Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398849.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2131.0, 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: 4646
ACGTcount: A:0.20, C:0.07, G:0.08, T:0.20
Warning! 2095 characters in sequence are not A, C, G, or T
Found at i:1254 original size:171 final size:169
Alignment explanation
Indices: 939--2325 Score: 1022
Period size: 171 Copynumber: 8.1 Consensus size: 169
929 NNNNNNNGCA
* * * *
939 TAAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATGAGGCTTTTGAAGGAATAGGAG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTG
* * * * *
1004 ACTGTAAATGGACTTTTCTTGC-CAATGAATGTTTGTTTCTTCAAGTTTCTCAAGGTAAACATTC
66 ACTATAAAT-GACTTTTCTT-CTCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAAGCATTC
* * *
1068 AACTATAGGCTGTTTTAACTAAAAATGTAAAACAATTCAACT
129 AATTATAGTCTGTTTTAACTAAAAATCTAAAA-AATTCAACT
* * * *
1110 TAAAATCAATTTAT-AGATTATAAATCAATTTAAAGCTAGTAATAAGGCTTTTGAAGGAATTGGT
1 TAAAATCAA-TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
* * *
1174 GACTAGAAATAGACTTTTCTTCTCAGTGAATGGCTT-TTTCTGCATGTTTC-CTGAGGTAAGCAT
65 GACTATAAAT-GACTTTTCTTCTCAATGAAT-GCTTGTTTCTTCATGTTTCTC-GAGGTAAGCAT
* * *
1237 CCTATTATAGTCTGTTTTAA-TGAAAAATGTAAAAGAATTCAACT
127 TCAATTATAGTCTGTTTTAACT-AAAAATCTAAAA-AATTCAACT
********** * *
1281 TAAAATCAATTANNNNNNNNNNAAACCATTTAAAGCGAGTAATAAGCCTTTTAAAGGAAT-GGTT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGG-T
* * * *
1345 AACTATAAATGAACTTTTCTTATCAATGAATGCTTGTTTCCTCACGTTTCTCGAGGT-AGACATT
65 GACTATAAATG-ACTTTTCTTCTCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAAG-CATT
* * **************
1409 TAATTATAGCCTGTTTTAACTAAAAANNNNNNNNNNNNNNNCT
128 CAATTATAGTCTGTTTTAACTAAAAA-TCTAAAAAATTCAACT
* * * *
1452 TAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATGAGGCTTTTCAAGGAATAAGAT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-AGGT
* * * * * **
1517 -ACTATAAATGGACTTTTCTGCT-AGTGAATGCTTGTTTCTTTAGGTTTCTCAAGGTAAATATTC
65 GACTATAAAT-GACTTTTCTTCTCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAAGCATTC
* *
1580 AATTATAGGCTGTTTTAACTAAAAATCTAAAACAATTAAACT
129 AATTATAGTCTGTTTTAACTAAAAATCTAAAA-AATTCAACT
********** * *
1622 TAAAATCAATTATGAGATTATAAANNNNNNNNNNGCGAATAATAAGGCTTTTGAAGGAATTGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTG
* * * *
1687 ACTAAAAATGGACTTTTCTTCTCAAGGAGCA-GCTT-TTT-TGGCATGTTTCTTGAGGTAAGCAT
66 ACTATAAAT-GACTTTTCTTCTCAATGA--ATGCTTGTTTCT-TCATGTTTCTCGAGGTAAGCAT
* * *
1749 CCAATTATAGTCTGTTTTAA-TGGAAAATGTAAAAAGATT-AAGCT
127 TCAATTATAGTCTGTTTTAACT-AAAAATCTAAAAA-ATTCAA-CT
