Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 45 of 211
Found at i:12024365 original size:41 final size:41
Alignment explanation
Indices: 12024249--12024365 Score: 105
Period size: 41 Copynumber: 2.9 Consensus size: 41
12024239 TTGCATAAAA
* *
12024249 CACCGGCATAAAGCCTGCTAGGCA-CAAAGCCTG-A-TACATTT
1 CACCGGCATAAAGCCGGCTAGACATC-AAGCCTGAATTA-A-TT
* *
12024290 CACCGGCATAAAGCCTGCTAGACATCAAGTCTGAATTAATT
1 CACCGGCATAAAGCCGGCTAGACATCAAGCCTGAATTAATT
* * * * *
12024331 CATCGGCATCAAGCCGGCTAGGCATTAGGCCTGAA
1 CACCGGCATAAAGCCGGCTAGACATCAAGCCTGAA
12024366 AATCTCAGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 59 0.92
42 3 0.05
43 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (41 bp):
CACCGGCATAAAGCCGGCTAGACATCAAGCCTGAATTAATT
Found at i:12032240 original size:41 final size:41
Alignment explanation
Indices: 12032177--12032293 Score: 171
Period size: 41 Copynumber: 2.9 Consensus size: 41
12032167 GATGAATTTT
* * *
12032177 TCAGACTATAAATCTAGCAGGCTAAGTGCCGGTGATCGGAA
1 TCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATAGGAA
* * *
12032218 TCAGGTTATAAACCTAGCAGGCTACGTGCCGGTGATATGAA
1 TCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATAGGAA
*
12032259 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 TCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGA
12032294 ATATGTTAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (41 bp):
TCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATAGGAA
Found at i:12044484 original size:10 final size:9
Alignment explanation
Indices: 12044468--12044509 Score: 75
Period size: 9 Copynumber: 4.6 Consensus size: 9
12044458 AATTATGAAA
12044468 TAAAAAATT
1 TAAAAAATT
12044477 TAAAAAAATT
1 T-AAAAAATT
12044487 TAAAAAATT
1 TAAAAAATT
12044496 TAAAAAATT
1 TAAAAAATT
12044505 TAAAA
1 TAAAA
12044510 TTTATTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 23 0.72
10 9 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAAATT
Found at i:12044517 original size:19 final size:19
Alignment explanation
Indices: 12044471--12044519 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
12044461 TATGAAATAA
12044471 AAAATTTA--AAAAAATTT
1 AAAATTTATTAAAAAATTT
**
12044488 AAAAAAT-TTAAAAAATTT
1 AAAATTTATTAAAAAATTT
12044506 AAAATTTATTAAAA
1 AAAATTTATTAAAA
12044520 TTTAGTCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.20
18 14 0.56
19 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTTATTAAAAAATTT
Found at i:12047551 original size:126 final size:126
Alignment explanation
Indices: 12047325--12047613 Score: 454
Period size: 126 Copynumber: 2.3 Consensus size: 126
12047315 GGCCAAATAA
* * *
12047325 GAACTACTGTAGCAAAAGAGTGTCCACGTGGGAGATTCTTTCAGTACTTTAGCTGACATTACATC
1 GAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTAGCTGACAATACATC
*
12047390 CTGCTTGAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCA-
66 CTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAT
* * *
12047450 GAAACTACTGTAGCAAAAGAACGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCAT
1 G-AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTAGCTGACAATACAT
* * * *
12047515 TCTGCTTAAAGCGTTTTTGACATTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTCAT
65 CCTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAT
*
12047577 GAACTACTGTAGCAAAAGAGCGTTCACGTGGGAGCTT
1 GAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
12047614 TTTAAAATTA
Statistics
Matches: 149, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
125 1 0.01
126 147 0.99
127 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (126 bp):
GAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTAGCTGACAATACATC
CTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAT
Found at i:12047760 original size:96 final size:96
Alignment explanation
Indices: 12047647--12047925 Score: 438
Period size: 96 Copynumber: 2.9 Consensus size: 96
12047637 TTAACCCTGG
**
12047647 ACCCCAAACCCTAATTTATTTAAATTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTT
1 ACCCCAAACCCTAATTTATTTATTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTT
12047712 TTTTAAAATTTATAATTAATTTACTCAAGTA
66 TTTTAAAATTTATAATTAATTTACTCAAGTA
* * *
12047743 ACCCCAAACCCTAATTTATTTTATTTTTTTCTT-AAAACCTTAAACCCTAAACCTTAATCTAATT
1 ACCCCAAACCCTAATTTA-TTTATTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATT
*
12047807 TTTTTAAAATTTATAATTAATTCACTCAAGTA
65 TTTTTAAAATTTATAATTAATTTACTCAAGTA
* *
12047839 ACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAA-T
1 ACCCCAAACCCTAATTTATTT-ATTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATT
*
12047903 TTCTT-AAATTTATAATTAATTTA
65 TTTTTAAAATTTATAATTAATTTA
12047926 ATTAAGAAAC
Statistics
Matches: 167, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
95 20 0.12
96 110 0.66
97 37 0.22
ACGTcount: A:0.38, C:0.20, G:0.01, T:0.41
Consensus pattern (96 bp):
ACCCCAAACCCTAATTTATTTATTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTT
TTTTAAAATTTATAATTAATTTACTCAAGTA
Found at i:12047846 original size:53 final size:53
Alignment explanation
Indices: 12047693--12047853 Score: 164
Period size: 53 Copynumber: 3.2 Consensus size: 53
12047683 ACCTTAAACA
*
12047693 CTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACC
1 CTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTCACTCAAGTAACC
* * * ** *
12047746 CCAAACCCTAAT-TTATTTTATTT----TTT-T-CTTAAAAC-CT-TA--AACC
1 CTAAACCCTAATCTAATTTT-TTTAAAATTTATAATTAATTCACTCAAGTAACC
*
12047789 CTAAACCTTAATCTAATTTTTTTAAAATTTATAATTAATTCACTCAAGTAACC
1 CTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTCACTCAAGTAACC
12047842 CTAAACCCTAAT
1 CTAAACCCTAAT
12047854 TTATTTGATT
Statistics
Matches: 81, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
43 17 0.21
44 6 0.07
45 1 0.01
46 2 0.02
47 7 0.09
48 2 0.02
49 8 0.10
50 2 0.02
51 1 0.01
52 6 0.07
53 29 0.36
ACGTcount: A:0.38, C:0.20, G:0.01, T:0.41
Consensus pattern (53 bp):
CTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTCACTCAAGTAACC
Found at i:12053710 original size:29 final size:28
Alignment explanation
Indices: 12053668--12053724 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
12053658 ATTCCTCCCA
* * *
12053668 AAAAATTCTCTTCTTTCATTCTCTCTCT
1 AAAAACTCTCTTCTCTCACTCTCTCTCT
*
12053696 AAAAACTCTCATTCTCTCGCTCTCTCTCT
1 AAAAACTCTC-TTCTCTCACTCTCTCTCT
12053725 CTCTCTCTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.21, C:0.33, G:0.02, T:0.44
Consensus pattern (28 bp):
AAAAACTCTCTTCTCTCACTCTCTCTCT
Found at i:12053713 original size:2 final size:2
Alignment explanation
Indices: 12053708--12053756 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
12053698 AAACTCTCAT
*
12053708 TC TC TC GC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12053750 TC TC TC T
1 TC TC TC T
12053757 TTCTTCACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:12054111 original size:2 final size:2
Alignment explanation
Indices: 12054106--12054130 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12054096 TTTTTTTTTT
12054106 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
12054131 CTGTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12060162 original size:21 final size:21
Alignment explanation
Indices: 12060138--12060178 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12060128 TAACGGGGCC
12060138 GCTGATGTGG-CAAGTTAACTA
1 GCTGATGTGGCCAA-TTAACTA
12060159 GCTGATGTGGCCAATTAACT
1 GCTGATGTGGCCAATTAACT
12060179 TGTCACGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (21 bp):
GCTGATGTGGCCAATTAACTA
Found at i:12060584 original size:16 final size:17
Alignment explanation
Indices: 12060553--12060597 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
12060543 CCGATATAAT
* * *
12060553 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
12060570 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
12060586 AAATATTTTTAA
1 AAATATTTTTAA
12060598 AATACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:12060626 original size:30 final size:29
Alignment explanation
Indices: 12060592--12060691 Score: 114
Period size: 28 Copynumber: 3.3 Consensus size: 29
12060582 TTTAAAATAT
**
12060592 TTTTAAAATACTTTTTTTTTTATTTTTTAA
1 TTTTAAAATACTTTTTTAATT-TTTTTTAA
12060622 TTTTAAAATAC-TTTTTAATTTTTTTTAA
1 TTTTAAAATACTTTTTTAATTTTTTTTAA
*
12060650 TTTTAAAATA-TTTTTAAAATACTTTTTTTAA
1 TTTTAAAATACTTTTT-TAAT--TTTTTTTAA
12060681 TTTTTAAAATA
1 -TTTTAAAATA
12060692 AATTTTTGGT
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
28 22 0.35
29 10 0.16
30 11 0.18
31 9 0.15
32 10 0.16
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTAAAATACTTTTTTAATTTTTTTTAA
Found at i:12060697 original size:21 final size:21
Alignment explanation
Indices: 12060659--12060698 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12060649 ATTTTAAAAT
**
12060659 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
12060680 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
12060699 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:12060705 original size:22 final size:21
Alignment explanation
Indices: 12060658--12060716 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
12060648 AATTTTAAAA
* *
12060658 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
12060678 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
12060701 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
12060717 GGGTCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:12062587 original size:18 final size:17
Alignment explanation
Indices: 12062566--12062609 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
12062556 TTAAAAAAAA
*
12062566 TATAAATTGTTGAATTTT
1 TATAAATT-TGGAATTTT
12062584 TATAAATATTGGAATTTT
1 TATAAAT-TTGGAATTTT
12062602 TATAAATT
1 TATAAATT
12062610 ACTTTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
TATAAATTTGGAATTTT
Found at i:12066484 original size:20 final size:21
Alignment explanation
