Multiple sequence alignment - TraesCS1D01G128000

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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 TraesCS1D01G128000 chr1D 100.000 4839 0 0 1 4839 141273457 141278295 0.000000e+00 8937.0
1 TraesCS1D01G128000 chr1D 91.833 502 39 2 4337 4837 262846530 262847030 0.000000e+00 699.0
2 TraesCS1D01G128000 chr1B 95.934 2607 68 10 220 2798 196465820 196463224 0.000000e+00 4193.0
3 TraesCS1D01G128000 chr1B 95.166 1262 36 5 2792 4030 196463147 196461888 0.000000e+00 1969.0
4 TraesCS1D01G128000 chr1A 94.862 1557 37 9 200 1724 149515600 149514055 0.000000e+00 2392.0
5 TraesCS1D01G128000 chr1A 94.975 1393 43 11 1789 3162 149513465 149512081 0.000000e+00 2159.0
6 TraesCS1D01G128000 chr1A 93.255 1364 64 13 3421 4780 149510847 149509508 0.000000e+00 1984.0
7 TraesCS1D01G128000 chr1A 97.535 284 7 0 3155 3438 149511148 149510865 2.020000e-133 486.0
8 TraesCS1D01G128000 chr3D 92.490 506 38 0 4334 4839 370207987 370207482 0.000000e+00 725.0
9 TraesCS1D01G128000 chr3D 92.000 500 39 1 4337 4835 467510794 467510295 0.000000e+00 701.0
10 TraesCS1D01G128000 chr3D 91.176 68 5 1 4271 4337 363308637 363308704 1.850000e-14 91.6
11 TraesCS1D01G128000 chr5D 92.786 499 35 1 4338 4835 224859535 224860033 0.000000e+00 721.0
12 TraesCS1D01G128000 chr4A 92.585 499 37 0 4337 4835 61099942 61100440 0.000000e+00 717.0
13 TraesCS1D01G128000 chr4B 92.400 500 38 0 4338 4837 433069266 433069765 0.000000e+00 713.0
14 TraesCS1D01G128000 chr5A 91.881 505 40 1 4336 4839 484553969 484553465 0.000000e+00 704.0
15 TraesCS1D01G128000 chr6D 91.667 504 42 0 4334 4837 394370062 394370565 0.000000e+00 699.0
16 TraesCS1D01G128000 chr4D 91.816 501 41 0 4337 4837 102844922 102844422 0.000000e+00 699.0
17 TraesCS1D01G128000 chr4D 94.444 72 2 2 4268 4337 451244498 451244427 5.120000e-20 110.0
18 TraesCS1D01G128000 chr4D 91.176 68 5 1 4271 4337 64834759 64834826 1.850000e-14 91.6
19 TraesCS1D01G128000 chr7A 94.118 68 3 1 4271 4337 405886272 405886205 8.570000e-18 102.0
20 TraesCS1D01G128000 chr7A 92.647 68 4 1 4271 4337 142341989 142342056 3.990000e-16 97.1
21 TraesCS1D01G128000 chr6B 94.118 68 3 1 4271 4337 384498929 384498862 8.570000e-18 102.0
22 TraesCS1D01G128000 chr7B 92.647 68 4 1 4271 4337 95986944 95986877 3.990000e-16 97.1
23 TraesCS1D01G128000 chr5B 92.647 68 4 1 4271 4337 103940453 103940520 3.990000e-16 97.1
24 TraesCS1D01G128000 chr3A 92.647 68 4 1 4271 4337 581282957 581283024 3.990000e-16 97.1


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 TraesCS1D01G128000 chr1D 141273457 141278295 4838 False 8937.00 8937 100.00000 1 4839 1 chr1D.!!$F1 4838
1 TraesCS1D01G128000 chr1D 262846530 262847030 500 False 699.00 699 91.83300 4337 4837 1 chr1D.!!$F2 500
2 TraesCS1D01G128000 chr1B 196461888 196465820 3932 True 3081.00 4193 95.55000 220 4030 2 chr1B.!!$R1 3810
3 TraesCS1D01G128000 chr1A 149509508 149515600 6092 True 1755.25 2392 95.15675 200 4780 4 chr1A.!!$R1 4580
4 TraesCS1D01G128000 chr3D 370207482 370207987 505 True 725.00 725 92.49000 4334 4839 1 chr3D.!!$R1 505
5 TraesCS1D01G128000 chr5A 484553465 484553969 504 True 704.00 704 91.88100 4336 4839 1 chr5A.!!$R1 503
6 TraesCS1D01G128000 chr6D 394370062 394370565 503 False 699.00 699 91.66700 4334 4837 1 chr6D.!!$F1 503
