Multiple sequence alignment - TraesCS6D01G241600

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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 TraesCS6D01G241600 chr6D 100.000 8102 0 0 1 8102 343944751 343952852 0.000000e+00 14962.0
1 TraesCS6D01G241600 chr6B 95.861 4156 93 17 866 4986 519138173 519142284 0.000000e+00 6649.0
2 TraesCS6D01G241600 chr6B 93.553 1272 42 14 5980 7223 519149998 519151257 0.000000e+00 1858.0
3 TraesCS6D01G241600 chr6B 96.521 1006 21 4 4982 5981 519148972 519149969 0.000000e+00 1652.0
4 TraesCS6D01G241600 chr6B 93.388 605 34 5 1265 1868 43646680 43646081 0.000000e+00 891.0
5 TraesCS6D01G241600 chr6B 83.958 854 101 23 3 845 519135067 519135895 0.000000e+00 785.0
6 TraesCS6D01G241600 chr6B 88.745 462 32 8 7392 7838 519151435 519151891 1.540000e-151 547.0
7 TraesCS6D01G241600 chr6B 76.857 821 122 40 29 828 135116804 135117577 1.270000e-107 401.0
8 TraesCS6D01G241600 chr6B 86.738 279 16 4 7844 8102 519152078 519152355 2.860000e-74 291.0
9 TraesCS6D01G241600 chr6B 95.041 121 6 0 7254 7374 519151251 519151371 2.980000e-44 191.0
10 TraesCS6D01G241600 chr6A 89.782 4179 264 63 34 4140 484274235 484278322 0.000000e+00 5201.0
11 TraesCS6D01G241600 chr6A 95.231 1300 43 8 5980 7270 484280183 484281472 0.000000e+00 2039.0
12 TraesCS6D01G241600 chr6A 93.367 588 36 1 4249 4833 484278321 484278908 0.000000e+00 867.0
13 TraesCS6D01G241600 chr6A 93.281 506 24 6 5485 5981 484279650 484280154 0.000000e+00 737.0
14 TraesCS6D01G241600 chr6A 92.138 318 14 6 7525 7831 484311637 484311954 9.650000e-119 438.0
15 TraesCS6D01G241600 chr6A 91.176 306 26 1 5190 5495 484279327 484279631 1.630000e-111 414.0
16 TraesCS6D01G241600 chr6A 95.089 224 11 0 4964 5187 484279019 484279242 3.600000e-93 353.0
17 TraesCS6D01G241600 chr6A 96.244 213 4 2 7320 7529 484281475 484281686 6.020000e-91 346.0
18 TraesCS6D01G241600 chr6A 95.082 183 6 3 7839 8020 484314683 484314863 1.330000e-72 285.0
19 TraesCS6D01G241600 chr6A 95.312 64 3 0 4835 4898 484278934 484278997 1.440000e-17 102.0
20 TraesCS6D01G241600 chr6A 100.000 34 0 0 8019 8052 484314880 484314913 6.790000e-06 63.9
21 TraesCS6D01G241600 chr6A 100.000 28 0 0 8075 8102 484314911 484314938 1.500000e-02 52.8
22 TraesCS6D01G241600 chr3B 89.943 875 50 20 5853 6693 582281553 582280683 0.000000e+00 1094.0
23 TraesCS6D01G241600 chr3B 87.571 885 46 35 5853 6693 327394290 327393426 0.000000e+00 966.0
24 TraesCS6D01G241600 chr3B 94.667 75 2 2 33 107 46784041 46784113 1.850000e-21 115.0
25 TraesCS6D01G241600 chr4B 89.444 900 44 28 5841 6693 128793080 128793975 0.000000e+00 1088.0
26 TraesCS6D01G241600 chr1B 89.234 901 45 26 5841 6693 258765436 258764540 0.000000e+00 1079.0
27 TraesCS6D01G241600 chr3D 78.213 638 92 27 40 672 602278900 602278305 1.660000e-96 364.0
28 TraesCS6D01G241600 chr3D 87.273 55 4 3 830 882 444483995 444484048 8.780000e-05 60.2
29 TraesCS6D01G241600 chr3A 90.667 75 5 2 33 107 37813993 37814065 1.860000e-16 99.0
30 TraesCS6D01G241600 chr5B 97.059 34 0 1 830 863 537531786 537531754 1.000000e-03 56.5


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 TraesCS6D01G241600 chr6D 343944751 343952852 8101 False 14962.000 14962 100.00000 1 8102 1 chr6D.!!$F1 8101
1 TraesCS6D01G241600 chr6B 519135067 519142284 7217 False 3717.000 6649 89.90950 3 4986 2 chr6B.!!$F2 4983
2 TraesCS6D01G241600 chr6B 519148972 519152355 3383 False 907.800 1858 92.11960 4982 8102 5 chr6B.!!$F3 3120
3 TraesCS6D01G241600 chr6B 43646081 43646680 599 True 891.000 891 93.38800 1265 1868 1 chr6B.!!$R1 603
