Multiple sequence alignment - TraesCS3A01G221700

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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 TraesCS3A01G221700 chr3A 100.000 9527 0 0 1 9527 412367720 412377246 0.000000e+00 17594.0
1 TraesCS3A01G221700 chr3A 93.396 106 7 0 2343 2448 32479621 32479516 3.560000e-34 158.0
2 TraesCS3A01G221700 chr3A 92.157 51 4 0 148 198 39860591 39860641 1.330000e-08 73.1
3 TraesCS3A01G221700 chr3A 93.023 43 1 2 569 611 521727250 521727210 2.870000e-05 62.1
4 TraesCS3A01G221700 chr3D 96.444 6243 140 36 756 6954 316566370 316560166 0.000000e+00 10224.0
5 TraesCS3A01G221700 chr3D 96.802 2595 58 12 6955 9527 316560115 316557524 0.000000e+00 4309.0
6 TraesCS3A01G221700 chr3D 89.890 544 46 7 1 537 316567413 316566872 0.000000e+00 691.0
7 TraesCS3A01G221700 chr3D 91.837 196 9 5 581 769 316566600 316566405 5.670000e-67 267.0
8 TraesCS3A01G221700 chr3D 78.333 120 16 7 498 608 542914348 542914466 1.720000e-07 69.4
9 TraesCS3A01G221700 chr3B 93.966 2602 97 20 2877 5436 403106587 403109170 0.000000e+00 3880.0
10 TraesCS3A01G221700 chr3B 96.204 2318 47 8 6955 9261 403110637 403112924 0.000000e+00 3755.0
11 TraesCS3A01G221700 chr3B 94.771 2161 70 22 756 2886 403104359 403106506 0.000000e+00 3325.0
12 TraesCS3A01G221700 chr3B 94.313 1442 50 11 5521 6954 403109169 403110586 0.000000e+00 2180.0
13 TraesCS3A01G221700 chr3B 83.294 425 55 7 1 411 403088230 403088652 2.510000e-100 377.0
14 TraesCS3A01G221700 chr3B 91.803 183 10 2 9269 9451 403112974 403113151 5.710000e-62 250.0
15 TraesCS3A01G221700 chr3B 88.430 121 7 5 385 498 373962197 373962077 1.290000e-28 139.0
16 TraesCS3A01G221700 chr1B 88.757 507 40 10 3530 4027 470895111 470895609 1.060000e-168 604.0
17 TraesCS3A01G221700 chr1B 97.368 38 1 0 573 610 644579552 644579589 2.220000e-06 65.8
18 TraesCS3A01G221700 chr7A 90.323 248 14 4 3788 4026 672010849 672010603 5.550000e-82 316.0
19 TraesCS3A01G221700 chr7A 85.022 227 23 6 3530 3754 672011058 672010841 4.480000e-53 220.0
20 TraesCS3A01G221700 chr7A 93.182 44 3 0 497 540 57736230 57736273 2.220000e-06 65.8
21 TraesCS3A01G221700 chr4D 86.765 136 9 7 369 495 73776795 73776930 9.970000e-30 143.0
22 TraesCS3A01G221700 chr4D 93.407 91 3 1 5435 5525 190653953 190654040 2.160000e-26 132.0
23 TraesCS3A01G221700 chr4D 92.683 41 3 0 570 610 124052107 124052147 1.030000e-04 60.2
24 TraesCS3A01G221700 chr7B 86.131 137 12 5 369 498 70637413 70637277 3.590000e-29 141.0
25 TraesCS3A01G221700 chr7B 78.151 119 20 4 103 218 91780724 91780609 4.770000e-08 71.3
26 TraesCS3A01G221700 chr5A 88.889 117 7 4 382 492 350085413 350085529 1.290000e-28 139.0
27 TraesCS3A01G221700 chr5A 92.632 95 3 3 5435 5528 155735564 155735655 6.000000e-27 134.0
28 TraesCS3A01G221700 chr6B 78.409 264 20 24 383 610 182272676 182272414 4.640000e-28 137.0
29 TraesCS3A01G221700 chr6B 86.992 123 9 4 383 498 207462174 207462052 2.160000e-26 132.0
30 TraesCS3A01G221700 chr6B 84.058 138 14 6 369 498 403890002 403889865 1.000000e-24 126.0
31 TraesCS3A01G221700 chr5B 88.333 120 7 5 383 495 308836173 308836292 4.640000e-28 137.0
32 TraesCS3A01G221700 chr2A 88.793 116 7 5 383 492 454737705 454737820 4.640000e-28 137.0