Indices: 12066459--12066509 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
12066449 AAGTTTTATA
*
12066459 ATATATATTCATTA-TAACAT
1 ATATATATTCAATAGTAACAT
* *
12066479 ATATATGTACAATAGTTAACAT
1 ATATATATTCAATAG-TAACAT
12066501 ATATATATT
1 ATATATATT
12066510 TACATATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 11 0.46
22 13 0.54
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (21 bp):
ATATATATTCAATAGTAACAT
Found at i:12073776 original size:47 final size:48
Alignment explanation
Indices: 12073724--12073825 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 48
12073714 TCATTTTTTC
* *
12073724 CTTTTTCTAATTTT-TTTATTTATTTGTCCTTT-TTTGTTTTTTATTT
1 CTTTTTCTAATTTTATTTATTTATTTCTCCTTTATTTATTTTTTATTT
*
12073770 ACTTTTTC-AGTTTTATTTATTTATTTCTCCTTTATTTATTTTTTATTT
1 -CTTTTTCTAATTTTATTTATTTATTTCTCCTTTATTTATTTTTTATTT
12073818 CTTTTTCT
1 CTTTTTCT
12073826 TTATTTCTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
46 5 0.10
47 31 0.63
48 13 0.27
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.74
Consensus pattern (48 bp):
CTTTTTCTAATTTTATTTATTTATTTCTCCTTTATTTATTTTTTATTT
Found at i:12073796 original size:19 final size:18
Alignment explanation
Indices: 12073762--12073813 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
12073752 CTTTTTTGTT
* *
12073762 TTTTATTTACTTTTTCAG
1 TTTTATTTATTTTTTCAC
*
12073780 TTTTATTTATTTATTTCTC
1 TTTTATTTATTT-TTTCAC
*
12073799 CTTTATTTATTTTTT
1 TTTTATTTATTTTTT
12073814 ATTTCTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTATTTATTTTTTCAC
Found at i:12073841 original size:15 final size:14
Alignment explanation
Indices: 12073811--12073837 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12073801 TTATTTATTT
12073811 TTTATTTCTTTTTC
1 TTTATTTCTTTTTC
12073825 TTTATTTCTTTTT
1 TTTATTTCTTTTT
12073838 TCTTCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTCTTTTTC
Found at i:12073848 original size:25 final size:25
Alignment explanation
Indices: 12073735--12073847 Score: 85
Period size: 25 Copynumber: 4.6 Consensus size: 25
12073725 TTTTTCTAAT
* * *
12073735 TTTTTTATTTATTTGTCCTTT-TTTG
1 TTTTTTATTTCTTT-TTCTTTATTTA
**
12073760 TTTTTTATTTACTTTTTCAGT-TTTA
1 TTTTTTATTT-CTTTTTCTTTATTTA
*
12073785 TTTATTTATTTC---TCCTTTATTTA
1 TTT-TTTATTTCTTTTTCTTTATTTA
*
12073808 TTTTTTATTTCTTTTTCTTTATTTC
1 TTTTTTATTTCTTTTTCTTTATTTA
*
12073833 TTTTTT-CTTCTTTTT
1 TTTTTTATTTCTTTTT
12073848 TATTTGTTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
22 11 0.15
23 7 0.10
24 8 0.11
25 35 0.49
26 10 0.14
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (25 bp):
TTTTTTATTTCTTTTTCTTTATTTA
Found at i:12073848 original size:36 final size:34
Alignment explanation
Indices: 12073690--12073852 Score: 114
Period size: 36 Copynumber: 4.6 Consensus size: 34
12073680 TCCAACAACC
*
12073690 TTTTCTTTATTTTTTATTTGTTTTTCATTTTTTCCT
1 TTTTCTTTATTTTTTATTT-TTTTTC-TTTTTTCTT
* * *
12073726 TTTTC-TAATTTTTTTATTTATTTGTCCTTTTTTGTT
1 TTTTCTTTA-TTTTTTATTT-TTT-TTCTTTTTTCTT
* * * * *
12073762 TTTTATTTACTTTTTCAGTTTTATTTATTTATTTCTC
1 TTTTCTTTA-TTTTTTA-TTTTTTTTCTTT-TTTCTT
* *
12073799 CTTTATTTATTTTTTATTTCTTTTTCTTTATTTCTT
1 TTTTCTTTATTTTTTATTT-TTTTTCTTT-TTTCTT
*
12073835 TTTTC-TTCTTTTTTATTT
1 TTTTCTTTATTTTTTATTT
12073853 GTTTAATAAT
Statistics
Matches: 99, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
35 17 0.17
36 55 0.56
37 24 0.24
38 3 0.03
ACGTcount: A:0.11, C:0.10, G:0.02, T:0.76
Consensus pattern (34 bp):
TTTTCTTTATTTTTTATTTTTTTTCTTTTTTCTT
Found at i:12074357 original size:7 final size:7
Alignment explanation
Indices: 12074345--12074384 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
12074335 TAGTAAGGTA
*
12074345 TTTATAG
1 TTTATAT
12074352 TTTATAT
1 TTTATAT
*
12074359 TTTGTAT
1 TTTATAT
12074366 TTTATAT
1 TTTATAT
12074373 TTTATAT
1 TTTATAT
12074380 TTTAT
1 TTTAT
12074385 TGTTATTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (7 bp):
TTTATAT
Found at i:12076246 original size:3 final size:3
Alignment explanation
Indices: 12076228--12076275 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
12076218 CAAATTTTGG
* * * *
12076228 ATT ATC ATT GTT ATT ATT ATT GTT ATT ATT ATT ATT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12076276 TATTCGTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:12080607 original size:13 final size:13
Alignment explanation
Indices: 12080589--12080634 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
12080579 AGATCCGATC
12080589 AAAAAATATTTCA
1 AAAAAATATTTCA
**
12080602 AAAAAATCAAAATCA
1 AAAAAAT--ATTTCA
12080617 AAAAAATATTTCA
1 AAAAAATATTTCA
12080630 AAAAA
1 AAAAA
12080635 TGAAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 16 0.59
15 11 0.41
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAAAATATTTCA
Found at i:12080641 original size:9 final size:9
Alignment explanation
Indices: 12080629--12080658 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
12080619 AAAATATTTC
12080629 AAAAAATGA
1 AAAAAATGA
12080638 AAAAAATGA
1 AAAAAATGA
12080647 AAAAAATGA
1 AAAAAATGA
12080656 AAA
1 AAA
12080659 TGAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:12080681 original size:17 final size:17
Alignment explanation
Indices: 12080661--12080697 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12080651 AATGAAAATG
*
12080661 AAGAAAAAGAGAAGAAA
1 AAGAAAAAGAAAAGAAA
*
12080678 AAGAAAAGGAAAAGAAA
1 AAGAAAAAGAAAAGAAA
12080695 AAG
1 AAG
12080698 GAGATGCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAAGAAA
Found at i:12080682 original size:9 final size:10
Alignment explanation
Indices: 12080629--12080682 Score: 53
Period size: 9 Copynumber: 5.7 Consensus size: 10
12080619 AAAATATTTC
12080629 AAAA-AATGA
1 AAAAGAATGA
12080638 AAAA-AATGA
1 AAAAGAATGA
12080647 AAAA-AATGA
1 AAAAGAATGA
*
12080656 AAATGAA-GA
1 AAAAGAATGA
*
12080665 AAAAGAGAAGA
1 AAAAGA-ATGA
12080676 AAAAGAA
1 AAAAGAA
12080683 AAGGAAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
9 28 0.70
10 4 0.10
11 8 0.20
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (10 bp):
AAAAGAATGA
Found at i:12080693 original size:11 final size:11
Alignment explanation
Indices: 12080661--12080695 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12080651 AATGAAAATG
*
12080661 AAGAAAAAGAG
1 AAGAAAAAGAA
12080672 AAGAAAAAGAA
1 AAGAAAAAGAA
*
12080683 AAGGAAAAGAA
1 AAGAAAAAGAA
12080694 AA
1 AA
12080696 AGGAGATGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:12082300 original size:66 final size:66
Alignment explanation
Indices: 12082194--12082331 Score: 276
Period size: 66 Copynumber: 2.1 Consensus size: 66
12082184 GGAAGTAGAT
12082194 TTAAGCCACCAGGCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTC
1 TTAAGCCACCAGGCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTC
12082259 C
66 C
12082260 TTAAGCCACCAGGCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTC
1 TTAAGCCACCAGGCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTC
12082325 C
66 C
12082326 TTAAGC
1 TTAAGC
12082332 AGTGGTTGAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (66 bp):
TTAAGCCACCAGGCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTC
C
Found at i:12082476 original size:51 final size:51
Alignment explanation
Indices: 12082348--12082476 Score: 118
Period size: 51 Copynumber: 2.5 Consensus size: 51
12082338 TGAGCAGATC
* * * * * *
12082348 GAAGGCAGCGAATCATATCTCTTTGGCGTTACAGTGGAACAGATTAAAGCT
1 GAAGGCTGCTAATCTTATCTCTCTGGCATTACAGCGGAACAGATTAAAGCT
* * * * * *
12082399 AAAGG-TAG-TGAATCTTGTTTCCCTGGCATTGCAGCGGAGCAGATTAAAGCT
1 GAAGGCT-GCT-AATCTTATCTCTCTGGCATTACAGCGGAACAGATTAAAGCT
12082450 GAAGGCTGCTAATCTTATCTCTCTGGC
1 GAAGGCTGCTAATCTTATCTCTCTGGC
12082477 CTTAAAGCTA
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
51 56 0.97
52 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (51 bp):
GAAGGCTGCTAATCTTATCTCTCTGGCATTACAGCGGAACAGATTAAAGCT
Found at i:12082840 original size:132 final size:132
Alignment explanation
Indices: 12082486--12082843 Score: 558
Period size: 132 Copynumber: 2.7 Consensus size: 132
12082476 CCTTAAAGCT
* * *
12082486 AAAGATAGTGAATCTTAT-TTTCCCAAGGTAGTAGGGAAGTAGATTTAAGCCACCAGTCTTATCT
1 AAAGATGGTGAATCTTATCTTT-CCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCT
* *
12082550 CCCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCTCTAAGCAGTAGTGAAGCAA
65 CCCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGAAGCAA
12082615 ATC
130 ATC
*
12082618 AAAGACGGTGAATCTTATC-TTCTCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCT
1 AAAGATGGTGAATCTTATCTTTC-CAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCT
* *
12082682 CCCTGAGCAACAGTAGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAA
65 CCCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGAAGCAA
12082747 ATC
130 ATC
* *
12082750 AAAGATGGTGAATCTTATCTTTCCAAGGTAGTAGAGAAGCAGATTTAAGCCACCAGTCCTATCTT
1 AAAGATGGTGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTC
** * *
12082815 CCTGAGCGGCAGTGGAGCAGCTTGAAGAT
66 CCTGAGCAACAGTGGAGTAGGTTGAAGAT
12082844 ACCAACTTTA
Statistics
Matches: 207, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
131 1 0.00
132 203 0.98
133 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (132 bp):
AAAGATGGTGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTC
CCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGAAGCAAA
TC
Found at i:12082876 original size:44 final size:44
Alignment explanation
Indices: 12082823--12082969 Score: 188
Period size: 44 Copynumber: 3.3 Consensus size: 44
12082813 TTCCTGAGCG
* *
12082823 GCAGTGGAGCAGCTTGAAGATACCAACTTTATCTCCTTGAAGTT
1 GCAGTGGAGCAGATTGAAGATACCAACTTTATCTCCCTGAAGTT
*
12082867 GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCCTGAAGTT
1 GCAGTGGAGCAGATTGAAGATACCAACTTTATCTCCCTGAAGTT
* ** * *
12082911 GCAGTGGAGCAGATTGAAGCTATTAA-TCCTATCACCCTGAAGTT
1 GCAGTGGAGCAGATTGAAGATACCAACT-TTATCTCCCTGAAGTT
