Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019671.1 Corchorus olitorius cultivar O-4 contig19704, 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: 34291
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:7082 original size:2 final size:2
Alignment explanation
Indices: 7075--7104 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7065 TTATAGAACA
7075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7105 CTTTCAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12185 original size:18 final size:17
Alignment explanation
Indices: 12157--12200 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
12147 TTCAACCAGG
12157 TTTTC-TTTCTTCTTCA
1 TTTTCTTTTCTTCTTCA
* *
12173 TTTTCATTTTCTTTTTCG
1 TTTTC-TTTTCTTCTTCA
12191 TTTTCTTTTC
1 TTTTCTTTTC
12201 AATCTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 5 0.21
18 14 0.58
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTCTTTTCTTCTTCA
Found at i:12856 original size:33 final size:33
Alignment explanation
Indices: 12814--12879 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
12804 CGTTATTACC
12814 TGTTATTATTTGTTGATGGATTCCAACAATTAA
1 TGTTATTATTTGTTGATGGATTCCAACAATTAA
12847 TGTTATTATTTGTTGATGGATTCCAACAATTAA
1 TGTTATTATTTGTTGATGGATTCCAACAATTAA
12880 CTCATTTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTTATTATTTGTTGATGGATTCCAACAATTAA
Found at i:26020 original size:10 final size:10
Alignment explanation
Indices: 26005--26029 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25995 CATATGAGTT
26005 TTTTTTTTAA
1 TTTTTTTTAA
26015 TTTTTTTTAA
1 TTTTTTTTAA
26025 TTTTT
1 TTTTT
26030 AAACCTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:26394 original size:36 final size:36
Alignment explanation
Indices: 26347--26418 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
26337 ACCAGTTGAG
26347 CTAACAACTCGGGTGCTGCAACGTGATATTAATGAT
1 CTAACAACTCGGGTGCTGCAACGTGATATTAATGAT
26383 CTAACAACTCGGGTGCTGCAACGTGATATTAATGAT
1 CTAACAACTCGGGTGCTGCAACGTGATATTAATGAT
26419 TTAAAATCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (36 bp):
CTAACAACTCGGGTGCTGCAACGTGATATTAATGAT
Found at i:28186 original size:178 final size:178
Alignment explanation
Indices: 27874--28211 Score: 459
Period size: 178 Copynumber: 1.9 Consensus size: 178
27864 TTCCACCATA
* * * * *
27874 AGCATAAATTATGTAATATTAAGTAGACCGTCTATTTCCTTTAACTAAAACAACTAATTCTTTGG
1 AGCATAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGG
* * *
27939 AAGTAATTTTTATACCTCGAACATTAGATTTGGTTTTCGAGCCCTTCATGAAAGTTGTAGATTAT
66 AAGTAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAGATGAT
*
28004 GGAACAACCTTTCAAGAGACACTTGAATCATCTCAATCACAAATCTGG
131 GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATCACAAATCTGG
* *
28052 AGCA-AAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTC
1 AGCATAAA-TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTT-
* * *
28115 GGAAG-CATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGA
64 GGAAGTAATTTTT-ATACCTCG-AACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAGA
* * *
28178 TGATGGAACAATCTTTTAATAGACACTTAAATCA
127 TGATGGAACAACCTTTCAAGAGACACTTAAATCA
28212 CCTTAATCGG
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
177 15 0.11
178 124 0.89
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (178 bp):
AGCATAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGG
AAGTAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAGATGAT
GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATCACAAATCTGG
Found at i:28244 original size:178 final size:178
Alignment explanation
Indices: 27874--28256 Score: 452
Period size: 178 Copynumber: 2.2 Consensus size: 178
27864 TTCCACCATA
* * * * * *
27874 AGCATAAATTATGTAATATTAAGTAGACCGTCTATTTCCTTTAACTAAAACAACTAATTCTTTGG
1 AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGG
* * *
27939 AAGTAATTTTTATACCTCGAACATTAGATTTGGTTTTCGAGCCCTTCATGAAAGTTGTAGATTAT
66 AAGTAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAGATGAT
* * *
28004 GGAACAACCTTTCAAGAGACACTTGAATCATCTCAATCACAAATCTGG
131 GGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCACAAATCCGG
* * *
28052 AGCAAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCG
1 AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTT-G
* * *
28116 GAAG-CATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGAT
65 GAAGTAATTTTT-ATACCTCG-AACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAGAT
* * * * **
28179 GATGGAACAATCTTTTAATAGACACTTAAATCACCTTAATCGGATAA-CCGG
128 GATGGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCACA-AATCCGG
* *
28230 AG-AGAAAATTATATAATGTTAAATAGA
1 AGCA-AAAATTATATAATATTAAGTAGA
28257 TCGTTTAGTC
Statistics
Matches: 172, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
177 13 0.08
178 157 0.91
179 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (178 bp):
AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGG
AAGTAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAGATGAT
GGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCACAAATCCGG
Done.