Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 7 of 17
Found at i:1493137 original size:11 final size:12
Alignment explanation
Indices: 1493123--1493154 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1493113 AATTAATAAA
1493123 AAATTTATTAT-
1 AAATTTATTATG
1493134 AAATTTATT-TG
1 AAATTTATTATG
1493145 AAATTTATTA
1 AAATTTATTA
1493155 CACATGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 18 0.95
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
AAATTTATTATG
Found at i:1493753 original size:18 final size:18
Alignment explanation
Indices: 1493730--1493796 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
1493720 ATTACTATGT
*
1493730 TATAAAAATAACATA-ATA
1 TATAAAAATAA-ATATAGA
*
1493748 TATAAATATAAATATAGA
1 TATAAAAATAAATATAGA
*
1493766 TATAAAATATATTATATA-A
1 TATAAAA-ATA-AATATAGA
1493785 T-TAAAAATAAAT
1 TATAAAAATAAAT
1493797 CAAATTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.05
17 6 0.15
18 23 0.56
19 5 0.12
20 5 0.12
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (18 bp):
TATAAAAATAAATATAGA
Found at i:1493903 original size:30 final size:28
Alignment explanation
Indices: 1493837--1493903 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 28
1493827 AAATCAAAAT
* *
1493837 TTAACTTATTTTTTAAATAAATTTTTTA
1 TTAATTTATTTTTAAAATAAATTTTTTA
*
1493865 TCTAAATTTATTTTTAAAATTTAATATTTTTA
1 T-T-AATTTATTTTTAAAA-TAAAT-TTTTTA
1493897 TTAATTT
1 TTAATTT
1493904 TTTAATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
28 1 0.03
29 1 0.03
30 18 0.56
31 5 0.16
32 7 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (28 bp):
TTAATTTATTTTTAAAATAAATTTTTTA
Found at i:1493937 original size:28 final size:29
Alignment explanation
Indices: 1493906--1493965 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1493896 ATTAATTTTT
*
1493906 TAATTATTAAAT-AACTTTTAAACTTAAA
1 TAATTATTAAATAAAATTTTAAACTTAAA
* *
1493934 TAATTATTAAATAAAATTTTAAATTTTAA
1 TAATTATTAAATAAAATTTTAAACTTAAA
1493963 TAA
1 TAA
1493966 ATAATCTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATTATTAAATAAAATTTTAAACTTAAA
Found at i:1494407 original size:30 final size:30
Alignment explanation
Indices: 1494371--1494442 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
1494361 TTAAGAAAAC
*
1494371 AATTATTTTTATATGATTAATATTATAA-TA-
1 AATTATTTTTATAT--TTAATAATATAATTAT
* *
1494401 AATTATTATTAAATTTAATAATATAATTAT
1 AATTATTTTTATATTTAATAATATAATTAT
*
1494431 ATTTATTTTTAT
1 AATTATTTTTAT
1494443 GTGAAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 11 0.32
29 2 0.06
30 21 0.62
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (30 bp):
AATTATTTTTATATTTAATAATATAATTAT
Found at i:1494499 original size:35 final size:34
Alignment explanation
Indices: 1494458--1494543 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
1494448 ATTTAAATTG
1494458 ATTTAATAT-T-TTTATTATAATGATAAAAATATTAT
1 ATTTAATATATATTTA--ATAATGA-AAAAATATTAT
* * *
1494493 TTTTAATATATATTTAATAATTAAAAAATTTTAT
1 ATTTAATATATATTTAATAATGAAAAAATATTAT
* *
1494527 ATTTAATAAATAGTTAA
1 ATTTAATATATATTTAA
1494544 AATTTTTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
34 24 0.56
35 14 0.33
36 1 0.02
37 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (34 bp):
ATTTAATATATATTTAATAATGAAAAAATATTAT
Found at i:1494532 original size:34 final size:33
Alignment explanation
Indices: 1494482--1494547 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
1494472 TTATAATGAT
* * *
1494482 AAAAATATTATTTTTAATATATATTTAATAATTA
1 AAAAATATTATATTTAATAAATAGTTAA-AATTA
*
1494516 AAAAATTTTATATTTAATAAATAGTTAAAATT
1 AAAAATATTATATTTAATAAATAGTTAAAATT
1494548 TTTTAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (33 bp):
AAAAATATTATATTTAATAAATAGTTAAAATTA
Found at i:1494736 original size:36 final size:33
Alignment explanation
Indices: 1494645--1494713 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1494635 AAAAATTACG
1494645 TAAGTATTTAAACAAAATTAATTTTCTTATTAT
1 TAAGTATTTAAACAAAATTAATTTTCTTATTAT
1494678 TAAGTATTTAAACAAAATTAATTTTCTTATTAT
1 TAAGTATTTAAACAAAATTAATTTTCTTATTAT
1494711 TAA
1 TAA
1494714 AAGTGTTTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (33 bp):
TAAGTATTTAAACAAAATTAATTTTCTTATTAT
Found at i:1495536 original size:17 final size:18
Alignment explanation
Indices: 1495502--1495545 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1495492 TTTATCAATA
1495502 AAATTTATATTAATATGT
1 AAATTTATATTAATATGT
*
1495520 AAATTTAT-TTTATATGT
1 AAATTTATATTAATATGT
1495537 AAA-TTATAT
1 AAATTTATAT
1495546 CAAATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 12 0.50
18 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
AAATTTATATTAATATGT
Found at i:1495665 original size:31 final size:29
Alignment explanation
Indices: 1495621--1495738 Score: 112
Period size: 31 Copynumber: 3.8 Consensus size: 29
1495611 GTAAGCTTTA
*
1495621 ATTTTTTTTATTAATCAAATAATTTTATTT
1 ATTTTTTTCATTAATCAAA-AATTTTATTT
* *
1495651 ATTTTTTATCATTAATGAAAAATATGTAAGCTTT
1 ATTTTTT-TCATTAATCAAAAAT-T-TTA--TTT
1495685 AATTTTTTT-ATTAATCAAATAATTTTATTT
1 -ATTTTTTTCATTAATCAAA-AATTTTATTT
*
1495715 ATTTTTTATCATTAATGAAAAATT
1 ATTTTTT-TCATTAATCAAAAATT
1495739 AAAACTTTGA
Statistics
Matches: 73, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
29 7 0.10
30 18 0.25
31 20 0.27
32 4 0.05
33 10 0.14
34 7 0.10
35 7 0.10
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTTTTCATTAATCAAAAATTTTATTT
Found at i:1495706 original size:64 final size:65
Alignment explanation
Indices: 1495609--1495737 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 65
1495599 AATAAATGTA
1495609 ATGTAAGCTTTAATTTTTTTTATTAATCAAATAATTTTATTTATTTTTTATCATTAATGAAAAAT
1 ATGTAAGCTTTAATTTTTTTTATTAATCAAATAATTTTATTTATTTTTTATCATTAATGAAAAAT
1495674 ATGTAAGCTTTAA-TTTTTTTATTAATCAAATAATTTTATTTATTTTTTATCATTAATGAAAAAT
1 ATGTAAGCTTTAATTTTTTTTATTAATCAAATAATTTTATTTATTTTTTATCATTAATGAAAAAT
1495738 TAAAACTTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 51 0.80
65 13 0.20
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (65 bp):
ATGTAAGCTTTAATTTTTTTTATTAATCAAATAATTTTATTTATTTTTTATCATTAATGAAAAAT
Found at i:1495921 original size:25 final size:25
Alignment explanation
Indices: 1495889--1495939 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1495879 TTTATTGTCA
* *
1495889 TACTTTTATATGTGCTAGTATTCGT
1 TACTTTTATATATGCTAATATTCGT
1495914 TACTTTTATATATGCTAATATTCGT
1 TACTTTTATATATGCTAATATTCGT
1495939 T
1 T
1495940 GTTATGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (25 bp):
TACTTTTATATATGCTAATATTCGT
Found at i:1499243 original size:29 final size:29
Alignment explanation
Indices: 1499188--1499243 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1499178 ATTGTATTAA
*
1499188 ATTTTTTATTATTATATCATATTTTTGTT
1 ATTTTTTATTATTATATCATATGTTTGTT
*
1499217 ATTTTTTA-TATTGTATCATGATGTTTG
1 ATTTTTTATTATTATATCAT-ATGTTTG
1499244 AAATTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (29 bp):
ATTTTTTATTATTATATCATATGTTTGTT
Found at i:1499395 original size:28 final size:23
Alignment explanation
