Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 6 of 26
Found at i:1031751 original size:33 final size:33
Alignment explanation
Indices: 1031703--1031776 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 33
1031693 CATCACAGGA
1031703 TATATTTATATAATTTT-T-TAAATATTATTAATT
1 TATATTTATATAATTTTATATAAATATTA-T-ATT
1031736 TATA-TTATATAAATTTTATAATAAATATTATATT
1 TATATTTATAT-AATTTTAT-ATAAATATTATATT
1031770 TATATTT
1 TATATTT
1031777 TTTACGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
32 6 0.17
33 10 0.28
34 8 0.22
35 3 0.08
36 9 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TATATTTATATAATTTTATATAAATATTATATT
Found at i:1031761 original size:12 final size:12
Alignment explanation
Indices: 1031721--1031767 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1031711 TATAATTTTT
1031721 TAAATATTATTAA
1 TAAATATTA-TAA
**
1031734 TTTATATTAT-A
1 TAAATATTATAA
*
1031745 TAAATTTTATAA
1 TAAATATTATAA
1031757 TAAATATTATA
1 TAAATATTATA
1031768 TTTATATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
11 8 0.30
12 12 0.44
13 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAAATATTATAA
Found at i:1032399 original size:19 final size:19
Alignment explanation
Indices: 1032377--1032414 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1032367 TATAATTATA
1032377 TTTAA-ATAAAATATATAAT
1 TTTAATATAAAA-ATATAAT
*
1032396 TTTAATTTAAAAATATAAT
1 TTTAATATAAAAATATAAT
1032415 CCAAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAATATAAAAATATAAT
Found at i:1035716 original size:17 final size:17
Alignment explanation
Indices: 1035694--1035735 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1035684 TAAATATAAA
* *
1035694 TAAAAAATAT-TATTTT
1 TAAAAAATATAAAATTT
*
1035710 TTAAAAATATAAAATTT
1 TAAAAAATATAAAATTT
1035727 TAAAAAATA
1 TAAAAAATA
1035736 AAATATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAAAATATAAAATTT
Found at i:1035727 original size:16 final size:15
Alignment explanation
Indices: 1035708--1035739 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1035698 AAATATTATT
1035708 TTTTAAAAATATAAAA
1 TTTTAAAAA-ATAAAA
1035724 TTTTAAAAAATAAAA
1 TTTTAAAAAATAAAA
1035739 T
1 T
1035740 ATATTTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTTAAAAAATAAAA
Found at i:1036728 original size:2 final size:2
Alignment explanation
Indices: 1036721--1036751 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1036711 AAGAGATAAC
1036721 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
1036752 GTTTAATGTT
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:1039911 original size:33 final size:33
Alignment explanation
Indices: 1039869--1039936 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
1039859 TTGTGAGAAC
1039869 CTGGTCAACAACTTCCCAAAATAGCATCTCTCT
1 CTGGTCAACAACTTCCCAAAATAGCATCTCTCT
*
1039902 CTGGTCAACAACTTCTCAAAATAGCATCTCTCT
1 CTGGTCAACAACTTCCCAAAATAGCATCTCTCT
1039935 CT
1 CT
1039937 TTTCAGAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.29
Consensus pattern (33 bp):
CTGGTCAACAACTTCCCAAAATAGCATCTCTCT
Found at i:1040452 original size:2 final size:2
Alignment explanation
Indices: 1040447--1040475 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1040437 AAAAGTAAAC
1040447 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 A
1040476 ATTATTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1045859 original size:19 final size:19
Alignment explanation
Indices: 1045835--1045880 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1045825 ATTAATAATT
1045835 TATATTCTATAAATTT-TAA
1 TATATT-TATAAATTTATAA
* *
1045854 TATATTTATATATTTATAT
1 TATATTTATAAATTTATAA
1045873 TATATTTA
1 TATATTTA
1045881 AATTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTTATAAATTTATAA
Found at i:1045878 original size:11 final size:11
Alignment explanation
Indices: 1045862--1045912 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
1045852 AATATATTTA
1045862 TATATTTATAT
1 TATATTTATAT
*
1045873 TATATTTAAAT
1 TATATTTATAT
* *
1045884 TAT-TTTTTAA
1 TATATTTATAT
*
1045894 TATATTATATTT
1 TATATT-TATAT
1045906 TATATTT
1 TATATTT
1045913 TATCTTAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
10 7 0.23
11 16 0.52
12 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1045892 original size:40 final size:38
Alignment explanation
Indices: 1045848--1045926 Score: 115
Period size: 38 Copynumber: 2.0 Consensus size: 38
1045838 ATTCTATAAA
1045848 TTTTAATATATTTATATATTTATATTATAT-TTAAATTATT
1 TTTTAATATA-TTATAT-TTTATATTATATCTT-AATTATT
*
1045888 TTTTAATATATTATATTTTATATTTTATCTTAATTATT
1 TTTTAATATATTATATTTTATATTATATCTTAATTATT
1045926 T
1 T
1045927 AAAAAATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
38 19 0.51
39 8 0.22
40 10 0.27
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (38 bp):
TTTTAATATATTATATTTTATATTATATCTTAATTATT
Found at i:1046462 original size:27 final size:28
Alignment explanation
Indices: 1046372--1046482 Score: 83
Period size: 27 Copynumber: 4.1 Consensus size: 28
1046362 TATTTAATAA
1046372 ATTATA-TATTTATATATATTTA-A-TAT
1 ATTATATTATTTATATAT-TTTATATTAT
* * * * *
1046398 ATTA-ATAATTTATATAATATAAATTTT
1 ATTATATTATTTATATATTTTATATTAT
*
1046425 AATATATTTATTTATAT-TTTTATATTAT
1 ATTATA-TTATTTATATATTTTATATTAT
*
1046453 ATTATATTA-TAAT-TATTTTTATATTAT
1 ATTATATTATTTATATA-TTTTATATTAT
1046480 ATT
1 ATT
1046483 TTATGACCAA
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
25 5 0.08
26 17 0.26
27 22 0.33
28 13 0.20
29 9 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTATATTATTTATATATTTTATATTAT
Found at i:1047297 original size:17 final size:17
Alignment explanation
Indices: 1047275--1047323 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1047265 TTGAATTTTT
1047275 TTTATAAATTAAATTAA
1 TTTATAAATTAAATTAA
* **
1047292 TTTATAATTTAAAAAAA
1 TTTATAAATTAAATTAA
*
1047309 TTTA-AAATTTAATTA
1 TTTATAAATTAAATTA
1047324 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTATAAATTAAATTAA
Found at i:1047442 original size:20 final size:20
Alignment explanation
Indices: 1047417--1047475 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1047407 ATTAAATTTA
1047417 AATAAAAAATTATTTTAATT
1 AATAAAAAATTATTTTAATT
* * *
1047437 AATAAATAATAATTTAAATT
1 AATAAAAAATTATTTTAATT
1047457 ACATAAATAAATTATTTTA
1 A-ATAAA-AAATTATTTTA
1047476 CTTTTAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 18 0.58
21 5 0.16
22 8 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAAAAAATTATTTTAATT
Found at i:1047464 original size:21 final size:20
Alignment explanation
Indices: 1047404--1047466 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
1047394 ATATATTTTT
*
1047404 ATAA-TTAAATTTAAATAAAAA
1 ATAATTTAAA-TT-AATAAATA
* *
1047425 ATTATTTTAATTAATAAATA
1 ATAATTTAAATTAATAAATA
1047445 ATAATTTAAATTACATAAATA
1 ATAATTTAAATTA-ATAAATA
1047466 A
1 A
1047467 ATTATTTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 18 0.51
21 13 0.37
22 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATTTAAATTAATAAATA
Found at i:1047679 original size:2 final size:2
Alignment explanation
Indices: 1047672--1047698 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1047662 CATTCCACAT
1047672 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 T
1047699 TTTTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1048010 original size:25 final size:26
Alignment explanation
Indices: 1047980--1048037 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1047970 TTGATTTAAT
*
1047980 AAAAATAAATAAA-CT-ATTTAAATTA
1 AAAAATAAA-AAATCTAATTTAAACTA
*
1048005 AAAAATAAAAAATTTAATTTAAACTA
1 AAAAATAAAAAATCTAATTTAAACTA
1048031 AAAAATA
1 AAAAATA
1048038 TTAAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 3 0.10
25 10 0.34
26 16 0.55
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAATAAAAAATCTAATTTAAACTA
Found at i:1048012 original size:21 final size:21
Alignment explanation
Indices: 1047986--1048027 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1047976 TAATAAAAAT
