Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400423.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3620.0, 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: 2677
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.25
Warning! 786 characters in sequence are not A, C, G, or T
Found at i:335 original size:171 final size:170
Alignment explanation
Indices: 6--1290 Score: 1226
Period size: 171 Copynumber: 7.5 Consensus size: 170
1 TTACA
* * * * * *
6 AATGAATACTTTTGTCTTCATGTTTCTCGAGATAAACAGTCAATTATTG-CTTGTTTTAATCAAA
1 AATGAATACTTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTC-TGTTTTAATGAAA
* * * *
70 TATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTCAAGCAAGTAATAAG
65 AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT-AAACGAGTAATAAG
* * * *
135 GCCTTCGAAGGAATGGGAGGCTGTAAATAGACTTTTCTTGCC
129 GCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCC
* * * *
177 AATGAATGCTTTTTTCTTCATGCTTCTCAAGGCAAACATTCAATTATAGTCTTTTTTAATGAAAA
1 AATGAATACTTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAA
* * * *
242 ATGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATTTAGAACGAGTAAAAAAG
66 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA-AACGAGTAATAAGG
* * * * **
307 CTGTTGAAGGACTGGGAGCCTATAAATAGACTTTTGTTATC
130 CTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCC
* * * * * * **
348 AATGAATACTTTTTTCTTCTTGATTCT-AGAGGCAAACATTCAATTATGGCCTATTTTAACAAAA
1 AATGAATACTTTTTTCTTCATGTTTCTCA-AGGTAAACATTCAATTATAGTCTGTTTTAATGAAA
* *
412 AATATAAAAAAATTCAACTTAAAATCAATTATGAGACTAGAAAACCATTTAAAGCGAGTAATAAG
65 AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA-CGAGTAATAAG
* * * * *
477 GCTTTTGACGGAATGTGTGACTATAAATGGGCTTTTCTTGCC
129 GCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCC
* ** * * * *
519 GATGAATACTTTTGCCTTCATGTTTCTCAAGATAAACAGTCAATTATTGTCTGTTTTAATCAAAA
1 AATGAATACTTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAA
* * * * * *
584 ATATAAAAAAATTCTACTTAAAATGAATTATTAGATTATAAAACCATTTCAAGCAAGCAATAAGG
66 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT-AAACGAGTAATAAGG
* *
649 CCTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTGCC
130 CTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCC
* * *
690 AATGAATGCTTTTTTCTTCACT-TTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAATGAAA
1 AATGAATACTTTTTTCTTCA-TGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATGAAA
* * * * * * ** *
754 AAGT-TAAAAAACATTGAACTTAAAATTAATTATGAGGTTATGAAGCCGTTTAGATTGAGTAAAA
65 AA-TATAAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA-AACGAGTAATA
* * * **
818 AGGCTATT-AGAGGAATGAGAGACTATAAAT-GCACTTTTTTTATC
127 AGGCTTTTGA-AGGAATGGGAGACTATAAATAG-ACTTTTCTTGCC
* * * * *** * *
862 AATGAATGCTTTTTTCTTCACGTTTATCAAGGCAAGTGTTCAATTATAGGCTATTTTAATGAAAA
1 AATGAATACTTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAA
* * * * * * *
927 ATGTAAAAAATTTCAAATTAAAATCAATTATTATATTAT-AAACTATTTAAA-GTAAGTAATAAA
66 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAACG--AGTAATAAG
* * * *
990 ACTTTTGAAGGAATGGGTA-ACAATAAATAGATTTTTCTTACC
129 GCTTTTGAAGGAATGGG-AGACTATAAATAGACTTTTCTTGCC
* * ** *
1032 AATTAAT-GTGTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATGAAA
1 AATGAATACT-TTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATGAAA
* * * * * * *
1096 AATATACAAAAACTCAACTTCAAATCAATTATGACATTATAAAATCATTTAAAGTGAGTCATAAG
65 AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA-CGAGTAATAAG
* * **
1161 GATTTTGAAGGAATAGGTA-ACTATAAAT-GCACTTTTCTTGAT
129 GCTTTTGAAGGAAT-GGGAGACTATAAATAG-ACTTTTCTTGCC
* * ** * * * * *
1203 AATGAATACTTTTTCCTTCATGTTGCTTGAGATAGACATTCAATTATTGTCTGCTTTAATCAAAA
1 AATGAATACTTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAA
*
1268 ATGTAAAAAAATTCAACTTAAAA
66 ATATAAAAAAATTCAACTTAAAA
1291 NNNNNNNNNN
Statistics
Matches: 903, Mismatches: 185, Indels: 52
0.79 0.16 0.05
Matches are distributed among these distances:
168 1 0.00
169 2 0.00
170 129 0.14
171 629 0.70
172 141 0.16
173 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
AATGAATACTTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAA
ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAACGAGTAATAAGGC
TTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCC
Found at i:977 original size:513 final size:513
Alignment explanation
Indices: 1--1290 Score: 1560
Period size: 513 Copynumber: 2.5 Consensus size: 513
*
1 TTACAAATGAATACTTTTGTCTTCATGTTTCTCGAGATAAACAGTCAATTATTG-CTTGTTTTAA
1 TTACCAATGAATACTTTTGTCTTCATGTTTCTCGAGATAAACAGTCAATTATTGTC-TGTTTTAA
* *
65 TCAAATATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTCAAGCAAGTA
65 TCAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTCAAGCAAGCA
* *
130 ATAAGGCCTTCGAAGGAATGGGAGGCTGTAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTT
130 ATAAGGCCTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTT
* * * * *
195 CATGCTTCTCAAGGCAAACATTCAATTATAGTCTTTTTTAATGAAAAATGTAAAAAAATTAAACT
195 CATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTAAACT
* * *
260 TAAAATCAATTATGAGATTATAAAACCATTTAGAACGAGTAAAAAAGCTGTTGAAGGACTGGGAG
260 TAAAATCAATTATGAGATTATAAAACCATTTAGAACGAGTAAAAAAGCTATTGAAGGAATGAGAG
* ** *
325 CCTATAAATAGACTTTTGTTATCAATGAATACTTTTTTCTTCTTGATTCTAGAGGCAAACATTCA
325 ACTATAAATAGACTTTTGTTATCAATGAATACTTTTTTCTTCACGATTATAGAGGCAAACATTCA
*
390 ATTATGGCCTATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGACTAGAAA
390 ATTATGGCCTATTTTAACAAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGACTAGAAA
* ** * * * * * *
455 ACCATTTAAAGCGAGTAATAAGGCTTTTGACGGAATGTGTGACTATAAATGGGCTTTTC
455 ACCATTTAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTAACAATAAATAGACTTTTC
* * * *
514 TTGCCGATGAATACTTTTGCCTTCATGTTTCTCAAGATAAACAGTCAATTATTGTCTGTTTTAAT
1 TTACCAATGAATACTTTTGTCTTCATGTTTCTCGAGATAAACAGTCAATTATTGTCTGTTTTAAT
* *
579 CAAAAATATAAAAAAATTCTACTTAAAATGAATTATTAGATTATAAAACCATTTCAAGCAAGCAA
66 CAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTCAAGCAAGCAA
644 TAAGGCCTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTC
131 TAAGGCCTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTC
*
709 ACT-TTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAA-GTTAAAAAACATTGAA
196 A-TGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATG-TAAAAAA-ATTAAA
* * * * * ** *
772 CTTAAAATTAATTATGAGGTTATGAAGCCGTTTAGATTGAGTAAAAAGGCTATT-AGAGGAATGA
258 CTTAAAATCAATTATGAGATTATAAAACCATTTAGAACGAGTAAAAAAGCTATTGA-AGGAATGA
* * * **
836 GAGACTATAAAT-GCACTTTTTTTATCAATGAATGCTTTTTTCTTCACGTTTATCA-AGGCAAGT
322 GAGACTATAAATAG-ACTTTTGTTATCAATGAATACTTTTTTCTTCACGATTAT-AGAGGCAAAC
* ** * * * * *
899 GTTCAATTATAGG-CTATTTTAATGAAAAATGTAAAAAATTTCAAATTAAAATCAATTATTATAT
385 ATTCAATTAT-GGCCTATTTTAACAAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGAC
* * * *
963 TA-TAAACTATTTAAAGTAAGTAATAAAACTTTTGAAGGAATGGGTAACAATAAATAGATTTTTC
449 TAGAAAACCATTTAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTAACAATAAATAGACTTTTC
* * * * * * * *
1027 TTACCAATTAAT-GTGTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAA
1 TTACCAATGAATACT-TTTGTCTTCATGTTTCTCGAGATAAACAGTCAATTATTGTCTGTTTTAA
* * * * * * * * **
1091 TGAAAAATATACAAAAACTCAACTTCAAATCAATTATGACATTATAAAATCATTTAAAGTGAGTC
65 TCAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTCAAGCAAG-C
** * * ** * *
1156 -ATAAGGATTTTGAAGGAATAGGTA-ACTATAAAT-GCACTTTTCTTGATAATGAATACTTTTTC
129 AATAAGGCCTTTGAAGGAAT-GGGAGGCTATAAATAG-ACTTTTCTTGCCAATGAATGCTTTTTT
* * * * * * *
1218 CTTCATGTTGCTTGAGATAGACATTCAATTATTGTCTGCTTTAATCAAAAATGTAAAAAAATTCA
192 CTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTAA
1283 ACTTAAAA
257 ACTTAAAA
1291 NNNNNNNNNN
Statistics
Matches: 665, Mismatches: 98, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
512 16 0.02
513 479 0.72
514 167 0.25
515 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (513 bp):
TTACCAATGAATACTTTTGTCTTCATGTTTCTCGAGATAAACAGTCAATTATTGTCTGTTTTAAT
CAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTCAAGCAAGCAA
TAAGGCCTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTC
ATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTAAACTT
AAAATCAATTATGAGATTATAAAACCATTTAGAACGAGTAAAAAAGCTATTGAAGGAATGAGAGA
CTATAAATAGACTTTTGTTATCAATGAATACTTTTTTCTTCACGATTATAGAGGCAAACATTCAA
TTATGGCCTATTTTAACAAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGACTAGAAAA
CCATTTAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTAACAATAAATAGACTTTTC
Done.