Multiple sequence alignment - TraesCS4D01G018200

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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 TraesCS4D01G018200 chr4D 100.000 2223 0 0 927 3149 7893183 7890961 0.000000e+00 4106
1 TraesCS4D01G018200 chr4D 100.000 705 0 0 1 705 7894109 7893405 0.000000e+00 1303
2 TraesCS4D01G018200 chr4D 85.612 139 15 4 413 550 416450133 416449999 1.180000e-29 141
3 TraesCS4D01G018200 chr4A 93.231 2157 124 10 927 3070 595422800 595424947 0.000000e+00 3155
4 TraesCS4D01G018200 chr4A 95.881 437 15 3 2712 3146 595425357 595425792 0.000000e+00 704
5 TraesCS4D01G018200 chr4A 82.426 643 49 28 1 612 595422079 595422688 1.300000e-138 503
6 TraesCS4D01G018200 chr4A 95.690 116 5 0 2537 2652 595425226 595425341 1.490000e-43 187
7 TraesCS4D01G018200 chr4A 86.466 133 14 4 413 544 47628254 47628383 3.270000e-30 143
8 TraesCS4D01G018200 chr4B 92.714 2141 129 12 940 3070 14013144 14015267 0.000000e+00 3064
9 TraesCS4D01G018200 chr4B 85.507 138 16 3 414 550 513099933 513099799 1.180000e-29 141
10 TraesCS4D01G018200 chr7A 91.565 1470 106 9 927 2383 635684178 635685642 0.000000e+00 2012
11 TraesCS4D01G018200 chr7A 78.939 622 72 36 2438 3055 635685842 635686408 4.960000e-98 368
12 TraesCS4D01G018200 chr7B 91.361 1470 111 8 927 2383 594954984 594956450 0.000000e+00 1997
13 TraesCS4D01G018200 chr7B 79.051 611 69 26 2438 3045 594956662 594957216 6.420000e-97 364
14 TraesCS4D01G018200 chr7D 91.020 1470 116 9 927 2383 550266047 550267513 0.000000e+00 1969
15 TraesCS4D01G018200 chr7D 79.214 611 69 35 2438 3045 550267742 550268297 3.840000e-99 372
16 TraesCS4D01G018200 chr1A 86.466 133 13 5 413 544 508198897 508199025 1.180000e-29 141
17 TraesCS4D01G018200 chr2A 85.714 133 12 4 431 563 612758574 612758699 1.970000e-27 134
18 TraesCS4D01G018200 chr1B 87.156 109 12 2 431 539 529576039 529575933 4.270000e-24 122


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 TraesCS4D01G018200 chr4D 7890961 7894109 3148 True 2704.50 4106 100.000 1 3149 2 chr4D.!!$R2 3148
1 TraesCS4D01G018200 chr4A 595422079 595425792 3713 False 1137.25 3155 91.807 1 3146 4 chr4A.!!$F2 3145
2 TraesCS4D01G018200 chr4B 14013144 14015267 2123 False 3064.00 3064 92.714 940 3070 1 chr4B.!!$F1 2130
3 TraesCS4D01G018200 chr7A 635684178 635686408 2230 False 1190.00 2012 85.252 927 3055 2 chr7A.!!$F1 2128
4 TraesCS4D01G018200 chr7B 594954984 594957216 2232 False 1180.50 1997 85.206 927 3045 2 chr7B.!!$F1 2118
5 TraesCS4D01G018200 chr7D 550266047 550268297 2250 False 1170.50 1969 85.117 927 3045 2 chr7D.!!$F1 2118

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
964 1001 0.535335 TGAATGCTCGGGACCTACAC 59.465 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2855 3105 0.251165 TTTACAGGTGCCTTCTGCCC 60.251 55.0 0.0 0.0 40.16 5.36 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
27 28 2.049063 GCACGAGCGGTCTTCTGT 60.049 61.111 13.48 0.00 0.00 3.41
30 31 2.202492 CGAGCGGTCTTCTGTCCG 60.202 66.667 13.48 0.00 45.25 4.79
32 33 1.642037 CGAGCGGTCTTCTGTCCGTA 61.642 60.000 13.48 0.00 44.52 4.02
38 39 1.067776 GGTCTTCTGTCCGTACCACTG 60.068 57.143 0.00 0.00 0.00 3.66
87 88 1.292541 GAGGACCTGAACACGACCC 59.707 63.158 0.00 0.00 0.00 4.46
89 90 1.301479 GGACCTGAACACGACCCAC 60.301 63.158 0.00 0.00 0.00 4.61
92 93 1.068417 CCTGAACACGACCCACGAA 59.932 57.895 0.00 0.00 45.77 3.85
