Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011578.1 Corchorus capsularis cultivar CVL-1 contig11599, whole genome shotgun sequence
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: 10672
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Found at i:1112 original size:29 final size:30
Alignment explanation
Indices: 1079--1154 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
1069 ACTTGTAGTG
*
1079 TTTGGACGTTTTGT-CCCATGAACTTCAAT
1 TTTGGACGTTTTGTCCCCATCAACTTCAAT
*
1108 TTTGGACATTTT-TCCCCATCAACTTCAAT
1 TTTGGACGTTTTGTCCCCATCAACTTCAAT
1137 TTTGGGACGTTTTG-CCCC
1 TTT-GGACGTTTTGTCCCC
1155 TTAGACTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.02
29 28 0.68
30 12 0.29
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (30 bp):
TTTGGACGTTTTGTCCCCATCAACTTCAAT
Found at i:2102 original size:2 final size:2
Alignment explanation
Indices: 2091--2126 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2081 GCTTTACTTG
2091 AT AT -T AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2127 TGACTCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5210 original size:18 final size:18
Alignment explanation
Indices: 5187--5232 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
5177 CAAAATCTGA
5187 CCCGAACCCGATAACCCG
1 CCCGAACCCGATAACCCG
*
5205 CCCGAACCC-AAAACCCG
1 CCCGAACCCGATAACCCG
5222 CCC-AACCCGAT
1 CCCGAACCCGAT
5233 TTGATCAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.20
17 11 0.44
18 9 0.36
ACGTcount: A:0.30, C:0.52, G:0.13, T:0.04
Consensus pattern (18 bp):
CCCGAACCCGATAACCCG
Found at i:5470 original size:22 final size:21
Alignment explanation
Indices: 5426--5469 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5416 CTAAACTGGA
*
5426 TTGCTAAACACCGCCCCCCTT
1 TTGCTAAACACCACCCCCCTT
*
5447 TTGCTAAATACCACCCCCCTT
1 TTGCTAAACACCACCCCCCTT
5468 TT
1 TT
5470 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.43, G:0.07, T:0.30
Consensus pattern (21 bp):
TTGCTAAACACCACCCCCCTT
Found at i:5599 original size:24 final size:24
Alignment explanation
Indices: 5540--5597 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
5530 TTCAAACCTT
* **
5540 AAACTTCATTTCTAACAACTTTTC
1 AAACTTCATTTCTAACAAATCATC
5564 AAACTTCATTTCTAACAAATCATC
1 AAACTTCATTTCTAACAAATCATC
5588 AAA-TTCATTT
1 AAACTTCATTT
5598 TCCTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 7 0.23
24 24 0.77
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCATC
Found at i:5638 original size:26 final size:26
Alignment explanation
Indices: 5607--5674 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
5597 TTCCTTCATT
*
5607 TTAATCATAAACTAATTAAATACTTA
1 TTAATCATAAACTAATTAAATACTAA
5633 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
5659 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
5675 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:5650 original size:15 final size:14
Alignment explanation
Indices: 5607--5674 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
5597 TTCCTTCATT
5607 TTAATCATAAACTAA
1 TTAA-CATAAACTAA
*
5622 TTAA-AT--ACTTA
1 TTAACATAAACTAA
5633 TTAATCATAAACTAA
1 TTAA-CATAAACTAA
5648 TTAA-AT--ACTAA
1 TTAACATAAACTAA
5659 TTAAACATAAACTAA
1 TT-AACATAAACTAA
5674 T
1 T
5675 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 15 0.35
12 2 0.05
13 8 0.19
15 18 0.42
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAACATAAACTAA
Found at i:5835 original size:10 final size:10
Alignment explanation
Indices: 5820--5859 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
5810 TTATTTATTT
5820 ATTTTTTTGA
1 ATTTTTTTGA
5830 ATTTTTTTTGA
1 A-TTTTTTTGA
*
5841 ATTTTTTTAA
1 ATTTTTTTGA
5851 ATATTTTTT
1 AT-TTTTTT
5860 ACCTCATTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 11 0.41
11 16 0.59
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (10 bp):
ATTTTTTTGA
Found at i:5837 original size:11 final size:11
Alignment explanation
