Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402728.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_579.0, 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: 1701
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.29
Warning! 295 characters in sequence are not A, C, G, or T
Found at i:552 original size:172 final size:172
Alignment explanation
Indices: 10--1264 Score: 936
Period size: 172 Copynumber: 7.3 Consensus size: 172
1 AATTACGGC
* * * * * *
10 ATTACAAAACCATTTAAAGTGAGTTATAATGCTTTTGAAGGTATGAGTGACTATAAATGGACTTT
1 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTT
** * * * ********** * * *
75 TCTTGAAAATAAATGCATTTTTCTTCATGATTNNNNNNNNNNACATTCAATTCTAGCCTATTTTA
66 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTA
* * * *
140 ACAAAAAATGAACAATGAAATCAAATTTAAAAT-AATTTTGAG
131 ACCAAAAATGTACAAAGAATTCAAA-TTAAAATCAATTTTGAG
* * * * *
182 ATTAGAAAGCAATTTAAAGTGAGTAATAAGGCTTTGGAAGGAATGAGTGACTATAAATAGACTTT
1 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTT
* ** * * * *
247 TGTTGCCAATGAATGC-CATTACTTTACGTTTCT-AGAGGTAAACATTCAATTATAGTCTG-TTT
66 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCA-AGGTAGACATTCAATTATAGTCTGTTTT
* * * * * *
309 AACCAAAAATGTAAAAAATAATTTAACTTAAAATCAATTATGAC
130 AACCAAAAATGT-ACAAAGAATTCAAATTAAAATCAATTTTGAG
* ** * * * *
353 ATTACAAAACCATTTAAAGCAAGTAATAATGCTTTTGAGGGTATGGGTGACTATAAGTAGACTTT
1 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTT
*
418 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTCA-AGTCTGTTTT
66 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATT-ATAGTCTGTTTT
*
482 AACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAG
130 AACCAAAAATGTACAAAGAATTCAAATTAAAATCAATTTTGAG
* * * * * * * *
525 ATTATAAAAACATTTAAAGGGAGTAATAAGACTTTTAAAGGAATAGGTGTCTATAAATAGAGTTC
1 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTT
* * ** * * * * * *
590 TCTTACCTATGAATGCTTACTTCTTTATATTTCTCGAA-CTAGACATTTAATTATAATATGTTTT
66 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTC-AAGGTAGACATTCAATTATAGTCTGTTTT
* * * * *
654 AACTAGAAAA-GTA-AAAAAATTTGAACTTAAAATCAATTTTAAG
130 AACCA-AAAATGTACAAAGAA-TTCAAATTAAAATCAATTTTGAG
* * * * * *
697 AATATAAAATCATTTAAAGTGATTAATTAGGCTTTTGAAGTAATAGGTGACTATAAATAGACTTT
1 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTT
* * * * * *
762 TCTTGCCAATGAATACTTTTTCCTTCATGTTTCTCAAGGTCGACATTCAATTCTACTCTATTTTA
66 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTA
* * ** *
827 ACCATAAATGTGCAAAGTTTTCAAATTTAAATCAA-TTTGAG
131 ACCAAAAATGTACAAAGAATTCAAATTAAAATCAATTTTGAG
** * ** * * *
868 ATTATAAAATTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGACTGACTATAAATGGACCTC
1 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTT
* * * * ** * * *
933 TCTTACCCATGAATGCTCTCTTCTTTGTGTTTCTCAGGGTAGACGA-TCAATTATAATATGTTTT
66 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGAC-ATTCAATTATAGTCTGTTTT
* * * * * *
997 AACTAAAAAAGCA-AAAAATATTTAAACTTAAAATCAATTTGGAG
130 AACCAAAAATGTACAAAGA-ATTCAAA-TTAAAATCAATTTTGAG
* * * * * * ****
1041 ATTATAAAACCATTTAAAGTGACTGATAAGGCTTTTGATGCAATGGGTGACCATAAATGGANNNN
1 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTT
****** * * * * * * * *
1106 NNNNNNCAATGAATGCCTTTTTATTTACGTTTATCGAGGTAGACATTCAATTATAATCTTTTTTA
66 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTA
* * * * *
1171 ACCAAAAGTATA-AAAAAACTT-AACTTAAAATCAATTAT-AG
131 ACCAAAAATGTACAAAGAA-TTCAAATTAAAATCAATTTTGAG
* * * * *
1211 CATTACAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTA
1 -ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTA
1265 NNNNNNNNNN
Statistics
Matches: 843, Mismatches: 219, Indels: 43
0.76 0.20 0.04
Matches are distributed among these distances:
170 25 0.03
171 293 0.35
172 384 0.46
