Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013176.1 Corchorus olitorius cultivar O-4 contig13209, 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: 30337
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1346 original size:21 final size:21
Alignment explanation
Indices: 1322--1374 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1312 AGGATAGCTT
1322 GGATGGCCGGGAAGATGGCGC
1 GGATGGCCGGGAAGATGGCGC
* *
1343 GGATGGCCGGGCATATGGCGC
1 GGATGGCCGGGAAGATGGCGC
* *
1364 GGCTGACCGGG
1 GGATGGCCGGG
1375 CCATGGCCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.15, C:0.23, G:0.51, T:0.11
Consensus pattern (21 bp):
GGATGGCCGGGAAGATGGCGC
Found at i:4345 original size:20 final size:20
Alignment explanation
Indices: 4320--4364 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
4310 ATTTTTTTTT
4320 AAATTAAAAACGCAAACA-CA
1 AAATTAAAAACGCAAA-ATCA
*
4340 AAATTAAAAACGGAAAATCA
1 AAATTAAAAACGCAAAATCA
4360 AAATT
1 AAATT
4365 TTTTTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.64, C:0.13, G:0.07, T:0.16
Consensus pattern (20 bp):
AAATTAAAAACGCAAAATCA
Found at i:4721 original size:15 final size:14
Alignment explanation
Indices: 4696--4727 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
4686 AAAGCGGAGG
4696 TTAAAAGAAAGCAA
1 TTAAAAGAAAGCAA
4710 TTAAACAGAAAGCAA
1 TTAAA-AGAAAGCAA
4725 TTA
1 TTA
4728 TACTAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.19
Consensus pattern (14 bp):
TTAAAAGAAAGCAA
Found at i:5519 original size:11 final size:11
Alignment explanation
Indices: 5503--5528 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5493 CTTTGCCTAA
5503 AAAACTAGAAG
1 AAAACTAGAAG
5514 AAAACTAGAAG
1 AAAACTAGAAG
5525 AAAA
1 AAAA
5529 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:7331 original size:5 final size:5
Alignment explanation
Indices: 7317--7354 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
7307 AATAAAACAC
* *
7317 CAAAA C-AAA CAAAA CAAAA CAAAC CAAAA CAACA CAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAA
7355 GCAACCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:7919 original size:41 final size:40
Alignment explanation
Indices: 7872--8433 Score: 557
Period size: 41 Copynumber: 13.8 Consensus size: 40
7862 AGGAATAGGA
* * * *
7872 ACAACACCTCCCGATGAGGGAGGGCAAACTGAGAAATGCAG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTG-GAAATGCTG
* * * * *
7913 GCAACACATTCCGATGAGGAAGGGCAAACTGGTGAA--CTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-AAATGC-T-G
*
7954 ACAATACCTTCCGATGAGGAAGGGCAAATTGCGAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTG-GAAATGCTG
* * * * * *
7995 ACATCACCTTTCGATGAGGAAGGGCAAACTGAACAAAGAC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGA-AATG-CTG
* * * * *
8036 ACTACACCTCCCAATGAAGCAGGGCAAATTGGTAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-AAATGCTG
8077 ACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-AAATGCTG
*
8118 ACAACACCTTCCGATGATGAAGGGCAAATTGGTAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-AAATGCTG
* *
