Multiple sequence alignment - TraesCS6A01G353800

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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 TraesCS6A01G353800 chr6A 100.000 4852 0 0 1 4852 585433549 585428698 0.000000e+00 8961.0
1 TraesCS6A01G353800 chr6A 85.646 209 15 4 962 1170 391629150 391628957 6.370000e-49 206.0
2 TraesCS6A01G353800 chr6B 91.713 4163 207 68 726 4852 661343750 661339690 0.000000e+00 5650.0
3 TraesCS6A01G353800 chr6B 86.901 626 72 4 40 656 661400934 661400310 0.000000e+00 693.0
4 TraesCS6A01G353800 chr6B 83.333 192 31 1 49 240 661459570 661459380 4.990000e-40 176.0
5 TraesCS6A01G353800 chr6B 100.000 28 0 0 677 704 661400322 661400295 9.000000e-03 52.8
6 TraesCS6A01G353800 chr6D 92.829 3263 149 34 1630 4852 437168406 437165189 0.000000e+00 4650.0
7 TraesCS6A01G353800 chr6D 90.863 996 42 28 726 1717 437169352 437168402 0.000000e+00 1290.0
8 TraesCS6A01G353800 chr6D 87.810 484 49 6 1 478 437172204 437171725 4.240000e-155 558.0
9 TraesCS6A01G353800 chr4B 93.431 274 18 0 4579 4852 429270121 429269848 1.630000e-109 407.0
10 TraesCS6A01G353800 chr4A 91.513 271 23 0 4582 4852 589150554 589150284 1.650000e-99 374.0
11 TraesCS6A01G353800 chr3A 90.110 273 21 4 4579 4851 681626852 681626586 2.780000e-92 350.0
12 TraesCS6A01G353800 chr7A 95.385 195 9 0 4658 4852 130190243 130190049 1.310000e-80 311.0
13 TraesCS6A01G353800 chr7A 93.151 146 7 1 4664 4809 130190537 130190395 1.370000e-50 211.0
14 TraesCS6A01G353800 chr5A 86.603 209 13 1 962 1170 522677036 522676843 2.940000e-52 217.0
15 TraesCS6A01G353800 chr5A 85.646 209 15 8 962 1170 149695587 149695394 6.370000e-49 206.0
16 TraesCS6A01G353800 chr1A 87.302 189 9 3 982 1170 565924523 565924696 8.230000e-48 202.0


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 TraesCS6A01G353800 chr6A 585428698 585433549 4851 True 8961.0 8961 100.000000 1 4852 1 chr6A.!!$R2 4851
1 TraesCS6A01G353800 chr6B 661339690 661343750 4060 True 5650.0 5650 91.713000 726 4852 1 chr6B.!!$R1 4126
2 TraesCS6A01G353800 chr6B 661400295 661400934 639 True 372.9 693 93.450500 40 704 2 chr6B.!!$R3 664
3 TraesCS6A01G353800 chr6D 437165189 437172204 7015 True 2166.0 4650 90.500667 1 4852 3 chr6D.!!$R1 4851

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
527 629 0.030092 AGCCTGCCCTATGGGTCTAA 60.030 55.0 4.42 0.00 46.51 2.10 F
902 3061 0.037590 CCCAAATCGAACCCCAGACA 59.962 55.0 0.00 0.00 0.00 3.41 F
1523 3692 0.522180 CGTCAGCTTCTACGGTGAGT 59.478 55.0 5.35 0.00 41.53 3.41 F
2105 4375 1.246649 AATGTTGGCGCTGTCAATCA 58.753 45.0 7.64 5.15 27.28 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 3696 0.771755 AGCGGAAGGAAAAAGGGTCT 59.228 50.000 0.00 0.0 0.00 3.85 R
1833 4093 1.064017 TGTTTGGTCCAAGAAGTGCCT 60.064 47.619 4.09 0.0 0.00 4.75 R
2352 4638 2.159037 GCGAACAGCTAGGTTAAACCAC 59.841 50.000 0.00 0.0 41.38 4.16 R
3926 6218 0.375454 CACAGCCAAAACACGTTCGA 59.625 50.000 0.00 0.0 0.00 3.71 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
26 27 4.437390 GCATCGCCAAACATATATACAGCC 60.437 45.833 0.00 0.00 0.00 4.85
27 28 4.344359 TCGCCAAACATATATACAGCCA 57.656 40.909 0.00 0.00 0.00 4.75
