Multiple sequence alignment - TraesCS7A01G178300

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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 TraesCS7A01G178300 chr7A 100.000 2639 0 0 1 2639 131938231 131935593 0.000000e+00 4874.0
1 TraesCS7A01G178300 chr7A 90.286 175 16 1 2095 2269 115807514 115807687 7.350000e-56 228.0
2 TraesCS7A01G178300 chr7A 92.727 55 2 2 1 54 602020371 602020318 7.830000e-11 78.7
3 TraesCS7A01G178300 chr7B 94.295 1788 62 14 38 1808 94631669 94629905 0.000000e+00 2700.0
4 TraesCS7A01G178300 chr7B 89.224 232 23 1 2409 2638 94629808 94629577 3.320000e-74 289.0
5 TraesCS7A01G178300 chr7D 95.045 1675 45 16 209 1866 133328444 133326791 0.000000e+00 2599.0
6 TraesCS7A01G178300 chr7D 90.171 234 20 2 2409 2639 133323889 133323656 4.270000e-78 302.0
7 TraesCS7A01G178300 chr7D 83.465 254 28 5 1863 2115 133326549 133326309 9.510000e-55 224.0
8 TraesCS7A01G178300 chr7D 97.826 46 0 1 1 45 473622852 473622897 7.830000e-11 78.7
9 TraesCS7A01G178300 chr7D 94.118 51 2 1 1 51 25492787 25492738 2.820000e-10 76.8
10 TraesCS7A01G178300 chr2D 90.409 709 61 7 937 1640 30980131 30979425 0.000000e+00 926.0
11 TraesCS7A01G178300 chr2D 87.377 713 64 11 937 1640 30935633 30934938 0.000000e+00 795.0
12 TraesCS7A01G178300 chr2D 90.286 175 17 0 2102 2276 309971586 309971412 2.040000e-56 230.0
13 TraesCS7A01G178300 chr2D 97.826 46 0 1 1 46 226926231 226926187 7.830000e-11 78.7
14 TraesCS7A01G178300 chr2D 95.833 48 1 1 1 48 474745233 474745279 2.820000e-10 76.8
15 TraesCS7A01G178300 chr2B 90.254 708 60 7 937 1639 51228693 51229396 0.000000e+00 917.0
16 TraesCS7A01G178300 chr2B 89.444 180 17 2 2096 2275 514027851 514028028 2.640000e-55 226.0
17 TraesCS7A01G178300 chr2A 89.888 712 62 9 937 1640 33271086 33270377 0.000000e+00 907.0
18 TraesCS7A01G178300 chr5A 92.262 168 13 0 2102 2269 456897905 456897738 3.390000e-59 239.0
19 TraesCS7A01G178300 chr3B 91.011 178 15 1 2096 2272 139194441 139194264 3.390000e-59 239.0
20 TraesCS7A01G178300 chr1D 89.503 181 17 2 2100 2279 393753279 393753458 7.350000e-56 228.0
21 TraesCS7A01G178300 chr1D 96.078 51 0 2 1 49 448103174 448103124 6.050000e-12 82.4
22 TraesCS7A01G178300 chr3D 89.385 179 19 0 2093 2271 185002595 185002773 2.640000e-55 226.0
23 TraesCS7A01G178300 chr3D 88.649 185 18 2 2099 2283 522773206 522773387 3.420000e-54 222.0
24 TraesCS7A01G178300 chr3D 100.000 43 0 0 1 43 48422632 48422674 2.180000e-11 80.5
25 TraesCS7A01G178300 chr4D 87.766 188 21 2 2104 2291 46028702 46028517 4.420000e-53 219.0
26 TraesCS7A01G178300 chr4B 97.826 46 1 0 1 46 14840396 14840351 2.180000e-11 80.5
27 TraesCS7A01G178300 chr6A 95.745 47 2 0 1 47 362119226 362119272 2.820000e-10 76.8


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 TraesCS7A01G178300 chr7A 131935593 131938231 2638 True 4874.000000 4874 100.000000 1 2639 1 chr7A.!!$R1 2638
1 TraesCS7A01G178300 chr7B 94629577 94631669 2092 True 1494.500000 2700 91.759500 38 2638 2 chr7B.!!$R1 2600
2 TraesCS7A01G178300 chr7D 133323656 133328444 4788 True 1041.666667 2599 89.560333 209 2639 3 chr7D.!!$R2 2430
3 TraesCS7A01G178300 chr2D 30979425 30980131 706 True 926.000000 926 90.409000 937 1640 1 chr2D.!!$R2 703
4 TraesCS7A01G178300 chr2D 30934938 30935633 695 True 795.000000 795 87.377000 937 1640 1 chr2D.!!$R1 703
5 TraesCS7A01G178300 chr2B 51228693 51229396 703 False 917.000000 917 90.254000 937 1639 1 chr2B.!!$F1 702
6 TraesCS7A01G178300 chr2A 33270377 33271086 709 True 907.000000 907 89.888000 937 1640 1 chr2A.!!$R1 703


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
453 459 0.173935 ATTTCACATGCATGGCCACG 59.826 50.0 29.41 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 5023 0.172803 ACGCGAGTGGGAGTATCAAC 59.827 55.0 15.93 0.0 46.97 3.18 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
20 21 3.650070 TCCAAATTAACGTGCATTGCA 57.350 38.095 7.38 7.38 35.60 4.08
31 32 2.328655 TGCATTGCACGTACACATTG 57.671 45.000 7.38 0.00 31.71 2.82
32 33 1.876156 TGCATTGCACGTACACATTGA 59.124 42.857 7.38 0.00 31.71 2.57
33 34 2.241722 GCATTGCACGTACACATTGAC 58.758 47.619 3.15 1.49 0.00 3.18
34 35 2.095768 GCATTGCACGTACACATTGACT 60.096 45.455 3.15 0.00 0.00 3.41
35 36 3.124466 GCATTGCACGTACACATTGACTA 59.876 43.478 3.15 0.00 0.00 2.59
36 37 4.724885 GCATTGCACGTACACATTGACTAG 60.725 45.833 3.15 0.00 0.00 2.57
91 94 8.336801 TGAAAGAGAAAAACTAATAAGAGCCC 57.663 34.615 0.00 0.00 0.00 5.19
111 114 4.141287 CCCAGAAATGCCCGACATATTAA 58.859 43.478 0.00 0.00 38.34 1.40
112 115 4.766891 CCCAGAAATGCCCGACATATTAAT 59.233 41.667 0.00 0.00 38.34 1.40
114 117 6.603201 CCCAGAAATGCCCGACATATTAATAT 59.397 38.462 1.91 1.91 38.34 1.28
