Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold684
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: 61720
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Found at i:705 original size:2 final size:2
Alignment explanation
Indices: 698--726 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
688 ATGACCACAA
698 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
727 GCCCTTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2421 original size:50 final size:50
Alignment explanation
Indices: 2322--2429 Score: 144
Period size: 50 Copynumber: 2.2 Consensus size: 50
2312 TTGTTTAGAG
* ** ** *
2322 TCAACAATTACGATTATCTCTCTCGATTGTCAAAGGTTTGTAAAGAATAA
1 TCAACAATTACGATCATCTCTCTCGATTGTCAAAAATTAATAAAAAATAA
*
2372 TCAACACTTACGATCATCTCTCTCGATTGTCAAAAATTAATAAAAAATAA
1 TCAACAATTACGATCATCTCTCTCGATTGTCAAAAATTAATAAAAAATAA
*
2422 TTAACAAT
1 TCAACAAT
2430 GATAATACCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (50 bp):
TCAACAATTACGATCATCTCTCTCGATTGTCAAAAATTAATAAAAAATAA
Found at i:4556 original size:16 final size:16
Alignment explanation
Indices: 4532--4566 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
4522 ATTGAATCTT
*
4532 AAATGATATAAACTTA
1 AAATAATATAAACTTA
4548 AAATAATATAAACTTA
1 AAATAATATAAACTTA
4564 AAA
1 AAA
4567 AAATTTGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATAATATAAACTTA
Found at i:4584 original size:15 final size:16
Alignment explanation
Indices: 4562--4598 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4552 AATATAAACT
*
4562 TAAAAAAATTTGAACC
1 TAAAAAATTTTGAACC
*
4578 TAAAAAATTTTGAACT
1 TAAAAAATTTTGAACC
4594 TAAAA
1 TAAAA
4599 TTGACTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (16 bp):
TAAAAAATTTTGAACC
Found at i:5667 original size:20 final size:19
Alignment explanation
Indices: 5637--5675 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
5627 TTAAAACTTA
5637 ATTTTATAAATAAATATAG
1 ATTTTATAAATAAATATAG
5656 ATTTTAATAAATAAATATAG
1 ATTTT-ATAAATAAATATAG
5676 TAAAAATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTTTATAAATAAATATAG
Found at i:5879 original size:16 final size:17
Alignment explanation
Indices: 5860--5891 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5850 AAAAGATTTG
5860 AATTCAAACTC-AAAAA
1 AATTCAAACTCGAAAAA
5876 AATTCAAACTCGAAAA
1 AATTCAAACTCGAAAA
5892 GCTCTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (17 bp):
AATTCAAACTCGAAAAA
Found at i:7448 original size:7 final size:7
Alignment explanation
Indices: 7438--7482 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
7428 AATAGTAAAT
7438 ATTTATA
1 ATTTATA
7445 ATTTATA
1 ATTTATA
7452 ATTTATA
1 ATTTATA
7459 ATTTATA
1 ATTTATA
* *
7466 ATTTTTT
1 ATTTATA
7473 ATTTA-A
1 ATTTATA
7479 ATTT
1 ATTT
7483 TTATTTACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
6 4 0.12
7 30 0.88
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTATA
Found at i:7485 original size:12 final size:12
Alignment explanation
Indices: 7445--7509 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
7435 AATATTTATA
*
7445 ATTTATAATTTATA
1 ATTTA-AATTT-TT
7459 ATTTATAATTTTTT
1 ATTTA-AA-TTTTT
7473 ATTTAAATTTTT
1 ATTTAAATTTTT
*
7485 ATTTACATTTTT
1 ATTTAAATTTTT
*
7497 -TTTGAAAGTTTT
1 ATTT-AAATTTTT
7509 A
1 A
7510 AATATTAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
11 3 0.07
12 22 0.50
13 2 0.05
14 14 0.32
15 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (12 bp):
ATTTAAATTTTT
Found at i:10199 original size:15 final size:15
Alignment explanation
Indices: 10179--10211 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10169 TGACGTGTTC
10179 TTGTGAGATTTGCCA
1 TTGTGAGATTTGCCA
10194 TTGTGAGATTTGCCA
1 TTGTGAGATTTGCCA
10209 TTG
1 TTG
10212 ATAGCTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.42
Consensus pattern (15 bp):
TTGTGAGATTTGCCA
Found at i:11910 original size:15 final size:15
Alignment explanation
Indices: 11890--11919 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11880 AAAAAATATA
*
11890 ATTTTATATTTAAAT
1 ATTTTATAATTAAAT
11905 ATTTTATAATTAAAT
1 ATTTTATAATTAAAT
11920 TTAAATAAAA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTATAATTAAAT
Found at i:12052 original size:13 final size:13
Alignment explanation
Indices: 12034--12058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12024 ATATTTTAAT
12034 TTTTTATAATAAA
1 TTTTTATAATAAA
12047 TTTTTATAATAA
1 TTTTTATAATAA
12059 TATTAAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTATAATAAA
Found at i:12212 original size:58 final size:59
Alignment explanation
Indices: 12134--12255 Score: 212
Period size: 58 Copynumber: 2.1 Consensus size: 59
12124 CAAATTTTAC
12134 CATCT-CAATTTTTTAAAAAAAAAATATTACCAAATTATCCCTAAGCAAATTTAATCTA
1 CATCTCCAATTTTTTAAAAAAAAAATATTACCAAATTATCCCTAAGCAAATTTAATCTA
* *
12192 CATCTCCAATTTTTT-TAAAAAGAATATTACCAAATTATCCCTAAGCAAATTTAATCTA
1 CATCTCCAATTTTTTAAAAAAAAAATATTACCAAATTATCCCTAAGCAAATTTAATCTA
12250 CATCTC
1 CATCTC
12256 ACAGCCTATG
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
58 52 0.85
59 9 0.15
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (59 bp):
CATCTCCAATTTTTTAAAAAAAAAATATTACCAAATTATCCCTAAGCAAATTTAATCTA
Found at i:17168 original size:11 final size:10
Alignment explanation
Indices: 17151--17186 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
17141 TAAAATTTTT
17151 AATTTAATTA
1 AATTTAATTA
17161 ATATTTAATTA
1 A-ATTTAATTA
17172 AATATTAATTA
1 AAT-TTAATTA
17183 AATT
1 AATT
17187 AAAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTTAATTA
Found at i:18094 original size:21 final size:23
Alignment explanation
Indices: 18046--18094 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
18036 ATTCGTATTT
*
18046 TAAAA-TTTATATTAATATAATT
1 TAAAATTTTATATTAATATAATA
*
18068 TAAAATTTTATATT-ATA-ACTA
1 TAAAATTTTATATTAATATAATA
18089 TAAAAT
1 TAAAAT
18095 CATATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 8 0.33
23 8 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAAATTTTATATTAATATAATA
Found at i:18622 original size:16 final size:17
Alignment explanation
Indices: 18593--18684 Score: 57
Period size: 16 Copynumber: 5.4 Consensus size: 17
18583 AATAAAATTT
*
18593 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
18610 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
*
18625 ATCAAATTTAT--TTAA
1 ATAAAATTTATAATTAA
* * *
18640 AAATAAATATATTATTAA
1 ATA-AAATTTATAATTAA
* *
18658 TATATAAATTTTTTATTAA
1 -ATA-AAATTTATAATTAA
18677 ATTAAAAT
1 A-TAAAAT
18685 ATTTTAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
14 2 0.03
15 8 0.13
16 18 0.30
17 6 0.10
18 9 0.15
19 17 0.28
