Multiple sequence alignment - TraesCS2B01G399200

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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 TraesCS2B01G399200 chr2B 100.000 2778 0 0 714 3491 567034404 567037181 0.000000e+00 5131.0
1 TraesCS2B01G399200 chr2B 100.000 353 0 0 1 353 567033691 567034043 0.000000e+00 652.0
2 TraesCS2B01G399200 chr2B 87.879 132 16 0 1246 1377 661851523 661851654 4.670000e-34 156.0
3 TraesCS2B01G399200 chr2B 86.111 144 17 3 1240 1381 489849188 489849330 6.040000e-33 152.0
4 TraesCS2B01G399200 chr2D 91.437 2721 124 58 714 3384 482789516 482792177 0.000000e+00 3633.0
5 TraesCS2B01G399200 chr2D 93.294 343 17 4 1078 1414 636638755 636639097 5.200000e-138 501.0
6 TraesCS2B01G399200 chr2D 91.795 195 14 2 42 235 482788550 482788743 1.600000e-68 270.0
7 TraesCS2B01G399200 chr2D 88.636 132 15 0 1246 1377 555395468 555395599 1.000000e-35 161.0
8 TraesCS2B01G399200 chr2D 86.525 141 17 2 1242 1381 417625367 417625506 1.680000e-33 154.0
9 TraesCS2B01G399200 chr2A 88.184 2759 141 70 716 3378 625243022 625245691 0.000000e+00 3118.0
10 TraesCS2B01G399200 chr2A 86.667 150 8 6 146 294 625242848 625242986 4.670000e-34 156.0
11 TraesCS2B01G399200 chr2A 94.000 100 6 0 3392 3491 625245885 625245984 6.040000e-33 152.0
12 TraesCS2B01G399200 chr3B 91.789 341 22 4 1080 1414 757671768 757672108 1.470000e-128 470.0
13 TraesCS2B01G399200 chr1B 91.319 288 19 4 1136 1417 491634633 491634346 4.230000e-104 388.0
14 TraesCS2B01G399200 chr6D 92.308 91 7 0 1915 2005 297407114 297407024 2.830000e-26 130.0
15 TraesCS2B01G399200 chr6D 92.308 91 7 0 1915 2005 297489643 297489553 2.830000e-26 130.0
16 TraesCS2B01G399200 chr6D 92.222 90 7 0 1915 2004 296993295 296993206 1.020000e-25 128.0
17 TraesCS2B01G399200 chr6D 92.222 90 7 0 1915 2004 298207020 298206931 1.020000e-25 128.0
18 TraesCS2B01G399200 chr6D 92.222 90 7 0 1915 2004 298444548 298444459 1.020000e-25 128.0
19 TraesCS2B01G399200 chr6A 91.209 91 8 0 1915 2005 421226325 421226415 1.320000e-24 124.0
20 TraesCS2B01G399200 chr6B 85.366 82 12 0 1915 1996 526100915 526100834 6.210000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G399200 chr2B 567033691 567037181 3490 False 2891.5 5131 100.000 1 3491 2 chr2B.!!$F3 3490
1 TraesCS2B01G399200 chr2D 482788550 482792177 3627 False 1951.5 3633 91.616 42 3384 2 chr2D.!!$F4 3342
2 TraesCS2B01G399200 chr2A 625242848 625245984 3136 False 1142.0 3118 89.617 146 3491 3 chr2A.!!$F1 3345

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
247 248 0.038166 GCCCCCTCACATGTCAGAAA 59.962 55.0 0.0 0.0 0.0 2.52 F
1718 2474 0.095935 CTCTTGATTTCAGTGCCGCG 59.904 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2849 0.250234 TCCTCATCTTGACCTTGCCG 59.750 55.0 0.0 0.0 0.0 5.69 R
3007 3798 0.318699 GTTTTTCAGGCTCGGTTGGC 60.319 55.0 0.0 0.0 0.0 4.52 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
22 23 5.382618 GATTTACCGATATGTACCTCCGT 57.617 43.478 0.00 0.00 0.00 4.69
23 24 6.500684 GATTTACCGATATGTACCTCCGTA 57.499 41.667 0.00 0.00 0.00 4.02
24 25 7.093322 GATTTACCGATATGTACCTCCGTAT 57.907 40.000 0.00 0.00 0.00 3.06
25 26 6.899393 TTTACCGATATGTACCTCCGTATT 57.101 37.500 0.00 0.00 0.00 1.89
26 27 4.778534 ACCGATATGTACCTCCGTATTG 57.221 45.455 0.00 0.00 0.00 1.90
