Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007368.1 Corchorus capsularis cultivar CVL-1 contig07389, 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: 18053
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:1147 original size:22 final size:21
Alignment explanation
Indices: 1122--1355 Score: 97
Period size: 22 Copynumber: 10.7 Consensus size: 21
1112 TAGTAGCTCC
*
1122 CTATGAAATTTTGATTATTACA
1 CTATGAAATTTTGATAATT-CA
* *
1144 CTATAAAATTTTGATAACCTT-G
1 CTATGAAATTTTGATAA--TTCA
*
1166 CTATGAAATTTTGATAA-CCA
1 CTATGAAATTTTGATAATTCA
* * *
1186 CCCTATAAAAGTTTGATAACCTTGA
1 --CTATGAAATTTTGATAA--TTCA
*
1211 -TATGAAATTTTGATAA-CCA
1 CTATGAAATTTTGATAATTCA
1230 CCCTATGAAATTTTGATAACATTC-
1 --CTATGAAATTTTGAT-A-ATTCA
* * * *
1254 CTATGAAAGTTTGGTTACTTCT
1 CTATGAAA-TTTTGATAATTCA
**
1276 CTAT-AAACTTTT-ACTTTTTACA
1 CTATGAAA-TTTTGA-TAATT-CA
**
1298 CTATGAAATTTTGGA-AACCACA
1 CTATGAAATTTT-GATAA-TTCA
1320 CTATGAAATTTTGATAATCTCA
1 CTATGAAATTTTGATAAT-TCA
*
1342 TTATGAAATTTTGA
1 CTATGAAATTTTGA
1356 CAACCACATT
Statistics
Matches: 157, Mismatches: 31, Indels: 48
0.67 0.13 0.20
Matches are distributed among these distances:
19 1 0.01
21 14 0.09
22 127 0.81
23 9 0.06
24 4 0.03
25 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
CTATGAAATTTTGATAATTCA
Found at i:1172 original size:44 final size:44
Alignment explanation
Indices: 1122--1266 Score: 200
Period size: 44 Copynumber: 3.3 Consensus size: 44
1112 TAGTAGCTCC
* ** *
1122 CTATGAAATTTTGATTATTACACTATAAAATTTTGATAACCTTG
1 CTATGAAATTTTGATAACCACCCTATAAAATTTTGATAACCTTG
*
1166 CTATGAAATTTTGATAACCACCCTATAAAAGTTTGATAACCTTG
1 CTATGAAATTTTGATAACCACCCTATAAAATTTTGATAACCTTG
* * * *
1210 ATATGAAATTTTGATAACCACCCTATGAAATTTTGATAACATTC
1 CTATGAAATTTTGATAACCACCCTATAAAATTTTGATAACCTTG
*
1254 CTATGAAAGTTTG
1 CTATGAAATTTTG
1267 GTTACTTCTC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 89 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACCCTATAAAATTTTGATAACCTTG
Found at i:1365 original size:22 final size:21
Alignment explanation
Indices: 1299--1366 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 21
1289 CTTTTTACAC
*
1299 TATGAAATTTTGGAAACCACAC
1 TATGAAATTTT-GAAACCACAT
* *
1321 TATGAAATTTTGATAATCTCAT
1 TATGAAATTTTGA-AACCACAT
1343 TATGAAATTTTGACAACCACAT
1 TATGAAATTTTGA-AACCACAT
1365 TA
1 TA
1367 ATACAACAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 2 0.05
22 37 0.95
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (21 bp):
TATGAAATTTTGAAACCACAT
Found at i:6733 original size:20 final size:20
Alignment explanation
Indices: 6690--6726 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6680 AATTTTCTGA
*
6690 TTTTCCTTTTTCCTTTTTTC
1 TTTTCCTTCTTCCTTTTTTC
6710 TTTTCCTTCTT-CTTTTT
1 TTTTCCTTCTTCCTTTTT
6727 GTTTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCCTTCTTCCTTTTTTC
Found at i:10967 original size:24 final size:24
Alignment explanation
Indices: 10938--10984 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
10928 CTTATTGTGA
