Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 136 of 153
Found at i:42796890 original size:120 final size:119
Alignment explanation
Indices: 42796668--42796930 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
42796658 TCCTCGTTCA
* * *
42796668 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
42796733 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
42796786 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
42796851 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
42796907 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
42796931 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:42796939 original size:41 final size:41
Alignment explanation
Indices: 42796862--42796939 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42796852 TTTGTATCTC
* * *
42796862 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42796903 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42796940 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42804662 original size:39 final size:40
Alignment explanation
Indices: 42804617--42804788 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
42804607 GCTCCTCGTT
* * *
42804617 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
42804657 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
42804696 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
42804736 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
42804776 CAAATGCCTTCGG
1 CAAATGCCTTCGG
42804789 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:42804717 original size:40 final size:39
Alignment explanation
Indices: 42804619--42804841 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
42804609 TCCTCGTTCA
* * * *
42804619 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
42804658 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
42804697 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
42804737 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
42804777 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
42804818 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42804842 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:42804801 original size:80 final size:79
Alignment explanation
Indices: 42804617--42804841 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
42804607 GCTCCTCGTT
* * * * *
42804617 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
42804681 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
42804696 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
42804761 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
42804776 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
42804840 GA
63 GA
42804842 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:42804850 original size:41 final size:41
Alignment explanation
Indices: 42804773--42804850 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42804763 TTTGTATCTC
* * *
42804773 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42804814 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42804851 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42812268 original size:14 final size:14
Alignment explanation
Indices: 42812251--42812282 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
42812241 GAGAAAAATA
42812251 TAATAAAATAACTC
1 TAATAAAATAACTC
*
42812265 TAATAAACTAACTC
1 TAATAAAATAACTC
42812279 TAAT
1 TAAT
42812283 TTCACTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATAAAATAACTC
Found at i:42812405 original size:17 final size:16
Alignment explanation
Indices: 42812383--42812417 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
42812373 TTTTATTTAC
42812383 AACTAAAAGTAAAATGT
1 AACTAAAAGTAAAA-GT
*
42812400 AACTAAAATTAAAAGT
1 AACTAAAAGTAAAAGT
42812416 AA
1 AA
42812418 AAATAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.23
Consensus pattern (16 bp):
AACTAAAAGTAAAAGT
Found at i:42824220 original size:50 final size:50
Alignment explanation
Indices: 42824143--42824287 Score: 146
Period size: 50 Copynumber: 2.9 Consensus size: 50
42824133 TTCTTGTACT
* * * ** *
42824143 GCCAATGCCATATCCTAGATATGGTCTTACATGAGAGTTCTCATATCGGC
1 GCCAACGCCATGTCCTAGACATGGTCTTACATGAGACCTCCCATATCGGC
* * ** * * *
42824193 GCCCACGCCATGTCTTAGACATGGTCTTACGGGGGACCTCCCATCTCGGT
1 GCCAACGCCATGTCCTAGACATGGTCTTACATGAGACCTCCCATATCGGC
* * *
42824243 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 GCCAACGCCATGTCCTAGACATGGTCTTACATGAGACCTCCCATA
42824288 ATCTCAATAA
Statistics
Matches: 75, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
GCCAACGCCATGTCCTAGACATGGTCTTACATGAGACCTCCCATATCGGC
Found at i:42833082 original size:26 final size:26
Alignment explanation
Indices: 42833010--42833068 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
42833000 TCTCATCCCA
* *
42833010 ATTTTACTCCCAATAAAATTTAGATG
1 ATTTTACTCCCGATAAAATTTAGACG
*
42833036 ATTTTACTCCCGATAAAATTTTGACG
1 ATTTTACTCCCGATAAAATTTAGACG
42833062 ATTTTAC
1 ATTTTAC
42833069 CCTTGGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (26 bp):
ATTTTACTCCCGATAAAATTTAGACG
Found at i:42833251 original size:6 final size:6
Alignment explanation
Indices: 42833237--42833271 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
42833227 GAATCATTGT
*
42833237 CATTGC CATTTC CATTTC CATTTC CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
42833272 TTGGAAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.31, G:0.03, T:0.49
Consensus pattern (6 bp):
CATTTC
Found at i:42836495 original size:25 final size:25
Alignment explanation
Indices: 42836467--42836516 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42836457 TGGGTGGATT
42836467 AGTTATTGATTAACCAATTATTACC
1 AGTTATTGATTAACCAATTATTACC
42836492 AGTTATTGATTAACCAATTATTACC
1 AGTTATTGATTAACCAATTATTACC
42836517 TTACTTAACT
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (25 bp):
AGTTATTGATTAACCAATTATTACC
Found at i:42836507 original size:15 final size:15
Alignment explanation
Indices: 42836467--42836513 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
42836457 TGGGTGGATT
42836467 AGTTATTGATTAACC
1 AGTTATTGATTAACC
42836482 A---ATT-ATT-ACC
1 AGTTATTGATTAACC
42836492 AGTTATTGATTAACC
1 AGTTATTGATTAACC
*
42836507 AATTATT
1 AGTTATT
42836514 ACCTTACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
10 4 0.15
11 3 0.12
12 3 0.12
13 3 0.12
14 3 0.12
15 10 0.38
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (15 bp):
AGTTATTGATTAACC
Found at i:42838109 original size:50 final size:50
Alignment explanation
Indices: 42837996--42838109 Score: 165
Period size: 50 Copynumber: 2.3 Consensus size: 50
42837986 CCTAGATATT
** * *
42837996 GTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATG
1 GTCTTACATGGGACCTCTCATATCGGTACCAATGCCATGTCCCAGACATG
** *
42838046 GTCTTACGGGGGACCTCTCATCTCGGTACCAATGCCATGTCCCAGACATG
1 GTCTTACATGGGACCTCTCATATCGGTACCAATGCCATGTCCCAGACATG
42838096 GTCTTACATGGGAC
1 GTCTTACATGGGAC
42838110 TAGACCTCTC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (50 bp):
GTCTTACATGGGACCTCTCATATCGGTACCAATGCCATGTCCCAGACATG
Found at i:42838545 original size:30 final size:30
Alignment explanation
Indices: 42838511--42838568 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
42838501 TCATTGACTC
42838511 AAAC-TTTGACATAATTACAATTTTGCCCCT
1 AAACTTTTG-CATAATTACAATTTTGCCCCT
* *
42838541 AAACTTTTGCATATTTACACTTTTGCCC
1 AAACTTTTGCATAATTACAATTTTGCCC
42838569 GAAAGCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (30 bp):
AAACTTTTGCATAATTACAATTTTGCCCCT
Found at i:42844084 original size:33 final size:33
Alignment explanation
Indices: 42844042--42844162 Score: 125
Period size: 33 Copynumber: 3.7 Consensus size: 33
42844032 ATGCTCACCT
* * *
42844042 AAGCCAATCCCTCCAACACACTAATGCTCATAA
1 AAGCTAATCCATCCAACACACCAATGCTCATAA
* * *
42844075 AAGCTAATCCAACCATCACACCAATGCTTATAA
1 AAGCTAATCCATCCAACACACCAATGCTCATAA
* * *
42844108 GAGCTAATCCATCCATCACACCAATGCTCAGAA
1 AAGCTAATCCATCCAACACACCAATGCTCATAA
* * * *
42844141 GAGCTAAACCAACCAGCACACC
1 AAGCTAATCCATCCAACACACC
42844163 GAATAGAGAG
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.40, C:0.35, G:0.09, T:0.17
Consensus pattern (33 bp):
AAGCTAATCCATCCAACACACCAATGCTCATAA
Found at i:42851098 original size:118 final size:118
Alignment explanation
Indices: 42850924--42851154 Score: 444
Period size: 118 Copynumber: 2.0 Consensus size: 118
42850914 TGATTGATGA
*
42850924 GAAATTGTGTTGAATGAAGAATATTATCTATGGTTGTGACATATATGCAAACTATGATTCATGTT
1 GAAATTATGTTGAATGAAGAATATTATCTATGGTTGTGACATATATGCAAACTATGATTCATGTT
42850989 GGCATATCTTGAAACTTAGAATAAAATTTTCAAAATGTTTGTATATGAAATAG
66 GGCATATCTTGAAACTTAGAATAAAATTTTCAAAATGTTTGTATATGAAATAG
*
42851042 GAAATTATGTTGAATGAAGAATGTTATCTATGGTTGTGACATATATGCAAACTATGATTCATGTT
1 GAAATTATGTTGAATGAAGAATATTATCTATGGTTGTGACATATATGCAAACTATGATTCATGTT
42851107 GGCATATCTTGAAACTTAGAATAAAATTTTCAAAATGTTTGTATATGA
66 GGCATATCTTGAAACTTAGAATAAAATTTTCAAAATGTTTGTATATGA
42851155 GTTACTTGTT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 111 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (118 bp):
GAAATTATGTTGAATGAAGAATATTATCTATGGTTGTGACATATATGCAAACTATGATTCATGTT
GGCATATCTTGAAACTTAGAATAAAATTTTCAAAATGTTTGTATATGAAATAG
Found at i:42858226 original size:35 final size:35
Alignment explanation
Indices: 42858178--42858316 Score: 197
Period size: 35 Copynumber: 4.0 Consensus size: 35
42858168 TACACGGTTA
*
42858178 ACCATCCAACACACCACATGCTCATAAGAGCCAGT
1 ACCATCCAACACACCAAATGCTCATAAGAGCCAGT
* *
42858213 ACCATCTAGCACACCAAATGCTCATAAGAGCCAGT
1 ACCATCCAACACACCAAATGCTCATAAGAGCCAGT
* * * * *
42858248 ACCATCCAGCATACTAGATGCTCATAAGAGCCAAT
1 ACCATCCAACACACCAAATGCTCATAAGAGCCAGT
*
42858283 ACCATTCAACACACCAAATGCTCATAAGAGCCAG
1 ACCATCCAACACACCAAATGCTCATAAGAGCCAG
42858317 ACCTACCGAT
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 90 1.00
ACGTcount: A:0.38, C:0.32, G:0.13, T:0.17
Consensus pattern (35 bp):
ACCATCCAACACACCAAATGCTCATAAGAGCCAGT
Found at i:42864543 original size:26 final size:26
Alignment explanation
Indices: 42864463--42864543 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
42864453 GATGGTCACG
42864463 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
42864489 CGTGTA-T-CGGATAGTG-ATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
42864514 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
42864540 TGTG
1 TGTG
42864544 AACCGATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:42864619 original size:46 final size:44
Alignment explanation
Indices: 42864548--42864637 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 44
42864538 TATGTGAACC
*
42864548 GATATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCCACCG
1 GATATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CCACCG
* *
