Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399608.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2861.0, 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: 2108
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.24
Warning! 668 characters in sequence are not A, C, G, or T
Found at i:302 original size:171 final size:168
Alignment explanation
Indices: 1--512 Score: 397
Period size: 171 Copynumber: 3.0 Consensus size: 168
* * * *
1 CTATAAATGA-GCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCCCAAGGAAAACAGTCA
1 CTATAAA-GAGGCTTTTCTTGCCAATGAATGGATTTTTCTTCACGTTTTCCAAGGAAAACATTCA
** ** ********** * * *
65 ATTATGTTCTATTTTAAACAAAANNNNNNNNNNATTCAACTTAAAATCAATTTTGAG-GTCATAA
65 ATTATAATCTGGTTT-AACAAAAAAGTAAAAAAATTTAACTTAAAATCAATTATGAGAAT-ATAA
*
129 AACTATTTATAGAGAGTAATAAGGCTTTAGAAGGCTTTGGTGA
128 AACTATTTA-AGAGAATAATAAGGCTTT-GAAGGCTTTGGTGA
** * * *
172 CTATATATTA-GCTTTTCTTGCCAATGATTGTATTTTTCTTCACG-TTTCCAAAGGTAAACATTC
1 CTATA-AAGAGGCTTTTCTTGCCAATGAATGGATTTTTCTTCACGTTTTCC-AAGGAAAACATTC
* *
235 AATTATAATCTGTTTTAATCAAATTAA-TAAAAAAATTTAACTTAAAATCAATTATGAGAATATA
64 AATTATAATCTGGTTTAA-CAAA-AAAGTAAAAAAATTTAACTTAAAATCAATTATGAGAATATA
*********
299 AAACTATNNNNNNNNNNTAATAAGGCTTTTGAAGGC-TTGGATGA
127 AAACTAT-TTAAGAGAATAATAAGGC-TTTGAAGGCTTTGG-TGA
* * * *
343 CTATAAAGAGGCTTTTCTTGCTAATGAATGGGTTTTTCTTCATGTTTTCCAAGGAAAACATTCAC
1 CTATAAAGAGGCTTTTCTTGCCAATGAATGGATTTTTCTTCACGTTTTCCAAGGAAAACATTCAA
* * * * *
408 TTATATTCTGGTTTAACAAAAAATGTGAAAACATTTAACTTAAAATCAATTATGAGATTGTAAAA
66 TTATAATCTGGTTTAACAAAAAA-GTAAAAAAATTTAACTTAAAATCAATTATGAGAATATAAAA
* * *
473 CCATTTAATGAGAATAATAAGACATTTGAAGGCTTGGGTG
130 CTATTTAA-GAGAATAATAAGGC-TTTGAAGGCTTTGGTG
513 NNNNNNNNNN
Statistics
Matches: 264, Mismatches: 63, Indels: 28
0.74 0.18 0.08
Matches are distributed among these distances:
169 2 0.01
170 16 0.06
171 233 0.88
172 13 0.05
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.35
Consensus pattern (168 bp):
CTATAAAGAGGCTTTTCTTGCCAATGAATGGATTTTTCTTCACGTTTTCCAAGGAAAACATTCAA
TTATAATCTGGTTTAACAAAAAAGTAAAAAAATTTAACTTAAAATCAATTATGAGAATATAAAAC
TATTTAAGAGAATAATAAGGCTTTGAAGGCTTTGGTGA
Found at i:1337 original size:169 final size:161
Alignment explanation
Indices: 1025--1338 Score: 332
Period size: 171 Copynumber: 1.9 Consensus size: 161
1015 CATTCAGCTT
* * * *
1025 AAAATCAATTATGGCACTACAAAACCATTTAAAGCGCGTAATAGGGCTTTTGAAAACTTGAGTGA
1 AAAATCAATTATGGCACTACAAAACCATTTAAAGAGAGTAATAAGGCTGTTGAAAACTTGAGTGA
* * * * *
1090 CTATAAATGCGCTTTTCTTGTCAATAAATATGTTTTTCTTCATGTTTTCAAAGGCAAACATTCAA
66 CTATAAATGAGCTTTTCTTGCCAACAAATATGGTTTTCTTCATCTTTTCAAAGGCAAACATTCAA
1155 TTATAATCTGTTTTAACTAAAAATATAAAAA
131 TTATAATCTGTTTTAACTAAAAATATAAAAA
* * *
