Multiple sequence alignment - TraesCS2D01G198800

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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 TraesCS2D01G198800 chr2D 100.000 3634 0 0 1 3634 147936936 147940569 0.000000e+00 6711.0
1 TraesCS2D01G198800 chr2D 92.478 1715 107 9 964 2657 147425998 147427711 0.000000e+00 2433.0
2 TraesCS2D01G198800 chr2D 80.025 1582 281 27 1000 2557 147953508 147955078 0.000000e+00 1138.0
3 TraesCS2D01G198800 chr2D 82.095 525 54 22 458 958 147424527 147425035 2.610000e-111 412.0
4 TraesCS2D01G198800 chr2D 85.549 173 21 4 1 170 553406250 553406079 1.040000e-40 178.0
5 TraesCS2D01G198800 chr2B 95.178 2302 71 11 451 2742 207470683 207472954 0.000000e+00 3600.0
6 TraesCS2D01G198800 chr2B 90.316 2024 143 23 677 2657 207100118 207102131 0.000000e+00 2603.0
7 TraesCS2D01G198800 chr2B 91.333 300 16 9 1 296 207468262 207468555 5.650000e-108 401.0
8 TraesCS2D01G198800 chr2B 87.560 209 16 6 459 665 207099651 207099851 2.180000e-57 233.0
9 TraesCS2D01G198800 chr2B 81.579 152 18 9 310 456 32940452 32940306 2.290000e-22 117.0
10 TraesCS2D01G198800 chr2A 90.625 2176 142 30 490 2619 155075410 155073251 0.000000e+00 2832.0
11 TraesCS2D01G198800 chr2A 95.076 1767 81 4 1000 2763 154849656 154847893 0.000000e+00 2776.0
12 TraesCS2D01G198800 chr2A 81.825 1359 237 8 1207 2560 154422555 154421202 0.000000e+00 1133.0
13 TraesCS2D01G198800 chr2A 91.237 776 60 6 2862 3634 552103172 552102402 0.000000e+00 1050.0
14 TraesCS2D01G198800 chr2A 94.212 501 16 4 448 946 154850148 154849659 0.000000e+00 752.0
15 TraesCS2D01G198800 chr2A 91.582 297 15 7 1 290 154850451 154850158 5.650000e-108 401.0
16 TraesCS2D01G198800 chr2A 88.356 146 14 3 307 450 656838365 656838509 4.820000e-39 172.0
17 TraesCS2D01G198800 chr2A 84.314 153 19 5 307 457 588287739 588287590 1.050000e-30 145.0
18 TraesCS2D01G198800 chr1D 81.342 1356 249 4 1195 2548 483972823 483974176 0.000000e+00 1099.0
19 TraesCS2D01G198800 chr1D 86.228 167 19 3 1 163 443093998 443094164 1.040000e-40 178.0
20 TraesCS2D01G198800 chr1A 81.195 1356 251 4 1195 2548 580988491 580989844 0.000000e+00 1088.0
21 TraesCS2D01G198800 chr1A 72.517 735 180 20 2887 3610 15527831 15527108 6.110000e-53 219.0
22 TraesCS2D01G198800 chr1A 88.194 144 16 1 307 449 533762203 533762346 1.740000e-38 171.0
23 TraesCS2D01G198800 chr1A 82.955 176 24 5 1 170 8020552 8020727 1.750000e-33 154.0
24 TraesCS2D01G198800 chr6B 90.206 776 70 5 2862 3634 664199161 664199933 0.000000e+00 1007.0
25 TraesCS2D01G198800 chrUn 90.052 573 51 5 3065 3634 86966047 86965478 0.000000e+00 737.0
26 TraesCS2D01G198800 chrUn 87.838 74 7 2 2705 2777 326826628 326826556 6.470000e-13 86.1
27 TraesCS2D01G198800 chrUn 87.838 74 7 2 2705 2777 362639288 362639216 6.470000e-13 86.1
28 TraesCS2D01G198800 chr7B 73.046 742 170 25 2887 3613 32554946 32555672 6.070000e-58 235.0
29 TraesCS2D01G198800 chr7B 72.458 777 187 23 2862 3625 312388125 312387363 1.310000e-54 224.0
30 TraesCS2D01G198800 chr7B 88.276 145 16 1 307 450 596898866 596898722 4.820000e-39 172.0
31 TraesCS2D01G198800 chr7B 94.545 55 2 1 2705 2759 566744009 566743956 2.330000e-12 84.2
32 TraesCS2D01G198800 chr5B 72.500 760 181 25 2889 3634 382369964 382369219 1.700000e-53 220.0
33 TraesCS2D01G198800 chr3B 72.162 740 180 23 2887 3613 828531787 828531061 6.150000e-48 202.0
34 TraesCS2D01G198800 chr3A 71.611 782 191 28 2861 3625 730874915 730874148 6.200000e-43 185.0
35 TraesCS2D01G198800 chr3A 88.276 145 14 3 307 449 554736122 554735979 1.740000e-38 171.0
36 TraesCS2D01G198800 chr4D 88.966 145 15 1 307 450 300311201 300311057 1.040000e-40 178.0
