Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397512.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4817.0, 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: 11005
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.34
Warning! 817 characters in sequence are not A, C, G, or T
Found at i:736 original size:343 final size:342
Alignment explanation
Indices: 1--1312 Score: 1312
Period size: 343 Copynumber: 3.8 Consensus size: 342
* * *
1 ATTATGAGATTATAAAACCATTTAAAGTGTGTAATAAGGCTTTTGAACGAATGGATGACTATAAA
1 ATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAA
* *
66 TAGACTTTTCTTG-CAAATGAATG--TGTTTTACTTCATGTTT-TTCAAGGTAGACATTCAATTA
66 TAGACTTTTCTTGTCAAATGAATGCTTG-TTT-CTTCACGTTTCTT-AAGGTAAACATTCAATTA
* * * * * * * ** *
127 TAATATGTTTTTACCAATAATGCAATAAAAATT-TACTTAAAATCAAGCATTAGATTATAAAACA
128 TAGTCTGTTTTAACCAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACA
* * * * * * *
191 ATTTAAAGTAAGGAATAAGCCTTTAAAACGAATGGGTGACTATAGATGGACTTTTCCT-CTAAAT
193 ATTTAAAGCAAGTAATAAGGCTTTTAAA-GAATGGGTGACTATAAATGGACTTTTCTTGC-CAAT
* * ** * * *
255 GATTGGATTTTTTGCACGTTTTTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAATATGT
256 AAATGCTTTTTTTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGT
* * *
320 AAAAATATTCAATTTAAAATTA
321 AAAAACATTCAACTTAAAATCA
* * * * * * *
342 AATATGAGATTATAAAACAACTTAAAGTGAGTAAAAAAGTTTTTGCAGGAATAGG-TGATTATAA
1 ATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGATGACTATAA
* *
406 ATAGACTTTTCTTGTC-AATGAATGCTTGTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATA
65 ATAGACTTTTCTTGTCAAATGAATGCTTGTTTCTTCACGTTTCTTAAGGTAAACATTCAATTATA
* * *
470 GTCTGTTTTAGCAAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAAT
130 GTCTGTTTTAACCAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAAT
* * * *
535 TTAAAGCAAGTAATAAGGCTTTTAAAGAAATAGGAGACTATAAATAGACTTTTCTTGCTAATAAA
195 TTAAAGCAAGTAATAAGGCTTTTAAAG-AATGGGTGACTATAAATGGACTTTTCTTGCCAATAAA
* * * *
600 TGCTTTTTTCTTTACGTTTCTCAAGGTACACATTCAATTATAGTCTATTTTAACCAAAAATCTAA
259 TGCTTTTTT-TTCACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGTAA
665 AAACATTCAACTTAAAATCA
323 AAACATTCAACTTAAAATCA
* * *
685 ATTATGAGATTATAAAATC-ATTTAAAGCGAGTAATAATGCTTTT-ACAGGAATGGACGACTATA
1 ATTATGAGATTATAAAA-CAATTTAAAGTGAGTAATAAGGCTTTTGA-AGGAATGGATGACTATA
* * * * * ** * *
748 AATGGAC-TTT-TTGTGCTAGTGAATATCTT-TTTCTTTACGTTTCTGGAGGTAAACCTTCCATT
64 AATAGACTTTTCTTGT-CAAATGAAT-GCTTGTTTCTTCACGTTTCTTAAGGTAAACATTCAATT
* * *
810 ATAGTCTATTTTAACCAAAAATG-AAAAAAAATTCAACTTCAAGTCAATTATGAGATTATAAAAC
127 ATAGTCTGTTTTAACCAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * ** * *
874 CATTTAAAGCAAGTAATATGGCTTTCGAAGGATGGGTGACTATAAATGAACTTTTCTTGCCAATG
192 AATTTAAAGCAAGTAATAAGGCTTTTAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT-
* * * * * * * * * *
939 AGTAT-CTTTTTATTCATGTTACTCAAGCTAGACAATCAATTATAATATTTTTTACCCAATAATG
256 A-AATGCTTTTTTTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATG
* *
1003 TAAAAAACAATTGAACCTAAAATCA
320 T-AAAAAC-ATTCAACTTAAAATCA
* * *
1028 ATTTTGAGATTATAAAGCTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGA-GACTATAA
