Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018717.1 Corchorus olitorius cultivar O-4 contig18750, 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: 3411
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Found at i:866 original size:11 final size:11
Alignment explanation
Indices: 852--885 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
842 TAAAGGAAAA
852 AGCTAGGAAGG
1 AGCTAGGAAGG
863 AGCTAGGAAGG
1 AGCTAGGAAGG
874 AGCTAGGAAGG
1 AGCTAGGAAGG
885 A
1 A
886 CCCTACTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09
Consensus pattern (11 bp):
AGCTAGGAAGG
Found at i:1613 original size:16 final size:16
Alignment explanation
Indices: 1592--1648 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
1582 GGCTTTGTAG
*
1592 GTGAGTATCT-CACTAA
1 GTGAGTAT-TACACCAA
1608 GTGAGTATTACACCAA
1 GTGAGTATTACACCAA
***
1624 GTGAGTATGGTACCAA
1 GTGAGTATTACACCAA
1640 GTGAGTATT
1 GTGAGTATT
1649 TTGTTGGGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 1 0.03
16 34 0.97
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (16 bp):
GTGAGTATTACACCAA
Found at i:2552 original size:25 final size:25
Alignment explanation
Indices: 2518--2587 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
2508 GGGAGTCTCC
2518 CAGGTGAGTCTCACCTAGCGCACAG
1 CAGGTGAGTCTCACCTAGCGCACAG
* *
2543 CAGGTGAGTCTCACTTAGCGCATAG
1 CAGGTGAGTCTCACCTAGCGCACAG
2568 CAGGTGAGTCTCACCTAGCG
1 CAGGTGAGTCTCACCTAGCG
2588 TGTGGAGTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.20
Consensus pattern (25 bp):
CAGGTGAGTCTCACCTAGCGCACAG
Found at i:2833 original size:14 final size:15
Alignment explanation
Indices: 2804--2836 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2794 AGCAAGAGAC
2804 TCTCCCTCAGGGGAG
1 TCTCCCTCAGGGGAG
2819 TCTCCCTCA-GGGAG
1 TCTCCCTCAGGGGAG
2833 TCTC
1 TCTC
2837 TCCCCTAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.12, C:0.36, G:0.27, T:0.24
Consensus pattern (15 bp):
TCTCCCTCAGGGGAG
Found at i:3135 original size:42 final size:42
Alignment explanation
Indices: 3063--3179 Score: 121
Period size: 40 Copynumber: 2.8 Consensus size: 42
3053 CGAAGGTTGG
* * * * *
3063 GGAGTCTCCCCTAGCGCATATCAAGGGAGTCTCTCCCTCAGA
1 GGAGTCTCCTCTAACGCAGAACAAGAGAGTCTCTCCCTCAGA
* ** * *
3105 GGAGTCTCCTTTAACGTGGAGCAAGAGAG--TCTCCCTCAGG
1 GGAGTCTCCTCTAACGCAGAACAAGAGAGTCTCTCCCTCAGA
*
3145 GGAGTCTCCTCTAACGCAGAACAAAAGAGTCTCTC
1 GGAGTCTCCTCTAACGCAGAACAAGAGAGTCTCTC
3180 TCAGGAGAGT
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
40 34 0.58
42 25 0.42
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (42 bp):
GGAGTCTCCTCTAACGCAGAACAAGAGAGTCTCTCCCTCAGA
Found at i:3149 original size:40 final size:40
Alignment explanation
Indices: 3094--3196 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 40
3084 CAAGGGAGTC
* * ** * *
3094 TCTCCCTCAGAGGAGTCTCCTTTAACGTGGAGCAAGAGAG
1 TCTCCCTCAGGGGAGTCTCCTCTAACGCAGAACAAAAGAG
3134 TCTCCCTCAGGGGAGTCTCCTCTAACGCAGAACAAAAGAG
1 TCTCCCTCAGGGGAGTCTCCTCTAACGCAGAACAAAAGAG
* *
3174 TCTCTCTCAGGAGAGTCTTCCTC
1 TCTCCCTCAGGGGAGTC-TCCTC
3197 AAGGAAGTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
40 49 0.91
41 5 0.09
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
TCTCCCTCAGGGGAGTCTCCTCTAACGCAGAACAAAAGAG
Found at i:3206 original size:30 final size:30
Alignment explanation
Indices: 3172--3229 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3162 AGAACAAAAG
* *
3172 AGTCTCTCTCAGGAGAGTCTTCCTCAAGGA
1 AGTCTCCCTAAGGAGAGTCTTCCTCAAGGA
*
3202 AGTCTCCCTAAGGGGAGTCTTCCTCAAG
1 AGTCTCCCTAAGGAGAGTCTTCCTCAAG
3230 TTAGATTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (30 bp):
AGTCTCCCTAAGGAGAGTCTTCCTCAAGGA
Found at i:3275 original size:34 final size:34
Alignment explanation
Indices: 3237--3302 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
3227 AAGTTAGATT
*
3237 GGAAGGGGG-GAAAACCCCTCCCCCATTAAAAATG
1 GGAAGGGGGCG-AAACACCTCCCCCATTAAAAATG
* *
3271 GGAAGGGGGCGTAACACTTCCCCCATTAAAAA
1 GGAAGGGGGCGAAACACCTCCCCCATTAAAAA
3303 AATTTGGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.14
Consensus pattern (34 bp):
GGAAGGGGGCGAAACACCTCCCCCATTAAAAATG
Done.