Multiple sequence alignment - TraesCS3A01G076800

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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 TraesCS3A01G076800 chr3A 100.000 7516 0 0 1 7516 47523317 47530832 0.000000e+00 13880
1 TraesCS3A01G076800 chr3A 96.102 4028 137 10 2806 6821 47553813 47557832 0.000000e+00 6551
2 TraesCS3A01G076800 chr3A 94.295 3576 150 24 3828 7369 47583521 47587076 0.000000e+00 5424
3 TraesCS3A01G076800 chr3A 90.524 1678 116 16 408 2057 47579831 47581493 0.000000e+00 2178
4 TraesCS3A01G076800 chr3A 91.633 1470 88 13 612 2057 47551522 47552980 0.000000e+00 2001
5 TraesCS3A01G076800 chr3A 93.665 1105 46 16 6420 7516 47557831 47558919 0.000000e+00 1631
6 TraesCS3A01G076800 chr3A 93.527 1035 56 6 2806 3835 47582327 47583355 0.000000e+00 1530
7 TraesCS3A01G076800 chr3A 94.459 758 40 1 2055 2810 47553018 47553775 0.000000e+00 1166
8 TraesCS3A01G076800 chr3A 94.327 758 41 1 2055 2810 47581531 47582288 0.000000e+00 1160
9 TraesCS3A01G076800 chr3A 85.644 404 50 4 1 397 47544625 47545027 1.170000e-112 418
10 TraesCS3A01G076800 chr3A 87.580 314 31 4 91 397 47579463 47579775 2.580000e-94 357
11 TraesCS3A01G076800 chr3B 93.617 4042 196 20 2806 6827 59751512 59755511 0.000000e+00 5978
12 TraesCS3A01G076800 chr3B 92.624 1654 91 17 2811 4460 59996800 59995174 0.000000e+00 2350
13 TraesCS3A01G076800 chr3B 89.690 1678 119 15 398 2057 59749033 59750674 0.000000e+00 2091
14 TraesCS3A01G076800 chr3B 95.661 1014 39 2 4640 5649 59968849 59967837 0.000000e+00 1624
15 TraesCS3A01G076800 chr3B 93.026 760 47 2 2055 2808 59750712 59751471 0.000000e+00 1105
16 TraesCS3A01G076800 chr3B 85.755 1046 112 18 5648 6691 59962210 59961200 0.000000e+00 1072
17 TraesCS3A01G076800 chr3B 85.938 384 33 9 2435 2815 59997204 59996839 2.540000e-104 390
18 TraesCS3A01G076800 chr3B 87.544 281 17 6 6994 7258 59757051 59757329 7.320000e-80 309
19 TraesCS3A01G076800 chr3B 92.793 111 8 0 7257 7367 59757413 59757523 2.170000e-35 161
20 TraesCS3A01G076800 chr3B 82.143 168 17 10 7126 7285 59942156 59941994 1.700000e-26 132
21 TraesCS3A01G076800 chr3B 93.023 86 6 0 7284 7369 59940937 59940852 7.920000e-25 126
22 TraesCS3A01G076800 chr3B 94.366 71 1 1 6891 6961 59755542 59755609 1.030000e-18 106
23 TraesCS3A01G076800 chr3D 93.538 4039 206 29 2806 6815 37268398 37272410 0.000000e+00 5962
24 TraesCS3A01G076800 chr3D 94.020 3127 169 12 2806 5927 37453092 37449979 0.000000e+00 4723
25 TraesCS3A01G076800 chr3D 93.878 3022 146 19 3815 6815 37246892 37249895 0.000000e+00 4519
26 TraesCS3A01G076800 chr3D 94.484 2375 101 12 2806 5152 37287538 37289910 0.000000e+00 3633
27 TraesCS3A01G076800 chr3D 94.798 2057 78 6 1 2057 37242975 37245002 0.000000e+00 3179
28 TraesCS3A01G076800 chr3D 94.652 2057 78 8 1 2057 37265572 37267596 0.000000e+00 3160
29 TraesCS3A01G076800 chr3D 91.837 2254 136 21 5143 7369 37442307 37440075 0.000000e+00 3099
30 TraesCS3A01G076800 chr3D 93.515 2097 101 13 2806 4895 37546185 37544117 0.000000e+00 3086
31 TraesCS3A01G076800 chr3D 89.119 1691 130 24 399 2057 37455544 37453876 0.000000e+00 2054
32 TraesCS3A01G076800 chr3D 88.342 1321 96 21 762 2057 37548273 37546986 0.000000e+00 1533
33 TraesCS3A01G076800 chr3D 88.124 1322 98 23 762 2057 37534705 37533417 0.000000e+00 1517
34 TraesCS3A01G076800 chr3D 91.467 1043 62 7 2806 3828 37245836 37246871 0.000000e+00 1408