115 118 7.773224 CCCAGAAATGCCCGACATATTAATATA 59.227 37.037 7.65 0.00 38.34 0.86
116 119 9.342308 CCAGAAATGCCCGACATATTAATATAT 57.658 33.333 7.65 0.00 38.34 0.86
142 145 9.930158 TTATAAAGGCCCACTCTATTTTACATT 57.070 29.630 0.00 0.00 0.00 2.71
183 188 6.520792 GTCTAGAGACGCTTTTGTTTTACA 57.479 37.500 0.00 0.00 35.12 2.41
187 192 4.873827 AGAGACGCTTTTGTTTTACACAGA 59.126 37.500 0.00 0.00 36.48 3.41
190 195 4.905269 ACGCTTTTGTTTTACACAGAGTC 58.095 39.130 0.00 0.00 36.48 3.36
198 203 6.436261 TTGTTTTACACAGAGTCTAGAGACG 58.564 40.000 4.07 0.00 42.47 4.18
303 308 1.021390 CCGTTGCATCCAGACAGGTC 61.021 60.000 0.00 0.00 39.02 3.85
391 396 5.478332 ACATATCACTCTCGGAATATGCTGA 59.522 40.000 6.56 0.00 0.00 4.26
411 416 3.189080 TGAGCATGAACCACAAAATCTCG 59.811 43.478 0.00 0.00 0.00 4.04
425 430 3.444703 AATCTCGAAGATCTTGGACCG 57.555 47.619 14.00 10.28 32.89 4.79
446 452 3.611986 CGGCGTTAAAATTTCACATGCAT 59.388 39.130 0.00 0.00 0.00 3.96
447 453 4.490639 CGGCGTTAAAATTTCACATGCATG 60.491 41.667 25.09 25.09 0.00 4.06
448 454 4.201705 GGCGTTAAAATTTCACATGCATGG 60.202 41.667 29.41 18.30 0.00 3.66
449 455 4.724602 GCGTTAAAATTTCACATGCATGGC 60.725 41.667 29.41 14.62 0.00 4.40
450 456 4.201705 CGTTAAAATTTCACATGCATGGCC 60.202 41.667 29.41 0.00 0.00 5.36
451 457 3.420300 AAAATTTCACATGCATGGCCA 57.580 38.095 29.41 8.56 0.00 5.36
452 458 2.389962 AATTTCACATGCATGGCCAC 57.610 45.000 29.41 0.00 0.00 5.01
453 459 0.173935 ATTTCACATGCATGGCCACG 59.826 50.000 29.41 0.00 0.00 4.94
454 460 2.489539 TTTCACATGCATGGCCACGC 62.490 55.000 29.41 18.86 0.00 5.34
455 461 3.750155 CACATGCATGGCCACGCA 61.750 61.111 30.82 30.82 43.45 5.24
456 462 3.751246 ACATGCATGGCCACGCAC 61.751 61.111 31.34 9.03 41.79 5.34
457 463 4.501714 CATGCATGGCCACGCACC 62.502 66.667 31.34 5.79 41.79 5.01
482 488 3.340034 ACCCGATATCTCGTTTTGCAAA 58.660 40.909 8.05 8.05 43.49 3.68
669 679 2.569059 CTGCATGAGACAATGGGTAGG 58.431 52.381 0.00 0.00 0.00 3.18
674 684 1.548719 TGAGACAATGGGTAGGTCACG 59.451 52.381 0.00 0.00 34.04 4.35
773 783 4.078980 AGCTTTCCCTATTTCATGGACCAT 60.079 41.667 0.00 0.00 0.00 3.55
867 877 0.175760 GCATGTGAACCCTAGCTCGA 59.824 55.000 0.00 0.00 0.00 4.04
1468 1494 3.629883 TACCAGTACAACGGCGGCG 62.630 63.158 31.06 31.06 0.00 6.46
1643 1669 2.709475 CGGCAGCGGCTAATTGAC 59.291 61.111 9.17 0.00 40.87 3.18
1748 1781 4.142687 CGAGTCTGTTCCAAGTTGTGTTTT 60.143 41.667 1.45 0.00 0.00 2.43
1822 1855 2.249309 AGAAGGTTGTACCCTCGGAT 57.751 50.000 0.00 0.00 39.75 4.18
1848 1881 4.801330 TCTCGATTGATGTACACAACCT 57.199 40.909 0.00 0.00 0.00 3.50
1852 1885 6.147164 TCTCGATTGATGTACACAACCTTTTC 59.853 38.462 0.00 0.00 0.00 2.29
1857 1890 6.951062 TGATGTACACAACCTTTTCATTGA 57.049 33.333 0.00 0.00 0.00 2.57
1904 2182 0.465460 ACATGGCCACACGAACAAGT 60.465 50.000 8.16 0.00 0.00 3.16
1917 2195 8.592998 CCACACGAACAAGTTATAGAGATTTAC 58.407 37.037 0.00 0.00 0.00 2.01
1968 2246 8.121086 CCTATTGCTATGCTATCATTCAAATCG 58.879 37.037 0.00 0.00 34.22 3.34
1971 2249 5.409520 TGCTATGCTATCATTCAAATCGGTC 59.590 40.000 0.00 0.00 34.22 4.79
1990 2268 2.801679 GTCGAATAAAACCCGTGTGACA 59.198 45.455 0.00 0.00 0.00 3.58
1991 2269 3.061322 TCGAATAAAACCCGTGTGACAG 58.939 45.455 0.00 0.00 0.00 3.51
1994 2272 2.243602 TAAAACCCGTGTGACAGTCC 57.756 50.000 0.00 0.00 0.00 3.85
2001 2279 1.002659 CCGTGTGACAGTCCCCAAATA 59.997 52.381 0.00 0.00 0.00 1.40
2003 2281 2.289444 CGTGTGACAGTCCCCAAATAGT 60.289 50.000 0.00 0.00 0.00 2.12
2004 2282 3.751518 GTGTGACAGTCCCCAAATAGTT 58.248 45.455 0.00 0.00 0.00 2.24
2005 2283 3.502211 GTGTGACAGTCCCCAAATAGTTG 59.498 47.826 0.00 0.00 34.25 3.16
2007 2285 2.107378 TGACAGTCCCCAAATAGTTGCA 59.893 45.455 0.00 0.00 33.01 4.08
2008 2286 3.245229 TGACAGTCCCCAAATAGTTGCAT 60.245 43.478 0.00 0.00 33.01 3.96
2009 2287 3.356290 ACAGTCCCCAAATAGTTGCATC 58.644 45.455 0.00 0.00 33.01 3.91
2010 2288 3.010584 ACAGTCCCCAAATAGTTGCATCT 59.989 43.478 2.28 2.28 33.01 2.90
2011 2289 4.227300 ACAGTCCCCAAATAGTTGCATCTA 59.773 41.667 6.95 6.95 33.01 1.98
2012 2290 4.818546 CAGTCCCCAAATAGTTGCATCTAG 59.181 45.833 10.16 0.00 33.01 2.43
2013 2291 4.721776 AGTCCCCAAATAGTTGCATCTAGA 59.278 41.667 10.16 0.00 33.01 2.43
2014 2292 5.059833 GTCCCCAAATAGTTGCATCTAGAG 58.940 45.833 10.16 3.20 33.01 2.43
2015 2293 4.721776 TCCCCAAATAGTTGCATCTAGAGT 59.278 41.667 10.16 0.00 33.01 3.24
2016 2294 5.059833 CCCCAAATAGTTGCATCTAGAGTC 58.940 45.833 10.16 0.00 33.01 3.36
2017 2295 5.163258 CCCCAAATAGTTGCATCTAGAGTCT 60.163 44.000 10.16 0.00 33.01 3.24
2033 2311 8.570068 TCTAGAGTCTAGAAGAAAAGAACTCC 57.430 38.462 24.66 0.00 0.00 3.85
2057 2335 3.000727 AGCATCCACACGCTAAAGTAAC 58.999 45.455 0.00 0.00 36.50 2.50
2061 2339 1.723003 CCACACGCTAAAGTAACGACC 59.277 52.381 0.00 0.00 0.00 4.79
