Multiple sequence alignment - TraesCS6B01G306000

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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 TraesCS6B01G306000 chr6B 100.000 5985 0 0 1 5985 549081678 549087662 0.000000e+00 11053.0
1 TraesCS6B01G306000 chr6B 90.647 139 12 1 2245 2382 549083879 549084017 3.680000e-42 183.0
2 TraesCS6B01G306000 chr6B 90.647 139 12 1 2202 2340 549083922 549084059 3.680000e-42 183.0
3 TraesCS6B01G306000 chr6D 97.053 2681 53 11 2383 5056 364101640 364104301 0.000000e+00 4490.0
4 TraesCS6B01G306000 chr6D 97.231 1914 43 5 560 2470 364099733 364101639 0.000000e+00 3232.0
5 TraesCS6B01G306000 chr6D 89.722 720 40 12 5080 5777 364104292 364104999 0.000000e+00 889.0
6 TraesCS6B01G306000 chr6D 94.089 203 12 0 5766 5968 364105051 364105253 5.830000e-80 309.0
7 TraesCS6B01G306000 chr6D 81.231 325 39 11 168 473 364099325 364099646 5.990000e-60 243.0
8 TraesCS6B01G306000 chr6D 92.763 152 10 1 3 153 364099121 364099272 1.010000e-52 219.0
9 TraesCS6B01G306000 chr6D 90.647 139 12 1 2245 2382 364101371 364101509 3.680000e-42 183.0
10 TraesCS6B01G306000 chr6D 90.647 139 12 1 2202 2340 364101414 364101551 3.680000e-42 183.0
11 TraesCS6B01G306000 chr6D 100.000 32 0 0 5954 5985 364105270 364105301 6.480000e-05 60.2
12 TraesCS6B01G306000 chr6A 94.656 2788 111 16 3184 5958 505440258 505437496 0.000000e+00 4289.0
13 TraesCS6B01G306000 chr6A 93.771 2649 94 17 545 3152 505443129 505440511 0.000000e+00 3912.0
14 TraesCS6B01G306000 chr6A 94.231 104 6 0 2254 2357 505441469 505441366 6.210000e-35 159.0
15 TraesCS6B01G306000 chr6A 100.000 43 0 0 5943 5985 505437480 505437438 4.970000e-11 80.5
16 TraesCS6B01G306000 chr6A 100.000 37 0 0 3151 3187 505440407 505440371 1.080000e-07 69.4
17 TraesCS6B01G306000 chr6A 93.023 43 3 0 5141 5183 465229014 465228972 5.010000e-06 63.9
18 TraesCS6B01G306000 chr5D 92.523 107 7 1 3 108 46380487 46380593 1.040000e-32 152.0
19 TraesCS6B01G306000 chr5D 77.941 204 25 10 296 493 91556678 91556489 6.340000e-20 110.0
20 TraesCS6B01G306000 chr5B 92.453 106 6 2 3 106 101426950 101426845 3.740000e-32 150.0
21 TraesCS6B01G306000 chr2B 78.838 241 33 6 228 460 569128025 569128255 4.830000e-31 147.0
22 TraesCS6B01G306000 chr2A 91.509 106 7 2 3 106 624293458 624293563 1.740000e-30 145.0
23 TraesCS6B01G306000 chr2A 90.090 111 8 3 3 110 726998207 726998097 2.250000e-29 141.0
24 TraesCS6B01G306000 chr7D 90.654 107 10 0 3 109 211599322 211599216 6.250000e-30 143.0
25 TraesCS6B01G306000 chr2D 90.000 110 10 1 1 109 250757500 250757609 2.250000e-29 141.0
26 TraesCS6B01G306000 chr3D 89.815 108 10 1 3 109 309734011 309733904 2.910000e-28 137.0
27 TraesCS6B01G306000 chr3B 89.381 113 7 3 3 110 487878315 487878427 2.910000e-28 137.0
28 TraesCS6B01G306000 chr1A 81.461 178 20 4 296 473 474646776 474646612 3.760000e-27 134.0
29 TraesCS6B01G306000 chr1D 93.878 49 2 1 5136 5183 345266676 345266724 8.320000e-09 73.1
30 TraesCS6B01G306000 chr1D 93.333 45 3 0 5139 5183 128528627 128528671 3.870000e-07 67.6
31 TraesCS6B01G306000 chr7B 91.837 49 3 1 5136 5183 282334361 282334409 3.870000e-07 67.6
