Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 200 of 292
Found at i:59721797 original size:42 final size:42
Alignment explanation
Indices: 59721738--59721822 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
59721728 ATTCCAATAC
*
59721738 TAAAATCACCACATTACCAAGATCAACTCGAAAGTACAGTCA
1 TAAAATCACCACATTACCAAGATCAAATCGAAAGTACAGTCA
* *
59721780 TAAAATCACCACATTACCAAGATCAAATCGGAAGTATAGTCA
1 TAAAATCACCACATTACCAAGATCAAATCGAAAGTACAGTCA
59721822 T
1 T
59721823 GCTTGTCATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.21
Consensus pattern (42 bp):
TAAAATCACCACATTACCAAGATCAAATCGAAAGTACAGTCA
Found at i:59722124 original size:9 final size:9
Alignment explanation
Indices: 59722110--59722140 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
59722100 GAAGAAATAG
59722110 TATCATACA
1 TATCATACA
59722119 TATCATACA
1 TATCATACA
59722128 TATCATACA
1 TATCATACA
59722137 TATC
1 TATC
59722141 CTCTCATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
TATCATACA
Found at i:59725179 original size:20 final size:20
Alignment explanation
Indices: 59725154--59725204 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
59725144 AATATGTTTA
59725154 CTTAAAGTATCTGTACTTTG
1 CTTAAAGTATCTGTACTTTG
59725174 CTTAAAGTATCTGTACTTTG
1 CTTAAAGTATCTGTACTTTG
59725194 CTTAAAGTATC
1 CTTAAAGTATC
59725205 GATACCTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
CTTAAAGTATCTGTACTTTG
Found at i:59725220 original size:20 final size:20
Alignment explanation
Indices: 59725197--59725234 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59725187 TACTTTGCTT
59725197 AAAGTATCGATACCTTTAAC
1 AAAGTATCGATACCTTTAAC
* *
59725217 AAAGTTTCGATATCTTTA
1 AAAGTATCGATACCTTTA
59725235 TTCTGGTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
AAAGTATCGATACCTTTAAC
Found at i:59731066 original size:15 final size:17
Alignment explanation
Indices: 59731046--59731078 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
59731036 AAAAATATTA
59731046 TAAAAGTT-T-TTGTAT
1 TAAAAGTTGTATTGTAT
59731061 TAAAAGTTGTATTGTAT
1 TAAAAGTTGTATTGTAT
59731078 T
1 T
59731079 TTATTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (17 bp):
TAAAAGTTGTATTGTAT
Found at i:59742500 original size:17 final size:16
Alignment explanation
Indices: 59742478--59742522 Score: 72
Period size: 17 Copynumber: 2.7 Consensus size: 16
59742468 ATAATTAATT
59742478 ATTTTTAAAATTTAAA
1 ATTTTTAAAATTTAAA
59742494 ATATTTTAAAATTTAAA
1 AT-TTTTAAAATTTAAA
59742511 ATTATTTAAAAT
1 ATT-TTTAAAAT
59742523 ATATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.11
17 24 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTTAAAATTTAAA
Found at i:59742544 original size:27 final size:28
Alignment explanation
Indices: 59742486--59742544 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
59742476 TTATTTTTAA
* * *
59742486 AATTTAAAATATTTTAAAATTTAAAATT
1 AATTTAAAATATATAAAAATATAAAATT
*
59742514 -ATTTAAAATATATAAAAATAT-CAATT
1 AATTTAAAATATATAAAAATATAAAATT
59742540 AATTT
1 AATTT
59742545 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
AATTTAAAATATATAAAAATATAAAATT
Found at i:59749892 original size:18 final size:19
Alignment explanation
Indices: 59749856--59749893 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
59749846 TTGAAGCTTT
*
59749856 ATTTTAATATTTTTTATAC
1 ATTTTAATATTTATTATAC
59749875 ATTTTAAT-TTTATTATAC
1 ATTTTAATATTTATTATAC
59749893 A
1 A
59749894 CATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATATTTATTATAC
Found at i:59749898 original size:20 final size:19
Alignment explanation
Indices: 59749856--59749900 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
59749846 TTGAAGCTTT
*
59749856 ATTTTAATATTTTTTATAC
1 ATTTTAATATTTTTTACAC
59749875 ATTTTAAT-TTTATTATACAC
1 ATTTTAATATTT-TT-TACAC
59749895 ATTTTA
1 ATTTTA
59749901 TTACTTCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 10 0.43
20 10 0.43
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTAATATTTTTTACAC
Found at i:59752664 original size:20 final size:19
Alignment explanation
Indices: 59752620--59752664 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
59752610 GCTAGGTTTG
*
59752620 ATATCTTTTCTTTTTTATTA
1 ATAT-TTTTCTTTTTTATGA
*
59752640 TTATTTTTCTTTTTTAATGA
1 ATATTTTTCTTTTTT-ATGA
59752660 ATATT
1 ATATT
59752665 ACTATCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (19 bp):
ATATTTTTCTTTTTTATGA
Found at i:59758441 original size:15 final size:16
Alignment explanation
Indices: 59758423--59758473 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
59758413 TAAAATTTAA
59758423 ATAAA-TAAAAAATAT
1 ATAAATTAAAAAATAT
**
59758438 ATAAAATTATTAAATAT
1 AT-AAATTAAAAAATAT
*
59758455 -TAAATTAAAAATTAT
1 ATAAATTAAAAAATAT
59758470 ATAA
1 ATAA
59758474 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 13 0.46
16 7 0.25
17 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATTAAAAAATAT
Found at i:59758491 original size:34 final size:32
Alignment explanation
Indices: 59758424--59758496 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
59758414 AAAATTTAAA
*
59758424 TAAA-TAAAAAATATATAAAATTATTAAATAT
1 TAAATTAAAAAATATATAAAATTATTAAAAAT
* * *
59758455 TAAATTAAAAATTATATAATATTTTTAAAAAAAT
1 TAAATTAAAAAATATATAAAATTATT--AAAAAT
59758489 TAAATTAA
1 TAAATTAA
59758497 TATGAGTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.11
32 18 0.51
34 13 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAATTAAAAAATATATAAAATTATTAAAAAT
Found at i:59761092 original size:23 final size:21
Alignment explanation
Indices: 59761058--59761100 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
59761048 ACGTAAGTTT
59761058 CTTTTTTTTTTTATTTTTTTA
1 CTTTTTTTTTTTATTTTTTTA
*
59761079 CTTTTTTTACTTTTGTTTTTTT
1 CTTTTTTT--TTTTATTTTTTT
59761101 TATGTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (21 bp):
CTTTTTTTTTTTATTTTTTTA
Found at i:59761108 original size:9 final size:8
Alignment explanation
Indices: 59761059--59761108 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
59761049 CGTAAGTTTC
59761059 TTTT-TTT
1 TTTTATTT
59761066 TTTTATTT
1 TTTTATTT
59761074 TTTTACTTT
1 TTTTA-TTT
*
59761083 TTTTACTT
1 TTTTATTT
*
59761091 TTGT-TTT
1 TTTTATTT
*
59761098 TTTTATGT
1 TTTTATTT
59761106 TTT
1 TTT
59761109 GTCTTTTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
7 9 0.26
8 18 0.51
9 8 0.23
ACGTcount: A:0.08, C:0.04, G:0.04, T:0.84
Consensus pattern (8 bp):
TTTTATTT
Found at i:59761246 original size:15 final size:15
Alignment explanation
Indices: 59761228--59761262 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
59761218 ATTTTAAATT
59761228 TTTTAATTCAATCAG
1 TTTTAATTCAATCAG
59761243 TTTTAATTCAATCAG
1 TTTTAATTCAATCAG
59761258 TTTTA
1 TTTTA
59761263 TTGGAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (15 bp):
TTTTAATTCAATCAG
Found at i:59763147 original size:20 final size:20
Alignment explanation
Indices: 59763122--59763165 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
59763112 TAAGATACAG
59763122 TGAAGG-AAAAGAAATAACTT
1 TGAAGGTAAAAGAAATAA-TT
*
59763142 TGAAGGTAAAAGTAATAATT
1 TGAAGGTAAAAGAAATAATT
59763162 TGAA
1 TGAA
59763166 TTCATTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.52, C:0.02, G:0.20, T:0.25
Consensus pattern (20 bp):
TGAAGGTAAAAGAAATAATT
Found at i:59768576 original size:18 final size:19
Alignment explanation
Indices: 59768549--59768598 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
59768539 TTTATTGCAT
*
59768549 TTTA-TTTTTGTTTT-TAG
1 TTTATTTTTTGTTTTCTAA
59768566 TTTATTTTTTGTTTTCTAA
1 TTTATTTTTTGTTTTCTAA
59768585 TTT-TTCTTTTGTTT
1 TTTATT-TTTTGTTT
59768599 GCTTTTGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 12 0.41
19 13 0.45
ACGTcount: A:0.10, C:0.04, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTATTTTTTGTTTTCTAA
Found at i:59772128 original size:10 final size:10
Alignment explanation
Indices: 59772113--59772143 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
