Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398614.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1901.0, 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: 2891
ACGTcount: A:0.23, C:0.10, G:0.09, T:0.22
Warning! 1037 characters in sequence are not A, C, G, or T
Found at i:1761 original size:171 final size:172
Alignment explanation
Indices: 1439--2208 Score: 651
Period size: 171 Copynumber: 4.5 Consensus size: 172
1429 NNNNNNNNNN
* * *
1439 GAATTCTTTGTACATTGTT-GGTCAACAA-AGATTATAATTGAATGTCAACCTCCAA-AAACGTG
1 GAATTCTTTGTACATT-TTATGTTAA-AACATATTATAATTGAATGTCAACCT-CAAGAAACGTG
* ** * * * **
1501 ACGGTAAAGGCATTCATTGGGAAGAAAAGTCCATTAATACTCACCCATTCCTTCAAAAGCCTCTT
63 AAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCCTTCAAAAGCCTAAT
* *
1566 TACTTACTTTAAAGGGTTTTATAATCTCAAAATTGATTTAAATTT
128 TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTT
* *
1611 GAATTCTTTGTGCATTTTATGTTAAAACATATTATAATTGAATGTCAACCTCAAGAAACCTGAAG
1 GAATTCTTTGTACATTTTATGTTAAAACATATTATAATTGAATGTCAACCTCAAGAAACGTGAAG
** * * *
1676 AAAAAAGCACACATTGGCAAGAAAAATCCGTTTAT-GTCACCCATTCCTTCAAAAGCCTAATTAC
66 AAAAAAGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCCTTCAAAAGCCTAATTAC
* ** ****
1740 TCGCTTTAAATGGTTTTATAATGC-CGTAATTGATTTTTCGTT
131 TCACTTTAAATGGTTTTATAAT-CTCAAAATTGATTTAAATTT
* * ** * **
1782 GAAGTT-TTT-TACATTTT-TGGTTAAAACAGATAATAATTGAATGTCAATATCGAGAAACGAAA
1 GAA-TTCTTTGTACATTTTAT-GTTAAAACATATTATAATTGAATGTCAACCTCAAGAAACGTGA
* ** ** * *
1844 AGAAAAAAGTATTTGTTGGCAAGAAAAGTTTATTTATAGTCACCCATTCATTCAAAAGCCTTAA-
64 AGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCCTTCAAAAGCC-TAAT
* * * *
1908 -ACCTCACTTTCAATGGTTTTGTAATCTTAAAATTGATTGAAATTT
128 TA-CTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTT
* * *
1953 GAATTCTTTGTACATTTTAAGTTAAAGA-ATATTATAATTGAATGT-AAACTCAAGAAACATGAA
1 GAATTCTTTGTACATTTTATGTTAAA-ACATATTATAATTGAATGTCAACCTCAAGAAACGTGAA
* * * * *
2016 GGAAAAGGCATTCAATGGCAAGAAAAGTCCATTAATAGTCACCTATTCCTTCAAAAAGCCTTATT
65 GAAAAAAGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCCTTC-AAAAGCCTAATT
* * * * * * * *
2081 CCTCGCTTTACATGGTTTTCTATTAC-CACAATTGATTTTAAGTT
129 ACTCACTTTAAATGGTTTTATAAT-CTCAAAATTGATTTAAATTT
* * * * * *
2125 GAACTT-TTT-TACATTTT-TAGTTAAAATAGACTAGAATTG-ATGTCTACC-CGGAGAAACGT-
1 GAA-TTCTTTGTACATTTTAT-GTTAAAACATATTATAATTGAATGTCAACCTC-AAGAAACGTG
* *
2184 AACAAAAAAGGCATTCGTTGGCAAG
63 AAGAAAAAA-GCATTCATTGGCAAG
2209 NNNNNNNNNN
Statistics
Matches: 472, Mismatches: 102, Indels: 49
0.76 0.16 0.08
Matches are distributed among these distances:
169 1 0.00
170 86 0.18
171 227 0.48
172 154 0.33
173 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (172 bp):
