Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 19 of 333
Found at i:5590185 original size:47 final size:45
Alignment explanation
Indices: 5590134--5590225 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 45
5590124 CTAATAAATT
* *
5590134 ATAAAATTAATA-AAACATGTTTAAAATTTTATAAAAACAT-ATAAAAA
1 ATAAAATTAATATAAAC-T-TTGAAAA-ATTATAAAAA-ATCATAAAAA
*
5590181 ATAAATTTAATATAAACTTTGAAAAATTATAAAAAATCATAAAAA
1 ATAAAATTAATATAAACTTTGAAAAATTATAAAAAATCATAAAAA
5590226 CTTGAATTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
44 2 0.05
45 16 0.40
46 6 0.15
47 12 0.30
48 4 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (45 bp):
ATAAAATTAATATAAACTTTGAAAAATTATAAAAAATCATAAAAA
Found at i:5590880 original size:20 final size:19
Alignment explanation
Indices: 5590830--5590880 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
5590820 TTTAATTTTT
*
5590830 AATTTTTTATAACTTTTAT
1 AATTTTTTATAACTTTTAG
*
5590849 AATTTGTATATAACTTATTAG
1 AATTT-TTTATAACTT-TTAG
5590870 AATTTTTTATA
1 AATTTTTTATA
5590881 TTATTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 14 0.52
21 8 0.30
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (19 bp):
AATTTTTTATAACTTTTAG
Found at i:5590927 original size:31 final size:29
Alignment explanation
Indices: 5590843--5590927 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 29
5590833 TTTTTATAAC
* *
5590843 TTTTATAATTTGTATATAACTTATTAGAATT
1 TTTTATAATTTTTATA-AAATT-TTAGAATT
5590874 TTTTAT-ATTATTTAT-AAATTTTAGGAATT
1 TTTTATAATT-TTTATAAAATTTTA-GAATT
5590903 TTTTATAAGTTTTTATAAAATTTTA
1 TTTTATAA-TTTTTATAAAATTTTA
5590928 AATACATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
28 3 0.06
29 15 0.32
30 9 0.19
31 20 0.43
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (29 bp):
TTTTATAATTTTTATAAAATTTTAGAATT
Found at i:5592723 original size:15 final size:16
Alignment explanation
Indices: 5592703--5592747 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
5592693 ATAACAATCC
5592703 ATAATTTAAAATT-AA
1 ATAATTTAAAATTAAA
*
5592718 ATAATTTAAATTTAAA
1 ATAATTTAAAATTAAA
5592734 ATATATTTTAAAAT
1 ATA-A-TTTAAAAT
5592748 AGTAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.48
16 5 0.20
17 1 0.04
18 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTTAAAATTAAA
Found at i:5595423 original size:24 final size:24
Alignment explanation
Indices: 5595385--5595433 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5595375 GGTTCCCTCG
* *
5595385 GCCTCTTAGGAGAATCTGTTGGAA
1 GCCTCTCAGGAGAATCAGTTGGAA
*
5595409 GCCTCTCAGGCGAATCAGTTGGAA
1 GCCTCTCAGGAGAATCAGTTGGAA
5595433 G
1 G
5595434 TCTTTGCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (24 bp):
GCCTCTCAGGAGAATCAGTTGGAA
Found at i:5613436 original size:18 final size:18
Alignment explanation
Indices: 5613389--5613436 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
5613379 TAGGGTGGGA
5613389 AAAAGAAAAAG---AGGG
1 AAAAGAAAAAGAAAAGGG
*
5613404 AAAATGAGAAA-AAAAGGG
1 AAAA-GAAAAAGAAAAGGG
5613422 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
5613437 AGTAGGGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 5 0.19
18 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGGG
Found at i:5616575 original size:15 final size:15
Alignment explanation
Indices: 5616553--5616590 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
5616543 TCTGTTCTTT
*
5616553 TTTCTATTGTTTTTTA
1 TTTCTATT-TCTTTTA
5616569 TTT-TATTTCTTTTA
1 TTTCTATTTCTTTTA
5616583 TTTCTATT
1 TTTCTATT
5616591 ATGTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 8 0.40
16 3 0.15
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTCTATTTCTTTTA
Found at i:5618717 original size:24 final size:23
Alignment explanation
Indices: 5618690--5618743 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
5618680 TTTTTCTCAC
*
5618690 ATTTTTATTTCTT-GTTTTCTTTTT
1 ATTTTTA-TTCTTCCTTTT-TTTTT
5618714 ATTTTCTATTCTTCCTTTTTTTTT
1 ATTTT-TATTCTTCCTTTTTTTTT
5618738 ATTTTT
1 ATTTTT
5618744 TTATTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 20 0.74
25 6 0.22
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (23 bp):
ATTTTTATTCTTCCTTTTTTTTT
Found at i:5618732 original size:25 final size:25
Alignment explanation
Indices: 5618704--5618751 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5618694 TTATTTCTTG
5618704 TTTTCTTTTTA-TTTTCTATTCTTCC
1 TTTT-TTTTTATTTTTCTATTCTTCC
*
5618729 TTTTTTTTTATTTTTTTATTCTT
1 TTTTTTTTTATTTTTCTATTCTT
5618752 TTCTGCAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTTTTTATTTTTCTATTCTTCC
Found at i:5625773 original size:20 final size:21
Alignment explanation
Indices: 5625748--5625798 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
5625738 AGGGGCACAT
*
5625748 GCCCGTGTGGCT-TGGGACAC
1 GCCCGTGTGGCTCTGGAACAC
*
5625768 GCCCGTGTGG-TCTGGAACAT
1 GCCCGTGTGGCTCTGGAACAC
5625788 GCCCGTGTGGC
1 GCCCGTGTGGC
5625799 CTGCCCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.10, C:0.29, G:0.39, T:0.22
Consensus pattern (21 bp):
GCCCGTGTGGCTCTGGAACAC
Found at i:5626673 original size:53 final size:52
Alignment explanation
Indices: 5626541--5626750 Score: 193
Period size: 52 Copynumber: 4.1 Consensus size: 52
5626531 TTCATTATCA
* * * *
5626541 CACATCACACACTGAAGCCATAGCCCTGCCATGGTCTTATACAG-ATCACATAT
1 CACATCACAC-C-GATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATAT
* * * *
5626594 --CAT---ACCGATGCAATATCCTAGATATGGTCTTATACGGAATCACATTAT
1 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACA-TAT
* *
5626642 CACATCACACCGATGCCATAGCTCAGCTATGGTCTTATACGGGAA-CACAAAT
1 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATAC-GGAATCACATAT
*** *
5626694 CACATTGTACCGATGCCATAGCCCGGCTATGGTCTTATACGG-ATCACATAT
1 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATAT
*
5626745 CTCATC
1 CACATC
5626751 TTTTTCGTCA
Statistics
Matches: 126, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
46 23 0.18
47 7 0.06
48 5 0.04
50 4 0.03
51 15 0.12
52 37 0.29
53 31 0.25
54 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (52 bp):
CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATAT
Found at i:5628979 original size:13 final size:13
Alignment explanation
Indices: 5628963--5628995 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5628953 TTTAATTTAA
*
5628963 TTAGTTAATTAGT
1 TTAGATAATTAGT
5628976 TTAGATAATTAGT
1 TTAGATAATTAGT
5628989 TTA-ATAA
1 TTAGATAA
5628996 ACAAACCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:5637384 original size:3 final size:3
Alignment explanation
Indices: 5637372--5637427 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
5637362 TCCTATCTTT
*
5637372 TTA TTT TTA TTA TTA TT- TTA TTA TTA TT- TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5637417 TTA TTA TTA TT
1 TTA TTA TTA TT
5637428 TTTCTTTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 6 0.12
3 42 0.88
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:5637392 original size:11 final size:11
Alignment explanation
Indices: 5637376--5637427 Score: 95
Period size: 11 Copynumber: 4.6 Consensus size: 11
5637366 ATCTTTTTAT
5637376 TTTTATTATTA
1 TTTTATTATTA
5637387 TTTTATTATTA
1 TTTTATTATTA
5637398 TTTTATTATTA
1 TTTTATTATTA
5637409 TTTTATTATTA
1 TTTTATTATTA
5637420 TTATTATT
1 TT-TTATT
5637428 TTTCTTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
11 35 0.88
12 5 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:5637451 original size:6 final size:6
Alignment explanation
Indices: 5637369--5637442 Score: 64
Period size: 6 Copynumber: 12.8 Consensus size: 6
5637359 TCCTCCTATC
* * *
5637369 TTTTTA TTTTTA TTATTA -TTTTA TTATTA -TTTTA TTATTA -TTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
5637414 TTATTA TTATTA TTTTTC TTTTTC TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
5637443 TTATTTTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
