Multiple sequence alignment - TraesCS2A01G583700

Loading Multiple Alignment...

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 TraesCS2A01G583700 chr2A 100.000 7198 0 0 1 7198 775443293 775436096 0.000000e+00 13293.0
1 TraesCS2A01G583700 chr2D 97.296 3920 83 9 1868 5779 649304210 649308114 0.000000e+00 6630.0
2 TraesCS2A01G583700 chr2D 92.173 1086 49 16 769 1838 649303060 649304125 0.000000e+00 1502.0
3 TraesCS2A01G583700 chr2D 94.978 916 31 7 6288 7198 649308913 649309818 0.000000e+00 1423.0
4 TraesCS2A01G583700 chr2D 88.235 714 65 8 66 770 649302267 649302970 0.000000e+00 835.0
5 TraesCS2A01G583700 chr2D 94.184 533 15 4 5807 6335 649308397 649308917 0.000000e+00 798.0
6 TraesCS2A01G583700 chr2D 87.165 709 64 14 227 932 649301388 649302072 0.000000e+00 780.0
7 TraesCS2A01G583700 chr2D 85.797 690 73 11 82 767 649154877 649155545 0.000000e+00 708.0
8 TraesCS2A01G583700 chr2B 93.677 4381 212 38 1423 5779 785188983 785193322 0.000000e+00 6495.0
9 TraesCS2A01G583700 chr2B 91.631 944 37 17 6288 7198 785194194 785195128 0.000000e+00 1267.0
10 TraesCS2A01G583700 chr2B 87.478 1126 92 20 66 1170 785160267 785161364 0.000000e+00 1253.0
11 TraesCS2A01G583700 chr2B 90.506 948 59 7 430 1371 785188046 785188968 0.000000e+00 1223.0
12 TraesCS2A01G583700 chr2B 88.154 937 84 12 3 932 785159149 785160065 0.000000e+00 1090.0
13 TraesCS2A01G583700 chr2B 88.617 817 62 8 3 817 785183527 785184314 0.000000e+00 965.0
14 TraesCS2A01G583700 chr2B 86.635 853 85 12 90 932 785186424 785187257 0.000000e+00 917.0
15 TraesCS2A01G583700 chr2B 95.248 484 18 3 5856 6335 785193716 785194198 0.000000e+00 761.0
16 TraesCS2A01G583700 chr2B 87.521 593 62 6 66 651 785187457 785188044 0.000000e+00 675.0
17 TraesCS2A01G583700 chr2B 91.954 87 6 1 3 88 785160237 785160323 3.530000e-23 121.0
18 TraesCS2A01G583700 chr2B 89.655 87 8 1 3 88 785187427 785187513 7.630000e-20 110.0
19 TraesCS2A01G583700 chr2B 80.952 105 15 4 8 110 798126559 798126458 2.150000e-10 78.7
20 TraesCS2A01G583700 chr6A 85.227 88 12 1 8 94 163201156 163201243 9.950000e-14 89.8
21 TraesCS2A01G583700 chr6A 84.884 86 13 0 3 88 207632580 207632665 3.580000e-13 87.9
22 TraesCS2A01G583700 chrUn 83.721 86 14 0 3 88 13405866 13405781 1.660000e-11 82.4
23 TraesCS2A01G583700 chr7B 83.146 89 13 2 3 90 14870190 14870277 5.990000e-11 80.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G583700 chr2A 775436096 775443293 7197 True 13293.000000 13293 100.000000 1 7198 1 chr2A.!!$R1 7197
1 TraesCS2A01G583700 chr2D 649301388 649309818 8430 False 1994.666667 6630 92.338500 66 7198 6 chr2D.!!$F2 7132
2 TraesCS2A01G583700 chr2D 649154877 649155545 668 False 708.000000 708 85.797000 82 767 1 chr2D.!!$F1 685
3 TraesCS2A01G583700 chr2B 785183527 785195128 11601 False 1551.625000 6495 90.436250 3 7198 8 chr2B.!!$F2 7195
4 TraesCS2A01G583700 chr2B 785159149 785161364 2215 False 821.333333 1253 89.195333 3 1170 3 chr2B.!!$F1 1167

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
513 3329 0.315869 GCACAACCGTGAGAACGTTG 60.316 55.000 5.00 0.00 46.80 4.10 F
