Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 84 of 103
Found at i:31136664 original size:24 final size:24
Alignment explanation
Indices: 31136632--31136731 Score: 103
Period size: 24 Copynumber: 4.1 Consensus size: 24
31136622 ATCCTCCTTT
31136632 CCCTC-TTCTCTCAGCCGATCTTC
1 CCCTCTTTCTCTCAGCCGATCTTC
*
31136655 CCCTCTTTCTCTTAGCCGATCTTC
1 CCCTCTTTCTCTCAGCCGATCTTC
* * * *
31136679 CCTTCTTTCTCTCTCTGCTGCTCTTC
1 CCCTC-TT-TCTCTCAGCCGATCTTC
* * *
31136705 CCCTTTTTCTCTCAACCGCTCTTC
1 CCCTCTTTCTCTCAGCCGATCTTC
31136729 CCC
1 CCC
31136732 ACTCTTCCCC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
23 5 0.08
24 38 0.60
25 4 0.06
26 16 0.25
ACGTcount: A:0.06, C:0.46, G:0.07, T:0.41
Consensus pattern (24 bp):
CCCTCTTTCTCTCAGCCGATCTTC
Found at i:31136737 original size:34 final size:34
Alignment explanation
Indices: 31136699--31136770 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
31136689 CTCTCTGCTG
*
31136699 CTCTTCCCCTTTTTCTCTCAACCGCTCTTCCCCA
1 CTCTTCCCCTCTTTCTCTCAACCGCTCTTCCCCA
* * *
31136733 CTCTTCCCCTCTTTCTGTCAGCCGCTCTTCCCCT
1 CTCTTCCCCTCTTTCTCTCAACCGCTCTTCCCCA
31136767 CTCT
1 CTCT
31136771 CTCTCAACCG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.06, C:0.50, G:0.06, T:0.39
Consensus pattern (34 bp):
CTCTTCCCCTCTTTCTCTCAACCGCTCTTCCCCA
Found at i:31136765 original size:24 final size:24
Alignment explanation
Indices: 31136733--31136794 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
31136723 CTCTTCCCCA
* * *
31136733 CTCTTCCCCTCTTTCTGTCAGCCG
1 CTCTTCCCCTCTCTCTCTCAACCG
31136757 CTCTTCCCCTCTCTCTCTCAACCG
1 CTCTTCCCCTCTCTCTCTCAACCG
* *
31136781 TTCTTCCCCGCTCT
1 CTCTTCCCCTCTCT
31136795 TCCCTTCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.05, C:0.50, G:0.08, T:0.37
Consensus pattern (24 bp):
CTCTTCCCCTCTCTCTCTCAACCG
Found at i:31136819 original size:58 final size:58
Alignment explanation
Indices: 31136674--31136821 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 58
31136664 TCTTAGCCGA
* *
31136674 TCTTCCCTTCTTTCTCTCTC-TGCTGCTCTTCCCCTTTTTCTCTCAACCGCTCTTCCCCAC
1 TCTTCCCTTCTTTCTCTC-CAT-C-GCTCTTCCCCTCTCTCTCTCAACCGCTCTTCCCCAC
* * * * *
31136734 TCTTCCCCTCTTTCTGT-CAGCCGCTCTTCCCCTCTCTCTCTCAACCGTTCTTCCCCGC
1 TCTTCCCTTCTTTCTCTCCA-TCGCTCTTCCCCTCTCTCTCTCAACCGCTCTTCCCCAC
*
31136792 TCTTCCCTTCTTTCTCTCCATCACTCTTCC
1 TCTTCCCTTCTTTCTCTCCATCGCTCTTCC
31136822 ACTGTTTGGG
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
58 56 0.76
59 3 0.04
60 15 0.20
ACGTcount: A:0.05, C:0.48, G:0.05, T:0.41
Consensus pattern (58 bp):
TCTTCCCTTCTTTCTCTCCATCGCTCTTCCCCTCTCTCTCTCAACCGCTCTTCCCCAC
Found at i:31136820 original size:34 final size:34
Alignment explanation
Indices: 31136754--31136821 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
31136744 TTTCTGTCAG
**
31136754 CCGCTCTTCCCCTCTCTCTCTCAACCGTTCTTCC
1 CCGCTCTTCCCCTCTCTCTCTCAACCACTCTTCC
* * * *
31136788 CCGCTCTTCCCTTCTTTCTCTCCATCACTCTTCC
1 CCGCTCTTCCCCTCTCTCTCTCAACCACTCTTCC
31136822 ACTGTTTGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.06, C:0.51, G:0.04, T:0.38
Consensus pattern (34 bp):
CCGCTCTTCCCCTCTCTCTCTCAACCACTCTTCC
Found at i:31142718 original size:101 final size:102
Alignment explanation
Indices: 31142537--31142743 Score: 335
Period size: 101 Copynumber: 2.0 Consensus size: 102
31142527 CTTTTTTCCA
* * *
31142537 TTACACTTAATTCTTTATATTTGAGTCAAAAATATAATTTTTTTTTAATTTTTGACCAAGACCCA
1 TTACACTTAATTCTTCATATTTGAGCCAAAAATATAA--TTTTTTGAATTTTTGACCAAGACCCA
*
31142602 TATCCATAATTCATGGTTGATTGGATAATAATAACAAAC
64 TATACATAATTCATGGTTGATTGGATAATAATAACAAAC
*
31142641 TTACACTTAATTCTTCATATTTGTGCCAAAAATATAA-TTTTTGAATTTTTGACCAAGACCCATA
1 TTACACTTAATTCTTCATATTTGAGCCAAAAATATAATTTTTTGAATTTTTGACCAAGACCCATA
*
31142705 TATATAATTCATGGTTGATTGGATAATAATAACAAAC
66 TACATAATTCATGGTTGATTGGATAATAATAACAAAC
31142742 TT
1 TT
31142744 GCGGTTAAAA
Statistics
Matches: 97, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
101 63 0.65
104 34 0.35
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.41
Consensus pattern (102 bp):
TTACACTTAATTCTTCATATTTGAGCCAAAAATATAATTTTTTGAATTTTTGACCAAGACCCATA
TACATAATTCATGGTTGATTGGATAATAATAACAAAC
Found at i:31149520 original size:7 final size:7
Alignment explanation
Indices: 31149510--31149536 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
31149500 TTATATTTTT
31149510 TTATTTA
1 TTATTTA
31149517 TTATTTA
1 TTATTTA
31149524 TTATTTA
1 TTATTTA
31149531 TTATTT
1 TTATTT
31149537 CATTTTATAT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:31149754 original size:13 final size:13
Alignment explanation
Indices: 31149736--31149780 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
31149726 TTCTACTTCT
31149736 TTTTATTATTATA
1 TTTTATTATTATA
*
31149749 TTTTATTAATATA
1 TTTTATTATTATA
* *
31149762 TTTT-TTCTTATT
1 TTTTATTATTATA
31149774 TTTTATT
1 TTTTATT
31149781 TCTTTATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATTATTATA
Found at i:31149853 original size:16 final size:17
Alignment explanation
Indices: 31149832--31149877 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
31149822 TTTATATTTG
*
31149832 TATTATGATTT-TTTAA
1 TATTATCATTTATTTAA
31149848 TATTATCATTTATTT-A
1 TATTATCATTTATTTAA
*
31149864 T-TTATTATTTATTT
1 TATTATCATTTATTT
31149878 TTATTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 12 0.44
16 12 0.44
17 3 0.11
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATCATTTATTTAA
Found at i:31150188 original size:13 final size:13
Alignment explanation
Indices: 31150167--31150209 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
31150157 CAAAATCTTT
*
31150167 TTTCCTTCTTTTC
1 TTTCTTTCTTTTC
31150180 TTTCTTTCTTTTTC
1 TTTCTTTC-TTTTC
*
31150194 TTT-TTTCTTCTC
1 TTTCTTTCTTTTC
31150206 TTTC
1 TTTC
31150210 CCAACCGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 7 0.27
13 11 0.42
14 8 0.31
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Found at i:31150209 original size:16 final size:15
Alignment explanation
Indices: 31150162--31150209 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
31150152 GACCCCAAAA
31150162 TCTTTTTTCCTTCTTT
1 TCTTTTTT-CTTCTTT
31150178 TCTTTCTTTC-T-TTT
1 TCTTT-TTTCTTCTTT
31150192 TCTTTTTTCTTCTCTT
1 TCTTTTTTCTTCT-TT
31150208 TC
1 TC
31150210 CCAACCGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 4 0.14
14 9 0.32
15 2 0.07
16 10 0.36
17 3 0.11
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TCTTTTTTCTTCTTT
Found at i:31162519 original size:23 final size:23
Alignment explanation
Indices: 31162489--31162536 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
31162479 ACATATAGGC
31162489 AGGTGGATTTAAGATTTTGTATG
1 AGGTGGATTTAAGATTTTGTATG
31162512 AGGTGGATTTAAGATTTTGTATG
1 AGGTGGATTTAAGATTTTGTATG
31162535 AG
1 AG
31162537 ATGTGGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (23 bp):
AGGTGGATTTAAGATTTTGTATG
Found at i:31162655 original size:29 final size:29
Alignment explanation
Indices: 31162623--31162683 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
31162613 AAATAATCAT
31162623 TTTTAT-ATAAAA-GTAAATTTAACATAAAA
1 TTTTATCA-AAAATGTAAATTT-ACATAAAA
* *
31162652 TTTTATCAAAAATTTAAATTTATATAAAA
1 TTTTATCAAAAATGTAAATTTACATAAAA
31162681 TTT
1 TTT
31162684 CAGATTCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (29 bp):
TTTTATCAAAAATGTAAATTTACATAAAA
Found at i:31166772 original size:23 final size:23
Alignment explanation
Indices: 31166746--31166791 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
31166736 ATACCATAAC
*
31166746 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
31166769 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
31166792 TGTTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:31166929 original size:10 final size:10
Alignment explanation
Indices: 31166916--31166949 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
31166906 AAAAGAGATC
31166916 AAAAAAAGAA
1 AAAAAAAGAA
31166926 AAAAAAAGAGA
1 AAAAAAAGA-A
31166937 AAAAAAAGAA
1 AAAAAAAGAA
31166947 AAA
1 AAA
31166950 TAATACCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:31166930 original size:11 final size:11
Alignment explanation
Indices: 31166916--31166949 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31166906 AAAAGAGATC
31166916 AAAAAAAG-AA
1 AAAAAAAGAAA
*
31166926 AAAAAAAGAGA
1 AAAAAAAGAAA
31166937 AAAAAAAGAAA
1 AAAAAAAGAAA
31166948 AA
1 AA
31166950 TAATACCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:31166930 original size:21 final size:21
Alignment explanation
Indices: 31166906--31166949 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
31166896 GCACATTTAT
31166906 AAAAGAGATCAAAAAAAGAAAAA
1 AAAAGAGA--AAAAAAAGAAAAA
31166929 AAAAGAGAAAAAAAAGAAAAA
1 AAAAGAGAAAAAAAAGAAAAA
31166950 TAATACCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.62
23 8 0.38
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAGAGAAAAAAAAGAAAAA
Found at i:31167513 original size:17 final size:17
Alignment explanation
Indices: 31167472--31167535 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
31167462 AAAATAATAT
31167472 AATATTT-AAATA-TTA
1 AATATTTAAAATATTTA
*
31167487 ATTA-TTAAAATATTTA
1 AATATTTAAAATATTTA
31167503 AATATTTAAAATTATTTA
1 AATATTTAAAA-TATTTA
*
31167521 AA-ATTTAAATTATTT
1 AATATTTAAAATATTT
31167536 TATAAAAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
14 2 0.05
15 8 0.19
16 11 0.26
17 13 0.31
18 8 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTTAAAATATTTA
Found at i:31167520 original size:10 final size:10
