Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 23 of 259
Found at i:6275080 original size:60 final size:60
Alignment explanation
Indices: 6274985--6275100 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
6274975 CCTCAACAAC
*
6274985 CTGAGTACTGTCAGGAGCTGAATGGGAATCTGAACATA-CAGCAACTGGAGAAGAATCAAT
1 CTGAGTACTGCCAGGAGCTGAATGGGAATCTGAACA-AGCAGCAACTGGAGAAGAATCAAT
* * *
6275045 CTGAGTATTGCCAGGAGCTGAATGGGAAT-TAGAACAAGCATCAGCTGGAGAAGAAT
1 CTGAGTACTGCCAGGAGCTGAATGGGAATCT-GAACAAGCAGCAACTGGAGAAGAAT
6275101 GTGGTGTAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 48 0.96
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (60 bp):
CTGAGTACTGCCAGGAGCTGAATGGGAATCTGAACAAGCAGCAACTGGAGAAGAATCAAT
Found at i:6281427 original size:15 final size:15
Alignment explanation
Indices: 6281415--6281467 Score: 88
Period size: 15 Copynumber: 3.5 Consensus size: 15
6281405 GACTTCATGC
*
6281415 TTTGACTTGTCATCT
1 TTTGATTTGTCATCT
*
6281430 TTTGATTTGTCGTCT
1 TTTGATTTGTCATCT
6281445 TTTGATTTGTCATCT
1 TTTGATTTGTCATCT
6281460 TTTGATTT
1 TTTGATTT
6281468 TTTGCCATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.11, C:0.13, G:0.15, T:0.60
Consensus pattern (15 bp):
TTTGATTTGTCATCT
Found at i:6294591 original size:27 final size:26
Alignment explanation
Indices: 6294554--6294668 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
6294544 AGCATGGCTG
* *
6294554 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
6294580 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
6294608 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
6294635 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
6294662 CCAGAAC
1 CCAGAAC
6294669 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:6294613 original size:54 final size:54
Alignment explanation
Indices: 6294554--6294668 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
6294544 AGCATGGCTG
*
6294554 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
6294608 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
6294662 CCAGAAC
1 CCAGAAC
6294669 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:6296311 original size:26 final size:26
Alignment explanation
Indices: 6296275--6296384 Score: 161
Period size: 26 Copynumber: 4.2 Consensus size: 26
6296265 CATGAAATTC
6296275 TTATCATGAAACATTTACCTAACAC-A
1 TTATCATGAAACATTTACCTAAC-CTA
*
6296301 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
6296327 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
6296353 TTATCATTG-AACAATTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCTA
6296379 TTATCA
1 TTATCA
6296385 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
25 1 0.01
26 76 0.96
27 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:6300000 original size:25 final size:25
Alignment explanation
Indices: 6299965--6300026 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
6299955 ATTTTTGTCT
* *
6299965 TTTTTGTTCACCCAACTATCTTGGA
1 TTTTTGGTCACCAAACTATCTTGGA
6299990 TTTTTGGTCACCAAACTATCTTGGA
1 TTTTTGGTCACCAAACTATCTTGGA
6300015 TTTTTGGTCACC
1 TTTTTGGTCACC
6300027 TATAACCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.44
Consensus pattern (25 bp):
TTTTTGGTCACCAAACTATCTTGGA
Found at i:6300328 original size:6 final size:6
Alignment explanation
Indices: 6300317--6300345 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
6300307 AGTTATTCTA
6300317 AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
6300346 ATAGCTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:6308685 original size:40 final size:40
Alignment explanation
Indices: 6308641--6308826 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
6308631 GCTACTCGTT
* * *
6308641 CAAATGCCTTCGGGACATAGCCCAG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
6308681 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
6308721 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
6308761 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
6308802 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
6308827 CATCATTCAA
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 116 0.88
41 13 0.10
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:6311600 original size:32 final size:32
Alignment explanation
Indices: 6311559--6311624 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
6311549 ATCAATTAAC
6311559 ATTATTTTATTCTCAATTTATCATATAACACA
1 ATTATTTTATTCTCAATTTATCATATAACACA
6311591 ATTATTTTATTCTCAATTTATCATATAACACA
1 ATTATTTTATTCTCAATTTATCATATAACACA
6311623 AT
1 AT
6311625 ATGCTTCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (32 bp):
ATTATTTTATTCTCAATTTATCATATAACACA
Found at i:6314415 original size:13 final size:14
Alignment explanation
Indices: 6314397--6314474 Score: 58
Period size: 13 Copynumber: 5.9 Consensus size: 14
6314387 GAAAAAAATT
*
6314397 TTATAT-GAATTAG
1 TTATATGGAAATAG
*
6314410 TTATATGGAAATAA
1 TTATATGGAAATAG
* *
6314424 ATATATGG-AATGG
1 TTATATGGAAATAG
*
6314437 TTATAT-G-AATCGG
1 TTATATGGAAAT-AG
6314450 TTATATGGAAATAG
1 TTATATGGAAATAG
*
6314464 ATATAT-GAAAT
1 TTATATGGAAAT
6314475 GGAACATTGG
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
12 4 0.08
13 27 0.51
14 19 0.36
15 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATATGGAAATAG
Found at i:6314453 original size:40 final size:40
Alignment explanation
Indices: 6314397--6314476 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
6314387 GAAAAAAATT
* *
6314397 TTATATGAATTAGTTATATGGAAATAAATATATGGAATGG
1 TTATATGAATCAGTTATATGGAAATAAATATATGAAATGG
* *
6314437 TTATATGAATCGGTTATATGGAAATAGATATATGAAATGG
1 TTATATGAATCAGTTATATGGAAATAAATATATGAAATGG
6314477 AACATTGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.36
Consensus pattern (40 bp):
TTATATGAATCAGTTATATGGAAATAAATATATGAAATGG
Found at i:6319764 original size:7 final size:7
Alignment explanation
Indices: 6319747--6319789 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
6319737 TTCAAACTAC
6319747 TTTTTATT
1 TTTTTA-T
6319755 TTTTTATT
1 TTTTTA-T
6319763 TTTTTAT
1 TTTTTAT
*
6319770 TTTTTAA
1 TTTTTAT
6319777 TTTTTAT
1 TTTTTAT
6319784 TTTTTA
1 TTTTTA
6319790 GCAGATCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
7 19 0.58
8 14 0.42
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTAT
Found at i:6319788 original size:8 final size:8
Alignment explanation
Indices: 6319747--6319781 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
6319737 TTCAAACTAC
6319747 TTTTTATT
1 TTTTTATT
6319755 TTTTTATT
1 TTTTTATT
6319763 TTTTTATT
1 TTTTTATT
*
6319771 TTTTAATT
1 TTTTTATT
6319779 TTT
1 TTT
6319782 ATTTTTTAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTATT
Found at i:6326700 original size:7 final size:8
Alignment explanation
Indices: 6326681--6326723 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 8
6326671 TGCAAATGGT
6326681 AATTTTTAA
1 AATTTTT-A
6326690 TAATTTTTAA
1 -AATTTTT-A
6326700 TAATTTTTA
1 -AATTTTTA
6326709 AATTTTTA
1 AATTTTTA
6326717 AATTTTT
1 AATTTTT
6326724 TTTAATAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 15 0.45
9 1 0.03
10 17 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
AATTTTTA
Found at i:6326705 original size:20 final size:18
Alignment explanation
Indices: 6326680--6326717 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
6326670 TTGCAAATGG
6326680 TAATTTTTAATAATTTTTAA
1 TAATTTTT-A-AATTTTTAA
6326700 TAATTTTTAAATTTTTAA
1 TAATTTTTAAATTTTTAA
6326718 ATTTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATTTTTAAATTTTTAA
Found at i:6326723 original size:8 final size:10
Alignment explanation
Indices: 6326680--6326717 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
6326670 TTGCAAATGG
6326680 TAATTTTTAA
1 TAATTTTTAA
6326690 TAATTTTTAA
1 TAATTTTTAA
6326700 TAATTTTT-A
1 TAATTTTTAA
6326709 -AATTTTTAA
1 TAATTTTTAA
6326718 ATTTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 7 0.26
9 2 0.07
10 18 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:6331461 original size:15 final size:15
Alignment explanation
Indices: 6331441--6331514 Score: 121
Period size: 15 Copynumber: 4.9 Consensus size: 15
6331431 CAATGGCGAA
6331441 AAATCAAAAGATGAC
1 AAATCAAAAGATGAC
6331456 AAATCAAAAGATGAC
1 AAATCAAAAGATGAC
*
6331471 AAATCAAAAGACGAC
1 AAATCAAAAGATGAC
6331486 AAATCAAAAGATGAC
1 AAATCAAAAGATGAC
* *
6331501 AAGTCAAAACATGA
1 AAATCAAAAGATGA
6331515 AGTCGGAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.59, C:0.15, G:0.14, T:0.12
Consensus pattern (15 bp):
AAATCAAAAGATGAC
Found at i:6336333 original size:10 final size:10
Alignment explanation
Indices: 6336306--6336345 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
6336296 TTAAATTCTA
6336306 AAAGATAAAT
1 AAAGATAAAT
6336316 ACAA-ATAAAT
1 A-AAGATAAAT
*
6336326 AAAGATAATT
1 AAAGATAAAT
6336336 AAAGATAAAT
1 AAAGATAAAT
6336346 GAGGATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:6338082 original size:40 final size:39
Alignment explanation
Indices: 6338014--6338091 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 39
6338004 ATATAGACAC
*
6338014 TTCATATAATCATTTCGTATATCTATTTCCACATAATCAA
1 TTCATATAACCATTTCGTATATCTATTT-CACATAATCAA
*
6338054 TTCATATAACCATTTCATGTA-ATC-ATTTCATATAATCA
1 TTCATATAACCATTTC--GTATATCTATTTCACATAATCA
6338092 TTCTGTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 9 0.26
40 19 0.56
41 3 0.09
42 3 0.09
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (39 bp):
TTCATATAACCATTTCGTATATCTATTTCACATAATCAA
Found at i:6338089 original size:13 final size:13
Alignment explanation
Indices: 6337990--6338155 Score: 110
Period size: 13 Copynumber: 12.7 Consensus size: 13
6337980 TGTCCATATC
6337990 CATATAAAT-ATTT
1 CATAT-AATCATTT
*
6338003 CATATAGA-CACTT
1 CATATA-ATCATTT
6338016 CATATAATCATTT
1 CATATAATCATTT
*
6338029 CGTAT-ATCTATTT
1 CATATAATC-ATTT
* *
6338042 CCACATAATCAATT
1 -CATATAATCATTT
