Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401481.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4608.0, 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: 2256
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.28
Warning! 527 characters in sequence are not A, C, G, or T
Found at i:1499 original size:172 final size:171
Alignment explanation
Indices: 839--2164 Score: 832
Period size: 172 Copynumber: 7.8 Consensus size: 171
829 NNNGAGGTAG
** * ** * *
839 ACATTCAATTATAATCTGTTTTAATAAAAAATA-TAAAAAATTCAACACAAAATTAGTTATGAGA
1 ACATTCAATTATAATCTGTTTTAACCAAAAATAGAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * ** * * * * * **
903 TTGTGAAACCACGTAAAGCGACTTAA-AAGGGTTTCGAAGGCATGGGTGTCTACCAATGGACTTT
66 TTATAAAAACATTTAAAGCGA-GTAATAAGGCTTTTGAAGGGATGGGTGACTATAAATGGACTTT
* **
967 TCTTGCGAATGAA-ATTCTTTTTCTTCATGTTTCACT-A-GTTAA
130 TCTTAC-AATGAATA-TCTTTTTCTTCATGTTTC-CTCAGGGCAA
* * * ***
1009 ACATTCAATTATAATTTGTTTTAA-TAAAATATA-TAAAAAATTCAACTTAAAATCAATTATNNN
1 ACATTCAATTATAATCTGTTTTAACCAAAA-ATAGAAAAAAATTCAACTTAAAATCAATTATGAG
******* ** *
1072 NNNNNNNAAA-ATTTAAAGCGAGTAATAAGGCTTTTGAAGATATGGGTGACTATAAATGGATTTT
65 ATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGGATGGGTGACTATAAATGGACTTT
* * ***********
1136 TCTTGCCAATGGATATCTTTTTCTTCATG-TTNNNNNNNNNNN
130 TCTT-ACAATGAATATCTTTTTCTTCATGTTTCCTCAGGGCAA
******* * *
1178 NNNNNNNATTATTATCTGTTTTAACCAAAAAT-GTAAAAAAATTCAACTTAAAATCAATTTTTTG
1 ACATTCAATTATAATCTGTTTTAACCAAAAATAG-AAAAAAATTCAACTTAAAATCAA--TTATG
*
1242 AGATTATAAAAACATTTAAAGCGAGTAATAAGGTTTTTGAAGGGATGGGTGGA-TATAAATGGAC
63 AGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGGATGGGT-GACTATAAATGGAC
1306 TTTTCTTATCAATGAATATCTTTTTCTTCATGTTTCCT-AGGGCAA
127 TTTTCTTA-CAATGAATATCTTTTTCTTCATGTTTCCTCAGGGCAA
*
1351 ACATTCAATTATTATCTGTTTTAACCAAAAATAGAAAAAAATTCAACTTAAAAATCAATTATGAG
1 ACATTCAATTATAATCTGTTTTAACCAAAAATAGAAAAAAATTCAACTT-AAAATCAATTATGAG
* * * *
1416 ATTA-AAAAATCATTTAAAGCGAGTAATAACGG-ATTCGAAGGGATGGGTGACTATAAATAGTCT
65 ATTATAAAAA-CATTTAAAGCGAGTAATAA-GGCTTTTGAAGGGATGGGTGACTATAAATGGACT
* * * * *
1479 TTTCTTACCAATGGATATCTTGTTCTTCATGTTTCTTGAGGTC-A
128 TTTCTTA-CAATGAATATCTTTTTCTTCATGTTTCCTCAGGGCAA
* * * *
1523 ACATTCAATTATAATTTGTTTTTACCAAAAATGTAAAAAAAAATT-AACTTAAAATGAATTATGA
1 ACATTCAATTATAATCTGTTTTAACCAAAAA--TAGAAAAAAATTCAACTTAAAATCAATTATGA
* * *
1587 GATTATAAAAACATTTAAAGCTAGTAATAAGGCTTTTGAAGGCAAGGGTGACTATAAATGGACTT
64 GATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGGATGGGTGACTATAAATGGACTT
* ** * *
1652 TTCTTGA-AAGTGAATATCTTTTTTTTCATGTTT-CTCAACGTAG
129 TTCTT-ACAA-TGAATATCTTTTTCTTCATGTTTCCTCAGGGCAA
* ** * * * *
1695 ATATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAA-TCAAGTCAAAATTAATTATGAGA
1 ACATTCAATTATAATCTGTTTTAACCAAAAATAGAAAAAAATTCAACTTAAAATCAATTATGAGA