Indices: 1499342--1499385 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1499332 CATGTAATTA
1499342 AATTATTTTTTATGTTATATTTT
1 AATTATTTTTTATGTTATATTTT
*
1499365 AATTATTTTTTATTTTATATT
1 AATTATTTTTTATGTTATATT
1499386 AGTGTATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
AATTATTTTTTATGTTATATTTT
Found at i:1499808 original size:21 final size:21
Alignment explanation
Indices: 1499782--1499821 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1499772 AATAAATTAG
1499782 ATTTATA-TATATTTATATTTT
1 ATTTATACTAT-TTTATATTTT
1499803 ATTTATACTATTTTATATT
1 ATTTATACTATTTTATATT
1499822 CATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTATACTATTTTATATTTT
Found at i:1499829 original size:13 final size:13
Alignment explanation
Indices: 1499789--1499835 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
1499779 TAGATTTATA
1499789 TATATTTATATTT
1 TATATTTATATTT
1499802 TAT-TTATACTATTT
1 TATATT-TA-TATTT
*
1499816 TATATTCATATTT
1 TATATTTATATTT
1499829 TAT-TTTA
1 TATATTTA
1499836 AAAGTTATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 5 0.17
13 13 0.45
14 9 0.31
15 2 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (13 bp):
TATATTTATATTT
Found at i:1500193 original size:25 final size:25
Alignment explanation
Indices: 1500165--1500213 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1500155 AAAATAATTT
1500165 TATTTATCTT-TTAAAGTTTTAATAA
1 TATTTATCTTCTTAAAG-TTTAATAA
* *
1500190 TATTTTTTTTCTTAAAGTTTAATA
1 TATTTATCTTCTTAAAGTTTAATA
1500214 CAAAATCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (25 bp):
TATTTATCTTCTTAAAGTTTAATAA
Found at i:1500202 original size:28 final size:30
Alignment explanation
Indices: 1500144--1500213 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
1500134 ATTATTATTT
*
1500144 TTTTAAA-TTTAAAAATAATTTTATTTATC
1 TTTTAAAGTTTAATAATAATTTTATTTATC
1500173 TTTTAAAGTTTTAATAAT-ATTTT-TTT-TC
1 TTTTAAAG-TTTAATAATAATTTTATTTATC
1500201 --TTAAAGTTTAATA
1 TTTTAAAGTTTAATA
1500214 CAAAATCTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
25 7 0.18
26 6 0.16
28 2 0.05
29 10 0.26
30 5 0.13
31 8 0.21
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (30 bp):
TTTTAAAGTTTAATAATAATTTTATTTATC
Found at i:1501093 original size:30 final size:29
Alignment explanation
Indices: 1501059--1501152 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 29
1501049 AGAATAATAA
*
1501059 TTTAAAAGATAAGTATATTTTTTATCAAAT
1 TTTAAAAGATAAATATATTTTTTAT-AAAT
* *
1501089 TTTAAAAGAATAAATGA-ATAGTTTT-TAAAC
1 TTTAAAAG-ATAAAT-ATAT-TTTTTATAAAT
1501119 TTTAAATA-ATAAATATATTTTTTATAAAAT
1 TTTAAA-AGATAAATATATTTTTTAT-AAAT
1501149 TTTA
1 TTTA
1501153 GAGGATGAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
28 5 0.10
29 9 0.17
30 24 0.46
31 9 0.17
32 5 0.10
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTAAAAGATAAATATATTTTTTATAAAT
Found at i:1501848 original size:18 final size:18
Alignment explanation
Indices: 1501827--1501867 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1501817 GAGTACAAAT
1501827 TTAAAATATATTTT-TATA
1 TTAAAATATATTTTATA-A
*
1501845 TTAATATATATTTTATAA
1 TTAAAATATATTTTATAA
1501863 TTAAA
1 TTAAA
1501868 TTTAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAAAATATATTTTATAA
Found at i:1502889 original size:2 final size:2
Alignment explanation
Indices: 1502878--1502914 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1502868 GAGGGCATCA
1502878 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1502915 GAGGGAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1508088 original size:30 final size:30
Alignment explanation
Indices: 1508030--1508089 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1508020 GGTGGAGGCA
* * * *
1508030 CATGCGAAGATTGGCCTGTTTGTGAAGGTG
1 CATGAGAAGATTGGACTGTTGGTAAAGGTG
*
1508060 CATGAGAAGATTGGAGTGTTGGTAAAGGTG
1 CATGAGAAGATTGGACTGTTGGTAAAGGTG
1508090 TATCAGCTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.38, T:0.28
Consensus pattern (30 bp):
CATGAGAAGATTGGACTGTTGGTAAAGGTG
Found at i:1511075 original size:2 final size:2
Alignment explanation
Indices: 1511070--1511097 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1511060 AGAGGGAATG
1511070 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1511098 ATGCGCTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1511153 original size:2 final size:2
Alignment explanation
Indices: 1511146--1511171 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1511136 GTATCGTATG
1511146 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1511172 TTATAAACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1511852 original size:12 final size:12
Alignment explanation
Indices: 1511835--1511860 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1511825 GACTAGGCCA
1511835 AAACTAGCTCTT
1 AAACTAGCTCTT
1511847 AAACTAGCTCTT
1 AAACTAGCTCTT
1511859 AA
1 AA
1511861 TTGTTGCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (12 bp):
AAACTAGCTCTT
Found at i:1514106 original size:90 final size:90
Alignment explanation
Indices: 1513971--1514141 Score: 261
Period size: 90 Copynumber: 1.9 Consensus size: 90
1513961 GAAATCTGAA
* * *
1513971 GCATCTCCAGTAGATTCATCTGCAGAAAGGAAGTTAACTCCTCCTGCTAAAGAGGTTTTGTGTCA
1 GCATCTCCAGCAGATTCATCTGCAGAAAGGAAATTAACTCCTCCTGCGAAAGAGGTTTTGTGTCA
1514036 TTCTAAAAGCACAAAGAAGCTTGAT
66 TTCTAAAAGCACAAAGAAGCTTGAT
* * * *
1514061 GCATCTCTAGCAGATTCTTCTGCAGAAAGGAAATTAGCTCCTCCTGCGAATGAGGTTTTGTGTCA
1 GCATCTCCAGCAGATTCATCTGCAGAAAGGAAATTAACTCCTCCTGCGAAAGAGGTTTTGTGTCA
* *
1514126 TTCTAAGATCACAAAG
66 TTCTAAAAGCACAAAG
1514142 TCTGAACAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 72 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (90 bp):
GCATCTCCAGCAGATTCATCTGCAGAAAGGAAATTAACTCCTCCTGCGAAAGAGGTTTTGTGTCA
TTCTAAAAGCACAAAGAAGCTTGAT
Found at i:1526623 original size:2 final size:2
Alignment explanation
Indices: 1526616--1526657 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1526606 ATGTAATCCA
1526616 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1526658 ACACACGCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1527813 original size:20 final size:19
Alignment explanation
Indices: 1527781--1527845 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
1527771 AAAAATATTT
1527781 TAATTTTTAACTTTAAAAAA
1 TAATTTTT-ACTTTAAAAAA
*
1527801 TAATTATTTAC-TT-AAAAT
1 TAATT-TTTACTTTAAAAAA
* *
1527819 TACTTTTTATTTTAAAAAA
1 TAATTTTTACTTTAAAAAA
*
1527838 TTATTTTT
1 TAATTTTT
1527846 TTTACCCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
17 4 0.11
18 10 0.28
19 12 0.33
20 7 0.19
21 3 0.08
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTTTTACTTTAAAAAA
Found at i:1532823 original size:14 final size:14
Alignment explanation
Indices: 1532801--1532835 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1532791 GAGAAAGTAT
1532801 TGAAGCCCAAAGGC
1 TGAAGCCCAAAGGC
*
1532815 TGGAGCCCAAAGGC
1 TGAAGCCCAAAGGC
1532829 TGAAGCC
1 TGAAGCC
1532836 TAACTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.31, T:0.09
Consensus pattern (14 bp):
TGAAGCCCAAAGGC
Found at i:1537542 original size:15 final size:14
