Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402797.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5854.0, 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, 856
Length: 1427
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.31
Warning! 287 characters in sequence are not A, C, G, or T
Found at i:500 original size:173 final size:160
Alignment explanation
Indices: 276--586 Score: 381
Period size: 173 Copynumber: 1.9 Consensus size: 160
266 NNNNNNNTTC
* * *
276 CTTCAAAAGCCTTATTACTCAATTTCAATAGTTTTATTATCTCAAAATTGATTTTGTGTTCAATT
1 CTTCAAAAGCCTTATTACTCAAGTTAAATAGTTTTATTATCTCAAAATTGATTTTATGTTCAA-T
* * *
341 TTTTTGTACATTTT-TGCTTAAAACATATTATAATTGAAAGTCTACCTTGAGAAATGTAAAGAAA
65 GTTTT-TAC-TTTTGTGCTT-AAACAGATTATAATTGAAAGTCTACCATGAGAAATGTAAAGAAA
405 AAGGCATTCATTAGCAAGANNNNNNNNNNTATAGTCACCCATTT
127 AAGGCATTCATTAGCAAGA----------TATAGTCACCCATTT
**
449 CTTCAAAAGCCTTATTACTTGAGTTAAATAGTTTTATTATCTCAAAATTGATTTTATGTTCAATG
1 CTTCAAAAGCCTTATTACTCAAGTTAAATAGTTTTATTATCTCAAAATTGATTTTATGTTCAATG
* * * *
514 TTTTTACTTTTGTGGTTAAACAGATTATAATTGAATGTCTACGATGAGAAATGTGAAGAAAAAGG
66 TTTTTACTTTTGTGCTTAAACAGATTATAATTGAAAGTCTACCATGAGAAATGTAAAGAAAAAGG
579 CATTCATT
131 CATTCATT
587 GACAAGAAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
170 55 0.44
171 7 0.06
172 5 0.04
173 58 0.46
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.39
Consensus pattern (160 bp):
CTTCAAAAGCCTTATTACTCAAGTTAAATAGTTTTATTATCTCAAAATTGATTTTATGTTCAATG
TTTTTACTTTTGTGCTTAAACAGATTATAATTGAAAGTCTACCATGAGAAATGTAAAGAAAAAGG
CATTCATTAGCAAGATATAGTCACCCATTT
Found at i:770 original size:173 final size:171
Alignment explanation
Indices: 1--1016 Score: 768
Period size: 170 Copynumber: 5.9 Consensus size: 171
* * * **
1 TTTTTTACATTATTGGTTAAAATAGATTATAATTGAATGGCTACCTCAAGAAACATGAAGAAAAA
1 TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGAAGAAAAA
* * * *
66 GGCATTAATTGGCATGAAAAGTCCATTTATAGTCACCCATTTTTTCAAAAGCCTTATTACACACT
66 GGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCCTTATTACTCA-T
* **********
131 TTAAATGGTTTTATNNNNNNNNNNTTGATTTTAAGTTCAATT
130 TTAAATAGTTTTATTATCTCAAAATTGATTTTAAGTTCAATT
* * * *
173 TTTTTTACATTTTTGGTTCAAACAAACTATAATTGAATGTCTACCTTAAGAAATGTGAAGAAAAA
1 TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGAAGAAAAA
* ********** *
238 ---A-TCATTGGCAAGAAAAGTCTATTTANNNNNNNNNNTTCCTTCAAAAGCCTTATTACTCAAT
66 GGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCCTTATTACTC-AT
* **
299 TTCAATAGTTTTATTATCTCAAAATTGATTTTGTGTTCAATT
130 TTAAATAGTTTTATTATCTCAAAATTGATTTTAAGTTCAATT
* * * ** *
341 TTTTTGTACATTTTTGCTTAAAACATATTATAATTGAAAGTCTACCTTGAGAAATGTAAAGAAAA
1 TTTTT-TACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGAAGAAAA
* ********** *
406 AGGCATTCATTAGCAAGANNNNNNNNNNTATAGTCACCCATTTCTTCAAAAGCCTTATTACTTGA
65 AGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCCTTATTAC-TCA
* *
471 GTTAAATAGTTTTATTATCTCAAAATTGATTTTATGTTCAA-T
129 TTTAAATAGTTTTATTATCTCAAAATTGATTTTAAGTTCAATT
* * *
513 GTTTTTAC-TTTTGTGGTT-AAACAGATTATAATTGAATGTCTACGAT-GAGAAATGTGAAGAAA
1 TTTTTTACATTTT-TGGTTAAAACAGATTATAATTGAATGTCTAC-CTCAAGAAATGTGAAGAAA
* * * * *
575 AAGGCATTCATTGACAAGAAAAGTCCATTTATAGTTAGCCC-TTGCTTCGAAAGCCCTATTACTC
64 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCA-CCCATTTCTTCAAAAGCCTTATTACTC
* * *
639 ATTTCAAGTGGTTTTATAATCTCAAAATTGATTTTAAGTTCAACTT
128 ATTT-AAATAGTTTTATTATCTCAAAATTGATTTTAAGTTCAA-TT
** * * * *
685 TTTTTTACATTTTTGGTTAAAACAGGCTACAGTTGAATGTCTACCTCAAGAAACGTTAAGAAAAA
1 TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGAAGAAAAA
* * ********** *
750 TGCATTCATTGGCTAGAAAAGTCCATTTATAGTCNNNNNNNNNNTCAAAAGCCTTATTACTCCCT
66 GGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCCTTATTACT-CAT
* * ** *
