Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015066.1 Corchorus olitorius cultivar O-4 contig15099, 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: 37401
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:16358 original size:6 final size:6
Alignment explanation
Indices: 16347--16388 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
16337 CAATATCACG
16347 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
16389 GGTAAAACCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:18794 original size:21 final size:21
Alignment explanation
Indices: 18770--18810 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18760 TTGTAAATGT
*
18770 AACAAAACTCACATAAAGTGA
1 AACAAAACCCACATAAAGTGA
*
18791 AACAAAGCCCACATAAAGTG
1 AACAAAACCCACATAAAGTG
18811 GGATAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.22, G:0.12, T:0.12
Consensus pattern (21 bp):
AACAAAACCCACATAAAGTGA
Found at i:21234 original size:37 final size:37
Alignment explanation
Indices: 21151--21234 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
21141 TTAGAAATCC
* * * *
21151 GGCACTCAATCCGGCACTAAATATTTAGTATATTTCT
1 GGCACTAAATACGGCACTAAATATTTAGTACATTACT
21188 GGCACTAAATACGGCACTAAATATTTAGTACATATAC-
1 GGCACTAAATACGGCACTAAATATTTAGTACAT-TACT
*
21225 GGCAGTAAAT
1 GGCACTAAAT
21235 TGTAAGTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 39 0.95
38 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (37 bp):
GGCACTAAATACGGCACTAAATATTTAGTACATTACT
Found at i:26473 original size:27 final size:27
Alignment explanation
Indices: 26443--26502 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
26433 ACAAGTATGA
26443 AATTTAATTACAAACTACTGTTTATAT
1 AATTTAATTACAAACTACTGTTTATAT
*
26470 AATTTAATTACAAACTATTGTTTATAT
1 AATTTAATTACAAACTACTGTTTATAT
26497 AATTTA
1 AATTTA
26503 CCAAGTATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (27 bp):
AATTTAATTACAAACTACTGTTTATAT
Found at i:27286 original size:4 final size:4
Alignment explanation
Indices: 27277--27301 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27267 TTTATAGTTA
27277 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
27302 TTTTCACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:30164 original size:17 final size:17
Alignment explanation
Indices: 30144--30176 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30134 CAAATGGGAA
30144 GTGAAATTAAATATAAC
1 GTGAAATTAAATATAAC
30161 GTGAAATTAAATATAA
1 GTGAAATTAAATATAA
30177 GTTTCAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (17 bp):
GTGAAATTAAATATAAC
Found at i:31833 original size:65 final size:66
Alignment explanation
Indices: 31728--31861 Score: 252
Period size: 65 Copynumber: 2.0 Consensus size: 66
31718 GAGTAACCTA
*
31728 CTTTTTTCACCTTGTAAAGGTTTTCAAATGTAGAATCAGCTTTTATTTTAGCTTTAGAACAATGA
1 CTTTTTTCAACTTGTAAAGGTTTTCAAATGTAGAATCAGCTTTTATTTTAGCTTTAGAACAATGA
31793 G
66 G
31794 CTTTTTTCAACTTGTAAAGG-TTTCAAATGTAGAATCAGCTTTTATTTTAGCTTTAGAACAATGA
1 CTTTTTTCAACTTGTAAAGGTTTTCAAATGTAGAATCAGCTTTTATTTTAGCTTTAGAACAATGA
31858 G
66 G
31859 CTT
1 CTT
31862 GTTAGTTGTT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 48 0.72
66 19 0.28
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (66 bp):
CTTTTTTCAACTTGTAAAGGTTTTCAAATGTAGAATCAGCTTTTATTTTAGCTTTAGAACAATGA
G
Found at i:32461 original size:26 final size:26
Alignment explanation
Indices: 32425--32476 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
32415 ATTTAAATAA
32425 ACAGAGAAACAACTTATCATCAATCT
1 ACAGAGAAACAACTTATCATCAATCT
32451 ACAGAGAAACAACTTATCATCAATCT
1 ACAGAGAAACAACTTATCATCAATCT
32477 CTAAAATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (26 bp):
ACAGAGAAACAACTTATCATCAATCT
Found at i:36762 original size:31 final size:31
Alignment explanation
Indices: 36727--36798 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
36717 CAATTTGGGC
36727 CTAAACCTTTTTAAGGTTGCCCAATTCCAGT
1 CTAAACCTTTTTAAGGTTGCCCAATTCCAGT
36758 CTAAACCTTTTTAAGGTTGCCCAATTCCAGT
1 CTAAACCTTTTTAAGGTTGCCCAATTCCAGT
36789 CTAAACCTTT
1 CTAAACCTTT
36799 AAATAGATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.36
Consensus pattern (31 bp):
CTAAACCTTTTTAAGGTTGCCCAATTCCAGT
Done.