Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400272.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3480.0, 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: 2850
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.28
Warning! 527 characters in sequence are not A, C, G, or T
Found at i:318 original size:171 final size:171
Alignment explanation
Indices: 140--773 Score: 482
Period size: 171 Copynumber: 3.7 Consensus size: 171
130 ATGAGTGACT
* * * *
140 ATAAATGGACTTTTCTTGCTAATGATTGTC-TTTTTCTTCACATTTCTCAAGGTAGACATTTAAT
1 ATAAATGGACTTTTCTTACCAATGAATG-CATTTTTCTTCACATTTCTCAAGGTAGACATTCAAT
* * * * * * *
204 TATAATTTGTGT-TAACCAAGAATGTAAAAAAATTCAACTTAAAATCAATTATGAGGTTCTCAAA
65 TATAATCTGT-TCTAACCAAAAATATAAAAAAATTCAACTCAAAATCAATTATGAGATTATAAAA
268 CCATTTAAAAT-AAGTAACAAGGCTTTTGAAGGAATGGGT-GAAA
129 CCATTT-AAATGAAGTAACAAGGCTTTTGAAGGAATGGGTAG-AA
* ***
311 ATAAATGGACTTTTTTTACCAATGAATGCATTTTTCTTCGTGTTTCTCAAGGTAGACATTCAATT
1 ATAAATGGACTTTTCTTACCAATGAATGCATTTTTCTTCACATTTCTCAAGGTAGACATTCAATT
* * *
376 ATAATCTGTTCTAACCAAAAATATGAAAATATTTAACTCAAAATCAATTATGAGATTATAAAACC
66 ATAATCTGTTCTAACCAAAAATATAAAAAAATTCAACTCAAAATCAATTATGAGATTATAAAACC
* * * **
441 ATTTAAATGGAGTAATAAGGCTTTTGAAGGAATGTGTAGCT
131 ATTTAAATGAAGTAACAAGGCTTTTGAAGGAATGGGTAGAA
********** * *
482 ATAAATGGACTTTTCTTACCAATGAATGCNNNNNNNNNNACGTTTCTTAAGGTAGACATTCAATT
1 ATAAATGGACTTTTCTTACCAATGAATGCATTTTTCTTCACATTTCTCAAGGTAGACATTCAATT
* * * * * * **********
547 ACAGTATGTATAATAA--AAAAATGTAAAAAAATTCAACTTAAAATCAANNNNNNNNNNATAAAA
66 ATAATCTGT-T-CTAACCAAAAATATAAAAAAATTCAACTCAAAATCAATTATGAGATTATAAAA
* * * *
610 CCATTTAAA-GTAAGTAATAAAGCTTTTGAAGGAATTGGT-GACT
129 CCATTTAAATG-AAGTAACAAGGCTTTTGAAGGAATGGGTAGA-A
* * * * * * * * * *
653 ATAATTGGAATTTTCTTGCCAATAAATACCTTGTTCTT--CATGTTC-CGAAAGCAAACATTCAA
1 ATAAATGGACTTTTCTTACCAATGAATGCATTTTTCTTCACAT-TTCTC-AAGGTAGACATTCAA
* *
715 TTATAATCTATTCTAACCAAAAATGTAAAAAAATTCAAC-CTAAAATCAATTATGAGATT
64 TTATAATCTGTTCTAACCAAAAATATAAAAAAATTCAACTC-AAAATCAATTATGAGATT
774 NNNNNNNNNN
Statistics
Matches: 354, Mismatches: 96, Indels: 27
0.74 0.20 0.06
Matches are distributed among these distances:
168 3 0.01
169 3 0.01
170 59 0.17
171 284 0.80
172 2 0.01
173 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.33
Consensus pattern (171 bp):
ATAAATGGACTTTTCTTACCAATGAATGCATTTTTCTTCACATTTCTCAAGGTAGACATTCAATT
ATAATCTGTTCTAACCAAAAATATAAAAAAATTCAACTCAAAATCAATTATGAGATTATAAAACC
ATTTAAATGAAGTAACAAGGCTTTTGAAGGAATGGGTAGAA
Found at i:1923 original size:170 final size:169
Alignment explanation
Indices: 967--1992 Score: 781
Period size: 169 Copynumber: 6.0 Consensus size: 169
957 NNNNNNNNNN
** * *
967 TTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA-TGATAAATGGACTTT
1 TTATAAAACCATTTAAAGCAAGTAAGAAGGCTTTTGAAGGAATGAGTGACT-ATAAATGGACTTT
* * * * * * ** * **
1031 TCTTTCCAATCAAT-ACATTTTCCTTAATGTTTCCAGAGACAGACATTTAATTATAGTTTATTTT
65 TCTTGCCAATGAATGGC-TTTTGCTTCATGTTCCCA-AGGTAGACATTCAATTATAGCCT-TTTT
* * *
1095 AATAAAAAATATAAAAAAA-T-AACTTAAAATC-AGTATGAGA
127 AACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGA
* * * * * * * *
