Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 40 of 228
Found at i:12203757 original size:5 final size:5
Alignment explanation
Indices: 12203747--12203792 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
12203737 AGAGTTGCCC
*
12203747 ATAAT ATAAT ATAGT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
12203793 TGCAACTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:12203774 original size:19 final size:19
Alignment explanation
Indices: 12203750--12203788 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12203740 GTTGCCCATA
*
12203750 ATATAATATAGTATAATAT
1 ATATAATATAATATAATAT
12203769 ATATAATATAATATAATAT
1 ATATAATATAATATAATAT
12203788 A
1 A
12203789 ATATTGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
ATATAATATAATATAATAT
Found at i:12203775 original size:24 final size:24
Alignment explanation
Indices: 12203747--12203792 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
12203737 AGAGTTGCCC
*
12203747 ATAATATAATATAGTATAATATAT
1 ATAATATAATATAATATAATATAT
12203771 ATAATATAATATAATATAATAT
1 ATAATATAATATAATATAATAT
12203793 TGCAACTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
ATAATATAATATAATATAATATAT
Found at i:12206486 original size:22 final size:24
Alignment explanation
Indices: 12206462--12206506 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12206452 ATTTAAACTT
*
12206462 AAATTTACATG-TATTTAAAAATA
1 AAATTCACATGCTATTTAAAAATA
12206485 AAATTCACATGCTA-TTAAAAAT
1 AAATTCACATGCTATTTAAAAAT
12206507 TCATATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (24 bp):
AAATTCACATGCTATTTAAAAATA
Found at i:12207077 original size:31 final size:29
Alignment explanation
Indices: 12207042--12207112 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
12207032 TTAAATTAGT
* *
12207042 AATGATAAAATTGTACTTTAGTCTCCTTAAA
1 AATGATAAAATT-TAATTTAATC-CCTTAAA
*
12207073 AATGATAAAAATTTAATTTAATCCTTTAAA
1 AATGAT-AAAATTTAATTTAATCCCTTAAA
*
12207103 AATTATAAAA
1 AATGATAAAA
12207113 ATATAGACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.11
30 11 0.31
31 14 0.40
32 6 0.17
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (29 bp):
AATGATAAAATTTAATTTAATCCCTTAAA
Found at i:12207104 original size:30 final size:32
Alignment explanation
Indices: 12207042--12207114 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 32
12207032 TTAAATTAGT
* *
12207042 AATGAT-AAAATTGTACTTTAGTCTCCTTAAA
1 AATGATAAAAATTGTAATTTAATCTCCTTAAA
*
12207073 AATGATAAAAATT-TAATTTAATC-CTTTAAA
1 AATGATAAAAATTGTAATTTAATCTCCTTAAA
*
12207103 AATTATAAAAAT
1 AATGATAAAAAT
12207115 ATAGACTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 17 0.46
31 14 0.38
32 6 0.16
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (32 bp):
AATGATAAAAATTGTAATTTAATCTCCTTAAA
Found at i:12213401 original size:31 final size:29
Alignment explanation
Indices: 12213324--12213404 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
12213314 CTTTTTTTGC
12213324 TCAAAT-T-ACATTTTAGTCACTTATGTT
1 TCAAATGTAACATTTTAGTCACTTATGTT
* * *
12213351 TGAAATGTTACGTTTTAGTCACTTATGTT
1 TCAAATGTAACATTTTAGTCACTTATGTT
**
12213380 ATCACGTTGTAACATTTTAGTCACT
1 -TCA-AATGTAACATTTTAGTCACT
12213405 GAGCCGTTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 19 0.44
30 2 0.05
31 16 0.37
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (29 bp):
TCAAATGTAACATTTTAGTCACTTATGTT
Found at i:12215730 original size:78 final size:78
Alignment explanation
Indices: 12215601--12215758 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
12215591 AAAACTATAA
12215601 AAAACCCCCCACCTTTCATTTTTTTCACAAATTAATCATTTCTCTATTATTCTCTTGACAACATC
1 AAAACCCCCCACCTTTCATTTTTTTCACAAATTAATCATTTCTCTATTATTCTCTTGACAACATC
12215666 TCAATTTCCTCTC
66 TCAATTTCCTCTC
12215679 AAAACCCCCCACCTTTCATTTTTTTCACAAATTAATCATTTCTCTATTATTCTCTTGACAACATC
1 AAAACCCCCCACCTTTCATTTTTTTCACAAATTAATCATTTCTCTATTATTCTCTTGACAACATC
12215744 TCAATTTCCTCTC
66 TCAATTTCCTCTC
12215757 AA
1 AA
12215759 TTTGCTCTCA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.28, C:0.30, G:0.01, T:0.41
Consensus pattern (78 bp):
AAAACCCCCCACCTTTCATTTTTTTCACAAATTAATCATTTCTCTATTATTCTCTTGACAACATC
TCAATTTCCTCTC
Found at i:12215758 original size:11 final size:11
Alignment explanation
Indices: 12215742--12215836 Score: 67
Period size: 11 Copynumber: 8.9 Consensus size: 11
12215732 CTTGACAACA
12215742 TCTCAATTTCC
1 TCTCAATTTCC
*
12215753 TCTCAATTTGC
1 TCTCAATTTCC
12215764 TCTCAATTTCC
1 TCTCAATTTCC
12215775 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
12215786 TCTCAA-ATCC
1 TCTCAATTTCC
**
12215796 -CT--ATTTAA
1 TCTCAATTTCC
*
12215804 TCTCAATTTGC
1 TCTCAATTTCC
*
12215815 TCTCAATTTGC
1 TCTCAATTTCC
12215826 TCTCAAATTTC
1 TCTC-AATTTC
12215837 TCTTAAATAT
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 5 0.08
10 4 0.06
11 44 0.67
12 11 0.17
ACGTcount: A:0.23, C:0.29, G:0.03, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:12215767 original size:22 final size:22
Alignment explanation
Indices: 12215742--12215836 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
12215732 CTTGACAACA
12215742 TCTCAATTTCCTCTCAATTTGC
1 TCTCAATTTCCTCTCAATTTGC
12215764 TCTCAATTTCCT-TCCAAATTT-C
1 TCTCAATTTCCTCT-C-AATTTGC
* **
12215786 TCTCAA-ATCC-CT--ATTTAA
1 TCTCAATTTCCTCTCAATTTGC
*
12215804 TCTCAATTTGCTCTCAATTTGC
1 TCTCAATTTCCTCTCAATTTGC
12215826 TCTCAAATTTC
1 TCTC-AATTTC
12215837 TCTTAAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
17 4 0.07
18 6 0.11
19 2 0.04
20 2 0.04
21 5 0.09
22 28 0.49
23 10 0.18
ACGTcount: A:0.23, C:0.29, G:0.03, T:0.44
Consensus pattern (22 bp):
TCTCAATTTCCTCTCAATTTGC
Found at i:12215844 original size:11 final size:12
Alignment explanation
Indices: 12215804--12215844 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
12215794 CCCTATTTAA
12215804 TCTC-AATTTGC
1 TCTCAAATTTGC
12215815 TCTC-AATTTGC
1 TCTCAAATTTGC
12215826 TCTCAAATTT-C
1 TCTCAAATTTGC
*
12215837 TCTTAAAT
1 TCTCAAAT
12215845 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 23 0.82
12 5 0.18
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.46
Consensus pattern (12 bp):
TCTCAAATTTGC
Found at i:12217705 original size:18 final size:18
Alignment explanation
Indices: 12217682--12217724 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12217672 TGCCAGGTGC
* *
12217682 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
12217700 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
12217718 GTTTCCT
1 GTATCCT
12217725 TTTCTGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:12218005 original size:21 final size:21
Alignment explanation
Indices: 12217981--12218026 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
12217971 GATACCCTAT
* *
12217981 CGGAGGAACCAGAATCCCCGC
1 CGGAGCAACCAGAACCCCCGC
*
12218002 CGGAGCAACCATAACCCCCGC
1 CGGAGCAACCAGAACCCCCGC
12218023 CGGA
1 CGGA
12218027 AGCTGGACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.41, G:0.26, T:0.04
Consensus pattern (21 bp):
CGGAGCAACCAGAACCCCCGC
Found at i:12218729 original size:230 final size:230
Alignment explanation
Indices: 12218287--12219052 Score: 1291
Period size: 229 Copynumber: 3.3 Consensus size: 230
12218277 TCATATTTTG
* *
12218287 AAAAATAATAAACACAAAAACTAATCCAATTTTGAAAATTTTATAAATAATTTAATTGACAAACC
1 AAAAATAATAAACACAAAAACTAATCCAATTTTGAAATTTTTTTAAATAATTTAATTGACAAACC
12218352 CTAAACTCTAAACCCTAACTTATTTGATTTTTCCTTAAAAACCCTTAACTTAAAAACACCAAAAC
66 CTAAACTCTAAACCCTAACTTATTTGATTTTTCCTTAAAAACCCTTAACTTAAAAACACCAAAAC
12218417 CCTAACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAAATTTTTTAATTAAATTACTCAAG
131 CCTAACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAAATTTTTTAATTAAATTACTCAAG
12218482 TAACCCTAAACCACAATTTAATTAATTTTTTCTTA
196 TAACCCTAAACCACAATTTAATTAATTTTTTCTTA
* *
12218517 AAAAATAATAAACACGAAAACTAATCCAATTTT-TAATTTTTTTAAATAATTTAATTGACAAACC
1 AAAAATAATAAACACAAAAACTAATCCAATTTTGAAATTTTTTTAAATAATTTAATTGACAAACC
*
12218581 CTAAACTCTAAACTCTAACTTATTTGATTTTTCCTTAAAAACCCTTAACTTAAAAACACCAAAAC
66 CTAAACTCTAAACCCTAACTTATTTGATTTTTCCTTAAAAACCCTTAACTTAAAAACACCAAAAC
12218646 CCTAACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAAAATTTTTTAATTAAATTACTCAA
131 CCTAACAAAAACCCTAACCCTAACCCTAATCTAATTTTT-AAAATTTTTTAATTAAATTACTCAA
*
12218711 GTAACCCTAAATCACAATTTAATTAATTTTTTCTTA
195 GTAACCCTAAACCACAATTTAATTAATTTTTTCTTA
* *
12218747 AAAAATAATAAACACGAAAACTAATCCAATTTTGAAATTTTTTTAAATAATTTAATTGACAAATC
1 AAAAATAATAAACACAAAAACTAATCCAATTTTGAAATTTTTTTAAATAATTTAATTGACAAACC
*
12218812 CTAAACTCTAAACCCTAACTTATTTGATTTTTCCTTAAAAACCCTTAACTTAAAAACACTAAAAC
66 CTAAACTCTAAACCCTAACTTATTTGATTTTTCCTTAAAAACCCTTAACTTAAAAACACCAAAAC
* ** *
12218877 CCTAACAAAAACCCTAACCCTAACCCTAACCCTAATTTGATTTTTAATTTTTTAATTAAATTATT
131 CCTAACAAAAACCCTAACCCTAACCCTAA-TCTAA-TT--TTTAAAATTTTTTAATTAAATTACT
* * * *
12218942 CAAATAACCCTAAACCATAATTTAATTGATTTTTCCTTA
192 CAAGTAACCCTAAACCACAATTTAATTAATTTTTTCTTA
* * * *
12218981 AAAATTAATAAACACAAAAACTAATCTAATTTCGAAATTTTTTTAAATTATTTAATTGACAAACC
1 AAAAATAATAAACACAAAAACTAATCCAATTTTGAAATTTTTTTAAATAATTTAATTGACAAACC
12219046 CTAAACT
66 CTAAACT
12219053 AGAGGTGTTC
Statistics
Matches: 505, Mismatches: 25, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
229 131 0.26
230 125 0.25
231 121 0.24
232 4 0.01
233 2 0.00
234 119 0.24
235 3 0.01
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (230 bp):
AAAAATAATAAACACAAAAACTAATCCAATTTTGAAATTTTTTTAAATAATTTAATTGACAAACC
