Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 173 of 189
Found at i:51397004 original size:18 final size:17
Alignment explanation
Indices: 51396969--51397019 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
51396959 TTTAACCCTA
51396969 AATTTAATTATAATTAT
1 AATTTAATTATAATTAT
*
51396986 AATTATAATTATTAATATAA
1 AATT-TAATTA-TAAT-TAT
*
51397006 AATTTTATT-TAATT
1 AATTTAATTATAATT
51397020 TTTGCACTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 1 0.03
17 8 0.28
18 6 0.21
19 8 0.28
20 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTAATTATAATTAT
Found at i:51404612 original size:43 final size:43
Alignment explanation
Indices: 51404565--51404706 Score: 167
Period size: 43 Copynumber: 3.3 Consensus size: 43
51404555 CATTAAATAA
* ** *
51404565 CATGTTCTTTAGTGATGTTTGTGGGGAAAGCGTCGTTAAAGGT
1 CATGTTCTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGGT
*
51404608 CATGTTTTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGGT
1 CATGTTCTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGGT
* * * * ** *
51404651 CATGTTCTTTAGCGGCGTTTGTAGGAAAAGCACCACTAAAGGT
1 CATGTTCTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGGT
*
51404694 CATGTTCTATAGC
1 CATGTTCTTTAGC
51404707 AGCGTTTTTC
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 85 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (43 bp):
CATGTTCTTTAGCGACATTTGTGGGGAAAGCGTCGCTAAAGGT
Found at i:51408679 original size:45 final size:45
Alignment explanation
Indices: 51408612--51408788 Score: 216
Period size: 45 Copynumber: 4.0 Consensus size: 45
51408602 GTGTACTGAG
* *
51408612 TATCATTGATTATAAAGGTGGTTGTTATGTGTTGATTCCACCGGG
1 TATCATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGA
* * *
51408657 TACCATTGATTATAAAGGTGGTTGTTATGTGCTGACTCCACTGGA
1 TATCATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGA
* ** * *
51408702 AATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
1 TATCATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGA
*
51408747 TATAATTGATTATAAAGGGTGG-TGCTT-TGTGCTGA-TCCACCG
1 TATCATTGATTATAAA-GGTGGTTG-TTATGTGCTGATTCCACCG
51408789 TGTAACGGTT
Statistics
Matches: 112, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
44 7 0.06
45 99 0.88
46 6 0.05
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (45 bp):
TATCATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGA
Found at i:51414611 original size:15 final size:15
Alignment explanation
Indices: 51414591--51414624 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
51414581 CTAAAAGCTC
*
51414591 TTATTGTGACCATTG
1 TTATTGTCACCATTG
51414606 TTATTGTCACCATTG
1 TTATTGTCACCATTG
51414621 TTAT
1 TTAT
51414625 CGACCAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.50
Consensus pattern (15 bp):
TTATTGTCACCATTG
Found at i:51415056 original size:18 final size:17
Alignment explanation
Indices: 51415017--51415059 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
51415007 AAAAACTATT
51415017 TTAAAAATTAAAAATCA
1 TTAAAAATTAAAAATCA
*
51415034 TTAAAAGATTATAAAATTA
1 TTAAAA-ATTA-AAAATCA
51415053 -TAAAAAT
1 TTAAAAAT
51415060 ATTTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 9 0.39
19 6 0.26
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
TTAAAAATTAAAAATCA
Found at i:51415626 original size:29 final size:30
Alignment explanation
Indices: 51415594--51415650 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
51415584 AATTAATAAA
*
51415594 AATAAAATTATAATTTAA-CCTTTAAAAGT
1 AATAAAATTATAATTTAATCATTTAAAAGT
*
51415623 AATAAAATTTTAATTTAATCATTTAAAA
1 AATAAAATTATAATTTAATCATTTAAAA
51415651 ATTACATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (30 bp):
AATAAAATTATAATTTAATCATTTAAAAGT
Found at i:51424474 original size:190 final size:190
Alignment explanation
Indices: 51424151--51424531 Score: 699
Period size: 190 Copynumber: 2.0 Consensus size: 190
51424141 ACTTCCAATC
51424151 AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
1 AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
51424216 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
66 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
51424281 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
131 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
*
51424341 AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATTAGATATTCCAACTTTCTTTCTTAACA
1 AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
* ** *
51424406 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTGTTCTGGCAACGATCCCAGCTTGGAAT
66 ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
* *
51424471 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAACCCAAACTCTAAAAGTG
131 CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
51424531 A
1 A
51424532 CGGCAAGAAG
Statistics
Matches: 184, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
190 184 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (190 bp):
AGCGAACTTTAGGTAAGCTTCAGAATTGGGTTACTAATCAGATATTCCAACTTTCTTTCTTAACA
ATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTATGATGGCAACGATCCCAGCGTGGAAT
CTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAGTG
Found at i:51425900 original size:25 final size:25
Alignment explanation
Indices: 51425872--51425926 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
51425862 GTACCAAATT
* *
51425872 AAAAAAAATT-AACATCAAATTTTAA
1 AAAAAAAATTAAAAACCAAA-TTTAA
*
51425897 AAAAAAACTTAAAAACCAAATTTAA
1 AAAAAAAATTAAAAACCAAATTTAA
51425922 AAAAA
1 AAAAA
51425927 TTGCGAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (25 bp):
AAAAAAAATTAAAAACCAAATTTAA
Found at i:51432584 original size:21 final size:21
Alignment explanation
Indices: 51432516--51432584 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
51432506 AAGCCCAAAG
* *
51432516 GCTGAATAGAAGCTCATGAGA
1 GCTGAATGGAAGCTCATAAGA
* * * *
51432537 GCTAAATGGAAACCCATAAGG
1 GCTGAATGGAAGCTCATAAGA
* *
51432558 GTTGAATGGAAGCTCGTAAGA
1 GCTGAATGGAAGCTCATAAGA
51432579 GCTGAA
1 GCTGAA
51432585 CGAAAAATCA
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.19
Consensus pattern (21 bp):
GCTGAATGGAAGCTCATAAGA
Found at i:51432647 original size:42 final size:42
Alignment explanation
Indices: 51432534--51432674 Score: 106
Period size: 42 Copynumber: 3.4 Consensus size: 42
51432524 GAAGCTCATG
* * * * ** * **
51432534 AGAGCTAAATGGAAACCCATAAGGGTTGAATGGAAGCTCGTA
1 AGAGCTGAACGGAAAACCATAAGGGTTAAACAGAAACTCAAA
* * *
51432576 AGAGCTGAACGAAAAATCATAAGGTTTAAACA-AAAGCTCAAA
1 AGAGCTGAACGGAAAACCATAAGGGTTAAACAGAAA-CTCAAA
* *
51432618 AGAGCTGAACGGAAACCCA-ATAGGGTTAAATAGAAACTCAAA
1 AGAGCTGAACGGAAAACCATA-AGGGTTAAACAGAAACTCAAA
* *
51432660 AGTGCTAAACGGAAA
1 AGAGCTGAACGGAAA
51432675 GAAAACACGA
Statistics
Matches: 77, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
41 3 0.04
42 71 0.92
43 3 0.04
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.16
Consensus pattern (42 bp):
AGAGCTGAACGGAAAACCATAAGGGTTAAACAGAAACTCAAA
Found at i:51432674 original size:21 final size:21
Alignment explanation
Indices: 51432612--51432674 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
51432602 TAAACAAAAG
*
51432612 CTCAAAAGAGCTGAACGGAAA
1 CTCAAAAGAGCTAAACGGAAA
* * * * **
51432633 CCCAATAGGGTTAAATAGAAA
1 CTCAAAAGAGCTAAACGGAAA
*
51432654 CTCAAAAGTGCTAAACGGAAA
1 CTCAAAAGAGCTAAACGGAAA
51432675 GAAAACACGA
Statistics
Matches: 29, Mismatches: 13, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (21 bp):
CTCAAAAGAGCTAAACGGAAA
Found at i:51432795 original size:24 final size:24
Alignment explanation
Indices: 51432733--51432795 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
51432723 AATTTGCCAT
* *
51432733 CAATTCATCCTTTGAATATACCGT
1 CAATTCATCCTTTGCATATACCGC
*
51432757 CAATTCATCCTTTGCATTTACCGC
1 CAATTCATCCTTTGCATATACCGC
51432781 CAATTCATCCTTTGC
1 CAATTCATCCTTTGC
51432796 CACAGAACGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.24, C:0.30, G:0.08, T:0.38
Consensus pattern (24 bp):
CAATTCATCCTTTGCATATACCGC
Found at i:51434715 original size:10 final size:11
Alignment explanation
Indices: 51434691--51434746 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
51434681 TTATATACTA
51434691 AATAAAATAAT
1 AATAAAATAAT