4 TraesCS6D01G241600 chr6B 135116804 135117577 773 False 401.000 401 76.85700 29 828 1 chr6B.!!$F1 799
5 TraesCS6D01G241600 chr6A 484274235 484281686 7451 False 1257.375 5201 93.68525 34 7529 8 chr6A.!!$F1 7495
6 TraesCS6D01G241600 chr6A 484311637 484314938 3301 False 209.925 438 96.80500 7525 8102 4 chr6A.!!$F2 577
7 TraesCS6D01G241600 chr3B 582280683 582281553 870 True 1094.000 1094 89.94300 5853 6693 1 chr3B.!!$R2 840
8 TraesCS6D01G241600 chr3B 327393426 327394290 864 True 966.000 966 87.57100 5853 6693 1 chr3B.!!$R1 840
9 TraesCS6D01G241600 chr4B 128793080 128793975 895 False 1088.000 1088 89.44400 5841 6693 1 chr4B.!!$F1 852
10 TraesCS6D01G241600 chr1B 258764540 258765436 896 True 1079.000 1079 89.23400 5841 6693 1 chr1B.!!$R1 852
11 TraesCS6D01G241600 chr3D 602278305 602278900 595 True 364.000 364 78.21300 40 672 1 chr3D.!!$R1 632

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
611 636 0.318275 GGAATGAAAACAACGCGGCA 60.318 50.000 12.47 0.00 0.00 5.69 F
778 810 0.320160 GACCGTCCTGTAAAACCGCT 60.320 55.000 0.00 0.00 0.00 5.52 F
1934 4258 0.393537 GCACAGTAGCAGGGCATTCT 60.394 55.000 0.00 0.00 0.00 2.40 F
3289 5638 0.470833 AGTCACCAGCTCAGACCTGT 60.471 55.000 6.19 0.00 32.82 4.00 F
3929 6282 0.174389 ATCTCTCGCTGCGTTCACAT 59.826 50.000 22.48 6.22 0.00 3.21 F
4611 6969 0.750546 TTCATCATGGGAGCAGCAGC 60.751 55.000 0.00 0.00 42.56 5.25 F
5259 7726 1.069090 GCAGTTCCGGTGACTGACA 59.931 57.895 31.13 0.00 45.72 3.58 F
5476 7943 1.228459 GGTTCGAAGGGGTTTGCCT 60.228 57.895 0.00 0.00 34.45 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 4539 0.251341 AAGTGTCCCCAAGTGCCATC 60.251 55.000 0.00 0.00 0.00 3.51 R
2968 5294 1.442526 GCAAGCTGAGCATGGCGTAT 61.443 55.000 11.88 0.00 0.00 3.06 R
3436 5785 0.314935 TCCGTGTCCACCTAAACGTC 59.685 55.000 0.00 0.00 34.30 4.34 R
5242 7709 0.946221 GCTGTCAGTCACCGGAACTG 60.946 60.000 25.94 25.94 0.00 3.16 R
5602 8099 0.716108 GATGTCAGTGCTTTCCGACG 59.284 55.000 0.00 0.00 0.00 5.12 R
6108 8644 2.604174 GGACGAAACACACTGCCCG 61.604 63.158 0.00 0.00 0.00 6.13 R
6973 9529 0.110486 TTCAGCTCCAACCTTCCACC 59.890 55.000 0.00 0.00 0.00 4.61 R
7583 10223 0.957395 GCAGGCAGTGTACACATGCT 60.957 55.000 31.18 21.63 36.45 3.79 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.839121 TCAAACATAGCATACCGGAGTTT 58.161 39.130 9.46 3.05 0.00 2.66
107 109 3.118519 ACTTAAACGGGGTGCATACTAGG 60.119 47.826 0.00 0.00 0.00 3.02
253 257 1.660167 CATGCCGAGCTTCATCTTCA 58.340 50.000 0.00 0.00 0.00 3.02
289 293 2.668550 GCCTCGAACCACGCCTTT 60.669 61.111 0.00 0.00 42.26 3.11
294 298 2.248835 CGAACCACGCCTTTTCCGT 61.249 57.895 0.00 0.00 39.91 4.69
410 420 1.528824 GCCTGCTCCTTCTGCCATA 59.471 57.895 0.00 0.00 0.00 2.74
412 422 0.835941 CCTGCTCCTTCTGCCATACT 59.164 55.000 0.00 0.00 0.00 2.12
421 431 4.777896 TCCTTCTGCCATACTTTCACTAGT 59.222 41.667 0.00 0.00 0.00 2.57
521 546 3.550431 CTCCCGGATCCCGTGCAT 61.550 66.667 0.73 0.00 46.80 3.96
601 626 2.413502 CGATTTGACGCCGGAATGAAAA 60.414 45.455 5.05 0.00 0.00 2.29
611 636 0.318275 GGAATGAAAACAACGCGGCA 60.318 50.000 12.47 0.00 0.00 5.69
616 648 3.194272 AAAACAACGCGGCAGAGGC 62.194 57.895 12.47 0.00 40.13 4.70
632 664 1.070914 GAGGCGGATAGGGGAAAAGAG 59.929 57.143 0.00 0.00 0.00 2.85
661 693 1.400530 CCCTAAATCGTCCCGGAGCT 61.401 60.000 0.73 0.00 0.00 4.09
672 704 2.500098 GTCCCGGAGCTGGCATATATAA 59.500 50.000 0.73 0.00 0.00 0.98
681 713 4.225042 AGCTGGCATATATAACCGGAATCA 59.775 41.667 9.46 0.00 30.92 2.57
694 726 0.674269 GGAATCACGGGCGGTTTACA 60.674 55.000 0.00 0.00 0.00 2.41
