Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398594.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1885.0, 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: 3179
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.31
Warning! 546 characters in sequence are not A, C, G, or T
Found at i:311 original size:173 final size:173
Alignment explanation
Indices: 1--1028 Score: 535
Period size: 173 Copynumber: 6.0 Consensus size: 173
*
1 CAAAATTGATTTTATGTTCAATTTTTATTTATATTTTTTATTAAAACAGACTATGATTAAATGTC
1 CAAAATTGATTTTATGTTCAATTTTTATTTATATTTTTTATTAAAACAGACTATAATTAAATGTC
* * * * * **********
66 TACCTTGAGAAGTATGAAGAAAAATGCATTTATTGACAAGAAAAGTCTATTTNNNNNNNNNNATT
66 TACCTCGAGAAATATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATACTCACACATT
* *
131 CCTTCAAAAGCCTTATTACTCACTTGAAATTGTTTTATTACCC
131 CCTTCAAAAGCCTTATTACTCACTTGAAATGGTTTTATAACCC
* * * *
174 CAAAATTGATTTTATGTTCAATTTTTATTTATATTTTTTATTAAAATAGACTACAATTGAATATC
1 CAAAATTGATTTTATGTTCAATTTTTATTTATATTTTTTATTAAAACAGACTATAATTAAATGTC
* * * * *
239 TACCTCCAAAAATATTAAGACAAAA-GCATTCATTGGCAAGAAAAGTCTATTTATACTCACCCGT
66 TACCTCGAGAAATATGAAGA-AAAAGGCATTCATTGGCAAGAAAAGTCTATTTATACTCACACAT
* * * * * *
303 TGCTTCAAAAGCCTTATTACACACTTTAAATGGTTTTGTAATCT
130 TCCTTCAAAAGCCTTATTACTCACTTGAAATGGTTTTATAACCC
* * ** ** *
347 CAAAATTGATTTCAAGTTCAATTTTT-TTTACGTTTTTGGTTAAAACAGATTATAATTAAATGTC
1 CAAAATTGATTTTATGTTCAATTTTTATTTATATTTTTTATTAAAACAGACTATAATTAAATGTC
* ** * * * * *
411 TACATCGAGAAACGTGAGGAAAAAGGTATTCATTGGTAAGAAAAGTCTATTTATAGTCTCACATT
66 TACCTCGAGAAATATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATACTCACACATT
* **********************
476 CCTTCAAAGGCCTTATTACTCNNNNNNNNNNNNNNNNNNNNNN
131 CCTTCAAAAGCCTTATTACTCACTTGAAATGGTTTTATAACCC
* * * * * * *
519 NATAATTGATTTTAAGTTGAA--TTT-TTTACATTTTTTGTTAAAGCAGACTATAATTAAATG-C
1 CAAAATTGATTTTATGTTCAATTTTTATTTATATTTTTTATTAAAACAGACTATAATTAAATGTC
** * ** * ** * * * * **
580 TTGCT-TAGGAAACGTGTAGAAAAACACATTTATTAGG-AAGAAAAGTCCATTTATAGTCTCTTA
66 TACCTCGA-GAAATATGAAGAAAAAGGCATTCATT-GGCAAGAAAAGTCTATTTATACTCACACA
* * * * * * * *
643 TTTCC-TCAAAAGCCGTATTGCTCGCTTTAAATGGCTTTATCATCT
129 -TTCCTTCAAAAGCCTTATTACTCACTTGAAATGGTTTTATAACCC
* * * * *
688 CAAAATTGATTTTAAGTTCAATTTTT-TCTA-ACTTTTTTGGCTT-AAACATATTATAATTAAAT
1 CAAAATTGATTTTATGTTCAATTTTTATTTATA-TTTTTT--ATTAAAACAGACTATAATTAAAT
* * * * * * ***
750 TTCTACATCAAGAAATGTGAGGAAAAAGGCATTCATTGGCAA-AAAAGGTCTATTTATAGTCTTT
63 GTCTACCTCGAGAAATATGAAGAAAAAGGCATTCATTGGCAAGAAAA-GTCTATTTATACTCACA
* * * * *
814 CATTCCTTCAAAAGCCTTATTACTCTCTTTAAAAGGTCTTATAATCC
127 CATTCCTTCAAAAGCCTTATTACTCACTTGAAATGGTTTTATAACCC
* * * * * * ** * * * *
861 CATAACTGATTTTAAGTT-AAATTTT-TTTACACTTTTGGTTCAAACAAACCATAATTGAATGTC
1 CAAAATTGATTTTATGTTCAATTTTTATTTATATTTTTTATTAAAACAGACTATAATTAAATGTC
* ** * * ****
924 TACCTAGAGAAACGTGAAGGAAAAA-GTATTCATT-GCTAAGAAAAGT-TGATTTATAGTCTTTT
