Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397936.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1240.0, 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: 2927
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.28
Warning! 763 characters in sequence are not A, C, G, or T
Found at i:996 original size:171 final size:161
Alignment explanation
Indices: 677--996 Score: 340
Period size: 171 Copynumber: 1.9 Consensus size: 161
667 NNAGTTGAAA
* * *
677 TTTTTTACATTTTTCATTAAAATAGACTATAATTGAATGTTTGCCTTGACAAACATGAAGAAAAA
1 TTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTATGCCTGGACAAACATGAAGAAAAA
* * * * *
742 ATCATTCATTGATAAGAAAAGTCCATTTATAGCCTCCCATTTATTTAATAGCCTTTTTACTCATT
66 AGCATTCATTGACAAGAAAAGTCCATTTATAGCCTCCCATTCATTCAATAGCCTTATTACTCATT
807 CTAAATGGTTTCATAATCTCATAATTANNNNNNNNNNCAAT
131 CTAAATGGTTTCATAATCTCATAATTA----------CAAT
*
848 TTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTATGCCTGGAGAAA-AGTGAAGAAAA
1 TTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTATGCCTGGACAAACA-TGAAGAAAA
* * * * *
912 AAGCATTCATT-AGCAAGAAAGGTCTATTTATAGCCTCTCATTCCTTCAA-AGACCTTATTACTT
65 AAGCATTCATTGA-CAAGAAAAGTCCATTTATAGCCTCCCATTCATTCAATAG-CCTTATTACTC
* * * *
975 GTTTTAAATTGTTTTATAATCT
128 ATTCTAAATGGTTTCATAATCT
997 AAGAATTTAT
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
170 4 0.03
171 124 0.97
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.38
Consensus pattern (161 bp):
TTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTATGCCTGGACAAACATGAAGAAAAA
AGCATTCATTGACAAGAAAAGTCCATTTATAGCCTCCCATTCATTCAATAGCCTTATTACTCATT
CTAAATGGTTTCATAATCTCATAATTACAAT
Found at i:2266 original size:171 final size:170
Alignment explanation
Indices: 1912--2891 Score: 1014
Period size: 171 Copynumber: 5.7 Consensus size: 170
1902 NNNNNNNNNN
* *
1912 ATCTCATAATTGATTTTAAGTTCAATTTTTTTTACATTTTTCATTAAAACAGATTATAATTGAAT
1 ATCTCATAATTGATTTTAAGTTGAA--TTTTTTACATTTTTCATTAAAACAGACTATAATTGAAT
* * * ** * * * *
1977 GTTTACCTT-GAGAAGTATGAAGAAAAAAGCATTCATTTG-CAAGAAAACTCTATTTACAGCCTC
64 GTCTATCTTCAAGAAACATGAAGAAAAAAGCATTCA-TTGACAAGAAAAGTCCATTTATAGCCAC
* * * * *
2040 CCATTCCTTCGAAAGCCTTATTACTCACTTAAAATGGTTTTATA
128 CTATTCCTTCAAAAGCCTTATTACT-GCTTTAAATAGTTTTATA
* * * * *
2084 ATCTAATAATTGATTTTAAATTGAATTATTTTACATTTTTGATTAAAACAGACTATAATTAAATA
1 ATCTCATAATTGATTTTAAGTTGAATT-TTTTACATTTTTCATTAAAACAGACTATAATTGAATG
* * * *
2149 TCTATCTTGAA-AAACATGAAGAAAAGAGGATTCATTGACAAGAAAAGTCCATTTATAGTCACCT
65 TCTATCTTCAAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCCATTTATAGCCACCT
* *
2213 ATTCCTTTAAAAG-CTTAATTACATGCTTTAAATAGTTTTCTA
