Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016634.1 Corchorus olitorius cultivar O-4 contig16667, 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: 44514
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:10224 original size:63 final size:64
Alignment explanation
Indices: 10125--10252 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 64
10115 TTACTTAATT
* *
10125 TTACCAAAACTAGTAAAATCTTTTATGGTAAGTACATTGACTCTTGGATCCCGGT-GGGGCAGC
1 TTACCAAAACTAGTAAAATCTTTTATGGTAAATACATTGACTCTTGGATCCCAGTGGGGGCAGC
10188 TTACCAAAACTAGTAAAATCTTTTATGGTAAATACATTGACTCTTGGATCCCAGTGGGGGCAGC
1 TTACCAAAACTAGTAAAATCTTTTATGGTAAATACATTGACTCTTGGATCCCAGTGGGGGCAGC
10252 T
1 T
10253 GCCCCCACCG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 53 0.85
64 9 0.15
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (64 bp):
TTACCAAAACTAGTAAAATCTTTTATGGTAAATACATTGACTCTTGGATCCCAGTGGGGGCAGC
Found at i:15555 original size:6 final size:6
Alignment explanation
Indices: 15506--15568 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
15496 CAAGAGGAGG
* * * *
15506 AGAAGA AGAAGA AGAAGA AGAAATA AGGAAA AGAAAA GAGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAA-A AGAAAA AGAAAA -AGAAAA AGAAAA
* *
15556 ATAAAA ATAAAA A
1 AGAAAA AGAAAA A
15569 TAAAGGATAC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
6 40 0.78
7 11 0.22
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.05
Consensus pattern (6 bp):
AGAAAA
Found at i:15561 original size:12 final size:12
Alignment explanation
Indices: 15534--15572 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
15524 AGAAATAAGG
*
15534 AAAAGAAAAGAGA
1 AAAAGAAAA-ATA
15547 AAAAGAAAAATA
1 AAAAGAAAAATA
*
15559 AAAATAAAAATA
1 AAAAGAAAAATA
15571 AA
1 AA
15573 GGATACGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (12 bp):
AAAAGAAAAATA
Found at i:15798 original size:29 final size:31
Alignment explanation
Indices: 15756--15814 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
15746 GTAACGTAAA
15756 GAATTAATTTGTCCC-AAA-AAAAACATAAG
1 GAATTAATTTGTCCCAAAACAAAAACATAAG
*
15785 GAATTATTTTGTCCCAAAACAAAAACATAA
1 GAATTAATTTGTCCCAAAACAAAAACATAA
15815 TGGATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.52
30 3 0.11
31 10 0.37
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.25
Consensus pattern (31 bp):
GAATTAATTTGTCCCAAAACAAAAACATAAG
Found at i:16860 original size:15 final size:15
Alignment explanation
Indices: 16840--16868 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16830 TACAATATTC
16840 TCGCGATCCTCAGGT
1 TCGCGATCCTCAGGT
16855 TCGCGATCCTCAGG
1 TCGCGATCCTCAGG
16869 CTTCAGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (15 bp):
TCGCGATCCTCAGGT
Found at i:16981 original size:69 final size:69
Alignment explanation
Indices: 16865--17004 Score: 253
Period size: 69 Copynumber: 2.0 Consensus size: 69
16855 TCGCGATCCT
16865 CAGGCTTCAGATGAGATATGGCAGTCATGAATGACAGAGAGGATCGGATACTTGCAAGAAGTATA
1 CAGGCTTCAGATGAGATATGGCAGTCATGAATGACAGAGAGGATCGGATACTTGCAAGAAGTATA
16930 CTTA
66 CTTA
* * *
16934 CAGGTTTCAGATGAGATATGGCAGTCATGAATGACAGGGAGGATCGGATACTTGCAAGAAGTTTA
1 CAGGCTTCAGATGAGATATGGCAGTCATGAATGACAGAGAGGATCGGATACTTGCAAGAAGTATA
16999 CTTA
66 CTTA
17003 CA
1 CA
17005 AAATCGCTGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (69 bp):
CAGGCTTCAGATGAGATATGGCAGTCATGAATGACAGAGAGGATCGGATACTTGCAAGAAGTATA
CTTA
Found at i:17065 original size:36 final size:36
Alignment explanation
Indices: 17025--17098 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
17015 GCATAGGTGG
17025 CTCGGAAATAGGAGGCTTAGACACAATAGGAGACTC
1 CTCGGAAATAGGAGGCTTAGACACAATAGGAGACTC
* *
17061 CTCGGAAATAGGAGGCTTAGGCACAATGGGAGACTC
1 CTCGGAAATAGGAGGCTTAGACACAATAGGAGACTC
17097 CT
1 CT
17099 GAGACTCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (36 bp):