37 TraesCS2D01G198800 chr6D 88.889 144 15 1 307 449 8096705 8096562 3.730000e-40 176.0
38 TraesCS2D01G198800 chr5A 88.889 144 15 1 308 450 451879341 451879484 3.730000e-40 176.0
39 TraesCS2D01G198800 chr5A 84.713 157 18 4 10 162 130535346 130535500 6.280000e-33 152.0
40 TraesCS2D01G198800 chr4B 88.889 144 15 1 307 449 98740247 98740390 3.730000e-40 176.0
41 TraesCS2D01G198800 chr5D 88.276 145 15 2 307 449 244712857 244713001 4.820000e-39 172.0
42 TraesCS2D01G198800 chr5D 81.768 181 27 5 1 175 499691910 499692090 2.920000e-31 147.0
43 TraesCS2D01G198800 chr1B 85.897 156 21 1 10 165 306062606 306062452 8.070000e-37 165.0
44 TraesCS2D01G198800 chr6A 84.337 166 21 4 1 162 448700258 448700422 1.350000e-34 158.0
45 TraesCS2D01G198800 chr7A 85.235 149 21 1 307 454 55198882 55198734 6.280000e-33 152.0
46 TraesCS2D01G198800 chr7D 82.530 166 25 4 307 471 185184020 185184182 3.780000e-30 143.0


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 TraesCS2D01G198800 chr2D 147936936 147940569 3633 False 6711.000000 6711 100.000000 1 3634 1 chr2D.!!$F1 3633
1 TraesCS2D01G198800 chr2D 147424527 147427711 3184 False 1422.500000 2433 87.286500 458 2657 2 chr2D.!!$F3 2199
2 TraesCS2D01G198800 chr2D 147953508 147955078 1570 False 1138.000000 1138 80.025000 1000 2557 1 chr2D.!!$F2 1557
3 TraesCS2D01G198800 chr2B 207468262 207472954 4692 False 2000.500000 3600 93.255500 1 2742 2 chr2B.!!$F2 2741
4 TraesCS2D01G198800 chr2B 207099651 207102131 2480 False 1418.000000 2603 88.938000 459 2657 2 chr2B.!!$F1 2198
5 TraesCS2D01G198800 chr2A 155073251 155075410 2159 True 2832.000000 2832 90.625000 490 2619 1 chr2A.!!$R2 2129
6 TraesCS2D01G198800 chr2A 154847893 154850451 2558 True 1309.666667 2776 93.623333 1 2763 3 chr2A.!!$R5 2762
7 TraesCS2D01G198800 chr2A 154421202 154422555 1353 True 1133.000000 1133 81.825000 1207 2560 1 chr2A.!!$R1 1353
8 TraesCS2D01G198800 chr2A 552102402 552103172 770 True 1050.000000 1050 91.237000 2862 3634 1 chr2A.!!$R3 772
9 TraesCS2D01G198800 chr1D 483972823 483974176 1353 False 1099.000000 1099 81.342000 1195 2548 1 chr1D.!!$F2 1353
10 TraesCS2D01G198800 chr1A 580988491 580989844 1353 False 1088.000000 1088 81.195000 1195 2548 1 chr1A.!!$F3 1353
11 TraesCS2D01G198800 chr1A 15527108 15527831 723 True 219.000000 219 72.517000 2887 3610 1 chr1A.!!$R1 723
12 TraesCS2D01G198800 chr6B 664199161 664199933 772 False 1007.000000 1007 90.206000 2862 3634 1 chr6B.!!$F1 772
13 TraesCS2D01G198800 chrUn 86965478 86966047 569 True 737.000000 737 90.052000 3065 3634 1 chrUn.!!$R1 569
14 TraesCS2D01G198800 chr7B 32554946 32555672 726 False 235.000000 235 73.046000 2887 3613 1 chr7B.!!$F1 726
15 TraesCS2D01G198800 chr7B 312387363 312388125 762 True 224.000000 224 72.458000 2862 3625 1 chr7B.!!$R1 763
16 TraesCS2D01G198800 chr5B 382369219 382369964 745 True 220.000000 220 72.500000 2889 3634 1 chr5B.!!$R1 745
17 TraesCS2D01G198800 chr3B 828531061 828531787 726 True 202.000000 202 72.162000 2887 3613 1 chr3B.!!$R1 726

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
798 3048 0.03601 AAAGGTCCTGGCGATGTCAG 60.036 55.0 0.0 0.0 34.71 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2796 6089 0.035152 TTCTGCATGGGTGTGGCTAG 60.035 55.0 0.0 0.0 0.0 3.42 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
136 143 8.034215 TGAAAGTTGACAATGTTTGACTTTGAT 58.966 29.630 19.63 4.60 37.43 2.57
185 192 3.865745 CAGAAGGCGTACAAGAATACTGG 59.134 47.826 0.00 0.00 0.00 4.00
299 307 8.844244 TCCTAGACAAGTTTTACGATATACTCC 58.156 37.037 0.00 0.00 0.00 3.85
