Multiple sequence alignment - TraesCS6D01G016400

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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 TraesCS6D01G016400 chr6D 100.000 5607 0 0 1 5607 6823143 6828749 0.000000e+00 10355
1 TraesCS6D01G016400 chr6D 88.314 2242 204 43 1505 3730 360751653 360749454 0.000000e+00 2636
2 TraesCS6D01G016400 chr6D 97.861 187 4 0 5421 5607 106037245 106037431 1.950000e-84 324
3 TraesCS6D01G016400 chr6D 97.861 187 4 0 5421 5607 132900034 132900220 1.950000e-84 324
4 TraesCS6D01G016400 chr6D 97.861 187 4 0 5421 5607 453891079 453890893 1.950000e-84 324
5 TraesCS6D01G016400 chr6D 97.326 187 5 0 5421 5607 189904787 189904601 9.060000e-83 318
6 TraesCS6D01G016400 chr5A 95.993 5441 183 19 1 5421 553300544 553295119 0.000000e+00 8807
7 TraesCS6D01G016400 chr5A 89.238 446 47 1 4978 5423 370095082 370095526 1.760000e-154 556
8 TraesCS6D01G016400 chr7A 95.198 5435 214 21 1 5423 527904817 527910216 0.000000e+00 8547
9 TraesCS6D01G016400 chr7A 87.071 3759 402 40 1 3730 461485747 461482044 0.000000e+00 4172
10 TraesCS6D01G016400 chr7A 96.930 2215 57 5 1489 3695 270889778 270887567 0.000000e+00 3703
11 TraesCS6D01G016400 chr7A 94.825 1739 71 9 3693 5421 270883623 270881894 0.000000e+00 2695
12 TraesCS6D01G016400 chr7A 96.291 1510 48 4 1 1503 270891312 270889804 0.000000e+00 2471
13 TraesCS6D01G016400 chr7A 97.671 730 15 2 2886 3614 734698272 734699000 0.000000e+00 1253
14 TraesCS6D01G016400 chr7A 82.016 1012 116 30 4054 5015 622252617 622253612 0.000000e+00 800
15 TraesCS6D01G016400 chr2D 98.136 3327 42 6 1 3319 12731587 12728273 0.000000e+00 5782
16 TraesCS6D01G016400 chr2D 98.929 2054 22 0 3368 5421 12728279 12726226 0.000000e+00 3672
17 TraesCS6D01G016400 chr2D 97.279 1911 47 3 1582 3489 649294990 649296898 0.000000e+00 3236
18 TraesCS6D01G016400 chr2D 83.217 1001 114 21 4054 5016 417245710 417244726 0.000000e+00 869
19 TraesCS6D01G016400 chr3D 90.072 3767 273 49 1499 5196 573207412 573211146 0.000000e+00 4791
20 TraesCS6D01G016400 chr7D 88.303 3753 370 47 1 3730 346629938 346626232 0.000000e+00 4434
21 TraesCS6D01G016400 chr7D 83.249 991 128 17 4054 5016 608289855 608288875 0.000000e+00 876
22 TraesCS6D01G016400 chr2A 88.615 2187 207 31 1560 3730 171836744 171838904 0.000000e+00 2621
23 TraesCS6D01G016400 chr2B 88.564 2186 208 32 1560 3730 93122633 93124791 0.000000e+00 2614
24 TraesCS6D01G016400 chr2B 84.990 1479 159 27 3966 5400 726916038 726914579 0.000000e+00 1443
25 TraesCS6D01G016400 chr2B 83.629 1185 138 31 2778 3940 726917175 726916025 0.000000e+00 1062
26 TraesCS6D01G016400 chr4B 90.209 1481 137 6 1 1474 622887767 622886288 0.000000e+00 1925
27 TraesCS6D01G016400 chr4B 89.932 1480 141 6 1 1474 445327872 445329349 0.000000e+00 1901
28 TraesCS6D01G016400 chr3B 90.135 1480 139 5 1 1474 777040625 777039147 0.000000e+00 1917
29 TraesCS6D01G016400 chr6A 89.744 1482 142 7 1 1474 46108757 46110236 0.000000e+00 1886
30 TraesCS6D01G016400 chr6A 89.683 1483 142 8 1 1474 46139673 46141153 0.000000e+00 1881
31 TraesCS6D01G016400 chr3A 85.027 1496 170 29 3966 5421 352091206 352092687 0.000000e+00 1472
32 TraesCS6D01G016400 chr3A 88.686 1043 83 18 3625 4645 707859050 707860079 0.000000e+00 1240
33 TraesCS6D01G016400 chr3A 85.485 1123 143 13 4302 5422 554370181 554371285 0.000000e+00 1153
34 TraesCS6D01G016400 chr3A 83.398 1036 126 18 4382 5416 163166438 163165448 0.000000e+00 918
35 TraesCS6D01G016400 chr3A 81.682 333 33 6 3636 3940 163167356 163167024 9.320000e-63 252
36 TraesCS6D01G016400 chr4D 98.396 187 3 0 5421 5607 307310412 307310226 4.190000e-86 329
37 TraesCS6D01G016400 chr4D 97.861 187 4 0 5421 5607 12684603 12684789 1.950000e-84 324
