Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397988.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1292.0, 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: 2210
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.27
Warning! 498 characters in sequence are not A, C, G, or T
Found at i:348 original size:171 final size:169
Alignment explanation
Indices: 1--1396 Score: 1139
Period size: 171 Copynumber: 8.2 Consensus size: 169
* * * *
1 AAATGTAAAAAATTCAACTCAAAATCAATTATGAGATTATAAAACCGTTTAAAGTGAGTACTAAG
1 AAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
* * * *
66 GCTTTTGAAGGAACGGATGACTATAAATAGACTTTTCTTCCAAATAAATGGGTTTTTCTATACA-
66 GCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTCCAAATAAATGGGTTTTTCT-TACAT
* * * ** **
130 TTTCTTGAGGTAGACATTCAATTATTGACTACTTTAACCTT
130 TTTC-TAAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
* * *
171 AAATGTAAACAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTGATAA
1 AAATGTAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
* * * * *
236 GGCTTTTGAAAGAATGGGGGAGTATAAATGGACTCTTCATCCAAATAAATGGGTTTCTCTATACA
65 GGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTCCAAATAAATGGGTTTTTCT-TACA
** * * * * * *
301 TTTTCTAAGACAGGCAGTCATTTATAGTTTGTTTTAGCAAA
129 TTTTCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
* * * *
342 AAATGTAAAAAATGCAACTTAAAAGCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAA
1 AAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
* * * **
407 GCTTTCG-AAGAAATGAGTGACTATAAATGGACTTTTCTTGCC-AATGAATGTCTTTTTCCTT--
66 GCTTTTGAAAG-AATGGGTGACTATAAATGGACTTTTCTT-CCAAATAAATGGGTTTTT-CTTAC
* ** * *
468 ATGTTTCACAAGGTAGACATTCAATTATTTTCTATTTTAGCCAA
128 AT-TTTC-TAAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
* * * * * *
512 AAATGTAAAAAAAAAATTGAACTTAAAGTCAATTTTAAGATTATAAAACTATTTCAAGTC-AGTA
1 AAATGT----AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG-CGAGTA
* ** * * * * **
576 ATAAGGGTTTTGATGGAATGGGTGAGTATAAATAGACTTTTC-TCACCAATGAATGCCTTTTTCT
61 ATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTC-CAAATAAATGGGTTTTTCT
* * * *
640 T-CATGTTTTATAAGGTAGACATTTAATTATAATCTATTTTAACCAA
125 TACA--TTTTCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
* * * * * * * * *
686 AATTGTAAAAACAATTGAACTAAAAATCAATTTTGATATTATAAAGCTATTTTAAGTGAGTAATA
1 AAATGT-AAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * * *** *
751 AGGCTTTTGAAGGAATGGATGATTATGAATGGACTTTTCTTACC-AATGAATACCTTTTTCTT-T
64 AGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTT-CCAAATAAATGGGTTTTTCTTAC
* * * * * *
814 ATATTCTTGATGTAGACATTTAATTATAATCTGTTTTAACTAGA
128 ATTTTC-TAAGGTAGACATTCAATTATAGTCTGTTTTAACCA-A
* * * *
858 AAA-GAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAA
1 AAATG-TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
* * * ** * * ***
922 GGCTTTTGAAGGAATAGGTAACTATAAACAGACTTTCCTTGCC-AATGAATATATTTTTCTT-CA
65 GGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTT-CCAAATAAATGGGTTTTTCTTACA
* *
985 TATTTCTCAAGGCAGACATTGAATTATAGTCTGTTTTAACCAA
129 T-TTTCT-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
* * * * *
1028 AAATATAAAAAAATACAACTTTAAATCAATTATGACG-TTATAAAATCATTTAAAGCGAGAAATA
1 AAATGT-AAAAAATTCAACTTAAAATCAATTATGA-GATTATAAAACCATTTAAAGCGAGTAATA
* * * * *
1092 AGGCTTTTGAAAAAATGGGAGACTATAAATGGATTTTTTTTCAAAATAAATGGGTTTTTC-TACA
64 AGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTCCAAATAAATGGGTTTTTCTTACA
* **
1156 CGTTTTGC-AAGG-AAAGCATTCAATTATAGTCTGTTTTAATGAA
129 --TTTT-CTAAGGTAGA-CATTCAATTATAGTCTGTTTTAACCAA
* * *
1199 AAATGTAAAAAATTCAACTTAATATCAGTTATGAGATTA-ATAAACCATTTAAAGCGAGTAATTA
1 AAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATA-AAACCATTTAAAGCGAGTAATAA
*
1263 GGCTTCTG-AAGAAAT--GTGACTATAAATGGACTTTTCTTCCAAATAAATGGG-TTTTCTGTAC
65 GGCTTTTGAAAG-AATGGGTGACTATAAATGGACTTTTCTTCCAAATAAATGGGTTTTTCT-TAC
* * * * * **
1324 -GTTACT-AGAGCAGGCATTCAATTATAATCTGTTTTAATAAA
128 ATTTTCTAAG-GTAGACATTCAATTATAGTCTGTTTTAACCAA
*
1365 AAATGTAAAACATTCAACTTAAAATCAATTAT
1 AAATGTAAAAAATTCAACTTAAAATCAATTAT
1397 NNNNNNNNNN
Statistics
Matches: 1000, Mismatches: 182, Indels: 92
0.78 0.14 0.07
Matches are distributed among these distances:
165 3 0.00
166 57 0.06
167 6 0.01
168 34 0.03
169 14 0.01
170 300 0.30
171 336 0.34
172 108 0.11
173 9 0.01
174 127 0.13
175 5 0.00
176 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
AAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
GCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTCCAAATAAATGGGTTTTTCTTACATT
TTCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
Done.