300 308 8.848182 CCTAGACAAGTTTTACGATATACTCCT 58.152 37.037 0.00 0.00 0.00 3.69
301 309 9.881529 CTAGACAAGTTTTACGATATACTCCTC 57.118 37.037 0.00 0.00 0.00 3.71
302 310 7.714703 AGACAAGTTTTACGATATACTCCTCC 58.285 38.462 0.00 0.00 0.00 4.30
303 311 6.501781 ACAAGTTTTACGATATACTCCTCCG 58.498 40.000 0.00 0.00 0.00 4.63
305 313 6.705863 AGTTTTACGATATACTCCTCCGTT 57.294 37.500 0.00 0.00 35.05 4.44
306 314 7.105241 AGTTTTACGATATACTCCTCCGTTT 57.895 36.000 0.00 0.00 35.05 3.60
307 315 7.550712 AGTTTTACGATATACTCCTCCGTTTT 58.449 34.615 0.00 0.00 35.05 2.43
308 316 8.037166 AGTTTTACGATATACTCCTCCGTTTTT 58.963 33.333 0.00 0.00 35.05 1.94
309 317 7.760131 TTTACGATATACTCCTCCGTTTTTG 57.240 36.000 0.00 0.00 35.05 2.44
310 318 5.334724 ACGATATACTCCTCCGTTTTTGT 57.665 39.130 0.00 0.00 0.00 2.83
311 319 5.346522 ACGATATACTCCTCCGTTTTTGTC 58.653 41.667 0.00 0.00 0.00 3.18
312 320 5.126707 ACGATATACTCCTCCGTTTTTGTCT 59.873 40.000 0.00 0.00 0.00 3.41
313 321 6.040878 CGATATACTCCTCCGTTTTTGTCTT 58.959 40.000 0.00 0.00 0.00 3.01
314 322 6.534079 CGATATACTCCTCCGTTTTTGTCTTT 59.466 38.462 0.00 0.00 0.00 2.52
315 323 7.064253 CGATATACTCCTCCGTTTTTGTCTTTT 59.936 37.037 0.00 0.00 0.00 2.27
316 324 6.954487 ATACTCCTCCGTTTTTGTCTTTTT 57.046 33.333 0.00 0.00 0.00 1.94
317 325 9.729281 ATATACTCCTCCGTTTTTGTCTTTTTA 57.271 29.630 0.00 0.00 0.00 1.52
318 326 6.373186 ACTCCTCCGTTTTTGTCTTTTTAG 57.627 37.500 0.00 0.00 0.00 1.85
320 328 6.771267 ACTCCTCCGTTTTTGTCTTTTTAGAT 59.229 34.615 0.00 0.00 0.00 1.98
321 329 7.935210 ACTCCTCCGTTTTTGTCTTTTTAGATA 59.065 33.333 0.00 0.00 0.00 1.98
322 330 8.857694 TCCTCCGTTTTTGTCTTTTTAGATAT 57.142 30.769 0.00 0.00 0.00 1.63
323 331 9.292195 TCCTCCGTTTTTGTCTTTTTAGATATT 57.708 29.630 0.00 0.00 0.00 1.28
324 332 9.908152 CCTCCGTTTTTGTCTTTTTAGATATTT 57.092 29.630 0.00 0.00 0.00 1.40
443 2183 8.244113 AGAAAAGCAAATATTTAGAAACGGAGG 58.756 33.333 0.00 0.00 0.00 4.30
446 2186 7.321745 AGCAAATATTTAGAAACGGAGGAAG 57.678 36.000 0.00 0.00 0.00 3.46
518 2500 2.038269 CGTGGATGTTTCACCGGGG 61.038 63.158 6.32 0.00 0.00 5.73
578 2561 9.746711 GATAGTAATAGAATATTTGTTGCAGCG 57.253 33.333 0.00 0.00 0.00 5.18
583 2566 1.544724 ATATTTGTTGCAGCGGGTGT 58.455 45.000 9.16 0.00 0.00 4.16
590 2573 2.746277 GCAGCGGGTGTAGGTTGG 60.746 66.667 9.16 0.00 0.00 3.77
591 2574 2.747686 CAGCGGGTGTAGGTTGGT 59.252 61.111 0.00 0.00 0.00 3.67
592 2575 1.976898 CAGCGGGTGTAGGTTGGTA 59.023 57.895 0.00 0.00 0.00 3.25
593 2576 0.108329 CAGCGGGTGTAGGTTGGTAG 60.108 60.000 0.00 0.00 0.00 3.18
594 2577 1.219935 GCGGGTGTAGGTTGGTAGG 59.780 63.158 0.00 0.00 0.00 3.18
595 2578 1.259840 GCGGGTGTAGGTTGGTAGGA 61.260 60.000 0.00 0.00 0.00 2.94
798 3048 0.036010 AAAGGTCCTGGCGATGTCAG 60.036 55.000 0.00 0.00 34.71 3.51
924 3195 6.129179 CACCATCCCTCATGTTTAATTAGGT 58.871 40.000 0.00 0.00 0.00 3.08
935 3206 8.293867 TCATGTTTAATTAGGTTCCAAACTTCG 58.706 33.333 0.00 0.00 31.85 3.79
943 3214 2.231235 GGTTCCAAACTTCGCCAATCAT 59.769 45.455 0.00 0.00 0.00 2.45
946 3217 4.695217 TCCAAACTTCGCCAATCATTAC 57.305 40.909 0.00 0.00 0.00 1.89
958 3229 3.067180 CCAATCATTACACCATGGTCAGC 59.933 47.826 16.53 0.00 0.00 4.26
1122 4356 0.394762 TCCTCGGCTACGGTACACAT 60.395 55.000 0.00 0.00 41.39 3.21
1144 4418 1.871080 CTGCCATTATCACCTCGTCC 58.129 55.000 0.00 0.00 0.00 4.79
1188 4477 6.954944 TGGCTATATGAAGTGTTTATTTCGC 58.045 36.000 0.00 0.00 0.00 4.70
1392 4684 1.133823 TCTTCTTCTTTGCTGGTGCCA 60.134 47.619 0.00 0.00 38.71 4.92
2282 5574 2.555199 GTGTCATTCTTCTCCATCGGG 58.445 52.381 0.00 0.00 0.00 5.14
2330 5622 2.786495 GGAGATCTTCCCGCTGCGA 61.786 63.158 25.45 2.65 40.37 5.10
2643 5935 0.035458 CTCGCCTTGACCCAGAGTTT 59.965 55.000 0.00 0.00 0.00 2.66