CTAAACTCTAAACCCTAACTTATTTGATTTTTCCTTAAAAACCCTTAACTTAAAAACACCAAAAC
CCTAACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAAATTTTTTAATTAAATTACTCAAG
TAACCCTAAACCACAATTTAATTAATTTTTTCTTA
Found at i:12218897 original size:6 final size:6
Alignment explanation
Indices: 12218886--12218911 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12218876 CCCTAACAAA
12218886 AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AA
12218912 TTTGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:12219559 original size:15 final size:15
Alignment explanation
Indices: 12219541--12219573 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12219531 CATAAACCAT
*
12219541 AAACCCTAAAACCTA
1 AAACCCTAAAACCCA
12219556 AAACCCTAAAACCCA
1 AAACCCTAAAACCCA
12219571 AAA
1 AAA
12219574 ACGAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.33, G:0.00, T:0.09
Consensus pattern (15 bp):
AAACCCTAAAACCCA
Found at i:12219563 original size:8 final size:8
Alignment explanation
Indices: 12219541--12219575 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
12219531 CATAAACCAT
12219541 AAACCCTA
1 AAACCCTA
12219549 AAA-CCTA
1 AAACCCTA
12219556 AAACCCTA
1 AAACCCTA
*
12219564 AAACCCAA
1 AAACCCTA
12219572 AAAC
1 AAAC
12219576 GAGAAAAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.57, C:0.34, G:0.00, T:0.09
Consensus pattern (8 bp):
AAACCCTA
Found at i:12222988 original size:4 final size:4
Alignment explanation
Indices: 12222979--12223022 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
12222969 TTTACATGCT
*
12222979 TACA TACA TACA TACA TACA TACA TACA TACA TACA TCCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
12223023 CCCTTTTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:12225138 original size:151 final size:151
Alignment explanation
Indices: 12224864--12225164 Score: 548
Period size: 151 Copynumber: 2.0 Consensus size: 151
12224854 AAAAAGTAGG
* * *
12224864 GAATTTCAAGTAGTTTTTGAGATAGGGAAGATGTCTAATATTTTTAAAGTTTTAAATTCGCTACT
1 GAATTTCAAGTAGTTTTTGAAATAGGGAAGATGGCTAATATTTTTAAAGCTTTAAATTCGCTACT
*
12224929 TGGATTATTTATGCTGTTTAGTATTATTTTAGTGTGAATTTTCAATGTATGATTATCTGTAAATT
66 TGGATTATCTATGCTGTTTAGTATTATTTTAGTGTGAATTTTCAATGTATGATTATCTGTAAATT
12224994 ATACTAAGACAATATCAGTGT
131 ATACTAAGACAATATCAGTGT
12225015 GAATTTCAAGTAGTTTTTGAAATAGGGAAGATGGCTAATATTTTTAAAGCTTTAAATTCGCTACT
1 GAATTTCAAGTAGTTTTTGAAATAGGGAAGATGGCTAATATTTTTAAAGCTTTAAATTCGCTACT
*
12225080 TGGATTGTCTATGCTGTTTAGTATTATTTTAGTGTGAATTTTCAATGTATGATTATCTGTAAATT
66 TGGATTATCTATGCTGTTTAGTATTATTTTAGTGTGAATTTTCAATGTATGATTATCTGTAAATT
*
12225145 ATATTAAGACAATATCAGTG
131 ATACTAAGACAATATCAGTG
12225165 AAAACAATTA
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
151 144 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (151 bp):
GAATTTCAAGTAGTTTTTGAAATAGGGAAGATGGCTAATATTTTTAAAGCTTTAAATTCGCTACT
TGGATTATCTATGCTGTTTAGTATTATTTTAGTGTGAATTTTCAATGTATGATTATCTGTAAATT
ATACTAAGACAATATCAGTGT
Found at i:12226656 original size:17 final size:18
Alignment explanation
Indices: 12226623--12226660 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
12226613 AAAACTTAAA
12226623 ATTTTTATATAAAAATGT
1 ATTTTTATATAAAAATGT
12226641 ATTTTTA-A-AAATAATGT
1 ATTTTTATATAAA-AATGT
12226658 ATT
1 ATT
12226661 GATTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 9 0.47
18 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTTATATAAAAATGT
Found at i:12228531 original size:21 final size:22
Alignment explanation
Indices: 12228501--12228545 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
12228491 GAACAAATTG
12228501 TTGATTCTATTTCTTTCTTG-AT
1 TTGATTCTA-TTCTTTCTTGTAT
*
12228523 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTCTTGTAT
12228544 TT
1 TT
12228546 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCTTTCTTGTAT
Found at i:12228928 original size:21 final size:22
Alignment explanation
Indices: 12228888--12228942 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
12228878 AAAGCTTAAG
*
12228888 TTTGGAAACTTGATTGTGAAAA
1 TTTGGAAACTTAATTGTGAAAA
*
12228910 TTTGAAAACTTAATT-TGAAAA
1 TTTGGAAACTTAATTGTGAAAA
12228931 TTTGGAAACTTA
1 TTTGGAAACTTA
12228943 GAAATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.38
Consensus pattern (22 bp):
TTTGGAAACTTAATTGTGAAAA
Found at i:12229221 original size:35 final size:35
Alignment explanation
Indices: 12229177--12229343 Score: 239
Period size: 35 Copynumber: 4.8 Consensus size: 35
12229167 TTCACTTGTC
* * *
12229177 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
12229212 TTTTGTTGCAAGGAATCTCTCCTGTTCACAC-TTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATT-A
* *
12229247 -TTTCTTACAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
12229281 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
12229316 TGTTGTTGCAGGGAATCTCTCCTGTTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCA
12229344 TGTATCATTT
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
34 29 0.25
35 88 0.75
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:12229278 original size:69 final size:69
Alignment explanation
Indices: 12229178--12229343 Score: 253
Period size: 69 Copynumber: 2.4 Consensus size: 69
12229168 TCACTTGTCT
* *
12229178 TTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTTTGTTGCAAGGAATCTCTCCTGTTCACAC
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAAGGAATCTCTCCTGTTCACAC
12229243 -TTCA
66 ATT-A
* * *
12229247 TTTCTTACAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACGC
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAAGGAATCTCTCCTGTTCACAC
12229312 ATTA
66 ATTA
*
12229316 TGTTGTTGCAGGGAATCTCTCCTGTTCA
1 T-TTCTTGCAGGGAATCTCTCCTGTTCA
12229344 TGTATCATTT
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
69 62 0.70
70 26 0.30
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (69 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAAGGAATCTCTCCTGTTCACAC
ATTA
Found at i:12232162 original size:21 final size:22
Alignment explanation
Indices: 12232132--12232176 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
12232122 GAACAAATTG
12232132 TTGATTCTATTTCTTTCTTG-AT
1 TTGATTCTA-TTCTTTCTTGTAT
*
12232154 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTCTTGTAT
12232175 TT
1 TT
12232177 CTCTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCTTTCTTGTAT
Found at i:12235998 original size:34 final size:35
Alignment explanation
Indices: 12235911--12236002 Score: 123
Period size: 35 Copynumber: 2.7 Consensus size: 35
12235901 TTCACTTGTC
* * * *
12235911 TTTTCTTGCAGGGAATATTTCCTGTTCACTCATTA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
*
12235946 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATCA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
*
12235981 -TTTCTTGTAGGGAATCTCTCCT
1 TTTTCTTGCAGGGAATCTCTCCT
12236003 ATTACGAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 20 0.40
35 30 0.60
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.42
Consensus pattern (35 bp):
TTTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
Found at i:12237269 original size:37 final size:38
Alignment explanation
Indices: 12237204--12237282 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
12237194 TGTCAATTTA
* * *
12237204 TTACTTCGGATTTATTCGATGAGGCACTGGGTGGCAAT
1 TTACTTCGGATTTAATCAATGAGACACTGGGTGGCAAT
*
12237242 TTACTTCGG-TTTAATCAATGAGACACTGGGTGTCAAT
1 TTACTTCGGATTTAATCAATGAGACACTGGGTGGCAAT
12237279 TTAC
1 TTAC
12237283 CACTTCGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 28 0.76
38 9 0.24
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (38 bp):
TTACTTCGGATTTAATCAATGAGACACTGGGTGGCAAT
Found at i:12238062 original size:21 final size:20
Alignment explanation
Indices: 12238020--12238062 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
12238010 ATTTAAAATG
* * *
12238020 ATGATTTGAATGATGTTTTA
1 ATGATATGAATGATGATGTA
12238040 ATGATATGAAATGATGATGTA
1 ATGATATG-AATGATGATGTA
12238061 AT
1 AT
12238063 TGTGGTACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (20 bp):
ATGATATGAATGATGATGTA
Found at i:12240873 original size:31 final size:31
Alignment explanation
Indices: 12240829--12240897 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
12240819 TTGCCCAAGA
12240829 GTAAATA-CTCAAAATTTGAGGGGTTAAAGT
1 GTAAATATCTCAAAATTTGAGGGGTTAAAGT
12240859 GTAAATATCTCAAAATTTGAGGGGTTAAAGT
1 GTAAATATCTCAAAATTTGAGGGGTTAAAGT
12240890 GTAAATAT
1 GTAAATAT
12240898 GAAAAATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 7 0.18
31 31 0.82
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (31 bp):
GTAAATATCTCAAAATTTGAGGGGTTAAAGT
Found at i:12240906 original size:30 final size:31
Alignment explanation
Indices: 12240839--12240906 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
12240829 GTAAATACTC
**
12240839 AAAATTTGAGGGGTTAAAGTGTAAATATCTC
1 AAAATTTGAGGGGTTAAAGTGTAAATATCGA
12240870 AAAATTTGAGGGGTTAAAGTGTAAATAT-GA
1 AAAATTTGAGGGGTTAAAGTGTAAATATCGA
12240900 AAAATTT
1 AAAATTT
12240907 AAAGGACCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (31 bp):
AAAATTTGAGGGGTTAAAGTGTAAATATCGA
Found at i:12266558 original size:17 final size:18
Alignment explanation
Indices: 12266523--12266559 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12266513 AAAGCAAAAA
12266523 GAGATTGAAAAAGAAATT
1 GAGATTGAAAAAGAAATT
*
12266541 GAGATTGAGAAA-AAATT
1 GAGATTGAAAAAGAAATT
12266558 GA
1 GA
12266560 AAAAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (18 bp):
