Multiple sequence alignment - TraesCS3B01G355000

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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 TraesCS3B01G355000 chr3B 100.000 4022 0 0 1 4022 565275541 565271520 0.000000e+00 7428.0
1 TraesCS3B01G355000 chr3B 92.857 154 11 0 1339 1492 565276760 565276607 1.450000e-54 224.0
2 TraesCS3B01G355000 chr3B 85.849 212 16 7 942 1151 565276949 565276750 3.150000e-51 213.0
3 TraesCS3B01G355000 chr3B 90.083 121 11 1 2939 3058 565272474 565272354 5.380000e-34 156.0
4 TraesCS3B01G355000 chr3B 90.083 121 11 1 3068 3188 565272603 565272484 5.380000e-34 156.0
5 TraesCS3B01G355000 chr3D 96.150 3091 91 11 937 4022 433142422 433139355 0.000000e+00 5024.0
6 TraesCS3B01G355000 chr3D 91.667 120 10 0 2939 3058 433140297 433140178 2.490000e-37 167.0
7 TraesCS3B01G355000 chr3D 88.430 121 13 1 3068 3188 433140426 433140307 1.170000e-30 145.0
8 TraesCS3B01G355000 chr3A 95.115 3009 97 22 860 3829 571184384 571181387 0.000000e+00 4697.0
9 TraesCS3B01G355000 chr3A 97.406 347 9 0 3676 4022 571181394 571181048 3.460000e-165 592.0
10 TraesCS3B01G355000 chr3A 74.449 771 128 44 1 744 344994673 344995401 6.630000e-68 268.0
11 TraesCS3B01G355000 chr3A 87.705 122 12 3 3068 3188 571182276 571182157 5.420000e-29 139.0
12 TraesCS3B01G355000 chr1A 76.671 823 147 34 1 808 425049106 425049898 8.040000e-112 414.0
13 TraesCS3B01G355000 chr1A 76.983 517 80 26 1 503 406658057 406657566 3.990000e-65 259.0
14 TraesCS3B01G355000 chr1A 83.529 85 12 2 52 134 152052725 152052641 1.200000e-10 78.7
15 TraesCS3B01G355000 chr1B 76.067 890 153 36 1 860 299034224 299035083 3.740000e-110 409.0
16 TraesCS3B01G355000 chr1B 75.827 877 152 37 1 848 299014773 299015618 1.360000e-104 390.0
17 TraesCS3B01G355000 chr2B 76.222 757 142 25 1 745 266768499 266767769 2.280000e-97 366.0
18 TraesCS3B01G355000 chr6B 76.910 576 106 23 187 745 210288713 210289278 6.530000e-78 302.0
19 TraesCS3B01G355000 chr2D 75.575 696 125 30 188 860 282951224 282951897 6.530000e-78 302.0
20 TraesCS3B01G355000 chr2D 93.388 121 8 0 1410 1530 539005212 539005092 3.190000e-41 180.0
21 TraesCS3B01G355000 chr1D 75.777 611 108 31 225 808 167377752 167377155 5.120000e-69 272.0
22 TraesCS3B01G355000 chr1D 84.239 184 16 6 12 182 313346324 313346507 2.490000e-37 167.0
23 TraesCS3B01G355000 chr1D 84.239 184 16 6 12 182 313350807 313350990 2.490000e-37 167.0
24 TraesCS3B01G355000 chr1D 83.077 195 19 6 1 182 233067921 233067728 8.940000e-37 165.0
25 TraesCS3B01G355000 chrUn 75.120 627 95 38 1 602 33188199 33188789 1.870000e-58 237.0
26 TraesCS3B01G355000 chrUn 86.010 193 16 7 1 182 73053540 73053348 3.170000e-46 196.0
27 TraesCS3B01G355000 chrUn 86.585 164 11 6 30 182 388387985 388388148 1.920000e-38 171.0
28 TraesCS3B01G355000 chr7B 85.000 180 17 5 1 171 304113461 304113639 1.490000e-39 174.0
29 TraesCS3B01G355000 chr7B 85.542 83 10 2 54 134 336417403 336417321 7.160000e-13 86.1
30 TraesCS3B01G355000 chr4A 86.164 159 11 5 35 182 334762468 334762310 1.160000e-35 161.0
31 TraesCS3B01G355000 chr6D 88.976 127 14 0 1402 1528 10717840 10717966 1.500000e-34 158.0
32 TraesCS3B01G355000 chr2A 90.588 85 8 0 1268 1352 681484528 681484444 3.290000e-21 113.0
