Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015052.1 Corchorus capsularis cultivar CVL-1 contig15073, 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: 63602
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:4294 original size:2 final size:2
Alignment explanation
Indices: 4287--4323 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
4277 CCTCTTGGCA
* *
4287 TG TG TG TG TG TG TG TG AG TT TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4324 TAATTTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:4330 original size:22 final size:22
Alignment explanation
Indices: 4287--4330 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4277 CCTCTTGGCA
*
4287 TGTGTGTGTGTGTGTGAGTTTG
1 TGTGTGTGTGTGTGTGAATTTG
*
4309 TGTGTGTGTGTGTGTTAATTTG
1 TGTGTGTGTGTGTGTGAATTTG
4331 AAATAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.00, G:0.41, T:0.52
Consensus pattern (22 bp):
TGTGTGTGTGTGTGTGAATTTG
Found at i:24546 original size:154 final size:154
Alignment explanation
Indices: 24266--24573 Score: 526
Period size: 154 Copynumber: 2.0 Consensus size: 154
24256 GAAGTTTGAA
* *
24266 GAGATTTTCATATATTAATTCAATCTCTTTACATCATGATGAACCAAGAAACGTATGACTTATAA
1 GAGATTTTCATATATTAATTCAATCTCTTTACACCATGATGAACCAAGAAACATATGACTTATAA
* *
24331 TTAGCATTGATCATAACAACAGGATTTCAGCTATCAAACCGATTGATCTGATGACCAAACAAAAC
66 TTAGCATTCATCATAACAACAGGATTTCAGCTATCAAACCAATTGATCTGATGACCAAACAAAAC
24396 TCAAATCTTTCTGCAGCATAATGT
131 TCAAATCTTTCTGCAGCATAATGT
* *
24420 GAGATTTTCATATATTAATTCAATCTCTTTACACCATGGTGAACCAAGAGACATATGACTTATAA
1 GAGATTTTCATATATTAATTCAATCTCTTTACACCATGATGAACCAAGAAACATATGACTTATAA
* *
24485 TTAGCATTCATCATAACAGCAGGATTTCAGTTATCAAACCAATTGATCTGATGACCAAACAAAAC
66 TTAGCATTCATCATAACAACAGGATTTCAGCTATCAAACCAATTGATCTGATGACCAAACAAAAC
* *
24550 TGAAATCTTTCTGCGGCATAATGT
131 TCAAATCTTTCTGCAGCATAATGT
24574 CTATAAATAT
Statistics
Matches: 144, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
154 144 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (154 bp):
GAGATTTTCATATATTAATTCAATCTCTTTACACCATGATGAACCAAGAAACATATGACTTATAA
TTAGCATTCATCATAACAACAGGATTTCAGCTATCAAACCAATTGATCTGATGACCAAACAAAAC
TCAAATCTTTCTGCAGCATAATGT
Found at i:26808 original size:168 final size:165
Alignment explanation
Indices: 26440--26871 Score: 573
Period size: 168 Copynumber: 2.6 Consensus size: 165
26430 GTGATTTGTA
*
26440 AATTGAGAAATGACCAAAAATTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTA
1 AATTGAGAAATGACCAAAAA-GTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTA
* * * ** * *
26505 AGTAATCTGCCAAGTTGGTAAAGAC-AAAAAAAATTAGTTCTCTATCTCATCATCAATCCTTGAT
65 AGTAATCTGCCAAG-TGGAAAAGACGAAAAAAAATAAGTTATCTATCTCAAAAGCAAACCTTGAT
* *
26569 GGGGATCTTTTATTAATTCCACTACTCTATTCAAATC
129 AGGGATCTTTTAGTAATTCCACTACTCTATTCAAATC
* * * *
26606 CATTGAGAAATTACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTA
1 AATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTA
26671 AGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAATAAGTTATCT-TACTCCAAAAGCAAACCTTG
65 AGTAATCTGCCAAGT-GGAAAAGACGAAAAAAAATAAGTTATCTAT-CT-CAAAAGCAAACCTTG
* *
26735 GTAGGGATCTTTTAGTAATTCCACTACTTTATT-AAAGTC
127 ATAGGGATCTTTTAGTAATTCCACTACTCTATTCAAA-TC
* * *
26774 AATTGAGAAATGACCTAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGGCATTTA
1 AATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTA
* *
26839 AGTAATCGGTCAAGTGTGAAAAGACGAAAAAAA
65 AGTAATCTGCCAAGTG-GAAAAGACGAAAAAAA
26872 TTAGTTCTCT
Statistics
