Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398473.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_177.0, 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: 7685
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.30
Warning! 1469 characters in sequence are not A, C, G, or T
Found at i:2518 original size:171 final size:171
Alignment explanation
Indices: 2231--2713 Score: 422
Period size: 171 Copynumber: 2.8 Consensus size: 171
2221 NNNNNNNNTT
* * * * * * * *
2231 ATATTTTTTATTAAAATAGATTATAATTGAATATCTAC-CTTGAGAAACGTGAGGAAAAAGATAT
1 ATATTTTTGATTAAAACAGATAATAATTAAATATCT-CTCTCGAGAAAGGTGAAGAAAAAGACAT
* * * * ** * * *
2295 CCATT-G-ATACGAAAAGTCTACTTATAGTCACCTACACCTTCAAAAGCCTTATTACTCGCTTTA
65 CCATTAGCA-A-GAAAAGTCCAGTCATAGTCACCAATGCATTCGAAACCCTTATTACTCGCTTTA
*
2358 AATGTTTTTATAATCTCATAAATAATTTTCAA-TTGAATTTTTTC
128 AATGTTTTTATAATCTCATAAATAA-TTTAAAGTTGAATTTTTTC
* * * * *
2402 ATATTTTTGGA-TAAAACAGATAATAATTGAATATCTGTCTTGATAAAGGTGAAGAAAAAGCCAT
1 ATATTTTT-GATTAAAACAGATAATAATTAAATATCTCTCTCGAGAAAGGTGAAGAAAAAGACAT
* ** * * * * * *
2466 TCATTA-TTAGAAAAAGTCCATTTATAGTTACCCATGCATTTGAAACCCTTATTACTCGGTTTAA
65 CCATTAGCAAG-AAAAGTCCAGTCATAGTCACCAATGCATTCGAAACCCTTATTACTCGCTTTAA
* * * * *
2530 ATGATTTTT-TAACCTCATAATTGATTTAAAGTTGAGTTTTTTT
129 ATG-TTTTTATAATCTCATAAATAATTTAAAGTTGAATTTTTTC
* * * * * *
2573 ATATTTTTTATTAAAATAGATTATAATTAAATGTCTCTCTCGAGAAATGTGAAGAAAAAGATATC
1 ATATTTTTGATTAAAACAGATAATAATTAAATATCTCTCTCGAGAAAGGTGAAGAAAAAGACATC
* * * *
2638 CATTGGCAAGAAATGTCCAGTCATAGTCACCAATGCCTTCGAAAGCCTTATTACTCGCTTTAAAT
66 CATTAGCAAGAAAAGTCCAGTCATAGTCACCAATGCATTCGAAACCCTTATTACTCGCTTTAAAT
*
2703 GGTTTTATAAT
131 GTTTTTATAAT
2714 NNNNNNNNNN
Statistics
Matches: 248, Mismatches: 54, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
170 11 0.04
171 229 0.92
172 8 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (171 bp):
ATATTTTTGATTAAAACAGATAATAATTAAATATCTCTCTCGAGAAAGGTGAAGAAAAAGACATC
CATTAGCAAGAAAAGTCCAGTCATAGTCACCAATGCATTCGAAACCCTTATTACTCGCTTTAAAT
GTTTTTATAATCTCATAAATAATTTAAAGTTGAATTTTTTC
Found at i:3614 original size:172 final size:172
Alignment explanation
Indices: 3285--3815 Score: 573
Period size: 172 Copynumber: 3.1 Consensus size: 172
3275 NNNNNNNNNN
* * * * * * * * * *
3285 AAATGTTTTTAGAATCTTGTAATTGATTTTAACTTGAATTTTTATACATTTTTTGTTAAAACATA
1 AAATATTTTTATAATCTCGAAATTGATTTTAAATTAAATTTTTTTACGTTTTTCGTTAAAACAGA
* *
3350 TAATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAGGATATCCTTTGGCAAGAAAAGTCCA
66 TAATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGATATCCATTGGCAAGAAAAGTCCA
*
3415 TTTATAGTCACCCATGACTTCAAAAGCCTTATTCCTCTATTT
131 TTTATAGTCACCCATGACTTCAAAAGCCTTATTACTCTATTT
* * *
3457 AAATATTTTTATAATCTC-ATAATT-ACTTTTAAATTAAATTTTTTTATGTTTTTGGTTAAAACG
1 AAATATTTTTATAATCTCGA-AATTGA-TTTTAAATTAAATTTTTTTACGTTTTTCGTTAAAACA
* **
