Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400133.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3349.0, 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: 6229
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.23
Warning! 2475 characters in sequence are not A, C, G, or T
Found at i:2247 original size:171 final size:171
Alignment explanation
Indices: 1937--2305 Score: 424
Period size: 171 Copynumber: 2.2 Consensus size: 171
1927 NNNNNNNNNN
* * * *
1937 TACTGGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGCTGAAATTTTTGACATTTTTTG
1 TACTCGCTTTAAACAGTTTTATAATCTCATAATTGATTTTAAGATGAAATTTTTGACATTTTTTA
* * *
2002 TTAAAACTGACTATTATTAAATTCTTGCCTTGAAAAACAAGCATAAAAAACCATTCATTGAGAAG
66 TTAAAACTGACTATAATTAAATTCTTGCCTTGAAAAACAAGAAGAAAAAACCATTCATTGAGAAG
* *
2067 AAAAGTCCATTTAAAGTCACCCATTCCTTCAAAAAGTTTAT
131 AAAAGTCCATTTAAAGTCACCCACTCCTTCAAAAAGCTTAT
* * * * * *
2108 TACTTGCTTTAAACGGTTTTGTAATCTCATAATTGATTTTAA-ATTAAATTTTTTTACGTTTTTT
1 TACTCGCTTTAAACAGTTTTATAATCTCATAATTGATTTTAAGATGAAA-TTTTTGACATTTTTT
* * ** * * *
2172 ATTAACATCT-ACTATAATTAAAAGTT-TT-CCTTGAGAAACGTGAAGAAACAAGCGTTCATTG-
65 ATTAA-AACTGACTATAATT-AAA-TTCTTGCCTTGAAAAACAAGAAGAAAAAACCATTCATTGA
* * *
2233 GCAAGAATAGTCCATTTATAGTCACCTACTCCTTCAAAAAGCTTAT
127 G-AAGAAAAGTCCATTTAAAGTCACCCACTCCTTCAAAAAGCTTAT
*
2279 TACTCACTTTAAACAGTTTTATAATCT
1 TACTCGCTTTAAACAGTTTTATAATCT
2306 NNNNNNNNNN
Statistics
Matches: 165, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
170 5 0.03
171 150 0.91
172 8 0.05
173 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (171 bp):
TACTCGCTTTAAACAGTTTTATAATCTCATAATTGATTTTAAGATGAAATTTTTGACATTTTTTA
TTAAAACTGACTATAATTAAATTCTTGCCTTGAAAAACAAGAAGAAAAAACCATTCATTGAGAAG
AAAAGTCCATTTAAAGTCACCCACTCCTTCAAAAAGCTTAT
Found at i:2929 original size:171 final size:170
Alignment explanation
Indices: 2626--2979 Score: 437
Period size: 171 Copynumber: 2.1 Consensus size: 170
2616 NNNNNNNNNN
* *
2626 AAATGGTTTTATAATCTCACAATTAATTTTAAGTTGAATGTTTTTACATTTTTTGTTAAAACAGA
1 AAATGGTTTTATAATCTCACAAATAATTTTAAGTTGAATGTTTTTACATTTTTAGTTAAAACAGA
* ** * *
2691 CTGTAATTAAATTTTTACCTCAGGAACTAGCAAGAAACAAGCATTCATTGACAAGAAAAGCCCAT
66 CTATAATTAAATACTTACCTCAGAAACTA-CAAGAAACAAGCATTCATTGACAAAAAAAGCCCAT
**
2756 TTAGAGTCACCCATTGCTTCAAAAAGCTTATTACTCGCTGT
130 TTAGAGTCACCCATCCCTTCAAAAAGCTTATTACTCGCTGT
* * ** *
2797 AAATAGTTTTATAATCTCATAAATGCTTTTAAGTTGAAT-TGTTTTACATTTTTAGTTAAAACAT
1 AAATGGTTTTATAATCTCACAAATAATTTTAAGTTGAATGT-TTTTACATTTTTAGTTAAAACAG
*
2861 ACTATAATTAAATACTTACCTCGAGAAACGT-CTAA-AAA-AAGCTATTCATTGACAAAAAAAGG
65 ACTATAATTAAATACTTACCTC-AGAAAC-TAC-AAGAAACAAGC-ATTCATTGACAAAAAAAGC
* * * * * *
2923 CCATTTATAGTCACTCATCCCTTTAAAAGGCTTATTACTTGCTTT
126 CCATTTAGAGTCACCCATCCCTTCAAAAAGCTTATTACTCGCTGT
2968 AAATGGTTTTAT
1 AAATGGTTTTAT
2980 NNNNNNNNNN
Statistics
Matches: 156, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
170 5 0.03
171 143 0.92
172 7 0.04
173 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (170 bp):
AAATGGTTTTATAATCTCACAAATAATTTTAAGTTGAATGTTTTTACATTTTTAGTTAAAACAGA
CTATAATTAAATACTTACCTCAGAAACTACAAGAAACAAGCATTCATTGACAAAAAAAGCCCATT
TAGAGTCACCCATCCCTTCAAAAAGCTTATTACTCGCTGT
Found at i:5385 original size:170 final size:157
Alignment explanation
Indices: 5171--5502 Score: 310
Period size: 170 Copynumber: 2.0 Consensus size: 157
5161 AATTAAACTT
* *
5171 AAAATCAATTATGAGGTTATAAAACCATTTAAAGCGAATAATAAGCCTTTTAAAGGGATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAGCCTTTTAAAGGCATGGGTGA
* * ** * * **
5236 CTATAAATGGAATTTTTTTGTCAATGAATAG-T-TTTTTTGGACATTTCTTGA-GGTAAGCATTT
66 CTATAAATGGAATTTTCTTGTCAATGAAT-GCTGTTTCTTCCA-AGTTCCT-ATGGTAAAAATTT
*
5298 AATTATAGTCTGTTTTAACCAAAAATGTAA
128 AATTATAGTCTGTTTTAACAAAAAATGTAA
* * * * * *
5328 AANNNNNNNNNNNNNAATCATTTATGAGATTATAAAACTATTTAGAGCGAGTAATAAGCTTTTTG
1 AA-------------AATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAGCCTTTTA
* **
5393 AAGGCATGGGTGACTCTAAATGGGCTTTTCTTGTCAATGAATGCCTGTTTCTTCCAAGTTCCTAT
53 AAGGCATGGGTGACTATAAATGGAATTTTCTTGTCAATGAATG-CTGTTTCTTCCAAGTTCCTAT
5458 GGTAAAAATTTAATTATAGTCTGTTTTAACAAAAAATGTAA
117 GGTAAAAATTTAATTATAGTCTGTTTTAACAAAAAATGTAA
5499 AAAA
1 AAAA
5503 ATTCAACTTN
Statistics
Matches: 138, Mismatches: 20, Indels: 33
0.72 0.10 0.17
Matches are distributed among these distances:
157 2 0.01
158 2 0.01
169 1 0.01
170 81 0.59
171 46 0.33
172 6 0.04
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.35
Consensus pattern (157 bp):
AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAGCCTTTTAAAGGCATGGGTGA
CTATAAATGGAATTTTCTTGTCAATGAATGCTGTTTCTTCCAAGTTCCTATGGTAAAAATTTAAT
TATAGTCTGTTTTAACAAAAAATGTAA
Done.