Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399973.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3200.0, 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: 6728
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.20
Warning! 3039 characters in sequence are not A, C, G, or T
Found at i:2541 original size:169 final size:168
Alignment explanation
Indices: 2252--3324 Score: 809
Period size: 170 Copynumber: 6.3 Consensus size: 168
2242 NNNNNNNNNN
* ** *
2252 ATTCAAATTAAAATCAATTATGAGATTATAAAATCATTTAAAGCTTGTAATAAGCCTTTCGAAGA
1 ATTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAG-CTTTCGAAGG
* * * ** ********** *
2317 CGTAGGTGACTATAAATGGACTTTTCTTATCAATGGANNNNNNNNNNTTCACATTTCTTGAGGTA
65 CATGGGTGACTATAAATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGAGGTA
* * * *
2382 GACATTCAATTATAATTTATTTTAACATAAATATAAAAA
130 GACATTCAATTATAATATGTTTTAATAAAAATATAAAAA
* * *
2421 ATTCAATTTAAAATCAATTATGAAGTTATAAAATCATTTAAAGCGAGTAATAAGCTTTTCGTAGG
1 ATTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGC-TTTCGAAGG
* ** * * *
2486 TATGGGCAAATATAAATGAACTTTTCTTACCAATGGATATCTTTTTCTACACATTTCTCGAGGTA
65 CATGGGTGACTATAAATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGAGGTA
* * *
2551 GACATTTAATGAAAATATGTTTTAATAAAAATATAAAAA
130 GACATTCAATTATAATATGTTTTAATAAAAATATAAAAA
****************************** *
2590 ATTCAAATTAAAATCAATTATGAGGTTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTAGG
1 ATTCAAATTAAAATCAATTATGAGGTTA-TAAAATCATTTAAAGCGAGTAATAAGCTTTCGAAGG
* ** * * * *
2655 TATGGGCAAATATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTACACATTTCTCGAGGTA
65 CATGGGTGACTATAAATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGAGGTA
*
2720 GACATTCAATTAAAATATGTTTTAATAAAAATATAAAAAA
130 GACATTCAATTATAATATGTTTTAATAAAAATAT-AAAAA
********** *
2760 ATTCNNNNNNNNNNCAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGGAGG
1 ATTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAA-GCTTTCGAAGG
* * * * * *
2825 AATGGGTGACCATAAATGAACTTTTCTTGTCAATGGATATCTTTTTCTTCACGTCTCTCAAGGTA
65 CATGGGTGACTATAAATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGAGGTA
* * * *
2890 GACACTCAATTATAATCTATTGTAATAAAAATATAAAAAA
130 GACATTCAATTATAATATGTTTTAATAAAAATAT-AAAAA
* ********** * * * *
2930 ATTTAAATTNNNNNNNNNNATTAGGTTATAAAATCATTTAATGCAAGTAATAAAGGTTTCGAAGG
1 ATTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCGAGTAAT-AAGCTTTCGAAGG
* *** * *
2995 CATGGGTGACTATAAATGGACTTTTCTTGCCAACAAATATCTTTTTCTTCACGTTTCTTGAGGTA
65 CATGGGTGACTATAAATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGAGGTA
** *
3060 GACATTCAATTATAACCTGTTTGAATAAAAATATTAAAAA
130 GACATTCAATTATAATATGTTTTAATAAAAATA-TAAAAA
* * **
3100 ATTCAAATTAAAATCAATTATGAGATTATAAAATCATATAAAGCTTGTAATAAGCCTTTCGAAGG
1 ATTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAG-CTTTCGAAGG
* * * * * * *
3165 CGTAGGTGACTGTAAATGGAA-TTTTCTTGTCAATGGATATCTTTTTCTTCACGTTTCTGGAGAT
65 CATGGGTGACTATAAAT-GAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGAGGT
* *
3229 AAACACTT-AATTATAATTTGTTTTAATAAAAATATAGAAAA
129 AGACA-TTCAATTATAATATGTTTTAATAAAAATATA-AAAA
* *
3270 GTTCAATTTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGC
1 ATTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGC
3325 NNNNNNNNNN
Statistics
Matches: 698, Mismatches: 196, Indels: 20
0.76 0.21 0.02
Matches are distributed among these distances:
168 1 0.00
169 267 0.38
170 423 0.61
171 7 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34
Consensus pattern (168 bp):
ATTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGCTTTCGAAGGC
ATGGGTGACTATAAATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGAGGTAG
ACATTCAATTATAATATGTTTTAATAAAAATATAAAAA
Found at i:4164 original size:21 final size:21
Alignment explanation
Indices: 4140--4180 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4130 AAGAAACATA
4140 AAGAAAAAGATATCCATTGAG
1 AAGAAAAAGATATCCATTGAG
4161 AAGAAAAAGATATCCATTGA
1 AAGAAAAAGATATCCATTGA
4181 CAANNNNNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.20
Consensus pattern (21 bp):
AAGAAAAAGATATCCATTGAG
Found at i:6374 original size:170 final size:170
Alignment explanation
Indices: 6067--6715 Score: 731
Period size: 170 Copynumber: 3.8 Consensus size: 170
6057 NNNNNNNNNN
* * * * **
6067 ATTTTAAGTTGAAGTTTTTTACATTTTTTATTAAAACAGATTATAATTGAAAGTTTTCCTCGTGA
1 ATTTTAAGTTGAATTTTTTTATA-TTTTTATTAAAACAGATTATAATTGAATGTTTACCTCAAGA
* * * **
6132 AACATGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTACAGTCACTTACGCCTTCGAAAG
65 AACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCACGCCTTCGAAAG
*
6197 GCTTATTACAAGCTTTAAATGATTTTATAATCTCATAATTG
130 CCTTATTACAAGCTTTAAATGATTTTATAATCTCATAATTG
* * * *
6238 ATGTTAATTTGAATTTTTTTATATTTTTATTAAAACAGATAATAATTGAATGTCTACCTCAAGAA
1 ATTTTAAGTTGAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAATGTTTACCTCAAGAA
* * **
6303 ACGTGAAGAACAAGATATCCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCGAAAGC
66 ACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCACGCCTTCGAAAGC
*
6368 CTTATTATAAGCTTTAAATGATTTTATAATCTCATAATTG
131 CTTATTACAAGCTTTAAATGATTTTATAATCTCATAATTG
* * * **********
6408 ATTTTAATTTCAATTTTTTTATATTGTTATTAAAACAGATTATAATTGAATGTNNNNNNNNNNAA
1 ATTTTAAGTTGAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAATGTTTACCTCAAGAA
* * * * *
6473 ACGTGAAGAAAAAGATATCCGTTGGTAAGAAAAGTCCATTTATAGTCACCTACGCTTTCGAAAGG
66 ACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCACGCCTTCGAAAGC
* *
6538 CTTATTACAAGCTTTAAATGATTTTATAACCTCATAAATG
131 CTTATTACAAGCTTTAAATGATTTTATAATCTCATAATTG
********** * *
6578 ATTTTAAGTTGAATTTTTTTNNNNNNNNNNTAAAACAGATTATAATTGAATGTTTAGCTCAACAA
1 ATTTTAAGTTGAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAATGTTTACCTCAAGAA
* * ** * * ** *
6643 ACGTGAAGAAAAAGATATCCATTAGTAAGACTAGTCTATTTATAGTCACTCATACCTTCGACAGC
66 ACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCACGCCTTCGAAAGC
6708 CTTATTAC
131 CTTATTAC
6716 TCGTATTAAA
Statistics
Matches: 399, Mismatches: 79, Indels: 1
0.83 0.16 0.00
Matches are distributed among these distances:
170 380 0.95
171 19 0.05
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.36
Consensus pattern (170 bp):
ATTTTAAGTTGAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAATGTTTACCTCAAGAA
ACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCACGCCTTCGAAAGC
CTTATTACAAGCTTTAAATGATTTTATAATCTCATAATTG
Done.