Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013741.1 Corchorus olitorius cultivar O-4 contig13774, 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: 7750
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Found at i:1365 original size:260 final size:262
Alignment explanation
Indices: 904--1422 Score: 916
Period size: 260 Copynumber: 2.0 Consensus size: 262
894 CTGCACTGCA
*
904 AATTCCTTGGGGTATACAGTAAGAACATCTTCATTGGCTCCAAAAGCATCTTAAAGATGTAATGA
1 AATTCCTTGGGGTATACAGTAAGAACATCTTCATTGACTCCAAAAGCATCTTAAAGATGTAATGA
969 GAGTACAAACATCCAGAAAATGAAATGTTCTGAGTTTAGAGAATGGAAATTATGTTTGTTTGAAT
66 GAGTACAAACATCCAGAAAATGAAATGTTCTGAGTTTAGAGAATGGAAATTATGTTTGTTTGAAT
* *
1034 ATCTTACTATGTTATTTGACATTCGACATTACCTGTGGCTCAGTCAGGAAGGAAAGAAAAAGGTC
131 ATCTTACTATGTTATTTGACATTCGACATTACCTGTGGCTCAGTCAGGAAGAAAAGAAAAAGGCC
*
1099 GTAGCAGATTAGAACAGCTAGCGATTAGAG-TTT-TTTTTTTTTGGCATTAAGAAAGGGAGCTAG
196 GTAGCAGATTAGAACAACTAGCGATTAGAGTTTTCTTTTTTTTTGGCATTAAGAAAGGGAGCTAG
1162 CG
261 CG
*
1164 AATTCCTTGGGGTATACAGTAAGAACATCTTCATTGACTCCAAAAGTATCTTAAAGATGTAATGA
1 AATTCCTTGGGGTATACAGTAAGAACATCTTCATTGACTCCAAAAGCATCTTAAAGATGTAATGA
*
1229 GAGTACAAACATCCAGAAAATGAAATGTTCTGAGTTTAGAGAATGGAATTTATGTTTGTTTGAAT
66 GAGTACAAACATCCAGAAAATGAAATGTTCTGAGTTTAGAGAATGGAAATTATGTTTGTTTGAAT
* * *
1294 ATCTTACTATGTTATTTGACATTCGACATTATCTGTGTCTCTGTCAGGAAGAAAAGAAAAAGGCC
131 ATCTTACTATGTTATTTGACATTCGACATTACCTGTGGCTCAGTCAGGAAGAAAAGAAAAAGGCC
1359 GTAGCAGATTAGAACAACTAGCGATTAGAGTTTTTTTCTTTTTTTTTGGCATTAAGAAAGGGAG
196 GTAGCAGATTAGAACAACTAGCGATTAGAG---TTTTCTTTTTTTTTGGCATTAAGAAAGGGAG
1423 ATAGTGATTA
Statistics
Matches: 245, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
260 216 0.88
264 3 0.01
265 26 0.11
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (262 bp):
AATTCCTTGGGGTATACAGTAAGAACATCTTCATTGACTCCAAAAGCATCTTAAAGATGTAATGA
GAGTACAAACATCCAGAAAATGAAATGTTCTGAGTTTAGAGAATGGAAATTATGTTTGTTTGAAT
ATCTTACTATGTTATTTGACATTCGACATTACCTGTGGCTCAGTCAGGAAGAAAAGAAAAAGGCC
GTAGCAGATTAGAACAACTAGCGATTAGAGTTTTCTTTTTTTTTGGCATTAAGAAAGGGAGCTAG
CG
Found at i:4618 original size:203 final size:205
Alignment explanation
Indices: 4234--4635 Score: 668
Period size: 203 Copynumber: 2.0 Consensus size: 205
4224 ATATAAATTG
*
4234 GATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATC
1 GATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTCAATAAATC
* * *
4299 AACCTACTAATGTTCAACTAATTAATTTTTTTGGTATAATTCTATATATATAATAGTAATGTGTT
66 AACCTACTAATGTTCAACTAACT-ATTTTTTTGGTATAATTCTATATATATAATAATAATGTGCT
4364 GCATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAATAACATTCACCATTGA
130 GCATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAATAACATTCACCATTGA
4429 TAAATAAATCA
195 TAAATAAATCA
4440 GATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTCAATAAAT
1 GATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTCAATAAAT
* * *
4505 CAACC-ACTAATGTTCAACT-ACT-TTTTTTT-GTATAGTTTTATGTATAATAATAATAATGTGC
65 CAACCTACTAATGTTCAACTAACTATTTTTTTGGTATAATTCTATATAT-ATAATAATAATGTGC
* *
4566 TGTATCTTATTCACTACAACTTTGTTAGTAATTTTAGACTTAAAAATTAATAACATTCACCATTG
129 TGCATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAATAACATTCACCATTG
4631 ATAAA
194 ATAAA
4636 GTTATTAAGC
Statistics
Matches: 185, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
202 13 0.07
203 88 0.48
205 2 0.01
206 18 0.10
207 64 0.35
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (205 bp):
GATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTCAATAAATC
AACCTACTAATGTTCAACTAACTATTTTTTTGGTATAATTCTATATATATAATAATAATGTGCTG
CATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAATAACATTCACCATTGAT
AAATAAATCA
Found at i:6571 original size:58 final size:58
Alignment explanation
Indices: 6468--6582 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 58
6458 ATAGCATCAT
*
6468 GCCTCGGTCCTAAAACATCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAA
1 GCCTCGGTCCGAAAACATCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAA
* * * *
6526 GCCTTGGTCCGAAAACGTCTTTTTTTATG-CATCTAAT-AAAGAACATGTCACTTGATA
1 GCCTCGGTCCGAAAACATC-TTTTTTA-GACATCTAATAAAAAAACATGTCACTCGATA
6583 TTTGATTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
58 34 0.68
59 15 0.30
60 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (58 bp):
GCCTCGGTCCGAAAACATCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAA
Done.