Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398050.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1359.0, 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: 3964
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.23
Warning! 1418 characters in sequence are not A, C, G, or T
Found at i:300 original size:171 final size:170
Alignment explanation
Indices: 1--970 Score: 942
Period size: 171 Copynumber: 5.7 Consensus size: 170
* * ** *
1 CTTAAAATCAATTATTAGATTATAAAACAATTTAAAGCAAGTAATAATCCTTTTAAAGGAAT-GC
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAA-AAGGCTTTTGAAGGAATAG-
* * * * * * * * *** *
65 GTGACTATAACTGGACTTTTCCT-CTAAATAAAAAGATT-TTT-TTGTACGTTTCCCAAGATAGA
64 GAGACTATAAATGGACTTTTCTTGC-CAAT-GAATGCTTGTTTCTT-CACGTTTCTTGAGGTAGA
*
127 CATTCAATTATAGTCTATTTTAATCAAAAAT-ATAAAAACATTCAA
126 CATTCAATTATAGTCTGTTTTAATCAAAAATGATAAAAA-ATTCAA
* * * * *
172 TTTAAAATCAGTTATGAGATTATAAAACAATTTAAAGCGAGTAGAAAGGATTTTGTAGGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTA-AAAGGCTTTTGAAGGAATAGG
* * * * *
237 TGACTATAAATGGACTTTTCTTGTCAAAGAATGCTTGTCTCTTCATGTTTCTTGAGGTAGACATT
65 AGACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCACGTTTCTTGAGGTAGACATT
*
302 CAATTATAGTCTGTTTTAGA-AAAAAATG-TAAAAAAATTCAA
130 CAATTATAGTCTGTTTTA-ATCAAAAATGAT-AAAAAATTCAA
* * * **
343 CTTAAAATCAATTATGAGAGTATAAAACAATTTAAAGCAAGTAAAAAGGCTTTTAAAAAAATAGG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGT-AAAAGGCTTTTGAAGGAATAGG
* * *
408 AGACTATAAATAGACTTTTCTTGCCAATGAATGCTTGTTTCTTTACGTTTCTCT-TGGTAGACAT
65 AGACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCACGTTTCT-TGAGGTAGACAT
* * * *
472 TCAAATATAGTCTGTTTT-ACCAAAAAATGTTAAAAAATTTAA
129 TCAATTATAGTCTGTTTTAATC-AAAAATGATAAAAAATTCAA
* **
514 CTTAAAATTAATTATGAGATTATAAAATTATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAGG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGT-AAAAGGCTTTTGAAGGAATAGG
* * * * * * * *
579 TGACTATAAATGAACTTTTCTTGTCAATGAATGGTTTTTTCTGCACGTTT-TTGAAG-ACAAGCA
65 AGACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCACGTTTCTTGAGGTA-GA-CA
** ** * *
642 TTCAATTATAACCTGTTTTAATCAAAAATGGGAAAAAAGTCAG
128 TTCAATTATAGTCTGTTTTAATCAAAAATGATAAAAAATTCAA
* ** * *
685 CTTAAAATCAATTATGATATTATAAAACAATTTAAAGTAAGTAATAAGGCTTTCGAAGGAATAAG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAA-AAGGCTTTTGAAGGAATAGG
* * * * * * * *
750 AGACTATAAATGGACTTATCTTGCCAATGAATACTTATTTCTTTACGTTTCTCGATGTAAATATT
65 AGACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCACGTTTCTTGAGGTAGACATT
*
815 CAATTATAGTCTGTTTTAAACGAAAAAGTGA-AAAAAA-TCAA
130 CAATTATAGTCTGTTTTAATC-AAAAA-TGATAAAAAATTCAA
* * ** *
856 CTCAAAATTAATTATGAGATTATAAAACAATTTAGGGCGAG-AAATATGGCTTTTGAAGGAATAT
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAA-A-GGCTTTTGAAGGAATAG
* * *
