Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398108.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1411.0, 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: 18082
ACGTcount: A:0.20, C:0.07, G:0.06, T:0.20
Warning! 8603 characters in sequence are not A, C, G, or T
Found at i:1780 original size:172 final size:171
Alignment explanation
Indices: 1411--1850 Score: 449
Period size: 172 Copynumber: 2.6 Consensus size: 171
1401 NNNNNNNNNN
* * *
1411 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTATGTTTCTCGAGAGAGACATTCAA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTAAT-TTTCTCTAGATAGACATTCAA
* * *
1476 TTATTATTTGTATTAATGAAAAATG-T-AAAAAAGTTCAATTTAAAATCAATTATGAGATTAGAA
65 TTATTATCTGTTTTAATGAAAAA-GATAAAAAAAATTCAATTTAAAATCAATTATGAGATTAGAA
********** * *
1539 AACCATTTAAAGCGAGTAATAAAGGNNNNNNNNNNATAGGTGA
129 AACCATTTAAAGCGAGTAATAAAGGCTTCTAAAGGATAAGAGA
*** *
1582 CTATAAAAAAACTTTTCTTGCCAATGAATGCTTTTTTCTTCAATTATCTCTAGATAGACATTCAA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTT-AATTTTCTCTAGATAGACATTCAA
* * * * * *
1647 ATATTATCTGTTTTCATCAAAAAGATAAAAAAAATTTAATTTAAAATCAATTATTAGATTATAAA
65 TTATTATCTGTTTTAATGAAAAAGATAAAAAAAATTCAATTTAAAATCAATTATGAGATTAGAAA
* * *
1712 ACTATTTAAAGCTATTAAT-AAGGCTTCTAAAGGACTAAGAGA
130 ACCATTTAAAGCGAGTAATAAAGGCTTCTAAAGGA-TAAGAGA
* * * *
1754 CTATAAATGGACTTTTCTTACCAATGAATGCTCTTTTCTTTACTTTTCT-TATGGTAGACATTCA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTC-TTAATTTTCTCTA-GATAGACATTCA
* *
1818 ATTA-TAGTCTATTTTAATGAAAAATATAAAAAA
64 ATTATTA-TCTGTTTTAATGAAAAAGATAAAAAA
1851 NNNNNNNNNN
Statistics
Matches: 218, Mismatches: 44, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
170 1 0.00
171 83 0.38
172 132 0.61
173 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.37
Consensus pattern (171 bp):
CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTAATTTTCTCTAGATAGACATTCAAT
TATTATCTGTTTTAATGAAAAAGATAAAAAAAATTCAATTTAAAATCAATTATGAGATTAGAAAA
CCATTTAAAGCGAGTAATAAAGGCTTCTAAAGGATAAGAGA
Found at i:4843 original size:133 final size:123
Alignment explanation
Indices: 4664--4916 Score: 240
Period size: 133 Copynumber: 2.0 Consensus size: 123
4654 ATGGTTTTAA
* * *
4664 AATCTAATAATTGATTTTAAGTGAAATTTGTTTAAATTTTTTATTAAAACAGACAATAATTG-AT
1 AATCTAATAATTAATTTTAAGTGAAATTTGTTTAAATTTTTCATTAAAACAAACAATAATTGTA-
* * *
4728 TGTCTAGCTCAAGAAACATTAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTNNNNNNNNN
65 TGTCTAGCTCAAGAAACATAAAGAAAAAAGCATTCATTGACAAGAAAAGTCCATTT---------
4793 NTCT
121 -TCT
* * * * * *
4797 AATCTCATAATTAATTTTAAGTTG-AATTTTTTTATATTTTTCATTAATACAAATAATAGTTGTA
1 AATCTAATAATTAATTTTAAG-TGAAATTTGTTTAAATTTTTCATTAAAACAAACAATAATTGTA
* ** *
4861 TGTCTATCTTGAGAAACATAAAGAAAAAAGCATTCGTTGACAAGAAAAGTCCATTT
