Multiple sequence alignment - TraesCS2D01G221300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G221300 chr2D 100.000 3054 0 0 1 3054 188814505 188811452 0.000000e+00 5640.0
1 TraesCS2D01G221300 chr2A 90.560 1875 94 30 621 2464 202879796 202877974 0.000000e+00 2405.0
2 TraesCS2D01G221300 chr2A 93.790 467 20 4 2596 3054 202877850 202877385 0.000000e+00 693.0
3 TraesCS2D01G221300 chr2A 94.180 189 6 2 225 413 202880022 202879839 1.790000e-72 283.0
4 TraesCS2D01G221300 chr2B 95.627 1372 35 9 433 1785 244882854 244881489 0.000000e+00 2178.0
5 TraesCS2D01G221300 chr2B 86.414 449 35 9 2613 3054 244881167 244880738 4.610000e-128 468.0
6 TraesCS2D01G221300 chr2B 94.203 207 12 0 1 207 210253699 210253905 1.770000e-82 316.0
7 TraesCS2D01G221300 chr2B 83.121 314 25 12 1816 2111 244881514 244881211 8.400000e-66 261.0
8 TraesCS2D01G221300 chr2B 95.294 85 4 0 208 292 244882935 244882851 5.310000e-28 135.0
9 TraesCS2D01G221300 chr3D 98.068 207 4 0 1 207 407813251 407813457 8.050000e-96 361.0
10 TraesCS2D01G221300 chr3D 95.652 207 7 2 1 207 74751244 74751040 6.310000e-87 331.0
11 TraesCS2D01G221300 chr3D 94.686 207 10 1 1 207 529876207 529876002 1.370000e-83 320.0
12 TraesCS2D01G221300 chrUn 97.073 205 6 0 3 207 461039521 461039725 2.250000e-91 346.0
13 TraesCS2D01G221300 chr7A 95.652 207 7 1 1 207 54761454 54761250 6.310000e-87 331.0
14 TraesCS2D01G221300 chr7A 94.203 207 12 0 1 207 7831181 7830975 1.770000e-82 316.0
15 TraesCS2D01G221300 chr7A 88.679 53 6 0 2133 2185 108219665 108219613 7.070000e-07 65.8
16 TraesCS2D01G221300 chr7A 96.970 33 0 1 2137 2168 174589311 174589343 2.000000e-03 54.7
17 TraesCS2D01G221300 chr6D 93.720 207 13 0 1 207 467982396 467982602 8.220000e-81 311.0
18 TraesCS2D01G221300 chr4D 93.720 207 13 0 1 207 54264801 54264595 8.220000e-81 311.0
19 TraesCS2D01G221300 chr7D 93.023 43 2 1 2319 2360 146234585 146234543 9.140000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G221300 chr2D 188811452 188814505 3053 True 5640.0 5640 100.000000 1 3054 1 chr2D.!!$R1 3053
1 TraesCS2D01G221300 chr2A 202877385 202880022 2637 True 1127.0 2405 92.843333 225 3054 3 chr2A.!!$R1 2829
2 TraesCS2D01G221300 chr2B 244880738 244882935 2197 True 760.5 2178 90.114000 208 3054 4 chr2B.!!$R1 2846

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
164 165 0.043940 AAGGAGAGCTGATCTGGGGT 59.956 55.0 0.00 0.0 38.84 4.95 F
754 759 0.394938 TCAACTTAGCACGGCTCCAA 59.605 50.0 1.46 0.0 40.44 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1826 1.135460 GGTAGCTCGAACTACAGCGTT 60.135 52.381 23.5 0.0 43.61 4.84 R
2534 2585 0.105039 GAATGGCTAGGGGACAGTCG 59.895 60.000 0.0 0.0 38.32 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.367023 GCCACCACCGTGCTCGTA 62.367 66.667 7.47 0.00 38.79 3.43
28 29 2.577059 CCACCACCGTGCTCGTAT 59.423 61.111 7.47 0.00 38.79 3.06
29 30 1.518572 CCACCACCGTGCTCGTATC 60.519 63.158 7.47 0.00 38.79 2.24
30 31 1.518572 CACCACCGTGCTCGTATCC 60.519 63.158 7.47 0.00 32.04 2.59
31 32 2.278596 CCACCGTGCTCGTATCCG 60.279 66.667 7.47 0.00 35.01 4.18
32 33 2.278596 CACCGTGCTCGTATCCGG 60.279 66.667 7.47 0.00 45.72 5.14
33 34 4.203076 ACCGTGCTCGTATCCGGC 62.203 66.667 7.47 0.00 44.14 6.13
34 35 4.201679 CCGTGCTCGTATCCGGCA 62.202 66.667 7.47 0.00 37.73 5.69
35 36 2.027605 CGTGCTCGTATCCGGCAT 59.972 61.111 0.00 0.00 40.56 4.40
36 37 2.016704 CGTGCTCGTATCCGGCATC 61.017 63.158 0.00 0.00 40.56 3.91
37 38 1.067416 GTGCTCGTATCCGGCATCA 59.933 57.895 0.00 0.00 40.56 3.07
38 39 1.067416 TGCTCGTATCCGGCATCAC 59.933 57.895 0.00 0.00 36.04 3.06
39 40 2.016704 GCTCGTATCCGGCATCACG 61.017 63.158 0.00 3.42 35.78 4.35
40 41 2.016704 CTCGTATCCGGCATCACGC 61.017 63.158 0.00 0.00 41.28 5.34
49 50 3.737172 GCATCACGCCAACGCCTT 61.737 61.111 0.00 0.00 45.53 4.35
50 51 2.480555 CATCACGCCAACGCCTTC 59.519 61.111 0.00 0.00 45.53 3.46
51 52 3.118454 ATCACGCCAACGCCTTCG 61.118 61.111 0.00 0.00 45.53 3.79
68 69 4.839706 GGCCGCCCCCAATCACAT 62.840 66.667 0.00 0.00 0.00 3.21
69 70 3.219198 GCCGCCCCCAATCACATC 61.219 66.667 0.00 0.00 0.00 3.06
70 71 2.275089 CCGCCCCCAATCACATCA 59.725 61.111 0.00 0.00 0.00 3.07
71 72 1.825191 CCGCCCCCAATCACATCAG 60.825 63.158 0.00 0.00 0.00 2.90
72 73 1.077501 CGCCCCCAATCACATCAGT 60.078 57.895 0.00 0.00 0.00 3.41
86 87 2.703007 ACATCAGTGAAGGAGGATAGCC 59.297 50.000 0.00 0.00 0.00 3.93