Alignment explanation
Indices: 31167486--31167525 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
31167476 TTTAAATATT
31167486 AATTA-TTAA
1 AATTATTTAA
31167495 AA-TATTT-A
1 AATTATTTAA
31167503 AA-TATTTAA
1 AATTATTTAA
31167512 AATTATTTAA
1 AATTATTTAA
31167522 AATT
1 AATT
31167526 TAAATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 10 0.36
9 7 0.25
10 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATTATTTAA
Found at i:31167534 original size:26 final size:26
Alignment explanation
Indices: 31167472--31167535 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
31167462 AAAATAATAT
31167472 AATATTTAAATA-TT--AATTATTAA
1 AATATTTAAATATTTAAAATTATTAA
*
31167495 AATATTTAAATATTTAAAATTATTTA
1 AATATTTAAATATTTAAAATTATTAA
31167521 AA-ATTTAAATTATTT
1 AATATTTAAA-TATTT
31167536 TATAAAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 12 0.33
24 2 0.06
25 7 0.19
26 15 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AATATTTAAATATTTAAAATTATTAA
Found at i:31167537 original size:10 final size:8
Alignment explanation
Indices: 31167472--31167535 Score: 69
Period size: 8 Copynumber: 7.9 Consensus size: 8
31167462 AAAATAATAT
31167472 AATATTTA
1 AATATTTA
31167480 AATA-TTA
1 AATATTTA
* *
31167487 ATTATTAA
1 AATATTTA
31167495 AATATTTA
1 AATATTTA
31167503 AATATTTAA
1 AATATTT-A
31167512 AATTATTTA
1 AA-TATTTA
31167521 AA-ATTTA
1 AATATTTA
31167528 AATTATTT
1 AA-TATTT
31167536 TATAAAAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
7 13 0.28
8 19 0.40
9 10 0.21
10 5 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AATATTTA
Found at i:31167664 original size:21 final size:21
Alignment explanation
Indices: 31167638--31167677 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
31167628 CCATGGGCGC
31167638 TTCTTTTTCTTTT-CTCCTTAT
1 TTCTTTTT-TTTTCCTCCTTAT
31167659 TTCTTTTTTTTTCCTCCTT
1 TTCTTTTTTTTTCCTCCTT
31167678 TCCATACCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (21 bp):
TTCTTTTTTTTTCCTCCTTAT
Found at i:31178858 original size:24 final size:23
Alignment explanation
Indices: 31178831--31178881 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
31178821 ATCTAGTTAG
* *
31178831 ATTAGAATAACAATTCTTAATTCT
1 ATTAGAATAA-AATTCCTAATTAT
* *
31178855 ATTAGGATAAGATTCCTAATTAT
1 ATTAGAATAAAATTCCTAATTAT
31178878 ATTA
1 ATTA
31178882 AGATAAGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (23 bp):
ATTAGAATAAAATTCCTAATTAT
Found at i:31178874 original size:23 final size:23
Alignment explanation
Indices: 31178843--31178888 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31178833 TAGAATAACA
* * *
31178843 ATTCTTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAAGATAAG
31178866 ATTCCTAATTATATTAAGATAAG
1 ATTCCTAATTATATTAAGATAAG
31178889 GTTATTGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (23 bp):
ATTCCTAATTATATTAAGATAAG
Found at i:31182499 original size:12 final size:13
Alignment explanation
Indices: 31182475--31182508 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
31182465 TGGTCATGGG
31182475 CTCTTCTTCTTTT
1 CTCTTCTTCTTTT
*
31182488 CT-TTCTTTTTTT
1 CTCTTCTTCTTTT
31182500 CTCTTCTTC
1 CTCTTCTTC
31182509 CTCTTTGCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
CTCTTCTTCTTTT
Found at i:31185749 original size:3 final size:3
Alignment explanation
Indices: 31185741--31185774 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
31185731 CAATGTTACA
31185741 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31185775 CGTTAGTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:31187912 original size:22 final size:22
Alignment explanation
Indices: 31187887--31187934 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
31187877 TTGTTAAATG
31187887 ATATGCATAT-TCTATTATAATA
1 ATATGCATATCTCT-TTATAATA
31187909 ATATGCATATCTCTTTATAATA
1 ATATGCATATCTCTTTATAATA
31187931 ATAT
1 ATAT
31187935 ATACATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATGCATATCTCTTTATAATA
Found at i:31197656 original size:2 final size:2
Alignment explanation
Indices: 31197649--31197704 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
31197639 GGTAGATCCT
* * **
31197649 AG AG AG AG AG AG AG AG AG AG AG -G AA AG AN CT ACG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG
31197691 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
31197705 GAAAAATAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
1 1 0.02
2 43 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.45, T:0.02
Consensus pattern (2 bp):
AG
Found at i:31203483 original size:11 final size:11
Alignment explanation
Indices: 31203467--31203517 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
31203457 AAAATGAGAA
*
31203467 AAATGCAAGTG
1 AAATGCAAATG
31203478 AAATGCAAATG
1 AAATGCAAATG
*
31203489 AAATG-AAAGTT
1 AAATGCAAA-TG
31203500 AAATG-AAATG
1 AAATGCAAATG
31203510 CAAATGCA
1 -AAATGCA
31203518 TGCATGGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 4 0.12
11 29 0.85
12 1 0.03
ACGTcount: A:0.53, C:0.08, G:0.20, T:0.20
Consensus pattern (11 bp):
AAATGCAAATG
Found at i:31203493 original size:22 final size:22
Alignment explanation
Indices: 31203467--31203517 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
31203457 AAAATGAGAA
31203467 AAATGCAAGTGAAATGCAAATG-
1 AAATGCAAGTGAAATG-AAATGC
* *
31203489 AAATGAAAGTTAAATGAAATGC
1 AAATGCAAGTGAAATGAAATGC
31203511 AAATGCA
1 AAATGCA
31203518 TGCATGGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.53, C:0.08, G:0.20, T:0.20
Consensus pattern (22 bp):
AAATGCAAGTGAAATGAAATGC
Found at i:31203680 original size:22 final size:23
Alignment explanation
Indices: 31203641--31203683 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
31203631 TAATGTGATA
31203641 AAAAGGAAAAGTGAAATGATGTG
1 AAAAGGAAAAGTGAAATGATGTG
* *
31203664 AAAA-GAAAGGTGTAATGATG
1 AAAAGGAAAAGTGAAATGATG
31203684 GCATGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (23 bp):
AAAAGGAAAAGTGAAATGATGTG
Found at i:31204862 original size:22 final size:24
Alignment explanation
Indices: 31204837--31204887 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
31204827 AATGCTATAC
31204837 CATC-TTTACACTTTT-CTTT-TCA
1 CATCATTT-CACTTTTCCTTTATCA
31204859 CATCATTTCACTTTTCCTTTATCA
1 CATCATTTCACTTTTCCTTTATCA
31204883 CATCA
1 CATCA
31204888 AATGCTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.42
23 7 0.27
24 8 0.31
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (24 bp):
CATCATTTCACTTTTCCTTTATCA
Found at i:31205277 original size:19 final size:19
Alignment explanation
Indices: 31205253--31205291 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31205243 TCAATCATAC
31205253 TCTTTTGATGTGCATGCAT
1 TCTTTTGATGTGCATGCAT
31205272 TCTTTTGATGTGCATGCAT
1 TCTTTTGATGTGCATGCAT
31205291 T
1 T
31205292 AAAATGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (19 bp):
TCTTTTGATGTGCATGCAT
Found at i:31209838 original size:13 final size:13
Alignment explanation
Indices: 31209820--31209846 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31209810 TACAGTTTGG
31209820 CATGGCTATGGCT
1 CATGGCTATGGCT
31209833 CATGGCTATGGCT
1 CATGGCTATGGCT
31209846 C
1 C
31209847 TCTGCCTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.30
Consensus pattern (13 bp):
CATGGCTATGGCT
Found at i:31218306 original size:6 final size:6
Alignment explanation
Indices: 31218297--31218322 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31218287 TATTAGTATT
31218297 ATTATC ATTATC ATTATC ATTATC AT
1 ATTATC ATTATC ATTATC ATTATC AT
31218323 CACATGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTATC
Found at i:31220204 original size:45 final size:45
Alignment explanation
Indices: 31220153--31220244 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
31220143 AAGGCATAAA
* * * *
31220153 TTGGTTCTAGAACTAATAATCCTATTTTGGAGATTTTATGTCTGC
1 TTGGTTCTAGAACTAATAATCCTAATTTGGAGAGTTTACGCCTGC
* *
31220198 TTGGTTCTAGATCTAATAATTCTAATTTGGAGAGTTTACGCCTGC
1 TTGGTTCTAGAACTAATAATCCTAATTTGGAGAGTTTACGCCTGC
31220243 TT
1 TT
31220245 CCTCTTGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.43
Consensus pattern (45 bp):
TTGGTTCTAGAACTAATAATCCTAATTTGGAGAGTTTACGCCTGC
Found at i:31223647 original size:62 final size:62
Alignment explanation
Indices: 31223550--31223677 Score: 222
Period size: 62 Copynumber: 2.1 Consensus size: 62
31223540 CAAAATTAAG
31223550 TATAATAAAATAAAAAAATAAAAGGGGAAAAGAAAAAAGTCACCCCTGGACCACTTCAATCA
1 TATAATAAAATAAAAAAATAAAAGGGGAAAAGAAAAAAGTCACCCCTGGACCACTTCAATCA
* *
31223612 TATAATAAAATAAAAAAATAAAA-GGGAAATTGAAAAGAGTCACCCCTGGACCACTTCAATCA
1 TATAATAAAATAAAAAAATAAAAGGGGAAA-AGAAAAAAGTCACCCCTGGACCACTTCAATCA
31223674 TATA
1 TATA
31223678 GACATCGCTA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 6 0.10
62 57 0.90
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (62 bp):
TATAATAAAATAAAAAAATAAAAGGGGAAAAGAAAAAAGTCACCCCTGGACCACTTCAATCA
Found at i:31229040 original size:81 final size:81
Alignment explanation
Indices: 31228905--31229124 Score: 325
Period size: 81 Copynumber: 2.7 Consensus size: 81
31228895 ACCTATTGGT
* *
31228905 AGATAATATTTAT-TTTTTGGACCAATCAAAAATTAGTCATTGGTCATTCAATTTATCTTTAAAT
1 AGATAATATTTATATTTTT-GACCAATCAAAAATTAGTTATTGGTCATTCAATTTATCTCTAAAT
31228969 AAATCAAAATAATTTAA
65 AAATCAAAATAATTTAA
* *
31228986 AGATAATATTTATATTTTTGATCAATCAAAAATTAGTTATTGGTCATCCAATTTATCTCTAAATA
1 AGATAATATTTATATTTTTGACCAATCAAAAATTAGTTATTGGTCATTCAATTTATCTCTAAATA
* *
31229051 AATCAAGATAATTTAG
66 AATCAAAATAATTTAA
* * * * *