46 52 1.407258 CAAAAAGAGGAACGGGCAACA 59.593 47.619 0.00 0.00 39.74 3.33
65 71 1.077716 GAGCAGGCGGGTTGGTAAT 60.078 57.895 0.00 0.00 0.00 1.89
126 132 1.609783 CCCACTCCCACCCAGAATC 59.390 63.158 0.00 0.00 0.00 2.52
144 150 1.497991 TCACGTGAGCGGAAGAAAAG 58.502 50.000 15.76 0.00 43.45 2.27
163 169 1.228124 CAAGGGAGCCGACCAAACA 60.228 57.895 0.00 0.00 0.00 2.83
175 181 4.453136 GCCGACCAAACAATTCACTTACTA 59.547 41.667 0.00 0.00 0.00 1.82
201 208 4.261572 GGAGAGTGAGATCAGTGAGCATAC 60.262 50.000 11.60 8.86 0.00 2.39
202 209 3.636300 AGAGTGAGATCAGTGAGCATACC 59.364 47.826 11.60 3.89 0.00 2.73
234 241 1.818060 TGCCAAATCCACCGATCAAAG 59.182 47.619 0.00 0.00 0.00 2.77
236 243 1.202177 CCAAATCCACCGATCAAAGCG 60.202 52.381 0.00 0.00 0.00 4.68
257 264 3.247442 GTTCGATCATACAACACGTCCA 58.753 45.455 0.00 0.00 0.00 4.02
277 284 3.711842 ACACACGCACGCCGAATG 61.712 61.111 2.93 3.56 41.02 2.67
286 293 0.871722 CACGCCGAATGAGAAAACCA 59.128 50.000 0.00 0.00 0.00 3.67
290 297 1.611491 GCCGAATGAGAAAACCAACCA 59.389 47.619 0.00 0.00 0.00 3.67
295 302 0.260230 TGAGAAAACCAACCAGGCCA 59.740 50.000 5.01 0.00 43.14 5.36
311 318 1.541588 GGCCACAGAGTCCAAAATCAC 59.458 52.381 0.00 0.00 0.00 3.06
315 322 2.224079 CACAGAGTCCAAAATCACGGTG 59.776 50.000 0.56 0.56 0.00 4.94
337 344 1.337823 ACGCTCTAAACACGCCATCTT 60.338 47.619 0.00 0.00 0.00 2.40
339 346 2.159627 CGCTCTAAACACGCCATCTTTT 59.840 45.455 0.00 0.00 0.00 2.27
366 382 0.890683 AACAACAATAGCAGGCCAGC 59.109 50.000 13.11 13.11 0.00 4.85
379 395 4.402851 CCAGCTAGGCAAAGCACA 57.597 55.556 13.41 0.00 45.30 4.57
471 487 3.976942 CAGCAAAAGGACGATTCAACAAG 59.023 43.478 0.00 0.00 0.00 3.16
489 591 3.201266 ACAAGGTAGACTCAACCAACCAA 59.799 43.478 0.00 0.00 39.64 3.67
499 601 0.845337 AACCAACCAACTAACCCCGA 59.155 50.000 0.00 0.00 0.00 5.14
504 606 1.740296 CCAACTAACCCCGACAGCG 60.740 63.158 0.00 0.00 37.24 5.18
527 629 0.030092 AGCCTGCCCTATGGGTCTAA 60.030 55.000 4.42 0.00 46.51 2.10
533 635 1.878102 GCCCTATGGGTCTAACATGCG 60.878 57.143 4.42 0.00 46.51 4.73
576 2697 4.701956 ACGATGTTCATTTAGCCTTTGG 57.298 40.909 0.00 0.00 0.00 3.28
588 2709 2.118076 CTTTGGCTGGCTTGGGGA 59.882 61.111 2.00 0.00 0.00 4.81
643 2764 3.019964 ATGCTTGGAGCGTGTTTCA 57.980 47.368 0.00 0.00 46.26 2.69
645 2766 1.317613 TGCTTGGAGCGTGTTTCATT 58.682 45.000 0.00 0.00 46.26 2.57
647 2768 1.266718 GCTTGGAGCGTGTTTCATTGA 59.733 47.619 0.00 0.00 0.00 2.57
648 2769 2.095059 GCTTGGAGCGTGTTTCATTGAT 60.095 45.455 0.00 0.00 0.00 2.57
650 2771 3.057969 TGGAGCGTGTTTCATTGATCT 57.942 42.857 0.00 0.00 0.00 2.75
652 2773 4.769688 TGGAGCGTGTTTCATTGATCTAT 58.230 39.130 0.00 0.00 0.00 1.98
653 2774 5.185454 TGGAGCGTGTTTCATTGATCTATT 58.815 37.500 0.00 0.00 0.00 1.73
654 2775 5.065090 TGGAGCGTGTTTCATTGATCTATTG 59.935 40.000 0.00 0.00 0.00 1.90
656 2777 6.017605 GGAGCGTGTTTCATTGATCTATTGAT 60.018 38.462 0.00 0.00 35.26 2.57
657 2778 7.325660 AGCGTGTTTCATTGATCTATTGATT 57.674 32.000 0.00 0.00 32.19 2.57
658 2779 7.765307 AGCGTGTTTCATTGATCTATTGATTT 58.235 30.769 0.00 0.00 32.19 2.17
715 2851 1.493022 ACCTGCAACCTACAACCAGAA 59.507 47.619 0.00 0.00 0.00 3.02