GAGATTGAAAAAGAAATT
Found at i:12272579 original size:15 final size:15
Alignment explanation
Indices: 12272559--12272588 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12272549 CAGAAGAATA
12272559 TTGGCATATCATTCT
1 TTGGCATATCATTCT
12272574 TTGGCATATCATTCT
1 TTGGCATATCATTCT
12272589 GAAGAAAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (15 bp):
TTGGCATATCATTCT
Found at i:12276797 original size:26 final size:26
Alignment explanation
Indices: 12276743--12276802 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
12276733 GAATTTGAGC
* **
12276743 TCATAAATTAATTAAAATAAAATTTA
1 TCATAAATTAATAAAAATAAAATCAA
*
12276769 TCATAAATTGATAAAAATAAAATCAA
1 TCATAAATTAATAAAAATAAAATCAA
*
12276795 TCAAAAAT
1 TCATAAAT
12276803 GAAGTAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.32
Consensus pattern (26 bp):
TCATAAATTAATAAAAATAAAATCAA
Found at i:12276816 original size:4 final size:4
Alignment explanation
Indices: 12276809--12276835 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12276799 AAATGAAGTA
12276809 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
12276836 GAAGAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:12277567 original size:57 final size:59
Alignment explanation
Indices: 12277453--12277567 Score: 132
Period size: 57 Copynumber: 2.0 Consensus size: 59
12277443 TGATTTAATA
* * *
12277453 TAATTATACATAATATATATTTTAAATACTTTTAATAATTAATAAATTATTTGTAAATT
1 TAATTATACATAATATACATTTTAAATACTTTTAATAAATAATAAATTATTTCTAAATT
*
12277512 TAATTATACATGA-A-ACATTTTAAA-A-TTTTAAATATAATAATAAA-TATTATCTAAAT
1 TAATTATACATAATATACATTTTAAATACTTTT-AATA-AATAATAAATTATT-TCTAAAT
12277568 AATTTAACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
55 4 0.08
56 9 0.18
57 23 0.47
58 1 0.02
59 12 0.24
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (59 bp):
TAATTATACATAATATACATTTTAAATACTTTTAATAAATAATAAATTATTTCTAAATT
Found at i:12277635 original size:33 final size:31
Alignment explanation
Indices: 12277596--12277667 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 31
12277586 TTGTAAACAA
*
12277596 ATTTAAATAAGTTAATACAATGGTACATTAAAT
1 ATTTAAATAAGTTAATACAATGATACA-T-AAT
* * * *
12277629 ATTTAAATGATTTAATATAATGATATATAAT
1 ATTTAAATAAGTTAATACAATGATACATAAT
12277660 ATTTAAAT
1 ATTTAAAT
12277668 TTATCCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 11 0.32
32 1 0.03
33 22 0.65
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTTAAATAAGTTAATACAATGATACATAAT
Found at i:12281983 original size:39 final size:39
Alignment explanation
Indices: 12281939--12282014 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
12281929 ATACTAATTA
12281939 CATAAAGGACTTATACAGTTTCGGGTGTTGATTTTGGTT
1 CATAAAGGACTTATACAGTTTCGGGTGTTGATTTTGGTT
12281978 CATAAAGGACTTATACAGTTTCGGGTGTTGATTTTGG
1 CATAAAGGACTTATACAGTTTCGGGTGTTGATTTTGG
12282015 ATGTCCTACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (39 bp):
CATAAAGGACTTATACAGTTTCGGGTGTTGATTTTGGTT
Found at i:12282314 original size:39 final size:39
Alignment explanation
Indices: 12282224--12282399 Score: 185
Period size: 39 Copynumber: 4.5 Consensus size: 39
12282214 CGAGTCTTGG
* * * *
12282224 GCCTAGTAGGCTTTATGCCGATGTATTGTATCGGGCCTTGA
1 GCCTAGTAGGCTTTGTGCCGATG-ACT-TATCAGGCTTTGA
* *
12282265 GCCTAATAGGCTTTGTGCCGGTGACTTATCAGGCTTTGA
1 GCCTAGTAGGCTTTGTGCCGATGACTTATCAGGCTTTGA
**
12282304 GCCTAGTAGGCTTCATGCCGATGACTTATCAGGCTTTGA
1 GCCTAGTAGGCTTTGTGCCGATGACTTATCAGGCTTTGA
* * * *
12282343 GCGTAATAGGCTTTGTGCCGATG-TTTATCGGGC-TTGA
1 GCCTAGTAGGCTTTGTGCCGATGACTTATCAGGCTTTGA
* *
12282380 TGCCTAGCAGGCTTCGTGCC
1 -GCCTAGTAGGCTTTGTGCC
12282400 TGTGTAATGA
Statistics
Matches: 114, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
37 4 0.04
38 23 0.20
39 65 0.57
40 2 0.02
41 20 0.18
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (39 bp):
GCCTAGTAGGCTTTGTGCCGATGACTTATCAGGCTTTGA
Found at i:12282361 original size:78 final size:79
Alignment explanation
Indices: 12282224--12282399 Score: 223
Period size: 78 Copynumber: 2.2 Consensus size: 79
12282214 CGAGTCTTGG
* * * *
12282224 GCCTAGTAGGCTTTATGCCGATGTATTGTATCGGGCCTTGAGCCTAATAGGCTTTGTGCCGGTGA
1 GCCTAGTAGGCTTCATGCCGATGTACTGTATCAGGCCTTGAGCCTAATAGGCTTTGTGCCGATG-
12282289 CTTATCAGGCTTTGA-
65 CTTATCAGGC-TTGAT
* * *
12282304 GCCTAGTAGGCTTCATGCCGATG-ACT-TATCAGGCTTTGAGCGTAATAGGCTTTGTGCCGATGT
1 GCCTAGTAGGCTTCATGCCGATGTACTGTATCAGGCCTTGAGCCTAATAGGCTTTGTGCCGATGC
*
12282367 TTATCGGGCTTGAT
66 TTATCAGGCTTGAT
* *
12282381 GCCTAGCAGGCTTCGTGCC
1 GCCTAGTAGGCTTCATGCC
12282400 TGTGTAATGA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
76 4 0.05
77 25 0.29
78 32 0.38
79 2 0.02
80 22 0.26
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (79 bp):
GCCTAGTAGGCTTCATGCCGATGTACTGTATCAGGCCTTGAGCCTAATAGGCTTTGTGCCGATGC
TTATCAGGCTTGAT
Found at i:12293634 original size:29 final size:31
Alignment explanation
Indices: 12293602--12293659 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12293592 GTAAATACTC
**
12293602 AAAATTT-AAGGGTTAA-AGTGTAAATATGA
1 AAAATTTAAAGGAATAATAGTGTAAATATGA
12293631 AAAATTTAAAGGAATAATAGTGTAAATAT
1 AAAATTTAAAGGAATAATAGTGTAAATAT
12293660 TTAATGGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 7 0.28
31 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (31 bp):
AAAATTTAAAGGAATAATAGTGTAAATATGA
Found at i:12305076 original size:6 final size:6
Alignment explanation
Indices: 12305065--12305096 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12305055 GTCCCTTCGG
*
12305065 TTTTAT TTTTAT TTTTAT TTTTAT TTTAAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
12305097 GACCACAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:12305453 original size:25 final size:25
Alignment explanation
Indices: 12305425--12305679 Score: 108
Period size: 26 Copynumber: 9.8 Consensus size: 25
12305415 ACTATTATCC
*
12305425 ATTTTAATTTTGTTATATATTATTT
1 ATTTTAATTTTTTTATATATTATTT
*** **
12305450 ATTTTTAAACCATCATATATATT-TTT
1 A-TTTT-AATTTTTTTATATATTATTT
12305476 CATTTTGAATTGTTTTTATATATATCATTT
1 -ATTTT-AATT-TTTTTATATAT-T-ATTT
* * *
12305506 -TTTTAAACTGTTTTGTATATTA-TT
1 ATTTT-AATTTTTTTATATATTATTT
* *
12305530 ATTTTAAACTTCTTTTTACATATTACTT
1 ATTTT-AA-TT-TTTTTATATATTATTT
* **
12305558 ATATTAAACTTTTTATATATTA--T
1 ATTTTAATTTTTTTATATATTATTT
* * * **
12305581 -TTTAAATTGTCTTATATGCTATTT
1 ATTTTAATTTTTTTATATATTATTT
** * *
12305605 ATTTTAAATTGCTTTGTATACTATTT
1 ATTTT-AATTTTTTTATATATTATTT
*
12305631 ATTTTAATTTTTTTTACATATTATTT
1 ATTTTAA-TTTTTTTATATATTATTT
*
12305657 ACTTTAAATTTTTTTATACTATT
1 A-TTTTAATTTTTTTATA-TATT
12305680 TACTTCGAAT
Statistics
Matches: 169, Mismatches: 43, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
22 13 0.08
23 1 0.01
24 3 0.02
25 26 0.15
26 59 0.35
27 50 0.30
28 14 0.08
30 3 0.02
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (25 bp):
ATTTTAATTTTTTTATATATTATTT
Found at i:12305581 original size:28 final size:27
Alignment explanation
Indices: 12305522--12305581 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
12305512 ACTGTTTTGT
* *
12305522 ATATTATTATTTTAAACTTCTTTTTAC
1 ATATTATTATATTAAACTTCTTTATAC
12305549 ATATTACTTATATTAAACTT-TTTAT--
1 ATATTA-TTATATTAAACTTCTTTATAC
12305574 ATATTATT
1 ATATTATT
12305582 TTAAATTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.07
25 6 0.20
27 10 0.33
28 12 0.40
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (27 bp):
ATATTATTATATTAAACTTCTTTATAC
Found at i:12305635 original size:52 final size:50
Alignment explanation
Indices: 12305507--12305681 Score: 126
Period size: 52 Copynumber: 3.5 Consensus size: 50
12305497 ATATCATTTT
* * * * *
12305507 TTTAAACTGTTTTGTATATTA-TTATTTTAAACTTCTTTTTACATATTACTTA-
1 TTTAAA-T-TTTTGTATACTATTTATTTTAAA-TT-GTCTTACATACTATTTAC
* * * *
12305559 TATTAAACTTTT-TATA-TA-TTATTTTAAATTGTCTTATATGCTATTTAT
1 T-TTAAATTTTTGTATACTATTTATTTTAAATTGTCTTACATACTATTTAC
* * * *
12305607 TTTAAATTGCTTTGTATACTATTTATTTTAATTTTTTTTACATATTATTTAC
1 TTTAAATT--TTTGTATACTATTTATTTTAAATTGTCTTACATACTATTTAC
*
12305659 TTTAAATTTTTTTATACTATTTA
1 TTTAAATTTTTGTATACTATTTA
12305682 CTTCGAATTG
Statistics
Matches: 100, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
47 17 0.17
48 3 0.03
49 15 0.15
50 22 0.22
51 6 0.06
52 32 0.32
53 5 0.05
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.60
Consensus pattern (50 bp):
TTTAAATTTTTGTATACTATTTATTTTAAATTGTCTTACATACTATTTAC
Found at i:12305679 original size:27 final size:25
Alignment explanation
Indices: 12305600--12305679 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 25
12305590 TCTTATATGC
* * *
12305600 TATTTATTTTAAATTGCTTTGTA-TAC
1 TATTTA-TTTAAATT-TTTTTTACTAT
*
12305626 TATTTATTTTAATTTTTTTTACATAT
1 TATTTATTTAAATTTTTTTTAC-TAT
12305652 TATTTACTTTAAATTTTTTTATACTAT
1 TATTTA-TTTAAATTTTTTT-TACTAT
12305679 T
1 T
12305680 TACTTCGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
24 5 0.11
25 7 0.16
26 14 0.31
27 16 0.36
28 3 0.07
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (25 bp):
TATTTATTTAAATTTTTTTTACTAT
Found at i:12305699 original size:50 final size:51
Alignment explanation
Indices: 12305600--12305706 Score: 128
Period size: 50 Copynumber: 2.1 Consensus size: 51
12305590 TCTTATATGC
* ** * *
12305600 TATTTATTTTAAATTGCTTTGTATACTATTTATTTTAATTTTTTTTACATAT
1 TATTTACTTTAAATT-CTTTGTATACTATTTATTCGAATTTGTTCTACATAT
*
12305652 TATTTACTTTAAATT-TTTTTATACTATTTACTTCGAA-TTGTTCTACATAT
1 TATTTACTTTAAATTCTTTGTATACTATTTA-TTCGAATTTGTTCTACATAT
