Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018899.1 Corchorus olitorius cultivar O-4 contig18932, 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: 39488
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5642 original size:35 final size:35
Alignment explanation
Indices: 5582--5652 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
5572 TCATGTAGTA
* * *
5582 TGGATGTTGTGGCAATGTAAGTCTTTAGTCTTATG
1 TGGATGTTATGGCAATGCAAATCTTTAGTCTTATG
* * *
5617 TGGATGTTATGGCAGTGCAAATCTTTATTTTTATG
1 TGGATGTTATGGCAATGCAAATCTTTAGTCTTATG
5652 T
1 T
5653 TCAAGGTGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.45
Consensus pattern (35 bp):
TGGATGTTATGGCAATGCAAATCTTTAGTCTTATG
Found at i:7781 original size:17 final size:18
Alignment explanation
Indices: 7759--7804 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
7749 ACTCCAAAGC
7759 AAAAAAAAAAAAACAA-A
1 AAAAAAAAAAAAACAAGA
*
7776 AAAAAACAAAAAACAAGA
1 AAAAAAAAAAAAACAAGA
7794 ACAAAAAAAAA
1 A-AAAAAAAAA
7805 TCTTGATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.60
18 2 0.08
19 8 0.32
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAACAAGA
Found at i:7796 original size:23 final size:23
Alignment explanation
Indices: 7760--7804 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
7750 CTCCAAAGCA
7760 AAAAAAAAAAAACAAAAAAAAAC
1 AAAAAAAAAAAACAAAAAAAAAC
* *
7783 AAAAAACAAGAACAAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAAA
7805 TCTTGATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAACAAAAAAAAAC
Found at i:10735 original size:20 final size:20
Alignment explanation
Indices: 10710--10762 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
10700 GAGAAAATAG
10710 AAACTGGGTTTTGTTGCTCA
1 AAACTGGGTTTTGTTGCTCA
10730 AAACTGGGTTTTGTTGCTCA
1 AAACTGGGTTTTGTTGCTCA
10750 AAACTGGGTTTTG
1 AAACTGGGTTTTG
10763 ATAAATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (20 bp):
AAACTGGGTTTTGTTGCTCA
Found at i:11813 original size:6 final size:6
Alignment explanation
Indices: 11799--11830 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
11789 ATTAATCAAG
*
11799 TTATTA TTATAA TTATAA TTATAA TTATAA TT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TT
11831 GTAAGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTATAA
Found at i:22224 original size:25 final size:24
Alignment explanation
Indices: 22196--22257 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
22186 GTGGATTGTA
*
22196 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
22221 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
22245 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
22258 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:24354 original size:41 final size:42
Alignment explanation
Indices: 24262--24385 Score: 214
Period size: 41 Copynumber: 3.0 Consensus size: 42
24252 GCTAAGTCTT
* *
24262 GAAAATTCTCTGTAAATTGAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
*
24304 GAAAATTCTTTGTAGATTAAGAAATACTCAACTC-AATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
24345 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCAT
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCAT
24386 GATCCTTAGC
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
41 40 0.52
42 37 0.48
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (42 bp):
GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:24521 original size:56 final size:59
Alignment explanation
Indices: 24453--24565 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 59
24443 TTTTGTAGAT
24453 TAATCAAGTAGAGATA-GGGGGATA-G-GATTTATTATAACATTTATTGTGTGAAAAAA
1 TAATCAAGTAGAGATAGGGGGGATATGAGATTTATTATAACATTTATTGTGTGAAAAAA
* * *
24509 TAATTAAGTAGAGATAGGGGGGATATGAATATTTATTATAATATTTATTGTGTGAAA
1 TAATCAAGTAGAGATAGGGGGGATATG-AGATTTATTATAACATTTATTGTGTGAAA
24566 GAAAACTAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
56 15 0.30
57 8 0.16
58 1 0.02
60 26 0.52
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (59 bp):
TAATCAAGTAGAGATAGGGGGGATATGAGATTTATTATAACATTTATTGTGTGAAAAAA
Found at i:24756 original size:2 final size:2
Alignment explanation
Indices: 24744--24814 Score: 88
Period size: 2 Copynumber: 33.5 Consensus size: 2
24734 GTTTCAAATA
* *
24744 AT AT GT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
24787 AT AT AGT AT AT AGT AT AT AGT AT AT AT A
1 AT AT A-T AT AT A-T AT AT A-T AT AT AT A
24815 ATTTCATACA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 53 0.87
3 8 0.13
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (2 bp):
AT
Found at i:26477 original size:21 final size:21
Alignment explanation
Indices: 26453--26495 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
26443 AAAATTTTTC
26453 TCAAGCTTCGGGCTCTTCTAG
1 TCAAGCTTCGGGCTCTTCTAG
*
26474 TCAAGCTTTGGGCTCTTCTAG
1 TCAAGCTTCGGGCTCTTCTAG
26495 T
1 T
26496 AAGGCCCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (21 bp):
TCAAGCTTCGGGCTCTTCTAG
Found at i:32908 original size:13 final size:13
Alignment explanation
Indices: 32892--32925 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
32882 AGAATGGCTA
*
32892 ATATAAATATTAT
1 ATATAAATAATAT
*
32905 ATATATATAATAT
1 ATATAAATAATAT
32918 ATATAAAT
1 ATATAAAT
32926 GTACTAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATAAATAATAT
Done.