Multiple sequence alignment - TraesCS7B01G279900

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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 TraesCS7B01G279900 chr7B 100.000 4176 0 0 435 4610 512749705 512753880 0.000000e+00 7712.0
1 TraesCS7B01G279900 chr7B 100.000 104 0 0 1 104 512749271 512749374 4.710000e-45 193.0
2 TraesCS7B01G279900 chr7B 94.286 35 2 0 2095 2129 183292141 183292107 2.000000e-03 54.7
3 TraesCS7B01G279900 chr7D 93.062 2796 132 25 646 3420 485095526 485098280 0.000000e+00 4032.0
4 TraesCS7B01G279900 chr7D 92.910 677 28 11 3419 4090 485098439 485099100 0.000000e+00 966.0
5 TraesCS7B01G279900 chr7D 93.220 354 11 7 4257 4610 485099395 485099735 4.110000e-140 508.0
6 TraesCS7B01G279900 chr7D 96.532 173 5 1 435 607 485095353 485095524 7.550000e-73 285.0
7 TraesCS7B01G279900 chr7D 95.652 92 4 0 1 92 485095232 485095323 1.030000e-31 148.0
8 TraesCS7B01G279900 chr7D 90.805 87 5 1 4162 4248 485099240 485099323 3.770000e-21 113.0
9 TraesCS7B01G279900 chr7D 94.595 37 1 1 4108 4144 629237937 629237972 6.440000e-04 56.5
10 TraesCS7B01G279900 chr7D 96.875 32 1 0 4112 4143 5069398 5069429 2.000000e-03 54.7
11 TraesCS7B01G279900 chr7A 94.587 2494 93 20 435 2927 553382459 553384911 0.000000e+00 3819.0
12 TraesCS7B01G279900 chr7A 82.502 1183 122 55 3457 4610 553385404 553386530 0.000000e+00 959.0
13 TraesCS7B01G279900 chr7A 93.376 468 25 5 2920 3387 553384938 553385399 0.000000e+00 688.0
14 TraesCS7B01G279900 chr7A 100.000 28 0 0 4117 4144 720848370 720848397 8.000000e-03 52.8
15 TraesCS7B01G279900 chr3A 82.906 117 16 3 2051 2167 647054754 647054866 8.160000e-18 102.0
16 TraesCS7B01G279900 chr3A 96.970 33 1 0 1323 1355 575133495 575133463 6.440000e-04 56.5
17 TraesCS7B01G279900 chr3A 100.000 29 0 0 4116 4144 31668531 31668503 2.000000e-03 54.7
18 TraesCS7B01G279900 chr3B 81.739 115 15 5 2054 2167 174726246 174726355 1.770000e-14 91.6
19 TraesCS7B01G279900 chr3B 96.970 33 1 0 1323 1355 572372369 572372337 6.440000e-04 56.5
20 TraesCS7B01G279900 chr6B 100.000 29 0 0 4079 4107 556748401 556748429 2.000000e-03 54.7
21 TraesCS7B01G279900 chr3D 100.000 29 0 0 4116 4144 22054047 22054019 2.000000e-03 54.7


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 TraesCS7B01G279900 chr7B 512749271 512753880 4609 False 3952.500000 7712 100.000000 1 4610 2 chr7B.!!$F1 4609
1 TraesCS7B01G279900 chr7D 485095232 485099735 4503 False 1008.666667 4032 93.696833 1 4610 6 chr7D.!!$F3 4609
2 TraesCS7B01G279900 chr7A 553382459 553386530 4071 False 1822.000000 3819 90.155000 435 4610 3 chr7A.!!$F2 4175

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
981 992 1.138883 TTCTTGCTCCGGATCGACG 59.861 57.895 3.57 0.0 0.00 5.12 F
1415 1427 0.174389 AAGATCACGCTGTGCTCGAT 59.826 50.000 0.00 0.0 34.41 3.59 F
1700 1712 0.604780 CACCCCACTCTGAAGCTGTG 60.605 60.000 0.00 0.0 0.00 3.66 F
