Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021943.1 Corchorus olitorius cultivar O-4 contig21976, 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: 3188
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Found at i:1835 original size:303 final size:303
Alignment explanation
Indices: 1287--1888 Score: 841
Period size: 303 Copynumber: 2.0 Consensus size: 303
1277 TCTCAAGCAC
* *** *
1287 AAGAAGATGGTCAAATGTCGATGACTGAGGCACAGGTGTTCCACGTTTTTGTACTCTTCTTTGCA
1 AAGAAGATGGTCAAATGTCGACGACTGAGGCACAGGTGTTCCACGTTTGAATACTCTTCTTCGCA
* * * *
1352 ATTGCTGACTCACTTAAGTTTTTATATATAGGGTCTTCAAAAGTCTTCTTAACAAATGCATCGTG
66 ATTGCTCACTCACTTAAGTCTTTATATAAAGGATCTTCAAAAGTCTTCTTAACAAATGCATCGTG
* * ** * *
1417 ACAAACTTTACCCAATACCTTGAGTTCACCGCAACACTTCTTAGTGACGGCTCCGGTTTTGAATA
131 ACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGCGACAACTCCGGTATAGAATA
* * * * * *
1482 TACTTGTGAAAACTTGCCTGGCACAGGACAGTTCCATTTTTGTTTTGCAATTGTTTTCCTTAATA
196 TACTTGTGAAAACCTCCCTGGAACAGGACAGCTCCATTTTTGTCTTGCAATTATTTTCCTTAATA
* * *
1547 ATCAAGTCGGGGTTTT-TCGCAGGTGAAATGACTCCGCTTACAG
261 ATCAAGTCGGGGTTTTCT-ACAGCTGAAACGACTCCGCTTACAG
* *
1590 AAGAAGATGGTGC-AATGTCGACGACTGAGGCACATGTGTTCCATGTTTGAATACTCTTCTTCGC
1 AAGAAGATGGT-CAAATGTCGACGACTGAGGCACAGGTGTTCCACGTTTGAATACTCTTCTTCGC
* * *
1654 AATTGTTCACTCGCTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGT
65 AATTGCTCACTCACTTAAGTCTTTATATAAAGGATCTTCAAAAGTCTTCTTAACAAATGCATCGT
* *
1719 GACAAACTTTACCGAATACCATGAGTTCACCGCAACACTTCTTTGCGACAACTCCGGTATAGAAT
130 GACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGCGACAACTCCGGTATAGAAT
* * *
1784 ATACTTTTGAAAACCTCCCTGGAACAGGCCAGGCT-CATTTTTGTCTTGCAATTATTTTGCTTAA
195 ATACTTGTGAAAACCTCCCTGGAACAGGACA-GCTCCATTTTTGTCTTGCAATTATTTTCCTTAA
*
1848 TAATCAAGTCTGGGTTTTCTACAGCTGAAACGACTCCGCTT
259 TAATCAAGTCGGGGTTTTCTACAGCTGAAACGACTCCGCTT
1889 GTTAAAACAA
Statistics
Matches: 261, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
303 257 0.98
304 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (303 bp):
AAGAAGATGGTCAAATGTCGACGACTGAGGCACAGGTGTTCCACGTTTGAATACTCTTCTTCGCA
ATTGCTCACTCACTTAAGTCTTTATATAAAGGATCTTCAAAAGTCTTCTTAACAAATGCATCGTG
ACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGCGACAACTCCGGTATAGAATA
TACTTGTGAAAACCTCCCTGGAACAGGACAGCTCCATTTTTGTCTTGCAATTATTTTCCTTAATA
ATCAAGTCGGGGTTTTCTACAGCTGAAACGACTCCGCTTACAG
Done.