32 TraesCS6B01G306000 chr7B 93.333 45 3 0 5139 5183 336907260 336907216 3.870000e-07 67.6
33 TraesCS6B01G306000 chr1B 91.837 49 3 1 5136 5183 465698835 465698787 3.870000e-07 67.6
34 TraesCS6B01G306000 chr5A 87.931 58 3 3 5131 5184 709675851 709675794 1.390000e-06 65.8
35 TraesCS6B01G306000 chrUn 87.719 57 3 3 5131 5183 100172165 100172221 5.010000e-06 63.9


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 TraesCS6B01G306000 chr6B 549081678 549087662 5984 False 3806.333333 11053 93.764667 1 5985 3 chr6B.!!$F1 5984
1 TraesCS6B01G306000 chr6D 364099121 364105301 6180 False 1089.800000 4490 92.598111 3 5985 9 chr6D.!!$F1 5982
2 TraesCS6B01G306000 chr6A 505437438 505443129 5691 True 1701.980000 4289 96.531600 545 5985 5 chr6A.!!$R2 5440

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
323 376 0.035439 GATTTCAGACCCAAGCCCGA 60.035 55.000 0.00 0.00 0.0 5.14 F
476 558 0.744771 CCGAGCTAGGCCAGGTTTTC 60.745 60.000 5.01 0.00 34.3 2.29 F
580 663 1.463674 AGATTGTTTGGCCGACATCC 58.536 50.000 12.01 7.57 0.0 3.51 F
2401 2525 1.478916 TGTCTCCTCAAACGTGTGTCA 59.521 47.619 5.45 0.00 0.0 3.58 F
3028 3240 1.143684 ACCAGACAGATGGCACTTTGT 59.856 47.619 0.00 0.00 44.8 2.83 F
3521 3957 0.768622 ACAACTTCCCCGACATGGAA 59.231 50.000 0.00 0.00 42.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1614 0.188587 TGGCCTCATAGTCGATCCCT 59.811 55.000 3.32 0.0 0.00 4.20 R
2470 2594 1.486310 TGAAAGAGGATACGCCAGCAT 59.514 47.619 0.00 0.0 46.39 3.79 R
2555 2767 7.280055 CCAACAATAAAACATTACAAACAGCG 58.720 34.615 0.00 0.0 0.00 5.18 R
3226 3660 2.095364 CAGTGAATCAAGCAAGCAGGTC 60.095 50.000 0.00 0.0 0.00 3.85 R
4210 4651 4.327680 ACTTGATTCCAGCTACCAAGAAC 58.672 43.478 15.12 0.0 38.02 3.01 R
5086 5528 0.987294 TGAAGCTCCTTTCCTCCAGG 59.013 55.000 0.00 0.0 0.00 4.45 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
41 42 2.642139 TCGTGATCTCAACCCGTTAC 57.358 50.000 0.00 0.00 0.00 2.50
68 69 4.883585 TCTTCATATTGATCTTGGGTGTGC 59.116 41.667 0.00 0.00 0.00 4.57
75 76 1.553690 ATCTTGGGTGTGCGTAGGCT 61.554 55.000 9.11 0.00 40.82 4.58
76 77 1.302511 CTTGGGTGTGCGTAGGCTT 60.303 57.895 9.11 0.00 40.82 4.35
82 84 2.490509 GGGTGTGCGTAGGCTTATTTTT 59.509 45.455 9.11 0.00 40.82 1.94
106 108 7.571080 TTTTGTTTCTACTACGTTTCCCAAT 57.429 32.000 0.00 0.00 0.00 3.16
159 161 3.807839 CCCGGGCATCCCATGTCA 61.808 66.667 8.08 0.00 45.83 3.58
160 162 2.203252 CCGGGCATCCCATGTCAG 60.203 66.667 0.00 0.00 45.83 3.51
163 165 2.520260 GGCATCCCATGTCAGGCC 60.520 66.667 0.00 0.00 34.33 5.19
164 166 2.276409 GCATCCCATGTCAGGCCA 59.724 61.111 5.01 0.00 0.00 5.36
165 167 1.826921 GCATCCCATGTCAGGCCAG 60.827 63.158 5.01 0.00 0.00 4.85
166 168 1.152819 CATCCCATGTCAGGCCAGG 60.153 63.158 5.01 0.00 0.00 4.45
178 218 4.373116 GCCAGGCGTTCGAGGTCA 62.373 66.667 0.00 0.00 0.00 4.02
179 219 2.125912 CCAGGCGTTCGAGGTCAG 60.126 66.667 0.00 0.00 0.00 3.51
187 227 1.269621 CGTTCGAGGTCAGTTTGAGGT 60.270 52.381 0.00 0.00 0.00 3.85
189 229 0.679505 TCGAGGTCAGTTTGAGGTGG 59.320 55.000 0.00 0.00 0.00 4.61
191 231 0.606673 GAGGTCAGTTTGAGGTGGCC 60.607 60.000 0.00 0.00 38.87 5.36
197 237 1.070786 GTTTGAGGTGGCCGTCTGA 59.929 57.895 0.00 0.00 0.00 3.27
