Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009861.1 Corchorus capsularis cultivar CVL-1 contig09882, 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: 84913
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5644 original size:21 final size:21
Alignment explanation
Indices: 5601--5644 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5591 TGAAAGGGGG
* *
5601 TTGCTAAATACCGCCCTAGTT
1 TTGCTAAATACCGCCCCACTT
5622 TTGCTAAATACCGCCCCACTT
1 TTGCTAAATACCGCCCCACTT
5643 TT
1 TT
5645 TACACTTTTT
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:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCACTT
Found at i:5840 original size:32 final size:34
Alignment explanation
Indices: 5777--5898 Score: 180
Period size: 32 Copynumber: 3.7 Consensus size: 34
5767 CCTATTCATA
* *
5777 GTGAAGCCACCCTAATGGGGCGGCCTGCCCAATG
1 GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCAATG
5811 GTGAAGCCGCCCTAGT-GGGC-GCCTGCCCAATG
1 GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCAATG
5843 GTGAAGCCGCCCTAGTGGGGCGGCCTGCCC-ATG
1 GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCAATG
**
5876 GT-AAGCCGCCCTCTTGGGGCGGC
1 GTGAAGCCGCCCTAGTGGGGCGGC
5899 ACGGGTCATC
Statistics
Matches: 82, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
32 47 0.57
33 13 0.16
34 22 0.27
ACGTcount: A:0.15, C:0.34, G:0.36, T:0.16
Consensus pattern (34 bp):
GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCAATG
Found at i:5854 original size:16 final size:16
Alignment explanation
Indices: 5803--5854 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5793 GGGGCGGCCT
5803 GCCCAATGGTGAAGCC
1 GCCCAATGGTGAAGCC
* *
5819 GCCCTAGTGG-G-CGCC
1 GCCC-AATGGTGAAGCC
5834 TGCCCAATGGTGAAGCC
1 -GCCCAATGGTGAAGCC
5851 GCCC
1 GCCC
5855 TAGTGGGGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.17, C:0.37, G:0.33, T:0.13
Consensus pattern (16 bp):
GCCCAATGGTGAAGCC
Found at i:8205 original size:34 final size:34
Alignment explanation
Indices: 8120--8221 Score: 177
Period size: 36 Copynumber: 2.9 Consensus size: 34
8110 CAAACAATTT
8120 TTGTAGTTTGCTTTTAATTTATCAACTAGATGGA
1 TTGTAGTTTGCTTTTAATTTATCAACTAGATGGA
8154 TTGTAGAATTTGCTTTTAATTTATCAACTAGATGGA
1 TTGTAG--TTTGCTTTTAATTTATCAACTAGATGGA
*
8190 TTGTAGTTTGCTTTTACTTTATCAACTAGATG
1 TTGTAGTTTGCTTTTAATTTATCAACTAGATG
8222 AGATATCTTT
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
34 31 0.48
36 34 0.52
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (34 bp):
TTGTAGTTTGCTTTTAATTTATCAACTAGATGGA
Found at i:11912 original size:1 final size:1
Alignment explanation
Indices: 11906--11932 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
11896 CAACTCAAAC
11906 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
11933 GACTTTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12043 original size:23 final size:23
Alignment explanation
Indices: 12013--12058 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
12003 AGCTCTCATG
12013 AATGGTAAATGGTTAGAAAAAAA
1 AATGGTAAATGGTTAGAAAAAAA
