Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold401
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: 1910012
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 12 of 13
Found at i:1730003 original size:19 final size:20
Alignment explanation
Indices: 1729979--1730019 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1729969 GCCATTGTAC
1729979 TTTTTTTA-TTCTTTATTCA
1 TTTTTTTATTTCTTTATTCA
*
1729998 -TTTTTTATTTCTTTATTTA
1 TTTTTTTATTTCTTTATTCA
1730017 TTT
1 TTT
1730020 CTTAAAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 7 0.37
19 10 0.53
20 2 0.11
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTTATTTCTTTATTCA
Found at i:1731319 original size:3 final size:3
Alignment explanation
Indices: 1731311--1731352 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1731301 TGGGCAAAAC
1731311 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1731353 TCTTTCTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1732180 original size:2 final size:2
Alignment explanation
Indices: 1732173--1732197 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1732163 GGGGTGTCCC
1732173 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1732198 ATGCCAAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1732954 original size:22 final size:25
Alignment explanation
Indices: 1732929--1732974 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 25
1732919 ATACTTTAAA
1732929 AATTAAATA-AT-TAT-TATATAAT
1 AATTAAATATATATATATATATAAT
1732951 AATTAAATATATATATATATATAA
1 AATTAAATATATATATATATATAA
1732975 AATGATGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 2 0.10
24 3 0.14
25 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTAAATATATATATATATATAAT
Found at i:1733640 original size:18 final size:16
Alignment explanation
Indices: 1733619--1733657 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1733609 TTTTCATTTA
*
1733619 CTTTTATTTTTGTTTTT
1 CTTTTATTTAT-TTTTT
1733636 GCTTTTATTTATTTTTT
1 -CTTTTATTTATTTTTT
1733653 CTTTT
1 CTTTT
1733658 CAAGTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 5 0.25
18 10 0.50
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (16 bp):
CTTTTATTTATTTTTT
Found at i:1735090 original size:10 final size:10
Alignment explanation
Indices: 1735075--1735113 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1735065 AGTTTAGCTC
*
1735075 ACATATACAT
1 ACATATATAT
1735085 ACATATATAT
1 ACATATATAT
*
1735095 AAATATATAT
1 ACATATATAT
*
1735105 ATATATATA
1 ACATATATA
1735114 GATTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (10 bp):
ACATATATAT
Found at i:1737408 original size:18 final size:17
Alignment explanation
Indices: 1737381--1737417 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1737371 TAAAAATATG
*
1737381 ATATATAAATTATTAAAT
1 ATATAAAAATT-TTAAAT
1737399 ATATAAAAATTTTAAAT
1 ATATAAAAATTTTAAAT
1737416 AT
1 AT
1737418 TAATATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAAAAATTTTAAAT
Found at i:1738412 original size:18 final size:18
Alignment explanation
Indices: 1738389--1738451 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 18
1738379 TTTAAATATG
1738389 AATATAATATATTTATTA
1 AATATAATATATTTATTA
1738407 AATATAACGTATTATTTATATTTA
1 AATATAA--TA-TA-TT-TA-TTA
*
1738431 AATATATTATATTTATTA
1 AATATAATATATTTATTA
1738449 AAT
1 AAT
1738452 TATAGAATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
18 13 0.34
19 2 0.05
20 4 0.11
21 4 0.11
22 4 0.11
23 2 0.05
24 9 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
AATATAATATATTTATTA
Found at i:1745396 original size:15 final size:14
Alignment explanation
Indices: 1745370--1745403 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1745360 TTAAAAATCG
*
1745370 AATTTAATAAATTT
1 AATTTAATAAATTA
1745384 AATTTATATAAATTA
1 AATTTA-ATAAATTA
1745399 AATTT
1 AATTT
1745404 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAATAAATTA
Found at i:1745418 original size:23 final size:26
Alignment explanation
Indices: 1745392--1745444 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 26
1745382 TTAATTTATA
*
1745392 TAAATTAAAT-TTTTAA-AAAAA-TT
1 TAAATTAAATATTTAAATAAAAATTT
1745415 TAAA--AAATATTTAAATAAAAATTT
1 TAAATTAAATATTTAAATAAAAATTT
1745439 TAAATT
1 TAAATT
1745445 TTAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
21 4 0.17
22 5 0.21
23 9 0.38
24 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAATTAAATATTTAAATAAAAATTT
Found at i:1748264 original size:16 final size:16
Alignment explanation
Indices: 1748239--1748269 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1748229 GATCATTATG
*
1748239 ATAAACTAAATAAAGT
1 ATAAAATAAATAAAGT
1748255 ATAAAATAAATAAAG
1 ATAAAATAAATAAAG
1748270 CCATGACATA
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:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (16 bp):
ATAAAATAAATAAAGT
Found at i:1749150 original size:18 final size:19
Alignment explanation
Indices: 1749129--1749168 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
1749119 ATATATTTAT
1749129 AATATAATAAAAA-ATATA
1 AATATAATAAAAATATATA
1749147 AATATAATAAAAATATATA
1 AATATAATAAAAATATATA
1749166 AAT
1 AAT
1749169 TATTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATAATAAAAATATATA
Found at i:1749699 original size:27 final size:30
Alignment explanation
Indices: 1749643--1749702 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1749633 TAGTTTAATT
*
1749643 TAAAATTTAAAATTTATTATTTATAAATTAA
1 TAAAATTTAAAAATTATTATTTAT-AATTAA
1749674 TAAAA-TTAAAAATTATT-TTTAT-ATTAA
1 TAAAATTTAAAAATTATTATTTATAATTAA
1749701 TA
1 TA
1749703 TTTATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.25
29 5 0.18
30 11 0.39
31 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAATTTAAAAATTATTATTTATAATTAA
Found at i:1749715 original size:22 final size:22
Alignment explanation
Indices: 1749687--1749728 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1749677 AATTAAAAAT
1749687 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1749709 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1749729 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1750421 original size:6 final size:6
Alignment explanation
Indices: 1750410--1750435 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1750400 ATTATATAAT
1750410 TTTATA TTTATA TTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA TT
1750436 ATGTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:1751068 original size:15 final size:16
Alignment explanation
Indices: 1751033--1751070 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1751023 AAAAATAATA
*
1751033 AAAATTATTTTTATAT
1 AAAATTATTTTCATAT
*
1751049 TAAATTATTTTCAT-T
1 AAAATTATTTTCATAT
1751064 AAAATTA
1 AAAATTA
1751071 CTGTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATTATTTTCATAT
Found at i:1751566 original size:21 final size:21
Alignment explanation
Indices: 1751542--1751611 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1751532 AAAAGTAGGG
1751542 TCAATTATAGATAGATTAGTA
1 TCAATTATAGATAGATTAGTA
* * * *
1751563 TCAATTACATCAAAG-GTAG-A
1 TCAATTATA-GATAGATTAGTA
*
1751583 GTCAATTATAGATGGATTAGTA
1 -TCAATTATAGATAGATTAGTA
1751605 TCAATTA
1 TCAATTA
1751612 CATCAAAGGA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
20 3 0.08
21 29 0.81
22 4 0.11
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (21 bp):
TCAATTATAGATAGATTAGTA
Found at i:1751619 original size:42 final size:42
Alignment explanation
Indices: 1751501--1751620 Score: 204
Period size: 42 Copynumber: 2.9 Consensus size: 42
1751491 AATTATTCTA
* * *
1751501 CAATTATAGACGGATTAGTATCAATTACATCAAAAGTAGGGT
1 CAATTATAGATGGATTAGTATCAATTACATCAAAGGTAGAGT
*
1751543 CAATTATAGATAGATTAGTATCAATTACATCAAAGGTAGAGT
1 CAATTATAGATGGATTAGTATCAATTACATCAAAGGTAGAGT
1751585 CAATTATAGATGGATTAGTATCAATTACATCAAAGG
1 CAATTATAGATGGATTAGTATCAATTACATCAAAGG
1751621 ATGAGTATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (42 bp):
CAATTATAGATGGATTAGTATCAATTACATCAAAGGTAGAGT
