Multiple sequence alignment - TraesCS4D01G096400

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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 TraesCS4D01G096400 chr4D 100.000 5607 0 0 1 5607 72907328 72912934 0.000000e+00 10355.0
1 TraesCS4D01G096400 chr4A 94.104 3528 157 18 684 4176 514433577 514430066 0.000000e+00 5315.0
2 TraesCS4D01G096400 chr4A 90.187 1447 72 28 4174 5607 514430013 514428624 0.000000e+00 1821.0
3 TraesCS4D01G096400 chr4A 81.899 674 117 5 7 678 615947530 615946860 1.050000e-156 564.0
4 TraesCS4D01G096400 chr4A 81.763 658 109 11 2 654 701347654 701347003 1.780000e-149 540.0
5 TraesCS4D01G096400 chr4B 95.208 2525 90 9 2424 4937 105958203 105960707 0.000000e+00 3964.0
6 TraesCS4D01G096400 chr4B 94.341 1767 62 23 678 2425 105956385 105958132 0.000000e+00 2675.0
7 TraesCS4D01G096400 chr4B 82.462 650 109 5 19 665 478572664 478573311 1.050000e-156 564.0
8 TraesCS4D01G096400 chr4B 87.302 504 46 13 5111 5607 105960761 105961253 1.360000e-155 560.0
9 TraesCS4D01G096400 chr6D 83.111 675 106 7 7 677 420622001 420621331 4.800000e-170 608.0
10 TraesCS4D01G096400 chr5D 81.460 685 114 13 2 678 549200907 549200228 2.950000e-152 549.0
11 TraesCS4D01G096400 chr5B 81.443 679 115 9 4 678 597101288 597101959 3.820000e-151 545.0
12 TraesCS4D01G096400 chr5B 94.595 37 2 0 5055 5091 539660168 539660132 2.180000e-04 58.4
13 TraesCS4D01G096400 chr2D 81.361 676 113 12 4 673 194713283 194713951 6.390000e-149 538.0
14 TraesCS4D01G096400 chr1D 81.121 678 121 6 4 678 6466324 6466997 2.300000e-148 536.0
15 TraesCS4D01G096400 chr1D 90.698 43 3 1 5041 5083 163775436 163775477 7.850000e-04 56.5
16 TraesCS4D01G096400 chr3D 80.352 682 124 10 2 678 32588323 32587647 5.010000e-140 508.0
17 TraesCS4D01G096400 chr3D 97.143 35 1 0 5056 5090 32753892 32753926 6.070000e-05 60.2
18 TraesCS4D01G096400 chr7D 91.304 46 4 0 5056 5101 593175490 593175535 4.690000e-06 63.9
19 TraesCS4D01G096400 chr7D 94.444 36 2 0 5055 5090 566448799 566448834 7.850000e-04 56.5
20 TraesCS4D01G096400 chr3B 94.595 37 2 0 5055 5091 510326974 510327010 2.180000e-04 58.4
21 TraesCS4D01G096400 chr3B 94.595 37 2 0 5054 5090 728752108 728752144 2.180000e-04 58.4
22 TraesCS4D01G096400 chr7B 92.500 40 2 1 5052 5090 319390011 319389972 7.850000e-04 56.5
23 TraesCS4D01G096400 chr6B 92.500 40 2 1 5052 5090 160815589 160815550 7.850000e-04 56.5


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 TraesCS4D01G096400 chr4D 72907328 72912934 5606 False 10355.000000 10355 100.000000 1 5607 1 chr4D.!!$F1 5606
1 TraesCS4D01G096400 chr4A 514428624 514433577 4953 True 3568.000000 5315 92.145500 684 5607 2 chr4A.!!$R3 4923
2 TraesCS4D01G096400 chr4A 615946860 615947530 670 True 564.000000 564 81.899000 7 678 1 chr4A.!!$R1 671
3 TraesCS4D01G096400 chr4A 701347003 701347654 651 True 540.000000 540 81.763000 2 654 1 chr4A.!!$R2 652
4 TraesCS4D01G096400 chr4B 105956385 105961253 4868 False 2399.666667 3964 92.283667 678 5607 3 chr4B.!!$F2 4929
