Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009961.1 Corchorus capsularis cultivar CVL-1 contig09982, 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: 5937
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Found at i:3094 original size:2 final size:2
Alignment explanation
Indices: 3064--3119 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
3054 CGAATGTATC
* * *
3064 TA TA TT TA TA TC TA TA TC TA TA CTA 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
3107 TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA
3120 AAAAGTACGA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 1 0.02
2 43 0.93
3 2 0.04
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3098 original size:25 final size:25
Alignment explanation
Indices: 3064--3119 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
3054 CGAATGTATC
* * *
3064 TATATTTATATCTATATCTATACTA
1 TATATATATATATATATATATACTA
*
3089 TATATATATATATATATATATATTA
1 TATATATATATATATATATATACTA
3114 TATATA
1 TATATA
3120 AAAAGTACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATATATATATATATATATACTA
Found at i:3548 original size:19 final size:20
Alignment explanation
Indices: 3521--3558 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3511 TACTATTATT
3521 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
3541 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
3559 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:3710 original size:24 final size:22
Alignment explanation
Indices: 3661--3748 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 22
3651 CACTTTGTTC
**
3661 AAAATTTCATA-GTGTGGTTACC
1 AAAATTTCATAGGT-TGGTTATT
3683 AAAATTTCATAGGATCAT-GTTATT
1 AAAATTTCATAGG-T--TGGTTATT
* *
3707 AAAATCTCTTAGGTTGGTTATT
1 AAAATTTCATAGGTTGGTTATT
* *
3729 GAAATTTCATAGGGTGGTTA
1 AAAATTTCATAGGTTGGTTA
3749 ATTATCACAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.02
22 33 0.62
23 2 0.04
24 16 0.30
25 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (22 bp):
AAAATTTCATAGGTTGGTTATT
Found at i:3838 original size:22 final size:22
Alignment explanation
Indices: 3788--3918 Score: 81
Period size: 22 Copynumber: 6.0 Consensus size: 22
3778 AAGAGATTAT
* *
3788 CAAAATATCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* * *
3811 -AGAATTTTATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
3832 CAAAATTTCATTAG-GAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * *
3853 CTAATATTTCATGGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * * *
3876 CAAAATTTTATTGTGTGGTTAC
1 CAAAATTTCATAGTGAGGTTAA
3898 CAAAATTTCATA-TGAAGGTTA
1 CAAAATTTCATAGTG-AGGTTA
3919 TAAAAGTCTC
Statistics
Matches: 82, Mismatches: 20, Indels: 13
0.71 0.17 0.11
Matches are distributed among these distances:
21 7 0.09
22 71 0.87
23 4 0.05
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:4089 original size:21 final size:22
Alignment explanation
Indices: 3929--4092 Score: 84
Period size: 22 Copynumber: 7.3 Consensus size: 22
3919 TAAAAGTCTC
* *
3929 AATTTCATAAGGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
3949 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * * *
3969 AATCTCATAGAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
*
3991 AATTTCATAGAGATCGGATTATCAAA
1 AATTTCATAAAGA--GG-TTATC-AA
* * * *
4017 ATTTATTTCATAGAGGGGTCAACAA
1 A---ATTTCATAAAGAGGTTATCAA
* *
4042 AATTTTATAATGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
4064 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
4086 ATTTTCA
1 AATTTCA
4093 AATGTGATTA
Statistics
Matches: 109, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
19 1 0.01
20 19 0.17
21 9 0.08
22 53 0.49
24 1 0.01
25 8 0.07
26 5 0.05
27 2 0.02
29 11 0.10
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:4244 original size:22 final size:22
Alignment explanation
Indices: 4197--4776 Score: 168
Period size: 22 Copynumber: 26.6 Consensus size: 22
4187 TTATGGAGTA
* *
4197 ATCAAAATTTCA-GTG-AGGAT
1 ATCAAAATTTCATATGAAGGTT
4217 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
4239 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
4261 TTCAAAATTTCACAAG-AGAGTT
1 ATCAAAATTTCATATGAAG-GTT
* * *
4283 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
4305 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
4327 AACAAAATTTCATAATGAA-GTT
1 ATCAAAATTTCAT-ATGAAGGTT
* ** * *
4349 ATTAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
4371 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * **
4387 ATCAAGATTTCATAAGAAATTT
1 ATCAAAATTTCATATGAAGGTT
* * * *
4409 ATCAAAATTTTATAGGGAGATTT
1 ATCAAAATTTCATATGAAG-GTT
* * *
4432 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
*
