Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399166.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2439.0, 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: 1855
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:330 original size:171 final size:171
Alignment explanation
Indices: 50--1853 Score: 1629
Period size: 171 Copynumber: 10.6 Consensus size: 171
40 TAATGCTATT
* * ** *
50 AAACCGTTTAAAGAGAATAATAAGGAATTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTTC
1 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
* * * * * * * **
115 CAATAAATGTGTTTTTCTTCAT-TTTTCCAAGGGTAAATATTCAATGATAATTTGTTTTGCCCAA
66 CAATGAATGGGTTTTTCTTCATGTTTCCCAA-GGCAAACATTCAATTATAATCTGTTTTAACCAA
* *
179 AAACAG-AAAAAAATTCAAGTTAAAATCAATTATGAGATTATA
130 AAA-TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* * * * * *
221 AAACCATTTAAAGAGAGCAATAAGGCTTTTGAAGGCTTAGGAGACTATAGATGCGCTTTTCATGC
1 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
* * * *
286 CAGTCAATGGGTTTTTCTTCATGCTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACTAAA
66 CAATGAATGGGTTTTTCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAA
* * *
351 AATGTAAAAAAATTCGAC-TAAGAATCAATTATAAGATTACA
131 AATGTAAAAAAATTCAACTTAA-AATCAATTATGAGATTATA
* * * *
392 AAACCATTTAATGAGAGTAATAAGGCTTTTGAAGGCTTGAGTGGCTATAAATGGGCTTTTCTTAC
1 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
* * ** * * * * *
457 CAATGAATAGCTCATTCTTCAGGTTTTCCATGGAAAACATTGAATTATAATCTGTTTTAACCAAA
66 CAATGAATGGGTTTTTCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAA
* * * * *
522 AATGTAAAAAAAATCAACTTAAAATCAATTTTGAGGTGATC
131 AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* *
563 AAACCATTTAAAGAGAGTAATAAGGATTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGT
1 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
* * * * *
628 TAATGAATGGGTTTTTCTTCATGTTTCTCAAGGTAAACATTGAATTATAATCTGTTTTAACTAAA
66 CAATGAATGGGTTTTTCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAA
* * * *
693 AATGTAAAATAATTAAACATAAAATCAATT-TTA-ATGCTATA
131 AATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT--TATA
* * * *
734 AAACCTTTTTAAGAGAGTAATAAGGCATTTGAAAGCTTGGGTGACTATAAATGGGCTTTTCTTGC
1 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
* * * ** * * * *
799 CAATAAATGAGTTTTTCTTCATGCTTCTTAAGGCAAACAATCAATTATAATCTGTGTTAACTATA
66 CAATGAATGGGTTTTTCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAA
* * * * * * *
864 AATATAAAATAATTCAACTTCAGATCAATTATTAAATTATG
131 AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* * * ** * *
905 AAATCATTTACAA-AGAGTAATATGGCTTTTGAAGGCTTCGGTGACTATAAATGCAC-TTTCGTA
1 AAACCATTTA-AAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTG
* * * * *
968 CCAATGAATGGGTTTTTCTTCATATTTCTCAAGG-TAA-ATTCAATTATAATCTATTTTAACTAA
65 CCAATGAATGGGTTTTTCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAA
* * * *
1031 AGATG-AAAAAAAGTAAACCTAAAATCAATTATGAGATTATA
130 AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* *
1072 AAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
1 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
* ** * * * ** * *
1137 CAATGATTTAGTCTTTCTTTATGTCT-CTTAGGCCAAACATTCAATTATAGTCTGTTTTAGCCAA
66 CAATGAATGGGTTTTTCTTCATGTTTCCCAAGG-CAAACATTCAATTATAATCTGTTTTAACCAA
* * * * * *
1201 CAATGTAATAATATTTAATTTAAAATCAATTTTGAGATTATA
130 AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* *
1243 AAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATTGGCTTTTCTTGC
1 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
* * * * *
1308 CAATGAATAGATTTTTCTTCAT-TTTCCCCAAGGAAAACATTCAATTGTAATATGTTTTAACCAA
66 CAATGAATGGGTTTTTCTTCATGTTT-CCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAA
* *
1372 AAATGTAAAAAAATTCAACTTAAGATCAATTATGAGATTATN
130 AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
*************************** *
1414 NNNNNNNNNNNNNNNNNNNNNNNNNNNTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
1 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
* * ** * * * * *
1479 CAATGAATGAGTTTTTGTTCATGTTTCTGAAGGTAAACATTGAATTATAATTTGTTTTCACTAAA
66 CAATGAATGGGTTTTTCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAA
* * * * * *********
1544 AATGTGAAACAATTAAACATAAAATCAATTTTNNNNNNNNN
131 AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* * * *
1585 NAACCGTTTAAAGAGAGTAATAAGGCATTTGAAGGCTTGAGTGACTATAAATGGGCTTTTCTTGC
1 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
********** * * * * * * * *
1650 CNNNNNNNNNNTTTTTCTTCATGCTTCTCAAGGCAATCAATCAAGTATAATCTGTGTTAGCTAAA
66 CAATGAATGGGTTTTTCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAA
*
1715 AATGTAAAATAAA-TCAACTTAAAATCAATTATGAGACTATA
131 AATGTAAAA-AAATTCAACTTAAAATCAATTATGAGATTATA
* * *
1756 TAACCATTTAAAGAGAGTAATATA-GATTTTGAAGGCTTGGGTGACAATAAATGGGCTTTTCTTG
1 AAACCATTTAAAGAGAGTAATA-AGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTG
*
1820 CCAATGAATGGATTTTTCTTCATGTTTCCCAAGG
65 CCAATGAATGGGTTTTTCTTCATGTTTCCCAAGG
1854 AA
Statistics
Matches: 1279, Mismatches: 334, Indels: 40
0.77 0.20 0.02
Matches are distributed among these distances:
166 2 0.00
167 76 0.06
168 50 0.04
169 5 0.00
170 67 0.05
171 1053 0.82
172 24 0.02
173 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.34
Consensus pattern (171 bp):
AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
CAATGAATGGGTTTTTCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAA
AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
Found at i:1829 original size:21 final size:21
Alignment explanation
Indices: 1800--1839 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1790 GCTTGGGTGA
*
1800 CAATAAATGGGCTTTTCTTGC
1 CAATAAATGGACTTTTCTTGC
* *
1821 CAATGAATGGATTTTTCTT
1 CAATAAATGGACTTTTCTT
1840 CATGTTTCCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (21 bp):
CAATAAATGGACTTTTCTTGC
Done.