33 TraesCS3A01G221700 chrUn 86.992 123 9 5 383 498 292646549 292646427 2.160000e-26 132.0
34 TraesCS3A01G221700 chrUn 91.579 95 4 2 5434 5527 100223824 100223733 2.790000e-25 128.0
35 TraesCS3A01G221700 chr6D 93.407 91 3 1 5435 5525 77298540 77298627 2.160000e-26 132.0
36 TraesCS3A01G221700 chr6D 88.182 110 8 3 5421 5528 412759772 412759666 1.000000e-24 126.0
37 TraesCS3A01G221700 chr6D 83.333 90 7 7 148 232 109901055 109900969 1.030000e-09 76.8
38 TraesCS3A01G221700 chr6D 97.222 36 1 0 573 608 237188364 237188329 2.870000e-05 62.1
39 TraesCS3A01G221700 chr2D 91.089 101 4 3 5435 5535 44481298 44481393 2.160000e-26 132.0
40 TraesCS3A01G221700 chr2D 85.915 71 6 4 147 214 190120719 190120788 1.330000e-08 73.1
41 TraesCS3A01G221700 chr2D 100.000 29 0 0 9020 9048 485048662 485048690 5.000000e-03 54.7
42 TraesCS3A01G221700 chr1A 90.291 103 5 3 5424 5526 579222359 579222262 7.760000e-26 130.0
43 TraesCS3A01G221700 chr7D 88.785 107 8 3 5427 5532 441864128 441864025 2.790000e-25 128.0
44 TraesCS3A01G221700 chr2B 82.308 130 19 3 94 221 141562311 141562184 1.010000e-19 110.0
45 TraesCS3A01G221700 chr4B 79.508 122 18 5 100 217 63764963 63765081 7.930000e-11 80.5
46 TraesCS3A01G221700 chr4B 94.737 38 2 0 573 610 188156480 188156443 1.030000e-04 60.2
47 TraesCS3A01G221700 chr1D 87.097 62 8 0 497 558 331539158 331539097 4.770000e-08 71.3
48 TraesCS3A01G221700 chr6A 83.562 73 10 2 127 198 617705623 617705552 6.170000e-07 67.6
49 TraesCS3A01G221700 chr6A 97.222 36 1 0 573 608 551628025 551627990 2.870000e-05 62.1


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 TraesCS3A01G221700 chr3A 412367720 412377246 9526 False 17594.00 17594 100.00000 1 9527 1 chr3A.!!$F2 9526
1 TraesCS3A01G221700 chr3D 316557524 316567413 9889 True 3872.75 10224 93.74325 1 9527 4 chr3D.!!$R1 9526
2 TraesCS3A01G221700 chr3B 403104359 403113151 8792 False 2678.00 3880 94.21140 756 9451 5 chr3B.!!$F2 8695

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
947 1259 0.108963 AACCAAATTCCCCGTCGACA 59.891 50.000 17.16 0.00 0.00 4.35 F
1437 1750 0.970937 TCTTCGCCTCCGTCTCCAAT 60.971 55.000 0.00 0.00 35.54 3.16 F
2435 2753 2.093306 TATCACCTGAGGTTGCAACG 57.907 50.000 22.67 11.30 31.02 4.10 F
2978 3404 1.268032 GCTTATAAGCGTGCGCATGTT 60.268 47.619 29.00 22.04 42.88 2.71 F
3460 3899 0.875908 ACTGCGTATATGCTGCGGTG 60.876 55.000 20.20 6.46 45.91 4.94 F
5288 5763 1.005037 TGGCACGTAGCTCAACCTG 60.005 57.895 9.31 0.00 44.79 4.00 F
5806 6282 2.561569 CCCTGTTAGGTTTCGCTATGG 58.438 52.381 0.00 0.00 31.93 2.74 F
7284 7834 0.380378 GTGTTGAGTTTGCTGCGGAA 59.620 50.000 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2518 0.923358 ACAAGGACCCAACCACAGAA 59.077 50.000 0.00 0.0 0.00 3.02 R
2535 2869 1.202580 GCCAGCCTAGACAGTATGGTG 60.203 57.143 0.00 0.0 43.62 4.17 R
3443 3882 1.594021 CCACCGCAGCATATACGCA 60.594 57.895 0.00 0.0 0.00 5.24 R
4857 5322 2.440409 CCAGGAATTTGAGGTGTGGAG 58.560 52.381 0.00 0.0 0.00 3.86 R
5430 5905 0.410663 TGGGACGGAGGGAGTAAGAA 59.589 55.000 0.00 0.0 0.00 2.52 R
6449 6925 1.409802 CCTGGCCATTCATCAAGAGCT 60.410 52.381 5.51 0.0 0.00 4.09 R
7788 8340 1.201647 GTAGACGCTGCAACCTGAGTA 59.798 52.381 0.00 0.0 0.00 2.59 R