51434702 AATAAAAT-AT
1 AATAAAATAAT
*
51434712 AATAAAA-AACA
1 AATAAAATAA-T
*
51434723 AATCAAAATATT
1 AAT-AAAATAAT
*
51434735 AATAAACTAAT
1 AATAAAATAAT
51434746 A
1 A
51434747 TTTATTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 10 0.28
11 18 0.50
12 7 0.19
13 1 0.03
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:51438724 original size:6 final size:6
Alignment explanation
Indices: 51438713--51438754 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
51438703 GTTTCTTTTC
*
51438713 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT CTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
51438755 GGTGTGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:51438736 original size:18 final size:17
Alignment explanation
Indices: 51438708--51438754 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
51438698 GTAAAGTTTC
*
51438708 TTTTCTTTCTTTTTCTT
1 TTTTTTTTCTTTTTCTT
51438725 TTTCTTTTTCTTTTTCTT
1 TTT-TTTTTCTTTTTCTT
*
51438743 TTTTTCTTCTTT
1 TTTTTTTTCTTT
51438755 GGTGTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCTTTTTCTT
Found at i:51442322 original size:15 final size:15
Alignment explanation
Indices: 51442302--51442334 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
51442292 ATTTGTTGGA
51442302 AACAACAGATTTCAG
1 AACAACAGATTTCAG
51442317 AACAACAGATTTCAG
1 AACAACAGATTTCAG
51442332 AAC
1 AAC
51442335 TCTCTCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.18
Consensus pattern (15 bp):
AACAACAGATTTCAG
Found at i:51450799 original size:15 final size:15
Alignment explanation
Indices: 51450751--51450802 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
51450741 TAACTCAGAT
51450751 ATTTA-TAATATTTATA
1 ATTTATTAAT-TTTA-A
*
51450767 ATTAATTTAATTTT-A
1 ATTTA-TTAATTTTAA
51450782 ATTTATTAATTTTAA
1 ATTTATTAATTTTAA
51450797 ATTTAT
1 ATTTAT
51450803 ATTATCCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 8 0.26
15 12 0.39
16 4 0.13
17 3 0.10
18 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTAATTTTAA
Found at i:51453835 original size:27 final size:27
Alignment explanation
Indices: 51453781--51453838 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
51453771 TATCAAAAGG
* *
51453781 ATATGTATATAATATAATATGAAAAAT
1 ATATGTACATAAGATAATATGAAAAAT
*
51453808 ATATGTACATAAGATAATGT-AAAGAAT
1 ATATGTACATAAGATAATATGAAA-AAT
51453835 ATAT
1 ATAT
51453839 ACGTAACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.34
Consensus pattern (27 bp):
ATATGTACATAAGATAATATGAAAAAT
Found at i:51453864 original size:23 final size:22
Alignment explanation
Indices: 51453838--51453880 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
51453828 AAAGAATATA
51453838 TACGTA-ACTAATAATATGAGAAG
1 TACGTACA-TAAT-ATATGAGAAG
51453861 TACGTACATAATATATGAGA
1 TACGTACATAATATATGAGA
51453881 TTGTGATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 10 0.53
24 1 0.05
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (22 bp):
TACGTACATAATATATGAGAAG
Found at i:51453879 original size:22 final size:23
Alignment explanation
Indices: 51453838--51453880 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
51453828 AAAGAATATA
51453838 TACGTAACTAATAATATGAGAAG
1 TACGTAACTAATAATATGAGAAG
51453861 TACGT-ACATAAT-ATATGAGA
1 TACGTAAC-TAATAATATGAGA
51453881 TTGTGATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (23 bp):
TACGTAACTAATAATATGAGAAG
Found at i:51454228 original size:3 final size:3
Alignment explanation
Indices: 51454214--51454264 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
51454204 AAACATAAAC
* *
51454214 TAA TACA TAA TAA TAT TAA TAA TAA TAA -AA TTAA TAA T-A TAA AAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
51454259 TAA TAA
1 TAA TAA
51454265 GAGTATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.77
4 5 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:51454246 original size:15 final size:15
Alignment explanation
Indices: 51454214--51454264 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
51454204 AAACATAAAC
*
51454214 TAATACATAATAATAT
1 TAATA-ATAATAAAAT
51454230 TAATAATAATAAAAT
1 TAATAATAATAAAAT
*
51454245 TAATAAT-ATAAAAA
1 TAATAATAATAAAAT
51454259 TAATAA
1 TAATAA
51454265 GAGTATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.36
15 16 0.48
16 5 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAATAATAAAAT
Found at i:51455452 original size:16 final size:16
Alignment explanation
Indices: 51455431--51455462 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51455421 TTTTGTGTAA
*
51455431 TGGGCTGTTAGTTTAG
1 TGGGCTGGTAGTTTAG
51455447 TGGGCTGGTAGTTTAG
1 TGGGCTGGTAGTTTAG
51455463 GTTATTGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (16 bp):
TGGGCTGGTAGTTTAG
Found at i:51455701 original size:16 final size:18
Alignment explanation
Indices: 51455664--51455702 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
51455654 AATTAATTGA
51455664 AAAATGTAATAAAATATT
1 AAAATGTAATAAAATATT
*
51455682 AAAAT-TAATAAGAT-TT
1 AAAATGTAATAAAATATT
51455698 AAAAT
1 AAAAT
51455703 AAAAATTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 8 0.40
18 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
AAAATGTAATAAAATATT
Found at i:51468153 original size:26 final size:26
Alignment explanation
Indices: 51468110--51468160 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
51468100 TGCAAAAATA
* * *
51468110 ATATTTTAATATATATATATATATAC
1 ATATCTTAATATAAATATAAATATAC
*
51468136 ATATCTTAATGTAAATATAAATATA
1 ATATCTTAATATAAATATAAATATA
51468161 TTAAACTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (26 bp):
ATATCTTAATATAAATATAAATATAC
Found at i:51483241 original size:20 final size:21
Alignment explanation
Indices: 51483210--51483248 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
51483200 ATAATATCAA
51483210 ATAAATCTGAATTTTCATTGT
1 ATAAATCTGAATTTTCATTGT
51483231 ATAAA-CTGAATTTTCATT
1 ATAAATCTGAATTTTCATT
51483249 AATATCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (21 bp):
ATAAATCTGAATTTTCATTGT
Found at i:51483816 original size:2 final size:2
Alignment explanation
Indices: 51483811--51483843 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51483801 TTTGTGAGTA
51483811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51483844 AAAAGACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51498294 original size:21 final size:21
Alignment explanation
Indices: 51498278--51498321 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
51498268 ATAAGAAACT
51498278 AGAATAACAAGAGAAGATAAA
1 AGAATAACAAGAGAAGATAAA
51498299 AGAATAACAAGAGAAGATAAA
1 AGAATAACAAGAGAAGATAAA
51498320 AG
1 AG
51498322 TGCATACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.66, C:0.05, G:0.20, T:0.09
Consensus pattern (21 bp):
AGAATAACAAGAGAAGATAAA
Found at i:51500478 original size:14 final size:12
Alignment explanation
Indices: 51500458--51500499 Score: 59
Period size: 11 Copynumber: 3.4 Consensus size: 12
51500448 TTACCCTTTG
51500458 TTTTTTGTTCTT
1 TTTTTTGTTCTT
51500470 TATTATTTGTTCTT
1 T-TT-TTTGTTCTT
51500484 TTTTTT-TTCTT
1 TTTTTTGTTCTT
51500495 TTTTT
1 TTTTT
51500500 GTGCTCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.36
12 4 0.14
13 4 0.14
14 10 0.36
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.83
Consensus pattern (12 bp):
TTTTTTGTTCTT
Found at i:51503014 original size:178 final size:179
Alignment explanation
Indices: 51502714--51503044 Score: 538
Period size: 178 Copynumber: 1.9 Consensus size: 179
51502704 TCAAAATAAT
* * * * * *
51502714 ATTGTAAAAATAGGTAGTCATAAATCCTAAATATGAACCGTAAATTAGATATGTATTAAGAAAAC
1 ATTGTAAAAATAGGTAATCATAAACCCCAAATATGAACCATAAATTAAAGATGTATTAAGAAAAC
*
51502779 ACATAAACTTGAACTATTATTTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
66 ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
* *
51502844 TAGGAGGAATAGTTATGAACCCCTAAAAAGTTCAAGCCTTAAAAATGAC
131 TAGGAGGAACAGTTATAAACCCCTAAAAAGTTCAAGCCTTAAAAATGAC
* * *
51502893 ATTGTAAAAATAGGTAATCATGAACCCCAAATATGAACTATAAATTAAAGATGTATT-AGTAAAC
1 ATTGTAAAAATAGGTAATCATAAACCCCAAATATGAACCATAAATTAAAGATGTATTAAGAAAAC
51502957 ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
66 ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