27 28 4.401022 ACCGATATGTACCTCCGTATTGA 58.599 43.478 0.00 0.00 0.00 2.57
28 29 4.217118 ACCGATATGTACCTCCGTATTGAC 59.783 45.833 0.00 0.00 0.00 3.18
29 30 4.380233 CCGATATGTACCTCCGTATTGACC 60.380 50.000 0.00 0.00 0.00 4.02
30 31 4.216902 CGATATGTACCTCCGTATTGACCA 59.783 45.833 0.00 0.00 0.00 4.02
31 32 5.105877 CGATATGTACCTCCGTATTGACCAT 60.106 44.000 0.00 0.00 0.00 3.55
32 33 6.571731 CGATATGTACCTCCGTATTGACCATT 60.572 42.308 0.00 0.00 0.00 3.16
33 34 4.395959 TGTACCTCCGTATTGACCATTC 57.604 45.455 0.00 0.00 0.00 2.67
34 35 3.770388 TGTACCTCCGTATTGACCATTCA 59.230 43.478 0.00 0.00 0.00 2.57
35 36 4.407621 TGTACCTCCGTATTGACCATTCAT 59.592 41.667 0.00 0.00 0.00 2.57
36 37 5.599242 TGTACCTCCGTATTGACCATTCATA 59.401 40.000 0.00 0.00 0.00 2.15
37 38 5.215252 ACCTCCGTATTGACCATTCATAG 57.785 43.478 0.00 0.00 0.00 2.23
38 39 4.899457 ACCTCCGTATTGACCATTCATAGA 59.101 41.667 0.00 0.00 0.00 1.98
39 40 5.011125 ACCTCCGTATTGACCATTCATAGAG 59.989 44.000 0.00 0.00 0.00 2.43
40 41 5.011125 CCTCCGTATTGACCATTCATAGAGT 59.989 44.000 0.00 0.00 0.00 3.24
41 42 6.208797 CCTCCGTATTGACCATTCATAGAGTA 59.791 42.308 0.00 0.00 0.00 2.59
42 43 7.255836 CCTCCGTATTGACCATTCATAGAGTAA 60.256 40.741 0.00 0.00 0.00 2.24
43 44 8.014070 TCCGTATTGACCATTCATAGAGTAAA 57.986 34.615 0.00 0.00 0.00 2.01
44 45 7.924412 TCCGTATTGACCATTCATAGAGTAAAC 59.076 37.037 0.00 0.00 0.00 2.01
45 46 7.709182 CCGTATTGACCATTCATAGAGTAAACA 59.291 37.037 0.00 0.00 0.00 2.83
46 47 9.093970 CGTATTGACCATTCATAGAGTAAACAA 57.906 33.333 0.00 0.00 0.00 2.83
108 109 2.239907 AGCACTAGGGACCCAAATCTTC 59.760 50.000 14.60 0.00 0.00 2.87
131 132 2.961062 GACCCCTCGCAGGTAAATACTA 59.039 50.000 2.18 0.00 37.88 1.82
143 144 6.518493 CAGGTAAATACTAATCACGGCCTTA 58.482 40.000 0.00 0.00 0.00 2.69
172 173 3.549471 CGATAGATAAGCCATCATCACGC 59.451 47.826 0.00 0.00 35.96 5.34
180 181 0.749049 CCATCATCACGCTCTCCAGA 59.251 55.000 0.00 0.00 0.00 3.86
235 236 1.446366 GATTAGACACCGCCCCCTC 59.554 63.158 0.00 0.00 0.00 4.30
237 238 1.623542 ATTAGACACCGCCCCCTCAC 61.624 60.000 0.00 0.00 0.00 3.51
239 240 2.815684 TAGACACCGCCCCCTCACAT 62.816 60.000 0.00 0.00 0.00 3.21
240 241 3.976701 GACACCGCCCCCTCACATG 62.977 68.421 0.00 0.00 0.00 3.21
241 242 4.033776 CACCGCCCCCTCACATGT 62.034 66.667 0.00 0.00 0.00 3.21
242 243 3.717294 ACCGCCCCCTCACATGTC 61.717 66.667 0.00 0.00 0.00 3.06
243 244 3.716195 CCGCCCCCTCACATGTCA 61.716 66.667 0.00 0.00 0.00 3.58
244 245 2.124983 CGCCCCCTCACATGTCAG 60.125 66.667 0.00 0.00 0.00 3.51
245 246 2.659063 CGCCCCCTCACATGTCAGA 61.659 63.158 0.00 0.00 0.00 3.27
246 247 1.685224 GCCCCCTCACATGTCAGAA 59.315 57.895 0.00 0.00 0.00 3.02
247 248 0.038166 GCCCCCTCACATGTCAGAAA 59.962 55.000 0.00 0.00 0.00 2.52
248 249 1.952367 GCCCCCTCACATGTCAGAAAG 60.952 57.143 0.00 0.00 0.00 2.62
249 250 1.630369 CCCCCTCACATGTCAGAAAGA 59.370 52.381 0.00 0.00 0.00 2.52
250 251 2.240667 CCCCCTCACATGTCAGAAAGAT 59.759 50.000 0.00 0.00 0.00 2.40
251 252 3.455910 CCCCCTCACATGTCAGAAAGATA 59.544 47.826 0.00 0.00 0.00 1.98
252 253 4.446371 CCCCTCACATGTCAGAAAGATAC 58.554 47.826 0.00 0.00 0.00 2.24
292 503 5.362143 TCTCAAGAGAGAGAGAGAGAGAGAG 59.638 48.000 0.00 0.00 45.73 3.20
300 511 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
