Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399315.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2583.0, 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: 1774
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.32
Warning! 184 characters in sequence are not A, C, G, or T
Found at i:310 original size:171 final size:168
Alignment explanation
Indices: 21--1247 Score: 1120
Period size: 171 Copynumber: 7.2 Consensus size: 168
11 TGAAGAAATG
* * * * *
21 GGTGACTATAAATGGACTTTTCTTGCCATTGAATGGTTTTTTCTTCACGTTTTTCAA-GTAAACA
1 GGTGACTATAAATGGACTTTTCTTGCCAATGAAT-GCTTTTTCTTCATGTTTCTCAAGGTAGACA
* * ** * * * *
85 TACAATTATAATCTGTTTTAACTTAAAATGTAAAAATATTTAATTTAAAATCAATTTTGAGGTTA
65 TTCAATTATAATCTATTTTAACAAAAAATGTAAAAA-ATTCAACTTAAAATCAATTATGAGATTA
* *
150 CAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGTCCTT
129 TAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAG-GCTT
*
191 GGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTACTTCATGTTTC-CTAAGGTAGAC
1 GGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTCTTCATGTTTCTC-AAGGTAGAC
* * ** *
255 ATTCAATTATAACCTATTTTAACCAAAAATGTAAAATAATTCAACTTAAAATCAATTACAAAATT
64 ATTCAATTATAATCTATTTTAACAAAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATT
* * * *
320 ATAAAACCATTTAAAGCTAGTGATAAGGCTTTCGAAGGCTT
128 ATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGCTT
* ** ** * * * *
361 GACTGACTATAAATGGACTTTTGATATCAAT-AGATGCCTTTTGCTTCATGATTCTTAAGGAAGA
1 G-GTGACTATAAATGGACTTTTCTTGCCAATGA-ATG-CTTTTTCTTCATGTTTCTCAAGGTAGA
* * * * **
425 CATTCAATTATAGTATATTGTAATTAAAAAA-GTAAAAAAAGTTTGACTTAAAATCAATTATGAG
63 CATTCAATTATAATCTATTTTAA-CAAAAAATGT-AAAAAA-TTCAACTTAAAATCAATTATGAG
* * *
489 ATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGACTT
125 ATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGCTT
* * * * *
533 GAGTGGCTATAAGTGGACATTTT-ATGTCAATTG-ATGACTTTTGT-TTCATGTTTCCCAAGGTA
1 G-GTGACTATAAATGGAC-TTTTCTTGCCAA-TGAATG-CTTTT-TCTTCATGTTTCTCAAGGTA
* * * * *
595 AACATTCAATTACAATATA-TTTAATC-AGAAATGTAAAAAAATTCAACTCAAAATCAATTATGA
61 GACATTCAATTATAATCTATTTTAA-CAAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGA
* * * *
658 GTTTATAAAACCAATTTAAAGCGTGTAAT-ATGACTTTCGAAGGCTT
124 GATTATAAAACC-ATTTAAAGCGAGTAATAAAG-CTTTTGAAGGCTT
* * * *
704 ACGTGACTATAAATGGACTTTTCTTGTCAATGAATAGCTTTTTCTTAATGTTTCTCAAGGCAGAC
1 -GGTGACTATAAATGGACTTTTCTTGCCAATGAAT-GCTTTTTCTTCATGTTTCTCAAGGTAGAC
* * *
769 ATTCAATTACAATCTATTTTAACAAAAAATGTAAAAAA--AAACCTAAAATCAATTATGAGATTA
64 ATTCAATTATAATCTATTTTAACAAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTA
* *
832 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTT
129 TAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGCTT
* * * * * * * * *
872 GGGTGACTATAAGTGGGCTCTTT-TTACAAATGAACGAATTTTTCTTCATGTTTCTCGAGATAAA
1 -GGTGACTATAAATGGACT-TTTCTTGCCAATGAATG-CTTTTTCTTCATGTTTCTCAAGGTAGA
* * * *
936 CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACCTAAAAGCAATTTTGAGAT
63 CATTCAATTATAATCTATTTTAACAAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGAT
* * *
1001 TGTAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATA
127 TATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGG-CTT
* * * * ** *
1044 GGTAATTATAATAT--ACTTTTCTTACCAATGAATGATTTATTCTTCATGTTTCTGGAGGCAGAC
1 GGTGACTATAA-ATGGACTTTTCTTGCCAATGAATGCTTT-TTCTTCATGTTTCTCAAGGTAGAC
* * * * * * *
1107 ACTT-AGTTAT-ATCCTGTTTTAATAAAAAATATAAGAAAATTTAACCTATAATCAATTATGAGA
64 A-TTCAATTATAAT-CTATTTTAACAAAAAATGTAA-AAAATTCAACTTAAAATCAATTATGAGA
* * * *
1170 TTACAAAACCATTTAAAGCGAGTAATAAAGCCTTCGAAGGCATG
126 TTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGC-TT
*
1214 GGTGACTATAAATGGACTTTTCTTGTCAATGAAT
1 GGTGACTATAAATGGACTTTTCTTGCCAATGAAT
1248 NNNNNNNNNN
Statistics
Matches: 874, Mismatches: 143, Indels: 79
0.80 0.13 0.07
Matches are distributed among these distances:
167 1 0.00
168 101 0.12
169 54 0.06
