Multiple sequence alignment - TraesCS3D01G260200

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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 TraesCS3D01G260200 chr3D 100.000 5329 0 0 1 5329 362202807 362197479 0.000000e+00 9841.0
1 TraesCS3D01G260200 chr3D 98.925 93 1 0 4731 4823 362197985 362197893 3.300000e-37 167.0
2 TraesCS3D01G260200 chr3D 98.925 93 1 0 4823 4915 362198077 362197985 3.300000e-37 167.0
3 TraesCS3D01G260200 chr3A 94.842 4866 141 46 1 4823 482407631 482402833 0.000000e+00 7494.0
4 TraesCS3D01G260200 chr3A 81.604 424 20 14 4823 5210 482402919 482402518 1.120000e-76 298.0
5 TraesCS3D01G260200 chr3A 92.118 203 15 1 1652 1854 17310870 17311071 8.740000e-73 285.0
6 TraesCS3D01G260200 chr3A 90.385 208 19 1 1652 1859 258745208 258745002 6.800000e-69 272.0
7 TraesCS3D01G260200 chr3A 91.176 102 8 1 5229 5329 482402255 482402154 2.590000e-28 137.0
8 TraesCS3D01G260200 chr3A 88.889 81 7 2 3102 3182 8632883 8632805 1.220000e-16 99.0
9 TraesCS3D01G260200 chr3B 94.517 4870 170 31 1 4823 472117050 472112231 0.000000e+00 7424.0
10 TraesCS3D01G260200 chr3B 85.266 414 31 8 4823 5216 472112323 472111920 2.990000e-107 399.0
11 TraesCS3D01G260200 chr3B 91.000 200 17 1 1655 1854 651678826 651678628 8.800000e-68 268.0
12 TraesCS3D01G260200 chr7A 84.557 790 92 19 944 1728 19470544 19471308 0.000000e+00 756.0
13 TraesCS3D01G260200 chr7A 90.148 203 19 1 1652 1854 584879354 584879555 4.090000e-66 263.0
14 TraesCS3D01G260200 chr7D 86.545 275 31 5 944 1214 343299536 343299808 1.120000e-76 298.0
15 TraesCS3D01G260200 chrUn 90.148 203 18 2 1652 1854 81680663 81680863 4.090000e-66 263.0
16 TraesCS3D01G260200 chr4B 89.163 203 15 4 1652 1854 201717448 201717253 4.120000e-61 246.0
17 TraesCS3D01G260200 chr1A 90.374 187 17 1 1652 1838 521035887 521036072 1.480000e-60 244.0
18 TraesCS3D01G260200 chr1A 88.608 79 9 0 1559 1637 402803169 402803091 4.390000e-16 97.1
19 TraesCS3D01G260200 chr6B 93.182 88 6 0 3095 3182 278674700 278674613 4.330000e-26 130.0
20 TraesCS3D01G260200 chr6B 88.889 81 8 1 3094 3174 565749824 565749903 1.220000e-16 99.0
21 TraesCS3D01G260200 chr6A 93.182 88 6 0 3095 3182 209391428 209391341 4.330000e-26 130.0
22 TraesCS3D01G260200 chr6D 92.045 88 7 0 3095 3182 155602048 155601961 2.020000e-24 124.0
23 TraesCS3D01G260200 chr1D 90.541 74 7 0 3097 3170 116546609 116546682 1.220000e-16 99.0
24 TraesCS3D01G260200 chr1D 87.342 79 10 0 1559 1637 320400163 320400241 2.040000e-14 91.6
25 TraesCS3D01G260200 chr4A 88.608 79 9 0 3094 3172 373806316 373806394 4.390000e-16 97.1
26 TraesCS3D01G260200 chr1B 87.342 79 10 0 1559 1637 433436059 433436137 2.040000e-14 91.6


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 TraesCS3D01G260200 chr3D 362197479 362202807 5328 True 9841.0 9841 100.000000 1 5329 1 chr3D.!!$R1 5328
1 TraesCS3D01G260200 chr3A 482402154 482407631 5477 True 2643.0 7494 89.207333 1 5329 3 chr3A.!!$R3 5328
2 TraesCS3D01G260200 chr3B 472111920 472117050 5130 True 3911.5 7424 89.891500 1 5216 2 chr3B.!!$R2 5215