302 513 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
303 514 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
307 518 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
308 519 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
310 521 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
311 522 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
313 524 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
320 531 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
322 533 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
324 535 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
340 996 4.344390 AGAGAGAGAAAACAGTAAACGGGT 59.656 41.667 0.00 0.00 0.00 5.28
352 1008 5.358725 ACAGTAAACGGGTGAGAAACAATTT 59.641 36.000 0.00 0.00 0.00 1.82
852 1514 2.607892 GCCATTACTCCGCGGCATC 61.608 63.158 23.51 0.00 44.25 3.91
853 1515 1.227527 CCATTACTCCGCGGCATCA 60.228 57.895 23.51 1.03 0.00 3.07
854 1516 1.498865 CCATTACTCCGCGGCATCAC 61.499 60.000 23.51 0.00 0.00 3.06
855 1517 1.591594 ATTACTCCGCGGCATCACG 60.592 57.895 23.51 6.56 0.00 4.35
958 1639 2.107750 CTCCGCATCTGCATCCGT 59.892 61.111 2.72 0.00 42.21 4.69
1154 1867 4.077180 GTCCCTCCCTCCCTCCGT 62.077 72.222 0.00 0.00 0.00 4.69
1173 1886 0.317160 TCTCACAAACGCATCTCCGT 59.683 50.000 0.00 0.00 44.41 4.69
1181 1894 1.586564 CGCATCTCCGTCGTCTTCC 60.587 63.158 0.00 0.00 0.00 3.46
1493 2227 2.030805 GCTTCAATCGCAAAACAGAGGT 60.031 45.455 0.00 0.00 0.00 3.85
1675 2431 1.818674 GATTCCATCTTGTTTGGCCGT 59.181 47.619 0.00 0.00 34.06 5.68
1718 2474 0.095935 CTCTTGATTTCAGTGCCGCG 59.904 55.000 0.00 0.00 0.00 6.46
1766 2524 3.875134 CCTACTTGGCATTAAACTACGGG 59.125 47.826 0.00 0.00 0.00 5.28
1852 2610 8.250538 ACAAACAAACACGAATTCATCTTTTT 57.749 26.923 6.22 0.00 0.00 1.94
1854 2612 7.463469 AACAAACACGAATTCATCTTTTTCC 57.537 32.000 6.22 0.00 0.00 3.13
2424 3197 2.353704 CGACATGGACTACTGGCTCAAA 60.354 50.000 0.00 0.00 0.00 2.69
2461 3237 3.301592 GCGACGACGACAACAACA 58.698 55.556 12.29 0.00 42.66 3.33
2524 3301 0.802607 CTAGTTTCGTCGCTGCTCCC 60.803 60.000 0.00 0.00 0.00 4.30
2563 3341 2.123854 TCTCTCTACCCGCGCCAT 60.124 61.111 0.00 0.00 0.00 4.40
2602 3380 2.751166 TGCTAACAGAGAAGAGTGCC 57.249 50.000 0.00 0.00 0.00 5.01
2607 3385 1.078567 CAGAGAAGAGTGCCCTGCC 60.079 63.158 0.00 0.00 0.00 4.85
2651 3429 1.267732 GCAAGAACGCGGATCATGAAG 60.268 52.381 19.15 0.00 0.00 3.02
2720 3507 7.599621 CCTTGCTGTATAGAAAGATGAGAGATG 59.400 40.741 8.76 0.00 41.44 2.90
2723 3510 6.808212 GCTGTATAGAAAGATGAGAGATGAGC 59.192 42.308 0.00 0.00 0.00 4.26
2751 3538 3.895232 ACCGATGCATTCTGAGTTAGT 57.105 42.857 0.00 0.00 0.00 2.24
2752 3539 5.339008 AACCGATGCATTCTGAGTTAGTA 57.661 39.130 0.00 0.00 0.00 1.82
2753 3540 4.938080 ACCGATGCATTCTGAGTTAGTAG 58.062 43.478 0.00 0.00 0.00 2.57
2754 3541 4.402793 ACCGATGCATTCTGAGTTAGTAGT 59.597 41.667 0.00 0.00 0.00 2.73
2812 3599 4.289672 AGTTTCTGTACCACCATGGAGATT 59.710 41.667 21.47 3.50 40.96 2.40
2813 3600 5.487488 AGTTTCTGTACCACCATGGAGATTA 59.513 40.000 21.47 2.44 40.96 1.75
2814 3601 5.353394 TTCTGTACCACCATGGAGATTAC 57.647 43.478 21.47 15.05 40.96 1.89
2831 3618 8.861086 TGGAGATTACTACTATCTGAAATGGAC 58.139 37.037 0.00 0.00 32.64 4.02
2851 3638 2.560105 ACTCTGCTTTTCTCATTTGGCC 59.440 45.455 0.00 0.00 0.00 5.36
