Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013718.1 Corchorus olitorius cultivar O-4 contig13751, 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: 33582
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:776 original size:13 final size:14
Alignment explanation
Indices: 746--783 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
736 AAATTGTAAA
746 ATTTAAAAAATATC
1 ATTTAAAAAATATC
760 ATTTAAAAAATAT-
1 ATTTAAAAAATATC
773 ATTTAAAAAAT
1 ATTTAAAAAAT
784 TCTAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTTAAAAAATATC
Found at i:1012 original size:121 final size:127
Alignment explanation
Indices: 765--1022 Score: 411
Period size: 121 Copynumber: 2.0 Consensus size: 127
755 ATATCATTTA
*
765 AAAAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAA
1 AAAAGTATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAA
*
830 TAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTG
66 T---ATA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTA
895 T
127 T
*
896 AAAAGTATATTTAAAAAATTCT-A-ATATATAATTTTTTTAATTAAAATAGTAAAATGGTAAAAA
1 AAAAGTATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAA
959 T-TA-TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
66 TATAGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
1017 AAAAGT
1 AAAAGT
1023 TCAAACAATG
Statistics
Matches: 124, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
121 56 0.45
122 2 0.02
123 2 0.02
125 2 0.02
129 40 0.32
130 1 0.01
131 21 0.17
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (127 bp):
AAAAGTATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAA
TATAGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
Found at i:2073 original size:73 final size:73
Alignment explanation
Indices: 1996--2145 Score: 221
Period size: 73 Copynumber: 2.1 Consensus size: 73
1986 TTTAAGAAAT
* ** *
1996 ATATTTAAAAAATAAGGGTATAATAG-GTGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAAT
1 ATATTTAAAAAATAAGGATATAAT-GCACGATTCAAAAGTTTTACAGCTGAACGTAATTTTTAAT
*
2060 ATAGTATAG
65 ATAATATAG
* *
2069 ATATTTGAAAAATAAGGATATAATGCACGATTCAAAAGTTTTACAGGTGAACGTAATTTTTAATA
1 ATATTTAAAAAATAAGGATATAATGCACGATTCAAAAGTTTTACAGCTGAACGTAATTTTTAATA
2134 TAATATAG
66 TAATATAG
2142 ATAT
1 ATAT
2146 AAAAATTAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 1 0.01
73 68 0.99
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (73 bp):
ATATTTAAAAAATAAGGATATAATGCACGATTCAAAAGTTTTACAGCTGAACGTAATTTTTAATA
TAATATAG
Found at i:12757 original size:16 final size:16
Alignment explanation
Indices: 12736--12773 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
12726 GGGAATGCCC
12736 TCCCCGCCCTGCACCG
1 TCCCCGCCCTGCACCG
12752 TCCCCGCCCTGCACCG
1 TCCCCGCCCTGCACCG
12768 TCCCCG
1 TCCCCG
12774 AAATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.05, C:0.63, G:0.18, T:0.13
Consensus pattern (16 bp):
TCCCCGCCCTGCACCG
Found at i:15709 original size:25 final size:26
Alignment explanation
Indices: 15664--15716 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
15654 TTTTGAACTC
*
15664 ATTATTTATTATTTAAAATATAT-TT
1 ATTATTTATTATATAAAATATATATT
*
15689 ATTATTTATT-TAATAATATATATATT
1 ATTATTTATTAT-ATAAAATATATATT
15715 AT
1 AT
15717 ATCTAAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 19 0.79
26 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTATTTATTATATAAAATATATATT
Found at i:15714 original size:23 final size:22
Alignment explanation
Indices: 15634--15716 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
15624 TATAGTAATT
*
15634 AAATATATATTATTTATTTATTTTG
1 AAATATATA-TA-TTATTTA-TTTA
*
15659 AACTCAT-TAT-TTA-TTATTTA
1 AAAT-ATATATATTATTTATTTA
*
15679 AAATATATTTATTATTTATTTA
1 AAATATATATATTATTTATTTA
15701 ATAATATATATATTAT
1 A-AATATATATATTAT
15717 ATCTAAGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.04
20 8 0.17
21 6 0.12
22 11 0.23
23 13 0.27
24 1 0.02
25 5 0.10
26 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (22 bp):
AAATATATATATTATTTATTTA
Done.