Multiple sequence alignment - TraesCS6D01G082100

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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 TraesCS6D01G082100 chr6D 100.000 7751 0 0 1 7751 47627447 47619697 0.000000e+00 14314.0
1 TraesCS6D01G082100 chr6D 77.941 204 41 4 4758 4958 5044095 5044297 2.940000e-24 124.0
2 TraesCS6D01G082100 chr6D 82.308 130 16 6 5484 5610 450176912 450177037 1.060000e-18 106.0
3 TraesCS6D01G082100 chr6A 96.286 6005 154 23 1 5973 68125845 68131812 0.000000e+00 9790.0
4 TraesCS6D01G082100 chr6A 94.741 1331 34 12 6077 7386 68131859 68133174 0.000000e+00 2037.0
5 TraesCS6D01G082100 chr6A 91.176 374 24 7 7382 7749 68133203 68133573 4.180000e-137 499.0
6 TraesCS6D01G082100 chr6A 83.889 180 29 0 3653 3832 4234174 4233995 1.030000e-38 172.0
7 TraesCS6D01G082100 chr6A 87.037 54 2 3 4917 4967 12016637 12016688 1.000000e-03 56.5
8 TraesCS6D01G082100 chr6B 96.823 3683 92 8 3354 7018 124083946 124087621 0.000000e+00 6130.0
9 TraesCS6D01G082100 chr6B 96.572 1021 27 4 1 1016 124080321 124081338 0.000000e+00 1685.0
10 TraesCS6D01G082100 chr6B 89.812 373 30 6 7382 7749 124088781 124089150 9.100000e-129 472.0
11 TraesCS6D01G082100 chr6B 93.827 243 11 3 7043 7284 124087615 124087854 5.720000e-96 363.0
12 TraesCS6D01G082100 chr6B 83.889 180 29 0 3653 3832 10852875 10852696 1.030000e-38 172.0
13 TraesCS6D01G082100 chr6B 94.565 92 3 1 7297 7386 124087943 124088034 2.920000e-29 141.0
14 TraesCS6D01G082100 chr5A 83.903 5032 605 115 510 5406 655075521 655070560 0.000000e+00 4615.0
15 TraesCS6D01G082100 chr5A 85.385 130 12 6 5484 5610 655070521 655070396 2.270000e-25 128.0
16 TraesCS6D01G082100 chr5B 85.552 3177 384 33 1839 4970 664379253 664376107 0.000000e+00 3254.0
17 TraesCS6D01G082100 chr5B 84.184 980 113 23 536 1483 664380570 664379601 0.000000e+00 913.0
18 TraesCS6D01G082100 chr5B 79.650 457 62 25 4966 5406 664376029 664375588 4.550000e-77 300.0
19 TraesCS6D01G082100 chr3D 84.247 2628 311 63 1030 3595 161712629 161710043 0.000000e+00 2464.0
20 TraesCS6D01G082100 chr3A 84.287 2622 309 63 1030 3590 191534206 191531627 0.000000e+00 2464.0
21 TraesCS6D01G082100 chr3A 75.966 233 49 7 7382 7610 79189896 79189667 6.360000e-21 113.0
22 TraesCS6D01G082100 chr3B 84.144 2630 306 68 1030 3595 238313877 238311295 0.000000e+00 2444.0
23 TraesCS6D01G082100 chr5D 86.880 1997 197 26 1846 3807 527606104 527604138 0.000000e+00 2176.0
24 TraesCS6D01G082100 chr5D 86.780 1997 199 26 1846 3807 527576499 527574533 0.000000e+00 2165.0
25 TraesCS6D01G082100 chr5D 83.261 1386 178 31 510 1854 527607501 527606129 0.000000e+00 1225.0
26 TraesCS6D01G082100 chr5D 83.189 1386 179 31 510 1854 527577896 527576524 0.000000e+00 1219.0
27 TraesCS6D01G082100 chr5D 83.447 1172 181 9 3809 4970 527573896 527572728 0.000000e+00 1077.0
