Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015617.1 Corchorus capsularis cultivar CVL-1 contig15638, 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: 75201
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3467 original size:35 final size:35
Alignment explanation
Indices: 3406--3472 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3396 CTAAAATAGT
*
3406 CAACTTTTTTTCAAATAAATCCCTTTCTTAAAAGA
1 CAACTTTTTTTCAAATAAATCCCTTTCATAAAAGA
*
3441 CAACTTTTTTTCAAATACA-CCACTTTCATAAA
1 CAACTTTTTTTCAAATAAATCC-CTTTCATAAA
3473 GGCAATAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 2 0.07
35 27 0.93
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.39
Consensus pattern (35 bp):
CAACTTTTTTTCAAATAAATCCCTTTCATAAAAGA
Found at i:18841 original size:12 final size:12
Alignment explanation
Indices: 18824--18848 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18814 TTTACTGTGC
18824 AAAAACAGGGGA
1 AAAAACAGGGGA
18836 AAAAACAGGGGA
1 AAAAACAGGGGA
18848 A
1 A
18849 GGGAAGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.32, T:0.00
Consensus pattern (12 bp):
AAAAACAGGGGA
Found at i:21703 original size:3 final size:3
Alignment explanation
Indices: 21695--21727 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
21685 CATATTATAT
21695 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21728 TCATATTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28434 original size:77 final size:75
Alignment explanation
Indices: 28327--28479 Score: 263
Period size: 77 Copynumber: 2.0 Consensus size: 75
28317 TTTAGGCTGG
*
28327 AAGAGTCATAGATAAAATTTTAGAAAGATTCCATGTGGGCTTCATACAGCAATTCAATACATAAA
1 AAGAGTCATAGATAAAATTTGAGAAAGATTCCATGTGGGCTTCATACAGCAATTCAAT---TAAA
28392 CTCAGAGTAGAAC
63 CTCAGAGTAGAAC
28405 AAGAGTCATAGAT-AAATTTGAGAAAGATTCCATGTGGGCTTCATACAGCAATTCAATTAAACTC
1 AAGAGTCATAGATAAAATTTGAGAAAGATTCCATGTGGGCTTCATACAGCAATTCAATTAAACTC
28469 AGAGTAGAAC
66 AGAGTAGAAC
28479 A
1 A
28480 TGTAATCTCA
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
74 18 0.24
77 43 0.58
78 13 0.18
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (75 bp):
AAGAGTCATAGATAAAATTTGAGAAAGATTCCATGTGGGCTTCATACAGCAATTCAATTAAACTC
AGAGTAGAAC
Found at i:35879 original size:2 final size:2
Alignment explanation
Indices: 35872--35898 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35862 AAAGGAAAGA
35872 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
35899 TGTTATTATG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42941 original size:22 final size:22
Alignment explanation
Indices: 42916--43424 Score: 149
Period size: 22 Copynumber: 23.5 Consensus size: 22
42906 GATTTCATTT
42916 TGAAATTTTGATAACCTTCCTA
1 TGAAATTTTGATAACCTTCCTA
* *** *
42938 TGAAATTTTAATAATGATACTA
1 TGAAATTTTGATAACCTTCCTA
* * * **
42960 TGGAATTTCGAGAACCTTTTTA
1 TGAAATTTTGATAACCTTCCTA
** *
42982 T-AAATTTTTTTAACCTTCTTA
1 TGAAATTTTGATAACCTTCCTA
* *
43003 TGAAATTTTGTTAACC-TCCCA
1 TGAAATTTTGATAACCTTCCTA
* * * *
43024 AGGAATTTTGATGACC-TCAATA
1 TGAAATTTTGATAACCTTC-CTA
*
43046 TGAAATTTTGATAA-CTTCCCAA
1 TGAAATTTTGATAACCTT-CCTA
**
43068 TGAAATTTTGATAACCAACACTA
1 TGAAATTTTGATAACCTTC-CTA
* * *
43091 TGAGATGTTGACAACC-TCCATA
1 TGAAATTTTGATAACCTTCC-TA
* * *
43113 TGATATATTGATAATCACGT--TA
1 TGAAATTTTGATAA-C-CTTCCTA
* * *
43135 TGAAAATTTAAAAACC-TCCATA
1 TGAAATTTTGATAACCTTCC-TA
43157 TG-AATTGTT-AGTAATCACATT-C--
1 TGAAATT-TTGA-TAA-C-C-TTCCTA
*
43179 TGAAATTTTGTTAA-C-TCGCTA
1 TGAAATTTTGATAACCTTC-CTA
**
43200 TGAAATTTTGATAAATATTCCTA