31229067 AGATAATATTCATATTTTTAACCAATCAAAATTTAATTATTGGTCATTTAATTTATCT
1 AGATAATATTTATATTTTTGACCAATCAAAAATTAGTTATTGGTCATTCAATTTATCT
31229125 ATAATAATGA
Statistics
Matches: 125, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
81 120 0.96
82 5 0.04
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (81 bp):
AGATAATATTTATATTTTTGACCAATCAAAAATTAGTTATTGGTCATTCAATTTATCTCTAAATA
AATCAAAATAATTTAA
Found at i:31229527 original size:25 final size:23
Alignment explanation
Indices: 31229472--31229529 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 23
31229462 AGCGATAATT
31229472 AAGTTCGTGATCAAGCAACAACG
1 AAGTTCGTGATCAAGCAACAACG
31229495 AAGTTCGTGATCAA-CATATCAAGCG
1 AAGTTCGTGATCAAGCA-A-CAA-CG
31229520 AAGTTCGTGA
1 AAGTTCGTGA
31229530 GGTAAAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 2 0.06
23 15 0.47
24 3 0.09
25 12 0.38
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (23 bp):
AAGTTCGTGATCAAGCAACAACG
Found at i:31230465 original size:43 final size:43
Alignment explanation
Indices: 31230418--31230524 Score: 173
Period size: 43 Copynumber: 2.5 Consensus size: 43
31230408 AACAATAAAC
31230418 TGAAAAATATGAAATAATAAATAAAGTTTCCAAAACCCAAAAA
1 TGAAAAATATGAAATAATAAATAAAGTTTCCAAAACCCAAAAA
31230461 TGAAAAATATGAAATAATAAATAAAGTTTCCAAAACCCAAAAA
1 TGAAAAATATGAAATAATAAATAAAGTTTCCAAAACCCAAAAA
*
31230504 --AAAGAATAATGAAAAAATAAA
1 TGAAA-AAT-ATGAAATAATAAA
31230525 AAACAAAACA
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
41 3 0.05
42 3 0.05
43 55 0.90
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (43 bp):
TGAAAAATATGAAATAATAAATAAAGTTTCCAAAACCCAAAAA
Found at i:31231861 original size:15 final size:16
Alignment explanation
Indices: 31231843--31231872 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31231833 TTGTTATGTG
31231843 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
31231858 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
31231873 AAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:31232111 original size:14 final size:13
Alignment explanation
Indices: 31232094--31232141 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
31232084 TTTATATATC
31232094 ATATTTAACTATTT
1 ATATTTAA-TATTT
*
31232108 ATATTTTATATATT
1 ATATTTAATAT-TT
31232122 ATAATTTAATATTT
1 AT-ATTTAATATTT
31232136 AGTATT
1 A-TATT
31232142 ATAAACTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 17 0.59
15 9 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (13 bp):
ATATTTAATATTT
Found at i:31232115 original size:28 final size:29
Alignment explanation
Indices: 31232082--31232141 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
31232072 AAAATTATTA
31232082 ATTTTATATATCAT-ATTTAACTATTTA-T
1 ATTTTATATATCATAATTTAA-TATTTAGT
*
31232110 ATTTTATATATTATAATTTAATATTTAGT
1 ATTTTATATATCATAATTTAATATTTAGT
31232139 ATT
1 ATT
31232142 ATAAACTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (29 bp):
ATTTTATATATCATAATTTAATATTTAGT
Found at i:31234990 original size:18 final size:18
Alignment explanation
Indices: 31234967--31235006 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
31234957 CAAGGAGGAG
31234967 GGAAAGAAAAAGA-AGAAA
1 GGAAAGAAAAAGAGAG-AA
31234985 GGAAAGAAAAAGAGAGAA
1 GGAAAGAAAAAGAGAGAA
31235003 GGAA
1 GGAA
31235007 GTTCAGCCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
GGAAAGAAAAAGAGAGAA
Found at i:31235060 original size:14 final size:14
Alignment explanation
Indices: 31235023--31235069 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
31235013 CCGAACCAAG
31235023 GAGA-GAAAAGAAA
1 GAGAGGAAAAGAAA
*
31235036 GA-AAG-AAAGAAA
1 GAGAGGAAAAGAAA
*
31235048 GGGAGGAAAAGAAA
1 GAGAGGAAAAGAAA
31235062 GAGAGGAA
1 GAGAGGAA
31235070 GCTGGACTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 9 0.32
13 5 0.18
14 14 0.50
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
GAGAGGAAAAGAAA
Found at i:31242888 original size:45 final size:45
Alignment explanation
Indices: 31242837--31242928 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
31242827 AAGGCATAAA
* * * *
31242837 TTGGTTCTAGAACTAATAATCCTATTTTGGAGATTTTATGTCTGC
1 TTGGTTCTAGAACTAATAATCCTAATTTGGAGAGTTTACGCCTGC
* *
31242882 TTGGTTCTAGATCTAATAATTCTAATTTGGAGAGTTTACGCCTGC
1 TTGGTTCTAGAACTAATAATCCTAATTTGGAGAGTTTACGCCTGC
31242927 TT
1 TT
31242929 CCTCTTGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.43
Consensus pattern (45 bp):
TTGGTTCTAGAACTAATAATCCTAATTTGGAGAGTTTACGCCTGC
Found at i:31246361 original size:59 final size:62
Alignment explanation
Indices: 31246251--31246376 Score: 195
Period size: 59 Copynumber: 2.1 Consensus size: 62
31246241 CAAAATTAAG
31246251 TATAATAAAATAAAAAAATAAAAGGAAAAAAGAAAAAAAGTCACCCCTGGACCACTTCAATCA
1 TATAATAAAAT-AAAAAATAAAAGGAAAAAAGAAAAAAAGTCACCCCTGGACCACTTCAATCA
* * *
31246314 TATAATAAAAT-AAAAA-AAAAGGTAAAATG-AAAAATGTCACCCCTGGACCACTTCAATCA
1 TATAATAAAATAAAAAATAAAAGGAAAAAAGAAAAAAAGTCACCCCTGGACCACTTCAATCA
31246373 TATA
1 TATA
31246377 GACATCGCTA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
59 33 0.55
60 11 0.18
61 5 0.08
63 11 0.18
ACGTcount: A:0.56, C:0.16, G:0.10, T:0.19
Consensus pattern (62 bp):
TATAATAAAATAAAAAATAAAAGGAAAAAAGAAAAAAAGTCACCCCTGGACCACTTCAATCA
Found at i:31251851 original size:17 final size:17
Alignment explanation
Indices: 31251829--31251862 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31251819 CTGAAAGAAA
* *
31251829 ATAAAAGAAAATAAAAG
1 ATAAAAAAAAACAAAAG
31251846 ATAAAAAAAAACAAAAG
1 ATAAAAAAAAACAAAAG
31251863 GAAAATCATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
ATAAAAAAAAACAAAAG
Found at i:31251854 original size:10 final size:10
Alignment explanation
Indices: 31251822--31251846 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31251812 ACTGAGACTG
31251822 AAAGAAAATA
1 AAAGAAAATA
31251832 AAAGAAAATA
1 AAAGAAAATA
31251842 AAAGA
1 AAAGA
31251847 TAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAGAAAATA
Found at i:31258853 original size:4 final size:4
Alignment explanation
Indices: 31258846--31258885 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
31258836 TATATATATA
* *
31258846 TATG TATG TAAG TATG TATG TATG TATG TATG TGTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
31258886 CATGGAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:31270901 original size:37 final size:37
Alignment explanation
Indices: 31270856--31270939 Score: 159
Period size: 37 Copynumber: 2.3 Consensus size: 37
31270846 TTAAATGATC
*
31270856 AAGCATAACCTTTCCAAACCACTACTTTTCATGGATT
1 AAGCATAACCTTTACAAACCACTACTTTTCATGGATT
31270893 AAGCATAACCTTTACAAACCACTACTTTTCATGGATT
1 AAGCATAACCTTTACAAACCACTACTTTTCATGGATT
31270930 AAGCATAACC
1 AAGCATAACC
31270940 CCTATCTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (37 bp):
AAGCATAACCTTTACAAACCACTACTTTTCATGGATT
Found at i:31270949 original size:28 final size:28
Alignment explanation
Indices: 31270909--31270995 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
31270899 AACCTTTACA
* * *
31270909 AACCACTA-CTTTTCATGGATTAAGCAT
1 AACCCCTATCTTTTCAAGGATCAAGCAT
* * *
31270936 AACCCCTATCTTTTTAAAGATCGAGCAT
1 AACCCCTATCTTTTCAAGGATCAAGCAT
* * *
31270964 AACTCTTGTCTTTTCAAGGATCAAGCAT
1 AACCCCTATCTTTTCAAGGATCAAGCAT
31270992 AACC
1 AACC
31270996 TTTACAAGCA
Statistics
Matches: 46, Mismatches: 13, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
27 7 0.15
28 39 0.85
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (28 bp):
AACCCCTATCTTTTCAAGGATCAAGCAT
Found at i:31271599 original size:22 final size:22
Alignment explanation
Indices: 31271538--31271602 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
31271528 GAATTGATTT
* *
31271538 TTCATTCTTGAGATATCGATTC
1 TTCATTCTTTAGATATCAATTC
* *
31271560 TTC-TTGTTCTGTGA-ATCAATTC
1 TTCATTCTT-T-AGATATCAATTC
31271582 TTCATTCTTTAGATATCAATT
1 TTCATTCTTTAGATATCAATT
31271603 TTTTGTGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
21 6 0.18
22 21 0.64
23 6 0.18
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (22 bp):
TTCATTCTTTAGATATCAATTC
Found at i:31271878 original size:20 final size:19
Alignment explanation
Indices: 31271849--31271886 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
31271839 AACACATCGA
31271849 AAGCATTCAAGGATCACTC
1 AAGCATTCAAGGATCACTC
31271868 AAGCTATTCAAGGATCACT
1 AAGC-ATTCAAGGATCACT
31271887 TAGACAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24
Consensus pattern (19 bp):
AAGCATTCAAGGATCACTC
Found at i:31276614 original size:339 final size:338
Alignment explanation
Indices: 31275993--31276622 Score: 1242
Period size: 339 Copynumber: 1.9 Consensus size: 338
31275983 ATTGTGAGTG
31275993 AGATACATTCAAGATTTACCTTACAAAAATAGTAAAGATAACGTCAATTATTTCAGTTAACCCAT
1 AGATACATTCAAGATTTACCTTACAAAAATAGTAAAGATAACGTCAATTATTTCAGTTAACCCAT
31276058 TTTAAATTTTTTAGCCAAATCAATCCAACTTTACCAACTCACTTAACTGAATTAACCGAACTTTT
66 TTTAAATTTTTTAGCCAAATCAATCCAACTTTACCAACTCACTTAACTGAATTAACCGAACTTTT
31276123 GTCGACTAACTCAAACAAAGTCAACTTTATCCAATTTTTTCTCACCTTTAATTGTACCCATTTAG
131 GTCGACTAACTCAAACAAAGTCAACTTTATCCAATTTTTTCTCACCTTTAATTGTACCCATTTAG
31276188 ATCCTTTTTTGTTTCTGTGTGTGTGTGTATGACATAATGCTTGAAAAAGTTCCTGAACTATTCAA
196 ATCCTTTTTTGTTTCTGTGTGTGTGTGTATGACATAATGCTTGAAAAAGTTCCTGAACTATTCAA
31276253 GAAAATAACAATAAACTCTTATTCTTCTATTACTTTCAATAAAGTTAGTATACTCTTATTTTGAA
261 GAAAATAACAATAAACTCTTATTCTTCTATTACTTTCAATAAAGTTAGTATACTCTTATTTTGAA
31276318 TCAAATAAACTTA
326 TCAAATAAACTTA
31276331 ANGATACATTCAAGATTTACCTTACAAAAATAGTAAAGATAACGTCAATTATTTCAGTTAACCCA
1 A-GATACATTCAAGATTTACCTTACAAAAATAGTAAAGATAACGTCAATTATTTCAGTTAACCCA
