Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397648.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4927.0, 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: 2554
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.34
Warning! 144 characters in sequence are not A, C, G, or T
Found at i:1238 original size:511 final size:491
Alignment explanation
Indices: 721--2183 Score: 1248
Period size: 511 Copynumber: 2.9 Consensus size: 491
711 AACAATTTTG
*
721 AAAAATTCAACCTAAAATCAATTATCAGACTAGAAAACCATTGGAAGCGAGTAATA-AGGCTTTT
1 AAAAATTCAACCTAAAATCAATTATCAGACTAGAAAACCATTGGAAGCAAGTAATATA-GCTTTT
********** * * *
785 GAAGNNNNNNNNNNCTATAAATGGACTTTTCTTGTCGATGAATGCTCTTTTTTTCACATTTCTTT
65 GAAGGAAAGGGTGACTATAAATGGACTTTTCTTGTCGATGAATGCTCTTTTCTTCACATTTATTA
* * * *
850 AGATAGATATTTAATTATAGTCTATTTTAATCAAAAATGTAAAAACTTTCAACTTAAAATTAATT
130 AGATAAATATTCAATTATAGTCTATTTTAATCAAAAATGTAAAAAATTTCAACTTAAAATCAATT
* *****
915 ATTAGATTATAAAACCATTTAAAGTGANNNNNNNNNNTTTTGAAGGAATGGGAGGCTGTAAACAG
195 ATTACATTATAAAACCATTTAAAGTGA-----AAGGCTTTTGAAGGAATGGGAGGCTGTAAACAG
* * * * *
980 ACTTTTCTTGCCAATGAGTGC-TTTTTCTTCATGCTTCTCAAGGCAAACATTCAATTATAGTTTA
255 ACTTTTCCTGACAATGAATGCTTTTTTCTTCATGCTTCTCAAGCCAAACATTCAATTATAGTCTA
* * * ******
1044 TTTTAATGAAAAACGTAAAAACTTTGAGCTTAAAATCAAGTATGAGATTATAAAACTATNNNNNN
320 TTTTAATGAAAAACGTAAAAAATTTGAACTTAAAATCAAGTATGAGATTATAAAACCATTTAAAG
**** *
1109 NNNNTAATAAGGCTTTTGAAGGAA-TGGCTGACTATGAACGGACTTTTCTTTATAATGAATACTT
385 TGAGTAATAAGGCTTTTGAAGGAATTGG-TGACTATAAACGGACTTTT-TTTATAATGAATACTT
1173 TTTCCTTCATGTTTCTCGAGATAAACATTCAATTATTGNNNNNNNNNNNNNNNATGTAA
448 TTTCCTTCATGTTTCTCGAGATAAACATTCAATTATTG---------------ATGTAA
* * * * *
1232 AAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTGAAGCAAGTAATATAGCTTTTG
1 AAAAATTCAACCTAAAATCAATTATCAGACTAGAAAACCATTGGAAGCAAGTAATATAGCTTTTG
*
1297 AAGGAAAGGGTGACTATAAATGGACTTTTCTTGTCGATGAATGCTCTTTTCTTCACGTTTATTAA
66 AAGGAAAGGGTGACTATAAATGGACTTTTCTTGTCGATGAATGCTCTTTTCTTCACATTTATTAA
* * * *
1362 GATAAATATTCAATTATAGTCTGTTTTAATTAAAAATTTAAAAAATTTTAACTTAAAATCAATTA
131 GATAAATATTCAATTATAGTCTATTTTAATCAAAAATGTAAAAAATTTCAACTTAAAATCAATTA
***** *
1427 TTACATTATAAAACCATTTAANNNNNNNNNNAAGGCTTTTGAAGGAATGGGAGGCTGTAAATAGA
196 TTACATTATAAAACCATTTAA-----AGTGAAAGGCTTTTGAAGGAATGGGAGGCTGTAAACAGA
* * * *
1492 CTTTTCCTGATAATGAATGCTTTTTTCTTCATGCTTTTCAAGCCAAACATTCGATTATAGTCTGT
256 CTTTTCCTGACAATGAATGCTTTTTTCTTCATGCTTCTCAAGCCAAACATTCAATTATAGTCTAT
*
1557 TTTAATGAAAAATGTAAAAAATTTGAACTTAAAATCAAGTATGAGATTATAAAACCATTTAAAGT
321 TTTAATGAAAAACGTAAAAAATTTGAACTTAAAATCAAGTATGAGATTATAAAACCATTTAAAGT
*
1622 GAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGGACTTTTTTTATAATGAATACTTTTT
386 GAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAACGGACTTTTTTTATAATGAATACTTTTT
1687 CCTTCATGTTTCTCGAGATAAACATTCAATTATTGTTTGTTTTAATAAAAATGTAA
451 CCTTCATGTTTCTCGAGATAAACATTCAATTA----TTG-----------ATGTAA
* * * * **
1743 AAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCAAGTAATA-AGGCTTTT
1 AAAAATTCAACCTAAAATCAATTATCAGACTAGAAAACCATTGGAAGCAAGTAATATA-GCTTTT
* * * * * * * * * * * **
1807 GAAAGAATGAGAGGCTATAAATAGACTTTTCTTGCCAATAAATGCTTTTTTCTTCACATTTCTCG
65 GAAGGAAAGGGTGACTATAAATGGACTTTTCTTGTCGATGAATGCTCTTTTCTTCACATTTATTA
** * * * * *
1872 AGGCAAACATTCAATTATAGCCTGTTTTAA-CGAAAAATAT-AAAAATATTCAACTTCAAATCAA
130 AGATAAATATTCAATTATAGTCTATTTTAATC-AAAAATGTAAAAAAT-TTCAACTTAAAATCAA
* * * * * * * * * * *
