Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014072.1 Corchorus olitorius cultivar O-4 contig14105, 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: 12733
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1927 original size:64 final size:65
Alignment explanation
Indices: 1849--2018 Score: 161
Period size: 64 Copynumber: 2.6 Consensus size: 65
1839 ACTGTGAAAG
* * * *
1849 TTTGATAACTACACTGTGAAATTTTGATAACCTCAGTGTG-AATTGTGATAATCTCC-C-TATAA
1 TTTGATAAC-ACACTATGAAATTTTGATAACCTCACTATGAAATTGTGATAACCTCCTCATA-AA
1911 AT
64 AT
* * * *
1913 TTTGATAATCACACTAT-AAA-ATTGGTAACCGCACTATGAAAATTTTGATAACCTCCTCATAAA
1 TTTGATAA-CACACTATGAAATTTTGATAACCTCACTATG-AAATTGTGATAACCTCCTCATAAA
1976 AT
64 AT
* * *
1978 TTTGATAACCACACCATGAAATTTTAATAACCTCCCTATGA
1 TTTGATAA-CACACTATGAAATTTTGATAACCTCACTATGA
2019 GAATGAAATT
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
62 13 0.15
63 3 0.04
64 28 0.33
65 21 0.25
66 6 0.07
67 13 0.15
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (65 bp):
TTTGATAACACACTATGAAATTTTGATAACCTCACTATGAAATTGTGATAACCTCCTCATAAAAT
Found at i:2343 original size:22 final size:22
Alignment explanation
Indices: 1762--2343 Score: 207
Period size: 22 Copynumber: 26.4 Consensus size: 22
1752 CGTAAACATA
* * *
1762 TTGATAATCACACTGTGAAAAT
1 TTGATAACCACACTATGAAATT
* * *
1784 TTGATAACCTCATTATGAAATC
1 TTGATAACCACACTATGAAATT
* *
1806 TGGATAA--ACTACTTATGAAAAT
1 TTGATAACCAC-AC-TATGAAATT
* *
1828 TTGATAACCACACTGTGAAAGT
1 TTGATAACCACACTATGAAATT
* *
1850 TTGATAACTACACTGTGAAATT
1 TTGATAACCACACTATGAAATT
* * *
1872 TTGATAACCTCAGTGTG-AATT
1 TTGATAACCACACTATGAAATT
* * * *
1893 GTGATAATCTCCCTAT-AAATT
1 TTGATAACCACACTATGAAATT
* *
1914 TTGATAATCACACTAT-AAA-A
1 TTGATAACCACACTATGAAATT
* *
1934 TTGGTAACCGCACTATGAAAATT
1 TTGATAACCACACTATG-AAATT
* *
1957 TTGATAACCTC-CTCATAAAATT
1 TTGATAACCACACT-ATGAAATT
*
1979 TTGATAACCACACCATGAAATT
1 TTGATAACCACACTATGAAATT
* * *
2001 TTAATAACCTCCCTATGAGAATGAAAT
1 TTGATAACCACACTATGA-AAT----T
* *** *
2028 TGTGATATCCTTTCTATGTAATT
1 T-TGATAACCACACTATGAAATT
* *
2051 TTGATAA-CATCTCTATAAAATT
1 TTGATAACCA-CACTATGAAATT
* * * * *
2073 TTCATAATCTCCCTATGATATT
1 TTGATAACCACACTATGAAATT
* * * *
2095 TTGTTAACCTCTCTAGGAAATT
1 TTGATAACCACACTATGAAATT
* *
2117 TTGATAAGCGCA--A-G---TT
1 TTGATAACCACACTATGAAATT
* *
2133 TTGATAATATCCCTCCCTATGAAATT
1 TTGAT-A-A--CCACACTATGAAATT
2159 TTGATAACCACACTAT-ATAATT
1 TTGATAACCACACTATGA-AATT
* ** *
2181 TCGATAATCTTC-GTATGAAATT
1 TTGATAA-CCACACTATGAAATT
* * *
2203 TTGTTAA-CATCTCTAAGAAATT
1 TTGATAACCA-CACTATGAAATT
****
2225 TTGATAACCTTTTTATGAAATTT
1 TTGATAACCACACTATGAAA-TT
*
2248 TTGA-AA-C-CTCTATGTAAAATT
1 TTGATAACCACACTATG--AAATT
* * *
2269 TTGATAACTACACTATGTAGTT
1 TTGATAACCACACTATGAAATT
**
2291 TTGATAACTTCTA-TATGAAATT
1 TTGATAACCAC-ACTATGAAATT
* *
2313 TTGGTAACCACACTATGAAATA
1 TTGATAACCACACTATGAAATT
2335 TTGATAACC
1 TTGATAACC
2344 TTCCTATGTA
Statistics
Matches: 417, Mismatches: 101, Indels: 84
0.69 0.17 0.14
Matches are distributed among these distances:
16 7 0.02
17 1 0.00
18 1 0.00
19 1 0.00
20 22 0.05
21 47 0.11
22 272 0.65
23 32 0.08
24 9 0.02
25 1 0.00
26 7 0.02
27 5 0.01
28 12 0.03
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
TTGATAACCACACTATGAAATT
Found at i:11928 original size:26 final size:26
Alignment explanation
Indices: 11899--11956 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
11889 GGCCAGTGCA
* *
11899 GCCCAGCGTGCTGGGCTAGGCATGCG
1 GCCCAGCGTGCTAGGCTAGGCACGCG
* *
11925 GCCCAGCGTGCTAGGCTTGGCGCGCG
1 GCCCAGCGTGCTAGGCTAGGCACGCG
11951 GCCCAG
1 GCCCAG
11957 TCCGCATGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.10, C:0.34, G:0.41, T:0.14
Consensus pattern (26 bp):
GCCCAGCGTGCTAGGCTAGGCACGCG
Done.