2032 2044 1.691434 CTGGGCTTCTAGTGGAGATCC 59.309 57.143 0.00 0.0 32.88 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2836 2851 0.255890 ACAACACTGACAGGCCTTGT 59.744 50.000 0.00 4.75 44.55 3.16 R
2933 2981 1.003355 GCTCAGCCTGCCTGTGTTA 60.003 57.895 0.00 0.00 42.38 2.41 R
2940 2988 1.943340 GTATTTACTGCTCAGCCTGCC 59.057 52.381 0.00 0.00 0.00 4.85 R
3901 4124 0.320771 GTCTCACGTGTCCAAGCCAT 60.321 55.000 16.51 0.00 0.00 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
92 93 3.900892 CCGATCCACCTCGTCCCG 61.901 72.222 0.00 0.00 36.93 5.14
93 94 3.138798 CGATCCACCTCGTCCCGT 61.139 66.667 0.00 0.00 34.00 5.28
96 97 3.595428 ATCCACCTCGTCCCGTCCA 62.595 63.158 0.00 0.00 0.00 4.02
98 99 2.989824 CACCTCGTCCCGTCCAGT 60.990 66.667 0.00 0.00 0.00 4.00
102 103 4.289101 TCGTCCCGTCCAGTCCCA 62.289 66.667 0.00 0.00 0.00 4.37
474 475 1.262151 TCGTCGCTAAGCAAACAAACC 59.738 47.619 0.00 0.00 0.00 3.27
607 608 2.424302 GTACGTGCCACTGGGTGT 59.576 61.111 0.00 0.00 36.17 4.16
608 609 1.959226 GTACGTGCCACTGGGTGTG 60.959 63.158 0.00 0.00 45.80 3.82
609 610 2.436544 TACGTGCCACTGGGTGTGT 61.437 57.895 0.00 0.00 44.81 3.72
610 611 2.652382 TACGTGCCACTGGGTGTGTG 62.652 60.000 0.00 0.00 44.81 3.82
666 667 1.744114 GCCGAGATTCCTTCTTGTCCC 60.744 57.143 0.00 0.00 34.41 4.46
695 696 2.676471 AGGCGGATTGGTTGGTGC 60.676 61.111 0.00 0.00 0.00 5.01
697 698 2.700773 GGCGGATTGGTTGGTGCTC 61.701 63.158 0.00 0.00 0.00 4.26
774 785 3.706373 GGCGGTGAGGAGAAGGCA 61.706 66.667 0.00 0.00 0.00 4.75
777 788 2.947532 CGGTGAGGAGAAGGCAGCA 61.948 63.158 0.00 0.00 0.00 4.41
942 953 2.813042 GACGCTGCTGCTCACTCC 60.813 66.667 14.03 0.00 36.97 3.85
961 972 2.743928 GTGCCCGTCTTCTGCCTG 60.744 66.667 0.00 0.00 0.00 4.85
979 990 1.254975 TGGTTCTTGCTCCGGATCGA 61.255 55.000 3.57 0.00 0.00 3.59
981 992 1.138883 TTCTTGCTCCGGATCGACG 59.861 57.895 3.57 0.00 0.00 5.12
1144 1155 9.209175 AGTGTTGTTTTGTCTAGATCATAGAAC 57.791 33.333 0.00 4.13 0.00 3.01
1168 1179 9.862371 AACTCATACATCAAGTTTACTGTCTAG 57.138 33.333 0.00 0.00 29.09 2.43
1415 1427 0.174389 AAGATCACGCTGTGCTCGAT 59.826 50.000 0.00 0.00 34.41 3.59
1452 1464 1.340017 GGCTCAACCTGGTCATTGCTA 60.340 52.381 0.00 0.00 34.51 3.49
1455 1467 3.877559 CTCAACCTGGTCATTGCTATCA 58.122 45.455 0.00 0.00 0.00 2.15
1476 1488 1.547372 ACAATGGGTTGCTGAATGCTC 59.453 47.619 0.00 0.00 43.37 4.26
1484 1496 1.139095 GCTGAATGCTCTTGCTGCC 59.861 57.895 0.00 0.00 40.48 4.85
1496 1508 0.890542 TTGCTGCCAATGAGAGCGTT 60.891 50.000 0.00 0.00 35.36 4.84
1524 1536 1.344438 ACTGGCTGAATGAGAACGTGA 59.656 47.619 0.00 0.00 0.00 4.35
1541 1553 4.579869 ACGTGAAGCCTTACATTTCTCAT 58.420 39.130 0.00 0.00 0.00 2.90
1685 1697 4.441792 ACAAAATTGAGCTTTTCACACCC 58.558 39.130 0.00 0.00 34.94 4.61
1700 1712 0.604780 CACCCCACTCTGAAGCTGTG 60.605 60.000 0.00 0.00 0.00 3.66
1718 1730 3.093814 TGTGTTCGCTACTTCCTATCCA 58.906 45.455 0.00 0.00 0.00 3.41
1763 1775 8.915057 AGGAAGAAATCATGGTGTATATGAAG 57.085 34.615 0.00 0.00 38.01 3.02
1766 1778 6.604171 AGAAATCATGGTGTATATGAAGCCA 58.396 36.000 0.00 0.00 38.01 4.75
