Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020259.1 Corchorus olitorius cultivar O-4 contig20292, 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: 77886
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:17180 original size:430 final size:430
Alignment explanation
Indices: 16380--17238 Score: 1531
Period size: 430 Copynumber: 2.0 Consensus size: 430
16370 TATAGAGAAA
*
16380 GGGATGAGCATCAACCCATGAGAGATCTGACATCTCTATCCTCTTATGAGAATCAAATCATATTG
1 GGGATGAGCATCAACCCATGAAAGATCTGACATCTCTATCCTCTTATGAGAATCAAATCATATTG
* *
16445 CTTTGGATCCAGGTAAATTTGATTCATTTATATGTGTTGACTTAACTGTGGTGACTAATTCCCAT
66 CTTTGGATCCAAGTAAATTTGATTCATTTATATGTGTGGACTTAACTGTGGTGACTAATTCCCAT
*
16510 CTTTATTTGGGAAGCTGGTGAAAGATAAGATGGCAACCTGCCAAAGTTGGATCAAGATAATGTCA
131 CTTTACTTGGGAAGCTGGTGAAAGATAAGATGGCAACCTGCCAAAGTTGGATCAAGATAATGTCA
*
16575 ATTATGAATATGCAAGAATTGTAATATGTTGGAAAAATAGGACAATAATATAGCTTGAGTCGTGT
196 ATTATGAATATGCAAGAATTGCAATATGTTGGAAAAATAGGACAATAATATAGCTTGAGTCGTGT
* * *
16640 AGGACACACTGTCCTAAAGGATAATTTTCGGCTATTAACGACTATCCCCCAAGATTAAACAAGCT
261 AGGACAAACTGTCCTAAAGGATAATTTCCGGCTATTAACGACTATCCCCCAAGATCAAACAAGCT
* * *
16705 CTTCTCGAAATTGAAATTCCGAGAGGCTAACAGGAACCACAATAACTAACCTAGCAGAAAAATGA
326 CTTCTCGAAATTGAAATTCCGAGAGACTAACAGGAACCACAATAACTAACCCAGCAGAAAAAGGA
16770 GAGGAAGATAATTTAGAAAGGAGAAAGAAGAGTTTATCAT
391 GAGGAAGATAATTTAGAAAGGAGAAAGAAGAGTTTATCAT
*
16810 GGGATGAGTATCAACCCATGAAAGATCTGACATCTCTATCCTCTTATGAGAATCAAATCATATTG
1 GGGATGAGCATCAACCCATGAAAGATCTGACATCTCTATCCTCTTATGAGAATCAAATCATATTG
* *
16875 CTTTGGGTCCAAGTAAATTTGATTCATTTATATGTGTGGACTTAACTGTTGTGACTAATTCCCAT
66 CTTTGGATCCAAGTAAATTTGATTCATTTATATGTGTGGACTTAACTGTGGTGACTAATTCCCAT
*
16940 CTTTAACTT-GGAAGCTGGTGAAAGATGAGATGGCAACCTGCCAAAGTTGGATCAAGATAATGTC
131 CTTT-ACTTGGGAAGCTGGTGAAAGATAAGATGGCAACCTGCCAAAGTTGGATCAAGATAATGTC
*
17004 AATTATGAATATGCAAGAATTGCAATATGTTGGAAAAATATGACAATAATATAGCTTGAGTCGTG
195 AATTATGAATATGCAAGAATTGCAATATGTTGGAAAAATAGGACAATAATATAGCTTGAGTCGTG
* *
17069 TAGGACAAACTGTCCTAAAGGATAATTTCCGGCTATTAACGGCTATCCCCCAGGATCAAACAAGC
260 TAGGACAAACTGTCCTAAAGGATAATTTCCGGCTATTAACGACTATCCCCCAAGATCAAACAAGC
*
17134 TCTTCTCGAAATTGAAATTCCGAGAGACTAATAGGAACCACAATAACTAACCCAGCAGAAAAAGG
325 TCTTCTCGAAATTGAAATTCCGAGAGACTAACAGGAACCACAATAACTAACCCAGCAGAAAAAGG
17199 AGAGGAAGATAATTTAGAAAGGAGAAAGAAGAGTTTATCA
390 AGAGGAAGATAATTTAGAAAGGAGAAAGAAGAGTTTATCA
17239 ATTGGTGTGG
Statistics
Matches: 409, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
430 406 0.99
431 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (430 bp):
GGGATGAGCATCAACCCATGAAAGATCTGACATCTCTATCCTCTTATGAGAATCAAATCATATTG
CTTTGGATCCAAGTAAATTTGATTCATTTATATGTGTGGACTTAACTGTGGTGACTAATTCCCAT
CTTTACTTGGGAAGCTGGTGAAAGATAAGATGGCAACCTGCCAAAGTTGGATCAAGATAATGTCA
ATTATGAATATGCAAGAATTGCAATATGTTGGAAAAATAGGACAATAATATAGCTTGAGTCGTGT
AGGACAAACTGTCCTAAAGGATAATTTCCGGCTATTAACGACTATCCCCCAAGATCAAACAAGCT
CTTCTCGAAATTGAAATTCCGAGAGACTAACAGGAACCACAATAACTAACCCAGCAGAAAAAGGA
GAGGAAGATAATTTAGAAAGGAGAAAGAAGAGTTTATCAT
Found at i:21582 original size:31 final size:31
Alignment explanation
Indices: 21546--21685 Score: 172
Period size: 31 Copynumber: 4.5 Consensus size: 31
21536 AGTATCCGAC
* *
21546 GTGGCATGCCACGTATACCGAAAAGCGACAT
1 GTGGCACGCCACGTGTACCGAAAAGCGACAT
* * *
21577 TTGGCACGTCACGTGTACCGAAAAGCGATAT
1 GTGGCACGCCACGTGTACCGAAAAGCGACAT
* *
21608 GTGACACGCCACGTGTACCAAAAAGCGACAT
1 GTGGCACGCCACGTGTACCGAAAAGCGACAT
* * *
21639 TTGGCACGCCACGTGTACCCAAAAGTGACAT
1 GTGGCACGCCACGTGTACCGAAAAGCGACAT
* *
21670 GTGGCATGCCATGTGT
1 GTGGCACGCCACGTGT
21686 TTCAAAAAGT