42864592 GATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCCACCG
1 GATATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCCACCG
42864638 TGTATCTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 13 0.32
45 2 0.05
46 23 0.57
47 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (44 bp):
GATATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCCACCG
Found at i:42864788 original size:16 final size:16
Alignment explanation
Indices: 42864767--42864798 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42864757 TGATTGAAAG
*
42864767 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
42864783 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
42864799 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:42868483 original size:6 final size:6
Alignment explanation
Indices: 42868474--42868520 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
42868464 TGTAATTAAT
42868474 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
42868521 TAGACACCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (6 bp):
CATTTC
Found at i:42871355 original size:7 final size:7
Alignment explanation
Indices: 42871343--42871386 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
42871333 ACAAATATGA
42871343 TTTATTT
1 TTTATTT
42871350 TTTATTT
1 TTTATTT
42871357 TTTATTT
1 TTTATTT
42871364 TTTATTT
1 TTTATTT
42871371 TTTATTT
1 TTTATTT
*
42871378 TTCATTT
1 TTTATTT
42871385 TT
1 TT
42871387 GCCATCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTATTT
Found at i:42873165 original size:21 final size:21
Alignment explanation
Indices: 42873141--42873183 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
42873131 TTCGATTGAT
* *
42873141 TAGTGTTTGGTTGGCTAGAAA
1 TAGTATTTAGTTGGCTAGAAA
42873162 TAGTATTTAGTTGGCTAGAAA
1 TAGTATTTAGTTGGCTAGAAA
42873183 T
1 T
42873184 GGACTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.40
Consensus pattern (21 bp):
TAGTATTTAGTTGGCTAGAAA
Found at i:42875438 original size:23 final size:24
Alignment explanation
Indices: 42875412--42875464 Score: 99
Period size: 23 Copynumber: 2.2 Consensus size: 24
42875402 AATTTCTATC
42875412 AATATAAAAATTAAATATATTA-T
1 AATATAAAAATTAAATATATTATT
42875435 AATATAAAAATTAAATATATTATT
1 AATATAAAAATTAAATATATTATT
42875459 AATATA
1 AATATA
42875465 TTTAATTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATAAAAATTAAATATATTATT
Found at i:42875942 original size:15 final size:15
Alignment explanation
Indices: 42875906--42875943 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
42875896 ATTAAATTTG
42875906 ATCAAAATAAAAATA
1 ATCAAAATAAAAATA
*
42875921 ATAAAAATAAATAA-A
1 ATCAAAATAAA-AATA
42875936 ATCAAAAT
1 ATCAAAAT
42875944 TGTGGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (15 bp):
ATCAAAATAAAAATA
Found at i:42883870 original size:21 final size:21
Alignment explanation
Indices: 42883844--42883887 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
42883834 TCCAGTCTTT
42883844 TTCCAAGAAACCCATCATATA
1 TTCCAAGAAACCCATCATATA
** *
42883865 TTCCAAGATTCCCATGATATA
1 TTCCAAGAAACCCATCATATA
42883886 TT
1 TT
42883888 TTTTGAACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (21 bp):
TTCCAAGAAACCCATCATATA
Found at i:42884211 original size:15 final size:15
Alignment explanation
Indices: 42884188--42884232 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
42884178 ACAAGACTCT
*
42884188 AAACCCTAAATTTAA
1 AAACTCTAAATTTAA
*
42884203 AAACTCT-AATTTAT
1 AAACTCTAAATTTAA
42884217 AAACTCTAAACTTTAA
1 AAACTCTAAA-TTTAA
42884233 TCCTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 13 0.52
15 8 0.32
16 4 0.16
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (15 bp):
AAACTCTAAATTTAA
Found at i:42884281 original size:21 final size:21
Alignment explanation
Indices: 42884230--42884282 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
42884220 CTCTAAACTT
*
42884230 TAATCCTAAAAAACAAAACCT
1 TAATCCTAAAAAACAAAACCC
* ** **
42884251 TACTTTTAAAAATTAAAACCC
1 TAATCCTAAAAAACAAAACCC
42884272 TAATCCTAAAA
1 TAATCCTAAAA
42884283 GGGAAACGCT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (21 bp):
TAATCCTAAAAAACAAAACCC
Found at i:42885455 original size:48 final size:51
Alignment explanation
Indices: 42885403--42885504 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 51
42885393 TTTTATAAAT
*
42885403 AAAAAAAAT-TATTCATTAA-A-AAGT-TGTAA-TAAAAATAAAAAAAACTTG
1 AAAAAAAATATATTCATTAATATAAATAT-TAATTAAAAAT-AAAAAAACTTG
*
42885451 -AAAAAAATATATTTATTAATTATAAATATTAATTAAAAATAAAAAAACTTG
1 AAAAAAAATATATTCATTAA-TATAAATATTAATTAAAAATAAAAAAACTTG
42885502 AAA
1 AAA
42885505 CAACATGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
47 8 0.18
48 9 0.20
50 1 0.02
51 17 0.38
52 10 0.22
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (51 bp):
AAAAAAAATATATTCATTAATATAAATATTAATTAAAAATAAAAAAACTTG
Found at i:42885703 original size:26 final size:26
Alignment explanation
Indices: 42885674--42885724 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
42885664 TAAAAAATAC
* * *
42885674 AAATGTGAGTAGGAAAAGAATCAAAG
1 AAATGTAAGTAGAAAAAAAATCAAAG
42885700 AAATGTAAGTAGAAAAAAAATCAAA
1 AAATGTAAGTAGAAAAAAAATCAAA
42885725 CCTCAGACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.61, C:0.04, G:0.20, T:0.16
Consensus pattern (26 bp):
AAATGTAAGTAGAAAAAAAATCAAAG
Found at i:42892846 original size:13 final size:13
Alignment explanation
Indices: 42892828--42892853 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42892818 TAAGTAAAAC
42892828 TATTATATTATTA
1 TATTATATTATTA
42892841 TATTATATTATTA
1 TATTATATTATTA
42892854 GAAAAAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:42893586 original size:21 final size:20
Alignment explanation
Indices: 42893562--42893623 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
42893552 GGCTTTGCCG
42893562 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCAC-TTATGTGTCGT
**
42893583 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCA-CTTATGTGTCGT
*
42893604 TTCAGGCACTTATGTGTCGT
1 ATCAGGCACTTATGTGTCGT
42893624 TTACTGATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 10 0.29
21 24 0.69
22 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (20 bp):
ATCAGGCACTTATGTGTCGT
Found at i:42897902 original size:35 final size:37
Alignment explanation
Indices: 42897863--42897939 Score: 104
Period size: 35 Copynumber: 2.1 Consensus size: 37
42897853 TGTGATGATG
**
42897863 ATATATAGGTCCTTCAGGGCGTTACCA-TTAAA-AAT
1 ATATATAGGTCCTTCAGGGCGACACCATTTAAACAAT
* *
42897898 ATATATAGGTCTTTTAGGGCGACACCATTTAAACAAT
1 ATATATAGGTCCTTCAGGGCGACACCATTTAAACAAT
42897935 ATATA
1 ATATA
42897940 GATTCTTTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 23 0.64
36 5 0.14
37 8 0.22
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (37 bp):
ATATATAGGTCCTTCAGGGCGACACCATTTAAACAAT
Found at i:42906357 original size:12 final size:12
Alignment explanation
Indices: 42906340--42906364 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42906330 ATCTTTACTA
42906340 TACTTCATACAC
1 TACTTCATACAC
42906352 TACTTCATACAC
1 TACTTCATACAC
42906364 T
1 T
42906365 TACCCGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (12 bp):
TACTTCATACAC
Found at i:42909417 original size:51 final size:51
Alignment explanation
Indices: 42909245--42909532 Score: 268
Period size: 50 Copynumber: 5.8 Consensus size: 51
42909235 CTTTTATCAT
* * * **
42909245 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGAGCAAGTTTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAACATTTA
* * * **
42909296 -CGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAACATTTA
* * * *
42909346 -CGGTTCACGTAGTAGCCTTCACTTAGAACTACACATGTGACCATCATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAACATTTA
* * * *
42909396 TCGATTCACGTAGTAGCCTTCACAGAGTACCACACATGTGACCAA-AGCTTC
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAACA-TTTA
* * * * * *
42909447 TCGGTACACATTGTAGCCTTCAC-T--TAGT--ACATGTGACCATCATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAACATTTA
* * *
42909493 TCGATTCACATGGTAGCCTTCACACAGTACTACACATGTG
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACATGTG
42909533 TTCATCGATA
Statistics
Matches: 196, Mismatches: 33, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
46 33 0.17
47 1 0.01
48 2 0.01
49 3 0.02
50 91 0.46
51 66 0.34
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (51 bp):
TCGATTCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAACATTTA
Found at i:42909503 original size:46 final size:47
Alignment explanation
Indices: 42909349--42909516 Score: 133
Period size: 51 Copynumber: 3.4 Consensus size: 47
42909339 AGTTTTACGG
* *
42909349 TTCACGTAGTAGCCTTCACTTAGAACTACACATGTGACCATCATTTATCGA
1 TTCACATAGTAGCCTTCAC--AG-AGT-CACATGTGACCATCATTTATCGA
* * * * *
42909400 TTCACGTAGTAGCCTTCACAGAGTACCACACATGTGACCA-AAGCTTCTCGG
1 TTCACATAGTAGCCTTCACAGAGT----CACATGTGACCATCA-TTTATCGA
* * **
42909451 TACACATTGTAGCCTTCACTTAGT-ACATGTGACCATCATTTATCGA
1 TTCACATAGTAGCCTTCACAGAGTCACATGTGACCATCATTTATCGA
*
42909497 TTCACATGGTAGCCTTCACA
1 TTCACATAGTAGCCTTCACA
42909517 CAGTACTACA
Statistics
Matches: 95, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
46 33 0.35
47 1 0.01
48 2 0.02
49 2 0.02
50 1 0.01
51 56 0.59
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (47 bp):
TTCACATAGTAGCCTTCACAGAGTCACATGTGACCATCATTTATCGA
Found at i:42909509 original size:97 final size:98
Alignment explanation
Indices: 42909299--42909532 Score: 294
Period size: 97 Copynumber: 2.4 Consensus size: 98
42909289 AGTTTTACGG
* * * * * * *
42909299 TTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTAGCCT
1 TTCACATAGTAGCCTTCACACAGTACTACACATGTGACCAAGTTCTACGGTACACATAGTAGCCT
42909364 TCACTTAGAACTACACATGTGACCATCATTTATCGA
66 TCACTTAG-A-TA-ACATGTGACCATCATTTATCGA
* * * *
42909400 TTCACGTAGTAGCCTTCACAGAGTACCACACATGTGACCAAAGCTTCT-CGGTACACATTGTAGC
1 TTCACATAGTAGCCTTCACACAGTACTACACATGTGACC-AAG-TTCTACGGTACACATAGTAGC
42909464 CTTCACTTAG-T-ACATGTGACCATCATTTATCGA
64 CTTCACTTAGATAACATGTGACCATCATTTATCGA
*
42909497 TTCACATGGTAGCCTTCACACAGTACTACACATGTG
1 TTCACATAGTAGCCTTCACACAGTACTACACATGTG
42909533 TTCATCGATA
Statistics
Matches: 119, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
97 54 0.45
99 1 0.01
101 35 0.29
102 26 0.22
103 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (98 bp):
TTCACATAGTAGCCTTCACACAGTACTACACATGTGACCAAGTTCTACGGTACACATAGTAGCCT
TCACTTAGATAACATGTGACCATCATTTATCGA
Found at i:42909522 original size:46 final size:46
Alignment explanation
Indices: 42909378--42909522 Score: 130
Period size: 46 Copynumber: 3.0 Consensus size: 46
42909368 TTAGAACTAC
* *
42909378 ACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACAGAGT
1 ACATGTGACCATCATTTATCGATTCACATAGTAGCCTTCACACAGT
* * * * * * **
42909424 ACCACACATGTGACCA-AAGCTTCTCGGTACACATTGTAGCCTTCACTTAGT
