Multiple sequence alignment - TraesCS3B01G389300

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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 TraesCS3B01G389300 chr3B 100.000 5076 0 0 1 5076 612416181 612411106 0.000000e+00 9374
1 TraesCS3B01G389300 chr3B 91.250 80 3 2 4619 4694 62010449 62010528 6.950000e-19 106
2 TraesCS3B01G389300 chr3B 100.000 57 0 0 4636 4692 532666374 532666318 6.950000e-19 106
3 TraesCS3B01G389300 chr3B 98.305 59 1 0 4636 4694 560713475 560713417 2.500000e-18 104
4 TraesCS3B01G389300 chr3B 96.721 61 2 0 4636 4696 190911705 190911765 8.990000e-18 102
5 TraesCS3B01G389300 chr3A 95.061 3503 108 24 821 4296 603933942 603930478 0.000000e+00 5450
6 TraesCS3B01G389300 chr3A 86.819 789 66 12 1 788 603934695 603933944 0.000000e+00 846
7 TraesCS3B01G389300 chr3A 96.382 387 6 4 4690 5076 603928607 603928229 9.270000e-177 630
8 TraesCS3B01G389300 chr3A 96.216 185 7 0 4437 4621 603928789 603928605 2.300000e-78 303
9 TraesCS3B01G389300 chr3A 83.562 292 45 3 4783 5074 701362227 701361939 2.330000e-68 270
10 TraesCS3B01G389300 chr3D 92.546 2911 115 30 1 2890 461669658 461666829 0.000000e+00 4080
11 TraesCS3B01G389300 chr3D 96.722 1495 29 3 2897 4378 461666860 461665373 0.000000e+00 2471
12 TraesCS3B01G389300 chr3D 95.866 387 7 5 4690 5076 461664640 461664263 7.220000e-173 617
13 TraesCS3B01G389300 chr3D 98.378 185 3 0 4437 4621 461664822 461664638 4.900000e-85 326
14 TraesCS3B01G389300 chr3D 83.916 286 41 5 4783 5067 568036694 568036413 8.380000e-68 268
15 TraesCS3B01G389300 chr3D 83.448 145 15 7 4925 5066 569804096 569804234 5.340000e-25 126
16 TraesCS3B01G389300 chrUn 81.849 292 46 4 4783 5074 41006112 41006396 6.570000e-59 239
17 TraesCS3B01G389300 chrUn 81.849 292 46 4 4783 5074 307831324 307831040 6.570000e-59 239
18 TraesCS3B01G389300 chrUn 84.699 183 19 8 4887 5066 40928434 40928610 1.880000e-39 174
19 TraesCS3B01G389300 chr6B 100.000 59 0 0 4636 4694 14779952 14779894 5.370000e-20 110
20 TraesCS3B01G389300 chr6B 100.000 57 0 0 4636 4692 285804257 285804313 6.950000e-19 106
21 TraesCS3B01G389300 chr6B 100.000 56 0 0 4636 4691 226867007 226867062 2.500000e-18 104
22 TraesCS3B01G389300 chr1A 98.305 59 1 0 4636 4694 495707963 495708021 2.500000e-18 104
23 TraesCS3B01G389300 chr6D 98.246 57 1 0 4636 4692 397360167 397360223 3.230000e-17 100


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 TraesCS3B01G389300 chr3B 612411106 612416181 5075 True 9374.00 9374 100.0000 1 5076 1 chr3B.!!$R3 5075
1 TraesCS3B01G389300 chr3A 603928229 603934695 6466 True 1807.25 5450 93.6195 1 5076 4 chr3A.!!$R2 5075
2 TraesCS3B01G389300 chr3D 461664263 461669658 5395 True 1873.50 4080 95.8780 1 5076 4 chr3D.!!$R2 5075

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
788 798 0.240678 TACTTGGCTTGTTGCATGCG 59.759 50.000 14.09 0.00 45.15 4.73 F
1164 1187 0.110104 CCATGCTCCATCCCTCCTTC 59.890 60.000 0.00 0.00 0.00 3.46 F
1165 1188 0.841961 CATGCTCCATCCCTCCTTCA 59.158 55.000 0.00 0.00 0.00 3.02 F
1800 1825 1.159285 TTGTTCAAGCCTCGATGCTG 58.841 50.000 16.23 10.24 41.80 4.41 F
2910 2940 3.036091 AGCATGGGAAGAATGAATTGGG 58.964 45.455 0.00 0.00 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1786 2.273370 TCGAGCAACCGATTGTAGAC 57.727 50.000 0.00 0.00 38.17 2.59 R
2791 2821 2.310538 ACACTTTGGCAAGGAAGAAGG 58.689 47.619 16.87 2.39 33.82 3.46 R
2939 2969 3.054166 CTGTGTGGCAAACATGAACATG 58.946 45.455 11.65 12.43 41.97 3.21 R
3400 3430 0.953471 GTGTTGTGTCTATGGCGCCA 60.953 55.000 34.80 34.80 0.00 5.69 R
