Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 174 of 198
Found at i:54501015 original size:11 final size:11
Alignment explanation
Indices: 54500995--54501061 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
54500985 TAAAAATTAA
54500995 AAAAAGTATTTT
1 AAAAA-TATTTT
54501007 AAAAATATTTT
1 AAAAATATTTT
*
54501018 --AAA-A-TTA
1 AAAAATATTTT
* *
54501025 AAAAATA-ATA
1 AAAAATATTTT
54501035 AAAAAGTATTTT
1 AAAAA-TATTTT
54501047 AAAAATATTTT
1 AAAAATATTTT
54501058 AAAA
1 AAAA
54501062 TTAAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 6 0.13
10 8 0.17
11 18 0.39
12 11 0.24
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:54501045 original size:40 final size:40
Alignment explanation
Indices: 54500986--54501077 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
54500976 AATTTATTTT
*
54500986 AAAAATTA-AAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAATTA
54501025 AAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAATTA
*
54501065 AAAAA-ATTAAAAA
1 AAAAATAATAAAAA
54501078 TAAATATATT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
39 14 0.28
40 36 0.72
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (40 bp):
AAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:54501096 original size:41 final size:39
Alignment explanation
Indices: 54500986--54501089 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 39
54500976 AATTTATTTT
*
54500986 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTAAAAAAAATATTTTAAAAATATTTTAAAATTA
54501025 AAAAA-TAATAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAA-AAAAAA-TATTTTAAAAATATTTTAAAATT-A
54501066 AAAAATTAAAAATAAATATATTTA
1 AAAAATTAAAAA-AAATAT-TTTA
54501090 TTATATTGGG
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
38 3 0.05
39 10 0.17
40 23 0.40
41 12 0.21
42 10 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (39 bp):
AAAAATTAAAAAAAATATTTTAAAAATATTTTAAAATTA
Found at i:54501671 original size:16 final size:16
Alignment explanation
Indices: 54501650--54501681 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54501640 TACACGAGAA
54501650 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
*
54501666 AAATAATAAATTAAAT
1 AAATAATAAAATAAAT
54501682 TAAAAAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:54501949 original size:26 final size:29
Alignment explanation
Indices: 54501913--54501976 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 29
54501903 GGCCCTGCCC
* *
54501913 ATTTTTAAAAT-AAACA-TTAAAAAAA-T
1 ATTTTAAAAATAAAAAATTTAAAAAAATT
54501939 ATTTTAAAAATAAAAAATTTAAAAAAATT
1 ATTTTAAAAATAAAAAATTTAAAAAAATT
54501968 ATTTTAAAA
1 ATTTTAAAA
54501977 GTATTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 10 0.30
27 4 0.12
28 9 0.27
29 10 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (29 bp):
ATTTTAAAAATAAAAAATTTAAAAAAATT
Found at i:54501976 original size:28 final size:25
Alignment explanation
Indices: 54501915--54501976 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 25
54501905 CCCTGCCCAT
*
54501915 TTTTAAAATAAACATTAAAAAAATA
1 TTTTAAAATAAAAATTAAAAAAATA
54501940 TTTTAAAAATAAAAAATTTAAAAAAATTA
1 TTTT-AAAAT-AAAAA-TTAAAAAAA-TA
54501969 TTTTAAAA
1 TTTTAAAA
54501977 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 4 0.12
26 5 0.16
27 4 0.12
28 13 0.41
29 6 0.19
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTTAAAATAAAAATTAAAAAAATA
Found at i:54509412 original size:2 final size:2
Alignment explanation
Indices: 54509405--54509439 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54509395 TTGTTGGTGG
54509405 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
54509440 TACATGTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:54515039 original size:23 final size:22
Alignment explanation
Indices: 54514988--54515039 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
54514978 ATACTAATTA
* *
54514988 GAAGAAGATCTAAGGGTACACT
1 GAAGAAGATCTAAGAGAACACT
54515010 GAGAGAAGAT-TGAAGAGAACACT
1 GA-AGAAGATCT-AAGAGAACACT
54515033 CGAAGAA
1 -GAAGAA
54515040 CGCCGGCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.12
23 20 0.80
24 2 0.08
ACGTcount: A:0.46, C:0.12, G:0.29, T:0.13
Consensus pattern (22 bp):
GAAGAAGATCTAAGAGAACACT
Found at i:54543989 original size:4 final size:4
Alignment explanation
Indices: 54543980--54544005 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
54543970 ATTTATATTC
54543980 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
54544006 TTAAAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:54545877 original size:14 final size:17
Alignment explanation
Indices: 54545844--54545892 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 17
54545834 AATGTAAAAT
54545844 TTAATAATATTATGTTA
1 TTAATAATATTATGTTA
54545861 TTAA-AATA-TAT-TTA
1 TTAATAATATTATGTTA
*
54545875 TT-ATAATCATTATATTA
1 TTAATAAT-ATTATGTTA
54545892 T
1 T
54545893 GTTAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.04
14 8 0.29
15 4 0.14
16 7 0.25
17 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAATAATATTATGTTA
Found at i:54545984 original size:12 final size:12
Alignment explanation
Indices: 54545967--54545997 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54545957 GAAGCAGGGG
54545967 AGAAAAAGCGAA
1 AGAAAAAGCGAA
*
54545979 AGAAAAAGGGAA
1 AGAAAAAGCGAA
54545991 AGAAAAA
1 AGAAAAA
54545998 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGCGAA
Found at i:54546755 original size:40 final size:40
Alignment explanation
Indices: 54546688--54546764 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
54546678 AATTGAATCT
*
54546688 AAGTGAAATTATCTGAACTGTGTATTGATTAAAAAGTGGA
1 AAGTGAAATTATCTGAACTGTGTATTGAATAAAAAGTGGA
* *
54546728 AAGTGAAATTAAAT-TGAATTGTG-ATTGAATCAAAAGT
1 AAGTGAAATT--ATCTGAACTGTGTATTGAATAAAAAGT
54546765 AAATTTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 22 0.69
41 8 0.25
42 2 0.06
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (40 bp):
AAGTGAAATTATCTGAACTGTGTATTGAATAAAAAGTGGA
Found at i:54547526 original size:80 final size:80
Alignment explanation
Indices: 54547389--54547552 Score: 292
Period size: 80 Copynumber: 2.0 Consensus size: 80
54547379 ACTCAGCGTA
* *
54547389 CGGTTTTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGTTCCGGTTCAGCATCCAGATCAATCCCG
1 CGGTTGTTTCCGTGCACAGGTCGATAGAAGTCAAAGGTTCCGGTTCAGCATCCAGATCAATCCCG
54547454 ACTTCAACATAACTT
66 ACTTCAACATAACTT
* *
54547469 CGGTTGTTTCCGTGCACAGGTCGATAGAAGTCAAAGGTTTCGGTTCAGCATCTAGATCAATCCCG
1 CGGTTGTTTCCGTGCACAGGTCGATAGAAGTCAAAGGTTCCGGTTCAGCATCCAGATCAATCCCG
54547534 ACTTCAACATAACTT
66 ACTTCAACATAACTT
54547549 CGGT
1 CGGT
54547553 GATGTATTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (80 bp):
CGGTTGTTTCCGTGCACAGGTCGATAGAAGTCAAAGGTTCCGGTTCAGCATCCAGATCAATCCCG
ACTTCAACATAACTT
Found at i:54555349 original size:13 final size:13
Alignment explanation
Indices: 54555331--54555359 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54555321 TTGATATATT
54555331 ATTATATTTCTAG
1 ATTATATTTCTAG
54555344 ATTATATTTCTAG
1 ATTATATTTCTAG
54555357 ATT
1 ATT
54555360 GATAGTCAGC
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:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTATATTTCTAG
Found at i:54566625 original size:42 final size:43
Alignment explanation
Indices: 54566533--54566623 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 43
54566523 AATATATTTA
* * *
54566533 TTTTTTTAAA-TTTGAAATATTTTTTTACATACTTTTTTAATT
1 TTTTTTTAAATTTTAAAATATTTTTTAAAATACTTTTTTAATT
54566575 TTTTTTTAAATTTTAAAATA-TTTTTAAAATACTTTTTTTAATT
1 TTTTTTTAAATTTTAAAATATTTTTTAAAATAC-TTTTTTAATT
54566618 TTTTTT
1 TTTTTT
54566624 AATTTTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 20 0.45
43 24 0.55
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (43 bp):
TTTTTTTAAATTTTAAAATATTTTTTAAAATACTTTTTTAATT
Found at i:54566631 original size:18 final size:18
Alignment explanation
Indices: 54566607--54566647 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 18
54566597 TTTAAAATAC
54566607 TTTTTTTAATTTTTTTTAA
1 TTTTTTTAA-TTTTTTTAA
54566626 TTTTTTTAATTTTTTTAA
1 TTTTTTTAATTTTTTTAA
54566644 TTTT
1 TTTT
54566648 AAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTAATTTTTTTAA
Found at i:54566641 original size:42 final size:42
Alignment explanation
Indices: 54566533--54566643 Score: 136
Period size: 42 Copynumber: 2.6 Consensus size: 42
54566523 AATATATTTA
* *
54566533 TTTTTTTAAATTTGAAATATTTTTTT-ACATACTTTTTTAATT
1 TTTTTTTAAATTTTAAA-ATTTTTTTAAAATACTTTTTTAATT
*
54566575 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA-T
1 TTTTTTTAAATTTTAAAATTTTTTTAAAATAC-TTTTTTAATT
* **
54566617 TTTTTTTAATTTTTTTAATTTTTTTAA
1 TTTTTTTAAATTTTAAAATTTTTTTAA
54566644 TTTTAAAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
41 7 0.12
42 45 0.75
43 8 0.13
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.67
Consensus pattern (42 bp):
TTTTTTTAAATTTTAAAATTTTTTTAAAATACTTTTTTAATT
Found at i:54566663 original size:59 final size:61
Alignment explanation
Indices: 54566565--54566680 Score: 200
Period size: 59 Copynumber: 1.9 Consensus size: 61
54566555 TTTTACATAC
*
54566565 TTTTTTAATTTTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTTAAT
1 TTTTTTAA-TTTTTTTTAAATTTTAAAATATTTTAAAAATACTTTTTTTAATTTTTTTTAAT
54566627 TTTTTTAA-TTTTTTT-AATTTTAAAATATTTTAAAAATACTTTTTTTAATTTTTT
1 TTTTTTAATTTTTTTTAAATTTTAAAATATTTTAAAAATACTTTTTTTAATTTTTT
54566681 AAAATTTATA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
59 38 0.72
60 7 0.13
62 8 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (61 bp):
TTTTTTAATTTTTTTTAAATTTTAAAATATTTTAAAAATACTTTTTTTAATTTTTTTTAAT
Found at i:54567729 original size:16 final size:16
Alignment explanation
Indices: 54567708--54567759 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
54567698 TTTGGTTCGC
54567708 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
54567724 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
54567740 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
54567756 TGTA