Found at i:1751627 original size:23 final size:22
Alignment explanation
Indices: 1751516--1751628 Score: 62
Period size: 21 Copynumber: 5.3 Consensus size: 22
1751506 ATAGACGGAT
*
1751516 TAGTATCAATTACATCAAAAG-
1 TAGTATCAATTACATCAAAGGA
** * * *
1751537 TAGGGTCAATTATA-GATA-GA
1 TAGTATCAATTACATCAAAGGA
1751557 TTAGTATCAATTACATCAAAGG-
1 -TAGTATCAATTACATCAAAGGA
*
1751579 TAG-AGTCAATT--AT-AGATGGA
1 TAGTA-TCAATTACATCA-AAGGA
1751599 TTAGTATCAATTACATCAAAGGA
1 -TAGTATCAATTACATCAAAGGA
1751622 TGAGTAT
1 T-AGTAT
1751629 TTTAACTTTA
Statistics
Matches: 67, Mismatches: 12, Indels: 24
0.65 0.12 0.23
Matches are distributed among these distances:
18 1 0.01
19 6 0.09
20 3 0.04
21 40 0.60
22 4 0.06
23 12 0.18
24 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.31
Consensus pattern (22 bp):
TAGTATCAATTACATCAAAGGA
Found at i:1752244 original size:35 final size:36
Alignment explanation
Indices: 1752159--1752244 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 36
1752149 ATTTGTTAAA
* * *
1752159 AATAAAATTATTTA-TATTTATTTTTTAAAAAATTT
1 AATAAAATTATATATTATTTATTTATTAAAAAATAT
*
1752194 AATAAAA-TA-ATATTATTTAATTTATT-AATAATAT
1 AATAAAATTATATATTATTT-ATTTATTAAAAAATAT
1752228 -ATAAAATTATATATTAT
1 AATAAAATTATATATTAT
1752245 CAATGTATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 8 0.19
34 15 0.35
35 20 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
AATAAAATTATATATTATTTATTTATTAAAAAATAT
Found at i:1753598 original size:15 final size:15
Alignment explanation
Indices: 1753578--1753608 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1753568 TTAGCAGTAG
1753578 ACGCATCTAACTATT
1 ACGCATCTAACTATT
*
1753593 ACGCATCTAATTATT
1 ACGCATCTAACTATT
1753608 A
1 A
1753609 GATAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (15 bp):
ACGCATCTAACTATT
Found at i:1753644 original size:20 final size:20
Alignment explanation
Indices: 1753621--1753754 Score: 93
Period size: 20 Copynumber: 6.8 Consensus size: 20
1753611 TAATTTTTAA
1753621 TATTTATATTATATTTATAT
1 TATTTATATTATATTTATAT
1753641 TATTTATATTATAATTT-TAT
1 TATTTATATTAT-ATTTATAT
1753661 T-TATTAT-TGTATAAATTTATAT
1 TAT-TTATAT-TAT--ATTTATAT
* * *
1753683 AATTTTTAATATA-TTA-AT
1 TATTTATATTATATTTATAT
* * *
1753701 AATTTATATTATATATTTTAA
1 TATTTATATTATAT-TTATAT
**
1753722 TATTTATACCATATTTAT-T
1 TATTTATATTATATTTATAT
1753741 T-TTTATATTATATT
1 TATTTATATTATATT
1753755 ATTTTATATT
Statistics
Matches: 90, Mismatches: 14, Indels: 22
0.71 0.11 0.17
Matches are distributed among these distances:
18 24 0.27
19 6 0.07
20 29 0.32
21 21 0.23
22 9 0.10
23 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (20 bp):
TATTTATATTATATTTATAT
Found at i:1753761 original size:10 final size:10
Alignment explanation
Indices: 1753624--1753799 Score: 62
Period size: 9 Copynumber: 18.6 Consensus size: 10
1753614 TTTTTAATAT
1753624 TTATATTATA
1 TTATATTATA
1753634 TTTATATTAT-
1 -TTATATTATA
1753644 TTATATTATAA
1 TTATATTAT-A
*
1753655 TTTTATT-TA
1 TTATATTATA
1753664 TTAT-TGTATA
1 TTATAT-TATA
*
1753674 -AAT-TTATA
1 TTATATTATA
* *
1753682 TAAT-TTTTA
1 TTATATTATA
*
1753691 ATATATTA-A
1 TTATATTATA
*
1753700 TAAT-TTATA
1 TTATATTATA
*
1753709 TTATA-TATT
1 TTATATTATA
1753718 TTAATATTTATA
1 TT-ATA-TTATA
**
1753730 CCATATT-TA
1 TTATATTATA
*
1753739 TT-TTTTATA
1 TTATATTATA
*
1753748 TTATATTATT
1 TTATATTATA
1753758 TTATATT-TCA
1 TTATATTAT-A
*
1753768 TTAAAATT-T-
1 TT-ATATTATA
1753777 TTATATTA-A
1 TTATATTATA
1753786 TTATA-TAT-
1 TTATATTATA
1753794 TTATAT
1 TTATAT
1753800 CGTTATGCAA
Statistics
Matches: 124, Mismatches: 22, Indels: 40
0.67 0.12 0.22
Matches are distributed among these distances:
8 22 0.18
9 52 0.42
10 24 0.19
11 23 0.19
12 3 0.02
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.61
Consensus pattern (10 bp):
TTATATTATA
Found at i:1753770 original size:15 final size:14
Alignment explanation
Indices: 1753615--1753770 Score: 55
Period size: 13 Copynumber: 11.0 Consensus size: 14
1753605 ATTAGATAAT
1753615 TTTTAATATTTA-TA
1 TTTT-ATATTTATTA
*
1753629 TTATAT-TTATATTA
1 TTTTATATT-TATTA
1753643 -TTTATA-TTA-TA
1 TTTTATATTTATTA
*
1753654 ATTT-TATTTATTA
1 TTTTATATTTATTA
*
1753667 TTGTATAAATTTATATAA
1 TT-T-TATATTTAT-T-A
*
1753685 TTTTTAATATATTAATA
1 -TTTT-ATAT-TTATTA
*
1753702 ATTTATA-TTATATA
1 TTTTATATTTAT-TA
1753716 TTTTAATATTTA-TA
1 TTTT-ATATTTATTA
**
1753730 --CCATATTTATT-
1 TTTTATATTTATTA
1753741 TTTTATATTATATTA
1 TTTTATATT-TATTA
1753756 TTTTATATTTCATTA
1 TTTTATATTT-ATTA
1753771 AAATTTTTAT
Statistics
Matches: 106, Mismatches: 13, Indels: 45
0.65 0.08 0.27
Matches are distributed among these distances:
11 11 0.10
12 11 0.10
13 20 0.19
14 18 0.17
15 20 0.19
16 12 0.11
17 3 0.03
18 6 0.06
19 5 0.05
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.62
Consensus pattern (14 bp):
TTTTATATTTATTA
Found at i:1757524 original size:2 final size:2
Alignment explanation
Indices: 1757517--1757562 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1757507 AAAATTCTGA
1757517 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
1757559 AT AT
1 AT AT
1757563 CCAGTGTCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1759509 original size:24 final size:23
Alignment explanation
Indices: 1759444--1759512 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
1759434 TACAAATTTA
*
1759444 TTAAATAAAAAATTTATTAAA-AT
1 TTAAATTAAAAA-TTATTAAATAT
*
1759467 TTAAATTATTAAATTATTAAATAT
1 TTAAATTA-AAAATTATTAAATAT
**
1759491 TTATTTTAAAAATTAATTAAAT
1 TTAAATTAAAAATT-ATTAAAT
1759513 TAAATTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAAATTAAAAATTATTAAATAT
Found at i:1759519 original size:23 final size:22
Alignment explanation
Indices: 1759451--1759519 Score: 52
Period size: 23 Copynumber: 3.0 Consensus size: 22
1759441 TTATTAAATA
1759451 AAAAATTTATTAAAATTTAAATTATT
1 AAAAA-TTATT-AAA-TTAAATT-TT
**
1759477 --AAATTATTAAATATTTATTTT
1 AAAAATTATTAAAT-TAAATTTT
1759498 AAAAATTAATTAAATTAAATTT
1 AAAAATT-ATTAAATTAAATTT
1759520 AAATTTAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
21 3 0.09
22 7 0.20
23 15 0.43
24 10 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAAATTATTAAATTAAATTTT
Found at i:1761285 original size:16 final size:17
Alignment explanation
Indices: 1761266--1761312 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 17
1761256 TTTTAAGATA
1761266 TTATTTTAAATATTT-T
1 TTATTTTAAATATTTAT
1761282 TTATTATTAAA-ATTTAT
1 TTATT-TTAAATATTTAT
1761299 TTAATTTATAAATA
1 TT-ATTT-TAAATA
1761313 ATAATTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.35
17 9 0.35
18 7 0.27
19 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTTTAAATATTTAT
Found at i:1762261 original size:16 final size:18
Alignment explanation
Indices: 1762242--1762349 Score: 70
Period size: 17 Copynumber: 6.3 Consensus size: 18
1762232 ATTTATTTAT
1762242 TTTTATATTTA-A-AATA
1 TTTTATATTTATATAATA
*
1762258 TTTTATTTTTATATAATA
1 TTTTATATTTATATAATA
* * *
1762276 TTTGATA--TGT-CAATA
1 TTTTATATTTATATAATA
*
1762291 CTTTATA-TTATATAA-A
1 TTTTATATTTATATAATA
*
1762307 TTTTAAAATATTTATATTATA
1 TTTT---ATATTTATATAATA
*
1762328 TTTTAT-TTTATATTATA
1 TTTTATATTTATATAATA
1762345 TTTTA
1 TTTTA
1762350 ATTATATTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
15 9 0.12
16 18 0.25
17 19 0.26
18 11 0.15
19 3 0.04
20 7 0.10
21 5 0.07
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTATATTTATATAATA
Found at i:1762338 original size:12 final size:12
Alignment explanation
Indices: 1762317--1762368 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
1762307 TTTTAAAATA
*
1762317 TTTATATTATAT
1 TTTATTTTATAT
1762329 TTTATTTTATAT
1 TTTATTTTATAT
*
1762341 TATATTTTA-AT
1 TTTATTTTATAT
*
1762352 TATATTTTTATAT
1 TTTA-TTTTATAT
1762365 TTTA
1 TTTA
1762369 AAATAATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
11 6 0.17
12 24 0.69
13 5 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATTTTATAT
Found at i:1762339 original size:17 final size:17
Alignment explanation
Indices: 1762317--1762368 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
