Multiple sequence alignment - TraesCS7D01G532800

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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 TraesCS7D01G532800 chr7D 100.000 2903 0 0 1 2903 626437415 626440317 0.000000e+00 5361.0
1 TraesCS7D01G532800 chr7D 83.925 1325 164 23 627 1922 626455891 626457195 0.000000e+00 1221.0
2 TraesCS7D01G532800 chr7D 82.733 1332 158 41 717 2006 626598256 626596955 0.000000e+00 1120.0
3 TraesCS7D01G532800 chr7D 88.291 316 35 2 1 314 626757304 626756989 7.590000e-101 377.0
4 TraesCS7D01G532800 chr7D 91.573 178 12 3 2012 2187 606683477 606683301 2.890000e-60 243.0
5 TraesCS7D01G532800 chr7D 87.755 196 11 4 2173 2355 578817773 578817968 1.750000e-52 217.0
6 TraesCS7D01G532800 chr7D 88.079 151 17 1 668 817 626756742 626756592 8.270000e-41 178.0
7 TraesCS7D01G532800 chr7D 80.617 227 26 7 2692 2902 561701403 561701179 2.990000e-35 159.0
8 TraesCS7D01G532800 chr7A 87.024 1734 155 45 308 2010 722018767 722020461 0.000000e+00 1892.0
9 TraesCS7D01G532800 chr7A 84.384 1364 165 30 665 2002 722127720 722129061 0.000000e+00 1295.0
10 TraesCS7D01G532800 chr7A 90.221 317 28 3 1 315 722018423 722018738 7.490000e-111 411.0
11 TraesCS7D01G532800 chr7A 79.907 214 36 6 2692 2902 646478798 646478589 1.800000e-32 150.0
12 TraesCS7D01G532800 chr7A 93.182 88 6 0 2360 2447 30061345 30061258 2.350000e-26 130.0
13 TraesCS7D01G532800 chr7A 93.750 80 5 0 2454 2533 722021366 722021445 1.410000e-23 121.0
14 TraesCS7D01G532800 chr7B 86.688 1540 134 30 418 1921 726422972 726424476 0.000000e+00 1642.0
15 TraesCS7D01G532800 chr7B 85.215 1231 142 21 811 2006 726754401 726755626 0.000000e+00 1229.0
16 TraesCS7D01G532800 chr7B 87.123 1095 112 8 920 2010 726492084 726493153 0.000000e+00 1214.0
17 TraesCS7D01G532800 chr7B 86.591 1059 125 7 966 2010 726268018 726266963 0.000000e+00 1153.0
18 TraesCS7D01G532800 chr7B 82.628 1324 164 33 717 2001 726887990 726886694 0.000000e+00 1110.0
19 TraesCS7D01G532800 chr7B 89.431 492 37 8 328 816 726610529 726611008 8.900000e-170 606.0
20 TraesCS7D01G532800 chr7B 86.755 453 38 6 897 1347 726748407 726748839 4.350000e-133 484.0
21 TraesCS7D01G532800 chr7B 94.025 318 16 2 1 315 726422322 726422639 2.020000e-131 479.0
22 TraesCS7D01G532800 chr7B 94.774 287 13 2 308 592 726297749 726298035 2.050000e-121 446.0
23 TraesCS7D01G532800 chr7B 90.536 317 28 2 1 315 726941940 726941624 4.470000e-113 418.0
24 TraesCS7D01G532800 chr7B 87.464 343 15 9 1 315 726297378 726297720 1.270000e-98 370.0
25 TraesCS7D01G532800 chr7B 83.123 397 27 17 2471 2842 726495546 726495927 2.790000e-85 326.0
26 TraesCS7D01G532800 chr7B 80.372 484 42 21 2444 2903 726303167 726303621 4.670000e-83 318.0
27 TraesCS7D01G532800 chr7B 84.950 299 41 2 2 300 726456902 726457196 1.690000e-77 300.0
28 TraesCS7D01G532800 chr7B 86.307 241 30 1 577 817 726941357 726941120 2.870000e-65 259.0