5 TraesCS4D01G096400 chr4B 478572664 478573311 647 False 564.000000 564 82.462000 19 665 1 chr4B.!!$F1 646
6 TraesCS4D01G096400 chr6D 420621331 420622001 670 True 608.000000 608 83.111000 7 677 1 chr6D.!!$R1 670
7 TraesCS4D01G096400 chr5D 549200228 549200907 679 True 549.000000 549 81.460000 2 678 1 chr5D.!!$R1 676
8 TraesCS4D01G096400 chr5B 597101288 597101959 671 False 545.000000 545 81.443000 4 678 1 chr5B.!!$F1 674
9 TraesCS4D01G096400 chr2D 194713283 194713951 668 False 538.000000 538 81.361000 4 673 1 chr2D.!!$F1 669
10 TraesCS4D01G096400 chr1D 6466324 6466997 673 False 536.000000 536 81.121000 4 678 1 chr1D.!!$F1 674
11 TraesCS4D01G096400 chr3D 32587647 32588323 676 True 508.000000 508 80.352000 2 678 1 chr3D.!!$R1 676

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
291 296 0.105964 TGTGGCACAAGCGAGTTACT 59.894 50.000 19.74 0.0 44.16 2.24 F
412 420 1.004918 GGGTGAAGACCTGTGTCCG 60.005 63.158 0.00 0.0 42.81 4.79 F
1573 1601 0.944386 TCTGCGGTGCTTCTTGAAAC 59.056 50.000 0.00 0.0 0.00 2.78 F
2279 2323 0.248054 GCATTACGCATCACCCAACG 60.248 55.000 0.00 0.0 41.79 4.10 F
3432 3584 0.832135 AGAAGCTCGTGGACCCAGAA 60.832 55.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 1213 1.129998 CACGCATTTTCAGCTCCTCTG 59.870 52.381 0.0 0.0 44.21 3.35 R
1725 1755 1.146263 GGCCCATAGGACCAGAACG 59.854 63.158 0.0 0.0 33.41 3.95 R
3399 3551 0.964358 GCTTCTGCTCCATTGCCACT 60.964 55.000 0.0 0.0 36.03 4.00 R
3603 3755 0.749818 TTTTCAGCACAAGGTCGCCA 60.750 50.000 0.0 0.0 0.00 5.69 R
4804 5014 1.927174 CAGATTAACGTCGGCCTTGAG 59.073 52.381 0.0 0.0 0.00 3.02 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
31 32 1.935873 CCTATCATGGTTGAGTGCGTG 59.064 52.381 0.00 0.00 34.73 5.34
40 42 0.179059 TTGAGTGCGTGGTGATGTGT 60.179 50.000 0.00 0.00 0.00 3.72
124 129 4.100084 TCTCCGGCAGGCACCATG 62.100 66.667 0.00 0.00 37.47 3.66
142 147 2.194597 GTGGTGGTGGTGGCTTCA 59.805 61.111 0.00 0.00 0.00 3.02
153 158 2.434774 GGCTTCACTCCCGGGTTT 59.565 61.111 22.86 5.42 0.00 3.27
177 182 2.356313 CAACGAGAGGTGCTGCGT 60.356 61.111 0.00 0.00 44.78 5.24
184 189 1.302192 GAGGTGCTGCGTTGGGTAA 60.302 57.895 0.00 0.00 0.00 2.85
193 198 1.864176 CGTTGGGTAACTTGGACGC 59.136 57.895 0.00 0.00 34.60 5.19
198 203 3.122971 GTAACTTGGACGCGCCCC 61.123 66.667 9.62 10.31 34.97 5.80
256 261 4.862092 CTGTCATCGCCGCGCTCT 62.862 66.667 8.21 0.00 0.00 4.09
283 288 2.639286 CCTCGTTGTGGCACAAGC 59.361 61.111 31.83 23.37 44.16 4.01
289 294 0.941542 GTTGTGGCACAAGCGAGTTA 59.058 50.000 31.83 6.80 44.16 2.24
291 296 0.105964 TGTGGCACAAGCGAGTTACT 59.894 50.000 19.74 0.00 44.16 2.24
312 320 3.655481 CGAAAGCTCCGTGCCTTT 58.345 55.556 0.00 0.00 44.23 3.11
412 420 1.004918 GGGTGAAGACCTGTGTCCG 60.005 63.158 0.00 0.00 42.81 4.79
488 499 3.256136 GTCGTGGAGCTTAGGTATGCTAT 59.744 47.826 0.00 0.00 39.91 2.97
522 535 2.486013 GGGTGTTTAGTTCTTCCGGTGT 60.486 50.000 0.00 0.00 0.00 4.16
524 537 4.379652 GGTGTTTAGTTCTTCCGGTGTTA 58.620 43.478 0.00 0.00 0.00 2.41
554 568 3.324170 CGTAGTCGCGTGGATTCTT 57.676 52.632 5.77 0.00 0.00 2.52
561 575 1.282248 CGCGTGGATTCTTCGTGTGT 61.282 55.000 0.00 0.00 0.00 3.72
