Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401631.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4749.0, 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: 1935
ACGTcount: A:0.23, C:0.09, G:0.10, T:0.24
Warning! 656 characters in sequence are not A, C, G, or T
Found at i:1198 original size:172 final size:172
Alignment explanation
Indices: 564--1498 Score: 540
Period size: 172 Copynumber: 5.5 Consensus size: 172
554 CATTGAAATC
* * * *
564 GAGTAATAAGGCTTTTGAAGCTATGAGTGACTATAAATGAACTTTTCTTGCCAATGAAAACTTTT
1 GAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTT
* * * * *
629 TTCATCATGTTTCTGATGGTAGACAATCAATCCTAGTCTGTTTTCACTAAAAACGTACAAAGAAT
66 TTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTGTTTTAACTAAAAATGTACAAAGAAT
* * **
694 TGAAATTTAAATCAATTTTGAGATTATAAAACAATTCCAAGT
131 TCAAATTTAAATCAATTTTAAGATTATAAAACAATTTAAAGT
********** * * * * * *
736 GNNNNNNNNNNCTTTTGAAGGAATGGGTGACTATAAATGGACTTCTCTTGCTAATGATTGCCTTT
1 GAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTT
* * ** * * *
801 TTCTTTATGTTTCTCG-AGATAGACATTCAATTATAATCT-TTTTAACTAAAAATATA-AAATAT
66 TTCTTCATGTTTCT-GAAGGTAGACATTCAATCCTAGTCTGTTTTAACTAAAAATGTACAAAGA-
* *********** * * *
863 ATTC-AACTTAANNNNNNNNNNNGCATTACAAAACCATTTAAAGC
129 ATTCAAATTTAAATCAATTTTAAG-ATTATAAAACAATTTAAAGT
* * *
907 GAGTAGTAAGGCTTTTGAAGGTATGGGTGACTCTAAATGTACTTTTCTTGCCAATGAATACTTTT
1 GAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTT
* * ************** *
972 TTCTTCATGTTTCTGAACGTGGACATTCANNNNNNNNNNNNNNTAACAAAAAATGTACAAAGAAT
66 TTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTGTTTTAACTAAAAATGTACAAAGAAT
*
1037 TCAAATTTAAATCAATTTTAAGATTATAAAACGATTTAAAGT
131 TCAAATTTAAATCAATTTTAAGATTATAAAACAATTTAAAGT
* * * * * *
1079 GAGTAATAAGACTTTTCAAGGGATGGGTGACTATAAATGGACTTTTCTAGCTAATGAATACTTTA
1 GAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTT
* * *
1144 TTCTTCATGTTTTTGAAGGTAGACATTCAATCCTTGTATGTTTTAACTAAAAATGTACAAAGAAT
66 TTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTGTTTTAACTAAAAATGTACAAAGAAT
********************** * *
1209 TCNNNNNNNNNNNNNNNNNNNNNNTATAAAACCATTTAAATT
131 TCAAATTTAAATCAATTTTAAGATTATAAAACAATTTAAAGT
* * * * * *
1251 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAATTGGACTTCTCGTGCCAATGAATGCCTTT
1 GAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTT
* * * ** * * * *
1316 TTATTTACGTTTCTCG-AGGTAGACATTCAATTATAGTCTG-TTTAACCAAAAGTATA-AAAAAA
66 TTCTTCATGTTTCT-GAAGGTAGACATTCAATCCTAGTCTGTTTTAACTAAAAATGTACAAAGAA
* * * * * * * * * *
1378 ATCAACTTAAAAT-GATTAT-GGCATTACATAACCATTGAAA-T
130 TTCAAATTTAAATCAATTTTAAG-ATTATAAAACAATTTAAAGT
* * **
1419 CGAGTAATAAGGCTTCTGAAGTTATCAGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTT
1 -GAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTT
1484 TTTCTTCATGTTTCT
65 TTTCTTCATGTTTCT
1499 NNNNNNNNNN
Statistics
Matches: 539, Mismatches: 214, Indels: 23
0.69 0.28 0.03
Matches are distributed among these distances:
168 1 0.00
169 79 0.15
170 19 0.04
171 115 0.21
172 312 0.58
173 13 0.02
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.34
Consensus pattern (172 bp):
GAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTT
TTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTGTTTTAACTAAAAATGTACAAAGAAT
TCAAATTTAAATCAATTTTAAGATTATAAAACAATTTAAAGT
Done.