65 TGTCTAGCTCAAGAAACATAAAGAAAAAAGCATTCATTGACAAGAAAAGTCCATTT
4917 ATAGTAACTC
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
133 99 0.97
134 3 0.03
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.36
Consensus pattern (123 bp):
AATCTAATAATTAATTTTAAGTGAAATTTGTTTAAATTTTTCATTAAAACAAACAATAATTGTAT
GTCTAGCTCAAGAAACATAAAGAAAAAAGCATTCATTGACAAGAAAAGTCCATTTTCT
Found at i:8011 original size:170 final size:171
Alignment explanation
Indices: 7702--8038 Score: 408
Period size: 170 Copynumber: 2.0 Consensus size: 171
7692 NNNNNNNNNN
* * * * * ** **
7702 AAAACAGACTATAATTGAATATCTACCACAAGAAACGTGAATAAAAGAGCATTCTTTGGTAAGAA
1 AAAACAGACTATAATTAAATATCTACCACAAGAAACATGAAGAAAAAAGCACTCACTAATAAGAA
* * * *
7767 AAGTCCTTTTATAGTCTTCCAATCCTTTAAAAACCTTATTACTCTCTTTAAATAGTTTTATAATC
66 AAGTCCATTTATAGCCTTCCAATCCTTCAAAAACCTTATTACTCTCTCTAAATAGTTTTATAATC
*
7832 TCGTAATTGATTTTAAGTTGAAGTTTTTTACATTTTTCATT
131 TCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTCATT
* * *
7873 AAAACAGACTATAATTAAATGTCTGCCTCAAG-AACATGAAGAAAAAAGCACTCACTAATAAGAA
1 AAAACAGACTATAATTAAATATCTACCACAAGAAACATGAAGAAAAAAGCACTCACTAATAAGAA
* * * * * * * *
7937 AAGTCCATTTATAGCCTTCTATTCCTTCAACAGCCTTTTTGCTCGT-TCTAAATGGTTTTATGAT
66 AAGTCCATTTATAGCCTTCCAATCCTTCAAAAACCTTATTACTC-TCTCTAAATAGTTTTATAAT
* *
8001 CTCATAATTGATTTTAAGTTTAATTTTTTTACATTTTT
130 CTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTT
8039 NNNNNNNNNN
Statistics
Matches: 138, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
170 109 0.79
171 29 0.21
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (171 bp):
AAAACAGACTATAATTAAATATCTACCACAAGAAACATGAAGAAAAAAGCACTCACTAATAAGAA
AAGTCCATTTATAGCCTTCCAATCCTTCAAAAACCTTATTACTCTCTCTAAATAGTTTTATAATC
TCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTCATT
Found at i:13509 original size:171 final size:170
Alignment explanation
Indices: 13224--13805 Score: 574
Period size: 171 Copynumber: 3.4 Consensus size: 170
13214 NNNNNNNGAG
* * ** * **
13224 CTATAAAAGGACTTTTCTTGCCCATGAATGCTCATTTATTCACGTTTCTCGCTG-TAGATATTCA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCT-TATGATAGATATTCA
* * *
13288 ATTATAATATGTTTTAATCAAAAATGAAAAAAAACTCAACTTAAAATCAATTATTAGATTATAAA
65 ATTATAGTATGTTTTAATCAAAAATG-TAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
************
13353 ACCATTTAAAGCTAGTNNNNNNNNNNNNGAAGGAATGGGTGA
129 ACCATTTAAAGCTAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * *
13395 CTATAAATGGACTTTTCTTGCCAATGATTGCTTTTTTCTTTACGTTTCTTATGATAAATATTCAA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTTATGATAGATATTCAA
* * ***
13460 TTATAGTCTGCTTTAATCAAAAATGTAAAAAAGTTCAACTTAAAATCAATTATTAGATTATANNN
66 TTATAGTATGTTTTAATCAAAAATGTAAAAAA-TTCAACTTAAAATCAATTATTAGATTATAAAA
*******
13525 NNNNNNNAAGCTAGTAATAAGGCTTTTGAAGGAATGGGTGA