920 GAGACTATAAATGAACTTTTCTTGCCAATGTATGCTTTTTTCTTCACGTTT
64 GAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCACGTTT
971 ATTTAACCAA
Statistics
Matches: 660, Mismatches: 115, Indels: 48
0.80 0.14 0.06
Matches are distributed among these distances:
169 4 0.01
170 13 0.02
171 608 0.92
172 32 0.05
173 3 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (170 bp):
CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAAAAGGCTTTTGAAGGAATAGGA
GACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCACGTTTCTTGAGGTAGACATTC
AATTATAGTCTGTTTTAATCAAAAATGATAAAAAATTCAA
Found at i:646 original size:342 final size:341
Alignment explanation
Indices: 1--970 Score: 1116
Period size: 342 Copynumber: 2.8 Consensus size: 341
* **
1 CTTAAAATCAATTATTAGATTATAAAACAATTTAAAGCAAGTAATAATCCTTTTAAAGGAAT-GC
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATAG-
* * * * * * * * * *
65 GTGACTATAACTGGACTTTTCCT-CTAAATAAAAAGATTTTT-TTGTACGTTTCCCAAGATAGAC
65 GAGACTATAAATGGACTTTTCTTGC-CAAT-GAATGCTTTTTCTT-TACGTTTCTCATGGTAGAC
* * * * * *
128 ATTCAATTATAGTCTATTTTAATCAAAAAT-ATAAAAACATTCAATTTAAAATCAGTTATGAGAT
127 ATTCAATTATAGTCTGTTTTAAACAAAAATGTTAAAAA-ATTCAACTTAAAATTAATTATGAGAT
* * * * *
192 TATAAAACAATTTAAAGCGAGTAGAAAGGATTTTGTAGGAATGGGTGACTATAAATGGACTTTTC
191 TATAAAACAATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTC
* * * * ** **
257 TTGTCAAAGAATGCTTGTCTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAGA
256 TTGTCAATGAATGCTTTTTTCTTCACGTTTCTTGAGCAAGACATTCAATTATAACCTGTTTTA-A
* *
322 -AAAAAATGTAAAAAAATTCAA
320 TAAAAAATGGAAAAAAAGTCAA
* * **
343 CTTAAAATCAATTATGAGAGTATAAAACAATTTAAAGCAAGTAAAAAGGCTTTTAAAAAAATAGG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATAGG
* *
408 AGACTATAAATAGACTTTTCTTGCCAATGAATGCTTGTTTCTTTACGTTTCTCTTGGTAGACATT
66 AGACTATAAATGGACTTTTCTTGCCAATGAATGCTT-TTTCTTTACGTTTCTCATGGTAGACATT
* * *
473 CAAATATAGTCTGTTTT-ACCAAAAAATGTTAAAAAATTTAACTTAAAATTAATTATGAGATTAT
130 CAATTATAGTCTGTTTTAAAC-AAAAATGTTAAAAAATTCAACTTAAAATTAATTATGAGATTAT
**
537 AAAATTATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTCTTG
194 AAAACAATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTCTTG
* * *
602 TCAATGAATGGTTTTTTCTGCACGTTT-TTGAAGACAAG-CATTCAATTATAACCTGTTTTAATC
259 TCAATGAATGCTTTTTTCTTCACGTTTCTTG-AG-CAAGACATTCAATTATAACCTGTTTTAATA
* *
665 AAAAATGGGAAAAAAGTCAG
322 AAAAATGGAAAAAAAGTCAA
* * ** *
685 CTTAAAATCAATTATGATATTATAAAACAATTTAAAGTAAGTAATAAGGCTTTCGAAGGAATAAG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATAGG
* * * *
750 AGACTATAAATGGACTTATCTTGCCAATGAATACTTATTTCTTTACGTTTCTCGAT-GTAAATAT
66 AGACTATAAATGGACTTTTCTTGCCAATGAATGCTT-TTTCTTTACGTTTCTC-ATGGTAGACAT
* * *
814 TCAATTATAGTCTGTTTTAAACGAAAAA-GTGAAAAAAATCAACTCAAAATTAATTATGAGATTA
129 TCAATTATAGTCTGTTTTAAAC-AAAAATGTTAAAAAATTCAACTTAAAATTAATTATGAGATTA