8892 9453 0.911769 TCACGAGGCCCATCAGATTT 59.088 50.000 0.00 0.0 0.00 2.17 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
52 53 4.853924 ACCAATTTCTCGCAAAGACATT 57.146 36.364 0.00 0.00 35.26 2.71
125 126 7.724305 ATAAGACGCTCAAACTTTTGTTCTA 57.276 32.000 1.75 0.00 42.67 2.10
130 131 5.907391 ACGCTCAAACTTTTGTTCTAAATCG 59.093 36.000 1.75 0.00 42.67 3.34
131 132 6.133392 CGCTCAAACTTTTGTTCTAAATCGA 58.867 36.000 1.75 0.00 42.67 3.59
135 136 8.280909 TCAAACTTTTGTTCTAAATCGAATGC 57.719 30.769 0.00 0.00 42.67 3.56
179 180 6.494842 TGTTTGTTCACTTATTTCAGTCTGC 58.505 36.000 0.00 0.00 0.00 4.26
186 187 7.953158 TCACTTATTTCAGTCTGCATATAGC 57.047 36.000 0.00 0.00 45.96 2.97
198 199 8.441608 CAGTCTGCATATAGCTCATATTGAAAC 58.558 37.037 0.00 0.00 45.94 2.78
242 243 5.047235 AGACGCAAGGAGTAGTACTTTTCAT 60.047 40.000 0.00 0.00 46.39 2.57
243 244 5.548406 ACGCAAGGAGTAGTACTTTTCATT 58.452 37.500 0.00 0.38 46.39 2.57
244 245 5.995897 ACGCAAGGAGTAGTACTTTTCATTT 59.004 36.000 0.00 0.00 46.39 2.32
273 274 9.672086 TTTCAAACCATATTAGTCAGTTTTTCG 57.328 29.630 0.00 0.00 0.00 3.46
275 276 6.753107 AACCATATTAGTCAGTTTTTCGGG 57.247 37.500 0.00 0.00 0.00 5.14
277 278 5.878669 ACCATATTAGTCAGTTTTTCGGGAC 59.121 40.000 0.00 0.00 0.00 4.46
352 353 5.570234 TTTGCGGGAACTTCATAATTACC 57.430 39.130 0.00 0.00 0.00 2.85
397 398 4.337555 TGTATCTCTAAGGCTGGTCGTAAC 59.662 45.833 0.00 0.00 0.00 2.50
419 426 6.112994 ACGAGAGTATCATAGATACGCATG 57.887 41.667 18.50 13.57 46.88 4.06
428 435 2.533266 AGATACGCATGCCAACTAGG 57.467 50.000 13.15 0.00 41.84 3.02
445 452 6.071391 CCAACTAGGCAAATTTAATGAGGTGT 60.071 38.462 0.00 0.00 0.00 4.16
510 518 2.998316 TCCGGATGTGTCATGCATAA 57.002 45.000 0.00 0.00 0.00 1.90
514 522 3.316029 CCGGATGTGTCATGCATAACAAT 59.684 43.478 3.65 0.96 0.00 2.71
555 563 7.039270 TGATACTAACTTACGACATTGTGCAT 58.961 34.615 0.00 0.00 0.00 3.96
560 568 9.542462 ACTAACTTACGACATTGTGCATTATAT 57.458 29.630 0.00 0.00 0.00 0.86
594 843 7.875327 TTATACTAGCATATGATACTCGCCA 57.125 36.000 6.97 0.00 0.00 5.69
612 861 2.683362 GCCATTACAACCAGCCTAACTC 59.317 50.000 0.00 0.00 0.00 3.01
616 865 0.320771 ACAACCAGCCTAACTCGCAG 60.321 55.000 0.00 0.00 0.00 5.18
623 872 2.866762 CAGCCTAACTCGCAGAATAACC 59.133 50.000 0.00 0.00 34.09 2.85
625 874 2.737679 GCCTAACTCGCAGAATAACCGT 60.738 50.000 0.00 0.00 34.09 4.83
650 899 8.068380 GTGTTCCTAATTGTTCACACTTCTAAC 58.932 37.037 0.00 0.00 33.28 2.34
652 901 7.074653 TCCTAATTGTTCACACTTCTAACCT 57.925 36.000 0.00 0.00 0.00 3.50
684 939 5.472148 TGTTGATACTTCCACGTTCGTAAT 58.528 37.500 0.00 0.00 0.00 1.89
686 941 7.089538 TGTTGATACTTCCACGTTCGTAATTA 58.910 34.615 0.00 0.00 0.00 1.40
777 1080 5.320277 CAACCTTTCATCCTTCCTCTCTTT 58.680 41.667 0.00 0.00 0.00 2.52
807 1110 3.798954 GAAGCATCCTCCTCGCGGG 62.799 68.421 6.13 0.59 0.00 6.13
811 1122 2.042843 ATCCTCCTCGCGGGTTCT 60.043 61.111 4.71 0.00 36.25 3.01
929 1241 1.758592 CGACCCCCAGAAGTTCCAA 59.241 57.895 0.00 0.00 0.00 3.53
931 1243 0.251209 GACCCCCAGAAGTTCCAACC 60.251 60.000 0.00 0.00 0.00 3.77
947 1259 0.108963 AACCAAATTCCCCGTCGACA 59.891 50.000 17.16 0.00 0.00 4.35
979 1292 4.959596 GCTCCCAGATCTCGCCGC 62.960 72.222 0.00 0.00 0.00 6.53
1437 1750 0.970937 TCTTCGCCTCCGTCTCCAAT 60.971 55.000 0.00 0.00 35.54 3.16
