Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold19
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: 2266706
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17655 characters in sequence are not A, C, G, or T
File 1 of 15
Found at i:758 original size:6 final size:6
Alignment explanation
Indices: 749--789 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
739 GTAGGTTTAG
749 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGG
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGG
790 CGGCGGCGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.00, G:0.68, T:0.15
Consensus pattern (6 bp):
GGAGGT
Found at i:3711 original size:16 final size:16
Alignment explanation
Indices: 3690--3721 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3680 TATTAAAAAG
3690 TAAAATATATATATAA
1 TAAAATATATATATAA
3706 TAAAATATATATATAA
1 TAAAATATATATATAA
3722 AATTTTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATATATATATAA
Found at i:4691 original size:43 final size:42
Alignment explanation
Indices: 4618--4702 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
4608 CCCACATTTT
*
4618 TTAATTTATAAGTTAAAATTAAACTCTTATAAAAACTAAAATA
1 TTAACTTATAAGTTAAAATTAAACTCTTATAAAAA-TAAAATA
* * *
4661 TTAACTTATAAGTTATAATTAAATTTTTATAAAAATAAAATA
1 TTAACTTATAAGTTAAAATTAAACTCTTATAAAAATAAAATA
4703 AAAATTATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 7 0.18
43 31 0.82
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (42 bp):
TTAACTTATAAGTTAAAATTAAACTCTTATAAAAATAAAATA
Found at i:7308 original size:72 final size:72
Alignment explanation
Indices: 7191--7475 Score: 340
Period size: 72 Copynumber: 3.9 Consensus size: 72
7181 CAATTATGTG
* * *
7191 AAAGAAATAA-AACAAATGGGAGAAATAAACAGTGAAAGAATCAAGATTCATAATAAAACTTGGA
1 AAAGAAA-AACAACAAATGGAAGAAATAAACACTGAAAGAATCAAGATTCATAGTAAAACTTGGA
7255 AAAATGAA
65 AAAATGAA
* *
7263 AAAGAAAAACAACAAATGGAAGAAATAAACACCGAAAGAATCAAGATTCATAGTAAAACCTGGAA
1 AAAGAAAAACAACAAATGGAAGAAATAAACACTGAAAGAATCAAGATTCATAGTAAAACTTGGAA
*
7328 ACAT-ATA
66 AAATGA-A
* * * * * *
7335 AGAGAAATACAAAAAATGAAAGAAATAAACAGTGAAAGAATCAAGATTCATAGTAAAACTTGGAG
1 AAAGAAAAACAACAAATGGAAGAAATAAACACTGAAAGAATCAAGATTCATAGTAAAACTTGGAA
* *
7400 ACATGTA
66 AAATGAA
* * * ** **
7407 AGAGAAATAGAACAAATGGAAGAAAGGAACACTGAAAGAATCAAGATTCACGGTAAAACTTGGGA
1 AAAGAAAAACAACAAATGGAAGAAATAAACACTGAAAGAATCAAGATTCATAGTAAAACTT-GGA
7472 AAAA
65 AAAA
7476 AATAGAATAC
Statistics
Matches: 184, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
71 3 0.02
72 176 0.96
73 5 0.03
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.15
Consensus pattern (72 bp):
AAAGAAAAACAACAAATGGAAGAAATAAACACTGAAAGAATCAAGATTCATAGTAAAACTTGGAA
AAATGAA
Found at i:7371 original size:144 final size:144
Alignment explanation
Indices: 7193--7465 Score: 404
Period size: 144 Copynumber: 1.9 Consensus size: 144
7183 ATTATGTGAA
**
7193 AGAAATAAAACAAATGGGAGAAATAAACAGTGAAAGAATCAAGATTCATAATAAAACTTGGAAAA
1 AGAAATAAAACAAATGAAAGAAATAAACAGTGAAAGAATCAAGATTCATAATAAAACTTGGAAAA
* *
7258 ATGAAAAAGAAAAACAACAAATGGAAGAAATAAACACCGAAAGAATCAAGATTCATAGTAAAACC
66 ATGAAAAAGAAAAACAACAAATGGAAGAAAGAAACACCGAAAGAATCAAGATTCACAGTAAAACC
7323 TGGAAACATATAAG
131 TGGAAACATATAAG
* *
7337 AGAAATACAAA-AAATGAAAGAAATAAACAGTGAAAGAATCAAGATTCATAGTAAAACTTGGAGA
1 AGAAATA-AAACAAATGAAAGAAATAAACAGTGAAAGAATCAAGATTCATAATAAAACTTGGAAA
* * * * * * * *
7401 CATGTAAGAGAAATAGAACAAATGGAAGAAAGGAACACTGAAAGAATCAAGATTCACGGTAAAAC
65 AATGAAAAAGAAAAACAACAAATGGAAGAAAGAAACACCGAAAGAATCAAGATTCACAGTAAAAC
7466 TTGGGAAAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
144 111 0.97
145 3 0.03
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.15
Consensus pattern (144 bp):
AGAAATAAAACAAATGAAAGAAATAAACAGTGAAAGAATCAAGATTCATAATAAAACTTGGAAAA
ATGAAAAAGAAAAACAACAAATGGAAGAAAGAAACACCGAAAGAATCAAGATTCACAGTAAAACC
TGGAAACATATAAG
Found at i:7652 original size:22 final size:22
Alignment explanation
Indices: 7627--7678 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
7617 ACAAACAATA
7627 TTTAAAAAAATAAACGAACTTG
1 TTTAAAAAAATAAACGAACTTG
7649 TTTAAAAAAATAAACGAACTTG
1 TTTAAAAAAATAAACGAACTTG
*
7671 TTTCAAAA
1 TTTAAAAA
7679 TGGCAGAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (22 bp):
TTTAAAAAAATAAACGAACTTG
Found at i:9432 original size:187 final size:187
Alignment explanation
Indices: 9116--9476 Score: 580
Period size: 187 Copynumber: 1.9 Consensus size: 187
9106 AATTATCATT
* *
9116 ATTATAATCACTATAAATTATAAATATTTTTAACTGATCAACTCATTTTATAATTTTACCAACCA
1 ATTATAATCACTATAAATTATAAATATTTTTAACAGATCAACTCATTTTATAATTTTACCAAACA
* *
9181 AAAAAATATCTTATTTATATATAATTATTATTTGATGAAAAAAAAATATAAACTTTTGGACATTA
66 AAAAAATATCATATTTATATATAATTATTATTTGATGAAAAAAAAATATAAACTTTTAGACATTA
9246 TTTATACTATTTATAATGTGTTTGAGTTTGAAGTTAAAAATTAAAAAAAAAGTATTA
131 TTTATACTATTTATAATGTGTTTGAGTTTGAAGTTAAAAATTAAAAAAAAAGTATTA
* * * * *
9303 ATTATAATCACTTTATATTATAAATATTTTTAAGAGATTAACTCATTTTATAATTTTATCAAACA
1 ATTATAATCACTATAAATTATAAATATTTTTAACAGATCAACTCATTTTATAATTTTACCAAACA
*
9368 AAAAAAT-TCATATTTATATATAATTATTATTTGATGAAAGAATAAATATAAACTTTTAGACATT
66 AAAAAATATCATATTTATATATAATTATTATTTGATGAAA-AAAAAATATAAACTTTTAGACATT
* * * *
9432 ATTTATATTGTTTGTAATGTGTTTGAGTTTGAAGTTACAAATTAA
130 ATTTATACTATTTATAATGTGTTTGAGTTTGAAGTTAAAAATTAA
9477 GTGAAATCAA
Statistics
Matches: 159, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
186 31 0.19
187 128 0.81
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (187 bp):
ATTATAATCACTATAAATTATAAATATTTTTAACAGATCAACTCATTTTATAATTTTACCAAACA
AAAAAATATCATATTTATATATAATTATTATTTGATGAAAAAAAAATATAAACTTTTAGACATTA
TTTATACTATTTATAATGTGTTTGAGTTTGAAGTTAAAAATTAAAAAAAAAGTATTA
Found at i:9924 original size:6 final size:6
Alignment explanation
Indices: 9913--9982 Score: 61
Period size: 6 Copynumber: 11.2 Consensus size: 6
9903 GAAATACAAG
* * *
9913 TATTTT TATTTTT TAACTTTT TA-TTT TATTTT TATTAT TATTAT TATTAT
1 TATTTT TA-TTTT T-A-TTTT TATTTT TATTTT TATTTT TATTTT TATTTT
*
9963 TATTAT TATTATT TATTTT T
1 TATTTT TATT-TT TATTTT T
9983 TTGAAAGTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
5 5 0.09
6 35 0.61
7 11 0.19
8 6 0.11
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:9950 original size:9 final size:9
Alignment explanation
Indices: 9913--9982 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
9903 GAAATACAAG
9913 TATTTTTAT
1 TATTTTTAT
*
9922 T-TTTTAACT
1 TATTTTTA-T
9931 T-TTTATT-T
1 TATTT-TTAT
9939 TATTTTTAT
1 TATTTTTAT
*
9948 TATTATTAT
1 TATTTTTAT
*
9957 TATTATTAT
1 TATTTTTAT
*
9966 TATTATTATT
1 TATTTTTA-T
9976 TATTTTT
1 TATTTTT
9983 TTGAAAGTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
8 9 0.17
9 35 0.67
10 8 0.15
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.74
Consensus pattern (9 bp):
TATTTTTAT
Found at i:9952 original size:3 final size:3
Alignment explanation
Indices: 9933--9975 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
9923 TTTTAACTTT
*
9933 TTA TT- TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9976 TATTTTTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:10684 original size:2 final size:2
Alignment explanation
Indices: 10677--10714 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
10667 CGATTTCATC
*
10677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10715 TGAAAAAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14273 original size:2 final size:2
Alignment explanation
Indices: 14266--14299 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
14256 GAAAGGCATA
*
14266 AT AT AT AT AT AC 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
14300 GGAACTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15631 original size:31 final size:28
Alignment explanation
Indices: 15596--15661 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
15586 ACATTATAAT
* *
15596 ATATTAATTTACAAGTTTTTCAATAATTTTG
1 ATATTAATTTA-AA-TATTT-AAAAATTTTG
15627 ATATTAATTTAAATATTTAAAAATTTTG
