Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398012.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1319.0, 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: 2095
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.31
Warning! 415 characters in sequence are not A, C, G, or T
Found at i:394 original size:171 final size:169
Alignment explanation
Indices: 1--402 Score: 457
Period size: 171 Copynumber: 2.4 Consensus size: 169
* * ** *
1 CCATTTATAGTCACTCAAGCCTTCAAAAAACTTATTACTACCTTTAAATTATTTTATAATTTCAC
1 CCATTTATAGTCACTCAAGCCTTCAAAAGACTTATTACTCCCTTTAAATGGTTTTATAATCTCAC
* * * * *
66 AATTGAATTTAAGTTAAATTTTTTATATTTTTGGTTAAAATAAATTATATTTTAATGTCTGCCTC
66 AATTGAATTTAAGTTAAATTTTTTACATTTTTGCTGAAAATAAATTATATTTGAATATCTGCCTC
* * * *
131 AGGAAATGTGAAGCAAAAGCCATCTATTGGTAAGAAAAGT
131 AGAAAATGT-AAGCAAAAGCCATCCATTGATAAGAAAAAT
* * * * *
171 CCATTTATAGTCACTCAAGACATT-AAAAGCCTTATTTCTCGCTTTCAATGGTTTTATAATCTCA
1 CCATTTATAGTCACTCAAG-CCTTCAAAAGACTTATTACTCCCTTTAAATGGTTTTATAATCTCA
* * * * **
235 TAATTGATTTTTAGTTAAATTGTTTTGCATTTTTGCTGAAAATAAATTATATTTGAATATCTTTC
65 CAATTGAATTTAAGTTAAATT-TTTTACATTTTTGCTGAAAATAAATTATATTTGAATATCTGCC
* *
300 TCGAGAAACATGT-AGCAAAAGCCCTCCATTGATAATAAAAAT
129 TC-AGAAA-ATGTAAGCAAAAGCCATCCATTGATAAGAAAAAT
** * * *
342 TTATTTCTAGTCATTCAAGCCTTCAAAAGACTTATTGCTCCCTTTAAATGGTTTTATAATC
1 CCATTTATAGTCACTCAAGCCTTCAAAAGACTTATTACTCCCTTTAAATGGTTTTATAATC
403 NNNNNNNNNN
Statistics
Matches: 191, Mismatches: 36, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
170 71 0.37
171 112 0.59
172 4 0.02
173 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (169 bp):
CCATTTATAGTCACTCAAGCCTTCAAAAGACTTATTACTCCCTTTAAATGGTTTTATAATCTCAC
AATTGAATTTAAGTTAAATTTTTTACATTTTTGCTGAAAATAAATTATATTTGAATATCTGCCTC
AGAAAATGTAAGCAAAAGCCATCCATTGATAAGAAAAAT
Found at i:1654 original size:513 final size:500
Alignment explanation
Indices: 677--1867 Score: 1249
Period size: 513 Copynumber: 2.3 Consensus size: 500
667 NNNNNNAATG
* *
677 TGAAGTAAAAGCCATCCATTTGCAAGTAAAGTCCATTTATAGTTACTCAAGCCCTCAAAAAACTT
1 TGAAGCAAAAGCCATCCATTTGCAAGCAAAGTCCATTTATAGTTACTCAAGCCCTCAAAAAACTT
* * *
742 ATTACTAGCTTTAAATTATTTTATAATTTTACAATTGAATTTAAGTTAAATTTTTTTACATTTTT
66 ATTACCAGCTTTAAATTATTTTATAATTTCACAATTGAATATAAGTTAAATTTTTTTACATTTTT
* * * *
807 GGTTAAAATAAATTATATTTCAATGTCTGCCTCAAGAAACTTGAAGCAAAAGCCATCCATTGGTA
131 GGTTAAAATAAATTATATTTCAAAGTCTACCTCAAGAAACGTAAAGCAAAAGCCATCCATTGGTA
* *********
872 AAAAAAGTCCATTGTAGTCACTCAAGACATTAAAAGCCTTATTTCTCACTNNNNNNNNNNTTATA
196 AAAAAAGTCCATTATAGTCACTCAAGACATTAAAAGCCTTATTTCTCACT-TAAATAGTTTTATA
* *
937 ATCTCATAATTGATTTTTAGTTAAATTGTTTTACATTTTTGGTGAAAAAAAATTATATGTGAATG
260 ATCTCATAATTGATTTTTAGTTAAATTGTTTTACATTTTTAGTGAAAAAAAATTATATGTAAATG
* * * *
1002 TCTCCCTCGAGAAACATGAAGTAAAAGCCCTCCATTGGCAACAAAAATTTATTTATAGTCATGCA