35 TraesCS3A01G076800 chr3D 88.648 1154 123 5 5540 6691 37526991 37525844 0.000000e+00 1399
36 TraesCS3A01G076800 chr3D 88.648 1154 123 5 5540 6691 37540860 37539713 0.000000e+00 1399
37 TraesCS3A01G076800 chr3D 92.875 814 56 1 438 1251 37285116 37285927 0.000000e+00 1181
38 TraesCS3A01G076800 chr3D 92.965 796 52 3 1263 2057 37285912 37286704 0.000000e+00 1157
39 TraesCS3A01G076800 chr3D 94.195 758 42 1 2055 2810 37245040 37245797 0.000000e+00 1155
40 TraesCS3A01G076800 chr3D 93.939 759 42 3 2055 2810 37286742 37287499 0.000000e+00 1144
41 TraesCS3A01G076800 chr3D 95.377 584 27 0 4961 5544 37532843 37532260 0.000000e+00 929
42 TraesCS3A01G076800 chr3D 90.170 529 29 7 6859 7369 37272418 37272941 0.000000e+00 667
43 TraesCS3A01G076800 chr3D 89.603 529 32 7 6859 7369 37249902 37250425 0.000000e+00 651
44 TraesCS3A01G076800 chr3D 92.627 434 32 0 2377 2810 37267926 37268359 6.400000e-175 625
45 TraesCS3A01G076800 chr3D 91.514 436 33 4 2382 2815 37546651 37546218 1.400000e-166 597
46 TraesCS3A01G076800 chr3D 90.950 442 32 3 2376 2813 37453565 37453128 8.400000e-164 588
47 TraesCS3A01G076800 chr3D 94.785 326 15 1 2055 2378 37267634 37267959 2.420000e-139 507
48 TraesCS3A01G076800 chr3D 93.865 326 18 1 2055 2378 37546948 37546623 2.440000e-134 490
49 TraesCS3A01G076800 chr3D 93.272 327 19 2 2055 2378 37533379 37533053 5.280000e-131 479
50 TraesCS3A01G076800 chr3D 90.645 310 24 3 91 397 37455895 37455588 2.520000e-109 407
51 TraesCS3A01G076800 chr3D 90.000 310 23 3 91 397 37550321 37550017 1.970000e-105 394
52 TraesCS3A01G076800 chr3D 88.957 326 16 5 2055 2378 37453838 37453531 1.180000e-102 385
53 TraesCS3A01G076800 chr3D 89.032 310 26 4 91 397 38107704 38107400 1.980000e-100 377
54 TraesCS3A01G076800 chr3D 98.561 139 2 0 4838 4976 37532995 37532857 5.820000e-61 246
55 TraesCS3A01G076800 chr3D 92.994 157 11 0 408 564 37549961 37549805 5.870000e-56 230
56 TraesCS3A01G076800 chr3D 92.357 157 12 0 408 564 38107344 38107188 2.730000e-54 224
57 TraesCS3A01G076800 chr3D 87.023 131 11 2 642 772 37549759 37549635 7.860000e-30 143
58 TraesCS3A01G076800 chr3D 86.260 131 12 2 642 772 38107142 38107018 3.660000e-28 137
59 TraesCS3A01G076800 chr3D 81.564 179 13 7 7211 7369 37292528 37292706 6.120000e-26 130


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 TraesCS3A01G076800 chr3A 47523317 47530832 7515 False 13880.00 13880 100.000000 1 7516 1 chr3A.!!$F1 7515
1 TraesCS3A01G076800 chr3A 47551522 47558919 7397 False 2837.25 6551 93.964750 612 7516 4 chr3A.!!$F3 6904
2 TraesCS3A01G076800 chr3A 47579463 47587076 7613 False 2129.80 5424 92.050600 91 7369 5 chr3A.!!$F4 7278
3 TraesCS3A01G076800 chr3B 59749033 59757523 8490 False 1625.00 5978 91.839333 398 7367 6 chr3B.!!$F1 6969
4 TraesCS3A01G076800 chr3B 59967837 59968849 1012 True 1624.00 1624 95.661000 4640 5649 1 chr3B.!!$R2 1009
5 TraesCS3A01G076800 chr3B 59995174 59997204 2030 True 1370.00 2350 89.281000 2435 4460 2 chr3B.!!$R4 2025
6 TraesCS3A01G076800 chr3B 59961200 59962210 1010 True 1072.00 1072 85.755000 5648 6691 1 chr3B.!!$R1 1043
7 TraesCS3A01G076800 chr3D 37440075 37442307 2232 True 3099.00 3099 91.837000 5143 7369 1 chr3D.!!$R1 2226
8 TraesCS3A01G076800 chr3D 37265572 37272941 7369 False 2184.20 5962 93.154400 1 7369 5 chr3D.!!$F2 7368
9 TraesCS3A01G076800 chr3D 37242975 37250425 7450 False 2182.40 4519 92.788200 1 7369 5 chr3D.!!$F1 7368
