Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019539.1 Corchorus olitorius cultivar O-4 contig19572, 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: 29345
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:1255 original size:22 final size:21
Alignment explanation
Indices: 1230--1350 Score: 93
Period size: 22 Copynumber: 5.6 Consensus size: 21
1220 TATTTTTATG
*
1230 AAATTTTGATAACTACCCTATT
1 AAATTTTGATAACTA-CCTATA
* * *
1252 AAATTTTGATAACCATCATATG
1 AAATTTTGATAACTA-CCTATA
*
1274 AAATTTTGATAATTACCTATA
1 AAATTTTGATAACTACCTATA
*
1295 AAATTGTGATAAACT-CC-ATA
1 AAATTTTGAT-AACTACCTATA
* *
1315 AGAATCTTTGATAACCTAACTATG
1 A-AAT-TTTGATAA-CTACCTATA
*
1339 AAATTTTAATAA
1 AAATTTTGATAA
1351 ACTTTCCAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
20 4 0.05
21 20 0.25
22 48 0.61
23 4 0.05
24 3 0.04
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.37
Consensus pattern (21 bp):
AAATTTTGATAACTACCTATA
Found at i:1325 original size:43 final size:44
Alignment explanation
Indices: 1229--1329 Score: 118
Period size: 43 Copynumber: 2.3 Consensus size: 44
1219 ATATTTTTAT
* * * *
1229 GAAATTTTGATAACTACCCTATTAAATTTTGATAACCATCATAT
1 GAAATTTTGATAACTACCCTATAAAATTGTGATAAACATCATAA
*
1273 GAAATTTTGATAATTA-CCTATAAAATTGTGATAAAC-TCCATAA
1 GAAATTTTGATAACTACCCTATAAAATTGTGATAAACAT-CATAA
1316 G-AATCTTTGATAAC
1 GAAAT-TTTGATAAC
1330 CTAACTATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 4 0.08
43 30 0.61
44 15 0.31
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (44 bp):
GAAATTTTGATAACTACCCTATAAAATTGTGATAAACATCATAA
Found at i:2461 original size:19 final size:19
Alignment explanation
Indices: 2437--2477 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2427 TACTAATTAA
2437 TTATTTTAATATTATATTT
1 TTATTTTAATATTATATTT
*
2456 TTATTTTTATATTATATTT
1 TTATTTTAATATTATATTT
2475 TTA
1 TTA
2478 CTTAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTAATATTATATTT
Found at i:2488 original size:19 final size:19
Alignment explanation
Indices: 2447--2489 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
2437 TTATTTTAAT
* ** *
2447 ATTATATTTTTATTTTTAT
1 ATTATATTTTTACTTAAAA
2466 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
2485 ATTAT
1 ATTAT
2490 TCCTAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:14000 original size:6 final size:6
Alignment explanation
Indices: 13989--14018 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
13979 ATTGTTACTA
13989 TATATC TATATC TATATC TATATAC TATAT
1 TATATC TATATC TATATC TATAT-C TATAT
14019 AAGTCTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:14358 original size:207 final size:207
Alignment explanation
Indices: 14003--14419 Score: 825
Period size: 207 Copynumber: 2.0 Consensus size: 207
13993 TCTATATCTA
14003 TATCTATATACTATATAAGTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAATAGCCTTTT
1 TATCTATATACTATATAAGTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAATAGCCTTTT
14068 TAATTTTAAAATTTTAGTTATATTTGTAAGGGTTAATATGTAATCTATCCAACCAGATTTTATTT
66 TAATTTTAAAATTTTAGTTATATTTGTAAGGGTTAATATGTAATCTATCCAACCAGATTTTATTT
14133 CCATATTAAAAAAGTCTAAAATAATAACAATTTATGTTAAACAACATATTATTATAATTATTAAA
131 CCATATTAAAAAAGTCTAAAATAATAACAATTTATGTTAAACAACATATTATTATAATTATTAAA
14198 ATTATTATTAGT
196 ATTATTATTAGT
14210 TATCTATATACTATATAAGTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAATAGCCTTTT
1 TATCTATATACTATATAAGTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAATAGCCTTTT
*
14275 TAATTTTAAAATTTTAGTTATATTTTTAAGGGTTAATATGTAATCTATCCAACCAGATTTTATTT
66 TAATTTTAAAATTTTAGTTATATTTGTAAGGGTTAATATGTAATCTATCCAACCAGATTTTATTT
14340 CCATATTAAAAAAGTCTAAAATAATAACAATTTATGTTAAACAACATATTATTATAATTATTAAA
131 CCATATTAAAAAAGTCTAAAATAATAACAATTTATGTTAAACAACATATTATTATAATTATTAAA
14405 ATTATTATTAGT
196 ATTATTATTAGT
14417 TAT
1 TAT
14420 AATATATATA
Statistics
Matches: 209, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 209 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (207 bp):
TATCTATATACTATATAAGTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAATAGCCTTTT
TAATTTTAAAATTTTAGTTATATTTGTAAGGGTTAATATGTAATCTATCCAACCAGATTTTATTT
CCATATTAAAAAAGTCTAAAATAATAACAATTTATGTTAAACAACATATTATTATAATTATTAAA
ATTATTATTAGT
Found at i:14582 original size:30 final size:29
Alignment explanation
Indices: 14504--14587 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
14494 TAATTTAGAG
14504 TTATTATTAT--TATAATAATTATTAAAA
1 TTATTATTATAATATAATAATTATTAAAA
** * *
14531 TTATTATTAGTGGTATTATAATTATTAAAC
1 TTATTATTA-TAATATAATAATTATTAAAA
14561 TTATTATTATAATAATAATAATTATTA
1 TTATTATTATAAT-ATAATAATTATTA
14588 GTGGTATGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
27 9 0.19
28 1 0.02
29 2 0.04
30 36 0.75
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (29 bp):
TTATTATTATAATATAATAATTATTAAAA
Found at i:14585 original size:21 final size:21
Alignment explanation
Indices: 14544--14587 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
14534 TTATTAGTGG
* *
14544 TATTATAATTATTAAACTTAT
1 TATTATAATTAATAAAATTAT
14565 TATTATAA-TAATAATAATTAT
1 TATTATAATTAATAA-AATTAT
14586 TA
1 TA
14588 GTGGTATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTATAATTAATAAAATTAT
Found at i:17326 original size:273 final size:274
Alignment explanation
Indices: 16838--17382 Score: 1029
Period size: 273 Copynumber: 2.0 Consensus size: 274
16828 GAACTAGCAT
*
16838 TGATATCTATAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGAATGCCGAGTTAAT
1 TGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGAATGCCGAGTTAAT
*
16903 CAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
66 CAAAGAAATAGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
16968 GGAAAAGAGAAAGCTCAAGAAAAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
131 GGAAAAGAGAAAGCTCAAGAAAAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
* *
17033 ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAATGAAAAAAGGA
196 ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAGA
17098 GTTGCAAGAAAAAC
261 GTTGCAAGAAAAAC
17112 TGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAA-AATGCCGAGTTAAT
1 TGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGAATGCCGAGTTAAT
17176 CAAAGAAATAGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
66 CAAAGAAATAGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
* *
17241 GGAAAAGAGAAAGTTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
131 GGAAAAGAGAAAGCTCAAGAAAAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
17306 ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAGA
196 ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAGA
17371 GTTGCAAGAAAA
261 GTTGCAAGAAAA
17383 GCCAAGTTAG
Statistics
Matches: 265, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
273 216 0.82
274 49 0.18
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (274 bp):
TGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGAATGCCGAGTTAAT
CAAAGAAATAGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGT
GGAAAAGAGAAAGCTCAAGAAAAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAG
ACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAGA
GTTGCAAGAAAAAC
Found at i:22241 original size:2 final size:2
Alignment explanation
Indices: 22234--22269 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22224 TCTTTACTAG
22234 TA TA TA TA TA TA TA 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 TA TA
22270 AACAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23552 original size:30 final size:30
Alignment explanation
Indices: 23513--23582 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
23503 CTTCTTTTGG
*
23513 TCTTT-CTCTCGATCCTTCCTCGCTTCCTT
1 TCTTTACTCTCGATCCTTCCTCGCTTCCTC
23542 TCTTTACTCTCGATCCTTCCTCGCTTCCTC
1 TCTTTACTCTCGATCCTTCCTCGCTTCCTC
23572 TCTTTACTCTC
1 TCTTTACTCTC
23583 TCTTCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.06, C:0.41, G:0.06, T:0.47
Consensus pattern (30 bp):
TCTTTACTCTCGATCCTTCCTCGCTTCCTC
Done.