Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007471.1 Corchorus capsularis cultivar CVL-1 contig07492, 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: 54547
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:1476 original size:7 final size:8
Alignment explanation
Indices: 1445--1479 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1435 CCCGCAAAGT
1445 TACAAAAA
1 TACAAAAA
*
1453 GAACAAAAA
1 -TACAAAAA
1462 TACAAAAA
1 TACAAAAA
1470 TACAAAAA
1 TACAAAAA
1478 TA
1 TA
1480 AAGTAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.11
Consensus pattern (8 bp):
TACAAAAA
Found at i:6888 original size:140 final size:140
Alignment explanation
Indices: 6717--6996 Score: 515
Period size: 140 Copynumber: 2.0 Consensus size: 140
6707 CGGGGTGGTG
*
6717 CAACAGTTTCTGGAAGGATTGGTCCAAGACCTGATGACATCCCTAGTGGCTTGGCACTTATTCAT
1 CAACAGTTTCTGGAAGGATTGGTCCAAGACCTGATGACATCCCTAGTGGCTTGCCACTTATTCAT
*
6782 GATATCTGGTACTTTATTGATTTTATTACTGAATTGAGTTTGCCTAACTTTTCTCACTTTCGAAT
66 GATATCTGGTACTTTATTGATTTTATTACTGAATTGAGTTTGCCTAACTTTTCTCACTTTCAAAT
*
6847 GAATCTGAAA
131 AAATCTGAAA
* *
6857 CAACAGTTTCTGGAAGGATTGGTCCAAGACCTGATGACATCTCTAGTGGCTTGCCGCTTATTCAT
1 CAACAGTTTCTGGAAGGATTGGTCCAAGACCTGATGACATCCCTAGTGGCTTGCCACTTATTCAT
6922 GATATCTGGTACTTTATTGATTTTATTACTGAATTGAGTTTGCCTAACTTTTCTCACTTTCAAAT
66 GATATCTGGTACTTTATTGATTTTATTACTGAATTGAGTTTGCCTAACTTTTCTCACTTTCAAAT
6987 AAATCTGAAA
131 AAATCTGAAA
6997 TAGCATGAGA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (140 bp):
CAACAGTTTCTGGAAGGATTGGTCCAAGACCTGATGACATCCCTAGTGGCTTGCCACTTATTCAT
GATATCTGGTACTTTATTGATTTTATTACTGAATTGAGTTTGCCTAACTTTTCTCACTTTCAAAT
AAATCTGAAA
Found at i:17036 original size:39 final size:40
Alignment explanation
Indices: 16993--17100 Score: 141
Period size: 39 Copynumber: 2.8 Consensus size: 40
16983 TCTCTCTCCC
* *
16993 CAAAGTCCCCAAACACATATAACATAGGGGCAACTAT-CT
1 CAAAGTCCCCAAACACATATAACACAGAGGCAACTATACT
* *
17032 CAAAGTCCTCAAACACATATAACACAGAGGCATCTATACT
1 CAAAGTCCCCAAACACATATAACACAGAGGCAACTATACT
* *
17072 -AAAGTCTCTAAACACATATAACACA-AGGC
1 CAAAGTCCCCAAACACATATAACACAGAGGC
17101 CAATTTTCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 4 0.07
39 55 0.90
40 2 0.03
ACGTcount: A:0.44, C:0.27, G:0.11, T:0.19
Consensus pattern (40 bp):
CAAAGTCCCCAAACACATATAACACAGAGGCAACTATACT
Found at i:17939 original size:21 final size:20
Alignment explanation
Indices: 17915--17964 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
17905 GCTCCATACA
17915 AAGAATCACAATACAT-ATATC
1 AAGAATCACAAT-C-TCATATC
*
17936 AAGAACCACAATCTCCATATC
1 AAGAATCACAATCT-CATATC
17957 AAGAATCA
1 AAGAATCA
17965 TCATCATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 23 0.92
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.20
Consensus pattern (20 bp):
AAGAATCACAATCTCATATC
Found at i:20954 original size:21 final size:21
