Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold170
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: 1632119
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 57634 characters in sequence are not A, C, G, or T
File 10 of 11
Found at i:1413084 original size:50 final size:54
Alignment explanation
Indices: 1412995--1413093 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 54
1412985 TTTAATAAAA
*
1412995 TTATTTTATATTATTATTTATATATTTTATAATTAAATTTAAATAAAAAATATT
1 TTATTTTATATTATTAATTATATATTTTATAATTAAATTTAAATAAAAAATATT
*
1413049 TTATTTTA-ATT-TATAATTAT-TATTTTAT-GTT-AATTTAAATAAAAA
1 TTATTTTATATTAT-TAATTATATATTTTATAATTAAATTTAAATAAAAA
1413094 TAAAAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
50 14 0.33
51 2 0.05
52 9 0.21
53 9 0.21
54 8 0.19
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (54 bp):
TTATTTTATATTATTAATTATATATTTTATAATTAAATTTAAATAAAAAATATT
Found at i:1413261 original size:10 final size:10
Alignment explanation
Indices: 1413235--1413272 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1413225 TTTTGATTAA
1413235 AATAAAA-AT
1 AATAAAATAT
1413244 AATAAAAATAT
1 AAT-AAAATAT
1413255 AATAAAATAT
1 AATAAAATAT
1413265 AA-AAAATA
1 AATAAAATA
1413273 ATATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.33
10 13 0.48
11 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AATAAAATAT
Found at i:1413278 original size:19 final size:19
Alignment explanation
Indices: 1413235--1413280 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1413225 TTTTGATTAA
1413235 AATA-AAAATAATAAAAAT
1 AATATAAAATAATAAAAAT
1413253 -ATAATAAAAT-ATAAAAAAT
1 AAT-ATAAAATAAT-AAAAAT
1413272 AATATAAAA
1 AATATAAAA
1413281 ATTTATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.08
18 3 0.12
19 17 0.71
20 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AATATAAAATAATAAAAAT
Found at i:1413287 original size:10 final size:10
Alignment explanation
Indices: 1413236--1413350 Score: 68
Period size: 9 Copynumber: 12.1 Consensus size: 10
1413226 TTTGATTAAA
1413236 ATAAAAATA-
1 ATAAAAATAT
1413245 ATAAAAATAT
1 ATAAAAATAT
1413255 A-ATAAAATAT
1 ATA-AAAATAT
1413265 A-AAAAATAAT
1 ATAAAAAT-AT
*
1413275 ATAAAAATTT
1 ATAAAAATAT
*
1413285 AT-ATAATAT
1 ATAAAAATAT
***
1413294 ATAATGCT-T
1 ATAAAAATAT
*
1413303 -TAAATATA-
1 ATAAAAATAT
* *
1413311 ATAATAACAT
1 ATAAAAATAT
1413321 A-AAAAATAAT
1 ATAAAAAT-AT
1413331 ATAAAAAT-T
1 ATAAAAATAT
1413340 ATAAAAATAT
1 ATAAAAATAT
1413350 A
1 A
1413351 AATAGAAAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
8 4 0.05
9 41 0.50
10 25 0.30
11 12 0.15
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:1413354 original size:23 final size:21
Alignment explanation
Indices: 1413319--1413363 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
1413309 TAATAATAAC
*
1413319 ATAAAAAATAATATAAAAATT
1 ATAAAAAATAATAGAAAAATT
*
1413340 ATAAAAATATAAATAGAAAGATT
1 ATAAAAA-AT-AATAGAAAAATT
1413363 A
1 A
1413364 ATAGTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAAAAATAATAGAAAAATT
Found at i:1417616 original size:19 final size:19
Alignment explanation
Indices: 1417559--1417610 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1417549 TTACATAATA
1417559 ATAA-TACATAAA-ATTATT
1 ATAATTACATAAATA-TATT
1417577 ATAATTACATAAATATATT
1 ATAATTACATAAATATATT
*
1417596 ATAAGTTATATAAAT
1 ATAA-TTACATAAAT
1417611 CTTTATGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 4 0.13
19 16 0.53
20 10 0.33
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAATTACATAAATATATT
Found at i:1418743 original size:27 final size:28
Alignment explanation
Indices: 1418666--1418745 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 28
1418656 AAATTCATAT
1418666 TATTAATTTTTTAAATATTAATTTTATTTAA
1 TATTAATTTTTT-AA-ATT-ATTTTATTTAA
1418697 TACTT-ATTTAATATTAAAATTA-TTTATTTAA
1 TA-TTAATTT--T-TT-AAATTATTTTATTTAA
1418728 TATTAATTTTTTAAATTA
1 TATTAATTTTTTAAATTA
1418746 AACAATCAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
27 6 0.14
28 2 0.05
29 1 0.02
30 2 0.05
31 21 0.48
32 3 0.07
33 4 0.09
34 5 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
TATTAATTTTTTAAATTATTTTATTTAA
Found at i:1423529 original size:2 final size:2
Alignment explanation
Indices: 1423522--1423561 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1423512 CTCAAATACC
*
1423522 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1423562 ACCACTGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1423847 original size:36 final size:36
Alignment explanation
Indices: 1423800--1423874 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
1423790 GATTATATAG
1423800 AACAGGATGTGTTGAAATTAGATTGTGTTGTCATTC
1 AACAGGATGTGTTGAAATTAGATTGTGTTGTCATTC
1423836 AACAGGATGTGTTGAAATTAGATTGTGTTGTCATTC
1 AACAGGATGTGTTGAAATTAGATTGTGTTGTCATTC
1423872 AAC
1 AAC
1423875 CCCAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.37
Consensus pattern (36 bp):
AACAGGATGTGTTGAAATTAGATTGTGTTGTCATTC
Found at i:1426220 original size:2 final size:2
Alignment explanation
Indices: 1426215--1426261 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1426205 ACACACACCC
1426215 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
1426257 AT AT A
1 AT AT A
1426262 AAGACACCAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1427092 original size:94 final size:93
Alignment explanation
Indices: 1426979--1427159 Score: 265
Period size: 92 Copynumber: 1.9 Consensus size: 93
1426969 CTGAGCTTCT
1426979 AGGAAACCAGGAAAGAAAAGTCAATGACTTGTCCAAAAAGAAAAACCAAATAAAAAAGAACTAAA
1 AGGAAACCAGGAAAGAAAAGTCAATGACTTGTCCAAAAAG-AAAACCAAA-AAAAAAGAACTAAA
* *
1427044 AAGCTGTAGTTTGGAAGTGAAAGACAGTCA
64 AAGCTGTAGATTGAAAGTGAAAGACAGTCA
* * * * * *
1427074 AGGAAA-CAGGAAATAAAAGTCAATTACTTGTCCAAAAAGAAAATCAAAGAAAAAGAATTAACAA
1 AGGAAACCAGGAAAGAAAAGTCAATGACTTGTCCAAAAAGAAAACCAAAAAAAAAGAACTAAAAA
1427138 GCTGTAGATTGAAAGTGAAAGA
66 GCTGTAGATTGAAAGTGAAAGA
1427160 AAGAGAATTA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
92 33 0.42
93 8 0.10
94 31 0.40
95 6 0.08
ACGTcount: A:0.54, C:0.11, G:0.19, T:0.16
Consensus pattern (93 bp):
AGGAAACCAGGAAAGAAAAGTCAATGACTTGTCCAAAAAGAAAACCAAAAAAAAAGAACTAAAAA
GCTGTAGATTGAAAGTGAAAGACAGTCA
Found at i:1428892 original size:2 final size:2
Alignment explanation
Indices: 1428887--1428925 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1428877 GTGTGTCTAC
* *
1428887 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1428926 TTAAGAGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1435562 original size:16 final size:17
Alignment explanation
Indices: 1435543--1435585 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1435533 ATTTAATTTT
*
1435543 TTAATTTAAT-TATTAA
1 TTAATTAAATATATTAA
*
1435559 TTAATTAAATATATTAT
1 TTAATTAAATATATTAA
*
1435576 TTTATTAAAT
1 TTAATTAAAT
1435586 TTAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTAAATATATTAA
Found at i:1435848 original size:25 final size:25
Alignment explanation
Indices: 1435792--1435850 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
1435782 TTTTTATTTT
** * *
1435792 ATTTTAATTTTATATTTTAATAATA
1 ATTTTAATTTTATAAATGAAAAATA
**
1435817 AGATTAATTTTATAAATGAAAAATA
1 ATTTTAATTTTATAAATGAAAAATA
1435842 ATTTTAATT
1 ATTTTAATT
1435851 ATATTGAATT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (25 bp):
ATTTTAATTTTATAAATGAAAAATA
Found at i:1435897 original size:15 final size:13
