Multiple sequence alignment - TraesCS6A01G034400

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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 TraesCS6A01G034400 chr6A 100.000 3161 0 0 1 3161 16627997 16631157 0.000000e+00 5838.0
1 TraesCS6A01G034400 chr6A 80.961 1166 189 21 968 2114 15647255 15648406 0.000000e+00 893.0
2 TraesCS6A01G034400 chr6A 95.385 65 2 1 844 908 14367539 14367476 5.580000e-18 102.0
3 TraesCS6A01G034400 chr6D 95.694 2206 75 6 967 3161 16368939 16371135 0.000000e+00 3530.0
4 TraesCS6A01G034400 chr6D 80.135 1188 215 16 968 2144 14941189 14940012 0.000000e+00 867.0
5 TraesCS6A01G034400 chr6B 94.086 2215 95 18 964 3161 28471427 28473622 0.000000e+00 3332.0
6 TraesCS6A01G034400 chr6B 93.777 1880 83 20 967 2832 59305351 59303492 0.000000e+00 2793.0
7 TraesCS6A01G034400 chr6B 94.476 1068 43 6 2104 3161 28746747 28745686 0.000000e+00 1631.0
8 TraesCS6A01G034400 chr6B 86.228 1169 150 9 942 2102 28748058 28746893 0.000000e+00 1256.0
9 TraesCS6A01G034400 chr6B 86.228 1169 150 9 942 2102 28753424 28752259 0.000000e+00 1256.0
10 TraesCS6A01G034400 chrUn 93.593 1077 44 7 2104 3161 76385706 76384636 0.000000e+00 1585.0
11 TraesCS6A01G034400 chrUn 86.228 1169 150 9 942 2102 76387452 76386287 0.000000e+00 1256.0
12 TraesCS6A01G034400 chrUn 96.154 520 15 4 2645 3161 76408887 76408370 0.000000e+00 845.0
13 TraesCS6A01G034400 chr1B 86.313 1074 121 14 1800 2855 48092874 48091809 0.000000e+00 1146.0
14 TraesCS6A01G034400 chr5B 88.298 846 89 8 2 842 447400057 447400897 0.000000e+00 1005.0
15 TraesCS6A01G034400 chr4B 79.360 1187 218 20 996 2165 575726100 575727276 0.000000e+00 809.0
16 TraesCS6A01G034400 chr4B 82.997 594 83 9 2274 2855 289619909 289620496 3.610000e-144 521.0
17 TraesCS6A01G034400 chr7B 84.295 745 100 14 2118 2855 397596592 397595858 0.000000e+00 712.0
18 TraesCS6A01G034400 chr3B 84.440 482 61 9 2380 2855 305802544 305803017 2.220000e-126 462.0
19 TraesCS6A01G034400 chr3B 84.134 479 63 12 2380 2854 441233888 441234357 4.810000e-123 451.0
20 TraesCS6A01G034400 chr3B 80.460 261 35 9 2856 3104 305803064 305803320 5.380000e-43 185.0
21 TraesCS6A01G034400 chr3B 80.153 262 36 10 2855 3104 262656515 262656258 6.960000e-42 182.0
22 TraesCS6A01G034400 chr3B 79.389 262 36 11 2855 3103 441234404 441234660 5.420000e-38 169.0
23 TraesCS6A01G034400 chr7D 75.312 320 58 15 2855 3158 591389794 591390108 1.980000e-27 134.0
24 TraesCS6A01G034400 chr7A 78.090 178 38 1 2075 2251 657023507 657023330 9.270000e-21 111.0
25 TraesCS6A01G034400 chr7A 96.825 63 2 0 844 906 110223644 110223706 4.310000e-19 106.0
26 TraesCS6A01G034400 chr7A 94.030 67 3 1 845 911 110222643 110222578 2.010000e-17 100.0
27 TraesCS6A01G034400 chr4A 98.387 62 1 0 846 907 314690028 314689967 3.330000e-20 110.0
28 TraesCS6A01G034400 chr4A 95.082 61 3 0 844 904 314691024 314691084 2.600000e-16 97.1
29 TraesCS6A01G034400 chr2B 98.387 62 1 0 845 906 283013393 283013454 3.330000e-20 110.0
30 TraesCS6A01G034400 chr2D 96.825 63 2 0 844 906 25877466 25877404 4.310000e-19 106.0
31 TraesCS6A01G034400 chr1A 96.721 61 2 0 844 904 552495660 552495720 5.580000e-18 102.0


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 TraesCS6A01G034400 chr6A 16627997 16631157 3160 False 5838.0 5838 100.0000 1 3161 1 chr6A.!!$F2 3160
1 TraesCS6A01G034400 chr6A 15647255 15648406 1151 False 893.0 893 80.9610 968 2114 1 chr6A.!!$F1 1146
2 TraesCS6A01G034400 chr6D 16368939 16371135 2196 False 3530.0 3530 95.6940 967 3161 1 chr6D.!!$F1 2194