2922 3712 5.579718 CATCATGTGATCTTTTGGAGAAGC 58.420 41.667 0.00 0.00 38.06 3.86
2937 3727 2.603560 GAGAAGCGTGAGGATTAAACCG 59.396 50.000 0.00 0.00 34.73 4.44
2944 3734 4.186159 CGTGAGGATTAAACCGGTGTATT 58.814 43.478 8.52 2.60 34.73 1.89
2945 3735 5.350633 CGTGAGGATTAAACCGGTGTATTA 58.649 41.667 8.52 0.00 34.73 0.98
2946 3736 5.232838 CGTGAGGATTAAACCGGTGTATTAC 59.767 44.000 8.52 3.95 34.73 1.89
2967 3758 2.632987 AGTACGGGCTTTTGTCTTGT 57.367 45.000 0.00 0.00 0.00 3.16
3003 3794 3.935872 GTGTGCACGCTTGTCGCA 61.936 61.111 22.93 0.00 43.23 5.10
3004 3795 3.639008 TGTGCACGCTTGTCGCAG 61.639 61.111 13.13 0.00 43.23 5.18
3006 3797 2.894879 TGCACGCTTGTCGCAGTT 60.895 55.556 0.00 0.00 43.23 3.16
3007 3798 2.425773 GCACGCTTGTCGCAGTTG 60.426 61.111 0.00 0.00 43.23 3.16
3008 3799 2.425773 CACGCTTGTCGCAGTTGC 60.426 61.111 0.00 0.00 43.23 4.17
3009 3800 3.649986 ACGCTTGTCGCAGTTGCC 61.650 61.111 0.00 0.00 43.23 4.52
3013 3804 1.008538 CTTGTCGCAGTTGCCAACC 60.009 57.895 3.45 0.00 37.91 3.77
3014 3805 2.715864 CTTGTCGCAGTTGCCAACCG 62.716 60.000 3.45 1.79 37.91 4.44
3042 3833 0.179004 AAACATGCGTTGGGACTGGA 60.179 50.000 0.00 0.00 34.86 3.86
3068 3860 1.613520 CGGAGGAAAGGTCCCTTTTCC 60.614 57.143 12.39 14.09 46.30 3.13
3071 3863 0.784495 GGAAAGGTCCCTTTTCCCCT 59.216 55.000 12.39 0.00 45.16 4.79
3072 3864 1.272536 GGAAAGGTCCCTTTTCCCCTC 60.273 57.143 12.39 0.00 45.16 4.30
3073 3865 0.784495 AAAGGTCCCTTTTCCCCTCC 59.216 55.000 5.47 0.00 42.93 4.30
3075 3867 1.921857 GGTCCCTTTTCCCCTCCGA 60.922 63.158 0.00 0.00 0.00 4.55
3175 3969 2.420628 AACGAACAACATGTGCCATG 57.579 45.000 0.00 12.06 0.00 3.66
3178 3972 1.403116 CGAACAACATGTGCCATGCAT 60.403 47.619 13.19 0.00 41.91 3.96
3179 3973 1.996898 GAACAACATGTGCCATGCATG 59.003 47.619 20.19 20.19 46.51 4.06
3180 3974 0.390603 ACAACATGTGCCATGCATGC 60.391 50.000 21.69 11.82 45.40 4.06
3181 3975 0.390472 CAACATGTGCCATGCATGCA 60.390 50.000 25.04 25.04 45.40 3.96
3182 3976 0.108377 AACATGTGCCATGCATGCAG 60.108 50.000 26.69 14.50 45.40 4.41
3184 3978 0.389025 CATGTGCCATGCATGCAGAT 59.611 50.000 26.69 20.85 42.75 2.90
3185 3979 1.119684 ATGTGCCATGCATGCAGATT 58.880 45.000 26.69 6.48 39.42 2.40
3190 3984 1.801395 GCCATGCATGCAGATTCACAC 60.801 52.381 26.69 5.58 0.00 3.82
3191 3985 1.474879 CCATGCATGCAGATTCACACA 59.525 47.619 26.69 0.00 0.00 3.72
3198 3992 6.056884 TGCATGCAGATTCACACAGATATAA 58.943 36.000 18.46 0.00 0.00 0.98
3199 3993 6.204108 TGCATGCAGATTCACACAGATATAAG 59.796 38.462 18.46 0.00 0.00 1.73
3201 3995 6.484364 TGCAGATTCACACAGATATAAGGA 57.516 37.500 0.00 0.00 0.00 3.36
3202 3996 6.519382 TGCAGATTCACACAGATATAAGGAG 58.481 40.000 0.00 0.00 0.00 3.69
3203 3997 6.098838 TGCAGATTCACACAGATATAAGGAGT 59.901 38.462 0.00 0.00 0.00 3.85
3204 3998 7.287696 TGCAGATTCACACAGATATAAGGAGTA 59.712 37.037 0.00 0.00 0.00 2.59
3205 3999 8.310382 GCAGATTCACACAGATATAAGGAGTAT 58.690 37.037 0.00 0.00 0.00 2.12
3210 4004 8.885693 TCACACAGATATAAGGAGTATATGCT 57.114 34.615 0.00 0.00 35.82 3.79
3211 4005 9.975218 TCACACAGATATAAGGAGTATATGCTA 57.025 33.333 0.00 0.00 35.82 3.49
3213 4007 9.755122 ACACAGATATAAGGAGTATATGCTACA 57.245 33.333 5.77 0.00 35.82 2.74
3227 4023 6.839820 ATATGCTACAGTAAAACGTTAGCC 57.160 37.500 12.93 0.00 34.47 3.93