770 2912 2.283809 CCAACCCAACCCAACCCA 59.716 61.111 0.00 0.00 0.00 4.51
773 2915 1.383386 AACCCAACCCAACCCAACC 60.383 57.895 0.00 0.00 0.00 3.77
774 2916 2.525629 CCCAACCCAACCCAACCC 60.526 66.667 0.00 0.00 0.00 4.11
775 2917 2.525629 CCAACCCAACCCAACCCC 60.526 66.667 0.00 0.00 0.00 4.95
776 2918 2.283809 CAACCCAACCCAACCCCA 59.716 61.111 0.00 0.00 0.00 4.96
817 2959 0.375803 AATAACAAATCCGCGACCGC 59.624 50.000 8.23 4.06 37.85 5.68
819 2961 0.949588 TAACAAATCCGCGACCGCAA 60.950 50.000 8.23 2.17 42.06 4.85
820 2962 2.202298 CAAATCCGCGACCGCAAC 60.202 61.111 8.23 0.00 42.06 4.17
821 2963 3.428282 AAATCCGCGACCGCAACC 61.428 61.111 8.23 0.00 42.06 3.77
826 2968 4.204891 CGCGACCGCAACCGAATC 62.205 66.667 14.91 0.00 42.06 2.52
827 2969 3.861263 GCGACCGCAACCGAATCC 61.861 66.667 9.73 0.00 41.49 3.01
828 2970 2.433491 CGACCGCAACCGAATCCA 60.433 61.111 0.00 0.00 36.29 3.41
829 2971 2.736682 CGACCGCAACCGAATCCAC 61.737 63.158 0.00 0.00 36.29 4.02
830 2972 1.375523 GACCGCAACCGAATCCACT 60.376 57.895 0.00 0.00 36.29 4.00
831 2973 0.953960 GACCGCAACCGAATCCACTT 60.954 55.000 0.00 0.00 36.29 3.16
832 2974 0.953960 ACCGCAACCGAATCCACTTC 60.954 55.000 0.00 0.00 36.29 3.01
836 2978 1.339151 GCAACCGAATCCACTTCTCCT 60.339 52.381 0.00 0.00 0.00 3.69
845 2987 0.689412 CCACTTCTCCTCCTCCTCCC 60.689 65.000 0.00 0.00 0.00 4.30
901 3060 0.679960 CCCCAAATCGAACCCCAGAC 60.680 60.000 0.00 0.00 0.00 3.51
902 3061 0.037590 CCCAAATCGAACCCCAGACA 59.962 55.000 0.00 0.00 0.00 3.41
903 3062 1.453155 CCAAATCGAACCCCAGACAG 58.547 55.000 0.00 0.00 0.00 3.51
904 3063 1.003118 CCAAATCGAACCCCAGACAGA 59.997 52.381 0.00 0.00 0.00 3.41
960 3122 0.870307 CGATTCGATTCGGTTCGGCT 60.870 55.000 19.25 0.00 39.56 5.52
989 3151 4.214327 GCCGCCGGAGAAGAGGAG 62.214 72.222 7.68 0.00 0.00 3.69
990 3152 2.440430 CCGCCGGAGAAGAGGAGA 60.440 66.667 5.05 0.00 0.00 3.71
1243 3406 2.398036 CCCGAATTCGTTTCCGCG 59.602 61.111 25.10 0.00 37.74 6.46
1523 3692 0.522180 CGTCAGCTTCTACGGTGAGT 59.478 55.000 5.35 0.00 41.53 3.41
1526 3695 1.813178 TCAGCTTCTACGGTGAGTGAG 59.187 52.381 0.00 0.00 36.58 3.51
1527 3696 1.813178 CAGCTTCTACGGTGAGTGAGA 59.187 52.381 0.00 0.00 34.46 3.27
1528 3697 2.088423 AGCTTCTACGGTGAGTGAGAG 58.912 52.381 0.00 0.00 0.00 3.20
1567 3736 2.603247 CGCACGCAGCTGGTTGTAA 61.603 57.895 17.12 0.00 42.61 2.41
1652 3821 7.056635 ACTAGGATGGATAACATTTGGTTGAG 58.943 38.462 0.00 0.00 40.72 3.02
1743 3996 1.644509 GTTGCCCCTTCCCTCAAAAT 58.355 50.000 0.00 0.00 0.00 1.82
1773 4026 1.271434 GGTTTCTTCAGGGGGTGACTC 60.271 57.143 0.00 0.00 33.71 3.36
1798 4051 9.086336 TCTTTTGTTTTGCACTTTTGATTCTAG 57.914 29.630 0.00 0.00 0.00 2.43
1817 4070 6.668541 TCTAGCATGCACTAGAAAATGAAC 57.331 37.500 21.98 0.00 44.38 3.18
1828 4088 4.848562 AGAAAATGAACGGAAAGGGTTC 57.151 40.909 0.00 0.00 43.13 3.62
1833 4093 3.773418 TGAACGGAAAGGGTTCATGTA 57.227 42.857 3.44 0.00 46.33 2.29
1840 4100 3.421844 GAAAGGGTTCATGTAGGCACTT 58.578 45.455 0.00 0.00 34.98 3.16
1845 4105 2.749621 GGTTCATGTAGGCACTTCTTGG 59.250 50.000 0.00 0.00 41.75 3.61
1897 4161 9.383519 TCACTGAATCAAAAGAATAGATGGTAC 57.616 33.333 0.00 0.00 0.00 3.34