87 88 2.550277 TCAGTGAAGGAGGATAGCCA 57.450 50.000 0.00 0.00 36.29 4.75
88 89 2.832838 TCAGTGAAGGAGGATAGCCAA 58.167 47.619 0.00 0.00 36.29 4.52
89 90 2.501723 TCAGTGAAGGAGGATAGCCAAC 59.498 50.000 0.00 0.00 36.29 3.77
90 91 1.482593 AGTGAAGGAGGATAGCCAACG 59.517 52.381 0.00 0.00 36.29 4.10
91 92 0.178068 TGAAGGAGGATAGCCAACGC 59.822 55.000 0.00 0.00 36.29 4.84
92 93 0.876342 GAAGGAGGATAGCCAACGCG 60.876 60.000 3.53 3.53 41.18 6.01
93 94 1.327690 AAGGAGGATAGCCAACGCGA 61.328 55.000 15.93 0.00 41.18 5.87
94 95 1.300233 GGAGGATAGCCAACGCGAG 60.300 63.158 15.93 4.40 41.18 5.03
95 96 1.951631 GAGGATAGCCAACGCGAGC 60.952 63.158 15.93 13.18 41.18 5.03
96 97 3.330853 GGATAGCCAACGCGAGCG 61.331 66.667 15.93 16.38 46.03 5.03
97 98 3.989595 GATAGCCAACGCGAGCGC 61.990 66.667 15.93 10.79 44.19 5.92
111 112 3.272334 GCGCCCATCACCGCTTAG 61.272 66.667 0.00 0.00 46.14 2.18
113 114 2.908015 GCCCATCACCGCTTAGGA 59.092 61.111 0.00 0.00 45.00 2.94
114 115 1.523938 GCCCATCACCGCTTAGGAC 60.524 63.158 0.00 0.00 45.00 3.85
115 116 1.146263 CCCATCACCGCTTAGGACC 59.854 63.158 0.00 0.00 45.00 4.46
116 117 1.227263 CCATCACCGCTTAGGACCG 60.227 63.158 0.00 0.00 45.00 4.79
117 118 1.883084 CATCACCGCTTAGGACCGC 60.883 63.158 0.00 0.00 45.00 5.68
118 119 3.090219 ATCACCGCTTAGGACCGCC 62.090 63.158 0.00 0.00 45.00 6.13
122 123 4.867599 CGCTTAGGACCGCCGGAC 62.868 72.222 11.71 2.52 39.96 4.79
123 124 4.867599 GCTTAGGACCGCCGGACG 62.868 72.222 11.71 8.73 39.96 4.79
147 148 4.452733 GAGCCCGACCACCCGAAG 62.453 72.222 0.00 0.00 0.00 3.79
161 162 3.963676 CGAAGGAGAGCTGATCTGG 57.036 57.895 0.00 0.00 38.84 3.86
162 163 0.388659 CGAAGGAGAGCTGATCTGGG 59.611 60.000 0.00 0.00 38.84 4.45
163 164 0.758123 GAAGGAGAGCTGATCTGGGG 59.242 60.000 0.00 0.00 38.84 4.96
164 165 0.043940 AAGGAGAGCTGATCTGGGGT 59.956 55.000 0.00 0.00 38.84 4.95
165 166 0.690411 AGGAGAGCTGATCTGGGGTG 60.690 60.000 0.00 0.00 38.84 4.61
166 167 1.694133 GGAGAGCTGATCTGGGGTGG 61.694 65.000 0.00 0.00 38.84 4.61
167 168 1.692042 AGAGCTGATCTGGGGTGGG 60.692 63.158 0.00 0.00 36.69 4.61
168 169 1.690633 GAGCTGATCTGGGGTGGGA 60.691 63.158 0.00 0.00 0.00 4.37
169 170 1.229951 AGCTGATCTGGGGTGGGAA 60.230 57.895 1.46 0.00 0.00 3.97
170 171 0.846427 AGCTGATCTGGGGTGGGAAA 60.846 55.000 1.46 0.00 0.00 3.13
171 172 0.681243 GCTGATCTGGGGTGGGAAAC 60.681 60.000 1.46 0.00 0.00 2.78
183 184 2.124278 GGAAACCCCAGATCCGCC 60.124 66.667 0.00 0.00 34.14 6.13
184 185 2.513897 GAAACCCCAGATCCGCCG 60.514 66.667 0.00 0.00 0.00 6.46
185 186 4.796495 AAACCCCAGATCCGCCGC 62.796 66.667 0.00 0.00 0.00 6.53
249 250 0.659957 GATCATGGGAAGCACGAAGC 59.340 55.000 0.00 0.00 46.19 3.86
290 291 2.125106 GGTACGGAGGCAGCAAGG 60.125 66.667 0.00 0.00 0.00 3.61
291 292 2.656069 GGTACGGAGGCAGCAAGGA 61.656 63.158 0.00 0.00 0.00 3.36
292 293 1.295423 GTACGGAGGCAGCAAGGAA 59.705 57.895 0.00 0.00 0.00 3.36
293 294 0.741221 GTACGGAGGCAGCAAGGAAG 60.741 60.000 0.00 0.00 0.00 3.46
375 376 8.817100 CAACTCATCTATATTGCGTTGAACTTA 58.183 33.333 10.78 0.00 40.49 2.24
400 401 7.895759 AGCCAGCTAAAATATGTCAAGAAAAA 58.104 30.769 0.00 0.00 0.00 1.94
401 402 7.814587 AGCCAGCTAAAATATGTCAAGAAAAAC 59.185 33.333 0.00 0.00 0.00 2.43
402 403 7.814587 GCCAGCTAAAATATGTCAAGAAAAACT 59.185 33.333 0.00 0.00 0.00 2.66
403 404 9.696917 CCAGCTAAAATATGTCAAGAAAAACTT 57.303 29.630 0.00 0.00 39.70 2.66
415 416 9.868277 TGTCAAGAAAAACTTACATTTGTTGAT 57.132 25.926 12.07 0.00 44.95 2.57
444 445 3.443329 TGCGTTCCACAAGATTATGCATT 59.557 39.130 3.54 0.00 0.00 3.56
446 447 5.124617 TGCGTTCCACAAGATTATGCATTTA 59.875 36.000 3.54 0.00 0.00 1.40
447 448 6.033341 GCGTTCCACAAGATTATGCATTTAA 58.967 36.000 3.54 0.00 0.00 1.52
482 483 9.690913 ATGGCTGTCAATATGCATAAACTATAT 57.309 29.630 11.13 0.00 0.00 0.86
510 515 4.632688 GTGTTGGCCGAGCTAGTTAATTAA 59.367 41.667 0.00 0.00 0.00 1.40
511 516 4.632688 TGTTGGCCGAGCTAGTTAATTAAC 59.367 41.667 18.77 18.77 36.46 2.01
516 521 4.442472 GCCGAGCTAGTTAATTAACCCTGA 60.442 45.833 21.92 7.08 36.88 3.86
639 644 6.915843 TCCTTTTTAAAATCTCAACTGTTCGC 59.084 34.615 0.55 0.00 0.00 4.70
644 649 1.073216 ATCTCAACTGTTCGCGCTCG 61.073 55.000 5.56 0.00 0.00 5.03
754 759 0.394938 TCAACTTAGCACGGCTCCAA 59.605 50.000 1.46 0.00 40.44 3.53
866 871 3.533547 CTGCAATCTCTCCTCTTTCCTG 58.466 50.000 0.00 0.00 0.00 3.86
894 904 3.687847 TGGCAGGCCATAAACACAT 57.312 47.368 9.35 0.00 41.89 3.21
