Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 12 of 325
Found at i:4360843 original size:15 final size:15
Alignment explanation
Indices: 4360823--4360866 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
4360813 ATTTATTTAG
4360823 AAAATTCAATTAATT
1 AAAATTCAATTAATT
*
4360838 AAAATT-ATTTAATT
1 AAAATTCAATTAATT
*
4360852 AAAAATCAATTAATT
1 AAAATTCAATTAATT
4360867 TACTTGGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTCAATTAATT
Found at i:4364394 original size:2 final size:2
Alignment explanation
Indices: 4364389--4364455 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
4364379 ACATATATAC
4364389 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4364431 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
4364456 CTGATAAGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4364674 original size:3 final size:3
Alignment explanation
Indices: 4364666--4364692 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4364656 AAACATTAAA
4364666 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
4364693 CTTATTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4366488 original size:12 final size:13
Alignment explanation
Indices: 4366461--4366485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4366451 CCACTCGTCA
4366461 AATTAATTTTTTT
1 AATTAATTTTTTT
4366474 AATTAATTTTTT
1 AATTAATTTTTT
4366486 AATAACTCAA
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTAATTTTTTT
Found at i:4366742 original size:16 final size:16
Alignment explanation
Indices: 4366718--4366748 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4366708 ACTTAATATT
*
4366718 ATTTTACATTTACTTA
1 ATTTGACATTTACTTA
4366734 ATTTGACATTTACTT
1 ATTTGACATTTACTT
4366749 GATGGCAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTTGACATTTACTTA
Found at i:4367786 original size:17 final size:18
Alignment explanation
Indices: 4367760--4367793 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4367750 TTTATTTGAT
4367760 TCTTAAT-AAATATTAAC
1 TCTTAATAAAATATTAAC
*
4367777 TCTTACTAAAATATTAA
1 TCTTAATAAAATATTAA
4367794 TGGTAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (18 bp):
TCTTAATAAAATATTAAC
Found at i:4372672 original size:6 final size:6
Alignment explanation
Indices: 4372661--4372688 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4372651 GTTGGTATGA
4372661 AAACTC AAACTC AAACTC AAACTC AAAC
1 AAACTC AAACTC AAACTC AAACTC AAAC
4372689 AAATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (6 bp):
AAACTC
Found at i:4388986 original size:17 final size:18
Alignment explanation
Indices: 4388954--4388987 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4388944 TTAAGCAATG
4388954 CAAACAAATAAATGCACA
1 CAAACAAATAAATGCACA
*
4388972 CAAACACAT-AATGCAC
1 CAAACAAATAAATGCAC
4388988 GTTCAGCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.26, G:0.06, T:0.12
Consensus pattern (18 bp):
CAAACAAATAAATGCACA
Found at i:4389762 original size:43 final size:43
Alignment explanation
Indices: 4389714--4389868 Score: 265
Period size: 43 Copynumber: 3.6 Consensus size: 43
4389704 CCGGCATTAC
*
4389714 GCCTGCTAGGCACGAAGGCCCGAATACACGTCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
4389757 GCCTGCTAGGCACGAAGGCCCAAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
4389800 GCCTACTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
4389843 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
4389869 TAATACCAGC
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 104 1.00
ACGTcount: A:0.30, C:0.34, G:0.25, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:4393191 original size:26 final size:26
Alignment explanation
Indices: 4393137--4393185 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
4393127 ATACTGATCC
* *
4393137 AAAAATAAAAAAATAATACTTTATTT
1 AAAAATAAAAAAATAATAATTTATAT
4393163 AAAAAT-AAAAAATAA-AATTTATA
1 AAAAATAAAAAAATAATAATTTATA
4393186 AATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 9 0.43
26 6 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAATAAAAAAATAATAATTTATAT
Found at i:4393302 original size:16 final size:16
Alignment explanation
Indices: 4393251--4393328 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
4393241 TGGGAATGGG
* *
4393251 AATGAAAATGAAATTAG
1 AATG-AAATAAAATTAA
* *
4393268 AATGAAATAAAGTTGA
1 AATGAAATAAAATTAA
4393284 AATGAAATAAAATTAA
1 AATGAAATAAAATTAA
* *
4393300 AATAAAATGAAAATGAA
1 AATGAAAT-AAAATTAA
4393317 AA-GAAATGAAAA
1 AATGAAAT-AAAA
4393329 AAAAAAGGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
16 38 0.75
17 13 0.25
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.21
Consensus pattern (16 bp):
AATGAAATAAAATTAA
Found at i:4393756 original size:23 final size:23
Alignment explanation
Indices: 4393712--4393756 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4393702 AATAATATGA
*
4393712 AAAAAATAATATGAAATGAATTG
1 AAAAAATAATATGAAATAAATTG
4393735 AAAAAATAAT-TGAAATTAAATT
1 AAAAAATAATATGAAA-TAAATT
4393757 AAATTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (23 bp):
AAAAAATAATATGAAATAAATTG
Found at i:4393988 original size:23 final size:23
Alignment explanation
Indices: 4393944--4393988 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4393934 AATAATATGA
*
4393944 AAAAAATAATATGAAATGAATTG
1 AAAAAATAATATGAAATAAATTG
4393967 AAAAAATAAT-TGAAATTAAATT
1 AAAAAATAATATGAAA-TAAATT
4393989 AAATTACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (23 bp):
AAAAAATAATATGAAATAAATTG
Found at i:4395929 original size:18 final size:17
Alignment explanation
Indices: 4395896--4395934 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
4395886 TTGTATAAAT
4395896 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
4395914 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
4395931 TGTG
1 TGTG
4395935 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:4396051 original size:8 final size:8
Alignment explanation
Indices: 4396038--4396066 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4396028 CACTAGAGAC
4396038 CAGTGTTA
1 CAGTGTTA
4396046 CAGTGTTA
1 CAGTGTTA
4396054 CAGTGTTA
1 CAGTGTTA
4396062 CAGTG
1 CAGTG
4396067 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:4396207 original size:22 final size:23
Alignment explanation
Indices: 4396152--4396226 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
4396142 AGTGTTATTG
4396152 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
4396175 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4396198 ATC-GTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4396220 ATCAGTG
1 ATCAGTG
4396227 TGCACTTATG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
22 22 0.45
23 27 0.55
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:4403258 original size:18 final size:17
Alignment explanation
Indices: 4403225--4403263 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
4403215 TTGTATAAAT
4403225 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
4403243 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
4403260 TGTG
1 TGTG
4403264 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:4403381 original size:8 final size:8
Alignment explanation
Indices: 4403368--4403396 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4403358 CACTAGAGAC
4403368 CAGTGTTA
1 CAGTGTTA
4403376 CAGTGTTA
1 CAGTGTTA
4403384 CAGTGTTA
1 CAGTGTTA
4403392 CAGTG
1 CAGTG
4403397 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:4403510 original size:23 final size:23
Alignment explanation
Indices: 4403483--4403558 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
4403473 AGTGTTATTG
4403483 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
4403506 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4403529 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4403552 ATCAGTG
1 ATCAGTG
4403559 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:4406030 original size:106 final size:106