1762307 TTTTAAAATA
1762317 TTTATATTATATTTTAT
1 TTTATATTATATTTTAT
1762334 TTTATATTATATTTTAAT
1 TTTATATTATATTTT-AT
* *
1762352 TATATTTTTATATTTTA
1 TTTA-TATTATATTTTA
1762369 AAATAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 15 0.48
18 6 0.19
19 10 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATATTATATTTTAT
Found at i:1767124 original size:30 final size:26
Alignment explanation
Indices: 1767080--1767150 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 26
1767070 AAAAAGTCAT
* *
1767080 ATTTTTTTA-ATATTTTATTGCCTTTATC
1 ATTTTTTTATTTATTTTATT--CTTTA-A
1767108 ATTTTTTTACTTTATTTTATTCTTTAA
1 ATTTTTTTA-TTTATTTTATTCTTTAA
1767135 ATTTTTTTATTTATTT
1 ATTTTTTTATTTATTT
1767151 AAATATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 7 0.18
27 9 0.23
28 14 0.36
30 9 0.23
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.70
Consensus pattern (26 bp):
ATTTTTTTATTTATTTTATTCTTTAA
Found at i:1767993 original size:255 final size:255
Alignment explanation
Indices: 1767542--1768054 Score: 1026
Period size: 255 Copynumber: 2.0 Consensus size: 255
1767532 TGGTGAAAAG
1767542 TTAGAATTTACACTCAATCTAGTTAATGAAAAACAAAAACGAAAGGAATGGAAAGAAAAATAAAA
1 TTAGAATTTACACTCAATCTAGTTAATGAAAAACAAAAACGAAAGGAATGGAAAGAAAAATAAAA
1767607 ATAAATGTCTTAGGCCTCTTAATTAGTATCCATTTCAATATCTTAATCAGTCAATAACTCTATTA
66 ATAAATGTCTTAGGCCTCTTAATTAGTATCCATTTCAATATCTTAATCAGTCAATAACTCTATTA
1767672 TTTAGATTATTTTGTTAGACCAAAGCTTCAGTTTATGATCGTCCAAGCAAGCAGGAATTTAAGTG
131 TTTAGATTATTTTGTTAGACCAAAGCTTCAGTTTATGATCGTCCAAGCAAGCAGGAATTTAAGTG
1767737 AATAATGAACTAACCTCATAAAAAATATTACAATTTAATGAGATTTGATATTCAATTTAC
196 AATAATGAACTAACCTCATAAAAAATATTACAATTTAATGAGATTTGATATTCAATTTAC
1767797 TTAGAATTTACACTCAATCTAGTTAATGAAAAACAAAAACGAAAGGAATGGAAAGAAAAATAAAA
1 TTAGAATTTACACTCAATCTAGTTAATGAAAAACAAAAACGAAAGGAATGGAAAGAAAAATAAAA
1767862 ATAAATGTCTTAGGCCTCTTAATTAGTATCCATTTCAATATCTTAATCAGTCAATAACTCTATTA
66 ATAAATGTCTTAGGCCTCTTAATTAGTATCCATTTCAATATCTTAATCAGTCAATAACTCTATTA
1767927 TTTAGATTATTTTGTTAGACCAAAGCTTCAGTTTATGATCGTCCAAGCAAGCAGGAATTTAAGTG
131 TTTAGATTATTTTGTTAGACCAAAGCTTCAGTTTATGATCGTCCAAGCAAGCAGGAATTTAAGTG
1767992 AATAATGAACTAACCTCATAAAAAATATTACAATTTAATGAGATTTGATATTCAATTTAC
196 AATAATGAACTAACCTCATAAAAAATATTACAATTTAATGAGATTTGATATTCAATTTAC
1768052 TTA
1 TTA
1768055 TATTTAAATA
Statistics
Matches: 258, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
255 258 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (255 bp):
TTAGAATTTACACTCAATCTAGTTAATGAAAAACAAAAACGAAAGGAATGGAAAGAAAAATAAAA
ATAAATGTCTTAGGCCTCTTAATTAGTATCCATTTCAATATCTTAATCAGTCAATAACTCTATTA
TTTAGATTATTTTGTTAGACCAAAGCTTCAGTTTATGATCGTCCAAGCAAGCAGGAATTTAAGTG
AATAATGAACTAACCTCATAAAAAATATTACAATTTAATGAGATTTGATATTCAATTTAC
Found at i:1768176 original size:20 final size:21
Alignment explanation
Indices: 1768138--1768179 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1768128 AACACTTAAA
1768138 AATAATCTCAACTTACAAATAC
1 AATAATCTCAAC-TACAAATAC
1768160 AATAATCTCAA-TACAAATAC
1 AATAATCTCAACTACAAATAC
1768180 CAAAAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (21 bp):
AATAATCTCAACTACAAATAC
Found at i:1770486 original size:21 final size:20
Alignment explanation
Indices: 1770441--1770488 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1770431 ATGAATTTAT
*
1770441 ATATTATAAAATATTATAATT
1 ATATT-TAAAATATTATAATA
*
1770462 ATATTTAAAATATTTTATATA
1 ATATTTAAAATATTATA-ATA
1770483 ATATTT
1 ATATTT
1770489 TAATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTTAAAATATTATAATA
Found at i:1770506 original size:20 final size:21
Alignment explanation
Indices: 1770440--1770506 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
1770430 GATGAATTTA
*
1770440 TATATTATAAAATATTATA-AT
1 TATATT-TAAAATATTTTAGAT
*
1770461 TATATTTAAAATATTTTATAT
1 TATATTTAAAATATTTTAGAT
* * *
1770482 AATATTT-TAATTTTTTAGAT
1 TATATTTAAAATATTTTAGAT
1770502 TATAT
1 TATAT
1770507 AAATGTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (21 bp):
TATATTTAAAATATTTTAGAT
Found at i:1770977 original size:2 final size:2
Alignment explanation
Indices: 1770972--1771003 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1770962 ACACACACAC
1770972 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
1771004 TATCAAATCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1771152 original size:6 final size:6
Alignment explanation
Indices: 1771141--1771169 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1771131 ATAATAATTC
1771141 AAAAGA AAAAGA AAAAGA AAAA-A AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1771170 GGTTTAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:1773066 original size:14 final size:13
Alignment explanation
Indices: 1773032--1773074 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1773022 AAAATTTTTT
1773032 TATATAAATTTAA
1 TATATAAATTTAA
1773045 T-TATAAATATTAA
1 TATATAAAT-TTAA
*
1773058 TATAAAAATTTTAA
1 TATATAAA-TTTAA
1773072 TAT
1 TAT
1773075 TATTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 7 0.27
13 6 0.23
14 12 0.46
15 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATAAATTTAA
Found at i:1773723 original size:2 final size:2
Alignment explanation
Indices: 1773716--1773744 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1773706 AACTATGTAC
1773716 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
1773745 TGACGTCCCT
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:1776817 original size:15 final size:15
Alignment explanation
Indices: 1776797--1776828 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1776787 GCTTTCGATA
1776797 TTGCTTTTCTCAAAG
1 TTGCTTTTCTCAAAG
*
1776812 TTGCTTTTTTCAAAG
1 TTGCTTTTCTCAAAG
1776827 TT
1 TT
1776829 TTCAGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (15 bp):
TTGCTTTTCTCAAAG
Found at i:1780459 original size:72 final size:72
Alignment explanation
Indices: 1780324--1780464 Score: 178
Period size: 72 Copynumber: 2.0 Consensus size: 72
1780314 TTATACTATC
* * * *
1780324 AGATTCATCTTCACAACCCTCATTCTCTGCAGTATCATTCTCAACAGTTTGATGTTCTCTGTAAT
1 AGATTCATCTTCACAACCCTCATTCTCTGCAGCATCATTCTCAACAGTTTGATATTCTATGTAAC
1780389 CCTTATA
66 CCTTATA
* * * *
1780396 AGATTCAT-TTCCATAACTCTCGTTCTCTGCAGCATCATTCTCGACAGTCTT-ATATTCTATGTA
1 AGATTCATCTT-CACAACCCTCATTCTCTGCAGCATCATTCTCAACAGT-TTGATATTCTATGTA
1780459 ACCCTT
64 ACCCTT
1780465 GTTCTCCACA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 2 0.03
72 55 0.93
73 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (72 bp):
AGATTCATCTTCACAACCCTCATTCTCTGCAGCATCATTCTCAACAGTTTGATATTCTATGTAAC
CCTTATA
Found at i:1780507 original size:48 final size:48
Alignment explanation
Indices: 1780425--1780550 Score: 166
Period size: 48 Copynumber: 2.6 Consensus size: 48
1780415 TCGTTCTCTG
* * **
1780425 CAGCATCATTCTCGACA-GTCTT-ATATTCTATGTAACCCTTGTTCTCCA
1 CAGCATCATTCTC-ACAGGT-TTGATCTTCTCTGTAACCCTCATTCTCCA
*
1780473 CAGCATCATTCTCACAGGTTTGATCTTCTCTGTAATCCTCATTCTCCA
1 CAGCATCATTCTCACAGGTTTGATCTTCTCTGTAACCCTCATTCTCCA
*
1780521 CAGCATCATTCTCACCGGTTTGATCTTCTC
1 CAGCATCATTCTCACAGGTTTGATCTTCTC
1780551 CACTTTGTTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
47 5 0.07
48 65 0.93
ACGTcount: A:0.21, C:0.31, G:0.11, T:0.37
Consensus pattern (48 bp):
CAGCATCATTCTCACAGGTTTGATCTTCTCTGTAACCCTCATTCTCCA
Found at i:1783569 original size:20 final size:20
Alignment explanation
Indices: 1783487--1783562 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
1783477 TACATTCGGT
* *
1783487 AATTTTTATATATTTTTATA
1 AATTTTAATATATTTATATA
* *
1783507 TATTATAAT-TACTTTA-A-A
1 AATTTTAATATA-TTTATATA
*
1783525 AATATT-ATATATTTATATA
1 AATTTTAATATATTTATATA
1783544 AATTTTAATATATTTATAT
1 AATTTTAATATATTTATAT
1783563 TATTTTTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
17 6 0.14
18 7 0.16
19 9 0.21
20 21 0.49
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTAATATATTTATATA
Found at i:1784600 original size:2 final size:2
Alignment explanation
