Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402433.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5512.0, 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, 925
Length: 1543
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:297 original size:171 final size:170
Alignment explanation
Indices: 21--1005 Score: 920
Period size: 171 Copynumber: 5.8 Consensus size: 170
11 AAGGCTTGGG
* * *
21 TGACTATAAATAGG-CTTTTCTTGCCAATGAATGACTTTTTCTTCACGTTTCTCAAGGTAAACAT
1 TGACTATAAAT-GGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACATTTCT-GAGGTAAACAT
* * * * *
85 TCAAATATACTCTGTTTTAACTAAAAATATAAAAAAATTCAA-TGTAAAGTCAATTATCAGATTA
64 TCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTCAACT-TAAAATCAATTATAAGATTA
149 TAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAGGTATAGA
128 TAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAGGTATAGA
* * * ** **
192 TGACTATAAATGGATTTTTCTTGCCAATGAATGGCTTTTTTTTTATGTTTTCTGAGGTAGGCATT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCA-CATTTCTGAGGTAAACATT
* * * *
257 CAATTATAATCTATTTTAACTAAAAATGTAAAACAATTCAACTTAAAATCAATTTTAAAATTATA
65 CAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATA
* *
322 AAA-ATATTTAAAGTAAGCAATAAGGCTTTCGAAGGTAT-GA
130 AAACA-ATTTAAAGCAAGTAATAAGGCTTTCGAAGGTATAGA
* * * * * *
362 GTGACTATAAACGGACTTTTATTACCAATGAAT--ATATTTTCTTCACATTTTCTAAGGTAGACA
1 -TGACTATAAATGGACTTTTCTTGCCAATGAATGGCT-TTTTCTTCACA-TTTCTGAGGTAAACA
* * *
425 TTCAATTATAATTTGTTTTAA-TAAAAAATGT-ACAAAATTCAACTTAAAATCAATTATGAGATT
63 TTCAATTATAATCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATT
* * * *
488 ATAAAA-ACATCTAAAGCAAGTAATAAGGCTTTTGAAGGTATGGG
127 ATAAAACA-ATTTAAAGCAAGTAATAAGGCTTTCGAAGGTATAGA
* * * ** **
532 TGACTATAAATAGACTTTTGTTGCCAATAAATATCTTTTTCTTCACATTTCTTGAGACAAACATT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACATTTC-TGAGGTAAACATT
* * * * * *
597 TAATTATTAA-CTATTTTAA-TAAAAAATGTAAAACAATTCCACTGAAAATCAATTATGAGATTA
65 CAATTA-TAATCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTA
* * * * * * *
660 TAAAACTATTGAAATCGAGTAATAAGGCTTTCAAAGGCATGGA
128 TAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAGGTATAGA
* * * * *
703 AGACTCTAAATGGACTTTTCTTGCAAATGAATGAG-TCTTTCTTCACATTTCTTGAGGTACACAT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATG-GCTTTTTCTTCACATTTC-TGAGGTAAACAT
* * * ** * * * *
767 TCAATTATAGTCTGTGTTAAC-CAAAATACAAAAAAAATCAACTTATAGTCAACTATAAGATTAT
64 TCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTAT
* * * * * * *
831 AAAACTATTTAAAGTAAATAATAAGCCTTTTGAAGGCATAGG