12305702 TATTT
1 TATTT
12305707 TTGTTTCGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 30 0.62
51 4 0.08
52 14 0.29
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (51 bp):
TATTTACTTTAAATTCTTTGTATACTATTTATTCGAATTTGTTCTACATAT
Found at i:12306875 original size:21 final size:22
Alignment explanation
Indices: 12306843--12306904 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
12306833 GTTTCCATTC
*
12306843 AGCTCTTTTGAGCTTCT-GTTTA
1 AGCTCTTATGAGCTTCTCG-TTA
*
12306865 A-CTCTTATGAG-TTTTCGTTA
1 AGCTCTTATGAGCTTCTCGTTA
12306885 AGCTCTTATGAGCTT-TCGTT
1 AGCTCTTATGAGCTTCTCGTT
12306905 CAACCCATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 7 0.20
21 25 0.71
22 3 0.09
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (22 bp):
AGCTCTTATGAGCTTCTCGTTA
Found at i:12308108 original size:10 final size:11
Alignment explanation
Indices: 12308080--12308117 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12308070 TTTATGATTG
*
12308080 GTTTTTGAAAT
1 GTTTATGAAAT
12308091 GTTTATGAAAT
1 GTTTATGAAAT
12308102 G-TTATGAAAT
1 GTTTATGAAAT
*
12308112 TTTTAT
1 GTTTAT
12308118 ATTTGATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (11 bp):
GTTTATGAAAT
Found at i:12309147 original size:20 final size:20
Alignment explanation
Indices: 12309122--12309163 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12309112 TAGAGTGCAA
12309122 TGGATATTTAAGGTGGGATT
1 TGGATATTTAAGGTGGGATT
12309142 TGGATATTTAAGGTGGGATT
1 TGGATATTTAAGGTGGGATT
12309162 TG
1 TG
12309164 CCTAGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (20 bp):
TGGATATTTAAGGTGGGATT
Found at i:12312366 original size:24 final size:25
Alignment explanation
Indices: 12312273--12312382 Score: 116
Period size: 25 Copynumber: 4.5 Consensus size: 25
12312263 GCTCAATCGA
* *
12312273 AACGGGAAGCTCTTCCGAGCCATAT
1 AACGGGAAGCTCATGCGAGCCATAT
* *
12312298 AACGGGAAGCTCATGTGAGCCATGT
1 AACGGGAAGCTCATGCGAGCCATAT
* ** *
12312323 AACGGGAAGATCATAAGAGCCCTAT
1 AACGGGAAGCTCATGCGAGCCATAT
*
12312348 -ACGGGAAGCTCATGCGAGCTA-AT
1 AACGGGAAGCTCATGCGAGCCATAT
*
12312371 ATCGGGAAGCTC
1 AACGGGAAGCTC
12312383 CGAAGATCCA
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
23 2 0.03
24 26 0.38
25 41 0.59
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (25 bp):
AACGGGAAGCTCATGCGAGCCATAT
Found at i:12312452 original size:25 final size:25
Alignment explanation
Indices: 12312289--12312457 Score: 80
Period size: 25 Copynumber: 6.8 Consensus size: 25
12312279 AAGCTCTTCC
* * *
12312289 GAGCCATATAACGGGAAGCTCATG-T
1 GAGCCATATATCGGGAAGCTC-CGAA
* * * **
12312314 GAGCCATGTAACGGGAAGATCATAA
1 GAGCCATATATCGGGAAGCTCCGAA
* * *
12312339 GAGCCCTATA-CGGGAAGCTCATG-C
1 GAGCCATATATCGGGAAGCTC-CGAA
*
12312363 GAGCTA-ATATCGGGAAGCTCCGAA
1 GAGCCATATATCGGGAAGCTCCGAA
* ** *
12312387 GATCCAT-TAATTAGGAAGCT-CGTAC
1 GAGCCATAT-ATCGGGAAGCTCCG-AA
* *
12312412 GAGCCATATGTCGGGAAGCTCCGGA
1 GAGCCATATATCGGGAAGCTCCGAA
* *
12312437 GAGCCATATATTGGGACGCTC
1 GAGCCATATATCGGGAAGCTC
12312458 ATAAGAGTTG
Statistics
Matches: 106, Mismatches: 29, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
23 4 0.04
24 30 0.28
25 69 0.65
26 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (25 bp):
GAGCCATATATCGGGAAGCTCCGAA
Found at i:12312569 original size:25 final size:24
Alignment explanation
Indices: 12312532--12312600 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
12312522 TATGTATCGG
**
12312532 GAAGCTCCGGAGAGCCAAATATCAA
1 GAAGCTCAAGAGAGCC-AATATCAA
* *
12312557 GAAGCTCAAGAGAGTCAATATCGA
1 GAAGCTCAAGAGAGCCAATATCAA
* * *
12312581 CAGGCTCAAGAGAGCTAATA
1 GAAGCTCAAGAGAGCCAATA
12312601 ACGGGATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 23 0.64
25 13 0.36
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (24 bp):
GAAGCTCAAGAGAGCCAATATCAA
Found at i:12318764 original size:25 final size:26
Alignment explanation
Indices: 12318719--12318793 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 26
12318709 GAATGCTCAA
* * *
12318719 TCGAGCACATA-AACAGAAAGCTC-TT
1 TCGAGC-CATATAACGGGAAGCTCATG
12318744 TCGAGCCATATAACGGGAAGCTCATG
1 TCGAGCCATATAACGGGAAGCTCATG
*
12318770 T-GAGCCATGTAACGGGAAGCTCAT
1 TCGAGCCATATAACGGGAAGCTCAT
12318794 AAGAGCCCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.09
25 38 0.86
26 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (26 bp):
TCGAGCCATATAACGGGAAGCTCATG
Found at i:12318799 original size:25 final size:25
Alignment explanation
Indices: 12318746--12318897 Score: 87
Period size: 25 Copynumber: 6.1 Consensus size: 25
12318736 AAGCTCTTTC
**
12318746 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATAA
*
12318771 GAGCCATGTAACGGGAAGCTCATAA
1 GAGCCATATAACGGGAAGCTCATAA
* * *
12318796 GAGCCCTAT-TCGAGAAGCTC-TAAA
1 GAGCCATATAACGGGAAGCTCAT-AA
* * ** * **
12318820 GAGTCGT-TAATCAAGAAGCTCGTGC
1 GAGCCATATAA-CGGGAAGCTCATAA
* * *
12318845 GAGCCGTATATCGGGAAGCTC-TGGA
1 GAGCCATATAACGGGAAGCTCAT-AA
* *
12318870 GAGCCATATATCGGGATGCTCATAA
1 GAGCCATATAACGGGAAGCTCATAA
12318895 GAG
1 GAG
12318898 TTGTAGTGTA
Statistics
Matches: 99, Mismatches: 21, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
23 2 0.02
24 17 0.17
25 76 0.77
26 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATAA
Found at i:12319027 original size:24 final size:23
Alignment explanation
Indices: 12318977--12319032 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
12318967 AGCTCCGGAT
*
12318977 AGCCAAATATCAGGAAGCTCAATG
1 AGCC-AATATCAGGAAGCTCAAAG
* *
12319001 AGCCAATATCGGGATGCTCATAAG
1 AGCCAATATCAGGAAGCTCA-AAG
*
12319025 AGCTAATA
1 AGCCAATA
12319033 ATGGGACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (23 bp):
AGCCAATATCAGGAAGCTCAAAG
Found at i:12319294 original size:21 final size:21
Alignment explanation
Indices: 12319270--12319309 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12319260 AATTTAAGAC
* *
12319270 CAATTTAATACAATTCATACT
1 CAATTCAATACAATACATACT
*
12319291 CAATTCAATCCAATACATA
1 CAATTCAATACAATACATA
12319310 TCTTTTGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (21 bp):
CAATTCAATACAATACATACT
Found at i:12332662 original size:3 final size:3
Alignment explanation
Indices: 12332656--12332683 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12332646 AGGAGAAAGA
12332656 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12332684 GGAGAGCGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12338478 original size:19 final size:19
Alignment explanation
Indices: 12338454--12338494 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
12338444 TATTTTAAAG
12338454 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
12338473 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
12338492 TTA
1 TTA
12338495 GAAGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:12338564 original size:41 final size:41
Alignment explanation
Indices: 12338532--12338613 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
12338522 ATATTTTATT
12338532 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
12338573 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
12338614 CAATTAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
Found at i:12339091 original size:32 final size:32
Alignment explanation
Indices: 12339050--12339119 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
12339040 AGAGCTAGTG
12339050 ATCACATAACTAGTAGTTATTTTTTTCAACTT
1 ATCACATAACTAGTAGTTATTTTTTTCAACTT
12339082 ATCACATAACTAGTAGTTATTTTTTTCAACTT
1 ATCACATAACTAGTAGTTATTTTTTTCAACTT
12339114 ACTCAC
1 A-TCAC
12339120 CTTGTGCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (32 bp):
ATCACATAACTAGTAGTTATTTTTTTCAACTT
Found at i:12339788 original size:170 final size:169
Alignment explanation
Indices: 12339506--12339844 Score: 615
Period size: 170 Copynumber: 2.0 Consensus size: 169
12339496 TTAAGATATT
12339506 TGTTACCCGATCTATTTAAAAATAAAAGTCCTTCTTCATATCACTGTGAATTTTGTGAATTGGCT
1 TGTTACCCGATCTATTTAAAAATAAAAGTCCTTCTTCATATCACTGTGAATTTTGTGAATTGGCT
*
12339571 AAACATCATCGGTTATTCTTCTCACCTCAAAAATATAAAGCTTCTAAACTTTTTTTCATTAATTC
66 AAACATCATCGGTCATTCTTCTCACCTCAAAAATATAAAGCTTCTAAAC-TTTTTTCATTAATTC
12339636 ATAGTGATGTTTGGGGACCTTCGAGAGTCTCAACTTTTTC
130 ATAGTGATGTTTGGGGACCTTCGAGAGTCTCAACTTTTTC
* * *
12339676 TGTTACCTGATTTGTTTAAAAATAAAAGTCCTTCTTCATATCACTGTGAATTTTGTGAATTGGCT
1 TGTTACCCGATCTATTTAAAAATAAAAGTCCTTCTTCATATCACTGTGAATTTTGTGAATTGGCT
* *
12339741 AAACATTATCGGTCATTTTTCTCACCTCAAAAATATAAAGCTTCTAAACTTTTTTCATTAATTCA
66 AAACATCATCGGTCATTCTTCTCACCTCAAAAATATAAAGCTTCTAAACTTTTTTCATTAATTCA
12339806 TAGTGATGTTTGGGGACCTTCGAGAGTCTCAACTTTTTC
131 TAGTGATGTTTGGGGACCTTCGAGAGTCTCAACTTTTTC
12339845 AGAAAAATGT
Statistics
Matches: 163, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
169 55 0.34
170 108 0.66
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (169 bp):
TGTTACCCGATCTATTTAAAAATAAAAGTCCTTCTTCATATCACTGTGAATTTTGTGAATTGGCT
AAACATCATCGGTCATTCTTCTCACCTCAAAAATATAAAGCTTCTAAACTTTTTTCATTAATTCA
TAGTGATGTTTGGGGACCTTCGAGAGTCTCAACTTTTTC
Found at i:12342530 original size:19 final size:19
Alignment explanation
Indices: 12342506--12342546 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
12342496 TATTTTAAAG
12342506 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
*
12342525 TTATTTAGGTATATAAATC
1 TTATTTAGGTAGATAAATC
12342544 TTA
1 TTA
12342547 GAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:12342631 original size:41 final size:41
