Multiple sequence alignment - TraesCS5B01G546700

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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 TraesCS5B01G546700 chr5B 100.000 5196 0 0 1 5196 699950441 699945246 0.000000e+00 9596.0
1 TraesCS5B01G546700 chr5B 92.699 2123 91 22 2326 4400 700232796 700234902 0.000000e+00 3003.0
2 TraesCS5B01G546700 chr5B 95.428 678 29 1 4401 5076 700235841 700236518 0.000000e+00 1079.0
3 TraesCS5B01G546700 chr5B 93.478 598 22 10 1788 2378 700232206 700232793 0.000000e+00 872.0
4 TraesCS5B01G546700 chr5B 86.598 776 57 16 1 769 700229162 700229897 0.000000e+00 813.0
5 TraesCS5B01G546700 chr5B 83.174 939 94 28 2546 3446 700223349 700224261 0.000000e+00 800.0
6 TraesCS5B01G546700 chr5B 84.192 854 82 27 1648 2496 700222445 700223250 0.000000e+00 780.0
7 TraesCS5B01G546700 chr5B 85.667 607 63 9 4401 5002 698258723 698258136 7.390000e-173 617.0
8 TraesCS5B01G546700 chr5B 84.910 391 52 7 3492 3878 700224259 700224646 6.310000e-104 388.0
9 TraesCS5B01G546700 chr5B 85.612 278 24 9 4055 4330 700224816 700225079 1.430000e-70 278.0
10 TraesCS5B01G546700 chr5B 82.126 207 26 8 1058 1261 700231037 700231235 3.220000e-37 167.0
11 TraesCS5B01G546700 chr5B 90.323 124 10 2 937 1060 700230820 700230941 1.500000e-35 161.0
12 TraesCS5B01G546700 chr5B 86.331 139 17 1 4262 4400 698260107 698259971 3.240000e-32 150.0
13 TraesCS5B01G546700 chr5B 90.909 55 4 1 1252 1306 700231260 700231313 7.220000e-09 73.1
14 TraesCS5B01G546700 chr5B 100.000 38 0 0 5022 5059 699945372 699945335 2.600000e-08 71.3
15 TraesCS5B01G546700 chr5B 100.000 38 0 0 5070 5107 699945420 699945383 2.600000e-08 71.3
16 TraesCS5B01G546700 chr5B 97.143 35 1 0 5157 5191 700238030 700238064 5.620000e-05 60.2
17 TraesCS5B01G546700 chr5B 97.059 34 1 0 5158 5191 700242295 700242328 2.020000e-04 58.4
18 TraesCS5B01G546700 chr5D 95.149 2783 81 14 1648 4386 552037287 552040059 0.000000e+00 4342.0
19 TraesCS5B01G546700 chr5D 93.359 768 45 6 1 766 552033242 552034005 0.000000e+00 1131.0
20 TraesCS5B01G546700 chr5D 95.118 676 28 1 4401 5076 552040788 552041458 0.000000e+00 1061.0
21 TraesCS5B01G546700 chr5D 95.447 637 25 3 4401 5035 551449446 551448812 0.000000e+00 1013.0
22 TraesCS5B01G546700 chr5D 85.802 817 71 22 2538 3339 551992274 551993060 0.000000e+00 824.0
23 TraesCS5B01G546700 chr5D 85.220 751 89 10 1 738 551988772 551989513 0.000000e+00 752.0
24 TraesCS5B01G546700 chr5D 85.714 602 63 10 4401 5002 552456231 552456809 9.560000e-172 614.0
25 TraesCS5B01G546700 chr5D 82.561 734 74 17 1648 2359 551991386 551992087 9.630000e-167 597.0
26 TraesCS5B01G546700 chr5D 84.694 392 53 7 3492 3878 551993188 551993577 8.160000e-103 385.0
27 TraesCS5B01G546700 chr5D 89.098 266 22 2 1389 1654 552036617 552036875 1.800000e-84 324.0
28 TraesCS5B01G546700 chr5D 84.906 265 26 9 4055 4318 551993747 551993998 6.680000e-64 255.0
29 TraesCS5B01G546700 chr5D 79.268 410 45 21 3981 4386 552455078 552455451 3.110000e-62 250.0
30 TraesCS5B01G546700 chr5D 76.327 452 85 15 85 522 551739104 551738661 6.770000e-54 222.0
31 TraesCS5B01G546700 chr5D 90.400 125 8 4 937 1060 552036268 552036389 1.500000e-35 161.0
32 TraesCS5B01G546700 chr5D 90.244 123 7 4 795 914 552034001 552034121 6.970000e-34 156.0
33 TraesCS5B01G546700 chr5D 95.604 91 4 0 5105 5195 552042993 552043083 4.190000e-31 147.0