Indices: 5821--5848 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5811 TATTTATTTA
5821 TTTTTTTGAAT
1 TTTTTTTGAAT
5832 TTTTTTTGAAT
1 TTTTTTTGAAT
5843 TTTTTT
1 TTTTTT
5849 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:5844 original size:21 final size:21
Alignment explanation
Indices: 5820--5859 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5810 TTATTTATTT
* *
5820 ATTTTTTTGAATTTTTTTTGA
1 ATTTTTTTAAATATTTTTTGA
5841 ATTTTTTTAAATATTTTTT
1 ATTTTTTTAAATATTTTTT
5860 ACCTCATTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (21 bp):
ATTTTTTTAAATATTTTTTGA
Found at i:6026 original size:20 final size:21
Alignment explanation
Indices: 5998--6041 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5988 CAAAAATTAT
5998 AAAA-AGGGGCGGTATTTAGC
1 AAAAGAGGGGCGGTATTTAGC
* *
6018 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGAGGGGCGGTATTTAGC
6039 AAA
1 AAA
6042 CCCCATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.34, C:0.09, G:0.39, T:0.18
Consensus pattern (21 bp):
AAAAGAGGGGCGGTATTTAGC
Found at i:6104 original size:21 final size:21
Alignment explanation
Indices: 6078--6125 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
6068 ATACAATTTA
6078 TATTATTAG-TATAATTTTACC
1 TATTATT-GTTATAATTTTACC
*
6099 TATTATTGTTATCATTTTACC
1 TATTATTGTTATAATTTTACC
6120 TATTAT
1 TATTAT
6126 AAATTGGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (21 bp):
TATTATTGTTATAATTTTACC
Found at i:6601 original size:16 final size:16
Alignment explanation
Indices: 6582--6646 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
6572 GACCTAGTAA
6582 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
** *
6598 ACCCG-GAACTTGTATG
1 ACCCGAG-ACCCGAATG
*
6614 ACCCGAGACCCGAATA
1 ACCCGAGACCCGAATG
*
6630 ACCCGA-ACCCAAATG
1 ACCCGAGACCCGAATG
6645 AC
1 AC
6647 TCAAAACTCG
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
15 10 0.26
16 27 0.71
17 1 0.03
ACGTcount: A:0.34, C:0.35, G:0.20, T:0.11
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:6602 original size:32 final size:33
Alignment explanation
Indices: 6565--6635 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
6555 GAACCCGCCC
*
6565 AACCCGAGACCTAGTA-AACCCGAGACCCGAAT
1 AACCCGAGAACTAGTATAACCCGAGACCCGAAT
* * *
6597 GACCCG-GAACTTGTATGACCCGAGACCCGAAT
1 AACCCGAGAACTAGTATAACCCGAGACCCGAAT
6629 AACCCGA
1 AACCCGA
6636 ACCCAAATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.34, C:0.34, G:0.21, T:0.11
Consensus pattern (33 bp):
AACCCGAGAACTAGTATAACCCGAGACCCGAAT
Found at i:7382 original size:2 final size:2
Alignment explanation
Indices: 7375--7405 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7365 CTTTGGTTGT
7375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7406 TCATCTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8308 original size:130 final size:130
Alignment explanation
Indices: 8075--8344 Score: 486
Period size: 130 Copynumber: 2.1 Consensus size: 130
8065 CCATGTACTT
8075 ACAAGAAAAAATTAATTTGGTCACTCAACTCAAAAAACGATCGATTTAGTCCCTCTACTTACAGG
1 ACAAGAAAAAATTAATTTGGTCACTCAACTCAAAAAACGATCGATTTAGTCCCTCTACTTACAGG
* *
8140 TTTGGGTAAATTGAGTCCCTCTACTTGCGAAATTTAGTCCATGTTGCCTTCTATCATGTTTGGTA
66 TTTGGGTAAATTGAGTCCCTCTACTTGCGAAATTTAGTCCATGTTACCTTCTATCATGATTGGTA
* *
8205 ACAAGAAAAAATTAATTTGGTCACTCAACTCAAAAAGCGATCGATTTAGTCTCTCTACTTACAGG
1 ACAAGAAAAAATTAATTTGGTCACTCAACTCAAAAAACGATCGATTTAGTCCCTCTACTTACAGG
* *
8270 TTTGGGTCAATTGAGTCTCTCTACTTGCGAAATTTAGTCCATGTTACCTTCTATCATGATTGGTA
66 TTTGGGTAAATTGAGTCCCTCTACTTGCGAAATTTAGTCCATGTTACCTTCTATCATGATTGGTA
8335 ACAAGAAAAA
1 ACAAGAAAAA
8345 GCAATATTTA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
130 134 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (130 bp):
ACAAGAAAAAATTAATTTGGTCACTCAACTCAAAAAACGATCGATTTAGTCCCTCTACTTACAGG
TTTGGGTAAATTGAGTCCCTCTACTTGCGAAATTTAGTCCATGTTACCTTCTATCATGATTGGTA