Alignment explanation
Indices: 12342584--12342662 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
12342574 ATATGTTATT
*
12342584 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAAAATAAGGGAATTATTTTCC
12342625 TTATCTTTTAGTAGTTTATTAAAATAAGGGAATTATTT
1 TTATCTTTTAGTAGTTTATTAAAATAAGGGAATTATTT
12342663 CTCAATTAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAAAATAAGGGAATTATTTTCC
Found at i:12347239 original size:14 final size:14
Alignment explanation
Indices: 12347220--12347252 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
12347210 TCAAAAAATA
12347220 TTATATTTTTTAAT
1 TTATATTTTTTAAT
12347234 TTATA-TTTTTAAT
1 TTATATTTTTTAAT
*
12347247 TAATAT
1 TTATAT
12347253 ATATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATATTTTTTAAT
Found at i:12349489 original size:85 final size:85
Alignment explanation
Indices: 12349346--12349511 Score: 332
Period size: 85 Copynumber: 2.0 Consensus size: 85
12349336 ACGTGAATTA
12349346 AATCATAAACAATCATGTACATATCATATAAACAACTTGGGTATGACATATTAAAAAACCAAACA
1 AATCATAAACAATCATGTACATATCATATAAACAACTTGGGTATGACATATTAAAAAACCAAACA
12349411 ATGTAATTGAAATTCAATAT
66 ATGTAATTGAAATTCAATAT
12349431 AATCATAAACAATCATGTACATATCATATAAACAACTTGGGTATGACATATTAAAAAACCAAACA
1 AATCATAAACAATCATGTACATATCATATAAACAACTTGGGTATGACATATTAAAAAACCAAACA
12349496 ATGTAATTGAAATTCA
66 ATGTAATTGAAATTCA
12349512 GTAAGGCTAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.28
Consensus pattern (85 bp):
AATCATAAACAATCATGTACATATCATATAAACAACTTGGGTATGACATATTAAAAAACCAAACA
ATGTAATTGAAATTCAATAT
Found at i:12357081 original size:30 final size:30
Alignment explanation
Indices: 12357016--12357078 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
12357006 AATTACTTAA
12357016 TTTAT-ATTTTATGATTAATTTAAAATAAT
1 TTTATAATTTTATGATTAATTTAAAATAAT
12357045 TTTATAATTTTAT-ATT-ATCTT-AAATAAT
1 TTTATAATTTTATGATTAAT-TTAAAATAAT
*
12357073 ATTATA
1 TTTATA
12357079 TAAAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 14 0.45
29 10 0.32
30 7 0.23
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTATAATTTTATGATTAATTTAAAATAAT
Found at i:12357923 original size:125 final size:124
Alignment explanation
Indices: 12357668--12358104 Score: 644
Period size: 125 Copynumber: 3.5 Consensus size: 124
12357658 AAAATCAAAG
* * * * * * * *
12357668 CAGGATGATTTATCAGAAGGATTTTTGCAGTCGCGCCCAT-GTGTACGCGCTTTTGCTACAGTAG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCC-TCGTGGACGCGCTTTTGCTACAGTTG
* * *
12357732 GTCTTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAA
65 GTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCTA
* * * *
12357792 GCAGGATGCTATATGCGAAGAATTTGTGAAATTGCGCCCTCCTGGACGCGCTTTTGCTACAGTTG
1 -CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTG
*
12357857 GTCCTGAAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA
65 GTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA
12357917 CTAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTG
1 C-AGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTG
* *
12357982 GTCCTGGAAGAAATTATTTCGAGTTAACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA
65 GTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA
*
12358042 CCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 -CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
12358105 AGCATGTTTG
Statistics
Matches: 284, Mismatches: 24, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
124 2 0.01
125 244 0.86
126 38 0.13
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (124 bp):
CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGG
TCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA
Found at i:12361321 original size:21 final size:20
Alignment explanation
Indices: 12361262--12361321 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
12361252 TATATTTAAC
* *
12361262 TTAAGGGTTAAGGTTTTAAAT
1 TTAAGGGTT-AGGGTTTAAAG
*
12361283 TTAAGGTTTTAGGGTTTAGAAG
1 TTAAGG-GTTAGGGTTTA-AAG
12361305 TTAAGGGTTAGGGTTTA
1 TTAAGGGTTAGGGTTTA
12361322 TGGTTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (20 bp):
TTAAGGGTTAGGGTTTAAAG
Found at i:12361321 original size:28 final size:28
Alignment explanation
Indices: 12361287--12361357 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
12361277 TTAAATTTAA
12361287 GGTTTTAGGGTTTAGAAGTTAAGGGTTAG
1 GGTTTTA-GGTTTAGAAGTTAAGGGTTAG
**
12361316 GG-TTTATGGTTTTTAAGTTAAGGGTTAG
1 GGTTTTA-GGTTTAGAAGTTAAGGGTTAG
12361344 GGTTTTAGGTTTAG
1 GGTTTTAGGTTTAG
12361358 GGTTATGGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 30 0.83
29 6 0.17
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (28 bp):
GGTTTTAGGTTTAGAAGTTAAGGGTTAG
Found at i:12361335 original size:21 final size:20
Alignment explanation
Indices: 12361311--12361483 Score: 103
Period size: 22 Copynumber: 8.5 Consensus size: 20
12361301 GAAGTTAAGG
12361311 GTTAGGGTTTATGGTTTTTAA
1 GTTAGGGTTTA-GGTTTTTAA
* *
12361332 GTTAAGGG-TTAGGGTTTTAG
1 GTT-AGGGTTTAGGTTTTTAA
*
12361352 GTTTAGGGTTATGGGTTTTTAA
1 G-TTAGGGTT-TAGGTTTTTAA
*
12361374 GTTTAGGGTTTTAGG-TTTTAG
1 G-TTAGGG-TTTAGGTTTTTAA
* *
12361395 GTTTATGGTTTAGGGTTTTAAA
1 G-TTAGGGTTTA-GGTTTTTAA
* *
12361417 GTTTAAGGTTTAGG-ATTT--
1 G-TTAGGGTTTAGGTTTTTAA
12361435 -TTA-GGTTTAGGGTTTTTAA
1 GTTAGGGTTTA-GGTTTTTAA
12361454 GTTAAGGG-TTAGTGTTTTTAA
1 GTT-AGGGTTTAG-GTTTTTAA
12361475 -TTAGGGTTT
1 GTTAGGGTTT
12361484 TTAAGTTAAG
Statistics
Matches: 122, Mismatches: 14, Indels: 33
0.72 0.08 0.20
Matches are distributed among these distances:
15 6 0.05
16 5 0.04
17 3 0.02
19 4 0.03
20 25 0.20
21 37 0.30
22 40 0.33
23 2 0.02
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.50
Consensus pattern (20 bp):
GTTAGGGTTTAGGTTTTTAA
Found at i:12361377 original size:22 final size:22
Alignment explanation
Indices: 12361312--12361448 Score: 115
Period size: 22 Copynumber: 6.4 Consensus size: 22
12361302 AAGTTAAGGG
12361312 TTAGGGTTTAT-GGTTTTTAAGT
1 TTAGGG-TTATGGGTTTTTAAGT
* *
12361334 TAAGGGTTA-GGG-TTTTAGGT
1 TTAGGGTTATGGGTTTTTAAGT
12361354 TTAGGGTTATGGGTTTTTAAGT
1 TTAGGGTTATGGGTTTTTAAGT
* * *
12361376 TTAGGGTTTTAGG-TTTTAGGT
1 TTAGGGTTATGGGTTTTTAAGT
* *
12361397 TTATGGTT-TAGGGTTTTAAAGT
1 TTAGGGTTAT-GGGTTTTTAAGT
* * *
12361419 TTAAGGTT-TAGGATTTTTAGGT
1 TTAGGGTTAT-GGGTTTTTAAGT
12361441 TTAGGGTT
1 TTAGGGTT
12361449 TTTAAGTTAA
Statistics
Matches: 94, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
20 16 0.17
21 24 0.26
22 54 0.57
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (22 bp):
TTAGGGTTATGGGTTTTTAAGT
Found at i:12361384 original size:7 final size:7
Alignment explanation
Indices: 12361290--12361449 Score: 57
Period size: 7 Copynumber: 22.4 Consensus size: 7
12361280 AATTTAAGGT
12361290 TTTAGGG
1 TTTAGGG
*
12361297 TTTAGAAG
1 TTTAG-GG
*
12361305 TTAAGGG
1 TTTAGGG
12361312 -TTAGGG
1 TTTAGGG
*
12361318 TTTATGGTT
1 TTTA-GG-G
*
12361327 TTTA-AG
1 TTTAGGG
*
12361333 TTAAGGG
1 TTTAGGG
12361340 -TTAGGG
1 TTTAGGG
12361346 TTTTA-GG
1 -TTTAGGG
12361353 TTTAGGG
1 TTTAGGG
12361360 -TTATGGG
1 TTTA-GGG
*
12361367 TTTTTA-AG
1 --TTTAGGG
12361375 TTTAGGG
1 TTTAGGG
*
12361382 TTTTAGGT
1 -TTTAGGG
12361390 TTTA-GG
1 TTTAGGG
*
12361396 TTTATGG
1 TTTAGGG
12361403 TTTAGGG
1 TTTAGGG
**
12361410 TTTTAAAG
1 -TTTAGGG
*
12361418 TTTAAGG
1 TTTAGGG
*
12361425 TTTAGGATT
1 TTTAGG--G
12361434 TTTA-GG
1 TTTAGGG
12361440 TTTAGGG
1 TTTAGGG
12361447 TTT
1 TTT
12361450 TTAAGTTAAG
Statistics
Matches: 113, Mismatches: 21, Indels: 38
0.66 0.12 0.22
Matches are distributed among these distances:
6 33 0.29
7 46 0.41
8 23 0.20
9 8 0.07
10 3 0.03
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:12361384 original size:15 final size:15
Alignment explanation
Indices: 12361364--12361427 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 15
12361354 TTAGGGTTAT
12361364 GGGTTTTTAAGTTTA
1 GGGTTTTTAAGTTTA
*
12361379 GGG-TTTTAGGTTTTA
1 GGGTTTTTAAG-TTTA
* *
12361394 -GGTTTAT-GGTTTA
1 GGGTTTTTAAGTTTA
*
12361407 GGGTTTTAAAGTTTA
1 GGGTTTTTAAGTTTA
*
12361422 AGGTTT
1 GGGTTT
12361428 AGGATTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.10
14 15 0.38
15 20 0.51
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.52
Consensus pattern (15 bp):
GGGTTTTTAAGTTTA
Found at i:12361405 original size:28 final size:29
Alignment explanation
Indices: 12361374--12361428 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
12361364 GGGTTTTTAA
* *
12361374 GTTTAGGGTTTT-AGGTTTTAGGTTTATG
1 GTTTAGGGTTTTAAAGTTTAAGGTTTATG
12361402 GTTTAGGGTTTTAAAGTTTAAGGTTTA
1 GTTTAGGGTTTTAAAGTTTAAGGTTTA
12361429 GGATTTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (29 bp):
GTTTAGGGTTTTAAAGTTTAAGGTTTATG
Found at i:12361461 original size:15 final size:15
Alignment explanation
Indices: 12361418--12361463 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
12361408 GGTTTTAAAG
*
12361418 TTTAAGGTTTAGGATT
1 TTTAA-GTTTAGGGTT
*
12361434 TTTAGGTTTAGGGTT
1 TTTAAGTTTAGGGTT
*
12361449 TTTAAGTTAAGGGTT
1 TTTAAGTTTAGGGTT
12361464 AGTGTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (15 bp):
TTTAAGTTTAGGGTT
Found at i:12361484 original size:34 final size:35
Alignment explanation
Indices: 12361404--12361525 Score: 126
Period size: 34 Copynumber: 3.5 Consensus size: 35
12361394 GGTTTATGGT
* * *
12361404 TTAGGGTTTTAAAGTTTAAGGTTTAGGATTTTTAGGT
1 TTAGGGTTTTTAAG-TTAAGGGTTAGGATTTTTA-GA
12361441 TTAGGGTTTTTAAGTTAAGGGTTAGTG-TTTTTA-A
1 TTAGGGTTTTTAAGTTAAGGGTTAG-GATTTTTAGA
