Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015931.1 Corchorus olitorius cultivar O-4 contig15964, 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: 35485
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:40 original size:21 final size:21
Alignment explanation
Indices: 7--55 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1 ATTGTA
**
7 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
27 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
48 GCATTCCT
1 GC-TTCCT
56 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:4585 original size:72 final size:72
Alignment explanation
Indices: 4498--4840 Score: 528
Period size: 72 Copynumber: 4.8 Consensus size: 72
4488 CCTCTTCTTC
*
4498 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGGGATAAT
1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
4563 CTTCCAT
66 CTTCCAT
* * * *
4570 ATTACGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
*
4635 CTTCCGT
66 CTTCCAT
* * * * *
4642 ATTGCGGTTGTAGCAGAGGCAGTTCCAACATTTGGCAGTCCTTCACACAATCCTTACATGATAAT
1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
4707 CTTCCAT
66 CTTCCAT
* *
4714 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
*
4779 C-TCCCT
66 CTTCCAT
*
4785 CATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCGCAATCCTTA
1 -ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
4841 ATCCCCAGGG
Statistics
Matches: 247, Mismatches: 23, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
71 28 0.11
72 219 0.89
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (72 bp):
ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGTGATAAT
CTTCCAT
Found at i:6091 original size:41 final size:42
Alignment explanation
Indices: 6022--6163 Score: 223
Period size: 43 Copynumber: 3.4 Consensus size: 42
6012 AAGTCCCTAG
*
6022 ACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAA
1 ACACATATATAACACAGGGGCA-CTCTATTACAAAGTCCTCAA
* *
6065 ACACATATATAACACAGAGGCA-TCTATTACAAAGTCCCCAA
1 ACACATATATAACACAGGGGCACTCTATTACAAAGTCCTCAA
6106 ACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAA
1 ACACATATATAACACAGGGGCA-CTCTATTACAAAGTCCTCAA
*
6149 ACGCATATATAACAC
1 ACACATATATAACAC
6164 CTGGATTGCT
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
41 38 0.42
43 53 0.58
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (42 bp):
ACACATATATAACACAGGGGCACTCTATTACAAAGTCCTCAA
Found at i:6292 original size:29 final size:28
Alignment explanation
Indices: 6248--6303 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
6238 TTCTTCAAAC
*
6248 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
*
6276 TTTCTAATCTTCAAGAACGTTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
6304 GTGGAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Found at i:18579 original size:30 final size:31
Alignment explanation
Indices: 18505--18579 Score: 82
Period size: 34 Copynumber: 2.4 Consensus size: 31
18495 TTTTACTTTG
18505 AAATATTTA-TTATACATGCACATTCATTCTAAA
1 AAATATTTATTTATACATGCACATTCA---TAAA
** *
18538 AAATAAATATTTATACATGCACATTCA-AAT
1 AAATATTTATTTATACATGCACATTCATAAA
18568 AAATATTTATTT
1 AAATATTTATTT
18580 GATTATGCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 12 0.33
33 7 0.19
34 17 0.47
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (31 bp):
AAATATTTATTTATACATGCACATTCATAAA
Found at i:24587 original size:166 final size:169
Alignment explanation
Indices: 24309--24646 Score: 567
Period size: 166 Copynumber: 2.0 Consensus size: 169
24299 AAGTTTATCC
*
24309 ATTACTGTCTGCTTTCAGTGACTCTTCCTTCCAATAAAATAAGTGTCATTTTAAGCCACACCCTT
1 ATTACTGTCTGATTTCAGTGAC-CTTCCTTCCAATAAAATAAGTGTCATTTTAAGCCACACCCTT
*
24374 TGATCATGTTACATTCACCTTTCAGTCCTCTTTGTTTTTTATTCACTATTGAATTGCTGATAACA
65 TGATCATGTTACATTCACCTTTCAGTCCTCTTTGTTTTTTATTCACTATCGAATTGCTGATAACA
*
24439 TTCTGGCCCATGACATGACACAATGATGAGGATATATGAA
130 TTCTGCCCCATGACATGACACAATGATGAGGATATATGAA
*
24479 ATTACTGTTTGATTTCAGTGA-C-T-CTTCCAATAAAATAAGTGTCATTTTAAGCCACACCCTTT
1 ATTACTGTCTGATTTCAGTGACCTTCCTTCCAATAAAATAAGTGTCATTTTAAGCCACACCCTTT
* *
24541 GCTCATG-TATATTCACCTTTCAGTCCTCTTTGTTTTTTAATTCACTATCGAATTGCTGATAACA
66 GATCATGTTACATTCACCTTTCAGTCCTCTTTGTTTTTT-ATTCACTATCGAATTGCTGATAACA
*
24605 TTCTGCCCCATGACATGACACAATGATGAGGATTTATGAA
130 TTCTGCCCCATGACATGACACAATGATGAGGATATATGAA
24645 AT
1 AT
24647 ATTTTTTTTC
Statistics
Matches: 160, Mismatches: 7, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
165 30 0.19
166 109 0.68
167 1 0.01
168 1 0.01
170 19 0.12
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (169 bp):
ATTACTGTCTGATTTCAGTGACCTTCCTTCCAATAAAATAAGTGTCATTTTAAGCCACACCCTTT
GATCATGTTACATTCACCTTTCAGTCCTCTTTGTTTTTTATTCACTATCGAATTGCTGATAACAT
TCTGCCCCATGACATGACACAATGATGAGGATATATGAA
Found at i:31486 original size:9 final size:8
Alignment explanation
Indices: 31458--31487 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
31448 CTTTTTAGCT
31458 TTTTTTTC
1 TTTTTTTC
31466 TTTTTTTC
1 TTTTTTTC
*
31474 TTTTTTCC
1 TTTTTTTC
31482 TTTTTT
1 TTTTTT
31488 GAGATTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:32501 original size:17 final size:17
Alignment explanation
Indices: 32479--32514 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
32469 ACACATATTT
32479 ATAAACTCCAAGAAACA
1 ATAAACTCCAAGAAACA
32496 ATAAACTCCAAGAAACA
1 ATAAACTCCAAGAAACA
32513 AT
1 AT
32515 GTTTTATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.22, G:0.06, T:0.14
Consensus pattern (17 bp):
ATAAACTCCAAGAAACA
Found at i:34689 original size:29 final size:30
Alignment explanation
Indices: 34650--34710 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
34640 TATAAATAAT
* *
34650 ATAATATAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
*
34679 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
34709 AT
1 AT
34711 TAATTAGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Done.