578 592 5.127031 TCGTGTGTCAGATATTTCAGGATCA 59.873 40.000 0.00 0.00 0.00 2.92
665 681 7.316544 CTTTATATATAAAGCGGGGCGAAAT 57.683 36.000 25.10 0.00 41.69 2.17
689 705 9.533831 AATCCTGTTTCAAGACCATATTACTTT 57.466 29.630 0.00 0.00 0.00 2.66
752 776 7.363793 GGTGCAAGTTATCCACCATTTCTTTAT 60.364 37.037 12.26 0.00 46.38 1.40
753 777 8.034804 GTGCAAGTTATCCACCATTTCTTTATT 58.965 33.333 0.00 0.00 0.00 1.40
868 892 2.735151 AATTGCAGCTCCCTTGCCCA 62.735 55.000 0.00 0.00 40.81 5.36
938 962 2.112190 CACTTCCTCTCCTAACCCTCC 58.888 57.143 0.00 0.00 0.00 4.30
943 967 1.412361 CCTCTCCTAACCCTCCTCCAG 60.412 61.905 0.00 0.00 0.00 3.86
962 986 1.034838 GCCCTTCTCTCGCTCTCTCA 61.035 60.000 0.00 0.00 0.00 3.27
1071 1097 3.311486 AACTTTTCTCTCCTCTCAGCG 57.689 47.619 0.00 0.00 0.00 5.18
1115 1141 4.030452 GCGCACGAAAGCTTGGCT 62.030 61.111 0.30 0.00 42.56 4.75
1140 1166 4.794648 CTTCCCCCAATCGCGCCA 62.795 66.667 0.00 0.00 0.00 5.69
1177 1205 4.582973 AAAGGAGAGGAATTTGGGAGAG 57.417 45.455 0.00 0.00 0.00 3.20
1178 1206 3.498614 AGGAGAGGAATTTGGGAGAGA 57.501 47.619 0.00 0.00 0.00 3.10
1185 1213 5.365314 AGAGGAATTTGGGAGAGAGATGTAC 59.635 44.000 0.00 0.00 0.00 2.90
1573 1601 0.944386 TCTGCGGTGCTTCTTGAAAC 59.056 50.000 0.00 0.00 0.00 2.78
1622 1650 8.617809 GGTAAATTAGTCAATCAATTAGCCGAA 58.382 33.333 0.00 0.00 0.00 4.30
1668 1698 4.717778 TCGGGTGTTTATCTCCTGGATTTA 59.282 41.667 0.00 0.00 36.88 1.40
1823 1854 6.475727 TCACACTTAAAAGACTTCAGACTTCG 59.524 38.462 0.00 0.00 0.00 3.79
1889 1929 7.335422 ACAGTGTCAATTATTTGAGATCTCACC 59.665 37.037 25.07 0.00 42.41 4.02
1890 1930 7.335171 CAGTGTCAATTATTTGAGATCTCACCA 59.665 37.037 25.07 14.92 42.41 4.17
2074 2115 5.332506 CGTCTGAAATTGATTTTGTGTTGCC 60.333 40.000 0.00 0.00 0.00 4.52
2075 2116 5.754890 GTCTGAAATTGATTTTGTGTTGCCT 59.245 36.000 0.00 0.00 0.00 4.75
2137 2181 5.461032 TTTACGATCAATTTGGTGCCTTT 57.539 34.783 0.00 0.00 0.00 3.11
2182 2226 7.087007 TCATCGAAAAGATCCAATCTCTATCG 58.913 38.462 0.00 10.32 39.08 2.92
2186 2230 6.697455 CGAAAAGATCCAATCTCTATCGAACA 59.303 38.462 10.78 0.00 39.08 3.18
2279 2323 0.248054 GCATTACGCATCACCCAACG 60.248 55.000 0.00 0.00 41.79 4.10
2523 2646 2.157279 GCGCTGCATCTAGAGCATTTAG 59.843 50.000 14.58 6.92 42.16 1.85
2534 2657 8.772705 CATCTAGAGCATTTAGGAAATTCAGTC 58.227 37.037 0.00 0.00 0.00 3.51
2536 2659 4.333926 AGAGCATTTAGGAAATTCAGTCGC 59.666 41.667 0.00 0.00 0.00 5.19
2577 2700 4.509600 GCATAGTTTACTGTCATCCAGAGC 59.490 45.833 0.00 0.00 44.49 4.09
2634 2757 5.468746 GTGCTGTCCAGATGTAAACAACTTA 59.531 40.000 0.00 0.00 0.00 2.24
2682 2806 3.953712 TCATTTTACTCGGTCAGCAGA 57.046 42.857 0.00 0.00 0.00 4.26
2966 3115 9.492973 AAAATGGTTTCTTACTCATTCAATTGG 57.507 29.630 5.42 0.00 30.97 3.16
2967 3116 6.588719 TGGTTTCTTACTCATTCAATTGGG 57.411 37.500 5.42 0.00 0.00 4.12
2968 3117 6.074648 TGGTTTCTTACTCATTCAATTGGGT 58.925 36.000 5.42 0.66 33.95 4.51
2969 3118 6.553100 TGGTTTCTTACTCATTCAATTGGGTT 59.447 34.615 5.42 0.00 31.31 4.11
2970 3119 7.726291 TGGTTTCTTACTCATTCAATTGGGTTA 59.274 33.333 5.42 0.00 31.31 2.85
