Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402011.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5107.0, 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, 747
Length: 1245
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Found at i:534 original size:171 final size:171
Alignment explanation
Indices: 17--1238 Score: 1227
Period size: 171 Copynumber: 7.1 Consensus size: 171
7 CATTTAGGAT
* * * *
17 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATGAATAGACTTTTCTTCTAAATGAATGATTTT
1 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTT
* * * * *
82 TTCTACACGTTTCTTGAGGCAGACATTCATTTATAGTCTGTTTTAATTAAAAATATAAAAAAATT
66 TTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATAGAAAAAAATT
* *
147 CAAATTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
131 TAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* * * * * * *
188 AAGTAATAAGGCTTTTGAAAGAATGGGTGACAACAAATAGACTTTTCTTGTTAATAAATGCCTTT
1 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGAC-TT
* * * *
253 TTTCTTCACGTTTCTTGACGTAGACATTCAATCATATTCTGTTTTAACCAAAAAAGTA-AAAAAA
65 TTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAA-TAAAAAA-TAGAAAAAA
* * * *
317 ATTTAACTTAAAATCAATTTTGATATTATAAAACCATTTAAAGT
128 ATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* *
361 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATACAGTTTTCTTCTCAATGAATGACTTT
1 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTT
* * * * * *
426 ATCTACACATTTCTTGAGGTA-AGCATTCATTTATAGTCTGTTTTAATGAAAGATAGAAAAAAAT
66 TTCTTCACGTTTCTTGAGGTAGA-CATTCAATTATAGTCTGTTTTAATAAAAAATAGAAAAAAAT
* * * *
490 TTAACTTGAAATGAATTATGAAATTATAAAACTATTTAAAGT
130 TTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* * *
532 GAGTAATAAGGCTTTTG-AAGCAATGGATGACTAT-AATGGACTTTTCTTAC-CAATAAAT-ACA
1 GAGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATAGACTTTTCTT-CTCAATGAATGAC-
** * * *
593 TTTTTCTTCATATTTGTTGAGGTAGACATTCAATTATTGTCTGTTTTAATAAAAAATATAAAAAA
63 TTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATAGAAAAAA
* * * * * *
658 ATTCAACTTAAAATAAATTATGGGATTATAAACCCATTTAAATC
128 ATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* ** * * *
702 GAGTAATAAGGCTTTTGAAGGAATGAATGACTATAAATAGACTTTTCTTTTCAATGAACGGCTTT
1 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTT
* * * * * * * * *
767 TTCCAT-AGGTTTCTTGAGGCAGGCAATCAATTATAGGCTATTTTAATAAAAAAT-GTAAAACAT
66 TT-CTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATAG-AAAAAAA
* * * * *
830 TTTTACTTAATATCAATTATTAGATTATAAAACCATTTATAGC
129 TTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* * *
873 GAGCAATAAGGCTTTT-AAAGGAATGTGTGACTGTAAATAGACTTTTCTTGCT-AATGAAT--CT
1 GAGTAATAAGGCTTTTGAAA-GAATGGGTGACTATAAATAGACTTTTCTT-CTCAATGAATGAC-
* ** * * ** **
934 TTTTTCCTTTACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATTTAAAAA
63 TTTTT-CTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATAGAAAAA
* * * *
