Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019576.1 Corchorus olitorius cultivar O-4 contig19609, 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: 18365
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:1569 original size:36 final size:36
Alignment explanation
Indices: 1516--1591 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1506 TTCAACTATT
* *
1516 CAGCTCTTAAATAAGTGGCCATTTGATGATCAAATG
1 CAGCTCTTAAATAAGTGGCCATTTGATCATAAAATG
* *
1552 CAGCTCTTACATTAGTGGCCATTTGATCATAAAATG
1 CAGCTCTTAAATAAGTGGCCATTTGATCATAAAATG
1588 CAGC
1 CAGC
1592 AAAATCATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (36 bp):
CAGCTCTTAAATAAGTGGCCATTTGATCATAAAATG
Found at i:1687 original size:72 final size:72
Alignment explanation
Indices: 1562--1726 Score: 201
Period size: 72 Copynumber: 2.3 Consensus size: 72
1552 CAGCTCTTAC
* * *
1562 ATTAGTGGCCATTTGATCATAAAATGCAGCAAAATCATCATAACAAAATATAAGTCCACTAGTTA
1 ATTAGTGGCCATTTGATCATAAAAT-CAGCAAAATCATCACAACAAAACATAAGTACACTAGTTA
1627 GCATCTAG
65 GCATCTAG
*
1635 ATTAGTGGCCATTTGAT-ATCAACAAT-AGCAAAATCATCACAATAAAACATAAGTACACTAGTT
1 ATTAGTGGCCATTTGATCAT-AA-AATCAGCAAAATCATCACAACAAAACATAAGTACACTAGTT
*
1698 AGC-TCCTAA
64 AGCAT-CTAG
* * *
1707 ATTAGAGACCTTTTGATCAT
1 ATTAGTGGCCATTTGATCAT
1727 CTAGTAGTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 55 0.69
73 21 0.26
74 3 0.04
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (72 bp):
ATTAGTGGCCATTTGATCATAAAATCAGCAAAATCATCACAACAAAACATAAGTACACTAGTTAG
CATCTAG
Found at i:4364 original size:27 final size:28
Alignment explanation
Indices: 4334--4386 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
4324 TAATCTGATT
4334 ATTTAT-TTT-GGTATTTTATGATTTCAG
1 ATTTATCTTTAGGT-TTTTATGATTTCAG
*
4361 ATTTATCTTTATGTTTTTATGATTTC
1 ATTTATCTTTAGGTTTTTATGATTTC
4387 TAATTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 15 0.65
29 2 0.09
ACGTcount: A:0.21, C:0.06, G:0.11, T:0.62
Consensus pattern (28 bp):
ATTTATCTTTAGGTTTTTATGATTTCAG
Found at i:4860 original size:24 final size:25
Alignment explanation
Indices: 4814--4864 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
4804 ATTGGAGTAT
*
4814 TTATTTATCTTGTTTCTCAATTTTA
1 TTATTTATCTTGTTTATCAATTTTA
**
4839 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTTATCAATTTTA
4863 TT
1 TT
4865 GTTACTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTTATCAATTTTA
Found at i:5449 original size:41 final size:41
Alignment explanation
Indices: 5390--5469 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
5380 TCTCCAAAAC
*
5390 CAAACTAACACATGTCCACATGCTCAGATCATGAAGTAATT
1 CAAACTAACACATATCCACATGCTCAGATCATGAAGTAATT
5431 CAAACTAACACATATCCACATGCTCAGATCATGAAGTAA
1 CAAACTAACACATATCCACATGCTCAGATCATGAAGTAA
5470 CCATGCAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (41 bp):
CAAACTAACACATATCCACATGCTCAGATCATGAAGTAATT
Found at i:5743 original size:12 final size:12
Alignment explanation
Indices: 5726--5751 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5716 TGCAACCATT
5726 AAGAGCAAAATG
1 AAGAGCAAAATG
5738 AAGAGCAAAATG
1 AAGAGCAAAATG
5750 AA
1 AA
5752 AGAAAGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.23, T:0.08
Consensus pattern (12 bp):
AAGAGCAAAATG
Found at i:8634 original size:2 final size:2
Alignment explanation
Indices: 8629--8667 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
8619 ATATATGTAT
* *
8629 AG AG AG AG AG AG AG AC AG AG AG AC AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8668 TAGACATGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9467 original size:18 final size:18
Alignment explanation
Indices: 9427--9468 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
9417 AACTTGTCAA
*
9427 GAGGCGTAGAATTATTTC
1 GAGGCATAGAATTATTTC
* *
9445 AAGGCATAGAATTATTTG
1 GAGGCATAGAATTATTTC
9463 GAGGCA
1 GAGGCA
9469 ACTTGTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (18 bp):
GAGGCATAGAATTATTTC
Found at i:10702 original size:2 final size:2
Alignment explanation
Indices: 10697--10725 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10687 ATATATATGT
10697 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10726 TAGACATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11525 original size:18 final size:18
Alignment explanation
Indices: 11485--11525 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
11475 AACTTGTCAA
11485 GAGGCGTAGAATTATTTC
1 GAGGCGTAGAATTATTTC
* * *
11503 AAGGCTTAGAATTATTTG
1 GAGGCGTAGAATTATTTC
11521 GAGGC
1 GAGGC
11526 AACTTGTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (18 bp):
GAGGCGTAGAATTATTTC
Found at i:14831 original size:2 final size:2
Alignment explanation
Indices: 14826--14873 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
14816 AAGATAAAAA
* * *
14826 AT AT AT AT AA AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14867 AT AT AT A
1 AT AT AT A
14874 GTTGGGTTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.