2062 2340 2.396601 CACACGCTAAAGTAACGACCA 58.603 47.619 0.00 0.00 0.00 4.02
2064 2342 2.223782 ACACGCTAAAGTAACGACCACA 60.224 45.455 0.00 0.00 0.00 4.17
2068 2346 2.154389 GCTAAAGTAACGACCACACACG 59.846 50.000 0.00 0.00 0.00 4.49
2070 2348 3.435105 AAAGTAACGACCACACACGTA 57.565 42.857 0.00 0.00 41.87 3.57
2071 2349 3.648339 AAGTAACGACCACACACGTAT 57.352 42.857 0.00 0.00 41.87 3.06
2075 2353 4.637534 AGTAACGACCACACACGTATCTAT 59.362 41.667 0.00 0.00 41.87 1.98
2076 2354 5.817296 AGTAACGACCACACACGTATCTATA 59.183 40.000 0.00 0.00 41.87 1.31
2077 2355 5.762825 AACGACCACACACGTATCTATAT 57.237 39.130 0.00 0.00 41.87 0.86
2078 2356 5.762825 ACGACCACACACGTATCTATATT 57.237 39.130 0.00 0.00 40.92 1.28
2081 2359 5.209818 ACCACACACGTATCTATATTGGG 57.790 43.478 0.00 0.00 0.00 4.12
2082 2360 4.652421 ACCACACACGTATCTATATTGGGT 59.348 41.667 0.00 0.00 0.00 4.51
2155 2433 9.396022 TCTTTCTAGAAATTTCAACAAGTGACT 57.604 29.630 18.02 0.00 35.39 3.41
2158 2436 9.607988 TTCTAGAAATTTCAACAAGTGACTACA 57.392 29.630 19.99 0.00 35.39 2.74
2159 2437 9.778741 TCTAGAAATTTCAACAAGTGACTACAT 57.221 29.630 19.99 0.00 35.39 2.29
2160 2438 9.817365 CTAGAAATTTCAACAAGTGACTACATG 57.183 33.333 19.99 0.00 35.39 3.21
2161 2439 7.141363 AGAAATTTCAACAAGTGACTACATGC 58.859 34.615 19.99 0.00 35.39 4.06
2162 2440 6.389830 AATTTCAACAAGTGACTACATGCA 57.610 33.333 0.00 0.00 35.39 3.96
2163 2441 5.422666 TTTCAACAAGTGACTACATGCAG 57.577 39.130 0.00 0.00 35.39 4.41
2164 2442 4.335400 TCAACAAGTGACTACATGCAGA 57.665 40.909 0.00 0.00 0.00 4.26
2165 2443 4.309933 TCAACAAGTGACTACATGCAGAG 58.690 43.478 0.00 0.00 0.00 3.35
2166 2444 2.693069 ACAAGTGACTACATGCAGAGC 58.307 47.619 0.00 0.00 0.00 4.09
2167 2445 2.037641 ACAAGTGACTACATGCAGAGCA 59.962 45.455 0.00 0.00 44.86 4.26
2168 2446 3.069289 CAAGTGACTACATGCAGAGCAA 58.931 45.455 0.00 0.00 43.62 3.91
2169 2447 3.407424 AGTGACTACATGCAGAGCAAA 57.593 42.857 0.00 0.00 43.62 3.68
2170 2448 3.743521 AGTGACTACATGCAGAGCAAAA 58.256 40.909 0.00 0.00 43.62 2.44
2171 2449 4.330250 AGTGACTACATGCAGAGCAAAAT 58.670 39.130 0.00 0.00 43.62 1.82
2172 2450 4.155462 AGTGACTACATGCAGAGCAAAATG 59.845 41.667 0.00 0.00 43.62 2.32
2173 2451 4.154737 GTGACTACATGCAGAGCAAAATGA 59.845 41.667 0.00 0.00 43.62 2.57
2174 2452 4.393990 TGACTACATGCAGAGCAAAATGAG 59.606 41.667 0.00 0.00 43.62 2.90
2175 2453 4.330250 ACTACATGCAGAGCAAAATGAGT 58.670 39.130 0.00 0.00 43.62 3.41
2176 2454 3.570926 ACATGCAGAGCAAAATGAGTG 57.429 42.857 0.00 0.00 43.62 3.51
2177 2455 3.151554 ACATGCAGAGCAAAATGAGTGA 58.848 40.909 0.00 0.00 43.62 3.41
2178 2456 3.570975 ACATGCAGAGCAAAATGAGTGAA 59.429 39.130 0.00 0.00 43.62 3.18
2179 2457 4.219944 ACATGCAGAGCAAAATGAGTGAAT 59.780 37.500 0.00 0.00 43.62 2.57
2180 2458 4.430137 TGCAGAGCAAAATGAGTGAATC 57.570 40.909 0.00 0.00 34.76 2.52
2181 2459 3.120095 TGCAGAGCAAAATGAGTGAATCG 60.120 43.478 0.00 0.00 34.76 3.34
2182 2460 3.125829 GCAGAGCAAAATGAGTGAATCGA 59.874 43.478 0.00 0.00 0.00 3.59
2183 2461 4.645956 CAGAGCAAAATGAGTGAATCGAC 58.354 43.478 0.00 0.00 0.00 4.20
2184 2462 4.152938 CAGAGCAAAATGAGTGAATCGACA 59.847 41.667 0.00 0.00 0.00 4.35
2185 2463 4.153117 AGAGCAAAATGAGTGAATCGACAC 59.847 41.667 0.00 0.00 40.60 3.67
2186 2464 3.189287 AGCAAAATGAGTGAATCGACACC 59.811 43.478 2.76 0.00 41.12 4.16
2187 2465 3.670627 GCAAAATGAGTGAATCGACACCC 60.671 47.826 2.76 0.00 41.12 4.61
2188 2466 3.703001 AAATGAGTGAATCGACACCCT 57.297 42.857 2.76 0.00 41.12 4.34
2189 2467 4.819105 AAATGAGTGAATCGACACCCTA 57.181 40.909 2.76 0.00 41.12 3.53
2190 2468 4.819105 AATGAGTGAATCGACACCCTAA 57.181 40.909 2.76 0.00 41.12 2.69
2191 2469 4.819105 ATGAGTGAATCGACACCCTAAA 57.181 40.909 2.76 0.00 41.12 1.85
2192 2470 4.610605 TGAGTGAATCGACACCCTAAAA 57.389 40.909 2.76 0.00 41.12 1.52
2193 2471 5.160607 TGAGTGAATCGACACCCTAAAAT 57.839 39.130 2.76 0.00 41.12 1.82
2194 2472 6.288941 TGAGTGAATCGACACCCTAAAATA 57.711 37.500 2.76 0.00 41.12 1.40
2195 2473 6.884832 TGAGTGAATCGACACCCTAAAATAT 58.115 36.000 2.76 0.00 41.12 1.28
2196 2474 6.761242 TGAGTGAATCGACACCCTAAAATATG 59.239 38.462 2.76 0.00 41.12 1.78
2197 2475 6.650120 AGTGAATCGACACCCTAAAATATGT 58.350 36.000 2.76 0.00 41.12 2.29
2198 2476 7.788026 AGTGAATCGACACCCTAAAATATGTA 58.212 34.615 2.76 0.00 41.12 2.29
2199 2477 8.429641 AGTGAATCGACACCCTAAAATATGTAT 58.570 33.333 2.76 0.00 41.12 2.29
2200 2478 9.701098 GTGAATCGACACCCTAAAATATGTATA 57.299 33.333 0.00 0.00 35.07 1.47
2267 2545 9.449719 AGACAAATATTTAGAAACGGATGAAGT 57.550 29.630 0.00 0.00 0.00 3.01
2305 2583 8.190122 TCCATATTAATTGCAGTTGCTTTAGTG 58.810 33.333 4.47 4.89 42.66 2.74
2306 2584 7.436080 CCATATTAATTGCAGTTGCTTTAGTGG 59.564 37.037 4.47 8.81 42.66 4.00
2308 2586 4.935352 AATTGCAGTTGCTTTAGTGGAA 57.065 36.364 5.62 0.00 42.66 3.53
