Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012068.1 Corchorus olitorius cultivar O-4 contig12101, 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: 37354
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1441 original size:204 final size:201
Alignment explanation
Indices: 1056--1465 Score: 721
Period size: 204 Copynumber: 2.0 Consensus size: 201
1046 GCTTAATAAC
1056 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
1121 GATACAACACATTATTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATATAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTG
1186 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTCCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTCCAAAATTATAAAAGATATT-AAGATC
1251 CGATTTA
195 CGATTTA
*
1258 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* * *
1323 GATACAACAGATTACTATTATATATATAGAACTATACAAAAAAAAATTAGTTGAATATTAGTGGT
66 GATACAACACATTACTATTATATATAT--AACTATACAAAAAAAAAGTAGTTGAACATTAGTGGT
* *
1388 TGGTTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTCCAAAATTATAAAAGATATTAAGAT
1453 CCGATTTA
194 CCGATTTA
1461 TTTAT
1 TTTAT
1466 TATTAAGGAA
Statistics
Matches: 198, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
202 89 0.45
203 18 0.09
204 91 0.46
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATATAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTCCAAAATTATAAAAGATATTAAGATCC
GATTTA
Found at i:1571 original size:24 final size:23
Alignment explanation
Indices: 1539--1584 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1529 ACGTTTGCAC
*
1539 AAATACCTAAGAATTTAAATTAAA
1 AAATACCTAAAAATTT-AATTAAA
1563 AAATACCTAAAAATTTAATTAA
1 AAATACCTAAAAATTTAATTAA
1585 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATACCTAAAAATTTAATTAAA
Found at i:1634 original size:39 final size:40
Alignment explanation
Indices: 1575--1655 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
1565 ATACCTAAAA
* * *
1575 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAATATTTCAGTTATTATATATATTAC
*
1614 ATTTAATTAATATAAATATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAATATTTCAGTTATTATATATATTAC
1654 AT
1 AT
1656 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATATAAATATTTCAGTTATTATATATATTAC
Found at i:13176 original size:12 final size:11
Alignment explanation
Indices: 13159--13196 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
13149 TTTCAAAAGG
13159 TTTTCTCTTTT
1 TTTTCTCTTTT
13170 CTTTTCT-TTTT
1 -TTTTCTCTTTT
13181 TTTTCTTCTTTT
1 TTTTC-TCTTTT
13193 TTTT
1 TTTT
13197 TGATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.21
11 5 0.21
12 14 0.58
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:13189 original size:13 final size:13
Alignment explanation
Indices: 13173--13197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13163 CTCTTTTCTT
13173 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
13186 TTCTTTTTTTTT
1 TTCTTTTTTTTT
13198 GATTTTTTTT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:13190 original size:23 final size:22
Alignment explanation
Indices: 13159--13207 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
13149 TTTCAAAAGG
*
13159 TTTTCTCTTTTCTTTTCTTTTT
1 TTTTCTCTTTTCTTTTCATTTT
* *
13181 TTTTCTTCTTTTTTTTTGATTTT
1 TTTTC-TCTTTTCTTTTCATTTT
13204 TTTT
1 TTTT
13208 AGTGATAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTCTCTTTTCTTTTCATTTT
Found at i:19636 original size:10 final size:10
Alignment explanation
Indices: 19621--19645 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19611 GAATTTGGTG
19621 AGATCAAGCC
1 AGATCAAGCC
19631 AGATCAAGCC
1 AGATCAAGCC
19641 AGATC
1 AGATC
19646 CACAAGCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.28, G:0.20, T:0.12
Consensus pattern (10 bp):
AGATCAAGCC
Found at i:29094 original size:31 final size:30
Alignment explanation
Indices: 29054--29148 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
29044 AGACACTTTG
29054 GCCCCTGAACTTGTAAGAAAGGGACAAATTA
1 GCCCCTGAACTTGTAA-AAAGGGACAAATTA
* * ** *
29085 GCCCTTGAACTT-CAAAAATTG-CCAATT-
1 GCCCCTGAACTTGTAAAAAGGGACAAATTA
29112 GCACGCCTGAACTTGTAAAAAAGGGACAAATTA
1 GC-C-CCTGAACTTGT-AAAAAGGGACAAATTA
29145 GCCC
1 GCCC
29149 TTTTGGGACG
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
27 2 0.04
28 6 0.12
29 12 0.25
30 2 0.04
31 18 0.38
32 6 0.12
33 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (30 bp):
GCCCCTGAACTTGTAAAAAGGGACAAATTA
Found at i:31944 original size:24 final size:26
Alignment explanation
Indices: 31892--31945 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
31882 TTACTACTTT
*
31892 AAACTAATATATATGTTTGATGCCAAAA
1 AAACTAATATATATGTTTCATG-C-AAA
31920 AAACTAATATATATG-TTCATG-AAA
1 AAACTAATATATATGTTTCATGCAAA
31944 AA
1 AA
31946 CTTGATAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 5 0.20
27 5 0.20
28 15 0.60
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (26 bp):
AAACTAATATATATGTTTCATGCAAA
Found at i:35454 original size:48 final size:48
Alignment explanation
Indices: 35398--35495 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
35388 CTATCAAGTG
35398 CATAGTCTGACGGTAGAATTATTGTTTTAAACTCTTAAATTTGATGAT
1 CATAGTCTGACGGTAGAATTATTGTTTTAAACTCTTAAATTTGATGAT
*
35446 CATAGTCTGACGGTAGAATTATTGTTTTAGACTCTTAAATTTGATGAT
1 CATAGTCTGACGGTAGAATTATTGTTTTAAACTCTTAAATTTGATGAT
35494 CA
1 CA
35496 GAATTCAAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (48 bp):
CATAGTCTGACGGTAGAATTATTGTTTTAAACTCTTAAATTTGATGAT
Done.