* * *
12361475 TTAGGGTTTTTAAGTTAAGGGTTAAGA--TTAAGG
1 TTAGGGTTTTTAAGTTAAGGGTTAGGATTTTTAGA
*
12361508 TTAGGGTTTTAAAGTTAA
1 TTAGGGTTTTTAAGTTAA
12361526 AGTTTTAGGG
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
32 3 0.04
33 18 0.24
34 24 0.32
36 16 0.21
37 14 0.19
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (35 bp):
TTAGGGTTTTTAAGTTAAGGGTTAGGATTTTTAGA
Found at i:12361554 original size:22 final size:22
Alignment explanation
Indices: 12361502--12361582 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
12361492 AGGGTTAAGA
12361502 TTAAGG-TTAGGGTTTTAAAG-T
1 TTAAGGTTTAGGG-TTTAAAGTT
* * *
12361523 TAAAGTTTTAGGGTTTACAATTT
1 TTAAGGTTTAGGGTTTA-AAGTT
* * *
12361546 TTAA-GTTTATGATTTAAGGTT
1 TTAAGGTTTAGGGTTTAAAGTT
12361567 TTAAGGTTTAGGGTTT
1 TTAAGGTTTAGGGTTT
12361583 GGGGTTTTAA
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
21 15 0.33
22 26 0.58
23 4 0.09
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.48
Consensus pattern (22 bp):
TTAAGGTTTAGGGTTTAAAGTT
Found at i:12361570 original size:21 final size:21
Alignment explanation
Indices: 12361544--12361799 Score: 93
Period size: 22 Copynumber: 12.1 Consensus size: 21
12361534 GGTTTACAAT
* *
12361544 TTTTAAGTTTATGATTTAAGG
1 TTTTAAGTTTAAGGTTTAAGG
* **
12361565 TTTTAAGGTTTAGGGTTTGGGG
1 TTTTAA-GTTTAAGGTTTAAGG
*
12361587 TTTTAAG-TTAA-GTATTAGGG
1 TTTTAAGTTTAAGGT-TTAAGG
12361607 TTTTTAAGTTTAAGGTTTAAGG
1 -TTTTAAGTTTAAGGTTTAAGG
* *
12361629 TTTTTAGGTTAAGAG-TT-AGG
1 TTTTAAGTTTAAG-GTTTAAGG
* * *
12361649 GTTTAGGTTTAAGG-TTAGGGG
1 TTTTAAGTTTAAGGTTTA-AGG
*
12361670 TTTTTAAGTTT-AGGGTT-AGG
1 -TTTTAAGTTTAAGGTTTAAGG
* * * * *
12361690 -ATTAGGGTTATGGTTTTAAAG
1 TTTTAAGTTTAAGG-TTTAAGG
** *
12361711 --TTAAGGTTTTGGGGTTTAGGG
1 TTTTAA-G-TTTAAGGTTTAAGG
*
12361732 TTTTTAAGTTTAAGGTTTATGG
1 -TTTTAAGTTTAAGGTTTAAGG
* * *
12361754 TTTTTAGGTTTAAGATTTGAGG
1 -TTTTAAGTTTAAGGTTTAAGG
* *
12361776 TTTTTAAG-TTAAGGGTTAGGG
1 -TTTTAAGTTTAAGGTTTAAGG
12361797 TTT
1 TTT
12361800 AGAGTTTTTA
Statistics
Matches: 176, Mismatches: 41, Indels: 37
0.69 0.16 0.15
Matches are distributed among these distances:
18 6 0.03
19 7 0.04
20 30 0.17
21 49 0.28
22 77 0.44
23 3 0.02
24 4 0.02
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
TTTTAAGTTTAAGGTTTAAGG
Found at i:12361655 original size:19 final size:19
Alignment explanation
Indices: 12361631--12361705 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 19
12361621 GTTTAAGGTT
12361631 TTTAGG-TTAAGAGTTAGGG
1 TTTAGGTTTAAG-GTTAGGG
12361650 TTTAGGTTTAAGGTTAGGG
1 TTTAGGTTTAAGGTTAGGG
* *
12361669 GTT---TTTAAGTTTAGGG
1 TTTAGGTTTAAGGTTAGGG
* * *
12361685 -TTAGGATTAGGGTTATGG
1 TTTAGGTTTAAGGTTAGGG
12361703 TTT
1 TTT
12361706 TAAAGTTAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
15 2 0.04
16 12 0.27
18 9 0.20
19 17 0.38
20 5 0.11
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (19 bp):
TTTAGGTTTAAGGTTAGGG
Found at i:12361687 original size:22 final size:21
Alignment explanation
Indices: 12361543--12361689 Score: 102
Period size: 22 Copynumber: 7.0 Consensus size: 21
12361533 GGGTTTACAA
** *
12361543 TTTTTAAGTTTATGATTTAAGG
1 TTTTTAAGTTTA-GGGTTAGGG
*
12361565 -TTTTAAGGTTTAGGGTTTGGG
1 TTTTTAA-GTTTAGGGTTAGGG
* * **
12361586 GTTTTAAGTTAAGTATTAGGG
1 TTTTTAAGTTTAGGGTTAGGG
* *
12361607 TTTTTAAGTTTAAGGTTTAAGG
1 TTTTTAAGTTT-AGGGTTAGGG
* * *
12361629 TTTTTAGGTTAAGAGTTAGGG
1 TTTTTAAGTTTAGGGTTAGGG
* *
12361650 --TTTAGGTTTAAGGTTAGGGG
1 TTTTTAAGTTTAGGGTTA-GGG
12361670 TTTTTAAGTTTAGGGTTAGG
1 TTTTTAAGTTTAGGGTTAGG
12361690 ATTAGGGTTA
Statistics
Matches: 96, Mismatches: 23, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
19 13 0.14
20 3 0.03
21 39 0.41
22 41 0.43
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
TTTTTAAGTTTAGGGTTAGGG
Found at i:12361689 original size:34 final size:34
Alignment explanation
Indices: 12361644--12361712 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
12361634 AGGTTAAGAG
* *
12361644 TTAGGGTTTAGGTTTAAGGTTAGGGGTTTTTAAGT
1 TTAGGGTTTAGGATTAAGGTTA-GGGTTTTAAAGT
* *
12361679 TTAGGG-TTAGGATTAGGGTTATGGTTTTAAAGT
1 TTAGGGTTTAGGATTAAGGTTAGGGTTTTAAAGT
12361712 T
1 T
12361713 AAGGTTTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 11 0.37
34 13 0.43
35 6 0.20
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (34 bp):
TTAGGGTTTAGGATTAAGGTTAGGGTTTTAAAGT
Found at i:12361748 original size:22 final size:22
Alignment explanation
Indices: 12361723--12361799 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
12361713 AAGGTTTTGG
12361723 GGTTTAGGGTTTTTAAGTTTAA
1 GGTTTAGGGTTTTTAAGTTTAA
* *
12361745 GGTTTATGGTTTTTAGGTTTAA
1 GGTTTAGGGTTTTTAAGTTTAA
*
12361767 GATTT-GAGGTTTTTAAG-TTAA
1 GGTTTAG-GGTTTTTAAGTTTAA
*
12361788 GGGTTAGGGTTT
1 GGTTTAGGGTTT
12361800 AGAGTTTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 12 0.26
22 34 0.74
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (22 bp):
GGTTTAGGGTTTTTAAGTTTAA
Found at i:12362981 original size:7 final size:7
Alignment explanation
Indices: 12362971--12363003 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
12362961 TTATATACAT
12362971 AATACTA
1 AATACTA
12362978 AATACTA
1 AATACTA
12362985 AATACTA
1 AATACTA
12362992 AATACTA
1 AATACTA
12362999 AATAC
1 AATAC
12363004 CAATCGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:12364263 original size:11 final size:11
Alignment explanation
Indices: 12364249--12364284 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
12364239 GAAATTTGGA
12364249 AGGAAATTGAG
1 AGGAAATTGAG
*
12364260 AGGATATTGAG
1 AGGAAATTGAG
12364271 AGGAAATTTGAG
1 AGGAAA-TTGAG
12364283 AG
1 AG
12364285 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:12364897 original size:9 final size:9
Alignment explanation
Indices: 12364880--12364916 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12364870 TGAGTTTTCG
12364880 AATTCGAAT
1 AATTCGAAT
*
12364889 AACTCGAAT
1 AATTCGAAT
12364898 AATTCGAAT
1 AATTCGAAT
12364907 AATTCGAAT
1 AATTCGAAT
12364916 A
1 A
12364917 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:12365173 original size:30 final size:31
Alignment explanation
Indices: 12365126--12365184 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
12365116 AACTTTTTAC
*
12365126 TTTCCTCCAAAATTTTTACTCCC-TCCCACT
1 TTTCCTCCAAAACTTTTACTCCCTTCCCACT
*
12365156 TTTCC-CCTAAAACTTTTATTCCCTTCCCA
1 TTTCCTCC-AAAACTTTTACTCCCTTCCCA
12365185 TCTCACCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.08
30 18 0.72
31 5 0.20
ACGTcount: A:0.20, C:0.39, G:0.00, T:0.41
Consensus pattern (31 bp):
TTTCCTCCAAAACTTTTACTCCCTTCCCACT
Found at i:12369046 original size:26 final size:26
Alignment explanation
Indices: 12369016--12369067 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12369006 ATTATAAAAC
12369016 AACACCAATTATCATATTTAAACATA
1 AACACCAATTATCATATTTAAACATA
12369042 AACACCAATTATCATATTTAAACATA
1 AACACCAATTATCATATTTAAACATA
12369068 TCATGGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (26 bp):
AACACCAATTATCATATTTAAACATA
Found at i:12383486 original size:14 final size:16
Alignment explanation
Indices: 12383460--12383497 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
12383450 CTAAATAGCG
*
12383460 TAATAATTAAAT-ATT
1 TAATAAATAAATAATT
12383475 TAA-AAATAAATAATT
1 TAATAAATAAATAATT
12383490 TAATAAAT
1 TAATAAAT
12383498 TTTCTTACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 9 0.45
16 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAAATAAATAATT
Found at i:12383669 original size:14 final size:14
Alignment explanation
Indices: 12383650--12383698 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
12383640 TTAAGGATTA
12383650 AAAATTTGAAATTG
1 AAAATTTGAAATTG
12383664 AAAATTTGAAGATTG
1 AAAATTTGAA-ATTG
* * *
12383679 AAAATATAAAATTC
1 AAAATTTGAAATTG
12383693 AAAATT
1 AAAATT
12383699 GGGGATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (14 bp):
AAAATTTGAAATTG
Found at i:12383678 original size:15 final size:15
Alignment explanation
Indices: 12383645--12383683 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
12383635 GAGGATTAAG
*
12383645 GATTAAAAATTTGAA
1 GATTGAAAATTTGAA
12383660 -ATTGAAAATTTGAA
1 GATTGAAAATTTGAA
12383674 GATTGAAAAT
1 GATTGAAAAT
12383684 ATAAAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (15 bp):
GATTGAAAATTTGAA
Found at i:12397692 original size:19 final size:19
Alignment explanation
Indices: 12397641--12397692 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
12397631 CTGCCTTCAA
*
12397641 TGTCGTGACACAGCCATGG
1 TGTCGTGACACAACCATGG
*
12397660 -GATGGTACGACACAACCATGG
1 TG-TCGT--GACACAACCATGG
12397681 TGTCGTGACACA
1 TGTCGTGACACA
12397693 CCCTTGAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
18 1 0.04
19 9 0.35
21 15 0.58
22 1 0.04
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.19
Consensus pattern (19 bp):
TGTCGTGACACAACCATGG
Found at i:12399139 original size:20 final size:21
Alignment explanation
Indices: 12399110--12399149 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12399100 TTTCTTAACA
12399110 AAAAAAGTAA-AATAAAAAAT
1 AAAAAAGTAACAATAAAAAAT
*
12399130 AAAAATGTAACAATAAAAAA
1 AAAAAAGTAACAATAAAAAA
12399150 ATCATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAAAAGTAACAATAAAAAAT
Found at i:12402784 original size:30 final size:30
Alignment explanation
Indices: 12402727--12402784 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
12402717 ATATAATATA