*
6338056 CATATAACCATTT
1 CATATAATCATTT
*
6338069 CATGTAATCATTT
1 CATATAATCATTT
6338082 CATATAATCA-TT
1 CATATAATCATTT
* *
6338094 CTGTATAA-CTATTC
1 C-ATATAATC-ATTT
* * *
6338108 CATCTAAACACTT
1 CATATAATCATTT
*
6338121 CATAT-TTCCATTT
1 CATATAAT-CATTT
*
6338134 CATGTAATCATTT
1 CATATAATCATTT
6338147 CATATAATC
1 CATATAATC
6338156 CTTCTGTATA
Statistics
Matches: 116, Mismatches: 25, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
12 9 0.08
13 94 0.81
14 10 0.09
15 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.42
Consensus pattern (13 bp):
CATATAATCATTT
Found at i:6338139 original size:65 final size:65
Alignment explanation
Indices: 6338014--6338201 Score: 240
Period size: 65 Copynumber: 2.9 Consensus size: 65
6338004 ATATAGACAC
* * **
6338014 TTCATATAATCATT-TCGTATATCTATTTCCA-CATAATCAATTCATATAACCATTTCATGTAAT
1 TTCATATAATCATTCT-GTATAACTA-TTCCATC-TAAACAATTCATATTTCCATTTCATGTAAT
6338077 CAT
63 CAT
*
6338080 TTCATATAATCATTCTGTATAACTATTCCATCTAAACACTTCATATTTCCATTTCATGTAATCAT
1 TTCATATAATCATTCTGTATAACTATTCCATCTAAACAATTCATATTTCCATTTCATGTAATCAT
* *
6338145 TTCATATAATCCTTCTGTATAACCATTCCATCTAAA-AATTTCAT-TTTACCATTTCAT
1 TTCATATAATCATTCTGTATAACTATTCCATCTAAACAA-TTCATATTT-CCATTTCAT
6338202 TTACACATTT
Statistics
Matches: 110, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
64 4 0.04
65 82 0.75
66 23 0.21
67 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (65 bp):
TTCATATAATCATTCTGTATAACTATTCCATCTAAACAATTCATATTTCCATTTCATGTAATCAT
Found at i:6341752 original size:37 final size:37
Alignment explanation
Indices: 6341702--6341781 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
6341692 CTTATTACGA
* *
6341702 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
6341739 AGTCTTACCCGGACAAAATTCCCACACGTAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
6341776 GGTCTT
1 AGTCTT
6341782 TAGAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:6341971 original size:47 final size:47
Alignment explanation
Indices: 6341912--6342847 Score: 1584
Period size: 47 Copynumber: 20.1 Consensus size: 47
6341902 TATCACATTT
* * * *
6341912 ATACAC-T-TTCACATTCATCACATCGGCCATTAGGCCTTATCTCAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
6341957 ATACACATGCTCACATTCATCACATTGGCCACTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
6342004 ATACACCTGTTCACTTTCATCACATTGGCCATTCGGCTTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
6342051 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
6342098 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
6342145 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
6342192 ATACACATGTTCAC-TTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
6342238 ATACACATGTTCACTTTCATCACATTGGCCATTCGG-CTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
6342284 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
6342331 ATATACATGTTCACTTTCATCACATTGGCCATTC-G-CTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
6342376 AT--ACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
6342421 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
6342468 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
6342515 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
6342562 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
6342609 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
6342656 ATATACATGTTCACTTTCATCACATTGGTCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
6342703 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
** *
6342750 ATATGCATGTTTACATTT-ATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCAC-TTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
6342797 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCCTATTCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTA-TCACAC
6342845 ATA
1 ATA
6342848 TACACTTTCA
Statistics
Matches: 847, Mismatches: 33, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
43 30 0.04
44 1 0.00
45 30 0.04
46 96 0.11
47 679 0.80
48 11 0.01
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.33
Consensus pattern (47 bp):
ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
Found at i:6342398 original size:21 final size:21
Alignment explanation
Indices: 6342333--6342398 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
6342323 TATCACACAT
6342333 ATACATGTTCACTTTCATCAC
1 ATACATGTTCACTTTCATCAC
* *
6342354 ATTGGCCA--TTCGCTTATCA-CAC
1 A-T--ACATGTTCACTT-TCATCAC
6342376 ATACATGTTCACTTTCATCAC
1 ATACATGTTCACTTTCATCAC
6342397 AT
1 AT
6342399 TGGCCATTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 13 0.38
22 11 0.32
23 3 0.09
24 2 0.06
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.36
Consensus pattern (21 bp):
ATACATGTTCACTTTCATCAC
Found at i:6344463 original size:13 final size:13
Alignment explanation
Indices: 6344445--6344469 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6344435 TACTAAATTT
6344445 TCATGGATTCAAG
1 TCATGGATTCAAG
6344458 TCATGGATTCAA
1 TCATGGATTCAA
6344470 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:6347050 original size:27 final size:27
Alignment explanation
Indices: 6347020--6347074 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
6347010 CAATTTTGAG
6347020 ATGTTTTCCCCCATTGTTATGAACTAA
1 ATGTTTTCCCCCATTGTTATGAACTAA
*
6347047 ATGTTTTCCCCCATTTTTATGAACTAA
1 ATGTTTTCCCCCATTGTTATGAACTAA
6347074 A
1 A
6347075 ATCCTTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (27 bp):
ATGTTTTCCCCCATTGTTATGAACTAA
Found at i:6358378 original size:26 final size:24
Alignment explanation
Indices: 6358334--6358383 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
6358324 ATTTGTTTTA
*
6358334 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
6358358 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
6358384 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:6371199 original size:26 final size:26
Alignment explanation
Indices: 6371168--6371275 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
6371158 TGAAATGCCC
*
6371168 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
6371194 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
6371220 ATTATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
6371246 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
6371272 ATCA
1 ATCA
6371276 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:6378291 original size:26 final size:26
Alignment explanation
Indices: 6378260--6378367 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
6378250 TGAAATGCCC
*
6378260 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
6378286 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
6378312 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
6378338 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
6378364 ATCA
1 ATCA
6378368 ATTTGTACCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:6384853 original size:81 final size:82
Alignment explanation
Indices: 6384760--6384930 Score: 308
Period size: 81 Copynumber: 2.1 Consensus size: 82
6384750 TATGTCCATC
* *
6384760 AGCATAAGGTACATATAGCATATTACATGTAATTGTTTGGTTAATCATGTCAATTTTAATAATAA
1 AGCATAAAGTACATATAGCATATTACATGTAATTGTTTAGTTAATCATGTCAATTTTAATAATAA
6384825 AATTAGATGAA-TTTTT
66 AATTAGATGAATTTTTT
6384841 AGCATAAAGTACATATAGCATATTACATGTAATTGTTTAGTTAATCATGTCAATTTTAATAATAA
1 AGCATAAAGTACATATAGCATATTACATGTAATTGTTTAGTTAATCATGTCAATTTTAATAATAA
6384906 AATTAGATGAATTTTTT
66 AATTAGATGAATTTTTT
*
6384923 AACATAAA
1 AGCATAAA
6384931 ATATCAGTTT
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
81 74 0.86
82 12 0.14
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.40
Consensus pattern (82 bp):
AGCATAAAGTACATATAGCATATTACATGTAATTGTTTAGTTAATCATGTCAATTTTAATAATAA
AATTAGATGAATTTTTT
Found at i:6390953 original size:24 final size:24
Alignment explanation
Indices: 6390926--6390985 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
6390916 ATTGTCACTA
6390926 TGAAATATCAAGTTCTTAGCTATT
1 TGAAATATCAAGTTCTTAGCTATT
6390950 TGAAATATCAAGTTCTTAGCTATT
1 TGAAATATCAAGTTCTTAGCTATT
*
6390974 TGAAGTAT-AAGT
1 TGAAATATCAAGT
6390986 GATGTATTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (24 bp):
TGAAATATCAAGTTCTTAGCTATT
Found at i:6392794 original size:16 final size:16
Alignment explanation
Indices: 6392773--6392820 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
6392763 CTGGCAATAG
6392773 TGAGGCTACTCTTCCC
1 TGAGGCTACTCTTCCC
*
6392789 TGAGGCTA----T-AC
1 TGAGGCTACTCTTCCC
6392800 TGAGGCTACTCTTCCC
1 TGAGGCTACTCTTCCC
6392816 TGAGG
1 TGAGG
6392821 ACCCTGACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
15 1 0.04
16 14 0.56
ACGTcount: A:0.17, C:0.29, G:0.25, T:0.29
Consensus pattern (16 bp):
TGAGGCTACTCTTCCC
Found at i:6396463 original size:20 final size:23
Alignment explanation
Indices: 6396438--6396486 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
6396428 ATATAAAATA
6396438 TTAAAATAA-ATA-AAT-ATTTT
1 TTAAAATAATATATAATGATTTT
*
6396458 TTAAAA-AATATATATTGATTTT
1 TTAAAATAATATATAATGATTTT
6396480 TTAAAAT
1 TTAAAAT
6396487 TATTTGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 9 0.38
21 2 0.08
22 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAAATAATATATAATGATTTT
Found at i:6399123 original size:9 final size:9
Alignment explanation
Indices: 6399108--6399178 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
6399098 AATAATTTTT
6399108 AAAATTTAA
1 AAAATTTAA
* *
6399117 AATATTTAT
1 AAAATTTAA
*
6399126 AAAATTAAA
1 AAAATTTAA
*
6399135 AAAATCTAA
1 AAAATTTAA
*
6399144 AATATATATAA
1 AA-A-ATTTAA
6399155 AAAAGTTT-A
1 AAAA-TTTAA
6399164 AAAA-TTAA
1 AAAATTTAA
6399172 AAAATTT
1 AAAATTT
6399179 TCTAGAATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 30 0.62
10 4 0.08
11 7 0.15
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (9 bp):
AAAATTTAA
Found at i:6399136 original size:18 final size:19
