Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397492.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_655.0, 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: 12644
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.21
Warning! 5461 characters in sequence are not A, C, G, or T
Found at i:5723 original size:169 final size:169
Alignment explanation
Indices: 5546--5987 Score: 426
Period size: 170 Copynumber: 2.6 Consensus size: 169
5536 NNNNNNNNNN
* * *
5546 CATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTTTAATATCATAATTAGTATTAAGTT
1 CATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTTTAATCTCATAATT-GTTTTAAGTT
* *
5611 -AATTTTTTATATTTGTTATTAAAACAGATTATAATTGAACGTCCGCCTT-AGGAAACATGAAGA
65 AAATTTTTTATATTTGTTATTAAAACAGATTATAATTGAACGTCCACCTTGA-GAAACATAAAGA
**********
5674 AAAAGATATCCACTNNNNNNNNNNGTCCATTTGTACTC-AC
129 AAAAGATATCCACTAGCAGAAAAGGTCCATTTGTACTCAAC
* * * *
5714 CTATGCCTTCGAAAGCCTCACTACTCAG-TTTAAATAGTTTTGTAATCTCGTAATTGATTTTAAG
1 C-ATGCCTTCGAAAGCCTTATTACTC-GCTTTAAATAGTTTTTTAATCTCATAATTG-TTTTAAG
********* * * * *
5778 TTAAATTNNNNNNNNNNT-TTATTAAAACATATTACAATTGAATGTCTACCTTGAGAAACATAAA
63 TTAAATT-TTTTATATTTGTTATTAAAACAGATTATAATTGAACGTCCACCTTGAGAAACATAAA
* *
5842 GAAAAAGATATCCATTAGCAGAAAAGGTCCATTTGTAGTCAAC
127 GAAAAAGATATCCACTAGCAGAAAAGGTCCATTTGTACTCAAC
* * * *
5885 CATGTCTTCGAAAGCCGTATTACTCACTTTAAATAGTTTTTTAATCTCATAATTGGTTTTCAGTT
1 CATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTTTAATCTCATAATT-GTTTTAAGTT
*
5950 AAACTTTTTTATATTTGTTATTAATACAGATTATAATT
65 AAA-TTTTTTATATTTGTTATTAAAACAGATTATAATT
5988 AAATATCTTC
Statistics
Matches: 209, Mismatches: 54, Indels: 19
0.74 0.19 0.07
Matches are distributed among these distances:
168 2 0.01
169 53 0.25
170 128 0.61
171 26 0.12
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.37
Consensus pattern (169 bp):
CATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTTTAATCTCATAATTGTTTTAAGTTA
AATTTTTTATATTTGTTATTAAAACAGATTATAATTGAACGTCCACCTTGAGAAACATAAAGAAA
AAGATATCCACTAGCAGAAAAGGTCCATTTGTACTCAAC
Found at i:10749 original size:171 final size:170
Alignment explanation
Indices: 10308--11447 Score: 771
Period size: 171 Copynumber: 6.7 Consensus size: 170
10298 NNNNNNNNNN
* * * * * * * * *
10308 TAAAACAGATTATAATTGAACGTCT-ACCTTAAAAAATATAAAGAAAATGATATCAATTGACAAT
1 TAAAACAGATTATAATTGAATGTCTGACCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAG
* * **********
10372 AAAACTCCATTTATAGTCACCCATACCTTCGAAAGCCTTATTACTCGNNNNNNNNNNTTTTATAA
66 AAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAA
*
10437 CCTCATAATT-GATTTTAAGTTGAATTTTTTTTATAATTTTTAT
131 TCTCATAATTAG-TTTTAAGTTGAA--TTTTTTAT-ATTTTTAT
* * * * ********** *
10480 TAAAACAGATTGTAACTAAATGTCT-ACCTCAAGAAACGTGAAGNNNNNNNNNNCCATTGGCAAA
1 TAAAACAGATTATAATTGAATGTCTGACCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAG
* * * * * *
10544 AAAAATCCATTTACAGTCACCCATGCTTTCGAAAGCCTTATTACTCGCTTTAGATGCTTTTTTAA
66 AAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAA
* * *
10609 TCTTATAATTAGTTTTAAGTTGAAATTTTTTACATTTTTTAC
131 TCTCATAATTAGTTTTAAGTTG-AATTTTTTATA-TTTTTAT
* * * * *
10651 TGAAACAGATTATGATTGAATGT-TGACCTCTAGAGACATGAAGAAAAAGATATCCGTTGGCAAG
1 TAAAACAGATTATAATTGAATGTCTGACCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAG
* * * * *
10715 AGAAGTCCATTTATTGTCACTCATG-CTGTCGAAAGCTTTATGACTCGCTTTAAATGATTTTATA
66 AAAAGTCCATTTATAGTCACCCATGCCT-TCGAAAGCCTTATTACTCGCTTTAAATGATTTTATA
* * *************
10779 ACCTCATAATTGGTTTTAAGTTGAATTNNNNNNNNNNNNNNNT
130 ATCTCATAATTAGTTTTAAGTTGAATT--TTTTATATTTTTAT
* * * * **
10822 TAAAATAAATTATAATTGAATGTCT-ATCTCAAGAAACGTGAAGAAAAAGATATAAATTGGCAAG
1 TAAAACAGATTATAATTGAATGTCTGACCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAG
* * * * * *
10886 AAAAGTCCATTTATAATCATCCATGCCTTCGAAAG-ATTATTACTCGTTTATTTAAATGCTTTTT
66 AAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCG---CTTTAAATGATTTTA
*
10950 TAATCTCATCATTAGTTTTAAGTTGAACTTTTTTATATTTTTAT
128 TAATCTCATAATTAGTTTTAAGTTGAA-TTTTTTATATTTTTAT
* * ** ** **
10994 TAAAACAGATTATAATTGAATGTCTG-CCTCAAAAAACATAAAGAAAGTGATATCTGTTGGGGAG
1 TAAAACAGATTATAATTGAATGTCTGACCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAG
* * * * * *
11058 AGAAGTCCATTTATAATCACCCATGCCTT-TAGAAGCCTTACTACTTGATTTAAATGATTTTATA
66 AAAAGTCCATTTATAGTCACCCATGCCTTCGA-AAGCCTTATTACTCGCTTTAAATGATTTTATA
*
11122 ATCTCATAATT-GATTTTAATTTGAATTTTTTATAATTTTTAT
130 ATCTCATAATTAG-TTTTAAGTTGAATTTTTTAT-ATTTTTAT
* ** * *
11164 TAAAACAGA-TATAATTGAATGT-TTACCTCGTGAAACGTGAA-AAAAATTATATCCATTAGG-A
1 TAAAACAGATTATAATTGAATGTCTGACCTCAAGAAACATGAAGAAAAA-GATATCCATT-GGCA
** * **
11225 AGAAAAGTATATTTATAGTCACCCATGCCTTAGAAAGCCTTATTACTCGCTTTAAATGATTTTNN
64 AGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTAT
**************** * *
11290 NNNNNNNNNNNNNNNNTTAATTTGAATTTTTTTATTTTTTTAT
129 AATCTCATAATTAGTTTTAAGTTGAA-TTTTTTATATTTTTAT
* * * * * *
11333 TAAAACAGATTATAATTGAATGTCT-ACCTTAAAAAACATAAAGAAAATGATATTCATTGGTAAG
1 TAAAACAGATTATAATTGAATGTCTGACCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAG
* * * *
11397 AGAAGTCCATTTATTGTCACCTATGCCTTCGAAAGCCTTATGACTCGCTTT
66 AAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTT
11448 NNNNNNNNNN
Statistics
Matches: 737, Mismatches: 203, Indels: 58
0.74 0.20 0.06
Matches are distributed among these distances:
168 4 0.01
169 121 0.16
170 159 0.22
171 210 0.28
172 194 0.26
173 47 0.06
174 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.36
Consensus pattern (170 bp):
TAAAACAGATTATAATTGAATGTCTGACCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAG
AAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAA
TCTCATAATTAGTTTTAAGTTGAATTTTTTATATTTTTAT
Done.