Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402299.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5381.0, 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: 2332
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.26
Warning! 741 characters in sequence are not A, C, G, or T
Found at i:733 original size:171 final size:161
Alignment explanation
Indices: 540--855 Score: 307
Period size: 172 Copynumber: 1.9 Consensus size: 161
530 TTTTTTTATA
** * * * *
540 ATTTTTGTTAAAAAAAACTATAATTAAATATCTACCTTGAGAAATATGAAGAAACAAG-CATTCA
1 ATTTTTGTTAAAAAAAACTATAATTAAATATCTACCTCAACAAACATGAAAAAACAAGAAATTCA
* *
604 TTAGGAAGAAAAC-TCTATTTACAGTCACCCATTCCT-TCAAAAAGCTTATTAC-CAGCTTTAAA
66 TTAAGAAGAAAACTTC-ATTCACAGTCACCCATT-CTGTCAAAAAGCTTATTACTC-GCTTTAAA
666 TAGTTTTATAATCTCATAATTGATTTTANNNNNNNNNNTTTTAC
128 TAGTTTTATAATCTCATAATTGATTTTA----------TTTTAC
* * * * *
710 ATTTTTGATTAAAACATACTATAATTGAATGTCTACCTCAACAAACATGAAAAAACCAGAAATTC
1 ATTTTTG-TTAAAAAAAACTATAATTAAATATCTACCTCAACAAACATGAAAAAACAAGAAATTC
* * * * * *
775 ATTAATAAGAAAAGTTCATTCAGAGTCACCCATTCTGTCAAAAGGTTTATTACTCGTTTTAAATA
65 ATTAAGAAGAAAACTTCATTCACAGTCACCCATTCTGTCAAAAAGCTTATTACTCGCTTTAAATA
840 GTTTTATAATCTCATA
130 GTTTTATAATCTCATA
856 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
170 7 0.06
171 43 0.35
172 69 0.57
173 3 0.02
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.34
Consensus pattern (161 bp):
ATTTTTGTTAAAAAAAACTATAATTAAATATCTACCTCAACAAACATGAAAAAACAAGAAATTCA
TTAAGAAGAAAACTTCATTCACAGTCACCCATTCTGTCAAAAAGCTTATTACTCGCTTTAAATAG
TTTTATAATCTCATAATTGATTTTATTTTAC
Found at i:1059 original size:171 final size:168
Alignment explanation
Indices: 127--1110 Score: 554
Period size: 171 Copynumber: 5.8 Consensus size: 168
117 NNNNNNNNNN
* * * *
127 TTCAAAAGGCTTATTACCCGCTTTTAATG-GTTTTATAATTTCATAATTGATTTTTAGTTGAATT
1 TTCAAAA-GCTTATTACTCGC-TTTAAAGAGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * * ** * * * * *
191 CTTTTGTACTTTTTGTTAAAA-AAGGCTATAATTGAATACCTGCTTTG-GAAAACATGCATAAA-
64 TTTTTATATTTTTTATTAAAACAA--CTATAATTGAATGTCTACCTCGAG-AAACATGAAAAAAC
* * * * *
253 AAGCTTATTCATTGAGAACAAAAGTTCATTAATAGTCACCCATTCC
126 AAGC--ATTCATT-ATAAGAAAAGTTCATTTAGAGTCACCCATTCT
* ********** *
299 TTCAAAAGCCTTATTACTCG-TCTT-AAGTGGTTTNNNNNNNNNNTAATTGATTTTAAGTTAAAT
1 TTCAAAAG-CTTATTACTCGCT-TTAAAG-AGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
* *** * * ** *
362 TTTTTTACATTTTTGGCTAAAACAGACTTTAATTAAATGTCTATATCGAGAAATATG--AAAA-A
63 TTTTTTATATTTTTTATTAAAACA-ACTATAATTGAATGTCTACCTCGAGAAACATGAAAAAACA
* * * ******
424 AGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACCNNNNNNN
127 AG-CATTCATT-ATAAGAAAAGTTCATTTAGAGTCACC-CATTCT
*** * * *
469 NNNAAAAGCTTATTACTTGCTTTAAACG-GTTTTAAAATCTCATAATTGATTTTGAGTTGAATTT
1 TTCAAAAGCTTATTACTCGCTTTAAA-GAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTT
* * * * * * * *
533 TTTTATAATTTTTGTTAAAAAAAACTATAATTAAATATCTACCTTGAGAAATATGAAGAAACAAG
65 TTTTATATTTTTTATT-AAAACAACTATAATTGAATGTCTACCTCGAGAAACATGAAAAAACAAG
* * * *
598 CATTCATTAGGAAGAAAA-CTCTATTTACAGTCACCCATTCC
129 CATTCATTA-TAAGAAAAGTTC-ATTTAGAGTCACCCATTCT
* *********
639 TTCAAAAAGCTTATTAC-CAGCTTTAAATAGTTTTATAATCTCATAATTGATTTTANNNNNNNNN
1 TTC-AAAAGCTTATTACTC-GCTTTAAAGAGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * * * *
703 NTTTTACATTTTTGATTAAAACATACTATAATTGAATGTCTACCTCAACAAACATGAAAAAACCA
64 TTTTTATATTTTTTATTAAAACA-ACTATAATTGAATGTCTACCTCGAGAAACATGAAAAAACAA
* *
768 GAAATTCATTAATAAGAAAAGTTCATTCAGAGTCACCCATTCT
128 G-CATTCATT-ATAAGAAAAGTTCATTTAGAGTCACCCATTCT
* * * * ********** *
811 GTCAAAAGGTTTATTACTCGTTTTAAATAGTTTTATAATCTCATANNNNNNNNNNAGCTGAATTT
1 TTCAAAA-GCTTATTACTCGCTTTAAAGAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTT
* * * * * * *
876 TTTTAAATTTTTTATTAAAACAGACTATAATTGATTGTCTACTTTGAGAAACGTCAAGAAACAAG
65 TTTTATATTTTTTATTAAAACA-ACTATAATTGAATGTCTACCTCGAGAAACATGAAAAAACAAG
*
941 CATTCATTGATAAGAAAAGTTCATTTAGAGTCACCCATTTT
129 CATTCATT-ATAAGAAAAGTTCATTTAGAGTCACCCATTCT
* * * *
982 TTCAACAAGCTTATTACTCGCTTTAGACGA-TTTTATAATCTAATACTTGATTTTAAGTTGAATG
1 TTCAA-AAGCTTATTACTCGCTTTA-AAGAGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * *
1046 TTTTTATATTTTTTGTTAAAACAAGCCATAATTGAATGTTTACCTCGAGAAACGTGAAAAAACAA
64 TTTTTATATTTTTTATTAAAACAA-CTATAATTGAATGTCTACCTCGAGAAACATGAAAAAACAA
1111 CTATNNNNNN
Statistics
Matches: 605, Mismatches: 177, Indels: 61
0.72 0.21 0.07
Matches are distributed among these distances:
169 106 0.18
170 30 0.05
171 262 0.43
172 200 0.33
173 6 0.01
174 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.36
Consensus pattern (168 bp):
TTCAAAAGCTTATTACTCGCTTTAAAGAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTT
TTTATATTTTTTATTAAAACAACTATAATTGAATGTCTACCTCGAGAAACATGAAAAAACAAGCA
TTCATTATAAGAAAAGTTCATTTAGAGTCACCCATTCT
Done.