** * * *
878 TAAAACAATTTAGGGCGAG-AAATATGGCTTTTGAAGGAATATGAGACTATAAATGAACTTTTCT
193 TAAAACAATTTAAAGCGAGTAAA-AAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTCT
* *
942 TGCCAATGTATGCTTTTTTCTTCACGTTT
257 TGTCAATGAATGCTTTTTTCTTCACGTTT
971 ATTTAACCAA
Statistics
Matches: 533, Mismatches: 83, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
341 14 0.03
342 499 0.94
343 20 0.04
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (341 bp):
CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATAGG
AGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTTACGTTTCTCATGGTAGACATTC
AATTATAGTCTGTTTTAAACAAAAATGTTAAAAAATTCAACTTAAAATTAATTATGAGATTATAA
AACAATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTCTTGTC
AATGAATGCTTTTTTCTTCACGTTTCTTGAGCAAGACATTCAATTATAACCTGTTTTAATAAAAA
ATGGAAAAAAAGTCAA
Found at i:1303 original size:173 final size:170
Alignment explanation
Indices: 972--1388 Score: 421
Period size: 173 Copynumber: 2.4 Consensus size: 170
962 TTCACGTTTA
* * * *
972 TTTAACCAAAAATGTAAAAAAATTCAACAT-AAATTAATTATGAGATTATAAAACCATTTAAAGT
1 TTTAA-CAAAAATGTAAAAAAATTCAACATAAAATCAATTATAAGATTATAAAACTATTTAAAGC
* * * * *
1036 GAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGAATTTTCTTCACTATGAATAGCTTT
65 GAGTAATAAGACTTTGAAAGGAATGAGTGACCATAAATGGAATTATCTTCACAATGAATAGCTTT
* * *
1101 TTCTTTATGTTACTTGAGCTAGACATTCAATTATAATCTTT
130 TTCTTCATGTTACTCGAGCTAGACATTCAATTATAATCTGT
* * * * * *
1142 TTTAATCAATAATGTTAAAAAAATTAAACCCTAAAATCAATTTTTAGATTATAAAACTATTTAAT
1 TTTAA-CAAAAATG-TAAAAAAATTCAA-CATAAAATCAATTATAAGATTATAAAACTATTTAAA
* * * **
1207 GCGAGTAATAAGACTTCTGAAA-GAGT-AGGTGACCATAAATGTACTTATCTTGTCAATGAAT-G
63 GCGAGTAATAAGACTT-TGAAAGGAATGA-GTGACCATAAATGGAATTATCTTCACAATGAATAG
* *
1269 CTTGTTTCTTCATGTTTCTCGATG-TAGACATTCAATTATAGTCTGT
126 CTT-TTTCTTCATGTTACTCGA-GCTAGACATTCAATTATAATCTGT
* * * * * * **
1315 TTCAGAGAAAAATGCAAAAAAATTCAACTTAAAGTCAATTCTAAGATTATAAAACTATTTAAATA
1 TTTA-ACAAAAATGTAAAAAAATTCAACATAAAATCAATTATAAGATTATAAAACTATTTAAAGC
1380 GAGTAATAA
65 GAGTAATAA
1389 AGCTTTTTAA
Statistics
Matches: 202, Mismatches: 37, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
170 12 0.06
171 52 0.26
172 18 0.09
173 114 0.56
174 6 0.03
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (170 bp):
TTTAACAAAAATGTAAAAAAATTCAACATAAAATCAATTATAAGATTATAAAACTATTTAAAGCG
AGTAATAAGACTTTGAAAGGAATGAGTGACCATAAATGGAATTATCTTCACAATGAATAGCTTTT
TCTTCATGTTACTCGAGCTAGACATTCAATTATAATCTGT
Found at i:1403 original size:486 final size:485
Alignment explanation
Indices: 494--1403 Score: 1107
Period size: 486 Copynumber: 1.9 Consensus size: 485
484 TGTTTTACCA
* * * **
494 AAAAATGTTAAAAAATTTAACTTAAAATTAATTATGAGATTATAAAATTATTTAAAGCGAGTAAA
1 AAAAATGTAAAAAAATTCAACATAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAAA
* ** * *
