Multiple sequence alignment - TraesCS5D01G429400

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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 TraesCS5D01G429400 chr5D 100.000 4675 0 0 1 4675 486900525 486895851 0.000000e+00 8634.0
1 TraesCS5D01G429400 chr5D 92.495 3691 223 27 602 4253 486910515 486906840 0.000000e+00 5232.0
2 TraesCS5D01G429400 chr5D 86.644 1475 131 27 2279 3720 487005991 487007432 0.000000e+00 1572.0
3 TraesCS5D01G429400 chr5D 88.866 988 77 17 2763 3720 487173149 487172165 0.000000e+00 1184.0
4 TraesCS5D01G429400 chr5D 85.973 1048 118 16 934 1974 487175365 487174340 0.000000e+00 1094.0
5 TraesCS5D01G429400 chr5D 84.981 1052 129 16 931 1974 487004661 487005691 0.000000e+00 1040.0
6 TraesCS5D01G429400 chr5D 85.837 699 83 11 224 912 12992447 12991755 0.000000e+00 728.0
7 TraesCS5D01G429400 chr5D 88.115 488 51 3 2281 2768 487174053 487173573 1.460000e-159 573.0
8 TraesCS5D01G429400 chr5D 90.625 352 24 5 4146 4494 486866664 486866319 4.260000e-125 459.0
9 TraesCS5D01G429400 chr5D 93.023 86 6 0 4040 4125 486873818 486873733 4.910000e-25 126.0
10 TraesCS5D01G429400 chr5B 92.505 3816 223 26 891 4675 598660542 598656759 0.000000e+00 5404.0
11 TraesCS5D01G429400 chr5B 88.624 1468 128 21 2280 3720 599123087 599121632 0.000000e+00 1749.0
12 TraesCS5D01G429400 chr5B 88.525 1403 129 18 2279 3664 598755594 598754207 0.000000e+00 1670.0
13 TraesCS5D01G429400 chr5B 89.289 971 53 14 3712 4675 598654166 598653240 0.000000e+00 1170.0
14 TraesCS5D01G429400 chr5B 85.741 1052 126 13 931 1974 599124426 599123391 0.000000e+00 1090.0
15 TraesCS5D01G429400 chr5B 84.455 1055 121 20 931 1974 598756919 598755897 0.000000e+00 1000.0
16 TraesCS5D01G429400 chr5B 87.649 672 69 13 224 890 692786279 692785617 0.000000e+00 769.0
17 TraesCS5D01G429400 chr5B 84.900 702 87 12 224 912 12860307 12859612 0.000000e+00 691.0
18 TraesCS5D01G429400 chr5B 88.750 240 20 5 1992 2228 599123329 599123094 2.130000e-73 287.0
19 TraesCS5D01G429400 chr5B 83.929 112 11 6 4 108 692786654 692786543 2.980000e-17 100.0
20 TraesCS5D01G429400 chr5A 91.806 2453 139 25 1545 3969 607578672 607576254 0.000000e+00 3360.0
21 TraesCS5D01G429400 chr5A 87.483 1470 132 24 2279 3720 607595487 607594042 0.000000e+00 1648.0
22 TraesCS5D01G429400 chr5A 84.814 1317 157 24 931 2228 607596785 607595493 0.000000e+00 1284.0
23 TraesCS5D01G429400 chr5A 89.102 679 71 3 877 1554 607588159 607587483 0.000000e+00 841.0
24 TraesCS5D01G429400 chr5A 84.943 704 85 14 224 912 9856588 9855891 0.000000e+00 693.0
25 TraesCS5D01G429400 chr5A 94.077 439 19 2 4053 4488 607576251 607575817 0.000000e+00 660.0
26 TraesCS5D01G429400 chr7D 78.347 1621 282 48 2074 3660 566321003 566322588 0.000000e+00 985.0
27 TraesCS5D01G429400 chr7D 88.126 699 56 17 224 913 591455314 591454634 0.000000e+00 806.0
28 TraesCS5D01G429400 chr7D 94.595 37 2 0 1946 1982 566201222 566201258 1.820000e-04 58.4
29 TraesCS5D01G429400 chr6A 88.567 691 57 9 224 912 579956112 579955442 0.000000e+00 819.0
30 TraesCS5D01G429400 chr6A 83.465 127 20 1 4178 4304 438582320 438582445 2.960000e-22 117.0
31 TraesCS5D01G429400 chr6A 100.000 28 0 0 4288 4315 26984006 26984033 8.000000e-03 52.8
32 TraesCS5D01G429400 chr6D 87.246 690 64 11 226 912 433769012 433768344 0.000000e+00 765.0
33 TraesCS5D01G429400 chr6D 76.987 239 19 18 4 212 389609357 389609125 2.300000e-18 104.0
34 TraesCS5D01G429400 chr6D 93.617 47 3 0 4258 4304 287023819 287023773 2.330000e-08 71.3