Matches: 233, Mismatches: 25, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
165 1 0.00
166 82 0.35
167 23 0.10
168 127 0.55
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (165 bp):
AATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAA
GTAATCTGCCAAGTGGAAAAGACGAAAAAAAATAAGTTATCTATCTCAAAAGCAAACCTTGATAG
GGATCTTTTAGTAATTCCACTACTCTATTCAAATC
Found at i:29881 original size:35 final size:35
Alignment explanation
Indices: 29842--30076 Score: 323
Period size: 35 Copynumber: 6.7 Consensus size: 35
29832 TTCTTACTAA
29842 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
29877 ACTTAATTACCCTGAATTAAGTTGATTACCGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
29912 ACTTAATTACCCTGAATTAAGTT-ACTCATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTG-ACTC
* *
29947 ACTTAATTACCCTGAATTAAGTT-ACTTATTAACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
29982 ACTTAATTACCCTGAATTAAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTC
** *
30018 ACTTAATTACCCTGAATTAAGTTGATTACCAACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
30053 GCGTAATTACCCTGAATTAAGTTG
1 ACTTAATTACCCTGAATTAAGTTG
30077 CTTATTACTG
Statistics
Matches: 182, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
34 4 0.02
35 143 0.79
36 34 0.19
37 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
Found at i:36495 original size:41 final size:45
Alignment explanation
Indices: 36438--36552 Score: 166
Period size: 45 Copynumber: 2.6 Consensus size: 45
36428 ATTTTATTAA
** *
36438 TTTCCAAAATCTTCTTTT-GAATTTGTTAA-A-AAAACTTTTG-T
1 TTTCCAAAATCTTCTTTTGGAATTACTTAAGAGAAAACCTTTGTT
36479 TTTCCAAAATCTTCTTTTGGAATTACTTAAGAGAAAACCTTTGTT
1 TTTCCAAAATCTTCTTTTGGAATTACTTAAGAGAAAACCTTTGTT
*
36524 TTTCCGAAATCTTCTTTTGGAATTACTTA
1 TTTCCAAAATCTTCTTTTGGAATTACTTA
36553 CATTGAAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
41 18 0.27
42 9 0.14
43 1 0.02
44 9 0.14
45 29 0.44
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.46
Consensus pattern (45 bp):
TTTCCAAAATCTTCTTTTGGAATTACTTAAGAGAAAACCTTTGTT
Found at i:40481 original size:36 final size:36
Alignment explanation
Indices: 40434--40520 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
40424 ACTAACCATC
40434 ACTAATGCAAATTAATGGAATATATGATGTGATATG
1 ACTAATGCAAATTAATGGAATATATGATGTGATATG
40470 ACTAATGCAAATTAATGGAATATATGATGTGATATG
1 ACTAATGCAAATTAATGGAATATATGATGTGATATG
*
40506 -CTAACGCGAAATTAA
1 ACTAATGC-AAATTAA
40521 AATGACTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 6 0.12
36 43 0.88
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (36 bp):
ACTAATGCAAATTAATGGAATATATGATGTGATATG
Found at i:43694 original size:28 final size:27
Alignment explanation
Indices: 43653--43762 Score: 132
Period size: 28 Copynumber: 4.0 Consensus size: 27
43643 TTCTTAAGGT
* *
43653 CATCCAGGGGCATTTTGGTCATTTTCA
1 CATCAAGGGGCATTTTGGTCATTTTTA
*
43680 CATCATAGGGTCATTTTGGTCATTTTTA
1 CATCA-AGGGGCATTTTGGTCATTTTTA
* *
43708 CATTC-AGGGGTATTTTGGTCATTTTTG
1 CA-TCAAGGGGCATTTTGGTCATTTTTA
*
43735 CATTAAAGGGGCATTTTGGTCATTTTTA
1 CA-TCAAGGGGCATTTTGGTCATTTTTA
43763 GTCCATTTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
27 27 0.38
28 42 0.59
29 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.44
Consensus pattern (27 bp):
CATCAAGGGGCATTTTGGTCATTTTTA
Found at i:43717 original size:55 final size:55
Alignment explanation
Indices: 43657--43762 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 55
43647 TAAGGTCATC
