Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016469.1 Corchorus olitorius cultivar O-4 contig16502, 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: 110808
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9216 original size:19 final size:19
Alignment explanation
Indices: 9170--9228 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
9160 CGTTGCCCTA
*
9170 ATAATCTCATATGTACAGT
1 ATAATCTAATATGTACAGT
*
9189 ACTTAATCTAATTTGTACAGT
1 A--TAATCTAATATGTACAGT
* *
9210 ATAATCTGATCTGTACAGT
1 ATAATCTAATATGTACAGT
9229 TACTAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (19 bp):
ATAATCTAATATGTACAGT
Found at i:10528 original size:21 final size:19
Alignment explanation
Indices: 10502--10560 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 19
10492 CGCTGCTCTA
*
10502 ATAATCTCATCTGTACAGT
1 ATAATCTAATCTGTACAGT
*
10521 ACATAATCTAATTTGTACAGT
1 --ATAATCTAATCTGTACAGT
* *
10542 GTAATCTTATCTGTACAGT
1 ATAATCTAATCTGTACAGT
10561 TGTTAAACAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (19 bp):
ATAATCTAATCTGTACAGT
Found at i:10548 original size:19 final size:19
Alignment explanation
Indices: 10503--10560 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
10493 GCTGCTCTAA
* *
10503 TAATCTCATCTGTACAGTACA
1 TAATCTAATCTGTACAGT--G
*
10524 TAATCTAATTTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
10543 TAATCTTATCTGTACAGT
1 TAATCTAATCTGTACAGT
10561 TGTTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:10665 original size:34 final size:34
Alignment explanation
Indices: 10622--10687 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
10612 CTTAATCCAC
10622 CTTGTTCAAATATTGTGAATTGAAAAAAAAAAAT
1 CTTGTTCAAATATTGTGAATTGAAAAAAAAAAAT
10656 CTTGTTCAAATATTGTGAATTGAAAAAAAAAA
1 CTTGTTCAAATATTGTGAATTGAAAAAAAAAA
10688 TAAGGATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (34 bp):
CTTGTTCAAATATTGTGAATTGAAAAAAAAAAAT
Found at i:13798 original size:14 final size:14
Alignment explanation
Indices: 13779--13805 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13769 TACATGACAT
13779 GAAAGAGAGAGAGA
1 GAAAGAGAGAGAGA
13793 GAAAGAGAGAGAG
1 GAAAGAGAGAGAG
13806 TGGAACGGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (14 bp):
GAAAGAGAGAGAGA
Found at i:20968 original size:31 final size:31
Alignment explanation
Indices: 20927--21041 Score: 140
Period size: 31 Copynumber: 3.7 Consensus size: 31
20917 GCATGTCATG
* * *
20927 TGTCACTTTTTGGTACATATGGCGTGACACA
1 TGTCGCTTTTTGATACATGTGGCGTGACACA
* *
20958 TGTCGCTTTTTGATACATGTGGCGTGTCACG
1 TGTCGCTTTTTGATACATGTGGCGTGACACA
*
20989 TGTCGCTTTTTGATACATGTGGCGTGCCACA
1 TGTCGCTTTTTGATACATGTGGCGTGACACA
* * * *
21020 TTTTGCTTTTTGGTACACGTGG
1 TGTCGCTTTTTGATACATGTGG
21042 TATGCCACGT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (31 bp):
TGTCGCTTTTTGATACATGTGGCGTGACACA
Found at i:20998 original size:62 final size:62
Alignment explanation
Indices: 20920--21041 Score: 163
Period size: 62 Copynumber: 2.0 Consensus size: 62
20910 GCACAAGGCA
* * *
20920 TGTCATGTGTCACTTTTTGGTACATATGGCGTGACACATGTCGCTTTTTGATACATGTGGCG
1 TGTCACGTGTCACTTTTTGATACATATGGCGTGACACATGTCGCTTTTTGATACACGTGGCG
* * * * * *
20982 TGTCACGTGTCGCTTTTTGATACATGTGGCGTGCCACATTTTGCTTTTTGGTACACGTGG
1 TGTCACGTGTCACTTTTTGATACATATGGCGTGACACATGTCGCTTTTTGATACACGTGG
21042 TATGCCACGT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (62 bp):
TGTCACGTGTCACTTTTTGATACATATGGCGTGACACATGTCGCTTTTTGATACACGTGGCG
Found at i:21051 original size:62 final size:62
Alignment explanation
Indices: 20916--21051 Score: 155
Period size: 62 Copynumber: 2.2 Consensus size: 62
20906 TTGTGCACAA
* * * *
20916 GGCATGTCATGTGTCACTTTTTGGTACATATGGCGTGACACATGTCGCTTTTTGATACATGT
1 GGCATGCCACGTGTCACTTTTTGATACATATGGCGTGACACATGTCGCTTTTTGATACACGT
* * * * * * * *
20978 GGCGTGTCACGTGTCGCTTTTTGATACATGTGGCGTGCCACATTTTGCTTTTTGGTACACGT
1 GGCATGCCACGTGTCACTTTTTGATACATATGGCGTGACACATGTCGCTTTTTGATACACGT
*
21040 GGTATGCCACGT
1 GGCATGCCACGT
21052 CGGACACCGT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (62 bp):
GGCATGCCACGTGTCACTTTTTGATACATATGGCGTGACACATGTCGCTTTTTGATACACGT
Found at i:29884 original size:156 final size:158
Alignment explanation
Indices: 29661--29958 Score: 456
Period size: 156 Copynumber: 1.9 Consensus size: 158
29651 AGTGTACTGT
*