2971 3120 8.581578 GGTTTCTTACTCATTCAATTGGGTTAA 58.418 33.333 5.42 0.00 31.31 2.01
2974 3123 9.527157 TTCTTACTCATTCAATTGGGTTAATGA 57.473 29.630 15.56 15.56 36.32 2.57
2975 3124 8.956426 TCTTACTCATTCAATTGGGTTAATGAC 58.044 33.333 13.46 0.00 34.34 3.06
2976 3125 8.642935 TTACTCATTCAATTGGGTTAATGACA 57.357 30.769 13.46 5.26 34.34 3.58
2977 3126 7.537596 ACTCATTCAATTGGGTTAATGACAA 57.462 32.000 13.46 0.00 34.34 3.18
2978 3127 8.137745 ACTCATTCAATTGGGTTAATGACAAT 57.862 30.769 13.46 3.70 34.34 2.71
3033 3182 2.668550 GTGTTCACCGGCCACTCC 60.669 66.667 0.00 0.00 0.00 3.85
3272 3424 1.877576 CTAGACGCTGTCCCAGTGCA 61.878 60.000 4.78 0.00 44.75 4.57
3319 3471 2.032681 GGCCAGGACACACTCACC 59.967 66.667 0.00 0.00 0.00 4.02
3405 3557 2.669229 CATGTCCGCACAGTGGCA 60.669 61.111 1.84 0.00 35.41 4.92
3432 3584 0.832135 AGAAGCTCGTGGACCCAGAA 60.832 55.000 0.00 0.00 0.00 3.02
3441 3593 2.107141 GACCCAGAATCGCGAGGG 59.893 66.667 25.14 25.14 46.96 4.30
3546 3698 2.812591 CCAGATGCTCTATGCCACATTC 59.187 50.000 0.00 0.00 42.00 2.67
3552 3704 2.896801 CTATGCCACATTCGCCGCC 61.897 63.158 0.00 0.00 0.00 6.13
3559 3711 2.511373 CATTCGCCGCCTGCTACA 60.511 61.111 0.00 0.00 38.05 2.74
3603 3755 1.450312 GGCCGCACACTCTTGCTAT 60.450 57.895 0.00 0.00 40.62 2.97
3609 3761 1.002366 CACACTCTTGCTATGGCGAC 58.998 55.000 0.00 0.00 42.25 5.19
3653 3805 4.400961 GCTCCTCAAGCGGCACCT 62.401 66.667 1.45 0.00 42.21 4.00
3843 3995 3.059982 CTCTCAACACGGCTGGGA 58.940 61.111 0.00 0.00 0.00 4.37
4107 4259 2.887568 GAGCCACTGGACATCGCG 60.888 66.667 0.00 0.00 0.00 5.87
4137 4289 1.388547 GCAACAACCTCCACAAGACA 58.611 50.000 0.00 0.00 0.00 3.41
4611 4819 3.244579 ACAGCGTCGTTGTTTTAGTTCTC 59.755 43.478 9.09 0.00 0.00 2.87
4762 4971 7.174772 ACTGCATTATGTTGTTGTATCAGTTCA 59.825 33.333 0.00 0.00 0.00 3.18
4813 5023 1.266989 GTTGTTTCTTCCTCAAGGCCG 59.733 52.381 0.00 0.00 34.44 6.13
4849 5059 2.715749 TTGAGCATCTGGGTGGTATG 57.284 50.000 0.00 0.00 34.92 2.39
4897 5107 8.083462 TGATATCAAAGTTTACATGATACCGC 57.917 34.615 1.98 5.25 38.48 5.68
4898 5108 7.713073 TGATATCAAAGTTTACATGATACCGCA 59.287 33.333 1.98 6.89 38.48 5.69
4922 5140 7.532884 GCATCTCAAAATTCAAATTTGCAAGTC 59.467 33.333 13.54 0.00 38.53 3.01
4958 5177 9.952030 TCCAACATATGTCTACAATCACTAAAA 57.048 29.630 9.23 0.00 0.00 1.52
5061 5293 8.746052 TTCAATTTTTGAGAACTTCTACTCCA 57.254 30.769 0.00 0.00 41.38 3.86
5062 5294 8.924511 TCAATTTTTGAGAACTTCTACTCCAT 57.075 30.769 0.00 0.00 34.08 3.41
5063 5295 9.003658 TCAATTTTTGAGAACTTCTACTCCATC 57.996 33.333 0.00 0.00 34.08 3.51
5064 5296 9.007901 CAATTTTTGAGAACTTCTACTCCATCT 57.992 33.333 0.00 0.00 32.84 2.90
5065 5297 7.969536 TTTTTGAGAACTTCTACTCCATCTG 57.030 36.000 0.00 0.00 32.84 2.90
5066 5298 6.672266 TTTGAGAACTTCTACTCCATCTGT 57.328 37.500 0.00 0.00 32.84 3.41
5067 5299 5.906113 TGAGAACTTCTACTCCATCTGTC 57.094 43.478 0.00 0.00 32.84 3.51
5068 5300 4.707448 TGAGAACTTCTACTCCATCTGTCC 59.293 45.833 0.00 0.00 32.84 4.02
5069 5301 4.027437 AGAACTTCTACTCCATCTGTCCC 58.973 47.826 0.00 0.00 0.00 4.46
