Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009012.1 Corchorus capsularis cultivar CVL-1 contig09033, 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: 57857
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:4163 original size:30 final size:32
Alignment explanation
Indices: 4118--4183 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
4108 TGGCAATTTA
*
4118 GAAATATGTTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
*
4149 GAAATATG-TTTTAAAAATAAGGGTATAATCG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
4180 GAAA
1 GAAA
4184 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (32 bp):
GAAATATGTTTTTAAAAATAAGGGTACAATCG
Found at i:7582 original size:19 final size:19
Alignment explanation
Indices: 7529--7605 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 19
7519 TATCTCAGGC
7529 AAGGAGAGGAACG-GGAAAGA
1 AAGGAGAGGAA-GAGG-AAGA
* *
7549 GAGGAG-GGACCGAGGAAGA
1 AAGGAGAGGA-AGAGGAAGA
* *
7568 AAGGAGAGGAAGAGGGAGG
1 AAGGAGAGGAAGAGGAAGA
* *
7587 AAGGAGGGGAAGAGAAAGA
1 AAGGAGAGGAAGAGGAAGA
7606 GGAAGGCCCG
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
19 34 0.77
20 10 0.23
ACGTcount: A:0.45, C:0.04, G:0.51, T:0.00
Consensus pattern (19 bp):
AAGGAGAGGAAGAGGAAGA
Found at i:9986 original size:18 final size:20
Alignment explanation
Indices: 9955--9993 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9945 TAAAAAACAG
9955 TTTTTTTGCTTTTTTG-TTTT
1 TTTTTTTGC-TTTTTGCTTTT
9975 TTTTTTTG-TTTTTGCTTTT
1 TTTTTTTGCTTTTTGCTTTT
9994 CTTTGAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (20 bp):
TTTTTTTGCTTTTTGCTTTT
Found at i:18193 original size:2 final size:2
Alignment explanation
Indices: 18186--18257 Score: 108
Period size: 2 Copynumber: 36.0 Consensus size: 2
18176 ATACAATGAC
* * *
18186 AT AT AT AT AT AT AT AT AT AT AC AT GT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
18228 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18258 GAGTGAAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20900 original size:5 final size:5
Alignment explanation
Indices: 20890--20924 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
20880 TCAAGTTTTT
* *
20890 AAAGG AAAGG AAGGG AAAGG AAAGG AAAGG GAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
20925 GAAGCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:20910 original size:15 final size:16
Alignment explanation
Indices: 20890--20927 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
20880 TCAAGTTTTT
20890 AAAGGAAAGG-AAGGG
1 AAAGGAAAGGAAAGGG
20905 AAAGGAAAGGAAAGGG
1 AAAGGAAAGGAAAGGG
*
20921 AAGGGAA
1 AAAGGAA
20928 GCTTTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (16 bp):
AAAGGAAAGGAAAGGG
Found at i:26187 original size:11 final size:12
Alignment explanation
Indices: 26148--26204 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
26138 AGGCACGCCA
*
26148 TTTTTTCTTTTA
1 TTTTTTCTTTTC
* *
26160 ATTTTCCTTTCTC
1 TTTTTTCTTT-TC
26173 TTTTTT-TTTTC
1 TTTTTTCTTTTC
*
26184 TTTTTTCTTTTG
1 TTTTTTCTTTTC
*
26196 TATTTTCTT
1 TTTTTTCTT
26205 CCACTTAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
11 8 0.22
12 23 0.64
13 5 0.14
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:33604 original size:92 final size:92
Alignment explanation
Indices: 33443--33632 Score: 373
Period size: 92 Copynumber: 2.1 Consensus size: 92
33433 GCAAAAGATA
33443 ATTC-TAAGCAATCGAGATGACTTGCATTTGTTTGAATCACTTAGCATAAAAATGTACATAAAAG
1 ATTCATAAGCAATCGAGATGACTTGCATTTGTTTGAATCACTTAGCATAAAAATGTACATAAAAG
33507 TGAACAAACATAAGAGCTAACAGACTT
66 TGAACAAACATAAGAGCTAACAGACTT
33534 ATTCATAAGCAATCGAGATGACTTGCATTTGTTTGAATCACTTAGCATAAAAATGTACATAAAAG
1 ATTCATAAGCAATCGAGATGACTTGCATTTGTTTGAATCACTTAGCATAAAAATGTACATAAAAG
33599 TGAACAAACATAAGAGCTAACAGACTT
66 TGAACAAACATAAGAGCTAACAGACTT
33626 ATTCATA
1 ATTCATA
33633 CCATAACAGC
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 4 0.04
92 94 0.96
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (92 bp):
ATTCATAAGCAATCGAGATGACTTGCATTTGTTTGAATCACTTAGCATAAAAATGTACATAAAAG
TGAACAAACATAAGAGCTAACAGACTT
Found at i:41296 original size:20 final size:20
Alignment explanation
Indices: 41271--41310 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41261 CAATTAATTT
41271 GATCAAATAAAATTAACACA
1 GATCAAATAAAATTAACACA
*
41291 GATCAACTAAAATTAACACA
1 GATCAAATAAAATTAACACA
41311 CAAATAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.20
Consensus pattern (20 bp):
GATCAAATAAAATTAACACA
Found at i:43322 original size:17 final size:17
Alignment explanation
Indices: 43300--43333 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43290 CCGCTGGCCC
*
43300 TCAGTTGGCCATGCGAA
1 TCAGTTGGCCATACGAA
43317 TCAGTTGGCCATACGAA
1 TCAGTTGGCCATACGAA
43334 AGAAGTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (17 bp):