34 TraesCS5B01G546700 chr5D 88.764 89 6 3 973 1060 551990473 551990558 7.120000e-19 106.0
35 TraesCS5B01G546700 chr5D 89.157 83 6 2 1071 1150 552036502 552036584 3.310000e-17 100.0
36 TraesCS5B01G546700 chr5D 94.118 51 3 0 5105 5155 551447160 551447110 1.550000e-10 78.7
37 TraesCS5B01G546700 chr5D 95.238 42 1 1 5067 5107 552041400 552041441 1.210000e-06 65.8
38 TraesCS5B01G546700 chr5D 97.143 35 1 0 5157 5191 551446955 551446921 5.620000e-05 60.2
39 TraesCS5B01G546700 chr4A 94.139 1962 73 10 1650 3577 616231489 616233442 0.000000e+00 2948.0
40 TraesCS5B01G546700 chr4A 92.987 770 49 5 1 768 616212303 616213069 0.000000e+00 1118.0
41 TraesCS5B01G546700 chr4A 95.794 642 25 1 4401 5040 616673369 616674010 0.000000e+00 1035.0
42 TraesCS5B01G546700 chr4A 89.655 783 59 14 1 780 616297933 616297170 0.000000e+00 977.0
43 TraesCS5B01G546700 chr4A 84.871 813 74 22 2543 3339 616312086 616311307 0.000000e+00 774.0
44 TraesCS5B01G546700 chr4A 82.016 873 90 30 1648 2494 616313010 616312179 0.000000e+00 680.0
45 TraesCS5B01G546700 chr4A 83.223 757 96 14 2 738 616315756 616315011 0.000000e+00 665.0
46 TraesCS5B01G546700 chr4A 82.137 627 57 30 1055 1661 616230520 616231111 2.180000e-133 486.0
47 TraesCS5B01G546700 chr4A 84.211 399 45 9 1648 2045 670382439 670382058 6.350000e-99 372.0
48 TraesCS5B01G546700 chr4A 84.474 380 54 5 3492 3868 616310946 616310569 2.290000e-98 370.0
49 TraesCS5B01G546700 chr4A 83.471 363 35 14 1116 1464 616313639 616313288 1.090000e-81 315.0
50 TraesCS5B01G546700 chr4A 85.766 274 23 6 4055 4327 616310422 616310164 5.130000e-70 276.0
51 TraesCS5B01G546700 chr4A 90.526 95 6 1 966 1060 616230337 616230428 7.070000e-24 122.0
52 TraesCS5B01G546700 chr4A 91.463 82 4 2 979 1060 616313858 616313780 5.500000e-20 110.0
53 TraesCS5B01G546700 chr6B 91.048 458 26 5 2311 2754 16926871 16926415 5.760000e-169 604.0
54 TraesCS5B01G546700 chr6B 84.634 410 42 6 1633 2042 672450426 672450814 6.310000e-104 388.0
55 TraesCS5B01G546700 chr6B 84.553 369 35 5 1633 1996 19861745 19862096 3.850000e-91 346.0
56 TraesCS5B01G546700 chr6B 82.237 152 19 3 2871 3021 239368319 239368175 1.960000e-24 124.0
57 TraesCS5B01G546700 chr1B 81.729 613 94 18 1 608 627719909 627719310 3.610000e-136 496.0
58 TraesCS5B01G546700 chr2D 82.075 636 51 25 1055 1652 420719783 420720393 7.820000e-133 484.0
59 TraesCS5B01G546700 chr2D 94.949 99 5 0 954 1052 420719580 420719678 6.970000e-34 156.0
60 TraesCS5B01G546700 chr5A 84.332 217 30 4 3652 3866 680212345 680212559 5.270000e-50 209.0
61 TraesCS5B01G546700 chr4D 84.211 209 29 4 3664 3870 499453744 499453950 3.170000e-47 200.0
62 TraesCS5B01G546700 chr1A 75.588 340 71 10 134 464 569657192 569656856 1.940000e-34 158.0


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 TraesCS5B01G546700 chr5B 699945246 699950441 5195 True 9596.000000 9596 100.000000 1 5196 1 chr5B.!!$R1 5195
1 TraesCS5B01G546700 chr5B 700229162 700238064 8902 False 778.537500 3003 91.088000 1 5191 8 chr5B.!!$F3 5190
2 TraesCS5B01G546700 chr5B 700222445 700225079 2634 False 561.500000 800 84.472000 1648 4330 4 chr5B.!!$F2 2682
3 TraesCS5B01G546700 chr5B 698258136 698260107 1971 True 383.500000 617 85.999000 4262 5002 2 chr5B.!!$R2 740
4 TraesCS5B01G546700 chr5D 552033242 552043083 9841 False 831.977778 4342 92.596333 1 5195 9 chr5D.!!$F2 5194