2309 2587 3.708563 TTGCAGTTGCTTTAGTGGAAC 57.291 42.857 5.62 0.00 42.66 3.62
2311 2589 4.079980 TGCAGTTGCTTTAGTGGAACTA 57.920 40.909 5.62 0.00 44.68 2.24
2313 2591 4.455533 TGCAGTTGCTTTAGTGGAACTATG 59.544 41.667 5.62 0.00 44.68 2.23
2314 2592 4.695455 GCAGTTGCTTTAGTGGAACTATGA 59.305 41.667 1.44 0.00 44.68 2.15
2315 2593 5.181245 GCAGTTGCTTTAGTGGAACTATGAA 59.819 40.000 1.44 0.00 44.68 2.57
2316 2594 6.127897 GCAGTTGCTTTAGTGGAACTATGAAT 60.128 38.462 1.44 0.00 44.68 2.57
2317 2595 7.575720 GCAGTTGCTTTAGTGGAACTATGAATT 60.576 37.037 1.44 0.00 44.68 2.17
2322 2600 2.475200 GTGGAACTATGAATTGCCGC 57.525 50.000 0.00 0.00 0.00 6.53
2323 2601 2.017049 GTGGAACTATGAATTGCCGCT 58.983 47.619 0.00 0.00 0.00 5.52
2326 2604 1.672881 GAACTATGAATTGCCGCTGCT 59.327 47.619 0.70 0.00 38.71 4.24
2327 2605 1.755179 ACTATGAATTGCCGCTGCTT 58.245 45.000 0.70 0.00 38.71 3.91
2328 2606 2.094675 ACTATGAATTGCCGCTGCTTT 58.905 42.857 0.70 0.00 38.71 3.51
2332 2637 2.705730 TGAATTGCCGCTGCTTTAGTA 58.294 42.857 0.70 0.00 38.71 1.82
2363 4999 6.878923 TCTCTTAAACACAACATCATTCCGAT 59.121 34.615 0.00 0.00 33.27 4.18
2369 5005 6.377327 ACACAACATCATTCCGATAATTCC 57.623 37.500 0.00 0.00 31.20 3.01
2370 5006 5.885352 ACACAACATCATTCCGATAATTCCA 59.115 36.000 0.00 0.00 31.20 3.53
2371 5007 6.376864 ACACAACATCATTCCGATAATTCCAA 59.623 34.615 0.00 0.00 31.20 3.53
2372 5008 6.914215 CACAACATCATTCCGATAATTCCAAG 59.086 38.462 0.00 0.00 31.20 3.61
2373 5009 6.603201 ACAACATCATTCCGATAATTCCAAGT 59.397 34.615 0.00 0.00 31.20 3.16
2374 5010 7.122650 ACAACATCATTCCGATAATTCCAAGTT 59.877 33.333 0.00 0.00 31.20 2.66
2375 5011 7.031226 ACATCATTCCGATAATTCCAAGTTG 57.969 36.000 0.00 0.00 31.20 3.16
2376 5012 6.603201 ACATCATTCCGATAATTCCAAGTTGT 59.397 34.615 1.45 0.00 31.20 3.32
2377 5013 6.677781 TCATTCCGATAATTCCAAGTTGTC 57.322 37.500 1.45 0.00 0.00 3.18
2378 5014 5.588648 TCATTCCGATAATTCCAAGTTGTCC 59.411 40.000 1.45 0.00 0.00 4.02
2379 5015 4.561500 TCCGATAATTCCAAGTTGTCCA 57.438 40.909 1.45 0.00 0.00 4.02
2380 5016 4.912586 TCCGATAATTCCAAGTTGTCCAA 58.087 39.130 1.45 0.00 0.00 3.53
2381 5017 4.698304 TCCGATAATTCCAAGTTGTCCAAC 59.302 41.667 1.45 1.90 41.45 3.77
2382 5018 4.457603 CCGATAATTCCAAGTTGTCCAACA 59.542 41.667 12.32 0.00 43.47 3.33
2383 5019 5.125417 CCGATAATTCCAAGTTGTCCAACAT 59.875 40.000 12.32 0.00 43.47 2.71
2384 5020 6.317642 CCGATAATTCCAAGTTGTCCAACATA 59.682 38.462 12.32 0.00 43.47 2.29
2385 5021 7.148154 CCGATAATTCCAAGTTGTCCAACATAA 60.148 37.037 12.32 2.03 43.47 1.90
2386 5022 7.910162 CGATAATTCCAAGTTGTCCAACATAAG 59.090 37.037 12.32 0.00 43.47 1.73
2387 5023 5.982890 ATTCCAAGTTGTCCAACATAAGG 57.017 39.130 12.32 8.00 43.47 2.69
2388 5024 4.447138 TCCAAGTTGTCCAACATAAGGT 57.553 40.909 12.32 0.00 43.47 3.50
2389 5025 4.798882 TCCAAGTTGTCCAACATAAGGTT 58.201 39.130 12.32 0.00 43.47 3.50
2402 5038 5.615925 ACATAAGGTTGATACTCCCACTC 57.384 43.478 0.00 0.00 0.00 3.51
2403 5039 4.099573 ACATAAGGTTGATACTCCCACTCG 59.900 45.833 0.00 0.00 0.00 4.18
2404 5040 0.824759 AGGTTGATACTCCCACTCGC 59.175 55.000 0.00 0.00 0.00 5.03
2405 5041 0.527817 GGTTGATACTCCCACTCGCG 60.528 60.000 0.00 0.00 0.00 5.87
2406 5042 0.172803 GTTGATACTCCCACTCGCGT 59.827 55.000 5.77 0.00 0.00 6.01
2407 5043 1.402968 GTTGATACTCCCACTCGCGTA 59.597 52.381 5.77 0.00 0.00 4.42
2408 5044 1.977056 TGATACTCCCACTCGCGTAT 58.023 50.000 5.77 0.00 0.00 3.06
2409 5045 1.878088 TGATACTCCCACTCGCGTATC 59.122 52.381 5.77 4.04 38.94 2.24
2410 5046 2.152830 GATACTCCCACTCGCGTATCT 58.847 52.381 5.77 0.00 36.76 1.98
2411 5047 2.048444 TACTCCCACTCGCGTATCTT 57.952 50.000 5.77 0.00 0.00 2.40
2412 5048 2.048444 ACTCCCACTCGCGTATCTTA 57.952 50.000 5.77 0.00 0.00 2.10
2413 5049 2.372264 ACTCCCACTCGCGTATCTTAA 58.628 47.619 5.77 0.00 0.00 1.85
2414 5050 2.756760 ACTCCCACTCGCGTATCTTAAA 59.243 45.455 5.77 0.00 0.00 1.52
2415 5051 3.114065 CTCCCACTCGCGTATCTTAAAC 58.886 50.000 5.77 0.00 0.00 2.01
2416 5052 2.492881 TCCCACTCGCGTATCTTAAACA 59.507 45.455 5.77 0.00 0.00 2.83
2417 5053 2.601763 CCCACTCGCGTATCTTAAACAC 59.398 50.000 5.77 0.00 0.00 3.32
2418 5054 3.247442 CCACTCGCGTATCTTAAACACA 58.753 45.455 5.77 0.00 0.00 3.72
2419 5055 3.676172 CCACTCGCGTATCTTAAACACAA 59.324 43.478 5.77 0.00 0.00 3.33
2420 5056 4.433805 CCACTCGCGTATCTTAAACACAAC 60.434 45.833 5.77 0.00 0.00 3.32
2421 5057 4.149221 CACTCGCGTATCTTAAACACAACA 59.851 41.667 5.77 0.00 0.00 3.33
2422 5058 4.927425 ACTCGCGTATCTTAAACACAACAT 59.073 37.500 5.77 0.00 0.00 2.71
2423 5059 5.061808 ACTCGCGTATCTTAAACACAACATC 59.938 40.000 5.77 0.00 0.00 3.06
2424 5060 4.924462 TCGCGTATCTTAAACACAACATCA 59.076 37.500 5.77 0.00 0.00 3.07
2425 5061 5.579119 TCGCGTATCTTAAACACAACATCAT 59.421 36.000 5.77 0.00 0.00 2.45
