alignment explanation
Indices: 41861493--41861531 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
41861483 ATGGAAATGG
* *
41861493 ATC ATC TTC ATC TTC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
41861532 TTCTTCTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:41862372 original size:14 final size:14
Alignment explanation
Indices: 41862353--41862382 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41862343 CAGATTAGGT
41862353 GTGGGAAAAGGTTA
1 GTGGGAAAAGGTTA
41862367 GTGGGAAAAGGTTA
1 GTGGGAAAAGGTTA
41862381 GT
1 GT
41862383 TGCTTTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.23
Consensus pattern (14 bp):
GTGGGAAAAGGTTA
Found at i:41868986 original size:47 final size:48
Alignment explanation
Indices: 41868932--41869033 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 48
41868922 AATACATAGA
*
41868932 TTTTTTAAAGTTATATTTATAAAAATTAGATAAAATTAAAAA-TTTAG
1 TTTTTTAAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAG
41868979 TTTTTT-AAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAG
1 TTTTTTAAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAG
41869026 TGTTTTTA
1 T-TTTTTA
41869034 TTTCATTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
46 34 0.67
47 12 0.24
48 5 0.10
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (48 bp):
TTTTTTAAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAG
Found at i:41869047 original size:25 final size:26
Alignment explanation
Indices: 41869019--41869071 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
41869009 AAAATTAAAA
*
41869019 ATTTTAGTGTTTTTATTTCATTT-TT
1 ATTTTAGTATTTTTATTTCATTTCTT
* *
41869044 ATTTTTGTATTTTTATTTTATTTCTT
1 ATTTTAGTATTTTTATTTCATTTCTT
41869070 AT
1 AT
41869072 AATTTGGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.74
Consensus pattern (26 bp):
ATTTTAGTATTTTTATTTCATTTCTT
Found at i:41869345 original size:115 final size:115
Alignment explanation
Indices: 41869209--41869630 Score: 819
Period size: 115 Copynumber: 3.7 Consensus size: 115
41869199 AACGCCGCTA
41869209 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
1 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
41869274 ATTGATTTTTTTGCGGCGCCGCTATTGCTTACCTTTAGCGGCAAAGAATT
66 ATTGATTTTTTTGCGGCGCCGCTATTGCTTACCTTTAGCGGCAAAGAATT
41869324 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
1 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
41869389 ATTGATTTTTTTGCGGCGCCGCTATTGCTTACCTTTAGCGGCAAAGAATT
66 ATTGATTTTTTTGCGGCGCCGCTATTGCTTACCTTTAGCGGCAAAGAATT
41869439 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
1 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
41869504 ATTGATTTTTTTGCGGCGCCGCTATTGCTTACCTTTAGCGGCAAAGAATT
66 ATTGATTTTTTTGCGGCGCCGCTATTGCTTACCTTTAGCGGCAAAGAATT
*
41869554 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTA-TTTTTTATAA
1 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
41869618 ATTGATTTATTTT
66 ATTGATTT-TTTT
41869631 TTGAAAAAAC
Statistics
Matches: 305, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
114 18 0.06
115 287 0.94
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (115 bp):
TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
ATTGATTTTTTTGCGGCGCCGCTATTGCTTACCTTTAGCGGCAAAGAATT
Found at i:41870508 original size:22 final size:22
Alignment explanation
Indices: 41870458--41870508 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
41870448 CTCATCCCTG
41870458 AATCCCTAAACCTTAACTCCTT
1 AATCCCTAAACCTTAACTCCTT
* *
41870480 AACCCCTAAACCCTTAACTTC-T
1 AATCCCTAAA-CCTTAACTCCTT
41870502 AATCCCT
1 AATCCCT
41870509 GACCCCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.29
Consensus pattern (22 bp):
AATCCCTAAACCTTAACTCCTT
Found at i:41870547 original size:20 final size:21
Alignment explanation
Indices: 41870510--41870549 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41870500 CTAATCCCTG
*
41870510 ACCCCTAAACCTTAAATCCCA
1 ACCCCTAAACCATAAATCCCA
*
41870531 ACCCTTAAACCAT-AATCCC
1 ACCCCTAAACCATAAATCCC
41870550 TAATTCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.20
Consensus pattern (21 bp):
ACCCCTAAACCATAAATCCCA
Found at i:41871405 original size:113 final size:114
Alignment explanation
Indices: 41871137--41871556 Score: 533
Period size: 114 Copynumber: 3.7 Consensus size: 114
41871127 TTTTTGGCCA
* * **
41871137 CTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTT-AGGCTTAGAATTTTTTGCGGCGCTTTCTCA
1 CTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGA-GCTTAGGTTTTTTTGCGGCGCTTTCTCA
* * * *
41871201 AAAATGCCACTAAAGCCCTGAA-CATTAGCGGCGCTTTATTAAAAACGCTG
65 AAAACGCCACTAAAG-CCTTAAGCATTAGCGGCGCTTTCTTAAAAACGCCG
* * *
41871251 CTAAATCCCCGAAAGCTCAGAAAACGGCGTTGTTGAACTTAGGTTTTTTTGCGGCGCTTTCTCAA
1 CTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGAGCTTAGGTTTTTTTGCGGCGCTTTCTCAA
* *
41871316 AAATGCCGCTAAAGCCTTAAGCATTAGCGGCGCTTTCTT-AAAACGCCG
66 AAACGCCACTAAAGCCTTAAGCATTAGCGGCGCTTTCTTAAAAACGCCG
* * * * * *
41871364 CTAAATCCTCGAAAGCTCACAAAACGACGTCGTTGAGCTTAGGTTTTCTTGCGGC-ATTTTTGAG
1 CTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGAGCTTAGGTTTTTTTGCGGCGCTTTCTCA-
* * *
41871428 AAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAATGCCG
65 AAAACGCCACTAAAGCCTTAAGCATTAGCGGCGCTTTCTTAAAAACGCCG
* * * * *
41871478 CTAAAACCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTATGTTTTTTTTGCGGTGCTTTCTCA
1 CTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGAGCTTA-GGTTTTTTTGCGGCGCTTTCTCA
41871543 AAAACGCCACTAAA
65 AAAACGCCACTAAA
41871557 TCCCCGAAAG
Statistics
Matches: 267, Mismatches: 33, Indels: 11
0.86 0.11 0.04
Matches are distributed among these distances:
112 5 0.02
113 100 0.37
114 132 0.49
115 25 0.09
116 5 0.02
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (114 bp):
CTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGAGCTTAGGTTTTTTTGCGGCGCTTTCTCAA
AAACGCCACTAAAGCCTTAAGCATTAGCGGCGCTTTCTTAAAAACGCCG
Found at i:41871588 original size:74 final size:72
Alignment explanation
Indices: 41871455--41871627 Score: 238
Period size: 74 Copynumber: 2.4 Consensus size: 72
41871445 TTGAGCATTA
* * *
41871455 GCGGCGCTTTCTTAAAAATGCCGCTAAAACCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAT
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAACCCCGAAAGCTCACAAAACGGCATCATTGGGCTTA-
*
41871520 GTTTTTTTT
65 G-GTTTTTT
* * * ** *
41871529 GCGGTGCTTTCTCAAAAACGCCACTAAATCCCCGAAAGCTCAGGAAACGGCGTCATTGGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAACCCCGAAAGCTCACAAAACGGCATCATTGGGCTTAG
41871594 GTTTTTT
66 GTTTTTT
41871601 GCGGCGCTTTCTCAAAAACGCCGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
41871628 TGCTTATTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 31 0.36
73 1 0.01
74 55 0.63
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (72 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAACCCCGAAAGCTCACAAAACGGCATCATTGGGCTTAG
GTTTTTT
Found at i:41871713 original size:12 final size:12
Alignment explanation
Indices: 41871696--41871721 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41871686 TTTTTTATCC
41871696 AAACGCCGCTAA
1 AAACGCCGCTAA
41871708 AAACGCCGCTAA
1 AAACGCCGCTAA
41871720 AA
1 AA
41871722 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:41876644 original size:20 final size:18
Alignment explanation
Indices: 41876597--41876645 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
41876587 CAAGATAAAC
41876597 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
41876614 ATTAAGA-TAATCATTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
41876634 ATTAAATTAATA
1 ATTAAATTAATA
41876646 AAATACTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:41886206 original size:19 final size:20
Alignment explanation
Indices: 41886182--41886220 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41886172 AAGTTTTTAG
*
41886182 GTTTATT-CAATTTAGTTCA
1 GTTTATTACAACTTAGTTCA
41886201 GTTTATTACAACTTAGTTCA
1 GTTTATTACAACTTAGTTCA
41886221 TCATCCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (20 bp):
GTTTATTACAACTTAGTTCA
Found at i:41886667 original size:20 final size:21
Alignment explanation
Indices: 41886634--41886672 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41886624 GAAGATGAAA
41886634 AATAAAAAACCCT-AGAAATT
1 AATAAAAAACCCTAAGAAATT
41886654 AATAAGAAAA-CCTAAGAAA
1 AATAA-AAAACCCTAAGAAA
41886673 AACTAAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (21 bp):
AATAAAAAACCCTAAGAAATT
Found at i:41888855 original size:16 final size:16
Alignment explanation
Indices: 41888822--41888882 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
41888812 GGAATGCTAT
*
41888822 ACACAAA-AATACACAA
1 ACACAAATAATA-AAAA
*
41888838 ACACACATACA-AAAAA
1 ACACAAATA-ATAAAAA
41888854 ACACAAATAATAAAAA
1 ACACAAATAATAAAAA
*
41888870 ACAAAAATAATAA
1 ACACAAATAATAA
41888883 TCAAGTCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 1 0.03
16 34 0.89
17 2 0.05
18 1 0.03
ACGTcount: A:0.72, C:0.18, G:0.00, T:0.10
Consensus pattern (16 bp):
ACACAAATAATAAAAA
Found at i:41905625 original size:119 final size:120
Alignment explanation
Indices: 41905376--41905633 Score: 337
Period size: 119 Copynumber: 2.2 Consensus size: 120
41905366 GCTACTCGTT
* * * *
