Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401314.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4453.0, 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: 2612
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.29
Warning! 460 characters in sequence are not A, C, G, or T
Found at i:435 original size:172 final size:171
Alignment explanation
Indices: 137--1413 Score: 1096
Period size: 172 Copynumber: 7.5 Consensus size: 171
127 TAATATATGA
* * * * * *
137 ACTTTTTTTGCAAATGAATGA-CTTTTTCTACACGTTT-TCTGAGGCGGGCATTAAATTATAATC
1 ACTTTTCTTGCCAATGAAT-ATCTTTTTCTTCACGTTTCTC-GAGGCAGACATTCAATTATAATC
* * * * *
200 TATTTTAGCTAAAAATGTAAAAAAAATTGAA-TTGAAAATCAAATT-TGAGGTAATAAAACCATT
64 TATTTTAACCAAAAATGT-AAAAAAATTCAACTT-AAAATC-AATTATGAGATTATAAAACCATT
* * *
263 TAAAGTAAGTAATAAAGCTTTTGAAGAAATAAGTGACTATAAACGG
126 TAAAGTGAGTAATAAAGCTTTTGAAGGAATAAGTGACTATAAATGG
* ** *
309 ACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTTTCGAGGTTGATATTCAATTATAATCTA
1 ACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATAATCTA
*
374 TTTTAACCAAAAATGTACAAAGAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
66 TTTTAACCAAAAATGTA-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * *
439 GTGAGTAATAAGGCTTTTGAAGGAATGAA-TGATTATAAATAG
130 GTGAGTAATAAAGCTTTTGAAGGAAT-AAGTGACTATAAATGG
* * * * * * *
481 ACTTTTCTTGTCAATGAA-AGCTTTTTCTTTATGTTTCTCAAAGCAGAAATTCAATTATAATCTA
1 ACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATAATCTA
* * * * * * ** *
545 TTTTAACTAAAAATGTAAAAATATTCAATTTCAAATTAATTCTGAGATTATAAAATAATTTAAAC
66 TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * *
610 TGAGTAATAAGGCTTTTGGAGGAATAGGTGACTATAAATGG
131 TGAGTAATAAAGCTTTTGAAGGAATAAGTGACTATAAATGG
* * * * * * *
651 ACTTTTCTTGCCAATGAAT-GCTTTTTTCTTCACATTTCTAGAGGTAAACATTCAATTCTAGTC-
1 ACTTTTCTTGCCAATGAATATC-TTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATAATCT
* * * *
714 AGTTTTAACTAAAAATGTAAAAAAAAATT-AACTTAAAATAAATTATTAGTTTATAAAACCATTT
65 A-TTTTAACCAAAAATGT--AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
*** * ** **
778 AAACCAAGTAATAAGGCTTTCCAAGGCTTCAA-TGACTATAAATGG
127 AAAGTGAGTAATAAAGCTTTTGAAGGAAT-AAGTGACTATAAATGG
* * * * * * * * * * **
823 ACTTTTCGTACTAAT-AGT-TGGGTTTTGCTTGACG-TTCTCCAAAGCAAACATTCAATTATAGC
1 ACTTTTCTTGCCAATGAATAT--CTTTTTCTTCACGTTTCT-CGAGGCAGACATTCAATTATAAT
* * * * *
885 CTTTTTTAATCAAAAATATAAAAAAAATCAACTTAAAATCAATTTTGAGATTATAAAACCATTTA
63 CTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * **
950 AAGTGAGTAAGAAAGCTTTTGAACGAATGGGTGACTATAAAT-G
128 AAGTGAGTAATAAAGCTTTTGAAGGAATAAGTGACTATAAATGG
* * * * * *
993 ATTTTTCTTACCAATAAATATCTTTTTCTTCACGTTTCCCAATGCAGACATTCAATTATAATCTA
1 ACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATAATCTA
* ** * * * *
1058 TTCTAACCAAAAACATTAAAAAATTCAACCTAAAAACAATTATGAGATTATAAAACCATTTATAG
66 TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * *
1123 CGAGTAAT-AAGCCTTTTAAAGGAATGAGTGACTATAAATAG
131 TGAGTAATAAAG-CTTTTGAAGGAATAAGTGACTATAAATGG
