Multiple sequence alignment - TraesCS2B01G540600

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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 TraesCS2B01G540600 chr2B 100.000 2867 0 0 1 2867 737098085 737095219 0.000000e+00 5295
1 TraesCS2B01G540600 chr2B 91.708 2243 129 22 1 2215 737109362 737107149 0.000000e+00 3059
2 TraesCS2B01G540600 chr2B 89.806 1550 87 27 697 2215 737160815 737159306 0.000000e+00 1921
3 TraesCS2B01G540600 chr2B 93.610 1252 57 11 643 1880 737227237 737225995 0.000000e+00 1847
4 TraesCS2B01G540600 chr2B 93.365 1266 57 13 630 1880 737246304 737245051 0.000000e+00 1847
5 TraesCS2B01G540600 chr2B 91.153 1232 77 10 806 2026 737272380 737271170 0.000000e+00 1642
6 TraesCS2B01G540600 chr2B 81.317 653 80 15 2 636 737229324 737228696 2.570000e-135 492
7 TraesCS2B01G540600 chr2B 81.346 654 78 17 2 636 737248378 737247750 2.570000e-135 492
8 TraesCS2B01G540600 chr2B 88.952 353 22 10 1878 2215 737244948 737244598 1.230000e-113 420
9 TraesCS2B01G540600 chr2B 88.669 353 23 10 1878 2215 737225892 737225542 5.720000e-112 414
10 TraesCS2B01G540600 chr2B 97.196 107 3 0 2663 2769 369499343 369499449 6.310000e-42 182
11 TraesCS2B01G540600 chr2B 89.583 144 14 1 2374 2517 737107155 737107013 6.310000e-42 182
12 TraesCS2B01G540600 chr2A 93.317 1631 82 13 601 2210 737735573 737733949 0.000000e+00 2383
13 TraesCS2B01G540600 chr2A 91.521 1545 96 17 696 2215 737880627 737879093 0.000000e+00 2095
14 TraesCS2B01G540600 chr2A 88.491 1425 124 21 806 2215 738007000 738005601 0.000000e+00 1687
15 TraesCS2B01G540600 chr2A 84.824 626 73 14 2 606 737736279 737735655 6.790000e-171 610
16 TraesCS2B01G540600 chr2A 96.815 157 5 0 2217 2373 470120177 470120333 2.190000e-66 263
17 TraesCS2B01G540600 chr2A 81.646 316 33 12 2374 2664 737837059 737836744 3.690000e-59 239
18 TraesCS2B01G540600 chr2A 81.646 316 33 12 2374 2664 737879099 737878784 3.690000e-59 239
19 TraesCS2B01G540600 chr2A 80.546 293 39 13 2374 2664 737733953 737733677 2.890000e-50 209
20 TraesCS2B01G540600 chr2A 87.578 161 18 2 2376 2535 738005605 738005446 4.880000e-43 185
21 TraesCS2B01G540600 chr2A 88.000 100 9 2 2768 2867 737733678 737733582 6.490000e-22 115
22 TraesCS2B01G540600 chr2A 88.421 95 8 2 2768 2862 737836745 737836654 8.400000e-21 111
23 TraesCS2B01G540600 chr2A 88.421 95 8 2 2768 2862 737878785 737878694 8.400000e-21 111
24 TraesCS2B01G540600 chr2D 89.622 1561 105 24 696 2214 606156651 606155106 0.000000e+00 1932
25 TraesCS2B01G540600 chr2D 82.793 709 97 13 2 690 606189790 606189087 6.790000e-171 610
26 TraesCS2B01G540600 chr2D 88.983 472 38 8 1757 2215 606162004 606161534 3.200000e-159 571
27 TraesCS2B01G540600 chr2D 87.097 279 26 6 2376 2647 606149387 606149112 9.980000e-80 307
28 TraesCS2B01G540600 chr2D 81.126 302 42 12 2374 2664 606161540 606161243 7.990000e-56 228
29 TraesCS2B01G540600 chr2D 80.731 301 44 11 2374 2664 606155111 606154815 3.720000e-54 222
30 TraesCS2B01G540600 chr2D 74.157 445 76 26 1294 1708 476731922 476731487 6.400000e-32 148
31 TraesCS2B01G540600 chr2D 94.872 78 2 1 1681 1756 606163087 606163010 1.400000e-23 121
32 TraesCS2B01G540600 chr2D 96.667 60 2 0 2808 2867 606136532 606136473 1.820000e-17 100
33 TraesCS2B01G540600 chrUn 93.029 1162 70 6 1064 2215 386125594 386124434 0.000000e+00 1687
34 TraesCS2B01G540600 chrUn 81.646 316 33 12 2374 2664 386124440 386124125 3.690000e-59 239
35 TraesCS2B01G540600 chrUn 88.325 197 22 1 440 636 477697385 477697190 4.780000e-58 235
36 TraesCS2B01G540600 chrUn 84.298 242 14 16 696 921 30267131 30266898 6.220000e-52 215
37 TraesCS2B01G540600 chrUn 88.421 95 8 2 2768 2862 386124126 386124035 8.400000e-21 111
38 TraesCS2B01G540600 chr3A 96.815 157 5 0 2217 2373 166842206 166842050 2.190000e-66 263
39 TraesCS2B01G540600 chr3A 93.902 164 9 1 2214 2376 640619459 640619296 2.210000e-61 246
40 TraesCS2B01G540600 chr7A 96.178 157 6 0 2217 2373 6443622 6443466 1.020000e-64 257
41 TraesCS2B01G540600 chr5A 96.178 157 6 0 2217 2373 41702793 41702637 1.020000e-64 257
42 TraesCS2B01G540600 chr5A 96.178 157 6 0 2217 2373 84025847 84026003 1.020000e-64 257
43 TraesCS2B01G540600 chr5A 96.178 157 6 0 2217 2373 566780748 566780592 1.020000e-64 257
44 TraesCS2B01G540600 chr5A 96.178 157 6 0 2217 2373 672696186 672696342 1.020000e-64 257
45 TraesCS2B01G540600 chr1A 96.178 157 6 0 2217 2373 68578500 68578656 1.020000e-64 257
46 TraesCS2B01G540600 chr4D 96.364 110 4 0 2663 2772 39410782 39410673 6.310000e-42 182
47 TraesCS2B01G540600 chr7B 96.296 108 4 0 2662 2769 316313683 316313790 8.160000e-41 178