**
1047986 AAATAAACTATTTAAATTAAA
1 AAATAAAAAATTTAAATTAAA
*
1048007 AAATAAAAAATTTAATTTAAA
1 AAATAAAAAATTTAAATTAAA
1048028 CTAAAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAAAAATTTAAATTAAA
Found at i:1048106 original size:17 final size:17
Alignment explanation
Indices: 1048081--1048124 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1048071 CTAATTAGTT
*
1048081 TAAAGTTAAATTAAATA
1 TAAATTTAAATTAAATA
* *
1048098 TAAATTTAAAATAATTA
1 TAAATTTAAATTAAATA
1048115 -AAATTTAAAT
1 TAAATTTAAAT
1048125 CTAACAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTAAATA
Found at i:1048535 original size:18 final size:18
Alignment explanation
Indices: 1048512--1048563 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
1048502 TAAATTTTTT
1048512 TTAATTTTAAATATAATA
1 TTAATTTTAAATATAATA
*
1048530 TTAATTAT-AATATAA-A
1 TTAATTTTAAATATAATA
1048546 TT-A--TTAAA-ATAATA
1 TTAATTTTAAATATAATA
1048560 TTAA
1 TTAA
1048564 AATAAATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 5 0.17
14 5 0.17
15 2 0.07
16 3 0.10
17 7 0.24
18 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATTTTAAATATAATA
Found at i:1048556 original size:15 final size:17
Alignment explanation
Indices: 1048520--1048556 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1048510 TTTTAATTTT
1048520 AAATATAATATTAATTA
1 AAATATAATATTAATTA
*
1048537 TAATATAA-ATT-ATTA
1 AAATATAATATTAATTA
1048552 AAATA
1 AAATA
1048557 ATATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 8 0.44
16 3 0.17
17 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATAATATTAATTA
Found at i:1049831 original size:19 final size:18
Alignment explanation
Indices: 1049783--1049833 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
1049773 TGTGTTCTTA
*
1049783 AAATTATTTAAAAATATT
1 AAATTATTTATAAATATT
**
1049801 AAATT-TAAATAAATATT
1 AAATTATTTATAAATATT
1049818 AAATGTATTTATAAAT
1 AAAT-TATTTATAAAT
1049834 TAAATTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 13 0.50
18 6 0.23
19 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATTATTTATAAATATT
Found at i:1061612 original size:3 final size:3
Alignment explanation
Indices: 1061604--1061629 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1061594 GTAGGATTGA
1061604 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1061630 GGATAATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1067700 original size:2 final size:2
Alignment explanation
Indices: 1067695--1067726 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1067685 TCAAAATTAA
1067695 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
1067727 TGTTCTGTTC
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:1068719 original size:19 final size:19
Alignment explanation
Indices: 1068695--1068737 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1068685 TGTTTTGTTG
1068695 GTTAATGAATCACTGAAGT
1 GTTAATGAATCACTGAAGT
1068714 GTTAATGAATCACTGAAGT
1 GTTAATGAATCACTGAAGT
1068733 GTTAA
1 GTTAA
1068738 AAGATCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (19 bp):
GTTAATGAATCACTGAAGT
Found at i:1073393 original size:199 final size:197
Alignment explanation
Indices: 1073050--1073646 Score: 1049
Period size: 199 Copynumber: 3.0 Consensus size: 197
1073040 GCTTCTCCAA
1073050 GAGCAGATCTAAGAAGTTAAGAATTCCTTCAGTGATTATTAGCACACATGGCAGGCTAATAAAAA
1 GAGCAGATCTAAGAAGTTAAGAATTCCTTCAGTGATTATTAGCACACATGGCAGGCTAAT---AA
* * *
1073115 ACAACAGGTCGATACACTCATTGGCTACTGAT-AAAGTAGTTTGAGGGAATTTCTGTCATAAAAA
63 ACAACAGGTCAATACACTCATTGGCTACTGATGAAA-TAGTTTGAGGGAATTTCTGTCATAAGAC
1073179 GATGCATTACCCATTGTGTATGATCACACACTGATTTCCAGTTATGGATTGACTCGATAATCTGG
127 GATGCATTACCCATTGTGTATGATCACACACTGATTTCCAGTTAT-GATTGA-TCGATAATCTGG
1073244 TCTAATAG
190 TCTAATAG
1073252 GAGCAGATCTAAGAAGTTAAGAATTCCTTCAGTGATTATTAGCACACATGGCAGGCTAATAAACA
1 GAGCAGATCTAAGAAGTTAAGAATTCCTTCAGTGATTATTAGCACACATGGCAGGCTAATAAACA
1073317 ACAGGTCAATACACTCATTGGCTACTGATGAAATAGTTTGAGGGAATTTCTGTCATAAGACGATG
66 ACAGGTCAATACACTCATTGGCTACTGATGAAATAGTTTGAGGGAATTTCTGTCATAAGACGATG
1073382 CATTACCCATTGTGTATGATCACACACTGATTTCCAGTTATAGATTGATGCGATAATCTGGTCTA
131 CATTACCCATTGTGTATGATCACACACTGATTTCCAGTTAT-GATTGAT-CGATAATCTGGTCTA
1073447 ATAG
194 ATAG
1073451 GAGCAGATCTAAGAAGTTAAGAATTCCTTCAGTGATTATTAGCACACATGGCAGGCTAATAAACA
1 GAGCAGATCTAAGAAGTTAAGAATTCCTTCAGTGATTATTAGCACACATGGCAGGCTAATAAACA
1073516 ACAGGTCAATACACTCATTGGCTACTGATGAAATAGTTTGAGGGAATTTCTGTCATAAGACGATG
66 ACAGGTCAATACACTCATTGGCTACTGATGAAATAGTTTGAGGGAATTTCTGTCATAAGACGATG
*
1073581 CATTACCCATTGTGTATGATCACACACTGATTTCCA-TT-T-ATAGATTCGATAATCTGGTCTAA
131 CATTACCCATTGTGTATGATCACACACTGATTTCCAGTTATGATTGA-TCGATAATCTGGTCTAA
1073643 TAG
195 TAG
1073646 G
1 G
1073647 CTCATAGCCA
Statistics
Matches: 387, Mismatches: 5, Indels: 13
0.96 0.01 0.03
Matches are distributed among these distances:
195 24 0.06
196 1 0.00
197 1 0.00
198 3 0.01
199 295 0.76
200 3 0.01
202 60 0.16
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (197 bp):
GAGCAGATCTAAGAAGTTAAGAATTCCTTCAGTGATTATTAGCACACATGGCAGGCTAATAAACA
ACAGGTCAATACACTCATTGGCTACTGATGAAATAGTTTGAGGGAATTTCTGTCATAAGACGATG
CATTACCCATTGTGTATGATCACACACTGATTTCCAGTTATGATTGATCGATAATCTGGTCTAAT
AG
Found at i:1077073 original size:2 final size:2
Alignment explanation
Indices: 1077066--1077103 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1077056 TAAAGTTAGA
* *
1077066 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1077104 GGACCGGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1078407 original size:86 final size:86
Alignment explanation
Indices: 1078262--1078433 Score: 308
Period size: 86 Copynumber: 2.0 Consensus size: 86
1078252 AGTGGTCCAT
1078262 GAGATGAAAAACAAGACATGCCACTCAACAAAATAAACAAGATAATAACACTCTAATTTCAATTG
1 GAGATGAAAAACAAGACATGCCACTCAACAAAATAAACAAGATAATAACACTCTAATTTCAATTG
*
1078327 ATTAAGCCTTCCATAAGCTTA
66 ATTAAACCTTCCATAAGCTTA
* * *
1078348 GAGATGAAAACCAAGACATGCCACTCGACAAAATAAACAAGATAATGACACTCTAATTTCAATTG
1 GAGATGAAAAACAAGACATGCCACTCAACAAAATAAACAAGATAATAACACTCTAATTTCAATTG
1078413 ATTAAACCTTCCATAAGCTTA
66 ATTAAACCTTCCATAAGCTTA
1078434 TGTCAACCAC
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.23
Consensus pattern (86 bp):
GAGATGAAAAACAAGACATGCCACTCAACAAAATAAACAAGATAATAACACTCTAATTTCAATTG
ATTAAACCTTCCATAAGCTTA
Found at i:1079774 original size:20 final size:20
Alignment explanation
Indices: 1079746--1079783 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1079736 TAATAAGTGC
*
1079746 TAGATAGATAGATATGATGT
1 TAGACAGATAGATATGATGT
*
1079766 TAGACAGATTGATATGAT
1 TAGACAGATAGATATGAT
1079784 ACTGATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (20 bp):
TAGACAGATAGATATGATGT
Found at i:1079957 original size:2 final size:2
Alignment explanation
Indices: 1079950--1079979 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1079940 ATAATTTATT
1079950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1079980 GATACAAAAA
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):
TA
Found at i:1080658 original size:90 final size:90
Alignment explanation
Indices: 1080505--1080684 Score: 360
Period size: 90 Copynumber: 2.0 Consensus size: 90
1080495 AATTTGTTAT
1080505 GAACATAAATGGTCTTCAGGTTGGCACTAAACTTCTGGGAAATCTTAAGATCTTGAAGACCACTT
1 GAACATAAATGGTCTTCAGGTTGGCACTAAACTTCTGGGAAATCTTAAGATCTTGAAGACCACTT
1080570 TTAATCAATTTCTTTCAGGGAAAAC
66 TTAATCAATTTCTTTCAGGGAAAAC
1080595 GAACATAAATGGTCTTCAGGTTGGCACTAAACTTCTGGGAAATCTTAAGATCTTGAAGACCACTT
1 GAACATAAATGGTCTTCAGGTTGGCACTAAACTTCTGGGAAATCTTAAGATCTTGAAGACCACTT
1080660 TTAATCAATTTCTTTCAGGGAAAAC
66 TTAATCAATTTCTTTCAGGGAAAAC
1080685 AGCATGAGGC
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (90 bp):
GAACATAAATGGTCTTCAGGTTGGCACTAAACTTCTGGGAAATCTTAAGATCTTGAAGACCACTT
TTAATCAATTTCTTTCAGGGAAAAC
Found at i:1086038 original size:15 final size:15
Alignment explanation
Indices: 1086014--1086049 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1086004 GCCAAAAGCC