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:18664 original size:19 final size:19
Alignment explanation
Indices: 18642--18693 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
18632 TTATTTAAAA
18642 ATAAATATATTATTAATAT
1 ATAAATATATTATTAATAT
* *
18661 ATAAATTTTTTATTAA-AT
1 ATAAATATATTATTAATAT
18679 -TAAA-ATATT-TTAATA
1 ATAAATATATTATTAATA
18694 AATTATATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 4 0.14
18 2 0.07
19 14 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAAATATATTATTAATAT
Found at i:18667 original size:35 final size:33
Alignment explanation
Indices: 18628--18693 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 33
18618 ATAATTAATC
18628 AAATTTATTTA-AAAATAAATATATTATTAATATAT
1 AAATTT-TTTATAAAATAAA-ATATT-TTAATATAT
*
18663 AAATTTTTTATTAAATTAAAATATTTTAATA
1 AAATTTTTTA-TAAAATAAAATATTTTAATA
18694 AATTATATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
34 10 0.36
35 11 0.39
36 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AAATTTTTTATAAAATAAAATATTTTAATATAT
Found at i:18689 original size:18 final size:19
Alignment explanation
Indices: 18642--18700 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
18632 TTATTTAAAA
*
18642 ATAAATATATTATT-AATAT
1 ATAAATATTTTATTAAAT-T
*
18661 ATAAATTTTTTATTAAATT
1 ATAAATATTTTATTAAATT
*
18680 A-AAATATTTTAATAAATT
1 ATAAATATTTTATTAAATT
18698 ATA
1 ATA
18701 TCAGATACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 16 0.47
19 15 0.44
20 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAAATATTTTATTAAATT
Found at i:19133 original size:12 final size:12
Alignment explanation
Indices: 19112--19144 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19102 ACATAAATTT
*
19112 TTTCTCTTTTTC
1 TTTCTTTTTTTC
19124 TTTCTTTTTTTC
1 TTTCTTTTTTTC
19136 TTT-TTTTTT
1 TTTCTTTTTT
19145 ATAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:19282 original size:9 final size:9
Alignment explanation
Indices: 19268--19307 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
19258 AAATAGTTAA
19268 TAATATTTT
1 TAATATTTT
19277 TAATATTTT
1 TAATATTTT
19286 TAATATTTT
1 TAATATTTT
*
19295 TATTA-TTT
1 TAATATTTT
19303 TAATA
1 TAATA
19308 AAAATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TAATATTTT
Found at i:19788 original size:27 final size:26
Alignment explanation
Indices: 19722--19896 Score: 106
Period size: 28 Copynumber: 6.4 Consensus size: 26
19712 TATTTTATTT
19722 TAATAATATAAAAAATAATAT--AAATA
1 TAAT-ATATAAAAAA-AATATAAAAATA
** * *
19748 CGATATTTATAAAAAAATATTTAAAATA
1 TAATATATA-AAAAAAATA-TAAAAATA
* *
19776 TAATATATAAAAATAATATAAATATACA
1 TAATATATAAAAAAAATATAAA-A-ATA
*
19804 TAA-ATATAAAAAATATATAAAAAATTA
1 TAATATATAAAAAAAATAT-AAAAA-TA
*
19831 TTAATATAT-AAAAAATTATAAAAATA
1 -TAATATATAAAAAAAATATAAAAATA
* * *
19857 TAATATTTTAAATAAAATAATATAAATA
1 TAATA-TATAAAAAAAAT-ATAAAAATA
*
19885 TAAATAAATAAA
1 T-AATATATAAA
19897 TATTTTTCAC
Statistics
Matches: 115, Mismatches: 20, Indels: 26
0.71 0.12 0.16
Matches are distributed among these distances:
25 13 0.11
26 16 0.14
27 35 0.30
28 43 0.37
29 8 0.07
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (26 bp):
TAATATATAAAAAAAATATAAAAATA
Found at i:19845 original size:18 final size:18
Alignment explanation
Indices: 19777--19859 Score: 85
Period size: 18 Copynumber: 4.5 Consensus size: 18
19767 TTTAAAATAT
*
19777 AATATATAAAAATAATATA
1 AATATATAAAAA-ATTATA
* * * *
19796 AATATACATAAATATAAAA
1 AATATATA-AAAAATTATA
*
19815 AATATATAAAAAATTATT
1 AATATATAAAAAATTATA
19833 AATATATAAAAAATTATA
1 AATATATAAAAAATTATA
*
19851 AAAATATAA
1 AATATATAA
19860 TATTTTAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
18 31 0.61
19 17 0.33
20 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (18 bp):
AATATATAAAAAATTATA
Found at i:19875 original size:14 final size:14
Alignment explanation
Indices: 19723--19898 Score: 81
Period size: 14 Copynumber: 12.9 Consensus size: 14
19713 ATTTTATTTT
19723 AATAATAT-AA-AA
1 AATAATATAAATAA
*
19735 AATAATATAAATAC
1 AATAATATAAATAA
* *
19749 GATATTTATAAA-AA
1 AATA-ATATAAATAA
*
19763 AAT-AT-TTAA-AA
1 AATAATATAAATAA
* *
19774 TATAATATATA-AA
1 AATAATATAAATAA
19787 AATAATATAAATATA
1 AATAATATAAATA-A
*
19802 CATAA-ATATAA-AA
1 AATAATATA-AATAA
19815 AAT-ATATAAA-AA
1 AATAATATAAATAA
19827 ATTATTAATATATAA-AA
1 A--A-TAATATA-AATAA
* * *
19844 AATTATAAAAATAT
1 AATAATATAAATAA
* *
19858 AATATTTTAAATAA
1 AATAATATAAATAA
19872 AATAATATAAATATA
1 AATAATATAAATA-A
19887 AATAA-ATAAATA
1 AATAATATAAATA
19899 TTTTTCACTT
Statistics
Matches: 124, Mismatches: 24, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
11 7 0.06
12 17 0.14
13 23 0.19
14 46 0.37
15 21 0.17
16 5 0.04
17 5 0.04
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (14 bp):
AATAATATAAATAA
Found at i:19891 original size:10 final size:10
Alignment explanation
Indices: 19782--19894 Score: 64
Period size: 10 Copynumber: 11.7 Consensus size: 10
19772 AATATAATAT
*
19782 ATAAAAATAA
1 ATAAATATAA
*
19792 TATAAATATAC
1 -ATAAATATAA
19803 ATAAATATAA
1 ATAAATATAA
19813 A-AAATATATA
1 ATAAATATA-A
*
19823 A-AAA-ATTA
1 ATAAATATAA
*
19831 TTAATATATAA
1 ATAA-ATATAA
19842 A-AAAT-TATA
1 ATAAATATA-A
19851 A-AAATAT-A
1 ATAAATATAA
* *
19859 AT-ATTTTAA
1 ATAAATATAA
19868 ATAAA-ATAA
1 ATAAATATAA
19877 TATAAATATAA
1 -ATAAATATAA
19888 ATAAATA
1 ATAAATA
19895 AATATTTTTC
Statistics
Matches: 80, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
8 8 0.10
9 25 0.31
10 32 0.40
11 15 0.19
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAAATATAA
Found at i:19896 original size:28 final size:28
Alignment explanation
Indices: 19771--19898 Score: 86
Period size: 30 Copynumber: 4.5 Consensus size: 28
19761 AAAATATTTA
*
19771 AAATATAATATATAAAAATAATATAAATAT
1 AAATA-AATAAAT-AAAATAATATAAATAT
*
19801 ACATAAATATAA-AAAAT-ATATAAA-A-
1 AAATAAATA-AATAAAATAATATAAATAT
* * *
19826 AATTATTAATATATAAAA-AATTATAAAAAT
1 AA--ATAAATAAATAAAATAA-TATAAATAT
**
19856 ATAATATTTTAAATAAAATAATATAAATAT
1 A-AATA-AATAAATAAAATAATATAAATAT
19886 AAATAAATAAATA
1 AAATAAATAAATA
19899 TTTTTCACTT
Statistics
Matches: 75, Mismatches: 12, Indels: 24
0.68 0.11 0.22
Matches are distributed among these distances:
25 1 0.01
26 2 0.03
27 18 0.24
28 17 0.23
29 11 0.15
30 23 0.31
31 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (28 bp):
AAATAAATAAATAAAATAATATAAATAT
Found at i:19925 original size:14 final size:15
Alignment explanation
Indices: 19906--19950 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
19896 ATATTTTTCA
19906 CTTTTT-TTTCTCTT
1 CTTTTTCTTTCTCTT
19920 CTTTTTCTTTC-CTT
1 CTTTTTCTTTCTCTT
19934 -TTCTTTCTTTCT-TT