Alignment explanation
Indices: 1537522--1537551 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1537512 ATACATTCAG
1537522 TTTTTCTTTTTCTTT
1 TTTTTCTTTTT-TTT
1537537 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
1537551 T
1 T
1537552 GCCTTTCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:1538327 original size:40 final size:40
Alignment explanation
Indices: 1538272--1538348 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
1538262 CCTGGTTCAG
1538272 ATAGCTTCTACAACACTGACTCAGTATTCCTTAAGCACAT
1 ATAGCTTCTACAACACTGACTCAGTATTCCTTAAGCACAT
1538312 ATAGCTTCTACAACACTGACTCAGTATTCCTTAAGCA
1 ATAGCTTCTACAACACTGACTCAGTATTCCTTAAGCA
1538349 TCAATTGGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.30
Consensus pattern (40 bp):
ATAGCTTCTACAACACTGACTCAGTATTCCTTAAGCACAT
Found at i:1539939 original size:3 final size:3
Alignment explanation
Indices: 1539931--1539972 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1539921 CAACTCAATA
1539931 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1539973 ACTATAATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1540115 original size:3 final size:3
Alignment explanation
Indices: 1540107--1540138 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1540097 GTTGGCAAAC
1540107 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1540139 CAACAACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1541464 original size:7 final size:7
Alignment explanation
Indices: 1541413--1541460 Score: 87
Period size: 7 Copynumber: 6.9 Consensus size: 7
1541403 CAATGAGCAA
1541413 TGGGGAC
1 TGGGGAC
1541420 TGGGGAC
1 TGGGGAC
1541427 TGGGGAC
1 TGGGGAC
1541434 TGGGGAC
1 TGGGGAC
1541441 TGGGGAC
1 TGGGGAC
*
1541448 TGGGGAA
1 TGGGGAC
1541455 TGGGGA
1 TGGGGA
1541461 ATGGAGAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.17, C:0.10, G:0.58, T:0.15
Consensus pattern (7 bp):
TGGGGAC
Found at i:1541469 original size:14 final size:14
Alignment explanation
Indices: 1541411--1541471 Score: 86
Period size: 14 Copynumber: 4.4 Consensus size: 14
1541401 GGCAATGAGC
1541411 AATGGGGACTGGGG
1 AATGGGGACTGGGG
*
1541425 ACTGGGGACTGGGG
1 AATGGGGACTGGGG
*
1541439 ACTGGGGACTGGGG
1 AATGGGGACTGGGG
* *
1541453 AATGGGGAATGGAG
1 AATGGGGACTGGGG
1541467 AATGG
1 AATGG
1541472 CATTTCTAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.23, C:0.08, G:0.54, T:0.15
Consensus pattern (14 bp):
AATGGGGACTGGGG
Found at i:1543979 original size:2 final size:2
Alignment explanation
Indices: 1543972--1544001 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1543962 AACTTGCGGC
1543972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1544002 GACATAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1544538 original size:13 final size:14
Alignment explanation
Indices: 1544509--1544548 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1544499 AATAAAATTT
1544509 AATTT-AAT-TTAA
1 AATTTAAATATTAA
1544521 AATTTAAA-ATTAA
1 AATTTAAATATTAA
*
1544534 TATTTAAATATTAA
1 AATTTAAATATTAA
1544548 A
1 A
1544549 TAATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 5 0.22
13 13 0.57
14 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTTAAATATTAA
Found at i:1544547 original size:20 final size:20
Alignment explanation
Indices: 1544515--1544595 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 20
1544505 ATTTAATTTA
1544515 ATTTAAA-ATTTAAAATTAAT
1 ATTTAAATA-TTAAAATTAAT
1544535 ATTTAAATATT-AAA-TAAT
1 ATTTAAATATTAAAATTAAT
** *
1544553 ATTTTTATATTAATATTTATAT
1 ATTTAAATATTAA-AATTA-AT
* * *
1544575 ATTTTATTATTAAATTTAAT
1 ATTTAAATATTAAAATTAAT
1544595 A
1 A
1544596 ATAATTTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
18 13 0.25
19 4 0.08
20 13 0.25
21 8 0.16
22 13 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAAATATTAAAATTAAT
Found at i:1544579 original size:22 final size:22
Alignment explanation
Indices: 1544537--1544612 Score: 77
Period size: 22 Copynumber: 3.3 Consensus size: 22
1544527 AAATTAATAT
1544537 TTAAATATTAAATAATATTTTTATA
1 TTAAAT-TT-AATAATA-TTTTATA
1544562 TTAATATTT-AT-ATATTTTATTA
1 TTAA-ATTTAATAATATTTTA-TA
1544584 TTAAATTTAATAATAATTTTA-A
1 TTAAATTTAATAAT-ATTTTATA
1544606 TTAAATT
1 TTAAATT
1544613 AATTTAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
21 9 0.20
22 19 0.41
23 4 0.09
24 6 0.13
25 6 0.13
26 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAAATTTAATAATATTTTATA
Found at i:1545398 original size:13 final size:14
Alignment explanation
Indices: 1545382--1545410 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1545372 ATATTAAATT
1545382 TTAATTTT-AATAA
1 TTAATTTTAAATAA
1545395 TTAATTTTAAATAA
1 TTAATTTTAAATAA
1545409 TT
1 TT
1545411 TTAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAATTTTAAATAA
Found at i:1545422 original size:2 final size:2
Alignment explanation
Indices: 1545415--1545444 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1545405 ATAATTTTAA
*
1545415 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1545445 GATGCAGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1550194 original size:18 final size:18
Alignment explanation
Indices: 1550158--1550196 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1550148 ACGACTAAGC
*
1550158 TTTATTTTCTCCACTCTT
1 TTTATTTTCTCCAATCTT
1550176 TTTATTTT-TCCAATACTT
1 TTTATTTTCTCCAAT-CTT
1550194 TTT
1 TTT
1550197 CTTAATGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATTTTCTCCAATCTT
Found at i:1551447 original size:11 final size:10
Alignment explanation
Indices: 1551413--1551446 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1551403 TTTACACTCA
1551413 TTTAAATATT
1 TTTAAATATT
*
1551423 TTTATCATATT
1 TTTA-AATATT
1551434 TTTAAATATT
1 TTTAAATATT
1551444 TTT
1 TTT
1551447 TTCAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTAAATATT
Found at i:1554436 original size:3 final size:3
Alignment explanation
Indices: 1554428--1554457 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1554418 TCAAATATGC
1554428 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1554458 GCCATCAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1554613 original size:19 final size:20
Alignment explanation
Indices: 1554591--1554635 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1554581 TTTATTACAA
1554591 TTGACA-GTGTTCTTAGGGT
1 TTGACACGTGTTCTTAGGGT
*
1554610 TTGAGAGACGTGTTCTTAGGGT
1 TT--GACACGTGTTCTTAGGGT
1554632 TTGA
1 TTGA
1554636 GAGACTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 2 0.09
21 3 0.14
22 15 0.68
ACGTcount: A:0.18, C:0.09, G:0.33, T:0.40
Consensus pattern (20 bp):
TTGACACGTGTTCTTAGGGT
Found at i:1554622 original size:22 final size:22
Alignment explanation
Indices: 1554597--1554640 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1554587 ACAATTGACA
1554597 GTGTTCTTAGGGTTTGAGAGAC
1 GTGTTCTTAGGGTTTGAGAGAC
1554619 GTGTTCTTAGGGTTTGAGAGAC
1 GTGTTCTTAGGGTTTGAGAGAC
1554641 TGATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.36, T:0.36
Consensus pattern (22 bp):
GTGTTCTTAGGGTTTGAGAGAC
Found at i:1554648 original size:2 final size:2