35 TraesCS5D01G429400 chr2A 87.556 667 56 18 254 914 691230952 691230307 0.000000e+00 747.0
36 TraesCS5D01G429400 chr3D 82.420 876 128 20 2292 3149 45931952 45932819 0.000000e+00 741.0
37 TraesCS5D01G429400 chr6B 77.348 1267 248 32 2409 3665 503007506 503008743 0.000000e+00 713.0
38 TraesCS5D01G429400 chr6B 84.800 125 19 0 4180 4304 447890134 447890010 4.910000e-25 126.0
39 TraesCS5D01G429400 chr1B 86.287 649 66 14 224 868 551720941 551721570 0.000000e+00 684.0
40 TraesCS5D01G429400 chr7B 80.077 778 133 18 1131 1892 617839533 617840304 4.090000e-155 558.0
41 TraesCS5D01G429400 chr4B 80.452 619 108 12 1247 1857 32970685 32971298 1.190000e-125 460.0
42 TraesCS5D01G429400 chr3A 78.283 396 78 6 1083 1474 57498815 57499206 1.000000e-61 248.0
43 TraesCS5D01G429400 chr4D 97.500 40 1 0 4231 4270 32061594 32061555 8.390000e-08 69.4
44 TraesCS5D01G429400 chr4A 95.349 43 2 0 2169 2211 611935162 611935120 8.390000e-08 69.4
45 TraesCS5D01G429400 chr1A 93.182 44 3 0 6 49 34192464 34192507 1.090000e-06 65.8


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 TraesCS5D01G429400 chr5D 486895851 486900525 4674 True 8634.000000 8634 100.000000 1 4675 1 chr5D.!!$R4 4674
1 TraesCS5D01G429400 chr5D 486906840 486910515 3675 True 5232.000000 5232 92.495000 602 4253 1 chr5D.!!$R5 3651
2 TraesCS5D01G429400 chr5D 487004661 487007432 2771 False 1306.000000 1572 85.812500 931 3720 2 chr5D.!!$F1 2789
3 TraesCS5D01G429400 chr5D 487172165 487175365 3200 True 950.333333 1184 87.651333 934 3720 3 chr5D.!!$R6 2786
4 TraesCS5D01G429400 chr5D 12991755 12992447 692 True 728.000000 728 85.837000 224 912 1 chr5D.!!$R1 688
5 TraesCS5D01G429400 chr5B 598653240 598660542 7302 True 3287.000000 5404 90.897000 891 4675 2 chr5B.!!$R2 3784
6 TraesCS5D01G429400 chr5B 598754207 598756919 2712 True 1335.000000 1670 86.490000 931 3664 2 chr5B.!!$R3 2733
7 TraesCS5D01G429400 chr5B 599121632 599124426 2794 True 1042.000000 1749 87.705000 931 3720 3 chr5B.!!$R4 2789
8 TraesCS5D01G429400 chr5B 12859612 12860307 695 True 691.000000 691 84.900000 224 912 1 chr5B.!!$R1 688
9 TraesCS5D01G429400 chr5B 692785617 692786654 1037 True 434.500000 769 85.789000 4 890 2 chr5B.!!$R5 886
10 TraesCS5D01G429400 chr5A 607575817 607578672 2855 True 2010.000000 3360 92.941500 1545 4488 2 chr5A.!!$R3 2943
11 TraesCS5D01G429400 chr5A 607594042 607596785 2743 True 1466.000000 1648 86.148500 931 3720 2 chr5A.!!$R4 2789
12 TraesCS5D01G429400 chr5A 607587483 607588159 676 True 841.000000 841 89.102000 877 1554 1 chr5A.!!$R2 677
13 TraesCS5D01G429400 chr5A 9855891 9856588 697 True 693.000000 693 84.943000 224 912 1 chr5A.!!$R1 688
14 TraesCS5D01G429400 chr7D 566321003 566322588 1585 False 985.000000 985 78.347000 2074 3660 1 chr7D.!!$F2 1586
15 TraesCS5D01G429400 chr7D 591454634 591455314 680 True 806.000000 806 88.126000 224 913 1 chr7D.!!$R1 689
16 TraesCS5D01G429400 chr6A 579955442 579956112 670 True 819.000000 819 88.567000 224 912 1 chr6A.!!$R1 688
17 TraesCS5D01G429400 chr6D 433768344 433769012 668 True 765.000000 765 87.246000 226 912 1 chr6D.!!$R3 686
18 TraesCS5D01G429400 chr2A 691230307 691230952 645 True 747.000000 747 87.556000 254 914 1 chr2A.!!$R1 660
19 TraesCS5D01G429400 chr3D 45931952 45932819 867 False 741.000000 741 82.420000 2292 3149 1 chr3D.!!$F1 857
20 TraesCS5D01G429400 chr6B 503007506 503008743 1237 False 713.000000 713 77.348000 2409 3665 1 chr6B.!!$F1 1256
21 TraesCS5D01G429400 chr1B 551720941 551721570 629 False 684.000000 684 86.287000 224 868 1 chr1B.!!$F1 644
