Multiple sequence alignment - TraesCS5B01G240400

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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 TraesCS5B01G240400 chr5B 100.000 3017 0 0 1 3017 420713265 420716281 0.000000e+00 5572.0
1 TraesCS5B01G240400 chr5B 76.914 849 160 26 1019 1846 83677609 83676776 1.650000e-122 449.0
2 TraesCS5B01G240400 chr5B 76.185 907 185 23 2016 2908 419948633 419947744 1.650000e-122 449.0
3 TraesCS5B01G240400 chr5B 76.218 862 169 32 2002 2852 420732031 420732867 1.000000e-114 424.0
4 TraesCS5B01G240400 chr5B 75.326 920 177 33 2000 2907 419728408 419727527 2.180000e-106 396.0
5 TraesCS5B01G240400 chr5D 95.049 1030 39 3 1983 3010 355795569 355796588 0.000000e+00 1609.0
6 TraesCS5B01G240400 chr5D 94.758 973 42 4 1012 1984 355794545 355795508 0.000000e+00 1506.0
7 TraesCS5B01G240400 chr5D 90.191 734 66 6 1 731 51029585 51030315 0.000000e+00 952.0
8 TraesCS5B01G240400 chr5D 89.445 739 69 7 1 733 532239366 532238631 0.000000e+00 924.0
9 TraesCS5B01G240400 chr5D 77.396 845 166 17 1019 1846 75354405 75353569 2.100000e-131 479.0
10 TraesCS5B01G240400 chr5D 76.923 845 159 28 2002 2835 355796874 355797693 5.930000e-122 448.0
11 TraesCS5B01G240400 chr5D 76.210 723 152 13 2199 2908 355077457 355076742 6.150000e-97 364.0
12 TraesCS5B01G240400 chr5D 89.789 284 12 7 744 1012 355794231 355794512 6.190000e-92 348.0
13 TraesCS5B01G240400 chr5D 74.551 334 70 14 1173 1500 356194557 356194233 6.790000e-27 132.0
14 TraesCS5B01G240400 chr5A 94.783 1035 44 2 1983 3017 457515754 457514730 0.000000e+00 1604.0
15 TraesCS5B01G240400 chr5A 94.656 973 46 4 1012 1984 457516786 457515820 0.000000e+00 1504.0
16 TraesCS5B01G240400 chr5A 77.988 845 161 17 1019 1846 70482968 70482132 9.650000e-140 507.0
17 TraesCS5B01G240400 chr5A 77.461 843 158 28 2002 2835 457512522 457511703 2.720000e-130 475.0
18 TraesCS5B01G240400 chr5A 75.858 787 155 26 2134 2907 457087128 457086364 4.750000e-98 368.0
19 TraesCS5B01G240400 chr5A 88.235 255 9 5 777 1012 457517071 457516819 4.920000e-73 285.0
20 TraesCS5B01G240400 chr5A 80.000 305 56 5 1066 1366 457086421 457086724 1.410000e-53 220.0
21 TraesCS5B01G240400 chr5A 93.939 66 4 0 747 812 457517157 457517092 1.910000e-17 100.0
22 TraesCS5B01G240400 chr1B 90.625 736 62 7 1 733 50225214 50225945 0.000000e+00 970.0
23 TraesCS5B01G240400 chr2B 90.730 712 60 6 1 708 92536763 92536054 0.000000e+00 944.0
24 TraesCS5B01G240400 chr7D 89.431 738 66 10 1 735 30855108 30854380 0.000000e+00 920.0
25 TraesCS5B01G240400 chr7D 77.663 291 49 12 1067 1352 125887916 125888195 2.410000e-36 163.0
26 TraesCS5B01G240400 chr7D 77.055 292 49 13 1067 1352 125909120 125909399 5.210000e-33 152.0
27 TraesCS5B01G240400 chr2A 89.417 737 67 10 1 733 9140255 9140984 0.000000e+00 918.0
28 TraesCS5B01G240400 chr2A 88.514 740 79 6 1 737 599777818 599778554 0.000000e+00 891.0
29 TraesCS5B01G240400 chr7B 88.934 741 76 6 1 738 522041399 522040662 0.000000e+00 909.0
30 TraesCS5B01G240400 chr7B 75.549 319 54 17 1175 1487 87138638 87138338 5.250000e-28 135.0
31 TraesCS5B01G240400 chr4D 89.130 736 67 11 1 733 151997510 151998235 0.000000e+00 904.0
32 TraesCS5B01G240400 chr4D 76.849 311 49 15 2454 2745 116131736 116132042 1.450000e-33 154.0
33 TraesCS5B01G240400 chr1D 83.000 200 34 0 1692 1891 402749978 402750177 6.640000e-42 182.0
34 TraesCS5B01G240400 chr4A 76.299 308 56 10 2454 2745 460460317 460460011 6.740000e-32 148.0
35 TraesCS5B01G240400 chr3A 88.496 113 13 0 1692 1804 657100578 657100466 1.460000e-28 137.0