3 TraesCS6A01G034400 chr6D 14940012 14941189 1177 True 867.0 867 80.1350 968 2144 1 chr6D.!!$R1 1176
4 TraesCS6A01G034400 chr6B 28471427 28473622 2195 False 3332.0 3332 94.0860 964 3161 1 chr6B.!!$F1 2197
5 TraesCS6A01G034400 chr6B 59303492 59305351 1859 True 2793.0 2793 93.7770 967 2832 1 chr6B.!!$R2 1865
6 TraesCS6A01G034400 chr6B 28745686 28748058 2372 True 1443.5 1631 90.3520 942 3161 2 chr6B.!!$R3 2219
7 TraesCS6A01G034400 chr6B 28752259 28753424 1165 True 1256.0 1256 86.2280 942 2102 1 chr6B.!!$R1 1160
8 TraesCS6A01G034400 chrUn 76384636 76387452 2816 True 1420.5 1585 89.9105 942 3161 2 chrUn.!!$R2 2219
9 TraesCS6A01G034400 chrUn 76408370 76408887 517 True 845.0 845 96.1540 2645 3161 1 chrUn.!!$R1 516
10 TraesCS6A01G034400 chr1B 48091809 48092874 1065 True 1146.0 1146 86.3130 1800 2855 1 chr1B.!!$R1 1055
11 TraesCS6A01G034400 chr5B 447400057 447400897 840 False 1005.0 1005 88.2980 2 842 1 chr5B.!!$F1 840
12 TraesCS6A01G034400 chr4B 575726100 575727276 1176 False 809.0 809 79.3600 996 2165 1 chr4B.!!$F2 1169
13 TraesCS6A01G034400 chr4B 289619909 289620496 587 False 521.0 521 82.9970 2274 2855 1 chr4B.!!$F1 581
14 TraesCS6A01G034400 chr7B 397595858 397596592 734 True 712.0 712 84.2950 2118 2855 1 chr7B.!!$R1 737
15 TraesCS6A01G034400 chr3B 305802544 305803320 776 False 323.5 462 82.4500 2380 3104 2 chr3B.!!$F1 724
16 TraesCS6A01G034400 chr3B 441233888 441234660 772 False 310.0 451 81.7615 2380 3103 2 chr3B.!!$F2 723

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
959 964 0.313043 GCCATTGCAATCCATCGGAG 59.687 55.000 9.53 0.0 34.08 4.63 F
1031 1042 1.289380 GAGAGTGCGTCGTTTCCCT 59.711 57.895 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 1886 0.390472 CAGGAACTCGGACTTGCTCC 60.39 60.0 0.00 0.00 34.6 4.70 R
3016 3714 2.480073 GCCACATCATCCGGAAACAATG 60.48 50.0 9.01 12.33 0.0 2.82 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
65 66 4.306600 CAATCTTTGTTACCTTTGGCACC 58.693 43.478 0.00 0.00 0.00 5.01
97 98 8.727149 TGATCTAAGGAAATTATCATGAAGGGT 58.273 33.333 0.00 0.00 0.00 4.34
115 116 6.389869 TGAAGGGTATTCCATCTACAAGGATT 59.610 38.462 0.00 0.00 38.24 3.01
211 212 6.000891 TCATCACTCAAATAAACACACAGC 57.999 37.500 0.00 0.00 0.00 4.40
214 215 3.976942 CACTCAAATAAACACACAGCTGC 59.023 43.478 15.27 0.00 0.00 5.25
224 225 4.271696 ACACACAGCTGCTACAGATTTA 57.728 40.909 15.27 0.00 32.44 1.40
225 226 4.641396 ACACACAGCTGCTACAGATTTAA 58.359 39.130 15.27 0.00 32.44 1.52
227 228 5.707298 ACACACAGCTGCTACAGATTTAAAT 59.293 36.000 15.27 0.00 32.44 1.40
230 231 7.272084 CACACAGCTGCTACAGATTTAAATTTC 59.728 37.037 15.27 0.00 32.44 2.17
231 232 7.040478 ACACAGCTGCTACAGATTTAAATTTCA 60.040 33.333 15.27 0.00 32.44 2.69
253 255 6.314018 TCAATTTCGTAGTTGCATTCATGTC 58.686 36.000 0.00 0.00 0.00 3.06
256 258 3.261580 TCGTAGTTGCATTCATGTCCTG 58.738 45.455 0.00 0.00 0.00 3.86
273 275 3.823304 GTCCTGAAAGCATGAACCTTCTT 59.177 43.478 0.00 0.00 0.00 2.52
274 276 4.074970 TCCTGAAAGCATGAACCTTCTTC 58.925 43.478 0.00 0.00 0.00 2.87
280 282 4.213564 AGCATGAACCTTCTTCCTACAG 57.786 45.455 0.00 0.00 0.00 2.74
285 287 6.404074 GCATGAACCTTCTTCCTACAGATTTG 60.404 42.308 0.00 0.00 0.00 2.32
292 294 6.481644 CCTTCTTCCTACAGATTTGAGTATGC 59.518 42.308 0.00 0.00 0.00 3.14
302 304 6.883217 ACAGATTTGAGTATGCTGATCAGTTT 59.117 34.615 23.38 13.57 0.00 2.66
303 305 7.065563 ACAGATTTGAGTATGCTGATCAGTTTC 59.934 37.037 23.38 13.75 0.00 2.78
341 343 3.379240 CTGTAGGATGACGAATCTGCAG 58.621 50.000 7.63 7.63 35.43 4.41