1 ATATTAATTTAAATATTTAAAAATTTTG
*
15655 ATCTTAA
1 ATATTAA
15662 AAATAGACGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 15 0.47
29 4 0.12
30 2 0.06
31 11 0.34
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (28 bp):
ATATTAATTTAAATATTTAAAAATTTTG
Found at i:17628 original size:21 final size:21
Alignment explanation
Indices: 17602--17657 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
17592 TATTGTATAG
*
17602 AAATAAAAATAAAATAAAATA
1 AAATAATAATAAAATAAAATA
** *
17623 AAATAATTTTAAAATAGAATA
1 AAATAATAATAAAATAAAATA
*
17644 AGATAATAATAAAA
1 AAATAATAATAAAA
17658 AATATTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (21 bp):
AAATAATAATAAAATAAAATA
Found at i:17747 original size:13 final size:13
Alignment explanation
Indices: 17708--17748 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
17698 ATTTTTATAA
*
17708 AAAATATAATTTTA
1 AAAA-ATAATTTTT
17722 AAAAATAATTTTT
1 AAAAATAATTTTT
*
17735 AAAGATAATTTTT
1 AAAAATAATTTTT
17748 A
1 A
17749 CAGTCTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
AAAAATAATTTTT
Found at i:18506 original size:2 final size:2
Alignment explanation
Indices: 18499--18530 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18489 ATCTCCCACA
18499 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
18531 TACTTCAGAA
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:18811 original size:24 final size:21
Alignment explanation
Indices: 18773--18820 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 21
18763 TCTAATAAAT
18773 TAAAATTTTAATTTTAATATTTA
1 TAAAATTTTAATTTTAA-A-TTA
*
18796 TAAAATTTTTATTTTTAAATTA
1 TAAAA-TTTTAATTTTAAATTA
18818 TAA
1 TAA
18821 TTTATTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 6 0.26
24 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAAATTTTAATTTTAAATTA
Found at i:19712 original size:15 final size:14
Alignment explanation
Indices: 19682--19717 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
19672 TTTAAATTTG
*
19682 AATTTAATTTAATT
1 AATTTAATTAAATT
19696 AATTTATATTAAATT
1 AATTTA-ATTAAATT
19711 AATTTAA
1 AATTTAA
19718 AATATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTAATTAAATT
Found at i:19990 original size:12 final size:12
Alignment explanation
Indices: 19973--20000 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19963 TTAACGTTAG
19973 ATATATAAATAT
1 ATATATAAATAT
19985 ATATATAAATAT
1 ATATATAAATAT
19997 ATAT
1 ATAT
20001 TTATATGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:22184 original size:24 final size:25
Alignment explanation
Indices: 22138--22185 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
22128 TTATTTTATT
* **
22138 AATTATGTAAATATAAATTTTTAAA
1 AATTATGTAAATAAAAAAATTTAAA
22163 AATTAT-TAAATAAAAAAATTTAA
1 AATTATGTAAATAAAAAAATTTAA
22186 TTATAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AATTATGTAAATAAAAAAATTTAAA
Found at i:22472 original size:20 final size:20
Alignment explanation
Indices: 22444--22486 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
22434 TATATTACGC
* *
22444 TATGTTTATTAATTATTTTA
1 TATGCTTATTAAATATTTTA
22464 TATGCTTATTAAATATTTTA
1 TATGCTTATTAAATATTTTA
22484 TAT
1 TAT
22487 ACATGTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
TATGCTTATTAAATATTTTA
Found at i:24014 original size:17 final size:17
Alignment explanation
Indices: 23992--24044 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
23982 TATTTAAGAT
23992 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
24009 ATTTTAATATGTA-AT-A
1 ATTTT-ATATTTATATAA
24025 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
24040 ATTTT
1 ATTTT
24045 GAAACACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 2 0.07
14 5 0.17
15 5 0.17
16 5 0.17
17 7 0.23
18 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:24399 original size:7 final size:7
Alignment explanation
Indices: 24389--24443 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
24379 AAAAATTCAA
24389 AAAAATT
1 AAAAATT
24396 AAAAA-T
1 AAAAATT
24402 AAAAATTTT
1 AAAAA--TT
24411 AAAAATT
1 AAAAATT
24418 AAAAATTT
1 AAAAA-TT
24426 AAAAA-T
1 AAAAATT
*
24432 AAAATTT
1 AAAAATT
24439 AAAAA
1 AAAAA
24444 ATTTAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
6 11 0.27
7 17 0.41
8 7 0.17
9 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAAATT
Found at i:24405 original size:22 final size:22
Alignment explanation
Indices: 24379--24423 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
24369 TTTTAATTCC
24379 AAAAATTCAAAAAAATTAAAAAT
1 AAAAATT-AAAAAAATTAAAAAT
**
24402 AAAAATTTTAAAAATTAAAAAT
1 AAAAATTAAAAAAATTAAAAAT
24424 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAATTAAAAAAATTAAAAAT
Found at i:24412 original size:15 final size:15
Alignment explanation
Indices: 24394--24445 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
24384 TTCAAAAAAA
24394 TTAAAAATAAAAATT
1 TTAAAAATAAAAATT
24409 TTAAAAATTAAAAA-T
1 TTAAAAA-TAAAAATT
24424 TTAAAAAT-AAAATT
1 TTAAAAATAAAAATT
*
24438 TAAAAAAT
1 TTAAAAAT
24446 TTAAAAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.12
14 9 0.26
15 15 0.44
16 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAATAAAAATT
Found at i:24461 original size:11 final size:9
Alignment explanation
Indices: 24402--24491 Score: 52
Period size: 9 Copynumber: 10.7 Consensus size: 9
24392 AATTAAAAAT
*
24402 AAAAATTTT
1 AAAAATTTA
24411 AAAAA-TT-
1 AAAAATTTA
24418 AAAAATTT-
1 AAAAATTTA
24426 AAAAA--T-
1 AAAAATTTA
24432 -AAAATTTA
1 AAAAATTTA
24440 AAAAATTTA
1 AAAAATTTA
*
24449 AAAAATCTA
1 AAAAATTTA
* *
24458 TAAAA-CTA
1 AAAAATTTA
24466 TAAAAATTATA
1 -AAAAATT-TA
* *
24477 TAAAATTAA
1 AAAAATTTA
24486 AAAAAT
1 AAAAAT
24492 AAAAAATAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
5 4 0.06
6 1 0.02
7 6 0.09
8 12 0.18
9 35 0.53
10 6 0.09
11 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTTA
Found at i:24469 original size:19 final size:19
Alignment explanation
Indices: 24447--24492 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
24437 TTAAAAAATT
*
24447 TAAAAAATCTATAAAACTA
1 TAAAAAATATATAAAACTA
* *
24466 TAAAAATTATATAAAATTA
1 TAAAAAATATATAAAACTA
24485 -AAAAAATA
1 TAAAAAATA
24493 AAAAATAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAATATATAAAACTA
Found at i:24489 original size:8 final size:8
Alignment explanation
Indices: 24388--24498 Score: 79
Period size: 8 Copynumber: 13.9 Consensus size: 8
24378 CAAAAATTCA
24388 AAAAAATT
1 AAAAAATT
24396 -AAAAA-T
1 AAAAAATT
*
24402 AAAAATTT
1 AAAAAATT
*
24410 TAAAAATT
1 AAAAAATT
24418 -AAAAATT
1 AAAAAATT
*
24425 TAAAAA-T
1 AAAAAATT
*
24432 -AAAATTT
1 AAAAAATT
24439 AAAAAATTT
1 AAAAAA-TT
24448 AAAAAATCT
1 AAAAAAT-T
* *
24457 ATAAAACT
1 AAAAAATT
24465 ATAAAAATT
1 A-AAAAATT
24474 ATATAAAATT
1 A-A-AAAATT
*
24484 AAAAAAAT
1 AAAAAATT
24492 AAAAAAT
1 AAAAAAT
24499 AGAAAATAGA
Statistics
Matches: 83, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
6 5 0.06
7 18 0.22
8 30 0.36
9 23 0.28
10 7 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAAAATT
Found at i:24649 original size:18 final size:17
Alignment explanation
Indices: 24604--24650 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
24594 ATTCAAAAAA
24604 TTATAATTTTTTTGAAAT
1 TTATAATTTTTTT-AAAT
24622 TTATACA-TTTTTTATAAT
1 TTATA-ATTTTTTTA-AAT
24640 TTAATAATTTT
1 TT-ATAATTTT
24651 CTTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 17 0.68
19 7 0.28
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TTATAATTTTTTTAAAT
Found at i:24685 original size:9 final size:9
Alignment explanation
Indices: 24671--24818 Score: 100
Period size: 9 Copynumber: 16.4 Consensus size: 9
24661 TTCTATATAA
24671 AATTTTTAT
1 AATTTTTAT
24680 AA-TTTTAT
1 AATTTTTAT
*
24688 AGATATTTTAA
1 A-AT-TTTTAT
*
24699 AATTTAT-T
1 AATTTTTAT
24707 AA-TTTT-T
1 AATTTTTAT
24714 -ATTTTTA-
1 AATTTTTAT
24721 AATTTTTAT
1 AATTTTTAT
24730 AA-TTTTAT
1 AATTTTTAT
24738 AGATTTTTAT
1 A-ATTTTTAT
