Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014008.1 Corchorus olitorius cultivar O-4 contig14041, 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, 848
Length: 1414
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Found at i:377 original size:72 final size:72
Alignment explanation
Indices: 260--404 Score: 238
Period size: 72 Copynumber: 2.0 Consensus size: 72
250 ATTTCGAAAG
260 AAGAAGAAAAGAAATAAAAATGAAAAAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
1 AAGAAGAAAAGAAATAAAAATGAAAAAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
325 TCCTAGT
66 TCCTAGT
* * * *
332 AAGAAGAAAAGTAAATATAAATG-AATAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCC
1 AAGAAGAAAAG-AAATAAAAATGAAAAAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCC
396 ATCCTAGT
65 ATCCTAGT
404 A
1 A
405 CTACTCTCGC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 58 0.85
73 10 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AAGAAGAAAAGAAATAAAAATGAAAAAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
TCCTAGT
Found at i:1260 original size:293 final size:290
Alignment explanation
Indices: 735--1414 Score: 1204
Period size: 293 Copynumber: 2.3 Consensus size: 290
725 GCCATACTAG
*
735 GACTTAATGCTTACTTGAAACGATTGTCTACCATTAGAAATTTCGAAAGTAAGTAAGAAAAGAAA
1 GACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAATTTCGAAAG-AAG-AAGAAAAGAAA
*
800 ATAAAAATG-AAAAAAGGGGTGCAACACGAGGACTTCCTAGGAGGTCACCCATCCTAGTACTACT
64 ATAAAAATGAAAAAAAGGGGTGCAACACGAGGACTTCCTAGGAGGTCACCCAACCTAGTACTACT
*
864 CTCGCCCAAGCACGCTTAACTGCGGAGTTCTAATGGGATCCGGTGCATTAGTGCTGGTATGACCG
129 CTCGCCAAAGCACGCTTAACTGCGGAGTTCTAATGGGATCCGGTGCATTAGTGCTGGTATGACCG
* * *
929 TACCCATCTGTCTTCGCATAATAAATATATATAAGCACATCTCATTGGATACGGTGTATTTTTGC
194 CACCCATCTGTCTTCGCATAATAAATATATATAAGCACATCTCATTGGATACGGTGCATTGTTGC
*
994 CGACATATGATCATACACGCCATACGTTTGAA
259 AGACATATGATCATACACGCCATACGTTTGAA
1026 GACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAAT
1 GACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAAT
1091 AAAAATAGAAAAAAGAAGGGGTGCAACACGAGGACTTCAC-AGGAGGTCACCCAACCTAGTACTA
66 AAAAAT-G-AAAAA-AAGGGGTGCAACACGAGGACTTC-CTAGGAGGTCACCCAACCTAGTACTA
* *
1155 CTCTCGCCAAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGAT
127 CTCTCGCCAAAGCACGCTTAACTGCGGAGTTCTAATGGGATCCGGTGCATTAGTGCTGGTATGAC
1220 CGCACCCATCTGTCTTCGCATAATAAATATATATAAGCACATCTCATTGGATACGGTGCATTGTT
192 CGCACCCATCTGTCTTCGCATAATAAATATATATAAGCACATCTCATTGGATACGGTGCATTGTT
1285 GCAGACATATGATCATACACGCCATACGTTTGAA
257 GCAGACATATGATCATACACGCCATACGTTTGAA
1319 GACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAAT
1 GACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAAT
1384 AAAAATGAAAAAAA-GGGTGCAACACGAGGAC
66 AAAAATGAAAAAAAGGGGTGCAACACGAGGAC
Statistics
Matches: 375, Mismatches: 9, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
289 36 0.10
290 6 0.02
291 53 0.14
292 5 0.01
293 274 0.73
294 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (290 bp):
GACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAATTTCGAAAGAAGAAGAAAAGAAAAT
AAAAATGAAAAAAAGGGGTGCAACACGAGGACTTCCTAGGAGGTCACCCAACCTAGTACTACTCT
CGCCAAAGCACGCTTAACTGCGGAGTTCTAATGGGATCCGGTGCATTAGTGCTGGTATGACCGCA
CCCATCTGTCTTCGCATAATAAATATATATAAGCACATCTCATTGGATACGGTGCATTGTTGCAG
ACATATGATCATACACGCCATACGTTTGAA
Done.