5 TraesCS5B01G546700 chr5D 551988772 551993998 5226 False 486.500000 824 85.324500 1 4318 6 chr5D.!!$F1 4317
6 TraesCS5B01G546700 chr5D 552455078 552456809 1731 False 432.000000 614 82.491000 3981 5002 2 chr5D.!!$F3 1021
7 TraesCS5B01G546700 chr5D 551446921 551449446 2525 True 383.966667 1013 95.569333 4401 5191 3 chr5D.!!$R2 790
8 TraesCS5B01G546700 chr4A 616230337 616233442 3105 False 1185.333333 2948 88.934000 966 3577 3 chr4A.!!$F3 2611
9 TraesCS5B01G546700 chr4A 616212303 616213069 766 False 1118.000000 1118 92.987000 1 768 1 chr4A.!!$F1 767
10 TraesCS5B01G546700 chr4A 616673369 616674010 641 False 1035.000000 1035 95.794000 4401 5040 1 chr4A.!!$F2 639
11 TraesCS5B01G546700 chr4A 616297170 616297933 763 True 977.000000 977 89.655000 1 780 1 chr4A.!!$R1 779
12 TraesCS5B01G546700 chr4A 616310164 616315756 5592 True 455.714286 774 85.040571 2 4327 7 chr4A.!!$R3 4325
13 TraesCS5B01G546700 chr1B 627719310 627719909 599 True 496.000000 496 81.729000 1 608 1 chr1B.!!$R1 607
14 TraesCS5B01G546700 chr2D 420719580 420720393 813 False 320.000000 484 88.512000 954 1652 2 chr2D.!!$F1 698

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
211 220 0.798776 CGCAGTTGTCAGGAATGTCC 59.201 55.0 0.00 0.00 36.58 4.02 F
1064 4855 0.031414 GGCTACACCTCCTCCCCTTA 60.031 60.0 0.00 0.00 34.51 2.69 F
1295 5292 0.037303 CATCTCCCCACTGCAACTGT 59.963 55.0 0.00 0.00 0.00 3.55 F
1344 5366 0.396695 CAAGGGGCAGCCATTCTGAT 60.397 55.0 15.19 0.00 45.72 2.90 F
1638 5870 0.403271 AGTCAACTGGCAGCCATTCT 59.597 50.0 16.64 6.39 30.82 2.40 F
1639 5871 0.524862 GTCAACTGGCAGCCATTCTG 59.475 55.0 16.64 12.61 45.62 3.02 F
3100 7930 2.159043 TGCATGTAAGGTAGAGCTCTGC 60.159 50.0 26.78 24.46 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 6483 0.108585 AGGCCTTCTTGCAAGAACGA 59.891 50.000 32.86 17.08 39.95 3.85 R
1962 6604 2.169832 TTCTTTTCGCAGACCTCTGG 57.830 50.000 4.49 0.00 43.94 3.86 R
3256 8090 0.106521 GCCAGTGCCCAAAACACAAT 59.893 50.000 0.00 0.00 40.59 2.71 R
3306 8147 8.316640 AGACAAACAATGAAGAGTAGAATCAC 57.683 34.615 0.00 0.00 0.00 3.06 R
3544 8647 4.503741 ACAATTCAGTCCATGTTTTCCG 57.496 40.909 0.00 0.00 0.00 4.30 R
3915 9044 9.221775 GAAACAAGCAACTAATAATATCCAACG 57.778 33.333 0.00 0.00 0.00 4.10 R
5146 13456 0.247736 AACAGTTTTGTTTGGCCGCA 59.752 45.000 0.00 0.00 45.01 5.69 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
45 46 2.036256 GAGTGCAGTGGCCCCATT 59.964 61.111 0.00 0.00 40.13 3.16
124 125 0.892063 AAACAACAAGGTGCGTTGGT 59.108 45.000 7.82 0.00 46.04 3.67
195 204 4.622260 GGTATTTATAGTTACCCCCGCA 57.378 45.455 3.02 0.00 33.20 5.69
202 211 1.071814 GTTACCCCCGCAGTTGTCA 59.928 57.895 0.00 0.00 0.00 3.58
211 220 0.798776 CGCAGTTGTCAGGAATGTCC 59.201 55.000 0.00 0.00 36.58 4.02
562 577 7.489574 TTTATGTTGATTTTGGAAGGTTTGC 57.510 32.000 0.00 0.00 0.00 3.68
570 585 2.642154 TGGAAGGTTTGCGTTTCCTA 57.358 45.000 4.36 0.00 0.00 2.94
585 600 3.328382 TTCCTACCAAGATTGACCACG 57.672 47.619 0.00 0.00 0.00 4.94
586 601 2.531771 TCCTACCAAGATTGACCACGA 58.468 47.619 0.00 0.00 0.00 4.35
629 654 6.014327 TCAAGGCTAGCCAAAGAATTGAAAAT 60.014 34.615 34.70 6.54 38.94 1.82
732 760 2.763645 AAGAGGCCAACCCGGTGTT 61.764 57.895 5.01 0.95 39.21 3.32
838 1662 4.212425 TGACGGCTACAAACAAAGTGTATG 59.788 41.667 0.00 0.00 31.27 2.39
872 1962 4.415332 CGGCTGTAGACGCGTGGT 62.415 66.667 20.70 6.13 40.91 4.16