703 735 1.302993 GCGGTTTACAGGCCTTCCA 60.303 57.895 0.00 0.00 33.74 3.53
704 736 0.679960 GCGGTTTACAGGCCTTCCAT 60.680 55.000 0.00 0.00 33.74 3.41
707 739 3.551846 CGGTTTACAGGCCTTCCATAAT 58.448 45.455 0.00 0.00 33.74 1.28
708 740 3.951680 CGGTTTACAGGCCTTCCATAATT 59.048 43.478 0.00 0.00 33.74 1.40
778 810 0.320160 GACCGTCCTGTAAAACCGCT 60.320 55.000 0.00 0.00 0.00 5.52
787 819 3.040099 CTGTAAAACCGCTGGAAAAACG 58.960 45.455 1.50 0.00 0.00 3.60
793 825 2.126850 GCTGGAAAAACGCGCCTC 60.127 61.111 5.73 0.00 0.00 4.70
795 827 1.207593 CTGGAAAAACGCGCCTCAG 59.792 57.895 5.73 1.88 0.00 3.35
796 828 1.507141 CTGGAAAAACGCGCCTCAGT 61.507 55.000 5.73 0.00 0.00 3.41
809 841 1.254026 CCTCAGTGAGGTTACACGGA 58.746 55.000 28.38 0.00 44.25 4.69
822 854 4.498345 GGTTACACGGAATCTGCTAGAGAG 60.498 50.000 0.00 0.00 32.80 3.20
829 861 3.243839 GGAATCTGCTAGAGAGGCTCTTG 60.244 52.174 19.80 12.86 41.50 3.02
830 862 2.816777 TCTGCTAGAGAGGCTCTTGA 57.183 50.000 19.80 8.75 41.50 3.02
832 864 3.023119 TCTGCTAGAGAGGCTCTTGAAG 58.977 50.000 19.80 16.28 41.50 3.02
838 870 4.972751 AGAGAGGCTCTTGAAGAACTTT 57.027 40.909 19.80 0.00 37.60 2.66
863 3135 6.014840 TCCCTAAATTATACAGTCATCCCGTC 60.015 42.308 0.00 0.00 0.00 4.79
974 3268 1.000145 CTTTTCCCGTCTAAGCTCGC 59.000 55.000 0.00 0.00 0.00 5.03
1328 3630 4.956075 AGTTTCACTTTGACAAATCCTGGT 59.044 37.500 0.05 0.00 0.00 4.00
1567 3871 5.063564 GTCGAAAATATCACCCAGAACTCAC 59.936 44.000 0.00 0.00 0.00 3.51
1578 3882 6.053005 CACCCAGAACTCACTAGTGTTTTTA 58.947 40.000 21.99 1.87 35.62 1.52
1620 3924 1.856265 GCAGAGCAGACCCAAAACGG 61.856 60.000 0.00 0.00 0.00 4.44
1678 3982 8.801882 TTATGTTTCTCCTGTTATAACCTTGG 57.198 34.615 13.01 11.89 0.00 3.61
1871 4175 3.412981 TTGTTTGATGTGAACCGTGTG 57.587 42.857 0.00 0.00 0.00 3.82
1872 4176 1.673400 TGTTTGATGTGAACCGTGTGG 59.327 47.619 0.00 0.00 42.84 4.17
1887 4191 4.503910 CCGTGTGGTTAATCTCAGATTCA 58.496 43.478 2.18 0.00 0.00 2.57
1888 4192 5.118990 CCGTGTGGTTAATCTCAGATTCAT 58.881 41.667 2.18 0.00 0.00 2.57
1889 4193 5.235186 CCGTGTGGTTAATCTCAGATTCATC 59.765 44.000 2.18 0.00 0.00 2.92
1890 4194 5.235186 CGTGTGGTTAATCTCAGATTCATCC 59.765 44.000 2.18 5.90 0.00 3.51
1931 4255 3.080641 TGCACAGTAGCAGGGCAT 58.919 55.556 0.00 0.00 40.11 4.40
1932 4256 1.379916 TGCACAGTAGCAGGGCATT 59.620 52.632 0.00 0.00 40.11 3.56
1933 4257 0.677731 TGCACAGTAGCAGGGCATTC 60.678 55.000 0.00 0.00 40.11 2.67
1934 4258 0.393537 GCACAGTAGCAGGGCATTCT 60.394 55.000 0.00 0.00 0.00 2.40
1935 4259 1.661341 CACAGTAGCAGGGCATTCTC 58.339 55.000 0.00 0.00 0.00 2.87
1936 4260 1.065926 CACAGTAGCAGGGCATTCTCA 60.066 52.381 0.00 0.00 0.00 3.27
1937 4261 1.630369 ACAGTAGCAGGGCATTCTCAA 59.370 47.619 0.00 0.00 0.00 3.02
1938 4262 2.240667 ACAGTAGCAGGGCATTCTCAAT 59.759 45.455 0.00 0.00 0.00 2.57
1939 4263 2.617308 CAGTAGCAGGGCATTCTCAATG 59.383 50.000 0.00 0.00 41.85 2.82
1940 4264 2.240667 AGTAGCAGGGCATTCTCAATGT 59.759 45.455 0.00 0.00 41.01 2.71
1941 4265 2.226962 AGCAGGGCATTCTCAATGTT 57.773 45.000 0.00 0.00 41.01 2.71
1942 4266 2.532843 AGCAGGGCATTCTCAATGTTT 58.467 42.857 0.00 0.00 41.01 2.83
1943 4267 2.232941 AGCAGGGCATTCTCAATGTTTG 59.767 45.455 0.00 0.00 41.01 2.93
1981 4306 3.056393 ACACATTGTGGCCTTCAATCATG 60.056 43.478 20.33 19.77 37.94 3.07
2017 4342 5.355350 GGAACTGTGAAGCTTTGCACTATAT 59.645 40.000 16.60 3.94 36.05 0.86
2099 4424 0.549950 ACCATCATAAGGCTGCTGCT 59.450 50.000 15.64 0.00 39.59 4.24
2113 4438 2.090760 TGCTGCTGAAAGTTGTGTGAA 58.909 42.857 0.00 0.00 35.30 3.18
