Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018089.1 Corchorus olitorius cultivar O-4 contig18122, 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: 17268
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:382 original size:2 final size:2
Alignment explanation
Indices: 375--401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
365 CTTTAACTAG
375 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
402 CATAATAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4279 original size:17 final size:17
Alignment explanation
Indices: 4257--4293 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
4247 GCATGTTGAG
4257 TGTCTCATTGAGCAGTT
1 TGTCTCATTGAGCAGTT
4274 TGTCTCATTGAGCAGTT
1 TGTCTCATTGAGCAGTT
4291 TGT
1 TGT
4294 TCTATTCAGG
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:0.16, C:0.16, G:0.24, T:0.43
Consensus pattern (17 bp):
TGTCTCATTGAGCAGTT
Found at i:7220 original size:28 final size:28
Alignment explanation
Indices: 7187--7241 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
7177 ATAGAACTCT
*
7187 TGATTCATGAATAATTACAATATTCATC
1 TGATTCATGAATAATCACAATATTCATC
7215 TGATTCATGAATAATCACAATATTCAT
1 TGATTCATGAATAATCACAATATTCAT
7242 TAATGACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (28 bp):
TGATTCATGAATAATCACAATATTCATC
Found at i:9662 original size:2 final size:2
Alignment explanation
Indices: 9655--9693 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9645 GATTAGAAAT
9655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9694 GGGGTTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9819 original size:16 final size:16
Alignment explanation
Indices: 9798--9830 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9788 GTAATCTCTT
*
9798 TAATAGGTTGTGTAAC
1 TAATAGGTTGTCTAAC
9814 TAATAGGTTGTCTAAC
1 TAATAGGTTGTCTAAC
9830 T
1 T
9831 TGTTAGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (16 bp):
TAATAGGTTGTCTAAC
Found at i:10367 original size:22 final size:22
Alignment explanation
Indices: 10315--10438 Score: 108
Period size: 22 Copynumber: 5.7 Consensus size: 22
10305 ATAATTTCGA
* *
10315 TTGAAATTTTGACAACCGGCC-T
1 TTGAAATTTTGATAACC-ACCAT
* * * *
10337 ATGAGATTTTGATAACTACCGT
1 TTGAAATTTTGATAACCACCAT
*
10359 TTGAAATTTTGAAAACCACCAT
1 TTGAAATTTTGATAACCACCAT
* * *
10381 TTGAAATTTTAATAACCGCTAT
1 TTGAAATTTTGATAACCACCAT
* * *
10403 TTGTAATTTTGATAACCTCGA-
1 TTGAAATTTTGATAACCACCAT
10424 TTGAAATTTTGATAA
1 TTGAAATTTTGATAA
10439 TGGCCATATA
Statistics
Matches: 82, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
21 16 0.20
22 66 0.80
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (22 bp):
TTGAAATTTTGATAACCACCAT
Found at i:10490 original size:22 final size:22
Alignment explanation
Indices: 10460--10559 Score: 73
Period size: 22 Copynumber: 4.6 Consensus size: 22
10450 ATATATATAT
10460 ATATATAATTTTGATAAGCACC
1 ATATATAATTTTGATAAGCACC
*
10482 ATATGTAATTTTGATAATG-ACGC
1 ATATATAATTTTGATAA-GCAC-C
* **
10505 -TATATAATTTTAATAA-CTTC
1 ATATATAATTTTGATAAGCACC
* * * *
10525 ATTTGTAATTTTGATAACCTCC
1 ATATATAATTTTGATAAGCACC
*
10547 AT-TAAAATTTTGA
1 ATATATAATTTTGA
10560 AAAATACCCC
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.02
21 22 0.35
22 37 0.60
23 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
ATATATAATTTTGATAAGCACC
Found at i:12728 original size:13 final size:13