151 152 5.648572 GGTAACTAGTGCGATTGTAGAAGT 58.351 41.667 0.00 0.00 0.00 3.01
152 153 5.742926 GGTAACTAGTGCGATTGTAGAAGTC 59.257 44.000 0.00 0.00 0.00 3.01
164 165 6.128254 CGATTGTAGAAGTCAGTACTGTCTCA 60.128 42.308 21.99 12.72 35.62 3.27
165 166 7.414651 CGATTGTAGAAGTCAGTACTGTCTCAT 60.415 40.741 21.99 15.15 35.62 2.90
182 185 5.478332 TGTCTCATTTCAGTCTTCAGAGCTA 59.522 40.000 0.00 0.00 0.00 3.32
183 186 6.035843 GTCTCATTTCAGTCTTCAGAGCTAG 58.964 44.000 0.00 0.00 0.00 3.42
193 196 5.648960 AGTCTTCAGAGCTAGTAGTTGGTAC 59.351 44.000 0.00 0.00 0.00 3.34
194 197 5.648960 GTCTTCAGAGCTAGTAGTTGGTACT 59.351 44.000 0.00 0.00 44.69 2.73
195 198 5.648526 TCTTCAGAGCTAGTAGTTGGTACTG 59.351 44.000 0.00 0.00 42.37 2.74
196 199 4.270834 TCAGAGCTAGTAGTTGGTACTGG 58.729 47.826 0.00 0.00 42.37 4.00
197 200 4.018688 TCAGAGCTAGTAGTTGGTACTGGA 60.019 45.833 0.00 0.00 41.68 3.86
198 201 4.336993 CAGAGCTAGTAGTTGGTACTGGAG 59.663 50.000 0.00 0.00 41.68 3.86
199 202 4.018233 AGAGCTAGTAGTTGGTACTGGAGT 60.018 45.833 0.00 0.00 41.68 3.85
200 203 5.191323 AGAGCTAGTAGTTGGTACTGGAGTA 59.809 44.000 0.00 0.00 41.68 2.59
216 219 9.786105 GTACTGGAGTACTAGTGAAGAATAAAC 57.214 37.037 5.39 0.00 45.47 2.01
217 220 7.838884 ACTGGAGTACTAGTGAAGAATAAACC 58.161 38.462 5.39 0.00 36.51 3.27
218 221 6.860080 TGGAGTACTAGTGAAGAATAAACCG 58.140 40.000 5.39 0.00 0.00 4.44
219 222 6.660521 TGGAGTACTAGTGAAGAATAAACCGA 59.339 38.462 5.39 0.00 0.00 4.69
220 223 7.341256 TGGAGTACTAGTGAAGAATAAACCGAT 59.659 37.037 5.39 0.00 0.00 4.18
221 224 8.844244 GGAGTACTAGTGAAGAATAAACCGATA 58.156 37.037 5.39 0.00 0.00 2.92
225 228 8.403606 ACTAGTGAAGAATAAACCGATAAACG 57.596 34.615 0.00 0.00 42.18 3.60
276 279 2.806434 TGCCTGCTTGGTGACATTTAT 58.194 42.857 0.00 0.00 42.32 1.40
283 286 4.218200 TGCTTGGTGACATTTATTGAGTGG 59.782 41.667 0.00 0.00 42.32 4.00
289 292 6.126623 TGGTGACATTTATTGAGTGGGCTATA 60.127 38.462 0.00 0.00 33.40 1.31
297 300 4.963318 TTGAGTGGGCTATATTCCTGAG 57.037 45.455 0.00 0.00 0.00 3.35
312 315 4.039603 TCCTGAGAGTGAGTGAAGATGA 57.960 45.455 0.00 0.00 0.00 2.92
313 316 4.608269 TCCTGAGAGTGAGTGAAGATGAT 58.392 43.478 0.00 0.00 0.00 2.45
314 317 5.760131 TCCTGAGAGTGAGTGAAGATGATA 58.240 41.667 0.00 0.00 0.00 2.15
315 318 5.592282 TCCTGAGAGTGAGTGAAGATGATAC 59.408 44.000 0.00 0.00 0.00 2.24
316 319 5.359292 CCTGAGAGTGAGTGAAGATGATACA 59.641 44.000 0.00 0.00 0.00 2.29
317 320 6.448207 TGAGAGTGAGTGAAGATGATACAG 57.552 41.667 0.00 0.00 0.00 2.74
336 339 8.246871 TGATACAGTATGATATAAGCAGCTGAC 58.753 37.037 20.43 9.11 39.69 3.51
366 369 2.418628 GGCAATGCAAAAGCGTAGAGTA 59.581 45.455 7.79 0.00 0.00 2.59
390 397 9.401873 GTAGTTTAATGTTGTGGATTTTGTACC 57.598 33.333 0.00 0.00 0.00 3.34
409 416 2.039084 ACCCATCTATTTCATCTCGCCC 59.961 50.000 0.00 0.00 0.00 6.13
410 417 2.038952 CCCATCTATTTCATCTCGCCCA 59.961 50.000 0.00 0.00 0.00 5.36
428 435 4.612712 CGCCCAACTAGTTGTGTTGTAATG 60.613 45.833 29.05 13.50 42.09 1.90
436 443 4.947645 AGTTGTGTTGTAATGCTTGCAAT 58.052 34.783 0.00 0.00 37.58 3.56
514 547 8.712285 ATATTGCTCTTTTGGTCAATTTCATG 57.288 30.769 0.00 0.00 32.20 3.07
515 548 4.885413 TGCTCTTTTGGTCAATTTCATGG 58.115 39.130 0.00 0.00 0.00 3.66
530 563 2.549926 TCATGGTATGCGTGTGATGTC 58.450 47.619 0.00 0.00 0.00 3.06
531 564 2.168313 TCATGGTATGCGTGTGATGTCT 59.832 45.455 0.00 0.00 0.00 3.41
