Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399236.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2505.0, 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: 9120
ACGTcount: A:0.23, C:0.08, G:0.07, T:0.25
Warning! 3307 characters in sequence are not A, C, G, or T
Found at i:5278 original size:17 final size:17
Alignment explanation
Indices: 5256--5292 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5246 GAAAATAATA
* *
5256 TCCATTGGGAAGAGAAG
1 TCCATTGGCAAGAAAAG
5273 TCCATTGGCAAGAAAAG
1 TCCATTGGCAAGAAAAG
5290 TCC
1 TCC
5293 GTTTATAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (17 bp):
TCCATTGGCAAGAAAAG
Found at i:5672 original size:171 final size:160
Alignment explanation
Indices: 5545--5918 Score: 345
Period size: 170 Copynumber: 2.2 Consensus size: 160
5535 NNNNNNNNNN
* *
5545 TTTTTTTATATTTTTTATTAAAATAAATTATAATTGAATGTCTATC-TCAAAAAACGTGAAGAAA
1 TTTTTTTATATTTTTTATT-AAACAAATTATAATTGAATGTCTACCTTC-AAAAACGTGAAGAAA
*
5609 AAGATATCCATTGGCAAGAAAAGTCTATTTATAGACGCNNNNNNNNNNAAAAGCCTTATTACTCG
64 AAGATATCCATTGACAAGAAAAGTCTATTTATAGACGC----------AAAAGCCTTATTACTCG
*
5674 CTTTAAATGATTTTATAACCTCATCATTGATTTTGATTTGAT
119 CTTTAAATGATTTTATAACCTCATAATTGATTTTGATTTGAT
* * * **
5716 TTTTTTTATATTTTTTATTAAACAGATTATAATTGAATGTTTCCCTTCGGAAACGTGAAGAAAAA
1 TTTTTTTATATTTTTTATTAAACAAATTATAATTGAATGTCTACCTTCAAAAACGTGAAGAAAAA
* * ** *
5781 GATATCCGTTGATAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGGTTTAGTACTCGCT
66 GATATCCATTGACAAGAAAAGTCTATTTATAG--A--C--G----CAAAAGCCTTATTACTCGCT
* * * * *
5846 TTAAATGATTTTAAAAGCTCATAATTCATTTTAATTTGAA
121 TTAAATGATTTTATAACCTCATAATTGATTTTGATTTGAT
* *
5886 TTTTTTTAAATTTTTTATTAAAACAGATTATAA
1 TTTTTTTATATTTTTTATT-AAACAAATTATAA
5919 NNNNNNNNNN
Statistics
Matches: 171, Mismatches: 20, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
170 133 0.78
171 34 0.20
172 1 0.01
174 1 0.01
176 1 0.01
180 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.40
Consensus pattern (160 bp):
TTTTTTTATATTTTTTATTAAACAAATTATAATTGAATGTCTACCTTCAAAAACGTGAAGAAAAA
GATATCCATTGACAAGAAAAGTCTATTTATAGACGCAAAAGCCTTATTACTCGCTTTAAATGATT
TTATAACCTCATAATTGATTTTGATTTGAT
Found at i:5992 original size:171 final size:170
Alignment explanation
Indices: 5349--6097 Score: 642
Period size: 171 Copynumber: 4.4 Consensus size: 170
5339 NNNNNNNNNN
* * *
5349 ACCTCATAATTGATTTTAATTTTAATTTTTTTATATTTTTTATTAAAACTGATTCTAATTGAATG
1 ACCTCATAATT-ATTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATG
* * * * * *
5414 TTTTCCATAAGAAAC-GGAAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTAACCC
65 TTTCCCTTAAGAAACATG-AAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCC
** * *
5478 ATGCCTTGGAAAG-TCTCATTACTCGCTTTAAAT-ATTTTTATA
129 ATGCCTTCAAAAGAT-TTAGTACTCGCTTTAAATGA-TTTTATA
* ********** * *
5520 ATCTCATAATTGATTNNNNNNNNNNTTTTTTTATATTTTTTATTAAAATAAATTATAATTGAATG
1 ACCTCATAATT-ATTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATG
* ** * * * * * * * ***
5585 TCTATCTCAAAAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCTATTTATAGACGCNNN
65 TTTCCCTTAAGAAACATGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCA
******* ** *
5650 NNNNNNNAAAAGCCTTATTACTCGCTTTAAATGATTTTATA
130 TGCCTTCAAAAGATTTAGTACTCGCTTTAAATGATTTTATA
* * *
5691 ACCTCATCATTGATTTTGATTTGATTTTTTTTATATTTTTTATT-AAACAGATTATAATTGAATG
1 ACCTCATAATT-ATTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATG
** * * * *
5755 TTTCCCTTCGGAAACGTGAAGAAAAAGATATCCGTTGATAAGAAAAGTCTATTTATAGTCACCCA
65 TTTCCCTTAAGAAACATGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCA
* *
5820 TGCCTTCAAAAGGTTTAGTACTCGCTTTAAATGATTTTAAA
130 TGCCTTCAAAAGATTTAGTACTCGCTTTAAATGATTTTATA
* * *******
5861 AGCTCATAATTCATTTTAATTTGAATTTTTTTAAATTTTTTATTAAAACAGATTATAANNNNNNN
1 ACCTCATAATT-ATTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATG
**** * * * *
5926 NNNGCCTTAAGAAACATGAAGAAAAAGCTATCCATTGGCAAGAAGAGTCCATTTATAGTTACCCA
65 TTTCCCTTAAGAAACATGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCA
* * **
5991 TGCCTTCAAAAGATTTATTAATATCTTTAAATGATTTTATA
130 TGCCTTCAAAAGATTTAGTACTCGCTTTAAATGATTTTATA
* * *
6032 ACCTCATAATTAGTTTTAATTTGAATTTTATTATATTTTTCATTAAAACAGATTATAGTTGAATG
1 ACCTCATAATTA-TTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATG
6097 T
65 T
6098 CNNNNNNNNN
Statistics
Matches: 447, Mismatches: 126, Indels: 10
0.77 0.22 0.02
Matches are distributed among these distances:
170 137 0.31
171 308 0.69
172 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.39
Consensus pattern (170 bp):
ACCTCATAATTATTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGT
TTCCCTTAAGAAACATGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCAT
GCCTTCAAAAGATTTAGTACTCGCTTTAAATGATTTTATA
Found at i:7826 original size:171 final size:168
Alignment explanation
Indices: 7649--9120 Score: 1034
Period size: 171 Copynumber: 8.7 Consensus size: 168
7639 NNNNNNNNNN
* * *
7649 GAAGAAAAAGATATCCATTGATAAAAAATGTCCATTTGTAGTCACCCATGCCTTCTAAAGCCTAA
1 GAAGAAAAAGATATCCATTGATAAAAAA-GTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
* * * *
7714 TTACTCGATTTAAATAGTTTTTA-AATCTCATAATT-AGTTTTAAGTTGAACTTTTTTATATTTT
65 TTACTCGCTTTAAAT-GATTTTATAACCTCATAATTGA-TTTTAATTTGAA-TTTTTTATATTTT
* *
7777 TTATTAAAATTGATTATAATTATATGTTTACCTCAAGAAACGT
127 TTATTAAAATAGATTATAATTA-ATGTTTACCTCGAGAAACGT
* * * * ** *
7820 GAAGAAAAAGATATCTATT-AGTAAAAAAACTCTATTTATAGACACTGATACCTTCAAAAGCCTT
1 GAAGAAAAAGATATCCATTGA-T-AAAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTT
* * * *********
7884 ATTCCTCGGTTTAAATGATTTTATAACCTCATAATTGATTTTGATTTNNNNNNNNNNATATTTTT
64 ATTACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAATTT-GAATTTTTTATA-TTTT
* * *
7949 TTATTAAAACAGATTATAATTGAATGTTTGCC-CTAGGAAACGT
127 TTATTAAAATAGATTATAATT-AATGTTTACCTCGA-GAAACGT
* * * *
7992 GAACAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCATCCATGCCTTCAAAAGCTTTA
1 GAAGAAAAAGATATCCATTGATAA-AAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
* ********** * * *
8057 GTACNNNNNNNNNNTGATTTTATAAGCTCATAATTGATGTTAATTTGAATTTTTTTAAATTTTTT
65 TTACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAA-TTTTTTATATTTTTT