31276396 TTTTAAATTTTTTAGCCAAATCAATCCAACTTTACCAACTCACTTAACTGAATTAACCGAACTTT
65 TTTTAAATTTTTTAGCCAAATCAATCCAACTTTACCAACTCACTTAACTGAATTAACCGAACTTT
31276461 TGTCGACTAACTCAAACAAAGTCAACTTTATCCAATTTTTTCTCACCTTTAATTGTACCCATTTA
130 TGTCGACTAACTCAAACAAAGTCAACTTTATCCAATTTTTTCTCACCTTTAATTGTACCCATTTA
*
31276526 GATCCTTTTTTGTTTCTGTGTGTGTGTGTATGACATAATGCTTGAAAAAGTTCTTGAACTATTCA
195 GATCCTTTTTTGTTTCTGTGTGTGTGTGTATGACATAATGCTTGAAAAAGTTCCTGAACTATTCA
31276591 AGAAAATAACAATAAACTCTTATTCTTCTATT
260 AGAAAATAACAATAAACTCTTATTCTTCTATT
31276623 GTATTTAATT
Statistics
Matches: 290, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
338 1 0.00
339 289 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (338 bp):
AGATACATTCAAGATTTACCTTACAAAAATAGTAAAGATAACGTCAATTATTTCAGTTAACCCAT
TTTAAATTTTTTAGCCAAATCAATCCAACTTTACCAACTCACTTAACTGAATTAACCGAACTTTT
GTCGACTAACTCAAACAAAGTCAACTTTATCCAATTTTTTCTCACCTTTAATTGTACCCATTTAG
ATCCTTTTTTGTTTCTGTGTGTGTGTGTATGACATAATGCTTGAAAAAGTTCCTGAACTATTCAA
GAAAATAACAATAAACTCTTATTCTTCTATTACTTTCAATAAAGTTAGTATACTCTTATTTTGAA
TCAAATAAACTTA
Found at i:31285951 original size:37 final size:37
Alignment explanation
Indices: 31285890--31285992 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
31285880 CACTATAAAA
* * * *
31285890 ACTACTTTTTAAATGATCAAGCATAACCTTTCCAAACC
1 ACTACTTTTCATA-GATAAAGCATAACCTTTACAAACC
* *
31285928 ATTACTTTTCAT-GAATTAAGCATAACCTTTACAAACC
1 ACTACTTTTCATAG-ATAAAGCATAACCTTTACAAACC
31285965 ACTACTTTTCATAGATAAAGCATAACCT
1 ACTACTTTTCATAGATAAAGCATAACCT
31285993 CTACCTTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
36 1 0.02
37 45 0.80
38 10 0.18
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (37 bp):
ACTACTTTTCATAGATAAAGCATAACCTTTACAAACC
Found at i:31285991 original size:27 final size:27
Alignment explanation
Indices: 31285961--31286017 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
31285951 AACCTTTACA
*
31285961 AACCACTA-CTTTTCATAGATAAAGCAT
1 AACCACTACCTTTT-AAAGATAAAGCAT
* *
31285988 AACCTCTACCTTTTAAAGATCAAGCAT
1 AACCACTACCTTTTAAAGATAAAGCAT
31286015 AAC
1 AAC
31286018 TATTGTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (27 bp):
AACCACTACCTTTTAAAGATAAAGCAT
Found at i:31291383 original size:2 final size:2
Alignment explanation
Indices: 31291372--31291408 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
31291362 ATCTTATAAG
31291372 AT AT -T 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
31291409 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:31299419 original size:17 final size:18
Alignment explanation
Indices: 31299369--31299427 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
31299359 TTTATTTTCC
31299369 AACATAATTATTTGAACA
1 AACATAATTATTTGAACA
* *
31299387 AACTTAATTGTTTGAACA
1 AACATAATTATTTGAACA
*
31299405 AACATAAGT-TTTGAACA
1 AACATAATTATTTGAACA
*
31299422 ATCATA
1 AACATA
31299428 TTGTTCAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 13 0.36
18 23 0.64
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (18 bp):
AACATAATTATTTGAACA
Found at i:31301017 original size:15 final size:15
Alignment explanation
Indices: 31300997--31301029 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
31300987 TAACATTACA
31300997 AAAATTA-TAACTTAT
1 AAAATTATTAA-TTAT
31301012 AAAATTATTAATTAT
1 AAAATTATTAATTAT
31301027 AAA
1 AAA
31301030 TATATATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTATTAATTAT
Found at i:31303618 original size:3 final size:3
Alignment explanation
Indices: 31303610--31303695 Score: 54
Period size: 3 Copynumber: 28.3 Consensus size: 3
31303600 GTATTTTTTG
* *
31303610 TTA TTA TTAA TTA TTT TTA TT- TTA TTA TATA TT- TTA TTA TCA -TA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * *
31303654 TT- TCCTA TTC TTGT TTC TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA T--TA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31303696 CTTTATCTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
2 6 0.09
3 50 0.76
4 9 0.14
5 1 0.02
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31303816 original size:15 final size:14
Alignment explanation
Indices: 31303790--31303837 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
31303780 GTGAACAAAA
31303790 ATTATATATTTTTT
1 ATTATATATTTTTT
31303804 ATTATACTA-TTTTT
1 ATTATA-TATTTTTT
31303818 ATTTCATATATTTTTAT
1 A-TT-ATATATTTTT-T
31303835 ATT
1 ATT
31303838 TTTTATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.41
15 6 0.21
16 9 0.31
17 2 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATATATTTTTT
Found at i:31305130 original size:25 final size:26
Alignment explanation
Indices: 31305056--31305131 Score: 129
Period size: 25 Copynumber: 3.0 Consensus size: 26
31305046 ACCCGTTTCT
*
31305056 TTTTTTGCTTTCTCACCCAAGATC-C
1 TTTTTTGCTCTCTCACCCAAGATCTC
31305081 TTTTTTGCTCTCTCACCCAAGATCTC
1 TTTTTTGCTCTCTCACCCAAGATCTC
31305107 -TTTTTGCTCTCTCACCCAAGATCTC
1 TTTTTTGCTCTCTCACCCAAGATCTC
31305132 CCCCTTCCTC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 48 0.98
26 1 0.02
ACGTcount: A:0.16, C:0.34, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTTTTGCTCTCTCACCCAAGATCTC
Found at i:31317322 original size:2 final size:2
Alignment explanation
Indices: 31317311--31317356 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
31317301 ATTTAAAGTA
31317311 AT AT -T AT AT AT AT AT AT AT AT ACT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
31317353 AT AT
1 AT AT
31317357 TTGTTAGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31317888 original size:55 final size:55
Alignment explanation
Indices: 31317758--31317888 Score: 149
Period size: 55 Copynumber: 2.4 Consensus size: 55
31317748 GTTAGAGTTA
* * * *
31317758 TTTTAGCGTGTCACGGTTGTTCCTGGCGTGTTGTGGGTTAACTAGTTTTTTAGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTAGATTTATAGGT
* * * *
31317813 TGTTAGCGTGTCATGACTGTTCCTGAG-GTGTCGTGGGTTAACTTA-ATTTATGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTG-GCGTGTCGTGGGTTAAC-TAGATTTATAGGT
*
31317868 TTTTGGCGTGTCACGGCTGTT
1 TTTTAGCGTGTCACGGCTGTT
31317889 GGTGTAATAA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
55 59 0.95
56 3 0.05
ACGTcount: A:0.12, C:0.14, G:0.31, T:0.43
Consensus pattern (55 bp):
TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTAGATTTATAGGT
Found at i:31317950 original size:23 final size:23
Alignment explanation
Indices: 31317920--31318071 Score: 171
Period size: 23 Copynumber: 6.3 Consensus size: 23
31317910 CAGTGATTGA
*
31317920 CGTGTCACGACAGTGATGCATGG
1 CGTGTCACGATAGTGATGCATGG
31317943 CGTGTCACCG-TAGTGATGCAGCATGG
1 CGTGTCA-CGATAGTGAT---GCATGG
*
31317969 CGTGTCACGACAGTGATGCATGG
1 CGTGTCACGATAGTGATGCATGG
*
31317992 CGTGTCACCATAGTGATACAGCATGG
1 CGTGTCACGATAGTGAT---GCATGG
*
31318018 CGTGTCATGATAGTGATGCATGG
1 CGTGTCACGATAGTGATGCATGG
* * *
31318041 CGTGTAACGATACTGATGCATGA
1 CGTGTCACGATAGTGATGCATGG
31318064 CGTGTCAC
1 CGTGTCAC
31318072 AACATTTGAC
Statistics
Matches: 110, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
23 66 0.60
24 2 0.02
25 2 0.02
26 40 0.36
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (23 bp):
CGTGTCACGATAGTGATGCATGG
Found at i:31317992 original size:49 final size:49
Alignment explanation
Indices: 31317920--31318045 Score: 216
Period size: 49 Copynumber: 2.6 Consensus size: 49
31317910 CAGTGATTGA
* *
31317920 CGTGTCACGACAGTGATGCATGGCGTGTCACCGTAGTGATGCAGCATGG
1 CGTGTCACGACAGTGATGCATGGCGTGTCACCATAGTGATACAGCATGG
31317969 CGTGTCACGACAGTGATGCATGGCGTGTCACCATAGTGATACAGCATGG
1 CGTGTCACGACAGTGATGCATGGCGTGTCACCATAGTGATACAGCATGG
* *
31318018 CGTGTCATGATAGTGATGCATGGCGTGT
1 CGTGTCACGACAGTGATGCATGGCGTGT
31318046 AACGATACTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (49 bp):
CGTGTCACGACAGTGATGCATGGCGTGTCACCATAGTGATACAGCATGG
Found at i:31318091 original size:31 final size:32
Alignment explanation
Indices: 31318056--31318137 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 32
31318046 AACGATACTG
31318056 ATGCATGA-CGTGTCACAACATTTGAC-TTGAT
1 ATGCATGAGCGTGTCACAACATTTGACGTT-AT
* * *
31318087 ATGCAT-AGTGTGTTACAACATTTTACGTTAT
1 ATGCATGAGCGTGTCACAACATTTGACGTTAT
* *
31318118 ATGCATG-GCGTCTAACAACA
1 ATGCATGAGCGTGTCACAACA
31318138 CAACTGATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
30 1 0.02
31 39 0.93
32 2 0.05
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (32 bp):
ATGCATGAGCGTGTCACAACATTTGACGTTAT
Found at i:31322185 original size:31 final size:31
Alignment explanation
Indices: 31322141--31322572 Score: 451
Period size: 31 Copynumber: 14.0 Consensus size: 31
31322131 AATAAGGAAT
* *
31322141 AAATG-TGAGACACGCCATGCAAAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
31322171 AAATGTTGTGACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
31322202 AAATATTATGACACTCCATGCATAACAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
31322233 AAATTTTATGACACGCCATGCATAAGAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
31322264 AAACGTTGTGACACGTCATGCATAACAATTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
31322295 AATTATTGTGACACGCCATGCATAACAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
31322326 AAACGTTGTGACACGCCATGCGTAACAATTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
31322357 AATTGTTCTAACTCGCCATGCATAACAAGT-
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
31322387 AAAT-TATGCTGACACGCCATGCATAACAAGTT
1 AAATGT-TG-TGACACGCCATGCATAACAAGTA
* *
31322419 AAACGTTGTGACACGCCATGCATAACAATTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
