Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019910.1 Corchorus olitorius cultivar O-4 contig19943, 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: 6796
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Found at i:2144 original size:43 final size:43
Alignment explanation
Indices: 2097--2426 Score: 424
Period size: 43 Copynumber: 7.8 Consensus size: 43
2087 ATAAGGAGAA
2097 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
2140 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATA-A-
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
*
2181 ATGGCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGA-
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
2223 ATTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTG-AATATAG
1 A-TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* *
2265 GTGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * * **
2308 GTGCCCCTGTGTTATATATGTGTTTGGGGACTTT-TGGT-GTAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG-AG
*
2350 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
2393 GTGCCACTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTT
2427 TGGTTTTTGG
Statistics
Matches: 250, Mismatches: 27, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
41 68 0.27
42 46 0.18
43 136 0.54
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (43 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
Found at i:2209 original size:84 final size:84
Alignment explanation
Indices: 2095--2426 Score: 524
Period size: 84 Copynumber: 3.9 Consensus size: 84
2085 CCATAAGGAG
*
2095 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATG
2160 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* *
2179 AAATGGCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAA-TTGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATA-AAGATGCCCCTGTGTTATATAT
2243 GTGTTTGGGGAC-TTGAATAT
65 GTGTTTGGGGACTTTG-ATAT
** *
2263 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATG
* *
2328 TGTTTGGGGACTTTTGGTGT
66 TGTTTGGGGAC-TTTGATAT
* * *
2348 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCACTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATG
2413 TGTTTGGGGACTTT
66 TGTTTGGGGACTTT
2427 TGGTTTTTGG
Statistics
Matches: 232, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
83 5 0.02
84 147 0.63
85 77 0.33
86 3 0.01
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT
Found at i:3824 original size:45 final size:45
Alignment explanation
Indices: 3775--3860 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
3765 CTTTATTATA
3775 TTTAGGCCTTTGAGTTTCTTATTCATGGTGTTCTGATTTTGTGAT
1 TTTAGGCCTTTGAGTTTCTTATTCATGGTGTTCTGATTTTGTGAT
* *
3820 TTTAGGCCTTTGAGTTTCTTATTCATGGTGTTTTGTTTTTG
1 TTTAGGCCTTTGAGTTTCTTATTCATGGTGTTCTGATTTTG
3861 CTGAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.12, C:0.10, G:0.22, T:0.56
Consensus pattern (45 bp):
TTTAGGCCTTTGAGTTTCTTATTCATGGTGTTCTGATTTTGTGAT
Found at i:4565 original size:1 final size:1
Alignment explanation
Indices: 4554--4597 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
4544 CACCTGCTTC
* * * *
4554 TTTTTTGTTTTTTTTTTGTTTTTGTTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4598 GCTTATGGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:4576 original size:12 final size:12
Alignment explanation
Indices: 4554--4594 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
4544 CACCTGCTTC
4554 TTTTTTG-TTTT
1 TTTTTTGTTTTT
4565 TTTTTTGTTTTT
1 TTTTTTGTTTTT
*
4577 GTTTTTGTTTTT
1 TTTTTTGTTTTT
4589 TTTTTT
1 TTTTTT
4595 TTTGCTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 7 0.26
12 20 0.74
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:4585 original size:23 final size:22
Alignment explanation
Indices: 4555--4597 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
4545 ACCTGCTTCT
4555 TTTTTGTTTTTTTTTTGTTTTTG
1 TTTTTGTTTTTTTTTT-TTTTTG
4578 TTTTTGTTTTTTTTTTTTTT
1 TTTTTGTTTTTTTTTTTTTT
4598 GCTTATGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (22 bp):
TTTTTGTTTTTTTTTTTTTTTG
Done.