3 TraesCS3D01G260200 chr7A 19470544 19471308 764 False 756.0 756 84.557000 944 1728 1 chr7A.!!$F1 784

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
409 416 0.469917 CGGGGCTGATTGTATCCAGT 59.530 55.000 0.00 0.0 33.19 4.00 F
495 518 0.880441 TGGTAGTGCGTAGTTGCGTA 59.120 50.000 0.00 0.0 37.81 4.42 F
709 732 1.203523 AGGTCGCACTCTGATTCTGAC 59.796 52.381 0.00 0.0 0.00 3.51 F
2328 2372 1.588674 CAGCAACCGTTGGAGTTGTA 58.411 50.000 13.12 0.0 45.14 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2006 2.838736 ACAGAAGTCGTGCACAATTCT 58.161 42.857 18.64 19.05 0.00 2.40 R
2291 2335 3.549471 TGCTGCAACACAAACAAAATACG 59.451 39.130 0.00 0.00 0.00 3.06 R
3156 3201 7.010339 ACCCTCTCTGTTCCTAAATATATGC 57.990 40.000 0.00 0.00 0.00 3.14 R
4678 4739 1.138069 CCACCTGGGGTTGAAAAACAC 59.862 52.381 0.00 0.00 37.54 3.32 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
194 200 0.577269 GATTTCTTCGATCGCCACCG 59.423 55.000 11.09 0.00 0.00 4.94
298 305 0.755327 ACAGGTGGTGGCAAGGTTTC 60.755 55.000 0.00 0.00 0.00 2.78
326 333 1.017701 AGAAATTCGCGGTTCGTCCC 61.018 55.000 6.13 0.00 39.67 4.46
409 416 0.469917 CGGGGCTGATTGTATCCAGT 59.530 55.000 0.00 0.00 33.19 4.00
410 417 1.134098 CGGGGCTGATTGTATCCAGTT 60.134 52.381 0.00 0.00 33.19 3.16
431 454 5.127194 AGTTTGTCTCATCTACGCCATAGAA 59.873 40.000 0.00 0.00 43.33 2.10
495 518 0.880441 TGGTAGTGCGTAGTTGCGTA 59.120 50.000 0.00 0.00 37.81 4.42
571 594 5.132502 CCTTTTGGGTATCATGCTCATGTA 58.867 41.667 9.41 0.38 36.70 2.29
578 601 7.062322 TGGGTATCATGCTCATGTAAGATTTT 58.938 34.615 9.41 0.00 39.72 1.82
709 732 1.203523 AGGTCGCACTCTGATTCTGAC 59.796 52.381 0.00 0.00 0.00 3.51
720 743 7.009999 GCACTCTGATTCTGACAGTTGTATTAG 59.990 40.741 1.59 0.05 36.81 1.73
826 849 6.121776 TCTTTCCTGTCAATTACTTAGGCA 57.878 37.500 0.00 0.00 0.00 4.75
827 850 6.539173 TCTTTCCTGTCAATTACTTAGGCAA 58.461 36.000 0.00 0.00 0.00 4.52
828 851 6.430000 TCTTTCCTGTCAATTACTTAGGCAAC 59.570 38.462 0.00 0.00 0.00 4.17
849 872 9.860898 GGCAACTGTCAGAATTTTATTCTATTT 57.139 29.630 6.91 0.00 0.00 1.40
927 954 4.156190 TGCGCCATTCTAGCTAGTAGTATC 59.844 45.833 20.10 6.62 0.00 2.24
1395 1431 5.049405 CGCTTTTGTTGAGGTCAGTATTCTT 60.049 40.000 0.00 0.00 0.00 2.52
1418 1454 9.045223 TCTTTCATGGTCATGTAGAATATTTCG 57.955 33.333 10.32 0.00 39.72 3.46
1442 1478 5.565834 GCTGTCCTATGAGGCTTATACTCAC 60.566 48.000 0.00 0.00 46.67 3.51
1963 2006 4.019411 TCATGGCAAGATCTCAAGGTACAA 60.019 41.667 0.00 0.00 0.00 2.41
2204 2248 5.588958 AGAAATTTGAGGAGCTAATTGCC 57.411 39.130 0.00 0.00 44.23 4.52
2291 2335 4.454678 TGCACTCCCTATTGATGACAATC 58.545 43.478 0.00 0.00 44.34 2.67
2328 2372 1.588674 CAGCAACCGTTGGAGTTGTA 58.411 50.000 13.12 0.00 45.14 2.41
3100 3145 6.261158 TCTTCGAATGGTTGTTTTGATGTACA 59.739 34.615 0.00 0.00 0.00 2.90
3156 3201 6.850317 CAGTTTAAATTGAAATGCCAAAACGG 59.150 34.615 4.78 0.00 38.11 4.44
3595 3640 6.490040 TCATATAATCACTAAAAGGCCCTTGC 59.510 38.462 0.00 0.00 0.00 4.01
3610 3655 5.063204 GGCCCTTGCTTTCATTAAACTTTT 58.937 37.500 0.00 0.00 37.74 2.27
3659 3704 8.140628 GCATTCTACTGTAGAGAAGATGAATGA 58.859 37.037 22.34 5.89 38.52 2.57