1 TGAAATTTTGAT-AACCTTCCTA
*
43223 TAAAATTTTGATATAAACCTTCCTA
1 TGAAATTTTG--AT-AACCTTCCTA
* * *
43248 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAACCTTCCTA
* *
43270 TGAAGTCTTGATAA-----CTA
1 TGAAATTTTGATAACCTTCCTA
* *
43287 -CAAATTTTAATAACC-T-C-A
1 TGAAATTTTGATAACCTTCCTA
*
43305 TG-ATTTCTTGATAACC-TCACTA
1 TGAAATT-TTGATAACCTTC-CTA
* * *
43327 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCTTCCTA
* **
43349 TGAAATTTTGATAACCCTATTA
1 TGAAATTTTGATAACCTTCCTA
* **
43371 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT-TCCTA
* *
43393 TGAAATTTTGATATCC-TCC-C
1 TGAAATTTTGATAACCTTCCTA
43413 TGAAATTTTGAT
1 TGAAATTTTGAT
43425 TACTCCATAA
Statistics
Matches: 356, Mismatches: 89, Indels: 86
0.67 0.17 0.16
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 4 0.01
19 13 0.04
20 13 0.04
21 55 0.15
22 188 0.53
23 43 0.12
24 4 0.01
25 23 0.06
26 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCCTA
Found at i:43031 original size:43 final size:43
Alignment explanation
Indices: 42984--43083 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 43
42974 CCTTTTTATA
* * *
42984 AATTTTTTTAACCTTC-TTATGAAATTTTGTTAACCTCCCAAGG
1 AATTTTTATAACC-TCAATATGAAATTTTGATAACCTCCCAAGG
* * * *
43027 AATTTTGATGACCTCAATATGAAATTTTGATAACTTCCCAATGA
1 AATTTTTATAACCTCAATATGAAATTTTGATAACCTCCCAA-GG
*
43071 AATTTTGATAACC
1 AATTTTTATAACC
43084 AACACTATGA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 2 0.04
43 32 0.68
44 13 0.28
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (43 bp):
AATTTTTATAACCTCAATATGAAATTTTGATAACCTCCCAAGG
Found at i:43245 original size:25 final size:23
Alignment explanation
Indices: 43197--43261 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 23
43187 TGTTAACTCG
*
43197 CTATGAAATTTTGATAAATATTC
1 CTATAAAATTTTGATAAATATTC
43220 CTATAAAATTTTGATATAA-ACCTTC
1 CTATAAAATTTTGATA-AATA--TTC
43245 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
43262 CTTTCTTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
23 16 0.42
24 3 0.08
25 19 0.50
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATATTC
Found at i:43555 original size:22 final size:22
Alignment explanation
Indices: 43530--43696 Score: 137
Period size: 22 Copynumber: 7.6 Consensus size: 22
43520 AATCACATTT
*
43530 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
43552 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
43574 TAAAATTTT-ATTGACCCCTCTA
1 TGAAATTTTGA-TAACCTCTTTA
* * *
43596 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
43618 TGCAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
43640 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
43662 TGAAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
43684 T-AAATTTTGATAA
1 TGAAATTTTGATAA
43697 TCTGATCTCT
Statistics
Matches: 116, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.01
21 14 0.12
22 98 0.84
23 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:43556 original size:44 final size:44
Alignment explanation
Indices: 43506--43698 Score: 150
Period size: 44 Copynumber: 4.4 Consensus size: 44
43496 GAAATACCAC
43506 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
* * * * * *
43550 TATGAAATTTTGATAACCTC-TTTAT-AAAATTTTATTGACCCCTC
1 TATGAAATTTTGATAATCACATTT-TGAAAATTTGA-TAACCTCTT
* * * *
43594 TATGAAATTTTGATAATCACATTATGCAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTC-TT
* * *
43639 T-TGAAATTTTGATAA-CAACACTATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAATC-ACATTTTGAAAATTTGATAACCTCTT