38 TraesCS6D01G016400 chr4D 97.326 187 5 0 5421 5607 13849532 13849718 9.060000e-83 318
39 TraesCS6D01G016400 chr4D 97.326 187 5 0 5421 5607 350392802 350392616 9.060000e-83 318
40 TraesCS6D01G016400 chr4D 97.326 187 5 0 5421 5607 423586884 423587070 9.060000e-83 318


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 TraesCS6D01G016400 chr6D 6823143 6828749 5606 False 10355.000000 10355 100.000000 1 5607 1 chr6D.!!$F1 5606
1 TraesCS6D01G016400 chr6D 360749454 360751653 2199 True 2636.000000 2636 88.314000 1505 3730 1 chr6D.!!$R2 2225
2 TraesCS6D01G016400 chr5A 553295119 553300544 5425 True 8807.000000 8807 95.993000 1 5421 1 chr5A.!!$R1 5420
3 TraesCS6D01G016400 chr7A 527904817 527910216 5399 False 8547.000000 8547 95.198000 1 5423 1 chr7A.!!$F1 5422
4 TraesCS6D01G016400 chr7A 461482044 461485747 3703 True 4172.000000 4172 87.071000 1 3730 1 chr7A.!!$R1 3729
5 TraesCS6D01G016400 chr7A 270881894 270891312 9418 True 2956.333333 3703 96.015333 1 5421 3 chr7A.!!$R2 5420
6 TraesCS6D01G016400 chr7A 734698272 734699000 728 False 1253.000000 1253 97.671000 2886 3614 1 chr7A.!!$F3 728
7 TraesCS6D01G016400 chr7A 622252617 622253612 995 False 800.000000 800 82.016000 4054 5015 1 chr7A.!!$F2 961
8 TraesCS6D01G016400 chr2D 12726226 12731587 5361 True 4727.000000 5782 98.532500 1 5421 2 chr2D.!!$R2 5420
9 TraesCS6D01G016400 chr2D 649294990 649296898 1908 False 3236.000000 3236 97.279000 1582 3489 1 chr2D.!!$F1 1907
10 TraesCS6D01G016400 chr2D 417244726 417245710 984 True 869.000000 869 83.217000 4054 5016 1 chr2D.!!$R1 962
11 TraesCS6D01G016400 chr3D 573207412 573211146 3734 False 4791.000000 4791 90.072000 1499 5196 1 chr3D.!!$F1 3697
12 TraesCS6D01G016400 chr7D 346626232 346629938 3706 True 4434.000000 4434 88.303000 1 3730 1 chr7D.!!$R1 3729
13 TraesCS6D01G016400 chr7D 608288875 608289855 980 True 876.000000 876 83.249000 4054 5016 1 chr7D.!!$R2 962
14 TraesCS6D01G016400 chr2A 171836744 171838904 2160 False 2621.000000 2621 88.615000 1560 3730 1 chr2A.!!$F1 2170
15 TraesCS6D01G016400 chr2B 93122633 93124791 2158 False 2614.000000 2614 88.564000 1560 3730 1 chr2B.!!$F1 2170
16 TraesCS6D01G016400 chr2B 726914579 726917175 2596 True 1252.500000 1443 84.309500 2778 5400 2 chr2B.!!$R1 2622
17 TraesCS6D01G016400 chr4B 622886288 622887767 1479 True 1925.000000 1925 90.209000 1 1474 1 chr4B.!!$R1 1473
18 TraesCS6D01G016400 chr4B 445327872 445329349 1477 False 1901.000000 1901 89.932000 1 1474 1 chr4B.!!$F1 1473
19 TraesCS6D01G016400 chr3B 777039147 777040625 1478 True 1917.000000 1917 90.135000 1 1474 1 chr3B.!!$R1 1473
20 TraesCS6D01G016400 chr6A 46108757 46110236 1479 False 1886.000000 1886 89.744000 1 1474 1 chr6A.!!$F1 1473
21 TraesCS6D01G016400 chr6A 46139673 46141153 1480 False 1881.000000 1881 89.683000 1 1474 1 chr6A.!!$F2 1473
22 TraesCS6D01G016400 chr3A 352091206 352092687 1481 False 1472.000000 1472 85.027000 3966 5421 1 chr3A.!!$F1 1455
23 TraesCS6D01G016400 chr3A 707859050 707860079 1029 False 1240.000000 1240 88.686000 3625 4645 1 chr3A.!!$F3 1020
24 TraesCS6D01G016400 chr3A 554370181 554371285 1104 False 1153.000000 1153 85.485000 4302 5422 1 chr3A.!!$F2 1120
25 TraesCS6D01G016400 chr3A 163165448 163167356 1908 True 585.000000 918 82.540000 3636 5416 2 chr3A.!!$R1 1780

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
492 494 2.158769 TGAGTCTGCTGAGCCAAGAAAA 60.159 45.455 0.23 0.00 0.00 2.29 F
1313 1329 0.525455 CGCTCGTGATCCATCAACGA 60.525 55.000 5.28 5.28 38.75 3.85 F
1349 1365 1.300931 CGGCAGATGTATCCACCGG 60.301 63.158 0.00 0.00 40.24 5.28 F
2791 2877 3.713248 TGAGTGGATAGGATTGTGCTGAT 59.287 43.478 0.00 0.00 0.00 2.90 F