Alignment explanation
Indices: 4405869--4406367 Score: 526
Period size: 105 Copynumber: 4.7 Consensus size: 106
4405859 TCGAGAATAT
* * * ***
4405869 ATTTTTTTTTTGCACTGGGTGCCGGCCATTGACAGGCTAGCACCAAAAAAATTTTTTTTT-TGGA
1 ATTTTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACC--CAAAATTTTTTTTTAAAAA
* *
4405933 ACTCGTA-TTTTCGAGAG-AAAAAAAAA-TTGAAAAAAATTTTA
64 ACTCGTATTTTTAGAGAGCAAAAAAAAATTTGAAAAAAA-TTGA
* *
4405974 AGTTTTTTTTTTGTACTGGGTGCTGGCCATTGATAGGCCAGCACCCAAAATTTTTTTTTAAAAAA
1 A-TTTTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTAAAAAA
*
4406039 CTCGTATTTTTTA-AGAGCAAAAAAAAAATTCGAAAAAAAATT--
65 CTCGTA-TTTTTAGAGAGC-AAAAAAAAATTTG-AAAAAAATTGA
* * * * *
4406081 A-CTTTTTTTTGTACTGAGTGCCAGCCATTGACAAGCCAGCATCCC-AAATTTTTTTTAAAAAAA
1 ATTTTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCCAAAATTTTTTTT-TAAAAA
* * *
4406144 AATCGTGTTTTTAGAGAGCAAAAAAAAATTTTAAAAAAAAATTGA
64 ACTCGTATTTTTAGAGAGCAAAAAAAAA-TTT-GAAAAAAATTGA
* *
4406189 ATTTTTGTTCTGGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA--TTTTTTT--AAAA
1 ATTTTT-TTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTAAAAAA
*
4406250 CTCGTATTTTTAGAGAGTAAAAAAAAATTTTTGAAAAAAAAGTTGA
65 CTCGTATTTTTAGAGAGCAAAAAAAAA--TTTG-AAAAAAA-TTGA
*
4406296 ATTTTTTTTATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC--AATTTTTTTTT-TAAAA
1 ATTTTTTTT-TTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTAAAAAA
4406358 CTCGTATTTT
65 CTCGTATTTT
4406368 GTATGCCAAT
Statistics
Matches: 335, Mismatches: 34, Indels: 47
0.81 0.08 0.11
Matches are distributed among these distances:
104 13 0.04
105 99 0.30
106 85 0.25
107 57 0.17
108 30 0.09
109 10 0.03
110 41 0.12
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (106 bp):
ATTTTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTAAAAAAC
TCGTATTTTTAGAGAGCAAAAAAAAATTTGAAAAAAATTGA
Found at i:4406087 original size:105 final size:106
Alignment explanation
Indices: 4405869--4406367 Score: 547
Period size: 106 Copynumber: 4.7 Consensus size: 106
4405859 TCGAGAATAT
* * * ***
4405869 ATTTTTTTTTTGCACTGGGTGCCGGCCATTGACAGGCTAGCACCAAAAAAATTTTTTTTTTGGAA
1 ATTTTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACC--CAAAATTTTTTTTTAAAAA
* *
4405934 CTCGTA-TTTTCGAGAG--AAAAAAAAA-TTGAAAAAAATTTTA
64 CTCGTATTTTTAGAGAGCAAAAAAAAAATTTGAAAAAAA-ATTA
* *
4405974 AGTTTTTTTTTTGTACTGGGTGCTGGCCATTGATAGGCCAGCACCCAAAATTTTTTTTTAAAAAA
1 A-TTTTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT-AAAAA
*
4406039 CTCGTATTTTTTA-AGAGCAAAAAAAAAATTCGAAAAAAAATT-
64 CTCGTA-TTTTTAGAGAGCAAAAAAAAAATTTGAAAAAAAATTA
* * * * *
4406081 A-CTTTTTTTTGTACTGAGTGCCAGCCATTGACAAGCCAGCATCCC-AAATTTTTTTTAAAAAAA
1 ATTTTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCCAAAATTTTTTTT--TAAAA
* * * *
4406144 AATCGTGTTTTTAGAGAGCAAAAAAAAATTTTAAAAAAAAATTGA
63 ACTCGTATTTTTAGAGAGCAAAAAAAAAATTTGAAAAAAAATT-A
* *
4406189 ATTTTTGTTCTGGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA--TTTTTTT-AAAAC
1 ATTTTT-TTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTAAAAAC
* *
4406251 TCGTATTTTTAGAGAGTAAAAAAAAATTTTTGAAAAAAAAGTTGA
65 TCGTATTTTTAGAGAGCAAAAAAAAA-ATTTGAAAAAAAA-TT-A
*
4406296 ATTTTTTTTATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC--AATTTTTTTTTTAAAAC
1 ATTTTTTTT-TTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTAAAAAC
4406359 TCGTATTTT
65 TCGTATTTT
4406368 GTATGCCAAT
Statistics
Matches: 336, Mismatches: 36, Indels: 41
0.81 0.09 0.10
Matches are distributed among these distances:
104 13 0.04
105 90 0.27
106 95 0.28
107 57 0.17
108 32 0.10
109 15 0.04
110 34 0.10
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (106 bp):
ATTTTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTAAAAACT
CGTATTTTTAGAGAGCAAAAAAAAAATTTGAAAAAAAATTA
Found at i:4411624 original size:25 final size:22
Alignment explanation
Indices: 4411596--4411640 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 22
4411586 TTTTTAAAAT
4411596 ATTTATAACAAAATATTATAATTAA
1 ATTTA-AACAAAA-A-TATAATTAA
*
4411621 ATTTAAATAAAAATATAATT
1 ATTTAAACAAAAATATAATT
4411641 TTTTTTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 6 0.32
25 5 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTAAACAAAAATATAATTAA
Found at i:4412018 original size:14 final size:14
Alignment explanation
Indices: 4411999--4412030 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4411989 ATGTCATTTA
4411999 GCCCAACCAAACTG
1 GCCCAACCAAACTG
4412013 GCCCAACCAAACTG
1 GCCCAACCAAACTG
4412027 GCCC
1 GCCC
4412031 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:4412310 original size:45 final size:45
Alignment explanation
Indices: 4412246--4412335 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
4412236 ATTCATTGAG
4412246 TTATTAATAAGAATTTTGAGAGTATTCACTCAAACTTTTCTCTCA
1 TTATTAATAAGAATTTTGAGAGTATTCACTCAAACTTTTCTCTCA
4412291 TTATTAATAAGAATTTTGAGAGTATTCACTCAAACTTTTCTCTCA
1 TTATTAATAAGAATTTTGAGAGTATTCACTCAAACTTTTCTCTCA
4412336 AGTGTTCTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (45 bp):
TTATTAATAAGAATTTTGAGAGTATTCACTCAAACTTTTCTCTCA
Found at i:4417180 original size:14 final size:14
Alignment explanation
Indices: 4417161--4417192 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4417151 AGGTCATTTA
4417161 GCCCAACCAAACTG
1 GCCCAACCAAACTG
4417175 GCCCAACCAAACTG
1 GCCCAACCAAACTG
4417189 GCCC
1 GCCC
4417193 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:4418906 original size:11 final size:11
Alignment explanation
Indices: 4418890--4418923 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
4418880 CGGGCCTTCC
4418890 TATATTAATTT
1 TATATTAATTT
*
4418901 TATATTATTTT
1 TATATTAATTT
4418912 TATA-TAATTT
1 TATATTAATTT
4418922 TA
1 TA
4418924 AAATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTAATTT
Found at i:4419162 original size:11 final size:11
Alignment explanation
Indices: 4419144--4419184 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
4419134 ACAATAACAA
4419144 CAAAATAGTAG
1 CAAAATAGTAG
*
4419155 CAACATAGTAG
1 CAAAATAGTAG
*
4419166 TAAAATAGTAG
1 CAAAATAGTAG
*
4419177 CAGAATAG
1 CAAAATAG
4419185 GTAGAAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:4419184 original size:22 final size:22
Alignment explanation
Indices: 4419145--4419192 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
4419135 CAATAACAAC
4419145 AAAATAGTAGCAACATA-GTAG
1 AAAATAGTAGCAACATAGGTAG
4419166 TAAAATAGTAGCAGA-ATAGGTAG
1 -AAAATAGTAGCA-ACATAGGTAG
4419189 AAAA
1 AAAA
4419193 CAATAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (22 bp):
AAAATAGTAGCAACATAGGTAG
Found at i:4419616 original size:15 final size:15
Alignment explanation
Indices: 4419590--4419632 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
4419580 TTTACTAAAG
4419590 TTTATGAAAAAA-AAT
1 TTTAT-AAAAAATAAT
4419605 TGTTATAAAAAATAAT
1 T-TTATAAAAAATAAT
*
4419621 TTAATAAAAAAT
1 TTTATAAAAAAT
4419633 CTATATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
TTTATAAAAAATAAT
Found at i:4431688 original size:60 final size:60
Alignment explanation
Indices: 4431590--4431750 Score: 252
Period size: 60 Copynumber: 2.7 Consensus size: 60
4431580 AGGAAAAGGG
*
4431590 AAGCCAGCGGGTGGCACTCATGTGAACGTTGG-GCGCAAAGGAGTTGGAGTGAACACGGGA
1 AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAG-GCAAAGGAGTTGGAGTGAACACGGGA
* * *
4431650 AAGCCAGGGGGTGGCACTCATGTGAATGTTGGAGGCAAAGGAGTTGGGGTGAACACTGGA
1 AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACACGGGA
* *
4431710 AAGCCAGGAGGTGGCACCCATGTGAACGTTGGAGGCAAAGG
1 AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGG
4431751 TGGAGGAGTA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.40, T:0.16
Consensus pattern (60 bp):
AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACACGGGA
Found at i:4436690 original size:18 final size:18
Alignment explanation
Indices: 4436676--4436710 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4436666 GAAAAAAAGT
4436676 AAAAAATAAA-TAAAATAG
