Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399423.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_269.0, 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: 7158
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.24
Warning! 2348 characters in sequence are not A, C, G, or T
Found at i:3136 original size:171 final size:169
Alignment explanation
Indices: 2649--3935 Score: 995
Period size: 171 Copynumber: 7.6 Consensus size: 169
2639 GAGTAATAAA
* * **
2649 ACTA-AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGGCATTCA
1 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTACACATTCA
* *
2713 ATTATAGTCTTTTTTAACTAAAAATAT-AAAAAAATTCAACTTAAAGTAAGTTATGAGATTATAA
66 ATTATAGTCTTTTTTAA-TAAAAA-ATGTAAAAAATTCAACTTAAAATAAGTTATGAGATTATAA
********* * *
2777 AACCATTTANNNNNNNNNNTAAACCTTTTTAAA-GAATGGGTG
129 AACCATTTA-AGCGAGTAATAAGCC-TTTTAAAGGAATGAGTG
* * * ** *
2819 ACTATAAATGGACTTTTCTTGCCAATGAATAAC-CTTTTCTTCACGTTTCTTGAGGTAGACATTC
1 ACTATAAATGGACTTTTCTTACCAATGAAT-GCTTTTTTCTTCACGTTTCTCAAGGTACACATTC
* * ** ** *
2883 AATTATTGTC-TGTTTAACCAAAAATGTAAAAAATTCAACTCGAAATCAGTTATGAGATTATAAA
65 AATTATAGTCTTTTTTAATAAAAAATGTAAAAAATTCAACTTAAAATAAGTTATGAGATTATAAA
* * *
2947 ATCATTTAAAGCGAGTAATAAGCCTTCTAAAGGAATAAGTG
130 ACCATTT-AAGCGAGTAATAAGCCTTTTAAAGGAATGAGTG
* * * * * * *
2988 GCCATAAATGGACTTTT-TTACCAATGAATACTTTTTTCTTTATGTTTGTCAAGGTTCACATTCA
1 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTACACATTCA
*
3052 ATTATAGTCTTTTTTAATAAAAAAATGTAGAAATATTCAACTTAAAATAAGTTATGAGATTATAA
66 ATTATAGTCTTTTTTAAT-AAAAAATGTA-AAAAATTCAACTTAAAATAAGTTATGAGATTATAA
* * * *
3117 AACCAATTTAAGTGAGTAATAAGTCTTTTCAAGGAATGGGTG
129 AACC-ATTTAAGCGAGTAATAAGCCTTTTAAAGGAATGAGTG
* * *
3159 ACTATAAATGGACTTTTCTTACCAGTGAATGCTTGTTTCTTCATGTTTCTCAAGGTACACATTCA
1 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTACACATTCA
* * ** * * * *
3224 ATTATTGT-TTGTTGTAACCAAAAATGTAAAACGATTTAACTTAAAATCAGTTATGAGATTAAAA
66 ATTATAGTCTT-TTTTAATAAAAAATGTAAAA-AATTCAACTTAAAATAAGTTATGAGATTATAA
*
3288 AACCATTTAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTG
129 AACCATTTAAGCGAGTAATAAGCCTTTTAAAGGAATGAGTG
* * *
3329 ATTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTACACGTTTCTCAA-G-ACATATTCA
1 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTACACATTCA
* * * *
3392 ATTGTAGTCTGTTTTAATAAAATATGTAAAACAATTCAACTTAAAATCAA-TTAGGAGATTATAA
66 ATTATAGTCTTTTTTAATAAAAAATGTAAAA-AATTCAACTTAAAAT-AAGTTATGAGATTATAA
* * ********** * *
3456 AATCATTTAAAGCAANNNNNNNNNNTTTTGAAGGAATGGGTG
129 AACCATTT-AAGCGAGTAATAAGCCTTTTAAAGGAATGAGTG
*** * * * * * * *
3498 ACTATAAACAAACTTTTCTTGCCAATGAATGCTTATTTCTTTATGTTTCTCTAGATACACATTAA
1 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTACACATTCA
* * **********
3563 ATTAT--TATTTGTT-ATAACCAAAAGTGTAAAACAATTCAACTTAAANNNNNNNNNNAGATTAT
66 ATTATAGTCTTTTTTAATAA--AAAA-TGTAAAA-AATTCAACTTAAAATAAGTTATGAGATTAT