* * * * * * *
1164 ACTTTTCTTGCCAATGAATGTATATTTCTGCATGTTTCTCGAGGTAGACATTCAATTATAATCTG
1 ACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATAATCTA
* * * *
1229 TTTTAACGAAAAATGTACAAAGAATTCAAAC-TAAAATCAATTTTGAGATTAGAAAACCATTTAA
66 TTTTAACCAAAAATGTA-AAAAAATTC-AACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* ** * * ** * * **
1293 AGAGAGTTGTAAGGCTTTTAAAGGAATGGGTGACAATAAGTAA
129 AGTGAGTAATAAAGCTTTTGAAGGAATAAGTGACTATAAATGG
** * * * *
1336 ACTTTTCTTGGTAATGAATACCTTTTTCTTCATGTTT-TCTAGGGCAGA-ATATCAATTATATTC
1 ACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGA-GGCAGACAT-TCAATTATAATC
* *
1399 TGTTCTAACCAAAAA
64 TATTTTAACCAAAAA
1414 NNNNNNNNNN
Statistics
Matches: 897, Mismatches: 179, Indels: 58
0.79 0.16 0.05
Matches are distributed among these distances:
169 4 0.00
170 232 0.26
171 247 0.28
172 394 0.44
173 20 0.02
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (171 bp):
ACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATAATCTA
TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
TGAGTAATAAAGCTTTTGAAGGAATAAGTGACTATAAATGG
Found at i:790 original size:342 final size:342
Alignment explanation
Indices: 190--1413 Score: 1220
Period size: 342 Copynumber: 3.6 Consensus size: 342
180 GCGGGCATTA
* * * * * *
190 AATTATAATCTATTTTAGCTAAAAATGTAAAAAAAATTGAATTGAAAATCAAATTTGAGGTAATA
1 AATTATAATCTATTTTAACTAAAAATGT-AAAAAAATTCAATTTAAAATCAATTTTGAGATTATA
* * * *
255 AAACCATTTAAAGTAAGTAATAAAGCTTTTGAAGAAATAAGTGACTATAAACGGACTTTTCTTGC
65 AAACCATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGC
* * * *
320 CAATGAATATCTTTTTCTTCACGTTTTTCGAGGTTGATATTCAATTATAATCTATTTTAACCAAA
130 CAATGAATATCTTTTTCTTCACGTTTCTAGAGGTAGACATTCAATTATAATCTATTTTAACCAAA
* * * *
385 AATGT-ACAAAGAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATA
195 AATGTAAAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
449 AGGCTTTTGAAGGAATGAATGATTATAAATAGACTTTTCTTGTCAATGAAAGCTTTTTCTTTATG
260 AGGCTTTTAAAGGAATGAATGACTATAAATAGACTTTTCTTGTCAATGAAAG-TTTTTCTTCATG
514 TTTCTCAAAGCAGAAATTC
324 TTTCTCAAAGCAGAAATTC
* * * *
533 AATTATAATCTATTTTAACTAAAAATGTAAAAATATTCAATTTCAAATTAATTCTGAGATTATAA
1 AATTATAATCTATTTTAACTAAAAATGTAAAAAAATTCAATTTAAAATCAATTTTGAGATTATAA
** * * *
598 AATAATTTAAACTGAGTAATAAGGCTTTTGGAGGAATAGGTGACTATAAATGGACTTTTCTTGCC
66 AACCATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCC
* * * * * *
663 AATGAAT-GCTTTTTTCTTCACATTTCTAGAGGTAAACATTCAATTCTAGTC-AGTTTTAACTAA
131 AATGAATATC-TTTTTCTTCACGTTTCTAGAGGTAGACATTCAATTATAATCTA-TTTTAACCAA
* * * *
726 AAATGTAAAAAAAAATT-AACTTAAAATAAATTATTAGTTTATAAAACCATTTAAACCAAGTAAT
194 AAATGTAAAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
** ** * * *** *
790 AAGGCTTTCCAAGGCTTCAATGACTATAAATGGACTTTTC--GTACTAATAGTTGGGTTTTGCTT
259 AAGGCTTTTAAAGGAATGAATGACTATAAATAGACTTTTCTTGT-C-AAT-G-AAAGTTTTTCTT
* *
853 GACG-TTCTCCAAAGCA-AACATTC
320 CATGTTTCT-CAAAGCAGAA-ATTC
** * * * *
876 AATTATAGCCTTTTTTAA-TCAAAAATATAAAAAAAATCAACTTAAAATCAATTTTGAGATTATA
