Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399504.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2764.0, 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: 6033
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.25
Warning! 1939 characters in sequence are not A, C, G, or T
Found at i:294 original size:171 final size:169
Alignment explanation
Indices: 45--411 Score: 394
Period size: 169 Copynumber: 2.2 Consensus size: 169
35 CATAAATGGT
* * * * * *
45 TTTTTCTACAAGTTTCTCAAGGCAGGCATTTAATTATAGTCTGTTTTAACAAAAAATGCAAACAA
1 TTTTTCTTCAAGTTTCTCAAGGTAGACATTTAATTATAGTCTATTTTAACAAAAAATGAAAAAAA
** * **********
110 TTTCAACTTAAAATCAATTATGAGATTATAAAATTATTTAAAGCAAGTAATANNNNNNNNNNAGG
66 TTTCAACTTAAAATCAATTATGA-A-TATAAAACAAATTAAAGCAAGTAATAAGGCTTTTGAAGG
* *
175 AATGGGTGACTATAAATTAACTTTTCTTGCCAATGAATGTC
129 AATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATATC
* * * * *
216 TTTTTCTTCATGTTTCTCAAGGTAGACGTTTAATTATATTCTATTTTAACCAAATATGTAAAAAA
1 TTTTTCTTCAAGTTTCTCAAGGTAGACATTTAATTATAGTCTATTTTAACAAAAAATG-AAAAAA
* * *
281 ATTT-TACTTAAAATCAATTATGAATATAAAACAAATTAAAGCTAGTAGTAAGGCTTTTGAAGGA
65 ATTTCAACTTAAAATCAATTATGAATATAAAACAAATTAAAGCAAGTAATAAGGCTTTTGAAGGA
* * * *
345 ATGGGTGATTATGAATGGACTTTTCTTGCCAATGAATATT
130 ATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATATC
*
385 TTTTTCTTCACGTTTCTCAAGGTAGAC
1 TTTTTCTTCAAGTTTCTCAAGGTAGAC
412 NNNNNNNNNN
Statistics
Matches: 161, Mismatches: 34, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
169 85 0.53
170 1 0.01
171 67 0.42
172 8 0.05
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.37
Consensus pattern (169 bp):
TTTTTCTTCAAGTTTCTCAAGGTAGACATTTAATTATAGTCTATTTTAACAAAAAATGAAAAAAA
TTTCAACTTAAAATCAATTATGAATATAAAACAAATTAAAGCAAGTAATAAGGCTTTTGAAGGAA
TGGGTGACTATAAATGAACTTTTCTTGCCAATGAATATC
Found at i:1961 original size:172 final size:170
Alignment explanation
Indices: 1266--1966 Score: 641
Period size: 171 Copynumber: 4.1 Consensus size: 170
1256 NNNNNNNNNN
* * * * * *
1266 TTTCTTGACAATGAATATCTTTTTCTCCACGTTTTTCTAGCTAGACATTCAATTATAATATGTTT
1 TTTCTTGCCAATGAATATCTTTTTCTTCATGTTCTT-GAGCTAGACATTCAATTATAATCTGTTT
* * * * *
1331 TAACC-AATATGTAAAAAAAATTGAACCTAACATCAATTTTGACATTATAAAATCATTTAAAGCG
65 TAACCAAAAATGT-AAAAAAATTGAACCTAAAATCAATTTTGAGATTATAAAACCATTTAATGCG
* ** * *
1395 ACTAATAAGGCTTTCGAAGAAATAGGAGT--CTATAAAT-AATCT
129 AGTAATAAGGCTTTTAAAGGAATA--AGTAACTATAAATGGA-CT
* * * * * * *
1437 TTTCTTGCCAATTAAT-GCTTTTTTCTTTACAT-TTCTTGTGGTAAACATTCAATTATACTCTAT
1 TTTCTTGCCAATGAATATC-TTTTTC-TT-CATGTTCTTGAGCTAGACATTCAATTATAATCTGT
* * * **********
1500 TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATNNNNNNNNNNTAAAACCATTTAAAT-
63 TTTAACCAAAAATGTAAAAAAATTGAACCTAAAATCAATTTTGAGATTATAAAACCATTT-AATG
* * *