59772103 CTCCCCACTT
59772113 CCCTTCATCA
1 CCCTTCATCA
59772123 CCCTTCATCA
1 CCCTTCATCA
*
59772133 CCCTTCCTCA
1 CCCTTCATCA
59772143 C
1 C
59772144 TCTCCTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.16, C:0.55, G:0.00, T:0.29
Consensus pattern (10 bp):
CCCTTCATCA
Found at i:59772432 original size:16 final size:15
Alignment explanation
Indices: 59772372--59772435 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
59772362 TACTACTCTT
59772372 ATTATTATCTTTTTT-
1 ATTATTAT-TTTTTTA
*
59772387 -TTGTTATTTTTTTTA
1 ATTATTA-TTTTTTTA
*
59772402 TTTATT-TGTTTTTTA
1 ATTATTAT-TTTTTTA
59772417 ATTATTATTTTCTTTA
1 ATTATTATTTT-TTTA
59772433 ATT
1 ATT
59772436 TCTTTCTTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
14 12 0.30
15 16 0.40
16 12 0.30
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (15 bp):
ATTATTATTTTTTTA
Found at i:59773627 original size:22 final size:21
Alignment explanation
Indices: 59773602--59773644 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
59773592 AATTATTAAC
*
59773602 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATT-ATTTT
*
59773624 ATAATAAATTTTGATTATTTT
1 ATAATAAATTTTAATTATTTT
59773645 CGACAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATAATAAATTTTAATTATTTT
Found at i:59786727 original size:190 final size:192
Alignment explanation
Indices: 59786367--59786742 Score: 479
Period size: 190 Copynumber: 2.0 Consensus size: 192
59786357 GAAAAATAAT
* ** * * *
59786367 GAGGAATAAGAGGACGTCACGTGGCAGTGTGCGATTAGCCAGCACTGCCACGTCAGCAAAAAAAT
1 GAGGAATAAGAGGACGTCACGCGGCAGCATGCGATTAGCCAACAATACCACGTCAGC-AAAAAAT
* ** *
59786432 TAACGTTCTTAGTCTCAAGTATCAATATAGTGGACAAAAAAAAGTTTGGGTACCAATCTGGGAAA
65 TAACGTTCTTAGTCTCAAGTATCAATATAGTAGACAAAAAAAAGTTTGAATACAAATCT--GAAA
* * * *
59786497 AAAAAATCATAAGTATCAATTTGGGAGAAATGGACAAATTCGAGTACCAATTTTATTAAGAAAAG
128 AAAAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTATTAAGAAAAG
* * * *
59786562 GAGGTATAAGAGGACGTCACGCGGCGGCATGTGATTGGCCAACAATACCACGTCAGC-AAAAATT
1 GAGGAATAAGAGGACGTCACGCGGCAGCATGCGATTAGCCAACAATACCACGTCAGCAAAAAATT
* * * *
59786626 AACGTTGTTAGTCTTAAGTATCGATATAGTAGACAGAAAAAAA-TTTGAATATAAATCT-AAAAA
66 AACGTTCTTAGTCTCAAGTATCAATATAGTAGACA-AAAAAAAGTTTGAATACAAATCTGAAAAA
* *
59786689 AAAACCATAAGTATAAATTTGGGAGAAGTGAACAAATTCGAATACTAATTTTAT
130 AAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTAT
59786743 ATTTAACCCT
Statistics
Matches: 156, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
190 53 0.34
193 49 0.31
194 7 0.04
195 47 0.30
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (192 bp):
GAGGAATAAGAGGACGTCACGCGGCAGCATGCGATTAGCCAACAATACCACGTCAGCAAAAAATT
AACGTTCTTAGTCTCAAGTATCAATATAGTAGACAAAAAAAAGTTTGAATACAAATCTGAAAAAA
AAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTATTAAGAAAAG
Found at i:59787627 original size:15 final size:17
Alignment explanation
Indices: 59787606--59787646 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
59787596 TAATCTTTTA
59787606 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
59787622 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
59787638 AAAATTATA
1 AAAATTATA
59787647 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:59790984 original size:19 final size:19
Alignment explanation
Indices: 59790960--59791003 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
59790950 AAAATTATAC
59790960 TTTTAAAACTA-ATTTAATT
1 TTTTAAAA-TATATTTAATT
*
59790979 TTTTAAAATATTTTTAATT
1 TTTTAAAATATATTTAATT
59790998 TTTTAA
1 TTTTAA
59791004 TTTATATCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAATATATTTAATT
Found at i:59793588 original size:23 final size:23
Alignment explanation
Indices: 59793561--59793605 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
59793551 CCCGTTACAT
*
59793561 GGCTCTTTGTGAGCTTCCTGATA
1 GGCTCTTCGTGAGCTTCCTGATA
59793584 GGCTCTTCGTGAGCTTCCTGAT
1 GGCTCTTCGTGAGCTTCCTGAT
59793606 TAAAAGTTCT
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:0.11, C:0.24, G:0.27, T:0.38
Consensus pattern (23 bp):
GGCTCTTCGTGAGCTTCCTGATA
Found at i:59793695 original size:72 final size:76
Alignment explanation
Indices: 59793595--59793733 Score: 178
Period size: 72 Copynumber: 1.9 Consensus size: 76
59793585 GCTCTTCGTG
* *** *
59793595 AGCTTCCTGATTAAAAGTTCTTTGTGAACTTTTTGATT-GTGACTC-TTATAAGCTTCCTGTTAT
1 AGCTTCCTGATT-AAAGCTCTTTGTGAACTTCCCGATTAATGACTCTTTATAAGCTTCCTGTTAT
59793658 ATAGCCCGGATA
65 ATAGCCCGGATA
* *
59793670 AGCTTCCTGA-T-AAGCTCTTTGTGAACTTCCCGATTAATGACTCTTTGTGAGCTTCCTGTTATA
1 AGCTTCCTGATTAAAGCTCTTTGTGAACTTCCCGATTAATGACTCTTTATAAGCTTCCTGTTATA
59793733 T
66 T
59793734 GGCTTGAGAG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
72 20 0.36
73 6 0.11
74 19 0.35
75 10 0.18
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (76 bp):
AGCTTCCTGATTAAAGCTCTTTGTGAACTTCCCGATTAATGACTCTTTATAAGCTTCCTGTTATA
TAGCCCGGATA
Found at i:59799114 original size:11 final size:12
Alignment explanation
Indices: 59799098--59799146 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 12
59799088 AATAAAGTCA
59799098 TTATTAT-TATT
1 TTATTATATATT
59799109 TTATTATATATT
1 TTATTATATATT
59799121 TTATATATATATAT
1 TTAT-TATATAT-T
*
59799135 ATATATATATAT
1 TTAT-TATATAT
59799147 ATATAAGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 7 0.21
12 8 0.24
13 7 0.21
14 12 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATTATATATT
Found at i:59799127 original size:2 final size:2
Alignment explanation
Indices: 59799113--59799151 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
59799103 ATTATTTTAT
*
59799113 TA TA TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59799152 AGTAAAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:59800425 original size:21 final size:21
Alignment explanation
Indices: 59800371--59800426 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
59800361 TATGAACTGG
* *
59800371 ATTGAATATTGATTATATTGA
1 ATTGATTATTGAATATATTGA
59800392 ATTGATT-TATGAATATATGTGA
1 ATTGATTAT-TGAATATAT-TGA
59800414 ATTG-TTATTGAAT
1 ATTGATTATTGAAT
59800427 TGAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 21 0.70
22 8 0.27
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (21 bp):
ATTGATTATTGAATATATTGA
Found at i:59801281 original size:45 final size:45
Alignment explanation
Indices: 59801217--59801548 Score: 475
Period size: 45 Copynumber: 7.4 Consensus size: 45
59801207 TACTGTTACC
* *
59801217 GTTACTGCTACTATTACCGATTCGGCACTTTGTGTGTCGAATTTT
1 GTTACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATT
* * *
59801262 GTTACTGCTACTGTTACCGATTTGACACTTTGTGTGTTGAATATT
1 GTTACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATT
*
59801307 GTTACTGCTACTGTTACCGATTCGGCACTGTGTGTGTCGAATATT
1 GTTACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATT
* * *
59801352 GTTACTGCTACTGTTACCGATTCGACATTTTGTGTGTCAAATATT
1 GTTACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATT
* *
59801397 GTTACTGCTACTGTTACCAATTCGGCACTGTGTGTGTCGAATATT
1 GTTACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATT
* ** *
59801442 GTTACTGTTACCATTACCGATTCGGCACTTTGTGTGTCAAATATT
1 GTTACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATT
* * * * *
59801487 GTTACTGTTACCGTTACCGATTCAGCACTTTGTGTGTTGAATACT
1 GTTACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATT
*
59801532 GTTACTGTTACTGTTAC
1 GTTACTGCTACTGTTAC
59801549 TGTTACTGTT
Statistics
Matches: 257, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 257 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
GTTACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATT
Found at i:59801539 original size:6 final size:6
Alignment explanation
Indices: 59801528--59801558 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
59801518 GTGTGTTGAA
59801528 TACTGT TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
59801559 CCGGATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TACTGT
