Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401367.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_450.0, 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: 2398
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.26
Warning! 707 characters in sequence are not A, C, G, or T
Found at i:316 original size:171 final size:171
Alignment explanation
Indices: 6--393 Score: 399
Period size: 171 Copynumber: 2.3 Consensus size: 171
1 TCACC
* * * * * * *** *
6 CATTCCTTCAAAAGCCTTAATACTTACTTTAAATGGTTTTATAGT-CTCAAAATTTG-TTAAAAT
1 CATTCCTTTAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATGC-CATAA-TTGATTTTTAG
* * * * **
69 TTGAA-TTCTTTGTAAATTTTTAGTTAAAACAGATTGTAATTGAATGTCAACCTTAAGAAACGTG
64 TTGAAGTT-TTT-TACATTTTTAGTTAAAACAGACTATAATTAAATGTCAACCTTAAGAAACGCA
** *
133 AAGAAAAAGGCATACATTGGCAAGAAAAATCTGTTTATAGTCAC-
127 AAGAAAAAGGCATACATTGGCAAGAAAAATCCATTTATAGTAACA
*
177 CTATT-CTTTCAAAAGCCTCATTACTCGCTTTAAATGGTTTTATAATGCCATAATTGATTTTTAG
1 C-ATTCCTTT-AAAAGCCTCATTACTCACTTTAAATGGTTTTATAATGCCATAATTGATTTTTAG
* * * *
241 TTGAAGTTTTTTACATTTTTGGTTAACACAGACTATAATTAAATGTCAATCTTGAGAAACGCAAA
64 TTGAAGTTTTTTACATTTTTAGTTAAAACAGACTATAATTAAATGTCAACCTTAAGAAACGCAAA
*** * *
306 GAAAAAGGCATTTGTTGGCATGAAAAGTCCATTTATAGTAACA
129 GAAAAAGGCATACATTGGCAAGAAAAATCCATTTATAGTAACA
** *
349 CATTCCTTTAAAAGCCTTTTTACTCACTTTAAATGGTTTTCTAAT
1 CATTCCTTTAAAAGCCTCATTACTCACTTTAAATGGTTTTATAAT
394 CTCAAAAGTG
Statistics
Matches: 177, Mismatches: 33, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
171 120 0.68
172 54 0.31
173 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (171 bp):
CATTCCTTTAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATGCCATAATTGATTTTTAGTT
GAAGTTTTTTACATTTTTAGTTAAAACAGACTATAATTAAATGTCAACCTTAAGAAACGCAAAGA
AAAAGGCATACATTGGCAAGAAAAATCCATTTATAGTAACA
Found at i:1838 original size:170 final size:171
Alignment explanation
Indices: 1545--2397 Score: 886
Period size: 170 Copynumber: 5.0 Consensus size: 171
1535 NNNNNNNNNG
* * * * * *
1545 AAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCTTTCAAAGGCGTTATTACA
1 AAAAGG-ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTCCAAAAGCCTTATTACT
* * *
1610 CACTTTAAATAGTTTTATAATCTGAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTA
65 CACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGCACATTTTTGGTTA
* * *
1675 AAATAGATTATCATTGAATGTTAACCTCAAGAAACATGAAGA
130 AAAAAGATTATAATTGAATGTCAACCTCAAGAAACATGAAGA
* * *
1717 AAAAGG-TTCATTGGGAAGAAAAGTCCATTTACAATCACCCATTCCTCCAAAAGCCTTATTACTC
1 AAAAGGATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTCCAAAAGCCTTATTACTC
* * * * * **
1781 ACTTTAAATGGATTTGTAATCTAAAAATTGATTAAAATTTGAATTTTTTGCACATTTTTTATTAA
66 ACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGCACATTTTTGGTTAA
* * ** *
1846 AAAAGACTATAATTCAATGTCAACCTCAAGAAATGTGAAGG
131 AAAAGATTATAATTGAATGTCAACCTCAAGAAACATGAAGA
* * * *
1887 TAAAGGCATTCATTGGCAAGAAAAGT-CATTAATAGTCACCCATTCCTTCAAAAAGCCTTATGAC
1 AAAAGG-ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCC-TCCAAAAGCCTTATTAC
** * * * * *
1951 TCACTTTGCATGGTTTTATAATGCT-ATAATTGATTTTAAGTTGAAGTT-TTT-TACATTTATGG
64 TCACTTTAAATGGTTTTATAAT-CTCAAAATTGATTTAAATTTGAA-TTCTTTGCACATTTTTGG
* * * * * ** * *
2013 TTAAAACATACTAGAATTG-ATGTCTACCTTGATAAACCT-AATGA
127 TTAAAAAAGATTATAATTGAATGTCAACCTCAAGAAACATGAA-GA
* * *
2057 AAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTAACCTATTCCTTCC-AAAGCCTTATTAC
1 AAAAGG-ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCC-TCCAAAAGCCTTATTAC
* * *
2121 TCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATGTGAATTCTTTGCACATCTTT-CTA
64 TCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGCACATTTTTGGT-
* *
2185 TAAAACAA-ATTACAATTGAATGTCAACCTCCAA-AAACATGAA-C
128 TAAAA-AAGATTATAATTGAATGTCAACCT-CAAGAAACATGAAGA
* * * * *
