Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398984.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2265.0, 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: 1814
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.38
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:335 original size:172 final size:174
Alignment explanation
Indices: 78--429 Score: 381
Period size: 172 Copynumber: 2.0 Consensus size: 174
68 AAATAGAATG
* * * * *
78 GAATGTCTACCATGAGAAACGTTACGAAAAAGCATTCATTGGTAAGAAAAATCCATAAATAGTCC
1 GAATGTCTACCATGAGAAACATAAAGAAAAAGCATTCATTAGCAAGAAAAATCCATAAATAGTCC
*
143 CACATTCCTTCAAAAGCCTTATTACTCACTTTAAATCATTTTATA-A-TCCAAAAATTGACTTTA
66 CACATTCCTTCAAAAGCCTTATCACTCACTTTAAATCATTTTATACACT-C-AAAATTGACTTTA
*
206 AGCTT-A-A-TTTTTTTTACATTTTTGGTTATAACAGATTATAATT
129 AGCTTAATATTTTTTTTTACATTTTTGGTTAAAACAGATTATAATT
* * * * * **
249 GAATGTCTACCCTGAGAAATATAAAGAAAAATGCATTCATTAGCAAGAGAAGTCTATTTATAGTC
1 GAATGTCTACCATGAGAAACATAAAGAAAAA-GCATTCATTAGCAAGAAAAATCCATAAATAGTC
* * * ** ** ** *
314 TCTCATTCCTTCATAAGCCTTATCACTTGCTTTAAATTGTTTTATACACTCTTAATTGATTTTAA
65 CCACATTCCTTCAAAAGCCTTATCACTCACTTTAAATCATTTTATACACTCAAAATTGACTTTAA
* * *
379 GTTTAATTTATTTTTTTTTATATTTTTGGTTAAAATAGATTATAATT
130 GCTTAA--TATTTTTTTTTACATTTTTGGTTAAAACAGATTATAATT
426 GAAT
1 GAAT
430 ATTTATCTCG
Statistics
Matches: 146, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
171 26 0.18
172 78 0.53
173 3 0.02
174 1 0.01
176 1 0.01
177 37 0.25
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (174 bp):
GAATGTCTACCATGAGAAACATAAAGAAAAAGCATTCATTAGCAAGAAAAATCCATAAATAGTCC
CACATTCCTTCAAAAGCCTTATCACTCACTTTAAATCATTTTATACACTCAAAATTGACTTTAAG
CTTAATATTTTTTTTTACATTTTTGGTTAAAACAGATTATAATT
Found at i:1101 original size:172 final size:170
Alignment explanation
Indices: 698--1426 Score: 569
Period size: 172 Copynumber: 4.3 Consensus size: 170
688 TAGCCTTAAA
* * * * *
698 TGGTTAAAATAGACTACAATTGAATGCCTA-CTTCGAGGAATGTGAAGAAAAAAGCATTCGTTGA
1 TGGTTAAAATAGACTATAATTGAATGCCTACCTT-GAGAAACGTGAAAAAAAAAGCATTCATTGA
* * * * * **********
762 CAAGAAAAGTCCATTTATAGTTTTTCATTTTTTCAAAAGCCTTATTACTCGCATTNNNNNNNNNN
65 CAAGAAAAGTCCATTTATAGTCTCTCATTCTTTCAAAAGCCTTATTACTCACTTTAAATGATTTT
* *
827 ATAATCTCATAATTGATTTTAAGTT-TATTTTTTTAACATTAT
130 ATAATCTCAAAATTGATTTTAAGTTCAATTTTTTT-ACATT-T
* * * * * * * * *
869 TGGTTAAAATAGATTATAATTAAATGTCTATCTCGAGAAACGTGAAACAAAAGGCATTTATTGAT
1 TGGTTAAAATAGACTATAATTGAATGCCTACCTTGAGAAACGTGAAAAAAAAAGCATTCATTGAC
* *
934 AAGAAAAGTCTATTTATAGTCTCTCATTCTTTCAAAAGCCTTGTTACTCACTTTAAATGATTTTA
66 AAGAAAAGTCCATTTATAGTCTCTCATTCTTTCAAAAGCCTTATTACTCACTTTAAATGATTTTA
* * * *
999 TTATCTCAAAATTGATTTCATGTTCAATTCCTTTTACAGTTT
131 TAATCTCAAAATTGATTTTAAGTTCAATT-TTTTTACA-TTT
* *
1041 TGGTTAAAATAGACTATAATTGAATGCCTACCTTGAGAAACGTGAAAAAAAAATCATTTATTAGA
1 TGGTTAAAATAGACTATAATTGAATGCCTACCTTGAGAAACGTGAAAAAAAAAGCATTCATT-GA
* * * * * * * * *
1106 -AAAAAAAGTCTATTTATAGTTTTTCATTCCTACAAAAGTCTTATTACTCGCTTTAAATGGTTTT
65 CAAGAAAAGTCCATTTATAGTCTCTCATTCTTTCAAAAGCCTTATTACTCACTTTAAATGATTTT
**
1170 ATAAT-AAAATAATTGATTTTAAGTTCAATTATTTTTACATTTT
130 ATAATCTCAA-AATTGATTTTAAGTTCAATT-TTTTTACA-TTT
* * * * * ** * *
1213 TGATTAAAACATA-TAATAATTGAATGTCTGCC--GCATGAAATATGAAGAAAAAGGCATTCATT
1 TGGTTAAAATAGACT-ATAATTGAATGCCTACCTTG-A-GAAACGTGAAAAAAAAAGCATTCATT
* * * * * *
1275 GGCAAGAAAAGTCCATTTATATTCACCCATTCTTTCAAAAGCTTTATTACTCATTTTAAAT-ATT
63 GACAAGAAAAGTCCATTTATAGTCTCTCATTCTTTCAAAAGCCTTATTACTCACTTTAAATGA-T
* * * *
1339 TTTAAAATCTCATAATTGATTTTAAGGTGAA-TTTTTTACATTTT
127 TTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTACA-TTT
** * * * * *
1383 TCATTAAAACAAATTATAATTGAAT-TCTCACCTTGGGAAACGTG
1 TGGTTAAAATAGACTATAATTGAATGCCT-ACCTTGAGAAACGTG
1427 TAGAAAAATT
Statistics
Matches: 443, Mismatches: 99, Indels: 33
0.77 0.17 0.06
Matches are distributed among these distances:
169 3 0.01
170 42 0.09
171 124 0.28
172 265 0.60
173 9 0.02
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (170 bp):
TGGTTAAAATAGACTATAATTGAATGCCTACCTTGAGAAACGTGAAAAAAAAAGCATTCATTGAC
AAGAAAAGTCCATTTATAGTCTCTCATTCTTTCAAAAGCCTTATTACTCACTTTAAATGATTTTA
TAATCTCAAAATTGATTTTAAGTTCAATTTTTTTACATTT
Found at i:1109 original size:20 final size:21
Alignment explanation
Indices: 1084--1122 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1074 TGAGAAACGT
1084 GAAAAAAAAATC-ATTTATTA
1 GAAAAAAAAATCTATTTATTA
*
1104 GAAAAAAAAGTCTATTTAT
1 GAAAAAAAAATCTATTTAT
1123 AGTTTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (21 bp):
GAAAAAAAAATCTATTTATTA
Done.