28 TraesCS6D01G082100 chr5D 83.447 1172 181 9 3809 4970 527603459 527602291 0.000000e+00 1077.0
29 TraesCS6D01G082100 chr5D 80.659 455 60 22 4966 5406 527572673 527572233 2.090000e-85 327.0
30 TraesCS6D01G082100 chr5D 80.659 455 60 22 4966 5406 527602236 527601796 2.090000e-85 327.0
31 TraesCS6D01G082100 chr5D 85.385 130 12 6 5484 5610 527572194 527572069 2.270000e-25 128.0
32 TraesCS6D01G082100 chr5D 85.385 130 12 6 5484 5610 527601757 527601632 2.270000e-25 128.0
33 TraesCS6D01G082100 chr5D 83.077 130 15 6 5484 5610 127927696 127927821 2.290000e-20 111.0
34 TraesCS6D01G082100 chr7B 82.261 2548 371 51 2310 4832 736138536 736141027 0.000000e+00 2126.0
35 TraesCS6D01G082100 chr7B 83.668 1145 122 35 1024 2148 736137396 736138495 0.000000e+00 1018.0
36 TraesCS6D01G082100 chr7B 79.506 810 89 42 1100 1889 736090760 736091512 8.980000e-139 505.0
37 TraesCS6D01G082100 chrUn 85.160 2062 254 32 1021 3046 62647021 62649066 0.000000e+00 2065.0
38 TraesCS6D01G082100 chrUn 83.987 1224 186 2 3609 4832 62649172 62650385 0.000000e+00 1166.0
39 TraesCS6D01G082100 chrUn 76.426 1175 246 25 3653 4817 62614022 62615175 2.390000e-169 606.0
40 TraesCS6D01G082100 chrUn 84.181 177 28 0 3653 3829 62408926 62409102 1.030000e-38 172.0
41 TraesCS6D01G082100 chrUn 84.181 177 28 0 3653 3829 62593206 62593382 1.030000e-38 172.0
42 TraesCS6D01G082100 chr1A 86.585 164 22 0 3612 3775 576353302 576353139 1.720000e-41 182.0
43 TraesCS6D01G082100 chr1D 89.000 100 9 2 583 682 41173230 41173133 1.060000e-23 122.0
44 TraesCS6D01G082100 chr1D 82.308 130 16 6 5484 5610 415607944 415607819 1.060000e-18 106.0
45 TraesCS6D01G082100 chr7D 83.077 130 15 6 5484 5610 340194300 340194175 2.290000e-20 111.0
46 TraesCS6D01G082100 chr4A 84.091 88 14 0 5476 5563 693213434 693213347 1.390000e-12 86.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G082100 chr6D 47619697 47627447 7750 True 14314.000000 14314 100.000000 1 7751 1 chr6D.!!$R1 7750
1 TraesCS6D01G082100 chr6A 68125845 68133573 7728 False 4108.666667 9790 94.067667 1 7749 3 chr6A.!!$F2 7748
2 TraesCS6D01G082100 chr6B 124080321 124089150 8829 False 1758.200000 6130 94.319800 1 7749 5 chr6B.!!$F1 7748
3 TraesCS6D01G082100 chr5A 655070396 655075521 5125 True 2371.500000 4615 84.644000 510 5610 2 chr5A.!!$R1 5100
4 TraesCS6D01G082100 chr5B 664375588 664380570 4982 True 1489.000000 3254 83.128667 536 5406 3 chr5B.!!$R1 4870
5 TraesCS6D01G082100 chr3D 161710043 161712629 2586 True 2464.000000 2464 84.247000 1030 3595 1 chr3D.!!$R1 2565
6 TraesCS6D01G082100 chr3A 191531627 191534206 2579 True 2464.000000 2464 84.287000 1030 3590 1 chr3A.!!$R2 2560
7 TraesCS6D01G082100 chr3B 238311295 238313877 2582 True 2444.000000 2444 84.144000 1030 3595 1 chr3B.!!$R1 2565
8 TraesCS6D01G082100 chr5D 527601632 527607501 5869 True 986.600000 2176 83.926400 510 5610 5 chr5D.!!$R2 5100