3229 4025 3.991773 TGCTACAGTAAAACGTTAGCCTG 59.008 43.478 12.93 14.28 34.47 4.85
3230 4026 4.240096 GCTACAGTAAAACGTTAGCCTGA 58.760 43.478 20.98 9.07 31.34 3.86
3232 4028 4.062677 ACAGTAAAACGTTAGCCTGACA 57.937 40.909 20.98 0.00 0.00 3.58
3248 4045 4.082733 GCCTGACAGTTTTCTATTCCAACC 60.083 45.833 0.93 0.00 0.00 3.77
3249 4046 5.070001 CCTGACAGTTTTCTATTCCAACCA 58.930 41.667 0.93 0.00 0.00 3.67
3271 4071 1.477700 TGCCAATTATGTTCAGGCTGC 59.522 47.619 10.34 0.00 45.42 5.25
3272 4072 1.202452 GCCAATTATGTTCAGGCTGCC 60.202 52.381 11.65 11.65 42.01 4.85
3285 4085 1.075374 AGGCTGCCCAAACAGTATTCA 59.925 47.619 16.57 0.00 39.96 2.57
3287 4090 2.497273 GGCTGCCCAAACAGTATTCAAT 59.503 45.455 7.66 0.00 39.96 2.57
3293 4096 4.929211 GCCCAAACAGTATTCAATTCAACC 59.071 41.667 0.00 0.00 0.00 3.77
3294 4097 5.279456 GCCCAAACAGTATTCAATTCAACCT 60.279 40.000 0.00 0.00 0.00 3.50
3295 4098 6.741240 GCCCAAACAGTATTCAATTCAACCTT 60.741 38.462 0.00 0.00 0.00 3.50
3363 4175 4.747810 CATGGCAGTTTTCTATTCCAACC 58.252 43.478 0.00 0.00 30.82 3.77
3364 4176 3.838565 TGGCAGTTTTCTATTCCAACCA 58.161 40.909 0.00 0.00 0.00 3.67
3367 4179 4.280929 GGCAGTTTTCTATTCCAACCAGTT 59.719 41.667 0.00 0.00 0.00 3.16
3386 4198 4.460382 CAGTTCCAATTATGTTCAGGCAGT 59.540 41.667 0.00 0.00 0.00 4.40
3387 4199 5.047802 CAGTTCCAATTATGTTCAGGCAGTT 60.048 40.000 0.00 0.00 0.00 3.16
3388 4200 5.539955 AGTTCCAATTATGTTCAGGCAGTTT 59.460 36.000 0.00 0.00 0.00 2.66
3389 4201 6.041979 AGTTCCAATTATGTTCAGGCAGTTTT 59.958 34.615 0.00 0.00 0.00 2.43
3390 4202 6.024552 TCCAATTATGTTCAGGCAGTTTTC 57.975 37.500 0.00 0.00 0.00 2.29
3401 4393 2.446435 GGCAGTTTTCTATGGCTGGAA 58.554 47.619 0.00 0.00 38.83 3.53
3448 4440 1.131126 GTTTCATGGCCATCACGACAG 59.869 52.381 17.61 2.45 0.00 3.51
3449 4441 1.026182 TTCATGGCCATCACGACAGC 61.026 55.000 17.61 0.00 0.00 4.40
3463 4455 1.517242 GACAGCCTGTCCTTGAACAG 58.483 55.000 14.04 0.00 45.10 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.382618 ACGGAGGTACATATCGGTAAATC 57.617 43.478 7.47 0.00 0.00 2.17
2 3 6.489700 TCAATACGGAGGTACATATCGGTAAA 59.510 38.462 12.88 4.18 35.64 2.01
3 4 6.003326 TCAATACGGAGGTACATATCGGTAA 58.997 40.000 12.88 0.00 35.64 2.85
4 5 5.412594 GTCAATACGGAGGTACATATCGGTA 59.587 44.000 11.88 11.88 36.21 4.02
6 7 4.380233 GGTCAATACGGAGGTACATATCGG 60.380 50.000 7.47 3.69 0.00 4.18
7 8 4.216902 TGGTCAATACGGAGGTACATATCG 59.783 45.833 0.00 0.00 0.00 2.92
8 9 5.717078 TGGTCAATACGGAGGTACATATC 57.283 43.478 0.00 0.00 0.00 1.63
9 10 6.269077 TGAATGGTCAATACGGAGGTACATAT 59.731 38.462 0.00 0.00 0.00 1.78
11 12 4.407621 TGAATGGTCAATACGGAGGTACAT 59.592 41.667 0.00 0.00 0.00 2.29
12 13 3.770388 TGAATGGTCAATACGGAGGTACA 59.230 43.478 0.00 0.00 0.00 2.90
13 14 4.395959 TGAATGGTCAATACGGAGGTAC 57.604 45.455 0.00 0.00 0.00 3.34
14 15 6.072649 TCTATGAATGGTCAATACGGAGGTA 58.927 40.000 0.00 0.00 37.30 3.08
15 16 4.899457 TCTATGAATGGTCAATACGGAGGT 59.101 41.667 0.00 0.00 37.30 3.85
16 17 5.011125 ACTCTATGAATGGTCAATACGGAGG 59.989 44.000 0.00 0.00 37.30 4.30
18 19 7.591421 TTACTCTATGAATGGTCAATACGGA 57.409 36.000 0.00 0.00 37.30 4.69
19 20 7.709182 TGTTTACTCTATGAATGGTCAATACGG 59.291 37.037 0.00 0.00 37.30 4.02
20 21 8.642908 TGTTTACTCTATGAATGGTCAATACG 57.357 34.615 0.00 0.00 37.30 3.06
