Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014685.1 Corchorus capsularis cultivar CVL-1 contig14706, 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: 32163
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2852 original size:25 final size:24
Alignment explanation
Indices: 2807--2866 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
2797 ATTGCTTCAT
* * *
2807 AAATTTTCGAACTATTGTAAATAAC
1 AAATTTTTGAACTATAGTAAA-AAA
2832 AAATTTTTGAACTA-AGATAAAAAA
1 AAATTTTTGAACTATAG-TAAAAAA
*
2856 AAATTGTTGAA
1 AAATTTTTGAA
2867 TTTAAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (24 bp):
AAATTTTTGAACTATAGTAAAAAA
Found at i:5386 original size:2 final size:2
Alignment explanation
Indices: 5379--5408 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5369 AATCAGTTAC
5379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5409 GTTTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5857 original size:33 final size:33
Alignment explanation
Indices: 5820--5886 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5810 AACTTATTGA
5820 TCTTCAATTCTCTTTAAATTTAAGCCTAGCATG
1 TCTTCAATTCTCTTTAAATTTAAGCCTAGCATG
5853 TCTTCAATTCTCTTTAAATTTAAGCCTAGCATG
1 TCTTCAATTCTCTTTAAATTTAAGCCTAGCATG
5886 T
1 T
5887 TCACTAGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (33 bp):
TCTTCAATTCTCTTTAAATTTAAGCCTAGCATG
Found at i:11005 original size:12 final size:12
Alignment explanation
Indices: 10988--11012 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10978 CACGGTTATA
10988 TGAATTGTCAGG
1 TGAATTGTCAGG
11000 TGAATTGTCAGG
1 TGAATTGTCAGG
11012 T
1 T
11013 CTATTAACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (12 bp):
TGAATTGTCAGG
Found at i:30407 original size:3 final size:3
Alignment explanation
Indices: 30346--30387 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
30336 TTTCGATTTC
30346 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30388 TTGAAGGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:30687 original size:29 final size:29
Alignment explanation
Indices: 30645--30762 Score: 182
Period size: 29 Copynumber: 4.1 Consensus size: 29
30635 ACAATTTTTT
*
30645 GGTCTAGATGATCTGAATGATAAATTGAA
1 GGTCCAGATGATCTGAATGATAAATTGAA
* * ***
30674 GGTCCAGATGATCTGAATGACAATTTTTT
1 GGTCCAGATGATCTGAATGATAAATTGAA
30703 GGTCCAGATGATCTGAATGATAAATTGAA
1 GGTCCAGATGATCTGAATGATAAATTGAA
30732 GGTCCAGATGATCTGAATGATAAATTGAA
1 GGTCCAGATGATCTGAATGATAAATTGAA
30761 GG
1 GG
30763 CAACACCATC
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (29 bp):
GGTCCAGATGATCTGAATGATAAATTGAA
Found at i:30701 original size:58 final size:58
Alignment explanation
Indices: 30634--30751 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
30624 ACATCATCAG
*
30634 GACAATTTTTTGGTCTAGATGATCTGAATGATAAATTGAAGGTCCAGATGATCTGAAT
1 GACAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGTCCAGATGATCTGAAT
30692 GACAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGTCCAGATGATCTGAAT
1 GACAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGTCCAGATGATCTGAAT
30750 GA
1 GA
30752 TAAATTGAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (58 bp):
GACAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGTCCAGATGATCTGAAT
Found at i:30865 original size:29 final size:29
Alignment explanation
Indices: 30842--30901 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
30832 CCAATTTTTT
30842 GGTCCAGATGATCTGAATGACAATTTGAA
1 GGTCCAGATGATCTGAATGACAATTTGAA
* *
30871 GGTCCAGATGATCTGAATGATAAATTGAA
1 GGTCCAGATGATCTGAATGACAATTTGAA
30900 GG
1 GG
30902 CAACACCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (29 bp):
GGTCCAGATGATCTGAATGACAATTTGAA
Found at i:32133 original size:20 final size:18
Alignment explanation
Indices: 32096--32134 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
32086 AAAATGAAAA
*
32096 TCGTATAATTATTCTTGT
1 TCGTATAATTAATCTTGT
32114 TCGTATAATGATAATCTTGT
1 TCGTATAAT--TAATCTTGT
32134 T
1 T
32135 TGTGATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (18 bp):
TCGTATAATTAATCTTGT
Done.