4423 8744 1.920835 GGGAAGCAGGACTGGAGGT 60.921 63.158 1.01 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1833 1.902508 TGAAACACTGCCAAAAACCCA 59.097 42.857 0.0 0.0 0.00 4.51 R
2815 2901 1.064825 GTCCACTCCCCCTTTCTCAA 58.935 55.000 0.0 0.0 0.00 3.02 R
2934 3022 8.697507 TCTGATGTAGACTGTGTATCATACAT 57.302 34.615 0.0 0.0 41.34 2.29 R
4481 8802 1.144057 GACCACCCTCGCCATAGTG 59.856 63.158 0.0 0.0 0.00 2.74 R
5569 9949 0.106708 TATGAGCATCCAGGTTCCGC 59.893 55.000 0.0 0.0 0.00 5.54 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
128 130 7.761249 GGAAATAATCAAATTGTCCTTCACAGG 59.239 37.037 0.00 0.00 42.50 4.00
178 180 4.023279 TCAAATGTCGTTGGTTTGATCCTG 60.023 41.667 0.00 0.00 37.05 3.86
250 252 6.635030 AGTCTTCAAGGCTTCGTAATTTTT 57.365 33.333 0.00 0.00 0.00 1.94
345 347 2.439880 TGATTGGAGGGTTGTGTACACA 59.560 45.455 24.62 24.62 39.98 3.72
433 435 9.965902 ATGAATATTTCCAAGAAGTTAGTCAGT 57.034 29.630 0.00 0.00 0.00 3.41
492 494 2.158769 TGAGTCTGCTGAGCCAAGAAAA 60.159 45.455 0.23 0.00 0.00 2.29
1046 1057 0.618680 TCAGTGCCTAGGCTGGACAT 60.619 55.000 33.07 11.20 42.51 3.06
1212 1226 8.614346 GGCGTGTAAGTATTAAATATTCCAACA 58.386 33.333 0.00 0.00 28.70 3.33
1313 1329 0.525455 CGCTCGTGATCCATCAACGA 60.525 55.000 5.28 5.28 38.75 3.85
1349 1365 1.300931 CGGCAGATGTATCCACCGG 60.301 63.158 0.00 0.00 40.24 5.28
1709 1771 5.796424 ATGAAGTGTTGGAAGCTTTGATT 57.204 34.783 0.00 0.00 0.00 2.57
2407 2490 6.860080 AGCTCATTTTAACCATCATGACAAG 58.140 36.000 0.00 0.00 0.00 3.16
2791 2877 3.713248 TGAGTGGATAGGATTGTGCTGAT 59.287 43.478 0.00 0.00 0.00 2.90
2815 2901 9.224267 GATATGCTGATGTTTATAGTCATTGGT 57.776 33.333 0.00 0.00 0.00 3.67
2934 3022 9.031537 TGGAACTATTAAGTGATGTGTCTTCTA 57.968 33.333 0.00 0.00 35.62 2.10
3855 7963 6.341316 TGACGCTTGCTATCTCTTAAAGATT 58.659 36.000 5.76 0.00 42.30 2.40
4210 8365 2.190488 CTTGGACAGTCCCTCCTGCC 62.190 65.000 17.59 0.00 35.03 4.85
4423 8744 1.920835 GGGAAGCAGGACTGGAGGT 60.921 63.158 1.01 0.00 0.00 3.85
4481 8802 1.005156 GGCAGCGAGGGAGATGATC 60.005 63.158 0.00 0.00 0.00 2.92
4542 8863 5.722290 TGATTACTATGGTGGTGAGGGATA 58.278 41.667 0.00 0.00 0.00 2.59
4543 8864 6.331032 TGATTACTATGGTGGTGAGGGATAT 58.669 40.000 0.00 0.00 0.00 1.63
4544 8865 7.483881 TGATTACTATGGTGGTGAGGGATATA 58.516 38.462 0.00 0.00 0.00 0.86
4988 9367 7.383843 GGTGAATTCATAAATTGACGGTGTTTT 59.616 33.333 12.12 0.00 39.16 2.43
5120 9499 7.357043 CGAATGTACCGTCGACTATTATGAAAC 60.357 40.741 14.70 0.00 39.64 2.78
5338 9717 0.818296 GAGATGGCCGACAGTGTACT 59.182 55.000 0.00 0.00 0.00 2.73
5435 9815 4.035843 GTGATCTCACCCGGGACT 57.964 61.111 32.02 1.07 40.85 3.85
5436 9816 1.817209 GTGATCTCACCCGGGACTC 59.183 63.158 32.02 15.73 40.85 3.36
5437 9817 1.381327 TGATCTCACCCGGGACTCC 60.381 63.158 32.02 11.34 0.00 3.85
5457 9837 3.770263 CGAACTACCTTCGGTACATCA 57.230 47.619 0.00 0.00 46.85 3.07
5458 9838 4.100707 CGAACTACCTTCGGTACATCAA 57.899 45.455 0.00 0.00 46.85 2.57
5459 9839 4.487948 CGAACTACCTTCGGTACATCAAA 58.512 43.478 0.00 0.00 46.85 2.69
5460 9840 5.107133 CGAACTACCTTCGGTACATCAAAT 58.893 41.667 0.00 0.00 46.85 2.32
5461 9841 5.231568 CGAACTACCTTCGGTACATCAAATC 59.768 44.000 0.00 0.00 46.85 2.17
5462 9842 5.670792 ACTACCTTCGGTACATCAAATCA 57.329 39.130 0.00 0.00 37.09 2.57
5463 9843 5.416947 ACTACCTTCGGTACATCAAATCAC 58.583 41.667 0.00 0.00 37.09 3.06
5464 9844 4.280436 ACCTTCGGTACATCAAATCACA 57.720 40.909 0.00 0.00 32.11 3.58
5465 9845 4.843728 ACCTTCGGTACATCAAATCACAT 58.156 39.130 0.00 0.00 32.11 3.21
5466 9846 5.984725 ACCTTCGGTACATCAAATCACATA 58.015 37.500 0.00 0.00 32.11 2.29
5467 9847 6.411376 ACCTTCGGTACATCAAATCACATAA 58.589 36.000 0.00 0.00 32.11 1.90
5468 9848 6.882140 ACCTTCGGTACATCAAATCACATAAA 59.118 34.615 0.00 0.00 32.11 1.40
