Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401974.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5071.0, 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, 665
Length: 1109
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:272 original size:21 final size:21
Alignment explanation
Indices: 239--278 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
229 GGGAAACATG
*
239 AAGAAAAATCCATTCATTGGT
1 AAGAAAAACCCATTCATTGGT
* *
260 AAGAAAAGCCCATTTATTG
1 AAGAAAAACCCATTCATTG
279 TCACCCAAGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
AAGAAAAACCCATTCATTGGT
Found at i:416 original size:171 final size:170
Alignment explanation
Indices: 20--1109 Score: 976
Period size: 171 Copynumber: 6.4 Consensus size: 170
10 ATTTTTTTAT
* * ** * *
20 ATTTTTTGTTAAAACAGATTATAATTGAATGTTTTTC-TCAGGAAACATGAAGAAAAATCCATTC
1 ATTTTTGGTTAAAACAGATTATAATTGAATATTTGCCTTGA-GAAGCATGAAGAAAAATCCATTC
* * * *
84 ATTGGTAAGAAAAGCCCATTTATAGTTACCCTAGCCTT-TAAAGCCTTATTACTCTCTTTAAATG
65 ATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATG
* * * * *
148 GTTTTATAACCTCAAAATTGATTTTTAGTAGAATTTTTGAAT
130 GTTTTATAATCTCAAAATTGATTTTGAATTGAATTTTT-AAC
* * * * * *
190 ATTTTTAGTTAAAACAGATTATAATTAAATGTTTTCCTTGGGAAACATGAAGAAAAATCCATTCA
1 ATTTTTGGTTAAAACAGATTATAATTGAATATTTGCCTTGAGAAGCATGAAGAAAAATCCATTCA
* * * *
255 TTGGTAAGAAAAGCCCATTTATTGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTTAATGC
66 TTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGG
320 TTTTATAA-CTGCAAAATTGATTTTGAATTGAATTTTATAAC
131 TTTTATAATCT-CAAAATTGATTTTGAATTGAATTTT-TAAC
* * * *** * ** *
361 ATTATTGGGTAAAACATACGGTAATTGAATATTTGCCTTGATAAGCACAAAG-AAAATCTATTCA
1 ATTTTTGGTTAAAACAGATTATAATTGAATATTTGCCTTGAGAAGCATGAAGAAAAATCCATTCA
* ** * * **
425 TTGACAAGAAAAGCTTATTTATAGTCACCGAAGCCTTCAAAAGCTTTATTACTCTCTGCAAATGG
66 TTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGG
* * * *
490 TTTTATAATCTCATAATTGA-TTTAAAGTTGAATTATTTTAT
131 TTTTATAATCTCAAAATTGATTTTGAA-TTGAATT-TTTAAC
* ** * * **
531 ATTTTTGGTTAACACAGATTATAATTGAATATTTGCCTCAAGAAGCAT-AAGGAAAACCCATTTG
1 ATTTTTGGTTAAAACAGATTATAATTGAATATTTGCCTTGAGAAGCATGAAGAAAAATCCATTCA
* * * *
595 TTGGCAAGAAAAACCCATTTATAGTCACCTAAGCCTTCAAAAGCCTATTATTACTCTATTTCAAT
66 TTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCC--TTATTACTCTCTTTAAAT
* *
660 GGTTTCATAATCTCATAAA-TGATTTT-AAGTTGAAATTTTT-TC
129 GGTTTTATAATCTCA-AAATTGATTTTGAA-TTG-AATTTTTAAC
** * * * * *
702 TATTTTTGGCCATACCAGATTATAATTGAATGTTTCCCATTG-GAAACATGAAGAAAAA--CATG
1 -ATTTTTGGTTAAAACAGATTATAATTGAATATTTGCC-TTGAGAAGCATGAAGAAAAATCCA--
* * * *
764 TTCATTGGCAAGAAAAGCTCATTTATAGTCACCCAAGCCTCCAAAAGCCTCATTACTCTCTGTAA
62 TTCATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAA
* * *
829 ATGGTTTGATAATCT-AATAATTGA-GTTGAAATTGAATTATTTTAC
127 ATGGTTTTATAATCTCAA-AATTGATTTTG-AATTGAATT-TTTAAC
* * * * ** * *
874 ATTTTTGGTTAACACAAACTATAACTGAA-AGTTTGCCTCAAGAAGCATGAAGAAATACCCATTC
1 ATTTTTGGTTAAAACAGATTATAATTGAATA-TTTGCCTTGAGAAGCATGAAGAAAAATCCATTC
** * *
938 ATTGAAAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTAATCACTCTCTTTAAATG
65 ATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATG
* * **
1003 GTTTTATAATCAT-ATAATTGATTTT-AAGTCGAATTTTTTTC
130 GTTTTATAATC-TCAAAATTGATTTTGAA-TTGAATTTTTAAC
** * * * *
1044 TATTTTTGGCCAAAACAGATTTTAATTGAATGTTTACCTTTG-GAAACATGAAGAAAAA-CACAT
1 -ATTTTTGGTTAAAACAGATTATAATTGAATATTTGCC-TTGAGAAGCATGAAGAAAAATC-CAT
1107 TCA
63 TCA
Statistics
Matches: 747, Mismatches: 138, Indels: 69
0.78 0.14 0.07
Matches are distributed among these distances:
169 9 0.01
170 286 0.38
171 305 0.41
172 85 0.11
173 62 0.08
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (170 bp):
ATTTTTGGTTAAAACAGATTATAATTGAATATTTGCCTTGAGAAGCATGAAGAAAAATCCATTCA
TTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGG
TTTTATAATCTCAAAATTGATTTTGAATTGAATTTTTAAC
Done.