********** * * *
1793 TAAAATCAATTATGAGATTATAAAACCATTTNNNNNNNNNNATATGGCTTTTGAAGGAATGGGTA
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTG
* * * *
1858 ACTATAAATAGACTTTTTTTGC-CAGTAAATGCCTT-TTTCTTAATGTTTCTC-ATGGT-AGACA
66 ACTATAAAT-GACTTTTCTT-CTCAATGAATG-CTTGTTTCTTCATGTTTCTCGA-GGTAAG-CA
* * * *
1919 TTCAACTATAGCCTGTTTTAACTAAAAATTTAAAAAAATCAACT
126 TTCAATTATAGTCTGTTTTAACTAAAAATCTAAAAAATTCAACT
* ********** * *
1963 TAAAATCAATTATGAGATTATAAAACTATTNNNNNNNNNNAATAAGCCTTTTGAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTG
* * *
2028 ACTATAAATGTACTTTTCTTATCAAAGAATGCTTGTTTCCTT-GTGTTTCTCGAGGT-AGACATT
66 ACTATAAATG-ACTTTTCTTCTCAATGAATGCTTGTTT-CTTCATGTTTCTCGAGGTAAG-CATT
* * * * **
2091 CATTTATTGTCTATTTTAACCAAAAATCTAAAAAAATTCTGCT
128 CAATTATAGTCTGTTTTAACTAAAAATCT-AAAAAATTCAACT
* * * * * *
2134 TAAAATCAATTATGAGATTATAAAACTATTTAAAGTGCGTAATGAGGCTTTTGAAGGAATAAGAG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTG
* * * **
2199 ACTATAAATGAACTTTTCATGC-CAATGAATGCTT-TTTCTTCAAGTTTCTTGAGGTAAAAATTC
66 ACTATAAATG-ACTTTTC-TTCTCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAAGCATTC
*
2262 AA-T-TAGTCTCTTTTAACTAAAAATCTAAAAAAATTCAACT
129 AATTATAGTCTGTTTTAACTAAAAATCT-AAAAAATTCAACT
2302 TAAAATCAATTATGAGATTATAAA
1 TAAAATCAATTATGAGATTATAAA
2326 NNNNNNNNNN
Statistics
Matches: 958, Mismatches: 215, Indels: 89
0.76 0.17 0.07
Matches are distributed among these distances:
168 56 0.06
169 11 0.01
170 295 0.31
171 575 0.60
172 19 0.02
173 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.34
Consensus pattern (169 bp):
TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTG
ACTATAAATGACTTTTCTTCTCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAAGCATTCAA
TTATAGTCTGTTTTAACTAAAAATCTAAAAAATTCAACT
Found at i:1797 original size:341 final size:333
Alignment explanation
Indices: 939--2325 Score: 899
Period size: 341 Copynumber: 4.1 Consensus size: 333
929 NNNNNNNGCA
* * * * * *
939 TAAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATGAGGCTTTTGAAGGAATAGGAG
1 TAAAATCAATTATGAGATTATAAAACTA-TT---GCGAATAATAAGCCTTTTGAAGGAATGGGTG
** ** * * *** * * *
1004 ACTGTAAATGGACTTTTCTTGCCAATGAATGTTTGTTTCTTCAAGTTTCTCAAGGTAAACATTCA
62 ACTAAAAATGGACTTTTCTTATCAAAGAATGCTTGTTTC-TGGTGTTTCTCGAGGTAGACATCCA
* * * * * *
1069 ACTATAGGCTGTTTTAACTAAAAATGTAAAACAATTCAA-CTTAAAATCAATTTAT-AGATTATA
126 ATTATAGTCTATTTTAACCAAAAATCTAAAAAAATT-AAGCTTAAAATCAA-TTATGAGATTATA
* * * * * * * * * *
1132 AATCAATTTAAAGCTAGTAATAAGGCTTTTGAAGGAAT-TGGTGACTAGAAATAGACTTTTCTTC
189 AAACCATTTAAAACGAGTAATGAGGCTTTTGAAGGAATAAGAT-ACTATAAATGGACTTTTCTGC
** * * ** * * *
1196 TCAGTGAATGGCTTTTTCTGCATGTTTC-CTGAGGTAAGCATCCTATTATAGTCTGTTTTAA-TG
