Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398154.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1457.0, 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: 5511
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.29
Warning! 1455 characters in sequence are not A, C, G, or T
Found at i:2929 original size:169 final size:169
Alignment explanation
Indices: 2441--3665 Score: 1010
Period size: 169 Copynumber: 7.2 Consensus size: 169
2431 NNNNNNNTAC
* * *
2441 AATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTCTTATGAAAACAGATTATAATTAAAT
1 AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTT-TTATTAAAACAGATTATAATTGAAT
* * ** * * * **********
2506 GTCTTCCTTGAGAAACATGAAG-AAAAGATATCCATTGGTAAGNNNNNNNNNNTTATAGTCACCC
65 ATCTACCTCAAGAAACGTGAAGAAAAAGATATCTATTGGCAAGAAAAGTCCATTTATAGTCACCC
* * * * *
2570 ATGCCTTCGAAAGTCTTATTAGTCGCTTTGAATGTTTTTAA
130 ATACCTTCGAAAGCCTTATTACTCGCTTTAAATG-TTTTAT
* * * * * * * *
2611 AATCTCATAATAGATTTTATGCTG-TTTTTTTTATATTTTTTATTCAAACAAATTATAATTTATT
1 AATCTCATAATTGATTTTAAGTTGAATTTTTTTATA-TTTTTATTAAAACAGATTATAATTGAAT
* * ** * *********** * *
2675 GTCTACCTC-TGAAAATATGAAGAAAAAGATATCCATTGGTNNNNNNNNNNCACTTATAGTCACA
65 ATCTACCTCAAG-AAACGTGAAGAAAAAGATATCTATTGGCAAGAAAAGTCCATTTATAGTCACC
*
2739 CATACCTTCCG-AAGTCTTATTACTCGCTTTAAATAGTTTTAT
129 CATACCTT-CGAAAGCCTTATTACTCGCTTTAAAT-GTTTTAT
* * * * * *
2781 AATTTTATAATTAATTTTAAGTT-AATTTTTTTATATTTTTATTAAAACTGATTAAAATTGAATG
1 AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAATA
* *
2845 TCTACCTCAAGAAACGTGAAGAAAAAAATATCTATTGGCAAGAAAAGTCTATTTATAGTCACCCA
66 TCTACCTCAAGAAACGTGAAGAAAAAGATATCTATTGGCAAGAAAAGTCCATTTATAGTCACCCA
* * * * **
2910 TGCCTTCGGATGCCTTATTACTCGTTTTAAATGGTTTTGC
131 TACCTTCGAAAGCCTTATTACTCGCTTTAAAT-GTTTTAT
* * * *
2950 AAACTCATAATTGATTTTATGTTGAA-TTTTTT-TATTTTTATTAAAACAAATTATAATTAAATA
1 AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAATA
* * * * * * * *
3013 TTTACCTCGAGAAAAGTGAAG-AAAAGACATCCATTGACAAGAAAAGTCAATTTATAATCACCCA
66 TCTACCTCAAGAAACGTGAAGAAAAAGATATCTATTGGCAAGAAAAGTCCATTTATAGTCACCCA
*
3077 TACCTTCGAAATG-CTTATTACTCGGTTTAAATGTTTTTAT
131 TACCTTCGAAA-GCCTTATTACTCGCTTTAAATG-TTTTAT
* * * *
3117 AATC-AATAATAGATTTTAAGCTT-AATTTTTTTATATCTTTTATTAAGACAGATTATAATTTAA
1 AATCTCATAATTGATTTTAAG-TTGAATTTTTTTATAT-TTTTATTAAAACAGATTATAATTGAA
* * * * * * *
3180 TATCTACTTCAGGAAACATAAAGAAAAAGATATCTATTAGTAAGAAAAGTCCATTTATAGCCA-C
64 TATCTACCTCAAGAAACGTGAAGAAAAAGATATCTATTGGCAAGAAAAGTCCATTTATAGTCACC
* * *
3244 CATTGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTATAT
129 CA-TACCTTCGAAAGCCTTATTACTCGCTTTAAAT-GTTTTAT
********* * *
3287 AATCTCATAATTGATTTTAAGTTNNNNNNNNNNTAT-TTTTTATTAAAATAGATTATAATTGAGT
1 AATCTCATAATTGATTTTAAGTT-GAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAAT
** * * * *
3351 ATCTACCTTGAGAAATGTGAAGAAAAAGATAT-TCATTGTCAAG-AAAGTTCATTTATAGTTACC
