Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006157.1 Corchorus capsularis cultivar CVL-1 contig06175, 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: 36428
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2501 original size:44 final size:44
Alignment explanation
Indices: 2443--2580 Score: 240
Period size: 44 Copynumber: 3.1 Consensus size: 44
2433 TTCACTGTTG
* *
2443 AATATAATATAACGTTGTAATGTAATCCCTATAATTTCTCCCTTG
1 AATAT-ATATAACGTTGTAATGTAATCCATATAATTTCTCCCTTA
*
2488 AATATATATAACGTTGTAATGTAATCCTTATAATTTCTCCCTTA
1 AATATATATAACGTTGTAATGTAATCCATATAATTTCTCCCTTA
2532 AATATATATAACGTTGTAATGTAATCCATATAATTTCTCCCTTA
1 AATATATATAACGTTGTAATGTAATCCATATAATTTCTCCCTTA
2576 AATAT
1 AATAT
2581 TACCTGTAAT
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
44 85 0.94
45 5 0.06
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (44 bp):
AATATATATAACGTTGTAATGTAATCCATATAATTTCTCCCTTA
Found at i:4160 original size:29 final size:29
Alignment explanation
Indices: 4098--4187 Score: 96
Period size: 31 Copynumber: 3.1 Consensus size: 29
4088 GGCACGTGGC
* *
4098 ATTTTTG-ACACGTGGCGTGCCATGTGTCCG
1 ATTTTTGTACACGTGGCATGCCA--TGTCGG
4128 --TTTTGTACACGTGGCATGCCATGTCGG
1 ATTTTTGTACACGTGGCATGCCATGTCGG
*
4155 ATTTTTTGGTACACGTGGCATGCCACGTCGG
1 A-TTTTT-GTACACGTGGCATGCCATGTCGG
4186 AT
1 AT
4188 GCCCGTTTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
27 5 0.10
28 5 0.10
29 14 0.27
30 5 0.10
31 23 0.44
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (29 bp):
ATTTTTGTACACGTGGCATGCCATGTCGG
Found at i:4170 original size:31 final size:30
Alignment explanation
Indices: 4128--4187 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
4118 CATGTGTCCG
*
4128 TTTTGTACACGTGGCATGCCATGTCGGATT
1 TTTTGTACACGTGGCATGCCACGTCGGATT
4158 TTTTGGTACACGTGGCATGCCACGTCGGAT
1 TTTT-GTACACGTGGCATGCCACGTCGGAT
4188 GCCCGTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (30 bp):
TTTTGTACACGTGGCATGCCACGTCGGATT
Found at i:10066 original size:23 final size:23
Alignment explanation
Indices: 10038--10088 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
10028 ATGAAGTAAG
10038 CTCCTTC-GCATAACATTGATTCC
1 CTCCTTCTG-ATAACATTGATTCC
* *
10061 TTCCTTCTGGTAACATTGATTCC
1 CTCCTTCTGATAACATTGATTCC
10084 CTCCT
1 CTCCT
10089 CCTGGTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.18, C:0.33, G:0.10, T:0.39
Consensus pattern (23 bp):
CTCCTTCTGATAACATTGATTCC
Found at i:10093 original size:23 final size:23
Alignment explanation
Indices: 10048--10094 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
10038 CTCCTTCGCA
* *
10048 TAACATTGATTCCTTCCTTCTGG
1 TAACATTGATTCCCTCCTCCTGG
10071 TAACATTGATTCCCTCCTCCTGG
1 TAACATTGATTCCCTCCTCCTGG
10094 T
1 T
10095 TGATCTGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.40
Consensus pattern (23 bp):
TAACATTGATTCCCTCCTCCTGG
Found at i:17252 original size:12 final size:12
Alignment explanation
Indices: 17235--17277 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
17225 TTAATACAGG
17235 TATCGATGGATA
1 TATCGATGGATA
*
17247 TATCGAATAGATA
1 TATCG-ATGGATA
*
17260 GATCGATGGATA
1 TATCGATGGATA
17272 TATCGA