347 349 4.063689 GGATGACGAATCTGCAGATTGAT 58.936 43.478 39.54 28.16 44.14 2.57
348 350 4.152045 GGATGACGAATCTGCAGATTGATC 59.848 45.833 39.54 32.67 44.14 2.92
349 351 4.397481 TGACGAATCTGCAGATTGATCT 57.603 40.909 39.54 20.78 44.14 2.75
353 355 3.741856 CGAATCTGCAGATTGATCTCTGG 59.258 47.826 39.54 16.56 44.14 3.86
359 361 3.139850 GCAGATTGATCTCTGGTGATGG 58.860 50.000 12.48 0.00 42.42 3.51
420 422 2.113774 CCAGCTGCCAGTTGGTGA 59.886 61.111 18.57 0.00 41.12 4.02
431 436 1.281867 CAGTTGGTGATCCCAGCCTAA 59.718 52.381 11.62 0.00 45.11 2.69
433 438 1.004277 GTTGGTGATCCCAGCCTAACA 59.996 52.381 5.98 0.00 46.31 2.41
461 466 1.019673 CAGGGAATTGGCGATCACAG 58.980 55.000 0.00 0.00 0.00 3.66
466 471 1.033746 AATTGGCGATCACAGCAGGG 61.034 55.000 0.00 0.00 36.08 4.45
503 508 6.183347 CCATTGAACTAGGTTTCCAGATCTT 58.817 40.000 0.00 0.00 0.00 2.40
504 509 6.660949 CCATTGAACTAGGTTTCCAGATCTTT 59.339 38.462 0.00 0.00 0.00 2.52
527 532 2.753989 TGCTGATGTTTGTTGTGTCG 57.246 45.000 0.00 0.00 0.00 4.35
530 535 1.333308 CTGATGTTTGTTGTGTCGCCA 59.667 47.619 0.00 0.00 0.00 5.69
546 551 6.014584 TGTGTCGCCATCCAGTTTATATAGAT 60.015 38.462 0.00 0.00 0.00 1.98
557 562 8.154203 TCCAGTTTATATAGATGCGATGGAAAA 58.846 33.333 0.00 0.00 30.50 2.29
592 597 2.592308 GCTGCGGGAGGGAAGAAT 59.408 61.111 0.00 0.00 0.00 2.40
616 621 2.227865 GCGCCAATAAGTTTGTTGAGGA 59.772 45.455 0.00 0.00 31.84 3.71
629 634 0.972983 TTGAGGAAGGAGCGGAGAGG 60.973 60.000 0.00 0.00 0.00 3.69
634 639 1.210722 GGAAGGAGCGGAGAGGAAAAT 59.789 52.381 0.00 0.00 0.00 1.82
637 642 1.208293 AGGAGCGGAGAGGAAAATGTC 59.792 52.381 0.00 0.00 0.00 3.06
639 644 2.275318 GAGCGGAGAGGAAAATGTCTG 58.725 52.381 0.00 0.00 0.00 3.51
644 649 3.612860 CGGAGAGGAAAATGTCTGTTACG 59.387 47.826 0.00 0.00 0.00 3.18
654 659 7.172019 GGAAAATGTCTGTTACGGAGAGTTTTA 59.828 37.037 15.77 0.00 32.17 1.52
656 661 9.715121 AAAATGTCTGTTACGGAGAGTTTTATA 57.285 29.630 10.27 0.00 28.62 0.98
727 732 2.151502 TTCCTGGCTTTGTGGAAACA 57.848 45.000 0.00 0.00 36.98 2.83
728 733 2.380064 TCCTGGCTTTGTGGAAACAT 57.620 45.000 0.00 0.00 46.14 2.71
734 739 6.495181 TCCTGGCTTTGTGGAAACATAATTTA 59.505 34.615 0.00 0.00 46.14 1.40
737 742 7.731054 TGGCTTTGTGGAAACATAATTTAAGT 58.269 30.769 0.00 0.00 46.14 2.24
759 764 7.174107 AGTTATCCATGATTTTGTTGAAGGG 57.826 36.000 0.00 0.00 0.00 3.95
766 771 3.393941 TGATTTTGTTGAAGGGCCCAAAT 59.606 39.130 27.56 18.77 0.00 2.32
770 775 3.464720 TGTTGAAGGGCCCAAATATGA 57.535 42.857 27.56 0.00 0.00 2.15
796 801 3.020984 AGTTTGTTGGGCGGTTATATGG 58.979 45.455 0.00 0.00 0.00 2.74
798 803 0.920438 TGTTGGGCGGTTATATGGGT 59.080 50.000 0.00 0.00 0.00 4.51
799 804 1.134037 TGTTGGGCGGTTATATGGGTC 60.134 52.381 0.00 0.00 0.00 4.46
803 808 0.470766 GGCGGTTATATGGGTCCACA 59.529 55.000 0.00 0.00 0.00 4.17
826 831 6.948309 ACAGAAAACTAGTTTGGCTAATCCAT 59.052 34.615 21.22 1.65 46.04 3.41
842 847 2.639065 TCCATCGTATCCAAACAAGGC 58.361 47.619 0.00 0.00 0.00 4.35
843 848 1.676006 CCATCGTATCCAAACAAGGCC 59.324 52.381 0.00 0.00 0.00 5.19
844 849 2.643551 CATCGTATCCAAACAAGGCCT 58.356 47.619 0.00 0.00 0.00 5.19
845 850 3.433031 CCATCGTATCCAAACAAGGCCTA 60.433 47.826 5.16 0.00 0.00 3.93
846 851 3.985019 TCGTATCCAAACAAGGCCTAA 57.015 42.857 5.16 0.00 0.00 2.69
847 852 3.602483 TCGTATCCAAACAAGGCCTAAC 58.398 45.455 5.16 0.00 0.00 2.34
848 853 3.262405 TCGTATCCAAACAAGGCCTAACT 59.738 43.478 5.16 0.00 0.00 2.24
849 854 4.467082 TCGTATCCAAACAAGGCCTAACTA 59.533 41.667 5.16 0.00 0.00 2.24