1847 1859 2.433239 GGCTTACTTAACTGATCCGGGA 59.567 50.000 0.00 0.00 0.00 5.14
1937 1949 4.789629 CACTATGACAACATGTTTGATGCG 59.210 41.667 8.77 0.00 37.87 4.73
2032 2044 1.691434 CTGGGCTTCTAGTGGAGATCC 59.309 57.143 0.00 0.00 32.88 3.36
2316 2328 7.787725 ATTAAGGTAAGCATTTACTTCTCGG 57.212 36.000 0.00 0.00 39.30 4.63
2317 2329 3.532542 AGGTAAGCATTTACTTCTCGGC 58.467 45.455 0.00 0.00 39.30 5.54
2318 2330 3.197983 AGGTAAGCATTTACTTCTCGGCT 59.802 43.478 0.00 0.00 39.30 5.52
2319 2331 3.939592 GGTAAGCATTTACTTCTCGGCTT 59.060 43.478 0.00 0.00 43.32 4.35
2320 2332 4.034163 GGTAAGCATTTACTTCTCGGCTTC 59.966 45.833 0.00 0.00 41.38 3.86
2321 2333 3.618690 AGCATTTACTTCTCGGCTTCT 57.381 42.857 0.00 0.00 0.00 2.85
2322 2334 3.526534 AGCATTTACTTCTCGGCTTCTC 58.473 45.455 0.00 0.00 0.00 2.87
2323 2335 2.282820 GCATTTACTTCTCGGCTTCTCG 59.717 50.000 0.00 0.00 0.00 4.04
2370 2382 9.612620 CTAGTCTTTGTTTTCATTGTATTGTCC 57.387 33.333 0.00 0.00 0.00 4.02
2371 2383 8.237811 AGTCTTTGTTTTCATTGTATTGTCCT 57.762 30.769 0.00 0.00 0.00 3.85
2374 2386 8.474025 TCTTTGTTTTCATTGTATTGTCCTGTT 58.526 29.630 0.00 0.00 0.00 3.16
2375 2387 9.097257 CTTTGTTTTCATTGTATTGTCCTGTTT 57.903 29.630 0.00 0.00 0.00 2.83
2376 2388 8.417780 TTGTTTTCATTGTATTGTCCTGTTTG 57.582 30.769 0.00 0.00 0.00 2.93
2377 2389 7.776107 TGTTTTCATTGTATTGTCCTGTTTGA 58.224 30.769 0.00 0.00 0.00 2.69
2378 2390 8.420222 TGTTTTCATTGTATTGTCCTGTTTGAT 58.580 29.630 0.00 0.00 0.00 2.57
2379 2391 8.702438 GTTTTCATTGTATTGTCCTGTTTGATG 58.298 33.333 0.00 0.00 0.00 3.07
2380 2392 6.513806 TCATTGTATTGTCCTGTTTGATGG 57.486 37.500 0.00 0.00 0.00 3.51
2381 2393 6.009589 TCATTGTATTGTCCTGTTTGATGGT 58.990 36.000 0.00 0.00 0.00 3.55
2382 2394 6.493115 TCATTGTATTGTCCTGTTTGATGGTT 59.507 34.615 0.00 0.00 0.00 3.67
2383 2395 7.667635 TCATTGTATTGTCCTGTTTGATGGTTA 59.332 33.333 0.00 0.00 0.00 2.85
2384 2396 8.469200 CATTGTATTGTCCTGTTTGATGGTTAT 58.531 33.333 0.00 0.00 0.00 1.89
2385 2397 8.415950 TTGTATTGTCCTGTTTGATGGTTATT 57.584 30.769 0.00 0.00 0.00 1.40
2386 2398 7.825681 TGTATTGTCCTGTTTGATGGTTATTG 58.174 34.615 0.00 0.00 0.00 1.90
2387 2399 5.720371 TTGTCCTGTTTGATGGTTATTGG 57.280 39.130 0.00 0.00 0.00 3.16
2388 2400 4.991776 TGTCCTGTTTGATGGTTATTGGA 58.008 39.130 0.00 0.00 0.00 3.53
2469 2481 7.855784 TCAAAGCAGATTAGAGGTGGATATA 57.144 36.000 0.00 0.00 0.00 0.86
2519 2531 6.710744 CACTCAAAAGGGTACAGTAGTCAATT 59.289 38.462 0.00 0.00 0.00 2.32
2587 2601 6.452594 AGGGGCCCTATCAATTTAATTTCTT 58.547 36.000 27.62 0.00 28.47 2.52
2816 2831 2.859165 ATCCAGGTCGTGAACATTGT 57.141 45.000 0.00 0.00 0.00 2.71
2866 2881 2.221055 GTCAGTGTTGTGGATGAACGTC 59.779 50.000 0.00 0.00 0.00 4.34
2874 2889 4.066646 TGTGGATGAACGTCTTCTTTGA 57.933 40.909 0.00 0.00 0.00 2.69
2916 2931 4.697514 TGTTGTCCAGAGAAGAACTTCAG 58.302 43.478 15.43 6.16 41.84 3.02
2942 2990 9.983804 GTTGTACTAAATAGAAATAACACAGGC 57.016 33.333 0.00 0.00 0.00 4.85