999 TATTCAACTTAAAATCAATTATGAGATTATAGAACTATTTAAACC
127 AATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* * * * * *
1044 GAGTAACAAGGATTTTAAAAGAATGGGTGAATATAAATAGACTTTTCCTAC-CAATAAAT-ACTT
1 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTT-CTTCTCAATGAATGACTT
* * * * * *
1107 TTT-TGTCACAATTTC-TGAGGCAGGCAATCAATTATAGTCTATTTTAATGAAAAAT-GTAAAAA
65 TTTCT-TCAC-GTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATAG-AAAAA
* * * * *
1169 TATTTCACTTAAAATTAGTTATTAGATTATAAAACTATTTAAAGC
127 AATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
1214 GAGTAATAAGGCTTTTGAAAGAATG
1 GAGTAATAAGGCTTTTGAAAGAATG
1239 AATGACT
Statistics
Matches: 865, Mismatches: 159, Indels: 55
0.80 0.15 0.05
Matches are distributed among these distances:
169 4 0.00
170 251 0.29
171 413 0.48
172 93 0.11
173 102 0.12
174 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTT
TTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATAGAAAAAAATT
TAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
Found at i:782 original size:341 final size:338
Alignment explanation
Indices: 17--1245 Score: 1346
Period size: 341 Copynumber: 3.6 Consensus size: 338
7 CATTTAGGAT
* * * *
17 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATGAATAGACTTTTCTTCTAAATGAATGATTTT
1 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTT
* * * * * * *
82 TTCTACACGTTTCTTGAGGC-AGACATTCATTTATAGTCTGTTTTAATTAAAAATATAAAAAAAT
66 TTCCACACATTTCTTGAGGCAAG-CAATCAATTATAGTCTATTTTAATGAAAAATGTAAAAAAAT
* * *
146 TCAAATTAAAATCAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAAGAA
130 TTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA
* * * * *
211 TGGGTGACAACAAATAGACTTTTCTTGTTAATAAATGCCTTTTTTCTTCACGTTTCTTGACGTAG
195 TGGATGACTA-TAATAGACTTTTCTTGCTAATAAAT--CTTTTTTCTTCACGTTTCTTGAGGTAG
* * *
276 ACATTCAATCATATTCTGTTTTAACCAAAAAAGTA-AAAAAAATTTAACTTAAAATCAATTTTGA
257 ACATTCAATTAT-TTCTGTTTTAA-CAAAAAA-TATAAAAAAATTCAACTTAAAATCAATTATGA
*
340 TATTATAAAACCATTTAAAGT-
319 GATTAT-AAACCATTTAAA-TC
* *
361 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATACAGTTTTCTTCTCAATGAATGACTTT
1 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTT
* * * * * * *
426 ATCTACACATTTCTTGAGGTAAGCATTCATTTATAGTCTGTTTTAATGAAAGATAG-AAAAAAAT
66 TTCCACACATTTCTTGAGGCAAGCAATCAATTATAGTCTATTTTAATGAAAAAT-GTAAAAAAAT
* * * *
490 TTAACTTGAAATGAATTATGAAATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTG-AAGCA
130 TTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAG-A
* * * * ** *
554 ATGGATGACTATAATGGACTTTTCTTACCAATAAATACATTTTTCTTCATATTTGTTGAGGTAGA
194 ATGGATGACTATAATAGACTTTTCTTGCTAATAAAT-CTTTTTTCTTCACGTTTCTTGAGGTAGA
* * *
619 CATTCAATTATTGTCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATAAATTATGGGAT
258 CATTCAATTATT-TCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
684 TATAAACCCATTTAAATC
322 TATAAA-CCATTTAAATC
* ** * * *
702 GAGTAATAAGGCTTTTGAAGGAATGAATGACTATAAATAGACTTTTCTTTTCAATGAACGGCTTT