941 957 4.757149 ACGATTGGAAGAGAAAGTCTTTGG 59.243 41.667 1.60 0.00 46.21 3.28
999 1015 0.731417 CTGGTTGTAGCAGCAGCATC 59.269 55.000 3.17 0.00 45.49 3.91
1794 1826 3.287312 ACAAACGGACGATTTCTACGA 57.713 42.857 0.00 0.00 34.70 3.43
1800 1832 1.582502 GGACGATTTCTACGAACGCTG 59.417 52.381 0.00 0.00 34.70 5.18
1904 1936 7.597288 ACTATTCTTTGTACCAAAGGCTTTT 57.403 32.000 10.36 0.00 0.00 2.27
1905 1937 8.018537 ACTATTCTTTGTACCAAAGGCTTTTT 57.981 30.769 10.36 2.84 0.00 1.94
1975 2007 6.513806 TTCCTTGTATTTGATGTGTGGATG 57.486 37.500 0.00 0.00 0.00 3.51
2090 2138 0.877071 ATCAGCTTTGGTTGCGTCAG 59.123 50.000 0.00 0.00 35.28 3.51
2101 2149 3.632604 TGGTTGCGTCAGTTATCCAAAAA 59.367 39.130 0.00 0.00 0.00 1.94
2127 2175 9.525409 AAATCTCAGATTAATGTGCAAAATAGC 57.475 29.630 7.71 0.00 0.00 2.97
2128 2176 7.870509 TCTCAGATTAATGTGCAAAATAGCT 57.129 32.000 7.71 0.00 34.99 3.32
2129 2177 8.284945 TCTCAGATTAATGTGCAAAATAGCTT 57.715 30.769 7.71 0.00 34.99 3.74
2130 2178 8.400947 TCTCAGATTAATGTGCAAAATAGCTTC 58.599 33.333 7.71 0.00 34.99 3.86
2131 2179 8.284945 TCAGATTAATGTGCAAAATAGCTTCT 57.715 30.769 7.71 0.00 34.99 2.85
2132 2180 9.394767 TCAGATTAATGTGCAAAATAGCTTCTA 57.605 29.630 7.71 0.00 34.99 2.10
2159 2207 4.398044 TCGCCTGAATTTAGAATTTGGGTC 59.602 41.667 0.00 0.00 0.00 4.46
2160 2208 4.157656 CGCCTGAATTTAGAATTTGGGTCA 59.842 41.667 0.00 0.00 0.00 4.02
2164 2212 6.403636 CCTGAATTTAGAATTTGGGTCAGTCG 60.404 42.308 0.00 0.00 31.40 4.18
2173 2221 5.982890 ATTTGGGTCAGTCGATTTTCATT 57.017 34.783 0.00 0.00 0.00 2.57
2188 2236 5.712152 TTTTCATTTGAAGGAAGGAGCTC 57.288 39.130 4.71 4.71 35.21 4.09
2198 2246 1.471684 GGAAGGAGCTCGTCGTCTTAA 59.528 52.381 9.78 0.00 0.00 1.85
2200 2248 1.096416 AGGAGCTCGTCGTCTTAAGG 58.904 55.000 7.83 0.00 0.00 2.69
2203 2251 2.008329 GAGCTCGTCGTCTTAAGGAGA 58.992 52.381 0.00 0.00 31.82 3.71
2213 2261 1.975680 TCTTAAGGAGACAAACGCCCT 59.024 47.619 1.85 0.00 39.30 5.19
2229 2278 7.228706 ACAAACGCCCTCATTATTTATCTTAGG 59.771 37.037 0.00 0.00 0.00 2.69
2232 2281 5.510430 GCCCTCATTATTTATCTTAGGGGG 58.490 45.833 6.64 0.00 42.12 5.40
2257 2306 1.977009 GGTGCTGCAGTTTACCCCC 60.977 63.158 16.64 0.00 0.00 5.40
2260 2309 0.105964 TGCTGCAGTTTACCCCCAAA 60.106 50.000 16.64 0.00 0.00 3.28
2279 2328 0.110486 AAAACTGGTCATCGCAGGGT 59.890 50.000 0.00 0.00 0.00 4.34
2299 2348 1.213296 TTAGAGGGATGGTCAAGGGC 58.787 55.000 0.00 0.00 0.00 5.19
2301 2350 3.406595 GAGGGATGGTCAAGGGCGG 62.407 68.421 0.00 0.00 0.00 6.13
2302 2351 4.506255 GGGATGGTCAAGGGCGGG 62.506 72.222 0.00 0.00 0.00 6.13
2327 2376 2.915659 AGCACGACGGTTGAGGGA 60.916 61.111 1.53 0.00 0.00 4.20
2328 2377 2.432628 GCACGACGGTTGAGGGAG 60.433 66.667 1.53 0.00 0.00 4.30
2331 2380 4.452733 CGACGGTTGAGGGAGGGC 62.453 72.222 0.00 0.00 0.00 5.19
2332 2381 4.452733 GACGGTTGAGGGAGGGCG 62.453 72.222 0.00 0.00 0.00 6.13
2357 2407 4.373116 GAGGCGGTCACGGAAGCA 62.373 66.667 0.00 0.00 41.36 3.91
2360 2410 4.980805 GCGGTCACGGAAGCACCA 62.981 66.667 1.20 0.00 41.36 4.17
2369 2419 4.947147 GAAGCACCACCGGCCACA 62.947 66.667 0.00 0.00 0.00 4.17
2414 2465 1.388547 GGCAGTTGTGAGTGGTTCAA 58.611 50.000 0.00 0.00 37.61 2.69
2428 2479 2.370519 TGGTTCAAATCGAGGTCAGGAA 59.629 45.455 0.00 0.00 0.00 3.36
2431 2482 1.002366 CAAATCGAGGTCAGGAAGCG 58.998 55.000 0.00 0.00 0.00 4.68
2441 2492 2.093658 GGTCAGGAAGCGGAAGACAATA 60.094 50.000 0.00 0.00 0.00 1.90
2458 2509 8.871686 AAGACAATAAACAATGTTTTCAGGAC 57.128 30.769 16.99 5.52 0.00 3.85
2466 2517 8.463930 AAACAATGTTTTCAGGACATAGAAGA 57.536 30.769 5.41 0.00 36.76 2.87
2467 2518 8.463930 AACAATGTTTTCAGGACATAGAAGAA 57.536 30.769 0.00 0.00 36.76 2.52
2468 2519 8.103948 ACAATGTTTTCAGGACATAGAAGAAG 57.896 34.615 0.00 0.00 36.76 2.85
2469 2520 7.939039 ACAATGTTTTCAGGACATAGAAGAAGA 59.061 33.333 0.00 0.00 36.76 2.87
2470 2521 8.954350 CAATGTTTTCAGGACATAGAAGAAGAT 58.046 33.333 0.00 0.00 36.76 2.40
2471 2522 8.729805 ATGTTTTCAGGACATAGAAGAAGATC 57.270 34.615 0.00 0.00 36.04 2.75
2472 2523 7.911651 TGTTTTCAGGACATAGAAGAAGATCT 58.088 34.615 0.00 0.00 0.00 2.75
2473 2524 9.035890 TGTTTTCAGGACATAGAAGAAGATCTA 57.964 33.333 0.00 0.00 36.41 1.98
2474 2525 9.877178 GTTTTCAGGACATAGAAGAAGATCTAA 57.123 33.333 0.00 0.00 35.64 2.10
2475 2526 9.877178 TTTTCAGGACATAGAAGAAGATCTAAC 57.123 33.333 0.00 0.00 35.64 2.34
2476 2527 7.265647 TCAGGACATAGAAGAAGATCTAACG 57.734 40.000 0.00 0.00 35.64 3.18
