Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015670.1 Corchorus capsularis cultivar CVL-1 contig15691, 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: 24525
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1603 original size:19 final size:20
Alignment explanation
Indices: 1579--1616 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1569 TGATTACTAA
1579 AAAACAATTAT-AGGTTATC
1 AAAACAATTATAAGGTTATC
1598 AAAACAATTATAAGGTTAT
1 AAAACAATTATAAGGTTAT
1617 TTATAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAACAATTATAAGGTTATC
Found at i:3455 original size:6 final size:6
Alignment explanation
Indices: 3444--3472 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3434 CTTATATAAT
3444 ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATA
3473 TCCCTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:5432 original size:166 final size:167
Alignment explanation
Indices: 5116--5437 Score: 416
Period size: 166 Copynumber: 1.9 Consensus size: 167
5106 TTGTCAATTG
* *
5116 AGAAATGACCAAAAAGTTTAGTTATGTAATCCCCTCACGAATAAAAAATTAGGACATTTAAGTAA
1 AGAAATGACCAAAAAGATTAGTTATGTAATCCCCTCAAGAATAAAAAATTAGGACATTTAAGTAA
* * * * ** ** *
5181 TATGCCAAGTAGGTAAAGACGAAAAAATGTTAGTTCTCTAGCTCATCATTAATCCTTGAAGGGGA
66 TATGCCAAGTAGGAAAAGACGAAAAAATATAAGTTCTCTAACTCAAAACCAAGCCTTGAAGGGGA
*
5246 TCATTTATTAATTCCACTACTCTATTCAAATCCATTT
131 TCATTTAGTAATTCCACTACTCTATTCAAATCCATTT
* * * *
5283 AGAAATGACCAAAAAGATTA-TTATTTAATCCGCTCAAGAATTAAAAGTTAGGACATTTAAGTAA
1 AGAAATGACCAAAAAGATTAGTTATGTAATCCCCTCAAGAATAAAAAATTAGGACATTTAAGTAA
* * *
5347 TCTGTCAAGTAGGAAAAGACGAAAAAA-ATAAGTTCTCTAACTCCAAAACCAAGCCTTGTTA-GG
66 TATGCCAAGTAGGAAAAGACGAAAAAATATAAGTTCTCTAACT-CAAAACCAAGCCTTG-AAGGG
* *
5410 GATCTTTTAGTAATTTCACTACTCTATT
129 GATCATTTAGTAATTCCACTACTCTATT
5438 AAAGTTTAGG
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
165 12 0.09
166 100 0.76
167 20 0.15
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (167 bp):
AGAAATGACCAAAAAGATTAGTTATGTAATCCCCTCAAGAATAAAAAATTAGGACATTTAAGTAA
TATGCCAAGTAGGAAAAGACGAAAAAATATAAGTTCTCTAACTCAAAACCAAGCCTTGAAGGGGA
TCATTTAGTAATTCCACTACTCTATTCAAATCCATTT
Found at i:5861 original size:45 final size:45
Alignment explanation
Indices: 5811--5900 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
5801 AATTACTTCT
* *
5811 CCAGCTCATCATTAATCTGTGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCTGGGGTAGAGATCTTTTAGTAATTCCAC
* * *
5856 CCAGCTTATCATTAATTTGGGGTAGAGATCTTTTATTAATTCCAC
1 CCAGCTCATCATTAATCTGGGGTAGAGATCTTTTAGTAATTCCAC
5901 TACTCTATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (45 bp):
CCAGCTCATCATTAATCTGGGGTAGAGATCTTTTAGTAATTCCAC
Found at i:5972 original size:324 final size:314
Alignment explanation
Indices: 5244--6023 Score: 1120
Period size: 324 Copynumber: 2.4 Consensus size: 314
5234 CCTTGAAGGG
* *
5244 GATCATTTATTAATTCCACTACTCTATTCAAATCCATTTAGAAATGACCAAAAAGATTATTATTT
1 GATCTTTTATTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTATTATTT
*
5309 AA-TCCGCTCAAGAATTAAAAGTTAGGACATTTAAGTAATCTG-TCAAGTAGGAAAAGACGAAAA
66 AATTCC-CTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCT-AAGTAGGAAAAGACGAAAA
* *
5372 AAATAAGTTCTCTAACTCCAAAACCAAGCCTTGTTAGGGATCTTTTAGTAATTTCACTACTCTAT
129 AAATAAGTTCTCTAACTCCAAAACCAAGCCTTGTTAGGGATCTTTCAGTAATTCCACTACTCTAT
* * *
5437 TAAAGTTTAGGACATTTAAGTAATCTGTCAAGTACGAAAAAGATTACTTCTCTAGCTCATCATTA
194 TAAAGTTTAGGACATTTAAGTAATCTGCCAAGTACGAAAAAAATTACTTCTCCAGCTCATCATTA
* *
5502 ATCCGGGTAAGGATCTTTTAGTAATTCCATCCAACTTATCATTAATTCGGGGTAGG
259 ATCCGGGTAAGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTAGA
*
5558 GAT-TTTTTTGTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTAT
1 GATCTTTTAT-TAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTA-TTAT
* * *