2658 5950 7.402054 ACCCAGAGTTTATTAATCACATGACA 58.598 34.615 0.00 0.00 0.00 3.58
2678 5970 4.184629 ACAGGATTGCTAAATCTCACGAC 58.815 43.478 0.00 0.00 41.74 4.34
2700 5992 8.244802 ACGACGCTATATTTATAAGATCTTGCT 58.755 33.333 18.47 7.81 0.00 3.91
2759 6052 7.508687 TCTTCTTCTTTATATGCTATGCCACA 58.491 34.615 0.00 0.00 0.00 4.17
2763 6056 9.440773 TCTTCTTTATATGCTATGCCACATAAG 57.559 33.333 0.00 0.00 32.77 1.73
2764 6057 9.224267 CTTCTTTATATGCTATGCCACATAAGT 57.776 33.333 0.00 0.00 32.77 2.24
2765 6058 8.552083 TCTTTATATGCTATGCCACATAAGTG 57.448 34.615 0.00 0.00 45.47 3.16
2779 6072 6.877611 CACATAAGTGGGAGTTGTTTAAGT 57.122 37.500 0.00 0.00 42.13 2.24
2780 6073 6.899114 CACATAAGTGGGAGTTGTTTAAGTC 58.101 40.000 0.00 0.00 42.13 3.01
2781 6074 6.710744 CACATAAGTGGGAGTTGTTTAAGTCT 59.289 38.462 0.00 0.00 42.13 3.24
2782 6075 7.228706 CACATAAGTGGGAGTTGTTTAAGTCTT 59.771 37.037 0.00 0.00 42.13 3.01
2783 6076 8.434392 ACATAAGTGGGAGTTGTTTAAGTCTTA 58.566 33.333 0.00 0.00 36.64 2.10
2784 6077 9.280174 CATAAGTGGGAGTTGTTTAAGTCTTAA 57.720 33.333 0.65 0.65 36.64 1.85
2785 6078 7.803279 AAGTGGGAGTTGTTTAAGTCTTAAG 57.197 36.000 5.23 0.00 36.64 1.85
2786 6079 5.763698 AGTGGGAGTTGTTTAAGTCTTAAGC 59.236 40.000 11.20 11.20 36.64 3.09
2787 6080 4.753107 TGGGAGTTGTTTAAGTCTTAAGCG 59.247 41.667 12.76 0.00 36.64 4.68
2788 6081 4.992951 GGGAGTTGTTTAAGTCTTAAGCGA 59.007 41.667 12.76 9.20 36.64 4.93
2789 6082 5.107182 GGGAGTTGTTTAAGTCTTAAGCGAC 60.107 44.000 22.74 22.74 39.58 5.19
2790 6083 5.695363 GGAGTTGTTTAAGTCTTAAGCGACT 59.305 40.000 28.67 28.67 46.92 4.18
2791 6084 6.346678 GGAGTTGTTTAAGTCTTAAGCGACTG 60.347 42.308 31.35 0.00 45.38 3.51
2792 6085 6.278363 AGTTGTTTAAGTCTTAAGCGACTGA 58.722 36.000 28.13 6.66 44.40 3.41
2793 6086 6.421202 AGTTGTTTAAGTCTTAAGCGACTGAG 59.579 38.462 28.13 0.00 44.40 3.35
2794 6087 6.080648 TGTTTAAGTCTTAAGCGACTGAGA 57.919 37.500 12.76 0.00 43.14 3.27
2795 6088 5.919141 TGTTTAAGTCTTAAGCGACTGAGAC 59.081 40.000 12.76 11.88 43.14 3.36
2796 6089 3.579335 AAGTCTTAAGCGACTGAGACC 57.421 47.619 0.00 4.30 43.14 3.85
2797 6090 2.797786 AGTCTTAAGCGACTGAGACCT 58.202 47.619 0.00 0.00 42.39 3.85
2798 6091 3.952931 AGTCTTAAGCGACTGAGACCTA 58.047 45.455 0.00 0.00 42.39 3.08
2799 6092 3.942748 AGTCTTAAGCGACTGAGACCTAG 59.057 47.826 0.00 0.00 42.39 3.02
2800 6093 2.683867 TCTTAAGCGACTGAGACCTAGC 59.316 50.000 0.00 0.00 0.00 3.42
2801 6094 1.390565 TAAGCGACTGAGACCTAGCC 58.609 55.000 0.00 0.00 0.00 3.93
2802 6095 0.612174 AAGCGACTGAGACCTAGCCA 60.612 55.000 0.00 0.00 0.00 4.75
2803 6096 1.139947 GCGACTGAGACCTAGCCAC 59.860 63.158 0.00 0.00 0.00 5.01
2804 6097 1.595993 GCGACTGAGACCTAGCCACA 61.596 60.000 0.00 0.00 0.00 4.17
2805 6098 0.171455 CGACTGAGACCTAGCCACAC 59.829 60.000 0.00 0.00 0.00 3.82
2806 6099 0.533032 GACTGAGACCTAGCCACACC 59.467 60.000 0.00 0.00 0.00 4.16
2807 6100 0.905337 ACTGAGACCTAGCCACACCC 60.905 60.000 0.00 0.00 0.00 4.61
2808 6101 0.904865 CTGAGACCTAGCCACACCCA 60.905 60.000 0.00 0.00 0.00 4.51
2809 6102 0.252696 TGAGACCTAGCCACACCCAT 60.253 55.000 0.00 0.00 0.00 4.00
2810 6103 0.179000 GAGACCTAGCCACACCCATG 59.821 60.000 0.00 0.00 0.00 3.66
2811 6104 1.452108 GACCTAGCCACACCCATGC 60.452 63.158 0.00 0.00 0.00 4.06
2812 6105 2.196997 GACCTAGCCACACCCATGCA 62.197 60.000 0.00 0.00 0.00 3.96
2813 6106 1.452651 CCTAGCCACACCCATGCAG 60.453 63.158 0.00 0.00 0.00 4.41
2814 6107 1.603842 CTAGCCACACCCATGCAGA 59.396 57.895 0.00 0.00 0.00 4.26
2815 6108 0.035152 CTAGCCACACCCATGCAGAA 60.035 55.000 0.00 0.00 0.00 3.02
2816 6109 0.403655 TAGCCACACCCATGCAGAAA 59.596 50.000 0.00 0.00 0.00 2.52