Alignment explanation
Indices: 1554643--1554673 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1554633 TGAGAGACTG
1554643 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 A
1554674 GGAACTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1555596 original size:20 final size:20
Alignment explanation
Indices: 1555573--1555638 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
1555563 AAGTATCCAG
1555573 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1555593 ATGTAGCGATACATGTATAA
1 ATGTATCGATACATTTTTCA
* *
1555613 ATGTATCAATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1555633 ATGTAT
1 ATGTAT
1555639 TATATTCTAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1569325 original size:17 final size:18
Alignment explanation
Indices: 1569299--1569353 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
1569289 TTTAAATATA
* *
1569299 ATATTTTATAATTTAAAT
1 ATATTATATAATATAAAT
1569317 -TATTATATAATATAAAT
1 ATATTATATAATATAAAT
* *
1569334 ATATTTATTTAATAAAAAT
1 ATA-TTATATAATATAAAT
1569353 A
1 A
1569354 ATTTTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 15 0.48
18 2 0.06
19 14 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTATATAATATAAAT
Found at i:1569330 original size:22 final size:21
Alignment explanation
Indices: 1569287--1569331 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1569277 AATTGAGATA
**
1569287 AATTTAAATATAATATTTTAT
1 AATTTAAATATAATATAATAT
*
1569308 AATTTAAATTATTATATAATAT
1 AATTTAAA-TATAATATAATAT
1569330 AA
1 AA
1569332 ATATATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTTAAATATAATATAATAT
Found at i:1569361 original size:17 final size:19
Alignment explanation
Indices: 1569319--1569361 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1569309 ATTTAAATTA
* *
1569319 TTATATAATATAAATATAT
1 TTATTTAATAAAAATATAT
1569338 TTATTTAATAAAAATA-AT
1 TTATTTAATAAAAATATAT
1569356 TT-TTTA
1 TTATTTA
1569362 TTTTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 4 0.18
19 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTTAATAAAAATATAT
Found at i:1569393 original size:29 final size:30
Alignment explanation
Indices: 1569335--1569394 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
1569325 AATATAAATA
* **
1569335 TATTTATTTAATAAAAATAATTTTTTATTT
1 TATTAATTTAATAAAAATAATTTTAAATTT
1569365 TATTAATTT-ATAAATAATAA-TTTAAATTT
1 TATTAATTTAATAAA-AATAATTTTAAATTT
1569394 T
1 T
1569395 TATATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TATTAATTTAATAAAAATAATTTTAAATTT
Found at i:1570255 original size:20 final size:18
Alignment explanation
Indices: 1570209--1570255 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1570199 ATTAATTTTT
*
1570209 TAAAAAAATTAGTTTTAC
1 TAAAAAATTTAGTTTTAC
*
1570227 TATAAAATTTATGTTTTACC
1 TAAAAAATTTA-GTTTTA-C
1570247 TAAAAAATT
1 TAAAAAATT
1570256 CTCACTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 6 0.25
20 9 0.38
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (18 bp):
TAAAAAATTTAGTTTTAC
Found at i:1571909 original size:2 final size:2
Alignment explanation
Indices: 1571902--1571942 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1571892 TTTCTTCTTC
1571902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1571943 GTTCTCAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1573668 original size:30 final size:29
Alignment explanation
Indices: 1573629--1573689 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
1573619 TTTAAAATAT
1573629 AAAAGATATTTATTTTTTAAAATTTTATAA
1 AAAAGATATTTATTTTTTAAAATTTTA-AA
* *
1573659 AAAATATATTTATTTTTTAATATTTTAAA
1 AAAAGATATTTATTTTTTAAAATTTTAAA
1573688 AA
1 AA
1573690 TACTCACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
AAAAGATATTTATTTTTTAAAATTTTAAA
Found at i:1573859 original size:16 final size:16
Alignment explanation
Indices: 1573846--1573878 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1573836 TAAAATTATT
1573846 TTAAATTATTATTAAA
1 TTAAATTATTATTAAA
1573862 TTAAATTATTATTAAA
1 TTAAATTATTATTAAA
1573878 T
1 T
1573879 AATATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAATTATTATTAAA
Found at i:1574740 original size:28 final size:28
Alignment explanation
Indices: 1574686--1574742 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1574676 AATTTGATTT
* *
1574686 AAAATTTTAAAATATTATTTATAATTAA
1 AAAATTATAAAATATTATTAATAATTAA
*
1574714 AAAATTATAAAATAGTT-TTAATTATTAA
1 AAAATTATAAAATA-TTATTAATAATTAA
1574742 A
1 A
1574743 TAATAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AAAATTATAAAATATTATTAATAATTAA
Found at i:1575993 original size:2 final size:2
Alignment explanation
Indices: 1575986--1576020 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1575976 TGCATGGATG
1575986 AT 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 AT A
1576021 GACGCCATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1576552 original size:2 final size:2
Alignment explanation
Indices: 1576539--1576584 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1576529 TGAGATACAG
* *
1576539 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1576581 AT AT
1 AT AT
1576585 CATTTATAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1576552 original size:10 final size:10
Alignment explanation
Indices: 1576533--1576575 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
1576523 AGAAGTTGAG
*
1576533 ATACAGATAT
1 ATACATATAT
1576543 ATACATATAT
1 ATACATATAT
*
1576553 ATATATATAT
1 ATACATATAT
*
1576563 ATATATATAT
1 ATACATATAT
1576573 ATA
1 ATA
1576576 TATGTATATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (10 bp):
ATACATATAT
Found at i:1577442 original size:45 final size:45
Alignment explanation
Indices: 1577387--1577477 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
1577377 TCAGTTTTCA
1577387 TACAAAAGCATTCCCGTTATCCTGCAAAGTTGTTAACAGTTCATC
1 TACAAAAGCATTCCCGTTATCCTGCAAAGTTGTTAACAGTTCATC
* *
1577432 TACATAAGCATTCCCGTTATCCTGTAAAGTTGTTAACAGTTCATC
1 TACAAAAGCATTCCCGTTATCCTGCAAAGTTGTTAACAGTTCATC
1577477 T
1 T
1577478 GGCCATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (45 bp):
TACAAAAGCATTCCCGTTATCCTGCAAAGTTGTTAACAGTTCATC
Found at i:1582552 original size:2 final size:2
Alignment explanation
Indices: 1582545--1582584 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1582535 ATTCTTGTTT
1582545 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1582585 GCTTCAAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1584127 original size:2 final size:2
Alignment explanation
Indices: 1584120--1584153 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1584110 CCAAAATGCC
1584120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1584154 TAATTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1589391 original size:25 final size:25
Alignment explanation
Indices: 1589363--1589470 Score: 77
Period size: 25 Copynumber: 4.4 Consensus size: 25
1589353 ACAAATTGTA
*
1589363 AAAATTATATTTATAAATAATTTTT
1 AAAATTATATTTATAAATAATTATT
*
1589388 AAAATTATA---ATAAATAA-TAAT
1 AAAATTATATTTATAAATAATTATT
* *
1589409 -AAATTAATAATTACT-CATAAATT-TT