1933 4197 8.757877 ACTAATATGCAAAACAAATGTGGGTAT 58.242 29.630 0.00 0.00 0.00 2.73
1943 4207 5.984725 ACAAATGTGGGTATGTCGATTCTA 58.015 37.500 0.00 0.00 0.00 2.10
1951 4215 6.527023 GTGGGTATGTCGATTCTATGTTATCG 59.473 42.308 0.00 0.00 43.67 2.92
2013 4283 7.542130 GGAAAGGCTAAACAATTGTGAATACAG 59.458 37.037 12.82 4.68 38.23 2.74
2102 4372 1.317613 AGAAATGTTGGCGCTGTCAA 58.682 45.000 7.64 0.00 0.00 3.18
2105 4375 1.246649 AATGTTGGCGCTGTCAATCA 58.753 45.000 7.64 5.15 27.28 2.57
2145 4415 2.050077 GCGTTGCAAGGCTGTTCC 60.050 61.111 31.20 6.65 36.89 3.62
2149 4419 1.604604 GTTGCAAGGCTGTTCCTACA 58.395 50.000 0.00 0.00 46.94 2.74
2169 4439 8.390921 TCCTACAAATATTTTCTGTCTCCCTTT 58.609 33.333 0.00 0.00 0.00 3.11
2170 4440 8.678199 CCTACAAATATTTTCTGTCTCCCTTTC 58.322 37.037 0.00 0.00 0.00 2.62
2177 4447 5.640158 TTTCTGTCTCCCTTTCCTTAACA 57.360 39.130 0.00 0.00 0.00 2.41
2182 4452 7.066781 TCTGTCTCCCTTTCCTTAACAAAATT 58.933 34.615 0.00 0.00 0.00 1.82
2184 4454 8.770010 TGTCTCCCTTTCCTTAACAAAATTTA 57.230 30.769 0.00 0.00 0.00 1.40
2283 4553 7.575414 TGCTTGTTTAATAAAACCTGAGTCA 57.425 32.000 0.00 0.00 43.66 3.41
2284 4554 8.177119 TGCTTGTTTAATAAAACCTGAGTCAT 57.823 30.769 0.00 0.00 43.66 3.06
2285 4555 8.081633 TGCTTGTTTAATAAAACCTGAGTCATG 58.918 33.333 0.00 0.00 43.66 3.07
2286 4556 7.542130 GCTTGTTTAATAAAACCTGAGTCATGG 59.458 37.037 0.00 0.00 43.66 3.66
2352 4638 4.074970 ACTGATACCCTTTTGCTGTCTTG 58.925 43.478 0.00 0.00 0.00 3.02
2361 4647 4.803613 CCTTTTGCTGTCTTGTGGTTTAAC 59.196 41.667 0.00 0.00 0.00 2.01
2373 4659 2.159037 GTGGTTTAACCTAGCTGTTCGC 59.841 50.000 15.68 0.00 39.58 4.70
2420 4706 3.914426 AGAACTCATAAACCATCGGCT 57.086 42.857 0.00 0.00 0.00 5.52
2493 4782 3.988379 TTGCTTTACTGGAAACTGCAG 57.012 42.857 13.48 13.48 41.93 4.41
2543 4832 3.006537 TGAAGGTGGTGCTTACTGTAGTC 59.993 47.826 0.00 0.00 0.00 2.59
2797 5088 2.949177 ACATGGCTCTGTTGGTTGTA 57.051 45.000 0.00 0.00 0.00 2.41
2866 5157 1.221840 CTGGTTCACTCCATCGGGG 59.778 63.158 0.00 0.00 36.84 5.73
2993 5284 7.958053 TCTCCTACAACTTAGCTTTTGTTAC 57.042 36.000 11.86 0.00 37.19 2.50
3070 5361 6.380995 TCACATGATTGTCTTTGTGCATTAC 58.619 36.000 0.00 0.00 32.34 1.89
3436 5728 1.601759 TGCTGGCTCTTCTGCAACC 60.602 57.895 0.00 0.00 38.36 3.77
3523 5815 1.424403 TATGTAGTGTGTGTGCGTGC 58.576 50.000 0.00 0.00 0.00 5.34
3550 5842 1.199097 CAACTTGCTAAATTCGCCGGT 59.801 47.619 1.90 0.00 0.00 5.28
3556 5848 1.467342 GCTAAATTCGCCGGTGTTTCT 59.533 47.619 16.01 1.34 0.00 2.52
3593 5885 0.538057 CACTGCTCCCCTTCAGCAAA 60.538 55.000 0.00 0.00 46.22 3.68
3596 5888 2.694760 GCTCCCCTTCAGCAAAGCG 61.695 63.158 0.00 0.00 36.82 4.68
3599 5891 2.335712 CCCCTTCAGCAAAGCGGAC 61.336 63.158 0.00 0.00 35.25 4.79
3608 5900 1.153745 CAAAGCGGACGAGGAGGAG 60.154 63.158 0.00 0.00 0.00 3.69
3623 5915 0.251653 AGGAGACTAAGGACGTGCCA 60.252 55.000 2.38 0.00 40.61 4.92
3686 5978 0.035152 CCCTGGCAAGCATGTACTCA 60.035 55.000 0.00 0.00 0.00 3.41
3815 6107 1.630878 GGTCTGTTCATCTGGTCCCTT 59.369 52.381 0.00 0.00 0.00 3.95
3818 6110 2.711009 TCTGTTCATCTGGTCCCTTGTT 59.289 45.455 0.00 0.00 0.00 2.83
3872 6164 1.471119 TCGACCTGGTTACCTGCTAG 58.529 55.000 0.00 0.00 0.00 3.42