Found at i:9185 original size:21 final size:21
Alignment explanation
Indices: 9171--9212 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9161 AATTATTATT
9171 CTTATATATATAATTATACTA
1 CTTATATATATAATTATACTA
9192 CTTATATATAT-ATATATACTA
1 CTTATATATATAAT-TATACTA
9213 GTTTTAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
CTTATATATATAATTATACTA
Found at i:9357 original size:22 final size:22
Alignment explanation
Indices: 9332--9396 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
9322 ATGATCCCAT
*
9332 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTAC
* **
9354 TATGAAAATTTTAATAACGATAC
1 TATG-AAATTTTGATAACCTTAC
* *
9377 TATGGAATTTTGAGAACCTT
1 TATGAAATTTTGATAACCTT
9397 TTTTATAATT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTAC
Found at i:9524 original size:22 final size:22
Alignment explanation
Indices: 9463--9524 Score: 52
Period size: 23 Copynumber: 2.8 Consensus size: 22
9453 GAAGATCTCA
*
9463 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * * **
9485 ACTATGAGATGTTAATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
9508 ATATGATATATTGATAA
1 ATATGAAATATTGATAA
9525 TTACGTTATG
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:9591 original size:22 final size:22
Alignment explanation
Indices: 9553--9612 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
9543 AAAATCTCCA
*
9553 TATG-AATTGTTACTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* * *
9575 TCTGAAATTTTGATAATCGCAC
1 TATGAAATTGTGATAATCACAC
9597 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
9613 CCTATGAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:9619 original size:18 final size:18
Alignment explanation
Indices: 9596--9630 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9586 GATAATCGCA
9596 CTATGAAATTGTGATAAC
1 CTATGAAATTGTGATAAC
*
9614 CTATGAAATTTTGATAA
1 CTATGAAATTGTGATAA
9631 ATCTTCCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (18 bp):
CTATGAAATTGTGATAAC
Found at i:9645 original size:23 final size:23
Alignment explanation
Indices: 9613--9698 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 23
9603 ATTGTGATAA
*
9613 CCTATGAAATTTTGATAAATCTT
1 CCTATAAAATTTTGATAAATCTT
*
9636 CCTATAAAATTTTGATAAA-CCT
1 CCTATAAAATTTTGATAAATCTT
* *
9658 CCTTATAAAATTTTAATAACT-TT
1 CC-TATAAAATTTTGATAAATCTT
* * *
9681 CTTATGAAATCTTGATAA
1 CCTATAAAATTTTGATAA
9699 CTACAAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
22 17 0.33
23 35 0.67
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (23 bp):
CCTATAAAATTTTGATAAATCTT
Found at i:9753 original size:22 final size:21
Alignment explanation
Indices: 9577--9905 Score: 137
Period size: 22 Copynumber: 15.6 Consensus size: 21
9567 AATCACACTC
*
9577 TGAAATTTTGATAATCGCAC-TA
1 TGAAATTTTGATAA-C-CTCTTA
*
9599 TGAAATTGTGATAA-C-C-TA
1 TGAAATTTTGATAACCTCTTA
* *
9617 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AA-CCTCTTA
*
9640 TAAAATTTTGATAAACCTCCTTA
1 TGAAATTTTGAT-AACCT-CTTA
* * *
9663 TAAAATTTTAATAACTTTCTTA
1 TGAAATTTTGATAAC-CTCTTA
*
9685 TGAAATCTTGATAA---C-TA
1 TGAAATTTTGATAACCTCTTA
*
9702 -CAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCT-TA
**
9723 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTC-TTA
* * *
9745 TGAAATTTTGTTAATCTACCTA
1 TGAAATTTTGATAACCT-CTTA
* * * *
9767 TGAAAATATGATCTACATAC-TA
1 TGAAATTTTGAT-AACCT-CTTA
*
9789 TGAAATTTTGATAACCCTCTTG
1 TGAAATTTTGATAA-CCTCTTA
* ***
9811 TGAAATTTTGA-AAACTAAAGAA
1 TGAAATTTTGATAACCT--CTTA
* *
9833 TGAAATTTTGATTACCTTCATA
1 TGAAATTTTGATAACC-TCTTA
* **
9855 TGAAATTTTGATATCCTC-CC
1 TGAAATTTTGATAACCTCTTA
* *
9875 TG-AATTTTGATATCCTCCT-
1 TGAAATTTTGATAACCTCTTA
9894 TGAAATTTTGAT
1 TGAAATTTTGAT
9906 TATTCCATAA
Statistics
Matches: 236, Mismatches: 47, Indels: 50
0.71 0.14 0.15
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 15 0.06
19 21 0.09
20 13 0.06
21 8 0.03
22 126 0.53
23 39 0.17
24 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCTTA
Found at i:9882 original size:19 final size:20
Alignment explanation
Indices: 9855--9905 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
9845 TACCTTCATA
9855 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
9875 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
9894 TGAAATTTTGAT
1 TGAAATTTTGAT
9906 TATTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:9994 original size:22 final size:22
Alignment explanation
Indices: 9969--10043 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
9959 CCATATTATT
*
9969 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCACTATGAAA
* *
9991 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCACTATGAAA
* * *
10013 TTTTTATAACCTCGCTATGACA
1 TTTTGATAACCTCACTATGAAA
10035 TTTTGATAA
1 TTTTGATAA
10044 TCTCTTTGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGAAA
Found at i:10111 original size:22 final size:22
Alignment explanation
Indices: 10052--10218 Score: 122
Period size: 22 Copynumber: 7.3 Consensus size: 22
10042 AATCTCTTTG
* *
10052 ATAACCTTTCTATGAAATTGTGATA
1 ATAACCATCCTATGAAATT-T--TA
* *
10077 ATTAACCACCCTATGAAATTTCA
1 A-TAACCATCCTATGAAATTTTA
* * *
10100 ATAACCAACCTAAGAGATTTTA
1 ATAACCATCCTATGAAATTTTA
*
10122 ATAACCTGATCCTATGAAATTTTG
1 ATAACC--ATCCTATGAAATTTTA
* *
10146 ATAACCA-CACTATGGAATTTTG
1 ATAACCATC-CTATGAAATTTTA
* *
10168 ATAACC-TCTTCATGAAATTATA
1 ATAACCATCCT-ATGAAATTTTA
* *
10190 ATAACCATCTTATGAAATTTTG
1 ATAACCATCCTATGAAATTTTA
10212 ATAACCA
1 ATAACCA
10219 CATAGAGACA
Statistics
Matches: 116, Mismatches: 19, Indels: 17
0.76 0.12 0.11
Matches are distributed among these distances:
21 2 0.02
22 73 0.63
23 6 0.05
24 18 0.16
25 2 0.02
26 15 0.13
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
ATAACCATCCTATGAAATTTTA
Found at i:10165 original size:68 final size:66
Alignment explanation
Indices: 10079--10220 Score: 160
Period size: 68 Copynumber: 2.1 Consensus size: 66
10069 TTGTGATAAT
* * *
10079 TAACCACCCTATGAAATTTCAATAACCAACCT-AAGAGATTTTAATAACCTGATCCTATGAAATT
1 TAACCACACTATGAAATTTCAATAACC-ACCTCAAGAAATTATAATAACC--ATCCTATGAAATT
10143 TTGA
63 TTGA
* ** * * * *
10147 TAACCACACTATGGAATTTTGATAACCTCTTCATGAAATTATAATAACCATCTTATGAAATTTTG
1 TAACCACACTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTG
10212 A
66 A
10213 TAACCACA
1 TAACCACA
10221 TAGAGACAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
66 24 0.38
67 2 0.03
68 37 0.59
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.32
Consensus pattern (66 bp):
TAACCACACTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTG
A
Found at i:10172 original size:46 final size:45
Alignment explanation
Indices: 10086--10217 Score: 119
Period size: 46 Copynumber: 2.9 Consensus size: 45
10076 AATTAACCAC
* * *
10086 CCTATGAAATTTCAATAACCA-ACCTA-AGAGATTTTAATAACCTGAT
1 CCTATGAAATTTTAATAACCACA-CTATGGA-ATTTTGATAACCT-AT
* *
10132 CCTATGAAATTTTGATAACCACACTATGGAATTTTGATAACCTCT
1 CCTATGAAATTTTAATAACCACACTATGGAATTTTGATAACCTAT
* * * *
10177 TC-ATGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 CCTATGAAATTTTAATAACCA-CACTATGGAATTTTGATAACC
10218 ACATAGAGAC
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
44 33 0.45
45 3 0.04
46 34 0.47
47 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (45 bp):
CCTATGAAATTTTAATAACCACACTATGGAATTTTGATAACCTAT
Found at i:10613 original size:36 final size:36
Alignment explanation
Indices: 10546--10621 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
10536 TTTAAGACCG
* *
10546 AAGACAAAGCAAAATTAAATACAAAGATTGGAAATA
1 AAGACAAAGAAAAATTAAATACAAAGATTGGAAACA
** *
10582 AAGACAAAAGAAAAATTAAATAGGACG-TTGGAAACA
1 AAGAC-AAAGAAAAATTAAATACAAAGATTGGAAACA
10618 AAGA
1 AAGA
10622 ATCAAATTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 17 0.50
37 17 0.50
ACGTcount: A:0.61, C:0.08, G:0.17, T:0.14
Consensus pattern (36 bp):
AAGACAAAGAAAAATTAAATACAAAGATTGGAAACA
Done.