7 TraesCS1D01G128000 chr4D 102844422 102844922 500 True 699.00 699 91.81600 4337 4837 1 chr4D.!!$R1 500

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
800 850 0.029567 GGATCACGTCCGCTCTAGTG 59.970 60.000 0.0 0.0 37.23 2.74 F
1114 1164 0.366871 CACATACTGTGTTCGCTCGC 59.633 55.000 0.0 0.0 43.08 5.03 F
1285 1338 0.752743 CGATACTGGTGTCCGGGGTA 60.753 60.000 0.0 0.0 33.40 3.69 F
2113 2692 1.899814 TGGAACGACCACAGCTTCTAT 59.100 47.619 0.0 0.0 44.64 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2607 3196 1.636003 GAAGGTCAACCCTCCTCCATT 59.364 52.381 0.00 0.00 45.47 3.16 R
2992 3666 0.972883 AGTTGCTCCTGGAGAGTGAC 59.027 55.000 27.53 16.98 45.21 3.67 R
3171 4795 3.770933 GCAATGTGGATGGGGCATATAAT 59.229 43.478 0.00 0.00 0.00 1.28 R
3870 5543 1.133598 CAGTATGTTCGGACGTAGGCA 59.866 52.381 0.00 0.00 0.00 4.75 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
25 26 8.561738 GATGACCAAGAACATAGACCTTTTAA 57.438 34.615 0.00 0.00 0.00 1.52
26 27 8.934023 ATGACCAAGAACATAGACCTTTTAAA 57.066 30.769 0.00 0.00 0.00 1.52
27 28 8.754991 TGACCAAGAACATAGACCTTTTAAAA 57.245 30.769 0.00 0.00 0.00 1.52
28 29 9.191479 TGACCAAGAACATAGACCTTTTAAAAA 57.809 29.630 1.66 0.00 0.00 1.94
35 36 9.983804 GAACATAGACCTTTTAAAAATACGAGG 57.016 33.333 1.66 1.11 0.00 4.63
36 37 9.511272 AACATAGACCTTTTAAAAATACGAGGT 57.489 29.630 6.70 6.70 40.04 3.85
39 40 6.187125 GACCTTTTAAAAATACGAGGTCCC 57.813 41.667 18.06 1.92 44.59 4.46
40 41 5.012239 ACCTTTTAAAAATACGAGGTCCCC 58.988 41.667 1.66 0.00 32.25 4.81
41 42 5.222192 ACCTTTTAAAAATACGAGGTCCCCT 60.222 40.000 1.66 0.00 32.25 4.79
42 43 5.124936 CCTTTTAAAAATACGAGGTCCCCTG 59.875 44.000 1.66 0.00 31.76 4.45
43 44 2.124277 AAAAATACGAGGTCCCCTGC 57.876 50.000 0.00 0.00 31.76 4.85
44 45 0.255033 AAAATACGAGGTCCCCTGCC 59.745 55.000 0.00 0.00 31.76 4.85
45 46 0.620700 AAATACGAGGTCCCCTGCCT 60.621 55.000 0.00 0.00 39.42 4.75
46 47 1.049289 AATACGAGGTCCCCTGCCTC 61.049 60.000 0.00 1.50 46.75 4.70
49 50 2.039624 GAGGTCCCCTGCCTCTCA 59.960 66.667 4.26 0.00 46.71 3.27
50 51 2.040278 AGGTCCCCTGCCTCTCAG 59.960 66.667 0.00 0.00 42.49 3.35
51 52 3.791586 GGTCCCCTGCCTCTCAGC 61.792 72.222 0.00 0.00 41.50 4.26
52 53 4.154347 GTCCCCTGCCTCTCAGCG 62.154 72.222 0.00 0.00 41.50 5.18
55 56 4.834453 CCCTGCCTCTCAGCGCTG 62.834 72.222 31.53 31.53 41.50 5.18
56 57 3.767806 CCTGCCTCTCAGCGCTGA 61.768 66.667 35.97 35.97 41.50 4.26
65 66 1.153686 TCAGCGCTGAGATGTGAGC 60.154 57.895 35.30 0.00 37.54 4.26
66 67 2.172372 CAGCGCTGAGATGTGAGCC 61.172 63.158 33.66 0.00 30.98 4.70
67 68 3.260483 GCGCTGAGATGTGAGCCG 61.260 66.667 0.00 0.00 30.98 5.52
68 69 2.491621 CGCTGAGATGTGAGCCGA 59.508 61.111 0.00 0.00 30.98 5.54
69 70 1.153765 CGCTGAGATGTGAGCCGAA 60.154 57.895 0.00 0.00 30.98 4.30
70 71 1.144565 CGCTGAGATGTGAGCCGAAG 61.145 60.000 0.00 0.00 30.98 3.79
125 126 3.118454 GCGGCTGCAGCTAACGAA 61.118 61.111 35.82 0.00 42.15 3.85
126 127 2.677003 GCGGCTGCAGCTAACGAAA 61.677 57.895 35.82 0.00 42.15 3.46
127 128 1.132640 CGGCTGCAGCTAACGAAAC 59.867 57.895 35.82 16.98 41.70 2.78
128 129 1.502190 GGCTGCAGCTAACGAAACC 59.498 57.895 35.82 14.01 41.70 3.27
129 130 1.502190 GCTGCAGCTAACGAAACCC 59.498 57.895 31.33 0.00 38.21 4.11
