Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398326.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1626.0, 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: 10526
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.21
Warning! 4219 characters in sequence are not A, C, G, or T
Found at i:4394 original size:170 final size:170
Alignment explanation
Indices: 4084--4440 Score: 427
Period size: 170 Copynumber: 2.1 Consensus size: 170
4074 CTCAAGGCAG
* *
4084 ACATTTAATTATAATCTATTTTAACTAAAATAAAAAAACATTCAACTTAAAATCATTTATGAGAT
1 ACATTTAATTATAATCTATTTTAACAAAAATAAAAAAACATTCAACTAAAAATCATTTATGAGAT
* * * **********
4149 TATAAAATCATTTAAATCGAGAAATAAGGCTTTTGAAGGCATGGGTGANNNNNNNNNNACTTGTC
66 TATAAAACCATTTAAAGCGAGAAATAAGGCTTTTGAAGGCAAGGGTGACTATAAATGGACTTGTC
** *
4214 TTGCAAATGAA-AGGCTTTTCCTTCACGTTT-TTGA-GACAA
131 TTAAAAATGAATA-GCTTTTCCTTCAAGTTTCTTGATG-CAA
*
4253 ACATTTAATTATAATCTATTTTAACCAAAAATACAAAAAA-ATTTAACTCAAAAAT-ATTTATGA
1 ACATTTAATTATAATCTATTTTAA-CAAAAATA-AAAAAACATTCAACT-AAAAATCATTTATGA
*
4316 GATTATAAAACCATTTAAAGCGAGAAATAAGGCTTTTGAAGGTAAGGGTGACTATAAATGGACTT
63 GATTATAAAACCATTTAAAGCGAGAAATAAGGCTTTTGAAGGCAAGGGTGACTATAAATGGACTT
* * *
4381 TTCTTAAAAATGAATAGCTTTTCCTTCAAGTTTCTTGATGTAG
128 GTCTTAAAAATGAATAGCTTTTCCTTCAAGTTTCTTGATGCAA
4424 ACATTTAATTATAATCT
1 ACATTTAATTATAATCT
4441 GNNNNNNNNN
Statistics
Matches: 159, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
169 24 0.15
170 100 0.63
171 34 0.21
172 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.34
Consensus pattern (170 bp):
ACATTTAATTATAATCTATTTTAACAAAAATAAAAAAACATTCAACTAAAAATCATTTATGAGAT
TATAAAACCATTTAAAGCGAGAAATAAGGCTTTTGAAGGCAAGGGTGACTATAAATGGACTTGTC
TTAAAAATGAATAGCTTTTCCTTCAAGTTTCTTGATGCAA
Found at i:5198 original size:171 final size:168
Alignment explanation
Indices: 4748--5210 Score: 454
Period size: 171 Copynumber: 2.7 Consensus size: 168
4738 NNNNNNNNNG
* *
4748 TTATAAAACCATTTAAAGCTAGTAATAAGGCTTTTGAAGGCT-T-AGGTGACTATAAATAGGA-T
1 TTATAAAACCATTTAAAGCGA-TAATAAGGCTTTTG-AGGGTATGA-GTGACTATAAAT-GGACT
* * * * * * *
4810 TTTCTTGTC-AATGAACATCTCTTT-CTTCATGTTTCTCGAGGCAGATATTTAATTATAATATAT
62 TTTCTT-TCAAATGAATAGCT-TTTCCTTCAAGTTTCTTGATGCAGACATTTAATTATAATCTAT
* * * *
4873 TTTAACTAAAATAAAAAAAATTCAACTTAAAATCATTTATGAGA
125 TTAAACAAAAATAAAAAAAACTCAACTCAAAATCATTTATGAGA
* ******** * * * * *
4917 TTATAAAATCANNNNNNNNNNG-TAATAAGGCTTTTGAAGGCATGGGTGGCTATAAATGGACTCT
1 TTATAAAACCA--TTTAAAGCGATAATAAGGCTTTTGAGGGTATGAGTGACTATAAATGGACTTT
* * * * *
4981 TCTTGCAAATGAATGGCTTTTCCTTCACGTTTTTTG-TGGCAGACATTTAATTTTAATCTATTTA
64 TCTTTCAAATGAATAGCTTTTCCTTCAAGTTTCTTGAT-GCAGACATTTAATTATAATCTATTTA