4733 6399 0.111835 GCACGTGAGTTCGTTCGTTC 60.112 55.000 22.23 0.00 46.40 3.95 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
43 44 1.737838 TCCTTCGTGGATCACAATGC 58.262 50.000 0.00 0.00 40.56 3.56
53 54 3.384532 CACAATGCCAGCCACCCC 61.385 66.667 0.00 0.00 0.00 4.95
55 56 4.738998 CAATGCCAGCCACCCCGA 62.739 66.667 0.00 0.00 0.00 5.14
98 99 3.186409 CGAGTCTCTTTTTCGCAAATGGA 59.814 43.478 0.00 0.00 0.00 3.41
101 102 4.520492 AGTCTCTTTTTCGCAAATGGATGT 59.480 37.500 0.00 0.00 0.00 3.06
104 105 5.009510 TCTCTTTTTCGCAAATGGATGTTGA 59.990 36.000 0.00 0.00 0.00 3.18
126 127 3.244700 ACTGAGGAGTTTGAGATTGTGGG 60.245 47.826 0.00 0.00 0.00 4.61
217 219 4.220382 TGGCAAAAGTGTTGCTTAGCATAT 59.780 37.500 17.48 0.00 44.36 1.78
225 227 9.449719 AAAGTGTTGCTTAGCATATTAGTAAGT 57.550 29.630 8.05 0.00 38.76 2.24
283 285 1.444119 AACACGCCAAACACGAGCAT 61.444 50.000 0.00 0.00 0.00 3.79
294 296 1.271379 ACACGAGCATAGAAACCACGA 59.729 47.619 0.00 0.00 0.00 4.35
302 304 2.089887 TAGAAACCACGAGCCGCACA 62.090 55.000 0.00 0.00 0.00 4.57
340 342 1.282875 TCGCGAGAGGCATCATACG 59.717 57.895 3.71 4.73 43.84 3.06
433 435 4.479993 GGACCAGGCAGCAGCGAT 62.480 66.667 0.00 0.00 43.41 4.58
437 439 2.758089 CCAGGCAGCAGCGATGTTC 61.758 63.158 1.22 0.00 43.41 3.18
479 481 5.296780 ACAATCATAAATCACGGCTCGAAAT 59.703 36.000 1.50 0.00 0.00 2.17
558 560 0.612453 GTAGCGCCCCTAGCCTCTAT 60.612 60.000 2.29 0.00 38.78 1.98
566 568 2.657143 CCCTAGCCTCTATATCGGTCC 58.343 57.143 0.00 0.00 0.00 4.46
567 569 2.290464 CCTAGCCTCTATATCGGTCCG 58.710 57.143 4.39 4.39 0.00 4.79
568 570 1.671845 CTAGCCTCTATATCGGTCCGC 59.328 57.143 6.34 0.00 0.00 5.54
583 585 3.913573 CGCGCACACGGTCATAGC 61.914 66.667 8.75 0.00 40.57 2.97
612 614 9.194271 GTAATAAAAACCGGCAAAAGAATTACA 57.806 29.630 0.00 0.00 0.00 2.41
647 649 7.348080 AGATAGAATCACGGATAGACACAAA 57.652 36.000 0.00 0.00 0.00 2.83
657 659 5.639506 ACGGATAGACACAAAGACAATTCTG 59.360 40.000 0.00 0.00 29.98 3.02
663 665 5.807011 AGACACAAAGACAATTCTGCAAAAC 59.193 36.000 0.00 0.00 29.98 2.43
788 798 0.240678 TACTTGGCTTGTTGCATGCG 59.759 50.000 14.09 0.00 45.15 4.73
793 803 1.434696 GCTTGTTGCATGCGGCTAT 59.565 52.632 14.09 0.00 45.15 2.97
978 990 4.471386 TCTTGATCTCTCCTCCGGAAATTT 59.529 41.667 5.23 0.00 0.00 1.82
987 999 3.142174 CCTCCGGAAATTTGCTATCCTC 58.858 50.000 5.23 0.00 0.00 3.71
1157 1180 1.091771 CACACGTCCATGCTCCATCC 61.092 60.000 0.00 0.00 0.00 3.51
1161 1184 1.453669 GTCCATGCTCCATCCCTCC 59.546 63.158 0.00 0.00 0.00 4.30
1162 1185 1.059006 GTCCATGCTCCATCCCTCCT 61.059 60.000 0.00 0.00 0.00 3.69
1164 1187 0.110104 CCATGCTCCATCCCTCCTTC 59.890 60.000 0.00 0.00 0.00 3.46
1165 1188 0.841961 CATGCTCCATCCCTCCTTCA 59.158 55.000 0.00 0.00 0.00 3.02
1166 1189 1.424302 CATGCTCCATCCCTCCTTCAT 59.576 52.381 0.00 0.00 0.00 2.57
1169 1192 1.347378 GCTCCATCCCTCCTTCATCTC 59.653 57.143 0.00 0.00 0.00 2.75
1213 1237 2.281761 CTGTTGCTGCCCGTCCTT 60.282 61.111 0.00 0.00 0.00 3.36
1318 1342 4.179579 GCGCGTGGGCAGATTTCC 62.180 66.667 8.43 0.00 39.92 3.13
1454 1478 2.010817 GCTTTGTTCGGTGCGCTTG 61.011 57.895 9.73 0.00 0.00 4.01
1645 1670 4.578928 AGAGCGGTTAGTTTTGACATTTGT 59.421 37.500 0.00 0.00 0.00 2.83
1646 1671 5.067283 AGAGCGGTTAGTTTTGACATTTGTT 59.933 36.000 0.00 0.00 0.00 2.83
1647 1672 5.040635 AGCGGTTAGTTTTGACATTTGTTG 58.959 37.500 0.00 0.00 0.00 3.33
1648 1673 4.801516 GCGGTTAGTTTTGACATTTGTTGT 59.198 37.500 0.00 0.00 42.79 3.32
1761 1786 2.885644 CCCATTGCGTCGACCTCG 60.886 66.667 10.58 0.00 41.45 4.63
1800 1825 1.159285 TTGTTCAAGCCTCGATGCTG 58.841 50.000 16.23 10.24 41.80 4.41
