Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007310.1 Corchorus capsularis cultivar CVL-1 contig07331, 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: 49161
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4178 original size:30 final size:30
Alignment explanation
Indices: 4144--4200 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
4134 GTGATGAAAT
*
4144 AAGTCAACTGTGTATTTACAGCAGGATGCA
1 AAGTCAACAGTGTATTTACAGCAGGATGCA
* * *
4174 AAGTCAACAGTTTGTTTACAGTAGGAT
1 AAGTCAACAGTGTATTTACAGCAGGAT
4201 CCAAGATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (30 bp):
AAGTCAACAGTGTATTTACAGCAGGATGCA
Found at i:6679 original size:2 final size:2
Alignment explanation
Indices: 6672--6698 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6662 AAAATCAATC
6672 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 A
6699 CATAGAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6999 original size:2 final size:2
Alignment explanation
Indices: 6992--7025 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6982 AACCAGAATA
6992 AT AT AT 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 AT AT AT
7026 TAATTTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7375 original size:20 final size:21
Alignment explanation
Indices: 7350--7391 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7340 TCTTAGGTTC
*
7350 TACTCTTAC-GAAATGTGAGT
1 TACTCTCACGGAAATGTGAGT
*
7370 TACTCTCACGGAATTGTGAGT
1 TACTCTCACGGAAATGTGAGT
7391 T
1 T
7392 TTCTTTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (21 bp):
TACTCTCACGGAAATGTGAGT
Found at i:8204 original size:31 final size:29
Alignment explanation
Indices: 8158--8215 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 29
8148 CATTTGTAAA
8158 AAAATTTTATTTATCTATATTTATGTTAC
1 AAAATTTTATTTATCTATATTTATGTTAC
8187 AAAATTTTCCATTTATCTATATTTATGTT
1 AAAATTTT--ATTTATCTATATTTATGTT
8216 TAATGGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 8 0.30
31 19 0.70
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (29 bp):
AAAATTTTATTTATCTATATTTATGTTAC
Found at i:8728 original size:21 final size:19
Alignment explanation
Indices: 8703--8757 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
8693 ATTTAATTTT
*
8703 TCATTACACCTAATAATGA
1 TCATTACACCTAATAAGGA
*
8722 TACCATTACACCTAAAAAGGA
1 T--CATTACACCTAATAAGGA
*
8743 TCATTACACCAAATA
1 TCATTACACCTAATA
8758 GGGACAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.25
Consensus pattern (19 bp):
TCATTACACCTAATAAGGA
Found at i:14314 original size:165 final size:165
Alignment explanation
Indices: 14039--14415 Score: 605
Period size: 165 Copynumber: 2.3 Consensus size: 165
14029 GTAATTAACC
* * *
14039 GACACTTGAA-CAACCTCAATCGGACAAAT-GGACTGAAAATTATACAATATTAAATAGACGGGC
1 GACACTTGAATC-ACCTTAATCGGACAAATAGAAC--AAAAAT-TACAATATTAAATAGACGGGC
*
14102 AATTGAAACCACAAAATTTCGGAAGCCTTTTTTAAAATCAAAACATTAAAATTGACTTCTAAATT
62 AATTGAAACCACAAAATTTCGGAAGCATTTTTTAAAATCAAAACATTAAAATTGACTTCTAAATT
*
14167 CTTCATGAAAGTTATATATCATGAAATCACATTTTAATA
127 CTTCATGAAAGTTATAGATCATGAAATCACATTTTAATA
**
14206 GACACTTGAATCACCTTAATCGGACAAATAGAACAAAAATTACAATATTAAATAGATTGGCAATT
1 GACACTTGAATCACCTTAATCGGACAAATAGAACAAAAATTACAATATTAAATAGACGGGCAATT
* *
14271 GAAACCACAAAATTTCGGAAGTATTTTTTAAAATCAGAACATTAAAATTGACTTCTAAATTCTTC
66 GAAACCACAAAATTTCGGAAGCATTTTTTAAAATCAAAACATTAAAATTGACTTCTAAATTCTTC
14336 ATGAAAGTTATAGATCATGAAATCACATTTTAATA
131 ATGAAAGTTATAGATCATGAAATCACATTTTAATA
* *