Indices: 1784595--1784625 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1784585 GTGTGTGTGT
1784595 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1784626 GATGTCGAAA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1786065 original size:18 final size:17
Alignment explanation
Indices: 1786023--1786066 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1786013 TTTTTATTTA
*
1786023 ATTTTAATTTTAAAATAT
1 ATTTTAA-TATAAAATAT
*
1786041 ATATTAATATAAAATAAT
1 ATTTTAATATAAAAT-AT
1786059 ATTTTAAT
1 ATTTTAAT
1786067 TTTTTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAATATAAAATAT
Found at i:1788974 original size:9 final size:10
Alignment explanation
Indices: 1788950--1788986 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1788940 ATATATACTG
*
1788950 TTTAAATATA
1 TTTAAAAATA
1788960 TTTAAAAAT-
1 TTTAAAAATA
1788969 TTTAAAAATA
1 TTTAAAAATA
1788979 TTTAAAAA
1 TTTAAAAA
1788987 ATAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:1788974 original size:19 final size:19
Alignment explanation
Indices: 1788950--1788986 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1788940 ATATATACTG
*
1788950 TTTAAATATATTTAAAAAT
1 TTTAAAAATATTTAAAAAT
1788969 TTTAAAAATATTTAAAAA
1 TTTAAAAATATTTAAAAA
1788987 ATAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAAAAATATTTAAAAAT
Found at i:1789788 original size:23 final size:21
Alignment explanation
Indices: 1789740--1789792 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1789730 ATTTGATCTC
*
1789740 AAAATTAAAATTTTTTATTTT
1 AAAATTAAAATTTTTTATTTA
* *
1789761 TAAATTATAATTTTTTATATTA
1 AAAATTAAAATTTTTTAT-TTA
*
1789783 AAAAATAAAA
1 AAAATTAAAA
1789793 ACATAAATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTAAAATTTTTTATTTA
Found at i:1789790 original size:20 final size:21
Alignment explanation
Indices: 1789748--1789790 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1789738 TCAAAATTAA
* **
1789748 AATTTTTTATTTTTAAATTAT
1 AATTTTTTATTATTAAAAAAT
1789769 AATTTTTTA-TATTAAAAAAT
1 AATTTTTTATTATTAAAAAAT
1789789 AA
1 AA
1789791 AAACATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTTTTTATTATTAAAAAAT
Found at i:1791879 original size:3 final size:3
Alignment explanation
Indices: 1791871--1791896 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1791861 TTTCATGTAA
1791871 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1791897 AATCTGGGTC
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1792902 original size:52 final size:52
Alignment explanation
Indices: 1792823--1792933 Score: 213
Period size: 52 Copynumber: 2.1 Consensus size: 52
1792813 TTTTGAGAAG
1792823 AGATGATCCTTTTTTCTATATATTAAGTATGGAAAAATTATGTTATTAGCTCA
1 AGATG-TCCTTTTTTCTATATATTAAGTATGGAAAAATTATGTTATTAGCTCA
1792876 AGATGTCCTTTTTTCTATATATTAAGTATGGAAAAATTATGTTATTAGCTCA
1 AGATGTCCTTTTTTCTATATATTAAGTATGGAAAAATTATGTTATTAGCTCA
1792928 AGATGT
1 AGATGT
1792934 GGTTTCGAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 53 0.91
53 5 0.09
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.43
Consensus pattern (52 bp):
AGATGTCCTTTTTTCTATATATTAAGTATGGAAAAATTATGTTATTAGCTCA
Found at i:1793118 original size:23 final size:23
Alignment explanation
Indices: 1793092--1793138 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1793082 TAACAAAGAA
1793092 ATTAAAAAAATAGGAGATCATTT
1 ATTAAAAAAATAGGAGATCATTT
1793115 ATTAAAAAAATAGGAGATCATTT
1 ATTAAAAAAATAGGAGATCATTT
1793138 A
1 A
1793139 GTTTAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.30
Consensus pattern (23 bp):
ATTAAAAAAATAGGAGATCATTT
Found at i:1794694 original size:16 final size:14
Alignment explanation
Indices: 1794652--1794694 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1794642 AAAGTTAAAG
1794652 TTTGATTTTTTATAA
1 TTTGATTTTTT-TAA
*
1794667 TTTAATTTTTTTAA
1 TTTGATTTTTTTAA
1794681 TCTTGATTTCTTTT
1 T-TTGATTT-TTTT
1794695 TAAAAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (14 bp):
TTTGATTTTTTTAA
Found at i:1795627 original size:15 final size:15
Alignment explanation
Indices: 1795607--1795667 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
1795597 GTAACATATT
*
1795607 ATTTAAATTAATTAA
1 ATTTAAATTAAATAA
1795622 ATTTAAATTAAATAA
1 ATTTAAATTAAATAA
* *
1795637 A--AAAATTATAAAAA
1 ATTTAAATTA-AATAA
*
1795651 ATTTAAATTTAATAA
1 ATTTAAATTAAATAA
1795666 AT
1 AT
1795668 ATATAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 6 0.16
14 5 0.14
15 21 0.57
16 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTTAAATTAAATAA
Found at i:1795781 original size:35 final size:37
Alignment explanation
Indices: 1795741--1795823 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 37
1795731 TTATATATTT
* *
1795741 TATTTAATAATATTT-AT-AAGTAAAATTAATTTAAA
1 TATTTAATAATATTTAATAAAATAAAATAAATTTAAA
* *
1795776 TATTTATTACTATTTAAATAAAAATAAAATAAATTTAAA
1 TATTTAATAATATTT-AAT-AAAATAAAATAAATTTAAA
*
1795815 TATTAAATA
1 TATTTAATA
1795824 TTCAAATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
35 13 0.34
37 2 0.05
39 23 0.61
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (37 bp):
TATTTAATAATATTTAATAAAATAAAATAAATTTAAA
Found at i:1799682 original size:2 final size:2
Alignment explanation
Indices: 1799636--1799665 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1799626 CACTGCGATT
1799636 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
1799666 CAGATATAAC
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:1799918 original size:2 final size:2
Alignment explanation
Indices: 1799911--1799937 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1799901 TTCTTTGATT
1799911 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
1799938 GCATATGCAA
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:1800200 original size:9 final size:9
Alignment explanation
Indices: 1800178--1800218 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1800168 TTAAAATTTA
1800178 AATTTAATTT
1 AATTTAA-TT
1800188 AATTTAATT
1 AATTTAATT
1800197 AATTT-ATAT
1 AATTTAAT-T
1800206 AA-TTAATT
1 AATTTAATT
1800214 AATTT
1 AATTT
1800219 TTAATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 7 0.25
9 14 0.50
10 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTAATT
Found at i:1800412 original size:20 final size:20
Alignment explanation
Indices: 1800387--1800426 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1800377 CTACATGTGA
1800387 ACTTGTCAATCTATATTTGG
1 ACTTGTCAATCTATATTTGG
1800407 ACTTGTCAATCTATATTTGG
1 ACTTGTCAATCTATATTTGG
1800427 TTTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (20 bp):
ACTTGTCAATCTATATTTGG
Found at i:1802169 original size:22 final size:22
Alignment explanation
Indices: 1802143--1802191 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1802133 AAGTGACGAT
1802143 CCAATTTAACCGAAATTGTGAC
1 CCAATTTAACCGAAATTGTGAC
*
1802165 CCAATTTAAGCGAAATTGTGAC
1 CCAATTTAACCGAAATTGTGAC
1802187 CCAAT
1 CCAAT
1802192 ACACCGATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (22 bp):
CCAATTTAACCGAAATTGTGAC
Found at i:1802367 original size:101 final size:101
Alignment explanation
Indices: 1802192--1802376 Score: 352
Period size: 101 Copynumber: 1.8 Consensus size: 101
1802182 GTGACCCAAT
* *
1802192 ACACCGATTAATCAAACTAAGAGTGAGGCTTAAAATGGCTAATAAAGCAAAGAGAATAGCCCTTG
1 ACACCGATTAATCAAACTAAGAGTAAGGCTTAAAATGGCTAATAAAGCAAAGAGAAAAGCCCTTG
1802257 AGCTTAATGGCTTTGATAAGCAAAATTGTTTCATTA
66 AGCTTAATGGCTTTGATAAGCAAAATTGTTTCATTA
1802293 ACACCGATTAATCAAACTAAGAGTAAGGCTTAAAATGGCTAATAAAGCAAAGAGAAAAGCCCTTG
1 ACACCGATTAATCAAACTAAGAGTAAGGCTTAAAATGGCTAATAAAGCAAAGAGAAAAGCCCTTG
1802358 AGCTTAATGGCTTTGATAA
66 AGCTTAATGGCTTTGATAA
1802377 TCCATATATA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (101 bp):
ACACCGATTAATCAAACTAAGAGTAAGGCTTAAAATGGCTAATAAAGCAAAGAGAAAAGCCCTTG
AGCTTAATGGCTTTGATAAGCAAAATTGTTTCATTA
Found at i:1803475 original size:2 final size:2
Alignment explanation
Indices: 1803468--1803492 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1803458 ATCAATATTG