33 TraesCS3B01G355000 chr2A 89.655 58 6 0 1445 1502 681484409 681484352 1.550000e-09 75.0


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 TraesCS3B01G355000 chr3B 565271520 565275541 4021 True 2580.000000 7428 93.388667 1 4022 3 chr3B.!!$R1 4021
1 TraesCS3B01G355000 chr3D 433139355 433142422 3067 True 1778.666667 5024 92.082333 937 4022 3 chr3D.!!$R1 3085
2 TraesCS3B01G355000 chr3A 571181048 571184384 3336 True 1809.333333 4697 93.408667 860 4022 3 chr3A.!!$R1 3162
3 TraesCS3B01G355000 chr3A 344994673 344995401 728 False 268.000000 268 74.449000 1 744 1 chr3A.!!$F1 743
4 TraesCS3B01G355000 chr1A 425049106 425049898 792 False 414.000000 414 76.671000 1 808 1 chr1A.!!$F1 807
5 TraesCS3B01G355000 chr1B 299034224 299035083 859 False 409.000000 409 76.067000 1 860 1 chr1B.!!$F2 859
6 TraesCS3B01G355000 chr1B 299014773 299015618 845 False 390.000000 390 75.827000 1 848 1 chr1B.!!$F1 847
7 TraesCS3B01G355000 chr2B 266767769 266768499 730 True 366.000000 366 76.222000 1 745 1 chr2B.!!$R1 744
8 TraesCS3B01G355000 chr6B 210288713 210289278 565 False 302.000000 302 76.910000 187 745 1 chr6B.!!$F1 558
9 TraesCS3B01G355000 chr2D 282951224 282951897 673 False 302.000000 302 75.575000 188 860 1 chr2D.!!$F1 672
10 TraesCS3B01G355000 chr1D 167377155 167377752 597 True 272.000000 272 75.777000 225 808 1 chr1D.!!$R1 583
11 TraesCS3B01G355000 chrUn 33188199 33188789 590 False 237.000000 237 75.120000 1 602 1 chrUn.!!$F1 601

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
518 547 0.032952 TACTCCACACGCCAGACAAC 59.967 55.000 0.00 0.0 0.00 3.32 F
1055 1113 0.605589 CTCTATCTGCCCCTAAGCGG 59.394 60.000 0.00 0.0 40.71 5.52 F
1806 1882 1.148273 GTCAGCTGTTGGGGTGTCA 59.852 57.895 14.67 0.0 36.29 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1882 0.034059 CAAAGCTCTCCACGTCTGGT 59.966 55.0 0.00 0.00 38.9 4.00 R
2352 2428 0.036164 TGCCGGCATCAAGTTGTAGT 59.964 50.0 29.03 0.00 0.0 2.73 R
3541 3623 0.038892 GTAGCTCAACGGACCGAACA 60.039 55.0 23.38 1.84 0.0 3.18 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
28 29 1.596496 ACCCCAAGGATCCTAGGTTG 58.404 55.000 23.13 14.95 36.73 3.77
33 34 3.973973 CCCAAGGATCCTAGGTTGACATA 59.026 47.826 16.55 0.00 0.00 2.29
86 91 1.833630 TCAGTGGTGCATTCTCTAGGG 59.166 52.381 0.00 0.00 0.00 3.53
89 94 1.834263 GTGGTGCATTCTCTAGGGACT 59.166 52.381 0.00 0.00 46.37 3.85
96 101 6.007703 GTGCATTCTCTAGGGACTATAGAGT 58.992 44.000 6.78 0.00 43.40 3.24
102 107 6.324544 TCTCTAGGGACTATAGAGTGCTCTA 58.675 44.000 8.98 10.88 44.39 2.43
111 116 2.310779 AGAGTGCTCTACCAAGGACA 57.689 50.000 0.00 0.00 39.82 4.02
119 125 3.610911 CTCTACCAAGGACAATTCACCC 58.389 50.000 0.00 0.00 0.00 4.61
127 133 5.047660 CCAAGGACAATTCACCCGATTTAAA 60.048 40.000 0.00 0.00 0.00 1.52
139 147 6.314400 TCACCCGATTTAAATTCCGAAACTAG 59.686 38.462 10.04 0.00 0.00 2.57
180 195 1.202698 GGCGCATTCTCTAGGGACAAT 60.203 52.381 10.83 0.00 0.00 2.71
181 196 2.037251 GGCGCATTCTCTAGGGACAATA 59.963 50.000 10.83 0.00 0.00 1.90
182 197 3.494398 GGCGCATTCTCTAGGGACAATAA 60.494 47.826 10.83 0.00 0.00 1.40
183 198 4.127171 GCGCATTCTCTAGGGACAATAAA 58.873 43.478 0.30 0.00 0.00 1.40
