Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402478.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5553.0, 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: 1948
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.33
Warning! 137 characters in sequence are not A, C, G, or T
Found at i:1097 original size:171 final size:171
Alignment explanation
Indices: 1--1116 Score: 850
Period size: 171 Copynumber: 6.6 Consensus size: 171
* * *
1 AAAAATGTAAAAAAATTTAACTTAAAATTAATTATGAGATTATAAAACAATTTAGAGCGAGCAAT
1 AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
* * ** *
66 AAGGCTTTCGAAAGAATGCATGACTATAAA-TGAACTTTTCTTCTCAATGAATGACTTTTTCTAC
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATTG-ACTTTTCTTCTCAATGAATGACTTTTTCTTC
* * *
130 ATGTTTCT-GAAGGCAGACATTCAATTATAGCCTGTTTGAACA
130 AAGTTTCTCG-AGGCAGACATTCAATTATAGTCTGTTTTAACA
**********
172 AAAAATGTAAAAAAATTTANNNNNNNNNNAATTATGAGATTATAAAACAATTTAAAG-GTAGTAA
1 AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCG-AGTAA
* * ** * * *
236 TAAGGCTTCTGAACGAATACGTAACTATAAA-AGAACTTTTCTTGC-CAATGAATGCCTTTTTCT
65 TAAGGCTTTTGAAGGAATGGGTGACTATAAATTG-ACTTTTCTT-CTCAATGAATGACTTTTTCT
* * * * * *
299 TCAAGTTTATTGAGGTAGACATTCAATTATATTCTATTTTAACT
128 TCAAGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAACA
********** * * *
343 AAAAATGTAAAAAAANNNNNNNNNNAATGAATTTTGAGATTATAAAACAATTTAAAGCGAGCAAT
1 AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
* * * *
408 AAGGCTTTTGAGGGAATGAGTTATTATAAATTGACTTTTCTTCTCAATGAATGACTTTTT-TT-A
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATTGACTTTTCTTCTCAATGAATGACTTTTTCTTCA
* * * * *
471 TTCGTTTCTTGAGGCAGGCATTCAATTATAGTCCT-CTTTAATA
131 --AGTTTCTCGAGGCAGACATTCAATTATAGT-CTGTTTTAACA
* * * * * * * ** *
514 AAAAATGT-AAAAAATTCAACGTAAAATTAATTTTAAGGTTATAAAACTATTTAAAGTTAGTACT
1 AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
** * ** * * *
578 AAGGCTTTTGAAAAAATGGGTGGCTAT-AATCAACTTTTCTTGT-AGATAAATG-CATTGTTCTT
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATTGACTTTTCTTCTCA-ATGAATGAC-TTTTTCTT
* * *
640 CACGTTTCTTC-AGGTAGACATTCAATTATAGTCTGTTTTAACC
129 CAAGTTTC-TCGAGGCAGACATTCAATTATAGTCTGTTTTAACA
* * * * *
683 GAAAATGTAAAAAAATTTAAATTAAAATCAATTATGAGATTGTTAAATAATTTAAAGCGAGTAAT
1 AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
********** * * *
748 AAGGCTTTTGANNNNNNNNNNGACTATAAATAGACTTTTCTTCTCTATGAATGACTTTTTCTACA
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATTGACTTTTCTTCTCAATGAATGACTTTTTCTTCA
* * * * *
813 TG-TTCTAGAGGCA-AGCACTCAATTATA-ACT-TGCTTAA-A
131 AGTTTCTCGAGGCAGA-CATTCAATTATAGTCTGT-TTTAACA
* * * * * *
851 AAATATATAAAAAAATTCAAATT-AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAGT
1 AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
*** * *
915 AAAATTTTTGAAGGAATGGGTGACTATAAATTGACTTTTCTTAC-CAACGAATGCCTTTTTCTTC
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATTGACTTTTCTT-CTCAATGAATGACTTTTTCTTC
* * * *
979 AAGTTGCTCGAGGTAAACATTCAATTATAGTCTGTTTTAACC
130 AAGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAACA
** * * * *
1021 AAAAATGTAAAACCATTTAACTTAAAATCAATCATGAGATTATAAAATAATTTAAAGGGACTAAT
1 AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
* * *
1086 AAGGATTTTGAAGAAATAGGTGACTATAAAT
66 AAGGCTTTTGAAGGAATGGGTGACTATAAAT
1117 AAATGCCTGT
Statistics
Matches: 732, Mismatches: 184, Indels: 58
0.75 0.19 0.06
Matches are distributed among these distances:
167 82 0.11
168 44 0.06
169 76 0.10
170 159 0.22
171 364 0.50
172 7 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.34
Consensus pattern (171 bp):
AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAT
AAGGCTTTTGAAGGAATGGGTGACTATAAATTGACTTTTCTTCTCAATGAATGACTTTTTCTTCA
AGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAACA
Found at i:1824 original size:170 final size:161
Alignment explanation
Indices: 1536--1857 Score: 346
Period size: 170 Copynumber: 1.9 Consensus size: 161
1526 TAAAACAATT
* * * *
1536 TAAAGCGAGGAATACGGCTTTTGAAGGAATGGGTGACTATAAGTGGCCTTTTCTTCTCAATGAAT
1 TAAAGCGAGGAATAAGGCTTTTGAAGGAATGGATGACTATAAGTGGACTTTTCTTCTAAATGAAT
* ** * * *
1601 GACTTTTTCAATATGTTTCTTGAGGTAGGTGTTCAATTATAGTCTGATTTAACCAACAATGTAAA
66 GACTTTTTCAATATATCGCTTGAGGTAGATATACAATTATAGTCTGATTTAACCAACAATGTAAA
1666 AAAATTCAGCTTAAAATCAATTTTGAGAATA
131 AAAATTCAGCTTAAAATCAATTTTGAGAATA
* **
1697 TANNNNNNNNNNAAGCGAGTAATAAGGCTTTTGAAGGTGTGGATGACTATAA-TGGACTTTTCTT
1 TA----------AAGCGAGGAATAAGGCTTTTGAAGGAATGGATGACTATAAGTGGACTTTTCTT
* *
1761 GC-AAATGAATG-CATTTTTC-TTCATATCGCTTGAGGTAGATATACAATTATAGTCTGTTTTAA
56 -CTAAATGAATGAC-TTTTTCAAT-ATATCGCTTGAGGTAGATATACAATTATAGTCTGATTTAA
* *
1823 CCGACAATGTAAGAAAATTCAGCTTAAAATCAATT
118 CCAACAATGTAAAAAAATTCAGCTTAAAATCAATT
1858 ATGNNNNNNN
Statistics
Matches: 131, Mismatches: 17, Indels: 17
0.79 0.10 0.10
Matches are distributed among these distances:
161 2 0.02
169 2 0.02
170 91 0.69
171 36 0.27
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.34
Consensus pattern (161 bp):
TAAAGCGAGGAATAAGGCTTTTGAAGGAATGGATGACTATAAGTGGACTTTTCTTCTAAATGAAT
GACTTTTTCAATATATCGCTTGAGGTAGATATACAATTATAGTCTGATTTAACCAACAATGTAAA
AAAATTCAGCTTAAAATCAATTTTGAGAATA
Done.