Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01004505.1 Corchorus olitorius cultivar O-4 contig04521, 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, 705
Length: 1176
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Found at i:190 original size:61 final size:61
Alignment explanation
Indices: 94--218 Score: 171
Period size: 61 Copynumber: 2.0 Consensus size: 61
84 ACACTTTTGC
* * * * * * *
94 CCTTTGCTTCATTTTCTTTAAACTTTCTAATTTCAAATCCTTTTAAACCTTCAAAGTAAAA
1 CCTTTACTTCATTTTCTTCAAACTTTCTAACTTCAAATCCTCTAAAACATTCAAACTAAAA
155 CCTTTACTTCATTTTCTTCAAATCTTT-TAACTTCAAATCCTCTAAAACATTCAAACTAAAA
1 CCTTTACTTCATTTTCTTCAAA-CTTTCTAACTTCAAATCCTCTAAAACATTCAAACTAAAA
216 CCT
1 CCT
219 CAAATTTTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
61 52 0.93
62 4 0.07
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.42
Consensus pattern (61 bp):
CCTTTACTTCATTTTCTTCAAACTTTCTAACTTCAAATCCTCTAAAACATTCAAACTAAAA
Found at i:450 original size:8 final size:8
Alignment explanation
Indices: 426--465 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
416 GCGGCCCCAG
*
426 TAATTTTT
1 TAATTATT
434 TAATATATT
1 TAAT-TATT
443 TAATTATT
1 TAATTATT
451 TAATTA-T
1 TAATTATT
458 TAATTATT
1 TAATTATT
466 ATTAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TAATTATT
Found at i:462 original size:15 final size:17
Alignment explanation
Indices: 426--465 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
416 GCGGCCCCAG
*
426 TAATTTTTTAATATATT
1 TAATTATTTAATATATT
443 TAATTATTTAAT-TA-T
1 TAATTATTTAATATATT
458 TAATTATT
1 TAATTATT
466 ATTAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 2 0.09
17 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTATTTAATATATT
Found at i:530 original size:8 final size:8
Alignment explanation
Indices: 508--563 Score: 60
Period size: 8 Copynumber: 6.6 Consensus size: 8
498 TTAAGATTAA
508 TTATT-GT
1 TTATTAGT
*
515 TAATTAGT
1 TTATTAGT
523 TTATTAGTT
1 TTATTAG-T
532 TTAATTAGT
1 TT-ATTAGT
541 TTATTAGT
1 TTATTAGT
549 GTTAATTAGT
1 -TT-ATTAGT
559 TTATT
1 TTATT
564 TACGATTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 4 0.10
8 17 0.40
9 10 0.24
10 11 0.26
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (8 bp):
TTATTAGT
Found at i:535 original size:18 final size:18
Alignment explanation
Indices: 507--563 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
497 ATTAAGATTA
*
507 ATTATTGTTAATTAGTTT
1 ATTAGTGTTAATTAGTTT
*
525 ATTAGTTTTAATTAGTTT
1 ATTAGTGTTAATTAGTTT
543 ATTAGTGTTAATTAGTTT
1 ATTAGTGTTAATTAGTTT
561 ATT
1 ATT
564 TACGATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (18 bp):
ATTAGTGTTAATTAGTTT
Found at i:555 original size:36 final size:38
Alignment explanation
Indices: 493--563 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 38
483 AATTGTGAAA
*
493 TTTAATTAAGATTAATTATTGTTAATTAGTTTATTAGT
1 TTTAATTAAGATTAATTAGTGTTAATTAGTTTATTAGT
*
531 TTTAATT-AG-TTTATTAGTGTTAATTAGTTTATT
1 TTTAATTAAGATTAATTAGTGTTAATTAGTTTATT
564 TACGATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 22 0.71
37 2 0.06
38 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (38 bp):
TTTAATTAAGATTAATTAGTGTTAATTAGTTTATTAGT
Done.