Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006874.1 Corchorus capsularis cultivar CVL-1 contig06895, 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: 36765
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:3682 original size:3 final size:3
Alignment explanation
Indices: 3674--3705 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3664 ATTTGCATGA
3674 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3706 AGGGATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4066 original size:75 final size:75
Alignment explanation
Indices: 3840--4055 Score: 290
Period size: 75 Copynumber: 2.9 Consensus size: 75
3830 TTATCTAGAC
* * * * *
3840 TGTGAGCAAAGGAATGATGAGTTTTAATTAAAATATGTTTCAAAATCAGTTTCAATCAAAACAAT
1 TGTGAGCAAAGGAATGTTGAGTTTTAATTAAAACATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
3905 GGTTTCGAGG
66 GGTTTCGAGG
* * * * *
3915 TGTGAGCAAAAGAATGTTGGGTTTTAATTAAAACATGTTTCAAAATAAG-TATCGATCAAAGCAA
1 TGTGAGCAAAGGAATGTTGAGTTTTAATTAAAACATGTTTCAAAATCAGTTTTAG-TCAAAGCAA
3979 TGGTTTCGAGG
65 TGGTTTCGAGG
* * * *
3990 TGTGAGCAAAGGGATGTTAAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
1 TGTGAGCAAAGGAATGTTGAGTTTTAATTAAAACATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
4055 G
66 G
4056 ATTTTAAGGT
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
74 1 0.01
75 116 0.97
76 3 0.03
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.31
Consensus pattern (75 bp):
TGTGAGCAAAGGAATGTTGAGTTTTAATTAAAACATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
GGTTTCGAGG
Found at i:4597 original size:19 final size:19
Alignment explanation
Indices: 4573--4643 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
4563 ATAAAATGAT
4573 TTTTCAAAAAGAGTCATGG
1 TTTTCAAAAAGAGTCATGG
* * *
4592 TTTTCAAAAGGTTGATAAAATGG
1 TTTTCAAAAAG-AG-T--CATGG
*
4615 TTTTTCAAAAAAAGTCATGG
1 -TTTTCAAAAAGAGTCATGG
4635 TTTTCAAAA
1 TTTTCAAAA
4644 GGTTTTGATA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
19 19 0.47
20 5 0.12
21 1 0.03
22 1 0.03
23 5 0.12
24 9 0.22
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (19 bp):
TTTTCAAAAAGAGTCATGG
Found at i:4607 original size:43 final size:44
Alignment explanation
Indices: 4529--4668 Score: 219
Period size: 45 Copynumber: 3.2 Consensus size: 44
4519 CAACGATGGA
* *
4529 TTTCAAAAAAAGTCATGATTTTCAAAAGGCTTTGATAAAATGATT
1 TTTCAAAAAAAGTCATGGTTTTCAAAAGG-TTTGATAAAATGGTT
*
4574 TTTCAAAAAGAGTCATGGTTTTCAAAAGG-TTGATAAAATGGTT
1 TTTCAAAAAAAGTCATGGTTTTCAAAAGGTTTGATAAAATGGTT
4617 TTTCAAAAAAAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTT
1 TTTCAAAAAAAGTCATGGTTTTCAAAAGG-TTTGATAAAATGGTT
*
4662 TTCCAAA
1 TTTCAAA
4669 GTTGTGTTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
43 41 0.47
45 47 0.53
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (44 bp):
TTTCAAAAAAAGTCATGGTTTTCAAAAGGTTTGATAAAATGGTT
Found at i:5013 original size:14 final size:14
Alignment explanation
Indices: 4988--5034 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
4978 CAAAGTCGAT
4988 AAAGATAAAAAAGAA
1 AAAGA-AAAAAAGAA
5003 AAAGAAAAAAA-AGA
1 AAAGAAAAAAAGA-A
*
5017 AGAGAAGAAAAAGAA
1 AAAGAA-AAAAAGAA
5032 AAA
1 AAA
5035 AGGTGAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 12 0.44
