Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011291.1 Corchorus olitorius cultivar O-4 contig11324, 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: 20566
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--27 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
28 GCTCTTGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13544 original size:4 final size:4
Alignment explanation
Indices: 13535--13579 Score: 81
Period size: 4 Copynumber: 11.0 Consensus size: 4
13525 TTGTAGGGTA
13535 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT
13580 TTTTTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 36 0.90
5 4 0.10
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:13587 original size:12 final size:12
Alignment explanation
Indices: 13536--13594 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
13526 TGTAGGGTAC
*
13536 TTTCTTTCTTTC
1 TTTCTTTCTTTT
*
13548 TTTCTTTCTTTC
1 TTTCTTTCTTTT
13560 TTTCTTTCTTTCT
1 TTTCTTTCTTT-T
13573 TTTCTTT-TTTT
1 TTTCTTTCTTTT
13584 TTT-TTT-TTTT
1 TTTCTTTCTTTT
13594 T
1 T
13595 ATGAATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
10 8 0.18
11 4 0.09
12 26 0.58
13 7 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTCTTTCTTTT
Found at i:20392 original size:14 final size:14
Alignment explanation
Indices: 20373--20411 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
20363 TTTTTAGTTG
20373 AGTAAAACTA-TAAA
1 AGTAAAA-TAGTAAA
20387 AGTAAAATAGTAAA
1 AGTAAAATAGTAAA
*
20401 AATAAAATAGT
1 AGTAAAATAGT
20412 TATAAGGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (14 bp):
AGTAAAATAGTAAA
Found at i:20400 original size:85 final size:85
Alignment explanation
Indices: 20302--20468 Score: 289
Period size: 85 Copynumber: 2.0 Consensus size: 85
20292 TAATTAAATT
* *
20302 AGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
*
20367 TAGTTGAGTAAAACTATAAA
66 TAGTTGACTAAAACTATAAA
* *
20387 AGTAAAATAGTAAAAATAAAATAGTTATAAGGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
20452 TAGTTGACTAAAACTAT
66 TAGTTGACTAAAACTAT
20469 GAATATATTC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 77 1.00
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (85 bp):
AGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
TAGTTGACTAAAACTATAAA
Found at i:20518 original size:31 final size:31
Alignment explanation
Indices: 20483--20544 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
20473 ATATTCCAAA
*
20483 AATAAGGGTATAATAGGCGATTCAAAAGTTT
1 AATAAGGATATAATAGGCGATTCAAAAGTTT
20514 AATAAGGATATAATAGGCGATTCAAAAGTTT
1 AATAAGGATATAATAGGCGATTCAAAAGTTT
20545 TACAAAACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (31 bp):
AATAAGGATATAATAGGCGATTCAAAAGTTT
Done.