Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012989.1 Corchorus capsularis cultivar CVL-1 contig13010, 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: 48353
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:9999 original size:22 final size:21
Alignment explanation
Indices: 9970--10013 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
9960 GTAAGTGATG
9970 AAGTAGTGAAATTGAAAATTA
1 AAGTAGTGAAATTGAAAATTA
* *
9991 AAGTGAGTGAATTTGAGAATTA
1 AAGT-AGTGAAATTGAAAATTA
10013 A
1 A
10014 GGTAATAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.30
Consensus pattern (21 bp):
AAGTAGTGAAATTGAAAATTA
Found at i:13621 original size:17 final size:18
Alignment explanation
Indices: 13593--13643 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
13583 AAGTAACTAA
*
13593 GAAAAATAAAAAGTAAAC
1 GAAAAATCAAAAGTAAAC
*
13611 TAAAAA-CAAAAG-AAAC
1 GAAAAATCAAAAGTAAAC
*
13627 GAAAAATTAAAAGTAAA
1 GAAAAATCAAAAGTAAA
13644 ATAACGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 9 0.33
17 10 0.37
18 8 0.30
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.12
Consensus pattern (18 bp):
GAAAAATCAAAAGTAAAC
Found at i:13637 original size:23 final size:22
Alignment explanation
Indices: 13611--13660 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
13601 AAAAGTAAAC
13611 TAAAAACAAAAGAAACGAAAAAT
1 TAAAAACAAAA-AAACGAAAAAT
** *
13634 TAAAAGTAAAATAACGAAAAAT
1 TAAAAACAAAAAAACGAAAAAT
13656 TAAAA
1 TAAAA
13661 GATAAAGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (22 bp):
TAAAAACAAAAAAACGAAAAAT
Found at i:13649 original size:22 final size:23
Alignment explanation
Indices: 13624--13666 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
13614 AAACAAAAGA
13624 AACGAAAAATTAAAAG-TAAAAT
1 AACGAAAAATTAAAAGATAAAAT
13646 AACGAAAAATTAAAAGATAAA
1 AACGAAAAATTAAAAGATAAA
13667 GGTAAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (23 bp):
AACGAAAAATTAAAAGATAAAAT
Found at i:18273 original size:21 final size:21
Alignment explanation
Indices: 18247--18295 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
18237 GCGCTGAGCG
18247 CCCATGTGGTATG-CTTGGCGA
1 CCCATGTGGTATGCCTT-GCGA
*
18268 CCCATGTGGTTTGCCTTGCGA
1 CCCATGTGGTATGCCTTGCGA
18289 CCCATGT
1 CCCATGT
18296 ACTCCAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.31
Consensus pattern (21 bp):
CCCATGTGGTATGCCTTGCGA
Found at i:26235 original size:21 final size:21
Alignment explanation
Indices: 26222--26262 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
26212 AGAAACTTTG
26222 AAATATAAATAAGAAACCTCT
1 AAATATAAATAAGAAACCTCT
*
26243 AAATATAAATAAGAGACCTC
1 AAATATAAATAAGAAACCTC
26263 CAACATAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (21 bp):
AAATATAAATAAGAAACCTCT
Found at i:28293 original size:20 final size:19
Alignment explanation
Indices: 28260--28297 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
28250 AAAAAGTTCT
*
28260 AAAACAAAATTAAAAATTA
1 AAAACAAAAATAAAAATTA
28279 AAAACAGAAAATAAAAATT
1 AAAACA-AAAATAAAAATT
28298 TTTTAGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAACAAAAATAAAAATTA
Found at i:29651 original size:28 final size:30
Alignment explanation
Indices: 29602--29659 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
29592 TAACTATCCA
29602 TTTTGGGACAAATTGGTCCCC-TAACTTTT
1 TTTTGGGACAAATTGGTCCCCTTAACTTTT
29631 TTTTGGGACAAATTGG-CCCCTTAACTTTT
1 TTTTGGGACAAATTGGTCCCCTTAACTTTT
29660 AAAAACGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (30 bp):
TTTTGGGACAAATTGGTCCCCTTAACTTTT
Found at i:33843 original size:20 final size:20
Alignment explanation
Indices: 33820--33869 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
33810 AAAACCAATG
*
33820 AAAATCCAAAAAAAAATGAA
1 AAAATCAAAAAAAAAATGAA
** *
33840 AAAAAGAAAAAAAAAATGAG
1 AAAATCAAAAAAAAAATGAA
*
33860 AAAATTAAAA
1 AAAATCAAAA
33870 GATGCAATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (20 bp):
AAAATCAAAAAAAAAATGAA
Found at i:39080 original size:30 final size:30
Alignment explanation
Indices: 39046--39107 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
39036 TCTTACCTGT
39046 TTTCACCTGGGATAGTTGCTACTAGGCCTA
1 TTTCACCTGGGATAGTTGCTACTAGGCCTA
39076 TTTCACCTGGGATAGTTGCTACTAGGCCTA
1 TTTCACCTGGGATAGTTGCTACTAGGCCTA
39106 TT
1 TT
39108 GACTTAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (30 bp):
TTTCACCTGGGATAGTTGCTACTAGGCCTA
Found at i:43897 original size:21 final size:21
Alignment explanation
Indices: 43871--43923 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
43861 GCACTGGAGT
* * *
43871 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
43892 ACATGGGGCGCCAAGCAAACC
1 ACATGGGGCGCCAAGCAAACC
43913 ACAT-GGGCGCC
1 ACATGGGGCGCC
43924 CAGCGCTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.28, C:0.32, G:0.32, T:0.08
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:46822 original size:21 final size:21
Alignment explanation
Indices: 46798--46839 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
46788 AAAGTTCTTG
* *
46798 CAAAATTGAACTTGTCACCAA
1 CAAAATTGAACCTGACACCAA
46819 CAAAATTGAACCTGACACCAA
1 CAAAATTGAACCTGACACCAA
46840 TATACATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (21 bp):
CAAAATTGAACCTGACACCAA
Done.