* *
12082955 GAAGTGGAGCGGATT
1 GCAGTGGAGCAGATT
12082970 AAAATGATGA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 1 0.01
44 91 0.99
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (44 bp):
GCAGTGGAGCAGATTGAAGATACCAACTTTATCTCCCTGAAGTT
Found at i:12082983 original size:44 final size:44
Alignment explanation
Indices: 12082860--12082994 Score: 114
Period size: 44 Copynumber: 3.1 Consensus size: 44
12082850 TTTATCTCCT
* * * ** * *
12082860 TGAAGTTGCAGTGGAGCAGGTTGAAGATACCAA-CTTTATCTCCC
1 TGAAGTTGAAGTGGAGCAGATTGAAAATATGAATC-CTATCACCC
* ** *
12082904 TGAAGTTGCAGTGGAGCAGATTGAAGCTATTAATCCTATCACCC
1 TGAAGTTGAAGTGGAGCAGATTGAAAATATGAATCCTATCACCC
*
12082948 TGAAGTTGAAGTGGAGCGGATT-AAAATGATGAATCCTAT-ACCTC
1 TGAAGTTGAAGTGGAGCAGATTGAAAAT-ATGAATCCTATCACC-C
12082992 TGA
1 TGA
12082995 TATTGCAGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
43 6 0.08
44 70 0.91
45 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
TGAAGTTGAAGTGGAGCAGATTGAAAATATGAATCCTATCACCC
Found at i:12084199 original size:3 final size:3
Alignment explanation
Indices: 12084181--12084260 Score: 79
Period size: 3 Copynumber: 26.0 Consensus size: 3
12084171 CAAATTTTGG
* * * * * * *
12084181 ATT ATC ATT GTT ATT ATT ATT GTT ATT GTT GTT GTT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12084229 ATT ATT ATT ATT ATT ATT ATTT ATT AGTT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT
12084261 TATTTTCCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
3 61 0.91
4 6 0.09
ACGTcount: A:0.25, C:0.01, G:0.09, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12084263 original size:15 final size:13
Alignment explanation
Indices: 12084218--12084265 Score: 64
Period size: 12 Copynumber: 3.7 Consensus size: 13
12084208 GTTGTTGTTG
12084218 TTATTA-TTATTA
1 TTATTATTTATTA
12084230 TTATTA-TTATTA
1 TTATTATTTATTA
12084242 TTATTATTTATTA
1 TTATTATTTATTA
12084255 GTTATTTATTT
1 -TTA-TTATTT
12084266 TCCTTTGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 18 0.55
13 6 0.18
14 3 0.09
15 6 0.18
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:12087544 original size:33 final size:32
Alignment explanation
Indices: 12087465--12087547 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 32
12087455 AAATATAATT
* *
12087465 TTTTAAAATTTTAAATATAATTTTAAAAAACA
1 TTTTAATATTTTAAAAATAATTTTAAAAAACA
* * *
12087497 TTTGAATTTCTTTAAAAATAA-TTTAAAAAATTA
1 TTTTAATAT-TTTAAAAATAATTTTAAAAAA-CA
12087530 TATTTAATATTTTAAAAA
1 T-TTTAATATTTTAAAAA
12087548 ATTATATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
32 15 0.37
33 20 0.49
34 6 0.15
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (32 bp):
TTTTAATATTTTAAAAATAATTTTAAAAAACA
Found at i:12087569 original size:23 final size:22
Alignment explanation
Indices: 12087513--12087591 Score: 131
Period size: 22 Copynumber: 3.5 Consensus size: 22
12087503 TTTCTTTAAA
*
12087513 AATAATTTAAAAAATTATATTT
1 AATATTTTAAAAAATTATATTT
12087535 AATATTTTAAAAAATTATATTT
1 AATATTTTAAAAAATTATATTT
12087557 AATATTTTAAAAAATTATATTTT
1 AATATTTTAAAAAATTATA-TTT
*
12087580 AAAATTTTAAAA
1 AATATTTTAAAA
12087592 TATACATTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
22 40 0.74
23 14 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATTTTAAAAAATTATATTT
Found at i:12087601 original size:44 final size:44
Alignment explanation
Indices: 12087513--12087811 Score: 133
Period size: 45 Copynumber: 6.8 Consensus size: 44
12087503 TTTCTTTAAA
* *
12087513 AATAATTTAAAAAATTATATTTAATATTTTAAAAAATTATATTT
1 AATAATTTAAAAAATTATATTTAAAATTTTAAAAAATTACATTT
* *
12087557 AATATTTTAAAAAATTATATTTTAAAATTTTAAAATA-TACATTT
1 AATAATTTAAAAAATTATA-TTTAAAATTTTAAAAAATTACATTT
* * * *
12087601 AA-AATATTATAAAACA-AATA-AT-AAATTTGAAAAGCA-TATC-TTT
1 AATAAT-TTA-AAAA-ATTATATTTAAAATTTTAAAA-AATTA-CATTT
* * * * * *
12087644 AAAAATAATATTTATAAA-TAT-TTTATAATATTAAAAATTTATATTT
1 ---AATAAT-TTAAAAAATTATATTTAAAATTTTAAAAAATTACATTT
* * * * *
12087690 AA-AATTTTAAAAATAATATTT-AAATTTTTAAAAATAATATTT
1 AATAATTTAAAAAATTATATTTAAAATTTTAAAAAATTACATTT
* * * *
12087732 AA-AA-TTAAAAAA-TAAATTTAAAATTTTTTTAAAAATAATATTAT
1 AATAATTTAAAAAATTATATTTAAAA--TTTTAAAAAATTACATT-T
* * *
12087776 AAAAAATTTAAAATA-TACATTTAAAATTTTAAAAAA
1 -AATAATTTAAAAAATTATATTTAAAATTTTAAAAAA
12087812 ATAATAAACA
Statistics
Matches: 200, Mismatches: 32, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
40 5 0.03
41 17 0.09
42 35 0.17
43 31 0.16
44 31 0.16
45 37 0.19
46 21 0.10
47 23 0.12
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (44 bp):
AATAATTTAAAAAATTATATTTAAAATTTTAAAAAATTACATTT
Found at i:12087704 original size:41 final size:40
Alignment explanation
Indices: 12087653--12087814 Score: 125
Period size: 43 Copynumber: 3.9 Consensus size: 40
12087643 TAAAAATAAT
* *
12087653 ATTTATAAATAT-TTTATAA-TATTAAAAATTTATATTTAAA
1 ATTTAAAAATATATTTA-AATTATTAAAAA-TAATATTTAAA
*
12087693 ATTTTAAAAATAATATTTAAATTTTTAAAAATAATATTTAAA
1 A-TTTAAAAAT-ATATTTAAATTATTAAAAATAATATTTAAA
* * *
12087735 ATTAAAAAATAAATTTAAAATTTTTTTAAAAATAATATTATAAAAA
1 ATTTAAAAATATATTT-AAA--TTATTAAAAATAATATT-T--AAA
*
12087781 ATTTAAAATATACATTTAAAATT-TTAAAAA-AATA
1 ATTTAAAA-ATATATTT-AAATTATTAAAAATAATA
12087815 ATAAACAAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
40 6 0.06
41 19 0.18
42 15 0.14
43 33 0.32
44 8 0.08
45 2 0.02
46 10 0.10
47 11 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (40 bp):
ATTTAAAAATATATTTAAATTATTAAAAATAATATTTAAA
Found at i:12087708 original size:21 final size:21
Alignment explanation
Indices: 12087516--12087814 Score: 170
Period size: 21 Copynumber: 13.8 Consensus size: 21
12087506 CTTTAAAAAT
* *
12087516 AATTTAAAAAATTATATTTAA
1 AATTTTAAAAATAATATTTAA
* *
12087537 TATTTTAAAAAATTATATTTAA
1 AATTTT-AAAAATAATATTTAA
* *
12087559 TATTTTAAAAAATTATATTTTAA
1 AATTTT-AAAAATAATA-TTTAA
*
12087582 AATTTT-AAAATATACATTTAA
1 AATTTTAAAAATA-ATATTTAA
*
12087603 AATATTATAAAACA-AATA-AT-A
1 AAT-TT-TAAAA-ATAATATTTAA
* *
12087624 AATTTGAAAAGCAT-ATCTTTAAAAA
1 AATTTTAAAA--ATAATATTT---AA
* *
12087649 TAATATTTATAAAT-AT-TTTAT
1 -AAT-TTTAAAAATAATATTTAA
* *
12087670 AATATTAAAAATTTATATTTAA
1 AATTTTAAAAA-TAATATTTAA
12087692 AATTTTAAAAATAATATTTAA
1 AATTTTAAAAATAATATTTAA
*
12087713 ATTTTTAAAAATAATATTTAA
1 AATTTTAAAAATAATATTTAA
*
12087734 AA-TTAAAAAATAA-ATTTAA
1 AATTTTAAAAATAATATTTAA
12087753 AATTTTTTTAAAAATAATATTATAAA
1 AA---TTTTAAAAATAATATT-T-AA
* *
12087779 AAATTT-AAAATATACATTTAA
1 AATTTTAAAAATA-ATATTTAA
12087800 AATTTTAAAAA-AATA
1 AATTTTAAAAATAATA
12087815 ATAAACAAAT
Statistics
Matches: 224, Mismatches: 26, Indels: 57
0.73 0.08 0.19
Matches are distributed among these distances:
19 18 0.08
20 22 0.10
21 63 0.28
22 62 0.28
23 30 0.13
24 10 0.04
25 7 0.03
26 7 0.03
27 5 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (21 bp):
AATTTTAAAAATAATATTTAA
Found at i:12087804 original size:47 final size:43
Alignment explanation
Indices: 12087674--12087805 Score: 144
Period size: 43 Copynumber: 3.0 Consensus size: 43
12087664 TTTTATAATA
* *
12087674 TTAAAAATTTATATTTAAAATTTTAAAAATAATATTT-AAA--TTT
1 TTAAAAA-TAATATTTAAAA-TTAAAAAATAA-ATTTAAAATTTTT
12087717 TTAAAAATAATATTTAAAATTAAAAAATAAATTTAAAATTTTT
1 TTAAAAATAATATTTAAAATTAAAAAATAAATTTAAAATTTTT
* *
12087760 TTAAAAATAATATTATAAAAAATTTAAAATATACATTTAAAATTTT
1 TTAAAAATAATATT-T--AAAA-TTAAAAAATAAATTTAAAATTTT
12087806 AAAAAAATAA
Statistics
Matches: 78, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
40 4 0.05
41 13 0.17
42 11 0.14
43 24 0.31
44 1 0.01
46 4 0.05
47 21 0.27
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (43 bp):
TTAAAAATAATATTTAAAATTAAAAAATAAATTTAAAATTTTT
Found at i:12087845 original size:26 final size:26
Alignment explanation
Indices: 12087815--12087911 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 26
12087805 TAAAAAAATA
*
12087815 ATAAACAAATAAAAGAGAAATAAAGG
1 ATAAACAAATAAAAAAGAAATAAAGG
*
12087841 ATAAATAAATAATTGAAAAAGTAAATAAA-G
1 ATAAACAAAT-A---AAAAAG-AAATAAAGG
*
12087871 AAAAACAAATAAAAAACG-AA-AAAGG
1 ATAAACAAATAAAAAA-GAAATAAAGG
*
12087896 ACAAACAAATAAAAAA
1 ATAAACAAATAAAAAA
12087912 ATCATAAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
24 3 0.05
25 18 0.31
26 14 0.24
27 2 0.03
29 1 0.02
30 14 0.24
31 7 0.12
ACGTcount: A:0.72, C:0.05, G:0.10, T:0.12
Consensus pattern (26 bp):
ATAAACAAATAAAAAAGAAATAAAGG
Found at i:12087852 original size:15 final size:14
Alignment explanation
Indices: 12087832--12087883 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
12087822 AATAAAAGAG
*
12087832 AAATAAAGGATAAAT
1 AAATAAA-GAAAAAT
*
12087847 AAATAATTGAAAAAGT
1 AAATAA-AGAAAAA-T
*
12087863 AAATAAAGAAAAAC
1 AAATAAAGAAAAAT
12087877 AAATAAA
1 AAATAAA
12087884 AAACGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 7 0.23
15 17 0.55
16 7 0.23
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (14 bp):
AAATAAAGAAAAAT
Found at i:12089251 original size:11 final size:11
Alignment explanation
Indices: 12089235--12089297 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
12089225 CTTTTAAAAT
12089235 TTAAAAAATTA
1 TTAAAAAATTA
*
12089246 TTAAAAAATCA
1 TTAAAAAATTA
12089257 -T-AAAAATTA
1 TTAAAAAATTA
*
12089266 TAAAAAAAATTA
1 T-TAAAAAATTA
*
12089278 -TAAAAATTTTA
1 TTAAAAA-ATTA
12089289 TTAAAAAAT
1 TTAAAAAAT
12089298 AACAAGACCT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
9 7 0.17
10 6 0.15
11 14 0.34
12 14 0.34
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
TTAAAAAATTA
Found at i:12089262 original size:21 final size:21
Alignment explanation
Indices: 12089236--12089297 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
12089226 TTTTAAAATT
12089236 TAAAAAATTATTAAAAAATCA
1 TAAAAAATTATTAAAAAATCA
* *
12089257 T-AAAAATTATAAAAAAAATTA
1 TAAAAAATTAT-TAAAAAATCA
*
12089278 TAAAAATTTTATTAAAAAAT
1 TAAAAA-ATTATTAAAAAAT
12089298 AACAAGACCT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.26
21 10 0.29
22 11 0.32