1534 1847 5.644644 GCCTTTGTTTGATCTCGATCATTT 58.355 37.500 10.15 0.00 46.12 2.32
1538 1851 7.148356 CCTTTGTTTGATCTCGATCATTTCTGA 60.148 37.037 10.15 0.00 46.12 3.27
1540 1853 7.065216 TGTTTGATCTCGATCATTTCTGAAC 57.935 36.000 10.15 10.44 46.12 3.18
1598 1911 3.740115 TGGAGGCTAGAGTTTGTGAAAC 58.260 45.455 0.00 0.00 41.69 2.78
1623 1936 6.636705 TGGCGATTTAGTTCAAGTATACTGT 58.363 36.000 6.06 0.00 0.00 3.55
1644 1957 2.634639 AGTATCAGTGTGGGTGGGTA 57.365 50.000 0.00 0.00 0.00 3.69
1768 2082 3.473923 AGTTTTGCCCAATTTGTCCAG 57.526 42.857 0.00 0.00 0.00 3.86
1853 2167 4.855715 TGTATCCGCAAATTTCACCAAA 57.144 36.364 0.00 0.00 0.00 3.28
1974 2288 5.938125 GGCATTTCTCCAGTCTTGTTACTTA 59.062 40.000 0.00 0.00 0.00 2.24
2201 2518 6.037172 GTCAACCAATGCACTCGTAAATATCT 59.963 38.462 0.00 0.00 0.00 1.98
2310 2628 7.981142 TCTACTATGGTTTGCTTATTTTTCGG 58.019 34.615 0.00 0.00 0.00 4.30
2435 2753 2.093306 TATCACCTGAGGTTGCAACG 57.907 50.000 22.67 11.30 31.02 4.10
2529 2863 8.241367 CCCGTCATTAAACTAGCTTTATTGTTT 58.759 33.333 0.00 0.00 36.69 2.83
2628 2962 8.992835 AAATCAATTCAAACCTTCTCTAATGC 57.007 30.769 0.00 0.00 0.00 3.56
2689 3023 8.514594 GGTAAATTTTCTGTTCTGACATCATGA 58.485 33.333 0.00 0.00 34.72 3.07
2804 3140 8.964772 CATCAGGAGTCTCCTTTCAAAATAAAT 58.035 33.333 19.46 0.00 46.91 1.40
2852 3188 7.982354 AGTATCTTAATGCAGTACTTCACTTCC 59.018 37.037 0.00 0.00 34.26 3.46
2903 3329 7.988028 GGCTAAGTGAGGACAGTTATAAGAAAT 59.012 37.037 0.00 0.00 39.96 2.17
2931 3357 7.913789 TGGGAGCAGTTTTTAGTCTATTCTAA 58.086 34.615 0.00 0.00 0.00 2.10
2978 3404 1.268032 GCTTATAAGCGTGCGCATGTT 60.268 47.619 29.00 22.04 42.88 2.71
3019 3445 3.281727 ACTTGGTCTCTTTTGCAGACA 57.718 42.857 5.52 0.00 41.94 3.41
3166 3593 8.922058 ACATTGTACTTCGTAAGTAATGTAGG 57.078 34.615 17.67 7.92 43.56 3.18
3186 3613 9.705290 ATGTAGGTGATTTGTTTTACCATTTTC 57.295 29.630 0.00 0.00 35.66 2.29
3188 3615 5.694458 AGGTGATTTGTTTTACCATTTTCGC 59.306 36.000 0.00 0.00 35.66 4.70
3222 3649 5.136105 AGTTGGCATCTTCTTTCTTTGAGT 58.864 37.500 0.00 0.00 0.00 3.41
3235 3662 9.477484 TTCTTTCTTTGAGTCATAACAGAGTAC 57.523 33.333 0.00 0.00 0.00 2.73
3271 3699 6.574350 TGCTTAGTATTCTCTTAAGTCCTGC 58.426 40.000 1.63 0.00 0.00 4.85
3443 3882 7.512992 ACATGGATTTGCTTAGCTCTATAACT 58.487 34.615 5.60 0.00 0.00 2.24
3460 3899 0.875908 ACTGCGTATATGCTGCGGTG 60.876 55.000 20.20 6.46 45.91 4.94
3517 3956 6.016610 GGTTTTGTGAACAGCTAAACATCCTA 60.017 38.462 7.97 0.00 34.78 2.94
3586 4025 4.503910 TGTCGCTGTGATTAGCAAAGTAT 58.496 39.130 0.00 0.00 43.87 2.12
3587 4026 5.656480 TGTCGCTGTGATTAGCAAAGTATA 58.344 37.500 0.00 0.00 43.87 1.47
4069 4508 3.695830 TGGCCTTCACAGGTAAAGTAG 57.304 47.619 3.32 0.00 43.18 2.57
4412 4874 6.814146 GCTTCAGTTACTTGCTAGACTGTTAT 59.186 38.462 13.82 0.00 40.21 1.89
4559 5021 8.757982 ATAAAGTATGTGCAATCCATTCTCTT 57.242 30.769 0.00 0.00 0.00 2.85
4569 5031 8.296713 GTGCAATCCATTCTCTTTACTTTGTTA 58.703 33.333 0.00 0.00 0.00 2.41
4576 5038 8.836413 CCATTCTCTTTACTTTGTTACAGTCAA 58.164 33.333 0.00 0.00 0.00 3.18
4642 5104 1.230324 ACTTGCTCTTTCGTGCCTTC 58.770 50.000 0.00 0.00 0.00 3.46
4828 5292 2.230660 GAGGCTGCCAACAACTAAAGT 58.769 47.619 22.65 0.00 0.00 2.66
5013 5478 3.423749 TGCACATGGTGTTCATCTGAAT 58.576 40.909 0.00 0.00 36.33 2.57