15 13 0.48
16 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:5747 original size:50 final size:50
Alignment explanation
Indices: 5684--5782 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
5674 AAGTTTTATA
* *
5684 ATAAGATTGCATTCCATTTATAAGTCCAATATCAAAATTCGATTTTCAAG
1 ATAAAATTGCATTCCATTTATAAGTCCAAGATCAAAATTCGATTTTCAAG
* * * *
5734 ATAAAATTGCATTCCATTTGTGAGTCCAAGATCAAAATTTGCTTTTCAA
1 ATAAAATTGCATTCCATTTATAAGTCCAAGATCAAAATTCGATTTTCAA
5783 AGGGCATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (50 bp):
ATAAAATTGCATTCCATTTATAAGTCCAAGATCAAAATTCGATTTTCAAG
Found at i:6329 original size:70 final size:70
Alignment explanation
Indices: 6252--6677 Score: 549
Period size: 70 Copynumber: 6.1 Consensus size: 70
6242 AATGCTTTGA
* * * * * *
6252 CTTTTCCATAAGTCAAACTCATTTACACACAAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
6317 AGGGG
66 AGGGG
* * * * *
6322 CTTTTCCACAAGCCAAACTCGTTTCCATAAGAGAT-TGTTCATGTTTTAGTTCCATCCAAGCATG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCATCCAAGCATG
6386 CAGGGG
65 CAGGGG
* *
6392 CTTTTCAATAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAAGCAT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCATCC-AAGCAT
*
6456 TCAGGGG
64 GCAGGGG
* * **
6463 CTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAGTTCAAGTTTTGGTTCCATCCAAGCATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
6528 AGGGG
66 AGGGG
* * * *
6533 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGACAGTT-TAGCCTTGGTTCCATCAAAGCA-GC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
6596 AGGGG
66 AGGGG
* *
6601 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-TAGCCTTGGTTCCATCCAAGCA-GT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATG-
*
6664 AAGGGG
65 CAGGGG
6670 CTTTTCCA
1 CTTTTCCA
6678 TAGGCCAAGT
Statistics
Matches: 317, Mismatches: 35, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
68 65 0.21
69 31 0.10
70 157 0.50
71 64 0.20
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (70 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
AGGGG
Found at i:6488 original size:141 final size:141
Alignment explanation
Indices: 6252--6685 Score: 560
Period size: 141 Copynumber: 3.1 Consensus size: 141
6242 AATGCTTTGA
* * * * *
6252 CTTTTCCATAAGTCAAACTCATTTACACACAAG-TCAGTTCAAGCTTTGGTTCCATCC-AAGCAT
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAAGCAT
* *
6315 GCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATAAGAGAT-TGTTCATGTTTTAGTTCCATCC
65 GCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATAAGAG-TCAGTTCAAGTTTTAGTTCCATCC
6379 AAGCATGCAGGGG
129 AAGCATGCAGGGG
* *
6392 CTTTTCAATAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAAGCATT
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAAGCATG
* * *
6457 CAGGGGCTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAGTTCAAGTTTTGGTTCCATCCAA
66 CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATAAGAGTCAGTTCAAGTTTTAGTTCCATCCAA
**
6522 GCATTTAGGGG
131 GCATGCAGGGG
* * * *
6533 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGACAGTT-TAGCCTTGGTTCCAT-CAAAGCA-G
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAAGCATG
* * ** *
6595 CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-TAGCCTTGGTTCCATCCAA