* *
5045 AACCAAAAATATAAAACAACTCAACTCAAAATTATTTATGAGA
128 AA-CAAAAATA-AAAAAAACTCAACTCAAAATCATTTATGAGA
5088 TTATAAAACCATTTAAAGCGATAAATAAGGCTTTTGAGGGTATGAGTGACTATAAATGGACTTTT
1 TTATAAAACCATTTAAAGCGAT-AATAAGGCTTTTGAGGGTATGAGTGACTATAAATGGACTTTT
*
5153 CTTTCAAATGAATAGCTTTTCCTTCAAGTTTCTTGATGTAGACATTTAATTATAATCT
65 CTTTCAAATGAATAGCTTTTCCTTCAAGTTTCTTGATGCAGACATTTAATTATAATCT
5211 GNNNNNNNNN
Statistics
Matches: 228, Mismatches: 53, Indels: 24
0.75 0.17 0.08
Matches are distributed among these distances:
168 9 0.04
169 86 0.38
170 8 0.04
171 124 0.54
172 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.36
Consensus pattern (168 bp):
TTATAAAACCATTTAAAGCGATAATAAGGCTTTTGAGGGTATGAGTGACTATAAATGGACTTTTC
TTTCAAATGAATAGCTTTTCCTTCAAGTTTCTTGATGCAGACATTTAATTATAATCTATTTAAAC
AAAAATAAAAAAAACTCAACTCAAAATCATTTATGAGA
Found at i:6525 original size:170 final size:169
Alignment explanation
Indices: 6228--6673 Score: 469
Period size: 170 Copynumber: 2.6 Consensus size: 169
6218 NNNNNNNNNN
* * * * *
6228 TTTAACCAAAAATGTAAAAAAATTCAAGTTAAAATCAATTATGAGATTACAAAATCATTCAAAGT
1 TTTAACC-AAAATGCAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAAACATT-AAAGT
*
6293 GAGTAATAAGGCTTTTGAAGGCATGGGTGATTATAAATATGCTTTTCTTGCAAATGAATGGCTCT
64 GAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATATGCTTTTCTTGCAAATGAATGGCTCT
* ********** *
6358 TTCTTCATGTTTCTTAAGGNNNNNNNNNNATTATTATCTAT
129 TTCTTCATATTTCTTAAGGTAGACATTTAATTATAATCTAT
* *
6399 TTTAACCAAAATGCAAAAAAATTCTACTTAAAATCAATTATAAGCTTATAAAAACACTTAAAGTG
1 TTTAACCAAAATGCAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAAACA-TTAAAGTG
********** * *
6464 AGTAATAAGGCTTTTGAAGGCATGGGTGACTNNNNNNNNNNTTTTCTTGCCAATGAATGGCTTTT
65 AGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATATGCTTTTCTTGCAAATGAATGGCTCTT
* *
6529 TCTTCATATTTCTTGAGGTAGACATTTAATTATAATCTGT
130 TCTTCATATTTCTTAAGGTAGACATTTAATTATAATCTAT
* * * *
6569 TTTAACCATAAATACCAAAAATAATTCAACTTAAAATCAATTATTAGGTTATAAAACCATATAAA
1 TTTAACCA-AAAT-GCAAAAA-AATTCAACTTAAAATCAATTATAAGATTATAAAAACAT-TAAA
* *
6634 GCGAGTAGTAAGGCTTTTGAAGGCATGGGTGACTATAAAT
62 GTGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAAT
6674 GGACTTTTCT
Statistics
Matches: 223, Mismatches: 47, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
170 134 0.60
171 13 0.06
172 7 0.03
173 69 0.31
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.33
Consensus pattern (169 bp):
TTTAACCAAAATGCAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAAACATTAAAGTGA
GTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATATGCTTTTCTTGCAAATGAATGGCTCTTT
CTTCATATTTCTTAAGGTAGACATTTAATTATAATCTAT
Done.