9 TraesCS6D01G082100 chr5D 527572069 527577896 5827 True 983.200000 2165 83.892000 510 5610 5 chr5D.!!$R1 5100
10 TraesCS6D01G082100 chr7B 736137396 736141027 3631 False 1572.000000 2126 82.964500 1024 4832 2 chr7B.!!$F2 3808
11 TraesCS6D01G082100 chr7B 736090760 736091512 752 False 505.000000 505 79.506000 1100 1889 1 chr7B.!!$F1 789
12 TraesCS6D01G082100 chrUn 62647021 62650385 3364 False 1615.500000 2065 84.573500 1021 4832 2 chrUn.!!$F4 3811
13 TraesCS6D01G082100 chrUn 62614022 62615175 1153 False 606.000000 606 76.426000 3653 4817 1 chrUn.!!$F3 1164

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
961 994 1.204786 TCCATGACGGGAACACCCAT 61.205 55.000 6.12 0.0 43.64 4.00 F
1005 1038 4.278669 GCAGAATCTGAGCATTTGATGGAT 59.721 41.667 15.38 0.0 32.44 3.41 F
1403 3635 4.624015 CATGTTCAGCACAATTTCAGGTT 58.376 39.130 0.00 0.0 39.50 3.50 F
2564 4908 1.649662 GCTCGCTAGAAGTGTTTCGAC 59.350 52.381 0.00 0.0 38.38 4.20 F
3238 5619 2.541556 GCCGAACTGATCACTTAGACC 58.458 52.381 0.00 0.0 0.00 3.85 F
4536 7632 0.634465 ACAAGGGGGACAACTGGTTT 59.366 50.000 0.00 0.0 0.00 3.27 F
4788 7884 1.002468 CTTAAGATGATTTGGCCGCCG 60.002 52.381 4.58 0.0 0.00 6.46 F
4841 7937 2.430694 GGTTTGTCTTTTGGCCTTCAGT 59.569 45.455 3.32 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 4341 1.997311 CAGAGGACCATGCTGGGGA 60.997 63.158 7.06 0.00 43.37 4.81 R
2424 4768 5.798125 TTGTCATAAAACCATGCCTTCAA 57.202 34.783 0.00 0.00 0.00 2.69 R
3238 5619 2.083774 TGGCTTTGCAGGATAGTTTCG 58.916 47.619 0.00 0.00 0.00 3.46 R
4005 7098 2.425592 CTGCGGTTGACCTGGTCA 59.574 61.111 25.12 25.12 41.09 4.02 R
4908 8005 0.255890 ACACCATCCCGCAGCTATTT 59.744 50.000 0.00 0.00 0.00 1.40 R
6000 9257 0.246635 AAACGACATCCGGGACTGAG 59.753 55.000 0.00 2.76 43.93 3.35 R
6309 9566 2.757314 TGATCTTGCTCTCATCGACACT 59.243 45.455 0.00 0.00 0.00 3.55 R
6804 10076 6.200286 CACTTGCAATTCATCTATCAAATGGC 59.800 38.462 0.00 0.00 31.29 4.40 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
302 303 3.734463 TGCTTTCACAGGAATCGTACAA 58.266 40.909 0.00 0.00 31.93 2.41
413 419 2.017668 ATCACCCCAGCCAACCACAA 62.018 55.000 0.00 0.00 0.00 3.33
515 522 4.983053 TCGTTTTTAGGGGGTATTTGACA 58.017 39.130 0.00 0.00 0.00 3.58
762 787 2.791383 TTCTGCAAACCAAATGACCG 57.209 45.000 0.00 0.00 0.00 4.79
802 827 6.975772 CCGTGTTTTTCATTCCTCTGTTTTTA 59.024 34.615 0.00 0.00 0.00 1.52
896 921 7.268199 AGCCTAATATGTGTCAATGTGATTG 57.732 36.000 0.00 0.00 41.57 2.67
961 994 1.204786 TCCATGACGGGAACACCCAT 61.205 55.000 6.12 0.00 43.64 4.00
975 1008 6.047231 GGAACACCCATCTATAACACACTAC 58.953 44.000 0.00 0.00 34.14 2.73
1005 1038 4.278669 GCAGAATCTGAGCATTTGATGGAT 59.721 41.667 15.38 0.00 32.44 3.41
1403 3635 4.624015 CATGTTCAGCACAATTTCAGGTT 58.376 39.130 0.00 0.00 39.50 3.50
2239 4571 6.092807 CCTTAGTCTGTATGCTTCAAAAGTCC 59.907 42.308 0.00 0.00 0.00 3.85