48 TraesCS2B01G540600 chr7B 93.913 115 6 1 2657 2770 152383896 152384010 3.800000e-39 172
49 TraesCS2B01G540600 chr6B 94.017 117 6 1 2657 2772 126722447 126722331 2.940000e-40 176
50 TraesCS2B01G540600 chr1B 94.643 112 6 0 2659 2770 6684252 6684363 1.060000e-39 174
51 TraesCS2B01G540600 chr5B 93.913 115 6 1 2657 2770 451858014 451858128 3.800000e-39 172
52 TraesCS2B01G540600 chr5B 89.313 131 12 2 2640 2769 355653036 355653165 2.290000e-36 163
53 TraesCS2B01G540600 chr4A 93.913 115 6 1 2657 2770 730795280 730795166 3.800000e-39 172


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 TraesCS2B01G540600 chr2B 737095219 737098085 2866 True 5295.000000 5295 100.000000 1 2867 1 chr2B.!!$R1 2866
1 TraesCS2B01G540600 chr2B 737159306 737160815 1509 True 1921.000000 1921 89.806000 697 2215 1 chr2B.!!$R2 1518
2 TraesCS2B01G540600 chr2B 737271170 737272380 1210 True 1642.000000 1642 91.153000 806 2026 1 chr2B.!!$R3 1220
3 TraesCS2B01G540600 chr2B 737107013 737109362 2349 True 1620.500000 3059 90.645500 1 2517 2 chr2B.!!$R4 2516
4 TraesCS2B01G540600 chr2B 737244598 737248378 3780 True 919.666667 1847 87.887667 2 2215 3 chr2B.!!$R6 2213
5 TraesCS2B01G540600 chr2B 737225542 737229324 3782 True 917.666667 1847 87.865333 2 2215 3 chr2B.!!$R5 2213
6 TraesCS2B01G540600 chr2A 738005446 738007000 1554 True 936.000000 1687 88.034500 806 2535 2 chr2A.!!$R4 1729
7 TraesCS2B01G540600 chr2A 737733582 737736279 2697 True 829.250000 2383 86.671750 2 2867 4 chr2A.!!$R1 2865
8 TraesCS2B01G540600 chr2A 737878694 737880627 1933 True 815.000000 2095 87.196000 696 2862 3 chr2A.!!$R3 2166
9 TraesCS2B01G540600 chr2D 606154815 606156651 1836 True 1077.000000 1932 85.176500 696 2664 2 chr2D.!!$R5 1968
10 TraesCS2B01G540600 chr2D 606189087 606189790 703 True 610.000000 610 82.793000 2 690 1 chr2D.!!$R4 688
11 TraesCS2B01G540600 chr2D 606161243 606163087 1844 True 306.666667 571 88.327000 1681 2664 3 chr2D.!!$R6 983
12 TraesCS2B01G540600 chrUn 386124035 386125594 1559 True 679.000000 1687 87.698667 1064 2862 3 chrUn.!!$R3 1798

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
794 2397 0.331278 ATTTGGGCTGGATTCGGACA 59.669 50.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2662 5490 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 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
19 20 1.638467 CTAGCTCGTGATTTGCGGC 59.362 57.895 0.00 0.00 0.00 6.53
26 27 1.874231 TCGTGATTTGCGGCTTGTAAA 59.126 42.857 0.00 0.00 36.57 2.01
51 52 0.874175 CGAGTTGCGGCCGATATTGA 60.874 55.000 33.48 3.63 36.03 2.57
77 78 2.026641 GCTCATTGCCCTATTGCTTCA 58.973 47.619 0.00 0.00 35.15 3.02
150 151 2.822701 GAAACCCGCGGTCATCCC 60.823 66.667 26.12 4.00 33.12 3.85
180 181 2.268920 CCGCACACCACTGGCTAT 59.731 61.111 0.00 0.00 0.00 2.97
195 196 2.021068 GCTATCACTCCTGCTCGCCA 62.021 60.000 0.00 0.00 0.00 5.69
198 199 0.684479 ATCACTCCTGCTCGCCACTA 60.684 55.000 0.00 0.00 0.00 2.74
260 284 2.352030 CGGTTGTAACACCTTCGAGCTA 60.352 50.000 0.00 0.00 34.22 3.32
374 400 3.127533 GTAGCGCTGGCAAGTGGG 61.128 66.667 22.90 0.00 43.41 4.61
437 480 2.309528 TTGTGTTGACTGAGCGAAGT 57.690 45.000 0.00 0.00 0.00 3.01
481 524 4.101448 GCTGGCCCACGAGGTGAT 62.101 66.667 0.00 0.00 38.26 3.06
597 642 6.564328 GCCAGATATAAGTGTTTCCCTTTTG 58.436 40.000 0.00 0.00 0.00 2.44
653 2239 0.456221 TTTTTGTCGGGCGCAAGAAA 59.544 45.000 10.83 0.00 43.02 2.52
667 2253 3.121362 CGCAAGAAAAAGCAAAACGATCC 60.121 43.478 0.00 0.00 43.02 3.36
682 2268 3.808728 ACGATCCACCATCCAAATACAG 58.191 45.455 0.00 0.00 0.00 2.74
794 2397 0.331278 ATTTGGGCTGGATTCGGACA 59.669 50.000 0.00 0.00 0.00 4.02
867 2490 4.198530 TCGGCCGACGGATACATATATAA 58.801 43.478 27.28 0.00 44.45 0.98
893 2519 2.756283 CGGCGGTCTCCTCCTCTT 60.756 66.667 0.00 0.00 0.00 2.85
1793 4450 2.977914 TCTCTTCATCAAGAAAGGCCG 58.022 47.619 0.00 0.00 38.23 6.13
1859 4522 1.668751 GGAAACAGCACAAGAACACGA 59.331 47.619 0.00 0.00 0.00 4.35
1875 4542 2.100989 CACGAACCCTAGCTAGTTCCT 58.899 52.381 19.31 5.90 39.36 3.36
1888 4661 3.368236 GCTAGTTCCTTAGTGTTCTTGCG 59.632 47.826 0.00 0.00 0.00 4.85
1891 4664 1.508632 TCCTTAGTGTTCTTGCGTGC 58.491 50.000 0.00 0.00 0.00 5.34
1973 4751 1.754803 AGTCGTGGTGTTGAGACTTGA 59.245 47.619 0.00 0.00 40.64 3.02
1986 4771 2.076863 AGACTTGAATGTAACCTGCGC 58.923 47.619 0.00 0.00 0.00 6.09
2010 4795 8.612619 CGCTGATATAATACAGTCCTTGTTTTT 58.387 33.333 0.00 0.00 41.29 1.94
2052 4840 8.862325 TTATCTCATTTAGTTTTTCTCTGGCA 57.138 30.769 0.00 0.00 0.00 4.92
2074 4866 5.172053 GCAAAAGAGACGACATTCAACAAAG 59.828 40.000 0.00 0.00 0.00 2.77