129 AAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAGGTATAGA
* * * * * **
873 TGACTATAAATGGACTTTTCTTGTCAATGATTGGCTTTTACTTCA-TTTTCCTTAGACAAACATT
1 TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACATTT-CTGAGGTAAACATT
* * * * * *
937 AAACTATAGTCTGTTTTAACCAAAACTCTAAAAAAATTCAACTTAAAATCAATTATGAA-ATTAT
65 CAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT-AAGATTAT
1001 AAAAC
129 AAAAC
1006 CGTTTAAATA
Statistics
Matches: 662, Mismatches: 130, Indels: 45
0.79 0.16 0.05
Matches are distributed among these distances:
169 126 0.19
170 235 0.35
171 295 0.45
172 6 0.01
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (170 bp):
TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACATTTCTGAGGTAAACATTC
AATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAA
AACAATTTAAAGCAAGTAATAAGGCTTTCGAAGGTATAGA
Found at i:934 original size:340 final size:334
Alignment explanation
Indices: 1--1024 Score: 1070
Period size: 340 Copynumber: 3.0 Consensus size: 334
* *
1 AAGGCTTTCAAAGGCTTGGGTGACTATAAATAGG-CTTTTCTTGCCAATGAATGACTTTTTCTTC
1 AAGGCTTTCAAAGGCATGGATGACTATAAAT-GGACTTTTCTTGCCAATGAATGA-TTTTTCTTC
* * * * *
65 ACGTTTCTCAAGGTAAACATTCAAATATACTCTGTTTTAACTAAAAATATAAAAAAATTCAA-TG
64 ACATTTCTTAAGGTAAACATTCAATTATAATCTGTTTTAAC-AAAAATACAAAAAAATTCAACT-
* * *
129 TAAAGTCAATTATCAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAGGTATAGATG
127 TAAAGTCAATTATAAGATTATAAAAC-ATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATAGGTG
* * * * ** ** *
194 ACTATAAATGGATTTTTCTTGCCAATGAATGGCTTTTTTTTTATGTTTTCTGAGGTAGGCATTCA
191 ACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCA--TTTTCTTAGACAAACATTAA
* *
259 ATTATAATCTATTTTAACTAAAAATGTAAAACAATTCAACTTAAAATCAATTTTAAAATTATAAA
254 ATTATAA-CTATTTTAA-TAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAAATTATAAA
* * *
324 AATATTTAAAGTAAGCAAT
317 ACTATTTAAA-TGAGTAAT
* * * * *
343 AAGGCTTTCGAAGGTAT-GAGTGACTATAAACGGACTTTTATTACCAATGAAT-ATATTTTCTTC
1 AAGGCTTTCAAAGGCATGGA-TGACTATAAATGGACTTTTCTTGCCAATGAATGAT-TTTTCTTC
* * * ** *
406 ACATTT-TCTAAGGTAGACATTCAATTATAATTTGTTTTAATAAAAA-ATGTACAAAATTCAACT
64 ACATTTCT-TAAGGTAAACATTCAATTATAATCTGTTTTAACAAAAATA-CAAAAAAATTCAACT
* * * *
469 TAAAATCAATTATGAGATTATAAAAACATCTAAAGCAAGTAATAAGGCTTTTGAAGGTATGGGTG
127 TAAAGTCAATTATAAGATTAT-AAAACATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATAGGTG
* * * ** * *
534 ACTATAAATAGACTTTTGTTGCCAATAAATATCTTTTTCTTCACATTTCTTGAGACAAACATTTA
191 ACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCA-TTTTCTT-AGACAAACATTAA