3018 3072 9.326339 GAAATTAACTTGCCTACTTCTAAAACG 57.674 33.333 0.00 0.00 0.00 3.60
3052 3106 6.120220 CCAATAAGGTCCGAATAAGTTTCCT 58.880 40.000 0.00 0.00 0.00 3.36
3180 3234 8.441312 TTCTTCGAAGGTAGTTTGTTGTTATT 57.559 30.769 24.37 0.00 0.00 1.40
3240 3294 8.292448 GCAAGTTCATGTTCTGAATTCTCTAAA 58.708 33.333 7.05 0.00 45.36 1.85
3267 3321 5.533112 TCCCCTGCAAATAATTTATGGGAA 58.467 37.500 9.35 0.00 36.61 3.97
3355 3410 8.739039 CCACTTATGTTCATTAAAATCACCTCA 58.261 33.333 0.00 0.00 0.00 3.86
3467 3682 6.001449 TGGTACTGCCTATTTCTTGCTTAT 57.999 37.500 0.00 0.00 38.35 1.73
3582 3797 0.605050 TTGCACACTATTCGGCTGCA 60.605 50.000 0.50 0.00 36.08 4.41
3684 3901 1.210478 TGAGGAGTTAGAATGCCTGCC 59.790 52.381 0.00 0.00 0.00 4.85
3685 3902 1.488393 GAGGAGTTAGAATGCCTGCCT 59.512 52.381 0.00 0.00 0.00 4.75
3686 3903 1.211457 AGGAGTTAGAATGCCTGCCTG 59.789 52.381 0.00 0.00 0.00 4.85
3687 3904 1.020437 GAGTTAGAATGCCTGCCTGC 58.980 55.000 0.00 0.00 0.00 4.85
3701 3918 1.168714 GCCTGCTTGTACTGGGAAAG 58.831 55.000 0.00 0.00 0.00 2.62
3708 3925 3.498777 GCTTGTACTGGGAAAGTCAGAAC 59.501 47.826 0.00 0.00 40.56 3.01
3740 3957 0.105760 AATGGTTCCCTGCACACCAA 60.106 50.000 6.44 0.00 43.85 3.67
3741 3958 0.827507 ATGGTTCCCTGCACACCAAC 60.828 55.000 6.44 0.00 43.85 3.77
3742 3959 2.200337 GGTTCCCTGCACACCAACC 61.200 63.158 0.00 0.00 0.00 3.77
3743 3960 1.454847 GTTCCCTGCACACCAACCA 60.455 57.895 0.00 0.00 0.00 3.67
3751 3968 0.028902 GCACACCAACCAGTTTCGTC 59.971 55.000 0.00 0.00 0.00 4.20
3796 4017 5.660460 ACCTGTGAAAAGAACATGGTTTTC 58.340 37.500 17.06 17.06 41.22 2.29
3920 4143 0.320771 ATGGCTTGGACACGTGAGAC 60.321 55.000 25.01 12.05 0.00 3.36
3946 4169 7.586300 CGCTTTTATCTTTTCTTTTTCTGACGA 59.414 33.333 0.00 0.00 0.00 4.20
3961 4184 4.373116 CGACCTGGTGGACGTGGG 62.373 72.222 2.82 0.00 44.19 4.61
3994 4217 1.340017 TGCCAGGCTGACAGGATTAAC 60.340 52.381 17.94 0.00 0.00 2.01
4000 4223 2.492088 GGCTGACAGGATTAACAAACCC 59.508 50.000 4.26 0.00 0.00 4.11
4001 4224 2.492088 GCTGACAGGATTAACAAACCCC 59.508 50.000 4.26 0.00 0.00 4.95
4002 4225 2.747446 CTGACAGGATTAACAAACCCCG 59.253 50.000 0.00 0.00 0.00 5.73
4034 4257 4.262335 CGTTTCTTCCCCAGTAAGTAGTGT 60.262 45.833 0.00 0.00 0.00 3.55
4039 4263 7.217028 TCTTCCCCAGTAAGTAGTGTATCTA 57.783 40.000 0.00 0.00 0.00 1.98
4040 4264 7.059156 TCTTCCCCAGTAAGTAGTGTATCTAC 58.941 42.308 0.00 0.00 46.68 2.59
4080 4304 1.268899 CTCAAGGCACCTGCTTTTCTG 59.731 52.381 0.00 0.00 38.33 3.02
4082 4306 0.468771 AAGGCACCTGCTTTTCTGCT 60.469 50.000 0.00 0.00 36.99 4.24
4090 4314 1.296715 GCTTTTCTGCTCCCTCCGA 59.703 57.895 0.00 0.00 0.00 4.55
4091 4315 0.107459 GCTTTTCTGCTCCCTCCGAT 60.107 55.000 0.00 0.00 0.00 4.18
4092 4316 1.946745 CTTTTCTGCTCCCTCCGATC 58.053 55.000 0.00 0.00 0.00 3.69
4093 4317 1.484240 CTTTTCTGCTCCCTCCGATCT 59.516 52.381 0.00 0.00 0.00 2.75
4094 4318 0.826715 TTTCTGCTCCCTCCGATCTG 59.173 55.000 0.00 0.00 0.00 2.90
4095 4319 0.033109 TTCTGCTCCCTCCGATCTGA 60.033 55.000 0.00 0.00 0.00 3.27