559 AAGGCTTTTGAAGGAATAGGTGACTATAAATGAACTTTTCTTGTCAATGAATGGTTTTTTCTGCA
66 AAGGCTTTTAAAGGAATAGGTGACTATAAATGAACTTTTCTTCACAATGAATAGCTTTTTCTGCA
* * * * *
624 CGTTTTTGAAGACAAGCATTCAATTATAACCTGTTTTAATCAAAAATGGGAAAAAAGTCAGCTTA
131 CGTTCTTGAAGACAAGCATTCAATTATAACCTGTTTTAATCAAAAATGGAAAAAAAGTAACCCTA
* * * *
689 AAATCAATTATGATATTATAAAACAATTTAAAGTAAGTAATAAGGCTTTCGAAGGAATAAGAGAC
196 AAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGACTTTCGAAAGAATAAGAGAC
* * *
754 TATAAATGGACTTATCTTGCCAATGAATACTTATTTCTTTACGTTTCTCGATGTAAATATTCAAT
261 CATAAATGGACTTATCTTGCCAATGAATACTTATTTCTTCACGTTTCTCGATGTAAACATTCAAT
* * *
819 TATAGTCTGTTTTAAACGAAAAAGTGAAAAAAATCAACTCAAAATTAATTATGAGATTATAAAAC
326 TATAGTCTGTTTCAAACGAAAAAGTGAAAAAAATCAACTCAAAATCAATTATAAGATTATAAAAC
** * **
884 AATTTAGGGCGAGAAATATGGCTTTTGAAGGAATATGAGACTATAAATGAACTTTTCTTGCCAAT
391 AATTTAAAGAGAGAAATAAAGCTTTTGAAGGAATATGAGACTATAAATGAACTTTTCTTGCCAAT
949 GTATGCTTTTTTCTTCACGTTTATTTAACC
456 GTATGCTTTTTTCTTCACGTTTATTTAACC
* *
979 AAAAATGTAAAAAAATTCAACAT-AAATTAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
1 AAAAATGTAAAAAAATTCAACATAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAAA
* *
1043 AAGGCTTTTAAAGGAAT-GAGTGACTATAAATGGAA-TTTTCTTCACTATGAATAGCTTTTTCTT
66 AAGGCTTTTAAAGGAATAG-GTGACTATAAAT-GAACTTTTCTTCACAATGAATAGCTTTTTCTG
* * * * * * * *
1106 TATGTTACTTG-AG-CTAGACATTCAATTATAATCTTTTTTAATCAATAATGTTAAAAAAATTAA
129 CACGTT-CTTGAAGACAAG-CATTCAATTATAACCTGTTTTAATCAAAAATG-GAAAAAAAGT-A
* * * * * *
1169 ACCCTAAAATCAATTTTTAGATTATAAAACTATTTAATGCGAGTAATAAGAC-TTCTGAAAGAGT
190 ACCCTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGACTTTC-GAAAGAAT
* * * * * * * *
1233 AGGTGACCATAAATGTACTTATCTTGTCAATGAATGCTTGTTTCTTCATGTTTCTCGATGTAGAC
254 AAGAGACCATAAATGGACTTATCTTGCCAATGAATACTTATTTCTTCACGTTTCTCGATGTAAAC
* * * *
1298 ATTCAATTATAGTCTGTTTCAGA-GAAAAA-TGCAAAAAAATTCAACTTAAAGTCAATTCTAAGA
319 ATTCAATTATAGTCTGTTTCAAACGAAAAAGTG-AAAAAAA-TCAACTCAAAATCAATTATAAGA
* * * *
1361 TTATAAAACTATTTAAATAGAGTAATAAAGCTTTTTAAGGAAT
382 TTATAAAACAATTTAAAGAGAGAAATAAAGCTTTTGAAGGAAT
1404 GGGNNNNNNN
Statistics
Matches: 352, Mismatches: 64, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
483 4 0.01
484 124 0.35
485 49 0.14
486 175 0.50
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (485 bp):
AAAAATGTAAAAAAATTCAACATAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAAA
AAGGCTTTTAAAGGAATAGGTGACTATAAATGAACTTTTCTTCACAATGAATAGCTTTTTCTGCA
CGTTCTTGAAGACAAGCATTCAATTATAACCTGTTTTAATCAAAAATGGAAAAAAAGTAACCCTA
AAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTAATAAGACTTTCGAAAGAATAAGAGAC
CATAAATGGACTTATCTTGCCAATGAATACTTATTTCTTCACGTTTCTCGATGTAAACATTCAAT
TATAGTCTGTTTCAAACGAAAAAGTGAAAAAAATCAACTCAAAATCAATTATAAGATTATAAAAC
AATTTAAAGAGAGAAATAAAGCTTTTGAAGGAATATGAGACTATAAATGAACTTTTCTTGCCAAT
GTATGCTTTTTTCTTCACGTTTATTTAACC
Done.