1 ATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGATGACTATAA
* * * * *
1092 ATGGACTTTTCTTG-CCAATGAATGCTTTTTTCTTTATGTTTCTTAAGGTAAACATTCAATTATA
65 ATAGACTTTTCTTGTCAAATGAATGCTTGTTTCTTCACGTTTCTTAAGGTAAACATTCAATTATA
* * * * ** * *
1156 GTCTGTATTAACTAAAAATCT-GAAAGCATTCAACTTAAAATCAATTATGATATTATAAAATC-G
130 GTCTGTTTTAACCAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CAA
* * ** * * * * *
1219 TTTAAAACGAGTAATAAAACTTTTGAAGGAATGAGTGACTTTAAATGGACTTTTTTTGCCAATGA
194 TTTAAAGCAAGTAATAAGGCTTTT-AAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAA
*
1284 ATGTCTTTTTTTTCATGTTTCTCAAGGTA
258 ATG-CTTTTTTTTCACGTTTCTCAAGGTA
1313 ATACTCTTTA
Statistics
Matches: 802, Mismatches: 139, Indels: 57
0.80 0.14 0.06
Matches are distributed among these distances:
341 198 0.25
342 181 0.23
343 355 0.44
344 65 0.08
345 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (342 bp):
ATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAA
TAGACTTTTCTTGTCAAATGAATGCTTGTTTCTTCACGTTTCTTAAGGTAAACATTCAATTATAG
TCTGTTTTAACCAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATT
TAAAGCAAGTAATAAGGCTTTTAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATG
CTTTTTTTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAA
CATTCAACTTAAAATCA
Found at i:1106 original size:514 final size:510
Alignment explanation
Indices: 1--1313 Score: 1424
Period size: 514 Copynumber: 2.6 Consensus size: 510
* * *
1 ATTATGAGATTATAAAACCATTTAAAGTGTGTAATAAGGCTTTTGAACGAAT-GGATGACTATAA
1 ATTATGAGATTAT-AAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGA-GACTATAA
* * * *
65 ATAGACTTTTCTTGCAAATGAATG-TGTTTTACTTCATGTTTTTCAAGGTAGACATTCAATTATA
64 ATAGACTTTTCTTGCAAATGAATGCT-TTTTTCTTTATGTTTCTCAAGGTAAACATTCAATTATA
* * * * * * ** *
129 ATATGTTTTTACCAATAATGC-AATAAAAATT-TACTTAAAATCAAGCATTAGATTATAAAA-CA
128 GTCTGTTTTAACCAAAAAT-CTAA-AAACATTCAACTTAAAATCAATTATGAGATTATAAAATC-
** * * * * * *
191 ATTTAAAGTAAGGAATAAGCCTTTAAAACGAATGGGTGACTATAGATGGACTTTTCCT-CTAAAT
190 ATTTAAAGCGAGTAATAAG-CTTT-TAAGGAATGGATGACTATAAATGGACTTTTTCTGCT-AAT
* ** * * * *
255 GATTGGATTTTTTGCACGTTTTTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAATATGT
252 GAATGTCTTTTTTGCACGTTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACCAAAAATGA
* * * ** *
320 AAAAATATTCAATTTAAAATTAAATATGAGATTATAAAACAACTTAAAGTGAGTAAAAAAGTTTT
317 AAAAAAATTCAACTTAAAATCAAATATGAGATTATAAAACAACTTAAAGCAAGTAAAAAAGCTTT
* * * * * * *
385 TGCAGGAATAGGTGATTATAAATAGACTTTTCTTGTCAATGAATGCTTGTTTCTTCACGTTTCTT
382 CGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTGTTTATTCACGTTACTC
* * * * * * *
450 GAGGTAGACATTCAATTATAGTCTGTTTTAGCAAAAAATGTAAAAAAAATTCAACTTAAAATCA
447 AAGCTAGACAATCAATTATAATATGTTTTACCAAAAAATGTAAAAAAAATTCAACCTAAAATCA
* ** * *
514 ATTATGAGATTATAAAATAATTTAAAGCAAGTAATAAGGCTTTTAAAGAAATAGGAGACTATAAA
1 ATTATGAGATTATAAACT-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAA
* * * *
579 TAGACTTTTCTTGCTAATAAATGCTTTTTTCTTTACGTTTCTCAAGGTACACATTCAATTATAGT
65 TAGACTTTTCTTGCAAATGAATGCTTTTTTCTTTATGTTTCTCAAGGTAAACATTCAATTATAGT
*
644 CTATTTTAACCAAAAATCTAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTA
130 CTGTTTTAACCAAAAATCTAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTA
* * * *
709 AAGCGAGTAATAATGCTTTTACAGGAATGGACGACTATAAATGGACTTTTTGTGCTAGTGAATAT
195 AAGCGAGTAATAA-GCTTTTA-AGGAATGGATGACTATAAATGGACTTTTTCTGCTAATGAATGT
** ** * * *
774 CTTTTTCTTTACGTTTCTGGAGGTAAACCTTCCATTATAGTCTATTTTAACCAAAAATGAAAAAA
258 CTTTTT-TGCACGTTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACCAAAAATGAAAAAA
* * * * * * **
839 AATTCAACTTCAAGTCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATATGGCTTTCGAAG
322 AATTCAACTTAAAATCAAATATGAGATTATAAAACAACTTAAAGCAAGTAAAAAAGCTTTCGAAG
* *
904 G-ATGGGTGACTATAAAT-GAACTTTTCTTGCCAATGAGTAT-CTT-TTTATTCATGTTACTCAA
387 GAATAGGTGACTATAAATAG-ACTTTTCTTGCCAATGA--ATGCTTGTTTATTCACGTTACTCAA
* * * *
965 GCTAGACAATCAATTATAATATTTTTTACCCAATAATGTAAAAAACAATTGAACCTAAAATCA
449 GCTAGACAATCAATTATAATATGTTTTACCAAAAAATGTAAAAAA-AATTCAACCTAAAATCA
*
1028 ATTTTGAGATTATAAAGCTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAA
1 ATTATGAGATTATAAA-CTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAA
* * *
1093 TGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTATGTTTCTTAAGGTAAACATTCAATTATAGT
65 TAGACTTTTCTTGCAAATGAATGCTTTTTTCTTTATGTTTCTCAAGGTAAACATTCAATTATAGT
* * * * * *
1158 CTGTATTAACTAAAAATCTGAAAGCATTCAACTTAAAATCAATTATGATATTATAAAATCGTTTA
130 CTGTTTTAACCAAAAATCTAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTA
* * * * *
1223 AAACGAGTAATAAAACTTTTGAAGGAAT-GAGTGACTTTAAATGGACTTTTTTTGCCAATGAATG
195 AAGCGAGTAAT-AAGCTTTT-AAGGAATGGA-TGACTATAAATGGACTTTTTCTGCTAATGAATG
* *
1287 TCTTTTTTTTCATGTTTCTCAAGGTAA
257 TC-TTTTTTGCACGTTTCTCAAGGTAA
1314 TACTCTTTAT
Statistics
Matches: 665, Mismatches: 116, Indels: 37
0.81 0.14 0.05
Matches are distributed among these distances:
512 12 0.02
513 280 0.42
514 362 0.54
515 11 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (510 bp):
ATTATGAGATTATAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAAT
AGACTTTTCTTGCAAATGAATGCTTTTTTCTTTATGTTTCTCAAGGTAAACATTCAATTATAGTC
TGTTTTAACCAAAAATCTAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAA
AGCGAGTAATAAGCTTTTAAGGAATGGATGACTATAAATGGACTTTTTCTGCTAATGAATGTCTT
TTTTGCACGTTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACCAAAAATGAAAAAAAATT
CAACTTAAAATCAAATATGAGATTATAAAACAACTTAAAGCAAGTAAAAAAGCTTTCGAAGGAAT
AGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTGTTTATTCACGTTACTCAAGCTAGAC
AATCAATTATAATATGTTTTACCAAAAAATGTAAAAAAAATTCAACCTAAAATCA
Found at i:1313 original size:171 final size:170
Alignment explanation
Indices: 1--1313 Score: 1196
Period size: 171 Copynumber: 7.7 Consensus size: 170
* * * *
1 ATTATGAGATTATAAAACCATTTAAAGTGTGTAATAAGGCTTTTGAACGAAT-GGATGACTATAA
1 ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGG-TGACTATAA
* * * * * *
65 ATAGACTTTTCTTGCAAATGAATG-TGTTTTACTTCATGTTTTTCAAGGTAGACATTCAATTATA
65 ATGGACTTTTCTTGCCAATGAATGCT-TTTT-TTTCACGTTTCTCAAGGTAAACATTCAATTATA
* * * * * * * *
129 ATATGTTTTTACCAATAATGCAATAAAAATT-TACTTAAAATCA
128 GTCTATTTTAACCAAAAATGTAA-AAACATTCAACTTAAAATCA
** * ** * * ** * * *
172 AGCATTAGATTATAAAA-CAATTTAAAGTAAGGAATAAGCCTTTAAAACGAATGGGTGACTATAG