1964 1989 8.894409 TCGATAATTGTTTTTATTCTGTGCTG 57.106 30.769 0.00 0.00 0.00 4.41
1982 2007 5.046231 TGTGCTGTTGGTGGTCATAGTATTA 60.046 40.000 0.00 0.00 0.00 0.98
2026 2051 9.095065 GAAATAGACGGACTGCTAATTTAGAAA 57.905 33.333 7.63 0.00 0.00 2.52
2088 2113 4.747108 AGCGATGCAGTACTAGCTTAAATG 59.253 41.667 15.28 0.00 0.00 2.32
2162 2191 3.403038 AGAGGAAGTGTTTGAATCCACG 58.597 45.455 0.00 0.00 36.69 4.94
2222 2251 6.210784 AGGTTGCAACTCTAGTATGTAACTCA 59.789 38.462 27.64 0.00 38.94 3.41
2226 2255 7.941919 TGCAACTCTAGTATGTAACTCATAGG 58.058 38.462 0.00 0.00 39.36 2.57
2246 2275 8.826765 TCATAGGTCCTTTCTCAAAGAAGTTAT 58.173 33.333 0.00 0.00 41.02 1.89
2489 2519 8.887036 AGGAAATGTTTTGTCTGAAATTTACC 57.113 30.769 0.00 0.00 0.00 2.85
2676 2706 6.801539 TTCATAACTCTGTTTAGGTTGCAG 57.198 37.500 0.00 0.00 0.00 4.41
2791 2821 9.933723 TTTTAACTCACTGTAAGGATTAGGTAC 57.066 33.333 0.00 0.00 39.30 3.34
2878 2908 9.856488 CATGTTGAAGAATGAATTGAATCTCTT 57.144 29.630 0.00 0.00 0.00 2.85
2885 2915 8.063200 AGAATGAATTGAATCTCTTGCATTGA 57.937 30.769 0.00 0.00 0.00 2.57
2910 2940 3.036091 AGCATGGGAAGAATGAATTGGG 58.964 45.455 0.00 0.00 0.00 4.12
3400 3430 3.971702 GGCCTCCCCAACTGCTGT 61.972 66.667 0.00 0.00 0.00 4.40
3748 3778 2.329678 AAGAGCGCGATCTGTCTCCG 62.330 60.000 29.44 0.00 0.00 4.63
3899 3929 0.033228 GATCATCTACGCCTGCTGCT 59.967 55.000 0.00 0.00 38.05 4.24
4006 4036 0.322816 AGTTCAGCAATGTGGCCGAT 60.323 50.000 0.00 0.00 0.00 4.18
4009 4039 0.107066 TCAGCAATGTGGCCGATGAT 60.107 50.000 0.00 0.00 0.00 2.45
4020 4050 2.202743 CGATGATGGTGCGGTCGT 60.203 61.111 0.00 0.00 0.00 4.34
4056 4086 1.821332 GCCAGTATGTCAGCAGGCC 60.821 63.158 0.00 0.00 36.17 5.19
4285 4328 1.199789 CTGCTTTGCTCGTTATTGGCA 59.800 47.619 0.00 0.00 0.00 4.92
4298 4341 7.425577 TCGTTATTGGCAATGATATTCTCAG 57.574 36.000 22.57 2.90 37.28 3.35
4314 4357 2.094675 CTCAGGCAAGGGTATTGTTGG 58.905 52.381 0.00 0.00 0.00 3.77
4326 4369 6.424032 AGGGTATTGTTGGAATTCTACCTTC 58.576 40.000 15.22 4.37 31.39 3.46
4368 4411 9.177608 CAACCTGAGATTTTGATTCCTTATGTA 57.822 33.333 0.00 0.00 0.00 2.29
4373 4416 9.605275 TGAGATTTTGATTCCTTATGTAGTCTG 57.395 33.333 0.00 0.00 0.00 3.51
4378 4421 9.739276 TTTTGATTCCTTATGTAGTCTGTGAAT 57.261 29.630 0.00 0.00 0.00 2.57
4380 4423 7.203218 TGATTCCTTATGTAGTCTGTGAATCG 58.797 38.462 0.00 0.00 39.60 3.34
4392 6037 4.563184 GTCTGTGAATCGTTCGATTAAGCT 59.437 41.667 18.20 0.00 35.29 3.74
4408 6053 6.690098 CGATTAAGCTGTTTTGGATGATTCAG 59.310 38.462 0.00 0.00 0.00 3.02
4502 6168 0.466739 CATGGGCTGCTGCTGGATTA 60.467 55.000 15.64 0.00 39.59 1.75
4618 6284 2.438434 GGCACTTAGGCCGCACAT 60.438 61.111 0.00 0.00 45.40 3.21
4619 6285 1.153249 GGCACTTAGGCCGCACATA 60.153 57.895 0.00 0.00 45.40 2.29
4620 6286 1.436983 GGCACTTAGGCCGCACATAC 61.437 60.000 0.00 0.00 45.40 2.39
4621 6287 0.462047 GCACTTAGGCCGCACATACT 60.462 55.000 0.00 0.00 0.00 2.12
4622 6288 1.571919 CACTTAGGCCGCACATACTC 58.428 55.000 0.00 0.00 0.00 2.59
4623 6289 0.464452 ACTTAGGCCGCACATACTCC 59.536 55.000 0.00 0.00 0.00 3.85
4624 6290 0.249911 CTTAGGCCGCACATACTCCC 60.250 60.000 0.00 0.00 0.00 4.30
4625 6291 0.689745 TTAGGCCGCACATACTCCCT 60.690 55.000 0.00 0.00 0.00 4.20
4626 6292 1.113517 TAGGCCGCACATACTCCCTC 61.114 60.000 0.00 0.00 0.00 4.30
4627 6293 2.109181 GCCGCACATACTCCCTCC 59.891 66.667 0.00 0.00 0.00 4.30
4628 6294 2.417516 CCGCACATACTCCCTCCG 59.582 66.667 0.00 0.00 0.00 4.63
4629 6295 2.423898 CCGCACATACTCCCTCCGT 61.424 63.158 0.00 0.00 0.00 4.69
4630 6296 1.515954 CGCACATACTCCCTCCGTT 59.484 57.895 0.00 0.00 0.00 4.44
4631 6297 0.527817 CGCACATACTCCCTCCGTTC 60.528 60.000 0.00 0.00 0.00 3.95