*
51503022 TAGGAGGGACAGTTATAAACCCC
131 TAGGAGGAACAGTTATAAACCCC
51503045 AAATTTGAAC
Statistics
Matches: 139, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
178 90 0.65
179 49 0.35
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (179 bp):
ATTGTAAAAATAGGTAATCATAAACCCCAAATATGAACCATAAATTAAAGATGTATTAAGAAAAC
ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
TAGGAGGAACAGTTATAAACCCCTAAAAAGTTCAAGCCTTAAAAATGAC
Found at i:51504304 original size:13 final size:13
Alignment explanation
Indices: 51504268--51504306 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
51504258 TCGAGTCATA
51504268 AATTATATTTAATT
1 AATTAT-TTTAATT
*
51504282 AATATATTTTTATT
1 AAT-TATTTTAATT
51504296 AATTATTTTAA
1 AATTATTTTAA
51504307 ATAAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 7 0.32
14 12 0.55
15 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTATTTTAATT
Found at i:51507014 original size:19 final size:20
Alignment explanation
Indices: 51506975--51507022 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
51506965 TTAAATTTTG
**
51506975 TTAATTTTAATAATGTTAAA
1 TTAATTTTTTTAATGTTAAA
*
51506995 TTTATTTTTTTAAT-TTAAA
1 TTAATTTTTTTAATGTTAAA
51507014 TTAATTTTT
1 TTAATTTTT
51507023 ATTGTGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTAATTTTTTTAATGTTAAA
Found at i:51509202 original size:9 final size:9
Alignment explanation
Indices: 51509185--51509221 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
51509175 TGAGTTTTCG
51509185 AATTCGAAT
1 AATTCGAAT
*
51509194 AACTCGAAT
1 AATTCGAAT
51509203 AATTCGAAT
1 AATTCGAAT
51509212 AATTCGAAT
1 AATTCGAAT
51509221 A
1 A
51509222 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:51509642 original size:20 final size:19
Alignment explanation
Indices: 51509574--51509642 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
51509564 ACTCCCCCTA
*
51509574 TTTACTT-TCCCTTAAACT
1 TTTACTTCTCCCCTAAACT
51509592 TTTA-TTC-CCCC-AAACTT
1 TTTACTTCTCCCCTAAAC-T
* *
51509609 TTTATTTTTCCCCTAAACT
1 TTTACTTCTCCCCTAAACT
51509628 TTTACTTCTCACCCT
1 TTTACTTCTC-CCCT
51509643 TTACTCTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 4 0.10
17 10 0.24
18 6 0.15
19 13 0.32
20 8 0.20
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTACTTCTCCCCTAAACT
Found at i:51513979 original size:20 final size:20
Alignment explanation
Indices: 51513954--51513991 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
51513944 TGGATCAATA
*
51513954 ATTTAATATATATAATTATT
1 ATTTAACATATATAATTATT
51513974 ATTTAACATATATAATTA
1 ATTTAACATATATAATTA
51513992 GTATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTAACATATATAATTATT
Found at i:51520993 original size:3 final size:3
Alignment explanation
Indices: 51520985--51521009 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
51520975 CTGTGCTGCC
51520985 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
51521010 AAACAAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:51527730 original size:24 final size:24
Alignment explanation
Indices: 51527700--51527769 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
51527690 GCAATATTGA
51527700 TTTTTGTAGATTTACGTTGGATTT
1 TTTTTGTAGATTTACGTTGGATTT
* * * *
51527724 TTTTTGTAAATTCATGGTGGATTT
1 TTTTTGTAGATTTACGTTGGATTT
* *
51527748 TTTTTTTGAGATTTACTTTGGA
1 TTTTTGT-AGATTTACGTTGGA
51527770 CTTTAGAGAT
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.19, C:0.04, G:0.20, T:0.57
Consensus pattern (24 bp):
TTTTTGTAGATTTACGTTGGATTT
Found at i:51532568 original size:11 final size:11
Alignment explanation
Indices: 51532527--51532576 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
51532517 AATTGACCAA
51532527 AACAAAACAAG
1 AACAAAACAAG
*
51532538 AAC-TAACACAG
1 AACAAAACA-AG
51532549 ATA-AAAACAAG
1 A-ACAAAACAAG
51532560 AACAAAACAA-
1 AACAAAACAAG
51532570 AACAAAA
1 AACAAAA
51532577 AATCATTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 12 0.36
11 16 0.48
12 5 0.15
ACGTcount: A:0.72, C:0.18, G:0.06, T:0.04
Consensus pattern (11 bp):
AACAAAACAAG
Found at i:51533442 original size:25 final size:27
Alignment explanation
Indices: 51533391--51533452 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
51533381 TTTAAAATAC
* *
51533391 TTTTAAAATAAATTTTTTTATTTTTTAT
1 TTTTAAAATAAA-TTTTTTAATGTTTAT
51533419 TTTTAAAAT-AA-TTTTTAATGTTTAT
1 TTTTAAAATAAATTTTTTAATGTTTAT
*
51533444 TTTAAAAAT
1 TTTTAAAAT
51533453 GGGCCAGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.65
27 2 0.06
28 9 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTAAAATAAATTTTTTAATGTTTAT
Found at i:51543683 original size:29 final size:29
Alignment explanation
Indices: 51543647--51543714 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
51543637 GGTTAATTGT
*
51543647 GTTGTGTGGGTCATATGGGCGTGTGT-AA
1 GTTGTGTGGGTCATACGGGCGTGTGTGAA
51543675 GGTTGTGTGGGTCATACGGGCGTGTGTGAA
1 -GTTGTGTGGGTCATACGGGCGTGTGTGAA
*
51543705 GTCGTGTGGG
1 GTTGTGTGGG
51543715 CCACCCGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.12, C:0.09, G:0.47, T:0.32
Consensus pattern (29 bp):
GTTGTGTGGGTCATACGGGCGTGTGTGAA
Found at i:51548969 original size:34 final size:34
Alignment explanation
Indices: 51548931--51549000 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
51548921 ATTGTTTACC
* *
51548931 ACTGTATTGTTTTGTTA-AAGACATATTAAATGCT
1 ACTGTATTGATCTGTTACAAG-CATATTAAATGCT
* *
51548965 ACTGTATTGATCTGTTACATGCATATTAATTGCT
1 ACTGTATTGATCTGTTACAAGCATATTAAATGCT
51548999 AC
1 AC
51549001 CATTTGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (34 bp):
ACTGTATTGATCTGTTACAAGCATATTAAATGCT
Found at i:51550550 original size:31 final size:31
Alignment explanation
Indices: 51550457--51550552 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
51550447 GGCAAATTAC
*
51550457 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
51550488 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
51550520 AAGAGTAATTGAATCATAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
51550551 AA
1 AA
51550553 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:51553626 original size:29 final size:29
Alignment explanation
Indices: 51553571--51553626 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
51553561 GTAGACAACT
* *
51553571 TTTTTTTTTTGCGCTTTTTTGCTTTTTGC
1 TTTTTTTTTTGCGCTTTTGTACTTTTTGC
51553600 TTTTTTTTTTGCGC-TTTGTACTCTTTT
1 TTTTTTTTTTGCGCTTTTGTACT-TTTT
51553627 TTTTTGCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.02, C:0.14, G:0.12, T:0.71
Consensus pattern (29 bp):
TTTTTTTTTTGCGCTTTTGTACTTTTTGC
Found at i:51553629 original size:22 final size:22
Alignment explanation
Indices: 51553591--51553696 Score: 92
Period size: 22 Copynumber: 4.9 Consensus size: 22
51553581 GCGCTTTTTT
* *
51553591 GCTTTTTGCTTTTTTTTTT-GC
1 GCTTTTTACTCTTTTTTTTTGC
*
51553612 GCTTTGTACTCTTTTTTTTTGC
1 GCTTTTTACTCTTTTTTTTTGC
* **
51553634 GATTTTTTTTGC-TTTTTTTTGC
1 GCTTTTTACT-CTTTTTTTTTGC
**
51553656 GCTTTTTACTC-TTTTTTTAAC
1 GCTTTTTACTCTTTTTTTTTGC
*
51553677 GCTTTTTTGCTCTTTTTTTT
1 GC-TTTTTACTCTTTTTTTT
51553697 GCTTTTATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
21 27 0.40
22 33 0.49
23 8 0.12
ACGTcount: A:0.05, C:0.15, G:0.11, T:0.69
Consensus pattern (22 bp):
GCTTTTTACTCTTTTTTTTTGC
Found at i:51553659 original size:12 final size:12
Alignment explanation
Indices: 51553624--51553662 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
51553614 TTTGTACTCT
*
51553624 TTTTTTTTGCGA
1 TTTTTTTTGCGC
51553636 TTTTTTTT--GC
1 TTTTTTTTGCGC
51553646 TTTTTTTTGCGC
1 TTTTTTTTGCGC
51553658 TTTTT
1 TTTTT
51553663 ACTCTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.03, C:0.10, G:0.13, T:0.74
Consensus pattern (12 bp):
TTTTTTTTGCGC
Found at i:51553684 original size:44 final size:44
Alignment explanation
Indices: 51553593--51553698 Score: 119
Period size: 44 Copynumber: 2.4 Consensus size: 44
51553583 GCTTTTTTGC
**
51553593 TTTTTGCTTTTTTTTTTGCGCTTTGTACTCTTTTTTTTTGCGATTT
1 TTTTTGC--TTTTTTTTGCGCTTTGTACTCTTTTTTTACGCGATTT
*
51553639 TTTTTGCTTTTTTTTGCGCTTTTTACTCTTTTTTTAACGC--TTT
1 TTTTTGCTTTTTTTTGCGCTTTGTACTCTTTTTTT-ACGCGATTT
*
51553682 TTTGCT-CTTTTTTTTGC
1 TTT-TTGCTTTTTTTTGC