*
1086014 GAGAAAAAGCCAGCA
1 GAGAAGAAGCCAGCA
*
1086029 GAGAAGAAGCCAGCT
1 GAGAAGAAGCCAGCA
1086044 GAGAAG
1 GAGAAG
1086050 CCAACGGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.33, T:0.03
Consensus pattern (15 bp):
GAGAAGAAGCCAGCA
Found at i:1087576 original size:29 final size:29
Alignment explanation
Indices: 1087514--1087603 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 29
1087504 TTATTTTAAC
* * * *
1087514 ATATATATT-TTTTAAAATTAG-ATTTTA
1 ATATATTTTATTTTAAAATTTGAATATAA
1087541 ATGATATTTTATTTTAAAATTTGAATATAA
1 AT-ATATTTTATTTTAAAATTTGAATATAA
* * *
1087571 ATATATTATAAATTTAAAATTTAAAATATAA
1 ATATATT-TTATTTTAAAATTT-GAATATAA
1087602 AT
1 AT
1087604 TAACATAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.04
28 6 0.12
29 16 0.31
30 18 0.35
31 9 0.18
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
ATATATTTTATTTTAAAATTTGAATATAA
Found at i:1087612 original size:30 final size:30
Alignment explanation
Indices: 1087553--1087630 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
1087543 GATATTTTAT
* **
1087553 TTTAAAATTTGAATATAAATATATTATAAA
1 TTTAAAATTTAAATATAAATATAACATAAA
1087583 TTTAAAATTTAAAATATAAAT-TAACATAAA
1 TTTAAAATTT-AAATATAAATATAACATAAA
** *
1087613 AATAATAATTTATATATA
1 TTTAA-AATTTAAATATA
1087631 TTTATAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 26 0.65
31 14 0.35
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (30 bp):
TTTAAAATTTAAATATAAATATAACATAAA
Found at i:1088170 original size:6 final size:6
Alignment explanation
Indices: 1088159--1088194 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1088149 ATTTATGTTA
* *
1088159 AAATTT AAATTT AATTTT GAATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
1088195 TTTAATACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:1088181 original size:18 final size:19
Alignment explanation
Indices: 1088160--1088195 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1088150 TTTATGTTAA
1088160 AATTTAAATTT-AATTTTG
1 AATTTAAATTTAAATTTTG
1088178 AATTTAAATTTAAATTTT
1 AATTTAAATTTAAATTTT
1088196 TTAATACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
AATTTAAATTTAAATTTTG
Found at i:1088886 original size:2 final size:2
Alignment explanation
Indices: 1088879--1088907 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1088869 TTTATAACAG
1088879 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 T
1088908 TTTAAAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1089110 original size:80 final size:80
Alignment explanation
Indices: 1089019--1089251 Score: 394
Period size: 80 Copynumber: 2.9 Consensus size: 80
1089009 TATTTTGATA
* *
1089019 GATTCACAAGATTTAATTAAATATATAATTAAAAAAATGATGATATTTGCTTTCAGATTAAGAAT
1 GATTCAAAAGATTTAATTAAATATATAATTAAAAAAATGATGATATTTGCTTTCAGATTAAGAAA
1089084 CCATTTTTCTTAATT
66 CCATTTTTCTTAATT
** *
1089099 GATTCAAAAGATTTAATTGGATATATAATTAAAAAAATGATGATATTTGCTTTCAGATTAAGAAG
1 GATTCAAAAGATTTAATTAAATATATAATTAAAAAAATGATGATATTTGCTTTCAGATTAAGAAA
1089164 CCATTTTTCTTAATT
66 CCATTTTTCTTAATT
* *
1089179 GATTCAAAAGATTTAATTAAATATATATTTAAAAAAAATGATGATATTTGCTTTCGGATTAAGAA
1 GATTCAAAAGATTTAATTAAATATATAATT-AAAAAAATGATGATATTTGCTTTCAGATTAAGAA
1089244 ACCATTTT
65 ACCATTTT
1089252 ATATTTTAAA
Statistics
Matches: 143, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 103 0.72
81 40 0.28
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (80 bp):
GATTCAAAAGATTTAATTAAATATATAATTAAAAAAATGATGATATTTGCTTTCAGATTAAGAAA
CCATTTTTCTTAATT
Found at i:1090517 original size:2 final size:2
Alignment explanation
Indices: 1090510--1090543 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1090500 TAATATTTTC
*
1090510 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1090544 CAACTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1093379 original size:21 final size:25
Alignment explanation
Indices: 1093332--1093382 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 25
1093322 GCATATTATA
*
1093332 TATATATATATTATACAATCAATTT
1 TATATATATAATATACAATCAATTT
1093357 TATATA-ATAATATA-AAT-AA-TT
1 TATATATATAATATACAATCAATTT
1093378 TATAT
1 TATAT
1093383 TTTAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
22 2 0.08
23 3 0.12
24 7 0.28
25 6 0.24
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATATATAATATACAATCAATTT
Found at i:1093480 original size:17 final size:18
Alignment explanation
Indices: 1093460--1093504 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1093450 TAATTAATTT
1093460 AATTTATTAAAATTT-TA
1 AATTTATTAAAATTTATA
* *
1093477 AATTTATTTAATTTTATA
1 AATTTATTAAAATTTATA
1093495 AATTT-TTAAA
1 AATTTATTAAA
1093505 CTTAACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTATTAAAATTTATA
Found at i:1093487 original size:26 final size:26
Alignment explanation
Indices: 1093451--1093509 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
1093441 ATTTTTTATT
1093451 AATTAATTTAA-TTTATTAAAATTTTA
1 AATTAATTTAATTTTA-TAAAATTTTA
* *
1093477 AATTTATTTAATTTTATAAATTTTTA
1 AATTAATTTAATTTTATAAAATTTTA
1093503 AACTTAA
1 AA-TTAA
1093510 CTAATTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
AATTAATTTAATTTTATAAAATTTTA
Found at i:1093514 original size:26 final size:27
Alignment explanation
Indices: 1093462--1093515 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1093452 ATTAATTTAA
* **
1093462 TTTATTAAAATTTTAAATTTATTTAAT
1 TTTATTAAAATTTTAAACTTAACTAAT
*
1093489 TTTA-TAAATTTTTAAACTTAACTAAT
1 TTTATTAAAATTTTAAACTTAACTAAT
1093515 T
1 T
1093516 GAATTTGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATTAAAATTTTAAACTTAACTAAT
Found at i:1094442 original size:18 final size:18
Alignment explanation
Indices: 1094419--1094502 Score: 63
Period size: 18 Copynumber: 4.7 Consensus size: 18
1094409 CCAAATAAAT
1094419 ATATAATATAAATTATTA
1 ATATAATATAAATTATTA
1094437 ATATAATA-AAATTTATTA
1 ATATAATATAAA-TTATTA
1094455 A-A-AATA-AATATT-TTA
1 ATATAATATAA-ATTATTA
* *
1094470 A-ATAATATATTAAAATATAA
1 ATAT-A-ATA-TAAATTATTA
1094490 ATATAATATAAAT
1 ATATAATATAAAT
1094503 ACCTATAGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
15 5 0.09
16 8 0.15
17 6 0.11
18 22 0.41
19 5 0.09
20 6 0.11
21 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAATATAAATTATTA
Found at i:1094492 original size:16 final size:16
Alignment explanation
Indices: 1094423--1094494 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 16
1094413 ATAAATATAT
1094423 AATATAAAT-TATTAA
1 AATATAAATATATTAA
* *
1094438 TATAATAAAATTTATTAA
1 AAT-AT-AAATATATTAA
*
1094456 AA-ATAAATAT-TT-T
1 AATATAAATATATTAA
1094469 AA-AT-AATATATTAA
1 AATATAAATATATTAA
1094483 AATATAAATATA
1 AATATAAATATA
1094495 ATATAAATAC
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
12 5 0.11
13 6 0.13
14 4 0.09
15 9 0.20
16 10 0.22
17 4 0.09
18 7 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATAAATATATTAA
Found at i:1099282 original size:93 final size:93
Alignment explanation
Indices: 1099115--1099296 Score: 256
Period size: 93 Copynumber: 2.0 Consensus size: 93
1099105 ATAATATTTA
* * * * *
1099115 TAAATTATCTTGATAGATTCACAAGATTGAATTAGATATATAATTAAAAAAATGATGATATTTGG
1 TAAATTATCTTGATAGATTAACAAGATTGAATTAAATATAAAATTAAAAAAATGATAATATTTGC
* **
1099180 TTTCGGATAAAGATGCCATTTGATGTTT
66 TTTCAGATAAAGAAACCATTTGATGTTT
* * * *
1099208 TAAATTTTCTTGATTGATTAACAATATTTAATTAAATATAAAATTAAAAAAATGATAATATTTGC
1 TAAATTATCTTGATAGATTAACAAGATTGAATTAAATATAAAATTAAAAAAATGATAATATTTGC
1099273 TTTCAGATAAAGAAACCATTTGAT
66 TTTCAGATAAAGAAACCATTTGAT
1099297 AGACAGATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (93 bp):
TAAATTATCTTGATAGATTAACAAGATTGAATTAAATATAAAATTAAAAAAATGATAATATTTGC
TTTCAGATAAAGAAACCATTTGATGTTT
Found at i:1099471 original size:21 final size:21
Alignment explanation
Indices: 1099447--1099493 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1099437 TAAATGTGTG
1099447 AATAAATAAAAAAATAA-TTTA
1 AATAAAT-AAAAAATAATTTTA
* * *
1099468 AATATATACAAATTAATTTTA
