Multiple sequence alignment - TraesCS6D01G041200

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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 TraesCS6D01G041200 chr6D 100.000 3149 0 0 1 3149 16776743 16773595 0.000000e+00 5816.0
1 TraesCS6D01G041200 chr6B 93.417 1352 82 3 1016 2361 29753721 29755071 0.000000e+00 1997.0
2 TraesCS6D01G041200 chr6B 91.340 612 40 4 2510 3119 29755626 29756226 0.000000e+00 824.0
3 TraesCS6D01G041200 chr6B 79.427 1186 221 18 971 2139 26389182 26390361 0.000000e+00 817.0
4 TraesCS6D01G041200 chr6B 79.247 1195 229 14 985 2174 26500512 26501692 0.000000e+00 815.0
5 TraesCS6D01G041200 chr6B 79.428 1118 215 14 966 2080 26794076 26792971 0.000000e+00 776.0
6 TraesCS6D01G041200 chr6B 78.947 1102 226 6 999 2097 53062512 53061414 0.000000e+00 745.0
7 TraesCS6D01G041200 chr6B 95.699 186 8 0 2962 3147 29427127 29426942 1.840000e-77 300.0
8 TraesCS6D01G041200 chr6B 85.204 196 18 7 665 851 29739705 29739898 1.150000e-44 191.0
9 TraesCS6D01G041200 chr6A 94.096 1101 42 9 2064 3147 17603997 17602903 0.000000e+00 1652.0
10 TraesCS6D01G041200 chr6A 87.484 799 60 27 1 797 17604879 17604119 0.000000e+00 885.0
11 TraesCS6D01G041200 chr6A 79.041 1231 222 29 958 2172 9364556 9365766 0.000000e+00 811.0
12 TraesCS6D01G041200 chr6A 79.313 1136 209 21 966 2091 9336007 9337126 0.000000e+00 773.0
13 TraesCS6D01G041200 chr6A 78.645 1166 216 28 987 2139 15914153 15913008 0.000000e+00 743.0
14 TraesCS6D01G041200 chr6A 91.016 256 22 1 408 662 76520677 76520932 8.360000e-91 344.0
15 TraesCS6D01G041200 chr6A 95.238 42 1 1 2091 2132 17604042 17604002 7.290000e-07 65.8
16 TraesCS6D01G041200 chr1B 79.609 1177 214 21 970 2134 48062374 48061212 0.000000e+00 821.0
17 TraesCS6D01G041200 chr1B 88.849 278 28 3 395 670 212061529 212061805 3.890000e-89 339.0
18 TraesCS6D01G041200 chr5B 91.406 256 21 1 408 662 317310044 317310299 1.800000e-92 350.0
19 TraesCS6D01G041200 chr5A 90.074 272 23 4 402 670 419685927 419686197 1.800000e-92 350.0
20 TraesCS6D01G041200 chr3A 90.226 266 25 1 407 671 600926563 600926828 2.320000e-91 346.0
21 TraesCS6D01G041200 chr3D 90.189 265 25 1 406 669 586579198 586578934 8.360000e-91 344.0
22 TraesCS6D01G041200 chr7D 89.630 270 27 1 408 676 182347678 182347409 3.010000e-90 342.0
23 TraesCS6D01G041200 chr7D 89.963 269 22 3 404 669 509242266 509242532 3.010000e-90 342.0


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 TraesCS6D01G041200 chr6D 16773595 16776743 3148 True 5816.0 5816 100.000000 1 3149 1 chr6D.!!$R1 3148
1 TraesCS6D01G041200 chr6B 29753721 29756226 2505 False 1410.5 1997 92.378500 1016 3119 2 chr6B.!!$F4 2103
2 TraesCS6D01G041200 chr6B 26389182 26390361 1179 False 817.0 817 79.427000 971 2139 1 chr6B.!!$F1 1168
3 TraesCS6D01G041200 chr6B 26500512 26501692 1180 False 815.0 815 79.247000 985 2174 1 chr6B.!!$F2 1189
4 TraesCS6D01G041200 chr6B 26792971 26794076 1105 True 776.0 776 79.428000 966 2080 1 chr6B.!!$R1 1114
5 TraesCS6D01G041200 chr6B 53061414 53062512 1098 True 745.0 745 78.947000 999 2097 1 chr6B.!!$R3 1098