24748 AATTTTTATTTT
1 AATTTTTA---T
*
24760 ACTTTTT-T
1 AATTTTTAT
*
24768 AATTTTTTTT
1 AA-TTTTTAT
24778 AATTTTTAT
1 AATTTTTAT
24787 AA-TTTTAT
1 AATTTTTAT
24795 AGATTTTT-T
1 A-ATTTTTAT
24804 AAATTTTTTAT
1 -AA-TTTTTAT
24815 AATT
1 AATT
24819 ATCTGAATTT
Statistics
Matches: 113, Mismatches: 7, Indels: 38
0.72 0.04 0.24
Matches are distributed among these distances:
6 1 0.01
7 8 0.07
8 32 0.28
9 34 0.30
10 24 0.21
11 7 0.06
12 7 0.06
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.66
Consensus pattern (9 bp):
AATTTTTAT
Found at i:24687 original size:8 final size:8
Alignment explanation
Indices: 24674--24801 Score: 65
Period size: 8 Copynumber: 15.5 Consensus size: 8
24664 TATATAAAAT
24674 TTTTATAA
1 TTTTATAA
24682 TTTTATAGA
1 TTTTATA-A
24691 TATTT-TAAA
1 T-TTTAT-AA
*
24700 ATTTATTAA
1 TTTTA-TAA
*
24709 TTTT-TAT
1 TTTTATAA
24716 TTTTA-AA
1 TTTTATAA
24723 TTTTTATAA
1 -TTTTATAA
24732 TTTTATAGA
1 TTTTATA-A
24741 TTTTTATAA
1 -TTTTATAA
24750 TTTT-T-A
1 TTTTATAA
24756 TTTTACT--
1 TTTTA-TAA
24763 TTTT-TAA
1 TTTTATAA
*
24770 TTTTTTTTAA
1 --TTTTATAA
24780 TTTTTATAA
1 -TTTTATAA
24789 TTTTATAGA
1 TTTTATA-A
24798 TTTT
1 TTTT
24802 TTAAATTTTT
Statistics
Matches: 97, Mismatches: 5, Indels: 35
0.71 0.04 0.26
Matches are distributed among these distances:
5 1 0.01
6 5 0.05
7 12 0.12
8 34 0.35
9 30 0.31
10 15 0.15
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (8 bp):
TTTTATAA
Found at i:24717 original size:22 final size:23
Alignment explanation
Indices: 24691--24735 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
24681 ATTTTATAGA
24691 TATTTTAAAATTTAT-TAATTTT
1 TATTTTAAAATTTATATAATTTT
* *
24713 TATTTTTAAATTTTTATAATTTT
1 TATTTTAAAATTTATATAATTTT
24736 ATAGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTTAAAATTTATATAATTTT
Found at i:24829 original size:27 final size:27
Alignment explanation
Indices: 24670--24838 Score: 88
Period size: 27 Copynumber: 6.4 Consensus size: 27
24660 ATTCTATATA
* *
24670 AAATTTTTATAATTTTATAGATATTTTA
1 AAATTTTTATAATTATATAGA-ATTTTT
* *
24698 AAATTTAT-TAATT-T-T--TATTTTT
1 AAATTTTTATAATTATATAGAATTTTT
*
24720 AAATTTTTATAATTTTATAG-ATTTTT
1 AAATTTTTATAATTATATAGAATTTTT
* * * *
24746 ATAATTTTTATTTTACTTTTTTA-ATTTTTTT
1 A-AATTTTTA---TAATTATATAGA-ATTTTT
* * *
24777 TAATTTTTATAATTTTATAGATTTTTT
1 AAATTTTTATAATTATATAGAATTTTT
*
24804 AAATTTTTTATAATTATCT-GAATTTTT
1 AAA-TTTTTATAATTATATAGAATTTTT
24831 --ATTTTTAT
1 AAATTTTTAT
24839 TTTTAAATTT
Statistics
Matches: 114, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
22 12 0.11
23 5 0.04
24 8 0.07
25 3 0.03
26 8 0.07
27 36 0.32
28 21 0.18
30 16 0.14
31 5 0.04
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.65
Consensus pattern (27 bp):
AAATTTTTATAATTATATAGAATTTTT
Found at i:24848 original size:57 final size:56
Alignment explanation
Indices: 24628--24848 Score: 171
Period size: 57 Copynumber: 3.8 Consensus size: 56
24618 AAATTTATAC
* * * * *
24628 ATTTTTTATAATTTAATAATTTTCTTTTTTTTATTCTATATAAAATTTTTATA-ATTTTATAG
1 ATTTTTTATAA-TTATTAA-TTT-TTATTTTTATT-T-T-TATAA-TTTTATAGATTTTTTAA
* *
24690 ATATTTTAAAATTTATTAATTTTTATTTTTAAATTTTTATAATTTTATAGATTTTTATAA
1 ATTTTTTATAA-TTATTAATTTTTATTTTT--ATTTTTATAATTTTATAGATTTTT-TAA
* * * * *
24750 TTTTTATTTTACTTTTTTAA-TTTT-TTTTAATTTTTATAATTTTATAGATTTTTTAA
1 ATTTT-TTATA-ATTATTAATTTTTATTTTTATTTTTATAATTTTATAGATTTTTTAA
24806 ATTTTTTATAATTATCTGAATTTTTATTTTTATTTTTA-AATTT
1 ATTTTTTATAATTAT-T-AATTTTTATTTTTATTTTTATAATTT
24849 GTTATTTTCA
Statistics
Matches: 130, Mismatches: 19, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
54 3 0.02
55 5 0.04
56 9 0.07
57 33 0.25
58 18 0.14
59 13 0.10
60 17 0.13
61 13 0.10
62 19 0.15
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (56 bp):
ATTTTTTATAATTATTAATTTTTATTTTTATTTTTATAATTTTATAGATTTTTTAA
Found at i:25504 original size:17 final size:17
Alignment explanation
Indices: 25481--25540 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
25471 TTAAAAATAT
*
25481 ATTT-AAAATAACTTAA
1 ATTTAAAAATAAATTAA
25497 ATTTTAAAAA-AAATTAA
1 A-TTTAAAAATAAATTAA
* *
25514 A-TAAAAAATAATTTAA
1 ATTTAAAAATAAATTAA
25530 ATTTAAAAATA
1 ATTTAAAAATA
25541 TACTAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
15 6 0.17
16 8 0.22
17 18 0.50
18 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAAATAAATTAA
Found at i:25537 original size:16 final size:16
Alignment explanation
Indices: 25481--25537 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
25471 TTAAAAATAT
*
25481 ATTTAAAATAACTTAA
1 ATTTAAAATAAATTAA
*
25497 ATTTTAAAAAAAATTAA
1 A-TTTAAAATAAATTAA
** *
25514 ATAAAAAATAATTTAA
1 ATTTAAAATAAATTAA
25530 ATTTAAAA
1 ATTTAAAA
25538 ATATACTAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTTAAAATAAATTAA
Found at i:35116 original size:52 final size:49
Alignment explanation
Indices: 35020--35115 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 49
35010 AATGTGATAA
*
35020 TAATTTTTTAAAATATTATTATTAAATAAAATATAAATTTTATTATTTG
1 TAATTTTTTAAAATATTATAATTAAATAAAATATAAATTTTATTATTTG
*
35069 TAATATTTTTAAAGATATTTATAATT-AAT-AAATATTAA-TTTATTATT
1 TAAT-TTTTTAAA-ATA-TTATAATTAAATAAAATATAAATTTTATTATT
35116 AAAAATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
49 13 0.31
50 16 0.38
51 6 0.14
52 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (49 bp):
TAATTTTTTAAAATATTATAATTAAATAAAATATAAATTTTATTATTTG
Found at i:35135 original size:20 final size:21
Alignment explanation
Indices: 35085--35124 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35075 TTTTAAAGAT
*
35085 ATTTATAATTAATAAATATTA
1 ATTTATTATTAATAAATATTA
35106 ATTTATTATTAA-AAATATT
1 ATTTATTATTAATAAATATT
35125 TTTTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTATTATTAATAAATATTA
Found at i:35276 original size:27 final size:26
Alignment explanation
Indices: 35223--35276 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
35213 AAATTAAAAA
*
35223 TAAATTTTAAATATTTAATATGTATT
1 TAAATTATAAATATTTAATATGTATT
35249 TAAATTATAATATAATTTAAT-TGTATT
1 TAAATTATAA-AT-ATTTAATATGTATT
35276 T
1 T
35277 CATAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 9 0.36
27 9 0.36
28 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TAAATTATAAATATTTAATATGTATT
Found at i:35458 original size:17 final size:18
Alignment explanation
Indices: 35428--35462 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35418 TCCATTATTA
35428 TAAAAAAGTAATTTTTTT
1 TAAAAAAGTAATTTTTTT
*
35446 TAAAAAA-TTATTTTTTT
1 TAAAAAAGTAATTTTTTT
35463 AGGAAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAAAAAAGTAATTTTTTT
Found at i:35627 original size:18 final size:18
Alignment explanation
Indices: 35604--35650 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
35594 TAAATTAAAA
* *
35604 TTTAAAAATTATCTATTT
1 TTTAAAAATTAACAATTT
*
35622 TTT-AAAATATAAGAATTT
1 TTTAAAAAT-TAACAATTT
35640 TTTAAAAATTA
1 TTTAAAAATTA
35651 CTTAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTAAAAATTAACAATTT
Found at i:35831 original size:14 final size:14
Alignment explanation
Indices: 35800--35830 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
35790 CTAATAATTA
35800 TTTTAAAATTTTAT
1 TTTTAAAATTTTAT
35814 TTTTAAAA-TTTAT
1 TTTTAAAATTTTAT
35827 TTTT
1 TTTT
35831 TGCAGCGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTAAAATTTTAT
Found at i:38552 original size:24 final size:25
Alignment explanation
Indices: 38518--38566 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
38508 ATCTGAATAT
38518 ATAAATGTATCAAAATATATATAAA
1 ATAAATGTATCAAAATATATATAAA
*
38543 ATAAAT-TATCAAAATTTATATAAA
1 ATAAATGTATCAAAATATATATAAA
38567 TTTATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAAATGTATCAAAATATATATAAA
Found at i:38688 original size:32 final size:31
Alignment explanation
Indices: 38637--38696 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
38627 TATAAATATG
*
38637 ATAAAAAAATTGAGTTAATAATTTTAATAAA
1 ATAAAAAAATTGAGGTAATAATTTTAATAAA