130 131 0.955919 GCTGCAGCTAACGAAACCCT 60.956 55.000 31.33 0.00 38.21 4.34
131 132 1.079503 CTGCAGCTAACGAAACCCTC 58.920 55.000 0.00 0.00 0.00 4.30
139 140 3.562635 CGAAACCCTCGGAAGCAC 58.437 61.111 0.00 0.00 44.20 4.40
140 141 2.380410 CGAAACCCTCGGAAGCACG 61.380 63.158 0.00 0.00 44.20 5.34
141 142 2.668550 AAACCCTCGGAAGCACGC 60.669 61.111 0.00 0.00 0.00 5.34
142 143 4.699522 AACCCTCGGAAGCACGCC 62.700 66.667 0.00 0.00 0.00 5.68
144 145 3.458163 CCCTCGGAAGCACGCCTA 61.458 66.667 0.00 0.00 0.00 3.93
145 146 2.577059 CCTCGGAAGCACGCCTAA 59.423 61.111 0.00 0.00 0.00 2.69
146 147 1.810030 CCTCGGAAGCACGCCTAAC 60.810 63.158 0.00 0.00 0.00 2.34
147 148 1.810030 CTCGGAAGCACGCCTAACC 60.810 63.158 0.00 0.00 0.00 2.85
148 149 2.227089 CTCGGAAGCACGCCTAACCT 62.227 60.000 0.00 0.00 0.00 3.50
149 150 1.810030 CGGAAGCACGCCTAACCTC 60.810 63.158 0.00 0.00 0.00 3.85
150 151 1.295423 GGAAGCACGCCTAACCTCA 59.705 57.895 0.00 0.00 0.00 3.86
151 152 0.741221 GGAAGCACGCCTAACCTCAG 60.741 60.000 0.00 0.00 0.00 3.35
152 153 0.246635 GAAGCACGCCTAACCTCAGA 59.753 55.000 0.00 0.00 0.00 3.27
153 154 0.905357 AAGCACGCCTAACCTCAGAT 59.095 50.000 0.00 0.00 0.00 2.90
154 155 0.905357 AGCACGCCTAACCTCAGATT 59.095 50.000 0.00 0.00 0.00 2.40
155 156 1.279271 AGCACGCCTAACCTCAGATTT 59.721 47.619 0.00 0.00 0.00 2.17
156 157 2.084546 GCACGCCTAACCTCAGATTTT 58.915 47.619 0.00 0.00 0.00 1.82
157 158 2.488153 GCACGCCTAACCTCAGATTTTT 59.512 45.455 0.00 0.00 0.00 1.94
178 179 4.974645 TTTTGAGAAGAGCCTAACCTCA 57.025 40.909 0.00 0.00 34.26 3.86
179 180 4.543590 TTTGAGAAGAGCCTAACCTCAG 57.456 45.455 0.00 0.00 35.60 3.35
180 181 3.458044 TGAGAAGAGCCTAACCTCAGA 57.542 47.619 0.00 0.00 34.26 3.27
181 182 3.987745 TGAGAAGAGCCTAACCTCAGAT 58.012 45.455 0.00 0.00 34.26 2.90
182 183 4.357325 TGAGAAGAGCCTAACCTCAGATT 58.643 43.478 0.00 0.00 34.26 2.40
183 184 4.780021 TGAGAAGAGCCTAACCTCAGATTT 59.220 41.667 0.00 0.00 34.26 2.17
184 185 5.249393 TGAGAAGAGCCTAACCTCAGATTTT 59.751 40.000 0.00 0.00 34.26 1.82
185 186 6.133253 AGAAGAGCCTAACCTCAGATTTTT 57.867 37.500 0.00 0.00 34.26 1.94
212 213 5.441718 TTGAGAAATGCCTAACCTCAGAT 57.558 39.130 0.00 0.00 35.60 2.90
225 226 7.254932 GCCTAACCTCAGATGAAATATGAACAC 60.255 40.741 0.00 0.00 44.97 3.32
237 239 5.890110 AATATGAACACTCGTAATCGCAG 57.110 39.130 0.00 0.00 36.96 5.18
263 272 1.216977 CGTATTCTGTGACCCGGCA 59.783 57.895 0.00 0.00 0.00 5.69
293 302 1.084370 CCATCGTTCTGAAGGCCGAC 61.084 60.000 0.00 0.00 31.43 4.79
386 398 1.068474 GTCGACATCGTTTCCCACTG 58.932 55.000 11.55 0.00 40.80 3.66
448 460 1.135094 AACCTCCGCCATCTCATGAT 58.865 50.000 0.00 0.00 0.00 2.45
579 591 1.609841 CCCCCTTGGAGAACAACGTAC 60.610 57.143 0.00 0.00 34.76 3.67
639 651 0.091344 CACGAATCGACGTTCAGCAC 59.909 55.000 10.55 0.00 44.76 4.40
736 786 2.319890 AAACGCGACCTGACAACCCT 62.320 55.000 15.93 0.00 0.00 4.34
800 850 0.029567 GGATCACGTCCGCTCTAGTG 59.970 60.000 0.00 0.00 37.23 2.74
909 959 2.514592 AAGGCATCCACCGCATCG 60.515 61.111 0.00 0.00 33.69 3.84
956 1006 3.522553 ACGAATCCATCTTTTCCGAGAC 58.477 45.455 0.00 0.00 0.00 3.36
999 1049 2.279784 GCTCGGGATTCTCAGGCG 60.280 66.667 0.00 0.00 0.00 5.52
1114 1164 0.366871 CACATACTGTGTTCGCTCGC 59.633 55.000 0.00 0.00 43.08 5.03
1116 1166 1.336887 ACATACTGTGTTCGCTCGCTT 60.337 47.619 0.00 0.00 38.01 4.68