1 TGTA
54567760 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:54572475 original size:29 final size:30
Alignment explanation
Indices: 54572437--54572507 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
54572427 CATTGGTAAA
*
54572437 TTTAAAATTT-AGTCCTTATATTTTT-AT-T
1 TTTAAAATTTAACT-CTTATATTTTTAATAT
*
54572465 TTTATAAATTTAACTCTTTTATTTTTAATAT
1 TTTA-AAATTTAACTCTTATATTTTTAATAT
54572496 TTTAAAATTTAA
1 TTTAAAATTTAA
54572508 ATTTAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 4 0.11
29 16 0.43
30 12 0.32
31 5 0.14
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTAAAATTTAACTCTTATATTTTTAATAT
Found at i:54575889 original size:51 final size:51
Alignment explanation
Indices: 54575813--54575916 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
54575803 CTTTTCAACC
* * *
54575813 ACACTGATCAGTTAATTTTCAGCTGGAGCAAATAGCAGCAGTTAGAGGCTT
1 ACACTGATCAGCTAATTCTCAGCTGGAGCAAATAGCAGCAATTAGAGGCTT
* *
54575864 ACACTGATCAGCTGATTCTCAGCTGGAGCAAATAGCAGTAATTAGAGGCTT
1 ACACTGATCAGCTAATTCTCAGCTGGAGCAAATAGCAGCAATTAGAGGCTT
54575915 AC
1 AC
54575917 TGAGCAGTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (51 bp):
ACACTGATCAGCTAATTCTCAGCTGGAGCAAATAGCAGCAATTAGAGGCTT
Found at i:54582261 original size:11 final size:11
Alignment explanation
Indices: 54582245--54582270 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54582235 AATTATAACT
54582245 ATTAAAAAAAA
1 ATTAAAAAAAA
54582256 ATTAAAAAAAA
1 ATTAAAAAAAA
54582267 ATTA
1 ATTA
54582271 TCATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
ATTAAAAAAAA
Found at i:54582535 original size:21 final size:21
Alignment explanation
Indices: 54582511--54582560 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
54582501 CATTGTTTCT
54582511 AATCTCACCGCTACAGTAACC
1 AATCTCACCGCTACAGTAACC
*
54582532 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
54582553 AATCTCAC
1 AATCTCAC
54582561 TGCCACTGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.36, G:0.08, T:0.22
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:54582646 original size:23 final size:23
Alignment explanation
Indices: 54582618--54582678 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
54582608 CAAACTAGCC
54582618 CTAAATCCCTAACAAGCAGCCCT
1 CTAAATCCCTAACAAGCAGCCCT
54582641 CTAAATCCCTAACAAGCAGCCCT
1 CTAAATCCCTAACAAGCAGCCCT
*
54582664 CTGAATCCCTAACAA
1 CTAAATCCCTAACAA
54582679 AAATATAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.38, G:0.08, T:0.18
Consensus pattern (23 bp):
CTAAATCCCTAACAAGCAGCCCT
Found at i:54582968 original size:17 final size:17
Alignment explanation
Indices: 54582948--54582989 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
54582938 TTAAAAAATT
54582948 ATTTTAAAAATAAAAAA
1 ATTTTAAAAATAAAAAA
*
54582965 A-TTTAAAAATAAAAAT
1 ATTTTAAAAATAAAAAA
54582981 ATTTTAAAA
1 ATTTTAAAA
54582990 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTTTAAAAATAAAAAA
Found at i:54584685 original size:24 final size:23
Alignment explanation
Indices: 54584658--54584718 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
54584648 AGTGGTTGAA
*
54584658 TAAAAAATAAAATATTTTATTTAT
1 TAAAAAATAAAATATTTTA-TTAC
54584682 TAAAAAAT-AAA-ATTTTATTAC
1 TAAAAAATAAAATATTTTATTAC
54584703 TAATAAAA-AAAATATT
1 TAA-AAAATAAAATATT
54584719 ACATTCGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 6 0.18
22 13 0.39
23 6 0.18
24 8 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAAAATAAAATATTTTATTAC
Found at i:54584710 original size:22 final size:22
Alignment explanation
Indices: 54584658--54584715 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
54584648 AGTGGTTGAA
*
54584658 TAAAAAATAAAATATTTTATTTAT
1 TAAAAAAT-AAA-ATTTTATTTAC
54584682 TAAAAAATAAAATTTTA-TTAC
1 TAAAAAATAAAATTTTATTTAC
54584703 TAATAAAA-AAAAT
1 TAA-AAAATAAAAT
54584716 ATTACATTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.34
22 10 0.31
23 3 0.09
24 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAAATAAAATTTTATTTAC
Found at i:54597862 original size:31 final size:29
Alignment explanation
Indices: 54597795--54597864 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
54597785 AAATTAAAAT
* * *
54597795 TTCATGTATAGAATTACACAAAATCAAAG
1 TTCATGTATACAATTACACAAAAACAAAC
*
54597824 TTCATGTATACAATTACACATTAAAACATAC
1 TTCATGTATACAATTACACA--AAAACAAAC
54597855 TTCATGTATA
1 TTCATGTATA
54597865 GTTTTGATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (29 bp):
TTCATGTATACAATTACACAAAAACAAAC
Found at i:54598143 original size:22 final size:22
Alignment explanation
Indices: 54598118--54598162 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54598108 TTAAAAGGTT
* *
54598118 TAAAAAAGTTGCCAAAATTATA
1 TAAAAAAGTTACCAAAATAATA
*
54598140 TAAAGAAGTTACCAAAATAATA
1 TAAAAAAGTTACCAAAATAATA
54598162 T
1 T
54598163 CGCACAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (22 bp):
TAAAAAAGTTACCAAAATAATA
Found at i:54599996 original size:24 final size:24
Alignment explanation
Indices: 54599969--54600020 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54599959 TTTATAGAAG
* *
54599969 ATTTAGCATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
54599993 ATTTAATATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
54600017 ATTT
1 ATTT
54600021 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:54600667 original size:42 final size:42
Alignment explanation
Indices: 54600608--54600858 Score: 342
Period size: 42 Copynumber: 5.8 Consensus size: 42
54600598 AGCGTTTACA
*
54600608 AAAAAAACGCTGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
*
54600650 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGTGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
54600692 AAAAAAACGCCTCTAAAGACCGTGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
*
54600734 AAAAAAACGCCGCTAAAGACCGTGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
54600776 AAAAAAAAAACGCCGCTAAAAGACCATATTTTTTAGCGGGCGCTTAG
1 ---AAAAAAACGCCGCT-AAAGACCATGTTCTTTAGC-GGCGCTTAG
* * *
54600823 AAAAAAAAACGCCGC-AAATATCATGTTTTTTAGCGG
1 --AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGG
54600859 GCGTTTTTTG
Statistics
Matches: 192, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
42 120 0.62
43 2 0.01
44 16 0.08
45 14 0.07
46 31 0.16
47 9 0.05
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
Found at i:54601583 original size:21 final size:21
Alignment explanation
Indices: 54601534--54601583 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
54601524 TTTTGGCCTG
*
54601534 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
54601555 TTCCGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
54601576 CTCTGCTT
1 CTCTGCTT
54601584 TAAGTTGTAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.46, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:54602412 original size:15 final size:14
Alignment explanation
Indices: 54602388--54602419 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
54602378 ATACCTCGCC
54602388 TTTCTACTATGAAA
1 TTTCTACTATGAAA
54602402 TTTCATACTATGAAA
1 TTTC-TACTATGAAA
54602417 TTT
1 TTT
54602420 TTAGTACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.47
Consensus pattern (14 bp):
TTTCTACTATGAAA
Found at i:54605119 original size:115 final size:114
Alignment explanation
Indices: 54604998--54605312 Score: 558
Period size: 114 Copynumber: 2.8 Consensus size: 114
54604988 TAATAATGTG
* * *
54604998 CTTCAGCGGCGATTTTATAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGTTTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
*
54605063 TGTTTAACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCA
66 TGTTTAACA-TTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATACA
*
54605113 CTTCAGCGGCGTTTTTACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGTTTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
*
54605178 TGTTTAACATTTTTTGCGGCGCTTACAAACAAATGCCGCTAATGATACA
66 TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATACA
*
54605227 CTTCAGCGGCGTTTTTACAGAAACGCCACTAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGTTTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
54605292 TGTTTAACATTTTTTGCGGCG
66 TGTTTAACATTTTTTGCGGCG
54605313 TTTTGACAGA
Statistics
Matches: 192, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
114 122 0.64
115 70 0.36
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (114 bp):
CTTCAGCGGCGTTTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
TGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATACA
Found at i:54605357 original size:75 final size:75
Alignment explanation
Indices: 54605232--54605387 Score: 269
Period size: 75 Copynumber: 2.1 Consensus size: 75
54605222 ATACACTTCA
* *
54605232 GCGGCGTTTTTACAGAAACGCCACTAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTGACAGAAACGCCACTAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTT
54605297 AACATTTTTT
66 AACATTTTTT
54605307 GCGGCGTTTTGACAGAAACGCCA-TCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTT
1 GCGGCGTTTTGACAGAAACGCCACT-AATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTT
54605371 TAACATTTTTT
65 TAACATTTTTT
*
54605382 ACGGCG
1 GCGGCG
54605388 CTTACAAACA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
74 1 0.01
75 76 0.99
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (75 bp):
GCGGCGTTTTGACAGAAACGCCACTAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTT
AACATTTTTT
Found at i:54605425 original size:114 final size:114
Alignment explanation
Indices: 54605307--54605749 Score: 760
Period size: 114 Copynumber: 3.9 Consensus size: 114
54605297 AACATTTTTT
* * *
54605307 GCGGCGTTTTGACAGAAACGCCATCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* *
54605372 AACATTTTTTACGGCGCTTACAAACAAATGCCGCTAATGATACACTTCA
66 AACATTTTTTACGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
*
54605421 GCGGCATTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* * *
54605486 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTATTTATCCACTTCA
66 AACATTTTTTACGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
*
54605535 GCGGTGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
54605600 AACATTTTTTACGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
66 AACATTTTTTACGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
* *
54605649 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACATCAATCTTGTACACTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* *
54605714 AACATTGTTTGCGGCGCTTACAAACAAACGCCGCTA
66 AACATTTTTTACGGCGCTTACAAACAAACGCCGCTA
54605750 CTGCCACTAT
Statistics
Matches: 310, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 310 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (114 bp):
GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
AACATTTTTTACGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
Found at i:54605438 original size:189 final size:189
Alignment explanation
Indices: 54605118--54605501 Score: 698
Period size: 189 Copynumber: 2.0 Consensus size: 189
54605108 ATCCACTTCA
* *
54605118 GCGGCGTTTTTACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTGACAGAAACGCCACAAATTCAACTATACCTCAATCCTGTACGCTGCGTTTTGTTT
* *
54605183 AACATTTTTTGCGGCGCTTACAAACAAATGCCGCTAATGATACACTTCAGCGGCGTTTTTACAGA
66 AACATTTTTTACGGCGCTTACAAACAAATGCCGCTAATGATACACTTCAGCGGCATTTTTACAGA
*
54605248 AACGCCACTAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
131 AACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
*
54605307 GCGGCGTTTTGACAGAAACGCCATC-AATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTT
1 GCGGCGTTTTGACAGAAACGCCA-CAAATTCAACTATACCTCAATCCTGTACGCTGCGTTTTGTT
54605371 TAACATTTTTTACGGCGCTTACAAACAAATGCCGCTAATGATACACTTCAGCGGCATTTTTACAG
65 TAACATTTTTTACGGCGCTTACAAACAAATGCCGCTAATGATACACTTCAGCGGCATTTTTACAG
54605436 AAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
130 AAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
54605496 GCGGCG
1 GCGGCG
54605502 CTTACAAACA
Statistics
Matches: 188, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
189 187 0.99
190 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (189 bp):
GCGGCGTTTTGACAGAAACGCCACAAATTCAACTATACCTCAATCCTGTACGCTGCGTTTTGTTT
AACATTTTTTACGGCGCTTACAAACAAATGCCGCTAATGATACACTTCAGCGGCATTTTTACAGA
AACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
Found at i:54605566 original size:303 final size:304
Alignment explanation
Indices: 54605003--54605615 Score: 1059
Period size: 303 Copynumber: 2.0 Consensus size: 304
54604993 ATGTGCTTCA
* *
54605003 GCGGCGATTTTATAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGATTTTACAGAAACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTT
* * *
54605068 AACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTTACAG
66 AACATTTTTTTACGGCGCTTACAAACAAACGCCGCTAATGATACACTTCAGCGGCATTTTTACAG
54605133 AAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGC
131 AAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGC
* *
54605198 GCTTACAAACAAATGCCGCTAATGATACACTTCAGCGGCGTTTTTACAGAAACGCCACTAATTCT
196 GCTTACAAACAAACGCCGCTAATGATACACTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCT
54605263 ACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
261 ACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
*
54605307 GCGGCG-TTTTGACAGAAACGCCATCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTT
1 GCGGCGATTTT-ACAGAAACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTT
*
54605371 TAACA-TTTTTTACGGCGCTTACAAACAAATGCCGCTAATGATACACTTCAGCGGCATTTTTACA
65 TAACATTTTTTTACGGCGCTTACAAACAAACGCCGCTAATGATACACTTCAGCGGCATTTTTACA
* *
54605435 GAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGG
130 GAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGG
* * * *
54605500 CGCTTACAAACAAACGCCGCTATTTATCCACTTCAGCGGTGTTTTTACAGAAACGCCACCAATTC
195 CGCTTACAAACAAACGCCGCTAATGATACACTTCAGCGGCGTTTTTACAGAAACGCCACCAATTC
54605565 TACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
260 TACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
*
54605610 ACGGCG
1 GCGGCG
54605616 CTTACAAACA
Statistics
Matches: 292, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
303 231 0.79
304 61 0.21
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (304 bp):
GCGGCGATTTTACAGAAACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTT
AACATTTTTTTACGGCGCTTACAAACAAACGCCGCTAATGATACACTTCAGCGGCATTTTTACAG
AAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGC
GCTTACAAACAAACGCCGCTAATGATACACTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCT
ACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
Found at i:54605783 original size:417 final size:418
Alignment explanation
Indices: 54604998--54605786 Score: 1278
Period size: 417 Copynumber: 1.9 Consensus size: 418
54604988 TAATAATGTG
*
54604998 CTTCAGCGGCGATTTTATAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
1 CTTCAGCGGCGATTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
54605063 TGTTTAACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTT
66 TGTTTAACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTT
54605128 TACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
131 TACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
* * *
54605193 GCGGCGCTTACAAACAAATGCCGCTAATGATACACTTCAGCGGCGTTTTTACAGAAACGCCACTA
196 ACGGCGCTTACAAACAAACGCCGCTAATGATACACTTCAGCGGCGTTTTTACAGAAACGCCACCA
* * * * ** * *
54605258 ATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGTTTTGACAGA
261 ATTCTACTATACATCAATCTTGTACACTGCGTTTTGTTTAACATTGTTTGCGGCGCTTACAAACA
* * * ** *
54605323 AACGCCATCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTTACGGCG
326 AACGCCATCAATGCCACTATACCTCAATACTAAACGATGCGTTTTGTTTAACATTTTTTACGGCG
54605388 CTTACAAACAAATGCCGCTAATGATACA
391 CTTACAAACAAATGCCGCTAATGATACA
54605416 CTTCAGCGGC-ATTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTT
1 CTTCAGCGGCGA-TTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTT
* * *
54605480 TTGTTTAACA-TTTTTTGCGGCGCTTACAAACAAACGCCGCTATTTATCCACTTCAGCGGTGTTT
65 TTGTTTAACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTT
* *
54605544 TTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTT
130 TTACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTT
*
54605609 TACGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTTACAGAAACGCCACC
195 TACGGCGCTTACAAACAAACGCCGCTAATGATACACTTCAGCGGCGTTTTTACAGAAACGCCACC
54605674 AATTCTACTATACATCAATCTTGTACACTGCGTTTTGTTTAACATTGTTTGCGGCGCTTACAAAC
260 AATTCTACTATACATCAATCTTGTACACTGCGTTTTGTTTAACATTGTTTGCGGCGCTTACAAAC
* * * * *
54605739 AAACGCC-GCTACTGCCACTATTCCTGAATATTAAACGATGCGTTTTGT
325 AAACGCCATC-AATGCCACTATACCTCAATACTAAACGATGCGTTTTGT
54605787 CAGATTTACT
Statistics
Matches: 340, Mismatches: 29, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
416 1 0.00
417 268 0.79
418 71 0.21
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (418 bp):
CTTCAGCGGCGATTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTT
TGTTTAACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTT
TACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
ACGGCGCTTACAAACAAACGCCGCTAATGATACACTTCAGCGGCGTTTTTACAGAAACGCCACCA
ATTCTACTATACATCAATCTTGTACACTGCGTTTTGTTTAACATTGTTTGCGGCGCTTACAAACA
AACGCCATCAATGCCACTATACCTCAATACTAAACGATGCGTTTTGTTTAACATTTTTTACGGCG
CTTACAAACAAATGCCGCTAATGATACA
Found at i:54611027 original size:16 final size:17
Alignment explanation
Indices: 54610995--54611030 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
54610985 TGTCATATTT
54610995 AAACTAAATTATATTAA
1 AAACTAAATTATATTAA
54611012 AAACTAAATTAT-TTAA
1 AAACTAAATTATATTAA
54611028 AAA
1 AAA
54611031 TTTATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
AAACTAAATTATATTAA
Found at i:54611029 original size:15 final size:15
Alignment explanation
Indices: 54610990--54611029 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
54610980 ACCTTTGTCA
54610990 TATTT-AAACTAAAT
1 TATTTAAAACTAAAT
54611004 TATATTAAAAACTAAAT
1 TAT-TT-AAAACTAAAT
54611021 TATTTAAAA
1 TATTTAAAA
54611030 ATTTATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 6 0.26
16 2 0.09
17 12 0.52
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
TATTTAAAACTAAAT
Found at i:54618000 original size:20 final size:19
Alignment explanation
Indices: 54617963--54618000 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
54617953 GAATTCGTTT
54617963 ATTATTCACATTAAATCTG
1 ATTATTCACATTAAATCTG
54617982 ATTA-TCACAGTTCAAATCT
1 ATTATTCACA-TT-AAATCT
54618001 ATACTCTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.39
Consensus pattern (19 bp):
ATTATTCACATTAAATCTG
Found at i:54629653 original size:24 final size:25
Alignment explanation
Indices: 54629626--54629681 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
54629616 TTGTGGAAAC
*
54629626 CAACCGCAACCATC-AAAG-GAAGAT
1 CAACCGCAACCATCTAAAGCG-ACAT
*
54629650 CAACCACAACCATCTAAAGCGACAT
1 CAACCGCAACCATCTAAAGCGACAT
54629675 CAACCGC
1 CAACCGC
54629682 CAGACAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 13 0.48
25 13 0.48
26 1 0.04
ACGTcount: A:0.43, C:0.36, G:0.12, T:0.09
Consensus pattern (25 bp):
CAACCGCAACCATCTAAAGCGACAT
Found at i:54636861 original size:21 final size:20
Alignment explanation
Indices: 54636837--54636906 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
54636827 TTTACTTTTC
54636837 GTTTAACTCTCACGAGCTTCT
1 GTTTAACTCT-ACGAGCTTCT
* *
54636858 GTTTAACTCATATGAGTTTCT
1 GTTTAACTC-TACGAGCTTCT
* * *
54636879 GTTCAGCTCTTACGAGCTTCA
1 GTTTAACTC-TACGAGCTTCT
54636900 GTTTAAC
1 GTTTAAC
54636907 CCTTATGGAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 37 0.97
22 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (20 bp):
GTTTAACTCTACGAGCTTCT
Found at i:54636920 original size:42 final size:42
Alignment explanation
Indices: 54636843--54637030 Score: 216
Period size: 42 Copynumber: 4.5 Consensus size: 42
54636833 TTTCGTTTAA
* * * * *
54636843 CTCTCACGAGCTTCTGTTTAACTCATAT-GAGTTTCTGTTCAG
1 CTCTTACGAGCTTCCGTTCAACCCTTATGGA-TTTCTGTTCAG
* *
54636885 CTCTTACGAGCTTCAGTTTAACCCTTATGGATTTCTGTTCAG
1 CTCTTACGAGCTTCCGTTCAACCCTTATGGATTTCTGTTCAG
