Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011751.1 Corchorus capsularis cultivar CVL-1 contig11772, 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: 40043
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3756 original size:21 final size:22
Alignment explanation
Indices: 3730--3772 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
3720 ACTTGTGTGC
3730 TTTCTTTGTGCCAAAA-AAAAA
1 TTTCTTTGTGCCAAAAGAAAAA
3751 TTTCTTTGTGCCAAAAGAAAAA
1 TTTCTTTGTGCCAAAAGAAAAA
3773 AAACATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
TTTCTTTGTGCCAAAAGAAAAA
Found at i:3811 original size:1 final size:1
Alignment explanation
Indices: 3805--3837 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
3795 CTCCTTCGTC
3805 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3838 CTTGCGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5959 original size:29 final size:27
Alignment explanation
Indices: 5892--5962 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
5882 TTACCCGGAA
*
5892 GGGGCAAATTGTCCTGAATTTAGAAAG
1 GGGGCAAATTGTCTTGAATTTAGAAAG
* * * *
5919 TGGGCAATTTGTCTTGATTTTAGTTTAAG
1 GGGGCAAATTGTCTTGAATTTAG--AAAG
5948 GGGGCAAATTGTCTT
1 GGGGCAAATTGTCTT
5963 TAGACCCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
27 19 0.54
29 16 0.46
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.37
Consensus pattern (27 bp):
GGGGCAAATTGTCTTGAATTTAGAAAG
Found at i:10995 original size:93 final size:93
Alignment explanation
Indices: 10834--11014 Score: 263
Period size: 93 Copynumber: 1.9 Consensus size: 93
10824 AACCTTCAAC
10834 TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTACATGGTCCTAGATGCCCACCC
1 TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTACATGGTCCTAGATGCCCACCC
10899 TCAATTAATTAACTCGTCAAAATGCCCA
66 TCAATTAATTAACTCGTCAAAATGCCCA
* * ** ** ** *
10927 TTTCTTAATATTTTGTATGTAATTTTACATGGTGTTCACCCTTATTTGGTCCTAGATGTTCACTC
1 TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTACATGGTCCTAGATGCCCACCC
* *
10992 TCAATTGATTAACTTGTCAAAAT
66 TCAATTAATTAACTCGTCAAAAT
11015 ATCTCTGAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (93 bp):
TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTACATGGTCCTAGATGCCCACCC
TCAATTAATTAACTCGTCAAAATGCCCA
Found at i:11716 original size:2 final size:2
Alignment explanation
Indices: 11709--11739 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11699 AAAGACAATC
11709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11740 TTGTCATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17268 original size:1 final size:1
Alignment explanation
Indices: 17262--17287 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
17252 CTCAGGATTT
17262 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
17288 CTTGTAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18283 original size:29 final size:29
Alignment explanation
Indices: 18244--18313 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
18234 TATGAACTGC
* *
18244 CACTTTGCACCCTACTTTTTTATTTTGAT
1 CACTTTGCACCCTAATGTTTTATTTTGAT
*
18273 CACTTTGCACCCTAATGTTTTATTTTGTT
1 CACTTTGCACCCTAATGTTTTATTTTGAT
*
18302 CTACGTTGCACC
1 C-ACTTTGCACC
18314 TTTTGTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.17, C:0.26, G:0.10, T:0.47
Consensus pattern (29 bp):
CACTTTGCACCCTAATGTTTTATTTTGAT
Found at i:22512 original size:13 final size:13
Alignment explanation
Indices: 22494--22522 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
22484 TCAGAATTGT
22494 TCAAATATACTAC
1 TCAAATATACTAC
22507 TCAAATATACTAC
1 TCAAATATACTAC
22520 TCA
1 TCA
22523 CACACACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (13 bp):
TCAAATATACTAC
Found at i:24500 original size:20 final size:20
Alignment explanation
Indices: 24458--24500 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
24448 TATCCACCTC
* **
24458 TTTTAATGACCTTATTATGT
1 TTTTAATGACCTTATAAAAT
*
24478 TTTTAGTGACCTTATAAAAT
1 TTTTAATGACCTTATAAAAT
24498 TTT
1 TTT
24501 AGTAAGCTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (20 bp):
TTTTAATGACCTTATAAAAT
Found at i:24510 original size:19 final size:19
Alignment explanation
Indices: 24478--24525 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
24468 CTTATTATGT
*
24478 TTTTAGTGACCTTA-TAAAA
1 TTTTAGTAACCTTACT-AAA
* *
24497 TTTTAGTAAGCTTACTAAG
1 TTTTAGTAACCTTACTAAA
24516 TTTTAGTAAC
1 TTTTAGTAAC
24526 TTTATTAACC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.44
Consensus pattern (19 bp):
TTTTAGTAACCTTACTAAA
Found at i:24919 original size:14 final size:14
Alignment explanation
Indices: 24882--24931 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
24872 TATACATTTT