* **
3625 AAAACCATTTAAAGCGAGTAATAAACCTTTCGAAGGAAT-ATGTG
127 AAAACCATTT-AAGCGAGTAATAAGCCTTTTAAAGGAATGA-GTG
* * * * * * *
3669 ACTATAAATAGACTTTTCTTGCGAATGAATACTTTTTTCTCCATGTTTCCCAA-G-ACACATTCA
1 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTACACATTCA
** * * ********** *
3732 ATTGCAGTCTGTTTTAATGAAAAATGTAAAACAATTCAACTTNNNNNNNNNNAGGAGATTATAAA
66 ATTATAGTCTTTTTTAATAAAAAATGTAAAA-AATTCAACTTAAAATAAGTTATGAGATTATAAA
* * * *
3797 ATCATTTCAAGCGAGTAATAAGGCTTTTGAAGGAATTAGTG
130 ACCATTT-AAGCGAGTAATAAGCCTTTTAAAGGAATGAGTG
* ** * * *** *
3838 ACTATAAATGGATTTTTCTTGTCAATGAATGCCTTTTTCTTCATGTTTCTTGCGGTAGACATTCA
1 ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTACACATTCA
* **
3903 ATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
66 ATTATAGTCTTTTTTAATAAAAAATGTAAAAAA
3936 NNNNNNNNNN
Statistics
Matches: 898, Mismatches: 190, Indels: 58
0.78 0.17 0.05
Matches are distributed among these distances:
167 2 0.00
168 118 0.13
169 270 0.30
170 115 0.13
171 332 0.37
172 61 0.07
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.35
Consensus pattern (169 bp):
ACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTACACATTCA
ATTATAGTCTTTTTTAATAAAAAATGTAAAAAATTCAACTTAAAATAAGTTATGAGATTATAAAA
CCATTTAAGCGAGTAATAAGCCTTTTAAAGGAATGAGTG
Found at i:3223 original size:340 final size:337
Alignment explanation
Indices: 2649--3933 Score: 1229
Period size: 340 Copynumber: 3.8 Consensus size: 337
2639 GAGTAATAAA
* * * **
2649 ACTA-AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGGCATTCA
1 ACTATAAATGGACTTTTCTTACCAATGAATACTTTTTTCTTCACGTTTCTCAA-G-ACACATTCA
* * * * *
2713 ATTATAGTCTTTTTTAACT-AAAAATATAAAAAAATTCAACTTAAAGTAAGTTATGAGATTATAA
64 ATTATAGTCTGTTTTAA-TAAAAAATGTAAAACAATTCAACTTAAAATAAGTTAGGAGATTATAA
********** * * *
2777 AACCATTTANNNNNNNNNNTAAACCTTTTTAAAGAATGGGTGACTATAAATGGACTTTTCTTGCC
128 AACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
* * * * *
2842 AATGAATAACCTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATTGTCTGTT-TAACCAAAA
193 AATGAAT-GCTTTTTCTTCATGTTTCTCGAGGTACACATTCAATTATTGTCTGTTATAACCAAAA
* *
2906 ATGTAAAA-AATTCAACTCGAAATCAGTTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGC
257 ATGTAAAACAATTCAACT-AAAATCAGTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGC
*
2970 CTTCTAAAGGAATAAGTG
321 CTT-TGAAGGAATAAGTG
* * * * * *
2988 GCCATAAATGGACTTTT-TTACCAATGAATACTTTTTTCTTTATGTTTGTCAAGGTTCACATTCA
1 ACTATAAATGGACTTTTCTTACCAATGAATACTTTTTTCTTCACGTTTCTCAA-G-ACACATTCA
* * *
3052 ATTATAGTCTTTTTTAATAAAAAAATGTAGAAA-TATTCAACTTAAAATAAGTTATGAGATTATA
64 ATTATAGTCTGTTTTAAT-AAAAAATGTA-AAACAATTCAACTTAAAATAAGTTAGGAGATTATA
* * * *
3116 AAACCAATTT-AAGTGAGTAATAAGTCTTTTCAAGGAATGGGTGACTATAAATGGACTTTTCTTA
127 AAACC-ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTG
* * * *
3180 CCAGTGAATGCTTGTTTCTTCATGTTTCTCAAGGTACACATTCAATTATTGTTTGTTGTAACCAA