5243 5718 3.953612 TGGATTATTGGCTAACAGCAAGG 59.046 43.478 0.00 0.00 44.75 3.61
5247 5722 1.604604 TTGGCTAACAGCAAGGTGTC 58.395 50.000 5.28 0.00 44.75 3.67
5288 5763 1.005037 TGGCACGTAGCTCAACCTG 60.005 57.895 9.31 0.00 44.79 4.00
5430 5905 8.889717 CCGTATGACACCTCAATTTAAAATAGT 58.110 33.333 0.00 0.00 0.00 2.12
5806 6282 2.561569 CCCTGTTAGGTTTCGCTATGG 58.438 52.381 0.00 0.00 31.93 2.74
6449 6925 8.676454 GTGCAACAAACGACCATAATAATAAA 57.324 30.769 0.00 0.00 36.32 1.40
6466 6942 5.526506 AATAAAGCTCTTGATGAATGGCC 57.473 39.130 0.00 0.00 0.00 5.36
6470 6946 1.030457 CTCTTGATGAATGGCCAGGC 58.970 55.000 13.05 1.26 0.00 4.85
6534 7010 4.852134 TTTAGCAGACACATTTGCACAT 57.148 36.364 0.00 0.00 42.67 3.21
6650 7148 7.840931 TCATTATCTGTCTTCTGCTCTGTTTA 58.159 34.615 0.00 0.00 0.00 2.01
6755 7253 6.092807 CCTTTCTAAGTTGCTCTGGACATTAC 59.907 42.308 0.00 0.00 0.00 1.89
7181 7731 9.005777 GTTACCCTTGATATGTTTGTTCACTAA 57.994 33.333 0.00 0.00 0.00 2.24
7233 7783 6.813293 TTATTTACCTTCTACCAGTACCCC 57.187 41.667 0.00 0.00 0.00 4.95
7284 7834 0.380378 GTGTTGAGTTTGCTGCGGAA 59.620 50.000 0.00 0.00 0.00 4.30
7347 7897 7.706423 AACAACTGAATGTACAGCAATTTGCG 61.706 38.462 15.31 12.49 39.77 4.85
7748 8300 3.023832 CAAACCAACCCTCAACACTTCT 58.976 45.455 0.00 0.00 0.00 2.85
7788 8340 1.016130 CGAAGCAGCCATCGACAGTT 61.016 55.000 11.79 0.00 41.43 3.16
7986 8538 4.971924 AGTAAATCTGGAGGGCTGTCTAAT 59.028 41.667 0.00 0.00 0.00 1.73
8149 8701 1.194772 GCAGTACTTCGCTTGGACAAC 59.805 52.381 0.00 0.00 0.00 3.32
8210 8762 9.985730 AAACAATACAAATATAATGGGCATGAG 57.014 29.630 0.00 0.00 0.00 2.90
8312 8864 3.431922 CAATGCAGCTAGTTCCATTGG 57.568 47.619 13.82 0.00 40.30 3.16
8374 8926 2.315925 ATCACAGTTATCCAGTGGCG 57.684 50.000 3.51 0.00 34.17 5.69
8768 9329 3.440173 GGGTTTTCTCGATTTCAGCATCA 59.560 43.478 0.00 0.00 0.00 3.07
8892 9453 7.757941 TTGAATGTTGAGAATGTATCACCAA 57.242 32.000 0.00 0.00 0.00 3.67
8928 9489 3.071892 TCGTGAAAGTGGAAACCCTACAT 59.928 43.478 0.00 0.00 0.00 2.29
9003 9565 1.489481 CCATCTGTACCTCTGCCTGA 58.511 55.000 0.00 0.00 0.00 3.86
9088 9650 8.730680 ACTGTCGAAGTGAATATGCTTATTTTT 58.269 29.630 6.33 2.94 37.88 1.94
9144 9706 7.531857 TTGCATTTCAGTTCCCAACTAATTA 57.468 32.000 0.00 0.00 40.46 1.40
9146 9708 7.771183 TGCATTTCAGTTCCCAACTAATTATC 58.229 34.615 0.00 0.00 40.46 1.75
9170 9732 6.377146 TCCTTTGTTTAGAAATGTATCCCTGC 59.623 38.462 0.00 0.00 0.00 4.85
9227 9791 2.440247 CGGGCAAATCTGGTCCCC 60.440 66.667 0.00 0.00 35.32 4.81
9265 9829 2.069273 GTCCATGAACCGTGACTGAAG 58.931 52.381 0.00 0.00 0.00 3.02
9266 9830 1.967779 TCCATGAACCGTGACTGAAGA 59.032 47.619 0.00 0.00 0.00 2.87
9353 9959 1.923356 TGTCCCTCAAAGCAAATCCC 58.077 50.000 0.00 0.00 0.00 3.85
9354 9960 1.428912 TGTCCCTCAAAGCAAATCCCT 59.571 47.619 0.00 0.00 0.00 4.20
9370 9976 6.567891 GCAAATCCCTAAATCCGTACTAATGC 60.568 42.308 0.00 0.00 0.00 3.56
9387 9994 6.700352 ACTAATGCCATGCAATGTTAAACTT 58.300 32.000 0.00 0.00 44.81 2.66
9429 10036 9.755804 CGCACATATATCATAGGAAGTTCATAT 57.244 33.333 4.22 4.22 0.00 1.78
9480 10087 9.947669 ACATGTTCTACTAGTTACGAATGATAC 57.052 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.469807 AGTATCTCTTATTAATGTCTTTGCGAG 57.530 33.333 0.00 0.00 0.00 5.03