36 TraesCS5B01G240400 chr2D 73.640 239 47 14 2460 2690 7696468 7696238 8.970000e-11 78.7


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 TraesCS5B01G240400 chr5B 420713265 420716281 3016 False 5572.00 5572 100.00000 1 3017 1 chr5B.!!$F1 3016
1 TraesCS5B01G240400 chr5B 83676776 83677609 833 True 449.00 449 76.91400 1019 1846 1 chr5B.!!$R1 827
2 TraesCS5B01G240400 chr5B 419947744 419948633 889 True 449.00 449 76.18500 2016 2908 1 chr5B.!!$R3 892
3 TraesCS5B01G240400 chr5B 420732031 420732867 836 False 424.00 424 76.21800 2002 2852 1 chr5B.!!$F2 850
4 TraesCS5B01G240400 chr5B 419727527 419728408 881 True 396.00 396 75.32600 2000 2907 1 chr5B.!!$R2 907
5 TraesCS5B01G240400 chr5D 355794231 355797693 3462 False 977.75 1609 89.12975 744 3010 4 chr5D.!!$F2 2266
6 TraesCS5B01G240400 chr5D 51029585 51030315 730 False 952.00 952 90.19100 1 731 1 chr5D.!!$F1 730
7 TraesCS5B01G240400 chr5D 532238631 532239366 735 True 924.00 924 89.44500 1 733 1 chr5D.!!$R4 732
8 TraesCS5B01G240400 chr5D 75353569 75354405 836 True 479.00 479 77.39600 1019 1846 1 chr5D.!!$R1 827
9 TraesCS5B01G240400 chr5D 355076742 355077457 715 True 364.00 364 76.21000 2199 2908 1 chr5D.!!$R2 709
10 TraesCS5B01G240400 chr5A 457511703 457517157 5454 True 793.60 1604 89.81480 747 3017 5 chr5A.!!$R3 2270
11 TraesCS5B01G240400 chr5A 70482132 70482968 836 True 507.00 507 77.98800 1019 1846 1 chr5A.!!$R1 827
12 TraesCS5B01G240400 chr5A 457086364 457087128 764 True 368.00 368 75.85800 2134 2907 1 chr5A.!!$R2 773
13 TraesCS5B01G240400 chr1B 50225214 50225945 731 False 970.00 970 90.62500 1 733 1 chr1B.!!$F1 732
14 TraesCS5B01G240400 chr2B 92536054 92536763 709 True 944.00 944 90.73000 1 708 1 chr2B.!!$R1 707
15 TraesCS5B01G240400 chr7D 30854380 30855108 728 True 920.00 920 89.43100 1 735 1 chr7D.!!$R1 734
16 TraesCS5B01G240400 chr2A 9140255 9140984 729 False 918.00 918 89.41700 1 733 1 chr2A.!!$F1 732
17 TraesCS5B01G240400 chr2A 599777818 599778554 736 False 891.00 891 88.51400 1 737 1 chr2A.!!$F2 736
18 TraesCS5B01G240400 chr7B 522040662 522041399 737 True 909.00 909 88.93400 1 738 1 chr7B.!!$R2 737
19 TraesCS5B01G240400 chr4D 151997510 151998235 725 False 904.00 904 89.13000 1 733 1 chr4D.!!$F2 732

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
447 456 0.868406 CTATCGAAGAAATGGCCGCC 59.132 55.0 1.04 1.04 43.58 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2437 5844 0.109086 CAACGTCCTCATGAGAGCGT 60.109 55.0 27.03 27.03 40.68 5.07 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 4.212913 GCAGGATCTCGCGCCTCA 62.213 66.667 0.00 0.00 30.41 3.86
237 238 2.434658 ATCGTGAGGACAAGCGTGCA 62.435 55.000 0.00 0.00 35.57 4.57
266 267 1.406539 GGCCGCTCAATTGAACATGAT 59.593 47.619 9.88 0.00 0.00 2.45
406 410 9.050601 CCTTTTCTTTTATCTGTCTATGCTAGG 57.949 37.037 0.00 0.00 0.00 3.02
447 456 0.868406 CTATCGAAGAAATGGCCGCC 59.132 55.000 1.04 1.04 43.58 6.13
507 516 1.217057 ATGGGGAGAGGCCAATGTGT 61.217 55.000 5.01 0.00 38.95 3.72
538 547 2.693017 GCCAGGGGAGGAGAGAGA 59.307 66.667 0.00 0.00 0.00 3.10
575 588 1.374252 GTCTTGTGTCCGTGCCGAT 60.374 57.895 0.00 0.00 0.00 4.18
588 601 4.454948 CCGATGCAAATCCGGCTA 57.545 55.556 0.00 0.00 36.62 3.93
674 689 1.004292 GTTGGACCGTCTTTTGTGTCG 60.004 52.381 0.00 0.00 0.00 4.35
716 731 1.211709 CGAACAAAATGGGTCGCCC 59.788 57.895 7.87 7.87 45.71 6.13
738 753 3.560025 CCCATTGGAGTTGCTCTAACAGT 60.560 47.826 3.62 0.00 41.88 3.55
