Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021805.1 Corchorus olitorius cultivar O-4 contig21838, 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: 25975
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:79 original size:3 final size:3
Alignment explanation
Indices: 71--96 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61 TCTTTTATGT
71 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
97 TAAAGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:935 original size:25 final size:25
Alignment explanation
Indices: 890--938 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
880 TTTTGAACTC
*
890 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
915 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
939 AAATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:938 original size:21 final size:21
Alignment explanation
Indices: 890--939 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
880 TTTTGAACTC
890 ATTATT-TATTATTTAAAATAT
1 ATTATTAT-TTATTTAAAATAT
911 ATTTATTATTTATTTAATAATAT
1 A-TTATTATTTATTTAA-AATAT
934 A-TATTA
1 ATTATTA
940 AATCTAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 6 0.23
22 13 0.50
23 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTATTTATTTAAAATAT
Found at i:4230 original size:15 final size:15
Alignment explanation
Indices: 4210--4241 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4200 TCCTCCTAAG
4210 ATTAAACTGAAGCCA
1 ATTAAACTGAAGCCA
*
4225 ATTAAATTGAAGCCA
1 ATTAAACTGAAGCCA
4240 AT
1 AT
4242 GTATTCTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (15 bp):
ATTAAACTGAAGCCA
Found at i:5374 original size:129 final size:129
Alignment explanation
Indices: 5125--5384 Score: 316
Period size: 129 Copynumber: 2.0 Consensus size: 129
5115 CATTGTTTAA
* *
5125 ACTTTTATAGTTTTACTAAACTAAAATCTCTATAATTATTTAATTCAATCTAATATCCTTATAAC
1 ACTTTTATAGTTTTACTAAACTAAAAACTCTATAATTATTTAATTCAATATAATATCCTTATAAC
* * * *
5190 TATTTAATATTTACCATTTTACTATTCTAATTAAAAACTTATATATATTATAATTTTTA-AATAT
66 TATTT-ATATTTACCATTTTACTATTCTAATTAAAAAATTATAGACATTAGAATTTTTAGAATAT
* *
5254 ACTTTTATAG-TTTACTCAACTAAAAACTCTATTTATTATTTAATT-AATTATAATATCCTTATA
1 ACTTTTATAGTTTTACTAAACTAAAAACTCTA-TAATTATTTAATTCAA-TATAATATCCTTATA
* * *
5317 CCTAATTT-TTTTTATCATTTTACTAATT-TAATTAAAAAATT-TAGACATGTCAGAATTTTTAG
64 ACT-ATTTATATTTACCATTTTACT-ATTCTAATTAAAAAATTATAGACAT-T-AGAATTTTTAG
5379 AATAT
125 AATAT
5384 A
1 A
5385 TTTCTTAAAT
Statistics
Matches: 113, Mismatches: 11, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
127 5 0.04
128 48 0.42
129 50 0.44
130 10 0.09
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (129 bp):
ACTTTTATAGTTTTACTAAACTAAAAACTCTATAATTATTTAATTCAATATAATATCCTTATAAC
TATTTATATTTACCATTTTACTATTCTAATTAAAAAATTATAGACATTAGAATTTTTAGAATAT
Found at i:6659 original size:20 final size:20
Alignment explanation
Indices: 6634--6674 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6624 AGGTATGTGC
6634 TCAAATAAATATTGGTTATA
1 TCAAATAAATATTGGTTATA
6654 TCAAATAAATATTGGTTATA
1 TCAAATAAATATTGGTTATA
6674 T
1 T
6675 AATATCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
TCAAATAAATATTGGTTATA
Found at i:10150 original size:1 final size:1
Alignment explanation
Indices: 10144--10168 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
10134 AGAATCTGTC
10144 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
10169 CTGTTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16956 original size:90 final size:90
Alignment explanation
Indices: 16831--17016 Score: 266
Period size: 90 Copynumber: 2.1 Consensus size: 90
16821 AGTGCTCAGC
* * *