200 240 1.407656 TTGAGGTGGCCGTCTGAGTT 61.408 55.000 0.00 0.00 0.00 3.01
202 242 2.358737 GGTGGCCGTCTGAGTTGG 60.359 66.667 0.00 0.00 0.00 3.77
207 247 1.029681 GGCCGTCTGAGTTGGTTTTT 58.970 50.000 0.00 0.00 0.00 1.94
208 248 1.001706 GGCCGTCTGAGTTGGTTTTTC 60.002 52.381 0.00 0.00 0.00 2.29
221 261 7.123547 TGAGTTGGTTTTTCTTTTACTGGTCAT 59.876 33.333 0.00 0.00 0.00 3.06
248 288 2.028385 GGTATACCTGGCCATAAGTCGG 60.028 54.545 15.09 5.16 0.00 4.79
251 296 0.617820 ACCTGGCCATAAGTCGGACT 60.618 55.000 5.51 4.45 30.26 3.85
254 299 1.146263 GGCCATAAGTCGGACTGGG 59.854 63.158 12.12 14.26 0.00 4.45
256 301 1.146263 CCATAAGTCGGACTGGGCC 59.854 63.158 12.12 0.00 0.00 5.80
264 309 3.489513 GGACTGGGCCGGGCTAAT 61.490 66.667 28.80 12.76 0.00 1.73
268 313 0.626916 ACTGGGCCGGGCTAATAAAA 59.373 50.000 28.80 4.20 0.00 1.52
323 376 0.035439 GATTTCAGACCCAAGCCCGA 60.035 55.000 0.00 0.00 0.00 5.14
331 384 2.124570 CCAAGCCCGACCCATCAG 60.125 66.667 0.00 0.00 0.00 2.90
334 387 2.971598 AAGCCCGACCCATCAGTGG 61.972 63.158 0.00 0.00 45.61 4.00
375 428 2.095212 GGCCAGACCGCTTTCTTAAAAG 60.095 50.000 0.00 0.00 43.99 2.27
376 429 2.095212 GCCAGACCGCTTTCTTAAAAGG 60.095 50.000 0.58 0.00 41.87 3.11
404 463 2.860971 AAGCCCAAGCCTGGTCCT 60.861 61.111 0.00 0.00 41.72 3.85
414 473 3.655211 CTGGTCCTGCCCAGCCTT 61.655 66.667 0.00 0.00 45.19 4.35
418 477 3.333219 TCCTGCCCAGCCTTCAGG 61.333 66.667 1.29 1.29 46.60 3.86
437 496 1.271926 GGCTCAAAACTTAGGCCCAGA 60.272 52.381 0.00 0.00 37.12 3.86
440 499 1.074889 TCAAAACTTAGGCCCAGACCC 59.925 52.381 0.00 0.00 0.00 4.46
441 500 1.154430 AAAACTTAGGCCCAGACCCA 58.846 50.000 0.00 0.00 0.00 4.51
442 501 1.154430 AAACTTAGGCCCAGACCCAA 58.846 50.000 0.00 0.00 0.00 4.12
463 522 2.270205 CATGGGCAAGACCGAGCT 59.730 61.111 0.00 0.00 40.62 4.09
464 523 1.522092 CATGGGCAAGACCGAGCTA 59.478 57.895 0.00 0.00 40.62 3.32
476 558 0.744771 CCGAGCTAGGCCAGGTTTTC 60.745 60.000 5.01 0.00 34.30 2.29
490 572 2.856231 AGGTTTTCCATGGCCAGGTATA 59.144 45.455 17.55 0.00 43.73 1.47
493 575 4.141344 GGTTTTCCATGGCCAGGTATAGTA 60.141 45.833 17.55 0.00 40.31 1.82
495 577 3.915346 TCCATGGCCAGGTATAGTAGA 57.085 47.619 17.55 1.02 0.00 2.59
496 578 4.207698 TCCATGGCCAGGTATAGTAGAA 57.792 45.455 17.55 0.00 0.00 2.10
501 583 2.590821 GCCAGGTATAGTAGAACCGGA 58.409 52.381 9.46 0.00 40.88 5.14
502 584 2.295629 GCCAGGTATAGTAGAACCGGAC 59.704 54.545 9.46 0.99 40.88 4.79
505 587 3.249559 CAGGTATAGTAGAACCGGACGTC 59.750 52.174 9.46 7.13 40.88 4.34
506 588 3.135530 AGGTATAGTAGAACCGGACGTCT 59.864 47.826 16.46 10.47 40.88 4.18
509 591 1.513586 GTAGAACCGGACGTCTGCG 60.514 63.158 19.31 12.81 44.93 5.18
520 602 3.660111 GTCTGCGCGGGCTTTTGT 61.660 61.111 25.62 0.00 40.82 2.83
541 623 4.357279 GCTTGGGGTGCCTGCTCT 62.357 66.667 0.00 0.00 0.00 4.09
542 624 2.971598 GCTTGGGGTGCCTGCTCTA 61.972 63.158 0.00 0.00 0.00 2.43
543 625 1.685224 CTTGGGGTGCCTGCTCTAA 59.315 57.895 0.00 0.00 0.00 2.10
550 632 2.164422 GGGTGCCTGCTCTAATGTTTTC 59.836 50.000 0.00 0.00 0.00 2.29
554 636 3.507233 TGCCTGCTCTAATGTTTTCCTTG 59.493 43.478 0.00 0.00 0.00 3.61