1803468 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1803493 CAACTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1804524 original size:30 final size:30
Alignment explanation
Indices: 1804490--1804621 Score: 80
Period size: 30 Copynumber: 4.3 Consensus size: 30
1804480 TATTCAATAA
*
1804490 AATTTTATATATTTTAAATTAATTAAAATT
1 AATTTTATATATTTTAAAATAATTAAAATT
1804520 AA-TTTAT-TATTATTAAAAATAATTAAAATAT
1 AATTTTATATATT-TT-AAAATAATTAAAAT-T
* * * * *
1804551 TATTTTATTTAAATTT--AAT-TTTAAAAAT
1 AATTTTATAT-ATTTTAAAATAATTAAAATT
1804579 AATTTT-TAATATTATTTAAAATAA-TAAAATT
1 AATTTTAT-ATA-T-TTTAAAATAATTAAAATT
1804610 AAAATTTTATAT
1 --AATTTTATAT
1804622 TAACTTAATC
Statistics
Matches: 77, Mismatches: 10, Indels: 27
0.68 0.09 0.24
Matches are distributed among these distances:
27 2 0.03
28 11 0.14
29 16 0.21
30 18 0.23
31 11 0.14
32 5 0.06
33 11 0.14
34 3 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AATTTTATATATTTTAAAATAATTAAAATT
Found at i:1804525 original size:20 final size:19
Alignment explanation
Indices: 1804502--1804552 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1804492 TTTTATATAT
*
1804502 TTTAAATTAATTAAAATTAA
1 TTTAAATT-ATTAAAAATAA
*
1804522 TTTATTATTATTAAAAATAA
1 TTTA-AATTATTAAAAATAA
*
1804542 -TTAAAATATTA
1 TTTAAATTATTA
1804553 TTTTATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.23
19 3 0.12
20 14 0.54
21 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAAATTATTAAAAATAA
Found at i:1805526 original size:21 final size:23
Alignment explanation
Indices: 1805491--1805532 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
1805481 TAAAAAATAA
1805491 AATTTAATAAATTTAATTTTTAT
1 AATTTAATAAATTTAATTTTTAT
1805514 AATTT-AT-AATTTAATTTTT
1 AATTTAATAAATTTAATTTTT
1805533 TATTCTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTTAATAAATTTAATTTTTAT
Found at i:1806223 original size:10 final size:10
Alignment explanation
Indices: 1806194--1806223 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1806184 ACACACACAC
*
1806194 ATATATATAT
1 ATATATATAA
1806204 ATATATATAA
1 ATATATATAA
1806214 ATATATATAA
1 ATATATATAA
1806224 TACTCAGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATAA
Found at i:1810507 original size:2 final size:2
Alignment explanation
Indices: 1810500--1810531 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1810490 AAATGAAGAA
*
1810500 AT AT AT AT AT AT AA 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
1810532 GTATGTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1812125 original size:26 final size:27
Alignment explanation
Indices: 1812089--1812143 Score: 103
Period size: 26 Copynumber: 2.1 Consensus size: 27
1812079 ATATTATATA
1812089 AAAAATATAATTAATATATTAT-TTTT
1 AAAAATATAATTAATATATTATATTTT
1812115 AAAAATATAATTAATATATTATATTTT
1 AAAAATATAATTAATATATTATATTTT
1812142 AA
1 AA
1812144 TATAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AAAAATATAATTAATATATTATATTTT
Found at i:1812145 original size:15 final size:15
Alignment explanation
Indices: 1812099--1812147 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
1812089 AAAAATATAA
1812099 TTAATATATTAT-TT
1 TTAATATATTATATT
* *
1812113 TTAA-A-AATATA-A
1 TTAATATATTATATT
1812125 TTAATATATTATATT
1 TTAATATATTATATT
1812140 TTAATATA
1 TTAATATA
1812148 AAATTTTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 9 0.33
15 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATATATTATATT
Found at i:1812152 original size:26 final size:26
Alignment explanation
Indices: 1812089--1812152 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
1812079 ATATTATATA
*
1812089 AAAAATATAATTAATATATTATTTTT
1 AAAAATAAAATTAATATATTATTTTT
*
1812115 AAAAATATAATTAATATATTATATTTT
1 AAAAATAAAATTAATATATTAT-TTTT
*
1812142 -AATATAAAATT
1 AAAAATAAAATT
1812153 TTGTTAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAAATAAAATTAATATATTATTTTT
Found at i:1813598 original size:23 final size:23
Alignment explanation
Indices: 1813570--1813614 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1813560 ACATTATCAG
**
1813570 TTATTATATTTAATATAATAATA
1 TTATTATAAATAATATAATAATA
*
1813593 TTATTATAAATAATATATTAAT
1 TTATTATAAATAATATAATAAT
1813615 TAATTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATTATAAATAATATAATAATA
Found at i:1813663 original size:18 final size:16
Alignment explanation
Indices: 1813636--1813674 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1813626 AGTTATCAAC
*
1813636 TAATATATTAACTATAAA
1 TAATAAATTAA-T-TAAA
1813654 TAATAAATTAATTAAA
1 TAATAAATTAATTAAA
1813670 TAATA
1 TAATA
1813675 TTCATTCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 10 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAAATTAATTAAA
Found at i:1815301 original size:196 final size:197
Alignment explanation
Indices: 1815064--1815448 Score: 614
Period size: 196 Copynumber: 2.0 Consensus size: 197
1815054 AAAGTGATTA
* *
1815064 ATAAAATTAATATATTATATTATACATAATGAATAAAGATGAATGAGATAAAATTAATTAGTCAA
1 ATAAAATTAATATATTATATTACACACAATGAATAAAGATGAATGAGATAAAATTAATTAGTCAA
1815129 ATTAATATTATACATTAAATTTAACAAATTATTTTTATAATATATGAAAAA-AATTTT-AAAAAA
66 ATTAATATTATACATTAAATTTAACAAATTATTTTTATAATATAT-AAAAATAATTTTAAAAAAA
* * *
1815192 TTCATAATACATATTAGTATTTATGTCAAAAAA-TTATATTATATATAAATTATATAGATGAGGT
130 TCCATAATAAATATTAATATTTATGT-AAAAAAGTTATATTATATATAAATTATATAGATGAGGT
1815256 TGAG
194 TGAG
* *
1815260 ATAAAATTAATATATTATATTACACACAATGAATGAAGATGAATGATATAAAATTAATTAGTCAA
1 ATAAAATTAATATATTATATTACACACAATGAATAAAGATGAATGAGATAAAATTAATTAGTCAA
* * *
1815325 ATTAATATTATACATTAAATTTAATAAATTATTTTTATATTATATAAAAATATTTTTAAAAAAAA
66 ATTAATATTATACATTAAATTTAACAAATTATTTTTATAATATATAAAAATAATTTT-AAAAAAA
* *
1815390 TCCATAATAAATATTAATATTTATGTAAAAAAGTTGTATTATATATATATTATATAGAT
130 TCCATAATAAATATTAATATTTATGTAAAAAAGTTATATTATATATAAATTATATAGAT
1815449 ATATATAGAT
Statistics
Matches: 173, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
195 5 0.03
196 109 0.63
197 6 0.03
198 53 0.31
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (197 bp):
ATAAAATTAATATATTATATTACACACAATGAATAAAGATGAATGAGATAAAATTAATTAGTCAA
ATTAATATTATACATTAAATTTAACAAATTATTTTTATAATATATAAAAATAATTTTAAAAAAAT
CCATAATAAATATTAATATTTATGTAAAAAAGTTATATTATATATAAATTATATAGATGAGGTTG
AG
Found at i:1816885 original size:16 final size:16
Alignment explanation
Indices: 1816844--1816983 Score: 53
Period size: 16 Copynumber: 8.8 Consensus size: 16
1816834 AATACGAAAT
*
1816844 TATTTTATAATATAAAA
1 TATTATATAAT-TAAAA
* *
1816861 -ATAAAATAATTAAAA
1 TATTATATAATTAAAA
*
1816876 TATTATATAAATAATAAA
1 TATTATAT-AATTA-AAA
* * *
1816894 TTTTTTATAATATAAAT
1 TATTATATAAT-TAAAA
*
1816911 TAATA-ATATATTAAAA
1 TATTATATA-ATTAAAA
*
1816927 T-TTATATAAATATAAA
1 TATTATATAATTA-AAA
* *
1816943 TATT-TTTAA-TATAAT
1 TATTATATAATTA-AAA
*
1816958 TATTATATTA-TAAAA
1 TATTATATAATTAAAA
1816973 TA-TATA-AATTA
1 TATTATATAATTA
1816984 TTAAAGTGAA
Statistics
Matches: 91, Mismatches: 22, Indels: 23
0.67 0.16 0.17
Matches are distributed among these distances:
13 1 0.01
14 6 0.07
15 23 0.25
16 36 0.40
17 15 0.16
18 10 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTATATAATTAAAA
Found at i:1816894 original size:27 final size:27
Alignment explanation
Indices: 1816853--1816944 Score: 74
Period size: 27 Copynumber: 3.6 Consensus size: 27
1816843 TTATTTTATA
1816853 ATATAAA-AATAAAATAATTAAAATATT
1 ATATAAATAAT-AAATAATTAAAATATT
** *
1816880 ATATAAATAATAAAT--TT--TTTATA
1 ATATAAATAATAAATAATTAAAATATT
1816903 ATATAAATTAAT-AATATATTAAAAT-TT
1 ATATAAA-TAATAAATA-ATTAAAATATT
1816930 ATATAAAT-ATAAATA
1 ATATAAATAATAAATA
1816945 TTTTTAATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
23 13 0.25
24 4 0.08
25 4 0.08
26 7 0.14
27 19 0.37
28 4 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATATAAATAATAAATAATTAAAATATT
Found at i:1816906 original size:50 final size:50
Alignment explanation
Indices: 1816840--1816956 Score: 161
Period size: 50 Copynumber: 2.4 Consensus size: 50
1816830 ATTAAATACG
1816840 AAATTATTTTATAATATAAAAATAA-AATA-ATTAAAATATTATATAAATAAT