Found at i:59801608 original size:6 final size:6
Alignment explanation
Indices: 59801593--59801629 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
59801583 CTGTGTACCG
*
59801593 TACTGC TACTGT TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT T
59801630 TCGGCTTCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (6 bp):
TACTGT
Found at i:59801761 original size:18 final size:18
Alignment explanation
Indices: 59801734--59802016 Score: 187
Period size: 18 Copynumber: 15.3 Consensus size: 18
59801724 AAAGGTATAA
* *
59801734 AATAACTGATTATTACTG
1 AATAATTGATTGTTACTG
59801752 AATAATTGATTGTTACTG
1 AATAATTGATTGTTACTG
* *
59801770 GATAATTGACTGTTACTG
1 AATAATTGATTGTTACTG
* *
59801788 GAT-ATTAGACTGTTACTG
1 AATAATT-GATTGTTACTG
* * *
59801806 AATAACTGAATATTACTG
1 AATAATTGATTGTTACTG
**
59801824 AATAATTGATCATTACTG
1 AATAATTGATTGTTACTG
* *
59801842 AATAACTGATTGTCACTG
1 AATAATTGATTGTTACTG
* *
59801860 AATGAA-TGACTGCTACTG
1 AAT-AATTGATTGTTACTG
* *
59801878 AATAACTTAATAGTTACTG
1 AATAA-TTGATTGTTACTG
59801897 AAT-ATCTGATT-TTACTG
1 AATAAT-TGATTGTTACTG
*
59801914 AATAATTGACTGTTACTGG
1 AATAATTGATTGTTACT-G
* *
59801933 ATAACCGATCAATTGATCGATACTG
1 ---A---AT-AATTGATTGTTACTG
* * * *
59801958 AATAACTGGTTATTATTG
1 AATAATTGATTGTTACTG
*
59801976 AATAATTGATTGTTACCG
1 AATAATTGATTGTTACTG
* *
59801994 AATAACTGACTGTTACTG
1 AATAATTGATTGTTACTG
59802012 AATAA
1 AATAA
59802017 ATAATTATTC
Statistics
Matches: 207, Mismatches: 42, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
17 19 0.09
18 154 0.74
19 18 0.09
22 2 0.01
25 3 0.01
26 11 0.05
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
AATAATTGATTGTTACTG
Found at i:59802014 original size:36 final size:36
Alignment explanation
Indices: 59801734--59802016 Score: 214
Period size: 36 Copynumber: 7.6 Consensus size: 36
59801724 AAAGGTATAA
* *
59801734 AATAACTGATTATTACTGAATAATTGATTGTTACTG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
* * * *
59801770 GATAATTGACTGTTACTGGAT-ATTAGACTGTTACTG
1 AATAACTGACTGTTACTGAATAATT-GATTGTTACTG
* * **
59801806 AATAACTGAATATTACTGAATAATTGATCATTACTG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
* * * *
59801842 AATAACTGATTGTCACTGAATGAA-TGACTGCTACTG
1 AATAACTGACTGTTACTGAAT-AATTGATTGTTACTG
* *
59801878 AATAACTTAATAGTTACTGAAT-ATCTGATT-TTACTG
1 AATAACTGACT-GTTACTGAATAAT-TGATTGTTACTG
* * *
59801914 AATAATTGACTGTTACTGGATAACCGATCAATTGATCGATACTG
1 AATAACTGACTGTTACT-G---A---AT-AATTGATTGTTACTG
** * * *
59801958 AATAACTGGTTATTATTGAATAATTGATTGTTACCG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
59801994 AATAACTGACTGTTACTGAATAA
1 AATAACTGACTGTTACTGAATAA
59802017 ATAATTATTC
Statistics
Matches: 188, Mismatches: 43, Indels: 32
0.71 0.16 0.12
Matches are distributed among these distances:
35 10 0.05
36 130 0.69
37 20 0.11
39 1 0.01
40 1 0.01
42 2 0.01
43 5 0.03
44 19 0.10
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (36 bp):
AATAACTGACTGTTACTGAATAATTGATTGTTACTG
Found at i:59804239 original size:46 final size:46
Alignment explanation
Indices: 59804189--59804364 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
59804179 TGGTTGAGCA
59804189 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
59804235 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
59804280 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
59804328 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
59804365 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:59804345 original size:93 final size:93
Alignment explanation
Indices: 59804186--59804357 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
59804176 GGATGGTTGA
* *
59804186 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
59804251 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
59804279 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
59804344 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
59804358 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59811812 original size:46 final size:46
Alignment explanation
Indices: 59811762--59811937 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
59811752 TGGTTGAGCA
59811762 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
59811808 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
59811853 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
59811901 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
59811938 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:59811918 original size:93 final size:93
Alignment explanation
Indices: 59811759--59811930 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
59811749 GGATGGTTGA
* *
59811759 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
59811824 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
59811852 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
59811917 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
59811931 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59814979 original size:23 final size:23
Alignment explanation
Indices: 59814952--59814997 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
59814942 ACAATAATTA
59814952 AAATTAATCAAATTAAAGTGTTG
1 AAATTAATCAAATTAAAGTGTTG
59814975 AAATTAATCAAATTAAAGTGTTG
1 AAATTAATCAAATTAAAGTGTTG
59814998 GACTAAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (23 bp):
AAATTAATCAAATTAAAGTGTTG
Found at i:59815006 original size:23 final size:23
Alignment explanation
Indices: 59814952--59815006 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
59814942 ACAATAATTA
*
59814952 AAATTAATCAAATTAAAGTGTTG
1 AAATAAATCAAATTAAAGTGTTG
*
59814975 AAATTAATCAAATTAAAGTGTTG
1 AAATAAATCAAATTAAAGTGTTG
* *
59814998 GACTAAATC
1 AAATAAATC
59815007 CGTAACTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (23 bp):
AAATAAATCAAATTAAAGTGTTG
Found at i:59816663 original size:317 final size:320
Alignment explanation
Indices: 59816069--59816751 Score: 862
Period size: 317 Copynumber: 2.1 Consensus size: 320
59816059 CAACGGTTTT
*
59816069 CTAATAGGG-AGGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTG
1 CTAATAGGGCA-GCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTC
* **
59816133 TTACATTTTATTAAAGAGAGAACATATATTCAGTAATGGAGTCCTTCTGTGGTGGGGGAAGGGCA
65 TTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCCATGGTGGGGGAAGGGCA
* * * *
59816198 AGGGCAGTCTACTCGTTGTCAGGTTGCAATAAGAAATGAAAACTAGTCATTGGAGGGAACACAAG
130 AGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAAG
** * * *
59816263 GCTAGAGGAGAGTGGCTTTGCATACGAGCCTTACTCTATAGGGTCATTAGAGTGCTACAGCTAGC
195 GCTAGAGGAGAGTGGCTTCACATAAGAGCCTTACTCTATAGGGACATTAGAGTGCTACAACTAGC
* *
59816328 ACTTTGAAGCCCGCTGAAAAACAGATG--TGCTCTACTAGCGCGCAATGG-TTTGAAGCTTTG
260 ACTTTGAAGCCAGCTGAAAAACAGATGCTTG--CTACTAGCGCGCAATGGTTTTCAAGCTTTG
* * * *** * ** *
59816388 CTGATAGGGCAGCTTTATGCTTATTCAATAATTGTGGTATTGCCTTGGATTTTCTGTTTAGGTTC
1 CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACG-TTGTCCATGTAGGTTC
*
59816453 TTACATTTTATTAAATAAAGAACATATATTCAGTAATGGAGTCCTTCCATGGTGGGGGAAGGGCA
65 TTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCCATGGTGGGGGAAGGGCA
** * * *
59816518 AGGGCAG-C-A-TCCTTGTTGGGTTGAAACAAGAAACGGAAACTAGTCGTTGGAGGGAACACGAG
130 AGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAAG
* * * * *
59816580 GCTTGTGGA-ATGTGG-TTCCACATAAGAGCCTTACTCTATAGTGACGTTAGTGTGCTACAACTA
195 GCTAGAGGAGA-GTGGCTT-CACATAAGAGCCTTACTCTATAGGGACATTAGAGTGCTACAACTA
* * * *
59816643 GCACTTTGAAGCCAGCTGAAAAACTGATGCTTGCTATTGGTGCGCAATGGTTTTCAAGCTTTG
258 GCACTTTGAAGCCAGCTGAAAAACAGATGCTTGCTACTAGCGCGCAATGGTTTTCAAGCTTTG
* *
59816706 CTAATAGTGCAGCTTTATTGCTTATTCGATAATTGTGCCATTGCCA
1 CTAATAGGGCAGCTTTA-TGCTTATTCGATAATTGTGGCATTGCCA
59816752 GCATTTTCCA
Statistics
Matches: 310, Mismatches: 46, Indels: 16
0.83 0.12 0.04
Matches are distributed among these distances:
316 3 0.01
317 133 0.43
318 27 0.09
319 67 0.22
320 80 0.26
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (320 bp):
CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTCT
TACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCCATGGTGGGGGAAGGGCAA
GGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAAGG
CTAGAGGAGAGTGGCTTCACATAAGAGCCTTACTCTATAGGGACATTAGAGTGCTACAACTAGCA
CTTTGAAGCCAGCTGAAAAACAGATGCTTGCTACTAGCGCGCAATGGTTTTCAAGCTTTG
Found at i:59818912 original size:14 final size:15
Alignment explanation
Indices: 59818893--59818921 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59818883 GATTTGCAAC
59818893 AGTTAAATT-TATTA
1 AGTTAAATTATATTA
59818907 AGTTAAATTATATTA
1 AGTTAAATTATATTA
59818922 TTTTCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AGTTAAATTATATTA
Found at i:59822527 original size:28 final size:28
Alignment explanation
Indices: 59822483--59822536 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
59822473 AGTCTCTTCA
59822483 TGTTAAAAATTCTATCTATTTAATTATC
1 TGTTAAAAATTCTATCTATTTAATTATC
*
59822511 TGTTAAAAACTTC-ATCTATTTTATTA
1 TGTTAAAAA-TTCTATCTATTTAATTA
59822537 GAATTAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (28 bp):
TGTTAAAAATTCTATCTATTTAATTATC
Found at i:59822680 original size:30 final size:30
Alignment explanation
Indices: 59822614--59822680 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
59822604 AATTTTTAAT
**
59822614 AAAATAATTAATTTATTTTTTATATAATGT
1 AAAATAATTAATTTATTTTTTATATAATAA
*
59822644 ATAATAATTAATTTATTTATTTAT-TAATAA
1 AAAATAATTAATTTATTT-TTTATATAATAA
59822674 AAAATAA
1 AAAATAA
59822681 AATACAATCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (30 bp):
AAAATAATTAATTTATTTTTTATATAATAA
Found at i:59826855 original size:13 final size:13
Alignment explanation
Indices: 59826825--59826859 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
59826815 AAGTTTGGCA
59826825 ATTTTT-TATTTT
1 ATTTTTATATTTT
59826837 AGTTTTTATATTTT
1 A-TTTTTATATTTT
59826851 ATTTTTATA
1 ATTTTTATA
59826860 CAAAGATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 13 0.62
14 7 0.33
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
ATTTTTATATTTT
Found at i:59828495 original size:24 final size:24
Alignment explanation
Indices: 59828447--59828508 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
59828437 ACCTCTTTGT
* *
59828447 TTGAACCGTTATATCAATCATTTC
1 TTGAACCATTATATCAATCAGTTC
* *
59828471 TTGAACCATTATATCGATTAGTTC
1 TTGAACCATTATATCAATCAGTTC
* *
59828495 TTGGACTATTATAT
1 TTGAACCATTATAT
59828509 TGATCAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (24 bp):
TTGAACCATTATATCAATCAGTTC
Found at i:59828848 original size:25 final size:25
Alignment explanation
Indices: 59828811--59828861 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
59828801 AAACTTTTCA
* * *
59828811 ATTTTTTTATATTTTTATAATTTAT
1 ATTTTTATATATTTTAAAAATTTAT
*
59828836 ATTTTTATGTATTTTAAAAATTTAT
1 ATTTTTATATATTTTAAAAATTTAT
59828861 A
1 A
59828862 GATTTTTCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTTATATATTTTAAAAATTTAT
Found at i:59830283 original size:15 final size:14
Alignment explanation
Indices: 59830263--59830290 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59830253 TCAAGATAAG
59830263 AAAAAAATCAACAT
1 AAAAAAATCAACAT
59830277 AAAAAAATCAACAT
1 AAAAAAATCAACAT
59830291 CATCATTTTC
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:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAAATCAACAT
Found at i:59830892 original size:11 final size:11
Alignment explanation
Indices: 59830876--59830905 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
59830866 AAAGAGAAAG
59830876 AAAAACGTAGA
1 AAAAACGTAGA
59830887 AAAAACGTAGA
1 AAAAACGTAGA
59830898 AAAAACGT
1 AAAAACGT
59830906 TTTCTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.10, G:0.17, T:0.10
Consensus pattern (11 bp):
AAAAACGTAGA
Found at i:59832082 original size:31 final size:31
Alignment explanation
Indices: 59832047--59832109 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
59832037 TTCATGGAGC
59832047 TAAGGTCCAAAATATAGAAAAAACAGGTGTT
1 TAAGGTCCAAAATATAGAAAAAACAGGTGTT
* * *
59832078 TAAGGTCCAAAATATGGAAGAAATAGGTGTT
1 TAAGGTCCAAAATATAGAAAAAACAGGTGTT
59832109 T
1 T
59832110 CCACAACTCT
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:0.44, C:0.08, G:0.22, T:0.25
Consensus pattern (31 bp):
TAAGGTCCAAAATATAGAAAAAACAGGTGTT
Found at i:59836076 original size:41 final size:41
Alignment explanation
Indices: 59836031--59836148 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
59836021 TGAAAGATAA
59836031 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
59836072 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
59836102 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
59836143 ATGTAG
1 ATGTAG
59836149 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:59836087 original size:71 final size:71
Alignment explanation
Indices: 59835999--59836162 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
59835989 GAGATGTATC
59835999 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
59836064 AGGACA
66 AGGACA
59836070 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
59836135 AGGACA
66 AGGACA
59836141 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
59836163 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:59845146 original size:26 final size:26
Alignment explanation
Indices: 59845110--59845193 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
59845100 CATGATATTC
59845110 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
59845136 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
59845162 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
59845188 TTATCA
1 TTATCA
59845194 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:59849205 original size:34 final size:34
Alignment explanation
Indices: 59849162--59849227 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
59849152 TCACCACCCG
59849162 TTAAATCTGATGAAGTAAATATAATAACATATTA
1 TTAAATCTGATGAAGTAAATATAATAACATATTA
59849196 TTAAATCTGATGAAGTAAATATAATAACATAT
1 TTAAATCTGATGAAGTAAATATAATAACATAT
59849228 GCGCAATGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (34 bp):
TTAAATCTGATGAAGTAAATATAATAACATATTA
Found at i:59852403 original size:31 final size:32
Alignment explanation
Indices: 59852354--59852413 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
59852344 ATTTAGATCG
* *
59852354 AAAAAAATATCACGATTTTGTCA-ATAAAGAT
1 AAAAAAATATCACAATTTTATCATATAAAGAT
* *
59852385 AAAAAAATCTCATAATTTTATCATATAAA
1 AAAAAAATATCACAATTTTATCATATAAA
59852414 AAATTATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 19 0.79
32 5 0.21
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (32 bp):
AAAAAAATATCACAATTTTATCATATAAAGAT
Found at i:59857041 original size:32 final size:31
Alignment explanation
Indices: 59857005--59857116 Score: 103
Period size: 32 Copynumber: 3.8 Consensus size: 31
59856995 AAATGCGTGG
59857005 TTTTGTGAAATGATAACAAATATCAACTTTCA
1 TTTTGTGAAATGATAACAAATATCAACTTT-A
* *
59857037 TTTTGTGAAATGCTAACAACT-TC-A----A
1 TTTTGTGAAATGATAACAAATATCAACTTTA
* *
59857062 TTTTGTAAAATGATAGCAAATATCAACTTTAA
1 TTTTGTGAAATGATAACAAATATCAACTTT-A
* *
59857094 TTTTGTTAAATGATGAC-AATATC
1 TTTTGTGAAATGATAACAAATATC
59857117 CCTCTGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
25 18 0.28
26 2 0.03
27 1 0.02
30 1 0.02
31 8 0.12
32 34 0.53
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (31 bp):
TTTTGTGAAATGATAACAAATATCAACTTTA
Found at i:59860112 original size:42 final size:42
Alignment explanation
Indices: 59860048--59860129 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
59860038 TTTTTGAGGC
59860048 TTTTCATAATTCAACATCAAAGACCAAGTGTTTTCTCAAAAT
1 TTTTCATAATTCAACATCAAAGACCAAGTGTTTTCTCAAAAT
*
59860090 TTTTCATAATTCAACATGAAAGACCAAGTGTTTTCTCAAA
1 TTTTCATAATTCAACATCAAAGACCAAGTGTTTTCTCAAA
59860130 TGATTTTGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (42 bp):
TTTTCATAATTCAACATCAAAGACCAAGTGTTTTCTCAAAAT
