Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1567.0, 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: 3254
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.26
Warning! 814 characters in sequence are not A, C, G, or T
Found at i:333 original size:172 final size:171
Alignment explanation
Indices: 2--1180 Score: 1110
Period size: 172 Copynumber: 6.9 Consensus size: 171
1 A
* * * * * * *
2 GACTATAAATAGACTTTTCTT-CCAAATAAATAG-GTTTTTCTAT-ACATTTCCAAAGGTAGGCA
1 GACTATAAATGGACTTTTCTTGCC-AATGAAT-GCCTTTTTCT-TCATATTTCTAGAGGTAGACA
* * * * * * *
64 TTCAATTACAACCTGTTTTAATAAAAAATGT-AAAAAATTCAACTCAAAATTAATTTTGAGATTA
63 TTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTA
* * * * *
128 TAAAGCTATTTAAAGTGAGTAATAAGACTTTTGAAGGAATGGAT
128 TAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATGGAT
* * * ** * *
172 GACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTTATATTTCTTGATATAAATATTC
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTTCTAGAGGTAGACATTC
* * * *
237 AAATATAATTTGTTTTAATCATAAAA-GTAAAACAAATTGAATTTAAAATCAATTTTGAGATTAT
66 AATTATAATCTGTTTTAATCA-AAAATGTAAAA-AAATTGAACTTAAAATCAATTATGAGATTAT
*
301 AAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAAT-GAGT
129 AAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATGGA-T
* * *
344 GACTATAAATAGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCA-AGGTAGACATT
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTTCT-AGAGGTAGACATT
* * ** *
408 CAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGGTTATA
65 CAATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATA
* * *
473 AAACCATTTAAAGCGAGTAGTAAGGCTTTTGAAGGAATGGGA-
130 AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAAT-GGAT
* * * * * * ** * * * **
515 GACTATATATGAACTTTTTTTTCTAATAAATGGGTTTTTCTACATGTTTCCCA-AGCCA-AGCAT
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTT-CTAGAGGTAGA-CAT
* ** ** * * * * *
578 TCAATTTTAGCCCATTTTAATGAAAAATGT-AAAAAATTTAACTTTAAATCAGTTATGAGGTTAT
64 TCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTAT
** *
642 AAAATTATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAGA-
129 AAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATG-GAT
* ** * * *
685 GACTATAAATGGACTTTTCTT-CCAAATAAATGGGTTTTT-TT-ATACGTTACTAGAGGCAGGCA
1 GACTATAAATGGACTTTTCTTGCC-AATGAATGCCTTTTTCTTCATA--TTTCTAGAGGTAGACA
* *
747 TTCAA-T-T-ATCTGTTTTAATGAAAAATGT-AAAAAATTTAACTTAAAATCAATTATGAGATTA
63 TTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTA
808 TAAAACCATTTAAA-AGAGTAATAAGGCTTTTGAAAGAATGGAT
128 TAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATGGAT
* * * * ** * *
851 GACTATAAATGAACTTTTCTTGCCAATGAATACC-TTTTCATCATGTTTCTAGACATAGATAGTC
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTTCTAGAGGTAGACATTC
* * *
915 AATTATAATATGTTTTAAAT-AAAAATGTAAAAAAAATTAAACTTAAAATCAATTTTGAGATTAT
66 AATTATAATCTGTTTT-AATCAAAAATGT-AAAAAAATTGAACTTAAAATCAATTATGAGATTAT
* * *
979 AAAATCATTTAAAGTGAGTAATAAGAG-TTTTGAAAGAATGGGT
129 AAAACCATTTAAAGAGAGTAATAAG-GCTTTTGAAAGAATGGAT
** * * * * *
1022 GGGTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACATTTCTTGACGTAGACATTT
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTTCTAGAGGTAGACATTC
* * * *
1087 AATTATAATATGTTTTAACCAAAAATGTAAAAAAAATTGAACTTAAAATGAATTATGAAATTATA
66 AATTATAATCTGTTTTAATCAAAAATGT-AAAAAAATTGAACTTAAAATCAATTATGAGATTATA
1152 AAACCATTTAAAGCA-AGTAATAAGGCTTT
130 AAACCATTTAAAG-AGAGTAATAAGGCTTT
1181 CGANNNNNNN
Statistics
Matches: 840, Mismatches: 134, Indels: 68
0.81 0.13 0.07
Matches are distributed among these distances:
165 20 0.02
166 53 0.06
167 64 0.08
168 19 0.02
169 11 0.01
170 221 0.26
171 205 0.24
172 245 0.29
173 2 0.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTTCTAGAGGTAGACATTC
AATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAA
AACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATGGAT
Found at i:1748 original size:170 final size:160
Alignment explanation
Indices: 1479--1798 Score: 297
Period size: 170 Copynumber: 1.9 Consensus size: 160
1469 AATCAATTAT
* * * * *
1479 GAGATTATAAAACTAATTAAAGCGAGTAACAAGGCTTTTGAAGGAATTAGAGACTATAAATGGAC
1 GAGATTATAAAACCAATTAAAACGAGTAACAAGGCTTTTGAAAGAATTAGAGACTATAAATAGAA
* *** * * *
1544 TTTTCTTCCAAATAAATTGGTTTTTTTACACATTTTCA-GAGGCAGCCATTCAATTATAGTCTGT
66 TTTTCTGCCAAATAAATACCTTTTTTTACACA-TTTCATGAGACAGACATTCAATTATAATCTGT
** *
1608 TTTAATGAAAAATGTAAAAAATTTAACTTAA
130 TTTAACCAAAAATATAAAAAATTTAACTTAA
* * *
1639 NNNNNNNNNNGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAAGAA-TGGATGAC
1 ----------GAGATTATAAAACCAATTAAAACGAGTAACAAGGCTTTTGAAAGAATTAGA-GAC
* * *
1703 TATAAATAGAATTTTCATGCC-AATGAATACCTTTTTCTT-CACATTTCATGAGATAGACTTTCA
55 TATAAATAGAATTTTC-TGCCAAATAAATACCTTTTT-TTACACATTTCATGAGACAGACATTCA
1766 ATTATAATCTGTTTTAACCAAAAATATAAAAAA
118 ATTATAATCTGTTTTAACCAAAAATATAAAAAA
1799 AATTGAACTT
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
169 8 0.06
170 112 0.90
171 5 0.04
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.33
Consensus pattern (160 bp):
GAGATTATAAAACCAATTAAAACGAGTAACAAGGCTTTTGAAAGAATTAGAGACTATAAATAGAA
TTTTCTGCCAAATAAATACCTTTTTTTACACATTTCATGAGACAGACATTCAATTATAATCTGTT
TTAACCAAAAATATAAAAAATTTAACTTAA
Done.