Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011965.1 Corchorus capsularis cultivar CVL-1 contig11986, 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: 36214
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:1413 original size:31 final size:31
Alignment explanation
Indices: 1375--1434 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
1365 TTACGTATTT
1375 ATCGAATCTAACATTTTTTCATTGAAGAATC
1 ATCGAATCTAACATTTTTTCATTGAAGAATC
1406 ATCGAATCTAACATTTTTTCATTGAAGAA
1 ATCGAATCTAACATTTTTTCATTGAAGAA
1435 GTTCAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (31 bp):
ATCGAATCTAACATTTTTTCATTGAAGAATC
Found at i:9354 original size:6 final size:6
Alignment explanation
Indices: 9345--9379 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
9335 TTTTTTCTTG
9345 TTTTAT TTTTAT TTTTAT TTTTAT TTTTACT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTT
9380 TGAAGAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:21519 original size:6 final size:6
Alignment explanation
Indices: 21508--21544 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
21498 TTGTCACCGC
21508 GTTGCG GTTGCG GTTGCG GTTGCG GTTGCG GTTGCG G
1 GTTGCG GTTGCG GTTGCG GTTGCG GTTGCG GTTGCG G
21545 ATGGTTCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GTTGCG
Found at i:29483 original size:28 final size:25
Alignment explanation
Indices: 29444--29504 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 25
29434 TACTAATTTG
*
29444 ATTTCTTTTCAAAATCAAAATATAATT
1 ATTTTTTTTCAAAA--AAAATATAATT
29471 ATTTTTTTATCAAAAAAAATATAATT
1 ATTTTTTT-TCAAAAAAAATATAATT
29497 ATTTTTTT
1 ATTTTTTT
29505 CATTTTTCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 19 0.59
27 7 0.22
28 6 0.19
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTTTTTTCAAAAAAAATATAATT
Found at i:31867 original size:2 final size:2
Alignment explanation
Indices: 31862--31888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31852 ATAATTACCC
31862 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
31889 AGTACGAATA
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:32461 original size:23 final size:23
Alignment explanation
Indices: 32431--32488 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
32421 TTTCATGAGG
* *
32431 TTATCAAAATTTTACAGGGAGTT
1 TTATCAAAATTTTACAGGAAGGT
**
32454 TTATCAAAATTTTATTGGAAGGT
1 TTATCAAAATTTTACAGGAAGGT
32477 TTATCAAAATTT
1 TTATCAAAATTT
32489 CATAGCGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (23 bp):
TTATCAAAATTTTACAGGAAGGT
Found at i:32499 original size:23 final size:21
Alignment explanation
Indices: 32225--32800 Score: 194
Period size: 22 Copynumber: 26.6 Consensus size: 21
32215 GGTTAAAATT
*
32225 TCAAAATTTCAT-GGAGGATA
1 TCAAAATTTCATAGGAGGTTA
* *
32245 TCAAAATTTCATATGAAAGTTA
1 TCAAAATTTCATA-GGAGGTTA
* * *
32267 TTAAAATTTCATAGTTTA-GTTT
1 TCAAAATTTCATAG--GAGGTTA
* *
32289 TCAAAATTTTATAAGAAGGTTA
1 TCAAAATTTCAT-AGGAGGTTA
* * *
32311 TCAAAATTTCATAGTATGTAGA
1 TCAAAATTTCATAGGAGGT-TA
*
32333 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATA-GGAGGTTA
* * *
32355 ACAAAATTTCATAATGAGATTA
1 TCAAAATTTCAT-AGGAGGTTA
*
32377 TCAACAA-ATCATAGGGAGGTTA
1 TCAA-AATTTCATA-GGAGGTTA
*
32399 TCAAAA-TT--T-GTA-GTTA
1 TCAAAATTTCATAGGAGGTTA
*
32415 TCAAGATTTCAT--GAGGTTA
1 TCAAAATTTCATAGGAGGTTA
* * *
32434 TCAAAATTTTACAGGGAGTTTTA
1 TCAAAATTTCATA-GGAG-GTTA
* *
32457 TCAAAATTTTATTGGAAGGTTTA
1 TCAAAATTTCATAGG-AGG-TTA
32480 TCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAG-GAGGTTA
* * *
32502 TCACAATTTCATAGTATGATTA
1 TCAAAATTTCATAGGA-GGTTA
* * *
32524 TCAAAATTTCAGAGTGTGATTA
1 TCAAAATTTCATAG-GAGGTTA
* * *
32546 CTGACAA-TTCATATGGAGGTTT
1 -TCAAAATTTCATA-GGAGGTTA
* ** * *