12036 AATGGTAAATGGTTAGAAAAAAA
1 AATGGTAAATGGTTAGAAAAAAA
12059 GGTAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22
Consensus pattern (23 bp):
AATGGTAAATGGTTAGAAAAAAA
Found at i:36755 original size:3 final size:3
Alignment explanation
Indices: 36747--36787 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
36737 ATTTAGGGTT
36747 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AGAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG A
36788 CAAAGGCAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:50931 original size:20 final size:20
Alignment explanation
Indices: 50906--50945 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
50896 TCTACTTACA
*
50906 CTAAAATAAATATTAGTCTT
1 CTAAAATAAATAATAGTCTT
50926 CTAAAATAAATAATAGTCTT
1 CTAAAATAAATAATAGTCTT
50946 AATATATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
CTAAAATAAATAATAGTCTT
Found at i:53757 original size:15 final size:15
Alignment explanation
Indices: 53737--53766 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53727 CAACATTCTT
53737 TTTTTTTTTTAAGAG
1 TTTTTTTTTTAAGAG
53752 TTTTTTTTTTAAGAG
1 TTTTTTTTTTAAGAG
53767 AATGTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (15 bp):
TTTTTTTTTTAAGAG
Found at i:54149 original size:31 final size:31
Alignment explanation
Indices: 54111--54175 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
54101 AACTGAACTA
* **
54111 ACTCAAACATCTAAGATTTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCGAAAGATCTGGAG
*
54142 ACTCAAACATCCAATATCGAAAGATCTGGAG
1 ACTCAAACATCCAAGATCGAAAGATCTGGAG
54173 ACT
1 ACT
54176 GATAACCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCGAAAGATCTGGAG
Found at i:55685 original size:20 final size:21
Alignment explanation
Indices: 55642--55685 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55632 CAATTTATTC
* *
55642 ATTCACCGAAAAAAAGTAATA
1 ATTCACCAAAAAAAAGTAACA
55663 ATTCACCAAAAAAAAG-AACA
1 ATTCACCAAAAAAAAGTAACA
55683 ATT
1 ATT
55686 TATTCTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.59, C:0.16, G:0.07, T:0.18
Consensus pattern (21 bp):
ATTCACCAAAAAAAAGTAACA
Found at i:57203 original size:54 final size:54
Alignment explanation
Indices: 57119--57225 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 54
57109 ATGGGTCTAA
*
57119 AGCTGACACTAATGGTGGGGATTCTATAGAAGCTGCTGTTGTTGATTCAAGTGG
1 AGCTGACACTAATGGTGGGGATTCTATAGAAGCTGCTATTGTTGATTCAAGTGG
* *
57173 AGCTGACGCTAATGGTGGGGATTCTTTAGAAGCTGCTATTGTTGATTCAAGTG
1 AGCTGACACTAATGGTGGGGATTCTATAGAAGCTGCTATTGTTGATTCAAGTG
57226 CTAAGAGTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (54 bp):
AGCTGACACTAATGGTGGGGATTCTATAGAAGCTGCTATTGTTGATTCAAGTGG
Found at i:57387 original size:69 final size:69
Alignment explanation
Indices: 57300--57441 Score: 239
Period size: 69 Copynumber: 2.1 Consensus size: 69
57290 TACAAAGTTG
* *
57300 GAAGAGAATGACTCTGAAATTGCTGTAGCTGCTGAAGAAGACACGGCATGTCTCGTTGGTTTAGG
1 GAAGAGAATGACTCTGAAATTGCTGTAGCTGCTGAAGAAGACACAGCATGTATCGTTGGTTTAGG
57365 GCAT
66 GCAT
* * *