2477 2528 6.263392 TCAGGACATAGAAGAAGATCTAACGG 59.737 42.308 0.00 0.00 35.64 4.44
2478 2529 6.039941 CAGGACATAGAAGAAGATCTAACGGT 59.960 42.308 0.00 0.00 35.64 4.83
2479 2530 6.608002 AGGACATAGAAGAAGATCTAACGGTT 59.392 38.462 0.00 0.00 35.64 4.44
2480 2531 6.919115 GGACATAGAAGAAGATCTAACGGTTC 59.081 42.308 0.00 0.00 35.64 3.62
2481 2532 6.807789 ACATAGAAGAAGATCTAACGGTTCC 58.192 40.000 0.00 0.00 35.64 3.62
2482 2533 6.608002 ACATAGAAGAAGATCTAACGGTTCCT 59.392 38.462 0.00 0.00 35.64 3.36
2483 2534 7.124448 ACATAGAAGAAGATCTAACGGTTCCTT 59.876 37.037 0.00 0.00 35.64 3.36
2484 2535 6.361768 AGAAGAAGATCTAACGGTTCCTTT 57.638 37.500 0.00 0.00 0.00 3.11
2485 2536 6.770542 AGAAGAAGATCTAACGGTTCCTTTT 58.229 36.000 0.00 0.00 0.00 2.27
2486 2537 6.874664 AGAAGAAGATCTAACGGTTCCTTTTC 59.125 38.462 0.00 0.00 0.00 2.29
2487 2538 5.489249 AGAAGATCTAACGGTTCCTTTTCC 58.511 41.667 0.00 0.00 0.00 3.13
2488 2539 4.903045 AGATCTAACGGTTCCTTTTCCA 57.097 40.909 0.00 0.00 0.00 3.53
2489 2540 5.437191 AGATCTAACGGTTCCTTTTCCAT 57.563 39.130 0.00 0.00 0.00 3.41
2490 2541 5.429130 AGATCTAACGGTTCCTTTTCCATC 58.571 41.667 0.00 0.00 0.00 3.51
2491 2542 3.946606 TCTAACGGTTCCTTTTCCATCC 58.053 45.455 0.00 0.00 0.00 3.51
2492 2543 2.668144 AACGGTTCCTTTTCCATCCA 57.332 45.000 0.00 0.00 0.00 3.41
2493 2544 2.668144 ACGGTTCCTTTTCCATCCAA 57.332 45.000 0.00 0.00 0.00 3.53
2494 2545 2.235891 ACGGTTCCTTTTCCATCCAAC 58.764 47.619 0.00 0.00 0.00 3.77
2495 2546 1.199097 CGGTTCCTTTTCCATCCAACG 59.801 52.381 0.00 0.00 0.00 4.10
2496 2547 2.235891 GGTTCCTTTTCCATCCAACGT 58.764 47.619 0.00 0.00 0.00 3.99
2497 2548 2.228103 GGTTCCTTTTCCATCCAACGTC 59.772 50.000 0.00 0.00 0.00 4.34
2498 2549 3.146847 GTTCCTTTTCCATCCAACGTCT 58.853 45.455 0.00 0.00 0.00 4.18
2499 2550 2.778299 TCCTTTTCCATCCAACGTCTG 58.222 47.619 0.00 0.00 0.00 3.51
2501 2552 1.812571 CTTTTCCATCCAACGTCTGGG 59.187 52.381 14.23 5.87 46.44 4.45
2502 2553 1.060729 TTTCCATCCAACGTCTGGGA 58.939 50.000 14.23 10.54 46.44 4.37
2503 2554 1.060729 TTCCATCCAACGTCTGGGAA 58.939 50.000 14.23 9.16 46.44 3.97
2504 2555 0.613260 TCCATCCAACGTCTGGGAAG 59.387 55.000 14.23 7.69 46.44 3.46
2505 2556 0.613260 CCATCCAACGTCTGGGAAGA 59.387 55.000 14.23 0.00 46.44 2.87
2506 2557 1.003118 CCATCCAACGTCTGGGAAGAA 59.997 52.381 14.23 0.00 46.44 2.52
2507 2558 2.552155 CCATCCAACGTCTGGGAAGAAA 60.552 50.000 14.23 0.00 46.44 2.52
2508 2559 3.347216 CATCCAACGTCTGGGAAGAAAT 58.653 45.455 14.23 0.75 46.44 2.17
2509 2560 3.053831 TCCAACGTCTGGGAAGAAATC 57.946 47.619 14.23 0.00 46.44 2.17
2510 2561 1.732259 CCAACGTCTGGGAAGAAATCG 59.268 52.381 8.40 0.00 42.17 3.34
2511 2562 2.611971 CCAACGTCTGGGAAGAAATCGA 60.612 50.000 8.40 0.00 42.17 3.59
2512 2563 2.365408 ACGTCTGGGAAGAAATCGAC 57.635 50.000 0.00 0.00 0.00 4.20
2513 2564 1.893801 ACGTCTGGGAAGAAATCGACT 59.106 47.619 0.00 0.00 0.00 4.18
2514 2565 2.263077 CGTCTGGGAAGAAATCGACTG 58.737 52.381 0.00 0.00 0.00 3.51
2515 2566 2.094700 CGTCTGGGAAGAAATCGACTGA 60.095 50.000 0.00 0.00 0.00 3.41
2516 2567 3.254892 GTCTGGGAAGAAATCGACTGAC 58.745 50.000 0.00 0.00 32.10 3.51
2517 2568 2.233922 TCTGGGAAGAAATCGACTGACC 59.766 50.000 0.00 0.00 0.00 4.02
2518 2569 1.974957 TGGGAAGAAATCGACTGACCA 59.025 47.619 0.00 0.00 0.00 4.02
2534 2585 6.031751 ACTGACCAGAGTCTAAATTCAGTC 57.968 41.667 14.76 5.92 43.91 3.51
2537 2588 5.061920 ACCAGAGTCTAAATTCAGTCGAC 57.938 43.478 7.70 7.70 0.00 4.20
2543 2594 4.082136 AGTCTAAATTCAGTCGACTGTCCC 60.082 45.833 37.21 20.24 44.12 4.46
2556 2607 0.695803 CTGTCCCCTAGCCATTCCCT 60.696 60.000 0.00 0.00 0.00 4.20
2562 2613 3.140144 TCCCCTAGCCATTCCCTAAATTG 59.860 47.826 0.00 0.00 0.00 2.32
2565 2616 3.319122 CCTAGCCATTCCCTAAATTGTGC 59.681 47.826 0.00 0.00 0.00 4.57
2574 2625 2.977169 CCCTAAATTGTGCGTGTTTTCG 59.023 45.455 0.00 0.00 0.00 3.46
2597 2648 6.538742 TCGGTCTCATCTTTTTGATTATGGTC 59.461 38.462 0.00 0.00 32.05 4.02
2598 2649 6.540189 CGGTCTCATCTTTTTGATTATGGTCT 59.460 38.462 0.00 0.00 32.05 3.85
2599 2650 7.254590 CGGTCTCATCTTTTTGATTATGGTCTC 60.255 40.741 0.00 0.00 32.05 3.36
2628 2729 4.707563 TCGATTATGAAAGTTGTGTTGCG 58.292 39.130 0.00 0.00 0.00 4.85
2657 2758 2.976490 ATTTGCTCCTGGAGGCGCT 61.976 57.895 24.43 0.00 45.66 5.92
2665 2766 1.826024 CTGGAGGCGCTAGGAACAT 59.174 57.895 7.64 0.00 0.00 2.71
2726 2827 6.031003 CACGCACTACATAAAAACGAAATGTC 59.969 38.462 0.00 0.00 35.54 3.06
2817 2923 5.574443 GCAGGAGAACATGAACAAATTTAGC 59.426 40.000 0.00 0.00 0.00 3.09