29 TraesCS7D01G532800 chr7B 93.678 174 10 1 2010 2182 743857446 743857273 2.870000e-65 259.0
30 TraesCS7D01G532800 chr7B 85.502 269 13 9 2444 2695 726266966 726266707 1.030000e-64 257.0
31 TraesCS7D01G532800 chr7B 87.963 216 21 4 589 802 726300718 726300930 1.730000e-62 250.0
32 TraesCS7D01G532800 chr7B 92.090 177 13 1 2010 2185 743916009 743915833 6.210000e-62 248.0
33 TraesCS7D01G532800 chr7B 83.051 236 33 5 2618 2848 327620023 327620256 1.050000e-49 207.0
34 TraesCS7D01G532800 chr7B 91.089 101 4 3 2436 2533 726613271 726613369 6.530000e-27 132.0
35 TraesCS7D01G532800 chr7B 90.526 95 9 0 327 421 726422683 726422777 3.040000e-25 126.0
36 TraesCS7D01G532800 chr7B 82.075 106 15 3 632 736 726752384 726752486 1.430000e-13 87.9
37 TraesCS7D01G532800 chr1D 84.000 375 35 13 2004 2355 466993799 466994171 1.290000e-88 337.0
38 TraesCS7D01G532800 chr1D 93.064 173 9 3 2011 2182 481701886 481702056 1.730000e-62 250.0
39 TraesCS7D01G532800 chr1D 83.333 168 24 4 2189 2355 404305811 404305647 5.010000e-33 152.0
40 TraesCS7D01G532800 chr3D 84.984 313 33 8 2592 2902 113818308 113818608 3.630000e-79 305.0
41 TraesCS7D01G532800 chr3D 89.691 97 9 1 2356 2452 400749702 400749607 3.930000e-24 122.0
42 TraesCS7D01G532800 chr2D 93.642 173 10 1 2011 2182 16987577 16987405 1.030000e-64 257.0
43 TraesCS7D01G532800 chr2D 86.702 188 11 5 2180 2355 628165448 628165633 2.280000e-46 196.0
44 TraesCS7D01G532800 chr2D 81.026 195 29 6 2172 2360 42732678 42732486 6.480000e-32 148.0
45 TraesCS7D01G532800 chr2D 92.473 93 6 1 2360 2452 500690044 500689953 6.530000e-27 132.0
46 TraesCS7D01G532800 chr3A 93.605 172 9 2 2012 2182 128084945 128084775 3.710000e-64 255.0
47 TraesCS7D01G532800 chr3A 80.000 315 36 15 2600 2902 47224846 47224547 1.050000e-49 207.0
48 TraesCS7D01G532800 chr3A 91.579 95 7 1 2359 2452 221948992 221948898 2.350000e-26 130.0
49 TraesCS7D01G532800 chr3A 92.308 91 7 0 2361 2451 697786521 697786431 2.350000e-26 130.0
50 TraesCS7D01G532800 chr3A 89.583 96 10 0 2354 2449 199541473 199541378 3.930000e-24 122.0
51 TraesCS7D01G532800 chr3A 80.814 172 18 7 2180 2338 253767470 253767639 1.410000e-23 121.0
52 TraesCS7D01G532800 chr2A 92.697 178 11 2 2011 2187 18463631 18463807 3.710000e-64 255.0
53 TraesCS7D01G532800 chr2A 85.644 202 15 7 2171 2359 281037486 281037686 1.760000e-47 200.0
54 TraesCS7D01G532800 chr2A 85.484 186 14 6 2182 2355 18463833 18464017 6.390000e-42 182.0
55 TraesCS7D01G532800 chr2A 92.473 93 7 0 2357 2449 695156861 695156769 1.810000e-27 134.0
56 TraesCS7D01G532800 chr2A 89.655 58 4 1 2817 2874 612689717 612689772 4.010000e-09 73.1
57 TraesCS7D01G532800 chr2B 92.529 174 11 2 2011 2182 28879362 28879189 6.210000e-62 248.0
58 TraesCS7D01G532800 chr2B 89.831 59 6 0 2816 2874 331692840 331692898 3.100000e-10 76.8
59 TraesCS7D01G532800 chr5D 91.908 173 12 2 2011 2182 512393780 512393609 1.040000e-59 241.0
60 TraesCS7D01G532800 chr5D 90.055 181 13 2 2180 2355 515033684 515033504 2.250000e-56 230.0