1 AAAAAA-AAACTAAAATAG
4436694 AAAAAAAAACTAAAATA
1 AAAAAAAAACTAAAATA
4436711 TGATAACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAAAAAACTAAAATAG
Found at i:4440450 original size:15 final size:15
Alignment explanation
Indices: 4440430--4440472 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
4440420 TTTAATTCTT
4440430 TAAAAATTATAAAAA
1 TAAAAATTATAAAAA
* *
4440445 TAAAAACTATTAAAA
1 TAAAAATTATAAAAA
4440460 TAATAAAATTATA
1 T-A-AAAATTATA
4440473 TTTTTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 1 0.05
17 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAATTATAAAAA
Found at i:4440858 original size:67 final size:67
Alignment explanation
Indices: 4440750--4440877 Score: 256
Period size: 67 Copynumber: 1.9 Consensus size: 67
4440740 TTCGTGGAGT
4440750 AAATATCAATAAACTCACAGTTATCAGTTATCACCATGGTAACTGACAACAAAAAAACAGTGGAT
1 AAATATCAATAAACTCACAGTTATCAGTTATCACCATGGTAACTGACAACAAAAAAACAGTGGAT
4440815 GG
66 GG
4440817 AAATATCAATAAACTCACAGTTATCAGTTATCACCATGGTAACTGACAACAAAAAAACAGT
1 AAATATCAATAAACTCACAGTTATCAGTTATCACCATGGTAACTGACAACAAAAAAACAGT
4440878 TATCAGTTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (67 bp):
AAATATCAATAAACTCACAGTTATCAGTTATCACCATGGTAACTGACAACAAAAAAACAGTGGAT
GG
Found at i:4442431 original size:30 final size:30
Alignment explanation
Indices: 4442396--4442455 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4442386 TTACCGAGTC
4442396 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
* * *
4442426 TAGGGGCAAAATTGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
4442456 CGTATTAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAATTATGCAAAAGTT
Found at i:4443001 original size:46 final size:47
Alignment explanation
Indices: 4442878--4443006 Score: 197
Period size: 47 Copynumber: 2.8 Consensus size: 47
4442868 GGTTGAACAT
* * *
4442878 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAACGC
*
4442925 CTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAACGC
* *
4442971 CCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4443007 GCGGGTTACA
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
46 36 0.48
47 39 0.52
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (47 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAACGC
Found at i:4443476 original size:20 final size:20
Alignment explanation
Indices: 4443451--4443500 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
4443441 TTTTTGGTAA
4443451 ATGGCTTGTAAAACTTAAGT
1 ATGGCTTGTAAAACTTAAGT
4443471 ATGGCTTGTAAAACTTAAGT
1 ATGGCTTGTAAAACTTAAGT
*
4443491 ATGGCATGTA
1 ATGGCTTGTA
4443501 TAGCAATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (20 bp):
ATGGCTTGTAAAACTTAAGT
Found at i:4449109 original size:47 final size:46
Alignment explanation
Indices: 4449052--4449187 Score: 218
Period size: 47 Copynumber: 2.9 Consensus size: 46
4449042 CTAGGATGGT
* *
4449052 TGAACATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATG
1 TGAACGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG
*
4449098 TGAAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG
1 TG-AACGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG
* *
4449145 TGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TGAACGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4449188 GCGGGTTACA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
46 40 0.48
47 43 0.52
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
TGAACGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG
Found at i:4449164 original size:41 final size:43
Alignment explanation
Indices: 4449072--4449187 Score: 117
Period size: 46 Copynumber: 2.5 Consensus size: 43
4449062 AACTCGTTGA
* * *
4449072 GTTGAGTCTGAGTTCACTTATGGATGTGAAATGTCCGAACTCGTTG
1 GTTGAGTCCGAGTTCACTTATGGATGTGAAACGCCCGAACTC---G
*
4449118 AGTTGAGTCCGAGTTCACTTATGGATGTG-AACGCCCGAGCTCGTTG
1 -GTTGAGTCCGAGTTCACTTATGGATGTGAAACGCCCGAACTC---G
4449164 AGTTGAGTCCGAGTTCACTTATGG
1 -GTTGAGTCCGAGTTCACTTATGG
4449188 GCGGGTTACA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 38 0.58
47 27 0.42
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (43 bp):
GTTGAGTCCGAGTTCACTTATGGATGTGAAACGCCCGAACTCG
Found at i:4451104 original size:18 final size:19
Alignment explanation
Indices: 4451081--4451119 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4451071 TACAAATACA
*
4451081 AACATT-ACATAATTATTT
1 AACATTCACATAATAATTT
*
4451099 AACATTCACATCATAATTT
1 AACATTCACATAATAATTT
4451118 AA
1 AA
4451120 TCATATTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (19 bp):
AACATTCACATAATAATTT
Found at i:4451667 original size:31 final size:31
Alignment explanation
Indices: 4451629--4451691 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
4451619 GTATTTACAA
* *
4451629 CATATTTCACTTTATATTTTCAATTCATTAT
1 CATATTTCACATTATATTTTCAATTCACTAT
*
4451660 CATATTTCACATTCTATTTTCAATTCACTAT
1 CATATTTCACATTATATTTTCAATTCACTAT
4451691 C
1 C
4451692 TCATATTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.51
Consensus pattern (31 bp):
CATATTTCACATTATATTTTCAATTCACTAT
Found at i:4451885 original size:27 final size:25
Alignment explanation
Indices: 4451821--4451878 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
4451811 ATGTACTAAA
* *
4451821 CAGATAGCAATAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAATAAT
4451846 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAATAAT
*
4451871 CAAAGAGC
1 CAGAGAGC
4451879 GCGCTAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (25 bp):
CAGAGAGCACTAACGTGCTAATAAT
Found at i:4452821 original size:7 final size:7
Alignment explanation
Indices: 4452799--4452831 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
4452789 TTATTATATA
4452799 ATATAAT
1 ATATAAT
4452806 ATA-ACAT
1 ATATA-AT
4452813 ATATAAT
1 ATATAAT
4452820 ATATAAT
1 ATATAAT
4452827 ATATA
1 ATATA
4452832 CTTAACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 22 0.92
8 1 0.04
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (7 bp):
ATATAAT
Found at i:4452865 original size:29 final size:28
Alignment explanation
Indices: 4452816--4452870 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
4452806 ATAACATATA
*
4452816 TAATATATAATATATACTTAACTTTTAAG
1 TAATATATAAGATATACTTAA-TTTTAAG
*
4452845 TAATATTATAAGATAT-TTTAATTTTA
1 TAATA-TATAAGATATACTTAATTTTA
4452871 GATTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 9 0.39
30 9 0.39
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (28 bp):
TAATATATAAGATATACTTAATTTTAAG
Found at i:4463582 original size:18 final size:18
Alignment explanation
Indices: 4463542--4463584 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4463532 CCCTCGCTAT
* *
4463542 TGAAGAAGAAGAGGAGGA
1 TGAAGAAGAAGAAGAAGA
*
4463560 GGAAGAAGAAGAAGAAGA
1 TGAAGAAGAAGAAGAAGA
4463578 TGAAGAA
1 TGAAGAA
4463585 CATCACGAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.05
Consensus pattern (18 bp):
TGAAGAAGAAGAAGAAGA
Found at i:4474064 original size:31 final size:29
Alignment explanation
Indices: 4474008--4474070 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
4473998 TTTTTAAATG
4474008 TATATAATTGAATCAAAATTAAAATTTTA
1 TATATAATTGAATCAAAATTAAAATTTTA
* * *
4474037 TATATACATATGAATTACAATTCAAATTTTA
1 TATATA-AT-TGAATCAAAATTAAAATTTTA
4474068 TAT
1 TAT
4474071 GTATAATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.21
30 2 0.07
31 21 0.72
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (29 bp):
TATATAATTGAATCAAAATTAAAATTTTA
Found at i:4474218 original size:19 final size:20
Alignment explanation
Indices: 4474184--4474226 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
4474174 AACTTCCCTT
*
4474184 TTTCCATTTTTACAATTAAC
1 TTTCCATTTTTACAATAAAC
*
4474204 TTTCC-TTTTTCCAATAAAC
1 TTTCCATTTTTACAATAAAC
4474223 TTTC
1 TTTC
4474227 TTAAATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTCCATTTTTACAATAAAC
Found at i:4476927 original size:29 final size:28
Alignment explanation
