Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402483.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5558.0, 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: 4455
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.28
Warning! 977 characters in sequence are not A, C, G, or T
Found at i:2608 original size:318 final size:318
Alignment explanation
Indices: 1847--2725 Score: 690
Period size: 318 Copynumber: 2.8 Consensus size: 318
1837 AGAATGGGTG
* * ** * *** *
1847 ACTATAAATAGACTTTTCTTGCTAATGGATATC-ATTTTCTTCATGTTTCTCCAGGCAAACATTC
1 ACTATAAATAGACTTTTCTTGCCAATGGATATCTA-TTTCTTCACGTTTCTTAAGACGGGCGTTC
* ** *
1911 AATTATAATCTGTTTTCGTAAAAAGATATAAAAAAATTCAAATTAAAATCAATTATGAGATTATA
65 AATTATAATCTATTTTAAT-AAAA-ATAT-AAAAAATTCAAATTAAAATCAATTATGAGGTTATA
* * ********** * * * * *
1976 AAATTATTTANNNNNNNNNNTAAGGCTTTTGAAGGCATCAGTGACTATAAATGGACTTTTCTTGC
127 AAATCATTAAATCCGAGTAATAAGGCTTTTGAAGGCATGAGAGACTACAAATGGACTTCTCTTGA
** * * * * *** * * *
2041 CAATGGGTGTCTTTTGCT-TCA-CGTTTCTCGATTTAAACATACTATTA-AATTCTGTTTTAATA
192 CAATGCATATC-TTT-CTATTATAGTTTCTTGAGACAGACATTCAATTATAATT-TGTTTTAATA
**
2103 ATAAATATAA--AAAAG-TTCAAGTAAAA--A-TTAAAGCAAGTAAAAAGGCTTTCGAAGGCATC
254 A-AAATATAATTATGAGATT-AA--AAAAGCATTTAAAGCAAGTAAAAAGGCTTTCGAAGGCATC
2162 GGTA
315 GGTA
*
2166 ACTATAAATAGACTTTTCTTGCCAATGGATATCTATTTCTTCACGTTTCTTGAGACGGGCGTTCA
1 ACTATAAATAGACTTTTCTTGCCAATGGATATCTATTTCTTCACGTTTCTTAAGACGGGCGTTCA
**********
2231 ATTATAATCTATTTTAATAAAAATATAAAAAATTCAAATTAAANNNNNNNNNNAGGTTATAAAAT
66 ATTATAATCTATTTTAATAAAAATATAAAAAATTCAAATTAAAATCAATTATGAGGTTATAAAAT
* * * *
2296 CATTTAAA-CCGAGTAATAAGGCTTTTGAAGGCTTG-GATGATTATAAATGGACTTCTCTTGCCA
131 CA-TTAAATCCGAGTAATAAGGCTTTTGAAGGCATGAGA-GACTACAAATGGACTTCTCTTGACA
*
2359 ATGGATATCATTCTCT-TTATAGTTT-TTGAGACAGACATTCAATTATAATTTGTTTTAATAAAA
194 ATGCATATC-TT-TCTATTATAGTTTCTTGAGACAGACATTCAATTATAATTTGTTTTAATAAAA
* * * *
2422 ATATAATTATGAGATTAAAAAAGCATTTAAAGCGAGTAATAAGGCTTTCGAAGAG-ATGGGTG
257 ATATAATTATGAGATTAAAAAAGCATTTAAAGCAAGTAAAAAGGCTTTCGAAG-GCATCGGTA
* * * * **********
2484 ACTATAAATTGACTTTTCTTGGCAATGGATATCTTTTTCTTCATGTTTCTTAANNNNNNNNNNCA
1 ACTATAAATAGACTTTTCTTGCCAATGGATATCTATTTCTTCACGTTTCTTAAGACGGGCGTTCA
* * *
2549 ATTATAATCTATTTTAATAAAAATATAAAACATTTAAATTAAAATCAATTATGAGGTTATAAAGT
66 ATTATAATCTATTTTAATAAAAATATAAAAAATTCAAATTAAAATCAATTATGAGGTTATAAAAT
* * * * *
2614 CATTAAATGCGAGTGATGAGGCTTTTGAAGGCATGAGAGACTACCAATGGACTTTTCTTGACAAT
131 CATTAAATCCGAGTAATAAGGCTTTTGAAGGCATGAGAGACTACAAATGGACTTCTCTTGACAAT
* * * * *
2679 TCATATCTTTTTATTCTGGTTTCTTGAGGCAGACATTCAATTATAAT
196 GCATATCTTTCTATTATAGTTTCTTGAGACAGACATTCAATTATAAT
2726 CNNNNNNNNN
Statistics
Matches: 443, Mismatches: 100, Indels: 35
0.77 0.17 0.06
