Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398600.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1890.0, 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: 2012
ACGTcount: A:0.22, C:0.09, G:0.08, T:0.25
Warning! 700 characters in sequence are not A, C, G, or T
Found at i:367 original size:170 final size:170
Alignment explanation
Indices: 20--597 Score: 524
Period size: 170 Copynumber: 3.4 Consensus size: 170
10 AGAAAAGTCC
* * * *
20 ATTTATAGTCACCCAAGCCTTT-AGAAGCCTTCTTACTCGCTTTAAATAATTTTATAATCTCATA
1 ATTTATAGTCACTCAAGCCTTTGA-AAGCTTTATTACTCGCTTTAAATAGTTTTATAATCTCATA
* * * * * *
84 ATTGATTTTGAA-TTGAATTTTTTTATATTTTTAATTAAAACATATTATAATTGAATGTCTATCT
65 ATTGATTTT-AAGTTGAAATTCTTGATATTTTTAACTAAAACATATTATAATTGAATGTATACCT
* * * *
148 CAAGAAAGGTGAAACAAAAGTCATCCGTTGACAAGAAAGTTT
129 CAAGAAACGTGAAACAAAAGCCATCCATTGACAAGAAACTTT
* * * * *
190 GTTTATAGTCACTCAACCCTTTGAAAGCTTTGTTGCTCGCTTTAAATAGTTTTATAATCTCCTAA
1 ATTTATAGTCACTCAAGCCTTTGAAAGCTTTATTACTCGCTTTAAATAGTTTTATAATCTCATAA
* * * * *
255 TCGATTTTAAGTT-AAATTCTTGATATTTTTACCTAAAATATATTATAATTGAATGTATGCCTTA
66 TTGATTTTAAGTTGAAATTCTTGATATTTTTAACTAAAACATATTATAATTGAATGTATACCTCA
* ** *
319 AGAAACGTGTAACAAAAGCCATCCATTGGTATGAAAACTTT
131 AGAAACGTGAAACAAAAGCCATCCATTGACAAG-AAACTTT
* * * * *
360 ATTTATAGTCACTCAAGCCTTCGAAAGCTTTATAACTTGCTTTAAATGGATTTATAATCTCATAA
1 ATTTATAGTCACTCAAGCCTTTGAAAGCTTTATTACTCGCTTTAAATAGTTTTATAATCTCATAA
* *** * * *
425 TTGATTTTAAGTTGAAA-TCAT-ATATGGTTTTGGTTGAAACAGATTATAATTGAATGTCTATCC
66 TTGATTTTAAGTTGAAATTCTTGATAT--TTTTAACTAAAACATATTATAATTGAATGTATA-CC
* * * * * **
488 T--AGGAACTATGAAGA-AAAAGCCATTCAATGACAAGAAAAGTCC
128 TCAAGAAAC-GTGAA-ACAAAAGCCATCCATTGACAAG-AAACTTT
* * * ** * * *
531 ATTTATAGTTACCCAAGTCTTCAAAAGCCTCATTACTCGCTTTAAATGGTTTTATAATCTCATAA
1 ATTTATAGTCACTCAAGCCTTTGAAAGCTTTATTACTCGCTTTAAATAGTTTTATAATCTCATAA
596 TT
66 TT
598 NNNNNNNNNN
Statistics
Matches: 332, Mismatches: 67, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
169 73 0.22
170 145 0.44
171 110 0.33
172 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (170 bp):
ATTTATAGTCACTCAAGCCTTTGAAAGCTTTATTACTCGCTTTAAATAGTTTTATAATCTCATAA
TTGATTTTAAGTTGAAATTCTTGATATTTTTAACTAAAACATATTATAATTGAATGTATACCTCA
AGAAACGTGAAACAAAAGCCATCCATTGACAAGAAACTTT
Found at i:1052 original size:170 final size:170
Alignment explanation
Indices: 763--1108 Score: 398
Period size: 170 Copynumber: 2.0 Consensus size: 170
753 NNNNNNNNNN
* * * *
763 TTAAGTTGAATTTTTTTATATTTTTAGTTAAAACATATTATAATTGAATGTTTATCTCAAGAAAG
1 TTAAGTTGAATTTTTTAATATTTTTAGTTAAAACATATTATAATTGAATATATACCTCAAGAAAG
* * * *
828 GTGAGAGAAAAGCCATCCGTTGACAAGAAAGTCTATTTATAGTCACTCAAGCCTTTGAACGCTTT
66 GTGAGAGAAAAGCCATCCATTGACAAGAAACTCTATTTATAGTCACTCAAGCCTTTGAAAGCCTT
* * * * *
893 GTTGCTCGCTTTTAAT-AGTTTTATAATCTCGTAATTGATT
131 ATTACTCGCTTTAAATGA-ATTTATAATCTCATAATTGATT
* *
933 TTAAGTTGAA-TTTTTAATATTTTT-GCTTAAAATATATTATAATTGAATATATACCT-TAGCAA
1 TTAAGTTGAATTTTTTAATATTTTTAG-TTAAAACATATTATAATTGAATATATACCTCAAG-AA
* * * * * *
995 ATGTGTA-ACGAAAA-CCATCCATTGGCATGAAAACTTTATTTATGGTCACTTAAGCCTTTGAAA
64 AGGTG-AGA-GAAAAGCCATCCATTGACAAG-AAACTCTATTTATAGTCACTCAAGCCTTTGAAA
*
1058 GCCTTATTACTTGCTTTAAATGAATTTATAATCTCATAATTGATT
126 GCCTTATTACTCGCTTTAAATGAATTTATAATCTCATAATTGATT
1103 TTAAGT
1 TTAAGT
1109 NNNNNNNNNN
Statistics
Matches: 148, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
168 3 0.02
169 58 0.39
170 86 0.58
171 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (170 bp):
TTAAGTTGAATTTTTTAATATTTTTAGTTAAAACATATTATAATTGAATATATACCTCAAGAAAG
GTGAGAGAAAAGCCATCCATTGACAAGAAACTCTATTTATAGTCACTCAAGCCTTTGAAAGCCTT
ATTACTCGCTTTAAATGAATTTATAATCTCATAATTGATT
Done.