2159 4958 5.772672 AGCAAATGTTAACATTCCCTACACA 59.227 36.000 29.10 0.00 45.06 3.72
2164 4963 7.589958 ATGTTAACATTCCCTACACAAAACA 57.410 32.000 15.47 0.00 31.37 2.83
2215 5016 1.406860 CCAGCTTCCTCCTCCTAGGC 61.407 65.000 2.96 0.00 36.51 3.93
2216 5017 1.074850 AGCTTCCTCCTCCTAGGCC 60.075 63.158 2.96 0.00 36.51 5.19
2217 5018 1.383248 GCTTCCTCCTCCTAGGCCA 60.383 63.158 5.01 0.00 36.51 5.36
2218 5019 1.406860 GCTTCCTCCTCCTAGGCCAG 61.407 65.000 5.01 0.00 36.51 4.85
2219 5020 0.031616 CTTCCTCCTCCTAGGCCAGT 60.032 60.000 5.01 0.00 36.51 4.00
2220 5021 0.325671 TTCCTCCTCCTAGGCCAGTG 60.326 60.000 5.01 0.00 36.51 3.66
2221 5022 1.764054 CCTCCTCCTAGGCCAGTGG 60.764 68.421 5.01 4.20 34.61 4.00
2241 5042 2.039327 CGGAGCTAGACGCAGATTAC 57.961 55.000 0.00 0.00 42.61 1.89
2242 5043 1.660614 CGGAGCTAGACGCAGATTACG 60.661 57.143 0.00 0.00 42.61 3.18
2250 5051 2.125664 CGCAGATTACGTCTAGCGC 58.874 57.895 0.00 0.00 42.73 5.92
2251 5052 0.317103 CGCAGATTACGTCTAGCGCT 60.317 55.000 17.26 17.26 42.73 5.92
2252 5053 1.124462 GCAGATTACGTCTAGCGCTG 58.876 55.000 22.90 10.49 46.11 5.18
2253 5054 1.534175 GCAGATTACGTCTAGCGCTGT 60.534 52.381 22.90 12.13 46.11 4.40
2254 5055 2.112522 CAGATTACGTCTAGCGCTGTG 58.887 52.381 22.90 13.21 46.11 3.66
2255 5056 0.847035 GATTACGTCTAGCGCTGTGC 59.153 55.000 22.90 4.76 46.11 4.57
2265 5066 2.460330 GCGCTGTGCTATGTTGAGT 58.540 52.632 5.84 0.00 41.73 3.41
2266 5067 0.095935 GCGCTGTGCTATGTTGAGTG 59.904 55.000 5.84 0.00 41.73 3.51
2267 5068 1.713597 CGCTGTGCTATGTTGAGTGA 58.286 50.000 0.00 0.00 0.00 3.41
2268 5069 2.274437 CGCTGTGCTATGTTGAGTGAT 58.726 47.619 0.00 0.00 0.00 3.06
2269 5070 3.447742 CGCTGTGCTATGTTGAGTGATA 58.552 45.455 0.00 0.00 0.00 2.15
2270 5071 3.865164 CGCTGTGCTATGTTGAGTGATAA 59.135 43.478 0.00 0.00 0.00 1.75
2271 5072 4.329801 CGCTGTGCTATGTTGAGTGATAAA 59.670 41.667 0.00 0.00 0.00 1.40
2272 5073 5.563842 GCTGTGCTATGTTGAGTGATAAAC 58.436 41.667 0.00 0.00 0.00 2.01
2273 5074 5.352569 GCTGTGCTATGTTGAGTGATAAACT 59.647 40.000 0.00 0.00 43.85 2.66
2274 5075 6.128172 GCTGTGCTATGTTGAGTGATAAACTT 60.128 38.462 0.00 0.00 40.07 2.66
2275 5076 7.364522 TGTGCTATGTTGAGTGATAAACTTC 57.635 36.000 0.00 0.00 40.07 3.01
2276 5077 7.161404 TGTGCTATGTTGAGTGATAAACTTCT 58.839 34.615 0.00 0.00 40.07 2.85
2277 5078 8.311109 TGTGCTATGTTGAGTGATAAACTTCTA 58.689 33.333 0.00 0.00 40.07 2.10
2278 5079 9.319143 GTGCTATGTTGAGTGATAAACTTCTAT 57.681 33.333 0.00 0.00 40.07 1.98
2279 5080 9.317936 TGCTATGTTGAGTGATAAACTTCTATG 57.682 33.333 0.00 0.00 40.07 2.23
2280 5081 9.534565 GCTATGTTGAGTGATAAACTTCTATGA 57.465 33.333 0.00 0.00 40.07 2.15
2295 5096 9.578439 AAACTTCTATGATTTTCTATGCTTTGC 57.422 29.630 0.00 0.00 0.00 3.68
2296 5097 8.284945 ACTTCTATGATTTTCTATGCTTTGCA 57.715 30.769 0.00 0.00 44.86 4.08
2328 5129 6.628919 TTACAAAGGAAGTTGTTTCTAGGC 57.371 37.500 0.00 0.00 41.84 3.93
2329 5130 3.889538 ACAAAGGAAGTTGTTTCTAGGCC 59.110 43.478 0.00 0.00 38.60 5.19
2330 5131 4.145052 CAAAGGAAGTTGTTTCTAGGCCT 58.855 43.478 11.78 11.78 36.03 5.19
2331 5132 3.425162 AGGAAGTTGTTTCTAGGCCTG 57.575 47.619 17.99 5.60 36.03 4.85
2332 5133 2.040412 AGGAAGTTGTTTCTAGGCCTGG 59.960 50.000 17.99 14.14 36.03 4.45
2333 5134 2.437413 GAAGTTGTTTCTAGGCCTGGG 58.563 52.381 17.99 8.50 32.83 4.45
2334 5135 0.698818 AGTTGTTTCTAGGCCTGGGG 59.301 55.000 17.99 5.64 0.00 4.96
2357 5158 3.561241 GCCCTAGCTACCCCAGGC 61.561 72.222 0.00 0.00 35.50 4.85
2358 5159 2.849646 CCCTAGCTACCCCAGGCC 60.850 72.222 0.00 0.00 0.00 5.19
2359 5160 2.287251 CCTAGCTACCCCAGGCCT 59.713 66.667 0.00 0.00 0.00 5.19
2360 5161 2.143419 CCTAGCTACCCCAGGCCTG 61.143 68.421 26.87 26.87 0.00 4.85
2361 5162 1.383248 CTAGCTACCCCAGGCCTGT 60.383 63.158 30.63 15.62 0.00 4.00
2362 5163 1.382695 TAGCTACCCCAGGCCTGTC 60.383 63.158 30.63 12.20 0.00 3.51
2363 5164 1.886730 TAGCTACCCCAGGCCTGTCT 61.887 60.000 30.63 17.97 0.00 3.41
2364 5165 2.736826 GCTACCCCAGGCCTGTCTC 61.737 68.421 30.63 10.05 0.00 3.36
2365 5166 2.040606 TACCCCAGGCCTGTCTCC 59.959 66.667 30.63 0.00 0.00 3.71
2366 5167 3.976490 TACCCCAGGCCTGTCTCCG 62.976 68.421 30.63 15.07 0.00 4.63
2372 5173 4.767255 GGCCTGTCTCCGCCACTG 62.767 72.222 0.00 0.00 45.01 3.66
2373 5174 4.008933 GCCTGTCTCCGCCACTGT 62.009 66.667 0.00 0.00 0.00 3.55
2374 5175 2.262915 CCTGTCTCCGCCACTGTC 59.737 66.667 0.00 0.00 0.00 3.51
2375 5176 2.262915 CTGTCTCCGCCACTGTCC 59.737 66.667 0.00 0.00 0.00 4.02
2376 5177 2.203640 TGTCTCCGCCACTGTCCT 60.204 61.111 0.00 0.00 0.00 3.85
2377 5178 0.965866 CTGTCTCCGCCACTGTCCTA 60.966 60.000 0.00 0.00 0.00 2.94