1564 CAAGTAATAAGGCTTTTGAAGGAATGAGTAACTATAAATGGACT
127 CGAGTAATAAGGCTTTTAAAGGAATAAGTAACTATAAATGGACT
* * * * *
1608 TTTTTTGCCAATGAATATCTTTTTGTTCATGTTTCTCGAGGTAGAGC-TTCAATTATAGTCTGTT
1 TTTCTTGCCAATGAATATCTTTTTCTTCATG-TTCTTGAGCTAGA-CATTCAATTATAATCTGTT
* * * * * *
1672 TTAACCAAAAATGTAAAAAAATTTAGCTTACAATCAATTATGAGATTATAAAACCATTTACA-GT
64 TTAACCAAAAATGTAAAAAAATTGAACCTAAAATCAATTTTGAGATTATAAAACCATTTA-ATGC
* ** *
1736 GAGTAATATGGCTTTTGAAA-GAATGGGTAACTATAAATGGACC
128 GAGTAATAAGGCTTTT-AAAGGAATAAGTAACTATAAATGGACT
* * *
1779 TTTCTTGCCAATAAATATCTTTTTCTTCATGTTACTTGAGCTAGACATTCAATTACAATCTGTGT
1 TTTCTTGCCAATGAATATCTTTTTCTTCATGTT-CTTGAGCTAGACATTCAATTATAATCTGTTT
*
1844 TAACCAATAATGTAAAAAAAGTTGAACCTAAAATCAATTTTGAGATTATAAAACCATTTAATGCG
65 TAACCAAAAATGTAAAAAAA-TTGAACCTAAAATCAATTTTGAGATTATAAAACCATTTAATGCG
* *
1909 AGAAATAAGGGTTTTAAAGGAATAAG-AGACTATAAATGGACT
129 AGTAATAAGGCTTTTAAAGGAATAAGTA-ACTATAAATGGACT
1951 TTTCTTGCCAATGAAT
1 TTTCTTGCCAATGAAT
1967 GCTTGTTNNN
Statistics
Matches: 422, Mismatches: 87, Indels: 41
0.77 0.16 0.07
Matches are distributed among these distances:
169 6 0.01
170 7 0.02
171 309 0.73
172 98 0.23
173 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.36
Consensus pattern (170 bp):
TTTCTTGCCAATGAATATCTTTTTCTTCATGTTCTTGAGCTAGACATTCAATTATAATCTGTTTT
AACCAAAAATGTAAAAAAATTGAACCTAAAATCAATTTTGAGATTATAAAACCATTTAATGCGAG
TAATAAGGCTTTTAAAGGAATAAGTAACTATAAATGGACT
Found at i:3366 original size:171 final size:169
Alignment explanation
Indices: 2989--3458 Score: 537
Period size: 171 Copynumber: 2.7 Consensus size: 169
2979 NNNNNNNNNN
*
2989 ATTATGAGATTATAAAACCATTTAAGGCGAGTAATAAGGCTTTTAAAGGAATGGATGACTATAAA
1 ATTATGAGATTATAAAACCATTTAA-GCGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAA
* * *
3054 TGGACTTTTCCTGCCAATGAATGCTTGTTTCTTAATGTTTCTTGAGGTAGACATTCAATTGTAGT
65 TGGACTTTTTCTGCCAATGAATGCTTG-TTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGT
* *
3119 GCGTTTTAACCAAAAATGTAAAAAAAATCAACTTAGAATCA
129 ACGTTTTAACCAAAAATGCAAAAAAAATCAACTTAGAATCA
********* * * *
3160 ATTATGAGATTATAANNNNNNNNNNAGCAAGTAATAAGGCTTTTGAAGGGATGGGTGACTATAAA
1 ATTATGAGATTATAA-AACCATTTAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAA
* * *
3225 TGGACTTTTTTTGCCAGTGAATGCCTTGTTCTTCATATTTCTTGAGGTAGACATTCAATTATAGT
65 TGGACTTTTTCTGCCAATGAATG-CTTGTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGT
* * * * *
3290 ATGTTTTAACCAGAAATGCAAAAAAATTTAACTTATAATCA
129 ACGTTTTAACCAAAAATGCAAAAAAAATCAACTTAGAATCA
* * * * *
3331 ATTATGAGATTATAAAACCCTTTGAAGCGAGTAATATGGCTTTTAAAAGAATTGGCGACTATAAA
1 ATTATGAGATTATAAAACCATTT-AAGCGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAA
* * * * **
3396 TGGACTTTTTCCT-CTAATGAATGTCTTTTTCTTCATGTTTCTAGAGCTACCCATTCAATTATA
65 TGGACTTTTT-CTGCCAATGAATG-CTTGTTCTTCATGTTTCTTGAGGTAGACATTCAATTATA