41905376 CAAATGCCTTTGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAACTCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* * *
41905440 GTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
65 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
41905496 CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* * * *
41905560 A-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
66 ATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCA
41905616 CAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
41905634 GCCCGGACAT
Statistics
Matches: 122, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
118 4 0.03
119 62 0.51
120 54 0.44
121 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:41905640 original size:40 final size:40
Alignment explanation
Indices: 41905357--41905640 Score: 353
Period size: 40 Copynumber: 7.1 Consensus size: 40
41905347 CGGAATTTAA
** * *
41905357 CCGGATATAGCT-ACTCGTTCAAATGCCTTTGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
41905397 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
41905437 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41905477 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
41905517 TCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41905556 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
41905596 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41905636 CCGGA
1 CCGGA
41905641 CATCATTCGA
Statistics
Matches: 216, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.14
40 171 0.79
41 12 0.06
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41910884 original size:24 final size:24
Alignment explanation
Indices: 41910851--41910907 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
41910841 AAAACTAATT
* *
41910851 CTAATCAATGTCAAATATATTATG
1 CTAATAAATGTCAAATATATTATA
*
41910875 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATATATTATA
41910899 CTAATAAAT
1 CTAATAAAT
41910908 ACTAAATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATA
Found at i:41910913 original size:24 final size:24
Alignment explanation
Indices: 41910863--41910914 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41910853 AATCAATGTC
* **
41910863 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
41910887 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATACT
41910911 AAAT
1 AAAT
41910915 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:41922150 original size:13 final size:14
Alignment explanation
Indices: 41922116--41922153 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
41922106 CGAAACTAAT
*
41922116 ATATGAAATGGAAC
1 ATATGAAATGTAAC
*
41922130 ACATGAAATGTAA-
1 ATATGAAATGTAAC
41922143 ATATGAAATGT
1 ATATGAAATGT
41922154 TGAATGGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.26
Consensus pattern (14 bp):
ATATGAAATGTAAC
Found at i:41928926 original size:3 final size:3
Alignment explanation
Indices: 41928920--41928991 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
41928910 TTTAGTTTAA
* * * *
41928920 TAT TAT T-T TATT TAT TAG TAT TAT TAT TGT TAT TAC TAT TAT TAC
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
41928965 TAT TAT TAT TGGT T-T TAT TAT T-T TAT T
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT T
41928992 TTTGTTTATA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 6 0.11
3 44 0.80
4 5 0.09
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:41931265 original size:46 final size:46
Alignment explanation
Indices: 41931170--41931369 Score: 226
Period size: 46 Copynumber: 4.3 Consensus size: 46
41931160 TGGGTATGAT
* * * *
41931170 CACTTATCAC-TTGTC-CCTGATTAGATAAGTGTAG-TTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAC
*
41931213 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAC
* * *
41931259 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAC
* *
41931305 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAC
*
41931357 CACCTATCACTTT
1 CACTTATCACTTT
41931370 CCACTTGTCA
Statistics
Matches: 135, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
43 10 0.07
44 5 0.04
45 17 0.13
46 60 0.44
48 1 0.01
50 1 0.01
52 41 0.30
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAC
Found at i:41931326 original size:52 final size:52
Alignment explanation
Indices: 41931270--41931386 Score: 191
Period size: 52 Copynumber: 2.3 Consensus size: 52
41931260 ACTTATCACT
* *
41931270 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACCTATCACTTTCCAC
* *
41931322 TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACCTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACCTATCACTTTCCAC
41931374 TTGTCACTT-ATCA
1 TTGTCACTTGATCA
41931387 CTGATCAGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 4 0.07
52 57 0.93
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (52 bp):
TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACCTATCACTTTCCAC
Found at i:41936577 original size:84 final size:84
Alignment explanation
Indices: 41936335--41936651 Score: 237
Period size: 84 Copynumber: 3.8 Consensus size: 84
41936325 AACAATATCG
* **** * *
41936335 AATAAAATCTTGTTAAACGGAAAAAATAAA-CCCCAAACAGATTTTATTTAA-TTTAA--AATAA
1 AATAAAATCTTCTTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTACTAA
* *
41936396 TTT--AGAA-ATAAAATAA
66 TTTGGACAACAAAAAATAA
* * * *
41936412 AATAAAATCTTGTTAAACAGCGGGAATAAATCTCAAAACAGATTTTATTTAA-TTTAA-TACTAA
1 AATAAAATCTTCTTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTACTAA
* *
41936475 TTTGGAAACAACATAAAATTA
66 TTTGG--ACAACAAAAAATAA
* * *
41936496 AATAAAATCTTCTTAAACGGCGGTAATAAATCCCGAAATAGATTTTATTTAATTTTAATTTCTCA
1 AATAAAATCTTCTTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTACT-A
*
41936561 TTTTTGG-CAA-AAAAAATCAA
65 -ATTTGGACAACAAAAAAT-AA
* * * *
41936581 AATGTAATAA-ATTCGTTGAACGGTGGGAATAAATCCTGAAACAGATTTTATTTTAATTTTAA-T
1 AA--TAA-AATCTTC-TTAAACGGCGGGAATAAATCCCGAAACAGATTTTA-TTTAATTTTAATT
*
41936644 ACTTATTT
61 ACTAATTT
41936652 TTGGTAATAA
Statistics
Matches: 194, Mismatches: 29, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
77 25 0.13
78 24 0.12
79 7 0.04
83 3 0.02
84 60 0.31
85 11 0.06
86 6 0.03
87 7 0.04
88 40 0.21
89 11 0.06
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (84 bp):
AATAAAATCTTCTTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTACTAA
TTTGGACAACAAAAAATAA
Found at i:41936704 original size:89 final size:88
Alignment explanation
Indices: 41936412--41936821 Score: 329
Period size: 88 Copynumber: 4.7 Consensus size: 88
41936402 AATAAAATAA
* * * *
41936412 AATAAAATCTTGTTAAACAGCGGGAATAAAT-CTCAAAACAGATTTTATTTAA-TTTAATAC-TA
1 AATAAAATC-CGTTGAACGGCGGGAATAAATCCT-GAAACAGATTTTATTTAATTTTAATACTTA
* * * *
41936474 -ATTTGGAAACAACAT-AAAATT-A
64 TTTTTGGAAATAAAATCAAAATTGT
* * * * * *
41936496 AATAAAATCTTC-TTAAACGGCGGTAATAAATCCCGAAATAGATTTTATTTAATTTTAATTTCTC
1 AATAAAATC--CGTTGAACGGCGGGAATAAATCCTGAAACAGATTTTATTTAATTTTAA-TACTT
*
41936560 ATTTTTGGCAAAAAAAATCAAAA-TGT
63 ATTTTTGG-AAATAAAATCAAAATTGT
* *
41936586 AAT-AAATTCGTTGAACGGTGGGAATAAATCCTGAAACAGATTTTATTTTAATTTTAATACTTAT
1 AATAAAATCCGTTGAACGGCGGGAATAAATCCTGAAACAGATTTTA-TTTAATTTTAATACTTAT
* *
41936650 TTTTGGTAATAAAATCAAAATTGG
65 TTTTGGAAATAAAATCAAAATTGT
* * ** * * * **
41936674 AATAAAATCCATTGAACGACGGGAATAAATCCCCAAACGGGTTTTATTTAACTTTAAT--TTCCC
1 AATAAAATCCGTTGAACGGCGGGAATAAATCCTGAAACAGATTTTATTTAATTTTAATACTT-AT
* * *
41936737 GTTTGGAAATAAAATTAAAAATAATAT
65 TTTTGGAAATAAAA-TCAAAAT--TGT
* * * *
41936764 AATAAAATCCGTTGAATGGCGGGAATAAATCATGAAACGGATTTTATTTACTTTTAAT
1 AATAAAATCCGTTGAACGGCGGGAATAAATCCTGAAACAGATTTTATTTAATTTTAAT
41936822 TTGGAAACAA
Statistics
Matches: 261, Mismatches: 48, Indels: 28
0.77 0.14 0.08
Matches are distributed among these distances:
84 42 0.16
85 7 0.03
86 4 0.02
87 26 0.10
88 68 0.26
89 57 0.22
90 57 0.22
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (88 bp):
AATAAAATCCGTTGAACGGCGGGAATAAATCCTGAAACAGATTTTATTTAATTTTAATACTTATT
TTTGGAAATAAAATCAAAATTGT
Found at i:41937320 original size:30 final size:30
Alignment explanation
Indices: 41937285--41937345 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
41937275 AGCACCTCTA
* *
41937285 CAACGATCAATGAATAAACGTTGCATTTTT
1 CAACGATCAACGAACAAACGTTGCATTTTT
41937315 CAACGATCAACGAACAAACGTTGCATTTTT
1 CAACGATCAACGAACAAACGTTGCATTTTT
41937345 C
1 C
41937346 TATCACCGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (30 bp):
CAACGATCAACGAACAAACGTTGCATTTTT
Found at i:41940361 original size:22 final size:24
Alignment explanation
Indices: 41940335--41940387 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
41940325 TGTTTCCGAG
*
41940335 CAAACTAATAAGA-AAATAGACAA
1 CAAACTAATAAGATAAAGAGACAA
* *
41940358 -AAACAAATAAGATAAAGAGATAA
1 CAAACTAATAAGATAAAGAGACAA
41940381 CAAACTA
1 CAAACTA
41940388 GAAAAAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 11 0.46
23 8 0.33
24 5 0.21
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.13
Consensus pattern (24 bp):
CAAACTAATAAGATAAAGAGACAA
Found at i:41960716 original size:17 final size:18
Alignment explanation
Indices: 41960683--41960719 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
41960673 TCATGACTTA
41960683 TTTTGAAGAGGTCTTATT
1 TTTTGAAGAGGTCTTATT
41960701 TTTTAGAAGA-GT-TTATT