32568 TTAACTTTTCATAACGTGGTTA
1 TCAAAATTTCAT-AGGAGGTTA
* * *
32590 TCAATATATCATATGAAGGTTA
1 TCAAAATTTCATA-GGAGGTTA
* *
32612 TCAACATCTT-ATAGTGTTGGTTA
1 TCAAAAT-TTCATAG-G-AGGTTA
* *
32635 TCAAAATTTCATTTGGAAGTTA
1 TCAAAATTTCA-TAGGAGGTTA
* *
32657 TTAAAACTTT-ATAGTGAGATCT-
1 TCAAAA-TTTCATAG-GAGGT-TA
* *
32679 TCAAAATTCCTTAGGGAGGTTAA
1 TCAAAATTTCATA-GGAGGTT-A
*
32702 T-AAAATTTCATAAGATGGTTA
1 TCAAAATTTCATAGGA-GGTTA
** * ** *
32723 AAAAAAATT-ATAAAAAGGTTC
1 TCAAAATTTCAT-AGGAGGTTA
* * *
32744 TCGAAATTTCATAGTATCGTTA
1 TCAAAATTTCATAGGA-GGTTA
**
32766 TTGAAATTTCATAGGAAGGTTA
1 TCAAAATTTCATAGG-AGGTTA
*
32788 TCAATATTTCATA
1 TCAAAATTTCATA
32801 AAGACGTCAT
Statistics
Matches: 408, Mismatches: 101, Indels: 92
0.68 0.17 0.15
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
18 1 0.00
19 15 0.04
20 12 0.03
21 37 0.09
22 257 0.63
23 70 0.17
24 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (21 bp):
TCAAAATTTCATAGGAGGTTA
Found at i:32837 original size:40 final size:40
Alignment explanation
Indices: 32785--32874 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 40
32775 CATAGGAAGG
32785 TTATCA-ATATTTCATAAAG-ACGTCATAAAAAATAGTGTAA
1 TTATCATA-ATTTCA-AAAGAACGTCATAAAAAATAGTGTAA
* * * *
32825 TTATCATAATTTCACAAGAAGGTTATCAAAAATAGTGTAA
1 TTATCATAATTTCAAAAGAACGTCATAAAAAATAGTGTAA
32865 TTATCATAAT
1 TTATCATAAT
32875 ATAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 3 0.07
40 40 0.91
41 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (40 bp):
TTATCATAATTTCAAAAGAACGTCATAAAAAATAGTGTAA
Found at i:32890 original size:40 final size:40
Alignment explanation
Indices: 32812--32892 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
32802 AGACGTCATA
* * *
32812 AAAAATAGTGTAATTATCATAATTTCACAAGAAGGTTATC
1 AAAAATAGTGTAATTATCATAATATAACAAAAAGGTTATC
* *
32852 AAAAATAGTGTAATTATCATAATATAATAAAAATGTTATC
1 AAAAATAGTGTAATTATCATAATATAACAAAAAGGTTATC
32892 A
1 A
32893 TAATTTCGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.33
Consensus pattern (40 bp):
AAAAATAGTGTAATTATCATAATATAACAAAAAGGTTATC
Found at i:33477 original size:24 final size:25
Alignment explanation
Indices: 33450--33514 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
33440 TCAAATACTA
*
33450 AGCATACAGCA-ATTTGGAATATTG
1 AGCATACAACAGATTTGGAATATTG
*
33474 AGCATACAACAGTTTTGGAATATTG
1 AGCATACAACAGATTTGGAATATTG
*
33499 AGTATACAACAG-TTTG
1 AGCATACAACAGATTTG
33515 ACGATAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 14 0.38
25 23 0.62
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (25 bp):
AGCATACAACAGATTTGGAATATTG
Found at i:33494 original size:25 final size:25
Alignment explanation
Indices: 33462--33513 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
33452 CATACAGCAA
33462 TTTGGAATATTGAGCATACAACAGT
1 TTTGGAATATTGAGCATACAACAGT
*
33487 TTTGGAATATTGAGTATACAACAGT
1 TTTGGAATATTGAGCATACAACAGT
33512 TT
1 TT
33514 GACGATAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (25 bp):
TTTGGAATATTGAGCATACAACAGT
Found at i:33795 original size:25 final size:25
Alignment explanation
Indices: 33755--33803 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
33745 ACAGCAATTT
*
33755 GGAATATTGAGCATACAACAGTTTC
1 GGAATATTAAGCATACAACAGTTTC
*
33780 GGAATATTAAGTATACAACAGTTT
1 GGAATATTAAGCATACAACAGTTT
33804 GACGATAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (25 bp):
GGAATATTAAGCATACAACAGTTTC
Found at i:34740 original size:5 final size:5
Alignment explanation
Indices: 34730--34755 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34720 GTATAATTTC
34730 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
34756 CACATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Done.