Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011826.1 Corchorus olitorius cultivar O-4 contig11859, 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: 9621
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Found at i:39 original size:31 final size:31
Alignment explanation
Indices: 1--85 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
** * *
1 TTTTGGTAAATGTGGTGTGCCACGTGTCACT
1 TTTTGGTAAACATGGCGTGCCACATGTCACT
* *
32 TTTTGGTACACATGGCGTGCCACATGTCGCT
1 TTTTGGTAAACATGGCGTGCCACATGTCACT
* * *
63 TTTTGGTACACGTGGCATGCCAC
1 TTTTGGTAAACATGGCGTGCCAC
86 GTCGGACACC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.34
Consensus pattern (31 bp):
TTTTGGTAAACATGGCGTGCCACATGTCACT
Found at i:2593 original size:3 final size:3
Alignment explanation
Indices: 2580--2698 Score: 202
Period size: 3 Copynumber: 38.7 Consensus size: 3
2570 GACTTTCATG
2580 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2626 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2674 TTA TTA TTA TATA CTA TATA TTA TT
1 TTA TTA TTA T-TA TTA T-TA TTA TT
2699 TTTAGTGACT
Statistics
Matches: 111, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
3 103 0.93
4 8 0.07
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3431 original size:3 final size:3
Alignment explanation
Indices: 3423--3460 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3413 GCCCTGCTTG
*
3423 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3461 GGCCAACCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4306 original size:21 final size:21
Alignment explanation
Indices: 4282--4321 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4272 GGGAGGTCAT
4282 AAAAAATCATAGGAAGGTTGC
1 AAAAAATCATAGGAAGGTTGC
**
4303 AAAATTTCATAGGAAGGTT
1 AAAAAATCATAGGAAGGTT
4322 TATTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (21 bp):
AAAAAATCATAGGAAGGTTGC
Found at i:4333 original size:23 final size:22
Alignment explanation
Indices: 4288--4473 Score: 123
Period size: 22 Copynumber: 8.2 Consensus size: 22
4278 TCATAAAAAA
* *
4288 TCATAGGAAGGTT-GCAAAATT
1 TCATAGGAAGTTTATCAAAATT
*
4309 TCATAGGAAGGTTTATTAAAATTTCATT
1 TCATAGGAA-GTTTA-TCAAA----ATT
*
4337 TCATAGGAAGGTTTATTAAAATT
1 TCATAGGAA-GTTTATCAAAATT
** *
4360 TCATAGTTAGATTATCAAAATT
1 TCATAGGAAGTTTATCAAAATT
*
4382 TCATATGG-AGTTTATCACAATT
1 TCATA-GGAAGTTTATCAAAATT
*
4404 TCATAGGTAA--TTATCAGAATT
1 TCATAGG-AAGTTTATCAAAATT
* *
4425 TCATAGTG-TGATTATCAAAATT
1 TCATAG-GAAGTTTATCAAAATT
*
4447 TAATAGGATAG-TTATCAAAATT
1 TCATAGGA-AGTTTATCAAAATT
4469 TCATA
1 TCATA
4474 AAAATATTCA
Statistics
Matches: 133, Mismatches: 17, Indels: 29
0.74 0.09 0.16
Matches are distributed among these distances:
21 28 0.21
22 67 0.50
23 13 0.10
24 3 0.02
27 4 0.03
28 18 0.14
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
TCATAGGAAGTTTATCAAAATT
Found at i:4338 original size:28 final size:28
Alignment explanation
Indices: 4306--4363 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
4296 AGGTTGCAAA
4306 ATTTCATAGGAAGGTTTATTAAAATTTC
1 ATTTCATAGGAAGGTTTATTAAAATTTC
4334 ATTTCATAGGAAGGTTTATTAAAATTTC
1 ATTTCATAGGAAGGTTTATTAAAATTTC
4362 AT
1 AT
4364 AGTTAGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (28 bp):
ATTTCATAGGAAGGTTTATTAAAATTTC
Found at i:4404 original size:44 final size:44
Alignment explanation
Indices: 4334--4473 Score: 146
Period size: 44 Copynumber: 3.2 Consensus size: 44
4324 TTAAAATTTC
* *
4334 ATTTCATA-GGAAGGTTTATTAAAATTTCATAGTTAGATTATCAAA
1 ATTTCATATGG-A-GTTTATCAAAATTTCATAGATAGATTATCAAA
* * *
4379 ATTTCATATGGAGTTTATCACAATTTCATAGGTA-ATTATCAGA
1 ATTTCATATGGAGTTTATCAAAATTTCATAGATAGATTATCAAA
*
4422 ATTTCATAGTGTGA--TTATCAAAATTTAATAGGATAG-TTATCAAA
1 ATTTCATA-TG-GAGTTTATCAAAATTTCATA-GATAGATTATCAAA
4466 ATTTCATA
1 ATTTCATA
4474 AAAATATTCA
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
43 30 0.37
44 39 0.48
45 11 0.13
46 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (44 bp):
ATTTCATATGGAGTTTATCAAAATTTCATAGATAGATTATCAAA
Done.