Found at i:59861433 original size:30 final size:30
Alignment explanation
Indices: 59861397--59861459 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
59861387 ACTTATTTTA
59861397 TTGTTAATTTAGTTATTATTTTAAAGGCAT
1 TTGTTAATTTAGTTATTATTTTAAAGGCAT
* *
59861427 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTAGTTATTATTTTAAAGGCAT
59861457 TTG
1 TTG
59861460 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTAGTTATTATTTTAAAGGCAT
Found at i:59861472 original size:30 final size:30
Alignment explanation
Indices: 59861397--59861476 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
59861387 ACTTATTTTA
*
59861397 TTGTTAATTTAGTTATTATTTTAAAGGCAT
1 TTGTTAATTAAGTTATTATTTTAAAGGCAT
** *
59861427 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTAAGTTATTATTTTAAAGGCAT
*
59861457 TTGCTT-GTTAAGTTA-TATTT
1 TTG-TTAATTAAGTTATTATTT
59861477 ATCTTAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 5 0.11
30 37 0.84
31 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.15, T:0.56
Consensus pattern (30 bp):
TTGTTAATTAAGTTATTATTTTAAAGGCAT
Found at i:59861596 original size:11 final size:11
Alignment explanation
Indices: 59861580--59861609 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
59861570 TATATATATT
59861580 TAAAAATTATA
1 TAAAAATTATA
*
59861591 TAAAAATAATA
1 TAAAAATTATA
59861602 TAAAAATT
1 TAAAAATT
59861610 TAATACGGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:59863004 original size:18 final size:18
Alignment explanation
Indices: 59862981--59863017 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
59862971 TTAAAGAGTT
59862981 AGCAATGTCCTCTCATTG
1 AGCAATGTCCTCTCATTG
59862999 AGCAATGTCCTCTCATTG
1 AGCAATGTCCTCTCATTG
59863017 A
1 A
59863018 CATTGTGTGG
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:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (18 bp):
AGCAATGTCCTCTCATTG
Found at i:59864067 original size:12 final size:12
Alignment explanation
Indices: 59864050--59864084 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
59864040 TTTTCATAAT
59864050 TTTAATATTAAA
1 TTTAATATTAAA
59864062 TTTAATATT-AA
1 TTTAATATTAAA
59864073 TTTAATATTAAA
1 TTTAATATTAAA
59864085 GTGATTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:59874780 original size:43 final size:44
Alignment explanation
Indices: 59874733--59874815 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
59874723 TCTTTCTATT
* *
59874733 ATTATTAGGTATCTTATT-TATTTCTTTATTGTTTATTATTATG
1 ATTATTAGGTATCTTATTCTATTTATTTACTGTTTATTATTATG
* * *
59874776 ATTATTAGTTATTTTATTCTCTTTATTTACTGTTTATTAT
1 ATTATTAGGTATCTTATTCTATTTATTTACTGTTTATTAT
59874816 CTATTTTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 16 0.47
44 18 0.53
ACGTcount: A:0.23, C:0.06, G:0.07, T:0.64
Consensus pattern (44 bp):
ATTATTAGGTATCTTATTCTATTTATTTACTGTTTATTATTATG
Found at i:59883115 original size:18 final size:18
Alignment explanation
Indices: 59883094--59883129 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
59883084 AATTCAAAAT
59883094 TTAAA-AATCAAATTTAAA
1 TTAAAGAAT-AAATTTAAA
59883112 TTAAAGAATAAATTTAAA
1 TTAAAGAATAAATTTAAA
59883130 CTAATTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
TTAAAGAATAAATTTAAA
Found at i:59886546 original size:14 final size:14
Alignment explanation
Indices: 59886510--59886552 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
59886500 ACTAAAAAAC
*
59886510 AAATTCAAGAATAAAA
1 AAATTCAA-AAT-TAA
59886526 AAATTCAAAATTAA
1 AAATTCAAAATTAA
*
59886540 AATTTCAAAATTA
1 AAATTCAAAATTA
59886553 GATAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 14 0.56
15 3 0.12
16 8 0.32
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (14 bp):
AAATTCAAAATTAA
Found at i:59886621 original size:31 final size:31
Alignment explanation
Indices: 59886582--59886650 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
59886572 AATTAAAAGG
* * *
59886582 TGAA-AGATCGATTGAATAAACAAATGGATA
1 TGAATAGATCAATCGAATAAACAAATAGATA
59886612 TGAATAGATCAATCGAATAAACAAATAGATA
1 TGAATAGATCAATCGAATAAACAAATAGATA
59886643 TGAATAGA
1 TGAATAGA
59886651 AGATAGTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.23
Consensus pattern (31 bp):
TGAATAGATCAATCGAATAAACAAATAGATA
Found at i:59888670 original size:36 final size:33
Alignment explanation
Indices: 59888606--59888697 Score: 129
Period size: 36 Copynumber: 2.8 Consensus size: 33
59888596 TTAACCCCCC
59888606 AAAA-AAAAACCTAACCC---AAAAAAAAAGAA
1 AAAAGAAAAACCTAACCCAAAAAAAAAAAAGAA
59888635 AAAAGAAAAACCTAACCCCCAAAAAAAAAAGAAGAA
1 AAAAGAAAAACCTAA--CCCAAAAAAAAAA-AAGAA
59888671 AAAAGAAAAACCTAACCCAAAAAAAAA
1 AAAAGAAAAACCTAACCCAAAAAAAAA
59888698 CTAAAAAAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
29 4 0.07
30 10 0.18
32 3 0.05
34 12 0.21
35 7 0.12
36 20 0.36
ACGTcount: A:0.73, C:0.18, G:0.05, T:0.03
Consensus pattern (33 bp):
AAAAGAAAAACCTAACCCAAAAAAAAAAAAGAA
Found at i:59895311 original size:40 final size:40
Alignment explanation
Indices: 59895203--59895412 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
59895193 CGGGATTTAA
* * * * *
59895203 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
59895243 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
59895283 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
59895323 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
59895363 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
59895403 CCGGATATAT
1 CCGGATATAT
59895413 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:59902528 original size:40 final size:40
Alignment explanation
Indices: 59902420--59902629 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
59902410 CGGGATTTAA
* * * * *
59902420 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
59902460 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
59902500 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
59902540 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
59902580 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
59902620 CCGGATATAT
1 CCGGATATAT
59902630 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:59905704 original size:18 final size:18
Alignment explanation
Indices: 59905683--59905748 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
59905673 TCCATCAATT
59905683 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
59905701 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
59905719 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
*
59905737 CGAACATCATTT
1 TGAACATCATTT
59905749 CTCACATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:59907994 original size:29 final size:29
Alignment explanation
Indices: 59907962--59908034 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
59907952 CTTCTAGCTC
* * *
59907962 GCACACCCAGTGTCGTATATTTTCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
59907991 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
59908020 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
59908035 ATCTCGTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:59914675 original size:13 final size:13
Alignment explanation
Indices: 59914657--59914682 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59914647 TGGTATATTT
59914657 TTTTTATTTTTTA
1 TTTTTATTTTTTA
59914670 TTTTTATTTTTTA
1 TTTTTATTTTTTA
59914683 GGAGTCGACA
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:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:59915764 original size:20 final size:20
Alignment explanation
Indices: 59915736--59915783 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
59915726 GTCCAATTTT
*
59915736 TTATTTTTAAAAATAATTAA
1 TTATATTTAAAAATAATTAA
* * *
59915756 TTTTATTTAATATTAATTAA
1 TTATATTTAAAAATAATTAA
59915776 TTATATTT
1 TTATATTT
59915784 GACTACAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATATTTAAAAATAATTAA
Found at i:59915948 original size:23 final size:27
Alignment explanation
