Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403074.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_739.0, 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: 6553
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.22
Warning! 2545 characters in sequence are not A, C, G, or T
Found at i:3109 original size:171 final size:172
Alignment explanation
Indices: 2817--3977 Score: 1305
Period size: 172 Copynumber: 6.8 Consensus size: 172
2807 NNNNNNNTTA
* * * * * * * *
2817 TAGTCTGTTTTAACC-AAAA-GTATAAACAAATTCAACTTAAAATCAATTATG-GCGTTACAAAA
1 TAGTCTATTTTAACCAAAAATGTACAAA-GAATTCAAATTTAAATCAATTTTGAG-ATTATAAAA
* * * **
2879 CCAGTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTCACTATAAATATACTTTTCTTGCCAA
64 CCATTTAAAGCGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAA
*
2944 TGAATGCTTTTTTCTTCATGTTTCACAAGGTAGACATTCAATTC
129 TGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTC
* * * * *
2988 TAGTATTTTTTAACCAAAAATGTACAAAGAA-TCAAATTTTAGTCAATTTTGAGATTATAAAACA
1 TAGTCTATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACC
*
3052 ATTTAAAGCGAGTAATAAGGCTTTTAAAGGTATGAGTGACTATAAATGGACTTTTCTTGCCAATG
66 ATTTAAAGCGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATG
* *
3117 AATAG-TTTTTTCCTCATGTTTCTCAAGGTAGACATTCATTTC
131 AAT-GCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTC
* * * *
3159 TAGTCTATTTTAACTAAAAAAGTACAAAGAATTCAAATTTAAATAAATTTTGAGATTATAAAACT
1 TAGTCTATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACC
* * * *
3224 ATTTAAA-CGCAGTAATAAGGCTTTTAAATGAATGCGTGACTATAAATGGACTTTTCTTGGCAAT
66 ATTTAAAGCG-AGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * *
3288 GAATACTTTTTTCTTCATGTTT-TCCAAGGTATAGATACAATTG
130 GAATGCTTTTTTCTTCATGTTTCT-CAAGGTAGACATTCAATTC
* * * *
3331 TAGTCTATTTTAACTAAAAATATGCAAA-ACATTTAAATTTAAATCAATTTTGAGATTATAAAAC
1 TAGTCTATTTTAACCAAAAATGTACAAAGA-ATTCAAATTTAAATCAATTTTGAGATTATAAAAC
* * * * *
3395 CATTTAAAGTGCGTATTATGGCTCTTAAAGG-AGTGGGTGACTATAAATGGACTTTTCTTGCCAA
65 CATTTAAAGCGAGTAATAAGGCTTTTAAAGGTA-TGGGTGACTATAAATGGACTTTTCTTGCCAA
* * * *
3459 TGAAT-ATCTTTTTCTTTATGTTTCTCAAGGTAGGCATTCAATTA
129 TGAATGCT-TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTC
* * * * * * * * ** *
3503 GAGT-T-TGTTTATCCAAAAATATAGAAA-ATATTTAACTTAAAATCTATTACG-GCATTACAAA
1 TAGTCTAT-TTTAACCAAAAATGTACAAAGA-ATTCAAATTTAAATCAATTTTGAG-ATTATAAA
* * ** *
3564 ACCATTTAATGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATACACTTTTCTT-CCC
63 ACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCA
*
3628 ATGAATGCTTTTTCCTTCATGTTTCTCAAGGTAGACATTCAATTC
128 ATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTC
* * * *
3673 TAGTCTGTTTTAACCAAAAATGCACAAAGAA-TCAAATTTAAGTCAATTTTGAGATTATACAACC
1 TAGTCTATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACC
* * * *
3737 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGTGTGTGTGACTGTAAATGGACTTTTCTTGCCAATG
66 ATTTAAAGCGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATG
* * *
3802 AATACTTTTTTCTTCATGTTTCTTAAGATAGACATTCAA-TC
131 AATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTC
* * * *
3843 TTGGTCTGTGTTAA-CAAAAGATGTACAAAGAATTCAAATTTCAATCAATTTTGAGATTATAAAA
1 -TAGTCTATTTTAACCAAAA-ATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAA
* * * * * *
3907 CTATTTAAAGTGATTACTAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAA
64 CCATTTAAAGCGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAA
3972 TGAATG
129 TGAATG
3978 NNNNNNNNNN
Statistics
Matches: 835, Mismatches: 130, Indels: 49
0.82 0.13 0.05
Matches are distributed among these distances:
170 126 0.15
171 339 0.41
172 362 0.43
173 8 0.01
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (172 bp):
TAGTCTATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACC
ATTTAAAGCGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATG
AATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTC
Found at i:5647 original size:172 final size:171
Alignment explanation
Indices: 5358--5676 Score: 408
Period size: 172 Copynumber: 1.9 Consensus size: 171
5348 NNNNNATGGG
* *
5358 TGACTATAAATAGACTTTTTCTGCCAATGAATATTTTTTCTTCATGTTTCTCATGGTATAAATTA
1 TGACTATAAATAGACTTTTTCTGCCAATGAATATTTTTTCTTCATGTTTCTCAAGGTAGAAATTA
* * *********** * *
5423 TATTCTAGTCTATTTTAACCAAAANNNNNNNNNNCATTTAAATTTAAATCAATTTTTAGATTATA
66 TATCCTAGTCTATTTTAACAAAAAATGGTCAAAGAATTCAAATTTAAATCAATTTTGAGATTATA
*
5488 AAACCATTTAAATTGAGCAATAAGGCTCTTGAAGGAATGAA
131 AAACCATTTAAAGTGAGCAATAAGGCTCTTGAAGGAATGAA
* *
5529 TGACTATAAATAGAC-TTTTCTTGCCAATGAATTATTTTTTCTTCATGTTTCTTAAGGTAGACAT
1 TGACTATAAATAGACTTTTTC-TGCCAATGAA-TATTTTTTCTTCATGTTTCTCAAGGTAGAAAT
5593 TCA-ATCCTAGTCTATTTTAACAAAAAATGGTCAAAGAATTCAAATTTAAATCAATTTTGAGATT
64 T-ATATCCTAGTCTATTTTAACAAAAAATGGTCAAAGAATTCAAATTTAAATCAATTTTGAGATT
*
5657 ATAAAATCATTTAAAGTGAG
128 ATAAAACCATTTAAAGTGAG
5677 NNNNNNNNNN
Statistics
Matches: 124, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
170 5 0.04
171 25 0.20
172 93 0.75
173 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.39
Consensus pattern (171 bp):
TGACTATAAATAGACTTTTTCTGCCAATGAATATTTTTTCTTCATGTTTCTCAAGGTAGAAATTA
TATCCTAGTCTATTTTAACAAAAAATGGTCAAAGAATTCAAATTTAAATCAATTTTGAGATTATA
AAACCATTTAAAGTGAGCAATAAGGCTCTTGAAGGAATGAA
Done.