Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011134.1 Corchorus capsularis cultivar CVL-1 contig11155, 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: 58910
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2422 original size:445 final size:450
Alignment explanation
Indices: 1325--2597 Score: 2243
Period size: 445 Copynumber: 2.8 Consensus size: 450
1315 ACCCCTCTCG
*
1325 TTTTTAATTATTTAAGTAGATTTACAACATCATGATGATATTAGCAACTATTGACCGACGGGTTA
1 TTTTTAATTATTTAAGTAGATTTACAACATCATGATGATGTTAGCAACTATTGACCGACGGGTTA
*
1390 GCTAACTAACTCGGGTTGCCCAACAGGTTATACCCAGTATATACATGGGTTTTTATTGTTACCCA
66 GCTAACTAACTCGGGTTGCCCAACAGGTTATACCCAGTATATACATGGGTTTTTATTGGTACCCA
*
1455 GTATATATGGGTTTTTACTCATTAATATAAAAATAAAAATTCTCTTTTAAACTCTTAATGAAACT
131 GTATATATGGGTTTTTACTCATTAATATAAAAATAAAAATTCTCTTTTGAACTCTTAATGAAACT
*
1520 TGTAGATCAAATTTAGCTTTCGGGTTCGTAGATGATGCAATAACC-TTTAACCGACACTTGAATA
196 TGTGGATCAAATTTAGCTTTCGGGTTCGTAGATGATGCAATAACCTTTTAACCGACACTTGAATA
*
1584 ATATTAATTGGACATGTGGACTGAAAAATAATATGATATATTAAATAGACTGGTAATTAAAATCA
261 ACATTAATTGGACATGTGGACTG-AAAATAATATGATATATTAAATAGACTGGTAATTAAAATCA
* *
1649 CCAAATTTCGGAAGCATTTTTTGGAATTGAAACATAAAAATTGAATTAAAATCATCAAATAGACT
325 CCAAATTTCGGAAGCATTTTTTGGAATTGAAACATAAAAATTGGATTAAAATCACCAAATAGACT
*
1714 AGTTATAATCATTAAGATTTGATAGTTCCATAACCTTTTCTAATTAATTTTCTGATTCGTAAATA
390 AG-TATAATCATTAAGATTTGATAGTTCCACAACCTTTTC--A-TAA-----T-ATTCGTAAATA
1779 TTATTA
445 TTATTA
*
1785 TTTTTAATTATTTAAGTAGATTTACAACATCATGATGATGTTGGCAACTATTGACCGACGGGTTA
1 TTTTTAATTATTTAAGTAGATTTACAACATCATGATGATGTTAGCAACTATTGACCGACGGGTTA
*
1850 GCTAATTAACTCGGGTTGCCCAACAGGTTATACCCAGTATATACATGGGTTTTTATTGGTACCCA
66 GCTAACTAACTCGGGTTGCCCAACAGGTTATACCCAGTATATACATGGGTTTTTATTGGTACCCA
1915 GTATATATGGGTTTTTACTCATTAATATAAAAATAAAAATTCTCTTTTGAACTCTTAATGAAACT
131 GTATATATGGGTTTTTACTCATTAATATAAAAATAAAAATTCTCTTTTGAACTCTTAATGAAACT
* *
1980 TGTGGATCAAATTTAGCTTTCGGGTTCGTAGATGATGCAATAACCTTTTAACCAACACTTAAATA
196 TGTGGATCAAATTTAGCTTTCGGGTTCGTAGATGATGCAATAACCTTTTAACCGACACTTGAATA
*
2045 ACATTAATTGGACATGTGGACTGAAAATAATATGATATATTAAATAGACTGGTAATTATAATCAC
261 ACATTAATTGGACATGTGGACTGAAAATAATATGATATATTAAATAGACTGGTAATTAAAATCAC
2110 CAAATTTCGGAAGCATTTTTTGGAATTGAAACATAAAAATTGGATTAAAATCACCAAATAGACT-
326 CAAATTTCGGAAGCATTTTTTGGAATTGAAACATAAAAATTGGATTAAAATCACCAAATAGACTA
2174 G-ATAATCATTAAGATTTGATAGTTCCACAACCTTTTC-T-A-ATTCGTAAATATTATTA
391 GTATAATCATTAAGATTTGATAGTTCCACAACCTTTTCATAATATTCGTAAATATTATTA
2230 TTTTTAATTATTTAAGTAGATTTACAACATCATGATGATGTTAGCAACTATTGACCGACGGGTTA
1 TTTTTAATTATTTAAGTAGATTTACAACATCATGATGATGTTAGCAACTATTGACCGACGGGTTA
*
2295 GCTAACTAACTCGGGTTGCCCAACAGGTTATACCCAGTATATATATGGGTTTTTATTGGTACCCA
66 GCTAACTAACTCGGGTTGCCCAACAGGTTATACCCAGTATATACATGGGTTTTTATTGGTACCCA
2360 GTATATATGGGTTTTTACTCATTAATATAAAAATAAAAATTCTCTTTTGAACTCTTAATGAAACT
131 GTATATATGGGTTTTTACTCATTAATATAAAAATAAAAATTCTCTTTTGAACTCTTAATGAAACT
*
2425 TGTGGATCAAATTTAGCTTTCGGGTTCATAGATGATGCAATAACCTTTTAACCGACACTTGAATA
196 TGTGGATCAAATTTAGCTTTCGGGTTCGTAGATGATGCAATAACCTTTTAACCGACACTTGAATA
