Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012018.1 Corchorus olitorius cultivar O-4 contig12051, 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: 14610
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Found at i:359 original size:30 final size:30
Alignment explanation
Indices: 323--382 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
313 TTAGGTTAAT
323 TTTGTATTAGGAACATTGAGTAATTTTCTA
1 TTTGTATTAGGAACATTGAGTAATTTTCTA
*
353 TTTGTATTAGGAACATTTAGTAATTTTCTA
1 TTTGTATTAGGAACATTGAGTAATTTTCTA
383 AAGCATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (30 bp):
TTTGTATTAGGAACATTGAGTAATTTTCTA
Found at i:685 original size:17 final size:17
Alignment explanation
Indices: 663--697 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
653 ATCGATTCAT
*
663 TCACGTGTACGTTTTAG
1 TCACGTGCACGTTTTAG
680 TCACGTGCACGTTTTAG
1 TCACGTGCACGTTTTAG
697 T
1 T
698 TAGGTTGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (17 bp):
TCACGTGCACGTTTTAG
Found at i:830 original size:29 final size:29
Alignment explanation
Indices: 788--846 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
778 TTTTCAATTT
788 CATAGTTATGGGAAAGGGGGAGGACTTGG
1 CATAGTTATGGGAAAGGGGGAGGACTTGG
817 CATAGTTATGGGAAAGGGGGAGGACTTGG
1 CATAGTTATGGGAAAGGGGGAGGACTTGG
846 C
1 C
847 TTTAGGCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.44, T:0.20
Consensus pattern (29 bp):
CATAGTTATGGGAAAGGGGGAGGACTTGG
Found at i:2086 original size:95 final size:95
Alignment explanation
Indices: 1974--2164 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
1964 TCTCGGAGCC
1974 ACCTGCACAAAAGGATAACAATGAATCGGTTAGGGAGGAAAGAGAAAATAAAAACAGAATTAATA
1 ACCTGCACAAAAGGATAACAATGAATCGGTTAGGGAGGAAAGAGAAAATAAAAACAGAATTAATA
2039 AAAAGGGAAGAAAATGAAATTACAGCTAGG
66 AAAAGGGAAGAAAATGAAATTACAGCTAGG
2069 ACCTGCACAAAAGGATAACAATGAATCGGTTAGGGAGGAAAGAGAAAATAAAAACAGAATTAATA
1 ACCTGCACAAAAGGATAACAATGAATCGGTTAGGGAGGAAAGAGAAAATAAAAACAGAATTAATA
*
2134 AAAGGGGAAGAAAATGAAATTACAGCTAGG
66 AAAAGGGAAGAAAATGAAATTACAGCTAGG
2164 A
1 A
2165 AGGGTGGGGA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.52, C:0.09, G:0.24, T:0.15
Consensus pattern (95 bp):
ACCTGCACAAAAGGATAACAATGAATCGGTTAGGGAGGAAAGAGAAAATAAAAACAGAATTAATA
AAAAGGGAAGAAAATGAAATTACAGCTAGG
Found at i:2778 original size:13 final size:13
Alignment explanation
Indices: 2760--2787 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2750 GAGAGTAGTG
2760 AGAAGGATTTATC
1 AGAAGGATTTATC
2773 AGAAGGATTTATC
1 AGAAGGATTTATC
2786 AG
1 AG
2788 GTGGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (13 bp):
AGAAGGATTTATC
Found at i:3406 original size:29 final size:28
Alignment explanation
Indices: 3351--3407 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3341 GGTCATTTTT
** * *
3351 TTAGGTTTAATTTCAATTAATTTAGAAA
1 TTAGGTTTAATTTCAACAAAATAAGAAA
3379 TTAGGTTTAACTTTCAACAAAATAAGAAA
1 TTAGGTTTAA-TTTCAACAAAATAAGAAA
3408 GAATTAAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (28 bp):
TTAGGTTTAATTTCAACAAAATAAGAAA
Found at i:14118 original size:12 final size:12
Alignment explanation
Indices: 14101--14138 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
14091 AAGCGGCCCT
14101 TTTTCTTCTTTC
1 TTTTCTTCTTTC
*
14113 TTTTC-TCTTTT
1 TTTTCTTCTTTC
14124 TTTTCTTC-TTC
1 TTTTCTTCTTTC
14135 TTTT
1 TTTT
14139 TTTTTTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:14130 original size:16 final size:16
Alignment explanation
Indices: 14109--14143 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
14099 CTTTTTCTTC
14109 TTTCTT-TTCTCTTTTT
1 TTTCTTCTTCT-TTTTT
14125 TTTCTTCTTCTTTTTT
1 TTTCTTCTTCTTTTTT
14141 TTT
1 TTT
14144 TAAAGATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTCTTCTTCTTTTTT
Found at i:14139 original size:12 final size:12
Alignment explanation
Indices: 14099--14139 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
14089 CCAAGCGGCC
14099 CTTTTTCTTCTT
1 CTTTTTCTTCTT
14111 -TCTTTTC-TCTT
1 CT-TTTTCTTCTT
*
14122 TTTTTTCTTCTT
1 CTTTTTCTTCTT
14134 CTTTTT
1 CTTTTT
14140 TTTTTAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
CTTTTTCTTCTT
Done.