Multiple sequence alignment - TraesCS4D01G258200

Loading Multiple Alignment...

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 TraesCS4D01G258200 chr4D 100.000 3218 0 0 1 3218 428398875 428395658 0.000000e+00 5943.0
1 TraesCS4D01G258200 chr4D 88.542 1475 128 9 730 2196 427322398 427323839 0.000000e+00 1749.0
2 TraesCS4D01G258200 chr4D 87.330 1547 136 22 730 2258 427014253 427015757 0.000000e+00 1716.0
3 TraesCS4D01G258200 chr4D 86.779 1543 132 23 736 2258 428558549 428557059 0.000000e+00 1653.0
4 TraesCS4D01G258200 chr4D 84.109 1246 133 31 958 2182 427267891 427269092 0.000000e+00 1144.0
5 TraesCS4D01G258200 chr4D 83.912 547 54 14 961 1497 426900454 426900976 2.880000e-135 492.0
6 TraesCS4D01G258200 chr4D 92.701 274 19 1 2320 2593 427323907 427324179 8.370000e-106 394.0
7 TraesCS4D01G258200 chr4D 91.632 239 12 3 2192 2429 427015745 427015976 1.110000e-84 324.0
8 TraesCS4D01G258200 chr4D 85.784 204 26 1 1930 2130 428552740 428552537 2.510000e-51 213.0
9 TraesCS4D01G258200 chr4D 92.593 135 10 0 234 368 426903360 426903494 9.110000e-46 195.0
10 TraesCS4D01G258200 chr4D 92.593 135 10 0 234 368 427270441 427270575 9.110000e-46 195.0
11 TraesCS4D01G258200 chr4D 94.000 100 6 0 81 180 428559066 428558967 5.560000e-33 152.0
12 TraesCS4D01G258200 chr4D 88.393 112 9 2 426 535 427013334 427013443 7.240000e-27 132.0
13 TraesCS4D01G258200 chr4D 87.500 112 10 2 426 535 427319941 427320050 3.370000e-25 126.0
14 TraesCS4D01G258200 chr4D 84.286 140 10 8 2123 2258 428547310 428547179 3.370000e-25 126.0
15 TraesCS4D01G258200 chr4D 96.610 59 2 0 364 422 427013222 427013280 7.350000e-17 99.0
16 TraesCS4D01G258200 chr4D 95.238 63 2 1 364 426 428558884 428558823 7.350000e-17 99.0
17 TraesCS4D01G258200 chr4D 95.000 60 3 0 1 60 428559114 428559055 9.500000e-16 95.3
18 TraesCS4D01G258200 chr4D 94.737 57 2 1 370 426 427319835 427319890 1.590000e-13 87.9
19 TraesCS4D01G258200 chr4B 93.287 2145 104 19 81 2196 524901789 524899656 0.000000e+00 3127.0
20 TraesCS4D01G258200 chr4B 88.316 1532 131 13 731 2258 522681968 522683455 0.000000e+00 1794.0
21 TraesCS4D01G258200 chr4B 85.173 1214 138 21 906 2107 522677159 522678342 0.000000e+00 1206.0
22 TraesCS4D01G258200 chr4B 92.857 252 17 1 2343 2593 524899512 524899261 6.560000e-97 364.0
23 TraesCS4D01G258200 chr4B 89.883 257 22 3 2320 2575 522683475 522683728 8.610000e-86 327.0
24 TraesCS4D01G258200 chr4B 86.722 241 20 10 2027 2260 522683960 522684195 1.150000e-64 257.0
25 TraesCS4D01G258200 chr4B 76.618 479 55 27 426 879 526959982 526960428 9.040000e-51 211.0
26 TraesCS4D01G258200 chr4B 96.117 103 4 0 78 180 522681323 522681425 5.520000e-38 169.0
27 TraesCS4D01G258200 chr4B 98.333 60 1 0 1 60 524901837 524901778 4.390000e-19 106.0