532 565 2.008752 TGGTATGCGTGTGATGTCTG 57.991 50.000 0.00 0.00 0.00 3.51
535 568 3.132111 TGGTATGCGTGTGATGTCTGTAT 59.868 43.478 0.00 0.00 0.00 2.29
538 571 5.064707 GGTATGCGTGTGATGTCTGTATTTT 59.935 40.000 0.00 0.00 0.00 1.82
539 572 4.403015 TGCGTGTGATGTCTGTATTTTG 57.597 40.909 0.00 0.00 0.00 2.44
542 575 4.612614 GCGTGTGATGTCTGTATTTTGTTG 59.387 41.667 0.00 0.00 0.00 3.33
545 578 6.140580 CGTGTGATGTCTGTATTTTGTTGTTG 59.859 38.462 0.00 0.00 0.00 3.33
553 586 4.282496 TGTATTTTGTTGTTGGAGGTGGT 58.718 39.130 0.00 0.00 0.00 4.16
554 587 5.446860 TGTATTTTGTTGTTGGAGGTGGTA 58.553 37.500 0.00 0.00 0.00 3.25
555 588 4.929819 ATTTTGTTGTTGGAGGTGGTAC 57.070 40.909 0.00 0.00 0.00 3.34
575 608 7.691213 TGGTACACCCTATAAAATGTTCTTCA 58.309 34.615 0.00 0.00 34.29 3.02
600 633 1.947678 GCCACTGCTGCTATGAGTTGT 60.948 52.381 0.00 0.00 33.53 3.32
610 643 5.180117 GCTGCTATGAGTTGTTCTTCTGAAA 59.820 40.000 0.00 0.00 33.52 2.69
611 644 6.128063 GCTGCTATGAGTTGTTCTTCTGAAAT 60.128 38.462 0.00 0.00 33.52 2.17
612 645 7.137490 TGCTATGAGTTGTTCTTCTGAAATG 57.863 36.000 0.00 0.00 33.52 2.32
613 646 6.936335 TGCTATGAGTTGTTCTTCTGAAATGA 59.064 34.615 0.00 0.00 33.52 2.57
614 647 7.118825 TGCTATGAGTTGTTCTTCTGAAATGAG 59.881 37.037 0.00 0.00 33.52 2.90
615 648 7.332926 GCTATGAGTTGTTCTTCTGAAATGAGA 59.667 37.037 0.00 0.00 33.52 3.27
616 649 9.212641 CTATGAGTTGTTCTTCTGAAATGAGAA 57.787 33.333 0.00 0.00 33.52 2.87
617 650 8.632906 ATGAGTTGTTCTTCTGAAATGAGAAT 57.367 30.769 0.00 0.00 33.52 2.40
618 651 8.455903 TGAGTTGTTCTTCTGAAATGAGAATT 57.544 30.769 0.00 0.00 33.52 2.17
619 652 8.347771 TGAGTTGTTCTTCTGAAATGAGAATTG 58.652 33.333 0.00 0.00 33.52 2.32
620 653 8.230472 AGTTGTTCTTCTGAAATGAGAATTGT 57.770 30.769 0.00 0.00 33.52 2.71
621 654 8.689972 AGTTGTTCTTCTGAAATGAGAATTGTT 58.310 29.630 0.00 0.00 33.52 2.83
622 655 8.749499 GTTGTTCTTCTGAAATGAGAATTGTTG 58.251 33.333 0.00 0.00 33.52 3.33
623 656 8.224389 TGTTCTTCTGAAATGAGAATTGTTGA 57.776 30.769 0.00 0.00 33.52 3.18
624 657 8.347771 TGTTCTTCTGAAATGAGAATTGTTGAG 58.652 33.333 0.00 0.00 33.52 3.02
625 658 8.562892 GTTCTTCTGAAATGAGAATTGTTGAGA 58.437 33.333 0.00 0.00 33.52 3.27
626 659 8.320396 TCTTCTGAAATGAGAATTGTTGAGAG 57.680 34.615 0.00 0.00 31.51 3.20
627 660 7.935755 TCTTCTGAAATGAGAATTGTTGAGAGT 59.064 33.333 0.00 0.00 31.51 3.24
628 661 8.455903 TTCTGAAATGAGAATTGTTGAGAGTT 57.544 30.769 0.00 0.00 0.00 3.01
629 662 7.868775 TCTGAAATGAGAATTGTTGAGAGTTG 58.131 34.615 0.00 0.00 0.00 3.16
630 663 7.716560 TCTGAAATGAGAATTGTTGAGAGTTGA 59.283 33.333 0.00 0.00 0.00 3.18
631 664 7.868775 TGAAATGAGAATTGTTGAGAGTTGAG 58.131 34.615 0.00 0.00 0.00 3.02
632 665 7.716560 TGAAATGAGAATTGTTGAGAGTTGAGA 59.283 33.333 0.00 0.00 0.00 3.27
633 666 7.432350 AATGAGAATTGTTGAGAGTTGAGAC 57.568 36.000 0.00 0.00 0.00 3.36
634 667 6.166984 TGAGAATTGTTGAGAGTTGAGACT 57.833 37.500 0.00 0.00 39.32 3.24
635 668 6.586344 TGAGAATTGTTGAGAGTTGAGACTT 58.414 36.000 0.00 0.00 35.88 3.01
636 669 6.481313 TGAGAATTGTTGAGAGTTGAGACTTG 59.519 38.462 0.00 0.00 35.88 3.16
637 670 6.586344 AGAATTGTTGAGAGTTGAGACTTGA 58.414 36.000 0.00 0.00 35.88 3.02
638 671 6.705381 AGAATTGTTGAGAGTTGAGACTTGAG 59.295 38.462 0.00 0.00 35.88 3.02
685 718 8.763049 AATTTTATTCCTTAGTTGCAAAGCTC 57.237 30.769 0.00 0.00 0.00 4.09
702 736 6.018016 GCAAAGCTCATGTTGTTTAAAATGGT 60.018 34.615 0.00 0.00 33.19 3.55