1 TATCGA
17278 GGTATCGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.30
Consensus pattern (12 bp):
TATCGATGGATA
Found at i:19371 original size:31 final size:30
Alignment explanation
Indices: 19309--19371 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
19299 TTTGATGATC
* *
19309 AAGTATAGCCTATTATTCCGACCTAAAAAA
1 AAGTATAGCCTATTAATCCGACCCAAAAAA
**
19339 AAGTATAGCCTATTAAATCTTACCCAAAAAA
1 AAGTATAGCCTATT-AATCCGACCCAAAAAA
19370 AA
1 AA
19372 AAAAGTATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (30 bp):
AAGTATAGCCTATTAATCCGACCCAAAAAA
Found at i:30598 original size:31 final size:31
Alignment explanation
Indices: 30527--30598 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
30517 AACTTTATGT
*
30527 TTTCCAATTGTACCCTTATTTTAAAAACATA
1 TTTCAAATTGTACCCTTATTTTAAAAACATA
* * ** *
30558 TTTCGAATTGTA-CCTTTTTTTTTAAATATA
1 TTTCAAATTGTACCCTTATTTTAAAAACATA
30588 TTTCTAAATTG
1 TTTC-AAATTG
30599 CTATTACTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (31 bp):
TTTCAAATTGTACCCTTATTTTAAAAACATA
Found at i:30819 original size:37 final size:38
Alignment explanation
Indices: 30749--30844 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 38
30739 AATTTGACTT
30749 TTTGTTTCCAACGTCCTATTTAATTTTGTC-TTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGTCTTTTTGTC
** *
30786 TTTGTTTCCAATCGTTGTGTTTAATTTTG-CTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGTCTTTTTGTC
* *
30824 TTCGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
30845 GGGCTTAGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.39
38 30 0.61
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.55
Consensus pattern (38 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGTCTTTTTGTC
Found at i:30974 original size:44 final size:44
Alignment explanation
Indices: 30926--31048 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 44
30916 TCGAGGTTTT
* * *
30926 CAAAATTACATAATTTGATTATCAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAATATGATTATCAAAATTTCATAGAGAGGTCAA
* * * * * *
30970 CAAAATTTTATAGAGA-GGTTATCAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATA-ATATGATTATCAAAATTTCATAGAGAGGTCAA
* * *
31014 CAAATTTTCAAAATATGATTACCAAAATTTCATAG
1 CAAAATTTCATAATATGATTATCAAAATTTCATAG
31049 TGGTATTTCT
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
43 2 0.03
44 58 0.95
45 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (44 bp):
CAAAATTTCATAATATGATTATCAAAATTTCATAGAGAGGTCAA
Found at i:31011 original size:22 final size:22
Alignment explanation
Indices: 30903--31047 Score: 105
Period size: 22 Copynumber: 6.6 Consensus size: 22
30893 TGGTCCAATT
* *
30903 TCAAAATTTCA-AATCGAGGTTT
1 TCAAAATTTCATAA-AGAGGTTA
* *** *
30925 TCAAAATTACATAATTTGATTA
1 TCAAAATTTCATAAAGAGGTTA
* * *
30947 TCAAAATTTCATAGAGGGGTCA
1 TCAAAATTTCATAAAGAGGTTA
* * *
30969 ACAAAATTTTATAGAGAGGTTA
1 TCAAAATTTCATAAAGAGGTTA
30991 TCAAAATTTCATAAAGAGGTTA
1 TCAAAATTTCATAAAGAGGTTA
* * *
31013 TCAAATTTTCA-AAATATGATTA
1 TCAAAATTTCATAAAGA-GGTTA
*
31035 CCAAAATTTCATA
1 TCAAAATTTCATA
31048 GTGGTATTTC
Statistics
Matches: 95, Mismatches: 25, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