1 -----ACATGTGACCATCA-TTTATCGATTCACATAGTAGCCTTCACACAGT
*
42909475 ACATGTGACCATCATTTATCGATTCACATGGTAGCCTTCACACAGT
1 ACATGTGACCATCATTTATCGATTCACATAGTAGCCTTCACACAGT
42909521 AC
1 AC
42909523 TACACATGTG
Statistics
Matches: 75, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
46 38 0.51
47 1 0.01
50 1 0.01
51 35 0.47
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (46 bp):
ACATGTGACCATCATTTATCGATTCACATAGTAGCCTTCACACAGT
Found at i:42912848 original size:27 final size:27
Alignment explanation
Indices: 42912794--42912861 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
42912784 AATATAATAT
*
42912794 AATTATAAAATAATTAAATTGTACTTA
1 AATTATAAAATAATTAAATTGTAATTA
* *
42912821 AATTATTAAAAT-ATTTAATTTTAATT-
1 AATTA-TAAAATAATTAAATTGTAATTA
*
42912847 AATTTTATAAATAAT
1 AATTATA-AAATAAT
42912862 ATTAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 2 0.06
26 8 0.24
27 18 0.53
28 6 0.18
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
AATTATAAAATAATTAAATTGTAATTA
Found at i:42916214 original size:47 final size:47
Alignment explanation
Indices: 42916099--42916218 Score: 125
Period size: 47 Copynumber: 2.6 Consensus size: 47
42916089 TATTTAATAA
* * * *
42916099 TCTATAAATTTGGTGGTTTATCCACAACTATATGCATTGGCAGCTTG
1 TCTATAAATTTGGTGGATTGTCCACAACTATATGAATTGGAAGCTTG
** * * *
42916146 TCT-GGAATTTCGATGGATTGTCTACAACTATGTGAATTGGAAGCTTG
1 TCTATAAATTT-GGTGGATTGTCCACAACTATATGAATTGGAAGCTTG
* *
42916193 TTTATAAATTTGGTGGCTTGTCCACA
1 TCTATAAATTTGGTGGATTGTCCACA
42916219 TATGTGCTGG
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
46 5 0.09
47 46 0.82
48 5 0.09
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (47 bp):
TCTATAAATTTGGTGGATTGTCCACAACTATATGAATTGGAAGCTTG
Found at i:42919146 original size:51 final size:50
Alignment explanation
Indices: 42919069--42919265 Score: 196
Period size: 51 Copynumber: 3.9 Consensus size: 50
42919059 CTATAAACAA
* *
42919069 GTGTGTAGTACTAAGTGCAGGCTACTACTTGTATCGATAGATAATGGTCAC
1 GTGTGTAGTACTACGTGCAGGCTACTACGTGTATCGA-AGATAATGGTCAC
* * * * * **
42919120 ATGTGTAGTACTACGTGCAGGATACTATGTGTACCGGAAGGTTTTGGTCAC
1 GTGTGTAGTACTACGTGCAGGCTACTACGTGTATC-GAAGATAATGGTCAC
* * * * ** * *
42919171 GTGTGTAGTACTATGTGCAAGCTACTACGTGCATCGAAAATTTTGATAAC
1 GTGTGTAGTACTACGTGCAGGCTACTACGTGTATCGAAGATAATGGTCAC
* *
42919221 GTGTGTAGTACTACGTGAAGGCTACTACGTGTGTCGAATGATAAT
1 GTGTGTAGTACTACGTGCAGGCTACTACGTGTATCGAA-GATAAT
42919266 AATTACACGG
Statistics
Matches: 116, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
50 44 0.38
51 70 0.60
52 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (50 bp):
GTGTGTAGTACTACGTGCAGGCTACTACGTGTATCGAAGATAATGGTCAC
Found at i:42923950 original size:27 final size:27
Alignment explanation
Indices: 42923920--42924206 Score: 237
Period size: 27 Copynumber: 10.7 Consensus size: 27
42923910 AATCGAAATG
* *
42923920 CCCCTATAAGGTAAAATGACCATAATA
1 CCCCTATAGGGTAAAATGACCGTAATA
* * *
42923947 CCCCTGTAGGGTAAAATGACTG-AAAA
1 CCCCTATAGGGTAAAATGACCGTAATA
* *
42923973 ACCCTCATAGGGTAAAATGACTC-TAATG
1 CCCCT-ATAGGGTAAAATGAC-CGTAATA
* *
42924001 CCCCTGTAGGGTAAAATGACCGTAATG
1 CCCCTATAGGGTAAAATGACCGTAATA
* **
42924028 CCCCTGTAATGTAAAATGACCGTAATA
1 CCCCTATAGGGTAAAATGACCGTAATA
* ** *
42924055 CCCCTGTAGGGTAAAATGA-TTTAAAAA
1 CCCCTATAGGGTAAAATGACCGT-AATA
* * *
42924082 CCCCCTATAGGGTAAAATGACTGTTATG
1 -CCCCTATAGGGTAAAATGACCGTAATA
* *
42924110 CCCTTATAGGGTAAAATAACCGTAATA
1 CCCCTATAGGGTAAAATGACCGTAATA
* * * *
42924137 CCCC-ATAGGATTAGATGACCGAAATA
1 CCCCTATAGGGTAAAATGACCGTAATA
*
42924163 CCCCT-TAAGGTAAAATGACCGTAAT-
1 CCCCTATAGGGTAAAATGACCGTAATA
* *
42924188 GCCCTAGAGGGT-AAATGAC
1 CCCCTATAGGGTAAAATGAC
42924207 TATTTCGCCC
Statistics
Matches: 207, Mismatches: 44, Indels: 20
0.76 0.16 0.07
Matches are distributed among these distances:
25 11 0.05
26 49 0.24
27 120 0.58
28 25 0.12
29 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (27 bp):
CCCCTATAGGGTAAAATGACCGTAATA
Found at i:42924297 original size:24 final size:24
Alignment explanation
Indices: 42924225--42924306 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
42924215 CCCTCAAGTG
* * *
42924225 TAAATGATTGATTTGTCCGTAATG
1 TAAATGACTGATTTGTCTGTAATT
* *
42924249 TAAATGACTGATTTGTATGTGATT
1 TAAATGACTGATTTGTCTGTAATT
*
42924273 TAAATGACTGATTTGTCTGTCATT
1 TAAATGACTGATTTGTCTGTAATT
**
42924297 TGTATGACTG
1 TAAATGACTG
42924307 CTTCTGAGCA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.44
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTAATT
Found at i:42924416 original size:27 final size:27
Alignment explanation
Indices: 42924378--42924437 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
42924368 GGAAGTACTG
* *
42924378 TACTGGTGGCTTTGCCACA-ATCACTAT
1 TACTGGTAGCTTGGCCACATAT-ACTAT
42924405 TACTGGTAGCTTGGCCACATATACTAT
1 TACTGGTAGCTTGGCCACATATACTAT
42924432 TACTGG
1 TACTGG
42924438 CAACTTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 28 0.93
28 2 0.07
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (27 bp):
TACTGGTAGCTTGGCCACATATACTAT
Found at i:42924569 original size:32 final size:32
Alignment explanation
Indices: 42924482--42924575 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
42924472 CTGTGATGCT
* * *
42924482 ACTGATGGCTTTGTACCGGTCATATTACCGCT
1 ACTGATGGCTTTGTGCCGGTCATATTACTGCA
* * * *
42924514 ACTGAGGGCTGTGTGCTGGTCATATCACTGCA
1 ACTGATGGCTTTGTGCCGGTCATATTACTGCA
**
42924546 ACTGATGGCTTTGTGCCAATCATATTACTG
1 ACTGATGGCTTTGTGCCGGTCATATTACTG
42924576 TACTTATGGC
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (32 bp):
ACTGATGGCTTTGTGCCGGTCATATTACTGCA
Found at i:42924604 original size:22 final size:22
Alignment explanation
Indices: 42924579--42924625 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
42924569 ATTACTGTAC
* * *
42924579 TTATGGCTTGTAGCCATTCTGT
1 TTATAGCTTATAGCCATCCTGT
*
42924601 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTTATAGCCATCCTGT
42924623 TTA
1 TTA
42924626 CTGTTCTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (22 bp):
TTATAGCTTATAGCCATCCTGT
Found at i:42931189 original size:136 final size:137
Alignment explanation
Indices: 42930944--42931214 Score: 337
Period size: 136 Copynumber: 2.0 Consensus size: 137
42930934 CTGTAAAATG
* * **
42930944 GGTCTGCTCACACAAGCTGATGGTCGGAATGTAAGCTACACGATGCTGCTCACATAAGCTAATGA
1 GGTCTGCTCACACAAGCTGACGGTCGGAATGTAAGCTACACGATGCTGCTCACACAAGCTAACAA
* ** * * *
42931009 GTATCCGCAACTAATGTCGGAGCTCAACCATTGGTAGGAAATTCAGGACCAGCACCGAAACATGG
66 GTATCCGCAACAAATGTCAAACCTCAACCATCGGTAGGAAATTCAGGACCAGCACCCAAACATGG
42931074 TAACCTA
131 TAACCTA
* * *
42931081 GGTCTGCTCACACAAGTTGACGGTCGGAATGT-AGCTACACGATGCTGCTCCCACAAGCTGACAA
1 GGTCTGCTCACACAAGCTGACGGTCGGAATGTAAGCTACACGATGCTGCTCACACAAGCTAACAA
* * * * * * * * *
42931145 GTCTCTGCAACAAATGTTAAACCTTAGCTATCGGTAGGACATTCAGGATCAGGACCCAAACATGG
66 GTATCCGCAACAAATGTCAAACCTCAACCATCGGTAGGAAATTCAGGACCAGCACCCAAACATGG
42931210 TAACC
131 TAACC
42931215 CTAATGATAT
Statistics
Matches: 112, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
136 82 0.73
137 30 0.27
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (137 bp):
GGTCTGCTCACACAAGCTGACGGTCGGAATGTAAGCTACACGATGCTGCTCACACAAGCTAACAA
GTATCCGCAACAAATGTCAAACCTCAACCATCGGTAGGAAATTCAGGACCAGCACCCAAACATGG
TAACCTA
Found at i:42937421 original size:18 final size:18
Alignment explanation
Indices: 42937390--42937424 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42937380 GCTCAGTTGG
* *
42937390 TTTCTTCTTTCCCTTAGC
1 TTTCTACTTCCCCTTAGC
42937408 TTTCTACTTCCCCTTAG
1 TTTCTACTTCCCCTTAG
42937425 AGGATGAGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.34, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTCTACTTCCCCTTAGC
Found at i:42948626 original size:39 final size:39
Alignment explanation
Indices: 42948580--42948717 Score: 195
Period size: 39 Copynumber: 3.5 Consensus size: 39
42948570 ATTCACTTTC
* * *
42948580 AAGCATATATCACATTACACATATAATTACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTT
* *
42948619 AAACATATATCACAATACTCATATAATCACATAACACTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTT
* * *
42948658 AAGCATATATCAAAATACTCATATAACCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTT
*
42948697 AAGCATATATCACATTACTCA
1 AAGCATATATCACAATACTCA
42948718 AAAACATGTT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTT
Found at i:42950273 original size:31 final size:31
Alignment explanation
Indices: 42950238--42950299 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
42950228 GACAAGAGAA
42950238 CACCATTCACAGAAGCATCTACCACCAACAT
1 CACCATTCACAGAAGCATCTACCACCAACAT
*
42950269 CACCATTCACAGAAGTATCTACCACCAACAT
1 CACCATTCACAGAAGCATCTACCACCAACAT
42950300 TGTGTGTGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.37, G:0.06, T:0.18
Consensus pattern (31 bp):
CACCATTCACAGAAGCATCTACCACCAACAT
Found at i:42954016 original size:19 final size:20
Alignment explanation
Indices: 42953968--42954018 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
42953958 GCTTTCGGAA
42953968 AATTATTTCTGGAAAATGACT
1 AATT-TTTCTGGAAAATGACT
*
42953989 TATTTTTCTGGAAAA-G-CT
1 AATTTTTCTGGAAAATGACT
42954007 AATATTTTCTGG
1 AAT-TTTTCTGG
42954019 TGTTTGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 9 0.33
20 11 0.41
21 3 0.11
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (20 bp):
AATTTTTCTGGAAAATGACT
Found at i:42954598 original size:18 final size:18
Alignment explanation
Indices: 42954560--42954595 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42954550 TTATTATTTT
*
42954560 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
42954578 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
42954596 TAATTTATTA
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:42955265 original size:29 final size:28
Alignment explanation
Indices: 42955205--42955287 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 28
42955195 TTTTGCATTT
***
42955205 TGACCCCTAAACTTTTAAAATTACATTT
1 TGACCCCTAAACTTTTAAAATTACACCA
**
42955233 TGACCCCTAAACTTTTAAAAATTGTACCA
1 TGACCCCTAAACTTTT-AAAATTACACCA
* * *
42955262 TGACCCCTGAGCTTTTTGAAATTACA
1 TGACCCCTAAAC-TTTTAAAATTACA
42955288 TTTTAACCCT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 16 0.37
29 23 0.53
30 4 0.09
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.35
Consensus pattern (28 bp):
TGACCCCTAAACTTTTAAAATTACACCA
Found at i:42955684 original size:3 final size:3
Alignment explanation
Indices: 42955670--42955720 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
42955660 GGGTTTCCGA
*
42955670 AAG AAG AA- AAG AAG AAG AAGG AAG AAG AAG AAG AAG AAAG AAA AAG
1 AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG -AAG AAG AAG
42955716 AAG AA
1 AAG AA
42955721 AAAATTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42955696 original size:13 final size:12