10 TraesCS3A01G076800 chr3D 37449979 37455895 5916 True 1631.40 4723 90.738200 91 5927 5 chr3D.!!$R3 5836
11 TraesCS3A01G076800 chr3D 37285116 37292706 7590 False 1449.00 3633 91.165400 438 7369 5 chr3D.!!$F3 6931
12 TraesCS3A01G076800 chr3D 37525844 37526991 1147 True 1399.00 1399 88.648000 5540 6691 1 chr3D.!!$R2 1151
13 TraesCS3A01G076800 chr3D 37539713 37550321 10608 True 984.00 3086 90.737625 91 6691 8 chr3D.!!$R5 6600
14 TraesCS3A01G076800 chr3D 37532260 37534705 2445 True 792.75 1517 93.833500 762 5544 4 chr3D.!!$R4 4782
15 TraesCS3A01G076800 chr3D 38107018 38107704 686 True 246.00 377 89.216333 91 772 3 chr3D.!!$R6 681

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
576 633 0.108615 AACTTGACGCTCGATCCAGG 60.109 55.000 0.00 0.0 0.00 4.45 F
1464 2932 0.984230 AGGCGAGGGTCTTTTGATGA 59.016 50.000 0.00 0.0 0.00 2.92 F
1581 3049 0.389391 CTGGTGCTATCGGAATCGGT 59.611 55.000 0.00 0.0 36.95 4.69 F
2825 4463 1.292992 GGGTAAAATTCGACGCGGAT 58.707 50.000 12.47 0.0 0.00 4.18 F
4008 5913 1.392589 CTGCCAACGGGAAGCATATT 58.607 50.000 0.00 0.0 31.32 1.28 F
4493 6405 1.355381 TGGGGAATCAGAATGTGCTGT 59.645 47.619 0.00 0.0 37.20 4.40 F
5624 10150 0.250727 ATGTTCCCACCACAGGTTCG 60.251 55.000 0.00 0.0 31.02 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 3033 1.663445 CGAGACCGATTCCGATAGCAC 60.663 57.143 0.00 0.00 38.22 4.40 R
2284 3804 2.287608 CGAAGCAAGGGTCTTGGTTTTC 60.288 50.000 20.96 11.85 39.83 2.29 R
3476 5160 2.107378 TGCCACACCAACTTATGAAGGA 59.893 45.455 0.00 0.00 0.00 3.36 R
4293 6201 0.107017 TATTTGGCTGCCTCTCCTGC 60.107 55.000 21.03 0.00 0.00 4.85 R
5624 10150 0.392461 TTGATACCCGAAGCCTGCAC 60.392 55.000 0.00 0.00 0.00 4.57 R
5666 10192 1.221021 CCGCTAGGAACCCAAGGAC 59.779 63.158 0.00 0.00 41.02 3.85 R
7181 14015 0.394216 GCATCCCACTGCACATGGTA 60.394 55.000 10.65 0.00 41.87 3.25 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.452833 GATGGCCACAAGGAGCTCC 60.453 63.158 26.22 26.22 36.89 4.70
38 39 3.640407 AAGGAGCTCCGCCTTGCA 61.640 61.111 26.95 0.00 41.83 4.08
59 60 1.228894 TCCTCAAGTCTCGCCCAGT 60.229 57.895 0.00 0.00 0.00 4.00
258 266 3.369576 GGACTAGTTTCCCTGGATGACAC 60.370 52.174 0.00 0.00 0.00 3.67
332 341 5.006552 CGTTCAAATGCACCAATCTTTTTGT 59.993 36.000 0.00 0.00 0.00 2.83
445 499 1.139853 CGAAGAGCTGCTAGGGGAAAT 59.860 52.381 0.15 0.00 0.00 2.17
480 534 7.066163 CCTTCAAATGCAACACTCATAGTATCA 59.934 37.037 0.00 0.00 0.00 2.15
537 594 5.233902 TCTTTGAAATTTGTTGAACGCCATG 59.766 36.000 0.00 0.00 0.00 3.66
576 633 0.108615 AACTTGACGCTCGATCCAGG 60.109 55.000 0.00 0.00 0.00 4.45
589 646 4.653868 TCGATCCAGGTTAGTATCTCTCC 58.346 47.826 0.00 0.00 0.00 3.71
594 653 4.105057 TCCAGGTTAGTATCTCTCCCTCTC 59.895 50.000 0.00 0.00 0.00 3.20
595 654 4.105697 CCAGGTTAGTATCTCTCCCTCTCT 59.894 50.000 0.00 0.00 0.00 3.10
875 2317 4.770795 AGAGCGTTCACCTATAAAAGCAT 58.229 39.130 1.01 0.00 33.15 3.79
1142 2592 1.604593 CCCTGTTCTGCAAGGTGGG 60.605 63.158 1.58 0.00 0.00 4.61
1208 2658 2.116238 ACTTGGGTACGCCTATGTGAT 58.884 47.619 7.55 0.00 33.47 3.06
1221 2671 5.109903 GCCTATGTGATTTTCTACAGTCGT 58.890 41.667 0.00 0.00 0.00 4.34
1247 2710 2.029828 ACGGTGAGTGTGTCTTCATCTC 60.030 50.000 0.00 0.00 0.00 2.75
1248 2711 2.230025 CGGTGAGTGTGTCTTCATCTCT 59.770 50.000 0.00 0.00 32.82 3.10
1305 2769 4.630644 TCATCTAATCAGGCTTGGATCC 57.369 45.455 4.20 4.20 0.00 3.36