5070 5302 3.474798 ACTTCTACTCCATCTGTCCCA 57.525 47.619 0.00 0.00 0.00 4.37
5071 5303 4.000928 ACTTCTACTCCATCTGTCCCAT 57.999 45.455 0.00 0.00 0.00 4.00
5072 5304 5.144159 ACTTCTACTCCATCTGTCCCATA 57.856 43.478 0.00 0.00 0.00 2.74
5073 5305 5.529289 ACTTCTACTCCATCTGTCCCATAA 58.471 41.667 0.00 0.00 0.00 1.90
5074 5306 6.146760 ACTTCTACTCCATCTGTCCCATAAT 58.853 40.000 0.00 0.00 0.00 1.28
5075 5307 7.306013 ACTTCTACTCCATCTGTCCCATAATA 58.694 38.462 0.00 0.00 0.00 0.98
5076 5308 7.958583 ACTTCTACTCCATCTGTCCCATAATAT 59.041 37.037 0.00 0.00 0.00 1.28
5077 5309 9.480861 CTTCTACTCCATCTGTCCCATAATATA 57.519 37.037 0.00 0.00 0.00 0.86
5078 5310 9.837681 TTCTACTCCATCTGTCCCATAATATAA 57.162 33.333 0.00 0.00 0.00 0.98
5079 5311 9.480861 TCTACTCCATCTGTCCCATAATATAAG 57.519 37.037 0.00 0.00 0.00 1.73
5080 5312 9.480861 CTACTCCATCTGTCCCATAATATAAGA 57.519 37.037 0.00 0.00 0.00 2.10
5081 5313 8.742125 ACTCCATCTGTCCCATAATATAAGAA 57.258 34.615 0.00 0.00 0.00 2.52
5082 5314 8.598041 ACTCCATCTGTCCCATAATATAAGAAC 58.402 37.037 0.00 0.00 0.00 3.01
5083 5315 8.504811 TCCATCTGTCCCATAATATAAGAACA 57.495 34.615 0.00 0.00 0.00 3.18
5084 5316 8.375506 TCCATCTGTCCCATAATATAAGAACAC 58.624 37.037 0.00 0.00 0.00 3.32
5085 5317 8.378565 CCATCTGTCCCATAATATAAGAACACT 58.621 37.037 0.00 0.00 0.00 3.55
5086 5318 9.784531 CATCTGTCCCATAATATAAGAACACTT 57.215 33.333 0.00 0.00 0.00 3.16
5090 5322 9.184523 TGTCCCATAATATAAGAACACTTTTGG 57.815 33.333 0.00 0.00 0.00 3.28
5091 5323 9.185680 GTCCCATAATATAAGAACACTTTTGGT 57.814 33.333 0.00 0.00 0.00 3.67
5153 5385 5.466728 GCAAACTGTGTGAGATGAGTCTTTA 59.533 40.000 1.19 0.00 33.97 1.85
5179 5412 5.033589 TCAAAAGGTGACATTTTTGCCAT 57.966 34.783 5.11 0.00 41.64 4.40
5186 5419 4.091800 GGTGACATTTTTGCCATGAATTCG 59.908 41.667 0.04 0.00 0.00 3.34
5239 5472 4.265056 AACGCCACCCACTCCACC 62.265 66.667 0.00 0.00 0.00 4.61
5268 5501 3.930336 TCTCTCAATCGCAACTGAACAT 58.070 40.909 0.00 0.00 0.00 2.71
5305 5538 5.953571 ACAGGGTTTTTACTCAGGAAGAAT 58.046 37.500 0.00 0.00 0.00 2.40
5327 5560 9.481340 AGAATGAAGAATTTTTGGTAAAAGCTC 57.519 29.630 0.00 0.00 36.73 4.09
5360 5593 4.428209 ACAGACTACAGCATTCTGAATCG 58.572 43.478 0.00 0.00 42.95 3.34
5382 5615 4.148696 CGAAATGACATTTTGGAACACAGC 59.851 41.667 17.34 0.88 39.29 4.40
5386 5619 3.384146 TGACATTTTGGAACACAGCACAT 59.616 39.130 0.00 0.00 39.29 3.21
5448 5681 3.003585 CACTGTGTTGCTTGTATTCAGCA 59.996 43.478 0.00 0.00 36.72 4.41
5449 5682 3.003689 ACTGTGTTGCTTGTATTCAGCAC 59.996 43.478 0.00 0.00 42.32 4.40
5450 5683 3.213506 TGTGTTGCTTGTATTCAGCACT 58.786 40.909 9.79 0.00 42.42 4.40
5451 5684 3.003585 TGTGTTGCTTGTATTCAGCACTG 59.996 43.478 9.79 0.00 42.42 3.66
5453 5686 4.074259 TGTTGCTTGTATTCAGCACTGAT 58.926 39.130 0.31 0.00 39.64 2.90
5454 5687 4.083164 TGTTGCTTGTATTCAGCACTGATG 60.083 41.667 0.31 0.00 39.64 3.07
5455 5688 3.678289 TGCTTGTATTCAGCACTGATGT 58.322 40.909 0.31 0.00 39.64 3.06
5456 5689 3.437741 TGCTTGTATTCAGCACTGATGTG 59.562 43.478 0.31 0.00 46.37 3.21
5580 5819 3.708563 TCACTCATGTCGAATATCGCA 57.291 42.857 0.00 0.00 40.21 5.10