739 754 4.074970 CCATTGGAGTTGCTCTAACAGTT 58.925 43.478 0.00 0.00 41.88 3.16
740 755 4.520492 CCATTGGAGTTGCTCTAACAGTTT 59.480 41.667 0.00 0.00 41.88 2.66
741 756 5.705441 CCATTGGAGTTGCTCTAACAGTTTA 59.295 40.000 0.00 0.00 41.88 2.01
742 757 6.348540 CCATTGGAGTTGCTCTAACAGTTTAC 60.349 42.308 0.00 0.00 41.88 2.01
745 760 6.999950 TGGAGTTGCTCTAACAGTTTACATA 58.000 36.000 0.00 0.00 41.88 2.29
887 960 4.522789 GGTTAATCAAAGACCAGGAAGCAA 59.477 41.667 0.00 0.00 33.61 3.91
891 964 4.589216 TCAAAGACCAGGAAGCAAATTG 57.411 40.909 0.00 0.00 0.00 2.32
892 965 3.960102 TCAAAGACCAGGAAGCAAATTGT 59.040 39.130 0.00 0.00 0.00 2.71
893 966 5.136828 TCAAAGACCAGGAAGCAAATTGTA 58.863 37.500 0.00 0.00 0.00 2.41
894 967 5.009610 TCAAAGACCAGGAAGCAAATTGTAC 59.990 40.000 0.00 0.00 0.00 2.90
908 981 5.982516 GCAAATTGTACAACACAGAAATGGA 59.017 36.000 11.22 0.00 38.72 3.41
936 1013 4.732285 AACAGTGAAGTAAGTGCGATTG 57.268 40.909 0.00 0.00 0.00 2.67
1224 1347 2.484203 GCTTACGTCGCCGAGTCT 59.516 61.111 0.00 0.00 37.88 3.24
1234 1357 2.896443 CCGAGTCTGCCTTCTCCC 59.104 66.667 0.00 0.00 0.00 4.30
1235 1358 1.684049 CCGAGTCTGCCTTCTCCCT 60.684 63.158 0.00 0.00 0.00 4.20
1597 1729 4.351938 CGTCGGAAGGCACGGACA 62.352 66.667 17.05 0.00 39.12 4.02
1660 1798 0.249120 CAAGTATGGGCTCGACCACA 59.751 55.000 0.00 0.00 44.72 4.17
1862 2000 6.294473 AGGAGCACATGTATTATTTCTCCAG 58.706 40.000 0.00 0.00 40.84 3.86
1971 2109 3.809832 CCAGTCCATCGGATTGTAACATC 59.190 47.826 5.01 0.00 37.68 3.06
2025 2230 1.522806 GCCGGTATGATGAACGCCA 60.523 57.895 1.90 0.00 0.00 5.69
2052 2257 3.004951 CCATGAGCTCCTTGGCCT 58.995 61.111 17.15 0.00 33.94 5.19
2054 2259 1.035932 CCATGAGCTCCTTGGCCTTG 61.036 60.000 17.15 0.00 33.94 3.61
2055 2260 1.035932 CATGAGCTCCTTGGCCTTGG 61.036 60.000 12.15 6.25 0.00 3.61
2185 2390 1.913951 TAGTACGCTCGGTCCCTGGA 61.914 60.000 0.00 0.00 0.00 3.86
2252 5653 2.062070 GAGATTCTCCATCCCCGGG 58.938 63.158 15.80 15.80 31.20 5.73
2330 5734 0.179100 ACGCGAACTCCCAGATCATG 60.179 55.000 15.93 0.00 0.00 3.07
2368 5772 2.492090 CTCGGCCTCACCTTCGAG 59.508 66.667 0.00 0.00 42.09 4.04
2378 5782 1.137479 TCACCTTCGAGGAACGTGTTT 59.863 47.619 7.76 0.00 37.67 2.83
2390 5794 0.178533 ACGTGTTTCCTCCGAACCAA 59.821 50.000 0.00 0.00 0.00 3.67
2393 5797 1.133363 TGTTTCCTCCGAACCAAGGA 58.867 50.000 0.00 0.00 39.94 3.36
2402 5806 1.339055 CCGAACCAAGGATGCAGAAGA 60.339 52.381 0.00 0.00 0.00 2.87
2411 5815 1.153289 ATGCAGAAGAATCGCGCCT 60.153 52.632 0.00 0.00 0.00 5.52
2423 5827 2.303676 CGCGCCTTCTATTCTCGGC 61.304 63.158 0.00 0.00 39.14 5.54
2426 5830 1.956678 GCCTTCTATTCTCGGCGCC 60.957 63.158 19.07 19.07 32.22 6.53
2428 5832 1.661821 CTTCTATTCTCGGCGCCGG 60.662 63.158 44.95 34.43 40.25 6.13
2429 5833 3.785189 TTCTATTCTCGGCGCCGGC 62.785 63.158 44.95 19.07 40.25 6.13
2450 5857 0.526524 GGAACGACGCTCTCATGAGG 60.527 60.000 22.42 13.87 40.53 3.86
2452 5859 0.171455 AACGACGCTCTCATGAGGAC 59.829 55.000 22.42 13.43 40.53 3.85
2455 5862 0.171455 GACGCTCTCATGAGGACGTT 59.829 55.000 30.90 20.61 38.48 3.99
2462 5869 0.602638 TCATGAGGACGTTGTGCACC 60.603 55.000 15.69 0.00 0.00 5.01
2469 5876 0.934436 GACGTTGTGCACCATGTTGC 60.934 55.000 16.18 8.51 43.31 4.17
2685 6098 1.534476 TTGTGGTACTGCGGGGAGA 60.534 57.895 0.00 0.00 0.00 3.71
2698 6111 4.176851 GGAGACGGCCGACTCGAC 62.177 72.222 38.17 27.13 37.69 4.20
2706 6119 2.100603 CCGACTCGACGAGGAAGC 59.899 66.667 27.39 13.13 33.35 3.86
2731 6144 0.818296 CCGTGGAAGAAGACGAGGAT 59.182 55.000 0.00 0.00 37.81 3.24
2745 6158 1.115467 GAGGATCGGGAGCTTCTTGA 58.885 55.000 0.00 0.00 0.00 3.02