5 12 0.21
6 44 0.79
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:5643864 original size:20 final size:19
Alignment explanation
Indices: 5643815--5643862 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
5643805 TAAACCTTAA
5643815 AAATAAAAATAATATAATT
1 AAATAAAAATAATATAATT
5643834 AGAATAAAAATAA-ACTAATT
1 A-AATAAAAATAATA-TAATT
5643854 AAATAAAAA
1 AAATAAAAA
5643863 ATTGGACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAATAAAAATAATATAATT
Found at i:5645683 original size:27 final size:26
Alignment explanation
Indices: 5645607--5645673 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
5645597 TTATATAATT
* **
5645607 TATTTATTTTAAAAA-ACTATACATA
1 TATTTATATTAAAAATACTATTTATA
5645632 TA-TTATTATTAAAAATACTATTTATA
1 TATTTA-TATTAAAAATACTATTTATA
5645658 TATTTATATTAAAAAT
1 TATTTATATTAAAAAT
5645674 TTTTATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.08
25 10 0.28
26 20 0.56
27 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTTATATTAAAAATACTATTTATA
Found at i:5645694 original size:27 final size:25
Alignment explanation
Indices: 5645604--5645694 Score: 73
Period size: 26 Copynumber: 3.6 Consensus size: 25
5645594 TTTTTATATA
5645604 ATTTAT-T-TATT-TTAAAAA-ACT
1 ATTTATATATATTATTAAAAATACT
**
5645625 ATACATATATTATTATTAAAAATACT
1 ATTTATATA-TATTATTAAAAATACT
* **
5645651 ATTTATATATTTATATTAAAAATTTTT
1 ATTTATATATAT-TATTAAAAA-TACT
5645678 ATTTATCATATATTATT
1 ATTTAT-ATATATTATT
5645695 TTCCTATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
21 4 0.07
22 1 0.02
24 4 0.07
25 9 0.17
26 19 0.35
27 12 0.22
28 5 0.09
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTATATATATTATTAAAAATACT
Found at i:5645757 original size:32 final size:32
Alignment explanation
Indices: 5645708--5645778 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
5645698 CTATATATTT
*
5645708 TTATTTTATTTTATTATATAAAATTTATTATA
1 TTATTTTATTTTATTATATAAAACTTATTATA
**
5645740 TT-TTTTATTTTTATTATATATTACTTATTATA
1 TTATTTTA-TTTTATTATATAAAACTTATTATA
5645772 TTATTTT
1 TTATTTT
5645779 TTATTCTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 5 0.15
32 25 0.74
33 4 0.12
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (32 bp):
TTATTTTATTTTATTATATAAAACTTATTATA
Found at i:5645777 original size:35 final size:34
Alignment explanation
Indices: 5645699--5645792 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 34
5645689 ATTATTTTCC
* *
5645699 TATATATTTTTATTTTA-TTTTATTATATAAAATT
1 TATATATTATT-TTTTATTTTTATTATATAAAACT
**
5645733 TAT-TA-TATTTTTTATTTTTATTATATATTACT
1 TATATATTATTTTTTATTTTTATTATATAAAACT
*
5645765 TATTATATTATTTTTTATTCTATATTAT
1 TA-TATATTATTTTTTATT-TTTATTAT
5645793 GTATATCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
31 5 0.10
32 19 0.38
33 3 0.06
34 5 0.10
35 11 0.22
36 7 0.14
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (34 bp):
TATATATTATTTTTTATTTTTATTATATAAAACT
Found at i:5649148 original size:30 final size:30
Alignment explanation
Indices: 5649113--5649275 Score: 129
Period size: 30 Copynumber: 5.5 Consensus size: 30
5649103 ATGGTCGTCA
5649113 CCATCCCTTTTCATAATTTGATAGTCGAAG
1 CCATCCCTTTTCATAATTTGATAGTCGAAG
* * ** **
5649143 TCATCCCTTTTCATAGTGCGATAACCGAAG
1 CCATCCCTTTTCATAATTTGATAGTCGAAG
* *
5649173 CCATCCCTTTTCATAATTTAATAGTCGTCA-
1 CCATCCCTTTTCATAATTTGATAGTCG-AAG
* *
5649203 CCATCCCTTTTCATAATATGATGGTC-ATCA-
1 CCATCCCTTTTCATAATTTGATAGTCGA--AG
* *
5649233 CCATCTCTTTTCATGA-TTGATAG-CGGAAG
1 CCATCCCTTTTCATAATTTGATAGTC-GAAG
**
5649262 TTATCCCTTTTCAT
1 CCATCCCTTTTCAT
5649276 TCGTCATTGA
Statistics
Matches: 102, Mismatches: 25, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
28 2 0.02
29 16 0.16
30 83 0.81
31 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.37
Consensus pattern (30 bp):
CCATCCCTTTTCATAATTTGATAGTCGAAG
Found at i:5649237 original size:60 final size:60
Alignment explanation
Indices: 5649101--5649246 Score: 145
Period size: 60 Copynumber: 2.4 Consensus size: 60
5649091 TTTCATTGTT
* * * * *
5649101 CGATGGTCGTCACCATCCCTTTTCATAATTTGATAGTCGAAGTCATCCCTTTTCATAGTG
1 CGATGGTCATCACCATCCCTTTTCATAATTTAATAGTCGAAGCCATCCCTTTTCATAATA
*** *
5649161 CGATAACCGA--AGCCATCCCTTTTCATAATTTAATAGTCGTCA-CCATCCCTTTTCATAATA
1 CGATGGTC-ATCA-CCATCCCTTTTCATAATTTAATAGTCG-AAGCCATCCCTTTTCATAATA
* *
5649221 TGATGGTCATCACCATCTCTTTTCAT
1 CGATGGTCATCACCATCCCTTTTCAT
5649247 GATTGATAGC
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
59 2 0.03
60 63 0.94
61 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (60 bp):
CGATGGTCATCACCATCCCTTTTCATAATTTAATAGTCGAAGCCATCCCTTTTCATAATA
Found at i:5656035 original size:33 final size:33
Alignment explanation
Indices: 5655998--5656064 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
5655988 AGTGACTATG
5655998 ACTCAAGTAGACATCTTTGAATGAACTATAAAT
1 ACTCAAGTAGACATCTTTGAATGAACTATAAAT
*
5656031 ACTCAAGTAGATATCTTTGAATGAACTATAAAT
1 ACTCAAGTAGACATCTTTGAATGAACTATAAAT
5656064 A
1 A
5656065 ATAGTGGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (33 bp):
ACTCAAGTAGACATCTTTGAATGAACTATAAAT
Found at i:5664377 original size:40 final size:40
Alignment explanation
Indices: 5664316--5664391 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
5664306 CGGTACTTTA
* *
5664316 TGGTGCGTAGGGTTAGATGGGTTGATTTTATCCCCATATT
1 TGGTGCGTAGGGATAGATGGGTCGATTTTATCCCCATATT
* *
5664356 TGGTGTGTAGGGATAGGTGGGTCGATTTTATCCCCA
1 TGGTGCGTAGGGATAGATGGGTCGATTTTATCCCCA
5664392 CATGGTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.17, C:0.13, G:0.33, T:0.37
Consensus pattern (40 bp):
TGGTGCGTAGGGATAGATGGGTCGATTTTATCCCCATATT
Found at i:5670391 original size:17 final size:19
Alignment explanation
Indices: 5670369--5670403 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
5670359 CTAAAATATT
5670369 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
5670386 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
5670404 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:5670475 original size:18 final size:19
Alignment explanation
Indices: 5670452--5670504 Score: 74
Period size: 17 Copynumber: 2.8 Consensus size: 19
5670442 AAATGATAGC
5670452 AAAATAGTAAAAAAAAAG-
1 AAAATAGTAAAAAAAAAGA
*
5670470 AAAATAG-AAAAAAACAGA
1 AAAATAGTAAAAAAAAAGA
5670488 AAGAATAGTAAAAAAAA
1 AA-AATAGTAAAAAAAA
5670505 CAACAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 9 0.30
18 9 0.30
19 5 0.17
20 7 0.23
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.09
Consensus pattern (19 bp):
AAAATAGTAAAAAAAAAGA
Found at i:5670482 original size:19 final size:19
Alignment explanation
Indices: 5670454--5670504 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
5670444 ATGATAGCAA
5670454 AATAGTAAAAAAAA-AGAA-
1 AATAGTAAAAAAAAGA-AAG
5670472 AATAG-AAAAAAACAGAAAG
1 AATAGTAAAAAAA-AGAAAG
5670491 AATAGTAAAAAAAA
1 AATAGTAAAAAAAA
5670505 CAACAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.24
18 8 0.28
19 7 0.24
20 7 0.24
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (19 bp):
AATAGTAAAAAAAAGAAAG
Found at i:5670492 original size:21 final size:21
Alignment explanation
Indices: 5670466--5670506 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5670456 TAGTAAAAAA
5670466 AAAGAA-AATAGAAAAAAACAG
1 AAAGAATAATA-AAAAAAACAG
*
5670487 AAAGAATAGTAAAAAAAACA
1 AAAGAATAATAAAAAAAACA
5670507 ACAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (21 bp):
AAAGAATAATAAAAAAAACAG
Found at i:5673776 original size:21 final size:20
Alignment explanation
Indices: 5673738--5673776 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5673728 GTATTAAATT
**
5673738 TATATTATAAAACTATTTCG
1 TATATTATAAAAAAATTTCG
5673758 TATATTAATAAAAAAATTT
1 TATATT-ATAAAAAAATTT
5673777 AAGTGTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
TATATTATAAAAAAATTTCG
Found at i:5674451 original size:24 final size:23
Alignment explanation