10938 AAAATGACCAAAATGCCCCTATGG
1 AAAATGACCAAAATGCCCCTATGG
10962 AAAATGACCAAAATGCCCCTATG
1 AAAATGACCAAAATGCCCCTATG
10985 TGACCCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.17
Consensus pattern (24 bp):
AAAATGACCAAAATGCCCCTATGG
Found at i:11289 original size:31 final size:31
Alignment explanation
Indices: 11254--11358 Score: 160
Period size: 31 Copynumber: 3.4 Consensus size: 31
11244 ATTGGGCGGG
* *
11254 TTCGGGCTCGGGTACTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
11285 TTCGGGTTCGGGTATTTTCGGGTTC-GGT-TT
1 TTCGGGTTCGGGTA-TTTCGGGTTCGGGTATT
11315 TGTCGGGTTCGGGTATTTCGGGTTCGGGTATT
1 T-TCGGGTTCGGGTATTTCGGGTTCGGGTATT
11347 TTCGGGTTCGGG
1 TTCGGGTTCGGG
11359 CTCGGATCGA
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
30 13 0.19
31 43 0.63
32 12 0.18
ACGTcount: A:0.05, C:0.15, G:0.40, T:0.40
Consensus pattern (31 bp):
TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
Found at i:11290 original size:16 final size:16
Alignment explanation
Indices: 11254--11358 Score: 155
Period size: 16 Copynumber: 6.8 Consensus size: 16
11244 ATTGGGCGGG
* *
11254 TTCGGGCTCGGGTA-C
1 TTCGGGTTCGGGTATT
11269 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
11285 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
11301 TTCGGGTTC-GGT-TT
1 TTCGGGTTCGGGTATT
11315 TGTCGGGTTCGGGTA-T
1 T-TCGGGTTCGGGTATT
11331 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
11347 TTCGGGTTCGGG
1 TTCGGGTTCGGG
11359 CTCGGATCGA
Statistics
Matches: 83, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
14 3 0.04
15 37 0.45
16 43 0.52
ACGTcount: A:0.05, C:0.15, G:0.40, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:11380 original size:23 final size:23
Alignment explanation
Indices: 11347--11401 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
11337 TTCGGGTATT
*
11347 TTCGGGTTCGGGCTCGGATCGAG
1 TTCGGGTTCGGGCCCGGATCGAG
* * *
11370 TTTGGGTTCGGGCCCGGGTCGGG
1 TTCGGGTTCGGGCCCGGATCGAG
11393 TTCGGGTTC
1 TTCGGGTTC
11402 ACTTTCGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.04, C:0.22, G:0.45, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCGGGCCCGGATCGAG
Found at i:14349 original size:16 final size:15
Alignment explanation
Indices: 14322--14351 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
14312 ATCTCGGGCT
14322 CGGGTTGGGTTCGGG
1 CGGGTTGGGTTCGGG
14337 CGGGTTCGGGTTCGG
1 CGGGTT-GGGTTCGG
14352 ATATTTTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.57, T:0.27
Consensus pattern (15 bp):
CGGGTTGGGTTCGGG
Found at i:14384 original size:16 final size:16
Alignment explanation
Indices: 14341--14385 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
14331 TTCGGGCGGG
* *
14341 TTCGGGTTCGGATATT
1 TTCGGGTTCGGGTAAT
14357 TTCGGGTTCGGGTAAT
1 TTCGGGTTCGGGTAAT
14373 TTCGGGTTCGGGT
1 TTCGGGTTCGGGT
14386 TCGGGCCGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.09, C:0.13, G:0.38, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTAAT
Found at i:16657 original size:26 final size:26
