Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403166.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_832.0, 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: 9616
ACGTcount: A:0.20, C:0.08, G:0.07, T:0.22
Warning! 4112 characters in sequence are not A, C, G, or T
Found at i:1203 original size:170 final size:171
Alignment explanation
Indices: 659--1223 Score: 449
Period size: 170 Copynumber: 3.3 Consensus size: 171
649 GATTTTAATG
* * ** *
659 ATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACAGTTTTCGTTAAAATAGACTATA
1 ATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTTATTAAAACAGACTATA
** * * * * * * * * ** *
724 ATTGAATACCTGCCATAGGAAACATGTAGAAAAAGCCTATTCATTGAGAAGAAAAGTTTATTTAT
66 ATTGAATGTCTACCTTAGAAAACGTGCAAAAAAAGCC-ATTCATTGACAACAAAAGTCCATTTAG
** * *
789 AGCCACCCATTCTTTCAAAAGCCTTATTACTCTG-TTTAAATA
130 AATCACCCATTCCTTCAAAAGCCTTATTAC-CCGCTTTAAATA
* ********** ** *
831 GTTTTANNNNNNNNNNATTGATTTTAAGTTGAATTTTTTTAT-TTTTTGGTTAAAATAGACTATA
1 ATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTTATTAAAACAGACTATA
* * * * * * *
895 ATTTATTGTCTACCTTAGAAAACGTGCAGAAAAAGCCATTCATTGAGAAGAAAAGTCTATTTATA
66 ATTGAATGTCTACCTTAGAAAACGTGCAAAAAAAGCCATTCATTGACAACAAAAGTCCATTTAGA
* * * *
960 GTGACTCATTCCTTCAAAAGCCTTATTACCCGCTTTAAATG
131 ATCACCCATTCCTTCAAAAGCCTTATTACCCGCTTTAAATA
* ********** *
1001 GTTTTATAATCTCATANNNNNNNNNNAGTTGAATTTTTTTATATTTTTTATTAAAACATACTATA
1 ATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTTATTAAAACAGACTATA
* *
1066 ATTGAATGTTTACC-TAGAGAAACGTG-AAAAACAAG-CATTCTTTGACAACAAAAGTCCATTTA
66 ATTGAATGTCTACCTTAGA-AAACGTGCAAAAA-AAGCCATTCATTGACAACAAAAGTCCATTTA
* *
1128 GAATCACCCATTCCTTCAAAAAG-CTTGTTACTCGCTTTAAATA
129 GAATCACCCATTCCTTC-AAAAGCCTTATTACCCGCTTTAAATA
* * *
1171 ATTTTATAATCTCGTAATTGATTTTAAGTTGAATTATTTTACATTTTTTATTA
1 ATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTTATTA
1224 NNNNNNNNNN
Statistics
Matches: 305, Mismatches: 83, Indels: 12
0.76 0.21 0.03
Matches are distributed among these distances:
169 2 0.01
170 181 0.59
171 92 0.30
172 30 0.10
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.39
Consensus pattern (171 bp):
ATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTTATTAAAACAGACTATA
ATTGAATGTCTACCTTAGAAAACGTGCAAAAAAAGCCATTCATTGACAACAAAAGTCCATTTAGA
ATCACCCATTCCTTCAAAAGCCTTATTACCCGCTTTAAATA
Found at i:6256 original size:171 final size:169
Alignment explanation
Indices: 5948--6678 Score: 594
Period size: 171 Copynumber: 4.3 Consensus size: 169
5938 NNNNNNNNNN
* * * **
5948 CTTCAAAAGGCTTATTACTCACTTTAAATAG-TTTTATAATCTCATAATTGATTGAAAGTTG-AT
1 CTTCAAAAAGCTTATTACTCCCTTTTAAT-GTTTTTATAATCTCATAATTGATTTTAAGTTGAAT
6011 TTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTA-CATTGAGAAACATGATG-AAA
65 TTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACCA-TGAG-AA-ATG-TGAAAA
* * *
6074 CAAGTATTCATTGATAAGAAAAGTCAATTTAGAGTCACTCATTC
126 AAAGCATTCATTGACAAGAAAAGTCAATTTAGAGTCACTCATTC
