Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397896.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1201.0, 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: 12497
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 4801 characters in sequence are not A, C, G, or T
Found at i:333 original size:170 final size:171
Alignment explanation
Indices: 1--334 Score: 447
Period size: 170 Copynumber: 2.0 Consensus size: 171
* *
1 TAATTAATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAAAAGACTATAATTAAATGTCTGTC
1 TAATTAATTTTAAGTTAAATTTTTTTACATTTTTAGTTAAAAAAGACTATAATTAAATGTCTGAC
* * * * * * * ** *
66 TTGGGGAACGTGAAGAAAAAGGTATTTATTGGCAAGAAAAGTCCATTTATAGCCACTTATTCTTT
66 TTGAGAAACATGAAGAAAAAGATAGTCATTGACAAGAAAAGTCCATTTATAGCCACCAATTCCTT
* *
131 TAAAAGCCTTATTACTCGCTTTAAACGATTTTATTATGTCA
131 CAAAAGCCTTATTACTCGCTTTAAAAGATTTTATTATGTCA
* * * * *
172 TAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGTTAAAAGAGATTATAATTGAATGTC-GAC
1 TAATTAATTTTAAGTTAAATTTTTTTACATTTTTAGTTAAAAAAGACTATAATTAAATGTCTGAC
* * *
236 TTGAGAAACATGAAGAAAAAGATAGTCATTGACAAGAATAGTCTA-TTAGTAGTCACCAATTCCT
66 TTGAGAAACATGAAGAAAAAGATAGTCATTGACAAGAAAAGTCCATTTA-TAGCCACCAATTCCT
300 TCAAAAGCCTTATTACTCGCTTTAAAAGATTTTAT
130 TCAAAAGCCTTATTACTCGCTTTAAAAGATTTTAT
335 AATCNNNNNN
Statistics
Matches: 140, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
169 3 0.02
170 82 0.59
171 55 0.39
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (171 bp):
TAATTAATTTTAAGTTAAATTTTTTTACATTTTTAGTTAAAAAAGACTATAATTAAATGTCTGAC
TTGAGAAACATGAAGAAAAAGATAGTCATTGACAAGAAAAGTCCATTTATAGCCACCAATTCCTT
CAAAAGCCTTATTACTCGCTTTAAAAGATTTTATTATGTCA
Found at i:2568 original size:171 final size:174
Alignment explanation
Indices: 2380--2755 Score: 501
Period size: 171 Copynumber: 2.2 Consensus size: 174
2370 NNNNNNNNNN
* * *
2380 TTATAAAACCATTTAAAGTGAGTAATAAG-GCTTTTAAAGGAATAGGTGATTGTCACTAGACTTT
1 TTATAAAACCTTTTAAAGCGAGTAATAAGAGCTTTTAAAGGAATAGGTGATTCTCACTAGACTTT
* ** * * *
2444 TCTTGCCAATAGATGCCTTTTTGTTCACATTCCCCAAGGTAG-CATTCAATGCTCGCTTTTTTTA
66 TCTTGCCAATAAATGCCTTTTTCATCACATTCCCCAAGGTAGACATTCAATGCTAGCCTTCTTTA
* * ***
2508 AATAAAAAAGTACAAA-AAAATTAACTTAAAATCAATTTTGACA
131 AACAAAAAAGTAAAAACAAAATTAACTTAAAATCAATGAAGACA
*
2551 TTATAAAACCTTTTAAAGCGAGTAAT-AGAGCTTTTAAAGGAATAGGTGATTCTCCCTAGACTTT
1 TTATAAAACCTTTTAAAGCGAGTAATAAGAGCTTTTAAAGGAATAGGTGATTCTCACTAGACTTT
* * * * *
2615 TCTTGTCAATAAATGCTTTTTTCATCACATTCCTCAAGGTAGACATTTAATTCTAGCCTTCTTTA
66 TCTTGCCAATAAATGCCTTTTTCATCACATTCCCCAAGGTAGACATTCAATGCTAGCCTTCTTTA
* * * *
2680 ACCAAAAATGTAAAAACAAAATTAACTTACAATCAATGAAGAGA
131 AACAAAAAAGTAAAAACAAAATTAACTTAAAATCAATGAAGACA
2724 TTATAAAACCTTTTAAAGCGAGTAATAA-AGCT
1 TTATAAAACCTTTTAAAGCGAGTAATAAGAGCT
2756 NNNNNNNNNN
Statistics
Matches: 177, Mismatches: 24, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
170 2 0.01
171 93 0.53
172 29 0.16
173 52 0.29
174 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (174 bp):
TTATAAAACCTTTTAAAGCGAGTAATAAGAGCTTTTAAAGGAATAGGTGATTCTCACTAGACTTT
TCTTGCCAATAAATGCCTTTTTCATCACATTCCCCAAGGTAGACATTCAATGCTAGCCTTCTTTA
AACAAAAAAGTAAAAACAAAATTAACTTAAAATCAATGAAGACA
Found at i:3984 original size:170 final size:172
Alignment explanation
Indices: 3759--4153 Score: 528
Period size: 170 Copynumber: 2.3 Consensus size: 172
3749 TAATTTTAAA
* * * * * *
3759 ATTATTAAACCATTTAAAGTGAGTAATAAGGCTTTTCAAGGAATAGGTGACTGTCACTATACTTT
1 ATTATAAAACCTTTTAAAGCGAGTAATAAGGC-TTTAAAGGAATAGGTGACTGTCACTAGACCTT