Indices: 4476877--4476934 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
4476867 GTGAAGTTAG
*
4476877 TCAATACATACTGGTCTTATACTCTTTA
1 TCAATACATACTAGTCTTATACTCTTTA
*
4476905 TCAATACATCACTAGTCTTATACTTTTTA
1 TCAATACAT-ACTAGTCTTATACTCTTTA
4476934 T
1 T
4476935 AATCTCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (28 bp):
TCAATACATACTAGTCTTATACTCTTTA
Found at i:4479789 original size:35 final size:35
Alignment explanation
Indices: 4479750--4480086 Score: 413
Period size: 35 Copynumber: 9.6 Consensus size: 35
4479740 CATGGCAAAG
* ** *
4479750 TGTGAAATGTAGGTATGACATTAACCATGCTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* * *
4479785 TGTGAAACGTATGTATGGTATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* *
4479820 TGTGAAACGTAGGTATAGTATTAACCATATTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* *
4479855 TGTGAAACTTAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
*
4479890 TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
*
4479925 TGTGAAACGTAGGTATAGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
*
4479960 TGTGAAACATAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* * * * *
4479995 TGTGAAATGGAGGGATGGTATTATCCATATTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
** ** ** *
4480030 TAAGAAACGTAGGTATGACATTTCCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
***
4480065 TGTGAAATACAGGTATGGTATT
1 TGTGAAACGTAGGTATGGTATT
4480087 TCAATAAGGA
Statistics
Matches: 257, Mismatches: 45, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 257 1.00
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
Found at i:4479932 original size:105 final size:105
Alignment explanation
Indices: 4479750--4480086 Score: 455
Period size: 105 Copynumber: 3.2 Consensus size: 105
4479740 CATGGCAAAG
** * * *
4479750 TGTGAAA-TGTAGGTATGACATTAACCATGCTGAGTTGTGAAACGTATGTATGGTATCATCCATA
1 TGTGAAACT-TAGGTATGGTATTAACCATACTGAGTTGTGAAACGTAGGTATGGTATTATCCATA
*
4479814 CTGAGTTGTGAAACGTAGGTATAGTATTAACCATATTGAGT
65 CTGAGTTGTGAAACGTAGGTATAGTATTAACCATACTGAGT
*
4479855 TGTGAAACTTAGGTATGGTATTATCCATACTGAGTTGTGAAACGTAGGTATGGTATTATCCATAC
1 TGTGAAACTTAGGTATGGTATTAACCATACTGAGTTGTGAAACGTAGGTATGGTATTATCCATAC
4479920 TGAGTTGTGAAACGTAGGTATAGTATTAACCATACTGAGT
66 TGAGTTGTGAAACGTAGGTATAGTATTAACCATACTGAGT
* * * * *
4479960 TGTGAAACATAGGTATGGTATTAACCATACTGAGTTGTGAAATGGAGGGATGGTATTATCCATAT
1 TGTGAAACTTAGGTATGGTATTAACCATACTGAGTTGTGAAACGTAGGTATGGTATTATCCATAC
** * ** *
4480025 TGAGTTAAGAAACGTAGGTAT-GACATTTCCCATACCGAGT
66 TGAGTTGTGAAACGTAGGTATAG-TATTAACCATACTGAGT
*
4480065 TGTGAAA-TACAGGTATGGTATT
1 TGTGAAACT-TAGGTATGGTATT
4480087 TCAATAAGGA
Statistics
Matches: 208, Mismatches: 21, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
104 1 0.00
105 206 0.99
106 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (105 bp):
TGTGAAACTTAGGTATGGTATTAACCATACTGAGTTGTGAAACGTAGGTATGGTATTATCCATAC
TGAGTTGTGAAACGTAGGTATAGTATTAACCATACTGAGT
Found at i:4482320 original size:37 final size:38
Alignment explanation
Indices: 4482278--4482374 Score: 90
Period size: 40 Copynumber: 2.5 Consensus size: 38
4482268 CGGATAGATT
*
4482278 CGATGAGGCATTGGTCGCCAC-TTTGCTTCG-GCTTAGC
1 CGATGAGGCATTGGTCGCCACTTTTGCTTCGAAC-TAGC
* * ** *
4482315 CGATGAGACGTTGGTCATCACTTATTTGCTTCGAACTATC
1 CGATGAGGCATTGGTCGCCAC-T-TTTGCTTCGAACTAGC
*
4482355 CGATGAGGCCTTGGTCGCCA
1 CGATGAGGCATTGGTCGCCA
4482375 TTCTGGTGTG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
37 17 0.37
40 28 0.61
41 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (38 bp):
CGATGAGGCATTGGTCGCCACTTTTGCTTCGAACTAGC
Found at i:4484061 original size:19 final size:20
Alignment explanation
Indices: 4484029--4484068 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4484019 AATGTAAAAT
* *
4484029 AATATTATTTAAAT-TATTA
1 AATATAATTAAAATATATTA
4484048 AATATAATTAAAATATATTA
1 AATATAATTAAAATATATTA
4484068 A
1 A
4484069 CTTACAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATAATTAAAATATATTA
Found at i:4490640 original size:38 final size:38
Alignment explanation
Indices: 4490598--4490673 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
4490588 GAAGATGAAG
4490598 ATAAACAACAAATGTAAATAGATTAAACAAGTCTTACT
1 ATAAACAACAAATGTAAATAGATTAAACAAGTCTTACT
4490636 ATAAACAACAAATGTAAATAGATTAAACAAGTCTTACT
1 ATAAACAACAAATGTAAATAGATTAAACAAGTCTTACT
4490674 TTGTTAATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (38 bp):
ATAAACAACAAATGTAAATAGATTAAACAAGTCTTACT
Found at i:4490664 original size:19 final size:19
Alignment explanation
Indices: 4490604--4490665 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
4490594 GAAGATAAAC
4490604 AACAAATGTAAATAGATTA
1 AACAAATGTAAATAGATTA
* * * * * *
4490623 AACAAGTCTTACTATA-AA
1 AACAAATGTAAATAGATTA
4490641 CAACAAATGTAAATAGATTA
1 -AACAAATGTAAATAGATTA
4490661 AACAA
1 AACAA
4490666 GTCTTACTTT
Statistics
Matches: 29, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 1 0.03
19 27 0.93
20 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.24
Consensus pattern (19 bp):
AACAAATGTAAATAGATTA
Found at i:4490859 original size:122 final size:123
Alignment explanation
Indices: 4490704--4490937 Score: 407
Period size: 122 Copynumber: 1.9 Consensus size: 123
4490694 TCAATAGCAC
4490704 GATCATATTCATCTGCATGATTATAAACCCATCATAAGTCGATCAATGTGCATTTAAT-AAAAAA
1 GATCATATTCATCTGCATGATTATAAACCCATCATAAGTCGATCAATGTGCATTTAATAAAAAAA
*
4490768 CAAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGTAGATCAATACTATTGAT
66 CAAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGCAGATCAATACTATTGAT
* *
4490826 GATCATATTTATCTGCATGATTATAAACTCATCATAAGTCGATCAATGTGCATTTAATAAAAAAA
1 GATCATATTCATCTGCATGATTATAAACCCATCATAAGTCGATCAATGTGCATTTAATAAAAAAA
* * *
4490891 CAAATGCTACAGTTTAACTAGACTACGAGCAAAAGCTGAGCAGATCA
66 CAAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGCAGATCA
4490938 CAGCTAAGAT
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
122 56 0.53
123 49 0.47
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (123 bp):
GATCATATTCATCTGCATGATTATAAACCCATCATAAGTCGATCAATGTGCATTTAATAAAAAAA
CAAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGCAGATCAATACTATTGAT
Found at i:4494996 original size:18 final size:18
Alignment explanation
Indices: 4494973--4495009 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4494963 TTGAATAAGA
4494973 ACACCAAAAATAGTTATG
1 ACACCAAAAATAGTTATG
4494991 ACACCAAAAATAGTTATG
1 ACACCAAAAATAGTTATG
4495009 A
1 A
4495010 TGTAATTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.22
Consensus pattern (18 bp):
ACACCAAAAATAGTTATG
Found at i:4517341 original size:20 final size:23
Alignment explanation
Indices: 4517304--4517370 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 23
4517294 ATAATGTGAT
*
4517304 TAATATTAAAA-AATTTAAATAA
1 TAATTTTAAAATAATTTAAATAA
*
4517326 -AATTTT-AAAT-ATTTAATTAA
1 TAATTTTAAAATAATTTAAATAA
*
4517346 TATTTTTAAAATAATTTAAA-AA
1 TAATTTTAAAATAATTTAAATAA
4517368 TAA
1 TAA
4517371 AAATATTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 12 0.33
21 10 0.28
22 8 0.22
23 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATTTTAAAATAATTTAAATAA
Found at i:4520502 original size:29 final size:29
Alignment explanation
Indices: 4520463--4520542 Score: 117
Period size: 28 Copynumber: 2.8 Consensus size: 29
4520453 CACTTTGTGC
4520463 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGATGGATTATAT
*
4520492 TATTCTGGTGTGTTTGGGA-GGATTATAT
1 TATTCTGGTGTGTTTTGGATGGATTATAT
* * *
4520520 GATACTGGTGTGTTTTGGTTGGA
1 TATTCTGGTGTGTTTTGGATGGA
4520543 CATTTTGGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 24 0.53
29 21 0.47
ACGTcount: A:0.16, C:0.04, G:0.33, T:0.47
Consensus pattern (29 bp):
TATTCTGGTGTGTTTTGGATGGATTATAT
Found at i:4520775 original size:21 final size:21
Alignment explanation
Indices: 4520727--4520834 Score: 110
Period size: 21 Copynumber: 5.1 Consensus size: 21
4520717 GGCTATACTG
* *
