Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398765.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2048.0, 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: 5555
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.23
Warning! 1875 characters in sequence are not A, C, G, or T
Found at i:673 original size:172 final size:171
Alignment explanation
Indices: 381--1333 Score: 1102
Period size: 172 Copynumber: 5.5 Consensus size: 171
371 NNNNNNNNNA
* * *
381 ATTCAAATTTAAATCAATTTTGAAATTATAAAA-ATATTTAAAGTGAGTAATAAAGCTTTTGAAG
1 ATTCAAATTTAAATCAATTTTGAGATTATAAAACA-ATTTAAACTGAGTAATAAGGCTTTTGAAG
* * *
445 GAATGGGTGACTAGAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTCCATGTTTCTCATGGT
65 GAATGGGTGACTATAAAT-GACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGT
*
510 AGACATTCAATTCTAGTCTATTTTAACGAAAAATGTACAAAAC
129 AGACATTCAATTCTAGTCTATTTTAACAAAAAATGTACAAAAC
* * *
553 ATTCAAATTTCAATAAATTTTGAGATTATAAAACAATTTAAACTGAGTAATAAGGTTTTTGAAGG
1 ATTCAAATTTAAATCAATTTTGAGATTATAAAACAATTTAAACTGAGTAATAAGGCTTTTGAAGG
* * *
618 AATGGGTGACTATAAATGCATTTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTA
66 AATGGGTGACTATAAATG-ACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTA
* * *
683 GAC-TCTCAATTCTAGTCTGTTTTAACCAAAAATGTTCAAAGA-
130 GACAT-TCAATTCTAGTCTATTTTAACAAAAAATGTACAAA-AC
* * *
725 ATTCAAATTTAAAGCAATTTTGAGAATATAAAACCATTTAAAGC-GAGTAATAAGGCTTTTGAAG
1 ATTCAAATTTAAATCAATTTTGAGATTATAAAACAATTTAAA-CTGAGTAATAAGGCTTTTGAAG
* * * * *
789 GACTGGGTGAATATAAATAGACTTCTCTTGCCAATGAATATTTTTTTCTTCATGTTTCTCATGGT
65 GAATGGGTGACTATAAAT-GACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGT
* *
854 GGACATT-ATATTCTAGTCTATTTTAACTAAAAATGTACAAAAC
129 AGACATTCA-ATTCTAGTCTATTTTAACAAAAAATGTACAAAAC
* * * *
897 ATTCAAATTTTAATCAATTTTGAGATTATAAAACCATTTAAACTAAGTAATAAGGCTCTTGAAGG
1 ATTCAAATTTAAATCAATTTTGAGATTATAAAACAATTTAAACTGAGTAATAAGGCTTTTGAAGG
* * * *
962 AATGAGTTACTATAAATGGACTTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTA
66 AATGGGTGACTATAAAT-GACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTA
* * *
1027 GACATTCAATCCTAGTCTGTTTTAACAAAAAATGTACAAAAA
130 GACATTCAATTCTAGTCTATTTTAACAAAAAATGTACAAAAC
* * *
1069 ATTCAAATTTAAATCAATTTTGAGACTATAAAACAATTAAAAGTGAGTAATAAGGCTTTTGAAGG
1 ATTCAAATTTAAATCAATTTTGAGATTATAAAACAATTTAAACTGAGTAATAAGGCTTTTGAAGG
* * * * * *
1134 AATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCCTTGC--GTTTGTCGAGC
66 AATGGGTGACTATAAAT-GACTTTTCTTGCCAATGAAT-ACTTTTTTCTT-CATGTTTCTCAAGG
* * * *
1197 CAGACATTCAATTATAGTCT-TTTTAA-AAATATATATATA-AAAAA
128 TAGACATTCAATTCTAGTCTATTTTAACAAA-A-A-ATGTACAAAAC
* * ** * * * * *
1241 ATTCAACTTAAAATCAATTACG-GCATTACAAAACTATTTAAAAC-AAGTAATAATGCTTTCGAA
1 ATTCAAATTTAAATCAATTTTGAG-ATTATAAAACAATTT-AAACTGAGTAATAAGGCTTTTGAA
* * *
1304 GGTATAGGTGAATATAAATGGACTTTTCTT
64 GGAATGGGTGACTATAAAT-GACTTTTCTT
1334 NNNNNNNNNN
Statistics
Matches: 675, Mismatches: 88, Indels: 36
0.84 0.11 0.05
Matches are distributed among these distances:
170 3 0.00
171 13 0.02
172 636 0.94
173 22 0.03