1 CTT-TTTCTTTCTCTT
19948 CTT
1 CTT
19951 CTCTCTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.07
14 19 0.70
15 6 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTCTTTCTCTT
Found at i:19927 original size:11 final size:11
Alignment explanation
Indices: 19899--19952 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
19889 TAAATAAATA
* *
19899 TTTTTCACTTT
1 TTTTTCTCTTC
19910 TTTTTCTCTTC
1 TTTTTCTCTTC
19921 TTTTTCT-TTC
1 TTTTTCTCTTC
*
19931 CTTTTCT-TTC
1 TTTTTCTCTTC
19941 TTTCTT-TCTTC
1 TTT-TTCTCTTC
19952 T
1 T
19953 CTCTTTTTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 15 0.41
11 22 0.59
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTCTCTTC
Found at i:19928 original size:9 final size:10
Alignment explanation
Indices: 19906--19943 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
19896 ATATTTTTCA
19906 CTTT-TTTTT
1 CTTTCTTTTT
19915 CTCTTCTTTTT
1 CT-TTCTTTTT
*
19926 CTTTCCTTTT
1 CTTTCTTTTT
19936 CTTTCTTT
1 CTTTCTTT
19944 CTTTCTTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.08
10 16 0.64
11 7 0.28
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:19940 original size:25 final size:25
Alignment explanation
Indices: 19901--19961 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
19891 AATAAATATT
*
19901 TTTCACTTTTTTTTCTCTTCTTT-TTC
1 TTTC-CTTTTCTTTCT-TTCTTTCTTC
19927 TTTCCTTTTCTTTCTTTCTTTCTTC
1 TTTCCTTTTCTTTCTTTCTTTCTTC
* *
19952 TCTCTTTTTC
1 TTTCCTTTTC
19962 GACTGAACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 21 0.68
26 4 0.13
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTCCTTTTCTTTCTTTCTTTCTTC
Found at i:19957 original size:15 final size:15
Alignment explanation
Indices: 19912--19958 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
19902 TTCACTTTTT
19912 TTTCTCTTCTT-TTTC
1 TTTCT-TTCTTCTTTC
*
19927 TTTCCTT-TTCTTTC
1 TTTCTTTCTTCTTTC
*
19941 TTTCTTTCTTCTCTC
1 TTTCTTTCTTCTTTC
19956 TTT
1 TTT
19959 TTCGACTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 2 0.07
14 12 0.44
15 13 0.48
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCTTTCTTCTTTC
Found at i:22958 original size:21 final size:22
Alignment explanation
Indices: 22914--22960 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
22904 ATTAAAAATT
*
22914 AATTTAAACTCAAACATAAAAA
1 AATTTAAACTAAAACATAAAAA
* *
22936 AATTTGAACTAAAAC-TCAAAA
1 AATTTAAACTAAAACATAAAAA
22957 AATT
1 AATT
22961 CAAATTCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.26
Consensus pattern (22 bp):
AATTTAAACTAAAACATAAAAA
Found at i:22985 original size:16 final size:15
Alignment explanation
Indices: 22947--22989 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
22937 ATTTGAACTA
*
22947 AAACTCAAAAAATTC
1 AAACTCGAAAAATTC
* *
22962 AAATTCGAAAAGTTC
1 AAACTCGAAAAATTC
22977 TAAACTCGAAAAA
1 -AAACTCGAAAAA
22990 ACTCAAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.21
Consensus pattern (15 bp):
AAACTCGAAAAATTC
Found at i:27592 original size:23 final size:25
Alignment explanation
Indices: 27544--27608 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 25
27534 TATAAAATAA
*
27544 TTTTATTATTTTCATTTCATTAATT
1 TTTTATTATTTTAATTTCATTAATT
27569 TTTTATTATTTTAA-TT-A-TATATT
1 TTTTATTATTTTAATTTCATTA-ATT
*
27592 TTTTAATATTTTAATTT
1 TTTTATTATTTTAATTT
27609 TTGGACAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 2 0.06
23 17 0.47
24 4 0.11
25 13 0.36
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATTATTTTAATTTCATTAATT
Found at i:29934 original size:34 final size:34
Alignment explanation
Indices: 29862--30080 Score: 235
Period size: 34 Copynumber: 6.5 Consensus size: 34
29852 AAGTGGGAGA
* * * *
29862 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACT
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * ** * *
29895 GTTGTTGATTAAATGGGTGATTTGGCGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
29929 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* **
29963 ATTGTTGATTAAATGGGAAATTTGGTAGCTTATT
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
29997 ATTGTTGATTAAATGGGTGATTTGATGGCTTACT
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
30031 ATTGTTGACTAAATGGGAGATTTGGTAAG-TTGCC
1 ATTGTTGATTAAATGGGAGATTTGGT-AGCTTACC
30065 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
30081 TGGTTTTTAC
Statistics
Matches: 155, Mismatches: 29, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
33 13 0.08
34 141 0.91
35 1 0.01
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:30037 original size:102 final size:101
Alignment explanation
Indices: 29862--30082 Score: 311
Period size: 102 Copynumber: 2.2 Consensus size: 101
29852 AAGTGGGAGA
* * * * *
29862 ATTGTTGATTAAATGGTGATTTAGTAGTTTACTGTTGTTGATTAAATGGGTGATTTGGCGGTTTG
1 ATTGTTGATTAAATGGTGATTTAGTAGCTTACTATTGTTGATTAAATGGGTGATTTGACGGCTTA
29927 CCATTGTTGACTAAATGGGAGATTTGGT-AGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAAG-TTACC
* * *
29963 ATTGTTGATTAAATGG-GAAATTTGGTAGCTTATTATTGTTGATTAAATGGGTGATTTGATGGCT
1 ATTGTTGATTAAATGGTG--ATTTAGTAGCTTACTATTGTTGATTAAATGGGTGATTTGACGGCT
* *
30027 TACTATTGTTGACTAAATGGGAGATTTGGTAAGTTGCC
64 TACCATTGTTGACTAAATGGGAGATTTGGTAAGTTACC
30065 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
30083 GTTTTTACCA
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
100 1 0.01
101 16 0.15
102 86 0.81
103 3 0.03
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTAGTAGCTTACTATTGTTGATTAAATGGGTGATTTGACGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAAGTTACC
Found at i:31412 original size:13 final size:13
Alignment explanation
Indices: 31394--31428 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
31384 TTTATGATGC
* *
31394 ATCGATATACTGT
1 ATCGATACAATGT
31407 ATCGATACAATGT
1 ATCGATACAATGT
31420 ATCGATACA
1 ATCGATACA
31429 TGAATAGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (13 bp):
ATCGATACAATGT
Found at i:31475 original size:14 final size:14
Alignment explanation
Indices: 31456--31485 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31446 TGATTTTTAA
31456 TGATACATGAATAG
1 TGATACATGAATAG
*
31470 TGATACGTGAATAG
1 TGATACATGAATAG
31484 TG
1 TG
31486 TGAACAGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (14 bp):
TGATACATGAATAG
Found at i:31540 original size:22 final size:22
Alignment explanation
Indices: 31486--31540 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
31476 GTGAATAGTG
31486 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
31508 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
31529 TGAACAGTGATG
1 TGAACAGTGATG