88 89 4.442706 AGCGTCTTATAACAGTGAATGGG 58.557 43.478 0.00 0.00 0.00 4.00
91 92 6.874134 AGTTTGAGCGTCTTATAACAGTGAAT 59.126 34.615 0.00 0.00 0.00 2.57
154 155 7.141363 GCAGACTGAAATAAGTGAACAAACAT 58.859 34.615 6.65 0.00 0.00 2.71
169 170 8.370182 TCAATATGAGCTATATGCAGACTGAAA 58.630 33.333 6.65 0.00 45.94 2.69
174 175 7.148340 GGGTTTCAATATGAGCTATATGCAGAC 60.148 40.741 0.00 0.00 45.94 3.51
179 180 8.025445 GCTTTGGGTTTCAATATGAGCTATATG 58.975 37.037 0.00 0.00 34.42 1.78
186 187 6.461110 AGATGCTTTGGGTTTCAATATGAG 57.539 37.500 0.00 0.00 34.98 2.90
198 199 6.662616 CGTCTGAATTATAAGATGCTTTGGG 58.337 40.000 0.00 0.00 0.00 4.12
260 261 3.256383 TCATCGTCCCGAAAAACTGACTA 59.744 43.478 0.00 0.00 39.99 2.59
273 274 2.643551 ACCATGAACATTCATCGTCCC 58.356 47.619 4.08 0.00 45.62 4.46
275 276 5.109210 TGACTACCATGAACATTCATCGTC 58.891 41.667 7.95 10.34 45.62 4.20
277 278 6.609237 ATTGACTACCATGAACATTCATCG 57.391 37.500 4.08 1.11 45.62 3.84
283 284 9.295825 TGTAGAAAAATTGACTACCATGAACAT 57.704 29.630 0.00 0.00 36.62 2.71
351 352 8.568732 ACACGTTAAAATGTTCAATTAACTGG 57.431 30.769 15.55 11.95 38.99 4.00
365 366 6.761714 CCAGCCTTAGAGATACACGTTAAAAT 59.238 38.462 0.00 0.00 0.00 1.82
370 371 3.097614 ACCAGCCTTAGAGATACACGTT 58.902 45.455 0.00 0.00 0.00 3.99
378 379 1.741706 CGTTACGACCAGCCTTAGAGA 59.258 52.381 0.00 0.00 0.00 3.10
397 398 4.966970 GCATGCGTATCTATGATACTCTCG 59.033 45.833 0.00 4.34 0.00 4.04
428 435 9.807649 AATTCTATGACACCTCATTAAATTTGC 57.192 29.630 0.00 0.00 38.21 3.68
492 499 2.287769 TGTTATGCATGACACATCCGG 58.712 47.619 19.43 0.00 0.00 5.14
494 501 8.136800 TCATTTATTGTTATGCATGACACATCC 58.863 33.333 22.61 0.00 0.00 3.51
496 503 9.524106 CTTCATTTATTGTTATGCATGACACAT 57.476 29.630 22.61 19.21 0.00 3.21
497 504 8.522003 ACTTCATTTATTGTTATGCATGACACA 58.478 29.630 22.61 14.41 0.00 3.72
527 535 9.027129 GCACAATGTCGTAAGTTAGTATCATAA 57.973 33.333 0.00 0.00 39.48 1.90
578 586 5.163854 GGTTGTAATGGCGAGTATCATATGC 60.164 44.000 0.00 0.00 33.17 3.14
579 587 5.931724 TGGTTGTAATGGCGAGTATCATATG 59.068 40.000 0.00 0.00 33.17 1.78
593 842 2.351726 GCGAGTTAGGCTGGTTGTAATG 59.648 50.000 0.00 0.00 0.00 1.90
594 843 2.027561 TGCGAGTTAGGCTGGTTGTAAT 60.028 45.455 0.00 0.00 0.00 1.89
612 861 1.722011 AGGAACACGGTTATTCTGCG 58.278 50.000 0.00 0.00 0.00 5.18
616 865 7.019418 GTGAACAATTAGGAACACGGTTATTC 58.981 38.462 0.00 0.00 0.00 1.75
623 872 5.236478 AGAAGTGTGAACAATTAGGAACACG 59.764 40.000 0.00 0.00 42.05 4.49
625 874 7.227910 GGTTAGAAGTGTGAACAATTAGGAACA 59.772 37.037 12.66 0.00 34.01 3.18
660 909 3.921677 ACGAACGTGGAAGTATCAACAT 58.078 40.909 0.00 0.00 29.15 2.71
684 939 6.072175 GGTGTCTGGTCAATGCAGTTAATTAA 60.072 38.462 0.00 0.00 0.00 1.40
686 941 4.218417 GGTGTCTGGTCAATGCAGTTAATT 59.782 41.667 0.00 0.00 0.00 1.40
777 1080 1.003839 ATGCTTCGTCGGCAAGGAA 60.004 52.632 0.25 0.00 43.14 3.36
807 1110 1.135333 GGGGACGAGACTCATGAGAAC 59.865 57.143 29.27 20.22 0.00 3.01
811 1122 0.252057 TTGGGGGACGAGACTCATGA 60.252 55.000 2.82 0.00 0.00 3.07
929 1241 0.108963 TTGTCGACGGGGAATTTGGT 59.891 50.000 11.62 0.00 0.00 3.67
931 1243 1.196808 CTGTTGTCGACGGGGAATTTG 59.803 52.381 11.62 0.00 0.00 2.32
994 1307 1.995484 CATGTTGAGCGACATCTCGTT 59.005 47.619 0.37 0.00 42.33 3.85