Alignment explanation
Indices: 16625--16677 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
16615 TGATTTGGCC
* *
16625 TTTAATATTAAGTTATT-TTTATTATT
1 TTTAATATCAA-TTATTAATTATTATT
16651 TTTAATATCAATTATTAATTATTATT
1 TTTAATATCAATTATTAATTATTATT
16677 T
1 T
16678 AGGTTTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTAATATCAATTATTAATTATTATT
Found at i:17068 original size:22 final size:21
Alignment explanation
Indices: 17018--17124 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 21
17008 GTCTTTGTGT
17018 GGTTATCAAAATTTCATAAAGGA
1 GGTTATC-AAATTTCAT-AAGGA
* *
17041 GATTATTATAATTTCATAAGGA
1 GGTTATCA-AATTTCATAAGGA
* *
17063 GGTTATCAATATTTTATATGGA
1 GGTTATCAA-ATTTCATAAGGA
*
17085 GGTTATCAGAATTTC-TTAGGAA
1 GGTTATCA-AATTTCATAAGG-A
*
17107 GATTATCAAAATTTCATA
1 GGTTATC-AAATTTCATA
17125 CTATGTTTAC
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
21 4 0.06
22 47 0.70
23 16 0.24
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (21 bp):
GGTTATCAAATTTCATAAGGA
Found at i:17140 original size:22 final size:22
Alignment explanation
Indices: 17113--17168 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
17103 GGAAGATTAT
* *
17113 CAAAATTTCATACTATGTTTAC
1 CAAAATTTCATACAATGGTTAC
* * *
17135 CGAAATTTCTTAGAATGGTTAC
1 CAAAATTTCATACAATGGTTAC
17157 CAAAATTTCATA
1 CAAAATTTCATA
17169 GGGTTAGTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
CAAAATTTCATACAATGGTTAC
Found at i:17226 original size:22 final size:22
Alignment explanation
Indices: 17199--17331 Score: 101
Period size: 22 Copynumber: 5.8 Consensus size: 22
17189 GCATTGGAAT
17199 GTTATCAAAATTTCATAAAGTA
1 GTTATCAAAATTTCATAAAGTA
**
17221 GTTATCAAAATTTCATAGGGTCAA
1 GTTATCAAAATTTCATAAAGT--A
* *
17245 GTTATTATAATTTCATTAGAAGCTA
1 GTTATCAAAATTTCA-TA-AAG-TA
**
17270 GTTATCAAAATTTCATAGCG-A
1 GTTATCAAAATTTCATAAAGTA
*
17291 GATTATCAGAATTTCAT--AGTA
1 G-TTATCAAAATTTCATAAAGTA
*
17312 TGATTATCAAAATTTTATAA
1 -G-TTATCAAAATTTCATAA
17332 GGAGTGTTGC
Statistics
Matches: 87, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 48 0.55
23 1 0.01
24 16 0.18
25 16 0.18
26 1 0.01
27 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAAGTA
Found at i:17304 original size:71 final size:69
Alignment explanation
Indices: 17152--17309 Score: 196
Period size: 71 Copynumber: 2.3 Consensus size: 69
17142 TCTTAGAATG
* * *
17152 GTTACCAAAATTTCATAGGGTTAGTTTATTATAATTTGCATTGGAATGTTATCAAAATTTCATAA
1 GTTATCAAAATTTCATAGGGTAAGTTTATTATAATTTGCATTAGAATGTTATCAAAATTTCATAA
17217 AGTA
66 AGTA
17221 GTTATCAAAATTTCATAGGGTCAAG-TTATTATAATTT-CATTAGAAGCTAGTTATCAAAATTTC
1 GTTATCAAAATTTCATAGGGT-AAGTTTATTATAATTTGCATTAGAA--T-GTTATCAAAATTTC
**
17284 ATAGCG-A
62 ATAAAGTA
*
17291 GATTATCAGAATTTCATAG
1 G-TTATCAAAATTTCATAG
17310 TATGATTATC
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
68 7 0.09
69 32 0.41
70 5 0.06
71 34 0.44
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (69 bp):
GTTATCAAAATTTCATAGGGTAAGTTTATTATAATTTGCATTAGAATGTTATCAAAATTTCATAA
AGTA
Done.