3873 6165 1.183549 CGACCTGGTTACCTGCTAGT 58.816 55.000 0.00 0.00 0.00 2.57
3874 6166 1.135083 CGACCTGGTTACCTGCTAGTG 60.135 57.143 0.00 0.00 0.00 2.74
3875 6167 0.613777 ACCTGGTTACCTGCTAGTGC 59.386 55.000 2.07 0.00 40.20 4.40
3917 6209 2.769663 TGATTGGAGCCACCTACGTATT 59.230 45.455 0.00 0.00 39.86 1.89
3924 6216 2.954318 AGCCACCTACGTATTGTATCGT 59.046 45.455 0.00 0.00 42.82 3.73
3925 6217 4.136796 AGCCACCTACGTATTGTATCGTA 58.863 43.478 0.00 0.00 40.70 3.43
3926 6218 4.763793 AGCCACCTACGTATTGTATCGTAT 59.236 41.667 0.00 0.00 40.76 3.06
3927 6219 5.091431 GCCACCTACGTATTGTATCGTATC 58.909 45.833 0.00 0.00 40.76 2.24
3928 6220 5.319139 CCACCTACGTATTGTATCGTATCG 58.681 45.833 0.00 0.00 40.76 2.92
3969 6261 6.268617 TGATGGCTAAGCTGACTATCTGTATT 59.731 38.462 8.17 0.00 0.00 1.89
4094 6386 6.371548 TGCCAGTATTTCAACAGTGAAGATAC 59.628 38.462 0.00 10.50 44.49 2.24
4152 6444 2.100584 TCTGTTTCATTGGTGTGTTGCC 59.899 45.455 0.00 0.00 0.00 4.52
4219 6514 8.534496 TCATGATTTCTAATCTGAACAGACTCA 58.466 33.333 6.67 3.24 40.75 3.41
4228 6523 9.868277 CTAATCTGAACAGACTCACTCTATTTT 57.132 33.333 6.67 0.00 40.75 1.82
4282 6581 4.117685 ACACTACGTGGAAGAAAGTGTTC 58.882 43.478 5.70 0.00 46.38 3.18
4304 6604 8.966868 TGTTCTTGAGAAGTTAAAAATCCAGTT 58.033 29.630 0.00 0.00 34.27 3.16
4309 6609 8.990163 TGAGAAGTTAAAAATCCAGTTTAGGT 57.010 30.769 0.00 0.00 0.00 3.08
4334 6634 9.896215 GTTTATGAACTCGTCTTGCCATGCAAT 62.896 40.741 1.49 0.00 39.02 3.56
4408 6708 5.335740 CGGAGAAGTGTTTCTAGCTGACTAA 60.336 44.000 0.00 0.00 43.63 2.24
4452 6758 0.533755 CTTATCCCGGCCTCTGCTTG 60.534 60.000 0.00 0.00 37.74 4.01
4508 6814 3.546724 TGTGATCAAAGAAACCACGGAA 58.453 40.909 0.00 0.00 0.00 4.30
4511 6817 1.301423 TCAAAGAAACCACGGAACCG 58.699 50.000 11.83 11.83 46.03 4.44
4655 6961 2.025418 GGCGGTGTACCTGTTGACG 61.025 63.158 0.00 0.00 0.00 4.35
4656 6962 2.025418 GCGGTGTACCTGTTGACGG 61.025 63.158 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.258543 CCGTTCCTCTTTTTGGCTGTATA 58.741 43.478 0.00 0.00 0.00 1.47
24 25 1.289066 GCCCGTTCCTCTTTTTGGC 59.711 57.895 0.00 0.00 0.00 4.52
26 27 1.407258 TGTTGCCCGTTCCTCTTTTTG 59.593 47.619 0.00 0.00 0.00 2.44
27 28 1.681264 CTGTTGCCCGTTCCTCTTTTT 59.319 47.619 0.00 0.00 0.00 1.94
46 52 1.562672 ATTACCAACCCGCCTGCTCT 61.563 55.000 0.00 0.00 0.00 4.09
65 71 0.387929 GAGTGTGTGGTCGGTCTTCA 59.612 55.000 0.00 0.00 0.00 3.02
126 132 0.110644 GCTTTTCTTCCGCTCACGTG 60.111 55.000 9.94 9.94 37.70 4.49
144 150 2.282180 TTTGGTCGGCTCCCTTGC 60.282 61.111 0.00 0.00 0.00 4.01
163 169 5.590818 TCACTCTCCCCTAGTAAGTGAATT 58.409 41.667 1.28 0.00 42.34 2.17
175 181 1.643286 TCACTGATCTCACTCTCCCCT 59.357 52.381 0.00 0.00 0.00 4.79
234 241 1.652124 ACGTGTTGTATGATCGAACGC 59.348 47.619 0.00 0.00 33.08 4.84
236 243 3.247442 TGGACGTGTTGTATGATCGAAC 58.753 45.455 0.00 0.00 0.00 3.95
277 284 0.673985 GTGGCCTGGTTGGTTTTCTC 59.326 55.000 3.32 0.00 38.35 2.87
286 293 1.352622 TTGGACTCTGTGGCCTGGTT 61.353 55.000 3.32 0.00 46.68 3.67
290 297 1.425066 TGATTTTGGACTCTGTGGCCT 59.575 47.619 3.32 0.00 46.68 5.19
295 302 2.494059 CACCGTGATTTTGGACTCTGT 58.506 47.619 0.00 0.00 0.00 3.41
