Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401205.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4354.0, 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: 2174
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:866 original size:170 final size:161
Alignment explanation
Indices: 649--1038 Score: 311
Period size: 170 Copynumber: 2.3 Consensus size: 161
639 GAGTAATGAG
* * ** **
649 GCTTTTGAAGGAATGGGTGACTATAACTGGACTTTTCTTCTCAATGAATGGTATTTTCTATATGT
1 GCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATAATATTTTCTATA-CA
* * ** *
714 TTCCT-TAGGTAGACATTTAATTATTGTCTATTTTATTGAA-AAATGTAAAAAAATGCAACATAA
65 TTCCTCTAAGTAGACATTCAATTATTGTCTATTTTA-ACAAGAAATATAAAAAAATGCAACATAA
* *
777 AATC-ATTATGAGATTATAAAACCATTTAAAGT
129 AATCAACTATGAGATCATAAAACCATTTAAAGT
* * *
809 GNNNNNNNNNNCTTTTGAAGGAATATGTGACTATAAATGGGCTTTTCTTGC-CAATGAATAATTT
1 G----------CTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTT-CTCAATGAATAATAT
* * * * *
873 TTTCTTTACATTGCTCTAATTCGACATTCAATTATTGTCTATTTTAACAAGAAATATAAAACAAT
55 TTTCTATACATTCCTCTAAGTAGACATTCAATTATTGTCTATTTTAACAAGAAATATAAAAAAAT
* *
938 TCAACTTAAAATCAACTATGAGATCATAAAACCATTTAAAACGAGTAAT
120 GCAACATAAAATCAACTATGAGATCATAAAACCATTT--AA--AG---T
* * *
987 AAGACTTTTGAAGGAATAAGTGGCTATAAATGGGCTTTTCTTCTCAATGAAT
1 --G-CTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAAT
1039 GGCTTTTCCT
Statistics
Matches: 180, Mismatches: 26, Indels: 37
0.74 0.11 0.15
Matches are distributed among these distances:
160 1 0.01
169 6 0.03
170 101 0.56
171 66 0.37
173 2 0.01
175 2 0.01
178 1 0.01
180 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.36
Consensus pattern (161 bp):
GCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATAATATTTTCTATACAT
TCCTCTAAGTAGACATTCAATTATTGTCTATTTTAACAAGAAATATAAAAAAATGCAACATAAAA
TCAACTATGAGATCATAAAACCATTTAAAGT
Found at i:1131 original size:171 final size:168
Alignment explanation
Indices: 629--2174 Score: 805
Period size: 172 Copynumber: 9.0 Consensus size: 168
619 NNNNNNNNAC
* * * *
629 CATTTAAAGCGAGTAATGAGGCTTTTGAAGGAATGGGTGACTATAACTGGACTTTTCTTCTCAAT
1 CATTTAAA-AGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAAT
* * * * * * * ** *** *
694 GAATGGTATTTTCTATATGTTTCCTTAGGTAGACATTTAATTATTGTCTATTTTATTGAAAAATG
65 GAATGG-CTTTTCTACACGTTTCCTAAGGCAGGCATTCAATTAAAGTC-ATTTTAACAAAAAATA
* * *
759 TAAAAAAATGCAACATAAAATC-ATTATGAGATTATAAAAC
128 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
* ******** * *
799 CATTT-AAAGTGNNNNNNNNNNCTTTTGAAGGAATATGTGACTATAAATGGGCTTTTCTTGC-CA
1 CATTTAAAAGAG--TAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTT-CTCA
*** ** * * ** * ** *
862 ATGAATAATTTTTTCTTTACATTGCTCTAATTC-GACATTCAATTATTGTCTATTTTAACAAGAA
63 ATGAAT-GGCTTTTCTACACGTTTC-CTAAGGCAGGCATTCAATTAAAGTC-ATTTTAACAAAAA
* * * *
926 ATATAAAACAATTCAACTTAAAATCAACTATGAGATCATAAAAC
125 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
* * * *
970 CATTTAAAACGAGTAATAAGACTTTTGAAGGAATAAGTGGCTATAAATGGGCTTTTCTTCTCAAT
1 CATTTAAAA-GAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAAT
* * * * *
1035 GAATGGCTTTTCCTACACGTTTCCTGAGGCAAGCATTCATTTAAAGTTCATTTTTACAAAAAATG