Indices: 5674396--5674461 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
5674386 TATATTACAT
5674396 TTAAAAATATATATAATTTTTAA
1 TTAAAAATATATATAATTTTTAA
* * * *
5674419 TGATCAAATATATAGAATTTTTAC
1 TTA-AAAATATATATAATTTTTAA
5674443 TCTAAAAATATATATAATT
1 T-TAAAAATATATATAATT
5674462 CTCGACTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.06
24 31 0.91
25 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (23 bp):
TTAAAAATATATATAATTTTTAA
Found at i:5678931 original size:10 final size:10
Alignment explanation
Indices: 5678918--5678943 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5678908 TAACAAACTC
5678918 TTTTAATTTA
1 TTTTAATTTA
5678928 TTTTAATTTA
1 TTTTAATTTA
5678938 TTTTAA
1 TTTTAA
5678944 AATTTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:5681644 original size:29 final size:29
Alignment explanation
Indices: 5681581--5681648 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
5681571 TAATCACCCA
* *
5681581 CGCACACTCAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTACCATGCACTTTAAACT
* **
5681610 CACACACTTAGTACCATGCA-TTTCAAGTT
1 CGCACACTTAGTACCATGCACTTT-AAACT
5681639 CGCACACTTA
1 CGCACACTTA
5681649 CCTTTTTCCG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTACCATGCACTTTAAACT
Found at i:5681790 original size:29 final size:30
Alignment explanation
Indices: 5681751--5681829 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
5681741 CTTAATAATC
5681751 AACCGCGCACACTTAGTGCCATGTAC-TGTA
1 AACC-CGCACACTTAGTGCCATGTACATGTA
* *
5681781 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATGTA
*
5681810 AACCCGCACGCTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
5681830 ATCTCATGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 31 0.76
30 4 0.10
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATGTA
Found at i:5701745 original size:40 final size:39
Alignment explanation
Indices: 5701696--5701810 Score: 169
Period size: 40 Copynumber: 2.9 Consensus size: 39
5701686 GCTATCTCGG
*
5701696 TTCGTACACTTAGTGCCTCA-TACAGCCGAAGCTATACCAT
1 TTCGCACACTTAGTG-CT-ATTACAGCCGAAGCTATACCAT
*
5701736 TTCGCACACTTAGTGCTATTTATAGCCGAAGCTATACCAT
1 TTCGCACACTTAGTGCTA-TTACAGCCGAAGCTATACCAT
5701776 TTCGCACACTTAGTGCTATTTACAGCCGAAGCTAT
1 TTCGCACACTTAGTGCTA-TTACAGCCGAAGCTAT
5701811 TTTGAACCGC
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
38 1 0.01
39 2 0.03
40 67 0.96
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (39 bp):
TTCGCACACTTAGTGCTATTACAGCCGAAGCTATACCAT
Found at i:5704855 original size:38 final size:38
Alignment explanation
Indices: 5704798--5704874 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
5704788 TATTGCATCA
5704798 AAACACATCCCAAACCGATCAACGATGCATCACTGTAG
1 AAACACATCCCAAACCGATCAACGATGCATCACTGTAG
* * *
5704836 AAACACATCCCAGATCGATCAACGATGCATTACTGTAG
1 AAACACATCCCAAACCGATCAACGATGCATCACTGTAG
5704874 A
1 A
5704875 TCAAAAATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (38 bp):
AAACACATCCCAAACCGATCAACGATGCATCACTGTAG
Found at i:5709856 original size:52 final size:52
Alignment explanation
Indices: 5709744--5709892 Score: 190
Period size: 52 Copynumber: 2.8 Consensus size: 52
5709734 TTCATTTATT
* * * * *
5709744 TGCCATATCCCAGATATAGTCTCATACGGAAGCACATAATCACATCTCACCGA
1 TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACAT-ATCACATCACACCGA
*
5709797 TGCCATAGCCCAGCTATGGTCTTATACAGAAGCACATATCACATCACACCGA
1 TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATCACACCGA
* * * * *
5709849 TTCCATAGTCTAGCTATGGTCTTATACGGAAACACATGTCACAT
1 TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACAT
5709893 ATTGCCAAGG
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 52 0.62
53 32 0.38
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (52 bp):
TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATCACACCGA
Found at i:5712651 original size:3 final size:3
Alignment explanation
Indices: 5712645--5712670 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5712635 GTTGTTTATA
5712645 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
5712671 TTGCAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:5715424 original size:17 final size:17
Alignment explanation
Indices: 5715414--5715449 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5715404 TTTTGTTTCT
5715414 TTTTATGTTTTATTTTA
1 TTTTATGTTTTATTTTA
*
5715431 TTTTATGTTTTATTATA
1 TTTTATGTTTTATTTTA
5715448 TT
1 TT
5715450 AATATTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTATGTTTTATTTTA
Found at i:5718392 original size:17 final size:17
Alignment explanation
Indices: 5718353--5718393 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5718343 ATGAAATGTT
* *
5718353 AATAATTTAAATTTTAA
1 AATATTTTAAATTTGAA
5718370 AATATTTTAAATTTGAA
1 AATATTTTAAATTTGAA
*
5718387 ATTATTT
1 AATATTT
5718394 AATTAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATATTTTAAATTTGAA
Found at i:5718490 original size:32 final size:31
Alignment explanation
Indices: 5718454--5718588 Score: 117
Period size: 32 Copynumber: 4.2 Consensus size: 31
5718444 AAAAATTACT
*
5718454 AATAATTATAATTTAAATTAAATCAAATTTAA
1 AATAATTAAAATTTAAATT-AATCAAATTTAA
* * * * *
5718486 AATAATTTAAACTTAAAATAACCAAAATCTAA
1 AATAATTAAAATTTAAATTAATC-AAATTTAA
* *
5718518 AATAATTAAAATTTAAAGCTAACACAAATTTAA
1 AATAATTAAAATTTAAA-TTAA-TCAAATTTAA
** * **
5718551 AATTTTTAAAATTCAAATTAATCAAATACAA
1 AATAATTAAAATTTAAATTAATCAAATTTAA
5718582 AATAATT
1 AATAATT
5718589 CAATCCATCT
Statistics
Matches: 80, Mismatches: 20, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
31 15 0.19
32 40 0.50
33 24 0.30
34 1 0.01
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (31 bp):
AATAATTAAAATTTAAATTAATCAAATTTAA
Found at i:5718528 original size:16 final size:16
Alignment explanation
Indices: 5718454--5718534 Score: 81
Period size: 16 Copynumber: 5.1 Consensus size: 16
5718444 AAAAATTACT
*
5718454 AATAATTATAATTTAA
1 AATAATTAAAATTTAA
* * *
5718470 ATTAAATCAAATTTAA
1 AATAATTAAAATTTAA
* *
5718486 AATAATTTAAACTTAA
1 AATAATTAAAATTTAA
** *
5718502 AATAACCAAAATCTAA
1 AATAATTAAAATTTAA
5718518 AATAATTAAAATTTAA
1 AATAATTAAAATTTAA
5718534 A
1 A
5718535 GCTAACACAA
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATTAAAATTTAA
Found at i:5722873 original size:37 final size:37
Alignment explanation
Indices: 5722816--5722967 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
5722806 TATGATCACT
*
5722816 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
5722851 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
5722888 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
5722933 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
5722968 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:5722951 original size:46 final size:46
Alignment explanation
Indices: 5722884--5723152 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
5722874 TAAGTGTAGC
* **
5722884 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
5722930 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
5722976 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
5723028 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
5723074 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
5723126 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
5723153 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:5723003 original size:52 final size:52
Alignment explanation
Indices: 5722927--5723146 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
5722917 TAGCTAAAGC
* *
5722927 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
5722980 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
5723032 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
5723078 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
5723130 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