2426 5062 6.091577 TCGCGTATCTTAAACACAACATCATT 59.908 34.615 5.77 0.00 0.00 2.57
2427 5063 6.408039 CGCGTATCTTAAACACAACATCATTC 59.592 38.462 0.00 0.00 0.00 2.67
2428 5064 6.687105 GCGTATCTTAAACACAACATCATTCC 59.313 38.462 0.00 0.00 0.00 3.01
2429 5065 6.899771 CGTATCTTAAACACAACATCATTCCG 59.100 38.462 0.00 0.00 0.00 4.30
2430 5066 7.201487 CGTATCTTAAACACAACATCATTCCGA 60.201 37.037 0.00 0.00 0.00 4.55
2431 5067 6.236017 TCTTAAACACAACATCATTCCGAC 57.764 37.500 0.00 0.00 0.00 4.79
2432 5068 5.760743 TCTTAAACACAACATCATTCCGACA 59.239 36.000 0.00 0.00 0.00 4.35
2433 5069 4.909696 AAACACAACATCATTCCGACAA 57.090 36.364 0.00 0.00 0.00 3.18
2434 5070 5.452078 AAACACAACATCATTCCGACAAT 57.548 34.783 0.00 0.00 0.00 2.71
2435 5071 5.452078 AACACAACATCATTCCGACAATT 57.548 34.783 0.00 0.00 0.00 2.32
2436 5072 5.046910 ACACAACATCATTCCGACAATTC 57.953 39.130 0.00 0.00 0.00 2.17
2449 5085 5.505780 TCCGACAATTCCAAGTTATCCAAT 58.494 37.500 0.00 0.00 0.00 3.16
2451 5087 7.113437 TCCGACAATTCCAAGTTATCCAATAA 58.887 34.615 0.00 0.00 0.00 1.40
2456 5092 9.100197 ACAATTCCAAGTTATCCAATAAAAGGT 57.900 29.630 0.00 0.00 0.00 3.50
2469 5105 5.949354 CCAATAAAAGGTTGATACTCCCACA 59.051 40.000 0.00 0.00 0.00 4.17
2470 5106 6.607198 CCAATAAAAGGTTGATACTCCCACAT 59.393 38.462 0.00 0.00 0.00 3.21
2483 5121 5.994416 ACTCCCACATGTATTTTATCCCT 57.006 39.130 0.00 0.00 0.00 4.20
2492 5130 6.835488 ACATGTATTTTATCCCTCATGCAACT 59.165 34.615 0.00 0.00 36.96 3.16
2499 5137 8.593945 TTTTATCCCTCATGCAACTAATTTCT 57.406 30.769 0.00 0.00 0.00 2.52
2501 5139 8.908786 TTATCCCTCATGCAACTAATTTCTAG 57.091 34.615 0.00 0.00 0.00 2.43
2576 5214 1.200020 GCCATAGCAAGCACGAAAACT 59.800 47.619 0.00 0.00 39.53 2.66
2598 5236 7.093322 ACTGGCAAAGAGAAATATGTGATTC 57.907 36.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.650070 TGCAATGCACGTTAATTTGGA 57.350 38.095 2.72 0.00 31.71 3.53
12 13 1.876156 TCAATGTGTACGTGCAATGCA 59.124 42.857 8.25 2.72 35.60 3.96
13 14 2.095768 AGTCAATGTGTACGTGCAATGC 60.096 45.455 8.25 0.00 0.00 3.56
14 15 3.811722 AGTCAATGTGTACGTGCAATG 57.188 42.857 8.25 8.35 0.00 2.82
15 16 4.566004 ACTAGTCAATGTGTACGTGCAAT 58.434 39.130 8.25 1.77 0.00 3.56
16 17 3.985008 ACTAGTCAATGTGTACGTGCAA 58.015 40.909 8.25 0.00 0.00 4.08
17 18 3.653539 ACTAGTCAATGTGTACGTGCA 57.346 42.857 0.82 0.82 0.00 4.57
48 49 9.739276 TCTCTTTCAACACAATATAAACAGGAT 57.261 29.630 0.00 0.00 0.00 3.24
116 119 9.930158 AATGTAAAATAGAGTGGGCCTTTATAA 57.070 29.630 4.53 0.00 0.00 0.98
117 120 9.930158 AAATGTAAAATAGAGTGGGCCTTTATA 57.070 29.630 4.53 0.00 0.00 0.98
118 121 8.838649 AAATGTAAAATAGAGTGGGCCTTTAT 57.161 30.769 4.53 0.00 0.00 1.40
119 122 9.403583 CTAAATGTAAAATAGAGTGGGCCTTTA 57.596 33.333 4.53 0.00 0.00 1.85
120 123 8.113462 TCTAAATGTAAAATAGAGTGGGCCTTT 58.887 33.333 4.53 0.00 0.00 3.11
121 124 7.639378 TCTAAATGTAAAATAGAGTGGGCCTT 58.361 34.615 4.53 0.00 0.00 4.35
122 125 7.208064 TCTAAATGTAAAATAGAGTGGGCCT 57.792 36.000 4.53 0.00 0.00 5.19
123 126 7.875327 TTCTAAATGTAAAATAGAGTGGGCC 57.125 36.000 0.00 0.00 0.00 5.80
124 127 8.957466 AGTTTCTAAATGTAAAATAGAGTGGGC 58.043 33.333 0.00 0.00 0.00 5.36
141 144 9.688592 CTCTAGACTACCGAAAAAGTTTCTAAA 57.311 33.333 0.00 0.00 0.00 1.85
142 145 9.071276 TCTCTAGACTACCGAAAAAGTTTCTAA 57.929 33.333 0.00 0.00 0.00 2.10
183 188 2.785562 ACAAGCGTCTCTAGACTCTGT 58.214 47.619 8.41 5.86 38.98 3.41
187 192 2.159544 GCGTAACAAGCGTCTCTAGACT 60.160 50.000 8.41 0.00 42.66 3.24
198 203 0.165944 ATCTTGCACGCGTAACAAGC 59.834 50.000 33.03 24.27 40.45 4.01
277 282 3.067106 GTCTGGATGCAACGGGTATATG 58.933 50.000 0.00 0.00 0.00 1.78
303 308 3.749665 TTTGTTTCTTGCTTGGATGGG 57.250 42.857 0.00 0.00 0.00 4.00
391 396 3.411446 TCGAGATTTTGTGGTTCATGCT 58.589 40.909 0.00 0.00 0.00 3.79
411 416 0.391263 AACGCCGGTCCAAGATCTTC 60.391 55.000 4.57 0.00 0.00 2.87
425 430 4.201705 CCATGCATGTGAAATTTTAACGCC 60.202 41.667 24.58 0.00 0.00 5.68
450 456 2.638330 ATATCGGGTTCGGGTGCGTG 62.638 60.000 0.00 0.00 36.95 5.34
451 457 2.359570 GATATCGGGTTCGGGTGCGT 62.360 60.000 0.00 0.00 36.95 5.24
452 458 1.663702 GATATCGGGTTCGGGTGCG 60.664 63.158 0.00 0.00 36.95 5.34
453 459 0.319641 GAGATATCGGGTTCGGGTGC 60.320 60.000 0.00 0.00 36.95 5.01
454 460 0.039437 CGAGATATCGGGTTCGGGTG 60.039 60.000 0.73 0.00 36.95 4.61
455 461 0.466922 ACGAGATATCGGGTTCGGGT 60.467 55.000 15.07 0.00 37.38 5.28
456 462 0.672342 AACGAGATATCGGGTTCGGG 59.328 55.000 15.07 0.00 37.38 5.14
457 463 2.503920 AAACGAGATATCGGGTTCGG 57.496 50.000 15.07 0.63 37.38 4.30
458 464 2.034001 GCAAAACGAGATATCGGGTTCG 60.034 50.000 15.07 11.31 38.88 3.95
459 465 2.933906 TGCAAAACGAGATATCGGGTTC 59.066 45.455 15.07 0.00 37.45 3.62
460 466 2.980568 TGCAAAACGAGATATCGGGTT 58.019 42.857 15.07 4.94 37.45 4.11