4632 6298 0.527817 GCACATACTCCCTCCGTTCG 60.528 60.000 0.00 0.00 0.00 3.95
4633 6299 0.102481 CACATACTCCCTCCGTTCGG 59.898 60.000 4.74 4.74 0.00 4.30
4634 6300 0.033796 ACATACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
4635 6301 1.108776 CATACTCCCTCCGTTCGGAA 58.891 55.000 14.79 0.00 33.41 4.30
4636 6302 1.687123 CATACTCCCTCCGTTCGGAAT 59.313 52.381 14.79 2.14 33.41 3.01
4637 6303 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
4638 6304 0.981943 ACTCCCTCCGTTCGGAATTT 59.018 50.000 14.79 0.00 33.41 1.82
4639 6305 1.350019 ACTCCCTCCGTTCGGAATTTT 59.650 47.619 14.79 0.00 33.41 1.82
4640 6306 2.568509 ACTCCCTCCGTTCGGAATTTTA 59.431 45.455 14.79 0.00 33.41 1.52
4641 6307 3.195661 CTCCCTCCGTTCGGAATTTTAG 58.804 50.000 14.79 2.64 33.41 1.85
4642 6308 2.568509 TCCCTCCGTTCGGAATTTTAGT 59.431 45.455 14.79 0.00 33.41 2.24
4643 6309 3.008266 TCCCTCCGTTCGGAATTTTAGTT 59.992 43.478 14.79 0.00 33.41 2.24
4644 6310 3.373130 CCCTCCGTTCGGAATTTTAGTTC 59.627 47.826 14.79 0.00 33.41 3.01
4645 6311 4.251268 CCTCCGTTCGGAATTTTAGTTCT 58.749 43.478 14.79 0.00 33.41 3.01
4646 6312 5.413499 CCTCCGTTCGGAATTTTAGTTCTA 58.587 41.667 14.79 0.00 33.41 2.10
4647 6313 5.519206 CCTCCGTTCGGAATTTTAGTTCTAG 59.481 44.000 14.79 0.00 33.41 2.43
4648 6314 6.271488 TCCGTTCGGAATTTTAGTTCTAGA 57.729 37.500 11.66 0.00 0.00 2.43
4649 6315 6.870769 TCCGTTCGGAATTTTAGTTCTAGAT 58.129 36.000 11.66 0.00 0.00 1.98
4650 6316 7.999679 TCCGTTCGGAATTTTAGTTCTAGATA 58.000 34.615 11.66 0.00 0.00 1.98
4651 6317 7.917505 TCCGTTCGGAATTTTAGTTCTAGATAC 59.082 37.037 11.66 0.00 0.00 2.24
4652 6318 7.703621 CCGTTCGGAATTTTAGTTCTAGATACA 59.296 37.037 5.19 0.00 0.00 2.29
4653 6319 9.245962 CGTTCGGAATTTTAGTTCTAGATACAT 57.754 33.333 0.00 0.00 0.00 2.29
4655 6321 9.760077 TTCGGAATTTTAGTTCTAGATACATCC 57.240 33.333 0.00 0.00 0.00 3.51
4656 6322 8.920174 TCGGAATTTTAGTTCTAGATACATCCA 58.080 33.333 0.00 0.00 0.00 3.41
4657 6323 9.712305 CGGAATTTTAGTTCTAGATACATCCAT 57.288 33.333 0.00 0.00 0.00 3.41
4666 6332 9.606631 AGTTCTAGATACATCCATTTTCAAGAC 57.393 33.333 0.00 0.00 0.00 3.01
4667 6333 9.383519 GTTCTAGATACATCCATTTTCAAGACA 57.616 33.333 0.00 0.00 0.00 3.41
4668 6334 9.958180 TTCTAGATACATCCATTTTCAAGACAA 57.042 29.630 0.00 0.00 0.00 3.18
4669 6335 9.605275 TCTAGATACATCCATTTTCAAGACAAG 57.395 33.333 0.00 0.00 0.00 3.16
4670 6336 9.388506 CTAGATACATCCATTTTCAAGACAAGT 57.611 33.333 0.00 0.00 0.00 3.16
4672 6338 9.739276 AGATACATCCATTTTCAAGACAAGTAA 57.261 29.630 0.00 0.00 0.00 2.24
4676 6342 9.696917 ACATCCATTTTCAAGACAAGTAATTTC 57.303 29.630 0.00 0.00 0.00 2.17
4677 6343 8.853345 CATCCATTTTCAAGACAAGTAATTTCG 58.147 33.333 0.00 0.00 0.00 3.46
4678 6344 8.160521 TCCATTTTCAAGACAAGTAATTTCGA 57.839 30.769 0.00 0.00 0.00 3.71
4679 6345 8.625651 TCCATTTTCAAGACAAGTAATTTCGAA 58.374 29.630 0.00 0.00 0.00 3.71
4680 6346 8.690840 CCATTTTCAAGACAAGTAATTTCGAAC 58.309 33.333 0.00 0.00 0.00 3.95
4681 6347 7.886191 TTTTCAAGACAAGTAATTTCGAACG 57.114 32.000 0.00 0.00 0.00 3.95
4682 6348 5.585500 TCAAGACAAGTAATTTCGAACGG 57.415 39.130 0.00 0.00 0.00 4.44
4683 6349 5.291178 TCAAGACAAGTAATTTCGAACGGA 58.709 37.500 0.00 0.00 0.00 4.69
4684 6350 5.404366 TCAAGACAAGTAATTTCGAACGGAG 59.596 40.000 0.00 0.00 0.00 4.63
4685 6351 4.243270 AGACAAGTAATTTCGAACGGAGG 58.757 43.478 0.00 0.00 0.00 4.30
4686 6352 3.332034 ACAAGTAATTTCGAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
4687 6353 3.007182 ACAAGTAATTTCGAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
4688 6354 3.521947 AGTAATTTCGAACGGAGGGAG 57.478 47.619 0.00 0.00 0.00 4.30
