Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401466.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4593.0, 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: 2082
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.31
Warning! 300 characters in sequence are not A, C, G, or T
Found at i:715 original size:341 final size:339
Alignment explanation
Indices: 129--857 Score: 837
Period size: 341 Copynumber: 2.1 Consensus size: 339
119 NNNNNNNNNN
* * * * * *
129 ATTATGAGATTATAAAACTATTTAAAACAAGTAATAAGCCTTTTGATGGAATGGGTGACTATGAA
1 ATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAA
* * ***
194 TGGACTTTTCTTGCCAATGAATGCTTTTTGTTTGCTTTTCTATGCGTAGACATTCAATAATAGTT
66 CGAACTTTTCTTGCCAATGAATGCTTTTTGTTTGC-TTTCTATGCGTAGACATTCAATAATAACC
* *
259 TGTTTTAACCAAAATATAAAAAAGTTCTACTTAAAATCAATTATGAGATTATAAAACCACTTAAA
130 TGTTTTAACAAAAATATAAAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAACCACTTAAA
* * *
324 GAAAGTAATAAGGCCTTTAAAGGAATGGGTGACAATAAACTGATTTTTTTTGCTAGTGAATGCCT
195 GAAAGTAATAAGGCCTTTAAAGGAATGGGTGACAATAAACTGATTTTTTTTACTAGTAAATACCT
* * * * * * * *
389 TTTTCTTCACTTTTCTCT-AGGTAGACATTCAATTATTATCTGTTTTAAACCAAAGTG-TAAAAA
260 TTTTCTTCACATTTCT-TGAGGCAGACATTCAATTATAATCTATTTGAAACAAAAATGAAAAAAA
* *
452 ATTCAAC-TTAAAATCA
324 AATC-ACTTTAAAATAA
* * * **
468 ATTATGCGATTATAAAGCCATTTAAAGCGAGTAATAAGTGTTTTGAAGGAATGAGTGACTATAAA
1 ATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAA
* * *
533 CGAACTTTTTTTGCCAATGAATGCTTTTTTGTTCATG-TTTCT-TCGGGTAGACATTCAATTATA
66 CGAACTTTTCTTGCCAATGAATGC-TTTTTGTT--TGCTTTCTAT-GCGTAGACATTCAATAATA
* *
596 ACCTGTTTTAACTAAAAATATACAAAAA-TTCAACTTAAATTCAATTATGAGATTATAAAACTA-
127 ACCTGTTTTAAC-AAAAATATA-AAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAACCAC
********* * *
659 TTNNNNNNNNNNAATAAGGCCTTTGAAGGAATGGGTGACTATAAA-T-ATACTTTTTTTACTAGT
190 TT-AAAGAAAGTAATAAGGCCTTTAAAGGAATGGGTGACAATAAACTGAT--TTTTTTTACTAGT
*
722 AAATACCTTTTTCTTCACATTTCTTGAGGCAGACATTCAATTATAATCTATTTGAATCAAAAATG
252 AAATACCTTTTTCTTCACATTTCTTGAGGCAGACATTCAATTATAATCTATTTGAAACAAAAATG
787 AAAAAAAAATCACTTTAAAATAA
317 AAAAAAAAATCACTTTAAAATAA
* *
810 ATTATGAGATTATAAAACCACTTAAAGTAAGTAATAAGACTTTTGAAG
1 ATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAG
858 NNNNNNNNNN
Statistics
Matches: 324, Mismatches: 54, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
339 79 0.24
340 43 0.13
341 138 0.43
342 64 0.20
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Consensus pattern (339 bp):
ATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAA
CGAACTTTTCTTGCCAATGAATGCTTTTTGTTTGCTTTCTATGCGTAGACATTCAATAATAACCT
GTTTTAACAAAAATATAAAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAACCACTTAAAG
AAAGTAATAAGGCCTTTAAAGGAATGGGTGACAATAAACTGATTTTTTTTACTAGTAAATACCTT
TTTCTTCACATTTCTTGAGGCAGACATTCAATTATAATCTATTTGAAACAAAAATGAAAAAAAAA
TCACTTTAAAATAA
Found at i:1297 original size:171 final size:171
Alignment explanation
Indices: 129--1298 Score: 854
Period size: 171 Copynumber: 6.9 Consensus size: 171
119 NNNNNNNNNN
* * * *
129 ATTATGAGATTATAAAACTATTTAAA-ACAAGTAATAA-GCCTTTTGATGGAATGGGTGACTATG
1 ATTATGAGATTATAAAACCACTTAAAGA-AAGTAATAAGGCC-TTTGAAGGAATGGGTGACTATA
** * * * ** * *
192 AATGGACTTTTCTTGCCAATGAATG-CTTTTTGTTTGC-TTT-TCTATGCGTAGACATTCAATAA