Alignment explanation
Indices: 20928--20969 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20918 CCTAGAAAAA
20928 CTAATGCTTAGGTAGCTTAGG
1 CTAATGCTTAGGTAGCTTAGG
20949 CTAATGCTTAGGTAGCTTAGG
1 CTAATGCTTAGGTAGCTTAGG
20970 GTTTTCTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (21 bp):
CTAATGCTTAGGTAGCTTAGG
Found at i:22426 original size:26 final size:25
Alignment explanation
Indices: 22382--22430 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
22372 ATGATTTAGG
*
22382 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACTCCCATTTT-TTTTGA
22408 GGTTACTAAC-CCTCATTTTTTTT
1 GGTTACTAACTCC-CATTTTTTTT
22431 CTTTTTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.16, C:0.22, G:0.10, T:0.51
Consensus pattern (25 bp):
GGTTACTAACTCCCATTTTTTTTGA
Found at i:24284 original size:35 final size:34
Alignment explanation
Indices: 24245--24329 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 34
24235 ATTTCATCAG
*
24245 ATTCAACACTTGGGGACTCCAACAACCCCTTCATC
1 ATTCAACACTTGGGG-CTCCAACAACCCATTCATC
* * * *
24280 ATTCAACAATTGGGTGCTCCAGCAACTCATTCTTC
1 ATTCAACACTTGGG-GCTCCAACAACCCATTCATC
24315 ATTC-ACTACTTGGGG
1 ATTCAAC-ACTTGGGG
24330 GCTTCAATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
34 3 0.07
35 38 0.90
36 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (34 bp):
ATTCAACACTTGGGGCTCCAACAACCCATTCATC
Found at i:29423 original size:30 final size:32
Alignment explanation
Indices: 29389--29454 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
29379 TTTAATAATA
*
29389 AAAGAAAGGTAG-G-AGGAGATTATGCATGAT
1 AAAGAAAGGTAGAGAAGGAGATCATGCATGAT
29419 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
1 AAAGAAAGGTAG-AGAAGGAGATCATGCATGAT
29452 AAA
1 AAA
29455 TAACTTTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 12 0.38
32 1 0.03
33 19 0.59
ACGTcount: A:0.48, C:0.05, G:0.30, T:0.17
Consensus pattern (32 bp):
AAAGAAAGGTAGAGAAGGAGATCATGCATGAT
Found at i:30390 original size:39 final size:39
Alignment explanation
Indices: 30347--30422 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
30337 AATCATGGTC
*
30347 AGATCCGACAGAGAGAGCAGCAAATCGGCATCCTCTAGT
1 AGATCCGACAGAGAGAGCAGCAAATCGACATCCTCTAGT
* * * *
30386 AGATCTGACAGTGAGAGCAGCGAATCTACATCCTCTA
1 AGATCCGACAGAGAGAGCAGCAAATCGACATCCTCTA
30423 TCAGCCAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (39 bp):
AGATCCGACAGAGAGAGCAGCAAATCGACATCCTCTAGT
Found at i:30751 original size:90 final size:90
Alignment explanation
Indices: 30598--30767 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 90
30588 GGGAAAAGTC
* *
30598 GAGATGTAGCCACTGCCAAAAGATGGGGCATACCAAGGACCGATGTTATGAAATCCTTGGATATC
1 GAGATGTAGCCACTGCCAAAAGATAGGGCATACCAAGGACCGATGTTATAAAATCCTTGGATATC
* *
30663 CTGTGGTGTGGCGTATAACCCAGTT
66 CTGCGGGGTGGCGTATAACCCAGTT
* *
30688 GAGATGTGGCCACTGCCAGAAGATAGGGCATACCAAGGACCGATGTTATAAAATCCTTGGATATC