4096 4320 0.033109 TCTGCTCCCTCCGATCTGAA 60.033 55.000 0.00 0.00 0.00 3.02
4098 4322 1.415659 CTGCTCCCTCCGATCTGAATT 59.584 52.381 0.00 0.00 0.00 2.17
4099 4323 2.630098 CTGCTCCCTCCGATCTGAATTA 59.370 50.000 0.00 0.00 0.00 1.40
4101 4325 3.648067 TGCTCCCTCCGATCTGAATTAAT 59.352 43.478 0.00 0.00 0.00 1.40
4102 4326 4.103153 TGCTCCCTCCGATCTGAATTAATT 59.897 41.667 0.00 0.00 0.00 1.40
4103 4327 4.453819 GCTCCCTCCGATCTGAATTAATTG 59.546 45.833 5.17 0.00 0.00 2.32
4104 4328 5.743130 GCTCCCTCCGATCTGAATTAATTGA 60.743 44.000 5.17 0.00 0.00 2.57
4105 4329 6.439636 TCCCTCCGATCTGAATTAATTGAT 57.560 37.500 5.17 3.10 0.00 2.57
4106 4330 6.233434 TCCCTCCGATCTGAATTAATTGATG 58.767 40.000 5.17 0.00 0.00 3.07
4107 4331 6.043127 TCCCTCCGATCTGAATTAATTGATGA 59.957 38.462 5.17 1.50 0.00 2.92
4114 4357 6.762702 TCTGAATTAATTGATGAAGCTGCA 57.237 33.333 5.17 0.00 0.00 4.41
4127 4370 7.173863 GATGAAGCTGCATCAATTAATTTGG 57.826 36.000 27.17 0.00 43.21 3.28
4139 4382 6.423182 TCAATTAATTTGGATCGAAGGGAGT 58.577 36.000 0.00 0.00 35.92 3.85
4144 4387 4.996788 TTTGGATCGAAGGGAGTACTAC 57.003 45.455 0.00 0.00 0.00 2.73
4145 4388 3.947612 TGGATCGAAGGGAGTACTACT 57.052 47.619 4.77 0.00 0.00 2.57
4146 4389 5.378230 TTGGATCGAAGGGAGTACTACTA 57.622 43.478 4.77 0.00 0.00 1.82
4147 4390 4.970711 TGGATCGAAGGGAGTACTACTAG 58.029 47.826 4.77 1.35 0.00 2.57
4148 4391 4.657504 TGGATCGAAGGGAGTACTACTAGA 59.342 45.833 4.77 6.38 0.00 2.43
4150 4393 4.414337 TCGAAGGGAGTACTACTAGACC 57.586 50.000 4.77 0.00 0.00 3.85
4151 4394 4.036518 TCGAAGGGAGTACTACTAGACCT 58.963 47.826 4.77 0.00 31.03 3.85
4152 4395 4.472833 TCGAAGGGAGTACTACTAGACCTT 59.527 45.833 4.77 14.64 38.67 3.50
4154 4397 5.990996 CGAAGGGAGTACTACTAGACCTTAG 59.009 48.000 4.77 12.30 37.18 2.18
4155 4398 6.183360 CGAAGGGAGTACTACTAGACCTTAGA 60.183 46.154 4.77 0.00 37.18 2.10
4159 4402 6.767423 GGGAGTACTACTAGACCTTAGAACTG 59.233 46.154 4.77 0.00 0.00 3.16
4160 4403 7.365473 GGGAGTACTACTAGACCTTAGAACTGA 60.365 44.444 4.77 0.00 0.00 3.41
4227 4523 8.627208 ATGTGACTTTCAATGTCTTTCATACT 57.373 30.769 5.13 0.00 35.48 2.12
4314 4672 6.446781 CAGCATGGTCAGATGATTTTACTT 57.553 37.500 0.00 0.00 0.00 2.24
4315 4673 6.493116 CAGCATGGTCAGATGATTTTACTTC 58.507 40.000 0.00 0.00 0.00 3.01
4342 4700 9.521841 TTCCAATAATTGTTGTACTTATGTCCA 57.478 29.630 13.13 0.00 0.00 4.02
4376 4734 4.375405 CGTGTAATAAGCATGATGAGTCGC 60.375 45.833 0.00 0.00 0.00 5.19
4382 4740 3.097877 AGCATGATGAGTCGCGATTTA 57.902 42.857 14.06 4.98 0.00 1.40
4388 4746 6.344468 GCATGATGAGTCGCGATTTATTTTTG 60.344 38.462 14.06 10.31 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
501 502 1.004862 GCCCTTTTCTCCAGGCTAACT 59.995 52.381 0.00 0.00 42.34 2.24
695 696 3.620821 GGAGAAAGAATCCGCAAGAAGAG 59.379 47.826 0.00 0.00 43.02 2.85
959 970 0.807667 CGATCCGGAGCAAGAACCAG 60.808 60.000 21.44 0.00 0.00 4.00
961 972 0.806492 GTCGATCCGGAGCAAGAACC 60.806 60.000 21.44 0.00 0.00 3.62
1102 1113 9.829507 AAAACAACACTGAATTGAATTGGATAA 57.170 25.926 0.00 0.00 0.00 1.75