61 TraesCS7D01G532800 chr5D 87.437 199 9 5 2173 2355 515004267 515004069 6.300000e-52 215.0
62 TraesCS7D01G532800 chr5D 89.691 97 9 1 2354 2449 331118935 331119031 3.930000e-24 122.0
63 TraesCS7D01G532800 chr5A 91.279 172 13 2 2180 2349 608341285 608341114 1.740000e-57 233.0
64 TraesCS7D01G532800 chr5A 88.136 177 20 1 2180 2355 578220344 578220520 2.930000e-50 209.0
65 TraesCS7D01G532800 chr3B 89.894 188 7 3 2180 2356 592691817 592691631 6.260000e-57 231.0
66 TraesCS7D01G532800 chr3B 87.179 195 14 2 2172 2355 398956691 398956885 8.150000e-51 211.0
67 TraesCS7D01G532800 chr3B 86.631 187 12 6 2180 2355 592690635 592690451 8.210000e-46 195.0
68 TraesCS7D01G532800 chr3B 86.364 88 9 2 2591 2675 167058734 167058647 3.080000e-15 93.5
69 TraesCS7D01G532800 chr6A 86.631 187 13 3 2180 2355 460450607 460450422 2.280000e-46 196.0
70 TraesCS7D01G532800 chr6A 79.139 302 35 15 2592 2879 16313839 16314126 1.780000e-42 183.0
71 TraesCS7D01G532800 chr6A 88.235 102 10 2 2357 2457 563252408 563252508 1.410000e-23 121.0
72 TraesCS7D01G532800 chr6A 80.488 123 12 6 2760 2874 311620323 311620441 1.850000e-12 84.2
73 TraesCS7D01G532800 chr6A 90.566 53 5 0 2822 2874 164715848 164715796 1.440000e-08 71.3
74 TraesCS7D01G532800 chr6D 81.633 196 22 7 2173 2355 395473869 395474063 1.800000e-32 150.0
75 TraesCS7D01G532800 chrUn 92.632 95 7 0 2359 2453 77489856 77489762 1.400000e-28 137.0
76 TraesCS7D01G532800 chr4A 93.333 90 6 0 2359 2448 112585132 112585043 1.810000e-27 134.0
77 TraesCS7D01G532800 chr5B 95.122 82 4 0 2369 2450 705462707 705462626 2.350000e-26 130.0
78 TraesCS7D01G532800 chr5B 89.691 97 9 1 2356 2452 345770202 345770297 3.930000e-24 122.0
79 TraesCS7D01G532800 chr5B 82.759 145 7 9 2538 2681 527246748 527246875 2.360000e-21 113.0
80 TraesCS7D01G532800 chr6B 90.566 53 5 0 2822 2874 316292243 316292191 1.440000e-08 71.3
81 TraesCS7D01G532800 chr1B 90.566 53 5 0 2822 2874 597778736 597778684 1.440000e-08 71.3


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 TraesCS7D01G532800 chr7D 626437415 626440317 2902 False 5361.0 5361 100.000000 1 2903 1 chr7D.!!$F2 2902
1 TraesCS7D01G532800 chr7D 626455891 626457195 1304 False 1221.0 1221 83.925000 627 1922 1 chr7D.!!$F3 1295
2 TraesCS7D01G532800 chr7D 626596955 626598256 1301 True 1120.0 1120 82.733000 717 2006 1 chr7D.!!$R3 1289
3 TraesCS7D01G532800 chr7D 626756592 626757304 712 True 277.5 377 88.185000 1 817 2 chr7D.!!$R4 816
4 TraesCS7D01G532800 chr7A 722127720 722129061 1341 False 1295.0 1295 84.384000 665 2002 1 chr7A.!!$F1 1337
5 TraesCS7D01G532800 chr7A 722018423 722021445 3022 False 808.0 1892 90.331667 1 2533 3 chr7A.!!$F2 2532
6 TraesCS7D01G532800 chr7B 726886694 726887990 1296 True 1110.0 1110 82.628000 717 2001 1 chr7B.!!$R1 1284
7 TraesCS7D01G532800 chr7B 726492084 726495927 3843 False 770.0 1214 85.123000 920 2842 2 chr7B.!!$F5 1922