4728 6394 0.249699 TCGACGAGCACCACAACAAT 60.250 50.000 0.00 0.00 0.00 2.71
4731 6397 2.683968 GACGAGCACCACAACAATAGA 58.316 47.619 0.00 0.00 0.00 1.98
4732 6398 2.412089 GACGAGCACCACAACAATAGAC 59.588 50.000 0.00 0.00 0.00 2.59
4733 6399 1.390123 CGAGCACCACAACAATAGACG 59.610 52.381 0.00 0.00 0.00 4.18
4734 6400 2.683968 GAGCACCACAACAATAGACGA 58.316 47.619 0.00 0.00 0.00 4.20
4775 6441 5.060200 GCAAAGATTCAAGTCATTTTCTCGC 59.940 40.000 0.00 0.00 0.00 5.03
4776 6442 6.376978 CAAAGATTCAAGTCATTTTCTCGCT 58.623 36.000 0.00 0.00 0.00 4.93
4777 6443 5.793026 AGATTCAAGTCATTTTCTCGCTC 57.207 39.130 0.00 0.00 0.00 5.03
4778 6444 5.486526 AGATTCAAGTCATTTTCTCGCTCT 58.513 37.500 0.00 0.00 0.00 4.09
4828 6494 3.202906 TGTGCTACAAGAGGAAACACAC 58.797 45.455 0.00 0.00 32.06 3.82
4844 6510 1.237285 ACACGAGTTCAATGCTGGGC 61.237 55.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.000819 TGTACTCGGGGTGGCTGG 61.001 66.667 0.00 0.00 0.00 4.85
53 54 5.060569 CGAAATAGTTGTTCTGGTGTACTCG 59.939 44.000 0.00 0.00 0.00 4.18
55 56 6.092955 TCGAAATAGTTGTTCTGGTGTACT 57.907 37.500 0.00 0.00 0.00 2.73
57 58 6.015688 AGACTCGAAATAGTTGTTCTGGTGTA 60.016 38.462 0.00 0.00 0.00 2.90
98 99 4.963318 TCTCAAACTCCTCAGTCAACAT 57.037 40.909 0.00 0.00 29.93 2.71
101 102 5.059161 CACAATCTCAAACTCCTCAGTCAA 58.941 41.667 0.00 0.00 29.93 3.18
104 105 3.244700 CCCACAATCTCAAACTCCTCAGT 60.245 47.826 0.00 0.00 0.00 3.41
217 219 9.899661 ATCACATTGTATTGGCTTACTTACTAA 57.100 29.630 0.00 0.00 0.00 2.24
225 227 5.009911 GCCATGATCACATTGTATTGGCTTA 59.990 40.000 20.41 0.00 36.12 3.09
283 285 1.373748 GTGCGGCTCGTGGTTTCTA 60.374 57.895 0.00 0.00 0.00 2.10
294 296 4.722700 GTGGACCCATGTGCGGCT 62.723 66.667 0.00 0.00 35.21 5.52
302 304 1.351017 AGTTCGTCAATGTGGACCCAT 59.649 47.619 0.00 0.00 34.24 4.00
338 340 2.031919 TGAGCCGATGGTTTGCGT 59.968 55.556 0.00 0.00 0.00 5.24
340 342 0.659957 GATCTGAGCCGATGGTTTGC 59.340 55.000 0.00 0.00 0.00 3.68
421 423 2.437359 GGAACATCGCTGCTGCCT 60.437 61.111 10.24 0.00 35.36 4.75
432 434 6.543100 TGTAACGTAAAAAGTTCAGGGAACAT 59.457 34.615 11.28 0.00 44.11 2.71
433 435 5.879223 TGTAACGTAAAAAGTTCAGGGAACA 59.121 36.000 11.28 0.00 44.11 3.18
437 439 6.961576 TGATTGTAACGTAAAAAGTTCAGGG 58.038 36.000 0.00 0.00 33.42 4.45
468 470 2.910688 ATCCACATATTTCGAGCCGT 57.089 45.000 0.00 0.00 0.00 5.68
505 507 3.373130 TGATAACACTCGTCTCGTCGATT 59.627 43.478 0.00 0.00 39.12 3.34
550 552 1.306642 CGCGGACCGATATAGAGGCT 61.307 60.000 20.50 0.00 40.02 4.58
558 560 4.840288 CGTGTGCGCGGACCGATA 62.840 66.667 28.22 6.33 40.02 2.92
566 568 3.913573 GCTATGACCGTGTGCGCG 61.914 66.667 0.00 0.00 36.67 6.86
567 569 2.296692 CTTGCTATGACCGTGTGCGC 62.297 60.000 0.00 0.00 36.67 6.09
568 570 1.014044 ACTTGCTATGACCGTGTGCG 61.014 55.000 0.00 0.00 37.95 5.34
583 585 7.701809 TTCTTTTGCCGGTTTTTATTACTTG 57.298 32.000 1.90 0.00 0.00 3.16
647 649 2.676748 TGGGGTTTTGCAGAATTGTCT 58.323 42.857 0.00 0.00 32.85 3.41
657 659 1.039856 TCAAGCTCTTGGGGTTTTGC 58.960 50.000 9.48 0.00 40.78 3.68
663 665 0.322008 GTCTGGTCAAGCTCTTGGGG 60.322 60.000 9.48 0.00 40.78 4.96
937 948 4.729918 AAAGCAGCCGAGGCAGGG 62.730 66.667 17.18 6.49 44.88 4.45
938 949 2.674380 AAAAGCAGCCGAGGCAGG 60.674 61.111 17.18 9.03 44.88 4.85
939 950 1.239968 AAGAAAAGCAGCCGAGGCAG 61.240 55.000 17.18 9.65 44.88 4.85
940 951 1.228245 AAGAAAAGCAGCCGAGGCA 60.228 52.632 17.18 0.00 44.88 4.75
941 952 1.211190 CAAGAAAAGCAGCCGAGGC 59.789 57.895 5.89 5.89 42.33 4.70
942 953 1.399791 GATCAAGAAAAGCAGCCGAGG 59.600 52.381 0.00 0.00 0.00 4.63