*********** *
6118 CTTCAAAAAGCTTATTACTCGNNNNNNNNNNTTTTATAATCTCATAATTGATTTTAGGTTGAATT
1 CTTCAAAAAGCTTATTACTCCCTTTTAATGTTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * *
6183 TTTTTATATATTTTG-TTAAAACAGACTATAATTGATTTTTTACCATGAGAAATGTGCAAAAAAA
66 TTTTTATAT-TTTTGATTAAAACATACTATAATTGAATGTCTACCATGAGAAATGTG-AAAAAAA
* ********** *
6247 GCCATTCATTGAGAAGNNNNNNNNNNTTATAGTCACTCATTC
129 G-CATTCATTGACAAGAAAAGTCAATTTAGAGTCACTCATTC
* *
6289 CTTCAAAAGGCTTATTACCCCCTTTTAATGTTTTTATAATCTCATAATTGATTTTAAGTT-AGAT
1 CTTCAAAAAGCTTATTACTCCCTTTTAATGTTTTTATAATCTCATAATTGATTTTAAGTTGA-AT
* * *
6353 TTTTTAATATTTTTGATTAAAATATACTATAATTGAATGTCTACCATGAGAAACGTGAAGCAAAA
65 TTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACCATGAGAAATGTGAA--AAAA
* *
6418 AGCATTCATTGCCAAGAAAAGTCCATTTAGAGTCACTCATTC
128 AGCATTCATTGACAAGAAAAGTCAATTTAGAGTCACTCATTC
* * ** * * ********** *
6460 CTTTAAAAAGCTTACTACTTGCTTTAAATGATTTTATAATCTCATAANNNNNNNNNNGTTGACTT
1 CTTCAAAAAGCTTATTACTCCCTTTTAATGTTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * * ** *
6525 TTTTTACATTTTTGATTAAAGCATACTATAATTGAATGTCTACCTTGATAAACATAAAGAAACAA
66 TTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACCATGAGAAATGTGAA-AAA-AA
* * * *
6590 GCATTCATTGACAACAAAAGTCCATTTAGAGTAACCCATTC
129 GCATTCATTGACAAGAAAAGTCAATTTAGAGTCACTCATTC
* * * ***
6631 CTTTAAAAGGCTTATTAC-CCGTTTTAAATAAATTTATAATCTCATAAT
1 CTTCAAAAAGCTTATTACTCCCTTTT-AATGTTTTTATAATCTCATAAT
6679 NNNNNNNNNN
Statistics
Matches: 440, Mismatches: 107, Indels: 27
0.77 0.19 0.05
Matches are distributed among these distances:
168 2 0.00
169 3 0.01
170 68 0.15
171 353 0.80
172 14 0.03
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (169 bp):
CTTCAAAAAGCTTATTACTCCCTTTTAATGTTTTTATAATCTCATAATTGATTTTAAGTTGAATT
TTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACCATGAGAAATGTGAAAAAAAGC
ATTCATTGACAAGAAAAGTCAATTTAGAGTCACTCATTC
Found at i:6632 original size:342 final size:340
Alignment explanation
Indices: 5948--6678 Score: 727
Period size: 342 Copynumber: 2.1 Consensus size: 340
5938 NNNNNNNNNN
* * *
5948 CTTCAAAAGGCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTGAAAGTTGATTT
1 CTTCAAAAGGCTTATTACCCCCTTTTAAT-GTTTTATAATCTCATAATTGATTGAAAGTTGATTT
* *
6013 TTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACATTGAGAAACATGATGAAACAAG
65 TTTAATATTTTTGATTAAAACATACTATAATTGAATGTCTACATTGAGAAACATGAAGAAACAAG
* * * ****
6078 TATTCATTGATAAGAAAAGTCAATTTAGAGTCACTCATTCCTTCAAAAAGCTTATTACTCGNNNN
130 CATTCATTGACAAGAAAAGTCAATTTAGAGTCACTCATTCCTTCAAAAAGCTTACTACTCGCTTT
****** *
6143 NNNNNNTTTTATAATCTCATAATTGATTTTAGGTTGAATTTTTTTATATATTTTGTTAAAACAGA
195 AAATGATTTTATAATCTCATAATTGATTTTAGGTTGAATTTTTTTACATATTTTGTTAAAACAGA
* * * ** * * ***********
6208 CTATAATTGATTTTTTACCATGAGAAATGTGCAAAAAAAGCCATTCATTGAGAAGNNNNNNNNNN
260 CTATAATTGAATGTCTACCATGAGAAACATGAAAAAAAAGCCATTCATTGACAACAAAAGTCCAT
* * *
6273 TTATAGTCACTCATTC
325 TTAGAGTAACCCATTC