850 855 5.046448 TCGTATCCAAACAAGGCCTAACTAA 60.046 40.000 5.16 0.00 0.00 2.24
851 856 5.644636 CGTATCCAAACAAGGCCTAACTAAA 59.355 40.000 5.16 0.00 0.00 1.85
852 857 6.183360 CGTATCCAAACAAGGCCTAACTAAAG 60.183 42.308 5.16 0.00 0.00 1.85
853 858 3.824443 TCCAAACAAGGCCTAACTAAAGC 59.176 43.478 5.16 0.00 0.00 3.51
854 859 3.572255 CCAAACAAGGCCTAACTAAAGCA 59.428 43.478 5.16 0.00 0.00 3.91
855 860 4.321230 CCAAACAAGGCCTAACTAAAGCAG 60.321 45.833 5.16 0.00 0.00 4.24
856 861 3.073274 ACAAGGCCTAACTAAAGCAGG 57.927 47.619 5.16 0.00 0.00 4.85
857 862 2.290960 ACAAGGCCTAACTAAAGCAGGG 60.291 50.000 5.16 0.00 0.00 4.45
858 863 2.795165 GGCCTAACTAAAGCAGGGC 58.205 57.895 0.00 8.46 46.28 5.19
859 864 3.569873 GCCTAACTAAAGCAGGGCA 57.430 52.632 0.00 0.00 39.38 5.36
860 865 1.834188 GCCTAACTAAAGCAGGGCAA 58.166 50.000 0.00 0.00 39.38 4.52
861 866 2.167662 GCCTAACTAAAGCAGGGCAAA 58.832 47.619 0.00 0.00 39.38 3.68
862 867 2.760650 GCCTAACTAAAGCAGGGCAAAT 59.239 45.455 0.00 0.00 39.38 2.32
863 868 3.181486 GCCTAACTAAAGCAGGGCAAATC 60.181 47.826 0.00 0.00 39.38 2.17
864 869 4.016444 CCTAACTAAAGCAGGGCAAATCA 58.984 43.478 0.00 0.00 0.00 2.57
865 870 4.646492 CCTAACTAAAGCAGGGCAAATCAT 59.354 41.667 0.00 0.00 0.00 2.45
866 871 4.725790 AACTAAAGCAGGGCAAATCATC 57.274 40.909 0.00 0.00 0.00 2.92
867 872 3.700538 ACTAAAGCAGGGCAAATCATCA 58.299 40.909 0.00 0.00 0.00 3.07
868 873 4.088634 ACTAAAGCAGGGCAAATCATCAA 58.911 39.130 0.00 0.00 0.00 2.57
869 874 3.323751 AAAGCAGGGCAAATCATCAAC 57.676 42.857 0.00 0.00 0.00 3.18
870 875 2.226962 AGCAGGGCAAATCATCAACT 57.773 45.000 0.00 0.00 0.00 3.16
871 876 2.097825 AGCAGGGCAAATCATCAACTC 58.902 47.619 0.00 0.00 0.00 3.01
872 877 1.135721 GCAGGGCAAATCATCAACTCC 59.864 52.381 0.00 0.00 0.00 3.85
873 878 1.753073 CAGGGCAAATCATCAACTCCC 59.247 52.381 0.00 0.00 0.00 4.30
874 879 1.642762 AGGGCAAATCATCAACTCCCT 59.357 47.619 0.00 0.00 37.77 4.20
875 880 2.852449 AGGGCAAATCATCAACTCCCTA 59.148 45.455 0.00 0.00 40.59 3.53
876 881 3.269381 AGGGCAAATCATCAACTCCCTAA 59.731 43.478 0.00 0.00 40.59 2.69
877 882 4.023291 GGGCAAATCATCAACTCCCTAAA 58.977 43.478 0.00 0.00 0.00 1.85
878 883 4.651045 GGGCAAATCATCAACTCCCTAAAT 59.349 41.667 0.00 0.00 0.00 1.40
879 884 5.833131 GGGCAAATCATCAACTCCCTAAATA 59.167 40.000 0.00 0.00 0.00 1.40
880 885 6.323739 GGGCAAATCATCAACTCCCTAAATAA 59.676 38.462 0.00 0.00 0.00 1.40
881 886 7.147742 GGGCAAATCATCAACTCCCTAAATAAA 60.148 37.037 0.00 0.00 0.00 1.40
882 887 7.922811 GGCAAATCATCAACTCCCTAAATAAAG 59.077 37.037 0.00 0.00 0.00 1.85
883 888 8.470002 GCAAATCATCAACTCCCTAAATAAAGT 58.530 33.333 0.00 0.00 0.00 2.66
884 889 9.793252 CAAATCATCAACTCCCTAAATAAAGTG 57.207 33.333 0.00 0.00 0.00 3.16
885 890 9.533831 AAATCATCAACTCCCTAAATAAAGTGT 57.466 29.630 0.00 0.00 0.00 3.55
886 891 7.921786 TCATCAACTCCCTAAATAAAGTGTG 57.078 36.000 0.00 0.00 0.00 3.82
887 892 6.884295 TCATCAACTCCCTAAATAAAGTGTGG 59.116 38.462 0.00 0.00 0.00 4.17
888 893 5.007682 TCAACTCCCTAAATAAAGTGTGGC 58.992 41.667 0.00 0.00 0.00 5.01
889 894 4.650972 ACTCCCTAAATAAAGTGTGGCA 57.349 40.909 0.00 0.00 0.00 4.92
890 895 4.993028 ACTCCCTAAATAAAGTGTGGCAA 58.007 39.130 0.00 0.00 0.00 4.52
891 896 5.390387 ACTCCCTAAATAAAGTGTGGCAAA 58.610 37.500 0.00 0.00 0.00 3.68
892 897 6.016555 ACTCCCTAAATAAAGTGTGGCAAAT 58.983 36.000 0.00 0.00 0.00 2.32
893 898 6.071391 ACTCCCTAAATAAAGTGTGGCAAATG 60.071 38.462 0.00 0.00 0.00 2.32
894 899 6.013379 TCCCTAAATAAAGTGTGGCAAATGA 58.987 36.000 0.00 0.00 0.00 2.57
