Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399182.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2452.0, 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: 2316
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.26
Warning! 599 characters in sequence are not A, C, G, or T
Found at i:294 original size:153 final size:152
Alignment explanation
Indices: 16--323 Score: 409
Period size: 153 Copynumber: 2.0 Consensus size: 152
6 TTATAAAACT
* * *
16 ATTTAAAGTGAGTAATAAGACTTTTGAAGGAATGGGTGATTATAAATAGACTTTTCCTACCAATG
1 ATTTAAAGTGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAAAAGACTTTTCCTACCAATG
* * * * *
81 ATTGCCATTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTATACTCTGTTTTAGCCAAAAATGT
66 AATACCATTTTCTTCAAGTTTCTCAAGGAAGACATTCAATTATACTCTGTTTTAACCAAAAATGT
*
146 AAAGAAAATTGAACTTAAAATCA
131 AAA-AAAATTCAACTTAAAATCA
* * * *
169 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAAAGATTTTTCTTGCCAATG
1 ATTTAAAGTGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAAAAGACTTTTCCTACCAATG
** * * * * * * *
234 AATACGTTTTTCTTCACGTTTCTTAAGGAAGAGATTCACTTATAGTTTGTTTTAATCAAAAATGT
66 AATACCATTTTCTTCAAGTTTCTCAAGGAAGACATTCAATTATACTCTGTTTTAACCAAAAATGT
299 AAAAAAATTCAACTTAAAATCA
131 AAAAAAATTCAACTTAAAATCA
321 ATT
1 ATT
324 ATGAGATTAT
Statistics
Matches: 133, Mismatches: 22, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
152 21 0.16
153 112 0.84
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (152 bp):
ATTTAAAGTGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAAAAGACTTTTCCTACCAATG
AATACCATTTTCTTCAAGTTTCTCAAGGAAGACATTCAATTATACTCTGTTTTAACCAAAAATGT
AAAAAAATTCAACTTAAAATCA
Found at i:460 original size:171 final size:168
Alignment explanation
Indices: 169--1141 Score: 852
Period size: 171 Copynumber: 5.7 Consensus size: 168
159 CTTAAAATCA
** *
169 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAAAGATTTTTCTTGCCAATG
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGA-TGACTATAAATGGACTTTTCTTGCCAATG
* * * * * * *
234 AATACGTTTTTCTTCACGTTTCTTAAGGAAGAGATTCACTTATAGTTTGTTTTAATCAAAAATGT
65 AATAC-TTTTTCTTCACGTTTCTTGAGGCAGACATTCAATTATAATCTATTTTAATCAAAAATGT
299 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT
129 AAAAAAATT-AACTTAAAATCAATTATGAGATTATAAAACT
* * * ** * *
340 ATTTAAAATGAGTAATAAGACTTTTGAAGGAATAGAAGACCGTAAATGGATTTTTCGTT-TCAAT
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GATGACTATAAATGGACTTTTC-TTGCCAAT
* * * *
404 GAATGACTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATAATAATATATTTTAAT-AAAAATT
64 GAAT-ACTTTTTCTTCACGTTTCTTGAGGCAGACATTCAATTATAATCTATTTTAATCAAAAATG
* * * * * *
468 TAAAAAAAATAAGCTTAAAATAAATTTTAAGATAATATAAC-
128 TAAAAAAATTAA-CTTAAAATCAATTATGAGATTATAAAACT
* * * *
509 AGTTTAAAGTGAGTAATAAGGCTTTCGAAGGTATGGGTGACTACAAATGGACTTTTCTTGCCAAT
1 A-TTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GATGACTATAAATGGACTTTTCTTGCCAAT
* * * * *
574 GAATACCTTTTTC-TCTATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAAT
64 GAATA-CTTTTTCTTC-ACGTTTCTTGAGGCAGACATTCAATTATAATCTATTTTAATCAAAAAT
* * * *
638 ATAAAAAAATTCAACCTAAAATTAATTATGCGATTATAAAA-T
127 GTAAAAAAATT-AACTTAAAATCAATTATGAGATTATAAAACT
* * * *
680 CATTTAAAGTGAGTAATACA-ACTTTTGAAAGAATGAGAGACCATAAATGGACTTTTCTT-CCTA
1 -ATTTAAAGTGAGTAATA-AGGCTTTTGAAGGAATGA-TGACTATAAATGGACTTTTCTTGCC-A