Statistics
Matches: 92, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 92 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (31 bp):
GTGGCACGCCACGTGTACCGAAAAGCGACAT
Found at i:21694 original size:31 final size:31
Alignment explanation
Indices: 21546--21715 Score: 160
Period size: 31 Copynumber: 5.5 Consensus size: 31
21536 AGTATCCGAC
* * *
21546 GTGGCATGCCACGTATACCGAAAAGCGACAT
1 GTGGCATGCCACGTGTACCAAAAAGTGACAT
* * * * * *
21577 TTGGCACGTCACGTGTACCGAAAAGCGATAT
1 GTGGCATGCCACGTGTACCAAAAAGTGACAT
* * *
21608 GTGACACGCCACGTGTACCAAAAAGCGACAT
1 GTGGCATGCCACGTGTACCAAAAAGTGACAT
* * *
21639 TTGGCACGCCACGTGTACCCAAAAGTGACAT
1 GTGGCATGCCACGTGTACCAAAAAGTGACAT
* ** *
21670 GTGGCATGCCATGTGTTTCAAAAAGTGACAC
1 GTGGCATGCCACGTGTACCAAAAAGTGACAT
*
21701 GTGGCATGTCACGTG
1 GTGGCATGCCACGTG
21716 CACAAAAGGA
Statistics
Matches: 116, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 116 1.00
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (31 bp):
GTGGCATGCCACGTGTACCAAAAAGTGACAT
Found at i:24490 original size:3 final size:3
Alignment explanation
Indices: 24482--24517 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
24472 TGCAACAGCT
24482 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GA
24518 CACCATCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:26628 original size:13 final size:13
Alignment explanation
Indices: 26610--26636 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26600 AAACGGAAAA
26610 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
26623 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
26636 T
1 T
26637 TCAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:41160 original size:39 final size:39
Alignment explanation
Indices: 41105--41219 Score: 203
Period size: 39 Copynumber: 2.9 Consensus size: 39
41095 CAAACCGCAG
*
41105 ATTCAAGAGAGTTTTCGCAGAGGTAACTGAAAGAGAGAGA
1 ATTC-AGAGAGTTTTCGCAGAGGTAATTGAAAGAGAGAGA
*
41145 ATTCAGAGAGTTTTCGCAGAGGTAATTGAAAGAAAGAGA
1 ATTCAGAGAGTTTTCGCAGAGGTAATTGAAAGAGAGAGA
41184 ATTCAGAGAGTTTTCGCAGAGGTAATTGAAAGAGAG
1 ATTCAGAGAGTTTTCGCAGAGGTAATTGAAAGAGAG
41220 TTTAGCGTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 68 0.94
40 4 0.06
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.23
Consensus pattern (39 bp):
ATTCAGAGAGTTTTCGCAGAGGTAATTGAAAGAGAGAGA
Found at i:42744 original size:33 final size:33
Alignment explanation
Indices: 42707--42769 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
42697 GCCGCCGGTA
42707 TTAACCAGCCACTCCACACCAACACTGGCGGCG
1 TTAACCAGCCACTCCACACCAACACTGGCGGCG
*
42740 TTAACCAGCCACTCCACACCAACCCTGGCG
1 TTAACCAGCCACTCCACACCAACACTGGCG
42770 TTAACCAGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (33 bp):
TTAACCAGCCACTCCACACCAACACTGGCGGCG
Found at i:42772 original size:30 final size:30
Alignment explanation
Indices: 42707--42829 Score: 111
Period size: 30 Copynumber: 4.0 Consensus size: 30
42697 GCCGCCGGTA
*
42707 TTAACCAGCCACTCCACACCAACACTGGCGGCG
1 TTAACCAGCCACTCCACACCAACCCT---GGCG
42740 TTAACCAGCCACTCCACACCAACCCTGGCG
1 TTAACCAGCCACTCCACACCAACCCTGGCG
* ** * * *
42770 TTAACCAGCCGCTTTATAGCAACCCTGGTG
1 TTAACCAGCCACTCCACACCAACCCTGGCG
* * * * *
42800 CTAATCAGCCACTCCATAGCACCCCTGGCG
1 TTAACCAGCCACTCCACACCAACCCTGGCG
42830 GCCTTGGGCA
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
30 51 0.67
33 25 0.33
ACGTcount: A:0.25, C:0.41, G:0.17, T:0.17
Consensus pattern (30 bp):
TTAACCAGCCACTCCACACCAACCCTGGCG
Found at i:57969 original size:4 final size:4
Alignment explanation
Indices: 57960--57993 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