6 TraesCS6D01G041200 chr6A 17602903 17604879 1976 True 867.6 1652 92.272667 1 3147 3 chr6A.!!$R2 3146
7 TraesCS6D01G041200 chr6A 9364556 9365766 1210 False 811.0 811 79.041000 958 2172 1 chr6A.!!$F2 1214
8 TraesCS6D01G041200 chr6A 9336007 9337126 1119 False 773.0 773 79.313000 966 2091 1 chr6A.!!$F1 1125
9 TraesCS6D01G041200 chr6A 15913008 15914153 1145 True 743.0 743 78.645000 987 2139 1 chr6A.!!$R1 1152
10 TraesCS6D01G041200 chr1B 48061212 48062374 1162 True 821.0 821 79.609000 970 2134 1 chr1B.!!$R1 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
904 907 0.099436 CGAACCAATTAGCAGCTGGC 59.901 55.0 17.12 7.98 45.3 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2500 2687 0.319405 GAGCCATGCTTGTTTTGCCT 59.681 50.0 0.0 0.0 39.88 4.75 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
30 31 2.930040 GGCGATTCTCTTCGATCAACAA 59.070 45.455 0.00 0.00 41.62 2.83
47 48 1.455217 AAGGCATCCTGAGCATGGC 60.455 57.895 1.03 1.03 45.08 4.40
58 59 3.555377 CCTGAGCATGGCAATTTTCACAA 60.555 43.478 0.00 0.00 0.00 3.33
60 61 4.449131 TGAGCATGGCAATTTTCACAAAA 58.551 34.783 0.00 0.00 34.41 2.44
86 87 8.518430 AAACAATTTAGGTTGGCAATTTTTCT 57.482 26.923 1.92 0.00 33.40 2.52
118 119 1.889829 TGCTAAATCCCCCAAAACACG 59.110 47.619 0.00 0.00 0.00 4.49
144 145 5.156355 CCAATTACTCTGTTGCAACATGAC 58.844 41.667 31.17 5.54 38.41 3.06
154 155 7.140705 TCTGTTGCAACATGACAATTTTCTAG 58.859 34.615 31.17 14.82 38.41 2.43
179 180 6.510157 GCAATCGTTCCTATACAACATGACAG 60.510 42.308 0.00 0.00 0.00 3.51
200 201 6.866480 ACAGTAAACATGGCAAATCCTTATG 58.134 36.000 0.00 0.00 35.26 1.90
203 204 8.131100 CAGTAAACATGGCAAATCCTTATGTAG 58.869 37.037 0.00 0.00 32.17 2.74
215 216 6.872628 ATCCTTATGTAGCAACATGACATG 57.127 37.500 14.02 14.02 45.99 3.21
254 255 1.948104 CAATCCCGGAGCATTCGTTA 58.052 50.000 0.73 0.00 32.93 3.18
264 265 4.192317 GGAGCATTCGTTAGGAGTGATTT 58.808 43.478 1.71 0.00 34.50 2.17
308 309 3.900116 CGTTTGTTGCGATAGTTTGTCTG 59.100 43.478 0.00 0.00 39.35 3.51
311 312 1.130561 GTTGCGATAGTTTGTCTGGGC 59.869 52.381 0.00 0.00 39.35 5.36
315 316 1.135083 CGATAGTTTGTCTGGGCGACT 60.135 52.381 0.00 0.00 43.25 4.18
322 323 1.191489 TGTCTGGGCGACTTCCATGA 61.191 55.000 0.00 0.00 43.25 3.07
359 360 4.098196 CGTTACTGGGGTTCAAAGGAAAAA 59.902 41.667 0.00 0.00 34.13 1.94
367 368 4.469552 GGTTCAAAGGAAAAACCGATACG 58.530 43.478 0.00 0.00 44.74 3.06
371 372 4.095610 CAAAGGAAAAACCGATACGCATC 58.904 43.478 0.00 0.00 44.74 3.91
372 373 2.980568 AGGAAAAACCGATACGCATCA 58.019 42.857 0.00 0.00 44.74 3.07
390 391 7.578852 ACGCATCATCATACTAAAATCACATG 58.421 34.615 0.00 0.00 0.00 3.21
441 442 7.496591 TCCGTTTCTTTTTACTCCGCATATAAT 59.503 33.333 0.00 0.00 0.00 1.28
442 443 8.126700 CCGTTTCTTTTTACTCCGCATATAATT 58.873 33.333 0.00 0.00 0.00 1.40
481 482 8.840833 AAACTACACAAAGTTTGACCAAATTT 57.159 26.923 22.23 11.30 45.60 1.82
482 483 9.930693 AAACTACACAAAGTTTGACCAAATTTA 57.069 25.926 22.23 0.00 45.60 1.40
623 624 9.392259 AGTTAGTCAAACTTTACAAAGCTTACT 57.608 29.630 0.00 0.00 46.61 2.24
644 646 8.715191 TTACTTTGGCCAAATTTTATATGCAG 57.285 30.769 30.46 16.49 0.00 4.41