2214 4539 2.597455 ACCATGTTTTCAGTTGGGAGG 58.403 47.619 0.00 0.00 35.06 4.30
2675 5000 2.784347 GCAGTAGCACTTCCTCCTTTT 58.216 47.619 0.00 0.00 41.58 2.27
3178 5527 2.746362 GCTGAAGTTCCTCCAATCACTG 59.254 50.000 0.00 0.00 0.00 3.66
3289 5638 0.470833 AGTCACCAGCTCAGACCTGT 60.471 55.000 6.19 0.00 32.82 4.00
3311 5660 4.976925 CGGCCCTAGCATGCCTCG 62.977 72.222 15.66 5.84 45.71 4.63
3391 5740 4.749245 GTGAACAACCACTCCAAGTATG 57.251 45.455 0.00 0.00 34.38 2.39
3425 5774 1.688311 CCCCGTCCTCTCCAGATACAA 60.688 57.143 0.00 0.00 0.00 2.41
3633 5985 0.946221 GCTATCCATCTCAACGCGGG 60.946 60.000 12.47 1.49 0.00 6.13
3773 6126 0.666374 CAACCAACGTTTCCAGGGAC 59.334 55.000 8.47 0.00 0.00 4.46
3779 6132 2.671963 GTTTCCAGGGACGGCCAC 60.672 66.667 11.00 0.00 35.15 5.01
3853 6206 4.391216 CGTCTTGTGCTTGAAGAGATTGAT 59.609 41.667 0.00 0.00 30.01 2.57
3897 6250 3.520402 CGAGAGCTCCTCCTCCAC 58.480 66.667 10.93 0.00 38.71 4.02
3929 6282 0.174389 ATCTCTCGCTGCGTTCACAT 59.826 50.000 22.48 6.22 0.00 3.21
3970 6323 3.068165 TCAAGCAGAAGACACGAGAGAAA 59.932 43.478 0.00 0.00 0.00 2.52
3971 6324 3.735237 AGCAGAAGACACGAGAGAAAA 57.265 42.857 0.00 0.00 0.00 2.29
4156 6510 1.154454 ACCTAGGACGGTGGTGTGA 59.846 57.895 17.98 0.00 35.52 3.58
4166 6520 1.797348 CGGTGGTGTGAAACTTTGTGC 60.797 52.381 0.00 0.00 38.04 4.57
4211 6568 1.144276 TTGTCGCGGAAGGTGTGAA 59.856 52.632 6.13 0.00 0.00 3.18
4224 6581 4.581309 AGGTGTGAATCTGATTCCACAT 57.419 40.909 30.68 26.63 39.78 3.21
4258 6615 1.080772 GTGCGGAGACATGACGACA 60.081 57.895 0.00 0.00 0.00 4.35
4340 6697 1.803519 CACTCGTCGCTCTCTTGCC 60.804 63.158 0.00 0.00 0.00 4.52
4392 6750 7.437713 TCTACACATTGTATTTGGAGAGGAT 57.562 36.000 0.00 0.00 31.66 3.24
4452 6810 3.875727 GCTGATAGATTGAGCTTGAAGCA 59.124 43.478 20.45 0.00 45.56 3.91
4611 6969 0.750546 TTCATCATGGGAGCAGCAGC 60.751 55.000 0.00 0.00 42.56 5.25
4682 7040 2.756400 GGGTCACTGGACATGGCA 59.244 61.111 0.00 0.00 46.17 4.92
4880 7265 2.367567 ACTGTGTCGACCCAACATAGTT 59.632 45.455 14.12 0.00 43.79 2.24
4905 7290 6.403049 TGATCAAACTTAGAGAATGGCGTTA 58.597 36.000 0.00 0.00 0.00 3.18
4980 7365 4.287552 TGGACCTCTGAACCTATTAGGAC 58.712 47.826 16.80 10.04 37.67 3.85
5004 7389 1.360185 TAGGTTAAAGGTTCGGCCCA 58.640 50.000 0.00 0.00 38.26 5.36
5154 7539 5.240403 AGAAGAAGATGACAAAGAAACTGGC 59.760 40.000 0.00 0.00 0.00 4.85
5156 7541 5.075493 AGAAGATGACAAAGAAACTGGCAT 58.925 37.500 0.00 0.00 45.46 4.40
5208 7675 2.784682 ACCTAATCTACTCCGAGGAGGT 59.215 50.000 21.79 0.00 45.88 3.85
5259 7726 1.069090 GCAGTTCCGGTGACTGACA 59.931 57.895 31.13 0.00 45.72 3.58
5476 7943 1.228459 GGTTCGAAGGGGTTTGCCT 60.228 57.895 0.00 0.00 34.45 4.75
5589 8086 8.043113 TGACTTCTAGTGCTTGATGATTACATT 58.957 33.333 0.00 0.00 36.82 2.71
5949 8452 5.443230 TGTTATGTCAACATCCCATGGTA 57.557 39.130 11.73 0.00 37.76 3.25
6241 8784 6.542370 GGTACTAATCAATCTGCCAAAGCTTA 59.458 38.462 0.00 0.00 40.80 3.09
6388 8933 7.389803 TGTTTATCCACACACATTCTAATGG 57.610 36.000 7.56 0.00 40.70 3.16
6414 8959 5.068723 TGGTCCTCTTAACTTAGGATAAGCG 59.931 44.000 0.00 0.00 43.63 4.68
6593 9145 5.896678 CCCCAATTTGTCTATTGAACCCATA 59.103 40.000 0.00 0.00 37.65 2.74
6595 9147 6.461509 CCCAATTTGTCTATTGAACCCATAGC 60.462 42.308 0.00 0.00 37.65 2.97
6630 9182 9.419297 CTTCTGCATTATTTCCCATTCATTATG 57.581 33.333 0.00 0.00 0.00 1.90
6742 9298 9.939802 GTATATAAAGTCCCCGAGTTGAATAAT 57.060 33.333 0.00 0.00 0.00 1.28
6810 9366 3.202595 ACGACTTCTATCTCCCAGGTACT 59.797 47.826 0.00 0.00 43.88 2.73
6851 9407 4.347000 TCCAGTGTTGAACTACCTTAGCTT 59.653 41.667 0.00 0.00 36.83 3.74
