Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022404.1 Corchorus olitorius cultivar O-4 contig22437, 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: 24778
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:6271 original size:5 final size:5
Alignment explanation
Indices: 6261--6295 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
6251 CCATCTCTTC
6261 TTTCT TTTCT TTTCT TTTCTT TTTCTT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTC-T TTTC-T TTTCT TTT
6296 TGTTGCAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:6286 original size:6 final size:6
Alignment explanation
Indices: 6256--6296 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
6246 ACTCTCCATC
6256 TCTTCTT TC-TTT TC-TTT TC-TTT TCTTTT TCTTTT TCTTTT T
1 TCTT-TT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T
6297 GTTGCAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 14 0.42
6 17 0.52
7 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:9886 original size:12 final size:12
Alignment explanation
Indices: 9869--9894 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9859 CAGCCTTCAA
9869 GGCTTTCATGGT
1 GGCTTTCATGGT
9881 GGCTTTCATGGT
1 GGCTTTCATGGT
9893 GG
1 GG
9895 GAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.38, T:0.38
Consensus pattern (12 bp):
GGCTTTCATGGT
Found at i:19446 original size:31 final size:31
Alignment explanation
Indices: 19405--19483 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
19395 GGCACCTTTT
* *
19405 TTTAGCCTCAAATTGGTCAACTTTTGAAAGG
1 TTTAGACTCAAATTGGTCAACTTTTAAAAGG
**
19436 TTTAGACTCAAATTGACCAACTTTTAAAAGG
1 TTTAGACTCAAATTGGTCAACTTTTAAAAGG
19467 TTTAGACTCAAATTGGT
1 TTTAGACTCAAATTGGT
19484 GGTTAAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (31 bp):
TTTAGACTCAAATTGGTCAACTTTTAAAAGG
Found at i:21238 original size:19 final size:19
Alignment explanation
Indices: 21202--21241 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21192 GTTAAGACTT
*
21202 ATTAATTTAGTCACGTGGA
1 ATTAATTTAGCCACGTGGA
* *
21221 ATTAATTTGGCCAGGTGGA
1 ATTAATTTAGCCACGTGGA
21240 AT
1 AT
21242 ATTATTTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (19 bp):
ATTAATTTAGCCACGTGGA
Found at i:21373 original size:13 final size:13
Alignment explanation
Indices: 21355--21379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21345 TTCCAGAATT
21355 TTAGGGTTTGGAG
1 TTAGGGTTTGGAG
21368 TTAGGGTTTGGA
1 TTAGGGTTTGGA
21380 AATGATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
TTAGGGTTTGGAG
Found at i:22655 original size:34 final size:34
Alignment explanation
Indices: 22612--22695 Score: 168
Period size: 34 Copynumber: 2.5 Consensus size: 34
22602 AGGGTCTTCT
22612 TCTTCTTCTTCTTCTTCTTCTTCTTCTTTTAGGG
1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTTTAGGG
22646 TCTTCTTCTTCTTCTTCTTCTTCTTCTTTTAGGG
1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTTTAGGG
22680 TCTTCTTCTTCTTCTT
1 TCTTCTTCTTCTTCTT
22696 TTAGGGTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.02, C:0.27, G:0.07, T:0.63
Consensus pattern (34 bp):
TCTTCTTCTTCTTCTTCTTCTTCTTCTTTTAGGG
Found at i:22683 original size:25 final size:25
Alignment explanation
Indices: 22655--22710 Score: 91
Period size: 22 Copynumber: 2.4 Consensus size: 25
22645 GTCTTCTTCT
22655 TCTTCTTCTTCTTCTTCTTTTAGGG
1 TCTTCTTCTTCTTCTTCTTTTAGGG
22680 ---TCTTCTTCTTCTTCTTTTAGGG
1 TCTTCTTCTTCTTCTTCTTTTAGGG
22702 TCTTCTTCT
1 TCTTCTTCT
22711 GCTCTATCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 22 0.79
25 6 0.21
ACGTcount: A:0.04, C:0.25, G:0.11, T:0.61
Consensus pattern (25 bp):
TCTTCTTCTTCTTCTTCTTTTAGGG
Found at i:22710 original size:3 final size:3
Alignment explanation
Indices: 22606--22695 Score: 94
Period size: 3 Copynumber: 29.3 Consensus size: 3
22596 AACTTTAGGG
**
22606 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T TAGGG TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T--CT TCT TCT
**
22652 TCT TCT TCT TCT TCT TCT TCT T-T TAGGG TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T--CT TCT TCT TCT TCT TCT T
22696 TTAGGGTCTT
Statistics
Matches: 75, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.05
3 69 0.92
5 2 0.03
ACGTcount: A:0.02, C:0.28, G:0.07, T:0.63
Consensus pattern (3 bp):
TCT
Done.