31541 AATAGTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:31547 original size:10 final size:10
Alignment explanation
Indices: 31528--31558 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
31518 GTATCGATAC
31528 ATGAACAGTG
1 ATGAACAGTG
*
31538 ATGAATAGTG
1 ATGAACAGTG
31548 ATGAACAGTG
1 ATGAACAGTG
31558 A
1 A
31559 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:31650 original size:53 final size:53
Alignment explanation
Indices: 31585--31718 Score: 205
Period size: 53 Copynumber: 2.5 Consensus size: 53
31575 CTACCAATGC
* * *
31585 ATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGTCAGTGACCTGT
1 ATCGATACATATTTTGTGTATCGATACAAATTTGACTACTGCCAATGACCTGT
* * *
31638 ATTGATACATATTGTGTGTATCGATACAAATTTGACTACTGCCAATGTCCTGT
1 ATCGATACATATTTTGTGTATCGATACAAATTTGACTACTGCCAATGACCTGT
31691 ATCGATACATATTTGTGTGTATCGATAC
1 ATCGATACATATTT-TGTGTATCGATAC
31719 TATGCAATCT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
53 59 0.82
54 13 0.18
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (53 bp):
ATCGATACATATTTTGTGTATCGATACAAATTTGACTACTGCCAATGACCTGT
Found at i:31754 original size:21 final size:20
Alignment explanation
Indices: 31706--31760 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
31696 TACATATTTG
**
31706 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATAAAA
* *
31726 TCTGTATCGATACATTTAAAA
1 TGTGTATCGATAC-TATAAAA
31747 TGTGTATCGATACT
1 TGTGTATCGATACT
31761 TTTCAGGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (20 bp):
TGTGTATCGATACTATAAAA
Found at i:31823 original size:21 final size:21
Alignment explanation
Indices: 31799--31839 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31789 GTCAACCTTG
31799 TGTATTAATACTAATA-GTATA
1 TGTATTAATAC-AATACGTATA
*
31820 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
31840 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:32140 original size:23 final size:25
Alignment explanation
Indices: 32092--32156 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 25
32082 TATAAAATAA
*
32092 TTTTATTATTTTCATTTCATTAATT
1 TTTTATTATTTTAATTTCATTAATT
32117 TTTTATTATTTTAA-TT-A-TATATT
1 TTTTATTATTTTAATTTCATTA-ATT
*
32140 TTTTAATATTTTAATTT
1 TTTTATTATTTTAATTT
32157 TTTACAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 2 0.06
23 17 0.47
24 4 0.11
25 13 0.36
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATTATTTTAATTTCATTAATT
Found at i:33294 original size:2 final size:2
Alignment explanation
Indices: 33287--33314 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33277 AAGTGAATAA
33287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33315 GCACATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34300 original size:18 final size:18
Alignment explanation
Indices: 34265--34323 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
34255 GTTTAAAATA
34265 TTATAA-AT-TTATATAAT
1 TTATAATATATTA-ATAAT
34282 TTATAATATATTAATAAT
1 TTATAATATATTAATAAT
*
34300 TTATATTATA-TAA-AAT
1 TTATAATATATTAATAAT
34316 TTAATAAT
1 TT-ATAAT
34324 TTATATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 5 0.14
17 13 0.35
18 16 0.43
19 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATAATATATTAATAAT
Found at i:34324 original size:24 final size:25
Alignment explanation
Indices: 34258--34329 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 25
34248 TTATTATGTT
*
34258 TAAAATATT-ATAAATTTATATAATTTA
1 TAAAATATTAAT-AATTTATAT--TATA
*
34285 TAATATATTAATAATTTATATTATA
1 TAAAATATTAATAATTTATATTATA
34310 TAAAAT-TTAATAATTTATAT
1 TAAAATATTAATAATTTATAT
34330 ATTTATACAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 14 0.34
25 8 0.20
27 17 0.41
28 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAAATATTAATAATTTATATTATA
Found at i:34335 original size:27 final size:27
Alignment explanation
Indices: 34258--34336 Score: 89
Period size: 25 Copynumber: 3.1 Consensus size: 27
34248 TTATTATGTT
34258 TAAAATATT-ATAAATTTATATAATT-TA
1 TAAAATATTAAT-AATTTATAT-ATTATA
*
34285 TAATATATTAATAA-TT-TATATTATA
1 TAAAATATTAATAATTTATATATTATA
34310 TAAAAT-TTAATAATTTATATATT-TA
1 TAAAATATTAATAATTTATATATTATA
34335 TA
1 TA
34337 CATATTCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
24 10 0.22
25 16 0.35
26 8 0.17
27 10 0.22
28 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAAAATATTAATAATTTATATATTATA
Found at i:35801 original size:34 final size:34
Alignment explanation
Indices: 35763--35827 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
35753 TAATTGTAAT
*
35763 TTAAA-AATAAAAAATAAATTATATAGATTAAATA
1 TTAAATAATAAAAAAT-AATTATATAAATTAAATA
**
35797 TTAAATTTTAAAAAATAATTATATAAATTAA
1 TTAAATAATAAAAAATAATTATATAAATTAA
35828 TTAAATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 19 0.70
35 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (34 bp):
TTAAATAATAAAAAATAATTATATAAATTAAATA
Found at i:36226 original size:19 final size:18
Alignment explanation
Indices: 36204--36261 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 18
36194 TAAAATAATA
36204 TTTAAATTTAAATATTATT
1 TTTAAATTTAAATA-TATT
*
36223 TTTAAATTT--ATATATA
1 TTTAAATTTAAATATATT
* *
36239 ATTAAATTTAAATAAATT
1 TTTAAATTTAAATATATT
36257 TTTAA
1 TTTAA
36262 TATATAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 11 0.34
17 3 0.09
18 9 0.28
19 9 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATTTAAATATATT
Found at i:36279 original size:35 final size:35
Alignment explanation
Indices: 36192--36281 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 35
36182 AAGTTTATAT
*
36192 TATAAAATAATATTTAAATTTAAATATTATTTTTAAA
1 TATAAAAT-A-ATTTAAATTTAAATATAATTTTTAAA
* *
36229 TTTATATATAA-TTAAATTTAAATA-AATTTTTAATA
1 TATA-AAATAATTTAAATTTAAATATAATTTTTAA-A
36264 TATAAAATAATTTAAATT
1 TATAAAATAATTTAAATT
36282 AATTTAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
34 13 0.29
35 24 0.53
36 1 0.02
37 4 0.09
38 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TATAAAATAATTTAAATTTAAATATAATTTTTAAA
Found at i:36287 original size:27 final size:27
Alignment explanation
Indices: 36225--36316 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 27
36215 ATATTATTTT
*
36225 TAAATTT-ATATAT-AATTAAATTTAAA
1 TAAATTTAATATATAAAAT-AATTTAAA
36251 TAAATTTTTAATATATAAAATAATTTAAA
1 TAAA--TTTAATATATAAAATAATTTAAA
* * **
36280 TTAATTTAA-ATTATAAAATATTTTATT
1 TAAATTTAATA-TATAAAATAATTTAAA
36307 TAAATTTAAT
1 TAAATTTAAT
36317 TAAATATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
26 5 0.09
27 26 0.48
28 3 0.06
29 17 0.31
30 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TAAATTTAATATATAAAATAATTTAAA
Found at i:36294 original size:29 final size:32
Alignment explanation