184 199 4.574828 GCGCATTCTCTAGGGACAATAAAA 59.425 41.667 0.30 0.00 0.00 1.52
185 200 5.504173 GCGCATTCTCTAGGGACAATAAAAC 60.504 44.000 0.30 0.00 0.00 2.43
207 222 4.161565 ACACGCATTCTCTAGGGACAATAA 59.838 41.667 0.00 0.00 0.00 1.40
209 224 5.584649 CACGCATTCTCTAGGGACAATAAAA 59.415 40.000 0.00 0.00 0.00 1.52
217 232 6.156949 TCTCTAGGGACAATAAAATGCTCTGT 59.843 38.462 0.00 0.00 0.00 3.41
220 235 5.324409 AGGGACAATAAAATGCTCTGTCAA 58.676 37.500 3.23 0.00 38.50 3.18
221 236 5.416952 AGGGACAATAAAATGCTCTGTCAAG 59.583 40.000 3.23 0.00 38.50 3.02
223 238 5.393461 GGACAATAAAATGCTCTGTCAAGGG 60.393 44.000 3.23 0.00 38.50 3.95
270 285 5.041940 CGAGCCTACAACTATAAACACTCC 58.958 45.833 0.00 0.00 0.00 3.85
271 286 5.163540 CGAGCCTACAACTATAAACACTCCT 60.164 44.000 0.00 0.00 0.00 3.69
284 299 7.678947 ATAAACACTCCTCACTTTCATGAAG 57.321 36.000 8.41 5.87 41.32 3.02
296 318 1.896220 TCATGAAGCACTCAACACCC 58.104 50.000 0.00 0.00 37.67 4.61
302 324 1.846007 AGCACTCAACACCCAAACAA 58.154 45.000 0.00 0.00 0.00 2.83
303 325 1.750778 AGCACTCAACACCCAAACAAG 59.249 47.619 0.00 0.00 0.00 3.16
312 334 2.242708 ACACCCAAACAAGGTCTACCAA 59.757 45.455 1.26 0.00 34.56 3.67
318 340 5.337652 CCCAAACAAGGTCTACCAAAACAAA 60.338 40.000 1.26 0.00 38.89 2.83
320 342 4.649088 ACAAGGTCTACCAAAACAAAGC 57.351 40.909 1.26 0.00 38.89 3.51
321 343 4.278310 ACAAGGTCTACCAAAACAAAGCT 58.722 39.130 1.26 0.00 38.89 3.74
327 349 5.048013 GGTCTACCAAAACAAAGCTAAGCAT 60.048 40.000 0.00 0.00 35.64 3.79
329 351 7.148069 GGTCTACCAAAACAAAGCTAAGCATAT 60.148 37.037 0.00 0.00 35.64 1.78
331 353 9.109393 TCTACCAAAACAAAGCTAAGCATATAG 57.891 33.333 0.00 0.00 0.00 1.31
333 355 8.122472 ACCAAAACAAAGCTAAGCATATAGTT 57.878 30.769 0.00 0.00 0.00 2.24
334 356 8.028938 ACCAAAACAAAGCTAAGCATATAGTTG 58.971 33.333 0.00 0.00 0.00 3.16
345 367 7.800380 GCTAAGCATATAGTTGCACAATACAAG 59.200 37.037 1.38 0.00 45.23 3.16
356 378 6.285790 TGCACAATACAAGCAATATCTACG 57.714 37.500 0.00 0.00 34.97 3.51
359 381 7.042992 TGCACAATACAAGCAATATCTACGTAC 60.043 37.037 0.00 0.00 34.97 3.67
361 383 7.166970 CACAATACAAGCAATATCTACGTACGT 59.833 37.037 25.98 25.98 0.00 3.57
363 385 4.277258 ACAAGCAATATCTACGTACGTCG 58.723 43.478 26.53 19.38 46.00 5.12
367 390 3.620761 CAATATCTACGTACGTCGGCAA 58.379 45.455 26.53 5.84 44.69 4.52
403 429 8.437360 TCAGACCAAACACATAAATAGCATAG 57.563 34.615 0.00 0.00 0.00 2.23
409 436 9.507280 CCAAACACATAAATAGCATAGAAACTG 57.493 33.333 0.00 0.00 0.00 3.16
416 443 8.562052 CATAAATAGCATAGAAACTGCACATGA 58.438 33.333 0.00 0.00 42.15 3.07
417 444 5.998454 ATAGCATAGAAACTGCACATGAC 57.002 39.130 0.00 0.00 42.15 3.06
434 462 6.286758 CACATGACTAGCAGAACATAGGATT 58.713 40.000 0.00 0.00 0.00 3.01
436 464 7.928167 CACATGACTAGCAGAACATAGGATTAA 59.072 37.037 0.00 0.00 0.00 1.40
438 466 7.661536 TGACTAGCAGAACATAGGATTAACT 57.338 36.000 0.00 0.00 0.00 2.24
440 468 9.368416 TGACTAGCAGAACATAGGATTAACTAT 57.632 33.333 0.00 0.00 34.06 2.12
468 497 0.033781 TGCAACTTGCCTTGGAATGC 59.966 50.000 11.29 0.00 44.23 3.56
474 503 1.865788 TTGCCTTGGAATGCGCTGAC 61.866 55.000 9.73 0.00 0.00 3.51
500 529 6.630444 ACTCTAACGCTTAATTCCGATCTA 57.370 37.500 0.00 0.00 0.00 1.98
503 532 6.666417 TCTAACGCTTAATTCCGATCTACTC 58.334 40.000 0.00 0.00 0.00 2.59
