Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009985.1 Corchorus capsularis cultivar CVL-1 contig10006, 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: 71770
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:8828 original size:12 final size:12
Alignment explanation
Indices: 8811--8836 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8801 TATTTTGTTC
8811 ATGTGAAAAATT
1 ATGTGAAAAATT
8823 ATGTGAAAAATT
1 ATGTGAAAAATT
8835 AT
1 AT
8837 CAAAATCATA
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:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGTGAAAAATT
Found at i:10513 original size:25 final size:25
Alignment explanation
Indices: 10485--10533 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
10475 GATATGTAAA
10485 TCTGTAGATTTATCATATACTGTTT
1 TCTGTAGATTTATCATATACTGTTT
*
10510 TCTGTAGATTTATCCTATACTGTT
1 TCTGTAGATTTATCATATACTGTT
10534 AGCTATCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.51
Consensus pattern (25 bp):
TCTGTAGATTTATCATATACTGTTT
Found at i:19040 original size:4 final size:4
Alignment explanation
Indices: 19031--19057 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19021 GGAATATTAG
19031 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
19058 GTAAAAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:20049 original size:17 final size:17
Alignment explanation
Indices: 19993--20051 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
19983 AAGTTTTTCC
19993 AAGTTTTCAAATTGGGA
1 AAGTTTTCAAATTGGGA
* * **
20010 AAGTTCCCATCAAGTTGTCA
1 AAGTT---TTCAAATTGGGA
20030 AAGTTTTCAAATTGGGA
1 AAGTTTTCAAATTGGGA
20047 AAGTT
1 AAGTT
20052 CCCATCAGAT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
17 18 0.58
20 13 0.42
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (17 bp):
AAGTTTTCAAATTGGGA
Found at i:20106 original size:34 final size:34
Alignment explanation
Indices: 19997--20106 Score: 98
Period size: 37 Copynumber: 3.1 Consensus size: 34
19987 TTTTCCAAGT
* *
19997 TTTCAAATTGGGAAAGTTCCCATCA-AGTTGTCAAAGT
1 TTTCAAATTGGGAAAGTTCCCACCAGA-TT-TC--AGG
* * *
20034 TTTCAAATTGGGAAAGTTCCCATCAGATTTTAGT
1 TTTCAAATTGGGAAAGTTCCCACCAGATTTCAGG
* *
20068 TTTCAATTTAGGGAAAGTTCCCGCCAG-TTTCAGG
1 TTTCAAATT-GGGAAAGTTCCCACCAGATTTCAGG
20102 TTTCA
1 TTTCA
20107 GTTTTCAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
34 21 0.32
35 15 0.23
36 1 0.02
37 27 0.42
38 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (34 bp):
TTTCAAATTGGGAAAGTTCCCACCAGATTTCAGG
Found at i:21605 original size:42 final size:42
Alignment explanation
Indices: 21546--21647 Score: 204
Period size: 42 Copynumber: 2.4 Consensus size: 42
21536 TTTGGAGCAA
21546 GAATATTCCAATCGATTCTATGTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTATGTCTACTACAATCGATTCTAG
21588 GAATATTCCAATCGATTCTATGTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTATGTCTACTACAATCGATTCTAG
21630 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
21648 CAAGATATGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (42 bp):
GAATATTCCAATCGATTCTATGTCTACTACAATCGATTCTAG
Found at i:21641 original size:21 final size:21
Alignment explanation
Indices: 21546--21647 Score: 114
Period size: 21 Copynumber: 4.9 Consensus size: 21
21536 TTTGGAGCAA
*
21546 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * *
21567 GTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTAG
*
21588 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * *
21609 GTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTAG
21630 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
21648 CAAGATATGC
Statistics
Matches: 62, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATATTCCAATCGATTCTAG
Found at i:27403 original size:33 final size:33
Alignment explanation
Indices: 27327--27429 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
27317 GAAAAGAGTG
* * *
