Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399183.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2453.0, 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: 3336
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.27
Warning! 832 characters in sequence are not A, C, G, or T
Found at i:568 original size:172 final size:170
Alignment explanation
Indices: 4--1221 Score: 713
Period size: 172 Copynumber: 7.1 Consensus size: 170
1 ATG
* * *** *
4 TACAAAGAATTCAAATTTAAATCAATTTTCAAATTATAAAACCATTTAAAGCGAGTAATAAGGCT
1 TACAAAGAATTCAAATTAAAATCAATTATGGCATTATAAAACCATTTAAATCGAGTAATAAGGCT
* * * * * *
69 TCTGAATGTAT-GGCTGAATATAAATGGACTTTTCTTACTAATGAATACTTTTTTCTTCATGTTT
66 TTTGAAGGTATAGG-TGACTATAAATGGACTTTTCTTGCCAATGAATAC-TTTTTCTTTATGTTT
* * *****
133 CTAAAGGTAGACATTCAATCATAGTCTGTTTTAACCAANNNNN
129 CT-GAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATA
***** * * * *
176 NNNNNAGAATTCAAACTT-AAATAAATTTTGAG-ATTAT-AAATCATTGAAAGT-GAGTAATAAG
1 TACAAAGAATTCAAA-TTAAAATCAATTATG-GCATTATAAAACCATTTAAA-TCGAGTAATAAG
********** * * * * *
237 GCTTTTGAANNNNNNNNNNACTATAAATGGACTTCTCTTGCCAAAGAATGTCTTTGTCTTTACGT
63 GCTTTTGAAGGTATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT-ACTTTTTCTTTATGT
* * * *
302 TTATTAAGATAGACATTCAAT--TAACGTCT-ATTTAACCAAAAATA
127 TT-CTGAGGTAGACATTCAATCCT-A-GTCTGTTTTAACCAAAAATA
* * * **********
346 TAAAAAAACATTCAACTTAAAATCAATTATGGCNNNNNNNNNNCATTTAAATCGAGTAATAAGGC
1 TACAAAGA-ATTCAAATTAAAATCAATTATGGCATTATAAAACCATTTAAATCGAGTAATAAGGC
* *
411 TTTTGAAGCTATAGGTGACTATAAATGGAGTTTTCTTGCCAATGAATACTCTTTTCTTTATGTTT
65 TTTTGAAGGTATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATACT-TTTTCTTTATGTTT
*
476 ATGAAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATA
129 CTG-AGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATA
* * ** * * ***********
519 TACAAAGAATTGAAATTCAAATTTATTTTGAG-ATTATAAAACAATTTAAAGNNNNNNNNNNGGC
1 TACAAAGAATTCAAATTAAAATCAATTATG-GCATTATAAAACCATTTAAATCGAGTAATAAGGC
* * * * *
583 TTTTGAAGGAAT-GGCTGACTATAATTGGACTTCTCTTGCCAATGAATAACTTTTTATTTACGTT
65 TTTTGAAGGTATAGG-TGACTATAAATGGACTTTTCTTGCCAATGAAT-ACTTTTTCTTTATGTT
* * *
647 TCTCGAGGTACACATTC-ATCGATAGTCT-ATTTAACCAAAAATA
128 TCT-GAGGTAGACATTCAATC-CTAGTCTGTTTTAACCAAAAATA
* * * * * **
690 TA-AAGAAAATTTAACTTAAAATCAATTATGGCATTACAAAACCATTGAAATCGAGTAATGGGGC
1 TACAA-AGAATTCAAATTAAAATCAATTATGGCATTATAAAACCATTTAAATCGAGTAATAAGGC
* * * *
754 TTTTGAAGGTATGGGTGACTATAATTGGACTTTTCTTGCCAATAAATACTTGTTTCTTCATGTTT
65 TTTTGAAGGTATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTT-TTTCTTTATGTTT
* * * * *
819 CTAAAGGTAGATATTCAATACTAGTTTGTTTTAACCAAAAATG
129 CT-GAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATA
* * ********** * *
862 TACAAAGACTTCAAATTTAAATCNNNNNNNNNNTTATAAAACCATTTCAAGT-GAGTAATAAGAC