1135 TTATAAAGCCATTTAAAGCGAGTAATACA-GCTTTTGAAAGAATGGGTTACTATTAATGGACGTT
1 TTATAAAACCATTTAAAGCAAGTAAGA-AGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTT
* * * * *
1199 TCCTGTCAATGAATAGCTTTTTCTTCATGTTTCCCAAGGTAGACATTTAATTATAGCCTTTTTGA
65 TCTTGCCAATGAATGGCTTTTGCTTCATG-TTCCCAAGGTAGACATTCAATTATAGCCTTTTT-A
* * * * * **
1264 ACTAAAAATGTAAAAAATATTGAACTCAAAATTAATTATTACC
128 ACAAAAAATATAAAAAA-ATTCAACTTAAAATCAATTATTAGA
* * * ** **
1307 TTATAAAACTATTTAAAGCAAGCAAGAAGGCTTTCGAAGGCTTGAGCAACTATAAATGGACTTTT
1 TTATAAAACCATTTAAAGCAAGTAAGAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTT
* * ** * * * *
1372 CGTGCCAAT-AGATGGCTTTTGTTTCACATACCCTAAGGCAGATATTCAATTATAGCATTTTTAA
66 CTTGCCAATGA-ATGGCTTTTGCTTCATGTTCCC-AAGGTAGACATTCAATTATAGCCTTTTTAA
* * * * *
1436 C-CAAAATACAAAAACACTCAACTTAAAATCAATTATGAGA
129 CAAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGA
* * * * * * *
1476 TTATAAAACCACTTAACA-CGAGTAATAATGTTTTTGAAGGAATGGGTGACTATAAATGGACTAT
1 TTATAAAACCATTTAA-AGCAAGTAAGAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTT
* * * * * * * * **
1540 TCTTACCAA-AAAT-ACTTTTTACTTCACGTTTCTCAAGGTAAACATTCAATTGTA-ATTTGTTT
65 TCTTGCCAATGAATGGC-TTTTGCTTCATG-TTCCCAAGGTAGACATTCAATTATAGCCTT-TTT
* * * *
1602 AACTAAAAATATAAAAAAATTAAACTTAAAATTAGTT-TTGAGA
127 AACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATT-AGA
* * * *
1645 TTATAAAATCATTTACAATG--AGTAATAAGGCTTTTGAAGGAATG-GATGACTATTAATGGGCT
1 TTATAAAACCATTTA-AA-GCAAGTAAGAAGGCTTTTGAAGGAATGAG-TGACTATAAATGGACT
* * ** * *
1707 TTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTGTCAAAGTAGACATTCAATTATAGTCTGTTT
63 TTTCTTGCCAATGAATGGCTTTTGCTTCATG-TTCCCAAGGTAGACATTCAATTATAGCCT-TTT
* * * * * *
1772 TAGCAAAAAATGTAAATATATTCAACCTAAAATCAATTATTAGT
126 TAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGA
*** * *
1816 TTATAAAACCATTTAAAGCAAGTAAGAAGGCTTTTGAAGCCTTAAGTGACTATAAATGAAC-TTT
1 TTATAAAACCATTTAAAGCAAGTAAGAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTT
* * *
1880 CATGCCAATGAATGGCTTTTGCTTTATGTTCCACAAGGTAGACATTCAATTACAGCCTTTTTTAA
66 CTTGCCAATGAATGGCTTTTGCTTCATGTTCC-CAAGGTAGACATTCAATTATAGCC-TTTTTAA
* * *
1945 TAAAAAATAAAAAAAAATTCAACTTAAAATCAATTATGAGA
129 CAAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGA
1986 TTATAAA
1 TTATAAA
1993 NNNNNNNNNN
Statistics
Matches: 670, Mismatches: 155, Indels: 64
0.75 0.17 0.07
Matches are distributed among these distances:
167 7 0.01
168 143 0.21
169 177 0.26
170 143 0.21
171 99 0.15
172 101 0.15
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (169 bp):
TTATAAAACCATTTAAAGCAAGTAAGAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTT
CTTGCCAATGAATGGCTTTTGCTTCATGTTCCCAAGGTAGACATTCAATTATAGCCTTTTTAACA
AAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGA
Found at i:1944 original size:509 final size:510
Alignment explanation
Indices: 967--1992 Score: 1222
Period size: 509 Copynumber: 2.0 Consensus size: 510
957 NNNNNNNNNN
* * *
967 TTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATGATAAATGGACTTTT
1 TTATAAAACCACTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGATGATAAATGGACTATT
* * * * * * * *