Alignment explanation
Indices: 1435868--1435910 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
1435858 ATTATAGTCA
1435868 TTTATGATAAATTT
1 TTTATGAT-AATTT
1435882 TTTGAATGATAATTT
1 TTT--ATGATAATTT
1435897 TTTA-GATAATTT
1 TTTATGATAATTT
1435909 TT
1 TT
1435911 AATTAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 10 0.37
13 1 0.04
14 3 0.11
15 8 0.30
16 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (13 bp):
TTTATGATAATTT
Found at i:1435998 original size:21 final size:21
Alignment explanation
Indices: 1435966--1436020 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
1435956 TTTTAAAAAT
* *
1435966 TATAA-ATTATTTTATTTTTA
1 TATAATATAATTTTAATTTTA
1435986 TATAATATAATTTTAAATTTTA
1 TATAATATAATTTT-AATTTTA
1436008 -ATAAT-TAATTTTA
1 TATAATATAATTTTA
1436021 CAGATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.39
21 12 0.39
22 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATAATATAATTTTAATTTTA
Found at i:1436018 original size:20 final size:22
Alignment explanation
Indices: 1435981--1436020 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1435971 ATTATTTTAT
1435981 TTTTATATAATATAATTTTAAA
1 TTTTATATAATATAATTTTAAA
1436003 TTTTA-ATAAT-TAATTTTA
1 TTTTATATAATATAATTTTA
1436021 CAGATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTATATAATATAATTTTAAA
Found at i:1436955 original size:19 final size:20
Alignment explanation
Indices: 1436919--1436964 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1436909 TTATTAATAA
1436919 AATAAAATTATAACTATTAT
1 AATAAAATTATAACTATTAT
*
1436939 TATAAAA-TATATA-TATTAT
1 AATAAAATTATA-ACTATTAT
1436958 AATAAAA
1 AATAAAA
1436965 ACATAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAAAATTATAACTATTAT
Found at i:1437320 original size:41 final size:40
Alignment explanation
Indices: 1437272--1437363 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 40
1437262 AAAATTATTT
1437272 TTATTTAAATTTAATTA-TAAATATAAAAAATATTAATAT-AA
1 TTATTTAAATTT-ATTATTAAATATAAAAAATA--AATATAAA
* * * *
1437313 TTTTTTAAAATTTTTTATTAATTATAAATAATAAATATAAA
1 TTATTT-AAATTTATTATTAAATATAAAAAATAAATATAAA
1437354 TTATTTAAAT
1 TTATTTAAAT
1437364 GACTTTAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
40 9 0.21
41 15 0.35
42 19 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (40 bp):
TTATTTAAATTTATTATTAAATATAAAAAATAAATATAAA
Found at i:1437915 original size:17 final size:17
Alignment explanation
Indices: 1437893--1437934 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1437883 CAACAAATTT
1437893 TATATAT-TCATATTAAA
1 TATATATCT-ATATTAAA
*
1437910 TATATATCTATATTTAA
1 TATATATCTATATTAAA
*
1437927 TATTTATC
1 TATATATC
1437935 AAGAATCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATCTATATTAAA
Found at i:1438361 original size:65 final size:65
Alignment explanation
Indices: 1438244--1438367 Score: 160
Period size: 65 Copynumber: 1.9 Consensus size: 65
1438234 ACATATATTC
* * * *
1438244 ATATTTAATATTTTTTTTAAAATTTAAACAATATACTTAATAAAAATAAAGTATTATATACACTT
1 ATATTTAATATTCTTTTTAAAATCTAAACAACATACTTAATAAAAATAAAGTACTATATACACTT
* * * *
1438309 ATATTTAATATTCTTTTT-AAATCTGAGCAACATTCTTAATAGAAATAGAAGTACTATAT
1 ATATTTAATATTCTTTTTAAAATCTAAACAACATACTTAATAAAAATA-AAGTACTATAT
1438368 TGTTAGGCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
64 23 0.46
65 27 0.54
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (65 bp):
ATATTTAATATTCTTTTTAAAATCTAAACAACATACTTAATAAAAATAAAGTACTATATACACTT
Found at i:1438568 original size:2 final size:2
Alignment explanation
Indices: 1438561--1438593 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1438551 CTTGCCCCAC
*
1438561 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1438594 CACCAGCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1440377 original size:22 final size:22
Alignment explanation
Indices: 1440352--1440394 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1440342 ACTACAAATC
1440352 CGATACCGATGTCA-AAAATTCT
1 CGATACCGATGT-AGAAAATTCT
*
1440374 CGATACCTATGTAGAAAATTC
1 CGATACCGATGTAGAAAATTC
1440395 ATTTTCTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (22 bp):
CGATACCGATGTAGAAAATTCT
Found at i:1444787 original size:22 final size:22
Alignment explanation
Indices: 1444747--1444788 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1444737 ATTTAAATCA
*
1444747 TTTTTAATTTAAATTATTAATT
1 TTTTTAATTTAAATAATTAATT
1444769 TTTTTAA-TTAAATAAATTAA
1 TTTTTAATTTAAAT-AATTAA
1444789 ATTAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTAATTTAAATAATTAATT
Found at i:1445208 original size:21 final size:20
Alignment explanation
Indices: 1445181--1445220 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1445171 AATTATAAAA
1445181 TTAT-TTTTAT-ATTAATATT
1 TTATATTTTATAATTAA-ATT
1445200 TTATATTTTATAATTAAATT
1 TTATATTTTATAATTAAATT
1445220 T
1 T
1445221 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATATTTTATAATTAAATT
Found at i:1445232 original size:34 final size:34
Alignment explanation
Indices: 1445194--1445258 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1445184 TTTTTATATT
*
1445194 AATATT-TTATATTTTATAATTA-AATTTAAATAAA
1 AATATTATTAT-TTTTA-AATAATAATTTAAATAAA
1445228 AATATTATTATTTTTAAATAATAATTTAAAT
1 AATATTATTATTTTTAAATAATAATTTAAAT
1445259 CGATCTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 4 0.14
34 20 0.71
35 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
AATATTATTATTTTTAAATAATAATTTAAATAAA
Found at i:1446047 original size:22 final size:23
Alignment explanation
Indices: 1446003--1446062 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
1445993 TTAACGATTG
*
1446003 ATTAATATATTATT--TATAATA
1 ATTAATATTTTATTAATATAATA
*
1446024 A-TAATATTTTATTAATATAGTA
1 ATTAATATTTTATTAATATAATA
*
1446046 ATTCATATTTT-TTAATA
1 ATTAATATTTTATTAATA
1446063 GATGAGATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 11 0.33
21 1 0.03
22 13 0.39
23 8 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTAATATTTTATTAATATAATA
Found at i:1447245 original size:17 final size:17
Alignment explanation
Indices: 1447223--1447261 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1447213 TTTGAATTTA
1447223 AAATAAATATTAAATAT
1 AAATAAATATTAAATAT
* * *
1447240 AAATAATTATTTAATTT
1 AAATAAATATTAAATAT
1447257 AAATA
1 AAATA
1447262 TATTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATAAATATTAAATAT
Found at i:1447311 original size:25 final size:24
Alignment explanation
Indices: 1447277--1447324 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1447267 ATTTTTTTAT
1447277 ATATTTAAATA-ATTATATTAATATC
1 ATATTTAAATATA-TA-ATTAATATC
1447302 ATATTTAAATATATAATTAATAT
1 ATATTTAAATATATAATTAATAT
1447325 AATTATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 13 0.59
26 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTTAAATATATAATTAATATC
Found at i:1447331 original size:25 final size:25
Alignment explanation
Indices: 1447277--1447339 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
1447267 ATTTTTTTAT
*
1447277 ATATTTAAATAATTATATTAATATC
1 ATATTTAAATAATTATATTAATATA
1447302 ATATTTAAAT-A-TATAATTAATATA
1 ATATTTAAATAATTAT-ATTAATATA
1447326 AT-TATTAAA-AATTA
1 ATAT-TTAAATAATTA
1447340 AAAATTTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
23 4 0.12
24 17 0.52
25 12 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATTTAAATAATTATATTAATATA
Found at i:1447353 original size:39 final size:40
Alignment explanation
Indices: 1447304--1447383 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
1447294 TTAATATCAT
1447304 ATTTAAATATATAATTAATATAATTA-TTAAAAATTAAAA
1 ATTTAAATATATAATTAATATAATTATTTAAAAATTAAAA
* *
1447343 ATTTAGATATATAATTAATATAATTATTTAAATATTAAAA
1 ATTTAAATATATAATTAATATAATTATTTAAAAATTAAAA
1447383 A
1 A
1447384 AAATTGAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 25 0.66
40 13 0.34
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (40 bp):
ATTTAAATATATAATTAATATAATTATTTAAAAATTAAAA
Found at i:1447534 original size:17 final size:17
Alignment explanation
Indices: 1447509--1447544 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1447499 TTAAATATAA
1447509 AATAAAAAATATAATAT
1 AATAAAAAATATAATAT
* *
1447526 AATATAAAATTTAATAT
1 AATAAAAAATATAATAT
1447543 AA
1 AA
1447545 ATTATTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAAAAATATAATAT
Found at i:1447578 original size:33 final size:35
Alignment explanation
Indices: 1447493--1447602 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 35
1447483 ACTTTTAAAT
* *
1447493 ATTTATTTAAATATAAAATA-AAAAATATAATATAA
1 ATTTATTT-AATATAAAATATATAAATATATTATAA
** *
1447528 TATAAAATTTAATAT-AAAT-TATTAATATATTA-AA
1 -AT-TTATTTAATATAAAATATATAAATATATTATAA
*
1447562 ATTTATTTAAATATAAAATATATAAATATTTTATAA
1 ATTTATTT-AATATAAAATATATAAATATATTATAA
1447598 ATTTA
1 ATTTA
1447603 CGAAGCTAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
32 4 0.07
33 7 0.12
34 6 0.10
35 24 0.41
36 14 0.24
37 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
ATTTATTTAATATAAAATATATAAATATATTATAA
Found at i:1447581 original size:27 final size:28
Alignment explanation
Indices: 1447515--1447599 Score: 74
Period size: 27 Copynumber: 3.1 Consensus size: 28
1447505 ATAAAATAAA
*
1447515 AAATATAATATA-ATATAAAATTTAATAT
1 AAATATAAAATATAT-TAAAATTTAATAT
* *
1447543 AAAT-TATTAATATATTAAAATTT-ATTT
1 AAATATA-AAATATATTAAAATTTAATAT
1447570 AAATATAAAATATA-TAAATATTT--TAT
1 AAATATAAAATATATTAAA-ATTTAATAT
1447596 AAAT
1 AAAT
1447600 TTACGAAGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 10 0.21
27 19 0.40
28 17 0.35
29 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATATAAAATATATTAAAATTTAATAT
Found at i:1448178 original size:20 final size:20
Alignment explanation
Indices: 1448148--1448185 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1448138 TATGATTATT
1448148 ATAATTATAAAT-TAAAAAA
1 ATAATTATAAATATAAAAAA
1448167 ATAATATATAAATATAAAA
1 ATAAT-TATAAATATAAAA
1448186 TTATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAATTATAAATATAAAAAA
Found at i:1448384 original size:2 final size:2
Alignment explanation
Indices: 1448379--1448417 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1448369 TATGTGTGTC
* * *
1448379 TA TA TA CA TA CA TA TT 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 T
1448418 CCGAAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1448832 original size:19 final size:19
Alignment explanation
Indices: 1448810--1448851 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1448800 TATTTAATTT
1448810 TAAAAATAAATATTAAATA
1 TAAAAATAAATATTAAATA
* * *
1448829 TAAATATATATTTTAAATA
1 TAAAAATAAATATTAAATA
1448848 -AAAA
1 TAAAA
1448852 CTCTTAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAATAAATATTAAATA
Found at i:1449588 original size:30 final size:31
Alignment explanation
Indices: 1449545--1449605 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
1449535 TATCTAATAC
*
1449545 AAAAGTTTATAAAATTATTTTA-AATAATATT
1 AAAAGTTTATAAAAAT-TTTTATAATAATATT
* *
1449576 AAAA-TTTTTAAAAATTTTTATATTAATATT
1 AAAAGTTTATAAAAATTTTTATAATAATATT
1449606 TATAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 5 0.19
30 17 0.65
31 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
AAAAGTTTATAAAAATTTTTATAATAATATT
Found at i:1449910 original size:30 final size:28
Alignment explanation
Indices: 1449876--1449957 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 28
1449866 TTTGAATATT
1449876 TATTTAAAATAAAATTATATATTTATATCA
1 TATTT-AAATAAAATT-TATATTTATATCA
* * *
1449906 TATTTAAATAAATTTTTAATATTTATTTTA
1 TATTTAAATAAA-ATTT-ATATTTATATCA
1449936 TATTTAAATAAAATTT-TATTTA
1 TATTTAAATAAAATTTATATTTA
1449958 AATTCAAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 6 0.13
29 11 0.24
30 29 0.63
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (28 bp):
TATTTAAATAAAATTTATATTTATATCA
Found at i:1449957 original size:22 final size:24
Alignment explanation
Indices: 1449927--1449971 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
1449917 ATTTTTAATA
* *
1449927 TTTATTTTATATTTAAAT-AAAAT
1 TTTATTTTAAATTCAAATCAAAAT
1449950 TTTA-TTTAAATTCAAATCAAAA
1 TTTATTTTAAATTCAAATCAAAA
1449972 AGTAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTATTTTAAATTCAAATCAAAAT
Found at i:1450587 original size:23 final size:22
Alignment explanation
Indices: 1450538--1450593 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
1450528 TAAATAAGAT
1450538 ATTTATATTAAAAAAATTATATAA
1 ATTTA-ATT-AAAAAATTATATAA
* *
1450562 ATTTAATTAAAAGATTATATTTA
1 ATTTAATTAAAAAATTATA-TAA
1450585 ATTTAATTA
1 ATTTAATTA
1450594 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 10 0.34
23 14 0.48
24 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTAATTAAAAAATTATATAA
Found at i:1450596 original size:18 final size:18
Alignment explanation
Indices: 1450552--1450611 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
1450542 ATATTAAAAA
* *
1450552 AATTATATAAATTTAATTA
1 AATTAT-TATATTTAATTT
**
1450571 AAAGATTATATTTAATTT
1 AATTATTATATTTAATTT
* *
1450589 AATTATTAT-TTAAAATT
1 AATTATTATATTTAATTT
1450606 AATTAT
1 AATTAT
1450612 AAATAATCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
17 12 0.36
18 17 0.52
19 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATTATTATATTTAATTT
Found at i:1450670 original size:18 final size:18
Alignment explanation
Indices: 1450630--1450675 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1450620 ATAATTTAAG
1450630 TATTTTAATAAATAATTT
1 TATTTTAATAAATAATTT
* * *
1450648 AATTTTAATATATATTTT
1 TATTTTAATAAATAATTT
1450666 TATTTATAAT
1 TATTT-TAAT
1450676 TGATATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTAATAAATAATTT
Found at i:1450771 original size:15 final size:15
Alignment explanation
Indices: 1450746--1450817 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 15
1450736 ATTGAATACA
1450746 TTTAAATAATTTAAAT
1 TTTAAA-AATTTAAAT
1450762 TTTAAAAA-TTAAAT
1 TTTAAAAATTTAAAT
*
1450776 TAAATTAAATTAAATTAAAT
1 T---TTAAA--AATTTAAAT
*
1450796 TTT--AAATTTTAAT
1 TTTAAAAATTTAAAT
1450809 TTTAAAAAT
1 TTTAAAAAT
1450818 AAAATTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
13 10 0.22
14 7 0.15
15 7 0.15
16 6 0.13
17 7 0.15
19 2 0.04
20 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAAAATTTAAAT
Found at i:1450777 original size:5 final size:5
Alignment explanation
Indices: 1450767--1450796 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1450757 TAAATTTTAA
1450767 AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
1450797 TTAAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:1452972 original size:20 final size:20
Alignment explanation
Indices: 1452948--1453002 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
1452938 ATTATATGAC
1452948 TTTAATTTAAATTATTATTTA
