Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018482.1 Corchorus olitorius cultivar O-4 contig18515, 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: 37134
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--90 Score: 155
Period size: 2 Copynumber: 45.5 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
43 CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
84 CC CT CT C
1 CT CT CT C
91 CCTCCCTCCC
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
1 1 0.01
2 82 0.99
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:99 original size:18 final size:18
Alignment explanation
Indices: 67--106 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
57 CTCTCTCTCT
* *
67 CCTCTCTCTCTCTCCCTC
1 CCTCTCCCTCCCTCCCTC
85 CCTCTCCCTCCCTCCCTC
1 CCTCTCCCTCCCTCCCTC
103 CCTC
1 CCTC
107 CCCATGCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.33
Consensus pattern (18 bp):
CCTCTCCCTCCCTCCCTC
Found at i:4530 original size:211 final size:211
Alignment explanation
Indices: 4125--4509 Score: 589
Period size: 212 Copynumber: 1.8 Consensus size: 211
4115 GTTATTCGCA
* *
4125 CTTCAATTTGTTGTAAAAAATACCTTTGATTCATTTTCTTATGAGATTGACCGATTTGAATGGTT
1 CTTCAATTTGTTGTAAAAAATACCTTTGATCCATTTTCTTATGAGATTGACCGATTTGAATGATT
* * * *
4190 TATGCTGCCTTTTTTCAGGGTATTGCTGTTGTTTTCTTTTACACAGGTTTGTATCTCCTTTACGC
66 TATGCTGCCTCTTTTCAGGGTATTGCTATTGTTTTCTCTAACACAGGTTTGTATCTCCTTTACGC
* * *
4255 TATTCTTGCAATTGCATTTGTTTTTGGATTAAGTTGTTTTGTTCCAAAAATCTGATGAGTCTAAT
131 TATTCCTGCAATCGCATTTCTTTTTGGATTAAGTTGTTTTGTTCCAAAAATCTGATGAGTCTAAT
4320 ACTTGGTGTTCTTGGC
196 ACTTGGTGTTCTTGGC
*
4336 CTTCAATTTGTTGTAAAAAAATACCTTTGATCCATCTTT-TTATGAGATTGACTGATGTTG-ATG
1 CTTCAATTTGTTGT-AAAAAATACCTTTGATCCAT-TTTCTTATGAGATTGACCGAT-TTGAATG
**
4399 ATTTATGCTTTCTCTTTTCAGGGTATTGCTATTGTTTTCTCTAACACAGG-TTGTATCTCCTTTG
63 ATTTATGCTGCCTCTTTTCAGGGTATTGCTATTGTTTTCTCTAACACAGGTTTGTATCTCCTTT-
*
4463 A-GTTATTCCTGCAATCGCATTTCTTTTTGGATTAAGTTGTTTTGTTC
127 ACGCTATTCCTGCAATCGCATTTCTTTTTGGATTAAGTTGTTTTGTTC
4510 TGAGCATGTG
Statistics
Matches: 157, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
211 69 0.44
212 82 0.52
213 6 0.04
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (211 bp):
CTTCAATTTGTTGTAAAAAATACCTTTGATCCATTTTCTTATGAGATTGACCGATTTGAATGATT
TATGCTGCCTCTTTTCAGGGTATTGCTATTGTTTTCTCTAACACAGGTTTGTATCTCCTTTACGC
TATTCCTGCAATCGCATTTCTTTTTGGATTAAGTTGTTTTGTTCCAAAAATCTGATGAGTCTAAT
ACTTGGTGTTCTTGGC
Found at i:6298 original size:22 final size:20
Alignment explanation
Indices: 6255--6298 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
6245 ACGTTAGAAA
*
6255 GCAAGGTTGCCCGCGCATGG
1 GCAAGGTTGCCCGCGCACGG
*
6275 GCAAGAGTTGGCCCGCGCGCGG
1 GCAAG-GTT-GCCCGCGCACGG
6297 GC
1 GC
6299 TACCACAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 3 0.15
22 12 0.60
ACGTcount: A:0.14, C:0.32, G:0.43, T:0.11
Consensus pattern (20 bp):
GCAAGGTTGCCCGCGCACGG
Found at i:8004 original size:26 final size:26
Alignment explanation
Indices: 7975--8032 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
7965 AATGCAATGC
7975 ATGCAAACA-AAA-AGAAAATGAAAAA
1 ATGCAAACATAAACA-AAAATGAAAAA
*
8000 TATGCAAACATAAACAAAAATGCAAAA
1 -ATGCAAACATAAACAAAAATGAAAAA
8027 ATGCAA
1 ATGCAA
8033 TTTTTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 15 0.52
27 13 0.45
28 1 0.03
ACGTcount: A:0.66, C:0.12, G:0.10, T:0.12
Consensus pattern (26 bp):
ATGCAAACATAAACAAAAATGAAAAA
Found at i:8329 original size:19 final size:18
Alignment explanation
Indices: 8301--8336 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8291 AGAATTAAAT
8301 TAAAAGAAAACATAAAAAC
1 TAAAAGAAAA-ATAAAAAC
*
8320 TAAAATAAAAATAAAAA
1 TAAAAGAAAAATAAAAA
8337 TAAGTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.14
Consensus pattern (18 bp):
TAAAAGAAAAATAAAAAC
Found at i:12439 original size:22 final size:20
Alignment explanation
Indices: 12396--12439 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
12386 ACGTCAGAAA
*
12396 GCAAGGTTGCCCGCGCATGG
1 GCAAGGTTGCCCGCGCACGG
*
12416 GCAAGAGTTGGCCCGCGCGCGG
1 GCAAG-GTT-GCCCGCGCACGG
12438 GC
1 GC
12440 TACCATAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 3 0.15
22 12 0.60
ACGTcount: A:0.14, C:0.32, G:0.43, T:0.11
Consensus pattern (20 bp):
GCAAGGTTGCCCGCGCACGG
Found at i:33585 original size:11 final size:11
Alignment explanation
Indices: 33569--33593 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33559 AATATACTTA
33569 TTTTGTAATTG
1 TTTTGTAATTG
33580 TTTTGTAATTG
1 TTTTGTAATTG
33591 TTT
1 TTT
33594 CACTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTTGTAATTG
Done.