556 638 4.379918 GCCTGCTCTAATGTTTTCCTTGTC 60.380 45.833 0.00 0.00 0.00 3.18
580 663 1.463674 AGATTGTTTGGCCGACATCC 58.536 50.000 12.01 7.57 0.00 3.51
601 684 3.181450 CCCCAGGAGGATGTGAACTATTC 60.181 52.174 0.00 0.00 38.24 1.75
1698 1797 4.039092 AGGGCCATTGCAGCGTCT 62.039 61.111 6.18 0.00 40.13 4.18
1916 2015 2.294233 TGCCTTCTTTTGCTGTCATGTC 59.706 45.455 0.00 0.00 0.00 3.06
1936 2035 6.312399 TGTCATGTTTTCAGTATTGGTGTC 57.688 37.500 0.00 0.00 0.00 3.67
1988 2087 4.387559 GTGTTTTTAAATCCGGTGATTGCC 59.612 41.667 0.00 0.00 40.34 4.52
1989 2088 4.039245 TGTTTTTAAATCCGGTGATTGCCA 59.961 37.500 0.00 0.00 40.34 4.92
1990 2089 3.859411 TTTAAATCCGGTGATTGCCAC 57.141 42.857 0.00 0.00 40.34 5.01
2021 2121 7.523709 GCAAGTCCCTTTCTCATTTTGTTGATA 60.524 37.037 0.00 0.00 0.00 2.15
2034 2134 5.522315 TTTGTTGATAATGGGGTAGTGGA 57.478 39.130 0.00 0.00 0.00 4.02
2118 2218 4.993584 CCACATATTGAGGCATCAGTAGAC 59.006 45.833 9.48 0.00 36.61 2.59
2195 2299 6.636850 GCGTATACCTTTTCTGCATTATTTGG 59.363 38.462 0.00 0.00 0.00 3.28
2198 2302 3.840078 ACCTTTTCTGCATTATTTGGCCT 59.160 39.130 3.32 0.00 0.00 5.19
2364 2488 2.107552 TGTTTCCTCAAACCTCGGGAAT 59.892 45.455 0.00 0.00 41.25 3.01
2401 2525 1.478916 TGTCTCCTCAAACGTGTGTCA 59.521 47.619 5.45 0.00 0.00 3.58
2470 2594 2.871022 TGCACTTTAAACCGTTAGCGAA 59.129 40.909 0.00 0.00 41.33 4.70
2555 2767 4.090210 GCGTTTAGACTCAGCTTGTTACTC 59.910 45.833 0.00 0.00 0.00 2.59
2738 2950 8.754991 TTATAATTGGGGTATTGTTCGTTCAT 57.245 30.769 0.00 0.00 0.00 2.57
2980 3192 7.762159 TGCATCGTATACTGTCAAATTACTCAA 59.238 33.333 0.56 0.00 0.00 3.02
3020 3232 5.047306 TCTGTTGTTAGTACCAGACAGATGG 60.047 44.000 9.65 0.00 46.47 3.51
3027 3239 1.901591 ACCAGACAGATGGCACTTTG 58.098 50.000 0.00 0.00 44.80 2.77
3028 3240 1.143684 ACCAGACAGATGGCACTTTGT 59.856 47.619 0.00 0.00 44.80 2.83
3031 3243 3.551454 CCAGACAGATGGCACTTTGTTTG 60.551 47.826 9.84 9.84 32.48 2.93
3069 3282 6.341316 TGCTTTGGTGCTAATGTTTAAACAA 58.659 32.000 23.97 8.69 43.03 2.83
3230 3664 6.324254 ACTTCTACGCCTAGATAATTTGACCT 59.676 38.462 0.00 0.00 0.00 3.85
3254 3688 4.612259 GCTTGCTTGATTCACTGTGTACTG 60.612 45.833 7.79 0.00 0.00 2.74
3258 3692 2.403259 TGATTCACTGTGTACTGTGCG 58.597 47.619 14.76 0.00 42.96 5.34
3327 3761 4.156008 CCTCTGTAGCAATTGTAACAACCC 59.844 45.833 7.40 0.00 0.00 4.11
3521 3957 0.768622 ACAACTTCCCCGACATGGAA 59.231 50.000 0.00 0.00 42.00 3.53
3542 3978 5.008415 GGAAGTCATCAGCATATCTGGTTTG 59.992 44.000 0.00 1.19 43.06 2.93
3635 4071 1.890489 TGCACTGCTTTGCTGATCAAT 59.110 42.857 10.83 0.00 43.41 2.57
3697 4133 7.614494 AGCAAACTTACCGTAGTCCTTTTATA 58.386 34.615 0.00 0.00 0.00 0.98
3792 4233 9.031537 TGTATAGTAGTACCCAATATCACCATG 57.968 37.037 0.00 0.00 0.00 3.66
3800 4241 5.341169 ACCCAATATCACCATGGTTCTTTT 58.659 37.500 16.84 4.31 32.13 2.27
3819 4260 7.862512 TCTTTTGTCCAGCATTTGAAAAATT 57.137 28.000 0.00 0.00 0.00 1.82
4210 4651 4.347607 AGGTGATCCCATTTTCCTTTCTG 58.652 43.478 3.45 0.00 34.66 3.02
4328 4769 6.703165 AGTCTTTGCTGAATCATTTGTTTTCC 59.297 34.615 0.00 0.00 0.00 3.13
4912 5354 0.665835 TTTGTTTGTGTAGCCCTGCG 59.334 50.000 0.00 0.00 0.00 5.18
5007 5449 9.486497 TCAGAATATCAGATTAGCTTGTGATTC 57.514 33.333 3.61 4.68 32.01 2.52