2378 5179 0.965866 TGTCTCCGCCACTGTCCTAG 60.966 60.000 0.00 0.00 0.00 3.02
2379 5180 1.379977 TCTCCGCCACTGTCCTAGG 60.380 63.158 0.82 0.82 0.00 3.02
2380 5181 3.075005 TCCGCCACTGTCCTAGGC 61.075 66.667 2.96 0.00 44.89 3.93
2458 5261 1.803519 CTCCTCTCGTGCGCAGAAC 60.804 63.158 12.22 0.00 0.00 3.01
2465 5268 1.083401 CGTGCGCAGAACTGACAAC 60.083 57.895 12.22 0.00 0.00 3.32
2468 5271 1.002468 GTGCGCAGAACTGACAACAAT 60.002 47.619 12.22 0.00 0.00 2.71
2473 5276 4.319477 GCGCAGAACTGACAACAATCTTTA 60.319 41.667 0.30 0.00 0.00 1.85
2483 5288 8.143835 ACTGACAACAATCTTTATTTTCCTTGG 58.856 33.333 0.00 0.00 0.00 3.61
2484 5289 8.017418 TGACAACAATCTTTATTTTCCTTGGT 57.983 30.769 0.00 0.00 0.00 3.67
2496 5301 1.314730 TCCTTGGTTTCCGCTTTCAC 58.685 50.000 0.00 0.00 0.00 3.18
2500 5305 1.757682 TGGTTTCCGCTTTCACACTT 58.242 45.000 0.00 0.00 0.00 3.16
2522 5327 9.559958 CACTTTTTGAATAATGCTAATTCGTCT 57.440 29.630 0.00 0.00 36.35 4.18
2535 5340 7.648142 TGCTAATTCGTCTTTGTCAAATTCTT 58.352 30.769 0.00 0.00 0.00 2.52
2536 5341 8.134895 TGCTAATTCGTCTTTGTCAAATTCTTT 58.865 29.630 0.00 0.00 0.00 2.52
2537 5342 8.968242 GCTAATTCGTCTTTGTCAAATTCTTTT 58.032 29.630 0.00 0.00 0.00 2.27
2566 5376 6.385649 TCAAATTGAAAGCGTTTTCTAGGT 57.614 33.333 22.71 7.58 42.56 3.08
2568 5378 3.619233 TTGAAAGCGTTTTCTAGGTGC 57.381 42.857 22.71 0.00 42.56 5.01
2569 5379 1.529438 TGAAAGCGTTTTCTAGGTGCG 59.471 47.619 22.71 0.00 42.56 5.34
2570 5380 0.872388 AAAGCGTTTTCTAGGTGCGG 59.128 50.000 0.00 0.00 0.00 5.69
2572 5382 0.250166 AGCGTTTTCTAGGTGCGGTT 60.250 50.000 0.00 0.00 0.00 4.44
2573 5383 0.110373 GCGTTTTCTAGGTGCGGTTG 60.110 55.000 0.00 0.00 0.00 3.77
2590 5417 4.259690 GCGGTTGCGATACAAAGTTAGTAG 60.260 45.833 0.00 0.00 40.82 2.57
2596 5423 4.738839 GCGATACAAAGTTAGTAGGGGGTC 60.739 50.000 0.00 0.00 0.00 4.46
2640 5467 8.306038 CCAAAGATCACCATAAACTCATCAAAA 58.694 33.333 0.00 0.00 0.00 2.44
2656 5484 7.498900 ACTCATCAAAATGACACTTTGACTGTA 59.501 33.333 13.81 0.66 43.57 2.74
2667 5495 9.431887 TGACACTTTGACTGTATTTAATACTCC 57.568 33.333 15.05 6.02 36.70 3.85
2668 5496 8.788325 ACACTTTGACTGTATTTAATACTCCC 57.212 34.615 15.05 5.73 36.70 4.30
2669 5497 8.603304 ACACTTTGACTGTATTTAATACTCCCT 58.397 33.333 15.05 0.00 36.70 4.20
2670 5498 9.099454 CACTTTGACTGTATTTAATACTCCCTC 57.901 37.037 15.05 6.02 36.70 4.30
2671 5499 8.265764 ACTTTGACTGTATTTAATACTCCCTCC 58.734 37.037 15.05 1.75 36.70 4.30
2672 5500 6.401047 TGACTGTATTTAATACTCCCTCCG 57.599 41.667 15.05 0.38 36.70 4.63
2673 5501 5.895534 TGACTGTATTTAATACTCCCTCCGT 59.104 40.000 15.05 2.94 36.70 4.69
2674 5502 6.040166 TGACTGTATTTAATACTCCCTCCGTC 59.960 42.308 15.05 10.17 36.70 4.79
2675 5503 5.303845 ACTGTATTTAATACTCCCTCCGTCC 59.696 44.000 15.05 0.00 36.70 4.79
2676 5504 4.279169 TGTATTTAATACTCCCTCCGTCCG 59.721 45.833 15.05 0.00 36.70 4.79
2677 5505 1.696063 TTAATACTCCCTCCGTCCGG 58.304 55.000 0.00 0.00 0.00 5.14
2678 5506 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
2679 5507 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2680 5508 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2681 5509 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2682 5510 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2683 5511 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2684 5512 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2685 5513 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2686 5514 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2687 5515 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2688 5516 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2689 5517 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2690 5518 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2691 5519 3.055675 TCCGTCCGGAAATACTTGTCATT 60.056 43.478 5.23 0.00 42.05 2.57
2692 5520 3.063452 CCGTCCGGAAATACTTGTCATTG 59.937 47.826 5.23 0.00 37.50 2.82
2693 5521 3.930229 CGTCCGGAAATACTTGTCATTGA 59.070 43.478 5.23 0.00 0.00 2.57
2694 5522 4.390603 CGTCCGGAAATACTTGTCATTGAA 59.609 41.667 5.23 0.00 0.00 2.69
2695 5523 5.106869 CGTCCGGAAATACTTGTCATTGAAA 60.107 40.000 5.23 0.00 0.00 2.69
2696 5524 6.403200 CGTCCGGAAATACTTGTCATTGAAAT 60.403 38.462 5.23 0.00 0.00 2.17
2697 5525 6.747280 GTCCGGAAATACTTGTCATTGAAATG 59.253 38.462 5.23 0.00 37.75 2.32
2698 5526 6.035843 CCGGAAATACTTGTCATTGAAATGG 58.964 40.000 0.00 0.00 37.03 3.16
2699 5527 6.127758 CCGGAAATACTTGTCATTGAAATGGA 60.128 38.462 0.00 0.00 37.03 3.41
2700 5528 7.416664 CCGGAAATACTTGTCATTGAAATGGAT 60.417 37.037 0.00 0.00 37.03 3.41
2701 5529 7.433131 CGGAAATACTTGTCATTGAAATGGATG 59.567 37.037 3.31 0.00 37.03 3.51