21 4 0.04
22 88 0.93
23 3 0.03
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (22 bp):
TCAAAATTTCATAAAGAGGTTA
Found at i:31236 original size:44 final size:43
Alignment explanation
Indices: 31142--31244 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 43
31132 TCAGGGAGGA
* *
31142 TATCAAAATTTCATATGAAAGTTATTAAAATTTCAGAGTTTAG
1 TATCAAAATTTCATAAGAAAGTTATCAAAATTTCAGAGTTTAG
* ** *
31185 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAAGAAAGTTATCAAAATTTCAGAGT-T-TAG
31231 -ATCAAAATTTCATA
1 TATCAAAATTTCATA
31245 GGGAGAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 46 0.92
45 1 0.02
46 3 0.06
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.39
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAAAGTTATCAAAATTTCAGAGTTTAG
Found at i:31328 original size:22 final size:21
Alignment explanation
Indices: 31303--31420 Score: 92
Period size: 22 Copynumber: 5.3 Consensus size: 21
31293 AGTTATTAAG
*
31303 ATTTCATAAGGAGCTTATCAAA
1 ATTTCAT-AGGAGTTTATCAAA
* *
31325 ATTTTATAGGGAGATTTATCCAA
1 ATTTCATA-GGAG-TTTATCAAA
*
31348 ATTTTATAGGATGGTTTATCAAA
1 ATTTCATAGGA--GTTTATCAAA
* * *
31371 ATTTCTTAGCGAGGTTATCACA
1 ATTTCATAG-GAGTTTATCAAA
* *
31393 ATTTCATAGTGTGATTATCAAA
1 ATTTCATAG-GAGTTTATCAAA
31415 ATTTCA
1 ATTTCA
31421 GAGTGTGATT
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.01
22 44 0.56
23 30 0.38
24 3 0.04
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (21 bp):
ATTTCATAGGAGTTTATCAAA
Found at i:31386 original size:23 final size:23
Alignment explanation
Indices: 31317--31419 Score: 83
Period size: 23 Copynumber: 4.6 Consensus size: 23
31307 CATAAGGAGC
*
31317 TTATCAAAATTT-TATAGGGAGAT
1 TTATCAAAATTTCTATA-GGAGGT
*
31340 TTATCCAAATTT-TATAGGATGGT
1 TTATCAAAATTTCTATAGGA-GGT
31363 TTATCAAAATTTCT-TAGCGAGG-
1 TTATCAAAATTTCTATAG-GAGGT
* * *
31385 TTATCACAATTTC-ATAGTG-TGA
1 TTATCAAAATTTCTATAG-GAGGT
31407 TTATCAAAATTTC
1 TTATCAAAATTTC
31420 AGAGTGTGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.01
22 31 0.46
23 33 0.49
24 3 0.04
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTCTATAGGAGGT
Found at i:31442 original size:22 final size:22
Alignment explanation
Indices: 31385--31440 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
31375 CTTAGCGAGG
*
31385 TTATCACAATTTCATAGTGTGA
1 TTATCACAATTTCAGAGTGTGA
*
31407 TTATCAAAATTTCAGAGTGTGA
1 TTATCACAATTTCAGAGTGTGA
*
31429 TTACTGACAATT
1 TTA-TCACAATT
31441 CATATGGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCACAATTTCAGAGTGTGA
Found at i:31487 original size:22 final size:22
Alignment explanation
Indices: 31462--31524 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
31452 TTTTAAATTT
*
31462 TCATAATGTGGTTATCAATATA
1 TCATAATGTGGTTATCAACATA
* *
31484 TCAT-ATGGAGGTTATCAACATC
1 TCATAAT-GTGGTTATCAACATA
* *
31506 TTATAGTGTTGGTTATCAA
1 TCATAATG-TGGTTATCAA
31525 AATTTCATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 2 0.06
22 20 0.62
23 10 0.31
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (22 bp):
TCATAATGTGGTTATCAACATA
Found at i:31543 original size:45 final size:45
Alignment explanation