5583 5822 5.954335 TCACTCATGTCGAATATCGCATAT 58.046 37.500 8.54 0.00 40.21 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.933886 ACCATGATAGGAGGAGTGATGT 58.066 45.455 0.00 0.00 0.00 3.06
40 42 1.435925 CTAGATACCGTGTGCCGCA 59.564 57.895 0.00 0.00 34.38 5.69
124 129 2.597510 GAAGCCACCACCACCACC 60.598 66.667 0.00 0.00 0.00 4.61
142 147 2.518933 CCCACAAAACCCGGGAGT 59.481 61.111 32.02 17.03 43.21 3.85
153 158 1.227823 CACCTCTCGTTGCCCACAA 60.228 57.895 0.00 0.00 0.00 3.33
172 177 0.872388 GTCCAAGTTACCCAACGCAG 59.128 55.000 0.00 0.00 39.78 5.18
177 182 1.962306 GCGCGTCCAAGTTACCCAA 60.962 57.895 8.43 0.00 0.00 4.12
256 261 4.697756 CAACGAGGCCGCCAGGAA 62.698 66.667 13.15 0.00 41.02 3.36
280 285 2.329379 CTTTCGCTCAGTAACTCGCTT 58.671 47.619 0.00 0.00 0.00 4.68
283 288 1.983972 AGCTTTCGCTCAGTAACTCG 58.016 50.000 0.00 0.00 45.15 4.18
488 499 1.457823 AACACCCTCACGCTACGACA 61.458 55.000 0.00 0.00 0.00 4.35
500 511 2.052468 ACCGGAAGAACTAAACACCCT 58.948 47.619 9.46 0.00 0.00 4.34
522 535 1.133025 GACTACGCTACCGGCAACTAA 59.867 52.381 0.00 0.00 41.91 2.24
524 537 1.509923 GACTACGCTACCGGCAACT 59.490 57.895 0.00 0.00 41.91 3.16
548 561 7.254252 CCTGAAATATCTGACACACGAAGAATC 60.254 40.741 0.00 0.00 0.00 2.52
549 562 6.536582 CCTGAAATATCTGACACACGAAGAAT 59.463 38.462 0.00 0.00 0.00 2.40
554 568 5.127031 TGATCCTGAAATATCTGACACACGA 59.873 40.000 0.00 0.00 0.00 4.35
561 575 6.656902 ACAAAGCTGATCCTGAAATATCTGA 58.343 36.000 0.00 0.00 0.00 3.27
578 592 2.552367 AGGTAGCCCTCTTACAAAGCT 58.448 47.619 0.00 0.00 35.62 3.74
665 681 8.934023 AAAAGTAATATGGTCTTGAAACAGGA 57.066 30.769 0.00 0.00 0.00 3.86
701 721 8.997323 CCTGAATAGATAACTTGCTTCCAATAG 58.003 37.037 0.00 0.00 0.00 1.73
752 776 6.982852 TCGTAGGGAAAATGCAATGTTTTAA 58.017 32.000 0.00 0.00 0.00 1.52
753 777 6.431543 TCTCGTAGGGAAAATGCAATGTTTTA 59.568 34.615 0.00 0.00 0.00 1.52
798 822 2.606108 GACTTTGCATTTAAAGGCCCG 58.394 47.619 21.02 11.84 39.31 6.13
868 892 4.218686 GGTGTGGTGGGGGCAACT 62.219 66.667 0.00 0.00 0.00 3.16
938 962 2.015227 GAGCGAGAGAAGGGCTGGAG 62.015 65.000 0.00 0.00 37.10 3.86
943 967 1.034838 TGAGAGAGCGAGAGAAGGGC 61.035 60.000 0.00 0.00 0.00 5.19
1071 1097 3.057315 TGCGCCGGGAAGTACTTATATAC 60.057 47.826 8.42 0.00 0.00 1.47
1115 1141 1.681780 CGATTGGGGGAAGCTAAAGCA 60.682 52.381 4.54 0.00 45.16 3.91
1127 1153 1.737355 AAATCATGGCGCGATTGGGG 61.737 55.000 12.10 0.00 33.41 4.96
1140 1166 6.139679 TCTCCTTTTCTACCACCAAATCAT 57.860 37.500 0.00 0.00 0.00 2.45
1177 1205 4.727507 TTTCAGCTCCTCTGTACATCTC 57.272 45.455 0.00 0.00 43.32 2.75
1178 1206 5.426504 CATTTTCAGCTCCTCTGTACATCT 58.573 41.667 0.00 0.00 43.32 2.90
1185 1213 1.129998 CACGCATTTTCAGCTCCTCTG 59.870 52.381 0.00 0.00 44.21 3.35
1573 1601 4.463879 CTCAGGGGAGCCGCACAG 62.464 72.222 6.35 0.00 33.67 3.66
1622 1650 8.890718 CCGATTAAATGCTGATTGATGAGATAT 58.109 33.333 0.00 0.00 0.00 1.63
1623 1651 7.335171 CCCGATTAAATGCTGATTGATGAGATA 59.665 37.037 0.00 0.00 0.00 1.98
1668 1698 8.125978 TCACAAGGAAAAATGATTAAGCTGAT 57.874 30.769 0.00 0.00 0.00 2.90
