Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397718.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1017.0, 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: 6046
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.27
Warning! 1897 characters in sequence are not A, C, G, or T
Found at i:821 original size:170 final size:169
Alignment explanation
Indices: 397--861 Score: 482
Period size: 170 Copynumber: 2.7 Consensus size: 169
387 NNNNNNNNNN
** *** * * * *
397 TAAAACAGACTATAATTGAATGCTTGTGTCATGAGACGTGTAGGAAAAGCCATTTATTTAGAAGA
1 TAAAACAGACTATAATTGAATGCTTGCCTTGGGAAACGTGTAGAAAAATCCATTTATTT-GAAAA
* *********
462 AAAATCCATTTATAGTCT-CTCATTCCTTTAAAAGCCTTATTAATCGCTTTAAATGNNNNNNNNN
65 AAAATCCATTTATAGTCTCCT-ATTCCTTTAAAAGCCTTATTACTCGCTTTAAATGGTTTTAAAA
* * *
526 NCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTCAT
129 TCTCATAATTAATTTTAAGTTAAATTTTTTACATTTTTCAT
* * * * *
567 TGAAACATACTATAATTGAATGCTTACCTTGGGAAACGTGTAGAACAATACATTTATTTGAAAGA
1 TAAAACAGACTATAATTGAATGCTTGCCTTGGGAAACGTGTAGAAAAATCCATTTATTTGAAA-A
********** *
632 AAANNNNNNNNNNAGTCTCCTATTCCTTTAAAAGCCTTATTACTTGCTTTAAATGGTTTTAAAAT
65 AAAATCCATTTATAGTCTCCTATTCCTTTAAAAGCCTTATTACTCGCTTTAAATGGTTTTAAAAT
*
697 CTCATAATTAATTTTTAGTTAAATTTTTTACATTTTTCAT
130 CTCATAATTAATTTTAAGTTAAATTTTTTACATTTTTCAT
*
737 TAAAACAGACTATAATTGAATGCCTGCCTTGGGAAACGTGTAGAAAAATCCATTTATTTGAAAAA
1 TAAAACAGACTATAATTGAATGCTTGCCTTGGGAAACGTGTAGAAAAATCCATTTATTTGAAAAA
* * * * *
802 AAAGTTCATTTATAGTCTCCCATTCCATCAAAAGCCATATTACTCGCTTTAAATGGTTTT
66 AAA-TCCATTTATAGTCTCCTATTCCTTTAAAAGCCTTATTACTCGCTTTAAATGGTTTT
862 NNNNNNNNNN
Statistics
Matches: 232, Mismatches: 60, Indels: 6
0.78 0.20 0.02
Matches are distributed among these distances:
169 7 0.03
170 223 0.96
171 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.37
Consensus pattern (169 bp):
TAAAACAGACTATAATTGAATGCTTGCCTTGGGAAACGTGTAGAAAAATCCATTTATTTGAAAAA
AAATCCATTTATAGTCTCCTATTCCTTTAAAAGCCTTATTACTCGCTTTAAATGGTTTTAAAATC
TCATAATTAATTTTAAGTTAAATTTTTTACATTTTTCAT
Found at i:1872 original size:171 final size:170
Alignment explanation
Indices: 1324--2016 Score: 414
Period size: 170 Copynumber: 4.1 Consensus size: 170
1314 NNNNNNNNNN
* * * * * * *
1324 CTTCAAAAGTCTTATTACTAATTTTAAAAGGTTTTATAATCTCATAATT-AATTTAAAATTGAAT
1 CTTCAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGA-TGAA-
* ** * ** * *
1388 TTTTTTACATTTCACATTAAAACAAACTATAATTGAATA-CT-TGT-TGTGAAAAACTGTAGAAA
64 TTTTTTATATTTTTCATTAAAACAGACTATAATTGAATACCTACCTCAG-GAAACA-TGTAGAAA
* * *
1450 AA-CTCATTTATTTGGAAGAAAACTCAATTTATAGTCTCTCATTC
127 AACCT-ATTTATTTGGAAGAAAAGTCCATTTATAGTCTCACATTC
* ********** * * * *
1494 CTTCAAAAATCCT-NNNNNNNNNNTTAAATGCTTTTCTATTCTCATAATTGATTTTAAG-TAAAA
1 CTTC-AAAAGCCTCATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGAT-GAA