Alignment explanation
Indices: 12689--12732 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
12679 TCATGCACCC
12689 AAAACAATTTAATT
1 AAAACAATTTAA-T
*
12703 AAAA-TATTT-AT
1 AAAACAATTTAAT
12714 AAAACAATTTAAT
1 AAAACAATTTAAT
12727 AAAACA
1 AAAACA
12733 GTAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 5 0.19
12 5 0.19
13 12 0.46
14 4 0.15
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:14423 original size:413 final size:417
Alignment explanation
Indices: 13640--14472 Score: 1397
Period size: 413 Copynumber: 2.0 Consensus size: 417
13630 GTGCTATAAA
13640 TTAGTAAATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCC
1 TTAGTAAATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCC
* *
13705 TCCTTTTGGCTTTTTTTTTTGTCTTTTCACACTATTCGAGTGACTAAAAAGGCCCTTGATAAATT
66 TCCTTTTGGC-TTTTTTTTGGTCTGTTCACACTATTCGAGTGACTAAAAAGGCCCTTGATAAATT
**
13770 TCCTCCCTTACTTTTCCTGCTGCCCATTTTTGTAATTTACTATTTCTATATTTATGATTAAGTGT
130 TCCTCCC-T-CTTTTCCTGCAACCCATTTTTGTAATTTACTATTTCTATATTTATGATTAAGTGT
* *
13835 GTATTAATTAATCACATAATATTAATTGTGTGTGGACATTAGGATTTATCGGTTCAATTCCTCTG
193 GTATTAATTAATCAC--AATATTAATTGTGTGTGGACATTAGGATTTATCAGTTCAACTCCTCTG
*
13900 CCGGAATTCCAAAGGATTGGTGCTATAAATGTATCTGCAATAATGATTGATTCATGGGTAAACTA
256 CCGGAATTCCAAAGGATTGGTGCTATAAATATATCTGCAATAATGATTGATTCATGGGTAAACTA
*
13965 TTGACATTTCAATTCTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGAGTTTTTTCTTCCCTAA
321 TTGACATTCCAATTCTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGAGTTTTTTCTTCCCTAA
14030 CATTTCTCTAAATTGGTTTCACATGGACTCCG
386 CATTTCTCTAAATTGGTTTCACATGGACTCCG
*
14062 TTAGTATATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCC
1 TTAGTAAATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCC
* *
14127 TCCTTTTGGC-TTTTTTTGGTCTGTTCACACTTTTCG-GATGACTAAAAAGGCCCTTGATGAATT
66 TCCTTTTGGCTTTTTTTTGGTCTGTTCACACTATTCGAG-TGACTAAAAAGGCCCTTGATAAATT
14190 TCCT-CC-CTTTTCCTGCAACCCATTTTTGTAATTTACTATTTCTATATTTATGATTAAGTGTGT
130 TCCTCCCTCTTTTCCTGCAACCCATTTTTGTAATTTACTATTTCTATATTTATGATTAAGTGTGT
* * *
14253 TTTAATTAATCAC-ATATTAATTGTGTGTGGATATTAGGATTTATCAGTTTAACTCCTCTGCCGG
195 ATTAATTAATCACAATATTAATTGTGTGTGGACATTAGGATTTATCAGTTCAACTCCTCTGCCGG
* *
14317 AATTCCAAAGGATTGGTGTTATAAATATATCTGCAATAATGGTTGATTCATGGGTAAACTATTGA
260 AATTCCAAAGGATTGGTGCTATAAATATATCTGCAATAATGATTGATTCATGGGTAAACTATTGA
* * *
14382 CATTCCAGTTTTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGGGTTTTTTCTTCCCTAACATT
325 CATTCCAATTCTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGAGTTTTTTCTTCCCTAACATT
*
14447 TCTCTGAATTGGTTTCACATGGACTC
390 TCTCTAAATTGGTTTCACATGGACTC
14473 TGTTCTGTTT
Statistics
Matches: 390, Mismatches: 20, Indels: 11
0.93 0.05 0.03
Matches are distributed among these distances:
413 195 0.50
416 67 0.17
419 3 0.01
420 51 0.13
422 74 0.19
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (417 bp):
TTAGTAAATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCC
TCCTTTTGGCTTTTTTTTGGTCTGTTCACACTATTCGAGTGACTAAAAAGGCCCTTGATAAATTT
CCTCCCTCTTTTCCTGCAACCCATTTTTGTAATTTACTATTTCTATATTTATGATTAAGTGTGTA
TTAATTAATCACAATATTAATTGTGTGTGGACATTAGGATTTATCAGTTCAACTCCTCTGCCGGA
ATTCCAAAGGATTGGTGCTATAAATATATCTGCAATAATGATTGATTCATGGGTAAACTATTGAC
ATTCCAATTCTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGAGTTTTTTCTTCCCTAACATTT
CTCTAAATTGGTTTCACATGGACTCCG
Done.