*
12402727 TATTTTTTTAATTTTAAAATACTTTTTTTT
1 TATTTTTTTAATTTTAAAATACATTTTTTT
*
12402757 TATTTTTTTATTTTTAAAATGA-ATTTTT
1 TATTTTTTTAATTTTAAAAT-ACATTTTT
12402785 GGTGTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (30 bp):
TATTTTTTTAATTTTAAAATACATTTTTTT
Found at i:12418037 original size:32 final size:29
Alignment explanation
Indices: 12417996--12418070 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 29
12417986 TAAGGGTTAA
*
12417996 TTTTA-ATTTTTTTAATATTATTTAATATT
1 TTTTATATTTTTTTAAT-TTAATTAATATT
* *
12418025 TTTATTTCATTTTTGTAATTTAATTAATATT
1 TTT-TAT-ATTTTTTTAATTTAATTAATATT
12418056 TTTTATATTTTTTTA
1 TTTTATATTTTTTTA
12418071 TAACAATCGG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 11 0.29
30 3 0.08
31 14 0.37
32 10 0.26
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (29 bp):
TTTTATATTTTTTTAATTTAATTAATATT
Found at i:12418570 original size:34 final size:34
Alignment explanation
Indices: 12418527--12418591 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
12418517 GCATATGTAC
12418527 AAATTAAACATCAAACGAATCATAATTCATTACT
1 AAATTAAACATCAAACGAATCATAATTCATTACT
12418561 AAATTAAACATCAAACGAATCATAATTCATT
1 AAATTAAACATCAAACGAATCATAATTCATT
12418592 TATACAGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.29
Consensus pattern (34 bp):
AAATTAAACATCAAACGAATCATAATTCATTACT
Found at i:12423157 original size:58 final size:59
Alignment explanation
Indices: 12423067--12423233 Score: 187
Period size: 59 Copynumber: 2.8 Consensus size: 59
12423057 GCATTAATTT
* *
12423067 TTTTGAATATATTTATACAAACTGTTTTTATATTGTTTCATTTAAT-AAACAGAAGTTG
1 TTTTGAATATATTTATACAAACTATTTTTATATTGTTTCATTTAATAAAACAGAAGTTC
* * * * *
12423125 TTTTGAATATTTTTGTAGAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATATTTATACAAACTATTTTTATATTGTTTCATTTAATAAAACAGAAGTTC
*** * *
12423184 TTTTGAATA-AGACAATACAAATTATTTTT-TCATTGTTTTATTTAATAAAA
1 TTTTGAATATA-TTTATACAAACTATTTTTAT-ATTGTTTCATTTAATAAAA
12423234 TTATGAGTTA
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
58 42 0.46
59 50 0.54
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (59 bp):
TTTTGAATATATTTATACAAACTATTTTTATATTGTTTCATTTAATAAAACAGAAGTTC
Found at i:12426640 original size:29 final size:29
Alignment explanation
Indices: 12426594--12426666 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
12426584 TATCAAAATA
12426594 ATTTTTTCAGAACACATCACGTCAAATTT
1 ATTTTTTCAGAACACATCACGTCAAATTT
* * * **
12426623 ATTTTTTCATATCCCATCTTGTCAAATTT
1 ATTTTTTCAGAACACATCACGTCAAATTT
*
12426652 ATTTCTTCTAGAACA
1 ATTTTTTC-AGAACA
12426667 ATACTTACCA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
29 31 0.91
30 3 0.09
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (29 bp):
ATTTTTTCAGAACACATCACGTCAAATTT
Found at i:12426733 original size:28 final size:29
Alignment explanation
Indices: 12426701--12426755 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12426691 ACCCTAAAAC
*
12426701 AAACCCTAA-TTATTTTTTTAAAAACCTT
1 AAACCCTAATTTATTCTTTTAAAAACCTT
*
12426729 AAACCTTAATTTATTCTTTTAAAAACC
1 AAACCCTAATTTATTCTTTTAAAAACC
12426756 ATAATCCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (29 bp):
AAACCCTAATTTATTCTTTTAAAAACCTT
Found at i:12429413 original size:332 final size:332
Alignment explanation
Indices: 12428807--12429465 Score: 1318
Period size: 332 Copynumber: 2.0 Consensus size: 332
12428797 TTTCATGTTC
12428807 ATCAAGGAAGGGAAGATTGTGGACAAAGTGACGGGAGCAAAGAAAGAAGAGCTTCAGCAGACTGT
1 ATCAAGGAAGGGAAGATTGTGGACAAAGTGACGGGAGCAAAGAAAGAAGAGCTTCAGCAGACTGT
12428872 GATAAAGCATATGGCTGCCACCAGTACTACTTCTTCAGCTTGATTTTATGATAATTATTAGTTCA
66 GATAAAGCATATGGCTGCCACCAGTACTACTTCTTCAGCTTGATTTTATGATAATTATTAGTTCA
12428937 ACTGTTTTTATCTTTAATGTTTGGAGGAACTTGACCTCATGATTATGTCCTGCTACATCTCTTAT
131 ACTGTTTTTATCTTTAATGTTTGGAGGAACTTGACCTCATGATTATGTCCTGCTACATCTCTTAT
12429002 GTTATTAGACCTTAAGTTTCTTTATCTATGGATCTTTCATTTTATTTAAAGCATGCATATATTAT
196 GTTATTAGACCTTAAGTTTCTTTATCTATGGATCTTTCATTTTATTTAAAGCATGCATATATTAT
12429067 CAGCGTTCTTCGTTCTTTACAGTATCTAGTATACGTTTTTTAAACTATCTTATAGCATTTTAGCT
261 CAGCGTTCTTCGTTCTTTACAGTATCTAGTATACGTTTTTTAAACTATCTTATAGCATTTTAGCT
12429132 TTACAGT
326 TTACAGT
12429139 ATCAAGGAAGGGAAGATTGTGGACAAAGTGACGGGAGCAAAGAAAGAAGAGCTTCAGCAGACTGT
1 ATCAAGGAAGGGAAGATTGTGGACAAAGTGACGGGAGCAAAGAAAGAAGAGCTTCAGCAGACTGT
12429204 GATAAAGCATATGGCTGCCACCAGTACTACTTCTTCAGCTTGATTTTATGATAATTATTAGTTCA
66 GATAAAGCATATGGCTGCCACCAGTACTACTTCTTCAGCTTGATTTTATGATAATTATTAGTTCA
12429269 ACTGTTTTTATCTTTAATGTTTGGAGGAACTTGACCTCATGATTATGTCCTGCTACATCTCTTAT
131 ACTGTTTTTATCTTTAATGTTTGGAGGAACTTGACCTCATGATTATGTCCTGCTACATCTCTTAT
12429334 GTTATTAGACCTTAAGTTTCTTTATCTATGGATCTTTCATTTTATTTAAAGCATGCATATATTAT
196 GTTATTAGACCTTAAGTTTCTTTATCTATGGATCTTTCATTTTATTTAAAGCATGCATATATTAT
12429399 CAGCGTTCTTCGTTCTTTACAGTATCTAGTATACGTTTTTTAAACTATCTTATAGCATTTTAGCT
261 CAGCGTTCTTCGTTCTTTACAGTATCTAGTATACGTTTTTTAAACTATCTTATAGCATTTTAGCT
12429464 TT
326 TT
12429466 CAAATCTTGA
Statistics
Matches: 327, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
332 327 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (332 bp):
ATCAAGGAAGGGAAGATTGTGGACAAAGTGACGGGAGCAAAGAAAGAAGAGCTTCAGCAGACTGT
GATAAAGCATATGGCTGCCACCAGTACTACTTCTTCAGCTTGATTTTATGATAATTATTAGTTCA
ACTGTTTTTATCTTTAATGTTTGGAGGAACTTGACCTCATGATTATGTCCTGCTACATCTCTTAT
GTTATTAGACCTTAAGTTTCTTTATCTATGGATCTTTCATTTTATTTAAAGCATGCATATATTAT
CAGCGTTCTTCGTTCTTTACAGTATCTAGTATACGTTTTTTAAACTATCTTATAGCATTTTAGCT
TTACAGT
Found at i:12430582 original size:33 final size:33
Alignment explanation
Indices: 12430545--12430612 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
12430535 ATTAATCTAA
12430545 AACTTAACAGGGTGGTTAACTTTATATTAACTG
1 AACTTAACAGGGTGGTTAACTTTATATTAACTG
*
12430578 AACTTAATAGGGTGGTTAACTTTATATTAACTG
1 AACTTAACAGGGTGGTTAACTTTATATTAACTG
12430611 AA
1 AA
12430613 ATAGCGACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (33 bp):
AACTTAACAGGGTGGTTAACTTTATATTAACTG
Found at i:12432698 original size:6 final size:6
Alignment explanation
Indices: 12432687--12432718 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12432677 AGCGGACCCA
*
12432687 GAAAAG GAAAAG GAAAAG GAAAAG GAAGAG GA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GA
12432719 TATTGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:12443661 original size:129 final size:129
Alignment explanation
Indices: 12443431--12443673 Score: 371
Period size: 129 Copynumber: 1.9 Consensus size: 129
12443421 CCTGAAGAAC
* ** **
12443431 GCCACAGGATTGAAATTGTTAATAGAATTCAAACTGAAAACTATCTCAATTAACATAGATTAAAG
1 GCCACAAGATTGAAATTGTTAATAGAAAACAAACCAAAAACTATCTCAATTAACATAGATTAAAG
*
12443496 GTCAATCCAACCTAGCATCAGCAGTGAGAACACGAGTACATAACTAATTTAACATCAATTGAAG
66 GCCAATCCAACCTAGCATCAGCAGTGAGAACACGAGTACATAACTAATTTAACATCAATTGAAG
*
12443560 GCCACAAGATTGAAATTGTTAATAGAAAACAAACCAAAAACTATCTCAATTAACATCA-ATTAAG
1 GCCACAAGATTGAAATTGTTAATAGAAAACAAACCAAAAACTATCTCAATTAACAT-AGATTAAA
* * * *
12443624 GGCCAATTCAACCTAGCATCAGCAGTGAGAATACGAGTACCTGACTAATT
65 GGCCAATCCAACCTAGCATCAGCAGTGAGAACACGAGTACATAACTAATT
12443674 CAAACCAAGA
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
129 101 0.99
130 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (129 bp):
GCCACAAGATTGAAATTGTTAATAGAAAACAAACCAAAAACTATCTCAATTAACATAGATTAAAG
GCCAATCCAACCTAGCATCAGCAGTGAGAACACGAGTACATAACTAATTTAACATCAATTGAAG
Found at i:12445441 original size:12 final size:12
Alignment explanation
Indices: 12445426--12445466 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
12445416 AATCTAATAA
12445426 AAAATTAATTTT
1 AAAATTAATTTT
**
12445438 AAAATT-A-TAA
1 AAAATTAATTTT
12445448 AAAATTAATTTT
1 AAAATTAATTTT
12445460 AAAATTA
1 AAAATTA
12445467 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 7 0.30
11 2 0.09
12 14 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTT
Found at i:12445448 original size:22 final size:22
Alignment explanation
Indices: 12445422--12445477 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
12445412 TATAAATCTA
12445422 ATAAAAAATTAATTTTAAAATT
1 ATAAAAAATTAATTTTAAAATT
12445444 ATAAAAAATTAATTTTAAAATT
1 ATAAAAAATTAATTTTAAAATT
12445466 ATAAAAAATTAA
1 ATAAAAAATTAA
12445478 AAAGTTCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAAAATTAATTTTAAAATT
Found at i:12452359 original size:62 final size:62
Alignment explanation
Indices: 12452262--12452462 Score: 375
Period size: 62 Copynumber: 3.2 Consensus size: 62
12452252 CACCAAGATA
12452262 AAAGCAGATTCCTATCTGCTGAGTCATGTCCTTTAAGTCATGTCTGTAATTAGTATGTTTGT
1 AAAGCAGATTCCTATCTGCTGAGTCATGTCCTTTAAGTCATGTCTGTAATTAGTATGTTTGT
12452324 AAAGCAGATTCCTATCTGCTGAGTCATGTCCTTTAAGTCATGTCTGTAATTAGTATGTTTGT
1 AAAGCAGATTCCTATCTGCTGAGTCATGTCCTTTAAGTCATGTCTGTAATTAGTATGTTTGT
* * *
12452386 AAAACCGATTCCTATCTGCTGAGTCATGTCCTTTAAGTCATGTCTGTAATTAGTATATTTGT
1 AAAGCAGATTCCTATCTGCTGAGTCATGTCCTTTAAGTCATGTCTGTAATTAGTATGTTTGT
12452448 AAAGCAGATTCCTAT
1 AAAGCAGATTCCTAT
12452463 ATATCTACTC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 134 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (62 bp):
AAAGCAGATTCCTATCTGCTGAGTCATGTCCTTTAAGTCATGTCTGTAATTAGTATGTTTGT
Found at i:12453062 original size:17 final size:17
Alignment explanation
Indices: 12453040--12453072 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12453030 ATTTATTTTT
12453040 ATCCAATTATGTTAACC
1 ATCCAATTATGTTAACC
*
12453057 ATCCAATTCTGTTAAC
1 ATCCAATTATGTTAAC
12453073 TATTATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (17 bp):