1117 1167 1.726791 CATACTGTGTTCGCTCGCTTT 59.273 47.619 0.00 0.00 0.00 3.51
1118 1168 1.136690 TACTGTGTTCGCTCGCTTTG 58.863 50.000 0.00 0.00 0.00 2.77
1121 1171 1.082756 GTGTTCGCTCGCTTTGTGG 60.083 57.895 0.00 0.00 0.00 4.17
1122 1172 1.522806 TGTTCGCTCGCTTTGTGGT 60.523 52.632 0.00 0.00 0.00 4.16
1138 1188 1.860950 GTGGTTGATCCGATCGATGTG 59.139 52.381 18.66 0.00 39.52 3.21
1285 1338 0.752743 CGATACTGGTGTCCGGGGTA 60.753 60.000 0.00 0.00 33.40 3.69
1450 1503 4.608514 TCCAACCCCTGCCTCCCA 62.609 66.667 0.00 0.00 0.00 4.37
1507 1560 3.270839 GCCATGCTCGCTGCTCTC 61.271 66.667 0.00 0.00 43.37 3.20
1534 1587 2.338015 GGTGCTCGACGTCCTGGTA 61.338 63.158 10.58 0.00 0.00 3.25
1730 1783 2.125952 CGCATGGTCACGAGCTGA 60.126 61.111 0.00 0.00 0.00 4.26
1935 2513 2.584391 GCTTGGGGTGTCTCGGAGT 61.584 63.158 4.69 0.00 0.00 3.85
2044 2622 6.429385 GGTGAGGAATTCAGTATGGATTGATC 59.571 42.308 7.93 0.00 46.50 2.92
2113 2692 1.899814 TGGAACGACCACAGCTTCTAT 59.100 47.619 0.00 0.00 44.64 1.98
2121 2708 3.490348 ACCACAGCTTCTATTGTTTGCT 58.510 40.909 0.00 0.00 0.00 3.91
2194 2781 5.467399 CCATTTTTCACAGTGATGCAACATT 59.533 36.000 3.45 0.00 0.00 2.71
2195 2782 6.347079 CCATTTTTCACAGTGATGCAACATTC 60.347 38.462 3.45 0.00 0.00 2.67
2309 2898 3.079578 CACATGCAACAGAGAAGGATGT 58.920 45.455 0.00 0.00 43.65 3.06
2368 2957 8.202137 AGCTGGAAATATCAAGATTTTCATTGG 58.798 33.333 14.04 6.85 34.49 3.16
2509 3098 2.025605 ACATGAGCTGTCAATCCACCAT 60.026 45.455 0.00 0.00 35.88 3.55
2581 3170 7.499232 ACTTGCATGTAGTTCTAGTTTTTGTCT 59.501 33.333 2.92 0.00 0.00 3.41
2607 3196 4.837860 AGGGATTGCACCTTTGTTAATTGA 59.162 37.500 0.00 0.00 33.64 2.57
2672 3261 2.496899 AATTTGAGGCTGTGATCGGT 57.503 45.000 0.00 0.00 0.00 4.69
2902 3575 3.200605 TCTGTGATGAGGCACATAACCAT 59.799 43.478 9.57 0.00 46.64 3.55
2981 3655 7.681168 TCCTTCTAAAACTTTAGGTCCAGGATA 59.319 37.037 8.90 0.00 40.35 2.59
2983 3657 9.384764 CTTCTAAAACTTTAGGTCCAGGATAAG 57.615 37.037 8.90 0.00 40.35 1.73
2992 3666 2.359900 GTCCAGGATAAGTTGTGGCTG 58.640 52.381 0.00 0.00 0.00 4.85
3036 3710 6.203530 TGTCTGCTACTGAACTCTTTTGATTG 59.796 38.462 0.00 0.00 0.00 2.67
3091 3774 4.393680 ACTCAACGCTTAATCGGCAAAATA 59.606 37.500 3.51 0.00 0.00 1.40
3153 3837 9.832445 CTTCCAAATAACTTGCTCTTATACCTA 57.168 33.333 0.00 0.00 33.27 3.08
3168 4792 8.625786 TCTTATACCTATATGTGCAACGTCTA 57.374 34.615 0.00 0.00 42.39 2.59
3171 4795 5.333299 ACCTATATGTGCAACGTCTAACA 57.667 39.130 0.00 0.00 42.39 2.41
3214 4838 3.056821 GCTCCCTGGTGTTTCCAAAATAC 60.057 47.826 0.00 0.00 46.59 1.89
3318 4942 7.439356 CACTAAAATCAGACGATCATACCACAT 59.561 37.037 0.00 0.00 0.00 3.21
3373 4997 7.917597 TGTTTAAGTTGCTAATGTGACGTAAA 58.082 30.769 0.00 0.00 0.00 2.01
3571 5244 1.450134 GGCAGTCATGATGGCGTCA 60.450 57.895 12.53 12.53 42.06 4.35
3661 5334 1.616628 CCCCAGGGCTCTAGTGGTT 60.617 63.158 0.00 0.00 0.00 3.67
3676 5349 0.911769 TGGTTGAAGGCATCCTCGAT 59.088 50.000 0.00 0.00 35.36 3.59
3811 5484 0.898326 TGTTCCTAGGTGCGCTCTCA 60.898 55.000 9.73 0.00 0.00 3.27
3870 5543 0.178987 AGATGGAGGTAGCGGACGAT 60.179 55.000 0.00 0.00 0.00 3.73
3994 5667 0.622136 ATGGGCATGAGAGAACAGCA 59.378 50.000 0.00 0.00 0.00 4.41
4055 5728 6.816640 TGTGTATACTCTTGCTAAATCACCAC 59.183 38.462 4.17 0.00 0.00 4.16