665 667 5.639931 GCAGACTAAAAAGAAACGGAGAGAT 59.360 40.000 0.00 0.00 0.00 2.75
705 707 9.554053 TCCCTTAAATATTTTCTGGAATGGAAA 57.446 29.630 5.91 0.00 0.00 3.13
788 791 2.926838 GGAAGAAGCGACTCTCATTGTC 59.073 50.000 0.00 0.00 0.00 3.18
792 795 3.256879 AGAAGCGACTCTCATTGTCAGAA 59.743 43.478 0.00 0.00 34.37 3.02
793 796 3.229276 AGCGACTCTCATTGTCAGAAG 57.771 47.619 0.00 0.00 34.37 2.85
794 797 2.094286 AGCGACTCTCATTGTCAGAAGG 60.094 50.000 0.00 0.00 34.37 3.46
795 798 2.266554 CGACTCTCATTGTCAGAAGGC 58.733 52.381 0.00 0.00 34.37 4.35
796 799 2.626840 GACTCTCATTGTCAGAAGGCC 58.373 52.381 0.00 0.00 34.80 5.19
797 800 1.066573 ACTCTCATTGTCAGAAGGCCG 60.067 52.381 0.00 0.00 0.00 6.13
798 801 0.250234 TCTCATTGTCAGAAGGCCGG 59.750 55.000 0.00 0.00 0.00 6.13
799 802 1.372087 CTCATTGTCAGAAGGCCGGC 61.372 60.000 21.18 21.18 0.00 6.13
800 803 1.377725 CATTGTCAGAAGGCCGGCT 60.378 57.895 28.56 7.30 0.00 5.52
801 804 0.107703 CATTGTCAGAAGGCCGGCTA 60.108 55.000 28.56 2.01 0.00 3.93
802 805 0.107654 ATTGTCAGAAGGCCGGCTAC 60.108 55.000 28.56 17.41 0.00 3.58
803 806 2.202756 GTCAGAAGGCCGGCTACG 60.203 66.667 28.56 10.89 40.55 3.51
804 807 2.361992 TCAGAAGGCCGGCTACGA 60.362 61.111 28.56 13.17 44.60 3.43
805 808 2.202756 CAGAAGGCCGGCTACGAC 60.203 66.667 28.56 9.28 44.60 4.34
806 809 2.362632 AGAAGGCCGGCTACGACT 60.363 61.111 28.56 11.88 44.60 4.18
807 810 1.077212 AGAAGGCCGGCTACGACTA 60.077 57.895 28.56 0.00 44.60 2.59
808 811 1.065436 GAAGGCCGGCTACGACTAC 59.935 63.158 28.56 6.68 44.60 2.73
809 812 2.659017 GAAGGCCGGCTACGACTACG 62.659 65.000 28.56 0.00 44.60 3.51
811 814 4.261781 GCCGGCTACGACTACGGG 62.262 72.222 22.15 4.29 46.04 5.28
812 815 4.261781 CCGGCTACGACTACGGGC 62.262 72.222 0.00 0.00 44.60 6.13
815 818 3.142838 GCTACGACTACGGGCCCA 61.143 66.667 24.92 0.93 44.46 5.36
816 819 2.713967 GCTACGACTACGGGCCCAA 61.714 63.158 24.92 8.33 44.46 4.12
817 820 2.024590 GCTACGACTACGGGCCCAAT 62.025 60.000 24.92 12.25 44.46 3.16
818 821 1.321474 CTACGACTACGGGCCCAATA 58.679 55.000 24.92 12.82 44.46 1.90
819 822 1.682854 CTACGACTACGGGCCCAATAA 59.317 52.381 24.92 1.92 44.46 1.40
820 823 0.176449 ACGACTACGGGCCCAATAAC 59.824 55.000 24.92 8.91 44.46 1.89
821 824 0.462789 CGACTACGGGCCCAATAACT 59.537 55.000 24.92 1.01 35.72 2.24
822 825 1.537562 CGACTACGGGCCCAATAACTC 60.538 57.143 24.92 9.51 35.72 3.01
823 826 1.483415 GACTACGGGCCCAATAACTCA 59.517 52.381 24.92 0.00 0.00 3.41
824 827 1.208776 ACTACGGGCCCAATAACTCAC 59.791 52.381 24.92 0.00 0.00 3.51
825 828 1.208535 CTACGGGCCCAATAACTCACA 59.791 52.381 24.92 0.00 0.00 3.58
826 829 0.402504 ACGGGCCCAATAACTCACAA 59.597 50.000 24.92 0.00 0.00 3.33
827 830 1.094785 CGGGCCCAATAACTCACAAG 58.905 55.000 24.92 0.00 0.00 3.16
828 831 0.817654 GGGCCCAATAACTCACAAGC 59.182 55.000 19.95 0.00 0.00 4.01
829 832 1.616994 GGGCCCAATAACTCACAAGCT 60.617 52.381 19.95 0.00 0.00 3.74
830 833 1.474077 GGCCCAATAACTCACAAGCTG 59.526 52.381 0.00 0.00 0.00 4.24
831 834 1.474077 GCCCAATAACTCACAAGCTGG 59.526 52.381 0.00 0.00 0.00 4.85
832 835 2.879756 GCCCAATAACTCACAAGCTGGA 60.880 50.000 0.00 0.00 0.00 3.86