66 CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATAAGAGTCAGTTCAAGTTTTAGTTCCATCCAA
*
6659 GCA-GTAAGGGG
131 GCATG-CAGGGG
*
6670 CTTTTCCATAGGCCAA
1 CTTTTCCATAAGCCAA
6686 GTTCATTTCC
Statistics
Matches: 262, Mismatches: 28, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
137 38 0.15
138 44 0.17
139 7 0.03
140 63 0.24
141 110 0.42
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (141 bp):
CTTTTCCATAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAAGCATG
CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATAAGAGTCAGTTCAAGTTTTAGTTCCATCCAA
GCATGCAGGGG
Found at i:11367 original size:32 final size:32
Alignment explanation
Indices: 11326--11481 Score: 222
Period size: 32 Copynumber: 4.8 Consensus size: 32
11316 CTTTATTGAC
11326 TCCACTTAATTACCCTGAATTAAGTTCTTTAT
1 TCCACTTAATTACCCTGAATTAAGTTCTTTAT
11358 TCCACTTAATTACCCTGAATTAAGTTCTTTAT
1 TCCACTTAATTACCCTGAATTAAGTTCTTTAT
* * *
11390 TCTACTTAATTACCCTGAATTAAGCCTTTTATTGAC
1 TCCACTTAATTACCCTGAATTAAG--TTCT-TT-AT
*
11426 TCCACTTAATTACCCTGAATTAAGTTCTTGAT
1 TCCACTTAATTACCCTGAATTAAGTTCTTTAT
* *
11458 TCTACTTAATTACCTTGAATTAAG
1 TCCACTTAATTACCCTGAATTAAG
11482 CCATTTATTG
Statistics
Matches: 111, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
32 78 0.70
33 1 0.01
34 6 0.05
35 2 0.02
36 24 0.22
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (32 bp):
TCCACTTAATTACCCTGAATTAAGTTCTTTAT
Found at i:11388 original size:68 final size:67
Alignment explanation
Indices: 11329--11504 Score: 243
Period size: 68 Copynumber: 2.6 Consensus size: 67
11319 TATTGACTCC
*
11329 ACTTAATTACCCTGAATTAAG-TTCT-TT-ATTCCACTTAATTACCCTGAATTAAGTTCTTTATT
1 ACTTAATTACCCTGAATTAAGCTTCTATTGACTCCACTTAATTACCCTGAATTAAGTTCTTTATT
11391 CT
66 CT
* *
11393 ACTTAATTACCCTGAATTAAGCCTTTTATTGACTCCACTTAATTACCCTGAATTAAGTTCTTGAT
1 ACTTAATTACCCTGAATTAAG-CTTCTATTGACTCCACTTAATTACCCTGAATTAAGTTCTTTAT
11458 TCT
65 TCT
* * *
11461 ACTTAATTACCTTGAATTAAGCCATT-TATTGACTCTACTAAATT
1 ACTTAATTACCCTGAATTAAG-C-TTCTATTGACTCCACTTAATT
11505 TCCTTCCCTG
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
64 21 0.21
66 3 0.03
67 2 0.02
68 73 0.72
69 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (67 bp):
ACTTAATTACCCTGAATTAAGCTTCTATTGACTCCACTTAATTACCCTGAATTAAGTTCTTTATT
CT
Found at i:11546 original size:41 final size:40
Alignment explanation
Indices: 11501--12436 Score: 1265
Period size: 41 Copynumber: 23.1 Consensus size: 40
11491 GACTCTACTA
* *
11501 AATTTCCTTCCCTGAAATTAAGTTTGTGCTTGTCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTT-TCTTTACCT
*
11542 AA--T--TTCCTTGAAATTAAGTCTGTGCCTATCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTG-CTTTCTTTACCT
*
11579 AATTTCCTTCCTTGAAATTAAGTCTATGCTTTACTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTT-CTTTACCT
* * *
11620 AATTTCCTTCCTTGAAATTAAGTTTGTGCTTACTTTACTT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTCTTTACCT
* *
11660 AATTTCCCTCCTTGAAATTAAGTCTGTGCTTACTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTCTTTACCT
* *
11700 AATTTCCTTCATTGAAATTAAGTCTGTGCTTACTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTCTTTACCT
* *
11740 AATTTCCTTCCTTGAAATTAAATCTGTGCTTACTTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTC-TTTACCT
