Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400089.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3308.0, 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: 3694
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.28
Warning! 954 characters in sequence are not A, C, G, or T
Found at i:387 original size:164 final size:154
Alignment explanation
Indices: 165--462 Score: 371
Period size: 164 Copynumber: 1.9 Consensus size: 154
155 AATCAATTGA
* *
165 GAGATTATAAAATAAGTTAAAGCGAGTAATAAGGTTTTTAAAGGAATGGGTCACTATAAATGGAC
1 GAGATTATAAAATAAGTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTCACTATAAATGAAC
* * *
230 TTTTCTTCCCAATGATTGCCTTTTTCTTCAAGTTTCCTGAGGTAAACATTCAATTATTGTCTGTT
66 TTTTCCTCCCAATGAATGCCTTTTTCTTCAAGTTTCCTGAGCTAAACATTCAATTATTGTCTGTT
295 TTAATTAAAAAANNNNNNNNNNAAAATTAATTAT
131 TTAATTAAAAAA----------AAAATTAATTAT
* * * *
329 GAGATTATAAAATAATTTTAAGCGAGTAATAAGGCTTTTAAAGGAATTGGTGACTATAAATGAAC
1 GAGATTATAAAATAAGTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTCACTATAAATGAAC
** * * * *
394 TTTTCCTGTCAATGAATGTCTTTTTCTTCATGTTTCTTGAGCTAGACATTCAATTATTGTCTGTT
66 TTTTCCTCCCAATGAATGCCTTTTTCTTCAAGTTTCCTGAGCTAAACATTCAATTATTGTCTGTT
459 TTAA
131 TTAA
463 CTAANNNNNN
Statistics
Matches: 119, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
164 119 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.38
Consensus pattern (154 bp):
GAGATTATAAAATAAGTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTCACTATAAATGAAC
TTTTCCTCCCAATGAATGCCTTTTTCTTCAAGTTTCCTGAGCTAAACATTCAATTATTGTCTGTT
TTAATTAAAAAAAAAATTAATTAT
Found at i:1568 original size:170 final size:167
Alignment explanation
Indices: 1230--1904 Score: 569
Period size: 170 Copynumber: 4.0 Consensus size: 167
1220 TAAAGTGAGT
* ** * * * *
1230 AATAAGGCTTTTTAAGGAATGACTGACTATAAATGGACTTTT-TTTCTCAATGAAAGACTTTTTT
1 AATAA-GCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCT-AATGAATG-CCTTTTT
* ** * * * *
1294 TTACACATTTCTTAAGGCATG-CATTCAATTA-TAGTATGTTTTAACCATAAATGCATAAAAAAA
63 TT-CATATTTCTCGAGGTA-GACATTAAATTATTA-TCTGTTTTAACCAAAAATG---AAAAAAA
* *
1357 TTAACTTAAAATCAATTTTGAGATTATAAAATAATTTAAAGCGAAT
122 TTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAAA
* * *
1403 AATAAGTCTTTTAAAGGAATGAGTGACTATAAATAAATTTTTCTTGCTAATGAATGCCTTTTGTT
1 AATAAG-CTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCTAATGAATGCCTTTT-TT
* * *
1468 TCATATTTGTCGCGGTAAACATTAAATTATTATC-GATTTTAACCAAAATAT-AAAAAAATTAAA
64 TCATATTTCTCGAGGTAGACATTAAATTATTATCTG-TTTTAACCAAAA-ATGAAAAAAATT-AA
* * *
1531 CTTAAAATTAGTTATGAGTTTATAAAAGT-ATTTAAAGC-AAGA
126 CTTAAAATCAATTATGAGATTATAAAA-TAATTTAAAGCGAA-A
* * * * * * *
1573 AATATCGCTTCTGAAGGAATGGGTGACCATAAATGGACTTTTCTT-CTCTAGGAATAG-CTTTTT
1 AATA-AGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCT-AATGAAT-GCCTTTTT