3884 3935 7.984050 AGTTTCATATTCAGTAGTCACATCTGG 59.016 37.037 0.50 0.00 0.00 3.86
3992 4043 1.847737 TGGGTAAGGTTGTCAGGTTGT 59.152 47.619 0.00 0.00 0.00 3.32
4157 4208 3.433274 CACTTGTTCGAAGCAGCTAATGA 59.567 43.478 0.00 0.00 0.00 2.57
4159 4210 4.083802 ACTTGTTCGAAGCAGCTAATGAAC 60.084 41.667 19.89 19.89 36.98 3.18
4160 4211 3.664107 TGTTCGAAGCAGCTAATGAACT 58.336 40.909 23.92 0.00 37.27 3.01
4161 4212 3.433274 TGTTCGAAGCAGCTAATGAACTG 59.567 43.478 23.92 0.00 37.27 3.16
4162 4213 3.319137 TCGAAGCAGCTAATGAACTGT 57.681 42.857 0.00 0.00 36.26 3.55
4164 4215 3.679980 TCGAAGCAGCTAATGAACTGTTC 59.320 43.478 13.49 13.49 36.26 3.18
4241 4293 4.697514 GCTCTGCATCTCCTGTAATACAA 58.302 43.478 0.00 0.00 0.00 2.41
4242 4294 5.303971 GCTCTGCATCTCCTGTAATACAAT 58.696 41.667 0.00 0.00 0.00 2.71
4250 4302 6.073327 TCTCCTGTAATACAATAGCACTCG 57.927 41.667 0.00 0.00 0.00 4.18
4263 4315 2.155194 CACTCGCTCGCCTCTTTCG 61.155 63.158 0.00 0.00 0.00 3.46
4264 4316 2.179517 CTCGCTCGCCTCTTTCGT 59.820 61.111 0.00 0.00 0.00 3.85
4271 4323 2.930682 GCTCGCCTCTTTCGTAGAAATT 59.069 45.455 0.00 0.00 45.90 1.82
4279 4331 6.719365 CCTCTTTCGTAGAAATTGCTTATGG 58.281 40.000 0.00 0.00 45.90 2.74
4304 4356 7.767198 GGTTAACTTGTGCTAATATGGTGTCTA 59.233 37.037 5.42 0.00 0.00 2.59
4315 4367 0.253044 TGGTGTCTATTCTGGCAGGC 59.747 55.000 15.73 0.00 0.00 4.85
4337 4389 0.107214 GGTCGGATTGATCTTGGGCA 60.107 55.000 0.00 0.00 0.00 5.36
4356 4408 1.302033 CACCTGGAAGCAGCGAGTT 60.302 57.895 0.00 0.00 0.00 3.01
4410 4463 6.306199 AGGTGGTTGCATATGCTTTATCATA 58.694 36.000 27.13 2.54 42.66 2.15
4448 4501 0.035317 TTGCGAGACTGGAGCATTGT 59.965 50.000 0.00 0.00 40.83 2.71
4489 4543 5.346281 GTCTGTCTACTTGTTATGTGTCTGC 59.654 44.000 0.00 0.00 0.00 4.26
4590 4650 5.306937 TGGTAACTTGAATTCAGAGGAGACA 59.693 40.000 8.41 1.96 37.61 3.41
4760 4827 1.978617 CCAATGCCACTGGTGTCCC 60.979 63.158 0.00 0.00 0.00 4.46
4780 4847 1.764723 CAGGTGCTCTGATGGGTATGA 59.235 52.381 2.14 0.00 46.18 2.15
4782 4849 3.580022 CAGGTGCTCTGATGGGTATGATA 59.420 47.826 2.14 0.00 46.18 2.15
4813 4880 2.267642 GCCGAGTGCCCACATACA 59.732 61.111 0.82 0.00 0.00 2.29
4814 4881 1.153168 GCCGAGTGCCCACATACAT 60.153 57.895 0.82 0.00 0.00 2.29
4815 4882 0.105964 GCCGAGTGCCCACATACATA 59.894 55.000 0.82 0.00 0.00 2.29
4816 4883 1.873903 GCCGAGTGCCCACATACATAG 60.874 57.143 0.82 0.00 0.00 2.23
4817 4884 1.270305 CCGAGTGCCCACATACATAGG 60.270 57.143 0.82 0.00 0.00 2.57
4818 4885 1.873903 CGAGTGCCCACATACATAGGC 60.874 57.143 0.82 0.00 45.96 3.93
4821 4888 3.935993 GCCCACATACATAGGCGAT 57.064 52.632 0.00 0.00 35.30 4.58
4822 4889 1.726853 GCCCACATACATAGGCGATC 58.273 55.000 0.00 0.00 35.30 3.69
4823 4890 1.676014 GCCCACATACATAGGCGATCC 60.676 57.143 0.00 0.00 35.30 3.36
4824 4891 1.623311 CCCACATACATAGGCGATCCA 59.377 52.381 0.00 0.00 33.74 3.41
4825 4892 2.237143 CCCACATACATAGGCGATCCAT 59.763 50.000 0.00 0.00 33.74 3.41
4826 4893 3.264947 CCACATACATAGGCGATCCATG 58.735 50.000 0.00 0.00 33.74 3.66
4827 4894 2.674852 CACATACATAGGCGATCCATGC 59.325 50.000 0.00 0.00 33.74 4.06