********** * * * * *
1759 TTATAAAAACATTNNNNNNNNNNAATAATGCTTTTAAAGGCATGGGCGGCTATAAATGGACTTTT
66 TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGGATGGGTGACTATAAATGGACTTTT
* * * * * ***
1824 CTTGCCAATGGATATCGTTTTCTTCATGTTTTCT-AAGGTNN
131 CTT-ACAATGAATATCTTTTTCTTCATGTTTCCTCAGGGCAA
******** * * * *
1865 NNNNNNNNTTATTATCTGTTTTAACTAAAAA-AGTAAAACAATTCAAGTTAAAATCAATTATGAG
1 ACATTCAATTATAATCTGTTTTAACCAAAAATAG-AAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * * * * *
1929 GTTATAAAAATATTTAAAGCGAGTCATAAGGCTTTTAAAGGCATGAGTAACAATAAATAGAGTTT
65 ATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGGATGGGTGACTATAAATGGACTTT
* * ** * *
1994 TCTTATTAATGGATATTCTTTTT-TTCA-CATTCCTC-GAGACAG
130 TCTTA-CAATGAATA-TCTTTTTCTTCATGTTTCCTCAG-GGCAA
* ** * * * * * *
2036 ACATTCAATTATTATCTGTTTTCGCTATAAATATAAAAAAATTCAAGTCAAAATCAATTTTGA-A
1 ACATTCAATTATAATCTGTTTTAACCAAAAATAGAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * * *
2100 GTTAT-AAAACTATTTAAAGTGAGTAACAAGACTTTTGAAGGTATGAGTAACTATAAATGGACTT
66 -TTATAAAAAC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGGATGGGTGACTATAAATGGACTT
2164 T
129 T
2165 GTTTGTCAAT
Statistics
Matches: 896, Mismatches: 220, Indels: 79
0.75 0.18 0.07
Matches are distributed among these distances:
168 5 0.01
169 85 0.09
170 218 0.24
171 193 0.22
172 241 0.27
173 130 0.15
174 24 0.03
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
ACATTCAATTATAATCTGTTTTAACCAAAAATAGAAAAAAATTCAACTTAAAATCAATTATGAGA
TTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGGATGGGTGACTATAAATGGACTTTT
CTTACAATGAATATCTTTTTCTTCATGTTTCCTCAGGGCAA
Found at i:2050 original size:171 final size:170
Alignment explanation
Indices: 837--2186 Score: 815
Period size: 171 Copynumber: 7.9 Consensus size: 170
827 NNNNNGAGGT
* * ** * *
837 AGACATTCAATTATAATCTGTTTTAA-TAAAAAA-TATAAAAAATTCAACACAAAATTAGTTATG
1 AGACATTCAATTATTATCTGTTTTAACCAAAAAAGTA-AAAAAATTCAACTTAAAATCAATTATG
* * * ** * * * * **
900 AGATTGTGAAACCACGTAAAGCGACTTAA-AAGGGTTTCGAAGGCATGGGTGTCTACCAATGGAC
65 AGATTATAAAAACATTTAAAGCGA-GTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGAC
* * * * * * **
964 TTTTCTTGCGAAT-GAAATTCTTTTTCTTCATGTTTCACTAGTT
129 TTTTCTTACCAATGGATA-TCTTTTT-TTCATGTTCCTCGAGAC
* * * * * *
1007 AAACATTCAATTATAATTTGTTTTAA-TAAAATA-TATAAAAAATTCAACTTAAAATCAATTATN
1 AGACATTCAATTATTATCTGTTTTAACCAAAAAAGTA-AAAAAATTCAACTTAAAATCAATTATG
********* ** *
1070 NNNNNNNNNAAA-ATTTAAAGCGAGTAATAAGGCTTTTGAAGATATGGGTGACTATAAATGGATT
65 AGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGACT
* *********
1134 TTTCTTGCCAATGGATATCTTTTTCTTCATGTTNNNNNNNNN
130 TTTCTTACCAATGGATATCTTTTT-TTCATGTTCCTCGAGAC
********* * *
1176 NNNNNNNNNATTATTATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTTT
1 AGACATTCAATTATTATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAA--TTAT