31322450 AATTGTTCTAACCCGCCATGCATAACAAGT-
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
31322480 AAAT-TATGCTGACACGCCATGCATAACAAGTT
1 AAATGT-TG-TGACACGCCATGCATAACAAGTA
* *
31322512 AAACGTTGTGACACGCCATGCATAACAATTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
31322543 AATTGTTCTGACCCGCCATGCATGACAAGT
1 AAATGTTGTGACACGCCATGCATAACAAGT
31322573 TCTGGTGTGT
Statistics
Matches: 328, Mismatches: 65, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
29 2 0.01
30 13 0.04
31 301 0.92
32 10 0.03
33 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:31322308 original size:93 final size:93
Alignment explanation
Indices: 31322149--31322572 Score: 573
Period size: 93 Copynumber: 4.6 Consensus size: 93
31322139 ATAAATGTGA
* * * * * * * **
31322149 GACACGCCATGCAAAACAAGTAAAATGTTGTGACACGCCATGCATATCAAGTAAAATATTATGAC
1 GACACGCCATGCATAACAATTAAATTGTTCTAACACGCCATGCATAACAAGTAAATTATGCTGAC
* ** ** *
31322214 ACTCCATGCATAACAAGCAAAATTTTAT
66 ACGCCATGCATAACAAGTTAAACGTTGT
* * * * * *
31322242 GACACGCCATGCATAAGAAGTTAAA-CGTTGTGACACGTCATGCATAACAATTAAATTATTG-TG
1 GACACGCCATGCATAACAA-TTAAATTGTTCTAACACGCCATGCATAACAAGTAAATTA-TGCTG
31322305 ACACGCCATGCATAACAAGTTAAACGTTGT
64 ACACGCCATGCATAACAAGTTAAACGTTGT
* *
31322335 GACACGCCATGCGTAACAATTAAATTGTTCTAACTCGCCATGCATAACAAGTAAATTATGCTGAC
1 GACACGCCATGCATAACAATTAAATTGTTCTAACACGCCATGCATAACAAGTAAATTATGCTGAC
31322400 ACGCCATGCATAACAAGTTAAACGTTGT
66 ACGCCATGCATAACAAGTTAAACGTTGT
*
31322428 GACACGCCATGCATAACAATTAAATTGTTCTAACCCGCCATGCATAACAAGTAAATTATGCTGAC
1 GACACGCCATGCATAACAATTAAATTGTTCTAACACGCCATGCATAACAAGTAAATTATGCTGAC
31322493 ACGCCATGCATAACAAGTTAAACGTTGT
66 ACGCCATGCATAACAAGTTAAACGTTGT
* * *
31322521 GACACGCCATGCATAACAATTAAATTGTTCTGACCCGCCATGCATGACAAGT
1 GACACGCCATGCATAACAATTAAATTGTTCTAACACGCCATGCATAACAAGT
31322573 TCTGGTGTGT
Statistics
Matches: 300, Mismatches: 27, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
92 7 0.02
93 288 0.96
94 5 0.02
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (93 bp):
GACACGCCATGCATAACAATTAAATTGTTCTAACACGCCATGCATAACAAGTAAATTATGCTGAC
ACGCCATGCATAACAAGTTAAACGTTGT
Found at i:31323409 original size:31 final size:31
Alignment explanation
Indices: 31323321--31323397 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
31323311 CCCAATTGTT
* *
31323321 CTGACACGCTGAGTGGAAGTAGATTTATGGG
1 CTGACACGCTGAGTGGAAGTAGATTTATCGA
* * *
31323352 CTGACACGCTAAGTGGAAGCAAATTTATCGA
1 CTGACACGCTGAGTGGAAGTAGATTTATCGA
31323383 CTGACACGCTGAGTG
1 CTGACACGCTGAGTG
31323398 TTAGTGGATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (31 bp):
CTGACACGCTGAGTGGAAGTAGATTTATCGA
Found at i:31323467 original size:31 final size:31
Alignment explanation
Indices: 31323322--31323490 Score: 99
Period size: 31 Copynumber: 5.5 Consensus size: 31
31323312 CCAATTGTTC
* * * *
31323322 TGACACGCTGAGTGGAAGTAGATTTATGGGC
1 TGACACGCTGAGTGCAAGCAAATTTATGGGG
* * * **
31323353 TGACACGCTAAGTGGAAGCAAATTTATCGAC
1 TGACACGCTGAGTGCAAGCAAATTTATGGGG
** *** * *
31323384 TGACACGCTGAGTGTTAGTGGATTTACGGTG
1 TGACACGCTGAGTGCAAGCAAATTTATGGGG
* * * **
31323415 TCACACACTGACCT-CTTGCAAATTTATGGGG
1 TGACACGCTGA-GTGCAAGCAAATTTATGGGG
*
31323446 TGACACGCTGAGTGCAAGCAAATGTATGTGGG
1 TGACACGCTGAGTGCAAGCAAATTTATG-GGG
*
31323478 -GACACGTTGAGTG
1 TGACACGCTGAGTG
31323491 GTATCATATT
Statistics
Matches: 103, Mismatches: 32, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
30 1 0.01
31 98 0.95
32 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (31 bp):
TGACACGCTGAGTGCAAGCAAATTTATGGGG
Found at i:31323675 original size:14 final size:13
Alignment explanation
Indices: 31323656--31323717 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 13
31323646 GTTTACAATG
31323656 AATTGTATAAAATA
1 AATTGTATAAAA-A
*
31323670 AATTGTGTGTACAAAA
1 AA-T-TGTATA-AAAA
*
31323686 AATGTGTATAAAATT
1 AAT-TGTATAAAA-A
31323701 AATTGTATAAAAA
1 AATTGTATAAAAA
31323714 AATT
1 AATT
31323718 CGGTATACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 4 0.10
14 14 0.35
15 11 0.28
16 8 0.20
17 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (13 bp):
AATTGTATAAAAA
Found at i:31325306 original size:31 final size:31
Alignment explanation
Indices: 31325271--31325548 Score: 259
Period size: 31 Copynumber: 8.6 Consensus size: 31
31325261 AACCATAAAT
* *
31325271 AGTAAAATATTGTGACACGCCATGCATATCA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * *
31325302 AGTAAAATGTTGTCACACGCCATGCAAAATA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
*
31325333 ATGCATAACAAGATAAACTTTGTGACACGCCATGCATAACA
1 A-G--T-A-AA-AT----GTTGTGACACGCCATGCATAACA
31325374 AGTAAAATGTTGTGACACGCCATGCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * *
31325405 AGTTAAACGTTGTGACATGCCATCCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * * *
31325436 AGCAAATTGTTGTCACACGCCAAGGATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * *
31325467 AGCAAAATGTTGTGACATGCCATGCATATCA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * * *
31325498 AATCAAACGTTGTGACACACCATGAATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
31325529 AGTAAAATGTTGTGACACGC
1 AGTAAAATGTTGTGACACGC
31325549 TAAGGCTAAC
Statistics
Matches: 196, Mismatches: 41, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
31 162 0.83
32 1 0.01
34 1 0.01
35 3 0.02
36 4 0.02
37 3 0.02
38 1 0.01
40 1 0.01
41 20 0.10
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (31 bp):
AGTAAAATGTTGTGACACGCCATGCATAACA
Found at i:31326197 original size:156 final size:156
Alignment explanation
Indices: 31325903--31326256 Score: 487
Period size: 156 Copynumber: 2.3 Consensus size: 156
31325893 CGACTAGGTC
* *
31325903 AACTACAATAACATATATAACTGTGTTATTCAATAATCATATATGAAATTGTTGAACATTAACCA
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATATATGAAATTGTTGAACATTAACCA
*
31325968 TTACAACTTTAATATCCTAACCAGCGACTCATTAGCATTCTGCGGTGGAGCCGAACCGATCGGTG
66 TTACAACTTTAATATCCTAACCAGCGACTCATTAGCATTCTGCGATGGAGCCGAACCGATCGGTG
* *
31326033 CTTGAGGACTTGTCGTCACTTTCCCA
131 CTTGAGGACCTATCGTCACTTTCCCA
* *
31326059 AACTGTAATTACATATATAACTGTGTTATTCAATAATCATATATGAAATTGTTGAACATTAACCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATATATGAAATTGTTGAACATTAACCA
* * * * *
31326124 TTACAACTTTAATATCCTTACC-GTCGGCTCGTTAGC-TGTCTGCGATTGAGTCGAACCGATCGG
66 TTACAACTTTAATATCCTAACCAG-CGACTCATTAGCAT-TCTGCGATGGAGCCGAACCGATCGG
* **
31326187 TGCTTGAGGACCTATCGTCGCTTTCGTA
129 TGCTTGAGGACCTATCGTCACTTTCCCA
* * * * * *
31326215 AACTGCAATTACAGAAATTACTGTGTTACTCGATAAACATAT
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATAT
31326257 GTGGGAATGT
Statistics
Matches: 174, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
155 2 0.01
156 172 0.99
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (156 bp):
AACTGCAATTACATATATAACTGTGTTATTCAATAATCATATATGAAATTGTTGAACATTAACCA
TTACAACTTTAATATCCTAACCAGCGACTCATTAGCATTCTGCGATGGAGCCGAACCGATCGGTG
CTTGAGGACCTATCGTCACTTTCCCA
Found at i:31330515 original size:31 final size:31
Alignment explanation
Indices: 31330477--31330649 Score: 213
Period size: 31 Copynumber: 5.6 Consensus size: 31
31330467 AATAAAGAAT
* **
31330477 AAATGTTGTGACACGTCATGCATTGCAA-TCA
1 AAATGTTGTGACACGCCATGCATAACAAGT-A
31330508 AAATGTTGTGACACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
31330539 AAATGTTGTCACACACCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
31330570 AAATGCTGTGACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
31330601 AAATGTTGTCACATGCTATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
31330632 AAATATTGTCACACGCCA
1 AAATGTTGTGACACGCCA
31330650 ATACCAACTA
Statistics
Matches: 125, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
31 124 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:31330641 original size:93 final size:93
Alignment explanation
Indices: 31330477--31330645 Score: 243
Period size: 93 Copynumber: 1.8 Consensus size: 93
31330467 AATAAAGAAT
* * *
31330477 AAATGTTGTGACACGTCATGCATTGCAATCAAAATGTTGTGACACGCCATGCATAACAAGTAAAA
1 AAATGCTGTGACACGCCATGCATTGCAATCAAAATGTTGTCACACGCCATGCATAACAAGTAAAA
*
31330542 TGTTGTCACACACCATGCATAACAAGTA
66 TATTGTCACACACCATGCATAACAAGTA
* * *
31330570 AAATGCTGTGACACGCCATGCATAT-CAAGT-AAAATGTTGTCACATGCTATGCATATCAAGTAA
1 AAATGCTGTGACACGCCATGCAT-TGCAA-TCAAAATGTTGTCACACGCCATGCATAACAAGTAA
31330633 AATATTGTCACAC
64 AATATTGTCACAC
31330646 GCCAATACCA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
93 65 0.97
94 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (93 bp):
AAATGCTGTGACACGCCATGCATTGCAATCAAAATGTTGTCACACGCCATGCATAACAAGTAAAA
TATTGTCACACACCATGCATAACAAGTA
Found at i:31331251 original size:24 final size:24
Alignment explanation
Indices: 31331224--31331422 Score: 103
Period size: 24 Copynumber: 8.5 Consensus size: 24
31331214 AACATGACCA
31331224 TGGCGTGTCACCAACTATGAACTC
1 TGGCGTGTCACCAACTATGAACTC
*
31331248 TGGCGTGTCA-CAGCTTATG-AC-C
1 TGGCGTGTCACCAAC-TATGAACTC
*
31331270 ATGGCGTGTCACCAACTCTGAACTC
1 -TGGCGTGTCACCAACTATGAACTC
* ***
31331295 TGGCATGTCA-CAA--ATTTCCTCC
1 TGGCGTGTCACCAACTATGAACT-C
* * * *
31331317 ATGGCGTCTCACGAACTCTGAACGC
1 -TGGCGTGTCACCAACTATGAACTC
***
31331342 TGGCGTGTCA-CAA--ATTCCCTC
1 TGGCGTGTCACCAACTATGAACTC
* * *
31331363 TATGGCGTGTC-CCAACTCTTAACGC
1 --TGGCGTGTCACCAACTATGAACTC
* * *
31331388 TGACGTGTCACCAACTCTTAACTC
1 TGGCGTGTCACCAACTATGAACTC
31331412 TGGCGTGTCAC
1 TGGCGTGTCAC
31331423 AGATTCCATC
Statistics
Matches: 129, Mismatches: 30, Indels: 32
0.68 0.16 0.17
Matches are distributed among these distances:
21 6 0.05
22 2 0.02
23 51 0.40