Alignment explanation
Indices: 42955670--42955720 Score: 68
Period size: 13 Copynumber: 4.2 Consensus size: 12
42955660 GGGTTTCCGA
42955670 AAGAAGAA-AAG
1 AAGAAGAAGAAG
42955681 AAGAAGAAGGAAG
1 AAGAAGAA-GAAG
42955694 AAGAAGAAGAAG
1 AAGAAGAAGAAG
*
42955706 AAAGAAAAAGAAG
1 -AAGAAGAAGAAG
42955719 AA
1 AA
42955721 AAAATTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
11 8 0.22
12 6 0.17
13 22 0.61
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAG
Found at i:42955699 original size:16 final size:16
Alignment explanation
Indices: 42955670--42955720 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
42955660 GGGTTTCCGA
42955670 AAGAA-GAA-AAGAAG
1 AAGAAGGAAGAAGAAG
42955684 AAGAAGGAAGAAGAAG
1 AAGAAGGAAGAAGAAG
* *
42955700 AAGAAGAAAGAAAAAG
1 AAGAAGGAAGAAGAAG
42955716 AAGAA
1 AAGAA
42955721 AAAATTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.15
15 3 0.09
16 25 0.76
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AAGAAGGAAGAAGAAG
Found at i:42956007 original size:19 final size:19
Alignment explanation
Indices: 42955969--42956010 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42955959 GCAGCAAGCC
* **
42955969 AAAAAAAGAAAAGAGGGAA
1 AAAAAAAGAAAAAAAAGAA
42955988 AAAAAAAGAAAAAAAAGAA
1 AAAAAAAGAAAAAAAAGAA
42956007 AAAA
1 AAAA
42956011 GCCAAGTCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAGAA
Found at i:42956381 original size:18 final size:17
Alignment explanation
Indices: 42956344--42956402 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
42956334 TTTTTGTGTC
42956344 TTCAAAAATCCTCGTAT
1 TTCAAAAATCCTCGTAT
42956361 TTCAAAAATCCTCATGT-T
1 TTCAAAAATCCTC--GTAT
*
42956379 TTCAAAAATTCC-GGTAT
1 TTCAAAAA-TCCTCGTAT
42956396 TTCAAAA
1 TTCAAAA
42956403 TTTTTGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 2 0.05
17 21 0.57
18 9 0.24
19 5 0.14
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (17 bp):
TTCAAAAATCCTCGTAT
Found at i:42956582 original size:16 final size:17
Alignment explanation
Indices: 42956420--42956827 Score: 193
Period size: 17 Copynumber: 23.2 Consensus size: 17
42956410 ATTTTAAAAT
42956420 AAAATTC-CTGTGTTTTA
1 AAAATTCTC-GTGTTTTA
* *
42956437 AAAATTTTCGTGTTTCA
1 AAAATTCTCGTGTTTTA
* *
42956454 ACAATTCTCGTGTTTTG
1 AAAATTCTCGTGTTTTA
* * *
42956471 TAAATTTTCGTGTTTTTT
1 AAAATTCTCGTG-TTTTA
* * *
42956489 TAAATTCTCGT-ATTAA
1 AAAATTCTCGTGTTTTA
*
42956505 AAAATTCTCGTGTTTCA
1 AAAATTCTCGTGTTTTA
* * * *
42956522 CAAATCTTCGCGTTTTTTTT
1 -AAA-ATTCTCG-TGTTTTA
*
42956542 AAAATCCTCGTGTTTTCAA
1 AAAATTCTCGTGTTTT--A
* *
42956561 AAAAATCTCTTGTTTTA
1 AAAATTCTCGTGTTTTA
42956578 AAAATTCTCGTG-TTTA
1 AAAATTCTCGTGTTTTA
* *
42956594 CAAAACTTCTCGAGTTTTG
1 -AAAA-TTCTCGTGTTTTA
* * *
42956613 TAAATTTTCGTGTTTTT
1 AAAATTCTCGTGTTTTA
* *
42956630 AAAATTCTCGTATTTCA
1 AAAATTCTCGTGTTTTA
42956647 AAAAGTT-TCCGTGTTTTAAA
1 AAAA-TTCT-CGTGTTTT--A
42956667 AAAATTCTCGTGTTTT-
1 AAAATTCTCGTGTTTTA
*
42956683 AAAATAT-TCGTGTTCTCAA
1 AAAAT-TCTCGTGTT-T-TA
*
42956702 AAAATTTCTCGTGTTTCA
1 AAAA-TTCTCGTGTTTTA
* * *
42956720 AAAATTGTCGCGTTTTG
1 AAAATTCTCGTGTTTTA
* * *
42956737 CAAATTTTTGTGTTTTA
1 AAAATTCTCGTGTTTTA
* * *
42956754 AGAATTTTCGGGTTTTTA
1 AAAATTCTCGTG-TTTTA
* *
42956772 AAAGTTTTCGTGTTTCT-
1 AAAATTCTCGTGTTT-TA
* * *
42956789 ATAATTCTCGTATTTCA
1 AAAATTCTCGTGTTTTA
*
42956806 AAAAGTT-TCTGTGCTTTA
1 AAAA-TTCTC-GTGTTTTA
42956824 AAAA
1 AAAA
42956828 AAATTCTCTT
Statistics
Matches: 292, Mismatches: 72, Indels: 53
0.70 0.17 0.13
Matches are distributed among these distances:
16 28 0.10
17 135 0.46
18 71 0.24
19 40 0.14
20 18 0.06
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (17 bp):
AAAATTCTCGTGTTTTA
Found at i:42956611 original size:35 final size:34
Alignment explanation
Indices: 42956420--42956808 Score: 166
Period size: 35 Copynumber: 11.1 Consensus size: 34
42956410 ATTTTAAAAT
*
42956420 AAAATTC-CTGTGTTTTAAAAATTTTCGTGTTT-C
1 AAAATTCTC-GTGTTTTAAAAATTCTCGTGTTTAC
** * **
42956453 AACAATTCTCGTGTTTTGTAAATTTTCGTGTTTTTT
1 AA-AATTCTCGTGTTTTAAAAATTCTCGTG-TTTAC
* * *
42956489 TAAATTCTCGT-ATTAAAAAATTCTCGTGTTTCAC
1 AAAATTCTCGTGTTTTAAAAATTCTCGTGTTT-AC
* * * * * *
42956523 AAATCTTCGCGTTTTTTTTAAAATCCTCGTGTTTTCAA
1 AAA-ATTCTCG-TGTTTTAAAAATTCTCGTG-TTT-AC
* *
42956561 AAAAATCTCTTGTTTTAAAAATTCTCGTGTTTAC
1 AAAATTCTCGTGTTTTAAAAATTCTCGTGTTTAC
* ** * **
42956595 AAAACTTCTCGAGTTTTGTAAATTTTCGTGTTTTT
1 AAAA-TTCTCGTGTTTTAAAAATTCTCGTGTTTAC
* * *
42956630 AAAATTCTCGTATTTCAAAAAGTT-TCCGTGTTTTAAA
1 AAAATTCTCGTGTTTTAAAAA-TTCT-CGTG-TTT-AC
*
42956667 AAAATTCTCGTGTTTT-AAAATAT-TCGTGTTCTCAA
1 AAAATTCTCGTGTTTTAAAAAT-TCTCGTGTT-T-AC
* * * *
42956702 AAAATTTCTCGTGTTTCAAAAATTGTCGCGTTTTGC
1 AAAA-TTCTCGTGTTTTAAAAATTCTCGTG-TTTAC
* * * * * **
42956738 -AAATTTTTGTGTTTTAAGAATTTTCGGGTTTTT
1 AAAATTCTCGTGTTTTAAAAATTCTCGTGTTTAC
* * *
42956771 AAAAGTTTTCGTGTTTCT-ATAATTCTCGTATTT-C
1 AAAA-TTCTCGTGTTT-TAAAAATTCTCGTGTTTAC
42956805 AAAA
1 AAAA
42956809 AGTTTCTGTG
Statistics
Matches: 270, Mismatches: 63, Indels: 45
0.71 0.17 0.12
Matches are distributed among these distances:
33 8 0.03
34 83 0.31
35 89 0.33
36 40 0.15
37 40 0.15
38 10 0.04
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (34 bp):
AAAATTCTCGTGTTTTAAAAATTCTCGTGTTTAC
Found at i:42956702 original size:54 final size:55
Alignment explanation
Indices: 42956548--42956868 Score: 173
Period size: 52 Copynumber: 5.9 Consensus size: 55
42956538 TTTTAAAATC
* * * * *
42956548 CTCGTGTTTTCAAAAAAA-TCTCTTGTTTTAAAAATTCTCGTGTTT-ACAAAACTT
1 CTCGTG-TTTCAAAAAAATTCTCGTGTTTTTAAAATTCTCGTATTTCAAAAAATTT
* *** * *
42956602 CTCGAGTTT--TGTAAATTTTCGTGTTTTTAAAATTCTCGTATTTCAAAAAGTTT
1 CTCGTGTTTCAAAAAAATTCTCGTGTTTTTAAAATTCTCGTATTTCAAAAAATTT
* *
42956655 C-CGTGTTTTAAAAAAATTCTCGTG-TTTTAAAATAT-TCGTGTTCTCAAAAAATTT
1 CTCGTGTTTCAAAAAAATTCTCGTGTTTTTAAAAT-TCTCGTATT-TCAAAAAATTT
* * ** * * * * *
42956709 CTCGTGTTTC--AAAAATTGTCGCGTTTTGCAAATTTTTGTGTTT-TAAGAATTT
1 CTCGTGTTTCAAAAAAATTCTCGTGTTTTTAAAATTCTCGTATTTCAAAAAATTT
* ** * * * * *
42956761 -TCGGGTTT-TTAAAAGTTTTCGTGTTTCTATAATTCTCGTATTTCAAAAAGTTT
1 CTCGTGTTTCAAAAAAATTCTCGTGTTTTTAAAATTCTCGTATTTCAAAAAATTT
* * ** *
42956814 CT-GTGCTTTAAAAAAAATTCTCTTGTTTCAAAAAAATTTTCGTATTTTCAAAAAA
1 CTCGTG-TTTCAAAAAAATTCTCGTGTTT--TTAAAATTCTCGTA-TTTCAAAAAA
42956869 ATATTGTCTC
Statistics
Matches: 198, Mismatches: 51, Indels: 32
0.70 0.18 0.11
Matches are distributed among these distances:
51 10 0.05
52 59 0.30
53 46 0.23
54 44 0.22
55 20 0.10
57 10 0.05
58 9 0.05
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (55 bp):
CTCGTGTTTCAAAAAAATTCTCGTGTTTTTAAAATTCTCGTATTTCAAAAAATTT
Found at i:42956740 original size:19 final size:18
Alignment explanation
Indices: 42956642--42956732 Score: 55
Period size: 19 Copynumber: 4.9 Consensus size: 18
42956632 AATTCTCGTA
42956642 TTTCAAAAAGTTTC-CGTG
1 TTTCAAAAA-TTTCGCGTG
* * *
42956660 TTTTAAAAAAATTCTCGTG
1 -TTTCAAAAATTTCGCGTG
*
42956679 TTT-TAAAATATT--CGTG
1 TTTCAAAAAT-TTCGCGTG
*
42956695 TTCTCAAAAAATTTCTCGTG
1 TT-TC-AAAAATTTCGCGTG
42956715 TTTCAAAAATTGTCGCGT
1 TTTCAAAAATT-TCGCGT
42956733 TTTGCAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
16 6 0.10
17 5 0.09
18 17 0.29
19 24 0.41
20 6 0.10
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (18 bp):
TTTCAAAAATTTCGCGTG
Found at i:42956846 original size:19 final size:20
Alignment explanation
Indices: 42956824--42956870 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
42956814 CTGTGCTTTA
42956824 AAAAAAATTCTC-T-TGTTTC
1 AAAAAAATTCTCGTAT-TTTC
*
42956843 AAAAAAATTTTCGTATTTTC
1 AAAAAAATTCTCGTATTTTC
42956863 AAAAAAAT
1 AAAAAAAT
42956871 ATTGTCTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 11 0.44
20 13 0.52
21 1 0.04
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAAAAATTCTCGTATTTTC
Found at i:42957823 original size:18 final size:17
Alignment explanation
Indices: 42957786--42957828 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
42957776 ATAAAATTCC
*
42957786 CGTGTTTTAAAAATTTT
1 CGTGTTTTAAAAATTAT
*
42957803 CGTGTTTTCAAGAATTAT
1 CGTGTTTT-AAAAATTAT
42957821 CGTGTTTT
1 CGTGTTTT
42957829 GTAAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.51
Consensus pattern (17 bp):
CGTGTTTTAAAAATTAT
Found at i:42957923 original size:19 final size:18
Alignment explanation
Indices: 42957896--42957959 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
42957886 CTTCGTCTTT
*
42957896 TTTTAAAAAAATCCTCCTG
1 TTTTCAAAAAAT-CTCCTG
*
42957915 TTTTCAAAAAAATCTCTTG
1 TTTTC-AAAAAATCTCCTG
*
42957934 -TTT-AAAAAATTCTCGTG
1 TTTTCAAAAAA-TCTCCTG
42957951 TTTTCAAAA
1 TTTTCAAAA
42957960 CTTCTCGAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 6 0.16
17 6 0.16
18 6 0.16
19 13 0.34
20 7 0.18
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (18 bp):
TTTTCAAAAAATCTCCTG
Found at i:42957959 original size:18 final size:18
Alignment explanation
Indices: 42957697--42958137 Score: 144
Period size: 17 Copynumber: 24.7 Consensus size: 18
42957687 TGTGTTTTTT
* *
42957697 GTGTCTTCAAAAATCCTC
1 GTGTTTTCAAAAATTCTC
* *
42957715 GT-ATTTCAAAAATCCTC
1 GTGTTTTCAAAAATTCTC
* *
42957732 ATGTTTTCAAAAATTCTG
1 GTGTTTTCAAAAATTCTC
* *
42957750 GTG-TTTCAAAATTTGT-
1 GTGTTTTCAAAAATTCTC
* * *
42957766 GTATTTTAAAATAAAATTCCC
1 GTGTTTT--CA-AAAATTCTC
*
42957787 GTGTTTT-AAAAATTTTC
1 GTGTTTTCAAAAATTCTC
* *
42957804 GTGTTTTCAAGAATTATC
1 GTGTTTTCAAAAATTCTC
** *
42957822 GTGTTTT-GTAAATTTTC
1 GTGTTTTCAAAAATTCTC
* ****
42957839 ATGTTTTTTTTAATTCTC
1 GTGTTTTCAAAAATTCTC
* *
42957857 --GTATTAAAAAATTCTC
1 GTGTTTTCAAAAATTCTC
*
42957873 GTG-TTTCACAAATCTTCGTC
1 GTGTTTTCA-AAA-ATTC-TC
* * * *
42957893 TTTTTTTAAAAAAATCCTC
1 GTGTTTT-CAAAAATTCTC
* *
42957912 CTGTTTTCAAAAAAATCTC
1 GTGTTTTC-AAAAATTCTC
* *
42957931 TTG-TTTAAAAAATTCTC
1 GTGTTTTCAAAAATTCTC
*
42957948 GTGTTTTCAAAACTTCTC
1 GTGTTTTCAAAAATTCTC
* ** *
42957966 GAGTTTT-GTAAATTTTC
1 GTGTTTTCAAAAATTCTC
*
42957983 GTGTTCTCAAAAAAATTTCTC
1 GTGTTTTC--AAAAA-TTCTC
* *
42958004 ATG-TTTCAAAAATTGTC
1 GTGTTTTCAAAAATTCTC
* *
42958021 GCGTTTTGC--AAATTTTC
1 GTGTTTT-CAAAAATTCTC
* *
42958038 GTGTTTT-AAGAATTTTC
1 GTGTTTTCAAAAATTCTC
* * *
42958055 GGGTTTTCAAAAGTTTTC
1 GTGTTTTCAAAAATTCTC
* *
42958073 ATG-TTTCTAAAATTCTC
1 GTGTTTTCAAAAATTCTC
*
42958090 GT-ATTTCAAAAAGTTC-C
1 GTGTTTTCAAAAA-TTCTC
**
42958107 GTGCTTTAAAAAAATTCTC
1 GTG-TTTTCAAAAATTCTC
*
42958126 TTG-TTTCAAAAA
1 GTGTTTTCAAAAA
42958138 AATTTTCGTA
Statistics
Matches: 307, Mismatches: 85, Indels: 63
0.67 0.19 0.14
Matches are distributed among these distances:
16 13 0.04
17 140 0.46
18 87 0.28
19 32 0.10
20 16 0.05
21 18 0.06
22 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (18 bp):
GTGTTTTCAAAAATTCTC
Found at i:42958013 original size:55 final size:55
Alignment explanation