833 836 3.012518 CCCAATAACTCACAAGCTGGAG 58.987 50.000 0.00 1.55 37.18 3.86
834 837 3.012518 CCAATAACTCACAAGCTGGAGG 58.987 50.000 13.09 0.00 35.45 4.30
835 838 2.409948 ATAACTCACAAGCTGGAGGC 57.590 50.000 13.09 0.00 42.19 4.70
836 839 0.324943 TAACTCACAAGCTGGAGGCC 59.675 55.000 13.09 0.00 43.05 5.19
837 840 2.045536 CTCACAAGCTGGAGGCCC 60.046 66.667 0.00 0.00 43.05 5.80
838 841 2.853542 TCACAAGCTGGAGGCCCA 60.854 61.111 0.00 0.00 43.05 5.36
839 842 2.115910 CACAAGCTGGAGGCCCAA 59.884 61.111 0.00 0.00 42.98 4.12
840 843 1.304713 CACAAGCTGGAGGCCCAAT 60.305 57.895 0.00 0.00 42.98 3.16
841 844 1.304713 ACAAGCTGGAGGCCCAATG 60.305 57.895 0.00 0.00 42.98 2.82
842 845 2.363406 AAGCTGGAGGCCCAATGC 60.363 61.111 0.00 0.00 42.98 3.56
843 846 3.228243 AAGCTGGAGGCCCAATGCA 62.228 57.895 0.00 0.00 42.98 3.96
844 847 3.455469 GCTGGAGGCCCAATGCAC 61.455 66.667 0.00 0.00 42.98 4.57
845 848 2.036098 CTGGAGGCCCAATGCACA 59.964 61.111 0.00 0.00 42.98 4.57
846 849 1.607178 CTGGAGGCCCAATGCACAA 60.607 57.895 0.00 0.00 42.98 3.33
847 850 1.601419 CTGGAGGCCCAATGCACAAG 61.601 60.000 0.00 0.00 42.98 3.16
848 851 2.575461 GAGGCCCAATGCACAAGC 59.425 61.111 0.00 0.00 43.89 4.01
881 884 0.659427 CCAACGAATCGCAGCATCAT 59.341 50.000 1.15 0.00 0.00 2.45
894 897 3.243301 GCAGCATCATCATCGAACCAATT 60.243 43.478 0.00 0.00 0.00 2.32
895 898 4.023792 GCAGCATCATCATCGAACCAATTA 60.024 41.667 0.00 0.00 0.00 1.40
896 899 5.686834 CAGCATCATCATCGAACCAATTAG 58.313 41.667 0.00 0.00 0.00 1.73
897 900 4.214971 AGCATCATCATCGAACCAATTAGC 59.785 41.667 0.00 0.00 0.00 3.09
898 901 4.023792 GCATCATCATCGAACCAATTAGCA 60.024 41.667 0.00 0.00 0.00 3.49
899 902 5.686834 CATCATCATCGAACCAATTAGCAG 58.313 41.667 0.00 0.00 0.00 4.24
900 903 3.561310 TCATCATCGAACCAATTAGCAGC 59.439 43.478 0.00 0.00 0.00 5.25
901 904 3.266510 TCATCGAACCAATTAGCAGCT 57.733 42.857 0.00 0.00 0.00 4.24
902 905 2.938451 TCATCGAACCAATTAGCAGCTG 59.062 45.455 10.11 10.11 0.00 4.24
903 906 1.737838 TCGAACCAATTAGCAGCTGG 58.262 50.000 17.12 0.16 36.24 4.85
904 907 0.099436 CGAACCAATTAGCAGCTGGC 59.901 55.000 17.12 7.98 45.30 4.85
905 908 0.457443 GAACCAATTAGCAGCTGGCC 59.543 55.000 17.12 0.00 46.50 5.36
906 909 0.251742 AACCAATTAGCAGCTGGCCA 60.252 50.000 17.12 4.71 46.50 5.36
907 910 0.967380 ACCAATTAGCAGCTGGCCAC 60.967 55.000 17.12 0.00 46.50 5.01
908 911 1.669999 CCAATTAGCAGCTGGCCACC 61.670 60.000 17.12 0.00 46.50 4.61
909 912 1.380380 AATTAGCAGCTGGCCACCC 60.380 57.895 17.12 0.00 46.50 4.61
910 913 2.861271 AATTAGCAGCTGGCCACCCC 62.861 60.000 17.12 0.00 46.50 4.95
912 915 3.634157 TAGCAGCTGGCCACCCCTA 62.634 63.158 17.12 3.30 46.50 3.53
913 916 4.047125 GCAGCTGGCCACCCCTAA 62.047 66.667 17.12 0.00 36.11 2.69
914 917 2.763215 CAGCTGGCCACCCCTAAA 59.237 61.111 0.00 0.00 0.00 1.85
915 918 1.076549 CAGCTGGCCACCCCTAAAA 59.923 57.895 0.00 0.00 0.00 1.52
916 919 0.541764 CAGCTGGCCACCCCTAAAAA 60.542 55.000 0.00 0.00 0.00 1.94
966 969 4.097361 GGACTTCCCCGTCCCTGC 62.097 72.222 0.00 0.00 46.19 4.85
1039 1054 1.383109 ATCCTCACCCATCTCGCCA 60.383 57.895 0.00 0.00 0.00 5.69
1211 1238 1.601171 CCAAGCTCTCCCACCTCAG 59.399 63.158 0.00 0.00 0.00 3.35