38668 ATAAAAATAATTGAGGTAATAATTTTAAT
1 ATAAAAA-AATTGAGGTAATAATTTTAAT
38697 TTATTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (31 bp):
ATAAAAAAATTGAGGTAATAATTTTAATAAA
Found at i:40416 original size:20 final size:20
Alignment explanation
Indices: 40391--40431 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40381 TATTTTATAT
40391 TTTATTGAAATTAAAT-TAAA
1 TTTATT-AAATTAAATGTAAA
*
40411 TTTATTAAATTTAATGTAAA
1 TTTATTAAATTAAATGTAAA
40431 T
1 T
40432 AAATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTATTAAATTAAATGTAAA
Found at i:40977 original size:19 final size:19
Alignment explanation
Indices: 40953--40990 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40943 ATGATACATT
40953 TAATAAATATAAAATAATA
1 TAATAAATATAAAATAATA
*
40972 TAATAAATATAAGATAATA
1 TAATAAATATAAAATAATA
40991 CATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAATAAATATAAAATAATA
Found at i:41076 original size:18 final size:17
Alignment explanation
Indices: 41037--41079 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41027 CTATTATATT
*
41037 TATATTTAAAATTTTGA
1 TATATTTAAAATTATGA
41054 TATATTTAATAATTATG-
1 TATATTTAA-AATTATGA
41071 TGATATTTA
1 T-ATATTTA
41080 TATTTACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
TATATTTAAAATTATGA
Found at i:42738 original size:3 final size:3
Alignment explanation
Indices: 42730--42768 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
42720 CATTTTATTA
42730 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42769 GGTCAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43059 original size:82 final size:83
Alignment explanation
Indices: 42962--43131 Score: 279
Period size: 82 Copynumber: 2.1 Consensus size: 83
42952 ATATACATTA
*
42962 AATTTATCATGAAAAATATTGTATTTTTTAAAATGTAATAAATAAAAAATGGGTGAATA-ATTTT
1 AATTTATCATGAAAAATATTGTATTTTTTAAAAAGTAATAAATAAAAAATGGGTGAATACATTTT
43026 TTTTTAGTGAATGGTTTT
66 TTTTTAGTGAATGGTTTT
* * * *
43044 AATTTATTATGAAAAATATTGTGTTTTTTAAAAAGTAATGAATAAAAAATGGGTGAATACTTTTT
1 AATTTATCATGAAAAATATTGTATTTTTTAAAAAGTAATAAATAAAAAATGGGTGAATACATTTT
43109 TTTTTAGTGAATGGTTTT
66 TTTTTAGTGAATGGTTTT
*
43127 TATTT
1 AATTT
43132 TTTAAATTAA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 55 0.68
83 26 0.32
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.46
Consensus pattern (83 bp):
AATTTATCATGAAAAATATTGTATTTTTTAAAAAGTAATAAATAAAAAATGGGTGAATACATTTT
TTTTTAGTGAATGGTTTT
Found at i:44714 original size:3 final size:3
Alignment explanation
Indices: 44706--44731 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44696 CTCTATTTTA
44706 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
44732 GAACTTTTAA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:49952 original size:2 final size:2
Alignment explanation
Indices: 49945--49973 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49935 ATCGCATAAC
49945 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
49974 AGGGCTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52276 original size:38 final size:38
Alignment explanation
Indices: 52231--52306 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
52221 TTTAAAATAA
52231 CATAAAATAGTATGTATTTATGTTAATAAAATAAAATT
1 CATAAAATAGTATGTATTTATGTTAATAAAATAAAATT
52269 CATAAAATAGTATGTATTTATGTTAATAAAATAAAATT
1 CATAAAATAGTATGTATTTATGTTAATAAAATAAAATT
52307 GTAAATGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (38 bp):
CATAAAATAGTATGTATTTATGTTAATAAAATAAAATT
Found at i:52931 original size:17 final size:17
Alignment explanation
Indices: 52901--52933 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52891 ATTTTTATTT
52901 TTTTATATTATATTATA
1 TTTTATATTATATTATA
52918 TTTTA-ATTATTATTAT
1 TTTTATATTA-TATTAT
52934 TTTATGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATATTATATTATA
Found at i:53328 original size:21 final size:23
Alignment explanation
Indices: 53290--53331 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
53280 AGGTGTTGAA
53290 TAAAAAAATTAATGATTAAATAG
1 TAAAAAAATTAATGATTAAATAG
53313 TAAAAAAATT-AT-ATTAAAT
1 TAAAAAAATTAATGATTAAAT
53332 GATGTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TAAAAAAATTAATGATTAAATAG
Found at i:53973 original size:25 final size:25
Alignment explanation
Indices: 53900--53978 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
53890 TCGATTTTAT
* *
53900 AATAAATTTAAGTAGTATATTGATA
1 AATAAATTTTAGTAATATATTGATA
* *
53925 AATAAA--ATATTAAT-T-TT-AT-
1 AATAAATTTTAGTAATATATTGATA
53944 AATAAATTTTAGTAATATATTGATA
1 AATAAATTTTAGTAATATATTGATA
53969 AATAAATTTT
1 AATAAATTTT
53979 TTTATTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 6 0.14
20 2 0.05
21 8 0.19
22 2 0.05
23 6 0.14
24 2 0.05
25 16 0.38
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.44
Consensus pattern (25 bp):
AATAAATTTTAGTAATATATTGATA
Found at i:62163 original size:24 final size:25
Alignment explanation
Indices: 62136--62209 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 25
62126 AATATTAATA
62136 ATTTATTATTAATAATA-TAAAAAT
1 ATTTATTATTAATAATATTAAAAAT
62160 ATTTATGT-TTAATAATATTTAAAAAAT
1 ATTTAT-TATTAATAATA-TT-AAAAAT
**
62187 ATTTAAAATTAA-AATATTAAAAA
1 ATTTATTATTAATAATATTAAAAA
62210 CTTTTTACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
24 20 0.47
25 3 0.07
26 5 0.12
27 15 0.35
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
ATTTATTATTAATAATATTAAAAAT
Found at i:62202 original size:26 final size:26
Alignment explanation
Indices: 62143--62209 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 26
62133 ATAATTTATT
**
62143 ATTAATAATA-T-AAAAATATTTATG
1 ATTAATAATATTAAAAAATATTTAAA
*
62167 TTTAATAATATTTAAAAAATATTTAAA
1 ATTAATAATA-TTAAAAAATATTTAAA
62194 ATTAA-AATATTAAAAA
1 ATTAATAATATTAAAAA
62210 CTTTTTACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 9 0.25
25 7 0.19
26 5 0.14
27 15 0.42
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (26 bp):
ATTAATAATATTAAAAAATATTTAAA
Found at i:63450 original size:21 final size:22
Alignment explanation
Indices: 63425--63474 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
63415 TTCTAGTAAG
63425 TTTAATATTTA-TTTATTTATT
1 TTTAATATTTAGTTTATTTATT
*
63446 TTTAA-ATTTAGTTTTTTTATT
1 TTTAATATTTAGTTTATTTATT
63467 TTTAATAT
1 TTTAATAT
63475 ATAATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 19 0.73
22 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTAATATTTAGTTTATTTATT
Found at i:65335 original size:55 final size:56
Alignment explanation
Indices: 65240--65345 Score: 128
Period size: 55 Copynumber: 1.9 Consensus size: 56
65230 AAATTATATA
* *
65240 AAAATAATATAAATATAATTTTATACAATTTATATGAACAT-ATTATTAATATGGT
1 AAAATAATATAAATATAATTTTATAAAAATTATATGAACATAATTATTAATATGGT
* *
65295 AAAATTATATAAATATATATTATTTTAAAAATTAT-T-AACATAAATTATTAA
1 AAAATAATATAAATATA-ATT-TTATAAAAATTATATGAACAT-AATTATTAA
65346 ATTATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
55 21 0.49
56 4 0.09
57 18 0.42
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (56 bp):
AAAATAATATAAATATAATTTTATAAAAATTATATGAACATAATTATTAATATGGT
Found at i:65395 original size:13 final size:13
Alignment explanation
Indices: 65366--65408 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
65356 TTAAATATGA
*
65366 TATATATAAAA-T
1 TATATAAAAAATT
*
65378 TATATTAAAAATT
1 TATATAAAAAATT
65391 TATATAAATAAATT
1 TATATAAA-AAATT
65405 TATA
1 TATA
65409 ACTTGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 9 0.35
13 8 0.31
14 9 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATAAAAAATT
Found at i:65452 original size:15 final size:15
Alignment explanation
Indices: 65432--65476 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
65422 GTTGTTACTT
65432 TAAAAATTATTAATA
1 TAAAAATTATTAATA
*
65447 TAAAAAAATCATTAATA
1 T--AAAAATTATTAATA
*
65464 TAGAAATTATTAA
1 TAAAAATTATTAA
65477 ATCTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
TAAAAATTATTAATA
Found at i:65453 original size:17 final size:17