1 TTTAATTTAAATTATT-TTTA
*
1452969 -TTAA-TAAAATATATTTTTA
1 TTTAATTTAAAT-TATTTTTA
1452988 TTTAAATTT-AATTAT
1 TTT-AATTTAAATTAT
1453003 AAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
19 9 0.32
20 13 0.46
21 5 0.18
22 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTTAAATTATTTTTA
Found at i:1453309 original size:14 final size:14
Alignment explanation
Indices: 1453292--1453353 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
1453282 TTTTTAATAA
*
1453292 AAAAATTATAATTT
1 AAAAATTAAAATTT
*
1453306 AAAAATAAAAAATTAT
1 AAAAAT-TAAAATT-T
*
1453322 AAATATTAAAATTT
1 AAAAATTAAAATTT
*
1453336 AAAATTTAAAATTT
1 AAAAATTAAAATTT
1453350 AAAA
1 AAAA
1453354 TTATTAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 23 0.57
15 11 0.28
16 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAATTAAAATTT
Found at i:1453315 original size:21 final size:21
Alignment explanation
Indices: 1453291--1453375 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
1453281 TTTTTTAATA
1453291 AAAAAATTATAATTTAAAAAT
1 AAAAAATTATAATTTAAAAAT
*
1453312 AAAAAATTATAAATATTAAAATT
1 AAAAAATTAT-AAT-TTAAAAAT
* * * *
1453335 TAAAATTTAAAATTTAAAATT
1 AAAAAATTATAATTTAAAAAT
** *
1453356 ATTAAA-TATTATTTAAAAAT
1 AAAAAATTATAATTTAAAAAT
1453376 GATTAAATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
20 11 0.22
21 20 0.39
22 6 0.12
23 14 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAAATTATAATTTAAAAAT
Found at i:1453325 original size:7 final size:7
Alignment explanation
Indices: 1453292--1453353 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
1453282 TTTTTAATAA
1453292 AAAAATT
1 AAAAATT
* *
1453299 ATAATTT
1 AAAAATT
*
1453306 AAAAATA
1 AAAAATT
1453313 AAAAATT
1 AAAAATT
1453320 ATAAATATT
1 A-AAA-ATT
*
1453329 AAAATTT
1 AAAAATT
*
1453336 AAAATTT
1 AAAAATT
*
1453343 AAAATTT
1 AAAAATT
1453350 AAAA
1 AAAA
1453354 TTATTAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
7 36 0.78
8 6 0.13
9 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
AAAAATT
Found at i:1453335 original size:30 final size:30
Alignment explanation
Indices: 1453296--1453361 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1453286 TAATAAAAAA
*
1453296 ATTATAATTTAAAAATAAAAAATTATAAA-T
1 ATTAAAATTTAAAAATAAAAAATTA-AAATT
* * *
1453326 ATTAAAATTTAAAATTTAAAATTTAAAATT
1 ATTAAAATTTAAAAATAAAAAATTAAAATT
1453356 ATTAAA
1 ATTAAA
1453362 TATTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
ATTAAAATTTAAAAATAAAAAATTAAAATT
Found at i:1453366 original size:7 final size:7
Alignment explanation
Indices: 1453301--1453355 Score: 65
Period size: 7 Copynumber: 7.6 Consensus size: 7
1453291 AAAAAATTAT
1453301 AATTTAA
1 AATTTAA
* *
1453308 AAATAAA
1 AATTTAA
*
1453315 AAATTATA
1 AATTTA-A
1453323 AATATTAA
1 AAT-TTAA
1453331 AATTTAA
1 AATTTAA
1453338 AATTTAA
1 AATTTAA
1453345 AATTTAA
1 AATTTAA
1453352 AATT
1 AATT
1453356 ATTAAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 32 0.76
8 7 0.17
9 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATTTAA
Found at i:1453371 original size:20 final size:21
Alignment explanation
Indices: 1453346--1453384 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1453336 AAAATTTAAA
*
1453346 ATTT-AAAATTATTAAATATT
1 ATTTAAAAATGATTAAATATT
1453366 ATTTAAAAATGATTAAATA
1 ATTTAAAAATGATTAAATA
1453385 AATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
ATTTAAAAATGATTAAATATT
Found at i:1454125 original size:50 final size:48
Alignment explanation
Indices: 1454037--1454131 Score: 111
Period size: 50 Copynumber: 1.9 Consensus size: 48
1454027 AATTACAATT
* * *
1454037 TATTAATAAAAATATATTTTATTTAAATTTAATTATAAAATTAAAAAA
1 TATTAATAAAAATATATTTTATATAAATTTAATAATAAAAATAAAAAA
**
1454085 TATTAATATAAAATAATATTTTA-ATATTTTTAAATAATAAAAATAAA
1 TATTAATA-AAAAT-ATATTTTATATAAATTT-AATAATAAAAATAAA
1454132 TTATTAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
48 8 0.21
49 10 0.26
50 21 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (48 bp):
TATTAATAAAAATATATTTTATATAAATTTAATAATAAAAATAAAAAA
Found at i:1455545 original size:30 final size:30
Alignment explanation
Indices: 1455510--1455605 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 30
1455500 ATATTAAGGA
*
1455510 TTTATTTAAATATAAATCAAAAGTTAAAAG
1 TTTATTTAAATATAAATTAAAAGTTAAAAG
*** * * * *
1455540 TTTATTTGGGTACAATTTAAAATTTAATAG
1 TTTATTTAAATATAAATTAAAAGTTAAAAG
* * *
1455570 CTTATTTAATTATAAATTAAATGTTAAAAG
1 TTTATTTAAATATAAATTAAAAGTTAAAAG
1455600 TTTATT
1 TTTATT
1455606 CATATGTAAA
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (30 bp):
TTTATTTAAATATAAATTAAAAGTTAAAAG
Found at i:1455818 original size:20 final size:21
Alignment explanation
Indices: 1455773--1455828 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1455763 TATGAATTTG
*
1455773 ATTAAATTTAAAATAAGTTAA
1 ATTAAATTTAAATTAAGTTAA
* *
1455794 TTTAAATTTGAATTAA-TTAA
1 ATTAAATTTAAATTAAGTTAA
1455814 ATTAAATTTAAATTA
1 ATTAAATTTAAATTA
1455829 TTATTTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTAAATTTAAATTAAGTTAA
Found at i:1457912 original size:17 final size:17
Alignment explanation
Indices: 1457890--1457922 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1457880 ATTACATAAA
*
1457890 TTAATTAAATTAAATTT
1 TTAATTAAATCAAATTT
1457907 TTAATTAAATCAAATT
1 TTAATTAAATCAAATT
1457923 ATGAACACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATTAAATCAAATTT
Found at i:1458292 original size:20 final size:21
Alignment explanation
Indices: 1458269--1458307 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1458259 TTAGTAGATT
*
1458269 AAATATCATTATTT-TATTAA
1 AAATATAATTATTTATATTAA
1458289 AAATATAATTATTTATATT
1 AAATATAATTATTTATATT
1458308 TATATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATATAATTATTTATATTAA
Found at i:1458366 original size:43 final size:41
Alignment explanation
Indices: 1458279--1458363 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 41
1458269 AAATATCATT
*
1458279 ATTTTATTAAAAATATAATTATTTATATTTATATTTATAAA
1 ATTTTATTAAAAATATAATTATTTATATTAATATTTATAAA
*
1458320 ATTTTAATTAAATAATATAATTTATTT-TATTAATAATTTTTAAA
1 ATTTT-ATTAAA-AATATAA-TTATTTATATTAAT-ATTTATAAA
1458364 TTTATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
41 5 0.13
42 6 0.16
43 13 0.34
44 14 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (41 bp):
ATTTTATTAAAAATATAATTATTTATATTAATATTTATAAA
Found at i:1459292 original size:19 final size:20
Alignment explanation
Indices: 1459270--1459308 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1459260 GATATTAATG
*
1459270 ATATATTA-AATATAAAAAT
1 ATATATTATAATAAAAAAAT
1459289 ATATATTATAATAAAAAAAT
1 ATATATTATAATAAAAAAAT
1459309 TAATTCAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATATTATAATAAAAAAAT
Found at i:1459384 original size:18 final size:18
Alignment explanation
Indices: 1459370--1459423 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
1459360 AACATATTAT
1459370 ATAAAAATAATATATTTA
1 ATAAAAATAATATATTTA
* **
1459388 ATAAAAATAAAATA-AAA
1 ATAAAAATAATATATTTA
1459405 ATAAAAAT-ATA-ATTTA
1 ATAAAAATAATATATTTA
1459421 ATA
1 ATA
1459424 TATATATGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 1 0.03
16 6 0.21
17 9 0.31
18 13 0.45
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATAATATATTTA
Found at i:1459428 original size:14 final size:14
Alignment explanation
