Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012034.1 Corchorus olitorius cultivar O-4 contig12067, 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: 25151
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:7829 original size:42 final size:42
Alignment explanation
Indices: 7651--7854 Score: 256
Period size: 40 Copynumber: 4.9 Consensus size: 42
7641 CAAAGCCGAC
**
7651 GGGATCTTTCCCTAAATTGAAAACTTTTTGAAAAACTTCTTGAT
1 GGGATCTTTCCCTAAATTGAAAAC-TTTTG-AAAACTTGATGAT
* * *
7695 GGCATCTTTCCCTAAATTGAAAACTTTTGAAAA-TT-TTCAT
1 GGGATCTTTCCCTAAATTGAAAACTTTTGAAAACTTGATGAT
* * **
7735 GGGATCTTTCCCTAAATTGGAAAC--TGGACGACTTGATGAT
1 GGGATCTTTCCCTAAATTGAAAACTTTTGAAAACTTGATGAT
7775 GGGATCTTTCCCTAAATTGAAAAC-TTTGAAAAACTTGATGAT
1 GGGATCTTTCCCTAAATTGAAAACTTTTG-AAAACTTGATGAT
*
7817 GGGATCTCTCCCTAAATTGAAAACTTTTGAAAACTTGA
1 GGGATCTTTCCCTAAATTGAAAACTTTTGAAAACTTGA
7855 ATTGATTTTG
Statistics
Matches: 141, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
38 4 0.03
39 2 0.01
40 52 0.37
41 4 0.03
42 47 0.33
43 9 0.06
44 23 0.16
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (42 bp):
GGGATCTTTCCCTAAATTGAAAACTTTTGAAAACTTGATGAT
Found at i:9857 original size:11 final size:11
Alignment explanation
Indices: 9841--9866 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9831 AGATAATTTC
9841 TTTTCTTCTAG
1 TTTTCTTCTAG
9852 TTTTCTTCTAG
1 TTTTCTTCTAG
9863 TTTT
1 TTTT
9867 TTTTAGGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:11100 original size:28 final size:29
Alignment explanation
Indices: 11060--11115 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
11050 TTTGTTTTGT
*
11060 GTTTTTGCGTTTTT-CTAAAAAAAAAAGG
1 GTTTTTGCATTTTTACTAAAAAAAAAAGG
* *
11088 GTTTTTGCATTTTTATTTAAAAAAAAAG
1 GTTTTTGCATTTTTACTAAAAAAAAAAG
11116 TTTCTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (29 bp):
GTTTTTGCATTTTTACTAAAAAAAAAAGG
Found at i:15430 original size:19 final size:18
Alignment explanation
Indices: 15406--15441 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
15396 TGAAGACCAT
15406 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
15425 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
15442 TCTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:18523 original size:18 final size:19
Alignment explanation
Indices: 18489--18527 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
18479 CTCCTCTATC
*
18489 ATGAAAACACTTTTTTTTA
1 ATGAAAACACATTTTTTTA
18508 ATGAAAACA-ATTTTTTTA
1 ATGAAAACACATTTTTTTA
18526 AT
1 AT
18528 TACCCTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (19 bp):
ATGAAAACACATTTTTTTA
Found at i:18977 original size:97 final size:97
Alignment explanation
Indices: 18870--19063 Score: 379
Period size: 97 Copynumber: 2.0 Consensus size: 97
18860 TCAAAAATTG
18870 GGGAAAATAAGATCAATCCAAAAATACTCAAATTCTATCCTAGGTTCTCATGCAAACAAGGACTA
1 GGGAAAATAAGATCAATCCAAAAATACTCAAATTCTATCCTAGGTTCTCATGCAAACAAGGACTA
18935 TCATATGACTCAATTATTCAAGTAATACCCCT
66 TCATATGACTCAATTATTCAAGTAATACCCCT
*
18967 GGGAAAATAAGATCAATCCAAAAATACTCAAATTTTATCCTAGGTTCTCATGCAAACAAGGACTA
1 GGGAAAATAAGATCAATCCAAAAATACTCAAATTCTATCCTAGGTTCTCATGCAAACAAGGACTA
19032 TCATATGACTCAATTATTCAAGTAATACCCCT
66 TCATATGACTCAATTATTCAAGTAATACCCCT
19064 ATCAAGAAAA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.27
Consensus pattern (97 bp):
GGGAAAATAAGATCAATCCAAAAATACTCAAATTCTATCCTAGGTTCTCATGCAAACAAGGACTA
TCATATGACTCAATTATTCAAGTAATACCCCT
Found at i:20358 original size:21 final size:22
Alignment explanation
Indices: 20318--20358 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20308 CTTGTCGACG
**
20318 ATTTTGCTTCCCTTGGTCGATA
1 ATTTTGCTTCCCTTAATCGATA
20340 ATTTTGC-TCCCTTAATCGA
1 ATTTTGCTTCCCTTAATCGA
20359 ATCTTGGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (22 bp):
ATTTTGCTTCCCTTAATCGATA
Found at i:21195 original size:18 final size:19
Alignment explanation
Indices: 21161--21201 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
21151 AACTCAAAGA
21161 AAAAATTACTGTAAAAATT
1 AAAAATTACTGTAAAAATT
21180 AAAAATTA-TG-ATAAAATT
1 AAAAATTACTGTA-AAAATT
21198 AAAA
1 AAAA
21202 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.05
18 12 0.57
19 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAAATTACTGTAAAAATT
Found at i:24136 original size:17 final size:18
Alignment explanation
Indices: 24101--24136 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24091 CTCCTCTATC
*
24101 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
24119 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
24136 A
1 A
24137 ATTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Done.