57369 GAAGAGGATGACTCTGAAATTGCTGTAGCTGCTGAAGAGGACACAGCATGTATCGTTGGTTTGGG
1 GAAGAGAATGACTCTGAAATTGCTGTAGCTGCTGAAGAAGACACAGCATGTATCGTTGGTTTAGG
57434 GCAT
66 GCAT
57438 GAAG
1 GAAG
57442 TGGACGGGGT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.25
Consensus pattern (69 bp):
GAAGAGAATGACTCTGAAATTGCTGTAGCTGCTGAAGAAGACACAGCATGTATCGTTGGTTTAGG
GCAT
Found at i:57577 original size:27 final size:27
Alignment explanation
Indices: 57537--57594 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
57527 TCAACCATCA
* *
57537 GATGGTAATAGAGATTGCCCTGTTTCG
1 GATGGCAATAGAGATTGCACTGTTTCG
*
57564 GATGGCAATGGAGATTGCACTGTTTCG
1 GATGGCAATAGAGATTGCACTGTTTCG
57591 GATG
1 GATG
57595 CTCCCAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (27 bp):
GATGGCAATAGAGATTGCACTGTTTCG
Found at i:57706 original size:21 final size:21
Alignment explanation
Indices: 57677--57738 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
57667 CCAAAACTCC
* *
57677 TGAGAAACTAGTAGTAGGAGT
1 TGAGAAACTAGAATTAGGAGT
*
57698 TGAGGAACTAGAATTAGGAGT
1 TGAGAAACTAGAATTAGGAGT
57719 TGAGAAACTAGAATTAGGAG
1 TGAGAAACTAGAATTAGGAG
57739 ATGTTATAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.32, T:0.23
Consensus pattern (21 bp):
TGAGAAACTAGAATTAGGAGT
Found at i:58136 original size:45 final size:45
Alignment explanation
Indices: 58072--58202 Score: 232
Period size: 45 Copynumber: 3.0 Consensus size: 45
58062 TCTAGCGGCC
58072 TTGCTGAATCTAAATGTGAAGTTGATGATGTGGTCGCAGATTCGG
1 TTGCTGAATCTAAATGTGAAGTTGATGATGTGGTCGCAGATTCGG
*
58117 TTGCTGAATCTAAATGTGAAGTTGATGATGTGGTTGCAGATTCGG
1 TTGCTGAATCTAAATGTGAAGTTGATGATGTGGTCGCAGATTCGG
58162 TTGCTGAATCTAAATGTGAAG-T--TGATGTGGTCGCAGATTCG
1 TTGCTGAATCTAAATGTGAAGTTGATGATGTGGTCGCAGATTCG
58203 ATTCCCTCCT
Statistics
Matches: 84, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
42 18 0.21
44 1 0.01
45 65 0.77
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.34
Consensus pattern (45 bp):
TTGCTGAATCTAAATGTGAAGTTGATGATGTGGTCGCAGATTCGG
Found at i:58276 original size:15 final size:15
Alignment explanation
Indices: 58256--58285 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58246 CATCCCCTGT
58256 GAGCAAGGATATTCC
1 GAGCAAGGATATTCC
58271 GAGCAAGGATATTCC
1 GAGCAAGGATATTCC
58286 TATCAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (15 bp):
GAGCAAGGATATTCC
Found at i:60137 original size:12 final size:12
Alignment explanation
Indices: 60120--60144 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60110 CAGCCTGTTA
60120 TTCCTCAAGTAG
1 TTCCTCAAGTAG
60132 TTCCTCAAGTAG
1 TTCCTCAAGTAG
60144 T
1 T
60145 AAATGGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TTCCTCAAGTAG
Found at i:60170 original size:18 final size:18
Alignment explanation
Indices: 60147--60184 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
60137 CAAGTAGTAA
60147 ATGGAAGAGTGGCCAAGG
1 ATGGAAGAGTGGCCAAGG
60165 ATGGAAGAGTGGCCAAGG
1 ATGGAAGAGTGGCCAAGG
60183 AT
1 AT
60185 CACACAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.42, T:0.13
