Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397844.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1145.0, 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: 8059
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.24
Warning! 2850 characters in sequence are not A, C, G, or T
Found at i:5655 original size:170 final size:171
Alignment explanation
Indices: 5373--5845 Score: 641
Period size: 171 Copynumber: 2.8 Consensus size: 171
5363 AACAGGCTTG
*
5373 AATTGAATGCTTGCCTTAGGAAACGTGTAG-AAATAATCATTCATTT-AGAAGAAAAGTCCATTT
1 AATTGAATGCTTGCCTTAGGAAACATGTAGAAAAT-ATCATTCATTTGA-AAGAAAAGTCCATTT
* * * * *
5436 ATAGTCT-TCCATTCCTTCAAAAGTCTTGTTACTCACTTTAAATGGTTTTATAATCTCATAATTG
64 ATAGTCTCT-CATTCCTTCAAAAGCCTTATCATTCACTTTAAAAGGTTTTATAATCTCATAATTG
* * * *
5500 ATTTTAGGTTAAATG-TTTGAAATCCTTTGTTAAGACAGACTAT
128 ATTTTAGATTAAATGTTTTGAAATCCTTTATTAAGACAAACCAT
* * * * *
5543 AATTGAATTCCTGCCTTAGGAAATATTTAGAAAATACCATTCATTTGAAAGAAAAGTCCATTTAT
1 AATTGAATGCTTGCCTTAGGAAACATGTAGAAAATATCATTCATTTGAAAGAAAAGTCCATTTAT
* * *
5608 AGTCTCTCATTCCTTCAATAGCCTTATCATTCGCTTTAAAAGGTTTTAAAATCTCATAATTGATT
66 AGTCTCTCATTCCTTCAAAAGCCTTATCATTCACTTTAAAAGGTTTTATAATCTCATAATTGATT
* * ** *
5673 TTAGATTAAATGTTTTTATATTTTTTATTAAGATAAACCAT
131 TTAGATTAAATGTTTTGAAATCCTTTATTAAGACAAACCAT
* *
5714 AATTGAATGCTTGCC-TCGAGAAACATGTAGAAAACATCATTCATTTGAAAGAAAAGTCCATTTA
1 AATTGAATGCTTGCCTTAG-GAAACATGTAGAAAATATCATTCATTTGAAAGAAAAGTCCATTTA
*
5778 TAGTCTCTCATTCCTTCAAAAGCCTTATCATTCACTTTAAAAGATTTTATAATCTCATAATTGAT
65 TAGTCTCTCATTCCTTCAAAAGCCTTATCATTCACTTTAAAAGGTTTTATAATCTCATAATTGAT
5843 TTT
130 TTT
5846 TTCACTTTTT
Statistics
Matches: 264, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
170 120 0.45
171 144 0.55
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (171 bp):
AATTGAATGCTTGCCTTAGGAAACATGTAGAAAATATCATTCATTTGAAAGAAAAGTCCATTTAT
AGTCTCTCATTCCTTCAAAAGCCTTATCATTCACTTTAAAAGGTTTTATAATCTCATAATTGATT
TTAGATTAAATGTTTTGAAATCCTTTATTAAGACAAACCAT
Found at i:5969 original size:168 final size:168
Alignment explanation
Indices: 5410--6037 Score: 521
Period size: 171 Copynumber: 3.7 Consensus size: 168
5400 TAGAAATAAT
* * * *
5410 CATTCATTT-AGAAGAAAAGTCCATTTATAGTCT-TCCATTCCTTCAAAAGTCTTGTTACTCACT
1 CATTCATTTGA-AAGAAAAGTCCATTTATAGTCTCT-CATTCCTTCAAAAGCCTTATCATTCACT
* * * * * * *
5473 TTAAATGGTTTTATAATCTCATAATTGATTTTAGGTTAAATG-TTTGAAATCCTTT-GTTAAGAC
64 TTAAAAGATTTTATAATCTCATAATTGATTTTA--TTAAATGTTTTTACAT-TTTTCATTAAGAT
* * * ** * * * ** * *
5536 AGACTATAATTGAATTCCTGCCT-TAGGAAATATTTAGAAAATAC
126 AAACCATAAGTGAA-GGCTTCCTCGA-GAAACATGAAGAAAACAG
* *
5580 CATTCATTTGAAAGAAAAGTCCATTTATAGTCTCTCATTCCTTCAATAGCCTTATCATTCGCTTT
1 CATTCATTTGAAAGAAAAGTCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATCATTCACTTT
* * * *
5645 AAAAGGTTTTAAAATCTCATAATTGATTTTAGATTAAATGTTTTTATATTTTTTATTAAGATAAA
66 AAAAGATTTTATAATCTCATAATTGATTTT--ATTAAATGTTTTTACATTTTTCATTAAGATAAA
* * * *
5710 CCATAATTGAATGCTTGCCTCGAGAAACATGTAGAAAACAT
129 CCATAAGTGAAGGCTT-CCTCGAGAAACATGAAGAAAACAG
5751 CATTCATTTGAAAGAAAAGTCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATCATTCACTTT
1 CATTCATTTGAAAGAAAAGTCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATCATTCACTTT
* * * * *
5816 AAAAGATTTTATAATCTCATAATTGATTTT-TTCACTTTTTTTACATTTTTCATTAA-ATTATAT
66 AAAAGATTTTATAATCTCATAATTGATTTTATTAAATGTTTTTACATTTTTCATTAAGA-TAAAC
* **
5879 TATAAGTGAAGGTCTAT-CTCGAGAAAGGTGAAGAAAA-AGG
130 CATAAGTGAAGG-CT-TCCTCGAGAAACATGAAGAAAACA-G
** * * * *
5919 CATTCATTTCCAAGAAAAGTCGATTTATAGT-TAC-CTATT-TTTCTAAAAGCCTTATTACTCAC
1 CATTCATTTGAAAGAAAAGTCCATTTATAGTCT-CTC-ATTCCTTC-AAAAGCCTTATCATTCAC
5981 TTTAAATA-ATTTTATAATCTCCA-AATTGATTTTAATTTAAAT-TCCTTTTACATTTTT
63 TTTAAA-AGATTTTATAATCT-CATAATTGATTTT-A-TTAAATGT--TTTTACATTTTT
6038 GGAACAAACA
Statistics
Matches: 388, Mismatches: 48, Indels: 42
0.81 0.10 0.09
Matches are distributed among these distances:
167 7 0.02
168 126 0.32
169 5 0.01
170 98 0.25
171 138 0.36
172 14 0.04
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (168 bp):
CATTCATTTGAAAGAAAAGTCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATCATTCACTTT
AAAAGATTTTATAATCTCATAATTGATTTTATTAAATGTTTTTACATTTTTCATTAAGATAAACC
ATAAGTGAAGGCTTCCTCGAGAAACATGAAGAAAACAG
Found at i:6581 original size:170 final size:172
Alignment explanation
Indices: 6267--6773 Score: 494
Period size: 170 Copynumber: 3.0 Consensus size: 172
6257 NNNNNNNNNN
* * * * *
6267 TATAATCTCCAAATTGATTTTAATTTGAA-TTCCTTTTACA-TTTTGGTTAAAACATATTATAAT
1 TATAATCTCAAAATTGATATTAAGTTGAAGTT--TTTTACATTTTTAGTTAAAACAGATTATAAT
* ** ** * * * * * *
6330 TGAAT-GCTTGTCTTGAGAAACTTATAGAATAAGCCATTCATTTGG--ATAAAAAGTCCATTTAT
64 TGAATATC-TACCTCAAGAAACATAAAAAAAAAGACATTCA-TTGGCAAAAAAAAGTCCATTTAT
* **
6392 AGT-ATCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTC
127 AGTCA-CTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATACTTC
* * * * *
6438 TCTAATCTCATAATTGATATTAGGTTGAAGTTTTTTACATTTTTAG-TAAGAGCATATTATAATT
1 TATAATCTCAAAATTGATATTAAGTTGAAGTTTTTTACATTTTTAGTTAA-AACAGATTATAATT
* * * * ** *
6502 GAATATCTACCTTAGGAAACAT-GAAGAAAAGGTATTCATAT-G-TAAAAAAAGTCCATTTATAG
65 GAATATCTACCTCAAGAAACATAAAAAAAAAGACATTCAT-TGGCAAAAAAAAGTCCATTTATAG
* *
6564 TCACTCATTCATTCAAAAGCCTTATTACTCACTTTAAATACTTT
129 TCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATACTTC
* * * *
6608 TATAATCTCAAAATTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACGGATTATAATTG
1 TATAATCTCAAAATTGATATTAAGTTGAAGTTTTTTACATTTTTAGTTAAAACAGATTATAATTG
* *
6673 AATGTTTACCTCAAGAAACATAAAAAAAAAGACATTCATTGGCAAAAAAAAGTCCATTTATAGTC
66 AATATCTACCTCAAGAAACATAAAAAAAAAGACATTCATTGGCAAAAAAAAGTCCATTTATAGTC
* * * *
6738 ACTCATACCTTTAAAAGCTTTATTACCCACTTTAAA
131 ACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAA
6774 NNNNNNNNNN
Statistics
Matches: 276, Mismatches: 49, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
169 2 0.01
170 146 0.53
171 73 0.26
172 55 0.20
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (172 bp):
TATAATCTCAAAATTGATATTAAGTTGAAGTTTTTTACATTTTTAGTTAAAACAGATTATAATTG
AATATCTACCTCAAGAAACATAAAAAAAAAGACATTCATTGGCAAAAAAAAGTCCATTTATAGTC
ACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATACTTC
Done.