1103 1114 9.258826 CAAAACAACACTGAATTGAATTGGATA 57.741 29.630 0.00 0.00 0.00 2.59
1144 1155 8.194104 AGCTAGACAGTAAACTTGATGTATGAG 58.806 37.037 0.00 0.00 0.00 2.90
1168 1179 0.942884 GTTGCAAAAGCCTGCTCAGC 60.943 55.000 0.00 0.00 43.07 4.26
1404 1416 1.900585 TTGAACGCATCGAGCACAGC 61.901 55.000 7.47 0.00 46.13 4.40
1415 1427 1.228124 CCCTGTCCCTTTGAACGCA 60.228 57.895 0.00 0.00 0.00 5.24
1455 1467 2.460757 GCATTCAGCAACCCATTGTT 57.539 45.000 0.00 0.00 44.79 2.83
1476 1488 1.303799 ACGCTCTCATTGGCAGCAAG 61.304 55.000 0.00 0.00 32.27 4.01
1484 1496 1.394572 TCAATCGCAACGCTCTCATTG 59.605 47.619 0.00 0.00 0.00 2.82
1496 1508 1.089112 CATTCAGCCAGTCAATCGCA 58.911 50.000 0.00 0.00 0.00 5.10
1524 1536 4.332819 GCGTGTATGAGAAATGTAAGGCTT 59.667 41.667 4.58 4.58 0.00 4.35
1541 1553 1.996898 GTGATTCCAACGATGCGTGTA 59.003 47.619 0.00 0.00 39.99 2.90
1685 1697 1.143305 CGAACACAGCTTCAGAGTGG 58.857 55.000 6.15 0.00 37.58 4.00
1700 1712 2.223994 GGGTGGATAGGAAGTAGCGAAC 60.224 54.545 0.00 0.00 0.00 3.95
1718 1730 2.363306 TGAAAACACATGCAGAGGGT 57.637 45.000 0.00 0.00 0.00 4.34
1763 1775 0.746659 AAAACAAGTCCAGCAGTGGC 59.253 50.000 0.00 0.00 44.60 5.01
1766 1778 1.670811 CGTGAAAACAAGTCCAGCAGT 59.329 47.619 0.00 0.00 0.00 4.40
1847 1859 7.665690 AGAGAGCATAATTAATGTCGATCTGT 58.334 34.615 4.35 0.00 37.93 3.41
1972 1984 5.820423 CGGACTTCCATGTCATTATAACCAA 59.180 40.000 0.00 0.00 38.61 3.67
2032 2044 2.753452 ACTGATGCTCCTGCTTGATTTG 59.247 45.455 0.00 0.00 40.48 2.32
2317 2329 2.969628 ACAAGTAGATGGGCGAGAAG 57.030 50.000 0.00 0.00 0.00 2.85
2318 2330 3.334691 CAAACAAGTAGATGGGCGAGAA 58.665 45.455 0.00 0.00 0.00 2.87
2319 2331 2.935238 GCAAACAAGTAGATGGGCGAGA 60.935 50.000 0.00 0.00 0.00 4.04
2320 2332 1.398390 GCAAACAAGTAGATGGGCGAG 59.602 52.381 0.00 0.00 0.00 5.03
2321 2333 1.448985 GCAAACAAGTAGATGGGCGA 58.551 50.000 0.00 0.00 0.00 5.54
2322 2334 0.451783 GGCAAACAAGTAGATGGGCG 59.548 55.000 0.00 0.00 0.00 6.13
2323 2335 0.817654 GGGCAAACAAGTAGATGGGC 59.182 55.000 0.00 0.00 0.00 5.36
2469 2481 6.260714 GGCAATTGATGACTTTGGAACTTTTT 59.739 34.615 10.34 0.00 32.61 1.94
2519 2531 5.938125 GGTTTGGACTTGAAAGCTATGTCTA 59.062 40.000 0.00 0.00 0.00 2.59
2587 2601 1.543871 CCATGATCCATGATGCACGGA 60.544 52.381 8.38 0.00 43.81 4.69
2680 2694 4.586841 CCAAGACAGGGATGGTGTTTTTAA 59.413 41.667 0.00 0.00 0.00 1.52
2681 2695 4.148838 CCAAGACAGGGATGGTGTTTTTA 58.851 43.478 0.00 0.00 0.00 1.52
2721 2736 4.498520 CAGACCTCGCGGCGTCAT 62.499 66.667 22.90 8.49 0.00 3.06
2836 2851 0.255890 ACAACACTGACAGGCCTTGT 59.744 50.000 0.00 4.75 44.55 3.16
2866 2881 5.520376 ACCAATCCTGTTTGTCAAAGAAG 57.480 39.130 0.00 0.00 0.00 2.85
2874 2889 4.479158 ACATTGGTACCAATCCTGTTTGT 58.521 39.130 32.88 24.83 43.92 2.83
2916 2931 9.983804 GCCTGTGTTATTTCTATTTAGTACAAC 57.016 33.333 0.00 0.00 0.00 3.32
2933 2981 1.003355 GCTCAGCCTGCCTGTGTTA 60.003 57.895 0.00 0.00 42.38 2.41