1 AATAAATAAAAAATAATTTTA
1099489 AATAA
1 AATAA
1099494 TAATTATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAAATAAAAAATAATTTTA
Found at i:1099787 original size:2 final size:2
Alignment explanation
Indices: 1099780--1099812 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1099770 TTAATAGTAC
1099780 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 T
1099813 GAGATTAGAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1100785 original size:2 final size:2
Alignment explanation
Indices: 1100778--1100808 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1100768 CTTTTAAAAG
1100778 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 T
1100809 TAATAGCTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1101640 original size:44 final size:44
Alignment explanation
Indices: 1101591--1101690 Score: 139
Period size: 44 Copynumber: 2.2 Consensus size: 44
1101581 AAATTTTTTT
*
1101591 ATTTTTTATTTGTTTAGTTTTGATTTAATTATTAATAATGTT-AA
1 ATTTTTTATTT-TTTAGTTTTGATTTAATTATTAATAATATTAAA
* *
1101635 ATTTTTATATTTTTTATTTTTTATTTAATTATTAATAATATTAAA
1 ATTTTT-TATTTTTTAGTTTTGATTTAATTATTAATAATATTAAA
1101680 AGTTTTTTATT
1 A-TTTTTTATT
1101691 AATTTATTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 33 0.66
45 12 0.24
46 5 0.10
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (44 bp):
ATTTTTTATTTTTTAGTTTTGATTTAATTATTAATAATATTAAA
Found at i:1106718 original size:21 final size:25
Alignment explanation
Indices: 1106671--1106721 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 25
1106661 TTGCATATTA
*
1106671 TATATATATATTATACAATCAATTT
1 TATATATATAATATACAATCAATTT
1106696 TATATA-ATAATATA-AAT-AA-TT
1 TATATATATAATATACAATCAATTT
1106717 TATAT
1 TATAT
1106722 TTTAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
22 2 0.08
23 3 0.12
24 7 0.28
25 6 0.24
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATATATAATATACAATCAATTT
Found at i:1106820 original size:16 final size:16
Alignment explanation
Indices: 1106799--1106830 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1106789 TAATTAATTT
1106799 AATTTATTAAATTTTA
1 AATTTATTAAATTTTA
*
1106815 AATTTATTTAATTTTA
1 AATTTATTAAATTTTA
1106831 CAAAATTTTA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTATTAAATTTTA
Found at i:1106824 original size:25 final size:26
Alignment explanation
Indices: 1106790--1106856 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
1106780 ATTTTTTATT
**
1106790 AATTAATTTAA-TTTATTAAATTTTA
1 AATTAATTTAATTTTACAAAATTTTA
*
1106815 AATTTATTTAATTTTACAAAATTTTA
1 AATTAATTTAATTTTACAAAATTTTA
*
1106841 AACTTAA-CTAATTTTA
1 AA-TTAATTTAATTTTA
1106857 AACGTAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 10 0.29
26 22 0.63
27 3 0.09
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
AATTAATTTAATTTTACAAAATTTTA
Found at i:1107194 original size:2 final size:2
Alignment explanation
Indices: 1107189--1107228 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1107179 TTAAACTCTT
* *
1107189 TA TA TA TG TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1107229 ATAGTTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1107506 original size:21 final size:22
Alignment explanation
Indices: 1107477--1107531 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
1107467 TAAAATTTAT
* *
1107477 TAAAAATAAATAT-TTTAAATA
1 TAAATATAAATATATTAAAATA
*
1107498 TAATTAT-AATATATTAAAATA
1 TAAATATAAATATATTAAAATA
1107519 TAAATAT-AATATA
1 TAAATATAAATATA
1107532 AATACCTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATAAATATATTAAAATA
Found at i:1107510 original size:11 final size:11
Alignment explanation
Indices: 1107494--1107532 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1107484 AAATATTTTA
1107494 AATATAATTAT
1 AATATAATTAT
*
1107505 AATAT-ATTAA
1 AATATAATTAT
*
1107515 AATATAAATAT
1 AATATAATTAT
1107526 AATATAA
1 AATATAA
1107533 ATACCTATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATAATTAT
Found at i:1114447 original size:3 final size:3
Alignment explanation
Indices: 1114434--1114467 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1114424 TAGATACTTG
*
1114434 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1114468 AACACAGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1115023 original size:23 final size:23
Alignment explanation
Indices: 1114997--1115040 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1114987 TATAAATAAT
1114997 TTAAATAAAAATATT-TTTTATTA
1 TTAAATAAAAAT-TTATTTTATTA
*
1115020 TTAAATAATAATTTATTTTAT
1 TTAAATAAAAATTTATTTTAT
1115041 AGAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAATAAAAATTTATTTTATTA
Found at i:1122165 original size:16 final size:16
Alignment explanation
Indices: 1122141--1122206 Score: 89
Period size: 16 Copynumber: 4.2 Consensus size: 16
1122131 TAAAAGAATT
*
1122141 AAAATATTATGATATA
1 AAAATATTATTATATA
* **
1122157 AAAAAATTAAAATAT-
1 AAAATATTATTATATA
1122172 AAAATATTATTATATA
1 AAAATATTATTATATA
1122188 AAAATATTATTATATA
1 AAAATATTATTATATA
1122204 AAA
1 AAA
1122207 TATAATATGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.28
16 31 0.72
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AAAATATTATTATATA
Found at i:1122178 original size:31 final size:31
Alignment explanation
Indices: 1122140--1122235 Score: 111
Period size: 31 Copynumber: 3.0 Consensus size: 31
1122130 ATAAAAGAAT
1122140 TAAAATATTATGATATAAAAAAATTAAAATA
1 TAAAATATTATGATATAAAAAAATTAAAATA
* * **
1122171 TAAAATATTATTATATAAAAATATTATTATA
1 TAAAATATTATGATATAAAAAAATTAAAATA
**
1122202 TAAAATATAATATGACGTAAAAATAATTAAAATA
1 TAAAATAT--TATGATATAAAAA-AATTAAAATA
1122236 ATATTTAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 35 0.67
33 10 0.19
34 7 0.13
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (31 bp):
TAAAATATTATGATATAAAAAAATTAAAATA
Found at i:1122246 original size:38 final size:35
Alignment explanation
Indices: 1122204--1122277 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 35
1122194 TTATTATATA
* *
1122204 AAATATAATATGACGTAAAAATAATTAAAATAATATTT
1 AAATATAATATAACATAAAAATAA-T-AAATAA-ATTT
*
1122242 AAATATAATATAATATAAAAATAATAAATAAATTT
1 AAATATAATATAACATAAAAATAATAAATAAATTT
1122277 A
1 A
1122278 TAAATTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 5 0.15
36 6 0.18
37 1 0.03
38 21 0.64
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (35 bp):
AAATATAATATAACATAAAAATAATAAATAAATTT
Found at i:1122260 original size:16 final size:16
Alignment explanation
Indices: 1122167--1122271 Score: 52
Period size: 16 Copynumber: 6.2 Consensus size: 16
1122157 AAAAAATTAA
*
1122167 AATATAAA-ATATTAT
1 AATATAAATATAATAT
* * *
1122182 TATATAAAAATATTAT
1 AATATAAATATAATAT
*
1122198 TATATAAAATATAATAT
1 AATAT-AAATATAATAT
* * *
1122215 GACGTAAAAATAATTAAAAT
1 -A-ATATAAAT-A-TAATAT
1122235 AATATTTAAATATAATAT
1 AATA--TAAATATAATAT
*
1122253 AATATAAAAATAATA-
1 AATATAAATATAATAT
1122268 AATA
1 AATA
1122272 AATTTATAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
15 11 0.15
16 22 0.31
17 9 0.13
18 15 0.21
19 5 0.07
20 9 0.13
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (16 bp):
AATATAAATATAATAT
Found at i:1122272 original size:18 final size:18
Alignment explanation
Indices: 1122219--1122272 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1122209 TAATATGACG
1122219 TAAAAATAATTAAAATAATA
1 TAAAAATAA-T-AAATAATA
**
1122239 TTTAAAT-ATAATATAATA
1 TAAAAATAATAA-ATAATA
1122257 TAAAAATAATAAATAA
1 TAAAAATAATAAATAA
1122273 ATTTATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 2 0.07
18 16 0.57
19 5 0.18
20 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATAATAAATAATA
Found at i:1122513 original size:21 final size:21
Alignment explanation
Indices: 1122454--1122510 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 21
1122444 AATATTTTAA
1122454 AATATAAATAATTTGATATATTTTC
1 AATATAAATAA-TT-A-AT-TTTTC
*
1122479 AATATAAATAATTAATTTTTT
1 AATATAAATAATTAATTTTTC