509 538 3.438297 AATTCCGATCTACTCCACACG 57.562 47.619 0.00 0.00 0.00 4.49
518 547 0.032952 TACTCCACACGCCAGACAAC 59.967 55.000 0.00 0.00 0.00 3.32
528 557 3.555956 CACGCCAGACAACCTATACATTC 59.444 47.826 0.00 0.00 0.00 2.67
534 563 6.488006 GCCAGACAACCTATACATTCAATGAT 59.512 38.462 3.79 0.00 0.00 2.45
548 577 7.663827 ACATTCAATGATGGCATCGATAAATT 58.336 30.769 21.65 12.61 32.35 1.82
573 602 7.575414 AATTGTACTCACATAACACCACAAA 57.425 32.000 0.00 0.00 33.76 2.83
575 604 6.612247 TGTACTCACATAACACCACAAAAG 57.388 37.500 0.00 0.00 0.00 2.27
577 606 5.751243 ACTCACATAACACCACAAAAGTC 57.249 39.130 0.00 0.00 0.00 3.01
578 607 5.189928 ACTCACATAACACCACAAAAGTCA 58.810 37.500 0.00 0.00 0.00 3.41
579 608 5.650266 ACTCACATAACACCACAAAAGTCAA 59.350 36.000 0.00 0.00 0.00 3.18
580 609 6.321181 ACTCACATAACACCACAAAAGTCAAT 59.679 34.615 0.00 0.00 0.00 2.57
581 610 6.734137 TCACATAACACCACAAAAGTCAATC 58.266 36.000 0.00 0.00 0.00 2.67
582 611 6.319911 TCACATAACACCACAAAAGTCAATCA 59.680 34.615 0.00 0.00 0.00 2.57
584 613 6.978080 ACATAACACCACAAAAGTCAATCAAC 59.022 34.615 0.00 0.00 0.00 3.18
585 614 5.398603 AACACCACAAAAGTCAATCAACA 57.601 34.783 0.00 0.00 0.00 3.33
587 616 5.410067 ACACCACAAAAGTCAATCAACAAG 58.590 37.500 0.00 0.00 0.00 3.16
591 620 6.127083 ACCACAAAAGTCAATCAACAAGGAAT 60.127 34.615 0.00 0.00 0.00 3.01
593 622 7.042523 CCACAAAAGTCAATCAACAAGGAATTC 60.043 37.037 0.00 0.00 0.00 2.17
663 693 7.879070 TCTAAATGCTAATAGGATCGTAACGT 58.121 34.615 0.00 0.00 0.00 3.99
679 709 7.393551 TCGTAACGTAAAAAGAACCAACTAG 57.606 36.000 0.00 0.00 0.00 2.57
729 759 6.144175 TGGCGTTCGAAAGGTTAATTTTAAG 58.856 36.000 13.01 0.00 0.00 1.85
756 800 6.272318 TGACCAAATTCAAGATGTGTGAAAC 58.728 36.000 0.00 0.00 38.44 2.78
761 805 7.278424 CCAAATTCAAGATGTGTGAAACTTTGT 59.722 33.333 10.17 0.00 38.44 2.83
769 813 7.697691 AGATGTGTGAAACTTTGTTTCTACTG 58.302 34.615 19.52 0.00 38.04 2.74
777 821 5.234466 ACTTTGTTTCTACTGGATGCTCT 57.766 39.130 0.00 0.00 0.00 4.09
797 841 5.180117 GCTCTTGTTCAACATGAGTACACAT 59.820 40.000 26.17 0.00 46.23 3.21
829 873 8.237267 AGAATTGATGAATTTGAAGTTACGGAC 58.763 33.333 0.00 0.00 31.58 4.79
839 883 5.320549 TGAAGTTACGGACCTCAAGATAC 57.679 43.478 0.00 0.00 0.00 2.24
841 885 4.985538 AGTTACGGACCTCAAGATACAG 57.014 45.455 0.00 0.00 0.00 2.74
843 887 0.824759 ACGGACCTCAAGATACAGCC 59.175 55.000 0.00 0.00 0.00 4.85
844 888 1.115467 CGGACCTCAAGATACAGCCT 58.885 55.000 0.00 0.00 0.00 4.58
847 891 3.132289 CGGACCTCAAGATACAGCCTAAA 59.868 47.826 0.00 0.00 0.00 1.85
848 892 4.443621 GGACCTCAAGATACAGCCTAAAC 58.556 47.826 0.00 0.00 0.00 2.01
851 895 5.876357 ACCTCAAGATACAGCCTAAACAAA 58.124 37.500 0.00 0.00 0.00 2.83
855 899 7.756722 CCTCAAGATACAGCCTAAACAAAATTG 59.243 37.037 0.00 0.00 0.00 2.32
860 904 8.903820 AGATACAGCCTAAACAAAATTGGATAC 58.096 33.333 0.00 0.00 0.00 2.24
884 928 6.992123 ACAAATAGTCAGACTGATGTTCAACA 59.008 34.615 13.84 0.00 0.00 3.33
908 952 3.843999 TGTTGCAAAACTGACTCCAAAC 58.156 40.909 0.00 0.00 0.00 2.93
933 979 5.227152 AGTTTTCATGTAAAAATCCCACGC 58.773 37.500 0.00 0.00 38.76 5.34
934 980 3.479505 TTCATGTAAAAATCCCACGCG 57.520 42.857 3.53 3.53 0.00 6.01
978 1036 1.647084 GCAAACGCTCGAACACCTT 59.353 52.632 0.00 0.00 0.00 3.50