1 TACAAAGAATTCAAATTAAAATCAATTATGGCATTATAAAACCATTT-AAATCGAGTAATAAGGC
* * * *
926 TTTTGAAGGTATGGGTGACTATAAATGGACTTCTCTTGCCAATGACTGTCTTTTTCTTTATGTTT
65 TTTTGAAGGTATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT-ACTTTTTCTTTATGTTT
** * * **
991 CTCGAGGTAGACATTCAATTATAATCTG-TTCAATTAAAAATA
129 CT-GAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATA
* * * ********** * *
1033 TA-AAAAATATTCAACTTAAAATGAATTATGGCATTANNNNNNNNNNTAAAGCGAGTAGTAAGGC
1 TACAAAGA-ATTCAAATTAAAATCAATTATGGCATTATAAAACCATTTAAATCGAGTAATAAGGC
* * * * *
1097 TTTTGAAGGTATAGGTGACTACAAATGGACTTTTCTTGCCAATGAAAACTTTATCCTTCATGTGT
65 TTTTGAAGGTATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTT-TTCTTTATGTTT
* * * *
1162 CTATAGGTAGACATTCAATCCTTGTCAGTTTTAACTAAAAATA
129 CT-GAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATA
1205 TACAAAGAATTCAAATT
1 TACAAAGAATTCAAATT
1222 TAANNNNNNN
Statistics
Matches: 768, Mismatches: 241, Indels: 74
0.71 0.22 0.07
Matches are distributed among these distances:
169 1 0.00
170 32 0.04
171 338 0.44
172 356 0.46
173 40 0.05
174 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.34
Consensus pattern (170 bp):
TACAAAGAATTCAAATTAAAATCAATTATGGCATTATAAAACCATTTAAATCGAGTAATAAGGCT
TTTGAAGGTATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTCTTTATGTTTCT
GAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATA
Found at i:1222 original size:343 final size:336
Alignment explanation
Indices: 36--1373 Score: 896
Period size: 343 Copynumber: 3.9 Consensus size: 336
26 CAATTTTCAA
* * * * * *
36 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTCTGAATGTAT-GGCTGAATATAAATGGACTT
1 ATTACAAAACCATTGAAAGCGAGTAATAAGGCTTTTGAAGGTATAGG-TGACTACAAATGGACTT
* * * * * * *
100 TTCTTACTAATGAATACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAAT-CATAGTCTGTTT
65 TTCTTGCCAATAAATACTTGTTCCTTCATGTGTCTAAAGGTAGACATTCAATAC-TAGTCAGTTT
********** * * *
164 TAACCAANNNNNNNNNNAGAATTCAAACTTAAATAAATTTTGAGATTAT-AAATCATTGAAAGTG
129 TAACCAAAAATATACAAAGAATTCAAA-TT---TAAA---TCAGATTATAAAACCATTTAAAGTG
* ********** * * * *
228 AGTAATAAGGCTTTTGAANNNNNNNNNNACTATAAATGGACTTCTCTTGCCAAAGAATGTCTTTG
187 AGTAATAAGACTTTTGAAGGAATGGGTGACTATAATTGGACTTCTCTTGCCAATGAATGACTTTT
* * ** * * * *
293 TCTTTACGTTTATTAAGATAGACATTCAATTA-ACGTCTATTTAACCAAAAATATAAAAAAACAT
252 TATTTACGTTTCTCGAGGTAGACATTCAATTATA-ATCTATTCAACCAAAAATATAAAGAAA-AT
357 TCAACTTAAAATCAATTATGGC
315 TCAACTTAAAATCAATTATGGC
********** * * * * *
379 NNNNNNNNNNCATTTAAATCGAGTAATAAGGCTTTTGAAGCTATAGGTGACTATAAATGGAGTTT
1 ATTACAAAACCATTGAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTACAAATGGACTTT
* * * * * * * *
444 TCTTGCCAATGAATACTCT-TTTCTTTATGTTTATGAAGGTAGACATTCAATCCTAGTCTGTTTT
66 TCTTGCCAATAAATACT-TGTTCCTTCATGTGTCTAAAGGTAGACATTCAATACTAGTCAGTTTT
** * * ***
508 AACCAAAAATATACAAAGAATTGAAATTCAAATTTATTTTGAGATTATAAAACAATTTAAAGNNN
