Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013214.1 Corchorus capsularis cultivar CVL-1 contig13235, 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: 33777
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Found at i:29 original size:22 final size:22
Alignment explanation
Indices: 1--227 Score: 97
Period size: 22 Copynumber: 10.5 Consensus size: 22
1 AAAATTTCATAAGAGGGTTATC
1 AAAATTTCATAAGAGGGTTATC
* *
23 AAAATTTCAT-AGTA-TGTAGATC
1 AAAATTTCATAAG-AGGGT-TATC
*
45 AAAATTTCAT-AG-GGAGATTAAC
1 AAAATTTCATAAGAGG-G-TTATC
67 AAAATTTCATAATGA-GGTTATC
1 AAAATTTCATAA-GAGGGTTATC
*
89 AAAAAATT-AT-AG-GGAGCTTATC
1 -AAAATTTCATAAGAGG-G-TTATC
*
111 AAAA-TT--T-ACA--GTTATC
1 AAAATTTCATAAGAGGGTTATC
* **
127 AAGATTTCATAAGAAAGTTATC
1 AAAATTTCATAAGAGGGTTATC
* * *
149 AAAATTTTATAGAAAGGTTTATC
1 AAAATTTCATA-AGAGGGTTATC
* * **
172 AAAATTTTATAGGGAGATTTATC
1 AAAATTTCATA-AGAGGGTTATC
*
195 AAAATTTCATAACGA-GGTTATT
1 AAAATTTCATAA-GAGGGTTATC
*
217 ACAATTTCATA
1 AAAATTTCATA
228 GTGTGATTAT
Statistics
Matches: 159, Mismatches: 25, Indels: 42
0.70 0.11 0.19
Matches are distributed among these distances:
16 8 0.05
17 3 0.02
19 3 0.02
20 6 0.04
21 10 0.06
22 79 0.50
23 48 0.30
24 2 0.01
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAAGAGGGTTATC
Found at i:172 original size:23 final size:23
Alignment explanation
Indices: 122--201 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
112 AAATTTACAG
* *
122 TTATCAAGATTTCATAAGAAA-G-
1 TTATCAAAATTTTAT-AGAAAGGT
144 TTATCAAAATTTTATAGAAAGGT
1 TTATCAAAATTTTATAGAAAGGT
** *
167 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTTATAGAAAGGT
190 TTATCAAAATTT
1 TTATCAAAATTT
202 CATAACGAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
21 5 0.10
22 14 0.27
23 32 0.63
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAAAGGT
Found at i:213 original size:46 final size:44
Alignment explanation
Indices: 1--247 Score: 151
Period size: 44 Copynumber: 5.7 Consensus size: 44
* * *
1 AAAATTTCATAAGAGG-G-TTATCAAAATTTCATAG-TATGTAGATC
1 AAAATTTCAT-AG-GGAGATTATCAAAATTTCATAGAAAGGT-TATC
* *
45 AAAATTTCATAGGGAGATTAACAAAATTTCATA-ATGAGGTTATC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGA-AAGGTTATC
* * *
89 AAAAAATT-ATAGGGAGCTTATCAAAA-TT--T--ACA-GTTATC
1 -AAAATTTCATAGGGAGATTATCAAAATTTCATAGAAAGGTTATC
* * * *
127 AAGATTTCATA-AGAAAGTTATCAAAATTTTATAGAAAGGTTTATC
1 AAAATTTCATAGGGAGA-TTATCAAAATTTCATAGAAAGG-TTATC
* * *
172 AAAATTTTATAGGGAGATTTATCAAAATTTCATA-ACGAGGTTATT
1 AAAATTTCATAGGGAGA-TTATCAAAATTTCATAGA-AAGGTTATC
* * * *
217 ACAATTTCATAGTGTGATTATCAATATTTCA
1 AAAATTTCATAGGGAGATTATCAAAATTTCA
248 GAGTGTGATT
Statistics
Matches: 160, Mismatches: 27, Indels: 32
0.73 0.12 0.15
Matches are distributed among these distances:
37 7 0.04
38 18 0.11
39 3 0.02
40 1 0.01
41 2 0.01
42 2 0.01
43 7 0.04
44 58 0.36
45 41 0.26
46 21 0.13
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (44 bp):
AAAATTTCATAGGGAGATTATCAAAATTTCATAGAAAGGTTATC
Found at i:237 original size:22 final size:22
Alignment explanation
Indices: 212--271 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
202 CATAACGAGG
*
212 TTATTACAATTTCATAGTGTGA
1 TTATAACAATTTCATAGTGTGA
* *
234 TTATCAA-TATTTCAGAGTGTGA
1 TTAT-AACAATTTCATAGTGTGA
256 TTACTAACAA-TTCATA
1 TTA-TAACAATTTCATA
272 TGTAAGTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (22 bp):
TTATAACAATTTCATAGTGTGA
Found at i:314 original size:22 final size:22
Alignment explanation
Indices: 289--351 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
279 TTTTAAATTT
*
289 TCATAACGTGGTTATCAATATA
1 TCATAACGTGGTTATCAACATA
** * *
311 TCATATGGAGGTTATCAACATC
1 TCATAACGTGGTTATCAACATA
**
333 TCATAGTGTTGGTTATCAA
1 TCATAACG-TGGTTATCAA
352 AATTTCATTG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (22 bp):
TCATAACGTGGTTATCAACATA
Found at i:350 original size:23 final size:22
Alignment explanation
Indices: 296--351 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
286 TTTTCATAAC
*
296 GTGGTTATCAATATATCATATG
1 GTGGTTATCAACATATCATATG
* *
318 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAACATATCATA-TG
*
341 TTGGTTATCAA
1 GTGGTTATCAA
352 AATTTCATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAACATATCATATG
Found at i:382 original size:45 final size:44
Alignment explanation
Indices: 267--382 Score: 108
Period size: 45 Copynumber: 2.6 Consensus size: 44
257 TACTAACAAT
* * * *
267 TCATATGTAAGTTTTTAAATTTTCATAACGTGGTTATCAATATA
1 TCATATGGAAGTTATTAAAATTTCATAACGTGGTTATCAAAATA
* * * * ** *
311 TCATATGGAGGTTATCAACATCTCATAGTGTTGGTTATCAAAATT
