Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015730.1 Corchorus olitorius cultivar O-4 contig15763, 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: 33523
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:183 original size:105 final size:105
Alignment explanation
Indices: 9--284 Score: 502
Period size: 105 Copynumber: 2.6 Consensus size: 105
1 TAATAATT
* *
9 TATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
1 TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
*
74 ATTTTATTTTTATTTTAAGGGTAAATTGCATAATTAATAA
66 ATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAA
114 TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
1 TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
179 ATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAA
66 ATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAA
*
219 TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAG-CCCACATTAAA
1 TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
282 ATT
66 ATT
285 AAATGATGTA
Statistics
Matches: 167, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
103 13 0.08
104 14 0.08
105 140 0.84
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (105 bp):
TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
ATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAA
Found at i:11023 original size:33 final size:34
Alignment explanation
Indices: 10984--11052 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
10974 CTAAACAAAT
10984 AAAGAGTCTAC-AAAGAGGTTTACTAATAAAAAC
1 AAAGAGTCTACAAAAGAGGTTTACTAATAAAAAC
11017 AAAGAGTCTACAAAAGAGGTTTACTAATAAAAAC
1 AAAGAGTCTACAAAAGAGGTTTACTAATAAAAAC
11051 AA
1 AA
11053 TTACATTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 11 0.31
34 24 0.69
ACGTcount: A:0.54, C:0.12, G:0.14, T:0.20
Consensus pattern (34 bp):
AAAGAGTCTACAAAAGAGGTTTACTAATAAAAAC
Found at i:11165 original size:24 final size:24
Alignment explanation
Indices: 11112--11177 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
11102 AAATGTCTGG
*
11112 AAAA-AAGAAAAGATTTTAAGAAGA
1 AAAAGAAGAAAA-ATTTTAAGAAAA
*
11136 AGAAGAAGAAAAATTTTGAA-AAAA
1 AAAAGAAGAAAAATTTT-AAGAAAA
* *
11160 AAAAGATGAAACATTTTA
1 AAAAGAAGAAAAATTTTA
11178 TACTAGGTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 25 0.71
25 9 0.26
ACGTcount: A:0.64, C:0.02, G:0.15, T:0.20
Consensus pattern (24 bp):
AAAAGAAGAAAAATTTTAAGAAAA
Found at i:12197 original size:26 final size:25
Alignment explanation
Indices: 12168--12217 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
12158 AGTAATCAGT
* * *
12168 TTTTATTTTATATATATAAGTATATA
1 TTTTATTATAAATAT-TAAATATATA
12194 TTTTATTATAAATATTAAATATAT
1 TTTTATTATAAATATTAAATATAT
12218 TTAAGATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTATTATAAATATTAAATATATA
Found at i:12233 original size:7 final size:7
Alignment explanation
Indices: 12223--12252 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12213 TATATTTAAG
12223 ATATATT
1 ATATATT
12230 ATATA-T
1 ATATATT
12236 ATATATT
1 ATATATT
12243 ATATATT
1 ATATATT
12250 ATA
1 ATA
12253 CATATACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
ATATATT
Found at i:12245 original size:9 final size:9
Alignment explanation
Indices: 12105--12257 Score: 67
Period size: 9 Copynumber: 17.3 Consensus size: 9
12095 ATATATATTT
*
12105 TATTATAAA
1 TATTATATA
*
12114 TATTAAATA
1 TATTATATA
12123 TATT-TA-A
1 TATTATATA
*
12130 GA-TATATA
1 TATTATATA
12138 TATTATATA
1 TATTATATA
12147 TA-T-TATA
1 TATTATATA
12154 TATTAGTA-A
1 TATTA-TATA
*
12163 TCAGTT-TTTA
1 T-A-TTATATA
*
12173 TTTTATATA
1 TATTATATA
12182 TA-TA-AGTA
1 TATTATA-TA
*
12190 TA-TAT-TT
1 TATTATATA
*
12197 TATTATAAA
1 TATTATATA
*
12206 TATTAAATA
1 TATTATATA
*
12215 TATTTAAGATA
1 TA-TT-ATATA
12226 TATTATATA
1 TATTATATA
12235 TATATATTATA
1 TAT-TA-TATA
*
12246 TATTATACA
1 TATTATATA
12255 TAT
1 TAT
12258 ACATGTATTG
Statistics
Matches: 109, Mismatches: 17, Indels: 36
0.67 0.10 0.22
Matches are distributed among these distances:
6 1 0.01
7 14 0.13
8 18 0.17
9 48 0.44
10 13 0.12
11 15 0.14
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (9 bp):
TATTATATA
Found at i:15361 original size:27 final size:28
Alignment explanation
Indices: 15314--15388 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
15304 CCCTGATTGG
*
15314 TAAAATTA-CGATTTTACCCCTATCATAAA
1 TAAAATTACCG-TTTT-GCCCTATCATAAA
* * **
15343 -AAAATTACTGTTTTGCCCTTTGTTAAA