24 62 0.48
25 6 0.05
26 2 0.02
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (24 bp):
TGGCGTGTCACCAACTATGAACTC
Found at i:31331278 original size:23 final size:22
Alignment explanation
Indices: 31331217--31331286 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 22
31331207 CACTCTAAAC
31331217 ATGACCATGGCGTGTCACCAACT
1 ATGACCATGGCGTGTCA-CAACT
*
31331240 ATGAACTC-TGGCGTGTCACAGCTT
1 ATG-AC-CATGGCGTGTCACAAC-T
31331264 ATGACCATGGCGTGTCACCAACT
1 ATGACCATGGCGTGTCA-CAACT
31331287 CTGAACTCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
22 1 0.03
23 19 0.47
24 19 0.47
25 1 0.03
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (22 bp):
ATGACCATGGCGTGTCACAACT
Found at i:31331395 original size:46 final size:47
Alignment explanation
Indices: 31331221--31331398 Score: 205
Period size: 47 Copynumber: 3.8 Consensus size: 47
31331211 CTAAACATGA
* * ** ****
31331221 CCATGGCGTGTCACCAACTATGAACTCTGGCGTGTCACAGCTTATGA
1 CCATGGCGTGTCACCAACTCTGAACGCTGGCGTGTCACAAATTCCCT
* * *
31331268 CCATGGCGTGTCACCAACTCTGAACTCTGGCATGTCACAAATTTCCT
1 CCATGGCGTGTCACCAACTCTGAACGCTGGCGTGTCACAAATTCCCT
* *
31331315 CCATGGCGTCTCACGAACTCTGAACGCTGGCGTGTCACAAATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACGCTGGCGTGTCACAAATTCCCT
* * *
31331362 CTATGGCGTGTC-CCAACTCTTAACGCTGACGTGTCAC
1 CCATGGCGTGTCACCAACTCTGAACGCTGGCGTGTCAC
31331399 CAACTCTTAA
Statistics
Matches: 113, Mismatches: 18, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
46 22 0.19
47 91 0.81
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (47 bp):
CCATGGCGTGTCACCAACTCTGAACGCTGGCGTGTCACAAATTCCCT
Found at i:31331454 original size:117 final size:118
Alignment explanation
Indices: 31331273--31331516 Score: 316
Period size: 117 Copynumber: 2.1 Consensus size: 118
31331263 TATGACCATG
* * *
31331273 GCGTGTCACCAACTCTGAACTCTGGCATGTCACAAATTTCCTCCATGGCGTCTCACGAACTCTGA
1 GCGTGTCACCAACTCTGAACTCTGGCATGTCACAAATTTCCTCCATAGCATCTCACCAACTCTGA
* * *
31331338 ACG-CTGGCGTGTCACAAATTCCCTCTATGGCGTGTC-CCAACTCTTAACGCT-
66 ACGTC-GACGTATCACAAATTCCCTCCATGGCGTGTCACCAACTCTTAACGCTA
* * *
31331389 GACGTGTCACCAACTCTTAACTCTGGCGTGTCACAGA-TTCCATCCATAGCATCTCACCAACTCT
1 G-CGTGTCACCAACTCTGAACTCTGGCATGTCACAAATTTCC-TCCATAGCATCTCACCAACTCT
* * * *
31331453 GAACGTCGACGTATCATAGATTCCCTCCATGTCGTGTCACCAACTCTTAACTCTA
64 GAACGTCGACGTATCACAAATTCCCTCCATGGCGTGTCACCAACTCTTAACGCTA
31331508 GCGTGTCAC
1 GCGTGTCAC
31331517 AAATTCTCTC
Statistics
Matches: 110, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
116 5 0.05
117 81 0.74
118 23 0.21
119 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (118 bp):
GCGTGTCACCAACTCTGAACTCTGGCATGTCACAAATTTCCTCCATAGCATCTCACCAACTCTGA
ACGTCGACGTATCACAAATTCCCTCCATGGCGTGTCACCAACTCTTAACGCTA
Found at i:31331514 original size:164 final size:164
Alignment explanation
Indices: 31331227--31331563 Score: 403
Period size: 164 Copynumber: 2.0 Consensus size: 164
31331217 ATGACCATGG
* * * *
31331227 CGTGTCACCAACTATGAACTCTGGCGTGTCACAGCTTATGACCATGGCGTGTCACCAACTCTGAA
1 CGTGTCACCAACTATGAACTCTGGCGTGTCACAGATTAT-ACCATAGCATCTCACCAACTCTGAA
* * * * *
31331292 CTCTGGCATGTCACAAATTTCCTCCATGGCGTCTCACGAACTCTGAACGCTGGCGTGTCACAAAT
65 CTCTGACATATCACAAATTCCCTCCATGGCGTCTCACCAACTCTGAACGCTAGCGTGTCACAAAT
* * *
31331357 TCCCTCTATGGCGTGTC-CCAACTCTTAACGCTGA-
130 TCCCTCCATGGCGTCTCACCAACTCTGAACGCT-AC
* *
31331391 CGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCAT-CCATAGCATCTCACCAACTCTGA
1 CGTGTCACCAACTATGAACTCTGGCGTGTCACAGATT--ATACCATAGCATCTCACCAACTCTGA
* * * * * * *
31331455 ACGTC-GACGTATCATAGATTCCCTCCATGTCGTGTCACCAACTCTTAACTCTAGCGTGTCACAA
64 AC-TCTGACATATCACAAATTCCCTCCATGGCGTCTCACCAACTCTGAACGCTAGCGTGTCACAA
*
31331519 ATTCTCTCCATGGCGTCTCACCAACTCTGAACGCTAC
128 ATTCCCTCCATGGCGTCTCACCAACTCTGAACGCTAC
31331556 CGTGTCAC
1 CGTGTCAC
31331564 ATATTCGCAC
Statistics
Matches: 146, Mismatches: 22, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
164 120 0.82
165 24 0.16
166 2 0.01
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.27
Consensus pattern (164 bp):
CGTGTCACCAACTATGAACTCTGGCGTGTCACAGATTATACCATAGCATCTCACCAACTCTGAAC
TCTGACATATCACAAATTCCCTCCATGGCGTCTCACCAACTCTGAACGCTAGCGTGTCACAAATT
CCCTCCATGGCGTCTCACCAACTCTGAACGCTAC
Found at i:31331577 original size:94 final size:92
Alignment explanation
Indices: 31331388--31331687 Score: 348
Period size: 94 Copynumber: 3.2 Consensus size: 92
31331378 CTCTTAACGC
* *
31331388 TGACGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCATCCATAGCATCTCACCAACTCT
1 TGACGTGTCACCAACTCTTAACTCTAGCGTGTCACAGATTCC-TCCATAGCGTCTCACCAACTCT
* * * * *
31331453 GAACGTCGACGTATCATAGATTCCCTCCA
65 GAACG-CTACGTGTCACACATTCCCACCA
* * *
31331482 TGTCGTGTCACCAACTCTTAACTCTAGCGTGTCACAAATTCTCTCCATGGCGTCTCACCAACTCT
1 TGACGTGTCACCAACTCTTAACTCTAGCGTGTCACAGATTC-CTCCATAGCGTCTCACCAACTCT
* *
31331547 GAACGCTACCGTGTCACATATTCGCACCA
65 GAACGCTA-CGTGTCACACATTCCCACCA
* * * * *
31331576 TGGCGTGTCACCAACTCTTAACTCTAGCGTCTCACAGGTTCCCTCTATTGCGTCTCACCAACTCT
1 TGACGTGTCACCAACTCTTAACTCTAGCGTGTCACAGATT-CCTCCATAGCGTCTCACCAACTCT
* * *
31331641 GAACGGTGTCGTGTCACACATTCCCAACA
65 GAACGCT-ACGTGTCACACATTCCCACCA
* *
31331670 TGACGTTTCACAAACTCT
1 TGACGTGTCACCAACTCT
31331688 AAAAACAGCC
Statistics
Matches: 177, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
93 2 0.01
94 173 0.98
95 2 0.01
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.28
Consensus pattern (92 bp):
TGACGTGTCACCAACTCTTAACTCTAGCGTGTCACAGATTCCTCCATAGCGTCTCACCAACTCTG
AACGCTACGTGTCACACATTCCCACCA
Found at i:31331654 original size:141 final size:141
Alignment explanation
Indices: 31331395--31331663 Score: 303
Period size: 141 Copynumber: 1.9 Consensus size: 141
31331385 CGCTGACGTG
* * **
31331395 TCACCAACTCTTAACTCTGGCGTGTCACAGATTCCATCCATAGCATCTCACCAACTCTGAACGTC
1 TCACCAACTCTGAACGCTACCGTGTCACAGATTCCATCCATAGCATCTCACCAACTCTGAACGTC
* * * *
31331460 GACGTATCATAGATTCCCTCCATGTCGTGTCACCAACTCTTAACTCTAGCGTGTCACAAATTCTC
66 GACGTATCACAGATTCCCTCCATGTCGTCTCACCAACTCTGAACGCTAGCGTGTCACAAATTCTC
31331525 TCCATGGCGTC
131 TCCATGGCGTC
* * * * *
31331536 TCACCAACTCTGAACGCTACCGTGTCACATATTCGCA-CCATGGCGTGTCACCAACTCTTAAC-T
1 TCACCAACTCTGAACGCTACCGTGTCACAGATTC-CATCCATAGCATCTCACCAACTCTGAACGT
* * * * * *
31331599 CTAGCGTCTCACAGGTTCCCTCTAT-TGCGTCTCACCAACTCTGAACGGT-GTCGTGTCACACAT
65 CGA-CGTATCACAGATTCCCTCCATGT-CGTCTCACCAACTCTGAACGCTAG-CGTGTCACAAAT
31331662 TC
127 TC
31331664 CCAACATGAC
Statistics
Matches: 105, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
140 5 0.05
141 98 0.93
142 2 0.02
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (141 bp):
TCACCAACTCTGAACGCTACCGTGTCACAGATTCCATCCATAGCATCTCACCAACTCTGAACGTC
GACGTATCACAGATTCCCTCCATGTCGTCTCACCAACTCTGAACGCTAGCGTGTCACAAATTCTC
TCCATGGCGTC
Found at i:31331665 original size:47 final size:47
Alignment explanation
Indices: 31331395--31331644 Score: 268
Period size: 47 Copynumber: 5.3 Consensus size: 47
31331385 CGCTGACGTG
* * * * *
31331395 TCACCAACTCTTAACTCTGGCGTGTCACAGATTCCATCCATAGCATC
1 TCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCGTC
* * * * *
31331442 TCACCAACTCTGAACGTCGA-CGTATCATAGATTCCCTCCATGTCGTG
1 TCACCAACTCTGAAC-TCTAGCGTGTCACAGATTCCCTCCATGGCGTC
* * *
31331489 TCACCAACTCTTAACTCTAGCGTGTCACAAATTCTCTCCATGGCGTC
1 TCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCGTC
* * * * * *
31331536 TCACCAACTCTGAACGCTACCGTGTCACATATTCGCACCATGGCGTG
1 TCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCGTC
* * * * *
31331583 TCACCAACTCTTAACTCTAGCGTCTCACAGGTTCCCTCTATTGCGTC
1 TCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCGTC
31331630 TCACCAACTCTGAAC
1 TCACCAACTCTGAAC
31331645 GGTGTCGTGT
Statistics
Matches: 164, Mismatches: 37, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
46 3 0.02
47 159 0.97
48 2 0.01
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (47 bp):
TCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCGTC
Found at i:31332556 original size:32 final size:32
Alignment explanation
Indices: 31332520--31332580 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
31332510 GTATTCGGAG
*
31332520 ACTCCAATAAGAAATTTACTTATTTACAGAAT
1 ACTCCAATAAGAAATTTACTTATTAACAGAAT
31332552 ACTCCAATAAGAAATTTACTTATTAACAG
1 ACTCCAATAAGAAATTTACTTATTAACAG
31332581 CAATGGAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (32 bp):
ACTCCAATAAGAAATTTACTTATTAACAGAAT
Found at i:31349373 original size:29 final size:29
Alignment explanation
Indices: 31349327--31349384 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
31349317 TGATAGTTTT
*
31349327 GGGGGACAAGAAAGTTGAAACATGACAAA
1 GGGGGACAAGAAAATTGAAACATGACAAA
*
31349356 GGGGGACAAGAAAATTGAAACGTGACAAA
1 GGGGGACAAGAAAATTGAAACATGACAAA
31349385 ACTTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.10, G:0.31, T:0.10
Consensus pattern (29 bp):
GGGGGACAAGAAAATTGAAACATGACAAA
Found at i:31350890 original size:5 final size:5
Alignment explanation
Indices: 31350880--31350904 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31350870 TTAGTAACAC
31350880 CTAGG CTAGG CTAGG CTAGG CTAGG
1 CTAGG CTAGG CTAGG CTAGG CTAGG
31350905 ATCTTATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (5 bp):
CTAGG
Found at i:31356720 original size:16 final size:16
Alignment explanation
Indices: 31356699--31356732 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31356689 TATTAAGAAG
*
31356699 AATTAATAGTAAACTT
1 AATTAATAATAAACTT
*
31356715 AATTAATAATATACTT
1 AATTAATAATAAACTT
31356731 AA
1 AA
31356733 AATATATTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTAATAATAAACTT
Found at i:31357403 original size:22 final size:21
Alignment explanation
Indices: 31357361--31357403 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
31357351 TGCCTTTTTT
31357361 TAATTTTTTATAAAAATATAA
1 TAATTTTTTATAAAAATATAA
31357382 TAATATTTTT-T-AAAAT-TAA
1 TAAT-TTTTTATAAAAATATAA
31357401 TAA
1 TAA
31357404 AAAAATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 5 0.24
21 5 0.24
22 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTTTTTATAAAAATATAA
Found at i:31357619 original size:18 final size:18
Alignment explanation
Indices: 31357583--31357626 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
31357573 ATGTTTCTTA
*
31357583 ATATATAATGTTATGAAT
1 ATATATAATGTTATAAAT
31357601 ATATATAAT-TGTATAAAT
1 ATATATAATGT-TATAAAT
31357619 ATTATATA
1 A-TATATA
31357627 TATACATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (18 bp):
ATATATAATGTTATAAAT
Found at i:31358054 original size:22 final size:23
Alignment explanation
Indices: 31358028--31358071 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
31358018 TTTGATCAAT
31358028 TTTGATCGATTT-TTTTTAAAAA
1 TTTGATCGATTTATTTTTAAAAA
*
31358050 TTTGATCTATTTGATTTTTAAA
1 TTTGATCGATTT-ATTTTTAAA
31358072 TATGATGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTGATCGATTTATTTTTAAAAA
Found at i:31360201 original size:23 final size:23
Alignment explanation
Indices: 31360171--31360219 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
31360161 TAGAATAACA
*
31360171 ATTCCTAATTCTATTAAGATAAG
1 ATTCCTAATTATATTAAGATAAG
31360194 ATTCCTAATTATATTAAGATAAG
1 ATTCCTAATTATATTAAGATAAG
31360217 ATT
1 ATT
31360220 ATTGTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (23 bp):
ATTCCTAATTATATTAAGATAAG
Found at i:31367187 original size:15 final size:15
Alignment explanation
Indices: 31367167--31367196 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31367157 TAACTGCTAA
*
31367167 CCTCAACAACCCTTT
1 CCTCAAAAACCCTTT
31367182 CCTCAAAAACCCTTT
1 CCTCAAAAACCCTTT
31367197 AAGCAAAACA
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:0.30, C:0.43, G:0.00, T:0.27
Consensus pattern (15 bp):
CCTCAAAAACCCTTT
Found at i:31375430 original size:16 final size:16
Alignment explanation
Indices: 31375409--31375443 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31375399 AATTTTTTTC
* *
31375409 TAATAATACTAATTAA
1 TAATAATAATAATAAA
31375425 TAATAATAATAATAAA
1 TAATAATAATAATAAA
31375441 TAA
1 TAA
31375444 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATAATAATAATAAA
Found at i:31376421 original size:23 final size:23
Alignment explanation
Indices: 31376378--31376421 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
31376368 AGGAAATTGT
*
31376378 GAACATGGGTTGTTACCGGGTGG
1 GAACATGGGTTGTTACAGGGTGG
* *
31376401 GAACGTGGGTTGTTGCAGGGT
1 GAACATGGGTTGTTACAGGGT
31376422 AGGGGTTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.45, T:0.27
Consensus pattern (23 bp):
GAACATGGGTTGTTACAGGGTGG
Found at i:31390585 original size:6 final size:6
Alignment explanation
Indices: 31390574--31390601 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31390564 TGTGACCAAA
31390574 AATAGT AATAGT AATAGT AATAGT AATA
1 AATAGT AATAGT AATAGT AATAGT AATA
31390602 AAATAAACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (6 bp):
AATAGT
Found at i:31394518 original size:21 final size:21
Alignment explanation
Indices: 31394480--31394533 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
31394470 ACTCAATTGT
**
31394480 GTTTTAGGATTTTTTGAATCG
1 GTTTTAGGATTTGATGAATCG
* *
31394501 GTTTTAGGGTTTGATGAATTTG
1 GTTTTAGGATTTGATGAA-TCG
31394523 G-TTTAGGATTT
1 GTTTTAGGATTT
31394534 CATGCATAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.19, C:0.02, G:0.28, T:0.52
Consensus pattern (21 bp):
GTTTTAGGATTTGATGAATCG
Found at i:31394643 original size:41 final size:42
Alignment explanation
Indices: 31394483--31394648 Score: 122
Period size: 42 Copynumber: 4.0 Consensus size: 42
31394473 CAATTGTGTT
** * * ** *
31394483 TTAGGATTTTTTGAATCGGTTTTAGGGTTTGATGAATTTGGT-
1 TTAGGATTTGGTGAATCGATTTTAAGGTTTCTTGAA-TCGGTC
** * * * *
31394525 TTAGGATTTCATGCATAGATTTTAAGGTTTCTTGAATTGGAC
1 TTAGGATTTGGTGAATCGATTTTAAGGTTTCTTGAATCGGTC
* * * *
31394567 TTAGGATTTGGTGAATCAAGTTTAAGATTTTTTGAATCGGTC
1 TTAGGATTTGGTGAATCGATTTTAAGGTTTCTTGAATCGGTC
* *
31394609 -TA-GAGTTTGGTGAATTGATTTTAGGGTTTCTTGAATCGGT
1 TTAGGA-TTTGGTGAATCGATTTTAAGGTTTCTTGAATCGGT
31394649 TTAACAAATC
Statistics
Matches: 97, Mismatches: 25, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
40 2 0.02
41 35 0.36
42 60 0.62
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (42 bp):
TTAGGATTTGGTGAATCGATTTTAAGGTTTCTTGAATCGGTC
Found at i:31394780 original size:21 final size:21
Alignment explanation
Indices: 31394756--31394814 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
31394746 GATTTCGTGC
* **
31394756 ATCGATTTTAAGGTTTCTTGA
1 ATCGATTTTAAGATTTAATGA
**
31394777 ATCGGGTTTAAGATTTAATGA
1 ATCGATTTTAAGATTTAATGA
* *
31394798 ATCGTTTTTAGGATTTA
1 ATCGATTTTAAGATTTA
31394815 GTAAATTAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (21 bp):
ATCGATTTTAAGATTTAATGA
Found at i:31394941 original size:21 final size:21
Alignment explanation
Indices: 31394917--31394970 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
31394907 GGGTTTGGTG
31394917 AATTGATTTTAGGATTTAATA
1 AATTGATTTTAGGATTTAATA
* * * **
31394938 AATTAATTTCAGGGTTTTCTA
1 AATTGATTTTAGGATTTAATA
*
31394959 AATTGAGTTTAG
1 AATTGATTTTAG
31394971 AGTTTAGTGA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
AATTGATTTTAGGATTTAATA
Found at i:31408055 original size:60 final size:59
Alignment explanation
Indices: 31407946--31408057 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
31407936 CTTTTTGTTC
* *
31407946 CTTTTTTCCACTTTATCATCAATCAGTGATTGCATTCAAGTGATAATTAAAGCTTATTA
1 CTTTTTTCCAATTTATCATCAATAAGTGATTGCATTCAAGTGATAATTAAAGCTTATTA
*
31408005 CTTTTTTCCAATTTATCATCAATAAGTGATTGCATTTCAAGTGATGATTAAAG
1 CTTTTTTCCAATTTATCATCAATAAGTGATTGCA-TTCAAGTGATAATTAAAG
31408058 TTGTGGAGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 32 0.65
60 17 0.35
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (59 bp):
CTTTTTTCCAATTTATCATCAATAAGTGATTGCATTCAAGTGATAATTAAAGCTTATTA
Found at i:31412727 original size:2 final size:2
Alignment explanation
Indices: 31412715--31412762 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
31412705 AGCTAACAGA
* *
31412715 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31412756 AT A- AT AT
1 AT AT AT AT
31412763 CATTATAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:31415988 original size:15 final size:14
Alignment explanation
Indices: 31415950--31416036 Score: 61
Period size: 14 Copynumber: 5.9 Consensus size: 14
31415940 TATTTTTTGG
31415950 ATTAAAAAAATAAA
1 ATTAAAAAAATAAA
* *
31415964 ACTATGAAAAATAAA
1 ATTA-AAAAAATAAA
* *
31415979 ATTTAAAAAATAGA
1 ATTAAAAAAATAAA
31415993 A-TAAAAACAA-AACA
1 ATTAAAAA-AATAA-A
31416007 ATTAACCAAAAATTAAA
1 ATTAA--AAAAA-TAAA
*
31416024 ATAAAAAAAATAA
1 ATTAAAAAAATAA
31416037 CGTGACTAAG
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
13 6 0.11
14 19 0.34
15 19 0.34
16 2 0.04
17 8 0.14
18 2 0.04
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (14 bp):
ATTAAAAAAATAAA
Found at i:31425012 original size:66 final size:66
Alignment explanation
Indices: 31424915--31425052 Score: 258
Period size: 66 Copynumber: 2.1 Consensus size: 66
31424905 AATTTTTTCC
*
31424915 TGAGGATTGCCCTTGATTTTTTTTTTGTTGAAAAACATTTTCATGGGTTTGTGCATTATTTTCTG
1 TGAGGATTGCCCTTGATTTTTTTTTTGTTGAAAAACATTTTCATGAGTTTGTGCATTATTTTCTG
31424980 A
66 A
*
31424981 TGAGGATTGCCCTTGATTTTTTTTTTGTTGAAAAACATTTTCTTGAGTTTGTGCATTATTTTCTG
1 TGAGGATTGCCCTTGATTTTTTTTTTGTTGAAAAACATTTTCATGAGTTTGTGCATTATTTTCTG
31425046 A
66 A
31425047 TGAGGA
1 TGAGGA
31425053 AATAACAATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.49
Consensus pattern (66 bp):
TGAGGATTGCCCTTGATTTTTTTTTTGTTGAAAAACATTTTCATGAGTTTGTGCATTATTTTCTG
A
Found at i:31434741 original size:24 final size:24
Alignment explanation
Indices: 31434709--31434764 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
31434699 ATCTTCTAAG
31434709 GATTCTGAGAAAGTGATTAATAAA
1 GATTCTGAGAAAGTGATTAATAAA
31434733 GATTCTGAGAAAGTGATTAATAAA
1 GATTCTGAGAAAGTGATTAATAAA
31434757 -AGTTCTGA
1 GA-TTCTGA
31434765 AGAATTGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.30
Consensus pattern (24 bp):
GATTCTGAGAAAGTGATTAATAAA
Found at i:31440798 original size:16 final size:15
Alignment explanation
Indices: 31440772--31440820 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
31440762 TTTTGATAAT
* *
31440772 AATTATATAAATACA
1 AATTTTATAAATATA
31440787 AATGTTTATAAAGTATA
1 AAT-TTTATAAA-TATA
31440804 AATTTTA-AAATATA
1 AATTTTATAAATATA
31440818 AAT
1 AAT
31440821 AATTGAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 7 0.23
15 6 0.20
16 11 0.37
17 6 0.20
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (15 bp):
AATTTTATAAATATA
Found at i:31440817 original size:14 final size:16
Alignment explanation
Indices: 31440777--31440820 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
31440767 ATAATAATTA
*
31440777 TATAAATACAAATGTT
1 TATAAATATAAATGTT
31440793 TATAAAGTATAAAT-TT
1 TATAAA-TATAAATGTT
31440809 TA-AAATATAAAT
1 TATAAATATAAAT
31440821 AATTGAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.27
15 3 0.12
16 10 0.38
17 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (16 bp):
