Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400207.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_342.0, 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: 4384
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.25
Warning! 1429 characters in sequence are not A, C, G, or T
Found at i:2186 original size:171 final size:171
Alignment explanation
Indices: 1632--2704 Score: 801
Period size: 171 Copynumber: 6.3 Consensus size: 171
1622 NNNNNNNNNN
* * * * **
1632 GTGAATATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTT-TCTAAGTTAGACA
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCTC-GAGGCAGACA
* * * * * * *
1696 TTCAATTATTATTTATTGTAACT-AAAAATGTAAAAAATTTTAGCTTAAAATCAATTATGAGATT
65 TTCAATTATTATCTGTTTTAA-TAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATT
** ** ** * *
1760 ATAAAATTATTTAAAATGAGTAATAAGGCTTCCGAAGACATGA
129 ATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGG
* ** * ** * * *
1803 GTGACTATAGATGGACTTTTCTTGTCAATGGATATCTTTCTCTTCCCGTTTCTTGAGGTAGACAN
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACAT
*************** *
1868 NNNNNNNNNNNNNNCTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGATTAT
66 TCAATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
1933 AAAGACATTTGAAGCAAGTAATAAGGCTTTTAAAGGTATGG
131 AAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGG
* ********** * *
1974 GTGACTATAAAAGGACTTTTNNNNNNNNNNGATAACTTTTTCTTCATGTTTC-CTGAGCCAGACA
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCTC-GAGGCAGACA
* * ** * * *
2038 TTCAATAATTATCTGTTTTAATAAAACACGTAAAAAAATTTAATTTAAAATCAATTATTAGATTA
65 TTCAATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * *
2103 CAAAAACATTGAAAGCGAGTAATAAGGCTTTTGAAGGCATGA
130 TAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGG
* * * * * *
2145 GCGACTATAAATGGACTTTACTTACCATTGGATATCTTTTTCTTCATATTTTTCAAGGCAGACAT
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACAT
* * * *
2210 TCAATTATTATTTATTTTAATGAAAAATATAAAATAATTTC-ACTTAAAATCAATTATGAGATTA
66 TCAATTATTATCTGTTTTAATAAAAAATATAAAA-AAATTCAACTTAAAATCAATTATGAGATTA
* * * * * *
2274 TAAAAATATTTAAAGTGACTAAAAAGCCTTTTGAAGGCACGG
130 TAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGG
* * * **
2316 GTGACTATAAATAGACTTTCCTTGCCAAT-GATATCTTTTTCTTCCCGTTTC-CTGAGGCAGACA
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCTC-GAGGCAGACA
* ********** *
2379 TTTAATTATTATCTGTTNNNNNNNNNNATGTAAAAAAATTCAACTTAAAATTCAA-TATGAGATT
65 TTCAATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAA-TCAATTATGAGATT
** * * **
2443 ATAAAAACATTTAAAGCTCGTAAAAATGCTTTTGAAGGTGTGG
129 ATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGG
* * * * **********
2486 TTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTNNNNNNNNNNAT
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACAT
* * * * *
2551 TCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATGAAATATGATATTAT
66 TCAATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
** * * **
2616 AAAGCCATTTAAAACGAGTAATAAGGCTTTCGAAATCATGG
131 AAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGG
2657 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATG
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATG
2705 NNNNNNNNNN
Statistics
Matches: 679, Mismatches: 212, Indels: 22
0.74 0.23 0.02
Matches are distributed among these distances:
169 6 0.01
170 128 0.19
171 539 0.79
172 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACAT
TCAATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
AAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGG
Found at i:3697 original size:171 final size:170
Alignment explanation
Indices: 3145--3992 Score: 719
Period size: 171 Copynumber: 5.0 Consensus size: 170
3135 NNNNNNNNNC
* * * *
3145 TTAAAATCAATTATAAGATTATAAAAATATTTAAAACGAGTAATAA-CGCTTTTAAAGGCATGGG
1 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAAAAAGC-CTTTTAAAGGCATGGG
* * * * *
3209 AGACTATAAATGAACTTTTCTTACAAATGGATATCTTTTTGTTCATGTTTCCTGAGGCAGACATT
65 TGACTATAAATGGACTTTTCTTGCCAATGGATAT-TTTTTCTTCATGTTTCCTGAGGCAGACATT
* * ** **********
3274 CAATAGTTATCAGTTTTAATGAAACACATAAANNNNNNNNNN
129 CAATAATTATCAGTTTTAATGAAAAATGTAAAAAAATTTAAT
* * * *
3316 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCTAG-AAATAAGACTTTTCAAGGCATGAG
1 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAAA-AAGCCTTTTAAAGGCATGGG
* * * *
3380 TGACTATAAATGAACTTTTCTTGCCATTGGAT-TTTTTT-TTCATGTTT-CTCGAGGTAGATATT
65 TGACTATAAATGGACTTTTCTTGCCAATGGATATTTTTTCTTCATGTTTCCT-GAGGCAGACATT
* * * * * *
3442 CAATTATTATTTA-TTTTAATCAAAAATATAAAAAAATTCAAC
129 CAATAATTA-TCAGTTTTAATGAAAAATGTAAAAAAATTTAAT
********** * * * *
3484 TTANNNNNNNNNNTGAGATTATAAAAACAATTAAAGCAAGTAAAAAGCCTTTTAAATGCGTGGGT
1 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAAAAAGCCTTTTAAAGGCATGGGT
* * *
3549 GACTATAAATGGACTTTTCTTGCTAATGGATGTCTTTTTCTTCATGTTTCCTGAGGCTGACATTC
66 GACTATAAATGGACTTTTCTTGCCAATGGATAT-TTTTTCTTCATGTTTCCTGAGGCAGACATTC
* *
3614 AATAATTATCAGTTTTAATGAAACACGTAAAAAAATTTAAT
130 AATAATTATCAGTTTTAATGAAAAATGTAAAAAAATTTAAT
* * * * *
3655 TTAAAATTAATTATGAGATTAAAAAAATATTTAAAACAAGTAATAAGGCTTTTAAAGGCATGGGT
1 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAAAAAGCCTTTTAAAGGCATGGGT
* * * * * ** *
3720 GACTATAAATGGACTTCTCTTGCCACTGCATATGTTTGTCTTTACATTT-CTCGAGACAGACATT
66 GACTATAAATGGACTTTTCTTGCCAATGGATAT-TTTTTCTTCATGTTTCCT-GAGGCAGACATT
* *
3784 CAATCATTAATTA-TTTTAATCG-AAAATGTAAAAAAATTTAACT
129 CAATAATT-ATCAGTTTTAAT-GAAAAATGTAAAAAAATTTAA-T
* * * ***
3827 TT-AAATTAATTATGAGATTATAAAAACATTTAAAGCTAGTAAAAAGCCTTTTAAAGATGTGGGT
1 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAAAAAGCCTTTTAAAGGCATGGGT
* * * ** ** *
3891 GACTATAAATAGACTTTTCTTGCTAATGAATATTTGTTTCTTCCCGTTTCCCAAGGCAGACATTT
66 GACTATAAATGGACTTTTCTTGCCAATGGATATTT-TTTCTTCATGTTTCCTGAGGCAGACATTC
* *
3956 AATTATTATCTGTTTTAACT-AAAAATGTAAAAAAATT
130 AATAATTATCAGTTTTAA-TGAAAAATGTAAAAAAATT
3993 CAACTNNNNN
Statistics
Matches: 538, Mismatches: 120, Indels: 38
0.77 0.17 0.05
Matches are distributed among these distances:
167 2 0.00
168 113 0.21
169 11 0.02
170 16 0.03
171 385 0.72
172 11 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAAAAAGCCTTTTAAAGGCATGGGT
GACTATAAATGGACTTTTCTTGCCAATGGATATTTTTTCTTCATGTTTCCTGAGGCAGACATTCA
ATAATTATCAGTTTTAATGAAAAATGTAAAAAAATTTAAT
Done.