Matches are distributed among these distances:
315 13 0.03
316 108 0.24
317 36 0.08
318 213 0.48
319 72 0.16
320 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.36
Consensus pattern (318 bp):
ACTATAAATAGACTTTTCTTGCCAATGGATATCTATTTCTTCACGTTTCTTAAGACGGGCGTTCA
ATTATAATCTATTTTAATAAAAATATAAAAAATTCAAATTAAAATCAATTATGAGGTTATAAAAT
CATTAAATCCGAGTAATAAGGCTTTTGAAGGCATGAGAGACTACAAATGGACTTCTCTTGACAAT
GCATATCTTTCTATTATAGTTTCTTGAGACAGACATTCAATTATAATTTGTTTTAATAAAAATAT
AATTATGAGATTAAAAAAGCATTTAAAGCAAGTAAAAAGGCTTTCGAAGGCATCGGTA
Found at i:3520 original size:172 final size:170
Alignment explanation
Indices: 2426--3991 Score: 804
Period size: 171 Copynumber: 9.2 Consensus size: 170
2416 ATAAAAATAT
* * * * *
2426 AATTATGAGATTAAAAAAGCATTTAAAGCGAGTAATAAGGCTTTCGAAGAG-ATGGGTGACTATA
1 AATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAAGCTTTTGAA-AGCATGGGTGACTATA
* * ** **********
2490 AATTGACTTTTCTTGGCAATGGATATCTTTTTCTTCATGTTTCTTAANNNNNNNNNNCAATTATA
65 AA-TGACTTTTCTTGCCAATGGATATCTTTTTCTTCAAGTTTCTCGAGGCAAACATTCAATTATA
* * *
2555 ATCTATTTTAAT-AAAAATAT-AAAACATTTAAATTAAAATC
129 ATCTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAATC
* * * * * * * **
2595 AATTATGAGGTTATAAAGTCA-TTAAATGCGAGTGATGAGGCTTTTGAAGGCATGAGAGACTACC
1 AATTATGAGGTTATAAAATCATTTAAA-GCGAGTAATAAAGCTTTTGAAAGCATGGGTGACTATA
* ** * ** * *
2659 AATGGACTTTTCTTGACAATTCATATCTTTTTATTCTGGTTTCTTGAGGCAGACATTCAATTATA
65 AAT-GACTTTTCTTGCCAATGGATATCTTTTTCTTCAAGTTTCTCGAGGCAAACATTCAATTATA
********** * * *
2724 ATCNNNNNNNNNNAAAATTGTAAAAAAATTCAACTTAAAA-C
129 ATCTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAATC
* ** * * * * *
2765 AAATTATGAGATTATACCATCAATTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGCGACAATA
1 -AATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAAGCATGGGTGACTAT-
* * * * *********
2830 AAAGGACTTTTTTTGCCAATGAATATCTTTTTCTTCACGTTTC-CTGANNNNNNNNNNT-AATTA
64 AAATGACTTTTCTTGCCAATGGATATCTTTTTCTTCAAGTTTCTC-GA-GGCAAACATTCAATTA
* ** *
2893 TAATCTATTTTAAT---AAA-A-AAAAATTTTCAACTTAAAAGT-
127 TAATCTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAA-TC
* * * * * * *********
2932 AATTATG-GTATTAAAAAAGCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCATGGNNNNNNNNN
1 AATTATGAG-GTTATAAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAAGCATGGGTGACTATA
* * * * * *
2996 NATGGACTTTTCTTGCCAATTGATATCTTTTTCCTT-ATGTTTCGT-AAGGTAGACATTCAATTA
65 AAT-GACTTTTCTTGCCAATGGATATCTTTTT-CTTCAAGTTTC-TCGAGGCAAACATTCAATTA
* * *********
3059 TAATCTATTTTAATAAAAAATATAAAAAAGTTCAANNNNNNNNN
127 TAATCTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAATC
********** * * * * * *
3103 NNNNNNNNNATTAAAAAAGCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTTACTATGA
1 AATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAAGCATGGGTGACTAT-A
* * * * * *
3168 ATTGAATTTT-TGTGCCAATGGATATCTTTTTCTTCATGTTTCCCGAGGCAGACATTCAATTCTA
65 AATGACTTTTCT-TGCCAATGGATATCTTTTTCTTCAAGTTTCTCGAGGCAAACATTCAATTATA
*
3232 ATCTGTTTTAATATAAAATATAAAAAAATTCAAATTAAAATC
129 ATCTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAATC
*************** * *
3274 AATTATGAGGNNNNNNNNNNNNNNNAGGCGAGTAATAAAGCTTTTGAAGGCATGGGTGACTATAA
1 AATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAAGCATGGGTGACTATAA
* * * * *
3339 ACGGACTTTTCTTGTCAATGCATATCTTTTTCTTCAAGTTTATCGAGGCAGACATTCAATTATAA
66 A-TGACTTTTCTTGCCAATGGATATCTTTTTCTTCAAGTTTCTCGAGGCAAACATTCAATTATAA
3404 TCTGTTTTAATAAAAAATATAAAAACAAATT-AAATTAAAATC
130 TCTGTTTTAATAAAAAATAT-AAAA-AAATTCAAATTAAAATC
*
3446 AATTATGAGGTTATAAAATCCA-TTAGAGCGAGTAATAAAGCTTTTGAAAGCATGGGTGACTATA
1 AATTATGAGGTTATAAAAT-CATTTAAAGCGAGTAATAAAGCTTTTGAAAGCATGGGTGACTATA
********** * **
3510 AATAGACTTTTCNNNNNNNNNNATATCTTTTTCTTCACGTTTCTCGAGATAAACATTCAATTATA
65 AAT-GACTTTTCTTGCCAATGGATATCTTTTTCTTCAAGTTTCTCGAGGCAAACATTCAATTATA
* *
3575 ATCTGTTTTTATAAAAAA-ATAAAAAAATTCAAATTAAAATT
129 ATCTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAATC
* * * * * * *
3616 AATTATGAGATTATAAAATCATTTAAAACGAGTAATAAGGCCTTTG-AAGCCATCGGTGGCTACA
1 AATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAAG-CATGGGTGACTATA
* * * *
3680 AATGAACTTTTTTTGCAAATGGATATCTTTTTCATCACA-TTTCTCGAGGCAAACATTTAATTAT
65 AATG-ACTTTTCTTGCCAATGGATATCTTTTTCTTCA-AGTTTCTCGAGGCAAACATTCAATTAT
* *
3744 AATTTGTTTTAATAAATAATATAAAAAAATTCAAATTAAAATC
128 AATCTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAATC
********** * * * *
3787 AATTATGNNNNNNNNNNATCATTTAAAGCGAGTAATAATGCTTTTGAAAGTATCGGTGGCTATAA
1 AATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAAGCATGGGTGACTATAA
* * * * * * *
3852 ATGAACTTTTCTTGCCAATGGATATATTTTTATTCACGTTTCTTGATGTAAACATACAATTATAA
66 ATG-ACTTTTCTTGCCAATGGATATCTTTTTCTTCAAGTTTCTCGAGGCAAACATTCAATTATAA
* * * * * *
3917 TCTCTTTTAATAATAAATATGAAAAAGTTCAACA-AAAAATT
130 TCTGTTTTAATAAAAAATATAAAAAAATTCAA-ATTAAAATC
* * * *
3958 AAGTATGAGATTA-AAAAACTATTTAAAGTGAGTA
1 AATTATGAGGTTATAAAATC-ATTTAAAGCGAGTA
3992 NNNNNNNNNN
Statistics
Matches: 1039, Mismatches: 313, Indels: 88
0.72 0.22 0.06
Matches are distributed among these distances:
165 3 0.00
166 115 0.11
167 3 0.00
168 9 0.01
169 107 0.10
170 140 0.13
171 517 0.50
172 140 0.13
173 5 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.34
Consensus pattern (170 bp):
AATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAAGCATGGGTGACTATAA
ATGACTTTTCTTGCCAATGGATATCTTTTTCTTCAAGTTTCTCGAGGCAAACATTCAATTATAAT
CTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAATC
Done.