*
2490 ACATTAATTGGACATGTGAACTGAAAATAATATGATATATTAAATAGACTGGTAATTAAAATCAC
261 ACATTAATTGGACATGTGGACTGAAAATAATATGATATATTAAATAGACTGGTAATTAAAATCAC
* *
2555 CAAATTCCGGAAGCATTTTTTGGAATTGAATCATAAAAATTGG
326 CAAATTTCGGAAGCATTTTTTGGAATTGAAACATAAAAATTGG
2598 TTTTTGAGTC
Statistics
Matches: 789, Mismatches: 23, Indels: 17
0.95 0.03 0.02
Matches are distributed among these distances:
445 375 0.48
452 1 0.00
453 1 0.00
457 35 0.04
459 1 0.00
460 337 0.43
461 39 0.05
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (450 bp):
TTTTTAATTATTTAAGTAGATTTACAACATCATGATGATGTTAGCAACTATTGACCGACGGGTTA
GCTAACTAACTCGGGTTGCCCAACAGGTTATACCCAGTATATACATGGGTTTTTATTGGTACCCA
GTATATATGGGTTTTTACTCATTAATATAAAAATAAAAATTCTCTTTTGAACTCTTAATGAAACT
TGTGGATCAAATTTAGCTTTCGGGTTCGTAGATGATGCAATAACCTTTTAACCGACACTTGAATA
ACATTAATTGGACATGTGGACTGAAAATAATATGATATATTAAATAGACTGGTAATTAAAATCAC
CAAATTTCGGAAGCATTTTTTGGAATTGAAACATAAAAATTGGATTAAAATCACCAAATAGACTA
GTATAATCATTAAGATTTGATAGTTCCACAACCTTTTCATAATATTCGTAAATATTATTA
Found at i:12839 original size:48 final size:44
Alignment explanation
Indices: 12740--12872 Score: 221
Period size: 44 Copynumber: 2.9 Consensus size: 44
12730 TTCTTTTTAA
12740 TCTTGAATGAATAGGATTGGCCACAATCTGTTTGTTTTATTGAT
1 TCTTGAATGAATAGGATTGGCCACAATCTGTTTGTTTTATTGAT
12784 TCTTGAATGAATAGGATTGGCCACAATCTGTTTGTTTTATTGAT
1 TCTTGAATGAATAGGATTGGCCACAATCTGTTTGTTTTATTGAT
*
12828 TCTTGAATGAATAGGACTGATTGGCCATAATCTGTTTGTTTTATT
1 TCTTGAATGAATA-G---GATTGGCCACAATCTGTTTGTTTTATT
12873 TCTTTAATCA
Statistics
Matches: 84, Mismatches: 1, Indels: 4
0.94 0.01 0.04
Matches are distributed among these distances:
44 57 0.68
45 1 0.01
48 26 0.31
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (44 bp):
TCTTGAATGAATAGGATTGGCCACAATCTGTTTGTTTTATTGAT
Found at i:23250 original size:183 final size:176
Alignment explanation
Indices: 22936--23287 Score: 497
Period size: 183 Copynumber: 2.0 Consensus size: 176
22926 TAATCTGAAA
*
22936 CAACTTAATGTTTTTGCTACAAAAGAATAAAAGCGTAAACTAAAACCTCTTACACCCTCTCATTT
1 CAACTTAATGTTTTTGCTACAAAAGAACAAAAGCGTAAACTAAAACCTCTTACACCCTCTCATTT
23001 CCTATCCTCTTCAAGTAGAAGTTGAACCGGAGGTTCCTCAAACCAACTCACCCCTCGGAGATTGT
66 CCTATCCTCTTCAAGTAGAAGTTGAACCGGAGGTTCCTCAAACCAACTCACCCCTCGGAGATTGT
* * * * *
23066 CATAAGTCGAAGTAGCCGAAAGGTCAACACACCTATTACACCAACT
131 CATAAGCCAAAATAACCAAAAGGTCAACACACCTATTACACCAACT
* *
23112 CAACTTAATTTTTTTGCTACAAAGGAACAAAAGCGTAAACTAAAACCTCATTACACCCTCTCATT
1 CAACTTAATGTTTTTGCTACAAAAGAACAAAAGCGTAAACTAAAACCTC-TTACACCCTCTCATT
* * * *
23177 TTCTATCCTCTTCAAGCATGGATAGAAGTTGAACTGGAGGTTTCTCAAACCAACTCACCTCTCGG
65 TCCTATCCTCTTC-A--A--G-TAGAAGTTGAACCGGAGGTTCCTCAAACCAACTCACCCCTCGG
* ** *
23242 GGATTGTCATGCGCCAAAATAACCAAAAGGTCAGCACACCTATTAC
124 AGATTGTCATAAGCCAAAATAACCAAAAGGTCAACACACCTATTAC
23288 GTACCTTCAT
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
176 46 0.30
177 27 0.18
178 1 0.01
180 1 0.01
182 1 0.01
183 77 0.50
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (176 bp):
CAACTTAATGTTTTTGCTACAAAAGAACAAAAGCGTAAACTAAAACCTCTTACACCCTCTCATTT