28 TraesCS4D01G258200 chr4B 96.721 61 2 0 2197 2257 524899618 524899558 5.680000e-18 102.0
29 TraesCS4D01G258200 chr4A 94.469 1844 75 17 426 2258 37999442 38001269 0.000000e+00 2815.0
30 TraesCS4D01G258200 chr4A 84.821 1792 153 53 426 2196 37833148 37834841 0.000000e+00 1692.0
31 TraesCS4D01G258200 chr4A 84.821 1792 153 53 426 2196 38663873 38662180 0.000000e+00 1692.0
32 TraesCS4D01G258200 chr4A 83.511 1407 134 44 896 2258 38675718 38674366 0.000000e+00 1223.0
33 TraesCS4D01G258200 chr4A 88.599 614 38 6 2633 3218 73141808 73142417 0.000000e+00 717.0
34 TraesCS4D01G258200 chr4A 91.029 379 23 5 2198 2575 38662121 38661753 4.790000e-138 501.0
35 TraesCS4D01G258200 chr4A 89.518 353 27 4 2194 2546 38001259 38001601 3.810000e-119 438.0
36 TraesCS4D01G258200 chr4A 96.732 153 5 0 81 233 37999122 37999274 4.120000e-64 255.0
37 TraesCS4D01G258200 chr4A 96.825 126 4 0 297 422 37999272 37999397 9.040000e-51 211.0
38 TraesCS4D01G258200 chr4A 88.889 144 15 1 112 255 38668527 38668385 3.300000e-40 176.0
39 TraesCS4D01G258200 chr4A 93.069 101 7 0 78 178 37832762 37832862 7.190000e-32 148.0
40 TraesCS4D01G258200 chr4A 100.000 60 0 0 1 60 37999074 37999133 9.440000e-21 111.0
41 TraesCS4D01G258200 chr4A 93.651 63 3 1 364 426 37833037 37833098 3.420000e-15 93.5
42 TraesCS4D01G258200 chr4A 98.148 54 0 1 373 426 38663975 38663923 3.420000e-15 93.5
43 TraesCS4D01G258200 chr1D 89.203 602 30 17 2649 3218 319516453 319517051 0.000000e+00 719.0
44 TraesCS4D01G258200 chr1D 88.275 597 39 7 2649 3218 113831373 113830781 0.000000e+00 686.0
45 TraesCS4D01G258200 chr1D 86.401 603 43 17 2649 3218 25749732 25750328 9.800000e-175 623.0
46 TraesCS4D01G258200 chr1D 94.737 342 15 2 2879 3218 228045737 228046077 2.200000e-146 529.0
47 TraesCS4D01G258200 chr7D 89.185 601 29 24 2649 3218 636307394 636306799 0.000000e+00 717.0
48 TraesCS4D01G258200 chr7D 88.424 622 33 17 2624 3215 62129050 62129662 0.000000e+00 713.0
49 TraesCS4D01G258200 chr7D 88.852 601 31 14 2649 3218 635691752 635692347 0.000000e+00 706.0
50 TraesCS4D01G258200 chrUn 88.455 615 37 21 2635 3218 121739683 121739072 0.000000e+00 712.0
51 TraesCS4D01G258200 chr3D 89.076 595 32 20 2651 3218 378029824 378029236 0.000000e+00 708.0
52 TraesCS4D01G258200 chr3D 88.186 601 35 21 2649 3218 591127820 591127225 0.000000e+00 684.0
53 TraesCS4D01G258200 chr2D 88.667 600 33 18 2649 3218 304653729 304653135 0.000000e+00 699.0
54 TraesCS4D01G258200 chr2D 88.508 496 23 21 2756 3218 53898941 53899435 1.300000e-158 569.0
55 TraesCS4D01G258200 chr5D 87.940 597 41 12 2649 3218 389375386 389374794 0.000000e+00 675.0
56 TraesCS4D01G258200 chr5D 87.458 598 37 11 2651 3218 554395062 554394473 0.000000e+00 654.0
57 TraesCS4D01G258200 chr3A 87.171 608 42 21 2640 3218 733495604 733495004 0.000000e+00 658.0