6906 9462 7.730364 AAGTATCGTGTTTGATTCTGTTTCT 57.270 32.000 0.00 0.00 0.00 2.52
6951 9507 1.981533 GAAACGCAAGCTCATTTCTGC 59.018 47.619 0.00 0.00 45.62 4.26
6973 9529 5.049198 TGCTTAGTGTTGCAGAATTTGAGAG 60.049 40.000 0.00 0.00 34.84 3.20
6992 9548 0.110486 GGTGGAAGGTTGGAGCTGAA 59.890 55.000 0.00 0.00 0.00 3.02
7074 9630 3.686916 AGTGCTAAGGTTCAGAAGGAC 57.313 47.619 0.00 0.00 0.00 3.85
7113 9679 3.442625 GGAGCGGCTAGGTTTTATGTTTT 59.557 43.478 0.60 0.00 0.00 2.43
7122 9688 2.614229 GGTTTTATGTTTTGGGGCGCAT 60.614 45.455 10.83 0.00 0.00 4.73
7278 9848 1.135859 GCTGAAACTGTTGAGCATCCG 60.136 52.381 16.05 0.00 42.88 4.18
7283 9853 1.230635 ACTGTTGAGCATCCGTGTGC 61.231 55.000 1.37 1.37 45.38 4.57
7317 9887 8.179509 TGTAGGCTAATCTAGACTTTATGGAC 57.820 38.462 0.00 0.00 43.04 4.02
7568 10197 2.929903 TTGGCGCCATGACAAAGGC 61.930 57.895 33.25 11.25 44.60 4.35
7575 10204 1.787012 CCATGACAAAGGCACAAAGC 58.213 50.000 0.00 0.00 44.65 3.51
7590 10230 4.109766 CACAAAGCAATGGATAGCATGTG 58.890 43.478 0.00 0.00 41.19 3.21
7599 10239 2.213499 GGATAGCATGTGTACACTGCC 58.787 52.381 30.12 21.15 36.68 4.85
7699 10339 1.152312 GCCCTTCTCCCCCGATCTA 60.152 63.158 0.00 0.00 0.00 1.98
7742 10382 1.807142 GCAGGCTACTGTTGTTTCTCC 59.193 52.381 0.00 0.00 46.62 3.71
7743 10383 2.551071 GCAGGCTACTGTTGTTTCTCCT 60.551 50.000 0.00 0.00 46.62 3.69
7789 10429 0.328258 TTGAGCCTTTAGGGGACAGC 59.672 55.000 0.00 0.00 35.18 4.40
7838 10478 5.701290 GTCTGTATTCCCATGGCACTAATAC 59.299 44.000 19.97 19.97 34.89 1.89
7839 10479 5.606749 TCTGTATTCCCATGGCACTAATACT 59.393 40.000 23.52 3.41 35.20 2.12
7840 10480 6.785466 TCTGTATTCCCATGGCACTAATACTA 59.215 38.462 23.52 15.71 35.20 1.82
7841 10481 7.004555 TGTATTCCCATGGCACTAATACTAG 57.995 40.000 23.52 0.00 35.20 2.57
7842 10482 6.785466 TGTATTCCCATGGCACTAATACTAGA 59.215 38.462 23.52 11.59 35.20 2.43
7844 10484 8.978472 GTATTCCCATGGCACTAATACTAGATA 58.022 37.037 19.73 0.00 32.70 1.98
7845 10485 7.482169 TTCCCATGGCACTAATACTAGATAG 57.518 40.000 6.09 0.00 0.00 2.08
7919 13280 7.701445 AGATGCAAACATATAGCAAGAGAAAC 58.299 34.615 0.00 0.00 42.15 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.560068 CCGGTATGCTATGTTTGAACTCC 59.440 47.826 0.00 0.00 0.00 3.85
1 2 4.439057 TCCGGTATGCTATGTTTGAACTC 58.561 43.478 0.00 0.00 0.00 3.01
107 109 4.871557 ACGGCGATGAGTAGATCTAGTATC 59.128 45.833 16.62 11.65 0.00 2.24
235 237 1.950828 CTGAAGATGAAGCTCGGCAT 58.049 50.000 0.00 0.00 0.00 4.40
315 319 1.004918 GACCGCATATTCTCCCCCG 60.005 63.158 0.00 0.00 0.00 5.73
404 414 2.355716 GCCCACTAGTGAAAGTATGGCA 60.356 50.000 24.68 0.00 42.20 4.92
410 420 0.608640 CTCCGCCCACTAGTGAAAGT 59.391 55.000 24.68 0.00 0.00 2.66
412 422 1.295423 GCTCCGCCCACTAGTGAAA 59.705 57.895 24.68 3.76 0.00 2.69
517 542 0.103755 GCGAGAGGAGATGTCATGCA 59.896 55.000 0.00 0.00 0.00 3.96
521 546 1.098129 CGAGGCGAGAGGAGATGTCA 61.098 60.000 0.00 0.00 0.00 3.58
568 593 0.524414 TCAAATCGAGCGACTTCCGA 59.476 50.000 0.00 0.00 41.76 4.55
611 636 1.132500 CTTTTCCCCTATCCGCCTCT 58.868 55.000 0.00 0.00 0.00 3.69
616 648 1.802553 TCCCTCTTTTCCCCTATCCG 58.197 55.000 0.00 0.00 0.00 4.18
621 653 0.123266 TCCCATCCCTCTTTTCCCCT 59.877 55.000 0.00 0.00 0.00 4.79
632 664 1.493446 ACGATTTAGGGTTCCCATCCC 59.507 52.381 10.73 0.00 44.90 3.85
661 693 4.500127 CGTGATTCCGGTTATATATGCCA 58.500 43.478 0.00 0.00 0.00 4.92
681 713 4.710167 GGCCTGTAAACCGCCCGT 62.710 66.667 0.00 0.00 36.63 5.28
713 745 5.064558 TCGATTAAAACAACCTGGCTGTAA 58.935 37.500 2.67 0.00 0.00 2.41
715 747 3.482436 TCGATTAAAACAACCTGGCTGT 58.518 40.909 0.00 0.00 0.00 4.40