1186 NNNNNNNNNNAAAATCAATTATGAG-ATTATAAAATCATTTAAAGAGAGTAATAAGGCTGTTGAA
1 ----------AAAATCAATTATG-GCACTACAAAACCATTTAAAGAGAGTAATAAGGCTGTTGAA
** *
1250 GGCTTG-GATGACTATAAAT-AGCTTTTCTTGCCAACGAAT-TGGTTTTCTTCATCTTTGTC-AA
55 AACTTGAG-TGACTATAAATGAGCTTTTCTTGCCAACAAATATGGTTTTCTTCATCTTT-TCAAA
*
1311 GGCTAACATTCAATTATAATCTGTTTTA
118 GGCAAACATTCAATTATAATCTGTTTTA
1339 TAAAAAAATG
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
169 44 0.35
170 19 0.15
171 60 0.48
172 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.35
Consensus pattern (161 bp):
AAAATCAATTATGGCACTACAAAACCATTTAAAGAGAGTAATAAGGCTGTTGAAAACTTGAGTGA
CTATAAATGAGCTTTTCTTGCCAACAAATATGGTTTTCTTCATCTTTTCAAAGGCAAACATTCAA
TTATAATCTGTTTTAACTAAAAATATAAAAA
Found at i:1371 original size:169 final size:171
Alignment explanation
Indices: 852--1418 Score: 436
Period size: 169 Copynumber: 3.3 Consensus size: 171
842 AGTTCTGCTT
* ** * * *
852 AAAATCAATTATGAGGTTATAAAACCATTTAAATAGAGTAATAAGGCTTTTTTAAATCTTGGGTG
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTTGAAAACTTGAGTG
* ** * * * * ****
917 AATATAAAT-AGGCTTTTCTTGCCAATGAAT-GGGTTTCTCTTCATGTTTCTC-GATGCAANNNN
65 ACTATAAATGA-GCTTTTCTTGCCAACAAATATGGTTT-TCTTCATCTTT-TCAAAGGCAAACAT
****** * * * * * *
979 NNNNNNATAATCTATTTTAACTAAATATAT-AAAAACCATTCAGCTT
127 TCAATTATAATCTGTTTTAACTAAAAAAATAAAAAAAC-TT-AACTC
* * * *
1025 AAAATCAATTATG-GCACTACAAAACCATTTAAAGCGCGTAATAGGGCTTTTGAAAACTTGAGTG
1 AAAATCAATTATGAG-ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAACTTGAGTG
* * * * *
1089 ACTATAAATGCGCTTTTCTTGTCAATAAATATGTTTTTCTTCATGTTTTCAAAGGCAAACATTCA
65 ACTATAAATGAGCTTTTCTTGCCAACAAATATGGTTTTCTTCATCTTTTCAAAGGCAAACATTCA
* **********
1154 ATTATAATCTGTTTTAACTAAAAATATAAAAANNNNNNNNNN
130 ATTATAATCTGTTTTAACTAAAAAAATAAAAAAACTTAACTC
* * * **
1196 AAAATCAATTATGAGATTATAAAATCATTTAAAGAGAGTAATAAGGCTGTTGAAGGCTTG-GATG
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAACTTGAG-TG
* *
1260 ACTATAAAT-AGCTTTTCTTGCCAACGAAT-TGGTTTTCTTCATCTTTGTC-AAGGCTAACATTC
65 ACTATAAATGAGCTTTTCTTGCCAACAAATATGGTTTTCTTCATCTTT-TCAAAGGCAAACATTC
1322 AATTATAATCTGTTTT-A-TAAAAAAATGCAAAAAAACTTAACTC
129 AATTATAATCTGTTTTAACTAAAAAAAT--AAAAAAACTTAACTC
* *
1365 AAAATCAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGACTTTTGAA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
1419 NNNNNNNNNN
Statistics
Matches: 312, Mismatches: 72, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
167 8 0.03
168 1 0.00
169 97 0.31
170 19 0.06
171 62 0.20
172 79 0.25
173 46 0.15
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.34
Consensus pattern (171 bp):
AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAACTTGAGTGA
CTATAAATGAGCTTTTCTTGCCAACAAATATGGTTTTCTTCATCTTTTCAAAGGCAAACATTCAA
TTATAATCTGTTTTAACTAAAAAAATAAAAAAACTTAACTC
Done.