Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017047.1 Corchorus olitorius cultivar O-4 contig17080, 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: 21678
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1590 original size:32 final size:32
Alignment explanation
Indices: 1554--1619 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1544 TACAATTAAT
1554 TTCTGCATATTGTGCATTTACTTGATAATTCA
1 TTCTGCATATTGTGCATTTACTTGATAATTCA
1586 TTCTGCATATTGTGCATTTACTTGATAATTCA
1 TTCTGCATATTGTGCATTTACTTGATAATTCA
1618 TT
1 TT
1620 TTAGGATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (32 bp):
TTCTGCATATTGTGCATTTACTTGATAATTCA
Found at i:3575 original size:11 final size:12
Alignment explanation
Indices: 3536--3575 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3526 CCAGGCGCGC
3536 GGGCCAGCGCTT
1 GGGCCAGCGCTT
* *
3548 GGCCCAGCGCCT
1 GGGCCAGCGCTT
3560 GGGCCAG-GCTT
1 GGGCCAGCGCTT
3571 GGGCC
1 GGGCC
3576 CTAAGCCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.07, C:0.38, G:0.42, T:0.12
Consensus pattern (12 bp):
GGGCCAGCGCTT
Found at i:7016 original size:17 final size:17
Alignment explanation
Indices: 6994--7027 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6984 GCAGGATTGA
6994 CTTCTTGGAATTTAAGC
1 CTTCTTGGAATTTAAGC
7011 CTTCTTGGAATTTAAGC
1 CTTCTTGGAATTTAAGC
7028 ACAAAAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (17 bp):
CTTCTTGGAATTTAAGC
Found at i:10857 original size:15 final size:15
Alignment explanation
Indices: 10839--10871 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
10829 GAAAAAAGAT
10839 AAAAGCACAAA-ATCC
1 AAAAGC-CAAATATCC
10854 AAAAGCCAAATATCC
1 AAAAGCCAAATATCC
10869 AAA
1 AAA
10872 CTACTTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.61, C:0.24, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAAGCCAAATATCC
Found at i:13230 original size:22 final size:22
Alignment explanation
Indices: 13205--13377 Score: 69
Period size: 22 Copynumber: 8.1 Consensus size: 22
13195 ATTTTTTATG
13205 ACCTCCTTATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
*
13227 ACCTTCC-TATGAAATTTTAATA
1 ACC-TCCTTATGAAATTTTGATA
* * * * *
13249 ACGATAC-TATGGAATTTCGAGA
1 AC-CTCCTTATGAAATTTTGATA
*
13271 A---CCTT-T-AAATTTT-TTA
1 ACCTCCTTATGAAATTTTGATA
* * * *
13287 ACCTTCTTATGGAACTTTGTTA
1 ACCTCCTTATGAAATTTTGATA
* *
13309 ACCTCCCTAAGGAAA-TTTGA-A
1 ACCT-CCTTATGAAATTTTGATA
** *
13330 GACCTCAATATGAAATGTTGATA
1 -ACCTCCTTATGAAATTTTGATA
* **
13353 ACATCCCAATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
13375 ACC
1 ACC
13378 AACACTATAA
Statistics
Matches: 107, Mismatches: 31, Indels: 26
0.65 0.19 0.16
Matches are distributed among these distances:
16 2 0.02
17 5 0.05
18 2 0.02
19 4 0.04
20 1 0.01
21 12 0.11
22 71 0.66
23 10 0.09
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (22 bp):
ACCTCCTTATGAAATTTTGATA
Found at i:13521 original size:22 final size:22
Alignment explanation
Indices: 13464--13766 Score: 153
Period size: 22 Copynumber: 14.0 Consensus size: 22
13454 AATCGCACTC
* * *
13464 TGAAATTTTGATAAACACACTA
1 TGAAATTTTGATAACCTCCCTA
* * *
13486 TGAAATTGTAATAACC-CCGTTA
1 TGAAATTTTGATAACCTCC-CTA
*
13508 TGAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AACCTCCCTA
*
13531 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTCCCTA
* * *
13554 TAAAAATTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTCCCTA
*
13576 TGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAACCTCCCTA
* * *
13593 -CAAATTGTGATAACCTCCCTG
1 TGAAATTTTGATAACCTCCCTA
* **
13614 T-AATTTTTTGATAACCTCATTA
1 TGAA-ATTTTGATAACCTCCCTA
* * *
13636 AGAAATTTT-ATTAATCTCTCTA
1 TGAAATTTTGA-TAACCTCCCTA
* * * *
13658 TAAAATTTTGATCTACAT-ACTA
1 TGAAATTTTGAT-AACCTCCCTA
*
13680 TGAAATTTTGATAACC-CTCTTA
1 TGAAATTTTGATAACCTC-CCTA
* * **
13702 TCAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT-CCCTA
* *
13724 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACCTCCCTA
*
13746 TGAAATTTTGATATCCTCCCT
1 TGAAATTTTGATAACCTCCCT
13767 GGAATTTTGA
Statistics
Matches: 207, Mismatches: 55, Indels: 38
0.69 0.18 0.13
Matches are distributed among these distances:
16 10 0.05
17 2 0.01
21 11 0.05
22 136 0.66
23 47 0.23
24 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCCTA
Found at i:13536 original size:23 final size:23
Alignment explanation
Indices: 13510--13589 Score: 101
Period size: 23 Copynumber: 3.5 Consensus size: 23
13500 CCCCGTTATG
13510 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
13533 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTTCCTATA
* *
13556 AAAATTTGAT-AACC-TCCTTATG
1 AAATTTTGATAAACCTTCC-TATA
*
13578 AAATCTTGATAA
1 AAATTTTGATAA
13590 CTACAAATTG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.04
22 15 0.31
23 32 0.65
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAACCTTCCTATA
Found at i:13936 original size:22 final size:22
Alignment explanation
Indices: 13892--13969 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
13882 ATATCCCTTT
* * * *
13892 TATGAAATTCTGATAACCTCTC
1 TATGAAATTTTGTTGACCCCTC
*
13914 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGTTGACCCCTC
* *
13936 TATGAAATTTTGTTTACCCTTC
1 TATGAAATTTTGTTGACCCCTC
*
13958 TATGAGATTTTG
1 TATGAAATTTTG
13970 ATAATCACAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGTTGACCCCTC
Found at i:14054 original size:21 final size:23
Alignment explanation
Indices: 14004--14062 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
13994 AGCCCTGTTT
14004 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAATCAACACTA
**
14026 TGAAATTTTGATAATCTTC-CTA
1 TGAAATTTTGATAATCAACACTA
14048 T-AAATTTTGATAATC
1 TGAAATTTTGATAATC
14063 CGATCTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 14 0.41
22 18 0.53
23 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (23 bp):
TGAAATTTTGATAATCAACACTA
Found at i:21371 original size:2 final size:2
Alignment explanation
Indices: 21366--21397 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21356 ACCTCAAAAA
*
21366 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21398 GAAGTACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Done.