1305 1332 2.263540 GTAGCCAAAGACCCGCGA 59.736 61.111 8.23 0.00 0.00 5.87
1322 1349 0.026803 CGATTACTCTGCGCCAAAGC 59.973 55.000 4.18 0.00 37.71 3.51
1615 1646 1.321474 CAAGTTGTGCATCCCTGTGT 58.679 50.000 0.00 0.00 0.00 3.72
1803 1839 1.153549 GTGGTCAGATGCCGAGGTC 60.154 63.158 0.00 0.00 0.00 3.85
2036 2072 5.050295 GCCGGAGCTACTATGTAATTTTCAC 60.050 44.000 5.05 0.00 35.50 3.18
2080 2116 4.892934 TGGAAAAATACATATGCCCTCACC 59.107 41.667 1.58 0.00 0.00 4.02
2235 2275 2.484264 GACAAGGCGCACTAGTTTGATT 59.516 45.455 10.83 0.00 0.00 2.57
2333 2373 7.138054 TCTAATTATCTTCCTGGAAGTTCCC 57.862 40.000 30.15 2.04 40.24 3.97
2344 2384 2.167487 TGGAAGTTCCCTTTTGTTGTGC 59.833 45.455 19.42 0.00 35.03 4.57
2367 2552 5.277345 GCGGTATCTATTTGCAAGTACAAGG 60.277 44.000 0.00 0.00 0.00 3.61
2372 2557 9.379791 GTATCTATTTGCAAGTACAAGGTAAGT 57.620 33.333 0.00 0.00 0.00 2.24
2374 2559 9.953565 ATCTATTTGCAAGTACAAGGTAAGTTA 57.046 29.630 0.00 0.00 0.00 2.24
2434 2621 7.230849 ACAAAATTGCCTGAACATTGAGATA 57.769 32.000 0.00 0.00 0.00 1.98
2435 2622 7.318141 ACAAAATTGCCTGAACATTGAGATAG 58.682 34.615 0.00 0.00 0.00 2.08
2436 2623 7.039504 ACAAAATTGCCTGAACATTGAGATAGT 60.040 33.333 0.00 0.00 0.00 2.12
2462 2649 6.645415 ACTGGTAATCGTAGCATTAGCAATAC 59.355 38.462 7.53 0.00 43.01 1.89
2472 2659 5.195940 AGCATTAGCAATACAGGTGAACAT 58.804 37.500 0.00 0.00 45.49 2.71
2479 2666 1.557099 TACAGGTGAACATCGAGGCT 58.443 50.000 0.00 0.00 0.00 4.58
2500 2687 7.575505 AGGCTTGTATCTGTAGTAGTAGAGAA 58.424 38.462 8.40 0.00 32.54 2.87
2581 3044 4.984785 GCTCTTTGTTCCCTGATTTGTTTC 59.015 41.667 0.00 0.00 0.00 2.78
2628 3091 0.179026 CTCCCATGCCTGATCCACAG 60.179 60.000 0.00 0.00 45.36 3.66
2689 3152 7.243487 CGCACTTGTACAGATCAATGTATTTT 58.757 34.615 0.00 0.00 37.93 1.82
2783 3246 2.034053 GCTATCGTCCCTGAAGAGTCTG 59.966 54.545 0.00 0.00 0.00 3.51
2985 3448 0.674895 CCACTGCCTTGAGTACTGCC 60.675 60.000 0.00 0.00 0.00 4.85
2996 3459 0.833287 AGTACTGCCGATGCCTCAAT 59.167 50.000 0.00 0.00 36.33 2.57
3041 3504 2.691409 TTCCTTTGCCTGTATCCTCG 57.309 50.000 0.00 0.00 0.00 4.63
3047 3510 2.396590 TGCCTGTATCCTCGAAAACC 57.603 50.000 0.00 0.00 0.00 3.27
3119 3582 8.291191 TGATATCCTGCAATGTTCAACAATAA 57.709 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.935203 TGCCTTGTTGATCGAAGAGAATC 59.065 43.478 0.00 0.00 43.63 2.52
30 31 2.195139 GCCATGCTCAGGATGCCT 59.805 61.111 0.00 0.00 34.76 4.75
60 61 8.965819 AGAAAAATTGCCAACCTAAATTGTTTT 58.034 25.926 0.00 0.00 0.00 2.43
64 65 7.929159 ACAAGAAAAATTGCCAACCTAAATTG 58.071 30.769 0.00 0.00 33.28 2.32
65 66 8.404765 CAACAAGAAAAATTGCCAACCTAAATT 58.595 29.630 0.00 0.00 33.28 1.82
66 67 7.468494 GCAACAAGAAAAATTGCCAACCTAAAT 60.468 33.333 0.00 0.00 42.32 1.40
67 68 6.183360 GCAACAAGAAAAATTGCCAACCTAAA 60.183 34.615 0.00 0.00 42.32 1.85
68 69 5.295540 GCAACAAGAAAAATTGCCAACCTAA 59.704 36.000 0.00 0.00 42.32 2.69
101 102 1.614413 GCACGTGTTTTGGGGGATTTA 59.386 47.619 18.38 0.00 0.00 1.40
118 119 3.243367 TGTTGCAACAGAGTAATTGGCAC 60.243 43.478 27.96 0.00 34.30 5.01
144 145 8.826710 TGTATAGGAACGATTGCTAGAAAATTG 58.173 33.333 0.00 0.00 37.01 2.32