1725 1755 1.146263 GGCCCATAGGACCAGAACG 59.854 63.158 0.00 0.00 33.41 3.95
2074 2115 9.073475 AGAAGATATACACTGAACTAGCCTTAG 57.927 37.037 0.00 0.00 0.00 2.18
2075 2116 8.998277 AGAAGATATACACTGAACTAGCCTTA 57.002 34.615 0.00 0.00 0.00 2.69
2137 2181 8.085909 TCGATGAACTTACAAACTCTATGTCAA 58.914 33.333 0.00 0.00 32.27 3.18
2182 2226 3.064324 AAGCTGGCCGCCATGTTC 61.064 61.111 13.86 2.85 40.39 3.18
2186 2230 3.052909 ATCTCAAGCTGGCCGCCAT 62.053 57.895 13.86 0.00 40.39 4.40
2279 2323 8.616076 ACAAAATAGCAATAGCATACAGACTTC 58.384 33.333 0.00 0.00 45.49 3.01
2503 2626 2.735663 CCTAAATGCTCTAGATGCAGCG 59.264 50.000 17.79 8.98 44.04 5.18
2523 2646 1.750193 TCATGGGCGACTGAATTTCC 58.250 50.000 0.00 0.00 0.00 3.13
2534 2657 3.814842 TGCACTATTATTCTTCATGGGCG 59.185 43.478 0.00 0.00 0.00 6.13
2536 2659 8.627208 AACTATGCACTATTATTCTTCATGGG 57.373 34.615 0.00 0.00 0.00 4.00
2577 2700 8.565416 AGTATATGTCATCAAAATCAGCATGTG 58.435 33.333 0.00 0.00 37.40 3.21
2596 2719 5.604565 TGGACAGCACATGAAGAGTATATG 58.395 41.667 0.00 0.00 0.00 1.78
2660 2784 4.268884 GTCTGCTGACCGAGTAAAATGATC 59.731 45.833 12.42 0.00 37.24 2.92
2682 2806 7.442969 TGTCAAGAAACAATTAAGGTCGTATGT 59.557 33.333 0.00 0.00 0.00 2.29
2964 3113 5.754782 AGCATCTGTATTGTCATTAACCCA 58.245 37.500 0.00 0.00 0.00 4.51
2965 3114 6.992715 AGTAGCATCTGTATTGTCATTAACCC 59.007 38.462 0.00 0.00 0.00 4.11
2966 3115 9.542462 TTAGTAGCATCTGTATTGTCATTAACC 57.458 33.333 0.00 0.00 0.00 2.85
2970 3119 9.836864 TGATTTAGTAGCATCTGTATTGTCATT 57.163 29.630 0.00 0.00 0.00 2.57
2971 3120 9.486497 CTGATTTAGTAGCATCTGTATTGTCAT 57.514 33.333 0.00 0.00 0.00 3.06
2972 3121 8.695456 TCTGATTTAGTAGCATCTGTATTGTCA 58.305 33.333 0.00 0.00 0.00 3.58
2973 3122 9.703892 ATCTGATTTAGTAGCATCTGTATTGTC 57.296 33.333 0.00 0.00 0.00 3.18
2974 3123 9.703892 GATCTGATTTAGTAGCATCTGTATTGT 57.296 33.333 0.00 0.00 0.00 2.71
2975 3124 9.149225 GGATCTGATTTAGTAGCATCTGTATTG 57.851 37.037 0.00 0.00 0.00 1.90
2976 3125 8.031864 CGGATCTGATTTAGTAGCATCTGTATT 58.968 37.037 0.00 0.00 0.00 1.89
2977 3126 7.363355 CCGGATCTGATTTAGTAGCATCTGTAT 60.363 40.741 2.08 0.00 0.00 2.29
2978 3127 6.071896 CCGGATCTGATTTAGTAGCATCTGTA 60.072 42.308 2.08 0.00 0.00 2.74
3033 3182 4.899239 GCGATGGCTCCACCGAGG 62.899 72.222 6.89 0.00 43.94 4.63
3272 3424 1.869754 GCTGCATACCGATGATGACGT 60.870 52.381 0.00 0.00 34.73 4.34
3399 3551 0.964358 GCTTCTGCTCCATTGCCACT 60.964 55.000 0.00 0.00 36.03 4.00
3441 3593 3.477346 GGACGGTAAGGGCTCCCC 61.477 72.222 0.32 0.00 45.90 4.81
3603 3755 0.749818 TTTTCAGCACAAGGTCGCCA 60.750 50.000 0.00 0.00 0.00 5.69
3609 3761 1.068895 TGTGGCATTTTCAGCACAAGG 59.931 47.619 0.00 0.00 0.00 3.61
3650 3802 2.438975 CGTCCATGGCATGCAGGT 60.439 61.111 22.02 0.92 0.00 4.00
3653 3805 1.603171 AACACGTCCATGGCATGCA 60.603 52.632 22.02 3.98 0.00 3.96
3843 3995 2.501128 CGGCATGGAGTGATCCGT 59.499 61.111 0.00 0.00 35.75 4.69
4107 4259 1.084289 GGTTGTTGCGGTGATAGTCC 58.916 55.000 0.00 0.00 0.00 3.85
4137 4289 1.522569 GGTGATGTAGCCGCCTCTT 59.477 57.895 0.00 0.00 0.00 2.85
