Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398855.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2137.0, 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: 2295
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.28
Warning! 617 characters in sequence are not A, C, G, or T
Found at i:1310 original size:171 final size:170
Alignment explanation
Indices: 720--1515 Score: 767
Period size: 171 Copynumber: 4.7 Consensus size: 170
710 NNNNNNNNAC
* * * * * *
720 ATTTTTGGTTAAAATAAATTATAATTGAATGGCTATCTCT-AGAAA-GTGAAGAAAAATG-CATT
1 ATTTTTGGTTAGAACAGATTATAATTGAATGTCTACCT-TGAGAAACATGAAGAAAAA-GACATT
* * * * * * *
782 CATTGGCAAGAAATGTCCATTTATAGTCACGCATTCCTTTAAAAGCCTTATTACACACTTTAAAT
64 CATTGACAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACATTAAAT
* * * ********** * *
847 GGTTTTCTAATCTCANNNNNNNNNNTAGTTTGAATTCTTTGTAC
129 GGCTATATAATCTCATAATTGATTTTAGATTGAATT-TTT-TAT
* * * * *
891 ATTTTTTGTTAGAACATATTATCATTGAAGGTCTACCTTGACAAA-ATGAAGAAAAAGACATTCA
1 ATTTTTGGTTAGAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCA
* * * * *
955 TTCACAAGAAAAGT-TCATTTATAGTCACCCATTCTTTTAAAATCCTTATTACTCACATTATATG
66 TTGACAAGAAAAGTCT-ATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACATTAAATG
* * * * *
1019 GCTTTATAATCTCATAATTAATTTTAGACTGATTTTTTTAA
130 GCTATATAATCTCATAATTGATTTTAGATTGAATTTTTTAT
* * * * **
1060 ATTTTTGGTTAGAATAGATTATAATTGAATGTCTGCCCTGTGAAACATGAAGAAAAAGGTATTCA
1 ATTTTTGGTTAGAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCA
* * * *
1125 TTGGCAAGAAAAGTCTACTTATAGTCACTCATTCCTTCAAAAGCCTTCTTACTCACATTAAATGG
66 TTGACAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACATTAAATGG
1190 CTATATAATCTCATAATTGATTTTAGATTGAATTTGTTTAT
131 CTATATAATCTCATAATTGATTTTAGATTGAATTT-TTTAT
* *
1231 ATTTTTGGTTAGAACAGATTATAATTGAATGTCTACCATGAGAAACGA-GAAGAAAAAGGCATTC
1 ATTTTTGGTTAGAACAGATTATAATTGAATGTCTACCTTGAGAAAC-ATGAAGAAAAAGACATTC
* * ********** *
1295 ATTGACAAAAAAAGTCCATTTNNNNNNNNNNATTCCTTCAAAAGCCTTATTACTCACCTTAAATG
65 ATTGACAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACATTAAATG
* * * *
1360 GTTGTATAATCTCAAAATTGATTTTAGATTAAATTTTTTCAT
130 GCTATATAATCTCATAATTGATTTTAGATTGAATTTTTT-AT
* * * * *
1402 ATTTTTGGTTAGAACATATTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAATATATTCA
1 ATTTTTGGTTAGAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCA
* *
1467 GTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
66 TTGACAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
1516 NNNNNNNNNN
Statistics
Matches: 509, Mismatches: 107, Indels: 18
0.80 0.17 0.03
Matches are distributed among these distances:
169 38 0.07
170 110 0.22
171 360 0.71
172 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.36
Consensus pattern (170 bp):
ATTTTTGGTTAGAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCA
TTGACAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACATTAAATGG
CTATATAATCTCATAATTGATTTTAGATTGAATTTTTTAT
Found at i:1972 original size:170 final size:170
Alignment explanation
Indices: 1675--2060 Score: 418
Period size: 170 Copynumber: 2.3 Consensus size: 170
1665 CCTATTCTTT
* ** * *
1675 CAAAAGCCTTATTACTTACTTTAAATAGTTTTACAATCTCCTAATTGATTTTAGGTTGAATTTTT
1 CAAAAGCCTTATTACTTACTTTAAATAGTTTTATAATCTCAAAATTAATTTGAGGTTGAATTTTT
* * * * * *
1740 GACATTTTTTATTAAAATATATTATAATTGAATATTTGCCTTGGGAAATATGAAGAAAAAGGTAT
66 GACATTTTTGATTAAAAGAGACTATAATTGAATATCTGCCTTGGGAAATATGAAGAAAAAGGTAA
* * * ***
1805 TCATTGACA-AACAAAGTCTATTTATGGTCACCCATTTCTG
131 CCATTGACACAA-AAAGTCCATTTATAGTCACCCAAGCCTG
* * * *
1845 CAAAAGCCTTATTACTCACTTAAAATGGCTTTATAATCTCAAAATTAATTTGAGGTT-AATTTTT
1 CAAAAGCCTTATTACTTACTTTAAATAGTTTTATAATCTCAAAATTAATTTGAGGTTGAA-TTTT
** * * * * *
1909 TTTCATTTTTGGTTAAAAGAGGCTATAATTGAATGTCTGCCTTGAGGAACT-TGAAGCAAAAGGT
65 TGACATTTTTGATTAAAAGAGACTATAATTGAATATCTGCCTTG-GGAAATATGAAGAAAAAGGT
* * * *
1973 AACCATTGGCACAAAAAGTCCATTTTTAGTCACTCAAGCCTT
129 AACCATTGACACAAAAAGTCCATTTATAGTCACCCAAGCCTG
* *
2015 CAAAAGTCTTATTACTTGCTTTAAATAGTTTTATAATCTCAAAATT
1 CAAAAGCCTTATTACTTACTTTAAATAGTTTTATAATCTCAAAATT
2061 NNNNNNNNNN
Statistics
Matches: 175, Mismatches: 38, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
169 2 0.01
170 166 0.95
171 7 0.04
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (170 bp):
CAAAAGCCTTATTACTTACTTTAAATAGTTTTATAATCTCAAAATTAATTTGAGGTTGAATTTTT
GACATTTTTGATTAAAAGAGACTATAATTGAATATCTGCCTTGGGAAATATGAAGAAAAAGGTAA
CCATTGACACAAAAAGTCCATTTATAGTCACCCAAGCCTG
Done.