815 TTAAAT-GATTTTATAATCTCATAATCAATTTTAAGTTGAA--
130 TTAAATAG-TTTTATTATCTCAAAATTGATTTTAAGTTCAATT
* * * * * * * *
855 TTGTTTACATTTTTTGTTAAAATAGACTATAATTGAATG-CATGCCT-TAGAAAACGTGTAGAAA
1 TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTC-TACCTCAAG-AAATGTGAAGAAA
** * * * *
918 AATCCATTTATTTGG-AAGAAAAGTCCATTTATAGTCTCCTA-TTCTTTCAAAAGCTTTATTACT
64 AAGGCATTCA-TTGGCAAGAAAAGTCCATTTATAGTCACCCATTTC-TTCAAAAGCCTTATTACT
* * * *
981 CGCTTTAAACAGTTTTATAATCTCATAATTGATTTT
127 C-ATTTAAATAGTTTTATTATCTCAAAATTGATTTT
1017 NNNNNNNNNN
Statistics
Matches: 663, Mismatches: 156, Indels: 52
0.76 0.18 0.06
Matches are distributed among these distances:
168 75 0.11
169 63 0.10
170 239 0.36
171 16 0.02
172 77 0.12
173 188 0.28
174 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.37
Consensus pattern (171 bp):
TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAATGTGAAGAAAAA
GGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCCTTATTACTCATT
TAAATAGTTTTATTATCTCAAAATTGATTTTAAGTTCAATT
Found at i:783 original size:343 final size:339
Alignment explanation
Indices: 1--783 Score: 793
Period size: 343 Copynumber: 2.3 Consensus size: 339
* * * * *
1 TTTTTTACATTATTGGTTAAAATAGATTATAATTGAATGGCTACCTCAAGAAACATGAAGAAAAA
1 TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACGTAAAGAAAAA
* * *
66 GGCATTAATTGGCATGAAAAGTCCATTTATAGTCACCCATTTTTTCAAAAGCCTTATTACACACT
66 GGCATTCATTGGCA-GAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCCTTATTACACACG
* ********** *
131 TTAAATGGTTTTATNNNNNNNNNNTTGATTTTAAGTTCAATTTTTTTTACATTTTTGGTTCAAAC
130 TTAAATAGTTTTATTATCTCAAAATTGATTTTAAGTTCAATTGTTTTTACATTTTTGGTTCAAAC
* * *
196 AAACTATAATTGAATGTCTACCTTAAGAAATGTGAAGAAAAAATCATTGGCAAGAAAAGTCTATT
195 AAACTATAATTGAATGTCTACCATAAGAAATGTGAAGAAAAAATCATTGACAAGAAAAGTCCATT
********** * *
261 TANNNNNNNNNNTTCCTTCAAAAGCCTTATTACTCAATTTCAATAGTTTTATTATCTCAAAATTG
260 TATAGTTAGCCCTTCCTTCAAAAGCCCTATTACTCAATTTCAATAGTTTTATAATCTCAAAATTG
**
326 ATTTTGTGTTCAATT
325 ATTTTAAGTTCAATT
* * * ** *
341 TTTTTGTACATTTTTGCTTAAAACATATTATAATTGAAAGTCTACCTTGAGAAATGTAAAGAAAA
1 TTTTT-TACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACGTAAAGAAAA
* ********** **
406 AGGCATTCATTAGCAAGANNNNNNNNNNTATAGTCACCCATTTCTTCAAAAGCCTTATTACTTGA
65 AGGCATTCATTGGC-AGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCCTTATTAC-ACA
*
471 -GTTAAATAGTTTTATTATCTCAAAATTGATTTTATGTTCAA-TGTTTTTAC-TTTTGTGGTT-A
128 CGTTAAATAGTTTTATTATCTCAAAATTGATTTTAAGTTCAATTGTTTTTACATTTT-TGGTTCA
* * * *
532 AACAGATTATAATTGAATGTCTACGATGAGAAATGTGAAGAAAAAGGCATTCATTGACAAGAAAA
192 AACAAACTATAATTGAATGTCTACCATAAGAAATGTGAAGAAAAA---A-TCATTGACAAGAAAA
* * *
597 GTCCATTTATAGTTAGCCCTTGCTTCGAAAGCCCTATTACTC-ATTTCAAGTGGTTTTATAATCT
253 GTCCATTTATAGTTAGCCCTTCCTTCAAAAGCCCTATTACTCAATTTCAA-TAGTTTTATAATCT
661 CAAAATTGATTTTAAGTTCAACTT
317 CAAAATTGATTTTAAGTTCAA-TT
** * * *
685 TTTTTTACATTTTTGGTTAAAACAGGCTACAGTTGAATGTCTACCTCAAGAAACGTTAAGAAAAA
1 TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACGTAAAGAAAAA
*
750 TGCATTCATTGGCTAGAAAAGTCCATTTATAGTC
66 GGCATTCATTGGC-AGAAAAGTCCATTTATAGTC
784 NNNNNNNNNN
Statistics
Matches: 345, Mismatches: 88, Indels: 17
0.77 0.20 0.04
Matches are distributed among these distances:
339 45 0.13
340 18 0.05
341 122 0.35
342 10 0.03
343 143 0.41
344 7 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.37
Consensus pattern (339 bp):
TTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACGTAAAGAAAAA
GGCATTCATTGGCAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCCTTATTACACACGT
TAAATAGTTTTATTATCTCAAAATTGATTTTAAGTTCAATTGTTTTTACATTTTTGGTTCAAACA
AACTATAATTGAATGTCTACCATAAGAAATGTGAAGAAAAAATCATTGACAAGAAAAGTCCATTT
ATAGTTAGCCCTTCCTTCAAAAGCCCTATTACTCAATTTCAATAGTTTTATAATCTCAAAATTGA
TTTTAAGTTCAATT
Done.