2882 2996 2.371179 TCACGTTGTACCCATTACCCAA 59.629 45.455 0.00 0.00 0.00 4.12
2883 2997 2.485038 CACGTTGTACCCATTACCCAAC 59.515 50.000 0.00 0.00 33.74 3.77
2884 2998 2.106166 ACGTTGTACCCATTACCCAACA 59.894 45.455 0.00 0.00 36.15 3.33
2885 2999 2.485038 CGTTGTACCCATTACCCAACAC 59.515 50.000 0.00 0.00 36.15 3.32
2886 3000 3.488363 GTTGTACCCATTACCCAACACA 58.512 45.455 0.00 0.00 36.35 3.72
2887 3001 3.878237 TGTACCCATTACCCAACACAA 57.122 42.857 0.00 0.00 0.00 3.33
2888 3002 3.488363 TGTACCCATTACCCAACACAAC 58.512 45.455 0.00 0.00 0.00 3.32
2889 3003 2.757894 ACCCATTACCCAACACAACA 57.242 45.000 0.00 0.00 0.00 3.33
2890 3004 3.252554 ACCCATTACCCAACACAACAT 57.747 42.857 0.00 0.00 0.00 2.71
2891 3005 4.390129 ACCCATTACCCAACACAACATA 57.610 40.909 0.00 0.00 0.00 2.29
2892 3006 4.083565 ACCCATTACCCAACACAACATAC 58.916 43.478 0.00 0.00 0.00 2.39
2957 3082 4.159377 TGCGTTTTCACATGGAAGAATC 57.841 40.909 0.00 0.00 36.72 2.52
2973 3098 0.252197 AATCGGTAGGCCAACTGGAC 59.748 55.000 5.01 0.00 46.16 4.02
3008 3133 7.289317 ACCAACTAATAGCTAGCACAACCTATA 59.711 37.037 18.83 0.00 0.00 1.31
3042 3167 1.180907 TTTTGACCTGCAGCACAACA 58.819 45.000 18.56 12.35 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.659089 ATACGAGCACGGTGGTGGC 62.659 63.158 18.66 3.19 44.54 5.01
11 12 1.518572 GATACGAGCACGGTGGTGG 60.519 63.158 18.66 18.68 44.54 4.61
13 14 2.890371 GGATACGAGCACGGTGGT 59.110 61.111 13.36 13.36 44.46 4.16
32 33 3.667429 GAAGGCGTTGGCGTGATGC 62.667 63.158 0.00 0.00 45.38 3.91
33 34 2.480555 GAAGGCGTTGGCGTGATG 59.519 61.111 0.00 0.00 41.24 3.07
34 35 3.118454 CGAAGGCGTTGGCGTGAT 61.118 61.111 0.00 0.00 41.24 3.06
51 52 4.839706 ATGTGATTGGGGGCGGCC 62.840 66.667 22.00 22.00 0.00 6.13
52 53 3.219198 GATGTGATTGGGGGCGGC 61.219 66.667 0.00 0.00 0.00 6.53
53 54 1.825191 CTGATGTGATTGGGGGCGG 60.825 63.158 0.00 0.00 0.00 6.13
54 55 1.077501 ACTGATGTGATTGGGGGCG 60.078 57.895 0.00 0.00 0.00 6.13
55 56 2.496942 CACTGATGTGATTGGGGGC 58.503 57.895 0.00 0.00 46.55 5.80
64 65 3.494048 GGCTATCCTCCTTCACTGATGTG 60.494 52.174 0.00 0.00 45.07 3.21
65 66 2.703007 GGCTATCCTCCTTCACTGATGT 59.297 50.000 0.00 0.00 0.00 3.06
66 67 2.702478 TGGCTATCCTCCTTCACTGATG 59.298 50.000 0.00 0.00 0.00 3.07
67 68 3.051940 TGGCTATCCTCCTTCACTGAT 57.948 47.619 0.00 0.00 0.00 2.90
68 69 2.501723 GTTGGCTATCCTCCTTCACTGA 59.498 50.000 0.00 0.00 0.00 3.41
69 70 2.739932 CGTTGGCTATCCTCCTTCACTG 60.740 54.545 0.00 0.00 0.00 3.66
70 71 1.482593 CGTTGGCTATCCTCCTTCACT 59.517 52.381 0.00 0.00 0.00 3.41
71 72 1.941325 CGTTGGCTATCCTCCTTCAC 58.059 55.000 0.00 0.00 0.00 3.18
72 73 0.178068 GCGTTGGCTATCCTCCTTCA 59.822 55.000 0.00 0.00 35.83 3.02
73 74 0.876342 CGCGTTGGCTATCCTCCTTC 60.876 60.000 0.00 0.00 36.88 3.46
74 75 1.144057 CGCGTTGGCTATCCTCCTT 59.856 57.895 0.00 0.00 36.88 3.36
75 76 1.739338 CTCGCGTTGGCTATCCTCCT 61.739 60.000 5.77 0.00 36.88 3.69
76 77 1.300233 CTCGCGTTGGCTATCCTCC 60.300 63.158 5.77 0.00 36.88 4.30
77 78 1.951631 GCTCGCGTTGGCTATCCTC 60.952 63.158 5.77 0.00 36.88 3.71
78 79 2.107141 GCTCGCGTTGGCTATCCT 59.893 61.111 5.77 0.00 36.88 3.24
79 80 3.330853 CGCTCGCGTTGGCTATCC 61.331 66.667 5.77 0.00 36.88 2.59
80 81 3.989595 GCGCTCGCGTTGGCTATC 61.990 66.667 13.18 0.00 42.09 2.08
92 93 3.733344 TAAGCGGTGATGGGCGCTC 62.733 63.158 7.64 2.47 36.64 5.03
93 94 3.740128 CTAAGCGGTGATGGGCGCT 62.740 63.158 7.64 0.00 39.55 5.92
94 95 3.272334 CTAAGCGGTGATGGGCGC 61.272 66.667 0.00 0.00 0.00 6.53
95 96 2.588877 CCTAAGCGGTGATGGGCG 60.589 66.667 0.00 0.00 0.00 6.13
96 97 1.523938 GTCCTAAGCGGTGATGGGC 60.524 63.158 0.00 0.00 0.00 5.36
97 98 1.146263 GGTCCTAAGCGGTGATGGG 59.854 63.158 0.00 0.00 0.00 4.00
98 99 1.227263 CGGTCCTAAGCGGTGATGG 60.227 63.158 0.00 0.00 42.53 3.51
99 100 1.883084 GCGGTCCTAAGCGGTGATG 60.883 63.158 0.00 0.00 46.20 3.07
100 101 2.499685 GCGGTCCTAAGCGGTGAT 59.500 61.111 0.00 0.00 46.20 3.06
101 102 3.766691 GGCGGTCCTAAGCGGTGA 61.767 66.667 0.00 0.00 46.20 4.02
106 107 4.867599 CGTCCGGCGGTCCTAAGC 62.868 72.222 27.32 7.54 36.85 3.09
130 131 4.452733 CTTCGGGTGGTCGGGCTC 62.453 72.222 0.00 0.00 0.00 4.70
133 134 3.771160 CTCCTTCGGGTGGTCGGG 61.771 72.222 0.00 0.00 36.28 5.14
134 135 2.678934 TCTCCTTCGGGTGGTCGG 60.679 66.667 0.00 0.00 36.28 4.79
135 136 2.885861 CTCTCCTTCGGGTGGTCG 59.114 66.667 0.00 0.00 36.28 4.79