** * * * * * ** *
743 ATGAATGGGTTTTTCTACACATTTCCTGAGGCAGGCATTCAATTATAGTCT-GGTTAATGAAAAA
62 ATGAAT-ACTTTTTCTTCACGTTTCTTGAGGCAGACATTCAATTATAATCTATTTTAATCAAAAA
* *
807 TGTAAAAAAAAATTAACTCAAAATCAATTTTGAGATTATAAAACT
126 TGT--AAAAAAATTAACTTAAAATCAATTATGAGATTATAAAACT
* *
852 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGTGTGACTATAAATGGACTCTTCTTGCCAATG
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATG-ATGACTATAAATGGACTTTTCTTGCCAATG
* * * * * * * *
917 AATACCTTTTTCTTCATGTATCCTAAGGCAGACATTCATTTACAATTTATTCTAA-CAAAAAATG
65 AATA-CTTTTTCTTCACGTTTCTTGAGGCAGACATTCAATTATAATCTATTTTAATC-AAAAATG
* * ** *
981 TAAAAATATTTAACCTAAAATCAA-TATGAGATGGTAAAACC
128 TAAAAA-AATTAACTTAAAATCAATTATGAGATTATAAAACT
* * * * * * * **
1022 ATTTAAAGCGAGTAATAAAGCTTTCGAAGGCATGGGTGATTATAAATGGACTTTTCTTACTGATG
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GATGACTATAAATGGACTTTTCTTGCCAATG
* * ** * * * *
1087 AATGCTTTTTTCTTCACGTATCTCAAAGTAG-TATTCAATTATAGTCTATTTTAAT
65 AATAC-TTTTTCTTCACGTTTCTTGAGGCAGACATTCAATTATAATCTATTTTAAT
1142 TACAAATTNN
Statistics
Matches: 644, Mismatches: 128, Indels: 61
0.77 0.15 0.07
Matches are distributed among these distances:
169 26 0.04
170 241 0.37
171 343 0.53
172 34 0.05
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (168 bp):
ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGATGACTATAAATGGACTTTTCTTGCCAATGA
ATACTTTTTCTTCACGTTTCTTGAGGCAGACATTCAATTATAATCTATTTTAATCAAAAATGTAA
AAAAATTAACTTAAAATCAATTATGAGATTATAAAACT
Found at i:815 original size:341 final size:340
Alignment explanation
Indices: 169--1096 Score: 1091
Period size: 341 Copynumber: 2.7 Consensus size: 340
159 CTTAAAATCA
** *
169 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAAAGATTTTTCTTGCCAATG
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATG
* * * * * * *
234 AATACGTTTTTCTTCACGTTTCTTAAGGAAGAGATTCACTTATAGTTTGTTTTAATCAAAAATGT
66 AATACCTTTTTCTTCATGTTTCTTAAGGAAGACATTCAATTATAATTTGTTCTAACCAAAAATGT
* *
299 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAATGAGTAATAAGACTTT
131 AAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAAC-ATTTAAAGTGAGTAATAA-ACTTT
* * * * *
364 TGAAGGAAT-AGAAGACCGTAAATGGATTTTTCGTTTC-AATGAATGACTTTTTCTTCACGTTTC
194 TGAAGGAATGAG-AGACCATAAATGGACTTTTC-TTACTAATGAATGACTTTTTCTACACATTTC
* * ** * *
427 TTGAGGTAGACATTCAATAATAATATATTTTAATAAAAAT-TTAAAAAAAA-TAAGCTTAAAATA
257 CTGAGGCAGACATTCAATAATAATATAGGTTAATAAAAATGTAAAAAAAAATTAA-CTCAAAATA
*
490 AATTTTAAGATAATATAAC-
321 AATTTTAAGATAATAAAACT
* * * *
509 AGTTTAAAGTGAGTAATAAGGCTTTCGAAGGTATGGGTGACTACAAATGGACTTTTCTTGCCAAT
1 A-TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
* * *
574 GAATACCTTTTTC-TCTATGTTTCTTGAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAAT
65 GAATACCTTTTTCTTC-ATGTTTCTTAAGGAAGACATTCAATTATAATTTGTTCTAACCAAAAAT
* * *
638 ATAAAAAAATTCAACCTAAAATTAATTATGCGATTATAAAATCATTTAAAGTGAGTAATACAACT
129 GTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAA-CATTTAAAGTGAGTAATA-AACT
* * **
703 TTTGAAAGAATGAGAGACCATAAATGGACTTTTCTTCCTAATGAATGGGTTTTTCTACACATTTC
192 TTTGAAGGAATGAGAGACCATAAATGGACTTTTCTTACTAATGAATGACTTTTTCTACACATTTC
* * * * *
768 CTGAGGCAGGCATTCAATTATAGTCT-GGTTAATGAAAAATGTAAAAAAAAATTAACTCAAAATC
257 CTGAGGCAGACATTCAATAATAATATAGGTTAAT-AAAAATGTAAAAAAAAATTAACTCAAAATA
* *
832 AATTTTGAGATTATAAAACT
321 AATTTTAAGATAATAAAACT
