Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015719.1 Corchorus olitorius cultivar O-4 contig15752, 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: 39862
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3829 original size:62 final size:62
Alignment explanation
Indices: 3763--3929 Score: 174
Period size: 62 Copynumber: 2.7 Consensus size: 62
3753 TGACACTAGT
* * *
3763 CTTTTTTGTGCACGAGGCATACCATGTGTCACTTTTTGGTACACATGACGTGACACGTGTCA
1 CTTTTTGGTACACGAGGCATACCACGTGTCACTTTTTGGTACACATGACGTGACACGTGTCA
* * * * * * *
3825 CTTTTTGGTACATGTGGCGTGCCACGTGTCACTTTTTGGTACACATGATGTGCCACGTGTCG
1 CTTTTTGGTACACGAGGCATACCACGTGTCACTTTTTGGTACACATGACGTGACACGTGTCA
* * * * * * *
3887 C-TTGTGGTACACGTGGCGTGCCACATGTCGCTTTTTGGCACAC
1 CTTTTTGGTACACGAGGCATACCACGTGTCACTTTTTGGTACAC
3930 GTGGCATGCC
Statistics
Matches: 90, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 37 0.41
62 53 0.59
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.34
Consensus pattern (62 bp):
CTTTTTGGTACACGAGGCATACCACGTGTCACTTTTTGGTACACATGACGTGACACGTGTCA
Found at i:3897 original size:30 final size:31
Alignment explanation
Indices: 3788--3943 Score: 170
Period size: 31 Copynumber: 5.1 Consensus size: 31
3778 GGCATACCAT
*
3788 GTGTCACTTTTTGGTACACATGACGTGACAC
1 GTGTCACTTTTTGGTACACATGACGTGCCAC
** *
3819 GTGTCACTTTTTGGTACATGTGGCGTGCCAC
1 GTGTCACTTTTTGGTACACATGACGTGCCAC
*
3850 GTGTCACTTTTTGGTACACATGATGTGCCAC
1 GTGTCACTTTTTGGTACACATGACGTGCCAC
* * * *
3881 GTGTCGC-TTGTGGTACACGTGGCGTGCCAC
1 GTGTCACTTTTTGGTACACATGACGTGCCAC
* * * * * *
3911 ATGTCGCTTTTTGGCACACGTGGCATGCCAC
1 GTGTCACTTTTTGGTACACATGACGTGCCAC
3942 GT
1 GT
3944 CAGACACTGT
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
30 25 0.24
31 81 0.76
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (31 bp):
GTGTCACTTTTTGGTACACATGACGTGCCAC
Found at i:3940 original size:61 final size:62
Alignment explanation
Indices: 3789--3943 Score: 204
Period size: 61 Copynumber: 2.5 Consensus size: 62
3779 GCATACCATG
* * * *
3789 TGTCACTTTTTGGTACACATGACGTGACACGTGTCACTTTTTGGTACATGTGGCGTGCCACG
1 TGTCACTTTTTGGTACACATGACGTGCCACGTGTCACTTTGTGGTACACGTGGCGTGCCACA
* *
3851 TGTCACTTTTTGGTACACATGATGTGCCACGTGTCGC-TTGTGGTACACGTGGCGTGCCACA
1 TGTCACTTTTTGGTACACATGACGTGCCACGTGTCACTTTGTGGTACACGTGGCGTGCCACA
* * * * *
3912 TGTCGCTTTTTGGCACACGTGGCATGCCACGT
1 TGTCACTTTTTGGTACACATGACGTGCCACGT
3944 CAGACACTGT
Statistics
Matches: 81, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
61 47 0.58
62 34 0.42
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (62 bp):
TGTCACTTTTTGGTACACATGACGTGCCACGTGTCACTTTGTGGTACACGTGGCGTGCCACA
Found at i:16090 original size:17 final size:16
Alignment explanation
Indices: 16050--16098 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
16040 CATGTAATCT
*
16050 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
16066 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
16083 TTAGATCACTAGTGAT
1 TT-GATCACTGGTGAT
16099 TTGGGGGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:16561 original size:21 final size:21
Alignment explanation
Indices: 16537--16587 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
16527 ATGAAGCTGT
16537 GGATGATATTCATGGTGGTGG
1 GGATGATATTCATGGTGGTGG
*
16558 GGATGCTATTCATGGTGGTGG
1 GGATGATATTCATGGTGGTGG
*
16579 GAATGATAT
1 GGATGATAT
16588 AGAAGTCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.06, G:0.39, T:0.33
Consensus pattern (21 bp):
GGATGATATTCATGGTGGTGG
Found at i:16677 original size:21 final size:21
Alignment explanation
Indices: 16652--16709 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
16642 TAATGTGGAA
16652 GGAGAAGCTCATCCTGCTGGT
1 GGAGAAGCTCATCCTGCTGGT
* *
16673 GGAGAAGCTCATTCTGGTGGT
1 GGAGAAGCTCATCCTGCTGGT
*