1 AAATT-TTTTATAATATAAAAATAATAATATATTAAAAT-TTATATAAAT-AT
*
1816891 AAATTTTTTATAATAT-AAATTAATAATATATTAAAATTTATATAAATAT
1 AAATTTTTTATAATATAAAAATAATAATATATTAAAATTTATATAAATAT
*
1816940 AAATATTTT-TAATATAA
1 AAATTTTTTATAATATAA
1816957 TTATTATATT
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
48 6 0.10
49 17 0.28
50 25 0.41
51 13 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (50 bp):
AAATTTTTTATAATATAAAAATAATAATATATTAAAATTTATATAAATAT
Found at i:1818039 original size:2 final size:2
Alignment explanation
Indices: 1818034--1818067 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1818024 AAAAAAATAC
1818034 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
1818068 GAACTGATAT
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:1826812 original size:20 final size:21
Alignment explanation
Indices: 1826789--1826829 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1826779 CATATTTAAT
1826789 ATTTATTTAATA-TTAAAATC
1 ATTTATTTAATATTTAAAATC
*
1826809 ATTTTTTTAATATTTAAAATC
1 ATTTATTTAATATTTAAAATC
1826830 TTGTTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTATTTAATATTTAAAATC
Found at i:1833796 original size:4 final size:4
Alignment explanation
Indices: 1833787--1833817 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1833777 AACAACTCCT
1833787 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1833818 TTTTGCTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1835263 original size:15 final size:15
Alignment explanation
Indices: 1835243--1835274 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1835233 TATATTTATT
1835243 TTCCTTGCCTATAAA
1 TTCCTTGCCTATAAA
1835258 TTCCTTGCCTATAAA
1 TTCCTTGCCTATAAA
1835273 TT
1 TT
1835275 TTAATAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (15 bp):
TTCCTTGCCTATAAA
Found at i:1835419 original size:14 final size:13
Alignment explanation
Indices: 1835402--1835436 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
1835392 TATAAATTAA
1835402 TTTTATAATAAAAT
1 TTTTA-AATAAAAT
1835416 TTTTAAATAAAAT
1 TTTTAAATAAAAT
1835429 TTTTAAAT
1 TTTTAAAT
1835437 TTTTTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTTAAATAAAAT
Found at i:1835656 original size:29 final size:32
Alignment explanation
Indices: 1835592--1835656 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 32
1835582 ATTTATATTT
* * *
1835592 TAAATTTTAATAAAAATTTAATTATTATAAAT
1 TAAATTTTAATAAAAATATAATTATTAAAAAA
*
1835624 TAAATTTTAA-AAATATATAA-T-TTAAAAAA
1 TAAATTTTAATAAAAATATAATTATTAAAAAA
1835653 TAAA
1 TAAA
1835657 AAAATACACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 10 0.34
30 1 0.03
31 8 0.28
32 10 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
TAAATTTTAATAAAAATATAATTATTAAAAAA
Found at i:1836492 original size:19 final size:18
Alignment explanation
Indices: 1836453--1836498 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1836443 AATTTGATAG
1836453 TAATTAAAAATTATTTTA
1 TAATTAAAAATTATTTTA
*
1836471 TAATTGAAAA-TATTTTA
1 TAATTAAAAATTATTTTA
1836488 -AA-TAAAAATTA
1 TAATTAAAAATTA
1836499 ATAATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 4 0.16
17 7 0.28
18 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATTAAAAATTATTTTA
Found at i:1839607 original size:19 final size:19
Alignment explanation
Indices: 1839575--1839669 Score: 67
Period size: 19 Copynumber: 5.0 Consensus size: 19
1839565 ATAAAATAAA
1839575 AAATA-AAAT-AATAATAT
1 AAATATAAATAAATAATAT
*
1839592 AAATATAAATATATAA-AT
1 AAATATAAATAAATAATAT
* *
1839610 ATAT-TAAATATATTAAATAT
1 AAATATAAATA-AAT-AATAT
1839630 AATTATAATAAA-AAATAATAT
1 AA--AT-ATAAATAAATAATAT
1839651 AAATATGAAA-AAATAATAT
1 AAATAT-AAATAAATAATAT
1839670 TTTTATTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
17 11 0.18
18 12 0.19
19 20 0.32
20 3 0.05
21 7 0.11
22 4 0.06
23 1 0.02
24 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (19 bp):
AAATATAAATAAATAATAT
Found at i:1839619 original size:9 final size:9
Alignment explanation
Indices: 1839597--1839630 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
1839587 AATATAAATA
1839597 TAAATATA-
1 TAAATATAT
1839605 TAAATATAT
1 TAAATATAT
1839614 TAAATATAT
1 TAAATATAT
1839623 TAAATATA
1 TAAATATA
1839631 ATTATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TAAATATAT
Found at i:1843294 original size:2 final size:2
Alignment explanation
Indices: 1843287--1843316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1843277 CAGCAGCGTA
1843287 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1843317 AGAGAGAGAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1843321 original size:2 final size:2
Alignment explanation
Indices: 1843316--1843341 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1843306 GTGTGTGTGT
1843316 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1843342 AACGAACAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1846956 original size:17 final size:19
Alignment explanation
Indices: 1846929--1846968 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
1846919 TCGGCATAAA
*
1846929 AAAATTATATTATAAT-TT
1 AAAATTATATTAAAATATT
1846947 AAAA-TATATTAAAATATT
1 AAAATTATATTAAAATATT
1846965 AAAA
1 AAAA
1846969 AATTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTATATTAAAATATT
Found at i:1846969 original size:19 final size:19
Alignment explanation
Indices: 1846928--1846980 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 19
1846918 TTCGGCATAA
*
1846928 AAAAATTATATTATAATTT
1 AAAAATTATATTAAAATTT
1846947 -AAAA-TATATTAAAATATT
1 AAAAATTATATTAAAAT-TT
1846965 AAAAAATTTATATTAA
1 -AAAAA-TTATATTAA
1846981 TTTTTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 10 0.36
18 6 0.21
20 4 0.14
22 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATTATATTAAAATTT
Found at i:1852426 original size:2 final size:2
Alignment explanation
Indices: 1852419--1852454 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1852409 TGAGGAATTC
1852419 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1852455 CGCAAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1853497 original size:11 final size:11
Alignment explanation
Indices: 1853477--1853519 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1853467 AATTTATAGA
1853477 TTAT-ATTATT
1 TTATAATTATT
1853487 TTATAATTATTT
1 TTATAATTA-TT
* *
1853499 TTAAAAATATT
1 TTATAATTATT
1853510 TTATAATTAT
1 TTATAATTAT
1853520 ATAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 4 0.15
11 14 0.52
12 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTATAATTATT
Found at i:1856845 original size:20 final size:21
Alignment explanation
Indices: 1856796--1856859 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 21
1856786 TTAAACATAA
* *
1856796 TATTTAATAATTTAAGTTATT
1 TATTTATTAATTTAAATTATT
1856817 T-TATT-TTAATTTAAATT-TT
1 TAT-TTATTAATTTAAATTATT
**
1856836 TATTTATTAAATAAAAATTATT
1 TATTTATT-AATTTAAATTATT
1856858 TA
1 TA
1856860 AATTAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 5 0.15
20 14 0.41
21 11 0.32
22 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TATTTATTAATTTAAATTATT
Found at i:1857883 original size:2 final size:2
Alignment explanation
Indices: 1857876--1857913 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1857866 GCCTAATTTT
1857876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1857914 ATGTTCTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1857990 original size:5 final size:5
Alignment explanation
Indices: 1857980--1858029 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
1857970 AAAACATAAA
* *
1857980 AATAT AATAT AAAAT AATAT -ATTT AATA- AATAT AA-A- AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1858026 AATA
1 AATA
1858030 AATGTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 2 0.05
4 9 0.24
5 26 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:1857993 original size:13 final size:13
Alignment explanation
Indices: 1857975--1858032 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
1857965 TATATAAAAC