5622 TTAATTCCCTCAAGAATCAAAAGTTAGGACATTTAAATAATATGCTAAGTAGAAAAAGACGAAAA
64 TTAATTCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCTAAGTAGGAAAAGACGAAAA
* *
5687 AAATAAGTTCTCTAACTCCAAAAGCAAGTCTTGTTAGGGATCTTTCAGTAATTCCACTACTCTAT
129 AAATAAGTTCTCTAACTCCAAAACCAAGCCTTGTTAGGGATCTTTCAGTAATTCCACTACTCTAT
5752 TAAAGTTTAGGACATTTAAGTAATCTGCCAGGTAGGTAAAGACGAAAAAAATTACTTCTCCAGCT
194 TAAAGTTTAGGACATTTAAGTAATCTGCCA---A-GT----ACGAAAAAAATTACTTCTCCAGCT
* * * *
5817 CATCATTAATCTGTGGTAGGGATCTTTTAGTAATTCCACCCAGCTTATCATTAATTTGGGGTAGA
251 CATCATTAATCCG-GGTAAGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTAGA
* *
5882 GATCTTTTATTAATTCCACTACTCTATT-AAAGTCAAATGAGAAATGACCAAAAAG-TCTAGTTA
1 GATCTTTTATTAATTCCACTACTCTATTCAAA-TCCATTGAGAAATGACCAAAAAGAT-TA-TTA
* * * * * *
5945 TTTAATTACCTTAAGAATCAAAAGTTAGGGCATTTAAGTAATCGGCCAAGTGGGAAAAGACGAAA
63 TTTAATTCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCTAAGTAGGAAAAGACGAAA
*
6010 AAAATTAGTTCTCT
128 AAAATAAGTTCTCT
6024 CGCTCCTCAT
Statistics
Matches: 416, Mismatches: 34, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
313 4 0.01
314 51 0.12
315 149 0.36
316 4 0.01
318 1 0.00
319 2 0.00
323 38 0.09
324 162 0.39
325 5 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (314 bp):
GATCTTTTATTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTATTATTT
AATTCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCTAAGTAGGAAAAGACGAAAAAA
ATAAGTTCTCTAACTCCAAAACCAAGCCTTGTTAGGGATCTTTCAGTAATTCCACTACTCTATTA
AAGTTTAGGACATTTAAGTAATCTGCCAAGTACGAAAAAAATTACTTCTCCAGCTCATCATTAAT
CCGGGTAAGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTAGA
Found at i:7061 original size:19 final size:20
Alignment explanation
Indices: 7037--7078 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
7027 TTTTTCACAT
*
7037 TTATATAT-TTGTAAACAAA
1 TTATATATCATGTAAACAAA
*
7056 TTATATGTCATGTAAACAAA
1 TTATATATCATGTAAACAAA
7076 TTA
1 TTA
7079 AGGGTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (20 bp):
TTATATATCATGTAAACAAA
Found at i:10735 original size:15 final size:15
Alignment explanation
Indices: 10715--10746 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10705 CATTGCTATT
*
10715 AAATTCTCAATTCTC
1 AAATTCCCAATTCTC
10730 AAATTCCCAATTCTC
1 AAATTCCCAATTCTC
10745 AA
1 AA
10747 GATACCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTCCCAATTCTC
Found at i:16374 original size:3 final size:3
Alignment explanation
Indices: 16366--16394 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16356 GTTTTCTCAA
16366 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16395 AGGAATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21448 original size:19 final size:19
Alignment explanation
Indices: 21424--21465 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
21414 TTTATATTAC
21424 ATTAGATTAATTAAATGAA
1 ATTAGATTAATTAAATGAA
21443 ATTAGATTAATTAAATGAA
1 ATTAGATTAATTAAATGAA
21462 ATTA
1 ATTA
21466 TTAGATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
ATTAGATTAATTAAATGAA
Found at i:22288 original size:29 final size:29
Alignment explanation
Indices: 22223--22288 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
22213 ACCCTTGACG
* ** *
22223 GTCCAAAATTGAAGTTCAGGAGGTAAAAT
1 GTCCAAACTTGAAGTTCAGGAGACAAAAC
*
22252 GTCCAAACTTGAAGTTTAGGAGACAAAAC
1 GTCCAAACTTGAAGTTCAGGAGACAAAAC
22281 GTCCAAAC
1 GTCCAAAC
22289 ACTACAAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (29 bp):
GTCCAAACTTGAAGTTCAGGAGACAAAAC
Found at i:22847 original size:3 final size:3
Alignment explanation
Indices: 22839--22878 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
22829 TTTAATATAG
* *
22839 AAT AAT AAT AAT AAT AAT AAT AAG AAT AAG AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
22879 TATGTTTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (3 bp):
AAT
Done.