108 109 0.541863 ATTTACCTGCGAGGGGTCAG 59.458 55.000 7.06 0.00 40.58 3.51
131 132 4.866508 TCGATTAGATAAGGCCGTGATT 57.133 40.909 0.00 0.00 0.00 2.57
143 144 9.140874 TGATGATGGCTTATCTATCGATTAGAT 57.859 33.333 1.71 12.05 46.99 1.98
235 236 9.586435 TTACTGTATGTATCTTTCTGACATGTG 57.414 33.333 1.15 0.00 35.48 3.21
239 240 8.301720 ACGTTTACTGTATGTATCTTTCTGACA 58.698 33.333 0.00 0.00 0.00 3.58
240 241 8.684973 ACGTTTACTGTATGTATCTTTCTGAC 57.315 34.615 0.00 0.00 0.00 3.51
241 242 9.135843 CAACGTTTACTGTATGTATCTTTCTGA 57.864 33.333 0.00 0.00 0.00 3.27
242 243 8.922676 ACAACGTTTACTGTATGTATCTTTCTG 58.077 33.333 0.00 0.00 0.00 3.02
243 244 9.136952 GACAACGTTTACTGTATGTATCTTTCT 57.863 33.333 0.00 0.00 0.00 2.52
244 245 9.136952 AGACAACGTTTACTGTATGTATCTTTC 57.863 33.333 0.00 0.00 0.00 2.62
245 246 9.136952 GAGACAACGTTTACTGTATGTATCTTT 57.863 33.333 0.00 0.00 0.00 2.52
246 247 8.301720 TGAGACAACGTTTACTGTATGTATCTT 58.698 33.333 0.00 0.00 32.06 2.40
247 248 7.823665 TGAGACAACGTTTACTGTATGTATCT 58.176 34.615 0.00 7.63 32.06 1.98
248 249 8.456904 TTGAGACAACGTTTACTGTATGTATC 57.543 34.615 0.00 0.00 31.59 2.24
249 250 8.301720 TCTTGAGACAACGTTTACTGTATGTAT 58.698 33.333 0.00 0.00 0.00 2.29
250 251 7.650890 TCTTGAGACAACGTTTACTGTATGTA 58.349 34.615 0.00 0.00 0.00 2.29
251 252 6.509656 TCTTGAGACAACGTTTACTGTATGT 58.490 36.000 0.00 0.00 0.00 2.29
252 253 6.861572 TCTCTTGAGACAACGTTTACTGTATG 59.138 38.462 0.00 0.00 0.00 2.39
288 292 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
292 503 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
300 511 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
302 513 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
303 514 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
307 518 6.126863 TGTTTTCTCTCTCTCTCTCTCTCT 57.873 41.667 0.00 0.00 0.00 3.10
308 519 5.940470 ACTGTTTTCTCTCTCTCTCTCTCTC 59.060 44.000 0.00 0.00 0.00 3.20
310 521 7.681939 TTACTGTTTTCTCTCTCTCTCTCTC 57.318 40.000 0.00 0.00 0.00 3.20
311 522 7.308348 CGTTTACTGTTTTCTCTCTCTCTCTCT 60.308 40.741 0.00 0.00 0.00 3.10
313 524 6.294286 CCGTTTACTGTTTTCTCTCTCTCTCT 60.294 42.308 0.00 0.00 0.00 3.10
320 531 4.374399 TCACCCGTTTACTGTTTTCTCTC 58.626 43.478 0.00 0.00 0.00 3.20
322 533 4.374399 TCTCACCCGTTTACTGTTTTCTC 58.626 43.478 0.00 0.00 0.00 2.87
324 535 5.163733 TGTTTCTCACCCGTTTACTGTTTTC 60.164 40.000 0.00 0.00 0.00 2.29
858 1520 4.871910 CTAGCCTGCCTGCCTGCC 62.872 72.222 0.00 0.00 0.00 4.85
890 1552 1.411074 GGGGGAGAGGAGAGAAGAGAC 60.411 61.905 0.00 0.00 0.00 3.36
1145 1850 0.388649 CGTTTGTGAGACGGAGGGAG 60.389 60.000 0.00 0.00 36.90 4.30
1154 1867 0.317160 ACGGAGATGCGTTTGTGAGA 59.683 50.000 0.00 0.00 0.00 3.27
1201 1924 2.496817 GGACGGATCTTGAGCGCT 59.503 61.111 11.27 11.27 0.00 5.92
1547 2297 5.810074 CCGCGATGGATGATAACATATTGTA 59.190 40.000 8.23 0.00 42.00 2.41
1614 2370 4.891168 TCATCAGTGATGCAATTAGCCATT 59.109 37.500 25.53 0.00 44.83 3.16
1616 2372 3.888583 TCATCAGTGATGCAATTAGCCA 58.111 40.909 25.53 4.90 44.83 4.75
1718 2474 1.299089 GTGGCGGCACAAAGTGTTC 60.299 57.895 34.40 5.93 35.75 3.18
1852 2610 0.252421 AGTCCAGACAGATGGCAGGA 60.252 55.000 0.00 0.00 40.41 3.86
1854 2612 0.612229 ACAGTCCAGACAGATGGCAG 59.388 55.000 0.00 0.00 40.41 4.85
