Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397882.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1187.0, 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: 6143
ACGTcount: A:0.21, C:0.08, G:0.09, T:0.21
Warning! 2538 characters in sequence are not A, C, G, or T
Found at i:2105 original size:172 final size:172
Alignment explanation
Indices: 1735--2813 Score: 1047
Period size: 172 Copynumber: 6.3 Consensus size: 172
1725 NNNNNNNNNN
* * * *
1735 GAAGGAATGGGTGACTATAAATGGATTTTTCTTGCCAATGTATGCCTTTTTC-TTGATGTTTTTT
1 GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATT-ATGTTTCTC
* * *
1799 GAGGTTGACATTCAATTATAATCTGTTTTAATAAAAAAATGTACAAAGAATGCAAATTTAAATCA
65 GAGGTTGACATTCAATTATAATCTGTTTTAA-CAAAAAATGTACAAAGAATTCAAATTAAAATCA
1864 ATTTTGAGATTATAAAACCATTTAAAGTGAGTAGA-AAGGCTTTT
129 ATTTTGAGATTATAAAACCATTTAAAGTGAGTA-ATAAGGCTTTT
* * * *
1908 GAAGGAATGGGTGACTACAAATGGACTTCTCTTGCCAACGAATGCCTTTTTCATTATGTTTCTCA
1 GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATTATGTTTCTCG
* * ** * * *
1973 AGGTAGACA-TCAATTCTCGTCTGTTTTAACCAAAAATGTA-AAA-ACGTTCAACTTAAAATCAA
66 AGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATGTACAAAGA-ATTCAAATTAAAATCAA
* * *
2035 TTTTG-GCAATATAAAACCATGTAAAGCGAGTAATAAGGCTCTTTT
130 TTTTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGG--CTTTT
* * * * ** * * *
2080 GAAGGAATGAGTGATTATTAATGGACTTTTCTAGCCAATGAATGCCTTTACCTTTACGTTTCTAG
1 GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATTATGTTTCTCG
* * * * * * * * **
2145 AGGTTGACTTTGACTTACAATCTTTTTTGACCAACAATGTACAAAGAATTCAAATTTCAATCAAT
66 AGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTAAAATCAAT
* * *
2210 TTTGAGATTACAAAACCATTTAAAGTAAGTATTAAGGCTTTT
131 TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
** * ** * ** *
2252 GAAGGAATGGGTCTCTATAAATGAACTTTTCTTGCCAACAAATACCTTTAGCTTTATGTTTCTCG
1 GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATTATGTTTCTCG
* * **** * ** * *
2317 AGATTGACATTCAATTATAGTCTGTTTTAACCCGGAATGTA-AAAAAAAACAACTAAAAATCAAT
66 AGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTAAAATCAAT
* * * *
2381 TATG-GTATTATAAAACCATTTCAAGAGAGTAATGAGGCTTTT
131 TTTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
* * * * * *
2423 GAAGGAATGAGTGACTATAAATGGATTTTTCTTACCAATGTATGCC-TTTTCCTTCATGTTTCTT
1 GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATT-ATGTTTCTC
* * *
2487 GAGGTTGACATTCAATTATAATCTGTTTAAATAAAAAATGTACAAAGAATTCAAATTCAAATCAA
65 GAGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTAAAATCAA
* *
2552 TTTTGAGATTATAAAAGCATTTAAAGTGAGTACA-AAGGATTTT
130 TTTTGAGATTATAAAACCATTTAAAGTGAGTA-ATAAGGCTTTT
* *
2595 GAAGGAATGGGTGACTATAAATGGAC-TTTCTTACCAACGAATGCCTTTTTCATTATGTTT-TCT
1 GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATTATGTTTCTC-
* * * * * *
2658 GGGGTTGACA-TAAATTCTAGTCTGTTTTAACAAAAAATGTACAAA-AGTTCAACTTAAAATCAA
65 GAGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTAAAATCAA
* * * **
2721 TTATG-GTATTATAAAATCATGTAAAGCAAGTAATAAGGCTTTTT
130 TTTTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGC-TTTT
* *** * *
2765 GAAGAAATAAATGATTA-ATAATAGACTTTTCTTGCCAATGAATGCCTTT
1 GAAGGAATGGGTGACTATA-AATGGACTTTTCTTGCCAATGAATGCCTTT
2814 ACCTTCACGT
Statistics
Matches: 728, Mismatches: 156, Indels: 46
0.78 0.17 0.05
Matches are distributed among these distances:
168 2 0.00
169 48 0.07
170 106 0.15
171 188 0.26
172 248 0.34
173 86 0.12
174 48 0.07
175 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (172 bp):
GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATTATGTTTCTCG
AGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTAAAATCAAT
TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
Found at i:2562 original size:343 final size:342
Alignment explanation
Indices: 1735--2827 Score: 1352
Period size: 343 Copynumber: 3.2 Consensus size: 342
1725 NNNNNNNNNN
* * * * ** * * *
1735 GAAGGAATGGGTGACTATAAATGGATTTTTCTTGCCAATGTATGCCTTTTTCTTGATGTTTTTTG
1 GAAGGAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTTACCTTCACGTTTCTTG
* *
1800 AGGTTGACATTCAATTATAATCTGTTTTAATAAAAAAATGTACAAAGAATGCAAATTTAAATCAA
66 AGGTTGACATTCAATTATAATCTGTTTTAAT-AAAAAATGTACAAAGAATTCAAATTCAAATCAA
* *
1865 TTTTGAGATTATAAAACCATTTAAAGTGAGTAGAAAGGCTTTTGAAGGAATGGGTGACTACAAAT
130 TTTTGAGATTATAAAACCATTTAAAGTGAGTACAAAGGCTTTTGAAGGAATGGGTGACTATAAAT
* * * *
1930 GGACTTCTCTTGCCAACGAATGCCTTTTTCATTATGTTTCTCAAGGTAGACATCAATTCTCGTCT
195 GGACTTTTCTTGCCAACGAATGCCTTTTTCATTATGTTTCTCGAGGTTGACATCAATTCTAGTCT
* * * *
1995 GTTTTAACCAAAAATGTAAAAACGTTCAACTTAAAATCAATTTTGGCAATATAAAACCATGTAAA
260 GTTTTAACCAAAAATGTAAAAAAGTTCAACTTAAAATCAATTATGGTATTATAAAACCATGTAAA
*
2060 GCGAGTAATAAGGCTCTTTT
325 GAGAGTAATAAGG--CTTTT
* * * *
2080 GAAGGAATGAGTGATTATTAATGGACTTTTC-TAGCCAATGAATGCCTTTACCTTTACGTTTCTA
1 GAAGGAATGAGTGACTATAAATGGACTTTTCTTA-CCAATGAATGCCTTTACCTTCACGTTTCTT
* * * * * * ** *
2144 GAGGTTGACTTTGACTTACAATCTTTTTTGACCAACAATGTACAAAGAATTCAAATTTC-AATCA
65 GAGGTTGACATTCAATTATAATCTGTTTTAATAAAAAATGTACAAAGAATTCAAA-TTCAAATCA
* * ** **
2208 ATTTTGAGATTACAAAACCATTTAAAGTAAGTATTAAGGCTTTTGAAGGAATGGGTCTCTATAAA
129 ATTTTGAGATTATAAAACCATTTAAAGTGAGTACAAAGGCTTTTGAAGGAATGGGTGACTATAAA
* * * ** * * *
2273 TGAACTTTTCTTGCCAACAAATACCTTTAGCTTTATGTTTCTCGAGATTGACATTCAATTATAGT
194 TGGACTTTTCTTGCCAACGAATGCCTTTTTCATTATGTTTCTCGAGGTTGACA-TCAATTCTAGT
*** *** * * *
2338 CTGTTTTAACCCGGAATGTAAAAAAAAACAACTAAAAATCAATTATGGTATTATAAAACCATTTC
258 CTGTTTTAACCAAAAATGTAAAAAAGTTCAACTTAAAATCAATTATGGTATTATAAAACCATGTA
*
2403 AAGAGAGTAATGAGGCTTTT
323 AAGAGAGTAATAAGGCTTTT
* * * *
2423 GAAGGAATGAGTGACTATAAATGGATTTTTCTTACCAATGTATGCCTTTTCCTTCATGTTTCTTG
1 GAAGGAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTTACCTTCACGTTTCTTG
*
2488 AGGTTGACATTCAATTATAATCTGTTTAAATAAAAAATGTACAAAGAATTCAAATTCAAATCAAT
66 AGGTTGACATTCAATTATAATCTGTTTTAATAAAAAATGTACAAAGAATTCAAATTCAAATCAAT
* *
2553 TTTGAGATTATAAAAGCATTTAAAGTGAGTACAAAGGATTTTGAAGGAATGGGTGACTATAAATG
131 TTTGAGATTATAAAACCATTTAAAGTGAGTACAAAGGCTTTTGAAGGAATGGGTGACTATAAATG
* * *
2618 GAC-TTTCTTACCAACGAATGCCTTTTTCATTATGTTT-TCTGGGGTTGACATAAATTCTAGTCT
196 GACTTTTCTTGCCAACGAATGCCTTTTTCATTATGTTTCTC-GAGGTTGACATCAATTCTAGTCT
* * *
2681 GTTTTAACAAAAAATGTACAAAAGTTCAACTTAAAATCAATTATGGTATTATAAAATCATGTAAA
260 GTTTTAACCAAAAATGTAAAAAAGTTCAACTTAAAATCAATTATGGTATTATAAAACCATGTAAA
2746 GCA-AGTAATAAGGCTTTTT
325 G-AGAGTAATAAGGC-TTTT
* * * * * *
2765 GAAGAAATAAATGATTA-ATAATAGACTTTTCTTGCCAATGAATGCCTTTACCTTCACGTTTCT
1 GAAGGAATGAGTGACTATA-AATGGACTTTTCTTACCAATGAATGCCTTTACCTTCACGTTTCT
2828 GGAGNNNNNN
Statistics
Matches: 622, Mismatches: 117, Indels: 21
0.82 0.15 0.03
Matches are distributed among these distances:
341 78 0.13
342 95 0.15
343 169 0.27
344 129 0.21
345 151 0.24
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (342 bp):
GAAGGAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTTACCTTCACGTTTCTTG
AGGTTGACATTCAATTATAATCTGTTTTAATAAAAAATGTACAAAGAATTCAAATTCAAATCAAT
TTTGAGATTATAAAACCATTTAAAGTGAGTACAAAGGCTTTTGAAGGAATGGGTGACTATAAATG
GACTTTTCTTGCCAACGAATGCCTTTTTCATTATGTTTCTCGAGGTTGACATCAATTCTAGTCTG
TTTTAACCAAAAATGTAAAAAAGTTCAACTTAAAATCAATTATGGTATTATAAAACCATGTAAAG
AGAGTAATAAGGCTTTT
Done.