*** *********** *
1557 TTTTTTGCGTTTTTCATTAAAACAGACTATAATTGAANNNNNNNNNNGGGAGACATGTAGAAAAA
64 TTTTTTATATTTTTCATTAAAACAGACTATAATTGAATACCTACCTCAGGAAACATGTAGAAAAA
* * *
1622 GCC-ATTTATTTCGAAGAAAAGTCCATTTATAGTATCCCATTC
129 -CCTATTTATTTGGAAGAAAAGTCCATTTATAGTCTCACATTC
* * *********** * *
1664 CTTCAAAAGCCTTATTAGTCGNNNNNNNNNNTTTTATAATCTCATAATTGATTTTAAGTTGGATT
1 CTTCAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGATGAATT
** * *** *
1729 TTTTATATTTTTTTGTTAAAACATACTATAATTGAATGTTTGCCTCAGGAAACATGTAGAAAAAC
66 TTTTATA-TTTTTCATTAAAACAGACTATAATTGAATACCTACCTCAGGAAACATGTAGAAAAAC
* *
1794 CTATTTATTTGGAAGAAAAGTCCATTTACAGTCTCTCATTC
130 CTATTTATTTGGAAGAAAAGTCCATTTATAGTCTCACATTC
**********
1835 CTTCAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATCTCNNNNNNNNNNTTAAGATGAATT
1 CTTCAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGATGAATT
* * * * *
1900 TTTTTTATTTTTCATTAAAACAGATTATAATTGAATACCTACCTCGGGAAACATATAGGAAAACC
66 TTTTATATTTTTCATTAAAACAGACTATAATTGAATACCTACCTCAGGAAACATGTA-GAAAAAC
1965 CT-TTTATTTGGAAGAAAAGTCCATTTATAGTCTCACATTC
130 CTATTTATTTGGAAGAAAAGTCCATTTATAGTCTCACATTC
*
2005 TTTCAAAAGCCT
1 CTTCAAAAGCCT
2017 TATTNNNNNN
Statistics
Matches: 388, Mismatches: 122, Indels: 26
0.72 0.23 0.05
Matches are distributed among these distances:
169 40 0.10
170 199 0.51
171 147 0.38
172 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.37
Consensus pattern (170 bp):
CTTCAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGATGAATT
TTTTATATTTTTCATTAAAACAGACTATAATTGAATACCTACCTCAGGAAACATGTAGAAAAACC
TATTTATTTGGAAGAAAAGTCCATTTATAGTCTCACATTC
Found at i:2214 original size:171 final size:162
Alignment explanation
Indices: 2037--2357 Score: 317
Period size: 172 Copynumber: 1.9 Consensus size: 162
2027 NNNNNNNNNN
*
2037 TTTATAATCTCATAATTGATTTTAAGTTGAATTGTTTTAT-ATTTTTAGCCAAAACAGAA-TATA
1 TTTATAATCTCATAATTGATTTTAAGTTCAATTGTTTTATCATTTTTAGCCAAAACA-AATTATA
* * * *
2100 ATTGAATTTCTACCTAAGGAAACGTGAGGA-ATAAAGCATTCATT-AGCAAGAAAGGTCCATTTA
65 ATTGAATATCTACCTAAGGAAACATGAAGAGA-AAAGCATTCATTGA-CAAGAAAAGTCCATTTA
* *
2163 TATTCTCCCATTCCTTCAAAAGCCTTAGTNNNNNNNNNNAATGGT
128 TAGTCACCCATTCCTTCAAAAGCCTTAGT----------AATGGT
* * * * * **
2208 TTTATAATCTCGTAATTGATTTTAAGTTCAATTTTTTTTTCCTTTTTGGTTAAAACAAATTATAA
1 TTTATAATCTCATAATTGATTTTAAGTTCAATTGTTTTATCATTTTTAGCCAAAACAAATTATAA
* * * *
2273 TTGAATATCTACCTTATGAAACATGAAGAGAAAGGCATTCATTGACAAGAAAAGTCTATTTATAG
66 TTGAATATCTACCTAAGGAAACATGAAGAGAAAAGCATTCATTGACAAGAAAAGTCCATTTATAG
* *
2338 TCACTCATTTCTTCAAAAGC
131 TCACCCATTCCTTCAAAAGC
2358 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
171 38 0.30
172 86 0.68
173 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.37
Consensus pattern (162 bp):
TTTATAATCTCATAATTGATTTTAAGTTCAATTGTTTTATCATTTTTAGCCAAAACAAATTATAA
TTGAATATCTACCTAAGGAAACATGAAGAGAAAAGCATTCATTGACAAGAAAAGTCCATTTATAG
TCACCCATTCCTTCAAAAGCCTTAGTAATGGT
Done.