3520 GATAATAATTGAATGTCTGCCTTGGGAAACATGAAGAAAAAAGATATCCATTGGCAAGAAAAGTC
64 GATAATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGATATCCATTGGCAAGAAAAGTC
********** * * *
3585 CATTTANNNNNNNNNNTGCCTTTAAAAGCCTTATTACTCTCTTT
129 CATTTATAGTCACCCATGACTTCAAAAGCCTTATTACTCTATTT
* *
3629 AAATATTTTTCTAATCTCGAAATTGATTTTAAATTGAATTTTTTTACGTTTTTCGTTAAAACAGA
1 AAATATTTTTATAATCTCGAAATTGATTTTAAATTAAATTTTTTTACGTTTTTCGTTAAAACAGA
********** **
3694 TAATAATTGAATGTNNNNNNNNNNAAACATGAAG-AAAAAGATATCCATCAGCAAGAAAAGTCCA
66 TAATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGATATCCATTGGCAAGAAAAGTCCA
** * *
3758 TTTATAGTCACTTATGATTTCAAAAGCCTTATTACTCGATTT
131 TTTATAGTCACCCATGACTTCAAAAGCCTTATTACTCTATTT
3800 AAATATTTTTATAATC
1 AAATATTTTTATAATC
3816 ATATAATTGN
Statistics
Matches: 291, Mismatches: 64, Indels: 9
0.80 0.18 0.02
Matches are distributed among these distances:
171 71 0.24
172 218 0.75
173 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.37
Consensus pattern (172 bp):
AAATATTTTTATAATCTCGAAATTGATTTTAAATTAAATTTTTTTACGTTTTTCGTTAAAACAGA
TAATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGATATCCATTGGCAAGAAAAGTCCA
TTTATAGTCACCCATGACTTCAAAAGCCTTATTACTCTATTT
Found at i:4424 original size:171 final size:171
Alignment explanation
Indices: 3925--5396 Score: 729
Period size: 171 Copynumber: 8.6 Consensus size: 171
3915 NNNNNNNNNN
* * * * * *
3925 GTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTTCTTCATGTTTCCTAAGGCAGACA
1 GTGACTATAAATGAACTTTTCTTACCAATGAATATC-TTTTTCTTCATGTTTTCTGAGGCAAACA
* * ** * **********
3990 TTTAATTATTATCTGTTTTAACCAAAAACGTAAAAAANNNNNNNNNNAAATCAATTATGAGATTA
65 TTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAGCTTAAAATCAATTATGAGATTA
* *
4055 TAAAAATATTTAAAT-AGAGTAATAAGGCTTTTGAAGTCATGG
130 TAAAAATATTT-AATGCGAGTAATAAGGCTTTTGAAGGCATGG
* * * * *
4097 GTGACTATAAATGGACTTTTCTTACCAAAGGATATCCTTTTTCTTCATGTTTTCTGAGGTAGACA
1 GTGACTATAAATGAACTTTTCTTACCAATGAATAT-CTTTTTCTTCATGTTTTCTGAGGCAAACA
* * ********** *
4162 TTCAATTATTATCTATTTTAACAAAAAATGTACAAAAANNNNNNNNNNAATCAATTATGAGATTC
65 TTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAGCTTAAAATCAATTATGAGATTA
* * **
4227 TAAAAATATTTTA-GCCACAAAATAAGGCTTTTGAAGGCATGG
130 TAAAAATATTTAATGCGA-GTAATAAGGCTTTTGAAGGCATGG
* * ** * * *
4269 GTGATTATAAATAAACTTTTCTGGCCAATGAATGTCTTTTTCTTTAGGTTTTCTGAGGCAAACAT
1 GTGACTATAAATGAACTTTTCTTACCAATGAATATCTTTTTCTTCATGTTTTCTGAGGCAAACAT
* * * * * * *
4334 TCAGTTCTTATTTATTTTAATTAAAAGTGTAAAAAAATTCAGCTTCAAATTAATTATGAGATTAT
66 TCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAGCTTAAAATCAATTATGAGATTAT
* ** * *
4399 AAAACTATTTAATGCGAGTAATAAGGCTTTCAAAGGCGTCG
131 AAAAATATTTAATGCGAGTAATAAGGCTTTTGAAGGCATGG
** * *
4440 GTGACTATAAATGGGCTTTTCTTACCAATGAATATCCTTTTCTTCATGTTTCTCT-AGGCAGACA
1 GTGACTATAAATGAACTTTTCTTACCAATGAATATCTTTTTCTTCATGTTT-TCTGAGGCAAACA
