Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013037.1 Corchorus capsularis cultivar CVL-1 contig13058, 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: 48041
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1613 original size:5 final size:5
Alignment explanation
Indices: 1603--1634 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1593 ATTGATATAT
1603 CAAAC CAAAC CAAAC CAAAC CAAAC CAAAC CA
1 CAAAC CAAAC CAAAC CAAAC CAAAC CAAAC CA
1635 GTACGACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAC
Found at i:4920 original size:14 final size:14
Alignment explanation
Indices: 4901--4928 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4891 AGTTAACGGA
4901 ACTTACAAGGTTTT
1 ACTTACAAGGTTTT
4915 ACTTACAAGGTTTT
1 ACTTACAAGGTTTT
4929 TCTAGTTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
ACTTACAAGGTTTT
Found at i:5879 original size:14 final size:14
Alignment explanation
Indices: 5846--5880 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5836 AAACGGTGCA
5846 GTTTTTGCTTTTTT
1 GTTTTTGCTTTTTT
*
5860 GCTTTTGCTTTTTT
1 GTTTTTGCTTTTTT
*
5874 TTTTTTG
1 GTTTTTG
5881 TTAGTTGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (14 bp):
GTTTTTGCTTTTTT
Found at i:6795 original size:11 final size:11
Alignment explanation
Indices: 6752--6789 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6742 TTCCTATATA
*
6752 AAATAAATTAT
1 AAATTAATTAT
6763 CAAA-TAATTAT
1 -AAATTAATTAT
6774 AAATTAATTAT
1 AAATTAATTAT
6785 AAATT
1 AAATT
6790 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:7146 original size:14 final size:14
Alignment explanation
Indices: 7101--7150 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
7091 ACAAAATTTC
7101 ATTTT-TTAACTAA
1 ATTTTCTTAACTAA
* **
7114 ATTTTCTAAACTTC
1 ATTTTCTTAACTAA
*
7128 A-TTTCTTAACTGA
1 ATTTTCTTAACTAA
7141 ATTTTCTTAA
1 ATTTTCTTAA
7151 AAGAATTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 15 0.52
14 14 0.48
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (14 bp):
ATTTTCTTAACTAA
Found at i:15345 original size:2 final size:2
Alignment explanation
Indices: 15332--15370 Score: 51
Period size: 2 Copynumber: 18.0 Consensus size: 2
15322 TTATAAATAA
15332 AT AT AT AGT AT AT AT AT AT AT AT ACT AT AT ACT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
15371 TATTTTTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 28 0.82
3 6 0.18
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15360 original size:7 final size:6
Alignment explanation
Indices: 15332--15370 Score: 51
Period size: 7 Copynumber: 6.0 Consensus size: 6
15322 TTATAAATAA
15332 ATATAT AGTATAT ATATAT ATATACT ATATACT ATATAT
1 ATATAT A-TATAT ATATAT ATATA-T ATATA-T ATATAT
15371 TATTTTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (6 bp):
ATATAT
Found at i:17841 original size:22 final size:22
Alignment explanation
Indices: 17813--17854 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
17803 TTATGTGAAT
17813 AGAAATTTAGGAAAATCAAAAA
1 AGAAATTTAGGAAAATCAAAAA
17835 AGAAATTTAGGAAAATCAAA
1 AGAAATTTAGGAAAATCAAA
17855 TGGCAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (22 bp):
AGAAATTTAGGAAAATCAAAAA
Found at i:18158 original size:1 final size:1
Alignment explanation
Indices: 18147--18190 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
18137 TTTCCCCATC
* * * *
18147 AAAACAAAAAAAAAAAAAAAAAATAAAAAATAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18191 TCTTCTTTCT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.02, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:18181 original size:21 final size:20
Alignment explanation
Indices: 18152--18191 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
18142 CCATCAAAAC
18152 AAAAAAAAAAAAAAAAAATA
1 AAAAAAAAAAAAAAAAAATA
*
18172 AAAAATAAAAGAAAAAAAAT
1 AAAAA-AAAAAAAAAAAAAT
18192 CTTCTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.90, C:0.00, G:0.03, T:0.07
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAAATA
Found at i:26020 original size:6 final size:6