311 318 1.342082 CGTGTTTAGAGCGTCCACCG 61.342 60.000 0.00 0.00 40.40 4.94
315 322 0.739813 ATGGCGTGTTTAGAGCGTCC 60.740 55.000 0.00 0.00 0.00 4.79
350 366 1.133976 CCTAGCTGGCCTGCTATTGTT 60.134 52.381 35.80 18.50 43.54 2.83
366 382 1.470098 GTGTGGATGTGCTTTGCCTAG 59.530 52.381 0.00 0.00 0.00 3.02
379 395 2.592993 CCGTCAGGTGGGTGTGGAT 61.593 63.158 0.00 0.00 0.00 3.41
471 487 3.487120 AGTTGGTTGGTTGAGTCTACC 57.513 47.619 15.94 15.94 36.17 3.18
489 591 1.952296 CTATACGCTGTCGGGGTTAGT 59.048 52.381 6.69 0.00 41.43 2.24
499 601 0.469331 TAGGGCAGGCTATACGCTGT 60.469 55.000 10.07 0.00 39.13 4.40
576 2697 0.686789 ATGTTTTTCCCCAAGCCAGC 59.313 50.000 0.00 0.00 0.00 4.85
588 2709 2.995258 CGCTGCATTTGGCTATGTTTTT 59.005 40.909 0.00 0.00 45.15 1.94
668 2789 6.713903 GCCATTCAATAGATCAATCTTCCTCA 59.286 38.462 0.00 0.00 38.32 3.86
669 2790 6.713903 TGCCATTCAATAGATCAATCTTCCTC 59.286 38.462 0.00 0.00 38.32 3.71
670 2791 6.607970 TGCCATTCAATAGATCAATCTTCCT 58.392 36.000 0.00 0.00 38.32 3.36
671 2792 6.889301 TGCCATTCAATAGATCAATCTTCC 57.111 37.500 0.00 0.00 38.32 3.46
672 2793 7.014038 AGGTTGCCATTCAATAGATCAATCTTC 59.986 37.037 0.00 0.00 38.32 2.87
673 2794 6.837568 AGGTTGCCATTCAATAGATCAATCTT 59.162 34.615 0.00 0.00 38.32 2.40
674 2795 6.264744 CAGGTTGCCATTCAATAGATCAATCT 59.735 38.462 0.00 0.00 40.86 2.40
704 2825 7.201617 GGTCCGATTAATCTTTTCTGGTTGTAG 60.202 40.741 13.45 0.00 0.00 2.74
705 2826 6.596497 GGTCCGATTAATCTTTTCTGGTTGTA 59.404 38.462 13.45 0.00 0.00 2.41
706 2827 5.414765 GGTCCGATTAATCTTTTCTGGTTGT 59.585 40.000 13.45 0.00 0.00 3.32
707 2828 5.163652 GGGTCCGATTAATCTTTTCTGGTTG 60.164 44.000 13.45 0.00 0.00 3.77
709 2830 4.524053 GGGTCCGATTAATCTTTTCTGGT 58.476 43.478 13.45 0.00 0.00 4.00
715 2851 2.770232 AGACCGGGTCCGATTAATCTTT 59.230 45.455 23.21 0.00 42.83 2.52
817 2959 2.622436 GAGGAGAAGTGGATTCGGTTG 58.378 52.381 0.00 0.00 43.16 3.77
819 2961 1.196012 GGAGGAGAAGTGGATTCGGT 58.804 55.000 0.00 0.00 43.16 4.69
820 2962 1.410882 GAGGAGGAGAAGTGGATTCGG 59.589 57.143 0.00 0.00 43.16 4.30
821 2963 1.410882 GGAGGAGGAGAAGTGGATTCG 59.589 57.143 0.00 0.00 43.16 3.34
822 2964 2.698274 GAGGAGGAGGAGAAGTGGATTC 59.302 54.545 0.00 0.00 38.28 2.52
823 2965 2.628290 GGAGGAGGAGGAGAAGTGGATT 60.628 54.545 0.00 0.00 0.00 3.01
824 2966 1.062505 GGAGGAGGAGGAGAAGTGGAT 60.063 57.143 0.00 0.00 0.00 3.41
825 2967 0.336737 GGAGGAGGAGGAGAAGTGGA 59.663 60.000 0.00 0.00 0.00 4.02
826 2968 0.689412 GGGAGGAGGAGGAGAAGTGG 60.689 65.000 0.00 0.00 0.00 4.00
827 2969 0.338120 AGGGAGGAGGAGGAGAAGTG 59.662 60.000 0.00 0.00 0.00 3.16
828 2970 0.338120 CAGGGAGGAGGAGGAGAAGT 59.662 60.000 0.00 0.00 0.00 3.01
829 2971 1.048160 GCAGGGAGGAGGAGGAGAAG 61.048 65.000 0.00 0.00 0.00 2.85
830 2972 1.002274 GCAGGGAGGAGGAGGAGAA 59.998 63.158 0.00 0.00 0.00 2.87
831 2973 2.693017 GCAGGGAGGAGGAGGAGA 59.307 66.667 0.00 0.00 0.00 3.71
832 2974 2.445654 GGCAGGGAGGAGGAGGAG 60.446 72.222 0.00 0.00 0.00 3.69
836 2978 4.779733 GGACGGCAGGGAGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
1264 3433 0.036388 TGATCCCTGCAACGGAGAAC 60.036 55.000 8.12 3.70 31.41 3.01
1265 3434 0.690192 TTGATCCCTGCAACGGAGAA 59.310 50.000 8.12 1.67 31.41 2.87