Indices: 36206--36294 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 32
36196 AAATAATATT
* *
36206 TAAATTTAAATATTATTTTTAAATTTATATATAAT
1 TAAATTTAAATA--AATTTTAAA-TTATATATAAA
*
36241 TAAATTTAAATAAATTTTTAA-TATATA-AAA
1 TAAATTTAAATAAATTTTAAATTATATATAAA
*
36271 T-AATTTAAATTAA-TTTAAATTATA
1 TAAATTTAAATAAATTTTAAATTATA
36295 AAATATTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
28 5 0.10
29 15 0.31
30 3 0.06
31 6 0.12
33 7 0.15
35 12 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TAAATTTAAATAAATTTTAAATTATATATAAA
Found at i:36369 original size:40 final size:42
Alignment explanation
Indices: 36275--36385 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 42
36265 ATAAAATAAT
*
36275 TTAAAT-TAATTTAAATTATAAAATATTTTATTTAAATTTAA
1 TTAAATATAATTTATATTATAAAATATTTTATTTAAATTTAA
* *
36316 TTAAATATAAATTTATATTTTTAAATA-TTT-TTTAAA-TTAA
1 TTAAATAT-AATTTATATTATAAAATATTTTATTTAAATTTAA
*
36356 TTAATTTATAATTTATATTAATAATAATAT
1 TTAA-ATATAATTTATATT-ATAA-AATAT
36386 ATTAAATATA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
40 18 0.31
41 17 0.29
42 8 0.14
43 15 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (42 bp):
TTAAATATAATTTATATTATAAAATATTTTATTTAAATTTAA
Found at i:36370 original size:21 final size:20
Alignment explanation
Indices: 36346--36409 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
36336 TTAAATATTT
*
36346 TTTAAATTAATTAATTTATAA
1 TTTAAATTAA-TAATTAATAA
*
36367 TTTATATTAATAA-TAAT-A
1 TTTAAATTAATAATTAATAA
36385 TATTAAATATAATAATTAATAA
1 T-TTAAAT-TAATAATTAATAA
36407 TTT
1 TTT
36410 TCTTTCACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.06
19 8 0.22
20 9 0.25
21 15 0.42
22 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAATTAATAATTAATAA
Found at i:36388 original size:14 final size:14
Alignment explanation
Indices: 36369--36407 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
36359 ATTTATAATT
36369 TATATTAATAATAA
1 TATATTAATAATAA
36383 TATATTAA-ATATAA
1 TATATTAATA-ATAA
36397 TA-ATTAATAAT
1 TATATTAATAAT
36408 TTTCTTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATTAATAATAA
Found at i:36461 original size:20 final size:21
Alignment explanation
Indices: 36436--36481 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
36426 TAAAAAATAA
* * *
36436 AAAAAATTAATAATTATT-TT
1 AAAAAATAAAAAATAATTCTT
36456 AAAAAATAAAAAATAATTCTT
1 AAAAAATAAAAAATAATTCTT
36477 AAAAA
1 AAAAA
36482 TTTTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAAATAAAAAATAATTCTT
Found at i:36489 original size:29 final size:29
Alignment explanation
Indices: 36419--36489 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
36409 TTCTTTCACT
36419 AAAATTTTAAAAAATAAAAAAAATTAATA
1 AAAATTTTAAAAAATAAAAAAAATTAATA
** **
36448 ATTATTTTAAAAAATAAAAAATAATTCTTA
1 AAAATTTTAAAAAATAAAAAA-AATTAATA
36478 AAAATTTTAAAA
1 AAAATTTTAAAA
36490 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAATTTTAAAAAATAAAAAAAATTAATA
Found at i:36539 original size:18 final size:17
Alignment explanation
Indices: 36516--36562 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
36506 CATCCTCTTC
36516 TAAAATATATTAATATTT
1 TAAAATATATTAAT-TTT
36534 TAAAATAATATT-ATTTT
1 TAAAAT-ATATTAATTTT
*
36551 TAATAT-TATTAA
1 TAAAATATATTAA
36563 ATTAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 1 0.04
17 8 0.31
18 8 0.31
19 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAAATATATTAATTTT
Found at i:36985 original size:3 final size:3
Alignment explanation
Indices: 36977--37012 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
36967 ATAAGGAGAT
36977 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
37013 GGGAGATGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:37760 original size:24 final size:25
Alignment explanation
Indices: 37716--37770 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
37706 AATTTATATT
* * *
37716 TTATATATTGTTAGTATAT-AAATA
1 TTATATATTATTAATATATAAAAAA
37740 TTATATATTATTAAT-TGATAAAAAA
1 TTATATATTATTAATAT-ATAAAAAA
37765 TTATAT
1 TTATAT
37771 TTTAAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 15 0.58
25 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (25 bp):
TTATATATTATTAATATATAAAAAA
Found at i:38438 original size:26 final size:27
Alignment explanation
Indices: 38409--38462 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
38399 TTTTAATATA
38409 ATATAATAAAATATTATA-TTAAAAAT
1 ATATAATAAAATATTATATTTAAAAAT
** *
38435 ATATTTTAATATATTATATTTAAAAAT
1 ATATAATAAAATATTATATTTAAAAAT
38462 A
1 A
38463 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATAATAAAATATTATATTTAAAAAT
Found at i:38454 original size:15 final size:14
Alignment explanation
Indices: 38417--38476 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
38407 TAATATAATA
38417 AAATATTATA--TT
1 AAATATTATATTTT
*
38429 AAA-AATATATTTT
1 AAATATTATATTTT
38442 AATATATTATA-TTT
1 AA-ATATTATATTTT
* *
38456 AAAAATAATATTTT
1 AAATATTATATTTT
38470 AAATATT
1 AAATATT
38477 TAGAGCTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
11 5 0.14
12 3 0.08
13 10 0.27
14 14 0.38
15 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATTATATTTT
Found at i:38469 original size:28 final size:25
Alignment explanation
Indices: 38417--38476 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 25
38407 TAATATAATA
38417 AAATATTATATTAAAAATATATTTT
1 AAATATTATATTAAAAATATATTTT
38442 AATATATTATATTTAAAAATAATATTTT
1 AA-ATATTATA-TTAAAAAT-ATATTTT
38470 AAATATT
1 AAATATT
38477 TAGAGCTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 2 0.06
26 8 0.25
27 13 0.41
28 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATATTATATTAAAAATATATTTT
Found at i:38486 original size:28 final size:27
Alignment explanation
Indices: 38428--38486 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
38418 AATATTATAT
* **
38428 TAAAAATATATTTTAATATATTATATT
1 TAAAAATATATTTTAATATATTAGAGC
38455 TAAAAATAATATTTTAA-ATATTTAGAGC
1 TAAAAAT-ATATTTTAATATA-TTAGAGC
38483 TAAA
1 TAAA
38487 GCAGTATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (27 bp):
TAAAAATATATTTTAATATATTAGAGC
Found at i:38906 original size:23 final size:21
Alignment explanation
Indices: 38870--38925 Score: 94
Period size: 22 Copynumber: 2.6 Consensus size: 21
38860 ACGATATATG
38870 TAATATAAATATAATAAAAAA
1 TAATATAAATATAATAAAAAA
38891 TTAATATATAATATAATAAAAAA
1 -TAATATA-AATATAATAAAAAA
38914 TAATATAAATAT
1 TAATATAAATAT
38926 TATACAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 5 0.15
22 14 0.42
23 14 0.42
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATATAAATATAATAAAAAA
Found at i:39115 original size:19 final size:21