1 AATTATAATCTATTTTAACT-AAAAATGTAAAAAAATTCAATTTAAAATCAATTTTGAGATTATA
* * * * *
940 AAACCATTTAAAGTGAGTAAGAAAGCTTTTGAACGAATGGGTGACTATAAAT-GATTTTTCTTAC
65 AAACCATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGC
* * * * *
1004 CAATAAATATCTTTTTCTTCACGTTTCCCA-ATGCAGACATTCAATTATAATCTATTCTAACCAA
130 CAATGAATATCTTTTTCTTCACGTTT-CTAGAGGTAGACATTCAATTATAATCTATTTTAACCAA
* ** * *
1068 AAA--CATTAAAAAATTCAACCTAAAA-ACAATTATGAGATTATAAAACCATTTATAGCGAGTAA
194 AAATGTAAAAAAAAATTCAACTTAAAATA-AATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * * *
1130 TAAGCCTTTTAAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGTATATTTCTGC
258 TAAGGCTTTTAAAGGAATGAATGACTATAAATAGACTTTTCTTGTCAATGAAAGT-T-TTTCTTC
* * * *
1195 ATGTTTCTCGAGGTAGACATTC
321 ATGTTTCTCAAAGCAGAAATTC
* * * ** *
1217 AATTATAATCTGTTTTAACGAAAAATGTACAAAGAATTCAAACTAAAATCAATTTTGAGATTAGA
1 AATTATAATCTATTTTAACTAAAAATGTA-AAAAAATTCAATTTAAAATCAATTTTGAGATTATA
* ** * * * * * ** *
1282 AAACCATTTAAAGAGAGTTGTAAGGCTTTTAAAGGAATGGGTGACAATAAGTAAACTTTTCTTGG
65 AAACCATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGC
* * * * * * *
1347 TAATGAATACCTTTTTCTTCATGTTTTCTAG-GGCAGA-ATATCAATTATATTCTGTTCTAACCA
130 CAATGAATATCTTTTTCTTCACG-TTTCTAGAGGTAGACAT-TCAATTATAATCTATTTTAACCA
1410 AAAA
193 AAAA
1414 NNNNNNNNNN
Statistics
Matches: 713, Mismatches: 141, Indels: 54
0.79 0.16 0.06
Matches are distributed among these distances:
339 2 0.00
340 14 0.02
341 114 0.16
342 363 0.51
343 216 0.30
344 4 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (342 bp):
AATTATAATCTATTTTAACTAAAAATGTAAAAAAATTCAATTTAAAATCAATTTTGAGATTATAA
AACCATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCC
AATGAATATCTTTTTCTTCACGTTTCTAGAGGTAGACATTCAATTATAATCTATTTTAACCAAAA
ATGTAAAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
GGCTTTTAAAGGAATGAATGACTATAAATAGACTTTTCTTGTCAATGAAAGTTTTTCTTCATGTT
TCTCAAAGCAGAAATTC
Found at i:1393 original size:513 final size:512
Alignment explanation
Indices: 185--1413 Score: 1271
Period size: 513 Copynumber: 2.4 Consensus size: 512
175 CTGAGGCGGG
* * * * * *
185 CATTAAATTATAATCTATTTTAGCTAAAAATGTAAAAAAAATTGAATTGAAAATCAAATTTGAGG
1 CATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAAATT-AACT-AAAATCAATTTTGAGA
* * * * *
250 TAATAAAACCATTTAAAGTAAGTAATAAAGCTTTTGAAGAAATAAGTGACTATAAACGGACTTTT
64 TTATAAAACCATTTAAAG-AAGTAATAAGGCTTTTAAAGGAATAAGTGACTATAAATGGACTTTT
* * * ** *
315 CTTGCCAATGAATATCTTTTTCTTCACGTTTT-TCGAGGTTG-ATATTCAATTATAATCTATTTT
128 CTTGCTAATGAATACCTTTTTCTTCACGTTTTCTAG-GGCAGAATATTCAATTATAACCTATTTT
* * *
378 AACCAAAAATGTACAAAGAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGA
192 AACCAAAAATATACAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGA
* * * * ** *
443 GTAATAAGGCTTTTGAAGGAATGAATGATTATAAATAGACTTTTCTTGTCAATGAAAGCTTTTTC
257 GTAAGAAAGCTTTTGAACGAATGAATGACTATAAATAGACTTTTCTTACCAATAAAAGCTTTTTC
* * * * *
508 TTTATGTTTCTCAAAGCAGAAATTCAATTATAATCTATTTTAACTAAAAATGTAAAAATATTCAA