5469 9849 7.148306 ACCTTCGGTACATCAAATCACATAAAC 60.148 37.037 0.00 0.00 32.11 2.01
5470 9850 7.065803 CCTTCGGTACATCAAATCACATAAACT 59.934 37.037 0.00 0.00 0.00 2.66
5471 9851 7.534085 TCGGTACATCAAATCACATAAACTC 57.466 36.000 0.00 0.00 0.00 3.01
5472 9852 7.100409 TCGGTACATCAAATCACATAAACTCA 58.900 34.615 0.00 0.00 0.00 3.41
5473 9853 7.768582 TCGGTACATCAAATCACATAAACTCAT 59.231 33.333 0.00 0.00 0.00 2.90
5474 9854 9.040939 CGGTACATCAAATCACATAAACTCATA 57.959 33.333 0.00 0.00 0.00 2.15
5481 9861 9.825109 TCAAATCACATAAACTCATAATACCGA 57.175 29.630 0.00 0.00 0.00 4.69
5482 9862 9.864034 CAAATCACATAAACTCATAATACCGAC 57.136 33.333 0.00 0.00 0.00 4.79
5483 9863 8.603242 AATCACATAAACTCATAATACCGACC 57.397 34.615 0.00 0.00 0.00 4.79
5484 9864 6.210796 TCACATAAACTCATAATACCGACCG 58.789 40.000 0.00 0.00 0.00 4.79
5485 9865 5.981315 CACATAAACTCATAATACCGACCGT 59.019 40.000 0.00 0.00 0.00 4.83
5486 9866 6.143438 CACATAAACTCATAATACCGACCGTC 59.857 42.308 0.00 0.00 0.00 4.79
5487 9867 4.724074 AAACTCATAATACCGACCGTCA 57.276 40.909 0.00 0.00 0.00 4.35
5488 9868 3.705043 ACTCATAATACCGACCGTCAC 57.295 47.619 0.00 0.00 0.00 3.67
5489 9869 2.360165 ACTCATAATACCGACCGTCACC 59.640 50.000 0.00 0.00 0.00 4.02
5490 9870 1.334556 TCATAATACCGACCGTCACCG 59.665 52.381 0.00 0.00 0.00 4.94
5491 9871 1.334556 CATAATACCGACCGTCACCGA 59.665 52.381 0.00 0.00 35.63 4.69
5492 9872 1.458398 TAATACCGACCGTCACCGAA 58.542 50.000 0.00 0.00 35.63 4.30
5493 9873 0.109132 AATACCGACCGTCACCGAAC 60.109 55.000 0.00 0.00 35.63 3.95
5494 9874 0.962356 ATACCGACCGTCACCGAACT 60.962 55.000 0.00 0.00 35.63 3.01
5495 9875 1.172180 TACCGACCGTCACCGAACTT 61.172 55.000 0.00 0.00 35.63 2.66
5496 9876 1.300388 CCGACCGTCACCGAACTTT 60.300 57.895 0.00 0.00 35.63 2.66
5497 9877 0.039256 CCGACCGTCACCGAACTTTA 60.039 55.000 0.00 0.00 35.63 1.85
5498 9878 1.602668 CCGACCGTCACCGAACTTTAA 60.603 52.381 0.00 0.00 35.63 1.52
5499 9879 1.717645 CGACCGTCACCGAACTTTAAG 59.282 52.381 0.00 0.00 35.63 1.85
5500 9880 1.458445 GACCGTCACCGAACTTTAAGC 59.542 52.381 0.00 0.00 35.63 3.09
5501 9881 0.437295 CCGTCACCGAACTTTAAGCG 59.563 55.000 0.00 0.00 35.63 4.68
5502 9882 1.134226 CGTCACCGAACTTTAAGCGT 58.866 50.000 0.00 0.00 35.63 5.07
5503 9883 1.136721 CGTCACCGAACTTTAAGCGTG 60.137 52.381 0.00 0.00 35.63 5.34
5504 9884 0.863144 TCACCGAACTTTAAGCGTGC 59.137 50.000 0.00 0.00 0.00 5.34
5505 9885 0.450482 CACCGAACTTTAAGCGTGCG 60.450 55.000 0.00 1.50 33.23 5.34
5506 9886 1.131826 CCGAACTTTAAGCGTGCGG 59.868 57.895 10.80 10.80 46.22 5.69
5507 9887 2.146954 CGAACTTTAAGCGTGCGGA 58.853 52.632 0.00 0.00 29.82 5.54
5508 9888 0.179258 CGAACTTTAAGCGTGCGGAC 60.179 55.000 0.00 0.00 29.82 4.79
5509 9889 0.165295 GAACTTTAAGCGTGCGGACC 59.835 55.000 0.00 0.00 0.00 4.46
5510 9890 1.232621 AACTTTAAGCGTGCGGACCC 61.233 55.000 0.00 0.00 0.00 4.46
5511 9891 1.375523 CTTTAAGCGTGCGGACCCT 60.376 57.895 0.00 0.00 0.00 4.34
5512 9892 0.108520 CTTTAAGCGTGCGGACCCTA 60.109 55.000 0.00 0.00 0.00 3.53
5513 9893 0.390209 TTTAAGCGTGCGGACCCTAC 60.390 55.000 0.00 0.00 0.00 3.18
5514 9894 2.546645 TTAAGCGTGCGGACCCTACG 62.547 60.000 0.00 10.04 40.52 3.51
5526 9906 2.576298 CCCTACGGGTTCGAGAACT 58.424 57.895 14.62 0.00 40.94 3.01
5527 9907 1.755179 CCCTACGGGTTCGAGAACTA 58.245 55.000 14.62 0.70 40.94 2.24
5528 9908 2.305009 CCCTACGGGTTCGAGAACTAT 58.695 52.381 14.62 4.68 40.94 2.12
5529 9909 2.034305 CCCTACGGGTTCGAGAACTATG 59.966 54.545 14.62 8.07 40.94 2.23
5530 9910 2.686915 CCTACGGGTTCGAGAACTATGT 59.313 50.000 14.62 12.47 40.94 2.29
5531 9911 3.879295 CCTACGGGTTCGAGAACTATGTA 59.121 47.826 14.62 12.83 40.94 2.29
5532 9912 4.024218 CCTACGGGTTCGAGAACTATGTAG 60.024 50.000 21.42 21.42 40.94 2.74
