Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013220.1 Corchorus capsularis cultivar CVL-1 contig13241, 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: 6493
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:3133 original size:30 final size:30
Alignment explanation
Indices: 3097--3162 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
3087 ACATCGCACG
3097 GGCCATCGCACAAGCCATCCGGCCACAACC
1 GGCCATCGCACAAGCCATCCGGCCACAACC
***
3127 GGCCATCGCATGGGCCATCCGGCCACAACC
1 GGCCATCGCACAAGCCATCCGGCCACAACC
3157 GGCCAT
1 GGCCAT
3163 TCGATTCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.44, G:0.24, T:0.09
Consensus pattern (30 bp):
GGCCATCGCACAAGCCATCCGGCCACAACC
Found at i:4133 original size:18 final size:17
Alignment explanation
Indices: 4086--4137 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
4076 AAAAACAAAT
*
4086 AAAAAGAGA-AATA-AA
1 AAAAAGAGAGAAAAGAA
4101 AAAAAGAGAGAAAAGGAA
1 AAAAAGAGAGAAAA-GAA
4119 AAAAAGAG-GACAAAGAA
1 AAAAAGAGAGA-AAAGAA
4136 AA
1 AA
4138 GAGGCCCTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 9 0.28
16 3 0.09
17 7 0.22
18 13 0.41
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAAGAGAGAAAAGAA
Found at i:4478 original size:50 final size:50
Alignment explanation
Indices: 4410--4508 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
4400 AAGTTTTATA
* *
4410 ATAAGATTCCATTTCATTTGT-AAGTCCAATATCAAAATTCGATTTTCAAG
1 ATAAGATTCCATTCCATTTGTGAA-TCCAAGATCAAAATTCGATTTTCAAG
* * *
4460 ATAAGATTGCATTCCATTTGTGAATCCAAGATCAAAATTTGCTTTTCAA
1 ATAAGATTCCATTCCATTTGTGAATCCAAGATCAAAATTCGATTTTCAA
4509 AGGGCATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 41 0.95
51 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (50 bp):
ATAAGATTCCATTCCATTTGTGAATCCAAGATCAAAATTCGATTTTCAAG
Found at i:5157 original size:69 final size:69
Alignment explanation
Indices: 4979--5663 Score: 941
Period size: 70 Copynumber: 9.9 Consensus size: 69
4969 AATGCTTTGA
* ** * **
4979 CTTTTCCATAAGTAAAACTCGTTTCCACACGAGTCAGTTCAAGTTTTGGTTCCATCCAAGCATGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
*
5044 AGGGG
65 AAGGG
* * *
5049 CTTCTCCACAAGCTAAACTCGTTTTCATACGAGAT-AGTTCAAGCCTTGGTTCCATCCAAGCAGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCCTTGGTTCCATCCAAGCAGC
5113 AAGGG
65 AAGGG
* * * **
5118 CATTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAACATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
*
5183 AGGGG
65 AAGGG
*
5188 CTTTTCCACAAGCCAAACTCCTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGC-
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
5252 AGCAG
66 AG-GG
* * *
5257 CTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
5322 -AGGAG
65 AAGG-G
5327 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
5392 AGGG
66 AGGG
* * * **
5396 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TAGCCTTGGTTCCATCTGAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
5460 AGGA
66 AGGG
* * * *
5464 CTTTTCCACAAGGCAAACTCGTTTCCATATGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
5529 AAGGG
65 AAGGG
* *
5534 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-TAGCCTTGGTTCCATACAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
5598 AGGG
66 AGGG
* * *
5602 CTTTTCCACAAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCCAAGCAG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
5664 GGGTTTTTCC
Statistics
Matches: 547, Mismatches: 59, Indels: 20
0.87 0.09 0.03
Matches are distributed among these distances:
68 127 0.23
69 196 0.36
70 223 0.41
71 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
AGGG
Found at i:5231 original size:139 final size:139
Alignment explanation
Indices: 4979--5663 Score: 970
Period size: 139 Copynumber: 5.0 Consensus size: 139
4969 AATGCTTTGA
* ** * *
4979 CTTTTCCATAAGTAAAACTCGTTTCCACACGAGTCAGTTCAAGTTTTGGTTCCATCCAAGCATGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
* * *
5044 AGGGGCTTCTCCACAAGCTAAACTCGTTTTCATACGAGAT-AGTTCAAGCCTTGGTTCCATCCAA
66 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCCTTGGTTCCATCCAA
5108 GCAGCAAGGG
130 GCAGCAAGGG
* * **
5118 CATTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAACATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
*
5183 AGGGGCTTTTCCACAAGCCAAACTCCTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
66 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
*
5248 CAGC-AGCAG
131 CAGCAAG-GG
* *
5257 CTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
*
5322 AGGAGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
66 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
5387 CAGCAAGGG
131 CAGCAAGGG
* * * * **
5396 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TAGCCTTGGTTCCATCTGAGCA-GC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
* * * * *
5459 AAGGACTTTTCCACAAGGCAAACTCGTTTCCATATGAGTCAGTTCAAGCTTTGGTTCCATCCAAG
66 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
*
5524 CATTCAAGGG
131 CA-GCAAGGG
* * *
5534 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-TAGCCTTGGTTCCATACAAGCA-GC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
* * * *
5597 AAGGGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCCAAG
66 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
5661 CAG
131 CAG
5664 GGGTTTTTCC
Statistics
Matches: 495, Mismatches: 47, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
137 82 0.17
138 126 0.25
139 285 0.58
140 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (139 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
CAGCAAGGG
Done.