1 GAGATGTAGCCACTGCCAAAAGATAGGGCATACCAAGGACCGATGTTATAAAATCCTTGGATATC
30753 CTGCGGGGTGGCGTA
66 CTGCGGGGTGGCGTA
30768 AAAACCTGCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (90 bp):
GAGATGTAGCCACTGCCAAAAGATAGGGCATACCAAGGACCGATGTTATAAAATCCTTGGATATC
CTGCGGGGTGGCGTATAACCCAGTT
Found at i:33340 original size:21 final size:21
Alignment explanation
Indices: 33314--33362 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
33304 TTGCTGGGGG
* * *
33314 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
33335 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
33356 CCCATGT
1 CCCATGT
33363 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:46141 original size:22 final size:22
Alignment explanation
Indices: 46115--46168 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
46105 ACTCTTTATC
46115 TTTTATTTTTCGTTATT-TTCCT
1 TTTTATTTTTCGTT-TTGTTCCT
**
46137 TTTTATTTTTCGTTTTGTTTGT
1 TTTTATTTTTCGTTTTGTTCCT
46159 TTTTATTTTT
1 TTTTATTTTT
46169 ATTTTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (22 bp):
TTTTATTTTTCGTTTTGTTCCT
Found at i:47343 original size:21 final size:22
Alignment explanation
Indices: 47304--47344 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
47294 TCAATGCATT
**
47304 AGGAATGCAAGAGGGATTTCAA
1 AGGAATGCAAGAGCCATTTCAA
47326 AGGAA-GCAAGAGCCATTTC
1 AGGAATGCAAGAGCCATTTC
47345 CAAGAAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (22 bp):
AGGAATGCAAGAGCCATTTCAA
Found at i:49864 original size:22 final size:20
Alignment explanation
Indices: 49831--49875 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
49821 CTTCTATTAC
49831 CTTTATTCTCAAATTCACTCA
1 CTTTATTCTCAAATTCACT-A
* *
49852 CTTTGATTTTCAATTTCACTA
1 CTTT-ATTCTCAAATTCACTA
49873 CTT
1 CTT
49876 CATCACATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.49
Consensus pattern (20 bp):
CTTTATTCTCAAATTCACTA
Found at i:50430 original size:128 final size:128
Alignment explanation
Indices: 50198--50432 Score: 443
Period size: 128 Copynumber: 1.8 Consensus size: 128
50188 GAGCATCAAC
50198 GTCACAAGCCGCACCAATTGAGGAGGACAATGTCGCTCAACCATTCCTTAATGTGCCGCCACCTA
1 GTCACAAGCCGCACCAATTGAGGAGGACAATGTCGCTCAACCATTCCTTAATGTGCCGCCACCTA
50263 TTTTTGTTGACAATGATTGTCAAGAGTGGTATGAAGCAAGGTGTGAAGCAAGGTATAATGATT
66 TTTTTGTTGACAATGATTGTCAAGAGTGGTATGAAGCAAGGTGTGAAGCAAGGTATAATGATT
* *
50326 GTCACAAGTCGCACCAATTGAGGAGGACAATGTCGCTCAACCATTCCTTAATGTGTCGCCACCTA
1 GTCACAAGCCGCACCAATTGAGGAGGACAATGTCGCTCAACCATTCCTTAATGTGCCGCCACCTA
*
50391 TTTTTGTTGACAATGATTGTCAAGAGTGGTATGACGCAAGGT
66 TTTTTGTTGACAATGATTGTCAAGAGTGGTATGAAGCAAGGT
50433 ATAATAATTC
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 104 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (128 bp):
GTCACAAGCCGCACCAATTGAGGAGGACAATGTCGCTCAACCATTCCTTAATGTGCCGCCACCTA
TTTTTGTTGACAATGATTGTCAAGAGTGGTATGAAGCAAGGTGTGAAGCAAGGTATAATGATT
Done.