23 4 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAAAAATTATTAAAAAATCA
Found at i:12089275 original size:12 final size:12
Alignment explanation
Indices: 12089258--12089283 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12089248 AAAAAATCAT
12089258 AAAAATTATAAA
1 AAAAATTATAAA
12089270 AAAAATTATAAA
1 AAAAATTATAAA
12089282 AA
1 AA
12089284 TTTTATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:12090691 original size:23 final size:23
Alignment explanation
Indices: 12090665--12090724 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
12090655 AAAAGACAGT
12090665 TGAACAATGAAGATTCTCT-GCGA
1 TGAACAATGAAGATTCTCTAGC-A
* * *
12090688 TGAATAGT-AAAATTCTCTAGCA
1 TGAACAATGAAGATTCTCTAGCA
12090710 TGAACAATGAAGATT
1 TGAACAATGAAGATT
12090725 TTCCGTAGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (23 bp):
TGAACAATGAAGATTCTCTAGCA
Found at i:12093558 original size:9 final size:9
Alignment explanation
Indices: 12093541--12093577 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12093531 TGAGTTTTCG
12093541 AATTCGAAT
1 AATTCGAAT
*
12093550 AACTCGAAT
1 AATTCGAAT
12093559 AATTCGAAT
1 AATTCGAAT
12093568 AATTCGAAT
1 AATTCGAAT
12093577 A
1 A
12093578 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12094714 original size:19 final size:19
Alignment explanation
Indices: 12094680--12094716 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12094670 GCTTTAGGGT
* *
12094680 TTTTAATTTTTTTTTGGGG
1 TTTTAATTTGTATTTGGGG
12094699 TTTTAATTTGTATTTGGG
1 TTTTAATTTGTATTTGGG
12094717 CTGAAGTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.22, T:0.65
Consensus pattern (19 bp):
TTTTAATTTGTATTTGGGG
Found at i:12097676 original size:113 final size:114
Alignment explanation
Indices: 12097530--12097765 Score: 282
Period size: 113 Copynumber: 2.1 Consensus size: 114
12097520 CAGATTCAAA
* * *
12097530 GACATTAGTGGCGCTTTAAAGAAAACGCCGCAAAAGA-GAAACATTAGCGACGCTTTCTACAAAA
1 GACATTAGTGGCGATTTAAAGAAAACGCCGCAAAAGATCAAACATTAGCGACGCGTTC-ACAAAA
* *
12097594 GCGCCGCAAAAGTGATTAACAGACGATG-C-CGTATTGATTTACGTTTGAT
65 GCGCCGCAAAACTGATTAACAGACGACGACTCGT-TTGATTTACGTTTGAT
* * *** * *
12097643 GACATTAGTGGC-ATTTATAAGTAAACGTCGCAAAAGATCATGTATTCGCGGCGCGTTCACAAAA
1 GACATTAGTGGCGATTTA-AAGAAAACGCCGCAAAAGATCAAACATTAGCGACGCGTTCACAAAA
* * *
12097707 GCGCCGCAGATCTGATTAACAGACGACGACTTGTTTGATTTACGTTTGAT
65 GCGCCGCAAAACTGATTAACAGACGACGACTCGTTTGATTTACGTTTGAT
12097757 GACATTAGT
1 GACATTAGT
12097766 AGCGTTTTCG
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
112 4 0.04
113 59 0.57
114 39 0.38
115 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (114 bp):
GACATTAGTGGCGATTTAAAGAAAACGCCGCAAAAGATCAAACATTAGCGACGCGTTCACAAAAG
CGCCGCAAAACTGATTAACAGACGACGACTCGTTTGATTTACGTTTGAT
Found at i:12098580 original size:21 final size:21
Alignment explanation
Indices: 12098498--12098581 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
12098488 ATGCATTGGC
*
12098498 GGTTTAGGGATTATGGATTT-A
1 GGTTTAGGGTTTATGG-TTTAA
* * *
12098519 GGTCTTACGGTTTATTGTTTAT
1 GGT-TTAGGGTTTATGGTTTAA
* *
12098541 TGTTTAAGGGTTGA-GGTTTAA
1 GGTTT-AGGGTTTATGGTTTAA
*
12098562 GGTTTAGGGTTTATAGTTTA
1 GGTTTAGGGTTTATGGTTTA
12098582 TATATATTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
20 7 0.15
21 22 0.47
22 18 0.38
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (21 bp):
GGTTTAGGGTTTATGGTTTAA
Found at i:12098974 original size:21 final size:21
Alignment explanation
Indices: 12098918--12098980 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
12098908 TCTAGGTCAA
*
12098918 TTTAGGG-TTAAGGGTTTAATG
1 TTTAGGGTTTAA-GGTTTAAGG
* *
12098939 TTAAGGGTTAAAGGTTTAAGG
1 TTTAGGGTTTAAGGTTTAAGG
*
12098960 TTTAGGGTTTAAGGTCTAAGG
1 TTTAGGGTTTAAGGTTTAAGG
12098981 AATATAGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.33, T:0.38
Consensus pattern (21 bp):
TTTAGGGTTTAAGGTTTAAGG
Found at i:12098979 original size:7 final size:7
Alignment explanation
Indices: 12098925--12098980 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
12098915 CAATTTAGGG
12098925 TTAAGGGT
1 TTAA-GGT
*
12098933 TTAATG-
1 TTAAGGT
12098939 TTAAGGGT
1 TTAA-GGT
*
12098947 TAAAGGT
1 TTAAGGT
12098954 TTAAGGT
1 TTAAGGT
*
12098961 TTAGGGT
1 TTAAGGT
12098968 TTAAGGT
1 TTAAGGT
*
12098975 CTAAGG
1 TTAAGG
12098981 AATATAGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
6 4 0.10
7 28 0.72
8 7 0.18
ACGTcount: A:0.29, C:0.02, G:0.32, T:0.38
Consensus pattern (7 bp):
TTAAGGT
Found at i:12101949 original size:9 final size:9
Alignment explanation
Indices: 12101931--12102022 Score: 130
Period size: 9 Copynumber: 10.2 Consensus size: 9
12101921 CTTATATATA
*
12101931 AACTTGCAT
1 AACTTACAT
12101940 AACTTACAT
1 AACTTACAT
* *
12101949 AAATTAAAT
1 AACTTACAT
12101958 AACTTACAT
1 AACTTACAT
12101967 AACTTACAT
1 AACTTACAT
* *
12101976 AAATTAAAT
1 AACTTACAT
12101985 AACTTACAT
1 AACTTACAT
12101994 AACTTACAT
1 AACTTACAT
*
12102003 AACTTAAAT
1 AACTTACAT
12102012 AACTTACAT
1 AACTTACAT
12102021 AA
1 AA
12102023 TACATAAGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 72 1.00
ACGTcount: A:0.50, C:0.16, G:0.01, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:12101956 original size:54 final size:55
Alignment explanation
Indices: 12101867--12102029 Score: 205
Period size: 54 Copynumber: 3.0 Consensus size: 55
12101857 ATCATATCAT
* *
12101867 AACTTATATATAAACTTACATAA--TACATAAGTTAAATAACATAC-AATACATA
1 AACTTATATATAAACTTACATAACTTACATAAATTAAATAACTTACAAATACATA
*
12101919 AACTTATATATAAACTTGCATAACTTACATAAATTAAATAACTTACATAACTTACATA
1 AACTTATATATAAACTTACATAACTTACATAAATTAAATAACTTACA-AA--TACATA
*
12101977 AA-TTA-A-AT-AACTTACATAACTTACATAACTTAAATAACTTACATAATACATA
1 AACTTATATATAAACTTACATAACTTACATAAATTAAATAACTTACA-AATACATA
12102029 A
1 A
12102030 GTTTACTTAC
Statistics
Matches: 100, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
52 29 0.29
54 55 0.55
55 2 0.02
56 3 0.03
57 3 0.03
58 8 0.08
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.33
Consensus pattern (55 bp):
AACTTATATATAAACTTACATAACTTACATAAATTAAATAACTTACAAATACATA
Found at i:12101967 original size:27 final size:25
Alignment explanation
Indices: 12101879--12102029 Score: 162
Period size: 27 Copynumber: 5.7 Consensus size: 25
12101869 CTTATATATA
*
12101879 AACTTACATAATACATAAGTTAAAT
1 AACTTACATAATACATAAATTAAAT
*
12101904 AACATAC--AATACATAAACTTATATAT
1 AACTTACATAATACATAAA-TTA-A-AT
*
12101930 AAACTTGCATAACTTACATAAATTAAAT
1 -AACTTACATAA--TACATAAATTAAAT
12101958 AACTTACATAACTTACATAAATTAAAT
1 AACTTACATAA--TACATAAATTAAAT
*
12101985 AACTTACATAACTTACATAACTTAAAT
1 AACTTACATAA--TACATAAATTAAAT
12102012 AACTTACATAATACATAA
1 AACTTACATAATACATAA
12102030 GTTTACTTAC
Statistics
Matches: 112, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.08
24 3 0.03
25 14 0.12
26 2 0.02
27 68 0.61
28 2 0.02
29 3 0.03
30 3 0.03
31 8 0.07
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (25 bp):
AACTTACATAATACATAAATTAAAT
Found at i:12105242 original size:41 final size:41
Alignment explanation
Indices: 12105194--12105352 Score: 205
Period size: 41 Copynumber: 3.9 Consensus size: 41
12105184 GTGAAATTAT
* * *
12105194 TCAGACTATACGTCTAGCAGGCTAAGTGTCGGTGAATTGAA
1 TCAGGCTATACGCCTAGCAGGCTAAGTGCCGGTGAATTGAA
*
12105235 TC-GGACTATACGTCC-AGCAGGCTAAGTGCCGGTGAGTTGAA
1 TCAGG-CTATACG-CCTAGCAGGCTAAGTGCCGGTGAATTGAA
* * * *
12105276 TCAGGCTACAAGCCTAGCAGGCTAAGTGCTGGTGAACTGAA
1 TCAGGCTATACGCCTAGCAGGCTAAGTGCCGGTGAATTGAA
*
12105317 TCAGGCTATAGGCCTAGCAGGCTAAGTGCCGGTGAA
1 TCAGGCTATACGCCTAGCAGGCTAAGTGCCGGTGAA
12105353 CGGAATTAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
40 3 0.03
41 96 0.94
42 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (41 bp):
TCAGGCTATACGCCTAGCAGGCTAAGTGCCGGTGAATTGAA
Found at i:12105353 original size:41 final size:41
Alignment explanation
Indices: 12105207--12105393 Score: 200
Period size: 41 Copynumber: 4.6 Consensus size: 41
12105197 GACTATACGT
* * *
12105207 CTAGCAGGCTAAGTGTCGGTGAATTGAATC-GGACTATACGTC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGG-CTATAAG-C
** *
12105249 C-AGCAGGCTAAGTGCCGGTGAGTTGAATCAGGCTACAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
* *
12105289 CTAGCAGGCTAAGTGCTGGTGAACTGAATCAGGCTATAGGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
* * **
12105330 CTAGCAGGCTAAGTGCCGGTGAACGGAATTAAACTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
* *
12105371 CTATCAGG-TGAAGTGCCAGTGAA
1 CTAGCAGGCT-AAGTGCCGGTGAA
12105394 TCTGTTTAAA
Statistics
Matches: 125, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.02
41 119 0.95
42 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
Found at i:12106758 original size:21 final size:20
Alignment explanation
Indices: 12106732--12106797 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 20
12106722 CAACTTAAAA
*
12106732 CAGAGGCGGCAGCGAGGGAAG
1 CAGAGGC-GCAGCGAGAGAAG
*
12106753 CAGAGGCTGCAACGAGAGAAG
1 CAGAGGC-GCAGCGAGAGAAG
12106774 CAGAGGTCGCAGCGAGAGAAG
1 CAGAGG-CGCAGCGAGAGAAG
12106795 CAG
1 CAG
12106798 CGAGAGAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.44, T:0.03
Consensus pattern (20 bp):
CAGAGGCGCAGCGAGAGAAG
Found at i:12106799 original size:12 final size:12
Alignment explanation
Indices: 12106782--12106809 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12106772 AGCAGAGGTC
12106782 GCAGCGAGAGAA
1 GCAGCGAGAGAA
12106794 GCAGCGAGAGAA
1 GCAGCGAGAGAA
12106806 GCAG
1 GCAG
12106810 AGGTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:12107348 original size:42 final size:42
Alignment explanation
Indices: 12107245--12107539 Score: 267
Period size: 43 Copynumber: 7.0 Consensus size: 42
12107235 GTTTGTGAAA
* * * * ***
12107245 TAAGCGCCGCGAAAGAACACT-ACTTTTAGCGGTGTTTGTAGA
1 TAAGCGCCACTAAAGAACA-TGACTTTTAGCGGCGTTTTTTCC
* *
12107287 TGAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
1 T-AAGCGCCACTAAAGAACATGACTTTTAGCGGCGTTTTTT-CC
* * *
