Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019777.1 Corchorus olitorius cultivar O-4 contig19810, 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: 29241
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1572 original size:14 final size:14
Alignment explanation
Indices: 1550--1587 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1540 ATGGGATTTT
1550 TAATAATTATTTAA
1 TAATAATTATTTAA
*
1564 TAATTATTATTTAA
1 TAATAATTATTTAA
1578 TTAATAATTA
1 -TAATAATTA
1588 ATTTCAGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATAATTATTTAA
Found at i:2171 original size:5 final size:5
Alignment explanation
Indices: 2147--2243 Score: 58
Period size: 5 Copynumber: 19.2 Consensus size: 5
2137 TAAACTTTAC
* * * * *
2147 TATAT TAGA- TATAA TATAT TCTAT TATAT TATA- -CTAT TATAT TCTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* *
2194 TATAT TATACT AATAT ATACTAT TATAT TATAC TAT-T ATACTAT TATAT
1 TATAT TATA-T TATAT -TA-TAT TATAT TATAT TATAT -TA-TAT TATAT
2243 T
1 T
2244 CCCATAATCG
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
3 2 0.03
4 3 0.04
5 51 0.73
6 10 0.14
7 4 0.06
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (5 bp):
TATAT
Found at i:2186 original size:8 final size:8
Alignment explanation
Indices: 2173--2241 Score: 60
Period size: 8 Copynumber: 8.9 Consensus size: 8
2163 TATTCTATTA
2173 TATTATAC
1 TATTATAC
2181 TATTATA-
1 TATTATAC
2188 T-TCTATTA-
1 TAT-TA-TAC
2196 TATTATAC
1 TATTATAC
2204 TAATATATAC
1 T-AT-TATAC
2214 TA-T-TA-
1 TATTATAC
2219 TATTATAC
1 TATTATAC
2227 TATTATAC
1 TATTATAC
2235 TATTATA
1 TATTATA
2242 TTCCCATAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
5 2 0.04
6 4 0.08
7 8 0.15
8 28 0.54
9 4 0.08
10 6 0.12
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (8 bp):
TATTATAC
Found at i:2190 original size:23 final size:23
Alignment explanation
Indices: 2161--2243 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
2151 TTAGATATAA
2161 TATATTCTATTATATTATACTAT
1 TATATTCTATTATATTATACTAT
*
2184 TATATTCTATTATATTATACTAA
1 TATATTCTATTATATTATACTAT
*
2207 TATATACTATTATATTATACTAT
1 TATATTCTATTATATTATACTAT
2230 TATA--CTATTATATT
1 TATATTCTATTATATT
2244 CCCATAATCG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
21 10 0.18
23 47 0.82
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATTCTATTATATTATACTAT
Found at i:2243 original size:13 final size:13
Alignment explanation
Indices: 2167--2233 Score: 92
Period size: 13 Copynumber: 5.6 Consensus size: 13
2157 ATAATATATT
2167 CTATTATATTATA
1 CTATTATATTATA
2180 CTATTATA-T-T-
1 CTATTATATTATA
2190 CTATTATATTATA
1 CTATTATATTATA
2203 CTA--ATA-TATA
1 CTATTATATTATA
2213 CTATTATATTATA
1 CTATTATATTATA
2226 CTATTATA
1 CTATTATA
2234 CTATTATATT
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 15 0.31
11 5 0.10
12 5 0.10
13 23 0.48
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (13 bp):
CTATTATATTATA
Found at i:6877 original size:26 final size:25
Alignment explanation
Indices: 6818--6882 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 25
6808 CATGAATCAA
* *
6818 AAACGCAATCTCAGCTACGACCCTC
1 AAACGCAATCTCAGATACGACCCAC
* * *
6843 AGACACAATCTCAGATGACGACCCAG
1 AAACGCAATCTCAGAT-ACGACCCAC
6869 AAACGCAATCTCAG
1 AAACGCAATCTCAG
6883 CTATGACATC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 13 0.41
26 19 0.59
ACGTcount: A:0.37, C:0.34, G:0.15, T:0.14
Consensus pattern (25 bp):
AAACGCAATCTCAGATACGACCCAC
Found at i:7579 original size:6 final size:6
Alignment explanation
Indices: 7570--7625 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
7560 TAGAAGAGAA
* * *
7570 AAAAAG AAAAAAG GAAAAG AAAAATG AAAAATG AAAAGG AAAATG AAAAA-
1 AAAAAG -AAAAAG AAAAAG AAAAA-G AAAAA-G AAAAAG AAAAAG AAAAAG