130 AACCAAAAATATAC--A-AA--G-AATTCAAATTTA-AATCAGATTATAAAACCATTTAAAGTGA
******* * * *
573 NNNNNNNGGCTTTTGAAGGAATGGCTGACTATAATTGGACTTCTCTTGCCAATGAATAACTTTTT
188 GTAATAAGACTTTTGAAGGAATGGGTGACTATAATTGGACTTCTCTTGCCAATGAATGACTTTTT
* * * * *
638 ATTTACGTTTCTCGAGGTACACATTC-ATCGATAGTCTATTTAACCAAAAATATAAAGAAAATTT
253 ATTTACGTTTCTCGAGGTAGACATTCAAT-TATAATCTATTCAACCAAAAATATAAAGAAAATTC
702 AACTTAAAATCAATTATGGC
317 AACTTAAAATCAATTATGGC
* ** * * *
722 ATTACAAAACCATTGAAATCGAGTAATGGGGCTTTTGAAGGTATGGGTGACTATAATTGGACTTT
1 ATTACAAAACCATTGAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTACAAATGGACTTT
* * * **
787 TCTTGCCAATAAATACTTGTTTCTTCATGTTTCTAAAGGTAGATATTCAATACTAGTTTGTTTTA
66 TCTTGCCAATAAATACTTGTTCCTTCATGTGTCTAAAGGTAGACATTCAATACTAGTCAGTTTTA
* * *** *
852 ACCAAAAATGTACAAAGACTTCAAATTTAAATCNNNNNNNNNNTTATAAAACCATTTCAAGTGAG
131 ACCAAAAATATACAAAGAATTCAAATTTAAATC-------AGATTATAAAACCATTTAAAGTGAG
* * * * *
917 TAATAAGACTTTTGAAGGTATGGGTGACTATAAATGGACTTCTCTTGCCAATGACTGTCTTTTTC
189 TAATAAGACTTTTGAAGGAATGGGTGACTATAATTGGACTTCTCTTGCCAATGAATGACTTTTTA
* * **
982 TTTATGTTTCTCGAGGTAGACATTCAATTATAATCTGTTCAATTAAAAATATAAA-AAATATTCA
254 TTTACGTTTCTCGAGGTAGACATTCAATTATAATCTATTCAACCAAAAATATAAAGAAA-ATTCA
*
1046 ACTTAAAATGAATTATGGC
318 ACTTAAAATCAATTATGGC
********* *
1065 ATTANNNNNNNNNNT-AAAGCGAGTAGTAAGGCTTTTGAAGGTATAGGTGACTACAAATGGACTT
1 ATTA-CAAAACCATTGAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTACAAATGGACTT
* * *
1129 TTCTTGCCAATGAAA-ACTT-TATCCTTCATGTGTCTATAGGTAGACATTCAATCCTTGTCAGTT
65 TTCTTGCCAAT-AAATACTTGT-TCCTTCATGTGTCTAAAGGTAGACATTCAATACTAGTCAGTT
* *** *
1192 TTAACTAAAAATATACAAAGAATTCAAATTTAANNNNNNNNNNAGATTATAAAATCATTTAAAGT
128 TTAACCAAAAATATACAAAGAATTCAAATTTAA-------ATCAGATTATAAAACCATTTAAAGT
* * * * * *
1257 GAGTAATAAGGCTTTCGAAGGAATGTGTGACTATAATTTGACTTCTCTTGCCAATGAATGCCGTT
186 GAGTAATAAGACTTTTGAAGGAATGGGTGACTATAATTGGACTTCTCTTGCCAATGAATGACTTT
* * * ** * *
1322 TTATTTACATTGCTCGAAGTAGACATTCAATTATTGTCTGTTTAACCAAAAA
251 TTATTTACGTTTCTCGAGGTAGACATTCAATTATAATCTATTCAACCAAAAA
1374 AAAAAAAAAA
Statistics
Matches: 776, Mismatches: 186, Indels: 66
0.75 0.18 0.06
Matches are distributed among these distances:
336 1 0.00
337 11 0.01
338 1 0.00
340 2 0.00
341 1 0.00
342 5 0.01
343 630 0.81
344 110 0.14
345 3 0.00
346 1 0.00
348 3 0.00
349 8 0.01
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.34
Consensus pattern (336 bp):
ATTACAAAACCATTGAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTGACTACAAATGGACTTT
TCTTGCCAATAAATACTTGTTCCTTCATGTGTCTAAAGGTAGACATTCAATACTAGTCAGTTTTA
ACCAAAAATATACAAAGAATTCAAATTTAAATCAGATTATAAAACCATTTAAAGTGAGTAATAAG
ACTTTTGAAGGAATGGGTGACTATAATTGGACTTCTCTTGCCAATGAATGACTTTTTATTTACGT
TTCTCGAGGTAGACATTCAATTATAATCTATTCAACCAAAAATATAAAGAAAATTCAACTTAAAA
TCAATTATGGC
Done.