14371 GACACTTGAATCACCTTAATCGAACAAATAGAACAAAAAATACAA
1 GACACTTGAATCACCTTAATCGGACAAATAGAACAAAAATTACAA
14416 AAATGAAAGG
Statistics
Matches: 197, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
165 162 0.82
166 5 0.03
167 26 0.13
168 4 0.02
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (165 bp):
GACACTTGAATCACCTTAATCGGACAAATAGAACAAAAATTACAATATTAAATAGACGGGCAATT
GAAACCACAAAATTTCGGAAGCATTTTTTAAAATCAAAACATTAAAATTGACTTCTAAATTCTTC
ATGAAAGTTATAGATCATGAAATCACATTTTAATA
Found at i:15088 original size:8 final size:9
Alignment explanation
Indices: 15030--15086 Score: 82
Period size: 9 Copynumber: 6.4 Consensus size: 9
15020 TACGTGGCAT
15030 TTTTTAATA
1 TTTTTAATA
15039 TTTTTAATA
1 TTTTTAATA
*
15048 TTTTTTATAA
1 TTTTTAAT-A
15058 TTTTTAAT-
1 TTTTTAATA
15066 TTTTTAAT-
1 TTTTTAATA
15074 TTTTTAATA
1 TTTTTAATA
15083 TTTT
1 TTTT
15087 AAACCGGCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 16 0.36
9 20 0.45
10 8 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTAATA
Found at i:16469 original size:2 final size:2
Alignment explanation
Indices: 16462--16489 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16452 TTATACCAGA
16462 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
16490 GCACTTTCCA
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:18683 original size:2 final size:2
Alignment explanation
Indices: 18671--18707 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
18661 AACTTTAATG
18671 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18708 CACTACTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22607 original size:12 final size:12
Alignment explanation
Indices: 22590--22623 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
22580 CCACATGCCA
22590 GAAATGGCAATG
1 GAAATGGCAATG
22602 GAAATGGCAATG
1 GAAATGGCAATG
*
22614 AAAATGGCAA
1 GAAATGGCAA
22624 GGGTGCCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.29, T:0.15
Consensus pattern (12 bp):
GAAATGGCAATG
Found at i:36556 original size:179 final size:178
Alignment explanation
Indices: 36247--36647 Score: 500
Period size: 179 Copynumber: 2.3 Consensus size: 178
36237 CAAAATTTGG
* * * * *
36247 GTTGTAG-TCATGGAAAAATCTTTTAACAGATACTTGAATCATCTCAATCAGACATATGAAGCAA
1 GTTGTAGATCATGGAACAATCTTTTAAAAGACACTTAAATCACCTCAATCAGACATATGAAGCAA
** * * * * *
36311 AAATTATATAATATTAAGTAGATTATAGATTCCCGTTAACCGAAACAATTAATTCTTCGTAAGCA
66 AAATTATATAATATTAAGTAGACCATACATTCACGATAACCGAAACAACTAATTCTTCGAAAGCA
* * * *
36376 TTTTTTTATACTTTAAACATTAAATTTAGCTTTT-GAGTCCTTCATAAAA
131 -TTTTTGATACTTGAAACATTAAATTTA-ATTTTCAAGTCCTTCATAAAA
* * * *
36425 GTTGTAGATCATGGAACAACCTTTTAAAAGACACCTAAATCACCTCAATCAGACATCTGGAGCAA
1 GTTGTAGATCATGGAACAATCTTTTAAAAGACACTTAAATCACCTCAATCAGACATATGAAGCAA
* * * * * * *
36490 AAGTTATGTAATATTAAGTGGACCGTCCATTCATGATAACCGAAACAACTAATTTTTCGAAAGCA
66 AAATTATATAATATTAAGTAGACCATACATTCACGATAACCGAAACAACTAATTCTTCGAAAGCA
*
36555 TTTTTGATACTTGAAACATTAAATTTAATTTTCAAGTCCTTCATGAAA
131 TTTTTGATACTTGAAACATTAAATTTAATTTTCAAGTCCTTCATAAAA
* *
36603 GTTGTAGATCATGAAACAATCTTTTAATAGACACTTAAATCACCT
1 GTTGTAGATCATGGAACAATCTTTTAAAAGACACTTAAATCACCT
36648 TGATCGGATA
Statistics
Matches: 189, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
177 4 0.02
178 86 0.46
179 99 0.52
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (178 bp):
GTTGTAGATCATGGAACAATCTTTTAAAAGACACTTAAATCACCTCAATCAGACATATGAAGCAA
AAATTATATAATATTAAGTAGACCATACATTCACGATAACCGAAACAACTAATTCTTCGAAAGCA
TTTTTGATACTTGAAACATTAAATTTAATTTTCAAGTCCTTCATAAAA
Done.