1497 1810 3.674997 ACAAAGGCGTGAGTGATATGTT 58.325 40.909 0.00 0.00 0.00 2.71
1503 1816 2.031258 TCAAACAAAGGCGTGAGTGA 57.969 45.000 0.00 0.00 0.00 3.41
1534 1847 3.840666 AGGTCCAAAGCTAGATGTTCAGA 59.159 43.478 0.00 0.00 0.00 3.27
1538 1851 3.600388 CGAAGGTCCAAAGCTAGATGTT 58.400 45.455 0.00 0.00 31.54 2.71
1540 1853 1.936547 GCGAAGGTCCAAAGCTAGATG 59.063 52.381 0.00 0.00 31.54 2.90
1598 1911 6.757010 ACAGTATACTTGAACTAAATCGCCAG 59.243 38.462 1.56 0.00 0.00 4.85
1623 1936 2.910544 ACCCACCCACACTGATACTAA 58.089 47.619 0.00 0.00 0.00 2.24
1644 1957 6.869206 ACTACCAGTGAGTAATGTAACCAT 57.131 37.500 0.00 0.00 0.00 3.55
1768 2082 4.499696 GGCATTCACCATGGTGCTAAATAC 60.500 45.833 35.73 24.09 45.04 1.89
1974 2288 7.250569 CCACGAGATTTTTACAAATAGTGCAT 58.749 34.615 0.00 0.00 34.39 3.96
2201 2518 0.923358 ACAAGGACCCAACCACAGAA 59.077 50.000 0.00 0.00 0.00 3.02
2276 2594 4.201822 GCAAACCATAGTAGAGGCGAAAAG 60.202 45.833 0.00 0.00 0.00 2.27
2283 2601 8.122952 CGAAAAATAAGCAAACCATAGTAGAGG 58.877 37.037 0.00 0.00 0.00 3.69
2482 2816 3.572255 GGGGAAACTAATGAGTGCACAAA 59.428 43.478 21.04 6.80 35.52 2.83
2499 2833 2.841881 AGCTAGTTTAATGACGGGGGAA 59.158 45.455 0.00 0.00 0.00 3.97
2529 2863 4.408921 AGCCTAGACAGTATGGTGCAAATA 59.591 41.667 0.00 0.00 43.62 1.40
2535 2869 1.202580 GCCAGCCTAGACAGTATGGTG 60.203 57.143 0.00 0.00 43.62 4.17
2674 3008 4.877823 GCTACCAATCATGATGTCAGAACA 59.122 41.667 9.46 0.00 40.38 3.18
2689 3023 7.985752 GGTACTATTAAACTCTGTGCTACCAAT 59.014 37.037 0.00 0.00 0.00 3.16
2756 3092 3.810743 GCCAGGGACAGTTGTAGTGAAAT 60.811 47.826 0.00 0.00 0.00 2.17
2852 3188 9.956720 CCTATTCTAAAGCATTAATGAGGTTTG 57.043 33.333 19.73 9.66 36.84 2.93
2903 3329 8.548877 AGAATAGACTAAAAACTGCTCCCATTA 58.451 33.333 0.00 0.00 0.00 1.90
2978 3404 8.946085 CCAAGTTATTACAGCATAGAAGTGAAA 58.054 33.333 0.00 0.00 0.00 2.69
3166 3593 6.763303 AGCGAAAATGGTAAAACAAATCAC 57.237 33.333 0.00 0.00 0.00 3.06
3186 3613 7.815068 AGAAGATGCCAACTAGTTAATATAGCG 59.185 37.037 8.04 0.00 0.00 4.26
3249 3676 7.354751 AGGCAGGACTTAAGAGAATACTAAG 57.645 40.000 10.09 0.00 0.00 2.18
3271 3699 3.181462 TGCTCCAGTGCAATCTACATAGG 60.181 47.826 0.00 0.00 40.29 2.57
3329 3759 8.752005 TTCATGACTAGGAAAAATTCTATGGG 57.248 34.615 0.00 0.00 0.00 4.00
3443 3882 1.594021 CCACCGCAGCATATACGCA 60.594 57.895 0.00 0.00 0.00 5.24
3478 3917 8.253810 TGTTCACAAAACCATTCTGAACAAATA 58.746 29.630 8.66 0.00 44.73 1.40
4069 4508 3.738791 CCAAATAAGGAAAACACAACCGC 59.261 43.478 0.00 0.00 0.00 5.68
4569 5031 4.276926 GCTCCTCTGAACAATTTTGACTGT 59.723 41.667 0.00 0.00 0.00 3.55
4576 5038 7.148407 CGTAATTACAGCTCCTCTGAACAATTT 60.148 37.037 15.67 0.00 45.72 1.82
4642 5104 9.459640 CAATAAAGTTTTATCATGCATCTGAGG 57.540 33.333 0.00 0.00 32.46 3.86
4709 5171 5.164620 TGAGCACTGGATACTTGATTGAA 57.835 39.130 0.00 0.00 37.61 2.69
4857 5322 2.440409 CCAGGAATTTGAGGTGTGGAG 58.560 52.381 0.00 0.00 0.00 3.86
5061 5526 9.635520 AATGAGTCAGCTATCAAAAAGAAAATG 57.364 29.630 0.00 0.00 0.00 2.32
5247 5722 9.301153 GCCAGTTGTTAGAATTAATTAACCATG 57.699 33.333 0.00 2.90 0.00 3.66
5288 5763 5.476091 AACTAGCCAGATAAGCAGATACC 57.524 43.478 0.00 0.00 0.00 2.73
5331 5806 4.962155 ACCACAGAAAGAGAGGTTACAAG 58.038 43.478 0.00 0.00 0.00 3.16