508 518 0.321653 CCTCGGGAAGTTTGTGGAGG 60.322 60.000 0.00 0.00 35.56 4.30
669 679 3.627732 ACGATGAGATGGATACGTGAC 57.372 47.619 0.00 0.00 42.51 3.67
674 684 6.480320 AGCTGTTTTTACGATGAGATGGATAC 59.520 38.462 0.00 0.00 0.00 2.24
851 861 0.738975 CGATCGAGCTAGGGTTCACA 59.261 55.000 10.26 0.00 0.00 3.58
867 877 3.804325 CGTGAGTGATATTCTTTGGCGAT 59.196 43.478 0.00 0.00 0.00 4.58
1643 1669 2.213499 ACGAACTTTGCTGAGAACTGG 58.787 47.619 0.00 0.00 0.00 4.00
1822 1855 6.978659 GGTTGTGTACATCAATCGAGATAGAA 59.021 38.462 0.00 0.00 0.00 2.10
1882 2160 1.968704 TGTTCGTGTGGCCATGTTTA 58.031 45.000 9.72 0.00 0.00 2.01
1887 2165 2.264005 TAACTTGTTCGTGTGGCCAT 57.736 45.000 9.72 0.00 0.00 4.40
1888 2166 2.264005 ATAACTTGTTCGTGTGGCCA 57.736 45.000 0.00 0.00 0.00 5.36
1917 2195 3.508762 AGTAACGCACCAGAGATTTACG 58.491 45.455 0.00 0.00 0.00 3.18
1928 2206 4.377897 AGCAATAGGATTAGTAACGCACC 58.622 43.478 0.00 0.00 0.00 5.01
1961 2239 4.950434 GGGTTTTATTCGACCGATTTGA 57.050 40.909 0.00 0.00 36.78 2.69
1968 2246 2.158254 GTCACACGGGTTTTATTCGACC 59.842 50.000 0.00 0.00 35.14 4.79
1971 2249 2.803956 ACTGTCACACGGGTTTTATTCG 59.196 45.455 0.00 0.00 0.00 3.34
1990 2268 4.721776 TCTAGATGCAACTATTTGGGGACT 59.278 41.667 3.95 0.00 32.81 3.85
1991 2269 5.036117 TCTAGATGCAACTATTTGGGGAC 57.964 43.478 3.95 0.00 32.81 4.46
1994 2272 5.923204 AGACTCTAGATGCAACTATTTGGG 58.077 41.667 3.95 0.00 32.81 4.12
2001 2279 7.710676 TTTCTTCTAGACTCTAGATGCAACT 57.289 36.000 15.27 0.86 0.00 3.16
2003 2281 8.354711 TCTTTTCTTCTAGACTCTAGATGCAA 57.645 34.615 15.27 11.68 0.00 4.08
2004 2282 7.946381 TCTTTTCTTCTAGACTCTAGATGCA 57.054 36.000 15.27 6.86 0.00 3.96
2005 2283 8.466798 AGTTCTTTTCTTCTAGACTCTAGATGC 58.533 37.037 15.27 5.07 0.00 3.91
2007 2285 9.185680 GGAGTTCTTTTCTTCTAGACTCTAGAT 57.814 37.037 15.27 0.00 0.00 1.98
2008 2286 8.387813 AGGAGTTCTTTTCTTCTAGACTCTAGA 58.612 37.037 11.23 11.23 0.00 2.43
2009 2287 8.458843 CAGGAGTTCTTTTCTTCTAGACTCTAG 58.541 40.741 6.74 6.74 0.00 2.43
2010 2288 8.164733 TCAGGAGTTCTTTTCTTCTAGACTCTA 58.835 37.037 0.00 0.00 0.00 2.43
2011 2289 7.007723 TCAGGAGTTCTTTTCTTCTAGACTCT 58.992 38.462 0.00 0.00 0.00 3.24
2012 2290 7.222000 TCAGGAGTTCTTTTCTTCTAGACTC 57.778 40.000 0.00 0.00 0.00 3.36
2013 2291 6.295067 GCTCAGGAGTTCTTTTCTTCTAGACT 60.295 42.308 0.00 0.00 0.00 3.24
2014 2292 5.867174 GCTCAGGAGTTCTTTTCTTCTAGAC 59.133 44.000 0.00 0.00 0.00 2.59
2015 2293 5.540337 TGCTCAGGAGTTCTTTTCTTCTAGA 59.460 40.000 0.00 0.00 0.00 2.43
2016 2294 5.788450 TGCTCAGGAGTTCTTTTCTTCTAG 58.212 41.667 0.00 0.00 0.00 2.43
2017 2295 5.808366 TGCTCAGGAGTTCTTTTCTTCTA 57.192 39.130 0.00 0.00 0.00 2.10
2033 2311 1.662629 CTTTAGCGTGTGGATGCTCAG 59.337 52.381 0.00 0.00 43.77 3.35
2057 2335 4.915667 CCAATATAGATACGTGTGTGGTCG 59.084 45.833 0.00 0.00 0.00 4.79
2061 2339 6.643770 GGTTACCCAATATAGATACGTGTGTG 59.356 42.308 0.00 0.00 0.00 3.82
2062 2340 6.324512 TGGTTACCCAATATAGATACGTGTGT 59.675 38.462 0.00 0.00 37.98 3.72
2064 2342 6.982160 TGGTTACCCAATATAGATACGTGT 57.018 37.500 0.00 0.00 37.98 4.49
2068 2346 7.913789 TCCACATGGTTACCCAATATAGATAC 58.086 38.462 0.00 0.00 46.04 2.24
2070 2348 7.588866 ATCCACATGGTTACCCAATATAGAT 57.411 36.000 0.00 0.00 46.04 1.98
2071 2349 8.513139 TTATCCACATGGTTACCCAATATAGA 57.487 34.615 0.00 0.00 46.04 1.98
2129 2407 9.396022 AGTCACTTGTTGAAATTTCTAGAAAGA 57.604 29.630 21.75 15.31 35.39 2.52
2132 2410 9.607988 TGTAGTCACTTGTTGAAATTTCTAGAA 57.392 29.630 18.64 14.37 35.39 2.10
2133 2411 9.778741 ATGTAGTCACTTGTTGAAATTTCTAGA 57.221 29.630 18.64 7.52 35.39 2.43
2134 2412 9.817365 CATGTAGTCACTTGTTGAAATTTCTAG 57.183 33.333 18.64 12.38 35.39 2.43
2135 2413 8.289618 GCATGTAGTCACTTGTTGAAATTTCTA 58.710 33.333 18.64 8.95 35.39 2.10
2136 2414 7.141363 GCATGTAGTCACTTGTTGAAATTTCT 58.859 34.615 18.64 0.00 35.39 2.52
2137 2415 6.917477 TGCATGTAGTCACTTGTTGAAATTTC 59.083 34.615 11.41 11.41 35.39 2.17
2138 2416 6.804677 TGCATGTAGTCACTTGTTGAAATTT 58.195 32.000 0.00 0.00 35.39 1.82
2139 2417 6.262944 TCTGCATGTAGTCACTTGTTGAAATT 59.737 34.615 10.80 0.00 35.39 1.82
2140 2418 5.764686 TCTGCATGTAGTCACTTGTTGAAAT 59.235 36.000 10.80 0.00 35.39 2.17
2141 2419 5.122519 TCTGCATGTAGTCACTTGTTGAAA 58.877 37.500 10.80 0.00 35.39 2.69
2142 2420 4.702831 TCTGCATGTAGTCACTTGTTGAA 58.297 39.130 10.80 0.00 35.39 2.69
2143 2421 4.309933 CTCTGCATGTAGTCACTTGTTGA 58.690 43.478 10.80 0.00 33.46 3.18
2144 2422 3.120408 GCTCTGCATGTAGTCACTTGTTG 60.120 47.826 10.80 0.00 33.46 3.33
2145 2423 3.070018 GCTCTGCATGTAGTCACTTGTT 58.930 45.455 10.80 0.00 33.46 2.83
2146 2424 2.037641 TGCTCTGCATGTAGTCACTTGT 59.962 45.455 10.80 0.00 31.71 3.16
2147 2425 2.691927 TGCTCTGCATGTAGTCACTTG 58.308 47.619 10.80 0.00 31.71 3.16