22 TraesCS5D01G429400 chr7B 617839533 617840304 771 False 558.000000 558 80.077000 1131 1892 1 chr7B.!!$F1 761
23 TraesCS5D01G429400 chr4B 32970685 32971298 613 False 460.000000 460 80.452000 1247 1857 1 chr4B.!!$F1 610

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
682 870 0.178961 ACCCCTTTGGAACTTGGAGC 60.179 55.0 0.00 0.00 38.00 4.70 F
726 914 0.624500 ATTGGAGGGGCTTGGAGCTA 60.625 55.0 0.00 0.00 41.99 3.32 F
2358 2665 0.036732 TTCCTCCCAGTCACATGTGC 59.963 55.0 21.38 15.51 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 2651 0.450583 GCAGATGCACATGTGACTGG 59.549 55.000 29.80 14.14 41.59 4.00 R
2498 2811 2.437359 AACTCGCTCATGCAGCCC 60.437 61.111 10.34 0.00 46.74 5.19 R
3732 4546 0.609131 ACAAGGTCTTGAATGCGGGG 60.609 55.000 16.55 0.00 42.93 5.73 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
34 35 1.301716 CCGGCGACCATTCCATAGG 60.302 63.158 9.30 0.00 0.00 2.57
58 59 0.251653 TAGCCACCACTCCTTCGTCT 60.252 55.000 0.00 0.00 0.00 4.18
61 76 1.001633 GCCACCACTCCTTCGTCTTTA 59.998 52.381 0.00 0.00 0.00 1.85
80 95 0.719015 ACTCCCTCTTCCCTCATCCA 59.281 55.000 0.00 0.00 0.00 3.41
86 130 0.719015 TCTTCCCTCATCCACCCTCT 59.281 55.000 0.00 0.00 0.00 3.69
97 141 0.689412 CCACCCTCTCTCCTTCCTCC 60.689 65.000 0.00 0.00 0.00 4.30
110 154 1.138661 CTTCCTCCTGCATCCTCTGTC 59.861 57.143 0.00 0.00 0.00 3.51
115 159 1.277273 TCCTGCATCCTCTGTCTGTTG 59.723 52.381 0.00 0.00 0.00 3.33
117 161 2.093075 CCTGCATCCTCTGTCTGTTGAT 60.093 50.000 0.00 0.00 0.00 2.57
118 162 3.607741 CTGCATCCTCTGTCTGTTGATT 58.392 45.455 0.00 0.00 0.00 2.57
119 163 4.008330 CTGCATCCTCTGTCTGTTGATTT 58.992 43.478 0.00 0.00 0.00 2.17
120 164 4.401022 TGCATCCTCTGTCTGTTGATTTT 58.599 39.130 0.00 0.00 0.00 1.82
121 165 4.828939 TGCATCCTCTGTCTGTTGATTTTT 59.171 37.500 0.00 0.00 0.00 1.94
143 187 5.538849 TTTCCCTGGTTTTTGTATTGGAC 57.461 39.130 0.00 0.00 0.00 4.02
144 188 4.463050 TCCCTGGTTTTTGTATTGGACT 57.537 40.909 0.00 0.00 0.00 3.85
149 193 5.508994 CCTGGTTTTTGTATTGGACTTGGAC 60.509 44.000 0.00 0.00 0.00 4.02
156 200 4.084287 TGTATTGGACTTGGACGAGTACT 58.916 43.478 0.00 0.00 31.46 2.73
157 201 3.870633 ATTGGACTTGGACGAGTACTC 57.129 47.619 13.18 13.18 31.46 2.59
170 214 4.274421 CGAGTACTCGCTGTAGATTTGA 57.726 45.455 30.44 0.00 46.50 2.69
173 217 6.604012 CGAGTACTCGCTGTAGATTTGATAT 58.396 40.000 30.44 0.00 46.50 1.63
181 225 6.920210 TCGCTGTAGATTTGATATTGTGAGAG 59.080 38.462 0.00 0.00 0.00 3.20
183 227 7.862873 CGCTGTAGATTTGATATTGTGAGAGTA 59.137 37.037 0.00 0.00 0.00 2.59
213 257 8.649973 AATGATTATTTCTTGACGAGTACTCC 57.350 34.615 17.23 4.79 0.00 3.85
216 260 4.722361 ATTTCTTGACGAGTACTCCCTC 57.278 45.455 17.23 11.96 0.00 4.30
230 392 0.399075 TCCCTCGGGTCTTTTTGGTC 59.601 55.000 1.18 0.00 36.47 4.02
250 412 5.700832 TGGTCTAAACATGTTAGCAGTGAAG 59.299 40.000 12.39 0.51 0.00 3.02
280 442 9.121517 GCAATGATTGACGATATATGAAAAAGG 57.878 33.333 9.76 0.00 0.00 3.11
324 498 1.880027 GCACCGTCTTGACCTGAAATT 59.120 47.619 0.00 0.00 0.00 1.82
385 560 4.217550 GCTTTGTCTTTGTTATACTGGCCA 59.782 41.667 4.71 4.71 0.00 5.36
472 655 7.872061 ATGATTGGGAATATAGTGGTACTGA 57.128 36.000 0.00 0.00 0.00 3.41
485 668 3.063997 GTGGTACTGATATGCTGTGTTGC 59.936 47.826 0.00 0.00 0.00 4.17
499 686 4.442073 GCTGTGTTGCTGATTTTAACAGTG 59.558 41.667 0.00 0.00 36.72 3.66
517 704 9.871238 TTAACAGTGAGACCTAAAATATCACTC 57.129 33.333 0.00 0.00 45.60 3.51
682 870 0.178961 ACCCCTTTGGAACTTGGAGC 60.179 55.000 0.00 0.00 38.00 4.70
726 914 0.624500 ATTGGAGGGGCTTGGAGCTA 60.625 55.000 0.00 0.00 41.99 3.32