51553699 TTTTATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
43 17 0.31
44 28 0.52
45 2 0.04
46 7 0.13
ACGTcount: A:0.05, C:0.15, G:0.11, T:0.69
Consensus pattern (44 bp):
TTTTTGCTTTTTTTTGCGCTTTGTACTCTTTTTTTACGCGATTT
Found at i:51554351 original size:31 final size:31
Alignment explanation
Indices: 51554261--51554354 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
51554251 AAATTACAAG
* *
51554261 AGTAATTGAATCCTAATAAAACTCTTTCAAG
1 AGTAATTGAATCCTAATAAAACTCTTTAAAA
51554292 AGTAATTGAATCCTAATAAAAACTCTTTAAAA
1 AGTAATTGAATCCTAAT-AAAACTCTTTAAAA
51554324 AGTAATTGAATCCTAATAAAACTCTTTAAAA
1 AGTAATTGAATCCTAATAAAACTCTTTAAAA
51554355 TTATCTAAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 31 0.52
32 29 0.48
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (31 bp):
AGTAATTGAATCCTAATAAAACTCTTTAAAA
Found at i:51557316 original size:24 final size:25
Alignment explanation
Indices: 51557269--51557318 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
51557259 TTTATAGTTA
* *
51557269 AATAGATATTTACTCAAAATTGAAT
1 AATAGATATTTACTAAAAAATGAAT
*
51557294 AATAGATATTT-TTAAAAAATGAAT
1 AATAGATATTTACTAAAAAATGAAT
51557318 A
1 A
51557319 GTGTTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (25 bp):
AATAGATATTTACTAAAAAATGAAT
Found at i:51566465 original size:48 final size:48
Alignment explanation
Indices: 51566409--51566506 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
51566399 ATTTAGGTAT
51566409 TCACTTAATTTTACTAGGTATAGGTGCTTTTCTTCTTGTATTCAAGCC
1 TCACTTAATTTTACTAGGTATAGGTGCTTTTCTTCTTGTATTCAAGCC
*
51566457 TCACTTAATTTTACTAGGTATAGGTGCTTTTCTTCTTTTATTCAAGCC
1 TCACTTAATTTTACTAGGTATAGGTGCTTTTCTTCTTGTATTCAAGCC
51566505 TC
1 TC
51566507 TTTATTTTGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.47
Consensus pattern (48 bp):
TCACTTAATTTTACTAGGTATAGGTGCTTTTCTTCTTGTATTCAAGCC
Found at i:51567545 original size:12 final size:12
Alignment explanation
Indices: 51567528--51567552 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51567518 CAGCAGAAAG
51567528 GAGTGAAGAGAA
1 GAGTGAAGAGAA
51567540 GAGTGAAGAGAA
1 GAGTGAAGAGAA
51567552 G
1 G
51567553 GCATTTCAAG
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:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGTGAAGAGAA
Found at i:51577523 original size:20 final size:20
Alignment explanation
Indices: 51577495--51577532 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
51577485 TTATATATTC
51577495 TTTACAATTTTTTTAAAAAA
1 TTTACAATTTTTTTAAAAAA
*
51577515 TTTATAATTTTTTTAAAA
1 TTTACAATTTTTTTAAAA
51577533 TATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTACAATTTTTTTAAAAAA
Found at i:51577590 original size:11 final size:12
Alignment explanation
Indices: 51577568--51577601 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
51577558 TATTTAAATT
51577568 TTTTGAAATTTA
1 TTTTGAAATTTA
51577580 TTTTG-AATTTA
1 TTTTGAAATTTA
*
51577591 TTTTGTAATTT
1 TTTTGAAATTT
51577602 TTTATGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (12 bp):
TTTTGAAATTTA
Found at i:51587111 original size:3 final size:3
Alignment explanation
Indices: 51587103--51587143 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
51587093 AATCATTAAA
* *
51587103 AAT AAT AAT AAT AAT AAT ATT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
51587144 AATTTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:51587948 original size:5 final size:5
Alignment explanation
Indices: 51587940--51587974 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
51587930 TTTTTTTCTT
*
51587940 ATATA ATATA ATACA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
51587975 TAAAACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:51596125 original size:6 final size:6
Alignment explanation
Indices: 51596114--51596152 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
51596104 TTTTACATCG
51596114 ATAAAT ATAAAT ATAAAT ATAAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT AT
51596153 TCTTTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:51596140 original size:13 final size:13
Alignment explanation
Indices: 51596114--51596149 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
51596104 TTTTACATCG
51596114 ATAAATAT-AAAT
1 ATAAATATAAAAT
51596126 ATAAATATAAAAT
1 ATAAATATAAAAT
51596139 ATAAATATAAA
1 ATAAATATAAA
51596150 TATTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAATATAAAAT
Found at i:51596140 original size:19 final size:19
Alignment explanation
Indices: 51596116--51596152 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
51596106 TTACATCGAT
51596116 AAATATAAATATAAATATA
1 AAATATAAATATAAATATA
51596135 AAATATAAATATAAATAT
1 AAATATAAATATAAATAT
51596153 TCTTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATATAAATATAAATATA
Found at i:51600535 original size:7 final size:7
Alignment explanation
Indices: 51600525--51600552 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
51600515 CACTGCTGAA
51600525 CTCCTCC
1 CTCCTCC
51600532 CTCCTCC
1 CTCCTCC
51600539 CTCCTCC
1 CTCCTCC
51600546 CTCCTCC
1 CTCCTCC
51600553 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.71, G:0.00, T:0.29
Consensus pattern (7 bp):
CTCCTCC
Found at i:51601468 original size:6 final size:6
Alignment explanation
Indices: 51601457--51601504 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
51601447 CGGTAACGGA
* *
51601457 TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGTTG TTGCTG CTGCTG
1 TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG
51601505 ATGGTGAGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.17, G:0.33, T:0.50
Consensus pattern (6 bp):
TTGCTG
Found at i:51607246 original size:19 final size:18
Alignment explanation
Indices: 51607208--51607300 Score: 66
Period size: 19 Copynumber: 5.1 Consensus size: 18
51607198 CATGTGACAA
*
51607208 AAAAAATTATAAAAA-AT
1 AAAAAATAATAAAAATAT
51607225 AAAAAATAATAAAAATATT
1 AAAAAATAATAAAAATA-T
***
51607244 AAATTTTAATAAAAATAT
1 AAAAAATAATAAAAATAT
* * *
51607262 AAAATAT-TTAAAATTTACT
1 AAAAAATAATAAAA-ATA-T
51607281 AAAAAATAGA-AAAAATAT
1 AAAAAATA-ATAAAAATAT
51607299 AA
1 AA
51607301 GAATCATAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
17 19 0.32
18 12 0.20
19 24 0.41
20 4 0.07
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (18 bp):
AAAAAATAATAAAAATAT
Found at i:51607257 original size:27 final size:28
Alignment explanation
Indices: 51607227--51607293 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
51607217 TAAAAAATAA
*
51607227 AAAATAATA-AAAATA-TTAAATTTTAAT
1 AAAA-AATAGAAAATATTTAAAATTTAAT
* *
51607254 -AAAAATATAAAATATTTAAAATTTACT
1 AAAAAATAGAAAATATTTAAAATTTAAT
51607281 AAAAAATAGAAAA
1 AAAAAATAGAAAA
51607294 AATATAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 4 0.12
26 9 0.26
27 10 0.29
28 11 0.32
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (28 bp):
AAAAAATAGAAAATATTTAAAATTTAAT
Found at i:51607257 original size:28 final size:29
Alignment explanation
Indices: 51607222--51607298 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 29
51607212 AATTATAAAA
*
51607222 AATAAAAAATAATAAAAATATTAAATTTT
1 AATAAAAAATAATAAAAATATTAAAATTT
51607251 AAT-AAAAAT-AT-AAAATATTTAAAATTT
1 AATAAAAAATAATAAAAATA-TTAAAATTT
*
51607278 ACTAAAAAATAGA-AAAAATAT
1 AATAAAAAATA-ATAAAAATAT
51607299 AAGAATCATA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
26 6 0.15
27 12 0.29
28 12 0.29
29 4 0.10
30 7 0.17
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (29 bp):
AATAAAAAATAATAAAAATATTAAAATTT
Found at i:51614429 original size:36 final size:36
Alignment explanation
Indices: 51614377--51614449 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
51614367 AACTTAACTT
* * *
51614377 AAAAAATGAACGATAGGTTGATATTTATGTTTGATA
1 AAAAAATAAACAATAGGTTGATATTTATGGTTGATA
51614413 AAAAAATAAACAATAGGTTGATATTTATGGTTGATA
1 AAAAAATAAACAATAGGTTGATATTTATGGTTGATA
51614449 A
1 A
51614450 TGTCGATAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (36 bp):
AAAAAATAAACAATAGGTTGATATTTATGGTTGATA
Found at i:51617318 original size:14 final size:15
Alignment explanation
Indices: 51617291--51617319 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
51617281 CGTGGCATCC
51617291 TTCTTATATCTTTTT