5059 5501 8.637986 TGCTAGATTTTAAATTTTGTCTGTGGT 58.362 29.630 0.00 0.00 0.00 4.16
5077 5519 2.708861 TGGTATGAAGGTCCAGTGTGTT 59.291 45.455 0.00 0.00 0.00 3.32
5078 5520 3.137544 TGGTATGAAGGTCCAGTGTGTTT 59.862 43.478 0.00 0.00 0.00 2.83
5079 5521 4.348461 TGGTATGAAGGTCCAGTGTGTTTA 59.652 41.667 0.00 0.00 0.00 2.01
5123 5565 1.006043 TCACGGCCCCATTTCCATTAA 59.994 47.619 0.00 0.00 0.00 1.40
5129 5571 3.118775 GGCCCCATTTCCATTAAACTGAC 60.119 47.826 0.00 0.00 0.00 3.51
5162 5608 2.227865 GGATTTAGTTGCCGCTCAAACA 59.772 45.455 0.00 0.00 36.26 2.83
5184 5630 7.117285 ACAGATGTATCTAGCACTGAAATGA 57.883 36.000 0.00 0.00 34.85 2.57
5189 5635 7.175347 TGTATCTAGCACTGAAATGAAGAGT 57.825 36.000 0.00 0.00 0.00 3.24
5245 5697 5.492895 TCCGAATAAAAACAGCCTACATCA 58.507 37.500 0.00 0.00 0.00 3.07
5269 5721 1.971695 GTGCTAACCCGCCAAGCTT 60.972 57.895 0.00 0.00 37.16 3.74
5285 5737 7.302524 CGCCAAGCTTAGTGTAAAATCTTTTA 58.697 34.615 0.00 0.00 0.00 1.52
5321 5773 5.770162 AGTAACTTGCAAAAGCTAACCTGAT 59.230 36.000 0.00 0.00 0.00 2.90
5362 5814 3.936453 CTCTTACACAGCGAGAGACTAGT 59.064 47.826 0.00 0.00 39.36 2.57
5375 5835 5.984323 CGAGAGACTAGTACATACTACAGCA 59.016 44.000 0.00 0.00 37.73 4.41
5376 5836 6.144886 CGAGAGACTAGTACATACTACAGCAG 59.855 46.154 0.00 0.00 37.73 4.24
5451 5911 7.885399 ACTAGCAGAATTCAGGAACAGTAAATT 59.115 33.333 8.44 0.00 0.00 1.82
5492 5952 0.698238 AGCATTTCCTACCCACTGCA 59.302 50.000 0.00 0.00 32.18 4.41
5493 5953 0.811281 GCATTTCCTACCCACTGCAC 59.189 55.000 0.00 0.00 0.00 4.57
5494 5954 1.614317 GCATTTCCTACCCACTGCACT 60.614 52.381 0.00 0.00 0.00 4.40
5495 5955 2.086869 CATTTCCTACCCACTGCACTG 58.913 52.381 0.00 0.00 0.00 3.66
5496 5956 1.136828 TTTCCTACCCACTGCACTGT 58.863 50.000 0.00 0.00 0.00 3.55
5497 5957 0.396435 TTCCTACCCACTGCACTGTG 59.604 55.000 2.76 2.76 37.66 3.66
5498 5958 1.672356 CCTACCCACTGCACTGTGC 60.672 63.158 25.15 25.15 45.29 4.57
5558 6022 3.958798 AGGGATCAATGCTTTCTTCCATG 59.041 43.478 10.53 0.00 0.00 3.66
5580 6044 4.835615 TGCAACATAACCCACAATTACCTT 59.164 37.500 0.00 0.00 0.00 3.50
5584 6048 7.414436 CAACATAACCCACAATTACCTTATCG 58.586 38.462 0.00 0.00 0.00 2.92
5608 6072 7.125204 TCGTCCCATCCTCTTTTCTTAAGATTA 59.875 37.037 5.89 0.00 0.00 1.75
5748 6213 2.125773 TAGAGAGACTTCACCGGGAC 57.874 55.000 6.32 0.00 0.00 4.46
5781 6309 5.243060 ACTTGGTTAAAAGCCATACAACCTC 59.757 40.000 0.00 0.00 39.51 3.85
5786 6314 4.546829 AAAAGCCATACAACCTCGTCTA 57.453 40.909 0.00 0.00 0.00 2.59
5798 6326 5.465724 ACAACCTCGTCTAGTTCATTGTTTC 59.534 40.000 0.00 0.00 0.00 2.78
5813 6341 1.483004 TGTTTCGAGTCACCTGACCAA 59.517 47.619 1.66 0.00 45.85 3.67
5814 6342 2.135933 GTTTCGAGTCACCTGACCAAG 58.864 52.381 1.66 0.00 45.85 3.61
5854 6382 3.119137 TCCACATATCCAACGTGTCAGAG 60.119 47.826 0.00 0.00 0.00 3.35
5857 6385 3.509967 ACATATCCAACGTGTCAGAGTGA 59.490 43.478 0.00 0.00 0.00 3.41
5916 6444 4.991687 CCTAAAAACTTTGGCGGCATTAAA 59.008 37.500 14.32 3.00 0.00 1.52
5925 6453 2.297315 TGGCGGCATTAAAATGTTGACA 59.703 40.909 7.97 3.28 38.65 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.069296 CGTTACCGTCACCGAGTTGTA 60.069 52.381 0.00 0.00 35.63 2.41
