Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014827.1 Corchorus olitorius cultivar O-4 contig14860, 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: 44481
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:1407 original size:17 final size:17
Alignment explanation
Indices: 1380--1424 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
1370 ATAATCATGT
1380 TAATATA-TATATATA-
1 TAATATATTATATATAC
*
1395 T-ATATATTATATACAC
1 TAATATATTATATATAC
1411 TAATATATTA-ATAT
1 TAATATATTATATAT
1425 TTTTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.20
15 8 0.32
16 4 0.16
17 8 0.32
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATATTATATATAC
Found at i:10456 original size:30 final size:30
Alignment explanation
Indices: 10422--10482 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
10412 TTTTGTATAG
*
10422 CTCAACTGGT-AAGTGTACTGTGCCATGAAC
1 CTCAACTGGTGAA-TGCACTGTGCCATGAAC
10452 CTCAACTGGTGAATGCACTGTGCCATGAAC
1 CTCAACTGGTGAATGCACTGTGCCATGAAC
10482 C
1 C
10483 ATGAGGTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (30 bp):
CTCAACTGGTGAATGCACTGTGCCATGAAC
Found at i:11485 original size:6 final size:6
Alignment explanation
Indices: 11476--11500 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11466 TTTCTTTTTA
11476 TTTGTT TTTGTT TTTGTT TTTGTT T
1 TTTGTT TTTGTT TTTGTT TTTGTT T
11501 ATTTCTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTGTT
Found at i:21523 original size:22 final size:23
Alignment explanation
Indices: 21476--21520 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
21466 CCAGATCAAT
21476 TTTCCAGATCTAATAAATAAAAA
1 TTTCCAGATCTAATAAATAAAAA
*
21499 TTTCCAGATCTAATAGATAAAA
1 TTTCCAGATCTAATAAATAAAA
21521 TTTATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (23 bp):
TTTCCAGATCTAATAAATAAAAA
Found at i:22147 original size:23 final size:23
Alignment explanation
Indices: 22118--22162 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
22108 TTCAAAGGAG
*
22118 AAGAAAGGAGATCAAAGGGGAAA
1 AAGAAAGGAGAACAAAGGGGAAA
*
22141 AAGAAAGGGGAACAAAGGGGAA
1 AAGAAAGGAGAACAAAGGGGAA
22163 GAATATCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.04, G:0.38, T:0.02
Consensus pattern (23 bp):
AAGAAAGGAGAACAAAGGGGAAA
Found at i:23812 original size:5 final size:5
Alignment explanation
Indices: 23802--23839 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
23792 ATATATTACT
23802 ATATA ATATA ATATA ATATA ATATA ATAT- ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT
23840 TCATATAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:23846 original size:15 final size:14
Alignment explanation
Indices: 23787--23839 Score: 72
Period size: 15 Copynumber: 3.7 Consensus size: 14
23777 TAAATATGAG
*
23787 TATAT-ATATATTA
1 TATATAATATAATA
23800 CTATATAATATAATA
1 -TATATAATATAATA
23815 TAATATAATATAATA
1 T-ATATAATATAATA
23830 TATATAATAT
1 TATATAATAT
23840 TCATATAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 15 0.42
15 21 0.58
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAATATAATA
Found at i:31404 original size:2 final size:2
Alignment explanation
Indices: 31397--31429 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31387 TCAATATAGA
31397 AT AT AT 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 AT AT AT A
31430 CTTTCATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43142 original size:648 final size:648
Alignment explanation
Indices: 41907--43200 Score: 2477
Period size: 648 Copynumber: 2.0 Consensus size: 648
41897 TTCTAAAAAT
*
41907 TATTGTAAGAGAATATATTTTAAAAATTCTAATATATCTAATTTTTTTTTAATTAAAATAGTAAA
1 TATTGTAAGAGAATATATTTTAAAAATTCTAATATATCTAATGTTTTTTTAATTAAAATAGTAAA
41972 ATGATAACAACAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
66 ATGATAACAACAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
42037 AGTAAAACTATAAAAGTATATTTAAAATTTTCTAATACATCTAAGTTTTTTTTAATTAAAATAGT