5533 9913 3.614092 ACGGGTTCGAGAACTATGTAGA 58.386 45.455 14.62 0.00 40.94 2.59
5534 9914 3.376546 ACGGGTTCGAGAACTATGTAGAC 59.623 47.826 14.62 0.00 40.94 2.59
5535 9915 3.376234 CGGGTTCGAGAACTATGTAGACA 59.624 47.826 14.62 0.00 40.94 3.41
5536 9916 4.036498 CGGGTTCGAGAACTATGTAGACAT 59.964 45.833 14.62 0.08 40.94 3.06
5537 9917 5.282510 GGGTTCGAGAACTATGTAGACATG 58.717 45.833 14.62 0.00 40.94 3.21
5538 9918 5.067413 GGGTTCGAGAACTATGTAGACATGA 59.933 44.000 14.62 0.00 40.94 3.07
5539 9919 5.972382 GGTTCGAGAACTATGTAGACATGAC 59.028 44.000 14.62 0.00 40.94 3.06
5540 9920 5.752892 TCGAGAACTATGTAGACATGACC 57.247 43.478 0.00 0.00 37.15 4.02
5541 9921 4.272748 TCGAGAACTATGTAGACATGACCG 59.727 45.833 0.00 1.67 37.15 4.79
5542 9922 4.272748 CGAGAACTATGTAGACATGACCGA 59.727 45.833 0.00 0.00 37.15 4.69
5543 9923 5.559225 CGAGAACTATGTAGACATGACCGAG 60.559 48.000 0.00 0.00 37.15 4.63
5544 9924 5.437946 AGAACTATGTAGACATGACCGAGA 58.562 41.667 0.00 0.00 37.15 4.04
5545 9925 5.297278 AGAACTATGTAGACATGACCGAGAC 59.703 44.000 0.00 0.00 37.15 3.36
5546 9926 4.524053 ACTATGTAGACATGACCGAGACA 58.476 43.478 0.00 0.00 37.15 3.41
5547 9927 3.784701 ATGTAGACATGACCGAGACAC 57.215 47.619 0.00 0.00 34.83 3.67
5548 9928 1.467342 TGTAGACATGACCGAGACACG 59.533 52.381 0.00 0.00 42.18 4.49
5549 9929 1.467734 GTAGACATGACCGAGACACGT 59.532 52.381 0.00 0.00 40.78 4.49
5550 9930 0.522180 AGACATGACCGAGACACGTC 59.478 55.000 0.00 0.00 40.78 4.34
5551 9931 0.522180 GACATGACCGAGACACGTCT 59.478 55.000 0.00 0.00 43.78 4.18
5552 9932 0.959553 ACATGACCGAGACACGTCTT 59.040 50.000 0.00 0.00 40.61 3.01
5553 9933 1.068472 ACATGACCGAGACACGTCTTC 60.068 52.381 0.00 0.00 40.61 2.87
5554 9934 0.168348 ATGACCGAGACACGTCTTCG 59.832 55.000 0.38 6.61 40.61 3.79
5555 9935 1.154263 GACCGAGACACGTCTTCGG 60.154 63.158 23.02 23.02 46.21 4.30
5556 9936 2.952245 CCGAGACACGTCTTCGGT 59.048 61.111 18.73 0.00 41.27 4.69
5557 9937 1.285023 CCGAGACACGTCTTCGGTT 59.715 57.895 18.73 0.00 41.27 4.44
5558 9938 0.518636 CCGAGACACGTCTTCGGTTA 59.481 55.000 18.73 0.00 41.27 2.85
5559 9939 1.069022 CCGAGACACGTCTTCGGTTAA 60.069 52.381 18.73 0.00 41.27 2.01
5560 9940 2.415090 CCGAGACACGTCTTCGGTTAAT 60.415 50.000 18.73 0.00 41.27 1.40
5561 9941 3.181507 CCGAGACACGTCTTCGGTTAATA 60.182 47.826 18.73 0.00 41.27 0.98
5562 9942 4.406069 CGAGACACGTCTTCGGTTAATAA 58.594 43.478 0.38 0.00 40.61 1.40
5563 9943 4.261581 CGAGACACGTCTTCGGTTAATAAC 59.738 45.833 0.38 0.00 40.61 1.89
5564 9944 4.488879 AGACACGTCTTCGGTTAATAACC 58.511 43.478 12.02 12.02 41.86 2.85
5565 9945 4.022068 AGACACGTCTTCGGTTAATAACCA 60.022 41.667 20.78 6.61 44.03 3.67
5566 9946 5.509501 AGACACGTCTTCGGTTAATAACCAA 60.510 40.000 20.78 12.96 44.03 3.67
5567 9947 6.795287 AGACACGTCTTCGGTTAATAACCAAT 60.795 38.462 20.78 0.79 44.03 3.16
5568 9948 7.577426 AGACACGTCTTCGGTTAATAACCAATA 60.577 37.037 20.78 4.17 44.03 1.90
5578 9958 6.056428 GTTAATAACCAATAGCGGAACCTG 57.944 41.667 0.00 0.00 0.00 4.00
5579 9959 2.702592 TAACCAATAGCGGAACCTGG 57.297 50.000 0.00 0.00 0.00 4.45
5580 9960 0.988832 AACCAATAGCGGAACCTGGA 59.011 50.000 0.00 0.00 0.00 3.86
5581 9961 1.213296 ACCAATAGCGGAACCTGGAT 58.787 50.000 0.00 0.00 0.00 3.41
5582 9962 1.134098 ACCAATAGCGGAACCTGGATG 60.134 52.381 0.00 0.00 0.00 3.51
5583 9963 0.947244 CAATAGCGGAACCTGGATGC 59.053 55.000 0.00 0.00 0.00 3.91
5584 9964 0.839946 AATAGCGGAACCTGGATGCT 59.160 50.000 0.00 6.34 39.59 3.79
5585 9965 0.394565 ATAGCGGAACCTGGATGCTC 59.605 55.000 0.00 0.00 37.12 4.26
5586 9966 0.975556 TAGCGGAACCTGGATGCTCA 60.976 55.000 0.00 0.00 37.12 4.26
5587 9967 1.153086 GCGGAACCTGGATGCTCAT 60.153 57.895 0.00 0.00 0.00 2.90
5588 9968 0.106708 GCGGAACCTGGATGCTCATA 59.893 55.000 0.00 0.00 0.00 2.15