4828 4895 2.568956 ACATACATAGGCGATCCATGCT 59.431 45.455 0.00 0.00 33.74 3.79
4829 4896 2.749280 TACATAGGCGATCCATGCTG 57.251 50.000 0.00 0.00 33.74 4.41
4830 4897 0.761187 ACATAGGCGATCCATGCTGT 59.239 50.000 0.00 0.00 33.74 4.40
4831 4898 1.154197 CATAGGCGATCCATGCTGTG 58.846 55.000 0.00 0.00 33.74 3.66
4832 4899 0.604780 ATAGGCGATCCATGCTGTGC 60.605 55.000 0.00 0.00 33.74 4.57
4833 4900 2.976692 TAGGCGATCCATGCTGTGCG 62.977 60.000 0.00 0.00 33.74 5.34
4834 4901 4.602696 GCGATCCATGCTGTGCGC 62.603 66.667 0.00 0.00 37.60 6.09
4835 4902 3.945434 CGATCCATGCTGTGCGCC 61.945 66.667 4.18 0.00 38.05 6.53
4836 4903 2.825387 GATCCATGCTGTGCGCCA 60.825 61.111 4.18 0.90 38.05 5.69
4837 4904 2.361483 ATCCATGCTGTGCGCCAA 60.361 55.556 4.18 0.00 38.05 4.52
4838 4905 1.731433 GATCCATGCTGTGCGCCAAT 61.731 55.000 4.18 0.00 38.05 3.16
4839 4906 2.011741 ATCCATGCTGTGCGCCAATG 62.012 55.000 4.18 4.40 38.05 2.82
4840 4907 2.883730 CATGCTGTGCGCCAATGC 60.884 61.111 4.18 4.77 38.05 3.56
4841 4908 4.137872 ATGCTGTGCGCCAATGCC 62.138 61.111 4.18 0.00 38.05 4.40
4844 4911 3.367743 CTGTGCGCCAATGCCACT 61.368 61.111 4.18 0.00 38.61 4.00
4845 4912 3.620300 CTGTGCGCCAATGCCACTG 62.620 63.158 4.18 0.00 38.61 3.66
4846 4913 4.424566 GTGCGCCAATGCCACTGG 62.425 66.667 4.18 0.00 36.40 4.00
4847 4914 4.972733 TGCGCCAATGCCACTGGT 62.973 61.111 4.18 0.00 36.24 4.00
4848 4915 4.424566 GCGCCAATGCCACTGGTG 62.425 66.667 0.42 0.42 45.53 4.17
4849 4916 2.985282 CGCCAATGCCACTGGTGT 60.985 61.111 0.00 0.00 39.23 4.16
4850 4917 2.964978 GCCAATGCCACTGGTGTC 59.035 61.111 0.00 0.00 36.24 3.67
4851 4918 2.639327 GCCAATGCCACTGGTGTCC 61.639 63.158 0.00 0.00 36.24 4.02
4852 4919 1.978617 CCAATGCCACTGGTGTCCC 60.979 63.158 0.00 0.00 0.00 4.46
4853 4920 1.228521 CAATGCCACTGGTGTCCCA 60.229 57.895 0.00 0.00 38.87 4.37
4861 4928 2.122413 TGGTGTCCCAGGTGCTCT 60.122 61.111 0.00 0.00 35.17 4.09
4862 4929 2.348998 GGTGTCCCAGGTGCTCTG 59.651 66.667 1.44 1.44 43.00 3.35
4863 4930 2.217038 GGTGTCCCAGGTGCTCTGA 61.217 63.158 8.81 0.00 46.18 3.27
4864 4931 1.557269 GGTGTCCCAGGTGCTCTGAT 61.557 60.000 8.81 0.00 46.18 2.90
4865 4932 0.392193 GTGTCCCAGGTGCTCTGATG 60.392 60.000 8.81 1.54 46.18 3.07
4866 4933 1.451028 GTCCCAGGTGCTCTGATGC 60.451 63.158 8.81 0.00 46.18 3.91
4867 4934 2.513204 CCCAGGTGCTCTGATGCG 60.513 66.667 8.81 0.00 46.18 4.73
4868 4935 2.267006 CCAGGTGCTCTGATGCGT 59.733 61.111 8.81 0.00 46.18 5.24
4869 4936 1.517361 CCAGGTGCTCTGATGCGTA 59.483 57.895 8.81 0.00 46.18 4.42
4870 4937 0.105593 CCAGGTGCTCTGATGCGTAT 59.894 55.000 8.81 0.00 46.18 3.06
4871 4938 1.215244 CAGGTGCTCTGATGCGTATG 58.785 55.000 0.00 0.00 46.18 2.39
4872 4939 1.114627 AGGTGCTCTGATGCGTATGA 58.885 50.000 0.00 0.00 35.36 2.15
4873 4940 1.690893 AGGTGCTCTGATGCGTATGAT 59.309 47.619 0.00 0.00 35.36 2.45
4874 4941 2.893489 AGGTGCTCTGATGCGTATGATA 59.107 45.455 0.00 0.00 35.36 2.15
4875 4942 3.056962 AGGTGCTCTGATGCGTATGATAG 60.057 47.826 0.00 0.00 35.36 2.08
4876 4943 2.665537 GTGCTCTGATGCGTATGATAGC 59.334 50.000 3.70 3.70 35.36 2.97
