Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021994.1 Corchorus olitorius cultivar O-4 contig22027, 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: 17767
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:6915 original size:27 final size:27
Alignment explanation
Indices: 6877--6954 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
6867 AGTGTACTTG
*
6877 AAATGACCAAAATGCCCTTGGATGTGC
1 AAATGACCAAAATGCCCCTGGATGTGC
**
6904 AAATGACCAAAATGCCCCTGGACATGC
1 AAATGACCAAAATGCCCCTGGATGTGC
6931 AAATGACCAAAATGCCCCTGGATG
1 AAATGACCAAAATGCCCCTGGATG
6955 ACCCTAATGC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATGTGC
Found at i:9626 original size:2 final size:2
Alignment explanation
Indices: 9619--9663 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
9609 ATAATTTCGA
* *
9619 AG AG AG AG AG AG AG AG AG AG AG AG AC TG ATG AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG AG
9661 AG A
1 AG A
9664 AATAGTTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.47, T:0.04
Consensus pattern (2 bp):
AG
Found at i:9950 original size:17 final size:16
Alignment explanation
Indices: 9876--9957 Score: 52
Period size: 15 Copynumber: 5.4 Consensus size: 16
9866 AATTAGGTAT
*
9876 TATATTTAT-AAATTA
1 TATATTAATGAAATTA
9891 TATATGTAATGAAATT-
1 TATAT-TAATGAAATTA
* * *
9907 T-TATT-TTTAAAATA
1 TATATTAATGAAATTA
*
9921 -ATATTTA-GAAATTA
1 TATATTAATGAAATTA
9935 TATATGTAATGAAATTA
1 TATAT-TAATGAAATTA
9952 TA-ATTA
1 TATATTA
9958 GAATATAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
13 5 0.10
14 10 0.20
15 14 0.27
16 8 0.16
17 14 0.27
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
TATATTAATGAAATTA
Found at i:9960 original size:30 final size:28
Alignment explanation
Indices: 9829--9981 Score: 82
Period size: 30 Copynumber: 5.3 Consensus size: 28
9819 TTATATGAGA
* * *
9829 AAATAATATTTAGAAATGATATATGTAATT
1 AAATTATAATTAGAAATTATATAT-TAA-T
**
9859 AAATTATAATTAGGTATTATAT-TT-AT
1 AAATTATAATTAGAAATTATATATTAAT
* * *
9885 AAATTATATATGTAATGAAATTTTATTTTTA-
1 AAATTATA-AT-T-A-GAAATTATATATTAAT
* *
9916 AAATAATATTTAGAAATTATATATGTAAT
1 AAATTATAATTAGAAATTATATAT-TAAT
* *
9945 GAAATTATAATTAG-AA-TATAATATTTAG
1 -AAATTATAATTAGAAATTAT-ATATTAAT
9973 AAATTATAA
1 AAATTATAA
9982 ATGTTTAGAA
Statistics
Matches: 96, Mismatches: 17, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
26 9 0.09
27 22 0.23
28 10 0.10
29 9 0.09
30 36 0.38
31 9 0.09
32 1 0.01
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (28 bp):
AAATTATAATTAGAAATTATATATTAAT
Found at i:9974 original size:14 final size:14
Alignment explanation
Indices: 9955--10029 Score: 68
Period size: 14 Copynumber: 5.4 Consensus size: 14
9945 GAAATTATAA
9955 TTAGAATATAATAT
1 TTAGAATATAATAT
*
9969 TTAGAAATTATAAATGT
1 TTAG-AA-TAT-AATAT
*
9986 TTAGAA-ATTATAT
1 TTAGAATATAATAT
9999 TTAG-AT-T-ATAT
1 TTAGAATATAATAT
*
10010 TTAGAAAATAATAT
1 TTAGAATATAATAT
10024 TTAGAA
1 TTAGAA
10030 ATTATAAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
11 8 0.16
12 3 0.06
13 8 0.16
14 16 0.32
15 2 0.04
16 5 0.10
17 8 0.16
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (14 bp):
TTAGAATATAATAT
Found at i:9993 original size:44 final size:44
Alignment explanation
Indices: 9814--10036 Score: 182
Period size: 44 Copynumber: 5.2 Consensus size: 44
9804 AAAATTGGTC
* * *
9814 AGAAATTAT-ATGAGAAAATAATATTTAGAAATGATATATGTAATT
1 AGAAATTATAATTAGAATATAATATTTAGAAATTATATATGT--TT
* * * *
9859 --AAATTATAATTAG-GTATTATATTTATAAATTATATATG-TA
1 AGAAATTATAATTAGAATATAATATTTAGAAATTATATATGTTT
* * ** * *
9899 ATGAAATTTTATTTTTAAAATAATATTTAGAAATTATATATG-TA
1 A-GAAATTATAATTAGAATATAATATTTAGAAATTATATATGTTT
