Multiple sequence alignment - TraesCS7D01G503100

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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 TraesCS7D01G503100 chr7D 100.000 5359 0 0 1 5359 608293643 608288285 0.000000e+00 9897.0
1 TraesCS7D01G503100 chr7D 97.686 3717 78 3 1500 5210 346628465 346624751 0.000000e+00 6381.0
2 TraesCS7D01G503100 chr7D 98.190 1050 19 0 430 1479 346629479 346628430 0.000000e+00 1834.0
3 TraesCS7D01G503100 chr7D 98.485 396 6 0 4 399 346632755 346632360 0.000000e+00 699.0
4 TraesCS7D01G503100 chr7D 100.000 33 0 0 397 429 346629529 346629497 1.610000e-05 62.1
5 TraesCS7D01G503100 chr1D 96.552 4786 136 9 431 5210 162594685 162599447 0.000000e+00 7897.0
6 TraesCS7D01G503100 chr1D 98.106 3749 63 3 1472 5214 485426358 485422612 0.000000e+00 6523.0
7 TraesCS7D01G503100 chr1D 97.647 3740 73 4 1484 5211 42042677 42038941 0.000000e+00 6405.0
8 TraesCS7D01G503100 chr1D 98.302 1060 16 2 430 1489 42043689 42042632 0.000000e+00 1857.0
9 TraesCS7D01G503100 chr1D 99.248 399 3 0 1 399 42046967 42046569 0.000000e+00 721.0
10 TraesCS7D01G503100 chr1D 98.747 399 5 0 1 399 162591501 162591899 0.000000e+00 710.0
11 TraesCS7D01G503100 chr1D 98.496 399 6 0 1 399 485429362 485428964 0.000000e+00 704.0
12 TraesCS7D01G503100 chr1D 100.000 33 0 0 397 429 42043739 42043707 1.610000e-05 62.1
13 TraesCS7D01G503100 chr1D 100.000 33 0 0 397 429 162594634 162594666 1.610000e-05 62.1
14 TraesCS7D01G503100 chr6D 95.749 4775 144 21 430 5185 360752728 360747994 0.000000e+00 7638.0
15 TraesCS7D01G503100 chr6D 96.639 1071 31 2 430 1495 360745867 360746937 0.000000e+00 1773.0
16 TraesCS7D01G503100 chr6D 98.997 399 4 0 1 399 360714395 360714793 0.000000e+00 715.0
17 TraesCS7D01G503100 chr6D 97.995 399 8 0 1 399 360756006 360755608 0.000000e+00 693.0
18 TraesCS7D01G503100 chr2A 95.732 3046 108 10 1542 4572 171836712 171839750 0.000000e+00 4885.0
19 TraesCS7D01G503100 chr2A 97.647 1020 19 2 430 1444 171835688 171836707 0.000000e+00 1746.0
20 TraesCS7D01G503100 chr2A 95.033 604 30 0 4608 5211 171839748 171840351 0.000000e+00 950.0
21 TraesCS7D01G503100 chr2A 82.927 123 19 2 5231 5352 738028298 738028177 5.670000e-20 110.0
22 TraesCS7D01G503100 chr4B 95.632 3045 112 10 1542 4572 445329352 445332389 0.000000e+00 4867.0
23 TraesCS7D01G503100 chr4B 95.599 3045 110 13 1542 4571 622886285 622883250 0.000000e+00 4859.0
24 TraesCS7D01G503100 chr4B 97.745 1020 17 3 430 1444 622887308 622886290 0.000000e+00 1751.0
25 TraesCS7D01G503100 chr4B 97.451 1020 18 3 430 1444 445328331 445329347 0.000000e+00 1733.0
26 TraesCS7D01G503100 chr4B 98.246 399 7 0 1 399 445325235 445325633 0.000000e+00 699.0
27 TraesCS7D01G503100 chr4B 100.000 33 0 0 397 429 622887358 622887326 1.610000e-05 62.1
28 TraesCS7D01G503100 chr5A 95.601 3046 112 11 1542 4572 617310922 617307884 0.000000e+00 4863.0
29 TraesCS7D01G503100 chr5A 93.229 1861 90 16 3365 5210 370093685 370095524 0.000000e+00 2706.0
30 TraesCS7D01G503100 chrUn 95.498 3043 118 9 1542 4572 269556353 269559388 0.000000e+00 4843.0