Alignment explanation
Indices: 39093--39137 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
39083 ATTAAAATTT
39093 ATATAATAAAATATTT-T-AA
1 ATATAATAAAATATTTATAAA
* *
39112 ATATAATTATATATTTATAAA
1 ATATAATAAAATATTTATAAA
39133 ATATA
1 ATATA
39138 TGAATATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 1 0.05
21 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATAATAAAATATTTATAAA
Found at i:39169 original size:17 final size:19
Alignment explanation
Indices: 39129--39171 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
39119 TATATATTTA
39129 TAAAATATATGAATATAAT
1 TAAAATATATGAATATAAT
* *
39148 AAAAATATAT-AA-ATTAT
1 TAAAATATATGAATATAAT
39165 TAAAATA
1 TAAAATA
39172 ACTTGTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAAATATATGAATATAAT
Found at i:39315 original size:11 final size:10
Alignment explanation
Indices: 39298--39333 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
39288 AAAATTTTTT
39298 AATTTAATTA
1 AATTTAATTA
39308 ATATTTAATTA
1 A-ATTTAATTA
39319 AATATTAATTA
1 AAT-TTAATTA
39330 AATT
1 AATT
39334 AAAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTTAATTA
Found at i:40248 original size:21 final size:23
Alignment explanation
Indices: 40200--40248 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
40190 ATTCGTATTT
*
40200 TAAAA-TTTATATTAATATAATT
1 TAAAATTTTATATTAATATAATA
*
40222 TAAAATTTTATATT-ATA-ACTA
1 TAAAATTTTATATTAATATAATA
40243 TAAAAT
1 TAAAAT
40249 CATATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 8 0.33
23 8 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAAATTTTATATTAATATAATA
Found at i:40776 original size:16 final size:17
Alignment explanation
Indices: 40747--40838 Score: 57
Period size: 16 Copynumber: 5.4 Consensus size: 17
40737 AATAAAATTT
*
40747 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
40764 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
*
40779 ATCAAATTTAT--TTAA
1 ATAAAATTTATAATTAA
* * *
40794 AAATAAATATATTATTAA
1 ATA-AAATTTATAATTAA
* *
40812 TATATAAATTTTTTATTAA
1 -ATA-AAATTTATAATTAA
40831 ATTAAAAT
1 A-TAAAAT
40839 ATTTTAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
14 2 0.03
15 8 0.13
16 18 0.30
17 6 0.10
18 9 0.15
19 17 0.28
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:40818 original size:19 final size:19
Alignment explanation
Indices: 40796--40847 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
40786 TTATTTAAAA
40796 ATAAATATATTATTAATAT
1 ATAAATATATTATTAATAT
* *
40815 ATAAATTTTTTATTAA-AT
1 ATAAATATATTATTAATAT
40833 -TAAA-ATATT-TTAATA
1 ATAAATATATTATTAATA
40848 AATTATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 4 0.14
18 2 0.07
19 14 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAAATATATTATTAATAT
Found at i:40821 original size:35 final size:33
Alignment explanation
Indices: 40782--40847 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 33
40772 ATAATTAATC
40782 AAATTTATTTA-AAAATAAATATATTATTAATATAT
1 AAATTT-TTTATAAAATAAA-ATATT-TTAATATAT
*
40817 AAATTTTTTATTAAATTAAAATATTTTAATA
1 AAATTTTTTA-TAAAATAAAATATTTTAATA
40848 AATTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
34 10 0.36
35 11 0.39
36 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AAATTTTTTATAAAATAAAATATTTTAATATAT
Found at i:40843 original size:18 final size:19
Alignment explanation
Indices: 40796--40854 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
40786 TTATTTAAAA
*
40796 ATAAATATATTATT-AATAT
1 ATAAATATTTTATTAAAT-T
*
40815 ATAAATTTTTTATTAAATT
1 ATAAATATTTTATTAAATT
*
40834 A-AAATATTTTAATAAATT
1 ATAAATATTTTATTAAATT
40852 ATA
1 ATA
40855 TATAGTAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 16 0.47
19 15 0.44
20 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAAATATTTTATTAAATT
Found at i:41287 original size:22 final size:24
Alignment explanation
Indices: 41246--41290 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
41236 AAATTTATAT
*
41246 AAAAATATAATATTTAGAATACAA
1 AAAAATATAATATATAGAATACAA
41270 AAAAATATAA-ATAT-GAATACA
1 AAAAATATAATATATAGAATACA
41291 TAAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 10 0.50
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (24 bp):
AAAAATATAATATATAGAATACAA
Found at i:42511 original size:17 final size:17
Alignment explanation
Indices: 42489--42568 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 17
42479 ATTTATATTA
42489 TAAATAATATTTAAAAT
1 TAAATAATATTTAAAAT
* * *
42506 TAAATATTATTTTTATAT
1 TAAATAATA-TTTAAAAT
* *
42524 T-AATATATAATTAAATT
1 TAAATA-ATATTTAAAAT
*
42541 TAAATAATTTTTAATACAT
1 TAAATAATATTTAA-A-AT
42560 ATAAATAAT
1 -TAAATAAT
42569 TTAAATTATA
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
17 23 0.50
18 14 0.30
19 1 0.02
20 8 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATAATATTTAAAAT
Found at i:42573 original size:35 final size:37
Alignment explanation
Indices: 42487--42587 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 37
42477 AAATTTATAT
*
42487 TATAAATAATATTTAAAATTAAATATTATTTTTATATTAA
1 TATAAAT-A-ATTTAAATTTAAATA-TATTTTTATATTAA
42527 TAT--ATAA-TTAAATTTAAATA-ATTTTTA-A-TACA
1 TATAAATAATTTAAATTTAAATATATTTTTATATTA-A
42559 TATAAATAATTTAAATTATAAA-ATATTTT
1 TATAAATAATTTAAATT-TAAATATATTTT
42588 ATTTAAATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
31 2 0.04
32 5 0.09
33 7 0.13
34 4 0.07
35 20 0.37
36 10 0.19
37 1 0.02
38 2 0.04
40 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (37 bp):
TATAAATAATTTAAATTTAAATATATTTTTATATTAA
Found at i:42734 original size:23 final size:22
Alignment explanation
Indices: 42708--42776 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 22
42698 TAAAAAAATA
42708 AAAAATTAAAAATAATTATTTTT
1 AAAAATT-AAAATAATTATTTTT
* * *
42731 AAAAAATAAAAT-ATCATTCTT
1 AAAAATTAAAATAATTATTTTT
* *
42752 AAAAATTTTAAAATATTTTTTTTT
1 AAAAA--TTAAAATAATTATTTTT
42776 A
1 A
42777 TTTTTAACAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 12 0.34
22 5 0.14
23 12 0.34
24 6 0.17
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAATTAAAATAATTATTTTT
Found at i:42755 original size:21 final size:24
Alignment explanation
Indices: 42706--42766 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 24
42696 TTTAAAAAAA
* *
42706 TAAAAAATTAAAAATAATTATTTT
1 TAAAAAATTAAAAATAATCATTCT
42730 TAAAAAA-T-AAAAT-ATCATTCT
1 TAAAAAATTAAAAATAATCATTCT
* *
42751 TAAAAATTTTAAAATA
1 TAAAAAATTAAAAATA
42767 TTTTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 12 0.39
22 6 0.19
23 6 0.19
24 7 0.23
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAAAATTAAAAATAATCATTCT
Found at i:43088 original size:162 final size:162