1389 5643 0.107703 TCCGCCTTGCTTTGATCGAT 60.108 50.000 0.00 0.00 0.00 3.59 F
1770 6043 0.319125 GATCGGAGCCGGTGAAGATC 60.319 60.000 9.29 9.63 40.25 2.75 F
2088 6437 0.322816 TGCCCATTCCTGCAGAAGAC 60.323 55.000 17.39 0.00 38.07 3.01 F
2952 7308 0.536233 TTGCAGTGCGGTGTTACCAT 60.536 50.000 11.20 0.00 38.47 3.55 F
4587 8945 2.235650 CTGGTCTCTGAAATCTCTGGCA 59.764 50.000 0.00 0.00 0.00 4.92 F
4934 9293 0.460722 GCACAATGCATGCCCACATA 59.539 50.000 16.68 0.00 44.26 2.29 F
5779 10140 2.466846 TGCCTCAGCAGTATTAGTGGA 58.533 47.619 0.85 0.00 46.52 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 5850 0.179119 GCGCCGAGTAACACCAGTAT 60.179 55.000 0.00 0.0 0.00 2.12 R
2415 6771 0.615850 AGCCAGTAAGACCCTTGCTC 59.384 55.000 0.00 0.0 0.00 4.26 R
3750 8108 0.316841 TGGATTGGCTTGAAAACGGC 59.683 50.000 0.00 0.0 0.00 5.68 R
3813 8171 2.093783 GTCGTTCGCCAACCTAAATCTG 59.906 50.000 0.00 0.0 0.00 2.90 R
4934 9293 5.253330 ACATGTTAATGGAAACTGGACGAT 58.747 37.500 0.00 0.0 38.19 3.73 R
5781 10142 0.403271 CCCCTCCCCAATAGAGCATG 59.597 60.000 0.00 0.0 0.00 4.06 R
5782 10143 0.773700 CCCCCTCCCCAATAGAGCAT 60.774 60.000 0.00 0.0 0.00 3.79 R
6671 11399 2.038952 ACTGCAGAGCAACACCTCATAA 59.961 45.455 23.35 0.0 38.41 1.90 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
94 95 7.204604 TCAATATACAGCCATGCATGAAAAAG 58.795 34.615 28.31 11.71 0.00 2.27
112 113 8.208718 TGAAAAAGGTTCCATCTCAATATACG 57.791 34.615 0.00 0.00 0.00 3.06
267 3083 4.073200 GCTGGCCAACCACATGCC 62.073 66.667 7.01 0.00 42.67 4.40
281 3097 1.133823 ACATGCCTGTGGAAGTTGTGA 60.134 47.619 0.00 0.00 33.22 3.58
322 3138 2.606961 CGTGTCACCAATGCGCAGT 61.607 57.895 18.32 11.60 0.00 4.40
439 3255 0.322816 ATCAACACCGCTGGCAATCT 60.323 50.000 0.00 0.00 0.00 2.40
444 3260 2.117156 ACCGCTGGCAATCTCATGC 61.117 57.895 0.00 0.00 45.67 4.06
463 3279 1.136690 CGCGTGAAAGTTGTGCTAGA 58.863 50.000 0.00 0.00 0.00 2.43
475 3291 3.134574 TGTGCTAGAAAAACCGATGGT 57.865 42.857 0.00 0.00 37.65 3.55
504 3320 4.326766 CGCTTGGGCACAACCGTG 62.327 66.667 8.26 0.00 46.56 4.94
513 3329 0.315869 GCACAACCGTGAGAACGTTG 60.316 55.000 5.00 0.00 46.80 4.10
524 3340 4.378616 CGTGAGAACGTTGGCAAAATAAAG 59.621 41.667 5.00 0.00 0.00 1.85
526 3342 5.398416 GTGAGAACGTTGGCAAAATAAAGTC 59.602 40.000 5.00 0.00 0.00 3.01
532 3348 6.386654 ACGTTGGCAAAATAAAGTCTTATGG 58.613 36.000 0.00 0.00 0.00 2.74
549 3365 8.535335 AGTCTTATGGATAATGATAAGCATCGT 58.465 33.333 0.00 0.00 35.78 3.73
566 3382 5.981174 GCATCGTATCGGTAAATGCTTTAA 58.019 37.500 14.17 0.00 39.62 1.52
583 3399 9.941325 AATGCTTTAATTACATTGAAACATCCA 57.059 25.926 0.00 0.00 32.94 3.41
584 3400 9.941325 ATGCTTTAATTACATTGAAACATCCAA 57.059 25.926 0.00 0.00 0.00 3.53
589 3405 3.665745 ACATTGAAACATCCAACAGGC 57.334 42.857 0.00 0.00 0.00 4.85
607 3423 2.194597 AGCACCGCTGGAAACCAA 59.805 55.556 1.50 0.00 37.57 3.67
621 3437 2.507339 AACCAAATGCACGTGAAAGG 57.493 45.000 22.23 15.28 0.00 3.11
624 3440 1.130955 CAAATGCACGTGAAAGGCAC 58.869 50.000 22.23 0.00 40.83 5.01
634 3450 1.281656 GAAAGGCACGTGGAAACCG 59.718 57.895 18.88 0.00 0.00 4.44
697 3513 6.198403 TCGTAAGTGCAATAAGATTTAGCGAG 59.802 38.462 0.00 0.00 39.48 5.03