5589 9969 1.271054 GCGGAACCTGGATGCTCATAT 60.271 52.381 0.00 0.00 0.00 1.78
5590 9970 2.811873 GCGGAACCTGGATGCTCATATT 60.812 50.000 0.00 0.00 0.00 1.28
5591 9971 2.810274 CGGAACCTGGATGCTCATATTG 59.190 50.000 0.00 0.00 0.00 1.90
5592 9972 3.152341 GGAACCTGGATGCTCATATTGG 58.848 50.000 0.00 0.00 0.00 3.16
5593 9973 2.283145 ACCTGGATGCTCATATTGGC 57.717 50.000 0.00 0.00 0.00 4.52
5594 9974 1.779092 ACCTGGATGCTCATATTGGCT 59.221 47.619 0.00 0.00 0.00 4.75
5595 9975 2.224719 ACCTGGATGCTCATATTGGCTC 60.225 50.000 0.00 0.00 0.00 4.70
5596 9976 2.434428 CTGGATGCTCATATTGGCTCC 58.566 52.381 0.00 0.00 0.00 4.70
5597 9977 1.074405 TGGATGCTCATATTGGCTCCC 59.926 52.381 0.00 0.00 0.00 4.30
5598 9978 1.074405 GGATGCTCATATTGGCTCCCA 59.926 52.381 0.00 0.00 0.00 4.37
5599 9979 2.157738 GATGCTCATATTGGCTCCCAC 58.842 52.381 0.00 0.00 30.78 4.61
5600 9980 0.918258 TGCTCATATTGGCTCCCACA 59.082 50.000 0.00 0.00 30.78 4.17
5601 9981 1.496001 TGCTCATATTGGCTCCCACAT 59.504 47.619 0.00 0.00 30.78 3.21
5602 9982 2.710471 TGCTCATATTGGCTCCCACATA 59.290 45.455 0.00 0.00 30.78 2.29
5603 9983 3.331591 TGCTCATATTGGCTCCCACATAT 59.668 43.478 0.00 0.00 30.78 1.78
5604 9984 4.202599 TGCTCATATTGGCTCCCACATATT 60.203 41.667 0.00 0.00 30.78 1.28
5605 9985 4.397417 GCTCATATTGGCTCCCACATATTC 59.603 45.833 0.00 0.00 30.78 1.75
5606 9986 5.805751 GCTCATATTGGCTCCCACATATTCT 60.806 44.000 0.00 0.00 30.78 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 130 7.824779 AGAGTACCATCTCAATTTTTCTACCAC 59.175 37.037 0.00 0.00 36.97 4.16
178 180 3.740832 GCATTTGGCTTCACACCTTTTAC 59.259 43.478 0.00 0.00 40.25 2.01
227 229 6.635030 AAAAATTACGAAGCCTTGAAGACT 57.365 33.333 0.00 0.00 0.00 3.24
250 252 1.824230 GTGAGCCATGGCAAATGGTTA 59.176 47.619 37.18 10.69 44.88 2.85
286 288 6.582636 TCGAGGATGCATACTTCAAGTAATT 58.417 36.000 14.07 0.00 33.89 1.40
345 347 1.590147 GCTGCTGCTTGGCTGAATT 59.410 52.632 8.53 0.00 36.03 2.17
433 435 6.488683 CCAACATCTACAGAAAAACTACCCAA 59.511 38.462 0.00 0.00 0.00 4.12
467 469 0.535797 TGGCTCAGCAGACTCATCAG 59.464 55.000 0.00 0.00 0.00 2.90
492 494 4.161754 TCAAGCATCACATCATCTGACTCT 59.838 41.667 0.00 0.00 0.00 3.24
1212 1226 6.434028 TGAATATTGCTCCAACAAGTAAAGCT 59.566 34.615 0.00 0.00 34.11 3.74
1624 1686 7.227049 CAAAGAATTGTAACTACCACCCATT 57.773 36.000 0.00 0.00 0.00 3.16
1768 1833 1.902508 TGAAACACTGCCAAAAACCCA 59.097 42.857 0.00 0.00 0.00 4.51
1769 1834 2.682155 TGAAACACTGCCAAAAACCC 57.318 45.000 0.00 0.00 0.00 4.11
2407 2490 8.844441 TGTAAACTAAAGTGTTGTGCAAATAC 57.156 30.769 0.00 0.00 0.00 1.89
2791 2877 8.839343 CAACCAATGACTATAAACATCAGCATA 58.161 33.333 0.00 0.00 0.00 3.14
2815 2901 1.064825 GTCCACTCCCCCTTTCTCAA 58.935 55.000 0.00 0.00 0.00 3.02
2934 3022 8.697507 TCTGATGTAGACTGTGTATCATACAT 57.302 34.615 0.00 0.00 41.34 2.29
3777 7874 5.010314 ACAGATGTGCATGTGATCTTGTTTT 59.990 36.000 14.88 0.00 35.83 2.43
3855 7963 4.895668 TGATCATGAGCATGTATGGCTA 57.104 40.909 10.16 0.00 42.78 3.93
4074 8189 5.531122 TGGCTAGTTCGAGCATATAACTT 57.469 39.130 1.01 0.00 44.76 2.66
4210 8365 6.615088 AGATTTTCACAGGAAACATGAATCG 58.385 36.000 0.00 0.00 42.48 3.34
4481 8802 1.144057 GACCACCCTCGCCATAGTG 59.856 63.158 0.00 0.00 0.00 2.74
4988 9367 2.512896 ACCTATTAGTCGAGGGGTGAGA 59.487 50.000 0.00 0.00 37.14 3.27
5120 9499 2.102588 ACGGTTATTGATTCTCCTCGGG 59.897 50.000 0.00 0.00 0.00 5.14
5338 9717 5.863397 CCGTCAACTATTACTAAAACCGACA 59.137 40.000 0.00 0.00 0.00 4.35
5445 9825 7.974675 AGTTTATGTGATTTGATGTACCGAAG 58.025 34.615 0.00 0.00 0.00 3.79
5446 9826 7.604545 TGAGTTTATGTGATTTGATGTACCGAA 59.395 33.333 0.00 0.00 0.00 4.30
5447 9827 7.100409 TGAGTTTATGTGATTTGATGTACCGA 58.900 34.615 0.00 0.00 0.00 4.69
5448 9828 7.302350 TGAGTTTATGTGATTTGATGTACCG 57.698 36.000 0.00 0.00 0.00 4.02