170 222 0.25
171 350 0.40
172 141 0.16
173 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (168 bp):
GGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTCATGTTTCTCAAGGTAGACAT
TCAATTATAATCTATTTTAACAAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATA
AAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGCTT
Found at i:677 original size:343 final size:332
Alignment explanation
Indices: 129--1247 Score: 995
Period size: 343 Copynumber: 3.3 Consensus size: 332
119 AATATTTAAT
* * * * *
129 TTAAAATCAATTTTGAGGTTACAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGTCCTTGGT
1 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG-ACTTGGT
* * * * * *
194 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTACTTCATGTTTCCTAAGGTAGACATTC
65 GACTATAAGTGGAC-TTT-TTGTCAATGAATGACTTTT-TTTCATGTTTCCCAAGGTAAACATTC
* * ** *
259 AATTATAACCTATTTTAACCAAAAATGTAAAATAATTCAACTTAAAATCAATTACAAAATTATAA
127 AATTATAA--TATTTTAA-CAAAAATGTAAAAAAATTCAACTCAAAATCAATTATGAGATTATAA
* *
324 AACCATTTAAAGCTAGTGATAAGGCTTTCGAAGGCTTGAC-TGACTATAAATGGACTTTTGATAT
189 AACCATTTAAAGCTAGTAATAAGGCTTTCGAAGGCTT-ACGTGACTATAAATGGACTTTTCATAT
* * * * *
388 CAAT-AGAT-GCCTTTTGCTTCATGATTCTTAAGGAAGACATTCAATTATAGTATATTGTAATTA
253 CAATGA-ATAG-CTTTTGCTTAATGATTCTCAAGGAAGACATTCAATTACAATATATTGTAA-CA
*
451 AAAAA-GTAAAAAAAGTTTGAC
315 AAAAATGTAAAAAAA----AAC
*
472 TTAAAATCAATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGACTTGAGT
1 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGACTTG-GT
*
537 GGCTATAAGTGGACATTTTATGTCAATTG-ATGACTTTTGTTTCATGTTTCCCAAGGTAAACATT
65 GACTATAAGTGGAC-TTTT-TGTCAA-TGAATGACTTTT-TTTCATGTTTCCCAAGGTAAACATT
* * *
601 CAATTACAATATATTTAATCAGAAATGTAAAAAAATTCAACTCAAAATCAATTATGAGTTTATAA
126 CAATTATAATAT-TTTAA-CAAAAATGTAAAAAAATTCAACTCAAAATCAATTATGAGATTATAA
* * * *
666 AACCAATTTAAAGCGT-GTAATATGACTTTCGAAGGCTTACGTGACTATAAATGGACTTTTCTTG
189 AACC-ATTTAAAGC-TAGTAATAAGGCTTTCGAAGGCTTACGTGACTATAAATGGACTTTTCATA
* * * * *
730 TCAATGAATAGCTTTTTCTTAATGTTTCTCAAGGCAGACATTCAATTACAATCTATTTTAACAAA
252 TCAATGAATAGCTTTTGCTTAATGATTCTCAAGGAAGACATTCAATTACAATATATTGTAACAAA
795 AAATGTAAAAAAAAAC
317 AAATGTAAAAAAAAAC
* * *
811 CTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTGGGT
1 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGACTT-GGT
* * * * * *
876 GACTATAAGTGGGCTCTTTT-TACAAATGAACGAATTTTTCTTCATGTTTCTCGAGATAAACATT
65 GACTATAAGTGGACT-TTTTGT-C-AATGAATGACTTTTT-TTCATGTTTCCCAAGGTAAACATT
* * * *
940 CAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAAC-CTAAAAGCAATTTTGAGATTGT
126 CAATTATAA--TATTTTAAC-AAAAATGTAAAAAAATTCAACTC-AAAATCAATTATGAGATTAT
* * * ** * * * *
1004 AAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATAGGTAATTATAATAT--ACTTTTCTT
187 AAAACCATTTAAAGCTAGTAATAAGGCTTTCGAAGGCTTACGTGACTATAA-ATGGACTTTTCAT
* * * * * ** * * * * * *
1067 ACCAATGAAT-GATTTATTCTTCATGTTTCTGGAGGCAGACACTT-AGTTA-TATCCTGTTTTAA
251 ATCAATGAATAGCTTT-TGCTTAATGATTCTCAAGGAAGACA-TTCAATTACAAT-ATATTGTAA
* * *
1129 TAAAAAATATAAGAAAATTTAAC
313 CAAAAAATGTAA-AAAA--AAAC
* * * * * * * *
1152 CTATAATCAATTATGAGATTACAAAACCATTTAAAGCGAGTAATAAAGCCTTCGAAGGCATGGGT
1 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAC-TTGGT
*
1217 GACTATAAATGGACTTTTCTTGTCAATGAAT
65 GACTATAAGTGGAC-TTT-TTGTCAATGAAT
1248 NNNNNNNNNN
Statistics
Matches: 653, Mismatches: 91, Indels: 66
0.81 0.11 0.08
Matches are distributed among these distances:
337 7 0.01
338 67 0.10
339 156 0.24
340 50 0.08
341 84 0.13
342 66 0.10
343 218 0.33
344 5 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (332 bp):
TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGACTTGGTG
ACTATAAGTGGACTTTTTGTCAATGAATGACTTTTTTTCATGTTTCCCAAGGTAAACATTCAATT
ATAATATTTTAACAAAAATGTAAAAAAATTCAACTCAAAATCAATTATGAGATTATAAAACCATT
TAAAGCTAGTAATAAGGCTTTCGAAGGCTTACGTGACTATAAATGGACTTTTCATATCAATGAAT
AGCTTTTGCTTAATGATTCTCAAGGAAGACATTCAATTACAATATATTGTAACAAAAAATGTAAA
AAAAAAC
Done.