Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018926.1 Corchorus olitorius cultivar O-4 contig18959, 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: 37326
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:1097 original size:31 final size:33
Alignment explanation
Indices: 1018--1099 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 33
1008 GGATTTTTTA
* *
1018 TTATATATATGATTTATAAAAATTAATTATTCATG
1 TTATATATAT-ATAT-TACAAATTAATTATTCATG
1053 TTATATATATATATTACAAATTAA-TA-TCAT-
1 TTATATATATATATTACAAATTAATTATTCATG
*
1083 TTAGTATATTTATATTA
1 TTA-TATATATATATTA
1100 TTTTAATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 3 0.07
31 16 0.37
32 2 0.05
33 9 0.21
34 3 0.07
35 10 0.23
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (33 bp):
TTATATATATATATTACAAATTAATTATTCATG
Found at i:3709 original size:2 final size:2
Alignment explanation
Indices: 3702--3739 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3692 ACATATAAAG
3702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3740 TTGAAGCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6566 original size:21 final size:20
Alignment explanation
Indices: 6541--6580 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
6531 CATATAAACT
* *
6541 AATTAATCAGAATATATATCA
1 AATTAAACAAAATA-ATATCA
6562 AATTAAACAAAATAATATC
1 AATTAAACAAAATAATATC
6581 TAGAGATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (20 bp):
AATTAAACAAAATAATATCA
Found at i:16280 original size:2 final size:2
Alignment explanation
Indices: 16273--16309 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16263 ATTTCCTTTA
16273 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 A
16310 AGTACTTCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18295 original size:19 final size:19
Alignment explanation
Indices: 18245--18295 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
18235 TGTGGGATTT
18245 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
18263 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
18282 TTAATAATTAATTA
1 TTAATAATTAATTA
18296 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:19239 original size:11 final size:11
Alignment explanation
Indices: 19223--19264 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
19213 ATATCTAGGG
19223 TTTTCTTTTTC
1 TTTTCTTTTTC
*
19234 TTTTCTTTTTT
1 TTTTCTTTTTC
*
19245 TTTTCATTTTCC
1 TTTTC-TTTTTC
19257 TTTT-TTTT
1 TTTTCTTTT
19265 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 4 0.15
11 15 0.56
12 8 0.30
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:19248 original size:17 final size:18
Alignment explanation
Indices: 19223--19264 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
19213 ATATCTAGGG
*
19223 TTTTCTTTTTC-TTTT-C
1 TTTTTTTTTTCATTTTCC
19239 TTTTTTTTTTCATTTTCC
1 TTTTTTTTTTCATTTTCC
19257 TTTTTTTT
1 TTTTTTTT
19265 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.43
17 4 0.17
18 9 0.39
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTTCATTTTCC
Found at i:23275 original size:48 final size:48
Alignment explanation
Indices: 23223--23324 Score: 129
Period size: 48 Copynumber: 2.1 Consensus size: 48
23213 ACAGTCACCA
23223 AAACCAATGTCA-TCCTCCTTT-TCAGCATCCACAAA-CTTCATCGAAACC
1 AAACCAATGTCACT-CT-CTTTCTCAGCATCCACAAATC-TCATCGAAACC
* * *
23271 AAACCAATGTCACTCTCTTTCTCAGCATCCTCAAATCTCATTGACACC
1 AAACCAATGTCACTCTCTTTCTCAGCATCCACAAATCTCATCGAAACC
23319 AAACCA
1 AAACCA
23325 TTTCCACCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
47 4 0.08
48 42 0.88
49 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.06, T:0.25
Consensus pattern (48 bp):
AAACCAATGTCACTCTCTTTCTCAGCATCCACAAATCTCATCGAAACC