4056 5729 6.816640 GTGTATACTCTTGCTAAATCACCACA 59.183 38.462 4.17 0.00 0.00 4.17
4057 5730 7.333423 GTGTATACTCTTGCTAAATCACCACAA 59.667 37.037 4.17 0.00 0.00 3.33
4058 5731 6.992063 ATACTCTTGCTAAATCACCACAAG 57.008 37.500 0.00 0.00 39.22 3.16
4060 5733 3.485394 TCTTGCTAAATCACCACAAGCA 58.515 40.909 0.00 0.00 41.19 3.91
4061 5734 4.081406 TCTTGCTAAATCACCACAAGCAT 58.919 39.130 0.00 0.00 42.34 3.79
4106 5779 2.410939 GACGACAGTGGTTTTCCTACC 58.589 52.381 0.00 0.00 41.38 3.18
4107 5780 1.764134 ACGACAGTGGTTTTCCTACCA 59.236 47.619 0.00 0.00 45.73 3.25
4132 5805 3.011085 CATGCATGCATCTACCGGT 57.989 52.632 30.07 13.98 33.90 5.28
4208 5881 6.631971 TTCAGAGTGTTGCATAATGTTTCA 57.368 33.333 0.00 0.00 0.00 2.69
4235 5908 9.256477 GTAGTTTTATTTTCTTGTTCCAAAGGG 57.744 33.333 0.00 0.00 0.00 3.95
4239 5912 9.990360 TTTTATTTTCTTGTTCCAAAGGGTATC 57.010 29.630 0.00 0.00 34.93 2.24
4285 5958 3.478540 GCTAAATGCCCGAGGTCTT 57.521 52.632 0.00 0.00 35.15 3.01
4286 5959 1.300481 GCTAAATGCCCGAGGTCTTC 58.700 55.000 0.00 0.00 35.15 2.87
4287 5960 1.406887 GCTAAATGCCCGAGGTCTTCA 60.407 52.381 0.00 0.00 35.15 3.02
4288 5961 2.746472 GCTAAATGCCCGAGGTCTTCAT 60.746 50.000 0.00 0.00 35.15 2.57
4289 5962 3.494398 GCTAAATGCCCGAGGTCTTCATA 60.494 47.826 0.00 0.00 35.15 2.15
4306 5979 7.769044 GGTCTTCATAAGCAAGTAAGTTGGATA 59.231 37.037 0.00 0.00 36.56 2.59
4325 5998 4.390909 GGATACACACCCACTTAGTTTTCG 59.609 45.833 0.00 0.00 0.00 3.46
4351 6024 5.012239 TGAGCTTTCTGTTGGAAATATGCT 58.988 37.500 0.00 0.00 42.03 3.79
4481 6154 4.929479 ACATAAGCAAATACCAAGTCCCA 58.071 39.130 0.00 0.00 0.00 4.37
4483 6156 5.777732 ACATAAGCAAATACCAAGTCCCAAA 59.222 36.000 0.00 0.00 0.00 3.28
4505 6178 7.014808 CCAAATAAGCCTCTACTAGACTAGCTT 59.985 40.741 9.52 9.10 41.59 3.74
4531 6204 8.482128 TGTTGATCAAAAGATGGTTAAGGTTTT 58.518 29.630 10.35 0.00 0.00 2.43
4627 6300 6.883217 CCCATCTGTTAGCTTAGCATATGATT 59.117 38.462 6.97 0.00 29.20 2.57
4639 6312 9.604626 GCTTAGCATATGATTGTTCAGTTTATC 57.395 33.333 6.97 0.00 34.73 1.75
4657 6333 8.391106 CAGTTTATCGCTACTGCTTTCTTAATT 58.609 33.333 0.00 0.00 35.79 1.40
4729 6407 4.060038 AGGAATACCTTGTGTGCTATCG 57.940 45.455 0.00 0.00 45.36 2.92
4831 6509 1.890876 TTGGGATTTGTCACTCCGTG 58.109 50.000 0.00 0.00 31.95 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.561738 TTAAAAGGTCTATGTTCTTGGTCATC 57.438 34.615 0.00 0.00 0.00 2.92
1 2 8.934023 TTTAAAAGGTCTATGTTCTTGGTCAT 57.066 30.769 0.00 0.00 0.00 3.06
2 3 8.754991 TTTTAAAAGGTCTATGTTCTTGGTCA 57.245 30.769 0.00 0.00 0.00 4.02
9 10 9.983804 CCTCGTATTTTTAAAAGGTCTATGTTC 57.016 33.333 0.14 0.00 0.00 3.18
10 11 9.511272 ACCTCGTATTTTTAAAAGGTCTATGTT 57.489 29.630 0.14 0.00 31.58 2.71
11 12 9.159364 GACCTCGTATTTTTAAAAGGTCTATGT 57.841 33.333 20.22 8.17 45.98 2.29
39 40 3.767806 TCAGCGCTGAGAGGCAGG 61.768 66.667 35.30 7.71 45.03 4.85
47 48 1.153686 GCTCACATCTCAGCGCTGA 60.154 57.895 35.97 35.97 38.06 4.26
48 49 2.172372 GGCTCACATCTCAGCGCTG 61.172 63.158 31.53 31.53 36.41 5.18
49 50 2.186384 GGCTCACATCTCAGCGCT 59.814 61.111 2.64 2.64 36.41 5.92
50 51 3.260483 CGGCTCACATCTCAGCGC 61.260 66.667 0.00 0.00 36.41 5.92
51 52 1.144565 CTTCGGCTCACATCTCAGCG 61.145 60.000 0.00 0.00 36.41 5.18
52 53 0.809241 CCTTCGGCTCACATCTCAGC 60.809 60.000 0.00 0.00 34.65 4.26