* *
54636927 CTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTCAG
1 CTCTTACGAGCTTCCGTTCAACCCTTATGGATTTCTGTTCAG
* * *
54636969 CTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAG
1 CTCTTACGAGCTTCCGTTCAACCCTTATGGATTTCTGTTCAG
* * * *
54637011 CACTTATGTGCTTCTGTTCA
1 CTCTTACGAGCTTCCGTTCA
54637031 GCCTTCGGGC
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
42 131 0.98
43 2 0.02
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.41
Consensus pattern (42 bp):
CTCTTACGAGCTTCCGTTCAACCCTTATGGATTTCTGTTCAG
Found at i:54636934 original size:21 final size:21
Alignment explanation
Indices: 54636875--54637033 Score: 92
Period size: 21 Copynumber: 7.6 Consensus size: 21
54636865 TCATATGAGT
* *
54636875 TTCTGTTCAGCTCTTA-CGAGC
1 TTCTGTTCAGCCCTTATGGA-C
* * * *
54636896 TTCAGTTTAACCCTTATGGAT
1 TTCTGTTCAGCCCTTATGGAC
*
54636917 TTCTGTTCAGCTCTTAT-GAGC
1 TTCTGTTCAGCCCTTATGGA-C
* * **
54636938 TTCCGTTCAACCCTTATGGGT
1 TTCTGTTCAGCCCTTATGGAC
*
54636959 TTCTGTTCAGCTCTTAT-GAGC
1 TTCTGTTCAGCCCTTATGGA-C
* * **
54636980 TTCCGTTCAACCCTTATGGGT
1 TTCTGTTCAGCCCTTATGGAC
* *
54637001 TTCTGTTTAGCACTTATGTG-C
1 TTCTGTTCAGCCCTTATG-GAC
54637022 TTCTGTTCAGCC
1 TTCTGTTCAGCC
54637034 TTCGGGCTTC
Statistics
Matches: 99, Mismatches: 33, Indels: 12
0.69 0.23 0.08
Matches are distributed among these distances:
20 3 0.03
21 91 0.92
22 5 0.05
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (21 bp):
TTCTGTTCAGCCCTTATGGAC
Found at i:54636992 original size:84 final size:84
Alignment explanation
Indices: 54636850--54637030 Score: 254
Period size: 84 Copynumber: 2.2 Consensus size: 84
54636840 TAACTCTCAC
* * *
54636850 GAGCTTCTGTTTAACTCATATGAGTTTCTGTTCAGCTCTTACGAGCTTCAGTTTAACCCTTATGG
1 GAGCTTCTGTTCAACCCATATGAGTTTCTGTTCAGCTCTTACGAGCTTCAGTTCAACCCTTATGG
*
54636915 ATTTCTGTTCAGCTCTTAT
66 ATTTCTGTTCAGCACTTAT
* * * * *
54636934 GAGCTTCCGTTCAACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATGG
1 GAGCTTCTGTTCAACCCATATGAGTTTCTGTTCAGCTCTTACGAGCTTCAGTTCAACCCTTATGG
* *
54636999 GTTTCTGTTTAGCACTTAT
66 ATTTCTGTTCAGCACTTAT
*
54637018 GTGCTTCTGTTCA
1 GAGCTTCTGTTCA
54637031 GCCTTCGGGC
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (84 bp):
GAGCTTCTGTTCAACCCATATGAGTTTCTGTTCAGCTCTTACGAGCTTCAGTTCAACCCTTATGG
ATTTCTGTTCAGCACTTAT
Found at i:54644808 original size:25 final size:24
Alignment explanation
Indices: 54644780--54644886 Score: 101
Period size: 25 Copynumber: 4.3 Consensus size: 24
54644770 AAGATCTTCC
* *
54644780 GAGCTATACATCGGGAAGCTCATGT
1 GAGCCATA-ATCGGGAAGCTCATGA
* * *
54644805 GAGCAATGTAAT-AGGAAGCTCATAA
1 GAGCCA--TAATCGGGAAGCTCATGA
*
54644830 GAGCCAT-ATACGGGAAGCTCAAGA
1 GAGCCATAAT-CGGGAAGCTCATGA
54644854 GAGCCATTAATCGGGAAGCTCATGA
1 GAGCCA-TAATCGGGAAGCTCATGA
54644879 GAGCCATA
1 GAGCCATA
54644887 TAATGGGATG
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
22 2 0.03
23 1 0.01
24 18 0.27
25 40 0.60
26 4 0.06
27 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.19
Consensus pattern (24 bp):
GAGCCATAATCGGGAAGCTCATGA
Found at i:54644849 original size:49 final size:49
Alignment explanation
Indices: 54644791--54644888 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
54644781 AGCTATACAT
* *
54644791 CGGGAAGCTCATGTGAGCAATGTAAT-AGGAAGCTCATAAGAGCCATATA
1 CGGGAAGCTCAAGAGAGCAAT-TAATCAGGAAGCTCATAAGAGCCATATA
* * *
54644840 CGGGAAGCTCAAGAGAGCCATTAATCGGGAAGCTCATGAGAGCCATATA
1 CGGGAAGCTCAAGAGAGCAATTAATCAGGAAGCTCATAAGAGCCATATA
54644889 ATGGGATGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 4 0.09
49 39 0.91
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (49 bp):
CGGGAAGCTCAAGAGAGCAATTAATCAGGAAGCTCATAAGAGCCATATA
Found at i:54644894 original size:25 final size:25
Alignment explanation
Indices: 54644792--54644894 Score: 120
Period size: 25 Copynumber: 4.2 Consensus size: 25
54644782 GCTATACATC
* * *
54644792 GGGAAGCTCATGTGAGCAATGTAAT
1 GGGAAGCTCATGAGAGCCATATAAT
* * *
54644817 AGGAAGCTCATAAGAGCCATAT-AC
1 GGGAAGCTCATGAGAGCCATATAAT
*
54644841 GGGAAGCTCAAGAGAGCCAT-TAAT
1 GGGAAGCTCATGAGAGCCATATAAT
54644865 CGGGAAGCTCATGAGAGCCATATAAT
1 -GGGAAGCTCATGAGAGCCATATAAT
54644891 GGGA
1 GGGA
54644895 TGATCATAAG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
23 1 0.02
24 19 0.30
25 40 0.62
26 4 0.06
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (25 bp):
GGGAAGCTCATGAGAGCCATATAAT
Found at i:54644901 original size:25 final size:25
Alignment explanation
Indices: 54644792--54644907 Score: 112
Period size: 25 Copynumber: 4.7 Consensus size: 25
54644782 GCTATACATC
** * *
54644792 GGGAAGCTCATGTGAGCAATGTAAT
1 GGGAAGCTCATAAGAGCCATATAAT
* *
54644817 AGGAAGCTCATAAGAGCCATAT-AC
1 GGGAAGCTCATAAGAGCCATATAAT
54644841 GGGAAGCTCA-AGAGAGCCAT-TAAT
1 GGGAAGCTCATA-AGAGCCATATAAT
*
54644865 CGGGAAGCTCATGAGAGCCATATAAT
1 -GGGAAGCTCATAAGAGCCATATAAT
* *
54644891 GGGATGATCATAAGAGC
1 GGGAAGCTCATAAGAGC
54644908 TGTGGTGTGT
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
23 2 0.03
24 19 0.26
25 49 0.66
26 4 0.05
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.19
Consensus pattern (25 bp):
GGGAAGCTCATAAGAGCCATATAAT
Found at i:54645273 original size:21 final size:21
Alignment explanation
Indices: 54645230--54645273 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
54645220 AATGAATTTG
* **
54645230 ACTCAATTTAATACAATTCAT
1 ACTCAATTCAATACAATAAAT
*
54645251 ACTCAATTCAATTCAATAAAT
1 ACTCAATTCAATACAATAAAT
54645272 AC
1 AC
54645274 CTTTGGAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (21 bp):
ACTCAATTCAATACAATAAAT
Found at i:54647965 original size:23 final size:23
Alignment explanation
Indices: 54647939--54647990 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
54647929 AAGTCAACTT
*
54647939 CTGTAATATCCCGAAAATTACTA
1 CTGTAATACCCCGAAAATTACTA
*
54647962 CTGTACTACCCCGAAAATTACTA
1 CTGTAATACCCCGAAAATTACTA
*
54647985 CAGTAA
1 CTGTAA
54647991 GAAAGTAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (23 bp):
CTGTAATACCCCGAAAATTACTA
Found at i:54668505 original size:9 final size:9
Alignment explanation
Indices: 54668491--54668520 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
54668481 ATAACTTAGT
54668491 AATTCATAC
1 AATTCATAC
*
54668500 AATTCACAC
1 AATTCATAC
54668509 AATTCATAC
1 AATTCATAC
54668518 AAT
1 AAT
54668521 ATACCATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (9 bp):
AATTCATAC
Found at i:54670263 original size:16 final size:16
Alignment explanation
Indices: 54670242--54670274 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54670232 GAATGGTCTC
*
54670242 TGTTTCTTTTCTTCTT
1 TGTTTCTTTTATTCTT
54670258 TGTTTCTTTTATTCTT
1 TGTTTCTTTTATTCTT
54670274 T
1 T
54670275 TATTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTTATTCTT
Found at i:54672268 original size:6 final size:6
Alignment explanation
Indices: 54672259--54672292 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
54672249 AAAATTTATG
54672259 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
54672293 AATCAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:54672293 original size:18 final size:18
Alignment explanation
Indices: 54672259--54672292 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
54672249 AAAATTTATG
54672259 AAAAATAAAAATAAAAAT
1 AAAAATAAAAATAAAAAT
54672277 AAAAAT-AAAATAAAAA
1 AAAAATAAAAATAAAAA
54672293 AATCAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAATAAAAATAAAAAT
Found at i:54681215 original size:19 final size:20
Alignment explanation
Indices: 54681178--54681215 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54681168 TGTAAATAAA
54681178 TAAATATTTTTTGAGTTTAT
1 TAAATATTTTTTGAGTTTAT
54681198 TAAA-ATTTATTTGA-TTTA
1 TAAATATTT-TTTGAGTTTA
54681216 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TAAATATTTTTTGAGTTTAT
Found at i:54683347 original size:46 final size:46
Alignment explanation
Indices: 54683297--54683441 Score: 118
Period size: 46 Copynumber: 3.1 Consensus size: 46
54683287 TTGAAATCTG
54683297 TTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTT
1 TTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTT
** ** * * ** * * *
54683343 TTCA-CC-ATGAAAAAAATTATTACTAGCAAATAGTAA--AATGAAATCTG
1 TTCACCCAAT-ATTATCA-TATT-TTATCTCATAATAACCATTG-AAT-TT
54683390 TTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTT
1 TTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTT
54683436 TTCACC
1 TTCACC
54683442 ATGAAAAAAA
Statistics
Matches: 68, Mismatches: 22, Indels: 18
0.63 0.20 0.17
Matches are distributed among these distances:
44 2 0.03
45 8 0.12
46 27 0.40
47 21 0.31
48 8 0.12
49 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.38
Consensus pattern (46 bp):
TTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTT
Found at i:54683404 original size:93 final size:93
Alignment explanation
Indices: 54683288--54683479 Score: 375
Period size: 93 Copynumber: 2.1 Consensus size: 93
54683278 CTCTTTTGGT
54683288 TGAAATCTGTTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTTTTCACCATGA
1 TGAAATCTGTTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTTTTCACCATGA
54683353 AAAAAATTATTACTAGCAAATAGTAAAA
66 AAAAAATTATTACTAGCAAATAGTAAAA
54683381 TGAAATCTGTTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTTTTCACCATGA
1 TGAAATCTGTTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTTTTCACCATGA
54683446 AAAAAATTATTACTAGCAAATAGTAAAA
66 AAAAAATTATTACTAGCAAATAGTAAAA
*
54683474 TAAAAT
1 TGAAAT
54683480 TTTCGTCTTG
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 98 1.00
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (93 bp):
TGAAATCTGTTCACCCAATATTATCATATTTTATCTCATAATAACCATTGAATTTTTCACCATGA
AAAAAATTATTACTAGCAAATAGTAAAA
Found at i:54685039 original size:35 final size:36
Alignment explanation
Indices: 54685000--54685067 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
54684990 TAGGATCATA
*
54685000 TATCTCTG-AAGATCACCTTCCATATTTGCCAAACC
1 TATCTCTGAAAGATCACCTTCCATATTTACCAAACC
* * *
54685035 TATCTTTGAAAGATCACTTTTCATATTTACCAA
1 TATCTCTGAAAGATCACCTTCCATATTTACCAA