31 TraesCS7D01G503100 chrUn 96.909 647 14 3 430 1071 455329657 455329012 0.000000e+00 1079.0
32 TraesCS7D01G503100 chr7A 92.028 1869 107 14 3364 5210 622252206 622254054 0.000000e+00 2588.0
33 TraesCS7D01G503100 chr2B 97.843 1020 17 2 430 1444 93121577 93122596 0.000000e+00 1757.0
34 TraesCS7D01G503100 chr2B 97.995 399 8 0 1 399 93119690 93120088 0.000000e+00 693.0
35 TraesCS7D01G503100 chr2B 84.848 66 9 1 5292 5357 658176692 658176628 1.250000e-06 65.8
36 TraesCS7D01G503100 chr3B 97.843 1020 15 3 430 1444 777040166 777039149 0.000000e+00 1755.0
37 TraesCS7D01G503100 chr3B 100.000 33 0 0 397 429 777040216 777040184 1.610000e-05 62.1
38 TraesCS7D01G503100 chr6A 97.549 1020 19 3 430 1444 46109216 46110234 0.000000e+00 1740.0
39 TraesCS7D01G503100 chr6A 97.451 1020 20 3 430 1444 46140133 46141151 0.000000e+00 1735.0
40 TraesCS7D01G503100 chr6A 98.237 397 7 0 3 399 46105938 46106334 0.000000e+00 695.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G503100 chr7D 608288285 608293643 5358 True 9897.000000 9897 100.000000 1 5359 1 chr7D.!!$R1 5358
1 TraesCS7D01G503100 chr7D 346624751 346632755 8004 True 2244.025000 6381 98.590250 4 5210 4 chr7D.!!$R2 5206
2 TraesCS7D01G503100 chr1D 485422612 485429362 6750 True 3613.500000 6523 98.301000 1 5214 2 chr1D.!!$R2 5213
3 TraesCS7D01G503100 chr1D 162591501 162599447 7946 False 2889.700000 7897 98.433000 1 5210 3 chr1D.!!$F1 5209
4 TraesCS7D01G503100 chr1D 42038941 42046967 8026 True 2261.275000 6405 98.799250 1 5211 4 chr1D.!!$R1 5210
5 TraesCS7D01G503100 chr6D 360747994 360756006 8012 True 4165.500000 7638 96.872000 1 5185 2 chr6D.!!$R1 5184
6 TraesCS7D01G503100 chr6D 360745867 360746937 1070 False 1773.000000 1773 96.639000 430 1495 1 chr6D.!!$F2 1065
7 TraesCS7D01G503100 chr2A 171835688 171840351 4663 False 2527.000000 4885 96.137333 430 5211 3 chr2A.!!$F1 4781
8 TraesCS7D01G503100 chr4B 445325235 445332389 7154 False 2433.000000 4867 97.109667 1 4572 3 chr4B.!!$F1 4571
9 TraesCS7D01G503100 chr4B 622883250 622887358 4108 True 2224.033333 4859 97.781333 397 4571 3 chr4B.!!$R1 4174
10 TraesCS7D01G503100 chr5A 617307884 617310922 3038 True 4863.000000 4863 95.601000 1542 4572 1 chr5A.!!$R1 3030
11 TraesCS7D01G503100 chr5A 370093685 370095524 1839 False 2706.000000 2706 93.229000 3365 5210 1 chr5A.!!$F1 1845
12 TraesCS7D01G503100 chrUn 269556353 269559388 3035 False 4843.000000 4843 95.498000 1542 4572 1 chrUn.!!$F1 3030
13 TraesCS7D01G503100 chrUn 455329012 455329657 645 True 1079.000000 1079 96.909000 430 1071 1 chrUn.!!$R1 641
14 TraesCS7D01G503100 chr7A 622252206 622254054 1848 False 2588.000000 2588 92.028000 3364 5210 1 chr7A.!!$F1 1846
15 TraesCS7D01G503100 chr2B 93119690 93122596 2906 False 1225.000000 1757 97.919000 1 1444 2 chr2B.!!$F1 1443
16 TraesCS7D01G503100 chr3B 777039149 777040216 1067 True 908.550000 1755 98.921500 397 1444 2 chr3B.!!$R1 1047
17 TraesCS7D01G503100 chr6A 46140133 46141151 1018 False 1735.000000 1735 97.451000 430 1444 1 chr6A.!!$F1 1014
18 TraesCS7D01G503100 chr6A 46105938 46110234 4296 False 1217.500000 1740 97.893000 3 1444 2 chr6A.!!$F2 1441