* *
43657 CAGGGGCATTTTGGTCATTTTCACATCATAGGGTCATTTTGGTCATTTTTACATT
1 CAGGGGCATTTTGGTCATTTTCACATCAAAGGGGCATTTTGGTCATTTTTACATT
* ** *
43712 CAGGGGTATTTTGGTCATTTTTGCATTAAAGGGGCATTTTGGTCATTTTTA
1 CAGGGGCATTTTGGTCATTTTCACATCAAAGGGGCATTTTGGTCATTTTTA
43763 GTCCATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (55 bp):
CAGGGGCATTTTGGTCATTTTCACATCAAAGGGGCATTTTGGTCATTTTTACATT
Found at i:50027 original size:50 final size:50
Alignment explanation
Indices: 49967--50340 Score: 252
Period size: 50 Copynumber: 7.6 Consensus size: 50
49957 CCATCTCCCG
* * * *
49967 ATTCATTCTTAAAAAAACCGTCTTCCGATCATCTTTCGAACTGTCTTCCA
1 ATTCATTCTTAAAAGAATCGTCTTCCGATTATCTTTCGAATTGTCTTCCA
* * * *
50017 ATTCATTCTTATAAAGAATTGTCTTCCGATCATC-TTC-CATTCATCTTTCTCTA
1 ATTCATTCTTA-AAAGAATCGTCTTCCGATTATCTTTCGAATT-GTC-TTC-C-A
* * **
50070 ATTC--TC-T----GAATCATCTTCCGCTTATCCCTCGAATTGTC-TCTCA
1 ATTCATTCTTAAAAGAATCGTCTTCCGATTATCTTTCGAATTGTCTTC-CA
* * * * * *
50113 ATTCCATTCATGAGAGGATCGTCTTCCGATTTTCTTTCGAACTGTCTTCCA
1 ATT-CATTCTTAAAAGAATCGTCTTCCGATTATCTTTCGAATTGTCTTCCA
* * * * *
50164 ATTCAATCTTAAAAGGACCGTCTCCCGCTTATCCTTT-GAATTGTCTTCCA
1 ATTCATTCTTAAAAGAATCGTCTTCCGATTAT-CTTTCGAATTGTCTTCCA
* * * * * *
50214 ATCCCATTATTAAGAGGATCGTCTTCCGATTCTCTTTCGAATTGTCTTCTA
1 AT-TCATTCTTAAAAGAATCGTCTTCCGATTATCTTTCGAATTGTCTTCCA
* * * * *
50265 ATTCAATCTTAAAAGGACCGTCTTCCGTTTATCCTTCGAATTGTCTTCCA
1 ATTCATTCTTAAAAGAATCGTCTTCCGATTATCTTTCGAATTGTCTTCCA
* *
50315 ATTCGTTC-TAATA-AATCGTCTTCCGA
1 ATTCATTCTTAAAAGAATCGTCTTCCGA
50341 CCTATTCCTG
Statistics
Matches: 252, Mismatches: 53, Indels: 40
0.73 0.15 0.12
Matches are distributed among these distances:
43 4 0.02
44 5 0.02
45 15 0.06
46 6 0.02
47 4 0.02
48 10 0.04
49 6 0.02
50 101 0.40
51 93 0.37
52 3 0.01
53 5 0.02
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.39
Consensus pattern (50 bp):
ATTCATTCTTAAAAGAATCGTCTTCCGATTATCTTTCGAATTGTCTTCCA
Found at i:50205 original size:101 final size:101
Alignment explanation
Indices: 50087--50318 Score: 351
Period size: 101 Copynumber: 2.3 Consensus size: 101
50077 GAATCATCTT
* * *
50087 CCGCTTATCCCTCGAATTGTC-TCTCAATTCCATTCA-TGAGAGGATCGTCTTCCGATTTTCTTT
1 CCGCTTATCCTTCGAATTGTCTTC-CAATTCCATT-ATTAAGAGGATCGTCTTCCGATTCTCTTT
50150 CGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTC
64 CGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTC
* *
50188 CCGCTTATCCTTTGAATTGTCTTCCAATCCCATTATTAAGAGGATCGTCTTCCGATTCTCTTTCG
1 CCGCTTATCCTTCGAATTGTCTTCCAATTCCATTATTAAGAGGATCGTCTTCCGATTCTCTTTCG
* * *
50253 AATTGTCTTCTAATTCAATCTTAAAAGGACCGTCTT
66 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTC
*
50289 CCGTTTATCCTTCGAATTGTCTTCCAATTC
1 CCGCTTATCCTTCGAATTGTCTTCCAATTC
50319 GTTCTAATAA
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
100 1 0.01
101 115 0.97
102 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (101 bp):
CCGCTTATCCTTCGAATTGTCTTCCAATTCCATTATTAAGAGGATCGTCTTCCGATTCTCTTTCG
AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTC
Found at i:59391 original size:28 final size:28
Alignment explanation
Indices: 59360--59424 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
59350 AGGTTTAAAA
*
59360 CACCACATCATTCAAACTTTAAATACAT
1 CACCAAATCATTCAAACTTTAAATACAT
* * *
59388 CACCAAATCGTTCAAATTTTAATTACAAT
1 CACCAAATCATTCAAACTTTAAATAC-AT
*
59417 CTCCAAAT
1 CACCAAAT
59425 ATATTTTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.31
Consensus pattern (28 bp):
CACCAAATCATTCAAACTTTAAATACAT
Done.