54685068 GCTTCGTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 7 0.25
36 21 0.75
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (36 bp):
TATCTCTGAAAGATCACCTTCCATATTTACCAAACC
Found at i:54685887 original size:2 final size:2
Alignment explanation
Indices: 54685880--54685906 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54685870 GATGGCATTA
54685880 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
54685907 ACACCAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54688060 original size:30 final size:30
Alignment explanation
Indices: 54688026--54688087 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
54688016 ACTTATTTTA
*
54688026 TTGTTAATTTTGTTATTATTTTA-AAGACAT
1 TTGTTAATTTTATTATTATTTTAGAAG-CAT
54688056 TTGTTAATTTTATTATTATTTTAGAAGCAT
1 TTGTTAATTTTATTATTATTTTAGAAGCAT
54688086 TT
1 TT
54688088 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAGAAGCAT
Found at i:54688242 original size:12 final size:12
Alignment explanation
Indices: 54688212--54688244 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
54688202 TATATATTTT
54688212 AAAATT-ATATA
1 AAAATTAATATA
54688223 AAAA-TAATATA
1 AAAATTAATATA
54688234 AAAATTAATAT
1 AAAATTAATAT
54688245 GGGCGGACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:54694015 original size:20 final size:19
Alignment explanation
Indices: 54693992--54694062 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
54693982 ATTGAATTAA
54693992 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
54694011 CAAAAATACAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
* *
54694031 AAAATTTTAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
54694050 AAAAATTTCAAAA
1 AAAAA-TTCAAAA
54694063 AATATCCTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 4 0.09
19 15 0.35
20 24 0.56
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:54694064 original size:10 final size:9
Alignment explanation
Indices: 54693986--54694110 Score: 52
Period size: 9 Copynumber: 12.6 Consensus size: 9
54693976 GAACAAATTG
*
54693986 AATTAAAAA
1 AATTTAAAA
*
54693995 AATTCAAAA
1 AATTTAAAA
*
54694004 TAATTTTCAAA
1 -AA-TTTAAAA
**
54694015 AATACAAAA
1 AATTTAAAA
*
54694024 TAATTTTAAA
1 -AATTTAAAA
*
54694034 ATTTTAAAA
1 AATTTAAAA
*
54694043 TATTTATAAA
1 AATTTA-AAA
54694053 AATTTCAAAAA
1 AATTT--AAAA
54694064 ATATCCTTAAAA
1 A-AT--TTAAAA
*
54694076 ATATATAAAA
1 A-ATTTAAAA
54694086 GAAGTTTAAAA
1 -AA-TTTAAAA
*
54694097 AAATTAAAA
1 AATTTAAAA
54694106 AATTT
1 AATTT
54694111 CTAGAATAAT
Statistics
Matches: 87, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
9 33 0.38
10 25 0.29
11 16 0.18
12 11 0.13
14 2 0.02
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (9 bp):
AATTTAAAA
Found at i:54694310 original size:22 final size:22
Alignment explanation
Indices: 54694268--54694312 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54694258 TGTAATAAGA
**
54694268 TTTTAATTTAACATGTTTAATT
1 TTTTAATTTAACATGAATAATT
*
54694290 TTTTAATTTAACTTGAATAATT
1 TTTTAATTTAACATGAATAATT
54694312 T
1 T
54694313 CACTCGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (22 bp):
TTTTAATTTAACATGAATAATT
Found at i:54695604 original size:13 final size:13
Alignment explanation
Indices: 54695591--54695637 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
54695581 AAGTTATTAA
54695591 TTAAGTTTAATAAT
1 TTAA-TTTAATAAT
54695605 TTAATTTAATAACT
1 TTAATTTAATAA-T
*
54695619 ATTAATTTTA-AAT
1 -TTAATTTAATAAT
54695632 TTAATT
1 TTAATT
54695638 ATAGAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 6 0.20
13 9 0.30
14 7 0.23
15 8 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (13 bp):
TTAATTTAATAAT
Found at i:54703846 original size:2 final size:2
Alignment explanation
Indices: 54703839--54703863 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54703829 GTTAAAAATC
54703839 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
54703864 AAGTTAACAC
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:54714875 original size:6 final size:6
Alignment explanation
Indices: 54714864--54714894 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
54714854 TAATTGATAC
54714864 TAATAT TAATAT TAATAT TAATAT TAA-AT TA
1 TAATAT TAATAT TAATAT TAATAT TAATAT TA
54714895 TAAAATCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAATAT
Found at i:54719395 original size:19 final size:19
Alignment explanation
Indices: 54719373--54719410 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
54719363 AATAAAATTC
54719373 AAAATT-CAAAATATTTATA
1 AAAATTCCAAAA-ATTTATA
54719392 AAAATTCCAAAAATTTATA
1 AAAATTCCAAAAATTTATA
54719411 TACTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTCCAAAAATTTATA
Found at i:54719440 original size:19 final size:18
Alignment explanation
Indices: 54719400--54719442 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
54719390 TAAAAATTCC
* * *
54719400 AAAAATTTATATACTTTT
1 AAAAAATTATATAATTTA
54719418 AAAAAATTATAGTAATTTA
1 AAAAAATTATA-TAATTTA
54719437 AAAAAA
1 AAAAAA
54719443 ATTCTAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAAAATTATATAATTTA
Found at i:54725144 original size:46 final size:46
Alignment explanation
Indices: 54725081--54725179 Score: 180
Period size: 46 Copynumber: 2.2 Consensus size: 46
54725071 CAAAAAATTG
* *
54725081 TATTAATTGTATTAATGGTTAGTAAATTTATCAAATTATATAAAAT
1 TATTAATTGTATCAATGGTTAGTAAAATTATCAAATTATATAAAAT
54725127 TATTAATTGTATCAATGGTTAGTAAAATTATCAAATTATATAAAAT
1 TATTAATTGTATCAATGGTTAGTAAAATTATCAAATTATATAAAAT
54725173 TATTAAT
1 TATTAAT
54725180 GATTAGTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (46 bp):
TATTAATTGTATCAATGGTTAGTAAAATTATCAAATTATATAAAAT
Found at i:54725195 original size:19 final size:19
Alignment explanation
Indices: 54725140--54725197 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
54725130 TAATTGTATC
* *
54725140 AATGGTTAGTAAAATTATC
1 AATGATTAGTAAAATTATT
*
54725159 AA--ATTATATAAAATTATT
1 AATGATTA-GTAAAATTATT
54725177 AATGATTAGTAAAATTATT
1 AATGATTAGTAAAATTATT
54725196 AA
1 AA
54725198 ATTAGGTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 3 0.09
18 11 0.34
19 14 0.44
20 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.40
Consensus pattern (19 bp):
AATGATTAGTAAAATTATT
Found at i:54725269 original size:28 final size:29
Alignment explanation
Indices: 54725196--54725726 Score: 340
Period size: 29 Copynumber: 17.0 Consensus size: 29
54725186 TAAAATTATT
54725196 AAATTAGGTTAGGGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
54725225 AAATTAGGTTAGGGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
54725254 AAATTAGGTTA-GGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
54725282 AAATTAGGTTAGGGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
*
54725311 AAATTAGGTTA-GGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
* *
54725339 AAATTAGGTTTAATCAAATTAGGTTAGGGTTTTTAATTA
1 AAATTAGG--T--T---A--GGGTTAGGGTTTTTAA-TC
54725378 AATTAGGTTAGGTTAGGGTTAGGGTTTTTAATC
1 AA--A--TTAGGTTAGGGTTAGGGTTTTTAATC
* *
54725411 AAATTAGGTTAGAGTTAGTGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
*** * *
54725440 AAATTAGGTTTAATCAAATTA-GGTTAGGTTTAGGGTTTT
1 AAATTAGG-TT-A--GGGTTAGGGTT---TTTA----ATC
* * ** *
54725479 TAATCAAATTAGGTTAGATTAGGGTTTTTATTC
1 AAATTAGGTTAGG---G-TTAGGGTTTTTAATC
* *
54725512 AAATTATGTTA-GGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
* *
54725540 AAATTAGGTTTAATCAAATTAGGTTAGAGTTAGGGTTT--T-
1 AAATTAGG--T--T---A--GGGTTAGGGTT----TTTAATC
* * **
54725579 TAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
1 AAAT-TAGGT----TAGGGTTAGGGTTTTTAATC
54725613 AAATTAGGTTA-GGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
54725641 AAATTAGGTTAGGGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
* *
54725670 AAATTAGGTTAGGGGTAGGCTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATC
* *
54725699 AAATTAGGTTAGGGGTAGGCTTTTTAAT
1 AAATTAGGTTAGGGTTAGGGTTTTTAAT
54725727 TACATCAAAT
Statistics
Matches: 408, Mismatches: 41, Indels: 106
0.74 0.07 0.19
Matches are distributed among these distances:
28 100 0.25
29 175 0.43
30 4 0.01
31 5 0.01
32 6 0.01
33 19 0.05
34 18 0.04
35 15 0.04
36 1 0.00
37 6 0.01
38 27 0.07
39 15 0.04
40 7 0.02
41 2 0.00
42 3 0.01
43 5 0.01
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.43
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATC
Found at i:54725277 original size:57 final size:58
Alignment explanation
Indices: 54725196--54725726 Score: 514
Period size: 57 Copynumber: 8.5 Consensus size: 58
54725186 TAAAATTATT
54725196 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
54725254 AAATTAGGTTA-GGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
* *
54725311 AAATTAGGTTA-GGTTAGGGTTTTTAATTAAATTAGGTTTAATCAAATTAGGTTAGGGTTTTTAA
1 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGG--T--T---A--GGGTTAGGGTTTTTAA
*
54725375 TTA
57 -TC
* *
54725378 AATTAGGTTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGAGTTAGTGTTTTTAATC
1 AA--A--TTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
*
54725440 AAATTAGGTTTAATCAAATTAGGTTAGGTTTAGGGTTTTTAATCAAATTAGGTTA-GATTAGGGT
1 AAATTAGG----------TTA-G---GG-TTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGT
*
54725504 TTTTATTC
51 TTTTAATC
* *
54725512 AAATTATGTTA-GGTTAGGGTTTTTAATTAAATTAGGTTTAATCAAATTAGGTTAGAGTTAGGGT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGG----------TTA-G---G-GTTAGGGT
54725576 TTTTAATC
51 TTTTAATC
54725584 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTA-GGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
* *
54725641 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGGTAGGCTTTTTAATC
1 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
* *
54725699 AAATTAGGTTAGGGGTAGGCTTTTTAAT
1 AAATTAGGTTAGGGTTAGGGTTTTTAAT
54725727 TACATCAAAT
Statistics
Matches: 403, Mismatches: 22, Indels: 96
0.77 0.04 0.18
Matches are distributed among these distances:
56 22 0.05
57 139 0.34
58 58 0.14
59 1 0.00
60 1 0.00
61 1 0.00
62 6 0.01
63 16 0.04
64 1 0.00
65 1 0.00