16831 TTTAAGCTCTGGCCTTCCAGAATCTAGTAACTCTTCAGACACAGTTTGTTCC-TTTGTATCACCC
1 TTTAAGCTCTGGACTGCCAGAATCTAATAACTCTTCAGACACAGTTTGTTCCGTTT-TATCACCC
**
16895 TCTGTGTTTCCAACCTCACTTTCTTG
65 TCTGCCTTTCCAACCTCACTTTCTTG
** *
16921 TTTAAGCTCTGGACTGCCAGAATCTAATAACTCTTCAGATGCAGTTTGTTCCGTTTTATCATCCT
1 TTTAAGCTCTGGACTGCCAGAATCTAATAACTCTTCAGACACAGTTTGTTCCGTTTTATCACCCT
* *
16986 CTGCCTTTCCAAGCTCAGTTTCTTG
66 CTGCCTTTCCAACCTCACTTTCTTG
17011 TTTAAG
1 TTTAAG
17017 AAAATCACCT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 82 0.96
91 3 0.04
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (90 bp):
TTTAAGCTCTGGACTGCCAGAATCTAATAACTCTTCAGACACAGTTTGTTCCGTTTTATCACCCT
CTGCCTTTCCAACCTCACTTTCTTG
Found at i:19616 original size:10 final size:10
Alignment explanation
Indices: 19601--19666 Score: 55
Period size: 10 Copynumber: 6.3 Consensus size: 10
19591 CCGTTTAATA
19601 ATTATATATT
1 ATTATATATT
19611 ATTATATATGT
1 ATTATATAT-T
19622 AATTATATA-T
1 -ATTATATATT
19632 ATCTA-ATATT
1 AT-TATATATT
*
19642 ATTTTATATAT
1 ATTATATAT-T
*
19653 ATATATATAAT
1 AT-TATATATT
19664 ATT
1 ATT
19667 TAATTATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
9 6 0.13
10 20 0.43
11 7 0.15
12 13 0.28
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (10 bp):
ATTATATATT
Found at i:19654 original size:14 final size:14
Alignment explanation
Indices: 19603--19666 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 14
19593 GTTTAATAAT
19603 TATATATTATTATA
1 TATATATTATTATA
*
19617 TATGTAATTATATATA
1 TATAT-ATTAT-TATA
* *
19633 TCTAATATTATTTTA
1 TAT-ATATTATTATA
19648 TATATA-TA-TATA
1 TATATATTATTATA
19660 TA-ATATT
1 TATATATT
19667 TAATTATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
11 3 0.08
12 6 0.15
13 2 0.05
14 7 0.17
15 10 0.25
16 11 0.28
17 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
TATATATTATTATA
Found at i:19660 original size:31 final size:32
Alignment explanation
Indices: 19606--19670 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
19596 TAATAATTAT
*
19606 ATATTATTATATATGTAATTATAT-ATATCTA
1 ATATTATTATATATATAATTATATAATATCTA
* *
19637 ATATTATTTTATATAT-ATATATATAATATTTA
1 ATATTATTATATATATAAT-TATATAATATCTA
19669 AT
1 AT
19671 TATAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 2 0.07
31 19 0.66
32 8 0.28
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (32 bp):
ATATTATTATATATATAATTATATAATATCTA
Found at i:19673 original size:25 final size:25
Alignment explanation
Indices: 19599--19679 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 25
19589 AACCGTTTAA
*
19599 TAATTATATAT-TAT-TAT-ATATG
1 TAATTATATATATATATATAATATT
* *
19621 TAATTATATATATCTA-ATATTA-T
1 TAATTATATATATATATATAATATT
19644 T--TTATATATATATATATAATATT
1 TAATTATATATATATATATAATATT
*
19667 TAATTATAAATAT
1 TAATTATATATAT
19680 TACTAAACGG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
21 12 0.26
22 16 0.35
23 7 0.15
24 2 0.04
25 9 0.20
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
TAATTATATATATATATATAATATT
Found at i:20180 original size:61 final size:61
Alignment explanation
Indices: 20085--20208 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
20075 TACTAGGCAA
20085 ATTATACAATACACCGGCGGTGGAGTTTAGCAAACTACACAAGCGGGTCCTGAAGGGTGAC
1 ATTATACAATACACCGGCGGTGGAGTTTAGCAAACTACACAAGCGGGTCCTGAAGGGTGAC
20146 ATTATACAATACACCGGCGGTGGAGTTTAGCAAACTACACAAGCGGGTCCTGAAGGGTGAC
1 ATTATACAATACACCGGCGGTGGAGTTTAGCAAACTACACAAGCGGGTCCTGAAGGGTGAC
20207 AT
1 AT
20209 GTGTCCTTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.20
Consensus pattern (61 bp):
ATTATACAATACACCGGCGGTGGAGTTTAGCAAACTACACAAGCGGGTCCTGAAGGGTGAC
Done.