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 TraesCS4D01G258200 chr4D 428395658 428398875 3217 True 5943.000000 5943 100.000000 1 3218 1 chr4D.!!$R1 3217
1 TraesCS4D01G258200 chr4D 427267891 427270575 2684 False 669.500000 1144 88.351000 234 2182 2 chr4D.!!$F3 1948
2 TraesCS4D01G258200 chr4D 427319835 427324179 4344 False 589.225000 1749 90.870000 370 2593 4 chr4D.!!$F4 2223
3 TraesCS4D01G258200 chr4D 427013222 427015976 2754 False 567.750000 1716 90.991250 364 2429 4 chr4D.!!$F2 2065
4 TraesCS4D01G258200 chr4D 428557059 428559114 2055 True 499.825000 1653 92.754250 1 2258 4 chr4D.!!$R4 2257
5 TraesCS4D01G258200 chr4D 426900454 426903494 3040 False 343.500000 492 88.252500 234 1497 2 chr4D.!!$F1 1263
6 TraesCS4D01G258200 chr4B 524899261 524901837 2576 True 924.750000 3127 95.299500 1 2593 4 chr4B.!!$R1 2592
7 TraesCS4D01G258200 chr4B 522677159 522684195 7036 False 750.600000 1794 89.242200 78 2575 5 chr4B.!!$F2 2497
8 TraesCS4D01G258200 chr4A 38674366 38675718 1352 True 1223.000000 1223 83.511000 896 2258 1 chr4A.!!$R2 1362
9 TraesCS4D01G258200 chr4A 37999074 38001601 2527 False 766.000000 2815 95.508800 1 2546 5 chr4A.!!$F3 2545
10 TraesCS4D01G258200 chr4A 38661753 38663975 2222 True 762.166667 1692 91.332667 373 2575 3 chr4A.!!$R3 2202
11 TraesCS4D01G258200 chr4A 73141808 73142417 609 False 717.000000 717 88.599000 2633 3218 1 chr4A.!!$F1 585
12 TraesCS4D01G258200 chr4A 37832762 37834841 2079 False 644.500000 1692 90.513667 78 2196 3 chr4A.!!$F2 2118
13 TraesCS4D01G258200 chr1D 319516453 319517051 598 False 719.000000 719 89.203000 2649 3218 1 chr1D.!!$F3 569
14 TraesCS4D01G258200 chr1D 113830781 113831373 592 True 686.000000 686 88.275000 2649 3218 1 chr1D.!!$R1 569
15 TraesCS4D01G258200 chr1D 25749732 25750328 596 False 623.000000 623 86.401000 2649 3218 1 chr1D.!!$F1 569
16 TraesCS4D01G258200 chr7D 636306799 636307394 595 True 717.000000 717 89.185000 2649 3218 1 chr7D.!!$R1 569
17 TraesCS4D01G258200 chr7D 62129050 62129662 612 False 713.000000 713 88.424000 2624 3215 1 chr7D.!!$F1 591
18 TraesCS4D01G258200 chr7D 635691752 635692347 595 False 706.000000 706 88.852000 2649 3218 1 chr7D.!!$F2 569
19 TraesCS4D01G258200 chrUn 121739072 121739683 611 True 712.000000 712 88.455000 2635 3218 1 chrUn.!!$R1 583
20 TraesCS4D01G258200 chr3D 378029236 378029824 588 True 708.000000 708 89.076000 2651 3218 1 chr3D.!!$R1 567
21 TraesCS4D01G258200 chr3D 591127225 591127820 595 True 684.000000 684 88.186000 2649 3218 1 chr3D.!!$R2 569
22 TraesCS4D01G258200 chr2D 304653135 304653729 594 True 699.000000 699 88.667000 2649 3218 1 chr2D.!!$R1 569
23 TraesCS4D01G258200 chr5D 389374794 389375386 592 True 675.000000 675 87.940000 2649 3218 1 chr5D.!!$R1 569
