Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015555.1 Corchorus olitorius cultivar O-4 contig15588, 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: 22466
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:6401 original size:22 final size:22
Alignment explanation
Indices: 6134--6410 Score: 168
Period size: 22 Copynumber: 12.6 Consensus size: 22
6124 CTCCAACGTA
* * **
6134 GAAATATTGATAATCACACTGC
1 GAAATTTTGATAACCACACTAT
* * * *
6156 GAAAATTTGATAACCTCATTGT
1 GAAATTTTGATAACCACACTAT
* * *
6178 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* * * *
6200 TAAAATTTGATAACCACAGTGT
1 GAAATTTTGATAACCACACTAT
*
6222 GAAATTTTGATAACCACACTGT
1 GAAATTTTGATAACCACACTAT
*
6244 GAAATTCTGATAACCACA-TAAT
1 GAAATTTTGATAACCACACT-AT
* * *
6266 GAAGTTTTGATAACCTC-CGTGT
1 GAAATTTTGATAACCACAC-TAT
* * *
6288 GAAATTTTGATAATCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* * *
6310 GAAATTTTGATTATCACATTAT
1 GAAATTTTGATAACCACACTAT
* * * * *
6332 -AAA-ATTGGTAATCGCACTAC
1 GAAATTTTGATAACCACACTAT
*
6352 GAAAATTTTGATAACCTC-CTCAT
1 G-AAATTTTGATAACCACACT-AT
* *
6375 AAAATTTTGATAACCACACTAA
1 GAAATTTTGATAACCACACTAT
*
6397 GAAATTTCGATAAC
1 GAAATTTTGATAAC
6411 TTCCCTATGA
Statistics
Matches: 196, Mismatches: 50, Indels: 18
0.74 0.19 0.07
Matches are distributed among these distances:
20 11 0.06
21 4 0.02
22 168 0.86
23 13 0.07
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:6475 original size:22 final size:22
Alignment explanation
Indices: 6444--6783 Score: 121
Period size: 22 Copynumber: 15.5 Consensus size: 22
6434 ATATCATCTT
*
6444 TATGTAATTTTGATAACCTCTCC
1 TATGAAATTTTGATAACCTC-CC
*
6467 -AT-AACATTTTCATAACCTCCC
1 TATGAA-ATTTTGATAACCTCCC
* *
6488 TATGAAATTTTGTTAACCTTCC
1 TATGAAATTTTGATAACCTCCC
* *
6510 TAGGAAATTTTG---A--T-CA
1 TATGAAATTTTGATAACCTCCC
* **
6526 GAACAAATTTTGATAACCTCCCTCCC
1 TATGAAATTTTGATAA----CCTCCC
* * *
6552 TATG-AATTTTGTTAACAT-TC
1 TATGAAATTTTGATAACCTCCC
* * * **
6572 TAAT-TAATTTTGATAATCACAT
1 T-ATGAAATTTTGATAACCTCCC
* ** * *
6594 TATAAAATTTCAATAACCTTCG
1 TATGAAATTTTGATAACCTCCC
6616 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * **
6638 TAAGCAATTTTGATAACCT-TT
1 TATGAAATTTTGATAACCTCCC
* * * **
6659 TAATAAAATTTTGGTATCCTCTA
1 T-ATGAAATTTTGATAACCTCCC
*
6682 TATGAAATTTTGATAA-CTACAC
1 TATGAAATTTTGATAACCT-CCC
* * *
6704 TATGAAGTTTTAATAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * *
6726 TATGAAATTCTGGTAACCACACAC
1 TATGAAATTTTGATAACCTC-C-C
* *
6750 TATGAAATTTTAATAACCTTCC
1 TATGAAATTTTGATAACCTCCC
*
6772 TATGTAATTTTG
1 TATGAAATTTTG
6784 GTTTGATTTT
Statistics
Matches: 226, Mismatches: 68, Indels: 47
0.66 0.20 0.14
Matches are distributed among these distances:
16 10 0.04
17 1 0.00
19 2 0.01
20 2 0.01
21 22 0.10
22 153 0.68
23 8 0.04
24 15 0.07
25 11 0.05
26 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:7179 original size:2 final size:2
Alignment explanation
Indices: 7174--7207 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7164 ATTACGTGTG
7174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7208 CACCATGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7430 original size:22 final size:22
Alignment explanation
Indices: 7348--7431 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
7338 CAAAAAACTG
* *