53 54 0.179089 CCCTTCGGCTCACATCTCAG 60.179 60.000 0.00 0.00 0.00 3.35
54 55 0.904865 ACCCTTCGGCTCACATCTCA 60.905 55.000 0.00 0.00 0.00 3.27
55 56 0.460987 CACCCTTCGGCTCACATCTC 60.461 60.000 0.00 0.00 0.00 2.75
56 57 1.599047 CACCCTTCGGCTCACATCT 59.401 57.895 0.00 0.00 0.00 2.90
57 58 2.109126 GCACCCTTCGGCTCACATC 61.109 63.158 0.00 0.00 0.00 3.06
58 59 2.045926 GCACCCTTCGGCTCACAT 60.046 61.111 0.00 0.00 0.00 3.21
59 60 4.329545 GGCACCCTTCGGCTCACA 62.330 66.667 0.00 0.00 0.00 3.58
62 63 4.821589 CTCGGCACCCTTCGGCTC 62.822 72.222 0.00 0.00 0.00 4.70
108 109 2.677003 TTTCGTTAGCTGCAGCCGC 61.677 57.895 34.39 22.41 43.38 6.53
109 110 1.132640 GTTTCGTTAGCTGCAGCCG 59.867 57.895 34.39 28.74 43.38 5.52
110 111 1.502190 GGTTTCGTTAGCTGCAGCC 59.498 57.895 34.39 18.66 43.38 4.85
111 112 0.955919 AGGGTTTCGTTAGCTGCAGC 60.956 55.000 31.53 31.53 42.49 5.25
112 113 1.079503 GAGGGTTTCGTTAGCTGCAG 58.920 55.000 10.11 10.11 0.00 4.41
113 114 0.669318 CGAGGGTTTCGTTAGCTGCA 60.669 55.000 1.02 0.00 44.27 4.41
114 115 2.079049 CGAGGGTTTCGTTAGCTGC 58.921 57.895 0.00 0.00 44.27 5.25
123 124 2.677979 GCGTGCTTCCGAGGGTTTC 61.678 63.158 0.00 0.00 0.00 2.78
124 125 2.668550 GCGTGCTTCCGAGGGTTT 60.669 61.111 0.00 0.00 0.00 3.27
125 126 4.699522 GGCGTGCTTCCGAGGGTT 62.700 66.667 0.00 0.00 0.00 4.11
127 128 3.014085 TTAGGCGTGCTTCCGAGGG 62.014 63.158 0.00 0.00 0.00 4.30
128 129 1.810030 GTTAGGCGTGCTTCCGAGG 60.810 63.158 0.00 0.00 0.00 4.63
129 130 1.810030 GGTTAGGCGTGCTTCCGAG 60.810 63.158 0.00 0.00 0.00 4.63
130 131 2.221906 GAGGTTAGGCGTGCTTCCGA 62.222 60.000 0.00 0.00 0.00 4.55
131 132 1.810030 GAGGTTAGGCGTGCTTCCG 60.810 63.158 0.00 0.00 0.00 4.30
132 133 0.741221 CTGAGGTTAGGCGTGCTTCC 60.741 60.000 0.00 0.00 0.00 3.46
133 134 0.246635 TCTGAGGTTAGGCGTGCTTC 59.753 55.000 0.00 0.00 0.00 3.86
134 135 0.905357 ATCTGAGGTTAGGCGTGCTT 59.095 50.000 0.00 0.00 0.00 3.91
135 136 0.905357 AATCTGAGGTTAGGCGTGCT 59.095 50.000 0.00 0.00 0.00 4.40
136 137 1.739067 AAATCTGAGGTTAGGCGTGC 58.261 50.000 0.00 0.00 0.00 5.34
156 157 5.071788 TCTGAGGTTAGGCTCTTCTCAAAAA 59.928 40.000 12.44 2.61 34.58 1.94
157 158 4.593206 TCTGAGGTTAGGCTCTTCTCAAAA 59.407 41.667 12.44 4.38 34.58 2.44
158 159 4.160329 TCTGAGGTTAGGCTCTTCTCAAA 58.840 43.478 12.44 0.65 34.58 2.69
159 160 3.779444 TCTGAGGTTAGGCTCTTCTCAA 58.221 45.455 12.44 4.51 34.58 3.02
160 161 3.458044 TCTGAGGTTAGGCTCTTCTCA 57.542 47.619 11.35 11.35 33.96 3.27
161 162 5.351948 AAATCTGAGGTTAGGCTCTTCTC 57.648 43.478 0.00 0.00 0.00 2.87
162 163 5.770685 AAAATCTGAGGTTAGGCTCTTCT 57.229 39.130 0.00 0.00 0.00 2.85
187 188 6.068010 TCTGAGGTTAGGCATTTCTCAAAAA 58.932 36.000 0.00 0.00 34.58 1.94
188 189 5.630121 TCTGAGGTTAGGCATTTCTCAAAA 58.370 37.500 0.00 0.00 34.58 2.44
189 190 5.241403 TCTGAGGTTAGGCATTTCTCAAA 57.759 39.130 0.00 0.00 34.58 2.69
190 191 4.908601 TCTGAGGTTAGGCATTTCTCAA 57.091 40.909 0.00 0.00 34.58 3.02
191 192 4.471025 TCATCTGAGGTTAGGCATTTCTCA 59.529 41.667 0.00 0.00 33.96 3.27
192 193 5.028549 TCATCTGAGGTTAGGCATTTCTC 57.971 43.478 0.00 0.00 0.00 2.87
193 194 5.441718 TTCATCTGAGGTTAGGCATTTCT 57.558 39.130 0.00 0.00 0.00 2.52
194 195 6.705863 ATTTCATCTGAGGTTAGGCATTTC 57.294 37.500 0.00 0.00 0.00 2.17
195 196 8.000709 TCATATTTCATCTGAGGTTAGGCATTT 58.999 33.333 0.00 0.00 0.00 2.32