29661 ATATATTAGATACTTTTTAACATTAATACTATGTATAATATTAGATTATTAGTCCTATATATCAT
1 ATATATTAGATACTTTTTAACATTAATACTATGTATAATATTAGATTATTAGTACTATATATCAT
* * * * *
29726 AGAGTTTTGTTATATGACCAGAAAAATTGACCCGAAATTTAATTCCTATGACGTATTCTTACATG
66 AGAGTTTTGCTACATGACCAGAAAAATTGACCCGAAATTTAATCCCCATGACGTATTCTTACACG
*
29791 GTTGGTTCAGCACTCAGCAGACTCTATA
131 GTTGGTCCAGCACTCAGCAGACTCTATA
* *
29819 ATATATTAGATACTTTTTAACA-T-ATATTATGTATAATATTAGATTATTAGTACTATATATTAT
1 ATATATTAGATACTTTTTAACATTAATACTATGTATAATATTAGATTATTAGTACTATATATCAT
* * ** *
29882 AGAGTTTTGCTACGTGATCAGAAAAATTGACCCGAAATTTGGTCCCCATGACGTGTTCTTACACG
66 AGAGTTTTGCTACATGACCAGAAAAATTGACCCGAAATTTAATCCCCATGACGTATTCTTACACG
29947 GTTGGTCCAGCA
131 GTTGGTCCAGCA
29959 GACTGGTTCC
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
156 103 0.82
157 1 0.01
158 22 0.17
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (158 bp):
ATATATTAGATACTTTTTAACATTAATACTATGTATAATATTAGATTATTAGTACTATATATCAT
AGAGTTTTGCTACATGACCAGAAAAATTGACCCGAAATTTAATCCCCATGACGTATTCTTACACG
GTTGGTCCAGCACTCAGCAGACTCTATA
Found at i:30103 original size:25 final size:24
Alignment explanation
Indices: 30069--30117 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
30059 TGGAATTTTT
30069 CTATATTATAA-TAATATATATACTA
1 CTATATTATAAGTAA-AT-TATACTA
*
30094 CTATTTTATAAGTAAATTATACTA
1 CTATATTATAAGTAAATTATACTA
30118 GTAAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 12 0.55
26 3 0.14
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (24 bp):
CTATATTATAAGTAAATTATACTA
Found at i:35293 original size:2 final size:2
Alignment explanation
Indices: 35286--35318 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35276 TACTATTTAG
35286 TA 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 TA T
35319 TCTCTCTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42035 original size:17 final size:17
Alignment explanation
Indices: 42013--42047 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42003 TTTTTTGACA
42013 GACTGTACCAGTCTATG
1 GACTGTACCAGTCTATG
42030 GACTGTACCAGTCTATG
1 GACTGTACCAGTCTATG
42047 G
1 G
42048 GTTCTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (17 bp):
GACTGTACCAGTCTATG
Found at i:52547 original size:27 final size:27
Alignment explanation
Indices: 52490--52551 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
52480 GTTATCAAGG
* *
52490 GGACCCGACATGAAGCCTCTTTCAATC
1 GGACCCGACATGAACCCTCTTTCAATA
*
52517 GGACCTGACATGAACCCTCTTTCCAA-A
1 GGACCCGACATGAACCCTCTTT-CAATA
52544 GGACCCGA
1 GGACCCGA
52552 ACCCGGAACG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.19
Consensus pattern (27 bp):
GGACCCGACATGAACCCTCTTTCAATA
Found at i:64612 original size:2 final size:2
Alignment explanation
Indices: 64605--64643 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
64595 GTAATACTGC
*
64605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64644 ATTTCATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:76787 original size:21 final size:24
Alignment explanation
Indices: 76761--76804 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 24
76751 AATCCGAACT
76761 CTCACTCTC-CTCT-T-CCTCCTC
1 CTCACTCTCACTCTCTACCTCCTC
76782 CTCACTCTCACTCTCTACCTCCT
1 CTCACTCTCACTCTCTACCTCCT
76805 TGTTCCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 1 0.05
24 6 0.30
ACGTcount: A:0.09, C:0.55, G:0.00, T:0.36
Consensus pattern (24 bp):
CTCACTCTCACTCTCTACCTCCTC
Found at i:85777 original size:19 final size:19
Alignment explanation
Indices: 85741--85782 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
85731 ATTCAAAACA
*
85741 AAATAAAAACTATCTATTTT
1 AAATAAAAACTAACTA-TTT
*
85761 AAAT-AAAACTAAGTATTT
1 AAATAAAAACTAACTATTT
85779 AAAT
1 AAAT
85783 TTTATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
AAATAAAAACTAACTATTT
Found at i:107619 original size:13 final size:13
Alignment explanation
Indices: 107601--107626 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
107591 AGAATTATTA
107601 TTTTCATTAGTCT
1 TTTTCATTAGTCT
107614 TTTTCATTAGTCT
1 TTTTCATTAGTCT
107627 GGCGTGGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (13 bp):
TTTTCATTAGTCT
Found at i:110775 original size:2 final size:2
Alignment explanation
Indices: 110768--110808 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
110758 CAGTGACTGA
110768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.