CTCGGAAATAGGAGGCTTAGACACAATAGGAGACTC
Found at i:21263 original size:8 final size:8
Alignment explanation
Indices: 21250--21299 Score: 73
Period size: 8 Copynumber: 6.0 Consensus size: 8
21240 TTATATTATA
21250 ATCTTACT
1 ATCTTACT
*
21258 ATCTTATT
1 ATCTTACT
21266 ATCTTATCTT
1 ATCTTA-C-T
21276 ATCTTACT
1 ATCTTACT
21284 ATCTTACT
1 ATCTTACT
21292 ATCTTACT
1 ATCTTACT
21300 TACTACTAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 30 0.79
9 1 0.03
10 7 0.18
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (8 bp):
ATCTTACT
Found at i:21283 original size:26 final size:25
Alignment explanation
Indices: 21250--21301 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
21240 TTATATTATA
*
21250 ATCTTACTATCTTATTATCTTATCTT
1 ATCTTACTATCTTACTATCTTA-CTT
21276 ATCTTACTATCTTACTATCTTACTT
1 ATCTTACTATCTTACTATCTTACTT
21301 A
1 A
21302 CTACTAGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (25 bp):
ATCTTACTATCTTACTATCTTACTT
Found at i:21913 original size:25 final size:24
Alignment explanation
Indices: 21885--21946 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
21875 GTGTATTGTA
*
21885 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
21910 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
21934 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
21947 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:24315 original size:15 final size:15
Alignment explanation
Indices: 24292--24321 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24282 TTTAAATGAA
24292 TTTTCTTTTTTTTCC
1 TTTTCTTTTTTTTCC
*
24307 TTTTGTTTTTTTTCC
1 TTTTCTTTTTTTTCC
24322 AAATTGTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTTTCC
Found at i:26003 original size:136 final size:136
Alignment explanation
Indices: 25826--26098 Score: 510
Period size: 136 Copynumber: 2.0 Consensus size: 136
25816 ACTAGACAAT
25826 TATGTTTTAAAGAATGTAACTAAATATACTTCTTACTAGAAAAAGATGTTACTATTATATCCATA
1 TATGTTTTAAAGAATGTAACTAAATATACTTCTTACTAGAAAAAGATGTTACTATTATATCCATA
* *
25891 ATATATATAAATCTTAAATAAATAATTTAATTGTTTTGACTTATATTAATTTAAGAAATAAAGTA
66 ATATATATAAATCTTAAATAAATAATTTAATTGTTCTGACTTATATTAATTTAAAAAATAAAGTA
25956 TATTAA
131 TATTAA
*
25962 TATGTTTTAAAGAATGTAGCTAAATATACTTCTTACTAGAAAAAGATGTTACTATTATATCCATA
1 TATGTTTTAAAGAATGTAACTAAATATACTTCTTACTAGAAAAAGATGTTACTATTATATCCATA
*
26027 ATATATATAAATCTTGAATAAATAATTTAATTGTTCTGACTTATATTAATTTAAAAAATAAAGTA
66 ATATATATAAATCTTAAATAAATAATTTAATTGTTCTGACTTATATTAATTTAAAAAATAAAGTA
26092 TATTAA
131 TATTAA
26098 T
1 T
26099 TAGTGCAATG
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 133 1.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (136 bp):
TATGTTTTAAAGAATGTAACTAAATATACTTCTTACTAGAAAAAGATGTTACTATTATATCCATA
ATATATATAAATCTTAAATAAATAATTTAATTGTTCTGACTTATATTAATTTAAAAAATAAAGTA
TATTAA
Found at i:26279 original size:60 final size:60
Alignment explanation
Indices: 26186--26349 Score: 179
Period size: 60 Copynumber: 2.7 Consensus size: 60
26176 TAATTTGATC
* ** * *
26186 ATGCTCAAATAAGTGCCCAACGTTTGTGAAAATGTTTAAATAAGGGCCCAAAGAAAAAAA
1 ATGCTCAAATAAGTGCCCAACATTTACGAAAATGCTCAAATAAGGGCCCAAAGAAAAAAA
* * *
26246 ATGCTCAAATCAG-GACCCAACATTTACGAAAATGCTCAAATAAGTGTCCAAAGAAAAAAA
1 ATGCTCAAATAAGTG-CCCAACATTTACGAAAATGCTCAAATAAGGGCCCAAAGAAAAAAA
* * * **
26306 AAGCTCAAATAAGGGTCCAATTTTTA-GAAAATTGCTCAAATAAG
1 ATGCTCAAATAAGTGCCCAACATTTACGAAAA-TGCTCAAATAAG
26350 CTTCTGCGGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 6 0.07
60 81 0.92
61 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (60 bp):
ATGCTCAAATAAGTGCCCAACATTTACGAAAATGCTCAAATAAGGGCCCAAAGAAAAAAA
Found at i:26323 original size:29 final size:29
Alignment explanation
Indices: 26214--26325 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 29
26204 AACGTTTGTG
* *
26214 AAAATGTTTAAATAAGGGCCCAAAGAAAA
1 AAAATGCTCAAATAAGGGCCCAAAGAAAA