1346 2813 7.490657 ACAAGGTTGTGTGGTTATAGATCTA 57.509 36.000 4.57 4.57 40.49 1.98
1355 2822 9.826574 TGTGTGGTTATAGATCTATTTGGTTAC 57.173 33.333 20.13 13.07 0.00 2.50
1464 2932 0.984230 AGGCGAGGGTCTTTTGATGA 59.016 50.000 0.00 0.00 0.00 2.92
1496 2964 3.832490 AGATAGTGTGTTGACCTGCAGTA 59.168 43.478 13.81 0.00 0.00 2.74
1530 2998 4.238514 GTGTCACTAACATGAGGAGTGTC 58.761 47.826 18.93 15.75 40.80 3.67
1565 3033 3.063452 CGATTCGGGTTTGTGTAATCTGG 59.937 47.826 0.00 0.00 0.00 3.86
1581 3049 0.389391 CTGGTGCTATCGGAATCGGT 59.611 55.000 0.00 0.00 36.95 4.69
1627 3096 4.121317 CAAAAGCAAATGGACACACACAT 58.879 39.130 0.00 0.00 0.00 3.21
1675 3144 7.078249 ACCTACATGCCATATATTTCTGTCA 57.922 36.000 0.00 0.00 0.00 3.58
1678 3147 9.322773 CCTACATGCCATATATTTCTGTCATAG 57.677 37.037 0.00 0.00 0.00 2.23
1950 3426 4.262164 GGGGTAGAAAATCGCCGTAGATAA 60.262 45.833 0.00 0.00 0.00 1.75
1951 3427 5.476614 GGGTAGAAAATCGCCGTAGATAAT 58.523 41.667 0.00 0.00 0.00 1.28
2021 3499 9.394477 GGAAAAATAAGTAGACACACACAATTC 57.606 33.333 0.00 0.00 0.00 2.17
2073 3591 8.414003 TCGCTGAGTTGTCTATCTTATTTATGT 58.586 33.333 0.00 0.00 0.00 2.29
2138 3658 9.783256 AGTTTTTATTAAATTAGGTCGCATGAC 57.217 29.630 0.00 0.00 44.72 3.06
2235 3755 6.830873 AGGAAGAGAATGGAATTTTGACTG 57.169 37.500 0.00 0.00 36.07 3.51
2284 3804 5.850557 TGGGTTTATGCACATTCCATAAG 57.149 39.130 0.00 0.00 36.74 1.73
2299 3820 5.333566 TCCATAAGAAAACCAAGACCCTT 57.666 39.130 0.00 0.00 0.00 3.95
2373 3958 5.392811 GGAAGAGAATGGAATCAGCAGTTTG 60.393 44.000 0.00 0.00 0.00 2.93
2374 3959 3.442977 AGAGAATGGAATCAGCAGTTTGC 59.557 43.478 0.00 0.00 45.46 3.68
2382 3967 1.822990 ATCAGCAGTTTGCAGATTGGG 59.177 47.619 3.67 0.00 45.46 4.12
2383 3968 2.555892 ATCAGCAGTTTGCAGATTGGGA 60.556 45.455 3.67 0.00 45.46 4.37
2384 3969 4.068135 ATCAGCAGTTTGCAGATTGGGAA 61.068 43.478 3.67 0.00 45.46 3.97
2385 3970 2.358939 GCAGTTTGCAGATTGGGAAG 57.641 50.000 1.89 0.00 44.26 3.46
2386 3971 1.888512 GCAGTTTGCAGATTGGGAAGA 59.111 47.619 1.89 0.00 44.26 2.87
2387 3972 2.094854 GCAGTTTGCAGATTGGGAAGAG 60.095 50.000 1.89 0.00 44.26 2.85
2388 3973 3.415212 CAGTTTGCAGATTGGGAAGAGA 58.585 45.455 0.00 0.00 0.00 3.10
2389 3974 3.822735 CAGTTTGCAGATTGGGAAGAGAA 59.177 43.478 0.00 0.00 0.00 2.87
2390 3975 4.461781 CAGTTTGCAGATTGGGAAGAGAAT 59.538 41.667 0.00 0.00 0.00 2.40
2391 3976 4.461781 AGTTTGCAGATTGGGAAGAGAATG 59.538 41.667 0.00 0.00 0.00 2.67
2392 3977 3.008835 TGCAGATTGGGAAGAGAATGG 57.991 47.619 0.00 0.00 0.00 3.16
2393 3978 2.577563 TGCAGATTGGGAAGAGAATGGA 59.422 45.455 0.00 0.00 0.00 3.41
2394 3979 3.010472 TGCAGATTGGGAAGAGAATGGAA 59.990 43.478 0.00 0.00 0.00 3.53
2395 3980 4.213513 GCAGATTGGGAAGAGAATGGAAT 58.786 43.478 0.00 0.00 0.00 3.01
2396 3981 4.277921 GCAGATTGGGAAGAGAATGGAATC 59.722 45.833 0.00 0.00 0.00 2.52
2397 3982 5.443283 CAGATTGGGAAGAGAATGGAATCA 58.557 41.667 0.00 0.00 0.00 2.57
2398 3983 5.531659 CAGATTGGGAAGAGAATGGAATCAG 59.468 44.000 0.00 0.00 0.00 2.90
2399 3984 3.287867 TGGGAAGAGAATGGAATCAGC 57.712 47.619 0.00 0.00 0.00 4.26
2400 3985 2.577563 TGGGAAGAGAATGGAATCAGCA 59.422 45.455 0.00 0.00 0.00 4.41
2401 3986 3.010472 TGGGAAGAGAATGGAATCAGCAA 59.990 43.478 0.00 0.00 0.00 3.91
2402 3987 3.379688 GGGAAGAGAATGGAATCAGCAAC 59.620 47.826 0.00 0.00 0.00 4.17
2403 3988 4.268359 GGAAGAGAATGGAATCAGCAACT 58.732 43.478 0.00 0.00 0.00 3.16
2404 3989 4.704057 GGAAGAGAATGGAATCAGCAACTT 59.296 41.667 0.00 0.00 0.00 2.66