2817 6110 0.251922 AGCCACACCCATGCAGAAAT 60.252 50.000 0.00 0.00 0.00 2.17
2818 6111 0.108520 GCCACACCCATGCAGAAATG 60.109 55.000 0.00 0.00 0.00 2.32
2819 6112 0.108520 CCACACCCATGCAGAAATGC 60.109 55.000 0.00 0.00 0.00 3.56
2820 6113 0.892755 CACACCCATGCAGAAATGCT 59.107 50.000 1.53 0.00 35.49 3.79
2821 6114 2.093890 CACACCCATGCAGAAATGCTA 58.906 47.619 1.53 0.00 35.49 3.49
2822 6115 2.492881 CACACCCATGCAGAAATGCTAA 59.507 45.455 1.53 0.00 35.49 3.09
2823 6116 3.056678 CACACCCATGCAGAAATGCTAAA 60.057 43.478 1.53 0.00 35.49 1.85
2824 6117 3.770933 ACACCCATGCAGAAATGCTAAAT 59.229 39.130 1.53 0.00 35.49 1.40
2825 6118 4.142093 ACACCCATGCAGAAATGCTAAATC 60.142 41.667 1.53 0.00 35.49 2.17
2826 6119 4.098960 CACCCATGCAGAAATGCTAAATCT 59.901 41.667 1.53 0.00 35.49 2.40
2827 6120 4.340381 ACCCATGCAGAAATGCTAAATCTC 59.660 41.667 1.53 0.00 35.49 2.75
2828 6121 4.340097 CCCATGCAGAAATGCTAAATCTCA 59.660 41.667 1.53 0.00 35.49 3.27
2829 6122 5.507482 CCCATGCAGAAATGCTAAATCTCAG 60.507 44.000 1.53 0.00 35.49 3.35
2830 6123 5.067413 CCATGCAGAAATGCTAAATCTCAGT 59.933 40.000 1.53 0.00 35.49 3.41
2831 6124 5.808042 TGCAGAAATGCTAAATCTCAGTC 57.192 39.130 1.53 0.00 35.49 3.51
2832 6125 5.247862 TGCAGAAATGCTAAATCTCAGTCA 58.752 37.500 1.53 0.00 35.49 3.41
2833 6126 5.706833 TGCAGAAATGCTAAATCTCAGTCAA 59.293 36.000 1.53 0.00 35.49 3.18
2834 6127 6.128090 TGCAGAAATGCTAAATCTCAGTCAAG 60.128 38.462 1.53 0.00 35.49 3.02
2835 6128 6.128063 GCAGAAATGCTAAATCTCAGTCAAGT 60.128 38.462 0.00 0.00 0.00 3.16
2836 6129 7.242079 CAGAAATGCTAAATCTCAGTCAAGTG 58.758 38.462 0.00 0.00 0.00 3.16
2837 6130 7.118825 CAGAAATGCTAAATCTCAGTCAAGTGA 59.881 37.037 0.00 0.00 0.00 3.41
2838 6131 6.981762 AATGCTAAATCTCAGTCAAGTGAG 57.018 37.500 8.30 8.30 44.71 3.51
2846 6139 5.950758 TCTCAGTCAAGTGAGACTTAGTC 57.049 43.478 12.48 3.85 46.52 2.59
2847 6140 4.452795 TCTCAGTCAAGTGAGACTTAGTCG 59.547 45.833 12.48 0.00 46.52 4.18
2848 6141 4.135306 TCAGTCAAGTGAGACTTAGTCGT 58.865 43.478 6.73 0.00 46.26 4.34
2849 6142 4.579340 TCAGTCAAGTGAGACTTAGTCGTT 59.421 41.667 6.73 0.00 46.26 3.85
2850 6143 5.761726 TCAGTCAAGTGAGACTTAGTCGTTA 59.238 40.000 6.73 0.00 46.26 3.18
2851 6144 6.261603 TCAGTCAAGTGAGACTTAGTCGTTAA 59.738 38.462 6.73 0.00 46.26 2.01
2852 6145 6.579292 CAGTCAAGTGAGACTTAGTCGTTAAG 59.421 42.308 6.73 7.57 46.26 1.85
2885 6178 5.092554 TGCTGACCGAATGTTAATTAGGA 57.907 39.130 4.83 0.00 40.10 2.94
2920 6213 2.166664 ACTTGATGAACTCCTCTACCGC 59.833 50.000 0.00 0.00 0.00 5.68
3016 6309 4.994471 CAGGCTGTGTGGCGAGCA 62.994 66.667 6.28 0.00 46.88 4.26
3017 6310 4.025858 AGGCTGTGTGGCGAGCAT 62.026 61.111 0.00 0.00 46.88 3.79
3138 6431 2.900546 ACACAAAGGACCCTACTCTGAG 59.099 50.000 2.45 2.45 0.00 3.35
3146 6439 0.394488 CCCTACTCTGAGAGTCCGCA 60.394 60.000 19.83 0.00 42.40 5.69
3223 6516 1.202687 TGCTCAGTTCACACAAGAGGG 60.203 52.381 0.00 0.00 31.36 4.30
3266 6559 0.536460 TCGGTCCTTTGAAAGCACCC 60.536 55.000 12.20 4.42 0.00 4.61
3267 6560 1.524008 CGGTCCTTTGAAAGCACCCC 61.524 60.000 12.20 2.15 0.00 4.95
3318 6611 4.757799 CAACGTAATTGGGTTGTGATGA 57.242 40.909 12.66 0.00 38.89 2.92
3388 6682 1.475751 GCCGGATGGAGTGAATCACAT 60.476 52.381 16.38 0.01 37.49 3.21
3418 6712 3.370061 GTCCTAATTCCGAAAGTTCCACG 59.630 47.826 0.00 0.00 0.00 4.94
3517 6814 1.135083 CGCCTTCGACCACTGTTATCT 60.135 52.381 0.00 0.00 38.10 1.98
3518 6815 2.541556 GCCTTCGACCACTGTTATCTC 58.458 52.381 0.00 0.00 0.00 2.75
3546 6843 5.877012 TCTTATCTCTGAAAATCAAAGCGCT 59.123 36.000 2.64 2.64 0.00 5.92
3548 6845 7.549134 TCTTATCTCTGAAAATCAAAGCGCTTA 59.451 33.333 25.33 9.45 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 118 7.810766 TCAAAGTCAAACATTGTCAACTTTC 57.189 32.000 15.57 0.00 34.78 2.62