* * ** **
26243 AAAATGCTCAAATCAGGACCCAACATTTACG
1 AAAATGCTCAAATAAGGGCCCAA-A-GAAAA
* *
26274 AAAATGCTCAAATAAGTGTCCAAAGAAAA
1 AAAATGCTCAAATAAGGGCCCAAAGAAAA
* *
26303 AAAAAGCTCAAATAAGGGTCCAA
1 AAAATGCTCAAATAAGGGCCCAA
26326 TTTTTAGAAA
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
29 41 0.65
30 2 0.03
31 20 0.32
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (29 bp):
AAAATGCTCAAATAAGGGCCCAAAGAAAA
Found at i:29308 original size:3 final size:3
Alignment explanation
Indices: 29300--29337 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
29290 CTCTTGTATA
29300 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29338 GATTTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:29714 original size:16 final size:15
Alignment explanation
Indices: 29693--29722 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29683 AATGGTGCTG
29693 ATGAACATATTATCAC
1 ATGAACATA-TATCAC
29709 ATGAACATATATCA
1 ATGAACATATATCA
29723 GAAGCTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (15 bp):
ATGAACATATATCAC
Found at i:31248 original size:54 final size:54
Alignment explanation
Indices: 31166--31274 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
31156 AATAGGAGGC
*
31166 TTACAATAATCTCGCTATCTTCAGGTTCGCGATCCTCAGGTTTCAGATGAGATA
1 TTACAATAATCTCGCGATCTTCAGGTTCGCGATCCTCAGGTTTCAGATGAGATA
*
31220 TTACAATATTCTCGCGATCTTCAGGTTCGCGATCCTCAGGTTTCAGATGAGATA
1 TTACAATAATCTCGCGATCTTCAGGTTCGCGATCCTCAGGTTTCAGATGAGATA
31274 T
1 T
31275 GGCAGTCATG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (54 bp):
TTACAATAATCTCGCGATCTTCAGGTTCGCGATCCTCAGGTTTCAGATGAGATA
Found at i:31251 original size:15 final size:15
Alignment explanation
Indices: 31231--31261 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31221 TACAATATTC
*
31231 TCGCGATCTTCAGGT
1 TCGCGATCCTCAGGT
31246 TCGCGATCCTCAGGT
1 TCGCGATCCTCAGGT
31261 T
1 T
31262 TCAGATGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.29, G:0.26, T:0.32
Consensus pattern (15 bp):
TCGCGATCCTCAGGT
Found at i:31367 original size:69 final size:69
Alignment explanation
Indices: 31256--31386 Score: 235
Period size: 69 Copynumber: 1.9 Consensus size: 69
31246 TCGCGATCCT
* *
31256 CAGGTTTCAGATGAGATATGGCAGTCATGAATGACAGAGAGGATCGGATAGTTGCAAGAAGTATA
1 CAGGTTTCAGATGAGATATGGCAATCATGAATGACAGAGAGGATCGGATACTTGCAAGAAGTATA
31321 CTTA
66 CTTA
*
31325 CAGGTTTCAGATGAGATATGGCAATCATGAATGACAGGGAGGATCGGATACTTGCAAGAAGT
1 CAGGTTTCAGATGAGATATGGCAATCATGAATGACAGAGAGGATCGGATACTTGCAAGAAGT
31387 TTAGCTGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.24
Consensus pattern (69 bp):
CAGGTTTCAGATGAGATATGGCAATCATGAATGACAGAGAGGATCGGATACTTGCAAGAAGTATA
CTTA
Found at i:32006 original size:23 final size:24
Alignment explanation
Indices: 31972--32017 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
31962 GGTTTTGATT
31972 ACAAAGGAACGGGTTGATCGATCA
1 ACAAAGGAACGGGTTGATCGATCA
31996 ACAAA-GAACGGGTTGATCGATC
1 ACAAAGGAACGGGTTGATCGATC
32018 GGTTAAGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (24 bp):
ACAAAGGAACGGGTTGATCGATCA
Found at i:33375 original size:32 final size:32
Alignment explanation
Indices: 33334--33394 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
33324 TTTTTTTTTT
*
33334 ATAACTTAATAATAATATATTAAGGAAAGAAA
1 ATAACTTAATAATAATATATTAAGCAAAGAAA
33366 ATAACTTAATAATAATATATTAAGCAAAG
1 ATAACTTAATAATAATATATTAAGCAAAG
33395 CAGCAGTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (32 bp):
ATAACTTAATAATAATATATTAAGCAAAGAAA
Found at i:39675 original size:7 final size:7
Alignment explanation
Indices: 39659--39688 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
39649 TGATCTATCC
39659 AAAA-AA
1 AAAAGAA
39665 AAAAGAA
1 AAAAGAA
39672 AAAAGAA
1 AAAAGAA
39679 AAAAGAA
1 AAAAGAA
39686 AAA
1 AAA
39689 TAGTAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Done.