66 18 0.04
67 3 0.01
68 4 0.01
69 2 0.00
70 1 0.00
71 9 0.02
72 70 0.17
73 50 0.12
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.43
Consensus pattern (58 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
Found at i:54725351 original size:43 final size:38
Alignment explanation
Indices: 54725319--54725467 Score: 137
Period size: 38 Copynumber: 4.3 Consensus size: 38
54725309 TCAAATTAGG
54725319 TTAGGTTAGGGTTTTTAATTAAATTAGGTTTAATCAAA
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTTAATCAAA
**
54725357 TTAGGTTAGGGTTTTTAATTAAATTAGG--T--T-AGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTTAATCAAA
*
54725390 TTAGGGTTAGGGTTTTTAATCAAATTAGG--T--T---A
1 TTA-GGTTAGGGTTTTTAATTAAATTAGGTTTAATCAAA
* * *
54725422 -GA-GTTAGTGTTTTTAATCAAATTAGGTTTAATCAAA
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTTAATCAAA
54725458 TTAGGTTAGG
1 TTAGGTTAGG
54725468 TTTAGGGTTT
Statistics
Matches: 93, Mismatches: 8, Indels: 20
0.77 0.07 0.17
Matches are distributed among these distances:
29 23 0.25
31 2 0.02
33 5 0.05
34 27 0.29
36 2 0.02
37 1 0.01
38 33 0.35
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.44
Consensus pattern (38 bp):
TTAGGTTAGGGTTTTTAATTAAATTAGGTTTAATCAAA
Found at i:54725352 original size:15 final size:15
Alignment explanation
Indices: 54725332--54725363 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54725322 GGTTAGGGTT
*
54725332 TTTAATTAAATTAGG
1 TTTAATCAAATTAGG
54725347 TTTAATCAAATTAGG
1 TTTAATCAAATTAGG
54725362 TT
1 TT
54725364 AGGGTTTTTA
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:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (15 bp):
TTTAATCAAATTAGG
Found at i:54725363 original size:129 final size:127
Alignment explanation
Indices: 54725218--54725728 Score: 422
Period size: 129 Copynumber: 4.0 Consensus size: 127
54725208 GGTTAGGGTT
54725218 TTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTA-GGTTAGGGTTTTTAATC
1 TTTAATCAAATTAGGTTA-GGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
*
54725282 AAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTA-GGTTAGGGTTTTTAATTAAATTAG
65 AAATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGG-TTTTAATT--ATTAG
54725346 G
127 G
*
54725347 TTTAATC-AA--A--TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTT
1 TTTAATCAAATTAGGTTAGGTTAGGGTTTTTAA-TCAA--A--TTAGGTTAGGGTTAGGGTTTTT
* *** **
54725407 AATCAAATTAGGTTAGAGTTAGTGTTTTTAATCAAATTAGGTTTAATCAAATTA-GG--TTAGGT
61 AATCAAATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGG-TT-A--GGGTTAGGGTTTTAATT
54725469 -TTAGGG
122 ATTA-GG
* * *
54725475 TTTTTAATCAAATTAGGTTAGATTAGGGTTTTTATTCAAATTATGTTA-GGTTAGGGTTTTTAAT
1 --TTTAATCAAATTAGGTTAGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGG--------
54725539 TAAATTAGGTTTAATCAAATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGG
56 ----TT---TTTAATCAAATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGG
54725604 ---------TT---
114 TTTTAATTATTAGG
54725606 TTTAATCAAATTAGGTTAGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCA
1 TTTAATCAAATTAGGTTAGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCA
* * * * *
54725671 AATTAGGTTAGGGGTAGGCTTTTTAATCAAATTAGGTTAGGGGTAGGCTTTTTAATTA
66 AATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGG-GTTTTAATTA
54725729 CATCAAATAA
Statistics
Matches: 313, Mismatches: 23, Indels: 96
0.72 0.05 0.22
Matches are distributed among these distances:
115 51 0.16
118 2 0.01
123 15 0.05
124 6 0.02
126 2 0.01
127 3 0.01
128 12 0.04
129 110 0.35
130 28 0.09
131 3 0.01
132 1 0.00
133 3 0.01
134 6 0.02
135 18 0.06
140 3 0.01
141 4 0.01
142 1 0.00
143 2 0.01
144 43 0.14
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.43
Consensus pattern (127 bp):
TTTAATCAAATTAGGTTAGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCA
AATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTAATTATTAGG
Found at i:54725453 original size:15 final size:15
Alignment explanation
Indices: 54725433--54725464 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
54725423 AGTTAGTGTT
54725433 TTTAATCAAATTAGG
1 TTTAATCAAATTAGG
54725448 TTTAATCAAATTAGG
1 TTTAATCAAATTAGG
54725463 TT
1 TT
54725465 AGGTTTAGGG
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:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (15 bp):
TTTAATCAAATTAGG
Found at i:54725454 original size:44 final size:44
Alignment explanation
Indices: 54725404--54725593 Score: 186
Period size: 44 Copynumber: 4.0 Consensus size: 44
54725394 GGTTAGGGTT
*
54725404 TTTAATCAAATTAGGTTAGAGTTAGTGTTTTTAATCAAATTAGG
1 TTTAATCAAATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGG
54725448 TTTAATCAAATTAGGTTAG-GTTTAGGGTTTTTAATCAAATTAGG
1 TTTAATCAAATTAGGTTAGAG-TTAGGGTTTTTAATCAAATTAGG
* * ** *
54725492 -TTAGATTAGGGTTTTTATTCAAATTATGTTAGGTTAGGGTTTTTAATTAAATTAGG
1 TTTA-ATCA-------AATT-AGGTTA-G--A-GTTAGGGTTTTTAATCAAATTAGG
54725548 TTTAATCAAATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGG
1 TTTAATCAAATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGG
54725592 TT
1 TT
54725594 AGGGTTAGGG
Statistics
Matches: 119, Mismatches: 11, Indels: 32
0.73 0.07 0.20
Matches are distributed among these distances:
43 4 0.03
44 69 0.58
45 1 0.01
47 1 0.01
48 4 0.03
49 3 0.03
51 3 0.03
52 4 0.03
53 1 0.01
56 25 0.21
57 4 0.03
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.45
Consensus pattern (44 bp):
TTTAATCAAATTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGG
Found at i:54725490 original size:173 final size:164
Alignment explanation
Indices: 54725247--54725726 Score: 192
Period size: 173 Copynumber: 2.9 Consensus size: 164
54725237 GGTTAGGGTT
* * *
54725247 TTTAATCAAATTAGGTTA-GGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC
1 TTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTA-GATTAGGGTTTTTATTA
** * **
54725311 AAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTTAATCAAATTAG-GTTAGGGTTTTTAA
65 AAATTATATTAGGTTAGGGTTTTTAATTAAATTAGG----ATTAGGTTAGAGTTAGGGTTTTTAA
*
54725375 TTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGG
126 TCAAATTAGGTTA-G--A--GTTAGGGTTTTTAATCAAATTAGG
* * *** *
54725419 -TT-A--GAGTTAGTGTTTTTAATCAAATTA-GG--TTTAATCAAATTAGGTTAGGTTTAGGGTT
1 TTTAATCAAATTAG-G---TT-A--GGGTTAGGGTTTTTAATCAAATTAGGTTA-GATTAGGGTT
* * ** *
54725477 TTTAATCAAATTAGGTTAGATTAGGGTTTTT-ATTCAAATT---A-T--GTTAG-GTTAGGGTTT
58 TTTATTAAAATTATATTAGGTTAGGGTTTTTAATT-AAATTAGGATTAGGTTAGAGTTAGGGTTT
* * * * *
54725534 TTAATTAAATTAGGTTTAATCAAATTA-GG---TT-A--GAGTTAGGG
122 TTAATCAAATTAGG-TT-A--GAGTTAGGGTTTTTAATCAAATTA-GG
* *
54725575 TTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGTTAGGGTTTTTAAT
1 --TTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGATTAGGGTTTTTATT
* ** * *
54725640 CAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGG-TTAGG---G-G-TAGGCTTTTTAATC
64 AAAATTATATTA-GGTTAGGGTTTTTAATTAAATTAGGATTAGGTTAGAGTTAGGGTTTTTAATC
* * *
54725699 AAATTAGGTTAGGGGTAGGCTTTTTAAT
128 AAATTAGGTTAGAGTTAGGGTTTTTAAT
54725727 TACATCAAAT
Statistics
Matches: 244, Mismatches: 28, Indels: 83
0.69 0.08 0.23
Matches are distributed among these distances:
155 9 0.04
156 5 0.02
157 30 0.12
158 41 0.17
159 26 0.11
160 4 0.02
161 4 0.02
162 8 0.03
163 29 0.12
164 3 0.01
165 1 0.00
166 1 0.00
168 5 0.02
169 1 0.00
170 1 0.00
171 2 0.01
172 5 0.02
173 64 0.26
175 2 0.01
176 3 0.01
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.43
Consensus pattern (164 bp):
TTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGATTAGGGTTTTTATTAA
AATTATATTAGGTTAGGGTTTTTAATTAAATTAGGATTAGGTTAGAGTTAGGGTTTTTAATCAAA
TTAGGTTAGAGTTAGGGTTTTTAATCAAATTAGG
Found at i:54725553 original size:15 final size:15
Alignment explanation
Indices: 54725533--54725564 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54725523 GGTTAGGGTT
*
54725533 TTTAATTAAATTAGG
1 TTTAATCAAATTAGG
54725548 TTTAATCAAATTAGG
1 TTTAATCAAATTAGG
54725563 TT
1 TT
54725565 AGAGTTAGGG
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:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (15 bp):
TTTAATCAAATTAGG
Found at i:54725833 original size:25 final size:25
Alignment explanation
Indices: 54725761--54725826 Score: 132
Period size: 25 Copynumber: 2.6 Consensus size: 25
54725751 TCGAAAAAAT
54725761 TTCTATTTTATTACATAAAATAAAC
1 TTCTATTTTATTACATAAAATAAAC
54725786 TTCTATTTTATTACATAAAATAAAC
1 TTCTATTTTATTACATAAAATAAAC
54725811 TTCTATTTTATTACAT
1 TTCTATTTTATTACAT
54725827 CGAATAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (25 bp):
TTCTATTTTATTACATAAAATAAAC
Found at i:54726333 original size:18 final size:18
Alignment explanation
Indices: 54726310--54726344 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54726300 CGAAAAAGGA
*
54726310 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
54726328 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
54726345 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:54728245 original size:12 final size:11
Alignment explanation
Indices: 54728211--54728245 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
54728201 GAATTTTGGA
54728211 AGGAAATTGAG
1 AGGAAATTGAG
54728222 AGG-AATTGAG
1 AGGAAATTGAG
54728232 AGGAAATATGAG
1 AGGAAAT-TGAG
54728244 AG
1 AG
54728246 AGAATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:54730849 original size:61 final size:61
Alignment explanation
Indices: 54730710--54730851 Score: 266
Period size: 61 Copynumber: 2.3 Consensus size: 61
54730700 ATTTAGATCT
*
54730710 CCCCAATTCCCAGAGAGTCGAGGGAGAAAATGCCAAGTCGGTCAGTTGTTATTAATGTTAG
1 CCCCAATTCCCAGAGGGTCGAGGGAGAAAATGCCAAGTCGGTCAGTTGTTATTAATGTTAG
54730771 CCCCAATTCCCAGAGGGTCGAGGGAGAAAATGCCAAGTCGGTCAGTTGTTATTAATGTTAG
1 CCCCAATTCCCAGAGGGTCGAGGGAGAAAATGCCAAGTCGGTCAGTTGTTATTAATGTTAG
*
54730832 CCCCAATTCCCAAAGGGTCG
1 CCCCAATTCCCAGAGGGTCG
54730852 TGGACTACTC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 79 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (61 bp):
CCCCAATTCCCAGAGGGTCGAGGGAGAAAATGCCAAGTCGGTCAGTTGTTATTAATGTTAG