8 TraesCS7D01G532800 chr7B 726422322 726424476 2154 False 749.0 1642 90.413000 1 1921 3 chr7B.!!$F4 1920
9 TraesCS7D01G532800 chr7B 726266707 726268018 1311 True 705.0 1153 86.046500 966 2695 2 chr7B.!!$R4 1729
10 TraesCS7D01G532800 chr7B 726748407 726755626 7219 False 600.3 1229 84.681667 632 2006 3 chr7B.!!$F7 1374
11 TraesCS7D01G532800 chr7B 726610529 726613369 2840 False 369.0 606 90.260000 328 2533 2 chr7B.!!$F6 2205
12 TraesCS7D01G532800 chr7B 726297378 726303621 6243 False 346.0 446 87.643250 1 2903 4 chr7B.!!$F3 2902
13 TraesCS7D01G532800 chr7B 726941120 726941940 820 True 338.5 418 88.421500 1 817 2 chr7B.!!$R5 816
14 TraesCS7D01G532800 chr3B 592690451 592691817 1366 True 213.0 231 88.262500 2180 2356 2 chr3B.!!$R2 176

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
440 707 0.107459 CTGCAACTAGGAGGAAGGGC 60.107 60.0 0.0 0.0 31.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 9185 0.10741 GTACCCGGTTCATCCATGCA 60.107 55.0 0.0 0.0 35.57 3.96 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
148 179 7.967854 CACAATGCATTTCTCCGTAAATCTAAA 59.032 33.333 9.83 0.00 0.00 1.85
350 419 1.674817 CGTTACCGGAGCTTCCAACAT 60.675 52.381 9.46 0.00 35.91 2.71
440 707 0.107459 CTGCAACTAGGAGGAAGGGC 60.107 60.000 0.00 0.00 31.00 5.19
475 745 7.941919 TGAGCCCTCGTTGCTAATATATATAG 58.058 38.462 0.00 0.00 39.69 1.31
614 3594 1.278413 GGGGAGTGTCCTTACAACCTC 59.722 57.143 0.00 0.00 37.36 3.85
665 4019 3.548770 TCAGAAAGCTGATTATGCTGGG 58.451 45.455 0.00 0.00 45.88 4.45
666 4020 2.034305 CAGAAAGCTGATTATGCTGGGC 59.966 50.000 0.00 0.00 45.17 5.36
667 4021 2.026641 GAAAGCTGATTATGCTGGGCA 58.973 47.619 0.00 0.00 44.86 5.36
669 4023 0.841961 AGCTGATTATGCTGGGCAGA 59.158 50.000 0.00 0.00 43.65 4.26
1065 7405 2.600769 AGGTCTCCCAAGTCGCGT 60.601 61.111 5.77 0.00 0.00 6.01
1335 8191 2.726351 GGACTCCTTCCTCCGCCTG 61.726 68.421 0.00 0.00 41.95 4.85
1372 8228 4.954118 TCCAGGAGGCCGTGGTGT 62.954 66.667 18.21 0.00 45.84 4.16
1533 8389 2.028190 CCCTCGCGCCTGAGTATG 59.972 66.667 0.00 0.00 34.04 2.39
1712 8568 1.372683 CCCTGGTGTGTCTGGTGAG 59.627 63.158 0.00 0.00 0.00 3.51
1714 8570 1.302033 CTGGTGTGTCTGGTGAGGC 60.302 63.158 0.00 0.00 0.00 4.70
1758 8617 2.039137 AGGTCGGGGGAAGAGGAC 59.961 66.667 0.00 0.00 0.00 3.85
1760 8619 2.359967 GGTCGGGGGAAGAGGACAG 61.360 68.421 0.00 0.00 0.00 3.51
1802 8664 2.686835 GCTGGAGGAGCTGGAGGT 60.687 66.667 0.00 0.00 45.21 3.85
1812 8674 0.247736 AGCTGGAGGTGTTCATCGAC 59.752 55.000 0.00 0.00 0.00 4.20
2013 9181 8.903059 ATAGAAGAAGGAATATGTAGTAGGGG 57.097 38.462 0.00 0.00 0.00 4.79
2014 9182 6.935036 AGAAGAAGGAATATGTAGTAGGGGA 58.065 40.000 0.00 0.00 0.00 4.81
2017 9185 6.694611 AGAAGGAATATGTAGTAGGGGAAGT 58.305 40.000 0.00 0.00 0.00 3.01
2019 9187 4.593634 AGGAATATGTAGTAGGGGAAGTGC 59.406 45.833 0.00 0.00 0.00 4.40
2020 9188 4.347000 GGAATATGTAGTAGGGGAAGTGCA 59.653 45.833 0.00 0.00 0.00 4.57
2022 9190 3.845781 ATGTAGTAGGGGAAGTGCATG 57.154 47.619 0.00 0.00 0.00 4.06
