Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402817.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5872.0, 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, 848
Length: 1414
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.33
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:329 original size:171 final size:171
Alignment explanation
Indices: 3--1180 Score: 1325
Period size: 171 Copynumber: 6.9 Consensus size: 171
1 AA
* * *
3 TCAACTTCAAATCAATTATGAGATTATAAAATCATTTAAAGAGAGTAATAAGACTTTTGAAGGCT
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
* * * * * * *
68 TGAGTGACTATAAATGGGCTTTTCTTTCCAATGAATGACTTTTTCTTCAAGTTTCCCATGG-AAA
66 TGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCATGCTTCTCAAGGCAAA
* * *
132 CCATTCAATTGTAGTCTGTTTTAACTAAAAATATAAACA-AAT
131 -CATTCAATTATAATCTGTTTTAACCAAAAATATAAA-ATAAT
* **
174 TCAACTTAAAATCAATTTTGAGGCTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
* * * * * * * *
239 TAGGTTG-CTATAAATGTGTTTTTCTTGCCAATGAATGGGTTTCTCTTCATGCTACTCGAGGCAG
66 T-GGGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCATGCTTCTCAAGGCAA
* * * * *
303 ACATTTAAATATAATCTGTGTTAACTAAAAATGTAAAATAAT
130 ACATTCAATTATAATCTGTTTTAACCAAAAATATAAAATAAT
* * ** * *
345 TCACCTTCAAATCAATTAAAAGATTATAAAACCATTGACAGAGAGTAATAAGGCTTTTGAAGGCT
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
** * * * * * *
410 TGGGTGACTATAAATGCACTATTCTTGCCAATGAATGGCTCTTTCTTCAGGTTTCCCAAGGAAAA
66 TGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCATGCTTCTCAAGGCAAA
* * *
475 CATTCAATTATAATATGTTTTAACCAAAAATACAAAAAAAT
131 CATTCAATTATAATCTGTTTTAACCAAAAATATAAAATAAT
* * * *
516 T-AACTTAAAATTCAATTATGAGATTATAAAACTATTTAAAGAGAGTAAAAAGACTTTTGAAGGA
1 TCAACTTAAAA-TCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGC
** * * * * *
580 TTAAGTGATTATAAATGGGTTTTTCTTGTCAATGAATGGGTTTTTCTTCATACTTCTCAAGGCAA
65 TTGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCATGCTTCTCAAGGCAA
* * * *
645 ACATTCAAGTATAATCTGTGTTAACCAAAAATGTAAAATAAA
130 ACATTCAATTATAATCTGTTTTAACCAAAAATATAAAATAAT
* * *
687 TCAACTTCAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGTT
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
* * * * * * * **
752 TGGGTGACTATAAATGGGGTTTTCTTGTCAATGAATGGCTTTTTCTTTAGGTTTCCCATGAAAAA
66 TGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCATGCTTCTCAAGGCAAA
* * *
817 CATTCAATTATAGTCTGTTTTGACCAAAAATAGAAAA-AAGT
131 CATTCAATTATAATCTGTTTTAACCAAAAATATAAAATAA-T
*
858 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATTAGGCTTTTGAAGGCT
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
* * * *
923 TGGATGACCATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTCCTTCATGCTTCTCAAGGCAAA
66 TGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCATGCTTCTCAAGGCAAA
* * *
988 CAATCAATTATAATCT-TCATTAACTAAAAATATAAAATAAT
131 CATTCAATTATAATCTGT-TTTAACCAAAAATATAAAATAAT
* * *
1029 TCAACTTTAAATCAATTATGAGATTATAAAGCTATTTATAA-AGAGTAATAAGGCTTTTGAAGGC
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTA-AAGAGAGTAATAAGGCTTTTGAAGGC
*** * * * ** *
1093 TTGGGTGACTATAAATACAC-TTTCTTACCAATAAATGGGTTTTTCTTCATATTTCT-ACAGG-T
65 TTGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCATGCTTCTCA-AGGCA
* *
1155 AA-ATTCAATTTTAATCTATTTTAACC
129 AACATTCAATTATAATCTGTTTTAACC
1181 NNNNNNNNNN
Statistics
Matches: 838, Mismatches: 157, Indels: 27
0.82 0.15 0.03
Matches are distributed among these distances:
168 18 0.02
169 4 0.00
170 49 0.06
171 750 0.89
172 17 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (171 bp):
TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
TGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCATGCTTCTCAAGGCAAA
CATTCAATTATAATCTGTTTTAACCAAAAATATAAAATAAT
Found at i:660 original size:342 final size:343
Alignment explanation
Indices: 3--1141 Score: 1572
Period size: 342 Copynumber: 3.3 Consensus size: 343
1 AA
* *
3 TCAACTTCAAATCAATTATGAGATTATAAAATCATTTAAAGAGAGTAATAAGACTTTTGAAGGCT
1 TCAACTTCAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
* ** * * * *
68 TGAGTGACTATAAATGGGCTTTTCTTTCCAATGAATGACTTTTTCTTCAAGTTTCCCATGGAAAC
66 TGGGTGACTATAAATGCACTTTTCTTGCCAATGAATGGCTTTTTCTTCAGGTTTCCCATGGAAAA
* * * * * **
133 CATTCAATTGTAGTCTGTTTTAACTAAAAATATAAACAAATTCAACTTAAAATCAATTTTGAGGC
131 CATTCAATTATAGTCTGTTTTAACCAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGAT
* *
198 TATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTAGGTTG-CTATAAATGTGTTTTT
196 TATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTAGGATGACTATAAATGGGTTTTT
* * * * *
262 CTTGCCAATGAATGGGTTTCTCTTCATGCTACTCGAGGCAGACATTTAAATATAATCTGTGTTAA
261 CTTGCCAATGAATGGGTTTTTCTTCATGCTTCTCAAGGCAAACATTCAAATATAATCTGTGTTAA
327 CTAAAAATGTAAAATAAT
326 CTAAAAATGTAAAATAAT
* ** * *
345 TCACCTTCAAATCAATTAAAAGATTATAAAACCATTGACAGAGAGTAATAAGGCTTTTGAAGGCT
1 TCAACTTCAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
* * *
410 TGGGTGACTATAAATGCACTATTCTTGCCAATGAATGGCTCTTTCTTCAGGTTTCCCAAGGAAAA
66 TGGGTGACTATAAATGCACTTTTCTTGCCAATGAATGGCTTTTTCTTCAGGTTTCCCATGGAAAA
* *
475 CATTCAATTATAATATGTTTTAACCAAAAATACAAAAAAATT-AACTTAAAATTCAATTATGAGA
131 CATTCAATTATAGTCTGTTTTAACCAAAAATACAAAAAAATTCAACTTAAAA-TCAATTATGAGA
* * * * * *
539 TTATAAAACTATTTAAAGAGAGTAAAAAGACTTTTGAAGGATTAAG-TGATTATAAATGGGTTTT
195 TTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTAGGATGACTATAAATGGGTTTT
* * *
603 TCTTGTCAATGAATGGGTTTTTCTTCATACTTCTCAAGGCAAACATTCAAGTATAATCTGTGTTA
260 TCTTGCCAATGAATGGGTTTTTCTTCATGCTTCTCAAGGCAAACATTCAAATATAATCTGTGTTA
* *
668 ACCAAAAATGTAAAATAAA
325 ACTAAAAATGTAAAATAAT
* *
687 TCAACTTCAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGTT
1 TCAACTTCAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
*** * * *
752 TGGGTGACTATAAATGGGGTTTTCTTGTCAATGAATGGCTTTTTCTTTAGGTTTCCCATGAAAAA
66 TGGGTGACTATAAATGCACTTTTCTTGCCAATGAATGGCTTTTTCTTCAGGTTTCCCATGGAAAA
* * *
817 CATTCAATTATAGTCTGTTTTGACCAAAAATAGAAAAAAGTTCAACTTAAAATCAATTATGAGAT
131 CATTCAATTATAGTCTGTTTTAACCAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * *
882 TATAAAACCATTTAAAGAGAGTAATTAGGCTTTTGAAGGCTT-GGATGACCATAAATGGGCTTTT
196 TATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTAGGATGACTATAAATGGGTTTTT
* * * *
946 CTTGCCAATGAATGGGTTTTCCTTCATGCTTCTCAAGGCAAACAATCAATTATAATCT-TCATTA
261 CTTGCCAATGAATGGGTTTTTCTTCATGCTTCTCAAGGCAAACATTCAAATATAATCTGT-GTTA
*
1010 ACTAAAAATATAAAATAAT
325 ACTAAAAATGTAAAATAAT
* * *
1029 TCAACTTTAAATCAATTATGAGATTATAAAGCTATTTATAA-AGAGTAATAAGGCTTTTGAAGGC
1 TCAACTTCAAATCAATTATGAGATTATAAAACCATTTA-AAGAGAGTAATAAGGCTTTTGAAGGC
* * * *
1093 TTGGGTGACTATAAATACAC-TTTCTTACCAATAAATGGGTTTTTCTTCA
65 TTGGGTGACTATAAATGCACTTTTCTTGCCAATGAATGGCTTTTTCTTCA
1142 TATTTCTACA
Statistics
Matches: 697, Mismatches: 94, Indels: 13
0.87 0.12 0.02
Matches are distributed among these distances:
341 37 0.05
342 649 0.93
343 11 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (343 bp):
TCAACTTCAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCT
TGGGTGACTATAAATGCACTTTTCTTGCCAATGAATGGCTTTTTCTTCAGGTTTCCCATGGAAAA
CATTCAATTATAGTCTGTTTTAACCAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGAT
TATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTAGGATGACTATAAATGGGTTTTT
CTTGCCAATGAATGGGTTTTTCTTCATGCTTCTCAAGGCAAACATTCAAATATAATCTGTGTTAA
CTAAAAATGTAAAATAAT
Done.