4877 4944 2.266554 GCTCTGATGCGTATGATAGCC 58.733 52.381 0.00 0.00 0.00 3.93
4878 4945 2.353109 GCTCTGATGCGTATGATAGCCA 60.353 50.000 0.00 0.00 0.00 4.75
4879 4946 3.862264 GCTCTGATGCGTATGATAGCCAA 60.862 47.826 0.00 0.00 0.00 4.52
4880 4947 3.653344 TCTGATGCGTATGATAGCCAAC 58.347 45.455 0.00 0.00 0.00 3.77
4881 4948 2.738846 CTGATGCGTATGATAGCCAACC 59.261 50.000 0.00 0.00 0.00 3.77
4882 4949 2.076863 GATGCGTATGATAGCCAACCC 58.923 52.381 0.00 0.00 0.00 4.11
4883 4950 1.128200 TGCGTATGATAGCCAACCCT 58.872 50.000 0.00 0.00 0.00 4.34
4884 4951 1.202639 TGCGTATGATAGCCAACCCTG 60.203 52.381 0.00 0.00 0.00 4.45
4885 4952 1.878102 GCGTATGATAGCCAACCCTGG 60.878 57.143 0.00 0.00 46.65 4.45
4903 4970 4.155733 CCGCCGAGTGCCCACATA 62.156 66.667 0.82 0.00 36.24 2.29
4904 4971 2.890474 CGCCGAGTGCCCACATAC 60.890 66.667 0.82 0.00 36.24 2.39
4928 4995 1.272781 GCGATCGAGGTTGTCTCTTG 58.727 55.000 21.57 0.00 40.30 3.02
4937 5004 1.079503 GTTGTCTCTTGGTGCGATCC 58.920 55.000 0.00 0.00 0.00 3.36
4963 5047 2.458951 GCGCATTGTTTTTGACTGACA 58.541 42.857 0.30 0.00 0.00 3.58
4988 5072 0.319900 CCTGTGAACCGACAGACTGG 60.320 60.000 7.51 0.00 45.39 4.00
4995 5079 1.267121 ACCGACAGACTGGTATGCTT 58.733 50.000 7.51 0.00 36.50 3.91
5016 5100 5.447010 GCTTGTATTTCAGCTAAGAGCACAG 60.447 44.000 0.64 0.00 45.56 3.66
5036 5123 6.961554 GCACAGATTAGTTGGAAAGAATTACG 59.038 38.462 0.00 0.00 0.00 3.18
5106 5212 4.094887 ACATCGTTGACATTGCTATGTTCC 59.905 41.667 14.96 4.34 44.90 3.62
5116 5222 5.415701 ACATTGCTATGTTCCCAACTTGTAG 59.584 40.000 8.03 0.00 42.29 2.74
5117 5223 4.634012 TGCTATGTTCCCAACTTGTAGT 57.366 40.909 0.00 0.00 0.00 2.73
5118 5224 5.748670 TGCTATGTTCCCAACTTGTAGTA 57.251 39.130 0.00 0.00 0.00 1.82
5141 5247 0.664166 CATTGCTTGCACGGGTTGTC 60.664 55.000 0.00 0.00 0.00 3.18
5216 5322 4.475135 GCGGGCTGGGAAGGAGAC 62.475 72.222 0.00 0.00 0.00 3.36
5218 5324 2.671682 GGGCTGGGAAGGAGACAC 59.328 66.667 0.00 0.00 0.00 3.67
5219 5325 2.224159 GGGCTGGGAAGGAGACACA 61.224 63.158 0.00 0.00 0.00 3.72
5220 5326 1.003233 GGCTGGGAAGGAGACACAC 60.003 63.158 0.00 0.00 0.00 3.82
5221 5327 1.003233 GCTGGGAAGGAGACACACC 60.003 63.158 0.00 0.00 0.00 4.16
5222 5328 1.768684 GCTGGGAAGGAGACACACCA 61.769 60.000 0.00 0.00 0.00 4.17
5223 5329 0.764890 CTGGGAAGGAGACACACCAA 59.235 55.000 0.00 0.00 0.00 3.67
5225 5331 0.036875 GGGAAGGAGACACACCAAGG 59.963 60.000 0.00 0.00 0.00 3.61
5226 5332 0.036875 GGAAGGAGACACACCAAGGG 59.963 60.000 0.00 0.00 0.00 3.95
5227 5333 0.036875 GAAGGAGACACACCAAGGGG 59.963 60.000 0.00 0.00 41.29 4.79
5248 5598 9.853177 AAGGGGTTATTCTATCTTGATAGTTTG 57.147 33.333 14.90 0.00 0.00 2.93
5259 5610 7.759489 ATCTTGATAGTTTGTAAGTGCCAAA 57.241 32.000 0.00 0.00 0.00 3.28
5261 5612 8.177119 TCTTGATAGTTTGTAAGTGCCAAATT 57.823 30.769 0.00 0.00 34.59 1.82
5279 5630 5.875910 CCAAATTGGTTGATGTGCATTGTAT 59.124 36.000 3.34 0.00 39.87 2.29
5314 5665 1.009389 GCTCGTCGAGTTCACAAGGG 61.009 60.000 22.61 0.00 31.39 3.95
5315 5666 1.006571 TCGTCGAGTTCACAAGGGC 60.007 57.895 0.00 0.00 0.00 5.19