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
372 373 2.421424 GGACGATGCTGCAAAAGATCTT 59.579 45.455 6.36 0.88 0.00 2.40 F
1448 4310 2.143008 TGGGTAAGTATATGCACGCG 57.857 50.000 3.53 3.53 0.00 6.01 F
2163 5053 0.317436 GAAATGTTTGTCGCCACGCA 60.317 50.000 0.00 0.00 0.00 5.24 F
3060 5952 1.446099 ATTGTCGTCGTGCTCGCAT 60.446 52.632 2.69 0.00 36.96 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 4314 0.096976 GTGTCTGTGTGTGTGTGTGC 59.903 55.000 0.00 0.00 0.00 4.57 R
3060 5952 0.991920 GGAAAGGTCATCCCCAGACA 59.008 55.000 0.00 0.00 37.74 3.41 R
3076 5968 5.144100 ACACATAAATGGTGGAACAAGGAA 58.856 37.500 0.00 0.00 44.16 3.36 R
4819 7758 1.132643 AGCTCGTTAGATGGTCGACAC 59.867 52.381 18.91 7.49 0.00 3.67 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
98 99 6.048073 TGAAAATGTAGAGCATGATAACGC 57.952 37.500 0.00 0.00 37.96 4.84
282 283 6.876257 CCATTGTAGGAAGGCTAATGACTATC 59.124 42.308 6.93 0.00 32.05 2.08
372 373 2.421424 GGACGATGCTGCAAAAGATCTT 59.579 45.455 6.36 0.88 0.00 2.40
1040 3902 3.054582 TCTTCTTCTAGTGCCTCCGTAGA 60.055 47.826 0.00 0.00 0.00 2.59
1105 3967 4.875561 AGAACACCAAGAACTAGGACTC 57.124 45.455 0.00 0.00 0.00 3.36
1448 4310 2.143008 TGGGTAAGTATATGCACGCG 57.857 50.000 3.53 3.53 0.00 6.01
1466 4328 3.858989 CGCGCACACACACACACA 61.859 61.111 8.75 0.00 0.00 3.72
1467 4329 2.023181 GCGCACACACACACACAG 59.977 61.111 0.30 0.00 0.00 3.66
1468 4330 2.460275 GCGCACACACACACACAGA 61.460 57.895 0.30 0.00 0.00 3.41
1482 4344 1.270571 ACACAGACACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
1489 4351 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1895 4785 4.521146 CAGATGCTACATGAGGAAAAGGT 58.479 43.478 0.00 0.00 0.00 3.50
1948 4838 5.648092 GGACAATTGCCTACAGAACTAACAT 59.352 40.000 5.05 0.00 0.00 2.71
1971 4861 2.091278 AGAGGATGAGGATGGTAACCGA 60.091 50.000 0.00 0.00 0.00 4.69
2132 5022 1.979308 TGGGAACACGGTCTTCCATTA 59.021 47.619 15.67 0.88 39.29 1.90
2152 5042 6.071952 CCATTACAGTGGTGCTAGAAATGTTT 60.072 38.462 0.00 0.00 34.46 2.83
2163 5053 0.317436 GAAATGTTTGTCGCCACGCA 60.317 50.000 0.00 0.00 0.00 5.24
2274 5164 6.866480 TCTTGAAATGCAGAAACTCAAAACT 58.134 32.000 0.00 0.00 0.00 2.66
2549 5440 4.934001 CCGGATTTAGATGGACAGATCATG 59.066 45.833 0.00 0.00 0.00 3.07
3060 5952 1.446099 ATTGTCGTCGTGCTCGCAT 60.446 52.632 2.69 0.00 36.96 4.73
3076 5968 0.257039 GCATGTCTGGGGATGACCTT 59.743 55.000 0.00 0.00 40.03 3.50
3310 6202 6.947644 ATGACTGATGCTGCATGTAAATAA 57.052 33.333 21.53 0.00 0.00 1.40
3625 6521 9.704098 GGAACGAATTATTAGACATGAAAGAAC 57.296 33.333 0.00 0.00 0.00 3.01
4202 7102 5.430886 ACGAGTCATGGAAATGATGATGAA 58.569 37.500 0.00 0.00 32.53 2.57
4304 7204 4.265073 GCCATGGGGAATATGATGACTAC 58.735 47.826 15.13 0.00 35.59 2.73
4484 7423 1.945394 CACAATGTGGCCTATCTCAGC 59.055 52.381 5.29 0.00 0.00 4.26
4915 7854 4.084952 CGTCGACTATTTTGAAAACCGACA 60.085 41.667 23.01 0.00 43.40 4.35
4921 7860 5.826208 ACTATTTTGAAAACCGACAGGAAGT 59.174 36.000 0.00 0.00 41.02 3.01
4925 7864 5.682943 TTGAAAACCGACAGGAAGTAATG 57.317 39.130 0.00 0.00 41.02 1.90