1 TTTT-GAAGAGGTCTTATT
41960718 TT
1 TT
41960720 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.24, C:0.03, G:0.19, T:0.54
Consensus pattern (18 bp):
TTTTGAAGAGGTCTTATT
Found at i:41960724 original size:19 final size:20
Alignment explanation
Indices: 41960680--41960724 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
41960670 TTTTCATGAC
*
41960680 TTATTTTGAAGAGGTCTTAT
1 TTATTTAGAAGAGGTCTTAT
41960700 TT-TTTAGAAGA-GT-TTATT
1 TTATTTAGAAGAGGTCTTA-T
41960718 TTATTTA
1 TTATTTA
41960725 TTTATTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 3 0.14
18 5 0.23
19 12 0.55
20 2 0.09
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.56
Consensus pattern (20 bp):
TTATTTAGAAGAGGTCTTAT
Found at i:41961486 original size:19 final size:20
Alignment explanation
Indices: 41961459--41961506 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
41961449 TTTATAATGT
*
41961459 TATATTTTA-ATATTTAAAA
1 TATATTTTATATATTCAAAA
* *
41961478 TATAATTTATATATTCAAAT
1 TATATTTTATATATTCAAAA
41961498 TATATTTTA
1 TATATTTTA
41961507 CAAATACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTTTATATATTCAAAA
Found at i:41963124 original size:30 final size:30
Alignment explanation
Indices: 41963088--41963156 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
41963078 TATTCATAAA
* *
41963088 AATTGGTAAAGTGAGGCGATAATTTGGAAT
1 AATTGGTAAAGTAAGACGATAATTTGGAAT
*
41963118 AATTGGTAAAGTAAGATGATAATTTGGAAT
1 AATTGGTAAAGTAAGACGATAATTTGGAAT
41963148 AATCTGGTA
1 AAT-TGGTA
41963157 TCCAACTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (30 bp):
AATTGGTAAAGTAAGACGATAATTTGGAAT
Found at i:41967931 original size:17 final size:16
Alignment explanation
Indices: 41967888--41967934 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
41967878 AAAGTTATTC
*
41967888 AAAATTATAAAAATAT
1 AAAATTATAAAAATAA
* *
41967904 AAATTTTTAAATAATAA
1 AAAATTATAAA-AATAA
41967921 AAAATTATAAAAAT
1 AAAATTATAAAAAT
41967935 TGCAAACAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATTATAAAAATAA
Found at i:41967934 original size:9 final size:9
Alignment explanation
Indices: 41967888--41967980 Score: 59
Period size: 9 Copynumber: 10.4 Consensus size: 9
41967878 AAAGTTATTC
41967888 AAAATTATA
1 AAAATTATA
41967897 AAAA-TAT-
1 AAAATTATA
* *
41967904 AAATTTTTA
1 AAAATTATA
41967913 AATAA-TA-A
1 AA-AATTATA
41967921 AAAATTATA
1 AAAATTATA
**
41967930 AAAATTGCA
1 AAAATTATA
*
41967939 AACAATTATG
1 AA-AATTATA
* *
41967949 AAAATTTTT
1 AAAATTATA
41967958 AAAATTATTA
1 AAAATTA-TA
*
41967968 AAAATTTTA
1 AAAATTATA
41967977 AAAA
1 AAAA
41967981 ATAAAATTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 14
0.69 0.15 0.15
Matches are distributed among these distances:
7 5 0.08
8 10 0.16
9 34 0.54
10 14 0.22
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:41972132 original size:16 final size:19
Alignment explanation
Indices: 41972099--41972135 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
41972089 ATAACGTATT
41972099 ATAAAATAAAAGACAGAGA
1 ATAAAATAAAAGACAGAGA
41972118 ATAAAA-AAAA-A-AGAGA
1 ATAAAATAAAAGACAGAGA
41972134 AT
1 AT
41972136 GGGAGAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 4 0.22
19 6 0.33
ACGTcount: A:0.73, C:0.03, G:0.14, T:0.11
Consensus pattern (19 bp):
ATAAAATAAAAGACAGAGA
Found at i:41980822 original size:29 final size:29
Alignment explanation
Indices: 41980780--41980837 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
41980770 CGTTTTAGAG
41980780 GAGAAGGGATGATTTCCTTTCCAGCCGCT
1 GAGAAGGGATGATTTCCTTTCCAGCCGCT
41980809 GAGAAGGGATGATTTCCTTTCCAGCCGCT
1 GAGAAGGGATGATTTCCTTTCCAGCCGCT
41980838 CTATGTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (29 bp):
GAGAAGGGATGATTTCCTTTCCAGCCGCT
Found at i:41981027 original size:28 final size:27
Alignment explanation
Indices: 41980973--41981042 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
41980963 AAATATAATT
* * *
41980973 ATAATTTTTATTATTTATTTATTTTTTA
1 ATAATTTTTA-TATTAATTAATGTTTTA
*
41981001 ATAATTTTTATATGTAATTAATGTTTTC
1 ATAATTTTTATAT-TAATTAATGTTTTA
*
41981029 ATAATTTATATATT
1 ATAATTTTTATATT
41981043 TCTATAATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.11
28 32 0.89
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (27 bp):
ATAATTTTTATATTAATTAATGTTTTA
Found at i:41981562 original size:13 final size:14
Alignment explanation
Indices: 41981529--41981565 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
41981519 TTTTTTATGA
41981529 ATATTAGTTTCGTTT
1 ATATTA-TTTCGTTT
41981544 AT-TTATTT-GTTT
1 ATATTATTTCGTTT
41981556 ATATTATTTC
1 ATATTATTTC
41981566 TATGCAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 3 0.15
15 2 0.10
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (14 bp):
ATATTATTTCGTTT
Found at i:41984103 original size:72 final size:71
Alignment explanation
Indices: 41984011--41984277 Score: 324
Period size: 72 Copynumber: 3.7 Consensus size: 71
41984001 CAATGCTAAA
*
41984011 CTAGTTTTATCAATAGTTGTTTATGTTTTGTTTTTGAATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTTGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
41984076 GTGTAAT
66 GT-TAAT
* * *
41984083 CTAGTTTTATCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGGTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTTGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
41984148 GCTTAAGGT
66 G-TTAA--T
* * * *
41984157 C-ATTTTTATCAATAATTGTTTATGTTTTTTTTTTTTGGATATTGAATTTATGTTCTACTTAGTT
1 CTAGTTTTATCAATAGTTGTTTATG--TTTTGTTTTTGGATATTGAATTTATGTTCTACTTATTT
* *
41984221 ATACTAAAT
64 AT-GTTAAT
* * **
41984230 -TAGTTTTATCAATAGTTGTTTAT-ATTTGATTTTGGATATAAAATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTTGTTTTTGGATATTGAATTTAT
41984278 TCATAGATGA
Statistics
Matches: 168, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
70 20 0.12
72 65 0.39
73 42 0.25
74 2 0.01
75 39 0.23
ACGTcount: A:0.25, C:0.06, G:0.14, T:0.55
Consensus pattern (71 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTTGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTTAAT
Found at i:41984263 original size:145 final size:145
Alignment explanation
Indices: 41984015--41984277 Score: 379
Period size: 147 Copynumber: 1.8 Consensus size: 145
41984005 GCTAAACTAG
* * * *
41984015 TTTTATCAATAGTTGTTTATGTTTTGTTTTTGAATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAATTGTTTATGTTTTGTTTTTGAATATTGAATTTATGTTCTACTTAGTTATCTGA
* * * **
41984080 AATCTAGTTTTATCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGGTCTACTTATT
66 AATCTAGTTTTATCAATAGTTGTTTATATTTGGATTTTGGATATAAAATTTATGGTCTACTTATT
41984145 TATGCTTAAGGTCAT
131 TATGCTTAAGGTCAT
* *
41984160 TTTTATCAATAATTGTTTATGTTTTTTTTTTTTGGATATTGAATTTATGTTCTACTTAGTTATAC
1 TTTTATCAATAATTGTTTATG--TTTTGTTTTTGAATATTGAATTTATGTTCTACTTAGTTAT-C
41984225 T-AAAT-TAGTTTTATCAATAGTTGTTTATATTT-GATTTTGGATATAAAATTTAT
63 TGAAATCTAGTTTTATCAATAGTTGTTTATATTTGGATTTTGGATATAAAATTTAT
41984278 TCATAGATGA
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
145 38 0.37
146 25 0.24
147 40 0.38
148 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (145 bp):
TTTTATCAATAATTGTTTATGTTTTGTTTTTGAATATTGAATTTATGTTCTACTTAGTTATCTGA
AATCTAGTTTTATCAATAGTTGTTTATATTTGGATTTTGGATATAAAATTTATGGTCTACTTATT
TATGCTTAAGGTCAT
Found at i:41986125 original size:21 final size:20
Alignment explanation
Indices: 41986083--41986125 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41986073 ATTTTAAAAG
*
41986083 TTTTTTGTATTTTTTTATGT
1 TTTTTTGTATTTTATTATGT
41986103 TTTTCTTGTATTATTATTA-GT
1 TTTT-TTGTATT-TTATTATGT
41986124 TT
1 TT
41986126 ATCATCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.74
Consensus pattern (20 bp):
TTTTTTGTATTTTATTATGT
Found at i:41987337 original size:14 final size:14
Alignment explanation
Indices: 41987318--41987346 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41987308 CGACTCCATT
41987318 TTTCAAAATAAAAA
1 TTTCAAAATAAAAA
41987332 TTTCAAAATAAAAA
1 TTTCAAAATAAAAA
41987346 T
1 T
41987347 GGTTTAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
TTTCAAAATAAAAA
Found at i:41998905 original size:44 final size:44
Alignment explanation
Indices: 41998726--41998879 Score: 193
Period size: 44 Copynumber: 3.5 Consensus size: 44
41998716 GAAAACCTAT
* * **
41998726 TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-CACATCTTA
1 TCTCCCTGAAGTTGCAATGGAGCAGATTGAAGAAACCA-ATCTTA
* * * * *
41998770 TCTCCCTGAAGTTACAGTGGAACAGACTGAATAAACCAATCTTA
1 TCTCCCTGAAGTTGCAATGGAGCAGATTGAAGAAACCAATCTTA
*
41998814 TCTCCCTGAAGTTGCAATGGAGCAGATTGAAGAAACCAATCATA
1 TCTCCCTGAAGTTGCAATGGAGCAGATTGAAGAAACCAATCTTA
*
41998858 TCTCCCTGAAGTTGCAGTGGAG
1 TCTCCCTGAAGTTGCAATGGAG
41998880 TGGATTAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
44 93 0.98
45 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
TCTCCCTGAAGTTGCAATGGAGCAGATTGAAGAAACCAATCTTA
Found at i:41999250 original size:44 final size:42
Alignment explanation
Indices: 41999202--41999321 Score: 111
Period size: 41 Copynumber: 2.9 Consensus size: 42
41999192 AGCCACCAGC
* * *
41999202 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTTAAATGATGGAT
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAAATTCAAATCA-GG-T
* * * **
41999246 CTTATCTCTCT-AAGGTTGTAGTAGAGCAGA-TCGCATCAGGT