191 CCAATGAATGCTT-TTTCTTCATGTTTCTCGAGGTACACATTCAATTATTGTCTGTTATAACCAA
* * *
3245 AAATGTAAAACGATTTAACTTAAAATCAGTTATGAGATTAAAAAACCATTT-AAGCGAGTAATAA
255 AAATGTAAAACAATTCAAC-TAAAATCAGTTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
*
3309 GCCTTTTGAAGGAATGAGTG
319 GCC-TTTGAAGGAATAAGTG
* * * *
3329 ATTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTACACGTTTCTCAAGACATATTCAAT
1 ACTATAAATGGACTTTTCTTACCAATGAATACTTTTTTCTTCACGTTTCTCAAGACACATTCAAT
* *
3394 TGTAGTCTGTTTTAATAAAATATGTAAAACAATTCAACTTAAAATCAA-TTAGGAGATTATAAAA
66 TATAGTCTGTTTTAATAAAAAATGTAAAACAATTCAACTTAAAAT-AAGTTAGGAGATTATAAAA
* * ********** ***
3458 TCATTTAAAGCAANNNNNNNNNNTTTTGAAGGAATGGGTGACTATAAACAAACTTTTCTTGCCAA
130 CCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAA
* * * * * * *
3523 TGAATGCTTATTTCTTTATGTTTCTCTAGATACACATTAAATTATTATTTGTTATAACCAAAAGT
195 TGAATGCTT-TTTCTTCATGTTTCTCGAGGTACACATTCAATTATTGTCTGTTATAACCAAAAAT
********** *
3588 GTAAAACAATTCAACTTAAANNNNNNNNNNAGATTATAAAACCATTTAAAGCGAGTAATAAACCT
259 GTAAAACAATTCAAC-TAAAATCAGTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCT
*
3653 TTCGAAGGAATATGTG
323 TT-GAAGGAATAAGTG
* * * * * *
3669 ACTATAAATAGACTTTTCTTGCGAATGAATACTTTTTTCTCCATGTTTCCCAAGACACATTCAAT
1 ACTATAAATGGACTTTTCTTACCAATGAATACTTTTTTCTTCACGTTTCTCAAGACACATTCAAT
** * ********** *
3734 TGCAGTCTGTTTTAATGAAAAATGTAAAACAATTCAACTTNNNNNNNNNNAGGAGATTATAAAAT
66 TATAGTCTGTTTTAATAAAAAATGTAAAACAATTCAACTTAAAATAAGTTAGGAGATTATAAAAC
* * ** * *
3799 CATTTCAAGCGAGTAATAAGGCTTTTGAAGGAATTAGTGACTATAAATGGATTTTTCTTGTCAAT
131 CATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * *
3864 GAATGCCTTTTTCTTCATGTTTCTTGCGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG
196 GAATG-CTTTTTCTTCATGTTTCTCGAGGTACACATTCAATTATTGTCTGTTATAACCAAAAATG
3929 TAAAA
260 TAAAA
3934 AANNNNNNNN
Statistics
Matches: 774, Mismatches: 154, Indels: 35
0.80 0.16 0.04
Matches are distributed among these distances:
338 8 0.01
339 232 0.30
340 398 0.51
341 70 0.09
342 65 0.08
343 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.35
Consensus pattern (337 bp):
ACTATAAATGGACTTTTCTTACCAATGAATACTTTTTTCTTCACGTTTCTCAAGACACATTCAAT
TATAGTCTGTTTTAATAAAAAATGTAAAACAATTCAACTTAAAATAAGTTAGGAGATTATAAAAC
CATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
GAATGCTTTTTCTTCATGTTTCTCGAGGTACACATTCAATTATTGTCTGTTATAACCAAAAATGT
AAAACAATTCAACTAAAATCAGTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTG
AAGGAATAAGTG
Found at i:6363 original size:170 final size:170
Alignment explanation
Indices: 5434--6461 Score: 943
Period size: 171 Copynumber: 6.0 Consensus size: 170
5424 NNNNNNNNNN
* **
5434 AAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTAAATTAATGGGTGA
1 AAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAAT-GGTGA
* ** * *
5499 CTATAAATGGACTTTTCTTGCCAATAAATATTTTTTTC-TCACGTTTCTCAAGGTACACATTCAA