1 AAAATT-ATATTTA-TAAAT-AATTATT
*
1589434 AAAAATTATATTTATAAATAATAATT
1 -AAAATTATATTTATAAATAATTATT
*
1589460 AAAATTGTATT
1 AAAATTATATT
1589471 GAATAATAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
20 5 0.08
21 5 0.08
22 8 0.12
24 3 0.05
25 27 0.42
26 11 0.17
27 5 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (25 bp):
AAAATTATATTTATAAATAATTATT
Found at i:1589437 original size:72 final size:72
Alignment explanation
Indices: 1589349--1589483 Score: 207
Period size: 72 Copynumber: 1.9 Consensus size: 72
1589339 CATTGCACTC
**
1589349 ACTCACAAATTGTAAAAATTATATTTATAAATAATTTTTAAAATTATAATAAATAATAATAAATT
1 ACTCACAAATTGTAAAAATTATATTTATAAATAATAATTAAAATTATAATAAATAATAATAAATT
1589414 AATAATT
66 AATAATT
* * * * *
1589421 ACTCATAAATTTTAAAAATTATATTTATAAATAATAATTAAAATTGTATTGAATAATAATAAA
1 ACTCACAAATTGTAAAAATTATATTTATAAATAATAATTAAAATTATAATAAATAATAATAAA
1589484 AAAATAAAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (72 bp):
ACTCACAAATTGTAAAAATTATATTTATAAATAATAATTAAAATTATAATAAATAATAATAAATT
AATAATT
Found at i:1597772 original size:2 final size:2
Alignment explanation
Indices: 1597765--1597794 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1597755 AAATTTATGA
1597765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1597795 CCATAGTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1598399 original size:21 final size:21
Alignment explanation
Indices: 1598374--1598413 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1598364 ATTTTTTATT
1598374 TAAAT-TTAATTATAAAATATA
1 TAAATATTAATTA-AAAATATA
1598395 TAAATATTAATTAAAAATA
1 TAAATATTAATTAAAAATA
1598414 AAAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATTAAAAATATA
Found at i:1609198 original size:20 final size:20
Alignment explanation
Indices: 1609162--1609215 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1609152 ATATTAATCT
* *
1609162 TAAC-ATAAAGTAGTAATAA
1 TAACAATAAATTAATAATAA
1609181 TAACAATAAATTAATAATAA
1 TAACAATAAATTAATAATAA
*
1609201 TAAAAATAAATTAAT
1 TAACAATAAATTAAT
1609216 TAACTAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (20 bp):
TAACAATAAATTAATAATAA
Found at i:1610731 original size:11 final size:11
Alignment explanation
Indices: 1610708--1610741 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1610698 AAAATCATAA
1610708 TTATTTAAATTT
1 TTATTT-AATTT
1610720 TTATTTAATTT
1 TTATTTAATTT
*
1610731 TTAATTAATTT
1 TTATTTAATTT
1610742 AAAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTAATTT
Found at i:1611273 original size:20 final size:19
Alignment explanation
Indices: 1611237--1611276 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1611227 CAAAAAGATG
1611237 TATATTTTAAAAATTTTAT
1 TATATTTTAAAAATTTTAT
* *
1611256 TATATTTT-TAAATTTTTT
1 TATATTTTAAAAATTTTAT
1611274 TAT
1 TAT
1611277 TTCTCACTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATATTTTAAAAATTTTAT
Found at i:1613868 original size:2 final size:2
Alignment explanation
Indices: 1613857--1613891 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1613847 TGCCCCAGGT
*
1613857 TC TC -C TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1613892 AAGTTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1617433 original size:2 final size:2
Alignment explanation
Indices: 1617426--1617453 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1617416 TGAAAATTTA
1617426 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1617454 TAAAACCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1618661 original size:37 final size:34
Alignment explanation
Indices: 1618583--1618661 Score: 86
Period size: 37 Copynumber: 2.2 Consensus size: 34
1618573 TTAATTTAAA
*
1618583 TTTTATAATGTTTTATTTTATTAAATTAAATTAT
1 TTTTATAATATTTTATTTTATTAAATTAAATTAT
** **
1618617 TGGTATAATAATTTTATTTTATTTTAAATTATTTTAT
1 TTTTATAAT-ATTTTATTTTA--TTAAATTAAATTAT
1618654 TTTTATAA
1 TTTTATAA
1618662 AATAATTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
34 7 0.20
35 10 0.29
37 18 0.51
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTTTATAATATTTTATTTTATTAAATTAAATTAT
Found at i:1619074 original size:22 final size:21
Alignment explanation
Indices: 1619049--1619094 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1619039 TTTGAGTTTT
*
1619049 TTTAAAATTTAAATTAATTTGA
1 TTTAAAATTCAAATT-ATTTGA
* *
1619071 TTTAATATTCCAATTATTTGA
1 TTTAAAATTCAAATTATTTGA
1619092 TTT
1 TTT
1619095 TGATTTTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTAAAATTCAAATTATTTGA
Found at i:1619846 original size:21 final size:21
Alignment explanation
Indices: 1619820--1619869 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1619810 TATATTTTTA
1619820 TATAAAT-TTAATTATAAAAAT
1 TATAAATATTAA-TATAAAAAT
1619841 TATAAATATTAATATAAAAAT
1 TATAAATATTAATATAAAAAT
*
1619862 TTTAAATA
1 TATAAATA
1619870 ATAAAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TATAAATATTAATATAAAAAT
Found at i:1627368 original size:2 final size:2
Alignment explanation
Indices: 1627361--1627392 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1627351 ACTTTTGTTC
1627361 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1627393 TTTTGTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1629182 original size:24 final size:25
Alignment explanation
Indices: 1629153--1629201 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1629143 TGATATAAAA
*
1629153 TATT-AATT-ATATAAAATTTATTTT
1 TATTAAATTGATA-AAAAATTATTTT
1629177 TATTAAATTGATAAAAAATTATTTT
1 TATTAAATTGATAAAAAATTATTTT
1629202 AAATAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 15 0.68
26 3 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATTAAATTGATAAAAAATTATTTT
Found at i:1637441 original size:3 final size:3
Alignment explanation
Indices: 1637433--1637473 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1637423 TTTATTTGGC
1637433 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1637474 GGCCAAGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1638965 original size:25 final size:25
Alignment explanation
Indices: 1638918--1638966 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1638908 TATTAATATT
* *
1638918 TATATATTTTTATAATTAAATTAAA
1 TATATATTTATATAATAAAATTAAA
1638943 TATATATTTAT-TAATAAATATTAA
1 TATATATTTATATAATAAA-ATTAA
1638967 TTCGACAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TATATATTTATATAATAAAATTAAA
Found at i:1639624 original size:2 final size:2
Alignment explanation
Indices: 1639605--1639639 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1639595 ACATCCATAC
* *
1639605 AT AT AA AT AT AA 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 AT A
1639640 ATCTTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1640295 original size:2 final size:2
Alignment explanation
Indices: 1640288--1640332 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1640278 TTTGAATTGA
1640288 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1640330 AT A
1 AT A
1640333 ATTAAAGTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1644124 original size:37 final size:37
Alignment explanation