136 137 1.985116 AGCTCTCCTTCGGGTGGTC 60.985 63.158 0.00 0.00 36.28 4.02
137 138 2.120718 AGCTCTCCTTCGGGTGGT 59.879 61.111 0.00 0.00 36.28 4.16
138 139 1.333636 ATCAGCTCTCCTTCGGGTGG 61.334 60.000 0.00 0.00 36.28 4.61
139 140 0.103937 GATCAGCTCTCCTTCGGGTG 59.896 60.000 0.00 0.00 36.28 4.61
140 141 0.032615 AGATCAGCTCTCCTTCGGGT 60.033 55.000 0.00 0.00 36.28 5.28
141 142 0.388659 CAGATCAGCTCTCCTTCGGG 59.611 60.000 0.00 0.00 29.16 5.14
142 143 0.388659 CCAGATCAGCTCTCCTTCGG 59.611 60.000 0.00 0.00 29.16 4.30
143 144 0.388659 CCCAGATCAGCTCTCCTTCG 59.611 60.000 0.00 0.00 29.16 3.79
144 145 0.758123 CCCCAGATCAGCTCTCCTTC 59.242 60.000 0.00 0.00 29.16 3.46
145 146 0.043940 ACCCCAGATCAGCTCTCCTT 59.956 55.000 0.00 0.00 29.16 3.36
146 147 0.690411 CACCCCAGATCAGCTCTCCT 60.690 60.000 0.00 0.00 29.16 3.69
147 148 1.694133 CCACCCCAGATCAGCTCTCC 61.694 65.000 0.00 0.00 29.16 3.71
148 149 1.694133 CCCACCCCAGATCAGCTCTC 61.694 65.000 0.00 0.00 29.16 3.20
149 150 1.692042 CCCACCCCAGATCAGCTCT 60.692 63.158 0.00 0.00 33.14 4.09
150 151 1.274703 TTCCCACCCCAGATCAGCTC 61.275 60.000 0.00 0.00 0.00 4.09
151 152 0.846427 TTTCCCACCCCAGATCAGCT 60.846 55.000 0.00 0.00 0.00 4.24
152 153 0.681243 GTTTCCCACCCCAGATCAGC 60.681 60.000 0.00 0.00 0.00 4.26
153 154 0.034089 GGTTTCCCACCCCAGATCAG 60.034 60.000 0.00 0.00 40.19 2.90
154 155 2.083715 GGTTTCCCACCCCAGATCA 58.916 57.895 0.00 0.00 40.19 2.92
166 167 2.124278 GGCGGATCTGGGGTTTCC 60.124 66.667 3.14 0.00 0.00 3.13
167 168 2.513897 CGGCGGATCTGGGGTTTC 60.514 66.667 3.14 0.00 0.00 2.78
168 169 4.796495 GCGGCGGATCTGGGGTTT 62.796 66.667 9.78 0.00 0.00 3.27
197 198 1.279527 TACATTATACGCGGCGCTGC 61.280 55.000 31.30 31.30 0.00 5.25
198 199 1.059122 CATACATTATACGCGGCGCTG 59.941 52.381 30.54 24.12 0.00 5.18
199 200 1.336517 ACATACATTATACGCGGCGCT 60.337 47.619 30.54 18.74 0.00 5.92
200 201 1.065358 ACATACATTATACGCGGCGC 58.935 50.000 24.21 24.21 0.00 6.53
201 202 2.278094 GCTACATACATTATACGCGGCG 59.722 50.000 22.36 22.36 0.00 6.46
202 203 2.601763 GGCTACATACATTATACGCGGC 59.398 50.000 12.47 0.00 0.00 6.53
203 204 4.103357 GAGGCTACATACATTATACGCGG 58.897 47.826 12.47 0.00 0.00 6.46
204 205 3.784468 CGAGGCTACATACATTATACGCG 59.216 47.826 3.53 3.53 0.00 6.01
205 206 4.978186 TCGAGGCTACATACATTATACGC 58.022 43.478 0.00 0.00 0.00 4.42
206 207 5.902432 CGATCGAGGCTACATACATTATACG 59.098 44.000 10.26 0.00 0.00 3.06
249 250 1.516386 ATGACTCGCGCGTTAGTGG 60.516 57.895 30.98 15.38 0.00 4.00
290 291 0.249911 ACGTGAGCACAAGTCCCTTC 60.250 55.000 0.00 0.00 33.92 3.46
291 292 1.000955 CTACGTGAGCACAAGTCCCTT 59.999 52.381 5.94 0.00 39.24 3.95
292 293 0.603569 CTACGTGAGCACAAGTCCCT 59.396 55.000 5.94 0.00 39.24 4.20
293 294 0.601558 TCTACGTGAGCACAAGTCCC 59.398 55.000 5.94 0.00 39.24 4.46
334 335 3.930336 TGAGTTGACATGCGAGATTCTT 58.070 40.909 0.00 0.00 0.00 2.52
375 376 7.466746 TTTTCTTGACATATTTTAGCTGGCT 57.533 32.000 0.00 0.00 0.00 4.75
423 424 3.698029 ATGCATAATCTTGTGGAACGC 57.302 42.857 0.00 0.00 42.39 4.84
424 425 8.633075 AATTAAATGCATAATCTTGTGGAACG 57.367 30.769 0.00 0.00 42.39 3.95
425 426 9.585099 TGAATTAAATGCATAATCTTGTGGAAC 57.415 29.630 0.00 0.00 37.35 3.62
428 429 9.590451 AGTTGAATTAAATGCATAATCTTGTGG 57.410 29.630 0.00 0.00 0.00 4.17
446 447 7.147863 TGCATATTGACAGCCATTAGTTGAATT 60.148 33.333 0.00 0.00 0.00 2.17
447 448 6.321945 TGCATATTGACAGCCATTAGTTGAAT 59.678 34.615 0.00 0.00 0.00 2.57
482 483 0.978667 TAGCTCGGCCAACACCCATA 60.979 55.000 2.24 0.00 0.00 2.74
483 484 2.257409 CTAGCTCGGCCAACACCCAT 62.257 60.000 2.24 0.00 0.00 4.00
510 515 3.508793 CAGAGAATGCATGTTTTCAGGGT 59.491 43.478 0.00 0.00 31.73 4.34
511 516 3.508793 ACAGAGAATGCATGTTTTCAGGG 59.491 43.478 0.00 0.00 31.73 4.45
516 521 5.014858 AGATGGACAGAGAATGCATGTTTT 58.985 37.500 0.00 0.00 0.00 2.43
568 573 6.399039 CGTCGCAAGCTCAACATATATACTTC 60.399 42.308 0.00 0.00 37.18 3.01
639 644 6.577800 ACTCAAATAATACGAAGATACGAGCG 59.422 38.462 0.00 0.00 37.03 5.03
754 759 1.909700 ACATCGCACCTGGTTCATTT 58.090 45.000 0.00 0.00 0.00 2.32
866 871 1.153509 GGCCTGCCATGAAACATGC 60.154 57.895 2.58 0.00 35.81 4.06
941 957 4.868314 ATATACCGGGAGCTAGAACAAC 57.132 45.455 6.32 0.00 0.00 3.32
975 991 0.035317 TGCTGCTACAACCAGACCAG 59.965 55.000 0.00 0.00 32.03 4.00
999 1015 2.029020 TGGTTCTGTGATCGTCTGAAGG 60.029 50.000 9.16 0.00 0.00 3.46
1794 1826 1.135460 GGTAGCTCGAACTACAGCGTT 60.135 52.381 23.50 0.00 43.61 4.84