CCTATCCTCTTCAAGTAGAAGTTGAACCGGAGGTTCCTCAAACCAACTCACCCCTCGGAGATTGT
CATAAGCCAAAATAACCAAAAGGTCAACACACCTATTACACCAACT
Found at i:28726 original size:40 final size:40
Alignment explanation
Indices: 28671--28747 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
28661 TTGTTGATTT
*
28671 TGCATTAATTCTTCATCTCTCAATCACTAGGCCTAGGGAG
1 TGCATTAATTCTTCATCTCTCAATCACTAGGCATAGGGAG
28711 TGCATTAATTCTTCATCTCTCAATCACTAGGCATAGG
1 TGCATTAATTCTTCATCTCTCAATCACTAGGCATAGG
28748 AAGAAGTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (40 bp):
TGCATTAATTCTTCATCTCTCAATCACTAGGCATAGGGAG
Found at i:30111 original size:2 final size:2
Alignment explanation
Indices: 30059--30091 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30049 CAGCTTGAAC
*
30059 AT AT AT AT AA AT A- 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
30092 TTTTTGGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:43576 original size:20 final size:20
Alignment explanation
Indices: 43551--43593 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
43541 CAGTGGATTT
43551 TTATCCTCTCCAAATTAAGC
1 TTATCCTCTCCAAATTAAGC
43571 TTATCCTCTCCAAATTAAGC
1 TTATCCTCTCCAAATTAAGC
43591 TTA
1 TTA
43594 AATTGAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (20 bp):
TTATCCTCTCCAAATTAAGC
Found at i:50053 original size:13 final size:13
Alignment explanation
Indices: 50035--50063 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
50025 CTTTCTTTAC
50035 TGAATGGAGTAAG
1 TGAATGGAGTAAG
50048 TGAATGGAGTAAG
1 TGAATGGAGTAAG
50061 TGA
1 TGA
50064 TAGTGGGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (13 bp):
TGAATGGAGTAAG
Found at i:50781 original size:47 final size:48
Alignment explanation
Indices: 50730--50832 Score: 129
Period size: 48 Copynumber: 2.2 Consensus size: 48
50720 TTTGGTCAAG
* * * *
50730 TTTGGCCTC-GAG-GATCATTATGGTTAGTCTTGCTCATTTTGACTAAA
1 TTTGGCCTCTGAGAG-TCATGATGGTTACTCTCGCTCATTTTAACTAAA
* *
50777 TTTGGCCACTGAGAGTCATGATGGTTACTCTCGGTCATTTTAACTAAA
1 TTTGGCCTCTGAGAGTCATGATGGTTACTCTCGCTCATTTTAACTAAA
50825 TTTGGCCT
1 TTTGGCCT
50833 TGGTCATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
47 8 0.17
48 38 0.81
49 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (48 bp):
TTTGGCCTCTGAGAGTCATGATGGTTACTCTCGCTCATTTTAACTAAA
Found at i:51055 original size:11 final size:11
Alignment explanation
Indices: 51012--51049 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
51002 TTCCTATATA
*
51012 AAATAAATTAT
1 AAATTAATTAT
51023 CAAA-TAATTAT
1 -AAATTAATTAT
51034 AAATTAATTAT
1 AAATTAATTAT
51045 AAATT
1 AAATT
51050 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:56697 original size:2 final size:2
Alignment explanation
Indices: 56684--56736 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
56674 CAATTCAACC
* * * *
56684 AT AT AT AC AT AT AT AT AT AT AT AT CT GT TT A- 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 AT AT
56725 AT AT AT AT AT AT
1 AT AT AT AT AT AT
56737 TATGTAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Done.