1 TAAAATTACCGTTTTGCCCTATCATAAA
15370 TAAAATTACCGTTTTGCCC
1 TAAAATTACCGTTTTGCCC
15389 CTGTAGACCT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 9 0.24
28 28 0.74
29 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (28 bp):
TAAAATTACCGTTTTGCCCTATCATAAA
Found at i:21379 original size:247 final size:247
Alignment explanation
Indices: 20942--21437 Score: 866
Period size: 247 Copynumber: 2.0 Consensus size: 247
20932 TCAAATATGG
20942 ATCTTCAATGATTCAAGCTTCCTTCAAGGCTTAATGGGCTCCAATGGGCTCACTGGGCTAAAAAT
1 ATCTTCAATGATTCAAGCTTCCTTCAAGGCTTAATGGGCTCCAATGGGCTCACTGGGCTAAAAAT
* *
21007 GGCCAAAATCAGTAGTTTCTCCAAATTGATCCAAAATCGCTCCAAATCTCCATAATCTTAACTAA
66 GGCCAAAATCAGTAATTTCTCCAAATTGATCCAAAATCGCTCCAAATCTCCATAATCTTAAATAA
* * * *
21072 TGGCTCTAAATGGTCCTGAAAACAGAAATATGAGAAATATGAGGGTAAATAGATACTTATGACTA
131 TGACTCTAAATGGTCCTGAAAACACAAATATGAGAAATATGAGGATAAATAGAAACTTATGACTA
*
21137 CCAAAACAAGGCAAAATCATATAAAAAATAAGCATTAAATTAGGTCTTATCA
196 CCAAAACAAGACAAAATCATATAAAAAATAAGCATTAAATTAGGTCTTATCA
*
21189 ATCTTCAATGATTCAAGCTTCCTTCAGGGCTTAATGGGCTCCAATGGGCTCACTGGGCTAAAAAT
1 ATCTTCAATGATTCAAGCTTCCTTCAAGGCTTAATGGGCTCCAATGGGCTCACTGGGCTAAAAAT
* * *
21254 GGCCAAAATCAGTAATTTCTCCAAATTGATCCAAAATTGCTTCAAATCTTCATAATCTTAAATAA
66 GGCCAAAATCAGTAATTTCTCCAAATTGATCCAAAATCGCTCCAAATCTCCATAATCTTAAATAA
* *
21319 TGACTCTATATGGTCCTGAAAACACAAATATGAGAAATATGAGGATAACTAGAAACTTATGACTA
131 TGACTCTAAATGGTCCTGAAAACACAAATATGAGAAATATGAGGATAAATAGAAACTTATGACTA
*
21384 CCAAAACAAGACAAAATCATATAGAAAATAAGCATTAAATTAGGTCTTATCA
196 CCAAAACAAGACAAAATCATATAAAAAATAAGCATTAAATTAGGTCTTATCA
21436 AT
1 AT
21438 TCAATATATT
Statistics
Matches: 235, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
247 235 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (247 bp):
ATCTTCAATGATTCAAGCTTCCTTCAAGGCTTAATGGGCTCCAATGGGCTCACTGGGCTAAAAAT
GGCCAAAATCAGTAATTTCTCCAAATTGATCCAAAATCGCTCCAAATCTCCATAATCTTAAATAA
TGACTCTAAATGGTCCTGAAAACACAAATATGAGAAATATGAGGATAAATAGAAACTTATGACTA
CCAAAACAAGACAAAATCATATAAAAAATAAGCATTAAATTAGGTCTTATCA
Found at i:21841 original size:19 final size:19
Alignment explanation
Indices: 21817--21855 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21807 TTCATTTTCT
21817 AACTCTCAAAACTTCTTCA
1 AACTCTCAAAACTTCTTCA
*
21836 AACTCTCTAAACTTCTTCA
1 AACTCTCAAAACTTCTTCA
21855 A
1 A
21856 GAACATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (19 bp):
AACTCTCAAAACTTCTTCA
Found at i:22235 original size:17 final size:17
Alignment explanation
Indices: 22213--22245 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22203 TTATTATTTG
22213 ACTATAATTAATTATTC
1 ACTATAATTAATTATTC
*
22230 ACTATAATTATTTATT
1 ACTATAATTAATTATT
22246 ATTGTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
ACTATAATTAATTATTC
Found at i:26193 original size:19 final size:19
Alignment explanation
Indices: 26171--26225 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
26161 ATATGAATAC
26171 ATTAATAAATAATAATAAA
1 ATTAATAAATAATAATAAA
* **
26190 ATTAAT-AATAAATATTACG
1 ATTAATAAAT-AATAATAAA
*
26209 ACTAATAAATAATAATA
1 ATTAATAAATAATAATA
26226 CCACCTGATG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 3 0.10
19 23 0.79
20 3 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
ATTAATAAATAATAATAAA
Found at i:28697 original size:56 final size:56
Alignment explanation
Indices: 28625--28738 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
28615 TTTATTTTAT
* *
28625 AGAATAATTAAGTAGAGATATGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
28681 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
28737 AG
1 AG
28739 GAAATGGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
Found at i:31491 original size:69 final size:71
Alignment explanation
Indices: 31374--31513 Score: 194
Period size: 70 Copynumber: 2.0 Consensus size: 71
31364 AAGGCTGCGC
*
31374 ATTTAAGGCATAATTCTTTTTTTAACTGTGAATGATAAAGATGGAAA-TTTTATTAAATGTGCAT
1 ATTTAAGGCATAATTCTTTTTTTAACTGAGAATGATAAAGATGGAAATTTTTATTAAATGTGCAT
*
31438 TGGGGT
66 TAGGGT
* * * * * *
31444 ATTTAAGGCATAATTC-TTTTTTGATTGAGAATGATGAATATGGAAATTTTTATTGATTGTGCAT
1 ATTTAAGGCATAATTCTTTTTTTAACTGAGAATGATAAAGATGGAAATTTTTATTAAATGTGCAT
31508 TAGGGT
66 TAGGGT
31514 TGGAGGGGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 25 0.41
70 36 0.59
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (71 bp):
ATTTAAGGCATAATTCTTTTTTTAACTGAGAATGATAAAGATGGAAATTTTTATTAAATGTGCAT
TAGGGT
Done.