4507 4715 3.554692 GGCGCAAGGACGTCGATG 61.555 66.667 10.83 11.85 38.28 3.84
4611 4819 4.750952 CTGCTCCAGCTAATTCATCATG 57.249 45.455 0.00 0.00 42.66 3.07
4690 4899 3.429881 GCGTATTTACAACCGCCTATACC 59.570 47.826 0.00 0.00 40.25 2.73
4804 5014 1.927174 CAGATTAACGTCGGCCTTGAG 59.073 52.381 0.00 0.00 0.00 3.02
4813 5023 6.048073 TGCTCAATAATGCAGATTAACGTC 57.952 37.500 0.00 0.00 34.84 4.34
4849 5059 2.246719 GCTGATCATACAGGGACACC 57.753 55.000 0.00 0.00 38.22 4.16
4882 5092 5.984233 TTGAGATGCGGTATCATGTAAAC 57.016 39.130 8.78 0.00 38.31 2.01
4897 5107 8.770828 AGACTTGCAAATTTGAATTTTGAGATG 58.229 29.630 22.31 6.56 36.52 2.90
4898 5108 8.897872 AGACTTGCAAATTTGAATTTTGAGAT 57.102 26.923 22.31 0.00 36.52 2.75
5060 5292 9.784531 AAGTGTTCTTATATTATGGGACAGATG 57.215 33.333 0.00 0.00 34.77 2.90
5064 5296 9.184523 CCAAAAGTGTTCTTATATTATGGGACA 57.815 33.333 0.00 0.00 36.45 4.02
5065 5297 9.185680 ACCAAAAGTGTTCTTATATTATGGGAC 57.814 33.333 0.00 0.00 33.09 4.46
5087 5319 9.575868 TGTCTCCAAATGTTAATTTACTACCAA 57.424 29.630 0.00 0.00 34.14 3.67
5088 5320 9.747898 ATGTCTCCAAATGTTAATTTACTACCA 57.252 29.630 0.00 0.00 34.14 3.25
5102 5334 9.551734 TTGATCTAGAATACATGTCTCCAAATG 57.448 33.333 0.00 0.00 0.00 2.32
5153 5385 5.759763 GGCAAAAATGTCACCTTTTGATTCT 59.240 36.000 19.24 0.00 42.53 2.40
5159 5391 5.033589 TCATGGCAAAAATGTCACCTTTT 57.966 34.783 0.00 0.00 0.00 2.27
5179 5412 7.041721 AGAATACTGTAAGCATCACGAATTCA 58.958 34.615 6.22 0.00 37.60 2.57
5186 5419 9.352784 GATGATCTAGAATACTGTAAGCATCAC 57.647 37.037 0.00 0.00 37.60 3.06
5254 5487 5.724328 TCTCTTAAGATGTTCAGTTGCGAT 58.276 37.500 5.44 0.00 0.00 4.58
5305 5538 7.920682 GTGAGAGCTTTTACCAAAAATTCTTCA 59.079 33.333 0.00 0.00 34.18 3.02
5323 5556 4.946478 AGTCTGTAAGTTTGTGAGAGCT 57.054 40.909 0.00 0.00 33.76 4.09
5327 5560 5.289595 TGCTGTAGTCTGTAAGTTTGTGAG 58.710 41.667 0.00 0.00 33.76 3.51
5360 5593 5.049167 TGCTGTGTTCCAAAATGTCATTTC 58.951 37.500 11.19 0.00 0.00 2.17
5382 5615 7.286508 GCTTCGTTGTCAATCAGATATATGTG 58.713 38.462 3.46 3.46 0.00 3.21
5386 5619 5.827666 TCGCTTCGTTGTCAATCAGATATA 58.172 37.500 0.00 0.00 0.00 0.86
5448 5681 2.224597 TGTTCCTGACATGCACATCAGT 60.225 45.455 21.64 3.37 40.70 3.41
5449 5682 2.418976 CTGTTCCTGACATGCACATCAG 59.581 50.000 18.21 18.21 41.75 2.90
5450 5683 2.038820 TCTGTTCCTGACATGCACATCA 59.961 45.455 0.00 0.00 37.69 3.07
5451 5684 2.417933 GTCTGTTCCTGACATGCACATC 59.582 50.000 0.00 0.00 37.69 3.06
5453 5686 1.417517 AGTCTGTTCCTGACATGCACA 59.582 47.619 0.00 0.00 37.69 4.57
5454 5687 2.175878 AGTCTGTTCCTGACATGCAC 57.824 50.000 0.00 0.00 37.69 4.57
5455 5688 4.558226 ATTAGTCTGTTCCTGACATGCA 57.442 40.909 0.00 0.00 37.69 3.96
5456 5689 6.283694 TGATATTAGTCTGTTCCTGACATGC 58.716 40.000 0.00 0.00 37.69 4.06
5457 5690 6.423302 GCTGATATTAGTCTGTTCCTGACATG 59.577 42.308 0.00 0.00 37.69 3.21
5545 5784 1.215647 GTGATGAGTCGGTCCGCTT 59.784 57.895 6.34 0.00 0.00 4.68
5580 5819 3.983494 AGCGCGCCGAGCTCATAT 61.983 61.111 30.33 0.79 41.83 1.78


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

AutoCloner maintained by Alex Coulton.