Alignment explanation
Indices: 65433--65465 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
65423 TTGTTACTTT
*
65433 AAAAATTATTAATATAA
1 AAAAATCATTAATATAA
65450 AAAAATCATTAATATA
1 AAAAATCATTAATATA
65466 GAAATTATTA
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:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATCATTAATATAA
Found at i:71253 original size:2 final size:2
Alignment explanation
Indices: 71246--71273 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
71236 CCTGTTGTCG
71246 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
71274 CATTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:82801 original size:17 final size:16
Alignment explanation
Indices: 82754--82801 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
82744 GAAATAATTT
*
82754 AAATAAT-TATTTTTA
1 AAATAATATAATTTTA
* *
82769 AAATAATTTAAATTTA
1 AAATAATATAATTTTA
82785 AATATAATATAATTTTA
1 AA-ATAATATAATTTTA
82802 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 7 0.26
16 8 0.30
17 12 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATAATATAATTTTA
Found at i:82844 original size:7 final size:7
Alignment explanation
Indices: 82834--82860 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
82824 AAAAATAAAA
82834 ATAATTT
1 ATAATTT
82841 ATAATTT
1 ATAATTT
82848 ATAATTT
1 ATAATTT
82855 ATAATT
1 ATAATT
82861 ATCATTTTCA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATAATTT
Found at i:84356 original size:16 final size:15
Alignment explanation
Indices: 84298--84377 Score: 85
Period size: 15 Copynumber: 5.3 Consensus size: 15
84288 AAATCTATCC
84298 AAAT-ATTAAATTT-
1 AAATAATTAAATTTA
* *
84311 AATTAATTTAAA-TAA
1 AAATAA-TTAAATTTA
84326 AAATAATTAAATTTA
1 AAATAATTAAATTTA
*
84341 AAATAAATAAATTTTA
1 AAATAATTAAA-TTTA
84357 AAATAATTTAAATTTA
1 AAATAA-TTAAATTTA
84373 AAATA
1 AAATA
84378 TATTTAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
13 3 0.05
14 7 0.13
15 22 0.40
16 19 0.35
17 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAATTAAATTTA
Found at i:89801 original size:12 final size:13
Alignment explanation
Indices: 89754--89802 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 13
89744 GATACGGTTC
89754 AAATATAACATAA
1 AAATATAACATAA
*
89767 AAA-AT-A-ATTA
1 AAATATAACATAA
*
89777 AAATATAATATAA
1 AAATATAACATAA
89790 AAAT-TAACATAA
1 AAATATAACATAA
89802 A
1 A
89803 CATGATAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
10 6 0.20
11 3 0.10
12 11 0.37
13 10 0.33
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATATAACATAA
Found at i:91253 original size:17 final size:16
Alignment explanation
Indices: 91230--91281 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
91220 AAATAAACTA
91230 ATTATTAAAATATTAT
1 ATTATTAAAATATTAT
* * *
91246 TTTGATTAATAT-TTCT
1 ATT-ATTAAAATATTAT
91262 ATTATTAAAATATTAAT
1 ATTATTAAAATATT-AT
91279 ATT
1 ATT
91282 TTATATTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
15 7 0.26
16 9 0.33
17 11 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTATTAAAATATTAT
Found at i:91290 original size:21 final size:23
Alignment explanation
Indices: 91250--91292 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
91240 TATTATTTTG
91250 ATTAATATTTCTATTATTAAAAT
1 ATTAATATTTCTATTATTAAAAT
91273 ATTAATATTT-TA-TATTAAAA
1 ATTAATATTTCTATTATTAAAA
91293 ACAATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
22 2 0.10
23 10 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTAATATTTCTATTATTAAAAT
Found at i:92109 original size:19 final size:20
Alignment explanation
Indices: 92084--92128 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
92074 TTATGATTAA
92084 AATTTTAAATATTTT-ATTT
1 AATTTTAAATATTTTAATTT
* * *
92103 TATTTTATATTTTTTAATTT
1 AATTTTAAATATTTTAATTT
92123 AATTTT
1 AATTTT
92129 TTAATTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
AATTTTAAATATTTTAATTT
Found at i:92127 original size:13 final size:14
Alignment explanation
Indices: 92100--92134 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
92090 AAATATTTTA
*
92100 TTTTATTTTATATT
1 TTTTAATTTATATT
92114 TTTTAATTTA-ATT
1 TTTTAATTTATATT
92127 TTTTAATT
1 TTTTAATT
92135 ATTTTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTAATTTATATT
Found at i:93651 original size:33 final size:34
Alignment explanation
Indices: 93603--93690 Score: 108
Period size: 32 Copynumber: 2.6 Consensus size: 34
93593 TATAATCTTA
* * *
93603 ATTAAAATATTTTATATTTATATAAATTTTGATAT
1 ATTAAAATA-TTTATATTTATATAAATATTAAAAT
*
93638 ATT-AATTATTTATA-TTATATAAATATTAAAAT
1 ATTAAAATATTTATATTTATATAAATATTAAAAT
93670 ATTAAAATATTTATATATTAT
1 ATTAAAATATTTATAT-TTAT
93691 TTATGTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
32 18 0.40
33 16 0.36
34 4 0.09
35 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (34 bp):
ATTAAAATATTTATATTTATATAAATATTAAAAT
Found at i:93687 original size:16 final size:16
Alignment explanation
Indices: 93603--93689 Score: 63
Period size: 16 Copynumber: 5.2 Consensus size: 16
93593 TATAATCTTA
93603 ATTAAAATATTTTATAT
1 ATTAAAATA-TTTATAT
*
93620 TTATATAAAT-TTTGATAT
1 AT-TA-AAATATTT-ATAT
*
93638 ATT-AATTATTTATAT
1 ATTAAAATATTTATAT
* *
93653 -TATATAAATATTAAAAT
1 AT-TA-AAATATTTATAT
93670 ATTAAAATATTTATAT
1 ATTAAAATATTTATAT
93686 ATTA
1 ATTA
93690 TTTATGTTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
14 1 0.02
15 8 0.15
16 17 0.31
17 16 0.30
18 8 0.15
19 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
ATTAAAATATTTATAT
Found at i:93761 original size:15 final size:15
Alignment explanation
Indices: 93734--93770 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
93724 TTTTTATATC
*
93734 ATCTAAT-TTATTAT
1 ATCTAATATTATTAG
93748 ATCTAATATTATTAG
1 ATCTAATATTATTAG
93763 ATCTAATA
1 ATCTAATA
93771 ATTTTAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (15 bp):
ATCTAATATTATTAG
Found at i:94771 original size:24 final size:26
Alignment explanation
Indices: 94744--94814 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 26
94734 AATATAACTG
94744 TTTTAATAATA-TATA-TTAAATATT
1 TTTTAATAATATTATATTTAAATATT
*
94768 TTTTAATAAATATTATATTTTAATATT
1 TTTTAAT-AATATTATATTTAAATATT
*
94795 TATATTAATAAAAATTATAT
1 T-T-TTAAT-AATATTATAT
94815 GAATATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.17
25 4 0.10
26 4 0.10
27 9 0.22
28 1 0.03
29 15 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTAATAATATTATATTTAAATATT
Found at i:94811 original size:29 final size:28
Alignment explanation
Indices: 94753--94814 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
94743 GTTTTAATAA
*
94753 TATATATTAAATATTTTTTAATAAATAT
1 TATATATTAAATATTTTTTAATAAAAAT
*
94781 TATAT-TTTAATATTTATATTAATAAAAAT
1 TATATATTAAATATTT-T-TTAATAAAAAT
94810 TATAT
1 TATAT
94815 GAATATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 9 0.30
28 6 0.20
29 15 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TATATATTAAATATTTTTTAATAAAAAT
Found at i:94827 original size:27 final size:27
Alignment explanation
Indices: 94755--94827 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
94745 TTTAATAATA
* *
94755 TATATTAAATATTTT-TTAATAAATAT
1 TATATTGAATATTTTATTAATAAAAAT
*
94781 TATATTTTAATATTTATATTAATAAAAAT
1 TATA-TTGAATATTT-TATTAATAAAAAT
94810 TATA-TGAATATTATTATT
1 TATATTGAATATT-TTATT
94828 TTAAATATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.10
27 20 0.50
28 2 0.05
29 14 0.35
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
TATATTGAATATTTTATTAATAAAAAT
Found at i:95514 original size:33 final size:33
Alignment explanation
Indices: 95477--95575 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 33
95467 TTATGTATAG
95477 AATATTTTATATTTATATATATTTTGATATATT
1 AATATTTTATATTTATATATATTTTGATATATT
* * * *
95510 AATA-TTTATA-TTATATAAATTATGAAACATT
1 AATATTTTATATTTATATATATTTTGATATATT
* * *
95541 TATATATTAATATTGTAT-TATATTTTAATTATATT
1 AATAT-TTTATATT-TATATATATTTTGA-TATATT