1122500 AATAATAAATA
1 AAT-ATAAATA
1122511 TTATATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.23
22 9 0.30
23 1 0.03
24 2 0.07
25 11 0.37
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AATATAAATAATTAATTTTTC
Found at i:1122527 original size:24 final size:24
Alignment explanation
Indices: 1122500--1122555 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
1122490 TTAATTTTTT
1122500 AATAATAAATATTATATA-AATATA
1 AATAATAAATATTATATATAAT-TA
1122524 AAT-ATAAA-ATTATATATTAATTA
1 AATAATAAATATTATATA-TAATTA
1122547 AA-AATAAAT
1 AATAATAAAT
1122556 CAAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATAATAAATATTATATATAATTA
Found at i:1122736 original size:23 final size:23
Alignment explanation
Indices: 1122705--1122802 Score: 83
Period size: 23 Copynumber: 4.0 Consensus size: 23
1122695 TAAAATAATT
*
1122705 TAATTTATAAATATTTTAAAATA
1 TAATATATAAATATTTTAAAATA
*
1122728 TAATATATAAATATTTT-AAATT
1 TAATATATAAATATTTTAAAATA
*
1122750 TATATAATATAAAT-TATTAATATATTA
1 TA-AT-ATATAAATATTTTAA-A-A-TA
1122777 TAATTTATATAAATATTTTCAAAATA
1 TAA--TATATAAATATTTT-AAAATA
1122803 ATTAAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
22 6 0.10
23 21 0.35
24 9 0.15
25 1 0.02
26 4 0.07
27 12 0.20
28 5 0.08
29 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATATATAAATATTTTAAAATA
Found at i:1122759 original size:31 final size:32
Alignment explanation
Indices: 1122724--1122788 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
1122714 AATATTTTAA
*
1122724 AATAT-AATATATAAATATTTTA-AATTTATAT
1 AATATAAAT-TATAAATATATTATAATTTATAT
*
1122755 AATATAAATTATTAATATATTATAATTTATAT
1 AATATAAATTATAAATATATTATAATTTATAT
1122787 AA
1 AA
1122789 ATATTTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 16 0.53
32 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
AATATAAATTATAAATATATTATAATTTATAT
Found at i:1122792 original size:18 final size:18
Alignment explanation
Indices: 1122731--1122793 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
1122721 TAAAATATAA
*
1122731 TATATAAATATTTTAAATT
1 TATATAAATATTAT-AATT
1122750 TATAT-AATA-TA-AA-T
1 TATATAAATATTATAATT
1122764 TAT-TAATATATTATAATT
1 TATATAA-ATATTATAATT
1122782 TATATAAATATT
1 TATATAAATATT
1122794 TTCAAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 5 0.14
16 2 0.05
17 3 0.08
18 13 0.35
19 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATAAATATTATAATT
Found at i:1123130 original size:2 final size:2
Alignment explanation
Indices: 1123123--1123157 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1123113 TGGTCTTGTT
1123123 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1123158 TTTTCTGTAA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1137677 original size:149 final size:149
Alignment explanation
Indices: 1137402--1137699 Score: 508
Period size: 149 Copynumber: 2.0 Consensus size: 149
1137392 GAAGGGAGTG
* * * * ** *
1137402 GCCAAGTTTTGGTTGCTACTGTGGGTCTCTTTACATAGGCATTTGCTGGAAGATGTTAAGGGCCC
1 GCCAAGTTTTGGCTGCCACTGTGGGTCTCTTTACACAGGCATTTGCTCGAAGAAATTAAAGGCCC
1137467 AAACCATCTCATGGCTTGCCTATCCAATTTTGGGTGTGAAACTCTGGGTCTTAAATCTTTAA-GT
66 AAACCATCTCATGGCTTGCCTATCCAATTTTGGGTGTGAAACTCTGGGTCTTAAATCTTTAAGGT
1137531 TTAGGAATTTGATCGGATCA
131 TTA-GAATTTGATCGGATCA
*
1137551 GCCAGGTTTTGGCTGCCACTGTGGGTCTCTTTACACAGGCATTTGCTCGAAGAAATTAAAGGCCC
1 GCCAAGTTTTGGCTGCCACTGTGGGTCTCTTTACACAGGCATTTGCTCGAAGAAATTAAAGGCCC
1137616 AAACCATCTCATGGCTTGCCTATCCAATTTTGGGTGTGAAACTCTGGGTCTTAAATCTTTAAGGT
66 AAACCATCTCATGGCTTGCCTATCCAATTTTGGGTGTGAAACTCTGGGTCTTAAATCTTTAAGGT
1137681 TTAGAATTTGATCGGATCA
131 TTAGAATTTGATCGGATCA
1137700 ATCGTTTACC
Statistics
Matches: 140, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
149 135 0.96
150 5 0.04
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (149 bp):
GCCAAGTTTTGGCTGCCACTGTGGGTCTCTTTACACAGGCATTTGCTCGAAGAAATTAAAGGCCC
AAACCATCTCATGGCTTGCCTATCCAATTTTGGGTGTGAAACTCTGGGTCTTAAATCTTTAAGGT
TTAGAATTTGATCGGATCA
Found at i:1139124 original size:2 final size:2
Alignment explanation
Indices: 1139117--1139150 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1139107 CAAAACCCAG
1139117 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
1139151 TCAGGAGATG
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:1141687 original size:13 final size:13
Alignment explanation
Indices: 1141665--1141703 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1141655 TTTTATATTT
1141665 ATATTTAATAAAA
1 ATATTTAATAAAA
* *
1141678 ATATTAAATATAA
1 ATATTTAATAAAA
1141691 ATATTTAATAAAA
1 ATATTTAATAAAA
1141704 TAAAGGTTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATTTAATAAAA
Found at i:1142470 original size:25 final size:24
Alignment explanation
Indices: 1142442--1142491 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1142432 ATGCATAAAA
*
1142442 TATTTATTGATATTAAAAATTGTAT
1 TATTTATTGAAATTAAAAATT-TAT
* *
1142467 TATTTATTTAAATTTAAAATTTAT
1 TATTTATTGAAATTAAAAATTTAT
1142491 T
1 T
1142492 TTAAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
TATTTATTGAAATTAAAAATTTAT
Found at i:1142627 original size:15 final size:15
Alignment explanation
Indices: 1142607--1142648 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1142597 ATTCGATTTG
* *
1142607 ATATATTTTTTAATT
1 ATATATTATATAATT
1142622 ATATATTATATAATT
1 ATATATTATATAATT
*
1142637 -TATATCATATAA
1 ATATATTATATAA
1142649 AAATTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATATTATATAATT
Found at i:1142753 original size:32 final size:29
Alignment explanation
Indices: 1142712--1142775 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 29
1142702 AGTGTTTTAG
1142712 AATTTAATAAAATAAAAAATAAAATTATTAAA
1 AATTTAATAAAA-AAAAAATAAAA-TA-TAAA
* *
1142744 AATTTAATAAAAAATAATTAAAATATAAA
1 AATTTAATAAAAAAAAAATAAAATATAAA
1142773 AAT
1 AAT
1142776 ATAAATAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 7 0.23
30 2 0.07
31 9 0.30
32 12 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
AATTTAATAAAAAAAAAATAAAATATAAA
Found at i:1142860 original size:20 final size:20
Alignment explanation
Indices: 1142831--1142868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1142821 TAAATTTAGA
1142831 TAAATATATAAATATTAAGG
1 TAAATATATAAATATTAAGG
* *
1142851 TAAATTTATAGATATTAA
1 TAAATATATAAATATTAA
1142869 AATTAAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (20 bp):
TAAATATATAAATATTAAGG
Found at i:1146273 original size:242 final size:242
Alignment explanation
Indices: 1145838--1146303 Score: 641
Period size: 242 Copynumber: 1.9 Consensus size: 242
1145828 TATTCATTAA
* * * * * * *
1145838 GTTTTGAGTCAAGTCGCATTCTGTTACGTTTTCAGAGCAGGTACTCTTGCTTTCACTGTGGATTC
1 GTTTTGAGTCAAGTCACACTCTGTCACATTCTCAGAGCAGGGACTCATGCTTTCACTGTGGATTC
* *
1145903 TTCGCTTTTCAAAGCCAATTTCAATTTGTGTGATTGGCTACATGAGTTTTAAAGGAACTTGTTGT
66 TTCACTTTTCAAAGCCAATTTCAATTTGTGTGATTGGCTACATGAGTTTGAAAGGAACTTGTTGT
* * *
1145968 GCTTAGCAAGGGTTGACTTTGTGAATCTCTCTTTATTGTATCCTTATGGACTGGCAGTGTAACAT
131 GCTTAGCAAGGGTTGACTTTGTGAATCTCTCTGTATTATATCCTTATGGACTGGCAATGTAACAT
*
1146033 GCCAAG-TATTTTGGTAACTATAATTGCATTATATGCATTTGTATATG
196 GCCAAGCT-TTCTGGTAACTATAATTGCATTATATGCATTTGTATATG
* * * * *
1146080 GTTTTGAGTCAAGTCACACTCTGTCATATTCTCAGAGCAGGGATTCATGCTTTCAGTTTTGATTC
1 GTTTTGAGTCAAGTCACACTCTGTCACATTCTCAGAGCAGGGACTCATGCTTTCACTGTGGATTC
* * * *
1146145 TTCAC-TTTCTAAAGCCAATTTCGATTTTTGTGATTGGCTGCTTGAGTTTGAAAGGAACTTGTTG
66 TTCACTTTTC-AAAGCCAATTTCAATTTGTGTGATTGGCTACATGAGTTTGAAAGGAACTTGTTG
* *
1146209 TGCTTAGCAAGGGTTGCCTTTGTGAATCTCTCTGTATTATAT-CTATATGGACTTGCAATGTAAC
130 TGCTTAGCAAGGGTTGACTTTGTGAATCTCTCTGTATTATATCCT-TATGGACTGGCAATGTAAC
* * *
1146273 ATGCTAAGCTTTCTGGTTATTATAATTGCAT
194 ATGCCAAGCTTTCTGGTAACTATAATTGCAT
1146304 ATGTATATGA
Statistics
Matches: 194, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
241 6 0.03
242 187 0.96
243 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.41
Consensus pattern (242 bp):
GTTTTGAGTCAAGTCACACTCTGTCACATTCTCAGAGCAGGGACTCATGCTTTCACTGTGGATTC