65 GAATGGCTTTT-CTACACGTTTCCTAAGGCAGGCATTCAATTAAAG-TCATTTTAACAAAAAATA
* *
1100 TAAAAAAACTCAACTCAAAA-CTAATTATGAGATTATAAAAT
128 TAAAAAAATTCAACTTAAAATC-AATTATGAGATTATAAAAT
* * * * *** *
1141 TATTTAAGGAGAGTAATAAGGCTTTTAAAAGAAT-GGTGACTATAAAAATACTTTTCTTCTTAAT
1 CATTTAA-AAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAAT
* * * * * **
1205 GAATGGCTTTTTTCACATGTTTCCCAAGGCAGGTAGTCAATTATAA-TCTATTTTAATGAAAAAT
65 GAATGGCTTTTCT-ACACGTTTCCTAAGGCAGGCATTCAATTA-AAGTC-ATTTTAACAAAAAAT
* * *
1269 GTAAAAACATTCAACTTAAAATCAATGATGAGATTATAAAAT
127 ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
* * * * * *
1311 CTTTTAAAGAAAGTAATAAGGCTTTTCAAGGAATGGGTGACTATAAATGAACTTTT-TTTTACCA
1 CATTTAAA-AGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCT--CA
* * * * * * * **
1375 ATAAATGCCTTTTTCTTCACGTTTCCTAAGGTAGGCATTTAATTATAGTCTGTTTTAAGTAAAAA
63 ATGAATGGC-TTTTCTACACGTTTCCTAAGGCAGGCATTCAATTAAAGTC-ATTTTAACAAAAAA
* * * *
1440 TACAAAACAATTCAATTTAAAATTAATTATGAGATTATAAAAT
126 TATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
* * * *
1483 CATTTAAAGTGACTAATAAGGCTTTTGAAGGAATAGGTGACTATAAGTGGACTTTTCTTGC-CAC
1 CATTTAAA-AGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTT-CTCAA
* ** * * * * * * *
1547 TGAAT-GCTTTCCTTTTTATGTTT-CTCAAAGTAGACATTCAATCATAGTCTGTTTTAATC-AAA
64 TGAATGGCTTT--TCTACACGTTTCCT-AAGGCAGGCATTCAATTAAAGTC-ATTTTAA-CAAAA
* ********** * *
1609 AATGTAAAAAAATTCAACNNNNNNNNNNTTATTAGACTATAAAA-
124 AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
* * * *
1653 CTATTT-AAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACAATAAATAGACTTTTCTTGC-C
1 C-ATTTAAAAG--AGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTT-CTC
* * * * *** * **
1716 AATGAAAGCCTTTT-TCATCATGTTTCTTAATATAGACATTCAATTATAA-T-ATGTTTTANNNN
62 AATGAATGGCTTTTCT-A-CACGTTTCCTAAGGCAGGCATTCAATTA-AAGTCA--TTTTA--AC
****** * * * *
1778 NNNNNNTA-AAAAAAATTAAACTTAAAATCAGTTTTGAGATTATAAAAC
120 AAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
* * * * *
1826 CATTT-AAAGCCAATAATAAGGCTTTTGAAGAAAT-GAGTGACTATAAATAGATTTTTCTTCTTA
1 CATTTAAAAG--AGTAATAAGGCTTTTGAAGGAATAG-GTGACTATAAATGGACTTTTCTTCTCA
* * * * * * * **
1889 ATGAATGTCTTTTTCTACACGTTTCATAATGAAGACATTCAATTATAGACTATTTTATTAAAAAA
63 ATGAATGGC-TTTTCTACACGTTTCCTAAGGCAGGCATTCAATTAAAGTC-ATTTTAACAAAAAA
* * *
1954 TGTAAAAAAAACTCAACTTAAAATCAATTATGAGATTATAAAAG
126 TAT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
* **********
1998 CATTTAAATCGAGTAATAAGGCTTTTGAAGGANNNNNNNNNNATAAATGGACTTTTCTTCTCAAT
1 CATTTAAA-AGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAAT
* ** * * * **
2063 GAATGGCATTTTCTATACGTTTCCTGAA-GCACACATTTAATTATAGTCCGTTTTAATGAAAAAT
65 GAATGGC-TTTTCTACACGTTTCCT-AAGGCAGGCATTCAATTAAAGT-CATTTTAACAAAAAAT
* * * *
2127 GTTAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAAC
127 ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
2169 CATTTA
1 CATTTA
Statistics
Matches: 1053, Mismatches: 265, Indels: 115
0.73 0.18 0.08
Matches are distributed among these distances:
168 2 0.00
169 10 0.01
170 257 0.24
171 379 0.36
172 381 0.36
173 21 0.02
174 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.35
Consensus pattern (168 bp):
CATTTAAAAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAATG
AATGGCTTTTCTACACGTTTCCTAAGGCAGGCATTCAATTAAAGTCATTTTAACAAAAAATATAA
AAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
Found at i:1480 original size:172 final size:170
Alignment explanation
Indices: 120--2174 Score: 901
Period size: 171 Copynumber: 12.1 Consensus size: 170
110 NNNNNNNNNN
* * * *
120 AAAAGCATTTAAAGTGAATAATAAGGCTTTTGAAGAAAT-GGTTGACTATAAATGAACTTTTTTT
1 AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGG-TGACTATAAATGAACTTTTTTT
* * * ** * * * *
184 CTCC-ATGAATGGCATTTTT-TAT-AGGTTTCCCAAGGTAGATATTTAATTCTAGTATGTTTTAA
65 -TCCAATGAATGGC-TTTTTCT-TCACGTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTAA
* * * * *
246 TAAATTATGTAAAAGAATTCAACTTCAAATCAATTATAAGATTAT
127 TAAA-AATATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
* ********** * * * * * *
291 AAAACCATTTANNNNNNNNNNTAAGGCTTTTAAAAGAATGGGTGACTCTAAATGGACTTTTTTTG
1 AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTTTTT
* ** * * * **
356 CCAATGAATGCCTTTTTCTTCATATTT-CTTAGGTTAAGCATTCAATTATAGTC-CGTTT--T-A
66 CCAATGAATGGCTTTTTCTTCACGTTTCCTAAGG-CAGGCATTCAATTATAGTCTATTTTAATAA
* *
416 ACA-A-AAAA-AATT-AACTTAAAATTAATTATGAGATTAT
130 AAATATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
453 AAAAGT-ATTTAAAGCGAGTAATAGGGCTTTTGAAGAAATGGGTGACCATAAAT-AGACTTTTCT
1 AAAA-TCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGA-ACTTTTTT
* * * ********* * * * * * * * *
516 TGCCAATAAAT-GATTTNNNNNNNNNNTTTCTTGAGGTAGACATTTAATTATTGTCTGTTTGAAC
64 TTCCAATGAATGGCTTT-TTCTTCACGTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTAA-
* * *******
580 AAAAAATGTAAAACAATTCAACTTAAAATCAATTATGNNNNNNN
127 TAAAAATATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
*** * * * * * * *
624 NNNACCATTTAAAGCGAGTAATGAGGCTTTTGAAGGAATGGGTGACTATAACTGGAC-TTTTCTT
1 AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTTTTT
* * * * * * *
688 CTCAATGAATGG-TATTTTCTAT-ATGTTTCCTTAGGTAGACATTTAATTATTGTCTATTTTATT
66 C-CAATGAATGGCT-TTTTCT-TCACGTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTAAT
* * * *
751 GAAAAATGTAAAAAAATGCAACATAAAATC-ATTATGAGATTAT
128 -AAAAATATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
* * ********** * ** * *
794 AAAACCATTTAAAGTGNNNNNNNNNNCTTTTGAAGGAATATGTGACTATAAATGGGCTTTTCTTG
1 AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTTTTT
*** * * * ** * * *
859 CCAATGAATAATTTTTTCTTTACATTGCTCTAATTC-GACATTCAATTATTGTCTATTTTAACAA
66 CCAATGAATGGCTTTTTCTTCACGTTTC-CTAAGGCAGGCATTCAATTATAGTCTATTTTAATAA
* *
923 GAAATATAAAACAATTCAACTTAAAATCAACTATGAGATCAT
130 -AAATATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
* * * * ** *
965 AAAACCATTTAAA-ACGAGTAATAAGACTTTTGAAGGAATAAGTGGCTATAAATGGGC-TTTTCT
1 AAAATCATTTAAAGA-GAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTTTT
* * * * * *
1028 TCTCAATGAATGGCTTTTCCTACACGTTTCCTGAGGCAAGCATTCATTTAAAGT-TCATTTTTAC
65 TC-CAATGAATGGCTTTTTCTTCACGTTTCCTAAGGCAGGCATTCAATTATAGTCT-A-TTTTA-
* * * *
1092 A-AAAAATGTAAAAAAACTCAACTCAAAA-CTAATTATGAGATTAT
126 ATAAAAATATAAAACAATTCAACTTAAAATC-AATTATGAGATTAT
* * * * *
1136 AAAATTATTTAAGGAGAGTAATAAGGCTTTTAAAAGAAT-GGTGACTATAAA-AATACTTTTCTT