903 2518 1.444553 GGTGACGACTTGCCGAGAG 60.445 63.158 0.00 0.00 0.00 3.20
904 2519 1.579932 GTGACGACTTGCCGAGAGA 59.420 57.895 0.00 0.00 0.00 3.10
1060 4851 3.155167 CGGGCTACACCTCCTCCC 61.155 72.222 0.00 0.00 39.10 4.30
1061 4852 2.768769 GGGCTACACCTCCTCCCC 60.769 72.222 0.00 0.00 39.10 4.81
1062 4853 2.369001 GGCTACACCTCCTCCCCT 59.631 66.667 0.00 0.00 34.51 4.79
1063 4854 1.307084 GGCTACACCTCCTCCCCTT 60.307 63.158 0.00 0.00 34.51 3.95
1064 4855 0.031414 GGCTACACCTCCTCCCCTTA 60.031 60.000 0.00 0.00 34.51 2.69
1295 5292 0.037303 CATCTCCCCACTGCAACTGT 59.963 55.000 0.00 0.00 0.00 3.55
1296 5293 1.278985 CATCTCCCCACTGCAACTGTA 59.721 52.381 0.00 0.00 0.00 2.74
1297 5294 1.656587 TCTCCCCACTGCAACTGTAT 58.343 50.000 0.00 0.00 0.00 2.29
1344 5366 0.396695 CAAGGGGCAGCCATTCTGAT 60.397 55.000 15.19 0.00 45.72 2.90
1365 5387 7.610305 TCTGATCTGTGAATTTAAAACTACCCC 59.390 37.037 0.00 0.00 0.00 4.95
1366 5388 6.661805 TGATCTGTGAATTTAAAACTACCCCC 59.338 38.462 0.00 0.00 0.00 5.40
1367 5389 5.005094 TCTGTGAATTTAAAACTACCCCCG 58.995 41.667 0.00 0.00 0.00 5.73
1368 5390 4.080687 TGTGAATTTAAAACTACCCCCGG 58.919 43.478 0.00 0.00 0.00 5.73
1373 5395 1.898330 TAAAACTACCCCCGGCCGAC 61.898 60.000 30.73 0.00 0.00 4.79
1386 5408 1.145803 GGCCGACTTCGCATAATACC 58.854 55.000 0.00 0.00 38.18 2.73
1387 5409 1.270147 GGCCGACTTCGCATAATACCT 60.270 52.381 0.00 0.00 38.18 3.08
1577 5792 0.681733 TCTGGCTCTGTTCACTCACC 59.318 55.000 0.00 0.00 0.00 4.02
1591 5809 3.334581 TCACTCACCCCCTACTACAACTA 59.665 47.826 0.00 0.00 0.00 2.24
1592 5810 3.700038 CACTCACCCCCTACTACAACTAG 59.300 52.174 0.00 0.00 0.00 2.57
1593 5811 3.336088 ACTCACCCCCTACTACAACTAGT 59.664 47.826 0.00 0.00 37.04 2.57
1594 5812 4.541714 ACTCACCCCCTACTACAACTAGTA 59.458 45.833 0.00 0.00 34.79 1.82
1595 5813 5.195349 ACTCACCCCCTACTACAACTAGTAT 59.805 44.000 0.00 0.00 35.34 2.12
1596 5814 6.391055 ACTCACCCCCTACTACAACTAGTATA 59.609 42.308 0.00 0.00 35.34 1.47
1637 5869 0.807496 GAGTCAACTGGCAGCCATTC 59.193 55.000 16.64 4.06 30.82 2.67
1638 5870 0.403271 AGTCAACTGGCAGCCATTCT 59.597 50.000 16.64 6.39 30.82 2.40
1639 5871 0.524862 GTCAACTGGCAGCCATTCTG 59.475 55.000 16.64 12.61 45.62 3.02
1652 6290 5.124457 GCAGCCATTCTGACTTCTGAATTAA 59.876 40.000 8.24 0.00 45.72 1.40
1782 6424 5.908341 TGTTCTGTGTACTTATGTGTGTCA 58.092 37.500 0.00 0.00 0.00 3.58
1962 6604 3.807622 TGACGAGACATGGTTTTCAAGTC 59.192 43.478 0.00 0.51 42.53 3.01
1992 6634 7.494952 AGGTCTGCGAAAAGAATAAGGTAATAC 59.505 37.037 0.00 0.00 0.00 1.89
1999 6641 8.179615 CGAAAAGAATAAGGTAATACGCCTTTT 58.820 33.333 1.73 0.00 43.24 2.27
2014 6656 3.338249 GCCTTTTCTGTGCTCATAGACA 58.662 45.455 0.00 0.00 0.00 3.41
2023 6665 2.287373 GTGCTCATAGACATCTGCTTGC 59.713 50.000 0.00 0.00 0.00 4.01
2181 6887 9.330063 CAAATGCACCTCTACTGAAATAGAATA 57.670 33.333 0.00 0.00 30.76 1.75
2232 6939 6.568869 TGTTATTGAAGACCTTGGTTTTGTG 58.431 36.000 0.07 0.00 0.00 3.33
2233 6940 6.153680 TGTTATTGAAGACCTTGGTTTTGTGT 59.846 34.615 0.07 0.00 0.00 3.72
2234 6941 5.675684 ATTGAAGACCTTGGTTTTGTGTT 57.324 34.783 0.07 0.00 0.00 3.32
2235 6942 5.476091 TTGAAGACCTTGGTTTTGTGTTT 57.524 34.783 0.07 0.00 0.00 2.83
2236 6943 5.476091 TGAAGACCTTGGTTTTGTGTTTT 57.524 34.783 0.07 0.00 0.00 2.43
2237 6944 5.474825 TGAAGACCTTGGTTTTGTGTTTTC 58.525 37.500 0.07 0.00 0.00 2.29
2238 6945 5.011125 TGAAGACCTTGGTTTTGTGTTTTCA 59.989 36.000 0.07 0.00 30.52 2.69