716 748 4.226761 GTTCGATTAAAACAACCTGGCTG 58.773 43.478 0.00 0.00 0.00 4.85
724 756 4.038162 CCCAACCAGGTTCGATTAAAACAA 59.962 41.667 0.12 0.00 34.66 2.83
725 757 3.570550 CCCAACCAGGTTCGATTAAAACA 59.429 43.478 0.12 0.00 34.66 2.83
731 763 1.304134 GGCCCAACCAGGTTCGATT 60.304 57.895 0.12 0.00 38.86 3.34
733 765 4.323477 CGGCCCAACCAGGTTCGA 62.323 66.667 0.12 0.00 39.03 3.71
767 799 2.795331 GCGTTTTTCCAGCGGTTTTACA 60.795 45.455 0.00 0.00 0.00 2.41
778 810 1.525077 ACTGAGGCGCGTTTTTCCA 60.525 52.632 8.43 0.00 0.00 3.53
793 825 3.254060 CAGATTCCGTGTAACCTCACTG 58.746 50.000 0.00 0.00 36.33 3.66
795 827 2.000447 GCAGATTCCGTGTAACCTCAC 59.000 52.381 0.00 0.00 35.28 3.51
796 828 1.899814 AGCAGATTCCGTGTAACCTCA 59.100 47.619 0.00 0.00 0.00 3.86
804 836 1.269517 GCCTCTCTAGCAGATTCCGTG 60.270 57.143 0.00 0.00 0.00 4.94
809 841 3.641046 TCAAGAGCCTCTCTAGCAGATT 58.359 45.455 0.00 0.00 40.28 2.40
822 854 3.147553 AGGGAAAGTTCTTCAAGAGCC 57.852 47.619 0.00 0.00 0.00 4.70
838 870 5.842328 ACGGGATGACTGTATAATTTAGGGA 59.158 40.000 0.00 0.00 36.76 4.20
1031 3325 2.890474 GGTACAGCACGGCCGATG 60.890 66.667 35.90 27.38 0.00 3.84
1328 3630 6.000891 TCTAGCTTAAACGAACTAACGACA 57.999 37.500 0.00 0.00 37.03 4.35
1368 3670 1.134521 GGTCGGGATACAGATTGCACA 60.135 52.381 0.00 0.00 44.55 4.57
1620 3924 7.059147 CGTTTTTCTTTTAAGGTACAAGATCGC 59.941 37.037 0.00 0.00 0.00 4.58
1655 3959 6.790319 ACCAAGGTTATAACAGGAGAAACAT 58.210 36.000 20.99 1.92 0.00 2.71
1678 3982 4.809673 CTGCAAAAGGAAACCCATAAGAC 58.190 43.478 0.00 0.00 0.00 3.01
1871 4175 5.215252 TCCGGATGAATCTGAGATTAACC 57.785 43.478 7.82 10.41 35.13 2.85
1872 4176 6.146837 CACATCCGGATGAATCTGAGATTAAC 59.853 42.308 43.42 2.86 41.20 2.01
1873 4177 6.041979 TCACATCCGGATGAATCTGAGATTAA 59.958 38.462 43.42 16.19 41.20 1.40
1874 4178 5.539955 TCACATCCGGATGAATCTGAGATTA 59.460 40.000 43.42 16.83 41.20 1.75
1875 4179 4.346127 TCACATCCGGATGAATCTGAGATT 59.654 41.667 43.42 19.54 41.20 2.40
1876 4180 3.899980 TCACATCCGGATGAATCTGAGAT 59.100 43.478 43.42 20.25 41.20 2.75
1877 4181 3.299503 TCACATCCGGATGAATCTGAGA 58.700 45.455 43.42 25.76 41.20 3.27
1878 4182 3.740631 TCACATCCGGATGAATCTGAG 57.259 47.619 43.42 24.30 41.20 3.35
1879 4183 4.346127 AGAATCACATCCGGATGAATCTGA 59.654 41.667 43.42 34.92 41.20 3.27
1880 4184 4.639334 AGAATCACATCCGGATGAATCTG 58.361 43.478 43.42 31.65 41.20 2.90
1881 4185 4.970860 AGAATCACATCCGGATGAATCT 57.029 40.909 43.42 32.97 41.20 2.40
1882 4186 4.453819 GGAAGAATCACATCCGGATGAATC 59.546 45.833 43.42 31.70 41.20 2.52
1883 4187 4.103785 AGGAAGAATCACATCCGGATGAAT 59.896 41.667 43.42 32.07 40.80 2.57
1884 4188 3.455910 AGGAAGAATCACATCCGGATGAA 59.544 43.478 43.42 31.46 40.80 2.57
1885 4189 3.041211 AGGAAGAATCACATCCGGATGA 58.959 45.455 43.42 28.17 40.80 2.92
1886 4190 3.482156 AGGAAGAATCACATCCGGATG 57.518 47.619 37.23 37.23 40.80 3.51
1887 4191 5.832539 ATTAGGAAGAATCACATCCGGAT 57.167 39.130 12.38 12.38 40.80 4.18
1888 4192 5.630415 AATTAGGAAGAATCACATCCGGA 57.370 39.130 6.61 6.61 40.80 5.14
1889 4193 6.699575 AAAATTAGGAAGAATCACATCCGG 57.300 37.500 0.00 0.00 40.80 5.14
1890 4194 7.805071 GCATAAAATTAGGAAGAATCACATCCG 59.195 37.037 0.00 0.00 40.80 4.18
1931 4255 8.034215 ACAAACATTGAGAACAAACATTGAGAA 58.966 29.630 0.00 0.00 39.54 2.87
1932 4256 7.546358 ACAAACATTGAGAACAAACATTGAGA 58.454 30.769 0.00 0.00 39.54 3.27
1933 4257 7.760131 ACAAACATTGAGAACAAACATTGAG 57.240 32.000 0.00 0.00 39.54 3.02
1934 4258 9.081997 GTTACAAACATTGAGAACAAACATTGA 57.918 29.630 0.00 0.00 39.54 2.57