Consensus pattern (18 bp):
ATGGAAGAGTGGCCAAGG
Found at i:61554 original size:26 final size:26
Alignment explanation
Indices: 61525--61577 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
61515 AATCCCAAGG
61525 CCCATGTATTAGTATGAAGTATTTGA
1 CCCATGTATTAGTATGAAGTATTTGA
61551 CCCATGTATTAGTATGAAGTATTTGA
1 CCCATGTATTAGTATGAAGTATTTGA
61577 C
1 C
61578 ATTTACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (26 bp):
CCCATGTATTAGTATGAAGTATTTGA
Found at i:61615 original size:26 final size:26
Alignment explanation
Indices: 61579--61632 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
61569 GTATTTGACA
61579 TTTACCAAATAAAAGATGCCACCACT
1 TTTACCAAATAAAAGATGCCACCACT
61605 TTTACCAAATAAAAGATGCCACCACT
1 TTTACCAAATAAAAGATGCCACCACT
61631 TT
1 TT
61633 CAACTGAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (26 bp):
TTTACCAAATAAAAGATGCCACCACT
Found at i:72486 original size:30 final size:30
Alignment explanation
Indices: 72450--72510 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
72440 CTTAATAATT
*
72450 CCATTACAACTTCGAAATAAAAGACTAAAA
1 CCATTACAACTTCAAAATAAAAGACTAAAA
*
72480 CCATTACAACTTCAAAATTAAAGACTAAAA
1 CCATTACAACTTCAAAATAAAAGACTAAAA
72510 C
1 C
72511 TGCGAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.21, G:0.05, T:0.21
Consensus pattern (30 bp):
CCATTACAACTTCAAAATAAAAGACTAAAA
Found at i:72511 original size:21 final size:21
Alignment explanation
Indices: 72487--72534 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
72477 AAACCATTAC
*
72487 AACTTCAAAATTAAAGACTAA
1 AACTTCAAAATAAAAGACTAA
* *
72508 AACTGCGAAATAAAAGACTAA
1 AACTTCAAAATAAAAGACTAA
72529 AGACTT
1 A-ACTT
72535 AATATCCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (21 bp):
AACTTCAAAATAAAAGACTAA
Found at i:72604 original size:29 final size:29
Alignment explanation
Indices: 72566--72628 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
72556 ACTTGTAGTG
* * * *
72566 TTTGGGCATTTTGCCCCCTGATCTTTAAT
1 TTTGGACATTTTGCCCCATGAACTTCAAT
72595 TTTGGACATTTTGCCCCATGAACTTCAAT
1 TTTGGACATTTTGCCCCATGAACTTCAAT
72624 TTTGG
1 TTTGG
72629 GACGTTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCATGAACTTCAAT
Found at i:72851 original size:29 final size:28
Alignment explanation
Indices: 72778--72853 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
72768 CAAAATTGAG
72778 GGGGCAAAACATCTCAAAATTGAAGTTCA
1 GGGGCAAAACATC-CAAAATTGAAGTTCA
* **
72807 TGGTGCAAAATGTCCAAAATTGAAGTTCA
1 -GGGGCAAAACATCCAAAATTGAAGTTCA
72836 GGGGACAAAACATCCAAA
1 GGGG-CAAAACATCCAAA
72854 CGCTACAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
28 3 0.08
29 26 0.67
30 10 0.26
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (28 bp):
GGGGCAAAACATCCAAAATTGAAGTTCA
Found at i:75905 original size:2 final size:2
Alignment explanation
Indices: 75895--75929 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
75885 ACACACACAC
75895 AT AT A- AT AT AT -T 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 AT AT AT AT A