988 1046 1.868498 TCGAACACCTTAACGGCAAAG 59.132 47.619 0.00 0.00 35.61 2.77
1055 1113 0.605589 CTCTATCTGCCCCTAAGCGG 59.394 60.000 0.00 0.00 40.71 5.52
1064 1122 3.090532 CCTAAGCGGGAGGCCCTT 61.091 66.667 0.00 0.00 42.67 3.95
1084 1142 2.197324 CCTCCTCCTCCTCCTCCG 59.803 72.222 0.00 0.00 0.00 4.63
1085 1143 2.387772 CCTCCTCCTCCTCCTCCGA 61.388 68.421 0.00 0.00 0.00 4.55
1110 1186 1.755395 CCACGAGATCCCCACCGTA 60.755 63.158 0.00 0.00 33.62 4.02
1443 1519 2.286732 AAGAGCCCCCATGCCTCT 60.287 61.111 0.00 0.00 0.00 3.69
1789 1865 5.396213 GCTGAGAAGGTCTTGGAGATTATGT 60.396 44.000 0.00 0.00 0.00 2.29
1806 1882 1.148273 GTCAGCTGTTGGGGTGTCA 59.852 57.895 14.67 0.00 36.29 3.58
1854 1930 1.656652 CCTTCTTGTATGCGTGGAGG 58.343 55.000 0.00 0.00 0.00 4.30
1994 2070 3.752412 TTCGTCGATCATACTTCGTGT 57.248 42.857 0.00 0.00 37.82 4.49
1995 2071 3.314763 TCGTCGATCATACTTCGTGTC 57.685 47.619 0.00 0.00 37.82 3.67
2015 2091 2.163509 CGTGGAGGAGAGAAGAGTTGA 58.836 52.381 0.00 0.00 0.00 3.18
2055 2131 3.296854 TGATGAGTGCTATACCGAGGTT 58.703 45.455 0.00 0.00 0.00 3.50
2079 2155 4.330620 GCACAATGCTTTGTTGATAATGGG 59.669 41.667 14.80 2.88 43.57 4.00
2137 2213 5.402398 CACAAGAGATTGAGTCGACACATA 58.598 41.667 19.50 9.05 0.00 2.29
2147 2223 2.420022 AGTCGACACATAAATTGCTGGC 59.580 45.455 19.50 0.00 0.00 4.85
2150 2226 2.533266 GACACATAAATTGCTGGCAGC 58.467 47.619 31.91 31.91 42.82 5.25
2219 2295 5.674525 TGGTCTATTGAACAAGGCTCATAG 58.325 41.667 0.00 0.00 36.90 2.23
2367 2443 1.740025 GCAGGACTACAACTTGATGCC 59.260 52.381 0.00 0.00 0.00 4.40
2397 2473 7.937942 AGTTATGATGCTCTTATTGATGCTTCT 59.062 33.333 0.88 0.00 32.92 2.85
2478 2554 3.707102 GGCTACCAGATCTTAGGACAAGT 59.293 47.826 6.11 0.00 0.00 3.16
2547 2623 1.031571 TGGCATCATTCTTGGACGCC 61.032 55.000 0.00 0.00 38.56 5.68
2985 3061 6.616017 CAACTTTAGGAAAATGGAAGCTCTC 58.384 40.000 0.00 0.00 0.00 3.20
3026 3102 4.035208 GGCGGGTCTTAACTCATAACATTG 59.965 45.833 0.00 0.00 0.00 2.82
3027 3103 4.495844 GCGGGTCTTAACTCATAACATTGC 60.496 45.833 0.00 0.00 0.00 3.56
3116 3192 6.488715 ACTTTAGGAAAATGGAAGCTCTGAT 58.511 36.000 0.00 0.00 0.00 2.90
3144 3220 6.223852 TGTTAAAGAACTGAGCTGGTCTTAG 58.776 40.000 4.88 0.70 36.45 2.18
3333 3414 2.137523 GGAAGCTGGTGCATTTTTGTG 58.862 47.619 0.00 0.00 42.74 3.33
3435 3516 7.290248 TGTTAACCTCCAAATCCCATGTAAAAA 59.710 33.333 2.48 0.00 0.00 1.94
3450 3531 9.855021 CCCATGTAAAAATTCTTAAGTTAGTGG 57.145 33.333 1.63 5.19 0.00 4.00
3466 3547 8.667076 AAGTTAGTGGATACGTAACAAGTTTT 57.333 30.769 0.00 0.00 42.51 2.43
3554 3636 3.881780 TTATGTTTGTTCGGTCCGTTG 57.118 42.857 11.88 0.00 0.00 4.10
3581 3663 4.149598 ACCCTTGTAATGTTTTCACTCCC 58.850 43.478 0.00 0.00 0.00 4.30
3730 3812 2.899900 GGGAAAAGTGAAGGCAGGAATT 59.100 45.455 0.00 0.00 0.00 2.17
3826 4055 8.567948 AGAGTTGACAAAACACCACAATATTAG 58.432 33.333 0.00 0.00 0.00 1.73
3928 4157 1.071128 CATCTAGCAGGGGAGCTGC 59.929 63.158 0.00 0.00 46.11 5.25
4004 4233 4.751767 TGCCAAATCAACAGGAAAAGTT 57.248 36.364 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.629639 CCTAGGATCCTTGGGGTTCTCA 60.630 54.545 28.99 4.01 35.74 3.27
16 17 6.235231 TCTTGTTATGTCAACCTAGGATCC 57.765 41.667 17.98 2.48 0.00 3.36