* * *
11781 AATTTCCTTCCTTGAAATTAAGTATGTGCTTACTTTAGCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTCTTTACCT
* *
11821 AATTTCCTTCTTTGAAATTAAGTCTGTGCTTACTTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTC-TTTACCT
* *
11862 AATTTTCTTCCTTGAAATTAAGTCTGTGCTATACTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
*
11903 AATTTCCTTCCTTGAAATT-A--CTGTGCTATACTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCT-TTCTTTACCT
* *
11941 AATTTCCTTTCTTGAAATTAAGTATGTGCTTTACTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTT-CTTTACCT
* *
11982 AATTTCCTTCCTTGAAATTAAGTCTGTGCCTATCTTTACTT
1 AATTTCCTTCCTTGAAATTAAGTCTGTG-CTTTCTTTACCT
* * *
12023 AATTTACTTCCTTGAAATTAAGTCTGTGCCTATCTTTACTT
1 AATTTCCTTCCTTGAAATTAAGTCTGTG-CTTTCTTTACCT
* * *
12064 AATTTCCTTCCTTGAAATTAAATTTGTGCTTTACTTTACTT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTT-CTTTACCT
*
12105 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTGTCTTTTCCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTT-TCTTTACCT
*
12146 AATTTCCTTCCTTGAAATTAAGTATGTGCTTGTCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTT-TCTTTACCT
12187 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTT-CTTTACCT
* * *
12228 AATTTCCTTCCTTGAAATTAAGTCTGTGTTTGTCTTTTCTT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTT-TCTTTACCT
*
12269 AATATCCTTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTT-TCTTTACCT
12310 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTT-CTTTACCT
* *
12351 AATTTCCTTCCTTGAAATTAAGTATGTGCTTGTCCTTACCT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTT-TCTTTACCT
* * * *
12392 AGTTTCCTTCCTTGAAATTATGTTTGTGCTTTACTTTACTT
1 AATTTCCTTCCTTGAAATTAAGTCTGTGCTTT-CTTTACCT
12433 AATT
1 AATT
12437 ACCATGAATT
Statistics
Matches: 814, Mismatches: 60, Indels: 42
0.89 0.07 0.05
Matches are distributed among these distances:
37 30 0.04
38 38 0.05
39 3 0.00
40 161 0.20
41 573 0.70
42 9 0.01
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.47
Consensus pattern (40 bp):
AATTTCCTTCCTTGAAATTAAGTCTGTGCTTTCTTTACCT
Found at i:12468 original size:37 final size:37
Alignment explanation
Indices: 12426--12674 Score: 349
Period size: 37 Copynumber: 6.6 Consensus size: 37
12416 TGTGCTTTAC
*
12426 TTTACTTAATTACCATGAATTAAGTCCTTTTACTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTGACTGCT
*
12463 TTTACTTAATTACCATGAATTAAGTCCTTTTACTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTGACTGCT
12500 TTTACTTAATTACCATGAATTAAGTCCTTTGACTGCTGT
1 TTTACTTAATTACCATGAATTAAGTCCTTTGACTGC--T
* *
12539 GTTTACTTAATTTCCTTGAATTAAGTCCTTTGACTGCT
1 -TTTACTTAATTACCATGAATTAAGTCCTTTGACTGCT
* * *
12577 TTTACTTAATTATCATGAATTAAGTCTTTTAACTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTGACTGCT
* *
12614 TTTACTTAATAACCCTGAATTAAGTCCTTTGACTG-T
1 TTTACTTAATTACCATGAATTAAGTCCTTTGACTGCT
*
12650 TGTTACTTAATTTCTC-TGAATTAAG
1 T-TTACTTAATTAC-CATGAATTAAG
12675 ACTTTGATTG
Statistics
Matches: 192, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
36 2 0.01
37 153 0.80
38 2 0.01
39 1 0.01
40 34 0.18
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (37 bp):
TTTACTTAATTACCATGAATTAAGTCCTTTGACTGCT