Indices: 1459411--1459460 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1459401 AAAAATAAAA
1459411 ATATAATTTAATAT
1 ATATAATTTAATAT
1459425 ATAT-ATGATTAATAT
1 ATATAAT--TTAATAT
1459440 A-ATATATTTAATAT
1 ATATA-ATTTAATAT
1459454 AT-TAATT
1 ATATAATT
1459461 ATATTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.16
14 16 0.52
15 8 0.26
16 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
ATATAATTTAATAT
Found at i:1459451 original size:9 final size:9
Alignment explanation
Indices: 1459439--1459518 Score: 64
Period size: 9 Copynumber: 9.2 Consensus size: 9
1459429 ATGATTAATA
1459439 TAATATATT
1 TAATATATT
1459448 TAATATA-T
1 TAATATATT
1459456 TAAT-TATAT
1 TAATATAT-T
1459465 T--TATATT
1 TAATATATT
*
1459472 TAAAAT-TT
1 TAATATATT
1459480 TAATATATT
1 TAATATATT
*
1459489 TAATAATTTT
1 TAAT-ATATT
*
1459499 TATTATATT
1 TAATATATT
1459508 T-ATAATATT
1 TAAT-ATATT
1459517 TA
1 TA
1459519 TAAAACTAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
7 5 0.09
8 16 0.29
9 28 0.50
10 7 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TAATATATT
Found at i:1459463 original size:18 final size:18
Alignment explanation
Indices: 1459439--1459518 Score: 80
Period size: 18 Copynumber: 4.7 Consensus size: 18
1459429 ATGATTAATA
1459439 TAAT-ATATTTAATATAT
1 TAATAATATTTAATATAT
*
1459456 TAATTATATTT-ATAT-T
1 TAATAATATTTAATATAT
1459472 TAA-AAT-TTTAATATATT
1 TAATAATATTTAATATA-T
* *
1459489 TAATAATTTTTATTATAT
1 TAATAATATTTAATATAT
*
1459507 TTATAATATTTA
1 TAATAATATTTA
1459519 TAAAACTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
14 3 0.06
15 6 0.11
16 4 0.08
17 12 0.23
18 20 0.38
19 8 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATAATATTTAATATAT
Found at i:1459474 original size:24 final size:23
Alignment explanation
Indices: 1459432--1459490 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
1459422 TATATATATG
* *
1459432 ATTAATATA-ATATATTTAATAT
1 ATTAATATATTTATATTTAAAAT
1459454 ATTAATTATATTTATATTTAAAAT
1 ATTAA-TATATTTATATTTAAAAT
*
1459478 TTTAATATATTTA
1 ATTAATATATTTA
1459491 ATAATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.16
23 12 0.38
24 15 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTAATATATTTATATTTAAAAT
Found at i:1460135 original size:20 final size:20
Alignment explanation
Indices: 1460112--1460156 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1460102 AAATAATTTT
* *
1460112 AATATTTAGTAAATATTAAA
1 AATATTTAATAAATAATAAA
* *
1460132 AATAATTAATAATTAATAAA
1 AATATTTAATAAATAATAAA
1460152 AATAT
1 AATAT
1460157 ATTTAATTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AATATTTAATAAATAATAAA
Found at i:1460151 original size:27 final size:29
Alignment explanation
Indices: 1460086--1460176 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 29
1460076 ATTTATATAA
*
1460086 AATT-ATATATATTATAAAATAATTTTAAT
1 AATTAATAAATATTATAAAATAA-TTTAAT
* *
1460115 ATTTAGTAAATATTA-AAAATAA-TTAAT
1 AATTAATAAATATTATAAAATAATTTAAT
* **
1460142 AATTAATAAA-AATAT-ATTTAATTTAAT
1 AATTAATAAATATTATAAAATAATTTAAT
1460169 AATATAAT
1 AAT-TAAT
1460177 TTTTAATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
26 7 0.14
27 21 0.42
28 4 0.08
29 10 0.20
30 8 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (29 bp):
AATTAATAAATATTATAAAATAATTTAAT
Found at i:1460163 original size:19 final size:20
Alignment explanation
Indices: 1460128--1460170 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1460118 TAGTAAATAT
1460128 TAAAAATAATTAATAA-TTAA
1 TAAAAATAATT-ATAATTTAA
1460148 TAAAAATATATT-TAATTTAA
1 TAAAAATA-ATTATAATTTAA
1460168 TAA
1 TAA
1460171 TATAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.14
20 15 0.71
21 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAATAATTATAATTTAA
Found at i:1460546 original size:6 final size:7
Alignment explanation
Indices: 1460518--1460544 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1460508 AATTGGAATA
1460518 ATTTTTT
1 ATTTTTT
1460525 ATTTTTT
1 ATTTTTT
1460532 ATTTTTT
1 ATTTTTT
1460539 ATTTTT
1 ATTTTT
1460545 ATCAAAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:1461112 original size:14 final size:13
Alignment explanation
Indices: 1461083--1461133 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
1461073 GAAGTTCATT
*
1461083 ATTTAAAGATTTTA
1 ATTTAAA-AATTTA
1461097 ATATTAAAAATTTA
1 AT-TTAAAAATTTA
*
1461111 ATTTTAAAAAATT-
1 A-TTTAAAAATTTA
1461124 ATTTAAAAAT
1 ATTTAAAAAT
1461134 AATATATTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 8 0.25
13 1 0.03
14 17 0.53
15 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (13 bp):
ATTTAAAAATTTA
Found at i:1461348 original size:20 final size:20
Alignment explanation
Indices: 1461319--1461416 Score: 57
Period size: 18 Copynumber: 5.0 Consensus size: 20
1461309 AAATTAAAAT
1461319 ATATTATTAAAAATAATATAA
1 ATATT-TTAAAAATAATATAA
*
1461340 ATATTTTAAATTTATAATATAA
1 ATATTTTAAA--AATAATATAA
* *
1461362 AT-TATT-AACAT-ATA-AA
1 ATATTTTAAAAATAATATAA
*
1461378 A-ATTTATATAAAT-ATAT-A
1 ATATTT-TAAAAATAATATAA
*
1461396 ATATTTTAAATATAATTATAA
1 ATATTTTAAAAATAA-TATAA
1461417 TAAAATATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
16 5 0.08
17 4 0.07
18 15 0.25
19 5 0.08
20 10 0.17
21 9 0.15
22 11 0.19
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTTTAAAAATAATATAA
Found at i:1461410 original size:22 final size:21
Alignment explanation
Indices: 1461355--1461473 Score: 80
Period size: 22 Copynumber: 5.4 Consensus size: 21
1461345 TTAAATTTAT
* *
1461355 AATATAAATTATTAACATATAA
1 AATATAAA-TATAAATATATAA
**
1461377 AA-ATTTATATAAATATATAA
1 AATATAAATATAAATATATAA
* * *
1461397 TATTTTAAATATAATTATAATAA
1 -AATATAAATATAAATAT-ATAA
1461420 AATATAAATATAAATATAATAAA
1 AATATAAATATAAATAT-AT-AA
*
1461443 ATATATAAATTATTAAATTTATAA
1 A-ATATAAA-TA-TAAATATATAA
1461467 AA-ATAAA
1 AATATAAA
1461474 AAGAACTGAG
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
20 11 0.14
21 4 0.05
22 34 0.44
23 8 0.10
24 10 0.13
25 4 0.05
26 6 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATAAATATAAATATATAA
Found at i:1461417 original size:6 final size:6
Alignment explanation
Indices: 1461355--1461447 Score: 59
Period size: 6 Copynumber: 15.0 Consensus size: 6
1461345 TTAAATTTAT
* * *
1461355 AATATA AATTATTA ACATATA AAAATT TATATA AATATA TAATATTTTA
1 AATATA AA-TA-TA A-ATATA AATATA AATATA AATATA -AATA---TA
*
1461404 AATATA ATTAT- AATA-A AATATA AATATA AATAT- AATA-A AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
1461448 TAAATTATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 22
0.69 0.08 0.22
Matches are distributed among these distances:
5 15 0.22
6 32 0.47
7 9 0.13
8 5 0.07
9 5 0.07
10 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (6 bp):
AATATA
Found at i:1461444 original size:16 final size:16
Alignment explanation
Indices: 1461355--1461473 Score: 61
Period size: 16 Copynumber: 7.5 Consensus size: 16
1461345 TTAAATTTAT
*
1461355 AATATAAAT-TATTAA
1 AATATAAATATAATAA
* * *
1461370 CATATAAAAATTTATATA
1 AATATAAATA-TAATA-A
* *
1461388 AATATATAATAT-TTTA
1 AATATA-AATATAATAA
*
1461404 AATATAATTATAATAA
1 AATATAAATATAATAA
*
1461420 AATATAAATATAAATAT
1 AATATAAATAT-AATAA
1461437 AATA-AAATAT-ATAA
1 AATATAAATATAATAA
* *
1461451 ATTATTAAAT-TTATAA
1 AATA-TAAATATAATAA
1461467 AA-ATAAA
1 AATATAAA
1461474 AAGAACTGAG
Statistics
Matches: 79, Mismatches: 16, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