*
3824 TCTTACCAATAAATACCTTTTTCTTCACATTCCCCAAGGTAG-CAATCAATTCTAGCCTT-TTCT
65 TCTTACCAATAAATACCTTTTTCTTCACATTCCCCAAGGTAGACAATCAACTCTAGCCTTCTT-T
* * *
3887 GAA-TAGAAATGTAAAAT-ACAATCAACCTAAAATCAATTATGAG
129 -AACTAAAAATGTAAAATCAAAATCAACCTAAAATCAATTAAGAG
*
3930 ATTATAAAACCTTTTAAAGCGAGTAATAGGGCTTTAAAGGAATAGGTGACTGTCACTAGACCTTT
1 ATTATAAAACCTTTTAAAGCGAGTAATAAGGCTTTAAAGGAATAGGTGACTGTCACTAGACCTTT
** * * *
3995 CTTGTCAATAAATGCCTTTTTCTTTACATTCCCCAAGGTAGACATTCAACTCTAGCCTTCTTTAA
66 CTTACCAATAAATACCTTTTTCTTCACATTCCCCAAGGTAGACAATCAACTCTAGCCTTCTTTAA
* *
4060 CTAAAAATGTAAAATCAAAATCAACTTACAATCAATTAAGAG
131 CTAAAAATGTAAAATCAAAATCAACCTAAAATCAATTAAGAG
* * * *
4102 ATTATAAAACCTTTTAAAGCAAGTAATAAAGCTTCTGAAGGAATGGGTGACT
1 ATTATAAAACCTTTTAAAGCGAGTAATAAGGCTT-TAAAGGAATAGGTGACT
4154 ATAAATGGAN
Statistics
Matches: 196, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
170 69 0.35
171 57 0.29
172 55 0.28
173 15 0.08
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.32
Consensus pattern (172 bp):
ATTATAAAACCTTTTAAAGCGAGTAATAAGGCTTTAAAGGAATAGGTGACTGTCACTAGACCTTT
CTTACCAATAAATACCTTTTTCTTCACATTCCCCAAGGTAGACAATCAACTCTAGCCTTCTTTAA
CTAAAAATGTAAAATCAAAATCAACCTAAAATCAATTAAGAG
Found at i:5317 original size:170 final size:172
Alignment explanation
Indices: 4927--5536 Score: 472
Period size: 172 Copynumber: 3.5 Consensus size: 172
4917 NCAAAAGCTT
* ** * * * * *
4927 TATTACTCGCTTTAAAAGGTTTTATAATCTCTTAACTGATTGTAAG-AGTATTTTGTTTTTACAT
1 TATTACTCACTTTAAAAGGTTTTATAATCTCAAAATTGATTTTAAGTTG-A-ATTCTTTTTACAT
* * * * *
4991 TTTTGGTTAAAGAAGGCTAGAATTGAATGTCTACCTTAGGGAATGTGAAGAAAAAGGCTTTTATT
64 TTTTAGTTAAAAAAGACTAGAATTGAATGTCTACCTCAGGGAATGTGAAGAAAAAGGCATTTATT
*
5056 GACAAGAAAAGTCTAGTGACAATCACCTATTCCTTTAAAAGCCC
129 GGCAAGAAAAGTCTAGTGACAATCACCTATTCCTTTAAAAGCCC
* ********** *
5100 TATTACTCGCTTTAAAAGGTTTTATAATCTCNNNNNNNNNNTTAAGTTG-ATTTTTTTTACATTT
1 TATTACTCACTTTAAAAGGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTCTTTTTACATTT
* * *
5164 TTATTTAAAAAAGACTAGAATTGAATG-CTACCTCGGGGAATGTGAAGAAAAAAGCATTTATTGG
66 TTAGTTAAAAAAGACTAGAATTGAATGTCTACCTCAGGGAATGTGAAGAAAAAGGCATTTATTGG
** *
5228 CAAGAAAAGTCTAGTGACTGTCACCTATTCCTTTAAAAGCCT
131 CAAGAAAAGTCTAGTGACAATCACCTATTCCTTTAAAAGCCC
********** * ** *
5270 TATTACTCACTTNNNNNNNNNNTATAATTTCAAAATTGATTTTAAGTTGAATTCTTTAAATATTT
1 TATTACTCACTTTAAAAGGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTCTTTTTACATTT
* * * * * * * * *
5335 TTAGTTAAAATAGATTATAATTAAATGTCTACCTCAAGAAACGTCAAGAAAAAGGCATTCATTGG
66 TTAGTTAAAAAAGACTAGAATTGAATGTCTACCTCAGGGAATGTGAAGAAAAAGGCATTTATTGG
* * ** * * * * * *
5400 CAAGAAAAGT-TCATTTATTACCACCCATTTCTTCAAAAGTCT
131 CAAGAAAAGTCT-AGTGACAATCACCTATTCCTTTAAAAGCCC
* * * * * * * * *
5442 TATTATTCGCTTTAAAAGGTTTTATAATTTCATAACTGATTTCATGTTGAATTTTTTTTCAAATT
1 TATTACTCACTTTAAAAGGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTCTTTTT-ACATT
* *
5507 TTTAGTTAAAGAAGGCTAGAATTGAATGTC
65 TTTAGTTAAAAAAGACTAGAATTGAATGTC
5537 GACCCTGGAA
Statistics
Matches: 333, Mismatches: 99, Indels: 10
0.75 0.22 0.02
Matches are distributed among these distances:
170 98 0.29
171 70 0.21
172 101 0.30
173 63 0.19
174 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.37
Consensus pattern (172 bp):
TATTACTCACTTTAAAAGGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTCTTTTTACATTT
TTAGTTAAAAAAGACTAGAATTGAATGTCTACCTCAGGGAATGTGAAGAAAAAGGCATTTATTGG
CAAGAAAAGTCTAGTGACAATCACCTATTCCTTTAAAAGCCC
Done.