3459 ATCTATTTTA
Statistics
Matches: 243, Mismatches: 52, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
171 237 0.98
172 6 0.02
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (169 bp):
ATTATGAGATTATAAAACCATTTAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAAT
GGACTTTTTCTGCCAATGAATGCTTGTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTAC
GTTTTAACCAAAAATGCAAAAAAAATCAACTTAGAATCA
Found at i:3470 original size:171 final size:170
Alignment explanation
Indices: 2989--3678 Score: 534
Period size: 171 Copynumber: 4.0 Consensus size: 170
2979 NNNNNNNNNN
2989 ATTATGAGATTATAAAACCATTTAAGGCGAGTAATAAGGCTTTTAAAGGAA-TGGATGACTATAA
1 ATTATGAGATTATAAAACCATTTAA-GCGAGTAATAAGGCTTTTAAAGGAATTGG-TGACTATAA
* *
3053 ATGGAC-TTTTCCTGCCAATGAATGCTTGTTTCTTAATGTTTCTTGAGGTAGACATTCAATTGTA
64 ATGGACTTTTTCCTGCCAATGAATGCTT-TTTCTTCATGTTTCTTGAGGTAGACATTCAATTATA
*
3117 GTGC-GTTTTAACCAAAAATGTAAAAAAAATCAACTTAGAATCA
128 GT-CTGTTTTAACCAAAAATGCAAAAAAAATCAACTTAGAATCA
********* * * * *
3160 ATTATGAGATTATAANNNNNNNNNNAGCAAGTAATAAGGCTTTTGAAGGGATGGGTGACTATAAA
1 ATTATGAGATTATAA-AACCATTTAAGCGAGTAATAAGGCTTTTAAAGGAATTGGTGACTATAAA
* * * *
3225 TGGACTTTTT-TTGCCAGTGAATGCCTTGTTCTTCATATTTCTTGAGGTAGACATTCAATTATAG
65 TGGACTTTTTCCTGCCAATGAATG-CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAG
* * * * *
3289 TATGTTTTAACCAGAAATGCAAAAAAATTTAACTTATAATCA
129 TCTGTTTTAACCAAAAATGCAAAAAAAATCAACTTAGAATCA
* * * *
3331 ATTATGAGATTATAAAACCCTTTGAAGCGAGTAATATGGCTTTTAAAAGAATTGGCGACTATAAA
1 ATTATGAGATTATAAAACCATTT-AAGCGAGTAATAAGGCTTTTAAAGGAATTGGTGACTATAAA
* * * ** *
3396 TGGACTTTTTCCT-CTAATGAATGTCTTTTTCTTCATGTTTCTAGAGCTACCCATTCAATTATAA
65 TGGACTTTTTCCTGCCAATGAATG-CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAG
* * * * * * * * *
3460 TCTATTTTAACTAATAAGGTAAAAACAATTGAA-TGTAAAATTA
129 TCTGTTTTAACCAAAAATGCAAAAA-AAATCAACT-TAGAATCA
* ********* * * * **
3503 ATTTTGAGATTATAAAANNNNNNNNNNCGTGTAATAAGGCTTTTGAAGGAATAGAAGACTATAAA
1 ATTATGAGATTATAAAA-CCATTTAAGCGAGTAATAAGGCTTTTAAAGGAATTGGTGACTATAAA
* * * * * * * *
3568 TGGAC-TTTTCTTGCCAACGAATGCTTTTTTCTTTACGTTTCCCT-AGGTAAACATTCAACTATT
65 TGGACTTTTTCCTGCCAATGAATGC-TTTTTCTTCATGTTT-CTTGAGGTAGACATTCAATTATA
**** * * *
3631 GTCTGTTTTATTGTAAAAT-CAAAAAAATTTAACTTAAAATCA
128 GTCTGTTTTAACCAAAAATGCAAAAAAAATCAACTTAGAATCA
3673 ATTATG
1 ATTATG
3679 NNNNNNNNNN
Statistics
Matches: 402, Mismatches: 103, Indels: 29
0.75 0.19 0.05
Matches are distributed among these distances:
170 18 0.04
171 262 0.65
172 121 0.30
173 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.35
Consensus pattern (170 bp):
ATTATGAGATTATAAAACCATTTAAGCGAGTAATAAGGCTTTTAAAGGAATTGGTGACTATAAAT
GGACTTTTTCCTGCCAATGAATGCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTC
TGTTTTAACCAAAAATGCAAAAAAAATCAACTTAGAATCA
Done.