2702 5530 8.253113 GGAAATACTTGTCATTGAAATGGATGT 58.747 33.333 3.31 2.77 37.03 3.06
2706 5534 9.857656 ATACTTGTCATTGAAATGGATGTATCT 57.142 29.630 3.31 0.00 37.03 1.98
2708 5536 9.334947 ACTTGTCATTGAAATGGATGTATCTAG 57.665 33.333 3.31 0.00 37.03 2.43
2709 5537 9.551734 CTTGTCATTGAAATGGATGTATCTAGA 57.448 33.333 0.00 0.00 37.03 2.43
2744 5572 9.167311 AGTTCTAGATACATCCATTTTGTTGAC 57.833 33.333 0.00 0.00 0.00 3.18
2745 5573 7.770801 TCTAGATACATCCATTTTGTTGACG 57.229 36.000 0.00 0.00 0.00 4.35
2746 5574 7.552459 TCTAGATACATCCATTTTGTTGACGA 58.448 34.615 0.00 0.00 0.00 4.20
2747 5575 6.668541 AGATACATCCATTTTGTTGACGAG 57.331 37.500 0.00 0.00 0.00 4.18
2748 5576 6.173339 AGATACATCCATTTTGTTGACGAGT 58.827 36.000 0.00 0.00 0.00 4.18
2749 5577 7.327975 AGATACATCCATTTTGTTGACGAGTA 58.672 34.615 0.00 0.00 0.00 2.59
2750 5578 7.822334 AGATACATCCATTTTGTTGACGAGTAA 59.178 33.333 0.00 0.00 0.00 2.24
2751 5579 6.817765 ACATCCATTTTGTTGACGAGTAAT 57.182 33.333 0.00 0.00 0.00 1.89
2752 5580 7.214467 ACATCCATTTTGTTGACGAGTAATT 57.786 32.000 0.00 0.00 0.00 1.40
2753 5581 7.305474 ACATCCATTTTGTTGACGAGTAATTC 58.695 34.615 0.00 0.00 0.00 2.17
2754 5582 7.174946 ACATCCATTTTGTTGACGAGTAATTCT 59.825 33.333 0.00 0.00 0.00 2.40
2755 5583 6.898041 TCCATTTTGTTGACGAGTAATTCTG 58.102 36.000 0.00 0.00 0.00 3.02
2756 5584 6.072728 TCCATTTTGTTGACGAGTAATTCTGG 60.073 38.462 0.00 0.00 0.00 3.86
2757 5585 6.072728 CCATTTTGTTGACGAGTAATTCTGGA 60.073 38.462 0.00 0.00 0.00 3.86
2758 5586 5.917541 TTTGTTGACGAGTAATTCTGGAC 57.082 39.130 0.00 0.00 0.00 4.02
2759 5587 3.571571 TGTTGACGAGTAATTCTGGACG 58.428 45.455 0.00 0.00 0.00 4.79
2760 5588 2.921754 GTTGACGAGTAATTCTGGACGG 59.078 50.000 0.00 0.00 0.00 4.79
2761 5589 2.439409 TGACGAGTAATTCTGGACGGA 58.561 47.619 0.00 0.00 0.00 4.69
2762 5590 2.422479 TGACGAGTAATTCTGGACGGAG 59.578 50.000 0.00 0.00 0.00 4.63
2763 5591 1.749634 ACGAGTAATTCTGGACGGAGG 59.250 52.381 0.00 0.00 0.00 4.30
2764 5592 1.067212 CGAGTAATTCTGGACGGAGGG 59.933 57.143 0.00 0.00 0.00 4.30
2765 5593 2.385803 GAGTAATTCTGGACGGAGGGA 58.614 52.381 0.00 0.00 0.00 4.20
2766 5594 2.362717 GAGTAATTCTGGACGGAGGGAG 59.637 54.545 0.00 0.00 0.00 4.30
2778 5606 1.685180 CGGAGGGAGTATGTGAGGTCA 60.685 57.143 0.00 0.00 0.00 4.02
2783 5611 3.708631 AGGGAGTATGTGAGGTCATCTTG 59.291 47.826 0.00 0.00 0.00 3.02
2791 5619 5.147330 TGTGAGGTCATCTTGTTTATCGT 57.853 39.130 0.00 0.00 0.00 3.73
2800 5628 9.472361 GGTCATCTTGTTTATCGTAGCTTAATA 57.528 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.668656 GCAACTCGAACATTTTACAAGCC 59.331 43.478 0.00 0.00 0.00 4.35
19 20 3.906008 CCGCAACTCGAACATTTTACAAG 59.094 43.478 0.00 0.00 41.67 3.16
26 27 2.677003 CGGCCGCAACTCGAACATT 61.677 57.895 14.67 0.00 41.67 2.71
51 52 2.364324 CAATAGGGCAATGAGCTGCAAT 59.636 45.455 1.02 0.00 44.52 3.56
77 78 0.394565 ACTTGCCGACAGAGAAGCTT 59.605 50.000 0.00 0.00 0.00 3.74
174 175 2.021068 GCGAGCAGGAGTGATAGCCA 62.021 60.000 0.00 0.00 34.92 4.75
180 181 0.684479 ATAGTGGCGAGCAGGAGTGA 60.684 55.000 0.00 0.00 0.00 3.41
195 196 2.798499 GCGTCGACCATGCTACAATAGT 60.798 50.000 10.58 0.00 33.71 2.12
198 199 0.810031 GGCGTCGACCATGCTACAAT 60.810 55.000 10.58 0.00 37.18 2.71
236 260 0.940519 CGAAGGTGTTACAACCGCGA 60.941 55.000 8.23 0.00 45.53 5.87
260 284 0.995024 ACCCAGCTTGCTATTCCTGT 59.005 50.000 0.00 0.00 0.00 4.00
284 308 0.251121 ATCCATTTGTGTGGCCGTGA 60.251 50.000 0.00 0.00 39.19 4.35
297 321 3.301222 AAGCGGCCACCCATCCATT 62.301 57.895 2.24 0.00 0.00 3.16
328 352 4.660938 GACACCACCCACCTGCCC 62.661 72.222 0.00 0.00 0.00 5.36
378 404 4.704833 CACACCCCCTGTCGGCTG 62.705 72.222 0.00 0.00 0.00 4.85
384 410 1.136329 AATCAGAGCACACCCCCTGT 61.136 55.000 0.00 0.00 0.00 4.00
437 480 1.035385 TCGCAGCGTCTCCCTTATCA 61.035 55.000 15.93 0.00 0.00 2.15
481 524 2.149803 CTACGTCTTCCCACCACGCA 62.150 60.000 0.00 0.00 37.02 5.24
568 612 1.852942 ACACTTATATCTGGCGTGCG 58.147 50.000 0.00 0.00 0.00 5.34
597 642 6.018262 GCCAAAATTTCAAGGGACACTTTAAC 60.018 38.462 0.00 0.00 37.29 2.01
653 2239 2.231235 GGATGGTGGATCGTTTTGCTTT 59.769 45.455 0.00 0.00 30.87 3.51
667 2253 7.362920 CCCTAGAAAAACTGTATTTGGATGGTG 60.363 40.741 0.00 0.00 0.00 4.17
682 2268 4.569719 TGGATGGTCTCCCTAGAAAAAC 57.430 45.455 0.00 0.00 44.23 2.43
759 2361 2.223782 CCAAATCCGGTTCCGTATCGTA 60.224 50.000 0.00 0.00 0.00 3.43
794 2397 8.298729 TCGAATACCAGATGAATAGATGCTAT 57.701 34.615 0.00 0.00 0.00 2.97
853 2476 5.277683 CGACGTCCCCTTATATATGTATCCG 60.278 48.000 10.58 0.00 0.00 4.18
893 2519 2.811504 GCGACAATGGATGGATGGATGA 60.812 50.000 0.00 0.00 0.00 2.92