253 -CAGTGAAT-GCTTTTTCTTAAAGTTTCTC-AAGGTAAAAATTC-AATATAGCCTGTTTTAACT-
*
1259 AAAAATGTAAAAGAATTCAACT
313 AAAAATCTAAAA-AATTCAACT
********** * * * * *
1281 TAAAATCAATTANNNNNNNNNNAAACCATTTAAAGCGAGTAATAAGCCTTTTAAAGGAATGGTTA
1 TAAAATCAATTATGAGATTATAAAACTA-TT---GCGAATAATAAGCCTTTTGAAGGAATGGGTG
* * * *** **
1346 ACTATAAATGAACTTTTCTTATCAATGAATGCTTGTTTCCTCACGTTTCTCGAGGTAGACATTTA
62 ACTAAAAATGGACTTTTCTTATCAAAGAATGCTTGTTT-CTGGTGTTTCTCGAGGTAGACATCCA
* * * ***************
1411 ATTATAGCCTGTTTTAACTAAAAANNNNNNNNNNNNNNNCTTAAAATCAATTATGAGATTATAAA
126 ATTATAGTCTATTTTAACCAAAAATCTAAAAAAATTAAGCTTAAAATCAATTATGAGATTATAAA
* *
1476 ACCATTTAAAACGAGTAATGAGGCTTTTCAAGGAATAAGATACTATAAATGGACTTTTCTGCTAG
191 ACCATTTAAAACGAGTAATGAGGCTTTTGAAGGAATAAGATACTATAAATGGACTTTTCTGCCAG
* * * *
1541 TGAATGCTTGTTTCTTTAGGTTTCTCAAGGTAAATATTCAATTATAGGCTGTTTTAACTAAAAAT
256 TGAATGCTT-TTTCTTAAAGTTTCTCAAGGTAAAAATTCAA-TATAGCCTGTTTTAACTAAAAAT
*
1606 CTAAAACAATTAAACT
319 CTAAAA-AATTCAACT
****** * *
1622 TAAAATCAATTATGAGATTATAAANNNNNNNNNNGCGAATAATAAGGCTTTTGAAGGAATTGGTG
1 TAAAATCAATTATGAGATTATAAA----ACTATTGCGAATAATAAGCCTTTTGAAGGAATGGGTG
* * *
1687 ACTAAAAATGGACTTTTCTTCTCAAGGAGCA-GCTT-TTT-TGGCATGTTTCTTGAGGTA-AGCA
62 ACTAAAAATGGACTTTTCTTATCAA--AGAATGCTTGTTTCTGG--TGTTTCTCGAGGTAGA-CA
* *** * *
1748 TCCAATTATAGTCTGTTTTAATGGAAAATGTAAAAAGATTAAGCTTAAAATCAATTATGAGATTA
122 TCCAATTATAGTCTATTTTAACCAAAAATCTAAAAAAATTAAGCTTAAAATCAATTATGAGATTA
********** * * *
1813 TAAAACCATTTNNNNNNNNNNAT-ATGGCTTTTGAAGGAAT-GGGTAACTATAAATAGACTTTTT
187 TAAAACCATTTAAAACGAGTAATGA-GGCTTTTGAAGGAATAAGAT-ACTATAAATGGAC-TTTT
* * * * * *
1876 TTGCCAGTAAATGCCTTTTTCTTAATGTTTCTCATGGTAGACATTCAACTATAGCCTGTTTTAAC
249 CTGCCAGTGAATG-CTTTTTCTTAAAGTTTCTCAAGGTAAAAATTCAA-TATAGCCTGTTTTAAC
* *
1941 TAAAAATTTAAAAAAATCAACT
312 TAAAAATCTAAAAAATTCAACT
******
1963 TAAAATCAATTATGAGATTATAAAACTATTNNNNNNNNNNAATAAGCCTTTTGAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAACTATT----GCGAATAATAAGCCTTTTGAAGGAATGGGTG
* * * *
2028 ACTATAAATGTACTTTTCTTATCAAAGAATGCTTGTTTCCTTGTGTTTCTCGAGGTAGACATTCA
62 ACTAAAAATGGACTTTTCTTATCAAAGAATGCTTGTTT-CTGGTGTTTCTCGAGGTAGACATCCA
* * **
2093 TTTATTGTCTATTTTAACCAAAAATCTAAAAAAATTCTGCTTAAAATCAATTATGAGATTATAAA
126 ATTATAGTCTATTTTAACCAAAAATCTAAAAAAATTAAGCTTAAAATCAATTATGAGATTATAAA
* ** * * *
2158 ACTATTTAAAGTGCGTAATGAGGCTTTTGAAGGAATAAGAGACTATAAATGAACTTTTCATGCCA
191 ACCATTTAAAACGAGTAATGAGGCTTTTGAAGGAATAAGATACTATAAATGGACTTTTC-TGCCA
* * ** * *
2223 ATGAATGCTTTTTCTTCAAGTTTCTTGAGGTAAAAATTCAAT-TAGTCTCTTTTAACTAAAAATC
255 GTGAATGCTTTTTCTTAAAGTTTCTCAAGGTAAAAATTCAATATAGCCTGTTTTAACTAAAAATC