154 155 5.293324 TGTCATGTTGTATAGGAACGATTGC 59.707 40.000 0.00 0.00 0.00 3.56
179 180 6.918022 GCTACATAAGGATTTGCCATGTTTAC 59.082 38.462 0.00 0.00 40.02 2.01
215 216 5.921004 TTGCCATGCAAAAACAGATAAAC 57.079 34.783 0.00 0.00 45.96 2.01
229 230 3.599704 GCTCCGGGATTGCCATGC 61.600 66.667 0.00 0.00 35.15 4.06
241 242 1.134367 TCACTCCTAACGAATGCTCCG 59.866 52.381 0.00 0.00 0.00 4.63
273 274 4.316377 CGCAACAAACGAACATTTCAGTTC 60.316 41.667 0.00 0.00 43.39 3.01
286 287 3.900116 CAGACAAACTATCGCAACAAACG 59.100 43.478 0.00 0.00 0.00 3.60
294 295 0.459585 TCGCCCAGACAAACTATCGC 60.460 55.000 0.00 0.00 0.00 4.58
308 309 0.537188 TTCTCTCATGGAAGTCGCCC 59.463 55.000 0.00 0.00 0.00 6.13
311 312 2.095212 TGACGTTCTCTCATGGAAGTCG 60.095 50.000 0.00 4.03 0.00 4.18
315 316 3.390135 GTGTTGACGTTCTCTCATGGAA 58.610 45.455 0.00 0.00 0.00 3.53
345 346 4.469552 CGTATCGGTTTTTCCTTTGAACC 58.530 43.478 0.00 0.00 39.50 3.62
359 360 5.638596 TTAGTATGATGATGCGTATCGGT 57.361 39.130 9.02 0.00 36.04 4.69
367 368 9.770503 GATCATGTGATTTTAGTATGATGATGC 57.229 33.333 0.00 0.00 38.28 3.91
390 391 7.787028 AGGGAGTACTTAACAGAATTCTGATC 58.213 38.462 36.15 19.86 46.59 2.92
559 560 4.904116 TCAACGTTCGCAATATGAAATCC 58.096 39.130 0.00 0.00 0.00 3.01
621 622 6.818142 GTCTGCATATAAAATTTGGCCAAAGT 59.182 34.615 32.85 29.07 33.32 2.66
622 623 7.043565 AGTCTGCATATAAAATTTGGCCAAAG 58.956 34.615 32.85 18.94 33.32 2.77
623 624 6.945218 AGTCTGCATATAAAATTTGGCCAAA 58.055 32.000 32.12 32.12 34.46 3.28
626 627 8.940768 TTTTAGTCTGCATATAAAATTTGGCC 57.059 30.769 0.00 0.00 0.00 5.36
759 762 3.192844 AGAGTCGCTTCTTCCGTTGATTA 59.807 43.478 0.00 0.00 0.00 1.75
768 771 3.579709 TGACAATGAGAGTCGCTTCTTC 58.420 45.455 0.00 0.00 38.83 2.87
788 791 1.381928 TAGTCGTAGCCGGCCTTCTG 61.382 60.000 26.15 9.27 40.30 3.02
792 795 3.207669 CGTAGTCGTAGCCGGCCT 61.208 66.667 26.15 15.54 40.30 5.19
793 796 4.261781 CCGTAGTCGTAGCCGGCC 62.262 72.222 26.15 7.92 40.30 6.13
794 797 4.261781 CCCGTAGTCGTAGCCGGC 62.262 72.222 21.89 21.89 39.12 6.13
795 798 4.261781 GCCCGTAGTCGTAGCCGG 62.262 72.222 0.00 0.00 40.12 6.13
796 799 4.261781 GGCCCGTAGTCGTAGCCG 62.262 72.222 0.00 0.00 41.91 5.52
797 800 3.909285 GGGCCCGTAGTCGTAGCC 61.909 72.222 5.69 9.38 46.67 3.93
798 801 2.024590 ATTGGGCCCGTAGTCGTAGC 62.025 60.000 19.37 0.00 34.95 3.58
799 802 1.321474 TATTGGGCCCGTAGTCGTAG 58.679 55.000 19.37 0.00 35.01 3.51
800 803 1.408702 GTTATTGGGCCCGTAGTCGTA 59.591 52.381 19.37 0.00 35.01 3.43
801 804 0.176449 GTTATTGGGCCCGTAGTCGT 59.824 55.000 19.37 0.00 35.01 4.34
802 805 0.462789 AGTTATTGGGCCCGTAGTCG 59.537 55.000 19.37 0.00 0.00 4.18
803 806 1.483415 TGAGTTATTGGGCCCGTAGTC 59.517 52.381 19.37 14.29 0.00 2.59
804 807 1.208776 GTGAGTTATTGGGCCCGTAGT 59.791 52.381 19.37 4.68 0.00 2.73
805 808 1.208535 TGTGAGTTATTGGGCCCGTAG 59.791 52.381 19.37 0.00 0.00 3.51
806 809 1.277579 TGTGAGTTATTGGGCCCGTA 58.722 50.000 19.37 10.22 0.00 4.02
807 810 0.402504 TTGTGAGTTATTGGGCCCGT 59.597 50.000 19.37 11.40 0.00 5.28
808 811 1.094785 CTTGTGAGTTATTGGGCCCG 58.905 55.000 19.37 0.00 0.00 6.13