Indices: 59915899--59915951 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
59915889 TATATGATAT
59915899 AAATAATATAATATATAAACCAAATGAA
1 AAATAATATAATATATAAACC-AATGAA
59915927 AAATAATAT-AT-TATAAA-C-ATGAA
1 AAATAATATAATATATAAACCAATGAA
59915950 AA
1 AA
59915952 CAAGTCAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 7 0.28
25 1 0.04
26 6 0.24
27 2 0.08
28 9 0.36
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
AAATAATATAATATATAAACCAATGAA
Found at i:59917706 original size:21 final size:21
Alignment explanation
Indices: 59917665--59917706 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
59917655 TTAAGCACCC
* **
59917665 ATTAAAATTTTATTTTTTTAA
1 ATTAAAATTTTAATTCATTAA
59917686 ATTAAAATTTTAATTCATTAA
1 ATTAAAATTTTAATTCATTAA
59917707 CATATTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAAAATTTTAATTCATTAA
Found at i:59918388 original size:19 final size:21
Alignment explanation
Indices: 59918349--59918390 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
59918339 TTTCTTTAAC
*
59918349 TTTTTAAAAATTATTATAATT
1 TTTTTAAAAAATATTATAATT
59918370 TTTTTAAAAAATA-TA-AATT
1 TTTTTAAAAAATATTATAATT
59918389 TT
1 TT
59918391 GGATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTAAAAAATATTATAATT
Found at i:59918411 original size:20 final size:21
Alignment explanation
Indices: 59918349--59918439 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 21
59918339 TTTCTTTAAC
* *
59918349 TTTTTAAAAATTATTAT-AATT
1 TTTTTAAAAATTATTTTGGA-T
59918370 TTTTTAAAAAATATAAATTTTGGAT
1 TTTTT-AAAAAT-T--ATTTTGGAT
* *
59918395 TTTTTATAAA-TATTTT-GAA
1 TTTTTAAAAATTATTTTGGAT
* *
59918414 TTTTGAAAAATTATTTTGAAT
1 TTTTTAAAAATTATTTTGGAT
59918435 TTTTT
1 TTTTT
59918440 TTTATAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
19 10 0.19
20 11 0.20
21 10 0.19
22 7 0.13
23 1 0.02
24 4 0.07
25 10 0.19
26 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTTAAAAATTATTTTGGAT
Found at i:59918782 original size:6 final size:6
Alignment explanation
Indices: 59918771--59918797 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
59918761 AAAATAAGCA
59918771 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
59918798 TTGAACAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:59919251 original size:27 final size:27
Alignment explanation
Indices: 59919213--59919267 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
59919203 TGACAATTGG
*
59919213 CATTGTCACAACTTAAGCACGATGTAT
1 CATTGTCACAACTCAAGCACGATGTAT
59919240 CATTGTCACAACTCAAGCACGATGTAT
1 CATTGTCACAACTCAAGCACGATGTAT
59919267 C
1 C
59919268 TAGAGTGATT
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:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (27 bp):
CATTGTCACAACTCAAGCACGATGTAT
Found at i:59934130 original size:12 final size:12
Alignment explanation
Indices: 59934113--59934137 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59934103 TTTTAAAATT
59934113 ATGAATAATATA
1 ATGAATAATATA
59934125 ATGAATAATATA
1 ATGAATAATATA
59934137 A
1 A
59934138 AACATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAATAATATA
Found at i:59934194 original size:11 final size:11
Alignment explanation
Indices: 59934178--59934253 Score: 64
Period size: 11 Copynumber: 6.5 Consensus size: 11
59934168 TATACATAAC
59934178 ATATAATAAAA
1 ATATAATAAAA
*
59934189 AAATAATAAGTAA
1 ATATAATAA--AA
59934202 TATATAATAAAA
1 -ATATAATAAAA
*
59934214 ATATAATAAATGTT
1 ATATAATAAA---A
59934228 ATATAAT-AAA
1 ATATAATAAAA
*
59934238 ATATAATATAA
1 ATATAATAAAA
59934249 ATATA
1 ATATA
59934254 TATAGGAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 7 0.13
11 25 0.47
12 2 0.04
13 4 0.08
14 15 0.28
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
ATATAATAAAA
Found at i:59934208 original size:14 final size:13
Alignment explanation
Indices: 59934120--59934242 Score: 53
Period size: 14 Copynumber: 9.2 Consensus size: 13
59934110 ATTATGAATA
59934120 ATATAATGAATAAT
1 ATATAAT-AATAAT
59934134 ATA-AA-ACATAAAT
1 ATATAATA-AT-AAT
*
59934147 AATATAACAAATAAT
1 -ATATAA-TAATAAT
* *
59934162 ATACGATATACATAAC
1 ATA-TA-ATA-ATAAT
59934178 ATATAATAA-AA-
1 ATATAATAATAAT
*
59934189 AAATAATAAGTAAT
1 ATATAATAA-TAAT
59934203 ATATAATAA-AA-
1 ATATAATAATAAT
**
59934214 ATATAATAAATGTT
1 ATATAAT-AATAAT
59934228 ATATAATAA-AAT
1 ATATAATAATAAT
59934240 ATA
1 ATA
59934243 ATATAAATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 32
0.67 0.08 0.25
Matches are distributed among these distances:
11 16 0.19
12 12 0.14
13 10 0.12
14 27 0.32
15 8 0.10
16 10 0.12
17 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:59934208 original size:25 final size:25
Alignment explanation
Indices: 59934173--59934257 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
59934163 TACGATATAC
*
59934173 ATAACATATAATAAAAAAATAATAA
1 ATAATATATAATAAAAAAATAATAA
* *
59934198 GTAATATATAATAAAAATATAATAA
1 ATAATATATAATAAAAAAATAATAA
**
59934223 ATGTTATATAATAAAATATAAT-ATAA
1 ATAATATATAATAAAA-A-AATAATAA
59934249 AT-ATATATA
1 ATAATATATA
59934258 GGAAAATAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 41 0.82
26 7 0.14
27 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (25 bp):
ATAATATATAATAAAAAAATAATAA
Found at i:59934331 original size:26 final size:25
Alignment explanation
Indices: 59934284--59934348 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
59934274 TAAATAAAAA
*
59934284 TTTTATATAAATATATAAATAGTAC
1 TTTTATAAAAATATATAAATAGTAC
** **
59934309 TTTTAATAAAAATATATGCATAGTTT
1 TTTT-ATAAAAATATATAAATAGTAC
59934335 TTTTATAATAAATA
1 TTTTATAA-AAATA
59934349 AATTATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 8 0.24
26 25 0.76
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (25 bp):
TTTTATAAAAATATATAAATAGTAC
Found at i:59934388 original size:18 final size:17
Alignment explanation
Indices: 59934360--59934393 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
59934350 ATTATATATA
59934360 TAAAAAATAAAAAAATT
1 TAAAAAATAAAAAAATT
*
59934377 TAAAATAATAAAGAAAT
1 TAAAA-AATAAAAAAAT
59934394 GGCTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
TAAAAAATAAAAAAATT
Found at i:59941875 original size:14 final size:14
Alignment explanation
Indices: 59941856--59941890 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
59941846 AGATTTTCAG
59941856 TTCAATCGGTATCA
1 TTCAATCGGTATCA
59941870 TTCAATCGGTATCA
1 TTCAATCGGTATCA
59941884 TTCAATC
1 TTCAATC
59941891 TTTAGTACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (14 bp):
TTCAATCGGTATCA
Found at i:59943002 original size:23 final size:22
Alignment explanation
Indices: 59942970--59943037 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 22
59942960 TATGTTTTAC
*
59942970 TTAATTAATATAATATATTATAA-
1 TTAATAAATAT-ATATATTA-AAG
*
59942993 TTAATAAATATCTTATACTTAAAG
1 TTAATAAATAT-ATATA-TTAAAG
59943017 TATAAGTAAATATATATATTA
1 T-TAA-TAAATATATATATTA
59943038 CATTTGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 16 0.43
24 7 0.19
25 7 0.19
26 7 0.19
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (22 bp):
TTAATAAATATATATATTAAAG
Found at i:59943008 original size:18 final size:19
Alignment explanation
Indices: 59942971--59943014 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
59942961 ATGTTTTACT
59942971 TAATTAATATAATATATTA
1 TAATTAATATAATATATTA
*
59942990 TAATTAATA-AATATCTTA
1 TAATTAATATAATATATTA
*
59943008 TACTTAA
1 TAATTAA
59943015 AGTATAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATTAATATAATATATTA
Found at i:59944640 original size:17 final size:16
Alignment explanation
Indices: 59944607--59944637 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59944597 GCGCTGAAAC
59944607 ATATTATGTCAAAAAG
1 ATATTATGTCAAAAAG
*
59944623 ATATTGTGTCAAAAA
1 ATATTATGTCAAAAA
59944638 AGAATAAATA
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:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (16 bp):
ATATTATGTCAAAAAG
Found at i:59948098 original size:23 final size:24