5723147 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:5723049 original size:98 final size:98
Alignment explanation
Indices: 5722884--5723152 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
5722874 TAAGTGTAGC
* * *
5722884 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
5722949 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
5722983 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
5723048 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
5723081 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
5723146 GATCAGA
66 GATCAGA
5723153 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:5731884 original size:6 final size:6
Alignment explanation
Indices: 5731873--5731911 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
5731863 CTTATATACA
5731873 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTC
5731912 ACCACTCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:5737388 original size:10 final size:9
Alignment explanation
Indices: 5737354--5737430 Score: 52
Period size: 10 Copynumber: 8.3 Consensus size: 9
5737344 TTAAAAAAAA
5737354 TTTATAAATT
1 TTTAT-AATT
*
5737364 TATATCAATT
1 TTTAT-AATT
* *
5737374 CTAATAATT
1 TTTATAATT
5737383 TTTAATAA--
1 TTT-ATAATT
5737391 TTT-TAATT
1 TTTATAATT
5737399 TTTAATAATAT
1 TTT-ATAAT-T
*
5737410 TTTATGATT
1 TTTATAATT
5737419 TTTATAATT
1 TTTATAATT
5737428 TTT
1 TTT
5737431 TTCTAATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
6 3 0.06
8 6 0.12
9 17 0.33
10 22 0.42
11 4 0.08
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTATAATT
Found at i:5737399 original size:16 final size:16
Alignment explanation
Indices: 5737378--5737429 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
5737368 TCAATTCTAA
5737378 TAATTTTTAATAATTT
1 TAATTTTTAATAATTT
5737394 TAATTTTTAATAATATTT
1 TAATTTTTAAT-A-ATTT
5737412 TATGATTTTT-ATAATTT
1 TA--ATTTTTAATAATTT
5737429 T
1 T
5737430 TTTCTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.34
17 6 0.19
18 7 0.22
19 2 0.06
20 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TAATTTTTAATAATTT
Found at i:5741461 original size:17 final size:16
Alignment explanation
Indices: 5741435--5741469 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5741425 TCAATTAACC
*
5741435 AATCAACTTAAATCTT
1 AATCAACTTAAACCTT
5741451 AATCAAACTTAAACCTT
1 AATC-AACTTAAACCTT
5741468 AA
1 AA
5741470 CTGATTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (16 bp):
AATCAACTTAAACCTT
Found at i:5748878 original size:29 final size:27
Alignment explanation
Indices: 5748834--5748888 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5748824 ATTTTACCAA
*
5748834 TTTTTTTTAAAAAAAATTCATATAAAC
1 TTTTTTTTAAAAAAAATGCATATAAAC
*
5748861 TTTTTTTTAAAAGTAAAATGCTTATAAA
1 TTTTTTTTAAAA--AAAATGCATATAAA
5748889 ATATAGAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
29 12 0.50
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (27 bp):
TTTTTTTTAAAAAAAATGCATATAAAC
Found at i:5751055 original size:114 final size:114
Alignment explanation
Indices: 5750855--5751082 Score: 456
Period size: 114 Copynumber: 2.0 Consensus size: 114
5750845 GTGTAGGAAA
5750855 ACACGTCCAGTTTTAAGTTGCTTTTTTAAAATTTTTTAATATAATTCGTTTCTTTGGTTAAATGT
1 ACACGTCCAGTTTTAAGTTGCTTTTTTAAAATTTTTTAATATAATTCGTTTCTTTGGTTAAATGT
5750920 TATTAATTTTGTCATTAAGTCTTAGGTTCAATTTCTCTCTCACTCACAT
66 TATTAATTTTGTCATTAAGTCTTAGGTTCAATTTCTCTCTCACTCACAT
5750969 ACACGTCCAGTTTTAAGTTGCTTTTTTAAAATTTTTTAATATAATTCGTTTCTTTGGTTAAATGT
1 ACACGTCCAGTTTTAAGTTGCTTTTTTAAAATTTTTTAATATAATTCGTTTCTTTGGTTAAATGT
5751034 TATTAATTTTGTCATTAAGTCTTAGGTTCAATTTCTCTCTCACTCACAT
66 TATTAATTTTGTCATTAAGTCTTAGGTTCAATTTCTCTCTCACTCACAT
5751083 TTATATTTTT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (114 bp):
ACACGTCCAGTTTTAAGTTGCTTTTTTAAAATTTTTTAATATAATTCGTTTCTTTGGTTAAATGT
TATTAATTTTGTCATTAAGTCTTAGGTTCAATTTCTCTCTCACTCACAT
Found at i:5751311 original size:13 final size:13
Alignment explanation
Indices: 5751293--5751317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5751283 AATTTTTTTA
5751293 TTTTTAATTAATC
1 TTTTTAATTAATC
5751306 TTTTTAATTAAT
1 TTTTTAATTAAT
5751318 AACTCTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:5756479 original size:17 final size:18
Alignment explanation
Indices: 5756442--5756480 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5756432 AAAATTTTAA
* *
5756442 ATTAATTTATATTGTTGC
1 ATTAAATTATATTGGTGC
5756460 ATTAAATTAT-TTGGTGC
1 ATTAAATTATATTGGTGC
5756477 ATTA
1 ATTA
5756481 CCATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (18 bp):
ATTAAATTATATTGGTGC
Found at i:5756511 original size:22 final size:25
Alignment explanation
Indices: 5756483--5756540 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
5756473 GTGCATTACC
5756483 ATTTATT-TTAAAAATA-AT-TTAT
1 ATTTATTATTAAAAATATATGTTAT
* *
5756505 ATTTATTATTTAAAATATATGTTTT
1 ATTTATTATTAAAAATATATGTTAT
*
5756530 ATTTATCATTA
1 ATTTATTATTA
5756541 TATTAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
24 2 0.07
25 12 0.41
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTATTATTAAAAATATATGTTAT
Found at i:5756519 original size:24 final size:24
Alignment explanation
Indices: 5756489--5756554 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 24
5756479 TACCATTTAT
*
5756489 TTTAAAAATAATTTATATTTATTA
1 TTTAAAAATAATTTATATTTATCA
*
5756513 TTT-AAAATATATGTTTTATTTATCA
1 TTTAAAAATA-AT-TTATATTTATCA
*
5756538 TTATATTAAATAATTTA
1 TT-TA-AAAATAATTTA
5756555 AAATTTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
23 6 0.18
24 5 0.15
25 12 0.36
26 3 0.09
27 2 0.06
28 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTAAAAATAATTTATATTTATCA
Found at i:5756924 original size:32 final size:32
Alignment explanation
Indices: 5756888--5756950 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
5756878 AATTCAGACA
*
5756888 AATTTAAACACAAAACAATATAAACCTAAATT
1 AATTTAAACACAAAACAATATAAACCCAAATT
* * *
5756920 AATTTGAACTCAAAACAATTTAAACCCAAAT
1 AATTTAAACACAAAACAATATAAACCCAAAT
5756951 CATCAAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.25
Consensus pattern (32 bp):
AATTTAAACACAAAACAATATAAACCCAAATT
Found at i:5756949 original size:16 final size:16
Alignment explanation
Indices: 5756888--5756949 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
5756878 AATTCAGACA
*
5756888 AATTTAAACACAAAAC
1 AATTTAAACCCAAAAC
* * **
5756904 AATATAAACCTAAATT
1 AATTTAAACCCAAAAC
* *
5756920 AATTTGAACTCAAAAC
1 AATTTAAACCCAAAAC
5756936 AATTTAAACCCAAA
1 AATTTAAACCCAAA
5756950 TCATCAAACT
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.24
Consensus pattern (16 bp):
AATTTAAACCCAAAAC
Found at i:5764841 original size:2 final size:2
Alignment explanation
Indices: 5764834--5764858 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5764824 TAATATGCAT
5764834 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 A
5764859 AAAGTACAGC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5777524 original size:30 final size:30
Alignment explanation
Indices: 5777488--5777662 Score: 296
Period size: 30 Copynumber: 5.8 Consensus size: 30
5777478 TAGGCACAAG
* *
5777488 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
5777518 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
5777548 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
5777578 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
5777608 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
5777638 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
5777663 TGAGAAAAGT
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 135 1.00
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:5777581 original size:60 final size:60
Alignment explanation
Indices: 5777488--5777662 Score: 332
Period size: 60 Copynumber: 2.9 Consensus size: 60
5777478 TAGGCACAAG
*