163 170 3.865745 CCAGTATTCTTGTACGCCTTCTG 59.134 47.826 0.00 0.00 0.00 3.02
164 171 3.767673 TCCAGTATTCTTGTACGCCTTCT 59.232 43.478 0.00 0.00 0.00 2.85
167 174 4.546829 TTTCCAGTATTCTTGTACGCCT 57.453 40.909 0.00 0.00 0.00 5.52
202 210 8.099364 TCAGAACTCTAAGCGATTTTGAAAAT 57.901 30.769 2.27 2.27 0.00 1.82
296 304 6.613755 TCTAAAAAGACAAAAACGGAGGAG 57.386 37.500 0.00 0.00 0.00 3.69
298 306 9.908152 AAATATCTAAAAAGACAAAAACGGAGG 57.092 29.630 0.00 0.00 0.00 4.30
417 2157 8.244113 CCTCCGTTTCTAAATATTTGCTTTTCT 58.756 33.333 11.05 0.00 0.00 2.52
418 2158 8.241367 TCCTCCGTTTCTAAATATTTGCTTTTC 58.759 33.333 11.05 0.00 0.00 2.29
419 2159 8.117813 TCCTCCGTTTCTAAATATTTGCTTTT 57.882 30.769 11.05 0.00 0.00 2.27
420 2160 7.696992 TCCTCCGTTTCTAAATATTTGCTTT 57.303 32.000 11.05 0.00 0.00 3.51
421 2161 7.393515 ACTTCCTCCGTTTCTAAATATTTGCTT 59.606 33.333 11.05 0.00 0.00 3.91
422 2162 6.884836 ACTTCCTCCGTTTCTAAATATTTGCT 59.115 34.615 11.05 0.00 0.00 3.91
423 2163 7.085052 ACTTCCTCCGTTTCTAAATATTTGC 57.915 36.000 11.05 0.00 0.00 3.68
426 2166 9.597170 GTTCTACTTCCTCCGTTTCTAAATATT 57.403 33.333 0.00 0.00 0.00 1.28
427 2167 8.979534 AGTTCTACTTCCTCCGTTTCTAAATAT 58.020 33.333 0.00 0.00 0.00 1.28
428 2168 8.248945 CAGTTCTACTTCCTCCGTTTCTAAATA 58.751 37.037 0.00 0.00 0.00 1.40
431 2171 5.537674 ACAGTTCTACTTCCTCCGTTTCTAA 59.462 40.000 0.00 0.00 0.00 2.10
432 2172 5.075493 ACAGTTCTACTTCCTCCGTTTCTA 58.925 41.667 0.00 0.00 0.00 2.10
434 2174 4.254402 ACAGTTCTACTTCCTCCGTTTC 57.746 45.455 0.00 0.00 0.00 2.78
435 2175 4.321824 GCTACAGTTCTACTTCCTCCGTTT 60.322 45.833 0.00 0.00 0.00 3.60
437 2177 2.754002 GCTACAGTTCTACTTCCTCCGT 59.246 50.000 0.00 0.00 0.00 4.69
438 2178 2.099427 GGCTACAGTTCTACTTCCTCCG 59.901 54.545 0.00 0.00 0.00 4.63
439 2179 2.431419 GGGCTACAGTTCTACTTCCTCC 59.569 54.545 0.00 0.00 0.00 4.30
442 2182 3.367321 AGAGGGCTACAGTTCTACTTCC 58.633 50.000 0.00 0.00 0.00 3.46
443 2183 5.172205 CAAAGAGGGCTACAGTTCTACTTC 58.828 45.833 0.00 0.00 0.00 3.01
446 2186 3.863041 CCAAAGAGGGCTACAGTTCTAC 58.137 50.000 0.00 0.00 0.00 2.59
518 2500 4.416738 GCTGAGCCCACCCACCTC 62.417 72.222 0.00 0.00 0.00 3.85
578 2561 1.948391 ACTCCTACCAACCTACACCC 58.052 55.000 0.00 0.00 0.00 4.61
590 2573 4.423625 AGGCAAATGATGGTACTCCTAC 57.576 45.455 0.00 0.00 34.23 3.18
591 2574 6.533730 CATTAGGCAAATGATGGTACTCCTA 58.466 40.000 5.33 0.00 46.81 2.94
592 2575 5.380043 CATTAGGCAAATGATGGTACTCCT 58.620 41.667 5.33 0.00 46.81 3.69
593 2576 4.022849 GCATTAGGCAAATGATGGTACTCC 60.023 45.833 13.53 0.00 46.81 3.85
594 2577 5.113502 GCATTAGGCAAATGATGGTACTC 57.886 43.478 13.53 0.00 46.81 2.59
798 3048 3.496331 TCCTGACCTTGTTTGATTTCCC 58.504 45.455 0.00 0.00 0.00 3.97
924 3195 4.520874 TGTAATGATTGGCGAAGTTTGGAA 59.479 37.500 0.00 0.00 0.00 3.53
935 3206 3.023119 TGACCATGGTGTAATGATTGGC 58.977 45.455 25.52 3.21 0.00 4.52
943 3214 1.376683 GGCGCTGACCATGGTGTAA 60.377 57.895 25.52 6.73 0.00 2.41
946 3217 2.360350 AAGGCGCTGACCATGGTG 60.360 61.111 25.52 10.36 0.00 4.17
958 3229 0.391263 GTCCTTACACAGGGAAGGCG 60.391 60.000 0.63 0.00 44.12 5.52
1028 4259 3.008330 CTCTTCTTCATCTTGGGTGCTG 58.992 50.000 0.00 0.00 0.00 4.41
1122 4356 1.065491 ACGAGGTGATAATGGCAGCAA 60.065 47.619 0.00 0.00 36.28 3.91
1144 4418 3.677121 CCAAACACGAGACAGAATCAGAG 59.323 47.826 0.00 0.00 0.00 3.35
2078 5370 0.324614 ACATGGCGACCAAGATGACA 59.675 50.000 7.87 0.00 36.95 3.58
2513 5805 3.036429 GCCCATCTCCTCCAGCGTT 62.036 63.158 0.00 0.00 0.00 4.84
2643 5935 9.625747 TTTAGCAATCCTGTCATGTGATTAATA 57.374 29.630 0.00 0.00 0.00 0.98
