Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398284.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1588.0, 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, 908
Length: 1514
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.35
Warning! 87 characters in sequence are not A, C, G, or T
Found at i:701 original size:170 final size:171
Alignment explanation
Indices: 263--1148 Score: 989
Period size: 171 Copynumber: 5.2 Consensus size: 171
253 NNNNNNNNNN
* * * * **
263 TTTAGTTAAAACAGATTGTAATTAAATGTTTTCCTTGAGAAACATGTAGAAAAATACATTCATTG
1 TTTAGTTAAAACAGATTATAATTGAATGTTTGCCTTGAGAAACATGAAGAAAAACCCATTCATTG
* * *
328 GCTAGAAAAGCCCATTTATAGTCACCTAAGCCTTCAAAAGCCTTATTACTCTCTGTAACTAGTTT
66 GCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTGTAAATAGTTT
*
393 TATAATCTCATAATTGATTTGAAATTGAATTATTTTATATT
131 TATAATCTCATAATTGATTTGAAGTTGAATTATTTTATATT
* **
434 TTTGGTTAACTCAGATTATAATTGAATGTTTGCCTTGAGAAGTACA--AAGAAAAACCCATTCAT
1 TTTAGTTAAAACAGATTATAATTGAATGTTTGCCTTGAGAA--ACATGAAGAAAAACCCATTCAT
* * * * *
497 TGGTAAGAAAAGCTCATTTATAGCCACCCAAGCCTTCAAAAGACTTATTAGTCTCTGTAAAT-GA
64 TGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTGTAAATAG-
* * *
561 TTTTATAGTCTTATAGTTGATTTGAAGTTGAATTATTTTATA-T
128 TTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTATATT
* * * * * * *
604 TTTGGTTAACACAGAATATAATTGATTGTTTGCCTTGAGAAGCATGAGGAAAAACCCATTCACTG
1 TTTAGTTAAAACAGATTATAATTGAATGTTTGCCTTGAGAAACATGAAGAAAAACCCATTCATTG
* * * * *
669 GCAAGAAAAGCCCCTGTATAGTCACACAAGCCTTCAAAAGCCTAATATTACTCCCTTTAAATAGT
66 GCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCT--TATTACTCTCTGTAAATAGT
* * * * * *
734 TTTATAATCTCATAATTTATTTTAAGATGATTTTTTTTCTATT
129 TTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTATATT
* * *
777 TTTAGTCAAAACAGATTATAATTGAATGTTTGCCTTTG-GAAACATGAAG-AAAACACATTTATT
1 TTTAGTTAAAACAGATTATAATTGAATGTTTGCC-TTGAGAAACATGAAGAAAAACCCATTCATT
* * *
840 GGCAAGAAAAGGCCATTTATAGTCACTCAAACCTTCAAAAGCCTTATTACTCTCCT-TAAATAGT
65 GGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCT-CTGTAAATAGT
* * * *
904 TTTATAACCTCAAAATTGATTTTAAGTTGAATTTTTTTATATT
129 TTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTATATT
* * * * * * * *
947 TTTATTTAAAACATATTAGAATTGAATGTTTTCCATGGGAAACTTGAGGAAAAACCCATTCATTG
1 TTTAGTTAAAACAGATTATAATTGAATGTTTGCCTTGAGAAACATGAAGAAAAACCCATTCATTG
* *** * * * * *
1012 GCAACAAAAGAGTATTTATAGTCACCCAAGCCTTCAAAAACCTAATTACTCTTTTTAAATGGTTT
66 GCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTGTAAATAGTTT
* * *
1077 TATAATCTCATAATTGATTCT-AAGTTAAATTGTTTTGTATT
131 TATAATCTCATAATTGATT-TGAAGTTGAATTATTTTATATT
* *
1118 TTTCA-TCAAAATAGATTATAATTGAATGTTT
1 TTT-AGTTAAAACAGATTATAATTGAATGTTT
1149 ATGTTTGGAA
Statistics
Matches: 602, Mismatches: 97, Indels: 32
0.82 0.13 0.04
Matches are distributed among these distances:
168 2 0.00
169 2 0.00
170 185 0.31
171 268 0.45
172 99 0.16
173 43 0.07
174 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (171 bp):
TTTAGTTAAAACAGATTATAATTGAATGTTTGCCTTGAGAAACATGAAGAAAAACCCATTCATTG
GCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTGTAAATAGTTT
TATAATCTCATAATTGATTTGAAGTTGAATTATTTTATATT
Found at i:1488 original size:172 final size:168
Alignment explanation
Indices: 1164--1514 Score: 526
Period size: 172 Copynumber: 2.1 Consensus size: 168
1154 TGGAAACATA
* *
1164 AAGAAAAGCACATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCCGTAAATGATTTTT
1 AAGAAAA-CCCATTTATAGTCACCCAAGCCTTCAAAAGCATTATTACTCTCCGTAAATGATTTTT
* * * *
1229 AATCTTATAATTTATTTCAAGTTGGATTATTTACTTTTTTGGTTAACAATGATTATAATTGAATG
65 AATCTTATAATTGATTTAAAGTTGAATTATTTACTTTTTTGGTTAACAATGATTATAATAGAATG
*
1294 TTTGGCTAGAGAAGCATGAAGAAAAACCCATTCATTGGC
130 TTTGCCTAGAGAAGCATGAAGAAAAACCCATTCATTGGC
** *
1333 AAGACAAACCCATTTATAGTCACCCAAGCCTTCAAAAGCATTATTACTCTTTGTAAATGGTTTTA
1 AAGA-AAACCCATTTATAGTCACCCAAGCCTTCAAAAGCATTATTACTCTCCGTAAATGATTTT-
1398 TAATCTTATAATTGATTTAAAGTTGAATTATTTTACATTTTTTGGTTAAC-ATGGATTATAATAG
64 TAATCTTATAATTGATTTAAAGTTGAATTA-TTTAC-TTTTTTGGTTAACAAT-GATTATAATAG
*
1462 AATGTTTGCCTCA-AGAAGCATGAAGAAAAACCCATTCATTTGC
126 AATGTTTGCCT-AGAGAAGCATGAAGAAAAACCCATTCATTGGC
1505 AAGAAAACCC
1 AAGAAAACCC
Statistics
Matches: 165, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
169 55 0.33
170 30 0.18
171 13 0.08
172 66 0.40
173 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (168 bp):
AAGAAAACCCATTTATAGTCACCCAAGCCTTCAAAAGCATTATTACTCTCCGTAAATGATTTTTA
ATCTTATAATTGATTTAAAGTTGAATTATTTACTTTTTTGGTTAACAATGATTATAATAGAATGT
TTGCCTAGAGAAGCATGAAGAAAAACCCATTCATTGGC
Done.