2433 4020 2.068519 TGTTGCTTAGCACTGACATCG 58.931 47.619 6.34 0.00 38.71 3.84
2445 4032 4.748892 CACTGACATCGGTGTTAGAATCT 58.251 43.478 25.64 1.62 45.65 2.40
2450 4037 6.873997 TGACATCGGTGTTAGAATCTGTAAT 58.126 36.000 1.13 0.00 39.09 1.89
2465 4052 3.196039 TCTGTAATCGATTCGGGTTTCCA 59.804 43.478 15.25 0.00 0.00 3.53
2474 4061 1.757682 TCGGGTTTCCAATATGGCAC 58.242 50.000 0.00 0.00 37.47 5.01
2499 4087 7.653311 ACAAAATCTTAGTGGAAACAAATGCTC 59.347 33.333 0.00 0.00 46.06 4.26
2649 4239 3.344904 TGTCTATCTTACTTACGCCGC 57.655 47.619 0.00 0.00 0.00 6.53
2825 4463 1.292992 GGGTAAAATTCGACGCGGAT 58.707 50.000 12.47 0.00 0.00 4.18
2856 4494 2.989840 GCCGAATATGTCAGAATCCGAG 59.010 50.000 0.00 0.00 0.00 4.63
2998 4649 4.494690 CGGCGTCGTCTATCTTACTTACAA 60.495 45.833 0.00 0.00 0.00 2.41
3025 4676 5.692115 ACTTTTGGGAGTTGAATTGGTTT 57.308 34.783 0.00 0.00 0.00 3.27
3087 4742 9.569122 ACACGGTTTATTTATAAGATAGCCAAT 57.431 29.630 0.00 0.00 0.00 3.16
3197 4870 4.219264 TGCATGGTGTAGAACATCATCA 57.781 40.909 2.84 2.98 46.26 3.07
3356 5040 6.872920 ACATGTTTCTGTTATTGGTGTTGTT 58.127 32.000 0.00 0.00 0.00 2.83
3361 5045 8.138712 TGTTTCTGTTATTGGTGTTGTTTATCC 58.861 33.333 0.00 0.00 0.00 2.59
3403 5087 3.071167 GGGAGTTGACTTGGTTAGTGAGT 59.929 47.826 0.00 0.00 37.17 3.41
3406 5090 5.511545 GGAGTTGACTTGGTTAGTGAGTGAT 60.512 44.000 0.00 0.00 37.17 3.06
3440 5124 7.341445 AGTTTAGTCCATGCAGTTTGTTTTA 57.659 32.000 0.00 0.00 0.00 1.52
3450 5134 9.469807 CCATGCAGTTTGTTTTATAGTTTAACA 57.530 29.630 0.00 0.00 0.00 2.41
3510 5194 4.636249 TGGTGTGGCAATTTGGAAAATAC 58.364 39.130 0.00 0.00 0.00 1.89
3519 5203 7.718753 TGGCAATTTGGAAAATACAAACAAGAT 59.281 29.630 0.00 0.00 40.25 2.40
3571 5257 9.296400 GTTAAGAATTTTTCTAGTTTGTGCACA 57.704 29.630 17.42 17.42 39.61 4.57
3648 5335 7.470192 CCCCATGGATTTCATAGTTAACCTAT 58.530 38.462 15.22 0.00 36.79 2.57
3876 5775 7.710907 ACCTTAACCTGATTTCTTTTTCTTTGC 59.289 33.333 0.00 0.00 0.00 3.68
4008 5913 1.392589 CTGCCAACGGGAAGCATATT 58.607 50.000 0.00 0.00 31.32 1.28
4124 6030 4.910195 AGCTTGAGTGATATGTTTGGTCA 58.090 39.130 0.00 0.00 0.00 4.02
4125 6031 4.940046 AGCTTGAGTGATATGTTTGGTCAG 59.060 41.667 0.00 0.00 0.00 3.51
4203 6109 2.399396 ACGGATTTGTTCAGTTTGCG 57.601 45.000 0.00 0.00 27.16 4.85
4206 6112 2.661594 GGATTTGTTCAGTTTGCGGAC 58.338 47.619 0.00 0.00 0.00 4.79
4293 6201 2.422479 TGTAGGTCTCTTCATTCGTCGG 59.578 50.000 0.00 0.00 0.00 4.79
4461 6373 3.897239 TGGAATATCCAAATGCTTCGGT 58.103 40.909 0.00 0.00 45.00 4.69
4493 6405 1.355381 TGGGGAATCAGAATGTGCTGT 59.645 47.619 0.00 0.00 37.20 4.40
4523 6435 7.233348 AGCTGTGAAAATTCTTAATGGGAAGAA 59.767 33.333 1.38 1.38 46.63 2.52
4603 6515 6.151817 AGCAGAACTGAAAGAAAACTTTGAGT 59.848 34.615 8.49 8.49 41.25 3.41
4799 6712 5.452078 TGGCTCACCTTCTTAACATTTTG 57.548 39.130 0.00 0.00 36.63 2.44
4912 6826 5.778862 ACATGGTTTAGTTGTATGCAAACC 58.221 37.500 7.86 7.86 46.59 3.27
5125 8228 6.422400 GCCTTCTGCTGATAAGTGATAAGTAC 59.578 42.308 0.00 0.00 36.87 2.73
5624 10150 0.250727 ATGTTCCCACCACAGGTTCG 60.251 55.000 0.00 0.00 31.02 3.95
5658 10184 4.282195 GGGTATCAACAATTCCCACAACAA 59.718 41.667 0.00 0.00 43.03 2.83
5666 10192 5.358922 ACAATTCCCACAACAACATTTCAG 58.641 37.500 0.00 0.00 0.00 3.02
5764 10291 6.656270 TGTGCATCAAGAAATCAATCTACACT 59.344 34.615 0.00 0.00 0.00 3.55
5845 10372 2.097142 GCATCAGCTACTCTTGCAAAGG 59.903 50.000 0.00 0.00 40.52 3.11