1 AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGA-ACTTTT-TT
* * * *
1199 CTT--AATGAATGGC-TTTT-TTCACATGTTTCCCAAGGCAGGTAGTCAATTATAATCTATTTTA
64 -TTCCAATGAATGGCTTTTTCTTCAC--GTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTA
* *
1260 ATGAAAAATGTAAAA-ACATTCAACTTAAAATCAATGATGAGATTAT
126 AT-AAAAATATAAAACA-ATTCAACTTAAAATCAATTATGAGATTAT
* * * *
1306 AAAATCTTTTAAAGAAAGTAATAAGGCTTTTCAAGGAATGGGTGACTATAAATGAACTTTTTTTT
1 AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTTTTT
* * * * *
1371 ACCAATAAATGCCTTTTTCTTCACGTTTCCTAAGGTAGGCATTTAATTATAGTCTGTTTTAAGTA
66 -CCAATGAATGGCTTTTTCTTCACGTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTAA-TA
* * *
1436 AAAATACAAAACAATTCAATTTAAAATTAATTATGAGATTAT
129 AAAATATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
1478 AAAATCATTTAAAGTGACTAATAAGGCTTTTGAAGGAATAGGTGACTATAAGTGGACTTTTCTTG
1 AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTTTTT
* * * * * * * *
1543 CCACTGAAT-GCTTTCCTT-TTTATGTTT-CTCAAAGTAGACATTCAATCATAGTCTGTTTTAAT
66 CCAATGAATGGCTTT--TTCTTCACGTTTCCT-AAGGCAGGCATTCAATTATAGTCTATTTTAAT
* * ********** * *
1605 CAAAAATGTAAAAAAATTCAACNNNNNNNNNNTTATTAGACTAT
128 -AAAAATATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
* * * *
1649 AAAA-CTATTTAAAGCA-AGTAATAAGACTTTTGAAGGAATGGGTGACAATAAAT-AGACTTTTC
1 AAAATC-ATTTAAAG-AGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGA-ACTTTTT
* * * * * * *** * * * *
1711 TTGCCAATGAAAGCCTTTTTCATCATGTTTCTTAATATAGACATTCAATTATAATATGTTTTANN
63 TTTCCAATGAATGGCTTTTTCTTCACGTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTA--
******* * * * *
1776 NNNNNNNNTA-AAAAAAATTAAACTTAAAATCAGTTTTGAGATTAT
126 -ATAAAAATATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
* ** * * *
1821 AAAACCATTTAAAGCCAATAATAAGGCTTTTGAAGAAAT-GAGTGACTATAAAT-AGA-TTTTTC
1 AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAG-GTGACTATAAATGA-ACTTTTTT
* * * * * * * * *
1883 TTCTTAATGAATGTCTTTTTCTACACGTTTCATAATGAAGACATTCAATTATAGACTATTTTATT
64 TTC-CAATGAATGGCTTTTTCTTCACGTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTAAT
* * *
1948 AAAAAATGTAAAAAAAACTCAACTTAAAATCAATTATGAGATTAT
128 -AAAAATAT-AAAACAATTCAACTTAAAATCAATTATGAGATTAT
* ** ********** * *
1993 AAAAGCATTTAAATCGAGTAATAAGGCTTTTGAAGGANNNNNNNNNNATAAATGGAC-TTTTCTT
1 AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTTTTT
* ** * **
2057 CTCAATGAATGGCATTTTCTAT-ACGTTTCCTGAA-GCACACATTTAATTATAGTCCGTTTTAAT
66 C-CAATGAATGGCTTTTTCT-TCACGTTTCCT-AAGGCAGGCATTCAATTATAGTCTATTTTAAT
* *
2120 GAAAAATGTTAAAA-AATTCAACTTAAAATCAATTATTAGATTAT
128 -AAAAAT-ATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
*
2164 AAAACCATTTA
1 AAAATCATTTA
Statistics
Matches: 1412, Mismatches: 387, Indels: 170
0.72 0.20 0.09
Matches are distributed among these distances:
161 3 0.00
162 92 0.07
163 10 0.01
164 4 0.00
166 1 0.00
167 5 0.00
168 6 0.00
169 18 0.01
170 269 0.19
171 586 0.42
172 399 0.28
173 14 0.01
174 5 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
AAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTTTTT
CCAATGAATGGCTTTTTCTTCACGTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTAATAAA
AATATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
Done.