65 ATCTACCTCAAGAAACGTGAAGAAAAAGATATCT-ATTGGCAAGAAAAGTCCATTTATAGTCACC
* *
3414 CATACCTTCGAAAGCCTTTTTACTCGTTTTAAATAGTTTTAT
129 CATACCTTCGAAAGCCTTATTACTCGCTTTAAAT-GTTTTAT
* * *
3456 AATCTCATAATTTATTTTATGTTGAA-TTTTTTATATTTTTATTAAAACAGATTATATTTGAATA
1 AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAATA
* * * * * * *
3520 TCTACCTTAGGAAACATGAAGAAAAATATAT-TCATTAGCAAGAAAAGTCCATTTATA-TTATTC
66 TCTACCTCAAGAAACGTGAAGAAAAAGATATCT-ATTGGCAAGAAAAGTCCATTTATAGTCA-CC
* * *
3583 CATGCCTTCAAAAGCCTTATTAGTCGCTTTAAATGTTTTGAT
129 CATACCTTCGAAAGCCTTATTACTCGCTTTAAATGTTTT-AT
* *
3625 AATCTCATTATTGATTTTAAGTTGAATTTTTTTACATTTTT
1 AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTT
3666 GGTTGAAATA
Statistics
Matches: 847, Mismatches: 179, Indels: 58
0.78 0.17 0.05
Matches are distributed among these distances:
166 16 0.02
167 81 0.10
168 120 0.14
169 348 0.41
170 260 0.31
171 19 0.02
172 3 0.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.40
Consensus pattern (169 bp):
AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAATA
TCTACCTCAAGAAACGTGAAGAAAAAGATATCTATTGGCAAGAAAAGTCCATTTATAGTCACCCA
TACCTTCGAAAGCCTTATTACTCGCTTTAAATGTTTTAT
Found at i:4795 original size:171 final size:168
Alignment explanation
Indices: 4325--4799 Score: 492
Period size: 170 Copynumber: 2.8 Consensus size: 168
4315 NNNNNNNNNN
* * * * * * * * * *
4325 AGTTGAATTTTTTTACATTTTTTGTTGAAACAGATAATAATTGAATGTCTGCCTCAAAAACATAA
1 AGTTGAATTTGTTTAAATTTTTTATTAAAATAAATTATAATTGAATGTTTACCT-TAAAACATAA
* * * * **
4390 AGAAAAAGTTATTCATTGGCAAGAAAAGTTCATTTATAATCAGTCATGCCTTCG-AAGCCCTTAT
65 AG-AAAAGATATCCATTGGAAAGAAAAGTTCATTTATAGTCACCCATGCCTTCGAAAG-CCTTAT
*
4454 TACTCGCTATGAATAGTTTTACAATCCAATAATTAATTTTA
128 TACTCGCTATGAATAGTTTTAAAATCCAATAATTAATTTTA
* * * *
4495 AGTTGAATTTGTTTATATTTTTTATTAAAATATATTATAATTGAATGTTTTCCTTAGGAAACATG
1 AGTTGAATTTGTTTAAATTTTTTATTAAAATAAATTATAATTGAATGTTTACCTTA--AAACATA
* * * *
4560 AAGAAAAGATATCCATTCGAAAGAAAAGTCCATTTATTGTCACCCATGCCATCGAAAGCCTTATT
64 AAGAAAAGATATCCATTGGAAAGAAAAGTTCATTTATAGTCACCCATGCCTTCGAAAGCCTTATT
* *
4625 ATTCGCTTTGAAT-GTTTTTAAAATCTC-ATAA-TAGATTTTA
129 ACTCGCTATGAATAG-TTTTAAAATC-CAATAATTA-ATTTTA
** *
4665 AGTTGAATTT-TTTAAAATTTTTTATTCCAATAAATTATAATTTAATGTTTACCTCTCAAAACAT
1 AGTTGAATTTGTTT-AAATTTTTTATTAAAATAAATTATAATTGAATGTTTACCT-T-AAAACAT
* * * * *
4729 AAAGCAAAAGATATCCATTGGTAAGAAAAATTCACTTATAGTCACCCATACCTTTGAAAGCCTTA
63 AAAG-AAAAGATATCCATTGGAAAGAAAAGTTCATTTATAGTCACCCATGCCTTCGAAAGCCTTA
4794 TTACTC
127 TTACTC
4800 NNNNNNNNNN
Statistics
Matches: 254, Mismatches: 41, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
169 7 0.03
170 176 0.69
171 70 0.28
172 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (168 bp):
AGTTGAATTTGTTTAAATTTTTTATTAAAATAAATTATAATTGAATGTTTACCTTAAAACATAAA
GAAAAGATATCCATTGGAAAGAAAAGTTCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTAC
TCGCTATGAATAGTTTTAAAATCCAATAATTAATTTTA
Done.