2287 TAAAAAAATTCAACT
320 T-AAAAAATTCAACT
2302 TAAAATCAATTATGAGATTATAAA
1 TAAAATCAATTATGAGATTATAAA
2326 NNNNNNNNNN
Statistics
Matches: 803, Mismatches: 208, Indels: 71
0.74 0.19 0.07
Matches are distributed among these distances:
338 20 0.02
339 41 0.05
340 44 0.05
341 421 0.52
342 267 0.33
343 10 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.34
Consensus pattern (333 bp):
TAAAATCAATTATGAGATTATAAAACTATTGCGAATAATAAGCCTTTTGAAGGAATGGGTGACTA
AAAATGGACTTTTCTTATCAAAGAATGCTTGTTTCTGGTGTTTCTCGAGGTAGACATCCAATTAT
AGTCTATTTTAACCAAAAATCTAAAAAAATTAAGCTTAAAATCAATTATGAGATTATAAAACCAT
TTAAAACGAGTAATGAGGCTTTTGAAGGAATAAGATACTATAAATGGACTTTTCTGCCAGTGAAT
GCTTTTTCTTAAAGTTTCTCAAGGTAAAAATTCAATATAGCCTGTTTTAACTAAAAATCTAAAAA
ATTCAACT
Found at i:1908 original size:512 final size:498
Alignment explanation
Indices: 939--2325 Score: 1134
Period size: 512 Copynumber: 2.7 Consensus size: 498
929 NNNNNNNGCA
* * * * *
939 TAAAATCAGTTATGAGATTATAAAACTATTTAAAGCGAGTAATGAGGCTTTTGAAGGAATAGGAG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATGAGGCTTTTCAAGGAATAAGAG
* *
1004 ACTGTAAATGGACTTTTCTTGCCAATGAATGTTTGTTTCTTCAAGTTTCTCAAGGTAAACATTCA
66 ACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCAAGTTTCTCAAGGTAAACATTCA
* *
1069 ACTATAGGCTGTTTTAACTAAAAATGTAAAACAATTCAACTTAAAATCAATTTATAGATTATAAA
131 ACTATAGGCTGTTTTAACTAAAAATCTAAAACAATTAAACTTAAAATCAATTTATAGATTATAAA
* * *
1134 TCAATTTAAAGCTAGTAATAAGGCTTTTGAAGGAATTGGTGACTAGAAATAGACTTTTCTTCTCA
196 TCAATTTAAAGCGAATAATAAGGCTTTTGAAGGAATTGGTGACTAAAAATAGACTTTTCTTCTCA
** *
1199 GTGAATGGCTTTTTCTGCATGTTTCCTGAGGTAAGCATCCTATTATAGTCTGTTTTAATGAAAAA
261 GTGAACAGCTTTTTCTGCATGTTTCCTGAGGTAAGCATCCAATTATAGTCTGTTTTAATGAAAAA
**********
1264 TGTAAAAGAATTCAACTTAAAATCAATTANNNNNNNNNNAAACCATTTAAAGCGAGTAATAAGCC
326 TGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCC
* * * *
1329 TTTTAAAGGAATGGTTAACTATAAATGAACTTTTCTTATCAATGAATGCTTGTTTCCTCACGTTT
391 TTTTAAAGGAATGGGTAACTATAAATGAACTTTTCTTACCAATAAATGCTTGTTTCCTAACGTTT
* *
1394 CTCGA-GGTAGACATTTAATTATAGCCTGTTTTAACTAAAAANNNNNNNNNNNNNNNCT
456 CTC-ATGGTAGACATTCAACTATAGCCTGTTTTAACTAAAAA---------------CT
*
1452 TAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATGAGGCTTTTCAAGGAATAAGAT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATGAGGCTTTTCAAGGAATAAGAG
* * * * *
1517 ACTATAAATGGACTTTTC-TGCTAGTGAATGCTTGTTTCTTTAGGTTTCTCAAGGTAAATATTCA
66 ACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCAAGTTTCTCAAGGTAAACATTCA
*
1581 ATTATAGGCTGTTTTAACTAAAAATCTAAAACAATTAAACTTAAAATCAA-TTATGAGATTATAA
131 ACTATAGGCTGTTTTAACTAAAAATCTAAAACAATTAAACTTAAAATCAATTTAT-AGATTATAA