95576 TATAATCATA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
31 20 0.40
32 6 0.12
33 9 0.18
34 8 0.16
35 7 0.14
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (33 bp):
AATATTTTATATTTATATATATTTTGATATATT
Found at i:95576 original size:11 final size:12
Alignment explanation
Indices: 95557--95589 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
95547 TTAATATTGT
95557 ATTATATTT-TA
1 ATTATATTTATA
95568 ATTATATTTATA
1 ATTATATTTATA
*
95580 ATCATATTTA
1 ATTATATTTA
95590 ATATTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATATTTATA
Found at i:95903 original size:2 final size:2
Alignment explanation
Indices: 95896--95931 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
95886 TCTACCTTTA
95896 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
95932 CTCTACATAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96921 original size:13 final size:13
Alignment explanation
Indices: 96903--96930 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
96893 ATAATTAAAT
96903 AAATTCAATATAA
1 AAATTCAATATAA
96916 AAATTCAATATAA
1 AAATTCAATATAA
96929 AA
1 AA
96931 TAAATTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATTCAATATAA
Found at i:96937 original size:16 final size:16
Alignment explanation
Indices: 96899--96943 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
96889 ATATATAATT
96899 AAATAAATTCAATAT-
1 AAATAAATTCAATATA
96914 -AA-AAATTCAATATA
1 AAATAAATTCAATATA
96928 AAATAAATTCAATATA
1 AAATAAATTCAATATA
96944 TATTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 11 0.41
14 2 0.07
15 2 0.07
16 12 0.44
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAAATTCAATATA
Found at i:97039 original size:2 final size:2
Alignment explanation
Indices: 96986--97025 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
96976 CTTAAGCACC
96986 TA 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 TA
97026 AGGATCCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:97114 original size:4 final size:4
Alignment explanation
Indices: 97101--97131 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
97091 CAATGGGTTA
97101 ATTT -TTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
97132 TTACTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
ATTT
Found at i:99219 original size:18 final size:18
Alignment explanation
Indices: 99196--99233 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
99186 ATAATTACTC
99196 AAAAGAGAATGCCTTTTG
1 AAAAGAGAATGCCTTTTG
99214 AAAAGAGAATGCCTTTTG
1 AAAAGAGAATGCCTTTTG
99232 AA
1 AA
99234 TTTAATCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (18 bp):
AAAAGAGAATGCCTTTTG
Found at i:99968 original size:35 final size:35
Alignment explanation
Indices: 99876--99969 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 35
99866 TTTAAATAAT
*
99876 TTCTTATAGTAAGGTATATTGTTTTTATGATTATG
1 TTCTTATAGTAAGGTATATTGTTTTTATAATTATG
* ** * *
99911 TTCCTATA-TAA-AAATAATT-TTTTCA-AATTTTG
1 TTCTTATAGTAAGGTAT-ATTGTTTTTATAATTATG
99943 TTCTTATAGTAAGGTATATTGTTTTTA
1 TTCTTATAGTAAGGTATATTGTTTTTA
99970 CGGTTATGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
32 12 0.27
33 13 0.29
34 13 0.29
35 7 0.16
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (35 bp):
TTCTTATAGTAAGGTATATTGTTTTTATAATTATG
Found at i:101651 original size:13 final size:13
Alignment explanation
Indices: 101635--101663 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
101625 TAGAGAGAGT
101635 ATTAAGAGATAAA
1 ATTAAGAGATAAA
101648 ATTAAGAGATAAA
1 ATTAAGAGATAAA
101661 ATT
1 ATT
101664 GTGAGGATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (13 bp):
ATTAAGAGATAAA
Found at i:105999 original size:1 final size:1
Alignment explanation
Indices: 105993--106032 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
105983 AAAGTGTTTG
***
105993 AAAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
106033 TTTAAATGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.93, C:0.00, G:0.03, T:0.05
Consensus pattern (1 bp):
A
Found at i:106021 original size:20 final size:20
Alignment explanation
Indices: 105996--106034 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
105986 GTGTTTGAAA
105996 AAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAATTG
106016 AAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAATT
106035 TAAATGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAATTG
Found at i:106152 original size:19 final size:19
Alignment explanation
Indices: 106128--106195 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
106118 AATTCAACAA
106128 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
106147 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
106162 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
106179 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
106196 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:106167 original size:13 final size:13
Alignment explanation
Indices: 106149--106173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106139 ACATAAGTTT
106149 TGTATCGATACAA
1 TGTATCGATACAA
106162 TGTATCGATACA
1 TGTATCGATACA
106174 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:106171 original size:32 final size:32
Alignment explanation
Indices: 106130--106192 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
106120 TTCAACAATT
*
106130 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
106162 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
106193 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:106253 original size:13 final size:13
Alignment explanation
Indices: 106235--106260 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
106225 CATTTTTCTG
106235 TGTATCGATACAT
1 TGTATCGATACAT
106248 TGTATCGATACAT
1 TGTATCGATACAT
106261 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:106257 original size:33 final size:33
Alignment explanation
Indices: 106215--106281 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
106205 GCCAAGGAAA
***
106215 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
106248 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
106281 T
1 T
106282 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:108744 original size:28 final size:27
Alignment explanation
Indices: 108677--108749 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
108667 CTTCACAATC
* *
108677 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
108704 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
108732 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
108750 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:108794 original size:51 final size:51
Alignment explanation
Indices: 108732--108902 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
108722 TTATTTCTGA
* * *
108732 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * * *
108783 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCCATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
108836 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
108888 GAGGATACTCCAACC
1 GGGGATACTCCAACC
108903 TCGTTATTTC
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 36 0.38
52 18 0.19
53 32 0.33
54 10 0.10
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:108921 original size:28 final size:28
Alignment explanation
Indices: 108885--108966 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
108875 ATTTTTCACA
*
108885 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
108913 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
108941 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
108967 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:112148 original size:22 final size:20
Alignment explanation
Indices: 112096--112163 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 20
112086 ATTATTATTT
* *
112096 TTAATAAAATTAAAAATAATAT
1 TTAAT-AAATTAAAAA-ATTAA
112118 TTAATTAAATTTAAAAAATTACA
1 TTAA-TAAA-TTAAAAAATTA-A