1 2 0.318107 CGTTACCGTCACCGAGTTGT 60.318 55.000 0.00 0.00 35.63 3.32
41 42 6.931281 ACACCCAAGATCAATATGAAGATACG 59.069 38.462 0.00 0.00 0.00 3.06
82 84 6.998968 TTGGGAAACGTAGTAGAAACAAAA 57.001 33.333 0.00 0.00 45.00 2.44
85 87 6.400568 CCTATTGGGAAACGTAGTAGAAACA 58.599 40.000 0.00 0.00 37.09 2.83
86 88 6.898912 CCTATTGGGAAACGTAGTAGAAAC 57.101 41.667 0.00 0.00 37.09 2.78
106 108 2.281091 CCCGACAGGCCTACCCTA 59.719 66.667 3.98 0.00 44.09 3.53
153 155 2.360350 AACGCCTGGCCTGACATG 60.360 61.111 14.12 0.00 0.00 3.21
154 156 2.045926 GAACGCCTGGCCTGACAT 60.046 61.111 14.12 0.00 0.00 3.06
156 158 4.373116 TCGAACGCCTGGCCTGAC 62.373 66.667 14.12 0.00 0.00 3.51
157 159 4.069232 CTCGAACGCCTGGCCTGA 62.069 66.667 14.12 4.93 0.00 3.86
163 165 0.600255 AAACTGACCTCGAACGCCTG 60.600 55.000 0.00 0.00 0.00 4.85
164 166 0.600255 CAAACTGACCTCGAACGCCT 60.600 55.000 0.00 0.00 0.00 5.52
165 167 0.599204 TCAAACTGACCTCGAACGCC 60.599 55.000 0.00 0.00 0.00 5.68
166 168 0.784778 CTCAAACTGACCTCGAACGC 59.215 55.000 0.00 0.00 0.00 4.84
178 218 1.071471 CAGACGGCCACCTCAAACT 59.929 57.895 2.24 0.00 0.00 2.66
179 219 0.951040 CTCAGACGGCCACCTCAAAC 60.951 60.000 2.24 0.00 0.00 2.93
187 227 0.106918 AAAACCAACTCAGACGGCCA 60.107 50.000 2.24 0.00 0.00 5.36
189 229 1.947456 AGAAAAACCAACTCAGACGGC 59.053 47.619 0.00 0.00 0.00 5.68
191 231 6.687105 CAGTAAAAGAAAAACCAACTCAGACG 59.313 38.462 0.00 0.00 0.00 4.18
197 237 6.844097 TGACCAGTAAAAGAAAAACCAACT 57.156 33.333 0.00 0.00 0.00 3.16
200 240 7.262048 GTCAATGACCAGTAAAAGAAAAACCA 58.738 34.615 1.10 0.00 0.00 3.67
221 261 0.618107 TGGCCAGGTATACCGGTCAA 60.618 55.000 27.11 16.15 39.84 3.18
227 267 2.028385 CCGACTTATGGCCAGGTATACC 60.028 54.545 13.05 14.54 0.00 2.73
233 273 0.179073 CAGTCCGACTTATGGCCAGG 60.179 60.000 13.05 5.74 0.00 4.45
248 288 0.181824 TTTATTAGCCCGGCCCAGTC 59.818 55.000 5.55 0.00 0.00 3.51
251 296 0.396001 GGTTTTATTAGCCCGGCCCA 60.396 55.000 5.55 0.00 0.00 5.36
293 338 0.753262 TCTGAAATCTAGGCCCGAGC 59.247 55.000 0.00 0.00 38.76 5.03
294 339 1.069358 GGTCTGAAATCTAGGCCCGAG 59.931 57.143 0.00 0.00 33.79 4.63
331 384 3.603365 CCCGATGGGCTTTTCCAC 58.397 61.111 0.00 0.00 39.97 4.02
354 407 1.530323 TTTAAGAAAGCGGTCTGGCC 58.470 50.000 0.00 0.00 0.00 5.36
356 409 2.095212 GCCTTTTAAGAAAGCGGTCTGG 60.095 50.000 0.00 0.00 40.75 3.86
358 411 2.858745 TGCCTTTTAAGAAAGCGGTCT 58.141 42.857 0.00 0.00 40.75 3.85
360 413 4.600692 ATTTGCCTTTTAAGAAAGCGGT 57.399 36.364 0.00 0.00 40.75 5.68
376 429 2.075904 GCTTGGGCTTGGCATATTTGC 61.076 52.381 0.00 0.00 40.80 3.68
414 473 1.271926 GGGCCTAAGTTTTGAGCCTGA 60.272 52.381 0.84 0.00 43.36 3.86
418 477 1.813178 GTCTGGGCCTAAGTTTTGAGC 59.187 52.381 4.53 0.00 0.00 4.26
463 522 3.998560 CCATGGAAAACCTGGCCTA 57.001 52.632 5.56 0.00 0.00 3.93
464 523 4.872293 CCATGGAAAACCTGGCCT 57.128 55.556 5.56 0.00 0.00 5.19
476 558 3.008049 GGTTCTACTATACCTGGCCATGG 59.992 52.174 5.51 13.05 0.00 3.66
490 572 1.881602 GCAGACGTCCGGTTCTACT 59.118 57.895 13.01 0.00 0.00 2.57
493 575 4.719369 GCGCAGACGTCCGGTTCT 62.719 66.667 13.01 0.00 42.83 3.01
502 584 4.741781 CAAAAGCCCGCGCAGACG 62.742 66.667 8.75 0.00 44.07 4.18