174 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
ATTCAAATTTAAATCAATTTTGAGATTATAAAACAATTTAAACTGAGTAATAAGGCTTTTGAAGG
AATGGGTGACTATAAATGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAG
ACATTCAATTCTAGTCTATTTTAACAAAAAATGTACAAAAC
Found at i:1007 original size:344 final size:344
Alignment explanation
Indices: 380--1180 Score: 1250
Period size: 344 Copynumber: 2.3 Consensus size: 344
370 NNNNNNNNNN
*
380 AATTCAAATTTAAATCAATTTTGA-AATTATAAAA-ATATTTAAAGTGAGTAATAAAGCTTTTGA
1 AATTCAAATTTAAATCAATTTTGAGAA-TATAAAACA-ATTTAAAGTGAGTAATAAGGCTTTTGA
*
443 AGGAATGGGTGACTAGAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTCCATGTTTCTCATG
64 AGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTCCATGTTTCTCATG
508 GTAGACATTCAATTCTAGTCTATTTTAACGAAAAATGTACAAAACATTCAAATTTCAATAAATTT
129 GTAGACATTCAATTCTAGTCTATTTTAACGAAAAATGTACAAAACATTCAAATTTCAATAAATTT
* * * *
573 TGAGATTATAAAACAATTTAAACTGAGTAATAAGGTTTTTGAAGGAATGGGTGACTATAAATGCA
194 TGAGATTATAAAACAATTTAAACTAAGTAATAAGGCTCTTGAAGGAATGAGTGACTATAAATGCA
* *
638 TTTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGAC-TCTCAATTCTAGTCTG
259 CTTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACAT-TCAATCCTAGTCTG
* * *
702 TTTTAACCAAAAATGTTCAAAG
323 TTTTAACAAAAAATGTACAAAA
* * *
724 AATTCAAATTTAAAGCAATTTTGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
1 AATTCAAATTTAAATCAATTTTGAGAATATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * * *
789 GACTGGGTGAATATAAATAGACTTCTCTTGCCAATGAATATTTTTTTCTTCATGTTTCTCATGGT
66 GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTCCATGTTTCTCATGGT
* * * *
854 GGACATT-ATATTCTAGTCTATTTTAACTAAAAATGTACAAAACATTCAAATTTTAATCAATTTT
131 AGACATTCA-ATTCTAGTCTATTTTAACGAAAAATGTACAAAACATTCAAATTTCAATAAATTTT
* * *
918 GAGATTATAAAACCATTTAAACTAAGTAATAAGGCTCTTGAAGGAATGAGTTACTATAAATGGAC
195 GAGATTATAAAACAATTTAAACTAAGTAATAAGGCTCTTGAAGGAATGAGTGACTATAAATGCAC
983 TTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTGTT
260 TTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTGTT
1048 TTAACAAAAAATGTACAAAA
325 TTAACAAAAAATGTACAAAA
* *
1068 AATTCAAATTTAAATCAATTTTGAGACTATAAAACAATTAAAAGTGAGTAATAAGGCTTTTGAAG
1 AATTCAAATTTAAATCAATTTTGAGAATATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * *
1133 GAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTC
66 GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTC
1181 CTTGCGTTTG
Statistics
Matches: 414, Mismatches: 39, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
343 1 0.00
344 410 0.99
345 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (344 bp):
AATTCAAATTTAAATCAATTTTGAGAATATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAG
GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTCCATGTTTCTCATGGT
AGACATTCAATTCTAGTCTATTTTAACGAAAAATGTACAAAACATTCAAATTTCAATAAATTTTG
AGATTATAAAACAATTTAAACTAAGTAATAAGGCTCTTGAAGGAATGAGTGACTATAAATGCACT
TTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTGTTT
TAACAAAAAATGTACAAAA
Found at i:1258 original size:344 final size:341
Alignment explanation