Alignment explanation
Indices: 6399091--6399174 Score: 61
Period size: 18 Copynumber: 4.5 Consensus size: 19
6399081 TTTACGAAAT
* *
6399091 AATTCAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
*
6399110 AATTTAAAAT-ATTTATAA
1 AATTAAAAATAATTTATAA
*
6399128 AATTAAAAA-AATCTA-AA
1 AATTAAAAATAATTTATAA
6399145 ATATATATAAAA-AAGTTTA-AA
1 A-AT-TA-AAAATAA-TTTATAA
6399166 AATTAAAAA
1 AATTAAAAA
6399175 ATTTTCTAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
17 3 0.05
18 25 0.45
19 13 0.24
20 8 0.15
21 6 0.11
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:6401621 original size:32 final size:32
Alignment explanation
Indices: 6401585--6401646 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
6401575 TTTGTATGTG
6401585 TATTTAAAATATTTCACATAT-AAACATAATGA
1 TATTTAAAATATTTCACATATGAAA-ATAATGA
*
6401617 TATTTAAAATATTTTACATATGAAAATAAT
1 TATTTAAAATATTTCACATATGAAAATAAT
6401647 AATTGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (32 bp):
TATTTAAAATATTTCACATATGAAAATAATGA
Found at i:6402004 original size:95 final size:95
Alignment explanation
Indices: 6401835--6402006 Score: 210
Period size: 95 Copynumber: 1.8 Consensus size: 95
6401825 ATAATTATTA
* * ** *
6401835 ATTTATTTATATAAATAAAAGAGTTATTAATTTTAAATATCTTAAAATAATTATTTATATAATAT
1 ATTTATTTATATAAATAAAAGAGTTATTAATTTAAAATATATTAAAATAAAAATTTATATAACAT
*
6401900 ATATTTTTATTATATAATTACATATTTAAT
66 ATATATTTATTATATAATTACATATTTAAT
6401930 ATTTGATTT-TATAAATAAAAGAGTTATTAA-TTAAAATATGAATTAAAAATTAAAAATTTA-A-
1 ATTT-ATTTATATAAATAAAAGAGTTATTAATTTAAAATAT--ATT-AAAA-TAAAAATTTATAT
6401991 AACA-ATATATTTATTA
61 AACATATATATTTATTA
6402007 ATTAAAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
94 8 0.12
95 36 0.55
96 9 0.14
97 5 0.08
98 8 0.12
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (95 bp):
ATTTATTTATATAAATAAAAGAGTTATTAATTTAAAATATATTAAAATAAAAATTTATATAACAT
ATATATTTATTATATAATTACATATTTAAT
Found at i:6403507 original size:108 final size:109
Alignment explanation
Indices: 6403309--6403511 Score: 302
Period size: 108 Copynumber: 1.9 Consensus size: 109
6403299 ATAAGGTCCT
* * *
6403309 TCGGGGCGACACCTCAAGGAGGTTTAAGGTGTAAGACATAGCTCGACTTTGGCAACCAATAGAGT
1 TCGGGGCGACACCTCAAGGAGGTTTAAGGTGTAAGACATAGCTCGACTATGACAACCAACAGAGT
*
6403374 CCGCCAGGACATTAAACATGAGGTTATATTAAGCAAGACCATAG
66 CCACCAGGACATTAAACATGAGGTTATATTAAGCAAGACCATAG
* *
6403418 TCGGGG-GACACCTCAATGAGGTTTAAGGTGTCAA-ACATAGCTCGACTATGACAACCAACAGTG
1 TCGGGGCGACACCTCAAGGAGGTTTAAGGTGT-AAGACATAGCTCGACTATGACAACCAACAGAG
* * *
6403481 TCCACCAGGACCTTAAATATGGGGTTATATT
65 TCCACCAGGACATTAAACATGAGGTTATATT
6403512 GTTTAAGAGC
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 76 0.90
109 8 0.10
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (109 bp):
TCGGGGCGACACCTCAAGGAGGTTTAAGGTGTAAGACATAGCTCGACTATGACAACCAACAGAGT
CCACCAGGACATTAAACATGAGGTTATATTAAGCAAGACCATAG
Found at i:6405299 original size:6 final size:6
Alignment explanation
Indices: 6405288--6405371 Score: 86
Period size: 6 Copynumber: 14.2 Consensus size: 6
6405278 ATGTTACAAG
* *
6405288 GAAAAA GAAAAAA GAAAAA -AAAAG GAAAAA G-AAAA -AAAAT GAAAAA
1 GAAAAA G-AAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
*
6405334 TGAAAAA TGAAAAA G-AAAA TAAAAA GAAAAA GAAAAA G
1 -GAAAAA -GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
6405372 CTGCAAATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
5 15 0.23
6 32 0.48
7 19 0.29
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:6405311 original size:17 final size:17
Alignment explanation
Indices: 6405289--6405370 Score: 85
Period size: 17 Copynumber: 4.6 Consensus size: 17
6405279 TGTTACAAGG
6405289 AAAAAGAAAAAAGAAAA
1 AAAAAGAAAAAAGAAAA
*
6405306 AAAAAGGAAAAAGAAAA
1 AAAAAGAAAAAAGAAAA
* *
6405323 AAAATGAAAAATGAAAAA
1 AAAAAGAAAAAAG-AAAA
*
6405341 TGAAAAAGAAAATAA-AAAG
1 --AAAAAGAAAA-AAGAAAA
6405360 AAAAAGAAAAA
1 AAAAAGAAAAA
6405371 GCTGCAAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
16 1 0.02
17 36 0.67
18 4 0.07
19 3 0.06
20 9 0.17
21 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAAAAGAAAA
Found at i:6408067 original size:17 final size:19
Alignment explanation
Indices: 6408025--6408070 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
6408015 TAAATAGTTC
6408025 TTTAGATTTTATATAAATT
1 TTTAGATTTTATATAAATT
*
6408044 TTT--ATTTT-T-TAATTT
1 TTTAGATTTTATATAAATT
6408059 TTTAGATTTTAT
1 TTTAGATTTTAT
6408071 TCAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 10 0.43
18 1 0.04
19 3 0.13
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTAGATTTTATATAAATT
Found at i:6413932 original size:16 final size:16
Alignment explanation
Indices: 6413911--6413954 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
6413901 GAGTTGTTGC
6413911 TGGTTTTGTTTTGTTT
1 TGGTTTTGTTTTGTTT
*
6413927 TGGTTTT-TTTTTTTT
1 TGGTTTTGTTTTGTTT
6413942 TGAGGTTTTGTTT
1 T--GGTTTTGTTT
6413955 AAGCATTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.33
16 7 0.29
17 6 0.25
18 3 0.12
ACGTcount: A:0.02, C:0.00, G:0.23, T:0.75
Consensus pattern (16 bp):
TGGTTTTGTTTTGTTT
Found at i:6413934 original size:17 final size:17
Alignment explanation
Indices: 6413912--6413954 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
6413902 AGTTGTTGCT
6413912 GGTTTTGTTTTGTTTT--
1 GGTTTTGTTTT-TTTTGA
*
6413928 GGTTTTTTTTTTTTTGA
1 GGTTTTGTTTTTTTTGA
6413945 GGTTTTGTTT
1 GGTTTTGTTT
6413955 AAGCATTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 9 0.39
ACGTcount: A:0.02, C:0.00, G:0.23, T:0.74
Consensus pattern (17 bp):
GGTTTTGTTTTTTTTGA
Found at i:6423416 original size:21 final size:22
Alignment explanation
Indices: 6423376--6423417 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6423366 TTTTAATCCG
6423376 TTAATTATAAAAGATTTTCAAT
1 TTAATTATAAAAGATTTTCAAT
*
6423398 TTAATTATTAAAG-TTTTCAA
1 TTAATTATAAAAGATTTTCAA
6423418 AATATTAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (22 bp):
TTAATTATAAAAGATTTTCAAT
Found at i:6429715 original size:26 final size:28
Alignment explanation
Indices: 6429686--6429765 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
6429676 ATGATGCACA
*
6429686 AAAAAATTTAAAA-A-ATGATATATATG
1 AAAAAATTTAAAATAGATAATATATATG
*
6429712 AAAAATTTTAAAATAGATAATATATAT-
1 AAAAAATTTAAAATAGATAATATATATG
* * * *
6429739 ATAATAGTGTAAAATAAATAATATATA
1 A-AAAAATTTAAAATAGATAATATATA
6429766 AAAAACCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 12 0.27
27 2 0.04
28 31 0.69
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (28 bp):
AAAAAATTTAAAATAGATAATATATATG
Found at i:6430081 original size:26 final size:26
Alignment explanation
Indices: 6430023--6430125 Score: 93
Period size: 26 Copynumber: 3.9 Consensus size: 26
6430013 GTATAAAAGC
*
6430023 TTAAAATAAATAATATGTGGAAAAAGAACT
1 TTAAAATAAATAATATAT--AAAAAG-A-T
*
6430053 TTAAAATAAATAATATATAAAAAGTT
1 TTAAAATAAATAATATATAAAAAGAT
** * *
6430079 TTAACGTGAATAATATATAAAAA-AC
1 TTAAAATAAATAATATATAAAAAGAT
*
6430104 TTAAAATGAATAATA-ATAAAAA
1 TTAAAATAAATAATATATAAAAA
6430126 AAATAGTTCT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.11
25 13 0.20
26 21 0.33
28 6 0.09
30 17 0.27
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAAAGAT
Found at i:6430127 original size:25 final size:25
Alignment explanation
Indices: 6430043--6430127 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
6430033 TAATATGTGG
*
6430043 AAAAAGAACTTTAAAATAAATAATATAT
1 AAAAA-AAC-TTAAAATGAATAATA-AT
*** **
6430071 AAAAAGTTTTAACGTGAATAAT-AT
1 AAAAAAACTTAAAATGAATAATAAT
6430095 ATAAAAAACTTAAAATGAATAATAAT
1 A-AAAAAACTTAAAATGAATAATAAT
6430121 AAAAAAA
1 AAAAAAA
6430128 ATAGTTCTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
24 3 0.07
25 22 0.50
26 14 0.32
28 5 0.11
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.27
Consensus pattern (25 bp):
AAAAAAACTTAAAATGAATAATAAT
Found at i:6434616 original size:20 final size:20
Alignment explanation
Indices: 6434579--6434616 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6434569 TGATGGGGAG
*
6434579 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
6434599 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
6434617 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:6436565 original size:46 final size:46
Alignment explanation
Indices: 6436513--6436694 Score: 249
Period size: 46 Copynumber: 4.0 Consensus size: 46
6436503 AGTGTGCTCT
*
6436513 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
6436559 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
6436605 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
6436651 ATGACA-GAAAATGGGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
6436695 TCATGTCAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 121 0.99
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:6437507 original size:20 final size:20
Alignment explanation
Indices: 6437458--6437509 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
6437448 TGGGTAGGGG
** *
6437458 ACACGGGCGCATCCCGAAGC
1 ACACGGGCGTGTCCCCAAGC
6437478 ACACGGGCGTGTCCCCAAGC
1 ACACGGGCGTGTCCCCAAGC
6437498 ACACGGGCGTGT
1 ACACGGGCGTGT
6437510 GCTATGTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.21, C:0.37, G:0.33, T:0.10
Consensus pattern (20 bp):
ACACGGGCGTGTCCCCAAGC
Found at i:6437527 original size:23 final size:23
Alignment explanation
Indices: 6437497--6437556 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
6437487 TGTCCCCAAG
6437497 CACACGGGCGTGTGCTATGTCTT
1 CACACGGGCGTGTGCTATGTCTT
6437520 CACACGGGCGTGTGCTATGTCTT
1 CACACGGGCGTGTGCTATGTCTT
6437543 CACACGGGCGTGTG
1 CACACGGGCGTGTG
6437557 AGACACTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (23 bp):
CACACGGGCGTGTGCTATGTCTT
Found at i:6441354 original size:68 final size:69
Alignment explanation
Indices: 6441279--6441413 Score: 159
Period size: 70 Copynumber: 2.0 Consensus size: 69