**
6289 CTTCAAAAGGCTTATTACCCCCTTTTAATGTTTTTATAATCTCATAATTGATTTTAAGTTAGATT
1 CTTCAAAAGGCTTATTACCCCCTTTTAATG-TTTTATAATCTCATAATTGATTGAAAGTT-GATT
* *
6354 TTTTAATATTTTTGATTAAAATATACTATAATTGAATGTCTACCA-TGAGAAACGTGAAGCAAA-
64 TTTTAATATTTTTGATTAAAACATACTATAATTGAATGTCTA-CATTGAGAAACATGAAG-AAAC
* * * *
6417 AAGCATTCATTGCCAAGAAAAGTCCATTTAGAGTCACTCATTCCTTTAAAAAGCTTACTACTTGC
127 AAGCATTCATTGACAAGAAAAGTCAATTTAGAGTCACTCATTCCTTCAAAAAGCTTACTACTCGC
********** * *
6482 TTTAAATGATTTTATAATCTCATAANNNNNNNNNNGTTGACTTTTTTTACAT-TTTTGATTAAAG
192 TTTAAATGATTTTATAATCTCATAATTGATTTTAGGTTGAATTTTTTTACATATTTTG-TTAAAA
* * *
6546 CATACTATAATTGAATGTCTACCTTGATAAACAT-AAAGAAACAAG-CATTCATTGACAACAAAA
256 CAGACTATAATTGAATGTCTACCATGAGAAACATGAAA-AAA-AAGCCATTCATTGACAACAAAA
6609 GTCCATTTAGAGTAACCCATTC
319 GTCCATTTAGAGTAACCCATTC
* * **
6631 CTTTAAAAGGCTTATTA-CCCGTTTTAAATAAATTTATAATCTCATAAT
1 CTTCAAAAGGCTTATTACCCCCTTTT-AAT-GTTTTATAATCTCATAAT
6679 NNNNNNNNNN
Statistics
Matches: 314, Mismatches: 67, Indels: 17
0.79 0.17 0.04
Matches are distributed among these distances:
340 1 0.00
341 67 0.21
342 238 0.76
343 8 0.03
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (340 bp):
CTTCAAAAGGCTTATTACCCCCTTTTAATGTTTTATAATCTCATAATTGATTGAAAGTTGATTTT
TTAATATTTTTGATTAAAACATACTATAATTGAATGTCTACATTGAGAAACATGAAGAAACAAGC
ATTCATTGACAAGAAAAGTCAATTTAGAGTCACTCATTCCTTCAAAAAGCTTACTACTCGCTTTA
AATGATTTTATAATCTCATAATTGATTTTAGGTTGAATTTTTTTACATATTTTGTTAAAACAGAC
TATAATTGAATGTCTACCATGAGAAACATGAAAAAAAAGCCATTCATTGACAACAAAAGTCCATT
TAGAGTAACCCATTC
Found at i:6875 original size:171 final size:161
Alignment explanation
Indices: 6698--7027 Score: 346
Period size: 171 Copynumber: 2.0 Consensus size: 161
6688 NNNNNNNNNN
** * *
6698 TTTACATTTTT-TGTTAAAACAGACTATAATTG-AATGTTTGCCTCAGGAAACATGTTGAAAAAG
1 TTTACATTTTTCT-TTAAAACAGACTATAATTGCAA-GCCTACCTCAGGAAACATGTAGAAAAAG
* *
6761 CCATTCATTAG-GAAGAAAAGCCCATTTATAGTCACTCATTCCTTTAAAAGCCTTATTAC-CCGC
64 CCATTCA-TAGAGAAGAAAAACCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTCCG-
6824 TTTAAAT-AGTTTCATAATCTCATAATTAATTTTNNNNNNNNNNTT
127 TTTAAATGA-TTTCATAATCTCATAATTAATTTT----------TT
**
6869 TTTACATTTTTCTTTAAAACAGACTATAATTGCAAGCCTACCTCAGGAAAGGTGTAGAAAAAGCC
1 TTTACATTTTTCTTTAAAACAGACTATAATTGCAAGCCTACCTCAGGAAACATGTAGAAAAAGCC
* ** * * *
6934 TTTCATAGAGAAGAAAAATTCATTTTTAGTCACCCATTCTTTTGAAAGCCTTATTACTCCGTTTA
66 ATTCATAGAGAAGAAAAACCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTCCGTTTA
* *
6999 AATGATTTTATAATCTCATAATTGATTTT
131 AATGATTTCATAATCTCATAATTAATTTT
7028 AAGTTTAACT
Statistics
Matches: 138, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
170 3 0.02
171 128 0.93
172 7 0.05
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.37
Consensus pattern (161 bp):
TTTACATTTTTCTTTAAAACAGACTATAATTGCAAGCCTACCTCAGGAAACATGTAGAAAAAGCC
ATTCATAGAGAAGAAAAACCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTCCGTTTA
AATGATTTCATAATCTCATAATTAATTTTTT
Done.