Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010285.1 Corchorus olitorius cultivar O-4 contig10317, 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: 6092
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Found at i:2169 original size:24 final size:24
Alignment explanation
Indices: 2102--2174 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
2092 AATTAATTGA
*
2102 GTTAATTTCTGATTGA-TTTAATT
1 GTTAATTTCTAATTGAGTTTAATT
*
2125 GAGTTAATTACTAAATT-AGTTTAATT
1 --GTTAATTTCT-AATTGAGTTTAATT
*
2151 -TCTAATTTCTAATTGAGTTGAATT
1 GT-TAATTTCTAATTGAGTTTAATT
2175 CATTGATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
23 5 0.12
24 15 0.38
25 10 0.25
26 10 0.25
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (24 bp):
GTTAATTTCTAATTGAGTTTAATT
Found at i:2511 original size:82 final size:82
Alignment explanation
Indices: 2371--2534 Score: 256
Period size: 82 Copynumber: 2.0 Consensus size: 82
2361 ATTTGTAGTT
*
2371 GAGTAATGCTAAACAACCCGCCTATTTAACCCGTAAAATGTCCCGCCTGACGTAGCATTGGAAAA
1 GAGTAATGCTAAACAACCCGCCTATTTAACCCGCAAAATGTCCCGCCTGACGTAGCATTGGAAAA
*
2436 AGTTATCAAAATTTCTA
66 AGTTACCAAAATTTCTA
* * * * *
2453 GAGTAATGCTACACAACCCGTCTATTTGACCCGCAAAATGTCCCGTCTGACGTGGCATTGGAAAA
1 GAGTAATGCTAAACAACCCGCCTATTTAACCCGCAAAATGTCCCGCCTGACGTAGCATTGGAAAA
*
2518 AGTTACCATAATTTCTA
66 AGTTACCAAAATTTCTA
2535 AAATCCTATT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (82 bp):
GAGTAATGCTAAACAACCCGCCTATTTAACCCGCAAAATGTCCCGCCTGACGTAGCATTGGAAAA
AGTTACCAAAATTTCTA
Found at i:2792 original size:161 final size:161
Alignment explanation
Indices: 2527--2848 Score: 484
Period size: 161 Copynumber: 2.0 Consensus size: 161
2517 AAGTTACCAT
* * *
2527 AATTTCTAAAATCCTATTTAATAATACCCTAAAATCAAAAAATTTACCCTGCAAACCCTCCTTAT
1 AATTTCTAAAACCCTATTTAACAATACCCTAAAATCAAAAAATTTACCCTACAAACCCTCCTTAT
* * * * * * *
2592 ATATAATTAGGGGCTAAATCTGGAATTAATTTGTTACCTTAATTATTAGGCGGGATAACTGGTGG
66 ATATAACTAAGGGCTAAACCTGAAATTAATTTATTACCTTAAATAATAGGCGGGATAACTGGTGG
2657 TAAAATCAGACGGGTCAAAAAGTATTTTCCA
131 TAAAATCAGACGGGTCAAAAAGTATTTTCCA
***
2688 AATTTCTAAAACCCTATTTAACAATACCCTAAAATCAAGGGATTTACCCTACAAACCCTCCTTAT
1 AATTTCTAAAACCCTATTTAACAATACCCTAAAATCAAAAAATTTACCCTACAAACCCTCCTTAT
* *
2753 TTATAACTAAGGGCTAAACCT-AAATTTAATTTATTACCTTAAATAATAGGCGGGTTAACTGGTG
66 ATATAACTAAGGGCTAAACCTGAAA-TTAATTTATTACCTTAAATAATAGGCGGGATAACTGGTG
*
2817 TTAAAATCAGACGGGTCAAAAAGTATTTTCCA
130 GTAAAATCAGACGGGTCAAAAAGTATTTTCCA
2849 TTTACATAGT
Statistics
Matches: 144, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
160 2 0.01
161 142 0.99
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (161 bp):
AATTTCTAAAACCCTATTTAACAATACCCTAAAATCAAAAAATTTACCCTACAAACCCTCCTTAT
ATATAACTAAGGGCTAAACCTGAAATTAATTTATTACCTTAAATAATAGGCGGGATAACTGGTGG
TAAAATCAGACGGGTCAAAAAGTATTTTCCA
Found at i:3186 original size:49 final size:49
Alignment explanation
Indices: 3119--3212 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
3109 ACCCTAGTGG
* * *
3119 TTAAACCTTGTGATTTCTTGTAGGAGGTCCCGGGTTCGAATCCTGGGAT
1 TTAAACCTTGGGACTTCTTGTAGGAGGTCCCGGATTCGAATCCTGGGAT
*
3168 TTAAAGCTTGGGACTTCTTGTAGGAGGTCCCGGATTCGAATCCTG
1 TTAAACCTTGGGACTTCTTGTAGGAGGTCCCGGATTCGAATCCTG
3213 AAATGAGCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (49 bp):
TTAAACCTTGGGACTTCTTGTAGGAGGTCCCGGATTCGAATCCTGGGAT
Found at i:3229 original size:49 final size:49
Alignment explanation
Indices: 3133--3229 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 49
3123 ACCTTGTGAT
* * * * **
3133 TTCTTGTAGGAGGTCCCGGGTTCGAATCCTGGGATTTAAAGCTTGGGAC
1 TTCTTGTAGGAGGTCCCGGATTCGAATCCTGGAAATGAAAGAATGGGAC
*
3182 TTCTTGTAGGAGGTCCCGGATTCGAATCCT-GAAATGAGCAGAATGGGA
1 TTCTTGTAGGAGGTCCCGGATTCGAATCCTGGAAATGA-AAGAATGGGA
3230 TTATAGACCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 4 0.10
49 36 0.90
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.28
Consensus pattern (49 bp):
TTCTTGTAGGAGGTCCCGGATTCGAATCCTGGAAATGAAAGAATGGGAC
Found at i:4038 original size:3 final size:3
Alignment explanation
Indices: 4030--4115 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
4020 GCTTCATCTA
4030 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4078 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4116 GGTCTATTGA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5850 original size:103 final size:103
Alignment explanation
Indices: 5671--5878 Score: 398
Period size: 103 Copynumber: 2.0 Consensus size: 103
5661 CCTTTTTAAT
*
5671 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTTCA
1 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAACTTTTAAGGTTCA
5736 ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
66 ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
*
5774 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAACTTTTAAGGTTTA
1 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAACTTTTAAGGTTCA
5839 ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
66 ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
5877 TT
1 TT
5879 ATATTACAAT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (103 bp):
TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAACTTTTAAGGTTCA
ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
Found at i:5993 original size:39 final size:40
Alignment explanation
Indices: 5937--6017 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
5927 TTTAATTCCT
*
5937 ATGTAATATATATAATAACTAAAATGCTTACATCAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
* * *
5977 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
6016 AT
1 AT
6018 TCTTAGGTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
Done.