24 TraesCS4D01G258200 chr5D 554394473 554395062 589 True 654.000000 654 87.458000 2651 3218 1 chr5D.!!$R2 567
25 TraesCS4D01G258200 chr3A 733495004 733495604 600 True 658.000000 658 87.171000 2640 3218 1 chr3A.!!$R1 578

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
61 62 0.121197 TCCCATCTTGGTTCCCTCCT 59.879 55.0 0.0 0.0 35.17 3.69 F
62 63 0.257039 CCCATCTTGGTTCCCTCCTG 59.743 60.0 0.0 0.0 35.17 3.86 F
68 69 0.263172 TTGGTTCCCTCCTGCCAAAA 59.737 50.0 0.0 0.0 37.97 2.44 F
290 4382 0.770590 CGACACACAAGAAGACGACG 59.229 55.0 0.0 0.0 0.00 5.12 F
632 4828 0.902516 GAGGGGATCGAGATGGAGGG 60.903 65.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 8451 0.452585 CGTCTTCCTCCTCGTCTTCC 59.547 60.000 0.00 0.00 0.00 3.46 R
1812 8511 1.965754 GCACTCGGAAGATGCTCCCT 61.966 60.000 2.29 0.00 39.71 4.20 R
1990 8689 2.753029 GTTGCACCTGAGGAGCCT 59.247 61.111 18.18 0.00 38.50 4.58 R
2077 9511 2.434359 GACCTTCTCAACGGCGGG 60.434 66.667 13.24 2.75 0.00 6.13 R
2609 10111 0.108756 GTAGTTCCCTGGACGCACTC 60.109 60.000 0.00 0.00 0.00 3.51 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
46 47 6.376299 CAGAATTCTTCAATCAGACAATCCCA 59.624 38.462 4.86 0.00 0.00 4.37
50 51 6.070951 TCTTCAATCAGACAATCCCATCTT 57.929 37.500 0.00 0.00 0.00 2.40
51 52 5.884232 TCTTCAATCAGACAATCCCATCTTG 59.116 40.000 0.00 0.00 0.00 3.02
52 53 4.529897 TCAATCAGACAATCCCATCTTGG 58.470 43.478 0.00 0.00 37.25 3.61
53 54 4.018141 TCAATCAGACAATCCCATCTTGGT 60.018 41.667 0.00 0.00 35.17 3.67
54 55 4.598036 ATCAGACAATCCCATCTTGGTT 57.402 40.909 0.00 0.00 35.17 3.67
60 61 1.226311 ATCCCATCTTGGTTCCCTCC 58.774 55.000 0.00 0.00 35.17 4.30
61 62 0.121197 TCCCATCTTGGTTCCCTCCT 59.879 55.000 0.00 0.00 35.17 3.69
62 63 0.257039 CCCATCTTGGTTCCCTCCTG 59.743 60.000 0.00 0.00 35.17 3.86
63 64 0.394899 CCATCTTGGTTCCCTCCTGC 60.395 60.000 0.00 0.00 31.35 4.85
64 65 0.394899 CATCTTGGTTCCCTCCTGCC 60.395 60.000 0.00 0.00 0.00 4.85
65 66 0.846427 ATCTTGGTTCCCTCCTGCCA 60.846 55.000 0.00 0.00 0.00 4.92
68 69 0.263172 TTGGTTCCCTCCTGCCAAAA 59.737 50.000 0.00 0.00 37.97 2.44
69 70 0.263172 TGGTTCCCTCCTGCCAAAAA 59.737 50.000 0.00 0.00 0.00 1.94
180 4268 8.690203 TGAACCTGAACATTTCTGAAGAATTA 57.310 30.769 0.00 0.00 33.54 1.40
185 4273 8.786898 CCTGAACATTTCTGAAGAATTAGACAA 58.213 33.333 0.00 0.00 33.54 3.18
276 4368 3.807622 TCACAAAAGGAGATCAACGACAC 59.192 43.478 0.00 0.00 0.00 3.67
279 4371 3.469008 AAAGGAGATCAACGACACACA 57.531 42.857 0.00 0.00 0.00 3.72
286 4378 4.051922 AGATCAACGACACACAAGAAGAC 58.948 43.478 0.00 0.00 0.00 3.01
290 4382 0.770590 CGACACACAAGAAGACGACG 59.229 55.000 0.00 0.00 0.00 5.12
348 4440 2.551032 CTGATGCTTGCTTCACAACTGA 59.449 45.455 7.03 0.00 33.68 3.41
368 4465 5.011840 ACTGAAGTTAACTCCAGTAAGTCCC 59.988 44.000 24.25 0.00 38.02 4.46