Indices: 1644071--1644170 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 37
1644061 TTATGTAATG
*
1644071 ATATTTAAATTT-TTTAATTATTTAAATTTATATTAA
1 ATATTTTAATTTATTTAATTATTTAAATTTATATTAA
* *
1644107 ATATTATT-ATTTATTTAAATATTT--ATTTTTATTAA
1 ATATT-TTAATTTATTTAATTATTTAAATTTATATTAA
1644142 ATATTTTAATTTTATTTTAATTA-TTAAAT
1 ATATTTTAA-TTTA-TTTAATTATTTAAAT
1644171 AATTCGATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
34 2 0.04
35 16 0.30
36 15 0.28
37 18 0.34
38 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (37 bp):
ATATTTTAATTTATTTAATTATTTAAATTTATATTAA
Found at i:1644133 original size:29 final size:28
Alignment explanation
Indices: 1644075--1644157 Score: 77
Period size: 29 Copynumber: 3.1 Consensus size: 28
1644065 GTAATGATAT
*
1644075 TTAAATTTTTTAATTATTTAAATTTATA
1 TTAAATTTATTAATTATTTAAATTTATA
*
1644103 TTAAATATTATTATTTATTTAAATATT-TA
1 TTAAAT-TTATTAATTATTTAAAT-TTATA
* *
1644132 TT---TTTATTAAATATTTTAATTT-TA
1 TTAAATTTATTAATTATTTAAATTTATA
1644156 TT
1 TT
1644158 TTAATTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 6 0.12
25 14 0.29
26 1 0.02
28 6 0.12
29 19 0.40
30 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTAAATTTATTAATTATTTAAATTTATA
Found at i:1644138 original size:25 final size:24
Alignment explanation
Indices: 1644110--1644166 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
1644100 ATATTAAATA
1644110 TTATTATTTATTTAAATATTTATTT
1 TTATTATTTATTTAAAT-TTTATTT
** *
1644135 TTATTAAATATTTTAATTTTATTT
1 TTATTATTTATTTAAATTTTATTT
*
1644159 TAATTATT
1 TTATTATT
1644167 AAATAATTCG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTATTATTTATTTAAATTTTATTT
Found at i:1644154 original size:18 final size:18
Alignment explanation
Indices: 1644071--1644157 Score: 83
Period size: 18 Copynumber: 4.9 Consensus size: 18
1644061 TTATGTAATG
*
1644071 ATATTTAAATTTT-TTAA
1 ATATTTTAATTTTATTAA
* *
1644088 TTATTTAAATTTATATTAA
1 ATATTTTAATTT-TATTAA
1644107 ATATTATT-A-TTTATTTAA
1 ATATT-TTAATTTTA-TTAA
*
1644125 ATA-TTTATTTTTATTAA
1 ATATTTTAATTTTATTAA
1644142 ATATTTTAATTTTATT
1 ATATTTTAATTTTATT
1644158 TTAATTATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
16 2 0.03
17 21 0.36
18 25 0.43
19 9 0.16
20 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTTAATTTTATTAA
Found at i:1644168 original size:18 final size:18
Alignment explanation
Indices: 1644082--1644168 Score: 52
Period size: 19 Copynumber: 4.7 Consensus size: 18
1644072 TATTTAAATT
*
1644082 TTTTAATTATTTAAATTTA
1 TTTTAATTA-TTAATTTTA
* * *
1644101 TATTAAATATTATTATTTA
1 TTTTAATTATTAAT-TTTA
* *
1644120 -TTTAAATATTTATTTT-
1 TTTTAATTATTAATTTTA
* *
1644136 TATTAAATATTTTAATTTTA
1 T-TTTAAT-TATTAATTTTA
1644156 TTTTAATTATTAA
1 TTTTAATTATTAA
1644169 ATAATTCGAT
Statistics
Matches: 50, Mismatches: 13, Indels: 11
0.68 0.18 0.15
Matches are distributed among these distances:
17 3 0.06
18 22 0.44
19 24 0.48
20 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTAATTATTAATTTTA
Found at i:1646270 original size:8 final size:8
Alignment explanation
Indices: 1646257--1646299 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
1646247 CATAATTTTA
*
1646257 ATATATTC
1 ATATATTT
1646265 ATATATTT
1 ATATATTT
1646273 ATATTATTT
1 ATA-TATTT
1646282 ATATATTTT
1 ATATA-TTT
1646291 ATCATATTT
1 AT-ATATTT
1646300 TTATTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 12 0.39
9 16 0.52
10 3 0.10
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATATTT
Found at i:1655918 original size:25 final size:24
Alignment explanation
Indices: 1655890--1655938 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1655880 AAGATTAATT
1655890 CTTAAGAAAAAGTTTTATAATTTTA
1 CTTAA-AAAAAGTTTTATAATTTTA
* * *
1655915 CTTAAATAAATTTTTATATTTTTA
1 CTTAAAAAAAGTTTTATAATTTTA
1655939 TTTTACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (24 bp):
CTTAAAAAAAGTTTTATAATTTTA
Found at i:1656833 original size:2 final size:2
Alignment explanation
Indices: 1656826--1656850 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1656816 ATCATTAACA
1656826 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 A
1656851 ATACATCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1660441 original size:16 final size:16
Alignment explanation
Indices: 1660410--1660440 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1660400 ATTTTGTATC
1660410 CTTTATTTTTCTTTTT
1 CTTTATTTTTCTTTTT
1660426 CTTTATTTTT-TTTTT
1 CTTTATTTTTCTTTTT
1660441 TTGGCCCCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTTATTTTTCTTTTT
Found at i:1665692 original size:20 final size:20
Alignment explanation
Indices: 1665655--1665695 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1665645 AGGTGAAAAA
* *
1665655 ACACACACACACATACAAAT
1 ACACACACAAACACACAAAT
*
1665675 ACACAGACAAACACACAAAT
1 ACACACACAAACACACAAAT
1665695 A
1 A
1665696 TTACCCCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.32, G:0.02, T:0.07
Consensus pattern (20 bp):
ACACACACAAACACACAAAT
Found at i:1668690 original size:17 final size:17
Alignment explanation
Indices: 1668657--1668690 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1668647 AGATTATAAT
* *
1668657 CAAAATGAAAAGAAAAA
1 CAAAAAGAAAAAAAAAA
1668674 CAAAAAGAAAAAAAAAA
1 CAAAAAGAAAAAAAAAA
1668691 TTCTAAAAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (17 bp):
CAAAAAGAAAAAAAAAA
Found at i:1671128 original size:12 final size:12
Alignment explanation
Indices: 1671107--1671141 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1671097 GCCTTGTAAA
*
1671107 AATAAAAATAAT
1 AATAACAATAAT
1671119 AATAACAATAAT
1 AATAACAATAAT
*
1671131 GATAACAATAA
1 AATAACAATAA
1671142 ATGGGGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (12 bp):
AATAACAATAAT
Found at i:1673434 original size:5 final size:5
Alignment explanation
Indices: 1673424--1673462 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
1673414 CCATTGCCTC
*
1673424 CTTTT CTTTT CTTTT CTTTT CTTTT CCTTT -TTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1673463 TAATTCCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 28 0.90
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
CTTTT
Found at i:1676246 original size:7 final size:7
Alignment explanation
Indices: 1676234--1676263 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1676224 TAAATTTAAA
1676234 TTTATTT
1 TTTATTT
1676241 TTTATTT
1 TTTATTT
1676248 TTTATTT
1 TTTATTT
1676255 TTTATTT
1 TTTATTT
1676262 TT
1 TT
1676264 AAGTTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTATTT
Found at i:1677110 original size:34 final size:34
Alignment explanation
Indices: 1677066--1677152 Score: 81
Period size: 35 Copynumber: 2.6 Consensus size: 34
1677056 AAATTTTATG
* * *
1677066 TATTAGTATTTATGTTATTTTTTTCGTATTTAA-AA
1 TATTA-TATTTATATTATTTTTTACATA-TTAATAA
*
1677101 TATTATATTTTTATATATTTTTTACATATTAATAA
1 TATTATATTTATAT-TATTTTTTACATATTAATAA
*
1677136 T-TTAT-TTTATTTTATTT
1 TATTATATTTATATTATTT
1677153 ATATTTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
32 5 0.11
33 5 0.11
34 15 0.34
35 19 0.43
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.64