322 TTCACGTTTCCCAAAGCAGAAATTCAATTATAATCTATTCTAACAAAAAATGTAAAAATATTCAA
** * ** * * * **
573 TTTCAAATTAATTCTGAGATTATAAAATAATTTAAACTGAGTAATAAGGCTTTTGGAGGAATAGG
387 CCTAAAAACAATTATGAGATTATAAAACAATTTAAACTGAGTAATAAGCCTTTTAAAGGAATAGG
* * *
638 TGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTCTAGAGGTAAA
452 TGACTATAAATAGACTTTTCTTGCCAATGAATGCTTATTTCTGCACATTTCTAGAGGTAAA
* * * *
699 CATTCAATTCTAGTCAGTTTTAACTAAAAATGTAAAAAAAAATTAACTTAAAATAAATTATT-AG
1 CATTCAATTATAATCTGTTTTAACTAAAAATGT-AAAAAAAATTAAC-TAAAATCAATT-TTGAG
* * ** **
763 TTTATAAAACCATTTAAACCAAGTAATAAGGCTTTCCAAGGCTTCAA-TGACTATAAATGGACTT
63 ATTATAAAACCATTTAAA-GAAGTAATAAGGCTTTTAAAGGAAT-AAGTGACTATAAATGGACTT
* * * *** * * * * ** * * *
827 TTCGTACTAAT-AGTTGGGTTTTGCTTGACGTTCTCCAAAGCA-AACATTCAATTATAGCCTTTT
126 TTCTTGCTAATGA-ATACCTTTTTCTTCACGTTTTCTAGGGCAGAATATTCAATTATAACCTATT
* *
890 TTAATCAAAAATATA-AAAAAAATCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGT
190 TTAACCAAAAATATACAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGT
** * *
954 GAGTAAGAAAGCTTTTGAACGAATGGGTGACTATAAAT-GATTTTTCTTACCAATAAATATCTTT
255 GAGTAAGAAAGCTTTTGAACGAATGAATGACTATAAATAGACTTTTCTTACCAATAAA-AGCTTT
* *
1018 TTCTTCACGTTTCCCAATGCAGACATTCAATTATAATCTATTCTAACCAAAAACAT-TAAAAA-A
319 TTCTTCACGTTTCCCAAAGCAGAAATTCAATTATAATCTATTCTAA-CAAAAA-ATGTAAAAATA
* *
1081 TTCAACCTAAAAACAATTATGAGATTATAAAACCATTTATAGC-GAGTAATAAGCCTTTTAAAGG
382 TTCAACCTAAAAACAATTATGAGATTATAAAACAATTTA-AACTGAGTAATAAGCCTTTTAAAGG
** *
1145 AAT-GAGTGACTATAAATAGACTTTTCTTGCCAATGAATG-TATATTTCTGCATGTTTCTCGAGG
446 AATAG-GTGACTATAAATAGACTTTTCTTGCCAATGAATGCT-TATTTCTGCACATTTCTAGAGG
*
1208 TAGA
509 TAAA
* * *
1212 CATTCAATTATAATCTGTTTTAACGAAAAATGTACAAAGAATTCAAACTAAAATCAATTTTGAGA
1 CATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAAATT--AACTAAAATCAATTTTGAGA
* ** ** * * **
1277 TTAGAAAACCATTTAAAGAGAGTTGTAAGGCTTTTAAAGGAATGGGTGACAATAAGTAAACTTTT
64 TTATAAAACCATTTAAAGA-AGTAATAAGGCTTTTAAAGGAATAAGTGACTATAAATGGACTTTT
* * ** * *
1342 CTTGGTAATGAATACCTTTTTCTTCATGTTTTCTAGGGCAGAATA-TCAATTATATTCTGTTCTA
128 CTTGCTAATGAATACCTTTTTCTTCACGTTTTCTAGGGCAGAATATTCAATTATAACCTATTTTA
1406 ACCAAAAA
193 ACCAAAAA
1414 NNNNNNNNNN
Statistics
Matches: 571, Mismatches: 123, Indels: 43
0.77 0.17 0.06
Matches are distributed among these distances:
512 28 0.05
513 365 0.64
514 161 0.28
515 17 0.03
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (512 bp):
CATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAAATTAACTAAAATCAATTTTGAGATT
ATAAAACCATTTAAAGAAGTAATAAGGCTTTTAAAGGAATAAGTGACTATAAATGGACTTTTCTT
GCTAATGAATACCTTTTTCTTCACGTTTTCTAGGGCAGAATATTCAATTATAACCTATTTTAACC
AAAAATATACAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAA
GAAAGCTTTTGAACGAATGAATGACTATAAATAGACTTTTCTTACCAATAAAAGCTTTTTCTTCA
CGTTTCCCAAAGCAGAAATTCAATTATAATCTATTCTAACAAAAAATGTAAAAATATTCAACCTA
AAAACAATTATGAGATTATAAAACAATTTAAACTGAGTAATAAGCCTTTTAAAGGAATAGGTGAC
TATAAATAGACTTTTCTTGCCAATGAATGCTTATTTCTGCACATTTCTAGAGGTAAA
Done.