2076 2849 0.250234 TCCTCATCTTGACCTTGCCG 59.750 55.000 0.00 0.00 0.00 5.69
2164 2937 2.175322 GGACGTCGACTCGGTGAC 59.825 66.667 14.70 0.00 34.94 3.67
2238 3011 3.685214 CTCCTCCTTGACGGACGCG 62.685 68.421 3.53 3.53 36.69 6.01
2424 3197 2.671070 CCGCCCTCCATGAACACT 59.329 61.111 0.00 0.00 0.00 3.55
2461 3237 1.515736 GTAAGTCTAGCGCGCCGTT 60.516 57.895 30.33 12.78 0.00 4.44
2563 3341 4.020617 CCCTCCGGTGCAGCAAGA 62.021 66.667 17.33 10.89 0.00 3.02
2607 3385 2.480845 CTACTAATTTTCCTCCGCGGG 58.519 52.381 27.83 16.14 0.00 6.13
2611 3389 2.872858 GCTGGCTACTAATTTTCCTCCG 59.127 50.000 0.00 0.00 0.00 4.63
2720 3507 2.303676 GCATCGGTTCCGATCGCTC 61.304 63.158 25.54 14.12 45.80 5.03
2723 3510 0.508641 GAATGCATCGGTTCCGATCG 59.491 55.000 21.61 17.42 45.80 3.69
2751 3538 6.036470 CGTGCAGAAGAACAGATAATCACTA 58.964 40.000 0.00 0.00 0.00 2.74
2752 3539 4.867047 CGTGCAGAAGAACAGATAATCACT 59.133 41.667 0.00 0.00 0.00 3.41
2753 3540 4.033358 CCGTGCAGAAGAACAGATAATCAC 59.967 45.833 0.00 0.00 0.00 3.06
2754 3541 4.183865 CCGTGCAGAAGAACAGATAATCA 58.816 43.478 0.00 0.00 0.00 2.57
2812 3599 7.063593 AGCAGAGTCCATTTCAGATAGTAGTA 58.936 38.462 0.00 0.00 0.00 1.82
2813 3600 5.896678 AGCAGAGTCCATTTCAGATAGTAGT 59.103 40.000 0.00 0.00 0.00 2.73
2814 3601 6.403866 AGCAGAGTCCATTTCAGATAGTAG 57.596 41.667 0.00 0.00 0.00 2.57
2831 3618 2.415090 CGGCCAAATGAGAAAAGCAGAG 60.415 50.000 2.24 0.00 0.00 3.35
2910 3699 2.169832 TCCTCACGCTTCTCCAAAAG 57.830 50.000 0.00 0.00 0.00 2.27
2922 3712 2.088950 ACACCGGTTTAATCCTCACG 57.911 50.000 2.97 0.00 0.00 4.35
2937 3727 4.926140 AAGCCCGTACTAGTAATACACC 57.074 45.455 3.61 0.00 0.00 4.16
2944 3734 4.281688 ACAAGACAAAAGCCCGTACTAGTA 59.718 41.667 0.00 0.00 0.00 1.82
2945 3735 3.070590 ACAAGACAAAAGCCCGTACTAGT 59.929 43.478 0.00 0.00 0.00 2.57
2946 3736 3.660865 ACAAGACAAAAGCCCGTACTAG 58.339 45.455 0.00 0.00 0.00 2.57
2967 3758 4.513692 CACACACCGGAAAAGAACAGATAA 59.486 41.667 9.46 0.00 0.00 1.75
3003 3794 2.281761 CAGGCTCGGTTGGCAACT 60.282 61.111 27.77 6.03 37.61 3.16
3004 3795 1.452145 TTTCAGGCTCGGTTGGCAAC 61.452 55.000 21.92 21.92 34.73 4.17
3006 3797 0.753479 TTTTTCAGGCTCGGTTGGCA 60.753 50.000 0.00 0.00 34.73 4.92
3007 3798 0.318699 GTTTTTCAGGCTCGGTTGGC 60.319 55.000 0.00 0.00 0.00 4.52
3008 3799 1.028905 TGTTTTTCAGGCTCGGTTGG 58.971 50.000 0.00 0.00 0.00 3.77
3009 3800 2.664916 CATGTTTTTCAGGCTCGGTTG 58.335 47.619 0.00 0.00 0.00 3.77
3042 3833 1.479942 GGGACCTTTCCTCCGGTTTTT 60.480 52.381 0.00 0.00 42.38 1.94
3068 3860 6.183360 TGTCATTATTTAACTCTCTCGGAGGG 60.183 42.308 4.96 0.81 45.83 4.30
3071 3863 6.263344 CGTGTCATTATTTAACTCTCTCGGA 58.737 40.000 0.00 0.00 0.00 4.55
3072 3864 5.459107 CCGTGTCATTATTTAACTCTCTCGG 59.541 44.000 0.00 0.00 0.00 4.63
3073 3865 6.196724 GTCCGTGTCATTATTTAACTCTCTCG 59.803 42.308 0.00 0.00 0.00 4.04
3075 3867 6.931838 TGTCCGTGTCATTATTTAACTCTCT 58.068 36.000 0.00 0.00 0.00 3.10
3175 3969 6.348295 CCTTATATCTGTGTGAATCTGCATGC 60.348 42.308 11.82 11.82 0.00 4.06
3178 3972 6.098838 ACTCCTTATATCTGTGTGAATCTGCA 59.901 38.462 0.00 0.00 0.00 4.41
3179 3973 6.520272 ACTCCTTATATCTGTGTGAATCTGC 58.480 40.000 0.00 0.00 0.00 4.26
3184 3978 9.314133 AGCATATACTCCTTATATCTGTGTGAA 57.686 33.333 0.00 0.00 31.83 3.18
