Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008146.1 Corchorus capsularis cultivar CVL-1 contig08167, 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: 35828
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1038 original size:45 final size:45
Alignment explanation
Indices: 987--1077 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
977 TTAATAATCT
*
987 TACATTTTAGTAACTTTATTAAATTTTCGTCAGTGGAGAAGGTTA
1 TACATTTTAGTAACTTTATTAAATTATCGTCAGTGGAGAAGGTTA
*
1032 TACATTTTAGTAACTTTATTAAATTATCGTTAGTGGAGAAGGTTA
1 TACATTTTAGTAACTTTATTAAATTATCGTCAGTGGAGAAGGTTA
1077 T
1 T
1078 TTTTTTATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.43
Consensus pattern (45 bp):
TACATTTTAGTAACTTTATTAAATTATCGTCAGTGGAGAAGGTTA
Found at i:1271 original size:24 final size:24
Alignment explanation
Indices: 1239--1317 Score: 149
Period size: 24 Copynumber: 3.2 Consensus size: 24
1229 ATTAGCAATC
1239 TAAAGACTATCTTCTCTTCTTGTA
1 TAAAGACTATCTTCTCTTCTTGTA
1263 TAAAGACTATCTTCTCTTCTTGTA
1 TAAAGACTATCTTCTCTTCTTGTA
1287 TAAAGACTATCTTCTCTTCTTGTA
1 TAAAGACTATCTTCTCTTCTTGTA
1311 TATAAGA
1 TA-AAGA
1318 AATTAACAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 50 0.93
25 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (24 bp):
TAAAGACTATCTTCTCTTCTTGTA
Found at i:2157 original size:37 final size:37
Alignment explanation
Indices: 2115--2185 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
2105 ACATGATTAT
* *
2115 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
2152 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
2186 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:3408 original size:31 final size:32
Alignment explanation
Indices: 3370--3431 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
3360 TGGGGGTGTC
3370 TTGGTTTCTTAAAGAAAC-AAAGAGATATATG
1 TTGGTTTCTTAAAGAAACAAAAGAGATATATG
* *
3401 TTGGTTTCTTAGAGAAACAAAAGAGTTATAT
1 TTGGTTTCTTAAAGAAACAAAAGAGATATAT
3432 CACTATGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (32 bp):
TTGGTTTCTTAAAGAAACAAAAGAGATATATG
Found at i:12728 original size:19 final size:18
Alignment explanation
Indices: 12691--12729 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12681 TTCTTGAAAT
*
12691 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
12709 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
12728 AA
1 AA
12730 ATAATATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:13872 original size:17 final size:18
Alignment explanation
Indices: 13840--13875 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13830 CTCCTCTTGC
*
13840 ATGAAAGCACTTTTTTTT
1 ATGAAAACACTTTTTTTT
13858 ATGAAAACA-TTTTTTTT
1 ATGAAAACACTTTTTTTT
13875 A
1 A
13876 ACTACCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (18 bp):
ATGAAAACACTTTTTTTT
Found at i:14704 original size:21 final size:21
Alignment explanation
Indices: 14658--14705 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
14648 GATAGCCTGA
* *
14658 GATGACCGGTGGTGGCATGGT
1 GATGGCCGGTGGTGGCACGGT
*
14679 GATGGCCGGTGGTGGCGCGGT
1 GATGGCCGGTGGTGGCACGGT
*
14700 TATGGC
1 GATGGC
14706 TGCGCGTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.10, C:0.17, G:0.50, T:0.23
Consensus pattern (21 bp):
GATGGCCGGTGGTGGCACGGT
Found at i:16497 original size:22 final size:23
Alignment explanation
Indices: 16471--16513 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
16461 GTCATTTTCT
16471 AATTCACT-TTTGGCATTTAGTA
1 AATTCACTCTTTGGCATTTAGTA
*
16493 AATTCACTCTTTGGCCTTTAG
1 AATTCACTCTTTGGCATTTAG
16514 CATAACATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (23 bp):
AATTCACTCTTTGGCATTTAGTA
Found at i:19740 original size:43 final size:43
Alignment explanation