* *
852 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGTGTGACTATAAATGGACTCTTCTTGCCAATG
1 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATG
* * * * * * *
917 AATACCTTTTTCTTCATGTATCCTAAGGCAGACATTCATTTACAATTTATTCTAACAAAAAATGT
66 AATACCTTTTTCTTCATGTTTCTTAAGGAAGACATTCAATTATAATTTGTTCTAACCAAAAATGT
* * ** *
982 AAAAATATTTAACCTAAAATCAA-TATGAGATGGTAAAACCATTTAAAGCGAGTAATAAAGCTTT
131 AAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAA-CATTTAAAGTGAGTAATAAA-CTTT
* * * * ** *
1046 CGAAGGCATGGGTGATTATAAATGGACTTTTCTTACTGATGAATG-CTTTTT
194 TGAAGGAATGAGAGACCATAAATGGACTTTTCTTACTAATGAATGACTTTTT
1097 TCTTCACGTA
Statistics
Matches: 499, Mismatches: 77, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
340 18 0.04
341 308 0.62
342 167 0.33
343 6 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (340 bp):
ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATG
AATACCTTTTTCTTCATGTTTCTTAAGGAAGACATTCAATTATAATTTGTTCTAACCAAAAATGT
AAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACATTTAAAGTGAGTAATAAACTTTTG
AAGGAATGAGAGACCATAAATGGACTTTTCTTACTAATGAATGACTTTTTCTACACATTTCCTGA
GGCAGACATTCAATAATAATATAGGTTAATAAAAATGTAAAAAAAAATTAACTCAAAATAAATTT
TAAGATAATAAAACT
Found at i:2040 original size:171 final size:171
Alignment explanation
Indices: 1749--2315 Score: 557
Period size: 171 Copynumber: 3.4 Consensus size: 171
1739 NNNNNNNNNN
* * * * * ** *
1749 AAGGAATGAGTGACTATAAA-AGGACTTTTGTTATCAATGAATACATTTTTCTTCATATTTCTCA
1 AAGGAATGGGTGACTATAAATA-GACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTTA
* * * ** * *
1813 AGGTAGACATTCAATTATAATTTTTTTTAACCAAAAACGTGAAAAAATTCAACTTAAAATCAATT
65 AGGCAGACATTCAATTATAGTCTTTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATT
* * ** *
1878 TTGAGATTAGAAAGCCATTTAAAGAGAATAATAAGGCTTTTG
130 TTGAGATTATAAAACCATTTAAAGAGAGGAATAAGACTTTTG
* *
1920 AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAGTGCCTTTTTCTTCATGTTTCTTAA
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTTAA
* * *
1985 AGCAGACATTCAATTACAGTCTCTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATTA
66 GGCAGACATTCAATTATAGTCTTTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATT-
* *
2050 TT-TGTTTATAAAACCATTTAAAGCA-AGGAATAAGACTTTT-
130 TTGAGATTATAAAACCATTTAAAG-AGAGGAATAAGACTTTTG
* * * * * * * * * * *
2090 ---G-A---GTAACTAT-AATAAATTTTTCGTGCTAATGGATGGCTTTTGCCTT-ACGTTCCTTG
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTT-TCTTCACGTTTCTTA
* * * *
2146 AGGCAGACATTCAATTATAGCCTTTTTTAACTAAAAATATAAAAAAATTTAACTCAAAGTCAATT
65 AGGCAGACATTCAATTATAGTCTTTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATT
* *
2211 TTGAGATTATAAAACTATTTAAAGTGAGGAATAAGACTTTTG
130 TTGAGATTATAAAACCATTTAAAGAGAGGAATAAGACTTTTG
* * * * * *
2253 AAGAAATAGATGACTATAAATAGACTTTTCATGCCAATGAATGTCTTTTTCTTCACGTTTCTT
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTT
2316 G
Statistics
Matches: 320, Mismatches: 60, Indels: 32
0.78 0.15 0.08
Matches are distributed among these distances:
161 2 0.01
162 121 0.38
163 10 0.03
166 1 0.00
167 2 0.01
170 9 0.03
171 171 0.53
172 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (171 bp):
AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTTAA
GGCAGACATTCAATTATAGTCTTTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATCAATTT
TGAGATTATAAAACCATTTAAAGAGAGGAATAAGACTTTTG
Done.