2490 7259 5.430886 TGCATAACAACTCTGCATCTACAT 58.569 37.500 0.00 0.00 40.75 2.29
2532 7327 4.976116 TCATAGATGTTGAAGCGACATACG 59.024 41.667 0.51 0.00 38.45 3.06
2579 7397 8.331022 GCACTTGTAATCATAAGTACATCACTG 58.669 37.037 0.00 0.00 36.00 3.66
2626 7444 9.049523 CATGCACTTGTCATTATAAGTACATCT 57.950 33.333 0.00 0.00 38.21 2.90
2674 7492 7.295340 TGGTTCCTCATACTGACTATAAGCTA 58.705 38.462 0.00 0.00 0.00 3.32
2689 7509 9.145865 GACTATAAGCTACCATAATTTCTGCTC 57.854 37.037 0.00 0.00 0.00 4.26
2713 7533 4.965119 ACAGGGTTCTTTCGATATTTGC 57.035 40.909 0.00 0.00 0.00 3.68
2801 7623 9.270640 TCCACATCCTTTTGTATTTCAATTTTG 57.729 29.630 0.00 0.00 35.84 2.44
2936 7762 6.857964 GGAAGTACGCAAATGATAATGGATTG 59.142 38.462 0.00 0.00 0.00 2.67
3001 7827 5.104941 TGTTGCAGCCTACACTGAATACTAT 60.105 40.000 0.00 0.00 40.25 2.12
3100 7930 2.159043 TGCATGTAAGGTAGAGCTCTGC 60.159 50.000 26.78 24.46 0.00 4.26
3153 7983 2.981859 TTCGAGAGAATACCCAAGCC 57.018 50.000 0.00 0.00 46.92 4.35
3256 8090 7.873719 TGTTTCTTTCATTTCCTTCTGTGTA 57.126 32.000 0.00 0.00 0.00 2.90
3306 8147 6.148976 CACTGTGAGATATTGCCATATTGGAG 59.851 42.308 0.32 0.00 40.96 3.86
3345 8209 7.919091 TCATTGTTTGTCTAGCTAATAGGTACG 59.081 37.037 0.00 0.00 31.83 3.67
3487 8589 8.459521 TTTGCGTTCATTTATTTGGATACTTG 57.540 30.769 0.00 0.00 37.61 3.16
3500 8603 3.196469 TGGATACTTGGAGCTTCAGAGTG 59.804 47.826 15.90 3.40 37.61 3.51
3544 8647 6.238759 GGCATAGAGGATGTTTAATGACCAAC 60.239 42.308 0.00 0.00 37.90 3.77
3555 8658 3.658757 AATGACCAACGGAAAACATGG 57.341 42.857 0.00 0.00 38.91 3.66
3902 9031 5.582953 AGTGAATCCCTTGGAATTGAATCA 58.417 37.500 0.00 0.00 34.34 2.57
3915 9044 8.506168 TGGAATTGAATCAAGAACAGTATACC 57.494 34.615 1.10 0.00 0.00 2.73
4386 9558 5.463724 GGATTCAAGTTCCGAGACATGTATC 59.536 44.000 10.51 10.51 29.73 2.24
4387 9559 4.386867 TCAAGTTCCGAGACATGTATCC 57.613 45.455 14.60 0.87 0.00 2.59
4388 9560 4.023980 TCAAGTTCCGAGACATGTATCCT 58.976 43.478 14.60 3.24 0.00 3.24
4389 9561 4.115516 CAAGTTCCGAGACATGTATCCTG 58.884 47.826 14.60 6.61 0.00 3.86
4390 9562 2.101582 AGTTCCGAGACATGTATCCTGC 59.898 50.000 14.60 3.39 0.00 4.85
4391 9563 1.040646 TCCGAGACATGTATCCTGCC 58.959 55.000 14.60 0.00 0.00 4.85
4392 9564 0.752658 CCGAGACATGTATCCTGCCA 59.247 55.000 14.60 0.00 0.00 4.92
4393 9565 1.269988 CCGAGACATGTATCCTGCCAG 60.270 57.143 14.60 0.00 0.00 4.85
4394 9566 1.410517 CGAGACATGTATCCTGCCAGT 59.589 52.381 14.60 0.00 0.00 4.00
4398 9570 3.133003 AGACATGTATCCTGCCAGTACAC 59.867 47.826 0.00 0.00 31.79 2.90
4483 11112 8.768397 TCTACAACAGGGTACATCAAATTAGAT 58.232 33.333 0.00 0.00 0.00 1.98
4516 11145 3.744660 AGATAATCAATTCACTCGGCCC 58.255 45.455 0.00 0.00 0.00 5.80
4720 11357 1.472082 CCACACATTCTTAATGCGCCA 59.528 47.619 4.18 0.00 42.69 5.69
4728 11365 1.202817 TCTTAATGCGCCACGTCACTA 59.797 47.619 4.18 0.00 0.00 2.74
4758 11395 4.280929 ACCCTTTCTGCAAACATAGGTTTC 59.719 41.667 1.81 0.00 45.18 2.78
4852 11493 2.088423 ACGGCACTCAAAGTTTGTTCA 58.912 42.857 15.08 0.00 0.00 3.18
4880 11521 8.428063 ACCCATTTCAAACATAACTTTCAATCA 58.572 29.630 0.00 0.00 0.00 2.57
4959 11600 3.384467 AGTTGTTCCCACATCACAAAAGG 59.616 43.478 0.00 0.00 32.32 3.11
5079 11722 9.832445 TGTAGTGACTTCAGATTAAACTTTTCT 57.168 29.630 0.00 0.00 0.00 2.52
5082 11725 9.267084 AGTGACTTCAGATTAAACTTTTCTCTC 57.733 33.333 0.00 0.00 0.00 3.20