28 29 7.653713 TGAGACTTCTGAAGTTCTTGTTATGTC 59.346 37.037 22.80 7.11 43.03 3.06
33 34 6.314896 CACTTGAGACTTCTGAAGTTCTTGTT 59.685 38.462 22.80 5.80 45.79 2.83
86 91 5.239963 GTCCTTGGTAGAGCACTCTATAGTC 59.760 48.000 10.44 0.00 43.32 2.59
89 94 5.125367 TGTCCTTGGTAGAGCACTCTATA 57.875 43.478 10.44 1.39 43.32 1.31
96 101 3.559171 GGTGAATTGTCCTTGGTAGAGCA 60.559 47.826 0.00 0.00 0.00 4.26
102 107 0.768622 TCGGGTGAATTGTCCTTGGT 59.231 50.000 0.00 0.00 0.00 3.67
111 116 6.518208 TTCGGAATTTAAATCGGGTGAATT 57.482 33.333 0.10 0.00 0.00 2.17
119 125 7.000575 TGAGCTAGTTTCGGAATTTAAATCG 57.999 36.000 0.10 2.12 0.00 3.34
127 133 3.003480 GCACTTGAGCTAGTTTCGGAAT 58.997 45.455 0.00 0.00 0.00 3.01
139 147 1.224069 TTGACAGAGCGCACTTGAGC 61.224 55.000 11.47 0.00 41.28 4.26
180 195 4.020928 TGTCCCTAGAGAATGCGTGTTTTA 60.021 41.667 0.00 0.00 0.00 1.52
181 196 3.244422 TGTCCCTAGAGAATGCGTGTTTT 60.244 43.478 0.00 0.00 0.00 2.43
182 197 2.301870 TGTCCCTAGAGAATGCGTGTTT 59.698 45.455 0.00 0.00 0.00 2.83
183 198 1.899814 TGTCCCTAGAGAATGCGTGTT 59.100 47.619 0.00 0.00 0.00 3.32
184 199 1.557099 TGTCCCTAGAGAATGCGTGT 58.443 50.000 0.00 0.00 0.00 4.49
185 200 2.672961 TTGTCCCTAGAGAATGCGTG 57.327 50.000 0.00 0.00 0.00 5.34
207 222 1.589716 GCGCCCTTGACAGAGCATTT 61.590 55.000 0.00 0.00 0.00 2.32
209 224 2.437359 GCGCCCTTGACAGAGCAT 60.437 61.111 0.00 0.00 0.00 3.79
217 232 1.675310 CAGGTGAATGCGCCCTTGA 60.675 57.895 4.18 0.00 46.09 3.02
220 235 1.847798 TTACCAGGTGAATGCGCCCT 61.848 55.000 4.18 0.00 46.09 5.19
221 236 0.963355 TTTACCAGGTGAATGCGCCC 60.963 55.000 4.18 0.00 46.09 6.13
223 238 2.030274 ACTTTTTACCAGGTGAATGCGC 60.030 45.455 0.76 0.00 0.00 6.09
270 285 4.274214 TGTTGAGTGCTTCATGAAAGTGAG 59.726 41.667 9.88 0.00 37.31 3.51
271 286 4.035558 GTGTTGAGTGCTTCATGAAAGTGA 59.964 41.667 9.88 0.00 37.31 3.41
284 299 1.202405 CCTTGTTTGGGTGTTGAGTGC 60.202 52.381 0.00 0.00 0.00 4.40
296 318 5.290885 GCTTTGTTTTGGTAGACCTTGTTTG 59.709 40.000 0.00 0.00 36.82 2.93
302 324 4.519350 GCTTAGCTTTGTTTTGGTAGACCT 59.481 41.667 0.00 0.00 36.82 3.85
303 325 4.277423 TGCTTAGCTTTGTTTTGGTAGACC 59.723 41.667 5.60 0.00 0.00 3.85
312 334 7.029563 GTGCAACTATATGCTTAGCTTTGTTT 58.970 34.615 5.60 0.00 46.54 2.83
318 340 6.992123 TGTATTGTGCAACTATATGCTTAGCT 59.008 34.615 5.60 0.00 46.54 3.32
320 342 7.800380 GCTTGTATTGTGCAACTATATGCTTAG 59.200 37.037 0.00 0.00 46.54 2.18
321 343 7.281999 TGCTTGTATTGTGCAACTATATGCTTA 59.718 33.333 0.00 0.00 46.54 3.09
333 355 5.815222 ACGTAGATATTGCTTGTATTGTGCA 59.185 36.000 0.00 0.00 34.69 4.57
334 356 6.287107 ACGTAGATATTGCTTGTATTGTGC 57.713 37.500 0.00 0.00 0.00 4.57
345 367 1.974680 GCCGACGTACGTAGATATTGC 59.025 52.381 27.05 17.89 40.78 3.56
355 377 5.624715 TTTATATTCTTTGCCGACGTACG 57.375 39.130 15.01 15.01 42.18 3.67
356 378 7.168637 TCTGATTTATATTCTTTGCCGACGTAC 59.831 37.037 0.00 0.00 0.00 3.67
359 381 6.355638 GTCTGATTTATATTCTTTGCCGACG 58.644 40.000 0.00 0.00 0.00 5.12
361 383 6.353323 TGGTCTGATTTATATTCTTTGCCGA 58.647 36.000 0.00 0.00 0.00 5.54
363 385 8.250332 TGTTTGGTCTGATTTATATTCTTTGCC 58.750 33.333 0.00 0.00 0.00 4.52
403 429 3.736530 CTGCTAGTCATGTGCAGTTTC 57.263 47.619 17.63 0.00 46.23 2.78