Found at i:12559 original size:114 final size:112
Alignment explanation
Indices: 12426--12674 Score: 387
Period size: 114 Copynumber: 2.2 Consensus size: 112
12416 TGTGCTTTAC
* * *
12426 TTTACTTAATTACCATGAATTAAGTCCTTTTACTGCTTTTACTTAATTACCATGAATTAAGTCCT
1 TTTACTTAATTTCCTTGAATTAAGTCCTTTGACTGCTTTTACTTAATTACCATGAATTAAGT-CT
*
12491 TTT-ACTGCTTTTACTTAATTACCATGAATTAAGTCCTTTGACTGCTGTG
65 TTTAACTGCTTTTACTTAATAACCATGAATTAAGTCCTTTGACTG-T-TG
*
12540 TTTACTTAATTTCCTTGAATTAAGTCCTTTGACTGCTTTTACTTAATTATCATGAATTAAGTCTT
1 TTTACTTAATTTCCTTGAATTAAGTCCTTTGACTGCTTTTACTTAATTACCATGAATTAAGTCTT
*
12605 TTAACTGCTTTTACTTAATAACCCTGAATTAAGTCCTTTGACTGTTG
66 TTAACTGCTTTTACTTAATAACCATGAATTAAGTCCTTTGACTGTTG
12652 -TTACTTAATTT-CTCTGAATTAAG
1 TTTACTTAATTTCCT-TGAATTAAG
12675 ACTTTGATTG
Statistics
Matches: 127, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
110 2 0.02
111 20 0.16
112 2 0.02
113 6 0.05
114 97 0.76
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (112 bp):
TTTACTTAATTTCCTTGAATTAAGTCCTTTGACTGCTTTTACTTAATTACCATGAATTAAGTCTT
TTAACTGCTTTTACTTAATAACCATGAATTAAGTCCTTTGACTGTTG
Found at i:12710 original size:41 final size:41
Alignment explanation
Indices: 12655--12764 Score: 159
Period size: 40 Copynumber: 2.7 Consensus size: 41
12645 ACTGTTGTTA
* * *
12655 CTTAATTTCTCTGAATTAAGACTTTGATTGTGTTTACTCTT
1 CTTAATTACCCTGAATTAAGACTTTGACTGTGTTTACTCTT
* *
12696 CTTAATTACCCTGAATTAAGAC-TTCACTGTGTTTACTTTT
1 CTTAATTACCCTGAATTAAGACTTTGACTGTGTTTACTCTT
*
12736 CTTAATTACCCTGAATTAAGAATTTGACT
1 CTTAATTACCCTGAATTAAGACTTTGACT
12765 ATATTTATGG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 36 0.59
41 25 0.41
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45
Consensus pattern (41 bp):
CTTAATTACCCTGAATTAAGACTTTGACTGTGTTTACTCTT
Found at i:13274 original size:18 final size:18
Alignment explanation
Indices: 13247--13281 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13237 CAAAGCTGCC
13247 TTCTTCCTCTTCAAAACT
1 TTCTTCCTCTTCAAAACT
* *
13265 TTCTTTCTCTTCCAAAC
1 TTCTTCCTCTTCAAAAC
13282 CCTAGCCGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.46
Consensus pattern (18 bp):
TTCTTCCTCTTCAAAACT
Found at i:16744 original size:15 final size:15
Alignment explanation
Indices: 16721--16750 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16711 ATCGGTTGAA
*
16721 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
16736 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
16751 GCGGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:22014 original size:15 final size:15
Alignment explanation
Indices: 21991--22020 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21981 ATCGGTTGAA
*
21991 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
22006 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
22021 GTGGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:34584 original size:21 final size:21
Alignment explanation
Indices: 34546--34590 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34536 GGCACCCACA
* *
34546 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAAGACCCAAG
**
34567 TGGTTTGCCTGATTACCCAAG
1 TGGTTTGCCTGAAGACCCAAG
34588 TGG
1 TGG
34591 GCAGTGTCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAAGACCCAAG
Done.