4520727 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTGTGTGTCGT
4520748 ATTTCAGGCACCTTGTGTGTCGT
1 A--TCAGGCACCTTGTGTGTCGT
* *
4520771 ATCAGGCACCTCGTGTGTTGT
1 ATCAGGCACCTTGTGTGTCGT
* * *
4520792 TTCAGGTACCTCGTGTGTCGT
1 ATCAGGCACCTTGTGTGTCGT
* *
4520813 TTCAGGCA-CTTATGTGTCGT
1 ATCAGGCACCTTGTGTGTCGT
4520833 AT
1 AT
4520835 ACTGATCAGG
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.15
21 44 0.59
23 19 0.26
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (21 bp):
ATCAGGCACCTTGTGTGTCGT
Found at i:4522074 original size:46 final size:48
Alignment explanation
Indices: 4521916--4522102 Score: 154
Period size: 46 Copynumber: 3.9 Consensus size: 48
4521906 TGGTTGGACC
4521916 ATGGCATCA-A-TGTGATATGTGA-TCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTC-GTGTAAGACCATAGCTGGGCT
* * * * *
4521962 ATGGCATCAGAGATATGTGATTACGTGCTTCCGTATAAGACCATATCTGGGAT
1 ATGGCATCAGAG---TGTGA-TATGTGATT-CGTGTAAGACCATAGCTGGGCT
* *
4522015 ATGACATC--AGTGTGATATGTGATTCGTGTAAGACCATGGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
* * *
4522061 ATGGC-TACGGTGTGTGATATGTGACTAT-GTGCAAGACCATAG
1 ATGGCAT-CAGAGTGTGATATGTGA-T-TCGTGTAAGACCATAG
4522103 TTTTACTATG
Statistics
Matches: 112, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
45 1 0.01
46 32 0.29
47 8 0.07
48 18 0.16
49 13 0.12
50 1 0.01
51 7 0.06
52 5 0.04
53 26 0.23
54 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (48 bp):
ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
Found at i:4528642 original size:39 final size:39
Alignment explanation
Indices: 4528599--4528711 Score: 99
Period size: 39 Copynumber: 2.9 Consensus size: 39
4528589 TCGGATAGTT
4528599 CGAAGTAATAGTTGACACCCAATGTCTCATCGACCTAGC
1 CGAAGTAATAGTTGACACCCAATGTCTCATCGACCTAGC
** * *
4528638 CGAAGTAA-AGTTGGTA-CCAA-GTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAATGT--CTCATCG-ACCTAGC
* *
4528677 CGAAGAAATTTAG-TGACACCCAGTGTCTCATCGAC
1 CGAAGTAA--TAGTTGACACCCAATGTCTCATCGAC
4528712 TCGAGGTCGA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
36 2 0.04
37 4 0.07
38 13 0.23
39 20 0.35
40 1 0.02
41 10 0.18
42 5 0.09
43 2 0.04
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (39 bp):
CGAAGTAATAGTTGACACCCAATGTCTCATCGACCTAGC
Found at i:4529628 original size:12 final size:12
Alignment explanation
Indices: 4529613--4529643 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4529603 TTCTCTTTTA
4529613 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
4529625 TTTTTCTTTCTC
1 TTTTTCTTTCCC
4529637 TTTTTCT
1 TTTTTCT
4529644 CCCCTCCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:4534410 original size:28 final size:28
Alignment explanation
Indices: 4534378--4534432 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4534368 ATCATACACA
4534378 TTTAAATAAATAAATAT-ATTAATTTATT
1 TTTAAATAAATAAATATAATT-ATTTATT
*
4534406 TTTAATTAAATAAATATAATTATTTAT
1 TTTAAATAAATAAATATAATTATTTAT
4534433 ATATACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAAATAAATAAATATAATTATTTATT
Found at i:4547830 original size:34 final size:34
Alignment explanation
Indices: 4547792--4547860 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
4547782 AATATTAACC
4547792 ATTGTACTTTTTAAAACTTGAAATTTTAGTCTTA
1 ATTGTACTTTTTAAAACTTGAAATTTTAGTCTTA
4547826 ATTGTACTTTTTAAAACTTGAAATTTTAGTCTTA
1 ATTGTACTTTTTAAAACTTGAAATTTTAGTCTTA
4547860 A
1 A
4547861 CCTAAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (34 bp):
ATTGTACTTTTTAAAACTTGAAATTTTAGTCTTA
Found at i:4547975 original size:18 final size:18
Alignment explanation
Indices: 4547949--4547983 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4547939 AGTATTTCTC
*
4547949 AATTGGATATTTTTAAGA
1 AATTCGATATTTTTAAGA
4547967 AATTCGATATTTTTAAG
1 AATTCGATATTTTTAAG
4547984 TTTTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (18 bp):
AATTCGATATTTTTAAGA
Found at i:4559535 original size:28 final size:28
Alignment explanation
Indices: 4559480--4559563 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
4559470 TTAAATTTTA
* * *
4559480 TCCACGTGTTATTCAACATCCTATGTTG
1 TCCACATGTCATTCGACATCCTATGTTG
* *
4559508 TTCACATGTCGTTCGACATCCTATGTTG
1 TCCACATGTCATTCGACATCCTATGTTG
*
4559536 TCCACGTGTCATTCGACATCCTATGTTG
1 TCCACATGTCATTCGACATCCTATGTTG
4559564 AAAGCTTAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (28 bp):
TCCACATGTCATTCGACATCCTATGTTG
Found at i:4563980 original size:44 final size:44
Alignment explanation
Indices: 4563917--4564047 Score: 253
Period size: 44 Copynumber: 3.0 Consensus size: 44
4563907 TCTGCTAGTG
4563917 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCGTGAATTTT
1 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCGTGAATTTT
*
4563961 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCATGAATTTT
1 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCGTGAATTTT
4564005 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCGTGAATTT
1 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCGTGAATTT
4564048 GCACATCATT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 85 1.00
ACGTcount: A:0.19, C:0.27, G:0.13, T:0.40
Consensus pattern (44 bp):
TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCGTGAATTTT
Found at i:4566042 original size:14 final size:14
Alignment explanation
Indices: 4566023--4566050 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4566013 ACTCACTGTT
4566023 TATCCGTGCATATG
1 TATCCGTGCATATG
4566037 TATCCGTGCATATG
1 TATCCGTGCATATG
4566051 CAGATCATGC
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:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
TATCCGTGCATATG
Found at i:4576212 original size:33 final size:33
Alignment explanation
Indices: 4576174--4576239 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
4576164 GACTGAGTGG
* *
4576174 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTGGTTGCTAGACAGGAGCTAGAATGT
*
4576207 GAGTGTTTGGTTGCTAGATAGGAGCTAGAATGT
1 GAGTGTTTGGTTGCTAGACAGGAGCTAGAATGT
4576240 CAAGAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.21, C:0.08, G:0.39, T:0.32
Consensus pattern (33 bp):
GAGTGTTTGGTTGCTAGACAGGAGCTAGAATGT
Found at i:4584730 original size:29 final size:30
Alignment explanation
Indices: 4584671--4584728 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4584661 TCCGAGCCTT
*
4584671 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
4584701 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
4584729 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:4584958 original size:13 final size:13
Alignment explanation
Indices: 4584940--4584971 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4584930 TTTCCAGCAA
4584940 TTATGAATTTATT
1 TTATGAATTTATT
4584953 TTATGAATTTATT
1 TTATGAATTTATT
*
4584966 TGATGA
1 TTATGA
4584972 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:4585179 original size:50 final size:50
Alignment explanation
Indices: 4585066--4585307 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
4585056 ATTTGGGTAA
* * *
4585066 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
4585122 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
4585172 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
4585222 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
4585272 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
4585308 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:4585255 original size:100 final size:103
Alignment explanation
Indices: 4585066--4585315 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
4585056 ATTTGGGTAA
4585066 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
4585131 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
4585172 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
4585234 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
4585272 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
4585316 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:4588010 original size:22 final size:23