5777488 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
5777548 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
*
5777608 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGT
5777663 TGAGAAAAGT
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 113 1.00
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.25
Consensus pattern (60 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:5785337 original size:9 final size:8
Alignment explanation
Indices: 5785308--5785337 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
5785298 TATCGTTATT
5785308 AAAATTTC
1 AAAATTTC
5785316 AAAATTTC
1 AAAATTTC
5785324 AAAATTTGC
1 AAAATTT-C
5785333 AAAAT
1 AAAAT
5785338 ACAACTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (8 bp):
AAAATTTC
Found at i:5795953 original size:30 final size:30
Alignment explanation
Indices: 5795919--5795976 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5795909 CAGCAAGTAC
*
5795919 TAGAAGTGGAAGAGGAAATCGAAGAAGAAG
1 TAGAAGTAGAAGAGGAAATCGAAGAAGAAG
* *
5795949 TAGAAGTAGAAGAGGAATTTGAAGAAGA
1 TAGAAGTAGAAGAGGAAATCGAAGAAGA
5795977 GGAGGAGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.34, T:0.14
Consensus pattern (30 bp):
TAGAAGTAGAAGAGGAAATCGAAGAAGAAG
Found at i:5796956 original size:27 final size:27
Alignment explanation
Indices: 5796926--5796983 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
5796916 GCCTGCTGGA
* *
5796926 GCTGGGTTCAACCATGGTGTTGCTCCT
1 GCTGGGTTCAACCATGGAGTGGCTCCT
* * *
5796953 GCTGGGTTTAACCCTGGAGTGGCTGCT
1 GCTGGGTTCAACCATGGAGTGGCTCCT
5796980 GCTG
1 GCTG
5796984 CTGCACCGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.10, C:0.24, G:0.34, T:0.31
Consensus pattern (27 bp):
GCTGGGTTCAACCATGGAGTGGCTCCT
Found at i:5812165 original size:30 final size:30
Alignment explanation
Indices: 5812108--5812166 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
5812098 ATAAATTTCA
* *
5812108 AATTTAATCTCCCTACTTTTATTTTTTAAG
1 AATTTAATCACCCTACTTTTATATTTTAAG
*
5812138 AATTTAATCACTCTACTTTTCA-ATTTTAA
1 AATTTAATCACCCTACTTTT-ATATTTTAA
5812167 AAATCCAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.51
Consensus pattern (30 bp):
AATTTAATCACCCTACTTTTATATTTTAAG
Found at i:5812699 original size:14 final size:14
Alignment explanation
Indices: 5812680--5812711 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5812670 CAATTTATTT
5812680 TAAAAATTAAATTA
1 TAAAAATTAAATTA
*
5812694 TAAAAATTAAATTT
1 TAAAAATTAAATTA
5812708 TAAA
1 TAAA
5812712 TTTAAGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAATTAAATTA
Found at i:5817219 original size:35 final size:35
Alignment explanation
Indices: 5817173--5817243 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
5817163 TTTAGGATCA
* * *
5817173 CATATCTTTGAAGATCCCCTTCCATATTTGCCAAG
1 CATATATTTGAAGATCACCTTCCATATTTACCAAG
* *
5817208 CATATATTTGAAGATCACTTTTCATATTTACCAAG
1 CATATATTTGAAGATCACCTTCCATATTTACCAAG
5817243 C
1 C
5817244 TCTAGAGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37
Consensus pattern (35 bp):
CATATATTTGAAGATCACCTTCCATATTTACCAAG
Found at i:5821818 original size:48 final size:48
Alignment explanation
Indices: 5821694--5821800 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
5821684 TTAGGGAATT
* * * *
5821694 CATTGATTTTGCTCCGG-GACATGATATCAGCACTTCAGGTGCTAGTTA
1 CATTGATTTGGCTTCGGAG-CATGATATCGGCACTTCAGGTGCGAGTTA
5821742 CATTGATTTGGCTTCGGAGCATGATATCGGCACTTC-GGATGCGAGTTA
1 CATTGATTTGGCTTCGGAGCATGATATCGGCACTTCAGG-TGCGAGTTA
*
5821790 TATTGATTTGG
1 CATTGATTTGG
5821801 TTTTGGGCCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
47 2 0.04
48 49 0.94
49 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (48 bp):
CATTGATTTGGCTTCGGAGCATGATATCGGCACTTCAGGTGCGAGTTA
Found at i:5825178 original size:35 final size:35
Alignment explanation
Indices: 5825120--5825190 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
5825110 CCTAGGATCA
* *
5825120 CATATATTTGAAGATACCCTTCCATGTTTGCCAAG
1 CATATATTTGAAGATACCCTTCCATATTTACCAAG
*
5825155 CATATATTTGAAGAT-CACTTTCCATATTTACCAAG
1 CATATATTTGAAGATAC-CCTTCCATATTTACCAAG
5825190 C
1 C
5825191 TCCGAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (35 bp):
CATATATTTGAAGATACCCTTCCATATTTACCAAG
Found at i:5831956 original size:57 final size:55
Alignment explanation
Indices: 5831876--5832020 Score: 150
Period size: 57 Copynumber: 2.6 Consensus size: 55
5831866 AACTTCACAC
* * *
5831876 TTTTCTTAATTTGGTAT-TTAGTTTTTTTTTTTAATTTAGTACT-TGAATTTGATACAT
1 TTTTC-TAATTTGGTATCTAAGTTTTTTTTTTCAATTTAATA-TATGAATTTG--ACAT
* *
5831933 TTTTCTAATTTGGTATCTAAGTTTTCTTTGTCCAATTTAATATATGAATTTGACAT
1 TTTTCTAATTTGGTATCTAAGTTTT-TTTTTTCAATTTAATATATGAATTTGACAT
* * *
5831989 TTTTCCTAATTTGATACCTAAGGTTTTTTTTT
1 TTTT-CTAATTTGGTATCTAAGTTTTTTTTTT
5832021 GTGTGTTCTA
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
56 23 0.31
57 31 0.42
58 20 0.27
ACGTcount: A:0.23, C:0.09, G:0.10, T:0.57
Consensus pattern (55 bp):
TTTTCTAATTTGGTATCTAAGTTTTTTTTTTCAATTTAATATATGAATTTGACAT
Found at i:5834831 original size:19 final size:19
Alignment explanation
Indices: 5834791--5834837 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5834781 ATTTTATTTT
* *
5834791 ATTTTTTAAATTTTTATGA
1 ATTTTTTTAATTTTTATAA
5834810 ATTTTTTTAATATTTTA-AA
1 ATTTTTTTAAT-TTTTATAA
*
5834829 ATTTATTTA
1 ATTTTTTTA
5834838 TTTATTGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTTTAATTTTTATAA
Found at i:5835721 original size:17 final size:19
Alignment explanation
Indices: 5835687--5835735 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5835677 GTCCACGTGT
*
5835687 ATATTATAAAAATTTTAAA
1 ATATTATAAAAATCTTAAA
5835706 ATATTA-AAAAA-CTTAAA
1 ATATTATAAAAATCTTAAA
*
5835723 AAATTCATAAAAA
1 ATATT-ATAAAAA
5835736 AAAAGTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.35
18 6 0.23
19 11 0.42
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATTATAAAAATCTTAAA
Found at i:5835912 original size:24 final size:22
Alignment explanation
Indices: 5835860--5835912 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
5835850 GGATAAACAT
*
5835860 TAAAAAGCTAAAATTTTTAAAT
1 TAAAAAGCTAAAATTTTTAAAA
5835882 TAGAAAAGGACTAAAA-TTTTAGAAA
1 TA-AAAA-G-CTAAAATTTTTA-AAA
5835907 TAAAAA
1 TAAAAA
5835913 TAGAAAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 2 0.08
23 4 0.15
24 10 0.38
25 10 0.38
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.28
Consensus pattern (22 bp):
TAAAAAGCTAAAATTTTTAAAA
Found at i:5836110 original size:2 final size:2
Alignment explanation
Indices: 5836093--5836152 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
5836083 CTCCTTCCCA
* * *
5836093 TC TC -C TC TC TA T- TC TC TC TC TC TT TC TC TC TC TC TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5836133 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
5836153 CTACACTAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5836112 original size:16 final size:16
Alignment explanation
Indices: 5836105--5836152 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
5836095 TCCTCTCTAT
5836105 TCTCTCTCTCTTTCTC
1 TCTCTCTCTCTTTCTC
5836121 TCTCTCTCTCTTTCTC
1 TCTCTCTCTCTTTCTC
*
5836137 TCTCTCTCTCTCTCTC
1 TCTCTCTCTCTTTCTC
5836153 CTACACTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (16 bp):
TCTCTCTCTCTTTCTC
Found at i:5836211 original size:2 final size:2
Alignment explanation
Indices: 5836204--5836244 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5836194 GGGATAATAT
5836204 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5836245 GAAATTATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5840880 original size:32 final size:31
Alignment explanation
Indices: 5840802--5840880 Score: 74
Period size: 32 Copynumber: 2.5 Consensus size: 31
5840792 TTATTTAGAA
*
5840802 ATAATAAAAATATAAA-ATATTTTTATATTTT
1 ATAATAAAAA-ATAAATAAATTTTTATATTTT
