Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007233.1 Corchorus capsularis cultivar CVL-1 contig07254, 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: 32393
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:721 original size:15 final size:15
Alignment explanation
Indices: 681--724 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
671 TTTTACGTTA
681 TTTTCCTTTTCTTTT
1 TTTTCCTTTTCTTTT
* *
696 TCTTCCCTTTCTTTT
1 TTTTCCTTTTCTTTT
*
711 TTTTCGTTTTCTTT
1 TTTTCCTTTTCTTT
725 GCTTCGTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTTCCTTTTCTTTT
Found at i:1376 original size:15 final size:15
Alignment explanation
Indices: 1352--1401 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1342 GAATGGCGCA
1352 AACAACAATGGTGCG
1 AACAACAATGGTGCG
* *
1367 AACCATAATGGTGCG
1 AACAACAATGGTGCG
*
1382 AACAACCATGGTGCG
1 AACAACAATGGTGCG
1397 AACAA
1 AACAA
1402 TCATGTTGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.14
Consensus pattern (15 bp):
AACAACAATGGTGCG
Found at i:1386 original size:30 final size:30
Alignment explanation
Indices: 1343--1399 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1333 TGCTAGGGTG
1343 AATGGCGCAAACAACAATGGTGCGAACCAT
1 AATGGCGCAAACAACAATGGTGCGAACCAT
* * *
1373 AATGGTGCGAACAACCATGGTGCGAAC
1 AATGGCGCAAACAACAATGGTGCGAAC
1400 AATCATGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (30 bp):
AATGGCGCAAACAACAATGGTGCGAACCAT
Found at i:1406 original size:15 final size:15
Alignment explanation
Indices: 1359--1406 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
1349 GCAAACAACA
* *
1359 ATGGTGCGAACCATA
1 ATGGTGCGAACAATC
*
1374 ATGGTGCGAACAACC
1 ATGGTGCGAACAATC
1389 ATGGTGCGAACAATC
1 ATGGTGCGAACAATC
1404 ATG
1 ATG
1407 TTGTGCAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (15 bp):
ATGGTGCGAACAATC
Found at i:15845 original size:34 final size:34
Alignment explanation
Indices: 15799--15867 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
15789 TCCAAGAATT
* *
15799 AGTTTTTGCTTTTTTCG-TTTTCTCTAAAAAAAAA
1 AGTTTTTCCTTTTTCCGATTTT-TCTAAAAAAAAA
15833 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAA
1 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAA
15867 A
1 A
15868 ATTAAGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (34 bp):
AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAA
Found at i:19857 original size:17 final size:18
Alignment explanation
Indices: 19827--19861 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
19817 AGGAACAGAA
*
19827 AAGAAAGAGGAAAAGGAG
1 AAGAAAGAGAAAAAGGAG
19845 AAGAAA-AGAAAAAGGAG
1 AAGAAAGAGAAAAAGGAG
19862 TCGATATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
AAGAAAGAGAAAAAGGAG
Found at i:20205 original size:54 final size:52
Alignment explanation
Indices: 20138--20285 Score: 169
Period size: 50 Copynumber: 2.8 Consensus size: 52
20128 CTTTGTGTTG
20138 AAAGATTAAATCTTTGGAATGATTTGTGAATAAAAATTGAATTTTTTTTAAGTA
1 AAAGATTAAATCTTT-GAATGATTTGTGAATAAAAATTGAA-TTTTTTTAAGTA
** * * *
20192 AAAGATTGGATCTTTTAA-GTAGTTTGTGAATGAAAATTGAA---TTTTAAGTG
1 AAAGATTAAATCTTTGAATG-A-TTTGTGAATAAAAATTGAATTTTTTTAAGTA
*
20242 AAAGATTAAATCTTTGAAGTGATTTGTGAATAAAGATTGAATTT
1 AAAGATTAAATCTTTGAA-TGATTTGTGAATAAAAATTGAATTT
20286 CTAATTAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
50 40 0.52
51 1 0.01
52 2 0.03
53 3 0.04
54 31 0.40
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (52 bp):
AAAGATTAAATCTTTGAATGATTTGTGAATAAAAATTGAATTTTTTTAAGTA
Found at i:20262 original size:21 final size:19
Alignment explanation
Indices: 20218--20263 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
20208 AAGTAGTTTG
*
20218 TGAA-TGAAAATTGAATTT
1 TGAAGTGAAAATTAAATTT
20236 T-AAGTGAAAGATTAAATCTT
1 TGAAGTGAAA-ATTAAAT-TT
20256 TGAAGTGA
1 TGAAGTGA
20264 TTTGTGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 6 0.26
19 6 0.26
20 3 0.13
21 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (19 bp):
TGAAGTGAAAATTAAATTT
Found at i:21080 original size:47 final size:43
Alignment explanation
Indices: 21006--21589 Score: 413
Period size: 47 Copynumber: 13.7 Consensus size: 43
20996 ATTTGTCGGT
*
21006 TTTGTCCTT-CCCAGTCGGAAGGTGTTGTTTAGTTATCAAATTACCAG
1 TTTGCCCTTCCCCA-TCGGAAGGTGTTGTTTAGTT-TC---TTACCAG