1193 2843 0.606401 CACTGCCTTGATGGGTTCGT 60.606 55.000 0.00 0.00 36.00 3.85
1197 2847 2.036256 GGCACTGCCTTGATGGGT 59.964 61.111 13.28 0.00 46.69 4.51
1237 2887 4.869440 CGGCGGCTCAGCTCTCTG 62.869 72.222 7.61 0.00 41.67 3.35
1762 4419 6.174049 TCTTGATGAAGAGAACGTAGAGAGA 58.826 40.000 0.00 0.00 32.98 3.10
1793 4450 1.645402 ATGGGGTGGTGGTAGCATCC 61.645 60.000 2.07 1.77 45.83 3.51
1859 4522 4.685807 ACACTAAGGAACTAGCTAGGGTT 58.314 43.478 24.35 11.64 38.49 4.11
1875 4542 2.232756 TCTGCACGCAAGAACACTAA 57.767 45.000 0.00 0.00 43.62 2.24
1888 4661 4.568152 ACAGGTTTGTACAATTCTGCAC 57.432 40.909 25.68 14.69 35.25 4.57
1973 4751 7.158697 TGTATTATATCAGCGCAGGTTACATT 58.841 34.615 11.47 0.00 33.74 2.71
2027 4815 8.862325 TGCCAGAGAAAAACTAAATGAGATAA 57.138 30.769 0.00 0.00 0.00 1.75
2052 4840 5.163663 TGCTTTGTTGAATGTCGTCTCTTTT 60.164 36.000 0.00 0.00 0.00 2.27
2118 4914 6.150140 ACATTTGCTCCAGTATTCTTCACTTC 59.850 38.462 0.00 0.00 0.00 3.01
2159 4958 9.820229 CACATGTATGATACGTAGTTTTGTTTT 57.180 29.630 0.00 0.00 37.78 2.43
2164 4963 6.592220 TGCACACATGTATGATACGTAGTTTT 59.408 34.615 8.67 0.00 37.78 2.43
2215 5016 2.496817 GTCTAGCTCCGCCACTGG 59.503 66.667 0.00 0.00 0.00 4.00
2216 5017 2.103143 CGTCTAGCTCCGCCACTG 59.897 66.667 0.00 0.00 0.00 3.66
2217 5018 3.827898 GCGTCTAGCTCCGCCACT 61.828 66.667 12.74 0.00 43.96 4.00
2231 5032 3.528594 CGCTAGACGTAATCTGCGT 57.471 52.632 11.03 0.00 43.73 5.24
2233 5034 1.124462 CAGCGCTAGACGTAATCTGC 58.876 55.000 10.99 0.00 46.11 4.26
2234 5035 2.112522 CACAGCGCTAGACGTAATCTG 58.887 52.381 10.99 0.00 46.11 2.90
2235 5036 1.534175 GCACAGCGCTAGACGTAATCT 60.534 52.381 10.99 0.00 46.11 2.40
2236 5037 0.847035 GCACAGCGCTAGACGTAATC 59.153 55.000 10.99 0.00 46.11 1.75
2237 5038 2.959275 GCACAGCGCTAGACGTAAT 58.041 52.632 10.99 0.00 46.11 1.89
2238 5039 4.470876 GCACAGCGCTAGACGTAA 57.529 55.556 10.99 0.00 46.11 3.18
2247 5048 0.095935 CACTCAACATAGCACAGCGC 59.904 55.000 0.00 0.00 42.91 5.92
2248 5049 1.713597 TCACTCAACATAGCACAGCG 58.286 50.000 0.00 0.00 0.00 5.18
2249 5050 5.352569 AGTTTATCACTCAACATAGCACAGC 59.647 40.000 0.00 0.00 0.00 4.40
2250 5051 6.974932 AGTTTATCACTCAACATAGCACAG 57.025 37.500 0.00 0.00 0.00 3.66
2251 5052 7.161404 AGAAGTTTATCACTCAACATAGCACA 58.839 34.615 0.00 0.00 32.94 4.57
2252 5053 7.602517 AGAAGTTTATCACTCAACATAGCAC 57.397 36.000 0.00 0.00 32.94 4.40
2253 5054 9.317936 CATAGAAGTTTATCACTCAACATAGCA 57.682 33.333 0.00 0.00 32.94 3.49
2254 5055 9.534565 TCATAGAAGTTTATCACTCAACATAGC 57.465 33.333 0.00 0.00 32.94 2.97
2269 5070 9.578439 GCAAAGCATAGAAAATCATAGAAGTTT 57.422 29.630 0.00 0.00 0.00 2.66
2270 5071 8.742777 TGCAAAGCATAGAAAATCATAGAAGTT 58.257 29.630 0.00 0.00 31.71 2.66
2271 5072 8.284945 TGCAAAGCATAGAAAATCATAGAAGT 57.715 30.769 0.00 0.00 31.71 3.01
2302 5103 8.141909 GCCTAGAAACAACTTCCTTTGTAATTT 58.858 33.333 0.00 0.00 38.82 1.82
2303 5104 7.255836 GGCCTAGAAACAACTTCCTTTGTAATT 60.256 37.037 0.00 0.00 38.82 1.40
2304 5105 6.208797 GGCCTAGAAACAACTTCCTTTGTAAT 59.791 38.462 0.00 0.00 38.82 1.89
2305 5106 5.533528 GGCCTAGAAACAACTTCCTTTGTAA 59.466 40.000 0.00 0.00 38.82 2.41
2306 5107 5.067954 GGCCTAGAAACAACTTCCTTTGTA 58.932 41.667 0.00 0.00 38.82 2.41
2307 5108 3.889538 GGCCTAGAAACAACTTCCTTTGT 59.110 43.478 0.00 0.00 41.62 2.83
2308 5109 4.022849 CAGGCCTAGAAACAACTTCCTTTG 60.023 45.833 3.98 0.00 34.21 2.77
2309 5110 4.145052 CAGGCCTAGAAACAACTTCCTTT 58.855 43.478 3.98 0.00 34.21 3.11
2310 5111 3.498661 CCAGGCCTAGAAACAACTTCCTT 60.499 47.826 3.98 0.00 34.21 3.36
2311 5112 2.040412 CCAGGCCTAGAAACAACTTCCT 59.960 50.000 3.98 0.00 34.21 3.36
2312 5113 2.437413 CCAGGCCTAGAAACAACTTCC 58.563 52.381 3.98 0.00 34.21 3.46
2313 5114 2.437413 CCCAGGCCTAGAAACAACTTC 58.563 52.381 3.98 0.00 0.00 3.01
2314 5115 1.075536 CCCCAGGCCTAGAAACAACTT 59.924 52.381 3.98 0.00 0.00 2.66
2315 5116 0.698818 CCCCAGGCCTAGAAACAACT 59.301 55.000 3.98 0.00 0.00 3.16
2316 5117 0.965866 GCCCCAGGCCTAGAAACAAC 60.966 60.000 3.98 0.00 44.06 3.32
2317 5118 1.382629 GCCCCAGGCCTAGAAACAA 59.617 57.895 3.98 0.00 44.06 2.83
2318 5119 3.087065 GCCCCAGGCCTAGAAACA 58.913 61.111 3.98 0.00 44.06 2.83
2340 5141 3.561241 GCCTGGGGTAGCTAGGGC 61.561 72.222 14.62 10.83 39.06 5.19
2341 5142 2.849646 GGCCTGGGGTAGCTAGGG 60.850 72.222 14.62 5.82 32.15 3.53
2342 5143 2.143419 CAGGCCTGGGGTAGCTAGG 61.143 68.421 26.14 10.26 34.67 3.02
2343 5144 1.383248 ACAGGCCTGGGGTAGCTAG 60.383 63.158 35.42 7.82 34.19 3.42
2344 5145 1.382695 GACAGGCCTGGGGTAGCTA 60.383 63.158 35.42 0.00 34.19 3.32
2345 5146 2.689034 GACAGGCCTGGGGTAGCT 60.689 66.667 35.42 13.88 34.19 3.32