66 TACCTCGAGAAATATGAA-GAAAAAGGCATTCATTGGC-AAGAAAAGTCT-ATTTATACTCACAC
* * * *
986 ATTTCTCCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAA
128 ATTCCTTCAAAAGCCTTATTACTCACTTGAAATGGTTTTATAA
1029 TATCATAATT
Statistics
Matches: 653, Mismatches: 181, Indels: 44
0.74 0.21 0.05
Matches are distributed among these distances:
168 1 0.00
169 79 0.12
170 47 0.07
171 108 0.17
172 160 0.25
173 253 0.39
174 5 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.38
Consensus pattern (173 bp):
CAAAATTGATTTTATGTTCAATTTTTATTTATATTTTTTATTAAAACAGACTATAATTAAATGTC
TACCTCGAGAAATATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATACTCACACATT
CCTTCAAAAGCCTTATTACTCACTTGAAATGGTTTTATAACCC
Found at i:873 original size:342 final size:342
Alignment explanation
Indices: 307--1039 Score: 762
Period size: 342 Copynumber: 2.1 Consensus size: 342
297 ACCCGTTGCT
* * *
307 TCAAAAGCCTTATTACACACTTTAAATGGTTTTGTAATCTCAAAATTGATTTCAAGTTCAATTTT
1 TCAAAAGCCTTATTACTCACTTTAAATGGCTTTATAATCTCAAAATTGATTTCAAGTTCAATTTT
* *
372 TTTTACGTTTTTGGTTAAAACAGATTATAATTAAATGTCTACATCGAGAAACGTGAGGAAAAAGG
66 TTTAACGTTTTTGGTTAAAACAGATTATAATTAAATGTCTACATCAAGAAACGTGAGGAAAAAGG
* * * *****
437 TATTCATTGGTAAGAAAAGTCTATTTATAGTCTCACATTCCTTCAAAGGCCTTATTACTCNNNNN
131 CATTCATTGGCAAGAAAAGTCTATTTATAGTCTCACATTCCTTCAAAAGCCTTATTACTCTCTTT
****************** * * * * *
502 NNNNNNNNNNNNNNNNNNATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTTGTT-AAAGCAG
196 AAAAGGTCTTATAATCCCATAACTGATTTTAAGTTAAATTTTTTTACACTTTTGGTTCAAA-CAA
* * * * *
565 ACTATAATTAAATG-CTTGCTTAG-GAAACGTGTA-GAAAAACACATTTATTAG-GAAGAAAAGT
260 ACCATAATTAAATGTC-TACCTAGAGAAACGTGAAGGAAAAA-ACATTCATT-GCGAAGAAAAGT
626 CCATTTATAGTCTCTTATTTCC
322 CCATTTATAGTCTCTTATTT-C
* * * * *
648 TCAAAAGCCGTATTGCTCGCTTTAAATGGCTTTATCATCTCAAAATTGATTTTAAGTTCAATTTT
1 TCAAAAGCCTTATTACTCACTTTAAATGGCTTTATAATCTCAAAATTGATTTCAAGTTCAATTTT
* * * *
713 TTCTAACTTTTTTGGCTT-AAACATATTATAATTAAATTTCTACATCAAGAAATGTGAGGAAAAA
66 TT-TAACGTTTTTGG-TTAAAACAGATTATAATTAAATGTCTACATCAAGAAACGTGAGGAAAAA
**
777 GGCATTCATTGGCAA-AAAAGGTCTATTTATAGTCTTTCATTCCTTCAAAAGCCTTATTACTCTC
129 GGCATTCATTGGCAAGAAAA-GTCTATTTATAGTCTCACATTCCTTCAAAAGCCTTATTACTCTC
841 TTTAAAAGGTCTTATAATCCCATAACTGATTTTAAGTTAAATTTTTTTACACTTTTGGTTCAAAC
193 TTTAAAAGGTCTTATAATCCCATAACTGATTTTAAGTTAAATTTTTTTACACTTTTGGTTCAAAC
* ** * *
906 AAACCATAATTGAATGTCTACCTAGAGAAACGTGAAGGAAAAAGTATTCATTGCTAAGAAAAGTT
258 AAACCATAATTAAATGTCTACCTAGAGAAACGTGAAGGAAAAAACATTCATTGCGAAGAAAAGTC
* *
971 GATTTATAGTCTTTTATTTC
323 CATTTATAGTCTCTTATTTC
* * * *
991 TCCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATATCATAATTG
1 T-CAAAAGCCTTATTACTCACTTTAAATGGCTTTATAATCTCAAAATTG
1040 NNNNNNNNNN
Statistics
Matches: 315, Mismatches: 67, Indels: 17
0.79 0.17 0.04
Matches are distributed among these distances:
341 63 0.20