Found at i:54732659 original size:18 final size:17
Alignment explanation
Indices: 54732638--54732672 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54732628 TTATTATTAA
*
54732638 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54732656 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54732673 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54732779 original size:18 final size:17
Alignment explanation
Indices: 54732756--54732792 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
54732746 AATTATTATT
54732756 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
54732772 AAATATATGATTTAATA
1 AAATATATGATTTAATA
54732789 AAAT
1 AAAT
54732793 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:54732790 original size:59 final size:57
Alignment explanation
Indices: 54732624--54732816 Score: 169
Period size: 57 Copynumber: 3.3 Consensus size: 57
54732614 ATATTTTAAC
*
54732624 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
* * * * * * *
54732681 ATCAATT-TTCTTATATGA-ATTTACTCAAATCATAATATATGATACT-ATAAAATATAATTTGA
1 AT-AATTATTATTAAAT-ATATTT--T--AATTAAAATATATGAT-TTAATAAAAT-T--CTTAA
54732743 -A
56 TA
54732744 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
* * *
54732801 ATTATTACTAATAAAT
1 ATAATTATTATTAAAT
54732817 TTTCTTATAT
Statistics
Matches: 104, Mismatches: 18, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
56 3 0.03
57 27 0.26
58 7 0.07
59 22 0.21
61 21 0.20
62 7 0.07
63 14 0.13
64 3 0.03
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (57 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
Found at i:54732848 original size:47 final size:46
Alignment explanation
Indices: 54732797--54732942 Score: 151
Period size: 47 Copynumber: 3.2 Consensus size: 46
54732787 TAAAATTCTT
*
54732797 AATAATTATTACTAATAAATTTTCTTATATGAATTTGTATAATTTAA
1 AATAATTATTA-TAATAAATTTTCTTATATGAATTTATATAATTTAA
* * *
54732844 AATAATTATTAT--TAAATATAAT-TTA-AT-AATAATATATAATTTCAT
1 AATAATTATTATAATAAAT-T-TTCTTATATGAAT-TTATATAATTT-AA
*
54732889 AA-AATTCTTGATAATAAATTTTCTTATATGAATTTATATAATTTAA
1 AATAATTATT-ATAATAAATTTTCTTATATGAATTTATATAATTTAA
54732935 AATAATTA
1 AATAATTA
54732943 ATATTAAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
43 3 0.04
44 22 0.28
45 10 0.13
46 9 0.11
47 32 0.41
48 3 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (46 bp):
AATAATTATTATAATAAATTTTCTTATATGAATTTATATAATTTAA
Found at i:54732853 original size:101 final size:96
Alignment explanation
Indices: 54732732--54733015 Score: 356
Period size: 91 Copynumber: 3.0 Consensus size: 96
54732722 ATACTATAAA
* * * *
54732732 ATATAATTTGAAATAATTATTATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTCT
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTC-
*
54732796 TAATAATTATTACTAATAAATTTTCTTATATGAATTT
64 T--TAATT-TGA-TAATAAATTTTCTTATATGAATTT
*
54732833 GTATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTC--
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
54732896 ---TTGATAATAAATTTTCTTATATGAATTT
66 AATTTGATAATAAATTTTCTTATATGAATTT
* *
54732924 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTT
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
*
54732989 AA--TGATAA-ATA-TTT-TTATATGAATTT
66 AATTTGATAATAAATTTTCTTATATGAATTT
54733015 A
1 A
54733016 CTAAAATCAT
Statistics
Matches: 168, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
91 97 0.58
92 5 0.03
93 3 0.02
94 6 0.04
100 3 0.02
101 54 0.32
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (96 bp):
ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
AATTTGATAATAAATTTTCTTATATGAATTT
Found at i:54732883 original size:44 final size:43
Alignment explanation
Indices: 54732834--54732976 Score: 139
Period size: 44 Copynumber: 3.2 Consensus size: 43
54732824 TATGAATTTG
54732834 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
* * * *
54732878 TATAATTTCATAA-AATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-AT--TAAATATAAT-TTA-AT-AATATA
*
54732925 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
54732969 TATAATTT
1 TATAATTT
54732977 CATAAAATTC
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
43 3 0.04
44 31 0.39
45 10 0.13
46 10 0.13
47 22 0.28
48 3 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (43 bp):
TATAATTTAAAATAATTATTATTAAATATAATTTAATAATATA
Found at i:54732998 original size:47 final size:45
Alignment explanation
Indices: 54732856--54733000 Score: 138
Period size: 47 Copynumber: 3.2 Consensus size: 45
54732846 TAATTATTAT
*
54732856 TAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAA
1 TAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAAT-A
* * **
54732903 TAAAT-T-TTCTTATATGAATTTATATAA-TT--TAAAATAATTAATA
1 TAAATATAAT-TTA-AT-AATATATATAATTTCATAAAATTCTTAATA
54732946 TTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATGA
1 -TAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAAT-A
54732994 TAAATAT
1 TAAATAT
54733001 TTTTATATGA
Statistics
Matches: 78, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
43 4 0.05
44 24 0.31
45 7 0.09
46 7 0.09
47 32 0.41
48 4 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (45 bp):
TAAATATAATTTAATAATATATATAATTTCATAAAATTCTTAATA
Found at i:54734894 original size:21 final size:21
Alignment explanation
Indices: 54734868--54734919 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
54734858 CTCCAAAACA
*
54734868 AGGGAAAATGGGTTACATTTT
1 AGGGAAAATGGGCTACATTTT
54734889 AGGGAAAATGGGCTACATTTT
1 AGGGAAAATGGGCTACATTTT
54734910 AGGGAAAATG
1 AGGGAAAATG
54734920 TCTTACCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.31, T:0.27
Consensus pattern (21 bp):
AGGGAAAATGGGCTACATTTT
Found at i:54741310 original size:24 final size:24
Alignment explanation
Indices: 54741283--54741334 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
54741273 TTAGTAAGTC
*
54741283 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54741307 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54741331 AAAT
1 AAAT
54741335 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54750549 original size:8 final size:7
Alignment explanation
Indices: 54750501--54750547 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
54750491 TACATTAATA
54750501 CATTTCC
1 CATTTCC
54750508 CATTTCC
1 CATTTCC
54750515 C--TTCC
1 CATTTCC
* *
54750520 C-CTCCC
1 CATTTCC
54750526 CATTTCC
1 CATTTCC
54750533 CATTTCC
1 CATTTCC
54750540 CATTTCC
1 CATTTCC
54750547 C
1 C
54750548 CAACCCCGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 5 0.14
6 4 0.11
7 26 0.74
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.38
Consensus pattern (7 bp):
CATTTCC
Found at i:54751383 original size:28 final size:29
Alignment explanation
Indices: 54751352--54751408 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
54751342 TTAATAATTT
* **
54751352 TTAATAAAAATGTGTATT-AAGGACTAAA
1 TTAAGAAAAATGTAAATTGAAGGACTAAA
*
54751380 TTAAGAAAAGTGTAAATTGAAGGACTAAA
1 TTAAGAAAAATGTAAATTGAAGGACTAAA
54751409 ATGTGAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.28
Consensus pattern (29 bp):
TTAAGAAAAATGTAAATTGAAGGACTAAA
Found at i:54751533 original size:37 final size:37
Alignment explanation
Indices: 54751480--54751554 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
54751470 GTACAATGAA
*
54751480 AGTTTGTTAATTTTTGTATTTTTGTGAAATAGAGACT
1 AGTTTGTTAATCTTTGTATTTTTGTGAAATAGAGACT
54751517 AGTTTGTTAATCTTTGTATTTTTGTGAAATAGAGACT
1 AGTTTGTTAATCTTTGTATTTTTGTGAAATAGAGACT
54751554 A
1 A
54751555 AATTGCAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (37 bp):
AGTTTGTTAATCTTTGTATTTTTGTGAAATAGAGACT
Found at i:54751982 original size:43 final size:42
Alignment explanation
Indices: 54751919--54752035 Score: 148
Period size: 43 Copynumber: 2.7 Consensus size: 42
54751909 GGATTTCCGA
*
54751919 TATGTGTTATCGTGTAAGACCACGTCTGGGACAGTGGCATCGAC
1 TATGTGTTA-CGTGTAAGACCACATCTGGGACAGTGGCATCG-C
*
54751963 T-TGTGTTTACGTGTAAGACC-CTATCTGGGACAGTGGCATCGG
1 TATGTG-TTACGTGTAAGACCAC-ATCTGGGACAGTGGCATCGC
*
54752005 TATGTGATTACATGTAAGACCACATCTGGGA
1 TATGTG-TTACGTGTAAGACCACATCTGGGA
54752036 TGTTGGCATT
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
42 2 0.03
43 58 0.89
44 5 0.08
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
TATGTGTTACGTGTAAGACCACATCTGGGACAGTGGCATCGC
Found at i:54752925 original size:46 final size:46
Alignment explanation
Indices: 54752872--54753070 Score: 371
Period size: 46 Copynumber: 4.3 Consensus size: 46
54752862 GATGGATTGA
* *
54752872 TTTGATGCATAAATGCTGCCCAATTTGTTGCATAATGCTGTCCAAT
1 TTTGATGCTTAAATGCTGCCCAATTTGTTACATAATGCTGTCCAAT
54752918 TTTGATGCTTAAATGCTGCCCAATTTGTTACATAATGCTGTCCAAT
1 TTTGATGCTTAAATGCTGCCCAATTTGTTACATAATGCTGTCCAAT
*
54752964 TTTGATGCCTAAATGCTGCCCAATTTGTTACATAATGCTGTCCAAT
1 TTTGATGCTTAAATGCTGCCCAATTTGTTACATAATGCTGTCCAAT
54753010 TTTGATGCTTAAATGCTGCCCAATTTGTTACATAATGCTGTCCAAT
1 TTTGATGCTTAAATGCTGCCCAATTTGTTACATAATGCTGTCCAAT
54753056 TTTGATGCTTAAATG
1 TTTGATGCTTAAATG
54753071 NNNNNNNNNN
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 149 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (46 bp):
TTTGATGCTTAAATGCTGCCCAATTTGTTACATAATGCTGTCCAAT
Found at i:54753239 original size:23 final size:23
Alignment explanation
Indices: 54753171--54753295 Score: 88
Period size: 24 Copynumber: 5.3 Consensus size: 23
54753161 NNNNNNNNNN
54753171 GCCCAATTTGTTACATATATGCT
1 GCCCAATTTGTTACATATATGCT
** * * * *
54753194 GTTCAATTTTGATGCCTAAATGCT
1 GCCCAA-TTTGTTACATATATGCT
54753218 GCCCAATTTGTTACATATATGCT
1 GCCCAATTTGTTACATATATGCT
* * * * *
54753241 GTCCAATTTTGATGCTTAAATGCT
1 GCCCAA-TTTGTTACATATATGCT
* * *
54753265 ACCCAAATTGTTGTATATATATGCT
1 GCCCAATTTG-T-TACATATATGCT
54753290 GCCCAA
1 GCCCAA
54753296 ATTGATGAAT
Statistics
Matches: 72, Mismatches: 26, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
23 25 0.35
24 34 0.47
25 13 0.18
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (23 bp):
GCCCAATTTGTTACATATATGCT
Found at i:54753240 original size:47 final size:47
Alignment explanation