2346 5147 2.689034 AGACAGGCCTGGGGTAGC 60.689 66.667 35.42 16.91 34.19 3.58
2347 5148 2.066999 GGAGACAGGCCTGGGGTAG 61.067 68.421 35.42 11.04 34.19 3.18
2348 5149 2.040606 GGAGACAGGCCTGGGGTA 59.959 66.667 35.42 0.00 34.19 3.69
2360 5161 1.668101 CCTAGGACAGTGGCGGAGAC 61.668 65.000 1.05 0.00 0.00 3.36
2361 5162 1.379977 CCTAGGACAGTGGCGGAGA 60.380 63.158 1.05 0.00 0.00 3.71
2362 5163 3.082579 GCCTAGGACAGTGGCGGAG 62.083 68.421 14.75 0.00 37.11 4.63
2363 5164 3.075005 GCCTAGGACAGTGGCGGA 61.075 66.667 14.75 0.00 37.11 5.54
2366 5167 1.153549 CTTCGCCTAGGACAGTGGC 60.154 63.158 14.75 0.00 42.94 5.01
2367 5168 1.115467 ATCTTCGCCTAGGACAGTGG 58.885 55.000 14.75 0.00 0.00 4.00
2368 5169 2.969628 AATCTTCGCCTAGGACAGTG 57.030 50.000 14.75 0.00 0.00 3.66
2369 5170 4.382793 GGTTTAATCTTCGCCTAGGACAGT 60.383 45.833 14.75 0.00 0.00 3.55
2370 5171 4.120589 GGTTTAATCTTCGCCTAGGACAG 58.879 47.826 14.75 4.36 0.00 3.51
2371 5172 3.773119 AGGTTTAATCTTCGCCTAGGACA 59.227 43.478 14.75 0.00 0.00 4.02
2372 5173 4.142004 TGAGGTTTAATCTTCGCCTAGGAC 60.142 45.833 14.75 2.72 0.00 3.85
2373 5174 4.028131 TGAGGTTTAATCTTCGCCTAGGA 58.972 43.478 14.75 0.00 0.00 2.94
2374 5175 4.402056 TGAGGTTTAATCTTCGCCTAGG 57.598 45.455 3.67 3.67 0.00 3.02
2375 5176 6.049149 TGATTGAGGTTTAATCTTCGCCTAG 58.951 40.000 0.00 0.00 35.94 3.02
2376 5177 5.984725 TGATTGAGGTTTAATCTTCGCCTA 58.015 37.500 0.00 0.00 35.94 3.93
2377 5178 4.843728 TGATTGAGGTTTAATCTTCGCCT 58.156 39.130 0.00 0.00 35.94 5.52
2378 5179 5.559035 CGATGATTGAGGTTTAATCTTCGCC 60.559 44.000 17.09 0.00 45.91 5.54
2379 5180 5.435557 CGATGATTGAGGTTTAATCTTCGC 58.564 41.667 17.09 0.00 45.91 4.70
2452 5254 8.579682 AAAATAAAGATTGTTGTCAGTTCTGC 57.420 30.769 0.00 0.00 0.00 4.26
2458 5261 8.143835 ACCAAGGAAAATAAAGATTGTTGTCAG 58.856 33.333 0.00 0.00 0.00 3.51
2465 5268 6.090763 GCGGAAACCAAGGAAAATAAAGATTG 59.909 38.462 0.00 0.00 0.00 2.67
2468 5271 4.830600 AGCGGAAACCAAGGAAAATAAAGA 59.169 37.500 0.00 0.00 0.00 2.52
2473 5276 3.386402 TGAAAGCGGAAACCAAGGAAAAT 59.614 39.130 0.00 0.00 0.00 1.82
2483 5288 4.170256 TCAAAAAGTGTGAAAGCGGAAAC 58.830 39.130 0.00 0.00 0.00 2.78
2484 5289 4.442375 TCAAAAAGTGTGAAAGCGGAAA 57.558 36.364 0.00 0.00 0.00 3.13
2496 5301 9.559958 AGACGAATTAGCATTATTCAAAAAGTG 57.440 29.630 0.00 0.00 32.72 3.16
2500 5305 9.906660 ACAAAGACGAATTAGCATTATTCAAAA 57.093 25.926 0.00 0.00 32.72 2.44
2550 5360 1.136057 CCGCACCTAGAAAACGCTTTC 60.136 52.381 3.04 3.04 41.19 2.62
2554 5364 0.110373 CAACCGCACCTAGAAAACGC 60.110 55.000 0.00 0.00 0.00 4.84
2555 5365 0.110373 GCAACCGCACCTAGAAAACG 60.110 55.000 0.00 0.00 38.36 3.60
2566 5376 1.231221 AACTTTGTATCGCAACCGCA 58.769 45.000 0.00 0.00 36.72 5.69
2568 5378 4.266976 CCTACTAACTTTGTATCGCAACCG 59.733 45.833 0.00 0.00 36.72 4.44
2569 5379 4.569564 CCCTACTAACTTTGTATCGCAACC 59.430 45.833 0.00 0.00 36.72 3.77
2570 5380 4.569564 CCCCTACTAACTTTGTATCGCAAC 59.430 45.833 0.00 0.00 36.72 4.17
2572 5382 3.133362 CCCCCTACTAACTTTGTATCGCA 59.867 47.826 0.00 0.00 0.00 5.10
2573 5383 3.133542 ACCCCCTACTAACTTTGTATCGC 59.866 47.826 0.00 0.00 0.00 4.58
2585 5412 2.158564 CCATCGTACAGACCCCCTACTA 60.159 54.545 0.00 0.00 0.00 1.82
2590 5417 0.686769 AGACCATCGTACAGACCCCC 60.687 60.000 0.00 0.00 0.00 5.40
2629 5456 7.148018 ACAGTCAAAGTGTCATTTTGATGAGTT 60.148 33.333 21.92 7.01 43.90 3.01
2656 5484 2.631545 CCGGACGGAGGGAGTATTAAAT 59.368 50.000 4.40 0.00 37.50 1.40
2662 5490 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2663 5491 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2664 5492 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2665 5493 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2666 5494 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2667 5495 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2668 5496 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2669 5497 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2670 5498 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2671 5499 3.930229 TCAATGACAAGTATTTCCGGACG 59.070 43.478 1.83 0.00 0.00 4.79
2672 5500 5.873179 TTCAATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 0.00 4.79
2673 5501 6.127758 CCATTTCAATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 38.70 5.14
2674 5502 6.035843 CCATTTCAATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 38.70 5.14
2675 5503 6.851609 TCCATTTCAATGACAAGTATTTCCG 58.148 36.000 0.81 0.00 38.70 4.30
2676 5504 8.253113 ACATCCATTTCAATGACAAGTATTTCC 58.747 33.333 0.81 0.00 38.70 3.13
2680 5508 9.857656 AGATACATCCATTTCAATGACAAGTAT 57.142 29.630 0.81 4.50 38.70 2.12