5430 5905 0.410663 TGGGACGGAGGGAGTAAGAA 59.589 55.000 0.00 0.00 0.00 2.52
5496 5971 6.791371 ACTCCCTCCGTCTCATAATATAAGA 58.209 40.000 0.00 0.00 0.00 2.10
5497 5972 7.830201 ACTACTCCCTCCGTCTCATAATATAAG 59.170 40.741 0.00 0.00 0.00 1.73
5498 5973 7.696981 ACTACTCCCTCCGTCTCATAATATAA 58.303 38.462 0.00 0.00 0.00 0.98
5509 5984 4.996788 TTCAATAACTACTCCCTCCGTC 57.003 45.455 0.00 0.00 0.00 4.79
5601 6077 2.165998 GCAGAACAGAAAGAGGGCATT 58.834 47.619 0.00 0.00 0.00 3.56
5602 6078 1.074405 TGCAGAACAGAAAGAGGGCAT 59.926 47.619 0.00 0.00 0.00 4.40
5806 6282 6.255020 GGATCAAGATCAACATTGCATTCAAC 59.745 38.462 11.78 0.00 39.54 3.18
6090 6566 5.695816 GCAATTAAAACTCAATGGCTGTTCA 59.304 36.000 0.00 0.00 30.88 3.18
6280 6756 4.256920 TCAGTAGCTGCAAGAAGAAATCC 58.743 43.478 4.12 0.00 34.07 3.01
6424 6900 8.676454 TTTATTATTATGGTCGTTTGTTGCAC 57.324 30.769 0.00 0.00 0.00 4.57
6449 6925 1.409802 CCTGGCCATTCATCAAGAGCT 60.410 52.381 5.51 0.00 0.00 4.09
6755 7253 7.396540 AGGTAAACCTTAATTCAGCAATCAG 57.603 36.000 0.00 0.00 46.09 2.90
7284 7834 3.515901 GGAAGACTAGAGGAACCACATGT 59.484 47.826 0.00 0.00 0.00 3.21
7748 8300 6.732531 TCGTTTGAGTACTAAGATCGAAGA 57.267 37.500 0.00 0.00 45.75 2.87
7788 8340 1.201647 GTAGACGCTGCAACCTGAGTA 59.798 52.381 0.00 0.00 0.00 2.59
7863 8415 2.228822 ACATGAACCGGAAGTTTGATGC 59.771 45.455 9.46 0.00 39.40 3.91
7986 8538 3.735720 TCAACATCATCAACCCCATCA 57.264 42.857 0.00 0.00 0.00 3.07
8149 8701 2.689983 AGCTCACCTGGTTTGTTTTCAG 59.310 45.455 0.00 0.00 0.00 3.02
8210 8762 4.229876 GTTCAAATAGCTGGCAGTTGAAC 58.770 43.478 29.54 29.54 46.13 3.18
8290 8842 2.062971 ATGGAACTAGCTGCATTGGG 57.937 50.000 1.02 0.00 0.00 4.12
8768 9329 2.765969 CTGCCTCACCACCCCAAT 59.234 61.111 0.00 0.00 0.00 3.16
8886 9447 1.358787 AGGCCCATCAGATTTTGGTGA 59.641 47.619 0.00 0.00 40.55 4.02
8892 9453 0.911769 TCACGAGGCCCATCAGATTT 59.088 50.000 0.00 0.00 0.00 2.17
8928 9489 5.042463 TCCCGGCTTAAATGAATACATCA 57.958 39.130 0.00 0.00 43.67 3.07
9003 9565 4.019771 ACAAGTGTTTCCACCCACATTTTT 60.020 37.500 0.00 0.00 42.88 1.94
9125 9687 8.802267 CAAAGGATAATTAGTTGGGAACTGAAA 58.198 33.333 0.00 0.00 42.84 2.69
9144 9706 7.068716 GCAGGGATACATTTCTAAACAAAGGAT 59.931 37.037 0.00 0.00 39.74 3.24
9146 9708 6.405842 GGCAGGGATACATTTCTAAACAAAGG 60.406 42.308 0.00 0.00 39.74 3.11
9170 9732 2.565046 ACATTTTTGGTTGGGCATGG 57.435 45.000 0.00 0.00 0.00 3.66
9227 9791 5.289917 TGGACACGTTTGCAAATGTATAG 57.710 39.130 31.06 22.59 36.43 1.31
9280 9886 7.997803 TGACCCAAAATTTTCCTGAAAATCAAT 59.002 29.630 15.96 5.69 46.76 2.57
9353 9959 4.754618 TGCATGGCATTAGTACGGATTTAG 59.245 41.667 0.00 0.00 31.71 1.85
9354 9960 4.709250 TGCATGGCATTAGTACGGATTTA 58.291 39.130 0.00 0.00 31.71 1.40
9370 9976 5.060816 CGTGCTTAAGTTTAACATTGCATGG 59.939 40.000 4.02 0.00 33.97 3.66
9387 9994 1.788308 GTGCGTTGAACTACGTGCTTA 59.212 47.619 0.00 0.00 43.22 3.09
9432 10039 7.747155 TGTTTAATTTTGGTAGTCCGATGAA 57.253 32.000 0.00 0.00 36.30 2.57
9452 10059 9.871238 ATCATTCGTAACTAGTAGAACATGTTT 57.129 29.630 13.36 5.60 0.00 2.83
9480 10087 2.420022 GGGTGAAGTTCATCCATTGTCG 59.580 50.000 27.24 0.00 46.88 4.35


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

AutoCloner maintained by Alex Coulton.