5217 8156 9.890629 AATGAAATATCTAGTAGTGCTCACAAA 57.109 29.630 2.63 0.00 0.00 2.83
5219 8158 9.890629 TGAAATATCTAGTAGTGCTCACAAATT 57.109 29.630 2.63 0.00 0.00 1.82
5221 8160 9.890629 AAATATCTAGTAGTGCTCACAAATTGA 57.109 29.630 0.00 0.00 0.00 2.57
5222 8161 9.890629 AATATCTAGTAGTGCTCACAAATTGAA 57.109 29.630 0.00 0.00 32.21 2.69
5223 8162 7.840342 ATCTAGTAGTGCTCACAAATTGAAG 57.160 36.000 0.00 0.00 32.21 3.02
5224 8163 6.993079 TCTAGTAGTGCTCACAAATTGAAGA 58.007 36.000 0.00 0.00 32.21 2.87
5225 8164 5.931441 AGTAGTGCTCACAAATTGAAGAC 57.069 39.130 0.00 0.00 32.21 3.01
5226 8165 5.368145 AGTAGTGCTCACAAATTGAAGACA 58.632 37.500 0.00 0.00 32.21 3.41
5227 8166 4.558538 AGTGCTCACAAATTGAAGACAC 57.441 40.909 0.00 9.03 32.21 3.67
5228 8167 3.947196 AGTGCTCACAAATTGAAGACACA 59.053 39.130 0.00 0.00 32.21 3.72
5229 8168 4.037690 GTGCTCACAAATTGAAGACACAC 58.962 43.478 0.00 3.57 32.21 3.82
5230 8169 3.242706 TGCTCACAAATTGAAGACACACG 60.243 43.478 0.00 0.00 32.21 4.49
5231 8170 3.242739 GCTCACAAATTGAAGACACACGT 60.243 43.478 0.00 0.00 32.21 4.49
5232 8171 4.271590 TCACAAATTGAAGACACACGTG 57.728 40.909 15.48 15.48 0.00 4.49
5233 8172 3.064682 TCACAAATTGAAGACACACGTGG 59.935 43.478 21.57 11.39 34.19 4.94
5234 8173 2.357637 ACAAATTGAAGACACACGTGGG 59.642 45.455 18.21 18.21 34.19 4.61
5235 8174 1.604604 AATTGAAGACACACGTGGGG 58.395 50.000 24.03 15.18 34.19 4.96
5236 8175 0.762418 ATTGAAGACACACGTGGGGA 59.238 50.000 24.03 0.65 34.19 4.81
5237 8176 0.105964 TTGAAGACACACGTGGGGAG 59.894 55.000 24.03 10.23 34.19 4.30
5238 8177 1.668151 GAAGACACACGTGGGGAGC 60.668 63.158 24.03 11.09 34.19 4.70
5239 8178 2.100879 GAAGACACACGTGGGGAGCT 62.101 60.000 24.03 13.35 34.19 4.09
5240 8179 1.696097 AAGACACACGTGGGGAGCTT 61.696 55.000 24.03 18.44 34.19 3.74
5241 8180 1.227853 GACACACGTGGGGAGCTTT 60.228 57.895 24.03 0.00 34.19 3.51
5242 8181 1.507141 GACACACGTGGGGAGCTTTG 61.507 60.000 24.03 9.85 34.19 2.77
5243 8182 2.594592 ACACGTGGGGAGCTTTGC 60.595 61.111 21.57 0.00 0.00 3.68
5244 8183 3.726517 CACGTGGGGAGCTTTGCG 61.727 66.667 7.95 0.00 0.00 4.85
5247 8186 4.344865 GTGGGGAGCTTTGCGGGA 62.345 66.667 0.00 0.00 0.00 5.14
5248 8187 4.033776 TGGGGAGCTTTGCGGGAG 62.034 66.667 0.00 0.00 0.00 4.30
5249 8188 4.035102 GGGGAGCTTTGCGGGAGT 62.035 66.667 0.00 0.00 0.00 3.85
5250 8189 2.436824 GGGAGCTTTGCGGGAGTC 60.437 66.667 0.00 0.00 0.00 3.36
5251 8190 2.436824 GGAGCTTTGCGGGAGTCC 60.437 66.667 0.00 0.00 0.00 3.85
5261 8200 3.308705 GGGAGTCCGGACCGTTGT 61.309 66.667 30.82 12.40 0.00 3.32
5262 8201 2.260743 GGAGTCCGGACCGTTGTC 59.739 66.667 30.82 20.32 40.98 3.18
5263 8202 2.567497 GGAGTCCGGACCGTTGTCA 61.567 63.158 30.82 0.00 43.65 3.58
5264 8203 1.372623 GAGTCCGGACCGTTGTCAC 60.373 63.158 30.82 3.19 43.65 3.67
5265 8204 2.732094 GTCCGGACCGTTGTCACG 60.732 66.667 24.75 0.00 46.71 4.35
5266 8205 4.651008 TCCGGACCGTTGTCACGC 62.651 66.667 13.94 0.00 45.72 5.34
5267 8206 4.657824 CCGGACCGTTGTCACGCT 62.658 66.667 13.94 0.00 45.72 5.07
5268 8207 3.103911 CGGACCGTTGTCACGCTC 61.104 66.667 5.48 0.00 45.72 5.03
5269 8208 3.103911 GGACCGTTGTCACGCTCG 61.104 66.667 0.00 0.00 45.72 5.03
