Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398158.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1461.0, 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: 4906
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.25
Warning! 1747 characters in sequence are not A, C, G, or T
Found at i:406 original size:173 final size:161
Alignment explanation
Indices: 144--590 Score: 378
Period size: 173 Copynumber: 2.6 Consensus size: 161
134 NNNNNTTTTT
* * * ** * ** **
144 ACATTTTTGGTTCAAACAGACTATAATTAAATCTTTACCTCGAGAAATGTG-AGAAAAAATACAT
1 ACATTTTT-GTTAAAACAGACTATAATCAAATGTCCACCTCAAGAAACATGAAG-AAAAAGGCAT
*
208 TCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTNNNNNNNNNNCCTTATTACTCGCTTTAAA
64 TCATTGGCAAGAAAAGTCCATTTATAGTCACCTATT---------GCCTTATTACTCGCTTTAAA
** *
273 TTGTTTTATAATCTCATAATTGATTGCAAGTTCAATTTTTTTTTGG
120 TTGTTTTATAATCTCATAATTGATTGCAAG-T-AA-AATTGTTT-G
* * * * * *
319 A-TTTTTTGTTAAAACAGACTATAATTAAATGTCTACTTCAAGCAACATGAAGGAAAAGGCATTC
1 ACATTTTTGTTAAAACAGACTATAATCAAATGTCCACCTCAAGAAACATGAAGAAAAAGGCATTC
* *
383 ATTGGCAAGAAAAGTCCATTTATAGTCACCTATNNNNNNNNNNGCCTTATTACTCGTTTTAAATT
66 ATTGGCAAGAAAAGTCCATTTATAGTCACCTAT---------TGCCTTATTACTCGCTTTAAATT
**
448 GTTTTATAATCTCATAATTGATTTTAAGTAAAATTGTTTG
122 GTTTTATAATCTCATAATTGATTGCAAGTAAAATTGTTTG
* * * *
488 ACATTTTTGTTAAAATAGACTATAATCGAATGTCCACCTCAAGAAATATGAAGAAAAAGTCATTC
1 ACATTTTTGTTAAAACAGACTATAATCAAATGTCCACCTCAAGAAACATGAAGAAAAAGGCATTC
* * *
553 ATTGGTAAGAAAAGTCTATTTATAGTCACCAATT-CCTT
66 ATTGGCAAGAAAAGTCCATTTATAGTCACCTATTGCCTT
591 CAAANNNNNN
Statistics
Matches: 227, Mismatches: 34, Indels: 37
0.76 0.11 0.12
Matches are distributed among these distances:
160 4 0.02
169 2 0.01
170 88 0.39
171 2 0.01
172 1 0.00
173 122 0.54
174 7 0.03
175 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.36
Consensus pattern (161 bp):
ACATTTTTGTTAAAACAGACTATAATCAAATGTCCACCTCAAGAAACATGAAGAAAAAGGCATTC
ATTGGCAAGAAAAGTCCATTTATAGTCACCTATTGCCTTATTACTCGCTTTAAATTGTTTTATAA
TCTCATAATTGATTGCAAGTAAAATTGTTTG
Found at i:2831 original size:172 final size:168
Alignment explanation
Indices: 2077--2900 Score: 592
Period size: 171 Copynumber: 4.8 Consensus size: 168
2067 NNNNNNNNTG
* * ** ** * * * *
2077 GTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAATGTGAAGAACAAGGGATTCATTGGTAA
1 GTTAAAATAAACTATAATT-AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTAGCAA
* * * *
2142 GAAAAGTCCAATTATAGTCATCCATTCCTTCA-AAACGCTTATTACTCGCTTTAAATTATTTTGT
65 GAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGC-CTTATTACTCGCTTTAAATTATTTTAT
********* * * *
2206 AATCTCNNNNNNNNNNTTAAATTTAGTTTTTTTACATTTTTT
129 AATCTC-ATAATTGATTTAAGTTTAATTTTTTTA-AATTTTT
* * * * * * * *
2248 GTTAAAACAAACTATAATTGAATCTTTACTTCAAAAAACGTAAAGAAAAAGGCATTCATTGGCAA
1 GTTAAAATAAACTATAATT-AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTAGCAA
* * ********** * *
2313 TAAAAGTCTATTTATAGTCANNNNNNNNNNCAAAAGCCTTATTACTCACTTTAAATTATTTTATA
65 GAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACTCGCTTTAAATTATTTTATA
*
2378 ATCTCATAATTGATATTAAGTTTAATTTTTTTACATTTTTT
