Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400298.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3504.0, 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: 8367
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.26
Warning! 2188 characters in sequence are not A, C, G, or T
Found at i:5002 original size:173 final size:161
Alignment explanation
Indices: 4695--5024 Score: 301
Period size: 173 Copynumber: 2.0 Consensus size: 161
4685 AAAATTTTAG
* * *
4695 CTTAAAATCAATTATTAGATTATAAAACTATTAAAGTGAGTAATAAGGCTTTTGAAGGAATTGAA
1 CTTAAAATCAAGTATGAGATTATAAAACTATTAAAGTGAGTAATAAGACTTTTGAAGGAATTGAA
* * * ** *
4760 GGCTACAAATCGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATTTTTCTCAAGGAAAACATTC
66 GACTACAAATCGACTTTTCTTGCCAATGAATACTTTTTCCTTCACGTTTCTCAAGGAAAACACTC
4825 AATTA-TAGTCTGTTTTAATGAAAAATGTNNNNNNNNNNTGAA
131 AATTATTA-TCTGTTTTAAT-AAAAATGT----------TGAA
*
4867 CTTAAAATCAAGTATGAGATTATAAAA-TCATTTAAAGTGAGTAATGAGACTTTTGAAGGAA-TG
1 CTTAAAATCAAGTATGAGATTATAAAACT-A-TTAAAGTGAGTAATAAGACTTTTGAAGGAATTG
* * * * * ** *
4930 -AGTTACTATAAATGGACTTTTCTTTG-TAATGAGTACTTTTTCCTTCACGTTTCTCGAGTTAGA
64 AAG--ACTACAAATCGACTTTTC-TTGCCAATGAATACTTTTTCCTTCACGTTTCTCAAGGAAAA
*
4993 CACTCAATTATTATTTGTTTTAATAAAAATGT
126 CACTCAATTATTATCTGTTTTAATAAAAATGT
5025 AAAAACATTC
Statistics
Matches: 133, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
171 3 0.02
172 36 0.27
173 89 0.67
174 5 0.04
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.38
Consensus pattern (161 bp):
CTTAAAATCAAGTATGAGATTATAAAACTATTAAAGTGAGTAATAAGACTTTTGAAGGAATTGAA
GACTACAAATCGACTTTTCTTGCCAATGAATACTTTTTCCTTCACGTTTCTCAAGGAAAACACTC
AATTATTATCTGTTTTAATAAAAATGTTGAA
Found at i:5097 original size:170 final size:166
Alignment explanation
Indices: 4570--5398 Score: 592
Period size: 170 Copynumber: 4.8 Consensus size: 166
4560 NNNNNNNNNN
* * *
4570 AGGCTTTTGAAGGAATGGGTGACTATAAATGCACTTTTCTTGTCAATGAATGCTCTTTTCTTTAC
1 AGGCTTTTGAAGGAATGAGT-ACTATAAATGGACTTTTCTTGT-AATGAATGCT-TTTTCTTCAC
* * *
4635 GTTTCTCGAGATAGATC-TTCAATTATAGTCTGTTTTAATAAAGAATCTAAAAAATTTTAGCTTA
63 GTTTCTCGAGATAGA-CATTCAATTATAGTCTGTTTTAATAAA-AATGTAAAAAA-TTCAACTTA
* *
4699 AAATCAATTATTAGATTATAAAACTA-TTAAAGTGAGTAATA
125 AAATCAACTATTAGATTATAAAACCATTTAAAGTGAGTAATA
* * * *
4740 AGGCTTTTGAAGGAATTGAAG-GCTACAAATCGACTTTTCTTGCCAATGAATGCTTTTTTCTTCA
1 AGGCTTTTGAAGGAA-TG-AGTACTATAAATGGACTTTTCTTG-TAATGAATGC-TTTTTCTTCA
** * * ******* *
4804 TTTTTCTCAAGGA-AAACATTCAATTATAGTCTGTTTTAATGAAAAATGTNNNNNNNNNNTGAAC
62 CGTTTCTCGA-GATAGACATTCAATTATAGTCTGTTTTAAT-AAAAATGT---AAAAAATTCAAC
* * * *
4868 TTAAAATCAAGTATGAGATTATAAAATCATTTAAAGTGAGTAATG
122 TTAAAATCAACTATTAGATTATAAAACCATTTAAAGTGAGTAATA
* * *
4913 AGACTTTTGAAGGAATGAGTTACTATAAATGGACTTTTCTTTGTAATGAGTACTTTTTCCTTCAC
1 AGGCTTTTGAAGGAATGAG-TACTATAAATGGACTTTTC-TTGTAATGAATGCTTTTT-CTTCAC
* * * *
4978 GTTTCTCGAGTTAGACACTCAATTATTA-TTTGTTTTAATAAAAATGTAAAAACATTCAACTCAA
63 GTTTCTCGAGATAGACATTCAATTA-TAGTCTGTTTTAATAAAAATGTAAAAA-ATTCAACTTAA
**
5042 AATCAACTATTAGATTATAAAACCATTTAAAGCAAGTAATA
126 AATCAACTATTAGATTATAAAACCATTTAAAGTGAGTAATA
********* * *
5083 AGGCTTTTGAAGGAATGNNNNNNNNNNAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCAC
1 AGGCTTTTGAAGGAATG-AGTACTATAAATGGACTTTTCTTG-TAATGAATGC-TTTTTCTTCAC
* * * *
5148 ATTTCTCGAGA-AAAAATTTCAATTATAGCCTGTTTTAATGAAAAATG-AGAAAACATTCAACTT
63 GTTTCTCGAGATAGACA-TTCAATTATAGTCTGTTTTAAT-AAAAATGTA-AAAA-ATTCAACTT
* * **********
5211 AAAATCAATTATGAGATTATAANNNNNNNNNNAGTGAGTAATA
124 AAAATCAACTATTAGATTATAAAACCATTTAAAGTGAGTAATA
* * * * * * *
5254 TGGCTTTTGAAGGAAAGGGTGACTAGAAATGGACTTTTCTTGTCAGTGAATACTTTTTTCTTCAA
1 AGGCTTTTGAAGGAATGAGT-ACTATAAATGGACTTTTCTTGT-AATGAATGC-TTTTTCTTCAC
* * * * * * * *
5319 GTTTCTTGAGACAAATATTCAATTATAGTTTGTTTGAATAATAAATGCAAAAAAATTCAACCTAA
63 GTTTCTCGAGATAGACATTCAATTATAGTCTGTTTTAATAA-AAATG-TAAAAAATTCAACTTAA
* *
5384 AATCAATTATGAGAT
126 AATCAACTATTAGAT
5399 NNNNNNNNNN
Statistics
Matches: 514, Mismatches: 114, Indels: 61
0.75 0.17 0.09
Matches are distributed among these distances:
169 9 0.02
170 194 0.38
171 169 0.33
172 53 0.10
173 84 0.16
174 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.36
Consensus pattern (166 bp):
AGGCTTTTGAAGGAATGAGTACTATAAATGGACTTTTCTTGTAATGAATGCTTTTTCTTCACGTT
TCTCGAGATAGACATTCAATTATAGTCTGTTTTAATAAAAATGTAAAAAATTCAACTTAAAATCA
ACTATTAGATTATAAAACCATTTAAAGTGAGTAATA
Found at i:6520 original size:171 final size:171
Alignment explanation
Indices: 6119--6707 Score: 480
Period size: 171 Copynumber: 3.4 Consensus size: 171
6109 NNNNNNNNNN
* * * * * *
6119 CAACTTAAAATCAATTATGAGATTATAAAACCATTTGAAGTGAGTAATATGGCTATAGAAGGAAA
1 CAACCTAAAATCAATTATGAGATTAGAAAACCATTTGAAGTGAGTAATAAGGCTTTTGAAGGAAT
* * * * *
6184 AGATGACTATAAATGGACTTTTCTTGTCAGTGAATGCTCTTTTTTTTACGTTTCTTAAGATAAAT
66 GGATGACTATAAATGGACTTTTCTTGTCAATAAATGCTCTTTTCTTCACGTTTCTTAAGATAAAT
*
6249 ATTCAATTATAGTCTGTTTGAATCAGAAATGTAAAAAAATC
131 ATTCAATTATAGTCTGTTTGAATCAAAAATGTAAAAAAATC
* * **********
6290 CAACCTAAAATCAATTATGAGATTAGAAAACCATTGGAAGCGANNNNNNNNNNTTTTGAAGGAAT
1 CAACCTAAAATCAATTATGAGATTAGAAAACCATTTGAAGTGAGTAATAAGGCTTTTGAAGGAAT
* * *
6355 GGGTGATTATAAATGGACTTTTCTTGTCAATAAATGCTCTTTTCTTCACGTTTC-TATAGATAGA
66 GGATGACTATAAATGGACTTTTCTTGTCAATAAATGCTCTTTTCTTCACGTTTCTTA-AGATAAA
* * * *
6419 TATTTAATTATAGTCTGTTTTAATCAAAAATGTAAAAAATTT
130 TATTCAATTATAGTCTGTTTGAATCAAAAATGTAAAAAAATC
* ********** *
6461 CAACTTAAAATCAATTNNNNNNNNNNAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
1 CAACCTAAAATCAATTATGAGATTAGAAAACCATTTGAAGTGAGTAATAAGGCTTTTGAAGGAAT
* ** * * * * * * * ** **
6526 GAGA-GGCTGCAAATAGACTTTTCTAGCCAATGAATGCTTTTTTCTTCATGCTTCCCAAGGCAAA
66 G-GATGACTATAAATGGACTTTTCTTGTCAATAAATGCTCTTTTCTTCACGTTTCTTAAGATAAA
* * * ** * *
6590 CATTCAATTATAGCCTGTTTTAAAGAAAAATATAAAAAAAATT
130 TATTCAATTATAGTCTGTTTGAATCAAAAATGT-AAAAAAATC
* * * * * * * *
6633 GAACTTAAAATCAAGTAAGAAATTATAAAACCATTTCAAGTGAGTAATAAGGCTTTTGAAAGAAT
1 CAACCTAAAATCAATTATGAGATTAGAAAACCATTTGAAGTGAGTAATAAGGCTTTTGAAGGAAT
*
6698 GGGTGACTAT
66 GGATGACTAT
6708 NNNNNNNNNN
Statistics
Matches: 318, Mismatches: 95, Indels: 9
0.75 0.23 0.02
Matches are distributed among these distances:
170 2 0.01
171 251 0.79
172 65 0.20
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.33
Consensus pattern (171 bp):
CAACCTAAAATCAATTATGAGATTAGAAAACCATTTGAAGTGAGTAATAAGGCTTTTGAAGGAAT
GGATGACTATAAATGGACTTTTCTTGTCAATAAATGCTCTTTTCTTCACGTTTCTTAAGATAAAT
ATTCAATTATAGTCTGTTTGAATCAAAAATGTAAAAAAATC
Done.