Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398672.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1958.0, 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, 687
Length: 1146
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.38
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:297 original size:172 final size:170
Alignment explanation
Indices: 1--1146 Score: 720
Period size: 171 Copynumber: 6.7 Consensus size: 170
* * * * * *
1 TAAATGATTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTACTTTTTCATTAAAACAT
1 TAAATGATTTTATAATCTCATAATTGATTTTAAGTT-AAATTTTTTTAATTTTTTATTAAAATAG
* * * * * * *
66 ATTATAATTGAATGTCTACATTGAGAAACGTAAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCA
65 ACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCCA
** * * *
131 TTTATTGTCACCTATTCCTTCGAAAGCCTTATTAC-CAACTC
130 TTTATAATCACCCATTCCTTCAAAAGCCTTATTACTC-ACTT
* * * * *
172 TAAATGGTTTTATAAACTCAAAATTGATTTTTAGTTTAAATTTTTTTAATTTTTTAGTTAAAACA
1 TAAATGATTTTATAATCTCATAATTGATTTTAAG-TTAAATTTTTTTAATTTTTTA-TTAAAATA
*
237 GACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAAGCATTCATTGATAAGAAAAGTCC
64 GACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCC
* * **
302 ATTCATAGTCACCCATTCCTTCAAAAGGGTTATTACTCACTT
129 ATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCACTT
* *
344 TAAATGTTTTTATAATTTCATAATTGATTTTAAGTTAAATTTTTTT-ATTTTTTCATTAAAATAG
1 TAAATGATTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTAATTTTTT-ATTAAAATAG
* * * * * * ** * *
408 ACCATAGTTGAATGCCTGCTTC-AGAAA-ATG-TGTAGAAAAAGCCATTTGTTAAGAAGAAAAGT
65 ACTATAATTGAATGTCTACCTCGAGAAACATGAAG-A-AAAAAG-CATTCATTGACAAGAAAAGT
* ***
470 TCATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTTGTTT
127 CCATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCACTT
* * ***
514 TAAAT-AGTTTTATAATC-CTATAATTGATTTTAAGTTGAATTGTTTTATATTTTTGGCTAAAAT
1 TAAATGA-TTTTATAATCTC-ATAATTGATTTTAAGTTAAATTTTTTTA-ATTTTTTATTAAAAT
* * * * * ** * * * *
577 AGGA-AATAATTTACTCTCTACCACGAGAAATGTGAAGAAAAAAACATTCATTGGCAACAAAACT
63 A-GACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGT
** * **
641 CCATTTATAATCACCCATTAGTTCTAAAGGTTTATTACTCACTT
127 CCATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCACTT
* * * * * * *
685 TAAATGATTTTATGATTTCATAATAGATTTTAGGTTGAATTTTTTTATATTTTTCATTCAAATAG
1 TAAATGATTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTA-ATTTTTTATTAAAATAG
* * ** * * * * *
750 ACTATAATTGAATGCCT-GCTTTAGGAAACGA-GTAGAAAAAATCATTTATTGAGAAGAAAAGTG
65 ACTATAATTGAATGTCTACCTCGA-GAAAC-ATGAAGAAAAAAGCATTCATTGACAAGAAAAGTC
********************* *
813 NNNNNNNNNNNNNNNNNNNNNTCAAAAGCCTTATTACTCGCTT
128 CATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCACTT
* * * * * *
856 TAAATGGTTTTATAATCCCGTAATTGATTTTATGTTAAATGTTTTTACA-TTTTTAGTTAAAACA
1 TAAATGATTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTA-ATTTTTTA-TTAAAATA
* * * *
920 GA-TAATAATTGACT-TCTACCTTGAGAAACGTGAAGAAAAATA-CATTCATTGATAAGAAAAGT
64 GACT-ATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAA-AGCATTCATTGACAAGAAAAGT
* * * * * * * *
982 CTATTTGTAGTCACCCATTCTTTTAAAAGGCTTATTATTCGCTT
127 CCATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCACTT
* ********** * * * *
1026 TAAATGGTTTTATAATCNNNNNNNNNNTTTTAAGTTGAATTTTTTTACATTTTTTGTTTAAACAG
1 TAAATGATTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTA-ATTTTTTATTAAAATAG
* * * * * *