632 4828 0.902516 GAGGGGATCGAGATGGAGGG 60.903 65.000 0.00 0.00 0.00 4.30
698 7074 5.407691 TGTGGATCGTCTCGTCAGTATATAC 59.592 44.000 4.60 4.60 0.00 1.47
745 7121 3.092301 GGAAGGGAAATGAAGAACCTGG 58.908 50.000 0.00 0.00 0.00 4.45
1427 7843 1.609635 TTATTGTGGGAGAGGCGCGA 61.610 55.000 12.10 0.00 0.00 5.87
1767 8451 2.100631 GCTGTTCATGGTCGACCCG 61.101 63.158 31.19 21.87 35.15 5.28
1812 8511 4.994852 ACAAAGAATGACGTAAAGCAGCTA 59.005 37.500 0.00 0.00 0.00 3.32
1962 8661 3.864789 TTGTTCCCTCAAGAGAAGCTT 57.135 42.857 0.00 0.00 37.29 3.74
1990 8689 2.380064 AGGATTCCAGGTGTTGCAAA 57.620 45.000 0.00 0.00 0.00 3.68
2150 9584 1.910580 ATCAAGTTCATCCCGCCGGT 61.911 55.000 1.90 0.00 0.00 5.28
2307 9799 7.733773 TCCATCAAGTAGAAGTTGATCCTTA 57.266 36.000 6.94 0.00 42.84 2.69
2311 9803 6.634805 TCAAGTAGAAGTTGATCCTTAGCAG 58.365 40.000 0.00 0.00 32.96 4.24
2312 9804 6.211584 TCAAGTAGAAGTTGATCCTTAGCAGT 59.788 38.462 0.00 0.00 32.96 4.40
2313 9805 6.613153 AGTAGAAGTTGATCCTTAGCAGTT 57.387 37.500 0.00 0.00 0.00 3.16
2314 9806 7.719871 AGTAGAAGTTGATCCTTAGCAGTTA 57.280 36.000 0.00 0.00 0.00 2.24
2315 9807 7.777095 AGTAGAAGTTGATCCTTAGCAGTTAG 58.223 38.462 0.00 0.00 0.00 2.34
2316 9808 5.423886 AGAAGTTGATCCTTAGCAGTTAGC 58.576 41.667 0.00 0.00 46.19 3.09
2356 9848 1.270252 CCATTTGTGTTGGCCTGGTTC 60.270 52.381 3.32 0.00 0.00 3.62
2383 9875 4.604843 ATTCTATGTGTCATTGTGCACG 57.395 40.909 13.13 0.00 38.36 5.34
2402 9894 3.917380 CACGTGTTCAGAGAATCAGAGAC 59.083 47.826 7.58 0.00 37.82 3.36
2470 9972 8.856153 ACATATGTTGTTTACATGGTCAGTTA 57.144 30.769 1.41 0.00 46.81 2.24
2522 10024 6.847956 TGTTTTTCAAAAATCATGAGCTGG 57.152 33.333 0.09 0.00 0.00 4.85
2558 10060 4.379793 GCAGTTCAAATGTTCTAAGCAACG 59.620 41.667 0.00 0.00 0.00 4.10
2567 10069 7.681939 AATGTTCTAAGCAACGGAAATCTAA 57.318 32.000 0.00 0.00 0.00 2.10
2575 10077 4.691216 AGCAACGGAAATCTAAAGAGTGAC 59.309 41.667 0.00 0.00 0.00 3.67
2578 10080 3.187700 CGGAAATCTAAAGAGTGACGGG 58.812 50.000 0.00 0.00 0.00 5.28
2593 10095 5.611374 AGTGACGGGTGGATTGATATTAAG 58.389 41.667 0.00 0.00 0.00 1.85
2594 10096 4.213482 GTGACGGGTGGATTGATATTAAGC 59.787 45.833 0.00 0.00 0.00 3.09
2595 10097 4.141597 TGACGGGTGGATTGATATTAAGCA 60.142 41.667 0.00 0.00 0.00 3.91
2596 10098 4.787551 ACGGGTGGATTGATATTAAGCAA 58.212 39.130 0.00 0.00 35.06 3.91
2597 10099 4.578928 ACGGGTGGATTGATATTAAGCAAC 59.421 41.667 0.00 0.00 32.99 4.17
2598 10100 4.578516 CGGGTGGATTGATATTAAGCAACA 59.421 41.667 5.49 0.00 32.99 3.33
2599 10101 5.277974 CGGGTGGATTGATATTAAGCAACAG 60.278 44.000 5.49 0.00 32.99 3.16
2600 10102 5.827797 GGGTGGATTGATATTAAGCAACAGA 59.172 40.000 5.49 0.00 32.99 3.41
2601 10103 6.321181 GGGTGGATTGATATTAAGCAACAGAA 59.679 38.462 5.49 0.00 32.99 3.02