342 122 0.39
343 40 0.13
344 84 0.27
345 6 0.02
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.37
Consensus pattern (342 bp):
TCAAAAGCCTTATTACTCACTTTAAATGGCTTTATAATCTCAAAATTGATTTCAAGTTCAATTTT
TTTAACGTTTTTGGTTAAAACAGATTATAATTAAATGTCTACATCAAGAAACGTGAGGAAAAAGG
CATTCATTGGCAAGAAAAGTCTATTTATAGTCTCACATTCCTTCAAAAGCCTTATTACTCTCTTT
AAAAGGTCTTATAATCCCATAACTGATTTTAAGTTAAATTTTTTTACACTTTTGGTTCAAACAAA
CCATAATTAAATGTCTACCTAGAGAAACGTGAAGGAAAAAACATTCATTGCGAAGAAAAGTCCAT
TTATAGTCTCTTATTTC
Found at i:1953 original size:172 final size:169
Alignment explanation
Indices: 1663--2322 Score: 706
Period size: 171 Copynumber: 3.9 Consensus size: 169
1653 NNNNNNNNNN
* * ** * *
1663 CATTTTTCATTAAAATAGACTATAATTGAATGCCTGTCTCAGAAAAAATGTAG-AAAAAGCTATT
1 CATTTTT-ATTAAAACAGACTATAATTGAATGTCTACCTCAG-AAACATGAAGAAAAAAGC-ATT
* * * * * * *
1727 TACTTGG-AAGAAAAGTCCATTTATAATCTCTCATACTTTTAAAAGCCCTATTACT-ACCTTTTA
63 CA-TTGGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTAAAAGCCTTATTACTCA-CTTTAA
* * *
1790 ATGGTTTTGTAATCTCATAATTGCA-TTTAACTTAAATTTTTTTTA
126 ATGGTTTTATAATCTCATAATTG-ATTTTAAGTTGAA-TTTTTTTA
* * *** *
1835 CATTTTTCATTAAAAC-GAAATATAATTGAATG-CTTACATCATGAAGTGTGTAG-AAAAAGCCA
1 CATTTTT-ATTAAAACAG-ACTATAATTGAATGTC-TACCTCA-GAAACATGAAGAAAAAAG-CA
*
1897 TTCATTGGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTGAAAGCCTTATTACTCACTTTAA
61 TTCATTGGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTAAAAGCCTTATTACTCACTTTAA
* *
1962 ATGGTTTTATAATCTCATAACTGATTTTAAGTTGAATTTTTTGA
126 ATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTA
* ** * * * *
2006 TAGTTTTGGTTAAAACAGACTATGATTGAATGTCTACCTCGAGAAACATAAAGAAAAAAGTATTT
1 CA-TTTTTATTAAAACAGACTATAATTGAATGTCTACCTC-AGAAACATGAAGAAAAAAGCATTC
* * * * *
2071 ATTGACGAGAAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAACCTTAGTACTCACTTTAAATG
64 ATTGGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTAAAAGCCTTATTACTCACTTTAAATG
* *
2136 GTTTTATAATCTCATAATTTATTTTAAGTTGAATTTGTTTA
129 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTA
* * *
2177 CATTTTTAGTTAAAACAGACTATAATTGAGTGTCCACCTTAAGAAACATGAAGAAAAAAGCATTC
1 CATTTTTA-TTAAAACAGACTATAATTGAATGTCTACC-TCAGAAACATGAAGAAAAAAGCATTC
* * *
2242 ATTTGCAAGAAAAGTCCATTTATA-TCTCCCATTCCTTTGAAAGCCTTATTACTCGCTTTAAATG
64 ATTGGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTAAAAGCCTTATTACTCACTTTAAATG
*
2306 GTTTTATATTCTCATAA
129 GTTTTATAATCTCATAA
2323 NNNNNNNNNN
Statistics
Matches: 411, Mismatches: 63, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
170 55 0.13
171 213 0.52
172 140 0.34
173 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (169 bp):
CATTTTTATTAAAACAGACTATAATTGAATGTCTACCTCAGAAACATGAAGAAAAAAGCATTCAT
TGGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTAAAAGCCTTATTACTCACTTTAAATGGT
TTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTA
Done.