Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397534.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2412.0, 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: 9704
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.22
Warning! 3802 characters in sequence are not A, C, G, or T
Found at i:3523 original size:172 final size:171
Alignment explanation
Indices: 3215--3538 Score: 393
Period size: 172 Copynumber: 1.9 Consensus size: 171
3205 NNNNNNNNNN
* **
3215 TATTGCTCACTTTAAATGGTTTTATAATCTCAAAATTAATTCTAAGTTCAAATTTTCTACATTTT
1 TATTACTCACTTTAAATAATTTTATAATCTCAAAATTAATTCTAAGTTCAAATTTTCTACATTTT
* * * * * *
3280 TGGTCAAAATAAATTATAATTGAATGCCTACCTCAAGAAATGTAAAGAAAAGGGCATTCATTGAG
66 TGGTCAAAACAAATTATAACTAAATGCCTACCTCAAGAAACGTAAAGAAAAAGGCATTCATTGAC
*
3345 AAGAAAATTCTATTTACAGTCACCCATTGCTTCAAAAGTCT
131 AAGAAAAGTCTATTTACAGTCACCCATTGCTTCAAAAGTCT
* * * *
3386 TATTACTCACTTTAAATAATTTTATAATCTCAAGATTGATTTTAAGTTCAAATTGTTTTACATTT
1 TATTACTCACTTTAAATAATTTTATAATCTCAAAATTAATTCTAAGTTCAAATT-TTCTACATTT
* * ** * * *
3451 GTT-GTTAAAACATATTATAACTAAATGTGTAGCTCGAA-TAACGTGAAGAAAAAGGCATTCATT
65 -TTGGTCAAAACAAATTATAACTAAATGCCTACCTC-AAGAAACGTAAAGAAAAAGGCATTCA-T
*
3514 TG-CAAGAAAAGTCTATTTATAGTCA
127 TGACAAGAAAAGTCTATTTACAGTCA
3539 NNNNNNNNNN
Statistics
Matches: 127, Mismatches: 22, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
171 48 0.38
172 72 0.57
173 7 0.06
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (171 bp):
TATTACTCACTTTAAATAATTTTATAATCTCAAAATTAATTCTAAGTTCAAATTTTCTACATTTT
TGGTCAAAACAAATTATAACTAAATGCCTACCTCAAGAAACGTAAAGAAAAAGGCATTCATTGAC
AAGAAAAGTCTATTTACAGTCACCCATTGCTTCAAAAGTCT
Found at i:6164 original size:171 final size:161
Alignment explanation
Indices: 5850--6171 Score: 305
Period size: 171 Copynumber: 1.9 Consensus size: 161
5840 NNNNNNNGTT
*
5850 TATAAAACCATTTAAAGCAAGTAATAATGCTTTCGAAGACTTGACAGACTATAAATGGACTTTCT
1 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGACTTGACAGACTATAAATGGACTTTCT
* * * * *
5915 GTGCCAATAGTTGGCTTTTGCTTCACGTTCCCCATGGCAAGAACTCGATTATAGCCTTTTTTAAC
66 ATGCCAATAGTTGCCTTTTGCTTCACGTTCCCCATGGCAAGAACTCGATTATAACCTGTTCTAAC
* * *
5980 GAAAAATGTAAAAACATTCAACTTAAACTCA
131 CAAAAACGTAAAAAAATTCAACTTAAACTCA
* ** *
6011 NNNNNNNNNNTATAAAGCCATTTAAAGTGAGTAATAAGGCATTT-GAAGGCTTGAGCA-ACTATA
1 ----------TATAAAACCATTTAAAGCAAGTAATAAGGC-TTTCGAAGACTTGA-CAGACTATA
* * *
6074 AATGGACTTCTCTAT-CCAATGAG-TGCCTTTTTCTTCACGTTTCCCATGGCAA-ACATTC-AGT
54 AATGGACTT-TCTATGCCAAT-AGTTGCCTTTTGCTTCACGTTCCCCATGGCAAGA-ACTCGA-T
*
6135 TATAATCTGTTCTAACCAAAAACGTAAAAAAATTCAA
115 TATAACCTGTTCTAACCAAAAACGTAAAAAAATTCAA
6172 GGTAAAATCA
Statistics
Matches: 128, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
170 2 0.02
171 115 0.90
172 11 0.09
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.30
Consensus pattern (161 bp):
TATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGACTTGACAGACTATAAATGGACTTTCT
ATGCCAATAGTTGCCTTTTGCTTCACGTTCCCCATGGCAAGAACTCGATTATAACCTGTTCTAAC
CAAAAACGTAAAAAAATTCAACTTAAACTCA
Found at i:7516 original size:172 final size:170
Alignment explanation
Indices: 7208--8370 Score: 899
Period size: 172 Copynumber: 6.8 Consensus size: 170
7198 NNNNNNNNNN
* * *
7208 ATTCAGTTATAATATGTTTTAACAAAAAATGTAAAATAATTTGAACTTAAAATCAATCTTGAGAT