2602 10104 7.147915 GGGTGGATTGATATTAAGCAACAGAAA 60.148 37.037 5.49 0.00 32.99 2.52
2603 10105 8.416329 GGTGGATTGATATTAAGCAACAGAAAT 58.584 33.333 5.49 0.00 32.99 2.17
2604 10106 9.455847 GTGGATTGATATTAAGCAACAGAAATC 57.544 33.333 0.00 0.00 32.99 2.17
2605 10107 9.412460 TGGATTGATATTAAGCAACAGAAATCT 57.588 29.630 0.00 0.00 32.99 2.40
2614 10116 6.917217 AAGCAACAGAAATCTATAGAGTGC 57.083 37.500 8.70 4.16 0.00 4.40
2615 10117 5.046529 AGCAACAGAAATCTATAGAGTGCG 58.953 41.667 8.70 3.89 0.00 5.34
2616 10118 4.806247 GCAACAGAAATCTATAGAGTGCGT 59.194 41.667 8.70 4.49 0.00 5.24
2617 10119 5.051374 GCAACAGAAATCTATAGAGTGCGTC 60.051 44.000 8.70 0.64 0.00 5.19
2618 10120 5.189659 ACAGAAATCTATAGAGTGCGTCC 57.810 43.478 8.70 0.00 0.00 4.79
2619 10121 4.645136 ACAGAAATCTATAGAGTGCGTCCA 59.355 41.667 8.70 0.00 0.00 4.02
2620 10122 5.218885 CAGAAATCTATAGAGTGCGTCCAG 58.781 45.833 8.70 0.00 0.00 3.86
2621 10123 4.279671 AGAAATCTATAGAGTGCGTCCAGG 59.720 45.833 8.70 0.00 0.00 4.45
2622 10124 1.982660 TCTATAGAGTGCGTCCAGGG 58.017 55.000 0.00 0.00 0.00 4.45
2627 10129 0.251653 AGAGTGCGTCCAGGGAACTA 60.252 55.000 0.00 0.00 40.21 2.24
2629 10131 0.830444 AGTGCGTCCAGGGAACTACA 60.830 55.000 0.00 0.00 40.21 2.74
2647 10149 4.075793 CCCGACCTCTCTCCCCCA 62.076 72.222 0.00 0.00 0.00 4.96
2664 10171 1.609501 CACCCGACCTCTCTCCCAA 60.610 63.158 0.00 0.00 0.00 4.12
2729 10237 2.041405 CCTCAGTCCTCCCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
2730 10238 2.780693 CTCAGTCCTCCCCCTCCA 59.219 66.667 0.00 0.00 0.00 3.86
2731 10239 1.316266 CTCAGTCCTCCCCCTCCAT 59.684 63.158 0.00 0.00 0.00 3.41
2862 10801 0.614979 CTCCCTCCTCCTCCAACGAA 60.615 60.000 0.00 0.00 0.00 3.85
2896 10859 4.778143 GCGGGTTGGCGGATGAGT 62.778 66.667 0.00 0.00 0.00 3.41
2947 10926 2.628657 CCGAGGGGTTTAGATCGAGATT 59.371 50.000 0.00 0.00 37.35 2.40
2959 10938 1.446792 CGAGATTCACTGCGGCTGT 60.447 57.895 6.70 6.70 0.00 4.40
3158 11139 1.135083 AGACATAGTCGCCGGTGAAAG 60.135 52.381 21.49 12.11 37.67 2.62
3170 11151 1.668151 GTGAAAGCCGAGCCGACTT 60.668 57.895 0.00 0.00 29.61 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 4268 2.572191 TTTCGTCAGTGTCGTTGTCT 57.428 45.000 9.53 0.00 0.00 3.41
185 4273 1.002142 TGTCGATTTCGTCAGTGTCGT 60.002 47.619 9.53 0.00 40.80 4.34
276 4368 0.508641 CAAGCCGTCGTCTTCTTGTG 59.491 55.000 0.00 0.00 33.27 3.33
279 4371 1.004918 CCCAAGCCGTCGTCTTCTT 60.005 57.895 0.00 0.00 0.00 2.52
286 4378 0.596082 AAATCAAACCCAAGCCGTCG 59.404 50.000 0.00 0.00 0.00 5.12
290 4382 0.246360 CCGGAAATCAAACCCAAGCC 59.754 55.000 0.00 0.00 0.00 4.35
348 4440 3.899980 ACGGGACTTACTGGAGTTAACTT 59.100 43.478 10.02 0.00 0.00 2.66
359 4451 3.285371 CGGCTGACGGGACTTACT 58.715 61.111 0.00 0.00 39.42 2.24
422 4519 2.748647 TCCGGCATCGTCGTCTGA 60.749 61.111 0.00 0.00 33.95 3.27