43680 CCTAT-AAATTTTGATAATC
1 --TATGAAATTTTGATAATC
43699 TGATCTCTAT
Statistics
Matches: 119, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 30 0.25
44 77 0.65
45 9 0.08
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
Found at i:43646 original size:66 final size:66
Alignment explanation
Indices: 43530--43677 Score: 165
Period size: 66 Copynumber: 2.2 Consensus size: 66
43520 AATCACATTT
* * * * * * ** *
43530 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTT-ATTGACCCCTC
1 TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCCTTATAAAATTTTGA-TAACAACAC
43594 TA
65 TA
* *
43596 TGAAATTTTGATAATCACATTATGCAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACAC
1 TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACAC
43660 TA
65 TA
43662 TGAAATTTTGATAATC
1 TGAAATTTTGATAATC
43678 TTCCTATAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
66 66 0.96
67 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (66 bp):
TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACT
A
Found at i:43668 original size:88 final size:88
Alignment explanation
Indices: 43505--43670 Score: 219
Period size: 88 Copynumber: 1.9 Consensus size: 88
43495 AGAAATACCA
* * **
43505 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
43570 TTTATAAAATTTTATTGACCCCT
66 ACTATAAAATTTTATTGACCCCT
* *
43593 CTATGAAA-TTTTGATAATCACATTATGCAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTTTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
43656 ACACTATGAAATTTT
64 ACACTATAAAATTTT
43671 GATAATCTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 5 0.07
88 60 0.90
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTATTGACCCCT
Found at i:43690 original size:21 final size:23
Alignment explanation
Indices: 43593--43742 Score: 125
Period size: 22 Copynumber: 6.7 Consensus size: 23
43583 ATTGACCCCT
43593 CTATGAAATTTTGATAATC-ACA
1 CTATGAAATTTTGATAATCTACA
* * * *
43615 TTATGCAATTTTGATAACCT-CG
1 CTATGAAATTTTGATAATCTACA
* *
43637 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATCTACA
*
43659 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATCTACA
*
43681 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATCT-A-CA
* * *
43705 CTATGACATTTCGATAATC-ACT
1 CTATGAAATTTTGATAATCTACA
*
43727 CTATGATA-TTTGATAA
1 CTATGAAATTTTGATAA
43743 CCTTCTATCA
Statistics
Matches: 104, Mismatches: 17, Indels: 15
0.76 0.12 0.11
Matches are distributed among these distances:
21 23 0.22
22 61 0.59
23 4 0.04
24 4 0.04
25 12 0.12
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCTACA
Found at i:44009 original size:31 final size:31
Alignment explanation
Indices: 43973--44035 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
43963 TAATGGTAAT
*
43973 TTAGAAATATGTTTTAAAAAAAAGGGTACAA
1 TTAGAAATATATTTTAAAAAAAAGGGTACAA
* *
44004 TTAGAAATATATTTTAAAAATAAGGTTACAA
1 TTAGAAATATATTTTAAAAAAAAGGGTACAA
44035 T
1 T
44036 CGAAAAATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (31 bp):
TTAGAAATATATTTTAAAAAAAAGGGTACAA
Found at i:65228 original size:22 final size:24
Alignment explanation
Indices: 65185--65231 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
65175 AAGAATAAAC
65185 TGTATTTGATAAAAAAATGTATTA
1 TGTATTTGATAAAAAAATGTATTA
*
65209 TGTA-TTGAT-AAATAATGTATTA
1 TGTATTTGATAAAAAAATGTATTA
65231 T
1 T
65232 CAGACTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 5 0.23
24 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.45
Consensus pattern (24 bp):
TGTATTTGATAAAAAAATGTATTA
Done.