7620 AAAAAG
1 AAAAAG
7626 CCACGTAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
5 5 0.12
6 19 0.45
7 18 0.43
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:7587 original size:13 final size:13
Alignment explanation
Indices: 7571--7620 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
7561 AGAAGAGAAA
7571 AAAAGAAAAAAGG
1 AAAAGAAAAAAGG
*
7584 AAAAG-AAAAATG
1 AAAAGAAAAAAGG
*
7596 AAAA-ATGAAAAGG
1 AAAAGA-AAAAAGG
7609 AAAATGAAAAAA
1 AAAA-GAAAAAA
7621 AAAAGCCACG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
12 10 0.34
13 14 0.48
14 4 0.14
15 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (13 bp):
AAAAGAAAAAAGG
Found at i:7592 original size:19 final size:20
Alignment explanation
Indices: 7570--7620 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
7560 TAGAAGAGAA
7570 AAAAAGAAAAAAGGAAAA-G
1 AAAAAGAAAAAAGGAAAAGG
*
7589 AAAAATG-AAAAATGAAAAGG
1 AAAAA-GAAAAAAGGAAAAGG
*
7609 AAAATGAAAAAA
1 AAAAAGAAAAAA
7621 AAAAGCCACG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (20 bp):
AAAAAGAAAAAAGGAAAAGG
Found at i:14545 original size:13 final size:13
Alignment explanation
Indices: 14527--14556 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
14517 CTTGTAATAA
14527 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
14540 AAAAAAGAAAAAG
1 AAAAAAAAAAAAG
14553 AAAA
1 AAAA
14557 TTATAGCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:15454 original size:17 final size:18
Alignment explanation
Indices: 15432--15470 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
15422 TTATGCAATT
* *
15432 TTTCATGA-ATGTTTTTA
1 TTTCATGATATGCTTTAA
15449 TTTCATGATATGCTTTAA
1 TTTCATGATATGCTTTAA
15467 TTTC
1 TTTC
15471 TTGAGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (18 bp):
TTTCATGATATGCTTTAA
Found at i:19502 original size:32 final size:32
Alignment explanation
Indices: 19487--19572 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
19477 TCTTTTCTTG
*
19487 CTTATTCGACTAAGTTTAAGATTCTTGTCATA
1 CTTATTCAACTAAGTTTAAGATTCTTGTCATA
19519 CTTATTCAACTAAGTTTAAGATTCTTGTCATA
1 CTTATTCAACTAAGTTTAAGATTCTTGTCATA
19551 CTTATTCAACTAAGTTTAAGAT
1 CTTATTCAACTAAGTTTAAGAT
19573 ATTGGGAATG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.43
Consensus pattern (32 bp):
CTTATTCAACTAAGTTTAAGATTCTTGTCATA
Found at i:23051 original size:31 final size:31
Alignment explanation
Indices: 23010--23156 Score: 143
Period size: 31 Copynumber: 4.7 Consensus size: 31
23000 GACGTGGCTT
* *
23010 GCCACATGTACCAAAAAGCAACATGTAGCAC
1 GCCACGTGTACCAAAAAGCGACATGTAGCAC
*
23041 GCCACGTGTACCAAAAAACGACATG-AGGCAC
1 GCCACGTGTACCAAAAAGCGACATGTA-GCAC
* * *
23072 GTCACGTGTACCAAAAAGTGACATGTATCAC
1 GCCACGTGTACCAAAAAGCGACATGTAGCAC
* * * * *
23103 GCCATGTGTACCCAAAAGTGACATGTGGCAT
1 GCCACGTGTACCAAAAAGCGACATGTAGCAC
* ** *
23134 GCCATGTGTTTCAAAAAGTGACA
1 GCCACGTGTACCAAAAAGCGACA
23157 CATGGCATGC
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
30 1 0.01
31 96 0.98
32 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGCGACATGTAGCAC
Found at i:23113 original size:62 final size:62
Alignment explanation
Indices: 23010--23156 Score: 168
Period size: 62 Copynumber: 2.4 Consensus size: 62
23000 GACGTGGCTT
* **
23010 GCCACATGTACCAAAAAGCAACATGTAGCACGCCACGTGTACCAAAAAACGACATGAGGCAC
1 GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAACGACATGAGGCAC
* * * * ** * *
23072 GTCACGTGTACCAAAAAGTGACATGTATCACGCCATGTGTACCCAAAAGTGACATGTGGCAT
1 GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAACGACATGAGGCAC
* **
23134 GCCATGTGTTTCAAAAAGTGACA
1 GCCACGTGTACCAAAAAGTGACA
23157 CATGGCATGC
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (62 bp):
GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAACGACATGAGGCAC
Found at i:23742 original size:54 final size:54
Alignment explanation
Indices: 23643--23750 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
23633 GCGTATAGGT
* * *
23643 TTTGTGCTGCTTTGTTAGTTTGTGTTTAATTGTTATAATGGAGATCAACAAGAA
1 TTTGTGCTGATTTGTTAGTTTGTGTTTAATTGCTATAATGAAGATCAACAAGAA
** *
23697 TTTGTGCTGATTTGTTAGTTTGTGTTTAATTGCTATCGTGAAGATCAACGAGAA
1 TTTGTGCTGATTTGTTAGTTTGTGTTTAATTGCTATAATGAAGATCAACAAGAA
23751 GGAACCAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (54 bp):
TTTGTGCTGATTTGTTAGTTTGTGTTTAATTGCTATAATGAAGATCAACAAGAA
Found at i:23796 original size:45 final size:45
Alignment explanation
Indices: 23727--23816 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
23717 TGTGTTTAAT
* * *
23727 TGCTATCGTGAAGATCAACGAGAAGGAACCAATGTTATGGGAATG
1 TGCTATCATGAAGATCAACAAGAAGGAACCAATGTTATGGAAATG
*
23772 TGCTATCATGGAGATCAACAAGAAGGAACCAATGTTATGGAAATG
1 TGCTATCATGAAGATCAACAAGAAGGAACCAATGTTATGGAAATG
23817 AGCTTTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (45 bp):
TGCTATCATGAAGATCAACAAGAAGGAACCAATGTTATGGAAATG
Found at i:23940 original size:2 final size:2
Alignment explanation
Indices: 23933--23981 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
23923 TACATAATAA
23933 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23975 AG AG AG A
1 AG AG AG A
23982 AATTGTTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:24008 original size:15 final size:15
Alignment explanation
Indices: 23988--24020 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
23978 GAGAAATTGT
23988 TAATAAAACCGAACC
1 TAATAAAACCGAACC
24003 TAATAAAACCGAACC
1 TAATAAAACCGAACC
24018 TAA
1 TAA
24021 AAATCAAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.24, G:0.06, T:0.15
Consensus pattern (15 bp):
TAATAAAACCGAACC
Found at i:25416 original size:16 final size:17
Alignment explanation
Indices: 25395--25426 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
25385 CCTAAAGTAA
25395 AAAAAGAAAAA-AAAAC
1 AAAAAGAAAAACAAAAC
25411 AAAAAGAAAAACAAAA
1 AAAAAGAAAAACAAAA
25427 TGGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAACAAAAC
Found at i:25697 original size:16 final size:15
Alignment explanation
Indices: 25662--25706 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
25652 CTCGGGTGGG
*
25662 TTCGAGTTCGGGCTTT
1 TTCGAGTTCGGG-TTA
25678 TTCGAGTTCGGGTTCA
1 TTCGAGTTCGGGTT-A
*
25694 TTCGGGTTCGGGT
1 TTCGAGTTCGGGT
25707 ATTTTCAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 2 0.08
16 24 0.92
ACGTcount: A:0.07, C:0.18, G:0.36, T:0.40
Consensus pattern (15 bp):
TTCGAGTTCGGGTTA
Found at i:25712 original size:32 final size:31
Alignment explanation
Indices: 25662--25753 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 31
25652 CTCGGGTGGG
*
25662 TTCGAGTTCGGGCT-TTTTCGAGTTCGGGTTCA
1 TTCGGGTTCGGG-TATTTTCGAGTTCGGGTT-A
*
25694 TTCGGGTTCGGGTATTTTC-AGGCTCGGGTTA
1 TTCGGGTTCGGGTATTTTCGA-GTTCGGGTTA
* * *
25725 TATAGGGTCCGGGTATTTTCGGGTTCGGG
1 T-TCGGGTTCGGGTATTTTCGAGTTCGGG
25754 CTCAGATTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
31 4 0.08
32 46 0.92
ACGTcount: A:0.10, C:0.16, G:0.36, T:0.38
Consensus pattern (31 bp):
TTCGGGTTCGGGTATTTTCGAGTTCGGGTTA
Found at i:27435 original size:31 final size:31
Alignment explanation
Indices: 27400--27471 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
27390 TAAATTATTG
* *
27400 CAAATTAAAACAAAT-TAAGTATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGCATTAAATTAAA
* *
27431 CAAA-TAATTAAAATGAAAGCCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGCATTAAATTAAA
27462 CAAATTAAAA
1 CAAATTAAAA
27472 GCTGATAGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 7 0.21
31 23 0.70
32 3 0.09
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGCATTAAATTAAA
Done.