943 954 2.351111 GAGATCAAGAAAAGCAGCCGAG 59.649 50.000 0.00 0.00 0.00 4.63
978 990 0.111446 CGAGGAGGAGGAGGATAGCA 59.889 60.000 0.00 0.00 0.00 3.49
987 999 2.060383 TGCCATGACGAGGAGGAGG 61.060 63.158 0.00 0.00 0.00 4.30
1157 1180 4.187694 CGGAAAGAAAGAGATGAAGGAGG 58.812 47.826 0.00 0.00 0.00 4.30
1161 1184 4.867608 GGAGACGGAAAGAAAGAGATGAAG 59.132 45.833 0.00 0.00 0.00 3.02
1162 1185 4.322801 GGGAGACGGAAAGAAAGAGATGAA 60.323 45.833 0.00 0.00 0.00 2.57
1164 1187 3.196685 AGGGAGACGGAAAGAAAGAGATG 59.803 47.826 0.00 0.00 0.00 2.90
1165 1188 3.196685 CAGGGAGACGGAAAGAAAGAGAT 59.803 47.826 0.00 0.00 0.00 2.75
1166 1189 2.563179 CAGGGAGACGGAAAGAAAGAGA 59.437 50.000 0.00 0.00 0.00 3.10
1169 1192 2.808543 CAACAGGGAGACGGAAAGAAAG 59.191 50.000 0.00 0.00 0.00 2.62
1318 1342 4.758251 TGATCCAGCACCACCGCG 62.758 66.667 0.00 0.00 36.85 6.46
1378 1402 3.426963 GGATTAAGCAACGCCATCGAAAA 60.427 43.478 0.00 0.00 39.41 2.29
1379 1403 2.096819 GGATTAAGCAACGCCATCGAAA 59.903 45.455 0.00 0.00 39.41 3.46
1389 1413 1.654023 AAGGCCGCGGATTAAGCAAC 61.654 55.000 33.48 7.28 34.19 4.17
1454 1478 4.717313 GCCGACCACCCCTCCAAC 62.717 72.222 0.00 0.00 0.00 3.77
1645 1670 3.759618 ACGAAGAACCAAGAAAACCACAA 59.240 39.130 0.00 0.00 0.00 3.33
1646 1671 3.349022 ACGAAGAACCAAGAAAACCACA 58.651 40.909 0.00 0.00 0.00 4.17
1647 1672 3.626217 AGACGAAGAACCAAGAAAACCAC 59.374 43.478 0.00 0.00 0.00 4.16
1648 1673 3.875134 GAGACGAAGAACCAAGAAAACCA 59.125 43.478 0.00 0.00 0.00 3.67
1761 1786 2.273370 TCGAGCAACCGATTGTAGAC 57.727 50.000 0.00 0.00 38.17 2.59
1800 1825 6.392625 AGAAAAAGAAGGGTTAGTTCTTGC 57.607 37.500 0.00 0.00 42.25 4.01
1864 1889 6.862209 TGTACAGCAACTTTTGACTGAATTT 58.138 32.000 13.64 0.17 37.84 1.82
1964 1989 7.931948 AGTAGCAATAATACTATGACCACCAAC 59.068 37.037 0.00 0.00 31.71 3.77
1982 2007 9.780186 GTCTATTTCTACCCAAATAGTAGCAAT 57.220 33.333 11.06 0.00 43.00 3.56
2026 2051 4.283467 TCTGTATGAGCCACAGTAACTGTT 59.717 41.667 0.00 0.00 42.59 3.16
2088 2113 8.004087 AGTTTTAAGAGTTACCCTGGAAAAAC 57.996 34.615 0.00 0.00 0.00 2.43
2131 2156 8.658499 TTCAAACACTTCCTCTTCTTAAGTAC 57.342 34.615 1.63 0.00 32.35 2.73
2132 2157 9.490379 GATTCAAACACTTCCTCTTCTTAAGTA 57.510 33.333 1.63 0.00 32.35 2.24
2133 2158 7.445707 GGATTCAAACACTTCCTCTTCTTAAGT 59.554 37.037 1.63 0.00 33.82 2.24
2134 2159 7.445402 TGGATTCAAACACTTCCTCTTCTTAAG 59.555 37.037 0.00 0.00 0.00 1.85
2199 2228 9.239002 CTATGAGTTACATACTAGAGTTGCAAC 57.761 37.037 22.17 22.17 40.07 4.17
2222 2251 9.052365 AGATAACTTCTTTGAGAAAGGACCTAT 57.948 33.333 0.00 0.00 39.01 2.57
2226 2255 7.971183 ACAGATAACTTCTTTGAGAAAGGAC 57.029 36.000 0.00 0.00 39.01 3.85
2423 2452 5.825593 AAATCCACTGTCTAAGGACTTGA 57.174 39.130 0.00 0.00 42.54 3.02
2489 2519 4.816385 TCAGCACTCAGTTTAAAGAGTTGG 59.184 41.667 7.24 0.76 42.87 3.77
2616 2646 8.617290 ACTGGTACAAGAAATGGTTAAACTAG 57.383 34.615 3.64 0.00 38.70 2.57
2791 2821 2.310538 ACACTTTGGCAAGGAAGAAGG 58.689 47.619 16.87 2.39 33.82 3.46
2847 2877 9.938280 ATTCAATTCATTCTTCAACATGAACAT 57.062 25.926 0.00 0.00 41.18 2.71
2878 2908 3.324268 TCTTCCCATGCTTTTTCAATGCA 59.676 39.130 0.00 0.00 44.26 3.96
2885 2915 5.941647 CCAATTCATTCTTCCCATGCTTTTT 59.058 36.000 0.00 0.00 0.00 1.94
2939 2969 3.054166 CTGTGTGGCAAACATGAACATG 58.946 45.455 11.65 12.43 41.97 3.21
3008 3038 5.104859 TGGAGTAGTGTCCTGTGTAAACAAA 60.105 40.000 0.00 0.00 37.52 2.83
3163 3193 3.071874 TGATCCTCCAACGCAAGAATT 57.928 42.857 0.00 0.00 43.62 2.17
3400 3430 0.953471 GTGTTGTGTCTATGGCGCCA 60.953 55.000 34.80 34.80 0.00 5.69
3748 3778 1.868469 TGTTGAATGCTGCTTTTGCC 58.132 45.000 0.00 0.00 46.87 4.52