* * * * * *
1636 TACACATTTCTCAAGGTAGGCATTCAATTA-TAGCCTGTTTTAACCAAAAATTGAAAAAAATCTA
63 TTCATATTTCTCGAGGTAGACATTAAATTATTA-TCTGTTTTAACCAAAAA-TGAAAAAAAT-TA
* * * **
1700 ACTTCAAATCAATTTTGGGATTATAAAATAATTTAAAGCGAGC
125 ACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAAA
* * * * *
1743 AATAAGGCTTTTAAAGGAGTGGGTGCCTATAAATGAACTTTTCTTGCCAATGATTTCCTTTTTCT
1 AATAA-GCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCTAATGAATGCCTTTTT-T
* * * ** *
1808 TCATGTTTCTTGAGGTAGACATTTAATTATTATCTGTTTTAATTAAAAATGTAAAAAATTTAACT
64 TCATATTTCTCGAGGTAGACATTAAATTATTATCTGTTTTAACCAAAAATG-AAAAAAATTAACT
1873 TAAAATCAATTATGAGATTATAAAATAATTTA
128 TAAAATCAATTATGAGATTATAAAATAATTTA
1905 NNNNNNNNNN
Statistics
Matches: 400, Mismatches: 76, Indels: 55
0.75 0.14 0.10
Matches are distributed among these distances:
168 3 0.01
169 51 0.13
170 203 0.51
171 51 0.13
172 39 0.10
173 49 0.12
174 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37
Consensus pattern (167 bp):
AATAAGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCTAATGAATGCCTTTTTTTC
ATATTTCTCGAGGTAGACATTAAATTATTATCTGTTTTAACCAAAAATGAAAAAAATTAACTTAA
AATCAATTATGAGATTATAAAATAATTTAAAGCGAAA
Found at i:1957 original size:340 final size:340
Alignment explanation
Indices: 1243--1897 Score: 845
Period size: 340 Copynumber: 1.9 Consensus size: 340
1233 AAGGCTTTTT
* * * *
1243 AAGGAATGACTGACTATAAATGGACTTTTTTTCTCAATGAAAGACTTTTTTTTACACATTTCTTA
1 AAGGAATGACTGACCATAAATGGACTTTTCTTCTCAAGGAAAGAC-TTTTTTTACACATTTCTCA
* * *
1308 AGGCATGCATTCAATTATAGTATGTTTTAACCATAAATGCATAAAAAAATTAACTTAAAATCAAT
65 AGGCAGGCATTCAATTATAGCATGTTTTAACCAAAAATG-A-AAAAAAATTAACTTAAAATCAAT
* *
1373 TTTGAGATTATAAAATAATTTAAAGCGAATAATAAGTCTTTTAAAGGAATGAGTGACTATAAATA
128 TTTGAGATTATAAAATAATTTAAAGCGAACAATAAGGCTTTTAAAGGAATGAGTGACTATAAATA
* * * *
1438 AATTTTTCTTGCTAATGAATGCCTTTTGTTTCATATTTGTCGCGGTAAACATTAAATTATTATCG
193 AACTTTTCTTGCCAATGAATGCCTTTTGTTTCATATTTCTCGAGGTAAACATTAAATTATTATCG
* * *
1503 ATTTTAACCAAAATATAAAAAAATTAAACTTAAAATTAGTTATGAGTTTATAAAAGTATTTAAAG
258 ATTTTAACCAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAAGTATTTAAAG
1568 CAAGAAATATCGCTTCTG
323 CAAGAAATATCGCTTCTG
** *
1586 AAGGAATGGGTGACCATAAATGGACTTTTCTTCTCTAGGAATAG-C-TTTTTTACACATTTCTCA
1 AAGGAATGACTGACCATAAATGGACTTTTCTTCTCAAGGAA-AGACTTTTTTTACACATTTCTCA
* * *
1649 AGGTAGGCATTCAATTATAGCCTGTTTTAACCAAAAATTG-AAAAAAATCTAACTTCAAATCAAT
65 AGGCAGGCATTCAATTATAGCATGTTTTAACCAAAAA-TGAAAAAAAAT-TAACTTAAAATCAAT
* * * * * *
1713 TTTGGGATTATAAAATAATTTAAAGCGAGCAATAAGGCTTTTAAAGGAGTGGGTGCCTATAAATG
128 TTTGAGATTATAAAATAATTTAAAGCGAACAATAAGGCTTTTAAAGGAATGAGTGACTATAAATA
* * * * * *
1778 AACTTTTCTTGCCAATGATTTCCTTTT-TCTTCATGTTTCTTGAGGTAGACATTTAATTATTATC
193 AACTTTTCTTGCCAATGAATGCCTTTTGT-TTCATATTTCTCGAGGTAAACATTAAATTATTATC