1800 1832 2.626088 ACAACGGTAGCTCGAACTAC 57.374 50.000 16.07 16.07 41.54 2.73
1975 2007 2.966516 AGGTTACATAGTAGGGAGCTGC 59.033 50.000 0.00 0.00 0.00 5.25
2048 2096 9.791820 TGATCAAAATGTAGTATCAAATTGCTG 57.208 29.630 0.00 0.00 0.00 4.41
2101 2149 9.525409 GCTATTTTGCACATTAATCTGAGATTT 57.475 29.630 13.54 0.00 0.00 2.17
2103 2151 8.461249 AGCTATTTTGCACATTAATCTGAGAT 57.539 30.769 0.00 0.00 34.99 2.75
2111 2159 9.840427 GACTTTAGAAGCTATTTTGCACATTAA 57.160 29.630 0.00 0.00 34.99 1.40
2112 2160 8.175069 CGACTTTAGAAGCTATTTTGCACATTA 58.825 33.333 0.00 0.00 34.99 1.90
2113 2161 7.023575 CGACTTTAGAAGCTATTTTGCACATT 58.976 34.615 0.00 0.00 34.99 2.71
2114 2162 6.546395 CGACTTTAGAAGCTATTTTGCACAT 58.454 36.000 0.00 0.00 34.99 3.21
2116 2164 4.788609 GCGACTTTAGAAGCTATTTTGCAC 59.211 41.667 0.00 0.00 34.99 4.57
2117 2165 4.142687 GGCGACTTTAGAAGCTATTTTGCA 60.143 41.667 0.00 0.00 34.99 4.08
2118 2166 4.095036 AGGCGACTTTAGAAGCTATTTTGC 59.905 41.667 0.00 0.00 37.44 3.68
2119 2167 5.351465 TCAGGCGACTTTAGAAGCTATTTTG 59.649 40.000 0.00 0.00 40.21 2.44
2120 2168 5.488341 TCAGGCGACTTTAGAAGCTATTTT 58.512 37.500 0.00 0.00 40.21 1.82
2121 2169 5.086104 TCAGGCGACTTTAGAAGCTATTT 57.914 39.130 0.00 0.00 40.21 1.40
2122 2170 4.737855 TCAGGCGACTTTAGAAGCTATT 57.262 40.909 0.00 0.00 40.21 1.73
2123 2171 4.737855 TTCAGGCGACTTTAGAAGCTAT 57.262 40.909 0.00 0.00 40.21 2.97
2124 2172 4.737855 ATTCAGGCGACTTTAGAAGCTA 57.262 40.909 0.00 0.00 40.21 3.32
2125 2173 3.618690 ATTCAGGCGACTTTAGAAGCT 57.381 42.857 0.00 0.00 40.21 3.74
2126 2174 4.686839 AAATTCAGGCGACTTTAGAAGC 57.313 40.909 0.00 0.00 40.21 3.86
2129 2177 8.450964 CAAATTCTAAATTCAGGCGACTTTAGA 58.549 33.333 18.37 18.37 44.88 2.10
2130 2178 7.698130 CCAAATTCTAAATTCAGGCGACTTTAG 59.302 37.037 15.85 15.85 41.94 1.85
2131 2179 7.362574 CCCAAATTCTAAATTCAGGCGACTTTA 60.363 37.037 0.00 0.00 40.21 1.85
2132 2180 6.389906 CCAAATTCTAAATTCAGGCGACTTT 58.610 36.000 0.00 0.00 40.21 2.66
2159 2207 6.072508 TCCTTCCTTCAAATGAAAATCGACTG 60.073 38.462 0.00 0.00 33.07 3.51
2160 2208 6.003950 TCCTTCCTTCAAATGAAAATCGACT 58.996 36.000 0.00 0.00 33.07 4.18
2164 2212 6.278172 AGCTCCTTCCTTCAAATGAAAATC 57.722 37.500 0.00 0.00 33.07 2.17
2173 2221 0.243907 CGACGAGCTCCTTCCTTCAA 59.756 55.000 8.47 0.00 0.00 2.69
2198 2246 0.693049 AATGAGGGCGTTTGTCTCCT 59.307 50.000 0.00 0.00 0.00 3.69
2200 2248 4.965119 AAATAATGAGGGCGTTTGTCTC 57.035 40.909 0.00 0.00 0.00 3.36
2203 2251 7.228706 CCTAAGATAAATAATGAGGGCGTTTGT 59.771 37.037 0.00 0.00 0.00 2.83
2207 2255 5.280521 CCCCTAAGATAAATAATGAGGGCGT 60.281 44.000 0.00 0.00 40.81 5.68
2208 2256 5.186198 CCCCTAAGATAAATAATGAGGGCG 58.814 45.833 0.00 0.00 40.81 6.13
2240 2289 0.825840 TTGGGGGTAAACTGCAGCAC 60.826 55.000 15.27 9.40 0.00 4.40
2260 2309 0.110486 ACCCTGCGATGACCAGTTTT 59.890 50.000 0.00 0.00 0.00 2.43
2267 2316 1.473434 CCCTCTAAACCCTGCGATGAC 60.473 57.143 0.00 0.00 0.00 3.06
2275 2324 2.661176 TGACCATCCCTCTAAACCCT 57.339 50.000 0.00 0.00 0.00 4.34
2276 2325 2.092375 CCTTGACCATCCCTCTAAACCC 60.092 54.545 0.00 0.00 0.00 4.11
2279 2328 1.564348 GCCCTTGACCATCCCTCTAAA 59.436 52.381 0.00 0.00 0.00 1.85
2307 2356 3.414700 CTCAACCGTCGTGCTGCC 61.415 66.667 0.00 0.00 0.00 4.85
2337 2386 3.934391 CTTCCGTGACCGCCTCACC 62.934 68.421 6.02 0.00 46.01 4.02
2338 2387 2.432628 CTTCCGTGACCGCCTCAC 60.433 66.667 2.18 2.18 45.38 3.51
2347 2397 4.308458 CCGGTGGTGCTTCCGTGA 62.308 66.667 0.00 0.00 44.51 4.35
2394 2445 0.813610 TGAACCACTCACAACTGCCG 60.814 55.000 0.00 0.00 0.00 5.69
2414 2465 0.970937 TCCGCTTCCTGACCTCGATT 60.971 55.000 0.00 0.00 0.00 3.34
2428 2479 5.705609 AACATTGTTTATTGTCTTCCGCT 57.294 34.783 0.00 0.00 0.00 5.52
2431 2482 8.141268 TCCTGAAAACATTGTTTATTGTCTTCC 58.859 33.333 14.81 0.00 0.00 3.46
2441 2492 8.463930 TCTTCTATGTCCTGAAAACATTGTTT 57.536 30.769 8.97 8.97 38.31 2.83
2458 2509 7.045126 AGGAACCGTTAGATCTTCTTCTATG 57.955 40.000 0.00 0.00 0.00 2.23
2464 2515 5.012768 TGGAAAAGGAACCGTTAGATCTTCT 59.987 40.000 0.00 0.00 0.00 2.85
2466 2517 5.237236 TGGAAAAGGAACCGTTAGATCTT 57.763 39.130 0.00 0.00 0.00 2.40
2467 2518 4.903045 TGGAAAAGGAACCGTTAGATCT 57.097 40.909 0.00 0.00 0.00 2.75
2468 2519 4.575236 GGATGGAAAAGGAACCGTTAGATC 59.425 45.833 0.00 0.00 0.00 2.75
2469 2520 4.018779 TGGATGGAAAAGGAACCGTTAGAT 60.019 41.667 0.00 0.00 0.00 1.98
2470 2521 3.328343 TGGATGGAAAAGGAACCGTTAGA 59.672 43.478 0.00 0.00 0.00 2.10