Consensus pattern (34 bp):
TATTATATTTATATTATTTTTTACATATTAATAA
Found at i:1677349 original size:18 final size:20
Alignment explanation
Indices: 1677321--1677365 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1677311 GTTTAGGAGG
1677321 AAAAAGAGAGA-AAGAAAGA-
1 AAAAAGAGAGACAA-AAAGAT
1677340 AAAAAG-GAGACAAAAAGAT
1 AAAAAGAGAGACAAAAAGAT
1677359 AAAAAGA
1 AAAAAGA
1677366 AAAAGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (20 bp):
AAAAAGAGAGACAAAAAGAT
Found at i:1677376 original size:22 final size:22
Alignment explanation
Indices: 1677320--1677377 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
1677310 CGTTTAGGAG
*
1677320 GAAAAAGAGAGAAAGAAAGAAA
1 GAAAAAGAGAAAAAGAAAGAAA
* *
1677342 -AAAGGAGACAAAAAGATAA-AAA
1 GAAA-AAGAGAAAAAGA-AAGAAA
1677364 GAAAAAGAGAAAAA
1 GAAAAAGAGAAAAA
1677378 ATTTATGTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
21 3 0.11
22 20 0.71
23 5 0.18
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.02
Consensus pattern (22 bp):
GAAAAAGAGAAAAAGAAAGAAA
Found at i:1677435 original size:19 final size:18
Alignment explanation
Indices: 1677413--1677465 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
1677403 TTTATATGTA
1677413 AAATATTTTATTTTTATAT
1 AAATATTTTATTTTTA-AT
* *
1677432 AAATTTTTTATATATTAAT
1 AAATATTTTAT-TTTTAAT
*
1677451 AATTCATTTTATTTT
1 AAAT-ATTTTATTTT
1677466 ATGTATATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
AAATATTTTATTTTTAAT
Found at i:1677465 original size:317 final size:318
Alignment explanation
Indices: 1677013--1677600 Score: 809
Period size: 317 Copynumber: 1.9 Consensus size: 318
1677003 ATAAAAAAAA
* * * *
1677013 AGAAAGAAAGAAAGAAATGAGAGAAAAAGAAAAAAGAAATAAAAAATTTTATGTATTAGTATTTA
1 AGAAAGAAAGAAAGAAAGGAGACAAAAAGAAAAAAGAAAGAAAAAAATTTATGTATTAGTATTTA
* * *
1677078 TGTTATTTTTTTCGTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTT
66 TGTTATTTTTTTCATATGTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTCATTT
* * * *
1677143 TATTTTATTTATATTTTTATATATACATATATTTGTATT-ATGTATATATTATTTTTAT-ATTAT
131 TATTTTATGTATATTTTTATACATACATATATTCGT-TTCATGTACATATTA-TTTTATCATTAT
* *
1677206 ATTTTAAAT-TTTTTTATAAATATCATATTTATA-TTTTTATAT-TTAAAATAAAATAAATTTAT
194 ATTATAAATATTTTTTATAAATATCATAGTTATATTTTTTAT-TGTTAAAATAAAATAAATTTAT
1677268 ATAAATTTTTACATTGACGTGACACTTAAATTTTTTGTTTTACGTTTAGGAGGAAAAAGAG
258 ATAAATTTTTACATTGACGTGACACTTAAATTTTTTGTTTTACGTTTAGGAGGAAAAAGAG
* *
1677329 AGAAAGAAAGAAA-AAAGGAGACAAAAAGATAAAAAGAAAAAGAGAAAAAATTTATGTCTTTGTA
1 AGAAAGAAAGAAAGAAAGGAGACAAAAAGA-AAAAAG--AAAGA-AAAAAATTTATGTATTAGTA
* *
1677393 -TT-TG-TATTTTTTT-ATATGTAAAATATTTTATTTTTATATAAATTTTTTATATATTAATAAT
62 TTTATGTTATTTTTTTCATATGTAAAATATTATATTTTTATAT--ATTTTTTACATATTAATAAT
* * *
1677454 TCATTTTATTTTATGTATATTTTTATACGTACTTATATTCGTTTCATGTGCATATTATTTTATCA
125 TCATTTTATTTTATGTATATTTTTATACATACATATATTCGTTTCATGTACATATTATTTTATCA
* * *
1677519 TTATGTTATAAATATTTTTTATAAATATCATGGTTATGTTTTTTATTGTTAAAATAAAATAAATT
190 TTATATTATAAATATTTTTTATAAATATCATAGTTATATTTTTTATTGTTAAAATAAAATAAATT
*
1677584 TATGTAAATTTTTACAT
255 TATATAAATTTTTACAT
1677601 GTTAATTATT
Statistics
Matches: 237, Mismatches: 24, Indels: 19
0.85 0.09 0.07
Matches are distributed among these distances:
315 37 0.16
316 36 0.15
317 79 0.33
318 28 0.12
319 57 0.24
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (318 bp):
AGAAAGAAAGAAAGAAAGGAGACAAAAAGAAAAAAGAAAGAAAAAAATTTATGTATTAGTATTTA
TGTTATTTTTTTCATATGTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTCATTT
TATTTTATGTATATTTTTATACATACATATATTCGTTTCATGTACATATTATTTTATCATTATAT
TATAAATATTTTTTATAAATATCATAGTTATATTTTTTATTGTTAAAATAAAATAAATTTATATA
AATTTTTACATTGACGTGACACTTAAATTTTTTGTTTTACGTTTAGGAGGAAAAAGAG
Found at i:1677476 original size:38 final size:36
Alignment explanation
Indices: 1677397--1677477 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 36
1677387 TTTGTATTTG
1677397 TATTTTTTTATATGTAAAATATTTTATTTTTATATA
1 TATTTTTTTATATGTAAAATATTTTATTTTTATATA
* *
1677433 AATTTTTTATATAT-TAATAATTCATTTTA-TTTTATGTA
1 TATTTTTT-TATATGTAA-AA-T-ATTTTATTTTTATATA
1677471 TATTTTT
1 TATTTTT
1677478 ATACGTACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
36 10 0.26
37 7 0.18
38 15 0.39
39 6 0.16
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (36 bp):
TATTTTTTTATATGTAAAATATTTTATTTTTATATA
Found at i:1677477 original size:37 final size:36
Alignment explanation
Indices: 1677397--1677480 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 36
1677387 TTTGTATTTG
*
1677397 TATTTTTTTATATGTAAAATATTTTATTTTTATATA
1 TATTTTTATATATGTAAAATATTTTATTTTTATATA
* *
1677433 AATTTTTTATATAT-TAATAATTCATTTTA-TTTTATGTA
1 TA-TTTTTATATATGTAA-AA-T-ATTTTATTTTTATATA
1677471 TATTTTTATA
1 TATTTTTATA
1677481 CGTACTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
36 4 0.10
37 20 0.50
38 10 0.25
39 6 0.15
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (36 bp):
TATTTTTATATATGTAAAATATTTTATTTTTATATA
Found at i:1677705 original size:9 final size:8
Alignment explanation
Indices: 1677686--1677745 Score: 66
Period size: 8 Copynumber: 7.1 Consensus size: 8
1677676 AGAAAGATGG
1677686 AAAGAAAA
1 AAAGAAAA
*
1677694 AAATAGAAA
1 AAAGA-AAA
1677703 AAAGAAAA
1 AAAGAAAA
1677711 GAAAGAAAA
1 -AAAGAAAA
1677720 AAAGAAAA
1 AAAGAAAA
**
1677728 GGAGAAATA
1 AAAGAAA-A
1677737 AAAGAAAA
1 AAAGAAAA
1677745 A
1 A
1677746 GTTAATGTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 22 0.51
9 21 0.49
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:1677705 original size:12 final size:11
Alignment explanation
Indices: 1677686--1677727 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
1677676 AGAAAGATGG
1677686 AAAG-AAAAAA
1 AAAGAAAAAAA
*
1677696 ATAGAAAAAAGA
1 AAAGAAAAAA-A
1677708 AAAGAAAGAAAA
1 AAAGAAA-AAAA
1677720 AAAGAAAA
1 AAAGAAAA
1677728 GGAGAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.11
11 6 0.22
12 15 0.56
13 3 0.11
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:1677708 original size:17 final size:17
Alignment explanation
Indices: 1677686--1677745 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1677676 AGAAAGATGG
1677686 AAAGAAAAAAATAG-AAA
1 AAAGAAAAAAA-AGAAAA
*
1677703 AAAGAAAAGAAAGAAAA
1 AAAGAAAAAAAAGAAAA
**
1677720 AAAG-AAAAGGAGAAATA
1 AAAGAAAAAAAAGAAA-A
1677737 AAAGAAAAA
1 AAAGAAAAA
1677746 GTTAATGTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.28
17 22 0.61
18 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAGAAAAAAAAGAAAA
Found at i:1677733 original size:25 final size:26
Alignment explanation
Indices: 1677685--1677745 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
1677675 GAGAAAGATG
1677685 GAAAGAAAAAAATAGAAAAAAGAAA-A
1 GAAAG-AAAAAATAGAAAAAAGAAATA
*
1677711 GAAAGAAAAAA-AGAAAAGGAGAAATA
1 GAAAGAAAAAATAGAAAA-AAGAAATA
1677737 -AAAGAAAAA
1 GAAAGAAAAA
1677746 GTTAATGTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.19
25 20 0.62
26 6 0.19
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (26 bp):
GAAAGAAAAAATAGAAAAAAGAAATA
Found at i:1679145 original size:12 final size:12
Alignment explanation