2564 4908 1.649662 GCTCGCTAGAAGTGTTTCGAC 59.350 52.381 0.00 0.00 38.38 4.20
2920 5288 6.573434 TGTAGCAATCTAACCTCTGTACATG 58.427 40.000 0.00 0.00 0.00 3.21
3138 5506 4.263068 CCTTCTATTGTCAGGACAGGTTGT 60.263 45.833 2.01 0.00 42.94 3.32
3153 5521 4.595781 ACAGGTTGTGGGTATAGTTTCAGA 59.404 41.667 0.00 0.00 0.00 3.27
3155 5523 6.180472 CAGGTTGTGGGTATAGTTTCAGAAT 58.820 40.000 0.00 0.00 0.00 2.40
3238 5619 2.541556 GCCGAACTGATCACTTAGACC 58.458 52.381 0.00 0.00 0.00 3.85
4005 7098 4.440880 GCAGAGTCTTCATCAGCTTGTAT 58.559 43.478 0.00 0.00 0.00 2.29
4049 7142 3.560251 AGTTGGGGCGCACAGTCT 61.560 61.111 13.89 2.43 0.00 3.24
4248 7344 2.114670 GTGGCGACATGGTGATGGG 61.115 63.158 0.00 0.00 46.14 4.00
4536 7632 0.634465 ACAAGGGGGACAACTGGTTT 59.366 50.000 0.00 0.00 0.00 3.27
4635 7731 2.205911 GCTCCTCTTCGGATAAAGCAC 58.794 52.381 0.00 0.00 42.12 4.40
4655 7751 1.737029 CGTGGGTGACTATGCTGAGTG 60.737 57.143 0.00 0.00 0.00 3.51
4686 7782 2.512286 ATGGGTCGATGCGCACTG 60.512 61.111 14.90 8.62 34.18 3.66
4747 7843 3.777106 TCATGGCAGAAGAAGAAGTGT 57.223 42.857 0.00 0.00 0.00 3.55
4788 7884 1.002468 CTTAAGATGATTTGGCCGCCG 60.002 52.381 4.58 0.00 0.00 6.46
4841 7937 2.430694 GGTTTGTCTTTTGGCCTTCAGT 59.569 45.455 3.32 0.00 0.00 3.41
4908 8005 4.511454 GTGCACTACTCATTGACTGTTTGA 59.489 41.667 10.32 0.00 0.00 2.69
4909 8006 5.007626 GTGCACTACTCATTGACTGTTTGAA 59.992 40.000 10.32 0.00 0.00 2.69
5006 8194 7.211966 AGATAATGCTTGCATTAAGATGTCC 57.788 36.000 25.43 12.39 38.76 4.02
5147 8337 6.599244 TGACCACTTCATTGTCCTGAAATATC 59.401 38.462 0.00 0.00 34.86 1.63
5249 8440 4.304110 TCAAGCTTACGAGACGTTTTCAT 58.696 39.130 0.00 0.00 41.54 2.57
5269 8493 9.853555 TTTTCATTGAACTTATGTATGCGATTT 57.146 25.926 0.00 0.00 0.00 2.17
5270 8494 9.853555 TTTCATTGAACTTATGTATGCGATTTT 57.146 25.926 0.00 0.00 0.00 1.82
5284 8508 9.906660 TGTATGCGATTTTATTTTCTGAAACTT 57.093 25.926 1.58 0.00 0.00 2.66
5342 8567 7.865385 TGCATGAGGTTGTTAATACTTGTTTTC 59.135 33.333 0.00 0.00 0.00 2.29
5406 8633 7.327214 ACACAAGTGGTTGTTGATTTTACATT 58.673 30.769 5.08 0.00 45.00 2.71
5519 8746 8.055279 TCTTTGGATGATCAGGTATTTGTTTC 57.945 34.615 0.09 0.00 0.00 2.78
5521 8748 7.959658 TTGGATGATCAGGTATTTGTTTCAT 57.040 32.000 0.09 0.00 0.00 2.57
5739 8975 9.973450 ATATAATTAGCTGCTAACTCCATATCG 57.027 33.333 23.20 0.00 0.00 2.92
5969 9205 4.881273 TCTGCTTCAGTTTCAGTTTTGCTA 59.119 37.500 0.00 0.00 32.61 3.49
5970 9206 5.008019 TCTGCTTCAGTTTCAGTTTTGCTAG 59.992 40.000 0.00 0.00 32.61 3.42
5971 9207 4.640201 TGCTTCAGTTTCAGTTTTGCTAGT 59.360 37.500 0.00 0.00 0.00 2.57
5972 9208 5.820423 TGCTTCAGTTTCAGTTTTGCTAGTA 59.180 36.000 0.00 0.00 0.00 1.82
5973 9209 6.317642 TGCTTCAGTTTCAGTTTTGCTAGTAA 59.682 34.615 0.00 0.00 0.00 2.24
5974 9210 7.013274 TGCTTCAGTTTCAGTTTTGCTAGTAAT 59.987 33.333 0.00 0.00 0.00 1.89
5975 9211 8.504005 GCTTCAGTTTCAGTTTTGCTAGTAATA 58.496 33.333 0.00 0.00 0.00 0.98