GAATTCTTTGTACATTTTATGTTAAAACATATTATAATTGAATGTCAACCTCAAGAAACGTGAAG
AAAAAAGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCCTTCAAAAGCCTAATTAC
TCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTT
Found at i:2181 original size:342 final size:341
Alignment explanation
Indices: 1510--2208 Score: 845
Period size: 342 Copynumber: 2.0 Consensus size: 341
1500 GACGGTAAAG
* * * ** *
1510 GCATTCATTGGGAAGAAAAGTCCATTAATACTCACCCATTCCTTCAAAAGCCTCTTTACTTACTT
1 GCATTCGTTGGCAAGAAAAGTCCATTAATACTCACCCATTCATTCAAAAGCCTCTAAACTCACTT
* * *
1575 TAAAGGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTGCATTTTATGTTAAAACA
66 TAAAGGGTTTTATAATCTCAAAATTGATTGAAATTTGAATTCTTTGTACATTTTAAGTTAAAACA
* * *
1640 TATTATAATTGAATGTCAACCTCAAGAAACCTGAAGAAAAAAGCACACATTGGCAAGAAAAATCC
131 TATTATAATTGAATGTCAAACTCAAGAAACATGAAGAAAAAAGCACACAATGGCAAGAAAAATCC
* * * **
1705 GTTTATGTCACCCATTCCTTCAAAAGCCTAATTACTCGCTTTAAATGGTTTTATAATGCCGTAAT
196 ATTAATGTCACCCATTCCTTCAAAAGCCTAATTACTCGCTTTAAATGGTTTTATAATACCACAAT
** * * * *
1770 TGATTTTTCGTTGAAGTTTTTTACATTTTTGGTTAAAACAGATAATAATTGAATGTCAATATCGA
261 TGATTTTAAGTTGAACTTTTTTACATTTTTAGTTAAAACAGATAAGAATTGAATGTC-ATACCGA
1835 GAAACG-AAAAGAAAAAA
325 GAAACGTAAAA-AAAAAA
* * ** * *
1852 GTATTTGTTGGCAAGAAAAGTTTATTTATAGTCACCCATTCATTCAAAAGCCT-TAAACCTCACT
1 GCATTCGTTGGCAAGAAAAGTCCATTAATACTCACCCATTCATTCAAAAGCCTCTAAA-CTCACT
* * * *
1916 TTCAATGGTTTTGTAATCTTAAAATTGATTGAAATTTGAATTCTTTGTACATTTTAAGTTAAAGA
65 TTAAAGGGTTTTATAATCTCAAAATTGATTGAAATTTGAATTCTTTGTACATTTTAAGTTAAA-A
* * ** *
1981 -ATATTATAATTGAATGT-AAACTCAAGAAACATGAAGGAAAAGGCATTCAATGGCAAGAAAAGT
129 CATATTATAATTGAATGTCAAACTCAAGAAACATGAAGAAAAAAGCACACAATGGCAAGAAAAAT
* * * * * *
2044 CCATTAATAGTCACCTATTCCTTCAAAAAGCCTTATTCCTCGCTTTACATGGTTTTCTATTACCA
194 CCATTAAT-GTCACCCATTCCTTC-AAAAGCCTAATTACTCGCTTTAAATGGTTTTATAATACCA
*
2109 CAATTGATTTTAAGTTGAACTTTTTTACATTTTTAGTTAAAATAGACT-AGAATTG-ATGTC-TA
257 CAATTGATTTTAAGTTGAACTTTTTTACATTTTTAGTTAAAACAGA-TAAGAATTGAATGTCATA
* *
2171 CCCGGAGAAACGTAACAAAAAAG
321 -CC-GAGAAACGTAAAAAAAAAA
2194 GCATTCGTTGGCAAG
1 GCATTCGTTGGCAAG
2209 NNNNNNNNNN
Statistics
Matches: 300, Mismatches: 49, Indels: 16
0.82 0.13 0.04
Matches are distributed among these distances:
340 2 0.01
341 47 0.16
342 167 0.56
343 83 0.28
344 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (341 bp):
GCATTCGTTGGCAAGAAAAGTCCATTAATACTCACCCATTCATTCAAAAGCCTCTAAACTCACTT
TAAAGGGTTTTATAATCTCAAAATTGATTGAAATTTGAATTCTTTGTACATTTTAAGTTAAAACA
TATTATAATTGAATGTCAAACTCAAGAAACATGAAGAAAAAAGCACACAATGGCAAGAAAAATCC
ATTAATGTCACCCATTCCTTCAAAAGCCTAATTACTCGCTTTAAATGGTTTTATAATACCACAAT
TGATTTTAAGTTGAACTTTTTTACATTTTTAGTTAAAACAGATAAGAATTGAATGTCATACCGAG
AAACGTAAAAAAAAAA
Done.