Indices: 1679106--1679149 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1679096 ACACCATCAG
1679106 TATTTATATATA
1 TATTTATATATA
*
1679118 TATATATATATA
1 TATTTATATATA
* *
1679130 TATTTATTTATT
1 TATTTATATATA
1679142 TATTTATA
1 TATTTATA
1679150 AAATATATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTTATATATA
Found at i:1679148 original size:8 final size:8
Alignment explanation
Indices: 1679106--1679144 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1679096 ACACCATCAG
1679106 TATTTATA
1 TATTTATA
*
1679114 TATATATA
1 TATTTATA
*
1679122 TATATATA
1 TATTTATA
*
1679130 TATTTATT
1 TATTTATA
1679138 TATTTAT
1 TATTTAT
1679145 TTATAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTATA
Found at i:1688350 original size:14 final size:14
Alignment explanation
Indices: 1688331--1688374 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1688321 ATTTTTTACA
*
1688331 TTAAAAATTATAAT
1 TTAAAAATTAAAAT
* *
1688345 TTAAAAATAAAAAA
1 TTAAAAATTAAAAT
1688359 TT-AAAATTAAAAT
1 TTAAAAATTAAAAT
1688372 TTA
1 TTA
1688375 TTAATATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAAAATTAAAAT
Found at i:1688692 original size:19 final size:21
Alignment explanation
Indices: 1688665--1688711 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1688655 TATATTATGC
* *
1688665 ATATGTTATTTATA-TATT-T
1 ATATATTATTAATATTATTAT
1688684 ATATATTATTAATATTATTAT
1 ATATATTATTAATATTATTAT
1688705 ATATATT
1 ATATATT
1688712 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
20 4 0.17
21 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATATTATTAATATTATTAT
Found at i:1688700 original size:9 final size:10
Alignment explanation
Indices: 1688655--1688708 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 10
1688645 TTAAGAGGAT
*
1688655 TATATTATGCA
1 TATATTAT-TA
*
1688666 TATGTTATT-
1 TATATTATTA
1688675 TATA-TATTTA
1 TATATTA-TTA
1688685 TATATTATTA
1 TATATTATTA
1688695 -ATATTATTA
1 TATATTATTA
1688704 TATAT
1 TATAT
1688709 ATTTAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
8 2 0.06
9 14 0.39
10 11 0.31
11 9 0.25
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (10 bp):
TATATTATTA
Found at i:1689509 original size:13 final size:13
Alignment explanation
Indices: 1689493--1689550 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
1689483 TATAAATTTT
1689493 ATAAATAAAATTA
1 ATAAATAAAATTA
**
1689506 ATAAAATAACTTTTA
1 AT-AAATAA-AATTA
* *
1689521 AT-AATAAATTTT
1 ATAAATAAAATTA
1689533 ATAAATAAAATTA
1 ATAAATAAAATTA
1689546 ATAAA
1 ATAAA
1689551 ATAACTTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
12 5 0.14
13 20 0.56
14 6 0.17
15 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAAATAAAATTA
Found at i:1689519 original size:27 final size:27
Alignment explanation
Indices: 1689484--1689549 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
1689474 AATAAATTTT
1689484 ATAAATTTT-ATAAATAAAATTAATAAA
1 ATAAATTTTAAT-AATAAAATTAATAAA
* * *
1689511 ATAACTTTTAATAATAAATTTTAT-AA
1 ATAAATTTTAATAATAAAATTAATAAA
*
1689537 ATAAA-ATTAATAA
1 ATAAATTTTAATAA
1689550 AATAACTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 7 0.21
26 6 0.18
27 18 0.55
28 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
ATAAATTTTAATAATAAAATTAATAAA
Found at i:1689765 original size:12 final size:12
Alignment explanation
Indices: 1689748--1689773 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1689738 ACAAATAATA
1689748 ATAATTATTATT
1 ATAATTATTATT
1689760 ATAATTATTATT
1 ATAATTATTATT
1689772 AT
1 AT
1689774 TATTTTGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATAATTATTATT
Found at i:1689982 original size:19 final size:20
Alignment explanation
Indices: 1689958--1690007 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1689948 GACACCAATA
1689958 AATTTAAAAATATAAAT-TT
1 AATTTAAAAATATAAATGTT
* *
1689977 AATTTATTAAATATAATTGTT
1 AATTTA-AAAATATAAATGTT
1689998 AA-TTAAAAAT
1 AATTTAAAAAT
1690008 GAAATGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATTTAAAAATATAAATGTT
Found at i:1690095 original size:17 final size:17
Alignment explanation
Indices: 1690075--1690108 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1690065 ATTTATTTTT
1690075 TTAATAT-AATATAAAAA
1 TTAATATGAA-ATAAAAA
1690092 TTAATATGAAATAAAAA
1 TTAATATGAAATAAAAA
1690109 GGAAATAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
TTAATATGAAATAAAAA
Found at i:1691462 original size:165 final size:170
Alignment explanation
Indices: 1691137--1691474 Score: 474
Period size: 165 Copynumber: 2.0 Consensus size: 170
1691127 GTGGTAGTCA
* *** *
1691137 TGTTAGTTCCTGTTGTCATGGTGCATTACATGGGTTTCTGCCTTGCACCGTACATCACTTGTTGA
1 TGTTAGTTCCTCTTGTCA--GTGCATTACATGGGTTTCTGCCGAACACCATACATCACTTGTTGA
*
1691202 GTTAGTTCTGCTTTTAAACTTGCATGCGTTTTTTGCTATTGTATCTGAATGTTTTGATCTCTTAA
64 GTTAGTTCTGCTTTTAAACTTGCATGCGTTTTTTGCTATTGTATCTGAATGTTTTGATCTCCTAA
*
1691267 CATAAGTATACTATTGACTTTATGCAGTTTTGAAATCCTTGT
129 CATAAGTATACTATTGACTGTATGCAGTTTTGAAATCCTTGT
*
1691309 TGTTAGTTCCTCTTGTCA-TG-ATTACATGGGTTTCTGCCGAACATCATACATCA-TTGTTGAGT
1 TGTTAGTTCCTCTTGTCAGTGCATTACATGGGTTTCTGCCGAACACCATACATCACTTGTTGAGT
* * *
1691371 TAGTT-TAGCTTTTAAACTTGCATGTG-TTTTTGCT-TTGTATCTGAATTTTTTGATC-CGCTGA
66 TAGTTCT-GCTTTTAAACTTGCATGCGTTTTTTGCTATTGTATCTGAATGTTTTGATCTC-CTAA
* *
1691432 CATAATTATACTGTTGACTGTATGCAGTTTTGAAATCCTTGT
129 CATAAGTATACTATTGACTGTATGCAGTTTTGAAATCCTTGT
1691474 T
1 T
1691475 CTGATTGAAC
Statistics
Matches: 151, Mismatches: 13, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
164 1 0.01
165 62 0.41
166 9 0.06
167 32 0.21
168 28 0.19
169 2 0.01
172 17 0.11
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (170 bp):
TGTTAGTTCCTCTTGTCAGTGCATTACATGGGTTTCTGCCGAACACCATACATCACTTGTTGAGT
TAGTTCTGCTTTTAAACTTGCATGCGTTTTTTGCTATTGTATCTGAATGTTTTGATCTCCTAACA
TAAGTATACTATTGACTGTATGCAGTTTTGAAATCCTTGT
Found at i:1694271 original size:26 final size:26
Alignment explanation
Indices: 1694241--1694292 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1694231 TTGTTTGCAA
1694241 GAACTTTTTCTAACATTCCTGTATCT
1 GAACTTTTTCTAACATTCCTGTATCT
1694267 GAACTTTTTCTAACATTCCTGTATCT
1 GAACTTTTTCTAACATTCCTGTATCT
1694293 TTTCACAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (26 bp):
GAACTTTTTCTAACATTCCTGTATCT
Found at i:1698928 original size:8 final size:8
Alignment explanation
Indices: 1698910--1698952 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
1698900 CAGTTTGTTT
1698910 TATAT-CA
1 TATATACA
1698917 TATATACA
1 TATATACA
1698925 TATATACA
1 TATATACA
1698933 TATATACA
1 TATATACA
*
1698941 TATATATA
1 TATATACA
1698949 TATA
1 TATA
1698953 GTAAAATGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 5 0.15
8 29 0.85
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (8 bp):
TATATACA
Found at i:1698929 original size:2 final size:2
Alignment explanation
Indices: 1698910--1698952 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1698900 CAGTTTGTTT
* * *
1698910 TA TA TCA TA TA TA CA TA TA TA CA TA TA TA CA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1698953 GTAAAATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Done.