Indices: 42957937--42958042 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 55
42957927 TCTCTTGTTT
* * *
42957937 AAAAAATTCTCGTGTTTTCAAAACTTCTCGAGTTTTGTAAATTTTCGTGTTCTCA
1 AAAAAATTCTCATGTTTTCAAAAATTCTCGAGTTTTGCAAATTTTCGTGTTCTCA
* *
42957992 AAAAAATTTCTCATG-TTTCAAAAATTGTCGCGTTTTGCAAATTTTCGTGTT
1 AAAAAA-TTCTCATGTTTTCAAAAATTCTCGAGTTTTGCAAATTTTCGTGTT
42958043 TTAAGAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 38 0.84
56 7 0.16
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (55 bp):
AAAAAATTCTCATGTTTTCAAAAATTCTCGAGTTTTGCAAATTTTCGTGTTCTCA
Found at i:42958015 original size:21 final size:20
Alignment explanation
Indices: 42957975--42958015 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
42957965 CGAGTTTTGT
*
42957975 AAATTTTCGTGTTCTCAAAA
1 AAATTTTCATGTTCTCAAAA
42957995 AAATTTCTCATGTT-TCAAAA
1 AAATTT-TCATGTTCTCAAAA
42958015 A
1 A
42958016 TTGTCGCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (20 bp):
AAATTTTCATGTTCTCAAAA
Found at i:42958156 original size:20 final size:19
Alignment explanation
Indices: 42958111--42958160 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
42958101 AGTTCCGTGC
42958111 TTTAAAAAAATTCTCTTGT
1 TTTAAAAAAATTCTCTTGT
* *
42958130 TTCAAAAAAATTTTCGTAT-T
1 TTTAAAAAAATTCTC-T-TGT
42958150 TTTAAAAAAAT
1 TTTAAAAAAAT
42958161 ATTGTCTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 13 0.50
20 12 0.46
21 1 0.04
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (19 bp):
TTTAAAAAAATTCTCTTGT
Found at i:42964919 original size:14 final size:14
Alignment explanation
Indices: 42964900--42964939 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42964890 TTGTTTGGCA
42964900 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
42964914 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
42964928 GGAAAATGTTTT
1 GTAAAATGTTTT
42964940 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:42964948 original size:20 final size:20
Alignment explanation
Indices: 42964923--42964982 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
42964913 CGTAAAATGA
42964923 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGTTTTACT
*
42964943 TTTCTGGAAAATGTTTTATT
1 TTTCTGGAAAATGTTTTACT
* *
42964963 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGTTTTACT
42964983 GGAAAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (20 bp):
TTTCTGGAAAATGTTTTACT
Found at i:42965111 original size:14 final size:14
Alignment explanation
Indices: 42965092--42965119 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42965082 ATTTTACATA
42965092 TATTAATATATATT
1 TATTAATATATATT
42965106 TATTAATATATATT
1 TATTAATATATATT
42965120 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:42965381 original size:39 final size:39
Alignment explanation
Indices: 42965332--42965453 Score: 116
Period size: 39 Copynumber: 3.3 Consensus size: 39
42965322 TAATTAATGG
42965332 TACACCACATAGTAACAACATTGTCCAAGTGCATAATAT
1 TACACCACATAGTAACAACATTGTCCAAGTGCATAATAT
* * * **
42965371 TACACCACATA-TATCCAA-A---TAC-A-T-AATTAATGG
1 TACACCACATAGTA-ACAACATTGTCCAAGTGCA-TAATAT
*
42965404 TACACCACATAGTAAGAACATTGTCCAAGTGCATAATAT
1 TACACCACATAGTAACAACATTGTCCAAGTGCATAATAT
42965443 TACACCACATA
1 TACACCACATA
42965454 AATGTATCAA
Statistics
Matches: 62, Mismatches: 11, Indels: 20
0.67 0.12 0.22
Matches are distributed among these distances:
32 1 0.02
33 18 0.29
34 4 0.06
35 2 0.03
37 2 0.03
38 4 0.06
39 30 0.48
40 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (39 bp):
TACACCACATAGTAACAACATTGTCCAAGTGCATAATAT
Found at i:42965427 original size:72 final size:72
Alignment explanation
Indices: 42965310--42965453 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
42965300 ATAATAATAT
42965310 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
42965375 CCACATA
66 CCACATA
*
42965382 TATCCAAATACATAATTAATGGTACACCACATAGTAAGAACATTGTCCAAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
42965447 CCACATA
66 CCACATA
42965454 AATGTATCAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (72 bp):
TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
CCACATA
Found at i:42965838 original size:27 final size:26
Alignment explanation
Indices: 42965808--42965869 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
42965798 AGTTATAATT
*
42965808 TTTAATATCAAAATTTATAGAGACCAA
1 TTTAATATCAAAA-TTATAGAGAACAA
* * *
42965835 TTTAAAATCTAGATTATAGAGAACAA
1 TTTAATATCAAAATTATAGAGAACAA
*
42965861 TTTGATATC
1 TTTAATATC
42965870 TAGATTCTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (26 bp):
TTTAATATCAAAATTATAGAGAACAA
Found at i:42965855 original size:26 final size:26
Alignment explanation
Indices: 42965822--42965875 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
42965812 ATATCAAAAT
*
42965822 TTATAGAGACCAATTTAAAATCTAGA
1 TTATAGAGAACAATTTAAAATCTAGA
* *
42965848 TTATAGAGAACAATTTGATATCTAGA
1 TTATAGAGAACAATTTAAAATCTAGA
42965874 TT
1 TT
42965876 CTAGTTTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (26 bp):
TTATAGAGAACAATTTAAAATCTAGA
Found at i:42973928 original size:75 final size:75
Alignment explanation
Indices: 42973635--42974549 Score: 828
Period size: 77 Copynumber: 11.9 Consensus size: 75
42973625 TTTCAAGAAA
* * *
42973635 TATTTTTCAATTTATGCTTTTTTTCAAAAATCAACTCAAAATACGAGAGGTGAGTTGAGCCTCGG
1 TATTTTT-AATTTCTG-TTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
** *
42973700 GTCACAATGAGA
64 GTCACGCTGAGG
42973712 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTTTTTTTT-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
42973777 TCACGCTGAGG
65 TCACGCTGAGG
* *
42973788 TATTTTTAATTTCTATCTTTTTTT--AAATCAACTCATAATACGAGAGGTGAGTAGAGCCTCGGG
1 TATTTTTAATTTCTGT-TTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
42973851 TCACGCTGAGG
65 TCACGCTGAGG
* * * *
42973862 TATTTTTAATTTCTGTCTTTTTTT-GAAATCAACTCATAATACAAAAGGTGAGTTGAGCCTTGGG
1 TATTTTTAATTTCTGT-TTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
42973926 TCACGCTGAGG
65 TCACGCTGAGG
* * *
42973937 TATTTTTTATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTTAATTTCTGTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
42974002 CACGCTGAGG
66 CACGCTGAGG
* * *
42974012 TATTTTTTAAATTTTTGTTTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TA-TTTTT-AATTTCTGTTTTTTTT--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
42974077 GGGTCACACGCTGAGG
62 GGGT--CACGCTGAGG
* * * *
42974093 TATTTCTTTTAAATTTCTATTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TA--T-TTTT-AATTTCTGTTTTTTT---TAAAAATCAACTCATAATACGAGAGGTGAGTTGAGC
*** * *
42974158 CTCGAACCATGCCGAGG
59 CTCGGGTCACGCTGAGG
* ** * * *
42974175 TATTTCTTTTAAATTTATG-TTTTTCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTC
1 TA--T-TTTT-AATTTCTGTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
** * *
42974239 GGACCATGCCGAGG
62 GGGTCACGCTGAGG
** * ** *
42974253 TATTTCCTTTAAATTTCTG--TTTTTCGAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTT
1 TA-TT--TTT-AATTTCTGTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
** * * *
42974316 GGACCATGCCGACG
62 GGGTCACGCTGAGG
* * *
42974330 TATTTTTTTTAAATTTC--TATTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TA---TTTTT-AATTTCTGTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
* *
42974393 GGGTCACGCCGATG
62 GGGTCACGCTGAGG
* * * * * *
42974407 TATTTTTCAA-TTCT-TGTTTTTCAAAAATCAACTCATACTGCGAGGGGTGAGTTGAGCCTCGAG
1 TATTTTT-AATTTCTGTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
* *
42974470 TCGCATGCCGAGG
65 T--CACGCTGAGG
* * * * *
42974483 TATTCTTTTCAAATTC--TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 TA-T-TTTT-AATTTCTGTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
42974546 GGTC
63 GGTC
42974550 GCACACCGAG
Statistics
Matches: 744, Mismatches: 67, Indels: 55
0.86 0.08 0.06
Matches are distributed among these distances:
73 3 0.00
74 130 0.17
75 116 0.16
76 87 0.12
77 144 0.19
78 117 0.16
79 46 0.06
81 17 0.02
82 27 0.04
83 18 0.02
84 39 0.05
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (75 bp):
TATTTTTAATTTCTGTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
CACGCTGAGG
Found at i:42973944 original size:150 final size:150
Alignment explanation
Indices: 42973652--42974549 Score: 891
Period size: 150 Copynumber: 5.8 Consensus size: 150
42973642 CAATTTATGC
* ** *
42973652 TTTTTTTCAAAAATCAACTCAAAATACGAGAGGTGAGTTGAGCCTCGGGTCACAATGAGATA-TT
1 TTTTTTT--AAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
* *
42973716 TTT-AATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCA
64 TTTAAATTTCTGTTTTTTTT--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
42973780 CGCTGAGGTA-TTTTTAATTTCTA
127 CGCTGAGGTATTTTTTAATTTCTA
* *
42973803 TCTTTTTTTAAATCAACTCATAATACGAGAGGTGAGTAGAGCCTCGGGTCACGCTGAGGTA-TTT
1 T-TTTTTTAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
* * * * * *
42973867 TT-AATTTCTGTCTTTTTTTGAAATCAACTCATAATACAAAAGGTGAGTTGAGCCTTGGGTCACG
65 TTAAATTTCTGT-TTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
42973931 CTGAGGTATTTTTT-ATTTCTA
129 CTGAGGTATTTTTTAATTTCTA
42973952 TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 TTTTTTT--AAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
42974017 TTTAAATTTTTGTTTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
64 TTTAAATTTCTGTTTTTTTT---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT-
42974082 ACACGCTGAGGTATTTCTTTTAAATTTCTA
125 -CACGCTGAGGTA-TT-TTTT-AATTTCTA
* * *** * *
42974112 TTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAACCATGCCGAGGTA
1 TTTTTTT-----AAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA
* *** * *
42974177 TTTCTTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGA
61 -TT-TTTTAAATTTCTGTTTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * * *
42974242 CCATGCCGAGGTATTTCCTTTAAATTTCTG
124 TCACGCTGAGGTATTT--TTT-AATTTCTA
** * ** * ** * * *
42974272 TTTTTCGAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGACCATGCCGACGTATTTTT
1 TTTTTTTAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--TTT
* *
42974337 TTTAAATTTCT-ATTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
64 TTTAAATTTCTGTTTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
* * *
42974401 CCGATGTATTTTTCAA-TTCT-
129 CTGAGGTATTTTTTAATTTCTA
* * * * * * *
42974421 TGTTTTTCAAAAATCAACTCATACTGCGAGGGGTGAGTTGAGCCTCGAGTCGCATGCCGAGGTAT
1 T-TTTTT-TAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTAT
* **
42974486 TCTTTTCAAA-TTCT-ATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
62 T-TTTT-AAATTTCTGTTTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
42974549 C
125 C
42974550 GCACACCGAG
Statistics
Matches: 653, Mismatches: 64, Indels: 59
0.84 0.08 0.08
Matches are distributed among these distances:
148 6 0.01
149 58 0.09
150 125 0.19
151 58 0.09
152 73 0.11