2750 6163 0.544357 TCGGGAGCTTCTTGAAGGGA 60.544 55.000 11.70 0.00 0.00 4.20
2754 6167 2.421248 GGGAGCTTCTTGAAGGGATCTG 60.421 54.545 11.70 0.00 0.00 2.90
2757 6170 2.021208 GCTTCTTGAAGGGATCTGGGC 61.021 57.143 11.70 0.00 0.00 5.36
2760 6176 0.106819 CTTGAAGGGATCTGGGCTGG 60.107 60.000 0.00 0.00 0.00 4.85
2777 6193 3.787001 GTGGGGAGGAAGAGGCGG 61.787 72.222 0.00 0.00 0.00 6.13
2783 6199 3.066233 GAGGAAGAGGCGGACGGAC 62.066 68.421 0.00 0.00 0.00 4.79
2807 6223 1.003233 GGTGGCAGAGTCAAGGACC 60.003 63.158 0.00 0.00 32.18 4.46
2813 6229 0.962489 CAGAGTCAAGGACCACGTCT 59.038 55.000 0.00 0.00 32.18 4.18
2819 6235 1.202604 TCAAGGACCACGTCTTTGGAC 60.203 52.381 14.34 0.00 45.48 4.02
2831 6247 2.752322 CTTTGGACGTGACGCCGGTA 62.752 60.000 4.25 0.00 0.00 4.02
2893 6309 2.892425 GTCCATCTTGCCGCTCCG 60.892 66.667 0.00 0.00 0.00 4.63
2904 6320 2.649034 CGCTCCGGTATATGCGGT 59.351 61.111 0.00 0.00 43.97 5.68
2908 6324 1.135460 GCTCCGGTATATGCGGTAGTC 60.135 57.143 0.00 0.00 0.00 2.59
2909 6325 2.156917 CTCCGGTATATGCGGTAGTCA 58.843 52.381 0.00 0.00 0.00 3.41
2910 6326 2.753452 CTCCGGTATATGCGGTAGTCAT 59.247 50.000 0.00 0.00 0.00 3.06
2911 6327 2.751259 TCCGGTATATGCGGTAGTCATC 59.249 50.000 0.00 0.00 0.00 2.92
2912 6328 2.477357 CCGGTATATGCGGTAGTCATCG 60.477 54.545 0.00 0.00 0.00 3.84
2918 6334 4.286967 CGGTAGTCATCGCAGTCG 57.713 61.111 0.00 0.00 0.00 4.18
2929 6345 2.327081 TCGCAGTCGAACACTACTTC 57.673 50.000 0.00 0.00 42.44 3.01
2930 6346 0.975544 CGCAGTCGAACACTACTTCG 59.024 55.000 0.00 0.00 43.65 3.79
2931 6347 1.662309 CGCAGTCGAACACTACTTCGT 60.662 52.381 0.00 0.00 42.97 3.85
2932 6348 1.977412 GCAGTCGAACACTACTTCGTC 59.023 52.381 0.00 0.00 42.97 4.20
2933 6349 2.231693 CAGTCGAACACTACTTCGTCG 58.768 52.381 0.00 0.00 42.97 5.12
2934 6350 1.196354 AGTCGAACACTACTTCGTCGG 59.804 52.381 0.00 0.00 42.97 4.79
2935 6351 0.110056 TCGAACACTACTTCGTCGGC 60.110 55.000 0.00 0.00 42.97 5.54
2936 6352 1.393597 CGAACACTACTTCGTCGGCG 61.394 60.000 1.15 1.15 38.58 6.46
2937 6353 1.671880 GAACACTACTTCGTCGGCGC 61.672 60.000 3.52 0.00 38.14 6.53
2938 6354 2.879462 CACTACTTCGTCGGCGCC 60.879 66.667 19.07 19.07 38.14 6.53
2939 6355 3.367743 ACTACTTCGTCGGCGCCA 61.368 61.111 28.98 11.20 38.14 5.69
2940 6356 2.579787 CTACTTCGTCGGCGCCAG 60.580 66.667 28.98 18.39 38.14 4.85
2941 6357 3.047718 CTACTTCGTCGGCGCCAGA 62.048 63.158 28.98 21.43 38.14 3.86
2942 6358 3.332493 TACTTCGTCGGCGCCAGAC 62.332 63.158 29.50 29.50 38.14 3.51
2943 6359 4.421479 CTTCGTCGGCGCCAGACT 62.421 66.667 32.91 0.00 36.53 3.24
2944 6360 4.415332 TTCGTCGGCGCCAGACTC 62.415 66.667 32.91 18.46 36.53 3.36
2947 6363 4.148825 GTCGGCGCCAGACTCCAT 62.149 66.667 30.94 0.00 35.84 3.41
2948 6364 4.147449 TCGGCGCCAGACTCCATG 62.147 66.667 28.98 6.54 0.00 3.66
2954 6370 3.628989 CCAGACTCCATGGCCGTA 58.371 61.111 6.96 0.00 0.00 4.02
2955 6371 1.443407 CCAGACTCCATGGCCGTAG 59.557 63.158 6.96 1.07 0.00 3.51
2956 6372 1.227380 CAGACTCCATGGCCGTAGC 60.227 63.158 6.96 0.00 38.76 3.58
2975 6391 4.899239 GGCTAGCCGCGCACAGAT 62.899 66.667 20.16 0.00 40.44 2.90
2976 6392 3.333969 GCTAGCCGCGCACAGATC 61.334 66.667 8.75 0.00 0.00 2.75
2977 6393 2.415010 CTAGCCGCGCACAGATCT 59.585 61.111 8.75 0.00 0.00 2.75
2978 6394 1.948138 CTAGCCGCGCACAGATCTG 60.948 63.158 21.37 21.37 0.00 2.90
2979 6395 2.341807 CTAGCCGCGCACAGATCTGA 62.342 60.000 29.27 2.20 0.00 3.27
2980 6396 1.944234 TAGCCGCGCACAGATCTGAA 61.944 55.000 29.27 0.35 0.00 3.02
2981 6397 2.806856 GCCGCGCACAGATCTGAAG 61.807 63.158 29.27 20.18 0.00 3.02
