Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397668.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4207.0, 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: 1785
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:991 original size:174 final size:169
Alignment explanation
Indices: 1--1782 Score: 1040
Period size: 171 Copynumber: 10.4 Consensus size: 169
* * * * * * * *
1 ACTTTTGTTGCCAGTGAATTCCTTTTTCTTCATGTTT-TTCAAGGTAAACATTCAAATATAATAT
1 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTT-GAGGCAAACATTTAATTATAATCT
* * **********
65 GTTTTAACCAAAAATGTAAAAAAATTAAACTTAAAATCAATTTTNNNNNNNNNNAACCATTTAAA
65 GTTTTAA-CAAAAATATAAAAAAA-TAAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
*
130 GCGAGTAATAAGGCTTTTAAAGGAATGGGTGA-TGATAAATAG
128 GCGAGTAATAAGGCTTTTGAAGGAATGGGTGACT-ATAAATAG
* * * ** * ** ** * **
172 ACTTTGCTTACCATTGAATGTGTTTTTCTTCACGTTTCTCAAGATAAACATTCAATTATTGTCTG
1 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCAAACATTTAATTATAATCTG
* * ********* * *
237 -TTTGACTAAAAATGTANNNNNNNNNNACTTAAAATCAATTATGAGATTATAAAATCAATTAAAG
66 TTTTAAC-AAAAATATA-AAAAAATAAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * *
301 TGAGTAATAAGGCTTTTGATGGAATGGGTAACTATAAATTG
129 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* * * * * * * * * * *
342 A-TTTTCTTACTTAATGAATGGC-TTTTCTACACGTTTCCTAAAGCAAATATTCAATTATAGTCT
1 ACTTTTCTTGC-CAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCAAACATTTAATTATAATCT
* * *
405 GTTTTAAAAAAATATATAAAAAAATTCAAA-TTATAATCAATTATGAGATTACAAAACCATTTAA
65 GTTTTAACAAAA-ATATAAAAAAA-T-AAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * * *
469 AGAGACTACTAAGGCTTTTGAAGGAATTGGTGACTACAAATAG
127 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* * * * * *
512 ACTTTTTTTTGCAAATGAATGACTTGTTCTTCATGTTTCTTGAGGTAGAC-TTTCAATTATAATC
1 AC-TTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCAAACATTT-AATTATAATC
* * ** * *
576 TGTTTTAAC-CAAGTA-AAAACATCTCAACTTAAAATCAATAATAGTGATAGATTAGTAAAATCA
64 TGTTTTAACAAAAATATAAAA-AAATAAACTTAAAATCAAT--TA-TG--AGATTA-TAAAACCA
* * * * * *
639 TTTAAAG-GGGCGAGTAA----TTTAAAGAAATGGGTGACTATAAATGG
122 TTTAAAGCGAG-TAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* * * * * ** * * * * *
683 ACTTTTCTTGTCAATGAATGGCTTTTTGTACATTTTTCCCGATG-TACCATTCAATTATAGTCTG
1 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCAAACATTTAATTATAATCTG
* *
747 TTTTAACAAAAA-ATATAAAAA-AAACTTAAAATCCATTATGAGATTATAAAACC-TTTCAAAGC
66 TTTTAACAAAAATATAAAAAAATAAACTTAAAATCAATTATGAGATTATAAAACCATTT-AAAGC
* *
809 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTGTAAATAG
130 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* * * * *
849 ACTTTTATTACCAATCAATGCCTTTTTCTTCATATTTCTTGAGGCAAACATTTAATTATAATATG
1 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCAAACATTTAATTATAATCTG
* * *
914 TTTTAACTAAAAATGTAAAAAAAAACTAGAACTTAAAATCAATTTTGAGAATATAAAACCATTTA
66 TTTTAAC-AAAAA--TATAAAAAAA-TA-AACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * *
979 AAGTGTGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGG
126 AAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* * * * * **
1023 ACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTTGAGGTAGACATTTAGTTATGCTCTG
1 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCAAACATTTAATTATAATCTG
* * * **
1088 TTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATTATGGGACTATAAAATAATTTAAAG
66 TTTTAA-CAAAAATATAAAAAAA-TAAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
*********** *
1153 CGAGTAATAAGGCTTTTGAAGGNNNNNNNNNNAATAAATGG
129 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* * ** * * * * *
1194 ACTATTCTTGCCAATGAATTCCTTTTTCTTCATGTTTCTCAATGTAGACA-TCAATTATAATATG
1 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCAAACATTTAATTATAATCTG
********* * * * * * *
1258 TTTTAACCAANNNNNNNNNNCAAATTGAACTTAAAATCAATTTTGTGGTTATAAAACTATTTAAA
66 TTTTAA-CAA--AAATATAAAAAAATAAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
** * * * * *
1323 TAGAGTAATAATGCTTTTGAAAGAATGAGAGACTATAAATAA
128 GCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* * * * * ** * * * * *
1365 ACTTTTCTTGCTAATTAATGCTTTTTTCTTCACGTTTTTTGAGATAGACATTCAATTTTAGTCTA
1 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCAAACATTTAATTATAATCTG
* * *
1430 TTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATTCCATTAATGAGATTGATATGAAA-CATT
66 TTTTAAC-AAAAATATAAAAAAA-TAAACTTAAAA-TCAATT-ATGAGATT-ATA--AAACCATT
* *
1494 T-AAGCGAGTAATCAAAGGCTTTTGAAGGAATGGGTAACTATAAATGG
124 TAAAGCGAGTAAT--AAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* ** * * **
1541 ACTTTTCTTGCCAATAAATGTTTTTTTCTTCATGTTTCATG-GG-ATAGAC-TTCAATTATTGTC
1 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCA-A-ACATTTAATTATAATC
* * * *
1603 TGTTTTAACAAAAAATGTAAAAATAATAAACTTATAATCAATTATGAGATTACAAAACCATTGAA
64 TGTTTTAAC-AAAAATATAAAAA-AATAAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* ** ** * *
1668 AGCGAGTAATAAGGGTTTTGAAAAAATAAGTGACTAAAAATGG
127 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* * * * * ** * *
1711 ACTTTTTTTGCTAGTAAATGCCTTTTTCTTCACGTTT-TCCAAGGTAAACATTCAATTATAATCT
1 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCT-TGAGGCAAACATTTAATTATAATCT
1775 GTTTTAAC
65 GTTTTAAC
1783 TAA
Statistics
Matches: 1223, Mismatches: 326, Indels: 124
0.73 0.19 0.07
Matches are distributed among these distances:
161 3 0.00
162 14 0.01
163 8 0.01
165 2 0.00
166 57 0.05
167 22 0.02
168 20 0.02
169 83 0.07
170 279 0.23
171 337 0.28
172 94 0.08
173 14 0.01
174 155 0.13
175 67 0.05
176 68 0.06
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Consensus pattern (169 bp):
ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGCAAACATTTAATTATAATCTG
TTTTAACAAAAATATAAAAAAATAAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
AGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
Done.