Alignment explanation
Indices: 4587984--4588028 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
4587974 ACCTGATCAG
4587984 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
4588006 AATACGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
4588029 TCAGTAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:4588314 original size:29 final size:28
Alignment explanation
Indices: 4588232--4588315 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
4588222 AAACACACAG
* * *
4588232 TATAATCCTCCAAAACACACTAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
4588260 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
4588288 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
4588316 GCACAAAGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 32 0.64
29 18 0.36
ACGTcount: A:0.46, C:0.30, G:0.04, T:0.20
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:4598392 original size:27 final size:26
Alignment explanation
Indices: 4598354--4598512 Score: 149
Period size: 27 Copynumber: 5.9 Consensus size: 26
4598344 GCGAGGCTGC
*
4598354 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGACAG-AGCCACCAGA-A
*
4598381 CAGATATTGTGACAGAGCCACCATAA
1 CAGATATTGTGACAGAGCCACCAGAA
** *
4598407 CAGATATATGTGGTAGAGCCACCAGAT
1 CAGATAT-TGTGACAGAGCCACCAGAA
* * *
4598434 CAGATAATTGTGGCATAGCCACCAGGA
1 CAGAT-ATTGTGACAGAGCCACCAGAA
* *
4598461 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGACAGAGCCACCAGAA
* *
4598488 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGACAGAGCCACCAG
4598513 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
26 10 0.09
27 98 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGACAGAGCCACCAGAA
Found at i:4598513 original size:54 final size:54
Alignment explanation
Indices: 4598372--4598515 Score: 227
Period size: 54 Copynumber: 2.7 Consensus size: 54
4598362 GTGACGAAGT
* * ** *
4598372 CACCAGATACAGAT-ATTGTGACAGAGCCACCATAACAGATATATGTGGTAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
4598426 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
4598480 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
4598516 GCTTCCTCTA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
53 5 0.06
54 79 0.94
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:4600136 original size:26 final size:26
Alignment explanation
Indices: 4600105--4600212 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
4600095 TGAAATGCCC
*
4600105 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
4600131 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
4600157 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
4600183 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
4600209 ATCA
1 ATCA
4600213 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:4605292 original size:18 final size:19
Alignment explanation
Indices: 4605269--4605308 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
4605259 TTCCTTTAAA
4605269 TTATTTCAT-TATTTA-TTT
1 TTATTTCATCT-TTTACTTT
4605287 TTATTTCATCTTTTACTTT
1 TTATTTCATCTTTTACTTT
4605306 TTA
1 TTA
4605309 CTTTTTACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTCATCTTTTACTTT
Found at i:4608485 original size:18 final size:19
Alignment explanation
Indices: 4608447--4608486 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
4608437 CCCATCTTTC
4608447 TCTTCTAATTGGAATTTTA
1 TCTTCTAATTGGAATTTTA
4608466 TCTTCTAATTGGAA-TTTA
1 TCTTCTAATTGGAATTTTA
4608484 TCT
1 TCT
4608487 GATTTTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (19 bp):
TCTTCTAATTGGAATTTTA
Found at i:4617190 original size:29 final size:31
Alignment explanation
Indices: 4617146--4617203 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
4617136 ATGATTGAAT
4617146 TATTCAAAAAATTTTATTCAAGTC-CTAAAC
1 TATTCAAAAAATTTTATTCAAGTCACTAAAC
* *
4617176 TATTC-AAAATTTTTATTTAAGTCACTAA
1 TATTCAAAAAATTTTATTCAAGTCACTAA
4617204 GCGGTTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.41
Consensus pattern (31 bp):
TATTCAAAAAATTTTATTCAAGTCACTAAAC
Found at i:4620287 original size:22 final size:23
Alignment explanation
Indices: 4620247--4620291 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
4620237 AATATAGTTG
4620247 TTTGATAAAAGTAAATATTATTT
1 TTTGATAAAAGTAAATATTATTT
* *
4620270 TTTGA-AAAATTAATTATTATTT
1 TTTGATAAAAGTAAATATTATTT
4620292 AATTTTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (23 bp):
TTTGATAAAAGTAAATATTATTT
Found at i:4628320 original size:15 final size:15
Alignment explanation
Indices: 4628302--4628344 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
4628292 ATTCAATGTT
*
4628302 TAATAATTTAAAAAG
1 TAATAATTTAAAAAA
*
4628317 TAATTATTTGAAAAAA
1 TAATAATTT-AAAAAA
*
4628333 TATTAATTTAAA
1 TAATAATTTAAA
4628345 TTGAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
TAATAATTTAAAAAA
Found at i:4628499 original size:21 final size:22
Alignment explanation
Indices: 4628460--4628503 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
4628450 GAATATAGTG
4628460 TTTGATAAAAGTAAATATTATT
1 TTTGATAAAAGTAAATATTATT
* *
4628482 TTTGA-AAAATTAATTATTATT
1 TTTGATAAAAGTAAATATTATT
4628503 T
1 T
4628504 AATTTTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTGATAAAAGTAAATATTATT
Found at i:4651013 original size:23 final size:23
Alignment explanation
Indices: 4650985--4651028 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
4650975 TTTATACTAT
4650985 TCTCTGTCTTTTAACACGCTTTC
1 TCTCTGTCTTTTAACACGCTTTC
*
4651008 TCTCTGTCTTTTGACACGCTT
1 TCTCTGTCTTTTAACACGCTT
4651029 CTTTCTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.11, T:0.48
Consensus pattern (23 bp):
TCTCTGTCTTTTAACACGCTTTC
Found at i:4651673 original size:23 final size:23
Alignment explanation
Indices: 4651645--4651689 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
4651635 AAGAGAAAGG
4651645 AGAAGATTGCGTTGAAAAATGGA
1 AGAAGATTGCGTTGAAAAATGGA
*
4651668 AGAAGATTGTGTTGAAAAATGG
1 AGAAGATTGCGTTGAAAAATGG
4651690 CAAATCTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.24
Consensus pattern (23 bp):
AGAAGATTGCGTTGAAAAATGGA
Found at i:4659746 original size:25 final size:25
Alignment explanation
Indices: 4659712--4659760 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
4659702 TGTAATTCTT
4659712 AAAAAAAAATAAGATTAAATATTTA
1 AAAAAAAAATAAGATTAAATATTTA
4659737 AAAAAAAAATAAGATTAAATATTT
1 AAAAAAAAATAAGATTAAATATTT
4659761 CTTTTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (25 bp):
AAAAAAAAATAAGATTAAATATTTA
Found at i:4661696 original size:37 final size:37
Alignment explanation
Indices: 4661655--4661728 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
4661645 TAGCTAGGCT
4661655 ACCACTTATCACTTTACCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTACCACTTGATCAGATAAGTGTA
****
4661692 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTACCACTTGATCAGATAAGTGTA
4661729 GCTAAAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (37 bp):
ACCACTTATCACTTTACCACTTGATCAGATAAGTGTA
Found at i:4661759 original size:83 final size:80
Alignment explanation
Indices: 4661616--4661766 Score: 230
Period size: 83 Copynumber: 1.9 Consensus size: 80
4661606 CATATGACCT
**
4661616 CTTATCACTTGTCCTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTACCACTTGATC
1 CTTATCACTTGTCCTTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTTACCACTTGATC
4661681 AGATAAGTGTAACCA
66 AGATAAGTGTAACCA
* **
4661696 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCACTTG
1 CTTATCAC-TTG-TCCTTGATCAGATAAGTGTAGCT-AAACTACCACTTATCACTTTACCACTTG
4661761 ATCAGA
63 ATCAGA
4661767 AGTACTCAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 8 0.13
81 3 0.05
82 22 0.35
83 30 0.48
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (80 bp):
CTTATCACTTGTCCTTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTTACCACTTGATC
AGATAAGTGTAACCA
Found at i:4669276 original size:37 final size:37
Alignment explanation