963 1000 0.824109 CTGAATGCTCGGGACCTACA 59.176 55.000 0.00 0.00 0.00 2.74
964 1001 0.535335 TGAATGCTCGGGACCTACAC 59.465 55.000 0.00 0.00 0.00 2.90
986 1023 2.553602 TGCCTACACAGACTTGCATTTG 59.446 45.455 0.00 0.00 0.00 2.32
998 1035 6.521133 CAGACTTGCATTTGAGACGTAAATTC 59.479 38.462 0.00 0.00 0.00 2.17
1011 1052 8.403236 TGAGACGTAAATTCGATGAGAAGATTA 58.597 33.333 0.00 0.00 42.92 1.75
1024 1065 8.272176 CGATGAGAAGATTAGCAGAACATTTAC 58.728 37.037 0.00 0.00 0.00 2.01
1026 1067 6.535150 TGAGAAGATTAGCAGAACATTTACCG 59.465 38.462 0.00 0.00 0.00 4.02
1033 1074 7.675962 TTAGCAGAACATTTACCGTACATTT 57.324 32.000 0.00 0.00 0.00 2.32
1042 1083 4.987408 TTACCGTACATTTCCAGATCGA 57.013 40.909 0.00 0.00 0.00 3.59
1083 1124 1.064654 GAAATGTCCTCATTCGCTGCC 59.935 52.381 0.00 0.00 42.60 4.85
1122 1163 3.181506 CCAAGAAGAAGCTTTATCACCGC 60.182 47.826 0.00 0.00 0.00 5.68
1131 1172 1.609635 TTTATCACCGCGAGCCTGGA 61.610 55.000 8.23 0.00 0.00 3.86
1346 1387 1.167851 CGTGAACCCATTGCTGTCAT 58.832 50.000 0.00 0.00 0.00 3.06
1388 1429 4.881019 ATATTTCTGGTGAGGAGATCCG 57.119 45.455 0.00 0.00 42.08 4.18
1591 1632 2.503356 AGAGGATTGGACCATCTGTGTC 59.497 50.000 0.00 0.00 0.00 3.67
1636 1677 1.789464 CAGTCACAGCACGAGAAGAAC 59.211 52.381 0.00 0.00 0.00 3.01
1731 1772 6.003950 TGCTTTCAAGTTAAAGTATCCAGCT 58.996 36.000 0.00 0.00 38.48 4.24
1886 1927 6.798427 TCTACATGAGGTCTTAAGCTTGAT 57.202 37.500 9.86 0.00 32.07 2.57
2007 2048 6.127026 GGATCTTCTACATCACTAACAAGGGT 60.127 42.308 0.00 0.00 0.00 4.34
2048 2089 3.766591 CTCAAGGAGGCCTACGATGATAT 59.233 47.826 22.28 0.00 31.13 1.63
2120 2161 1.846007 TTAATTGGACGGCCATGCTT 58.154 45.000 13.08 8.30 45.46 3.91
2157 2201 2.879646 ACTGGCAGTATAGCTCGAGTAC 59.120 50.000 20.61 8.85 34.17 2.73
2184 2228 6.647334 TTTACATGAGAAGCAAAACCATGA 57.353 33.333 0.00 0.00 38.29 3.07
2190 2234 4.341806 TGAGAAGCAAAACCATGATGTGTT 59.658 37.500 0.00 0.00 0.00 3.32
2191 2235 4.874970 AGAAGCAAAACCATGATGTGTTC 58.125 39.130 0.00 0.00 0.00 3.18
2193 2237 2.622942 AGCAAAACCATGATGTGTTCGT 59.377 40.909 0.00 0.00 0.00 3.85
2230 2274 3.151554 AGTTGATTGCTTGATGCTCACA 58.848 40.909 0.00 0.00 43.37 3.58
2231 2275 3.762288 AGTTGATTGCTTGATGCTCACAT 59.238 39.130 0.00 0.00 43.37 3.21
2272 2316 5.701290 ACAACAAACTATGTAAGTCCTCTGC 59.299 40.000 0.00 0.00 42.99 4.26
2300 2347 4.261801 GGATGTTTCTTGCACCTTAGCTA 58.738 43.478 0.00 0.00 34.99 3.32
2470 2703 9.908152 AGTTGTGTAGCTTATAATTCCAAAAAC 57.092 29.630 0.00 0.00 0.00 2.43
2533 2766 4.843220 AATGTTGAGTTTGCTTCTCCTG 57.157 40.909 0.00 0.00 0.00 3.86
2542 2775 0.986527 TGCTTCTCCTGCTTGGATGA 59.013 50.000 0.00 0.00 45.16 2.92
2556 2789 4.451096 GCTTGGATGACTTTCTACGTTTGA 59.549 41.667 0.00 0.00 0.00 2.69
2569 2802 9.318041 CTTTCTACGTTTGACTCATAAACAATG 57.682 33.333 0.00 0.00 37.78 2.82
2629 2862 4.638865 CCAATCTCATGTGATTCTGCTTGA 59.361 41.667 17.85 0.00 34.77 3.02
2642 2875 9.113838 GTGATTCTGCTTGAAGAAGGATATTTA 57.886 33.333 0.00 0.00 39.47 1.40
2681 2921 7.797819 ACTTAATTTTAGAGAGTTCTGCAACG 58.202 34.615 0.00 0.00 37.61 4.10
2719 2959 3.774766 TCACACAGCCATACCACTAGATT 59.225 43.478 0.00 0.00 0.00 2.40
2720 2960 4.959839 TCACACAGCCATACCACTAGATTA 59.040 41.667 0.00 0.00 0.00 1.75
2746 2986 7.213678 TCTTGGTTGGTTGGATGTTTTAAATC 58.786 34.615 0.00 0.00 0.00 2.17
2747 2987 6.739331 TGGTTGGTTGGATGTTTTAAATCT 57.261 33.333 0.00 0.00 0.00 2.40