** * *
1842 TG-TTTTAATTAAAA-ATGTAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAA
257 -GATTTTAACCAAAATAT-AAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAA
1898 TAATTTANNN
Statistics
Matches: 268, Mismatches: 38, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
339 11 0.04
340 167 0.62
341 50 0.19
342 2 0.01
343 36 0.13
344 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37
Consensus pattern (340 bp):
AAGGAATGACTGACCATAAATGGACTTTTCTTCTCAAGGAAAGACTTTTTTTACACATTTCTCAA
GGCAGGCATTCAATTATAGCATGTTTTAACCAAAAATGAAAAAAAATTAACTTAAAATCAATTTT
GAGATTATAAAATAATTTAAAGCGAACAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAAAC
TTTTCTTGCCAATGAATGCCTTTTGTTTCATATTTCTCGAGGTAAACATTAAATTATTATCGATT
TTAACCAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAAGTATTTAAAGCAA
GAAATATCGCTTCTG
Found at i:3281 original size:173 final size:169
Alignment explanation
Indices: 2909--3450 Score: 459
Period size: 173 Copynumber: 3.2 Consensus size: 169
2899 NNNNNNNNNT
** * * * * *
2909 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAATGAATGGGTGACCATTAAT-GAACTTT
1 TTATAAAATAATTTAAAGCGAGTAATAAGTCTTTTGAAGGAATGAGTGACTATAAATAG-ACTTT
* *
2973 TCTTCTCAATGAATAGCTTTTTTGCATGTTTCTCAAGGCAAGCATTCAATTATAGTTTGTTTTAA
65 TTTTCTCAATGAATAGCTTTTTTGCA-GTTTCTCAAGGCAAGCATTCAATTATAGTATGTTTTAA
* ** *
3038 CCAAAAATACCAAAATATTCAACTTAAAATCAATTATGAGA
129 CCAAAAACAAAAAAAAATTCAACTTAAAATCAATTATGAGA
** * *
3079 TTATAAAATAATTTAAAATGAGAAATAAGTCTTTTGAAGGAATGACTGACTATAAATAGACTTTT
1 TTATAAAATAATTTAAAGCGAGTAATAAGTCTTTTGAAGGAATGAGTGACTATAAATAGACTTTT
** * *
3144 TTTCTCAATGAATAATTTTTTTTACGCA-TTTCTTAAGGCAGGCATTCAATTATAGTATGTTTTA
66 TTTCTCAATGAAT-AGCTTTTTT--GCAGTTTCTCAAGGCAAGCATTCAATTATAGTATGTTTTA
* *
3208 ACCATAAAAGCAAAAAAAAATTTAACTTAAAATCAATTTTGAGA
128 ACCA-AAAA-CAAAAAAAAATTCAACTTAAAATCAATTATGAGA
********** *
3252 TTATAAANNNNNNNNNNGCGAGTAATAAGTCTTTTAAAGGAATGAGTGACTATAAATAGA-TTTT
1 TTATAAAATAATTTAAAGCGAGTAATAAGTCTTTTGAAGGAATGAGTGACTATAAATAGACTTTT
* * * * * * * * *
3316 TCTTGCT-AATAAAT-GCCTTTTGTTTCATGTTTGTCGAGGTAAACATTAAATTATTGTCA-ATT
66 T-TT-CTCAATGAATAG-CTTTT-TTGCA-GTTTCTCAAGGCAAGCATTCAATTATAGT-ATGTT
* * * * * * *
3378 TTAATCAAAAATATAAAAAAATTGAACTTAAAATTAATTATTAGT
125 TTAACCAAAAACAAAAAAAAATTCAACTTAAAATCAATTATGAGA
3423 TTATAAAACT-ATTTAAAGCGAGTAATAA
1 TTATAAAA-TAATTTAAAGCGAGTAATAA
3451 AGCTTTNNNN
Statistics
Matches: 290, Mismatches: 68, Indels: 27
0.75 0.18 0.07
Matches are distributed among these distances:
170 64 0.22
171 92 0.32
172 17 0.06
173 114 0.39
174 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.36
Consensus pattern (169 bp):
TTATAAAATAATTTAAAGCGAGTAATAAGTCTTTTGAAGGAATGAGTGACTATAAATAGACTTTT
TTTCTCAATGAATAGCTTTTTTGCAGTTTCTCAAGGCAAGCATTCAATTATAGTATGTTTTAACC
AAAAACAAAAAAAAATTCAACTTAAAATCAATTATGAGA
Done.