Alignment explanation
Indices: 42847--43191 Score: 629
Period size: 162 Copynumber: 2.1 Consensus size: 162
42837 TTAATACTAT
42847 TAAATTAAAAATAATATTTACCTTAATATAACTAAAAATAAATAAAAAATATTTTTTTAATCAAT
1 TAAATTAAAAATAATATTTACCTTAATATAACTAAAAATAAATAAAAAATATTTTTTTAATCAAT
42912 ACTTTATCTTATTCTTAAAATTTTTTAATATTTATCATTAAATAAAAATATTATTACATATAATA
66 ACTTTATCTTATTCTTAAAATTTTTTAATATTTATCATTAAATAAAAATATTATTACATATAATA
42977 TTTTTTAAAAATATTTTTCAAATATTCATGAA
131 TTTTTTAAAAATATTTTTCAAATATTCATGAA
43009 TAAAATTAAAAATAATATTTACCTTAATATAACTAAAAATAAAT-AAAAATATTTTTTTAATCAA
1 T-AAATTAAAAATAATATTTACCTTAATATAACTAAAAATAAATAAAAAATATTTTTTTAATCAA
* *
43073 TACTTTATCTTATTCTTGAAATTTTTTAATATTTATCATTAAATTAAAATATTATTACATATAAT
65 TACTTTATCTTATTCTTAAAATTTTTTAATATTTATCATTAAATAAAAATATTATTACATATAAT
*
43138 ATTTTTTAAAAATATTTTTCAAATATTCATTAA
130 ATTTTTTAAAAATATTTTTCAAATATTCATGAA
43171 TAAATTAAAAAATATATATTT
1 TAAATT-AAAAATA-ATATTT
43192 GTTTATCTAT
Statistics
Matches: 177, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
161 5 0.03
162 124 0.70
163 48 0.27
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.46
Consensus pattern (162 bp):
TAAATTAAAAATAATATTTACCTTAATATAACTAAAAATAAATAAAAAATATTTTTTTAATCAAT
ACTTTATCTTATTCTTAAAATTTTTTAATATTTATCATTAAATAAAAATATTATTACATATAATA
TTTTTTAAAAATATTTTTCAAATATTCATGAA
Found at i:44071 original size:17 final size:18
Alignment explanation
Indices: 44045--44078 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44035 ATAAAAATAA
44045 AAAAAAATAT-ATTTTAT
1 AAAAAAATATAATTTTAT
*
44062 AAAAATATATAATTTTA
1 AAAAAAATATAATTTTA
44079 AATTTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAAAATATAATTTTAT
Found at i:44187 original size:51 final size:52
Alignment explanation
Indices: 44129--44231 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 52
44119 CCCTTTTATT
44129 TTTATTTATTATTTAAAATTTATCAAATCAAATTTAAAAATAT-TTATAAAA
1 TTTATTTATTATTTAAAATTTATCAAATCAAATTTAAAAATATATTATAAAA
*
44180 TTTATTTATTATTTAAAATTTATCAAATCAAATTTAAAAATATATTTTAAAA
1 TTTATTTATTATTTAAAATTTATCAAATCAAATTTAAAAATATATTATAAAA
44232 AATTAAAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 43 0.86
52 7 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.48
Consensus pattern (52 bp):
TTTATTTATTATTTAAAATTTATCAAATCAAATTTAAAAATATATTATAAAA
Found at i:44251 original size:51 final size:50
Alignment explanation
Indices: 44142--44251 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 50
44132 ATTTATTATT
* * ** *
44142 TAAAATTTATCAAATCAAATTTAAAAATATTTATAAAATTTATTTATTATT
1 TAAAATTTATCAAATCAAATTTAAAAATATTTATAAAA-TAATTAAAAATA
*
44193 TAAAATTTATCAAATCAAATTTAAAAATATATTTTAAAA-AATTAAAAATA
1 TAAAATTTATCAAATCAAATTTAAAAATAT-TTATAAAATAATTAAAAATA
44243 TAATAATTT
1 TAA-AATTT
44252 TTTTAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
50 9 0.18
51 35 0.69
52 7 0.14
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (50 bp):
TAAAATTTATCAAATCAAATTTAAAAATATTTATAAAATAATTAAAAATA
Found at i:44268 original size:26 final size:27
Alignment explanation
Indices: 44224--44279 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
44214 TAAAAATATA
44224 TTTTAAAAAATTAAAAATA-TAATAATTT
1 TTTTAAAAAA-TAAAAATATTAA-AATTT
*
44252 TTTTAAAAAA-AATAATATTAAAATTT
1 TTTTAAAAAATAAAAATATTAAAATTT
44278 TT
1 TT
44280 ATTTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 13 0.50
27 3 0.12
28 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTTAAAAAATAAAAATATTAAAATTT
Found at i:44876 original size:12 final size:12
Alignment explanation
Indices: 44859--44899 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
44849 AAATATTGAT
44859 AATAAAAAATAA
1 AATAAAAAATAA
*
44871 AATAAATAATAA
1 AATAAAAAATAA
44883 CAATAAAAATATAA
1 -AATAAAAA-ATAA
44897 AAT
1 AAT
44900 TTAATTGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.44
13 10 0.40
14 4 0.16
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:45791 original size:19 final size:18
Alignment explanation
Indices: 45769--45805 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
45759 AATTTAATCT
*
45769 AATTTAATTTATTTATTTA
1 AATTTAAATTA-TTATTTA
45788 AATTTAAATTATTATTTA
1 AATTTAAATTATTATTTA
45806 TTTTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTAAATTATTATTTA
Found at i:45893 original size:21 final size:20
Alignment explanation
Indices: 45856--45896 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
45846 ATAATTAAAA
45856 TTAAATACAAATATATTATT
1 TTAAATACAAATATATTATT
45876 TTAATATA-AAATATTATTATT
1 TTAA-ATACAAATA-TATTATT
45897 AGCCAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATACAAATATATTATT
Found at i:47997 original size:19 final size:20
Alignment explanation
Indices: 47975--48017 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
47965 ATAAATTATT
*
47975 TAAAAATTAATTTT-ATAAA
1 TAAAAATAAATTTTAATAAA
*
47994 TAAATATAAATTTTAATAAA
1 TAAAAATAAATTTTAATAAA
48014 TAAA
1 TAAA
48018 TATATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAATAAATTTTAATAAA
Found at i:48013 original size:16 final size:16
Alignment explanation
Indices: 47992--48037 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
47982 TAATTTTATA
47992 AATAAATATAAATTTT
1 AATAAATATAAATTTT
*
48008 AATAAATA-AATATATT
1 AATAAATATAA-ATTTT
48024 AA-AAATAATAAATT
1 AATAAAT-ATAAATT
48038 ATAACAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 6 0.24
16 17 0.68
17 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAAATATAAATTTT
Found at i:48014 original size:20 final size:19
Alignment explanation
Indices: 47983--48021 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
47973 TTTAAAAATT
47983 AATTTTATAAATAAATATA
1 AATTTTATAAATAAATATA
48002 AATTTTAATAAATAAATATA
1 AATTTT-ATAAATAAATATA
48022 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTTTATAAATAAATATA
Found at i:48244 original size:16 final size:15
Alignment explanation
Indices: 48202--48244 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
48192 ACTCAAACTC
*
48202 AAAAATTCAAACTGA
1 AAAAATTTAAACTGA
*
48217 AAAAACTCTAAACTCGA
1 AAAAA-TTTAAACT-GA
48234 AAAAATTTAAA
1 AAAAATTTAAA
48245 TCATAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 11 0.48
17 7 0.30
ACGTcount: A:0.60, C:0.14, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAAATTTAAACTGA
Found at i:49305 original size:21 final size:20
Alignment explanation
Indices: 49281--49323 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
49271 GATGCATTGG
*
49281 TTGGATAAAAGAATGTATTTT
1 TTGGATAAAA-AATGTAATTT
49302 TTGGATAAAAAATGTAATTT
1 TTGGATAAAAAATGTAATTT
49322 TT
1 TT
49324 AATAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (20 bp):
