Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018483.1 Corchorus olitorius cultivar O-4 contig18516, 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: 30458
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:7800 original size:11 final size:9
Alignment explanation
Indices: 7778--7802 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
7768 ACTAAAAATA
7778 ATATATAGT
1 ATATATAGT
7787 ATATATAGT
1 ATATATAGT
7796 ATATATA
1 ATATATA
7803 AGTCTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
ATATATAGT
Found at i:8108 original size:24 final size:24
Alignment explanation
Indices: 8081--8126 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
8071 AAAATTTACG
8081 TTAAACATCTTATTATTATAATTA
1 TTAAACATCTTATTATTATAATTA
*
8105 TTAAACTTCTTATTATTATAAT
1 TTAAACATCTTATTATTATAAT
8127 AATAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAAACATCTTATTATTATAATTA
Found at i:8118 original size:103 final size:103
Alignment explanation
Indices: 7929--8124 Score: 288
Period size: 103 Copynumber: 1.9 Consensus size: 103
7919 TCCAACTAGA
* * **
7929 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTACTTTTACGTTAAACAATTTATTAT
1 TTTTATTTCCATACTAAAAAAGTCTAAAATAATAACAATAAAATTTACGTTAAACAATTTATTAT
7994 TATAATTATTAAAATTATTATTAGTTATATATCATTACG
66 TATAATTATTAAAATTATTATTA-TTATATATCATTACG
* *
8033 TTTTTTTTCCATACTAAAAAAGTCTAAAATAATAATAA-AAAATTTACGTTAAAC-ATCTTATTA
1 TTTTATTTCCATACTAAAAAAGTCTAAAATAATAACAATAAAATTTACGTTAAACAAT-TTATTA
* *
8096 TTATAATTATTAAACTTCTTATTATTATA
65 TTATAATTATTAAAATTATTATTATTATA
8125 ATAATAATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
102 7 0.08
103 41 0.49
104 35 0.42
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (103 bp):
TTTTATTTCCATACTAAAAAAGTCTAAAATAATAACAATAAAATTTACGTTAAACAATTTATTAT
TATAATTATTAAAATTATTATTATTATATATCATTACG
Found at i:9200 original size:23 final size:22
Alignment explanation
Indices: 9147--9188 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
9137 AAGATAATAA
*
9147 TATAGTTTTTAGAATAATCACT
1 TATACTTTTTAGAATAATCACT
9169 TATACTTTTTAGAATAATCA
1 TATACTTTTTAGAATAATCA
9189 TTGTAGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (22 bp):
TATACTTTTTAGAATAATCACT
Found at i:12351 original size:42 final size:42
Alignment explanation
Indices: 12292--12375 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
12282 CTCTGCAACA
12292 TCCCATGATGCTTGGCAGAAACTGTTGAAACTATTTGCGAAT
1 TCCCATGATGCTTGGCAGAAACTGTTGAAACTATTTGCGAAT
12334 TCCCATGATGCTTGGCAGAAACTGTTGAAACTATTTGCGAAT
1 TCCCATGATGCTTGGCAGAAACTGTTGAAACTATTTGCGAAT
12376 AAAACTCGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (42 bp):
TCCCATGATGCTTGGCAGAAACTGTTGAAACTATTTGCGAAT
Found at i:23702 original size:51 final size:51
Alignment explanation
Indices: 23605--23702 Score: 112
Period size: 51 Copynumber: 1.9 Consensus size: 51
23595 CTTCATATTT
* **
23605 TCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGTTTTTC
1 TCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGTTTTTC
*
23656 TCTTGTTTCA-ATCTTGTCTCTGGAC-ATACAAACACT-GTACACGTGTT
1 TCTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGTT
23703 CTTCATTCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
50 4 0.10
51 35 0.88
52 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.42
Consensus pattern (51 bp):
TCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGTTTTTC
Found at i:29983 original size:17 final size:17
Alignment explanation
Indices: 29961--29999 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
29951 AAAGCTTTAA
*
29961 TCCTTTCAGAGCCCATT
1 TCCTTTCAAAGCCCATT
*
29978 TCCTTTTAAAGCCCATT
1 TCCTTTCAAAGCCCATT
*
29995 CCCTT
1 TCCTT
30000 ATTAGCTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.36, G:0.08, T:0.38
Consensus pattern (17 bp):
TCCTTTCAAAGCCCATT
Done.