* ********** * *
4504 TTCAATTATTATCTGTTNNNNNNNNNNATATAAACAAATTC-GACTTAAAATCAATTATGAGATT
65 TTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAG-CTTAAAATCAATTATGAGATT
* * * *
4568 ATAAAAATA-TTAAGGCAAGTAATAAGGCTTTTGAAAGCATGA
129 ATAAAAATATTTAATGCGAGTAATAAGGCTTTTGAAGGCATGG
* * * *
4610 GTGACTATGAATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACG-TTTCTCGA-GCAAACA
1 GTGACTATAAATGAACTTTTCTTACCAATGAATATCTTTTTCTTCATGTTTTCT-GAGGCAAACA
* * * *****************
4673 TTCAATTATAATCTGTTTTAATAAAAAATGTAAAAAAATTCAACTTNNNNNNNNNNNNNNNNNTA
65 TTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAGCTTAAAATCAATTATGAGATTA
** * * *
4738 TAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATCG
130 TAAAAATATTTAATGCGAGTAATAAGGCTTTTGAAGGCATGG
* ** * * *
4780 GTGACTATAACTGGTCCTTTCTTGCCAATGGATATCTTTTTCTTCATG-TTTCTCGAGG-AAGAC
1 GTGACTATAAATGAACTTTTCTTACCAATGAATATCTTTTTCTTCATGTTTTCT-GAGGCAA-AC
* * *********** * * *
4843 ATTTAATTATAATCTATTTTAATAAAAAATANNNNNNNNNNCAACTTAAAATCAATTATAAGGTT
64 ATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAGCTTAAAATCAATTATGAGATT
** * * ** * *
4908 AT-AAAATCATTTAAACCTAGTAATAAGGGTTTCAAACGCATGC
129 ATAAAAAT-ATTTAATGCGAGTAATAAGGCTTTTGAAGGCATGG
* * * * ** ** * * * *
4951 GTAACTATAAATGGACTTTT-TCTAGCAATAAATGGCTTTTTCTTCACCTTTGT-TAAGACAGAT
1 GTGACTATAAATGAACTTTTCT-TACCAATGAATATCTTTTTCTTCATGTTT-TCTGAGGCAAAC
* * * * * * * *
5014 ATTCAATTATTATCT-GTTT-ATCCAAAAATATGAAAAAATTCAACTGAAAATTATTTATGAGAT
64 ATTCAATTATTATCTATTTTAAT-AAAAAATGTAAAAAAATTCAGCTTAAAATCAATTATGAGAT
* * **
5077 TATAAAAATATTTAAAGCGACTAATAAGGCTTTTGAAGGTGTGG
128 TATAAAAATATTTAATGCGAGTAATAAGGCTTTTGAAGGCATGG
* * * * *
5121 GTGACTATAAGT-AGACTTTTCGTT--CAATGGATATCTTTTTCTTCATG-TTTCTCAAGGTAGA
1 GTGACTATAAATGA-ACTTTTC-TTACCAATGAATATCTTTTTCTTCATGTTTTCT-GAGGCAAA
* * * ********** * * *
5182 TATTGAATTATAATCTATTTTAATAAAANNNNNNNNNNAATTCAACTTAAATTCAATTA-GAAGG
63 CATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAGCTTAAAATCAATTATG-AGA
* *
5246 TTAT-AAAATCATTTAAAGCGTGTAATAAGGCTTTTGAAGGCATGG
127 TTATAAAAAT-ATTTAATGCGAGTAATAAGGCTTTTGAAGGCATGG
********** * * * * *
5291 GTGACTATANNNNNNNNNNTCTTGCCAATGGATATCTTTTTCTTCACG-TTTCTTGAGGAAAACT
1 GTGACTATAAATGAACTTTTCTTACCAATGAATATCTTTTTCTTCATGTTTTC-TGAGGCAAACA
* * *
5355 TTCAATTATAATATGA-TTTAATAAAAAATATAAAAAAATTCA
65 TTCAATTATTATCT-ATTTTAATAAAAAATGTAAAAAAATTCA
5397 ACTTNNNNNN
Statistics
Matches: 971, Mismatches: 296, Indels: 67
0.73 0.22 0.05
Matches are distributed among these distances:
167 1 0.00
168 6 0.01
169 94 0.10
170 294 0.30
171 387 0.40
172 187 0.19
173 2 0.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
GTGACTATAAATGAACTTTTCTTACCAATGAATATCTTTTTCTTCATGTTTTCTGAGGCAAACAT
TCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATTCAGCTTAAAATCAATTATGAGATTAT
AAAAATATTTAATGCGAGTAATAAGGCTTTTGAAGGCATGG
Done.