409 436 3.806521 CCTATGTTCTGCTAGTCATGTGC 59.193 47.826 0.00 0.00 0.00 4.57
463 492 2.470196 TAGAGTACGTCAGCGCATTC 57.530 50.000 11.47 0.00 42.83 2.67
466 495 0.179207 CGTTAGAGTACGTCAGCGCA 60.179 55.000 11.47 0.00 42.83 6.09
468 497 0.096628 AGCGTTAGAGTACGTCAGCG 59.903 55.000 0.00 0.00 43.22 5.18
474 503 4.591202 TCGGAATTAAGCGTTAGAGTACG 58.409 43.478 0.00 0.00 44.09 3.67
500 529 1.227556 GTTGTCTGGCGTGTGGAGT 60.228 57.895 0.00 0.00 0.00 3.85
503 532 0.036388 ATAGGTTGTCTGGCGTGTGG 60.036 55.000 0.00 0.00 0.00 4.17
509 538 5.822519 TCATTGAATGTATAGGTTGTCTGGC 59.177 40.000 4.93 0.00 0.00 4.85
518 547 5.876460 TCGATGCCATCATTGAATGTATAGG 59.124 40.000 5.40 4.66 39.52 2.57
528 557 9.414295 ACAATTAATTTATCGATGCCATCATTG 57.586 29.630 8.54 11.76 35.77 2.82
534 563 8.556194 GTGAGTACAATTAATTTATCGATGCCA 58.444 33.333 8.54 0.00 0.00 4.92
548 577 8.678593 TTTGTGGTGTTATGTGAGTACAATTA 57.321 30.769 0.00 0.00 40.84 1.40
551 580 6.600032 ACTTTTGTGGTGTTATGTGAGTACAA 59.400 34.615 0.00 0.00 40.84 2.41
552 581 6.116806 ACTTTTGTGGTGTTATGTGAGTACA 58.883 36.000 0.00 0.00 41.89 2.90
642 672 8.876275 TTTTACGTTACGATCCTATTAGCATT 57.124 30.769 13.03 0.00 0.00 3.56
657 687 9.213819 CAAACTAGTTGGTTCTTTTTACGTTAC 57.786 33.333 9.34 0.00 33.18 2.50
711 741 8.684520 TGGTCAAACTTAAAATTAACCTTTCGA 58.315 29.630 0.00 0.00 0.00 3.71
729 759 6.272318 TCACACATCTTGAATTTGGTCAAAC 58.728 36.000 0.00 0.00 37.08 2.93
735 765 7.278424 ACAAAGTTTCACACATCTTGAATTTGG 59.722 33.333 12.38 1.85 37.31 3.28
745 775 6.912591 CCAGTAGAAACAAAGTTTCACACATC 59.087 38.462 20.71 7.55 0.00 3.06
747 791 5.941058 TCCAGTAGAAACAAAGTTTCACACA 59.059 36.000 20.71 4.48 0.00 3.72
756 800 5.471456 ACAAGAGCATCCAGTAGAAACAAAG 59.529 40.000 0.00 0.00 33.66 2.77
761 805 5.227569 TGAACAAGAGCATCCAGTAGAAA 57.772 39.130 0.00 0.00 33.66 2.52
769 813 3.755378 ACTCATGTTGAACAAGAGCATCC 59.245 43.478 25.16 0.00 45.01 3.51
777 821 6.934048 TTCATGTGTACTCATGTTGAACAA 57.066 33.333 28.06 16.30 43.70 2.83
829 873 6.817765 TTTTGTTTAGGCTGTATCTTGAGG 57.182 37.500 0.00 0.00 0.00 3.86
839 883 8.776376 ATTTGTATCCAATTTTGTTTAGGCTG 57.224 30.769 0.00 0.00 0.00 4.85
841 885 9.869757 ACTATTTGTATCCAATTTTGTTTAGGC 57.130 29.630 0.00 0.00 0.00 3.93
847 891 9.520515 AGTCTGACTATTTGTATCCAATTTTGT 57.479 29.630 8.91 0.00 0.00 2.83
848 892 9.778993 CAGTCTGACTATTTGTATCCAATTTTG 57.221 33.333 10.47 0.00 0.00 2.44
851 895 9.334947 CATCAGTCTGACTATTTGTATCCAATT 57.665 33.333 10.47 0.00 0.00 2.32
855 899 7.981789 TGAACATCAGTCTGACTATTTGTATCC 59.018 37.037 10.47 7.95 0.00 2.59
860 904 7.172190 AGTGTTGAACATCAGTCTGACTATTTG 59.828 37.037 10.47 10.48 0.00 2.32
861 905 7.220030 AGTGTTGAACATCAGTCTGACTATTT 58.780 34.615 10.47 1.36 0.00 1.40
862 906 6.763355 AGTGTTGAACATCAGTCTGACTATT 58.237 36.000 10.47 2.99 0.00 1.73
863 907 6.352016 AGTGTTGAACATCAGTCTGACTAT 57.648 37.500 10.47 2.36 0.00 2.12
864 908 5.791336 AGTGTTGAACATCAGTCTGACTA 57.209 39.130 10.47 0.00 0.00 2.59
865 909 4.679373 AGTGTTGAACATCAGTCTGACT 57.321 40.909 4.21 4.06 0.00 3.41
884 928 3.088532 TGGAGTCAGTTTTGCAACAAGT 58.911 40.909 0.00 0.00 35.05 3.16
908 952 5.567534 CGTGGGATTTTTACATGAAAACTCG 59.432 40.000 0.00 0.65 37.50 4.18
933 979 2.473378 CAGCGAAGTTGCAGCTCG 59.527 61.111 2.60 10.42 39.48 5.03