2940 2988 1.943340 GTATTTACTGCTCAGCCTGCC 59.057 52.381 0.00 0.00 0.00 4.85
2941 2989 2.611292 CAGTATTTACTGCTCAGCCTGC 59.389 50.000 4.88 0.00 46.03 4.85
3018 3072 6.385649 TCGGACCTTATTGGCATTTAAATC 57.614 37.500 0.00 0.00 40.22 2.17
3065 3119 7.067008 CCAACTGGGTAAAGAGGTTACATAATG 59.933 40.741 0.00 0.00 43.48 1.90
3145 3199 6.166982 ACTACCTTCGAAGAAAGGAATTGAG 58.833 40.000 26.61 7.36 45.90 3.02
3180 3234 7.564793 ACCTCATTCAATTATGCACTACACTA 58.435 34.615 0.00 0.00 0.00 2.74
3200 3254 5.164620 TGAACTTGCAGATCAATACCTCA 57.835 39.130 0.00 0.00 33.57 3.86
3240 3294 6.126796 CCCATAAATTATTTGCAGGGGAACTT 60.127 38.462 4.64 0.00 34.97 2.66
3242 3296 5.365314 TCCCATAAATTATTTGCAGGGGAAC 59.635 40.000 17.54 0.00 39.03 3.62
3355 3410 7.999450 TTTTTATTACACAATACCCGGAACT 57.001 32.000 0.73 0.00 0.00 3.01
3427 3642 7.251281 GCAGTACCAGAATCCAATAGAAAAAC 58.749 38.462 0.00 0.00 0.00 2.43
3467 3682 4.058124 GTGCTATCATCATACGCCAAAGA 58.942 43.478 0.00 0.00 0.00 2.52
3537 3752 2.729479 CCAGGCTCGCATCTCCTGT 61.729 63.158 6.74 0.00 44.41 4.00
3684 3901 3.070018 CTGACTTTCCCAGTACAAGCAG 58.930 50.000 0.00 0.00 35.01 4.24
3685 3902 2.703536 TCTGACTTTCCCAGTACAAGCA 59.296 45.455 0.00 0.00 35.01 3.91
3686 3903 3.402628 TCTGACTTTCCCAGTACAAGC 57.597 47.619 0.00 0.00 35.01 4.01
3687 3904 3.741344 CGTTCTGACTTTCCCAGTACAAG 59.259 47.826 0.00 0.00 35.01 3.16
3701 3918 7.312899 ACCATTATTTGAATTTCCGTTCTGAC 58.687 34.615 0.00 0.00 0.00 3.51
3740 3957 1.474498 GGGAACACAGACGAAACTGGT 60.474 52.381 11.80 5.98 41.59 4.00
3741 3958 1.226746 GGGAACACAGACGAAACTGG 58.773 55.000 11.80 5.53 41.59 4.00
3742 3959 1.202651 AGGGGAACACAGACGAAACTG 60.203 52.381 0.00 0.00 42.78 3.16
3743 3960 1.070289 GAGGGGAACACAGACGAAACT 59.930 52.381 0.00 0.00 0.00 2.66
3751 3968 1.059913 AAGGAGTGAGGGGAACACAG 58.940 55.000 0.00 0.00 40.25 3.66
3901 4124 0.320771 GTCTCACGTGTCCAAGCCAT 60.321 55.000 16.51 0.00 0.00 4.40
3902 4125 1.069090 GTCTCACGTGTCCAAGCCA 59.931 57.895 16.51 0.00 0.00 4.75
3904 4127 2.658707 GCGTCTCACGTGTCCAAGC 61.659 63.158 16.51 12.05 44.73 4.01
3920 4143 7.586300 TCGTCAGAAAAAGAAAAGATAAAAGCG 59.414 33.333 0.00 0.00 0.00 4.68
3946 4169 3.556306 CACCCACGTCCACCAGGT 61.556 66.667 0.00 0.00 35.89 4.00
3961 4184 0.883833 CCTGGCAGTTCAATGGACAC 59.116 55.000 14.43 0.00 0.00 3.67
3994 4217 1.357334 CGACCAACAACGGGGTTTG 59.643 57.895 0.00 0.00 37.57 2.93
4000 4223 1.003223 GGAAGAAACGACCAACAACGG 60.003 52.381 0.00 0.00 0.00 4.44
4001 4224 1.003223 GGGAAGAAACGACCAACAACG 60.003 52.381 0.00 0.00 0.00 4.10
4002 4225 1.335810 GGGGAAGAAACGACCAACAAC 59.664 52.381 0.00 0.00 0.00 3.32
4034 4257 6.092092 GCAACAACATGCAATTGTGTAGATA 58.908 36.000 17.62 0.00 45.70 1.98
4047 4271 1.774639 CCTTGAGTGCAACAACATGC 58.225 50.000 0.00 0.00 46.58 4.06
4048 4272 1.067364 TGCCTTGAGTGCAACAACATG 59.933 47.619 0.00 0.00 41.43 3.21
4049 4273 1.067516 GTGCCTTGAGTGCAACAACAT 59.932 47.619 0.00 0.00 41.06 2.71
4050 4274 0.455410 GTGCCTTGAGTGCAACAACA 59.545 50.000 0.00 0.00 41.06 3.33