2982 6398 2.169789 CCGCGCACAGATCTGAAGG 61.170 63.158 29.27 18.07 0.00 3.46
2983 6399 1.446792 CGCGCACAGATCTGAAGGT 60.447 57.895 29.27 3.48 0.00 3.50
2984 6400 0.179137 CGCGCACAGATCTGAAGGTA 60.179 55.000 29.27 0.00 0.00 3.08
2985 6401 1.536922 CGCGCACAGATCTGAAGGTAT 60.537 52.381 29.27 2.25 0.00 2.73
2986 6402 2.287608 CGCGCACAGATCTGAAGGTATA 60.288 50.000 29.27 0.00 0.00 1.47
2987 6403 3.312828 GCGCACAGATCTGAAGGTATAG 58.687 50.000 29.27 11.36 0.00 1.31
2988 6404 3.243569 GCGCACAGATCTGAAGGTATAGT 60.244 47.826 29.27 0.00 0.00 2.12
2989 6405 4.737946 GCGCACAGATCTGAAGGTATAGTT 60.738 45.833 29.27 0.00 0.00 2.24
2990 6406 5.352284 CGCACAGATCTGAAGGTATAGTTT 58.648 41.667 29.27 0.00 0.00 2.66
2991 6407 5.233050 CGCACAGATCTGAAGGTATAGTTTG 59.767 44.000 29.27 12.70 0.00 2.93
2992 6408 6.109359 GCACAGATCTGAAGGTATAGTTTGT 58.891 40.000 29.27 0.00 0.00 2.83
2993 6409 6.595716 GCACAGATCTGAAGGTATAGTTTGTT 59.404 38.462 29.27 0.00 0.00 2.83
2994 6410 7.413438 GCACAGATCTGAAGGTATAGTTTGTTG 60.413 40.741 29.27 11.47 0.00 3.33
2995 6411 7.819415 CACAGATCTGAAGGTATAGTTTGTTGA 59.181 37.037 29.27 0.00 0.00 3.18
2996 6412 8.037758 ACAGATCTGAAGGTATAGTTTGTTGAG 58.962 37.037 29.27 0.00 0.00 3.02
2997 6413 8.037758 CAGATCTGAAGGTATAGTTTGTTGAGT 58.962 37.037 18.34 0.00 0.00 3.41
2998 6414 8.037758 AGATCTGAAGGTATAGTTTGTTGAGTG 58.962 37.037 0.00 0.00 0.00 3.51
2999 6415 6.464222 TCTGAAGGTATAGTTTGTTGAGTGG 58.536 40.000 0.00 0.00 0.00 4.00
3000 6416 6.042781 TCTGAAGGTATAGTTTGTTGAGTGGT 59.957 38.462 0.00 0.00 0.00 4.16
3001 6417 6.597562 TGAAGGTATAGTTTGTTGAGTGGTT 58.402 36.000 0.00 0.00 0.00 3.67
3002 6418 6.485313 TGAAGGTATAGTTTGTTGAGTGGTTG 59.515 38.462 0.00 0.00 0.00 3.77
3003 6419 5.313712 AGGTATAGTTTGTTGAGTGGTTGG 58.686 41.667 0.00 0.00 0.00 3.77
3004 6420 5.067954 GGTATAGTTTGTTGAGTGGTTGGT 58.932 41.667 0.00 0.00 0.00 3.67
3005 6421 5.048991 GGTATAGTTTGTTGAGTGGTTGGTG 60.049 44.000 0.00 0.00 0.00 4.17
3006 6422 2.099405 AGTTTGTTGAGTGGTTGGTGG 58.901 47.619 0.00 0.00 0.00 4.61
3007 6423 0.820871 TTTGTTGAGTGGTTGGTGGC 59.179 50.000 0.00 0.00 0.00 5.01
3008 6424 0.323816 TTGTTGAGTGGTTGGTGGCA 60.324 50.000 0.00 0.00 0.00 4.92
3009 6425 0.751277 TGTTGAGTGGTTGGTGGCAG 60.751 55.000 0.00 0.00 0.00 4.85
3010 6426 0.751643 GTTGAGTGGTTGGTGGCAGT 60.752 55.000 0.00 0.00 0.00 4.40
3011 6427 0.751277 TTGAGTGGTTGGTGGCAGTG 60.751 55.000 0.00 0.00 0.00 3.66
3012 6428 1.898574 GAGTGGTTGGTGGCAGTGG 60.899 63.158 0.00 0.00 0.00 4.00
3013 6429 3.605664 GTGGTTGGTGGCAGTGGC 61.606 66.667 10.30 10.30 40.13 5.01
3014 6430 4.134785 TGGTTGGTGGCAGTGGCA 62.135 61.111 16.56 16.56 43.71 4.92
3015 6431 3.297620 GGTTGGTGGCAGTGGCAG 61.298 66.667 21.25 0.00 43.71 4.85
3016 6432 2.203337 GTTGGTGGCAGTGGCAGA 60.203 61.111 21.25 6.95 43.71 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 161 6.154706 TCCATCCTCCTTTACTTGTAGAACTC 59.845 42.308 0.00 0.00 0.00 3.01
222 223 2.661537 CGTGCACGCTTGTCCTCA 60.662 61.111 28.16 0.00 0.00 3.86
244 245 2.016318 CATGTTCAATTGAGCGGCCTA 58.984 47.619 16.27 0.26 0.00 3.93
266 267 1.654954 GGACGACGCTTCTCCTAGCA 61.655 60.000 0.00 0.00 41.28 3.49
369 373 9.273016 CAGATAAAAGAAAAGGTCAACTACTCA 57.727 33.333 0.00 0.00 0.00 3.41
380 384 9.050601 CCTAGCATAGACAGATAAAAGAAAAGG 57.949 37.037 0.00 0.00 42.77 3.11
428 436 0.868406 GGCGGCCATTTCTTCGATAG 59.132 55.000 15.62 0.00 0.00 2.08
429 437 0.878523 CGGCGGCCATTTCTTCGATA 60.879 55.000 20.71 0.00 0.00 2.92
430 438 2.180204 CGGCGGCCATTTCTTCGAT 61.180 57.895 20.71 0.00 0.00 3.59