6441269 TACCAAAATA
* *
6441279 TATAACTTTTATAAAATAT-AAGTACATAATTAG-ACC-AAAAATAATAAAAGTACCACATTAAA
1 TATAACTTTTATAAAATATGAA-TAC-TAATTAGAACCAAAAAATAACAAAAATACCACATTAAA
6441341 AAAGTG
64 AAAGTG
* * * * *
6441347 TATAACTTTTGTCAAATATGAATACTTATTTGAACCAAAAAAATAACAAAAATATCACATTAAAA
1 TATAACTTTTATAAAATATGAATACTAATTAGAACC-AAAAAATAACAAAAATACCACATTAAAA
6441412 AA
65 AA
6441414 TGTCAAACTC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
67 5 0.09
68 23 0.41
69 2 0.04
70 26 0.46
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (69 bp):
TATAACTTTTATAAAATATGAATACTAATTAGAACCAAAAAATAACAAAAATACCACATTAAAAA
AGTG
Found at i:6441973 original size:10 final size:10
Alignment explanation
Indices: 6441955--6441988 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
6441945 AATTTGTAAT
*
6441955 TTTTTTATAA
1 TTTTATATAA
6441965 TTTTATATAA
1 TTTTATATAA
6441975 TTTTATA-AA
1 TTTTATATAA
6441984 TTTTA
1 TTTTA
6441989 AATTGTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATATAA
Found at i:6451755 original size:26 final size:26
Alignment explanation
Indices: 6451719--6451770 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6451709 GTGATGTAGG
6451719 AGTTTGATTGCATTTTACCTTCTCTA
1 AGTTTGATTGCATTTTACCTTCTCTA
6451745 AGTTTGATTGCATTTTACCTTCTCTA
1 AGTTTGATTGCATTTTACCTTCTCTA
6451771 CTTAGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (26 bp):
AGTTTGATTGCATTTTACCTTCTCTA
Found at i:6452056 original size:10 final size:11
Alignment explanation
Indices: 6452041--6452085 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
6452031 TATATATTTG
6452041 AATTA-TAAGA
1 AATTATTAAGA
6452051 AATTATTAA-A
1 AATTATTAAGA
*
6452061 AAATATTAAG-
1 AATTATTAAGA
6452071 AATTA-TAAGA
1 AATTATTAAGA
6452081 AATTA
1 AATTA
6452086 ATAAAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 4 0.13
10 23 0.77
11 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (11 bp):
AATTATTAAGA
Found at i:6453405 original size:17 final size:17
Alignment explanation
Indices: 6453351--6453406 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
6453341 TTCATAATTG
* *
6453351 TAATTATATTGTATTTA
1 TAATTATACTATATTTA
* * *
6453368 TAACTATACGATACTTA
1 TAATTATACTATATTTA
*
6453385 TAATTATACTATATTTG
1 TAATTATACTATATTTA
6453402 TAATT
1 TAATT
6453407 GCAAATCTTT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (17 bp):
TAATTATACTATATTTA
Found at i:6454085 original size:30 final size:30
Alignment explanation
Indices: 6454028--6454086 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
6454018 GTAGTAATTA
* *
6454028 GTACTTAAATTATACTTCATTACTTAAATG
1 GTACTTAAACTATACTACATTACTTAAATG
* *
6454058 GTACTTAAACTATACTACGTTATTTAAAT
1 GTACTTAAACTATACTACATTACTTAAAT
6454087 TATTCTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (30 bp):
GTACTTAAACTATACTACATTACTTAAATG
Found at i:6454622 original size:25 final size:24
Alignment explanation
Indices: 6454558--6454619 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
6454548 ATTGAAATAG
* *
6454558 TTTAATTT-ATTTACATTTTATTTT
1 TTTAATTTAATTTA-ATTCTATTCT
*
6454582 TTATAATTCAATTTAATTCTATTCT
1 TT-TAATTTAATTTAATTCTATTCT
6454607 TTTAATTTAATTT
1 TTTAATTTAATTT
6454620 TAACTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 12 0.38
25 15 0.47
26 5 0.16
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTAATTTAATTTAATTCTATTCT
Found at i:6458756 original size:40 final size:40
Alignment explanation
Indices: 6458691--6458898 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
6458681 GGGCATGAAA
* * * ** *
6458691 GTGCATTCAGGCGTACCGAATTACAAACATCGGCACATAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* * * *
6458731 GTGCAATCAGGGGTACTGAAGTACAAATAGGGGAACATAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* ** * * * *
6458771 GTGCAATTAGGACTACCAAAGTAAAAATAGGGGCATGTAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* ** *
6458811 GTGTAATCAGGGGTACTAAAGTATAAACAGGGGCACGTAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* *
6458851 GTGCAATTAGGGGTACCGAAGTACAAA-AGGGACACGTAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
6458890 GTGCAATCA
1 GTGCAATCA
6458899 TACAATAATT
Statistics
Matches: 136, Mismatches: 32, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
39 19 0.14
40 117 0.86
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (40 bp):
GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
Found at i:6458781 original size:20 final size:20
Alignment explanation
Indices: 6458725--6458781 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
6458715 AAACATCGGC
* *
6458725 ACATATGTGCAATCAGGGGT
1 ACATATGTGCAATTAGGGGA
* * *
6458745 AC-TGAAGTACAAATAGGGGA
1 ACAT-ATGTGCAATTAGGGGA
6458765 ACATATGTGCAATTAGG
1 ACATATGTGCAATTAGG
6458782 ACTACCAAAG
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.23
Consensus pattern (20 bp):
ACATATGTGCAATTAGGGGA
Found at i:6458833 original size:80 final size:79
Alignment explanation
Indices: 6458728--6458898 Score: 225
Period size: 80 Copynumber: 2.2 Consensus size: 79
6458718 CATCGGCACA
* *
6458728 TATGTGCAATCAGGGGTACTGAAGTACAAATAGGGGAACATATGTGCAATTAGGACTACCAAAGT
1 TATGTGCAATCAGGGGTACTAAAGTACAAACAGGGGAACATATGTGCAATTAGGACTACCAAAGT
* *
6458793 AAAAATAGGGGCATG
66 AAAAA-AGGGACACG
* * * * ** *
6458808 TATGTGTAATCAGGGGTACTAAAGTATAAACAGGGGCACGTATGTGCAATTAGGGGTACCGAAGT
1 TATGTGCAATCAGGGGTACTAAAGTACAAACAGGGGAACATATGTGCAATTAGGACTACCAAAGT
*
6458873 ACAAAAGGGACACG
66 AAAAAAGGGACACG
6458887 TATGTGCAATCA
1 TATGTGCAATCA
6458899 TACAATAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 18 0.23
80 60 0.77
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (79 bp):
TATGTGCAATCAGGGGTACTAAAGTACAAACAGGGGAACATATGTGCAATTAGGACTACCAAAGT
AAAAAAGGGACACG
Found at i:6465889 original size:40 final size:39
Alignment explanation
Indices: 6465845--6466049 Score: 169
Period size: 40 Copynumber: 5.1 Consensus size: 39
6465835 ATGTTTGTAT
* *
6465845 AATCAAGAGTACCGAAGTACAAACATGGGAACATATGTGC
1 AATCAAGGGTACCGAAGTACAAACA-GGGAACGTATGTGC
* * * * *
6465885 AATC-AGTGGTACTGAAGTATAAACAGGGGCACGCATATGC
1 AATCAAG-GGTACCGAAGTACAAACA-GGGAACGTATGTGC
* * * * * *
6465925 AATCAGGGGCACTGAAGTAGAAACAGGAGCACGTGTGTGC
1 AATCAAGGGTACCGAAGTACAAACAGG-GAACGTATGTGC
* *
6465965 AATCAAGGGAACCGAAGTACAAACAGGGACACGTATGTAC
1 AATCAAGGGTACCGAAGTACAAACAGGGA-ACGTATGTGC
* * * * *
6466005 AACCAGGGGTATCGAAGTATAAATAGGGACACGTATGTGC
1 AATCAAGGGTACCGAAGTACAAACAGGGA-ACGTATGTGC
6466045 AATCA
1 AATCA
6466050 TACAATAATT
Statistics
Matches: 132, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
39 5 0.04
40 126 0.95
41 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (39 bp):
AATCAAGGGTACCGAAGTACAAACAGGGAACGTATGTGC
Found at i:6465942 original size:80 final size:78
Alignment explanation
Indices: 6465857--6466049 Score: 190
Period size: 80 Copynumber: 2.4 Consensus size: 78
6465847 TCAAGAGTAC
* * * * *
6465857 CGAAGTACAAACATGGGAACATATGTGCAATCAGTGGTACTGAAGTATAAACAGGGGCACGCATA
1 CGAAGTACAAACA-GGGAACGTATGTGCAATCAG-GGAACCGAAGTACAAACAGGGACACGCATA
* *
6465922 TGCAATCAGGGGCA-
64 TACAACCAGGGGCAT
* * * *
6465936 CTGAAGTAGAAACAGGAGCACGTGTGTGCAATCAAGGGAACCGAAGTACAAACAGGGACACGTAT
1 C-GAAGTACAAACAGG-GAACGTATGTGCAATC-AGGGAACCGAAGTACAAACAGGGACACGCAT
* *
6466001 GTACAACCAGGGGTAT
63 ATACAACCAGGGGCAT
* *
6466017 CGAAGTATAAATAGGGACACGTATGTGCAATCA
1 CGAAGTACAAACAGGGA-ACGTATGTGCAATCA
6466050 TACAATAATT
Statistics
Matches: 92, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
79 5 0.05
80 84 0.91
81 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (78 bp):
CGAAGTACAAACAGGGAACGTATGTGCAATCAGGGAACCGAAGTACAAACAGGGACACGCATATA
CAACCAGGGGCAT
Found at i:6465951 original size:20 final size:20
Alignment explanation
Indices: 6465895--6465956 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
6465885 AATCAGTGGT
*
6465895 ACTGAAGTATAAACAGGGGC
1 ACTGAAGTAGAAACAGGGGC
* *
6465915 AC-GCA-TATGCAATCAGGGGC
1 ACTGAAGTA-G-AAACAGGGGC
*
6465935 ACTGAAGTAGAAACAGGAGC
1 ACTGAAGTAGAAACAGGGGC
6465955 AC
1 AC
6465957 GTGTGTGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 23 0.72
21 3 0.09
22 2 0.06
ACGTcount: A:0.39, C:0.19, G:0.29, T:0.13
Consensus pattern (20 bp):
ACTGAAGTAGAAACAGGGGC
Found at i:6468096 original size:18 final size:18
Alignment explanation
Indices: 6468058--6468101 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6468048 TTTTTATTTT
6468058 TTAAATATTAATATAATTA
1 TTAAAT-TTAATATAATTA
*
6468077 TTTAATTTAATATTAA-TA
1 TTAAATTTAATA-TAATTA
6468095 TTAAATT
1 TTAAATT
6468102 ATTTTTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAATTTAATATAATTA
Found at i:6472163 original size:33 final size:35
Alignment explanation
Indices: 6472126--6472196 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
6472116 ACTACTTTTT
* *
6472126 TGTCACTG-TACTGAGATGGGATAAGGCCCAA-AC
1 TGTCACTGATACTGAAAAGGGATAAGGCCCAAGAC
* *
6472159 TGTCACTGATACTGAAAAGGGCTTAGGCCCAAGAC
1 TGTCACTGATACTGAAAAGGGATAAGGCCCAAGAC
6472194 TGT
1 TGT
6472197 TCAACTGTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 8 0.25
34 19 0.59
35 5 0.16
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (35 bp):
TGTCACTGATACTGAAAAGGGATAAGGCCCAAGAC
Found at i:6475777 original size:14 final size:15
Alignment explanation
Indices: 6475760--6475788 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6475750 AATTTTAATT
6475760 AAATAA-ATTATTAA
1 AAATAAGATTATTAA
6475774 AAATAAGATTATTAA
1 AAATAAGATTATTAA
6475789 CATCAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAATAAGATTATTAA
Found at i:6481679 original size:19 final size:18
Alignment explanation
Indices: 6481639--6481681 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
6481629 TTTTTGTTAC
**
6481639 ATATCTTATTTTTTTATTT
1 ATAT-TTATTTTTTTAAAT
6481658 ATATTTATATTTTTTAAAT
1 ATATTTAT-TTTTTTAAAT
6481677 ATATT
1 ATATT
6481682 CTAAGATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTTATTTTTTTAAAT
Found at i:6484003 original size:3 final size:3
Alignment explanation
Indices: 6483995--6484032 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6483985 CATGGACAAA
6483995 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6484033 CTTGTACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6485269 original size:24 final size:23
Alignment explanation
Indices: 6485202--6485269 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
6485192 TTTTAAATAT
* *
6485202 ATATAAAATATTGATAAATATCAA
1 ATATAAAATA-TAATAAATTTCAA
6485226 ATAATAAAAT-TAAATAAATTTCAA
1 AT-ATAAAATAT-AATAAATTTCAA
*
6485250 ATATAAAATAGTAATCAATT
1 ATATAAAATA-TAATAAATT
6485270 ATATAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 8 0.22
24 21 0.57
25 8 0.22
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATAAAATATAATAAATTTCAA
Found at i:6491634 original size:19 final size:19
Alignment explanation
Indices: 6491610--6491649 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
6491600 TTTACTCACA
6491610 AACTATTCAAATTCAACTC
1 AACTATTCAAATTCAACTC
*
6491629 AACTATTCGAATTCAACTC
1 AACTATTCAAATTCAACTC
6491648 AA
1 AA
6491650 ATCATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (19 bp):
AACTATTCAAATTCAACTC
Found at i:6492913 original size:3 final size:3
Alignment explanation
Indices: 6492907--6492938 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6492897 AATTATTAAA
6492907 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
6492939 AATTGAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6494320 original size:38 final size:38
Alignment explanation
Indices: 6494277--6494352 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
6494267 GTTATTATTA
*
6494277 TTTTTTAATTCATTAATAAATTACCTAATTTTAGTTTT
1 TTTTTTAATTCATTAATAAATTACCTAATTTTAATTTT
6494315 TTTTTTAATTCATTAATAAATTACCTAATTTTAATTTT
1 TTTTTTAATTCATTAATAAATTACCTAATTTTAATTTT
6494353 AATTGTAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.58
Consensus pattern (38 bp):
TTTTTTAATTCATTAATAAATTACCTAATTTTAATTTT
Found at i:6499349 original size:25 final size:26
Alignment explanation
Indices: 6499310--6499370 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
6499300 GTATAATTAG
6499310 AATATATATATTTAAAAAATTATAAA
1 AATATATATATTTAAAAAATTATAAA
* *
6499336 AATATAT-TATTTAATAAATTTTAAA
1 AATATATATATTTAAAAAATTATAAA
*
6499361 AATAAATATA
1 AATATATATA
6499371 GAAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 22 0.71
26 9 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATATATATATTTAAAAAATTATAAA
Found at i:6500849 original size:104 final size:104
Alignment explanation
Indices: 6500715--6501139 Score: 586
Period size: 104 Copynumber: 4.1 Consensus size: 104
6500705 GAATCTTAGT
* * * *
6500715 AAAATCAACTATGAACGTAGGTTAGCGAGCTGTTAGGAGTTGCGATATTAAATTAACGAACTCAA
1 AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCAA
* *
6500780 ATAATCGGAGGCTACAATCTTAAATCAGCTAGCCTTAAG
66 ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
* * * * * *
6500819 AAAATCAGCTATGAACGTAGGTCAGTGAGCTGTGAGGAGTTGCGATATTAAATTAGCTAACTCAA
1 AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCAA
*
6500884 ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTT-TG
66 ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
* * *
6500922 TAACATCAACTGTGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAAATCA
1 -AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCA
*
6500987 AATAATCGGAGGCTGCGATCTTAAATCACCTAG-CTTAA-
65 AATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
* * * * *
6501025 AACATTAACTATGAACGTAGGTCAGCGAGCTATTAAGAGTTGCGATCTTAAATCAACCAACTCAA
1 AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCAA
* * *
6501090 ATAATCGAAGGCTGCGATCTTAAATTAGCTAGCCTTAAT
66 ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
*
6501129 AACATCAACTA
1 AAAATCAACTA
6501140 CAAGTTCAAA
Statistics
Matches: 287, Mismatches: 30, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
102 88 0.31
103 9 0.03
104 190 0.66
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (104 bp):
AAAATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTAACTCAA
ATAATCGGAGGCTGCGATCTTAAATCAGCTAGCCTTAAG
Found at i:6501134 original size:206 final size:208
Alignment explanation
Indices: 6500709--6501139 Score: 623
Period size: 206 Copynumber: 2.1 Consensus size: 208
6500699 ATCAGTGAAT
* * * *
6500709 CTTAGTAAAATCAACTATGAACGTAGGTTAGCGAGCTGTTAGGAGTTGCGATATTAAATTAACGA
1 CTTAGTAACATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACGA
* * *
6500774 ACTCAAATAATCGGAGGCTACAATCTTAAATCAGCTAGCCTTAAGAAAATCAGCTATGAACGTAG
66 AATCAAATAATCGGAGGCTACAATCTTAAATCACCTAGCCTTAAGAAAATCAACTATGAACGTAG
* * * * * * *
6500839 GTCAGTGAGCTGTGAGGAGTTGCGATATTAAATTAGCTAACTCAAATAATCGGAGGCTGCGATCT
131 GTCAGCGAGCTATGAAGAGTTGCGATATTAAATCAACCAACTCAAATAATCGAAGGCTGCGATCT
6500904 TAAATCAGCTAGC
196 TAAATCAGCTAGC
* * *
6500917 CTTTGTAACATCAACTGTGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACTA
1 CTTAGTAACATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACGA
* * * *
6500982 AATCAAATAATCGGAGGCTGCGATCTTAAATCACCTAG-CTTAA-AACATTAACTATGAACGTAG
66 AATCAAATAATCGGAGGCTACAATCTTAAATCACCTAGCCTTAAGAAAATCAACTATGAACGTAG
* *
6501045 GTCAGCGAGCTATTAAGAGTTGCGATCTTAAATCAACCAACTCAAATAATCGAAGGCTGCGATCT
131 GTCAGCGAGCTATGAAGAGTTGCGATATTAAATCAACCAACTCAAATAATCGAAGGCTGCGATCT
*
6501110 TAAATTAGCTAGC
196 TAAATCAGCTAGC
*
6501123 CTTAATAACATCAACTA
1 CTTAGTAACATCAACTA
6501140 CAAGTTCAAA
Statistics
Matches: 196, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
206 99 0.51
207 5 0.03
208 92 0.47
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (208 bp):
CTTAGTAACATCAACTATGAACGTAGGTCAGCGAGCTATTAGGAGTTGCGATATTAAATCAACGA
AATCAAATAATCGGAGGCTACAATCTTAAATCACCTAGCCTTAAGAAAATCAACTATGAACGTAG
GTCAGCGAGCTATGAAGAGTTGCGATATTAAATCAACCAACTCAAATAATCGAAGGCTGCGATCT
TAAATCAGCTAGC
Found at i:6503010 original size:31 final size:30
Alignment explanation
Indices: 6502975--6503047 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
6502965 ATAAAAGTGA
6502975 TATTTGAATTTCTCTATTT-TTCTTAGATTGG
1 TATTTGAATTTCTCT-TTTGTT-TTAGATTGG
*
6503006 TATTT-AAGGTTTTTCTTTTGTTTTAGATTGG
1 TATTTGAA--TTTCTCTTTTGTTTTAGATTGG
*
6503037 TACTTGAATTT
1 TATTTGAATTT
6503048 TTATTCATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
30 5 0.14
31 21 0.58
32 10 0.28
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (30 bp):
TATTTGAATTTCTCTTTTGTTTTAGATTGG
Found at i:6503199 original size:15 final size:15
Alignment explanation
Indices: 6503181--6503209 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6503171 TAATTATCAT
6503181 AATTTAATTTTTTTA
1 AATTTAATTTTTTTA
6503196 AATTTAATTTTTTT
1 AATTTAATTTTTTT
6503210 GAAAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
AATTTAATTTTTTTA
Found at i:6509989 original size:6 final size:6
Alignment explanation
Indices: 6509978--6510052 Score: 77
Period size: 6 Copynumber: 12.7 Consensus size: 6
6509968 CCAATCTTTC
* *
6509978 TTTTTA TTTTTA TTTTTA TTTTTA TTTATTA -TTTT- TCTTTC TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA
6510025 TTTATTA TTTATTA -TTTTA -TTTTA TTTT
1 TTT-TTA TTT-TTA TTTTTA TTTTTA TTTT
6510053 AGTTAAATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
5 13 0.21
6 35 0.57
7 13 0.21
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:6509994 original size:7 final size:7
Alignment explanation
Indices: 6509978--6510042 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
6509968 CCAATCTTTC
6509978 TTTTTA-
1 TTTTTAT
6509984 TTTTTA-
1 TTTTTAT
6509990 TTTTTA-
1 TTTTTAT
6509996 TTTTTAT
1 TTTTTAT
*
6510003 TTATTAT
1 TTTTTAT
*
6510010 TTTTCTTT
1 TTTT-TAT
6510018 CTTTTTAT
1 -TTTTTAT
*
6510026 TTATTAT
1 TTTTTAT
*
6510033 TTATTAT
1 TTTTTAT
6510040 TTT
1 TTT
6510043 ATTTTATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
6 18 0.36
7 24 0.48
8 4 0.08
9 4 0.08
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTAT
Found at i:6510007 original size:10 final size:10
Alignment explanation
Indices: 6509986--6510052 Score: 61
Period size: 10 Copynumber: 6.8 Consensus size: 10
6509976 TCTTTTTATT
6509986 TTTATTTTTA
1 TTTATTTTTA
6509996 TTT-TTATTTA
1 TTTATT-TTTA
*
6510006 -TTATTTTTC
1 TTTATTTTTA
*
6510015 TTTCTTTTTA
1 TTTATTTTTA
6510025 TTTATTATTTA
1 TTTATT-TTTA
6510036 -TTA-TTTTA
1 TTTATTTTTA
6510044 TTTTATTTT
1 -TTTATTTT
6510053 AGTTAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
8 4 0.09
9 8 0.17
10 27 0.59
11 7 0.15
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:6510186 original size:20 final size:20
Alignment explanation
Indices: 6510161--6510202 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6510151 ATCCATGGTA
* *
6510161 CCAAACAGTTCTATTCCAGC
1 CCAAACAATCCTATTCCAGC
6510181 CCAAACAATCCTATTCCAGC
1 CCAAACAATCCTATTCCAGC
6510201 CC
1 CC
6510203 TAGAATCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.40, G:0.07, T:0.21
Consensus pattern (20 bp):
CCAAACAATCCTATTCCAGC
Found at i:6511190 original size:118 final size:118
Alignment explanation
Indices: 6510979--6511208 Score: 361
Period size: 118 Copynumber: 1.9 Consensus size: 118
6510969 TGTTTCCATT
* * *
6510979 GTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTC
1 GTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGCAGGGTGCTTGGGTTGTCATTC
*
6511044 TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGAG
66 TACTTCGCGTCAAAAGGTTGTGTAACGTGACAAGTAAAACTCCGCTAGCCGAG
* *
6511097 GTTATGAGTATAGCTCAAATCGTGACTGACTGAGTAACTGGGGCAGGGTGCTTGGGTTGTCATTC
1 GTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGCAGGGTGCTTGGGTTGTCATTC
* ****
6511162 TACTTCGCGTCAAAAGTTTGTGTAACGTGTTGGGTAAAACTCCGCTA
66 TACTTCGCGTCAAAAGGTTGTGTAACGTGACAAGTAAAACTCCGCTA
6511209 ACCGGAAATA
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
118 101 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (118 bp):
GTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGCAGGGTGCTTGGGTTGTCATTC
TACTTCGCGTCAAAAGGTTGTGTAACGTGACAAGTAAAACTCCGCTAGCCGAG
Found at i:6511972 original size:27 final size:28
Alignment explanation
Indices: 6511942--6511994 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
6511932 ATTTTATTTT
6511942 ATATTAGGA-TAATTAATATTAAGATAA
1 ATATTAGGATTAATTAATATTAAGATAA
* *
6511969 ATATTAGGATTATTTAATTTTAAGAT
1 ATATTAGGATTAATTAATATTAAGAT
6511995 TTTATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.43
Consensus pattern (28 bp):
ATATTAGGATTAATTAATATTAAGATAA
Found at i:6514713 original size:45 final size:45
Alignment explanation
Indices: 6514631--6514760 Score: 134
Period size: 45 Copynumber: 2.9 Consensus size: 45
6514621 ACCAGGAGTG
* * * * * *
6514631 AGTAAGACCATAGCTGAAACATACTATGCCATAATGATGATAATA
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
* * *
6514676 AGTAAGACCATAGCTGAAAGATGCTACGATATCATGATAAAAATG
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
* * * * *
6514721 AGTAAGACAATAGTTGAAAGACGCTATGGCATAATGATAA
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAA
6514761 GGGTGAGTAA
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
Found at i:6515812 original size:17 final size:17
Alignment explanation
Indices: 6515785--6515828 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
6515775 TCTGATACCA
* *
6515785 ATGGCGGATACCTATCT
1 ATGGCGAATACCTATCC
*
6515802 ATGGTGAATACCTATCC
1 ATGGCGAATACCTATCC
6515819 ATGGCGAATA
1 ATGGCGAATA
6515829 GTTTTTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (17 bp):
ATGGCGAATACCTATCC
Found at i:6523861 original size:129 final size:126
Alignment explanation
Indices: 6523609--6523937 Score: 385
Period size: 130 Copynumber: 2.6 Consensus size: 126
6523599 TTTTAAAATG
* ** * * * * *
6523609 ATATTCGATTGTTTGGTCAAACGGTAAATCGAAACCCAGCACG-TAGGGCACGTTTTCTCGGATT
1 ATATTCGATTATTTGAACAAACGGGAAATTGAAACCCAGCACGATAGGGCACGATTTCCCGAATT
* * *
6523673 CCCAAACATTGAACATTGCCTTGTTTTAGAATTTAGAAAACATGAGTGAAATTCTAAAGGA
66 TCCAAACATTGAACATTACCTTGTTTTAGAATTTAGAAAACATGAGTGAAATTCCAAAGGA
*
6523734 ATATTCGATTATTTGAACAAACGGGAAATTGTAACCCAGCACGATAGGGCACGATTTCCCGAATT
1 ATATTCGATTATTTGAACAAACGGGAAATTGAAACCCAGCACGATAGGGCACGATTTCCCGAATT
* ** *
6523799 TCCAAAC-TTCGAACGTTACCTTCGTTTTAAAGAATTTTTAAAACATGTGTGAAATTCCAAAGGA
66 TCCAAACATT-GAACATTACCTT-GTTTT--AGAATTTAGAAAACATGAGTGAAATTCCAAAGGA
* * * * *
6523863 ATATTCGATCATTTTGAACAAACGAGAAATTGCAACCCAGTACGACAGGGCACGA-TTCCTCGAA
1 ATATTCGATTA-TTTGAACAAACGGGAAATTGAAACCCAGCACGATAGGGCACGATTTCC-CGAA
*
6523927 TTTCTAAACAT
64 TTTCCAAACAT
6523938 CAAACATCGT
Statistics
Matches: 174, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
125 39 0.22
126 34 0.20
127 5 0.03
129 44 0.25
130 51 0.29
131 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (126 bp):
ATATTCGATTATTTGAACAAACGGGAAATTGAAACCCAGCACGATAGGGCACGATTTCCCGAATT
TCCAAACATTGAACATTACCTTGTTTTAGAATTTAGAAAACATGAGTGAAATTCCAAAGGA
Found at i:6524387 original size:24 final size:20
Alignment explanation
Indices: 6524344--6524392 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 20
6524334 TTAAAATCAT
6524344 TAATATAAAAGATAACAAAA
1 TAATATAAAAGATAACAAAA
6524364 TAATATAAATAGAATAACTTAAAA
1 TAATATAAA-AG-ATAAC--AAAA
6524388 TAATA
1 TAATA
6524393 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.36
21 2 0.08
22 5 0.20
24 9 0.36
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
TAATATAAAAGATAACAAAA
Found at i:6526485 original size:35 final size:33
Alignment explanation
Indices: 6526433--6526501 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 33
6526423 TTTTAACCTT
*
6526433 AAAAAAAATTTAGAACACCCAAAAATTTAAAGC
1 AAAAAAAATTTAAAACACCCAAAAATTTAAAGC
*
6526466 AAAAAAAACTTTTAAAACACTCAAAAATTTAAAGC
1 AAAAAAAA--TTTAAAACACCCAAAAATTTAAAGC
6526501 A
1 A
6526502 TCACCCTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 8 0.25
35 24 0.75
ACGTcount: A:0.61, C:0.14, G:0.04, T:0.20
Consensus pattern (33 bp):
AAAAAAAATTTAAAACACCCAAAAATTTAAAGC
Found at i:6531231 original size:42 final size:43
Alignment explanation
Indices: 6531133--6531238 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
6531123 AAATTTTAGC
* *
6531133 CTGTTACCCTACTGCTTAGGGAGTTAAGGCGTGTATCTTTAAT
1 CTGTTACCCTATTGCTTAGGGAGATAAGGCGTGTATCTTTAAT
* *
6531176 CTGCT-CCACTATTGCTTAGGGAGATAAGATC-TGTA-CTTTATAT
1 CTGTTACC-CTATTGCTTAGGGAGATAAG-GCGTGTATCTTTA-AT
6531219 -TGTTACCCTATTGCTTAGGG
1 CTGTTACCCTATTGCTTAGGG
6531239 GGTTAAAGCC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
42 23 0.43
43 30 0.56
44 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (43 bp):
CTGTTACCCTATTGCTTAGGGAGATAAGGCGTGTATCTTTAAT
Found at i:6531332 original size:85 final size:85
Alignment explanation
Indices: 6530269--6531329 Score: 1443
Period size: 85 Copynumber: 12.5 Consensus size: 85
6530259 AAGCTAAGAC
* *
6530269 CTGT-AATTTTAGCCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGACCTGCTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
* *
6530333 ACTGCTCGGAGAG-CCAGGAT
66 ACTACTCGGCGAGCCCA-GAT
* * * *** * * * * *
6530353 CTGTAAATTTTAGCCTGCT-CCATTCTTGCTTAGTAAAGATAAGGCTAGTCTTCAACTTGCTCCG
1 CTGTAAATTTTAGCCTGTTACCCTAC-TGCTTAG-GGGGTTAAGGCAAGTCTTCGACCTGCTCCA
** *
6530417 CCACTGTTCGGCGAGCCTAGAT
64 CCACTACTCGGCGAGCCCAGAT
*
6530439 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAATCTTCGACCTGCTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
6530504 ACTACTCGGCGAGCCCAGAT
66 ACTACTCGGCGAGCCCAGAT
* * *
6530524 CTGTAAATTTTAGCCTGTTACCCTACTGTTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCTACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
*
6530589 ACTACTCGGCGAGCCCAAAT
66 ACTACTCGGCGAGCCCAGAT
* * *
6530609 CTGTAAATTTTAGCCTGTTACCCTATTGCTTAGGGGGTTAAGGCAAGTCTTCGATCTACTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
* *
6530674 ACTGCTCCGCGAGCCCAGAT
66 ACTACTCGGCGAGCCCAGAT
* * * *
6530694 CTGTAAATTTTAGCCTATTACCCTACTACTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCGCC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
6530759 ACTACTCGGCGAGCCCAGAT
66 ACTACTCGGCGAGCCCAGAT
*
6530779 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCCGCTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
*
6530844 ACTACTCGACGAGCCCAGAT
66 ACTACTCGGCGAGCCCAGAT
* * *
6530864 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACGAGTCTTTGACCTGCTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
*
6530929 ACTACTCGGCAAGCCCAGAT
66 ACTACTCGGCGAGCCCAGAT
6530949 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
6531014 ACTACTCGGCGAGCCCAGAT
66 ACTACTCGGCGAGCCCAGAT
* **
6531034 CTGTAAATTTTAGCCTGTTACCTTACTATTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
6531099 ACTACTCGGCGAGCCCAGAT
66 ACTACTCGGCGAGCCCAGAT
* ** ** *
6531119 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCGTGTATCTTTAATCTGCTCCA
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAG--TCTTCGACCTGCTCCA
* * * * ***
6531184 CTATTGCTTAGG-GAGATAAGAT
64 CCACTAC-TCGGCGAGCCCAGAT
* * * * **
6531206 CTGT-ACTTTATA--TTGTTACCCTATTGCTTAGGGGGTTAAAGCCTGTCTTCGACCTGCTCCAC
1 CTGTAAATTT-TAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCAC
* *
6531268 CACTGCTCGACGAGCCCAGAT
65 CACTACTCGGCGAGCCCAGAT
*
6531289 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGAGTTAA
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAA
6531330 AGCTTGCTGA
Statistics
Matches: 856, Mismatches: 108, Indels: 25
0.87 0.11 0.03
Matches are distributed among these distances:
82 2 0.00
83 31 0.04
84 12 0.01
85 706 0.82
86 66 0.08
87 36 0.04
88 3 0.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (85 bp):
CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
ACTACTCGGCGAGCCCAGAT
Found at i:6539130 original size:21 final size:21
Alignment explanation
Indices: 6539104--6539148 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
6539094 GCTGGCTCAT
*
6539104 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
*
6539125 CATGTTTTTCTGGGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
6539146 CAT
1 CAT
6539149 TTGATCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:6544041 original size:35 final size:35
Alignment explanation
Indices: 6543995--6544065 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
6543985 TTTTAACCTT
*
6543995 AAAAAAAACTTTTAGAACACCCAAAAATTTAAAGC
1 AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
*
6544030 AAAAAAAACTTTTAAAACACTCAAAAATTTAAAGC
1 AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
6544065 A
1 A
6544066 TCACCCTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.59, C:0.15, G:0.04, T:0.21
Consensus pattern (35 bp):
AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
Found at i:6545041 original size:3 final size:3
Alignment explanation
Indices: 6545030--6545163 Score: 91
Period size: 3 Copynumber: 44.7 Consensus size: 3
6545020 TGATGATAGC
* * *
6545030 AAT AGT AAT AAT -AT AAT AAT AA- AGT AGAA AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * * * *
6545074 AAT ACGTT AAT AAG AAT AAT AAT AGT -AT ATT AAT AAT AAC AAT AAT
1 AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
6545120 AGA- AAGT AAT GAT AA- AAT AAT AAAT AAT AAT AAT AAT AA- AAT AA
1 A-AT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
6545164 AGAATAGTGC
Statistics
Matches: 101, Mismatches: 18, Indels: 24
0.71 0.13 0.17
Matches are distributed among these distances:
2 9 0.09
3 83 0.82
4 7 0.07
5 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:6545085 original size:23 final size:21
Alignment explanation
Indices: 6545030--6545247 Score: 108
Period size: 21 Copynumber: 10.0 Consensus size: 21
6545020 TGATGATAGC
6545030 AATAGTAATAAT-ATAATAAT
1 AATAGTAATAATAATAATAAT
*
6545050 AAAGTAGAAAATAATAATAATAAT
1 -AA-TAG-TAATAATAATAATAAT
*
6545074 AATACGTTAATAAGAATAATAAT
1 AATA-G-TAATAATAATAATAAT