2028 9196 1.002069 AGGGGAAGTGCATGGATGAA 58.998 50.000 0.00 0.00 0.00 2.57
2029 9197 1.106285 GGGGAAGTGCATGGATGAAC 58.894 55.000 0.00 0.00 36.55 3.18
2033 9201 0.680921 AAGTGCATGGATGAACCGGG 60.681 55.000 6.32 0.00 42.61 5.73
2034 9202 1.378514 GTGCATGGATGAACCGGGT 60.379 57.895 6.32 0.00 42.61 5.28
2036 9204 0.107410 TGCATGGATGAACCGGGTAC 60.107 55.000 6.32 0.00 42.61 3.34
2037 9205 0.107410 GCATGGATGAACCGGGTACA 60.107 55.000 6.32 2.78 42.61 2.90
2039 9207 2.221169 CATGGATGAACCGGGTACATG 58.779 52.381 6.32 8.95 42.61 3.21
2040 9208 1.281419 TGGATGAACCGGGTACATGT 58.719 50.000 6.32 2.69 42.61 3.21
2043 9211 2.355310 GGATGAACCGGGTACATGTGAA 60.355 50.000 9.11 0.00 0.00 3.18
2044 9212 2.172851 TGAACCGGGTACATGTGAAC 57.827 50.000 9.11 0.00 0.00 3.18
2045 9213 1.695242 TGAACCGGGTACATGTGAACT 59.305 47.619 9.11 0.00 0.00 3.01
2046 9214 2.289195 TGAACCGGGTACATGTGAACTC 60.289 50.000 9.11 0.00 0.00 3.01
2049 9217 1.275291 CCGGGTACATGTGAACTCACT 59.725 52.381 9.11 0.00 46.55 3.41
2050 9218 2.289444 CCGGGTACATGTGAACTCACTT 60.289 50.000 9.11 2.17 46.55 3.16
2051 9219 3.399330 CGGGTACATGTGAACTCACTTT 58.601 45.455 9.11 0.00 46.55 2.66
2056 9224 6.183360 GGGTACATGTGAACTCACTTTGAAAA 60.183 38.462 9.11 0.00 46.55 2.29
2058 9226 7.220108 GGTACATGTGAACTCACTTTGAAAAAC 59.780 37.037 9.11 0.00 46.55 2.43
2060 9228 6.586082 ACATGTGAACTCACTTTGAAAAACAC 59.414 34.615 10.99 0.00 46.55 3.32
2061 9229 6.078202 TGTGAACTCACTTTGAAAAACACA 57.922 33.333 10.99 0.00 46.55 3.72
2063 9231 7.151308 TGTGAACTCACTTTGAAAAACACATT 58.849 30.769 10.99 0.00 46.55 2.71
2064 9232 7.655328 TGTGAACTCACTTTGAAAAACACATTT 59.345 29.630 10.99 0.00 46.55 2.32
2065 9233 8.162245 GTGAACTCACTTTGAAAAACACATTTC 58.838 33.333 2.51 0.00 43.25 2.17
2066 9234 8.087750 TGAACTCACTTTGAAAAACACATTTCT 58.912 29.630 1.99 0.00 39.51 2.52
2068 9236 9.921637 AACTCACTTTGAAAAACACATTTCTAA 57.078 25.926 1.99 0.29 39.51 2.10
2102 9270 4.854587 AAAAAGGCGGCATGGGTA 57.145 50.000 13.08 0.00 0.00 3.69
2103 9271 3.298320 AAAAAGGCGGCATGGGTAT 57.702 47.368 13.08 0.00 0.00 2.73
2104 9272 0.823460 AAAAAGGCGGCATGGGTATG 59.177 50.000 13.08 0.00 37.36 2.39
2107 9275 0.771127 AAGGCGGCATGGGTATGTAT 59.229 50.000 13.08 0.00 36.65 2.29
2108 9276 0.771127 AGGCGGCATGGGTATGTATT 59.229 50.000 13.08 0.00 36.65 1.89
2109 9277 1.165270 GGCGGCATGGGTATGTATTC 58.835 55.000 3.07 0.00 36.65 1.75
2110 9278 1.544537 GGCGGCATGGGTATGTATTCA 60.545 52.381 3.07 0.00 36.65 2.57
2114 9282 3.820467 CGGCATGGGTATGTATTCATGTT 59.180 43.478 0.00 0.00 39.17 2.71
2115 9283 4.083324 CGGCATGGGTATGTATTCATGTTC 60.083 45.833 0.00 0.00 39.17 3.18
2118 9286 6.886459 GGCATGGGTATGTATTCATGTTCTAT 59.114 38.462 0.00 0.00 39.17 1.98
2119 9287 7.148188 GGCATGGGTATGTATTCATGTTCTATG 60.148 40.741 0.00 0.78 39.17 2.23
2122 9290 7.801104 TGGGTATGTATTCATGTTCTATGTGT 58.199 34.615 0.00 0.00 35.70 3.72
2123 9291 7.714813 TGGGTATGTATTCATGTTCTATGTGTG 59.285 37.037 0.00 0.00 35.70 3.82