895 900 6.667414 TCCCTAAATAAAGTGTGGCAAATGAT 59.333 34.615 0.00 0.00 0.00 2.45
896 901 6.980397 CCCTAAATAAAGTGTGGCAAATGATC 59.020 38.462 0.00 0.00 0.00 2.92
897 902 6.980397 CCTAAATAAAGTGTGGCAAATGATCC 59.020 38.462 0.00 0.00 0.00 3.36
898 903 5.999205 AATAAAGTGTGGCAAATGATCCA 57.001 34.783 0.00 0.00 0.00 3.41
899 904 5.999205 ATAAAGTGTGGCAAATGATCCAA 57.001 34.783 0.00 0.00 33.57 3.53
900 905 4.895668 AAAGTGTGGCAAATGATCCAAT 57.104 36.364 0.00 0.00 33.57 3.16
901 906 4.460948 AAGTGTGGCAAATGATCCAATC 57.539 40.909 0.00 0.00 33.57 2.67
902 907 3.705051 AGTGTGGCAAATGATCCAATCT 58.295 40.909 0.00 0.00 33.57 2.40
903 908 3.698040 AGTGTGGCAAATGATCCAATCTC 59.302 43.478 0.00 0.00 33.57 2.75
904 909 3.025978 TGTGGCAAATGATCCAATCTCC 58.974 45.455 0.00 0.00 33.57 3.71
905 910 2.363359 GTGGCAAATGATCCAATCTCCC 59.637 50.000 0.00 0.00 33.57 4.30
906 911 1.610522 GGCAAATGATCCAATCTCCCG 59.389 52.381 0.00 0.00 0.00 5.14
907 912 2.575532 GCAAATGATCCAATCTCCCGA 58.424 47.619 0.00 0.00 0.00 5.14
908 913 3.152341 GCAAATGATCCAATCTCCCGAT 58.848 45.455 0.00 0.00 0.00 4.18
909 914 4.326826 GCAAATGATCCAATCTCCCGATA 58.673 43.478 0.00 0.00 0.00 2.92
910 915 4.761739 GCAAATGATCCAATCTCCCGATAA 59.238 41.667 0.00 0.00 0.00 1.75
911 916 5.335191 GCAAATGATCCAATCTCCCGATAAC 60.335 44.000 0.00 0.00 0.00 1.89
912 917 4.559862 ATGATCCAATCTCCCGATAACC 57.440 45.455 0.00 0.00 0.00 2.85
913 918 2.299013 TGATCCAATCTCCCGATAACCG 59.701 50.000 0.00 0.00 38.18 4.44
922 927 3.891400 CGATAACCGGGACCGCGA 61.891 66.667 8.23 0.00 38.24 5.87
923 928 2.279054 GATAACCGGGACCGCGAC 60.279 66.667 8.23 0.17 38.24 5.19
924 929 3.067480 GATAACCGGGACCGCGACA 62.067 63.158 8.23 0.00 38.24 4.35
925 930 3.360956 ATAACCGGGACCGCGACAC 62.361 63.158 8.23 0.63 38.24 3.67
937 942 4.087892 CGACACCCAGGGGCAGAG 62.088 72.222 11.37 0.00 39.32 3.35
938 943 4.416738 GACACCCAGGGGCAGAGC 62.417 72.222 11.37 0.00 39.32 4.09
939 944 4.990910 ACACCCAGGGGCAGAGCT 62.991 66.667 11.37 0.00 39.32 4.09
940 945 4.421515 CACCCAGGGGCAGAGCTG 62.422 72.222 11.37 0.00 39.32 4.24
957 962 2.117257 TGCCATTGCAATCCATCGG 58.883 52.632 9.53 8.68 46.66 4.18
959 964 0.313043 GCCATTGCAATCCATCGGAG 59.687 55.000 9.53 0.00 34.08 4.63
961 966 2.511659 CCATTGCAATCCATCGGAGAT 58.488 47.619 9.53 0.00 45.12 2.75
1031 1042 1.289380 GAGAGTGCGTCGTTTCCCT 59.711 57.895 0.00 0.00 0.00 4.20
1047 1070 2.003830 TCCCTTCTCCTCTCTTCTCCA 58.996 52.381 0.00 0.00 0.00 3.86
1153 1176 2.823147 AGGAGTACCTCGTCGCCG 60.823 66.667 0.00 0.00 44.13 6.46
1539 1562 1.760613 TCGCGGGACCTTGATAAGATT 59.239 47.619 6.13 0.00 0.00 2.40
1597 1620 3.060003 GCTAGCTGCTTGTGATATTGTCG 60.060 47.826 7.79 0.00 38.95 4.35
1859 1886 2.551270 GTCAAAGGACACGCTGCG 59.449 61.111 21.91 21.91 43.73 5.18
2320 2928 9.928236 GCAGTTCAGTCTTCAATAATTAGATTC 57.072 33.333 0.00 0.00 0.00 2.52
2371 2979 8.940768 TTTTGGTTTCTTTCACCTTATTCTTG 57.059 30.769 0.00 0.00 35.07 3.02
2423 3038 0.469917 GGCTGTAGATGGCCTTGCTA 59.530 55.000 3.32 0.00 44.48 3.49
2462 3083 9.990360 TTTCTTCCAAATTTGATAAAGTAACCC 57.010 29.630 19.86 0.00 0.00 4.11
3010 3707 8.993121 TGATTACTGAAGTTCAAGAGAAACATC 58.007 33.333 7.06 1.87 35.08 3.06
3016 3714 6.263168 TGAAGTTCAAGAGAAACATCCCTTTC 59.737 38.462 2.20 0.00 35.08 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.940850 ACAAAGATTGCAGTATTTGTGTAACT 58.059 30.769 27.45 7.82 40.73 2.24
33 34 7.524717 AGGTAACAAAGATTGCAGTATTTGT 57.475 32.000 24.05 24.05 43.17 2.83
35 36 7.872483 CCAAAGGTAACAAAGATTGCAGTATTT 59.128 33.333 0.00 0.00 41.41 1.40