* *
6545097 AGTATATTAATAATAACAATAAT
1 A--ATAGTAATAATAATAATAAT
* *
6545120 AGAAAGTAATGATAA-AATAAT
1 A-ATAGTAATAATAATAATAAT
*
6545141 AAATAATAATAATAATAA-AAT
1 -AATAGTAATAATAATAATAAT
* *
6545162 AA-AG-AATAGTGCCAACAATAACAT
1 AATAGTAATAAT---AATAAT-A-AT
*
6545186 AAATAGTAATAGA-AA-AACAAT
1 -AATAGTAATA-ATAATAATAAT
* * *
6545207 AATAGAAACAGTAATAATAAT
1 AATAGTAATAATAATAATAAT
* *
6545228 AAAAGTAATAGTAATAATAA
1 AATAGTAATAATAATAATAA
6545248 ATGATTAAAA
Statistics
Matches: 151, Mismatches: 26, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
18 5 0.03
19 1 0.01
20 12 0.08
21 49 0.32
22 19 0.13
23 42 0.28
24 12 0.08
25 5 0.03
26 2 0.01
27 4 0.03
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (21 bp):
AATAGTAATAATAATAATAAT
Found at i:6545086 original size:20 final size:20
Alignment explanation
Indices: 6545060--6545157 Score: 85
Period size: 20 Copynumber: 4.9 Consensus size: 20
6545050 AAAGTAGAAA
6545060 ATAATAATAATAATAATACGT
1 ATAATAATAATAATAATA-GT
*
6545081 -TAATAAGAATAATAATAGT
1 ATAATAATAATAATAATAGT
* * *
6545100 ATATTAATAATAACAATAAT
1 ATAATAATAATAATAATAGT
* * *
6545120 AGAAAGTAATGATAA-AATAAT
1 A-TAA-TAATAATAATAATAGT
6545141 A-AATAATAATAATAATA
1 ATAATAATAATAATAATA
6545158 AAATAAAGAA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
18 8 0.12
19 8 0.12
20 32 0.50
21 8 0.12
22 8 0.12
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (20 bp):
ATAATAATAATAATAATAGT
Found at i:6555012 original size:24 final size:21
Alignment explanation
Indices: 6554985--6555031 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
6554975 CCCTTATGTT
6554985 CTTTCTCTATACTATTTCTCATCA
1 CTTTCTCT-TA-T-TTTCTCATCA
*
6555009 CTTTCTCTTATTTTCTCTTCA
1 CTTTCTCTTATTTTCTCATCA
6555030 CT
1 CT
6555032 AACATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 1 0.05
23 2 0.09
24 8 0.36
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.55
Consensus pattern (21 bp):
CTTTCTCTTATTTTCTCATCA
Found at i:6555460 original size:8 final size:8
Alignment explanation
Indices: 6555447--6555471 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6555437 ATATAGACTA
6555447 AATAAAAT
1 AATAAAAT
6555455 AATAAAAT
1 AATAAAAT
6555463 AATAAAAT
1 AATAAAAT
6555471 A
1 A
6555472 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:6555491 original size:29 final size:30
Alignment explanation
Indices: 6555450--6555523 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
6555440 TAGACTAAAT
*
6555450 AAAATAATAAAATAATAAAAT-ATCTTATTA
1 AAAATAATAAAATAA-AAAATAATCTAATTA
* *
6555480 AAAAT-ATTAAATAAATAATAATCTAATTA
1 AAAATAATAAAATAAAAAATAATCTAATTA
6555509 AATAACT-ATAAAATA
1 AA-AA-TAATAAAATA
6555524 TCACCAACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.11
29 18 0.49
30 7 0.19
31 8 0.22
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAATAATAAAATAAAAAATAATCTAATTA
Found at i:6555512 original size:16 final size:15
Alignment explanation
Indices: 6555468--6555513 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
6555458 AAAATAATAA
*
6555468 AATATCTTATTAAA-
1 AATATCTAATTAAAT
*
6555482 AATAT-TAAATAAAT
1 AATATCTAATTAAAT
6555496 AATAATCTAATTAAAT
1 AAT-ATCTAATTAAAT
6555512 AA
1 AA
6555514 CTATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 6 0.23
14 8 0.31
15 2 0.08
16 10 0.38
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATCTAATTAAAT
Found at i:6556861 original size:14 final size:15
Alignment explanation
Indices: 6556835--6556863 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6556825 CAAAGGTGAT
6556835 TCTTTTCATTTTTTA
1 TCTTTTCATTTTTTA
6556850 TCTTTT-ATTTTTTA
1 TCTTTTCATTTTTTA
6556864 GAAAAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
TCTTTTCATTTTTTA
Found at i:6561245 original size:23 final size:23
Alignment explanation
Indices: 6561215--6561301 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
6561205 GCTTTACTGA
* *
6561215 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
6561238 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
6561259 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
6561281 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
6561302 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:6576044 original size:96 final size:92
Alignment explanation
Indices: 6575819--6576328 Score: 335
Period size: 89 Copynumber: 5.5 Consensus size: 92
6575809 GTCACCATAG
* * *
6575819 CAAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACCATGGCGAATCTTATCTCCC
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG----CATAGCGAATCTTATCTCCC
* * *
6575884 TGAAGTTGCAGTGGAAAAGGTTAAAGCTACA
62 TAAAGTTGCAGTAGAAAAGATTAAAGCTACA
* * *
6575915 -AAA-CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAG-ATAGCGAATCTTATTTTCCTAAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAGCGAATCTTATCTCCCTAAA
*
6575977 GTTGCAGTAGAACAGATTAAAGCTACAAGTTA
66 GTTGCAGTAGAAAAGATTAAAGCTAC-----A
* * * *
6576009 CAAATCTAATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--T-GACAAATCTTATAC-CTCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAG-CGAATCTTAT-CTCCCTA
** * **** *
6576070 AAGTTATAGTGGGTCGGATTAAATCTACCA
64 AAGTTGCAGTAGAAAAGATTAAAGCTA-CA
* * * * * * * *
6576100 TAACGAGTCTTATTTCCTTGAAGTTGCAGTGGAACTGATTAAAGCTACAAGTCACAAATCTTATC
1 CAA--A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-A-TAG---CGAATCTTATC
* * ** *
6576165 TCCCTGAAGTTGCAGTGGAGTAGATTGAAGCT--A
58 TCCCTAAAGTTGCAGTAGAAAAGATTAAAGCTACA
*
6576198 CAAATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-TA-C-AGATCTTATCTCCCTAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAGCGA-ATCTTATCTCCCTAA
* * * * *
6576260 AGTTGCAGTGGAGAAGATTGAAGAT-GA
65 AGTTGCAGTAGAAAAGATTAAAGCTACA
* * * *
6576287 CAAATCTTATCTCTCTAAAGTTGCAATGAAGCAGATTGAAGC
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC
6576329 GACAAATCCT
Statistics
Matches: 334, Mismatches: 57, Indels: 53
0.75 0.13 0.12
Matches are distributed among these distances:
87 1 0.00
88 38 0.11
89 80 0.24
91 3 0.01
92 1 0.00
93 1 0.00
94 67 0.20
95 71 0.21
96 35 0.10
98 3 0.01
99 1 0.00
100 1 0.00
101 32 0.10
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (92 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAGCGAATCTTATCTCCCTAAA
GTTGCAGTAGAAAAGATTAAAGCTACA
Found at i:6576074 original size:44 final size:44
Alignment explanation
Indices: 6575819--6576359 Score: 281
Period size: 44 Copynumber: 11.6 Consensus size: 44
6575809 GTCACCATAG
* * *
6575819 CAAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACCATGG
1 CAAATCTTATCCT-CTGAAGTTGCAGTGGAGCAGATTGAAG----C-TGA
* * ** * *
6575869 CGAATCTTATCTCCCTGAAGTTGCAGTGGAAAAGGTTAAAGCT-A
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* * * *
6575913 CAAAACTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAT-A
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* ** * * * *
6575957 GCGAATCTTATTTTCCTAAAGTTGCAGTAGAACAGATTAAAGCTACAAGTTA
1 -CAAATCTTATCCT-CTGAAGTTGCAGTGGAGCAGATTGAAGCT----G--A
* * *
6576009 CAAATCTAATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TGA
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* ** * * *
6576053 CAAATCTTATACCTCTAAAGTTATAGTGG-GTCGGATTAAATCT-A
1 CAAATCTTAT-CCTCTGAAGTTGCAGTGGAG-CAGATTGAAGCTGA
* * *
6576097 CCATAACGAGTCTTATTTCCT-TGAAGTTGCAGTGGAACTGATTAAAGCTACAAGTCA
1 -C--AA--A-TCTTA--TCCTCTGAAGTTGCAGTGGAGCAGATTGAAGCT----G--A
* *
6576154 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCT-A
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
*
6576198 CAAATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT-A
1 CAAATCTTAT-CCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* * * * *
6576242 CAGATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGATGA
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* * *
6576287 CAAATCTTATCTCTCTAAAGTTGCAATGAAGCAGATTGAAGC-GA
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
*
6576331 CAAATCCTATACCTCTGAAGTTGCAGTGG
1 CAAATCTTAT-CCTCTGAAGTTGCAGTGG
6576360 GTAAGAATGA
Statistics
Matches: 387, Mismatches: 68, Indels: 78
0.73 0.13 0.15
Matches are distributed among these distances:
43 2 0.01
44 172 0.44
45 74 0.19
46 2 0.01
47 2 0.01
49 3 0.01
50 61 0.16
51 64 0.17
52 3 0.01
54 2 0.01
56 1 0.00
57 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
Found at i:6576226 original size:145 final size:140
Alignment explanation
Indices: 6575871--6576268 Score: 439
Period size: 145 Copynumber: 2.8 Consensus size: 140
6575861 TACCATGGCG
* * * *
6575871 AATCTTATCTCCCTGAAGTTGCAGTGGAAAAGGTTAAAGCTACAAAACTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAATCTTATCCCCCTGAAGTTG
* * *
6575936 TAGTGGAGCAGATTGAAGATAGCGAATCTTATTTTCCTAAAGTTGCAGTAGAACAGATTAAAGCT
66 TAGTGGAGCAGATTAAACATAACGAATCTTATTTTCCTAAAGTTGCAGTAGAACAGATTAAAGCT
*
6576001 ACAAGTTACA
131 ACAAGTCACA
* * * * *
6576011 AATCTAATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TGACAAATCTTATACCTCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCT-ACAAATCTTATCCCCCTGAAGTT
* * * * * *
6576075 ATAGTGG-GTCGGATTAAATCTACCATAACGAGTCTTA-TTTCCTTGAAGTTGCAGTGGAACTGA
65 GTAGTGGAG-CAGATT-AA---A-CATAACGAATCTTATTTTCC-TAAAGTTGCAGTAGAACAGA
6576138 TTAAAGCTACAAGTCACA
123 TTAAAGCTACAAGTCACA
* *
6576156 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCCCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAATCTTATCCCCCTGAAGTTG
* * * *
6576221 CAGTGGAGCAGATTGAAGC-T-AC-AGATCTTATCTCCCTAAAGTTGCAGT
66 TAGTGGAGCAGATT-AAACATAACGA-ATCTTATTTTCCTAAAGTTGCAGT
6576269 GGAGAAGATT
Statistics
Matches: 212, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
138 1 0.00
139 20 0.09
140 68 0.32
141 2 0.01
144 6 0.03
145 113 0.53
146 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (140 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAATCTTATCCCCCTGAAGTTG
TAGTGGAGCAGATTAAACATAACGAATCTTATTTTCCTAAAGTTGCAGTAGAACAGATTAAAGCT