1 CTTATCTCTCTGAA-GTTGCAGTGGAGCAAATTCAAATCAGGT
*
41999287 CTTATCTCTTTGAAGTTGCAGTGGAGCAAA-TCAAA
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAAATTCAAA
41999322 GCCAATAATC
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
41 27 0.45
42 4 0.07
43 6 0.10
44 23 0.38
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (42 bp):
CTTATCTCTCTGAAGTTGCAGTGGAGCAAATTCAAATCAGGT
Found at i:42000729 original size:25 final size:25
Alignment explanation
Indices: 42000695--42000744 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42000685 TGTGAAGGAG
42000695 AAGGGAATATTTTTCATTAAGTCCT
1 AAGGGAATATTTTTCATTAAGTCCT
42000720 AAGGGAATATTTTTCATTAAGTCCT
1 AAGGGAATATTTTTCATTAAGTCCT
42000745 CCATGTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (25 bp):
AAGGGAATATTTTTCATTAAGTCCT
Found at i:42001006 original size:21 final size:21
Alignment explanation
Indices: 42000982--42001026 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
42000972 TTTTAAAAGT
*
42000982 TTTTTTTTGTATTATT-TTATG
1 TTTTTCTTGTATTATTATTA-G
42001003 TTTTTCTTGTATTATTATTAG
1 TTTTTCTTGTATTATTATTAG
42001024 TTT
1 TTT
42001027 ATCATCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (21 bp):
TTTTTCTTGTATTATTATTAG
Found at i:42001433 original size:80 final size:80
Alignment explanation
Indices: 42001340--42001499 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 80
42001330 GTTTTAGATG
*
42001340 TCCTTTCTCTTATGATAATTTTTAAGTTTGCTATATTTTATTTGCATAATTTACTTAAGTATTTC
1 TCCTTTCTCTTATGATAATTTTTAAGTCTGCTATATTTTATTTGCATAATTTACTTAAGTATTTC
42001405 TTTCAATTTTTTACT
66 TTTCAATTTTTTACT
* * *
42001420 TCCTTTCTCTTATGATATTTTTTAAGTCTGCTATATTTTATTTGCGTAATTTGCTTAAGTATTTC
1 TCCTTTCTCTTATGATAATTTTTAAGTCTGCTATATTTTATTTGCATAATTTACTTAAGTATTTC
42001485 TTTCAATTTTTTACT
66 TTTCAATTTTTTACT
42001500 CACTTGCTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.57
Consensus pattern (80 bp):
TCCTTTCTCTTATGATAATTTTTAAGTCTGCTATATTTTATTTGCATAATTTACTTAAGTATTTC
TTTCAATTTTTTACT
Found at i:42003813 original size:13 final size:13
Alignment explanation
Indices: 42003795--42003835 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
42003785 AACAAAACTT
42003795 CTCAAAAGCACTA
1 CTCAAAAGCACTA
*
42003808 CTCAAAAGCACTT
1 CTCAAAAGCACTA
*
42003821 CTCAAAAGCAATA
1 CTCAAAAGCACTA
42003834 CT
1 CT
42003836 AAGCTAGACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (13 bp):
CTCAAAAGCACTA
Found at i:42005506 original size:29 final size:30
Alignment explanation
Indices: 42005444--42005514 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
42005434 TCATCAACGA
**
42005444 ATGAAAAAGGATAGCTTCGGCTATCAATCT
1 ATGAAAAAGGATAGCTTCAACTATCAATCT
* * *
42005474 ATGAAAATGGATAGTTTCAACTATCGAT-T
1 ATGAAAAAGGATAGCTTCAACTATCAATCT
*
42005503 ATGAAAAGGGAT
1 ATGAAAAAGGAT
42005515 GGTGACGACC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.28
Consensus pattern (30 bp):
ATGAAAAAGGATAGCTTCAACTATCAATCT
Found at i:42005598 original size:59 final size:60
Alignment explanation
Indices: 42005535--42005662 Score: 172
Period size: 59 Copynumber: 2.1 Consensus size: 60
42005525 ATCAATAATA
*
42005535 AAAAGGGATGGTGACGACCATCGA-ACTATG-AAAAGGAATAGCTTCAGTTATCGAT-TATG
1 AAAAGGGATGGTGACGACCATCGACA-TATGTAAAAGG-ATAGCTTCAGCTATCGATCTATG
* * *
42005594 AAAAGGGATGGTGACGACCATCGACATATGTAAAATGATGGCTTTAGCTATCGATCTATG
1 AAAAGGGATGGTGACGACCATCGACATATGTAAAAGGATAGCTTCAGCTATCGATCTATG
*
42005654 AAAGGGGAT
1 AAAAGGGAT
42005663 AGCTTCGGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
59 43 0.70
60 18 0.30
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (60 bp):
AAAAGGGATGGTGACGACCATCGACATATGTAAAAGGATAGCTTCAGCTATCGATCTATG
Found at i:42005616 original size:29 final size:29
Alignment explanation
Indices: 42005496--42005617 Score: 122
Period size: 29 Copynumber: 4.2 Consensus size: 29
42005486 AGTTTCAACT
42005496 ATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
* * *
42005525 ATCAATAATAAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
* * * * **
42005554 ATCGAACTATGAAAAGGAATAGCT-TC-AGTT
1 ATCG-ATTATGAAAAGGGAT-GGTGACGA-CC
42005584 ATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
42005613 ATCGA
1 ATCGA
42005618 CATATGTAAA
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
28 2 0.03
29 49 0.70
30 17 0.24
31 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (29 bp):
ATCGATTATGAAAAGGGATGGTGACGACC
Found at i:42005719 original size:29 final size:30
Alignment explanation
Indices: 42005684--42005752 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
42005674 TCAAATTATT
*
42005684 AAAAAGGATGGTGACAACCATCAAACAATG
1 AAAAGGGATGGTGACAACCATCAAACAATG
* ** *
42005714 AAAAGGGGTGGTGATGACCATCAAATAATG
1 AAAAGGGATGGTGACAACCATCAAACAATG
*
42005744 AACAGGGAT
1 AAAAGGGAT
42005753 AGCTTCGGCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.45, C:0.13, G:0.26, T:0.16
Consensus pattern (30 bp):
AAAAGGGATGGTGACAACCATCAAACAATG
Found at i:42013243 original size:30 final size:29
Alignment explanation
Indices: 42013192--42013259 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
42013182 TCGATGAATA
* *
42013192 AAAAGGGATAACTTCGACTATCGATCTATG
1 AAAAGGGATAACTCCGACTATCGAT-TACG
*
42013222 AAAAGGGATAGCTCC-AGCTATCGATTACG
1 AAAAGGGATAACTCCGA-CTATCGATTACG
42013251 AAAAGGGAT
1 AAAAGGGAT
42013260 GGAGACAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 13 0.38
30 21 0.62
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (29 bp):
AAAAGGGATAACTCCGACTATCGATTACG
Found at i:42013282 original size:29 final size:30
Alignment explanation
Indices: 42013250--42013320 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
42013240 TATCGATTAC
*
42013250 GAAAAGGGATGGAGACAACCAT-GAACAAT
1 GAAAAGGGATGGAGACAACCATCAAACAAT
* ** *
42013279 GAAAAGGGATGGGGACAATTATCAAACTAT
1 GAAAAGGGATGGAGACAACCATCAAACAAT
42013309 GAAAAGGGATGG
1 GAAAAGGGATGG
42013321 CTTCGACTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 19 0.53
30 17 0.47
ACGTcount: A:0.45, C:0.10, G:0.31, T:0.14
Consensus pattern (30 bp):
GAAAAGGGATGGAGACAACCATCAAACAAT
Found at i:42013340 original size:30 final size:30
Alignment explanation
Indices: 42013298--42013499 Score: 160
Period size: 30 Copynumber: 6.7 Consensus size: 30
42013288 TGGGGACAAT
*
42013298 TATCAAACTATGAAAAGGGATGGCTTCGAC
1 TATCAAATTATGAAAAGGGATGGCTTCGAC
** **
42013328 TAT-TGATATATGAAAAGGGATATCTTCGAC
1 TATCAAAT-TATGAAAAGGGATGGCTTCGAC
*
42013358 TATCAAATTATGAAAAGGGATGG-TGACGAC
1 TATCAAATTATGAAAAGGGATGGCT-TCGAC
** * * * *
42013388 CGTCGAAA-AATTAAAATGGATGG-TGACGAC
1 TATC-AAATTATGAAAAGGGATGGCT-TCGAC
* *
42013418 CATCAAATTATGAAAAGGGATAGCTTCGAC
1 TATCAAATTATGAAAAGGGATGGCTTCGAC
* * * ** *
42013448 TGTCGAACTATGAAAAGGGATAACTTCGAT
1 TATCAAATTATGAAAAGGGATGGCTTCGAC
42013478 TATCAAATTATGAAAAGGGATG
1 TATCAAATTATGAAAAGGGATG
42013500 TGTCAACCAT
Statistics
Matches: 135, Mismatches: 31, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
29 5 0.04
30 124 0.92
31 6 0.04
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (30 bp):
TATCAAATTATGAAAAGGGATGGCTTCGAC
Found at i:42013362 original size:60 final size:59
Alignment explanation
Indices: 42013298--42013499 Score: 210
Period size: 60 Copynumber: 3.4 Consensus size: 59
42013288 TGGGGACAAT
* * *
42013298 TATCAAACTATGAAAAGGGATGGCTTCGACTATTGATATATGAAAAGGGATATCTTCGAC
1 TATCAAATTATGAAAAGGGATGGCTTCGACTGTCGA-ATATGAAAAGGGATATCTTCGAC
* * * * * * **
42013358 TATCAAATTATGAAAAGGGATGG-TGACGACCGTCGAAAAATTAAAATGGATGGT-GACGAC
1 TATCAAATTATGAAAAGGGATGGCT-TCGACTGTCG-AATATGAAAAGGGAT-ATCTTCGAC
* * * *
42013418 CATCAAATTATGAAAAGGGATAGCTTCGACTGTCGAACTATGAAAAGGGATAACTTCGAT
1 TATCAAATTATGAAAAGGGATGGCTTCGACTGTCGAA-TATGAAAAGGGATATCTTCGAC
42013478 TATCAAATTATGAAAAGGGATG
1 TATCAAATTATGAAAAGGGATG
42013500 TGTCAACCAT
Statistics
Matches: 111, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
59 3 0.03
60 105 0.95
61 3 0.03
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (59 bp):
TATCAAATTATGAAAAGGGATGGCTTCGACTGTCGAATATGAAAAGGGATATCTTCGAC
Found at i:42013444 original size:120 final size:119
Alignment explanation
Indices: 42013192--42013499 Score: 370
Period size: 120 Copynumber: 2.6 Consensus size: 119
42013182 TCGATGAATA
* * * * * *
42013192 AAAAGGGATAACTTCGACTATCGATCTATGAAAAGGGATAGC-TCCAGCTATC-GATTACGAAAA
1 AAAAGGGATAGCTTCGACTATCGATATATGAAAAGGGATAACTTCGA-CTATCAAATTATGAAAA
* **
42013255 GGGATGGAGACAACCATGAACAATGAAAAGGGATGGGGACAATTATCAAACTATG
65 GGGATGGAGACAACCATGAAAAATGAAAAGGGATGGGGACAACCATCAAACTATG
* * *
42013310 AAAAGGGATGGCTTCGACTATTGATATATGAAAAGGGATATCTTCGACTATCAAATTATGAAAAG
1 AAAAGGGATAGCTTCGACTATCGATATATGAAAAGGGATAACTTCGACTATCAAATTATGAAAAG
* * * * * * * *
42013375 GGATGGTGACGACCGTCGAAAAATTAAAATGGATGGTGACGACCATCAAATTATG
66 GGATGGAGACAACCAT-GAAAAATGAAAAGGGATGGGGACAACCATCAAACTATG
* *
42013430 AAAAGGGATAGCTTCGACTGTCGA-ACTATGAAAAGGGATAACTTCGATTATCAAATTATGAAAA
1 AAAAGGGATAGCTTCGACTATCGATA-TATGAAAAGGGATAACTTCGACTATCAAATTATGAAAA
42013494 GGGATG
65 GGGATG
42013500 TGTCAACCAT
Statistics
Matches: 162, Mismatches: 24, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
118 42 0.26
119 27 0.17
120 93 0.57
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (119 bp):
AAAAGGGATAGCTTCGACTATCGATATATGAAAAGGGATAACTTCGACTATCAAATTATGAAAAG