8159 ACAACACCTTCCGATGAGGAAGAGC-AA-TGTAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGAAATGCTG
* * *
8197 ACAACACCTTCCGATGAGGAAGAGCAAACTGGACAATGGC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGA-AAT-GCTG
*
8238 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-AAATGCTG
* * *
8279 ACAACACCTTCCGATGAGGAAGAGCAAACTGGACAATGGC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGA-AAT-GCTG
* *
8320 ACAACACC-TCCTGATGAGGAAGAGCAAATTGGTAAATACTG
1 ACAACACCTTCC-GATGAGGAAGGGCAAATTGG-AAATGCTG
* *
8361 ACAACACCTTCCGATGAGGAAGGGCAAATTGGACAAAGGC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG--AAATGCTG
* *
8402 ACAACACCTCCCGATGAGGAACGGCAAATTGG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG
8434 TAAAAGTAGA
Statistics
Matches: 438, Mismatches: 60, Indels: 46
0.81 0.11 0.08
Matches are distributed among these distances:
38 33 0.08
39 5 0.01
40 15 0.03
41 367 0.84
42 17 0.04
43 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (40 bp):
ACAACACCTTCCGATGAGGAAGGGCAAATTGGAAATGCTG
Found at i:8526 original size:51 final size:51
Alignment explanation
Indices: 8402--8633 Score: 306
Period size: 51 Copynumber: 4.5 Consensus size: 51
8392 GACAAAGGCA
* * *
8402 ACAACACCTCCCGAT-GAGGAACGGCAAATTGGTAAAAGTAGACAAACCTTGG
1 ACAACACCTTCCGATGGA-GAAGGGCAAATTGGTAAAAGTAGAC-AACTTTGG
* *
8454 ACAACACCTTCCGATGAAGAAGGGCAAATTGGAAAAAGTAGACAACTTTGG
1 ACAACACCTTCCGATGGAGAAGGGCAAATTGGTAAAAGTAGACAACTTTGG
* * * **
8505 ACAACACCTTCCGATGGAGAAGGACAAATTGGTAGATGCCGACAACTTTGG
1 ACAACACCTTCCGATGGAGAAGGGCAAATTGGTAAAAGTAGACAACTTTGG
* *
8556 ACAACACCTTCCGATGGAGAAGGCCAAATTGGTAAATGCT-GACAACTTTGG
1 ACAACACCTTCCGATGGAGAAGGGCAAATTGGTAAAAG-TAGACAACTTTGG
*
8607 ACAACACCTTCCGATGGAGATGGGCAA
1 ACAACACCTTCCGATGGAGAAGGGCAA
8634 TTGTTTTTGA
Statistics
Matches: 161, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
51 123 0.76
52 37 0.23
53 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (51 bp):
ACAACACCTTCCGATGGAGAAGGGCAAATTGGTAAAAGTAGACAACTTTGG
Found at i:13969 original size:86 final size:86
Alignment explanation
Indices: 13824--13998 Score: 341
Period size: 86 Copynumber: 2.0 Consensus size: 86
13814 TCAGAGGTCC
*
13824 TTAATTTTATTCATTATTAGTAATTCTTTATTATTTATAATAAATGGTCTCTTTTCAACATATTC
1 TTAATTCTATTCATTATTAGTAATTCTTTATTATTTATAATAAATGGTCTCTTTTCAACATATTC
13889 TATCTTTATTCAAATTTGGGT
66 TATCTTTATTCAAATTTGGGT
13910 TTAATTCTATTCATTATTAGTAATTCTTTATTATTTATAATAAATGGTCTCTTTTCAACATATTC
1 TTAATTCTATTCATTATTAGTAATTCTTTATTATTTATAATAAATGGTCTCTTTTCAACATATTC
13975 TATCTTTATTCAAATTTGGGT
66 TATCTTTATTCAAATTTGGGT
13996 TTA
1 TTA
13999 GGGTTTATCA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (86 bp):
TTAATTCTATTCATTATTAGTAATTCTTTATTATTTATAATAAATGGTCTCTTTTCAACATATTC
TATCTTTATTCAAATTTGGGT
Found at i:29687 original size:14 final size:14
Alignment explanation
Indices: 29668--29696 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29658 TATTGACTTA
29668 TTGGGCTTTGGATT
1 TTGGGCTTTGGATT
29682 TTGGGCTTTGGATT
1 TTGGGCTTTGGATT
29696 T
1 T
29697 CTTTTGTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.34, T:0.52
Consensus pattern (14 bp):
TTGGGCTTTGGATT
Done.