97 98 5.912149 AGGCAATCCTTGTAGATGGAATA 57.088 39.130 0.00 0.00 40.66 1.75
101 102 7.170965 ACAATATAGGCAATCCTTGTAGATGG 58.829 38.462 0.00 0.00 40.66 3.51
181 182 9.500785 TGTGTTTATTTGAGTGATGAATAGACA 57.499 29.630 0.00 0.00 31.78 3.41
183 184 9.500785 TGTGTGTTTATTTGAGTGATGAATAGA 57.499 29.630 0.00 0.00 0.00 1.98
184 185 9.764870 CTGTGTGTTTATTTGAGTGATGAATAG 57.235 33.333 0.00 0.00 0.00 1.73
192 193 3.976942 GCAGCTGTGTGTTTATTTGAGTG 59.023 43.478 16.64 0.00 0.00 3.51
199 200 4.271696 TCTGTAGCAGCTGTGTGTTTAT 57.728 40.909 16.64 0.00 0.00 1.40
224 225 8.586570 TGAATGCAACTACGAAATTGAAATTT 57.413 26.923 0.68 0.68 41.06 1.82
225 226 8.649841 CATGAATGCAACTACGAAATTGAAATT 58.350 29.630 0.00 0.00 0.00 1.82
227 228 7.144661 ACATGAATGCAACTACGAAATTGAAA 58.855 30.769 0.00 0.00 0.00 2.69
230 231 5.512788 GGACATGAATGCAACTACGAAATTG 59.487 40.000 0.00 0.00 0.00 2.32
231 232 5.415701 AGGACATGAATGCAACTACGAAATT 59.584 36.000 0.00 0.00 0.00 1.82
253 255 3.192212 GGAAGAAGGTTCATGCTTTCAGG 59.808 47.826 0.00 0.00 0.00 3.86
256 258 5.003804 TGTAGGAAGAAGGTTCATGCTTTC 58.996 41.667 0.00 0.00 29.56 2.62
273 275 6.324770 TGATCAGCATACTCAAATCTGTAGGA 59.675 38.462 0.00 0.00 0.00 2.94
274 276 6.519382 TGATCAGCATACTCAAATCTGTAGG 58.481 40.000 0.00 0.00 0.00 3.18
280 282 7.279536 TCAGAAACTGATCAGCATACTCAAATC 59.720 37.037 22.83 4.90 35.39 2.17
302 304 5.839063 CCTACAGGTAAGGTCCATAATCAGA 59.161 44.000 0.00 0.00 0.00 3.27
303 305 5.839063 TCCTACAGGTAAGGTCCATAATCAG 59.161 44.000 0.00 0.00 36.34 2.90
314 316 4.585162 AGATTCGTCATCCTACAGGTAAGG 59.415 45.833 0.00 0.00 36.34 2.69
315 317 5.524284 CAGATTCGTCATCCTACAGGTAAG 58.476 45.833 0.00 0.00 36.34 2.34
341 343 5.188434 TGTTTCCATCACCAGAGATCAATC 58.812 41.667 0.00 0.00 0.00 2.67
347 349 4.136796 CAACTTGTTTCCATCACCAGAGA 58.863 43.478 0.00 0.00 0.00 3.10
348 350 3.254166 CCAACTTGTTTCCATCACCAGAG 59.746 47.826 0.00 0.00 0.00 3.35
349 351 3.221771 CCAACTTGTTTCCATCACCAGA 58.778 45.455 0.00 0.00 0.00 3.86
353 355 2.593026 TCCCCAACTTGTTTCCATCAC 58.407 47.619 0.00 0.00 0.00 3.06
359 361 4.086706 TCTCTCTTCCCCAACTTGTTTC 57.913 45.455 0.00 0.00 0.00 2.78
406 408 2.048603 GGGATCACCAACTGGCAGC 61.049 63.158 15.89 0.00 39.85 5.25
416 418 0.107165 GGTGTTAGGCTGGGATCACC 60.107 60.000 0.00 5.05 38.47 4.02
417 419 0.462047 CGGTGTTAGGCTGGGATCAC 60.462 60.000 0.00 0.00 0.00 3.06
418 420 1.622607 CCGGTGTTAGGCTGGGATCA 61.623 60.000 0.00 0.00 0.00 2.92
420 422 3.320359 CCGGTGTTAGGCTGGGAT 58.680 61.111 0.00 0.00 0.00 3.85
450 455 4.100084 CCCCTGCTGTGATCGCCA 62.100 66.667 3.31 0.00 0.00 5.69
452 457 0.811616 CTAACCCCTGCTGTGATCGC 60.812 60.000 0.00 0.00 0.00 4.58
453 458 0.811616 GCTAACCCCTGCTGTGATCG 60.812 60.000 0.00 0.00 0.00 3.69
461 466 2.109181 CTAGCCGCTAACCCCTGC 59.891 66.667 0.90 0.00 0.00 4.85
466 471 0.179056 TCAATGGCTAGCCGCTAACC 60.179 55.000 28.28 12.26 39.42 2.85
504 509 4.325741 CGACACAACAAACATCAGCAAAAA 59.674 37.500 0.00 0.00 0.00 1.94
511 516 1.383523 TGGCGACACAACAAACATCA 58.616 45.000 0.00 0.00 33.40 3.07
524 529 5.292101 GCATCTATATAAACTGGATGGCGAC 59.708 44.000 9.66 0.00 35.64 5.19
525 530 5.419542 GCATCTATATAAACTGGATGGCGA 58.580 41.667 9.66 0.00 35.64 5.54
527 532 5.419542 TCGCATCTATATAAACTGGATGGC 58.580 41.667 9.66 0.00 35.64 4.40
530 535 7.423844 TCCATCGCATCTATATAAACTGGAT 57.576 36.000 0.00 0.00 0.00 3.41
557 562 1.032114 GCCAGTTCTAGGCGCCATTT 61.032 55.000 31.54 11.17 43.15 2.32
566 571 1.142748 CTCCCGCAGCCAGTTCTAG 59.857 63.158 0.00 0.00 0.00 2.43
568 573 3.710722 CCTCCCGCAGCCAGTTCT 61.711 66.667 0.00 0.00 0.00 3.01