ATCCAATTATGTTAACC
Found at i:12453148 original size:32 final size:31
Alignment explanation
Indices: 12453085--12453148 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
12453075 TTATTAAATT
* **
12453085 TGTCATAAAAAATGACGTGACAATTTTAAAA
1 TGTCATAAAAAATGACATGACAATTCAAAAA
* *
12453116 TGTCATAGAAAAATGACATTATAATTCAAAAA
1 TGTCATA-AAAAATGACATGACAATTCAAAAA
12453148 T
1 T
12453149 TAACATGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (31 bp):
TGTCATAAAAAATGACATGACAATTCAAAAA
Found at i:12461645 original size:19 final size:19
Alignment explanation
Indices: 12461608--12461645 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12461598 GTAATTGAAC
* *
12461608 TTGAAAATTGGGTCTGAGA
1 TTGAAAATTGGGCCCGAGA
12461627 TTGAAAATTGGGCCCGAGA
1 TTGAAAATTGGGCCCGAGA
12461646 ATCCAAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.26
Consensus pattern (19 bp):
TTGAAAATTGGGCCCGAGA
Found at i:12466201 original size:41 final size:41
Alignment explanation
Indices: 12466063--12466214 Score: 182
Period size: 41 Copynumber: 3.7 Consensus size: 41
12466053 GTGAAATTGT
* * *
12466063 TCAGACTATACGTCTAGCAGGCTAAGTGTCGGTGAATTGAA
1 TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
*
12466104 TCGGACTATACGTCC-AGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATACG-CCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * *
12466145 TCAGGCTATAGGCCTAGCAGGCTAAGTGCCGGTGAACGGAA
1 TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * *
12466186 TTAGACTATAAGCCTATCAGG-TGAAGTGC
1 TCAGACTATACGCCTAGCAGGCT-AAGTGC
12466215 TAGTGAATCT
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.03
41 92 0.96
42 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.22
Consensus pattern (41 bp):
TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
Found at i:12466471 original size:27 final size:28
Alignment explanation
Indices: 12466411--12466472 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 28
12466401 TTTAAATGTG
*
12466411 TATATGTATGCATTTGGCATAGGTGGATATA
1 TATATGTATGCATTCGGCATAGGTGG--A-A
12466442 TATATGTATGCATTCGGCATAGGTGG-A
1 TATATGTATGCATTCGGCATAGGTGGAA
12466469 TATA
1 TATA
12466473 AGTGTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.17
31 25 0.83
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (28 bp):
TATATGTATGCATTCGGCATAGGTGGAA
Found at i:12466481 original size:37 final size:36
Alignment explanation
Indices: 12466411--12466530 Score: 150
Period size: 37 Copynumber: 3.5 Consensus size: 36
12466401 TTTAAATGTG
*
12466411 TATATGTATGCATTTGGCATAGGTGG-AT-A---TA
1 TATATGTATGCATTCGGCATAGGTGGTATAAGTGTA
12466442 TATATGTATGCATTCGGCATAGGTGGATATAAGTGTA
1 TATATGTATGCATTCGGCATAGGTGG-TATAAGTGTA
12466479 TATATGTATGCATTCGGCATAGGTGGGTATAAGTG-A
1 TATATGTATGCATTCGGCATAGGT-GGTATAAGTGTA
12466515 -ATATG--TGCATTCGGCA
1 TATATGTATGCATTCGGCA
12466531 CTTATAGTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
31 25 0.31
33 13 0.16
34 1 0.01
35 5 0.06
36 1 0.01
37 34 0.42
38 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (36 bp):
TATATGTATGCATTCGGCATAGGTGGTATAAGTGTA
Found at i:12467903 original size:16 final size:18
Alignment explanation
Indices: 12467877--12467909 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12467867 AAAAATCGGG
12467877 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
12467894 TTGA-AAAATTAATTTA
1 TTGAGAAAATTAATTTA
12467910 TGATGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:12468933 original size:184 final size:184
Alignment explanation
Indices: 12468612--12468967 Score: 460
Period size: 184 Copynumber: 1.9 Consensus size: 184
12468602 AAATAAAAAG
*
12468612 TTTTGGGGAGTAAAATATTGAGGGAAAGTAAATAGAGGGAGTAAAATTTTGGAGAGAAAATATTA
1 TTTTGGGGAGTAAAATATTGAGGGAAACTAAATAGAGGGAGTAAAATTTTGGAGAGAAAATATTA
** * * * *
12468677 AAAAAATGGGGGGGATGGGTTTAGGGTTGATGGGGGTGGGATGGGAGGGGAGTAAAAGTTTTAGG
66 AAAAAATGGGGGAAATGGATTCAGGGTAGATGGGGGTGGGATGGGAAGGGAGTAAAAGTTTTAGG
12468742 GGGAAAGTCG-G-AGAGAGTAAAAATTTTGCGGGAAAA-TAAAAATTTTTGAGGGT
131 GGGAAAGT-GAGAAG-GAGTAAAAATTTTGCGGGAAAAGTAAAAATTTTTGAGGGT
* *
12468795 TTTTGGGG-GT-AAA-ATTGAGGGAAACTAAAT-GTA-GGTGTAAAATTTTGGAGGGAAAATATT
1 TTTTGGGGAGTAAAATATTGAGGGAAACTAAATAG-AGGGAGTAAAATTTTGGAGAGAAAATATT
*
12468855 AAAAAAATTGGTGGGAAATGGATTCGGGGTAGATGGGGGAATTGGGATGGGAAGGGAGTAAAAGT
65 AAAAAAA-TGG-GGGAAATGGATTCAGGGTAGATGGGGG---TGGGATGGGAAGGGAGTAAAAGT
* *
12468920 TTT-GGGAGGAAAGTGAGAAGGAGTAAAAGTTTTGGGGGAAAAGTAAAA
125 TTTAGGG-GGAAAGTGAGAAGGAGTAAAAATTTTGCGGGAAAAGTAAAA
12468968 GGTTTGAGGA
Statistics
Matches: 151, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
179 33 0.22
180 20 0.13
181 24 0.16
182 2 0.01
183 12 0.08
184 53 0.35
185 7 0.05
ACGTcount: A:0.37, C:0.01, G:0.37, T:0.25
Consensus pattern (184 bp):
TTTTGGGGAGTAAAATATTGAGGGAAACTAAATAGAGGGAGTAAAATTTTGGAGAGAAAATATTA
AAAAAATGGGGGAAATGGATTCAGGGTAGATGGGGGTGGGATGGGAAGGGAGTAAAAGTTTTAGG
GGGAAAGTGAGAAGGAGTAAAAATTTTGCGGGAAAAGTAAAAATTTTTGAGGGT
Found at i:12472038 original size:45 final size:45
Alignment explanation
Indices: 12471983--12472068 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
12471973 GCTATACGGC
* * * * *
12471983 AAAATTAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATA
1 AAAATGAGTAAGACCAAAGCTGAAAGACGCTATGACATCATGATA
12472028 AAAATGAGTAAGACCAAAGCTGAAAGACGCTATGACATCAT
1 AAAATGAGTAAGACCAAAGCTGAAAGACGCTATGACATCAT
12472069 ATGAAAGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (45 bp):
AAAATGAGTAAGACCAAAGCTGAAAGACGCTATGACATCATGATA
Found at i:12472344 original size:74 final size:74
Alignment explanation
Indices: 12472109--12472340 Score: 331
Period size: 74 Copynumber: 3.1 Consensus size: 74
12472099 TAAAACCGTG
* * * * *
12472109 GCTGAAAGATACTATGACATCCTTTGATAGTCCGTTGGGATAATAAACATGGGGTTATCTTGTGT
1 GCTGAAAGATACTATGACATCCTTTGATAGTTCGTCGAGATAGTAAACATGGGGTTATATTGTGT
12472174 AAGACCATA
66 AAGACCATA
* * * * *
12472183 GCTGAAAGACACTATGACATCCTTTGATAGTTCATCGAGACAGTAAACACT-AGGTTATATTATG
1 GCTGAAAGATACTATGACATCCTTTGATAGTTCGTCGAGATAGTAAACA-TGGGGTTATATTGTG
12472247 TAAGACCATA
65 TAAGACCATA
** *
12472257 GCTGAAAGATGTTATGACATCCTTTGATAGTTTGTCGAGATAGTAAACATGGGGTTATATTGTGT
1 GCTGAAAGATACTATGACATCCTTTGATAGTTCGTCGAGATAGTAAACATGGGGTTATATTGTGT
12472322 AAGACCATA
66 AAGACCATA
12472331 GCTGAAAGAT
1 GCTGAAAGAT
12472341 GTTACAACAT
Statistics
Matches: 138, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
73 1 0.01
74 136 0.99
75 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (74 bp):
GCTGAAAGATACTATGACATCCTTTGATAGTTCGTCGAGATAGTAAACATGGGGTTATATTGTGT
AAGACCATA
Found at i:12472385 original size:27 final size:27
Alignment explanation
Indices: 12472354--12472443 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
12472344 ACAACATCAT
* * *
12472354 AGATAGACTATCGGGACACTAAACATG
1 AGATAGTCTAACGGGACATTAAACATG
*
12472381 AGATAGTCTAACGAGACATTAAACATG
1 AGATAGTCTAACGGGACATTAAACATG
* * *
12472408 GGATAGTCCAACGGGACATTAAACACG
1 AGATAGTCTAACGGGACATTAAACATG
12472435 AGATAGTCT
1 AGATAGTCT
12472444 GCTGGGACAG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (27 bp):
AGATAGTCTAACGGGACATTAAACATG
Found at i:12472450 original size:27 final size:26
Alignment explanation
Indices: 12472354--12472464 Score: 105
Period size: 27 Copynumber: 4.1 Consensus size: 26
12472344 ACAACATCAT
* *
12472354 AGATAGACTATCGGGACACTAAACATG
1 AGATAGTCTA-CGGGACATTAAACATG
*
12472381 AGATAGTCTAACGAGACATTAAACATG
1 AGATAGTCT-ACGGGACATTAAACATG
* * *
12472408 GGATAGTCCAACGGGACATTAAACACG
1 AGATAGT-CTACGGGACATTAAACATG
* * *
12472435 AGATAGTCTGCTGGGACAGTAAACGTG
1 AGATAGTCTAC-GGGACATTAAACATG
12472462 AGA
1 AGA
12472465 ATTTTGAGGT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
26 2 0.03
27 64 0.94
28 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (26 bp):
AGATAGTCTACGGGACATTAAACATG
Found at i:12487127 original size:12 final size:12
Alignment explanation
Indices: 12487106--12487138 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12487096 TTTTATTGCA
*
12487106 TTTTATTTTTAT
1 TTTTAGTTTTAT
12487118 TTTTAGTTTTAT
1 TTTTAGTTTTAT
12487130 TTTT-GTTTT
1 TTTTAGTTTT
12487139 CTAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (12 bp):
TTTTAGTTTTAT
Found at i:12487150 original size:18 final size:18
Alignment explanation
Indices: 12487105--12487154 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
12487095 TTTTTATTGC
12487105 ATTTTATTTTTATTTTTA
1 ATTTTATTTTTATTTTTA
* *
12487123 GTTTTATTTTTGTTTTCTA
1 ATTTTATTTTTATTTT-TA
12487142 A-TTT-TTTTTATTT
1 ATTTTATTTTTATTT
12487155 GCTTTTGGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 8 0.30
18 17 0.63
19 2 0.07
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (18 bp):
ATTTTATTTTTATTTTTA
Found at i:12489775 original size:64 final size:64
Alignment explanation
Indices: 12489668--12489792 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
12489658 GACACGGCAA
* * * * *
12489668 AGCCACACGGGCGTGTGGGATCTCACATGGGCGTGGAAGAAGCGAAGGAGATCACACACGGTCG
1 AGCCACACGGGCGTGTGGAATCTCACACGAGCATGGAAGAAGCGAAGGAAATCACACACGGTCG
*
12489732 AGCCACATGGGCGTGTGGAAT-TCCACACGAGCATGAGAA-AAGCGAAGGAAATCACACACGG
1 AGCCACACGGGCGTGTGGAATCT-CACACGAGCATG-GAAGAAGCGAAGGAAATCACACACGG
12489793 CCTGGACACA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.02
64 49 0.92
65 3 0.06
ACGTcount: A:0.31, C:0.23, G:0.34, T:0.12
Consensus pattern (64 bp):
AGCCACACGGGCGTGTGGAATCTCACACGAGCATGGAAGAAGCGAAGGAAATCACACACGGTCG
Done.