Indices: 4669235--4669345 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
4669225 TAGCTAGGCT
****
4669235 ACCACTTATCACTTTACCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
4669272 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
4669309 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
4669346 GCTAAAACTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:4679666 original size:46 final size:45
Alignment explanation
Indices: 4679608--4679696 Score: 101
Period size: 47 Copynumber: 2.0 Consensus size: 45
4679598 TAAACACCAT
4679608 TAAAAATAATAGA-AAATAAAAATTT-TAAAAATATAATATATATAA
1 TAAAAATAATAGATAAATAAAAATTTGT-AAAATAT-ATATATATAA
* * * *
4679653 TAAAATTATATAGATAATTTAATATTTGTAAAATATATATATAT
1 TAAAAATA-ATAGATAAATAAAAATTTGTAAAATATATATATAT
4679697 TTTTTACTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
45 7 0.19
46 13 0.35
47 16 0.43
48 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (45 bp):
TAAAAATAATAGATAAATAAAAATTTGTAAAATATATATATATAA
Found at i:4712174 original size:18 final size:18
Alignment explanation
Indices: 4712140--4712188 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
4712130 ACACATAAAG
4712140 TTAGATAAAAAAACACT-T
1 TTAGAT-AAAAAACACTAT
* *
4712158 TTGAGGTAAAAAGCACTAT
1 TT-AGATAAAAAACACTAT
4712177 TTAGATAAAAAA
1 TTAGATAAAAAA
4712189 AATATTGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (18 bp):
TTAGATAAAAAACACTAT
Found at i:4713564 original size:18 final size:19
Alignment explanation
Indices: 4713536--4713578 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4713526 TAGATATTGT
4713536 TTTTAATAATT-TTAA-AATA
1 TTTT-ATAATTCTTAATAA-A
4713555 TTTTATAATTCTTAATAAA
1 TTTTATAATTCTTAATAAA
4713574 TTTTA
1 TTTTA
4713579 ATCAATTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.27
19 14 0.64
20 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTATAATTCTTAATAAA
Found at i:4720486 original size:21 final size:21
Alignment explanation
Indices: 4720462--4720527 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
4720452 ACTCATATGA
*
4720462 GTTTCAGTTTAACCCTTCTGG
1 GTTTCAATTTAACCCTTCTGG
* * *
4720483 GTTTCAATTTAGCTCTTCTGA
1 GTTTCAATTTAACCCTTCTGG
* * *
4720504 GCTTCAAATTAA-CCTTATGG
1 GTTTCAATTTAACCCTTCTGG
4720524 GTTT
1 GTTT
4720528 TTGTTCAGCT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
20 8 0.24
21 26 0.76
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (21 bp):
GTTTCAATTTAACCCTTCTGG
Found at i:4720557 original size:41 final size:42
Alignment explanation
Indices: 4720457--4720570 Score: 122
Period size: 41 Copynumber: 2.7 Consensus size: 42
4720447 AGTTAACTCA
* * *
4720457 TATGAGTTTCAGTTTAACCCTTCTGGGTTTCAATTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCAATTCAGCTCT
* ** ***
4720499 TCTGAGCTTCAAATTAA-CCTTATGGGTTTTTGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCAATTCAGCTCT
* *
4720540 TATGAGCTTCCGTTTAACCCTTACGGGTTTC
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTC
4720571 TCTTTAACAC
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
41 32 0.57
42 24 0.43
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTCAATTCAGCTCT
Found at i:4724631 original size:49 final size:50
Alignment explanation
Indices: 4724576--4724695 Score: 163
Period size: 49 Copynumber: 2.4 Consensus size: 50
4724566 ATCTAGTACG
* **
4724576 CATAGTAGCCTGCACTTAGTACTACACATGCGA-CTAATTATCCAG-TACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCAT-CAGATACA
* * *
4724625 CGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCAGATACA
4724675 CATAGTAGCCTGCACTTAGTA
1 CATAGTAGCCTGCACTTAGTA
4724696 GTAGTCTGCA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 32 0.52
50 30 0.48
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCAGATACA
Found at i:4724699 original size:17 final size:17
Alignment explanation
Indices: 4724677--4724712 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4724667 CTGATACACA
4724677 TAGTAGCCTGCACTTAG
1 TAGTAGCCTGCACTTAG
*
4724694 TAGTAGTCTGCACTTAG
1 TAGTAGCCTGCACTTAG
4724711 TA
1 TA
4724713 CTACACACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (17 bp):
TAGTAGCCTGCACTTAG
Found at i:4727956 original size:102 final size:102
Alignment explanation
Indices: 4727780--4727981 Score: 386
Period size: 102 Copynumber: 2.0 Consensus size: 102
4727770 TGGTCATTCC
* *
4727780 AATGGCTAATCATTTACAAACCCTTTTCTTTCCAAACCATAGTCATATCATAAGATCATTTACAC
1 AATGGCCAATCATTTACAAACCCTTTTCTTTCCAAACCATAGCCATATCATAAGATCATTTACAC
4727845 AAAGTGAGCATTTTGCCATACATGCCACATTCAAAGG
66 AAAGTGAGCATTTTGCCATACATGCCACATTCAAAGG
4727882 AATGGCCAATCATTTACAAACCCTTTTCTTTCCAAACCATAGCCATATCATAAGATCATTTACAC
1 AATGGCCAATCATTTACAAACCCTTTTCTTTCCAAACCATAGCCATATCATAAGATCATTTACAC
4727947 AAAGTGAGCATTTTGCCATACATGCCACATTCAAA
66 AAAGTGAGCATTTTGCCATACATGCCACATTCAAA
4727982 ACACACAAGC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (102 bp):
AATGGCCAATCATTTACAAACCCTTTTCTTTCCAAACCATAGCCATATCATAAGATCATTTACAC
AAAGTGAGCATTTTGCCATACATGCCACATTCAAAGG
Found at i:4728563 original size:47 final size:49
Alignment explanation
Indices: 4728441--4728620 Score: 191
Period size: 47 Copynumber: 3.8 Consensus size: 49
4728431 TGTAACCCGC
* * * *
4728441 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-G-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
* *
4728487 CCATAAGTGAAATCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
*
4728537 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATT-CACAT
*
4728581 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
4728621 TCAACCATTC
Statistics
Matches: 112, Mismatches: 9, Indels: 22
0.78 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 5 0.04
45 1 0.01
46 34 0.30
47 59 0.53
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:4728609 original size:94 final size:93
Alignment explanation
Indices: 4728449--4728620 Score: 283
Period size: 94 Copynumber: 1.8 Consensus size: 93
4728439 GCCCATAAGT
* *
4728449 GAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAGTGAAATCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAGCATTCACATCCATAAGTGAAATCGGACTCAACTCAA
4728514 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
4728542 GAACTCGGACTCAACTCAACGAGTTCG-GACATTCCACATCCATAAGTGAACTCGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGCTCGAG-CATT-CACATCCATAAGTGAAATCGGACTCAACTC
4728606 AACGAGTTCGGATGC
64 AACGAGTTCGGATGC
4728621 TCAACCATTC
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
92 1 0.01
93 29 0.40
94 43 0.59
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAGCATTCACATCCATAAGTGAAATCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:4729073 original size:30 final size:30
Alignment explanation
Indices: 4729039--4729098 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4729029 CCTTAATACG
4729039 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
4729069 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
4729099 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:4731269 original size:13 final size:13
Alignment explanation
Indices: 4731248--4731277 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4731238 ATATAACCGA
4731248 TTCATATAGCCAT
1 TTCATATAGCCAT
*
4731261 TTCATATAGTCAT
1 TTCATATAGCCAT
4731274 TTCA
1 TTCA
4731278 AAGTGTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
TTCATATAGCCAT
Found at i:4747917 original size:47 final size:47
Alignment explanation
Indices: 4747808--4747918 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
4747798 CCGGGATAAG
* *
4747808 CACATAGTGCTTCATCGGAACAAATCCGGGACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
4747855 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
4747902 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
4747919 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:4755617 original size:22 final size:22
Alignment explanation
Indices: 4755589--4755633 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4755579 TGGGCTGGTG