5846 10373 3.341823 CATCAGCTACTCTTGCAAAGGT 58.658 45.455 0.00 4.91 46.24 3.50
5875 10402 2.549754 CCGTGCCCATGTTCAGATTATC 59.450 50.000 0.00 0.00 0.00 1.75
6584 11651 8.752005 TGGATAATGTTTAAGAAGATTCCTGG 57.248 34.615 0.00 0.00 31.85 4.45
6615 11682 6.095300 TGTTGCTTCATGATATTTTCGGTCAT 59.905 34.615 0.00 0.00 33.08 3.06
6629 11697 8.970691 ATTTTCGGTCATGAGTTTTATTCTTG 57.029 30.769 0.00 0.00 0.00 3.02
6630 11698 7.504924 TTTCGGTCATGAGTTTTATTCTTGT 57.495 32.000 0.00 0.00 0.00 3.16
6692 11760 9.998752 TTTTCCCCAATATTTAGGATAACTTCA 57.001 29.630 4.42 0.00 0.00 3.02
6732 11803 1.075659 GCCCTCTTCCTTTGGCAGT 59.924 57.895 0.00 0.00 43.46 4.40
6754 11828 7.934120 GCAGTGATCCTAGTTACTTCCAATATT 59.066 37.037 0.00 0.00 0.00 1.28
6758 11832 9.139734 TGATCCTAGTTACTTCCAATATTACGT 57.860 33.333 0.00 0.00 0.00 3.57
6827 11903 3.304996 CCTCACAAAACACACACACACAA 60.305 43.478 0.00 0.00 0.00 3.33
6912 11992 4.609301 TGATGCTAAACAGGGGCTTAATT 58.391 39.130 0.00 0.00 0.00 1.40
7085 13902 4.002982 TCCATGACAGAACGAAAATCCTG 58.997 43.478 0.00 0.00 0.00 3.86
7146 13978 1.288752 CCAAACGGTCAATGTGCCC 59.711 57.895 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.985116 GGGCGAGACTTGAGGACCT 60.985 63.158 0.00 0.00 0.00 3.85
40 41 1.216710 CTGGGCGAGACTTGAGGAC 59.783 63.158 0.00 0.00 0.00 3.85
59 60 2.909549 GCGGGGTTAGGGGTCCAAA 61.910 63.158 0.00 0.00 0.00 3.28
78 79 9.408069 CTATACCAAGTTATCGAGGTAATTCAC 57.592 37.037 3.41 0.00 39.80 3.18
258 266 1.133976 GGTCAGATCATGTCCCCTTGG 60.134 57.143 0.00 0.00 31.52 3.61
445 499 6.166984 TGTTGCATTTGAAGGGAACATAAA 57.833 33.333 10.61 0.00 44.01 1.40
480 534 7.846066 AGACAAAGATCAGAGTTTAGCACTAT 58.154 34.615 0.00 0.00 35.01 2.12
537 594 3.631145 TGTCAGCTCAGCATTTTGAAC 57.369 42.857 0.00 0.00 0.00 3.18
875 2317 1.345741 GATGGATTCATCGAGCAGGGA 59.654 52.381 0.00 0.00 40.15 4.20
1066 2516 2.549198 CGACGTATAGCGAGGCCCA 61.549 63.158 0.00 0.00 44.77 5.36
1221 2671 0.467474 AGACACACTCACCGTCCTCA 60.467 55.000 0.00 0.00 0.00 3.86
1305 2769 4.189231 CCTTGTAGGTTCTTTGTATCCCG 58.811 47.826 0.00 0.00 0.00 5.14
1346 2813 6.877611 AAATCACAGACTTCGTAACCAAAT 57.122 33.333 0.00 0.00 0.00 2.32
1355 2822 7.222999 GGGAAATCTAGTAAATCACAGACTTCG 59.777 40.741 0.00 0.00 29.23 3.79
1464 2932 3.293311 ACACACTATCTACGCACGTTT 57.707 42.857 0.00 0.00 0.00 3.60
1496 2964 5.593968 TGTTAGTGACACGTTGTTCTACAT 58.406 37.500 0.00 0.00 32.00 2.29
1556 3024 4.558697 CGATTCCGATAGCACCAGATTACA 60.559 45.833 0.00 0.00 38.22 2.41
1565 3033 1.663445 CGAGACCGATTCCGATAGCAC 60.663 57.143 0.00 0.00 38.22 4.40
1581 3049 6.173339 GCCAATCATTTATCCTATTCCGAGA 58.827 40.000 0.00 0.00 0.00 4.04
1627 3096 4.111375 ACACACGTTTAATTGCAACCAA 57.889 36.364 0.00 0.00 35.01 3.67
1897 3373 7.497249 GTGCACAATCTATGGAGAACTCTTAAT 59.503 37.037 13.17 0.00 34.61 1.40
2073 3591 5.533154 ACGATTCAACTCCCAAATGTTACAA 59.467 36.000 0.00 0.00 0.00 2.41
2138 3658 4.637483 TCTTGGCTGACTTGAAAACAAG 57.363 40.909 8.18 8.18 38.11 3.16
2284 3804 2.287608 CGAAGCAAGGGTCTTGGTTTTC 60.288 50.000 20.96 11.85 39.83 2.29
2299 3820 5.072040 TCTTGTTGTGATCTATCGAAGCA 57.928 39.130 0.00 0.00 0.00 3.91
2335 3856 7.730332 TCCATTCTCTTCCTAATCTATAGTGCA 59.270 37.037 0.00 0.00 0.00 4.57
2341 3862 8.320617 GCTGATTCCATTCTCTTCCTAATCTAT 58.679 37.037 0.00 0.00 0.00 1.98
2373 3958 3.287867 TCCATTCTCTTCCCAATCTGC 57.712 47.619 0.00 0.00 0.00 4.26
2374 3959 5.443283 TGATTCCATTCTCTTCCCAATCTG 58.557 41.667 0.00 0.00 0.00 2.90