* *
1241 GAGATTATAAAAACATTTAAAGCGAGTAATAAGGTTTTTGAAGGGATGGGTGGA-TATAAATGGA
64 GAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGT-GACTATAAATGGA
* * * *
1305 CTTTTCTTATCAATGAATATCTTTTTCTTCATGTTTCCTAG-GGC
128 CTTTTCTTACCAATGGATATCTTTTT-TTCATG-TTCCTCGAGAC
*
1349 AAACATTCAATTATTATCTGTTTTAACCAAAAATAG-AAAAAAATTCAACTTAAAAATCAATTAT
1 AGACATTCAATTATTATCTGTTTTAACCAAAAA-AGTAAAAAAATTCAACTT-AAAATCAATTAT
* * * *
1413 GAGATTA-AAAAATCATTTAAAGCGAGTAATAACGG-ATTCGAAGGGATGGGTGACTATAAATAG
64 GAGATTATAAAAA-CATTTAAAGCGAGTAATAA-GGCTTTTGAAGGCATGGGTGACTATAAATGG
* * * * *
1476 TCTTTTCTTACCAATGGATATCTTGTTCTTCATGTTTCTTGAGGTC
127 ACTTTTCTTACCAATGGATATCTT-TTTTTCATGTTCCTCGA-GAC
* * * * *
1522 A-ACATTCAATTATAATTTGTTTTTACCAAAAATGTAAAAAAAAATT-AACTTAAAATGAATTAT
1 AGACATTCAATTATTATCTGTTTTAACCAAAAAAGT--AAAAAAATTCAACTTAAAATCAATTAT
* *
1585 GAGATTATAAAAACATTTAAAGCTAGTAATAAGGCTTTTGAAGGCAAGGGTGACTATAAATGGAC
64 GAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGAC
* *
1650 TTTTCTTGA--AAGTGAATATCTTTTTTTTCATGTTTCTC-A-AC
129 TTTTCTT-ACCAA-TGGATATC-TTTTTTTCATGTTCCTCGAGAC
* * * * * * *
1691 GTAGATATTCAATTATAATCTGTTTTAA-TAAAAAA-TATAAAAAAATCAAGTCAAAATTAATTA
1 --AGACATTCAATTATTATCTGTTTTAACCAAAAAAGTA-AAAAAATTCAACTTAAAATCAATTA
********** * * * *
1754 TGAGATTATAAAAACATTNNNNNNNNNNAATAATGCTTTTAAAGGCATGGGCGGCTATAAATGGA
63 TGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGA
* * * * **
1819 CTTTTCTTGCCAATGGATATCGTTTTCTTCATGTT-TTCTAAGGT
128 CTTTTCTTACCAATGGATATC-TTTTTTTCATGTTCCTC-GAGAC
********** * * *
1863 NNNNNNNNNNTTATTATCTGTTTTAACTAAAAAAGTAAAACAATTCAAGTTAAAATCAATTATGA
1 AGACATTCAATTATTATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGA
* * * * * * * * *
1928 GGTTATAAAAATATTTAAAGCGAGTCATAAGGCTTTTAAAGGCATGAGTAACAATAAATAGAGTT
66 GATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGACTT
** **
1993 TTCTTATTAATGGATATTCTTTTTTTCACATTCCTCGAGAC
131 TTCTTACCAATGGATA-TCTTTTTTTCATGTTCCTCGAGAC
** * * * * *
2034 AGACATTCAATTATTATCTGTTTTCGCTATAAATA-TAAAAAAATTCAAGTCAAAATCAATTTTG
1 AGACATTCAATTATTATCTGTTTTAACCA-AAAAAGTAAAAAAATTCAACTTAAAATCAATTATG
* * * * * *
2098 A-AGTTAT-AAAACTATTTAAAGTGAGTAACAAGACTTTTGAAGGTATGAGTAACTATAAATGGA
65 AGA-TTATAAAAAC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGA
** *
2161 CTTTGT-TTGTCAATAGATATCTTTTT
128 CTTT-TCTTACCAATGGATATCTTTTT
2187 CTCAACATTT
Statistics
Matches: 913, Mismatches: 224, Indels: 86
0.75 0.18 0.07
Matches are distributed among these distances:
168 4 0.00
169 89 0.10
170 203 0.22
171 232 0.25
172 231 0.25
173 132 0.14
174 22 0.02
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
AGACATTCAATTATTATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGA
GATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATGGACTT
TTCTTACCAATGGATATCTTTTTTTCATGTTCCTCGAGAC
Done.