5270 8209 3.764049 GACCGTTGTCACGCTCGC 61.764 66.667 0.00 0.00 45.72 5.03
5271 8210 4.280494 ACCGTTGTCACGCTCGCT 62.280 61.111 0.00 0.00 45.72 4.93
5272 8211 3.036084 CCGTTGTCACGCTCGCTT 61.036 61.111 0.00 0.00 45.72 4.68
5273 8212 2.465920 CGTTGTCACGCTCGCTTC 59.534 61.111 0.00 0.00 40.18 3.86
5274 8213 2.016704 CGTTGTCACGCTCGCTTCT 61.017 57.895 0.00 0.00 40.18 2.85
5275 8214 1.488957 GTTGTCACGCTCGCTTCTG 59.511 57.895 0.00 0.00 0.00 3.02
5276 8215 1.067416 TTGTCACGCTCGCTTCTGT 59.933 52.632 0.00 0.00 0.00 3.41
5277 8216 0.939577 TTGTCACGCTCGCTTCTGTC 60.940 55.000 0.00 0.00 0.00 3.51
5278 8217 1.081108 GTCACGCTCGCTTCTGTCT 60.081 57.895 0.00 0.00 0.00 3.41
5279 8218 1.081175 TCACGCTCGCTTCTGTCTG 60.081 57.895 0.00 0.00 0.00 3.51
5280 8219 2.431601 ACGCTCGCTTCTGTCTGC 60.432 61.111 0.00 0.00 0.00 4.26
5281 8220 3.184683 CGCTCGCTTCTGTCTGCC 61.185 66.667 0.00 0.00 0.00 4.85
5282 8221 2.817396 GCTCGCTTCTGTCTGCCC 60.817 66.667 0.00 0.00 0.00 5.36
5283 8222 2.977178 CTCGCTTCTGTCTGCCCT 59.023 61.111 0.00 0.00 0.00 5.19
5284 8223 1.447489 CTCGCTTCTGTCTGCCCTG 60.447 63.158 0.00 0.00 0.00 4.45
5285 8224 2.435586 CGCTTCTGTCTGCCCTGG 60.436 66.667 0.00 0.00 0.00 4.45
5286 8225 2.749441 GCTTCTGTCTGCCCTGGC 60.749 66.667 0.00 0.00 42.35 4.85
5287 8226 3.076092 CTTCTGTCTGCCCTGGCT 58.924 61.111 9.97 0.00 42.51 4.75
5288 8227 1.078567 CTTCTGTCTGCCCTGGCTC 60.079 63.158 9.97 1.15 42.51 4.70
5289 8228 1.834856 CTTCTGTCTGCCCTGGCTCA 61.835 60.000 9.97 5.57 42.51 4.26
5290 8229 1.834856 TTCTGTCTGCCCTGGCTCAG 61.835 60.000 9.97 14.03 42.51 3.35
5291 8230 3.972971 CTGTCTGCCCTGGCTCAGC 62.973 68.421 9.97 0.00 42.51 4.26
5304 8243 2.713895 GCTCAGCCAAAAACCTTCTC 57.286 50.000 0.00 0.00 0.00 2.87
5305 8244 1.270826 GCTCAGCCAAAAACCTTCTCC 59.729 52.381 0.00 0.00 0.00 3.71
5306 8245 1.889170 CTCAGCCAAAAACCTTCTCCC 59.111 52.381 0.00 0.00 0.00 4.30
5307 8246 1.499007 TCAGCCAAAAACCTTCTCCCT 59.501 47.619 0.00 0.00 0.00 4.20
5308 8247 1.889170 CAGCCAAAAACCTTCTCCCTC 59.111 52.381 0.00 0.00 0.00 4.30
5309 8248 0.881796 GCCAAAAACCTTCTCCCTCG 59.118 55.000 0.00 0.00 0.00 4.63
5310 8249 0.881796 CCAAAAACCTTCTCCCTCGC 59.118 55.000 0.00 0.00 0.00 5.03
5311 8250 0.881796 CAAAAACCTTCTCCCTCGCC 59.118 55.000 0.00 0.00 0.00 5.54
5312 8251 0.251209 AAAAACCTTCTCCCTCGCCC 60.251 55.000 0.00 0.00 0.00 6.13
5313 8252 1.423794 AAAACCTTCTCCCTCGCCCA 61.424 55.000 0.00 0.00 0.00 5.36
5314 8253 2.125766 AAACCTTCTCCCTCGCCCAC 62.126 60.000 0.00 0.00 0.00 4.61
5315 8254 4.148825 CCTTCTCCCTCGCCCACG 62.149 72.222 0.00 0.00 42.01 4.94
5316 8255 4.821589 CTTCTCCCTCGCCCACGC 62.822 72.222 0.00 0.00 39.84 5.34
5347 8286 3.121030 GCGTCAGCTGTCCGCATT 61.121 61.111 32.88 0.00 46.26 3.56
5348 8287 3.084579 CGTCAGCTGTCCGCATTC 58.915 61.111 14.67 0.00 42.61 2.67
5349 8288 1.737735 CGTCAGCTGTCCGCATTCA 60.738 57.895 14.67 0.00 42.61 2.57
5350 8289 1.086067 CGTCAGCTGTCCGCATTCAT 61.086 55.000 14.67 0.00 42.61 2.57
5351 8290 0.376152 GTCAGCTGTCCGCATTCATG 59.624 55.000 14.67 0.00 42.61 3.07
5352 8291 0.036105 TCAGCTGTCCGCATTCATGT 60.036 50.000 14.67 0.00 42.61 3.21