1091 ACTATAAATGAATGTTTCCCTCAAGAAACGTGAAGAAAACAA-CATTCATTGGCAAG
65 ACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAA-AAGCATTCATTGACAAG
Statistics
Matches: 743, Mismatches: 203, Indels: 58
0.74 0.20 0.06
Matches are distributed among these distances:
167 1 0.00
168 4 0.01
169 12 0.02
170 238 0.32
171 334 0.45
172 149 0.20
173 4 0.01
174 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.38
Consensus pattern (170 bp):
TAAATGATTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTAATTTTTTATTAAAATAGA
CTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCCAT
TTATAATCACCCATTCCTTCAAAAGCCTTATTACTCACTT
Found at i:740 original size:342 final size:342
Alignment explanation
Indices: 1--811 Score: 871
Period size: 342 Copynumber: 2.4 Consensus size: 342
* * * * * * *
1 TAAATGATTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTACTTTTTCATTAAAACAT
1 TAAATGATTTTATAATTTCATAATAGATTTTAAGTT-AAATTTTTTTATTTTTTCATTAAAATAG
** * * * * ** * *
66 ATTATAATTGAATGTCTACATTGAG-AAACGTA-AAGAAAAAAGTATTCATT-GGCAAGAAAAGT
65 ACCATAATTGAATGCCTGC-TTCAGAAAACG-AGTAGAAAAAACCATTTATTAAG-AAGAAAAGT
** * * *
128 CCATTTATTGTCACCTATTCCTTCGAAAGCCTTATTACCAACTCTAAATGGTTTTATAAACTCAA
127 CCATTTATAATCACCCATTCCTTCAAAAGCCTTATTACCAACTCTAAATAGTTTTATAAACTCAA
* * * * *
193 AATTGATTTTTAGTTTAAATTTTTTTAATTTTTTAGTTAAAACAGACTATAATTGAATGTCTACC
192 AATTGATTTTAAGTTTAAATTGTTTTAATTTTTTAGCTAAAACAGACAATAATTGAATCTCTACC
* * * * * * *
258 TCGAGAAACATGAAGAAAAAAGCATTCATTGATAAGAAAAGTCCATTCATAGTCACCCATTCCTT
257 ACGAGAAACATGAAGAAAAAAACATTCATTGACAACAAAACTCCATTCATAATCACCCATTACTT
323 CAAAAGGGTTATTACTCACTT
322 CAAAAGGGTTATTACTCACTT
* *
344 TAAATGTTTTTATAATTTCATAATTGATTTTAAGTTAAATTTTTTTATTTTTTCATTAAAATAGA
1 TAAATGATTTTATAATTTCATAATAGATTTTAAGTTAAATTTTTTTATTTTTTCATTAAAATAGA
* * * * * *
409 CCATAGTTGAATGCCTGCTTCAGAAAATGTGTAGAAAAAGCCATTTGTTAAGAAGAAAAGTTCAT
66 CCATAATTGAATGCCTGCTTCAGAAAACGAGTAGAAAAAACCATTTATTAAGAAGAAAAGTCCAT
**** * * *
474 TTATAATCACCCATTCCTTCAAAAGCCTTATTACTTGTTTTAAATAGTTTTATAATC-CTATAAT
131 TTATAATCACCCATTCCTTCAAAAGCCTTATTACCAACTCTAAATAGTTTTATAAACTC-AAAAT
* * * * *
538 TGATTTTAAG-TTGAATTGTTTT-ATATTTTTGGCTAAAATAGGA-AATAATTTACTCTCTACCA
195 TGATTTTAAGTTTAAATTGTTTTAAT-TTTTTAGCTAAAACA-GACAATAATTGAATCTCTACCA
** * * *
600 CGAGAAATGTGAAGAAAAAAACATTCATTGGCAACAAAACTCCATTTATAATCACCCATTAGTTC
258 CGAGAAACATGAAGAAAAAAACATTCATTGACAACAAAACTCCATTCATAATCACCCATTACTTC
* *
665 TAAAGGTTTATTACTCACTT
323 AAAAGGGTTATTACTCACTT
* * * *
685 TAAATGATTTTATGATTTCATAATAGATTTTAGGTTGAATTTTTTTATATTTTTCATTCAAATAG
1 TAAATGATTTTATAATTTCATAATAGATTTTAAGTTAAATTTTTTTAT-TTTTTCATTAAAATAG
* * * * *
750 ACTATAATTGAATGCCTGCTTTAGGAAACGAGTAGAAAAAATCATTTATTGAGAAGAAAAGT
65 ACCATAATTGAATGCCTGCTTCAGAAAACGAGTAGAAAAAACCATTTATTAAGAAGAAAAGT
812 GNNNNNNNNN
Statistics
Matches: 386, Mismatches: 75, Indels: 15
0.81 0.16 0.03
Matches are distributed among these distances:
340 2 0.01
341 156 0.40
342 194 0.50
343 34 0.09
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.39
Consensus pattern (342 bp):
TAAATGATTTTATAATTTCATAATAGATTTTAAGTTAAATTTTTTTATTTTTTCATTAAAATAGA
CCATAATTGAATGCCTGCTTCAGAAAACGAGTAGAAAAAACCATTTATTAAGAAGAAAAGTCCAT
TTATAATCACCCATTCCTTCAAAAGCCTTATTACCAACTCTAAATAGTTTTATAAACTCAAAATT
GATTTTAAGTTTAAATTGTTTTAATTTTTTAGCTAAAACAGACAATAATTGAATCTCTACCACGA
GAAACATGAAGAAAAAAACATTCATTGACAACAAAACTCCATTCATAATCACCCATTACTTCAAA
AGGGTTATTACTCACTT
Done.