12107331 -AAGCGCCACTATAGAACATTACTTTTAGCGGTGTTTTTTCC
1 TAAGCGCCACTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
* * * * * *
12107372 TAAACGTCGCTAAAGATCATG-TTCTTTAGCGACGTTTTTTCC
1 TAAGCGCCACTAAAGAACATGACT-TTTAGCGGCGTTTTTTCC
* * *
12107414 AAAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTCC
1 TAAGCGCCACTAAAGAACATGACT-TTTAGCGGCG-TTTTTTCC
*
12107457 TAAGCGCCACTAAAGAACATGA-TCATTAGCGGCGTTTTTTTCC
1 TAAGCGCCACTAAAGAACATGACT-TTTAGCGGCG-TTTTTTCC
* *
12107500 TAAGCGCCACTAAAGAACATGACCTTTAACGGCGTTTTTT
1 TAAGCGCCACTAAAGAACATGACTTTTAGCGGCGTTTTTT
12107540 TCTGTAAGCG
Statistics
Matches: 216, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
41 3 0.01
42 101 0.47
43 112 0.52
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (42 bp):
TAAGCGCCACTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
Found at i:12107354 original size:85 final size:84
Alignment explanation
Indices: 12107246--12107558 Score: 274
Period size: 85 Copynumber: 3.7 Consensus size: 84
12107236 TTTGTGAAAT
* * * * ***
12107246 AAGCGCCGCGAAAGAACACTACTTTTAGCGGTGTTTGTAGATGAAGCGCCGCTAAAGAACATTAC
1 AAGCGCCACTAAAGAACATTACTTTTAGCGGTGTTTTTTCCT-AAGCGCCGCTAAAGAACATTAC
12107311 TTTTAGCGGCGTTTTTTACC-
65 TTTTAGCGGCGTTTTTT-CCA
* * * * *
12107331 AAGCGCCACTATAGAACATTACTTTTAGCGGTGTTTTTTCCTAAACGTCGCTAAAGATCATGTTC
1 AAGCGCCACTAAAGAACATTACTTTTAGCGGTGTTTTTTCCTAAGCGCCGCTAAAGAACAT-TAC
*
12107396 -TTTAGCGACGTTTTTTCCA
65 TTTTAGCGGCGTTTTTTCCA
* * * * * *
12107415 AAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTCCTAAGCGCCACTAAAGAACATGA
1 AAGCGCCACTAAAGAACATTACT-TTTAGCGGTG-TTTTTTCCTAAGCGCCGCTAAAGAACATTA
* *
12107479 -TCATTAGCGGCGTTTTTTTCCT
64 CT-TTTAGCGGCG-TTTTTTCCA
* * * * * *
12107501 AAGCGCCACTAAAGAACATGACCTTTAACGGCGTTTTTTTCTGTAAGCGCCGCAAAAG
1 AAGCGCCACTAAAGAACATTACTTTTAGCGGTG-TTTTTTC-CTAAGCGCCGCTAAAG
12107559 TTAGCGGCGT
Statistics
Matches: 185, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
83 3 0.02
84 57 0.31
85 68 0.37
86 44 0.24
87 13 0.07
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (84 bp):
AAGCGCCACTAAAGAACATTACTTTTAGCGGTGTTTTTTCCTAAGCGCCGCTAAAGAACATTACT
TTTAGCGGCGTTTTTTCCA
Found at i:12107470 original size:43 final size:43
Alignment explanation
Indices: 12107289--12107551 Score: 293
Period size: 43 Copynumber: 6.2 Consensus size: 43
12107279 TTTGTAGATG
* * *
12107289 AAGCGCCGCTAAAGAACATTA-CTTTTAGCGGCGTTTTTTACC-
1 AAGCGCCACTAAAGAACATGATC-TTTAGCGGCGTTTTTTTCCT
* * *
12107331 AAGCGCCACTATAGAACATTA-CTTTTAGCGGTG-TTTTTTCCT
1 AAGCGCCACTAAAGAACATGATC-TTTAGCGGCGTTTTTTTCCT
* * * * * * *
12107373 AAACGTCGCTAAAGATCATGTTCTTTAGCGACG-TTTTTTCCA
1 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCT
* *
12107415 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
1 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCT
*
12107458 AAGCGCCACTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
1 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCT
* * *
12107501 AAGCGCCACTAAAGAACATGACCTTTAACGGCGTTTTTTTCTGT
1 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-CT
12107545 AAGCGCC
1 AAGCGCC
12107552 GCAAAAGTTA
Statistics
Matches: 191, Mismatches: 26, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
41 7 0.04
42 87 0.46
43 89 0.47
44 8 0.04
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (43 bp):
AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCT
Found at i:12109633 original size:22 final size:21
Alignment explanation
Indices: 12109607--12109919 Score: 311
Period size: 22 Copynumber: 14.2 Consensus size: 21
12109597 AGAAATTATC
*
12109607 CAACATTCAGACAACATTTAAT
1 CAACATT-GGACAACATTTAAT
*
12109629 TAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
*
12109651 CAACAATTGGACAACATTCAAT
1 CAAC-ATTGGACAACATTTAAT
*
12109673 TAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
*
12109695 CAACAATTGGACAACATTCAAT
1 CAAC-ATTGGACAACATTTAAT
* *
12109717 CAATATTTGGACAGCATTTAAT
1 CAACA-TTGGACAACATTTAAT
* * *
12109739 CAACAATTGGACAGCACTAAAT
1 CAAC-ATTGGACAACATTTAAT
12109761 CAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
* * * *
12109783 CAAAAATTGGATAGCATTCAAT
1 C-AACATTGGACAACATTTAAT
*
12109805 CAATATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
* *
12109827 CAACAATTGGACAATATTAAAT
1 CAAC-ATTGGACAACATTTAAT
**
12109849 CAACATTTGGACAGTATTTAAT
1 CAACA-TTGGACAACATTTAAT
*
12109871 CAACAATTGGACAACATTCAAT
1 CAAC-ATTGGACAACATTTAAT
*
12109893 CAATATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
12109915 CAACA
1 CAACA
12109920 ATTTTTACTT
Statistics
Matches: 242, Mismatches: 36, Indels: 26
0.80 0.12 0.09
Matches are distributed among these distances:
21 8 0.03
22 224 0.93
23 10 0.04
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (21 bp):
CAACATTGGACAACATTTAAT
Found at i:12109644 original size:11 final size:11
Alignment explanation
Indices: 12109630--12109712 Score: 55
Period size: 11 Copynumber: 7.5 Consensus size: 11
12109620 ACATTTAATT
12109630 AACATTTGGAC
1 AACATTTGGAC
*
12109641 AACATTT-AATC
1 AACATTTGGA-C
*
12109652 AACAATTGGAC
1 AACATTTGGAC
** *
12109663 AACA-TTCAATT
1 AACATTTGGA-C
12109674 AACATTTGGAC
1 AACATTTGGAC
*
12109685 AACATTT-AATC
1 AACATTTGGA-C
*
12109696 AACAATTGGAC
1 AACATTTGGAC
12109707 AACATT
1 AACATT
12109713 CAATCAATAT
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
10 5 0.09
11 43 0.81
12 5 0.09
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (11 bp):
AACATTTGGAC
Found at i:12109664 original size:44 final size:44
Alignment explanation
Indices: 12109616--12109922 Score: 461
Period size: 44 Copynumber: 7.0 Consensus size: 44
12109606 CCAACATTCA
* *
12109616 GACAACATTTAATTAACATTTGGACAACATTTAATCAACAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
*
12109660 GACAACATTCAATTAACATTTGGACAACATTTAATCAACAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
* *
12109704 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
* * * *
12109748 GACAGCACTAAATCAACATTTGGACAACATTTAATCAAAAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
* * *
12109792 GATAGCATTCAATCAATATTTGGACAACATTTAATCAACAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
* * **
12109836 GACAATATTAAATCAACATTTGGACAGTATTTAATCAACAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
*
12109880 GACAACATTCAATCAATATTTGGACAACATTTAATCAACAATT
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATT
12109923 TTTACTTCAA
Statistics
Matches: 236, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 236 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (44 bp):
GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
Found at i:12110807 original size:42 final size:42
Alignment explanation
Indices: 12110701--12110856 Score: 129
Period size: 43 Copynumber: 3.6 Consensus size: 42
12110691 TCATACAATA
* * * * *
12110701 CCAACGTCCCAGACATGGTCTTTCATGTAATCAAACAACGATG
1 CCAACGTCCCAGACATGGTCTTACACGTAATCATA-AACTACG
*
12110744 CC-ACTGTCCCAGACA-GTGTCTTACACGTAATCATATACTACG
1 CCAAC-GTCCCAGACATG-GTCTTACACGTAATCATAAACTACG
* * * *
12110786 CCAATGTCCCAGATATGGTCTTACACGTAAATC-TCAAATTGAGG
1 CCAACGTCCCAGACATGGTCTTACACGT-AATCAT-AAACT-ACG
**
12110830 CCAACGTCCCAGATGTGGTCTTACACG
1 CCAACGTCCCAGACATGGTCTTACACG
12110857 ATGTCACATT
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
42 30 0.32
43 36 0.39
44 27 0.29
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (42 bp):
CCAACGTCCCAGACATGGTCTTACACGTAATCATAAACTACG
Found at i:12113620 original size:28 final size:28
Alignment explanation
Indices: 12113588--12113655 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
12113578 ATAAGATTTA
12113588 ATATTAAATTTAATCTAATATTAAATTG
1 ATATTAAATTTAATCTAATATTAAATTG
* * *
12113616 ATATTAGATTAAATTTAATATTAAATTG
1 ATATTAAATTTAATCTAATATTAAATTG
12113644 --ATTAAATTTAAT
1 ATATTAAATTTAAT
12113656 ATAGTTGAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 10 0.29
28 25 0.71
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (28 bp):
ATATTAAATTTAATCTAATATTAAATTG
Found at i:12117997 original size:20 final size:19
Alignment explanation
Indices: 12117949--12117998 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
12117939 TAACAGAAAT
*
12117949 TTATCCGTATCAACCGTAA
1 TTATCCATATCAACCGTAA
* *
12117968 CTTATACATATCAACGGTAA
1 -TTATCCATATCAACCGTAA
12117988 TTCATCCATAT
1 TT-ATCCATAT
12117999 AATTACATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (19 bp):
TTATCCATATCAACCGTAA
Found at i:12118200 original size:23 final size:23
Alignment explanation
Indices: 12118161--12118261 Score: 123
Period size: 23 Copynumber: 4.3 Consensus size: 23
12118151 AAGCTCATTC
*
12118161 CGAGCTGATAAACGGTAAACTCTAT
1 CGAGCTG--AAACGGTAAGCTCTAT
* *
12118186 CGAGCTGAAACGGTAAGTTCCAT
1 CGAGCTGAAACGGTAAGCTCTAT
*
12118209 AGAGCTGAAACGGTAAGCTCTAT
1 CGAGCTGAAACGGTAAGCTCTAT
*
12118232 AGAGCTGAAACGGTAAGCTC-AT
1 CGAGCTGAAACGGTAAGCTCTAT
12118254 ACGAGCTG
1 -CGAGCTG
12118262 TGGTGAGTCC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
22 2 0.03
23 59 0.87
25 7 0.10
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (23 bp):
CGAGCTGAAACGGTAAGCTCTAT
Found at i:12118222 original size:46 final size:46
Alignment explanation
Indices: 12118149--12118261 Score: 147
Period size: 46 Copynumber: 2.4 Consensus size: 46
12118139 GCCATGATCT
* *
12118149 GTAAGCTCATTCCGAGCTGATAAACGGTAAACTCTATCGAGCTGAAACG
1 GTAAGCTCA-TACGAGCTG--AAACGGTAAACTCTATAGAGCTGAAACG
* *
12118198 GTAAGTTCCATA-GAGCTGAAACGGTAAGCTCTATAGAGCTGAAACG
1 GTAAGCT-CATACGAGCTGAAACGGTAAACTCTATAGAGCTGAAACG
12118244 GTAAGCTCATACGAGCTG
1 GTAAGCTCATACGAGCTG
12118262 TGGTGAGTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
45 4 0.07
46 38 0.67
48 6 0.11
49 7 0.12
50 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (46 bp):
GTAAGCTCATACGAGCTGAAACGGTAAACTCTATAGAGCTGAAACG
Found at i:12119710 original size:24 final size:24
Alignment explanation
Indices: 12119678--12119733 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