3848 3878 1.228245 GCTTGTCAGGCCTCCACAA 60.228 57.895 20.87 20.87 0.00 3.33
3899 3929 2.679336 CGATCATGATGTTGGTGAGCAA 59.321 45.455 14.30 0.00 0.00 3.91
3952 3982 3.356639 ATCATGGTCGTGCGACGCT 62.357 57.895 22.08 5.44 45.41 5.07
4006 4036 4.306967 TGCACGACCGCACCATCA 62.307 61.111 0.00 0.00 36.86 3.07
4009 4039 4.662961 CTCTGCACGACCGCACCA 62.663 66.667 0.00 0.00 36.86 4.17
4020 4050 1.597854 CAAAGCACGTCCCTCTGCA 60.598 57.895 0.00 0.00 35.73 4.41
4073 4103 2.158593 AGCTAGAGGGCGAGAATCACTA 60.159 50.000 0.00 0.00 37.29 2.74
4285 4328 4.803329 ACCCTTGCCTGAGAATATCATT 57.197 40.909 0.00 0.00 37.28 2.57
4298 4341 3.769300 AGAATTCCAACAATACCCTTGCC 59.231 43.478 0.65 0.00 0.00 4.52
4314 4357 7.778470 ATTTCATGAGACGAAGGTAGAATTC 57.222 36.000 0.00 0.00 0.00 2.17
4326 4369 4.631377 TCAGGTTGCTAATTTCATGAGACG 59.369 41.667 0.00 0.00 0.00 4.18
4368 4411 4.563184 GCTTAATCGAACGATTCACAGACT 59.437 41.667 22.44 2.98 43.04 3.24
4373 4416 4.842139 ACAGCTTAATCGAACGATTCAC 57.158 40.909 22.44 14.30 43.04 3.18
4378 4421 4.059511 TCCAAAACAGCTTAATCGAACGA 58.940 39.130 0.00 0.00 0.00 3.85
4380 4423 5.938322 TCATCCAAAACAGCTTAATCGAAC 58.062 37.500 0.00 0.00 0.00 3.95
4408 6053 8.624776 CATTTGAGTTTTCCCCTATGATTCTAC 58.375 37.037 0.00 0.00 0.00 2.59
4420 6065 7.666623 TCCTGTTAAATCATTTGAGTTTTCCC 58.333 34.615 0.00 0.00 34.03 3.97
4502 6168 7.338800 CACCTCTCTTTTGGTGCATAATAAT 57.661 36.000 0.00 0.00 45.68 1.28
4618 6284 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
4619 6285 0.981943 AAATTCCGAACGGAGGGAGT 59.018 50.000 15.34 0.00 46.06 3.85
4620 6286 2.109425 AAAATTCCGAACGGAGGGAG 57.891 50.000 15.34 0.00 46.06 4.30
4621 6287 2.568509 ACTAAAATTCCGAACGGAGGGA 59.431 45.455 15.34 2.49 46.06 4.20
4622 6288 2.981898 ACTAAAATTCCGAACGGAGGG 58.018 47.619 15.34 6.79 46.06 4.30
4623 6289 4.251268 AGAACTAAAATTCCGAACGGAGG 58.749 43.478 15.34 6.50 46.06 4.30
4624 6290 6.327934 TCTAGAACTAAAATTCCGAACGGAG 58.672 40.000 15.34 6.26 46.06 4.63
4625 6291 6.271488 TCTAGAACTAAAATTCCGAACGGA 57.729 37.500 12.04 12.04 43.52 4.69
4626 6292 7.703621 TGTATCTAGAACTAAAATTCCGAACGG 59.296 37.037 6.94 6.94 0.00 4.44
4627 6293 8.624701 TGTATCTAGAACTAAAATTCCGAACG 57.375 34.615 0.00 0.00 0.00 3.95
4629 6295 9.760077 GGATGTATCTAGAACTAAAATTCCGAA 57.240 33.333 0.00 0.00 0.00 4.30
4630 6296 8.920174 TGGATGTATCTAGAACTAAAATTCCGA 58.080 33.333 0.00 0.00 0.00 4.55
4631 6297 9.712305 ATGGATGTATCTAGAACTAAAATTCCG 57.288 33.333 0.00 0.00 0.00 4.30
4640 6306 9.606631 GTCTTGAAAATGGATGTATCTAGAACT 57.393 33.333 0.00 0.00 0.00 3.01
4641 6307 9.383519 TGTCTTGAAAATGGATGTATCTAGAAC 57.616 33.333 0.00 0.00 0.00 3.01
4642 6308 9.958180 TTGTCTTGAAAATGGATGTATCTAGAA 57.042 29.630 0.00 0.00 0.00 2.10
4643 6309 9.605275 CTTGTCTTGAAAATGGATGTATCTAGA 57.395 33.333 0.00 0.00 0.00 2.43
4644 6310 9.388506 ACTTGTCTTGAAAATGGATGTATCTAG 57.611 33.333 0.00 0.00 0.00 2.43
4646 6312 9.739276 TTACTTGTCTTGAAAATGGATGTATCT 57.261 29.630 0.00 0.00 0.00 1.98
4650 6316 9.696917 GAAATTACTTGTCTTGAAAATGGATGT 57.303 29.630 0.00 0.00 0.00 3.06
4651 6317 8.853345 CGAAATTACTTGTCTTGAAAATGGATG 58.147 33.333 0.00 0.00 0.00 3.51
4652 6318 8.792633 TCGAAATTACTTGTCTTGAAAATGGAT 58.207 29.630 0.00 0.00 0.00 3.41
4653 6319 8.160521 TCGAAATTACTTGTCTTGAAAATGGA 57.839 30.769 0.00 0.00 0.00 3.41
4654 6320 8.690840 GTTCGAAATTACTTGTCTTGAAAATGG 58.309 33.333 0.00 0.00 0.00 3.16
4655 6321 8.409690 CGTTCGAAATTACTTGTCTTGAAAATG 58.590 33.333 0.00 0.00 0.00 2.32
4656 6322 7.589954 CCGTTCGAAATTACTTGTCTTGAAAAT 59.410 33.333 0.00 0.00 0.00 1.82