5353 8292 0.376152 CAGCTGTCCGCATTCATGTC 59.624 55.000 5.25 0.00 42.61 3.06
5354 8293 1.086067 AGCTGTCCGCATTCATGTCG 61.086 55.000 0.00 0.00 42.61 4.35
5355 8294 1.361668 GCTGTCCGCATTCATGTCGT 61.362 55.000 0.00 0.00 38.92 4.34
5356 8295 1.078709 CTGTCCGCATTCATGTCGTT 58.921 50.000 0.00 0.00 0.00 3.85
5357 8296 2.267426 CTGTCCGCATTCATGTCGTTA 58.733 47.619 0.00 0.00 0.00 3.18
5358 8297 2.866156 CTGTCCGCATTCATGTCGTTAT 59.134 45.455 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 2.540383 TCATTCTATCTCCATCCCCCG 58.460 52.381 0.00 0.00 0.00 5.73
282 283 7.113965 GCTTCTGACAGATTATGTTGTGTTTTG 59.886 37.037 5.87 0.00 44.17 2.44
372 373 2.026262 GGACCTATGGAAGTTTGCTGGA 60.026 50.000 0.00 0.00 0.00 3.86
863 3721 9.358872 AGAAGAAGAAAACAACAGAAAACATTC 57.641 29.630 0.00 0.00 0.00 2.67
1040 3902 6.322201 AGTTGACTGAGTTGATCCATTGTTTT 59.678 34.615 0.00 0.00 0.00 2.43
1105 3967 0.394488 TCTAGTCTGAGACCGGCTGG 60.394 60.000 11.02 11.02 42.84 4.85
1187 4049 4.099881 ACATGAACATTGCTCCAACAAGTT 59.900 37.500 0.00 0.00 31.96 2.66
1452 4314 0.096976 GTGTCTGTGTGTGTGTGTGC 59.903 55.000 0.00 0.00 0.00 4.57
1453 4315 1.128507 GTGTGTCTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1454 4316 1.270571 TGTGTGTCTGTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
1455 4317 1.128507 GTGTGTGTCTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1456 4318 1.270571 TGTGTGTGTCTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
1457 4319 1.128507 GTGTGTGTGTCTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1458 4320 1.270571 TGTGTGTGTGTCTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
1459 4321 1.128507 GTGTGTGTGTGTCTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1460 4322 1.270571 TGTGTGTGTGTGTCTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
1461 4323 1.128507 GTGTGTGTGTGTGTCTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1462 4324 1.270571 TGTGTGTGTGTGTGTCTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
1463 4325 1.128507 GTGTGTGTGTGTGTGTCTGTG 59.871 52.381 0.00 0.00 0.00 3.66
1464 4326 1.270571 TGTGTGTGTGTGTGTGTCTGT 60.271 47.619 0.00 0.00 0.00 3.41
1465 4327 1.128507 GTGTGTGTGTGTGTGTGTCTG 59.871 52.381 0.00 0.00 0.00 3.51
1466 4328 1.270571 TGTGTGTGTGTGTGTGTGTCT 60.271 47.619 0.00 0.00 0.00 3.41
1467 4329 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
1468 4330 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1482 4344 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1489 4351 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1620 4510 4.010349 CCATCCACCAGTTTTAGACTTCC 58.990 47.826 0.00 0.00 36.10 3.46
1895 4785 6.788598 TCTTTAATATTTTGATGGCTGCCA 57.211 33.333 25.65 25.65 38.19 4.92
1948 4838 3.895656 CGGTTACCATCCTCATCCTCTTA 59.104 47.826 1.13 0.00 0.00 2.10
1971 4861 2.907458 AAGCTTCCTTAGTTGGCCAT 57.093 45.000 6.09 0.00 0.00 4.40
2132 5022 4.207165 ACAAACATTTCTAGCACCACTGT 58.793 39.130 0.00 0.00 0.00 3.55
2152 5042 0.167908 GAAATTGATGCGTGGCGACA 59.832 50.000 0.00 0.00 38.70 4.35
2243 5133 2.703416 TCTGCATTTCAAGAGCGTGAT 58.297 42.857 0.00 0.00 0.00 3.06