Indices: 19649--19740 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
19639 TTAAATTTAA
* *
19649 ATAATTGGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
1 ATAATTGGGTAAACAACTTAATTCAGTGTAATTAAGCAAATTG
* * *
19692 GTAATTGGGTAATCAACTTAATTCAGTGTAATTAAGCAATTTG
1 ATAATTGGGTAAACAACTTAATTCAGTGTAATTAAGCAAATTG
19735 ATAATT
1 ATAATT
19741 AGATTAAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (43 bp):
ATAATTGGGTAAACAACTTAATTCAGTGTAATTAAGCAAATTG
Found at i:19746 original size:21 final size:21
Alignment explanation
Indices: 19722--19762 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19712 ATTCAGTGTA
*
19722 ATTAAGCAATTTGATAATTAG
1 ATTAAGCAACTTGATAATTAG
* *
19743 ATTAAGTAACTTGGTAATTA
1 ATTAAGCAACTTGATAATTA
19763 ACTTAATTCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (21 bp):
ATTAAGCAACTTGATAATTAG
Found at i:19815 original size:21 final size:21
Alignment explanation
Indices: 19777--19829 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
19767 AATTCGGTGC
* *
19777 AATTAAGAAAATT-GTAATTA
1 AATTAAGTAATTTGGTAATTA
*
19797 AGTTAAGTAATTTGGTAATTA
1 AATTAAGTAATTTGGTAATTA
19818 AATTAAGTAATT
1 AATTAAGTAATT
19830 AACTCAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (21 bp):
AATTAAGTAATTTGGTAATTA
Found at i:19816 original size:55 final size:56
Alignment explanation
Indices: 19692--19823 Score: 169
Period size: 56 Copynumber: 2.4 Consensus size: 56
19682 AAGTAAATTG
* * * * *
19692 GTAATTGGGTAATCAACTTAATTCAGTGTAATTAAGCAATTTGATAATTAGATTAA
1 GTAATTTGGTAATTAACTTAATTCAGTGCAATTAAGAAAATTGATAATTAGATTAA
* *
19748 GTAACTTGGTAATTAACTTAATTCGGTGCAATTAAGAAAATTG-TAATTA-AGTTAA
1 GTAATTTGGTAATTAACTTAATTCAGTGCAATTAAGAAAATTGATAATTAGA-TTAA
*
19803 GTAATTTGGTAATTAAATTAA
1 GTAATTTGGTAATTAACTTAA
19824 GTAATTAACT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
54 1 0.02
55 29 0.44
56 36 0.55
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (56 bp):
GTAATTTGGTAATTAACTTAATTCAGTGCAATTAAGAAAATTGATAATTAGATTAA
Found at i:19916 original size:35 final size:35
Alignment explanation
Indices: 19877--19943 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
19867 AGTAACTTGG
*
19877 TAATTAACTTAACTCAGTGTAATTAAGTAAATCAA
1 TAATTAACTTAACTCAGTGTAACTAAGTAAATCAA
** * **
19912 TAATTGGCTTAATTTGGTGTAACTAAGTAAAT
1 TAATTAACTTAACTCAGTGTAACTAAGTAAAT
19944 AAATGGCTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (35 bp):
TAATTAACTTAACTCAGTGTAACTAAGTAAATCAA
Found at i:20655 original size:21 final size:22
Alignment explanation
Indices: 20631--20677 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
20621 TTTATAACGC
20631 AAACCCTAATT-TTTT-AAGAAA
1 AAACCC-AATTCTTTTCAAGAAA
* *
20652 AAACGCAATTCTTTTCTAGAAA
1 AAACCCAATTCTTTTCAAGAAA
20674 AAAC
1 AAAC
20678 GCAAAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 9 0.41
22 9 0.41
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (22 bp):
AAACCCAATTCTTTTCAAGAAA
Found at i:21765 original size:27 final size:27
Alignment explanation
Indices: 21735--21805 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
21725 TAGGGTCATC
* * *
21735 CAGGAGCATTTTGGTCATTTTCACATT
1 CAGGGGCATTTTGGTCATTTGCACACT
* *
21762 CAGGGGCATTTAGGTCGTTTGCACACT
1 CAGGGGCATTTTGGTCATTTGCACACT
*
21789 CAGGGGTATTTTGGTCA
1 CAGGGGCATTTTGGTCA
21806 CATTATTCCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTGCACACT
Found at i:27097 original size:19 final size:18
Alignment explanation
Indices: 27060--27098 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
27050 TTCTTGAAAT
*
27060 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
27078 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
27097 AA
1 AA
27099 ATAATCTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Done.