153 14 0.02
154 91 0.14
155 60 0.09
156 15 0.02
157 2 0.00
158 5 0.01
159 2 0.00
160 40 0.06
162 38 0.06
163 47 0.07
164 2 0.00
165 17 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (150 bp):
TTTTTTTAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
TAAATTTCTGTTTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCT
GAGGTATTTTTTAATTTCTA
Found at i:42974245 original size:78 final size:76
Alignment explanation
Indices: 42973654--42974547 Score: 871
Period size: 78 Copynumber: 11.6 Consensus size: 76
42973644 ATTTATGCTT
* * * * *** *
42973654 TTTTTCAAAAATCAACTCAAAATACGAGAGGTGAGTTGAGCCTCGGGTCACAATGAGATA-TTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTATTTTT
* * *
42973718 TAATTTCTGTTT
66 TAAATTCT-ATG
* * * *
42973730 TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTATTTTT
* *
42973794 TAATTTCTATC
66 TAAATTCTATG
** * * * * *
42973805 TTTTT-TTAAATCAACTCATAATACGAGAGGTGAGTAGAGCCTCGGGTCACGCTGAGGTA-TTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTATTTTT
* * *
42973868 TAATTTCTGTC
66 TAAATTCTATG
*** * * * * * * *
42973879 TTTTTTTGAAATCAACTCATAATACAAAAGGTGAGTTGAGCCTTGGGTCACGCTGAGGTATTTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTATTTTT
* *
42973944 T-ATTTCTATT
66 TAAATTCTATG
* * * *
42973954 TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTATTTTT
*
42974019 TAAATT-TTTG
66 TAAATTCTATG
*
42974029 TTTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
1 ---TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-C-CACGCCGAGGT
*
42974094 ATTTCTTTTAAATTTCTATT
60 A-TT-TTTTAAA-TTCTATG
** *
42974114 TTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAACCATGCCGAGGTATT
1 TTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTA-T
42974179 TCTTTTAAATT-TATG
62 T-TTTTAAATTCTATG
* * *
42974194 TTTTTCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTC
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTATTT-
*
42974259 CTTTAAATT-TCTG
64 -TTTAAATTCTATG
* * * * * *
42974272 TTTTTCGAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGACCATGCCGACGTATTTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTA--TTT
42974337 TTTAAATTTCTAT-
64 TTTAAA-TTCTATG
* *
42974350 TTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGATGTA-TTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTATTTTT
*
42974413 TCAATTCT-TG
66 TAAATTCTATG
* * * *
42974423 TTTTTCAAAAATCAACTCATACTGCGAGGGGTGAGTTGAGCCTCGAGTCGCATGCCGAGGTATTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GGC-CACGCCGAGGTATT-
42974488 TTTTCAAATTCTA--
63 TTTT-AAATTCTATG
42974501 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
42974548 TCGCACACCG
Statistics
Matches: 726, Mismatches: 63, Indels: 57
0.86 0.07 0.07
Matches are distributed among these distances:
72 1 0.00
73 9 0.01
74 114 0.16
75 125 0.17
76 87 0.12
77 106 0.15
78 130 0.18
79 50 0.07
80 9 0.01
81 14 0.02
82 29 0.04
83 8 0.01
84 42 0.06
85 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (76 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACGCCGAGGTATTTTT
TAAATTCTATG
Found at i:42974788 original size:29 final size:29
Alignment explanation
Indices: 42974753--42974890 Score: 134
Period size: 29 Copynumber: 4.7 Consensus size: 29
42974743 AATTTTTTTG
42974753 CATTTTGACCCCTAAACTTTTTAAAATTA
1 CATTTTGACCCCTAAACTTTTTAAAATTA
*
42974782 CATTTTGACCCCTAAACTTTTTAAAATTG
1 CATTTTGACCCCTAAACTTTTTAAAATTA
*** * * * *
42974811 CACCATGAACCCTGAGCTTTTTGAAATTA
1 CATTTTGACCCCTAAACTTTTTAAAATTA
*
42974840 CATTTTGACCCTTAAA-TTTTCATAAAATTA
1 CATTTTGACCCCTAAACTTTT--TAAAATTA
* * * *
42974870 TATTTTGGCCCCAAAAGTTTT
1 CATTTTGACCCCTAAACTTTT
42974891 GTTGCAGTTG
Statistics
Matches: 85, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
28 4 0.05
29 58 0.68
30 19 0.22
31 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTTTAAAATTA
Found at i:42975225 original size:3 final size:3
Alignment explanation
Indices: 42975199--42975261 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
42975189 GGGTTTTCGA
* * *
42975199 AAG AAG AA- AAG TAG AAA AAGG AAG AAG AAG AAG AAG AAAG AAA AAG
1 AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG -AAG AAG AAG
* *
42975245 AAA AAG AAA AAG AAG AA
1 AAG AAG AAG AAG AAG AA
42975262 AAAATTTAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:42975239 original size:16 final size:15
Alignment explanation
Indices: 42975205--42975264 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 15
42975195 TCGAAAGAAG
*
42975205 AAAAGTAGAAAAAGGA
1 AAAAGAAGAAAAA-GA
* *
42975221 AGAAGAAGAAGAAGA
1 AAAAGAAGAAAAAGA
*
42975236 AAGAAAAAGAAAAAGA
1 AA-AAGAAGAAAAAGA
42975252 AAAAGAAGAAAAA
1 AAAAGAAGAAAAA
42975265 ATTTAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 13 0.36
16 23 0.64
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (15 bp):
AAAAGAAGAAAAAGA
Found at i:42975265 original size:16 final size:17
Alignment explanation
Indices: 42975198--42975263 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 17
42975188 AGGGTTTTCG
*
42975198 AAAGAAGAAAAGTAGAA
1 AAAGAAGAAAAGAAGAA
42975215 AAAGGAAGAAGAAGAAGAA
1 AAA-GAAGAA-AAGAAGAA
* *
42975234 GAAAGAAAAAGAAAAAGAA
1 -AAAGAAGAA-AAGAAGAA
42975253 AAAGAAGAAAA
1 AAAGAAGAAAA
42975264 AATTTAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.12
18 14 0.33
19 20 0.48
20 3 0.07
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (17 bp):
AAAGAAGAAAAGAAGAA
Found at i:42976002 original size:17 final size:18
Alignment explanation
Indices: 42975980--42976021 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
42975970 ATTTTAAAAT
42975980 AAAATTCCCGTGTTCT-A
1 AAAATTCCCGTGTTCTCA
** *
42975997 AAAATTTTCGTGTTTTCA
1 AAAATTCCCGTGTTCTCA
42976015 AAAATTC
1 AAAATTC
42976022 TCGTTTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (18 bp):
AAAATTCCCGTGTTCTCA
Found at i:42976029 original size:17 final size:17
Alignment explanation
Indices: 42975996--42976168 Score: 100
Period size: 18 Copynumber: 9.6 Consensus size: 17
42975986 CCCGTGTTCT
*
42975996 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGT-TTTTC
*
42976014 AAAAATTCTCGTTTTTT
1 AAAAATTCTCGTTTTTC
** * * *
42976031 GTAGATTTTCGTGTTTTTT
1 AAAAATTCTC--GTTTTTC
** *
42976050 TTAAATTCTCG-TATTC
1 AAAAATTCTCGTTTTTC
*
42976066 AAAAATTCTCGTGTTTC
1 AAAAATTCTCGTTTTTC
* *
42976083 ACAAA-TCTTCGTGTTTTTTTA
1 AAAAATTC-TC--G--TTTTTC
42976104 AAAAATTCTCGTGTTTTC
1 AAAAATTCTCGT-TTTTC
42976122 AAAAAATTCTC-TTGTTTC
1 -AAAAATTCTCGTT-TTTC
42976140 AAAAATTCTCGTGTTTTC
1 AAAAATTCTCGT-TTTTC
42976158 AAAAATTCTCG
1 AAAAATTCTCG
42976169 AGTTTTGTAA
Statistics
Matches: 121, Mismatches: 20, Indels: 28
0.72 0.12 0.17
Matches are distributed among these distances:
16 14 0.12
17 32 0.26
18 36 0.30
19 27 0.22
21 10 0.08
22 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.48
Consensus pattern (17 bp):
AAAAATTCTCGTTTTTC
Found at i:42976061 original size:19 final size:19
Alignment explanation
Indices: 42976016--42976061 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
42976006 GTGTTTTCAA
42976016 AAATTCTC--GTTTTTTGT
1 AAATTCTCGTGTTTTTTGT
* * *
42976033 AGATTTTCGTGTTTTTTTT
1 AAATTCTCGTGTTTTTTGT
42976052 AAATTCTCGT
1 AAATTCTCGT
42976062 ATTCAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
17 6 0.27
19 16 0.73
ACGTcount: A:0.17, C:0.11, G:0.13, T:0.59
Consensus pattern (19 bp):
AAATTCTCGTGTTTTTTGT
Found at i:42976197 original size:126 final size:125
Alignment explanation
Indices: 42976124--42976357 Score: 289
Period size: 126 Copynumber: 1.9 Consensus size: 125
42976114 GTGTTTTCAA
* * * *
42976124 AAAATTCTCTTGTT-TC-AAAAA-TTCTCGTGTTTTCAAAAATTCTCGAGTTTTGTAAATTTTTG
1 AAAATTCTCGTGTTCTCAAAAAATTTCTCATG-TTTCAAAAATTCTCGAGTTTTGCAAATTTTCG
42976186 TGTTTTTAAAATTCTCATATTTCAAAAAGTTTCCGTGTTTTAAAAAAAAATCTCCTGTTTT
65 TGTTTTTAAAATTCTCATATTTCAAAAAGTTTCCGTGTTTTAAAAAAAAATCTCCTGTTTT
* * *
42976247 AAAATTTTCGTGTTCTCAAAAAAATTTCTCATGTTTCAAAAATTGTCGCGTTTTGCAAATTTTCG
1 AAAATTCTCGTGTTCTC-AAAAAATTTCTCATGTTTCAAAAATTCTCGAGTTTTGCAAATTTTCG
* ** *
42976312 TG-TTTTAAGAATTTTTGTGTTTTC-AAAAGTTTCCGTGTTTCTAAAA
65 TGTTTTTAA-AATTCTCAT-ATTTCAAAAAGTTTCCGTGTTT-TAAAA
42976358 TTCTCGTATT
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
123 12 0.13
124 2 0.02
125 6 0.06
126 57 0.61
127 16 0.17
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.46
Consensus pattern (125 bp):
AAAATTCTCGTGTTCTCAAAAAATTTCTCATGTTTCAAAAATTCTCGAGTTTTGCAAATTTTCGT
GTTTTTAAAATTCTCATATTTCAAAAAGTTTCCGTGTTTTAAAAAAAAATCTCCTGTTTT
Found at i:42976247 original size:144 final size:142
Alignment explanation
Indices: 42975996--42976339 Score: 342
Period size: 144 Copynumber: 2.4 Consensus size: 142
42975986 CCCGTGTTCT
* * * * * *
42975996 AAAAATTTTCGTGTTTTCAAAAATTCTCGTTTTTTGTAGATTTTCGTGTTTTTTTTAAATTCTCG
1 AAAAATTCTCGTGTTTTCAAAAATTCTCGTGTTTTGTAAATTTT--TGTGTTTTTAAAATTCTCA
* * *** ** * *
42976061 TATTCAAAAATTCTCGTGTTTCACAAATCTTCGTGTTTTTTTAAAAAATTCTCGTGTTTTC-AAA
64 TATTCAAAAATTCTCGTGTTTAAAAAAAAATCGTCCTGTTTT--AAAATTCTCGTGTTCTCAAAA
*
42976125 AAA-TTCTCTTGTTTC
127 AAATTTCTCATGTTTC
*
42976140 AAAAATTCTCGTGTTTTCAAAAATTCTCGAGTTTTGTAAATTTTTGTGTTTTTAAAATTCTCATA
1 AAAAATTCTCGTGTTTTCAAAAATTCTCGTGTTTTGTAAATTTTTGTGTTTTTAAAATTCTCATA
*
42976205 TTTCAAAAAGTT-TCCGTGTTTTAAAAAAAAATC-TCCTGTTTTAAAATTTTCGTGTTCTCAAAA
66 -TTCAAAAA-TTCT-CGTG-TTTAAAAAAAAATCGTCCTGTTTTAAAATTCTCGTGTTCTCAAAA
42976268 AAATTTCTCATGTTTC
127 AAATTTCTCATGTTTC
* * * * *
42976284 AAAAATTGTCGCGTTTTGC--AAATTTTCGTGTTTT-AAGAATTTTTGTGTTTTCAAAA
1 AAAAATTCTCGTGTTTT-CAAAAATTCTCGTGTTTTGTA-AATTTTTGTGTTTTTAAAA
42976340 GTTTCCGTGT
Statistics
Matches: 168, Mismatches: 24, Indels: 17
0.80 0.11 0.08
Matches are distributed among these distances:
142 34 0.20
143 46 0.27
144 78 0.46
145 10 0.06
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (142 bp):
AAAAATTCTCGTGTTTTCAAAAATTCTCGTGTTTTGTAAATTTTTGTGTTTTTAAAATTCTCATA
TTCAAAAATTCTCGTGTTTAAAAAAAAATCGTCCTGTTTTAAAATTCTCGTGTTCTCAAAAAAAT
TTCTCATGTTTC
Found at i:42976267 original size:17 final size:16
Alignment explanation
Indices: 42976241--42976373 Score: 70
Period size: 17 Copynumber: 7.6 Consensus size: 16
42976231 AAAAATCTCC
*
42976241 TGTTTTAAAATTTTCG
1 TGTTTCAAAATTTTCG
*
42976257 TGTTCTCAAAAAAATTTCTCA
1 TGTT-TC---AAAATTT-TCG
*
42976278 TGTTTCAAAAATTGTCG
1 TGTTTC-AAAATTTTCG
*
42976295 CGTTTTGC-AAATTTTCG
1 TG-TTT-CAAAATTTTCG
* *
42976312 TGTTTTAAGAATTTTTG
1 TGTTTCAA-AATTTTCG
*
42976329 TGTTTTCAAAAGTTTCCG
1 TG-TTTCAAAA-TTTTCG
*
42976347 TGTTTCTAAAATTCTCG
1 TGTTTC-AAAATTTTCG
*
42976364 TATTTCAAAA
1 TGTTTCAAAA
42976374 AGTTTCCGTG
Statistics
Matches: 90, Mismatches: 15, Indels: 24
0.70 0.12 0.19
Matches are distributed among these distances:
16 12 0.13
17 37 0.41
18 25 0.28
19 1 0.01
20 9 0.10
21 6 0.07
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (16 bp):