TCAGTTGGCCATACGAA
Found at i:43702 original size:2 final size:2
Alignment explanation
Indices: 43697--43723 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43687 AAAGTAAAAA
43697 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
43724 GAAAAATTAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43956 original size:19 final size:19
Alignment explanation
Indices: 43932--43994 Score: 83
Period size: 19 Copynumber: 3.2 Consensus size: 19
43922 GAAAAAAAGA
*
43932 AATATAGTATATATAAT-AT
1 AATATAATATA-ATAATAAT
43951 AATATAATATAATAATAAT
1 AATATAATATAATAATAAT
43970 AATAATAATAATAATAATAAT
1 AAT-ATAAT-ATAATAATAAT
43991 AATA
1 AATA
43995 ATAACAACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 5 0.12
19 15 0.38
20 6 0.15
21 14 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AATATAATATAATAATAAT
Found at i:43967 original size:3 final size:3
Alignment explanation
Indices: 43944--43998 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
43934 TATAGTATAT
43944 ATA AT- ATA AT- ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
43989 ATA ATA ATA A
1 ATA ATA ATA A
43999 CAACAACAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.12
3 43 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:44387 original size:7 final size:7
Alignment explanation
Indices: 44375--44407 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
44365 TAAAAACCTT
44375 TTTTTTC
1 TTTTTTC
44382 TTTTTTC
1 TTTTTTC
44389 TTTTTTTC
1 -TTTTTTC
44397 TTTTTT-
1 TTTTTTC
44403 TTTTT
1 TTTTT
44408 GTAAAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 5 0.20
7 13 0.52
8 7 0.28
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTC
Found at i:44387 original size:8 final size:8
Alignment explanation
Indices: 44374--44407 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
44364 TTAAAAACCT
44374 TTTTTTTC
1 TTTTTTTC
44382 -TTTTTTC
1 TTTTTTTC
44389 TTTTTTTC
1 TTTTTTTC
44397 TTTTTTT-
1 TTTTTTTC
44404 TTTT
1 TTTT
44408 GTAAAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTTTTC
Found at i:44394 original size:15 final size:14
Alignment explanation
Indices: 44373--44407 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
44363 ATTAAAAACC
44373 TTTTTTTTCTTTTT
1 TTTTTTTTCTTTTT
44387 TCTTTTTTTCTTTTT
1 T-TTTTTTTCTTTTT
44402 TTTTTT
1 TTTTTT
44408 GTAAAATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTTTCTTTTT
Found at i:46422 original size:2 final size:2
Alignment explanation
Indices: 46417--46447 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46407 AAATGGATGA
46417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46448 ATAGTACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48472 original size:31 final size:31
Alignment explanation
Indices: 48404--48565 Score: 155
Period size: 31 Copynumber: 5.5 Consensus size: 31
48394 TCATTTTGTG
* * **
48404 CACGTGGCATGCCACGTGCCA-TTTTTGAAA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
48434 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
48465 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
*
48496 CA--T---GTGGCAC--G--ACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
48518 CATGTGGCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
48549 CACGTGGCGTGCCACGT
1 CACGTGGCGTGCCACGT
48566 CGGACACCGT
Statistics
Matches: 109, Mismatches: 13, Indels: 19
0.77 0.09 0.13
Matches are distributed among these distances:
22 13 0.12
24 2 0.02
26 5 0.05
27 6 0.06
29 2 0.02
30 19 0.17
31 62 0.57
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.32
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:48516 original size:53 final size:53
Alignment explanation
Indices: 48454--48556 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
48444 GCCACGTGTC
** *
48454 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
48507 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
48557 GTGCCACGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:50942 original size:16 final size:16
Alignment explanation
Indices: 50921--50952 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
50911 TATAAATTGT
*
50921 TATTTCCTTGTTAGTA
1 TATTTCCTTGTAAGTA
50937 TATTTCCTTGTAAGTA
1 TATTTCCTTGTAAGTA
50953 ATAAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (16 bp):
TATTTCCTTGTAAGTA
Found at i:51820 original size:30 final size:30
Alignment explanation
Indices: 51786--51846 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
51776 GTTGGCGACT
51786 TCTCTGCATTATCTACTATGCTTGTACTTG
1 TCTCTGCATTATCTACTATGCTTGTACTTG
*
51816 TCTCTGCATTATCTACTATGGTTGTACTTG
1 TCTCTGCATTATCTACTATGCTTGTACTTG
51846 T
1 T
51847 AGACGTACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.48
Consensus pattern (30 bp):
TCTCTGCATTATCTACTATGCTTGTACTTG
Done.