734 922 1.219393 GCTTGGAGCTACTTCGGCT 59.781 57.895 0.00 0.00 43.26 5.52
737 925 0.973632 TTGGAGCTACTTCGGCTTCA 59.026 50.000 0.00 0.00 42.80 3.02
863 1061 7.502226 TCTCCAAAATGCCGAATTTACATATCT 59.498 33.333 0.00 0.00 37.51 1.98
889 1087 2.945456 TCTGCCCGATACTGATACACT 58.055 47.619 0.00 0.00 0.00 3.55
914 1112 8.862325 TTATCCATATCGGTGCATTTTAGATT 57.138 30.769 0.00 0.00 35.57 2.40
953 1151 6.658816 AGGTACTCTCTCTGCATACATATGAG 59.341 42.308 10.38 0.00 35.75 2.90
964 1162 4.615223 GCATACATATGAGGCATTGCTGTG 60.615 45.833 10.38 0.00 35.75 3.66
971 1169 2.429971 TGAGGCATTGCTGTGTTTTTCA 59.570 40.909 8.82 0.00 0.00 2.69
974 1172 4.060205 AGGCATTGCTGTGTTTTTCATTC 58.940 39.130 8.82 0.00 0.00 2.67
981 1179 3.737774 GCTGTGTTTTTCATTCTTCAGGC 59.262 43.478 0.00 0.00 0.00 4.85
1061 1262 2.106338 TGCAAGGAACTGTCTTCCATCA 59.894 45.455 1.64 0.00 40.86 3.07
1081 1282 1.532604 GCTGGGGGCCTTGTTAACAC 61.533 60.000 8.07 0.00 34.27 3.32
1161 1362 3.012934 ACAGCTGTTAGTTTGGGTTGT 57.987 42.857 15.25 0.00 0.00 3.32
1239 1446 4.329545 GGCAAGGCAGTCGGACCA 62.330 66.667 4.14 0.00 0.00 4.02
1278 1485 2.728922 GAGATCGACCGCGTTATTTCT 58.271 47.619 4.92 1.19 38.98 2.52
1494 1701 1.590238 CGGATGAAGAGCGTGATCAAC 59.410 52.381 0.00 0.00 0.00 3.18
1565 1772 3.376918 GCTTCTTGGTGCTGGGGC 61.377 66.667 0.00 0.00 39.26 5.80
1569 1782 4.290622 CTTGGTGCTGGGGCTGGT 62.291 66.667 0.00 0.00 39.59 4.00
1590 1806 1.270094 CGTGGAGTTACTGGTGCTTCA 60.270 52.381 0.00 0.00 0.00 3.02
1592 1808 2.548480 GTGGAGTTACTGGTGCTTCAAC 59.452 50.000 0.00 0.00 0.00 3.18
1602 1818 1.340889 GGTGCTTCAACCATGCTGAAA 59.659 47.619 9.09 0.00 40.22 2.69
1877 2096 7.631717 AGGAATTTACTTGCTCCTATTGTTC 57.368 36.000 0.00 0.00 36.51 3.18
1880 2099 6.759497 ATTTACTTGCTCCTATTGTTCCAC 57.241 37.500 0.00 0.00 0.00 4.02
1903 2124 6.808704 CACGAGGTGATTAGGATGTACATATG 59.191 42.308 8.71 0.00 35.23 1.78
1904 2125 6.719829 ACGAGGTGATTAGGATGTACATATGA 59.280 38.462 8.71 0.00 0.00 2.15
1905 2126 7.397476 ACGAGGTGATTAGGATGTACATATGAT 59.603 37.037 8.71 3.03 0.00 2.45
1974 2203 7.919690 TCACATGCTAATTAAACTATCTGCAC 58.080 34.615 0.00 0.00 31.92 4.57
1975 2204 7.012327 TCACATGCTAATTAAACTATCTGCACC 59.988 37.037 0.00 0.00 31.92 5.01
1988 2274 0.793861 CTGCACCATTGTTGCATTGC 59.206 50.000 9.44 0.46 37.95 3.56
2084 2376 3.989817 GCACTGCAGTTTTTCCTTTATGG 59.010 43.478 18.94 1.79 37.10 2.74
2102 2394 2.562912 CGTGTTGCACCCATGAGC 59.437 61.111 0.00 0.00 0.00 4.26
2185 2491 1.602377 CGTCAATTTCCGGATAAGGCC 59.398 52.381 4.15 0.00 0.00 5.19
2250 2556 3.489355 TGATGCAGATTGACAACCAAGT 58.511 40.909 0.00 0.00 38.31 3.16
2258 2564 5.409826 CAGATTGACAACCAAGTAGAGGAAC 59.590 44.000 0.00 0.00 38.31 3.62
2345 2651 2.164422 GCACAAGTAGGCATTTTCCTCC 59.836 50.000 0.00 0.00 37.66 4.30
2350 2657 2.239907 AGTAGGCATTTTCCTCCCAGTC 59.760 50.000 0.00 0.00 37.66 3.51
2358 2665 0.036732 TTCCTCCCAGTCACATGTGC 59.963 55.000 21.38 15.51 0.00 4.57
2475 2788 1.163554 CTTGAGCAAGAGGACAAGGC 58.836 55.000 4.22 0.00 40.79 4.35
2498 2811 1.407979 AGTTAATCCACCTAGCGGACG 59.592 52.381 1.46 0.00 34.69 4.79
2521 2834 0.250252 TGCATGAGCGAGTTGTTGGA 60.250 50.000 0.00 0.00 46.23 3.53
2557 2870 1.884075 ATGTGGTCGCCGAAGCAGTA 61.884 55.000 0.00 0.00 39.83 2.74
2832 3594 7.758528 AGCTTGATTGATGTTAATGCTTCTTTC 59.241 33.333 0.00 0.00 0.00 2.62
2895 3663 4.529109 ACTGACTGAGAAAGTTAGGAGC 57.471 45.455 2.84 0.00 44.80 4.70
2901 3669 1.814169 GAAAGTTAGGAGCCGCCCG 60.814 63.158 0.00 0.00 37.37 6.13
2913 3681 1.079405 CCGCCCGTACAGTGTCATT 60.079 57.895 0.00 0.00 0.00 2.57