196 197 7.520798 TCATATTTCATCTGAGGTTAGGCATT 58.479 34.615 0.00 0.00 0.00 3.56
197 198 7.083062 TCATATTTCATCTGAGGTTAGGCAT 57.917 36.000 0.00 0.00 0.00 4.40
198 199 6.499106 TCATATTTCATCTGAGGTTAGGCA 57.501 37.500 0.00 0.00 0.00 4.75
208 209 8.210525 CGATTACGAGTGTTCATATTTCATCTG 58.789 37.037 0.00 0.00 42.66 2.90
212 213 5.808030 TGCGATTACGAGTGTTCATATTTCA 59.192 36.000 0.00 0.00 42.66 2.69
225 226 4.280461 ACGAGTTATTCTGCGATTACGAG 58.720 43.478 0.00 0.00 42.66 4.18
237 239 4.738740 CGGGTCACAGAATACGAGTTATTC 59.261 45.833 0.00 0.00 44.68 1.75
263 272 0.893727 GAACGATGGGCTGTTGGGTT 60.894 55.000 0.00 0.00 0.00 4.11
448 460 1.547675 GGGCCCATTTGTCAGTCTGAA 60.548 52.381 19.95 0.00 0.00 3.02
545 557 3.203716 CAAGGGGGTTCTAATACTTCGC 58.796 50.000 0.00 0.00 0.00 4.70
639 651 0.445436 GATGCACGAACTCCTTGCTG 59.555 55.000 0.00 0.00 37.16 4.41
728 778 1.742750 GCGATTCCACCTAGGGTTGTC 60.743 57.143 14.81 3.72 38.24 3.18
729 779 0.252197 GCGATTCCACCTAGGGTTGT 59.748 55.000 14.81 0.00 38.24 3.32
909 959 0.523519 CTTCGCCTGGCCTTTCTTTC 59.476 55.000 14.12 0.00 0.00 2.62
956 1006 4.695455 TGCTAAATTCCTCGAGGACAAAAG 59.305 41.667 33.75 25.93 45.39 2.27
999 1049 1.135046 CTGCGACACCGATCATCATC 58.865 55.000 0.00 0.00 38.22 2.92
1112 1162 1.062587 GATCGGATCAACCACAAAGCG 59.937 52.381 13.02 0.00 38.90 4.68
1113 1163 1.062587 CGATCGGATCAACCACAAAGC 59.937 52.381 17.53 0.00 38.90 3.51
1114 1164 2.616960 TCGATCGGATCAACCACAAAG 58.383 47.619 16.41 0.00 38.90 2.77
1116 1166 2.093711 ACATCGATCGGATCAACCACAA 60.094 45.455 16.41 0.00 38.90 3.33
1117 1167 1.480545 ACATCGATCGGATCAACCACA 59.519 47.619 16.41 0.00 38.90 4.17
1118 1168 1.860950 CACATCGATCGGATCAACCAC 59.139 52.381 16.41 0.00 38.90 4.16
1121 1171 1.202533 ACCCACATCGATCGGATCAAC 60.203 52.381 16.41 0.00 31.28 3.18
1122 1172 1.119684 ACCCACATCGATCGGATCAA 58.880 50.000 16.41 0.00 31.28 2.57
1138 1188 1.474330 CAATAAACCCTGAGCCACCC 58.526 55.000 0.00 0.00 0.00 4.61
1402 1455 4.450122 GCGTCGTGCAGCATGTGG 62.450 66.667 14.47 8.61 45.45 4.17
1534 1587 2.005370 TGGTCTCGTAGAACCTGGTT 57.995 50.000 12.82 12.82 38.12 3.67
1730 1783 2.616330 CGCGTCCTTGTGGTTGCAT 61.616 57.895 0.00 0.00 35.42 3.96
2044 2622 4.495679 CCCACAATCGTTCCACATTATTCG 60.496 45.833 0.00 0.00 0.00 3.34
2106 2685 7.133891 TCTACAAAGAGCAAACAATAGAAGC 57.866 36.000 0.00 0.00 0.00 3.86
2147 2734 6.606796 TGGACGTCCACATTAACCTATAAGTA 59.393 38.462 33.23 3.66 42.01 2.24
2148 2735 5.422970 TGGACGTCCACATTAACCTATAAGT 59.577 40.000 33.23 0.00 42.01 2.24
2149 2736 5.909477 TGGACGTCCACATTAACCTATAAG 58.091 41.667 33.23 0.00 42.01 1.73
2150 2737 5.936187 TGGACGTCCACATTAACCTATAA 57.064 39.130 33.23 5.20 42.01 0.98
2301 2890 7.214467 TGAGGTTTGTAAATTCACATCCTTC 57.786 36.000 7.23 0.00 35.04 3.46
2309 2898 6.061441 TCTGAGCTTGAGGTTTGTAAATTCA 58.939 36.000 0.00 0.00 0.00 2.57
2499 3088 8.906867 AGTTTAACATAATCAGATGGTGGATTG 58.093 33.333 0.00 0.00 35.49 2.67
2581 3170 2.380064 ACAAAGGTGCAATCCCTGAA 57.620 45.000 0.00 0.00 30.99 3.02
2607 3196 1.636003 GAAGGTCAACCCTCCTCCATT 59.364 52.381 0.00 0.00 45.47 3.16
2672 3261 5.894298 ACAAGCTGGTGATAGAATATCCA 57.106 39.130 0.00 0.00 0.00 3.41
2992 3666 0.972883 AGTTGCTCCTGGAGAGTGAC 59.027 55.000 27.53 16.98 45.21 3.67
3064 3738 4.878439 TGCCGATTAAGCGTTGAGTATAT 58.122 39.130 12.66 0.00 0.00 0.86