934 980 2.866028 CCAGCGAAGTTGCAGCTC 59.134 61.111 2.60 0.00 39.48 4.09
1064 1122 0.996762 GGAGGAGGAGGAGGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
1084 1142 1.141234 GGATCTCGTGGGTTCCGTC 59.859 63.158 0.00 0.00 0.00 4.79
1085 1143 2.356780 GGGATCTCGTGGGTTCCGT 61.357 63.158 0.00 0.00 0.00 4.69
1110 1186 3.310193 GTTAGGCTGGAGGAAGGAGTAT 58.690 50.000 0.00 0.00 0.00 2.12
1614 1690 3.479255 CTTCAAGAAGGCCGCAAAC 57.521 52.632 0.00 0.00 34.87 2.93
1789 1865 1.148273 GTGACACCCCAACAGCTGA 59.852 57.895 23.35 0.00 0.00 4.26
1806 1882 0.034059 CAAAGCTCTCCACGTCTGGT 59.966 55.000 0.00 0.00 38.90 4.00
1854 1930 4.660938 ACCCGGCTTGGAACAGCC 62.661 66.667 0.00 1.29 44.93 4.85
1994 2070 2.163509 CAACTCTTCTCTCCTCCACGA 58.836 52.381 0.00 0.00 0.00 4.35
1995 2071 2.163412 CTCAACTCTTCTCTCCTCCACG 59.837 54.545 0.00 0.00 0.00 4.94
2079 2155 1.492176 TGAGCCAATTCCCTGATCCTC 59.508 52.381 0.00 0.00 0.00 3.71
2137 2213 1.552578 TCATCAGCTGCCAGCAATTT 58.447 45.000 20.53 0.00 45.56 1.82
2147 2223 2.719739 ACCCAACAGAATCATCAGCTG 58.280 47.619 7.63 7.63 35.81 4.24
2150 2226 3.194116 CCCAAACCCAACAGAATCATCAG 59.806 47.826 0.00 0.00 0.00 2.90
2219 2295 4.498682 GGGCAGTCATTTCATCAAGTATGC 60.499 45.833 0.00 0.00 35.38 3.14
2264 2340 6.770785 TGCTTTCAAGATTGGGGTGTATATAC 59.229 38.462 5.89 5.89 0.00 1.47
2352 2428 0.036164 TGCCGGCATCAAGTTGTAGT 59.964 50.000 29.03 0.00 0.00 2.73
2358 2434 1.065491 TCATAACTGCCGGCATCAAGT 60.065 47.619 32.87 21.97 0.00 3.16
2367 2443 4.751600 TCAATAAGAGCATCATAACTGCCG 59.248 41.667 0.00 0.00 40.56 5.69
2397 2473 3.202818 ACTGGAAATCATGGGCTGTCATA 59.797 43.478 0.00 0.00 0.00 2.15
2478 2554 9.982651 GTCAAGCCTGTCATTATAGTAAGATAA 57.017 33.333 0.00 0.00 0.00 1.75
2985 3061 0.443869 CCCAGTTCTTGAACGCGATG 59.556 55.000 15.93 0.00 0.00 3.84
3026 3102 2.481952 GAGGAATCGCATGATAGGTTGC 59.518 50.000 0.00 0.00 33.40 4.17
3027 3103 2.733552 CGAGGAATCGCATGATAGGTTG 59.266 50.000 0.00 0.00 33.40 3.77
3116 3192 5.376625 ACCAGCTCAGTTCTTTAACATGAA 58.623 37.500 0.00 0.00 38.12 2.57
3144 3220 7.859377 CACATGATAGGTTGCAATCTTATGAAC 59.141 37.037 25.41 8.69 0.00 3.18
3300 3381 2.489073 CCAGCTTCCCTAACCTTGTTGT 60.489 50.000 0.00 0.00 0.00 3.32
3372 3453 5.467705 AGTAGTACAAAGTCAAGTTAGCCG 58.532 41.667 2.52 0.00 0.00 5.52
3450 3531 9.113876 CATTTCAGGAAAAACTTGTTACGTATC 57.886 33.333 0.00 0.00 33.56 2.24
3452 3533 6.913673 GCATTTCAGGAAAAACTTGTTACGTA 59.086 34.615 0.00 0.00 33.56 3.57
3453 3534 5.746721 GCATTTCAGGAAAAACTTGTTACGT 59.253 36.000 0.00 0.00 33.56 3.57
3454 3535 5.977129 AGCATTTCAGGAAAAACTTGTTACG 59.023 36.000 0.00 0.00 33.56 3.18
3455 3536 7.706607 AGAAGCATTTCAGGAAAAACTTGTTAC 59.293 33.333 13.86 4.22 35.70 2.50
3466 3547 4.206477 TCGATGAGAAGCATTTCAGGAA 57.794 40.909 0.00 0.00 37.34 3.36
3541 3623 0.038892 GTAGCTCAACGGACCGAACA 60.039 55.000 23.38 1.84 0.00 3.18
3554 3636 5.705905 AGTGAAAACATTACAAGGGTAGCTC 59.294 40.000 0.00 0.00 0.00 4.09
3581 3663 3.658351 GCTTCCATGTAACAGTAAGCG 57.342 47.619 0.00 0.00 31.14 4.68
3928 4157 5.920273 CCTTTAACTACACAAAGTTGGCATG 59.080 40.000 0.00 0.00 39.95 4.06


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

AutoCloner maintained by Alex Coulton.