**
5840833 ATAACT-AAATTTAAATACAATTTTTATTATTTT
1 ATAA-TAAAAAATAAATA-AATTTTTA-TATTTT
5840866 -TAATAAAAAATAAAT
1 ATAATAAAAAATAAAT
5840881 CATTTAACTG
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
30 4 0.11
31 9 0.24
32 19 0.50
33 6 0.16
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
ATAATAAAAAATAAATAAATTTTTATATTTT
Found at i:5843919 original size:23 final size:23
Alignment explanation
Indices: 5843892--5843948 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 23
5843882 ATTTTTAAAA
5843892 ATATTTAAAATTATTAAA-ATATC
1 ATATTTAAAATTATTAAATATA-C
*
5843915 ATATTTTTCAATATTATTAAATATAC
1 ATA--TTT-AAAATTATTAAATATAC
5843941 ATATTTAA
1 ATATTTAA
5843949 TTATTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
23 5 0.17
24 3 0.10
25 3 0.10
26 15 0.52
27 3 0.10
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTTAAAATTATTAAATATAC
Found at i:5844039 original size:13 final size:14
Alignment explanation
Indices: 5844014--5844061 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
5844004 TTTAATATTT
*
5844014 TAATATTATTTTAA
1 TAATATAATTTTAA
5844028 TAATA-AATTTTAA
1 TAATATAATTTTAA
* *
5844041 AAATAATAATTTAAA
1 TAAT-ATAATTTTAA
5844056 TAATAT
1 TAATAT
5844062 TTCAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 10 0.36
14 8 0.29
15 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATATAATTTTAA
Found at i:5844073 original size:23 final size:22
Alignment explanation
Indices: 5844042--5844100 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
5844032 AAATTTTAAA
*
5844042 AATAATAAT-TTAAATAATATTTC
1 AATATTAATATTAAA-AATA-TTC
*
5844065 AATATTAATATTCAAAATATTC
1 AATATTAATATTAAAAATATTC
5844087 ACATATTAATATTA
1 A-ATATTAATATTA
5844101 CAATTATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 4 0.13
23 23 0.74
24 4 0.13
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
AATATTAATATTAAAAATATTC
Found at i:5847018 original size:19 final size:19
Alignment explanation
Indices: 5846994--5847031 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5846984 GAAATGAATA
*
5846994 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
5847013 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
5847032 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:5847938 original size:19 final size:20
Alignment explanation
Indices: 5847905--5847944 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
5847895 ATGTATATAT
5847905 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
5847924 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
5847944 A
1 A
5847945 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:5848210 original size:18 final size:17
Alignment explanation
Indices: 5848187--5848232 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
5848177 AGAGGTAAGG
*
5848187 TTTTTTTCTTTTTCTTCA
1 TTTTTTTATTTTT-TTCA
*
5848205 TTTTTTTATTTTTTTTA
1 TTTTTTTATTTTTTTCA
5848222 -TTTTTTATTTT
1 TTTTTTTATTTT
5848233 GGGTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 3 0.12
18 12 0.46
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTATTTTTTTCA
Found at i:5854072 original size:10 final size:9
Alignment explanation
Indices: 5854037--5854074 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
5854027 ATTAATTAAT
*
5854037 TTTTAAAAT
1 TTTTAAAAA
*
5854046 TTTTTAAAA
1 TTTTAAAAA
5854055 TTTTAAAAA
1 TTTTAAAAA
5854064 TTTTAAAAA
1 TTTTAAAAA
5854073 TT
1 TT
5854075 AATTAATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:5866783 original size:26 final size:26
Alignment explanation
Indices: 5866745--5866854 Score: 157
Period size: 26 Copynumber: 4.2 Consensus size: 26
5866735 TGATACAAAT
* *
5866745 TGATAAAATGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5866771 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
5866797 TAATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5866823 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5866849 TGATAA
1 TGATAA
5866855 GAATTTCATG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5868369 original size:26 final size:26
Alignment explanation
Indices: 5868340--5868392 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5868330 TTTACAGTTT
5868340 TACCCTTAGGAGATAAATT-ACCGAAA
1 TACCCTTAGG-GATAAATTGACCGAAA
* *
5868366 TACCCTTAGGGTTAAATTGACCTAAA
1 TACCCTTAGGGATAAATTGACCGAAA
5868392 T
1 T
5868393 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (26 bp):
TACCCTTAGGGATAAATTGACCGAAA
Found at i:5870235 original size:30 final size:30
Alignment explanation
Indices: 5870201--5870262 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
5870191 ACTTATTTTA
*
5870201 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATGTTAAAGACAT
*
5870231 TTGTTAATTTTGTTATTATGTTAAAGATAT
1 TTGTTAATTTTGTTATTATGTTAAAGACAT
5870261 TT
1 TT
5870263 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATGTTAAAGACAT
Found at i:5870688 original size:26 final size:25
Alignment explanation
Indices: 5870635--5870692 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
5870625 AGAAAAAAAT
* **
5870635 TATTATATTATAAAAATATTTTTTA
1 TATTATATTATAAAAATAATTTACA
*
5870660 TATTTTATTATATAAAATAATTTACA
1 TATTATATTATA-AAAATAATTTACA
5870686 TATTATA
1 TATTATA
5870693 AAAGAGTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTATATTATAAAAATAATTTACA
Found at i:5879705 original size:26 final size:26
Alignment explanation
Indices: 5879647--5879697 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5879637 TTTATATTTA
5879647 ATTTTAAAAAATAAAAATACTAAAAT
1 ATTTTAAAAAATAAAAATACTAAAAT
*
5879673 ATTTT-TAAAATAAAAAATA-TAAAAT
1 ATTTTAAAAAAT-AAAAATACTAAAAT
5879698 GCATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
ATTTTAAAAAATAAAAATACTAAAAT
Found at i:5880041 original size:19 final size:20
Alignment explanation
Indices: 5880011--5880058 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 20
5880001 AAACATTGTG
5880011 GGAAAAAGAATCTTAGTGAA
1 GGAAAAAGAATCTTAGTGAA
5880031 GGAAAAA-AATCTTAGTGAA
1 GGAAAAAGAATCTTAGTGAA
5880050 GGAAAAAGA
1 GGAAAAAGA
5880059 GTACACTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.54, C:0.04, G:0.25, T:0.17
Consensus pattern (20 bp):
GGAAAAAGAATCTTAGTGAA
Found at i:5882580 original size:50 final size:49
Alignment explanation
Indices: 5882447--5882587 Score: 149
Period size: 50 Copynumber: 2.8 Consensus size: 49
5882437 GCCAATCCAA
* * * *
5882447 CCAAAAACAC-ACTTAGGCACCAAGTGTTTAGCCTGTAAGCTAACATCCTT
1 CCAAAAACACGA-TTGGGCACCAAGTG-TTAGCCCGTAGGCTAACATCCCT
* * * * *
5882497 TCAGAAACACGCTTGGGCACTAAGTGCCTAGCCCGTAGGCTAACATCCCT
1 CCAAAAACACGATTGGGCACCAAGTG-TTAGCCCGTAGGCTAACATCCCT
*
5882547 CCAAAAACATGATTGGGCACCAAGTGTTAAGCCCGTAGGCT
1 CCAAAAACACGATTGGGCACCAAGTGTT-AGCCCGTAGGCT
5882588 TTACATCCTC
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
49 1 0.01
50 72 0.99
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (49 bp):
CCAAAAACACGATTGGGCACCAAGTGTTAGCCCGTAGGCTAACATCCCT
Found at i:5884206 original size:38 final size:38
Alignment explanation
Indices: 5884157--5884233 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
5884147 ATCAACATAC
5884157 ACAACAATTATAACAAACTCCGAATTTGATCTTTTTAT
1 ACAACAATTATAACAAACTCCGAATTTGATCTTTTTAT
5884195 ACAACAATTATAACAAACTCCGAATTTGATCTTTTTAT
1 ACAACAATTATAACAAACTCCGAATTTGATCTTTTTAT
5884233 A
1 A
5884234 AAGACACATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36
Consensus pattern (38 bp):
ACAACAATTATAACAAACTCCGAATTTGATCTTTTTAT
Found at i:5887101 original size:11 final size:11
Alignment explanation
Indices: 5887085--5887109 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5887075 TCCTATATAC
5887085 ATATTTTTTTT
1 ATATTTTTTTT
5887096 ATATTTTTTTT
1 ATATTTTTTTT
5887107 ATA
1 ATA
5887110 GTGAAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
ATATTTTTTTT
Found at i:5892464 original size:21 final size:22
Alignment explanation