5979 9215 9.774742 CAGTTTCAGTTTTGCTAGTAATAATCC 57.225 33.333 0.00 0.00 0.00 3.01
5980 9216 9.515226 AGTTTCAGTTTTGCTAGTAATAATCCA 57.485 29.630 0.00 0.00 0.00 3.41
5983 9219 7.930217 TCAGTTTTGCTAGTAATAATCCATGC 58.070 34.615 0.00 0.00 0.00 4.06
5984 9220 6.852853 CAGTTTTGCTAGTAATAATCCATGCG 59.147 38.462 0.00 0.00 0.00 4.73
5985 9221 5.940192 TTTGCTAGTAATAATCCATGCGG 57.060 39.130 0.00 0.00 0.00 5.69
5986 9222 4.617253 TGCTAGTAATAATCCATGCGGT 57.383 40.909 0.00 0.00 0.00 5.68
5987 9223 4.314961 TGCTAGTAATAATCCATGCGGTG 58.685 43.478 0.00 0.00 0.00 4.94
5988 9224 4.202315 TGCTAGTAATAATCCATGCGGTGT 60.202 41.667 0.00 0.00 0.00 4.16
5989 9225 4.389077 GCTAGTAATAATCCATGCGGTGTC 59.611 45.833 0.00 0.00 0.00 3.67
6000 9257 3.179830 CATGCGGTGTCAGTAGTTAGTC 58.820 50.000 0.00 0.00 0.00 2.59
6037 9294 4.809958 TCGTTTTTATTCAGTTCCGTCACA 59.190 37.500 0.00 0.00 0.00 3.58
6046 9303 3.508402 TCAGTTCCGTCACATAGCTGTTA 59.492 43.478 0.00 0.00 31.62 2.41
6072 9329 7.389232 TCAGTTATATCATTGGCCTATGACAG 58.611 38.462 28.63 14.80 37.36 3.51
6309 9566 7.173562 ACCGTAGCAATTTGTTAGTTATTGTCA 59.826 33.333 0.00 0.00 33.04 3.58
6491 9760 4.182339 GCTTTCCCAGTTAGCAGTAGTAC 58.818 47.826 0.00 0.00 35.05 2.73
6529 9798 7.502561 GTGTAGTTTAGGGATGGAGCAATTATT 59.497 37.037 0.00 0.00 0.00 1.40
6620 9889 5.045215 CAGTGATGCACTTTTGTCATGTTT 58.955 37.500 0.00 0.00 42.59 2.83
6804 10076 4.154347 GAGGGGAGCCAGTCAGCG 62.154 72.222 0.00 0.00 38.01 5.18
6854 10126 5.986501 AGTGTACGAAGAGGAGAAGATTT 57.013 39.130 0.00 0.00 0.00 2.17
6923 10198 4.920781 TTTAGGGGGAGGATAGAAGAGT 57.079 45.455 0.00 0.00 0.00 3.24
6944 10219 4.140924 AGTTGGAAGGGAAGGTTGAAGAAT 60.141 41.667 0.00 0.00 0.00 2.40
6985 10260 1.867233 GCAACAAGAGCTCAAAGTCGA 59.133 47.619 17.77 0.00 0.00 4.20
7019 10294 3.438216 TCAGATTTTCAGTGGCATCCA 57.562 42.857 0.00 0.00 0.00 3.41
7083 10358 9.891828 CTTGCATTTATGTTAAGTTGTGACTAA 57.108 29.630 0.00 0.00 34.21 2.24
7084 10359 9.891828 TTGCATTTATGTTAAGTTGTGACTAAG 57.108 29.630 0.00 0.00 34.21 2.18
7085 10360 9.062524 TGCATTTATGTTAAGTTGTGACTAAGT 57.937 29.630 0.00 0.00 34.21 2.24
7220 10495 8.893727 GTTTTAGATATGTACTTGCAGTCCATT 58.106 33.333 0.00 0.00 27.58 3.16
7294 10569 5.653507 ACATCACAATACAATGCCATGTTC 58.346 37.500 0.00 0.00 34.75 3.18
7364 10715 1.856873 TGGGTCCAGCCTTCCCATT 60.857 57.895 0.00 0.00 45.19 3.16
7404 11508 0.034896 CGTGCCCACAGGAAAGTAGT 59.965 55.000 0.00 0.00 33.41 2.73
7471 11575 3.403038 ACAGCCAACATGTTACAGAGAC 58.597 45.455 11.53 0.00 0.00 3.36
7472 11576 2.413112 CAGCCAACATGTTACAGAGACG 59.587 50.000 11.53 0.00 0.00 4.18
7473 11577 2.037251 AGCCAACATGTTACAGAGACGT 59.963 45.455 11.53 0.00 0.00 4.34
7474 11578 2.412089 GCCAACATGTTACAGAGACGTC 59.588 50.000 11.53 7.70 0.00 4.34
7513 11619 1.676006 CCGCTCAAACTGGAACTTGTT 59.324 47.619 0.00 0.00 0.00 2.83