2375 3960 5.692928 CTGATTCCATTCTCTTCCCAATCT 58.307 41.667 0.00 0.00 0.00 2.40
2376 3961 4.277921 GCTGATTCCATTCTCTTCCCAATC 59.722 45.833 0.00 0.00 0.00 2.67
2377 3962 4.213513 GCTGATTCCATTCTCTTCCCAAT 58.786 43.478 0.00 0.00 0.00 3.16
2378 3963 3.010472 TGCTGATTCCATTCTCTTCCCAA 59.990 43.478 0.00 0.00 0.00 4.12
2379 3964 2.577563 TGCTGATTCCATTCTCTTCCCA 59.422 45.455 0.00 0.00 0.00 4.37
2380 3965 3.287867 TGCTGATTCCATTCTCTTCCC 57.712 47.619 0.00 0.00 0.00 3.97
2381 3966 4.268359 AGTTGCTGATTCCATTCTCTTCC 58.732 43.478 0.00 0.00 0.00 3.46
2382 3967 5.182760 ACAAGTTGCTGATTCCATTCTCTTC 59.817 40.000 1.81 0.00 0.00 2.87
2383 3968 5.075493 ACAAGTTGCTGATTCCATTCTCTT 58.925 37.500 1.81 0.00 0.00 2.85
2384 3969 4.660168 ACAAGTTGCTGATTCCATTCTCT 58.340 39.130 1.81 0.00 0.00 3.10
2385 3970 5.877012 TCTACAAGTTGCTGATTCCATTCTC 59.123 40.000 1.81 0.00 0.00 2.87
2386 3971 5.809001 TCTACAAGTTGCTGATTCCATTCT 58.191 37.500 1.81 0.00 0.00 2.40
2387 3972 6.072508 TGTTCTACAAGTTGCTGATTCCATTC 60.073 38.462 1.81 0.00 0.00 2.67
2388 3973 5.769662 TGTTCTACAAGTTGCTGATTCCATT 59.230 36.000 1.81 0.00 0.00 3.16
2389 3974 5.316167 TGTTCTACAAGTTGCTGATTCCAT 58.684 37.500 1.81 0.00 0.00 3.41
2390 3975 4.713553 TGTTCTACAAGTTGCTGATTCCA 58.286 39.130 1.81 0.00 0.00 3.53
2391 3976 5.182001 ACATGTTCTACAAGTTGCTGATTCC 59.818 40.000 1.81 0.00 0.00 3.01
2392 3977 6.246420 ACATGTTCTACAAGTTGCTGATTC 57.754 37.500 1.81 0.00 0.00 2.52
2393 3978 6.441274 CAACATGTTCTACAAGTTGCTGATT 58.559 36.000 8.48 0.00 46.20 2.57
2394 3979 6.005583 CAACATGTTCTACAAGTTGCTGAT 57.994 37.500 8.48 0.00 46.20 2.90
2395 3980 5.422666 CAACATGTTCTACAAGTTGCTGA 57.577 39.130 8.48 0.00 46.20 4.26
2400 3985 5.530915 TGCTAAGCAACATGTTCTACAAGTT 59.469 36.000 8.48 0.00 40.18 2.66
2401 3986 5.049405 GTGCTAAGCAACATGTTCTACAAGT 60.049 40.000 8.48 0.00 41.47 3.16
2402 3987 5.180117 AGTGCTAAGCAACATGTTCTACAAG 59.820 40.000 8.48 4.31 41.47 3.16
2403 3988 5.049474 CAGTGCTAAGCAACATGTTCTACAA 60.049 40.000 8.48 0.00 41.47 2.41
2404 3989 4.452114 CAGTGCTAAGCAACATGTTCTACA 59.548 41.667 8.48 6.26 41.47 2.74
2419 4006 2.831685 AACACCGATGTCAGTGCTAA 57.168 45.000 0.00 0.00 38.45 3.09
2420 4007 3.086282 TCTAACACCGATGTCAGTGCTA 58.914 45.455 0.00 0.00 38.45 3.49
2445 4032 3.613494 TGGAAACCCGAATCGATTACA 57.387 42.857 11.38 0.23 0.00 2.41
2450 4037 3.472652 CCATATTGGAAACCCGAATCGA 58.527 45.455 3.36 0.00 40.96 3.59
2465 4052 7.716799 TTCCACTAAGATTTTGTGCCATATT 57.283 32.000 0.00 0.00 0.00 1.28
2474 4061 7.869429 AGAGCATTTGTTTCCACTAAGATTTTG 59.131 33.333 0.00 0.00 0.00 2.44
2483 4071 4.090761 TCTGAGAGCATTTGTTTCCACT 57.909 40.909 0.00 0.00 0.00 4.00
2649 4239 5.781237 CGCTGACGATTCAATCCAAGTATTG 60.781 44.000 0.00 0.00 44.43 1.90
2750 4344 8.896744 CAGAAGAAATCTATGAAGCCATAAACA 58.103 33.333 0.00 0.00 36.32 2.83
2825 4463 8.669946 TTCTGACATATTCGGCAACATTATTA 57.330 30.769 0.00 0.00 0.00 0.98
2873 4511 8.637986 TGTGTGCCTACTATCTTTTTCAAAATT 58.362 29.630 0.00 0.00 0.00 1.82
2887 4525 9.674068 TGAAATAATAATTGTGTGTGCCTACTA 57.326 29.630 0.00 0.00 0.00 1.82
2998 4649 6.782494 ACCAATTCAACTCCCAAAAGTTAGAT 59.218 34.615 0.00 0.00 37.38 1.98
3025 4676 5.470098 ACAAAGAGCTAAATTTTCTCTCGCA 59.530 36.000 17.57 0.00 36.27 5.10
3087 4742 7.658525 AATTCCCATGTGCAATCTACAAATA 57.341 32.000 0.00 0.00 0.00 1.40
3197 4870 6.349280 CGGATTGTGACAATGTTAACTTCCAT 60.349 38.462 16.52 0.00 0.00 3.41