Indices: 5892439--5892479 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5892429 ACATTGTATC
* *
5892439 AATTTAGTTTT-AATTTTTAAA
1 AATTTAATTTTCAATGTTTAAA
5892460 AATTTAATTTTCAATGTTTA
1 AATTTAATTTTCAATGTTTA
5892480 CATAGTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
AATTTAATTTTCAATGTTTAAA
Found at i:5894568 original size:35 final size:35
Alignment explanation
Indices: 5894504--5894597 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 35
5894494 TAAATATTTT
*
5894504 TTATTAATTTTATATTTTTATAATTTATTTTAATTTA
1 TTATT-ATTTTATATTTTTATAA-TTATTTTAAGTTA
5894541 TTAGATT-TTTTATATTTTTATAA-TATTTTAAGTTA
1 TT--ATTATTTTATATTTTTATAATTATTTTAAGTTA
*
5894576 TTATTATTTTATAATTTTATAA
1 TTATTATTTTATATTTTTATAA
5894598 GTTTATATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
33 3 0.06
34 15 0.29
35 13 0.25
37 18 0.35
39 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (35 bp):
TTATTATTTTATATTTTTATAATTATTTTAAGTTA
Found at i:5894570 original size:10 final size:9
Alignment explanation
Indices: 5894375--5894659 Score: 101
Period size: 10 Copynumber: 31.0 Consensus size: 9
5894365 TACGATTTTG
5894375 TTTATAATT
1 TTTATAATT
5894384 TTTATAAATT
1 TTTAT-AATT
*
5894394 TATATTAATT
1 TTTA-TAATT
* *
5894404 TTAATACTT
1 TTTATAATT
* * *
5894413 CTAATCA-T
1 TTTATAATT
5894421 TTTATAATT
1 TTTATAATT
*
5894430 TTCAATAATTT
1 TT-TATAA-TT
*
5894441 TTTATGATTCT
1 TTTAT-AAT-T
5894452 TTTATAAGTT
1 TTTATAA-TT
*
5894462 TTTAAGAATT
1 TTT-ATAATT
*
5894472 TTTATATGTT
1 TTTATA-ATT
5894482 TTTATAAAATT
1 TTTAT--AATT
** *
5894493 GTAAATATTT
1 -TTTATAATT
5894503 TTTATTAA-T
1 TTTA-TAATT
5894512 TTTAT-ATT
1 TTTATAATT
5894520 TTTATAATT
1 TTTATAATT
*
5894529 TATTTTAATT
1 T-TTATAATT
* *
5894539 TATTAGATTT
1 T-TTATAATT
5894549 TTTAT-ATT
1 TTTATAATT
5894557 TTTATAATAT
1 TTTATAAT-T
*
5894567 TTTA-AGTT
1 TTTATAATT
* *
5894575 ATTATTA-T
1 TTTATAATT
5894583 TTTATAA-T
1 TTTATAATT
5894591 TTTATAAGTT
1 TTTATAA-TT
*
5894601 TATATCAATT
1 TTTAT-AATT
*
5894611 TTAATAA--
1 TTTATAATT
5894618 -TTAT--TT
1 TTTATAATT
*
5894624 TTTATGATT
1 TTTATAATT
5894633 TTTATAATT
1 TTTATAATT
*
5894642 TATTCTAATT
1 T-TTATAATT
5894652 TTT-TAATT
1 TTTATAATT
5894660 AATTTTATGA
Statistics
Matches: 205, Mismatches: 42, Indels: 59
0.67 0.14 0.19
Matches are distributed among these distances:
6 3 0.01
7 5 0.02
8 42 0.20
9 51 0.25
10 80 0.39
11 20 0.10
12 4 0.02
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTATAATT
Found at i:5894577 original size:45 final size:47
Alignment explanation
Indices: 5894499--5894587 Score: 112
Period size: 46 Copynumber: 1.9 Consensus size: 47
5894489 AATTGTAAAT
* *
5894499 ATTTTTTATTAATTTTATATTTTTATAATTTATT-TTAATTTATTAG
1 ATTTTTTATTAATTTTATATATTTATAAGTTATTATTAATTTATTAG
* *
5894545 ATTTTTTA-TATTTTTATAATATTT-TAAGTTATTATTATTTTAT
1 ATTTTTTATTAATTTTAT-ATATTTATAAGTTATTATTAATTTAT
5894588 AATTTTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 16 0.43
46 21 0.57
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (47 bp):
ATTTTTTATTAATTTTATATATTTATAAGTTATTATTAATTTATTAG
Found at i:5894592 original size:8 final size:8
Alignment explanation
Indices: 5894502--5894619 Score: 60
Period size: 8 Copynumber: 13.2 Consensus size: 8
5894492 TGTAAATATT
5894502 TTTTATTAA
1 TTTTA-TAA
*
5894511 TTTTATAT
1 TTTTATAA
5894519 TTTTATAA
1 TTTTATAA
*
5894527 TTTATTTTAA
1 -TT-TTATAA
5894537 -TTTATTAGA
1 TTTTA-TA-A
*
5894546 TTTTTTATAT
1 --TTTTATAA
5894556 TTTTATAA
1 TTTTATAA
5894564 TATTT-TAA
1 T-TTTATAA
*
5894572 GTTATTATTA
1 -TT-TTATAA
5894582 TTTTATAA
1 TTTTATAA
5894590 TTTTATAA
1 TTTTATAA
5894598 GTTTATATCAA
1 -TTT-TAT-AA
5894609 TTTTAATAA
1 TTTT-ATAA
5894618 TT
1 TT
5894620 ATTTTTTATG
Statistics
Matches: 86, Mismatches: 8, Indels: 30
0.69 0.06 0.24
Matches are distributed among these distances:
7 2 0.02
8 37 0.43
9 24 0.28
10 15 0.17
11 4 0.05
12 4 0.05
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.64
Consensus pattern (8 bp):
TTTTATAA
Found at i:5894603 original size:42 final size:40
Alignment explanation
Indices: 5894548--5894669 Score: 99
Period size: 42 Copynumber: 3.0 Consensus size: 40
5894538 TTATTAGATT
* *
5894548 TTTTAT-ATTTTTATAATATTTTAAGTTATTATTATTTTAT-AA
1 TTTTATAATTTATAT-A-ATTTTAA-TAATTATT-TTTTATGAA
*
5894590 TTTTATAAGTTTATATCAATTTTAATAATTATTTTTTATGAT
1 TTTTATAA-TTTATAT-AATTTTAATAATTATTTTTTATGAA
* * *
5894632 TTTTATAATTTATTCTAATTTT-TTAATTA-ATTTTATGA
1 TTTTATAATTTA-TATAATTTTAATAATTATTTTTTATGA
5894670 GAAAATATTA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
39 8 0.12
40 6 0.09
41 16 0.23
42 24 0.35
43 8 0.12
44 7 0.10
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (40 bp):
TTTTATAATTTATATAATTTTAATAATTATTTTTTATGAA
Found at i:5897896 original size:21 final size:21
Alignment explanation
Indices: 5897870--5897910 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5897860 ATCTGCTCAA
* *
5897870 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5897891 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5897911 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5904831 original size:20 final size:21
Alignment explanation
Indices: 5904808--5904853 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
5904798 TAGTATTTCA
5904808 ATTTTTTTTAT-TTTTAACAT
1 ATTTTTTTTATGTTTTAACAT
*
5904828 A-TTTTTTTATGTTTTTACAT
1 ATTTTTTTTATGTTTTAACAT
5904848 -TTTTTT
1 ATTTTTT
5904854 ACACGTCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (21 bp):
ATTTTTTTTATGTTTTAACAT
Found at i:5904832 original size:19 final size:19
Alignment explanation
Indices: 5904808--5904853 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
5904798 TAGTATTTCA
5904808 ATTTTTTTTAT-TTTTAAC
1 ATTTTTTTTATGTTTTAAC
*
5904826 ATATTTTTTTATGTTTTTAC
1 AT-TTTTTTTATGTTTTAAC
5904846 ATTTTTTT
1 ATTTTTTT
5904854 ACACGTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.60
20 8 0.32
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (19 bp):
ATTTTTTTTATGTTTTAAC
Found at i:5905023 original size:12 final size:12
Alignment explanation
Indices: 5905006--5905030 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5904996 ATCACATATG
5905006 TTTTACACAATT
1 TTTTACACAATT
5905018 TTTTACACAATT
1 TTTTACACAATT
5905030 T
1 T
5905031 GATAAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTACACAATT
Found at i:5909382 original size:13 final size:13
Alignment explanation
Indices: 5909364--5909389 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5909354 AATATTGCAT
5909364 GAAAATTTTTATC
1 GAAAATTTTTATC
5909377 GAAAATTTTTATC
1 GAAAATTTTTATC
5909390 AATTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
GAAAATTTTTATC
Found at i:5910615 original size:33 final size:33
Alignment explanation
Indices: 5910578--5910812 Score: 201
Period size: 33 Copynumber: 7.2 Consensus size: 33
5910568 TGGTACAACT
* * *
5910578 TGAAAAGGCTATGTACACTTTGTGTATACCATA
1 TGAAAAGGTTAGGTATACTTTGTGTATACCATA
** * *
5910611 TGAAAAGGAAAGGTACACTTTGTGTGTA-CACT-
1 TGAAAAGGTTAGGTATACTTTGTGTATACCA-TA
* * *
5910643 TGGAAAGGTTAGGTATACTTTGTGCATACCTTA
1 TGAAAAGGTTAGGTATACTTTGTGTATACCATA
** * * *
5910676 TGAAAAGGAAAAGTACACTTTGTGTGTA-CACT-
1 TGAAAAGGTTAGGTATACTTTGTGTATACCA-TA
*
5910708 TGGAAAGGTTAGGTATACTTTGTGTATACCATA
1 TGAAAAGGTTAGGTATACTTTGTGTATACCATA
* ** * *
5910741 TGAAAAAGAAAGATATACTTTGTGTGTACCACT-
1 TGAAAAGGTTAGGTATACTTTGTGTATACCA-TA
* *
5910774 TGGAAATGTTAGGTATACTTTGTGTATACCATA
1 TGAAAAGGTTAGGTATACTTTGTGTATACCATA
5910807 TGAAAA
1 TGAAAA
5910813 AGAAAGATCT
Statistics
Matches: 156, Mismatches: 38, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
32 50 0.32
33 105 0.67
34 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (33 bp):
TGAAAAGGTTAGGTATACTTTGTGTATACCATA
Found at i:5910663 original size:65 final size:65
Alignment explanation
Indices: 5910570--5910847 Score: 398
Period size: 65 Copynumber: 4.2 Consensus size: 65
