Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021761.1 Corchorus olitorius cultivar O-4 contig21794, 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: 25965
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:4271 original size:32 final size:32
Alignment explanation
Indices: 4227--4323 Score: 124
Period size: 32 Copynumber: 3.0 Consensus size: 32
4217 TTTTTGCAAA
* *
4227 TAGTGGCGTTTATTCAGTAAAACGCCACTAAT
1 TAGTGGCATTTATTAAGTAAAACGCCACTAAT
*
4259 TAGTGGCATTTATTGAGTAAAACGCCACTAAT
1 TAGTGGCATTTATTAAGTAAAACGCCACTAAT
* * *
4291 TAGTGGCGTTTTATGAAG-AAAACGCCCCTAAT
1 TAGTGGC-ATTTATTAAGTAAAACGCCACTAAT
4323 T
1 T
4324 TGCAATCCAG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 51 0.88
33 7 0.12
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (32 bp):
TAGTGGCATTTATTAAGTAAAACGCCACTAAT
Found at i:5075 original size:15 final size:15
Alignment explanation
Indices: 5055--5094 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
5045 TGAAGTTGGT
5055 GATGATGCAAATGTA
1 GATGATGCAAATGTA
5070 GATGATGCAAATGTA
1 GATGATGCAAATGTA
*
5085 GGTGATGCAA
1 GATGATGCAA
5095 GGGACGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.07, G:0.30, T:0.25
Consensus pattern (15 bp):
GATGATGCAAATGTA
Found at i:6155 original size:33 final size:33
Alignment explanation
Indices: 6118--6250 Score: 133
Period size: 33 Copynumber: 4.0 Consensus size: 33
6108 TAGAAAGGCA
* **
6118 ACAAGAGCTTGCAAGAATTGAAGAAGAAAGAAG
1 ACAAGAGCTGGCTCGAATTGAAGAAGAAAGAAG
* * *
6151 ACAAGAGCTGGCTCGCATTGAAGAAGATAGACG
1 ACAAGAGCTGGCTCGAATTGAAGAAGAAAGAAG
* * *
6184 ACAGGAGCTGGCTCGAGTTGAAGAAGAGAGAAG
1 ACAAGAGCTGGCTCGAATTGAAGAAGAAAGAAG
* ** *
6217 A-AATGAGCTAGCTCGCCTTGAAGAAGACAGAAG
1 ACAA-GAGCTGGCTCGAATTGAAGAAGAAAGAAG
6250 A
1 A
6251 AATGAGATTG
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
32 1 0.01
33 82 0.99
ACGTcount: A:0.41, C:0.14, G:0.31, T:0.14
Consensus pattern (33 bp):
ACAAGAGCTGGCTCGAATTGAAGAAGAAAGAAG
Found at i:6251 original size:33 final size:33
Alignment explanation
Indices: 6134--6256 Score: 142
Period size: 33 Copynumber: 3.7 Consensus size: 33
6124 GCTTGCAAGA
6134 ATTGAAGAAGAAAGAAGACAA-GAGCTGGCTCGC
1 ATTGAAGAAGAAAGAAGA-AATGAGCTGGCTCGC
* * * *
6167 ATTGAAGAAGATAGACGACAGGAGCTGGCTCG-
1 ATTGAAGAAGAAAGAAGAAATGAGCTGGCTCGC
* *
6199 AGTTGAAGAAGAGAGAAGAAATGAGCTAGCTCGC
1 A-TTGAAGAAGAAAGAAGAAATGAGCTGGCTCGC
* *
6233 CTTGAAGAAGACAGAAGAAATGAG
1 ATTGAAGAAGAAAGAAGAAATGAG
6257 ATTGATCGTT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.03
33 75 0.97
ACGTcount: A:0.41, C:0.13, G:0.32, T:0.14
Consensus pattern (33 bp):
ATTGAAGAAGAAAGAAGAAATGAGCTGGCTCGC
Found at i:6983 original size:32 final size:32
Alignment explanation
Indices: 6941--7226 Score: 401
Period size: 32 Copynumber: 8.9 Consensus size: 32
6931 ATGGTGTTTA
* * **
6941 TTGAATAAAACGCCACAAATCAGTGGCGTTCT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
*
6973 TTGAAGAAAACACCACTAATTTGTGGCGTTCT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
* *
7005 TTAAAGAAAACGCCACTAATCTGTGGCGTTCT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
*
7037 TTAAAGAAAACGCCACTAATTTGTGGCGTTCT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
* * *
7069 TTAAAGAAAATGCCACTAATTTGTGGCGTACT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
*
7101 TTGAAGAAAACGCCACTAATTTGTGGCGTACT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
*
7133 TTGAAGAAAAAGCCACTAATTTGTGGCGTTCT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
* * *
7165 TGGAAGAAAATGCCACTAATTTGTGGCGTACT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
* * *
7197 TTGATGAAAACGCCACCAATCTGTGGCGTT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTT
7227 TGTCTTTAAT
Statistics
Matches: 230, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 230 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (32 bp):
TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
Found at i:24769 original size:38 final size:38
Alignment explanation
Indices: 24673--24820 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
24663 GGCTGTGCAT
* *
24673 AGTGGACCCGTACCTCAGGGGGTTAAATTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* *
24712 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
24750 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
24788 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
24821 CTAGACTTGA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 9 0.09
38 62 0.61
39 31 0.30
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Done.