2549 5440 1.742761 TTCTGCCTGCTGCTTCATAC 58.257 50.000 0.00 0.00 42.00 2.39
2613 5504 3.665190 ACTTAAACTTCGCCTTCTCTGG 58.335 45.455 0.00 0.00 0.00 3.86
3060 5952 0.991920 GGAAAGGTCATCCCCAGACA 59.008 55.000 0.00 0.00 37.74 3.41
3076 5968 5.144100 ACACATAAATGGTGGAACAAGGAA 58.856 37.500 0.00 0.00 44.16 3.36
3625 6521 8.697507 AAAATATTCTGGATGGTTAGCCTAAG 57.302 34.615 0.00 0.00 32.18 2.18
4091 6991 5.938125 GCTGAAATTTAAGTGACCTACAGGA 59.062 40.000 1.29 0.00 38.94 3.86
4202 7102 3.328931 CCCCATTGCCATAGTAGTCATCT 59.671 47.826 0.00 0.00 0.00 2.90
4304 7204 2.094286 GCCATAGTCATCCTCATCTCCG 60.094 54.545 0.00 0.00 0.00 4.63
4453 7392 5.142639 AGGCCACATTGTGCATAAGATAAT 58.857 37.500 11.41 0.00 31.34 1.28
4484 7423 7.060600 TGTCGAATGCAGAACAAAATAGTAG 57.939 36.000 0.00 0.00 0.00 2.57
4812 7751 5.761726 TCGTTAGATGGTCGACACTGTATAT 59.238 40.000 18.91 3.50 0.00 0.86
4819 7758 1.132643 AGCTCGTTAGATGGTCGACAC 59.867 52.381 18.91 7.49 0.00 3.67
4883 7822 7.424227 TTCAAAATAGTCGACGGTACATTTT 57.576 32.000 10.46 13.86 0.00 1.82
4915 7854 1.749634 CTCCGACGGTCATTACTTCCT 59.250 52.381 14.79 0.00 0.00 3.36
4921 7860 4.735578 GCATTTACTCTCCGACGGTCATTA 60.736 45.833 14.79 0.00 0.00 1.90
4925 7864 1.557651 GCATTTACTCTCCGACGGTC 58.442 55.000 14.79 0.00 0.00 4.79
5088 8027 1.664649 CGTCAGCCTTGCTTCGTCA 60.665 57.895 0.00 0.00 36.40 4.35
5102 8041 3.458163 GTCGGCCATCTCCCGTCA 61.458 66.667 2.24 0.00 45.71 4.35
5211 8150 3.064682 CCACGTGTGTCTTCAATTTGTGA 59.935 43.478 15.65 0.00 0.00 3.58
5212 8151 3.362295 CCACGTGTGTCTTCAATTTGTG 58.638 45.455 15.65 0.00 0.00 3.33
5213 8152 2.357637 CCCACGTGTGTCTTCAATTTGT 59.642 45.455 15.65 0.00 0.00 2.83
5214 8153 2.287547 CCCCACGTGTGTCTTCAATTTG 60.288 50.000 15.65 0.00 0.00 2.32
5215 8154 1.953686 CCCCACGTGTGTCTTCAATTT 59.046 47.619 15.65 0.00 0.00 1.82
5216 8155 1.142060 TCCCCACGTGTGTCTTCAATT 59.858 47.619 15.65 0.00 0.00 2.32
5217 8156 0.762418 TCCCCACGTGTGTCTTCAAT 59.238 50.000 15.65 0.00 0.00 2.57
5218 8157 0.105964 CTCCCCACGTGTGTCTTCAA 59.894 55.000 15.65 0.00 0.00 2.69
5219 8158 1.745890 CTCCCCACGTGTGTCTTCA 59.254 57.895 15.65 0.00 0.00 3.02
5220 8159 1.668151 GCTCCCCACGTGTGTCTTC 60.668 63.158 15.65 0.00 0.00 2.87
5221 8160 1.696097 AAGCTCCCCACGTGTGTCTT 61.696 55.000 15.65 7.30 0.00 3.01
5222 8161 1.696097 AAAGCTCCCCACGTGTGTCT 61.696 55.000 15.65 1.16 0.00 3.41
5223 8162 1.227853 AAAGCTCCCCACGTGTGTC 60.228 57.895 15.65 0.00 0.00 3.67
5224 8163 1.525995 CAAAGCTCCCCACGTGTGT 60.526 57.895 15.65 0.00 0.00 3.72
5225 8164 2.908073 GCAAAGCTCCCCACGTGTG 61.908 63.158 15.65 2.09 0.00 3.82
5226 8165 2.594592 GCAAAGCTCCCCACGTGT 60.595 61.111 15.65 0.00 0.00 4.49
5227 8166 3.726517 CGCAAAGCTCCCCACGTG 61.727 66.667 9.08 9.08 0.00 4.49
5230 8169 4.344865 TCCCGCAAAGCTCCCCAC 62.345 66.667 0.00 0.00 0.00 4.61
5231 8170 4.033776 CTCCCGCAAAGCTCCCCA 62.034 66.667 0.00 0.00 0.00 4.96
5232 8171 3.978571 GACTCCCGCAAAGCTCCCC 62.979 68.421 0.00 0.00 0.00 4.81
5233 8172 2.436824 GACTCCCGCAAAGCTCCC 60.437 66.667 0.00 0.00 0.00 4.30
5234 8173 2.436824 GGACTCCCGCAAAGCTCC 60.437 66.667 0.00 0.00 0.00 4.70