Indices: 31470--31558 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
31460 TTTCATAATG
* * *
31470 TGGTTATCAATATATCATATGGAGGTTATCAACATCTTATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTTATAGTGT
* * *
31515 TGGTTATCAAAATTTCATTTGGAAGTTATCAAAATTTTATAGTG
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTTATAGTG
31559 AGGTCTTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.42
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTTATAGTGT
Found at i:31673 original size:22 final size:22
Alignment explanation
Indices: 31622--31686 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
31612 AAAATTATAA
*
31622 AAAGGTTCTCGAAATTTCATAG
1 AAAGGTTATCGAAATTTCATAG
* ** *
31644 TATCGTTATTGAAATTTCATAG
1 AAAGGTTATCGAAATTTCATAG
*
31666 AAAGGTTATCAAAATTTCATA
1 AAAGGTTATCGAAATTTCATA
31687 AGAATGTCAT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (22 bp):
AAAGGTTATCGAAATTTCATAG
Found at i:31722 original size:62 final size:62
Alignment explanation
Indices: 31656--31869 Score: 340
Period size: 62 Copynumber: 3.5 Consensus size: 62
31646 TCGTTATTGA
* *
31656 AATTTCATAGAAAGGTTATCAAAATTTCATAAGAATGTCATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGAAAGGTTATCAAAATTTCATAAGGATGTCATCAAAAATAGTGTAATTATCAT
* * *
31718 AATTTCATAGGAATGTTATCAAAATTTCACAAGGATGTCATCAAAAATAGTGTAATTATCAT
1 AATTTCATAGAAAGGTTATCAAAATTTCATAAGGATGTCATCAAAAATAGTGTAATTATCAT
31780 AATTTCATAAGAAA-GTTATCAAAATTTCATAAGGATGTCATCAAAAATAGTGTAATTATCAT
1 AATTTCAT-AGAAAGGTTATCAAAATTTCATAAGGATGTCATCAAAAATAGTGTAATTATCAT
* * *
31842 AATTTAATAGGAAGGTTATCATAATTTC
1 AATTTCATAGAAAGGTTATCAAAATTTC
31870 GTATGAATAT
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
61 4 0.03
62 132 0.94
63 4 0.03
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (62 bp):
AATTTCATAGAAAGGTTATCAAAATTTCATAAGGATGTCATCAAAAATAGTGTAATTATCAT
Found at i:31736 original size:22 final size:22
Alignment explanation
Indices: 31711--31869 Score: 67
Period size: 22 Copynumber: 7.6 Consensus size: 22
31701 AATAGTGTAA
31711 TTATCATAATTTCATAGGAATG
1 TTATCATAATTTCATAGGAATG
* *
31733 TTATCAAAATTTCACAAGG-ATG
1 TTATCATAATTTCA-TAGGAATG
* *
31755 TCATCA-AA---AATAGTGTAA--
1 TTATCATAATTTCATAG-G-AATG
* *
31773 TTATCATAATTTCATAAGAAAG
1 TTATCATAATTTCATAGGAATG
*
31795 TTATCAAAATTTCATAAGG-ATG
1 TTATCATAATTTCAT-AGGAATG
* *
31817 TCATCA-AA---AATAGTGTAA--
1 TTATCATAATTTCATAG-G-AATG
* *
31835 TTATCATAATTTAATAGGAAGG
1 TTATCATAATTTCATAGGAATG
31857 TTATCATAATTTC
1 TTATCATAATTTC
31870 GTATGAATAT
Statistics
Matches: 102, Mismatches: 15, Indels: 40
0.65 0.10 0.25
Matches are distributed among these distances:
17 4 0.04
18 15 0.15
19 4 0.04
20 6 0.06
21 6 0.06
22 62 0.61
23 5 0.05
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
TTATCATAATTTCATAGGAATG
Found at i:31941 original size:2 final size:2
Alignment explanation
Indices: 31934--31977 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
31924 ACTAAACTAG
* *
31934 TA TA TA TA TG TG 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 TA TA TA
31976 TA
1 TA
31978 ATTACAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Done.