ACAAGTCACA
Found at i:6576352 original size:89 final size:88
Alignment explanation
Indices: 6576153--6576359 Score: 272
Period size: 89 Copynumber: 2.3 Consensus size: 88
6576143 GCTACAAGTC
* * * *
6576153 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCCCCCTGAAG
1 ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACAAATCTTATCCCCCTAAAG
* * *
6576218 TTGCAGTGGAGCAGATTGAAGCT
66 TTGCAATGAAGCAGATTGAAGCG
* * * * *
6576241 ACAGATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGATGACAAATCTTATCTCTCTAAA
1 ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGAT-ACAAATCTTATCCCCCTAAA
6576306 GTTGCAATGAAGCAGATTGAAGCG
65 GTTGCAATGAAGCAGATTGAAGCG
*
6576330 ACAAATCCTATAC-CTCTGAAGTTGCAGTGG
1 ACAAATCCTAT-CTCCCTGAAGTTGCAGTGG
6576360 GTAAGAATGA
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
88 40 0.39
89 62 0.60
90 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (88 bp):
ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACAAATCTTATCCCCCTAAAG
TTGCAATGAAGCAGATTGAAGCG
Found at i:6580041 original size:9 final size:9
Alignment explanation
Indices: 6580027--6580054 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6580017 AATCAACCTT
6580027 AAAACGAAA
1 AAAACGAAA
6580036 AAAACGAAA
1 AAAACGAAA
6580045 AAAACGAAA
1 AAAACGAAA
6580054 A
1 A
6580055 CCTTAGAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAACGAAA
Found at i:6584386 original size:18 final size:16
Alignment explanation
Indices: 6584363--6584405 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
6584353 TGTCATTATT
*
6584363 CTTATTTTTTTCTCGTTG
1 CTTATTTTTTTCT--TTA
*
6584381 CTTATTTATTTCTTTA
1 CTTATTTTTTTCTTTA
6584397 CTTATTTTT
1 CTTATTTTT
6584406 ATACCTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
18 12 0.55
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.70
Consensus pattern (16 bp):
CTTATTTTTTTCTTTA
Found at i:6584563 original size:3 final size:3
Alignment explanation
Indices: 6584550--6584689 Score: 103
Period size: 3 Copynumber: 46.7 Consensus size: 3
6584540 GCACTATTCT
*
6584550 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TT- TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* * * *
6584594 CTT- TCTA TTA TTG TTA TTA TTA ATA -TA CTA TTA TTA TTC TTA TTAA
1 -TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * *
6584640 CGTA TTA TTA TTA TTA TTA TTT TCTA CT- TTA TTA TTA -TA TTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
*
6584685 CTA TT
1 TTA TT
6584690 GCTATCATCA
Statistics
Matches: 109, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
2 10 0.09
3 89 0.82
4 9 0.08
5 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:6584603 original size:43 final size:42
Alignment explanation
Indices: 6584556--6584675 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 42
6584546 TTCTTTATTT
* * *
6584556 TATTATTATTATTATTATTTATTATTATTTTATCATTACTT-TC-
1 TATTATTATTATTATTATTTACTATTATTAT-TC-TTA-TTAACG
* *
6584599 TATTATTGTTATTATTAATATACTATTATTATTCTTATTAACG
1 TATTATTATTATTATT-ATTTACTATTATTATTCTTATTAACG
*
6584642 TATTATTATTATTATTATTTTCTACTTTATTATT
1 TATTATTATTATTATTATTTACTA--TTATTATT
6584676 ATATTATTAC
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
41 2 0.03
42 10 0.16
43 32 0.50
44 20 0.31
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (42 bp):
TATTATTATTATTATTATTTACTATTATTATTCTTATTAACG
Found at i:6584681 original size:43 final size:41
Alignment explanation
Indices: 6584556--6584681 Score: 107
Period size: 46 Copynumber: 3.0 Consensus size: 41
6584546 TTCTTTATTT
6584556 TATTATTATTATTATTATTTATTA--TTATT-TTATCATT-AC
1 TATTATTATTATTATTATTT-TTACTTTATTATTAT-ATTAAC
* * * *
6584595 TTTCTATTATTGTTATTATTAATATACTATTATTATTCTTATTAAC
1 TAT-TATTATTATTATTATT--TTTACT-TTATTATT-ATATTAAC
6584641 GTATTATTATTATTATTATTTTCTACTTTATTATTATATTA
1 -TATTATTATTATTATTATTTT-TACTTTATTATTATATTA
6584682 TTACTATTGC
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
39 2 0.03
40 15 0.22
41 2 0.03
42 1 0.01
43 5 0.07
44 14 0.21
45 9 0.13
46 18 0.26
47 2 0.03
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (41 bp):
TATTATTATTATTATTATTTTTACTTTATTATTATATTAAC
Found at i:6585692 original size:35 final size:35
Alignment explanation
Indices: 6585653--6585723 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
6585643 AGGAGGGTGA
*
6585653 TGCTTTAAATTTTTGAGTGTTTTAAAAGTTTTTTT
1 TGCTTTAAATTTTTGAGTGTTCTAAAAGTTTTTTT
*
6585688 TGCTTTAAATTTTTGGGTGTTCTAAAAGTTTTTTT
1 TGCTTTAAATTTTTGAGTGTTCTAAAAGTTTTTTT
6585723 T
1 T
6585724 TAAGGTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.21, C:0.04, G:0.15, T:0.59
Consensus pattern (35 bp):
TGCTTTAAATTTTTGAGTGTTCTAAAAGTTTTTTT
Found at i:6587881 original size:3 final size:3
Alignment explanation
Indices: 6587867--6587960 Score: 59
Period size: 3 Copynumber: 31.3 Consensus size: 3
6587857 CCAAACTTTC
* * * * *
6587867 TAT TAT TGT TAT TAT TAA TA- TAC TAT TAT TAT TCT TAT TAACG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-A-T TAT
* * * *
6587913 TAT TTT TAT TAT TAT TAT TTT CTAC T-T TAT TAT TA- TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
6587957 TAT T
1 TAT T
6587961 GCTATCATCA
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
2 5 0.07
3 60 0.87
4 3 0.04
5 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:6587898 original size:20 final size:20
Alignment explanation
Indices: 6587870--6587923 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
6587860 AACTTTCTAT
*
6587870 TATTGTTATTATTAATATAC-
1 TATTATTATTATTAATA-ACG
* *
6587890 TATTATTATTCTTATTAACG
1 TATTATTATTATTAATAACG
*
6587910 TATTATTTTTATTA
1 TATTATTATTATTA
6587924 TTATTATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (20 bp):
TATTATTATTATTAATAACG
Found at i:6587916 original size:23 final size:23
Alignment explanation
Indices: 6587866--6587929 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
6587856 ACCAAACTTT
* *
6587866 CTATTATTGTTATTATTAATATA
1 CTATTATTATTATTATTAACATA
* *
6587889 CTATTATTATTCTTATTAACGTA
1 CTATTATTATTATTATTAACATA
* *
6587912 TTATTTTTATTATTATTA
1 CTATTATTATTATTATTA
6587930 TTTTCTACTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (23 bp):
CTATTATTATTATTATTAACATA
Found at i:6588047 original size:3 final size:3
Alignment explanation
Indices: 6588039--6588077 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
6588029 ATTTATTTAC
*
6588039 ATT ATT ATT GTT ATT -TCT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
6588078 TTTAGCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6588483 original size:24 final size:20
Alignment explanation
Indices: 6588456--6588504 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 20
6588446 ATTTTTTAAT
6588456 TATTATTTTAAGTTATTCTATTTA
1 TATTATTTT--GTTA-TCT-TTTA
6588480 TATTATTTTGTTATCTTTTA
1 TATTATTTTGTTATCTTTTA
6588500 TATTA
1 TATTA
6588505 ATGATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.36
21 3 0.12
22 4 0.16
24 9 0.36
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (20 bp):
TATTATTTTGTTATCTTTTA
Found at i:6589087 original size:130 final size:126
Alignment explanation
Indices: 6588910--6589238 Score: 385
Period size: 130 Copynumber: 2.6 Consensus size: 126
6588900 ACGATGTTTG
* * * * *
6588910 ATGTTTAGAAATTCGAGG-AATCGTGCCCTGTCGTACTGGGTTGCAATTTCTCGTTTGTTCAAAA
1 ATGTTTGGAAATTCG-GGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTC-AAA
* * *
6588974 TGATCGAATATTCCTTTGGAATTTCACACATGTTTTAAAAATTCTTTAAAACGAAGGTAACGTTC
64 TAATCGAATATTCCTTTAGAATTTCACACATGTTTTAAAAATTC--TAAAAC-AAGGCAACGTTC
6589039 GA
126 -A
6589041 A-GTTTGGAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATA
1 ATGTTTGGAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATA
* ** *
6589105 ATCGAATATTCCTTTAGAATTTCACTCATGTTTTCTAAATTCTAAAACAAGGCAATGTTCA
66 ATCGAATATTCCTTTAGAATTTCACACATGTTTTAAAAATTCTAAAACAAGGCAACGTTCA
* * * * * * * ** *
6589166 ATGTTTGGGAATCCGAGAAAACGTGCCCTA-CGTGCTGGGTTTCGATTTACCGTTTGACCAAACA
1 ATGTTTGGAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATA
6589230 ATCGAATAT
66 ATCGAATAT
6589239 CATTTTAAAA
Statistics
Matches: 174, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
125 39 0.22
126 34 0.20
127 6 0.03
129 44 0.25
130 50 0.29
131 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (126 bp):
ATGTTTGGAAATTCGGGAAATCGTGCCCTATCGTGCTGGGTTACAATTTCCCGTTTGTTCAAATA
ATCGAATATTCCTTTAGAATTTCACACATGTTTTAAAAATTCTAAAACAAGGCAACGTTCA
Found at i:6597041 original size:17 final size:17
Alignment explanation
Indices: 6597019--6597062 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
6597009 TTAGAAAAAC
*
6597019 TATTCGCCATGGATAGG
1 TATTCGCCATAGATAGG
6597036 TATTCGCCATAGATAGG
1 TATTCGCCATAGATAGG
*
6597053 TATCCGCCAT
1 TATTCGCCAT
6597063 TGGTATCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (17 bp):
TATTCGCCATAGATAGG
Found at i:6598136 original size:45 final size:45
Alignment explanation
Indices: 6598004--6598216 Score: 169
Period size: 45 Copynumber: 4.7 Consensus size: 45
6597994 ACTATCAAAG
* * * *
6598004 GATGTCATAGTGTCTTTCAACTATGGTCTTAGTC-TTATTTA-CTAT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATT-TTTATC-AT
* * * ***
6598049 GATGCCATAGCGTCTTTTAGCCATAGTCTTACTCACCCTTATCAT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCAT
* * *
6598094 TATGCCATAGCGTCTTTCAACTATTGTCTTACTCATTTTTATCAT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCAT
** * * * * *
6598139 GATATCGTAGCATCTTTCAGCTATGGTCTTACTTATTATCATCAT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCAT
* * ** *
6598184 TATGGCATAGTATGTTTCAGCTATGGTCTTACT
1 GATGCCATAGCGTCTTTCAGCTATGGTCTTACT
6598217 TACTCCTGGT
Statistics
Matches: 132, Mismatches: 34, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
45 131 0.99
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.43
Consensus pattern (45 bp):
GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTTATCAT
Done.