12119668 GGCTCAAGTG
12119678 GCCCAAATACAAAATTAACCCTAA
1 GCCCAAATACAAAATTAACCCTAA
12119702 GCCCAAATACAAAATTAACCCTAA
1 GCCCAAATACAAAATTAACCCTAA
12119726 GCCCAAAT
1 GCCCAAAT
12119734 CAACAGTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.30, G:0.05, T:0.16
Consensus pattern (24 bp):
GCCCAAATACAAAATTAACCCTAA
Found at i:12123417 original size:24 final size:25
Alignment explanation
Indices: 12123380--12123432 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
12123370 TCTTTTTGCA
* *
12123380 TTCATTCCATTCATCTGCATTACAT
1 TTCATTACATTCATCTGCATTAAAT
*
12123405 TTCATTACA-TCATTTGCATTAAAT
1 TTCATTACATTCATCTGCATTAAAT
12123429 TTCA
1 TTCA
12123433 CAAAAGAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (25 bp):
TTCATTACATTCATCTGCATTAAAT
Found at i:12126559 original size:8 final size:9
Alignment explanation
Indices: 12126540--12126585 Score: 55
Period size: 8 Copynumber: 5.6 Consensus size: 9
12126530 AAAATATTCT
12126540 AAAAA-AAG
1 AAAAATAAG
12126548 -AAAATAA-
1 AAAAATAAG
12126555 AAAAATAAG
1 AAAAATAAG
*
12126564 AAAAAGAAG
1 AAAAATAAG
12126573 AAAAA-AAG
1 AAAAATAAG
12126581 AAAAA
1 AAAAA
12126586 GAAATGAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 4 0.12
8 17 0.50
9 13 0.38
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (9 bp):
AAAAATAAG
Found at i:12126573 original size:9 final size:9
Alignment explanation
Indices: 12126555--12126588 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
12126545 AAGAAAATAA
*
12126555 AAAAATAAG
1 AAAAAGAAG
12126564 AAAAAGAAG
1 AAAAAGAAG
12126573 AAAAA-AAG
1 AAAAAGAAG
12126581 AAAAAGAA
1 AAAAAGAA
12126589 ATGAAAGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:12126576 original size:17 final size:17
Alignment explanation
Indices: 12126540--12126588 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
12126530 AAAATATTCT
12126540 AAAAAAAGAAAATA-AA-
1 AAAAAAAGAAAA-AGAAG
*
12126556 AAAATAAGAAAAAGAAG
1 AAAAAAAGAAAAAGAAG
12126573 AAAAAAAGAAAAAGAA
1 AAAAAAAGAAAAAGAA
12126589 ATGAAAGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 1 0.03
16 13 0.45
17 15 0.52
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (17 bp):
AAAAAAAGAAAAAGAAG
Found at i:12127653 original size:100 final size:100
Alignment explanation
Indices: 12127474--12128528 Score: 1106
Period size: 100 Copynumber: 10.7 Consensus size: 100
12127464 AAGGTTACAG
* * * *
12127474 TTAAAAAGATTGAAGCCACAAC-GACGAATCTTACTTCCCTAGCGGTGTAGTGGAACAAATTGAA
1 TTAAAAAGATTGAAGCCACAACAG-TGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAA
** *
12127538 GCTACAATTATGAATCTTGCTCCCCCGACATTGCAA
65 GCTACAACGATGAATCTTGCTTCCCCGACATTGCAA
* * * *
12127574 TTAAAAAGATTGAAGCTATAACATTGAATTTTACTTCCCTGGCGGTGCAGT-GAAGCAGATTGAA
1 TTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCGGTGCAGTGGAA-CAGATTGAA
* * ** ** * *
12127638 ACTACAATGGCGAATCTTGCTTTGCTGACTTTGCAA
65 GCTACAACGATGAATCTTGCTTCCCCGACATTGCAA
* * * * *
12127674 TTAAAAAGATTGAAGCCACAACTGTGAATCTTACTTCCCTGGTGGTACAGTGGAGCAGATTAAAG
1 TTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAG
* * *
12127739 CTACAACGGCT-AATCTTACTTCCCCGACATTACAA
66 CTACAAC-GATGAATCTTGCTTCCCCGACATTGCAA
* * * * *
12127774 TTAAAAAGATTGAATCTACAATAGTAAATCTTACTTCTCTGGCGGTGCAGTGGAACAGATTGAAG
1 TTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAG
* *
12127839 CTATAACGATGAATCTTGCTTCCTCGACATTGCAA
66 CTACAACGATGAATCTTGCTTCCCCGACATTGCAA
* ** * *
12127874 TTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTTTCTGGTGGTGCAGTGGAGCAGATTGAAG
1 TTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAG
* * *
12127939 CTACAACGACT-AATCTTGTTTTCCCGACATTGCAG
66 CTACAACGA-TGAATCTTGCTTCCCCGACATTGCAA
* * * * *
12127974 TTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCT----GTACAGTAGAATAGATTGAAG
1 TTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAG
* *
12128035 CTACAACGGTGAATATTGCTTCCCCGACATTGCAA
66 CTACAACGATGAATCTTGCTTCCCCGACATTGCAA
* * * * * *
12128070 TTAAAAAGGTTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTAGATCATATTGAAG
1 TTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAG
* * *
12128135 CTACAAC-AGTAAATCTTACTTCTCCGACATTGCAA
66 CTACAACGA-TGAATCTTGCTTCCCCGACATTGCAA
* * *
12128170 TTAAAAAGATTGAAGCCACAAC-GACGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGATTGAA
1 TTAAAAAGATTGAAGCCACAACAG-TGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAA
* **
12128234 ACTACAACGACAAATCTTGCTTCCCCGACATTG---
65 GCTACAACGATGAATCTTGCTTCCCCGACATTGCAA
* * *
12128267 -T----A-ATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAG
1 TTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAG
* * *
12128326 CTACGACGATGAATCTTGTTTCCCCGACATTGCAG
66 CTACAACGATGAATCTTGCTTCCCCGACATTGCAA
* * * * ** ** *
12128361 TTAAATAGATTAAAGCTACTAC-GACAAATCTTACTTCCCTGGCGGTATAGTGGAATAGATTGAA
1 TTAAAAAGATTGAAGCCACAACAG-TGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAA
* * * * *
12128425 GCTACGACGGTGAATCTTGTTTCCTCGACATTGCAG
65 GCTACAACGATGAATCTTGCTTCCCCGACATTGCAA
* * * * *
12128461 TTAAATAGATTGAAGCTACAACAGTGAATCTTACTTCCCTGGCGGTACAGTGGAACATATTAAAG
1 TTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAG
12128526 CTA
66 CTA
12128529 TAAATTACTG
Statistics
Matches: 796, Mismatches: 133, Indels: 52
0.81 0.14 0.05
Matches are distributed among these distances:
91 77 0.10
92 2 0.00
95 2 0.00
96 82 0.10
99 8 0.01
100 619 0.78
101 6 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (100 bp):
TTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAG
CTACAACGATGAATCTTGCTTCCCCGACATTGCAA
Found at i:12127734 original size:50 final size:50
Alignment explanation
Indices: 12127480--12128528 Score: 473
Period size: 50 Copynumber: 21.2 Consensus size: 50
12127470 ACAGTTAAAA
* ** * *
12127480 AGATTGAAGCCACAACGACGAATCTTACTTCCCTAGCGGTGTAGTGGAAC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* *** * * * * ** * ** *
12127530 AAATTGAAGCTACAATTATGAATCTTGCTCCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* ** *
12127580 AGATTGAAGCTATAACATTGAATTTTACTTCCCTGGCGGTGCAGT-GAAGC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAA-C
* * * * ** * ** * ** *
12127630 AGATTGAAACTACAATGGCGAATCTTGCTTTGCTGACTTTGCAATTAAAA
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * * *
12127680 AGATTGAAGCCACAACTGTGAATCTTACTTCCCTGGTGGTACAGTGGAGC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * ** * * ** *
12127730 AGATTAAAGCTACAACGGCT-AATCTTACTTCCCCGACATTACAATTAAAA
1 AGATTGAAGCTACAACGG-TGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* ** * *
12127780 AGATTGAATCTACAATAGTAAATCTTACTTCTCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * * ** * ** *
12127830 AGATTGAAGCTATAACGATGAATCTTGCTT-CCTCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCT-GGCGGTGCAGTGGAAC
* ** * *
12127880 AGATTGAAGCCACAACGGTGAATCTTACTTTTCTGGTGGTGCAGTGGAGC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* ** * ** ** *
12127930 AGATTGAAGCTACAACGACT-AATCTTGTTTTCCC-GACATTGCAGTTAAAA
1 AGATTGAAGCTACAACG-GTGAATCTT-ACTTCCCTGGCGGTGCAGTGGAAC
* * * * *
12127980 AGATTGAAGCTACAACAGCGAATCTTACTTCCCT----GTACAGTAGAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * * ** * ** *
12128026 AGATTGAAGCTACAACGGTGAATATTGCTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * * *
12128076 AGGTTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTAGATC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * * ** * ** *
12128126 ATATTGAAGCTACAACAGTAAATCTTACTTCTCC-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGTGAATCTTACTTC-CCTGGCGGTGCAGTGGAAC
* ** * *
12128176 AGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGGTGCAGTGGAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* *** * * * *
12128226 AGATTGAAACTACAACGACAAATCTTGCTTCCC---C-G-ACA-TTG--T
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* *
12128268 A-ATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * ** * * ** ** *
12128317 AGATTAAAGCTACGACGATGAATCTTGTTTCCCCGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * *** ** *
12128367 AGATTAAAGCTACTACGACAAATCTTACTTCCCTGGCGGTATAGTGGAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * * ** ** *
12128417 AGATTGAAGCTACGACGGTGAATCTT-GTTTCCTCGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCT-GGCGGTGCAGTGGAAC
* *
12128467 AGATTGAAGCTACAACAGTGAATCTTACTTCCCTGGCGGTACAGTGGAAC
1 AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* *
12128517 ATATTAAAGCTA
1 AGATTGAAGCTA
12128529 TAAATTACTG
Statistics
Matches: 711, Mismatches: 261, Indels: 54
0.69 0.25 0.05
Matches are distributed among these distances:
41 25 0.04
42 2 0.00
44 3 0.00
45 3 0.00
46 39 0.05
47 3 0.00
49 18 0.03
50 602 0.85
51 16 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
Found at i:12128699 original size:89 final size:89
Alignment explanation
Indices: 12128582--12128749 Score: 207
Period size: 89 Copynumber: 1.9 Consensus size: 89
12128572 CATATCAAAC
* * *
12128582 CTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAA-ATAACAAACCTTATCT-CTCTGAAGTTGC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGAT-ACAAACCATATCTCCT-TGAAGTTGC
*
12128645 AGTGAAGCAGGTTAAAGATACCCAAT
64 AGTGAAGCAGATTAAAGATACCCAAT
* * * *
12128671 CTTATCTCCCTGAAGTTGCTGT-GAAGCAGATTGAAGCTACTAATCATATCTCCTTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTAG-AGCAGATTGAAGATACAAACCATATCTCCTTGAAGTTGCA
*
12128735 GTGGAGCAGATTAAA
65 GTGAAGCAGATTAAA
12128750 ACGATGAATC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
88 1 0.01
89 63 0.94
90 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (89 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAACCATATCTCCTTGAAGTTGCAG
TGAAGCAGATTAAAGATACCCAAT
Found at i:12128743 original size:44 final size:44
Alignment explanation
Indices: 12128539--12128746 Score: 178
Period size: 44 Copynumber: 4.8 Consensus size: 44
12128529 TAAATTACTG
* * * *