1935 TTATGAGATTATAAAACTATTTGAAGTGAGTAGTATGGCTTTTAAAGAAAAGGGTGACTATAAAT
193 TTATTACATTATAAAACCATTTAAAGTGA--A--A-GGCTTTTGAAGGAATGGGAGGCTGTAAAC
* * * * * * * * * *
2000 GGACTTTTCTTGTCAATGAATGCTTTTTTTTTCACGTTTGTCGAGACAAATATTCAATTATAGTC
253 AGACTTTTCCTGACAATGAATGCTTTTTTCTTCATGCTTCTCAAGCCAAACATTCAATTATAGTC
* ** * * ** * * * **
2065 T-TTTTGAATCAAAAGTGTAAAAAAATTCAACCAAAAATCAATTATGAGATTAAAAAACTATTGG
318 TATTTT-AATGAAAAACGTAAAAAATTTGAACTTAAAATCAAGTATGAGATTATAAAACCATTTA
** * * *
2129 AAGCAAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTTTTAT
382 AAGTGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAACGGACTTTTTTTAT
2184 CGATAACTGC
Statistics
Matches: 790, Mismatches: 141, Indels: 42
0.81 0.14 0.04
Matches are distributed among these distances:
508 1 0.00
510 12 0.02
511 640 0.81
512 131 0.17
513 3 0.00
515 3 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35
Consensus pattern (491 bp):
AAAAATTCAACCTAAAATCAATTATCAGACTAGAAAACCATTGGAAGCAAGTAATATAGCTTTTG
AAGGAAAGGGTGACTATAAATGGACTTTTCTTGTCGATGAATGCTCTTTTCTTCACATTTATTAA
GATAAATATTCAATTATAGTCTATTTTAATCAAAAATGTAAAAAATTTCAACTTAAAATCAATTA
TTACATTATAAAACCATTTAAAGTGAAAGGCTTTTGAAGGAATGGGAGGCTGTAAACAGACTTTT
CCTGACAATGAATGCTTTTTTCTTCATGCTTCTCAAGCCAAACATTCAATTATAGTCTATTTTAA
TGAAAAACGTAAAAAATTTGAACTTAAAATCAAGTATGAGATTATAAAACCATTTAAAGTGAGTA
ATAAGGCTTTTGAAGGAATTGGTGACTATAAACGGACTTTTTTTATAATGAATACTTTTTCCTTC
ATGTTTCTCGAGATAAACATTCAATTATTGATGTAA
Found at i:1472 original size:171 final size:170
Alignment explanation
Indices: 585--2430 Score: 1305
Period size: 171 Copynumber: 10.8 Consensus size: 170
575 NNNNNNNNNN
* * * * * *
585 AAACCATTTAAAGCAAGTAAAAAGGCTTTTGAAGGAATGAGAGGCTATAAATAG-CTTTTCTTGC
1 AAACCATTT-AAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * * *
649 CAATGAATGCATTTTTCTTCACGTTTCTCAAGACAAATATTCAATTATAGTCTGTTTGAA-TAAA
65 CAATGAATGCTTTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTAAA
* * * * * *
713 CAATTTTGAAAAA-TTCAACCTAAAATCAATTATCAGACTAGA
130 -AA-TGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
* * **********
755 AAACCATTGGAAGCGAGTAATAAGGCTTTTGAAGNNNNNNNNNNCTATAAATGGACTTTTCTTGT
1 AAACCATT-TAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * ** * * * * * *
820 CGATGAATGCTCTTTTT-TTCACATTTCTTTAGATAGATATTTAATTATAGTCTATTTTAATCAA
65 CAATGAATGCT-TTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTAA
* * *
884 AAATGTAAAAACTTTCAACTTAAAATTAATTATTAGATTATA
129 AAATGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
** ********** * * * ** *
926 AAACCATTTAAAGTGANNNNNNNNNNTTTTGAAGGAATGGGAGGCTGTAAACAGACTTTTCTTGC
1 AAACCATTT-AAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * * * * * * *
991 CAATGAGTGC-TTTTTCTTCATGCTTCTCAAGGCAAACATTCAATTATAGTTTATTTTAATGAAA
65 CAATGAATGCTTTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTAAA
* * * * *
1055 AACGTAAAAACTTTGAGCTTAAAATCAAGTATGAGATTATA
130 AATGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
* ********* * * *
1096 AAACTATNNNNNNNNNNTAATAAGGCTTTTGAAGGAATGGCTGACTATGAACGGACTTTTCTT-T
1 AAACCAT-TTAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * * * * * *************
1160 ATAATGAATACTTTTTCCTTCATGTTTCTCGAGATAAACATTCAATTATTG-NNNNNNNNNNNNN
65 -CAATGAATGCTTTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTAA
** * *
1224 NNATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATA
129 AAATGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
*