*
112141 TTAATAAATTAAAATATTAA
1 TTAATAAATTAAAAAATTAA
112161 TTA
1 TTA
112164 CATGTTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.10
21 10 0.25
22 14 0.35
23 12 0.30
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAATAAATTAAAAAATTAA
Found at i:112179 original size:102 final size:105
Alignment explanation
Indices: 111991--112265 Score: 337
Period size: 102 Copynumber: 2.6 Consensus size: 105
111981 NNNNNNNNNN
* * *
111991 TTTTTAATAAAACTAAAAATAAT-TTTAATTAATTTTTAAAAATTTATATTAATAAATTAAAATA
1 TTTTTAATAAAA-TAAAAATAATATTTAATTAA-ATTTAAAAAATTACATTAATAAATTAAAATA
*
112055 TTAATTA-TTTTT-AAATTAAAAAA-GGTTTATTATTATTA-
64 TTAATTATTTTTTAAAATTAAAAAATGATTTATTATTATTAT
112093 TTTTTAATAAAATTAAAAATAATATTTAATTAAATTTAAAAAATTACATTAATAAATTAAAATAT
1 TTTTTAATAAAA-TAAAAATAATATTTAATTAAATTTAAAAAATTACATTAATAAATTAAAATAT
* * *
112158 TAATTACATGTTTTTATAAAAATAAAAAATTATTTTTTATTATTAT
65 TAATT--A--TTTTT-TAAAATTAAAAAATGATTTATTATTATTAT
* *
112204 TTTTTAAT-AAATAAAAATGATATTTAATTAAATTTAAAAAAATTTACATTAACAAATTAAAA
1 TTTTTAATAAAATAAAAATAATATTTAATTAAATTT-AAAAAA-TTACATTAATAAATTAAAA
112266 AAATAACATT
Statistics
Matches: 151, Mismatches: 10, Indels: 15
0.86 0.06 0.09
Matches are distributed among these distances:
102 56 0.37
103 9 0.06
104 1 0.01
107 4 0.03
108 1 0.01
109 33 0.22
110 21 0.14
111 26 0.17
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (105 bp):
TTTTTAATAAAATAAAAATAATATTTAATTAAATTTAAAAAATTACATTAATAAATTAAAATATT
AATTATTTTTTAAAATTAAAAAATGATTTATTATTATTAT
Found at i:112263 original size:23 final size:24
Alignment explanation
Indices: 112237--112295 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
112227 TTAATTAAAT
112237 TTAAAAAAATTTACA-TTAACAAA
1 TTAAAAAAATTTACATTTAACAAA
* **
112260 TTAAAAAAA-TAACATTTAAGGAA
1 TTAAAAAAATTTACATTTAACAAA
112283 TTAAAAAAATTTA
1 TTAAAAAAATTTA
112296 TTATTACTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 4 0.13
23 24 0.80
24 2 0.07
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (24 bp):
TTAAAAAAATTTACATTTAACAAA
Found at i:112290 original size:111 final size:110
Alignment explanation
Indices: 112084--112292 Score: 264
Period size: 109 Copynumber: 1.9 Consensus size: 110
112074 AAAAGGTTTA
*
112084 TTATTATTATTTTTAATAAAATTAAAAATAATATTTAATTAAATTTAAAAAATTACATTAATAAA
1 TTATTATTATTTTTAATAAAATTAAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAA
* * ***
112149 TTAAAATATTAATTACATGTTTTTATAAAAATAAAAAATTATTTT
66 TTAAAAAATAAATTACATGGAATTATAAAAATAAAAAATTATTTT
*
112194 TTATTATTATTTTTTAAT-AAA-TAAAAATGATATTTAATTAAATTTAAAAAAATTTACATTAAC
1 TTATTATTA-TTTTTAATAAAATTAAAAATAATATTTAATTAAATTT-AAAAAA-TTACATTAAC
*
112257 AAATTAAAAAAATAACATTTA-A-GGAATTAAAAAAAT
63 AAATT-AAAAAATAA-A-TTACATGGAATTATAAAAAT
112293 TTATTATTAC
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
109 23 0.27
110 18 0.21
111 22 0.26
112 17 0.20
113 2 0.02
114 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (110 bp):
TTATTATTATTTTTAATAAAATTAAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAA
TTAAAAAATAAATTACATGGAATTATAAAAATAAAAAATTATTTT
Found at i:112736 original size:123 final size:121
Alignment explanation
Indices: 112582--112833 Score: 364
Period size: 123 Copynumber: 2.1 Consensus size: 121
112572 AAAAAATATT
*
112582 ATTATAATAAAAAACTTTTTTTAATTTAAATTTTTT-TATTTTTAAAAACATAATAATTAATATT
1 ATTATAATAAAAAACTCTTTTTAATTTAAATTTTTTATATTTTTAAAAACATAATAATTAA-ATT
* * *
112646 TTAATTTGTCAATGTAAATTTTTAAATTTAATTAAATATTATTTTTTATTTTATTGAAA
65 TTAATTTGTCAATATAAATTTTTAAACTTAATTAAATATTA-TTTTAATTTTATT-AAA
* *
112705 ATTATAATAAAAAAC-CTTTTTATTTTAAAATTTTTTATTTTTTTAAAAACATAATAATTAAATT
1 ATTATAATAAAAAACTCTTTTTAATTT-AAATTTTTTATATTTTTAAAAACATAATAATTAAATT
* * *
112769 TTAATTTGTTAATATAATTTTTTTAACTTAATTAAATATTATTTTAATTTTATTAAA
65 TTAATTTGTCAATATAAATTTTTAAACTTAATTAAATATTATTTTAATTTTATTAAA
*
112826 ATAATAAT
1 ATTATAAT
112834 TGTCGCGACG
Statistics
Matches: 117, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
121 10 0.09
122 21 0.18
123 63 0.54
124 23 0.20
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (121 bp):
ATTATAATAAAAAACTCTTTTTAATTTAAATTTTTTATATTTTTAAAAACATAATAATTAAATTT
TAATTTGTCAATATAAATTTTTAAACTTAATTAAATATTATTTTAATTTTATTAAA
Found at i:112827 original size:22 final size:21
Alignment explanation
Indices: 112766--112828 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
112756 TAATAATTAA
* *
112766 ATTTTAATTTGTTAATATAATT
1 ATTTTAATTTATTAAAAT-ATT
* *
112788 TTTTTAACTTAATT-AAATATT
1 ATTTTAA-TTTATTAAAATATT
112809 ATTTTAATTTTATTAAAATA
1 ATTTTAA-TTTATTAAAATA
112829 ATAATTGTCG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 14 0.44
22 14 0.44
23 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTAATTTATTAAAATATT
Found at i:113877 original size:51 final size:51
Alignment explanation
Indices: 113808--113926 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 51
113798 GAGATAACAA
* * * * *
113808 CGGGGCTGGAGTACCCCTGATTATG-GAAAATCGATGTTCTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCTGATTATGAG-AAATCAATATTCTAGAAATAAAAC
* * * * *
113859 CGGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTAGGAATAAAGC
1 CGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTCTAGAAATAAAAC
113910 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
113927 CTTGGAAATA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTCTAGAAATAAAAC
Found at i:113994 original size:79 final size:79
Alignment explanation
Indices: 113859--114162 Score: 383
Period size: 79 Copynumber: 3.8 Consensus size: 79
113849 GAAATAAAAT
* * * *
113859 CGGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
*
113924 CCCCTTGGAAATAA
66 CCCCTCGGAAATAA
* **
113938 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAAAATAAAATTGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
*
114003 CCCCTCAGAAATAA
66 CCCCTCGGAAATAA
* * * ** *
114017 CAGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAGGCCGGGGTTGGAGCAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
*
114082 CCCCTCGAAAATAA
66 CCCCTCGGAAATAA
* * * * * * * *
114096 CGGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAAT-ATTTTAGAAATAAAACCGGGGTTGGAGTA
114161 TC
65 TC
114163 TCCGATTATA
Statistics
Matches: 190, Mismatches: 34, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
79 167 0.88
80 23 0.12
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGGAAATAA
Found at i:114169 original size:52 final size:52
Alignment explanation
Indices: 114100--114281 Score: 219
Period size: 51 Copynumber: 3.5 Consensus size: 52
114090 AAATAACGGG
* * *
114100 GTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAAAATAAAATCGGA
* * * *
114152 GTTGGAGTATCTCCGATTAT-AGAAATTTG-GTGTTTTGAAAATAAAA-CTGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGT-TTTTGAAAATAAAATC-GGA
* * *
114203 GTTAGAGTATCCCCGATTGTGAAAAATTAGTG-TTTCGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAAAATAAAATCGGA
*
114254 GTTGGAATATCCCCGATTATGAAAAATT
1 GTTGGAGTATCCCCGATTATGAAAAATT
114282 GAGAAACTTA
Statistics
Matches: 108, Mismatches: 17, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
50 3 0.03
51 79 0.73
52 25 0.23
53 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:114912 original size:10 final size:11
Alignment explanation
Indices: 114890--114918 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
114880 GCTCTTTGAG
114890 AGAAAAATATC
1 AGAAAAATATC
114901 AGAAAAAT-TC
1 AGAAAAATATC
114911 AGAAAAAT
1 AGAAAAAT
114919 CGTTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.66, C:0.07, G:0.10, T:0.17
Consensus pattern (11 bp):
AGAAAAATATC
Found at i:116636 original size:21 final size:21
Alignment explanation
Indices: 116610--116659 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
116600 ATCTGGGTAA
*
116610 ACTTCC-TAGATGTATCGATAC
1 ACTTCCTTA-ATGTACCGATAC
*
116631 ACTTCCTTAATGTACCGATAT
1 ACTTCCTTAATGTACCGATAC
*
116652 ATTTCCTT
1 ACTTCCTT