4455 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
4477 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
4499 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
4521 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * *
4543 TTTAAATTTTCATAATG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * *
4565 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * * **
4587 ATGAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
4610 ATCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
4632 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * * *
4655 -TCAAAATTCCTTAAGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* ** *
4676 AACCGAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * ** *
4698 -TAAAAAAATT-ATAAAAAGATT
1 AT-CAAAATTTCATATGAAGGTT
* * * **
4719 CTCGAAATTCCATAGTG-TCGTT
1 ATCAAAATTTCATA-TGAAGGTT
*
4741 ATTAAAATTTCATA-GAAAGGTT
1 ATCAAAATTTCATATG-AAGGTT
4763 ATCAAAATTTCATA
1 ATCAAAATTTCATA
4777 ATGGGGTCAT
Statistics
Matches: 416, Mismatches: 102, Indels: 82
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
20 16 0.04
21 34 0.08
22 280 0.67
23 71 0.17
24 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:4645 original size:45 final size:44
Alignment explanation
Indices: 4188--4662 Score: 252
Period size: 44 Copynumber: 10.9 Consensus size: 44
4178 AAACTTTTAT
* * *
4188 TATGG-AGTAATCAAAATTTC--AGTGAGGATATCAAAATTTCA
1 TATGGAAGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCA
* * *
4229 TAT-GAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCA
1 TATGGAA-GTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCA
* * * *
4273 CA-AGAGAGTTATCAAAATTTCATAGTAT-GTAGATCAAAATTTCA
1 TATGGA-AGTTATCAAAATTTCATAGTGTGGT-TATCAAAATTTCA
* * * ** * **
4317 TA-GGGAGATTAACAAAATTTCATAATGAAGTTATTAAAAAATCA
1 TATGGAAG-TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCA
* * * *
4361 TAGGGAGGTTATCAAAA--T--T--TGTAGTTATCAAGATTTCA
1 TATGGAAGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCA
* * * * * * * *
4399 TAAGAAATTTATCAAAATTTTATAGGGAGATTTATCAAAATTTTA
1 TATGGAAGTTATCAAAATTTCATAGTGTG-GTTATCAAAATTTCA
* * *
4444 TA-GGAAGATTTATCAAAATTTCATAGCGAGGTTATCACAATTTCA
1 TATGGAAG--TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCA
* *
4489 TAGTGTG-A-TTATCAAAATTTCAGAGTGTGATTA-CTAACAA-TTCA
1 TA-TG-GAAGTTATCAAAATTTCATAGTGTGGTTATC-AA-AATTTCA
* * * * * * *
4533 TATGGAGGTTTTTAAATTTTCATAATGTGGTTATCAATATATCA
1 TATGGAAGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCA
* * * *
4577 TATGGAGGTTATGAACATCTCATAGTGTTGGTTATCAAAATTTCA
1 TATGGAAGTTATCAAAATTTCATAGTG-TGGTTATCAAAATTTCA
* *
4622 T-TGGGAAGTTATCAAAATTTCATATTGAGGTCT-TCAAAATT
1 TAT-GGAAGTTATCAAAATTTCATAGTGTGGT-TATCAAAATT
4663 CCTTAAGGAG
Statistics
Matches: 329, Mismatches: 74, Indels: 59
0.71 0.16 0.13
Matches are distributed among these distances:
38 27 0.08
40 3 0.01
41 4 0.01
42 16 0.05
43 8 0.02
44 176 0.53
45 73 0.22
46 19 0.06
47 2 0.01
48 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (44 bp):
TATGGAAGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCA
Found at i:4805 original size:40 final size:40
Alignment explanation
Indices: 4761--4883 Score: 104
Period size: 40 Copynumber: 3.3 Consensus size: 40
4751 CATAGAAAGG
4761 TTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAA
1 TTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAA
* * * * * *
4801 TTATCATAGTTATTAAAAT---TTCAT--AGAA-AG-G---
1 TTATCAAAATT-TCATAATGGGGTCATAAAAAATAGTGTAA
4832 TTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAA
1 TTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAA
*
4872 TTATCATAATTT
1 TTATCAAAATTT
4884 AATAGAGAGG
Statistics
Matches: 59, Mismatches: 13, Indels: 22
0.63 0.14 0.23
Matches are distributed among these distances:
30 5 0.08
31 9 0.15
33 4 0.07
34 1 0.02
35 5 0.08
36 5 0.08
37 1 0.02
38 4 0.07
40 20 0.34
41 5 0.08
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (40 bp):
TTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAA
Found at i:4826 original size:71 final size:71
Alignment explanation
Indices: 4738--4879 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
4728 CCATAGTGTC
4738 GTTATTAAAATTTCATAGAAAGGTTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAATT
1 GTTATTAAAATTTCATAGAAAGGTTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAATT
4803 ATCATA
66 ATCATA
4809 GTTATTAAAATTTCATAGAAAGGTTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAATT
1 GTTATTAAAATTTCATAGAAAGGTTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAATT
4874 ATCATA
66 ATCATA
4880 ATTTAATAGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (71 bp):
GTTATTAAAATTTCATAGAAAGGTTATCAAAATTTCATAATGGGGTCATAAAAAATAGTGTAATT
ATCATA
Done.