GGATGGAGACAACCATGAAAAATGAAAAGGGATGGGGACAACCATCAAACTATG
Found at i:42016671 original size:15 final size:16
Alignment explanation
Indices: 42016638--42016692 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 16
42016628 TAAAAATGTT
* *
42016638 ATTAAATT-ATATATT
1 ATTAAATTAATACATA
42016653 ATTAAATTAATA-ATA
1 ATTAAATTAATACATA
* * *
42016668 ATTATATTAAAACATG
1 ATTAAATTAATACATA
42016684 ATTAAATTA
1 ATTAAATTA
42016693 TTTATTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 20 0.61
16 13 0.39
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTAAATTAATACATA
Found at i:42016904 original size:16 final size:16
Alignment explanation
Indices: 42016883--42016933 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
42016873 TGAATTACTG
*
42016883 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTCC
*
42016899 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
**
42016915 ATTACATTTCTATTCC
1 ATTACAGCTCTATTCC
42016931 ATT
1 ATT
42016934 CCAGTGAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.25, C:0.24, G:0.04, T:0.47
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:42020905 original size:21 final size:21
Alignment explanation
Indices: 42020881--42020923 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42020871 TGGTAAATAT
*
42020881 TGGAGAAT-TAAATTTATTATA
1 TGGAGAATATAAAATT-TTATA
*
42020902 TGGATAATATAAAATTTTATA
1 TGGAGAATATAAAATTTTATA
42020923 T
1 T
42020924 ATTTTTCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (21 bp):
TGGAGAATATAAAATTTTATA
Found at i:42026411 original size:18 final size:19
Alignment explanation
Indices: 42026376--42026411 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42026366 ATAAATTTTA
*
42026376 TTAAATATCTGTTTAATCT
1 TTAAATATCTGTTGAATCT
42026395 TTAAATAT-TGTTGAATC
1 TTAAATATCTGTTGAATC
42026412 ACACACTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAAATATCTGTTGAATCT
Found at i:42029816 original size:24 final size:22
Alignment explanation
Indices: 42029776--42029820 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42029766 TAAGTCTAAT
*
42029776 ATTTTTTTTAAAATTTAATTTG
1 ATTTCTTTTAAAATTTAATTTG
42029798 ATTTCTTTTAAGAAGTTTAATTT
1 ATTTCTTTTAA-AA-TTTAATTT
42029821 ATATAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 2 0.10
24 8 0.40
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
ATTTCTTTTAAAATTTAATTTG
Found at i:42031268 original size:13 final size:14
Alignment explanation
Indices: 42031237--42031269 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42031227 GGCTCACAAA
*
42031237 AAAATAATAAACCC
1 AAAATAATAAACAC
42031251 AAAATAATAAA-AC
1 AAAATAATAAACAC
42031264 AAAATA
1 AAAATA
42031270 TAAGTCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATAATAAACAC
Found at i:42031668 original size:4 final size:4
Alignment explanation
Indices: 42031659--42031686 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
42031649 CTCTGCGAAT
42031659 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
42031687 GCCCTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:42037157 original size:13 final size:13
Alignment explanation
Indices: 42037139--42037163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42037129 TACATATGCC
42037139 AGCTAAAATGCTT
1 AGCTAAAATGCTT
42037152 AGCTAAAATGCT
1 AGCTAAAATGCT
42037164 CCAAATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
AGCTAAAATGCTT
Found at i:42038762 original size:17 final size:17
Alignment explanation
Indices: 42038721--42038756 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42038711 TCAACTTTTC
42038721 ACCTTTCATCTTCCTTA
1 ACCTTTCATCTTCCTTA
*
42038738 ACCTTTCATTTTCCTTA
1 ACCTTTCATCTTCCTTA
42038755 AC
1 AC
42038757 TCTTCACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.47
Consensus pattern (17 bp):
ACCTTTCATCTTCCTTA
Found at i:42042292 original size:18 final size:17
Alignment explanation
Indices: 42042263--42042317 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 17
42042253 AAAAAAATTT
* *
42042263 AAAAAAAAAAGAAGAAG
1 AAAAAGAAAAGAAAAAG
42042280 AAGAAAGAAAAGAAAAAG
1 AA-AAAGAAAAGAAAAAG
42042298 AAAAAG--AAGAAAAAG
1 AAAAAGAAAAGAAAAAG
42042313 AAAAA
1 AAAAA
42042318 AGAGAGGCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 14 0.40
17 6 0.17
18 15 0.43
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAG
Found at i:42042295 original size:24 final size:24
Alignment explanation
Indices: 42042263--42042318 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
42042253 AAAAAAATTT
*
42042263 AAAAAAAAAAGAAGAAGAAGAAAG
1 AAAAAAAAAAGAAAAAGAAGAAAG
*
42042287 AAAAGAAAAAGAAAAAGAAGAAA-
1 AAAAAAAAAAGAAAAAGAAGAAAG
*
42042310 AAGAAAAAA
1 AAAAAAAAA
42042319 GAGAGGCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAGAAAAAGAAGAAAG
Found at i:42042298 original size:15 final size:15
Alignment explanation
Indices: 42042263--42042317 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
42042253 AAAAAAATTT
42042263 AAAAA-AAAAAGAAG
1 AAAAAGAAAAAGAAG
*
42042277 AAGAAGAAAGAA-AAG
1 AAAAAGAAA-AAGAAG
42042292 AAAAAGAAAAAGAAG
1 AAAAAGAAAAAGAAG
42042307 AAAAAGAAAAA
1 AAAAAGAAAAA
42042318 AGAGAGGCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 6 0.17
15 28 0.78
16 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAG
Found at i:42042298 original size:21 final size:21
Alignment explanation
Indices: 42042265--42042317 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
42042255 AAAAATTTAA
*
42042265 AAAAA-AAAGAAGAAGAAGAA-
1 AAAAAGAAA-AAGAAAAAGAAG
42042285 AGAAAAGAAAAAGAAAAAGAAG
1 A-AAAAGAAAAAGAAAAAGAAG
42042307 AAAAAGAAAAA
1 AAAAAGAAAAA
42042318 AGAGAGGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 24 0.83
22 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAGAAAAAGAAG
Found at i:42042315 original size:6 final size:6
Alignment explanation
Indices: 42042263--42042317 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
42042253 AAAAAAATTT
*
42042263 AAAAA- AAAAAG AAGAAG AAGAAAG -AAAAG AAAAAG AAAAAG ---AAG
1 AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG
42042307 AAAAAG AAAAA
1 AAAAAG AAAAA
42042318 AGAGAGGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.07
5 9 0.21
6 27 0.64
7 3 0.07
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:42043667 original size:72 final size:72
Alignment explanation
Indices: 42043532--42043668 Score: 229
Period size: 72 Copynumber: 1.9 Consensus size: 72
42043522 ACGTTGTAGC
* * *
42043532 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGTGGAATAGGTTAAAG
1 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAACAGATTAAAG
42043597 TTGAGGT
66 TTGAGGT
* *
42043604 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTTCCTGGCGTTGCAGCGGAGCAGATTAAAG
1 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAACAGATTAAAG
42043669 CTGAAGGCAG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (72 bp):
GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAACAGATTAAAG
TTGAGGT
Found at i:42043769 original size:50 final size:50
Alignment explanation
Indices: 42043709--42044361 Score: 567
Period size: 50 Copynumber: 13.0 Consensus size: 50
42043699 TTAAGACTAA
* * *
42043709 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCAACATTAC
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
* * * * **
42043759 GGTTAAATAGATTGAAGCTGCAATAGTGAATCTTGTTTCCCCGACATTGC
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
* * ** *
42043809 AGTTAAATAGATTGAAGCTATAACAGCGAATCTTATTTCCCTAACGTTGC
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
*** * * * * *
42043859 AGCGGAACAAATTAAAGCTA-AAGGTAGCGAGTCTTACTTCCCCGACATTGC
1 AGTTAAATAGATTGAAGCTACAA--CAGCGAATCTTACTTCCCCGACATTGC
* ** * **
42043910 AGTTAAATAGATTGAAGCTACAACAGCAAATCTTACTTCCTTGGCGGTGC
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
** * * * * *
42043960 AGTGGAACAGATTGAAGCTACAATAGTGAATCTTGCTTCCCCAACATTGC
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
* ** * *
42044010 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTATTTCCTTGGCGA-TGT
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGAC-ATTGC
** * * * *
42044060 AGTGGAACAGATTGAAGCTATAACAGCGAATCTTGCTTCCCCGATATTGC
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
* ** *
42044110 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTT-CCCTAGCGGTGT
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGA-CATTGC
** * * * * *
42044160 AGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTTCCCGACATTAC
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
* * * * * *
42044210 AGTTAAATAGGTTAAAGCTGCAACAGCGAATCTTACTT-CCCTAGCAGTGT
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGA-CATTGC
** * * * **
42044260 AGTGGAACAGATTAAAGCTACAACAGTGAATCTTGTTTCCCCGACATTGC
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
* * * *
42044310 AGTTAAATAGATTGAAGCTATAACAGCGAATCTTATTTCTCTGACATTGC
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
42044360 AG
1 AG
42044362 CAGAACAAAT
Statistics
Matches: 464, Mismatches: 130, Indels: 18
0.76 0.21 0.03
Matches are distributed among these distances:
49 11 0.02
50 407 0.88
51 44 0.09
52 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (50 bp):
AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGC
Found at i:42043834 original size:100 final size:99
Alignment explanation
Indices: 42043709--42044344 Score: 790
Period size: 100 Copynumber: 6.4 Consensus size: 99
42043699 TTAAGACTAA
* * * ** *
42043709 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCAACAT-TACGGTTAAATAGATTG
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCATGTA--GTGGAACAGATTG
* * *
42043773 AAGCTGCAATAGTGAATCTTGTTTCCCCGACATTGC
64 AAGCTACAACAGTGAATCTTGCTTCCCCGACATTGC
* * * * * * * *
42043809 AGTTAAATAGATTGAAGCTATAACAGCGAATCTTATTTCCCTAACGTTGCAGCGGAACAAATTAA
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGC-ATGTAGTGGAACAGATTGA
* * * *
42043874 AGCTA-AAGGTAGCGAGTCTTACTTCCCCGACATTGC
65 AGCTACAA--CAGTGAATCTTGCTTCCCCGACATTGC
* * * * *
42043910 AGTTAAATAGATTGAAGCTACAACAGCAAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGA
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGC-ATGTAGTGGAACAGATTGA
* *
42043975 AGCTACAATAGTGAATCTTGCTTCCCCAACATTGC
65 AGCTACAACAGTGAATCTTGCTTCCCCGACATTGC
* * *
42044010 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTATTTCCTTGGCGATGTAGTGGAACAGATTGA
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGC-ATGTAGTGGAACAGATTGA
* * *
42044075 AGCTATAACAGCGAATCTTGCTTCCCCGATATTGC
65 AGCTACAACAGTGAATCTTGCTTCCCCGACATTGC
*
42044110 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCGGTGTAGTGGAACAGATTGA
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGC-ATGTAGTGGAACAGATTGA
* *
42044175 AGCTACAACAGTGAATCTTGCTTTCCCGACATTAC
65 AGCTACAACAGTGAATCTTGCTTCCCCGACATTGC
* * * *
42044210 AGTTAAATAGGTTAAAGCTGCAACAGCGAATCTTACTTCCCTAGCAGTGTAGTGGAACAGATTAA
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCA-TGTAGTGGAACAGATTGA
*
42044275 AGCTACAACAGTGAATCTTGTTTCCCCGACATTGC
65 AGCTACAACAGTGAATCTTGCTTCCCCGACATTGC
*
42044310 AGTTAAATAGATTGAAGCTATAACAGCGAATCTTA
1 AGTTAAATAGATTGAAGCTACAACAGCGAATCTTA
42044345 TTTCTCTGAC
Statistics
Matches: 469, Mismatches: 61, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
99 2 0.00
100 380 0.81
101 84 0.18
102 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (99 bp):
AGTTAAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTAGCATGTAGTGGAACAGATTGAA
GCTACAACAGTGAATCTTGCTTCCCCGACATTGC
Found at i:42046480 original size:23 final size:22
Alignment explanation
Indices: 42046432--42046481 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
42046422 CACTAATACG
* *
42046432 TTATTATGCTATTATTTTTGTA
1 TTATTATGCTATTATTGTTATA
* *
42046454 TTATTATTGTTATTATTGTTATT
1 TTATTA-TGCTATTATTGTTATA
42046477 TTATT
1 TTATT
42046482 TATTTATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.68
Consensus pattern (22 bp):
TTATTATGCTATTATTGTTATA
Found at i:42046624 original size:27 final size:27
Alignment explanation
Indices: 42046568--42046624 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
42046558 AGATTTAATC
*
42046568 ATATATATACATACATATCTTTGATTT
1 ATATATATACATACATATATTTGATTT
* *
42046595 ATATATATACTTACTTATATTT--TTT
1 ATATATATACATACATATATTTGATTT
42046620 ATATA
1 ATATA
42046625 CTTTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 8 0.30
27 19 0.70
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.53
Consensus pattern (27 bp):
ATATATATACATACATATATTTGATTT
Found at i:42046849 original size:10 final size:10
Alignment explanation
Indices: 42046834--42046862 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
42046824 CAATTTTTAT
42046834 ATACATATAG
1 ATACATATAG
42046844 ATACATATAG
1 ATACATATAG
42046854 ATACATATA
1 ATACATATA
42046863 TATATGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (10 bp):
ATACATATAG
Found at i:42047370 original size:72 final size:72
Alignment explanation
Indices: 42047253--42047395 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 72
42047243 TCTTTTCAAA
* * *
42047253 CTCAAGTTTTAAACGATCTATGGAATTAAGAAGAGATCGTGTCCTAACTTATTGGGCACGATCCC
1 CTCAAGTTTTAAACGATCTACGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCACGATCCC
42047318 TTTTTTT
66 TTTTTTT
*
42047325 CTCAAGTTTTAAACGATCT-CGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
1 CTCAAGTTTTAAACGATCTACG-GAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCACGATCC
42047389 CTTTTTT
65 CTTTTTT
42047396 AAATCCGAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
71 1 0.02
72 65 0.98
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (72 bp):
CTCAAGTTTTAAACGATCTACGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCACGATCCC
TTTTTTT
Found at i:42048961 original size:10 final size:10
Alignment explanation
Indices: 42048946--42049036 Score: 55
Period size: 10 Copynumber: 9.3 Consensus size: 10
42048936 TAAAAACAAC
42048946 TATAAAAAAT
1 TATAAAAAAT
42048956 TAT--AAAAT
1 TATAAAAAAT
* *
42048964 TATTAGAAAT
1 TATAAAAAAT
* ***
42048974 TGTAAGGTAT
1 TATAAAAAAT
42048984 TATAAAAAAAT
1 TAT-AAAAAAT
42048995 TAT-AAAAAT
1 TATAAAAAAT
* *
42049004 TATTAGAAA-
1 TATAAAAAAT
42049013 TAGTAAAAAAT
1 TA-TAAAAAAT
*
42049024 TGTAAAAAAT
1 TATAAAAAAT
42049034 TAT
1 TAT
42049037 TCAAAATTTT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
8 8 0.13
9 11 0.18
10 34 0.56
11 8 0.13
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (10 bp):
TATAAAAAAT
Found at i:42049030 original size:40 final size:38
Alignment explanation
Indices: 42048946--42049062 Score: 135
Period size: 40 Copynumber: 3.0 Consensus size: 38
42048936 TAAAAACAAC
* ***
42048946 TATAAAAAATTATAAAATTATTAGAAATTGTAAGGTAT
1 TATAAAAAATTATAAAATTATTAGAAATAGTAAAAAAT
42048984 TATAAAAAAATTATAAAAATTATTAGAAATAGTAAAAAAT
1 TAT-AAAAAATTAT-AAAATTATTAGAAATAGTAAAAAAT
* * *
42049024 TGTAAAAAATTATTCAAAATTTTTAAAAATAGTAAAAAA
1 TATAAAAAATTA-T-AAAATTATTAGAAATAGTAAAAAA
42049063 AATTGTGGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 3 0.04
39 19 0.28
40 46 0.68
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (38 bp):
TATAAAAAATTATAAAATTATTAGAAATAGTAAAAAAT
Found at i:42049052 original size:10 final size:10
Alignment explanation
Indices: 42048989--42049053 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
42048979 GGTATTATAA
42048989 AAAAATTA-T
1 AAAAATTATT
42048998 AAAAATTATT
1 AAAAATTATT
* *
42049008 AGAAA-TAGTA
1 AAAAATTA-TT
* *
42049018 AAAAATTGTA
1 AAAAATTATT
42049028 AAAAATTATT
1 AAAAATTATT
* *
42049038 CAAAATTTTT
1 AAAAATTATT
42049048 AAAAAT
1 AAAAAT
42049054 AGTAAAAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
9 10 0.23
10 33 0.75
11 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.34
Consensus pattern (10 bp):
AAAAATTATT
Found at i:42057826 original size:9 final size:9
Alignment explanation
Indices: 42057750--42057804 Score: 67
Period size: 9 Copynumber: 6.2 Consensus size: 9
42057740 TTTGGTTAAA
*
42057750 AATTACCCG
1 AATTAACCG
*
42057759 AATTATCCG
1 AATTAACCG
*
42057768 AATTAACTG
1 AATTAACCG
*
42057777 AATTAACCA
1 AATTAACCG
42057786 AATTAACCG
1 AATTAACCG
42057795 AATT-ACCG
1 AATTAACCG
42057803 AA
1 AA
42057805 AAATACCCGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
8 6 0.15
9 34 0.85
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:42057985 original size:13 final size:13
Alignment explanation
Indices: 42057967--42057996 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
42057957 TTTTAGTTTT
42057967 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
42057980 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
42057993 ATTG
1 ATTG
42057997 AGTTTGAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:42058774 original size:40 final size:40
Alignment explanation
Indices: 42058714--42058853 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
42058704 AACACACCAG
* *
42058714 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
* * * *
42058754 TTTGACACCCAGTGTCTCATCGGTTAAACCAAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
** * *
42058792 -TTGGTACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCGGA-TAATCCGAAGTAATAA
* * *
42058832 ATTGACACCCAATGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
42058854 ACTCGAAGCC
Statistics
Matches: 78, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 18 0.23
38 11 0.14
39 1 0.01
40 31 0.40
41 17 0.22
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
Found at i:42058842 original size:41 final size:41
Alignment explanation
Indices: 42058719--42058854 Score: 138
Period size: 41 Copynumber: 3.4 Consensus size: 41
42058709 ACCAGTTTGG
* * * *
42058719 CACCCAGTGCCTCATCGGA-TAATTCGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
* * * *
42058759 CACCCAGTGTCTCATCG-GTTAAACC-AA--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
*
42058796 TACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
* *
42058837 CACCCAATGTCTCATCGA
1 CACCCAGTGCCTCATCGA
42058855 CTCGAAGCCG
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 22 0.29
38 6 0.08
39 4 0.05
40 20 0.26
41 24 0.32
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
Found at i:42059699 original size:4 final size:4
Alignment explanation
Indices: 42059692--42059760 Score: 56
Period size: 4 Copynumber: 17.0 Consensus size: 4
42059682 TTTCTCCTTC
42059692 CTTT CTTT -TCTT -TTT CTTT CTTTT CTTT CTTT C-TT -TTT CTTT CTATTT
1 CTTT CTTT CT-TT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT C--TTT