24882 TTTAAGAAAATTCA
1 TTTAAGAAAATTCA
* * *
24896 GTT-AGGAAATTCT
1 TTTAAGAAAATTCA
24909 TTTAAGAAAATTCA
1 TTTAAGAAAATTCA
*
24923 ATTAAGAAA
1 TTTAAGAAA
24932 TGAAATTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (14 bp):
TTTAAGAAAATTCA
Found at i:24919 original size:27 final size:27
Alignment explanation
Indices: 24881--24932 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
24871 TTATACATTT
* *
24881 TTTTAAGAAAATTCAGTTAGGAAATTC
1 TTTTAAGAAAATTCAATTAAGAAATTC
24908 TTTTAAGAAAATTCAATTAAGAAAT
1 TTTTAAGAAAATTCAATTAAGAAAT
24933 GAAATTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (27 bp):
TTTTAAGAAAATTCAATTAAGAAATTC
Found at i:25249 original size:19 final size:19
Alignment explanation
Indices: 25227--25268 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
25217 GGACATCCAC
25227 AACATACATGTATATTCAT
1 AACATACATGTATATTCAT
25246 AACATACATGTATATTCAT
1 AACATACATGTATATTCAT
25265 AACA
1 AACA
25269 AATTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (19 bp):
AACATACATGTATATTCAT
Found at i:27789 original size:23 final size:23
Alignment explanation
Indices: 27760--27834 Score: 123
Period size: 23 Copynumber: 3.2 Consensus size: 23
27750 TTTCTCTGTT
*
27760 TTTTTGGGACTCCTTAGTGAGAG
1 TTTTTGGGACTCCTTTGTGAGAG
*
27783 TTTTTGGAACTCCTTTGTGAGAG
1 TTTTTGGGACTCCTTTGTGAGAG
27806 TTTTTGGGACTCCTTTGTGAGAG
1 TTTTTGGGACTCCTTTGTGAGAG
27829 CTTTTT
1 -TTTTT
27835 CTATTGTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 43 0.90
24 5 0.10
ACGTcount: A:0.15, C:0.13, G:0.27, T:0.45
Consensus pattern (23 bp):
TTTTTGGGACTCCTTTGTGAGAG
Found at i:30148 original size:181 final size:179
Alignment explanation
Indices: 29839--30200 Score: 571
Period size: 181 Copynumber: 2.0 Consensus size: 179
29829 TTGACGATTA
* * * * * *
29839 TACCCTTATTTTTCGATTATATTTCTTAAACGCCATTGTTTAAATTTTTATAGTTTTACTCAACT
1 TACCCTTATTTTTCAAATATATTTCTTAAACGCCACTGTTTAAACTTTTACAATTTTACTCAACT
** * *
29904 AAAAACTCTATTTTTATTTAATTTAATCTAATATATTTATAAATATTTTATTTTTATCATTTTAC
66 AAAAACTCTATTTTTATTTAATCAAATCTAATATATCTATAAATATTTTATTTTTACCATTTTAC
29969 TATATTAATTTAAAAAACTTAGATATATTAGAATTTTTAAAATATATTTCT
131 TATATTAATTT-AAAAA-TTAGATATATTAGAATTTTTAAAATATATTTCT
* *
30020 TACCCTTATTTTTCAAATATATTTCTTAAATGCCACTGTTTAAACTTTTACAATTTTACTCAATT
1 TACCCTTATTTTTCAAATATATTTCTTAAACGCCACTGTTTAAACTTTTACAATTTTACTCAACT
*
30085 AAAAACTCTATTTTTATTTAATCAAATCTAATATATCTATAATTATTTTATTTTTACCATTTTAC
66 AAAAACTCTATTTTTATTTAATCAAATCTAATATATCTATAAATATTTTATTTTTACCATTTTAC
* *
30150 TATTTTAATTTAAAAATTAGATATATTAGAATTTTTTAAATATATTTCT
131 TATATTAATTTAAAAATTAGATATATTAGAATTTTTAAAATATATTTCT
30199 TA
1 TA
30201 AATGACATTA
Statistics
Matches: 166, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
179 34 0.20
180 5 0.03
181 127 0.77
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.51
Consensus pattern (179 bp):
TACCCTTATTTTTCAAATATATTTCTTAAACGCCACTGTTTAAACTTTTACAATTTTACTCAACT
AAAAACTCTATTTTTATTTAATCAAATCTAATATATCTATAAATATTTTATTTTTACCATTTTAC
TATATTAATTTAAAAATTAGATATATTAGAATTTTTAAAATATATTTCT
Found at i:30483 original size:31 final size:31
Alignment explanation
Indices: 30448--30508 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
30438 TAAATACTAA
* *
30448 AAAAATCCCTTATGTTTTTCTTTTGGGACAG
1 AAAAATCCCTTATGTTTTTATTTTAGGACAG
30479 AAAAATCCCTTATGTTTTTATTTTAGGACA
1 AAAAATCCCTTATGTTTTTATTTTAGGACA
30509 AATTAGTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (31 bp):
AAAAATCCCTTATGTTTTTATTTTAGGACAG
Found at i:39677 original size:29 final size:29
Alignment explanation
Indices: 39642--39719 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
39632 ACTTGTAGCG
*
39642 TTTGGACGTTTTGTCCCCTGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
** * *
39671 TTTGGACACTTTACCCCCAGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
39700 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACGTTTTGCCCCCT
39720 CAGACTAACG
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 27 0.69
30 12 0.31
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.37
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCCTGAACTTCAAT
Found at i:39915 original size:29 final size:29
Alignment explanation
Indices: 39865--39944 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
39855 TTAGACTAAC
39865 TAAGAGGGCAAAACGTCTCAAAATTGAAATT
1 TAAG-GGGCAAAACGTC-CAAAATTGAAATT
* *
39896 TAAGGGGCAAAATGTCCAAAATTGAAGTT
1 TAAGGGGCAAAACGTCCAAAATTGAAATT
*
39925 T-AGGAAGCAAAACGTCCAAA
1 TAAGG-GGCAAAACGTCCAAA
39945 CGCTACAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 3 0.07
29 26 0.59
30 11 0.25
31 4 0.09
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (29 bp):
TAAGGGGCAAAACGTCCAAAATTGAAATT
Done.