75930 AAGACAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76612 original size:78 final size:78
Alignment explanation
Indices: 76483--76627 Score: 290
Period size: 78 Copynumber: 1.9 Consensus size: 78
76473 TGCAATGATA
76483 TCAAACGTTTGACAAAATCCTAAGTTCTGAAGCACGGACACGGCTAGGGGGTCGCCGTATCCGTG
1 TCAAACGTTTGACAAAATCCTAAGTTCTGAAGCACGGACACGGCTAGGGGGTCGCCGTATCCGTG
76548 TCCGACTCCGATG
66 TCCGACTCCGATG
76561 TCAAACGTTTGACAAAATCCTAAGTTCTGAAGCACGGACACGGCTAGGGGGTCGCCGTATCCGTG
1 TCAAACGTTTGACAAAATCCTAAGTTCTGAAGCACGGACACGGCTAGGGGGTCGCCGTATCCGTG
76626 TC
66 TC
76628 GCACCGGAGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (78 bp):
TCAAACGTTTGACAAAATCCTAAGTTCTGAAGCACGGACACGGCTAGGGGGTCGCCGTATCCGTG
TCCGACTCCGATG
Found at i:81049 original size:7 final size:7
Alignment explanation
Indices: 81037--81062 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
81027 TAAACACTCG
81037 TTCAAGT
1 TTCAAGT
81044 TTCAAGT
1 TTCAAGT
81051 TTCAAGT
1 TTCAAGT
81058 TTCAA
1 TTCAA
81063 CTTAATTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (7 bp):
TTCAAGT
Found at i:82035 original size:21 final size:20
Alignment explanation
Indices: 82010--82055 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
82000 GTAAATTCTA
82010 ATATTTAAATTTTTTAAAAAT
1 ATATTTAAA-TTTTTAAAAAT
*
82031 ATA-TTATATTTTTAAAAAT
1 ATATTTAAATTTTTAAAAAT
82050 ATATTT
1 ATATTT
82056 TCTCAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 14 0.61
20 6 0.26
21 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTTAAATTTTTAAAAAT
Found at i:82156 original size:17 final size:16
Alignment explanation
Indices: 82106--82172 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 16
82096 TTAATAATCC
82106 ATTATAATTATAATTAATA
1 ATTAT-ATT-TAATT-ATA
* *
82125 ATT-TACTT-ATAATA
1 ATTATATTTAATTATA
*
82139 ATTATTTTTCAATTATA
1 ATTATATTT-AATTATA
82156 A-TATATTTAATTATA
1 ATTATATTTAATTATA
82171 AT
1 AT
82173 ATTATAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
14 6 0.16
15 13 0.34
16 7 0.18
17 8 0.21
18 1 0.03
19 3 0.08
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATATTTAATTATA
Found at i:82178 original size:18 final size:19
Alignment explanation
Indices: 82110--82183 Score: 61
Period size: 18 Copynumber: 4.1 Consensus size: 19
82100 TAATCCATTA
*
82110 TAATTATAAT-TAATAATT
1 TAATTATAATATTATAATT
* *
82128 TACTTATAATAATTAT-TTT
1 TAATTATAAT-ATTATAATT
82147 TCAATTAT-A-A-TAT-ATT
1 T-AATTATAATATTATAATT
82163 TAATTATAATATTATAATT
1 TAATTATAATATTATAATT
82182 TA
1 TA
82184 TAGTCATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
15 6 0.14
16 7 0.16
17 2 0.05
18 12 0.27
19 9 0.20
20 8 0.18
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATTATAATATTATAATT
Found at i:82185 original size:15 final size:15
Alignment explanation
Indices: 82149--82181 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
82139 ATTATTTTTC
*
82149 AATTATAATATATTT
1 AATTATAATATATAT
82164 AATTATAATAT-TAT
1 AATTATAATATATAT
82178 AATT
1 AATT
82182 TATAGTCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTATAATATATAT
Found at i:83399 original size:333 final size:331
Alignment explanation
Indices: 82794--84913 Score: 2889
Period size: 332 Copynumber: 6.4 Consensus size: 331
82784 TATGAGCATC
* * * *** ***
82794 TAAATCATATATATTTTATGAGTATTTTATCCGAAAATTGAGAAAAAAAAATTTTAAATCATTTT
1 TAAATCATATATAATTTATGAGTATTTTAT-CGAAAATTGTG-GAAAATTTTTTTGGGTCATTTT
* * *
82859 CAGCAAATTTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTCCGGA
64 CAGCAAATTTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTCGGCTAAAAATGCGTTCCGGA
* * * * * * * *
82924 GTTCCAGCTCAA-TTTTACATGATTTTTGGTGCAAAAACTCCTTGAAATAACTATATTCATCAAA
129 G-CCCGGCTCAATTTTTA-ATGATTTTTTGCGCTAAGACTTCTTGAAATATCTATATTCATCAAA
* * * * ** * * * * *
82988 CCAAATCTAAGCCACATTGGATATAAGGGTTTATTTTTACGAGCATCTGAATCTTGTTTAGATTT
192 CCAAATCTCAGCTACAGTGGATTTAAGAATTGATTTTTACGAGCATATAAATTTTGTTTCGATTT
* * *
83053 AATTAGAAATTAATTCAGAAAAAATATGAAAATTGAT-TTAAAAAAGTGAAAAGTCCTCAAATA-
257 AATTAGAAATTAATTCAGAAAAAATATGAAAATTGATATTAAAAAGGTGAAAAGTCCACCAATAT
83116 TTTTTGGTGT
322 TTTTTGGTGT
* * * *
83126 TAAATCATATATATTTTATGATTATTTTATCAGAAAATTGTGGAAAATTTTTTTGGATCATTGTC
1 TAAATCATATATAATTTATGAGTATTTTATC-GAAAATTGTGGAAAATTTTTTTGGGTCATTTTC
* * *
83191 AGCAAATTTTTAGCAAAAATCGTGCATAATAACCATCATAGTTTTCGGCTAAAAATGCGTTCCGG
65 AGCAAATTTTTAGCCAAAATCGTG--TACTAACCATCACAGTTTTCGGCTAAAAATGCGTTCCGG
*
83256 AGCACCGGCTCAATTTTTAATGATTTTTTGCGCTAAGACTTCATGAAATATCTATATTCATCAAA
128 AGC-CCGGCTCAATTTTTAATGATTTTTTGCGCTAAGACTTCTTGAAATATCTATATTCATCAAA
* *
83321 CCAAATCTCAGCTACGGTGGATTTAAGAATTGATTTTTACGAGCATATGAATTTTGTTTCGATTT
192 CCAAATCTCAGCTACAGTGGATTTAAGAATTGATTTTTACGAGCATATAAATTTTGTTTCGATTT
* *
83386 AATTAGAAATTAATTCAGAAAAAATACGAAAATTGATATTAAAAATGTGAAAAGTCCACCAATAT
257 AATTAGAAATTAATTCAGAAAAAATATGAAAATTGATATTAAAAAGGTGAAAAGTCCACCAATAT
83451 TTTTTGGTGT
322 TTTTTGGTGT
* * *
83461 TAAATAATATATAATTTATGACTATTTTATCCGAAAATTGAGGAAAATTTTTTTGGGTCATTTTC
1 TAAATCATATATAATTTATGAGTATTTTAT-CGAAAATTGTGGAAAATTTTTTTGGGTCATTTTC
* * * * *
83526 AGCAAATTTTTAGCCAAAATCATGTACGT---TATCACAATTTTCGGCTAAAAATGTGTTCCGAA
65 AGCAAATTTTTAGCCAAAATCGTGTAC-TAACCATCACAGTTTTCGGCTAAAAATGCGTTCCGGA
* * *
83588 GTCCCGGCTGAATTTTTAATGATTTTTTGTGCTAGGACTTCTTGAAATATCTATATTCATCAAAC
129 G-CCCGGCTCAATTTTTAATGATTTTTTGCGCTAAGACTTCTTGAAATATCTATATTCATCAAAC
*
83653 CAAATCTCAGCTACAGTGGATTTAAGAATTTATTTTTACGAGCATATAAAATTTTGTTTCGATTT
193 CAAATCTCAGCTACAGTGGATTTAAGAATTGATTTTTACGAGCATAT-AAATTTTGTTTCGATTT
83718 AATTAGAAATTAATTCAGAAAAAATATGAAAATTGATATTAAAAAGGTGAAAAGTCCACCAATAT
257 AATTAGAAATTAATTCAGAAAAAATATGAAAATTGATATTAAAAAGGTGAAAAGTCCACCAATA-
*
83783 TTTTTTGTTGT
321 TTTTTTGGTGT
* * *
83794 TAAATCATATATAATTTATGAGTATTTTATCCAAAATT-TGAGGAATTTTTTTTGGGTCATTTTC
1 TAAATCATATATAATTTATGAGTATTTTATCGAAAATTGTG-GAAAATTTTTTTGGGTCATTTTC
* *
83858 AGCAAATTTTTAGCCAAAATCGTGTAGTAACCATCACGGTTTTCGGCTAAAAATGCGTTCCGGAG
65 AGCAAATTTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTCGGCTAAAAATGCGTTCCGGAG
*
83923 CCTCGGCTCAATTTTTAATGATTTTTTGCGCCAAGACTTCTTGAAATATCTATATTCATCAAACC
