Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023511.1 Corchorus olitorius cultivar O-4 contig23544, 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: 18300
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:983 original size:33 final size:35
Alignment explanation
Indices: 925--991 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
915 ACAATCACAA
*
925 ATTTTTTTTTTAAAATTAAAGACGCAAAGAAAAAT
1 ATTTTTTTTTCAAAATTAAAGACGCAAAGAAAAAT
* *
960 ATTTTTTTTTCAGAA-TAAA-ACGCAGAGAAAAA
1 ATTTTTTTTTCAAAATTAAAGACGCAAAGAAAAA
992 GAAAAACGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 12 0.41
34 4 0.14
35 13 0.45
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.34
Consensus pattern (35 bp):
ATTTTTTTTTCAAAATTAAAGACGCAAAGAAAAAT
Found at i:1295 original size:15 final size:16
Alignment explanation
Indices: 1271--1310 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1261 AGAGGTTGAA
*
1271 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
1286 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
1302 AGAAAACAA
1 AGAAAACAA
1311 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:4360 original size:30 final size:30
Alignment explanation
Indices: 4326--4389 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
4316 AACAATTTCA
* *
4326 TCAAAACGGCAATAGCTTCTGCGTATTGAG
1 TCAAAACGGCAATAGCTCCTGCGTATTAAG
4356 TCAAAACGGCAATAGCTCCTGCGTATTAAG
1 TCAAAACGGCAATAGCTCCTGCGTATTAAG
4386 TCAA
1 TCAA
4390 CATAAATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (30 bp):
TCAAAACGGCAATAGCTCCTGCGTATTAAG
Found at i:5225 original size:21 final size:21
Alignment explanation
Indices: 5199--5269 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
5189 CTTAGGCAAT
*
5199 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
5220 TGCAATGAGCTTGGAATCTTC
1 TCCAATGAGCTTGGAACCTTC
*
5241 TCCAATGAGCTTGGAACGTTC
1 TCCAATGAGCTTGGAACCTTC
5262 TCCAATGA
1 TCCAATGA
5270 ACTCCTAGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:8237 original size:177 final size:177
Alignment explanation
Indices: 7921--8244 Score: 456
Period size: 177 Copynumber: 1.8 Consensus size: 177
7911 ACAAATTATG
* * * * *
7921 TAATATTAAGTAGACCGTCTATTTTCGTTAACCGAAACAACTAATTCTTTGTAATCATCTTTTAT
1 TAATATTAAGTAGACCATCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCATCTTTTAT
* * *
7986 ACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAGCCTTTC
66 ACCTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAACCTTTC
*
8051 AAGAGACACTTGAATCATCTCAATCAGACATCTGAAGCAAAAGTTTA
131 AAGAGACACTTAAATCATCTCAATCAGACATCTGAAGCAAAAGTTTA
* *
8098 TAATATTAAGTGGATCATCTATTTCCGTTAACCGAAACAACAAA-TCTTTTGGAAGCAT-TTTTG
1 TAATATTAAGTAGACCATCTATTTCCGTTAACCGAAACAACAAATTC-TTTGGAAGCATCTTTT-
* * *
8161 ATA-CTTAAAATATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATTAAACAATCT
64 ATACCTT-AAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAACCT
* *
8225 TTTAATAGACACTTAAATCA
128 TTCAAGAGACACTTAAATCA
8245 CCTTAAGCGG
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
176 9 0.07
177 119 0.93
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (177 bp):
TAATATTAAGTAGACCATCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCATCTTTTAT
ACCTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAACCTTTC
AAGAGACACTTAAATCATCTCAATCAGACATCTGAAGCAAAAGTTTA
Found at i:14998 original size:27 final size:27
Alignment explanation
Indices: 14953--15026 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
14943 TGTGAACTTA
* *
14953 AAATGACCAAAATGCCCCCTGAATATGC
1 AAATGACTAAAATG-CCCCTGAACATGC
* * *
14981 AAATGACTAAAACGCCCCTGGACGTGC
1 AAATGACTAAAATGCCCCTGAACATGC
15008 AAATGACTAAAATGCCCCT
1 AAATGACTAAAATGCCCCT
15027 AGGTGACCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 28 0.70
28 12 0.30
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAACATGC
Done.