2748 2988 6.520272 TGGTTGGTTGGATGTTTTAAATCTG 58.480 36.000 0.00 0.00 0.00 2.90
2763 3011 9.516314 GTTTTAAATCTGTTACCAGCATTATCC 57.484 33.333 0.00 0.00 38.66 2.59
2764 3012 7.817418 TTAAATCTGTTACCAGCATTATCCC 57.183 36.000 0.00 0.00 38.66 3.85
2791 3039 3.206150 GCATGAACTGACCATCGGTAAT 58.794 45.455 0.00 0.00 34.28 1.89
2793 3041 4.441792 CATGAACTGACCATCGGTAATGA 58.558 43.478 7.25 0.00 34.28 2.57
2808 3056 8.506437 CATCGGTAATGATTAGTGCATTAACAT 58.494 33.333 3.52 7.35 42.99 2.71
2827 3075 0.321919 TGCTGGCACCTCAATCAGTC 60.322 55.000 0.00 0.00 0.00 3.51
2828 3076 0.035630 GCTGGCACCTCAATCAGTCT 60.036 55.000 0.00 0.00 0.00 3.24
2830 3078 2.355108 GCTGGCACCTCAATCAGTCTTA 60.355 50.000 0.00 0.00 0.00 2.10
2855 3105 4.222886 TGTTGTTTTCGCATCCATTAACG 58.777 39.130 0.00 0.00 0.00 3.18
2863 3113 1.334869 GCATCCATTAACGGGCAGAAG 59.665 52.381 0.00 0.00 0.00 2.85
2887 3138 4.012374 CACCTGTAAAATGCTCCAGATGT 58.988 43.478 0.00 0.00 0.00 3.06
2895 3146 5.733620 AAATGCTCCAGATGTTGTCAATT 57.266 34.783 0.00 0.00 0.00 2.32
2905 3156 9.642327 TCCAGATGTTGTCAATTATTGAATTTG 57.358 29.630 9.39 5.31 42.15 2.32
2906 3157 9.642327 CCAGATGTTGTCAATTATTGAATTTGA 57.358 29.630 9.39 0.00 42.15 2.69
2931 3182 4.122046 TCGATCTAGCACATTGATTGGTG 58.878 43.478 0.00 0.00 38.05 4.17
2933 3184 4.333649 CGATCTAGCACATTGATTGGTGTT 59.666 41.667 0.00 0.00 37.35 3.32
2966 3217 7.977293 TCTGAATTTGTTGGCAATGATTATCTG 59.023 33.333 1.92 3.30 34.18 2.90
2967 3218 7.613585 TGAATTTGTTGGCAATGATTATCTGT 58.386 30.769 1.92 0.00 34.18 3.41
3100 4122 4.725490 AGGTGGCTTGTTTACTGTGTATT 58.275 39.130 0.00 0.00 0.00 1.89
3126 4148 4.022329 GGTGGCTTGCTTACTGTGTATTTT 60.022 41.667 0.00 0.00 0.00 1.82
3127 4149 4.917415 GTGGCTTGCTTACTGTGTATTTTG 59.083 41.667 0.00 0.00 0.00 2.44
3146 4168 3.202829 TGGGTGGTCTGTTTACTGAAC 57.797 47.619 0.00 0.00 38.78 3.18
3147 4169 2.506231 TGGGTGGTCTGTTTACTGAACA 59.494 45.455 3.71 3.71 45.70 3.18
3148 4170 3.054287 TGGGTGGTCTGTTTACTGAACAA 60.054 43.478 8.77 0.00 46.99 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.067776 CAGTGGTACGGACAGAAGACC 60.068 57.143 0.00 0.00 0.00 3.85
116 117 1.746220 CTAGTTACCTCGAGCAGCTGT 59.254 52.381 16.64 1.59 0.00 4.40
134 135 5.646793 AGTACTGACTTCTACAATCGCACTA 59.353 40.000 0.00 0.00 28.61 2.74
139 140 6.128254 TGAGACAGTACTGACTTCTACAATCG 60.128 42.308 29.30 0.00 35.86 3.34
151 152 6.265422 TGAAGACTGAAATGAGACAGTACTGA 59.735 38.462 29.30 7.19 45.54 3.41
152 153 6.450545 TGAAGACTGAAATGAGACAGTACTG 58.549 40.000 21.44 21.44 45.54 2.74
164 165 7.319646 CAACTACTAGCTCTGAAGACTGAAAT 58.680 38.462 0.00 0.00 0.00 2.17
165 166 6.294787 CCAACTACTAGCTCTGAAGACTGAAA 60.295 42.308 0.00 0.00 0.00 2.69
193 196 6.973474 CGGTTTATTCTTCACTAGTACTCCAG 59.027 42.308 0.00 0.00 0.00 3.86
194 197 6.660521 TCGGTTTATTCTTCACTAGTACTCCA 59.339 38.462 0.00 0.00 0.00 3.86
195 198 7.093322 TCGGTTTATTCTTCACTAGTACTCC 57.907 40.000 0.00 0.00 0.00 3.85
199 202 9.507280 CGTTTATCGGTTTATTCTTCACTAGTA 57.493 33.333 0.00 0.00 35.71 1.82
200 203 8.403606 CGTTTATCGGTTTATTCTTCACTAGT 57.596 34.615 0.00 0.00 35.71 2.57
217 220 1.469126 CTCGTCCGTGCCGTTTATCG 61.469 60.000 0.00 0.00 39.52 2.92
218 221 1.749609 GCTCGTCCGTGCCGTTTATC 61.750 60.000 2.54 0.00 0.00 1.75
219 222 1.808390 GCTCGTCCGTGCCGTTTAT 60.808 57.895 2.54 0.00 0.00 1.40
220 223 2.431260 GCTCGTCCGTGCCGTTTA 60.431 61.111 2.54 0.00 0.00 2.01