130 CC-CGGCTCAATTTTTAATGATTTTTTGCGCTAAGACTTCTTGAAATATCTATATTCATCAAACC
* * * **
83988 AAATCTCAGCTACAATGGATTTAAGAATTGATTTTTACGAGCATATGAATTTTATTTTTATTTAA
194 AAATCTCAGCTACAGTGGATTTAAGAATTGATTTTTACGAGCATATAAATTTTGTTTCGATTTAA
* * *
84053 TTAGAAATTAATTCAGAAAAAATTTGAAAATTGGTATTAAAAGGGTGAAAAGTCCACCAATATTT
259 TTAGAAATTAATTCAGAAAAAATATGAAAATTGATATTAAAAAGGTGAAAAGTCCACCAATATTT
*
84118 TTTCGTGT
324 TTTGGTGT
* * *
84126 TAAATCATATATAATTTATAAGTATTTTATTCGAAAATTGTGGAAAAAAAATTTTTGGGGTCATT
1 TAAATCATATATAATTTATGAGTATTTTA-TCGAAAATTGTGG---AAAATTTTTTTGGGTCATT
* * * *
84191 TTCAGCAAAATTTTTTAGCCAATATTGTGTACTAAACTATCACGGTTTTCGGCTAAAAATGCGTT
62 TTCAGC-AAA-TTTTTAGCCAAAATCGTGTACT-AACCATCACAGTTTTCGGCTAAAAATGCGTT
* * *
84256 CCGGAGCCCCGGCTCAGTTTTTAATGATTTTTTTGCGCCAAGATTTCTTGAAATATCTATATTCA
124 CCGGAG-CCCGGCTCAATTTTTAATGA-TTTTTTGCGCTAAGACTTCTTGAAATATCTATATTCA
* *
84321 TCAAACCAGATCTCAGCTACAGTGG-TTTCAAGAATTGATTTTTACAAGCATATAAATTTTGTTT
187 TCAAACCAAATCTCAGCTACAGTGGATTT-AAGAATTGATTTTTACGAGCATATAAATTTTGTTT
* * *
84385 CGATTTAATTAGAAATTAATTCTGAAAAAATACGAAAATTGATATTAAAAATGTGAAAAGTCCAC
251 CGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAATTGATATTAAAAAGGTGAAAAGTCCAC
*
84450 CAATATTTTTTAGTGT
316 CAATATTTTTTGGTGT
* * **
84466 TAAGTCATATATAATTTATGAATATTTTATCTGAAAATTGAAGAAAATTTTTTTGGGTCATTTTC
1 TAAATCATATATAATTTATGAGTATTTTATC-GAAAATTGTGGAAAATTTTTTTGGGTCATTTTC
* * *
84531 AGCAAATTTTTAGCCAAAATCATGTACGT---TATCACAGTTTTCGGCTAAAAATGCGTTCCGAA
65 AGCAAATTTTTAGCCAAAATCGTGTAC-TAACCATCACAGTTTTCGGCTAAAAATGCGTTCCGGA
* * *
84593 GTCCCGGCTGAATTTTTAATGATTTTTTGTGCTAGGACTTCTTGAAATATCTATATTCATCAAAC
129 G-CCCGGCTCAATTTTTAATGATTTTTTGCGCTAAGACTTCTTGAAATATCTATATTCATCAAAC
*
84658 CAAATCTCAGCTACAGTGGATTTAAGAATTTATTTTTACGAGCATATAAAATTTTGTTTCGATTT
193 CAAATCTCAGCTACAGTGGATTTAAGAATTGATTTTTACGAGCATAT-AAATTTTGTTTCGATTT
* *
84723 AATTAGAAATTAATTCAGAAAAAATAGGAAAATTGATATTAAAAAGGTGAAAAGTCCTCCAATAT
257 AATTAGAAATTAATTCAGAAAAAATATGAAAATTGATATTAAAAAGGTGAAAAGTCCACCAATAT
*
84788 TTTTTGTTGT
322 TTTTTGGTGT
* * *
84798 TAAATCATATATAATTTACGAGTATTTTATCCAAAATT-T-GAGGAATTTTTTTGGGTCATTTTC
1 TAAATCATATATAATTTATGAGTATTTTATCGAAAATTGTGGA-AAATTTTTTTGGGTCATTTTC
* *
84861 AGCAAATTTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCATAAAA
65 AGCAAATTTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTCGGC-TAAAA
Statistics
Matches: 1596, Mismatches: 155, Indels: 73
0.88 0.08 0.04
Matches are distributed among these distances:
329 3 0.00
330 46 0.03
331 259 0.16
332 387 0.24
333 303 0.19
334 162 0.10
335 107 0.07
336 26 0.02
337 26 0.02
338 19 0.01
339 58 0.04
340 200 0.13
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (331 bp):
TAAATCATATATAATTTATGAGTATTTTATCGAAAATTGTGGAAAATTTTTTTGGGTCATTTTCA
GCAAATTTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTCGGCTAAAAATGCGTTCCGGAGC
CCGGCTCAATTTTTAATGATTTTTTGCGCTAAGACTTCTTGAAATATCTATATTCATCAAACCAA
ATCTCAGCTACAGTGGATTTAAGAATTGATTTTTACGAGCATATAAATTTTGTTTCGATTTAATT
AGAAATTAATTCAGAAAAAATATGAAAATTGATATTAAAAAGGTGAAAAGTCCACCAATATTTTT
TGGTGT
Done.