4657 6323 6.908284 CCGTTCGAAATTACTTGTCTTGAAAA 59.092 34.615 0.00 0.00 0.00 2.29
4658 6324 6.258287 TCCGTTCGAAATTACTTGTCTTGAAA 59.742 34.615 0.00 0.00 0.00 2.69
4659 6325 5.754406 TCCGTTCGAAATTACTTGTCTTGAA 59.246 36.000 0.00 0.00 0.00 2.69
4660 6326 5.291178 TCCGTTCGAAATTACTTGTCTTGA 58.709 37.500 0.00 0.00 0.00 3.02
4661 6327 5.389516 CCTCCGTTCGAAATTACTTGTCTTG 60.390 44.000 0.00 0.00 0.00 3.02
4662 6328 4.689345 CCTCCGTTCGAAATTACTTGTCTT 59.311 41.667 0.00 0.00 0.00 3.01
4663 6329 4.243270 CCTCCGTTCGAAATTACTTGTCT 58.757 43.478 0.00 0.00 0.00 3.41
4664 6330 3.370061 CCCTCCGTTCGAAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
4665 6331 3.007182 TCCCTCCGTTCGAAATTACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
4666 6332 3.592059 TCCCTCCGTTCGAAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
4667 6333 3.260128 ACTCCCTCCGTTCGAAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
4668 6334 2.830321 ACTCCCTCCGTTCGAAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
4669 6335 3.242549 ACTCCCTCCGTTCGAAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
4670 6336 3.763360 TGTACTCCCTCCGTTCGAAATTA 59.237 43.478 0.00 0.00 0.00 1.40
4671 6337 2.564062 TGTACTCCCTCCGTTCGAAATT 59.436 45.455 0.00 0.00 0.00 1.82
4672 6338 2.173519 TGTACTCCCTCCGTTCGAAAT 58.826 47.619 0.00 0.00 0.00 2.17
4673 6339 1.619654 TGTACTCCCTCCGTTCGAAA 58.380 50.000 0.00 0.00 0.00 3.46
4674 6340 1.747355 GATGTACTCCCTCCGTTCGAA 59.253 52.381 0.00 0.00 0.00 3.71
4675 6341 1.064906 AGATGTACTCCCTCCGTTCGA 60.065 52.381 0.00 0.00 0.00 3.71
4676 6342 1.334243 GAGATGTACTCCCTCCGTTCG 59.666 57.143 0.00 0.00 39.53 3.95
4677 6343 2.359531 CAGAGATGTACTCCCTCCGTTC 59.640 54.545 0.00 0.00 45.96 3.95
4678 6344 2.379972 CAGAGATGTACTCCCTCCGTT 58.620 52.381 0.00 0.00 45.96 4.44
4679 6345 2.024825 GCAGAGATGTACTCCCTCCGT 61.025 57.143 0.00 0.00 45.96 4.69
4680 6346 0.671251 GCAGAGATGTACTCCCTCCG 59.329 60.000 0.00 0.00 45.96 4.63
4681 6347 0.671251 CGCAGAGATGTACTCCCTCC 59.329 60.000 0.00 0.00 45.96 4.30
4682 6348 1.335496 GTCGCAGAGATGTACTCCCTC 59.665 57.143 0.00 0.00 45.96 4.30
4683 6349 1.341089 TGTCGCAGAGATGTACTCCCT 60.341 52.381 0.00 0.00 45.96 4.20
4684 6350 1.103803 TGTCGCAGAGATGTACTCCC 58.896 55.000 0.00 0.00 45.96 4.30
4685 6351 2.941453 TTGTCGCAGAGATGTACTCC 57.059 50.000 0.00 0.00 45.96 3.85
4686 6352 4.627467 ACATTTTGTCGCAGAGATGTACTC 59.373 41.667 0.00 0.00 45.22 2.59
4687 6353 4.569943 ACATTTTGTCGCAGAGATGTACT 58.430 39.130 0.00 0.00 36.95 2.73
4688 6354 4.886971 GACATTTTGTCGCAGAGATGTAC 58.113 43.478 0.00 0.00 37.67 2.90
4728 6394 2.660094 CGTGAGTTCGTTCGTTCGTCTA 60.660 50.000 2.67 0.00 0.00 2.59
4731 6397 0.248215 ACGTGAGTTCGTTCGTTCGT 60.248 50.000 0.00 0.00 46.40 3.85
4732 6398 0.156035 CACGTGAGTTCGTTCGTTCG 59.844 55.000 10.90 0.00 46.40 3.95
4733 6399 0.111835 GCACGTGAGTTCGTTCGTTC 60.112 55.000 22.23 0.00 46.40 3.95
4734 6400 0.802994 TGCACGTGAGTTCGTTCGTT 60.803 50.000 22.23 0.00 46.40 3.85
4750 6416 6.144854 CGAGAAAATGACTTGAATCTTTGCA 58.855 36.000 0.00 0.00 0.00 4.08
4775 6441 7.859875 CCTAGTTTGCAAGAAAGAAAGAAAGAG 59.140 37.037 0.00 0.00 0.00 2.85
4776 6442 7.339466 ACCTAGTTTGCAAGAAAGAAAGAAAGA 59.661 33.333 0.00 0.00 0.00 2.52
4777 6443 7.433425 CACCTAGTTTGCAAGAAAGAAAGAAAG 59.567 37.037 0.00 0.00 0.00 2.62
4778 6444 7.257722 CACCTAGTTTGCAAGAAAGAAAGAAA 58.742 34.615 0.00 0.00 0.00 2.52
4828 6494 2.787249 CGCCCAGCATTGAACTCG 59.213 61.111 0.00 0.00 0.00 4.18
4844 6510 3.381169 CTTTCGGGTTGGCGATGCG 62.381 63.158 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.