3003 3775 0.179004 TGTTGACCGATGGCAAAGGT 60.179 50.000 15.70 15.70 41.63 3.50
3009 3781 1.079127 CGATGGCAAAGGTCGGACT 60.079 57.895 8.23 0.00 0.00 3.85
3101 3873 3.282021 CCGGAGAAATCACAATGGATGT 58.718 45.455 0.00 0.00 45.34 3.06
3173 3949 3.609409 GCGGCTCAGAAAACACTTAAAGG 60.609 47.826 0.00 0.00 0.00 3.11
3232 4008 2.687935 GGTTCAGAAACACTTCAAGCCA 59.312 45.455 0.00 0.00 37.10 4.75
3355 4131 0.833287 TAGCTGACAAGGGCATCTCC 59.167 55.000 0.00 0.00 0.00 3.71
3431 4207 2.763249 ACGCACAGCTTCTTTTCAAG 57.237 45.000 0.00 0.00 0.00 3.02
3732 4546 4.137543 GTCCCATAAACCATCCTCATGAC 58.862 47.826 0.00 0.00 30.57 3.06
3738 4552 2.745308 CCATCCTCATGACCCCGCA 61.745 63.158 0.00 0.00 30.57 5.69
3756 4570 3.181497 CCGCATTCAAGACCTTGTAATGG 60.181 47.826 21.77 16.21 41.16 3.16
3801 4615 5.437289 TCAGTTGTGCCTTTCTTTGTATG 57.563 39.130 0.00 0.00 0.00 2.39
3809 4623 3.309954 GCCTTTCTTTGTATGCTACCTCG 59.690 47.826 0.00 0.00 0.00 4.63
3820 4634 5.768662 TGTATGCTACCTCGAGCTAATACTT 59.231 40.000 6.99 0.00 43.27 2.24
3914 4737 9.527157 TTCTTCCATGTTTTGATCCTATACAAA 57.473 29.630 0.00 0.00 34.80 2.83
3916 4739 9.793252 CTTCCATGTTTTGATCCTATACAAAAG 57.207 33.333 0.00 0.00 43.39 2.27
3931 4754 9.638239 CCTATACAAAAGTTTGCAATGTAACAT 57.362 29.630 12.47 2.63 41.79 2.71
4133 8482 2.212652 TCTATCAATGGTGATGTGCGC 58.787 47.619 0.00 0.00 44.49 6.09
4183 8536 3.680937 CCTGCTTAACCATGCATGTTTTG 59.319 43.478 24.58 13.95 38.59 2.44
4186 8540 5.847304 TGCTTAACCATGCATGTTTTGTTA 58.153 33.333 24.58 20.33 33.94 2.41
4367 8721 0.886563 GCATTGCAGCTCTTTGGTCT 59.113 50.000 3.15 0.00 0.00 3.85
4370 8724 3.129988 GCATTGCAGCTCTTTGGTCTATT 59.870 43.478 3.15 0.00 0.00 1.73
4371 8725 4.336433 GCATTGCAGCTCTTTGGTCTATTA 59.664 41.667 3.15 0.00 0.00 0.98
4372 8726 5.009410 GCATTGCAGCTCTTTGGTCTATTAT 59.991 40.000 3.15 0.00 0.00 1.28
4373 8727 6.205464 GCATTGCAGCTCTTTGGTCTATTATA 59.795 38.462 3.15 0.00 0.00 0.98
4428 8782 1.518133 CTTGCTCCTCTCGAAGGCG 60.518 63.158 8.32 4.57 45.78 5.52
4442 8796 0.322187 AAGGCGTACCATCACAACCC 60.322 55.000 0.00 0.00 39.06 4.11
4482 8836 3.996921 ATGTGAGCCTCATCTGTTCTT 57.003 42.857 0.00 0.00 0.00 2.52
4488 8842 5.877012 GTGAGCCTCATCTGTTCTTTTATGA 59.123 40.000 0.00 0.00 0.00 2.15
4489 8843 6.036953 GTGAGCCTCATCTGTTCTTTTATGAG 59.963 42.308 0.00 0.00 43.17 2.90
4490 8844 4.880696 AGCCTCATCTGTTCTTTTATGAGC 59.119 41.667 0.00 0.00 42.53 4.26
4491 8845 4.036144 GCCTCATCTGTTCTTTTATGAGCC 59.964 45.833 0.00 0.00 42.53 4.70
4492 8846 5.435291 CCTCATCTGTTCTTTTATGAGCCT 58.565 41.667 0.00 0.00 42.53 4.58
4493 8847 5.526846 CCTCATCTGTTCTTTTATGAGCCTC 59.473 44.000 0.00 0.00 42.53 4.70
4494 8848 6.053632 TCATCTGTTCTTTTATGAGCCTCA 57.946 37.500 0.00 0.00 0.00 3.86
4495 8849 6.656902 TCATCTGTTCTTTTATGAGCCTCAT 58.343 36.000 12.62 12.62 40.72 2.90
4496 8850 6.765036 TCATCTGTTCTTTTATGAGCCTCATC 59.235 38.462 11.20 0.00 38.26 2.92
4497 8851 6.305272 TCTGTTCTTTTATGAGCCTCATCT 57.695 37.500 11.20 0.00 38.26 2.90
4498 8852 6.111382 TCTGTTCTTTTATGAGCCTCATCTG 58.889 40.000 11.20 0.00 38.26 2.90
4499 8853 5.809001 TGTTCTTTTATGAGCCTCATCTGT 58.191 37.500 11.20 0.00 38.26 3.41
4500 8854 6.240894 TGTTCTTTTATGAGCCTCATCTGTT 58.759 36.000 11.20 0.00 38.26 3.16
4501 8855 6.372659 TGTTCTTTTATGAGCCTCATCTGTTC 59.627 38.462 11.20 0.00 38.26 3.18
4502 8856 6.305272 TCTTTTATGAGCCTCATCTGTTCT 57.695 37.500 11.20 0.00 38.26 3.01
4503 8857 6.111382 TCTTTTATGAGCCTCATCTGTTCTG 58.889 40.000 11.20 0.00 38.26 3.02
4526 8880 5.934043 TGTTATGTGAACCTCATCTGTTCTG 59.066 40.000 4.94 0.00 42.04 3.02