*
21053 TTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTTTC-T--CAG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCTTACCAG
*
21093 TCTGCCCTTCCCCATCGGAA-G-G-TG-TT-G--T-TTACCAG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCTTACCAG
*
21128 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAG-TTC-T-CCTAG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCTTACC-AG
* * *
21169 TTTGCCCTTCCCCACCGGAAGGTGTTATCTAGTTGTCAAATTACCAG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTT-TC---TTACCAG
* *
21216 TTTGTCCTTCCCCATCGGAAGGTGTTGTCTAGTTTC-T--CAG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCTTACCAG
*
21256 TCTGCCCTTCCCCATCGGAA-G-G-TG-TT-G--T-TTACCAG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCTTACCAG
*
21291 TTTGCCCTTCCCTATCGGAAGGTGTTGTTTAGTATTC---CCAG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGT-TTCTTACCAG
* * *
21332 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTGTCAAATTACCAA
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTT-TC---TTACCAG
* * * ** *
21379 TTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGTTGCCAACTTCAA
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCTTAC--CAG
* * * *
21424 TTTGCCCTTCCCCA-CAGAAGGTGTTGTCTAAGTTGCCTTATCCCCG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGT-TTAGTT-TCTTA--CCAG
*
21470 TTTTGCCCTTCCCCATTGGAAGGTGTTGTTTAG-TT-TTACCAG
1 -TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCTTACCAG
* * * * *
21512 TTTGCGCTTCCCTACCAGAAGGTGTTGTTTATTTTGTCTTACTCATG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTA-GTT-TCTTAC-CA-G
* *
21559 TTTTGCCCTTCCCGATAGGAAGGTGTTGTTT
1 -TTTGCCCTTCCCCATCGGAAGGTGTTGTTT
21590 TGCCATGACC
Statistics
Matches: 435, Mismatches: 49, Indels: 105
0.74 0.08 0.18
Matches are distributed among these distances:
33 4 0.01
35 44 0.10
36 4 0.01
37 6 0.01
38 6 0.01
39 6 0.01
40 48 0.11
41 96 0.22
42 6 0.01
43 6 0.01
44 16 0.04
45 25 0.06
46 11 0.03
47 114 0.26
48 43 0.10
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (43 bp):
TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCTTACCAG
Found at i:21110 original size:40 final size:40
Alignment explanation
Indices: 21050--21539 Score: 349
Period size: 41 Copynumber: 11.8 Consensus size: 40
21040 ATCAAATTAC
21050 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCT
1 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCT
* *
21090 CAGTCTGCCCTTCCCCATCGGAAGGTGTTG--T--TTAC-
1 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCT
* *
21125 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAG-TTCT
1 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCT
* *
21164 CCTAGTTTGCCCTTCCCCACCGGAAGGTGTTATCTAGTTGTCAAATT
1 -C-AGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTT-TC----T
*
21211 ACCAGTTTGTCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCT
1 --CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCT
* *
21253 CAGTCTGCCCTTCCCCATCGGAAGGTGTTG--T--TTAC-
1 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCT
* * *
21288 CAGTTTGCCCTTCCCTATCGGAAGGTGTTGTTTAGTATTCC
1 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGT-TTCT
* * *
21329 CAGTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTGTCAAATT
1 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTT-TC----T
* * *
21374 ACCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGTTGCCAACTT
1 --CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTT----TC-T
* * *
21421 CAATTTGCCCTTCCCCA-CAGAAGGTGTTGTCTAAGTTGCCTTATCC
1 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCT-A---G--TT-TCT
* * *
21467 CCGTTTTGCCCTTCCCCATTGGAAGGTGTTGTTTAGTTT-T
1 CAG-TTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCT
* * * *
21507 ACCAGTTTGCGCTTCCCTACCAGAAGGTGTTGT
1 --CAGTTTGCCCTTCCCCATCGGAAGGTGTTGT
21540 TTATTTTGTC
Statistics
Matches: 370, Mismatches: 40, Indels: 79
0.76 0.08 0.16
Matches are distributed among these distances:
35 56 0.15
36 6 0.02
37 2 0.01
38 4 0.01
39 1 0.00
40 61 0.16
41 91 0.25
42 6 0.02
43 2 0.01
44 15 0.04
45 18 0.05
46 3 0.01
47 87 0.24
48 15 0.04
50 3 0.01
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.35
Consensus pattern (40 bp):
CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCT
Found at i:21141 original size:35 final size:35
Alignment explanation
Indices: 21046--21194 Score: 163
Period size: 35 Copynumber: 3.9 Consensus size: 35
21036 AGTTATCAAA
*
21046 TTACCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCT
1 TTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTG--T
* * *
21083 AGTTTCTCAGTCTGCCCTTCCCCATCGGAAGGTGTTGT
1 --TTAC-CAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
21121 TTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
1 TTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
21156 TTAGTTCTCCTAGTTTGCCCTTCCCCACCGGAAGGTGTT
1 TTA-----CC-AGTTTGCCCTTCCCCACCGGAAGGTGTT
21195 ATCTAGTTGT
Statistics
Matches: 98, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
35 32 0.33
36 3 0.03
38 1 0.01
39 3 0.03
40 31 0.32
41 28 0.29
ACGTcount: A:0.13, C:0.30, G:0.22, T:0.34
Consensus pattern (35 bp):
TTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
Found at i:21235 original size:88 final size:87
Alignment explanation
Indices: 21121--21281 Score: 252
Period size: 88 Copynumber: 1.8 Consensus size: 87
21111 AAGGTGTTGT
* *
21121 TTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAG-TTCTCCTAGTTTGCCCTTCCCCACC
1 TTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGTTTCT-C-AGTCTGCCCTTCCCCACC
21185 GGAAGGTGTTATCTAGTTGTCAAA
64 GGAAGGTGTTATCTAGTTGTCAAA
* * *
21209 TTACCAGTTTGTCCTTCCCCATCGGAAGGTGTTGTCTAGTTTCTCAGTCTGCCCTTCCCCATCGG
1 TTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGTTTCTCAGTCTGCCCTTCCCCACCGG
21274 AAGGTGTT
66 AAGGTGTT
21282 GTTTACCAGT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
87 26 0.39
88 37 0.55
89 4 0.06
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.35
Consensus pattern (87 bp):
TTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGTTTCTCAGTCTGCCCTTCCCCACCGG
AAGGTGTTATCTAGTTGTCAAA
Found at i:21281 original size:163 final size:163
Alignment explanation
Indices: 21021--21412 Score: 678
Period size: 163 Copynumber: 2.4 Consensus size: 163
21011 CCTTCCCAGT
*
21021 CGGAAGGTGTTGTTTAGTTATCAAATTACCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGT
1 CGGAAGGTGTTGTTTAGTTGTCAAATTACCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGT
21086 TTCTCAGTCTGCCCTTCCCCATCGGAAGGTGTTGTTTACCAGTTTGCCCTTCCCCACCGGAAGGT
66 TTCTCAGTCTGCCCTTCCCCATCGGAAGGTGTTGTTTACCAGTTTGCCCTTCCCCACCGGAAGGT
*
21151 GTTGTTTAGT-TCTCCTAGTTTGCCCTTCCCCAC
131 GTTGTTTAGTAT-TCCCAGTTTGCCCTTCCCCAC
* * *
21184 CGGAAGGTGTTATCTAGTTGTCAAATTACCAGTTTGTCCTTCCCCATCGGAAGGTGTTGTCTAGT
1 CGGAAGGTGTTGTTTAGTTGTCAAATTACCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGT
* *
21249 TTCTCAGTCTGCCCTTCCCCATCGGAAGGTGTTGTTTACCAGTTTGCCCTTCCCTATCGGAAGGT
66 TTCTCAGTCTGCCCTTCCCCATCGGAAGGTGTTGTTTACCAGTTTGCCCTTCCCCACCGGAAGGT
*
21314 GTTGTTTAGTATTCCCAGTTTGCCCTTCCTCAC
131 GTTGTTTAGTATTCCCAGTTTGCCCTTCCCCAC
* *
21347 CGGAAGGTGTTGTTTAGTTGTCAAATTACCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAGT
1 CGGAAGGTGTTGTTTAGTTGTCAAATTACCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGT
21412 T
66 T
21413 GCCAACTTCA
Statistics
Matches: 215, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
163 214 1.00
164 1 0.00
ACGTcount: A:0.16, C:0.26, G:0.22, T:0.35
Consensus pattern (163 bp):
CGGAAGGTGTTGTTTAGTTGTCAAATTACCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAGT
TTCTCAGTCTGCCCTTCCCCATCGGAAGGTGTTGTTTACCAGTTTGCCCTTCCCCACCGGAAGGT
GTTGTTTAGTATTCCCAGTTTGCCCTTCCCCAC
Found at i:27175 original size:6 final size:6
Alignment explanation
Indices: 27164--27195 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
27154 ATTAATCTGC
27164 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
27196 GCTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:31627 original size:48 final size:48
Alignment explanation
Indices: 31556--31648 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
31546 GAGATACCCA
31556 CTAATAATTGTTTTCCATGCCAACTTATATTGTGGAAAACCCTTGAGT
1 CTAATAATTGTTTTCCATGCCAACTTATATTGTGGAAAACCCTTGAGT
31604 CTAATAATTGTTTTCCATGCCAACTTATATTGTGGAAAACCCTTG
1 CTAATAATTGTTTTCCATGCCAACTTATATTGTGGAAAACCCTTG
31649 CTCTCAAGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (48 bp):
CTAATAATTGTTTTCCATGCCAACTTATATTGTGGAAAACCCTTGAGT
Done.