4051 4275 0.249031 GGTGCCTTGAGTGCAACAAC 60.249 55.000 0.00 0.00 45.74 3.32
4052 4276 2.114638 GGTGCCTTGAGTGCAACAA 58.885 52.632 7.25 7.25 45.74 2.83
4080 4304 3.753294 TTAATTCAGATCGGAGGGAGC 57.247 47.619 0.00 0.00 0.00 4.70
4082 4306 5.887214 TCAATTAATTCAGATCGGAGGGA 57.113 39.130 0.00 0.00 0.00 4.20
4090 4314 7.342769 TGCAGCTTCATCAATTAATTCAGAT 57.657 32.000 0.00 0.00 0.00 2.90
4091 4315 6.762702 TGCAGCTTCATCAATTAATTCAGA 57.237 33.333 0.00 0.00 0.00 3.27
4092 4316 7.200455 TGATGCAGCTTCATCAATTAATTCAG 58.800 34.615 24.12 0.00 46.84 3.02
4093 4317 7.102847 TGATGCAGCTTCATCAATTAATTCA 57.897 32.000 24.12 1.72 46.84 2.57
4103 4327 6.982141 TCCAAATTAATTGATGCAGCTTCATC 59.018 34.615 18.15 18.15 41.85 2.92
4104 4328 6.880484 TCCAAATTAATTGATGCAGCTTCAT 58.120 32.000 11.58 0.00 41.85 2.57
4105 4329 6.283544 TCCAAATTAATTGATGCAGCTTCA 57.716 33.333 2.53 6.89 41.85 3.02
4106 4330 6.143438 CGATCCAAATTAATTGATGCAGCTTC 59.857 38.462 2.53 1.18 41.85 3.86
4107 4331 5.981315 CGATCCAAATTAATTGATGCAGCTT 59.019 36.000 2.53 0.00 41.85 3.74
4114 4357 7.062957 ACTCCCTTCGATCCAAATTAATTGAT 58.937 34.615 0.39 1.14 41.85 2.57
4125 4368 3.947612 AGTAGTACTCCCTTCGATCCA 57.052 47.619 0.00 0.00 0.00 3.41
4127 4370 4.996758 GGTCTAGTAGTACTCCCTTCGATC 59.003 50.000 5.96 0.00 0.00 3.69
4146 4389 9.442047 CATGATTTTAAGTCAGTTCTAAGGTCT 57.558 33.333 0.00 0.00 0.00 3.85
4147 4390 8.669243 CCATGATTTTAAGTCAGTTCTAAGGTC 58.331 37.037 0.00 0.00 0.00 3.85
4148 4391 8.383175 TCCATGATTTTAAGTCAGTTCTAAGGT 58.617 33.333 0.00 0.00 0.00 3.50
4152 4395 9.010029 GGTTTCCATGATTTTAAGTCAGTTCTA 57.990 33.333 0.00 0.00 0.00 2.10
4154 4397 7.595130 GTGGTTTCCATGATTTTAAGTCAGTTC 59.405 37.037 0.00 0.00 35.28 3.01
4155 4398 7.069331 TGTGGTTTCCATGATTTTAAGTCAGTT 59.931 33.333 0.00 0.00 35.28 3.16
4159 4402 8.547894 GTTTTGTGGTTTCCATGATTTTAAGTC 58.452 33.333 0.00 0.00 35.28 3.01
4160 4403 7.497579 GGTTTTGTGGTTTCCATGATTTTAAGT 59.502 33.333 0.00 0.00 35.28 2.24
4205 4501 9.208022 CAGTAGTATGAAAGACATTGAAAGTCA 57.792 33.333 3.27 0.00 40.07 3.41
4225 4521 0.539051 CAGGCCAGCTTAGCAGTAGT 59.461 55.000 5.01 0.00 0.00 2.73
4226 4522 0.539051 ACAGGCCAGCTTAGCAGTAG 59.461 55.000 5.01 0.00 0.00 2.57
4227 4523 1.480954 GTACAGGCCAGCTTAGCAGTA 59.519 52.381 5.01 6.83 0.00 2.74
4342 4700 5.189928 TGCTTATTACACGTGGATCCAAAT 58.810 37.500 18.20 14.51 0.00 2.32
4382 4740 7.326789 CGACTCATCATGCTTTTGTACAAAAAT 59.673 33.333 28.52 19.66 39.49 1.82
4388 4746 4.928661 ACGACTCATCATGCTTTTGTAC 57.071 40.909 0.00 0.00 0.00 2.90
4574 4937 9.148879 CTTCTCCTTTTTCTCCCTGATAGTATA 57.851 37.037 0.00 0.00 0.00 1.47
4575 4938 7.625682 ACTTCTCCTTTTTCTCCCTGATAGTAT 59.374 37.037 0.00 0.00 0.00 2.12
4576 4939 6.960542 ACTTCTCCTTTTTCTCCCTGATAGTA 59.039 38.462 0.00 0.00 0.00 1.82
4577 4940 5.788014 ACTTCTCCTTTTTCTCCCTGATAGT 59.212 40.000 0.00 0.00 0.00 2.12
4578 4941 6.306643 ACTTCTCCTTTTTCTCCCTGATAG 57.693 41.667 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.