Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398655.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1940.0, 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: 4795
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.24
Warning! 1823 characters in sequence are not A, C, G, or T
Found at i:408 original size:172 final size:171
Alignment explanation
Indices: 16--1083 Score: 598
Period size: 172 Copynumber: 6.2 Consensus size: 171
6 ATGAAGAAAT
* ** * *
16 AAGCATTCATTCAGAAG-AAAGGCCTATTTAGATTCACTCATTCCTTCAAAAAG-CTTATTACTC
1 AAGCATTCATTTAGAAGAAAAGTTC-ATTTATAGTCACTCATTCCTTC-AAAAGCCTTATTAC-C
* * * * * *********
79 -GCTTCAAATAGTTTTATAACCTCATAATTGATTTTTAGTTGAATTTTTTTATA-TNNNNNNNNN
63 GGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAA
* * * * *
142 NAACGGTCTATAATTGAATGTCTACCT-TAGGAAACA-TGCAAAAA
128 AAACAGACTATAATTGATTGTCTACCTCGA-GAAA-AGTGCAAAAA
* *
186 AAGCCATTCATTTAGAAGAAAAGTTCATTTATAGGCACTCATACCTTCAAAAGCCTTATTACCGG
1 AAG-CATTCATTTAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACCGG
**********
251 CTTTAAATGGTTTTATANNNNNNNNNNTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAAAA
65 CTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAAAA
*
316 ACAGACTATAATTGATTGTTTACCTCGAGAAAAGTGCAAAAA
130 ACAGACTATAATTGATTGTCTACCTCGAGAAAAGTGCAAAAA
*
358 AAGTCATTC-TTTGATAAGAGAAA--TCTATTTATAGTCACTCATTCCTTCAAAAAG-CTTATTA
1 AAG-CATTCATTT-AGAAGA-AAAGTTC-ATTTATAGTCACTCATTCCTTC-AAAAGCCTTATTA
*********** *
419 CTNNNNNNNNNNGGTTTTATAATCTCATAATTGATTTTAAGTT-ACATTTTTTTACTTTTTTTAT
61 CCGGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGA-ATTTTTTTACATTTTTTAT
* * * * *
483 T-AAAACGGTCTATAATTGATTGTCTATCTC-AGGAAACGTGTAAAAA
125 TAAAAACAGACTATAATTGATTGTCTACCTCGA-GAAAAGTGCAAAAA
* ******
529 AAGCTATTCATTTAGAAGAAAAGTTCATTTATAGTCATTCATTCCTTCAAAAGCCTTATNNNNNN
1 AAGC-ATTCATTTAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACCGG
**** * * *
594 NNNNAAATGGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTTTAGATTTTTTGTTAAAA
65 CTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAAAA
* *
659 ACAGACAATAATTGATTGTCTACCTTGAGAAAAGTGCAAAAA
130 ACAGACTATAATTGATTGTCTACCTCGAGAAAAGTGCAAAAA
* * * * * *******
701 AAGACATTCATTGAAAAAAAAAG-TCTATTTATAGTCACCCATTCCTTCAAAAGGCTNNNNNNNN
1 AAG-CATTCATTTAGAAGAAAAGTTC-ATTTATAGTCACTCATTCCTTCAAAAGCCT-TATTACC
*** * *
765 NNTTTTAATTGTTTTTATAATCTCATAATTGATTTTAAGTT-AGATTTTTTT-CTATTTTTT-TG
63 GGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGA-ATTTTTTTAC-ATTTTTTAT-
* * * ** * * *
827 TTAAAATAGACTATAATTGAATACCTTCCT-TAGGAAACA-TGCAGAAA
125 TAAAAACAGACTATAATTGATTGTCTACCTCGA-GAAA-AGTGCAAAAA
* * * * **********
874 AAGCTTATTCATTGAGAACAAAAGTTTATTTATTGNNNNNNNNNNCTTCAAAAGCCTTATTACTC
1 AAGC--ATTCATTTAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTAC-C
* * * *
939 -GATTTAAATAGTTTTATAATCTTATAAATGATTTTAAGTTGAATTTTTTTACA-TTTTTAGTT-
63 GGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTA-TTA
* * * * * * * * *
1001 CAAACAGAATATAATTAAATGCCTCCCCCAACAAACA-TGCAAAAA
127 AAAACAGACTATAATTGATTGTCTACCTCGAGAAA-AGTGCAAAAA
* *
1046 AAGTCATTCATTGAGAAGAAAAGTCCATTTATAGTCAC
1 AAG-CATTCATTTAGAAGAAAAGTTCATTTATAGTCAC
1084 CCANNNNNNN
Statistics
Matches: 697, Mismatches: 162, Indels: 77
0.74 0.17 0.08