1266 3435 0.036388 GTTGATCCCTGCAACGGAGA 60.036 55.000 8.12 0.00 36.63 3.71
1267 3436 1.026718 GGTTGATCCCTGCAACGGAG 61.027 60.000 8.12 0.00 44.92 4.63
1268 3437 1.002624 GGTTGATCCCTGCAACGGA 60.003 57.895 4.71 4.71 44.92 4.69
1269 3438 1.303236 TGGTTGATCCCTGCAACGG 60.303 57.895 0.00 0.00 44.92 4.44
1270 3439 0.606401 AGTGGTTGATCCCTGCAACG 60.606 55.000 0.00 0.00 44.92 4.10
1523 3692 2.038557 CGGAAGGAAAAAGGGTCTCTCA 59.961 50.000 0.00 0.00 0.00 3.27
1526 3695 1.166129 GCGGAAGGAAAAAGGGTCTC 58.834 55.000 0.00 0.00 0.00 3.36
1527 3696 0.771755 AGCGGAAGGAAAAAGGGTCT 59.228 50.000 0.00 0.00 0.00 3.85
1528 3697 1.166129 GAGCGGAAGGAAAAAGGGTC 58.834 55.000 0.00 0.00 0.00 4.46
1565 3734 7.228906 GCAGATATCAGGCGGACTAGTATATTA 59.771 40.741 5.32 0.00 0.00 0.98
1567 3736 5.533154 GCAGATATCAGGCGGACTAGTATAT 59.467 44.000 5.32 0.00 0.00 0.86
1623 3792 6.942576 ACCAAATGTTATCCATCCTAGTATGC 59.057 38.462 0.00 0.00 31.75 3.14
1652 3821 7.766219 TCATTTAGGCGATTAGTAGTTTCAC 57.234 36.000 0.00 0.00 0.00 3.18
1743 3996 2.488347 CCTGAAGAAACCTTTCCGGGAA 60.488 50.000 5.09 5.09 37.92 3.97
1773 4026 7.847564 GCTAGAATCAAAAGTGCAAAACAAAAG 59.152 33.333 0.00 0.00 0.00 2.27
1798 4051 3.126858 TCCGTTCATTTTCTAGTGCATGC 59.873 43.478 11.82 11.82 0.00 4.06
1817 4070 1.339631 TGCCTACATGAACCCTTTCCG 60.340 52.381 0.00 0.00 0.00 4.30
1828 4088 2.290260 TGGTCCAAGAAGTGCCTACATG 60.290 50.000 0.00 0.00 0.00 3.21
1829 4089 1.985159 TGGTCCAAGAAGTGCCTACAT 59.015 47.619 0.00 0.00 0.00 2.29
1831 4091 2.552743 GTTTGGTCCAAGAAGTGCCTAC 59.447 50.000 4.09 0.00 0.00 3.18
1833 4093 1.064017 TGTTTGGTCCAAGAAGTGCCT 60.064 47.619 4.09 0.00 0.00 4.75
1840 4100 9.123902 CATCTGATATTATTGTTTGGTCCAAGA 57.876 33.333 4.09 0.00 0.00 3.02
1845 4105 7.004086 TCCCCATCTGATATTATTGTTTGGTC 58.996 38.462 0.00 0.00 0.00 4.02
1980 4246 6.211384 ACAATTGTTTAGCCTTTCCTTATGCT 59.789 34.615 4.92 0.00 37.84 3.79
1987 4253 7.375053 TGTATTCACAATTGTTTAGCCTTTCC 58.625 34.615 8.77 0.00 0.00 3.13
2013 4283 8.912988 TCACATTTTGACTAATTTCCATATCCC 58.087 33.333 0.00 0.00 0.00 3.85
2020 4290 8.031277 AGCTCAATCACATTTTGACTAATTTCC 58.969 33.333 0.00 0.00 36.92 3.13
2102 4372 6.042093 AGACTCCATACAACGATAACCATGAT 59.958 38.462 0.00 0.00 0.00 2.45
2105 4375 5.601662 CAGACTCCATACAACGATAACCAT 58.398 41.667 0.00 0.00 0.00 3.55
2145 4415 8.678199 GGAAAGGGAGACAGAAAATATTTGTAG 58.322 37.037 0.39 0.00 0.00 2.74
2149 4419 9.822727 TTAAGGAAAGGGAGACAGAAAATATTT 57.177 29.630 0.00 0.00 0.00 1.40
2352 4638 2.159037 GCGAACAGCTAGGTTAAACCAC 59.841 50.000 0.00 0.00 41.38 4.16
2373 4659 7.913674 ATTGCCTAAAGAAAGAGTACAGAAG 57.086 36.000 0.00 0.00 0.00 2.85
2529 4818 8.704234 GCAGAAATATATGACTACAGTAAGCAC 58.296 37.037 0.00 0.00 0.00 4.40
2543 4832 8.724229 TGGAAATCGATTCTGCAGAAATATATG 58.276 33.333 31.55 17.16 37.61 1.78
2797 5088 5.650266 TGAGCCAATATAACAAACAACCGAT 59.350 36.000 0.00 0.00 0.00 4.18
3070 5361 5.473931 AGCAGATCTACATAGCAATTACCG 58.526 41.667 0.00 0.00 0.00 4.02
3122 5413 6.710597 TCGATTGCTTGTATCCTAACTAGT 57.289 37.500 0.00 0.00 0.00 2.57
3466 5758 2.351738 GCCAGAGAACAAAATCCAACCG 60.352 50.000 0.00 0.00 0.00 4.44
