Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007685.1 Corchorus capsularis cultivar CVL-1 contig07706, 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: 57293
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1947 original size:31 final size:31
Alignment explanation
Indices: 1910--1994 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
1900 CTGACCTTCT
* * *
1910 AATCGGCTCAAATCAATCCCTAACGGTGTAA
1 AATCGGCTCAAATCAGTCCCTAACAGTGCAA
*
1941 AATCGGCTCAAATCAGTCCCTAACATTGCAA
1 AATCGGCTCAAATCAGTCCCTAACAGTGCAA
* *
1972 AATCGACTCAAATTAGTCCCTAA
1 AATCGGCTCAAATCAGTCCCTAA
1995 TGTCAATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (31 bp):
AATCGGCTCAAATCAGTCCCTAACAGTGCAA
Found at i:3480 original size:14 final size:13
Alignment explanation
Indices: 3461--3514 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 13
3451 CCACCACACG
3461 TCTTTCTCTCTCTT
1 TCTTTCTCTCT-TT
*
3475 TCTTTCTTTCTTT
1 TCTTTCTCTCTTT
3488 TGCTTTCTCT-TTT
1 T-CTTTCTCTCTTT
* *
3501 TCTCTCTCCCTTT
1 TCTTTCTCTCTTT
3514 T
1 T
3515 TCCCTATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
12 6 0.18
13 11 0.32
14 17 0.50
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (13 bp):
TCTTTCTCTCTTT
Found at i:18034 original size:17 final size:17
Alignment explanation
Indices: 18012--18046 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18002 AATGCAATGA
*
18012 GCAAATGATGCATGTAT
1 GCAAATGATGCATATAT
18029 GCAAATGATGCATATAT
1 GCAAATGATGCATATAT
18046 G
1 G
18047 AGGGATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (17 bp):
GCAAATGATGCATATAT
Found at i:19942 original size:13 final size:13
Alignment explanation
Indices: 19924--19951 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19914 TTTTTTTTGG
19924 CATCATAAAAAAA
1 CATCATAAAAAAA
19937 CATCATAAAAAAA
1 CATCATAAAAAAA
19950 CA
1 CA
19952 AAAAAAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.14
Consensus pattern (13 bp):
CATCATAAAAAAA
Found at i:21717 original size:54 final size:54
Alignment explanation
Indices: 21653--21761 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
21643 GAAAGAATAA
*
21653 TACTTTAACAAATTGCTATATAGTTTTTGAAAAAAAGATATAAATACATGCATC
1 TACTTTAACAAATTGCTATATAGTCTTTGAAAAAAAGATATAAATACATGCATC
21707 TACTTTAACAAATTGCTATATAGTCTTTGAAAAAAAGATATAAATACATGCATC
1 TACTTTAACAAATTGCTATATAGTCTTTGAAAAAAAGATATAAATACATGCATC
21761 T
1 T
21762 TATGATAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (54 bp):
TACTTTAACAAATTGCTATATAGTCTTTGAAAAAAAGATATAAATACATGCATC
Found at i:22783 original size:41 final size:42
Alignment explanation
Indices: 22724--22804 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 42
22714 GCGGCTGTTC
22724 TATTTTATAAATTCTTTTAAG-AAAATACAGTTAAGAAATTT
1 TATTTTATAAATTCTTTTAAGAAAAATACAGTTAAGAAATTT
* *
22765 TATTTTATAAATTGTTTTAAGAAAAATTCAGTTAAGAAAT
1 TATTTTATAAATTCTTTTAAGAAAAATACAGTTAAGAAAT
22805 AAAATTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 20 0.54
42 17 0.46
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (42 bp):
TATTTTATAAATTCTTTTAAGAAAAATACAGTTAAGAAATTT
Found at i:22812 original size:42 final size:41
Alignment explanation
Indices: 22725--22812 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
22715 CGGCTGTTCT
***
22725 ATTTTATAAATTCTTTTAAGAAAATACAGTTAAGAAATTTT
1 ATTTTATAAATTCTTTTAAGAAAATACAGTTAAGAAATAAA
* *
22766 ATTTTATAAATTGTTTTAAGAAAAATTCAGTTAAGAAATAAA
1 ATTTTATAAATTCTTTTAAG-AAAATACAGTTAAGAAATAAA
22808 ATTTT
1 ATTTT
22813 GTTGTGGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 19 0.46
42 22 0.54
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (41 bp):
ATTTTATAAATTCTTTTAAGAAAATACAGTTAAGAAATAAA
Found at i:23132 original size:11 final size:11
Alignment explanation
Indices: 23118--23155 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23108 ATTCATAACA
23118 AATTTATAATT
1 AATTTATAATT
23129 AATTTATAATT
1 AATTTATAATT
23140 -ATTTGATAATT
1 AATTT-ATAATT
*
23151 TATTT
1 AATTT
23156 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:24429 original size:15 final size:15
Alignment explanation
Indices: 24399--24448 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
24389 GAGGCATTGA
24399 AAACATTCTTTTCAAAC
1 AAACATTC--TTCAAAC
24416 AAACATTCTTCAAAC
1 AAACATTCTTCAAAC
**
24431 AAATCAAGCTTCAAAC
1 AAA-CATTCTTCAAAC
24447 AA
1 AA
24449 GTTTACAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 10 0.33
16 12 0.40
17 8 0.27
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (15 bp):
AAACATTCTTCAAAC
Found at i:30871 original size:16 final size:16
Alignment explanation
Indices: 30850--30884 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
30840 CATTCCCGGG
30850 AAACTTTCTCACTTGC
1 AAACTTTCTCACTTGC
30866 AAACTTTCTCACTTGC
1 AAACTTTCTCACTTGC
30882 AAA
1 AAA
30885 TTAATTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (16 bp):
AAACTTTCTCACTTGC
Found at i:31048 original size:51 final size:51
Alignment explanation
Indices: 30940--31035 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
30930 GTAAATAATA
* * * * *
30940 ATTTTTTCCATTCATAAGATTCAAATTCGAAATCTTCCTTAGAGGGAAATG
1 ATTTTTTCCATTCACAAGATTCAAACTCAAAACCTTACTTAGAGGGAAATG
*
30991 ATTTTTTCCATTCACAAGATTCAAACTCAAAACCTTATTTA-AGGG
1 ATTTTTTCCATTCACAAGATTCAAACTCAAAACCTTACTTAGAGGG
31036 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 4 0.10
51 35 0.90
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (51 bp):
ATTTTTTCCATTCACAAGATTCAAACTCAAAACCTTACTTAGAGGGAAATG
Found at i:34048 original size:32 final size:32
Alignment explanation
Indices: 34012--34075 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
34002 AATAGAAGTT
*
34012 GTTAAAGTTTCTGCTAGA-TTGTCAATTGTGCA
1 GTTAAAGTTTCTGCTA-ACTTATCAATTGTGCA
34044 GTTAAAGTTTCTGCTAACTTATCAATTGTGCA
1 GTTAAAGTTTCTGCTAACTTATCAATTGTGCA
34076 CGCTTGCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 1 0.03
32 29 0.97
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (32 bp):
GTTAAAGTTTCTGCTAACTTATCAATTGTGCA
Found at i:38246 original size:16 final size:15
Alignment explanation
Indices: 38222--38261 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
38212 ATGAAGAAAC
*
38222 TCAATTGAATGTTGTT
1 TCAA-TGAATGTTATT
38238 TCAAGTGAATGTTATT
1 TCAA-TGAATGTTATT
38254 TCAATGAA
1 TCAATGAA
38262 GTTTTTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (15 bp):
TCAATGAATGTTATT
Done.