Alignment explanation
Indices: 59948064--59948109 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
59948054 TCAAAATGCA
59948064 ATTTTTATTTTTTTAAAATTTTTT
1 ATTTTTATTTTTTTAAAATTTTTT
59948088 ATTTTTATTTTTTTAAAATTTT
1 ATTTTTATTTTTTTAAAATTTT
59948110 GAAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (24 bp):
ATTTTTATTTTTTTAAAATTTTTT
Found at i:59948955 original size:9 final size:9
Alignment explanation
Indices: 59948934--59948964 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
59948924 CTTTTAATTT
59948934 TTTATTATTA
1 TTTATT-TTA
59948944 TTTATTTTA
1 TTTATTTTA
59948953 TTTATTTTA
1 TTTATTTTA
59948962 TTT
1 TTT
59948965 TATGAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:59949391 original size:10 final size:11
Alignment explanation
Indices: 59949365--59949391 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
59949355 ACTATTAGTA
59949365 ATTTTTTAAAT
1 ATTTTTTAAAT
59949376 ATTTTTTAAAT
1 ATTTTTTAAAT
59949387 ATTTT
1 ATTTT
59949392 ACTATACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTTAAAT
Found at i:59950443 original size:20 final size:20
Alignment explanation
Indices: 59950402--59950440 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
59950392 AAAAAATTCA
59950402 AAAAATATAAAAAGTATTTT
1 AAAAATATAAAAAGTATTTT
*
59950422 AAAAGTATAAAAA-TATTTT
1 AAAAATATAAAAAGTATTTT
59950441 TAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAAATATAAAAAGTATTTT
Found at i:59953154 original size:14 final size:16
Alignment explanation
Indices: 59953130--59953161 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
59953120 TATTTAAAAG
59953130 ATAACATTAAAA-GAA
1 ATAACATTAAAATGAA
59953145 ATAA-ATTAAAATGAA
1 ATAACATTAAAATGAA
59953160 AT
1 AT
59953162 GAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (16 bp):
ATAACATTAAAATGAA
Found at i:59963511 original size:19 final size:19
Alignment explanation
Indices: 59963476--59963512 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59963466 CGTAAAATAT
* *
59963476 TAAAATAAATATTTATTAA
1 TAAAATAAAAATATATTAA
59963495 TAAAATAAAAATATATTA
1 TAAAATAAAAATATATTA
59963513 TAATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATAAAAATATATTAA
Found at i:59963648 original size:11 final size:11
Alignment explanation
Indices: 59963628--59963666 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
59963618 ATAACAACAA
59963628 CAAAATAATAG
1 CAAAATAATAG
* *
59963639 CAATATAATAA
1 CAAAATAATAG
59963650 CAAAATAATAG
1 CAAAATAATAG
59963661 CAAAAT
1 CAAAAT
59963667 GACAACAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:59963673 original size:22 final size:22
Alignment explanation
Indices: 59963623--59963687 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
59963613 TCCAAATAAC
*
59963623 AACAACAAAATAATAGCAATAT
1 AACAACAAAATAATAGCAAAAT
*
59963645 AATAACAAAATAATAGCAAAAT
1 AACAACAAAATAATAGCAAAAT
* * *
59963667 GACAACAAAACAACAGCAAAA
1 AACAACAAAATAATAGCAAAA
59963688 CAGCAGTAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.66, C:0.15, G:0.06, T:0.12
Consensus pattern (22 bp):
AACAACAAAATAATAGCAAAAT
Found at i:59969321 original size:34 final size:33
Alignment explanation
Indices: 59969265--59969330 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
59969255 TTTTCAAAAT
59969265 TTTTTTTAAATAATCAATATTAACTTT-ATTTAA
1 TTTTTTTAAATAATCAATATTAA-TTTAATTTAA
*
59969298 TTTTTTT-AATAATGACATAATTAATTTAATTTA
1 TTTTTTTAAATAATCA-AT-ATTAATTTAATTTA
59969331 GAAAAACGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 7 0.24
33 12 0.41
34 10 0.34
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (33 bp):
TTTTTTTAAATAATCAATATTAATTTAATTTAA
Found at i:59970608 original size:33 final size:33
Alignment explanation
Indices: 59970566--59970631 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
59970556 AAAATAAGTT
59970566 TAAAAATATAAAATCTTCAATTAGTTATGAAAA
1 TAAAAATATAAAATCTTCAATTAGTTATGAAAA
*
59970599 TAAAAATATAAAATTTTCAATTAGTTATGAAAA
1 TAAAAATATAAAATCTTCAATTAGTTATGAAAA
59970632 ATTAGTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.35
Consensus pattern (33 bp):
TAAAAATATAAAATCTTCAATTAGTTATGAAAA
Found at i:59970828 original size:31 final size:31
Alignment explanation
Indices: 59970770--59970829 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
59970760 TTAATAGTGG
*
59970770 CTTAAATAAAAATTTCTGAATAATTTAATGA
1 CTTAAATAAAAATTTCTAAATAATTTAATGA
* *
59970801 CTTAAATGAAAACTTTC-AAATAGTTTAAT
1 CTTAAAT-AAAAATTTCTAAATAATTTAAT
59970830 AATTATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (31 bp):
CTTAAATAAAAATTTCTAAATAATTTAATGA
Found at i:59974112 original size:16 final size:16
Alignment explanation
Indices: 59974087--59974117 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59974077 TCTTGAATAT
59974087 CTTGAATTATGTTTTA
1 CTTGAATTATGTTTTA
*
59974103 CTTGACTTATGTTTT
1 CTTGAATTATGTTTT
59974118 TAGGTTTTTC
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:0.19, C:0.10, G:0.13, T:0.58
Consensus pattern (16 bp):
CTTGAATTATGTTTTA
Found at i:59978905 original size:13 final size:13
Alignment explanation
Indices: 59978887--59978911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59978877 TTTCAAACTT
59978887 TTTTTAATTAATG
1 TTTTTAATTAATG
59978900 TTTTTAATTAAT
1 TTTTTAATTAAT
59978912 AAATATATTA
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:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:59979613 original size:6 final size:6
Alignment explanation
Indices: 59979602--59979639 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
59979592 GAGATCAGAA
*
59979602 AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AAAAGC AG
1 AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AG
59979640 GTGTTGACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.53, C:0.16, G:0.32, T:0.00
Consensus pattern (6 bp):
AGAAGC
Found at i:59992439 original size:22 final size:23
Alignment explanation
Indices: 59992382--59992439 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
59992372 GTGATTATAT
* *
59992382 TTTATTTCTATTTCCACAGGGTAG
1 TTTAGTTCTA-TTCCACAAGGTAG
*
59992406 GTTAGTTC-ATTCCACAAGGTAG
1 TTTAGTTCTATTCCACAAGGTAG
59992428 TTTA-TTCTATTC
1 TTTAGTTCTATTC
59992440 TGTGACTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.10
22 19 0.66
23 1 0.03
24 6 0.21
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (23 bp):
TTTAGTTCTATTCCACAAGGTAG
Found at i:59996645 original size:19 final size:19
Alignment explanation
Indices: 59996594--59996664 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
59996584 AAAATTACAA
* * *
59996594 AAAAATCAAAGTAATTTTC
1 AAAATTCAAAATAATTTTT
*
59996613 AAAATTTGAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTT
*
59996633 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
59996651 AGAAATTCTAAAAT
1 A-AAATTC-AAAAT
59996665 TTATATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 6 0.14
19 17 0.40
20 20 0.47
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:59996666 original size:18 final size:19
Alignment explanation
Indices: 59996621--59996669 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
59996611 TCAAAATTTG
*
59996621 AAAATAATTTTTA-AAATTC
1 AAAAT-ATTTATAGAAATTC
59996640 AAAATATTTATAGAAATTC
1 AAAATATTTATAGAAATTC
*
59996659 TAAA-ATTTATA
1 AAAATATTTATA
59996670 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATATTTATAGAAATTC
Found at i:59996718 original size:20 final size:20
Alignment explanation
Indices: 59996695--59996732 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59996685 TAAAATTTTT
59996695 AAAAAATCTAAAAAAATATA
1 AAAAAATCTAAAAAAATATA
* *
59996715 AAAAAATTTAATAAAATA
1 AAAAAATCTAAAAAAATA
59996733 ATAATTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAATCTAAAAAAATATA
Found at i:59996798 original size:3 final size:3
Alignment explanation
Indices: 59996790--59996825 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
59996780 CTAAAATATC