131 AGTAAAACTATAAAAGTATATTTAAAATTTTCTAATACATCTAAGTTTTTTTTAATTAAAATAGT
42102 AAAATGGTAAAAATGACATAGTTATAAGAATGTTAGATTTTTTTTAATTATACAGCAAGTTTTTA
196 AAAATGGTAAAAATGACATAGTTATAAGAATGTTAGATTTTTTTTAATTATACAGCAAGTTTTTA
42167 TCAAGCAAAAAATTAATTATAAGTCAAATAAAATAATTGCACATTAGGGTAAATAATAAAGTTTA
261 TCAAGCAAAAAATTAATTATAAGTCAAATAAAATAATTGCACATTAGGGTAAATAATAAAGTTTA
42232 ATCATAATACATTATTATAAACTATCAAATAGTAAGATGTCAATCATAATAACTTTATAAATTAA
326 ATCATAATACATTATTATAAACTATCAAATAGTAAGATGTCAATCATAATAACTTTATAAATTAA
42297 AATGGTAAAAAAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
391 AATGGTAAAAAAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
42362 ATAAAACTCTATATTTTGAAAAAAATAGTACAATGGTAAAAATAAAATAATTATAAAGATATTAA
456 ATAAAACTCTATATTTTGAAAAAAATAGTACAATGGTAAAAATAAAATAATTATAAAGATATTAA
42427 ATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATGGCATTTA
521 ATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATGGCATTTA
* *
42492 AGAAATATGTTTGAAAAATAAGGATATAATGGTCGATTCAATTAGGAAAATAAGGGTATAAAC
586 AGAAATATGTTTGAAAAATAAGGATATAATGGTCGATTCAATTAGAAAAATAAGGATATAAAC
42555 TATTGTAAGAGAATATATTTTAAAAATTCTAATATATCTAA-GTTTTTTTAATTAAAATAGTAAA
1 TATTGTAAGAGAATATATTTTAAAAATTCTAATATATCTAATGTTTTTTTAATTAAAATAGTAAA
42619 ATGATAACAACAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
66 ATGATAACAACAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
42684 AGTAAAACTATAAAAGTATATTTAAAATTTTCTAATACATCTAATGTTTTTTTTTAATTAAAATA
131 AGTAAAACTATAAAAGTATATTTAAAATTTTCTAATACATCTAA-G-TTTTTTTTAATTAAAATA
*
42749 GTAAAATGGTAAAAATGACATAGTTATAAGAATGTTAGATTTTTTTTAATTATATAGCAAGTTTT
194 GTAAAATGGTAAAAATGACATAGTTATAAGAATGTTAGATTTTTTTTAATTATACAGCAAGTTTT
42814 TATCAAGCAAAAAATTAATTATAAGTCAAATAAAATAATTGCACATTAGGG-AAATAATAAAGTT
259 TATCAAGCAAAAAATTAATTATAAGTCAAATAAAATAATTGCACATTAGGGTAAATAATAAAGTT
*
42878 TAATCATAATACATTATTATAAACTATCAAATAGTAAGATGTCAATCATAATAACTTTTTAAATT
324 TAATCATAATACATTATTATAAACTATCAAATAGTAAGATGTCAATCATAATAACTTTATAAATT
42943 AAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGT
389 AAAATGGTAAAAA-AAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGT
* *
43008 AGAATAAAACTCTATATTTTG-AAAAAATAGTACAATGGTAAAATTAAAGTAATTATAAAGATAT
453 AGAATAAAACTCTATATTTTGAAAAAAATAGTACAATGGTAAAAATAAAATAATTATAAAGATAT
43072 TAAATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATGGCAT
518 TAAATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATGGCAT
43137 TTAAGAAATATGTTTGAAAAATAAGGATATAATGGTCGATTCAATTAGAAAAATAAGGATATAA
583 TTAAGAAATATGTTTGAAAAATAAGGATATAATGGTCGATTCAATTAGAAAAATAAGGATATAA
43201 TAGACGATTC
Statistics
Matches: 636, Mismatches: 7, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
647 131 0.21
648 300 0.47
649 205 0.32
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (648 bp):
TATTGTAAGAGAATATATTTTAAAAATTCTAATATATCTAATGTTTTTTTAATTAAAATAGTAAA
ATGATAACAACAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
AGTAAAACTATAAAAGTATATTTAAAATTTTCTAATACATCTAAGTTTTTTTTAATTAAAATAGT
AAAATGGTAAAAATGACATAGTTATAAGAATGTTAGATTTTTTTTAATTATACAGCAAGTTTTTA
TCAAGCAAAAAATTAATTATAAGTCAAATAAAATAATTGCACATTAGGGTAAATAATAAAGTTTA
ATCATAATACATTATTATAAACTATCAAATAGTAAGATGTCAATCATAATAACTTTATAAATTAA
AATGGTAAAAAAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAACTCTATATTTTGAAAAAAATAGTACAATGGTAAAAATAAAATAATTATAAAGATATTAA
ATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATGGCATTTA
AGAAATATGTTTGAAAAATAAGGATATAATGGTCGATTCAATTAGAAAAATAAGGATATAAAC
Found at i:43193 original size:32 final size:32
Alignment explanation
Indices: 43152--43212 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
43142 AAATATGTTT
* *
43152 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGACGATTCAATTA
43184 GAAAAATAAGGATATAATAGACGATTCAA
1 GAAAAATAAGGATATAATAGACGATTCAA
43213 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.25
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGACGATTCAATTA
Done.