64 AACAGACTTTTTTTGCTAATGAATGCCTTTTTCTTCACGTTTCTCGA-G-GTAGACATTCAATTA
* *
254 TAGTTTGTTTTAACC-AAAAT-ATAAAAAAGTTCTACTTAAAATCA
127 TAGTCTGTTTTAACCAAAAATGATAAAAAA-TTCAACTTAAAATCA
* *
298 ATTATGAGATTATAAAACCACTTAAAGAAAGTAATAAGGCCTTTAAAGGAATGGGTGACAATAAA
1 ATTATGAGATTATAAAACCACTTAAAGAAAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAA
* * * * *
363 CTGATTTTTTTTGCTAGTGAATGCCTTTTTCTTCACTTTTCTCTAGGTAGACATTCAATTATTA-
66 CAGACTTTTTTTGCTAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTA-TAG
*
427 TCTGTTTTAAACC-AAAGTG-TAAAAAATTCAACTTAAAATCA
130 TCTGTTTT-AACCAAAAATGATAAAAAATTCAACTTAAAATCA
* * * ** * *
468 ATTATGCGATTATAAAGCCATTTAAAGCGAGTAATAAGTG-TTTTGAAGGAATGAGTGACTATAA
1 ATTATGAGATTATAAAACCACTTAAAGAAAGTAATAAG-GCCTTTGAAGGAATGGGTGACTATAA
* * * *
532 AC-GAACTTTTTTTGCCAATGAATGCTTTTTTGTTCATGTTTCTTCG-GGTAGACATTCAATTAT
65 ACAG-ACTTTTTTTGCTAATGAATGCCTTTTTCTTCACGTTTC-TCGAGGTAGACATTCAATTAT
** * *
595 AACCTGTTTTAACTAAAAAT-ATACAAAAATTCAACTTAAATTCA
128 AGTCTGTTTTAACCAAAAATGATA-AAAAATTCAACTTAAAATCA
* *********
639 ATTATGAGATTATAAAACTA-TTNNNNNNNNNNAATAAGGCCTTTGAAGGAATGGGTGACTATAA
1 ATTATGAGATTATAAAACCACTT-AAAGAAAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAA
* * * * * * * * * *
703 ATATACTTTTTTTACTAGTAAATACCTTTTTCTTCACATTTCTTGAGGCAGACATTCAATTATAA
65 ACAGACTTTTTTTGCTAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAG
* * * * * *
768 TCTATTTGAATCAAAAATGAAAAAAAAATC-ACTTTAAAATAA
130 TCTGTTTTAACCAAAAATGATAAAAAATTCAAC-TTAAAATCA
* * * **********
810 ATTATGAGATTATAAAACCACTTAAAGTAAGTAATAAGACTTTTGAAGNNNNNNNNNNCTATAAA
1 ATTATGAGATTATAAAACCACTTAAAGAAAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAA
** * * * * ** * *
875 TGGACTTTTCTTG-TCAATGAATGTCTTTTTGTTCATGTTTCTTAAGGTCA-ACATTCAATGAAA
66 CAGACTTTTTTTGCT-AATGAATGCCTTTTTCTTCACGTTTCTCGAGGT-AGACATTCAATTATA
* *
938 GTCTTTTTTAACCAAAAATG-TAAAAAAATTTAACCTT-AAATCA
129 GTCTGTTTTAACCAAAAATGAT-AAAAAATTCAA-CTTAAAATCA
** ** * ** ** * * * **
981 ATTATTTGATTATAAAATAATTTAAAGCGAGTAATAATACTTTTGAAGGAATGAGTGACTACANN
1 ATTATGAGATTATAAAACCACTTAAAGAAAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAA
******** * * * * * *
1046 NNNNNNNNTCTT-CTCAATGAATGGCTTTTTCTGCATGTTTC-CTGAGGCAGACATTTAATTATA
66 CAGACTTTTTTTGCT-AATGAATGCCTTTTTCTTCACGTTTCTC-GAGGTAGACATTCAATTATA
* * * *
1109 GTATGCTTTAACCAAAAATGTTAAAAAATTCAACTTAAAATGA
129 GTCTGTTTTAACCAAAAATGATAAAAAATTCAACTTAAAATCA
* *
1152 ATTATGAGATTACAAAACCACTTAAAGAAAGTAATAAGGCCTTTGAAGGAATGGGTAACTATAAA
1 ATTATGAGATTATAAAACCACTTAAAGAAAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAA
* * * * * *
1217 CAGATTTTTTTTGCTAGTGAATGCCTTTTTCTTGACGTTTCTCGAGATAGACATTTAATTATTGT
66 CAGACTTTTTTTGCTAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGT
1282 CTGTTTTAACCAAAAAT
131 CTGTTTTAACCAAAAAT
1299 ACNNNNNNNN
Statistics
Matches: 768, Mismatches: 199, Indels: 66
0.74 0.19 0.06
Matches are distributed among these distances:
169 76 0.10
170 175 0.23
171 500 0.65
172 16 0.02
173 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
ATTATGAGATTATAAAACCACTTAAAGAAAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAA
CAGACTTTTTTTGCTAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGT
CTGTTTTAACCAAAAATGATAAAAAATTCAACTTAAAATCA
Done.