5910560 TACCCAAATG
* * * * * *
5910570 GTACAACTTGAAAAGGCTATGTACACTTTGTGTATACCATATGAAAAGGAAAGGTACACTTTGTG
1 GTAC-ACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAAGAAAGATACACTTTGTG
5910635 T
65 T
* * *
5910636 GTACACTTGGAAAGGTTAGGTATACTTTGTGCATACCTTATGAAAAGGAAA-AGTACACTTTGTG
1 GTACACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAAGAAAGA-TACACTTTGTG
5910700 T
65 T
*
5910701 GTACACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAAGAAAGATATACTTTGTGT
1 GTACACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAAGAAAGATACACTTTGTGT
*
5910766 GTACCACTTGGAAATGTTAGGTATACTTTGTGTATACCATATGAAAAAGAAAGAT-CTACTTTGT
1 GTA-CACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAAGAAAGATAC-ACTTTGT
5910830 GT
64 GT
5910832 GTACCACTTGGAAAGG
1 GTA-CACTTGGAAAGG
5910848 AATGTACACT
Statistics
Matches: 194, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
65 115 0.59
66 79 0.41
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (65 bp):
GTACACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAAGAAAGATACACTTTGTGT
Found at i:5910826 original size:33 final size:33
Alignment explanation
Indices: 5910594--5910837 Score: 167
Period size: 33 Copynumber: 7.5 Consensus size: 33
5910584 GGCTATGTAC
* * *
5910594 ACTTTGTGTATACCATATGAAAAGGAAAGGTAC
1 ACTTTGTGTATACCATATGAAAAAGAAAGATAT
* * * ** *
5910627 ACTTTGTGTGTA-CACT-TGGAAAGGTTAGGTAT
1 ACTTTGTGTATACCA-TATGAAAAAGAAAGATAT
* * * *
5910659 ACTTTGTGCATACCTTATGAAAAGGAAA-AGTAC
1 ACTTTGTGTATACCATATGAAAAAGAAAGA-TAT
* * * ** *
5910692 ACTTTGTGTGTA-CACT-TGGAAAGGTTAGGTAT
1 ACTTTGTGTATACCA-TATGAAAAAGAAAGATAT
5910724 ACTTTGTGTATACCATATGAAAAAGAAAGATAT
1 ACTTTGTGTATACCATATGAAAAAGAAAGATAT
* * * ** *
5910757 ACTTTGTGTGTACCACT-TGGAAATGTTAGGTAT
1 ACTTTGTGTATACCA-TATGAAAAAGAAAGATAT
*
5910790 ACTTTGTGTATACCATATGAAAAAGAAAGATCT
1 ACTTTGTGTATACCATATGAAAAAGAAAGATAT
*
5910823 ACTTTGTGTGTACCA
1 ACTTTGTGTATACCA
5910838 CTTGGAAAGG
Statistics
Matches: 160, Mismatches: 41, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
32 49 0.31
33 110 0.69
34 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (33 bp):
ACTTTGTGTATACCATATGAAAAAGAAAGATAT
Found at i:5922388 original size:7 final size:7
Alignment explanation
Indices: 5922376--5922402 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5922366 TTTTTCATAC
5922376 TTATTTA
1 TTATTTA
5922383 TTATTTA
1 TTATTTA
5922390 TTATTTA
1 TTATTTA
5922397 TTATTT
1 TTATTT
5922403 GTTTAATTTT
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:5931495 original size:41 final size:41
Alignment explanation
Indices: 5931438--5931520 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
5931428 TGTAAACTTA
5931438 AGGTCCCGTTGGATGGGCAGTGTGTTTAATTACGTTAGTAT
1 AGGTCCCGTTGGATGGGCAGTGTGTTTAATTACGTTAGTAT
5931479 AGGTCCCGTTGGATGGGCAGTGTGTTTAATTACGTTAGTAT
1 AGGTCCCGTTGGATGGGCAGTGTGTTTAATTACGTTAGTAT
5931520 A
1 A
5931521 AAAACAACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.36
Consensus pattern (41 bp):
AGGTCCCGTTGGATGGGCAGTGTGTTTAATTACGTTAGTAT
Found at i:5931861 original size:9 final size:9
Alignment explanation
Indices: 5931847--5931885 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
5931837 AAATGCACAA
5931847 AAAAAAAAT
1 AAAAAAAAT
5931856 -AAAAAAAT
1 AAAAAAAAT
5931864 AAAAAAAAACT
1 -AAAAAAAA-T
5931875 AAAAAAAAT
1 AAAAAAAAT
5931884 AA
1 AA
5931886 CAACAGTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.30
9 3 0.11
10 15 0.56
11 1 0.04
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:5931861 original size:11 final size:11
Alignment explanation
Indices: 5931845--5931882 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5931835 TCAAATGCAC
5931845 AAAAAAAA-AA
1 AAAAAAAATAA
*
5931855 TAAAAAAATAA
1 AAAAAAAATAA
*
5931866 AAAAAAACTAA
1 AAAAAAAATAA
5931877 AAAAAA
1 AAAAAA
5931883 TAACAACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:5931885 original size:20 final size:19
Alignment explanation
Indices: 5931845--5931881 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5931835 TCAAATGCAC
5931845 AAAAAAAAAATAAAAAAAT
1 AAAAAAAAAATAAAAAAAT
*
5931864 AAAAAAAAACTAAAAAAA
1 AAAAAAAAAATAAAAAAA
5931882 ATAACAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAAAAAAAATAAAAAAAT
Found at i:5933012 original size:14 final size:14
Alignment explanation
Indices: 5932993--5933038 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
5932983 TTAAAAATTT
5932993 TAAATTAGTAAAGG
1 TAAATTAGTAAAGG
* ***
5933007 TAAATTTGTAATTT
1 TAAATTAGTAAAGG
5933021 TAAATTAGTAAAGG
1 TAAATTAGTAAAGG
5933035 TAAA
1 TAAA
5933039 ATTGTACTTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
TAAATTAGTAAAGG
Found at i:5933020 original size:28 final size:28
Alignment explanation
Indices: 5932988--5933044 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
5932978 ATTTTTTAAA
*
5932988 AATTTTAAATTAGTAAAGGTAAATTTGT
1 AATTTTAAATTAGTAAAGGTAAAATTGT
5933016 AATTTTAAATTAGTAAAGGTAAAATTGT
1 AATTTTAAATTAGTAAAGGTAAAATTGT
5933044 A
1 A
5933045 CTTTGCCCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (28 bp):
AATTTTAAATTAGTAAAGGTAAAATTGT
Found at i:5933528 original size:13 final size:13
Alignment explanation
Indices: 5933510--5933536 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5933500 TAGCAAAATT
5933510 TTAAGGCACGAAA
1 TTAAGGCACGAAA
5933523 TTAAGGCACGAAA
1 TTAAGGCACGAAA
5933536 T
1 T
5933537 AATTAGTAGG
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:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (13 bp):
TTAAGGCACGAAA
Found at i:5934337 original size:7 final size:7
Alignment explanation
Indices: 5934325--5934349 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5934315 AATTCATTTA
5934325 AAAAAAT
1 AAAAAAT
5934332 AAAAAAT
1 AAAAAAT
5934339 AAAAAAT
1 AAAAAAT
5934346 AAAA
1 AAAA
5934350 TAAAACCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:5934941 original size:21 final size:21
Alignment explanation
Indices: 5934915--5934954 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5934905 ACGAGGCAAG
5934915 TGACGTGGCCCA-TTAACTAGC
1 TGACGTGG-CCAGTTAACTAGC
5934936 TGACGTGGCCAGTTAACTA
1 TGACGTGGCCAGTTAACTA
5934955 CCCACGGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
TGACGTGGCCAGTTAACTAGC
Found at i:5935421 original size:3 final size:3
Alignment explanation
Indices: 5935413--5935459 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5935403 TTAACAGTAA
5935413 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
5935460 ATAAAGATGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5936621 original size:16 final size:16
Alignment explanation
Indices: 5936602--5936635 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5936592 AAAAAATTCT
5936602 AAAAACGA-AAAACCC
1 AAAAACGATAAAACCC
5936617 AAAAACGATAAAACCC
1 AAAAACGATAAAACCC
5936633 AAA
1 AAA
5936636 TCAAAGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.68, C:0.24, G:0.06, T:0.03
Consensus pattern (16 bp):
AAAAACGATAAAACCC
Found at i:5943511 original size:12 final size:12
Alignment explanation
Indices: 5943494--5943526 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
5943484 TTCCCTGTAA
5943494 AATAGTAAAAAT
1 AATAGTAAAAAT
5943506 AATAGTAAAAAT
1 AATAGTAAAAAT
5943518 AATAGTAAA
1 AATAGTAAA
5943527 GGGAAAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AATAGTAAAAAT
Found at i:5944450 original size:10 final size:10
Alignment explanation
Indices: 5944431--5944480 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
5944421 TGAAATTCTA
5944431 AAAGATAAAT
1 AAAGATAAAT
5944441 ACAA-ATAAAT
1 A-AAGATAAAT
5944451 AAAGATAAAT
1 AAAGATAAAT
5944461 AAAGATAAAT
1 AAAGATAAAT
5944471 GAAA-ATAAAT
1 -AAAGATAAAT
5944481 CCTAAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.05
10 30 0.81
11 5 0.14
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Done.