Indices: 54753171--54753295 Score: 178
Period size: 47 Copynumber: 2.6 Consensus size: 47
54753161 NNNNNNNNNN
*
54753171 GCCCAATTTGTTACATATATGCTGTTCAATTTTGATGCCTAAATGCT
1 GCCCAATTTGTTACATATATGCTGTCCAATTTTGATGCCTAAATGCT
*
54753218 GCCCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCT
1 GCCCAATTTGTTACATATATGCTGTCCAATTTTGATGCCTAAATGCT
* * * *
54753265 ACCCAAATTGTTGTATATATATGCTGCCCAA
1 GCCCAATTTG-T-TACATATATGCTGTCCAA
54753296 ATTGATGAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
47 53 0.76
48 1 0.01
49 16 0.23
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (47 bp):
GCCCAATTTGTTACATATATGCTGTCCAATTTTGATGCCTAAATGCT
Found at i:54760483 original size:22 final size:21
Alignment explanation
Indices: 54760462--54760509 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
54760452 AAGTGCAATA
* *
54760462 ATTAAATATTATTAAATTAAT
1 ATTAAATACTATTAAAATAAT
54760483 A--AAATACTATTAAAATAATT
1 ATTAAATACTATTAAAATAA-T
54760503 ATTAAAT
1 ATTAAAT
54760510 TAAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 15 0.68
20 2 0.09
21 1 0.05
22 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAAATACTATTAAAATAAT
Found at i:54760487 original size:19 final size:19
Alignment explanation
Indices: 54760458--54760501 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
54760448 ACACAAGTGC
* *
54760458 AATAATTAAATATTATTAA
1 AATAATAAAATACTATTAA
*
54760477 ATTAATAAAATACTATTAA
1 AATAATAAAATACTATTAA
54760496 AATAAT
1 AATAAT
54760502 TATTAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAATAAAATACTATTAA
Found at i:54761341 original size:74 final size:73
Alignment explanation
Indices: 54761196--54761339 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
54761186 TATCTACTTG
* * *
54761196 GTACTTAAGCTTTTTTTGGACCTAACTGGTACATAAACTTGAAAACCGTAAACCAAAGTGGTACT
1 GTACTTAAACTTTTTTTAGACCTAACTGGTACATAAACTTGAAAACCGTAAACCAAAGAGGTACT
54761261 TTTTTTAA
66 TTTTTTAA
* * * * *
54761269 GTACTTAAACTTTCTTTTAGACCTAATTGGTACTTGAACTTGAAAACC-TAAATCAAAGAGGTAT
1 GTACTTAAACTTT-TTTTAGACCTAACTGGTACATAAACTTGAAAACCGTAAACCAAAGAGGTAC
54761333 TTTTTTT
65 TTTTTTT
54761340 TAGATCCAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 32 0.52
74 30 0.48
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (73 bp):
GTACTTAAACTTTTTTTAGACCTAACTGGTACATAAACTTGAAAACCGTAAACCAAAGAGGTACT
TTTTTTAA
Found at i:54762079 original size:31 final size:31
Alignment explanation
Indices: 54762042--54762118 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
54762032 TATTTTTATT
* *
54762042 TTTTTGTCTAAATTCCTTTTTCGGATCTATA
1 TTTTTGTCTAAACTCATTTTTCGGATCTATA
54762073 TTTTTGTCTAAACTCATTTTTCGGATCTATA
1 TTTTTGTCTAAACTCATTTTTCGGATCTATA
54762104 TTTTTGT-TCAAACTC
1 TTTTTGTCT-AAACTC
54762119 TCTCACTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (31 bp):
TTTTTGTCTAAACTCATTTTTCGGATCTATA
Found at i:54772924 original size:16 final size:16
Alignment explanation
Indices: 54772904--54772940 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
54772894 AATTTTATTT
54772904 TAATAATAACTTTTAAA
1 TAATAATAA-TTTTAAA
54772921 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
54772936 TAATA
1 TAATA
54772941 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:54781121 original size:23 final size:23
Alignment explanation
Indices: 54781091--54781137 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
54781081 TCATAGTACT
54781091 GTAAAATATAATGTACATTTATC
1 GTAAAATATAATGTACATTTATC
54781114 GTAAAATATAATGTACATTTATC
1 GTAAAATATAATGTACATTTATC
54781137 G
1 G
54781138 ATACGTTGCT
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:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (23 bp):
GTAAAATATAATGTACATTTATC
Found at i:54792141 original size:3 final size:3
Alignment explanation
Indices: 54792133--54792176 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
54792123 ATTCTTTATA
54792133 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54792177 AAGAAACTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54805500 original size:19 final size:20
Alignment explanation
Indices: 54805476--54805521 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
54805466 ATAATGATCG
54805476 AAAATTAAAT-AAAAGCTAT
1 AAAATTAAATCAAAAGCTAT
* **
54805495 AAAATTATATCAATTGCTAT
1 AAAATTAAATCAAAAGCTAT
54805515 AAAATTA
1 AAAATTA
54805522 CACAAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATTAAATCAAAAGCTAT
Found at i:54807372 original size:2 final size:2
Alignment explanation
Indices: 54807365--54807406 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
54807355 CTTCACATGC
54807365 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
54807407 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54809038 original size:29 final size:30
Alignment explanation
Indices: 54808994--54809052 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
54808984 AAATTGAATC
* *
54808994 AAATCAAATTATCATATGTGAA-ATTGCACA
1 AAATCAAAGTATCATATAT-AACATTGCACA
54809024 AAATCAAAGT-TCATATATAACATTGCACA
1 AAATCAAAGTATCATATATAACATTGCACA
54809053 TAGACTCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.08
29 15 0.58
30 9 0.35
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (30 bp):
AAATCAAAGTATCATATATAACATTGCACA
Found at i:54810866 original size:23 final size:23
Alignment explanation
Indices: 54810840--54810883 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
54810830 TAAATATTAT
54810840 TTTATTAACATTTTATTTAGATA
1 TTTATTAACATTTTATTTAGATA
**
54810863 TTTATTATTATTTTATTTAGA
1 TTTATTAACATTTTATTTAGA
54810884 AAATGGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAACATTTTATTTAGATA
Found at i:54813440 original size:16 final size:16
Alignment explanation
Indices: 54813394--54813442 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
54813384 AAAACATGGA
54813394 TTTTATTTTATTAGTAT
1 TTTTATTTTATTA-TAT
*
54813411 TTTT-TATGTATTATAT
1 TTTTAT-TTTATTATAT
*
54813427 TTTTATTTTTTTATAT
1 TTTTATTTTATTATAT
54813443 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (16 bp):
TTTTATTTTATTATAT
Found at i:54824997 original size:30 final size:29
Alignment explanation
Indices: 54824958--54825024 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
54824948 ACCAAAAAAA
54824958 GCCACTTTTTTTAAAAAATTACCGAAATGG
1 GCCA-TTTTTTTAAAAAATTACCGAAATGG
* ** * *
54824988 GCCAGTTTTTTAATTATTTACCGGAATGG
1 GCCATTTTTTTAAAAAATTACCGAAATGG
54825017 GCCATTTT
1 GCCATTTT
54825025 CCCCGAAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (29 bp):
GCCATTTTTTTAAAAAATTACCGAAATGG
Found at i:54828754 original size:23 final size:23
Alignment explanation
Indices: 54828728--54828779 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
54828718 TTTTTAATTA
*
54828728 AATTAGGTTAGCTTAGGGATTTC
1 AATTAAGTTAGCTTAGGGATTTC
* * *
54828751 AATTAAGTTAGGTTAGGGTTTTT
1 AATTAAGTTAGCTTAGGGATTTC
54828774 AATTAA
1 AATTAA
54828780 ATTAAGTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.42
Consensus pattern (23 bp):
AATTAAGTTAGCTTAGGGATTTC
Found at i:54828755 original size:28 final size:28
Alignment explanation
Indices: 54828692--54828979 Score: 392
Period size: 28 Copynumber: 10.4 Consensus size: 28
54828682 AATTATTACA
* *
54828692 TTAATTCAAA-TAGGTTAGGGTTGGGGTTT
1 TTAATT-AAATTAAGTTA-GGTTAGGGTTT
* *
54828721 TTAATTAAATTAGGTTAGCTTAGGG---
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
* *
54828746 --ATTTCAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
54828772 TTAATTAAATTAAGTTAGGTTATGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
54828800 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAGTTA-GGTTAGGGTTT
*
54828829 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
54828857 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
54828885 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
54828913 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
54828941 TTAATTAAATT-AGTTTAGGGTTAGGGTTT
1 TTAATTAAATTAAG-TTA-GGTTAGGGTTT
*
54828970 TTAATCAAAT
1 TTAATTAAAT
54828980 AATGTCAAAA
Statistics
Matches: 235, Mismatches: 15, Indels: 18
0.88 0.06 0.07
Matches are distributed among these distances:
23 19 0.08
27 2 0.01
28 156 0.66
29 58 0.25
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.45
Consensus pattern (28 bp):
TTAATTAAATTAAGTTAGGTTAGGGTTT
Found at i:54828912 original size:113 final size:113
Alignment explanation
Indices: 54828692--54828979 Score: 419
Period size: 113 Copynumber: 2.6 Consensus size: 113
54828682 AATTATTACA
* * * * *
54828692 TTAATTCAAA-TAGGTTAGGGTTGGGGTTTTTAATTAAATTAGGTTAGCTTAGGG-----ATTTC
1 TTAATT-AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGTTAGGGTTTTTAATTA
*
54828751 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTATGGTTT
65 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTT
*
54828800 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAA
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGTTAGGGTTTTTAATTAA
54828865 ATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTT
66 ATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTT
* * *
54828913 TTAATTAAATTAAGTTA-GGTTAGGGTTTTTAATTAAATTAGTTTAGGGTTAGGGTTTTTAATCA
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGATTA-GGTTAGGGTTTTTAATTA
54828977 AAT
65 AAT
54828980 AATGTCAAAA
Statistics
Matches: 162, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
107 3 0.02
108 46 0.28
112 26 0.16
113 87 0.54
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.45
Consensus pattern (113 bp):
TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGATTAGGTTAGGGTTTTTAATTAA
ATTAAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTT
Found at i:54831206 original size:14 final size:15
Alignment explanation
Indices: 54831189--54831222 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54831179 AATAAATATC
54831189 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
54831203 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
54831218 TAAAA
1 TAAAA
54831223 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Done.