3072 3746 5.243426 ACATATTTTGCCGATTAAGCGTT 57.757 34.783 12.66 0.00 0.00 4.84
3091 3774 4.022589 CAGTGGAGCACATGAAAGAAACAT 60.023 41.667 0.00 0.00 36.74 2.71
3153 3837 8.443160 GCATATAATGTTAGACGTTGCACATAT 58.557 33.333 7.59 5.58 0.00 1.78
3168 4792 4.467861 TGTGGATGGGGCATATAATGTT 57.532 40.909 0.00 0.00 0.00 2.71
3171 4795 3.770933 GCAATGTGGATGGGGCATATAAT 59.229 43.478 0.00 0.00 0.00 1.28
3214 4838 6.287107 AGATCAACAAGTACACGAAAACAG 57.713 37.500 0.00 0.00 0.00 3.16
3318 4942 6.003950 GGCAATATAACCTCAGCCAATAAGA 58.996 40.000 0.00 0.00 41.63 2.10
3661 5334 1.833630 ACAGAATCGAGGATGCCTTCA 59.166 47.619 0.00 0.00 31.76 3.02
3676 5349 2.651105 TATGCCGGCCGACACAGAA 61.651 57.895 30.73 3.43 0.00 3.02
3811 5484 2.352030 CCAAACTGCAAGCGATGACATT 60.352 45.455 0.00 0.00 37.60 2.71
3870 5543 1.133598 CAGTATGTTCGGACGTAGGCA 59.866 52.381 0.00 0.00 0.00 4.75
3881 5554 5.118990 ACATGTATCACAGGCAGTATGTTC 58.881 41.667 0.00 0.00 39.31 3.18
3994 5667 3.530910 CTCAGGCGTTTCCACCGGT 62.531 63.158 0.00 0.00 37.29 5.28
4060 5733 2.564062 CACATCTCCCCAAAGCAACAAT 59.436 45.455 0.00 0.00 0.00 2.71
4061 5734 1.962807 CACATCTCCCCAAAGCAACAA 59.037 47.619 0.00 0.00 0.00 2.83
4125 5798 0.602638 TCACAAAGCAGCACCGGTAG 60.603 55.000 6.87 2.73 0.00 3.18
4132 5805 0.040157 GCACGAATCACAAAGCAGCA 60.040 50.000 0.00 0.00 0.00 4.41
4180 5853 9.630098 AAACATTATGCAACACTCTGAAATAAG 57.370 29.630 0.00 0.00 0.00 1.73
4234 5907 9.256477 TGATACACGATGAAACATTAAGATACC 57.744 33.333 0.00 0.00 0.00 2.73
4239 5912 7.408910 TGCATGATACACGATGAAACATTAAG 58.591 34.615 0.00 0.00 0.00 1.85
4281 5954 7.617041 ATCCAACTTACTTGCTTATGAAGAC 57.383 36.000 0.00 0.00 0.00 3.01
4282 5955 8.318412 TGTATCCAACTTACTTGCTTATGAAGA 58.682 33.333 0.00 0.00 0.00 2.87
4283 5956 8.391106 GTGTATCCAACTTACTTGCTTATGAAG 58.609 37.037 0.00 0.00 0.00 3.02
4284 5957 7.880713 TGTGTATCCAACTTACTTGCTTATGAA 59.119 33.333 0.00 0.00 0.00 2.57
4285 5958 7.333423 GTGTGTATCCAACTTACTTGCTTATGA 59.667 37.037 0.00 0.00 0.00 2.15
4286 5959 7.414098 GGTGTGTATCCAACTTACTTGCTTATG 60.414 40.741 0.00 0.00 0.00 1.90
4287 5960 6.598064 GGTGTGTATCCAACTTACTTGCTTAT 59.402 38.462 0.00 0.00 0.00 1.73
4288 5961 5.935789 GGTGTGTATCCAACTTACTTGCTTA 59.064 40.000 0.00 0.00 0.00 3.09
4289 5962 4.760204 GGTGTGTATCCAACTTACTTGCTT 59.240 41.667 0.00 0.00 0.00 3.91
4306 5979 2.092807 ACCGAAAACTAAGTGGGTGTGT 60.093 45.455 0.00 0.00 0.00 3.72
4312 5985 3.139077 AGCTCAACCGAAAACTAAGTGG 58.861 45.455 0.00 0.00 0.00 4.00
4313 5986 4.813296 AAGCTCAACCGAAAACTAAGTG 57.187 40.909 0.00 0.00 0.00 3.16
4320 5993 3.181491 CCAACAGAAAGCTCAACCGAAAA 60.181 43.478 0.00 0.00 0.00 2.29
4481 6154 7.562088 ACAAGCTAGTCTAGTAGAGGCTTATTT 59.438 37.037 23.08 13.96 36.38 1.40
4483 6156 6.607019 ACAAGCTAGTCTAGTAGAGGCTTAT 58.393 40.000 23.08 15.71 36.38 1.73
4505 6178 7.595819 AACCTTAACCATCTTTTGATCAACA 57.404 32.000 7.89 0.00 36.97 3.33
4580 6253 8.956446 TGGGTCTTATCTATCACATCATTCTA 57.044 34.615 0.00 0.00 0.00 2.10
4657 6333 7.990314 TCATGGTCGAAGGAATATGTATTTGAA 59.010 33.333 0.00 0.00 0.00 2.69
4729 6407 3.432252 CACCCAGTTATGAAGTGACGTTC 59.568 47.826 0.00 0.00 34.30 3.95
4796 6474 3.293337 TCCCAATCTTGATTCATGCCAG 58.707 45.455 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.