423 4520 2.278206 CTCCGGCATCGTCGTCTG 60.278 66.667 0.00 0.00 33.95 3.51
632 4828 1.784525 GTCCAATCCATCGATCGTCC 58.215 55.000 15.94 0.00 0.00 4.79
745 7121 1.316735 CGTTCGTTTCCGAGTCGAATC 59.683 52.381 15.64 2.01 45.24 2.52
841 7225 1.097232 CGCCATGGAATTCAGCTCAA 58.903 50.000 18.40 0.00 0.00 3.02
906 7290 2.288273 GGAGGAAGTTCCGTATGGATCG 60.288 54.545 16.31 0.00 45.91 3.69
1254 7670 1.646189 GCTCAAGATCTTGGACGTCC 58.354 55.000 30.33 28.17 40.78 4.79
1767 8451 0.452585 CGTCTTCCTCCTCGTCTTCC 59.547 60.000 0.00 0.00 0.00 3.46
1812 8511 1.965754 GCACTCGGAAGATGCTCCCT 61.966 60.000 2.29 0.00 39.71 4.20
1951 8650 3.501445 CCTTCCACTGAAAGCTTCTCTTG 59.499 47.826 0.00 0.00 37.60 3.02
1990 8689 2.753029 GTTGCACCTGAGGAGCCT 59.247 61.111 18.18 0.00 38.50 4.58
2077 9511 2.434359 GACCTTCTCAACGGCGGG 60.434 66.667 13.24 2.75 0.00 6.13
2150 9584 3.387962 AGTAGATTCTTCTGGGGCATCA 58.612 45.455 0.00 0.00 33.17 3.07
2307 9799 2.009042 GCGATCAAGGTGCTAACTGCT 61.009 52.381 0.00 0.00 43.37 4.24
2311 9803 1.429148 CCGGCGATCAAGGTGCTAAC 61.429 60.000 9.30 0.00 0.00 2.34
2312 9804 1.153449 CCGGCGATCAAGGTGCTAA 60.153 57.895 9.30 0.00 0.00 3.09
2313 9805 1.399744 ATCCGGCGATCAAGGTGCTA 61.400 55.000 9.30 0.00 0.00 3.49
2314 9806 2.650813 GATCCGGCGATCAAGGTGCT 62.651 60.000 9.30 0.00 43.87 4.40
2315 9807 2.203070 ATCCGGCGATCAAGGTGC 60.203 61.111 9.30 0.00 0.00 5.01
2316 9808 1.951130 CGATCCGGCGATCAAGGTG 60.951 63.158 9.30 0.00 44.55 4.00
2317 9809 2.417516 CGATCCGGCGATCAAGGT 59.582 61.111 9.30 0.00 44.55 3.50
2356 9848 5.449588 GCACAATGACACATAGAATTCAGGG 60.450 44.000 8.44 0.68 0.00 4.45
2383 9875 3.917380 CACGTCTCTGATTCTCTGAACAC 59.083 47.826 0.00 0.00 0.00 3.32
2402 9894 4.567558 TGAACACAACCTTACAGTTACACG 59.432 41.667 0.00 0.00 0.00 4.49
2470 9972 9.231297 ACAAATTGTGCAGTATAACTCAGTAAT 57.769 29.630 0.00 0.00 0.00 1.89
2508 10010 8.316214 ACATTTTTATCACCAGCTCATGATTTT 58.684 29.630 13.18 0.00 36.87 1.82
2522 10024 8.075593 ACATTTGAACTGCACATTTTTATCAC 57.924 30.769 0.00 0.00 0.00 3.06
2558 10060 3.933332 CACCCGTCACTCTTTAGATTTCC 59.067 47.826 0.00 0.00 0.00 3.13
2567 10069 1.348064 TCAATCCACCCGTCACTCTT 58.652 50.000 0.00 0.00 0.00 2.85
2575 10077 4.578516 TGTTGCTTAATATCAATCCACCCG 59.421 41.667 0.00 0.00 0.00 5.28
2578 10080 9.455847 GATTTCTGTTGCTTAATATCAATCCAC 57.544 33.333 0.00 0.00 0.00 4.02
2593 10095 4.806247 ACGCACTCTATAGATTTCTGTTGC 59.194 41.667 2.11 3.47 0.00 4.17
2594 10096 5.460419 GGACGCACTCTATAGATTTCTGTTG 59.540 44.000 2.11 0.00 0.00 3.33
2595 10097 5.127194 TGGACGCACTCTATAGATTTCTGTT 59.873 40.000 2.11 0.00 0.00 3.16
2596 10098 4.645136 TGGACGCACTCTATAGATTTCTGT 59.355 41.667 2.11 0.00 0.00 3.41
2597 10099 5.188327 TGGACGCACTCTATAGATTTCTG 57.812 43.478 2.11 0.00 0.00 3.02