4542 8896 4.065088 TGTTCTGTTATGTGAGCCTTGAC 58.935 43.478 0.00 0.00 0.00 3.18
4551 8905 1.220477 GAGCCTTGACCTCCTGAGC 59.780 63.158 0.00 0.00 0.00 4.26
4569 8923 3.256960 GGCCTTCACCCCTGTCCA 61.257 66.667 0.00 0.00 0.00 4.02
4619 8973 7.068716 GGCAAGGTAGTCAGATTGGAATTTTAT 59.931 37.037 0.00 0.00 0.00 1.40
4643 8997 4.808414 TCACTCTAGGTGGTGATTTCTG 57.192 45.455 10.33 0.00 45.38 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 3.246350 TGGATGAGGGAAGAGGGAGTAAA 60.246 47.826 0.00 0.00 0.00 2.01
61 76 0.719015 TGGATGAGGGAAGAGGGAGT 59.281 55.000 0.00 0.00 0.00 3.85
80 95 0.338120 CAGGAGGAAGGAGAGAGGGT 59.662 60.000 0.00 0.00 0.00 4.34
86 130 0.341258 AGGATGCAGGAGGAAGGAGA 59.659 55.000 0.00 0.00 0.00 3.71
97 141 2.756840 TCAACAGACAGAGGATGCAG 57.243 50.000 0.00 0.00 0.00 4.41
119 163 6.157123 AGTCCAATACAAAAACCAGGGAAAAA 59.843 34.615 0.00 0.00 0.00 1.94
120 164 5.663556 AGTCCAATACAAAAACCAGGGAAAA 59.336 36.000 0.00 0.00 0.00 2.29
121 165 5.212745 AGTCCAATACAAAAACCAGGGAAA 58.787 37.500 0.00 0.00 0.00 3.13
122 166 4.810345 AGTCCAATACAAAAACCAGGGAA 58.190 39.130 0.00 0.00 0.00 3.97
123 167 4.463050 AGTCCAATACAAAAACCAGGGA 57.537 40.909 0.00 0.00 0.00 4.20
124 168 4.262420 CCAAGTCCAATACAAAAACCAGGG 60.262 45.833 0.00 0.00 0.00 4.45
129 173 5.008316 ACTCGTCCAAGTCCAATACAAAAAC 59.992 40.000 0.00 0.00 0.00 2.43
132 176 4.345859 ACTCGTCCAAGTCCAATACAAA 57.654 40.909 0.00 0.00 0.00 2.83
133 177 4.525487 AGTACTCGTCCAAGTCCAATACAA 59.475 41.667 0.00 0.00 0.00 2.41
134 178 4.084287 AGTACTCGTCCAAGTCCAATACA 58.916 43.478 0.00 0.00 0.00 2.29
135 179 4.670347 GAGTACTCGTCCAAGTCCAATAC 58.330 47.826 7.22 0.00 0.00 1.89
136 180 3.376234 CGAGTACTCGTCCAAGTCCAATA 59.624 47.826 32.24 0.00 46.99 1.90
137 181 2.163815 CGAGTACTCGTCCAAGTCCAAT 59.836 50.000 32.24 0.00 46.99 3.16
140 184 3.992636 CGAGTACTCGTCCAAGTCC 57.007 57.895 32.24 0.00 46.99 3.85
156 200 6.805713 TCTCACAATATCAAATCTACAGCGA 58.194 36.000 0.00 0.00 0.00 4.93
157 201 6.699204 ACTCTCACAATATCAAATCTACAGCG 59.301 38.462 0.00 0.00 0.00 5.18
188 232 7.711339 GGGAGTACTCGTCAAGAAATAATCATT 59.289 37.037 16.56 0.00 0.00 2.57
212 256 0.400594 AGACCAAAAAGACCCGAGGG 59.599 55.000 6.63 6.63 42.03 4.30
213 257 3.412237 TTAGACCAAAAAGACCCGAGG 57.588 47.619 0.00 0.00 0.00 4.63
216 260 4.277423 ACATGTTTAGACCAAAAAGACCCG 59.723 41.667 0.00 0.00 0.00 5.28
217 261 5.784578 ACATGTTTAGACCAAAAAGACCC 57.215 39.130 0.00 0.00 0.00 4.46
218 262 6.861572 GCTAACATGTTTAGACCAAAAAGACC 59.138 38.462 17.78 0.00 0.00 3.85
219 263 7.422399 TGCTAACATGTTTAGACCAAAAAGAC 58.578 34.615 17.78 1.67 0.00 3.01
220 264 7.284489 ACTGCTAACATGTTTAGACCAAAAAGA 59.716 33.333 17.78 0.00 0.00 2.52
230 392 5.611796 TGCTTCACTGCTAACATGTTTAG 57.388 39.130 17.78 14.64 0.00 1.85
250 412 6.778108 TCATATATCGTCAATCATTGCATGC 58.222 36.000 11.82 11.82 0.00 4.06
294 457 4.393680 GGTCAAGACGGTGCATATAAACAA 59.606 41.667 0.00 0.00 0.00 2.83
296 459 4.034048 CAGGTCAAGACGGTGCATATAAAC 59.966 45.833 0.00 0.00 0.00 2.01
302 465 0.396435 TTCAGGTCAAGACGGTGCAT 59.604 50.000 0.00 0.00 0.00 3.96
324 498 6.757897 ATTGCATGTTACTGCTAAGCTTTA 57.242 33.333 3.20 0.00 42.75 1.85
385 560 6.664428 AGTACTAATGTGTTGCCCAATTTT 57.336 33.333 0.00 0.00 0.00 1.82
393 568 7.548075 ACAATACCACTAGTACTAATGTGTTGC 59.452 37.037 21.95 0.00 32.46 4.17
394 569 8.997621 ACAATACCACTAGTACTAATGTGTTG 57.002 34.615 21.18 21.18 32.46 3.33
472 655 6.923012 TGTTAAAATCAGCAACACAGCATAT 58.077 32.000 0.00 0.00 36.85 1.78
513 700 9.586435 AAAGGAAAACAATCACTTTAAAGAGTG 57.414 29.630 21.92 11.31 46.58 3.51