TTCACTTTTCAAAGCCAATTTCAATTTGTGTGATTGGCTACATGAGTTTGAAAGGAACTTGTTGT
GCTTAGCAAGGGTTGACTTTGTGAATCTCTCTGTATTATATCCTTATGGACTGGCAATGTAACAT
GCCAAGCTTTCTGGTAACTATAATTGCATTATATGCATTTGTATATG
Found at i:1150024 original size:7 final size:7
Alignment explanation
Indices: 1150012--1150037 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1150002 AAAATATTAA
1150012 AATTTAT
1 AATTTAT
1150019 AATTTAT
1 AATTTAT
1150026 AATTTAT
1 AATTTAT
1150033 AATTT
1 AATTT
1150038 TTTATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTAT
Found at i:1155526 original size:15 final size:15
Alignment explanation
Indices: 1155506--1155544 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1155496 TCTGTTTCTT
1155506 TTTCTTTTCTGTTAG
1 TTTCTTTTCTGTTAG
* *
1155521 TTTCTTTTCTTTTAT
1 TTTCTTTTCTGTTAG
1155536 TTTCTTTTC
1 TTTCTTTTC
1155545 AATGTGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.74
Consensus pattern (15 bp):
TTTCTTTTCTGTTAG
Found at i:1160543 original size:192 final size:192
Alignment explanation
Indices: 1160206--1160595 Score: 726
Period size: 192 Copynumber: 2.0 Consensus size: 192
1160196 TCACAACCTA
* *
1160206 AAGTGCAAATAGTGTTGTAATAAAATTCCAGTTTGGATGAGAAAAAGAGGGACAATCATTTTCAA
1 AAGT-CAAACAGTGTTGTAATAAAATTCCAGTTTGGATGAGAAAAAGAGGGACAATCATATTCAA
* *
1160271 TATGCCAAAATAAAAGTTGAAAAGGAAGATAAAAGCTGTAGTGTAACAGAAATTAAATTGCCCCA
65 TATGCCAAAATAAAAGTCGAAAAGGAAGATAAAAGCTGCAGTGTAACAGAAATTAAATTGCCCCA
1160336 GCATGGAACTTTAGCAAAACAAAAGAGTTAATTTGATCCTTGGAACTTCATATCCATTTATGC
130 GCATGGAACTTTAGCAAAACAAAAGAGTTAATTTGATCCTTGGAACTTCATATCCATTTATGC
1160399 AAGTCAAACAGTGTTGTAATAAAATTCCAGTTTGGATGAGAAAAAGAGGGACAATCATATTCAAT
1 AAGTCAAACAGTGTTGTAATAAAATTCCAGTTTGGATGAGAAAAAGAGGGACAATCATATTCAAT
1160464 ATGCCAAAATAAAAGTCGAAAAGGAAGATAAAAGCTGCAGTGTAACAGAAATTAAATTGCCCCAG
66 ATGCCAAAATAAAAGTCGAAAAGGAAGATAAAAGCTGCAGTGTAACAGAAATTAAATTGCCCCAG
*
1160529 CATGGAATTTTAGCAAAACAAAAGAGTTAATTTGATCCTTGGAACTTCATATCCATTTATGC
131 CATGGAACTTTAGCAAAACAAAAGAGTTAATTTGATCCTTGGAACTTCATATCCATTTATGC
1160591 AAGTC
1 AAGTC
1160596 CTTTTCAACA
Statistics
Matches: 192, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
192 188 0.98
193 4 0.02
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (192 bp):
AAGTCAAACAGTGTTGTAATAAAATTCCAGTTTGGATGAGAAAAAGAGGGACAATCATATTCAAT
ATGCCAAAATAAAAGTCGAAAAGGAAGATAAAAGCTGCAGTGTAACAGAAATTAAATTGCCCCAG
CATGGAACTTTAGCAAAACAAAAGAGTTAATTTGATCCTTGGAACTTCATATCCATTTATGC
Found at i:1163084 original size:27 final size:26
Alignment explanation
Indices: 1163054--1163115 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
1163044 TTAATATTCA
1163054 TAATAAATAAAAATTTATATAAATTAT
1 TAATAAATAAAAATTTATATAAA-TAT
* *
1163081 TAATATATTAAAATTTATATAAATAT
1 TAATAAATAAAAATTTATATAAATAT
*
1163107 AAATAAATA
1 TAATAAATA
1163116 TTTTATATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TAATAAATAAAAATTTATATAAATAT
Found at i:1163848 original size:24 final size:26
Alignment explanation
Indices: 1163794--1163850 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1163784 TAAGACATCA
*
1163794 ATAATTTAAATTTAATAAAATTAATT
1 ATAATTAAAATTTAATAAAATTAATT
* *
1163820 A-AATTAAAATTTAA-ATAATT-TTT
1 ATAATTAAAATTTAATAAAATTAATT
1163843 ATAATTAA
1 ATAATTAA
1163851 TTAATTATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.11
24 11 0.41
25 12 0.44
26 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAATTAAAATTTAATAAAATTAATT
Found at i:1164244 original size:34 final size:33
Alignment explanation
Indices: 1164196--1164416 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
1164186 TGGTAAAAAC
**
1164196 CACCATTTAATCAACAATGACAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1164229 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1164263 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1164297 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1164331 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
1164365 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1164399 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1164417 TCTCCCACTT
Statistics
Matches: 161, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.14
34 132 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1164312 original size:68 final size:67
Alignment explanation
Indices: 1164198--1164416 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
1164188 GTAAAAACCA
* * * *
1164198 CCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1164263 CAC
65 CAC
* * * *
1164266 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1164331 CTC
65 CAC
* * * *
1164334 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1164399 CA-
65 CAC
1164401 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1164417 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1164340 original size:102 final size:101
Alignment explanation
Indices: 1164196--1164416 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
1164186 TGGTAAAAAC
* *
1164196 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
1164261 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** ** * *
1164297 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
1164362 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1164399 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1164417 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1168866 original size:34 final size:34
Alignment explanation
Indices: 1168819--1169032 Score: 197
Period size: 34 Copynumber: 6.3 Consensus size: 34
1168809 GGTAAAAACC
* *
1168819 ACCATTTAATCAACAATGGCAACCTACTAAATCT
1 ACCATTTAATCAACAATGGTAACCTACCAAATCT
*
1168853 ACCATTTAGTCAACAATGGTAAGCC-ACCAAATC-
1 ACCATTTAATCAACAATGGTAA-CCTACCAAATCT
* *
1168886 ACCCATTTAATCAATAATGGTAAGCTACCAAAT-T
1 A-CCATTTAATCAACAATGGTAACCTACCAAATCT
* *
1168920 TCTCATTTAATCAACAATGGTAAGCTACCAAATCT
1 AC-CATTTAATCAACAATGGTAACCTACCAAATCT
* * *** *
1168955 CCCATTTAGTCAACAATAACAA-ATCACCAAATC-
1 ACCATTTAATCAACAATGGTAACCT-ACCAAATCT
* **
1168988 ATCCATTTAATCAACAATGATAAATTACCAAATC-
1 A-CCATTTAATCAACAATGGTAACCTACCAAATCT
1169022 ACCATTTAATC
1 ACCATTTAATC
1169033 GTCAAACGAA
Statistics
Matches: 152, Mismatches: 19, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
33 14 0.09
34 133 0.88
35 5 0.03
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.27
Consensus pattern (34 bp):
ACCATTTAATCAACAATGGTAACCTACCAAATCT
Found at i:1168934 original size:68 final size:67
Alignment explanation
Indices: 1168820--1169032 Score: 241
Period size: 68 Copynumber: 3.1 Consensus size: 67
1168810 GTAAAAACCA
* * * *
1168820 CCATTTAATCAACAATGGCAACCTACTAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAA-CTACCAAATCTTCCATTTAATCAACAATGGTAAGCTACCAAAT
1168885 CAC
65 CAC
* *
1168888 CCATTTAATCAATAATGGTAAGCTACCAAAT-TTCTCATTTAATCAACAATGGTAAGCTACCAAA
1 CCATTTAATCAACAATGGCAA-CTACCAAATCTTC-CATTTAATCAACAATGGTAAGCTACCAAA
*
1168952 TCTC
64 TCAC
* ** * * * **
1168956 CCATTTAGTCAACAATAACAAATCACCAAATCATCCATTTAATCAACAATGATAAATTACCAAAT
1 CCATTTAATCAACAATGGCAACT-ACCAAATCTTCCATTTAATCAACAATGGTAAGCTACCAAAT
1169021 CA-
65 CAC
1169023 CCATTTAATC
1 CCATTTAATC
1169033 GTCAAACGAA
Statistics
Matches: 122, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
67 12 0.10
68 108 0.89
69 2 0.02
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAACTACCAAATCTTCCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1168963 original size:102 final size:102
Alignment explanation
Indices: 1168821--1169020 Score: 274
Period size: 102 Copynumber: 2.0 Consensus size: 102
1168811 TAAAAACCAC
* *** *
1168821 CATTTAATCAACAATGGCAACCTACTAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAACAAACCACCAAATC
* * *
1168886 ACCCATTTAATCAATAATGGTAAGCTACCAAATTTCT
66 ACCCATTTAATCAACAATGATAAACTACCAAATTTCT
* * * *
1168923 CATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATAACAAATCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAACAAACCACCAAATC
* *
1168988 ATCCATTTAATCAACAATGATAAATTACCAAAT
66 ACCCATTTAATCAACAATGATAAACTACCAAAT
1169021 CACCATTTAA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 84 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (102 bp):
CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAACAAACCACCAAATC
ACCCATTTAATCAACAATGATAAACTACCAAATTTCT
Found at i:1169419 original size:18 final size:19
Alignment explanation
Indices: 1169398--1169434 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1169388 ATGTTTAATT
*
1169398 TATTTTTA-AAATTATATA
1 TATTTTTATAAATAATATA
1169416 TATTTTTATAAATAATATA
1 TATTTTTATAAATAATATA
1169435 ATTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTTATAAATAATATA
Found at i:1169433 original size:17 final size:17
Alignment explanation
Indices: 1169374--1169434 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
1169364 AGAAAATTGA
1169374 AAATAA-ATATTTTTAT
1 AAATAATATATTTTTAT
*** *
1169390 GTTTAATTTATTTTTA-
1 AAATAATATATTTTTAT
1169406 AAATTATATATATTTTTAT
1 AAA-TA-ATATATTTTTAT
1169425 AAATAATATA
1 AAATAATATA
1169435 ATTAAAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 12 0.36
19 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
AAATAATATATTTTTAT
Found at i:1169958 original size:6 final size:6
Alignment explanation
Indices: 1169928--1169976 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
1169918 TTATATTACT
*
1169928 TAAATA T-AATAA TAAATA TTGAATA TAAATA TAAATA T-AATA -AAATA
1 TAAATA TAAAT-A TAAATA -TAAATA TAAATA TAAATA TAAATA TAAATA
1169975 TA
1 TA
1169977 TTTAATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
5 11 0.31
6 17 0.47
7 8 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:1173682 original size:2 final size:2
Alignment explanation
Indices: 1173675--1173704 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1173665 GGACTGGATA
1173675 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
1173705 TATTCTTCTA
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:1176269 original size:2 final size:2
Alignment explanation
Indices: 1176262--1176291 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1176252 ATTAATTATC
1176262 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1176292 GAGAGAGAGA
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):
TA
Found at i:1176296 original size:2 final size:2
Alignment explanation
Indices: 1176291--1176317 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1176281 ATATATATAT
1176291 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1176318 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1176548 original size:6 final size:6
Alignment explanation
Indices: 1176537--1176561 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1176527 TACATTTAAC
1176537 ATATTT ATATTT ATATTT ATATTT A
1 ATATTT ATATTT ATATTT ATATTT A
1176562 AATGATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:1183691 original size:15 final size:16
Alignment explanation
Indices: 1183673--1183743 Score: 57
Period size: 15 Copynumber: 4.8 Consensus size: 16
1183663 TAAAAAACTG
1183673 TAAATATTAAAAAT-T
1 TAAATATTAAAAATAT
1183688 TAAA-ATTTAAAAATAT
1 TAAATA-TTAAAAATAT
* *
1183704 T-AATATT-AAATTAA
1 TAAATATTAAAAATAT
1183718 TAAA-ATTAAATAA-AT
1 TAAATATTAAA-AATAT
1183733 TAAAT-TTAAAA
1 TAAATATTAAAA
1183744 TTATGGATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
14 11 0.24
15 30 0.67
16 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATTAAAAATAT
Found at i:1187575 original size:10 final size:10
Alignment explanation
Indices: 1187536--1187582 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
1187526 GTGCATGTTA
1187536 AAAT-TATAT
1 AAATATATAT
*
1187545 AAAAAT-TA-
1 AAATATATAT
1187553 AAATATAATAT
1 AAATAT-ATAT
1187564 AAATATATAT
1 AAATATATAT
1187574 AAATATATA
1 AAATATATA
1187583 AATATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 5 0.16
9 5 0.16
10 16 0.50
11 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATATATAT
Found at i:1188478 original size:14 final size:14
Alignment explanation
Indices: 1188432--1188488 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 14
1188422 TGTAGATGTA
1188432 ATAAATATT-AT-T
1 ATAAATATTAATAT
*
1188444 ATAATTAATT-AT-T
1 ATAAAT-ATTAATAT
1188457 ATAAATATTAATAT
1 ATAAATATTAATAT
*
1188471 ATAGATATTAATA-
1 ATAAATATTAATAT
1188484 ATAAA
1 ATAAA
1188489 AAAATTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
12 8 0.21
13 17 0.45
14 13 0.34
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAAATATTAATAT
Found at i:1197120 original size:27 final size:27
Alignment explanation
Indices: 1197056--1197108 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1197046 ATTGCTATTA
*
1197056 TCAAGAGGACCCGACATGAACCCTCTC
1 TCAATAGGACCCGACATGAACCCTCTC
*
1197083 TCAATCGGACCCGACATGAACCCTCT
1 TCAATAGGACCCGACATGAACCCTCT
1197109 TTCTAAAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.38, G:0.17, T:0.17
Consensus pattern (27 bp):
TCAATAGGACCCGACATGAACCCTCTC
Found at i:1199043 original size:15 final size:15
Alignment explanation
Indices: 1199023--1199116 Score: 75
Period size: 15 Copynumber: 6.1 Consensus size: 15
1199013 ATCATGCCTT
*
1199023 TATTAAATTTAATAA
1 TATTAAATATAATAA
*
1199038 TATTAAATATAATTA
1 TATTAAATATAATAA
*
1199053 TA-TAAATATAACATA
1 TATTAAATATAATA-A
*
1199068 TATATATATATAATAA
1 TAT-TAAATATAATAA
* *
1199084 TA-AAAATATGATATA
1 TATTAAATATAATA-A
*
1199099 TATATATATATAATAA
1 TAT-TAAATATAATAA
1199115 TA
1 TA
1199117 AAAATATGAT
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
14 17 0.28
15 21 0.34
16 6 0.10
17 17 0.28
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (15 bp):
TATTAAATATAATAA
Found at i:1199068 original size:21 final size:23
Alignment explanation
Indices: 1199036--1199107 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
1199026 TAAATTTAAT
1199036 AATATTAAATATA-AT-TATATA
1 AATATTAAATATATATATATATA
1199057 AATA-TAACATATATATATATAT-
1 AATATTAA-ATATATATATATATA
* *
1199079 AATAATAAAAATATGATATATATA
1 AATATTAAATATAT-ATATATATA
*
1199103 TATAT
1 AATAT
1199108 ATAATAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.07
21 9 0.21
22 11 0.26
23 16 0.38
24 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (23 bp):
AATATTAAATATATATATATATA
Found at i:1199070 original size:2 final size:2
Alignment explanation
Indices: 1199051--1199132 Score: 57
Period size: 2 Copynumber: 42.5 Consensus size: 2
1199041 TAAATATAAT
* * * *
1199051 TA TA TA AA TA TA -A CA TA TA TA TA TA TA TA -A TA -A TA AA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1199090 TA TGA TA TA TA TA TA TA TA TA -A TA -A TA AA AA TA TGA TA TA TA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
1199132 T
1 T
1199133 GCATATTTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
1 5 0.08
2 57 0.86
3 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (2 bp):
TA
Found at i:1199076 original size:29 final size:29
Alignment explanation
Indices: 1199027--1199132 Score: 115
Period size: 31 Copynumber: 3.5 Consensus size: 29
1199017 TGCCTTTATT
* * * *
1199027 AAATTTAATA-ATATTAAATATAATTATAT
1 AAATATAATATATA-TATATATAATAATAA
1199056 AAATATAACATATATATATATATAATAATAA
1 AAATAT-A-ATATATATATATATAATAATAA
1199087 AAATATGATATATATATATATATAATAATAA
1 AAATAT-A-ATATATATATATATAATAATAA
*
1199118 AAATATGATATATAT
1 AAATATAATATATAT
1199133 GCATATTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
29 13 0.19
30 1 0.01
31 50 0.75
32 3 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.40
Consensus pattern (29 bp):
AAATATAATATATATATATATAATAATAA
Found at i:1199091 original size:31 final size:31
Alignment explanation
Indices: 1199044--1199132 Score: 142
Period size: 31 Copynumber: 2.9 Consensus size: 31
1199034 ATAATATTAA
* * * *
1199044 ATATAATTATATAAATATAACATATATATAT
1 ATATAATAATAAAAATATGATATATATATAT
1199075 ATATAATAATAAAAATATGATATATATATAT
1 ATATAATAATAAAAATATGATATATATATAT
1199106 ATATAATAATAAAAATATGATATATAT