*
9943 ATGAAATTATAATTAGAATATAATATTTAGAAATTATAAATGTTT
1 A-GAAATTATAATTAGAATATAATATTTAGAAATTATATATGTTT
* *
9988 AGAAATTATATTTAG-AT-T-ATATTTAGAAA--ATA-ATATTT
1 AGAAATTATAATTAGAATATAATATTTAGAAATTATATATGTTT
10026 AGAAATTATAA
1 AGAAATTATAA
10037 ATGTAATGAA
Statistics
Matches: 147, Mismatches: 25, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
38 15 0.10
39 3 0.02
40 1 0.01
41 11 0.07
42 1 0.01
43 38 0.26
44 76 0.52
45 2 0.01
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (44 bp):
AGAAATTATAATTAGAATATAATATTTAGAAATTATATATGTTT
Found at i:10001 original size:30 final size:30
Alignment explanation
Indices: 9955--10040 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 30
9945 GAAATTATAA
9955 TTAGAATATAATATTTAGAAATTATAAATGT
1 TTAGAA-ATAATATTTAGAAATTATAAATGT
*
9986 TTAGAAATTATATTTAG--ATTAT--A--T
1 TTAGAAATAATATTTAGAAATTATAAATGT
10010 TTAGAAAATAATATTTAGAAATTATAAATGT
1 TTAG-AAATAATATTTAGAAATTATAAATGT
10041 AATGAAATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
24 5 0.11
25 12 0.26
26 1 0.02
27 5 0.11
28 5 0.11
29 1 0.02
30 10 0.22
31 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (30 bp):
TTAGAAATAATATTTAGAAATTATAAATGT
Found at i:10014 original size:55 final size:55
Alignment explanation
Indices: 9948--10057 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
9938 ATGTAATGAA
* * *
9948 ATTATAATTAGAATATAATATTTAGAAATTATAAATGT-TTAGAAATTATATTTAG
1 ATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAAT-GAAATTATAATTAG
*
10003 ATTATATTTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTATAATTAG
1 ATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTATAATTAG
10058 GGGCGTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
55 49 0.98
56 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (55 bp):
ATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTATAATTAG
Found at i:10090 original size:32 final size:32
Alignment explanation
Indices: 10054--10130 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
10044 GAAATTATAA
*
10054 TTAGGGGCGTTTTAT-TTAGAAAACGCCACTAT
1 TTAGGGGCGTTTTATCCTA-AAAACGCCACTAT
* * * *
10086 TTAGGGGTGTTTTCTCCTATAAACGTCACTAT
1 TTAGGGGCGTTTTATCCTAAAAACGCCACTAT
*
10118 TTAGGGGCATTTT
1 TTAGGGGCGTTTT
10131 CTCCAGTAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
32 35 0.95
33 2 0.05
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (32 bp):
TTAGGGGCGTTTTATCCTAAAAACGCCACTAT
Found at i:10131 original size:32 final size:32
Alignment explanation
Indices: 10074--10215 Score: 99
Period size: 32 Copynumber: 4.4 Consensus size: 32
10064 TTTATTTAGA
**
10074 AAACGCCACTATTTAGGGGTGTTTTCTCCTAT
1 AAACGCCACTATTTAGGGGCATTTTCTCCTAT
*
10106 AAACGTCACTATTTAGGGGCATTTTCTCC-AGT
1 AAACGCCACTATTTAGGGGCATTTTCTCCTA-T
** * * * *
10138 AGGCGCCGCTATTTAGTGGCGTTTTCTTC-AGT
1 AAACGCCACTATTTAGGGGCATTTTCTCCTA-T
** * * * * *
10170 AGTCGCCGCTATTTAAGGGCGTTTTCTTCAAT
1 AAACGCCACTATTTAGGGGCATTTTCTCCTAT
*
10202 AAACGCCCCTATTT
1 AAACGCCACTATTT
10216 TGCAGCATTT
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
31 1 0.01
32 90 0.98
33 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (32 bp):
AAACGCCACTATTTAGGGGCATTTTCTCCTAT
Found at i:10255 original size:21 final size:20
Alignment explanation
Indices: 10222--10271 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
10212 ATTTTGCAGC
10222 ATTTTCTGCATAATCACCAAA
1 ATTTT-TGCATAATCACCAAA
**
10243 ATTTTTGCAATAATTGCCAAA
1 ATTTTTGC-ATAATCACCAAA
10264 ATTATTTG
1 ATT-TTTG
10272 GGTGCAGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.72
22 4 0.16
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (20 bp):
ATTTTTGCATAATCACCAAA
Done.