516 703 8.878769 GCAAAAGGAAAACAATCACTTTAAAGA 58.121 29.630 21.92 0.62 31.71 2.52
517 704 8.663911 TGCAAAAGGAAAACAATCACTTTAAAG 58.336 29.630 13.76 13.76 31.71 1.85
576 764 6.230472 TGTACATCTATCATGGCATAACACC 58.770 40.000 0.00 0.00 0.00 4.16
682 870 1.843368 ATGTTGATGCCCTGTTCCAG 58.157 50.000 0.00 0.00 0.00 3.86
726 914 2.610727 GCTCTACTGTTGAAGCCGAAGT 60.611 50.000 0.00 0.00 0.00 3.01
734 922 4.415881 TCCTGTTTGCTCTACTGTTGAA 57.584 40.909 0.00 0.00 0.00 2.69
737 925 3.136626 ACCTTCCTGTTTGCTCTACTGTT 59.863 43.478 0.00 0.00 0.00 3.16
833 1031 4.871933 AATTCGGCATTTTGGAGAAGTT 57.128 36.364 0.00 0.00 0.00 2.66
863 1061 6.095021 GTGTATCAGTATCGGGCAGATATACA 59.905 42.308 10.51 12.25 43.13 2.29
868 1066 3.501349 AGTGTATCAGTATCGGGCAGAT 58.499 45.455 5.28 5.28 43.19 2.90
869 1067 2.945456 AGTGTATCAGTATCGGGCAGA 58.055 47.619 0.00 0.00 0.00 4.26
889 1087 8.862325 AATCTAAAATGCACCGATATGGATAA 57.138 30.769 0.00 0.00 42.00 1.75
914 1112 4.344978 AGAGTACCTGAGAGTGCATGTAA 58.655 43.478 0.00 0.00 0.00 2.41
924 1122 3.660970 ATGCAGAGAGAGTACCTGAGA 57.339 47.619 0.00 0.00 0.00 3.27
953 1151 4.060205 AGAATGAAAAACACAGCAATGCC 58.940 39.130 0.00 0.00 0.00 4.40
964 1162 5.047731 AGCCTTAGCCTGAAGAATGAAAAAC 60.048 40.000 0.00 0.00 41.25 2.43
971 1169 3.883669 CAGAAGCCTTAGCCTGAAGAAT 58.116 45.455 0.00 0.00 41.25 2.40
974 1172 1.339438 TGCAGAAGCCTTAGCCTGAAG 60.339 52.381 0.00 0.00 41.25 3.02
981 1179 3.201290 CATACCTGTGCAGAAGCCTTAG 58.799 50.000 0.02 0.00 41.13 2.18
1061 1262 1.076727 GTTAACAAGGCCCCCAGCT 59.923 57.895 0.00 0.00 43.05 4.24
1081 1282 1.000283 GGACATATGACTCTGGGAGCG 60.000 57.143 10.38 0.00 32.04 5.03
1161 1362 2.397597 TCATAGTACCTCCATGCTGCA 58.602 47.619 4.13 4.13 0.00 4.41
1239 1446 1.374252 GTCATCACGGCCGACAACT 60.374 57.895 35.90 5.52 0.00 3.16
1278 1485 0.975556 TGGTCTTGCGGCAGAGGATA 60.976 55.000 1.67 0.00 0.00 2.59
1565 1772 0.966920 ACCAGTAACTCCACGACCAG 59.033 55.000 0.00 0.00 0.00 4.00
1569 1782 1.000506 GAAGCACCAGTAACTCCACGA 59.999 52.381 0.00 0.00 0.00 4.35
1877 2096 3.383505 TGTACATCCTAATCACCTCGTGG 59.616 47.826 0.99 0.99 39.83 4.94
1880 2099 7.158099 TCATATGTACATCCTAATCACCTCG 57.842 40.000 12.68 0.00 0.00 4.63
1903 2124 6.238759 GGCAGACCATAACCACAAAAGATATC 60.239 42.308 0.00 0.00 35.26 1.63
1904 2125 5.594317 GGCAGACCATAACCACAAAAGATAT 59.406 40.000 0.00 0.00 35.26 1.63
1905 2126 4.947388 GGCAGACCATAACCACAAAAGATA 59.053 41.667 0.00 0.00 35.26 1.98
1948 2175 8.066595 GTGCAGATAGTTTAATTAGCATGTGAG 58.933 37.037 0.00 0.00 32.98 3.51
2070 2361 3.183574 GCAACACGCCATAAAGGAAAAAC 59.816 43.478 0.00 0.00 41.22 2.43
2144 2450 3.865745 CGACCTATGGTAAAGACAGCAAG 59.134 47.826 0.00 0.00 35.25 4.01
2185 2491 3.813724 ACGCCTCATCAATCAGATCAATG 59.186 43.478 0.00 0.00 33.72 2.82
2250 2556 5.804639 TCTGCTTTGCATTAAGTTCCTCTA 58.195 37.500 0.36 0.00 38.13 2.43
2258 2564 2.417933 AGCGACTCTGCTTTGCATTAAG 59.582 45.455 0.00 0.00 44.46 1.85
2345 2651 0.450583 GCAGATGCACATGTGACTGG 59.549 55.000 29.80 14.14 41.59 4.00
2358 2665 4.694037 TCTCATTGACTGAAACTGCAGATG 59.306 41.667 23.35 10.25 39.20 2.90
2475 2788 4.618965 GTCCGCTAGGTGGATTAACTTAG 58.381 47.826 3.09 0.00 44.40 2.18
2498 2811 2.437359 AACTCGCTCATGCAGCCC 60.437 61.111 10.34 0.00 46.74 5.19
2521 2834 3.009723 CACATTTACCGCTTCATCCTGT 58.990 45.455 0.00 0.00 0.00 4.00
2557 2870 2.639327 GCCAGCCCTTGAACGCAAT 61.639 57.895 0.00 0.00 32.68 3.56
2832 3594 3.367025 CCTGACGGCTTTAAGAAGTTACG 59.633 47.826 0.00 0.00 35.25 3.18
2895 3663 1.079405 AATGACACTGTACGGGCGG 60.079 57.895 6.65 0.00 0.00 6.13