1857975 ATAAAAATATAAT
1 ATAAAAATATAAT
1857988 AT--AAA-ATAAT
1 ATAAAAATATAAT
**
1857998 ATATTTAATA-AAT
1 ATA-AAAATATAAT
1858011 ATAAAAATATAAT
1 ATAAAAATATAAT
1858024 ATAATAAAT
1 ATAA-AAAT
1858033 GTAAATATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
10 7 0.19
11 3 0.08
12 4 0.11
13 17 0.47
14 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAAAATATAAT
Found at i:1858037 original size:22 final size:21
Alignment explanation
Indices: 1857980--1858037 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
1857970 AAAACATAAA
*
1857980 AATATAATATAAAATAATATATTT
1 AATA-AATAT-AAA-AATATATAT
1858004 AATAAATATAAAAATATAATAT
1 AATAAATATAAAAATAT-ATAT
*
1858026 AATAAATGTAAA
1 AATAAATATAAA
1858038 TATGATACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.16
22 17 0.55
23 5 0.16
24 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAAATATAAAAATATATAT
Found at i:1858100 original size:17 final size:19
Alignment explanation
Indices: 1858065--1858110 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
1858055 ATATATTTTG
1858065 ATATATTTAATAGTTTATA
1 ATATATTTAATAGTTTATA
*
1858084 TTATATTT-ATA-TTTATA
1 ATATATTTAATAGTTTATA
*
1858101 ATATAATTAA
1 ATATATTTAA
1858111 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 12 0.52
18 4 0.17
19 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATATATTTAATAGTTTATA
Found at i:1859457 original size:16 final size:17
Alignment explanation
Indices: 1859449--1859480 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1859439 ATTTATTATA
1859449 TTTAATATTTATTTAAT
1 TTTAATATTTATTTAAT
1859466 TTTAATA-TTATTTAA
1 TTTAATATTTATTTAA
1859481 AAATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATATTTATTTAAT
Found at i:1860903 original size:5 final size:5
Alignment explanation
Indices: 1860887--1860915 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1860877 TAGCCAGTTG
1860887 TCTTT T-TTT TCTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
1860916 ATATGTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:1861544 original size:18 final size:18
Alignment explanation
Indices: 1861521--1861559 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1861511 TTCATTTTAT
1861521 TTTAAGATTATGATAATG
1 TTTAAGATTATGATAATG
1861539 TTTAAGATTATGATAATG
1 TTTAAGATTATGATAATG
1861557 TTT
1 TTT
1861560 TTGTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (18 bp):
TTTAAGATTATGATAATG
Found at i:1862283 original size:12 final size:13
Alignment explanation
Indices: 1862255--1862323 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 13
1862245 GTCGAGTAAG
1862255 GGAGAGGAGGGAGA
1 GGAG-GGAGGGAGA
1862269 GGAGGGAGGGA-A
1 GGAGGGAGGGAGA
1862281 GGAGGGA--GAGA
1 GGAGGGAGGGAGA
*
1862292 GGA--GAGGAAGA
1 GGAGGGAGGGAGA
1862303 GGAGGAGAGAGGAGA
1 GGAGG-GAG-GGAGA
1862318 GAGAGG
1 G-GAGG
1862324 AGAGAAGGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
9 2 0.04
10 2 0.04
11 10 0.22
12 8 0.18
13 7 0.16
14 7 0.16
15 5 0.11
16 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (13 bp):
GGAGGGAGGGAGA
Found at i:1862285 original size:21 final size:23
Alignment explanation
Indices: 1862253--1862328 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 23
1862243 TGGTCGAGTA
1862253 AGGGAGAGGAGGGAGAGGAGG-G
1 AGGGAGAGGAGGGAGAGGAGGAG
1862275 AGGGA-AGGAGGGAGA-GAGGAG
1 AGGGAGAGGAGGGAGAGGAGGAG
*
1862296 AGGAAGAGGAGGAGAGAGGAGAGAG
1 AGGGAGAGGAGG-GAGAGGAG-GAG
1862321 AGGAGAGA
1 AGG-GAGA
1862329 AGGATAGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.09
21 15 0.33
22 11 0.24
23 4 0.09
24 3 0.07
25 6 0.13
26 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (23 bp):
AGGGAGAGGAGGGAGAGGAGGAG
Found at i:1862287 original size:30 final size:34
Alignment explanation
Indices: 1862256--1862328 Score: 73
Period size: 37 Copynumber: 2.1 Consensus size: 34
1862246 TCGAGTAAGG
1862256 GAGAGGAGGGAGAGGAGGGAG-GG-A-AGGAGGGA
1 GAGAGGAGGGAGAGGAGGGAGAGGAAGAGGA-GGA
1862288 GAGAGGAGAGGAAGAGGAGGAGAGAGG-AGAGAGAGGA
1 GAGAGGAG-GG-AGAGGAGG-GAGAGGAAGAG-GAGGA
1862325 GAGA
1 GAGA
1862329 AGGATAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
32 8 0.23
33 2 0.06
34 8 0.23
35 3 0.09
36 3 0.09
37 9 0.26
38 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (34 bp):
GAGAGGAGGGAGAGGAGGGAGAGGAAGAGGAGGA
Found at i:1862309 original size:14 final size:16
Alignment explanation
Indices: 1862286--1862328 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1862276 GGGAAGGAGG
1862286 GAGAGAGGAGAG-GAA
1 GAGAGAGGAGAGAGAA
*
1862301 GAG-GAGGAGAGAGGA
1 GAGAGAGGAGAGAGAA
1862316 GAGAGAGGAGAGA
1 GAGAGAGGAGAGA
1862329 AGGATAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 8 0.32
16 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (16 bp):
GAGAGAGGAGAGAGAA
Found at i:1862326 original size:9 final size:9
Alignment explanation
Indices: 1862256--1862332 Score: 74
Period size: 9 Copynumber: 8.8 Consensus size: 9
1862246 TCGAGTAAGG
*
1862256 GAGAGGAGG
1 GAGAGGAGA
*
1862265 GAGAGGAGG
1 GAGAGGAGA
1862274 GAG-GGA-A
1 GAGAGGAGA
1862281 G-GAGG-GA
1 GAGAGGAGA
1862288 GAGAGGAGA
1 GAGAGGAGA
1862297 GGAAGAGGAGGA
1 -G-AGAGGA-GA
1862309 GAGAGGAGA
1 GAGAGGAGA
1862318 GAGAGGAGA
1 GAGAGGAGA
1862327 GA-AGGA
1 GAGAGGA
1862333 TAGATTGGCA
Statistics
Matches: 60, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
6 1 0.02
7 5 0.08
8 11 0.18
9 27 0.45
10 7 0.12
11 7 0.12
12 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (9 bp):
GAGAGGAGA
Found at i:1867460 original size:10 final size:10
Alignment explanation
Indices: 1867440--1867481 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
1867430 AAGGAGCCAT
1867440 GAAAGATAAAA
1 GAAA-ATAAAA
1867451 GAAAATAAAA
1 GAAAATAAAA
1867461 GAAAATTAGAAA
1 GAAAA-TA-AAA
1867473 -AAAATAAAA
1 GAAAATAAAA
1867482 AAGGAGGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.10
10 13 0.45
11 10 0.34
12 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (10 bp):
GAAAATAAAA
Found at i:1867973 original size:2 final size:2
Alignment explanation
Indices: 1867966--1867991 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1867956 AAGCAAGACC
1867966 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
1867992 GGTTTTTATT
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):
AT
Found at i:1868362 original size:21 final size:24
Alignment explanation
Indices: 1868319--1868362 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1868309 AAAAATAAAA
1868319 AAAAGTTATAATAAAACATATTAC
1 AAAAGTTATAATAAAACATATTAC
1868343 AAAA-TTA-AATAAAA-ATATTA
1 AAAAGTTATAATAAAACATATTA
1868363 TATTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 7 0.35
23 3 0.15
24 4 0.20
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAAGTTATAATAAAACATATTAC
Found at i:1868388 original size:36 final size:34
Alignment explanation
Indices: 1868296--1868389 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 34
1868286 AAATTAACTC
*
1868296 AAAAAATGATATAAAAAATAAA-AAAAAGTTATAAT
1 AAAAAAT-AT-TAAAAAATAAATAAAAAATTATAAT
* * *
1868331 AAAACATATTACAAAATTAAATAAAAATATTATATT
1 AAAAAATATTA-AAAAATAAATAAAAA-ATTATAAT
*
1868367 AAAATAATTTTAAAAAATAAATA
1 AAAA-AATATTAAAAAATAAATA
1868390 TATTTTATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
33 2 0.04
34 10 0.21
35 11 0.23
36 20 0.42
37 5 0.10
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (34 bp):
AAAAAATATTAAAAAATAAATAAAAAATTATAAT
Found at i:1868839 original size:17 final size:19
Alignment explanation
Indices: 1868817--1868862 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
1868807 TTTATGGAGA
1868817 ATTTTAAATAAAAT-AT-T
1 ATTTTAAATAAAATAATAT
1868834 ATTTTACAA-AAAATAATAT
1 ATTTTA-AATAAAATAATAT
*
1868853 GTTTTAAATA
1 ATTTTAAATA
1868863 TAGTATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 11 0.46
18 6 0.25
19 7 0.29
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTTAAATAAAATAATAT
Found at i:1871896 original size:15 final size:16
Alignment explanation
Indices: 1871873--1871914 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1871863 ACTCCAAATT