57950 AACACATAAT
*
57960 TTTC TTTC TTTC TTTC TTTC TTTA TTT- TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
57994 TAAATCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:67295 original size:48 final size:48
Alignment explanation
Indices: 67239--67340 Score: 204
Period size: 48 Copynumber: 2.1 Consensus size: 48
67229 GGAATTGTGG
67239 GAGTGTAAGCTGTGCCCAGAGAGCTTTTGATGACATGAGTGAGAAATA
1 GAGTGTAAGCTGTGCCCAGAGAGCTTTTGATGACATGAGTGAGAAATA
67287 GAGTGTAAGCTGTGCCCAGAGAGCTTTTGATGACATGAGTGAGAAATA
1 GAGTGTAAGCTGTGCCCAGAGAGCTTTTGATGACATGAGTGAGAAATA
67335 GAGTGT
1 GAGTGT
67341 CTTGGAATAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.25
Consensus pattern (48 bp):
GAGTGTAAGCTGTGCCCAGAGAGCTTTTGATGACATGAGTGAGAAATA
Found at i:74382 original size:1 final size:1
Alignment explanation
Indices: 74378--74408 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
74368 TTTTTTTTAG
74378 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
74409 CCTTTAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:74571 original size:14 final size:16
Alignment explanation
Indices: 74538--74571 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
74528 TCCTCTTCCA
*
74538 TTTTTCTCTCTTGGGT
1 TTTTTCTCTCGTGGGT
74554 TTTTTCTCTCGT-GGT
1 TTTTTCTCTCGTGGGT
74569 TTT
1 TTT
74572 AGGACAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.00, C:0.18, G:0.18, T:0.65
Consensus pattern (16 bp):
TTTTTCTCTCGTGGGT
Found at i:75981 original size:21 final size:21
Alignment explanation
Indices: 75935--75982 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
75925 CACCTTCACC
*
75935 GGCTCCGGCAGCTTCCCCCAA
1 GGCTTCGGCAGCTTCCCCCAA
75956 GGCTTCGGCAGCTTCCCCCAA
1 GGCTTCGGCAGCTTCCCCCAA
75977 GGCTTC
1 GGCTTC
75983 TTCACCTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.44, G:0.25, T:0.19
Consensus pattern (21 bp):
GGCTTCGGCAGCTTCCCCCAA
Found at i:75991 original size:21 final size:21
Alignment explanation
Indices: 75935--75992 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
75925 CACCTTCACC
* *
75935 GGCTCCGGCAGCTTCCCCCAA
1 GGCTTCGGCACCTTCCCCCAA
*
75956 GGCTTCGGCAGCTTCCCCCAA
1 GGCTTCGGCACCTTCCCCCAA
**
75977 GGCTTCTTCACCTTCC
1 GGCTTCGGCACCTTCC
75993 AAGTCAAAGT
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:0.12, C:0.45, G:0.21, T:0.22
Consensus pattern (21 bp):
GGCTTCGGCACCTTCCCCCAA
Found at i:76055 original size:14 final size:15
Alignment explanation
Indices: 76036--76064 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
76026 TCTCCCAAAT
76036 CCAACTCC-TCCTCC
1 CCAACTCCATCCTCC
76050 CCAACTCCATCCTCC
1 CCAACTCCATCCTCC
76065 AAGTCTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.17, C:0.62, G:0.00, T:0.21
Consensus pattern (15 bp):
CCAACTCCATCCTCC
Found at i:76219 original size:18 final size:18
Alignment explanation
Indices: 76192--76232 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
76182 TCCACCGATA
* *
76192 GCCCCACCGCCTCTGAGG
1 GCCCCACCGCCGCTGAAG
*
76210 GCCCCTCCGCCGCTGAAG
1 GCCCCACCGCCGCTGAAG
76228 GCCCC
1 GCCCC
76233 GATGTCGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.54, G:0.27, T:0.10
Consensus pattern (18 bp):
GCCCCACCGCCGCTGAAG
Found at i:77822 original size:29 final size:28
Alignment explanation
Indices: 77778--77833 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
77768 TTCTTCAAAC
*
77778 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
77806 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
77834 GTGGAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Done.