*
4755589 TAAGTCACATTTCATTGTTCAT
1 TAAGTCACATTTCATTGCTCAT
4755611 TAAGTCACATTTCATTGCTCAT
1 TAAGTCACATTTCATTGCTCAT
4755633 T
1 T
4755634 CGTGTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (22 bp):
TAAGTCACATTTCATTGCTCAT
Found at i:4770543 original size:21 final size:21
Alignment explanation
Indices: 4770517--4770557 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4770507 AGACGAGCAA
* *
4770517 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
4770538 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
4770558 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:4785822 original size:18 final size:16
Alignment explanation
Indices: 4785799--4785843 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
4785789 AGTATAAATG
4785799 ATATACAAAACAATATAT
1 ATATACAAAA-AATA-AT
4785817 ATATACAAATAAATAAT
1 ATATACAAA-AAATAAT
*
4785834 ATAAACAAAA
1 ATATACAAAA
4785844 TACAAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 10 0.40
18 13 0.52
19 1 0.04
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (16 bp):
ATATACAAAAAATAAT
Found at i:4785889 original size:23 final size:20
Alignment explanation
Indices: 4785859--4785900 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 20
4785849 ATAACTTAAT
4785859 ATAAATAATATATATAAAAATA
1 ATAAATAATAT-T-TAAAAATA
4785881 ATAATATAATATTTAAAAAT
1 ATAA-ATAATATTTAAAAAT
4785901 GTTCATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAATAATATTTAAAAATA
Found at i:4786439 original size:13 final size:13
Alignment explanation
Indices: 4786421--4786446 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4786411 GGTAATGGGG
4786421 TTAGTGGGGTGAT
1 TTAGTGGGGTGAT
4786434 TTAGTGGGGTGAT
1 TTAGTGGGGTGAT
4786447 GGAATTAGTA
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:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTAGTGGGGTGAT
Found at i:4791060 original size:23 final size:22
Alignment explanation
Indices: 4790999--4791064 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
4790989 ACCTGATCAG
4790999 AATACGACACATAAGTGCCTG-
1 AATACGACACATAAGTGCCTGA
* *
4791020 AA-ACGACACACGAGGTGCCTGA
1 AATACGACACA-TAAGTGCCTGA
4791042 AATACGACACATAAAGTGCCTGA
1 AATACGACACAT-AAGTGCCTGA
4791065 TCAGTAAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 8 0.22
21 10 0.27
22 2 0.05
23 17 0.46
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (22 bp):
AATACGACACATAAGTGCCTGA
Found at i:4791324 original size:23 final size:23
Alignment explanation
Indices: 4791255--4791352 Score: 70
Period size: 28 Copynumber: 3.8 Consensus size: 23
4791245 AAATGTCCAA
* *
4791255 CCAAAACACACTAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
4791278 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
4791306 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----A-ATAATCC-T
4791335 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
4791353 GCACAAAGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
23 13 0.21
24 3 0.05
25 1 0.02
28 32 0.51
29 14 0.22
ACGTcount: A:0.47, C:0.32, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:4791351 original size:29 final size:28
Alignment explanation
Indices: 4791269--4791352 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
4791259 AACACACTAG
* *
4791269 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
4791297 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
4791325 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
4791353 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:4799277 original size:31 final size:29
Alignment explanation
Indices: 4799242--4799312 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 29
4799232 TTAATAAAGG
*
4799242 TAAAATTATACTTTAATCCTCCCTAAAATTA
1 TAAAATTATA-TTTAATCCTCCAT-AAATTA
*
4799273 TAAAAATTCA-ATTTAATCCTTCATAAATTA
1 T-AAAATT-ATATTTAATCCTCCATAAATTA
*
4799303 TAAAAATATA
1 TAAAATTATA
4799313 AACTATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
28 1 0.03
29 6 0.18
30 7 0.21
31 12 0.35
32 7 0.21
33 1 0.03
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAAATTATATTTAATCCTCCATAAATTA
Found at i:4801488 original size:19 final size:19
Alignment explanation
Indices: 4801452--4801490 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
4801442 GAAATATTTA
*
4801452 TTTTGATGTTTTTAATATT
1 TTTTGATGTTTATAATATT
4801471 TTTTGATGTATTATATATAT
1 TTTTGATGT-TTATA-ATAT
4801491 AAATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (19 bp):
TTTTGATGTTTATAATATT
Found at i:4804134 original size:24 final size:23
Alignment explanation
Indices: 4804088--4804151 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
4804078 AAGATAAATT
*
4804088 AATAATAATTCAAAAAAATTTAAA
1 AATAATAATT-AAAAATATTTAAA
* *
4804112 AGTAATACTTAAAAATATATTAAA
1 AATAATAATTAAAAATAT-TTAAA
* *
4804136 AATTATATTTAAAAAT
1 AATAATAATTAAAAAT
4804152 TAAGAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (23 bp):
AATAATAATTAAAAATATTTAAA
Found at i:4804149 original size:13 final size:13
Alignment explanation
Indices: 4804105--4804153 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
4804095 ATTCAAAAAA
* *
4804105 ATTTAAAAGTAAT
1 ATTTAAAAATTAT
*
4804118 ACTTAAAAA-TAT
1 ATTTAAAAATTAT
4804130 A-TTAAAAATTAT
1 ATTTAAAAATTAT
4804142 ATTTAAAAATTA
1 ATTTAAAAATTA
4804154 AGAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 7 0.23
12 7 0.23
13 17 0.55
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
ATTTAAAAATTAT
Found at i:4819299 original size:20 final size:19
Alignment explanation
Indices: 4819269--4819311 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
4819259 GAATTAAATT
*
4819269 ATATTAAATTAAAGTATAA
1 ATATTAAATTAAAATATAA
*
4819288 ATATTAAAATTAAAATTTAA
1 ATATT-AAATTAAAATATAA
4819308 ATAT
1 ATAT
4819312 AGTAGAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATTAAATTAAAATATAA
Found at i:4826375 original size:47 final size:47
Alignment explanation
Indices: 4826322--4826415 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
4826312 ATTTTGACAG
4826322 TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
1 TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
4826369 TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
1 TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
4826416 CTCATTCAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (47 bp):
TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
Found at i:4838164 original size:17 final size:16
Alignment explanation
Indices: 4838140--4838179 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
4838130 ATATTTTAGA
*
4838140 AATTTAAATATAATAT
1 AATTTAAATAAAATAT
4838156 AATTATAAATAAAATAT
1 AATT-TAAATAAAATAT
*
4838173 AAATTAA
1 AATTTAA
4838180 TCTAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTTAAATAAAATAT
Found at i:4844218 original size:22 final size:22
Alignment explanation
Indices: 4844190--4844232 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4844180 CATTTTCTAA
*
4844190 TAGATTTAATGAATAAATTCAC
1 TAGATTTAATGAACAAATTCAC
4844212 TAGATTTAATGAACAAATTCA
1 TAGATTTAATGAACAAATTCA
4844233 ATATTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (22 bp):
TAGATTTAATGAACAAATTCAC
Found at i:4844849 original size:33 final size:33
Alignment explanation
Indices: 4844807--4844869 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
4844797 AAAAAAAAAT
*
4844807 TAACCATGGATTACAAATTTAATTATGGTAAAC
1 TAACCATGGATTACAAATTCAATTATGGTAAAC
4844840 TAACCATGGATTACAAATTCAATTATGGTA
1 TAACCATGGATTACAAATTCAATTATGGTA
4844870 CTATAACTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (33 bp):
TAACCATGGATTACAAATTCAATTATGGTAAAC
Found at i:4851508 original size:6 final size:6
Alignment explanation
Indices: 4851493--4851523 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
4851483 CTGTGTACCG
*
4851493 TACTGC TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
4851524 CTGGCTTCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Done.