2598 10100 4.279671 CCTGGACGCACTCTATAGATTTCT 59.720 45.833 2.11 0.00 0.00 2.52
2599 10101 4.551388 CCTGGACGCACTCTATAGATTTC 58.449 47.826 2.11 0.00 0.00 2.17
2600 10102 3.322254 CCCTGGACGCACTCTATAGATTT 59.678 47.826 2.11 0.00 0.00 2.17
2601 10103 2.894126 CCCTGGACGCACTCTATAGATT 59.106 50.000 2.11 0.00 0.00 2.40
2602 10104 2.108425 TCCCTGGACGCACTCTATAGAT 59.892 50.000 2.11 0.00 0.00 1.98
2603 10105 1.493446 TCCCTGGACGCACTCTATAGA 59.507 52.381 1.69 1.69 0.00 1.98
2604 10106 1.982660 TCCCTGGACGCACTCTATAG 58.017 55.000 0.00 0.00 0.00 1.31
2605 10107 2.029623 GTTCCCTGGACGCACTCTATA 58.970 52.381 0.00 0.00 0.00 1.31
2606 10108 0.824759 GTTCCCTGGACGCACTCTAT 59.175 55.000 0.00 0.00 0.00 1.98
2607 10109 0.251653 AGTTCCCTGGACGCACTCTA 60.252 55.000 0.00 0.00 0.00 2.43
2608 10110 0.251653 TAGTTCCCTGGACGCACTCT 60.252 55.000 0.00 0.00 0.00 3.24
2609 10111 0.108756 GTAGTTCCCTGGACGCACTC 60.109 60.000 0.00 0.00 0.00 3.51
2610 10112 0.830444 TGTAGTTCCCTGGACGCACT 60.830 55.000 0.00 0.00 0.00 4.40
2611 10113 0.669625 GTGTAGTTCCCTGGACGCAC 60.670 60.000 0.00 0.00 0.00 5.34
2612 10114 1.669440 GTGTAGTTCCCTGGACGCA 59.331 57.895 0.00 0.00 0.00 5.24
2613 10115 1.079336 GGTGTAGTTCCCTGGACGC 60.079 63.158 0.00 0.00 0.00 5.19
2614 10116 1.595357 GGGTGTAGTTCCCTGGACG 59.405 63.158 0.00 0.00 41.58 4.79
2615 10117 0.901580 TCGGGTGTAGTTCCCTGGAC 60.902 60.000 0.00 0.00 42.56 4.02
2616 10118 0.901580 GTCGGGTGTAGTTCCCTGGA 60.902 60.000 0.00 0.00 42.56 3.86
2617 10119 1.595357 GTCGGGTGTAGTTCCCTGG 59.405 63.158 0.00 0.00 42.56 4.45
2618 10120 0.903454 AGGTCGGGTGTAGTTCCCTG 60.903 60.000 0.00 0.00 42.56 4.45
2619 10121 0.614134 GAGGTCGGGTGTAGTTCCCT 60.614 60.000 0.00 0.00 42.56 4.20
2620 10122 0.614134 AGAGGTCGGGTGTAGTTCCC 60.614 60.000 0.00 0.00 41.41 3.97
2621 10123 0.816373 GAGAGGTCGGGTGTAGTTCC 59.184 60.000 0.00 0.00 0.00 3.62
2622 10124 1.744522 GAGAGAGGTCGGGTGTAGTTC 59.255 57.143 0.00 0.00 0.00 3.01
2627 10129 2.037527 GGGAGAGAGGTCGGGTGT 59.962 66.667 0.00 0.00 0.00 4.16
2629 10131 4.077180 GGGGGAGAGAGGTCGGGT 62.077 72.222 0.00 0.00 0.00 5.28
2647 10149 1.305381 CTTGGGAGAGAGGTCGGGT 60.305 63.158 0.00 0.00 0.00 5.28
2729 10237 0.034059 GGTAGTGGGAGGCGATGATG 59.966 60.000 0.00 0.00 0.00 3.07
2730 10238 1.464376 CGGTAGTGGGAGGCGATGAT 61.464 60.000 0.00 0.00 0.00 2.45
2731 10239 2.125326 CGGTAGTGGGAGGCGATGA 61.125 63.158 0.00 0.00 0.00 2.92
2827 10766 4.166888 AGATGGACGCCGCTGCAT 62.167 61.111 0.00 0.00 37.32 3.96
2896 10859 2.421073 CAGATCTCATCGCAGCCAAAAA 59.579 45.455 0.00 0.00 0.00 1.94
2959 10938 2.254350 CGTTGTCGAGACGAGGCA 59.746 61.111 14.23 0.00 42.82 4.75
3135 11116 1.076923 ACCGGCGACTATGTCTCCT 60.077 57.895 9.30 0.00 35.51 3.69


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

AutoCloner maintained by Alex Coulton.