1 TTCTTATATCTTTTT
51617306 TTCTTAT-TCTTTTT
1 TTCTTATATCTTTTT
51617320 ATTTCCCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTATATCTTTTT
Found at i:51620184 original size:21 final size:21
Alignment explanation
Indices: 51620158--51620197 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
51620148 ACACGCCAAT
51620158 AGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCATAAGAGCTGAAC
51620179 AGAAGCTCATAAGAGCTGA
1 AGAAGCTCATAAGAGCTGA
51620198 TCCACCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.15
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTGAAC
Found at i:51620495 original size:132 final size:138
Alignment explanation
Indices: 51620340--51620618 Score: 392
Period size: 144 Copynumber: 2.0 Consensus size: 138
51620330 CCTGTGTTCC
* *
51620340 ATTCAAATCGAAATCCAATTCAATGTTATAATTCCAACAACAATT-C-AT-TTC---CAACAATA
1 ATTCAAACCGAAATCCAATTCAATATTATAATTCCAACAACAATTACAATATTCATACAACAATA
*
51620399 GAATAAATAAATAATACCATTCATCAATTTATACAAAA-TATTAAATTTTAACTGTAAGAACTTA
66 GAAAAAATAAATAATACCATTCATCAATTTATA-AAAATTATTAAATTTTAACTGTAAGAACTTA
51620463 CCTGGCTAA
130 CCTGGCTAA
* * *
51620472 ATTCAAACCGAAATCCAATTCAATATTATAATTCCAACTATAATTCCAACAATAATTCATTTCCA
1 ATTCAAACCGAAATCCAATTCAATATTATAATTCCAACAACAATT---ACAAT-ATTCA--TACA
51620537 ACAATAGAAAAAATAAATAATACCATTCATCAATTTATAAAAATTATTAAATTTTAACTGTAAGA
60 ACAATAGAAAAAATAAATAATACCATTCATCAATTTATAAAAATTATTAAATTTTAACTGTAAGA
51620602 ACTTACCTGGCTAA
125 ACTTACCTGGCTAA
51620616 ATT
1 ATT
51620619 GCAGAAACAT
Statistics
Matches: 129, Mismatches: 5, Indels: 14
0.87 0.03 0.09
Matches are distributed among these distances:
132 41 0.32
136 1 0.01
137 2 0.02
139 3 0.02
143 4 0.03
144 78 0.60
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (138 bp):
ATTCAAACCGAAATCCAATTCAATATTATAATTCCAACAACAATTACAATATTCATACAACAATA
GAAAAAATAAATAATACCATTCATCAATTTATAAAAATTATTAAATTTTAACTGTAAGAACTTAC
CTGGCTAA
Found at i:51620515 original size:12 final size:12
Alignment explanation
Indices: 51620498--51620529 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
51620488 AATTCAATAT
51620498 TATAATTCCAAC
1 TATAATTCCAAC
51620510 TATAATTCCAAC
1 TATAATTCCAAC
*
51620522 AATAATTC
1 TATAATTC
51620530 ATTTCCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (12 bp):
TATAATTCCAAC
Found at i:51623228 original size:23 final size:23
Alignment explanation
Indices: 51623202--51623259 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
51623192 CTTAATAGTG
**
51623202 ATCATATAACCAGAATGACACAA
1 ATCATATAACCAGAACAACACAA
*
51623225 ATCACATAACCAGAACAACACAA
1 ATCATATAACCAGAACAACACAA
*
51623248 ATCGTATAACCA
1 ATCATATAACCA
51623260 AAAGAGAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.16
Consensus pattern (23 bp):
ATCATATAACCAGAACAACACAA
Found at i:51624407 original size:41 final size:41
Alignment explanation
Indices: 51624345--51624425 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 41
51624335 AATAGTGCCT
*
51624345 CACACGGTCTACCACACGGCCTAACATACGACCGTGTGGCA
1 CACACGGTCTACCACACGGCCTAACACACGACCGTGTGGCA
* * * * *
51624386 CACACGG-CATACCGCATGGCCTGACACATGGCCGTGTGGC
1 CACACGGTC-TACCACACGGCCTAACACACGACCGTGTGGC
51624426 GTCGAAGGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (41 bp):
CACACGGTCTACCACACGGCCTAACACACGACCGTGTGGCA
Found at i:51625581 original size:22 final size:20
Alignment explanation
Indices: 51625549--51625597 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
51625539 CCCGGCCCGT
51625549 AAAAAAATAAA-ATCAAAATA
1 AAAAAAATAAAGATCAAAA-A
*
51625569 AAAAAAATTTAAAGTTCAAAAA
1 AAAAAAA--TAAAGATCAAAAA
51625591 AAAAAAA
1 AAAAAAA
51625598 CATCAATCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
22 12 0.48
23 6 0.24
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAAATAAAGATCAAAAA
Found at i:51626871 original size:21 final size:22
Alignment explanation
Indices: 51626827--51626873 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
51626817 AAATTTAGTA
*
51626827 TATTTTAAATTTATTACAATAT
1 TATTTTAAATTTATAACAATAT
51626849 TATTTT-AATATTATAAC-ATAT
1 TATTTTAAAT-TTATAACAATAT
51626870 TATT
1 TATT
51626874 GTTCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAAATTTATAACAATAT
Found at i:51628399 original size:25 final size:24
Alignment explanation
Indices: 51628363--51628481 Score: 69
Period size: 25 Copynumber: 4.7 Consensus size: 24
51628353 CGAAATGATT
* *
51628363 AAAAACTTGATGGAAAATTTTATG
1 AAAAACTTGATGAAAAACTTTATG
*
51628387 AAAAGACTTGATGAAAAACTTTA-A
1 AAAA-ACTTGATGAAAAACTTTATG
* * * *
51628411 AAAGAACTTGCTGCAAAACTTGATAA
1 AAA-AACTTGATGAAAAACTTTAT-G
* * *
51628437 AAAAACTTGGTAATTAAAAACTTGATA
1 AAAAACTT-G--ATGAAAAACTTTATG
*
51628464 AAAGAACTAGATGAAAAA
1 AAA-AACTTGATGAAAAA
51628482 TACTTGAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
24 22 0.29
25 29 0.38
26 5 0.07
27 5 0.07
28 15 0.20
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (24 bp):
AAAAACTTGATGAAAAACTTTATG
Found at i:51628402 original size:13 final size:12
Alignment explanation
Indices: 51628358--51628481 Score: 70
Period size: 12 Copynumber: 9.8 Consensus size: 12
51628348 AAAAACGAAA
*
51628358 TGATTAAAAACT
1 TGATGAAAAACT
* *
51628370 TGATGGAAAATT
1 TGATGAAAAACT
*
51628382 TTATGAAAAGACT
1 TGATGAAAA-ACT
51628395 TGATGAAAAACT
1 TGATGAAAAACT
* *
51628407 TTA-AAAAGAACT
1 TGATGAAA-AACT
* *
51628419 TGCTGCAAAACT
1 TGATGAAAAACT
*
51628431 TGATAAAAAAACT
1 TGAT-GAAAAACT
*
51628444 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
51628459 TGATAAAAGAACT
1 TGATGAAA-AACT
*
51628472 AGATGAAAAA
1 TGATGAAAAA
51628482 TACTTGAAGA
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
11 3 0.04
12 40 0.48
13 29 0.35
14 2 0.02
15 8 0.10
16 2 0.02
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:51628457 original size:15 final size:13
Alignment explanation
Indices: 51628425--51628488 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
51628415 AACTTGCTGC
51628425 AAAACTTGATAAA
1 AAAACTTGATAAA
*
51628438 AAAACTTGGTAATTA
1 AAAACTTGATAA--A
51628453 AAAACTTGATAAA
1 AAAACTTGATAAA
* *
51628466 AGAACTAGATGAAA
1 AAAACTTGAT-AAA
*
51628480 AATACTTGA
1 AAAACTTGA
51628489 AGAAAGAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
13 20 0.49
14 9 0.22
15 12 0.29
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (13 bp):
AAAACTTGATAAA
Found at i:51628505 original size:19 final size:19
Alignment explanation
Indices: 51628477--51628514 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
51628467 GAACTAGATG
*
51628477 AAAAATACTTGAA-GAAAGA
1 AAAAACACTT-AATGAAAGA
51628496 AAAAACACTTAATGAAAGA
1 AAAAACACTTAATGAAAGA
51628515 CTTAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.63, C:0.08, G:0.13, T:0.16
Consensus pattern (19 bp):
AAAAACACTTAATGAAAGA
Found at i:51630710 original size:21 final size:23
Alignment explanation
Indices: 51630686--51630733 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
51630676 TTTAAAATTC
*
51630686 AAAAAATAAA-AAAA-ATAAATA
1 AAAAAATAAACAAAATATAAACA
*
51630707 AAAATATAAACAAAATATAAACA
1 AAAAAATAAACAAAATATAAACA
51630730 AAAA
1 AAAA
51630734 CTTCAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 10 0.43
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (23 bp):
AAAAAATAAACAAAATATAAACA
Found at i:51630722 original size:39 final size:39
Alignment explanation
Indices: 51630648--51630722 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
51630638 AAAAAATTTT
* ****
51630648 AAAAATAAAAAAATTAAGAAAAAATATCTTTAAAATTCA
1 AAAAATAAAAAAAATAAGAAAAAATATAAACAAAATTCA
51630687 AAAAATAAAAAAAATAA-ATAAAAATATAAACAAAAT
1 AAAAATAAAAAAAATAAGA-AAAAATATAAACAAAAT
51630723 ATAAACAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 1 0.03
39 29 0.97
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.21
Consensus pattern (39 bp):
AAAAATAAAAAAAATAAGAAAAAATATAAACAAAATTCA
Found at i:51630726 original size:19 final size:19
Alignment explanation
Indices: 51630686--51630727 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
51630676 TTTAAAATTC
51630686 AAAAAATAAAAAAAATAAAT
1 AAAAAATAAAAAAAAT-AAT
*
51630706 AAAAATATAAACAAAAT-AT
1 AAAAA-ATAAAAAAAATAAT
51630725 AAA
1 AAA
