Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012443.1 Corchorus olitorius cultivar O-4 contig12476, 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: 27985
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--44 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43 AT
1 AT
45 GACATGGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13190 original size:49 final size:47
Alignment explanation
Indices: 13089--13230 Score: 169
Period size: 49 Copynumber: 3.0 Consensus size: 47
13079 GAGCGTGCCA
* * * *
13089 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
13136 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
13185 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
13231 TGATTGCTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.34
49 42 0.51
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:27315 original size:16 final size:16
Alignment explanation
Indices: 27292--27397 Score: 117
Period size: 16 Copynumber: 6.6 Consensus size: 16
27282 GGCAATTGGG
27292 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
27308 CAGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* **
27324 CGGGCTCGGGT-TAAGT
1 CGGGTTCGGGTAT-TTT
*
27340 CGGATTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
27356 CGGGCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
27372 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
27388 CGGGTTCGGG
1 CGGGTTCGGG
27398 CTCGGGTAGG
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
15 2 0.03
16 68 0.94
17 2 0.03
ACGTcount: A:0.08, C:0.15, G:0.40, T:0.37
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:27348 original size:32 final size:32
Alignment explanation
Indices: 27312--27397 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
27302 TATTTTCAGG
27312 TTCGGGTATTTTCGGGCTCGGGTTAAGTCGGA
1 TTCGGGTATTTTCGGGCTCGGGTTAAGTCGGA
* *
27344 TTCGGGTATTTTCGGGCTCGGGTTATGTCGGG
1 TTCGGGTATTTTCGGGCTCGGGTTAAGTCGGA
*
27376 TTCGGGTATTTTCGGGTTCGGG
1 TTCGGGTATTTTCGGGCTCGGG
27398 CTCGGGTAGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.08, C:0.15, G:0.40, T:0.37
Consensus pattern (32 bp):
TTCGGGTATTTTCGGGCTCGGGTTAAGTCGGA
Found at i:27395 original size:6 final size:6
Alignment explanation
Indices: 27386--27428 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
27376 TTCGGGTATT
* * *
27386 TTCGGG TTCGGG CTCGGG -TAGGA TTCGGG TTCGGG TTCGGG TT
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TT
27429 TGATTTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 3 0.10
6 28 0.90
ACGTcount: A:0.05, C:0.16, G:0.47, T:0.33
Consensus pattern (6 bp):
TTCGGG
Found at i:27433 original size:23 final size:23
Alignment explanation
Indices: 27371--27433 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
27361 TCGGGTTATG
27371 TCGGGTTCGGGTATT--TTCGGGT
1 TCGGGTTCGGGT-TTGATTCGGGT
* **
27393 TCGGGCTCGGGTAGGATTCGGGT
1 TCGGGTTCGGGTTTGATTCGGGT
27416 TCGGGTTCGGGTTTGATT
1 TCGGGTTCGGGTTTGATT
27434 TTGATTCGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.06, C:0.14, G:0.43, T:0.37
Consensus pattern (23 bp):
TCGGGTTCGGGTTTGATTCGGGT
Found at i:27576 original size:13 final size:12
Alignment explanation
Indices: 27553--27599 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
27543 AAGTTTATTG
27553 ATAATATATAAT
1 ATAATATATAAT
27565 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
27578 ATAACAT-TATT
1 ATAATATATAAT
27589 ATCAATATATA
1 AT-AATATATA
27600 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:27888 original size:31 final size:31
Alignment explanation
Indices: 27853--27924 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
27843 TAAATTATTG
*
27853 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
27884 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
27915 CAAATTAAAA
1 CAAATTAAAA
27925 GCTCATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Done.