2124 9292 7.715249 GGGTATGTATTCATGTTCTATGTGTGT 59.285 37.037 0.00 0.00 35.70 3.72
2125 9293 8.551205 GGTATGTATTCATGTTCTATGTGTGTG 58.449 37.037 0.00 0.00 35.70 3.82
2126 9294 6.421377 TGTATTCATGTTCTATGTGTGTGC 57.579 37.500 0.00 0.00 0.00 4.57
2128 9296 6.598850 TGTATTCATGTTCTATGTGTGTGCAT 59.401 34.615 0.00 0.00 0.00 3.96
2129 9297 7.768120 TGTATTCATGTTCTATGTGTGTGCATA 59.232 33.333 0.00 0.00 0.00 3.14
2131 9299 7.446001 TTCATGTTCTATGTGTGTGCATAAA 57.554 32.000 0.00 0.00 31.76 1.40
2132 9300 7.075674 TCATGTTCTATGTGTGTGCATAAAG 57.924 36.000 0.00 0.00 31.76 1.85
2133 9301 6.654582 TCATGTTCTATGTGTGTGCATAAAGT 59.345 34.615 0.00 0.00 31.76 2.66
2134 9302 6.875948 TGTTCTATGTGTGTGCATAAAGTT 57.124 33.333 0.00 0.00 31.76 2.66
2135 9303 7.270757 TGTTCTATGTGTGTGCATAAAGTTT 57.729 32.000 0.00 0.00 31.76 2.66
2136 9304 7.359595 TGTTCTATGTGTGTGCATAAAGTTTC 58.640 34.615 0.00 0.00 31.76 2.78
2139 9307 3.946402 TGTGTGTGCATAAAGTTTCACG 58.054 40.909 0.00 0.00 32.48 4.35
2140 9308 3.623510 TGTGTGTGCATAAAGTTTCACGA 59.376 39.130 0.00 0.00 32.48 4.35
2141 9309 4.095036 TGTGTGTGCATAAAGTTTCACGAA 59.905 37.500 0.00 0.00 32.48 3.85
2142 9310 5.031578 GTGTGTGCATAAAGTTTCACGAAA 58.968 37.500 0.00 0.00 32.48 3.46
2143 9311 5.513495 GTGTGTGCATAAAGTTTCACGAAAA 59.487 36.000 0.00 0.00 32.48 2.29
2215 9387 5.643379 TGCAGAGACAAAACAAAAAGACT 57.357 34.783 0.00 0.00 0.00 3.24
2328 9556 5.860941 TTTTTGAAAAGTGGGTGCAGATA 57.139 34.783 0.00 0.00 0.00 1.98
2356 9584 1.476891 GTTCAGATCGTGCCCACTCTA 59.523 52.381 0.00 0.00 0.00 2.43
2358 9586 1.683385 TCAGATCGTGCCCACTCTATG 59.317 52.381 0.00 0.00 0.00 2.23
2359 9587 1.410517 CAGATCGTGCCCACTCTATGT 59.589 52.381 0.00 0.00 0.00 2.29
2360 9588 2.623416 CAGATCGTGCCCACTCTATGTA 59.377 50.000 0.00 0.00 0.00 2.29
2361 9589 2.887783 AGATCGTGCCCACTCTATGTAG 59.112 50.000 0.00 0.00 0.00 2.74
2362 9590 2.139323 TCGTGCCCACTCTATGTAGT 57.861 50.000 0.00 0.00 0.00 2.73
2363 9591 3.286329 TCGTGCCCACTCTATGTAGTA 57.714 47.619 0.00 0.00 0.00 1.82
2365 9593 2.950309 CGTGCCCACTCTATGTAGTAGT 59.050 50.000 0.00 0.00 0.00 2.73
2367 9595 4.208746 GTGCCCACTCTATGTAGTAGTCT 58.791 47.826 0.00 0.00 0.00 3.24
2368 9596 4.276431 GTGCCCACTCTATGTAGTAGTCTC 59.724 50.000 0.00 0.00 0.00 3.36
2369 9597 4.166337 TGCCCACTCTATGTAGTAGTCTCT 59.834 45.833 0.00 0.00 0.00 3.10
2370 9598 5.134661 GCCCACTCTATGTAGTAGTCTCTT 58.865 45.833 0.00 0.00 0.00 2.85
2371 9599 5.595133 GCCCACTCTATGTAGTAGTCTCTTT 59.405 44.000 0.00 0.00 0.00 2.52
2373 9601 6.603997 CCCACTCTATGTAGTAGTCTCTTTGT 59.396 42.308 0.00 0.00 0.00 2.83
2374 9602 7.774157 CCCACTCTATGTAGTAGTCTCTTTGTA 59.226 40.741 0.00 0.00 0.00 2.41
2535 12746 7.841729 AGAGAAGTGGAGAGTGATAAAATAGGA 59.158 37.037 0.00 0.00 0.00 2.94
2542 12753 8.548025 TGGAGAGTGATAAAATAGGAAATGACA 58.452 33.333 0.00 0.00 0.00 3.58
2596 13226 5.048643 CGATTCTATCTGTACCGTTGGATCT 60.049 44.000 0.00 0.00 0.00 2.75
