Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017138.1 Corchorus olitorius cultivar O-4 contig17171, 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: 21671
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:438 original size:39 final size:40
Alignment explanation
Indices: 384--464 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
374 ATACCTAAGA
* *
384 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATCAATGTAAGTATTTCAGTTATTATATATATTAC
*
423 ATTTAATCAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATCAATGTAAGTATTTCAGTTATTATATATATTAC
463 AT
1 AT
465 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (40 bp):
ATTTAATCAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:2918 original size:26 final size:26
Alignment explanation
Indices: 2889--2941 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2879 GTGAGAGTCT
2889 GGCAACGACGCGACTACGTATGCATG
1 GGCAACGACGCGACTACGTATGCATG
**
2915 GGCAACGGGGCGACTACGTATGCATG
1 GGCAACGACGCGACTACGTATGCATG
2941 G
1 G
2942 CAAGGTCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.36, T:0.15
Consensus pattern (26 bp):
GGCAACGACGCGACTACGTATGCATG
Found at i:9810 original size:31 final size:31
Alignment explanation
Indices: 9747--9914 Score: 156
Period size: 31 Copynumber: 5.4 Consensus size: 31
9737 TTTGTGCATG
* * ** *
9747 TGGCATGTCACGTGTCACTTTTTGAAATACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* * *
9778 TGACATGCCACGTGTCACTTTTGGGTACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* ** * * *
9809 TGGCGTGATACATGTCATTTTTTGGTATACG
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* * *
9840 TGACGTGCCACATGTCGCTTTTTGGTACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* * *
9871 TGGCGTGCCACATGTCGCTTTTTGGTACACG
1 TGGCATGCCACATGTCACTTTTTGGTACACA
9902 TGGCATGCCACAT
1 TGGCATGCCACAT
9915 CGGACACCGT
Statistics
Matches: 112, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 112 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (31 bp):
TGGCATGCCACATGTCACTTTTTGGTACACA
Found at i:9861 original size:62 final size:62
Alignment explanation
Indices: 9759--9914 Score: 195
Period size: 62 Copynumber: 2.5 Consensus size: 62
9749 GCATGTCACG
** * * *
9759 TGTCACTTTTTGAAATACATGACATGCCACGTGTCACTTTTGGGTACACATGGCGTGATACA
1 TGTCACTTTTTGGTATACGTGACATGCCACATGTCACTTTTGGGTACACATGGCGTGACACA
* * * * *
9821 TGTCATTTTTTGGTATACGTGACGTGCCACATGTCGCTTTTTGGTACACATGGCGTGCCACA
1 TGTCACTTTTTGGTATACGTGACATGCCACATGTCACTTTTGGGTACACATGGCGTGACACA
* * *
9883 TGTCGCTTTTTGGTACACGTGGCATGCCACAT
1 TGTCACTTTTTGGTATACGTGACATGCCACAT
9915 CGGACACCGT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 79 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (62 bp):
TGTCACTTTTTGGTATACGTGACATGCCACATGTCACTTTTGGGTACACATGGCGTGACACA
Found at i:10226 original size:11 final size:11
Alignment explanation
Indices: 10210--10234 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10200 GTTATTTTCT
10210 CAATACATAAG
1 CAATACATAAG
10221 CAATACATAAG
1 CAATACATAAG
10232 CAA
1 CAA
10235 GGGTTAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (11 bp):
CAATACATAAG
Found at i:14821 original size:18 final size:18
Alignment explanation
Indices: 14798--14866 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
14788 TACAAAATAT
14798 TGTTCCACTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
* * *
14816 TGTTCCACTACTGCAGAA
1 TGTTCCACTGCCGCAGGA
* *
14834 TGTTGCATTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
*
14852 TGTTCCGCTGCCGCA
1 TGTTCCACTGCCGCA
14867 AGAACCTTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.26
Consensus pattern (18 bp):
TGTTCCACTGCCGCAGGA
Found at i:16658 original size:17 final size:17
Alignment explanation
Indices: 16636--16671 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16626 TGATTTGTAA
16636 AGTTTGTTACACTAGAT
1 AGTTTGTTACACTAGAT
*
16653 AGTTTGTTATACTAGAT
1 AGTTTGTTACACTAGAT
16670 AG
1 AG
16672 CTCTTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (17 bp):
AGTTTGTTACACTAGAT
Found at i:20870 original size:16 final size:15
Alignment explanation
Indices: 20849--20878 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20839 ATTTTCAAAG
20849 TCAACTTCAGCAATTT
1 TCAACTTCAG-AATTT
20865 TCAACTTCAGAATT
1 TCAACTTCAGAATT
20879 GTGGAGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (15 bp):
TCAACTTCAGAATTT
Done.