809 812 0.817654 GCTTGTGAGTTATTGGGCCC 59.182 55.000 17.59 17.59 0.00 5.80
810 813 1.474077 CAGCTTGTGAGTTATTGGGCC 59.526 52.381 0.00 0.00 0.00 5.80
811 814 1.474077 CCAGCTTGTGAGTTATTGGGC 59.526 52.381 0.00 0.00 0.00 5.36
812 815 3.012518 CTCCAGCTTGTGAGTTATTGGG 58.987 50.000 0.00 0.00 0.00 4.12
813 816 3.012518 CCTCCAGCTTGTGAGTTATTGG 58.987 50.000 4.48 0.00 0.00 3.16
814 817 2.421424 GCCTCCAGCTTGTGAGTTATTG 59.579 50.000 4.48 0.00 38.99 1.90
815 818 2.619074 GGCCTCCAGCTTGTGAGTTATT 60.619 50.000 0.00 0.00 43.05 1.40
816 819 1.065126 GGCCTCCAGCTTGTGAGTTAT 60.065 52.381 0.00 0.00 43.05 1.89
817 820 0.324943 GGCCTCCAGCTTGTGAGTTA 59.675 55.000 0.00 0.00 43.05 2.24
818 821 1.073897 GGCCTCCAGCTTGTGAGTT 59.926 57.895 0.00 0.00 43.05 3.01
819 822 2.753029 GGCCTCCAGCTTGTGAGT 59.247 61.111 0.00 0.00 43.05 3.41
820 823 2.045536 GGGCCTCCAGCTTGTGAG 60.046 66.667 0.84 0.00 43.05 3.51
821 824 1.792757 ATTGGGCCTCCAGCTTGTGA 61.793 55.000 4.53 0.00 45.04 3.58
822 825 1.304713 ATTGGGCCTCCAGCTTGTG 60.305 57.895 4.53 0.00 45.04 3.33
823 826 1.304713 CATTGGGCCTCCAGCTTGT 60.305 57.895 4.53 0.00 45.04 3.16
824 827 2.718073 GCATTGGGCCTCCAGCTTG 61.718 63.158 4.53 0.00 45.04 4.01
825 828 2.363406 GCATTGGGCCTCCAGCTT 60.363 61.111 4.53 0.00 45.04 3.74
826 829 3.664888 TGCATTGGGCCTCCAGCT 61.665 61.111 4.53 0.00 45.04 4.24
827 830 3.455469 GTGCATTGGGCCTCCAGC 61.455 66.667 4.53 4.40 45.04 4.85
828 831 1.601419 CTTGTGCATTGGGCCTCCAG 61.601 60.000 4.53 0.00 45.04 3.86
829 832 1.607178 CTTGTGCATTGGGCCTCCA 60.607 57.895 4.53 0.00 43.89 3.86
830 833 3.010413 GCTTGTGCATTGGGCCTCC 62.010 63.158 4.53 0.00 43.89 4.30
831 834 2.277591 TGCTTGTGCATTGGGCCTC 61.278 57.895 4.53 0.00 45.31 4.70
832 835 2.203669 TGCTTGTGCATTGGGCCT 60.204 55.556 4.53 0.00 45.31 5.19
841 844 4.635765 TGGACTATGATTTACTGCTTGTGC 59.364 41.667 0.00 0.00 40.20 4.57
842 845 6.546395 GTTGGACTATGATTTACTGCTTGTG 58.454 40.000 0.00 0.00 0.00 3.33
843 846 5.351465 CGTTGGACTATGATTTACTGCTTGT 59.649 40.000 0.00 0.00 0.00 3.16
844 847 5.580691 TCGTTGGACTATGATTTACTGCTTG 59.419 40.000 0.00 0.00 0.00 4.01
845 848 5.730550 TCGTTGGACTATGATTTACTGCTT 58.269 37.500 0.00 0.00 0.00 3.91
846 849 5.339008 TCGTTGGACTATGATTTACTGCT 57.661 39.130 0.00 0.00 0.00 4.24
847 850 6.562270 CGATTCGTTGGACTATGATTTACTGC 60.562 42.308 0.00 0.00 0.00 4.40
848 851 6.562270 GCGATTCGTTGGACTATGATTTACTG 60.562 42.308 8.03 0.00 0.00 2.74
849 852 5.462398 GCGATTCGTTGGACTATGATTTACT 59.538 40.000 8.03 0.00 0.00 2.24
850 853 5.233476 TGCGATTCGTTGGACTATGATTTAC 59.767 40.000 8.03 0.00 0.00 2.01
851 854 5.353111 TGCGATTCGTTGGACTATGATTTA 58.647 37.500 8.03 0.00 0.00 1.40
852 855 4.188462 TGCGATTCGTTGGACTATGATTT 58.812 39.130 8.03 0.00 0.00 2.17
853 856 3.792401 TGCGATTCGTTGGACTATGATT 58.208 40.909 8.03 0.00 0.00 2.57
854 857 3.384668 CTGCGATTCGTTGGACTATGAT 58.615 45.455 8.03 0.00 0.00 2.45
855 858 2.809446 CTGCGATTCGTTGGACTATGA 58.191 47.619 8.03 0.00 0.00 2.15
856 859 1.258982 GCTGCGATTCGTTGGACTATG 59.741 52.381 8.03 0.00 0.00 2.23
857 860 1.134818 TGCTGCGATTCGTTGGACTAT 60.135 47.619 8.03 0.00 0.00 2.12