221 224 4.595538 TGCTCGTCCGTGCCGTTT 62.596 61.111 10.73 0.00 34.16 3.60
222 225 4.595538 TTGCTCGTCCGTGCCGTT 62.596 61.111 10.73 0.00 34.16 4.44
225 228 3.112709 GAGTTGCTCGTCCGTGCC 61.113 66.667 10.73 0.00 34.16 5.01
248 251 1.274167 CACCAAGCAGGCAATTGATGT 59.726 47.619 10.34 0.00 43.14 3.06
253 256 1.636148 ATGTCACCAAGCAGGCAATT 58.364 45.000 0.00 0.00 43.14 2.32
276 279 4.556697 TCTCAGGAATATAGCCCACTCAA 58.443 43.478 0.00 0.00 0.00 3.02
283 286 4.830046 TCACTCACTCTCAGGAATATAGCC 59.170 45.833 0.00 0.00 0.00 3.93
289 292 5.022122 TCATCTTCACTCACTCTCAGGAAT 58.978 41.667 0.00 0.00 0.00 3.01
297 300 7.935520 TCATACTGTATCATCTTCACTCACTC 58.064 38.462 0.00 0.00 0.00 3.51
312 315 7.254137 CGTCAGCTGCTTATATCATACTGTAT 58.746 38.462 9.47 0.00 0.00 2.29
313 316 6.612306 CGTCAGCTGCTTATATCATACTGTA 58.388 40.000 9.47 0.00 0.00 2.74
314 317 5.465051 CGTCAGCTGCTTATATCATACTGT 58.535 41.667 9.47 0.00 0.00 3.55
315 318 4.325741 GCGTCAGCTGCTTATATCATACTG 59.674 45.833 9.47 0.00 41.01 2.74
316 319 4.489810 GCGTCAGCTGCTTATATCATACT 58.510 43.478 9.47 0.00 41.01 2.12
317 320 4.831741 GCGTCAGCTGCTTATATCATAC 57.168 45.455 9.47 0.00 41.01 2.39
336 339 1.500108 TTTGCATTGCCAGAAAAGCG 58.500 45.000 6.12 0.00 0.00 4.68
366 369 7.070074 TGGGTACAAAATCCACAACATTAAACT 59.930 33.333 0.00 0.00 0.00 2.66
390 397 3.407424 TGGGCGAGATGAAATAGATGG 57.593 47.619 0.00 0.00 0.00 3.51
410 417 5.067153 TGCAAGCATTACAACACAACTAGTT 59.933 36.000 1.12 1.12 0.00 2.24
428 435 9.532697 CACTAAATATGTTTGAAAATTGCAAGC 57.467 29.630 4.94 0.00 0.00 4.01
500 533 3.761218 ACGCATACCATGAAATTGACCAA 59.239 39.130 0.00 0.00 0.00 3.67
504 537 4.006319 TCACACGCATACCATGAAATTGA 58.994 39.130 0.00 0.00 0.00 2.57
509 542 2.935849 GACATCACACGCATACCATGAA 59.064 45.455 0.00 0.00 0.00 2.57
510 543 2.168313 AGACATCACACGCATACCATGA 59.832 45.455 0.00 0.00 0.00 3.07
512 545 2.093500 ACAGACATCACACGCATACCAT 60.093 45.455 0.00 0.00 0.00 3.55
514 547 2.010145 ACAGACATCACACGCATACC 57.990 50.000 0.00 0.00 0.00 2.73
515 548 5.718649 AAATACAGACATCACACGCATAC 57.281 39.130 0.00 0.00 0.00 2.39
530 563 4.340950 ACCACCTCCAACAACAAAATACAG 59.659 41.667 0.00 0.00 0.00 2.74
531 564 4.282496 ACCACCTCCAACAACAAAATACA 58.718 39.130 0.00 0.00 0.00 2.29
532 565 4.929819 ACCACCTCCAACAACAAAATAC 57.070 40.909 0.00 0.00 0.00 1.89
535 568 3.444388 GTGTACCACCTCCAACAACAAAA 59.556 43.478 0.00 0.00 0.00 2.44
538 571 2.335316 GTGTACCACCTCCAACAACA 57.665 50.000 0.00 0.00 0.00 3.33
561 594 8.055754 GCAGTGGCAGAATGAAGAACATTTTAT 61.056 37.037 0.00 0.00 43.44 1.40
575 608 1.211212 TCATAGCAGCAGTGGCAGAAT 59.789 47.619 0.00 0.00 44.61 2.40
600 633 8.681486 TCTCAACAATTCTCATTTCAGAAGAA 57.319 30.769 0.00 0.00 35.83 2.52
610 643 6.767456 AGTCTCAACTCTCAACAATTCTCAT 58.233 36.000 0.00 0.00 0.00 2.90
611 644 6.166984 AGTCTCAACTCTCAACAATTCTCA 57.833 37.500 0.00 0.00 0.00 3.27
612 645 6.703607 TCAAGTCTCAACTCTCAACAATTCTC 59.296 38.462 0.00 0.00 33.48 2.87
613 646 6.586344 TCAAGTCTCAACTCTCAACAATTCT 58.414 36.000 0.00 0.00 33.48 2.40
614 647 6.703607 TCTCAAGTCTCAACTCTCAACAATTC 59.296 38.462 0.00 0.00 33.48 2.17
615 648 6.586344 TCTCAAGTCTCAACTCTCAACAATT 58.414 36.000 0.00 0.00 33.48 2.32
616 649 6.166984 TCTCAAGTCTCAACTCTCAACAAT 57.833 37.500 0.00 0.00 33.48 2.71
617 650 5.598416 TCTCAAGTCTCAACTCTCAACAA 57.402 39.130 0.00 0.00 33.48 2.83