7573 11679 2.030274 CGCCCTTTACAACCTCTTTTGG 60.030 50.000 0.00 0.00 0.00 3.28
7581 11687 0.634465 AACCTCTTTTGGGTGTGGGT 59.366 50.000 0.00 0.00 37.13 4.51
7589 11695 1.144691 TTGGGTGTGGGTTGAGATCA 58.855 50.000 0.00 0.00 0.00 2.92
7605 11712 2.306805 AGATCACACAGCCAATCTTCCA 59.693 45.455 0.00 0.00 0.00 3.53
7632 11739 6.162079 TCTAAGAGAGCAAGAAACACATCAG 58.838 40.000 0.00 0.00 0.00 2.90
7633 11740 4.613925 AGAGAGCAAGAAACACATCAGA 57.386 40.909 0.00 0.00 0.00 3.27
7634 11741 4.314121 AGAGAGCAAGAAACACATCAGAC 58.686 43.478 0.00 0.00 0.00 3.51
7635 11742 4.060900 GAGAGCAAGAAACACATCAGACA 58.939 43.478 0.00 0.00 0.00 3.41
7636 11743 4.649692 AGAGCAAGAAACACATCAGACAT 58.350 39.130 0.00 0.00 0.00 3.06
7637 11744 4.694509 AGAGCAAGAAACACATCAGACATC 59.305 41.667 0.00 0.00 0.00 3.06
7638 11745 4.392047 AGCAAGAAACACATCAGACATCA 58.608 39.130 0.00 0.00 0.00 3.07
7749 11864 3.253188 CCAATGGGTTTCATGTATAGCCG 59.747 47.826 0.00 0.00 35.99 5.52
7750 11865 4.133820 CAATGGGTTTCATGTATAGCCGA 58.866 43.478 0.00 0.00 35.99 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 6.322712 AGCAATTGAGGTTTTGTAGTTGGTAA 59.677 34.615 10.34 0.00 0.00 2.85
302 303 2.301870 TGCGAGTAGATGTTTGGAACCT 59.698 45.455 0.00 0.00 0.00 3.50
515 522 1.214424 ACTTAGGCACCCACACAAACT 59.786 47.619 0.00 0.00 0.00 2.66
778 803 6.885735 AAAAACAGAGGAATGAAAAACACG 57.114 33.333 0.00 0.00 0.00 4.49
802 827 6.101296 ACGGGAATAGAATAGGAATCAAGGTT 59.899 38.462 0.00 0.00 0.00 3.50
896 921 9.469807 CAATATAAGTACAGAACTGAGGTCATC 57.530 37.037 0.00 0.00 38.88 2.92
961 994 7.390823 TCTGCAATTTGGTAGTGTGTTATAGA 58.609 34.615 0.00 0.00 0.00 1.98
975 1008 3.861276 TGCTCAGATTCTGCAATTTGG 57.139 42.857 8.89 0.00 33.48 3.28
1073 3289 0.323302 TCCCTGTGATAGCGTGCAAA 59.677 50.000 0.00 0.00 0.00 3.68
1177 3397 6.508088 GCAAAGTTACGACTGCATCTATGTAC 60.508 42.308 0.00 0.00 35.91 2.90
1180 3400 4.329801 TGCAAAGTTACGACTGCATCTATG 59.670 41.667 5.26 0.00 35.91 2.23
1424 3675 5.925509 ACTACAAGTAAAAGCAACAGGAGA 58.074 37.500 0.00 0.00 0.00 3.71
1749 4013 7.255001 CCTCTACCACTTCACGTGTTTTATTTT 60.255 37.037 16.51 0.00 42.20 1.82
2012 4341 1.997311 CAGAGGACCATGCTGGGGA 60.997 63.158 7.06 0.00 43.37 4.81
2424 4768 5.798125 TTGTCATAAAACCATGCCTTCAA 57.202 34.783 0.00 0.00 0.00 2.69
2891 5253 5.882557 ACAGAGGTTAGATTGCTACAAATGG 59.117 40.000 0.00 0.00 0.00 3.16
3238 5619 2.083774 TGGCTTTGCAGGATAGTTTCG 58.916 47.619 0.00 0.00 0.00 3.46
4005 7098 2.425592 CTGCGGTTGACCTGGTCA 59.574 61.111 25.12 25.12 41.09 4.02
4635 7731 0.532573 ACTCAGCATAGTCACCCACG 59.467 55.000 0.00 0.00 0.00 4.94
4655 7751 4.766375 TCGACCCATCTCCAAGAAAATAC 58.234 43.478 0.00 0.00 0.00 1.89
4686 7782 3.795101 GCATGCACTTGACATCTAATTGC 59.205 43.478 14.21 0.00 35.18 3.56
4747 7843 4.047166 AGAGGATGGATATCACCCAAACA 58.953 43.478 4.83 0.00 37.22 2.83
4788 7884 1.070758 TCCTTGAGCGCAGGGAATATC 59.929 52.381 18.93 0.00 46.13 1.63