1 TCATATGGAAGTTATTAAAATTTCATAACG-TGGTTATCAAAATA
356 TCAT-TGGAAAGTTATTAAAATTTCATA
1 TCATATGG-AAGTTATTAAAATTTCATA
383 TTGAGGTCTT
Statistics
Matches: 55, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
44 24 0.44
45 31 0.56
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (44 bp):
TCATATGGAAGTTATTAAAATTTCATAACGTGGTTATCAAAATA
Found at i:635 original size:2 final size:2
Alignment explanation
Indices: 628--658 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
618 CTAAAACTAG
628 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
659 AACAAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1153 original size:42 final size:42
Alignment explanation
Indices: 1100--1182 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1090 TGGTTTGGTT
* *
1100 ATTAGTGTTTAATTTTAGTTTGATTTGAATCATATTTAGATC
1 ATTAATGTTTAATTTTAGTTTGATTTAAATCATATTTAGATC
1142 ATTAATGTTTAATTTTAGTTTGATTTAAATCATATTTAGAT
1 ATTAATGTTTAATTTTAGTTTGATTTAAATCATATTTAGAT
1183 TTAGTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (42 bp):
ATTAATGTTTAATTTTAGTTTGATTTAAATCATATTTAGATC
Found at i:5993 original size:2 final size:2
Alignment explanation
Indices: 5980--6014 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
5970 TGATGTCTTT
5980 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6015 GTTGCAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18618 original size:28 final size:28
Alignment explanation
Indices: 18586--18641 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
18576 TTGAGGGAAA
18586 ACTGATAAATCCTCCTATTAAAAAATTT
1 ACTGATAAATCCTCCTATTAAAAAATTT
* * *
18614 ACTGATGAATCCTCCTATTGACAAATTT
1 ACTGATAAATCCTCCTATTAAAAAATTT
18642 GTGAAATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (28 bp):
ACTGATAAATCCTCCTATTAAAAAATTT
Found at i:24183 original size:11 final size:10
Alignment explanation
Indices: 24165--24198 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
24155 AATTGTCTTC
24165 AAATCTTCAA
1 AAATCTTCAA
24175 AATATCTTCAA
1 AA-ATCTTCAA
24186 GAAATCTTCAA
1 -AAATCTTCAA
24197 AA
1 AA
24199 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:29542 original size:38 final size:38
Alignment explanation
Indices: 29465--29539 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
29455 TAAATAAAAA
* *
29465 ATTAAAAAGCAAAACAGAAAATAAAAATATATTCTTTT
1 ATTAAAAAGAAAAACAGAAAAGAAAAATATATTCTTTT
* * *
29503 ATTAAAAGGAAAAACGGAAAAGAAAAAT-TATTTTTTT
1 ATTAAAAAGAAAAACAGAAAAGAAAAATATATTCTTTT
29540 TATCGACGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 8 0.25
38 24 0.75
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.29
Consensus pattern (38 bp):
ATTAAAAAGAAAAACAGAAAAGAAAAATATATTCTTTT
Found at i:31243 original size:11 final size:10
Alignment explanation
Indices: 31225--31258 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
31215 AATTGTCTTC
31225 AAATCTTCAA
1 AAATCTTCAA
31235 AATATCTTCAA
1 AA-ATCTTCAA
31246 GAAATCTTCAA
1 -AAATCTTCAA
31257 AA
1 AA
31259 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:33271 original size:166 final size:164
Alignment explanation
Indices: 32794--33273 Score: 642
Period size: 164 Copynumber: 2.9 Consensus size: 164
32784 TGAGTCATTT
*
32794 GTCATTTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * * *
32859 TTAAATAATCTACCAAGTAAGTAAAGACGAAAAATATTAGTTCTCTAGCTCATCATCAATCATTG
65 TTAAGTAATCTGCCAAGT-AGGAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATCAATCCTGG
* *
32924 ATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
129 ATGGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * *
32960 GTCCACTGAGAAATGACCAAAAAGATTACTTATTTAAT-CCC-CAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * ** *
33023 TTAAGTAATCTGCCAAATAGGAAAGACGAAAAAAATAAGTTCTCTAACTCCAAATGCAAGCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCAT-CAATCC-TG
*
33088 G-TAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
128 GATGGGGATCTTTTAGTAATTCCACTACTCTATTAAA
33124 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * *
33189 TTAAGTAATCTGTCAAGTGGGAAAAGACGAAAAAAATTAGTTATCTCGCTCCTCATTAATCCGGG
65 TTAAGTAATCTGCCAAGTAGG-AAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATCAATCCTGG
33254 ATGGGGATCTTTTAGTAATT
129 ATGGGGATCTTTTAGTAATT
33274 TCACATGTTT
Statistics
Matches: 270, Mismatches: 37, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
163 31 0.11
164 106 0.39
165 10 0.04
166 95 0.35
167 28 0.10
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (164 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATCAATCCTGGAT
GGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Done.