5316 5667 2.027625 CGTCGAGTTCACAAGGGCC 61.028 63.158 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.699458 AGGTACGTATTGGTTTTCTCAACAG 59.301 40.000 0.00 0.00 0.00 3.16
91 93 2.261671 GCGGGTCGAGAAGCTTCA 59.738 61.111 27.57 4.98 0.00 3.02
127 129 1.529152 TTCGGCTGAAGTACCTGCGA 61.529 55.000 3.13 0.00 32.66 5.10
194 200 1.087501 GACGGAGAATTCAACTGGGC 58.912 55.000 8.44 0.67 0.00 5.36
204 210 1.204941 CGGGAGAAACTGACGGAGAAT 59.795 52.381 0.00 0.00 0.00 2.40
326 333 2.440409 CACAAATCAGAGGTGGAAGGG 58.560 52.381 0.00 0.00 0.00 3.95
409 416 5.348986 GTTCTATGGCGTAGATGAGACAAA 58.651 41.667 16.77 0.00 39.14 2.83
410 417 4.497507 CGTTCTATGGCGTAGATGAGACAA 60.498 45.833 16.77 0.00 39.14 3.18
584 607 7.279750 TGCACAGAACACCTTATATACGATA 57.720 36.000 0.00 0.00 0.00 2.92
585 608 6.156748 TGCACAGAACACCTTATATACGAT 57.843 37.500 0.00 0.00 0.00 3.73
884 907 5.673568 GCGCAGATAAACATAGAAGCACAAA 60.674 40.000 0.30 0.00 0.00 2.83
1395 1431 6.992123 AGCGAAATATTCTACATGACCATGAA 59.008 34.615 16.07 1.65 41.20 2.57
1418 1454 4.524714 TGAGTATAAGCCTCATAGGACAGC 59.475 45.833 0.00 0.00 37.67 4.40
1963 2006 2.838736 ACAGAAGTCGTGCACAATTCT 58.161 42.857 18.64 19.05 0.00 2.40
2063 2107 5.564063 CGTCGCATATGGTCCTGAATAAGTA 60.564 44.000 4.56 0.00 0.00 2.24
2291 2335 3.549471 TGCTGCAACACAAACAAAATACG 59.451 39.130 0.00 0.00 0.00 3.06
3156 3201 7.010339 ACCCTCTCTGTTCCTAAATATATGC 57.990 40.000 0.00 0.00 0.00 3.14
3884 3935 5.008712 GCATTTGGCTCTTTATACCTACCAC 59.991 44.000 0.00 0.00 40.25 4.16
3964 4015 3.773119 TGACAACCTTACCCATCCTCTAC 59.227 47.826 0.00 0.00 0.00 2.59
3978 4029 3.056179 CACCAAAAACAACCTGACAACCT 60.056 43.478 0.00 0.00 0.00 3.50
3992 4043 7.494625 TGCGTAATCCAAAATTAACACCAAAAA 59.505 29.630 0.00 0.00 0.00 1.94
4157 4208 2.092429 TCCAGAAACCTGCAGAACAGTT 60.092 45.455 17.39 7.84 45.68 3.16
4159 4210 2.260844 TCCAGAAACCTGCAGAACAG 57.739 50.000 17.39 0.00 46.77 3.16
4160 4211 2.727123 TTCCAGAAACCTGCAGAACA 57.273 45.000 17.39 0.00 0.00 3.18
4161 4212 4.550422 GATTTTCCAGAAACCTGCAGAAC 58.450 43.478 17.39 3.30 0.00 3.01
4162 4213 3.573967 GGATTTTCCAGAAACCTGCAGAA 59.426 43.478 17.39 0.00 36.28 3.02
4164 4215 2.095059 CGGATTTTCCAGAAACCTGCAG 60.095 50.000 6.78 6.78 35.91 4.41
4250 4302 1.992170 TTTCTACGAAAGAGGCGAGC 58.008 50.000 0.00 0.00 35.05 5.03
4263 4315 9.341899 CACAAGTTAACCATAAGCAATTTCTAC 57.658 33.333 0.88 0.00 0.00 2.59
4264 4316 8.026607 GCACAAGTTAACCATAAGCAATTTCTA 58.973 33.333 0.88 0.00 0.00 2.10
4271 4323 8.620416 CATATTAGCACAAGTTAACCATAAGCA 58.380 33.333 0.88 0.00 0.00 3.91
4279 4331 7.611213 AGACACCATATTAGCACAAGTTAAC 57.389 36.000 0.00 0.00 0.00 2.01
4304 4356 2.586792 GACCTCGCCTGCCAGAAT 59.413 61.111 0.00 0.00 0.00 2.40
4315 4367 1.539065 CCCAAGATCAATCCGACCTCG 60.539 57.143 0.00 0.00 39.44 4.63
4337 4389 2.044806 AACTCGCTGCTTCCAGGTGT 62.045 55.000 0.00 0.00 39.54 4.16
4356 4408 2.447443 ACTGCGATCCTGAAGTAGTCA 58.553 47.619 0.00 0.00 34.17 3.41
4448 4501 3.118149 ACAGACAGGCATCATGATAAGCA 60.118 43.478 17.11 0.00 0.00 3.91
4590 4650 4.935352 AACACATTACCACAAAGTGCAT 57.065 36.364 0.00 0.00 33.69 3.96