5083 11726 9.267084 GTGACTTCAGATTAAACTTTTCTCTCT 57.733 33.333 0.00 0.00 0.00 3.10
5085 11728 8.840833 ACTTCAGATTAAACTTTTCTCTCTCC 57.159 34.615 0.00 0.00 0.00 3.71
5086 11729 7.880713 ACTTCAGATTAAACTTTTCTCTCTCCC 59.119 37.037 0.00 0.00 0.00 4.30
5087 11730 7.316393 TCAGATTAAACTTTTCTCTCTCCCA 57.684 36.000 0.00 0.00 0.00 4.37
5088 11731 7.922382 TCAGATTAAACTTTTCTCTCTCCCAT 58.078 34.615 0.00 0.00 0.00 4.00
5089 11732 9.046846 TCAGATTAAACTTTTCTCTCTCCCATA 57.953 33.333 0.00 0.00 0.00 2.74
5092 11735 9.674068 GATTAAACTTTTCTCTCTCCCATACTT 57.326 33.333 0.00 0.00 0.00 2.24
5094 11737 7.987750 AAACTTTTCTCTCTCCCATACTTTC 57.012 36.000 0.00 0.00 0.00 2.62
5095 11738 6.943899 ACTTTTCTCTCTCCCATACTTTCT 57.056 37.500 0.00 0.00 0.00 2.52
5098 11741 5.941555 TTCTCTCTCCCATACTTTCTTCC 57.058 43.478 0.00 0.00 0.00 3.46
5099 11742 4.947883 TCTCTCTCCCATACTTTCTTCCA 58.052 43.478 0.00 0.00 0.00 3.53
5100 11743 4.712337 TCTCTCTCCCATACTTTCTTCCAC 59.288 45.833 0.00 0.00 0.00 4.02
5101 11744 4.689062 TCTCTCCCATACTTTCTTCCACT 58.311 43.478 0.00 0.00 0.00 4.00
5102 11745 4.467795 TCTCTCCCATACTTTCTTCCACTG 59.532 45.833 0.00 0.00 0.00 3.66
5103 11746 4.168101 TCTCCCATACTTTCTTCCACTGT 58.832 43.478 0.00 0.00 0.00 3.55
5161 13624 0.927537 GAAGTGCGGCCAAACAAAAC 59.072 50.000 2.24 0.00 0.00 2.43
5195 13658 1.296727 GAAACACATAGTAGCGGCCC 58.703 55.000 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 0.744057 TACGTCGATGGGCTACGTCA 60.744 55.000 9.90 0.00 44.34 4.35
64 65 3.243873 GCCAAAGAAAGCTAAAAGTGCCT 60.244 43.478 0.00 0.00 0.00 4.75
124 125 1.142870 CTCCTTCGGGATAATTGGGCA 59.857 52.381 0.00 0.00 44.11 5.36
195 204 0.396435 TGCGGACATTCCTGACAACT 59.604 50.000 0.00 0.00 33.30 3.16
202 211 0.035439 AATTCGGTGCGGACATTCCT 60.035 50.000 9.96 0.00 33.30 3.36
211 220 3.311080 CACCATGAAATTCGGTGCG 57.689 52.632 7.03 0.00 43.43 5.34
424 433 6.056428 GAACTACTCGAGGAGATCTTCTTC 57.944 45.833 31.50 18.14 33.32 2.87
562 577 3.435671 GTGGTCAATCTTGGTAGGAAACG 59.564 47.826 0.00 0.00 0.00 3.60
570 585 3.808728 CCATATCGTGGTCAATCTTGGT 58.191 45.455 0.00 0.00 43.44 3.67
585 600 0.179018 AGCTTTCGGTGGCCCATATC 60.179 55.000 0.00 0.00 0.00 1.63
586 601 0.179018 GAGCTTTCGGTGGCCCATAT 60.179 55.000 0.00 0.00 0.00 1.78
793 1617 9.530129 CGTCAGATTACTAGTTTGATCAAAAAC 57.470 33.333 22.07 11.97 39.80 2.43
794 1618 8.717821 CCGTCAGATTACTAGTTTGATCAAAAA 58.282 33.333 22.07 12.81 31.33 1.94
838 1662 1.527370 CGGACCCTCCATTTCCTCC 59.473 63.158 0.00 0.00 35.91 4.30
872 1962 0.041400 CGTCACCGTACACGTACACA 60.041 55.000 8.02 0.00 35.87 3.72
977 4755 3.393970 CCTCCTGCTCTTCCGGCA 61.394 66.667 0.00 0.00 38.10 5.69
1052 4843 1.796017 GGAAGAGTAAGGGGAGGAGG 58.204 60.000 0.00 0.00 0.00 4.30
1054 4845 0.686769 GCGGAAGAGTAAGGGGAGGA 60.687 60.000 0.00 0.00 0.00 3.71
1060 4851 0.179097 GAGCAGGCGGAAGAGTAAGG 60.179 60.000 0.00 0.00 0.00 2.69
1061 4852 0.820871 AGAGCAGGCGGAAGAGTAAG 59.179 55.000 0.00 0.00 0.00 2.34
1062 4853 2.025155 CTAGAGCAGGCGGAAGAGTAA 58.975 52.381 0.00 0.00 0.00 2.24
1063 4854 1.681538 CTAGAGCAGGCGGAAGAGTA 58.318 55.000 0.00 0.00 0.00 2.59
1064 4855 1.671901 GCTAGAGCAGGCGGAAGAGT 61.672 60.000 0.00 0.00 41.59 3.24
1132 5063 2.805099 GACTGAATCGATGAATCCCTGC 59.195 50.000 0.00 0.00 0.00 4.85
1163 5094 1.536644 AAACCTAGTTCCCCACCCAA 58.463 50.000 0.00 0.00 0.00 4.12
1228 5167 6.039717 TGCTAACAAATTCAGTCAGCTTCTTT 59.960 34.615 7.43 0.00 0.00 2.52