5455 9835 9.825109 TCGGTATTATGAGTTTATGTGATTTGA 57.175 29.630 0.00 0.00 0.00 2.69
5456 9836 9.864034 GTCGGTATTATGAGTTTATGTGATTTG 57.136 33.333 0.00 0.00 0.00 2.32
5457 9837 9.052759 GGTCGGTATTATGAGTTTATGTGATTT 57.947 33.333 0.00 0.00 0.00 2.17
5458 9838 7.384115 CGGTCGGTATTATGAGTTTATGTGATT 59.616 37.037 0.00 0.00 0.00 2.57
5459 9839 6.866770 CGGTCGGTATTATGAGTTTATGTGAT 59.133 38.462 0.00 0.00 0.00 3.06
5460 9840 6.183360 ACGGTCGGTATTATGAGTTTATGTGA 60.183 38.462 0.00 0.00 0.00 3.58
5461 9841 5.981315 ACGGTCGGTATTATGAGTTTATGTG 59.019 40.000 0.00 0.00 0.00 3.21
5462 9842 6.152932 ACGGTCGGTATTATGAGTTTATGT 57.847 37.500 0.00 0.00 0.00 2.29
5463 9843 6.143438 GTGACGGTCGGTATTATGAGTTTATG 59.857 42.308 3.34 0.00 0.00 1.90
5464 9844 6.211515 GTGACGGTCGGTATTATGAGTTTAT 58.788 40.000 3.34 0.00 0.00 1.40
5465 9845 5.450412 GGTGACGGTCGGTATTATGAGTTTA 60.450 44.000 3.34 0.00 0.00 2.01
5466 9846 4.427312 GTGACGGTCGGTATTATGAGTTT 58.573 43.478 3.34 0.00 0.00 2.66
5467 9847 3.181483 GGTGACGGTCGGTATTATGAGTT 60.181 47.826 3.34 0.00 0.00 3.01
5468 9848 2.360165 GGTGACGGTCGGTATTATGAGT 59.640 50.000 3.34 0.00 0.00 3.41
5469 9849 3.009301 GGTGACGGTCGGTATTATGAG 57.991 52.381 3.34 0.00 0.00 2.90
5484 9864 1.398071 GCACGCTTAAAGTTCGGTGAC 60.398 52.381 0.00 0.00 0.00 3.67
5485 9865 0.863144 GCACGCTTAAAGTTCGGTGA 59.137 50.000 0.00 0.00 0.00 4.02
5486 9866 0.450482 CGCACGCTTAAAGTTCGGTG 60.450 55.000 0.00 0.00 0.00 4.94
5487 9867 1.562575 CCGCACGCTTAAAGTTCGGT 61.563 55.000 11.64 0.00 42.00 4.69
5488 9868 1.131826 CCGCACGCTTAAAGTTCGG 59.868 57.895 7.25 7.25 41.35 4.30
5489 9869 0.179258 GTCCGCACGCTTAAAGTTCG 60.179 55.000 0.00 0.00 0.00 3.95
5490 9870 0.165295 GGTCCGCACGCTTAAAGTTC 59.835 55.000 0.00 0.00 0.00 3.01
5491 9871 1.232621 GGGTCCGCACGCTTAAAGTT 61.233 55.000 0.00 0.00 32.63 2.66
5492 9872 1.670083 GGGTCCGCACGCTTAAAGT 60.670 57.895 0.00 0.00 32.63 2.66
5493 9873 0.108520 TAGGGTCCGCACGCTTAAAG 60.109 55.000 0.00 0.00 43.11 1.85
5494 9874 0.390209 GTAGGGTCCGCACGCTTAAA 60.390 55.000 0.00 0.00 43.11 1.52
5495 9875 1.216178 GTAGGGTCCGCACGCTTAA 59.784 57.895 0.00 0.00 43.11 1.85
5496 9876 2.887360 GTAGGGTCCGCACGCTTA 59.113 61.111 0.00 0.00 43.11 3.09
5497 9877 4.430765 CGTAGGGTCCGCACGCTT 62.431 66.667 0.00 0.00 43.11 4.68
5510 9890 4.813161 TCTACATAGTTCTCGAACCCGTAG 59.187 45.833 16.66 16.66 42.06 3.51
5511 9891 4.572389 GTCTACATAGTTCTCGAACCCGTA 59.428 45.833 6.20 5.21 42.06 4.02
5512 9892 3.376546 GTCTACATAGTTCTCGAACCCGT 59.623 47.826 6.20 4.41 42.06 5.28
5513 9893 3.376234 TGTCTACATAGTTCTCGAACCCG 59.624 47.826 6.20 0.00 42.06 5.28
5514 9894 4.978083 TGTCTACATAGTTCTCGAACCC 57.022 45.455 6.20 0.00 42.06 4.11
5515 9895 5.972382 GTCATGTCTACATAGTTCTCGAACC 59.028 44.000 6.20 0.00 36.90 3.62
5516 9896 5.972382 GGTCATGTCTACATAGTTCTCGAAC 59.028 44.000 1.62 1.62 36.67 3.95
5517 9897 5.220796 CGGTCATGTCTACATAGTTCTCGAA 60.221 44.000 0.00 0.00 34.26 3.71
5518 9898 4.272748 CGGTCATGTCTACATAGTTCTCGA 59.727 45.833 0.00 0.00 34.26 4.04
5519 9899 4.272748 TCGGTCATGTCTACATAGTTCTCG 59.727 45.833 0.00 0.00 34.26 4.04
5520 9900 5.527951 TCTCGGTCATGTCTACATAGTTCTC 59.472 44.000 0.00 0.00 34.26 2.87
5521 9901 5.297278 GTCTCGGTCATGTCTACATAGTTCT 59.703 44.000 0.00 0.00 34.26 3.01
5522 9902 5.066117 TGTCTCGGTCATGTCTACATAGTTC 59.934 44.000 0.00 0.00 34.26 3.01
5523 9903 4.948004 TGTCTCGGTCATGTCTACATAGTT 59.052 41.667 0.00 0.00 34.26 2.24
5524 9904 4.335874 GTGTCTCGGTCATGTCTACATAGT 59.664 45.833 0.00 0.00 34.26 2.12
5525 9905 4.552961 CGTGTCTCGGTCATGTCTACATAG 60.553 50.000 0.00 0.00 33.77 2.23
5526 9906 3.311596 CGTGTCTCGGTCATGTCTACATA 59.688 47.826 0.00 0.00 33.77 2.29