130 ATCTCATAATTGAT-TTAAGTTTAATTTTTTTA-AATTTTT
* * * * ** * *
2419 GTTAAAACAGACTATAATTGAATCTCTACCTCTAGAAATGTGAAGAACAAGGCATTCA-TCGACA
1 GTTAAAATAAACTATAATT-AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTAG-CA
* * ** * *
2483 AGAAAATTCTATTTATAGTCACTTATTCCTTCAGAAGCCTTATTACTCGCTTTAAACTGTTTTAT
64 AGAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACTCGCTTTAAATTATTTTAT
** * *******
2548 AATCTCATAATTGATTTTAAGTAGAATTTTCTTANNNNNNNN
129 AATCTCATAATTGA-TTTAAGTTTAATTTTTTTA-AATTTTT
** * * * * *
2590 NNTAAAATAAACTATAATTAAATGTTTACCTCAAGAAACATGAAAAAAAAGACATTCATTGGTAA
1 GTTAAAATAAACTATAATT-AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTAGCAA
* **********
2655 GAAAAGTCCATTCATAGTCACCCATTCCTTNNNNNNNNNNATTACTCGCTTTAAATTATTTTATA
65 GAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACTCGCTTTAAATTATTTTATA
*
2720 ATCTCAGAATTGATTGTAAGTTTAATTTTTTTTAAATTTTT
130 ATCTCATAATTGATT-TAAGTTTAA-TTTTTTTAAATTTTT
*
2761 GATTAAAATAAACTATAATTAATTGTCTACCTCAAGAAACATGAAGAAAAAGGTATTCATTAGCA
1 G-TTAAAATAAACTATAATTAA-TGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTAGCA
* * * * *
2826 AGAAAAGTCCATTTATTGTCTCCCATTTCTTCAAAAACCTTATTACTCGCTTTAAA-TATTTTTA
64 AGAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACTCGCTTTAAATTA-TTTTA
2890 TAATCTCATAA
128 TAATCTCATAA
2901 NNNNNNNNNN
Statistics
Matches: 502, Mismatches: 141, Indels: 19
0.76 0.21 0.03
Matches are distributed among these distances:
170 4 0.01
171 375 0.75
172 123 0.25
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.36
Consensus pattern (168 bp):
GTTAAAATAAACTATAATTAATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTAGCAAG
AAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACTCGCTTTAAATTATTTTATAA
TCTCATAATTGATTTAAGTTTAATTTTTTTAAATTTTT
Found at i:3694 original size:171 final size:161
Alignment explanation
Indices: 3507--3829 Score: 366
Period size: 171 Copynumber: 1.9 Consensus size: 161
3497 NNNNNNNNNN
* * * *
3507 AATTATTTTGTAATCTCATAATTGATTTTAAATTTAATTTTTTTACATTTTTTGTTAAAACA-AA
1 AATTATTTTATAATCTCATAATCGATATTAAATTTAATTTTTTTACATTTTTTATTAAAACAGAA
* *
3571 TTATAATTGAATCTCTACCT-TAAGAAACATGAAGAAAAAGGCATTCATTG-GCAATAAAAGTCT
66 -TATAATTGAATCTCTACCTCT-AGAAACATGAAGAAAAAGGCATTCATCGAG-AAGAAAAGTCT
*
3634 ATTTATAGTCA-TCTATTCCTTCAAANNNNNNNNNNCTCACTTTA
128 ATTTAGAGTCACT-TATTCCTTCAAA----------CTCACTTTA
* *
3678 AATTGTTTTATAATCTCATAATCGATATTAAGTTTAATTTTTTTACATTTTTTATTAAAACAGAA
1 AATTATTTTATAATCTCATAATCGATATTAAATTTAATTTTTTTACATTTTTTATTAAAACAGAA
** * * *
3743 TATAATTGAATCTCTACCTCTAGAAATTTGAAGAACAAGGCATTCATCGAGAAGAAAATTTTATT
66 TATAATTGAATCTCTACCTCTAGAAACATGAAGAAAAAGGCATTCATCGAGAAGAAAAGTCTATT
3808 TAGAGTCACTTATTCCTTCAAA
131 TAGAGTCACTTATTCCTTCAAA
3830 AGCCTTATTA
Statistics
Matches: 134, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
171 129 0.96
172 5 0.04
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.40
Consensus pattern (161 bp):
AATTATTTTATAATCTCATAATCGATATTAAATTTAATTTTTTTACATTTTTTATTAAAACAGAA
TATAATTGAATCTCTACCTCTAGAAACATGAAGAAAAAGGCATTCATCGAGAAGAAAAGTCTATT
TAGAGTCACTTATTCCTTCAAACTCACTTTA
Done.