2658 5950 3.448686 CGTCGTGAGATTTAGCAATCCT 58.551 45.455 0.00 0.00 45.19 3.24
2732 6025 8.286097 GTGGCATAGCATATAAAGAAGAAGAAC 58.714 37.037 0.00 0.00 0.00 3.01
2759 6052 9.503399 CTTAAGACTTAAACAACTCCCACTTAT 57.497 33.333 8.92 0.00 0.00 1.73
2763 6056 5.333875 CGCTTAAGACTTAAACAACTCCCAC 60.334 44.000 6.67 0.00 0.00 4.61
2764 6057 4.753107 CGCTTAAGACTTAAACAACTCCCA 59.247 41.667 6.67 0.00 0.00 4.37
2765 6058 4.992951 TCGCTTAAGACTTAAACAACTCCC 59.007 41.667 6.67 0.00 0.00 4.30
2766 6059 5.913637 GTCGCTTAAGACTTAAACAACTCC 58.086 41.667 6.67 0.00 38.09 3.85
2778 6071 3.487879 GCTAGGTCTCAGTCGCTTAAGAC 60.488 52.174 6.67 0.00 41.23 3.01
2779 6072 2.683867 GCTAGGTCTCAGTCGCTTAAGA 59.316 50.000 6.67 0.00 0.00 2.10
2780 6073 2.223618 GGCTAGGTCTCAGTCGCTTAAG 60.224 54.545 0.00 0.00 0.00 1.85
2781 6074 1.749634 GGCTAGGTCTCAGTCGCTTAA 59.250 52.381 0.00 0.00 0.00 1.85
2782 6075 1.340697 TGGCTAGGTCTCAGTCGCTTA 60.341 52.381 0.00 0.00 0.00 3.09
2783 6076 0.612174 TGGCTAGGTCTCAGTCGCTT 60.612 55.000 0.00 0.00 0.00 4.68
2784 6077 1.000771 TGGCTAGGTCTCAGTCGCT 60.001 57.895 0.00 0.00 0.00 4.93
2785 6078 1.139947 GTGGCTAGGTCTCAGTCGC 59.860 63.158 0.00 0.00 0.00 5.19
2786 6079 0.171455 GTGTGGCTAGGTCTCAGTCG 59.829 60.000 0.00 0.00 0.00 4.18
2787 6080 0.533032 GGTGTGGCTAGGTCTCAGTC 59.467 60.000 0.00 0.00 0.00 3.51
2788 6081 0.905337 GGGTGTGGCTAGGTCTCAGT 60.905 60.000 0.00 0.00 0.00 3.41
2789 6082 0.904865 TGGGTGTGGCTAGGTCTCAG 60.905 60.000 0.00 0.00 0.00 3.35
2790 6083 0.252696 ATGGGTGTGGCTAGGTCTCA 60.253 55.000 0.00 0.00 0.00 3.27
2791 6084 0.179000 CATGGGTGTGGCTAGGTCTC 59.821 60.000 0.00 0.00 0.00 3.36
2792 6085 1.915078 GCATGGGTGTGGCTAGGTCT 61.915 60.000 0.00 0.00 0.00 3.85
2793 6086 1.452108 GCATGGGTGTGGCTAGGTC 60.452 63.158 0.00 0.00 0.00 3.85
2794 6087 2.202236 CTGCATGGGTGTGGCTAGGT 62.202 60.000 0.00 0.00 0.00 3.08
2795 6088 1.452651 CTGCATGGGTGTGGCTAGG 60.453 63.158 0.00 0.00 0.00 3.02
2796 6089 0.035152 TTCTGCATGGGTGTGGCTAG 60.035 55.000 0.00 0.00 0.00 3.42
2797 6090 0.403655 TTTCTGCATGGGTGTGGCTA 59.596 50.000 0.00 0.00 0.00 3.93
2798 6091 0.251922 ATTTCTGCATGGGTGTGGCT 60.252 50.000 0.00 0.00 0.00 4.75
2799 6092 0.108520 CATTTCTGCATGGGTGTGGC 60.109 55.000 0.00 0.00 0.00 5.01
2811 6104 7.118825 TCACTTGACTGAGATTTAGCATTTCTG 59.881 37.037 0.00 0.00 0.00 3.02
2812 6105 7.164122 TCACTTGACTGAGATTTAGCATTTCT 58.836 34.615 0.00 0.00 0.00 2.52
2813 6106 7.332926 TCTCACTTGACTGAGATTTAGCATTTC 59.667 37.037 0.00 0.00 41.49 2.17
2814 6107 7.118971 GTCTCACTTGACTGAGATTTAGCATTT 59.881 37.037 2.36 0.00 46.58 2.32
2815 6108 6.593382 GTCTCACTTGACTGAGATTTAGCATT 59.407 38.462 2.36 0.00 46.58 3.56
2816 6109 6.070881 AGTCTCACTTGACTGAGATTTAGCAT 60.071 38.462 2.36 0.00 46.58 3.79
2817 6110 5.244851 AGTCTCACTTGACTGAGATTTAGCA 59.755 40.000 2.36 0.00 46.58 3.49
2818 6111 5.719173 AGTCTCACTTGACTGAGATTTAGC 58.281 41.667 2.36 0.00 46.58 3.09
2820 6113 8.410673 ACTAAGTCTCACTTGACTGAGATTTA 57.589 34.615 14.05 11.45 46.58 1.40
2821 6114 7.296628 ACTAAGTCTCACTTGACTGAGATTT 57.703 36.000 14.05 10.59 46.58 2.17
2822 6115 6.348950 CGACTAAGTCTCACTTGACTGAGATT 60.349 42.308 14.05 0.00 46.58 2.40
2823 6116 5.123186 CGACTAAGTCTCACTTGACTGAGAT 59.877 44.000 14.05 1.49 46.58 2.75
2824 6117 4.452795 CGACTAAGTCTCACTTGACTGAGA 59.547 45.833 14.05 0.00 44.55 3.27
2825 6118 4.214545 ACGACTAAGTCTCACTTGACTGAG 59.785 45.833 7.32 7.32 46.25 3.35
2826 6119 4.135306 ACGACTAAGTCTCACTTGACTGA 58.865 43.478 0.00 0.00 45.49 3.41
2827 6120 4.491234 ACGACTAAGTCTCACTTGACTG 57.509 45.455 0.00 0.00 45.49 3.51
2828 6121 6.262720 ACTTAACGACTAAGTCTCACTTGACT 59.737 38.462 8.32 0.00 46.01 3.41