1344 5366 5.005094 CGGGGGTAGTTTTAAATTCACAGA 58.995 41.667 0.00 0.00 0.00 3.41
1365 5387 0.319211 TATTATGCGAAGTCGGCCGG 60.319 55.000 27.83 10.00 40.23 6.13
1366 5388 0.782384 GTATTATGCGAAGTCGGCCG 59.218 55.000 22.12 22.12 40.23 6.13
1367 5389 1.145803 GGTATTATGCGAAGTCGGCC 58.854 55.000 2.47 0.00 40.23 6.13
1368 5390 2.150397 AGGTATTATGCGAAGTCGGC 57.850 50.000 2.47 0.00 40.23 5.54
1373 5395 4.376413 CGCTAGCAAAGGTATTATGCGAAG 60.376 45.833 16.45 0.00 44.60 3.79
1377 5399 3.560068 ACACGCTAGCAAAGGTATTATGC 59.440 43.478 16.45 0.00 40.34 3.14
1616 5834 0.403271 ATGGCTGCCAGTTGACTCTT 59.597 50.000 27.20 3.44 36.75 2.85
1637 5869 9.956720 AAATGTTGTCTTTAATTCAGAAGTCAG 57.043 29.630 0.00 0.00 0.00 3.51
1638 5870 9.734620 CAAATGTTGTCTTTAATTCAGAAGTCA 57.265 29.630 0.00 0.00 0.00 3.41
1639 5871 8.694394 GCAAATGTTGTCTTTAATTCAGAAGTC 58.306 33.333 0.00 0.00 0.00 3.01
1641 5873 8.807667 AGCAAATGTTGTCTTTAATTCAGAAG 57.192 30.769 0.00 0.00 0.00 2.85
1642 5874 9.033481 CAAGCAAATGTTGTCTTTAATTCAGAA 57.967 29.630 0.00 0.00 0.00 3.02
1644 5876 8.356533 ACAAGCAAATGTTGTCTTTAATTCAG 57.643 30.769 0.00 0.00 32.53 3.02
1645 5877 8.715191 AACAAGCAAATGTTGTCTTTAATTCA 57.285 26.923 2.27 0.00 41.78 2.57
1646 5878 8.275632 GGAACAAGCAAATGTTGTCTTTAATTC 58.724 33.333 7.20 0.00 43.31 2.17
1652 6290 5.343307 AAGGAACAAGCAAATGTTGTCTT 57.657 34.783 7.20 7.83 43.31 3.01
1719 6361 7.898309 GCTGTTGTATTTACTAACTGAACATCG 59.102 37.037 0.00 0.00 0.00 3.84
1782 6424 4.899352 ACTCAGCCTGAAAGACAGTAAT 57.101 40.909 0.00 0.00 44.40 1.89
1841 6483 0.108585 AGGCCTTCTTGCAAGAACGA 59.891 50.000 32.86 17.08 39.95 3.85
1962 6604 2.169832 TTCTTTTCGCAGACCTCTGG 57.830 50.000 4.49 0.00 43.94 3.86
1992 6634 2.349886 GTCTATGAGCACAGAAAAGGCG 59.650 50.000 0.00 0.00 0.00 5.52
1999 6641 3.029570 AGCAGATGTCTATGAGCACAGA 58.970 45.455 0.00 0.00 0.00 3.41
2014 6656 4.951715 TCCATATGTGAAAAGCAAGCAGAT 59.048 37.500 1.24 0.00 0.00 2.90
2023 6665 5.125900 TGATTGCCACTCCATATGTGAAAAG 59.874 40.000 1.24 0.00 37.60 2.27
2181 6887 7.313731 TGGTATCACCCTCTTATCCTAAGAAT 58.686 38.462 0.00 0.00 37.50 2.40
2232 6939 6.099341 ACATCCTTGTGTGAAAACTGAAAAC 58.901 36.000 0.00 0.00 33.85 2.43
2233 6940 6.279513 ACATCCTTGTGTGAAAACTGAAAA 57.720 33.333 0.00 0.00 33.85 2.29
2234 6941 5.913137 ACATCCTTGTGTGAAAACTGAAA 57.087 34.783 0.00 0.00 33.85 2.69
2235 6942 5.530915 CCTACATCCTTGTGTGAAAACTGAA 59.469 40.000 0.00 0.00 36.53 3.02
2236 6943 5.063204 CCTACATCCTTGTGTGAAAACTGA 58.937 41.667 0.00 0.00 36.53 3.41
2237 6944 4.821805 ACCTACATCCTTGTGTGAAAACTG 59.178 41.667 0.00 0.00 36.53 3.16
2238 6945 5.048846 ACCTACATCCTTGTGTGAAAACT 57.951 39.130 0.00 0.00 36.53 2.66
2579 7397 6.347725 GCATGTGCCAGTTATACAGTAATAGC 60.348 42.308 0.00 0.00 34.31 2.97
2626 7444 4.524802 ATGCATATCCCCACTGAAGAAA 57.475 40.909 0.00 0.00 0.00 2.52
2674 7492 5.044846 ACCCTGTTAGAGCAGAAATTATGGT 60.045 40.000 0.00 0.00 38.70 3.55
2761 7581 7.839680 AAGGATGTGGAAGTAAAGTTTTGAT 57.160 32.000 0.00 0.00 0.00 2.57
2801 7623 5.185454 TGATGTACAGTCAACCATGGATTC 58.815 41.667 21.47 5.83 0.00 2.52
3001 7827 5.627499 AAACTTCAATATTGCTTCTGCGA 57.373 34.783 10.76 0.00 43.34 5.10
3076 7902 5.740224 GCAGAGCTCTACCTTACATGCATAA 60.740 44.000 17.75 0.00 0.00 1.90
3100 7930 3.450457 TGCAAAATGGGTATAGGGCAAAG 59.550 43.478 0.00 0.00 0.00 2.77
3153 7983 9.300681 TGGCTAATAGAAATTGGAATATCTTGG 57.699 33.333 0.00 0.00 0.00 3.61