2148 2426 3.407424 TTGCTCTGCATGTAGTCACTT 57.593 42.857 10.80 0.00 38.76 3.16
2149 2427 3.407424 TTTGCTCTGCATGTAGTCACT 57.593 42.857 10.80 0.00 38.76 3.41
2150 2428 4.154737 TCATTTTGCTCTGCATGTAGTCAC 59.845 41.667 10.80 2.57 38.76 3.67
2151 2429 4.325972 TCATTTTGCTCTGCATGTAGTCA 58.674 39.130 10.80 7.44 38.76 3.41
2152 2430 4.394300 ACTCATTTTGCTCTGCATGTAGTC 59.606 41.667 10.80 5.00 38.76 2.59
2153 2431 4.155462 CACTCATTTTGCTCTGCATGTAGT 59.845 41.667 10.80 0.00 38.76 2.73
2154 2432 4.393990 TCACTCATTTTGCTCTGCATGTAG 59.606 41.667 4.14 4.14 38.76 2.74
2155 2433 4.325972 TCACTCATTTTGCTCTGCATGTA 58.674 39.130 0.00 0.00 38.76 2.29
2156 2434 3.151554 TCACTCATTTTGCTCTGCATGT 58.848 40.909 0.00 0.00 38.76 3.21
2157 2435 3.842732 TCACTCATTTTGCTCTGCATG 57.157 42.857 0.00 0.00 38.76 4.06
2158 2436 4.438336 CGATTCACTCATTTTGCTCTGCAT 60.438 41.667 0.00 0.00 38.76 3.96
2159 2437 3.120095 CGATTCACTCATTTTGCTCTGCA 60.120 43.478 0.00 0.00 36.47 4.41
2160 2438 3.125829 TCGATTCACTCATTTTGCTCTGC 59.874 43.478 0.00 0.00 0.00 4.26
2161 2439 4.152938 TGTCGATTCACTCATTTTGCTCTG 59.847 41.667 0.00 0.00 0.00 3.35
2162 2440 4.153117 GTGTCGATTCACTCATTTTGCTCT 59.847 41.667 0.00 0.00 35.68 4.09
2163 2441 4.398247 GTGTCGATTCACTCATTTTGCTC 58.602 43.478 0.00 0.00 35.68 4.26
2164 2442 3.189287 GGTGTCGATTCACTCATTTTGCT 59.811 43.478 6.18 0.00 38.28 3.91
2165 2443 3.492313 GGTGTCGATTCACTCATTTTGC 58.508 45.455 6.18 0.00 38.28 3.68
2166 2444 3.753272 AGGGTGTCGATTCACTCATTTTG 59.247 43.478 8.58 0.00 40.86 2.44
2167 2445 4.021102 AGGGTGTCGATTCACTCATTTT 57.979 40.909 8.58 0.00 40.86 1.82
2168 2446 3.703001 AGGGTGTCGATTCACTCATTT 57.297 42.857 8.58 0.00 40.86 2.32
2169 2447 4.819105 TTAGGGTGTCGATTCACTCATT 57.181 40.909 8.58 0.00 40.86 2.57
2170 2448 4.819105 TTTAGGGTGTCGATTCACTCAT 57.181 40.909 8.58 0.00 40.86 2.90
2171 2449 4.610605 TTTTAGGGTGTCGATTCACTCA 57.389 40.909 8.58 0.00 40.86 3.41
2172 2450 6.761714 ACATATTTTAGGGTGTCGATTCACTC 59.238 38.462 6.18 2.26 38.92 3.51
2173 2451 6.650120 ACATATTTTAGGGTGTCGATTCACT 58.350 36.000 6.18 3.40 38.28 3.41
2174 2452 6.920569 ACATATTTTAGGGTGTCGATTCAC 57.079 37.500 0.00 0.00 37.57 3.18
2241 2519 9.449719 ACTTCATCCGTTTCTAAATATTTGTCT 57.550 29.630 11.05 0.00 0.00 3.41
2251 2529 9.582431 CATAAGAAGTACTTCATCCGTTTCTAA 57.418 33.333 31.80 7.38 41.84 2.10
2252 2530 8.963725 TCATAAGAAGTACTTCATCCGTTTCTA 58.036 33.333 31.80 8.03 41.84 2.10
2253 2531 7.837863 TCATAAGAAGTACTTCATCCGTTTCT 58.162 34.615 31.80 9.87 41.84 2.52
2254 2532 8.649973 ATCATAAGAAGTACTTCATCCGTTTC 57.350 34.615 31.80 7.74 41.84 2.78
2255 2533 7.711339 GGATCATAAGAAGTACTTCATCCGTTT 59.289 37.037 31.80 20.19 41.84 3.60
2256 2534 7.147724 TGGATCATAAGAAGTACTTCATCCGTT 60.148 37.037 31.80 20.79 39.62 4.44
2257 2535 6.323996 TGGATCATAAGAAGTACTTCATCCGT 59.676 38.462 31.80 16.05 39.62 4.69
2258 2536 6.749139 TGGATCATAAGAAGTACTTCATCCG 58.251 40.000 31.80 19.33 39.62 4.18
2272 2550 9.350357 GCAACTGCAATTAATATGGATCATAAG 57.650 33.333 0.00 0.00 41.59 1.73
2273 2551 9.081204 AGCAACTGCAATTAATATGGATCATAA 57.919 29.630 4.22 0.00 45.16 1.90
2274 2552 8.640063 AGCAACTGCAATTAATATGGATCATA 57.360 30.769 4.22 0.00 45.16 2.15
2275 2553 7.534723 AGCAACTGCAATTAATATGGATCAT 57.465 32.000 4.22 0.00 45.16 2.45
2276 2554 6.964807 AGCAACTGCAATTAATATGGATCA 57.035 33.333 4.22 0.00 45.16 2.92
2293 2571 7.575720 GCAATTCATAGTTCCACTAAAGCAACT 60.576 37.037 0.00 0.00 33.89 3.16
2295 2573 6.350110 GGCAATTCATAGTTCCACTAAAGCAA 60.350 38.462 0.00 0.00 33.89 3.91
2305 2583 1.268743 GCAGCGGCAATTCATAGTTCC 60.269 52.381 3.18 0.00 40.72 3.62
2306 2584 1.672881 AGCAGCGGCAATTCATAGTTC 59.327 47.619 12.44 0.00 44.61 3.01
2308 2586 1.755179 AAGCAGCGGCAATTCATAGT 58.245 45.000 12.44 0.00 44.61 2.12
2309 2587 2.857592 AAAGCAGCGGCAATTCATAG 57.142 45.000 12.44 0.00 44.61 2.23
2311 2589 2.094675 ACTAAAGCAGCGGCAATTCAT 58.905 42.857 12.44 0.00 44.61 2.57
2313 2591 2.678336 AGTACTAAAGCAGCGGCAATTC 59.322 45.455 12.44 0.00 44.61 2.17
2314 2592 2.711542 AGTACTAAAGCAGCGGCAATT 58.288 42.857 12.44 8.32 44.61 2.32
2315 2593 2.403252 AGTACTAAAGCAGCGGCAAT 57.597 45.000 12.44 1.25 44.61 3.56
2316 2594 2.997986 GTTAGTACTAAAGCAGCGGCAA 59.002 45.455 16.82 0.00 44.61 4.52
2317 2595 2.232941 AGTTAGTACTAAAGCAGCGGCA 59.767 45.455 16.82 0.00 36.01 5.69
2318 2596 2.858941 GAGTTAGTACTAAAGCAGCGGC 59.141 50.000 16.82 0.00 35.79 6.53
2319 2597 4.096682 AGAGAGTTAGTACTAAAGCAGCGG 59.903 45.833 16.82 0.00 33.84 5.52
2321 2599 8.862074 GTTTAAGAGAGTTAGTACTAAAGCAGC 58.138 37.037 16.82 4.65 33.84 5.25
2322 2600 9.909644 TGTTTAAGAGAGTTAGTACTAAAGCAG 57.090 33.333 16.82 0.00 33.84 4.24
2323 2601 9.688592 GTGTTTAAGAGAGTTAGTACTAAAGCA 57.311 33.333 16.82 4.77 33.84 3.91
