Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400515.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3710.0, 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, 768
Length: 1281
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.28
Warning! 241 characters in sequence are not A, C, G, or T
Found at i:705 original size:171 final size:171
Alignment explanation
Indices: 386--1281 Score: 1032
Period size: 171 Copynumber: 5.3 Consensus size: 171
376 NNNNNAAACG
* *
386 AATTATGAGATTATAGAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAAT-AGGTGACCATA
1 AATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGA-GTGACTATA
* * * * *
450 AATGGACTTTTCTTCTCAATCAATGGCTTTTTCTACACGTTCCTTGAGTTAGATATTCAATTATT
65 AATGGACTTTTCTTCTCAATCAATGGCTTTTTCTACACGTTTCTCGAGATAGACATTCAATTATA
*
515 GTCTAG-TTTAAAGAAAAATGTAAAAAAATTCAACTTTAAATC
130 GTCT-GTTTTAAAGAAAAATGTAAAAAAATTCAACTTAAAATC
* *
557 AATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTTAAGGAATGAGTGACTATAA
1 AATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGACTATAA
* * * * * * *
622 ATAGACTTTTCTTCTCAATGAATGACTTTTTTTGCACGTTTCTCGAGACAGACATTCAAATATAG
66 ATGGACTTTTCTTCTCAATCAATGGCTTTTTCTACACGTTTCTCGAGATAGACATTCAATTATAG
* *
687 TCTGTTCTAACA-AAAAATGTAGAAAAATTCAACTTAAAATC
131 TCTGTTTTAA-AGAAAAATGTAAAAAAATTCAACTTAAAATC
* * * *
728 AATTATGAGATTATAAAACTATTTAAAGCAAGTAATATGCCTTTTGAAGGAATGGGTGACTTCTA
1 AATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGAC-TATA
* * *
793 AATGGACTTTTCTTGTCAATCAATGGC-TTTTCTACAAGTTTCTCGAGATAGACATTCAATTATT
65 AATGGACTTTTCTTCTCAATCAATGGCTTTTTCTACACGTTTCTCGAGATAGACATTCAATTATA
* * *
857 TTCTGTTTTAAAGAAAAATGTAAAAAAATTCGACTTAAAATT
130 GTCTGTTTTAAAGAAAAATGTAAAAAAATTCAACTTAAAATC
* * * * * * * *
899 AATTATGAGATTATAAAATTATTTAAATCGAGTAATAAGGCTGTCGAAAGAATGGGTGACTAAAA
1 AATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGACTATAA
* * * * * *
964 ATGGATTTTTCTTCTGAATAAACGGCTTTTTCTATA---TTCAT-GAGGCA-AG-CTTTCAATTA
66 ATGGACTTTTCTTCTCAATCAATGGCTTTTTCTACACGTTTC-TCGA-G-ATAGACATTCAATTA
* * * * * *
1023 TGGCCCGTTTTAAAGAAAAAGGTAAAAAACTTCAACTCAAAATC
128 TAGTCTGTTTTAAAGAAAAATGTAAAAAAATTCAACTTAAAATC
* * * *
1067 AATTATGAGATTATAAAACCATTAAAAGCGGGTACTAAGCCTTTTGAAGGAATGAGTGACTATAA
1 AATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGACTATAA
* * * * *
1132 ATGAACTTTTTTTCTCAATGAATGGCTTTTTAC-GCACATTTCTCGATG-TAGACAATT-AATTA
66 ATGGACTTTTCTTCTCAATCAATGGCTTTTT-CTACACGTTTCTCGA-GATAGAC-ATTCAATTA
* * *
1194 TAATCTGTTTTAACA-AAAAA-GTGAAAAAATTCACCTTAAAATC
128 TAGTCTGTTTTAA-AGAAAAATGTAAAAAAATTCAACTTAAAATC
1237 AATTATGAGATTAT-AAACTATTTAAAGCGAGTAATAAGCCTTTTG
1 AATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTG
Statistics
Matches: 607, Mismatches: 100, Indels: 38
0.81 0.13 0.05
Matches are distributed among these distances:
168 128 0.21
169 32 0.05
170 63 0.10
171 353 0.58
172 31 0.05
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (171 bp):
AATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGACTATAA
ATGGACTTTTCTTCTCAATCAATGGCTTTTTCTACACGTTTCTCGAGATAGACATTCAATTATAG
TCTGTTTTAAAGAAAAATGTAAAAAAATTCAACTTAAAATC
Done.