1 ATTATGAGATTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * * ** * * * *
236 ATGGACTTTTCCT-CTAAATGATTGGATTTTTTGCACGTTTTTCAAGGTAGACATTCAATTATAA
65 ATGGACTTTTCTTGC-CAATGAATGCTTTTTTTTCACGTTTCTCAAGGTAAACATTCAATTATAG
* * * *
300 TCTATTTTAACCAAATATGTAAAAATATTCAATTTAAAATTA
129 TCTATTTTAACCAAAAATGTAAAAACATTCAACTTAAAATCA
* * * * * * * *
342 AATATGAGATTATAAAA-CAACTTAAAGTGAGTAAAAAAGTTTTTGCAGGAATAGGTGATTATAA
1 ATTATGAGATTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * * ** *
406 ATAGACTTTTCTTGTCAATGAATGCTTGTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAG
65 ATGGACTTTTCTTGCCAATGAATGCTT-TTTTTTCACGTTTCTCAAGGTAAACATTCAATTATAG
* * * *
471 TCTGTTTTAGCAAAAAATGTAAAAAAAATTCAACTTAAAATCA
129 TCTATTTTAACCAAAAATGT-AAAAACATTCAACTTAAAATCA
* * * * *
514 ATTATGAGATTATAAAATAATTTAAAGCAAGTAATAAGGCTTTTAAAGAAATAGGAGACTATAAA
1 ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAA
* * * * *
579 TAGACTTTTCTTGCTAATAAATGCTTTTTTCTTTACGTTTCTCAAGGTACACATTCAATTATAGT
66 TGGACTTTTCTTGCCAATGAATGCTTTTTT-TTCACGTTTCTCAAGGTAAACATTCAATTATAGT
*
644 CTATTTTAACCAAAAATCTAAAAACATTCAACTTAAAATCA
130 CTATTTTAACCAAAAATGTAAAAACATTCAACTTAAAATCA
* *
685 ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAATGCTTTT-ACAGGAAT-GGACGACTATA
1 ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATAGG-TGACTATA
* * * ** * *
748 AATGGACTTTT-TGTGCTAGTGAATATCTTTTTCTTT-ACGTTTCTGGAGGTAAACCTTCCATTA
64 AATGGACTTTTCT-TGCCAATGAAT-GCTTTTT-TTTCACGTTTCTCAAGGTAAACATTCAATTA
* * * *
811 TAGTCTATTTTAACCAAAAATGAAAAAAAATTCAACTTCAAGTCA
126 TAGTCTATTTTAACCAAAAATGTAAAAACATTCAACTTAAAATCA
* * * * *
856 ATTATGAGATTATAAAACCATTTAAAGCAAGTAATATGGCTTTCGAAGG-ATGGGTGACTATAAA
1 ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAA
* * * * * * * *
920 TGAACTTTTCTTGCCAATGAGTAT-CTTTTTATTCATGTTACTCAAGCTAGACAATCAATTATAA
66 TGGACTTTTCTTGCCAATGA--ATGCTTTTTTTTCACGTTTCTCAAGGTAAACATTCAATTATAG
* * * * * *
984 TATTTTTTACCCAATAATGTAAAAAACAATTGAACCTAAAATCA
129 TCTATTTTAACCAAAAATGT-AAAAAC-ATTCAACTTAAAATCA
* * * *
1028 ATTTTGAGATTAT-AAAGCTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAA
1 ATTATGAGATTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
* * *
1092 ATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTATGTTTCTTAAGGTAAACATTCAATTATAG
65 ATGGACTTTTCTTGCCAATGAATGCTTTTTT-TTCACGTTTCTCAAGGTAAACATTCAATTATAG
* * * * * *
1157 TCTGTATTAACTAAAAATCTGAAAGCATTCAACTTAAAATCA
129 TCTATTTTAACCAAAAATGTAAAAACATTCAACTTAAAATCA
* * * ** *
1199 ATTATGATATTATAAAATCGTTTAAAACGAGTAATAAAACTTTTGAAGGAAT-GAGTGACTTTAA
1 ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAG-GTGACTATAA
* *
1263 ATGGACTTTTTTTGCCAATGAATGTCTTTTTTTTCATGTTTCTCAAGGTAA
65 ATGGACTTTTCTTGCCAATGAATG-CTTTTTTTTCACGTTTCTCAAGGTAA
1314 TACTCTTTAT
Statistics
Matches: 932, Mismatches: 180, Indels: 60
0.80 0.15 0.05
Matches are distributed among these distances:
169 8 0.01
170 196 0.21
171 434 0.47
172 222 0.24
173 72 0.08
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
ATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAA
TGGACTTTTCTTGCCAATGAATGCTTTTTTTTCACGTTTCTCAAGGTAAACATTCAATTATAGTC
TATTTTAACCAAAAATGTAAAAACATTCAACTTAAAATCA
Done.