325 TCTCCCTCAAGAAACATGAAGTAAAAGCCCCCCATTGACAAAAAAAATTTATTTATAGTCATGCA
* *
1067 AACCTTTAAAAAACTTATTGCTCCCTTTAAATGGTTTTATAATCTTATGATTGATTTTAAGTTGA
390 AACCTTCAAAAAACTTATTGCTCCATTTAAATGGTTTTATAATCTTATGATTGATTTTAAGTTGA
1132 ATTTTTTTACANNNNNNNNNNAAATATATTATAACTGAATGTCTACCTTTGAAATA
455 ATTTTTTTACA----------AAATATATTATAACTGAATGTCTACCTTTGAAATA
* * * *
1188 TGAAGCAAAAGTCATCCATTTGTAAGCAAATTCTATTTATA-TTCACTCAAGCCCTCAAAAAACT
1 TGAAGCAAAAGCCATCCATTTGCAAGCAAAGTCCATTTATAGTT-ACTCAAGCCCTCAAAAAACT
1252 TATTACCAGCTTTAAATTATTTTATAATTTCACAATTGAATATAAGTTAAATTTTTTTTACATTT
65 TATTACCAGCTTTAAATTATTTTATAATTTCACAATTGAATATAAGTTAAA-TTTTTTTACATTT
* *
1317 TTGGTTAAAATAAATTATATTTCAAAGTCTACCTCAGGAAACGTAAAGCAAAAGCCATCTATTGG
129 TTGGTTAAAATAAATTATATTTCAAAGTCTACCTCAAGAAACGTAAAGCAAAAGCCATCCATTGG
* *******************
1382 TAAGAAAAGTCCATTTATAGTCACTCAAGACATTNNNNNNNNNNNNNNNNNNNNTAAATAGTTTT
194 TAAAAAAAGTCCA-TTATAGTCACTCAAGACATT-AAAAGCCTTATTTCTCACTTAAATAGTTTT
* *
1447 ATAATCTCATAATTGATTTTTAGTTAAATTGTTTTACATTTTTAGTGAAAACAAATTATATTTAA
257 ATAATCTCATAATTGATTTTTAGTTAAATTGTTTTACATTTTTAGTGAAAAAAAATTATATGTAA
* * *
1512 ATGTCTTCCTCAAGAAACATGAAGTCAAAGCCCCCCATTTACAAAAAAAATTTATTTATAGTCAT
322 ATGTCTCCCTCAAGAAACATGAAGTAAAAGCCCCCCATTGACAAAAAAAATTTATTTATAGTCAT
* **********
1577 GCAAACCTTCAAAAGACTTATTGCTCCATTTAAATGGTTTTATAATCNNNNNNNNNNTTTTAAGT
387 GCAAACCTTCAAAAAACTTATTGCTCCATTTAAATGGTTTTATAATCTTATGATTGATTTTAAGT
* * * *** *
1642 TGAATTTTTTTACATTTTCAGTTAAAACATATTATAACTAAATGTCTGCCCCGGAAATG
452 TGAATTTTTTT--A----C----AAAATATATTATAACTGAATGTCTACCTTTGAAATA
* * * ** * **
1701 TGAACCAAAAGCCATCTATTTGCAAGCAAAGTCCATTTATAGTCACTCAAGCGTTC-GAAGCCTT
1 TGAAGCAAAAGCCATCCATTTGCAAGCAAAGTCCATTTATAGTTACTCAAGCCCTCAAAAAACTT
** * * * *
1765 ATTA-CACGCTTTAAATGGTTTTATAATCAT-ATAATT-AACTTTAAGTTGAATTTTTTTACATT
66 ATTACCA-GCTTTAAATTATTTTATAAT-TTCACAATTGAA-TATAAGTTAAATTTTTTTACATT
* * * *
1827 TTTAGTTAAAATAAATTATAATTGAATGTCTACCTCAAGAA
128 TTTGGTTAAAATAAATTATATTTCAAAGTCTACCTCAAGAA
1868 NNNNNNNNNN
Statistics
Matches: 563, Mismatches: 99, Indels: 36
0.81 0.14 0.05
Matches are distributed among these distances:
510 2 0.00
511 155 0.28
512 125 0.22
513 277 0.49
514 1 0.00
515 1 0.00
519 1 0.00
523 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.36
Consensus pattern (500 bp):
TGAAGCAAAAGCCATCCATTTGCAAGCAAAGTCCATTTATAGTTACTCAAGCCCTCAAAAAACTT
ATTACCAGCTTTAAATTATTTTATAATTTCACAATTGAATATAAGTTAAATTTTTTTACATTTTT
GGTTAAAATAAATTATATTTCAAAGTCTACCTCAAGAAACGTAAAGCAAAAGCCATCCATTGGTA
AAAAAAGTCCATTATAGTCACTCAAGACATTAAAAGCCTTATTTCTCACTTAAATAGTTTTATAA
TCTCATAATTGATTTTTAGTTAAATTGTTTTACATTTTTAGTGAAAAAAAATTATATGTAAATGT
CTCCCTCAAGAAACATGAAGTAAAAGCCCCCCATTGACAAAAAAAATTTATTTATAGTCATGCAA
ACCTTCAAAAAACTTATTGCTCCATTTAAATGGTTTTATAATCTTATGATTGATTTTAAGTTGAA
TTTTTTTACAAAATATATTATAACTGAATGTCTACCTTTGAAATA
Done.