Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402184.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5273.0, 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: 3217
ACGTcount: A:0.22, C:0.09, G:0.08, T:0.23
Warning! 1208 characters in sequence are not A, C, G, or T
Found at i:1743 original size:171 final size:169
Alignment explanation
Indices: 1418--2108 Score: 629
Period size: 171 Copynumber: 4.0 Consensus size: 169
1408 NNNNNNNNNN
* * * * * * * * *
1418 TAAATAGTTTTATAATCTCAAAATTGATTTTAGGTTCAATTTTTT-TTACATTATGTGCTAGAAC
1 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTAATA-TTTTTG-GTTAAAAC
* * * * * * * * * * *
1482 AGATTATAATTG-ATGTCTAGCTCAAGTAACGT-AACGAAAAAGTTATTCATAGTGAATAAAAGT
64 AGACTATAGTTGAATGTATACCTCGAGAAACATGAA-GAAAAAG-CATTCATTG-GAAAAAAAAT
* * *
1545 CAATTTATTGTCACCCATTCCTTCAAAAGCCATATTACTTGCTT
126 CCATTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTT
* ** *
1589 TAAATGGTTTTATAATCTCGTAATTGATTTTAAGTTGAATTTTTTTGTATGTTTGGTTAAAACAG
1 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTGGTTAAAACAG
* * * * *
1654 ACTATAGTTGAACGTCTATCTCGAGAAACATGAAGAAAAAGCCATTCACTGGCAAAAAAAATTCA
66 ACTATAGTTGAATGTATACCTCGAGAAACATGAAGAAAAAG-CATTCATTGG-AAAAAAAATCCA
* ** **
1719 TTTTATAGTCACCCA-TCTTTCAAAAATCATATTACTATCTT
129 -TTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTT
* * * ** *
1760 TAAATTGTTTTATAATCTCATAATTGATTTTGAGTTGAATTTTTTCACCTTTTTAGTTAAAACAG
1 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTGGTTAAAACAG
* * * * * *
1825 ACTAGAATTGAATGTTTACCTCGAGAAACGTGAA-AAAAAGGCATTAATT-GATAAGAAAAGTCC
66 ACTATAGTTGAATGTATACCTCGAGAAACATGAAGAAAAA-GCATTCATTGGA-AA-AAAAATCC
* * *
1888 ATTTATAGTCACCTATTCCTTTAAAAGCCTTATTACTCGCTT
128 ATTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTT
* * * * *
1930 TAAATGGTATTATAATCTCATAATTAATTTTAAGTTAAAATTTTTAATATTTTTGGTTGAAACAG
1 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTGGTTAAAACAG
* * * **
1995 ACTATAGTTAAATGTATAGCTCGAGAAACATGAAGAAACAAGCATTCATTGGAAAGACAGGTCCA
66 ACTATAGTTGAATGTATACCTCGAGAAACATGAAGAAA-AAGCATTCATTGGAAA-AAAAATCCA
* ** *
2060 TTTATAGTCTCATATTCCTTCAAAAGCCTTATTACTCGCTT
129 TTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTT
2101 TAAATGGT
1 TAAATGGT
2109 NNNNNNNNNN
Statistics
Matches: 426, Mismatches: 82, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
168 1 0.00
169 16 0.04
170 136 0.32
171 252 0.59
172 21 0.05
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (169 bp):
TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTGGTTAAAACAG
ACTATAGTTGAATGTATACCTCGAGAAACATGAAGAAAAAGCATTCATTGGAAAAAAAATCCATT
TATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTT
Found at i:1995 original size:170 final size:170
Alignment explanation
Indices: 1539--2108 Score: 644
Period size: 171 Copynumber: 3.3 Consensus size: 170
1529 CATAGTGAAT
* * *
1539 AAAAGTCAATTTATTGTCACCCATTCCTTCAAAAGCCATATTACTTGCTTTAAATGGTTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGGTTTTATAA
* ** * *
1604 TCTCGTAATTGATTTTAAGTTGAATTTTTTTGTATGTTTGGTTAAAACAGACTATAGTTGAACGT
66 TCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTGGTTAAAACAGACTATAGTTGAATGT
* * * *
1669 CTATCTCGAGAAACATGAAGAAAAAGCCATTCACTGGCAAA-
131 ATACCTCGAGAAACATGAAGAAAAAGGCATTCA-TTG-AAAG
* * * ** ** *
1710 AAAAATTCATTTTATAGTCACCCA-TCTTTCAAAAATCATATTACTATCTTTAAATTGTTTTATA
1 AAAAGTCCA-TTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGGTTTTATA
* * ** * * *
1774 ATCTCATAATTGATTTTGAGTTGAATTTTTTCACCTTTTTAGTTAAAACAGACTAGAATTGAATG
65 ATCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTGGTTAAAACAGACTATAGTTGAATG
* * *
1839 TTTACCTCGAGAAACGTGAA-AAAAAGGCATTAATTGATAAG
130 TATACCTCGAGAAACATGAAGAAAAAGGCATTCATTGA-AAG
* * * *
1880 AAAAGTCCATTTATAGTCACCTATTCCTTTAAAAGCCTTATTACTCGCTTTAAATGGTATTATAA
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGGTTTTATAA
* * * * *
1945 TCTCATAATTAATTTTAAGTTAAAATTTTTAATATTTTTGGTTGAAACAGACTATAGTTAAATGT
66 TCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTGGTTAAAACAGACTATAGTTGAATGT
*
2010 ATAGCTCGAGAAACATGAAGAAACAA-GCATTCATTGGAAAG
131 ATACCTCGAGAAACATGAAGAAA-AAGGCATTCATT-GAAAG
* * * ** *
2051 ACAGGTCCATTTATAGTCTCATATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGT
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGGT
2109 NNNNNNNNNN
Statistics
Matches: 332, Mismatches: 60, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
168 1 0.00
169 17 0.05
170 119 0.36
171 178 0.54
172 17 0.05
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (170 bp):
AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCGCTTTAAATGGTTTTATAA
TCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTGGTTAAAACAGACTATAGTTGAATGT
ATACCTCGAGAAACATGAAGAAAAAGGCATTCATTGAAAG
Done.