51630728 CAAAAACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAAATAAAAAAAATAAT
Found at i:51643801 original size:12 final size:13
Alignment explanation
Indices: 51643779--51643807 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
51643769 AAGTTTTATT
51643779 TTTATTTTATTTA
1 TTTATTTTATTTA
51643792 TTTA-TTTATTTA
1 TTTATTTTATTTA
51643804 TTTA
1 TTTA
51643808 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:51662407 original size:26 final size:25
Alignment explanation
Indices: 51662378--51662435 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
51662368 TAAAAAAATG
51662378 AAAAAAATAAAAACTCTTTAAAATTC
1 AAAAAAA-AAAAACTCTTTAAAATTC
* * * *
51662404 AAAAATAAAAAGATTTTTTAAAATTT
1 AAAAA-AAAAAAACTCTTTAAAATTC
51662430 AAAAAA
1 AAAAAA
51662436 TTCCAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 24 0.89
27 2 0.07
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAAAAAAAAACTCTTTAAAATTC
Found at i:51662616 original size:21 final size:22
Alignment explanation
Indices: 51662592--51662632 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
51662582 CAGGTGGACA
*
51662592 GATTTTATAAT-TTTTATTTTT
1 GATTTTATAATAATTTATTTTT
*
51662613 GATTTTTTAATAATTTATTT
1 GATTTTATAATAATTTATTT
51662633 GCTTTGAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
GATTTTATAATAATTTATTTTT
Found at i:51664767 original size:45 final size:45
Alignment explanation
Indices: 51664669--51664856 Score: 247
Period size: 45 Copynumber: 4.2 Consensus size: 45
51664659 AATAATAACA
* * * *
51664669 GATACACGGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
* * *
51664712 GATACTCGGTGGAATCAGCACATAGCAACCACCTTCATAATCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
*
51664757 -AGTACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
1 GA-TACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
**
51664802 GATACCTAGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
*
51664847 GGTACCCGGT
1 GATACCCGGT
51664857 ACACGTAATA
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 11 0.09
44 14 0.11
45 101 0.80
46 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (45 bp):
GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
Found at i:51688483 original size:21 final size:21
Alignment explanation
Indices: 51688422--51688483 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
51688412 TTTTATAAAG
* *
51688422 TTGTAAAAAATATTA-AAAAAA
1 TTGTAAAAGA-ATTATAAAAAT
*
51688443 TTGT-AAAGAAATAT-AAAAT
1 TTGTAAAAGAATTATAAAAAT
51688462 TTGTAAAAGAATTATAAAAAT
1 TTGTAAAAGAATTATAAAAAT
51688483 T
1 T
51688484 ATCATATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.32
20 13 0.38
21 10 0.29
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (21 bp):
TTGTAAAAGAATTATAAAAAT
Found at i:51688533 original size:19 final size:18
Alignment explanation
Indices: 51688502--51688552 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
51688492 AAAATAAGTA
51688502 TTTTATAATATTTCTATGAT
1 TTTTATAATATTTCTAT--T
*
51688522 TTTTATAA-ATTTTTATT
1 TTTTATAATATTTCTATT
*
51688539 TTTTATAATTTTTC
1 TTTTATAATATTTC
51688553 GCCACATGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.33
18 3 0.11
19 7 0.26
20 8 0.30
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATAATATTTCTATT
Found at i:51688550 original size:9 final size:9
Alignment explanation
Indices: 51688502--51688551 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
51688492 AAAATAAGTA
51688502 TTTTATAAT
1 TTTTATAAT
*
51688511 ATTTCTATGAT
1 -TTT-TATAAT
51688522 TTTTATAAAT
1 TTTTAT-AAT
51688532 TTTTAT--T
1 TTTTATAAT
51688539 TTTTATAAT
1 TTTTATAAT
51688548 TTTT
1 TTTT
51688552 CGCCACATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
7 7 0.21
9 8 0.24
10 14 0.41
11 5 0.15
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTATAAT
Found at i:51688682 original size:10 final size:10
Alignment explanation
Indices: 51688669--51688808 Score: 56
Period size: 9 Copynumber: 14.7 Consensus size: 10
51688659 TTTTTGATGC
51688669 ATTTTATAAT
1 ATTTTATAAT
51688679 A-TTTATAA-
1 ATTTTATAAT
51688687 ATTTT-TACA-
1 ATTTTATA-AT
* *
51688696 ATTTTTTTAT
1 ATTTTATAAT
*
51688706 ATTTTTATACT
1 A-TTTTATAAT
*
51688717 ATTTTTATATT
1 A-TTTTATAAT
*
51688728 TTTTTCA-AAT
1 ATTTT-ATAAT
51688738 -TTTTAGTAA-
1 ATTTTA-TAAT
51688747 ATTTTA-AAT
1 ATTTTATAAT
51688756 ATTTT-T-AT
1 ATTTTATAAT
51688764 ATTTTTATTAA-
1 A-TTTTA-TAAT
*
51688775 A-GTT-TAAT
1 ATTTTATAAT
51688783 ATTTTATAAT
1 ATTTTATAAT
*
51688793 -TTTTATAAA
1 ATTTTATAAT
51688802 ATTTTAT
1 ATTTTAT
51688809 TTTTATAAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 38
0.68 0.07 0.26
Matches are distributed among these distances:
7 3 0.03
8 10 0.10
9 42 0.42
10 26 0.26
11 19 0.19
12 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:51688709 original size:19 final size:19
Alignment explanation
Indices: 51688670--51688770 Score: 89
Period size: 19 Copynumber: 5.3 Consensus size: 19
51688660 TTTTGATGCA
* * *
51688670 TTTTATAATATTTATAAAT
1 TTTTACAATATTTTTATAT
*
51688689 TTTTACAATTTTTTTATAT
1 TTTTACAATATTTTTATAT
* *
51688708 TTTTATACTATTTTTATATT
1 TTTTACAATATTTTTATA-T
* *
51688728 TTTTTCAA-ATTTTTAGTAAA
1 TTTTACAATATTTTTA-T-AT
51688748 TTTTA-AATATTTTTATAT
1 TTTTACAATATTTTTATAT
51688766 TTTTA
1 TTTTA
51688771 TTAAAGTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
18 6 0.09
19 40 0.62
20 18 0.28
21 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTACAATATTTTTATAT
Found at i:51688805 original size:19 final size:19
Alignment explanation
Indices: 51688669--51688808 Score: 58
Period size: 19 Copynumber: 7.4 Consensus size: 19
51688659 TTTTTGATGC
*
51688669 ATTTTATAATATTTATAAA
1 ATTTTATAATTTTTATAAA
* * * *
51688688 TTTTTACAATTTTTTTATA
1 ATTTTATAATTTTTATAAA
* **
51688707 TTTTTATACTATTTTTATATT
1 ATTTTATA--ATTTTTATAAA
*
51688728 TTTTTCA-AATTTTTAGT-AA
1 ATTTT-ATAATTTTTA-TAAA
*
51688747 ATTTTA-AATATTTT-TATA
1 ATTTTATAAT-TTTTATAAA
* ** *
51688765 TTTTTATTAA-AGTT-TAAT
1 ATTTTA-TAATTTTTATAAA
51688783 ATTTTATAATTTTTATAAA
1 ATTTTATAATTTTTATAAA
51688802 ATTTTAT
1 ATTTTAT
51688809 TTTTATAAAT
Statistics
Matches: 90, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
17 4 0.04
18 21 0.23
19 46 0.51
20 3 0.03
21 15 0.17
22 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (19 bp):
ATTTTATAATTTTTATAAA
Found at i:51688822 original size:10 final size:10
Alignment explanation
Indices: 51688670--51688808 Score: 68
Period size: 10 Copynumber: 14.6 Consensus size: 10
51688660 TTTTGATGCA
51688670 TTTTAT-AAT
1 TTTTATAAAT
*
51688679 ATTTATAAAT
1 TTTTATAAAT
*
51688689 TTTTA-CAAT
1 TTTTATAAAT
* *
51688698 TTTTTTATAT
1 TTTTATAAAT
*
51688708 TTTTATACTAT
1 TTTTATA-AAT
51688719 TTTTAT--AT
1 TTTTATAAAT
*
51688727 TTTTTTCAAAT
1 TTTTAT-AAAT
51688738 TTTTAGTAAA-
1 TTTTA-TAAAT
51688748 TTTTA-AATAT
1 TTTTATAA-AT
51688758 TTTTAT--AT
1 TTTTATAAAT
51688766 TTTTATTAAA-
1 TTTTA-TAAAT
* *
51688776 GTTTA-ATA-
1 TTTTATAAAT
51688784 TTTTAT-AAT
1 TTTTATAAAT
*
51688793 TTTTATAAAA
1 TTTTATAAAT
51688803 TTTTAT
1 TTTTAT
51688809 TTTTATAAAT
Statistics
Matches: 100, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
8 23 0.23
9 20 0.20
10 37 0.37
11 19 0.19
12 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:51688822 original size:16 final size:16
Alignment explanation
Indices: 51688791--51688821 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51688781 ATATTTTATA
51688791 ATTTTTATAAAATTTT
1 ATTTTTATAAAATTTT
51688807 ATTTTTAT-AAATTTT
1 ATTTTTATAAAATTTT
51688822 TTGTCACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTTATAAAATTTT
Found at i:51688823 original size:27 final size:27
Alignment explanation
Indices: 51688735--51688822 Score: 92
Period size: 26 Copynumber: 3.3 Consensus size: 27
51688725 ATTTTTTTCA
* *
51688735 AATTTTTAGTAAATTTTAAATATTTT-T
1 AATTTTTATTAAAATTT-AATATTTTAT
*
51688762 ATATTTTTATTAAAGTTTAATATTTTAT
1 A-ATTTTTATTAAAATTTAATATTTTAT
*
51688790 AATTTTTA-TAAAATTTTAT-TTTTAT
1 AATTTTTATTAAAATTTAATATTTTAT
51688815 AAATTTTT
1 -AATTTTT
51688823 TGTCACATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
25 6 0.11
26 16 0.30
27 16 0.30
28 16 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
AATTTTTATTAAAATTTAATATTTTAT