116660 GGCAGTAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (21 bp):
ACTTCCTTAATGTACCGATAC
Found at i:116705 original size:3 final size:3
Alignment explanation
Indices: 116697--116769 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
116687 ATAGATACAA
116697 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
116745 ATT AAT ACT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
116770 CAATTGAGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:117075 original size:16 final size:15
Alignment explanation
Indices: 117045--117074 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
117035 TTTTTTTATA
117045 AAAATAAAAAATTTT
1 AAAATAAAAAATTTT
*
117060 AAAATAAAAAGTTTT
1 AAAATAAAAAATTTT
117075 TTATTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAATAAAAAATTTT
Found at i:117107 original size:122 final size:120
Alignment explanation
Indices: 116850--117202 Score: 385
Period size: 122 Copynumber: 2.9 Consensus size: 120
116840 TATTTTTAAT
* * * *
116850 AAAA-AATATTTAATTAACTTTAAAGAAATTTATATCAACAAATTAAAATATTAATTATTTTG-T
1 AAAATAATATTTAATTAAGTTTAAA-AAA-TTACATTAACAAATTAAAATATTAATTATTATGTT
* * * *
116913 AATAATAAA-AAAATTTAAATAAAAATAAAAAAGGGTTTTTTATTATTATTTTTTAATAAAATTA
64 ATTAA-AAATAAAA---AAAT-AAAAT-AAAAA--GTTTTTTATTATAAATTTATAATAAAATTA
* * *
116977 AAAATAATATTTACTTAAGTTTAAAAAATTACATTAACAAATTAAAAT-TTAATTATTATTTTTT
1 AAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTA-TGTTA
*
117041 TATAAAAATAAAAAATTTTAAAATAAAAAGTTTTTTATTA-AAATTTATAATAAAA-TA
65 T-TAAAAATAAAAAA--ATAAAATAAAAAGTTTTTTATTATAAATTTATAATAAAATTA
*
117098 CAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTATGTTA
1 -AAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTATGTTA
* * *
117163 TTAAAAGTAAAAAAATAAATTAAAAATTTTTTTATTATAA
65 TTAAAAATAAAAAAATAAAATAAAAAGTTTTTTATTATAA
117203 TAATATTTTT
Statistics
Matches: 196, Mismatches: 20, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
119 20 0.10
120 2 0.01
121 14 0.07
122 62 0.32
123 21 0.11
125 16 0.08
126 24 0.12
127 12 0.06
128 25 0.13
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (120 bp):
AAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTATGTTAT
TAAAAATAAAAAAATAAAATAAAAAGTTTTTTATTATAAATTTATAATAAAATTA
Found at i:117677 original size:108 final size:114
Alignment explanation
Indices: 117521--117797 Score: 343
Period size: 108 Copynumber: 2.4 Consensus size: 114
117511 CTATGTTATT
* * * * *
117521 TTTTAATTTTTTAAAGTAAATTTTTTAAATTTTGATTAAATATCATTTTTTATTTTATTAAAAAA
1 TTTTAATTTATTAATGTAAATTTTTTAAA-TTTAATTAAATATTATTTTTAATTTTATTAAAAAA
* *
117586 TAATAA-AA-AAATACTTTTT-A-T-TTTTATAA-AAATATATAACTAATA
65 TAATAATAATAAACACTTTTTAATTATTTTATAATAAA-AAATAACTAATA
*
117631 TTTTAATTTGTTAATGT-AATTTTTTAAATTTAATTAAATATTATTTTTAATTTTATTAAAAAAT
1 TTTTAATTTATTAATGTAAATTTTTTAAATTTAATTAAATATTATTTTTAATTTTATTAAAAAAT
* *
117695 AATAATAATAAACACTTTTTAATTTAATTTTTTAATTTAAAAAATAATTAATA
66 AATAATAATAAACACTTTTTAA-TT-ATTTTATAA--TAAAAAATAACTAATA
* *
117748 TTTTAATTTATTAATGTAAATTTTTTAAAATTAATTAAATGTTATTTTTA
1 TTTTAATTTATTAATGTAAATTTTTTAAATTTAATTAAATATTATTTTTA
117798 TTAAAAAATA
Statistics
Matches: 144, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
108 38 0.26
109 13 0.09
110 25 0.17
111 1 0.01
113 1 0.01
115 7 0.05
117 26 0.18
118 33 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (114 bp):
TTTTAATTTATTAATGTAAATTTTTTAAATTTAATTAAATATTATTTTTAATTTTATTAAAAAAT
AATAATAATAAACACTTTTTAATTATTTTATAATAAAAAATAACTAATA
Found at i:117728 original size:13 final size:13
Alignment explanation
Indices: 117710--117734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
117700 TAATAAACAC
117710 TTTTTAATTTAAT
1 TTTTTAATTTAAT
117723 TTTTTAATTTAA
1 TTTTTAATTTAA
117735 AAAATAATTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:117779 original size:24 final size:26
Alignment explanation
Indices: 117752--117803 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
117742 TTAATATTTT
*
117752 AATTTATT-AATGTAAATTTT-TTAA
1 AATTAATTAAATGTAAATTTTATTAA
* *
117776 AATTAATTAAATGTTATTTTTATTAA
1 AATTAATTAAATGTAAATTTTATTAA
117802 AA
1 AA
117804 AATAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 10 0.43
26 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
AATTAATTAAATGTAAATTTTATTAA
Found at i:117805 original size:28 final size:31
Alignment explanation
Indices: 117774--117834 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
117764 TAAATTTTTT
*
117774 AAAAT-TAATTAA-ATGTTATT-TTTATTAA
1 AAAATATAATTAATATATTATTATTTATTAA
117802 AAAATAATAATTAATATATTATTATTTATTAA
1 AAAAT-ATAATTAATATATTATTATTTATTAA
117834 A
1 A
117835 TTTTTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 5 0.18
30 7 0.25
31 7 0.25
32 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
AAAATATAATTAATATATTATTATTTATTAA
Found at i:117985 original size:14 final size:14
Alignment explanation
Indices: 117966--118012 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
117956 ATTCATAAAC
117966 AAAAATTTATTTTA
1 AAAAATTTATTTTA
*
117980 AAAAATATT-TTATA
1 AAAAAT-TTATTTTA
*
117994 AAAAACTTA-TTTA
1 AAAAATTTATTTTA
118007 AAAAAT
1 AAAAAT
118013 AAAATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 10 0.37
14 15 0.56
15 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAATTTATTTTA
Found at i:118023 original size:27 final size:28
Alignment explanation
Indices: 117960--118025 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
117950 CAATATATTC
* **
117960 ATAAACAAAAATTTATTTTAAAAAATATT
1 ATAAA-AAAAACTTATTTTAAAAAATAAA
* *
117989 TTATAAAAAACTTA-TTTAAAAAATAAA
1 ATAAAAAAAACTTATTTTAAAAAATAAA
118016 ATAAAAAAAA
1 ATAAAAAAAA
118026 TCTATCACTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 19 0.63
28 8 0.27
29 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAAAAAAAACTTATTTTAAAAAATAAA
Found at i:119102 original size:68 final size:67
Alignment explanation
Indices: 119024--119173 Score: 191
Period size: 67 Copynumber: 2.3 Consensus size: 67
119014 GGTGCAGTAA
* * *
119024 TATATATTATTAATGAA-TAAAATGATGTCATCATATCATT-AAAATTTTTAAAAATAAATATAA
1 TATATATTATTAATGAATTAAAATAATATC-TC--ATCATTAAAAAATTTTAAAAATAAATATAA
119087 ATGAT
63 ATGAT
* *
119092 TATATATTATTAATAAATTAATATAATATCTCATCATTAAAAAATTTTAAAAATAAATATAAATG
1 TATATATTATTAATGAATTAAAATAATATCTCATCATTAAAAAATTTTAAAAATAAATATAAATG
119157 AT
66 AT
*
119159 T-T-TATTTTTAATGAA
1 TATATATTATTAATGAA
119174 ATGTTATCAT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
65 11 0.15
66 7 0.10
67 28 0.38
68 18 0.25
69 9 0.12
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (67 bp):
TATATATTATTAATGAATTAAAATAATATCTCATCATTAAAAAATTTTAAAAATAAATATAAATG
AT
Found at i:122946 original size:21 final size:21
Alignment explanation
Indices: 122914--122998 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
122904 AACTTAGATT
*
122914 TGATTTTGATAATTTTTAATA
1 TGATTTTTATAATTTTTAATA
* ** *
122935 TGGTTTTTATAATGCTTGATA
1 TGATTTTTATAATTTTTAATA
*
122956 TGATTTTTAAAATTTTTAATA
1 TGATTTTTATAATTTTTAATA
* *
122977 TGATTTTAATAATTTTTTATA
1 TGATTTTTATAATTTTTAATA
122998 T
1 T
122999 AATTAATTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.32, C:0.01, G:0.09, T:0.58
Consensus pattern (21 bp):
TGATTTTTATAATTTTTAATA
Found at i:123076 original size:21 final size:21
Alignment explanation
Indices: 123028--123138 Score: 68
Period size: 21 Copynumber: 5.4 Consensus size: 21
123018 TAACTTTTGG
* *
123028 TATAATATTGGTAACATTTAA
1 TATAATTTTGATAACATTTAA
*
123049 TATAATTTTGATAACTTTTAA
1 TATAATTTTGATAACATTTAA
* * *
123070 TTTAATTTTTATAA-A-CT-A
1 TATAATTTTGATAACATTTAA
* * *
123088 TATAATTTTAATAACTTTTGA
1 TATAATTTTGATAACATTTAA
* * * *
123109 TATTATCTTAATAAC-TTTGTA
1 TATAATTTTGATAACATTT-AA
123130 TATAATTTT
1 TATAATTTT
123139 AGTATATAAT
Statistics
Matches: 70, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
18 13 0.19
19 1 0.01
20 4 0.06
21 52 0.74
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
TATAATTTTGATAACATTTAA
Done.