12128539 ATCTTATCTCTTTGAAGTTGCAGT-AGAGCA-AAT-CATAT-CAA
1 ATCTTATCTCTCTGAAGTTGCAGTGA-AGCAGATTGAAGATACAA
* *
12128580 ACCTTATCTCTCTGAAGTTGCAGT-AGAGCAGGTTGAA-ATAACAA
1 ATCTTATCTCTCTGAAGTTGCAGTGA-AGCAGATTGAAGAT-ACAA
* * * *
12128624 ACCTTATCTCTCTGAAGTTGCAGTGAAGCAGGTTAAAGATACCCA
1 ATCTTATCTCTCTGAAGTTGCAGTGAAGCAGATTGAAGATA-CAA
* * * *
12128669 ATCTTATCTCCCTGAAGTTGCTGTGAAGCAGATTGAAGCTACTA
1 ATCTTATCTCTCTGAAGTTGCAGTGAAGCAGATTGAAGATACAA
* *
12128713 ATCATATCTC-CTTGAAGTTGCAGTGGAGCAGATT
1 ATCTTATCTCTC-TGAAGTTGCAGTGAAGCAGATT
12128747 AAAACGATGA
Statistics
Matches: 142, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
41 28 0.20
42 3 0.02
43 2 0.01
44 69 0.49
45 40 0.28
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCTCTGAAGTTGCAGTGAAGCAGATTGAAGATACAA
Found at i:12137237 original size:9 final size:9
Alignment explanation
Indices: 12137223--12137268 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
12137213 ACAAACAATC
12137223 CATGTAAAT
1 CATGTAAAT
**
12137232 CATGTATCT
1 CATGTAAAT
12137241 CATGTAAAT
1 CATGTAAAT
*
12137250 --TTTAAAT
1 CATGTAAAT
12137257 CATGTAAAT
1 CATGTAAAT
12137266 CAT
1 CAT
12137269 ATAACATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
7 6 0.21
9 23 0.79
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (9 bp):
CATGTAAAT
Found at i:12137268 original size:25 final size:26
Alignment explanation
Indices: 12137227--12137277 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
12137217 ACAATCCATG
** *
12137227 TAAATCATGTATCTCATGTAA-ATTT
1 TAAATCATGTAAATCATATAACATTT
12137252 TAAATCATGTAAATCATATAACATTT
1 TAAATCATGTAAATCATATAACATTT
12137278 ATATCAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (26 bp):
TAAATCATGTAAATCATATAACATTT
Found at i:12137380 original size:20 final size:19
Alignment explanation
Indices: 12137332--12137381 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
12137322 TAACAGAAAT
*
12137332 TTATCCGTATCAACCGTAA
1 TTATCCATATCAACCGTAA
* *
12137351 CTTATACATATCAACGGTAA
1 -TTATCCATATCAACCGTAA
12137371 TTCATCCATAT
1 TT-ATCCATAT
12137382 AATTGCATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (19 bp):
TTATCCATATCAACCGTAA
Found at i:12137560 original size:26 final size:23
Alignment explanation
Indices: 12137530--12137608 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
12137520 GAGCCATGAT
12137530 CGGTAAGCTC-ATTCCGAGCTGATAAA
1 CGGTAAGCTCTA-T-CGAGCTG--AAA
12137556 CGGTAAGCTCTATCGAGCTGAAA
1 CGGTAAGCTCTATCGAGCTGAAA
* * **
12137579 CGGAAAGCTCCATAAAGCTGAAA
1 CGGTAAGCTCTATCGAGCTGAAA
12137602 CGGTAAG
1 CGGTAAG
12137609 TTCATACGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 28 0.60
25 7 0.15
26 11 0.23
27 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (23 bp):
CGGTAAGCTCTATCGAGCTGAAA
Found at i:12139926 original size:15 final size:15
Alignment explanation
Indices: 12139906--12139934 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12139896 TGCTTTCATA
12139906 CACAACCATCAATTC
1 CACAACCATCAATTC
12139921 CACAACCATCAATT
1 CACAACCATCAATT
12139935 ATAATATTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (15 bp):
CACAACCATCAATTC
Found at i:12144930 original size:22 final size:22
Alignment explanation
Indices: 12144905--12144954 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
12144895 CCTAATCAAC
* *
12144905 TTAAATAATTGGGTTAGTACT-
1 TTAAATAATTGGATCAGTACTG
*
12144926 TTTAATAATTGGATCAGTACTG
1 TTAAATAATTGGATCAGTACTG
12144948 TTAAATA
1 TTAAATA
12144955 GAAAAGGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (22 bp):
TTAAATAATTGGATCAGTACTG
Found at i:12145745 original size:10 final size:10
Alignment explanation
Indices: 12145730--12145772 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
12145720 ATAACTTTAT
12145730 TTAAATATAA
1 TTAAATATAA
12145740 TTAAATAATAA
1 TTAAAT-ATAA
*
12145751 TTAATTATAA
1 TTAAATATAA
*
12145761 ATAAATACTAA
1 TTAAATA-TAA
12145772 T
1 T
12145773 AACTCTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 15 0.56
11 12 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAATATAA
Found at i:12145759 original size:21 final size:21
Alignment explanation
Indices: 12145730--12145772 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12145720 ATAACTTTAT
*
12145730 TTAAATATAATTAAATAATAA
1 TTAAATATAAATAAATAATAA
* *
12145751 TTAATTATAAATAAATACTAA
1 TTAAATATAAATAAATAATAA
12145772 T
1 T
12145773 AACTCTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATATAAATAAATAATAA
Found at i:12146703 original size:24 final size:24
Alignment explanation
Indices: 12146667--12146715 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
12146657 AAATTTTCAA
*
12146667 ATTTAATCTTTAAATTATT-ATTT
1 ATTTAATATTTAAATTATTAATTT
12146690 ATTTAGATATTTAAATTATTAATTT
1 ATTTA-ATATTTAAATTATTAATTT
12146715 A
1 A
12146716 GTCTCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
24 13 0.57
25 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTAATATTTAAATTATTAATTT
Found at i:12150893 original size:13 final size:14
Alignment explanation
Indices: 12150857--12150893 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
12150847 ATCAGAGGAG
12150857 TATTTTATTTTTAT
1 TATTTTATTTTTAT
*
12150871 T-TTTTATTTTTCT
1 TATTTTATTTTTAT
12150884 TATTTT-TTTT
1 TATTTTATTTT
12150894 GTTGAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.84
Consensus pattern (14 bp):
TATTTTATTTTTAT
Found at i:12151345 original size:6 final size:6
Alignment explanation
Indices: 12151334--12151384 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
12151324 GTTTTCATGC
*
12151334 AAAAAT AAAAAT AAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
12151384 A
1 A
12151385 GGATTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 5 0.12
6 23 0.57
7 7 0.17
8 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:12151381 original size:19 final size:19
Alignment explanation
Indices: 12151335--12151373 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12151325 TTTTCATGCA
12151335 AAAATAAAA-A-TAAAAAT
1 AAAATAAAATAGTAAAAAT
12151352 AAAATAAAATAGTAAAAAT
1 AAAATAAAATAGTAAAAAT
12151371 AAA
1 AAA
12151374 TAATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
19 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAATAAAATAGTAAAAAT
Found at i:12151384 original size:13 final size:13
Alignment explanation
Indices: 12151337--12151384 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
12151327 TTCATGCAAA
12151337 AATAAAAATAAA-
1 AATAAAAATAAAT
12151349 AAT-AAAATAAAAT
1 AATAAAAAT-AAAT
*
12151362 AGTAAAAATAAAT
1 AATAAAAATAAAT
*
12151375 AATAATAATA
1 AATAAAAATA
12151385 GGATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 5 0.17
12 6 0.20
13 14 0.47
14 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (13 bp):
AATAAAAATAAAT
Found at i:12162116 original size:9 final size:9
Alignment explanation
Indices: 12162102--12162133 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
12162092 TTTCGAATTT
12162102 GAATAACTC
1 GAATAACTC
*
12162111 GAATAATTC
1 GAATAACTC
12162120 GAATAACTC
1 GAATAACTC
12162129 GAATA
1 GAATA
12162134 TCAAACTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (9 bp):
GAATAACTC
Found at i:12162123 original size:18 final size:18
Alignment explanation
Indices: 12162097--12162133 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12162087 TGAGTTTTCG
*
12162097 AATTTGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
12162115 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
12162133 A
1 A
12162134 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:12163627 original size:2 final size:2
Alignment explanation
Indices: 12163622--12163680 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
12163612 TATGTCTTAA
* * * * *
12163622 AT AT AT AC AT AT AT AT AT AT A- AT AT TT CT -T AA AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12163662 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
12163681 AAAGGTACCA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12163642 original size:32 final size:32
Alignment explanation
Indices: 12163605--12163679 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
12163595 CATTTGTACT
12163605 TATATAATATGTCTTAAATATATACATATATA
1 TATATAATATGTCTTAAATATATACATATATA
*
12163637 TATATAATATTTCTTAAATATATACATATATA
1 TATATAATATGTCTTAAATATATACATATATA
12163669 TATATATATAT
1 TATATA-ATAT
12163680 AAAAGGTACC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 37 0.90
33 4 0.10
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (32 bp):
TATATAATATGTCTTAAATATATACATATATA
Found at i:12165192 original size:43 final size:43
Alignment explanation
Indices: 12165077--12165228 Score: 152
Period size: 43 Copynumber: 3.6 Consensus size: 43
12165067 TTTGTACAAC
* * * * *
12165077 GTCAACGTCCCAGACGTGGTCTTACATG-CAATCACAAATCGAT
1 GTCATCGTCCCAAACGTGGTCTTATATGAAAAT-ACAAGTCGAT
* *
12165120 GTCA-CTTCCTAGATA-G-GGTCTTACT-TGAAAATACAAGTCGAT
1 GTCATCGTCCCA-A-ACGTGGTCTTA-TATGAAAATACAAGTCGAT
*
12165162 GTCATCGTCCCAAACGTGGTCTTATATGAAAATACAAGTTGAT
1 GTCATCGTCCCAAACGTGGTCTTATATGAAAATACAAGTCGAT
*
12165205 GTCATCGTCCCAGACGTGGTCTTA
1 GTCATCGTCCCAAACGTGGTCTTA
12165229 CACAAAAACA
Statistics
Matches: 91, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
41 1 0.01
42 30 0.33
43 59 0.65
44 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (43 bp):
GTCATCGTCCCAAACGTGGTCTTATATGAAAATACAAGTCGAT
Found at i:12169118 original size:16 final size:16
Alignment explanation
Indices: 12169097--12169130 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12169087 TACTTAAAAG
12169097 TTAAAACTAATTGTTA
1 TTAAAACTAATTGTTA
*
12169113 TTAAAATTAATTGTTA
1 TTAAAACTAATTGTTA
12169129 TT
1 TT
12169131 GAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:12169231 original size:25 final size:25
Alignment explanation
Indices: 12169201--12169248 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12169191 AAGATTACTT