4678 4739 1.138069 CCACCTGGGGTTGAAAAACAC 59.862 52.381 0.00 0.00 37.54 3.32
4741 4808 2.639327 GGACACCAGTGGCATTGGC 61.639 63.158 26.94 12.12 41.42 4.52
4760 4827 1.764723 TCATACCCATCAGAGCACCTG 59.235 52.381 0.22 0.22 44.27 4.00
4813 4880 0.604780 GCACAGCATGGATCGCCTAT 60.605 55.000 0.00 0.00 43.62 2.57
4814 4881 1.227645 GCACAGCATGGATCGCCTA 60.228 57.895 0.00 0.00 43.62 3.93
4815 4882 2.515523 GCACAGCATGGATCGCCT 60.516 61.111 0.00 0.00 43.62 5.52
4816 4883 3.945434 CGCACAGCATGGATCGCC 61.945 66.667 0.00 0.00 43.62 5.54
4827 4894 3.367743 AGTGGCATTGGCGCACAG 61.368 61.111 23.55 0.00 41.06 3.66
4828 4895 3.672447 CAGTGGCATTGGCGCACA 61.672 61.111 23.55 1.22 41.06 4.57
4829 4896 4.424566 CCAGTGGCATTGGCGCAC 62.425 66.667 23.55 9.26 41.13 5.34
4830 4897 4.972733 ACCAGTGGCATTGGCGCA 62.973 61.111 26.94 0.00 41.13 6.09
4831 4898 4.424566 CACCAGTGGCATTGGCGC 62.425 66.667 26.94 15.34 42.47 6.53
4832 4899 2.981560 GACACCAGTGGCATTGGCG 61.982 63.158 26.94 20.79 42.47 5.69
4833 4900 2.639327 GGACACCAGTGGCATTGGC 61.639 63.158 26.94 12.12 41.42 4.52
4834 4901 1.978617 GGGACACCAGTGGCATTGG 60.979 63.158 25.63 25.63 41.42 3.16
4835 4902 1.228521 TGGGACACCAGTGGCATTG 60.229 57.895 9.78 2.55 43.37 2.82
4836 4903 3.260297 TGGGACACCAGTGGCATT 58.740 55.556 9.78 0.00 43.37 3.56
4844 4911 2.122413 AGAGCACCTGGGACACCA 60.122 61.111 0.00 0.00 46.94 4.17
4845 4912 1.557269 ATCAGAGCACCTGGGACACC 61.557 60.000 0.00 0.00 43.12 4.16
4846 4913 0.392193 CATCAGAGCACCTGGGACAC 60.392 60.000 0.00 0.00 43.12 3.67
4847 4914 1.985614 CATCAGAGCACCTGGGACA 59.014 57.895 0.00 0.00 43.12 4.02
4848 4915 1.451028 GCATCAGAGCACCTGGGAC 60.451 63.158 0.00 0.00 43.12 4.46
4849 4916 2.993008 GCATCAGAGCACCTGGGA 59.007 61.111 0.00 0.00 43.12 4.37
4850 4917 1.960040 TACGCATCAGAGCACCTGGG 61.960 60.000 0.00 0.19 43.12 4.45
4851 4918 0.105593 ATACGCATCAGAGCACCTGG 59.894 55.000 6.33 0.00 43.12 4.45
4852 4919 1.202452 TCATACGCATCAGAGCACCTG 60.202 52.381 0.22 0.22 44.27 4.00
4853 4920 1.114627 TCATACGCATCAGAGCACCT 58.885 50.000 0.00 0.00 0.00 4.00
4854 4921 2.160822 ATCATACGCATCAGAGCACC 57.839 50.000 0.00 0.00 0.00 5.01
4855 4922 2.665537 GCTATCATACGCATCAGAGCAC 59.334 50.000 0.00 0.00 0.00 4.40
4856 4923 2.353109 GGCTATCATACGCATCAGAGCA 60.353 50.000 0.00 0.00 0.00 4.26
4857 4924 2.266554 GGCTATCATACGCATCAGAGC 58.733 52.381 0.00 0.00 0.00 4.09
4858 4925 3.582714 TGGCTATCATACGCATCAGAG 57.417 47.619 0.00 0.00 0.00 3.35
4859 4926 3.554960 GGTTGGCTATCATACGCATCAGA 60.555 47.826 0.00 0.00 0.00 3.27
4860 4927 2.738846 GGTTGGCTATCATACGCATCAG 59.261 50.000 0.00 0.00 0.00 2.90
4861 4928 2.549992 GGGTTGGCTATCATACGCATCA 60.550 50.000 0.00 0.00 0.00 3.07
4862 4929 2.076863 GGGTTGGCTATCATACGCATC 58.923 52.381 0.00 0.00 0.00 3.91
4863 4930 1.699634 AGGGTTGGCTATCATACGCAT 59.300 47.619 0.00 0.00 0.00 4.73
4864 4931 1.128200 AGGGTTGGCTATCATACGCA 58.872 50.000 0.00 0.00 0.00 5.24
4865 4932 1.512926 CAGGGTTGGCTATCATACGC 58.487 55.000 0.00 0.00 0.00 4.42
4866 4933 2.169832 CCAGGGTTGGCTATCATACG 57.830 55.000 0.00 0.00 37.73 3.06