TGTTTCAAAATTTTCG
Found at i:42976282 original size:37 final size:36
Alignment explanation
Indices: 42976193--42976288 Score: 86
Period size: 38 Copynumber: 2.6 Consensus size: 36
42976183 TTGTGTTTTT
* *
42976193 AAAATTCTCATATTTCAAAAAGTTTCCGTGTTTTAAAA
1 AAAATTCTCATGTTT-AAAAAGTTTCCGTG-TTTCAAA
* * * *
42976231 AAAAATCTCCTGTTTTAAAA-TTTTCGTGTTCTCAAA
1 AAAATTCTCATGTTTAAAAAGTTTCCGTGTT-TCAAA
42976267 AAAATTTCTCATGTTTCAAAAA
1 AAAA-TTCTCATGTTT-AAAAA
42976289 TTGTCGCGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
35 2 0.04
36 15 0.33
37 13 0.28
38 16 0.35
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.40
Consensus pattern (36 bp):
AAAATTCTCATGTTTAAAAAGTTTCCGTGTTTCAAA
Found at i:42976288 original size:21 final size:20
Alignment explanation
Indices: 42976247--42976288 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
42976237 CTCCTGTTTT
*
42976247 AAAATTTTCGTGTTCTCAAA
1 AAAATTTTCATGTTCTCAAA
42976267 AAAATTTCTCATGTT-TCAAA
1 AAAATTT-TCATGTTCTCAAA
42976287 AA
1 AA
42976289 TTGTCGCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (20 bp):
AAAATTTTCATGTTCTCAAA
Found at i:42979331 original size:16 final size:16
Alignment explanation
Indices: 42979310--42979343 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42979300 TTTAGAAAAT
*
42979310 AGCAAAATAAAACTAA
1 AGCAAAAGAAAACTAA
*
42979326 AGCAAAAGAAAAGTAA
1 AGCAAAAGAAAACTAA
42979342 AG
1 AG
42979344 GATATCATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.09, G:0.15, T:0.09
Consensus pattern (16 bp):
AGCAAAAGAAAACTAA
Found at i:42980946 original size:51 final size:50
Alignment explanation
Indices: 42980763--42981106 Score: 340
Period size: 51 Copynumber: 6.8 Consensus size: 50
42980753 ATTTTTATCA
* * *
42980763 TTCGATACACGTAGTAGCCTTCACATAGTACTACATACGTGATC--AGTT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * *
42980811 TTACAGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
*
42980861 TTACGGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTT
1 TT-CGG-TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * * * * *
42980913 TTCGGTACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCATAGTT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * * *
42980963 TACCGATACACGTAGTAGCATTCACACAGTACTACACACGTG-CTCAAAGCTT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAG-TT
* * * *
42981015 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
** *
42981065 TATCAATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTG
42981107 TTCATCGACA
Statistics
Matches: 244, Mismatches: 40, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
48 2 0.01
49 38 0.16
50 52 0.21
51 143 0.59
52 9 0.04
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
Found at i:42981004 original size:102 final size:102
Alignment explanation
Indices: 42980765--42981106 Score: 428
Period size: 102 Copynumber: 3.4 Consensus size: 102
42980755 TTTTATCATT
* * * * * *
42980765 CGATACACGTAGTAGCCTTCACATAGTACTACATACGTGATC--AG-TTTTACAGTTCACGTAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAGT
* * *
42980827 AGCCTTCACATAGTACTACACACGTGATCA-AGTTTTAC
65 AGCCTTCACTTAGTACTACACATGTGACCATAG-TTTAC
* * * * * *
42980865 GGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGGTACCCATTGTA
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
*
42980929 GCCTTCACTTAGTACTACACATGTAACCATAGTTTAC
66 GCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
*
42980966 CGATACACGTAGTAGCATTCACACAGTACTACACACGTG-CTCAAAGCTTTTCGGTACACATAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGAC-CAAAGCTTTTCGGTACACATAGT
*
42981030 AGCCTTCACTTAGTACTACACATGTGACCATTA-TTTAT
65 AGCCTTCACTTAGTACTACACATGTGACCA-TAGTTTAC
*
42981068 CAATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
42981107 TTCATCGACA
Statistics
Matches: 212, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
99 36 0.17
100 2 0.01
101 44 0.21
102 128 0.60
103 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
Found at i:42981052 original size:26 final size:26
Alignment explanation
Indices: 42981020--42981102 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
42981010 AGCTTTTCGG
42981020 TACACATAGTAGCCTTCACTTAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
* *
42981046 TACACAT-GT-GACCATT-ATTTA-TCAA
1 TACACATAGTAG-CC-TTCACTTAGT-AC
* **
42981071 TACACGTAGTAGCCTTCACACAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
42981097 TACACA
1 TACACA
42981103 CGTGTTCATC
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 21 0.50
27 2 0.05
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.29
Consensus pattern (26 bp):
TACACATAGTAGCCTTCACTTAGTAC
Found at i:42981085 original size:153 final size:149
Alignment explanation
Indices: 42980767--42981105 Score: 380
Period size: 153 Copynumber: 2.2 Consensus size: 149
42980757 TTATCATTCG
* * * * *
42980767 ATACACGTAGTAGCCTTCACATAGTACTACATACGTGATCAGTTTTACAGTTCACGTAGTAGCCT
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTAACCAGTTTTACAGTACACGTAGTAGCAT
* *
42980832 TCACATAGTACTACACACGTGATCAAGTTTTACGGCTCACGTAGTAGCCTTCACATAGTACTACA
66 TCACACAGTACTACACACGTGATCAAGTTTTACGGCTCACATAGTAGCCTTCACATAGTACTACA
* *
42980897 TACGTGACCAAAGCTTTTCG
131 CACGTGACCAAA-CTTTTCA
* * * * * * *
42980917 GTACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCA-TAGTTTACCGATACACGTAGTAG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTAACCAGT--TTTACAG-TACACGTAGTAG
* *
42980981 CATTCACACAGTACTACACACGTGCTCAAAGCTTTT-CGG-TACACATAGTAGCCTTCACTTAGT
63 CATTCACACAGTACTACACACGTGATC-AAG-TTTTACGGCT-CACATAGTAGCCTTCACATAGT
* *
42981044 ACTACACATGTGACCATTA-TTTATCA
125 ACTACACACGTGACCA-AACTTT-TCA
*
42981070 ATACACGTAGTAGCCTTCACACAGTACTACACACGT
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGT
42981106 GTTCATCGAC
Statistics
Matches: 154, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
149 1 0.01
150 32 0.21
151 6 0.04
152 39 0.25
153 71 0.46
154 5 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (149 bp):
ATACACGTAGTAGCCTTCACATAGTACTACACACGTAACCAGTTTTACAGTACACGTAGTAGCAT
TCACACAGTACTACACACGTGATCAAGTTTTACGGCTCACATAGTAGCCTTCACATAGTACTACA
CACGTGACCAAACTTTTCA
Found at i:42981224 original size:15 final size:17
Alignment explanation
Indices: 42981204--42981236 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42981194 GTTATGAAAC
42981204 ATAACAA-A-AATAATT
1 ATAACAATATAATAATT
42981219 ATAACAATATAATAATT
1 ATAACAATATAATAATT
42981236 A
1 A
42981237 CATACAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAACAATATAATAATT
Found at i:42993246 original size:36 final size:36
Alignment explanation
Indices: 42993205--42993421 Score: 166
Period size: 35 Copynumber: 6.2 Consensus size: 36
42993195 ATACCGACAT
* *
42993205 TTAAAAAAGGTTGGGATAAACTCATCTAAGGCAATC
1 TTAAAAAAGGTTGGGATAAACTCATCTAAGACAACC
* * * *
42993241 TT-AAAAAGGTTGGGATAGACCCGTCTAAGACAAAC
1 TTAAAAAAGGTTGGGATAAACTCATCTAAGACAACC
* * *
42993276 TT-AAAAAGGCTGGGATAAACCTTATCTAAGGCAACC
1 TTAAAAAAGGTTGGGATAAA-CTCATCTAAGACAACC
** *
42993312 TTTAAAAAAATTTGGG------TCGTCTAAGACAACC
1 -TTAAAAAAGGTTGGGATAAACTCATCTAAGACAACC
* *
42993343 TTAAAAAA-GTTGGGATAGACCTTATCTAAGACAACC
1 TTAAAAAAGGTTGGGATA-AACTCATCTAAGACAACC
* * * * *
42993379 TTAAAAAA-GTTAGGATAGACACTTCTAAGGCAACC
1 TTAAAAAAGGTTGGGATAAACTCATCTAAGACAACC
42993414 TTAAAAAA
1 TTAAAAAA
42993422 ATTGGAATAG
Statistics
Matches: 143, Mismatches: 28, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
29 5 0.03
30 8 0.06
31 12 0.08
35 65 0.45
36 42 0.29
37 2 0.01
38 9 0.06
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (36 bp):
TTAAAAAAGGTTGGGATAAACTCATCTAAGACAACC
Found at i:42993347 original size:67 final size:66
Alignment explanation
Indices: 42993262--42993386 Score: 196
Period size: 67 Copynumber: 1.9 Consensus size: 66
42993252 GGGATAGACC
* *
42993262 CGTCTAAGACAAACTTAAAAAGGCTGGGATAAACCTTATCTAAGGCAACCTTTAAAAAAATTTGG
1 CGTCTAAGACAAACTTAAAAAAGCTGGGATAAACCTTATCTAAGACAACC-TTAAAAAAATTTGG
42993327 GT
65 GT
* * *
42993329 CGTCTAAGACAACCTTAAAAAAGTTGGGATAGACCTTATCTAAGACAACCTTAAAAAA
1 CGTCTAAGACAAACTTAAAAAAGCTGGGATAAACCTTATCTAAGACAACCTTAAAAAA
42993387 GTTAGGATAG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
66 8 0.15
67 45 0.85
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (66 bp):
CGTCTAAGACAAACTTAAAAAAGCTGGGATAAACCTTATCTAAGACAACCTTAAAAAAATTTGGG
T
Found at i:42993406 original size:102 final size:101
Alignment explanation
Indices: 42993229--42993424 Score: 261
Period size: 102 Copynumber: 1.9 Consensus size: 101
42993219 GATAAACTCA
* * * * * *
42993229 TCTAAGGCAATCTTAAAAAGGTTGGGATAGACCCGTCTAAGACAAACTTAAAAAGGCTGGGATAA
1 TCTAAGACAACCTTAAAAAAGTTGGGATAGACCCATCTAAGACAAACTTAAAAAAGCTAGGATAA
42993294 ACCTTATCTAAGGCAACCTTTAAAAAAATTTGGGTCG
66 ACCTTATCTAAGGCAACC-TTAAAAAAATTTGGGTCG
* * *
42993331 TCTAAGACAACCTTAAAAAAGTTGGGATAGACCTTATCTAAGACAACCTTAAAAAAGTTAGGATA
1 TCTAAGACAACCTTAAAAAAGTTGGGATAGACC-CATCTAAGACAAACTTAAAAAAGCTAGGATA
*
42993396 GACAC-T-TCTAAGGCAACCTTAAAAAAATT
65 AAC-CTTATCTAAGGCAACCTTAAAAAAATT
42993425 GGAATAGATA
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
101 11 0.13
102 42 0.51
103 28 0.34
104 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (101 bp):
TCTAAGACAACCTTAAAAAAGTTGGGATAGACCCATCTAAGACAAACTTAAAAAAGCTAGGATAA
ACCTTATCTAAGGCAACCTTAAAAAAATTTGGGTCG
Found at i:42993432 original size:35 final size:34
Alignment explanation
Indices: 42993331--42993442 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 34
42993321 ATTTGGGTCG
42993331 TCTAAGACAACCTTAAAAAAGTTGGGATAGAC-CTT
1 TCTAAGACAACCTTAAAAAAGTT-GGATAGACAC-T
42993366 ATCTAAGACAACCTTAAAAAAGTTAGGATAGACACT
1 -TCTAAGACAACCTTAAAAAAGTT-GGATAGACACT
* * * *
42993402 TCTAAGGCAACCTTAAAAAAATTGGAATAGATACG
1 TCTAAGACAACCTTAAAAAAGTTGG-ATAGACACT
42993437 TCTAAG
1 TCTAAG
42993443 GTAATTTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
34 2 0.03
35 34 0.49
36 32 0.46
37 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (34 bp):
TCTAAGACAACCTTAAAAAAGTTGGATAGACACT
Found at i:43000758 original size:62 final size:63
Alignment explanation
Indices: 43000687--43000805 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 63
43000677 AGTAGCCTTC
*
43000687 ACATAGTACTACACACGTAATC-AGTTTTACAGTTCACGTAGTAGCCTTCACATAGTGTGTAA
1 ACATAGTACTACACACGTAATCAAGTTTTACAGCTCACGTAGTAGCCTTCACATAGTGTGTAA
* * *
43000749 ACATAGTACTACACACGTGATCAAGTTTTACGGCTCACTTAGTAGCCTTCACATAGT
1 ACATAGTACTACACACGTAATCAAGTTTTACAGCTCACGTAGTAGCCTTCACATAGT
43000806 ACTACATACG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
62 21 0.40
63 31 0.60
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (63 bp):
ACATAGTACTACACACGTAATCAAGTTTTACAGCTCACGTAGTAGCCTTCACATAGTGTGTAA
Found at i:43000859 original size:51 final size:50
Alignment explanation
Indices: 43000749--43001017 Score: 217