5527 9907 2.097629 CGTGTCTCGGTCATGTCTACAT 59.902 50.000 0.00 0.00 34.74 2.29
5528 9908 1.467342 CGTGTCTCGGTCATGTCTACA 59.533 52.381 0.00 0.00 35.71 2.74
5529 9909 1.467734 ACGTGTCTCGGTCATGTCTAC 59.532 52.381 0.00 0.00 44.69 2.59
5530 9910 1.736126 GACGTGTCTCGGTCATGTCTA 59.264 52.381 0.00 0.00 43.95 2.59
5531 9911 0.522180 GACGTGTCTCGGTCATGTCT 59.478 55.000 0.00 0.00 43.95 3.41
5532 9912 0.522180 AGACGTGTCTCGGTCATGTC 59.478 55.000 14.86 14.86 46.16 3.06
5533 9913 0.959553 AAGACGTGTCTCGGTCATGT 59.040 50.000 2.48 0.00 44.69 3.21
5534 9914 1.618861 GAAGACGTGTCTCGGTCATG 58.381 55.000 2.48 0.00 44.69 3.07
5535 9915 0.168348 CGAAGACGTGTCTCGGTCAT 59.832 55.000 2.48 0.00 44.69 3.06
5536 9916 1.572941 CGAAGACGTGTCTCGGTCA 59.427 57.895 2.48 0.00 44.69 4.02
5537 9917 1.154263 CCGAAGACGTGTCTCGGTC 60.154 63.158 21.95 9.99 44.69 4.79
5538 9918 2.952245 CCGAAGACGTGTCTCGGT 59.048 61.111 21.95 3.39 44.69 4.69
5539 9919 0.518636 TAACCGAAGACGTGTCTCGG 59.481 55.000 25.46 25.46 46.21 4.63
5540 9920 2.320805 TTAACCGAAGACGTGTCTCG 57.679 50.000 2.48 8.54 39.39 4.04
5541 9921 4.560427 GGTTATTAACCGAAGACGTGTCTC 59.440 45.833 9.78 0.00 42.62 3.36
5542 9922 4.488879 GGTTATTAACCGAAGACGTGTCT 58.511 43.478 9.78 0.00 42.62 3.41
5543 9923 4.830015 GGTTATTAACCGAAGACGTGTC 57.170 45.455 9.78 0.00 42.62 3.67
5555 9935 5.008316 CCAGGTTCCGCTATTGGTTATTAAC 59.992 44.000 0.00 0.00 0.00 2.01
5556 9936 5.104444 TCCAGGTTCCGCTATTGGTTATTAA 60.104 40.000 0.00 0.00 0.00 1.40
5557 9937 4.409574 TCCAGGTTCCGCTATTGGTTATTA 59.590 41.667 0.00 0.00 0.00 0.98
5558 9938 3.201266 TCCAGGTTCCGCTATTGGTTATT 59.799 43.478 0.00 0.00 0.00 1.40
5559 9939 2.775384 TCCAGGTTCCGCTATTGGTTAT 59.225 45.455 0.00 0.00 0.00 1.89
5560 9940 2.189676 TCCAGGTTCCGCTATTGGTTA 58.810 47.619 0.00 0.00 0.00 2.85
5561 9941 0.988832 TCCAGGTTCCGCTATTGGTT 59.011 50.000 0.00 0.00 0.00 3.67
5562 9942 1.134098 CATCCAGGTTCCGCTATTGGT 60.134 52.381 0.00 0.00 0.00 3.67
5563 9943 1.597742 CATCCAGGTTCCGCTATTGG 58.402 55.000 0.00 0.00 0.00 3.16
5564 9944 0.947244 GCATCCAGGTTCCGCTATTG 59.053 55.000 0.00 0.00 0.00 1.90
5565 9945 0.839946 AGCATCCAGGTTCCGCTATT 59.160 50.000 0.00 0.00 0.00 1.73
5566 9946 0.394565 GAGCATCCAGGTTCCGCTAT 59.605 55.000 0.00 0.00 31.86 2.97
5567 9947 0.975556 TGAGCATCCAGGTTCCGCTA 60.976 55.000 0.00 0.00 31.86 4.26
5568 9948 1.630126 ATGAGCATCCAGGTTCCGCT 61.630 55.000 0.00 0.00 35.14 5.52
5569 9949 0.106708 TATGAGCATCCAGGTTCCGC 59.893 55.000 0.00 0.00 0.00 5.54
5570 9950 2.810274 CAATATGAGCATCCAGGTTCCG 59.190 50.000 0.00 0.00 0.00 4.30
5571 9951 3.152341 CCAATATGAGCATCCAGGTTCC 58.848 50.000 0.00 0.00 0.00 3.62
5572 9952 2.555757 GCCAATATGAGCATCCAGGTTC 59.444 50.000 0.00 0.00 0.00 3.62
5573 9953 2.176364 AGCCAATATGAGCATCCAGGTT 59.824 45.455 0.54 0.00 0.00 3.50
5574 9954 1.779092 AGCCAATATGAGCATCCAGGT 59.221 47.619 0.54 0.00 0.00 4.00
5575 9955 2.434428 GAGCCAATATGAGCATCCAGG 58.566 52.381 0.54 0.00 0.00 4.45
5576 9956 2.434428 GGAGCCAATATGAGCATCCAG 58.566 52.381 0.54 0.00 0.00 3.86
5577 9957 1.074405 GGGAGCCAATATGAGCATCCA 59.926 52.381 13.12 0.00 31.73 3.41
5578 9958 1.074405 TGGGAGCCAATATGAGCATCC 59.926 52.381 0.54 4.38 0.00 3.51
5579 9959 2.157738 GTGGGAGCCAATATGAGCATC 58.842 52.381 0.54 0.00 34.18 3.91
5580 9960 1.496001 TGTGGGAGCCAATATGAGCAT 59.504 47.619 0.54 0.00 34.18 3.79
5581 9961 0.918258 TGTGGGAGCCAATATGAGCA 59.082 50.000 0.54 0.00 34.18 4.26
5582 9962 2.283145 ATGTGGGAGCCAATATGAGC 57.717 50.000 0.00 0.00 34.18 4.26
5583 9963 5.813383 AGAATATGTGGGAGCCAATATGAG 58.187 41.667 0.00 0.00 34.18 2.90
5584 9964 5.848286 AGAATATGTGGGAGCCAATATGA 57.152 39.130 0.00 0.00 34.18 2.15


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

AutoCloner maintained by Alex Coulton.