Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020427.1 Corchorus olitorius cultivar O-4 contig20460, 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: 14253
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Found at i:3682 original size:16 final size:16
Alignment explanation
Indices: 3657--3692 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3647 TATGTGAAAC
3657 CACCAGATCACATTCT
1 CACCAGATCACATTCT
* *
3673 CACCATATCAGATTCT
1 CACCAGATCACATTCT
3689 CACC
1 CACC
3693 CTGCTTGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.39, G:0.06, T:0.25
Consensus pattern (16 bp):
CACCAGATCACATTCT
Found at i:5207 original size:20 final size:21
Alignment explanation
Indices: 5169--5207 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5159 TTCATTTCAC
5169 TTAGGGTTTGCCATTTCATGG
1 TTAGGGTTTGCCATTTCATGG
*
5190 TTAGGGTTTGTC-TTTCAT
1 TTAGGGTTTGCCATTTCAT
5208 CTCATGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.49
Consensus pattern (21 bp):
TTAGGGTTTGCCATTTCATGG
Found at i:5556 original size:77 final size:77
Alignment explanation
Indices: 5463--5619 Score: 296
Period size: 77 Copynumber: 2.0 Consensus size: 77
5453 ATTATAGATG
5463 TATATATAATAAGATAACATGTATATATTATTATGAGATTATTATGTAAGCTACATTATAGATTT
1 TATATATAATAAGATAACATGTATATATTATTATGAGATTATTATGTAAGCTACATTATAGATTT
5528 ATAGATGTATGA
66 ATAGATGTATGA
* *
5540 TATATATAATATGATAACATTTATATATTATTATGAGATTATTATGTAAGCTACATTATAGATTT
1 TATATATAATAAGATAACATGTATATATTATTATGAGATTATTATGTAAGCTACATTATAGATTT
5605 ATAGATGTATGA
66 ATAGATGTATGA
5617 TAT
1 TAT
5620 GTAAGCTACG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (77 bp):
TATATATAATAAGATAACATGTATATATTATTATGAGATTATTATGTAAGCTACATTATAGATTT
ATAGATGTATGA
Found at i:5621 original size:35 final size:35
Alignment explanation
Indices: 5505--5628 Score: 110
Period size: 35 Copynumber: 3.3 Consensus size: 35
5495 ATGAGATTAT
5505 TATGTAAGCTACATTATAGATTTATAGATGTATGATA
1 TATGTAAGCTACATTATAGATTTATAGATGTATG--A
* * *
5542 TATATAATATGATAACATTTATATATTATTATGAGAT-TAT--
1 TATGT-A-A-GCT-ACA-TTATAGA-T-TTAT-AGATGTATGA
5582 TATGTAAGCTACATTATAGATTTATAGATGTATGA
1 TATGTAAGCTACATTATAGATTTATAGATGTATGA
5617 TATGTAAGCTAC
1 TATGTAAGCTAC
5629 GTACAAACAA
Statistics
Matches: 70, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
32 4 0.06
33 7 0.10
34 1 0.01
35 18 0.26
36 3 0.04
37 6 0.09
38 2 0.03
39 2 0.03
40 6 0.09
41 3 0.04
42 6 0.09
43 1 0.01
44 7 0.10
45 4 0.06
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.42
Consensus pattern (35 bp):
TATGTAAGCTACATTATAGATTTATAGATGTATGA
Found at i:5902 original size:25 final size:24
Alignment explanation
Indices: 5860--5953 Score: 74
Period size: 25 Copynumber: 4.0 Consensus size: 24
5850 TGGATGACAT
5860 GTTAGGGTTTGGCTTTCATGTCATG
1 GTTAGGGTTT-GCTTTCATGTCATG
*
5885 GTTAGGGTTTAG-TCTTCATCTCA--
1 GTTAGGGTTT-GCT-TTCATGTCATG
* * *
5908 CTTAGGG-TT--TATCATTTCATG
1 GTTAGGGTTTGCTTTCATGTCATG
5929 GTTAGGGTTTGCCTTTCATGTCATG
1 GTTAGGGTTTG-CTTTCATGTCATG
5954 CCATTTTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
19 7 0.13
20 1 0.02
21 6 0.11
22 4 0.07
23 6 0.11
24 1 0.02
25 29 0.54
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.45
Consensus pattern (24 bp):
GTTAGGGTTTGCTTTCATGTCATG
Found at i:6324 original size:2 final size:2
Alignment explanation
Indices: 6279--6309 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6269 TAGATTTATG
6279 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6310 GATAACATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14205 original size:2 final size:2
Alignment explanation
Indices: 14198--14253 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
14188 TTATTGGAAA
14198 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
14240 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.