2471 2522 3.681593 TGGATGGAAAAGGAACCGTTAG 58.318 45.455 0.00 0.00 0.00 2.34
2472 2523 3.791953 TGGATGGAAAAGGAACCGTTA 57.208 42.857 0.00 0.00 0.00 3.18
2473 2524 2.626266 GTTGGATGGAAAAGGAACCGTT 59.374 45.455 0.00 0.00 0.00 4.44
2474 2525 2.235891 GTTGGATGGAAAAGGAACCGT 58.764 47.619 0.00 0.00 0.00 4.83
2475 2526 1.199097 CGTTGGATGGAAAAGGAACCG 59.801 52.381 0.00 0.00 0.00 4.44
2476 2527 2.228103 GACGTTGGATGGAAAAGGAACC 59.772 50.000 0.00 0.00 0.00 3.62
2477 2528 3.058224 CAGACGTTGGATGGAAAAGGAAC 60.058 47.826 0.00 0.00 0.00 3.62
2478 2529 3.146066 CAGACGTTGGATGGAAAAGGAA 58.854 45.455 0.00 0.00 0.00 3.36
2479 2530 2.778299 CAGACGTTGGATGGAAAAGGA 58.222 47.619 0.00 0.00 0.00 3.36
2491 2542 2.412089 GTCGATTTCTTCCCAGACGTTG 59.588 50.000 0.00 0.00 0.00 4.10
2492 2543 2.299297 AGTCGATTTCTTCCCAGACGTT 59.701 45.455 0.00 0.00 34.21 3.99
2493 2544 1.893801 AGTCGATTTCTTCCCAGACGT 59.106 47.619 0.00 0.00 34.21 4.34
2494 2545 2.094700 TCAGTCGATTTCTTCCCAGACG 60.095 50.000 0.00 0.00 34.21 4.18
2495 2546 3.254892 GTCAGTCGATTTCTTCCCAGAC 58.745 50.000 0.00 0.00 0.00 3.51
2496 2547 2.233922 GGTCAGTCGATTTCTTCCCAGA 59.766 50.000 0.00 0.00 0.00 3.86
2497 2548 2.028112 TGGTCAGTCGATTTCTTCCCAG 60.028 50.000 0.00 0.00 0.00 4.45
2498 2549 1.974957 TGGTCAGTCGATTTCTTCCCA 59.025 47.619 0.00 0.00 0.00 4.37
2499 2550 2.233922 TCTGGTCAGTCGATTTCTTCCC 59.766 50.000 0.00 0.00 0.00 3.97
2500 2551 3.056465 ACTCTGGTCAGTCGATTTCTTCC 60.056 47.826 0.00 0.00 0.00 3.46
2501 2552 4.082463 AGACTCTGGTCAGTCGATTTCTTC 60.082 45.833 0.00 0.00 46.52 2.87
2502 2553 3.829601 AGACTCTGGTCAGTCGATTTCTT 59.170 43.478 0.00 0.00 46.52 2.52
2503 2554 3.426615 AGACTCTGGTCAGTCGATTTCT 58.573 45.455 0.00 0.00 46.52 2.52
2504 2555 3.859411 AGACTCTGGTCAGTCGATTTC 57.141 47.619 0.00 0.00 46.52 2.17
2505 2556 5.723672 TTTAGACTCTGGTCAGTCGATTT 57.276 39.130 0.00 0.00 46.52 2.17
2506 2557 5.923733 ATTTAGACTCTGGTCAGTCGATT 57.076 39.130 0.00 0.00 46.52 3.34
2507 2558 5.419155 TGAATTTAGACTCTGGTCAGTCGAT 59.581 40.000 0.00 0.00 46.52 3.59
2508 2559 4.765339 TGAATTTAGACTCTGGTCAGTCGA 59.235 41.667 0.00 0.00 46.52 4.20
2509 2560 5.060662 TGAATTTAGACTCTGGTCAGTCG 57.939 43.478 0.00 0.00 46.52 4.18
2510 2561 6.031751 ACTGAATTTAGACTCTGGTCAGTC 57.968 41.667 3.94 0.00 39.97 3.51
2511 2562 5.336055 CGACTGAATTTAGACTCTGGTCAGT 60.336 44.000 3.94 10.10 45.08 3.41
2512 2563 5.098893 CGACTGAATTTAGACTCTGGTCAG 58.901 45.833 3.94 0.00 44.36 3.51
2513 2564 4.765339 TCGACTGAATTTAGACTCTGGTCA 59.235 41.667 3.94 0.00 44.36 4.02
2514 2565 5.096849 GTCGACTGAATTTAGACTCTGGTC 58.903 45.833 8.70 0.00 42.41 4.02
2515 2566 4.767928 AGTCGACTGAATTTAGACTCTGGT 59.232 41.667 19.30 0.00 37.61 4.00
2516 2567 5.098893 CAGTCGACTGAATTTAGACTCTGG 58.901 45.833 36.73 6.86 46.59 3.86
2517 2568 5.704888 ACAGTCGACTGAATTTAGACTCTG 58.295 41.667 43.55 19.18 46.59 3.35
2518 2569 5.106078 GGACAGTCGACTGAATTTAGACTCT 60.106 44.000 43.55 22.02 46.59 3.24
2534 2585 0.105039 GAATGGCTAGGGGACAGTCG 59.895 60.000 0.00 0.00 38.32 4.18
2537 2588 0.695803 AGGGAATGGCTAGGGGACAG 60.696 60.000 0.00 0.00 35.79 3.51
2543 2594 3.319122 GCACAATTTAGGGAATGGCTAGG 59.681 47.826 0.00 0.00 0.00 3.02
2556 2607 3.312973 AGACCGAAAACACGCACAATTTA 59.687 39.130 0.00 0.00 0.00 1.40
2562 2613 0.865769 ATGAGACCGAAAACACGCAC 59.134 50.000 0.00 0.00 0.00 5.34
2565 2616 4.468095 AAAAGATGAGACCGAAAACACG 57.532 40.909 0.00 0.00 0.00 4.49
2574 2625 7.554118 TGAGACCATAATCAAAAAGATGAGACC 59.446 37.037 0.00 0.00 36.96 3.85
2597 2648 9.270576 CACAACTTTCATAATCGAAAAGATGAG 57.729 33.333 18.15 10.17 40.02 2.90
2598 2649 8.783093 ACACAACTTTCATAATCGAAAAGATGA 58.217 29.630 18.15 9.67 40.02 2.92
2599 2650 8.955061 ACACAACTTTCATAATCGAAAAGATG 57.045 30.769 12.30 12.43 40.02 2.90
2657 2758 5.456619 GGATCATGTCCATTCCATGTTCCTA 60.457 44.000 17.28 0.00 46.38 2.94
2726 2827 1.531149 CAGCCAGTTACACCGTCTTTG 59.469 52.381 0.00 0.00 0.00 2.77
2817 2923 7.067615 ACGTGCCCTCTACTCATCTTATATATG 59.932 40.741 0.00 0.00 0.00 1.78
2882 2996 2.092646 ACCTGTGGTGTGTATGTTGTGT 60.093 45.455 0.00 0.00 32.98 3.72
2883 2997 2.571212 ACCTGTGGTGTGTATGTTGTG 58.429 47.619 0.00 0.00 32.98 3.33
2957 3082 2.125673 CGTCCAGTTGGCCTACCG 60.126 66.667 14.06 6.52 39.70 4.02
2973 3098 4.184629 AGCTATTAGTTGGTCTTCTTGCG 58.815 43.478 0.00 0.00 0.00 4.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.