431 439 2.817834 CGGCGGCCATTTCTTCGA 60.818 61.111 20.71 0.00 0.00 3.71
432 440 4.536687 GCGGCGGCCATTTCTTCG 62.537 66.667 20.71 3.11 0.00 3.79
640 655 4.383602 CAACGCGCCGACCCAAAG 62.384 66.667 5.73 0.00 0.00 2.77
674 689 4.629523 TCCGTTTGGGTCGGCACC 62.630 66.667 0.00 0.00 46.49 5.01
716 731 3.012518 CTGTTAGAGCAACTCCAATGGG 58.987 50.000 0.00 0.00 38.05 4.00
738 753 9.594478 TCAAAAGAAGTGATCGCTATATGTAAA 57.406 29.630 9.68 0.00 0.00 2.01
739 754 9.764363 ATCAAAAGAAGTGATCGCTATATGTAA 57.236 29.630 9.68 0.00 29.51 2.41
741 756 9.935241 ATATCAAAAGAAGTGATCGCTATATGT 57.065 29.630 9.68 0.00 37.01 2.29
887 960 7.765695 AGATCCATTTCTGTGTTGTACAATT 57.234 32.000 12.26 0.00 39.20 2.32
892 965 9.952030 TGTTTATAGATCCATTTCTGTGTTGTA 57.048 29.630 0.00 0.00 0.00 2.41
893 966 8.862325 TGTTTATAGATCCATTTCTGTGTTGT 57.138 30.769 0.00 0.00 0.00 3.32
894 967 8.950210 ACTGTTTATAGATCCATTTCTGTGTTG 58.050 33.333 0.00 0.00 0.00 3.33
908 981 7.544622 TCGCACTTACTTCACTGTTTATAGAT 58.455 34.615 0.00 0.00 0.00 1.98
936 1013 5.278022 GGAAATAATTGGTCTTCTGATCGCC 60.278 44.000 0.00 0.00 0.00 5.54
1087 1210 2.741092 GTCCTTGGAGGCGACACA 59.259 61.111 0.00 0.00 34.61 3.72
1089 1212 2.504274 AACGTCCTTGGAGGCGACA 61.504 57.895 14.52 0.00 37.97 4.35
1093 1216 0.321653 ATGACAACGTCCTTGGAGGC 60.322 55.000 9.03 0.00 34.61 4.70
1224 1347 0.116342 TGTACCTGAGGGAGAAGGCA 59.884 55.000 2.38 0.00 37.03 4.75
1234 1357 1.132643 GACGTAGCTGGTGTACCTGAG 59.867 57.143 11.56 0.00 37.15 3.35
1235 1358 1.171308 GACGTAGCTGGTGTACCTGA 58.829 55.000 11.56 0.00 37.15 3.86
1465 1591 2.027314 GTTGTGCGCCATGTTGCA 59.973 55.556 4.18 5.10 39.13 4.08
1638 1776 1.220749 GTCGAGCCCATACTTGCCA 59.779 57.895 0.00 0.00 0.00 4.92
1647 1785 3.509137 GAACGTGTGGTCGAGCCCA 62.509 63.158 12.85 3.38 36.04 5.36
1660 1798 2.342648 GAGCGGGTTGGAGAACGT 59.657 61.111 0.00 0.00 32.28 3.99
1833 1971 0.541392 AATACATGTGCTCCTCGCCA 59.459 50.000 9.11 0.00 38.05 5.69
1862 2000 1.590259 GAGTTGGATCTCGCGGCTC 60.590 63.158 6.13 0.02 0.00 4.70
1971 2109 2.158330 TGCGCGCAACGTAGATCTG 61.158 57.895 34.66 0.00 46.11 2.90
2012 2217 1.143373 GCGTCGTGGCGTTCATCATA 61.143 55.000 0.00 0.00 0.00 2.15
2013 2218 2.452813 GCGTCGTGGCGTTCATCAT 61.453 57.895 0.00 0.00 0.00 2.45
2014 2219 3.109547 GCGTCGTGGCGTTCATCA 61.110 61.111 0.00 0.00 0.00 3.07
2038 2243 2.759114 CCAAGGCCAAGGAGCTCA 59.241 61.111 17.19 0.00 0.00 4.26
2044 2249 2.203538 ACTGTGCCAAGGCCAAGG 60.204 61.111 5.01 7.44 41.09 3.61
2051 2256 2.281761 AAGCCGGACTGTGCCAAG 60.282 61.111 5.05 0.00 0.00 3.61
2052 2257 2.281484 GAAGCCGGACTGTGCCAA 60.281 61.111 5.05 0.00 0.00 4.52
2054 2259 2.032681 AAGAAGCCGGACTGTGCC 59.967 61.111 5.05 0.00 0.00 5.01
2055 2260 1.294659 CTGAAGAAGCCGGACTGTGC 61.295 60.000 5.05 0.00 0.00 4.57
2185 2390 2.925170 AGAAGGACTGGCTGGCGT 60.925 61.111 0.00 0.00 0.00 5.68
2237 5638 3.178611 GCCCCGGGGATGGAGAAT 61.179 66.667 44.86 0.00 37.50 2.40
2266 5667 2.038329 ACCCGAGGATGAACCCGA 59.962 61.111 0.00 0.00 40.05 5.14
2316 5720 1.133575 CATGGCCATGATCTGGGAGTT 60.134 52.381 37.84 0.00 46.06 3.01
2319 5723 0.475475 GACATGGCCATGATCTGGGA 59.525 55.000 44.72 3.19 46.06 4.37
2320 5724 0.538977 GGACATGGCCATGATCTGGG 60.539 60.000 44.72 22.22 46.06 4.45
2360 5764 1.861971 GAAACACGTTCCTCGAAGGT 58.138 50.000 0.00 0.00 40.55 3.50
2369 5773 0.863799 GGTTCGGAGGAAACACGTTC 59.136 55.000 0.00 0.00 39.74 3.95
2370 5774 0.178533 TGGTTCGGAGGAAACACGTT 59.821 50.000 0.00 0.00 44.70 3.99
2371 5775 1.824658 TGGTTCGGAGGAAACACGT 59.175 52.632 0.00 0.00 44.70 4.49