505 587 4.705519 CCACAAAAGCCCGCGCAG 62.706 66.667 8.75 0.00 37.52 5.18
525 607 0.257039 ATTAGAGCAGGCACCCCAAG 59.743 55.000 0.00 0.00 0.00 3.61
535 617 6.205464 TCAAGACAAGGAAAACATTAGAGCAG 59.795 38.462 0.00 0.00 0.00 4.24
536 618 6.061441 TCAAGACAAGGAAAACATTAGAGCA 58.939 36.000 0.00 0.00 0.00 4.26
538 620 8.383318 TCTTCAAGACAAGGAAAACATTAGAG 57.617 34.615 0.00 0.00 0.00 2.43
539 621 8.924511 ATCTTCAAGACAAGGAAAACATTAGA 57.075 30.769 0.00 0.00 0.00 2.10
540 622 9.403110 CAATCTTCAAGACAAGGAAAACATTAG 57.597 33.333 0.00 0.00 0.00 1.73
541 623 8.912988 ACAATCTTCAAGACAAGGAAAACATTA 58.087 29.630 0.00 0.00 0.00 1.90
542 624 7.785033 ACAATCTTCAAGACAAGGAAAACATT 58.215 30.769 0.00 0.00 0.00 2.71
543 625 7.352079 ACAATCTTCAAGACAAGGAAAACAT 57.648 32.000 0.00 0.00 0.00 2.71
550 632 4.301628 GCCAAACAATCTTCAAGACAAGG 58.698 43.478 0.00 0.00 0.00 3.61
554 636 2.552315 TCGGCCAAACAATCTTCAAGAC 59.448 45.455 2.24 0.00 0.00 3.01
556 638 2.293122 TGTCGGCCAAACAATCTTCAAG 59.707 45.455 2.24 0.00 0.00 3.02
580 663 3.181450 GGAATAGTTCACATCCTCCTGGG 60.181 52.174 0.00 0.00 0.00 4.45
594 677 5.184892 AGAGATGGCAAACAGGAATAGTT 57.815 39.130 0.00 0.00 0.00 2.24
601 684 1.363744 GACGAGAGATGGCAAACAGG 58.636 55.000 0.00 0.00 0.00 4.00
993 1088 3.853330 CGCGCGTCCATTGGTCTG 61.853 66.667 24.19 0.00 0.00 3.51
1416 1515 4.116328 CGAAGCCGCGACTCCAGA 62.116 66.667 8.23 0.00 0.00 3.86
1515 1614 0.188587 TGGCCTCATAGTCGATCCCT 59.811 55.000 3.32 0.00 0.00 4.20
1916 2015 5.574055 GCATGACACCAATACTGAAAACATG 59.426 40.000 0.00 0.00 35.85 3.21
1936 2035 4.922692 GTGCTACTTCTAGCTATGAGCATG 59.077 45.833 14.42 0.00 45.56 4.06
2021 2121 2.294263 ACCCTGTATCCACTACCCCATT 60.294 50.000 0.00 0.00 0.00 3.16
2034 2134 7.122650 GTGCAATATGGCAATAATACCCTGTAT 59.877 37.037 6.28 0.00 46.93 2.29
2118 2218 7.968956 GCAATCAGATGAATCAGGCAATATAAG 59.031 37.037 0.00 0.00 0.00 1.73
2195 2299 3.059166 ACGCAAAATGACAATTCAAGGC 58.941 40.909 0.00 0.00 34.61 4.35
2198 2302 6.533012 TGAAGAAACGCAAAATGACAATTCAA 59.467 30.769 0.00 0.00 34.61 2.69
2470 2594 1.486310 TGAAAGAGGATACGCCAGCAT 59.514 47.619 0.00 0.00 46.39 3.79
2555 2767 7.280055 CCAACAATAAAACATTACAAACAGCG 58.720 34.615 0.00 0.00 0.00 5.18
2738 2950 2.288948 ACGCCACAACTATGAAACGGTA 60.289 45.455 0.00 0.00 0.00 4.02
2980 3192 9.436957 CTAACAACAGACCATGTATCTAAACTT 57.563 33.333 0.00 0.00 43.00 2.66
3020 3232 5.730269 CAAACATCACATCAAACAAAGTGC 58.270 37.500 0.00 0.00 32.25 4.40
3027 3239 3.645884 AGCAGCAAACATCACATCAAAC 58.354 40.909 0.00 0.00 0.00 2.93
3028 3240 4.325028 AAGCAGCAAACATCACATCAAA 57.675 36.364 0.00 0.00 0.00 2.69
3031 3243 2.991190 CCAAAGCAGCAAACATCACATC 59.009 45.455 0.00 0.00 0.00 3.06
3069 3282 4.282703 AGCTGTTTGAGAAAATGCAATCCT 59.717 37.500 0.00 0.00 0.00 3.24
3213 3647 4.261363 GCAAGCAGGTCAAATTATCTAGGC 60.261 45.833 0.00 0.00 0.00 3.93
3226 3660 2.095364 CAGTGAATCAAGCAAGCAGGTC 60.095 50.000 0.00 0.00 0.00 3.85
3230 3664 2.300433 ACACAGTGAATCAAGCAAGCA 58.700 42.857 7.81 0.00 0.00 3.91
3254 3688 9.836076 AATTAATTTAGTTAAGAAAGGACGCAC 57.164 29.630 0.00 0.00 35.83 5.34
3327 3761 3.441496 ACCAGACAATGCAAACAACTG 57.559 42.857 0.00 0.00 0.00 3.16
