Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401855.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4960.0, 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: 3257
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.26
Warning! 944 characters in sequence are not A, C, G, or T
Found at i:935 original size:170 final size:167
Alignment explanation
Indices: 542--1273 Score: 468
Period size: 170 Copynumber: 4.3 Consensus size: 167
532 NNNNNNAATG
* * * **
542 AAAAATATATAAAAATTCAACTTAAAATCAATTATGT-GATTACAAAACTATTTAAAATGAGTAA
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTAT-TAGATTATAAAACCATTTAAAGCGAGTAA
* ********** *
606 TAAGACTTTTGAAGAAATGGGTGACTATAAATGGACTTTNNNNNNNNNNGAATACTTTTTTCTTC
65 TAAG-CTTTT-AAGAAATAGGTGACTATAAAT-GACTTTTCTTGTCAATGAATGCTTTTTTCTTC
* * ** * * *
671 ATGTTTC-CTAGGGTAGGCAATT-AATTGTAGTCTGTTTTAACC
127 ACGTTTCTC-AAGGTAAAC-ATTCAATTATAATC-GTTTTAACT
* * * ********** *
713 AAAAATA-CAAAAAATTCAACCTAAAATTAATTNNNNNNNNNNAAATCCATTTAAAGCGAGTAAT
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCGAGTAAT
* * *
777 AAAGCTTTTGAAGAAATTGGTGACTATAAATAGATTTTTCTTATCAATGAATGCTTTTTTCTTCA
66 -AAGCTTTT-AAGAAATAGGTGACTATAAAT-GACTTTTCTTGTCAATGAATGCTTTTTTCTTCA
*
842 CGTTTCTCAAGGTAAACATTCAATTATAATCATTTTAACT
128 CGTTTCTCAAGGTAAACATTCAATTATAATCGTTTTAACT
* * * *
882 AAAAATATAAAAAAATTTAACTTCAAATCAATTATTAGATTATAAGACCATTTAAAGCAAGTAAT
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * * *
947 ACGACTTTTAAAAGAATAGGTGACTATAAATGAACTTTTATTGCCAATGAATACATTTTTCTTCA
66 AAG-CTTTTAAGA-AATAGGTGACTATAAATG-ACTTTTCTTGTCAATGAATGCTTTTTTCTTCA
* * *
1012 TGTTTCTCAATGTAAACATTCAATTATAAACTGTTTTAACT
128 CGTTTCTCAAGGTAAACATTCAATTATAATC-GTTTTAACT
* * * * *
1053 AAAAAAGTAAAAAAAAAATTGAACTTAAAATCCATT-TTGATATTATAAAACCATTTAAAGTGAG
1 -AAAAA-T-ATAAAAAAATTCAACTTAAAATCAATTATT-AGATTATAAAACCATTTAAAGCGAG
******** * * * *
1117 TANNNNNNNNNNTAAAGGAATGGGTGACTAT-AATGGACTTTTCTTGTCAATGAATGTGTTTTTT
62 TA--ATAAGCTTTTAAGAAATAGGTGACTATAAAT-GACTTTTCTTGTCAATGAATG-CTTTTTT
* * ** * * * * **
1181 TTTCACATTTCTTGAGGTAGACATTCAATTTTAGTTTGTTTTAAGG
123 CTTCACGTTTCTCAAGGTAAACATTCAATTATA-ATCGTTTTAACT
*
1227 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAA
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAA
1274 TTATTTANNN
Statistics
Matches: 429, Mismatches: 113, Indels: 38
0.74 0.19 0.07
Matches are distributed among these distances:
169 23 0.05
170 219 0.51
171 52 0.12
172 8 0.02
173 28 0.07
174 96 0.22
175 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.35
Consensus pattern (167 bp):
AAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCGAGTAAT
AAGCTTTTAAGAAATAGGTGACTATAAATGACTTTTCTTGTCAATGAATGCTTTTTTCTTCACGT
TTCTCAAGGTAAACATTCAATTATAATCGTTTTAACT
Found at i:2487 original size:169 final size:169
Alignment explanation
Indices: 2048--2501 Score: 405
Period size: 170 Copynumber: 2.7 Consensus size: 169
2038 TTCTTTTGCT
* * * *
2048 AATGAATGTCTTTTTCTTTATGTTTCTTGAGGTAGGA-AATCAATTATAGTCTATTTTAA-TGAA
1 AATGAAT-ACTTTTTCTTCATGTTTCTTGAGGTA-GACATTCAATTATAGTCTGTTTTAACTG-A
* * * *
2111 AAATGTTAAACAATTTC-ACTTAAAATCAATTATTAGATTATAAAACCATTTAATGCGAGTAATA
63 AAATG-TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* ********** *
2175 AAGCTTTTGAAGGAATGNNNNNNNNNNAATGGACTTTTCTTGCC
127 AAGCTTTTGAAGAAATGAGGTAACTATAATGGAC-TTTCTTACC
* * ** * * * * *
2219 AATGAATAATTTTTTTTCATGTTTCTCAAGGTAGACATTCAGTTATTGCCTGTTTTAGCTAAAAA
1 AATGAATACTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTGAAAA
* ********** *
2284 TGTAAAACAATTCAACTTNNNNNNNNNNATGAGATTATAAAACCATTTAAAGCGAGTACTAAAGC
66 TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGC
2349 TTTTGAAGAAATG-GGTAACTATAAGTGGAC-TTCTTACC
131 TTTTGAAGAAATGAGGTAACTATAA-TGGACTTTCTTACC
* *
2387 AATGAATCCCTTTTTCTTCATGTTTATTGAGGTAGACATTCAATTATAGTCTGTTTTAACTGAAA
1 AATGAAT-ACTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTGAAA
* *
2452 ATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAATCATTTA
65 ATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
2502 NNNNNNNNNN
Statistics
Matches: 214, Mismatches: 64, Indels: 12
0.74 0.22 0.04
Matches are distributed among these distances:
168 14 0.07
169 95 0.44
170 97 0.45
171 8 0.04
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.36
Consensus pattern (169 bp):
AATGAATACTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTGAAAA
TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGC
TTTTGAAGAAATGAGGTAACTATAATGGACTTTCTTACC
Done.