Indices: 380--1333 Score: 1228
Period size: 344 Copynumber: 2.8 Consensus size: 341
370 NNNNNNNNNN
*
380 AATTCAAATTTAAATCAATTTTGA-AATTATAAAA-ATATTTAAAGTGAGTAATAAAGCTTTTGA
1 AATTCAAATTTAAATCAATTTTGAGAA-TATAAAACA-ATTTAAAGTGAGTAATAAGGCTTTTGA
* *
443 AGGAATGGGTGACTAGAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTCCATGTTTCTCATG
64 AGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCA-GTTTCTCATG
* *
508 GTAGACATTCAATTCTAGTCTATTTTAACGAAAAATGTACAAAACATTCAAATTTCAATAAATTT
128 GTAGACATTCAATTCTAGTCTATTTTAAC-AAAAATGTACAAAACATTCAAATTTAAATCAATTT
* * * *
573 TGAGATTATAAAACAATTTAAACTGAGTAATAAGGTTTTTGAAGGAATGGGTGACTATAAATGCA
192 TGAGATTATAAAACAATTTAAACTAAGTAATAAGG-CTTTGAAGGAATGAGTGACTATAAATGGA
* *
638 TTTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACTCTCAATTCTAGTCTGT
256 CTTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACTCTCAATCCTAGTCTGT
* * *
703 TTTAACCAAAAATGTTCAAAG
321 TTTAACAAAAAATGTACAAAA
* * *
724 AATTCAAATTTAAAGCAATTTTGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
1 AATTCAAATTTAAATCAATTTTGAGAATATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * *
789 GACTGGGTGAATATAAATAGACTTCTCTTGCCAATGAATATTTTTTTCTTCATGTTTCTCATGGT
66 GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCA-GTTTCTCATGGT
* *
854 GGACATT-ATATTCTAGTCTATTTTAACTAAAAATGTACAAAACATTCAAATTTTAATCAATTTT
130 AGACATTCA-ATTCTAGTCTATTTTAAC-AAAAATGTACAAAACATTCAAATTTAAATCAATTTT
* *
918 GAGATTATAAAACCATTTAAACTAAGTAATAAGGCTCTTGAAGGAATGAGTTACTATAAATGGAC
193 GAGATTATAAAACAATTTAAACTAAGTAATAAGGCT-TTGAAGGAATGAGTGACTATAAATGGAC
983 TTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACAT-TCAATCCTAGTCTGT
257 TTTTCTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGAC-TCTCAATCCTAGTCTGT
1047 TTTAACAAAAAATGTACAAAA
321 TTTAACAAAAAATGTACAAAA
* *
1068 AATTCAAATTTAAATCAATTTTGAGACTATAAAACAATTAAAAGTGAGTAATAAGGCTTTTGAAG
1 AATTCAAATTTAAATCAATTTTGAGAATATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * * *
1133 GAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCCTTGC-GTTTGTCGA-G
66 GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAAT-ACTTTTTTCTT-CAGTTTCTC-ATG
** * * * * * *
1196 CCAGACATTCAATTATAGTCT-TTTTAA-AAATATATATATAAAAAAATTCAACTTAAAATCAAT
128 GTAGACATTCAATTCTAGTCTATTTTAACAAA-A-ATGTA-CAAAACATTCAAATTTAAATCAAT
** * * * * *
1259 TACG-GCATTACAAAACTATTTAAAAC-AAGTAATAATGCTTTCGAAGGTAT-AGGTGAATATAA
190 TTTGAG-ATTATAAAACAATTT-AAACTAAGTAATAAGGCTTT-GAAGGAATGA-GTGACTATAA
1321 ATGGACTTTTCTT
251 ATGGACTTTTCTT
1334 NNNNNNNNNN
Statistics
Matches: 537, Mismatches: 57, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
341 3 0.01
342 1 0.00
343 16 0.03
344 499 0.93
345 17 0.03
346 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (341 bp):
AATTCAAATTTAAATCAATTTTGAGAATATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAG
GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCAGTTTCTCATGGTA
GACATTCAATTCTAGTCTATTTTAACAAAAATGTACAAAACATTCAAATTTAAATCAATTTTGAG
ATTATAAAACAATTTAAACTAAGTAATAAGGCTTTGAAGGAATGAGTGACTATAAATGGACTTTT
CTTGCGAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACTCTCAATCCTAGTCTGTTTTAA
CAAAAAATGTACAAAA
Found at i:2967 original size:172 final size:172
Alignment explanation
Indices: 2709--3126 Score: 417
Period size: 172 Copynumber: 2.4 Consensus size: 172
2699 CAAAGAACAT
* * * * * * * * *
2709 TCATTGGCAAGAAAGGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTGTCACTCACTTTAAA
1 TCATTAGCAAGAAAAGTCCATTTAGAGCCACCAATTCCTTCAAAAACATTATTACTCACTTTAAA
* * * ********** *
2774 T-GTTTTTATAATCTCAAAATTGATTTAAATTTGNNNNNNNNNNACATTTTTGGTTAAAATAGAC
66 TAG-TTTTATCACCTAAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGAC
* * * *
2838 T-AGAATTGAATGTCTACCTTGAGAAATATGAAGAAAAAAGCAG
130 TGAG-ATTGAATGTCTACCTTAAAAAACATGAAAAAAAAAGCAG
* * * ** * *
2881 TCATTAGTAAGAGAAGTCCATTTATAGTTACCCATTCCTTCAAAAACATTATTACTCACTTTGAA
1 TCATTAGCAAGAAAAGTCCATTTAGAGCCACCAATTCCTTCAAAAACATTATTACTCACTTTAAA
*
2946 TAGTTTTATCACCTAAAAATTGATTTAAATTTGAATTCTTTGTGCATTTTTGGTTAAAACAGACT
66 TAGTTTTATCACCTAAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACT
* * *
3011 GAGATTGAATGTTTACCTTAAAAAACATGAAAAAAAAAGTAT
131 GAGATTGAATGTCTACCTTAAAAAACATGAAAAAAAAAGCAG
* * * *
3053 TCATTGGCAAGAAAAGTTCATTTAGAGCCACCAATTCCTTCAAAAGCCTTATTACTCACTTTAAA
1 TCATTAGCAAGAAAAGTCCATTTAGAGCCACCAATTCCTTCAAAAACATTATTACTCACTTTAAA
*
3118 TGGTTTTAT
66 TAGTTTTAT
3127 AATCTNNNNN
Statistics
Matches: 200, Mismatches: 44, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
172 197 0.99
173 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.34
Consensus pattern (172 bp):
TCATTAGCAAGAAAAGTCCATTTAGAGCCACCAATTCCTTCAAAAACATTATTACTCACTTTAAA
TAGTTTTATCACCTAAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACT
GAGATTGAATGTCTACCTTAAAAAACATGAAAAAAAAAGCAG
Found at i:4258 original size:172 final size:161
Alignment explanation
Indices: 4039--4361 Score: 380
Period size: 172 Copynumber: 1.9 Consensus size: 161
4029 TTCAAGAGCC
* * *
4039 TTATTGCTCAGTTCAAATGGTTTTATAATCTCAAAATTAAGTTAAATTTGAATGT-TTTGTACA-
1 TTATTACTCAATTCAAATGGTTTTATAATCTCAAAATTAAGTTAAATTTGAAT-TCTTTATACAT
* * *
4102 TTTTACATTAAAATAGACTAGAATTGAATGTCTACCATGAGAAACAAGAAGAACAAAGTATTCAT
65 TTTTA-ATTAAAACAGACAAGAATTGAATGTCTACCATGAGAAACAAGAAGAA-AAAGCATTCAT
4167 TGGAAAGAAAAGTCCATTTATAGTCACTTANNNNNNNNNNAGCT
128 TGGAAAGAAAAGTCCATTTATAGTCACTTA----------AGCT
* * *
4211 TTATTACTCAATTTAAATGTTTTTATAATCTCAAAATTAATTTAAATTTGAATTCTTTATACATT
1 TTATTACTCAATTCAAATGGTTTTATAATCTCAAAATTAAGTTAAATTTGAATTCTTTATACATT
* * * * *
4276 TTTAGTTAGAACAGACAAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGCATTCGTTGG
66 TTTAATTAAAACAGACAAGAATTGAATGTCTACCATGAGAAACAAGAAGAAAAAGCATTCATTGG
*
4341 CAAGAAAAGTCCATTTATAGT
131 AAAGAAAAGTCCATTTATAGT
4362 TACTCNNNNN
Statistics
Matches: 134, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
171 33 0.25
172 96 0.72
173 5 0.04
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (161 bp):
TTATTACTCAATTCAAATGGTTTTATAATCTCAAAATTAAGTTAAATTTGAATTCTTTATACATT
TTTAATTAAAACAGACAAGAATTGAATGTCTACCATGAGAAACAAGAAGAAAAAGCATTCATTGG
AAAGAAAAGTCCATTTATAGTCACTTAAGCT
Done.