Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024854.1 Corchorus olitorius cultivar O-4 contig24887, 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: 24196
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:474 original size:21 final size:21
Alignment explanation
Indices: 448--602 Score: 226
Period size: 21 Copynumber: 7.4 Consensus size: 21
438 TGCTAGAAGT
448 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
469 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
490 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
511 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
532 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
553 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
574 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
595 TCATTGGA
1 TCATTGGA
603 ATTGCCTAAA
Statistics
Matches: 129, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
20 2 0.02
21 127 0.98
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:3591 original size:21 final size:21
Alignment explanation
Indices: 3567--3642 Score: 143
Period size: 21 Copynumber: 3.6 Consensus size: 21
3557 GAGCAAGTTC
3567 CAAGCTCATTGGAGAAGGTTT
1 CAAGCTCATTGGAGAAGGTTT
*
3588 CAAGCTCATTGGAGAAGGTTC
1 CAAGCTCATTGGAGAAGGTTT
3609 CAAGCTCATTGGAGAAGGTTT
1 CAAGCTCATTGGAGAAGGTTT
3630 CAAGCTCATTGGA
1 CAAGCTCATTGGA
3643 ATTGCCTAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (21 bp):
CAAGCTCATTGGAGAAGGTTT
Found at i:3609 original size:42 final size:42
Alignment explanation
Indices: 3555--3642 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
3545 AGGAGTTCAA
3555 TGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTTCAAGCTCAT
1 TGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTTCAAGCTCAT
3597 TGGAG-AAGGTTCCAAGCTCATTGGAGAAGGTTTCAAGCTCAT
1 TGGAGCAA-GTTCCAAGCTCATTGGAGAAGGTTTCAAGCTCAT
3639 TGGA
1 TGGA
3643 ATTGCCTAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 2 0.04
42 43 0.96
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (42 bp):
TGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTTCAAGCTCAT
Found at i:4778 original size:206 final size:206
Alignment explanation
Indices: 4421--4836 Score: 814
Period size: 206 Copynumber: 2.0 Consensus size: 206
4411 CGGGTCACAA
*
4421 GGGTGGATTTGAATCTTAAAACAACTAGATTCGCATCACATATGAAGGATCTTTACCTGACCATA
1 GGGTGGATTTGAATCTTAAAACAACTAGATTCGCATAACATATGAAGGATCTTTACCTGACCATA
4486 CTTTCTCTGGTATGTCAAAGGCTAAAGGAGCCGATGGAGACCTGTTGATAAGGTAGCAAGCAACC
66 CTTTCTCTGGTATGTCAAAGGCTAAAGGAGCCGATGGAGACCTGTTGATAAGGTAGCAAGCAACC
*
4551 TTGACTGCTTCACCTCAAAATGCCTTAGGCAATTTAGCCATCCTAAGCATGCATCTTGTCGCAAC
131 TTGACTGCTTCACCCCAAAATGCCTTAGGCAATTTAGCCATCCTAAGCATGCATCTTGTCGCAAC
4616 GTGTGGGTCCG
196 GTGTGGGTCCG
4627 GGGTGGATTTGAATCTTAAAACAACTAGATTCGCATAACATATGAAGGATCTTTACCTGACCATA
1 GGGTGGATTTGAATCTTAAAACAACTAGATTCGCATAACATATGAAGGATCTTTACCTGACCATA
4692 CTTTCTCTGGTATGTCAAAGGCTAAAGGAGCCGATGGAGACCTGTTGATAAGGTAGCAAGCAACC
66 CTTTCTCTGGTATGTCAAAGGCTAAAGGAGCCGATGGAGACCTGTTGATAAGGTAGCAAGCAACC
4757 TTGACTGCTTCACCCCAAAATGCCTTAGGCAATTTAGCCATCCTAAGCATGCATCTTGTCGCAAC
131 TTGACTGCTTCACCCCAAAATGCCTTAGGCAATTTAGCCATCCTAAGCATGCATCTTGTCGCAAC
4822 GTGTGGGTCCG
196 GTGTGGGTCCG
4833 GGGT
1 GGGT
4837 ACGAACCCTA
Statistics
Matches: 208, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