618 651 5.798125 ATCTCAAGTCTCAACTCTCAACA 57.202 39.130 0.00 0.00 33.48 3.33
619 652 6.682746 TGTATCTCAAGTCTCAACTCTCAAC 58.317 40.000 0.00 0.00 33.48 3.18
620 653 6.071672 CCTGTATCTCAAGTCTCAACTCTCAA 60.072 42.308 0.00 0.00 33.48 3.02
621 654 5.417266 CCTGTATCTCAAGTCTCAACTCTCA 59.583 44.000 0.00 0.00 33.48 3.27
622 655 5.678616 GCCTGTATCTCAAGTCTCAACTCTC 60.679 48.000 0.00 0.00 33.48 3.20
623 656 4.159506 GCCTGTATCTCAAGTCTCAACTCT 59.840 45.833 0.00 0.00 33.48 3.24
624 657 4.159506 AGCCTGTATCTCAAGTCTCAACTC 59.840 45.833 0.00 0.00 33.48 3.01
625 658 4.093011 AGCCTGTATCTCAAGTCTCAACT 58.907 43.478 0.00 0.00 37.32 3.16
626 659 4.464069 AGCCTGTATCTCAAGTCTCAAC 57.536 45.455 0.00 0.00 0.00 3.18
627 660 5.489792 AAAGCCTGTATCTCAAGTCTCAA 57.510 39.130 0.00 0.00 0.00 3.02
628 661 5.240891 CAAAAGCCTGTATCTCAAGTCTCA 58.759 41.667 0.00 0.00 0.00 3.27
629 662 4.633565 CCAAAAGCCTGTATCTCAAGTCTC 59.366 45.833 0.00 0.00 0.00 3.36
630 663 4.042187 ACCAAAAGCCTGTATCTCAAGTCT 59.958 41.667 0.00 0.00 0.00 3.24
631 664 4.327680 ACCAAAAGCCTGTATCTCAAGTC 58.672 43.478 0.00 0.00 0.00 3.01
632 665 4.373156 ACCAAAAGCCTGTATCTCAAGT 57.627 40.909 0.00 0.00 0.00 3.16
633 666 8.562892 CATAATACCAAAAGCCTGTATCTCAAG 58.437 37.037 0.00 0.00 0.00 3.02
634 667 8.271458 TCATAATACCAAAAGCCTGTATCTCAA 58.729 33.333 0.00 0.00 0.00 3.02
635 668 7.801104 TCATAATACCAAAAGCCTGTATCTCA 58.199 34.615 0.00 0.00 0.00 3.27
636 669 8.677148 TTCATAATACCAAAAGCCTGTATCTC 57.323 34.615 0.00 0.00 0.00 2.75
637 670 9.646522 AATTCATAATACCAAAAGCCTGTATCT 57.353 29.630 0.00 0.00 0.00 1.98
665 698 5.945784 ACATGAGCTTTGCAACTAAGGAATA 59.054 36.000 0.00 0.00 0.00 1.75
675 708 6.974932 TTTTAAACAACATGAGCTTTGCAA 57.025 29.167 0.00 0.00 0.00 4.08
938 972 1.817099 CCCGAGCATTCAGGAGTGC 60.817 63.158 8.54 8.54 43.34 4.40
961 998 1.541233 GCAAGTCTGTGTAGGCAGTGT 60.541 52.381 0.00 0.00 37.70 3.55
963 1000 0.758734 TGCAAGTCTGTGTAGGCAGT 59.241 50.000 0.00 0.00 37.70 4.40
964 1001 2.105006 ATGCAAGTCTGTGTAGGCAG 57.895 50.000 0.00 0.00 37.81 4.85
986 1023 7.687005 AATCTTCTCATCGAATTTACGTCTC 57.313 36.000 0.00 0.00 34.70 3.36
998 1035 6.841443 AATGTTCTGCTAATCTTCTCATCG 57.159 37.500 0.00 0.00 0.00 3.84
1011 1052 5.123344 GGAAATGTACGGTAAATGTTCTGCT 59.877 40.000 0.00 0.00 0.00 4.24
1024 1065 4.211374 GGAAATCGATCTGGAAATGTACGG 59.789 45.833 0.00 0.00 0.00 4.02
1026 1067 6.538742 TCAAGGAAATCGATCTGGAAATGTAC 59.461 38.462 0.00 0.00 0.00 2.90
1033 1074 5.869649 TGTATCAAGGAAATCGATCTGGA 57.130 39.130 0.00 0.00 0.00 3.86
1131 1172 1.296715 GTCCATGGCCTTGTCGAGT 59.703 57.895 16.81 0.00 0.00 4.18
1346 1387 1.644509 TCTGGCCTTCTCAGTAAGCA 58.355 50.000 3.32 0.00 34.15 3.91
1388 1429 2.284190 GTTCCATTAGCTCCTGTGCTC 58.716 52.381 0.00 0.00 42.97 4.26
1591 1632 3.262915 AGTGAAGAATCCCAACTCTCCAG 59.737 47.826 0.00 0.00 0.00 3.86
1636 1677 7.551035 TTTGGAAACCATCAAAGTTCAATTG 57.449 32.000 0.00 0.00 31.53 2.32
1731 1772 1.208844 TCCGGTTGGGCCTAAATCCA 61.209 55.000 1.74 0.00 35.24 3.41
1886 1927 4.627035 CAGATGTCAGTCGTTTCTGCATTA 59.373 41.667 0.00 0.00 34.77 1.90
2007 2048 3.069016 TGAGAAAGACGGTACTTCTTGCA 59.931 43.478 14.62 9.56 46.41 4.08
2048 2089 7.326454 CAGAGGACACTTCTCAATGAGATTAA 58.674 38.462 14.31 0.00 38.56 1.40
2120 2161 2.094182 GCCAGTGGAGTATTCAAGTCGA 60.094 50.000 15.20 0.00 0.00 4.20
2157 2201 6.680810 TGGTTTTGCTTCTCATGTAAATCAG 58.319 36.000 0.00 0.00 0.00 2.90
