Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021202.1 Corchorus olitorius cultivar O-4 contig21235, 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: 20399
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:493 original size:10 final size:10
Alignment explanation
Indices: 478--532 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
468 AGTAATTTCC
478 CTTCTTTTTT
1 CTTCTTTTTT
488 CTTCTTTTTT
1 CTTCTTTTTT
*
498 TTTCTTTTTT
1 CTTCTTTTTT
508 -TTCATTTTTTT
1 CTTC--TTTTTT
*
519 TTTCATTTTTT
1 CTTC-TTTTTT
530 CTT
1 CTT
533 ACCTTGTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
9 3 0.08
10 19 0.49
11 14 0.36
12 3 0.08
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.82
Consensus pattern (10 bp):
CTTCTTTTTT
Found at i:504 original size:20 final size:21
Alignment explanation
Indices: 479--532 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
469 GTAATTTCCC
479 TTCTTTTTTCTTC-TTTTTTT
1 TTCTTTTTTCTTCATTTTTTT
499 TTCTTTTTT-TTCATTTTTTTT
1 TTCTTTTTTCTTCA-TTTTTTT
520 TTCATTTTTTCTT
1 TTC-TTTTTTCTT
533 ACCTTGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.10
20 9 0.30
21 10 0.33
22 6 0.20
23 2 0.07
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (21 bp):
TTCTTTTTTCTTCATTTTTTT
Found at i:523 original size:12 final size:11
Alignment explanation
Indices: 482--529 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
472 ATTTCCCTTC
482 TTTTTTCTTCTT
1 TTTTTTCTT-TT
*
494 TTTTTT-TCTT
1 TTTTTTCTTTT
504 TTTTTTCATTTT
1 TTTTTTC-TTTT
516 TTTTTTCATTTT
1 TTTTTTC-TTTT
528 TT
1 TT
530 CTTACCTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 8 0.25
11 1 0.03
12 23 0.72
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:927 original size:28 final size:27
Alignment explanation
Indices: 875--973 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 27
865 TATGAAGTAC
*
875 AAATGACCAAAATGCCTTGGAATGTGTA
1 AAATGACCAAAATGCCCTGGAATGTG-A
*
903 AAATGACCAAAATGCCCCTGG-ATGTGC
1 AAATGACCAAAATG-CCCTGGAATGTGA
* * ** *
930 AAATGACTAAAATAACCCT-GAACATGC
1 AAATGACCAAAAT-GCCCTGGAATGTGA
*
957 AAATGACTAAAATGCCC
1 AAATGACCAAAATGCCC
974 CTGAACATGC
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.07
27 33 0.54
28 19 0.31
29 5 0.08
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCTGGAATGTGA
Found at i:941 original size:27 final size:27
Alignment explanation
Indices: 903--1000 Score: 133
Period size: 27 Copynumber: 3.6 Consensus size: 27
893 GGAATGTGTA
* * **
903 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACTAAAATGCCCCTGAACATGC
**
930 AAATGACTAAAATAACCCTGAACATGC
1 AAATGACTAAAATGCCCCTGAACATGC
957 AAATGACTAAAATGCCCCTGAACATGC
1 AAATGACTAAAATGCCCCTGAACATGC
*
984 AAAAGACTAAAATGCCC
1 AAATGACTAAAATGCCC
1001 ACCTAGGTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.17
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAACATGC
Found at i:10776 original size:35 final size:36
Alignment explanation
Indices: 10685--10865 Score: 233
Period size: 35 Copynumber: 5.1 Consensus size: 36
10675 AGGAAATATT
* * *
10685 AGGGCAGT-TTTTCTTTAGTTTATTTCAATTGATCC
1 AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCC
* *
10720 AGGGCGGTCTTTTCTTTAGTTTATTTTAGTTGATCC
1 AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCC
* * * *
10756 ATGACGTTC-TTTCTTCAGTTTATTTCAGTTGATCT
1 AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCC
* *
10791 AAGGCGGTC-TTTCTTCAGTTAATTTCAGTTGATCC
1 AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCC
*
10826 AGGGCGGTCTTTTCTTCAGTATATTTCAGTTGATCC
1 AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCC
10862 AGGG
1 AGGG
10866 AAATACCACC
Statistics
Matches: 127, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
35 68 0.54
36 59 0.46
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (36 bp):
AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCC
Found at i:10840 original size:71 final size:72
Alignment explanation
Indices: 10685--10862 Score: 227
Period size: 71 Copynumber: 2.5 Consensus size: 72
10675 AGGAAATATT
* * * * * * *
10685 AGGGCAGT-TTTTCTTTAGTTTATTTCAATTGATCCAGGGCGGTCTTTTCTTTAGTTTATTTTAG
1 AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCCAAGGCGGTCTTTTCTTCAGTTAATTTCAG
10749 TTGATCC
66 TTGATCC
* * * *
10756 ATGACGTTC-TTTCTTCAGTTTATTTCAGTTGATCTAAGGCGGTC-TTTCTTCAGTTAATTTCAG
1 AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCCAAGGCGGTCTTTTCTTCAGTTAATTTCAG
10819 TTGATCC
66 TTGATCC
*
10826 AGGGCGGTCTTTTCTTCAGTATATTTCAGTTGATCCA
1 AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCCA
10863 GGGAAATACC
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
70 29 0.33
71 60 0.67
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.46
Consensus pattern (72 bp):
AGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGATCCAAGGCGGTCTTTTCTTCAGTTAATTTCAG
TTGATCC
Found at i:15109 original size:16 final size:15
Alignment explanation
Indices: 15088--15125 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
15078 TTTAAAGGTT
15088 TTCTTTTTACTTTTAC
1 TTCTTTTTA-TTTTAC
*
15104 TTCTTTTTATTTTTC
1 TTCTTTTTATTTTAC
15119 -TCTTTTT
1 TTCTTTTT
15126 TGCAAGGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 5 0.24
16 9 0.43
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTTTATTTTAC
Found at i:19766 original size:15 final size:16
Alignment explanation
Indices: 19742--19778 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
19732 AGAGGTTGAA
*
19742 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
19757 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
19773 AGAAAA
1 AGAAAA
19779 TAAAGCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.14
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.