********** *
1645 ANNNNNNNNNNGCGAATAATAAGGCTTTTGAAGGAATTGGTGACTAAAAATGGACTTTTCTTCTC
195 ATCAATTTAAAGCGAATAATAAGGCTTTTGAAGGAATTGGTGACTAAAAATAGACTTTTCTTCTC
* * *
1710 AAG-GAGCAGCTTTTT-TGGCATGTTTCTTGAGGTAAGCATCCAATTATAGTCTGTTTTAATGGA
260 -AGTGAACAGCTTTTTCT-GCATGTTTCCTGAGGTAAGCATCCAATTATAGTCTGTTTTAATGAA
**********
1773 AAATGTAAAA-AGATT-AAGCTTAAAATCAATTATGAGATTATAAAACCATTTNNNNNNNNNNAT
323 AAATGTAAAAGA-ATTCAA-CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * * * *
1836 ATGGCTTTTGAAGGAATGGGTAACTATAAAT-AGACTTTTTTTGCCAGTAAATGCCTT-TTTCTT
386 AAGCCTTTTAAAGGAATGGGTAACTATAAATGA-ACTTTTCTTACCAATAAATG-CTTGTTTCCT
*
1899 AATGTTTCTCATGGTAGACATTCAACTATAGCCTGTTTTAACTAAAAATTTAAAAAAATCAACT
449 AACGTTTCTCATGGTAGACATTCAACTATAGCCTGTTTTAAC--------T----AAA--AACT
* ********** * * * ** *
1963 TAAAATCAATTATGAGATTATAAAACTATTNNNNNNNNNNAATAAGCCTTTTGAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATGAGGCTTTTCAAGGAATAAGAG
* ** * ** * *
2028 ACTATAAATGTACTTTTCTTATCAAAGAATGCTTGTTTCCTT-GTGTTTCTCGAGGTAGACATTC
66 ACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTT-CTTCAAGTTTCTCAAGGTAAACATTC
** * * * * * ***
2092 ATTTATTGTCTATTTTAACCAAAAATCTAAAAAAATTCTGCTTAAAATCAA-TTATGAGATTATA
130 AACTATAGGCTGTTTTAACTAAAAATCTAAAACAATTAAACTTAAAATCAATTTAT-AGATTATA
* * * ** * ** * * *
2156 AAACTATTTAAAGTGCGTAATGAGGCTTTTGAAGGAATAAGAGACTATAAAT-GAACTTTTCATG
194 AATCAATTTAAAGCGAATAATAAGGCTTTTGAAGGAATTGGTGACTAAAAATAG-ACTTTTC-TT
* * * * * ** * *
2220 C-CAATGAA-TGCTTTTTCTTCAAGTTTCTTGAGGTAAAAATTCAA-T-TAGTCTCTTTTAACT-
257 CTCAGTGAACAGCTTTTTCTGCATGTTTCCTGAGGTAAGCATCCAATTATAGTCTGTTTTAA-TG
* *
2280 AAAAATCTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
321 AAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAA
2326 NNNNNNNNNN
Statistics
Matches: 705, Mismatches: 138, Indels: 66
0.78 0.15 0.07
Matches are distributed among these distances:
509 51 0.07
510 5 0.01
511 106 0.15
512 451 0.64
513 86 0.12
520 1 0.00
524 3 0.00
526 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.34
Consensus pattern (498 bp):
TAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATGAGGCTTTTCAAGGAATAAGAG
ACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCAAGTTTCTCAAGGTAAACATTCA
ACTATAGGCTGTTTTAACTAAAAATCTAAAACAATTAAACTTAAAATCAATTTATAGATTATAAA
TCAATTTAAAGCGAATAATAAGGCTTTTGAAGGAATTGGTGACTAAAAATAGACTTTTCTTCTCA
GTGAACAGCTTTTTCTGCATGTTTCCTGAGGTAAGCATCCAATTATAGTCTGTTTTAATGAAAAA
TGTAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCC
TTTTAAAGGAATGGGTAACTATAAATGAACTTTTCTTACCAATAAATGCTTGTTTCCTAACGTTT
CTCATGGTAGACATTCAACTATAGCCTGTTTTAACTAAAAACT
Done.