Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015217.1 Corchorus olitorius cultivar O-4 contig15250, 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: 4390
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Found at i:739 original size:38 final size:38
Alignment explanation
Indices: 688--802 Score: 230
Period size: 38 Copynumber: 3.0 Consensus size: 38
678 TTTTTTTTGT
688 ATTTTTGGTTGAATCTGGTAAGTATGACTAGTTTTGGG
1 ATTTTTGGTTGAATCTGGTAAGTATGACTAGTTTTGGG
726 ATTTTTGGTTGAATCTGGTAAGTATGACTAGTTTTGGG
1 ATTTTTGGTTGAATCTGGTAAGTATGACTAGTTTTGGG
764 ATTTTTGGTTGAATCTGGTAAGTATGACTAGTTTTGGG
1 ATTTTTGGTTGAATCTGGTAAGTATGACTAGTTTTGGG
802 A
1 A
803 AGGAGAGCCT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 77 1.00
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (38 bp):
ATTTTTGGTTGAATCTGGTAAGTATGACTAGTTTTGGG
Found at i:2078 original size:58 final size:57
Alignment explanation
Indices: 1987--2164 Score: 270
Period size: 58 Copynumber: 3.1 Consensus size: 57
1977 GACCGAAATA
*
1987 CCCCTAGATGTGCAAAAATGACCAAAATGCCCCTGGATATGCAAAAGTGACTAAAATGT
1 CCCCTGGATGTGC-AAAATGACCAAAATGCCCCTGGATATGCAAAA-TGACTAAAATGT
* *
2046 CCCCTGGACGTGCAAAATGACCAGAATGCCCCTGGATATGCAAAAATGACTAAAATGT
1 CCCCTGGATGTGCAAAATGACCAAAATGCCCCTGGATATGC-AAAATGACTAAAATGT
*
2104 CCCCTGGATGTGCAAAATGACCAAAATGCCCCTGGTTATGCAAAATGA-TCAAAATG-
1 CCCCTGGATGTGCAAAATGACCAAAATGCCCCTGGATATGCAAAATGACT-AAAATGT
2160 CCCCT
1 CCCCT
2165 TTAAGTGACC
Statistics
Matches: 111, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
56 6 0.05
57 13 0.12
58 77 0.69
59 15 0.14
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (57 bp):
CCCCTGGATGTGCAAAATGACCAAAATGCCCCTGGATATGCAAAATGACTAAAATGT
Found at i:2087 original size:28 final size:28
Alignment explanation
Indices: 1973--2164 Score: 231
Period size: 29 Copynumber: 6.7 Consensus size: 28
1963 AGTGCACTTG
* * * *
1973 AAATGACCGAAATACCCCTAGATGTGCAA
1 AAATGACCAAAATGCCCCTGGATATGC-A
2002 AAATGACCAAAATGCCCCTGGATATGCA
1 AAATGACCAAAATGCCCCTGGATATGCA
* **
2030 AAAGTGACTAAAATGTCCCCTGGACGTGCA
1 AAA-TGACCAAAATG-CCCCTGGATATGCA
*
2060 AAATGACCAGAATGCCCCTGGATATGCAA
1 AAATGACCAAAATGCCCCTGGATATGC-A
* *
2089 AAATGACTAAAATGTCCCCTGGATGTGCA
1 AAATGACCAAAATG-CCCCTGGATATGCA
*
2118 AAATGACCAAAATGCCCCTGGTTATGCA
1 AAATGACCAAAATGCCCCTGGATATGCA
*
2146 AAATGATCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
2165 TTAAGTGACC
Statistics
Matches: 141, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
28 45 0.32
29 69 0.49
30 27 0.19
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGATATGCA
Found at i:2462 original size:35 final size:35
Alignment explanation
Indices: 2421--2732 Score: 360
Period size: 35 Copynumber: 8.9 Consensus size: 35
2411 TGAGTTCATA
* * *
2421 TTGAAGATGCTACACCAAGTCATCTGAATTCGTTT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* *
2456 TTGAAGATGCTACACCGAGTCACCTGAATTCATTT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* * * *
2491 TTGAAGAGGCTACACCGAG-CCTCCTGAATTCGTTTT
1 TTGAAGATGCTACACCGAGTCAT-CTGAATTC-ATCT
* *
2527 TTGAAGATGCTACACTGAGTCACCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* *
2562 TTGAAGATGCTACACCGAGTCACCTGAGTTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* *
2597 TTGAACATGCTACACCGAGTCATCTGGACTT-AT-T
1 TTGAAGATGCTACACCGAGTCATCT-GAATTCATCT
* * * * *
2631 TATGAGGATGCTACATCGAATCATCTGGATTTATCT
1 T-TGAAGATGCTACACCGAGTCATCTGAATTCATCT
* *
2667 TTGAAGATGCTACACCGAGTCATCTGGATTTATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
2702 TTGAAGATGCTACACCGAGTCATCTGGATTC
1 TTGAAGATGCTACACCGAGTCATCTGAATTC
2733 CTGAGAATTT
Statistics
Matches: 242, Mismatches: 28, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
34 6 0.02
35 201 0.83
36 34 0.14
37 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
Found at i:2568 original size:106 final size:104
Alignment explanation
Indices: 2421--2727 Score: 377
Period size: 106 Copynumber: 2.9 Consensus size: 104
2411 TGAGTTCATA
** * *
2421 TTGAAGATGCTACACCAAGTCATCTGAATTCGTTTTTGAAGATGCTACACCGAGTCACCTGAATT
1 TTGAAGATGCTACACTGAGTCATCTGAATTCATCTTTGAAGATGCTACACCGAGTCACCTGAATT
* * *
2486 CATTTTTGAAGAGGCTACACCGAG-CCTCCTGAATTCGTT-TT
66 CATCTTTGAAGATGCTACACCGAGTCAT-CTGAA--C-TTATT
* *
2527 TTGAAGATGCTACACTGAGTCACCTGAATTCATCTTTGAAGATGCTACACCGAGTCACCTGAGTT
1 TTGAAGATGCTACACTGAGTCATCTGAATTCATCTTTGAAGATGCTACACCGAGTCACCTGAATT
* *
2592 CATCTTTGAACATGCTACACCGAGTCATCTGGACTTATT
66 CATCTTTGAAGATGCTACACCGAGTCATCTGAACTTATT
* * * * * *
2631 TATGAGGATGCTACA-TCGAATCATCTGGATTTATCTTTGAAGATGCTACACCGAGTCATCTGGA
1 T-TGAAGATGCTACACT-GAGTCATCTGAATTCATCTTTGAAGATGCTACACCGAGTCACCTGAA
*
2695 TTTATCTTTGAAGATGCTACACCGAGTCATCTG
64 TTCATCTTTGAAGATGCTACACCGAGTCATCTG
2728 GATTCCTGAG
Statistics
Matches: 176, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
103 2 0.01
104 5 0.03
105 83 0.47
106 84 0.48
107 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (104 bp):
TTGAAGATGCTACACTGAGTCATCTGAATTCATCTTTGAAGATGCTACACCGAGTCACCTGAATT
CATCTTTGAAGATGCTACACCGAGTCATCTGAACTTATT
Done.