858 861 0.245266 TGCTGCGATTCGTTGGACTA 59.755 50.000 8.03 0.00 0.00 2.59
881 884 2.938451 CAGCTGCTAATTGGTTCGATGA 59.062 45.455 0.00 0.00 0.00 2.92
894 897 3.634157 TAGGGGTGGCCAGCTGCTA 62.634 63.158 32.43 9.82 40.92 3.49
896 899 3.583882 TTTAGGGGTGGCCAGCTGC 62.584 63.158 32.43 17.93 40.16 5.25
897 900 0.541764 TTTTTAGGGGTGGCCAGCTG 60.542 55.000 32.43 6.78 0.00 4.24
898 901 1.857777 TTTTTAGGGGTGGCCAGCT 59.142 52.632 32.43 17.80 0.00 4.24
899 902 4.531351 TTTTTAGGGGTGGCCAGC 57.469 55.556 27.04 27.04 0.00 4.85
926 929 1.478631 GGAGGCCAGCTGCTATTTTT 58.521 50.000 8.66 0.00 40.92 1.94
927 930 0.749454 CGGAGGCCAGCTGCTATTTT 60.749 55.000 8.66 0.00 40.92 1.82
928 931 1.153086 CGGAGGCCAGCTGCTATTT 60.153 57.895 8.66 0.00 40.92 1.40
929 932 2.507944 CGGAGGCCAGCTGCTATT 59.492 61.111 8.66 0.00 40.92 1.73
930 933 4.247380 GCGGAGGCCAGCTGCTAT 62.247 66.667 19.02 0.00 40.92 2.97
1290 1317 0.743345 GTAATCGCGGGTCTTTGGCT 60.743 55.000 6.13 0.00 0.00 4.75
1322 1349 2.570284 GGGGCCAAGGTTTTGTCCG 61.570 63.158 4.39 0.00 33.09 4.79
1627 1658 2.668550 GTGCTCGGGGTTGGTGAC 60.669 66.667 0.00 0.00 0.00 3.67
1803 1839 1.669779 GCCTTAGACAGAGCAATGCTG 59.330 52.381 14.48 1.99 39.88 4.41
2036 2072 3.121944 CACGAAAACCTTCTCAGTCATCG 59.878 47.826 0.00 0.00 33.78 3.84
2098 2134 2.294233 CGGCAGCATAGTATTTGGCAAT 59.706 45.455 0.00 0.00 36.04 3.56
2134 2170 1.890979 CAATCTAGCGGGCAGGCAG 60.891 63.158 0.00 0.00 34.64 4.85
2251 2291 6.428159 TGTCAAGATTTAGAACCTGCTCTTTC 59.572 38.462 0.00 0.00 0.00 2.62
2333 2373 5.286082 GCAAATAGATACCGCACAACAAAAG 59.714 40.000 0.00 0.00 0.00 2.27
2344 2384 5.815740 ACCTTGTACTTGCAAATAGATACCG 59.184 40.000 0.00 0.00 0.00 4.02
2367 2552 5.105877 GGCAATTTCTTGGGGAGTAACTTAC 60.106 44.000 0.00 0.00 32.72 2.34
2372 2557 3.825908 AGGCAATTTCTTGGGGAGTAA 57.174 42.857 0.00 0.00 32.72 2.24
2374 2559 2.702270 AAGGCAATTTCTTGGGGAGT 57.298 45.000 0.00 0.00 32.72 3.85
2434 2621 5.301045 TGCTAATGCTACGATTACCAGTACT 59.699 40.000 0.00 0.00 40.48 2.73
2435 2622 5.526115 TGCTAATGCTACGATTACCAGTAC 58.474 41.667 0.00 0.00 40.48 2.73
2436 2623 5.777850 TGCTAATGCTACGATTACCAGTA 57.222 39.130 0.00 0.00 40.48 2.74
2462 2649 1.081892 CAAGCCTCGATGTTCACCTG 58.918 55.000 0.00 0.00 0.00 4.00
2472 2659 4.778579 ACTACTACAGATACAAGCCTCGA 58.221 43.478 0.00 0.00 0.00 4.04
2479 2666 7.344134 TGCCTTCTCTACTACTACAGATACAA 58.656 38.462 0.00 0.00 0.00 2.41
2500 2687 0.319405 GAGCCATGCTTGTTTTGCCT 59.681 50.000 0.00 0.00 39.88 4.75
2551 3014 3.198635 TCAGGGAACAAAGAGCTCCATAG 59.801 47.826 10.93 0.49 0.00 2.23
2581 3044 5.645497 TCAACCTGGTTTTTGTTCCAAATTG 59.355 36.000 9.90 0.00 33.56 2.32
2783 3246 3.733337 AGATGATTTGTGGGATAGACGC 58.267 45.455 0.00 0.00 0.00 5.19
2985 3448 1.026584 TGCATGGAATTGAGGCATCG 58.973 50.000 0.00 0.00 0.00 3.84
2996 3459 3.196469 TGGTTTTCACAGTTTGCATGGAA 59.804 39.130 0.00 0.00 0.00 3.53
3041 3504 4.339530 GCAGGAGAGATAATTGGGGTTTTC 59.660 45.833 0.00 0.00 0.00 2.29
3047 3510 4.759183 GCTTAAGCAGGAGAGATAATTGGG 59.241 45.833 22.59 0.00 41.59 4.12


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

AutoCloner maintained by Alex Coulton.