2901 3669 6.183360 CCTCATCGAAAAGAATGACACTGTAC 60.183 42.308 0.00 0.00 0.00 2.90
2913 3681 3.055819 CCTTCTCCACCTCATCGAAAAGA 60.056 47.826 0.00 0.00 0.00 2.52
3003 3775 7.162761 TGGTATTCTTGAAATTTACAGTCCGA 58.837 34.615 0.00 0.00 0.00 4.55
3037 3809 4.096681 TCTGCTCCTAGATTTGAGGTCAA 58.903 43.478 0.00 0.00 35.40 3.18
3101 3873 0.950836 CATCAAAAGGTCACGTGCCA 59.049 50.000 24.48 9.27 0.00 4.92
3152 3924 3.609409 GCCTTTAAGTGTTTTCTGAGCCG 60.609 47.826 0.00 0.00 0.00 5.52
3232 4008 3.951775 CTCAGCCTGTTGAGTAACTCT 57.048 47.619 3.14 0.00 39.76 3.24
3431 4207 6.609533 CATGAGCCTAATCATTCATGTAAGC 58.390 40.000 5.41 0.00 41.09 3.09
3438 4219 7.649533 ATGAAAACATGAGCCTAATCATTCA 57.350 32.000 0.00 0.00 37.84 2.57
3694 4508 0.613260 GGACTGACCACAGCCACATA 59.387 55.000 0.00 0.00 46.95 2.29
3732 4546 0.609131 ACAAGGTCTTGAATGCGGGG 60.609 55.000 16.55 0.00 42.93 5.73
3738 4552 5.520748 ACTCCCATTACAAGGTCTTGAAT 57.479 39.130 16.55 9.25 42.93 2.57
3756 4570 5.886960 AGTGCAGTCATCAAAATAACTCC 57.113 39.130 0.00 0.00 0.00 3.85
3801 4615 8.266392 TCTAATAAGTATTAGCTCGAGGTAGC 57.734 38.462 22.31 16.52 42.95 3.58
3914 4737 6.623549 CGGAGATGATGTTACATTGCAAACTT 60.624 38.462 1.71 0.00 0.00 2.66
3916 4739 5.030295 CGGAGATGATGTTACATTGCAAAC 58.970 41.667 1.71 0.00 0.00 2.93
4183 8536 1.058695 CGTCTGAACGCCGTGATTAAC 59.941 52.381 0.00 0.00 42.82 2.01
4186 8540 3.856508 CGTCTGAACGCCGTGATT 58.143 55.556 0.00 0.00 42.82 2.57
4383 8737 4.395959 AGCTGCAAAATATGTTGATGGG 57.604 40.909 9.96 0.00 0.00 4.00
4428 8782 1.279271 AGCTCTGGGTTGTGATGGTAC 59.721 52.381 0.00 0.00 0.00 3.34
4482 8836 5.426689 ACAGAACAGATGAGGCTCATAAA 57.573 39.130 28.89 1.83 37.20 1.40
4488 8842 4.223700 TCACATAACAGAACAGATGAGGCT 59.776 41.667 0.00 0.00 0.00 4.58
4489 8843 4.507710 TCACATAACAGAACAGATGAGGC 58.492 43.478 0.00 0.00 0.00 4.70
4490 8844 5.352569 GGTTCACATAACAGAACAGATGAGG 59.647 44.000 7.49 0.00 44.46 3.86
4491 8845 6.169094 AGGTTCACATAACAGAACAGATGAG 58.831 40.000 7.49 0.00 44.46 2.90
4492 8846 6.114187 AGGTTCACATAACAGAACAGATGA 57.886 37.500 7.49 0.00 44.46 2.92
4493 8847 5.934043 TGAGGTTCACATAACAGAACAGATG 59.066 40.000 7.49 0.00 44.46 2.90
4494 8848 6.114187 TGAGGTTCACATAACAGAACAGAT 57.886 37.500 7.49 0.00 44.46 2.90
4495 8849 5.545063 TGAGGTTCACATAACAGAACAGA 57.455 39.130 7.49 0.00 44.46 3.41
4496 8850 6.091849 CAGATGAGGTTCACATAACAGAACAG 59.908 42.308 7.49 0.00 44.46 3.16
4497 8851 5.934043 CAGATGAGGTTCACATAACAGAACA 59.066 40.000 7.49 0.00 44.46 3.18
4498 8852 5.934625 ACAGATGAGGTTCACATAACAGAAC 59.065 40.000 0.00 0.00 42.51 3.01
4499 8853 6.114187 ACAGATGAGGTTCACATAACAGAA 57.886 37.500 0.00 0.00 0.00 3.02
4500 8854 5.745312 ACAGATGAGGTTCACATAACAGA 57.255 39.130 0.00 0.00 0.00 3.41
4501 8855 6.091849 CAGAACAGATGAGGTTCACATAACAG 59.908 42.308 7.87 0.00 45.45 3.16
4502 8856 5.934043 CAGAACAGATGAGGTTCACATAACA 59.066 40.000 7.87 0.00 45.45 2.41
4503 8857 5.934625 ACAGAACAGATGAGGTTCACATAAC 59.065 40.000 7.87 0.00 45.45 1.89
4526 8880 2.237392 AGGAGGTCAAGGCTCACATAAC 59.763 50.000 0.00 0.00 0.00 1.89
4542 8896 3.393970 TGAAGGCCGCTCAGGAGG 61.394 66.667 6.49 0.00 45.00 4.30
4551 8905 4.410400 GGACAGGGGTGAAGGCCG 62.410 72.222 0.00 0.00 0.00 6.13
4569 8923 3.131933 CCTCTGTCTTCTCGTGGATTGAT 59.868 47.826 0.00 0.00 0.00 2.57
4625 8979 5.420421 TCTCTTCAGAAATCACCACCTAGAG 59.580 44.000 0.00 0.00 0.00 2.43
4643 8997 1.134965 ACACTGCCTACGCATCTCTTC 60.135 52.381 0.00 0.00 46.11 2.87


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

AutoCloner maintained by Alex Coulton.