1935 4259 8.867935 TGTTACAAACATTGAGAACAAACATTG 58.132 29.630 10.60 0.00 39.54 2.82
1936 4260 8.868916 GTGTTACAAACATTGAGAACAAACATT 58.131 29.630 13.06 0.00 44.35 2.71
1937 4261 8.031864 TGTGTTACAAACATTGAGAACAAACAT 58.968 29.630 13.06 0.00 44.35 2.71
1938 4262 7.371159 TGTGTTACAAACATTGAGAACAAACA 58.629 30.769 13.06 8.24 44.35 2.83
1939 4263 7.804614 TGTGTTACAAACATTGAGAACAAAC 57.195 32.000 13.06 6.60 44.35 2.93
1940 4264 8.994429 AATGTGTTACAAACATTGAGAACAAA 57.006 26.923 13.06 10.27 44.51 2.83
1981 4306 5.858581 GCTTCACAGTTCCACAATATTCAAC 59.141 40.000 0.00 0.00 0.00 3.18
2129 4454 3.244181 GGCATGCCTCCTTTTTGAAAAGA 60.244 43.478 29.98 3.87 46.39 2.52
2214 4539 0.251341 AAGTGTCCCCAAGTGCCATC 60.251 55.000 0.00 0.00 0.00 3.51
2968 5294 1.442526 GCAAGCTGAGCATGGCGTAT 61.443 55.000 11.88 0.00 0.00 3.06
3178 5527 3.862991 GGGAGTAGCGGGGGAAGC 61.863 72.222 0.00 0.00 0.00 3.86
3289 5638 4.529219 CATGCTAGGGCCGACGCA 62.529 66.667 17.25 17.25 37.74 5.24
3311 5660 3.055719 CGTGGTGCATGGGTGGTC 61.056 66.667 0.00 0.00 0.00 4.02
3391 5740 0.611714 ACGGGGTACATGACTTGACC 59.388 55.000 0.00 0.00 0.00 4.02
3425 5774 2.159198 ACCTAAACGTCGTTCCGCATAT 60.159 45.455 11.71 0.00 0.00 1.78
3436 5785 0.314935 TCCGTGTCCACCTAAACGTC 59.685 55.000 0.00 0.00 34.30 4.34
3633 5985 1.008538 CTGGACAGTGCGCAAAACC 60.009 57.895 14.00 14.26 0.00 3.27
3658 6011 2.037144 GACTGTAGGGGGCGATTAGAA 58.963 52.381 0.00 0.00 0.00 2.10
3709 6062 2.814336 GAGGATTTGTCCAACACAGGTC 59.186 50.000 0.00 0.00 35.97 3.85
3773 6126 3.385749 ATAAGGAGCACCGTGGCCG 62.386 63.158 0.00 0.00 41.83 6.13
3779 6132 1.506493 GATCTGCATAAGGAGCACCG 58.494 55.000 0.00 0.00 41.83 4.94
3897 6250 2.094957 GCGAGAGATCCTTCCCTTATCG 60.095 54.545 0.00 0.00 0.00 2.92
3929 6282 6.936335 TGCTTGAAGAGATCACACTCATTTAA 59.064 34.615 0.00 0.00 37.92 1.52
3970 6323 0.673644 CTTTCCCGACCTCATGCGTT 60.674 55.000 0.00 0.00 0.00 4.84
3971 6324 1.079127 CTTTCCCGACCTCATGCGT 60.079 57.895 0.00 0.00 0.00 5.24
4146 6500 1.797348 GCACAAAGTTTCACACCACCG 60.797 52.381 0.00 0.00 0.00 4.94
4156 6510 4.397417 GCTATCCATCTCAGCACAAAGTTT 59.603 41.667 0.00 0.00 35.35 2.66
4166 6520 1.000283 GGGACGTGCTATCCATCTCAG 60.000 57.143 7.11 0.00 38.06 3.35
4211 6568 5.705905 CAGCATATCACATGTGGAATCAGAT 59.294 40.000 25.16 11.95 0.00 2.90
4224 6581 1.089112 GCACAGCACAGCATATCACA 58.911 50.000 0.00 0.00 0.00 3.58
4258 6615 1.464734 TCTCCGACGAGCTCTTTGAT 58.535 50.000 12.85 0.00 35.94 2.57
4392 6750 5.001874 AGTAGTGTCGACTCATGTACTTCA 58.998 41.667 17.92 0.00 33.21 3.02
4452 6810 4.718774 ACATCAACATCACCTCCTACATCT 59.281 41.667 0.00 0.00 0.00 2.90
4682 7040 2.297597 CGACAACCTCTTCCACTCTTCT 59.702 50.000 0.00 0.00 0.00 2.85
4819 7180 1.135527 CAGGTTACATGGCCAATGCAG 59.864 52.381 10.96 0.00 40.22 4.41
4880 7265 5.245531 ACGCCATTCTCTAAGTTTGATCAA 58.754 37.500 3.38 3.38 0.00 2.57
4901 7286 8.560576 AATTTTGGATTTATCAGCGAATAACG 57.439 30.769 0.00 0.00 45.66 3.18
4905 7290 7.492344 GGTTGAATTTTGGATTTATCAGCGAAT 59.508 33.333 0.00 0.00 0.00 3.34
4941 7326 1.553248 TCCAATAACAGGGTCAGACCG 59.447 52.381 13.80 3.17 39.83 4.79
4942 7327 2.355818 GGTCCAATAACAGGGTCAGACC 60.356 54.545 11.70 11.70 37.60 3.85
4943 7328 2.572104 AGGTCCAATAACAGGGTCAGAC 59.428 50.000 0.00 0.00 0.00 3.51
4944 7329 2.838202 GAGGTCCAATAACAGGGTCAGA 59.162 50.000 0.00 0.00 0.00 3.27
4945 7330 2.840651 AGAGGTCCAATAACAGGGTCAG 59.159 50.000 0.00 0.00 0.00 3.51
4980 7365 4.381185 GGGCCGAACCTTTAACCTAAATTG 60.381 45.833 0.00 0.00 39.10 2.32
5154 7539 3.021695 ACAGCATCAATTCACCCTCATG 58.978 45.455 0.00 0.00 0.00 3.07