Found at i:51697493 original size:25 final size:25
Alignment explanation
Indices: 51697455--51697523 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
51697445 TTTTTCGAGC
* *
51697455 CATATAACAAGAAGCTCATGTGAGT
1 CATATAACAGGAAGCTCATCTGAGT
* * * *
51697480 CATGTAACGGGAAGCTTATCTGGGT
1 CATATAACAGGAAGCTCATCTGAGT
*
51697505 TATATAACAGGAAGCTCAT
1 CATATAACAGGAAGCTCAT
51697524 AAGAGCCATA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (25 bp):
CATATAACAGGAAGCTCATCTGAGT
Found at i:51697543 original size:24 final size:24
Alignment explanation
Indices: 51697513--51697591 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
51697503 GTTATATAAC
51697513 AGGAAGCTCATAAGAGCCATAATT
1 AGGAAGCTCATAAGAGCCATAATT
* **
51697537 AGGAAGCTCGTGCGAGCCAATAA-T
1 AGGAAGCTCATAAGAGCC-ATAATT
* ** *
51697561 AGGTAGCTCCGAAGAGCCATTAATC
1 AGGAAGCTCATAAGAGCCA-TAATT
51697586 AGGAAG
1 AGGAAG
51697592 TTTCGGATAG
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
23 1 0.02
24 32 0.76
25 9 0.21
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.18
Consensus pattern (24 bp):
AGGAAGCTCATAAGAGCCATAATT
Found at i:51697711 original size:26 final size:26
Alignment explanation
Indices: 51697646--51697720 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
51697636 GAAACTCCAG
*
51697646 AGAGCCATTAATCAAGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* *
51697672 AGAGCCTTTAATCAGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
*
51697698 AGAGCCA-TATATCAGGATGCTCA
1 AGAGCCATTA-ATCAGGAAGCTCA
51697721 TAAGAGCTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 2 0.05
26 41 0.95
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:51705174 original size:4 final size:4
Alignment explanation
Indices: 51705165--51705205 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
51705155 GGTACTATAC
51705165 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA T-GA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
51705206 TACTAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (4 bp):
TAGA
Found at i:51710695 original size:6 final size:6
Alignment explanation
Indices: 51710684--51710726 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
51710674 TTAGTTATGT
*
51710684 AATATA AATATA AATATA AATATA AATATA AATATA TATATA A
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA A
51710727 CTAATATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:51711116 original size:88 final size:87
Alignment explanation
Indices: 51711012--51711228 Score: 285
Period size: 90 Copynumber: 2.4 Consensus size: 87
51711002 TAAGAGTGGT
*
51711012 GGCTTAATTGCTTTTTTGAAAAAATTTTGAGAGTCTTTTTTATGCATTTTGAAAGTTCAAGTACC
1 GGCTTAATTGCTTTTTT-AAAAAAATTTGAGAGTCTTTTTTATGCATTTTGAAAGTTCAAGTACC
51711077 CAATTAAGT-AAAAAAAAAGCAAG
65 CAATTAAGTGAAAAAAAAAG-AAG
* * * * *
51711100 GGCTCAATTGCTTTTTTATTGAAGAAGTTTGAGGGTCTTTTTTATGCATTTTGAAAGTTCAAGTG
1 GGCTTAATTGCTTTTTTA---AAAAAATTTGAGAGTCTTTTTTATGCATTTTGAAAGTTCAAGTA
* *
51711165 CCCAATTGAGTGAAAAAAAAAGAGG
63 CCCAATTAAGTGAAAAAAAAAGAAG
*
51711190 GGTTTAATTGCTTTTTTTAAAAAAATTTGAGAG-CTTTTT
1 GGCTTAATTGC-TTTTTTAAAAAAATTTGAGAGTCTTTTT
51711229 ACACCCTTAA
Statistics
Matches: 112, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
87 7 0.06
88 27 0.24
90 61 0.54
91 17 0.15
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (87 bp):
GGCTTAATTGCTTTTTTAAAAAAATTTGAGAGTCTTTTTTATGCATTTTGAAAGTTCAAGTACCC
AATTAAGTGAAAAAAAAAGAAG
Found at i:51714853 original size:18 final size:19
Alignment explanation
Indices: 51714830--51714866 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
51714820 ATTAAAAAAA
51714830 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
51714848 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
51714867 GGAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:51714865 original size:19 final size:18
Alignment explanation
Indices: 51714835--51714906 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 18
51714825 AAAAATATAA
51714835 ATTTTGGAATTTTTATAAAT
1 ATTTT-GAATTTTTA-AAAT
* *
51714855 ATTTTGAATTTTGGAAATT
1 ATTTTGAATTTT-TAAAAT
*
51714874 ATTTTGATTTTTTGAAAATT
1 ATTTTGAATTTTT-AAAA-T
*
51714894 ATTTTTAATTTTT
1 ATTTTGAATTTTT
51714907 GTTGAAAAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 24 0.57
20 18 0.43
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (18 bp):
ATTTTGAATTTTTAAAAT
Found at i:51714906 original size:20 final size:20
Alignment explanation
Indices: 51714835--51714907 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
51714825 AAAAATATAA
51714835 ATTTTGGAATTTTT-ATAAA-T
1 ATTTT-GAATTTTTGA-AAATT
*
51714855 ATTTTGAA-TTTTGGAAATT
1 ATTTTGAATTTTTGAAAATT
*
51714874 ATTTTGATTTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
*
51714894 ATTTTTAATTTTTG
1 ATTTTGAATTTTTG
51714908 TTGAAAAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 7 0.16
19 11 0.24
20 27 0.60
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:51715783 original size:19 final size:20
Alignment explanation
Indices: 51715759--51715805 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
51715749 ACTAGATCGA
51715759 TTAACCGAATTAAATCAA-T
1 TTAACCGAATTAAATCAATT
* *
51715778 TTAACCG-ATTAATTTAATT
1 TTAACCGAATTAAATCAATT
51715797 TTAACCGAA
1 TTAACCGAA
51715806 ATTTAAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.33
19 15 0.62
20 1 0.04
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (20 bp):
TTAACCGAATTAAATCAATT
Found at i:51715810 original size:17 final size:18
Alignment explanation
Indices: 51715777--51715811 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
51715767 ATTAAATCAA
51715777 TTTAACCGATTAATTTAAT
1 TTTAACCGA-TAATTTAAT
51715796 TTTAACCGA-AATTTAA
1 TTTAACCGATAATTTAA
51715812 ACACCCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTAACCGATAATTTAAT
Found at i:51717943 original size:20 final size:20
Alignment explanation
Indices: 51717923--51717958 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
51717913 TTTAATAATT
51717923 TTTTTAT-ATT-TTTAAATA
1 TTTTTATAATTATTTAAATA
51717941 TTTTTATAATTATTTAAA
1 TTTTTATAATTATTTAAA
51717959 AAAAATCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 3 0.19
20 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTATAATTATTTAAATA
Found at i:51718130 original size:97 final size:94
Alignment explanation
Indices: 51717995--51718203 Score: 235
Period size: 94 Copynumber: 2.2 Consensus size: 94
51717985 CTTAAGGGTG
* * * *
51717995 TAAAAA-GCCCTCAAACTTTTTTAAGAAAAGCAATTAAGC-CCTTGTTTTTTATTATTATTTTAC
1 TAAAAAGGCCCTCAAACTTTTTTAAAAAAAACAATTAAGCTCC-TGCTTTTT-TT-CT-TTTTAC
** **
51718058 ACTCAATTGGGTACTTAAACTTTCAAAATGCAT
62 ACTCAATTAAGTACTTAAACTGCCAAAATGCAT
* * *
51718091 TAAAAAGGCCCTTAAA-TTTTTTCAAAAAAAACAATTAAGCTGCTGCTTTTTTTCTTTTTGCACT
1 TAAAAAGGCCCTCAAACTTTTTT-AAAAAAAACAATTAAGCTCCTGCTTTTTTTCTTTTTACACT
*
51718155 CAATTAAGTACTTGAACTGCCAAAATGCAT
65 CAATTAAGTACTTAAACTGCCAAAATGCAT
*
51718185 CAAAAAGGCCCTCAAACTT
1 TAAAAAGGCCCTCAAACTT
51718204 AAAAAAAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
94 47 0.49
95 3 0.03
96 14 0.15
97 30 0.32
98 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (94 bp):
TAAAAAGGCCCTCAAACTTTTTTAAAAAAAACAATTAAGCTCCTGCTTTTTTTCTTTTTACACTC
AATTAAGTACTTAAACTGCCAAAATGCAT
Found at i:51719068 original size:91 final size:86
Alignment explanation
Indices: 51718885--51719068 Score: 187
Period size: 86 Copynumber: 2.1 Consensus size: 86
51718875 TTTTAAGGGT
* * * *
51718885 ATTTTTT-ATGCATTTTGACAATTCAAGTACCCAATTGATAGCAAAAAAAAAAAAACTCAATTGC
1 ATTTTTTAATACATTTTAAAAATTCAAATACCCAATTGATAGCAAAAAAAAAAAAACTCAATTGC
*
51718949 TTTTTTTAAAAGCTTTTAAAG
66 TTTTTTTAAAAGATTTTAAAG
* * * *
51718970 TTTTTTTAATACATTTTAAAAATTTAAATACCCAATTGAGTA-CAAAGCAAAAGCAAAAAGCTTA
1 ATTTTTTAATACATTTTAAAAATTCAAATACCCAATTGA-TAGCAAA--AAAA--AAAAAACTCA
51719034 ATTGCTTTTTTTTGAAAA-ATTTT-AAG
61 ATTGC-TTTTTTT-AAAAGATTTTAAAG
51719060 AATTTTTTA
1 -ATTTTTTA
51719069 CGCCCTTAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
85 6 0.08
86 30 0.38
87 2 0.03
88 4 0.05
90 16 0.20
91 18 0.22
92 4 0.05
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (86 bp):
ATTTTTTAATACATTTTAAAAATTCAAATACCCAATTGATAGCAAAAAAAAAAAAACTCAATTGC