206 208 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (206 bp):
GGGTGGATTTGAATCTTAAAACAACTAGATTCGCATAACATATGAAGGATCTTTACCTGACCATA
CTTTCTCTGGTATGTCAAAGGCTAAAGGAGCCGATGGAGACCTGTTGATAAGGTAGCAAGCAACC
TTGACTGCTTCACCCCAAAATGCCTTAGGCAATTTAGCCATCCTAAGCATGCATCTTGTCGCAAC
GTGTGGGTCCG
Found at i:5285 original size:40 final size:39
Alignment explanation
Indices: 5234--5542 Score: 141
Period size: 40 Copynumber: 7.7 Consensus size: 39
5224 AGACAAAATT
*
5234 AAACAACACCTTCCGACGGGGAAAGGC-GAATTGGGAACAA
1 AAACAACACCTTCCGATGGGGAAAGGCAGAA-TGGGAA-AA
* * * *
5274 AAACAACACCTTTCGGTGGGGAAGGGCAGAACAT-GAAAAA
1 AAACAACACCTTCCGATGGGGAAAGGCAG-A-ATGGGAAAA
* * *
5314 AAACAACACCTTTCGGTGGGG-AAGG-AAAACTGGGAAAA
1 AAACAACACCTTCCGATGGGGAAAGGCAGAA-TGGGAAAA
* * **
5352 GTAAACGACACCTTCCGATAGGGAAAGGCAGAACAGGAATAA
1 --AAACAACACCTTCCGATGGGGAAAGGCAGAATGGGAA-AA
* * * **
5394 AAACAACACCTTCCTG-TGAGGAAGGGCA-AACTGAGAATGT
1 AAACAACACCTTCC-GATGGGGAAAGGCAGAA-TGGGAA-AA
* * * * * *
5434 TAACAAGACCTTCCAACGAGG-AAGGACA-AACTGGGAATGA
1 AAACAACACCTTCCGATGGGGAAAGG-CAGAA-TGGGAA-AA
* * * *
5474 AAACAACACCTTCCGACGAGGAAGGGCA-AACTAGGAAATGA
1 AAACAACACCTTCCGATGGGGAAAGGCAGAA-TGGGAAA--A
* *
5515 AAACAACACCTTCCGATGAGGAAGGGCA
1 AAACAACACCTTCCGATGGGGAAAGGCA
5543 AACTGAGAAT
Statistics
Matches: 214, Mismatches: 38, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
36 1 0.00
37 2 0.01
38 6 0.03
39 8 0.04
40 145 0.68
41 44 0.21
42 7 0.03
43 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.12
Consensus pattern (39 bp):
AAACAACACCTTCCGATGGGGAAAGGCAGAATGGGAAAA
Found at i:5445 original size:80 final size:79
Alignment explanation
Indices: 5275--5673 Score: 367
Period size: 80 Copynumber: 5.0 Consensus size: 79
5265 TGGGAACAAA
* * * * ** * * *
5275 AACAACACCTTTCGGTGGGGAAGGGCAGAACATGAAAAAAAACAACACCTTTCGGTGGGGAA-GG
1 AACAACACCTTCCGATGAGGAAGGGCA-AACAGGAATGAAAACAACACCTTCCGATGAGGAAGGG
* * * *
5339 AAAACTGGGAAAAGTA
65 CAAACTGAG-AATGTT
* * *
5355 AACGACACCTTCCGAT-AGGGAAAGGCAGAACAGGAATAAAAACAACACCTTCCTG-TGAGGAAG
1 AACAACACCTTCCGATGA-GGAAGGGCA-AACAGGAATGAAAACAACACCTTCC-GATGAGGAAG
5418 GGCAAACTGAGAATGTT
63 GGCAAACTGAGAATGTT
* * * * * *
5435 AACAAGACCTTCCAACGAGGAAGGACAAACTGGGAATGAAAACAACACCTTCCGACGAGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAAC-AGGAATGAAAACAACACCTTCCGATGAGGAAGGG
**
5500 CAAACT-AGGAAATGAA
65 CAAACTGA-G-AATGTT
* ***
5516 AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGCTGACAACACCTTCCGATGAGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACAG-GAATGAAAACAACACCTTCCGATGAGGAAGGG
* *
5581 CAAACTGGGAATGCT
65 CAAACTGAGAATGTT
* * * **
5596 GACAACACCTTTCGATGAGGAAGGGCAAACTGGAATGCTAACAACACCTTCCGATGAGGAAGGGC
1 AACAACACCTTCCGATGAGGAAGGGCAAACAGGAATGAAAACAACACCTTCCGATGAGGAAGGGC
5661 AAACTG-GAATGTT
66 AAACTGAGAATGTT
5674 GAAAGAAAAT
Statistics
Matches: 269, Mismatches: 40, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
78 6 0.02
79 43 0.16
80 144 0.54
81 76 0.28
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (79 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACAGGAATGAAAACAACACCTTCCGATGAGGAAGGGC
AAACTGAGAATGTT
Found at i:5541 original size:121 final size:119
Alignment explanation
Indices: 5333--5673 Score: 422
Period size: 121 Copynumber: 2.8 Consensus size: 119