Alignment explanation
Indices: 26002--26035 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
25992 AGAATCAACC
*
26002 CCCCCA CCTCCA CCCCCA CCCCCA CCCCCA CCCC
1 CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA CCCC
26036 TTGTATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.82, G:0.00, T:0.03
Consensus pattern (6 bp):
CCCCCA
Found at i:31390 original size:89 final size:89
Alignment explanation
Indices: 31239--31403 Score: 330
Period size: 89 Copynumber: 1.9 Consensus size: 89
31229 GATAATTCCC
31239 TTTTTTTTTTGGCATCAATCAAATAATTCCTTTAATCAGCATATATGAACACAACTAGCTGTTCT
1 TTTTTTTTTTGGCATCAATCAAATAATTCCTTTAATCAGCATATATGAACACAACTAGCTGTTCT
31304 GTTATTTATTGCCTAAACAAAAAG
66 GTTATTTATTGCCTAAACAAAAAG
31328 TTTTTTTTTTGGCATCAATCAAATAATTCCTTTAATCAGCATATATGAACACAACTAGCTGTTCT
1 TTTTTTTTTTGGCATCAATCAAATAATTCCTTTAATCAGCATATATGAACACAACTAGCTGTTCT
31393 GTTATTTATTG
66 GTTATTTATTG
31404 TCACTTGTAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 76 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (89 bp):
TTTTTTTTTTGGCATCAATCAAATAATTCCTTTAATCAGCATATATGAACACAACTAGCTGTTCT
GTTATTTATTGCCTAAACAAAAAG
Found at i:37028 original size:19 final size:19
Alignment explanation
Indices: 36967--37019 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 19
36957 ATGAGATTTT
36967 TCATTACACCAAAAAAAGA
1 TCATTACACCAAAAAAAGA
*
36986 TGCCATTACACCAAATAAAGA
1 T--CATTACACCAAAAAAAGA
37007 TCATTACACCAAA
1 TCATTACACCAAA
37020 CAATGATCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.51, C:0.25, G:0.06, T:0.19
Consensus pattern (19 bp):
TCATTACACCAAAAAAAGA
Found at i:39737 original size:2 final size:2
Alignment explanation
Indices: 39730--39766 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39720 AAGACATTAA
39730 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
39767 ACATAGACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:45088 original size:30 final size:31
Alignment explanation
Indices: 45047--45108 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
45037 ATTTAGAAAT
* * * *
45047 ATATTTTTTAAAAA-AATGGTATAATTGGAA
1 ATATGTTTTAAAAATAAGGGTACAATCGGAA
45077 ATATGTTTTAAAAATAAGGGTACAATCGGAA
1 ATATGTTTTAAAAATAAGGGTACAATCGGAA
45108 A
1 A
45109 ACATAAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (31 bp):
ATATGTTTTAAAAATAAGGGTACAATCGGAA
Found at i:45928 original size:29 final size:29
Alignment explanation
Indices: 45870--45947 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
45860 TTCGGAACCT
***
45870 AGCTTTATTTCAATTAAATTATGTTTTCA
1 AGCTTTATTTCAATTAAATTATGAAATCA
* *
45899 AGCTTTATTTCAATTAAGTTTTGAAATCA
1 AGCTTTATTTCAATTAAATTATGAAATCA
* * *
45928 ATCTATATTTCCAATAAAAT
1 AGCTTTATTT-CAATTAAAT
45948 CTCATATAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 32 0.82
30 7 0.18
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (29 bp):
AGCTTTATTTCAATTAAATTATGAAATCA
Found at i:47210 original size:108 final size:107
Alignment explanation
Indices: 46962--47201 Score: 312
Period size: 108 Copynumber: 2.3 Consensus size: 107
46952 AGTTTAGCCT
* * * * *
46962 TAATTTCATTAAATTTAACCCCAAATTAACATTTTGTTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAATTTAGCCCCAAATTAAAATTTTGTTTTCATTTTAAGGGTAAATTCCAAAATT
47027 AATAATTTATTGTTATAAGGTTTTAGAAATAAAATATACAAAAC
66 AATAA-TTATTGTTATAAGGTTTTAGAAATAAAATATA-AAAAC
* * *
47071 TAATTTCACTGAGTTTAGCCCCAAATTAAAATTTT-TTTTCATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAATTTAGCCCCAAATTAAAATTTTGTTTTCATTTTAAGGGTAAATTCCAAAATT
* *
47135 AATAA-TATTGTTAT-AGGATTTTAGAAATAAAATAT-ATAAT
66 AATAATTATTGTTATAAGG-TTTTAGAAATAAAATATAAAAAC
*
47175 TAA-TTCACTAAATTTAG-CCTAAATTAA
1 TAATTTCACTAAATTTAGCCCCAAATTAA
47202 GATTAAAATC
Statistics
Matches: 117, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
102 9 0.08
103 12 0.10
104 6 0.05
105 3 0.03
106 26 0.22
108 31 0.26
109 30 0.26
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (107 bp):
TAATTTCACTAAATTTAGCCCCAAATTAAAATTTTGTTTTCATTTTAAGGGTAAATTCCAAAATT
AATAATTATTGTTATAAGGTTTTAGAAATAAAATATAAAAAC
Done.