2228 AAAAGGGTTCATTGGTAACAAAATTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTCA-TACT
1 AAAAGGATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTCCAAAAGCCTT-ATTACT
* * * * ** *
2292 CACTTTAAATAGTTTTGTAATCCCAAAATTGATTGAAATTTGAATTCTTTGGGCATTTTTAGTTA
65 CACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGCACATTTTTGGTTA
* *
2357 AAAAAGATTATAATTAAATGTCAACGTCAAGAAACATGAAG
130 AAAAAGATTATAATTGAATGTCAACCTCAAGAAACATGAAG
2398 G
Statistics
Matches: 560, Mismatches: 100, Indels: 43
0.80 0.14 0.06
Matches are distributed among these distances:
169 13 0.02
170 364 0.65
171 86 0.15
172 90 0.16
173 7 0.01
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (171 bp):
AAAAGGATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTCCAAAAGCCTTATTACTC
ACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGCACATTTTTGGTTAA
AAAAGATTATAATTGAATGTCAACCTCAAGAAACATGAAGA
Found at i:2175 original size:342 final size:340
Alignment explanation
Indices: 1545--2397 Score: 947
Period size: 342 Copynumber: 2.5 Consensus size: 340
1535 NNNNNNNNNG
* * * *
1545 AAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCTTTCAAAGGCGTTATTACA
1 AAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCCTTCAAAAGCCTTA-TACT
* *
1610 CACTTTAAATAGTTTTATAATCTGAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTA
65 CACTTTAAATAGTTTTATAATCTGAAAATTGATTTAAAGTTGAATTCTTTGTACATTTATGGTTA
* * ** *
1675 AAATAGATTATCATTGAATGTTAACCTCAAGAAACATGAAGAAAAAGGTTCATTGGGAAGAAAAG
130 AAACAGACTAGAATTGAATGTTAACCTCAAGAAACATGAAGAAAAAGGTTCATTGGCAAGAAAAG
* *
1740 TCCATTTACAATCACCCATTCCTCCAAAAGCCTTATTACTCACTTTAAATGGATTTGTAATCTAA
195 TCCATTTACAATAACCCATTCCTCCAAAAGCCTTATTACTCACTTTAAATGGATTTATAATCTAA
* * * *
1805 AAATTGATTAAAATTTGAATTTTTTGCACAT-TTTTTATTAAAA-AAGACTATAATTCAATGTCA
260 AAATTGATTAAAATGTGAATTCTTTGCACATCTTTCTA-TAAAACAA-ACTACAATTCAATGTCA
** *
1868 ACCT-CAAGAAATGTGAAGG
323 ACCTCCAA-AAACATGAA-C
*
1887 TAAAGGCATTCATTGGCAAGAAAAGT-CATTAATAGTCACCCATTCCTTCAAAAAGCCTTATGAC
1 AAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCCTTC-AAAAGCCTTAT-AC
** * * *
1951 TCACTTTGCATGGTTTTATAATGCT-ATAATTGATTTTAAGTTGAAGTT-TTT-TACATTTATGG
64 TCACTTTAAATAGTTTTATAAT-CTGAAAATTGATTTAAAGTTGAA-TTCTTTGTACATTTATGG
* ** * *
2013 TTAAAACATACTAGAATTG-ATGTCT-ACCTTGATAAACCT-AATGAAAAAGGCATTCATTGGCA
127 TTAAAACAGACTAGAATTGAATGT-TAACCTCAAGAAACATGAA-GAAAAAGG--TTCATTGGCA
* * * * *
2075 AGAAAAGTTCATTTATAGTAACCTATTCCTTCC-AAAGCCTTATTACTCACTTTAAATGGTTTTA
188 AGAAAAGTCCATTTACAATAACCCATTCC-TCCAAAAGCCTTATTACTCACTTTAAATGGATTTA
* * * *
2139 TAATCTCAAAATTGATTTAAATGTGAATTCTTTGCACATCTTTCTATAAAACAAATTACAATTGA
252 TAATCTAAAAATTGATTAAAATGTGAATTCTTTGCACATCTTTCTATAAAACAAACTACAATTCA
2204 ATGTCAACCTCCAAAAACATGAAC
317 ATGTCAACCTCCAAAAACATGAAC
* * * * *
2228 AAAAGG-GTTCATTGGTAACAAAATTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTCATACT
1 AAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCCTTCAAAAGCCTT-ATACT
* ** * * ** * *
2292 CACTTTAAATAGTTTTGTAATCCCAAAATTGATTGAAATTTGAATTCTTTGGGCATTTTTAGTTA
65 CACTTTAAATAGTTTTATAATCTGAAAATTGATTTAAAGTTGAATTCTTTGTACATTTATGGTTA
* * * * * *
2357 AAAAAGATTATAATTAAATGTCAACGTCAAGAAACATGAAG
130 AAACAGACTAGAATTGAATGTTAACCTCAAGAAACATGAAG
2398 G
Statistics
Matches: 421, Mismatches: 70, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
339 5 0.01
340 85 0.20
341 98 0.23
342 214 0.51
343 19 0.05
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (340 bp):
AAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCCTTCAAAAGCCTTATACTC
ACTTTAAATAGTTTTATAATCTGAAAATTGATTTAAAGTTGAATTCTTTGTACATTTATGGTTAA
AACAGACTAGAATTGAATGTTAACCTCAAGAAACATGAAGAAAAAGGTTCATTGGCAAGAAAAGT
CCATTTACAATAACCCATTCCTCCAAAAGCCTTATTACTCACTTTAAATGGATTTATAATCTAAA
AATTGATTAAAATGTGAATTCTTTGCACATCTTTCTATAAAACAAACTACAATTCAATGTCAACC
TCCAAAAACATGAAC
Done.