Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023501.1 Corchorus olitorius cultivar O-4 contig23534, 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: 7131
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Found at i:261 original size:28 final size:28
Alignment explanation
Indices: 229--300 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
219 GCACTTGAAG
229 TGACCAAAATGCCCCTGGAT-ATGCAAAA
1 TGACCAAAATGCCCCTGG-TCATGCAAAA
257 TGACCAAAATGCCCCTGGTCATGCAAAA
1 TGACCAAAATGCCCCTGGTCATGCAAAA
*
285 TGATCAAAATGCCCCT
1 TGACCAAAATGCCCCT
301 TTAAGTGACC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
27 1 0.02
28 41 0.98
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (28 bp):
TGACCAAAATGCCCCTGGTCATGCAAAA
Found at i:4206 original size:5 final size:5
Alignment explanation
Indices: 4194--4263 Score: 60
Period size: 5 Copynumber: 14.6 Consensus size: 5
4184 AAAAATAAAA
* **
4194 AAAT- AAATC AAATC AAATC AAAATC -AAT- AAA-A AAATC AAAT- AAAAA
1 AAATC AAATC AAATC AAATC -AAATC AAATC AAATC AAATC AAATC AAATC
4240 AAATC AAATC AAATC AAAATC AAA
1 AAATC AAATC AAATC -AAATC AAA
4264 AGAGAATTGA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
4 15 0.27
5 30 0.55
6 10 0.18
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (5 bp):
AAATC
Found at i:4215 original size:32 final size:32
Alignment explanation
Indices: 4179--4247 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
4169 ATCAAGAAAT
**
4179 TCAAAAAAAATAAAAAAAT-AAATCAAATCAAA
1 TCAAAAAAAATAAAAAAATCAAAT-AAAAAAAA
**
4211 TCAAAATCAATAAAAAAATCAAATAAAAAAAA
1 TCAAAAAAAATAAAAAAATCAAATAAAAAAAA
4243 TCAAA
1 TCAAA
4248 TCAAATCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (32 bp):
TCAAAAAAAATAAAAAAATCAAATAAAAAAAA
Found at i:4244 original size:42 final size:40
Alignment explanation
Indices: 4182--4262 Score: 135
Period size: 42 Copynumber: 2.0 Consensus size: 40
4172 AAGAAATTCA
*
4182 AAAAAAATAAAAAAATAAATCAAATCAAATCAAAATCAAT
1 AAAAAAATAAAAAAAAAAATCAAATCAAATCAAAATCAAT
4222 AAAAAAATCAAATAAAAAAAATCAAATCAAATCAAAATCAA
1 AAAAAAAT-AAA-AAAAAAAATCAAATCAAATCAAAATCAA
4263 AAGAGAATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 8 0.21
41 3 0.08
42 27 0.71
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (40 bp):
AAAAAAATAAAAAAAAAAATCAAATCAAATCAAAATCAAT
Found at i:4943 original size:51 final size:51
Alignment explanation
Indices: 4876--5073 Score: 278
Period size: 51 Copynumber: 3.9 Consensus size: 51
4866 GATTGCATTC
**
4876 CATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTTG
1 CATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTTG
*
4927 CATTTTTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTTG
1 CATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTTG
* * *
4978 CATTTGTGAGTTCAAGATCAAAATTTGCTTTTC-AAG-ACGAAATTGC-ATTC
1 CATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTA--AAATTGCTTTTG
*
5028 CATTTGTGAGTCCAAGATCAAAATTCGCTTTTCACAA-TAAAATTGC
1 CATTTGTGAGTTCAAGATCAAAATTCGCTTTTCA-AAGTAAAATTGC
5074 ACTACATTTG
Statistics
Matches: 133, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
49 1 0.01
50 43 0.32
51 86 0.65
52 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (51 bp):
CATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTTG
Found at i:5058 original size:50 final size:49
Alignment explanation
Indices: 4867--5099 Score: 270
Period size: 51 Copynumber: 4.6 Consensus size: 49
4857 TTACAATAAG
*
4867 ATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAA
1 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG-AAA
* * * *
4917 ATTGCTTTTGCATTTTTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAA
1 ATTGC-ATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG-AAA
* * * *
4968 ATTGCTTTTGCATTTGTGAGTTCAAGATCAAAATTTGCTTTTC-AAGACGAA
1 ATTGC-ATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGA--AA
*
5019 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCACAATAAA
1 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCA-AAGAAA
* * * *
5069 ATTGCACTACATTTGTGAGACCAAGACCAAA
1 ATTGCATTCCATTTGTGAGTCCAAGATCAAA
5100 GGTCGATTTT
Statistics
Matches: 162, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 70 0.43
51 88 0.54
52 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (49 bp):
ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGAAA
Found at i:5680 original size:50 final size:50
Alignment explanation
Indices: 5621--6293 Score: 1078
Period size: 50 Copynumber: 13.5 Consensus size: 50
5611 CGAATGCTTT
* *
5621 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
5671 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* *
5721 GACCTTTTCCATAAGCCAAACTCGTTTCCATACGATTCAATTATCAACACA
1 G-GCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
5772 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
5822 TGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* * *
5872 GGCTTTTCCATGAGCCAAACTCGTTTCCATATGAGTCAATGATCAACACA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
5922 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
5972 GGCTTTTCCATAAGCCAAACTCATTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* * * *
6022 GGCTTTTCCATAAGCCAAATTCATTTCCATACGAGTCAATTATCAATATA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* * * *
6072 GGCTTTTCCACAAGCCAAACTCGTTTGCATACGGGTCAATTATCAACATA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* * *
6122 GGCTTTTCCACAAGCCAAACTCGTCTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* **
6172 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACAGG
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* * *
6222 GGCTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAATTATCAAC-TA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
6271 GGCTTTTCCACAAGCCAAACTCG
1 GGCTTTTCCATAAGCCAAACTCG
6294 AGGATCTCTC
Statistics
Matches: 586, Mismatches: 36, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
49 22 0.04
50 517 0.88
51 47 0.08
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (50 bp):
GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
Found at i:6663 original size:26 final size:26
Alignment explanation
Indices: 6599--6695 Score: 113
Period size: 26 Copynumber: 3.7 Consensus size: 26
6589 AAAATCCAGA
6599 GGCATTTTGGTCATTTTTCACATTCAG
1 GGCATTTTGGTCATTTTT-ACATTCAG
* * *
6626 TGGCATTATGGTCATTTTTACACTAAG
1 -GGCATTTTGGTCATTTTTACATTCAG
** *
6653 GGCATTTTGGTCATTTGCATATTCAG
1 GGCATTTTGGTCATTTTTACATTCAG
*
6679 GGCATGTTGGTCATTTT
1 GGCATTTTGGTCATTTT
6696 GAGTCCACTG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 35 0.60
27 6 0.10
28 17 0.29
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (26 bp):
GGCATTTTGGTCATTTTTACATTCAG
Found at i:6863 original size:25 final size:25
Alignment explanation
Indices: 6834--6881 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
6824 GTATTTTGCG
*
6834 TTCATGTAGCTCAAAGCTAATTTCA
1 TTCATGAAGCTCAAAGCTAATTTCA
*
6859 TTCATGAAGCTCAAATCTAATTT
1 TTCATGAAGCTCAAAGCTAATTT
6882 GACATTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (25 bp):
TTCATGAAGCTCAAAGCTAATTTCA
Done.