Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016045.1 Corchorus capsularis cultivar CVL-1 contig16066, 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: 10871
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:404 original size:6 final size:6
Alignment explanation
Indices: 393--419 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
383 CCACCCTCAT
393 CAACAC CAACAC CAACAC CAACAC CAA
1 CAACAC CAACAC CAACAC CAACAC CAA
420 AATCACCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (6 bp):
CAACAC
Found at i:2065 original size:5 final size:6
Alignment explanation
Indices: 2048--2073 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2038 TTCTGGAGAT
2048 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
2074 TTGCTGCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:2303 original size:7 final size:7
Alignment explanation
Indices: 2291--2335 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
2281 ATTGCACTGT
2291 TGCCTGC
1 TGCCTGC
2298 TGCCTGC
1 TGCCTGC
2305 TGCCTGC
1 TGCCTGC
2312 TGCCTGC
1 TGCCTGC
2319 TGCCTGC
1 TGCCTGC
2326 TGCCTGC
1 TGCCTGC
2333 TGC
1 TGC
2336 TTAATGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.00, C:0.42, G:0.29, T:0.29
Consensus pattern (7 bp):
TGCCTGC
Found at i:5913 original size:41 final size:41
Alignment explanation
Indices: 5853--5931 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
5843 TGACATTCCT
* *
5853 AATAATTAAAGAAATAAATTAAATCCAGATTTAGCCCCCTA
1 AATAATTAAAGAAAGAAATTAAATCCAGATTTAACCCCCTA
* *
5894 AATAATTAAGGTAAGAAATTAAATCCAGATTTAACCCC
1 AATAATTAAAGAAAGAAATTAAATCCAGATTTAACCCC
5932 TAGTTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (41 bp):
AATAATTAAAGAAAGAAATTAAATCCAGATTTAACCCCCTA
Found at i:6632 original size:19 final size:19
Alignment explanation
Indices: 6608--6653 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
6598 TTTGCATTAC
6608 AATTAAATAAT-AATAAATA
1 AATTAAA-AATAAATAAATA
* *
6627 AATTAAAATTAAATGAATA
1 AATTAAAAATAAATAAATA
6646 AATTAAAA
1 AATTAAAA
6654 TTGGCTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AATTAAAAATAAATAAATA
Found at i:10607 original size:101 final size:100
Alignment explanation
Indices: 10484--10871 Score: 584
Period size: 101 Copynumber: 3.8 Consensus size: 100
10474 CTAAAAGATG
*
10484 TAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGATAAATAAAAATGTCATCTTTGGGTAAA
1 TAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAA
*
10549 AGATTGAA-CTTTTAGAGTGATTAGTAAATAAAATTT
66 AGATTGAATC-TTTAGAGTAATTAGTAAATAAAA-TT
* * *
10585 TAAGCTTTGAATAAAAGATTGAATTTTTAAGTAATT-GTAAGTAAAAATGTCATGTTTGGGTAAA
1 TAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAA
* * *
10649 AGATCGAATTTTTAGAGTAATTAGTAAATAAGGATT
66 AGATTGAATCTTTAGAGTAATTAGTAAATAA-AATT
*
10685 TAACCTTTGAATAAAACATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAA
1 TAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAA
10750 AGATTGAATCTTTAGAGTAATTAGTAAATAAAGATT
66 AGATTGAATCTTTAGAGTAATTAGTAAATAAA-ATT
* *
10786 TAACCTTTGAATAAAAGATTTGGA-TTTTAAGTAATTGGTAAATAAAAAATGTCGTCTTTGGGTA
1 TAACCTTTGAATAAAAGA-TTGAATTTTTAAGTAATTGGTAAAT-AAAAATGTCATCTTTGGGT-
10850 AAAAGATTGAAATCTTTAGAGT
63 AAAAGATTG-AATCTTTAGAGT
Statistics
Matches: 261, Mismatches: 18, Indels: 13
0.89 0.06 0.04
Matches are distributed among these distances:
100 88 0.34
101 130 0.50
102 22 0.08
103 9 0.03
104 12 0.05
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (100 bp):
TAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAA
AGATTGAATCTTTAGAGTAATTAGTAAATAAAATT
Found at i:10852 original size:51 final size:50
Alignment explanation
Indices: 10495--10860 Score: 378
Period size: 51 Copynumber: 7.2 Consensus size: 50
10485 AACCTTTGAA
10495 TAAAAGATTGAATTTTTAAGTAATT-GATAAATAAAAATGTCATCTTTGGG
1 TAAAAGATTGAATTTTTAAGTAATTAG-TAAATAAAAATGTCATCTTTGGG
* * * * * * **
10545 TAAAAGATTGAACTTTTAGAGTGATTAGTAAATAAAATTTTAAGCTTTGAA
1 TAAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAAATGTCATCTTTGGG
* *
10596 TAAAAGATTGAATTTTTAAGTAATT-GTAAGTAAAAATGTCATGTTTGGG
1 TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCATCTTTGGG
* ** * * * **
10645 TAAAAGATCGAATTTTTAGAGTAATTAGTAAATAAGGATTTAACCTTTGAA
1 TAAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAAATGTCATCTTTGGG
* *
10696 TAAAACATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGG
1 TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCATCTTTGGG
* * * * * **
10746 TAAAAGATTGAATCTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAA
1 TAAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAAATGTCATCTTTGGG
* * *
10797 TAAAAGATTTGGA-TTTTAAGTAATTGGTAAATAAAAAATGTCGTCTTTGGG
1 TAAAAGA-TTGAATTTTTAAGTAATTAGTAAAT-AAAAATGTCATCTTTGGG
10848 TAAAAAGATTGAA
1 T-AAAAGATTGAA
10861 ATCTTTAGAG
Statistics
Matches: 250, Mismatches: 58, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
49 33 0.13
50 83 0.33
51 123 0.49
52 11 0.04
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (50 bp):
TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCATCTTTGGG
Done.