Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021748.1 Corchorus olitorius cultivar O-4 contig21781, 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: 4398
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:1818 original size:303 final size:302
Alignment explanation
Indices: 1270--1838 Score: 854
Period size: 303 Copynumber: 1.9 Consensus size: 302
1260 TTCTCAAGAT
* *
1270 AAGAAGATGGTAAAATGACGATGACTGAGGCACAGGTGTTCCACGTTTTTGTACTCTTCTTTGCA
1 AAGAAGATGGTAAAATGACGACGACTGAGGCACAGGTGTTCCAC-TTTTTGTACTCTTCTTCGCA
* * *
1335 ATTGCTGACTCACTTAAGTTTTTATATAGAGGGTCTTCAAGAGTCTTCTTAACAAATGCATCGTG
65 ATTGCTGACTCACTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGTG
* * * * *
1400 ACAAACTTTACCCAATACCTTGGGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTTTGAATA
130 ACAAACTTTACACAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAATA
* * * * * *
1465 TACTTGTGAAAACTTCCCTGGCACAGGGCAGTTCCATTTTTGTTTTGCAATTGTTTTCCTTAATA
195 TACTTGTGAAAACTTCCCTAGAACAGGCCAGCTCCATTTTTGTCTTGCAATTATTTTCCTTAATA
1530 ATCAAGATGAGGTTTTTCTCAGGTGAAATGACTCCGCTTACAG
260 ATCAAGATGAGGTTTTTCTCAGGTGAAATGACTCCGCTTACAG
** * *
1573 AAGAAGATGGTGCAATGTCGACGACTGAGGCACATGTGTTCCA-TTTTTGAATACTCTTCTTCGC
1 AAGAAGATGGTAAAATGACGACGACTGAGGCACAGGTGTTCCACTTTTTG--TACTCTTCTTCGC
* *
1637 AATTGTTGACTCGCTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGT
64 AATTGCTGACTCACTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGT
* *
1702 GACAAACTTTACAGAATACCATGAGTTCACCGCAACACTTCTTTGTGACAGCTCCGGTATAGAAT
129 GACAAACTTTACACAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAAT
* *
1767 ATACTTTTGAAAACTTCCCTAGAACAGGCCATGCT-CATTTTTGTCTTGCAATTATTTTGCTTAA
194 ATACTTGTGAAAACTTCCCTAGAACAGGCCA-GCTCCATTTTTGTCTTGCAATTATTTTCCTTAA
1831 TAATCAAG
258 TAATCAAG
1839 GTCTGGGTTT
Statistics
Matches: 237, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
301 6 0.03
303 229 0.97
304 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (302 bp):
AAGAAGATGGTAAAATGACGACGACTGAGGCACAGGTGTTCCACTTTTTGTACTCTTCTTCGCAA
TTGCTGACTCACTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGTGA
CAAACTTTACACAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAATAT
ACTTGTGAAAACTTCCCTAGAACAGGCCAGCTCCATTTTTGTCTTGCAATTATTTTCCTTAATAA
TCAAGATGAGGTTTTTCTCAGGTGAAATGACTCCGCTTACAG
Done.