173 141 0.17
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (172 bp):
ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTT
TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTA
ACCAAAAATGTACAAAGAATTCAAATTAAAATCAATTTTGAG
Found at i:811 original size:344 final size:342
Alignment explanation
Indices: 117--1098 Score: 1140
Period size: 344 Copynumber: 2.9 Consensus size: 342
107 NNNNNNNNNN
* * * * *
117 ACATTCAATTCTAGCCTATTTTAACAAAAAATGAACAATGAAATCAAATTTAAAAT-AATTTTGA
1 ACATTCAATTCTAGTCTATTTTAACCAAAAATGTACAAAGAATTCAAATTT-AAATCAATTTTGA
* * **
181 GATTA-GAAAGCAATTTAAAGTGAGTAATAAGGCTTTGGAAGGAATGAGTGACTATAAATAGACT
65 GATTATAAAAAC-ATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACT
* * * * * * * * *
245 TTTGTTGCCAATGAATGC-CA-TTACTTTACGTTTCTAGAGGTAAACATTCAATTATAGTCTG-T
129 TCTCTTACCAATGAATGCTTACTT-CTTTATGTTTCTCGAGGTAGACATTCAATTATAATATGTT
* * * *
307 TTAACCAAAAATGTAAAAAATAATTTAACTTAAAATCAATTATGACATTACAAAACCATTTAAAG
193 TTAACTAAAAA-GT-AAAAA-AATTTAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAG
** * * * * *
372 CAAGTAATAATGCTTTTGAGGGT-ATGGGTGACTATAAGTAGACTTTTCTTGCCAATGAATGCTT
255 TGACTAATAAGGCTTTTGA-AGTAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTT
* *
436 TTTTCTTCATGTTTCTTAAGGTAG
319 TTTCCTTCATGTTTCTCAAGGTAG
* *
460 ACATTCAATTCAAGTCTGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAG
1 ACATTCAATTCTAGTCTATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAG
* * * *
525 ATTATAAAAACATTTAAAGGGAGTAATAAGACTTTTAAAGGAAT-AGGTGTCTATAAATAGAGTT
66 ATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGA-GTGACTATAAATAGACTT
* * ** *
589 CTCTTACCTATGAATGCTTACTTCTTTATATTTCTCGAACTAGACATTTAATTATAATATGTTTT
130 CTCTTACCAATGAATGCTTACTTCTTTATGTTTCTCGAGGTAGACATTCAATTATAATATGTTTT
* * *
654 AACTAGAAAAGTAAAAAAATTTGAACTTAAAATCAATTTTAAGAATATAAAATCATTTAAAGTGA
195 AACTA-AAAAGTAAAAAAATTT-AACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGA
* * *
719 TTAATTAGGCTTTTGAAGTAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTC
258 CTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTC
*
784 CTTCATGTTTCTCAAGGTCG
323 CTTCATGTTTCTCAAGGTAG
* * * **
804 ACATTCAATTCTACTCTATTTTAACCATAAATGTGCAAAGTTTTCAAATTTAAATCAA-TTTGAG
1 ACATTCAATTCTAGTCTATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAG
** * * *
868 ATTATAAAATTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGACTGACTATAAATGGACCTC
66 ATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTC
* *
933 TCTTACCCATGAATGCTCT-CTTCTTTGTGTTTCTC-AGGGTAGACGA-TCAATTATAATATGTT
131 TCTTACCAATGAATGCT-TACTTCTTTATGTTTCTCGA-GGTAGAC-ATTCAATTATAATATGTT
* *
995 TTAACTAAAAAAGCAAAAAATATTTAAACTTAAAATCAATTTGGAGATTATAAAACCATTTAAAG
193 TTAACT-AAAAAGTAAAAAA-ATTT-AACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAG
* * * *
1060 TGACTGATAAGGCTTTTGATGCAATGGGTGACCATAAAT
255 TGACTAATAAGGCTTTTGAAGTAATGGGTGACTATAAAT
1099 GGANNNNNNN
Statistics
Matches: 541, Mismatches: 83, Indels: 29
0.83 0.13 0.04
Matches are distributed among these distances:
342 6 0.01
343 249 0.46
344 271 0.50
345 11 0.02
346 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (342 bp):
ACATTCAATTCTAGTCTATTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAG
ATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTC
TCTTACCAATGAATGCTTACTTCTTTATGTTTCTCGAGGTAGACATTCAATTATAATATGTTTTA
ACTAAAAAGTAAAAAAATTTAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGACTA
ATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTCCTT
CATGTTTCTCAAGGTAG
Found at i:1153 original size:344 final size:343
Alignment explanation
Indices: 10--1264 Score: 1151
Period size: 343 Copynumber: 3.7 Consensus size: 343
1 AATTACGGC
* * * * ** * *
10 ATTACAAAACCATTTAAAGTGAGTTATAATGCTTTTGAAGGTATGAGTGACTATAAATGGACTTT