4886 4953 4.155733 TATGTGGGCACTCGGCGG 62.156 66.667 7.21 0.00 46.16 6.13
4887 4954 2.890474 GTATGTGGGCACTCGGCG 60.890 66.667 0.00 0.00 46.16 6.46
4888 4955 0.105964 TATGTATGTGGGCACTCGGC 59.894 55.000 0.00 0.00 43.74 5.54
4889 4956 1.270305 CCTATGTATGTGGGCACTCGG 60.270 57.143 0.00 0.00 0.00 4.63
4890 4957 1.873903 GCCTATGTATGTGGGCACTCG 60.874 57.143 0.00 0.00 43.59 4.18
4891 4958 1.873903 CGCCTATGTATGTGGGCACTC 60.874 57.143 0.00 0.00 44.27 3.51
4892 4959 0.106708 CGCCTATGTATGTGGGCACT 59.893 55.000 0.00 0.00 44.27 4.40
4893 4960 0.105964 TCGCCTATGTATGTGGGCAC 59.894 55.000 0.00 0.00 44.27 5.01
4894 4961 1.001974 GATCGCCTATGTATGTGGGCA 59.998 52.381 0.00 0.00 44.27 5.36
4895 4962 1.726853 GATCGCCTATGTATGTGGGC 58.273 55.000 0.00 0.00 41.02 5.36
4896 4963 1.544246 TCGATCGCCTATGTATGTGGG 59.456 52.381 11.09 0.00 0.00 4.61
4897 4964 2.416027 CCTCGATCGCCTATGTATGTGG 60.416 54.545 11.09 0.00 0.00 4.17
4898 4965 2.229062 ACCTCGATCGCCTATGTATGTG 59.771 50.000 11.09 0.00 0.00 3.21
4899 4966 2.515854 ACCTCGATCGCCTATGTATGT 58.484 47.619 11.09 0.00 0.00 2.29
4900 4967 3.245797 CAACCTCGATCGCCTATGTATG 58.754 50.000 11.09 0.00 0.00 2.39
4901 4968 2.891580 ACAACCTCGATCGCCTATGTAT 59.108 45.455 11.09 0.00 0.00 2.29
4902 4969 2.292569 GACAACCTCGATCGCCTATGTA 59.707 50.000 11.09 0.00 0.00 2.29
4903 4970 1.067212 GACAACCTCGATCGCCTATGT 59.933 52.381 11.09 12.67 0.00 2.29
4904 4971 1.338337 AGACAACCTCGATCGCCTATG 59.662 52.381 11.09 9.50 0.00 2.23
4937 5004 0.777631 CAAAAACAATGCGCCACGAG 59.222 50.000 4.18 0.00 0.00 4.18
4963 5047 0.834612 TGTCGGTTCACAGGGAGTTT 59.165 50.000 0.00 0.00 0.00 2.66
4988 5072 6.258727 TGCTCTTAGCTGAAATACAAGCATAC 59.741 38.462 0.00 0.00 42.97 2.39
4995 5079 5.405935 TCTGTGCTCTTAGCTGAAATACA 57.594 39.130 0.00 0.00 42.97 2.29
5016 5100 7.748847 TGCTTCGTAATTCTTTCCAACTAATC 58.251 34.615 0.00 0.00 0.00 1.75
5036 5123 1.270465 ACCTTGCCATTTGCTTGCTTC 60.270 47.619 0.00 0.00 42.00 3.86
5116 5222 1.396996 CCCGTGCAAGCAATGTAGTAC 59.603 52.381 0.00 0.00 0.00 2.73
5117 5223 1.002659 ACCCGTGCAAGCAATGTAGTA 59.997 47.619 0.00 0.00 0.00 1.82
5118 5224 0.250727 ACCCGTGCAAGCAATGTAGT 60.251 50.000 0.00 0.00 0.00 2.73
5210 5316 1.073706 ACCCCTTGGTGTGTCTCCT 60.074 57.895 0.00 0.00 45.58 3.69
5211 5317 3.576232 ACCCCTTGGTGTGTCTCC 58.424 61.111 0.00 0.00 45.58 3.71
5218 5324 7.880195 CTATCAAGATAGAATAACCCCTTGGTG 59.120 40.741 10.85 0.00 42.77 4.17
5219 5325 7.572861 ACTATCAAGATAGAATAACCCCTTGGT 59.427 37.037 20.71 0.00 44.18 3.67
5220 5326 7.978925 ACTATCAAGATAGAATAACCCCTTGG 58.021 38.462 20.71 0.00 42.55 3.61
5221 5327 9.853177 AAACTATCAAGATAGAATAACCCCTTG 57.147 33.333 20.71 0.00 42.55 3.61
5222 5328 9.853177 CAAACTATCAAGATAGAATAACCCCTT 57.147 33.333 20.71 2.14 42.55 3.95
5223 5329 9.004231 ACAAACTATCAAGATAGAATAACCCCT 57.996 33.333 20.71 0.00 42.55 4.79
5248 5598 4.685628 CACATCAACCAATTTGGCACTTAC 59.314 41.667 15.49 0.00 42.67 2.34
5254 5605 2.166821 TGCACATCAACCAATTTGGC 57.833 45.000 15.49 0.00 42.67 4.52


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

AutoCloner maintained by Alex Coulton.