7348 TATGATATTTTGATAACTACAC
1 TATGAAATTTTGATAACCACAC
*
7370 TAT-AAAGTTTTGATAACCTC-C
1 TATGAAA-TTTTGATAACCACAC
* * *
7391 ATATGGAATTATGGTAACCACAC
1 -TATGAAATTTTGATAACCACAC
*
7414 TATGAAATTTTAATAACC
1 TATGAAATTTTGATAACC
7432 TTCCTATGTA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
21 3 0.06
22 41 0.87
23 3 0.06
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:7430 original size:44 final size:44
Alignment explanation
Indices: 7361--7449 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
7351 GATATTTTGA
* *
7361 TAACTACACTATAAAGTTTTGATAACC-TCCATATGGAATTATGG
1 TAACCACACTATAAAGTTTTAATAACCTTCC-TATGGAATTATGG
* *
7405 TAACCACACTATGAAA-TTTTAATAACCTTCCTATGTAATTTTGG
1 TAACCACACTAT-AAAGTTTTAATAACCTTCCTATGGAATTATGG
7449 T
1 T
7450 TTGATTGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 33 0.85
45 6 0.15
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (44 bp):
TAACCACACTATAAAGTTTTAATAACCTTCCTATGGAATTATGG
Found at i:7781 original size:2 final size:2
Alignment explanation
Indices: 7776--7810 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7766 ACACACACAC
7776 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7811 CCATGTGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9811 original size:25 final size:25
Alignment explanation
Indices: 9779--9828 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
9769 GTAGATGGTT
* *
9779 TATTTATGCTAGTTACTTGGTTTGA
1 TATTTATGATAGTTACTTAGTTTGA
*
9804 TATTTATGATAGTTTCTTAGTTTGA
1 TATTTATGATAGTTACTTAGTTTGA
9829 GTTGATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.22, C:0.06, G:0.18, T:0.54
Consensus pattern (25 bp):
TATTTATGATAGTTACTTAGTTTGA
Found at i:12329 original size:42 final size:42
Alignment explanation
Indices: 12283--12363 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
12273 ATATTTAAAA
*
12283 TACCTTACTAAACGTATCATTTATTTGTGATTAGTTGGAAAT
1 TACCTTACTAAACGTATCATTTATTTGTGATTAGGTGGAAAT
*
12325 TACCTTACTAAACGTATCGTTTATTTGTGATTAGGTGGA
1 TACCTTACTAAACGTATCATTTATTTGTGATTAGGTGGA
12364 TGGAGCGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (42 bp):
TACCTTACTAAACGTATCATTTATTTGTGATTAGGTGGAAAT
Found at i:12467 original size:17 final size:17
Alignment explanation
Indices: 12445--12481 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
12435 TTTGCACCTC
12445 AAATCAGACAAATTAGA
1 AAATCAGACAAATTAGA
12462 AAATCAGACAAATTAGA
1 AAATCAGACAAATTAGA
12479 AAA
1 AAA
12482 GACGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (17 bp):
AAATCAGACAAATTAGA
Found at i:14638 original size:14 final size:14
Alignment explanation
Indices: 14619--14645 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14609 TAACCTTTTT
14619 TACGATAATATTAC
1 TACGATAATATTAC
14633 TACGATAATATTA
1 TACGATAATATTA
14646 TTGGTTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (14 bp):
TACGATAATATTAC
Found at i:17990 original size:17 final size:18
Alignment explanation
Indices: 17955--17990 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
17945 TTTCTAAAAC
17955 TTTATCTTTTAATAATTT
1 TTTATCTTTTAATAATTT
17973 TTTATC-TTTAA-AATTT
1 TTTATCTTTTAATAATTT
17989 TT
1 TT
17991 CATGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 5 0.28
18 6 0.33
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATCTTTTAATAATTT
Done.