5156 7541 2.885135 ACAGCATCAATTCACCCTCA 57.115 45.000 0.00 0.00 0.00 3.86
5242 7709 0.946221 GCTGTCAGTCACCGGAACTG 60.946 60.000 25.94 25.94 0.00 3.16
5525 8022 3.781307 CTGATCCGGTTCCGCCCA 61.781 66.667 10.02 2.65 0.00 5.36
5530 8027 3.268023 AGATTCAACTGATCCGGTTCC 57.732 47.619 10.02 0.00 29.62 3.62
5564 8061 8.430801 AATGTAATCATCAAGCACTAGAAGTC 57.569 34.615 0.00 0.00 32.56 3.01
5589 8086 4.673580 GCTTTCCGACGTCTACAATACAGA 60.674 45.833 14.70 0.00 0.00 3.41
5602 8099 0.716108 GATGTCAGTGCTTTCCGACG 59.284 55.000 0.00 0.00 0.00 5.12
5949 8452 7.288810 ACCACACTTTCAATTCACATACATT 57.711 32.000 0.00 0.00 0.00 2.71
6108 8644 2.604174 GGACGAAACACACTGCCCG 61.604 63.158 0.00 0.00 0.00 6.13
6241 8784 2.617276 CCAGATGCACTTCCACATCACT 60.617 50.000 5.84 0.00 44.16 3.41
6388 8933 6.481434 TTATCCTAAGTTAAGAGGACCAGC 57.519 41.667 3.38 0.00 44.64 4.85
6438 8983 5.240891 ACAGAACCAGTACTGTTCATGATG 58.759 41.667 26.08 20.56 43.52 3.07
6593 9145 3.717452 AATGCAGAAGAAAGAGAGGCT 57.283 42.857 0.00 0.00 0.00 4.58
6595 9147 6.039159 GGGAAATAATGCAGAAGAAAGAGAGG 59.961 42.308 0.00 0.00 0.00 3.69
6630 9182 9.031360 TGCAGTGAAGTCGAAATTATATCTTAC 57.969 33.333 0.00 0.00 0.00 2.34
6709 9265 5.387788 TCGGGGACTTTATATACTACAGCA 58.612 41.667 0.00 0.00 0.00 4.41
6742 9298 3.623060 GGCTGATTTTTAGCATCTCGTCA 59.377 43.478 0.00 0.00 42.88 4.35
6810 9366 5.649395 CACTGGAGATCCATAAGCAGAAAAA 59.351 40.000 1.15 0.00 46.46 1.94
6851 9407 2.593148 ACGCACACCCATTCGCAA 60.593 55.556 0.00 0.00 0.00 4.85
6906 9462 0.693092 CCCCCACCTCCGAATTCCTA 60.693 60.000 0.00 0.00 0.00 2.94
6951 9507 5.471456 ACCTCTCAAATTCTGCAACACTAAG 59.529 40.000 0.00 0.00 0.00 2.18
6953 9509 4.756642 CACCTCTCAAATTCTGCAACACTA 59.243 41.667 0.00 0.00 0.00 2.74
6973 9529 0.110486 TTCAGCTCCAACCTTCCACC 59.890 55.000 0.00 0.00 0.00 4.61
7074 9630 3.134458 GCTCCCATCCTTTGTATCTTCG 58.866 50.000 0.00 0.00 0.00 3.79
7122 9688 2.940158 CTCCTTTGCATGATGATGGGA 58.060 47.619 0.00 0.00 0.00 4.37
7278 9848 2.618709 AGCCTACAGAAAAAGTGCACAC 59.381 45.455 21.04 4.85 0.00 3.82
7283 9853 8.254508 AGTCTAGATTAGCCTACAGAAAAAGTG 58.745 37.037 0.00 0.00 0.00 3.16
7484 10112 1.556911 CTCCTTGGCCATGTCTACTGT 59.443 52.381 6.09 0.00 0.00 3.55
7568 10197 4.109766 CACATGCTATCCATTGCTTTGTG 58.890 43.478 11.77 11.77 37.20 3.33
7569 10198 3.765511 ACACATGCTATCCATTGCTTTGT 59.234 39.130 0.00 0.00 29.71 2.83
7570 10199 4.380841 ACACATGCTATCCATTGCTTTG 57.619 40.909 0.00 0.00 29.71 2.77
7571 10200 4.949238 TGTACACATGCTATCCATTGCTTT 59.051 37.500 0.00 0.00 29.71 3.51
7573 10202 3.879295 GTGTACACATGCTATCCATTGCT 59.121 43.478 21.14 0.00 29.71 3.91
7574 10203 3.879295 AGTGTACACATGCTATCCATTGC 59.121 43.478 27.06 0.00 29.71 3.56
7575 10204 4.260907 GCAGTGTACACATGCTATCCATTG 60.261 45.833 28.26 16.52 34.73 2.82
7577 10206 3.470709 GCAGTGTACACATGCTATCCAT 58.529 45.455 28.26 7.08 34.73 3.41
7583 10223 0.957395 GCAGGCAGTGTACACATGCT 60.957 55.000 31.18 21.63 36.45 3.79
7610 10250 1.103398 CAGGGCGCCTTTTGATAGGG 61.103 60.000 28.56 0.00 35.74 3.53
7699 10339 2.043046 CCATGTCGGGGCCCAAAT 60.043 61.111 26.86 9.74 0.00 2.32
7764 10404 4.726825 TGTCCCCTAAAGGCTCAAATAGAT 59.273 41.667 0.00 0.00 0.00 1.98
7859 13220 3.369385 GACGCGCTCTTAGCTGTAATAA 58.631 45.455 5.73 0.00 39.60 1.40
7869 13230 0.100682 GAGTCATGGACGCGCTCTTA 59.899 55.000 5.73 0.00 37.67 2.10
7919 13280 9.881529 GTCTAATTAATTACACTAGAGACCTCG 57.118 37.037 11.50 0.00 34.09 4.63
7964 13325 5.244402 TGCAAATGACCATTGAGTTTCAGAT 59.756 36.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.