65 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTAATGTTTCTCAAGGTACACATTCAA
* *
5563 TTATTA-TCTATTTTGAATAAAAATGT-AAAACAATTCAACTT
130 TTA-TAGTCTGTTTT-AATAAAAATGTAAAAAAAATTCAACTT
***************
5604 AAAATCAGTTATGAGATTATAAAA-TCATTTAAANNNNNNNNNNNNNNNTTTGAAGGAATGAGTG
1 AAAATCAGTTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATG-GTG
* * * ** **
5668 ACTATAAATGGACTTTTCTTGCCAATGAATCCCTTTTTGTTAATGGTTT-GAAAGGTAGGCATTC
64 ACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTAAT-GTTTCTCAAGGTACACATTC
*
5732 AATTATAGTCTGTTTTAACTAAAAATATAAAAAAAAATTCAACTT
128 AATTATAGTCTGTTTTAA-TAAAAATGT-AAAAAAAATTCAACTT
* *
5777 AAAATCAGTTATGAGATTATAAAACTATTTAGAGTGAGTAATAAGCCTTTTGAAGGAATAGGTGA
1 AAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAAT-GGTGA
* ** * * *
5842 CTACAAATAAACTTTTCTTGCAAATGAAT-CTCTTTTTCTTTAA-GTTTCTCGAGGTAAACATTC
65 CTATAAATGGACTTTTCTTGCCAATGAATGCT-TTTTTC-TTAATGTTTCTCAAGGTACACATTC
* * **
5905 AATTATATTCTGTTTTAGACAAAAATGT-AAAAAAATTTGACTT
128 AATTATAGTCTGTTTTA-ATAAAAATGTAAAAAAAATTCAACTT
* * * *
5948 AAAATCAGTTATGAGATTATTAAACTATTTAAAGCTAGTAATAAGCCTTTTAAAGTAATGGGTGA
1 AAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAAT-GGTGA
* * * * *
6013 CTATAAATGGAGTTTTCTTGCCAATGAATGTTTTTTTCTTCATGTTTCCCAAGGTACGCATTCAA
65 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTAATGTTTCTCAAGGTACACATTCAA
* * ** *
6078 TTATTGTATGTTTTAAATAAAAATGT-GCAACAATTCAA-TCT
130 TTATAGTCTGTTTT-AATAAAAATGTAAAAAAAATTCAACT-T
* * * * * * *
6119 AGAATTAGTTACGAGATTATAAAA-TCGTTTAAAGCGAGTAATATGCCTTTTGAAGGAATAAGTA
1 AAAATCAGTTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAAT-GGTG
*
6183 ACTATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTAATGTTTCTCAAGGTACACATTCA
64 ACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTAATGTTTCTCAAGGTACACATTCA
* * * ** *
6248 ATTGTAGTCTG-TTTAATGAAAAATGT-GAAACAGCTGAACTT
129 ATTATAGTCTGTTTTAAT-AAAAATGTAAAAAAAATTCAACTT
* * * * * *
6289 TAAATCAATTAGGATATTATAAAAACT-TTTAAAGCGAGTAACAAGGCTTTTGAAGGAATGGTTG
1 AAAATCAGTTATGAGATTAT-AAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGG-TG
* * * * * * * * *
6353 ACTGTAAATTGACTTTTCTTACGAATGAATGCCTTTTTCTTCACGTTTCTCAAGCTAGACATTCA
64 ACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTAATGTTTCTCAAGGTACACATTCA
* * *
6418 ATTATAGTCTTTTTTAACAAAAA-ATATAAAAAAATTCAACTT
129 ATTATAGTCTGTTTTAATAAAAATGTA-AAAAAAATTCAACTT
6460 AA
1 AA
6462 NNNNNNNNNN
Statistics
Matches: 686, Mismatches: 145, Indels: 53
0.78 0.16 0.06
Matches are distributed among these distances:
169 7 0.01
170 220 0.32
171 318 0.46
172 12 0.02
173 122 0.18
174 7 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
AAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGTGAC
TATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTAATGTTTCTCAAGGTACACATTCAAT
TATAGTCTGTTTTAATAAAAATGTAAAAAAAATTCAACTT
Done.