1266 AAACCATTTGAAGCAAGTAATATA-GCTTTTGAAGGAAAGGGTGACTATAAATGGACTTTTCTTG
1 AAACCATTT-AAGCAAGTAATA-AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTG
* * ** * *
1330 TCGATGAATGCTCTTTTCTTCACGTTTATTAAGATAAATATTCAATTATAGTCTGTTTTAATTAA
64 TCAATGAATGCTTTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTAA
* * * *
1395 AAATTTAAAAAATTTTAACTTAAAATCAATTATTACATTATA
129 AAATGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
********* * * * * *
1437 AAACCATTTAANNNNNNNNNNAAGGCTTTTGAAGGAATGGGAGGCTGTAAATAGACTTTTCCTGA
1 AAACCATTTAA-GCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTG-
* * * * *
1502 T-AATGAATGCTTTTTTCTTCATGCTTT-TCAAGCCAAACATTCGATTATAGTCTGTTTTAATGA
64 TCAATGAATGCTTTTTTCTTCACG-TTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTA
* *
1565 AAAATGTAAAAAATTTGAACTTAAAATCAAGTATGAGATTATA
128 AAAATGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
** * * *
1608 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGGACTTTTTTTAT
1 AAACCATTT-AAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * * * * *
1673 -AATGAATACTTTTTCCTTCATGTTTCTCGAGATAAACATTCAATTATTGTTTGTTTTAA-TAAA
65 CAATGAATGCTTTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTAAA
* *
1736 AATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATA
130 AATGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
* * * * * *
1777 AAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGAGGCTATAAATAGACTTTTCTTGC
1 AAACCATTT-AAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * * * **
1842 CAATAAATGCTTTTTTCTTCACATTTCTCGAGGCAAACATTCAATTATAGCCTGTTTTAACGAAA
65 CAATGAATGCTTTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTAAA
* *
1907 AATAT-AAAAATATTCAACTTCAAATCAATTATGAGATTATA
130 AATGTAAAAAAT-TTCAACTTAAAATCAATTATGAGATTATA
* ** * * * * *
1948 AAACTATTTGAAGTGAGTAGTATGGCTTTTAAAGAAAAGGGTGACTATAAATGGACTTTTCTTGT
1 AAACCATTT-AAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * *
2013 CAATGAATGCTTTTTTTTTCACGTTTGTCGAGACAAATATTCAATTATAGTCT-TTTTGAATCAA
65 CAATGAATGCTTTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTT-AATTAA
* * ** *
2077 AAGTGTAAAAAAATTCAACCAAAAATCAATTATGAGATTAAA
129 AAATGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
* * * * *
2119 AAACTATTGGAAGCAAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTTTTAT
1 AAACCATT-TAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * * * * *
2184 CGAT-AACTGCTCTTTTCTTCACGTTTCAT-GAGATAGATATTCAATTATAGTCTATTTTAATCA
65 CAATGAA-TGCTTTTTTCTTCACGTTT-ATCGAGACAAACATTCAATTATAGTCTGTTTTAATTA
* *
2247 AAATAT-AAAAAAATTTCAACTTAAAATCAATTATCAGATTATA
128 AAA-ATGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
********* * * ** * * *
2290 AAACCNNNNNNNNNNAGTAATAAGGCTTTTGAAGGAATGAGAGGTTGTAAATAGACATTTCTTGT
1 AAACC-ATTTAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * * *** * *
2355 CAATTAATGCTTTTTTCTTTACGTTTCTCAAGGTGAACATTCAATTATATTCTGTTTTAATGAAA
65 CAATGAATGCTTTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTAAA
2420 AATGTAAAAAA
130 AATGTAAAAAA
2431 ATTNNNNNNN
Statistics
Matches: 1291, Mismatches: 351, Indels: 67
0.76 0.21 0.04
Matches are distributed among these distances:
169 102 0.08
170 393 0.30
171 769 0.60
172 27 0.02
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
AAACCATTTAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTC
AATGAATGCTTTTTTCTTCACGTTTATCGAGACAAACATTCAATTATAGTCTGTTTTAATTAAAA
ATGTAAAAAATTTCAACTTAAAATCAATTATGAGATTATA
Done.