59996790 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59996826 CTTTGCTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59998550 original size:21 final size:21
Alignment explanation
Indices: 59998526--59998577 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
59998516 AGACAGGGAC
59998526 ACACGCCCGTGTGGAAGGGTT
1 ACACGCCCGTGTGGAAGGGTT
**
59998547 ACACGCTGGTGTGGAAGGGTT
1 ACACGCCCGTGTGGAAGGGTT
59998568 ACACGCCCGT
1 ACACGCCCGT
59998578 ATGTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (21 bp):
ACACGCCCGTGTGGAAGGGTT
Found at i:59999855 original size:48 final size:48
Alignment explanation
Indices: 59999784--60000067 Score: 225
Period size: 48 Copynumber: 5.9 Consensus size: 48
59999774 AGGGTAAATT
* *
59999784 GCCGATG-CATGTCCCAGATATGGTCTTACACTGGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAG
* * *** ** * *
59999831 GCCGATGCCATATCCCAAACATGGTCTTACACTAGCTTTTAACTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAG
** * * * * * *
59999879 ATCGATGCCATGTCCCAGTCATGATCTTACACTGGCTCTCATAAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-GTCGAG
* * * *
59999927 GTCGATGCCATATCCCAGACATGGTCTTACACTAG-TACACATGTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT-CACATGTCGAG
* * * * * * * *
59999975 ACCGATGCCATCTCCCAGACAAGGTCTTAAACTGGCTCTCATAAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-GTCGAG
*
60000023 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATGTC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTC
60000068 ACCTAAATAC
Statistics
Matches: 176, Mismatches: 54, Indels: 13
0.72 0.22 0.05
Matches are distributed among these distances:
47 10 0.06
48 163 0.93
49 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAG
Found at i:60000065 original size:96 final size:96
Alignment explanation
Indices: 59999785--60000068 Score: 365
Period size: 96 Copynumber: 3.0 Consensus size: 96
59999775 GGGTAAATTG
* * * *
59999785 CCGATG-CATGTCCCAGATATGGTCTTACACTGGCTCACAT-GTCGAGGCCGATGCCATATCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCCATATCCCA
* **** **
59999848 AACATGGTCTTACACTAGCTTTTAACTCAATA
65 GACATGGTCTTACACTAGCACACATGTCAATA
* * * *
59999880 TCGATGCCATGTCCCAGTCATGATCTTACACTGGCTCTCATAATGTGGTCGATGCCATATCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATATCCCAG
*
59999945 ACATGGTCTTACACTAGTACACATGTCAATA
66 ACATGGTCTTACACTAGCACACATGTCAATA
* * * *
59999976 CCGATGCCATCTCCCAGACAAGGTCTTAAACTGGCTCTCATAATGTGGCCGATGCCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATATCCCAG
60000041 ACATGGTCTTACACTAGCACACATGTCA
66 ACATGGTCTTACACTAGCACACATGTCA
60000069 CCTAAATACC
Statistics
Matches: 162, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
95 5 0.03
96 156 0.96
97 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (96 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATATCCCAG
ACATGGTCTTACACTAGCACACATGTCAATA
Found at i:60000661 original size:30 final size:30
Alignment explanation
Indices: 60000625--60000681 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
60000615 ACCAAGATTC
*
60000625 ATTTTCTTCCATAAAAATTCAGTAAAATTT
1 ATTTTCTTCCATAAAAATTCAGCAAAATTT
60000655 ATTTTCTTCCATAAAAATTCAGCAAAA
1 ATTTTCTTCCATAAAAATTCAGCAAAA
60000682 AATATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.39
Consensus pattern (30 bp):
ATTTTCTTCCATAAAAATTCAGCAAAATTT
Found at i:60002397 original size:41 final size:40
Alignment explanation
Indices: 60002326--60002404 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
60002316 TGTCGTAACT
**
60002326 TATGGTGTGTAGAGATGGATGGGTCAATTTTATTCCCCATA
1 TATGGTGTGTAGAGATGGATAAGTCAATTTTA-TCCCCATA
* *
60002367 TATGGTGTGTAGGGATTGG-TAAGTCGATTTTATCCCCA
1 TATGGTGTGTAGAGA-TGGATAAGTCAATTTTATCCCCA
60002405 CATGGTGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 6 0.18
41 24 0.73
42 3 0.09
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.37
Consensus pattern (40 bp):
TATGGTGTGTAGAGATGGATAAGTCAATTTTATCCCCATA
Found at i:60009578 original size:41 final size:41
Alignment explanation
Indices: 60009521--60009598 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
60009511 TACCGTACCT
60009521 TATGGTGTGTAGGGATGAATGGGTCGATTTTATTCCCCACA
1 TATGGTGTGTAGGGATGAATGGGTCGATTTTATTCCCCACA
** *
60009562 TATGGTGTGTAGGGATGGGTGGGTTGATTTTATTCCC
1 TATGGTGTGTAGGGATGAATGGGTCGATTTTATTCCC
60009599 ATATGGTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.18, C:0.12, G:0.33, T:0.37
Consensus pattern (41 bp):
TATGGTGTGTAGGGATGAATGGGTCGATTTTATTCCCCACA
Found at i:60016482 original size:18 final size:19
Alignment explanation
Indices: 60016467--60016502 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
60016457 CTAAAATAGT
60016467 AACAA-AATTA-ACAATAA
1 AACAAGAATTATACAATAA
60016484 AACAAGAATTATACAATAA
1 AACAAGAATTATACAATAA
60016503 CTAAACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (19 bp):
AACAAGAATTATACAATAA
Found at i:60018720 original size:100 final size:100
Alignment explanation
Indices: 60018547--60018750 Score: 401
Period size: 100 Copynumber: 2.0 Consensus size: 100
60018537 TTTCTTATCA
60018547 TAAATGTGATAGAATTGGCATCCGAGTTTGGAATATTTACATACCTGCTTGCGTTTCACTTACTT
1 TAAATGTGATAGAATTGGCATCCGAGTTTGGAATATTTACATACCTGCTTGCGTTTCACTTACTT
60018612 TACAGATTATGCGAAATTTGTGGCCAGACGGCTGG
66 TACAGATTATGCGAAATTTGTGGCCAGACGGCTGG
60018647 TAAATGTGATAGAATTGGCATCCGAGTTTGGAATATTTACATACCTGCTTGCGTTTCACTTACTT
1 TAAATGTGATAGAATTGGCATCCGAGTTTGGAATATTTACATACCTGCTTGCGTTTCACTTACTT
60018712 TACAGATTATGCGAAATTTGTGGCCAGACGGCTGG
66 TACAGATTATGCGAAATTTGTGGCCAGACGGCTGG
60018747 -AAAT
1 TAAAT
60018751 ATTACTGGTG
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 4 0.04
100 100 0.96
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (100 bp):
TAAATGTGATAGAATTGGCATCCGAGTTTGGAATATTTACATACCTGCTTGCGTTTCACTTACTT
TACAGATTATGCGAAATTTGTGGCCAGACGGCTGG
Found at i:60021309 original size:23 final size:23
Alignment explanation
Indices: 60021265--60021321 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
60021255 TTGTATAAGT
*
60021265 AAATAATAATTATTACTAAATATA
1 AAATAATAA-TATAACTAAATATA
*
60021289 ATATAATAATATAACTAAATATA
1 AAATAATAATATAACTAAATATA
60021312 AAATAA-AATA
1 AAATAATAATA
60021322 AAAAGAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 4 0.13
23 18 0.60
24 8 0.27
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATAATAATATAACTAAATATA
Found at i:60022249 original size:6 final size:6
Alignment explanation
Indices: 60022217--60022255 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
60022207 TGTGTACCGC
* * *
60022217 TACTGC TACTGC TACTGT TACTGT TACTAT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TAC
60022256 GGTGTATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:60023880 original size:33 final size:33
Alignment explanation
Indices: 60023818--60023886 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
60023808 GATGCTCTTA
* *
60023818 AAGCTATGATAACGACTTTGAAGGAGGAAACTG
1 AAGCTATAATAACGACTTTGAAGCAGGAAACTG
* *
60023851 AAGCTATAATGACGACTTTGAA-CACGGAAATTG
1 AAGCTATAATAACGACTTTGAAGCA-GGAAACTG
60023884 AAG
1 AAG
60023887 AACTCAAGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.22
Consensus pattern (33 bp):
AAGCTATAATAACGACTTTGAAGCAGGAAACTG
Found at i:60030609 original size:13 final size:13
Alignment explanation
Indices: 60030591--60030618 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
60030581 AATTCAATCC
60030591 ACATGGCCGTGTG
1 ACATGGCCGTGTG
60030604 ACATGGCCGTGTG
1 ACATGGCCGTGTG
60030617 AC
1 AC
60030619 GCACACGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.21
Consensus pattern (13 bp):
ACATGGCCGTGTG
Found at i:60037635 original size:4 final size:4
Alignment explanation
Indices: 60037628--60037670 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
60037618 TTAAAAAAAA
60037628 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
60037671 TTGGTGGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Done.