Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012380.1 Corchorus olitorius cultivar O-4 contig12413, 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: 8365
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1979 original size:75 final size:75
Alignment explanation
Indices: 1916--2066 Score: 205
Period size: 75 Copynumber: 2.0 Consensus size: 75
1906 TCTTTTTGTT
* * * *
1916 ACGCCATTTTATTATTGCTAATAG-ATTATATTTTACACAACAACTCAATATTGTTACGTAAAAA
1 ACGCCATTTTATTATTGATAAAAGAATTATATTTGACACAACAACTCAATATTGCTACGTAAAAA
1980 TATTTTAACA
66 TATTTTAACA
* * * * *
1990 ACGTCATTTTATTGTTTATAAAAGAATTTTATTTGACGCAACAACTCAATATTGCTACGTAAAAA
1 ACGCCATTTTATTATTGATAAAAGAATTATATTTGACACAACAACTCAATATTGCTACGTAAAAA
*
2055 AATTTTAACA
66 TATTTTAACA
2065 AC
1 AC
2067 AATATATATT
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 19 0.29
75 47 0.71
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (75 bp):
ACGCCATTTTATTATTGATAAAAGAATTATATTTGACACAACAACTCAATATTGCTACGTAAAAA
TATTTTAACA
Found at i:2087 original size:75 final size:75
Alignment explanation
Indices: 1920--2092 Score: 192
Period size: 75 Copynumber: 2.3 Consensus size: 75
1910 TTTGTTACGC
* * * * * * *
1920 CATTTTATTATTGCTAATAG-ATTATATTTTACACAACAACTCAATATTGTTACGTAAAAATATT
1 CATTATATTGTTGCTAAAAGAATTTTATTTGACACAACAACTCAATATTGCTACGTAAAAAAATT
*
1984 TTAACAACGT
66 TTAACAACAT
* ** *
1994 CATTTTATTGTTTATAAAAGAATTTTATTTGACGCAACAACTCAATATTGCTACGTAAAAAAATT
1 CATTATATTGTTGCTAAAAGAATTTTATTTGACACAACAACTCAATATTGCTACGTAAAAAAATT
2059 TTAACAACA-
66 TTAACAACAT
2068 -ATATATATTTGTTGCTAAAA-AATTT
1 CAT-TATA-TTGTTGCTAAAAGAATTT
2093 ATCTTACAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
73 2 0.02
74 24 0.29
75 57 0.69
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (75 bp):
CATTATATTGTTGCTAAAAGAATTTTATTTGACACAACAACTCAATATTGCTACGTAAAAAAATT
TTAACAACAT
Found at i:2892 original size:14 final size:14
Alignment explanation
Indices: 2873--2899 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2863 TTAAGGTTTG
2873 TTTGTTTTTTTTTC
1 TTTGTTTTTTTTTC
2887 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
2900 TAAGAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.04, G:0.07, T:0.89
Consensus pattern (14 bp):
TTTGTTTTTTTTTC
Found at i:3044 original size:54 final size:55
Alignment explanation
Indices: 2958--3066 Score: 127
Period size: 54 Copynumber: 2.0 Consensus size: 55
2948 AATCTATTTG
* * *
2958 GATCTAACCTTGTTAGGAACGGTTTGGAT-AAAACTAAGTTA-AAATTTGGGTTTA
1 GATCTAACCTTGTTAAGAACGGTTTAGATAAAAAC-AAGATAGAAATTTGGGTTTA
*
3012 GATCTAACCCTT-TTAAGAA-GGATTTAGATAAAAACCAGATAGAAATTTGGGTTTA
1 GATCTAA-CCTTGTTAAGAACGG-TTTAGATAAAAACAAGATAGAAATTTGGGTTTA
3067 AGAAATTGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
53 2 0.04
54 23 0.49
55 22 0.47
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (55 bp):
GATCTAACCTTGTTAAGAACGGTTTAGATAAAAACAAGATAGAAATTTGGGTTTA
Found at i:4460 original size:11 final size:11
Alignment explanation
Indices: 4444--4477 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4434 TCCACTATTG
4444 TTATTTTTTAA
1 TTATTTTTTAA
*
4455 TTATTTTTTAG
1 TTATTTTTTAA
4466 TTATTTATTTAA
1 TTATTT-TTTAA
4478 AATAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TTATTTTTTAA
Found at i:7557 original size:172 final size:174
Alignment explanation
Indices: 7368--7709 Score: 625
Period size: 172 Copynumber: 2.0 Consensus size: 174
7358 CAACTAAACC
* *
7368 AAACTCAAGAAACAAAGGACGAAGCCAAAAAAAAACAGTCTGCATATAAGATAATTTAAACAAGA
1 AAACTCAAGAAACAAAGGACGAAGCCAAAAAAAAACAGGCTGCATATAAGATAATCTAAACAAGA
*
7433 ATATAAGATAATCTAAACC-AAAAAAACAGTCTGCATATAAGATAATCT-AAAAAAACAGTCCAT
66 ATATAAGATAACCTAAACCAAAAAAAACAGTCTGCATATAAGATAATCTAAAAAAAACAGTCCAT
7496 CAAACAAGAATATATTATCTTACTAGAATCAAATCCAGTAAAGA
131 CAAACAAGAATATATTATCTTACTAGAATCAAATCCAGTAAAGA
7540 AAACTCAAGAAACAAAGGACGAAGCCAAAAAAAAACAGGCTGCATATAAGATAATCTAAACAAGA
1 AAACTCAAGAAACAAAGGACGAAGCCAAAAAAAAACAGGCTGCATATAAGATAATCTAAACAAGA
7605 ATATAAGATAACCTAAACCAAAAAAAAAACAGTCTGCATATAAGATAATCTAAAAAAAACAGTCC
66 ATATAAGATAACCTAAACC--AAAAAAAACAGTCTGCATATAAGATAATCTAAAAAAAACAGTCC
7670 ATCAAACAAGAATATATTATCTTACTAGAATCAAATCCAG
129 ATCAAACAAGAATATATTATCTTACTAGAATCAAATCCAG
7710 CAAACAAGAT
Statistics
Matches: 163, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
172 81 0.50
175 29 0.18
176 53 0.33
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (174 bp):
AAACTCAAGAAACAAAGGACGAAGCCAAAAAAAAACAGGCTGCATATAAGATAATCTAAACAAGA
ATATAAGATAACCTAAACCAAAAAAAACAGTCTGCATATAAGATAATCTAAAAAAAACAGTCCAT
CAAACAAGAATATATTATCTTACTAGAATCAAATCCAGTAAAGA
Done.