14 10 0.13
15 13 0.16
16 34 0.43
17 12 0.15
18 7 0.09
19 3 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATAAATATAATAA
Found at i:1461448 original size:12 final size:12
Alignment explanation
Indices: 1461412--1461450 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
1461402 TAAATATAAT
1461412 TATAATAAAATA
1 TATAATAAAATA
*
1461424 TA-AATATAA-A
1 TATAATAAAATA
1461434 TATAATAAAATA
1 TATAATAAAATA
1461446 TATAA
1 TATAA
1461451 ATTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 12 0.52
12 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TATAATAAAATA
Found at i:1461450 original size:54 final size:53
Alignment explanation
Indices: 1461300--1461461 Score: 138
Period size: 56 Copynumber: 3.0 Consensus size: 53
1461290 CAACACCTGA
* *
1461300 AATTA-AATAAAAT-TAAA-ATATAT-TATTAAAAATAATATAAATATTTTAAATT
1 AATTATAATAAAATATAAATATAAATATAAT-AAAAT-ATAT-AATATTTTAAATT
* * * * *
1461352 TATAAT-ATAAATTATTAACATATAAAAATTTATATAAATATATAATATTTTAAATAT
1 AATTATAATAAAATA-TAA-ATATAAATA-TAATA-AAATATATAATATTTTAAAT-T
1461409 AATTATAATAAAATATAAATATAAATATAATAAAATATATAA-ATTATTAAATT
1 AATTATAATAAAATATAAATATAAATATAATAAAATATATAATATT-TTAAATT
1461462 TATAAAAATA
Statistics
Matches: 87, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
52 9 0.10
53 4 0.05
54 19 0.22
55 5 0.06
56 24 0.28
57 13 0.15
58 13 0.15
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (53 bp):
AATTATAATAAAATATAAATATAAATATAATAAAATATATAATATTTTAAATT
Found at i:1465942 original size:13 final size:13
Alignment explanation
Indices: 1465924--1465948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1465914 ATTAAATATA
1465924 ATGAATATTAAAT
1 ATGAATATTAAAT
1465937 ATGAATATTAAA
1 ATGAATATTAAA
1465949 AAAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
ATGAATATTAAAT
Found at i:1470549 original size:10 final size:10
Alignment explanation
Indices: 1470534--1470605 Score: 56
Period size: 10 Copynumber: 6.6 Consensus size: 10
1470524 AATTTTTTTA
1470534 ATTTATATTT
1 ATTTATATTT
*
1470544 ATTTATATATAA
1 ATTTATAT-T-T
*
1470556 ATTTAAATTT
1 ATTTATATTT
1470566 ATTTATA-TT
1 ATTTATATTT
1470575 ATTAATATATAATT
1 ATT--TATAT--TT
1470589 ATTTATTATTT
1 ATTTA-TATTT
1470600 ATTTAT
1 ATTTAT
1470606 TTATTTTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
9 5 0.10
10 15 0.30
11 13 0.26
12 9 0.18
13 3 0.06
14 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTATATTT
Found at i:1470610 original size:15 final size:15
Alignment explanation
Indices: 1470562--1470615 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
1470552 ATAAATTTAA
1470562 ATTTATTTATATTATT
1 ATTTATTTAT-TTATT
*
1470578 AATATATAATTATTTATT
1 -AT-T-TATTTATTTATT
1470596 ATTTATTTATTTATT
1 ATTTATTTATTTATT
1470611 -TTTAT
1 ATTTAT
1470616 CTTTATGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 5 0.15
15 11 0.33
16 1 0.03
17 4 0.12
18 6 0.18
19 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTATTTATTTATT
Found at i:1476247 original size:2 final size:2
Alignment explanation
Indices: 1476240--1476265 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1476230 GTGAAACATT
1476240 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
1476266 ATTTTGTTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1477954 original size:17 final size:17
Alignment explanation
Indices: 1477934--1477969 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1477924 TATGAAAAGT
*
1477934 TTATAAATATTTTAAAA
1 TTATAAATATGTTAAAA
1477951 TTATAAATATGTTAAAA
1 TTATAAATATGTTAAAA
1477968 TT
1 TT
1477970 TATGTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTATAAATATGTTAAAA
Found at i:1478877 original size:46 final size:42
Alignment explanation
Indices: 1478827--1478916 Score: 99
Period size: 43 Copynumber: 2.0 Consensus size: 42
1478817 AAAAATCAAA
* *
1478827 TAAATTATAATATCAAATTATATAATAAAAATTATATTTATATTTT
1 TAAATTATAATAT-AAAATAT-TAA-AAAAATAATATTT-TATTTT
* * *
1478873 TAAATTTTTATATAAAATATTAAAAAAATAATATTTTTTTTT
1 TAAATTATAATATAAAATATTAAAAAAATAATATTTTATTTT
1478915 TA
1 TA
1478917 TGATTCAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
42 7 0.18
43 12 0.31
44 3 0.08
45 6 0.15
46 11 0.28
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (42 bp):
TAAATTATAATATAAAATATTAAAAAAATAATATTTTATTTT
Found at i:1480873 original size:16 final size:16
Alignment explanation
Indices: 1480852--1480882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1480842 AAACTATAAA
1480852 TAAATTAAAATTTAAT
1 TAAATTAAAATTTAAT
*
1480868 TAAATTAAATTTTAA
1 TAAATTAAAATTTAA
1480883 ATTTAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTAAAATTTAAT
Found at i:1481244 original size:17 final size:18
Alignment explanation
Indices: 1481215--1481248 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1481205 GATTTAGGTG
1481215 TTTCTTCTTCTTTTTTTT
1 TTTCTTCTTCTTTTTTTT
1481233 TTTCTT-TTCTTTTTTT
1 TTTCTTCTTCTTTTTTT
1481249 AATGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTCTTCTTCTTTTTTTT
Found at i:1482230 original size:16 final size:16
Alignment explanation
Indices: 1482125--1482254 Score: 84
Period size: 16 Copynumber: 8.0 Consensus size: 16
1482115 AACTATTATT
1482125 TTTAAA-ATAAAATAA
1 TTTAAATATAAAATAA
* *
1482140 TTAAAATATAATATAA
1 TTTAAATATAAAATAA
* **
1482156 TATAAATATATTATAAA
1 TTTAAATATAAAAT-AA
*
1482173 TTTAAATAATATAAATAC
1 TTTAAAT-ATA-AAATAA
* * *
1482191 TTT-CATTTAAAATTTA
1 TTTAAATATAAAA-TAA
* *
1482207 TATAAATATAAAATAT
1 TTTAAATATAAAATAA
**
1482223 TTTAAATATAATTTAA
1 TTTAAATATAAAATAA
*
1482239 TTTAAATATAACATAA
1 TTTAAATATAAAATAA
1482255 AATATATACA
Statistics
Matches: 85, Mismatches: 24, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
15 8 0.09
16 51 0.60
17 17 0.20
18 7 0.08
19 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAATATAAAATAA
Found at i:1483342 original size:13 final size:13
Alignment explanation
Indices: 1483324--1483353 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1483314 TTTTTTTAAA
1483324 AATATTTATATTT
1 AATATTTATATTT
*
1483337 AATATTTATGTTT
1 AATATTTATATTT
1483350 AATA
1 AATA
1483354 AATTTTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1483927 original size:9 final size:9
Alignment explanation
Indices: 1483909--1483963 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
1483899 TTATGAAAAA
*
1483909 TAATTTATT
1 TAATTAATT
1483918 TAATTAATT
1 TAATTAATT
* *
1483927 TTATTGATT
1 TAATTAATT
*
1483936 TAA-TAAGT
1 TAATTAATT
1483944 TAATTTAATT
1 TAA-TTAATT
1483954 TAATTAATT
1 TAATTAATT
1483963 T
1 T
1483964 TAAAAATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 6 0.16
9 24 0.65
10 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (9 bp):
TAATTAATT
Found at i:1484673 original size:13 final size:13
Alignment explanation
Indices: 1484655--1484689 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1484645 TTTTTTTAAA
*
1484655 AATATTTATATTT
1 AATATTTATATTC
1484668 AATATTTATATTC
1 AATATTTATATTC
1484681 AATATTTAT
1 AATATTTAT
1484690 TTAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATTTATATTC
Found at i:1484740 original size:19 final size:19
Alignment explanation
Indices: 1484716--1484757 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1484706 AGATATAATT
* *
1484716 TTTAAAATTTATTAAAAAA
1 TTTAAAAATAATTAAAAAA
*
1484735 TTTAAAAATAATTAAAATA
1 TTTAAAAATAATTAAAAAA
1484754 TTTA
1 TTTA