TATAAATATAAATGTT
Found at i:31440944 original size:16 final size:15
Alignment explanation
Indices: 31440923--31440964 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
31440913 ATTTTTATTT
31440923 ATATTTATAAATAAAA
1 ATATTTA-AAATAAAA
*
31440939 ATATTTAAAATGAAA
1 ATATTTAAAATAAAA
*
31440954 AT-TTAAAAATA
1 ATATTTAAAATA
31440965 TAATAGACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 7 0.30
15 9 0.39
16 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
ATATTTAAAATAAAA
Found at i:31442269 original size:27 final size:29
Alignment explanation
Indices: 31442239--31442314 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
31442229 AGGTATTAAA
* *
31442239 GTGTAATAA-AA-CGTTTTTGAATATGAC
1 GTGTAATAACAATAGTTTTTCAATATGAC
* * *
31442266 GTGTAACAACAATATTTTTTCAATATGGC
1 GTGTAATAACAATAGTTTTTCAATATGAC
* *
31442295 GTGTAATAATAATATTTTTT
1 GTGTAATAACAATAGTTTTT
31442315 TTCTATATGG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 8 0.20
28 2 0.05
29 30 0.75
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (29 bp):
GTGTAATAACAATAGTTTTTCAATATGAC
Found at i:31442324 original size:31 final size:29
Alignment explanation
Indices: 31442252--31442314 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
31442242 TAATAAAACG
* *
31442252 TTTTTGAATATGACGTGTAACAACAATAT
1 TTTTTCAATATGGCGTGTAACAACAATAT
* *
31442281 TTTTTCAATATGGCGTGTAATAATAATAT
1 TTTTTCAATATGGCGTGTAACAACAATAT
31442310 TTTTT
1 TTTTT
31442315 TTCTATATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (29 bp):
TTTTTCAATATGGCGTGTAACAACAATAT
Found at i:31442415 original size:54 final size:54
Alignment explanation
Indices: 31442332--31442441 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
31442322 TGGTATGTAA
* *
31442332 CAACTTAACCATGACGTGTCACATATTTTTGTACATGGCGTGTAACAACCTAAC
1 CAACTTAACCATGACATGTCACATATTTTTGTACATGGCATGTAACAACCTAAC
* * * * *
31442386 CAACTTAATCATGGCATGTCACATGTTTTTGTACATGGTATGTAACAATCTAAC
1 CAACTTAACCATGACATGTCACATATTTTTGTACATGGCATGTAACAACCTAAC
31442440 CA
1 CA
31442442 TGGCGTGTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (54 bp):
CAACTTAACCATGACATGTCACATATTTTTGTACATGGCATGTAACAACCTAAC
Found at i:31442450 original size:21 final size:21
Alignment explanation
Indices: 31442426--31442470 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
31442416 GTACATGGTA
*
31442426 TGTAACAATCTAACCATGGCG
1 TGTAACAACCTAACCATGGCG
31442447 TGTAACAACCTAACCATGGCG
1 TGTAACAACCTAACCATGGCG
31442468 TGT
1 TGT
31442471 CACATGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
TGTAACAACCTAACCATGGCG
Found at i:31442499 original size:24 final size:24
Alignment explanation
Indices: 31442465--31442511 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
31442455 CCTAACCATG
* *
31442465 GCGTGTCACATGTTTTTGTACATA
1 GCGTGTAACATATTTTTGTACATA
31442489 GCGTGTAACATATTTTTGTACAT
1 GCGTGTAACATATTTTTGTACAT
31442512 GACGTATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
GCGTGTAACATATTTTTGTACATA
Found at i:31442521 original size:24 final size:24
Alignment explanation
Indices: 31442472--31442522 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
31442462 ATGGCGTGTC
* *
31442472 ACATGTTTTTGTACATAGCGTGTA
1 ACATATTTTTGTACATAGCGTATA
31442496 ACATATTTTTGTACAT-GACGTATA
1 ACATATTTTTGTACATAG-CGTATA
31442520 ACA
1 ACA
31442523 ATCTAACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (24 bp):
ACATATTTTTGTACATAGCGTATA
Found at i:31443393 original size:21 final size:21
Alignment explanation
Indices: 31443369--31443410 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31443359 TTTGTGAAGT
*
31443369 TTATTT-TTATTTTGTTTTTTA
1 TTATTTATTA-TTTATTTTTTA
31443390 TTATTTATTATTTATTTTTTA
1 TTATTTATTATTTATTTTTTA
31443411 ACTAATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (21 bp):
TTATTTATTATTTATTTTTTA
Found at i:31444298 original size:37 final size:37
Alignment explanation
Indices: 31444220--31444390 Score: 215
Period size: 37 Copynumber: 4.6 Consensus size: 37
31444210 TGACAAACCC
*
31444220 TCTCTCTCTCTCTCCCTTTGTGCCAGCTGATCGGGTTTT
1 TCTCTCTCTCTCTCCCTTTGTGCCAGCCGATCGGG--TT
*
31444259 TCTCTCTCTCTCTCCCTTTGTGCCTGCCGATCGGGTT
1 TCTCTCTCTCTCTCCCTTTGTGCCAGCCGATCGGGTT
* *
31444296 TCTCT-T-TCTAT--CTTTAGTGCCAGTCGATCGGGTT
1 TCTCTCTCTCTCTCCCTTT-GTGCCAGCCGATCGGGTT
* * *
31444330 TTTCTCTCTCTCTTCCTTTGTGCCAGCCAATCGGGTT
1 TCTCTCTCTCTCTCCCTTTGTGCCAGCCGATCGGGTT
*
31444367 TCTCTCTATCTCTCCCTTTGTGCC
1 TCTCTCTCTCTCTCCCTTTGTGCC
31444391 TTTCCTCCTT
Statistics
Matches: 115, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
33 4 0.03
34 20 0.17
35 5 0.04
36 5 0.04
37 44 0.38
38 4 0.03
39 33 0.29
ACGTcount: A:0.06, C:0.33, G:0.17, T:0.43
Consensus pattern (37 bp):
TCTCTCTCTCTCTCCCTTTGTGCCAGCCGATCGGGTT
Found at i:31444373 original size:73 final size:72
Alignment explanation
Indices: 31444235--31444371 Score: 217
Period size: 73 Copynumber: 1.9 Consensus size: 72
31444225 CTCTCTCTCC
* *
31444235 CTTTGTGCCAGCTGATCGGGTTTTTCTCTCTCTCTCTCCCTTTGTGCCTGCCGATCGGGTTTCTC
1 CTTTGTGCCAGCTGATCGGGTTTTTCTCTCTCTCTCTCCCTTTGTGCCAGCCAATCGGGTTTCTC
31444300 TTTCTAT
66 TTTCTAT
31444307 CTTTAGTGCCAG-TCGATCGGGTTTTTCTCTCTCTCT-T-CCTTTGTGCCAGCCAATCGGGTTTC
1 CTTT-GTGCCAGCT-GATCGGGTTTTTCTCTCTCTCTCTCCCTTTGTGCCAGCCAATCGGGTTTC
31444369 TCT
64 TCT
31444372 CTATCTCTCC
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
71 26 0.43
72 6 0.10
73 29 0.48
ACGTcount: A:0.07, C:0.30, G:0.20, T:0.43
Consensus pattern (72 bp):
CTTTGTGCCAGCTGATCGGGTTTTTCTCTCTCTCTCTCCCTTTGTGCCAGCCAATCGGGTTTCTC
TTTCTAT
Found at i:31445373 original size:45 final size:45
Alignment explanation
Indices: 31445221--31445381 Score: 223
Period size: 45 Copynumber: 3.6 Consensus size: 45
31445211 TATACATGTC
* * *
31445221 ACATGTTTTTGTACATGGTGTGTAACAACCTAACCATGACGTGGA
1 ACATATTTTTGTACATGGCGTGTAACAACCTAACCATGACGTGTA
* * * *
31445266 ACATATTTTTTTACATGACATGTAACAACCTAACCATGACGTGTC
1 ACATATTTTTGTACATGGCGTGTAACAACCTAACCATGACGTGTA
* *
31445311 ACATATTTTTGTACATGGCGCGTAACAATCTAACCATGACGTGTA
1 ACATATTTTTGTACATGGCGTGTAACAACCTAACCATGACGTGTA
* *
31445356 ACATATTTTTATACATGGTGTGTAAC
1 ACATATTTTTGTACATGGCGTGTAAC
31445382 GTCATGACTT
Statistics
Matches: 100, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 100 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (45 bp):
ACATATTTTTGTACATGGCGTGTAACAACCTAACCATGACGTGTA
Found at i:31454195 original size:199 final size:198
Alignment explanation
Indices: 31453860--31454814 Score: 1051
Period size: 199 Copynumber: 4.8 Consensus size: 198
31453850 CAAGGGGAAC
* * *
31453860 GCACCATATAG-TAAGACTTCGAATTCACATATTGGCACCATTATACCCTAATGTATAATAGGAA
1 GCACCATAT-GCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAA
* * * * *
31453924 TGCCACATTCC-CGTACCTTAAAAG-TTTATTATTTCCATAAGTACCATTGTGCCATTATTGCAT
65 TGCCACATTCCAC--ACCTT-AAAGTTTTTTTATTTCTATAAGCACCATTGTGCCATTATTACAC
* * * ** *
31453987 AATAGGAATGCCAGGTCAAGTACTTTAAACATTTAATTTGCACCATTTTACCTTCAATCAAATAA
127 AATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTACACCTTCGATCAAATAA
* *
31454052 TAGGAAC
192 TAAGAAT
* * * * *
31454059 GCAACATATGCTCAGATTTCAAATTCAAATATTGACACCATTATACCGTAATGTATAATAGGAAT
1 GCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAAT
* * * * * *
31454124 GCCACATATCAAAACCTTAAAGTTTTTTTATGTCTGTGAGCACCATTGTGCCATAATTACACAAT
66 GCCACAT-TCCACACCTTAAAGTTTTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAAT
* * * * * *
31454189 AGGAATGCCACATCAAGCACTTTAAATATCGAATTTGAATCATTATACCTTCGATCAAATAATAT
130 AGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTACACCTTCGATCAAATAATA-
31454254 A-AAT
194 AGAAT
* * **
31454258 GCACCATATACTAAGATTTAAAATTCACGGATTGGCACCATTATACCTTAATGTATAATAGGAAT
1 GCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAAT
* * * * * * *
31454323 GCCACATGCTCACACACTTGATGTTTTTTTATTTTTGTAAGCACCATTATGCCGTTATTACACAA
66 GCCACATTC-CACAC-CTTAAAGTTTTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAA
* *
31454388 TAGAAATGCTACGTCAAGTACTTTAAATATCTAATTTGCACC-TT-CACTTCTTCGATCAAATAA
129 TAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTACAC--CTTCGATCAAATAA
31454451 TAAGAAT
192 TAAGAAT
* * * * *
31454458 GCATCATATACTAAGATTTCATATTCACATATAGGCACCATTATACCTTAATGTATAATAAGAAT
1 GCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAAT
* * * * *
31454523 GCCACATGCCCGCACCTTAAGGTTTTATTATTTTTATAAGCACCATTGTGCCATTATTACACAAT
66 GCCACAT-TCCACACCTTAAAGTTTTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAAT
* * ** * *
31454588 AGGAATGCCACGTCAAGTATTTTAAATATCTAATTTGCATCACCACACCTTCGATCGATTAATAA
130 AGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTACACCTTCGATCAAATAATAA
31454653 GAAT
195 GAAT
* * * * *
31454657 GCACCATATGCTAAGATTTCATATTCACATCTAGGCACCATTTTACCTTAATGTATAATAAGAAT
1 GCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAAT
* * ** * * **
31454722 GCCACATTTCCACACGTTAAAGTTTCATTT-TTTCTATAAGCACCATCATTCCAATATTACATGA
66 GCCACA-TTCCACACCTTAAAGTTT-TTTTATTTCTATAAGCACCATTGTGCCATTATTACACAA
* *
31454786 TAGGAATGCCATGTCAAGTACCTTAAATA
129 TAGGAATGCCACGTCAAGTACTTTAAATA
31454815 GGAATGCACT
Statistics
Matches: 640, Mismatches: 101, Indels: 30
0.83 0.13 0.04
Matches are distributed among these distances:
198 8 0.01
199 459 0.72
200 169 0.26
201 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (198 bp):
GCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAAT
GCCACATTCCACACCTTAAAGTTTTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAATA
GGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTACACCTTCGATCAAATAATAAG
AAT
Done.