1871873 AATATATTAAA-AATAA
1 AATA-ATTAAATAATAA
*
1871889 AATAATTAAATACTAA
1 AATAATTAAATAATAA
1871905 ATATAATTAA
1 A-ATAATTAA
1871915 TCTACTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 9 0.39
17 8 0.35
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATTAAATAATAA
Found at i:1872536 original size:19 final size:17
Alignment explanation
Indices: 1872501--1872554 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 17
1872491 ATTTATATTT
1872501 TTTTAA-TTTTATTATA
1 TTTTAATTTTTATTATA
1872517 TTTTAATTTTTATGTAATA
1 TTTTAATTTTTAT-T-ATA
1872536 TTTTAA-TTTTATT-TA
1 TTTTAATTTTTATTATA
1872551 TTTT
1 TTTT
1872555 GGATTCAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.17
16 6 0.17
17 7 0.20
18 7 0.20
19 9 0.26
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTAATTTTTATTATA
Found at i:1873367 original size:13 final size:13
Alignment explanation
Indices: 1873334--1873367 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1873324 CCATATTTGA
1873334 ATATATATTAAAC
1 ATATATATTAAAC
* *
1873347 ACAAATATTAAAC
1 ATATATATTAAAC
1873360 ATATATAT
1 ATATATAT
1873368 GTTAAAAAAA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATATATTAAAC
Found at i:1873534 original size:19 final size:19
Alignment explanation
Indices: 1873502--1873538 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1873492 TAATATTTTT
1873502 ATAATAAATATAATAATTA
1 ATAATAAATATAATAATTA
* *
1873521 ATAATTAATTTAATAATT
1 ATAATAAATATAATAATT
1873539 TTCACTGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATAAATATAATAATTA
Found at i:1874034 original size:2 final size:2
Alignment explanation
Indices: 1874029--1874072 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1874019 GTAGATAGAT
1874029 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1874071 AG
1 AG
1874073 TAAACTTGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1874907 original size:75 final size:75
Alignment explanation
Indices: 1874784--1875002 Score: 314
Period size: 75 Copynumber: 2.9 Consensus size: 75
1874774 GATAAAACGA
* * *
1874784 TAATCCGAGATAATCTGCACGATAACTACAATCAATAAATGTTTCTGCATATTTCACATTACTAC
1 TAATCCAAGATACTCTGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCACATTACTAC
*
1874849 TATCAGCAAC
66 TATCAACAAC
* *
1874859 TAATCCAAGATACTCTACACGATAACTACAATTAACAAATGTTTCTGCATATTTCACATTACTAC
1 TAATCCAAGATACTCTGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCACATTACTAC
*
1874924 TATCAATAAC
66 TATCAACAAC
* * * * *
1874934 TAATCTGAA-ATACTCTGTACGATAATTATAATCAACAAATATTTCTGCATATTTCACATTACTA
1 TAATC-CAAGATACTCTGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCACATTACTA
1874998 CTATC
65 CTATC
1875003 GAATACCATT
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
75 127 0.98
76 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.33
Consensus pattern (75 bp):
TAATCCAAGATACTCTGCACGATAACTACAATCAACAAATGTTTCTGCATATTTCACATTACTAC
TATCAACAAC
Found at i:1875751 original size:28 final size:28
Alignment explanation
Indices: 1875718--1875775 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
1875708 TCAAATATTT
*
1875718 TTTTAAACTCAAATTCTTAAATCTACTA
1 TTTTAAACTCAAATTCTTAAATCTAATA
1875746 TTTTAAACTCAAATTCTTAAATCTAATA
1 TTTTAAACTCAAATTCTTAAATCTAATA
1875774 TT
1 TT
1875776 AAAATTACCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.45
Consensus pattern (28 bp):
TTTTAAACTCAAATTCTTAAATCTAATA
Found at i:1875765 original size:14 final size:14
Alignment explanation
Indices: 1875720--1875766 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1875710 AAATATTTTT
1875720 TTAAACTCAAATTC
1 TTAAACTCAAATTC
*
1875734 TTAAA-TCTACTATT-
1 TTAAACTC-A-AATTC
1875748 TTAAACTCAAATTC
1 TTAAACTCAAATTC
1875762 TTAAA
1 TTAAA
1875767 TCTAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 5 0.19
14 17 0.63
15 5 0.19
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAACTCAAATTC
Found at i:1877033 original size:459 final size:459
Alignment explanation
Indices: 1876175--1877554 Score: 2634
Period size: 459 Copynumber: 3.0 Consensus size: 459
1876165 CGTTCTCAAC
*
1876175 ATAATCATTAGTTTGCAACTCAACAATTGTGCCTGGCATGTATTTTTTCATTGCCTCTAACCATC
1 ATAATCATTAGTTTGCAACTCAACAATTGTGCGTGGCATGTATTTTTTCATTGCCTCTAACCATC
*
1876240 TAGGCAATATCTCATAAGACTGATCCCAATCATAAAAAATTTTGACGATTGCTTTTTGCTTTGCC
66 TAGGCAATATCTCATAAGACTGATCCCAATCATCAAAAATTTTGACGATTGCTTTTTGCTTTGCC
*
1876305 TTCTAAATCTTTCGGTATGATACTTTATAAGAAAATTAACTTTGCATTCTTTCCTGAATTAATGC
131 TTCTAAGTCTTTCGGTATGATACTTTATAAGAAAATTAACTTTGCATTCTTTCCTGAATTAATGC
1876370 AATCGGCACATTTGATTTTTTCCGAACCATTTTCAAAATGCAAGAACATTTCATATTAGAGTCTA
196 AATCGGCACATTTGATTTTTTCCGAACCATTTTCAAAATGCAAGAACATTTCATATTAGAGTCTA
* *
1876435 ACTTTTTATGGTCTTGTGACAAAGCTGCATTTACATAACTATGCAGCCCATTGTATTTTGTAATT
261 ACTTTTTATGGTCTTGTGACAAAGCTGCATTTACACAACTATGCGGCCCATTGTATTTTGTAATT
1876500 TGTCACATTTTCGATTTTTTACTTAAAATAGTCCTCACTCTCCAATTACAACTATCACCAAATCG
326 TGTCACATTTTCGATTTTTTACTTAAAATAGTCCTCACTCTCCAATTACAACTATCACCAAATCG
1876565 AGGGCATCTAACAGATAATCTATTTCTATCAGATGCCACAACTTGATATACCTGATGCCTTTTTA
391 AGGGCATCTAACAGATAATCTATTTCTATCAGATGCCACAACTTGATATACCTGATGCCTTTTTA
1876630 AAGA
456 AAGA
1876634 ATAATCATTAGTTTGCAACTCAACAATTGTGCGTGGCATGTATTTTTTCATTGCCTCTAACCATC
1 ATAATCATTAGTTTGCAACTCAACAATTGTGCGTGGCATGTATTTTTTCATTGCCTCTAACCATC
*
1876699 TAGGCAATATCTCATAAGACTGATCCCAATCATCAAAAATTTTGACGATTGTTTTTTGCTTTGCC
66 TAGGCAATATCTCATAAGACTGATCCCAATCATCAAAAATTTTGACGATTGCTTTTTGCTTTGCC
1876764 TTCTAAGTCTTTCGGTATGATACTTTATAAGAAAATTAACTTTGCATTCTTTCCTGAATTAATGC
131 TTCTAAGTCTTTCGGTATGATACTTTATAAGAAAATTAACTTTGCATTCTTTCCTGAATTAATGC
*
1876829 AATCGGCACATTTGATTTTTTTCGAACCATTTTCAAAATGCAAGAACATTTCATATTAGAGTCTA
196 AATCGGCACATTTGATTTTTTCCGAACCATTTTCAAAATGCAAGAACATTTCATATTAGAGTCTA
*
1876894 ACTTTTTATGGTCTTGCGACAAAGCTGCATTTACACAACTATGCGGCCCATTGTATTTTGTAATT
261 ACTTTTTATGGTCTTGTGACAAAGCTGCATTTACACAACTATGCGGCCCATTGTATTTTGTAATT
1876959 TGTCACATTTTCGATTTTTTACTTAAAATAGTCCTCACTCTCCAATTACAACTATCACCAAATCG
326 TGTCACATTTTCGATTTTTTACTTAAAATAGTCCTCACTCTCCAATTACAACTATCACCAAATCG
* *
1877024 AGGGCATCTAACATATAATCTATTTCTATCAGATGCCACAACTTGATATACCTGATGCTTTTTTA
391 AGGGCATCTAACAGATAATCTATTTCTATCAGATGCCACAACTTGATATACCTGATGCCTTTTTA
1877089 AAGA
456 AAGA
1877093 ATAATCATTAGTTTGCAACTCAACAATTGTGCGTGGCATGTATTTTTTCATTGCCTCTAACCATC
1 ATAATCATTAGTTTGCAACTCAACAATTGTGCGTGGCATGTATTTTTTCATTGCCTCTAACCATC
1877158 TAGGCAATATCTCATAAGACTGATCCCAATCATCAAAAATTTTGACGATTGCTTTTTGCTTTGCC
66 TAGGCAATATCTCATAAGACTGATCCCAATCATCAAAAATTTTGACGATTGCTTTTTGCTTTGCC
1877223 TTCTAAGTCTTTCGGTATGATACTTTATAAGAAAATTAACTTTGCATTCTTTCCTGAATTAATGC
131 TTCTAAGTCTTTCGGTATGATACTTTATAAGAAAATTAACTTTGCATTCTTTCCTGAATTAATGC
1877288 AATCGGCACATTTGATTTTTTCCGAACCATTTTCAAAATGCAAGAACATTTCATATTAGAGTCTA
196 AATCGGCACATTTGATTTTTTCCGAACCATTTTCAAAATGCAAGAACATTTCATATTAGAGTCTA
* *
1877353 ACTTTTTAAGGTCTTGTGACAAAGCTACATTTACACAACTATGCGGCCCATTGTATTTTGTAATT
261 ACTTTTTATGGTCTTGTGACAAAGCTGCATTTACACAACTATGCGGCCCATTGTATTTTGTAATT
*
1877418 TATCACATTTTCGATTTTTTACTTAAAATAGTCCTCACTCTCCAATTACAACTATCACCAAATCG
326 TGTCACATTTTCGATTTTTTACTTAAAATAGTCCTCACTCTCCAATTACAACTATCACCAAATCG
*
1877483 AGGGCATCTAGCAGATAATCTATTTCTATCAGATGCCACAACTTGATATACCTGATGCCTTTTTA
391 AGGGCATCTAACAGATAATCTATTTCTATCAGATGCCACAACTTGATATACCTGATGCCTTTTTA
1877548 AAGA
456 AAGA
1877552 ATA
1 ATA
1877555 TTGCTTTAAT
Statistics
Matches: 902, Mismatches: 19, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
459 902 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (459 bp):
ATAATCATTAGTTTGCAACTCAACAATTGTGCGTGGCATGTATTTTTTCATTGCCTCTAACCATC
TAGGCAATATCTCATAAGACTGATCCCAATCATCAAAAATTTTGACGATTGCTTTTTGCTTTGCC
TTCTAAGTCTTTCGGTATGATACTTTATAAGAAAATTAACTTTGCATTCTTTCCTGAATTAATGC
AATCGGCACATTTGATTTTTTCCGAACCATTTTCAAAATGCAAGAACATTTCATATTAGAGTCTA
ACTTTTTATGGTCTTGTGACAAAGCTGCATTTACACAACTATGCGGCCCATTGTATTTTGTAATT
TGTCACATTTTCGATTTTTTACTTAAAATAGTCCTCACTCTCCAATTACAACTATCACCAAATCG
AGGGCATCTAACAGATAATCTATTTCTATCAGATGCCACAACTTGATATACCTGATGCCTTTTTA
AAGA
Done.