130 ATTCCTTCAAAAGCCTT-ATTAC-TGCTTTAAATAGTTTTATA
2255 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATG
1 ATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTCATTAAAACAGACTATAATTGAATG
* * * * * * * * *
2320 T-TGAAC-ACAAGAAACGTGAAGAAAAGAGCATTCATTGGCAGGAAAAGTTCATATATAGCCTCC
65 TCT-ATCTTCAAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCCATTTATAGCCACC
* * *
2383 CAATCCTTCAAAAGGCTTATTACTAGCTTTAAATAGTTTTATA
129 TATTCCTTCAAAAGCCTTATTACT-GCTTTAAATAGTTTTATA
* * * * * * *
2426 ATCTAATAATTGATTTTAAGTTAAATTTTTTATATTTATAATTAAAATAGACAATAATTGAATGT
1 ATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGT
** * * **
2491 CTAT-TTCAAGAAATGTGAAGAAAAAAGCA-TCATTGGCAAGAAAAGTCTATTTATAGCC-TTTC
66 CTATCTTCAAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCCATTTATAGCCACCT-
* *
2553 ACTCCTTCAAAAGCCTTATTACTTACTTTAAAT-GATTTTATA
130 ATTCCTTCAAAAGCCTTATTAC-TGCTTTAAATAG-TTTTATA
* * *
2595 ATCTCATAATTGATTTTAACTTGAATTTGTTTACATTTTTTATTAAAACAGACAATAATTGAATG
1 ATCTCATAATTGATTTTAAGTTGAATTT-TTTACATTTTTCATTAAAACAGACTATAATTGAATG
* * * * *
2660 TCTATC-TCAAGAAACGTGAAGGAAAAAGTATTCATT-ATCAAGAAAAGTTCATTTATAGTCACC
65 TCTATCTTCAAGAAACATGAAGAAAAAAGCATTCATTGA-CAAGAAAAGTCCATTTATAGCCACC
* *
2723 TATTCCTTCAAAAGCCTTATTACATGCTTTGAATGGTTTTTATA
129 TATTCCTTCAAAAGCCTTATTAC-TGCTTTAAATAG-TTTTATA
* * * * *
2767 ATGTCATAATTAATTTTAAGTTGAGCTTTTTTACATTTTTCGTTAAAACAGACTATAATTAAATG
1 ATCTCATAATTGATTTTAAGTTGA-ATTTTTTACATTTTTCATTAAAACAGACTATAATTGAATG
* * * * * * * *
2832 TCTACCTT-GACAACCATGAAGAAAAAAGCATTCATTGATAAGGAATGTCTATTTATAGCC
65 TCTATCTTCAAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCCATTTATAGCC
2892 TCCCATTTCT
Statistics
Matches: 675, Mismatches: 109, Indels: 48
0.81 0.13 0.06
Matches are distributed among these distances:
168 1 0.00
169 85 0.13
170 128 0.19
171 322 0.48
172 134 0.20
173 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (170 bp):
ATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGT
CTATCTTCAAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCCATTTATAGCCACCTA
TTCCTTCAAAAGCCTTATTACTGCTTTAAATAGTTTTATA
Found at i:2655 original size:340 final size:339
Alignment explanation
Indices: 1912--2889 Score: 1119
Period size: 340 Copynumber: 2.9 Consensus size: 339
1902 NNNNNNNNNN
* *
1912 ATCTCATAATTGATTTTAAGTTCAATTTTTTTTACATTTTTCATTAAAACAGATTATAATTGAAT
1 ATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTCATTAAAACAGACTATAATTGAAT
* ** *** * * *
1977 GTTTACCTTGAGAAGTATGAAGAAAAAAGCATTCATTTGCAAGAAAA-CTCTATTTACAGCCTCC
65 G-TTAACTCAAGAAACGTGAAG-AAAAAGCATTCATTAGCAAGAAAAGTTC-ATTTATAGCCTCC
* * *