3272 4956 9.691362 GACACACATTAATTGTAACCAAATTCT 57.309 29.630 0.00 0.00 36.57 2.40
3361 5045 7.666623 ACTCCCAAATGTTACACCATAAAAAG 58.333 34.615 0.00 0.00 0.00 2.27
3469 5153 7.339212 CCACACCAACTTATGAAGGAATCAATA 59.661 37.037 0.00 0.00 42.54 1.90
3476 5160 2.107378 TGCCACACCAACTTATGAAGGA 59.893 45.455 0.00 0.00 0.00 3.36
3510 5194 5.224888 CCACATTCAGTTCCATCTTGTTTG 58.775 41.667 0.00 0.00 0.00 2.93
3519 5203 5.205056 ACTTTTAACCCACATTCAGTTCCA 58.795 37.500 0.00 0.00 0.00 3.53
3571 5257 2.946329 TGTAGCACGTTTCAACACCATT 59.054 40.909 0.00 0.00 0.00 3.16
3648 5335 9.944663 GCACGGATAAACTAATGAATATTTGAA 57.055 29.630 0.00 0.00 0.00 2.69
3655 5342 5.527582 GTGGAGCACGGATAAACTAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
3876 5775 3.609853 TCTAGTAGGGCAAGCAAACATG 58.390 45.455 0.00 0.00 0.00 3.21
4124 6030 6.857437 TGCATGATAGTATAGTGCCATACT 57.143 37.500 13.67 7.59 42.85 2.12
4125 6031 7.604164 ACTTTGCATGATAGTATAGTGCCATAC 59.396 37.037 13.67 0.00 35.03 2.39
4167 6073 2.372504 TCCGTACCCTTTTGATTGACCA 59.627 45.455 0.00 0.00 0.00 4.02
4203 6109 1.134699 TCATTGGCAGATGTCTCGTCC 60.135 52.381 8.72 0.00 0.00 4.79
4206 6112 1.263484 GCATCATTGGCAGATGTCTCG 59.737 52.381 15.56 3.76 43.66 4.04
4293 6201 0.107017 TATTTGGCTGCCTCTCCTGC 60.107 55.000 21.03 0.00 0.00 4.85
4461 6373 6.302535 TCTGATTCCCCATAGTTAACGAAA 57.697 37.500 0.00 0.00 0.00 3.46
4493 6405 7.888021 TCCCATTAAGAATTTTCACAGCTTCTA 59.112 33.333 0.00 0.00 0.00 2.10
4548 6460 3.744660 TGACTTTTTCTGAGCTCTTCCC 58.255 45.455 16.19 0.00 0.00 3.97
4603 6515 5.687770 TTGAATTTCTCATTTCTCGCACA 57.312 34.783 0.00 0.00 32.78 4.57
4705 6617 5.357878 TGCATGATCCTATCTCACCAAAAAC 59.642 40.000 0.00 0.00 0.00 2.43
4799 6712 6.657541 TCCTTGTGAATCAACCATAACCTAAC 59.342 38.462 0.00 0.00 32.18 2.34
5246 9116 8.964476 AACAGAGTTTCTTTTAGTTCATCAGA 57.036 30.769 0.00 0.00 0.00 3.27
5317 9187 5.646793 CACTCATCCACATTGATTCTCAGTT 59.353 40.000 0.00 0.00 0.00 3.16
5624 10150 0.392461 TTGATACCCGAAGCCTGCAC 60.392 55.000 0.00 0.00 0.00 4.57
5658 10184 2.447047 AGGAACCCAAGGACTGAAATGT 59.553 45.455 0.00 0.00 0.00 2.71
5666 10192 1.221021 CCGCTAGGAACCCAAGGAC 59.779 63.158 0.00 0.00 41.02 3.85
5764 10291 4.901250 TCTCTCATGCCATAATACCTGTCA 59.099 41.667 0.00 0.00 0.00 3.58
5845 10372 3.704231 ATGGGCACGGCTGGATGAC 62.704 63.158 0.00 0.00 0.00 3.06
5846 10373 3.410628 ATGGGCACGGCTGGATGA 61.411 61.111 0.00 0.00 0.00 2.92
5875 10402 5.406780 GTCAGGTGAATTGACTACTTGTGAG 59.593 44.000 0.00 0.00 41.29 3.51
6584 11651 8.316046 CGAAAATATCATGAAGCAACATCAAAC 58.684 33.333 0.00 0.00 0.00 2.93
6627 11695 9.760077 TTAACCTAAGAACAAACAAACAAACAA 57.240 25.926 0.00 0.00 0.00 2.83
6628 11696 9.760077 TTTAACCTAAGAACAAACAAACAAACA 57.240 25.926 0.00 0.00 0.00 2.83
6630 11698 9.984190 ACTTTAACCTAAGAACAAACAAACAAA 57.016 25.926 0.00 0.00 0.00 2.83
6715 11786 0.401738 TCACTGCCAAAGGAAGAGGG 59.598 55.000 0.00 0.00 31.36 4.30
6732 11803 9.139734 ACGTAATATTGGAAGTAACTAGGATCA 57.860 33.333 0.00 0.00 0.00 2.92
6780 11856 8.362639 GGCCATCATGAATTGTTAAACAGATAT 58.637 33.333 0.00 0.00 0.00 1.63
6827 11903 4.444164 CCCTATTTGCACTTTTGGTTGGTT 60.444 41.667 0.00 0.00 0.00 3.67
6912 11992 3.921677 ACTACTTAGCAGTTTTAGCGCA 58.078 40.909 11.47 0.00 37.01 6.09
7181 14015 0.394216 GCATCCCACTGCACATGGTA 60.394 55.000 10.65 0.00 41.87 3.25
7467 15906 4.130118 GAGAAGGAGAAAGAAACACAGCA 58.870 43.478 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.