*
42059740 CGTTT CTAT CTTT CTTT CTTT
1 C-TTT CTTT CTTT CTTT CTTT
42059761 TTATTTTATT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
3 7 0.13
4 36 0.65
5 8 0.15
6 4 0.07
ACGTcount: A:0.03, C:0.22, G:0.01, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:42059740 original size:29 final size:29
Alignment explanation
Indices: 42059692--42059756 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
42059682 TTTCTCCTTC
* * * *
42059692 CTTTC-TTTTCTTTTTCTTTCTTTTCTTT
1 CTTTCTTTTTCTTTCTATTTCGTTTCTAT
42059720 CTTTCTTTTTCTTTCTATTTCGTTTCTAT
1 CTTTCTTTTTCTTTCTATTTCGTTTCTAT
42059749 CTTTCTTT
1 CTTTCTTT
42059757 CTTTTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.74
Consensus pattern (29 bp):
CTTTCTTTTTCTTTCTATTTCGTTTCTAT
Found at i:42059752 original size:33 final size:33
Alignment explanation
Indices: 42059693--42059774 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
42059683 TTCTCCTTCC
* *
42059693 TTTCTTTTCTTTTTCTTTCTTTTCTTTCTTTCTT
1 TTTC-TTTCTATTTCTTTCTTATCTTTCTTTCTT
42059727 TTTCTTTCTATTTCGTTTC-TATCTTTCTTTCTT
1 TTTCTTTCTATTTC-TTTCTTATCTTTCTTTCTT
*
42059760 TTTATTT-TA-TTCTTT
1 TTTCTTTCTATTTCTTT
42059775 ATTTTATCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 3 0.07
31 3 0.07
32 2 0.05
33 28 0.64
34 8 0.18
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.76
Consensus pattern (33 bp):
TTTCTTTCTATTTCTTTCTTATCTTTCTTTCTT
Found at i:42059793 original size:5 final size:5
Alignment explanation
Indices: 42059785--42060043 Score: 459
Period size: 5 Copynumber: 51.8 Consensus size: 5
42059775 ATTTTATCAT
42059785 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
42059835 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
42059885 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
42059935 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* * *
42059985 TATAA TATAA TATAA TATAA TATAA TA-AT TA-AGA TATAA TATTA TAATAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATAA TATAA T-ATAA
42060035 TATAA TATA
1 TATAA TATA
42060044 TATTTTAACT
Statistics
Matches: 245, Mismatches: 6, Indels: 6
0.95 0.02 0.02
Matches are distributed among these distances:
4 4 0.02
5 237 0.97
6 4 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:42061985 original size:38 final size:38
Alignment explanation
Indices: 42061934--42062023 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
42061924 CTCTGTCCAA
*
42061934 CCCTACATACCATGTGGGGATTAAATCAAGCCACCCAT
1 CCCTACACACCATGTGGGGATTAAATCAAGCCACCCAT
42061972 CCCTACACACCATGTGGGGATTAAATCAAGCCACCCAT
1 CCCTACACACCATGTGGGGATTAAATCAAGCCACCCAT
42062010 CCCTACACACCATG
1 CCCTACACACCATG
42062024 CTGTACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.31, C:0.36, G:0.14, T:0.19
Consensus pattern (38 bp):
CCCTACACACCATGTGGGGATTAAATCAAGCCACCCAT
Found at i:42066872 original size:16 final size:15
Alignment explanation
Indices: 42066851--42066912 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 15
42066841 TTCTCCTTCC
42066851 TTTCTTTCCTTTTTCT
1 TTTCTTT-CTTTTTCT
42066867 TTTCTTTCTTTTTCT
1 TTTCTTTCTTTTTCT
*
42066882 TTCTGTTTCGTTTCTATC-
1 TT-TCTTTC-TTT-T-TCT
42066900 TTTCTTTCTTTTT
1 TTTCTTTCTTTTT
42066913 ATTTATTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 1 0.03
15 11 0.28
16 15 0.38
17 8 0.20
18 3 0.08
19 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTCTTTCTTTTTCT
Found at i:42066895 original size:25 final size:26
Alignment explanation
Indices: 42066851--42066902 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
42066841 TTCTCCTTCC
* * *
42066851 TTTCTTTCCTTTTTCTTTTCTTTCTT
1 TTTCTTTCCTGTTTCGTTTCTATCTT
42066877 TTTCTTT-CTGTTTCGTTTCTATCTT
1 TTTCTTTCCTGTTTCGTTTCTATCTT
42066902 T
1 T
42066903 CTTTCTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTCTTTCCTGTTTCGTTTCTATCTT
Found at i:42066942 original size:5 final size:5
Alignment explanation
Indices: 42066934--42066974 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
42066924 ATTTTATCAT
42066934 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
42066975 TTAACTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:42067856 original size:24 final size:24
Alignment explanation
Indices: 42067813--42067861 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
42067803 TTTTGTCTAT
** *
42067813 ATAGTAATAGTGTGAGCTATGATG
1 ATAGTAATAGTGCAAACTATGATG
42067837 ATAGTAATAGTGCAAACTATGATG
1 ATAGTAATAGTGCAAACTATGATG
42067861 A
1 A
42067862 CATAGATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (24 bp):
ATAGTAATAGTGCAAACTATGATG
Found at i:42075332 original size:42 final size:42
Alignment explanation
Indices: 42075285--42075434 Score: 212
Period size: 42 Copynumber: 3.6 Consensus size: 42
42075275 ATAAGTTTTT
*
42075285 GTTTAACCCTTATGGGTTTCTATTCAGCTCTTTTGAGCTTCA
1 GTTTAACCCTTATGGGTTTCTGTTCAGCTCTTTTGAGCTTCA
* *
42075327 GTTTAACCCTTATCGGTTT-TCGTTCAACTCTTTTGAGCTTCA
1 GTTTAACCCTTATGGGTTTCT-GTTCAGCTCTTTTGAGCTTCA
* * **
42075369 ATTTAACCCTTATGGGTTTCCGTTCAGCTCTTACGAGCTTCA
1 GTTTAACCCTTATGGGTTTCTGTTCAGCTCTTTTGAGCTTCA
*
42075411 GTTCAACCCTTATGGGTTTCTGTT
1 GTTTAACCCTTATGGGTTTCTGTT
42075435 TAGCACTTAT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.01
42 93 0.99
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (42 bp):
GTTTAACCCTTATGGGTTTCTGTTCAGCTCTTTTGAGCTTCA
Found at i:42075422 original size:21 final size:21
Alignment explanation
Indices: 42075319--42075422 Score: 59
Period size: 21 Copynumber: 5.0 Consensus size: 21
42075309 CAGCTCTTTT
*
42075319 GAGCTTCAGTTTAACCCTTATC
1 GAGCTTCAGTTCAACCCTTA-C
* * **
42075341 G-GTTTTC-GTTCAACTCTTTT
1 GAG-CTTCAGTTCAACCCTTAC
* * *
42075361 GAGCTTCAATTTAACCCTTAT
1 GAGCTTCAGTTCAACCCTTAC
* * * * *
42075382 GGGTTTCCGTTCAGCTCTTAC
1 GAGCTTCAGTTCAACCCTTAC
42075403 GAGCTTCAGTTCAACCCTTA
1 GAGCTTCAGTTCAACCCTTA
42075423 TGGGTTTCTG
Statistics
Matches: 56, Mismatches: 23, Indels: 7
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.07
21 48 0.86
22 4 0.07
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.39
Consensus pattern (21 bp):
GAGCTTCAGTTCAACCCTTAC
Found at i:42075451 original size:42 final size:42
Alignment explanation
Indices: 42075289--42075460 Score: 193
Period size: 42 Copynumber: 4.1 Consensus size: 42
42075279 GTTTTTGTTT
* * *
42075289 AACCCTTATGGGTTTCTATTCAGCTCTTTTGAGCTTCAGTTT
1 AACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTTCAGTTC
* * * * *
42075331 AACCCTTATCGGTTT-TCGTTCAACTCTTTTGAGCTTCAATTT
1 AACCCTTATGGGTTTCT-GTTCAGCTCTTATGAGCTTCAGTTC
* *
42075373 AACCCTTATGGGTTTCCGTTCAGCTCTTACGAGCTTCAGTTC
1 AACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTTCAGTTC
* * * * *
42075415 AACCCTTATGGGTTTCTGTTTAGCACTTATGTGCTTCTGTGC
1 AACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTTCAGTTC
42075457 AACC
1 AACC
42075461 TTCGGGCTTC
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
41 1 0.01
42 109 0.99
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (42 bp):
AACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTTCAGTTC
Found at i:42075451 original size:84 final size:84
Alignment explanation
Indices: 42075286--42075451 Score: 217
Period size: 84 Copynumber: 2.0 Consensus size: 84
42075276 TAAGTTTTTG
* ** *
42075286 TTTAACCCTTATGGGTTTCTATTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATCGGTTTTCGTT
1 TTTAACCCTTATGGGTTTCCATTCAGCTCTTACGAGCTTCAGTTCAACCCTTATCGGTTTTCGTT
* *
42075351 CAACTCTTTTGAGCTTCAA
66 CAACACTTATGAGCTTCAA
* *
42075370 TTTAACCCTTATGGGTTTCCGTTCAGCTCTTACGAGCTTCAGTTCAACCCTTAT-GGGTTTCTGT
1 TTTAACCCTTATGGGTTTCCATTCAGCTCTTACGAGCTTCAGTTCAACCCTTATCGGTTTTC-GT
* * *
42075434 TTAGCACTTATGTGCTTC
65 TCAACACTTATGAGCTTC
42075452 TGTGCAACCT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
83 6 0.09
84 64 0.91
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.43
Consensus pattern (84 bp):
TTTAACCCTTATGGGTTTCCATTCAGCTCTTACGAGCTTCAGTTCAACCCTTATCGGTTTTCGTT
CAACACTTATGAGCTTCAA
Found at i:42077168 original size:27 final size:26
Alignment explanation
Indices: 42077138--42077223 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
42077128 AGGCTATCCC
42077138 TTCATAATTCGCCACAATGGTTTTTCT
1 TTCATAATTCGCCACAA-GGTTTTTCT
* * ** *
42077165 TTCATGATTCGTCACAAAATATTTCCT
1 TTCATAATTCGCCACAAGGT-TTTTCT
* * *
42077192 TTCATATTTCTCCACAAAGGCTTTTCT
1 TTCATAATTCGCCAC-AAGGTTTTTCT
42077219 TTCAT
1 TTCAT
42077224 GACTCACCAC
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
26 1 0.02
27 41 0.93
28 2 0.05
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.44
Consensus pattern (26 bp):
TTCATAATTCGCCACAAGGTTTTTCT
Found at i:42077249 original size:54 final size:54
Alignment explanation
Indices: 42077138--42077250 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 54
42077128 AGGCTATCCC
* * * ** * *
42077138 TTCATAATTCGCCACAATGGTTTTTCTTTCATGATTCGTCACAAAATATTTCCT
1 TTCATAATTCGCCACAAAGGCTTTTCTTTCATGACTCACCACAAAACATTTCAT
* *
42077192 TTCATATTTCTCCACAAAGGCTTTTCTTTCATGACTCACCACAAAAGCATTT-AT
1 TTCATAATTCGCCACAAAGGCTTTTCTTTCATGACTCACCACAAAA-CATTTCAT
42077246 TTCAT
1 TTCAT
42077251 GACGTGTTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 45 0.92
55 4 0.08
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (54 bp):
