Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399002.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2281.0, 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: 3039
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.29
Warning! 778 characters in sequence are not A, C, G, or T
Found at i:1822 original size:170 final size:171
Alignment explanation
Indices: 1529--1930 Score: 522
Period size: 170 Copynumber: 2.4 Consensus size: 171
1519 AAAATAGAGT
* * * *
1529 ATAATTGAATGTCTACCTCAAGAAACATGAAGAAACAAGCATCCATTGACAAGAGAAGTCAATTT
1 ATAATTGAATGTCTACCTCAAGAAACATGAAGAAATAAGCATTCATTGACAAGAAAAGTCCATTT
* **
1594 ATAGTCACCCATTCCTTTAAAAGGCATATTACTCCCTTTAAATTATTTTATAATCTCATAATTTA
66 ATAGTCACCCATTCCTTTAAAAGGCATATTACTCCCTTTAAATTATTGTATAATCTCATAATGGA
* *
1659 TTTTAAGTTAAAGTTTTTT-ACATTTTTTATTAAAACGGACC
131 TTTTAAGTTAAAGTTTTTTGA-ATTTTTGATTAAAACAGACC
* * * * *
1700 ATAATTTAAT-TCTACCTGAAGAAACGTGAAGAAATAAGTATTCATTGAGAAGAAAAGTCCATTT
1 ATAATTGAATGTCTACCTCAAGAAACATGAAGAAATAAGCATTCATTGACAAGAAAAGTCCATTT
* ** **
1764 ATAGTCACCCATTCTTTTAAAAGGGTTATTACTCGTTTTAAATGT-TTGTATAATCTCATAATGG
66 ATAGTCACCCATTCCTTTAAAAGGCATATTACTCCCTTTAAAT-TATTGTATAATCTCATAATGG
* * **
1828 ATTTTATGTTAAATTTTTTTGAATTTTTGATTAAAACAGAGT
130 ATTTTAAGTTAAAGTTTTTTGAATTTTTGATTAAAACAGACC
* * * *
1870 ATAATTGAATGTTTACCTTAAGAAACATGAACAAATAAGCATTCATTGATAAGAAAAGTCC
1 ATAATTGAATGTCTACCTCAAGAAACATGAAGAAATAAGCATTCATTGACAAGAAAAGTCC
1931 NNNNNNNNNN
Statistics
Matches: 198, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
170 143 0.72
171 55 0.28
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (171 bp):
ATAATTGAATGTCTACCTCAAGAAACATGAAGAAATAAGCATTCATTGACAAGAAAAGTCCATTT
ATAGTCACCCATTCCTTTAAAAGGCATATTACTCCCTTTAAATTATTGTATAATCTCATAATGGA
TTTTAAGTTAAAGTTTTTTGAATTTTTGATTAAAACAGACC
Found at i:2360 original size:171 final size:172
Alignment explanation
Indices: 2063--2761 Score: 439
Period size: 171 Copynumber: 4.1 Consensus size: 172
2053 NNNNNNNNNN
* *
2063 TTATAATCTCATAATTGATTTTAAGTTAAATT-TTTTAATATTTTTTG-TTAAAATAGACTATAA
1 TTATAATCTCATAATTGATTTTAAGTTAAATTGTTTTAATA-TTTTTGATTAAAATCGAGTATAA
* * * * ********** *
2126 TTGAATGTCTGCCTTGAGAAACGTGATGAAACAAGCATCCATTNNNNNNNNNNGTCTATTTATAG
65 TTGAATGTCTACCTTAAGAAACATGAGGAAACAAGCATCCATTGACAAGAAAAGTCCATTTATAG
** *
2191 -TCACCCATTCTTTCTGAAGGCTTATTACTCGCTTTAAATGGGT
130 ATCACCCATTC-TTCAAAAGGCTTATTACTCGCTTTAAATGAGT
* * *
2234 TTATAATCTCAAAATCGATTTTAAGTTGAATTGTTTT-ATATTTTTGATTAAAATCGAGTATAAT
1 TTATAATCTCATAATTGATTTTAAGTTAAATTGTTTTAATATTTTTGATTAAAATCGAGTATAAT
* * * *
2298 TGAATGTCTACCTCAAGAAACATGAGGAAACAAGCTTTCATTGACAAGAAAAGTCCATTTATAGN
66 TGAATGTCTACCTTAAGAAACATGAGGAAACAAGCATCCATTGACAAGAAAAGTCCATTTATAGA
********* * * *
2363 NNNNNNNNNCTTCAAAAGTCTTATTACTGGCTTTAAATGATT
131 TCACCCATTCTTCAAAAGGCTTATTACTCGCTTTAAATGAGT
* * * *
2405 TTATAATCTCATAGTTGATTTT-AGTTTAATTGTTTTCA-ATTTTTAATTAAAA-CAGAGTATAA
1 TTATAATCTCATAATTGATTTTAAGTTAAATTGTTTTAATATTTTTGATTAAAATC-GAGTATAA
* * ****************** * *
2467 TTGAATGTCTACCTTAAGAAACATTAAGAAAGNNNNNNNNNNNNNNNNNAAAATTCTATTTATAG
65 TTGAATGTCTACCTTAAGAAACATGAGGAAACAAGCATCCATTGACAAGAAAAGTCCATTTATAG
* * * **
2532 -TCACTCATTCCTTTAAAAGGCTTATTACTCGCTTTAAAAGTTT
130 ATCACCCATT-CTTCAAAAGGCTTATTACTCGCTTTAAATGAGT
* * * * *
2575 TTATAATCTCATAATTAATTTTACGTTAAATTTTTTTGA-ATTTTTGATTAAAATAGAGTATAAT
1 TTATAATCTCATAATTGATTTTAAGTTAAATTGTTTTAATATTTTTGATTAAAATCGAGTATAAT
** * ** * ** * * * **
2639 TGAATGTCTATGTTGAGAAATGTAAAAAAACAAGCATTCGTTGATAAGAAAAGTATATTTATAG-
66 TGAATGTCTACCTTAAGAAACATGAGGAAACAAGCATCCATTGACAAGAAAAGTCCATTTATAGA
* * * *
2703 CCACCTATTCCTTAAAAAGGATTATTACTCGCTTTAAATG-GTT
131 TCACCCATT-CTTCAAAAGGCTTATTACTCGCTTTAAATGAG-T
2746 TTATAATCTCATAATT
1 TTATAATCTCATAATT
2762 NNNNNNNNNN
Statistics
Matches: 397, Mismatches: 122, Indels: 18
0.74 0.23 0.03
Matches are distributed among these distances:
169 1 0.00
170 130 0.33
171 261 0.66
172 5 0.01
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.38
Consensus pattern (172 bp):
TTATAATCTCATAATTGATTTTAAGTTAAATTGTTTTAATATTTTTGATTAAAATCGAGTATAAT
TGAATGTCTACCTTAAGAAACATGAGGAAACAAGCATCCATTGACAAGAAAAGTCCATTTATAGA
TCACCCATTCTTCAAAAGGCTTATTACTCGCTTTAAATGAGT
Done.