1 ATTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGCAATGGGTGACTATAAATAGACTTT
** * * * ********** **
75 TCTTGAAAATAAATGCATTTTTCTTCATGATTNNNNNNNNNNACATTCAATTCTAGCCTATTTTA
66 TCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAATCTATTTTA
* * * * * * *
140 ACAAAAAATGAACAATGAAATCAAATTTAAAAT-AATTTTGAGATTAGAAAGCAATTTAAAGTGA
131 AC-CAAAATGTACAAAGAATTCAAATTT-AAATCAATTTTGAGATTATAAAACTATTTAAAGTGA
** * * *
204 GTAATAAGGCTTTGGAAGGAATGAGTGACTATAAATAGACTTTTGTTGCCAATGAATGC-CAT-T
194 GTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTCTCTTACCAATGAATGCTC-TCT
* * * * * * *
267 ACTTTACGTTTCT-AGAGGTAAACATTCAATTATAGTCTG-TTTAACCAAAAATGTAAAAAATAA
258 TCTTTATGTTTCTCAGAGGTAGACATTCAATTATAATATGTTTTAACTAAAAAAGTAAAAAAT-A
*
330 TTTAACTTAAAATCAATTATGAC
322 TTTAACTTAAAATCAATT-TGAG
* ** * * * ** *
353 ATTACAAAACCATTTAAAGCAAGTAATAATGCTTTTGAGGGTATGGGTGACTATAAGTAGACTTT
1 ATTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGCAATGGGTGACTATAAATAGACTTT
* * *
418 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTC-AAGTCTGTTTT
66 TCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAA-TCTATTTT
*
482 AACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAAAC-ATTTAAAGGG
130 AACC-AAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTAT-AAAACTATTTAAAGTG
* * * *
546 AGTAATAAGACTTTTAAAGGAAT-AGGTGTCTATAAATAGAGTTCTCTTACCTATGAATGCT-TA
193 AGTAATAAGGCTTTTAAAGGAATGA-GTGACTATAAATAGACTTCTCTTACCAATGAATGCTCT-
* ** * *
609 CTTCTTTATATTTCTC-GAACTAGACATTTAATTATAATATGTTTTAACTAGAAAAGTAAAAAA-
256 CTTCTTTATGTTTCTCAGAGGTAGACATTCAATTATAATATGTTTTAACTAAAAAAGTAAAAAAT
*
672 ATTTGAACTTAAAATCAATTTTAAG
321 ATTT-AACTTAAAATCAA-TTTGAG
* * * * * *
697 AATATAAAATCATTTAAAGTGATTAATTAGGCTTTTGAAGTAATAGGTGACTATAAATAGACTTT
1 ATTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGCAATGGGTGACTATAAATAGACTTT
* * *
762 TCTTGCCAATGAAT-ACTTTTTCCTTCATGTTTCTCAAGGTCGACATTCAATTCTACTCTATTTT
66 TCTTGCCAATGAATGCCTTTTT-CTTCATGTTTCTCAAGGTAGACATTCAATTCTAATCTATTTT
* ** *
826 AACCATAAATGTGCAAAGTTTTCAAATTTAAATCAA-TTTGAGATTATAAAATTATTTAAAGTGA
130 AACCA-AAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTAAAGTGA
* * * *
890 GTAATAAGGCTTTTAAAGGAATGACTGACTATAAATGGACCTCTCTTACCCATGAATGCTCTCTT
194 GTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTCTCTTACCAATGAATGCTCTCTT
* *
955 CTTTGTGTTTCTCAG-GGTAGACGA-TCAATTATAATATGTTTTAACTAAAAAAGCAAAAAATAT
259 CTTTATGTTTCTCAGAGGTAGAC-ATTCAATTATAATATGTTTTAACTAAAAAAGTAAAAAATAT
1018 TTAAACTTAAAATCAATTTGGAG
323 TT-AACTTAAAATCAATTT-GAG
* * * * ****
1041 ATTATAAAACCATTTAAAGTGACTGATAAGGCTTTTGATGCAATGGGTGACCATAAATGGANNNN
1 ATTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGCAATGGGTGACTATAAATAGACTTT
****** * * * * * * *
1106 NNNNNNCAATGAATGCCTTTTTATTTACGTTTATCGAGGTAGACATTCAATTATAATCTTTTTTA
66 TCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAATCTATTTTA
* * * * * * *
1171 ACCAAAA-GTATAAAAAAACTT-AACTTAAAATCAATTAT-AGCATTACAAAACTATTTAAAGCG
131 ACCAAAATGTA-CAAAGAA-TTCAAATTTAAATCAATTTTGAG-ATTATAAAACTATTTAAAGTG
* *
1233 AGTAATAAGGCTTTTGAAGGTATGAGTGACTA
193 AGTAATAAGGCTTTTAAAGGAATGAGTGACTA
1265 NNNNNNNNNN
Statistics
Matches: 746, Mismatches: 139, Indels: 53
0.80 0.15 0.06
Matches are distributed among these distances:
342 13 0.02
343 353 0.47
344 353 0.47
345 27 0.04
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (343 bp):
ATTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGCAATGGGTGACTATAAATAGACTTT
TCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAATCTATTTTA
ACCAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGT
AATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTCTCTTACCAATGAATGCTCTCTTCT
TTATGTTTCTCAGAGGTAGACATTCAATTATAATATGTTTTAACTAAAAAAGTAAAAAATATTTA
ACTTAAAATCAATTTGAG
Done.