1 ATTCAATTATAATATGTTTTAACAAAAAATGTAAAA-AATTTGAACTTAGAATCAATTTTGAGAT
* * * * * * * * *
7273 TATAAAATCGTTTAAAGAGAGTAATAAGGCTTTTGAAGCAATGGGTAACTGTAAATATAGTTTTT
65 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GACTTTTC
* ** * *
7338 TTGCCAATGAATGCCATTTTCTTTACATTTCTCGAGATAAAC
129 TTGCCAATGAATGCCTTTTTCTTTACATTTCTAAAGGTAGAC
* * * * *
7380 ATTCAATAATAATTTGTTTTAACTAAAAATGTAAAACAATTTGAGCTTAGAATAAATTTTGAGAT
1 ATTCAATTATAATATGTTTTAACAAAAAATGTAAAA-AATTTGAACTTAGAATCAATTTTGAGAT
* * * * *
7445 TATAAAACCATTGAAAGTGAGCAATAATG-TTACTGAAGGAATGAGTGACTATAAATGTACTTTT
65 TATAAAACCATTTAAAGTGAGTAATAAGGCTT-TTGAAGGAATGGGTGACTATAAATG-ACTTTT
* ** **********
7509 CTTGCCAATGAATGCTTTTTTCTTTATGTTTCTNNNNNNNNNN
128 CTTGCCAATGAATGCCTTTTTCTTTACATTTCTAAAGGTAGAC
* * * * * * *
7552 ATTCAATTATAGTCTATTTCAGCCAAAAATGTAAAAAAGTTT-AACTTAGAATC-TTTTATG-GC
1 ATTCAATTATAATATGTTTTAACAAAAAATGTAAAAAA-TTTGAACTTAGAATCAATTT-TGAG-
* * *
7614 ATTATAAAACCATTTAAAGTGAGTAATGAGGCTTTTAAAGGTATGGGTGACTATAAATAGACTTT
63 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GACTTT
* ** *
7679 TCTTGCCAATGAATGCTTTTTTCTTTATGTTTCTAAAGGTAGGC
127 TCTTGCCAATGAATGCCTTTTTCTTTACATTTCTAAAGGTAGAC
* * * * * * * ** * *
7723 ATTCAATTCTAGTCTGTTCTAATAAAAAATGATCGAAGAATTCAAATTTA-AATAAATTTTGAGA
1 ATTCAATTATAATATGTTTTAACAAAAAATG-T-AAAAAATTTGAACTTAGAATCAATTTTGAGA
* * * * * *********
7787 TTACAAAACCTTTTAAAGTCAGAAATAAGGCTTTTAAAGGAATGGGTGACNNNNNNNNNNCTTTT
64 TTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC-TATAAATGACTTTT
* * * * ** *
7852 TTTGCCAATGAATGCCTTCTTC-TT-CATGTTATTCAAGCCACAC
128 CTTGCCAATGAATGCCTTTTTCTTTACAT-TT-CTAAAGGTAGAC
* * * *
7895 ATTCAGTTATAATATGTTTTAACAAAAAATATAAAACAATTTGAACTTAAAATCAATCTTGAGAT
1 ATTCAATTATAATATGTTTTAACAAAAAATGTAAAA-AATTTGAACTTAGAATCAATTTTGAGAT
** * *
7960 TATAAAGGCATTTAAAGTGAGTAATAAGGCTTTTGAAGCAATGGGTGACTATAAATAGAATTTTC
65 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GACTTTTC
** ** *
8025 TTATCAATGAATGCCCGTTTCTTTACATTTCTAGAGGTAGAC
129 TTGCCAATGAATGCCTTTTTCTTTACATTTCTAAAGGTAGAC
* * *
8067 ATTCAATTATAATTTGTTTTAACCAAAAACGTAAAAACATTTGAACTTAGAATCAATTTTGAGAT
1 ATTCAATTATAATATGTTTTAACAAAAAATGTAAAAA-ATTTGAACTTAGAATCAATTTTGAGAT
* * *
8132 TATAAAACTATTTAAAGTGAGCAATAATGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTC
65 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GACTTTTC
* * ** * *
8197 TTACCATTGAATGCCTTTTTC-TTATGTTTCTCAAGGTAGAT
129 TTGCCAATGAATGCCTTTTTCTTTACATTTCTAAAGGTAGAC
* * * * * * * * *
8238 ATTTAATTATAGTCTACTTTT-GCCAAAAATGTAAAACAA-TTCAACTTAAAATCAATTATG-GC
1 ATTCAATTATAATAT-GTTTTAACAAAAAATGTAAAA-AATTTGAACTTAGAATCAATTTTGAG-
* ** * * **
8300 ATTGTAAAACCATTTAAAGCAAGTAATAAGGCTTTTTGATGGTATGAATGACTATAAATAGACTT
63 ATTATAAAACCATTTAAAGTGAGTAATAAGGC-TTTTGAAGGAATGGGTGACTATAAAT-GACTT
8365 TTCTTG
126 TTCTTG
8371 TNNNNNNNNN
Statistics
Matches: 773, Mismatches: 193, Indels: 51
0.76 0.19 0.05
Matches are distributed among these distances:
169 1 0.00
170 51 0.07
171 213 0.28
172 488 0.63
173 17 0.02
174 3 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
ATTCAATTATAATATGTTTTAACAAAAAATGTAAAAAATTTGAACTTAGAATCAATTTTGAGATT
ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGACTTTTCTT
GCCAATGAATGCCTTTTTCTTTACATTTCTAAAGGTAGAC
Done.