130 CCATTTAAAGCTAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * * * *
13566 CTATAAATGGACTTTTCATGCGAATGAATGCTTTTTTCTTCATGTTTCTTGA-GATAGACAATCA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTT-ATGATAGATATTCA
* * * * *
13630 ATTATTGTATGTTTTAATGAAAAACGTAAAACAATTTAACTTAAAATCAATTATTAGTTTATAAA
65 ATTATAGTATGTTTTAATCAAAAATGTAAAA-AATTCAACTTAAAATCAATTATTAGATTATAAA
* * * * *
13695 ACTATTTAAAGCTAGTAATGAGGCTTTTGAAGGACTCGGAGA
129 ACCATTTAAAGCTAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * * * * * *
13737 CTATAAATGGACTTTTCTTACCAATGAATGATCTTTTCTTCACATTTCTTGTGGTAGACATTCAA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTTATGATAGATATTCAA
13802 TTAT
66 TTAT
13806 CATCANNNNN
Statistics
Matches: 330, Mismatches: 76, Indels: 10
0.79 0.18 0.02
Matches are distributed among these distances:
170 8 0.02
171 319 0.97
172 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTTATGATAGATATTCAA
TTATAGTATGTTTTAATCAAAAATGTAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAAC
CATTTAAAGCTAGTAATAAGGCTTTTGAAGGAATGGGTGA
Found at i:15102 original size:170 final size:171
Alignment explanation
Indices: 14660--15107 Score: 436
Period size: 172 Copynumber: 2.6 Consensus size: 171
14650 NNNNNNNNNN
* * * *
14660 TTAATCAAAAATGT-AAAAAAGTTCAACTTAAAATCAATTATTAGATTATAAAACTATTTATAGC
1 TTAATGAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGC
* * *
14724 TAGTAATAAGGCTTTTGAAGGAATGAATGACTGTAAATGGACTTTTCTTACTAATGAATACTTTT
66 TAGTAATAAGGCTTTTGAAGGATTGGA-GACTATAAATGGACTTTTCTTACTAATGAATACTTTT
* *
14789 TTCTTCAAGTTTCTCAAGATAAACATTCAATTATTATTTGTA
130 TTCTTCAAGTTTCTCAAGATAAACAATCAATTATTATATGTA
* * **********
14831 TTAATGAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTAGAAANNNNNNNNNNGC
1 TTAATGAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGC
* * * * *
14896 GAGTAATAAGGGTTTTGAAGGAATTGGTGACTATAAATGGACTTTTCTTGCTAATGAATGC-TTT
66 TAGTAATAAGGCTTTTGAAGG-ATTGGAGACTATAAATGGACTTTTCTTACTAATGAATACTTTT
* * * * *
14960 TTCTTCATGTTTCTCGAGATAGACAATCAATTATTGTATGTT
130 TTCTTCAAGTTTCTCAAGATAAACAATCAATTATTATATGTA
* ********** *
15002 TTAAT-CAAANNNNNNNNNNAATTTAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGC
1 TTAATGAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGC
*
15066 TAGTAATGAA-GCTTTCGAAGGACTTGGAGACTATAAATGGAC
66 TAGTAAT-AAGGCTTTTGAAGGA-TTGGAGACTATAAATGGAC
15108 NNNNNNNNNN
Statistics
Matches: 216, Mismatches: 57, Indels: 9
0.77 0.20 0.03
Matches are distributed among these distances:
169 1 0.00
170 68 0.31
171 58 0.27
172 86 0.40
173 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.34
Consensus pattern (171 bp):
TTAATGAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGC
TAGTAATAAGGCTTTTGAAGGATTGGAGACTATAAATGGACTTTTCTTACTAATGAATACTTTTT
TCTTCAAGTTTCTCAAGATAAACAATCAATTATTATATGTA
Done.