TTTTTTTAAAAGATTTTAAAG
Found at i:51725082 original size:3 final size:3
Alignment explanation
Indices: 51725076--51725144 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
51725066 AGGAGAGATC
51725076 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
51725124 GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA
51725145 CGCCAGAAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:51725617 original size:8 final size:8
Alignment explanation
Indices: 51725604--51725631 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
51725594 GGAGGTGAGT
51725604 TGAGTAAG
1 TGAGTAAG
51725612 TGAGTAAG
1 TGAGTAAG
51725620 TGAGTAAG
1 TGAGTAAG
51725628 TGAG
1 TGAG
51725632 AGCGTGGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.25
Consensus pattern (8 bp):
TGAGTAAG
Found at i:51725995 original size:86 final size:84
Alignment explanation
Indices: 51725905--51726072 Score: 221
Period size: 86 Copynumber: 2.0 Consensus size: 84
51725895 AATTAAGTCT
* * * **
51725905 CTTTTTTCACTCAATTGAGCACTTAAATTTTTAAAATATATCAAAAAGACTTTC-AAATTTCTTC
1 CTTTTTTCACTCAATTGAGCACTTAAACTTTCAAAATACATCAAAAAGACCCTCAAAATTT-TTC
*
51725969 AAAAAACGCAATTAAGCCCCCG
65 -AAAAA-GCAATCAAGCCCCCG
* * *
51725991 CTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAGACCCTCAAAATTTTTCA
1 CTTTTTTCACTCAATTGAGCACTTAAACTTTCAAAATACATCAAAAAGACCCTCAAAATTTTTCA
51726056 AAAAGCAATCAAGCCCC
66 AAAAGCAATCAAGCCCC
51726073 TGCTCTTATT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
84 12 0.17
85 5 0.07
86 49 0.68
87 6 0.08
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.32
Consensus pattern (84 bp):
CTTTTTTCACTCAATTGAGCACTTAAACTTTCAAAATACATCAAAAAGACCCTCAAAATTTTTCA
AAAAGCAATCAAGCCCCCG
Found at i:51726146 original size:26 final size:25
Alignment explanation
Indices: 51726117--51726173 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
51726107 AAATTTTAGA
51726117 AAAATTATTA-AATTCTAATAAAAATT
1 AAAATTATTAGAATT-TAAT-AAAATT
**
51726143 AAAAAAATTAGAATTTAATAAAATT
1 AAAATTATTAGAATTTAATAAAATT
*
51726168 AGAATT
1 AAAATT
51726174 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 9 0.36
26 12 0.48
27 4 0.16
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
AAAATTATTAGAATTTAATAAAATT
Found at i:51726165 original size:16 final size:16
Alignment explanation
Indices: 51726141--51726174 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
51726131 CTAATAAAAA
51726141 TTAAAAAAATTAGAAT
1 TTAAAAAAATTAGAAT
*
51726157 TTAATAAAATTAGAAT
1 TTAAAAAAATTAGAAT
51726173 TT
1 TT
51726175 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
TTAAAAAAATTAGAAT
Found at i:51726441 original size:27 final size:28
Alignment explanation
Indices: 51726421--51726477 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
51726411 ATTTTATTTT
51726421 GACT-TTAT-AAAATTTATATTTTTTAC
1 GACTATTATAAAAATTTATATTTTTTAC
*
51726447 GATTATTATAAAAATTTATATTTTTTTAC
1 GACTATTATAAAAATTTATA-TTTTTTAC
51726476 GA
1 GA
51726478 TTTTTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 3 0.11
27 4 0.15
28 10 0.37
29 10 0.37
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (28 bp):
GACTATTATAAAAATTTATATTTTTTAC
Found at i:51726460 original size:28 final size:29
Alignment explanation
Indices: 51726425--51726485 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
51726415 TATTTTGACT
51726425 TTAT-AAAATTTATA-TTTTTTACGATTA
1 TTATAAAAATTTATATTTTTTTACGATTA
*
51726452 TTATAAAAATTTATATTTTTTTACGATTT
1 TTATAAAAATTTATATTTTTTTACGATTA
51726481 TTATA
1 TTATA
51726486 TTTTTTCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 4 0.13
28 10 0.32
29 17 0.55
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (29 bp):
TTATAAAAATTTATATTTTTTTACGATTA
Found at i:51726500 original size:19 final size:18
Alignment explanation
Indices: 51726461--51726506 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
51726451 ATTATAAAAA
51726461 TTTATATTTTTTTACGATT
1 TTTATATTTTTTTAC-ATT
51726480 TTTATATTTTTTCTA-ATT
1 TTTATATTTTTT-TACATT
51726498 TTTAATATT
1 TTT-ATATT
51726507 CAAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATATTTTTTTACATT
Found at i:51726693 original size:85 final size:86
Alignment explanation
Indices: 51726598--51726761 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 86
51726588 AAACCAGGGA
* * * * * * *
51726598 CTTAATTACTTATTTTT-TAAA-GTTTGAGGATC-TTTTTTATGCATTTTTAAAGTTCAAGTACT
1 CTTAATTACTT-TTTTTGAAAAGGTTTGAGG-GCATTTTTGATACATTTTAAAAATTCAAGTACC
*
51726660 CAATTGAGTACAAAAAGTAGAGG
64 CAAATGAGTACAAAAAGTAGAGG
51726683 CTTAATTACTTTTTTTGAAAAGGTTTGAGGGCATTTTTGATACATTTTAAAAATTCAAGTACCCA
1 CTTAATTACTTTTTTTGAAAAGGTTTGAGGGCATTTTTGATACATTTTAAAAATTCAAGTACCCA
*
51726748 AATGAGTGCAAAAA
66 AATGAGTACAAAAA
51726762 AAAGCAGGGG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 5 0.07
85 15 0.22
86 47 0.70
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (86 bp):
CTTAATTACTTTTTTTGAAAAGGTTTGAGGGCATTTTTGATACATTTTAAAAATTCAAGTACCCA
AATGAGTACAAAAAGTAGAGG
Found at i:51727203 original size:16 final size:18
Alignment explanation
Indices: 51727182--51727217 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
51727172 TTTCATATAG
51727182 TATAAAT-TAA-ATAATA
1 TATAAATATAATATAATA
51727198 TATAAATATAATATAATA
1 TATAAATATAATATAATA
51727216 TA
1 TA
51727218 ATATAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAAATATAATATAATA
Found at i:51727210 original size:5 final size:5
Alignment explanation
Indices: 51727192--51727223 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
51727182 TATAAATTAA
51727192 ATAAT AT-AT A-AAT ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
51727224 ACTTGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:51728232 original size:23 final size:22
Alignment explanation
Indices: 51728206--51728250 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
51728196 AGATATAATC
* *
51728206 AAAACCTATAATGAGATTATTAA
1 AAAACATATAAT-AAATTATTAA
*
51728229 AAAATATATAATAAATTATTAA
1 AAAACATATAATAAATTATTAA
51728251 TTTAGATAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAACATATAATAAATTATTAA
Found at i:51734230 original size:141 final size:141
Alignment explanation
Indices: 51733972--51734248 Score: 333
Period size: 141 Copynumber: 2.0 Consensus size: 141
51733962 GTGACTCGTA
** *
51733972 TACTTTGATGTAAGTAAAAGTTCGAGTTCAAATAGATAAACAGCCAAAAGTTGATGCATCGGGTA
1 TACTTTGATGTAAGTAAAACCTCGAGTTCAAATAGATAAACAACCAAAAGTTGATGCATCGGGTA
* * * * *
51734037 TACAACTTCTGAAGTATGTAGAGCCATTCATAATAGTAGAATTTATAGCCCGAGACATGATTAAA
66 TACAACTTCTGAAGTATGTAGAGCCATTCACAACAGTAGAATTCATAACCCGAGACATGAGTAAA
51734102 TGATATCCTTT
131 TGATATCCTTT
** * ** *
51734113 TACTTTGATGTAAGTAAAAACCT-GAGTTCAAATAGATAAGGAACCGAAAA-TTGGTGTGTTGGG
1 TACTTTGATGTAAGT-AAAACCTCGAGTTCAAATAGATAAACAACC-AAAAGTTGATGCATCGGG
** * * * * *
51734176 TATATGACTTCTGCAGTATGTAGTGTCATTCACAACAGTGGAATTCATAACCCGAGACATGGGTA
64 TATACAACTTCTGAAGTATGTAGAGCCATTCACAACAGTAGAATTCATAACCCGAGACATGAGTA
51734241 AATGATAT
129 AATGATAT
51734249 AATTTCATTA
Statistics
Matches: 113, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
141 104 0.92
142 9 0.08
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (141 bp):
TACTTTGATGTAAGTAAAACCTCGAGTTCAAATAGATAAACAACCAAAAGTTGATGCATCGGGTA
TACAACTTCTGAAGTATGTAGAGCCATTCACAACAGTAGAATTCATAACCCGAGACATGAGTAAA
TGATATCCTTT
Found at i:51736133 original size:17 final size:18
Alignment explanation
Indices: 51736113--51736161 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
51736103 AACTAGAACT
51736113 AATGAT-TTGAAATAGAA
1 AATGATATTGAAATAGAA
* *
51736130 AATGGTATTGAAAT-GAC
1 AATGATATTGAAATAGAA
*
51736147 AATGCTATTGAAATA
1 AATGATATTGAAATA
51736162 ACAAGTGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (18 bp):
AATGATATTGAAATAGAA
Found at i:51736165 original size:17 final size:17
Alignment explanation
Indices: 51736119--51736165 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
51736109 AACTAATGAT
* *
51736119 TTGAAATAGAAAATGGTA
1 TTGAAATA-ACAATGCTA
*
51736137 TTGAAATGACAATGCTA
1 TTGAAATAACAATGCTA
51736154 TTGAAATAACAA
1 TTGAAATAACAA
51736166 GTGAGATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (17 bp):
TTGAAATAACAATGCTA
Done.