Period size: 51 Copynumber: 5.3 Consensus size: 50
43000739 TAGTGTGTAA
* * *
43000749 ACATAGTACTACACACGTGATC-AAG-TTTTACGGCT-CACTTAGTAGCCTTC
1 ACATAGTACTACACACGTG-CCAAAGCTTTT-C-GATACACATAGTAGCCTTC
* * * *
43000799 ACATAGTACTACATACGTGGCCAAAGCTTTTCGGTACCCATTGTAGCCTTC
1 ACATAGTACTACACACGT-GCCAAAGCTTTTCGATACACATAGTAGCCTTC
* * * * * * *
43000850 ACTTAGTACTACACATGTAACCATAG-TTTACCGATACACGTAGTAGCATTC
1 ACATAGTACTACACACGT-GCCAAAGCTTT-TCGATACACATAGTAGCCTTC
*
43000901 ACACAGTACTACACACGTGCTCAAAGCTTTTCGATACACATAGTAGCCTTC
1 ACATAGTACTACACACGTGC-CAAAGCTTTTCGATACACATAGTAGCCTTC
* * * **
43000952 ACTTAGTACTACACATGTGACCATTA--TTTATCGATACATGTAGTAGCCTTC
1 ACATAGTACTACACACGTG-CCA-AAGCTTT-TCGATACACATAGTAGCCTTC
*
43001003 ACACAGTACTACACA
1 ACATAGTACTACACA
43001018 TGTGTTCATC
Statistics
Matches: 175, Mismatches: 34, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
50 27 0.15
51 139 0.79
52 9 0.05
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (50 bp):
ACATAGTACTACACACGTGCCAAAGCTTTTCGATACACATAGTAGCCTTC
Found at i:43000927 original size:102 final size:102
Alignment explanation
Indices: 43000788--43001017 Score: 347
Period size: 102 Copynumber: 2.3 Consensus size: 102
43000778 ACGGCTCACT
* * * * *
43000788 TAGTAGCCTTCACATAGTACTACATACGTGGCCAAAGCTTTTCGGTACCCATTGTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACACGTGGCCAAAGCTTTTCGATACACATAGTAGCCTTCACT
43000853 TAGTACTACACATGTAACCA-TAGTTTACCGATACACG
66 TAGTACTACACATGTAACCATTA-TTTACCGATACACG
*
43000890 TAGTAGCATTCACACAGTACTACACACGT-GCTCAAAGCTTTTCGATACACATAGTAGCCTTCAC
1 TAGTAGCCTTCACACAGTACTACACACGTGGC-CAAAGCTTTTCGATACACATAGTAGCCTTCAC
* * *
43000954 TTAGTACTACACATGTGACCATTATTTATCGATACATG
65 TTAGTACTACACATGTAACCATTATTTACCGATACACG
43000992 TAGTAGCCTTCACACAGTACTACACA
1 TAGTAGCCTTCACACAGTACTACACA
43001018 TGTGTTCATC
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
101 2 0.02
102 112 0.97
103 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (102 bp):
TAGTAGCCTTCACACAGTACTACACACGTGGCCAAAGCTTTTCGATACACATAGTAGCCTTCACT
TAGTACTACACATGTAACCATTATTTACCGATACACG
Found at i:43001018 original size:51 final size:51
Alignment explanation
Indices: 43000788--43001021 Score: 224
Period size: 51 Copynumber: 4.6 Consensus size: 51
43000778 ACGGCTCACT
* * * * * * * *
43000788 TAGTAGCCTTCACATAGTACTACATACGTGGCCAAAGCTTT-TCGGTACCCA
1 TAGTAGCCTTCACACAGTACTACACATGTGACCATAG-TTTATCGATACACG
* ** * *
43000839 TTGTAGCCTTCACTTAGTACTACACATGTAACCATAGTTTACCGATACACG
1 TAGTAGCCTTCACACAGTACTACACATGTGACCATAGTTTATCGATACACG
* * * *
43000890 TAGTAGCATTCACACAGTACTACACACGTG-CTCAAAGCTTT-TCGATACACA
1 TAGTAGCCTTCACACAGTACTACACATGTGAC-CATAG-TTTATCGATACACG
** *
43000941 TAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCGATACATG
1 TAGTAGCCTTCACACAGTACTACACATGTGACCA-TAGTTTATCGATACACG
43000992 TAGTAGCCTTCACACAGTACTACACATGTG
1 TAGTAGCCTTCACACAGTACTACACATGTG
43001022 TTCATCGACA
Statistics
Matches: 148, Mismatches: 29, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
50 7 0.05
51 136 0.92
52 5 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (51 bp):
TAGTAGCCTTCACACAGTACTACACATGTGACCATAGTTTATCGATACACG
Found at i:43004634 original size:20 final size:18
Alignment explanation
Indices: 43004584--43004635 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
43004574 CTGCAAGATA
43004584 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
43004601 AATATTAAGA-TAATCATTTT
1 AATATTAA-ATTAAT-A-TTT
43004621 AATATTAAATTAATA
1 AATATTAAATTAATA
43004636 AAATACCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:43005111 original size:18 final size:18
Alignment explanation
Indices: 43005088--43005122 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43005078 TATCATATTA
43005088 ATTTTAATTAATTTGATT
1 ATTTTAATTAATTTGATT
* *
43005106 ATTTTATTTTATTTGAT
1 ATTTTAATTAATTTGAT
43005123 CAAAATTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
ATTTTAATTAATTTGATT
Found at i:43010134 original size:50 final size:50
Alignment explanation
Indices: 43010006--43010252 Score: 237
Period size: 50 Copynumber: 4.8 Consensus size: 50
43009996 GATAATAACA
* ** * * *
43010006 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * **
43010055 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
43010105 TGCCCATGCCATGTCCCAGACATGATCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
43010155 TACCCACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
43010211 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
43010253 TTACCCAAAT
Statistics
Matches: 162, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 81 0.50
53 2 0.01
56 39 0.24
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:43019764 original size:23 final size:22
Alignment explanation
Indices: 43019722--43019773 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
43019712 TTTAGGCAGT
43019722 AGAAAAAGAAGAGAAAAAGAAAA
1 AGAAAAAGAAGAGAAAAAG-AAA
* * * *
43019745 AGAAAAAGAGGAGGAGAAGAAG
1 AGAAAAAGAAGAGAAAAAGAAA
43019767 AGAAAAA
1 AGAAAAA
43019774 AATGGAGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
AGAAAAAGAAGAGAAAAAGAAA
Found at i:43020851 original size:21 final size:21
Alignment explanation
Indices: 43020827--43020921 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
43020817 GCAGTTTGTA
* *
43020827 ACTGAGTTGGGGCAGCCTCTT
1 ACTGAGTTGGGGTAGACTCTT
* *
43020848 ACTGAGTTAGGGTAGTCTCTT
1 ACTGAGTTGGGGTAGACTCTT
* * * *
43020869 TCTAATTTGGGGTAGACTATT
1 ACTGAGTTGGGGTAGACTCTT
* * *
43020890 ACTGATTTGGGATAGACTGTT
1 ACTGAGTTGGGGTAGACTCTT
*
43020911 ATTGAGTTGGG
1 ACTGAGTTGGG
43020922 TAACCACTTG
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.37
Consensus pattern (21 bp):
ACTGAGTTGGGGTAGACTCTT
Found at i:43023237 original size:15 final size:15
Alignment explanation
Indices: 43023226--43023288 Score: 72
Period size: 15 Copynumber: 4.2 Consensus size: 15
43023216 ATCCTATTAA
43023226 ACACATCACTATCAG
1 ACACATCACTATCAG
* *
43023241 ACACATCATTAACAG
1 ACACATCACTATCAG
* *
43023256 AGACATCACTATTAG
1 ACACATCACTATCAG
**
43023271 ACACATCAAAATCAG
1 ACACATCACTATCAG
43023286 ACA
1 ACA
43023289 TTTCTTCTTC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.46, C:0.27, G:0.08, T:0.19
Consensus pattern (15 bp):
ACACATCACTATCAG
Found at i:43026181 original size:47 final size:47
Alignment explanation
Indices: 43026009--43026361 Score: 589
Period size: 47 Copynumber: 7.4 Consensus size: 47
43025999 ATTGATGTAC
* * * * *
43026009 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
43026056 AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
43026105 AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
43026154 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
43026201 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
43026248 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
* * *
43026295 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
*
43026342 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
43026362 TCCCGAAGGG
Statistics
Matches: 295, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 203 0.69
49 92 0.31
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
Found at i:43030634 original size:102 final size:103
Alignment explanation
Indices: 43030455--43030657 Score: 327
Period size: 102 Copynumber: 2.0 Consensus size: 103
43030445 AACAATAAAC
* * *
43030455 ATGACATACACAACAGTATATGCAACAAACAATAAACATGACATACACAGCATCATGCACATGGC
1 ATGACATACACAACAGCATATACAACAAACAATAAACATGACATACACAACATCATGCACATGGC
*
43030520 ATACCATGCACAGTATCTACCATTCAC-TTAATAACAA
66 ATACCATACACAGTATCTACCATTCACTTTAATAACAA
* * *
43030557 ATGACATACACAGCAGCATATACAACAAACAATAAATATGACATACACAACATCATGTACATGGC
1 ATGACATACACAACAGCATATACAACAAACAATAAACATGACATACACAACATCATGCACATGGC
*
43030622 ATACCATACACAGTATCTGCCATTCACTTTAATAAC
66 ATACCATACACAGTATCTACCATTCACTTTAATAAC
43030658 TAGACCTTAA
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 84 0.91
103 8 0.09
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (103 bp):
ATGACATACACAACAGCATATACAACAAACAATAAACATGACATACACAACATCATGCACATGGC
ATACCATACACAGTATCTACCATTCACTTTAATAACAA
Found at i:43031040 original size:40 final size:40
Alignment explanation
Indices: 43030982--43031092 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 40
43030972 AGAAAATATC
**
43030982 AATCGATTTCTAACCCTAAA-CCCTATTAATCAATTGTTG
1 AATCGATTTCTAACCCTAAACCCCTATTAATCAATTCCTG
*
43031021 AATTGATTTTCTAACCCTAAACCAACCTTATTAATCAATTCCTG
1 AATCGA-TTTCTAACCCTAAACC--CC-TATTAATCAATTCCTG
* *
43031065 AATCGATTTCTAA-CCGAAATCCCTATTA
1 AATCGATTTCTAACCCTAAACCCCTATTA
43031093 TTTTTTTTGC
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
39 10 0.16
40 16 0.26
41 1 0.02
42 6 0.10
43 9 0.15
44 19 0.31
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.35
Consensus pattern (40 bp):
AATCGATTTCTAACCCTAAACCCCTATTAATCAATTCCTG
Found at i:43031263 original size:21 final size:21
Alignment explanation
Indices: 43031239--43031279 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43031229 CGACATGGTA
*
43031239 AGTTAACTTGTCACATCAGCT
1 AGTTAACTTGCCACATCAGCT
43031260 AGTTAACTTGCCACATCAGC
1 AGTTAACTTGCCACATCAGC
43031280 GGTCTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:43033042 original size:12 final size:11
Alignment explanation
Indices: 43033025--43033049 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43033015 ATTCGATTCG
43033025 AAAAAAAAATT
1 AAAAAAAAATT
43033036 AAAAAAAAATT
1 AAAAAAAAATT
43033047 AAA
1 AAA
43033050 GAGTTACTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:43033306 original size:22 final size:22
Alignment explanation
Indices: 43033257--43033313 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
43033247 TATTTTTTTC
*
43033257 AAAAATTATAAAAATTTCAGAA
1 AAAAATTATAAAAATATCAGAA
*
43033279 AAAAATTATAAAAAGTAT-ATAA
1 AAAAATTATAAAAA-TATCAGAA
*
43033301 AGAAATT-TAAAAA
1 AAAAATTATAAAAA
43033314 ATTAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 23 0.74
23 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAAATTATAAAAATATCAGAA
Found at i:43039240 original size:15 final size:15
Alignment explanation
Indices: 43039220--43039253 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
43039210 GGTAAACTAC
43039220 ACTAGTAGCCACCCA
1 ACTAGTAGCCACCCA
43039235 ACTAGTAGCCACCCA
1 ACTAGTAGCCACCCA
43039250 ACTA
1 ACTA
43039254 TCATGTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (15 bp):
ACTAGTAGCCACCCA
Found at i:43040924 original size:14 final size:14
Alignment explanation
Indices: 43040905--43040932 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43040895 ATTATTAATA
43040905 TTATTAAATTTATT
1 TTATTAAATTTATT
43040919 TTATTAAATTTATT
1 TTATTAAATTTATT
43040933 GATATAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTAAATTTATT
Done.