TTCATAATTCGCCACAAAGGCTTTTCTTTCATGACTCACCACAAAACATTTCAT
Found at i:42082971 original size:18 final size:20
Alignment explanation
Indices: 42082933--42082971 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42082923 TCTTTTGAAG
*
42082933 TATTAAAAATCATATTTAGA
1 TATTAAAAATAATATTTAGA
42082953 TATTAAAAA-AATA-TTAGA
1 TATTAAAAATAATATTTAGA
42082971 T
1 T
42082972 GTAATGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
TATTAAAAATAATATTTAGA
Found at i:42093404 original size:25 final size:24
Alignment explanation
Indices: 42093368--42093438 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 24
42093358 ACACACCGCA
42093368 GCTCTTATGAGCGT-CCCGTTATATG
1 GCTCTTATGAGC-TACCCGTTAT-TG
*
42093393 GCTCTTCA-GAGCTATCCGTTATTG
1 GCTCTT-ATGAGCTACCCGTTATTG
** * *
42093417 GCTCACATGAGCTTCCTGTTAT
1 GCTCTTATGAGCTACCCGTTAT
42093439 ACAGCCCAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.03
24 18 0.49
25 17 0.46
26 1 0.03
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (24 bp):
GCTCTTATGAGCTACCCGTTATTG
Found at i:42093428 original size:24 final size:24
Alignment explanation
Indices: 42093383--42093439 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
42093373 TATGAGCGTC
*
42093383 CCGTTATATGGCTCTTCAGAGCTAT
1 CCGTTATATGGCTCTACAGAGCT-T
42093408 CCGTTAT-TGGCTC-ACATGAGCTT
1 CCGTTATATGGCTCTACA-GAGCTT
42093431 CCTGTTATA
1 CC-GTTATA
42093440 CAGCCCAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 5 0.18
24 16 0.57
25 7 0.25
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (24 bp):
CCGTTATATGGCTCTACAGAGCTT
Found at i:42093479 original size:25 final size:25
Alignment explanation
Indices: 42093374--42093496 Score: 117
Period size: 25 Copynumber: 5.0 Consensus size: 25
42093364 CGCAGCTCTT
* *
42093374 ATGAGCGTCCCGTTATATGGCTCTTC
1 ATGAGCTTCCCGTTATATGGCTC-AC
42093400 A-GAGCTAT-CCGTTAT-TGGCTCAC
1 ATGAGCT-TCCCGTTATATGGCTCAC
* ** * *
42093423 ATGAGCTTCCTGTTATACAGCCCAG
1 ATGAGCTTCCCGTTATATGGCTCAC
* *
42093448 ATAAGCTTCCCGTTACATGGCTCAC
1 ATGAGCTTCCCGTTATATGGCTCAC
*
42093473 ATGAGCTTCCCGTTATAAGGCTCA
1 ATGAGCTTCCCGTTATATGGCTCA
42093497 AGAGAGGGCT
Statistics
Matches: 76, Mismatches: 17, Indels: 9
0.75 0.17 0.09
Matches are distributed among these distances:
23 3 0.04
24 17 0.22
25 54 0.71
26 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGCTCAC
Found at i:42096146 original size:19 final size:19
Alignment explanation
Indices: 42096122--42096158 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
42096112 TTCTCCCGAA
42096122 ATTTTCCCCAAAACTTTTT
1 ATTTTCCCCAAAACTTTTT
42096141 ATTTTCCCCAAAACTTTT
1 ATTTTCCCCAAAACTTTT
42096159 ACTCCTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTCCCCAAAACTTTTT
Found at i:42106095 original size:27 final size:26
Alignment explanation
Indices: 42106037--42106102 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
42106027 CTCAAATTGA
*
42106037 TATAAAATGATTGTTATCCCCCACGT
1 TATAAAATGACTGTTATCCCCCACGT
** * *
42106063 GGTAAAATGACTGTTATGCCCCTATGT
1 TATAAAATGACTGTTAT-CCCCCACGT
*
42106090 TATAAAATAACTG
1 TATAAAATGACTG
42106103 CATGCTCTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
26 14 0.45
27 17 0.55
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (26 bp):
TATAAAATGACTGTTATCCCCCACGT
Found at i:42107906 original size:79 final size:81
Alignment explanation
Indices: 42107770--42107954 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
42107760 TTGAATGATG
*
42107770 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
42107834 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
42107849 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
42107911 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
42107929 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42107955 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:42107968 original size:40 final size:40
Alignment explanation
Indices: 42107771--42107954 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
42107761 TGAATGATGT
* * * *
42107771 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
42107811 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
42107851 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42107889 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42107930 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
42107955 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:42107976 original size:79 final size:79
Alignment explanation
Indices: 42107823--42107987 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
42107813 GGACTAAGAT
* **
42107823 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
42107888 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
42107902 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
42107965 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
42107981 CCGAAGG
1 CCGAAGG
42107988 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:42111456 original size:31 final size:31
Alignment explanation
Indices: 42111388--42111460 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
42111378 TGTGGGCCAT
* * * *
42111388 ACGGGCATGTGGGCCCACATAAGCAAGTCGT
1 ACGGGCGTGTGAGCCCACACAAGCAAGTCGC
* * *
42111419 ATGGGCGTGTGAGCCTACACAAGCATGTCGC
1 ACGGGCGTGTGAGCCCACACAAGCAAGTCGC
42111450 ACGGGCGTGTG
1 ACGGGCGTGTG
42111461 GGTCGTACGC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.22, C:0.25, G:0.36, T:0.18
Consensus pattern (31 bp):
ACGGGCGTGTGAGCCCACACAAGCAAGTCGC
Found at i:42114317 original size:7 final size:7
Alignment explanation
Indices: 42114307--42114331 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42114297 GAGAGATGAG
42114307 AGAATAA
1 AGAATAA
42114314 AGAATAA
1 AGAATAA
42114321 AGAATAA
1 AGAATAA
42114328 AGAA
1 AGAA
42114332 AATATGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (7 bp):
AGAATAA
Found at i:42115479 original size:41 final size:39
Alignment explanation
Indices: 42115391--42115471 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
42115381 AACTTGAGAG
42115391 ATTTGTGGTGTATAGGAGACAATTAAAACATATGAGCTA
1 ATTTGTGGTGTATAGGAGACAATTAAAACATATGAGCTA
* *
42115430 ATTTGTGGTGTGTAGGAGACAATTAAAGCATATGAGCTA
1 ATTTGTGGTGTATAGGAGACAATTAAAACATATGAGCTA
42115469 ATT
1 ATT
42115472 AGTGTGGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (39 bp):
ATTTGTGGTGTATAGGAGACAATTAAAACATATGAGCTA
Found at i:42117305 original size:41 final size:40
Alignment explanation
Indices: 42117260--42117361 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 40
42117250 TGATTCAGTA
42117260 CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCA-TTAGCCTGCTAGACATATAGTCTGAAATATTT
* * * *
42117301 CACCGGCATTAAGCCTGCTAGACATTTTGTCTGAAGTGTTT
1 CACCGGCATT-AGCCTGCTAGACATATAGTCTGAAATATTT
*
42117342 CACCGGCAATAAGCCTGCTA
1 CACCGGC-ATTAGCCTGCTA
42117362 AGCTCTAAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.04
41 50 0.93
42 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (40 bp):
CACCGGCATTAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:42121531 original size:92 final size:92
Alignment explanation
Indices: 42121374--42121553 Score: 306
Period size: 92 Copynumber: 2.0 Consensus size: 92
42121364 CAACTGTTTA
* * * *
42121374 TCTCGCAAAGTTTGTAACACAAGTCTCAGATGTTCAGCATGCTCATTTTCGTCTCGAGAGTAGAT
1 TCTCGCAAAGTTTGTAACACAAGTCTCAGATGATCAGCATGCTCAGTTTCATCACGAGAGTAGAT
*
42121439 CAAAATGTCATCAATAAATACTATTTT
66 CAAAATATCATCAATAAATACTATTTT
42121466 TCTCGCAAAGTTTGTAACACAAGTCTCAGATGATCAGCATGCTCAGTTTCATCACGAGAGTAGAT
1 TCTCGCAAAGTTTGTAACACAAGTCTCAGATGATCAGCATGCTCAGTTTCATCACGAGAGTAGAT
*
42121531 CAAAATATCATCTATAAATACTA
66 CAAAATATCATCAATAAATACTA
42121554 CCACAAACCG
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 82 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (92 bp):
TCTCGCAAAGTTTGTAACACAAGTCTCAGATGATCAGCATGCTCAGTTTCATCACGAGAGTAGAT
CAAAATATCATCAATAAATACTATTTT
Found at i:42126874 original size:41 final size:40
Alignment explanation
Indices: 42126829--42126930 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 40
42126819 TGATTCAGTA
42126829 CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCA-TTAGCCTGCTAGACATATAGTCTGAAATATTT
* * * *
42126870 CACCGGCATTAAGCCTGCTAGACATTTTGTCTGAAGTGTTT
1 CACCGGCATT-AGCCTGCTAGACATATAGTCTGAAATATTT
*
42126911 CACCGGCAATAAGCCTGCTA
1 CACCGGC-ATTAGCCTGCTA
42126931 AGCTCTAAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.04
41 50 0.93
42 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (40 bp):
CACCGGCATTAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:42131684 original size:38 final size:37
Alignment explanation
Indices: 42131575--42131684 Score: 114
Period size: 38 Copynumber: 2.9 Consensus size: 37
42131565 TAGTGTCTAG
* * *
42131575 CAGGCTTAGTGCTTAGTAGGCTTAGTATCGATGTTAAT
1 CAGGCTTAGTGCTTAGCAGGCTTA-TGTCGGTGTTAAT
* *
42131613 CAAGCTTAGTGCTTAGCAGGCTTA-GTGCTGGTGTTATT
1 CAGGCTTAGTGCTTAGCAGGCTTATGT-C-GGTGTTAAT
* *
42131651 CAGGCTTAGTGCGTAGCAAGCTTGATGTCGGTGT
1 CAGGCTTAGTGCTTAGCAGGCTT-ATGTCGGTGT
42131685 AGTAAATGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
36 1 0.02
37 1 0.02
38 54 0.90
39 2 0.03
40 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (37 bp):
CAGGCTTAGTGCTTAGCAGGCTTATGTCGGTGTTAAT
Done.