16694 GGAGAAGCTCTTCCTG
1 GGAGAAGCTCATCCTG
16710 GTGAAGGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.21, G:0.34, T:0.26
Consensus pattern (21 bp):
GGAGAAGCTCATCCTGCTGGT
Found at i:16751 original size:30 final size:30
Alignment explanation
Indices: 16715--16790 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
16705 TCCTGGTGAA
16715 GGTGAAGGCATAGATGGTGGTGTAGGTAAT
1 GGTGAAGGCATAGATGGTGGTGTAGGTAAT
16745 GGTGAAGGCATAGATGGTGGTGTAGGTAAT
1 GGTGAAGGCATAGATGGTGGTGTAGGTAAT
* *
16775 GGTGATGGTATAGATG
1 GGTGAAGGCATAGATG
16791 TTAGCTGTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.26, C:0.03, G:0.43, T:0.28
Consensus pattern (30 bp):
GGTGAAGGCATAGATGGTGGTGTAGGTAAT
Found at i:22476 original size:16 final size:16
Alignment explanation
Indices: 22451--22482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22441 CTAAATTATG
22451 ACAATGAAACAATCAA
1 ACAATGAAACAATCAA
*
22467 ACAATTAAACAATCAA
1 ACAATGAAACAATCAA
22483 TTTTAGTCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.19, G:0.03, T:0.16
Consensus pattern (16 bp):
ACAATGAAACAATCAA
Found at i:29109 original size:30 final size:30
Alignment explanation
Indices: 29060--29125 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
29050 AATAATTGAC
29060 AAAATGACCCTCGAACTATTGCTAAAAGGAT
1 AAAATGACCCTC-AACTATTGCTAAAAGGAT
29091 AAAATGACTCCT-AACTATTGCTAAAAGGAT
1 AAAATGAC-CCTCAACTATTGCTAAAAGGAT
29121 AAAAT
1 AAAAT
29126 AACCTCTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 23 0.68
31 8 0.24
32 3 0.09
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (30 bp):
AAAATGACCCTCAACTATTGCTAAAAGGAT
Found at i:31203 original size:7 final size:7
Alignment explanation
Indices: 31193--31228 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
31183 TGTCCCTGCA
31193 CTAAACC
1 CTAAACC
31200 CTAAACC
1 CTAAACC
31207 CTAAACC
1 CTAAACC
31214 CT-AACC
1 CTAAACC
31220 CTAAACC
1 CTAAACC
31227 CT
1 CT
31229 TACTCTGGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.39, C:0.44, G:0.00, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:31221 original size:13 final size:14
Alignment explanation
Indices: 31193--31228 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
31183 TGTCCCTGCA
31193 CTAAACCCTAAACC
1 CTAAACCCTAAACC
31207 CTAAACCCT-AACC
1 CTAAACCCTAAACC
31220 CTAAACCCT
1 CTAAACCCT
31229 TACTCTGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.39, C:0.44, G:0.00, T:0.17
Consensus pattern (14 bp):
CTAAACCCTAAACC
Found at i:37269 original size:81 final size:81
Alignment explanation
Indices: 37134--37301 Score: 291
Period size: 81 Copynumber: 2.1 Consensus size: 81
37124 TAATCATGTG
37134 ATTTTTATTATTCTTCAAAGGAAATCAATATGTGGATCAAATTAGATTTCTTGCCTTTTCTATTT
1 ATTTTTATTATTCTTCAAAGGAAATCAATATGTGGATCAAATTAGATTTCTTGCCTTTTCTATTT
37199 GAAGGTTCCAAATTCC
66 GAAGGTTCCAAATTCC
* * *
37215 ATTTTTATTTTTCTTCAAAGGAAATCAATTTGTGGATCACATTAGATTTCTTGCCTTTTCTATTT
1 ATTTTTATTATTCTTCAAAGGAAATCAATATGTGGATCAAATTAGATTTCTTGCCTTTTCTATTT
*
37280 GAAGGTTTCAAATTCC
66 GAAGGTTCCAAATTCC
*
37296 TTTTTT
1 ATTTTT
37302 CCCCATGTTG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (81 bp):
ATTTTTATTATTCTTCAAAGGAAATCAATATGTGGATCAAATTAGATTTCTTGCCTTTTCTATTT
GAAGGTTCCAAATTCC
Found at i:38663 original size:33 final size:33
Alignment explanation
Indices: 38619--38695 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
38609 TTATCACAGC
* * **
38619 ATCCAA-TCAGCAAAAGGTTAGTGAGTTGATTG
1 ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
*
38651 ATCCAAGTCAGCAAAATGTCAGTGAGATGATCA
1 ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
*
38684 ATCCAAGCCAGC
1 ATCCAAGTCAGC
38696 TGAAGGAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (33 bp):
ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
Done.