2598 13228 7.148222 CGATTCTATCTGTACCGTTGGATCTAT 60.148 40.741 0.00 0.00 0.00 1.98
2617 13264 5.745227 TCTATTCATCTTCCACCTCAAACC 58.255 41.667 0.00 0.00 0.00 3.27
2622 13306 0.107831 CTTCCACCTCAAACCCGACA 59.892 55.000 0.00 0.00 0.00 4.35
2786 13474 2.448542 GCCATCCCTCTAGGCCCA 60.449 66.667 0.00 0.00 42.58 5.36
2853 13542 3.637273 ACCGCCTCCACCCTGAAC 61.637 66.667 0.00 0.00 0.00 3.18
2883 13572 0.843309 ATAATGGGGTGATGACGGCA 59.157 50.000 0.00 0.00 0.00 5.69
2889 13578 3.134127 GTGATGACGGCAAGCCCC 61.134 66.667 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
350 419 3.438131 ACTCATGGGATCCCCTTTCTA 57.562 47.619 28.58 8.67 45.70 2.10
448 716 2.489938 ATTAGCAACGAGGGCTCAAA 57.510 45.000 3.71 0.00 42.62 2.69
475 745 9.817809 TGATACAAATATCTTACAGTTGAGTCC 57.182 33.333 0.00 0.00 38.47 3.85
575 869 3.947834 CCCCAACTTACATCCAGATTCAC 59.052 47.826 0.00 0.00 0.00 3.18
614 3594 1.233285 GCAGAGCAGGACCACAACAG 61.233 60.000 0.00 0.00 0.00 3.16
625 3605 2.223758 TGATCGAGATTCAGCAGAGCAG 60.224 50.000 0.00 0.00 0.00 4.24
1065 7405 3.801971 TACGACGACGATGGCGCA 61.802 61.111 15.32 0.00 42.48 6.09
1248 7588 3.640407 GGCAGGTCCAGCAGGTCA 61.640 66.667 8.70 0.00 35.89 4.02
1352 8208 3.322466 CCACGGCCTCCTGGAAGT 61.322 66.667 0.00 0.00 34.57 3.01
1372 8228 2.258591 GACGTCCTGCTTGAGCGA 59.741 61.111 3.51 0.00 45.83 4.93
1560 8416 2.214216 CCCGGTCACCTCAACCTCA 61.214 63.158 0.00 0.00 34.45 3.86
1690 8546 3.941188 CAGACACACCAGGGCCGT 61.941 66.667 0.00 0.00 0.00 5.68
1695 8551 1.372683 CCTCACCAGACACACCAGG 59.627 63.158 0.00 0.00 0.00 4.45
1704 8560 1.423584 TCTTGTTCTGCCTCACCAGA 58.576 50.000 0.00 0.00 39.94 3.86
1712 8568 1.770957 CGCCTTTTTCTTGTTCTGCC 58.229 50.000 0.00 0.00 0.00 4.85
1714 8570 1.770957 GGCGCCTTTTTCTTGTTCTG 58.229 50.000 22.15 0.00 0.00 3.02
1774 8636 3.160047 CTCCAGCCTCTCCGCCAT 61.160 66.667 0.00 0.00 0.00 4.40
1812 8674 4.560856 CTCCCGGCTTCGAGCTCG 62.561 72.222 30.03 30.03 41.99 5.03
2002 9170 2.439507 CCATGCACTTCCCCTACTACAT 59.560 50.000 0.00 0.00 0.00 2.29
2010 9178 1.106285 GTTCATCCATGCACTTCCCC 58.894 55.000 0.00 0.00 0.00 4.81
2011 9179 1.106285 GGTTCATCCATGCACTTCCC 58.894 55.000 0.00 0.00 35.97 3.97
2012 9180 0.734889 CGGTTCATCCATGCACTTCC 59.265 55.000 0.00 0.00 35.57 3.46
2013 9181 0.734889 CCGGTTCATCCATGCACTTC 59.265 55.000 0.00 0.00 35.57 3.01
2014 9182 0.680921 CCCGGTTCATCCATGCACTT 60.681 55.000 0.00 0.00 35.57 3.16
2017 9185 0.107410 GTACCCGGTTCATCCATGCA 60.107 55.000 0.00 0.00 35.57 3.96
2019 9187 2.221169 CATGTACCCGGTTCATCCATG 58.779 52.381 6.70 3.80 35.57 3.66
2020 9188 1.843851 ACATGTACCCGGTTCATCCAT 59.156 47.619 6.70 0.00 35.57 3.41
2022 9190 1.208535 TCACATGTACCCGGTTCATCC 59.791 52.381 6.70 0.00 0.00 3.51
2028 9196 1.001633 GTGAGTTCACATGTACCCGGT 59.998 52.381 0.00 0.00 45.75 5.28
2029 9197 1.722011 GTGAGTTCACATGTACCCGG 58.278 55.000 0.00 0.00 45.75 5.73
2039 9207 7.581011 AATGTGTTTTTCAAAGTGAGTTCAC 57.419 32.000 4.09 4.09 46.77 3.18
