Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002491.1 Corchorus olitorius cultivar O-4 contig02491, 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, 918
Length: 1530
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Found at i:267 original size:17 final size:17
Alignment explanation
Indices: 247--297 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
237 AACCAATTAA
247 CAATCTAAATTATATAT
1 CAATCTAAATTATATAT
264 CAAT-TCAAA-T-TA-A-
1 CAATCT-AAATTATATAT
277 CAATCTAAATTATATAT
1 CAATCTAAATTATATAT
294 CAAT
1 CAAT
298 TCAAATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
13 7 0.25
14 3 0.11
15 4 0.14
16 3 0.11
17 11 0.39
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (17 bp):
CAATCTAAATTATATAT
Found at i:275 original size:30 final size:30
Alignment explanation
Indices: 241--303 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
231 CTACTAAACC
241 AATTAACAATCTAAATTATATATCAATTCA
1 AATTAACAATCTAAATTATATATCAATTCA
271 AATTAACAATCTAAATTATATATCAATTCA
1 AATTAACAATCTAAATTATATATCAATTCA
301 AAT
1 AAT
304 GATTATCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37
Consensus pattern (30 bp):
AATTAACAATCTAAATTATATATCAATTCA
Found at i:303 original size:17 final size:17
Alignment explanation
Indices: 253--315 Score: 66
Period size: 17 Copynumber: 4.0 Consensus size: 17
243 TTAACAATCT
253 AAATTATATATCAATTC
1 AAATTATATATCAATTC
270 AAA-T-TA-A-CAA-TC
1 AAATTATATATCAATTC
282 TAAATTATATATCAATTC
1 -AAATTATATATCAATTC
*
300 AAATGAT-TATCAATTC
1 AAATTATATATCAATTC
316 TTACTATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
12 2 0.05
13 6 0.15
14 2 0.05
15 4 0.10
16 11 0.28
17 12 0.31
18 2 0.05
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATTATATATCAATTC
Found at i:328 original size:18 final size:18
Alignment explanation
Indices: 305--340 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
295 AATTCAAATG
305 ATTATCAATTCTTACTAT
1 ATTATCAATTCTTACTAT
323 ATTATCAATTCTTACTAT
1 ATTATCAATTCTTACTAT
341 CAATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATCAATTCTTACTAT
Found at i:372 original size:20 final size:20
Alignment explanation
Indices: 344--457 Score: 85
Period size: 20 Copynumber: 5.9 Consensus size: 20
334 TTACTATCAA
344 TTATTATTAATTTATATTAG
1 TTATTATTAATTTATATTAG
* * *
364 TTGTTATTAATTTCTATT-T
1 TTATTATTAATTTATATTAG
** *
383 TTATTCATTTTTTTTTATTA-
1 TTATT-ATTAATTTATATTAG
* * *
403 TTA-AATT--TTTATATCAA
1 TTATTATTAATTTATATTAG
420 TTATTATTAATTTATATTAG
1 TTATTATTAATTTATATTAG
* *
440 TTGTTATTAATTTCTATT
1 TTATTATTAATTTATATT
458 TTTATTCTAT
Statistics
Matches: 73, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
16 7 0.10
17 3 0.04
18 6 0.08
19 4 0.05
20 53 0.73
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (20 bp):
TTATTATTAATTTATATTAG
Found at i:420 original size:76 final size:77
Alignment explanation
Indices: 329--507 Score: 315
Period size: 76 Copynumber: 2.3 Consensus size: 77
319 CTATATTATC
*
329 AATTCTTACTATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTC-ATTT
1 AATTTTTA-TATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTCTATTT
393 TTTTTTATTATTA
65 TTTTTTATTATTA
406 AATTTTTATATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTCTATTTT
1 AATTTTTATATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTCTATTTT
471 TTTTTATTATTA
66 TTTTTATTATTA
* *
483 AATTTTTATATTATTTATTATTAAT
1 AATTTTTATATCAATTATTATTAAT
508 ACTTCTATTT
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
76 51 0.52
77 47 0.48
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (77 bp):
AATTTTTATATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTCTATTTT
TTTTTATTATTA
Found at i:534 original size:16 final size:16
Alignment explanation
Indices: 513--545 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
503 TTAATACTTC
513 TATTTCTATTAGAATA
1 TATTTCTATTAGAATA
*
529 TATTTCTATTATAATA
1 TATTTCTATTAGAATA
545 T
1 T
546 TAATATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATTTCTATTAGAATA
Found at i:550 original size:22 final size:24
Alignment explanation
Indices: 525--578 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
515 TTTCTATTAG
525 AATATATTTC--TATT-ATAATATT
1 AATATATTTCTATATTAATAATA-T
*
547 AATATAATTCTATATTAATAATAT
1 AATATATTTCTATATTAATAATAT
571 AATATATT
1 AATATATT
579 AATATATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.33
24 12 0.44
25 6 0.22
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
AATATATTTCTATATTAATAATAT
Found at i:561 original size:16 final size:16
Alignment explanation
Indices: 542--612 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
532 TTCTATTATA
542 ATATTAATATAATTCT
1 ATATTAATATAATTCT
**
558 ATATTAATA-ATATAAT
1 ATATTAATATA-ATTCT
* *
574 ATATTAATATATTTCG
1 ATATTAATATAATTCT
590 AT-TT-ATA-AA-TCT
1 ATATTAATATAATTCT
602 ATATTAGATAT
1 ATATTA-ATAT
613 TATTATATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
12 4 0.10
13 3 0.07
14 3 0.07
15 6 0.15
16 24 0.59
17 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATTAATATAATTCT
Found at i:584 original size:24 final size:24
Alignment explanation
Indices: 535--586 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
525 AATATATTTC
**
535 TATTATAATATTAATATAATTCTA
1 TATTATAATATTAATATAATAATA
*
559 TATTAATAATA-TAATATATTAATA
1 TATT-ATAATATTAATATAATAATA
583 TATT
1 TATT
587 TCGATTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTATAATATTAATATAATAATA
Found at i:735 original size:15 final size:16
Alignment explanation
Indices: 715--748 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
705 ATATAATTTC
715 TAAATAGAAATAT-TA
1 TAAATAGAAATATATA
730 TAAATAGAAATATATA
1 TAAATAGAAATATATA
746 TAA
1 TAA
749 TATAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
TAAATAGAAATATATA
Done.