Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399302.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2571.0, 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: 2271
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.29
Warning! 470 characters in sequence are not A, C, G, or T
Found at i:1339 original size:162 final size:157
Alignment explanation
Indices: 1078--1377 Score: 384
Period size: 162 Copynumber: 1.8 Consensus size: 157
1068 CTTATCAACG
*
1078 AATGCATTTTTCTTCACGTTTCTCCAAATTGAAATTCAATTATAGTTTGTTTTAGCCAAAAATAT
1 AATGCATTTTTCTTCACGTTTCTCCAAATTCAAATTCAATTATAGTTTGTTTTAGCCAAAAATAT
***** *
1143 AAAAAAATTNNNNNNNNNNTCAATTATAAGATTATAAAATAATTTAAAGCGAGTAATAAGGATTT
66 AAAAAAATT-----CAACTTCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAGGATTT
1208 TGAAGAATATAAATAGACTTTTCTTGCTAACA
126 TGAAGAATATAAATAGACTTTTCTTGCTAACA
*
1240 AATGCATTTTTCTTCACGTTTCTCCAAGTTCAAATTCAATTATAGTTTGTTTTAGCCAAAAATAT
1 AATGCATTTTTCTTCACGTTTCTCCAAATTCAAATTCAATTATAGTTTGTTTTAGCCAAAAATAT
***** *
1305 AAAAAAATTCAACTNNNNNNNNNNTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGATTT
66 AAAAAAATTCAACT-----TCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAGGATTT
1370 TGAAGAAT
126 TGAAGAAT
1378 GGGTGACTAT
Statistics
Matches: 119, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
162 119 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.34
Consensus pattern (157 bp):
AATGCATTTTTCTTCACGTTTCTCCAAATTCAAATTCAATTATAGTTTGTTTTAGCCAAAAATAT
AAAAAAATTCAACTTCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAGGATTTTGAAG
AATATAAATAGACTTTTCTTGCTAACA
Found at i:2090 original size:171 final size:171
Alignment explanation
Indices: 1741--2271 Score: 509
Period size: 171 Copynumber: 3.1 Consensus size: 171
1731 NNNNNNAAAG
* * * * * **
1741 TTTTCGAAGGACTGGGTGACTATAAATGGACTTTTCTTAC-AAATGAATACTTTTTTTTTTATGT
1 TTTT-GAAGGAATGGGTGACAATAAATGGACTTTTCTTACTCAATGAATAGTTTTTTTTTCACAT
* * * *
1805 TTCTCAAGGTAAACATTCAATTGTTGTCTATTTTAACCAAACATGTAAAAAAATTCAACTTAAAA
65 TTCTCAAGGCAAACATTCAATTATAGTCT-TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAA
* ******** *
1870 TCACTTATGAGATTATAAAATAATTTAAAGNNNNNNNNNNAA--T
129 TCAATTATGAGATTATAAAATAATTTAAAG--CGAGTAATAAGGC
1913 TTTTGAAGGAATGGGTGACAATAAATGGACTTTTCTT-CTCAATGAATAGTTTTTTTTTCACATT
1 TTTTGAAGGAATGGGTGACAATAAATGGACTTTTCTTACTCAATGAATAGTTTTTTTTTCACATT
* * *
1977 TCTCAAGGCAAGA-ATTCAATTATAGTCTGTTTTAACAAAAAAT-TAACACAAATTCAAATTAAA
66 TCTCAAGGCAA-ACATTCAATTATAGTCT-TTTTAACCAAAAATGTAA-AAAAATTCAACTTAAA
* * *
2040 ATCAATTATCAGATTATAAAACAATTTAAAGCTAGTAATAAGGC
128 ATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGC
********** * * *
2084 TTTTGAAGGAATGGGTNNNNNNNNNNGGACTTTT-TTCCTCAATGAATGGTTTTTTTTACACATT
1 TTTTGAAGGAATGGGTGACAATAAATGGACTTTTCTTACTCAATGAATAGTTTTTTTTTCACATT
** * * * *
2148 TCTGGAGGCAAACATTCGATTATAGTGTTTTTAACCATAAATGTAAAAAAATTCAACTTAAAATA
66 TCTCAAGGCAAACATTCAATTATAGTCTTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATC
* *
2213 AATTTTGAGATTAAAAAATAATTTAAAGCGAGTAATAAGGC
131 AATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGC
*
2254 TTTTAAAGGAATGGGTGA
1 TTTTGAAGGAATGGGTGA
Statistics
Matches: 295, Mismatches: 56, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
169 2 0.01
170 86 0.29
171 202 0.68
172 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
TTTTGAAGGAATGGGTGACAATAAATGGACTTTTCTTACTCAATGAATAGTTTTTTTTTCACATT
TCTCAAGGCAAACATTCAATTATAGTCTTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATC
AATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGC
Done.