2040 9208 8.087750 AGAAATGTGTTTTTCAAAGTGAGTTCA 58.912 29.630 0.00 0.00 37.93 3.18
2043 9211 9.921637 TTTAGAAATGTGTTTTTCAAAGTGAGT 57.078 25.926 0.00 0.00 37.93 3.41
2046 9214 9.424659 GCATTTAGAAATGTGTTTTTCAAAGTG 57.575 29.630 14.72 0.00 45.77 3.16
2090 9258 1.165270 GAATACATACCCATGCCGCC 58.835 55.000 0.00 0.00 35.39 6.13
2091 9259 1.890876 TGAATACATACCCATGCCGC 58.109 50.000 0.00 0.00 35.39 6.53
2092 9260 3.411446 ACATGAATACATACCCATGCCG 58.589 45.455 0.00 0.00 39.81 5.69
2093 9261 5.072741 AGAACATGAATACATACCCATGCC 58.927 41.667 0.00 0.00 39.81 4.40
2095 9263 8.724229 CACATAGAACATGAATACATACCCATG 58.276 37.037 0.00 0.00 41.40 3.66
2098 9266 7.715249 ACACACATAGAACATGAATACATACCC 59.285 37.037 0.00 0.00 35.09 3.69
2100 9268 8.064222 GCACACACATAGAACATGAATACATAC 58.936 37.037 0.00 0.00 35.09 2.39
2102 9270 6.598850 TGCACACACATAGAACATGAATACAT 59.401 34.615 0.00 0.00 37.19 2.29
2103 9271 5.936956 TGCACACACATAGAACATGAATACA 59.063 36.000 0.00 0.00 0.00 2.29
2104 9272 6.421377 TGCACACACATAGAACATGAATAC 57.579 37.500 0.00 0.00 0.00 1.89
2107 9275 7.174772 ACTTTATGCACACACATAGAACATGAA 59.825 33.333 0.00 0.00 34.15 2.57
2108 9276 6.654582 ACTTTATGCACACACATAGAACATGA 59.345 34.615 0.00 0.00 34.15 3.07
2109 9277 6.845302 ACTTTATGCACACACATAGAACATG 58.155 36.000 0.00 0.00 34.15 3.21
2110 9278 7.452880 AACTTTATGCACACACATAGAACAT 57.547 32.000 0.00 0.00 34.15 2.71
2114 9282 6.347321 CGTGAAACTTTATGCACACACATAGA 60.347 38.462 0.00 0.00 31.82 1.98
2115 9283 5.790003 CGTGAAACTTTATGCACACACATAG 59.210 40.000 0.00 0.00 31.82 2.23
2118 9286 3.623510 TCGTGAAACTTTATGCACACACA 59.376 39.130 0.00 0.00 31.75 3.72
2119 9287 4.203950 TCGTGAAACTTTATGCACACAC 57.796 40.909 0.00 0.00 31.75 3.82
2194 9362 6.951256 AAAGTCTTTTTGTTTTGTCTCTGC 57.049 33.333 0.00 0.00 0.00 4.26
2233 9405 3.590857 AAATGTGTGTGCGCGGCA 61.591 55.556 8.83 3.20 35.60 5.69
2430 10179 7.124448 CCAAGATTAGTACTCCCTCTGTAAACT 59.876 40.741 0.00 0.00 0.00 2.66
2433 10182 6.500336 ACCAAGATTAGTACTCCCTCTGTAA 58.500 40.000 0.00 0.00 0.00 2.41
2437 10186 5.659079 CAGAACCAAGATTAGTACTCCCTCT 59.341 44.000 0.00 0.00 0.00 3.69
2535 12746 4.816385 ACAATTCAGTCGACTGTGTCATTT 59.184 37.500 37.21 20.91 44.12 2.32
2542 12753 5.123186 TCACAAAAACAATTCAGTCGACTGT 59.877 36.000 37.21 21.85 44.12 3.55
2596 13226 4.625324 CGGGTTTGAGGTGGAAGATGAATA 60.625 45.833 0.00 0.00 0.00 1.75
2598 13228 2.552155 CGGGTTTGAGGTGGAAGATGAA 60.552 50.000 0.00 0.00 0.00 2.57
2617 13264 2.154854 AGATGAACAGTGTGTGTCGG 57.845 50.000 0.00 0.00 39.03 4.79
2622 13306 4.346418 AGAGGAAGAAGATGAACAGTGTGT 59.654 41.667 0.00 0.00 0.00 3.72
2786 13474 4.175962 TGAGAAGAAAACTAGATGGGGGT 58.824 43.478 0.00 0.00 0.00 4.95
2842 13531 2.576191 CAATCTTAGGGTTCAGGGTGGA 59.424 50.000 0.00 0.00 0.00 4.02
2853 13542 5.582950 TCACCCCATTATCAATCTTAGGG 57.417 43.478 0.00 0.00 39.33 3.53
2883 13572 1.307430 GGAGAGAAGGGAGGGGCTT 60.307 63.158 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.