2829 6122 6.437094 ACTTAACGACTAAGTCTCACTTGAC 58.563 40.000 8.32 0.00 46.01 3.18
2830 6123 6.630444 ACTTAACGACTAAGTCTCACTTGA 57.370 37.500 8.32 0.00 46.01 3.02
2840 6133 5.039480 TCGGTTGAGACTTAACGACTAAG 57.961 43.478 4.22 0.00 42.52 2.18
2841 6134 5.396484 CATCGGTTGAGACTTAACGACTAA 58.604 41.667 4.22 0.00 0.00 2.24
2842 6135 4.673580 GCATCGGTTGAGACTTAACGACTA 60.674 45.833 4.22 0.00 0.00 2.59
2843 6136 3.834610 CATCGGTTGAGACTTAACGACT 58.165 45.455 4.22 0.00 0.00 4.18
2844 6137 2.344741 GCATCGGTTGAGACTTAACGAC 59.655 50.000 4.22 0.00 0.00 4.34
2845 6138 2.230508 AGCATCGGTTGAGACTTAACGA 59.769 45.455 4.22 2.98 0.00 3.85
2846 6139 2.345641 CAGCATCGGTTGAGACTTAACG 59.654 50.000 4.22 0.00 0.00 3.18
2847 6140 3.368236 GTCAGCATCGGTTGAGACTTAAC 59.632 47.826 1.53 1.53 34.74 2.01
2848 6141 3.585862 GTCAGCATCGGTTGAGACTTAA 58.414 45.455 0.00 0.00 34.74 1.85
2849 6142 2.094182 GGTCAGCATCGGTTGAGACTTA 60.094 50.000 10.07 0.00 34.74 2.24
2850 6143 1.338200 GGTCAGCATCGGTTGAGACTT 60.338 52.381 10.07 0.00 34.74 3.01
2851 6144 0.247736 GGTCAGCATCGGTTGAGACT 59.752 55.000 10.07 0.00 34.74 3.24
2852 6145 1.078759 CGGTCAGCATCGGTTGAGAC 61.079 60.000 0.00 0.00 34.74 3.36
2853 6146 1.215382 CGGTCAGCATCGGTTGAGA 59.785 57.895 0.00 0.00 34.74 3.27
2854 6147 0.389817 TTCGGTCAGCATCGGTTGAG 60.390 55.000 0.00 0.00 34.74 3.02
2855 6148 0.249120 ATTCGGTCAGCATCGGTTGA 59.751 50.000 0.00 0.00 31.27 3.18
2856 6149 0.374758 CATTCGGTCAGCATCGGTTG 59.625 55.000 0.00 0.00 0.00 3.77
2857 6150 0.036388 ACATTCGGTCAGCATCGGTT 60.036 50.000 0.00 0.00 0.00 4.44
2858 6151 0.036388 AACATTCGGTCAGCATCGGT 60.036 50.000 0.00 0.00 0.00 4.69
2859 6152 1.934589 TAACATTCGGTCAGCATCGG 58.065 50.000 0.00 0.00 0.00 4.18
2860 6153 4.536364 AATTAACATTCGGTCAGCATCG 57.464 40.909 0.00 0.00 0.00 3.84
2885 6178 5.534207 TCATCAAGTTGGTGCATTTTCTT 57.466 34.783 11.48 0.00 0.00 2.52
2920 6213 1.712977 GCAGCCAAAGCATCTCCTCG 61.713 60.000 0.00 0.00 43.56 4.63
2985 6278 1.218047 GCCTGACGGTGCAGATACA 59.782 57.895 8.53 0.00 38.14 2.29
3016 6309 3.941483 GCCGCTGTATATAATTCCTGCAT 59.059 43.478 0.00 0.00 0.00 3.96
3017 6310 3.007940 AGCCGCTGTATATAATTCCTGCA 59.992 43.478 0.00 0.00 0.00 4.41
3043 6336 0.768622 TCCACGAACCATCCAACCTT 59.231 50.000 0.00 0.00 0.00 3.50
3048 6341 0.899720 GGTACTCCACGAACCATCCA 59.100 55.000 0.00 0.00 33.28 3.41
3098 6391 7.534085 TTGTGTACACTTCTTTGAAGTACAG 57.466 36.000 25.60 4.24 43.75 2.74
3099 6392 7.065324 CCTTTGTGTACACTTCTTTGAAGTACA 59.935 37.037 25.60 11.00 41.72 2.90
3146 6439 2.957402 TGATTCCTTCCAGCACACTT 57.043 45.000 0.00 0.00 0.00 3.16
3161 6454 4.021192 CCTTGTGTTACCTTTGGCATGATT 60.021 41.667 0.00 0.00 0.00 2.57
3216 6509 2.099756 GGGCATTCGAAATTCCCTCTTG 59.900 50.000 19.52 5.60 34.19 3.02
3223 6516 2.491693 TGGAACAGGGCATTCGAAATTC 59.508 45.455 0.00 0.00 0.00 2.17
3266 6559 2.140792 AGGGAATCCATCGGTCCGG 61.141 63.158 12.29 0.00 34.83 5.14
3267 6560 1.069765 CAGGGAATCCATCGGTCCG 59.930 63.158 4.39 4.39 34.83 4.79
3356 6650 1.202927 CCATCCGGCATTATCCCAGTT 60.203 52.381 0.00 0.00 0.00 3.16
3388 6682 7.120923 ACTTTCGGAATTAGGACTATAGCAA 57.879 36.000 0.00 0.00 0.00 3.91
3418 6712 3.653835 AATCCTTTAGCTCCTTGGGAC 57.346 47.619 0.00 0.00 0.00 4.46
3518 6815 8.063038 CGCTTTGATTTTCAGAGATAAGATCTG 58.937 37.037 0.00 0.00 44.57 2.90
3546 6843 7.039882 GTCAGAAATAAGACGACCAGGAATAA 58.960 38.462 0.00 0.00 0.00 1.40
3548 6845 5.046591 TGTCAGAAATAAGACGACCAGGAAT 60.047 40.000 0.00 0.00 37.58 3.01
3585 6884 5.476254 TGAATATGGTGAATGCACTCAAACA 59.524 36.000 0.00 2.54 44.52 2.83


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

AutoCloner maintained by Alex Coulton.