2041 CATTCCTTCGAAAGCCTTATTACTCA-CTTAAAATGGTTTTATAATCTAATAATTGATTTTAAAT
127 CATTCCTTCAAAAGCCTTATTACT-AGCTTTAAATGGTTTTATAATCTAATAATTGATTTTAAGT
* * * *
2105 TGAATTATTTTACATTTTTGATTAAAACAGACTATAATTAAATATCTATCTTGAAAAACATGAAG
191 TAAATT-TTTTACATTTTTAATTAAAACAGACTATAATTAAATGTCTATCTTCAAAAACATGAAG
* * * *
2170 AAAAGAGGATTCATTGACAAGAAAAGTCCATTTATAGTCACCTATTCCTTTAAAAGCTTAATTAC
255 AAAAAAGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCTACTCCTTCAAAAGCTTAATTAC
* *
2235 ATGCTTTAAATAGTTTTCTA
320 ATACTTTAAATAGTTTTATA
2255 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATG
1 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATG
* * * *
2320 TTGAACACAAGAAACGTGAAGAAAAGAGCATTCATTGGCAGGAAAAGTTCATATATAGCCTCCCA
66 TT-AACTCAAGAAACGTGAAGAAAA-AGCATTCATTAGCAAGAAAAGTTCATTTATAGCCTCCCA
* * *
2385 ATCCTTCAAAAGGCTTATTACTAGCTTTAAATAGTTTTATAATCTAATAATTGATTTTAAGTTAA
129 TTCCTTCAAAAGCCTTATTACTAGCTTTAAATGGTTTTATAATCTAATAATTGATTTTAAGTTAA
* * * * * **
2450 ATTTTTTATATTTATAATTAAAATAGACAATAATTGAATGTCTAT-TTCAAGAAATGTGAAGAAA
194 ATTTTTTACATTTTTAATTAAAACAGACTATAATTAAATGTCTATCTTCAA-AAACATGAAGAAA
* * *
2514 AAAGCA-TCATTGGCAAGAAAAGTCTATTTATAG-C-CTTTCACTCCTTCAAAAGCCTT-ATTAC
258 AAAGCATTCATTGACAAGAAAAGTCCATTTATAGTCAC-CT-ACTCCTTCAAAAG-CTTAATTAC
*
2575 TTACTTTAAAT-GATTTTATA
320 ATACTTTAAATAG-TTTTATA
* * * *
2595 ATCTCATAATTGATTTTAACTTGAATTTGTTTACATTTTTTATTAAAACAGACAATAATTGAATG
1 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATG
* * * * * *
2660 TCTATCTCAAGAAACGTGAAGGAAAAAGTATTCATTATCAAGAAAAGTTCATTTATAGTCACCTA
66 T-TAACTCAAGAAACGTGAA-GAAAAAGCATTCATTAGCAAGAAAAGTTCATTTATAGCCTCCCA
* * * *
2725 TTCCTTCAAAAGCCTTATTAC-ATGCTTTGAATGGTTTTTATAATGTCATAATTAATTTTAAGTT
129 TTCCTTCAAAAGCCTTATTACTA-GCTTTAAATGG-TTTTATAATCTAATAATTGATTTTAAGTT
** ** * * * *
2789 GAGCTTTTTTACATTTTTCGTTAAAACAGACTATAATTAAATGTCTACCTTGACAACCATGAAGA
192 -AAATTTTTTACATTTTTAATTAAAACAGACTATAATTAAATGTCTATCTTCAAAAACATGAAGA
* * * *
2854 AAAAAGCATTCATTGATAAGGAATGTCTATTTATAG
256 AAAAAGCATTCATTGACAAGAAAAGTCCATTTATAG
2890 CCTCCCATTT
Statistics
Matches: 538, Mismatches: 81, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
338 1 0.00
339 4 0.01
340 196 0.36
341 92 0.17
342 193 0.36
343 52 0.10
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (339 bp):
ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATG
TTAACTCAAGAAACGTGAAGAAAAAGCATTCATTAGCAAGAAAAGTTCATTTATAGCCTCCCATT
CCTTCAAAAGCCTTATTACTAGCTTTAAATGGTTTTATAATCTAATAATTGATTTTAAGTTAAAT
TTTTTACATTTTTAATTAAAACAGACTATAATTAAATGTCTATCTTCAAAAACATGAAGAAAAAA
GCATTCATTGACAAGAAAAGTCCATTTATAGTCACCTACTCCTTCAAAAGCTTAATTACATACTT
TAAATAGTTTTATA
Done.