5244 8183 3.292500 GACAACGGTCCGGACTCCC 62.293 68.421 32.52 16.79 38.12 4.30
5245 8184 2.260743 GACAACGGTCCGGACTCC 59.739 66.667 32.52 17.56 38.12 3.85
5246 8185 1.372623 GTGACAACGGTCCGGACTC 60.373 63.158 32.52 22.00 43.65 3.36
5247 8186 2.732658 GTGACAACGGTCCGGACT 59.267 61.111 32.52 14.04 43.65 3.85
5248 8187 2.732094 CGTGACAACGGTCCGGAC 60.732 66.667 27.04 27.04 46.25 4.79
5257 8196 1.215655 ACAGAAGCGAGCGTGACAAC 61.216 55.000 0.00 0.00 0.00 3.32
5258 8197 0.939577 GACAGAAGCGAGCGTGACAA 60.940 55.000 0.00 0.00 0.00 3.18
5259 8198 1.371758 GACAGAAGCGAGCGTGACA 60.372 57.895 0.00 0.00 0.00 3.58
5260 8199 1.081108 AGACAGAAGCGAGCGTGAC 60.081 57.895 0.00 0.00 0.00 3.67
5261 8200 1.081175 CAGACAGAAGCGAGCGTGA 60.081 57.895 0.00 0.00 0.00 4.35
5262 8201 2.724708 GCAGACAGAAGCGAGCGTG 61.725 63.158 0.00 0.00 0.00 5.34
5263 8202 2.431601 GCAGACAGAAGCGAGCGT 60.432 61.111 0.00 0.00 0.00 5.07
5264 8203 3.184683 GGCAGACAGAAGCGAGCG 61.185 66.667 0.00 0.00 0.00 5.03
5265 8204 2.817396 GGGCAGACAGAAGCGAGC 60.817 66.667 0.00 0.00 0.00 5.03
5266 8205 1.447489 CAGGGCAGACAGAAGCGAG 60.447 63.158 0.00 0.00 0.00 5.03
5267 8206 2.659016 CAGGGCAGACAGAAGCGA 59.341 61.111 0.00 0.00 0.00 4.93
5268 8207 2.435586 CCAGGGCAGACAGAAGCG 60.436 66.667 0.00 0.00 0.00 4.68
5269 8208 2.749441 GCCAGGGCAGACAGAAGC 60.749 66.667 5.20 0.00 41.49 3.86
5270 8209 1.078567 GAGCCAGGGCAGACAGAAG 60.079 63.158 13.63 0.00 44.88 2.85
5271 8210 1.834856 CTGAGCCAGGGCAGACAGAA 61.835 60.000 19.64 0.00 44.88 3.02
5272 8211 2.203832 TGAGCCAGGGCAGACAGA 60.204 61.111 13.63 0.00 44.88 3.41
5273 8212 2.268280 CTGAGCCAGGGCAGACAG 59.732 66.667 13.63 13.95 44.88 3.51
5274 8213 4.025858 GCTGAGCCAGGGCAGACA 62.026 66.667 13.63 8.61 44.88 3.41
5285 8224 1.270826 GGAGAAGGTTTTTGGCTGAGC 59.729 52.381 0.00 0.00 0.00 4.26
5286 8225 1.889170 GGGAGAAGGTTTTTGGCTGAG 59.111 52.381 0.00 0.00 0.00 3.35
5287 8226 1.499007 AGGGAGAAGGTTTTTGGCTGA 59.501 47.619 0.00 0.00 0.00 4.26
5288 8227 1.889170 GAGGGAGAAGGTTTTTGGCTG 59.111 52.381 0.00 0.00 0.00 4.85
5289 8228 1.545651 CGAGGGAGAAGGTTTTTGGCT 60.546 52.381 0.00 0.00 0.00 4.75
5290 8229 0.881796 CGAGGGAGAAGGTTTTTGGC 59.118 55.000 0.00 0.00 0.00 4.52
5291 8230 0.881796 GCGAGGGAGAAGGTTTTTGG 59.118 55.000 0.00 0.00 0.00 3.28
5292 8231 0.881796 GGCGAGGGAGAAGGTTTTTG 59.118 55.000 0.00 0.00 0.00 2.44
5293 8232 0.251209 GGGCGAGGGAGAAGGTTTTT 60.251 55.000 0.00 0.00 0.00 1.94
5294 8233 1.379146 GGGCGAGGGAGAAGGTTTT 59.621 57.895 0.00 0.00 0.00 2.43
5295 8234 1.846124 TGGGCGAGGGAGAAGGTTT 60.846 57.895 0.00 0.00 0.00 3.27
5296 8235 2.203938 TGGGCGAGGGAGAAGGTT 60.204 61.111 0.00 0.00 0.00 3.50
5297 8236 3.003763 GTGGGCGAGGGAGAAGGT 61.004 66.667 0.00 0.00 0.00 3.50
5298 8237 4.148825 CGTGGGCGAGGGAGAAGG 62.149 72.222 0.00 0.00 41.33 3.46
5299 8238 4.821589 GCGTGGGCGAGGGAGAAG 62.822 72.222 0.00 0.00 41.33 2.85
5337 8276 1.078709 AACGACATGAATGCGGACAG 58.921 50.000 0.00 0.00 33.70 3.51
5338 8277 2.371910 TAACGACATGAATGCGGACA 57.628 45.000 0.00 0.00 33.70 4.02


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

AutoCloner maintained by Alex Coulton.