27327 TTTTAGATGTTGTTTGCGATGATACTAAACCTAA
1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCT-A
* * * *
27361 TCTCA-GTGTTGTTTGCGATGACACTAAATCTG
1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
* *
27393 TTTTAGGTGTTGTTTGTGATGAAACAAAATCTA
1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
27426 TTTT
1 TTTT
27430 GGATGCTAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
32 3 0.05
33 50 0.89
34 3 0.05
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (33 bp):
TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA
Found at i:28051 original size:21 final size:21
Alignment explanation
Indices: 28012--28051 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28002 CAAGCACCAA
*
28012 GAAGATGCCATTCGATCCACG
1 GAAGATGCCATTAGATCCACG
28033 GAAGATGCCTATTAG-TCCA
1 GAAGATGCC-ATTAGATCCA
28052 ATGACAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
GAAGATGCCATTAGATCCACG
Found at i:40349 original size:21 final size:21
Alignment explanation
Indices: 40296--40355 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
40286 TTTGGAGCAA
*
40296 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * *
40317 GTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTAG
40338 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
40356 CAAGATATGC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATATTCCAATCGATTCTAG
Found at i:41481 original size:30 final size:30
Alignment explanation
Indices: 41464--41536 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
41454 AGTACTTGGT
41464 GCATCATTCCCTCCATGATAAGCTTTGGGC
1 GCATCATTCCCTCCATGATAAGCTTTGGGC
41494 GCATCATTCCCTCCATGATAAGCTTTGGGC
1 GCATCATTCCCTCCATGATAAGCTTTGGGC
41524 GCATCATTCCCTC
1 GCATCATTCCCTC
41537 GCCCTTGAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.19, C:0.33, G:0.18, T:0.30
Consensus pattern (30 bp):
GCATCATTCCCTCCATGATAAGCTTTGGGC
Found at i:43667 original size:30 final size:30
Alignment explanation
Indices: 43631--43691 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 30
43621 TGTCTTCTAG
43631 TCCATGATAAG-TACTT-GGCGCATCATTCCC
1 TCCATGATAAGCT--TTGGGCGCATCATTCCC
43661 TCCATGATAAGCTTTGGGCGCATCATTCCC
1 TCCATGATAAGCTTTGGGCGCATCATTCCC
43691 T
1 T
43692 TCCCTTGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 2 0.07
30 26 0.90
31 1 0.03
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (30 bp):
TCCATGATAAGCTTTGGGCGCATCATTCCC
Found at i:45870 original size:258 final size:258
Alignment explanation
Indices: 45542--46042 Score: 858
Period size: 258 Copynumber: 1.9 Consensus size: 258
45532 ATCAAGATGA
*
45542 GTTTGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTGTCATCGAACCTAA
1 GTTTGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTGTCATCGAACCAAA
* * *
45607 TGGCATCTTCAATGGATCAAATGACATGTTCTTGGTGCTTGGAACATGCTCAACGAGATCTCCAT
66 TGGCATCTTCAATAGATCAAATGACATCTTCTTGGTGCTTGGAACATGATCAACGAGATCTCCAT
* *
45672 GATCTTCATGCATCTTCATGCGTCCTTGCAGCCCATGCACATCATTTCCATGCTCTCCATGTTTG
131 GATCTTCATGCATCTCCATGCGTCCTTGCAGCCCATGCACATCATTTCCATGCTCTCCATGCTTG
* **
45737 TCTTCAAGTCCATGGTAAGTCCTTGGTGCATCATTCCCTCCATGATAACTTTTGATGGGACTT
196 TCTTCAAGTCCATGATAAGTCCTTGACGCATCATTCCCTCCATGATAACTTTTGATGGGACTT
*
45800 GTTTGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTGTCATCGGACCAAA
1 GTTTGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTGTCATCGAACCAAA
*
45865 TGGCATCTTCAATAGATCAAATGACATCTTCTTGGTGCTTGGAACATGATCAACGATATCTCCAT
66 TGGCATCTTCAATAGATCAAATGACATCTTCTTGGTGCTTGGAACATGATCAACGAGATCTCCAT
* * *
45930 GATCTTCATGCATCTCCATGCTTCCTTGCAGCCCATGCAGATCCTTTCCATGCTCTCCATGCTTG
131 GATCTTCATGCATCTCCATGCGTCCTTGCAGCCCATGCACATCATTTCCATGCTCTCCATGCTTG
* *
45995 TCTTCAAGTCCATGATAAGTCTTTGACGCATCATTCCCTCCGTGATAA
196 TCTTCAAGTCCATGATAAGTCCTTGACGCATCATTCCCTCCATGATAA
46043 GCATTAGGCG
Statistics
Matches: 227, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