* * *
599 ATTATTAACTATTTTAATAAAAAATGTAAAACAATTCCACTGAAAATCAATTATGAGATTATAAA
254 ATTA-TAACTATTTTAAT-AAAAATGTAAAACAATTCAACTTAAAATCAATTATGAAATTATAAA
*
664 ACTATTGAAATCGAGTAAT
317 ACTATTTAAAT-GAGTAAT
* * * *
683 AAGGCTTTCAAAGGCATGGAAGACTCTAAATGGACTTTTCTTGCAAATGAATGAGTCTTTCTTCA
1 AAGGCTTTCAAAGGCATGGATGACTATAAATGGACTTTTCTTGCCAATGAATGA-TTTTTCTTCA
* * * * * * *
748 CATTTCTTGAGGTACACATTCAATTATAGTCTGTGTTAACCAAAATACAAAAAAAATCAACTTAT
65 CATTTCTTAAGGTAAACATTCAATTATAATCTGTTTTAACAAAAATACAAAAAAATTCAACTTAA
* * * * *
813 AGTCAACTATAAGATTATAAAACTATTTAAAGTAAATAATAAGCCTTTTGAAGGCATAGGTGACT
130 AGTCAATTATAAGATTATAAAAC-ATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATAGGTGACT
* * * *
878 ATAAATGGACTTTTCTTGTCAATGATTGGCTTTTACTTCATTTTCCTTAGACAAACATTAAACTA
194 ATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATTTT-CTTAGACAAACATTAAATTA
* * * * * * **
943 TAGTCTGTTTTAACCAAAACTCTAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACCG
258 TA-ACTATTTTAA-TAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAAATTATAAAACTA
1008 TTTAAATAGAGTAAT
321 TTTAAAT-GAGTAAT
1023 AA
1 AA
1025 TACTTTTGAA
Statistics
Matches: 560, Mismatches: 102, Indels: 42
0.80 0.14 0.06
Matches are distributed among these distances:
339 10 0.02
340 309 0.55
341 198 0.35
342 43 0.08
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (334 bp):
AAGGCTTTCAAAGGCATGGATGACTATAAATGGACTTTTCTTGCCAATGAATGATTTTTCTTCAC
ATTTCTTAAGGTAAACATTCAATTATAATCTGTTTTAACAAAAATACAAAAAAATTCAACTTAAA
GTCAATTATAAGATTATAAAACATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATAGGTGACTAT
AAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATTTTCTTAGACAAACATTAAATTATAA
CTATTTTAATAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTAA
ATGAGTAAT
Found at i:975 original size:511 final size:510
Alignment explanation
Indices: 17--1004 Score: 1130
Period size: 511 Copynumber: 1.9 Consensus size: 510
7 TTCAAAGGCT
* * * **
17 TGGGTGACTATAAATAGGCTTTTCTTGCCAATGAATGACTTTTTCTTCACGTTTCTCAAGGTAAA
1 TGGGTGACTATAAATAGACTTTTCTTGCCAATAAATGACTTTTTCTTCACATTTCTCAAGACAAA
* * *
82 CATTCAAATATACTCTGTTTTAACTAAAAATATAAAAAAATTCAATGTAAAGTCAATTATCAGAT
66 CATTCAAATATACACTATTTTAACTAAAAATATAAAAAAATTCAATGTAAAATCAATTATCAGAT
* * * * *
147 TATAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAGGTATAGATGACTATAAATGGATTTTTC
131 TATAAAACAATTGAAAGCAAGTAATAAGGCTTTCAAAGGCATAGAAGACTATAAATGGACTTTTC
* * *** * ** *
212 TTGCCAATGAATGGCTTTTTTTTTATGTTTTCTGAGGTAGGCATTCAATTATAATCTATTTTAAC
196 TTGCAAATGAATGGCTTTCTTCACATGTTCTCTGAGGTACACATTCAATTATAATCTATGTTAAC
