Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400807.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3981.0, 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: 2690
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.21
Warning! 1087 characters in sequence are not A, C, G, or T
Found at i:1031 original size:171 final size:169
Alignment explanation
Indices: 556--1727 Score: 1139
Period size: 171 Copynumber: 6.9 Consensus size: 169
546 NNNNNNNNNN
* ** * **
556 TAAAATCAATTATGAGATTATAAAACAAGTTAAAGCGAGTAATAAGGCTTTTGACGGAATAAGTG
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * * *
621 ACTATAAAGGGACTTTTCTTGACAACGAATGAG--TTTTCTTCATGTTTCTCTAAGCAGATATTG
66 ACTATAAAAGGACTTTTCTTGCCAATGAATG-GCTTTTTCTTCA-CTTT-TCTAAGTAGACATTC
* * * * *
684 AATTATAGTTTATTTTAACTAAAAATTTAAACAAATTCAACT
128 AATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACT
* * * ** * * *
726 TAAAGTCAATTATCAAATTATAAAACAACAT-AAATGAGTAATATGGCTTTAGAAGGAATGAGTG
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * *
790 ACTATAAATGGACTTTTCTTGCCAACGAAT-GCGTTTTTCTTCTCGTTTCTGTAAGTAGACATTG
66 ACTATAAAAGGACTTTTCTTGCCAATGAATGGC-TTTTTCTTCAC-TTT-TCTAAGTAGACATTC
* ** *
854 AATTATACTCCCTTTTAACAAAAAATATAAAAAAATTCAACT
128 AATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACT
* *
896 TAAAATCAGTTATGAGATTATAAAACAATTTAAAATGAGTAATAAGGCTTTTAAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTG
** * * * * *
961 ACTATAAAAGGACTTTTCTTATCAATAAATGGCTTTTGCTGCACATTTTCTGAGGTAAACATTCA
66 ACTATAAAAGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCAC-TTTTCT-AAGTAGACATTCA
* * * *
1026 ATTATAGTCTGTTTTAACCAAAAACGTATAAATATTCAACT
129 ATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACT
*** * *
1067 TAAAATTTGTTATGAGATTATAAAATAATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * *
1132 ACTATAAAGGGACTTTTCTTGGCAATGAAT-GCATTTATCTTCA-TGGTTCTCTAAGTAGATATT
66 ACTATAAAAGGACTTTTCTTGCCAATGAATGGC-TTTTTCTTCACT--TT-TCTAAGTAGACATT
* * * *
1195 GAATTATAGTCCGTTTTAACTAAAATTGTAAAAAAATTCAACT
127 CAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACT
* * * * **
1238 TAAAATCAGTTATGAGATAATAAAGAC-ATTTAAAGCT-AGTAATAAGGCTTTCGAAGGAATAAG
1 TAAAATCAATTATGAGATTATAAA-ACAATTTAAA-ATGAGTAATAAGGCTTTTGAAGGAATGGG
* * * * *
1301 TGACTATAAATA-GACTTTTGTGGCCAATGAATGCCTTTTTCTTCACGTTTCTCAACTTAGACAT
64 TGACTATAAA-AGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACTTTTCT-AA-GTAGACAT
** *
1365 TCAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTCAGCT
126 TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACT
* * * * *
1409 TGAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATATGACTTTTGAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * *
1474 ACTATAAATGGACTTTTCTTGGCAATGAATGCCTTTTTCTTCA-TGCTTCTCAAGGTAGACATTC
66 ACTATAAAAGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACT-TTTCT-AA-GTAGACATTC
* * *
1538 AATTATAGTTTGTTTTCACAAAAAATGTAAAAAAATTTAACT
128 AATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACT
* * * *
1580 TAAAATCAATCATGAGATTATAAAACAATTT-AAATCGACTAATGAGGCTTTTAAAGGAATGGGT
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAAT-GAGTAATAAGGCTTTTGAAGGAATGGGT
* * * *
1644 GATTAT-AAAGAGACTTTT-TTGGCTAACGAATGTG-TTTTTCTTCACGTTTCTCGAAGTAGACA
65 GACTATAAAAG-GACTTTTCTT-GCCAATGAATG-GCTTTTTCTTCAC-TTT-TCTAAGTAGACA
* *
1706 TTGAATTATAGTCTATTTTAAC
125 TTCAATTATAGTCTGTTTTAAC
1728 TAANNNNNNN
Statistics
Matches: 827, Mismatches: 146, Indels: 57
0.80 0.14 0.06
Matches are distributed among these distances:
167 1 0.00
169 59 0.07
170 129 0.16
171 625 0.76
172 10 0.01
173 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (169 bp):
TAAAATCAATTATGAGATTATAAAACAATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTG
ACTATAAAAGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACTTTTCTAAGTAGACATTCAAT
TATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACT
Found at i:1538 original size:513 final size:509
Alignment explanation
Indices: 556--1730 Score: 1480
Period size: 513 Copynumber: 2.3 Consensus size: 509
546 NNNNNNNNNN
* * * **
556 TAAAATCAATTATGAGATTATAAAACAAGTTAAAGCGAGTAATAAGGCTTTTGACGGAATAAGTG
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
* *
621 ACTATAAAGGGACTTTTCTTGACAACGAATGAGTTTTCTTCATGTTTCTCTAAGCAGATATTGAA
66 ACTATAAAGGGACTTTTCTTGGCAACGAATGA-TTTTCTTCATGTTTCTCTAAGTAGATATTGAA
* * * *
686 TTATAGTTTATTTTAACTAAAAATTTAAACAAATTCAACTTAAAGTCAATTATCAAATTATAAAA
130 TTATAGTCTATTTTAACT-AAAATTTAAAAAAATTCAACTTAAAATCAATTATCAAATAATAAAA
* * * *
751 CAACATAAATGAGTAATATGGCTTTAGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAC
194 CAACATAAATGAGTAATAAGGCTTTAGAAGGAATAAGTGACTATAAATAGACTTTTCTGGCCAAC
* * * *
816 GAATGCGTTTTTCTTCTCGTTTCTGTAAGTAGACATTGAATTATACTCCCTTTTAACAAAAAATA
259 GAATGCCTTTTTCTTCACGTTTCTGCAAGTAGACATTCAATTATACTCCCTTTTAACAAAAAATA
* *
881 TAAAAAAATTCAACTTAAAATCAGTTATGAGATTATAAAACAATTTAAAATGAGTAATAAGGCTT
324 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAATGAGTAATAAGACTT
* * *
946 TTAAAGGAATGGGTGACTATAAAAGGACTTTTCTTATCAATAAATGGCTTTTGCTGCACATTTTC
389 TTAAAGGAATGGGTGACTATAAAAGGACTTTTCTTAGCAATAAATGCCTTTTGCTGCACATTCTC
* * * *
1011 TGAGGTAAACATTCAATTATAGTCTGTTTTAACCAAAAACGTATAAATATTCAACT
454 TAAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAACGTAAAAAAATTCAACT
*** *
1067 TAAAATTTGTTATGAGATTATAAAATAATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
* *
1132 ACTATAAAGGGACTTTTCTTGGCAATGAATGCATTTATCTTCATGGTTCTCTAAGTAGATATTGA
66 ACTATAAAGGGACTTTTCTTGGCAACGAATG-ATTT-TCTTCATGTTTCTCTAAGTAGATATTGA
** * * *
1197 ATTATAGTCCGTTTTAACTAAAATTGTAAAAAAATTCAACTTAAAATCAGTTATGAGATAATAAA
129 ATTATAGTCTATTTTAACTAAAATT-TAAAAAAATTCAACTTAAAATCAATTATCAAATAATAAA
** * *
1262 GAC-ATTTAAA-GCTAGTAATAAGGCTTTCGAAGGAATAAGTGACTATAAATAGACTTTTGTGGC
193 -ACAACATAAATG--AGTAATAAGGCTTTAGAAGGAATAAGTGACTATAAATAGACTTTTCTGGC
* * * ** **
1325 CAATGAATGCCTTTTTCTTCACGTTTCT-CAACTTAGACATTCAATTATAGTCTGTTTTAATGAA
255 CAACGAATGCCTTTTTCTTCACGTTTCTGCAA-GTAGACATTCAATTATACTCCCTTTTAACAAA
* * * * * *
1389 AAATGTAAAAAAATTCAGCTTGAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAT
319 AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAATGAGTAATAA
* * * * * *
1454 GACTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGGCAATGAATGCCTTTTTCTTCATG
384 GACTTTTAAAGGAATGGGTGACTATAAAAGGACTTTTCTTAGCAATAAATGCCTTTTGCTGCA--
* * * * *
1519 C-TTCTC-AAGGTAGACATTCAATTATAGTTTGTTTTCACAAAAAATGTAAAAAAATTTAACT
447 CATTCTCTAAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAACGTAAAAAAATTCAACT
* * * * *
1580 TAAAATCAATCATGAGATTATAAAACAATTTAAATCGACTAATGAGGCTTTTAAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * *
1645 ATTATAAAGAGACTTTT-TTGGCTAACGAATGTGTTTTTCTTCACGTTTCTCGAAGTAGACATTG
66 ACTATAAAGGGACTTTTCTTGGC-AACGAA--TGATTTTCTTCATGTTTCTCTAAGTAGATATTG
1709 AATTATAGTCTATTTTAACTAA
128 AATTATAGTCTATTTTAACTAA
1731 NNNNNNNNNN
Statistics
Matches: 566, Mismatches: 86, Indels: 22
0.84 0.13 0.03
Matches are distributed among these distances:
511 95 0.17
512 88 0.16
513 373 0.66
514 7 0.01
515 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (509 bp):
TAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
ACTATAAAGGGACTTTTCTTGGCAACGAATGATTTTCTTCATGTTTCTCTAAGTAGATATTGAAT
TATAGTCTATTTTAACTAAAATTTAAAAAAATTCAACTTAAAATCAATTATCAAATAATAAAACA
ACATAAATGAGTAATAAGGCTTTAGAAGGAATAAGTGACTATAAATAGACTTTTCTGGCCAACGA
ATGCCTTTTTCTTCACGTTTCTGCAAGTAGACATTCAATTATACTCCCTTTTAACAAAAAATATA
AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAATGAGTAATAAGACTTTT
AAAGGAATGGGTGACTATAAAAGGACTTTTCTTAGCAATAAATGCCTTTTGCTGCACATTCTCTA
AGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAACGTAAAAAAATTCAACT
Done.