Matches are distributed among these distances:
170 19 0.03
171 240 0.34
172 253 0.36
173 146 0.21
174 38 0.05
175 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (171 bp):
AAGCATTCATTTAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACCGGC
TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAAAAA
CAGACTATAATTGATTGTCTACCTCGAGAAAAGTGCAAAAA
Found at i:4162 original size:170 final size:172
Alignment explanation
Indices: 3285--4167 Score: 604
Period size: 171 Copynumber: 5.2 Consensus size: 172
3275 NNNTCACTTC
* * *
3285 AAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT--A-------TTAAAATAGG
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGA
* * * * * * * ** *
3341 CAATAATTGA-ATGTCTATCTCGGGAAACGTGTAAAAAAAGTTATTCATTGAGAAGAAAAGTCTA
66 CTATAATTGATATGCCTACCTTGAGAAACATGCAAAAAAAGCCATTCATTGAGAAGAAAAGTCCA
* * * * *
3405 TTTATAGTCACTCATTCCTACAAAAGTCTTATTACCCGCTTT
131 TTTAGAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTT
********** **
3447 AAATGGTTTTATAATCTCATAANNNNNNNNNNGTTGAATTTTTTTACATTTTTCTTTAAAACAGA
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGA
* * * *
3512 CTATAATT-AAATGCCTACAC-TAAGAAACATGC-AAAAAGGCCATTCATTGATAAGAAAAGTCC
66 CTATAATTGATATGCCTAC-CTTGAGAAACATGCAAAAAAAGCCATTCATTGAGAAGAAAAGTCC
** * * * *
3574 ATTTTTAGTCACTCATTCCTTCAAAAGCCATATTACTAGCTTT
130 ATTTAGAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTT
* *********** *
3617 TAATGGTTTTATAATCTCATAATTGNNNNNNNNNNAAATTTTTTTACATTTTTGATTAAAAC-GT
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAG-
** * *
3681 ACTATAATTGA-ATGTGTACCTTGAGAAACGTG-AAGAAACAAG-CATTCATTGATG-AGAGAAG
65 ACTATAATTGATATGCCTACCTTGAGAAACATGCAA-AAA-AAGCCATTCATTGA-GAAGAAAAG
* * *
3742 TCAATTTAGAGTCACCCATTCCTTCAAAAGGCCTATTGCTCGCTTT
127 TCCATTTAGAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTT
* * * *
3788 AAATAGTTTTATAATCTTATAATTGATTTTACA-TTGAATTTTTTTAAATTTTTTGTTAAAACAG
1 AAATGGTTTTATAATCTCATAATTGATTTTA-AGTTGAATTTTTTTACATTTTTGGTTAAAACAG
* ** ********** ** * * *
3852 ACTGTAATTGAT-TGTTTACNNNNNNNNNNATATAGAAAAAGTCATTCATTGAGAAGAGAAGTCC
65 ACTATAATTGATATGCCTACCTTGAGAAACATGCAAAAAAAGCCATTCATTGAGAAGAAAAGTCC
* * * *
3916 ATTTAGAGTCACCCTTTCCTTCAAAAAGTTTATTACACGCTTT
130 ATTTAGAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTT
** ********** * *
3959 AAACAGTTTTATAATCTNNNNNNNNNNTTTAAGTTGAATTTTTTTATATTTTTGGTTAAAATAGA
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGA
*
4024 CTATAATT-ATATG-CTGCCTTGAGAAACATGCAAAAAAAGCCATTCATTGAGAAGAAAAGTCCA
66 CTATAATTGATATGCCTACCTTGAGAAACATGCAAAAAAAGCCATTCATTGAGAAGAAAAGTCCA
* * * *
4087 TTTACAGTCACCCATTCCATCAAGAGGCTTATTCCTCGCTTT
131 TTTAGAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTT
*
4129 AAATGGTTTTACAATCTCATAATTGATTTTAAGTTGAAT
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
4168 NNNNNNNNNN
Statistics
Matches: 547, Mismatches: 148, Indels: 44
0.74 0.20 0.06
Matches are distributed among these distances:
162 34 0.06
164 1 0.00
169 2 0.00
170 240 0.44
171 265 0.48
172 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.36
Consensus pattern (172 bp):
AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGA
CTATAATTGATATGCCTACCTTGAGAAACATGCAAAAAAAGCCATTCATTGAGAAGAAAAGTCCA
TTTAGAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTT
Done.