12169201 ATTTGAATTTAATTACAAACAATTA
1 ATTTGAATTTAATTACAAACAATTA
12169226 ATTTGAATTTAATTACAAACAAT
1 ATTTGAATTTAATTACAAACAAT
12169249 CAAATCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTGAATTTAATTACAAACAATTA
Found at i:12169327 original size:8 final size:8
Alignment explanation
Indices: 12169314--12169338 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12169304 ATTTAATTAC
12169314 TTTTAACT
1 TTTTAACT
12169322 TTTTAACT
1 TTTTAACT
12169330 TTTTAACT
1 TTTTAACT
12169338 T
1 T
12169339 AAATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTAACT
Found at i:12170270 original size:8 final size:8
Alignment explanation
Indices: 12170259--12170290 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
12170249 TGAAGCACCA
12170259 TGGAGTCG
1 TGGAGTCG
12170267 TGGAGTCG
1 TGGAGTCG
12170275 TGGA--CG
1 TGGAGTCG
12170281 TGGAGTCG
1 TGGAGTCG
12170289 TG
1 TG
12170291 AATCGGTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.27
8 16 0.73
ACGTcount: A:0.12, C:0.12, G:0.50, T:0.25
Consensus pattern (8 bp):
TGGAGTCG
Found at i:12170287 original size:22 final size:22
Alignment explanation
Indices: 12170259--12170308 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12170249 TGAAGCACCA
*
12170259 TGGAGTCGTGGAGTC-GTGGACG
1 TGGAGTCGT-GAATCGGTGGACG
*
12170281 TGGAGTCGTGAATCGGTGGAGG
1 TGGAGTCGTGAATCGGTGGACG
12170303 TGGAGT
1 TGGAGT
12170309 TGGATCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.16, C:0.10, G:0.50, T:0.24
Consensus pattern (22 bp):
TGGAGTCGTGAATCGGTGGACG
Found at i:12176226 original size:13 final size:13
Alignment explanation
Indices: 12176208--12176233 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12176198 TAAGAATGGT
12176208 GTTTTTGGATTAA
1 GTTTTTGGATTAA
12176221 GTTTTTGGATTAA
1 GTTTTTGGATTAA
12176234 TGGACTAACT
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:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
GTTTTTGGATTAA
Found at i:12183777 original size:26 final size:26
Alignment explanation
Indices: 12183714--12183805 Score: 121
Period size: 27 Copynumber: 3.5 Consensus size: 26
12183704 CTTACGACCG
* *
12183714 AAGGGTAAAATAACCGAAATACCCTCG
1 AAGGGTAAAATGACCGAAATACCCT-A
* *
12183741 AAGGATAAAATGACCGATATACCCTA
1 AAGGGTAAAATGACCGAAATACCCTA
12183767 AAGGGTAAAATGACCGAAATACCCCTA
1 AAGGGTAAAATGACCGAAATA-CCCTA
*
12183794 TAGGGTAAAATG
1 AAGGGTAAAATG
12183806 TCTATTATAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 19 0.33
27 38 0.67
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (26 bp):
AAGGGTAAAATGACCGAAATACCCTA
Found at i:12184176 original size:28 final size:28
Alignment explanation
Indices: 12184144--12184233 Score: 117
Period size: 28 Copynumber: 3.2 Consensus size: 28
12184134 GTTACATTAT
* * *
12184144 CACACTGTTACTGTATCGAGCTAAGGTC
1 CACACTATTACTGTATCGGGCTAAGGCC
* **
12184172 CACACTATTACTGTATTGGGCTAATACC
1 CACACTATTACTGTATCGGGCTAAGGCC
*
12184200 CACACTATTACTGTATCGGGCTATGGCC
1 CACACTATTACTGTATCGGGCTAAGGCC
12184228 CACACT
1 CACACT
12184234 GTACTATTAT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (28 bp):
CACACTATTACTGTATCGGGCTAAGGCC
Found at i:12186243 original size:20 final size:20
Alignment explanation
Indices: 12186220--12186263 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
12186210 ATAGGGTATG
12186220 AGATCTGAGTATGGATGCCA
1 AGATCTGAGTATGGATGCCA
12186240 AGATCTGAGTATGGATGCCA
1 AGATCTGAGTATGGATGCCA
12186260 AGAT
1 AGAT
12186264 GGATTCTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (20 bp):
AGATCTGAGTATGGATGCCA
Found at i:12188359 original size:26 final size:26
Alignment explanation
Indices: 12188323--12188377 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
12188313 TGTTTAGTAC
12188323 TTTAGATATCACAACCAAGATCTTGT
1 TTTAGATATCACAACCAAGATCTTGT
12188349 TTTAGATATCACAACCAAGATCTTGT
1 TTTAGATATCACAACCAAGATCTTGT
12188375 TTT
1 TTT
12188378 GAAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (26 bp):
TTTAGATATCACAACCAAGATCTTGT
Found at i:12189069 original size:22 final size:23
Alignment explanation
Indices: 12189016--12189071 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
12189006 CTCAATTTTA
* * *
12189016 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
12189039 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
12189061 ATTAAAATTAA
1 ATTAAAATTAA
12189072 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:12189084 original size:16 final size:16
Alignment explanation
Indices: 12189047--12189086 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12189037 TTAATAAAAT
* *
12189047 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
12189063 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
12189079 TAAAATTA
1 TAAAATTA
12189087 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:12189171 original size:9 final size:9
Alignment explanation
Indices: 12189159--12189202 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
12189149 ATTATCAAAT
12189159 TATTAATTG
1 TATTAATTG
12189168 TATTAATTG
1 TATTAATTG
12189177 --TTAATTG
1 TATTAATTG
*
12189184 AATTAATTG
1 TATTAATTG
12189193 TATTAATTG
1 TATTAATTG
12189202 T
1 T
12189203 TGTAACAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 7 0.22
9 25 0.78
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (9 bp):
TATTAATTG
Found at i:12189180 original size:16 final size:16
Alignment explanation
Indices: 12189156--12189193 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
12189146 AAAATTATCA
* *
12189156 AATTATTAATTGTATT
1 AATTGTTAATTGAATT
12189172 AATTGTTAATTGAATT
1 AATTGTTAATTGAATT
12189188 AATTGT
1 AATTGT
12189194 ATTAATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (16 bp):
AATTGTTAATTGAATT
Found at i:12189299 original size:68 final size:68
Alignment explanation
Indices: 12189190--12189325 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
12189180 ATTGAATTAA
*
12189190 TTGTATTAATTGTTGTAACAAAACCTAACATTTGATTAGTAAAATAAACTTGATGTTTTATTATT
1 TTGTATTAATTGTTGTAACAAAACCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTATT
12189255 ATT
66 ATT
*
12189258 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTATT
1 TTGTATTAATTGTTGTAACAAAACCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTATT
12189323 ATT
66 ATT
12189326 ATTTTTTTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (68 bp):
TTGTATTAATTGTTGTAACAAAACCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTATT
ATT
Found at i:12197044 original size:29 final size:30
Alignment explanation
Indices: 12196980--12197050 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 30
12196970 AAATTTTTTA
* *
12196980 AATAATTTATTT-AATTATAAATAAAAATT
1 AATATTTTATTTAAATTATAAATAAAAAGT
* *
12197009 AAT-TTTTATTTAAATTAT-AGTAAATAGT
1 AATATTTTATTTAAATTATAAATAAAAAGT
*
12197037 AATATTTTCTTTAA
1 AATATTTTATTTAA
12197051 TTTTTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (30 bp):
AATATTTTATTTAAATTATAAATAAAAAGT
Found at i:12197052 original size:28 final size:29
Alignment explanation
Indices: 12196980--12197052 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
12196970 AAATTTTTTA
* *
12196980 AATAATTTATTTAATTATAAATAAAAATT
1 AATATTTTATTTAATTATAAATAAAAAGT
* *
12197009 AAT-TTTTATTTAAATTAT-AGTAAATAGT
1 AATATTTTATTT-AATTATAAATAAAAAGT
*
12197037 AATATTTTCTTTAATT
1 AATATTTTATTTAATT
12197053 TTTTTTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 21 0.57
29 16 0.43
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (29 bp):
AATATTTTATTTAATTATAAATAAAAAGT
Found at i:12202663 original size:41 final size:40
Alignment explanation
Indices: 12202611--12202767 Score: 161
Period size: 41 Copynumber: 3.9 Consensus size: 40
12202601 TTTAGCGGGG
* * * * *
12202611 TTTTTAAAAAGCGTCGCTAATACTCAGTGCTTTAGCAGCGC
1 TTTTTAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCAGC-A
* *
12202652 TTTTTAGAAAGCGCCGCGAATGCTCAGGGCTTTATCAGCA
1 TTTTTAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCA
** *
12202692 TTTTTGAGAAAGTACCGCTAATGCTCAGGGCTTTAGCGGCA
1 TTTTT-AGAAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCA
* * * *
12202733 TTTTTTATAAAGCGCCTCGAATGCTCAGGGATTTA
1 -TTTTTAGAAAGCGCCGCTAATGCTCAGGGCTTTA
12202768 AAATAATTTA
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
40 5 0.05
41 86 0.90
42 5 0.05
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (40 bp):
TTTTTAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCA
Found at i:12202953 original size:7 final size:7
Alignment explanation
Indices: 12202941--12202986 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
12202931 TATCACTATA
12202941 GTTTAGG
1 GTTTAGG
12202948 GTTTAGG
1 GTTTAGG
12202955 GTTTAGG
1 GTTTAGG
* *
12202962 GTATATG
1 GTTTAGG
*
12202969 GTTTAGA
1 GTTTAGG
12202976 GTTTAAGG
1 GTTT-AGG
12202984 GTT
1 GTT
12202987 AGGTGTTACC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:12203024 original size:15 final size:15
Alignment explanation
Indices: 12203004--12203033 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12202994 ACCATTTTAA
*
12203004 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
12203019 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
12203034 TTTATGGCTT
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:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:12203365 original size:21 final size:22
Alignment explanation
Indices: 12203340--12203423 Score: 61
Period size: 21 Copynumber: 4.0 Consensus size: 22
12203330 ATATATGGAT
*
12203340 TTAGGGA-TTATGGTTTTA-GGG
1 TTAGGGATTTAAGG-TTTAGGGG
12203361 TTA-GGATTTAAGGTTTAGGGG
1 TTAGGGATTTAAGGTTTAGGGG
* * *
12203382 TTA-GGAGTTAGGGGTTAGGGG
1 TTAGGGATTTAAGGTTTAGGGG
* *
12203403 TTA-AGAGTTAAGGATTTAGGG
1 TTAGGGATTTAAGG-TTTAGGG
12203424 ATTTAAGGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
20 7 0.13
21 40 0.75
22 6 0.11
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (22 bp):
TTAGGGATTTAAGGTTTAGGGG
Done.