TTGGATAAAAAATGTAATTT
Found at i:49317 original size:20 final size:22
Alignment explanation
Indices: 49281--49323 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
49271 GATGCATTGG
49281 TTGGATAAAAGAATGT-ATTTT
1 TTGGATAAAAGAATGTAATTTT
49302 TTGGATAAAA-AATGTAATTTT
1 TTGGATAAAAGAATGTAATTTT
49323 T
1 T
49324 AATAACCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (22 bp):
TTGGATAAAAGAATGTAATTTT
Found at i:56373 original size:21 final size:20
Alignment explanation
Indices: 56308--56384 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
56298 TTTTGCCTGC
*
56308 ATGTATCGATACATTTTATA
1 ATGTATCGATACATTTGATA
**
56328 ATGTATCGATACA-AAGATCA
1 ATGTATCGATACATTTGAT-A
56348 ATGTATCGATACATTTGAGTA
1 ATGTATCGATACATTTGA-TA
56369 ATGTATCGATACATTT
1 ATGTATCGATACATTT
56385 CCTTGGCAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.04
20 27 0.55
21 19 0.39
22 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTGATA
Found at i:56423 original size:13 final size:13
Alignment explanation
Indices: 56405--56488 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
56395 AGCTTCGTAG
56405 CGATACATTGTAT
1 CGATACATTGTAT
56418 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
56437 CGATACATTGTAT
1 CGATACATTGTAT
56450 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
56469 CGATACATTGTAT
1 CGATACATTGTAT
56482 CGATACA
1 CGATACA
56489 AATTGTTGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:56437 original size:19 final size:18
Alignment explanation
Indices: 56413--56475 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
56403 AGCGATACAT
56413 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
56432 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
56445 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
56464 TGTATCGATACA
1 TGTATCGATACA
56476 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:56446 original size:32 final size:32
Alignment explanation
Indices: 56405--56490 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
56395 AGCTTCGTAG
56405 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
56437 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
56469 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
56491 TTGTTGAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:57396 original size:49 final size:49
Alignment explanation
Indices: 57200--57623 Score: 272
Period size: 52 Copynumber: 8.6 Consensus size: 49
57190 AATTCACGAT
* * * * *
57200 CAGCGACATTAGTCTTGAAGATGAGAAGAATGCCAATGTGCTAATTCAAGGC
1 CAGCGACATTGGACTTAAAGATGA-AAG--TGCCGATGTGCTGATTCAAGGC
* ** * ** **
57252 CAACGACATTGGGTTTAAAGAAG-AA-TGCTAATGTGCTGAGACAAGGC
1 CAGCGACATTGGACTTAAAGATGAAAGTGCCGATGTGCTGATTCAAGGC
* * *** ** * *
57299 CAGCAACATTGGGCTTCGGGATGTTAAAGATGCTAATATGTTGATTCAAGGC
1 CAGCGACATTGGACTTAAAGATG--AAAG-TGCCGATGTGCTGATTCAAGGC
* * * * *
57351 CAACGATATCGGATTTAAAGATGAAAATGCCGATGTGCTGATTCAAGGC
1 CAGCGACATTGGACTTAAAGATGAAAGTGCCGATGTGCTGATTCAAGGC
* * * * *
57400 CAGCGACATTGAACTTAAAGATGACGAAGGCGCCAATATTCTGATTCAAGGC
1 CAGCGACATTGGACTTAAAGATGA--AA-GTGCCGATGTGCTGATTCAAGGC
* *
57452 CAGCGATATTGGACTTAAAGATGAAGGTGCCGATGTGCTGATTCAAGGC
1 CAGCGACATTGGACTTAAAGATGAAAGTGCCGATGTGCTGATTCAAGGC
* * * ** *
57501 CAGCGACATTGGACTTAAAGATGATA-TGCCAATATATTGACTCAAGGC
1 CAGCGACATTGGACTTAAAGATGAAAGTGCCGATGTGCTGATTCAAGGC
* * * *
57549 CAGCGATATTGGGCTTAAAGATG---GT--TGAGGTGCTGATTCAAGGC
1 CAGCGACATTGGACTTAAAGATGAAAGTGCCGATGTGCTGATTCAAGGC
* * *
57593 CAACGACATCGGTCTTAAAGAT-AAAGGTGCC
1 CAGCGACATTGGACTTAAAGATGAAA-GTGCC
57624 AATATGTCCA
Statistics
Matches: 283, Mismatches: 74, Indels: 33
0.73 0.19 0.08
Matches are distributed among these distances:
44 30 0.11
46 1 0.00
47 36 0.13
48 38 0.13
49 79 0.28
50 8 0.03
51 2 0.01
52 89 0.31
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
CAGCGACATTGGACTTAAAGATGAAAGTGCCGATGTGCTGATTCAAGGC
Found at i:57438 original size:101 final size:101
Alignment explanation
Indices: 57340--57524 Score: 316
Period size: 101 Copynumber: 1.8 Consensus size: 101
57330 GCTAATATGT
*
57340 TGATTCAAGGCCAACGATATCGGATTTAAAGATGAAAATGCCGATGTGCTGATTCAAGGCCAGCG
1 TGATTCAAGGCCAACGATATCGGACTTAAAGATGAAAATGCCGATGTGCTGATTCAAGGCCAGCG
57405 ACATTGAACTTAAAGATGACGAAGGCGCCAATATTC
66 ACATTGAACTTAAAGATGACGAAGGCGCCAATATTC
* * **
57441 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCGATGTGCTGATTCAAGGCCAGCG
1 TGATTCAAGGCCAACGATATCGGACTTAAAGATGAAAATGCCGATGTGCTGATTCAAGGCCAGCG
*
57506 ACATTGGACTTAAAGATGA
66 ACATTGAACTTAAAGATGA
57525 TATGCCAATA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 78 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (101 bp):
TGATTCAAGGCCAACGATATCGGACTTAAAGATGAAAATGCCGATGTGCTGATTCAAGGCCAGCG
ACATTGAACTTAAAGATGACGAAGGCGCCAATATTC
Found at i:57450 original size:52 final size:51
Alignment explanation
Indices: 57333--57571 Score: 222
Period size: 49 Copynumber: 4.8 Consensus size: 51
57323 TAAAGATGCT
* * * * * **
57333 AATATGTTGATTCAAGGCCAACGATATCGGATTTAAAGATGA-AA-ATGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGCGCC
* * *
57382 GATGTGCTGATTCAAGGCCAGCGACATTGAACTTAAAGATGACGAAGGCGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGGCGCC
* * *
57434 AATATTCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGCGCC
* * * *
57483 GATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-TA--TGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGCGCC
** * * *
57531 AATATATTGACTCAAGGCCAGCGATATTGGGCTTAAAGATG
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
57572 GTTGAGGTGC
Statistics
Matches: 157, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
48 38 0.24
49 78 0.50
50 1 0.01
51 2 0.01
52 38 0.24
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (51 bp):
AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGCGCC
Found at i:58992 original size:11 final size:11
Alignment explanation
Indices: 58976--59013 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
58966 AGTTGCAAAA
58976 TTCATAAAAGT
1 TTCATAAAAGT
*
58987 TTCATAAAAAT
1 TTCATAAAAGT
*
58998 TTTATAAAAGT
1 TTCATAAAAGT
59009 TTCAT
1 TTCAT
59014 TGTATCCTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (11 bp):
TTCATAAAAGT
Found at i:59741 original size:25 final size:25
Alignment explanation
Indices: 59687--59741 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
59677 AATATAAATA
* *
59687 AATTAAAATTTAATAATTTTATTTT
1 AATTTAAATTTAATAATTTAATTTT
* *
59712 TATTTAAATTTAATTA-TTAATTATT
1 AATTTAAATTTAATAATTTAATT-TT
59737 AATTT
1 AATTT
59742 TATATAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AATTTAAATTTAATAATTTAATTTT
Done.