3256 8090 0.106521 GCCAGTGCCCAAAACACAAT 59.893 50.000 0.00 0.00 40.59 2.71
3306 8147 8.316640 AGACAAACAATGAAGAGTAGAATCAC 57.683 34.615 0.00 0.00 0.00 3.06
3487 8589 8.313292 AGAATATATTCATCACTCTGAAGCTCC 58.687 37.037 24.00 0.00 38.47 4.70
3544 8647 4.503741 ACAATTCAGTCCATGTTTTCCG 57.496 40.909 0.00 0.00 0.00 4.30
3915 9044 9.221775 GAAACAAGCAACTAATAATATCCAACG 57.778 33.333 0.00 0.00 0.00 4.10
4141 9297 3.415087 GGGGTCAGCTCCATGCCT 61.415 66.667 0.00 0.00 44.23 4.75
4168 9325 2.035632 CTCGATAGTCCCTTGAGGCTT 58.964 52.381 0.00 0.00 34.51 4.35
4386 9558 2.550830 AACTCTTGTGTACTGGCAGG 57.449 50.000 20.34 0.58 0.00 4.85
4387 9559 4.900635 AAAAACTCTTGTGTACTGGCAG 57.099 40.909 14.16 14.16 0.00 4.85
4388 9560 6.761099 TTTAAAAACTCTTGTGTACTGGCA 57.239 33.333 0.00 0.00 0.00 4.92
4389 9561 7.169140 CCATTTTAAAAACTCTTGTGTACTGGC 59.831 37.037 4.44 0.00 0.00 4.85
4390 9562 8.194769 ACCATTTTAAAAACTCTTGTGTACTGG 58.805 33.333 4.44 5.86 0.00 4.00
4429 11058 4.212636 GCTTGAAAAAGCATTTGCAGACAT 59.787 37.500 5.20 0.00 44.85 3.06
4516 11145 4.058817 GCTTGATAATCTCCCGTGTTAGG 58.941 47.826 0.00 0.00 0.00 2.69
4720 11357 4.108673 GGTGACCCCTAGTGACGT 57.891 61.111 0.00 0.00 32.61 4.34
4758 11395 5.398236 TCCCCCTTCTAGAATCATACTGAG 58.602 45.833 5.44 0.00 0.00 3.35
4852 11493 7.118496 TGAAAGTTATGTTTGAAATGGGTGT 57.882 32.000 0.00 0.00 0.00 4.16
5072 11715 6.943899 AGAAAGTATGGGAGAGAGAAAAGT 57.056 37.500 0.00 0.00 0.00 2.66
5076 11719 5.187967 GTGGAAGAAAGTATGGGAGAGAGAA 59.812 44.000 0.00 0.00 0.00 2.87
5078 11721 4.714308 AGTGGAAGAAAGTATGGGAGAGAG 59.286 45.833 0.00 0.00 0.00 3.20
5079 11722 4.467795 CAGTGGAAGAAAGTATGGGAGAGA 59.532 45.833 0.00 0.00 0.00 3.10
5080 11723 4.223923 ACAGTGGAAGAAAGTATGGGAGAG 59.776 45.833 0.00 0.00 0.00 3.20
5082 11725 4.559862 ACAGTGGAAGAAAGTATGGGAG 57.440 45.455 0.00 0.00 0.00 4.30
5083 11726 5.091552 ACTACAGTGGAAGAAAGTATGGGA 58.908 41.667 0.00 0.00 0.00 4.37
5085 11728 8.883731 CAATTACTACAGTGGAAGAAAGTATGG 58.116 37.037 0.00 0.00 0.00 2.74
5086 11729 9.653287 TCAATTACTACAGTGGAAGAAAGTATG 57.347 33.333 0.00 0.00 0.00 2.39
5087 11730 9.877178 CTCAATTACTACAGTGGAAGAAAGTAT 57.123 33.333 0.00 0.00 0.00 2.12
5088 11731 8.311836 CCTCAATTACTACAGTGGAAGAAAGTA 58.688 37.037 0.00 0.00 0.00 2.24
5089 11732 7.016268 TCCTCAATTACTACAGTGGAAGAAAGT 59.984 37.037 0.00 0.00 0.00 2.66
5092 11735 6.070767 CCTCCTCAATTACTACAGTGGAAGAA 60.071 42.308 0.00 0.00 0.00 2.52
5094 11737 5.395768 CCCTCCTCAATTACTACAGTGGAAG 60.396 48.000 0.00 0.00 0.00 3.46
5095 11738 4.469945 CCCTCCTCAATTACTACAGTGGAA 59.530 45.833 0.00 0.00 0.00 3.53
5098 11741 3.432326 GCCCCTCCTCAATTACTACAGTG 60.432 52.174 0.00 0.00 0.00 3.66
5099 11742 2.772515 GCCCCTCCTCAATTACTACAGT 59.227 50.000 0.00 0.00 0.00 3.55
5100 11743 2.771943 TGCCCCTCCTCAATTACTACAG 59.228 50.000 0.00 0.00 0.00 2.74
5101 11744 2.840511 TGCCCCTCCTCAATTACTACA 58.159 47.619 0.00 0.00 0.00 2.74
5102 11745 3.433740 CCTTGCCCCTCCTCAATTACTAC 60.434 52.174 0.00 0.00 0.00 2.73
5103 11746 2.777692 CCTTGCCCCTCCTCAATTACTA 59.222 50.000 0.00 0.00 0.00 1.82
5143 13453 0.534873 AGTTTTGTTTGGCCGCACTT 59.465 45.000 0.00 0.00 0.00 3.16
5146 13456 0.247736 AACAGTTTTGTTTGGCCGCA 59.752 45.000 0.00 0.00 45.01 5.69
5161 13624 5.733226 TGTGTTTCAGTCATGTACAACAG 57.267 39.130 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.