3512 5804 2.647481 CAACACGCACGCACACAC 60.647 61.111 0.00 0.00 0.00 3.82
3550 5842 1.305201 GTCGGCACCTGAAAGAAACA 58.695 50.000 0.00 0.00 34.07 2.83
3556 5848 1.896660 GGCTTGTCGGCACCTGAAA 60.897 57.895 0.00 0.00 38.25 2.69
3593 5885 1.624479 TAGTCTCCTCCTCGTCCGCT 61.624 60.000 0.00 0.00 0.00 5.52
3596 5888 1.212441 TCCTTAGTCTCCTCCTCGTCC 59.788 57.143 0.00 0.00 0.00 4.79
3599 5891 1.301423 CGTCCTTAGTCTCCTCCTCG 58.699 60.000 0.00 0.00 0.00 4.63
3608 5900 0.796927 GCTTTGGCACGTCCTTAGTC 59.203 55.000 0.00 0.00 38.54 2.59
3611 5903 1.669760 CGGCTTTGGCACGTCCTTA 60.670 57.895 0.00 0.00 40.87 2.69
3623 5915 1.276622 AGGAGTATGTCACCGGCTTT 58.723 50.000 0.00 0.00 32.04 3.51
3686 5978 2.898738 CCAGTCAGGAGCATCGCT 59.101 61.111 0.00 0.00 43.88 4.93
3791 6083 1.277557 GACCAGATGAACAGACCTGCT 59.722 52.381 0.00 0.00 0.00 4.24
3815 6107 1.761174 GAACAGGAGGGGAGCAACA 59.239 57.895 0.00 0.00 0.00 3.33
3818 6110 2.610859 GGGAACAGGAGGGGAGCA 60.611 66.667 0.00 0.00 0.00 4.26
3882 6174 3.736720 TCCAATCAGATGATGCACTAGC 58.263 45.455 0.00 0.00 42.57 3.42
3883 6175 3.747010 GCTCCAATCAGATGATGCACTAG 59.253 47.826 0.00 0.00 34.49 2.57
3884 6176 3.495629 GGCTCCAATCAGATGATGCACTA 60.496 47.826 0.00 0.00 34.49 2.74
3885 6177 2.573369 GCTCCAATCAGATGATGCACT 58.427 47.619 0.00 0.00 34.49 4.40
3896 6188 1.855295 TACGTAGGTGGCTCCAATCA 58.145 50.000 8.51 0.00 39.02 2.57
3898 6190 2.504175 ACAATACGTAGGTGGCTCCAAT 59.496 45.455 8.51 0.00 39.02 3.16
3924 6216 2.222213 CACAGCCAAAACACGTTCGATA 59.778 45.455 0.00 0.00 0.00 2.92
3925 6217 1.002900 CACAGCCAAAACACGTTCGAT 60.003 47.619 0.00 0.00 0.00 3.59
3926 6218 0.375454 CACAGCCAAAACACGTTCGA 59.625 50.000 0.00 0.00 0.00 3.71
3927 6219 0.375454 TCACAGCCAAAACACGTTCG 59.625 50.000 0.00 0.00 0.00 3.95
3928 6220 2.384382 CATCACAGCCAAAACACGTTC 58.616 47.619 0.00 0.00 0.00 3.95
3938 6230 0.393402 CAGCTTAGCCATCACAGCCA 60.393 55.000 0.00 0.00 32.25 4.75
3969 6261 6.941857 TGCTTACACAATATTACAGACCAGA 58.058 36.000 0.00 0.00 0.00 3.86
3989 6281 0.471591 TCCTTGCCATGGGTTTGCTT 60.472 50.000 15.13 0.00 0.00 3.91
4011 6303 0.444651 ACAACGTCACACAAACACCG 59.555 50.000 0.00 0.00 0.00 4.94
4152 6444 5.334319 TGCATTTCATTCATTCGCACTTAG 58.666 37.500 0.00 0.00 0.00 2.18
4282 6581 9.899226 CCTAAACTGGATTTTTAACTTCTCAAG 57.101 33.333 0.00 0.00 0.00 3.02
4299 6599 6.164176 AGACGAGTTCATAAACCTAAACTGG 58.836 40.000 0.00 0.00 35.92 4.00
4304 6604 4.933400 GGCAAGACGAGTTCATAAACCTAA 59.067 41.667 0.00 0.00 35.92 2.69
4306 6606 3.244422 TGGCAAGACGAGTTCATAAACCT 60.244 43.478 0.00 0.00 35.92 3.50
4309 6609 3.126858 GCATGGCAAGACGAGTTCATAAA 59.873 43.478 0.00 0.00 0.00 1.40
4334 6634 4.811969 AGCATCATTTTGCCATCAGAAA 57.188 36.364 0.00 0.00 43.83 2.52
4385 6685 4.529109 AGTCAGCTAGAAACACTTCTCC 57.471 45.455 0.00 0.00 41.19 3.71
4408 6708 6.435430 TCATACTGTCAGCGCATTTTAATT 57.565 33.333 11.47 0.00 0.00 1.40
4452 6758 7.724305 TTAGGACACACAGAAGATTGTAAAC 57.276 36.000 0.00 0.00 0.00 2.01
4656 6962 2.282462 CAAGGGGTGCAGGGACAC 60.282 66.667 0.00 0.00 39.94 3.67


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

AutoCloner maintained by Alex Coulton.