2682 5510 9.334947 CTAGATACATCCATTTCAATGACAAGT 57.665 33.333 0.81 0.00 38.70 3.16
2683 5511 9.551734 TCTAGATACATCCATTTCAATGACAAG 57.448 33.333 0.81 0.00 38.70 3.16
2718 5546 9.167311 GTCAACAAAATGGATGTATCTAGAACT 57.833 33.333 0.00 0.00 0.00 3.01
2719 5547 8.116753 CGTCAACAAAATGGATGTATCTAGAAC 58.883 37.037 0.00 0.00 0.00 3.01
2720 5548 8.038351 TCGTCAACAAAATGGATGTATCTAGAA 58.962 33.333 0.00 0.00 0.00 2.10
2721 5549 7.552459 TCGTCAACAAAATGGATGTATCTAGA 58.448 34.615 0.00 0.00 0.00 2.43
2722 5550 7.492669 ACTCGTCAACAAAATGGATGTATCTAG 59.507 37.037 0.00 0.00 0.00 2.43
2723 5551 7.327975 ACTCGTCAACAAAATGGATGTATCTA 58.672 34.615 0.00 0.00 0.00 1.98
2724 5552 6.173339 ACTCGTCAACAAAATGGATGTATCT 58.827 36.000 0.00 0.00 0.00 1.98
2725 5553 6.422776 ACTCGTCAACAAAATGGATGTATC 57.577 37.500 0.00 0.00 0.00 2.24
2726 5554 7.915293 TTACTCGTCAACAAAATGGATGTAT 57.085 32.000 0.00 0.00 0.00 2.29
2727 5555 7.915293 ATTACTCGTCAACAAAATGGATGTA 57.085 32.000 0.00 0.00 0.00 2.29
2728 5556 6.817765 ATTACTCGTCAACAAAATGGATGT 57.182 33.333 0.00 0.00 0.00 3.06
2729 5557 7.482743 CAGAATTACTCGTCAACAAAATGGATG 59.517 37.037 0.00 0.00 0.00 3.51
2730 5558 7.362056 CCAGAATTACTCGTCAACAAAATGGAT 60.362 37.037 0.00 0.00 0.00 3.41
2731 5559 6.072728 CCAGAATTACTCGTCAACAAAATGGA 60.073 38.462 0.00 0.00 0.00 3.41
2732 5560 6.072728 TCCAGAATTACTCGTCAACAAAATGG 60.073 38.462 0.00 0.00 0.00 3.16
2733 5561 6.797033 GTCCAGAATTACTCGTCAACAAAATG 59.203 38.462 0.00 0.00 0.00 2.32
2734 5562 6.347402 CGTCCAGAATTACTCGTCAACAAAAT 60.347 38.462 0.00 0.00 0.00 1.82
2735 5563 5.050634 CGTCCAGAATTACTCGTCAACAAAA 60.051 40.000 0.00 0.00 0.00 2.44
2736 5564 4.446385 CGTCCAGAATTACTCGTCAACAAA 59.554 41.667 0.00 0.00 0.00 2.83
2737 5565 3.985279 CGTCCAGAATTACTCGTCAACAA 59.015 43.478 0.00 0.00 0.00 2.83
2738 5566 3.571571 CGTCCAGAATTACTCGTCAACA 58.428 45.455 0.00 0.00 0.00 3.33
2739 5567 2.921754 CCGTCCAGAATTACTCGTCAAC 59.078 50.000 0.00 0.00 0.00 3.18
2740 5568 2.821378 TCCGTCCAGAATTACTCGTCAA 59.179 45.455 0.00 0.00 0.00 3.18
2741 5569 2.422479 CTCCGTCCAGAATTACTCGTCA 59.578 50.000 0.00 0.00 0.00 4.35
2742 5570 2.223525 CCTCCGTCCAGAATTACTCGTC 60.224 54.545 0.00 0.00 0.00 4.20
2743 5571 1.749634 CCTCCGTCCAGAATTACTCGT 59.250 52.381 0.00 0.00 0.00 4.18
2744 5572 1.067212 CCCTCCGTCCAGAATTACTCG 59.933 57.143 0.00 0.00 0.00 4.18
2745 5573 2.362717 CTCCCTCCGTCCAGAATTACTC 59.637 54.545 0.00 0.00 0.00 2.59
2746 5574 2.292323 ACTCCCTCCGTCCAGAATTACT 60.292 50.000 0.00 0.00 0.00 2.24
2747 5575 2.108970 ACTCCCTCCGTCCAGAATTAC 58.891 52.381 0.00 0.00 0.00 1.89
2748 5576 2.544844 ACTCCCTCCGTCCAGAATTA 57.455 50.000 0.00 0.00 0.00 1.40
2749 5577 2.544844 TACTCCCTCCGTCCAGAATT 57.455 50.000 0.00 0.00 0.00 2.17
2750 5578 2.320781 CATACTCCCTCCGTCCAGAAT 58.679 52.381 0.00 0.00 0.00 2.40
2751 5579 1.006758 ACATACTCCCTCCGTCCAGAA 59.993 52.381 0.00 0.00 0.00 3.02
2752 5580 0.629596 ACATACTCCCTCCGTCCAGA 59.370 55.000 0.00 0.00 0.00 3.86
2753 5581 0.747255 CACATACTCCCTCCGTCCAG 59.253 60.000 0.00 0.00 0.00 3.86
2754 5582 0.333652 TCACATACTCCCTCCGTCCA 59.666 55.000 0.00 0.00 0.00 4.02
2755 5583 1.033574 CTCACATACTCCCTCCGTCC 58.966 60.000 0.00 0.00 0.00 4.79
2756 5584 1.033574 CCTCACATACTCCCTCCGTC 58.966 60.000 0.00 0.00 0.00 4.79
2757 5585 0.335361 ACCTCACATACTCCCTCCGT 59.665 55.000 0.00 0.00 0.00 4.69
2758 5586 1.033574 GACCTCACATACTCCCTCCG 58.966 60.000 0.00 0.00 0.00 4.63
2759 5587 2.160721 TGACCTCACATACTCCCTCC 57.839 55.000 0.00 0.00 0.00 4.30
2760 5588 3.571590 AGATGACCTCACATACTCCCTC 58.428 50.000 0.00 0.00 0.00 4.30
2761 5589 3.697190 AGATGACCTCACATACTCCCT 57.303 47.619 0.00 0.00 0.00 4.20
2762 5590 3.452627 ACAAGATGACCTCACATACTCCC 59.547 47.826 0.00 0.00 0.00 4.30
2763 5591 4.744795 ACAAGATGACCTCACATACTCC 57.255 45.455 0.00 0.00 0.00 3.85
2764 5592 7.168302 CGATAAACAAGATGACCTCACATACTC 59.832 40.741 0.00 0.00 0.00 2.59
2765 5593 6.980978 CGATAAACAAGATGACCTCACATACT 59.019 38.462 0.00 0.00 0.00 2.12
2766 5594 6.757010 ACGATAAACAAGATGACCTCACATAC 59.243 38.462 0.00 0.00 0.00 2.39
2800 5628 7.256475 CCTCAACACTGCTCCTAATAGGATTAT 60.256 40.741 9.80 0.00 44.81 1.28
2801 5629 6.042093 CCTCAACACTGCTCCTAATAGGATTA 59.958 42.308 9.80 1.24 44.81 1.75
2802 5630 5.163258 CCTCAACACTGCTCCTAATAGGATT 60.163 44.000 9.80 0.00 44.81 3.01
2804 5632 3.706594 CCTCAACACTGCTCCTAATAGGA 59.293 47.826 8.95 8.95 43.43 2.94
2805 5633 3.181461 CCCTCAACACTGCTCCTAATAGG 60.181 52.174 0.00 0.00 36.46 2.57
2806 5634 3.706594 TCCCTCAACACTGCTCCTAATAG 59.293 47.826 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.