2332 2637 9.561069 AATGATGTTGTGTTTAAGAGAGTTAGT 57.439 29.630 0.00 0.00 0.00 2.24
2363 4999 7.007723 ACCTTATGTTGGACAACTTGGAATTA 58.992 34.615 15.37 0.00 41.67 1.40
2379 5015 5.395324 CGAGTGGGAGTATCAACCTTATGTT 60.395 44.000 0.00 0.00 36.25 2.71
2380 5016 4.099573 CGAGTGGGAGTATCAACCTTATGT 59.900 45.833 0.00 0.00 36.25 2.29
2381 5017 4.621991 CGAGTGGGAGTATCAACCTTATG 58.378 47.826 0.00 0.00 36.25 1.90
2382 5018 3.069729 GCGAGTGGGAGTATCAACCTTAT 59.930 47.826 0.00 0.00 36.25 1.73
2383 5019 2.429610 GCGAGTGGGAGTATCAACCTTA 59.570 50.000 0.00 0.00 36.25 2.69
2384 5020 1.207329 GCGAGTGGGAGTATCAACCTT 59.793 52.381 0.00 0.00 36.25 3.50
2385 5021 0.824759 GCGAGTGGGAGTATCAACCT 59.175 55.000 0.00 0.00 36.25 3.50
2386 5022 0.527817 CGCGAGTGGGAGTATCAACC 60.528 60.000 0.00 0.00 36.25 3.77
2387 5023 0.172803 ACGCGAGTGGGAGTATCAAC 59.827 55.000 15.93 0.00 46.97 3.18
2388 5024 2.575108 ACGCGAGTGGGAGTATCAA 58.425 52.632 15.93 0.00 46.97 2.57
2389 5025 2.486727 AGATACGCGAGTGGGAGTATCA 60.487 50.000 15.93 0.00 46.02 2.15
2400 5036 4.896562 TGTTGTGTTTAAGATACGCGAG 57.103 40.909 15.93 0.00 0.00 5.03
2401 5037 4.924462 TGATGTTGTGTTTAAGATACGCGA 59.076 37.500 15.93 0.00 0.00 5.87
2402 5038 5.198116 TGATGTTGTGTTTAAGATACGCG 57.802 39.130 3.53 3.53 0.00 6.01
2403 5039 6.687105 GGAATGATGTTGTGTTTAAGATACGC 59.313 38.462 0.00 0.00 0.00 4.42
2404 5040 6.899771 CGGAATGATGTTGTGTTTAAGATACG 59.100 38.462 0.00 0.00 0.00 3.06
2405 5041 7.903431 GTCGGAATGATGTTGTGTTTAAGATAC 59.097 37.037 0.00 0.00 0.00 2.24
2406 5042 7.604545 TGTCGGAATGATGTTGTGTTTAAGATA 59.395 33.333 0.00 0.00 0.00 1.98
2407 5043 6.429692 TGTCGGAATGATGTTGTGTTTAAGAT 59.570 34.615 0.00 0.00 0.00 2.40
2408 5044 5.760743 TGTCGGAATGATGTTGTGTTTAAGA 59.239 36.000 0.00 0.00 0.00 2.10
2409 5045 5.996219 TGTCGGAATGATGTTGTGTTTAAG 58.004 37.500 0.00 0.00 0.00 1.85
2410 5046 6.378710 TTGTCGGAATGATGTTGTGTTTAA 57.621 33.333 0.00 0.00 0.00 1.52
2411 5047 6.567687 ATTGTCGGAATGATGTTGTGTTTA 57.432 33.333 0.00 0.00 0.00 2.01
2412 5048 4.909696 TTGTCGGAATGATGTTGTGTTT 57.090 36.364 0.00 0.00 0.00 2.83
2413 5049 5.452078 AATTGTCGGAATGATGTTGTGTT 57.548 34.783 0.00 0.00 0.00 3.32
2414 5050 4.082787 GGAATTGTCGGAATGATGTTGTGT 60.083 41.667 0.00 0.00 0.00 3.72
2415 5051 4.082841 TGGAATTGTCGGAATGATGTTGTG 60.083 41.667 0.00 0.00 0.00 3.33
2416 5052 4.078537 TGGAATTGTCGGAATGATGTTGT 58.921 39.130 0.00 0.00 0.00 3.32
2417 5053 4.700268 TGGAATTGTCGGAATGATGTTG 57.300 40.909 0.00 0.00 0.00 3.33
2418 5054 4.766891 ACTTGGAATTGTCGGAATGATGTT 59.233 37.500 0.00 0.00 0.00 2.71
2419 5055 4.335416 ACTTGGAATTGTCGGAATGATGT 58.665 39.130 0.00 0.00 0.00 3.06
2420 5056 4.970662 ACTTGGAATTGTCGGAATGATG 57.029 40.909 0.00 0.00 0.00 3.07
2421 5057 6.263168 GGATAACTTGGAATTGTCGGAATGAT 59.737 38.462 0.00 0.00 0.00 2.45
2422 5058 5.588648 GGATAACTTGGAATTGTCGGAATGA 59.411 40.000 0.00 0.00 0.00 2.57
2423 5059 5.356751 TGGATAACTTGGAATTGTCGGAATG 59.643 40.000 0.00 0.00 0.00 2.67
2424 5060 5.505780 TGGATAACTTGGAATTGTCGGAAT 58.494 37.500 0.00 0.00 0.00 3.01
2425 5061 4.912586 TGGATAACTTGGAATTGTCGGAA 58.087 39.130 0.00 0.00 0.00 4.30
2426 5062 4.561500 TGGATAACTTGGAATTGTCGGA 57.438 40.909 0.00 0.00 0.00 4.55
2427 5063 5.835113 ATTGGATAACTTGGAATTGTCGG 57.165 39.130 0.00 0.00 0.00 4.79
2428 5064 9.289303 CTTTTATTGGATAACTTGGAATTGTCG 57.711 33.333 0.00 0.00 0.00 4.35
2429 5065 9.586435 CCTTTTATTGGATAACTTGGAATTGTC 57.414 33.333 0.00 0.00 0.00 3.18
2430 5066 9.100197 ACCTTTTATTGGATAACTTGGAATTGT 57.900 29.630 0.00 0.00 0.00 2.71
2431 5067 9.942850 AACCTTTTATTGGATAACTTGGAATTG 57.057 29.630 0.00 0.00 0.00 2.32
2432 5068 9.942850 CAACCTTTTATTGGATAACTTGGAATT 57.057 29.630 0.00 0.00 0.00 2.17
2433 5069 9.320295 TCAACCTTTTATTGGATAACTTGGAAT 57.680 29.630 0.00 0.00 0.00 3.01
2434 5070 8.713708 TCAACCTTTTATTGGATAACTTGGAA 57.286 30.769 0.00 0.00 0.00 3.53
2435 5071 8.893563 ATCAACCTTTTATTGGATAACTTGGA 57.106 30.769 0.00 0.00 0.00 3.53
2449 5085 6.134535 ACATGTGGGAGTATCAACCTTTTA 57.865 37.500 0.00 0.00 36.25 1.52
2451 5087 4.657814 ACATGTGGGAGTATCAACCTTT 57.342 40.909 0.00 0.00 36.25 3.11
2456 5092 7.942341 GGGATAAAATACATGTGGGAGTATCAA 59.058 37.037 9.11 0.00 36.25 2.57
2469 5105 8.995027 TTAGTTGCATGAGGGATAAAATACAT 57.005 30.769 0.00 0.00 0.00 2.29
2470 5106 8.995027 ATTAGTTGCATGAGGGATAAAATACA 57.005 30.769 0.00 0.00 0.00 2.29
2519 5157 6.849085 TGCTTTTAATGTTCCACCACATAT 57.151 33.333 0.00 0.00 36.30 1.78
2576 5214 7.649533 ATGAATCACATATTTCTCTTTGCCA 57.350 32.000 0.00 0.00 37.46 4.92
2598 5236 9.628746 TGATGTTGTTAAGATGATGAAACAATG 57.371 29.630 3.16 0.00 42.07 2.82



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

AutoCloner maintained by Alex Coulton.