2378 5782 1.198094 TGCATCCTTGGTTCGGAGGA 61.198 55.000 0.00 0.00 45.57 3.71
2381 5785 0.690192 TTCTGCATCCTTGGTTCGGA 59.310 50.000 0.00 0.00 34.52 4.55
2390 5794 1.156645 GCGCGATTCTTCTGCATCCT 61.157 55.000 12.10 0.00 0.00 3.24
2393 5797 0.745845 AAGGCGCGATTCTTCTGCAT 60.746 50.000 12.10 0.00 0.00 3.96
2402 5806 1.603172 CCGAGAATAGAAGGCGCGATT 60.603 52.381 12.10 2.69 0.00 3.34
2426 5830 4.421479 AGAGCGTCGTTCCAGCCG 62.421 66.667 5.38 0.00 0.00 5.52
2428 5832 1.153745 ATGAGAGCGTCGTTCCAGC 60.154 57.895 5.38 0.00 0.00 4.85
2429 5833 0.171231 TCATGAGAGCGTCGTTCCAG 59.829 55.000 5.38 0.00 0.00 3.86
2431 5835 0.526524 CCTCATGAGAGCGTCGTTCC 60.527 60.000 24.62 0.00 40.68 3.62
2434 5838 1.803943 GTCCTCATGAGAGCGTCGT 59.196 57.895 24.62 0.00 40.68 4.34
2437 5844 0.109086 CAACGTCCTCATGAGAGCGT 60.109 55.000 27.03 27.03 40.68 5.07
2441 5848 0.678950 TGCACAACGTCCTCATGAGA 59.321 50.000 24.62 7.50 0.00 3.27
2450 5857 0.934436 GCAACATGGTGCACAACGTC 60.934 55.000 30.55 0.52 44.29 4.34
2452 5859 1.661197 GGCAACATGGTGCACAACG 60.661 57.895 35.07 1.24 46.81 4.10
2455 5862 3.976000 GCGGCAACATGGTGCACA 61.976 61.111 35.07 5.24 46.81 4.57
2606 6019 1.522355 CTCCGTCGAGTACCGCCTA 60.522 63.158 0.00 0.00 38.37 3.93
2615 6028 4.517703 GTCGCCGTCTCCGTCGAG 62.518 72.222 0.00 0.00 45.70 4.04
2657 6070 0.110056 AGTACCACAACTACGTCGCG 60.110 55.000 0.00 0.00 0.00 5.87
2658 6071 1.334054 CAGTACCACAACTACGTCGC 58.666 55.000 0.00 0.00 0.00 5.19
2659 6072 1.334054 GCAGTACCACAACTACGTCG 58.666 55.000 0.00 0.00 0.00 5.12
2706 6119 2.742372 CTTCTTCCACGGTGGCGG 60.742 66.667 22.42 15.99 37.47 6.13
2711 6124 0.538977 TCCTCGTCTTCTTCCACGGT 60.539 55.000 0.00 0.00 36.64 4.83
2721 6134 0.684805 AAGCTCCCGATCCTCGTCTT 60.685 55.000 0.00 0.00 38.40 3.01
2731 6144 0.544357 TCCCTTCAAGAAGCTCCCGA 60.544 55.000 4.30 0.00 37.11 5.14
2745 6158 2.311854 CCACCAGCCCAGATCCCTT 61.312 63.158 0.00 0.00 0.00 3.95
2750 6163 2.693864 CTCCCCACCAGCCCAGAT 60.694 66.667 0.00 0.00 0.00 2.90
2754 6167 3.732849 CTTCCTCCCCACCAGCCC 61.733 72.222 0.00 0.00 0.00 5.19
2757 6170 2.674220 GCCTCTTCCTCCCCACCAG 61.674 68.421 0.00 0.00 0.00 4.00
2760 6176 3.787001 CCGCCTCTTCCTCCCCAC 61.787 72.222 0.00 0.00 0.00 4.61
2769 6185 4.052229 CGTGTCCGTCCGCCTCTT 62.052 66.667 0.00 0.00 0.00 2.85
2793 6209 0.667792 GACGTGGTCCTTGACTCTGC 60.668 60.000 0.00 0.00 32.47 4.26
2795 6211 1.705873 AAGACGTGGTCCTTGACTCT 58.294 50.000 0.00 0.00 32.18 3.24
2797 6213 1.202651 CCAAAGACGTGGTCCTTGACT 60.203 52.381 8.31 0.00 36.44 3.41
2801 6217 3.700198 GTCCAAAGACGTGGTCCTT 57.300 52.632 0.00 0.00 39.88 3.36
2813 6229 2.752322 CTACCGGCGTCACGTCCAAA 62.752 60.000 6.01 0.00 0.00 3.28
2865 6281 1.949847 AAGATGGACCGCCTCTGTCG 61.950 60.000 0.00 0.00 33.46 4.35
2866 6282 0.460987 CAAGATGGACCGCCTCTGTC 60.461 60.000 0.00 0.00 34.31 3.51
2867 6283 1.599047 CAAGATGGACCGCCTCTGT 59.401 57.895 0.00 0.00 34.31 3.41
2868 6284 1.817099 GCAAGATGGACCGCCTCTG 60.817 63.158 0.00 0.00 34.31 3.35
2869 6285 2.586792 GCAAGATGGACCGCCTCT 59.413 61.111 0.00 0.00 34.31 3.69
2910 6326 2.327081 GAAGTAGTGTTCGACTGCGA 57.673 50.000 0.00 0.00 46.33 5.10
2926 6342 4.421479 AGTCTGGCGCCGACGAAG 62.421 66.667 31.25 20.90 43.93 3.79
2927 6343 4.415332 GAGTCTGGCGCCGACGAA 62.415 66.667 31.25 13.30 43.93 3.85
2930 6346 4.148825 ATGGAGTCTGGCGCCGAC 62.149 66.667 31.06 31.06 40.18 4.79
2931 6347 4.147449 CATGGAGTCTGGCGCCGA 62.147 66.667 23.90 19.11 40.18 5.54
2937 6353 1.443407 CTACGGCCATGGAGTCTGG 59.557 63.158 18.40 5.14 36.81 3.86