Found at i:24424 original size:2 final size:2
Alignment explanation
Indices: 24378--24408 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24368 TTTTTCCTTG
24378 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 A
24409 ATAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33309 original size:99 final size:99
Alignment explanation
Indices: 33192--33670 Score: 479
Period size: 99 Copynumber: 4.8 Consensus size: 99
33182 CATAACCTTC
* * * *
33192 ATCATCAGCAGCATATTCATCAACTTTGTTTGACGAGTTCAGTTTTGGCTTCCTCCCCCTTCGCT
1 ATCATCAGCATCAGATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGCT
* *
33257 TGGGTTCAATTCG-AGTAAGATCAACATCATCTTT
66 TGGGTTCAA-TAGAAGGAAGATCAACATCATCTTT
33291 ATCATCAGCATCAGATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGCT
1 ATCATCAGCATCAGATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGCT
* * *
33356 TGGTTTCAATAGAAGGCAGATCAGCATCAT-TTT
66 TGGGTTCAATAGAAGGAAGATCAACATCATCTTT
* * * * * * *
33389 CATCATCAG---CAGATTCCTCAACTTTATTAGACGAGCTCGGCTTGAGCTTTGGCTTTCTCCCT
1 -ATCATCAGCATCAGATTCATCAACTGTGTTTGACGA-----G-TTCAGCTTTGGCTTCCTCCCC
* * * * *
33451 CTTCGCTTGGGTTCAATTGGAGTAAGGTCAACATTATCTTT
59 CTTCGCTTGGGTTCAATAGAAGGAAGATCAACATCATCTTT
* *
33492 ATCATCAGCATCAAATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGTT
1 ATCATCAGCATCAGATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGCT
* * *
33557 TGGTTTCAATAGAAGGCAGATCAACATCATCTTC
66 TGGGTTCAATAGAAGGAAGATCAACATCATCTTT
* * * * * * *
33591 ATCATCAG---CAGATTCCTTAACTTTATTAGACGAGCTCGGCTTGAGCTTTGGCTTTCTCCCCC
1 ATCATCAGCATCAGATTCATCAACTGTGTTTGACGA-----G-TTCAGCTTTGGCTTCCTCCCCC
33653 TTCGCTTGGGTTCAATAG
60 TTCGCTTGGGTTCAATAG
33671 TAGCATCTTC
Statistics
Matches: 311, Mismatches: 51, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
96 40 0.13
98 5 0.02
99 149 0.48
100 1 0.00
101 2 0.01
102 91 0.29
103 3 0.01
105 20 0.06
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (99 bp):
ATCATCAGCATCAGATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGCT
TGGGTTCAATAGAAGGAAGATCAACATCATCTTT
Found at i:33594 original size:201 final size:201
Alignment explanation
Indices: 33235--33668 Score: 778
Period size: 201 Copynumber: 2.2 Consensus size: 201
33225 CGAGTTCAGT
*
33235 TTTGGCTTCCTCCCCCTTCGCTTGGGTTCAATTCGAGTAAGATCAACATCATCTTTATCATCAGC
1 TTTGGCTTTCTCCCCCTTCGCTTGGGTTCAATTCGAGTAAGATCAACATCATCTTTATCATCAGC
*
33300 ATCAGATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGCTTGGTTTCAA
66 ATCAAATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGCTTGGTTTCAA
* *
33365 TAGAAGGCAGATCAGCATCATTTTCATCATCAGCAGATTCCTCAACTTTATTAGACGAGCTCGGC
131 TAGAAGGCAGATCAACATCATCTTCATCATCAGCAGATTCCTCAACTTTATTAGACGAGCTCGGC
33430 TTGAGC
196 TTGAGC
* * * *
33436 TTTGGCTTTCTCCCTCTTCGCTTGGGTTCAATTGGAGTAAGGTCAACATTATCTTTATCATCAGC
1 TTTGGCTTTCTCCCCCTTCGCTTGGGTTCAATTCGAGTAAGATCAACATCATCTTTATCATCAGC
*
33501 ATCAAATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGTTTGGTTTCAA
66 ATCAAATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGCTTGGTTTCAA
*
33566 TAGAAGGCAGATCAACATCATCTTCATCATCAGCAGATTCCTTAACTTTATTAGACGAGCTCGGC
131 TAGAAGGCAGATCAACATCATCTTCATCATCAGCAGATTCCTCAACTTTATTAGACGAGCTCGGC
33631 TTGAGC
196 TTGAGC
33637 TTTGGCTTTCTCCCCCTTCGCTTGGGTTCAAT
1 TTTGGCTTTCTCCCCCTTCGCTTGGGTTCAAT
33669 AGTAGCATCT
Statistics
Matches: 222, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
201 222 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (201 bp):
TTTGGCTTTCTCCCCCTTCGCTTGGGTTCAATTCGAGTAAGATCAACATCATCTTTATCATCAGC
ATCAAATTCATCAACTGTGTTTGACGAGTTCAGCTTTGGCTTCCTCCCCCTTCGCTTGGTTTCAA
TAGAAGGCAGATCAACATCATCTTCATCATCAGCAGATTCCTCAACTTTATTAGACGAGCTCGGC
TTGAGC
Done.