572 577 4.479993 CTTCCCTCCCGCAGCCAG 62.480 72.222 0.00 0.00 0.00 4.85
592 597 2.362397 TCAACAAACTTATTGGCGCCAA 59.638 40.909 41.54 41.54 40.47 4.52
616 621 1.630878 ACATTTTCCTCTCCGCTCCTT 59.369 47.619 0.00 0.00 0.00 3.36
629 634 6.541111 AAACTCTCCGTAACAGACATTTTC 57.459 37.500 0.00 0.00 0.00 2.29
704 709 3.586470 TTCCACAAAGCCAGGAAACTA 57.414 42.857 0.00 0.00 40.21 2.24
710 715 4.806640 ATTATGTTTCCACAAAGCCAGG 57.193 40.909 0.00 0.00 36.16 4.45
734 739 7.614494 CCCTTCAACAAAATCATGGATAACTT 58.386 34.615 0.00 0.00 0.00 2.66
737 742 5.104982 GGCCCTTCAACAAAATCATGGATAA 60.105 40.000 0.00 0.00 0.00 1.75
746 751 5.250313 TCATATTTGGGCCCTTCAACAAAAT 59.750 36.000 25.70 19.75 36.53 1.82
759 764 7.065683 CCCAACAAACTAAAATCATATTTGGGC 59.934 37.037 0.00 0.00 42.17 5.36
766 771 4.767928 ACCGCCCAACAAACTAAAATCATA 59.232 37.500 0.00 0.00 0.00 2.15
770 775 5.731957 ATAACCGCCCAACAAACTAAAAT 57.268 34.783 0.00 0.00 0.00 1.82
796 801 3.004419 GCCAAACTAGTTTTCTGTGGACC 59.996 47.826 22.10 6.37 0.00 4.46
798 803 4.164843 AGCCAAACTAGTTTTCTGTGGA 57.835 40.909 22.10 0.00 0.00 4.02
799 804 6.349363 GGATTAGCCAAACTAGTTTTCTGTGG 60.349 42.308 18.25 16.96 36.34 4.17
826 831 3.262405 AGTTAGGCCTTGTTTGGATACGA 59.738 43.478 12.58 0.00 42.51 3.43
842 847 4.016444 TGATTTGCCCTGCTTTAGTTAGG 58.984 43.478 0.00 0.00 0.00 2.69
843 848 5.357878 TGATGATTTGCCCTGCTTTAGTTAG 59.642 40.000 0.00 0.00 0.00 2.34
844 849 5.260424 TGATGATTTGCCCTGCTTTAGTTA 58.740 37.500 0.00 0.00 0.00 2.24
845 850 4.088634 TGATGATTTGCCCTGCTTTAGTT 58.911 39.130 0.00 0.00 0.00 2.24
846 851 3.700538 TGATGATTTGCCCTGCTTTAGT 58.299 40.909 0.00 0.00 0.00 2.24
847 852 4.159135 AGTTGATGATTTGCCCTGCTTTAG 59.841 41.667 0.00 0.00 0.00 1.85
848 853 4.088634 AGTTGATGATTTGCCCTGCTTTA 58.911 39.130 0.00 0.00 0.00 1.85
849 854 2.901839 AGTTGATGATTTGCCCTGCTTT 59.098 40.909 0.00 0.00 0.00 3.51
850 855 2.494870 GAGTTGATGATTTGCCCTGCTT 59.505 45.455 0.00 0.00 0.00 3.91
851 856 2.097825 GAGTTGATGATTTGCCCTGCT 58.902 47.619 0.00 0.00 0.00 4.24
852 857 1.135721 GGAGTTGATGATTTGCCCTGC 59.864 52.381 0.00 0.00 0.00 4.85
853 858 1.753073 GGGAGTTGATGATTTGCCCTG 59.247 52.381 0.00 0.00 0.00 4.45
854 859 1.642762 AGGGAGTTGATGATTTGCCCT 59.357 47.619 0.00 0.00 39.53 5.19
855 860 2.149973 AGGGAGTTGATGATTTGCCC 57.850 50.000 0.00 0.00 0.00 5.36
856 861 5.859205 ATTTAGGGAGTTGATGATTTGCC 57.141 39.130 0.00 0.00 0.00 4.52
857 862 8.470002 ACTTTATTTAGGGAGTTGATGATTTGC 58.530 33.333 0.00 0.00 0.00 3.68
858 863 9.793252 CACTTTATTTAGGGAGTTGATGATTTG 57.207 33.333 0.00 0.00 0.00 2.32
859 864 9.533831 ACACTTTATTTAGGGAGTTGATGATTT 57.466 29.630 0.00 0.00 0.00 2.17
860 865 8.960591 CACACTTTATTTAGGGAGTTGATGATT 58.039 33.333 0.00 0.00 0.00 2.57
861 866 7.557719 CCACACTTTATTTAGGGAGTTGATGAT 59.442 37.037 0.00 0.00 0.00 2.45
862 867 6.884295 CCACACTTTATTTAGGGAGTTGATGA 59.116 38.462 0.00 0.00 0.00 2.92
863 868 6.404734 GCCACACTTTATTTAGGGAGTTGATG 60.405 42.308 0.00 0.00 0.00 3.07
864 869 5.652452 GCCACACTTTATTTAGGGAGTTGAT 59.348 40.000 0.00 0.00 0.00 2.57
865 870 5.007682 GCCACACTTTATTTAGGGAGTTGA 58.992 41.667 0.00 0.00 0.00 3.18
866 871 4.764823 TGCCACACTTTATTTAGGGAGTTG 59.235 41.667 0.00 0.00 0.00 3.16
867 872 4.993028 TGCCACACTTTATTTAGGGAGTT 58.007 39.130 0.00 0.00 0.00 3.01
868 873 4.650972 TGCCACACTTTATTTAGGGAGT 57.349 40.909 0.00 0.00 0.00 3.85
869 874 5.975693 TTTGCCACACTTTATTTAGGGAG 57.024 39.130 0.00 0.00 0.00 4.30
870 875 6.013379 TCATTTGCCACACTTTATTTAGGGA 58.987 36.000 0.00 0.00 0.00 4.20