5323 CTTTCGGTGG
* * * * * *
5333 GGAAGGA-AAACTGGGAAAAGTAAACGACACCTTCCGATAGGGAAAGGCAGAAC-AGGAATAAAA
1 GGAAGGACAAACTGGG-AATGAAAACAACACCTTCCGAGA-GGAAGGGCA-AACTAGGAATGAAA
*
5396 ACAACACCTTCCTG-TGAGGAAGGGCAAACTGAGAATGTTAACAAGACCTTCCAACGA
63 ACAACACCTTCC-GATGAGGAAGGGCAAACTGAGAATGTTAACAACACCTTCCAACGA
5453 GGAAGGACAAACTGGGAATGAAAACAACACCTTCCGACGAGGAAGGGCAAACTAGGAAATGAAAA
1 GGAAGGACAAACTGGGAATGAAAACAACACCTTCCGA-GAGGAAGGGCAAACTAGG-AATGAAAA
* * * *
5518 CAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGCTGACAACACCTTCCGATGA
64 CAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGTTAACAACACCTTCCAACGA
* *** * **
5574 GGAAGGGCAAACTGGGAATGCTGACAACACCTTTCGATGAGGAAGGGCAAACT-GGAATGCTAAC
1 GGAAGGACAAACTGGGAATGAAAACAACACCTTCCGA-GAGGAAGGGCAAACTAGGAATGAAAAC
5638 AACACCTTCCGATGAGGAAGGGCAAACTG-GAATGTT
65 AACACCTTCCGATGAGGAAGGGCAAACTGAGAATGTT
5674 GAAAGAAAAT
Statistics
Matches: 196, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
118 6 0.03
119 39 0.20
120 39 0.20
121 112 0.57
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (119 bp):
GGAAGGACAAACTGGGAATGAAAACAACACCTTCCGAGAGGAAGGGCAAACTAGGAATGAAAACA
ACACCTTCCGATGAGGAAGGGCAAACTGAGAATGTTAACAACACCTTCCAACGA
Found at i:5571 original size:40 final size:40
Alignment explanation
Indices: 5395--5671 Score: 364
Period size: 40 Copynumber: 7.0 Consensus size: 40
5385 CAGGAATAAA
*
5395 AACAACACCTTCCTG-TGAGGAAGGGCAAACTGAGAATGTT
1 AACAACACCTTCC-GATGAGGAAGGGCAAACTGAGAATGCT
* * * * * **
5435 AACAAGACCTTCCAACGAGGAAGGACAAACTGGGAATGAA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGCT
* **
5475 AACAACACCTTCCGACGAGGAAGGGCAAACT-AGGAAATGAA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGA-G-AATGCT
5516 AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGCT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGCT
* *
5556 GACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGCT
* *
5596 GACAACACCTTTCGATGAGGAAGGGCAAACTG-GAATGCT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGCT
5635 AACAACACCTTCCGATGAGGAAGGGCAAACTG-GAATG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATG
5672 TTGAAAGAAA
Statistics
Matches: 214, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
39 42 0.20
40 134 0.63
41 37 0.17
42 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.14
Consensus pattern (40 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATGCT
Found at i:9208 original size:28 final size:27
Alignment explanation
Indices: 9173--9246 Score: 105
Period size: 26 Copynumber: 2.7 Consensus size: 27
9163 AAGTGGACTT
*
9173 AAAATGACCAAAATGCCCCTTGAATGTG
1 AAAATGACCAAAATGCCCCTT-AATGTA
* *
9201 CAAATGACCAAAATG-CCCTTAGTGTA
1 AAAATGACCAAAATGCCCCTTAATGTA
9227 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
9247 AGGTGACCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 18 0.44
27 9 0.22
28 14 0.34
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTTAATGTA
Found at i:14233 original size:10 final size:11
Alignment explanation
Indices: 14208--14246 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
14198 TAGTTTAATC
**
14208 GAAAAATATCA
1 GAAAAATAAAA
14219 GAAAAATAAAA
1 GAAAAATAAAA
14230 -AAAAATAAAA
1 GAAAAATAAAA
14240 GAAAAAT
1 GAAAAAT
14247 TCGACCAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (11 bp):
GAAAAATAAAA
Done.