1484758 TATTAGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAAAAATAATTAAAAAA
Found at i:1488733 original size:19 final size:18
Alignment explanation
Indices: 1488709--1488754 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1488699 AGATATAATA
*
1488709 ATTTATTTATTCGTATTAT
1 ATTTATATATT-GTATTAT
*
1488728 ATTTATATATTTTATTAT
1 ATTTATATATTGTATTAT
1488746 ATATTATAT
1 AT-TTATAT
1488755 TTAAAAATTT
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:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTATATATTGTATTAT
Found at i:1488742 original size:28 final size:27
Alignment explanation
Indices: 1488710--1488776 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 27
1488700 GATATAATAA
* * *
1488710 TTTATTTATTCGTATTATATTTATATAT
1 TTTATTTATT-ATATTATATTTAAAAAT
1488738 TTTA-TTA-TATATTATATTTAAAAAT
1 TTTATTTATTATATTATATTTAAAAAT
1488763 TTT-TTTATTTATAT
1 TTTATTTA-TTATAT
1488777 AAATTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 20 0.61
26 1 0.03
27 8 0.24
28 4 0.12
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTATTTATTATATTATATTTAAAAAT
Found at i:1488747 original size:12 final size:12
Alignment explanation
Indices: 1488722--1488755 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1488712 TATTTATTCG
1488722 TATTATATTTATA
1 TATTATA-TTATA
*
1488735 TATTTTATTATA
1 TATTATATTATA
1488747 TATTATATT
1 TATTATATT
1488756 TAAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTATATTATA
Found at i:1492681 original size:21 final size:22
Alignment explanation
Indices: 1492652--1492697 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1492642 TGTTCAGACA
** *
1492652 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1492674 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1492695 AGT
1 AGT
1492698 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1494005 original size:25 final size:26
Alignment explanation
Indices: 1493951--1494006 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
1493941 TATTAATTTA
1493951 ATAAA-AAATATATATTTATAATAAT
1 ATAAATAAATATATATTTATAATAAT
* *
1493976 TTAAATAAATTTATA-TTATAA-ATAT
1 ATAAATAAATATATATTTATAATA-AT
1494001 ATAAAT
1 ATAAAT
1494007 TATTAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 1 0.04
25 17 0.65
26 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAATAAATATATATTTATAATAAT
Found at i:1494009 original size:20 final size:20
Alignment explanation
Indices: 1493929--1494009 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 20
1493919 TTAAATTTTA
*
1493929 TATATTATAAAT-TATTAAT
1 TATATTATAAATATATAAAT
* * *
1493948 T-TAATA-AAAAATATATAT
1 TATATTATAAATATATAAAT
* * *
1493966 T-TATAATAATTTAAATAAATT
1 TATATTATAA-ATATATAAA-T
1493987 TATATTATAAATATATAAAT
1 TATATTATAAATATATAAAT
1494007 TAT
1 TAT
1494010 TAAATTTAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 9
0.67 0.20 0.14
Matches are distributed among these distances:
17 3 0.07
18 13 0.30
19 3 0.07
20 9 0.20
21 9 0.20
22 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATTATAAATATATAAAT
Found at i:1494780 original size:14 final size:14
Alignment explanation
Indices: 1494739--1494785 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 14
1494729 TATAATTATT
* *
1494739 TTTAAAAAATAATA
1 TTTAAAAATTAAAA
1494753 TTTAATAAATTTAAAA
1 TTTAA-AAA-TTAAAA
1494769 TTTAAAAATT-AAA
1 TTTAAAAATTAAAA
1494782 TTTA
1 TTTA
1494786 TTATTTTCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 7 0.24
14 7 0.24
15 6 0.21
16 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAAAAATTAAAA
Found at i:1496099 original size:16 final size:16
Alignment explanation
Indices: 1496078--1496108 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1496068 AAACTATAAA
1496078 TAAATTAAAATTTAAT
1 TAAATTAAAATTTAAT
*
1496094 TAAATTAAATTTTAA
1 TAAATTAAAATTTAA
1496109 ATTTAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTAAAATTTAAT
Found at i:1496469 original size:16 final size:17
Alignment explanation
Indices: 1496441--1496473 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1496431 GATTTAGGTG
1496441 TTTCTTCTTCTTTTTTT
1 TTTCTTCTTCTTTTTTT
1496458 TTTCTT-TTCTTTTTTT
1 TTTCTTCTTCTTTTTTT
1496474 AATGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTCTTCTTCTTTTTTT
Found at i:1497383 original size:21 final size:23
Alignment explanation
Indices: 1497359--1497407 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1497349 TATTTTTAAA
1497359 ATAAAATAAT-TAAA-ATATAAT
1 ATAAAATAATATAAATATATAAT
* *
1497380 ATAATATAATATAAATATATATT
1 ATAAAATAATATAAATATATAAT
1497403 ATAAA
1 ATAAA
1497408 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 10 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAAAATAATATAAATATATAAT
Found at i:1497421 original size:5 final size:5
Alignment explanation
Indices: 1497372--1497421 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
1497362 AAATAATTAA
* *
1497372 AATAT AATAT AATAT AATAT AA-AT -ATAT ATTAT AAATTT AA-AT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
1497420 AA
1 AA
1497422 ATATTCTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 1 0.03
4 7 0.19
5 26 0.70
6 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:1497456 original size:32 final size:32
Alignment explanation
Indices: 1497398--1497458 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1497388 ATATAAATAT
1497398 ATATTATAAATTTAAATAATATAAATATTCTC
1 ATATTATAAATTTAAATAATATAAATATTCTC
* *
1497430 ATATTA-AAATTTATATAATGTAAAATATT
1 ATATTATAAATTTAAATAATAT-AAATATT
1497459 TTAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (32 bp):
ATATTATAAATTTAAATAATATAAATATTCTC
Found at i:1499986 original size:18 final size:19
Alignment explanation
Indices: 1499953--1499988 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1499943 AAATATAATT
*
1499953 TTTAAAATTTATTAAAAAA
1 TTTAAAATTAATTAAAAAA
1499972 TTTAAAA-TAATTAAAAA
1 TTTAAAATTAATTAAAAA
1499989 TATATATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTAAAATTAATTAAAAAA
Found at i:1501947 original size:23 final size:24
Alignment explanation
Indices: 1501916--1501969 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1501906 ATAATAAATA
*
1501916 ATAAGTTTTTT-TATTAAATT-ATT
1 ATAAATTTTTTATATT-AATTCATT
1501939 ATAAATTTTTTATATTAATTCATT
1 ATAAATTTTTTATATTAATTCATT
*
1501963 AAAAATT
1 ATAAATT
1501970 ATCAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATAAATTTTTTATATTAATTCATT
Found at i:1501950 original size:22 final size:24
Alignment explanation
Indices: 1501922--1501969 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1501912 AATAATAAGT
*
1501922 TTTTTTAT-TAAATT-ATTATAAA
1 TTTTTTATATAAATTCATTAAAAA
*
1501944 TTTTTTATATTAATTCATTAAAAA
1 TTTTTTATATAAATTCATTAAAAA
1501968 TT
1 TT
1501970 ATCAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTTTATATAAATTCATTAAAAA
Found at i:1502047 original size:15 final size:15
Alignment explanation
Indices: 1502027--1502072 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1502017 TTATTTTTTA
*
1502027 AATTTTATTAAACAT
1 AATTTTATTAAAAAT
1502042 AATTTTATTTAAAAAAT
1 AATTTTA-TT-AAAAAT
*
1502059 AATTTTTTTAAAAA
1 AATTTTATTAAAAA
1502073 AAAATAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTTATTAAAAAT
Found at i:1502074 original size:17 final size:17
Alignment explanation
Indices: 1502027--1502073 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
1502017 TTATTTTTTA
*