3185 3979 8.885693 AGCATATACTCCTTATATCTGTGTGA 57.114 34.615 0.00 0.00 31.83 3.58
3198 3992 7.344095 ACGTTTTACTGTAGCATATACTCCT 57.656 36.000 0.00 0.00 0.00 3.69
3199 3993 7.998753 AACGTTTTACTGTAGCATATACTCC 57.001 36.000 0.00 0.00 0.00 3.85
3201 3995 7.650903 GGCTAACGTTTTACTGTAGCATATACT 59.349 37.037 16.35 0.00 0.00 2.12
3202 3996 7.650903 AGGCTAACGTTTTACTGTAGCATATAC 59.349 37.037 16.35 1.96 0.00 1.47
3203 3997 7.650504 CAGGCTAACGTTTTACTGTAGCATATA 59.349 37.037 16.35 0.00 0.00 0.86
3204 3998 6.479001 CAGGCTAACGTTTTACTGTAGCATAT 59.521 38.462 16.35 2.26 0.00 1.78
3205 3999 5.808540 CAGGCTAACGTTTTACTGTAGCATA 59.191 40.000 16.35 0.00 0.00 3.14
3206 4000 4.630069 CAGGCTAACGTTTTACTGTAGCAT 59.370 41.667 16.35 8.47 0.00 3.79
3207 4001 3.991773 CAGGCTAACGTTTTACTGTAGCA 59.008 43.478 16.35 0.00 0.00 3.49
3208 4002 4.091075 GTCAGGCTAACGTTTTACTGTAGC 59.909 45.833 5.91 7.31 0.00 3.58
3209 4003 5.224888 TGTCAGGCTAACGTTTTACTGTAG 58.775 41.667 5.91 0.00 0.00 2.74
3210 4004 5.199024 TGTCAGGCTAACGTTTTACTGTA 57.801 39.130 5.91 4.22 0.00 2.74
3211 4005 4.056050 CTGTCAGGCTAACGTTTTACTGT 58.944 43.478 5.91 0.00 0.00 3.55
3212 4006 4.056050 ACTGTCAGGCTAACGTTTTACTG 58.944 43.478 5.91 12.32 0.00 2.74
3213 4007 4.332428 ACTGTCAGGCTAACGTTTTACT 57.668 40.909 5.91 0.00 0.00 2.24
3214 4008 5.413969 AAACTGTCAGGCTAACGTTTTAC 57.586 39.130 5.91 0.00 0.00 2.01
3227 4023 5.765182 ACTGGTTGGAATAGAAAACTGTCAG 59.235 40.000 0.00 0.00 0.00 3.51
3229 4025 5.562890 GCACTGGTTGGAATAGAAAACTGTC 60.563 44.000 0.00 0.00 0.00 3.51
3230 4026 4.278419 GCACTGGTTGGAATAGAAAACTGT 59.722 41.667 0.00 0.00 0.00 3.55
3232 4028 3.826729 GGCACTGGTTGGAATAGAAAACT 59.173 43.478 0.00 0.00 0.00 2.66
3248 4045 2.756760 AGCCTGAACATAATTGGCACTG 59.243 45.455 0.00 0.00 45.42 3.66
3249 4046 2.756760 CAGCCTGAACATAATTGGCACT 59.243 45.455 0.00 0.00 45.42 4.40
3271 4071 6.345096 AGGTTGAATTGAATACTGTTTGGG 57.655 37.500 0.00 0.00 0.00 4.12
3272 4072 8.661352 AAAAGGTTGAATTGAATACTGTTTGG 57.339 30.769 0.00 0.00 0.00 3.28
3322 4125 6.015519 TGCCATGCTACAAAACTTTCACTAAT 60.016 34.615 0.00 0.00 0.00 1.73
3330 4133 4.670896 AAACTGCCATGCTACAAAACTT 57.329 36.364 0.00 0.00 0.00 2.66
3336 4139 4.640201 GGAATAGAAAACTGCCATGCTACA 59.360 41.667 0.00 0.00 0.00 2.74
3363 4175 4.460382 ACTGCCTGAACATAATTGGAACTG 59.540 41.667 0.00 0.00 0.00 3.16
3364 4176 4.666512 ACTGCCTGAACATAATTGGAACT 58.333 39.130 0.00 0.00 0.00 3.01
3367 4179 5.774690 AGAAAACTGCCTGAACATAATTGGA 59.225 36.000 0.00 0.00 0.00 3.53
3386 4198 4.037446 GTGTGTTGTTCCAGCCATAGAAAA 59.963 41.667 0.00 0.00 0.00 2.29
3387 4199 3.568007 GTGTGTTGTTCCAGCCATAGAAA 59.432 43.478 0.00 0.00 0.00 2.52
3388 4200 3.146066 GTGTGTTGTTCCAGCCATAGAA 58.854 45.455 0.00 0.00 0.00 2.10
3389 4201 2.371841 AGTGTGTTGTTCCAGCCATAGA 59.628 45.455 0.00 0.00 0.00 1.98
3390 4202 2.485426 CAGTGTGTTGTTCCAGCCATAG 59.515 50.000 0.00 0.00 0.00 2.23
3398 4390 2.221169 TGATGAGCAGTGTGTTGTTCC 58.779 47.619 0.00 0.00 0.00 3.62
3401 4393 2.810274 GTGATGATGAGCAGTGTGTTGT 59.190 45.455 0.00 0.00 0.00 3.32
3448 4440 1.338200 ACGATCTGTTCAAGGACAGGC 60.338 52.381 8.57 1.33 45.54 4.85
3449 4441 2.341257 CACGATCTGTTCAAGGACAGG 58.659 52.381 8.57 0.00 45.54 4.00


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

AutoCloner maintained by Alex Coulton.