Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007101.1 Corchorus olitorius cultivar O-4 contig07126, 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: 2206
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:106 original size:47 final size:47
Alignment explanation
Indices: 55--186 Score: 149
Period size: 47 Copynumber: 2.8 Consensus size: 47
45 CACAGAGGCT
* *
55 AGTTTAATTCTAGGTAATTAAACTAAAAAGTAAAAGAGGAAGAAAAG
1 AGTTTAATTCTAGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAC
* * *
102 AGTTTAATTC-AGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
1 AGTTTAATTCTA-GGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAC
* * * * **
149 AGTTTGATTCTGGGTAATCAAGCTAAGCAGTAAAAGAA
1 AGTTTAATTCTAGGTAATTAAACTAAAAAGTAAAAGAA
187 AGCGTAATCA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
46 1 0.01
47 69 0.99
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (47 bp):
AGTTTAATTCTAGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAC
Found at i:208 original size:22 final size:22
Alignment explanation
Indices: 177--306 Score: 160
Period size: 22 Copynumber: 6.1 Consensus size: 22
167 CAAGCTAAGC
*
177 AGTAAAAGAAAGCGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
*
199 AGTAATAGAAAGAGTAATCAG-
1 AGTAAAAGAAAGAGTAATCAGA
* * *
220 AGTAAAAGGAAGAATAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
**
242 AGCCAAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
264 AG---AAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
*
283 AGTAAAAGAAAGATTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
305 AG
1 AG
307 ATTAGAGTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
19 19 0.21
21 17 0.18
22 56 0.61
ACGTcount: A:0.57, C:0.07, G:0.22, T:0.14
Consensus pattern (22 bp):
AGTAAAAGAAAGAGTAATCAGA
Found at i:225 original size:43 final size:42
Alignment explanation
Indices: 177--304 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 42
167 CAAGCTAAGC
*
177 AGTAAAAGAAAGCGTAATCAGAAGTAATAGAAAGAGTAATCAG
1 AGTAAAAGAAAGAGTAATCAGAAGTAA-AGAAAGAGTAATCAG
* * * *
220 AGTAAAAGGAAGAATAATCAAAAGCCAAAGAAAGAGTAATCAG
1 AGTAAAAGAAAGAGTAATCAGAAG-TAAAGAAAGAGTAATCAG
* *
263 A--AGAAGAAAGAGTAATCAGAAGTAAAAGAAAGATTAATCAG
1 AGTAAAAGAAAGAGTAATCAGAAGT-AAAGAAAGAGTAATCAG
304 A
1 A
305 AGATTAGAGT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 34 0.47
43 36 0.50
44 2 0.03
ACGTcount: A:0.57, C:0.07, G:0.22, T:0.14
Consensus pattern (42 bp):
AGTAAAAGAAAGAGTAATCAGAAGTAAAGAAAGAGTAATCAG
Found at i:283 original size:16 final size:17
Alignment explanation
Indices: 247--284 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
237 TCAAAAGCCA
247 AAGAAAGAGTAATCAGAAG
1 AAGAAAGAGTAATC--AAG
266 AAGAAAGAGTAATC-AG
1 AAGAAAGAGTAATCAAG
282 AAG
1 AAG
285 TAAAAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
19 14 0.74
ACGTcount: A:0.58, C:0.05, G:0.26, T:0.11
Consensus pattern (17 bp):
AAGAAAGAGTAATCAAG
Found at i:291 original size:41 final size:41
Alignment explanation
Indices: 182--307 Score: 153
Period size: 41 Copynumber: 3.0 Consensus size: 41
172 TAAGCAGTAA
* * *
182 AAGAAAGCGTAATCAGAAGTAATAGAAAGAGTAATCAGAGTAA
1 AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAGA--AG
* * * **
225 AAGGAAGAATAATCAAAAGCCAAAGAAAGAGTAATCAGAAG
1 AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAGAAG
*
266 AAGAAAGAGTAATCAGAAGTAAAAGAAAGATTAATCAGAAG
1 AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAGAAG
307 A
1 A
308 TTAGAGTAAT
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
41 37 0.54
43 32 0.46
ACGTcount: A:0.57, C:0.07, G:0.22, T:0.13
Consensus pattern (41 bp):
AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAGAAG
Found at i:333 original size:47 final size:44
Alignment explanation
Indices: 282--380 Score: 128
Period size: 47 Copynumber: 2.2 Consensus size: 44
272 GAGTAATCAG
*
282 AAGTAAAAGAAAGATTAATCAGAAGATTAGAG-TAATTAAGCTAAAA
1 AAGTAAAAGAAAGAGTAATCAGAAG--TAGAGTTAATTAAGCT-AAA
* *
328 CAAGTAAAAGCAAGAGTAATCAGTAGTAGAGTTAATTAAGCTAAA
1 -AAGTAAAAGAAAGAGTAATCAGAAGTAGAGTTAATTAAGCTAAA
373 AAGTAAAA
1 AAGTAAAA
381 AGTAATAACA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 8 0.17
45 8 0.17
46 10 0.21
47 22 0.46
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21
Consensus pattern (44 bp):
AAGTAAAAGAAAGAGTAATCAGAAGTAGAGTTAATTAAGCTAAA
Found at i:1686 original size:29 final size:29
Alignment explanation
Indices: 1569--1715 Score: 159
Period size: 29 Copynumber: 5.1 Consensus size: 29
1559 GCATTAGGGT
* * * *
1569 CACATCCAGGGGCATTATGATAATTTTCG
1 CACATCCAGGGGCATTTTGGTCATTTTTG
* * *
1598 CACCTCCAGGGGCATTATGGTCATTCTTG
1 CACATCCAGGGGCATTTTGGTCATTTTTG
* *
1627 CACCTCCAGGGGCATTTTGGTCATTTGTG
1 CACATCCAGGGGCATTTTGGTCATTTTTG
1656 CACATCCAGGGGCATTTTGGTCATTTTTG
1 CACATCCAGGGGCATTTTGGTCATTTTTG
** * * **
1685 CAGGTTCTGGGGCATTTTGGTTGTTTTTG
1 CACATCCAGGGGCATTTTGGTCATTTTTG
1714 CA
1 CA
1716 TACTTTAAGC
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 102 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (29 bp):
CACATCCAGGGGCATTTTGGTCATTTTTG
Found at i:1885 original size:15 final size:15
Alignment explanation
Indices: 1865--1898 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1855 GTACTATTTA
1865 CATTAGTCATGTTTG
1 CATTAGTCATGTTTG
1880 CATTAGTCATGTTTG
1 CATTAGTCATGTTTG
1895 CATT
1 CATT
1899 TTGGACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (15 bp):
CATTAGTCATGTTTG
Done.