Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014537.1 Corchorus olitorius cultivar O-4 contig14570, 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: 22931
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:1212 original size:4 final size:4
Alignment explanation
Indices: 1203--1227 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1193 AAAATTAAAC
1203 GCAG GCAG GCAG GCAG GCAG GCAG G
1 GCAG GCAG GCAG GCAG GCAG GCAG G
1228 AATGAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.52, T:0.00
Consensus pattern (4 bp):
GCAG
Found at i:2744 original size:21 final size:21
Alignment explanation
Indices: 2699--2744 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
2689 GTCTTTTAGG
*
2699 TTATAAAGTCTTTTATTTTAC
1 TTATAAAGTCTTTTAGTTTAC
2720 TTAT-AAGTCTTTAGTAGTTTA-
1 TTATAAAGTCTTT--TAGTTTAC
2741 TTAT
1 TTAT
2745 TGCTTATAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 8 0.36
21 8 0.36
22 6 0.27
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.57
Consensus pattern (21 bp):
TTATAAAGTCTTTTAGTTTAC
Found at i:5299 original size:1 final size:1
Alignment explanation
Indices: 5293--5364 Score: 81
Period size: 1 Copynumber: 72.0 Consensus size: 1
5283 TGTATAATTT
* * * * * **
5293 AAAAAAAAACAAAAAAAAACAAAAAAACAAAAAAACAAAAAAAAAAAACAAAAAAAGGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5358 AAAAAAA
1 AAAAAAA
5365 CTCAGAAGGG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:5335 original size:29 final size:28
Alignment explanation
Indices: 5293--5364 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 28
5283 TGTATAATTT
*
5293 AAAAAAAAACAAAAAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAAAAAACAAAAAAAC
*
5321 AAAAAAACAAAAAAAAAAAACAAAAAAAG
1 AAAAAAA-AAAAAAAAAAAACAAAAAAAC
*
5350 GAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAA
5365 CTCAGAAGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.38
29 25 0.62
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (28 bp):
AAAAAAAAAAAAAAAAAAACAAAAAAAC
Found at i:10981 original size:2 final size:2
Alignment explanation
Indices: 10943--10967 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10933 CTTAATTCTT
10943 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
10968 CGAAACGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13003 original size:151 final size:151
Alignment explanation
Indices: 12808--13109 Score: 604
Period size: 151 Copynumber: 2.0 Consensus size: 151
12798 ACTGGGATGG
12808 CTGGAACCACTGCATTTAAAAGAACCTAACCTCTCTACCCGCTTGCGAAAGGAACCTTCCTTTCC
1 CTGGAACCACTGCATTTAAAAGAACCTAACCTCTCTACCCGCTTGCGAAAGGAACCTTCCTTTCC
12873 ATGACTGAATTTTCGAGTGTATCCTTTGTAAGATACAAAGGAGCCTTTCCACCTTACTCCTACCC
66 ATGACTGAATTTTCGAGTGTATCCTTTGTAAGATACAAAGGAGCCTTTCCACCTTACTCCTACCC
12938 CACAATGAGGAAAGTCCCAGA
131 CACAATGAGGAAAGTCCCAGA
12959 CTGGAACCACTGCATTTAAAAGAACCTAACCTCTCTACCCGCTTGCGAAAGGAACCTTCCTTTCC
1 CTGGAACCACTGCATTTAAAAGAACCTAACCTCTCTACCCGCTTGCGAAAGGAACCTTCCTTTCC
13024 ATGACTGAATTTTCGAGTGTATCCTTTGTAAGATACAAAGGAGCCTTTCCACCTTACTCCTACCC
66 ATGACTGAATTTTCGAGTGTATCCTTTGTAAGATACAAAGGAGCCTTTCCACCTTACTCCTACCC
13089 CACAATGAGGAAAGTCCCAGA
131 CACAATGAGGAAAGTCCCAGA
13110 TAAACACTGT
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 151 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (151 bp):
CTGGAACCACTGCATTTAAAAGAACCTAACCTCTCTACCCGCTTGCGAAAGGAACCTTCCTTTCC
ATGACTGAATTTTCGAGTGTATCCTTTGTAAGATACAAAGGAGCCTTTCCACCTTACTCCTACCC
CACAATGAGGAAAGTCCCAGA
Found at i:13173 original size:21 final size:21
Alignment explanation
Indices: 13147--13187 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
13137 ACCCCAACAC
13147 CTCTAGTATGCTATCTGTCAT
1 CTCTAGTATGCTATCTGTCAT
13168 CTCTAGTATGCTATCTGTCA
1 CTCTAGTATGCTATCTGTCA
13188 CGGTCCACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (21 bp):
CTCTAGTATGCTATCTGTCAT
Found at i:14927 original size:34 final size:34
Alignment explanation
Indices: 14883--14998 Score: 153
Period size: 34 Copynumber: 3.4 Consensus size: 34
14873 CGCGGGTCGG
*
14883 ATCCGAATTAGGATTAGTCAAGACAAAGCCCTGA
1 ATCCGGATTAGGATTAGTCAAGACAAAGCCCTGA
* * *
14917 ATCCGGATTAGAATTAGTCAAGGCAAAGCCCTGG
1 ATCCGGATTAGGATTAGTCAAGACAAAGCCCTGA
** *
14951 ATCCGGATCCGGATTAGTCAAGACAAAGTCCTGA
1 ATCCGGATTAGGATTAGTCAAGACAAAGCCCTGA
14985 ATACCGGA-TAGGAT
1 AT-CCGGATTAGGAT
14999 ACCAAAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
34 64 0.93
35 5 0.07
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (34 bp):
ATCCGGATTAGGATTAGTCAAGACAAAGCCCTGA
Found at i:21142 original size:23 final size:20
Alignment explanation
Indices: 21122--21165 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
21112 GAAATAATCA
21122 TATAAAATAATAATAACTAAT
1 TATAAAA-AATAATAACTAAT
* *
21143 TTTTAAAAATAATAACTAAT
1 TATAAAAAATAATAACTAAT
21163 TAT
1 TAT
21166 TAATCTATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAAAAAATAATAACTAAT
Found at i:21155 original size:20 final size:20
Alignment explanation
Indices: 21130--21168 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21120 CATATAAAAT
*
21130 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
21150 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
21169 TCTATACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Done.