* * **
8122 ATTAAAACAGATTATAATTAAATGTCTACCTTAAGAAACGT
129 ATTAAAATAGATTATAATT-AATGTTTACCTCGAGAAACGT
* * **
8163 GAA-AAAAA-A-ATCAATT-AGTAAGAAAAGTCCATTTCTAGTCACCCATGCCTTCGTAAGCCTT
1 GAAGAAAAAGATATCCATTGA-TAA-AAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTT
* * * * * * * *
8224 ATTATTTGCTTTAAAT-ACTTTTTTAATCTTATAA-TAAGTTTTAACTTCAACTTTTTTATATTT
64 ATTACTCGCTTTAAATGA-TTTTATAACCTCATAATTGA-TTTTAATTTGAA-TTTTTTATATTT
* * * *
8287 ATTATTAAAATAAATTATAGTTATATGTTTACCTCGAGAAGCGT
126 TTTATTAAAATAGATTATAATTA-ATGTTTACCTCGAGAAACGT
* * * * *
8331 GAAAAAAAAGATATCCATTCG-CAAGAAAGTACA-TTATAGTCACCGATGCCTTCAAAAGCCTTA
1 GAAGAAAAAGATATCCATT-GATAAAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
********** *
8394 TTACTCGCTTTAAANNNNNNNNNNACCTCATAATTGATTTTAATTTGAATTTTTATATAATTTTT
65 TTACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTTTT-TATATTTTTT
* ** * * * *
8459 ATTCAAACGGATTATAATTGAATATCTGCCTCGAGAAACAT
129 ATTAAAATAGATTATAATT-AATGTTTACCTCGAGAAACGT
* * ********** * **
8500 GAAGAAAAAGATATTCATTGGTAAGAAAAGTCCNNNNNNNNNNACTCATGCCTTTGAAAGCCTTA
1 GAAGAAAAAGATATCCATTGATAA-AAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
* * *
8565 TTACTCGCTTTAAAT-ATTTTTATAAACTCGTAATTGATTTTAATTTGAAATTTTTTATATGTTT
65 TTACTCGCTTTAAATGA-TTTTATAACCTCATAATTGATTTTAATTTG-AATTTTTTATATTTTT
* * ** *
8629 TATTAAAATAGATTATAATCGAATTTTTGTCTTGAGAAACGT
128 TATTAAAATAGATTATAAT-TAATGTTTACCTCGAGAAACGT
********* * *
8671 GAAGAAAAAGATATCNNNNNNNNNNAAAAGTCCATTTATAGTCACCGATGCCATCAAAAGCCTTA
1 GAAGAAAAAGATATC-CATTGATAAAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
* *
8736 TTACTTGCTTTAAATGATTTTATAACCTCATAATTGATTTGAATTT-AGATTTTTTATA-TTTTT
65 TTACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGA-ATTTTTTATATTTTTT
* *
8799 ATTAAAATAGTTTATAATTGAATGTTTACCTCGAGAAATGT
129 ATTAAAATAGATTATAATT-AATGTTTACCTCGAGAAACGT
* ** * * * *
8840 GAAGAAAAATATATCCATTGGCAAGAAATGTCCATTTATAGTTACCCATCCCTTCAAAAGCTTTA
1 GAAGAAAAAGATATCCATTGATAA-AAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTA
********** *
8905 TTACTCGCTTTAAATGATTTTATANNNNNNNNNNTGATTTTAATTTAAATTTTTTTATATTTTTT
65 TTACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAA-TTTTTTATATTTTTT
* * * * ** *
8970 ACTAAAACAGATTATAATTGAATCTTTGCCTTAAGAAACAT
129 ATTAAAATAGATTATAATT-AATGTTTACCTCGAGAAACGT
* ** * * **
9011 GAAGAAAAAGCTATCCATTGGCAAAAAAGTCCATTTATAGT-AGCTCATGGCTTCGGAAGCCTTA
1 GAAGAAAAAGATATCCATTGATAAAAAAGTCCATTTATAGTCA-CCCATGCCTTCAAAAGCCTTA
* *
9075 TTACTCACTTTAAAT-ATTTTTATAAACTCATAATTGATTTTAATTT
65 TTACTCGCTTTAAATGA-TTTTATAACCTCATAATTGATTTTAATTT
Statistics
Matches: 984, Mismatches: 276, Indels: 83
0.73 0.21 0.06
Matches are distributed among these distances:
167 5 0.01
168 123 0.12
169 240 0.24
170 113 0.11
171 365 0.37
172 136 0.14
173 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (168 bp):
GAAGAAAAAGATATCCATTGATAAAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTAT
TACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTTTTTATATTTTTTAT
TAAAATAGATTATAATTAATGTTTACCTCGAGAAACGT
Done.