2184 2228 1.002430 AGATGCACCAGACGAACACAT 59.998 47.619 0.00 0.00 0.00 3.21
2190 2234 2.826128 ACTAAGAAGATGCACCAGACGA 59.174 45.455 0.00 0.00 0.00 4.20
2191 2235 3.238108 ACTAAGAAGATGCACCAGACG 57.762 47.619 0.00 0.00 0.00 4.18
2193 2237 4.890158 TCAACTAAGAAGATGCACCAGA 57.110 40.909 0.00 0.00 0.00 3.86
2230 2274 2.737544 TGTGTGCAAATGGGCTCATAT 58.262 42.857 0.00 0.00 39.20 1.78
2231 2275 2.212812 TGTGTGCAAATGGGCTCATA 57.787 45.000 0.00 0.00 39.20 2.15
2272 2316 3.006110 AGGTGCAAGAAACATCCATTGTG 59.994 43.478 0.00 0.00 38.99 3.33
2349 2396 1.177401 GCAACTTGATTCCTGGGGAC 58.823 55.000 0.00 0.00 0.00 4.46
2350 2397 0.776810 TGCAACTTGATTCCTGGGGA 59.223 50.000 0.00 0.00 0.00 4.81
2383 2430 1.843851 TCCAACTGAACCTGTGACCTT 59.156 47.619 0.00 0.00 0.00 3.50
2470 2703 7.865707 AGCAGAACTGATACTGTAACTTTTTG 58.134 34.615 5.97 0.00 36.62 2.44
2533 2766 4.451096 TCAAACGTAGAAAGTCATCCAAGC 59.549 41.667 0.00 0.00 0.00 4.01
2542 2775 8.428186 TTGTTTATGAGTCAAACGTAGAAAGT 57.572 30.769 0.00 0.00 38.46 2.66
2556 2789 3.758554 GTGCCTGACCATTGTTTATGAGT 59.241 43.478 0.00 0.00 36.26 3.41
2569 2802 4.142609 TCAGATAAATGAGTGCCTGACC 57.857 45.455 0.00 0.00 0.00 4.02
2609 2842 5.742063 TCTTCAAGCAGAATCACATGAGAT 58.258 37.500 0.00 0.00 35.25 2.75
2629 2862 8.211629 AGCGGAACAGTAATAAATATCCTTCTT 58.788 33.333 0.00 0.00 0.00 2.52
2642 2875 9.880157 TCTAAAATTAAGTAGCGGAACAGTAAT 57.120 29.630 0.00 0.00 0.00 1.89
2652 2892 7.275779 TGCAGAACTCTCTAAAATTAAGTAGCG 59.724 37.037 0.00 0.00 0.00 4.26
2681 2921 3.930229 TGTGTGAGTGTGACACAGTTTAC 59.070 43.478 18.95 17.53 46.80 2.01
2705 2945 6.936900 CCAACCAAGATAATCTAGTGGTATGG 59.063 42.308 2.24 7.98 36.79 2.74
2719 2959 7.841282 TTAAAACATCCAACCAACCAAGATA 57.159 32.000 0.00 0.00 0.00 1.98
2720 2960 6.739331 TTAAAACATCCAACCAACCAAGAT 57.261 33.333 0.00 0.00 0.00 2.40
2763 3011 0.967380 GGTCAGTTCATGCAAGGGGG 60.967 60.000 0.00 0.00 0.00 5.40
2764 3012 0.251297 TGGTCAGTTCATGCAAGGGG 60.251 55.000 0.00 0.00 0.00 4.79
2808 3056 0.321919 GACTGATTGAGGTGCCAGCA 60.322 55.000 0.00 0.00 0.00 4.41
2827 3075 6.949578 ATGGATGCGAAAACAACAAATAAG 57.050 33.333 0.00 0.00 0.00 1.73
2828 3076 8.704234 GTTAATGGATGCGAAAACAACAAATAA 58.296 29.630 0.00 0.00 0.00 1.40
2830 3078 6.128956 CGTTAATGGATGCGAAAACAACAAAT 60.129 34.615 0.00 0.00 0.00 2.32
2855 3105 0.251165 TTTACAGGTGCCTTCTGCCC 60.251 55.000 0.00 0.00 40.16 5.36
2863 3113 1.474077 CTGGAGCATTTTACAGGTGCC 59.526 52.381 0.00 0.00 39.62 5.01
2895 3146 7.763985 TGTGCTAGATCGAAGTCAAATTCAATA 59.236 33.333 0.00 0.00 0.00 1.90
2905 3156 5.050499 CCAATCAATGTGCTAGATCGAAGTC 60.050 44.000 0.00 0.00 0.00 3.01
2906 3157 4.813161 CCAATCAATGTGCTAGATCGAAGT 59.187 41.667 0.00 0.00 0.00 3.01
2931 3182 7.945033 TGCCAACAAATTCAGAAATTAGAAC 57.055 32.000 0.00 0.00 33.93 3.01
2933 3184 8.366401 TCATTGCCAACAAATTCAGAAATTAGA 58.634 29.630 0.00 0.00 39.77 2.10
2966 3217 6.072508 AGGACACAATCACATACAATGAACAC 60.073 38.462 0.00 0.00 0.00 3.32
2967 3218 6.003326 AGGACACAATCACATACAATGAACA 58.997 36.000 0.00 0.00 0.00 3.18
3100 4122 2.105821 ACACAGTAAGCAAGCCACCTAA 59.894 45.455 0.00 0.00 0.00 2.69
3126 4148 2.506231 TGTTCAGTAAACAGACCACCCA 59.494 45.455 0.00 0.00 42.95 4.51
3127 4149 3.202829 TGTTCAGTAAACAGACCACCC 57.797 47.619 0.00 0.00 42.95 4.61


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

AutoCloner maintained by Alex Coulton.