871 876 6.279513 TCATTTGCCACACTTTATTTAGGG 57.720 37.500 0.00 0.00 0.00 3.53
872 877 6.980397 GGATCATTTGCCACACTTTATTTAGG 59.020 38.462 0.00 0.00 0.00 2.69
873 878 7.546358 TGGATCATTTGCCACACTTTATTTAG 58.454 34.615 0.00 0.00 0.00 1.85
874 879 7.473735 TGGATCATTTGCCACACTTTATTTA 57.526 32.000 0.00 0.00 0.00 1.40
875 880 6.357579 TGGATCATTTGCCACACTTTATTT 57.642 33.333 0.00 0.00 0.00 1.40
876 881 5.999205 TGGATCATTTGCCACACTTTATT 57.001 34.783 0.00 0.00 0.00 1.40
877 882 5.999205 TTGGATCATTTGCCACACTTTAT 57.001 34.783 0.00 0.00 33.01 1.40
878 883 5.716228 AGATTGGATCATTTGCCACACTTTA 59.284 36.000 0.00 0.00 33.01 1.85
879 884 4.529377 AGATTGGATCATTTGCCACACTTT 59.471 37.500 0.00 0.00 33.01 2.66
880 885 4.091549 AGATTGGATCATTTGCCACACTT 58.908 39.130 0.00 0.00 33.01 3.16
881 886 3.698040 GAGATTGGATCATTTGCCACACT 59.302 43.478 0.00 0.00 33.01 3.55
882 887 3.181483 GGAGATTGGATCATTTGCCACAC 60.181 47.826 0.00 0.00 33.01 3.82
883 888 3.025978 GGAGATTGGATCATTTGCCACA 58.974 45.455 0.00 0.00 33.01 4.17
884 889 2.363359 GGGAGATTGGATCATTTGCCAC 59.637 50.000 0.00 0.00 33.01 5.01
885 890 2.669781 GGGAGATTGGATCATTTGCCA 58.330 47.619 0.00 0.00 0.00 4.92
886 891 1.610522 CGGGAGATTGGATCATTTGCC 59.389 52.381 0.00 0.00 0.00 4.52
887 892 2.575532 TCGGGAGATTGGATCATTTGC 58.424 47.619 0.00 0.00 0.00 3.68
905 910 3.891400 TCGCGGTCCCGGTTATCG 61.891 66.667 6.13 0.70 40.19 2.92
906 911 2.279054 GTCGCGGTCCCGGTTATC 60.279 66.667 6.13 0.00 40.19 1.75
907 912 3.069946 TGTCGCGGTCCCGGTTAT 61.070 61.111 6.13 0.00 40.19 1.89
908 913 4.054825 GTGTCGCGGTCCCGGTTA 62.055 66.667 6.13 0.00 40.19 2.85
920 925 4.087892 CTCTGCCCCTGGGTGTCG 62.088 72.222 12.71 0.00 37.65 4.35
921 926 4.416738 GCTCTGCCCCTGGGTGTC 62.417 72.222 12.71 0.85 37.65 3.67
922 927 4.990910 AGCTCTGCCCCTGGGTGT 62.991 66.667 12.71 0.00 37.65 4.16
923 928 4.421515 CAGCTCTGCCCCTGGGTG 62.422 72.222 12.71 4.35 37.65 4.61
940 945 0.313043 CTCCGATGGATTGCAATGGC 59.687 55.000 18.59 2.76 41.68 4.40
941 946 1.971481 TCTCCGATGGATTGCAATGG 58.029 50.000 18.59 11.54 0.00 3.16
942 947 5.183969 AGATATCTCCGATGGATTGCAATG 58.816 41.667 18.59 1.26 0.00 2.82
943 948 5.426504 GAGATATCTCCGATGGATTGCAAT 58.573 41.667 20.33 12.83 37.02 3.56
944 949 4.825422 GAGATATCTCCGATGGATTGCAA 58.175 43.478 20.33 0.00 37.02 4.08
945 950 4.462508 GAGATATCTCCGATGGATTGCA 57.537 45.455 20.33 0.00 37.02 4.08
957 962 2.179517 CGGCGGCGGAGATATCTC 59.820 66.667 25.36 22.41 42.14 2.75
1031 1042 3.370104 GTGGATGGAGAAGAGAGGAGAA 58.630 50.000 0.00 0.00 0.00 2.87
1047 1070 1.213926 GGGAAGATTGCAGAGGTGGAT 59.786 52.381 0.00 0.00 0.00 3.41
1539 1562 0.107897 ACGCGACATTGGGCTTGATA 60.108 50.000 15.93 0.00 0.00 2.15
1597 1620 0.807667 CGCCTGTACATGACCAGCTC 60.808 60.000 0.00 0.00 0.00 4.09
1859 1886 0.390472 CAGGAACTCGGACTTGCTCC 60.390 60.000 0.00 0.00 34.60 4.70
1972 1999 6.421801 CCATTTGCCTTGACAAACTTTAGAAG 59.578 38.462 0.00 0.00 42.01 2.85
2462 3083 5.633830 AATCTGTTGGTCATGCTTTAGTG 57.366 39.130 0.00 0.00 0.00 2.74
2689 3324 4.908736 ACAACTTTGATTTGAGTCACACG 58.091 39.130 0.00 0.00 0.00 4.49
2784 3421 5.237996 TGAAAAGACAGAGCATGAGAAACAG 59.762 40.000 0.00 0.00 0.00 3.16
2981 3678 6.672266 TCTCTTGAACTTCAGTAATCACCT 57.328 37.500 0.00 0.00 0.00 4.00
3010 3707 3.088532 TCATCCGGAAACAATGAAAGGG 58.911 45.455 9.01 0.00 31.38 3.95
3016 3714 2.480073 GCCACATCATCCGGAAACAATG 60.480 50.000 9.01 12.33 0.00 2.82


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

AutoCloner maintained by Alex Coulton.