1502027 AATTTTA-TT-AAACAT
1 AATTTTATTTAAAAAAT
1502042 AATTTTATTTAAAAAAT
1 AATTTTATTTAAAAAAT
1502059 AATTTT-TTTAAAAAA
1 AATTTTATTTAAAAAA
1502074 AAATAACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 7 0.24
16 11 0.38
17 11 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTATTTAAAAAAT
Found at i:1502555 original size:17 final size:17
Alignment explanation
Indices: 1502533--1502568 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1502523 ATATAACAAA
*
1502533 ATTTATATTAAATTTTT
1 ATTTATATTAAATATTT
*
1502550 ATTTATATTTAATATTT
1 ATTTATATTAAATATTT
1502567 AT
1 AT
1502569 CTTGAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATATTAAATATTT
Found at i:1504281 original size:19 final size:18
Alignment explanation
Indices: 1504257--1504300 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 18
1504247 GGATATAATA
1504257 ATTTATATATTTGTATTAT
1 ATTTATATATTT-TATTAT
1504276 ATTTATATATTTTATTAT
1 ATTTATATATTTTATTAT
1504294 ATATTAT
1 AT-TTAT
1504301 TTTTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:1504298 original size:25 final size:25
Alignment explanation
Indices: 1504270--1504318 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1504260 TATATATTTG
*
1504270 TATTATATTT-ATATATTTTATTATA
1 TATTATATTTAAAATATTTT-TTATA
*
1504295 TATTATTTTTAAAATATTTTTTAT
1 TATTATATTTAAAATATTTTTTAT
1504319 TTATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTATATTTAAAATATTTTTTATA
Found at i:1504339 original size:28 final size:29
Alignment explanation
Indices: 1504279--1504340 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
1504269 GTATTATATT
* * **
1504279 TATATATTTTATTATATATTATTTTTAAA
1 TATATTTTTTATTATATATAAAATTTAAA
1504308 -ATATTTTTTATT-TATATAAAATTTAAA
1 TATATTTTTTATTATATATAAAATTTAAA
1504335 TATATT
1 TATATT
1504341 AATAATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TATATTTTTTATTATATATAAAATTTAAA
Found at i:1505225 original size:30 final size:30
Alignment explanation
Indices: 1505189--1505261 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
1505179 TATTTATATA
* * *
1505189 TTTATAATCAAATTTAAATACAGTTATTAT
1 TTTATAATAAAATTTAAATAAAATTATTAT
*
1505219 TTTATAATTAAATTTAAATAAAATTATTAT
1 TTTATAATAAAATTTAAATAAAATTATTAT
1505249 TTTA-AATAAAATT
1 TTTATAATAAAATT
1505262 ACTTTGGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 8 0.21
30 31 0.79
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (30 bp):
TTTATAATAAAATTTAAATAAAATTATTAT
Found at i:1505785 original size:2 final size:2
Alignment explanation
Indices: 1505778--1505804 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1505768 GATTTTCTTT
1505778 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
1505805 GGATTTGGCT
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:1506904 original size:16 final size:16
Alignment explanation
Indices: 1506883--1506935 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1506873 ATAAATTTAT
1506883 TAAATTTTATATATCA
1 TAAATTTTATATATCA
*
1506899 TAAATTATTAATTTATCA
1 TAAATT-TT-ATATATCA
* * *
1506917 AAAATTATATATATAA
1 TAAATTTTATATATCA
1506933 TAA
1 TAA
1506936 TTTAAATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 14 0.48
17 3 0.10
18 12 0.41
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTTATATATCA
Found at i:1506967 original size:25 final size:26
Alignment explanation
Indices: 1506917--1506967 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
1506907 TAATTTATCA
**
1506917 AAAATTATATATATAATAATTTAAAT
1 AAAATTATATATATAATAATACAAAT
1506943 AAAATTATAT-TATAA-ATATACAAAT
1 AAAATTATATATATAATA-ATACAAAT
1506968 TACTAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 1 0.05
25 11 0.50
26 10 0.45
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AAAATTATATATATAATAATACAAAT
Found at i:1508651 original size:68 final size:68
Alignment explanation
Indices: 1508542--1508675 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 68
1508532 AGTTGTGATG
* * *
1508542 TTGATGATGATGGGATGGTGGTGTAGGTGCTAGGATATGGCTGGGCTGGGTTGCTGAGGAAGTAT
1 TTGATGATGATGGGACGGTGGTGCAGGTGCTAGGATATGGCTGAGCTGGGTTGCTGAGGAAGTAT
1508607 GTA
66 GTA
1508610 TTGATGATGATGGGACGGTGGTGCAGGTGCTAGGATATGGCTGAGCTGGGTTGCTGAGGAAGTAT
1 TTGATGATGATGGGACGGTGGTGCAGGTGCTAGGATATGGCTGAGCTGGGTTGCTGAGGAAGTAT
1508675 G
66 G
1508676 GATGCTAGAG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.19, C:0.07, G:0.44, T:0.29
Consensus pattern (68 bp):
TTGATGATGATGGGACGGTGGTGCAGGTGCTAGGATATGGCTGAGCTGGGTTGCTGAGGAAGTAT
GTA
Found at i:1508749 original size:31 final size:32
Alignment explanation
Indices: 1508711--1508779 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
1508701 ATTTAGTTTG
**
1508711 TTTAAA-TTAAAAGTTAATTTAATT-AATTAAT
1 TTTAAATTTAAAA-TTAAAATAATTAAATTAAT
1508742 TTTAAATTTAAAATTAAAATAATTAAATTAAT
1 TTTAAATTTAAAATTAAAATAATTAAATTAAT
*
1508774 ATTAAA
1 TTTAAA
1508780 ATCGGTGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 15 0.45
32 18 0.55
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
TTTAAATTTAAAATTAAAATAATTAAATTAAT
Found at i:1508777 original size:20 final size:21
Alignment explanation
Indices: 1508743--1508781 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1508733 TTAATTAATT
1508743 TTAAATTTAAAATTAAAATAA
1 TTAAATTTAAAATTAAAATAA
*
1508764 TTAAA-TTAATATTAAAAT
1 TTAAATTTAAAATTAAAAT
1508782 CGGTGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAATTTAAAATTAAAATAA
Found at i:1508876 original size:27 final size:26
Alignment explanation
Indices: 1508820--1508911 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 26
1508810 TTTAAAGTTA
*
1508820 TTTTTATTTTATTTAA-TTTACATATTTT
1 TTTTTATTTTAATTAAGTTT---TATTTT
*
1508848 TTTTTATTTTAATTGAGTTTTATTATT
1 TTTTTATTTTAATTAAGTTTTATT-TT
**
1508875 TTTTTATTTTAATTAAGTTTTATTGG
1 TTTTTATTTTAATTAAGTTTTATTTT
1508901 TTTTT-TTTTAA
1 TTTTTATTTTAA
1508912 ATTTTAATCT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.11
26 9 0.16
27 25 0.44
28 14 0.25
29 3 0.05
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.71
Consensus pattern (26 bp):
TTTTTATTTTAATTAAGTTTTATTTT
Found at i:1510236 original size:25 final size:25
Alignment explanation
Indices: 1510187--1510254 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
1510177 TCATATATTC
**
1510187 ATATTATATTTATCTATTTTATTAT
1 ATATTATATTTAAATATTTTATTAT
1510212 ATATTATATTTAAAATATTTT-TTAT
1 ATATTATATTT-AAATATTTTATTAT
* * *
1510237 TTATATACATTTTAATAT
1 ATAT-TATATTTAAATAT
1510255 GTTAATAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 23 0.64
26 13 0.36
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
ATATTATATTTAAATATTTTATTAT
Found at i:1511224 original size:16 final size:17
Alignment explanation
Indices: 1511187--1511225 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1511177 GTATTTTTCG
*
1511187 AATTTATTAGATAACTT
1 AATTTATTAGATAAATT
1511204 AATTT-TTAGATAAATT
1 AATTTATTAGATAAATT
*
1511220 TATTTA
1 AATTTA
1511226 CGAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTATTAGATAAATT
Found at i:1511336 original size:14 final size:14
Alignment explanation
Indices: 1511317--1511353 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1511307 AATTTTGCAC
1511317 ATGAATACTTTTAT
1 ATGAATACTTTTAT
1511331 ATGAATACTTTTAT
1 ATGAATACTTTTAT
*
1511345 ATGAGTACT
1 ATGAATACT
1511354 AAAGCACACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (14 bp):
ATGAATACTTTTAT
Done.