4826 7922 4.405358 ACAAATCAACTGAAGGCCAAAAGA 59.595 37.500 5.01 0.00 0.00 2.52
4841 7937 7.543868 CCCGAACAAAAGCAATATACAAATCAA 59.456 33.333 0.00 0.00 0.00 2.57
4908 8005 0.255890 ACACCATCCCGCAGCTATTT 59.744 50.000 0.00 0.00 0.00 1.40
4909 8006 0.255890 AACACCATCCCGCAGCTATT 59.744 50.000 0.00 0.00 0.00 1.73
5006 8194 6.750501 CCATCTTAATGCACAAGTGATTTCAG 59.249 38.462 4.04 0.00 0.00 3.02
5147 8337 5.163513 AGCTAAAATTTCAGGTTTGCGATG 58.836 37.500 0.00 0.00 0.00 3.84
5272 8496 9.340695 CAATCGCATACATAAAGTTTCAGAAAA 57.659 29.630 0.00 0.00 0.00 2.29
5273 8497 8.511321 ACAATCGCATACATAAAGTTTCAGAAA 58.489 29.630 0.00 0.00 0.00 2.52
5274 8498 8.039603 ACAATCGCATACATAAAGTTTCAGAA 57.960 30.769 0.00 0.00 0.00 3.02
5275 8499 7.609760 ACAATCGCATACATAAAGTTTCAGA 57.390 32.000 0.00 0.00 0.00 3.27
5276 8500 8.673626 AAACAATCGCATACATAAAGTTTCAG 57.326 30.769 0.00 0.00 0.00 3.02
5286 8510 9.289303 GTTTCAGAATAAAACAATCGCATACAT 57.711 29.630 0.00 0.00 36.76 2.29
5287 8511 8.511321 AGTTTCAGAATAAAACAATCGCATACA 58.489 29.630 2.05 0.00 38.73 2.29
5288 8512 8.895932 AGTTTCAGAATAAAACAATCGCATAC 57.104 30.769 2.05 0.00 38.73 2.39
5291 8515 9.340695 CATAAGTTTCAGAATAAAACAATCGCA 57.659 29.630 2.05 0.00 38.73 5.10
5292 8516 8.313931 GCATAAGTTTCAGAATAAAACAATCGC 58.686 33.333 2.05 0.00 38.73 4.58
5293 8517 9.340695 TGCATAAGTTTCAGAATAAAACAATCG 57.659 29.630 2.05 0.00 38.73 3.34
5406 8633 5.059161 GCATAAGCTCAATCATACCTGACA 58.941 41.667 0.00 0.00 37.91 3.58
5519 8746 6.575267 TCCATTTCATAGTTGCATTCCAATG 58.425 36.000 0.00 0.00 39.40 2.82
5521 8748 6.602410 TTCCATTTCATAGTTGCATTCCAA 57.398 33.333 0.00 0.00 0.00 3.53
5969 9205 4.141711 ACTGACACCGCATGGATTATTACT 60.142 41.667 0.00 0.00 39.21 2.24
5970 9206 4.127171 ACTGACACCGCATGGATTATTAC 58.873 43.478 0.00 0.00 39.21 1.89
5971 9207 4.415881 ACTGACACCGCATGGATTATTA 57.584 40.909 0.00 0.00 39.21 0.98
5972 9208 3.281727 ACTGACACCGCATGGATTATT 57.718 42.857 0.00 0.00 39.21 1.40
5973 9209 3.388024 ACTACTGACACCGCATGGATTAT 59.612 43.478 0.00 0.00 39.21 1.28
5974 9210 2.764010 ACTACTGACACCGCATGGATTA 59.236 45.455 0.00 0.00 39.21 1.75
5975 9211 1.555075 ACTACTGACACCGCATGGATT 59.445 47.619 0.00 0.00 39.21 3.01
5976 9212 1.195115 ACTACTGACACCGCATGGAT 58.805 50.000 0.00 0.00 39.21 3.41
5977 9213 0.973632 AACTACTGACACCGCATGGA 59.026 50.000 0.00 0.00 39.21 3.41
5978 9214 2.094182 ACTAACTACTGACACCGCATGG 60.094 50.000 0.00 0.00 42.84 3.66
5979 9215 3.119459 AGACTAACTACTGACACCGCATG 60.119 47.826 0.00 0.00 0.00 4.06
5980 9216 3.090037 AGACTAACTACTGACACCGCAT 58.910 45.455 0.00 0.00 0.00 4.73
5981 9217 2.486982 GAGACTAACTACTGACACCGCA 59.513 50.000 0.00 0.00 0.00 5.69
5982 9218 2.486982 TGAGACTAACTACTGACACCGC 59.513 50.000 0.00 0.00 0.00 5.68
5983 9219 3.752222 ACTGAGACTAACTACTGACACCG 59.248 47.826 0.00 0.00 0.00 4.94
5984 9220 4.156373 GGACTGAGACTAACTACTGACACC 59.844 50.000 0.00 0.00 0.00 4.16