** * * * * *
277 TAAAAATGTAAAACAATTCAACTTAAAATCAATTTTAAAATTATAAAAATATTTAAAGTAAGCAA
261 TAAAAATACAAAAAAAATCAACTTAAAATCAACTATAAAATTATAAAAATATTTAAAGTAAACAA
* * *
342 TAAGGCTTTCGAAGGTATGAGTGACTATAAACGGACTTTTATTACCAATGAATATATTTTCTTCA
326 TAAGCCTTTCGAAGGCATGAGTGACTATAAACGGACTTTTATTACCAATGAATAGATTTTCTT-A
** * * * * * * *
407 CATTTTCTAAGGTAGACATTCAATTATAATTTGTTTTAATAAAAAATGTACAAAATTCAACTTAA
390 CATTTTCTAAGACAAACATTAAACTATAATCTGTTTTAACAAAAAATCTAAAAAATTCAACTTAA
*
472 AATCAATTATGAGATTATAAAAACATCTAAAGCAAGTAATAAGGCTTTTGAAGGTA
455 AATCAATTATGAAATTATAAAAACATCTAAAGCAAGTAATAAGGCTTTTGAAGGTA
* **
528 TGGGTGACTATAAATAGACTTTTGTTGCCAATAAAT-ATCTTTTTCTTCACATTTCTTGAGACAA
1 TGGGTGACTATAAATAGACTTTTCTTGCCAATAAATGA-CTTTTTCTTCACATTTCTCAAGACAA
* * * * * *
592 ACATTTAATTATTA-ACTATTTTAA-TAAAAAATGTAAAACAATTCCACTG-AAAATCAATTATG
65 ACATTCAAATA-TACACTATTTTAACT-AAAAATATAAAAAAATT-CAATGTAAAATCAATTATC
* * * * *
654 AGATTATAAAACTATTGAAATCGAGTAATAAGGCTTTCAAAGGCATGGAAGACTCTAAATGGACT
127 AGATTATAAAACAATTGAAAGCAAGTAATAAGGCTTTCAAAGGCATAGAAGACTATAAATGGACT
* *
719 TTTCTTGCAAATGAATGAGTCTTTCTTCACAT-TTCT-TGAGGTACACATTCAATTATAGTCTGT
192 TTTCTTGCAAATGAATG-G-CTTTCTTCACATGTTCTCTGAGGTACACATTCAATTATAATCTAT
* * * * *
782 GTTAAC-CAAAATACAAAAAAAATCAACTTATAGTCAACTATAAGATTATAAAACTATTTAAAGT
255 GTTAACTAAAAATACAAAAAAAATCAACTTAAAATCAACTATAAAATTATAAAAATATTTAAAGT
* * * * ** * * *
846 AAATAATAAGCCTTTTGAAGGCAT-AGGTGACTATAAATGGACTTTTCTTGTCAATGATTGGCTT
320 AAACAATAAGCCTTTCGAAGGCATGA-GTGACTATAAACGGACTTTTATTACCAATGAATAGATT
* * * *
910 TTACTT-CATTTTCCTTAGACAAACATTAAACTATAGTCTGTTTTAACCAAAACTCTAAAAAAAT
384 TT-CTTACATTTT-CTAAGACAAACATTAAACTATAATCTGTTTTAACAAAAAATCT-AAAAAAT
974 TCAACTTAAAATCAATTATGAAATTATAAAA
446 TCAACTTAAAATCAATTATGAAATTATAAAA
1005 CCGTTTAAAT
Statistics
Matches: 391, Mismatches: 76, Indels: 20
0.80 0.16 0.04
Matches are distributed among these distances:
509 7 0.02
510 131 0.34
511 235 0.60
512 10 0.03
513 8 0.02
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (510 bp):
TGGGTGACTATAAATAGACTTTTCTTGCCAATAAATGACTTTTTCTTCACATTTCTCAAGACAAA
CATTCAAATATACACTATTTTAACTAAAAATATAAAAAAATTCAATGTAAAATCAATTATCAGAT
TATAAAACAATTGAAAGCAAGTAATAAGGCTTTCAAAGGCATAGAAGACTATAAATGGACTTTTC
TTGCAAATGAATGGCTTTCTTCACATGTTCTCTGAGGTACACATTCAATTATAATCTATGTTAAC
TAAAAATACAAAAAAAATCAACTTAAAATCAACTATAAAATTATAAAAATATTTAAAGTAAACAA
TAAGCCTTTCGAAGGCATGAGTGACTATAAACGGACTTTTATTACCAATGAATAGATTTTCTTAC
ATTTTCTAAGACAAACATTAAACTATAATCTGTTTTAACAAAAAATCTAAAAAATTCAACTTAAA
ATCAATTATGAAATTATAAAAACATCTAAAGCAAGTAATAAGGCTTTTGAAGGTA
Done.