1 ATATAATAATAAAAATATGATATATAT
1199133 GCATATTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (31 bp):
ATATAATAATAAAAATATGATATATATATAT
Found at i:1199974 original size:33 final size:32
Alignment explanation
Indices: 1199937--1200014 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
1199927 TTAAAATATA
1199937 ATATAAAATAAATATATAAATTT-TTTAAATTTT
1 ATATAAAATAAATATATAAATTTATTT-AA-TTT
* **
1199970 ATATAATATAAATA-ATTTATTTATTTAATTT
1 ATATAAAATAAATATATAAATTTATTTAATTT
1200001 ATATAAAA-AAATAT
1 ATATAAAATAAATAT
1200015 TTTAAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 5 0.13
31 10 0.26
32 8 0.21
33 16 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATATAAAATAAATATATAAATTTATTTAATTT
Found at i:1200030 original size:25 final size:25
Alignment explanation
Indices: 1200002--1200074 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 25
1199992 ATTTAATTTA
1200002 TATAAAAAAATATTTTAAATATAAT
1 TATAAAAAAATATTTTAAATATAAT
* * * *
1200027 TATAACATAATATGTATACATA-AAT
1 TATAAAAAAATAT-TTTAAATATAAT
* * *
1200052 TATTAAAACATTTTTTAAA-ATAA
1 TATAAAAAAATATTTTAAATATAA
1200075 AAATGAAAAA
Statistics
Matches: 35, Mismatches: 11, Indels: 5
0.69 0.22 0.10
Matches are distributed among these distances:
23 1 0.03
24 6 0.17
25 22 0.63
26 6 0.17
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (25 bp):
TATAAAAAAATATTTTAAATATAAT
Found at i:1202254 original size:17 final size:18
Alignment explanation
Indices: 1202226--1202260 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1202216 AAGCTGGAAT
*
1202226 TAAAATATAAAATTTTTA
1 TAAAATATAAAAATTTTA
1202244 TAAAA-ATAAAAATTTTA
1 TAAAATATAAAAATTTTA
1202261 ATAATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATATAAAAATTTTA
Found at i:1202255 original size:18 final size:19
Alignment explanation
Indices: 1202227--1202264 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1202217 AGCTGGAATT
*
1202227 AAAATATAAAATTTTTATA
1 AAAATATAAAATTTTAATA
1202246 AAAATA-AAAATTTTAATA
1 AAAATATAAAATTTTAATA
1202264 A
1 A
1202265 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATATAAAATTTTAATA
Found at i:1209358 original size:21 final size:21
Alignment explanation
Indices: 1209314--1209358 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1209304 ATTTATAATA
1209314 AATT-TTTAAAAATAAATTTT
1 AATTATTTAAAAATAAATTTT
1209334 -ATTATTTAAATAAT-AATTTT
1 AATTATTTAAA-AATAAATTTT
1209354 AATTA
1 AATTA
1209359 AAACAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.14
20 12 0.55
21 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTATTTAAAAATAAATTTT
Found at i:1212300 original size:23 final size:21
Alignment explanation
Indices: 1212274--1212330 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
1212264 TAATATACGA
1212274 AAATAAAATTTAA-TACATTTATT
1 AAAT-AAATTTAAGT-CATTTA-T
* *
1212297 AAATGAATTTTAAGTTATTTAT
1 AAAT-AAATTTAAGTCATTTAT
1212319 AAATAAATTTAA
1 AAATAAATTTAA
1212331 CATATTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.24
22 5 0.17
23 16 0.55
24 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (21 bp):
AAATAAATTTAAGTCATTTAT
Found at i:1213551 original size:63 final size:63
Alignment explanation
Indices: 1213452--1213578 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
1213442 AAAGAAGGTC
1213452 TCTCTTGAATGAGTCTGATGAGGTAAATAATATGATTAGGACCATTAGGTTTCTGGTTATTGT
1 TCTCTTGAATGAGTCTGATGAGGTAAATAATATGATTAGGACCATTAGGTTTCTGGTTATTGT
1213515 TCTCTTGAATGAGTCTGATGAGGTAAATAATATGATTAGGACCATTAGGTTTCTGGTTATTGT
1 TCTCTTGAATGAGTCTGATGAGGTAAATAATATGATTAGGACCATTAGGTTTCTGGTTATTGT
1213578 T
1 T
1213579 TGACGAATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (63 bp):
TCTCTTGAATGAGTCTGATGAGGTAAATAATATGATTAGGACCATTAGGTTTCTGGTTATTGT
Found at i:1215301 original size:2 final size:2
Alignment explanation
Indices: 1215294--1215328 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1215284 CATATACGTG
* *
1215294 TA TA TA TA TA TC TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1215329 TTATTTGCCA
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:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1217042 original size:16 final size:16
Alignment explanation
Indices: 1217023--1217077 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
1217013 TATGTCATAA
1217023 TTATATTTATAATATT
1 TTATATTTATAATATT
1217039 TTATATTTTATATATATT
1 TTATA-TTTATA-ATATT
* *
1217057 TTA-ATATATTAATAAT
1 TTATATTTA-TAATATT
1217073 TTATA
1 TTATA
1217078 ATAAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 15 0.45
17 10 0.30
18 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTTATAATATT
Found at i:1217054 original size:27 final size:27
Alignment explanation
Indices: 1217024--1217115 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 27
1217014 ATGTCATAAT
* *
1217024 TATATTTATAATAT-TTTATATTTTATA
1 TATATTT-TAATATATTAATAATTTATA
1217051 TATATTTTAATATATTAATAATTTATA
1 TATATTTTAATATATTAATAATTTATA
** *
1217078 -ATAAATTAATA-ATTAAT-A-TTATT
1 TATATTTTAATATATTAATAATTTATA
*
1217101 TAAATTTTAATATAT
1 TATATTTTAATATAT
1217116 ATTATATATT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
23 4 0.07
24 9 0.17
25 8 0.15
26 15 0.28
27 18 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATATTTTAATATATTAATAATTTATA
Found at i:1217085 original size:18 final size:17
Alignment explanation
Indices: 1217054--1217091 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1217044 TTTTATATAT
*
1217054 ATTTTAATATATTAATA
1 ATTTTAATAAATTAATA
1217071 ATTTATAATAAATTAATA
1 ATTT-TAATAAATTAATA
1217089 ATT
1 ATT
1217092 AATATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAATAAATTAATA
Found at i:1221711 original size:3 final size:3
Alignment explanation
Indices: 1221703--1221730 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1221693 GTTGTATTTA
1221703 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1221731 TTCTAGTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1225635 original size:21 final size:21
Alignment explanation
Indices: 1225596--1225636 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1225586 TTAATTATTT
**
1225596 TTAAATTAAAATTTGAAATTG
1 TTAAATTAAAATTAAAAATTG
*
1225617 TTAAATTAATATTAAAAATT
1 TTAAATTAAAATTAAAAATT
1225637 TATCTCAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TTAAATTAAAATTAAAAATTG
Found at i:1227439 original size:18 final size:18
Alignment explanation
Indices: 1227405--1227468 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
1227395 ACCATTTACG
*
1227405 TATAATATTAGTA-TAAAA
1 TATAAAATTA-TATTAAAA
1227423 TATAAAA-TATAATTAAAA
1 TATAAAATTAT-ATTAAAA
* *
1227441 TATAATATTATATAAAAA
1 TATAAAATTATATTAAAA
*
1227459 TATAATATTA
1 TATAAAATTA
1227469 ATATAATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.03
17 3 0.08
18 33 0.82
19 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
TATAAAATTATATTAAAA
Found at i:1227462 original size:29 final size:30
Alignment explanation
Indices: 1227421--1227499 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
1227411 ATTAGTATAA
1227421 AATAT-AAAATATAATTAAAATATAATATT
1 AATATAAAAATATAATTAAAATATAATATT
*
1227450 -ATATAAAAATATAA-TATTAATATAATATT
1 AATATAAAAATATAATTA-AAATATAATATT
**
1227479 AATATATGAATAT-ATTAAAAT
1 AATATAAAAATATAATTAAAAT
1227500 TTATATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
28 6 0.14
29 24 0.57
30 12 0.29
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
AATATAAAAATATAATTAAAATATAATATT
Found at i:1227473 original size:11 final size:11
Alignment explanation
Indices: 1227439--1227484 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
1227429 ATATAATTAA
1227439 AATATAATATT
1 AATATAATATT
1227450 -ATATAA-A--
1 AATATAATATT
1227457 AATATAATATT
1 AATATAATATT
1227468 AATATAATATT
1 AATATAATATT
1227479 AATATA
1 AATATA
1227485 TGAATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 6 0.19
11 17 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATAATATT
Done.