1032 CTTTCCAATCAATACATTTTCCTTAATGTTTCCAGAGACAGACATTTAATTATAGTTTATTTTAA
66 CTTACCAATAAATACATTTTACTTAACGTTTCCAGAGACAAACATTCAATTATAATTTAGTTTAA
*
1097 TAAAAAATATAAAAAAATAACTTAAAATCAGTATGAGATTATAAAGCCATTTAAAGCGAGTAATA
131 TAAAAAATATAAAAAAATAACTTAAAATCAGTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
1162 CAGCTTTTGAAAGAATGGGTTACTATTAATGGACGTTTCCTGTCAATGAATAGCTTTTTCTTCAT
196 CAGCTTTTGAAAGAATGGATGACTATTAATGGACGTTTCCTGCCAATGAATAGCTTTTTCTTCAT
* * * *
1227 GTTTCCCAAGGTAGACATTTAATTATAGCCTTTTTGAACTAAAAATGTAAAAAATATTGAACTCA
261 GTTTCCCAAAGTAGACATTCAATTATAGCCTTTTTGAACAAAAAATGTAAAAAATATTCAACTCA
* * * *
1292 AAATTAATTATTACCTTATAAAACTATTTAAAGCAAGCAAGAAGGCTTTCGAAGGCTTGAGCAAC
326 AAATCAATTATTACCTTATAAAACCATTTAAAGCAAGCAAGAAGGCTTTCGAAGCCTTAAGCAAC
* * *
1357 TATAAATGGACTTTTCGTGCCAATAGATGGCTTTTGTTTCACATACCCTAAGGCAGATATTCAAT
391 TATAAATGAACTTTTCATGCCAATAGATGGCTTTTGTTTCACATACCCTAAGGCAGACATTCAAT
* ** * *
1422 TATAGCATTTTTAA-CCAAAATACAAAAACACTCAACTTAAAATCAATTATGAGA
456 TACAGCATTTTTAATAAAAAATAAAAAAAAACTCAACTTAAAATCAATTATGAGA
* *
1476 TTATAAAACCACTTAACA-CGAGTAATAATGTTTTTGAAGGAATGGGTGACT-ATAAATGGACTA
1 TTATAAAACCACTTAA-AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA-TGATAAATGGACTA
* * ** *
1539 TTCTTACCAA-AAATACTTTTTACTTCACGTTTCTCA-AGGTAAACATTCAATTGTAATTT-GTT
64 TTCTTACCAATAAATACATTTTACTTAACGTTTC-CAGAGACAAACATTCAATTATAATTTAGTT
* * * *
1601 TAACT-AAAAATATAAAAAAATTAAACTTAAAATTAGTTTTGAGATTATAAAATCATTTACAA-T
128 TAA-TAAAAAATATAAAAAAA-T-AACTTAAAATCAG-TATGAGATTATAAAACCATTTA-AAGC
* * * *
1664 GAGTAATA-AGGCTTTTGAAGGAATGGATGACTATTAATGGGCTTTTCTTGCCAATGAAT-GCCT
188 GAGTAATACA-GCTTTTGAAAGAATGGATGACTATTAATGGACGTTTCCTGCCAATGAATAG-CT
** * * *
1727 TTTTCTTCATGTTTGTCAAAGTAGACATTCAATTATAGTCTGTTTT-AGCAAAAAATGT-AAATA
251 TTTTCTTCATGTTTCCCAAAGTAGACATTCAATTATAGCCT-TTTTGAACAAAAAATGTAAAAAA
** * *
1790 TATTCAAC-CTAAAATCAATTATTAGTTTATAAAACCATTTAAAGCAAGTAAGAAGGCTTTTGAA
315 TATTCAACTC-AAAATCAATTATTACCTTATAAAACCATTTAAAGCAAGCAAGAAGGCTTTCGAA
** ** *
1854 GCCTTAAGTGACTATAAATGAAC-TTTCATGCCAAT-GAATGGCTTTTGCTTT-ATGTTCCAC-A
379 GCCTTAAGCAACTATAAATGAACTTTTCATGCCAATAG-ATGGCTTTTG-TTTCACATACC-CTA
* * *
1915 AGGTAGACATTCAATTACAGCCTTTTTTAATAAAAAATAAAAAAAAATTCAACTTAAAATCAATT
441 AGGCAGACATTCAATTACAG-CATTTTTAATAAAAAATAAAAAAAAACTCAACTTAAAATCAATT
1980 ATGAGA
505 ATGAGA
1986 TTATAAA
1 TTATAAA
1993 NNNNNNNNNN
Statistics
Matches: 437, Mismatches: 63, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
507 21 0.05
508 81 0.19
509 168 0.38
510 161 0.37
511 6 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (510 bp):
TTATAAAACCACTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGATGATAAATGGACTATT
CTTACCAATAAATACATTTTACTTAACGTTTCCAGAGACAAACATTCAATTATAATTTAGTTTAA
TAAAAAATATAAAAAAATAACTTAAAATCAGTATGAGATTATAAAACCATTTAAAGCGAGTAATA
CAGCTTTTGAAAGAATGGATGACTATTAATGGACGTTTCCTGCCAATGAATAGCTTTTTCTTCAT
GTTTCCCAAAGTAGACATTCAATTATAGCCTTTTTGAACAAAAAATGTAAAAAATATTCAACTCA
AAATCAATTATTACCTTATAAAACCATTTAAAGCAAGCAAGAAGGCTTTCGAAGCCTTAAGCAAC
TATAAATGAACTTTTCATGCCAATAGATGGCTTTTGTTTCACATACCCTAAGGCAGACATTCAAT
TACAGCATTTTTAATAAAAAATAAAAAAAAACTCAACTTAAAATCAATTATGAGA
Done.