Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399022.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_23.1, 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: 3337
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.27
Warning! 794 characters in sequence are not A, C, G, or T
Found at i:1566 original size:171 final size:167
Alignment explanation
Indices: 994--1996 Score: 968
Period size: 171 Copynumber: 5.9 Consensus size: 167
984 NNNNNNNNNN
** * * **
994 ATAAAT-GAACTTTTCTTCATAATGAATGACTTTTTCTAGA-CGTTTATCGAGGTAGGTATTCAA
1 ATAAATGGAA-TTTTCTTCCCAATGAATG-CTTTTTCTACATC-TTTCT-GAGGTAGACATTCAA
** *
1057 TTATAGTCTGTTTTAATGAAAATTATAAAAAAAATT-AACTTAAAATCAATTATGAGATTGTAAA
62 TTATAGTCTGTTTTAAT-AAAA--ATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * *
1121 ACCATTT-AAGACGAGTAATTAGGCTTCTGAAGGAATGAGTGACT
124 ACCATTTAAAG-CAAGTAATAAGGCTTTTGAAGGAATGAGAGACT
* * *
1165 ATAAAT-GAACTTTTCTTCCCAATGAAAGCCTTTTTCTTCA-CGTTTCTTGAGGTAGACATTTAA
1 ATAAATGGAA-TTTTCTTCCCAATGAATG-CTTTTTCTACATC-TTTC-TGAGGTAGACATTCAA
* *
1228 TTATAGTCTG-TTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAGTTATGAGATTATAAAA
62 TTATAGTCTGTTTTAAT-AAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* * * * *
1292 TCA-TTAATGCTAGTAATAAGGCTTCTT-AAAGAATGAGTGACT
125 CCATTTAAAGCAAGTAATAAGGCTT-TTGAAGGAATGAGAGACT
* * * * * * **
1334 ATAAATGGACTTTTCTTTCCATTTAATGCCTTTTTCTTCA-CGTTTTTTGAGACAGACATTCAAT
1 ATAAATGGAATTTTCTTCCCAATGAATG-CTTTTTCTACATC--TTTCTGAGGTAGACATTCAAT
* * * * *
1398 TATAGTTTATTTTAACTAAAAATGTGAAAAAATTCACCTTAAAATCAATTATAAGATTATAAAGC
63 TATAGTCTGTTTTAA-TAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
*** * * * * *
1463 CATTTAAAATGAGTAATAAAGATTTTGAAGGGATGGGCGACT
126 CATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACT
* * * * * * *
1505 ATAGATAGACATTTT-TTGCCAATGAATAGCTTTTTCTACATCTTTCCCGAGGCAAACATTCAAC
1 ATAAATGGA-ATTTTCTTCCCAATGAAT-GCTTTTTCTACATCTTT-CTGAGGTAGACATTCAAT
* *
1569 TATAGTCTGTTTTAATAAAAAATGTAAAAAAATTCAAATTAATATCAATTATGAGATTATAAAAC
63 TATAGTCTGTTTTAAT-AAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
*
1634 CATTTAAAGCAAGTAATAAGGCTTTTGAAGGAAT-AGTGACT
126 CATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACT
* * *
1675 ATAAATGGATTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTTCTAAGGTAGACATTCAATT
1 ATAAATGGAATTTTCTTCCCAATGAAT-GCTTTTTCTACAT-CTTTCTGAGGTAGACATTCAATT
* * *
1740 ATAGTCTTTTTTTACAAAAAAATGTAAAATAATTCAACTTAAAATGAATTATGAGATTATAAAAC
64 ATAGTC-TGTTTTA-ATAAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAAC
* *
1805 CATTTAAACCAAGTAATAAGGCTTTTGAAGGAATGAGAGATT
126 CATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACT
* * * **
1847 ATAAATGGAATTTTCTTCCCAATGAATGACTTTTTTTACACCATTTTTGAGGTAGGTATTCAATT
1 ATAAATGGAATTTTCTTCCCAATGAATG-CTTTTTCTACATC-TTTCTGAGGTAGACATTCAATT
* * *
1912 ATAGTCTGTTTTAATGAAAATGTTAAACAAATTCAACTTCAAATCAAATATGAGATTATAAAACC
64 ATAGTCTGTTTTAATAAAAATG-TAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACC
* *
1977 ATTTGAAGCGAGTAATAAGG
127 ATTTAAAGCAAGTAATAAGG
1997 NNNNNNNNNN
Statistics
Matches: 693, Mismatches: 113, Indels: 52
0.81 0.13 0.06
Matches are distributed among these distances:
168 3 0.00
169 95 0.14
170 168 0.24
171 353 0.51
172 74 0.11
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (167 bp):
ATAAATGGAATTTTCTTCCCAATGAATGCTTTTTCTACATCTTTCTGAGGTAGACATTCAATTAT
AGTCTGTTTTAATAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
AAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACT
Found at i:1917 original size:342 final size:338
Alignment explanation
Indices: 994--1996 Score: 1096
Period size: 342 Copynumber: 2.9 Consensus size: 338
984 NNNNNNNNNN
* ** * **
994 ATAAATGAACTTTTCTTCATAATGAATGACTTTTTCTAGACGTTTATC-GAGGTAGGTATTCAAT
1 ATAAATGGACTTTTCTTCCCAATGAATGACTTTTTCTACACGTTT-TCTGAGGTAGACATTCAAT
* ** * * *
1058 TATAGTC-TGTTTTAATGAAAATTATAAAAAAAATT-AACTTAAAATCAATTATGAGATTGTAAA
65 TATAGTCTTATTTTAACAAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * *
1121 ACCATTTAAGACGAGTAATTAGGCTTCTGAAGGAATGAGTGACTATAAATGAACTTTTCTTCCCA
129 ACCATTTAA-ACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAA-TTTTCTTCCCA
* * *
1186 ATGAAAGCCTTTTTCTT-CACGTTTCTTGAGGTAGACATTTAATTATAGTCTG-TTTAATCAAAA
192 ATGAATGACTTTTT-TTACAC-TTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAAT-AAAA
* * * * *
1249 ATATAAAAAAATTCAACTTAAAATCAGTTATGAGATTATAAAATCA-TTAATGCTAGTAATAAGG
254 ATGTAAAAAAATTCAACTT-AAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGG
1313 CTTCTTAAAGAATGAGTGACT
318 CTTCTTAAAGAATGAGTGACT
* * * * * * **
1334 ATAAATGGACTTTTCTTTCCATTTAATGCCTTTTTCTTCACGTTTTTTGAGACAGACATTCAATT
1 ATAAATGGACTTTTCTTCCCAATGAATGACTTTTTCTACACGTTTTCTGAGGTAGACATTCAATT
* * * * *
1399 ATAGT-TTATTTTAACTAAAAATGTGAAAAAATTCACCTTAAAATCAATTATAAGATTATAAAGC
66 ATAGTCTTATTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * * * * * * *
1463 CATTTAAAATGAGTAATAAAGATTTTGAAGGGATGGGCGACTATAGATAGACATTTT-TTGCCAA
131 CATTT-AAACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAAT-GA-ATTTTCTTCCCAA
* ** * * *
1527 TGAAT-AGCTTTTTCTACATCTTTCCCGAGGCAAACATTCAACTATAGTCTGTTTTAATAAAAAA
193 TGAATGA-CTTTTTTTACA-CTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAAT-AAAAA
*
1591 TGTAAAAAAATTCAAATTAATATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
255 TGTAAAAAAATTCAACTTAA-ATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
*
1656 TT-TTGAAGGAAT-AGTGACT
319 TTCTT-AAAGAATGAGTGACT
* * * *
1675 ATAAATGGATTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTTCTAAGGTAGACATTCAATT
1 ATAAATGGACTTTTCTTCCCAATGAATGACTTTTTCTACACGTTTTCTGAGGTAGACATTCAATT
* * *
1740 ATAGTCTT-TTTTTACAAAAAAATGTAAAATAATTCAACTTAAAATGAATTATGAGATTATAAAA
66 ATAGTCTTATTTTAAC-AAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* *
1804 CCATTTAAACCAAGTAATAAGGCTTTTGAAGGAATGAGAGATTATAAATGGAATTTTCTTCCCAA
130 CCATTTAAA-CGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAAT-GAATTTTCTTCCCAA
** *
1869 TGAATGACTTTTTTTACACCATTT-TTGAGGTAGGTATTCAATTATAGTCTGTTTTAATGAAAAT
193 TGAATGACTTTTTTTACA-C-TTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAT
* * * *
1933 GTTAAACAAATTCAACTTCAAATCAAATATGAGATTATAAAACCATTTGAAGCGAGTAATAAGG
256 G-TAAAAAAATTCAACTT-AAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGG
1997 NNNNNNNNNN
Statistics
Matches: 546, Mismatches: 96, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
339 10 0.02
340 174 0.32
341 146 0.27
342 210 0.38
343 6 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (338 bp):
ATAAATGGACTTTTCTTCCCAATGAATGACTTTTTCTACACGTTTTCTGAGGTAGACATTCAATT
ATAGTCTTATTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
CATTTAAACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAATTTTCTTCCCAATGA
ATGACTTTTTTTACACTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAATGTAAA
AAAATTCAACTTAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTTAA
AGAATGAGTGACT
Done.