Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397781.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1081.0, 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: 3862
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.25
Warning! 1226 characters in sequence are not A, C, G, or T
Found at i:301 original size:171 final size:161
Alignment explanation
Indices: 1--326 Score: 339
Period size: 171 Copynumber: 2.0 Consensus size: 161
* * * * * *
1 AATTATGAGGTTATAAAATTATTTAAATCGAGTAATAAGGCTTTTGAAGGTATCAGTGTCTACAA
1 AATTATGAGATTAAAAAACTATTTAAATCGAGTAATAAGGCTTTCGAAGGCATCAGTGACTACAA
* * * *
66 ATAGACTTTTTTTACTAATGGATATCTTTTTCTTCACATTTCTTGAGGTAAACATATAATTATAA
66 ATAGACTTTTTTTACCAATGGATATCTTTTTCTTCACAGTTCTTAAGGCAAACATATAATTATAA
131 TCTATTTTAATAAAAAATATAAAAAGGTTCA
131 TCTATTTTAATAAAAAATATAAAAAGGTTCA
* **
162 ANNNNNNNNNNATTATGAGATTAAAAAACTATTTAAATCGAGTAATTAGGCTTTCGAAGGCATGT
1 A----------ATTATGAGATTAAAAAACTATTTAAATCGAGTAATAAGGCTTTCGAAGGCATCA
* * * * * ** *
227 GTGACTAGAAATTGAGTTTTTTTACCGATGGATATTTTTTTCTTCATGGTTCTTAAGGCAGACAT
56 GTGACTACAAATAGACTTTTTTTACCAATGGATATCTTTTTCTTCACAGTTCTTAAGGCAAACAT
* *
292 -TCGATTATAATCTGTTTTAATAAAAAATATAAAAA
121 AT-AATTATAATCTATTTTAATAAAAAATATAAAAA
327 AATTTAAATT
Statistics
Matches: 131, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
161 1 0.01
170 1 0.01
171 129 0.98
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.38
Consensus pattern (161 bp):
AATTATGAGATTAAAAAACTATTTAAATCGAGTAATAAGGCTTTCGAAGGCATCAGTGACTACAA
ATAGACTTTTTTTACCAATGGATATCTTTTTCTTCACAGTTCTTAAGGCAAACATATAATTATAA
TCTATTTTAATAAAAAATATAAAAAGGTTCA
Found at i:2015 original size:171 final size:171
Alignment explanation
Indices: 1651--2052 Score: 430
Period size: 171 Copynumber: 2.4 Consensus size: 171
1641 NNNNNNNNNN
* *
1651 TTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTACCAATGGATATC-TTTTCTTCACGTTT
1 TTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCACATTT
* * * * ** * *
1715 CTCAAGATAGACATGCAATTATAATCTATTTCAATAAAAAATATAAAAAATTTCAAATCAATATC
66 CTAAAGAGAAACATGCAATTATAATATATTTCAATAAAAAATATAAAAAAAATCAAATAAAAATC
* *
1780 AATTGTGAGATTATAAAAATATTTAAAGCGAGTAATAAGGC
131 AATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGCC
* * * *
1821 TTTCGAATGCATGGTTTACTATAAACGGACTTTTCTTACCAATGGATATCTTTTTCTTCACATTT
1 TTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCACATTT
* * * * * * *
1886 CTAAAGGGAAACATTCAATTATAATATGTTTTAATGAAAAATATAAAAAAAATGAAATAAAAATT
66 CTAAAGAGAAACATGCAATTATAATATATTTCAATAAAAAATATAAAAAAAATCAAATAAAAATC
* ********** *
1951 AATTATGAGGTTATAANNNNNNNNNNAGCGAGTAATAAATCC
131 AATTATGAGATTATAAAAATATTTAAAGCGAGTAAT-AAGCC
* * * *
1993 TTT-GAAGGCATGGGAGACTATAAATGGGCTTTTCTTGCCAAAGGATATCTTTTTCTTCAC
1 TTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCAC
2053 GTTTTTTGAG
Statistics
Matches: 187, Mismatches: 43, Indels: 3
0.80 0.18 0.01
Matches are distributed among these distances:
170 45 0.24
171 136 0.73
172 6 0.03
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (171 bp):
TTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCACATTT
CTAAAGAGAAACATGCAATTATAATATATTTCAATAAAAAATATAAAAAAAATCAAATAAAAATC
AATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGCC
Found at i:2918 original size:171 final size:169
Alignment explanation
Indices: 2618--3160 Score: 443
Period size: 171 Copynumber: 3.2 Consensus size: 169
2608 NNNNNNNNNN
* *
2618 TTGCCAATGGATATCTTTTTCTTCACATTTCTCAAGGCAAACATTCAATTATAA-CATGCTTTAA
1 TTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGGCAAACATTCAATTATAATCA---TTTAA
********** *
2682 TAAAAAATATAAAAAAATCTAAATTAAAATCAATTATGAGGTTATNNNNNNNNNNAAAGCGAGTA
63 TAAAAAATATAAAAAAATCTAAATTAAAATCAATTATGAGGTTATAAAAATATTTAAACCGAGTA
* * *
2747 ATAAGGCTTTTGATGGAATCG-GTGACTATAAATGGACTTTAT-
128 ATAAGGCTTTCGAAGGAAT-GAGTGACTATAAATAGACTTT-TC
* * *
2789 TTGCCAATGGATATCTTTTTTTTCACGTTTCTCGAGACAAACATTCGATTATAATCTATTGTAAT
1 TTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGGCAAACATTCAATTATAATC-ATT-TAAT
* * *
2854 AAAAAATAT-AAAAAATTTCAAATTAAAATCAATTATGAGTTTGTAAAAATATTTAAACCGAGTA
64 AAAAAATATAAAAAAATCT-AAATTAAAATCAATTATGAGGTTATAAAAATATTTAAACCGAGTA
* *
2918 ATAAGGCTTTCGAAGGCATGAGTTACTATAAATAGACTTTTC
128 ATAAGGCTTTCGAAGGAATGAGTGACTATAAATAGACTTTTC
* * * * * * * *
2960 TTACCAGTGAATATCTTTTTCGTCATGTTTCTGGAGGTAGACATTCAATTATAATCCGATTTAAT
1 TTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGGCAAACATTCAATTATAAT-C-ATTTAAT
********** * * *
3025 AAAAAATATANNNNNNNNNNAATTAAAATCAATTCTGAGGTTAT-AAAATCATTTAAAGCGAACT
64 AAAAAATATAAAAAAATCTAAATTAAAATCAATTATGAGGTTATAAAAAT-ATTTAAACCG-AGT
* * * * *
3089 -ATAAGGCTTTCGAAGGCATG-GATGACAACAAATGGACTTTTA
127 AATAAGGCTTTCGAAGGAATGAG-TGACTATAAATAGACTTTTC
* * *
3131 TTGCCTATGGATATCTATTTCTTCATGTTT
1 TTGCCAATGGATATCTTTTTCTTCACGTTT
3161 TTCAAGANNN
Statistics
Matches: 299, Mismatches: 62, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
170 18 0.06
171 273 0.91
172 7 0.02
173 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (169 bp):
TTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGGCAAACATTCAATTATAATCATTTAATAA
AAAATATAAAAAAATCTAAATTAAAATCAATTATGAGGTTATAAAAATATTTAAACCGAGTAATA
AGGCTTTCGAAGGAATGAGTGACTATAAATAGACTTTTC
Done.