5985 9221 4.156373 GGGACTGAGACTAACTACTGACAC 59.844 50.000 0.00 0.00 0.00 3.67
5986 9222 4.333690 GGGACTGAGACTAACTACTGACA 58.666 47.826 0.00 0.00 0.00 3.58
5987 9223 3.374678 CGGGACTGAGACTAACTACTGAC 59.625 52.174 0.00 0.00 0.00 3.51
5988 9224 3.607741 CGGGACTGAGACTAACTACTGA 58.392 50.000 0.00 0.00 0.00 3.41
5989 9225 2.683867 CCGGGACTGAGACTAACTACTG 59.316 54.545 0.00 0.00 0.00 2.74
6000 9257 0.246635 AAACGACATCCGGGACTGAG 59.753 55.000 0.00 2.76 43.93 3.35
6037 9294 9.388506 GCCAATGATATAACTGATAACAGCTAT 57.611 33.333 0.00 0.75 46.95 2.97
6046 9303 7.921304 TGTCATAGGCCAATGATATAACTGAT 58.079 34.615 5.01 0.00 38.13 2.90
6309 9566 2.757314 TGATCTTGCTCTCATCGACACT 59.243 45.455 0.00 0.00 0.00 3.55
6491 9760 7.447594 TCCCTAAACTACACTAGGTTTTTCTG 58.552 38.462 0.00 0.00 36.93 3.02
6556 9825 7.371126 TGAATAAACATTGCAAGTCGACATA 57.629 32.000 19.50 0.00 0.00 2.29
6804 10076 6.200286 CACTTGCAATTCATCTATCAAATGGC 59.800 38.462 0.00 0.00 31.29 4.40
6854 10126 7.284919 TCTTGTTCTTACATGACTACTGTGA 57.715 36.000 0.00 0.00 34.56 3.58
6923 10198 3.963476 TTCTTCAACCTTCCCTTCCAA 57.037 42.857 0.00 0.00 0.00 3.53
6944 10219 5.550290 TGCGCATCAATCCTTCTTATCATA 58.450 37.500 5.66 0.00 0.00 2.15
6958 10233 0.518636 GAGCTCTTGTTGCGCATCAA 59.481 50.000 27.19 27.19 35.28 2.57
6985 10260 8.936787 ACTGAAAATCTGATCATCTTATCTCCT 58.063 33.333 0.00 0.00 0.00 3.69
7019 10294 0.034574 TAATGCCAACACTGCCGGAT 60.035 50.000 5.05 0.00 0.00 4.18
7269 10544 6.135290 ACATGGCATTGTATTGTGATGTAC 57.865 37.500 0.00 0.00 0.00 2.90
7286 10561 0.889994 TGCTTGGTGATGAACATGGC 59.110 50.000 0.00 0.00 0.00 4.40
7294 10569 7.439056 AGTTTTGATTTACTTTGCTTGGTGATG 59.561 33.333 0.00 0.00 0.00 3.07
7364 10715 4.001652 CGGACTGTTACTCTGAGTGACTA 58.998 47.826 26.50 15.50 35.92 2.59
7404 11508 8.791675 TGTGCTTGAATGTAATGTAATTTCAGA 58.208 29.630 0.00 0.00 37.03 3.27
7447 11551 5.292101 GTCTCTGTAACATGTTGGCTGTATC 59.708 44.000 21.42 2.38 0.00 2.24
7471 11575 4.034510 GGCTTGGTAATCTCTGAATTGACG 59.965 45.833 0.00 0.00 0.00 4.35
7472 11576 4.034510 CGGCTTGGTAATCTCTGAATTGAC 59.965 45.833 0.00 0.00 0.00 3.18
7473 11577 4.191544 CGGCTTGGTAATCTCTGAATTGA 58.808 43.478 0.00 0.00 0.00 2.57
7474 11578 3.242870 GCGGCTTGGTAATCTCTGAATTG 60.243 47.826 0.00 0.00 0.00 2.32
7581 11687 3.708403 AGATTGGCTGTGTGATCTCAA 57.292 42.857 0.00 0.00 0.00 3.02
7589 11695 3.771216 AGAATTGGAAGATTGGCTGTGT 58.229 40.909 0.00 0.00 0.00 3.72
7605 11712 7.663081 TGATGTGTTTCTTGCTCTCTTAGAATT 59.337 33.333 0.00 0.00 0.00 2.17
7632 11739 4.214437 CAAGTCGCTTTTCTTGTGATGTC 58.786 43.478 0.00 0.00 37.04 3.06
7633 11740 4.214980 CAAGTCGCTTTTCTTGTGATGT 57.785 40.909 0.00 0.00 37.04 3.06
7715 11830 1.005450 ACCCATTGGCTATTCGTTGGT 59.995 47.619 0.00 0.00 33.59 3.67


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

AutoCloner maintained by Alex Coulton.