258 227 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (258 bp):
GTTTGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGCTCTTGTCATCGAACCAAA
TGGCATCTTCAATAGATCAAATGACATCTTCTTGGTGCTTGGAACATGATCAACGAGATCTCCAT
GATCTTCATGCATCTCCATGCGTCCTTGCAGCCCATGCACATCATTTCCATGCTCTCCATGCTTG
TCTTCAAGTCCATGATAAGTCCTTGACGCATCATTCCCTCCATGATAACTTTTGATGGGACTT
Found at i:54072 original size:22 final size:22
Alignment explanation
Indices: 54044--54089 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
54034 TTAAAAACTC
*
54044 GACACCCTTTTTCTTGTCTTGT
1 GACACCCATTTTCTTGTCTTGT
*
54066 GACACCCATTTTCTTGTTTTGT
1 GACACCCATTTTCTTGTCTTGT
54088 GA
1 GA
54090 GAGGTTGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.24, G:0.15, T:0.48
Consensus pattern (22 bp):
GACACCCATTTTCTTGTCTTGT
Found at i:54988 original size:6 final size:6
Alignment explanation
Indices: 54977--55018 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
54967 AGGAAGAAAG
*
54977 AAGGAA AAGGAAA AAGGAA AAGGAA AAAG-A AAGG-A AAGGAA A
1 AAGGAA AAGG-AA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA A
55019 GAAGGAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.28
6 17 0.53
7 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAGGAA
Found at i:55000 original size:30 final size:30
Alignment explanation
Indices: 54966--55024 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
54956 TTTTTAAAAT
54966 AAGGAAGAAAG-AAGGAAAAGGAAA-AAGGAA
1 AAGGAA-AAAGAAAGG-AAAGGAAAGAAGGAA
54996 AAGGAAAAAGAAAGGAAAGGAAAGAAGGA
1 AAGGAAAAAGAAAGGAAAGGAAAGAAGGA
55025 GAGAGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (30 bp):
AAGGAAAAAGAAAGGAAAGGAAAGAAGGAA
Found at i:55023 original size:13 final size:14
Alignment explanation
Indices: 54972--55024 Score: 65
Period size: 13 Copynumber: 3.7 Consensus size: 14
54962 AAATAAGGAA
54972 GAAAGAAGGAAAAG
1 GAAAGAAGGAAAAG
54986 GAAA-AAGGAAAAG
1 GAAAGAAGGAAAAG
54999 GAAAAAGAAAGG-AAAG
1 G--AAAG-AAGGAAAAG
55015 GAAAGAAGGA
1 GAAAGAAGGA
55025 GAGAGAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 14 0.41
14 8 0.24
15 3 0.09
16 5 0.15
17 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
GAAAGAAGGAAAAG
Found at i:56799 original size:21 final size:22
Alignment explanation
Indices: 56773--56827 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
56763 TGACCGGCCA
56773 CATGCCCGA-CCATCACCATCG
1 CATGCCCGAGCCATCACCATCG
*
56794 CATGCCC-AGCCATCACCATTG
1 CATGCCCGAGCCATCACCATCG
56815 CATGTCCCG-GCCA
1 CATG-CCCGAGCCA
56828 CATGATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 22 0.73
22 7 0.23
ACGTcount: A:0.22, C:0.45, G:0.16, T:0.16
Consensus pattern (22 bp):
CATGCCCGAGCCATCACCATCG
Found at i:59736 original size:7 final size:8
Alignment explanation
Indices: 59720--59747 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
59710 GAAAAATATC
59720 AAAATAAA
1 AAAATAAA
59728 AAAATAAA
1 AAAATAAA
59736 AAAATAAA
1 AAAATAAA
59744 AAAA
1 AAAA
59748 CAATTTCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:62354 original size:31 final size:31
Alignment explanation
Indices: 62316--62380 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
62306 GTGAATCATT
62316 GATCATGGACACTAAACATAAATTTGGCTTA
1 GATCATGGACACTAAACATAAATTTGGCTTA
62347 GATCATGGACACTAAACATAAATTTGGCTTA
1 GATCATGGACACTAAACATAAATTTGGCTTA
62378 GAT
1 GAT
62381 TGCAATCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (31 bp):
GATCATGGACACTAAACATAAATTTGGCTTA
Found at i:67215 original size:22 final size:21
Alignment explanation
Indices: 67154--67207 Score: 99
Period size: 21 Copynumber: 2.5 Consensus size: 21
67144 TGACCGGCCA
67154 CATGCCCGGCCATCACCATCG
1 CATGCCCGGCCATCACCATCG
67175 CATGCCCGGCCATCACCATCG
1 CATGCCCGGCCATCACCATCG
67196 CATGTCCCGGCC
1 CATG-CCCGGCC
67208 TTGCCCATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.17, C:0.48, G:0.20, T:0.15
Consensus pattern (21 bp):
CATGCCCGGCCATCACCATCG
Done.