3542 3978 4.096382 TCACAGTTTGCAAGGAAAGAGTTC 59.904 41.667 0.00 0.00 0.00 3.01
3635 4071 7.391554 AGAAAACTAGCAGATCTATTGTTTGCA 59.608 33.333 18.74 0.00 37.24 4.08
3792 4233 4.320608 TCAAATGCTGGACAAAAGAACC 57.679 40.909 0.00 0.00 0.00 3.62
4210 4651 4.327680 ACTTGATTCCAGCTACCAAGAAC 58.672 43.478 15.12 0.00 38.02 3.01
4328 4769 6.851222 ATTACGGATCAGAAAGCATAACAG 57.149 37.500 0.00 0.00 0.00 3.16
4912 5354 8.138712 TGGTTACACAAGAAAACATAAACATCC 58.861 33.333 0.00 0.00 0.00 3.51
5007 5449 6.336566 ACTGCATAGAGAGAACAGTAACATG 58.663 40.000 0.00 0.00 39.69 3.21
5056 5498 2.334977 ACACACTGGACCTTCATACCA 58.665 47.619 0.00 0.00 0.00 3.25
5059 5501 8.472007 AAAAATAAACACACTGGACCTTCATA 57.528 30.769 0.00 0.00 0.00 2.15
5086 5528 0.987294 TGAAGCTCCTTTCCTCCAGG 59.013 55.000 0.00 0.00 0.00 4.45
5162 5608 8.016301 TCTTCATTTCAGTGCTAGATACATCT 57.984 34.615 0.00 0.00 40.86 2.90
5184 5630 5.189145 AGGATATTTTGACCGGTACACTCTT 59.811 40.000 7.34 0.00 0.00 2.85
5245 5697 1.602605 GGCGGGTTAGCACCTTGTT 60.603 57.895 0.00 0.00 43.65 2.83
5362 5814 4.350245 ACTGTTCCCTGCTGTAGTATGTA 58.650 43.478 0.00 0.00 0.00 2.29
5375 5835 3.136626 AGCTGTCAGTTTTACTGTTCCCT 59.863 43.478 0.93 0.00 46.03 4.20
5376 5836 3.477530 AGCTGTCAGTTTTACTGTTCCC 58.522 45.455 0.93 0.00 46.03 3.97
5471 5931 2.307392 TGCAGTGGGTAGGAAATGCTAA 59.693 45.455 0.00 0.00 34.80 3.09
5494 5954 4.695455 GGCTAAATTTCTCTGTAGTGCACA 59.305 41.667 21.04 1.84 35.30 4.57
5495 5955 4.695455 TGGCTAAATTTCTCTGTAGTGCAC 59.305 41.667 9.40 9.40 0.00 4.57
5496 5956 4.905429 TGGCTAAATTTCTCTGTAGTGCA 58.095 39.130 0.00 0.00 0.00 4.57
5497 5957 5.178797 TCTGGCTAAATTTCTCTGTAGTGC 58.821 41.667 0.00 0.00 0.00 4.40
5498 5958 5.814705 CCTCTGGCTAAATTTCTCTGTAGTG 59.185 44.000 0.00 0.00 0.00 2.74
5502 5962 5.707066 ATCCTCTGGCTAAATTTCTCTGT 57.293 39.130 0.00 0.00 0.00 3.41
5558 6022 5.400066 AAGGTAATTGTGGGTTATGTTGC 57.600 39.130 0.00 0.00 0.00 4.17
5580 6044 6.610020 TCTTAAGAAAAGAGGATGGGACGATA 59.390 38.462 1.68 0.00 0.00 2.92
5584 6048 9.278978 GATAATCTTAAGAAAAGAGGATGGGAC 57.721 37.037 9.71 0.00 0.00 4.46
5608 6072 9.975218 TTTTAAGAATAGCACCCTTCTAAAGAT 57.025 29.630 0.00 0.00 31.60 2.40
5633 6097 7.913674 ATCGAAGATTTCTCTTTGCTAGTTT 57.086 32.000 0.00 0.00 45.12 2.66
5654 6118 9.884465 GGAGGATGAAAATGTATCTAAAAATCG 57.116 33.333 0.00 0.00 0.00 3.34
5666 6131 7.645058 AACGATATTTGGAGGATGAAAATGT 57.355 32.000 0.00 0.00 0.00 2.71
5748 6213 5.814705 TGGCTTTTAACCAAGTGAAATGTTG 59.185 36.000 0.00 0.00 33.12 3.33
5781 6309 4.915667 TGACTCGAAACAATGAACTAGACG 59.084 41.667 0.00 0.00 0.00 4.18
5786 6314 3.809832 CAGGTGACTCGAAACAATGAACT 59.190 43.478 0.00 0.00 40.21 3.01
5798 6326 3.380479 TTTACTTGGTCAGGTGACTCG 57.620 47.619 9.90 2.10 44.20 4.18
5854 6382 7.095060 TGCATTCTGTTCAGAAGATACTTTCAC 60.095 37.037 18.03 2.58 0.00 3.18
5857 6385 7.750229 TTGCATTCTGTTCAGAAGATACTTT 57.250 32.000 18.03 0.34 0.00 2.66
5916 6444 9.868277 TTTACAACTTGATCTTTTGTCAACATT 57.132 25.926 9.52 0.00 35.18 2.71
5925 6453 9.847224 TTCCTAGACTTTACAACTTGATCTTTT 57.153 29.630 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.