1 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTT
* ** * * * * *
767 TTCCATAGGTTTCTTGAGGCAGGCAATCAATTATAGGCTATTTTAATAAAAAATGTAAAACATTT
66 TTCCACACATTTCTTGAGGCAAGCAATCAATTATAGTCTATTTTAATGAAAAATGTAAAAAAATT
* * * * * *
832 TTACTTAATATCAATTATTAGATTATAAAACCATTTATAGCGAGCAATAAGGCTTTT-AAAGGAA
131 TAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAA-GAA
* * * **
896 TGTG-TGACTGTAAATAGACTTTTCTTGCTAATGAATCTTTTTTCCTTTACGTTTCTCAAGGTAG
195 TG-GATGACTAT-AATAGACTTTTCTTGCTAATAAATCTTTTTT-CTTCACGTTTCTTGAGGTAG
* * * * *
960 ACATTCAATTATAATCTATTTTAACCAAAAATTTAAAAATATTCAACTTAAAATCAATTATGAGA
257 ACATTCAATTAT-TTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
* *
1025 TTATAGAACTATTTAAACC
321 TTATA-AACCATTTAAATC
* * * * * *
1044 GAGTAACAAGGATTTTAAAAGAATGGGTGAATATAAATAGACTTTTCCTAC-CAATAAAT-ACTT
1 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTT-CTTCTCAATGAATGAC-T
* * *
1107 TTTTGTCACA-ATTTC-TGAGGCAGGCAATCAATTATAGTCTATTTTAATGAAAAATGTAAAAAT
64 TTTT-CCACACATTTCTTGAGGCAAGCAATCAATTATAGTCTATTTTAATGAAAAATGTAAAAAA
* * * *
1170 ATTTCACTTAAAATTAGTTATTAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAG
128 ATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAG
*
1235 AATGAATGACT
193 AATGGATGACT
Statistics
Matches: 743, Mismatches: 122, Indels: 43
0.82 0.13 0.05
Matches are distributed among these distances:
340 7 0.01
341 323 0.43
342 206 0.28
343 30 0.04
344 175 0.24
345 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (338 bp):
GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTT
TTCCACACATTTCTTGAGGCAAGCAATCAATTATAGTCTATTTTAATGAAAAATGTAAAAAAATT
TAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT
GGATGACTATAATAGACTTTTCTTGCTAATAAATCTTTTTTCTTCACGTTTCTTGAGGTAGACAT
TCAATTATTTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
AACCATTTAAATC
Found at i:1181 original size:512 final size:510
Alignment explanation
Indices: 17--1245 Score: 1354
Period size: 512 Copynumber: 2.4 Consensus size: 510
7 CATTTAGGAT
* *
17 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATGAATAGACTTTTCTTCTA--AATGAATGA--
1 GAGTAATAAGGCTTTT-AAAGAATGGGTGACTAT-AATAGACTTTTC--CTACCAATAAAT-ACT
* * *
78 TTTTTTCTACACGTTTCTTGAGGCAGACATTCATTTATAGTCTGTTTTAATTAAAAATATAAAAA
61 TTTTTTC-ACA-ATTTC-TGAGGCAGACATTCAATTATAGTCTGTTTTAATAAAAAATATAAAAA
* * *
143 AATTCAAATTAAAATCAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAA
123 AATTCAACTTAAAATAAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAA
** * * * *
208 GAATGGGTGACAACAAATAGACTTTTCTTGTTAATAAATGCCTTTTTTCTTCACGTTTCTTGACG
188 GAATGAATGACTACAAATAGACTTTTCTTGTTAATAAACGCCTTTTTCCATCACGTTTCTTGACG
* * ** *
273 TAGACATTCAATCATATTCTGTTTTAACCAAAAAAGTAAAAAAAATTTAACTTAAAATCAATTTT
253 CAGACAATCAATCATAGGCTATTTTAACCAAAAAAGTAAAAAAAATTTAACTTAAAATCAATTTT
* * * *
338 GATATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATACAG
318 GAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAATACAC
** * * *
403 TTTTCTTCTCAATGAATGACTTTATCTACACATTTCTTGAGGTAAGCATTCATTTATAGTCTGTT
383 TTTTCTTCTCAATGAAT-ACTTTATCTACACATTTCTCAAGGTAAGCATTCAATTATAATCTATT
** * * * * **
468 TTAATGAAAGATAGAAAAAAATTTAACTTGAAATGAATTATGAAATTATAAAACTATTTAAAGT
447 TTAACCAAAAATAGAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTAAACC
* * * *
532 GAGTAATAAGGCTTTTGAAGCAATGGATGACTATAATGGACTTTTCTTACCAATAAATACATTTT
1 GAGTAATAAGGCTTTTAAAG-AATGGGTGACTATAATAGACTTTTCCTACCAATAAATAC-TTTT
* * * *
597 TCTTCA-TATTTGTTGAGGTAGACATTCAATTATTGTCTGTTTTAATAAAAAATATAAAAAAATT
64 T-TTCACAATTT-CTGAGGCAGACATTCAATTATAGTCTGTTTTAATAAAAAATATAAAAAAATT
* * * * *
661 CAACTTAAAATAAATTATGGGATTATAAACCCATTTAAATCGAGTAATAAGGCTTTTGAAGGAAT
127 CAACTTAAAATAAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT
* * * * *
726 GAATGACTATAAATAGACTTTTCTT-TTCAATGAACGGCTTTTTCCAT-AGGTTTCTTGAGGCAG
192 GAATGACTACAAATAGACTTTTCTTGTT-AATAAACGCCTTTTTCCATCACGTTTCTTGACGCAG
* * * * * * *
789 GCAATCAATTATAGGCTATTTTAA-TAAAAAATGT-AAAACATTTTTACTTAATATCAATTATT-
256 ACAATCAATCATAGGCTATTTTAACCAAAAAA-GTAAAAAAAATTTAACTTAAAATCAATT-TTG
* * * *
851 AGATTATAAAACCATTTATAGCGAGCAATAAGGCTTTT-AAAGGAATGTGTGACTGTAAATAGAC
319 AGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTTGAAA-GAATGGGTGACTATAAATACAC
* ** *
915 TTTTCTTGCT-AATGAAT-CTTTTTTCCTTTACGTTTCTCAAGGT-AGACATTCAATTATAATCT
383 TTTTCTT-CTCAATGAATAC-TTTAT-CTACACATTTCTCAAGGTAAG-CATTCAATTATAATCT
** * * *
977 ATTTTAACCAAAAATTTAAAAATATTCAACTTAAAATCAATTATGAGATTATAGAACTATTTAAA
444 ATTTTAACCAAAAATAGAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTAAA
1042 CC
509 CC
* * *
1044 GAGTAACAAGGATTTTAAAAGAATGGGTGAATATAAATAGACTTTTCCTACCAATAAATACTTTT
1 GAGTAATAAGGCTTTT-AAAGAATGGGTGACTAT-AATAGACTTTTCCTACCAATAAATACTTTT
* * * * * *
1109 TTGTCACAATTTCTGAGGCAGGCAATCAATTATAGTCTATTTTAATGAAAAATGTAAAAATATTT
64 TT-TCACAATTTCTGAGGCAGACATTCAATTATAGTCTGTTTTAATAAAAAATATAAAAA-AATT
* * *
1174 C-ACTTAAAATTAGTTATTAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT
127 CAACTTAAAATAAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT
1238 GAATGACT
192 GAATGACT
Statistics
Matches: 594, Mismatches: 99, Indels: 45
0.80 0.13 0.06
Matches are distributed among these distances:
510 1 0.00
511 10 0.02
512 311 0.52
513 75 0.13
514 161 0.27
515 28 0.05
516 5 0.01
517 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (510 bp):
GAGTAATAAGGCTTTTAAAGAATGGGTGACTATAATAGACTTTTCCTACCAATAAATACTTTTTT
TCACAATTTCTGAGGCAGACATTCAATTATAGTCTGTTTTAATAAAAAATATAAAAAAATTCAAC
TTAAAATAAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAAT
GACTACAAATAGACTTTTCTTGTTAATAAACGCCTTTTTCCATCACGTTTCTTGACGCAGACAAT
CAATCATAGGCTATTTTAACCAAAAAAGTAAAAAAAATTTAACTTAAAATCAATTTTGAGATTAT
AAAACCATTTAAAGCGAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAATACACTTTTCTTC
TCAATGAATACTTTATCTACACATTTCTCAAGGTAAGCATTCAATTATAATCTATTTTAACCAAA
AATAGAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTAAACC
Done.