2938 6354 1.227380 GCTACGGCCATGGAGTCTG 60.227 63.158 18.40 5.43 0.00 3.51
2939 6355 3.221222 GCTACGGCCATGGAGTCT 58.779 61.111 18.40 0.00 0.00 3.24
2958 6374 4.899239 ATCTGTGCGCGGCTAGCC 62.899 66.667 24.75 24.75 44.76 3.93
2959 6375 3.333969 GATCTGTGCGCGGCTAGC 61.334 66.667 8.83 6.04 43.95 3.42
2960 6376 1.948138 CAGATCTGTGCGCGGCTAG 60.948 63.158 14.95 3.89 0.00 3.42
2961 6377 1.944234 TTCAGATCTGTGCGCGGCTA 61.944 55.000 21.92 0.00 0.00 3.93
2962 6378 3.300934 TTCAGATCTGTGCGCGGCT 62.301 57.895 21.92 0.00 0.00 5.52
2963 6379 2.806856 CTTCAGATCTGTGCGCGGC 61.807 63.158 21.92 0.00 0.00 6.53
2964 6380 2.169789 CCTTCAGATCTGTGCGCGG 61.170 63.158 21.92 12.04 0.00 6.46
2965 6381 0.179137 TACCTTCAGATCTGTGCGCG 60.179 55.000 21.92 0.00 0.00 6.86
2966 6382 2.231215 ATACCTTCAGATCTGTGCGC 57.769 50.000 21.92 0.00 0.00 6.09
2967 6383 4.576216 ACTATACCTTCAGATCTGTGCG 57.424 45.455 21.92 12.29 0.00 5.34
2968 6384 6.109359 ACAAACTATACCTTCAGATCTGTGC 58.891 40.000 21.92 0.00 0.00 4.57
2969 6385 7.819415 TCAACAAACTATACCTTCAGATCTGTG 59.181 37.037 21.92 15.25 0.00 3.66
2970 6386 7.907389 TCAACAAACTATACCTTCAGATCTGT 58.093 34.615 21.92 5.72 0.00 3.41
2971 6387 8.037758 ACTCAACAAACTATACCTTCAGATCTG 58.962 37.037 17.07 17.07 0.00 2.90
2972 6388 8.037758 CACTCAACAAACTATACCTTCAGATCT 58.962 37.037 0.00 0.00 0.00 2.75
2973 6389 7.278868 CCACTCAACAAACTATACCTTCAGATC 59.721 40.741 0.00 0.00 0.00 2.75
2974 6390 7.106239 CCACTCAACAAACTATACCTTCAGAT 58.894 38.462 0.00 0.00 0.00 2.90
2975 6391 6.042781 ACCACTCAACAAACTATACCTTCAGA 59.957 38.462 0.00 0.00 0.00 3.27
2976 6392 6.231211 ACCACTCAACAAACTATACCTTCAG 58.769 40.000 0.00 0.00 0.00 3.02
2977 6393 6.182507 ACCACTCAACAAACTATACCTTCA 57.817 37.500 0.00 0.00 0.00 3.02
2978 6394 6.072673 CCAACCACTCAACAAACTATACCTTC 60.073 42.308 0.00 0.00 0.00 3.46
2979 6395 5.768164 CCAACCACTCAACAAACTATACCTT 59.232 40.000 0.00 0.00 0.00 3.50
2980 6396 5.163131 ACCAACCACTCAACAAACTATACCT 60.163 40.000 0.00 0.00 0.00 3.08
2981 6397 5.048991 CACCAACCACTCAACAAACTATACC 60.049 44.000 0.00 0.00 0.00 2.73
2982 6398 5.048991 CCACCAACCACTCAACAAACTATAC 60.049 44.000 0.00 0.00 0.00 1.47
2983 6399 5.067273 CCACCAACCACTCAACAAACTATA 58.933 41.667 0.00 0.00 0.00 1.31
2984 6400 3.888930 CCACCAACCACTCAACAAACTAT 59.111 43.478 0.00 0.00 0.00 2.12
2985 6401 3.283751 CCACCAACCACTCAACAAACTA 58.716 45.455 0.00 0.00 0.00 2.24
2986 6402 2.099405 CCACCAACCACTCAACAAACT 58.901 47.619 0.00 0.00 0.00 2.66
2987 6403 1.470805 GCCACCAACCACTCAACAAAC 60.471 52.381 0.00 0.00 0.00 2.93
2988 6404 0.820871 GCCACCAACCACTCAACAAA 59.179 50.000 0.00 0.00 0.00 2.83
2989 6405 0.323816 TGCCACCAACCACTCAACAA 60.324 50.000 0.00 0.00 0.00 2.83
2990 6406 0.751277 CTGCCACCAACCACTCAACA 60.751 55.000 0.00 0.00 0.00 3.33
2991 6407 0.751643 ACTGCCACCAACCACTCAAC 60.752 55.000 0.00 0.00 0.00 3.18
2992 6408 0.751277 CACTGCCACCAACCACTCAA 60.751 55.000 0.00 0.00 0.00 3.02
2993 6409 1.152984 CACTGCCACCAACCACTCA 60.153 57.895 0.00 0.00 0.00 3.41
2994 6410 1.898574 CCACTGCCACCAACCACTC 60.899 63.158 0.00 0.00 0.00 3.51
2995 6411 2.195683 CCACTGCCACCAACCACT 59.804 61.111 0.00 0.00 0.00 4.00
2996 6412 3.605664 GCCACTGCCACCAACCAC 61.606 66.667 0.00 0.00 0.00 4.16
2997 6413 4.134785 TGCCACTGCCACCAACCA 62.135 61.111 0.00 0.00 36.33 3.67
2998 6414 3.297620 CTGCCACTGCCACCAACC 61.298 66.667 0.00 0.00 36.33 3.77
2999 6415 2.203337 TCTGCCACTGCCACCAAC 60.203 61.111 0.00 0.00 36.33 3.77


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

AutoCloner maintained by Alex Coulton.