698 3514 6.198403 CGTAAGTGCAATAAGATTTAGCGAGA 59.802 38.462 0.00 0.00 0.00 4.04
699 3515 6.595772 AAGTGCAATAAGATTTAGCGAGAG 57.404 37.500 0.00 0.00 0.00 3.20
702 3518 6.818644 AGTGCAATAAGATTTAGCGAGAGAAA 59.181 34.615 0.00 0.00 0.00 2.52
703 3519 7.497249 AGTGCAATAAGATTTAGCGAGAGAAAT 59.503 33.333 0.00 0.00 0.00 2.17
814 3630 6.882610 ACAATGAAGATTTTGTGTAGAGCA 57.117 33.333 0.00 0.00 34.87 4.26
815 3631 7.275888 ACAATGAAGATTTTGTGTAGAGCAA 57.724 32.000 0.00 0.00 34.87 3.91
816 3632 7.365741 ACAATGAAGATTTTGTGTAGAGCAAG 58.634 34.615 0.00 0.00 34.87 4.01
817 3633 7.229306 ACAATGAAGATTTTGTGTAGAGCAAGA 59.771 33.333 0.00 0.00 34.87 3.02
818 3634 6.791887 TGAAGATTTTGTGTAGAGCAAGAG 57.208 37.500 0.00 0.00 0.00 2.85
830 5051 0.331616 AGCAAGAGGGGCGGTTTATT 59.668 50.000 0.00 0.00 36.08 1.40
831 5052 1.182667 GCAAGAGGGGCGGTTTATTT 58.817 50.000 0.00 0.00 0.00 1.40
832 5053 2.025699 AGCAAGAGGGGCGGTTTATTTA 60.026 45.455 0.00 0.00 36.08 1.40
836 5057 2.174854 AGAGGGGCGGTTTATTTATGCT 59.825 45.455 0.00 0.00 0.00 3.79
837 5058 2.552743 GAGGGGCGGTTTATTTATGCTC 59.447 50.000 0.00 0.00 0.00 4.26
838 5059 2.174854 AGGGGCGGTTTATTTATGCTCT 59.825 45.455 0.00 0.00 0.00 4.09
839 5060 2.552743 GGGGCGGTTTATTTATGCTCTC 59.447 50.000 0.00 0.00 0.00 3.20
920 5164 4.042311 ACTCCTCCTCGATTATCTCTGCTA 59.958 45.833 0.00 0.00 0.00 3.49
921 5165 4.328536 TCCTCCTCGATTATCTCTGCTAC 58.671 47.826 0.00 0.00 0.00 3.58
922 5166 4.042311 TCCTCCTCGATTATCTCTGCTACT 59.958 45.833 0.00 0.00 0.00 2.57
923 5167 5.248705 TCCTCCTCGATTATCTCTGCTACTA 59.751 44.000 0.00 0.00 0.00 1.82
924 5168 5.353123 CCTCCTCGATTATCTCTGCTACTAC 59.647 48.000 0.00 0.00 0.00 2.73
925 5169 5.866207 TCCTCGATTATCTCTGCTACTACA 58.134 41.667 0.00 0.00 0.00 2.74
926 5170 6.477253 TCCTCGATTATCTCTGCTACTACAT 58.523 40.000 0.00 0.00 0.00 2.29
927 5171 7.621796 TCCTCGATTATCTCTGCTACTACATA 58.378 38.462 0.00 0.00 0.00 2.29
928 5172 8.268605 TCCTCGATTATCTCTGCTACTACATAT 58.731 37.037 0.00 0.00 0.00 1.78
929 5173 9.549078 CCTCGATTATCTCTGCTACTACATATA 57.451 37.037 0.00 0.00 0.00 0.86
938 5182 9.815306 TCTCTGCTACTACATATATTTTCCTCT 57.185 33.333 0.00 0.00 0.00 3.69
939 5183 9.853555 CTCTGCTACTACATATATTTTCCTCTG 57.146 37.037 0.00 0.00 0.00 3.35
940 5184 8.307483 TCTGCTACTACATATATTTTCCTCTGC 58.693 37.037 0.00 0.00 0.00 4.26
941 5185 8.195165 TGCTACTACATATATTTTCCTCTGCT 57.805 34.615 0.00 0.00 0.00 4.24
1176 5430 1.376683 CGCCCAGGTTCCGAATTCA 60.377 57.895 6.22 0.00 0.00 2.57
1372 5626 0.778223 GTACGTTCGTTGGTTCGTCC 59.222 55.000 2.62 0.00 37.66 4.79
1373 5627 0.660005 TACGTTCGTTGGTTCGTCCG 60.660 55.000 2.62 0.00 39.52 4.79
1375 5629 2.662527 TTCGTTGGTTCGTCCGCC 60.663 61.111 0.00 0.00 39.52 6.13
1377 5631 2.647680 TTCGTTGGTTCGTCCGCCTT 62.648 55.000 0.00 0.00 39.52 4.35
1378 5632 2.943653 GTTGGTTCGTCCGCCTTG 59.056 61.111 0.00 0.00 39.52 3.61
1379 5633 2.975799 TTGGTTCGTCCGCCTTGC 60.976 61.111 0.00 0.00 39.52 4.01
1382 5636 2.258726 GGTTCGTCCGCCTTGCTTT 61.259 57.895 0.00 0.00 0.00 3.51
1383 5637 1.082104 GTTCGTCCGCCTTGCTTTG 60.082 57.895 0.00 0.00 0.00 2.77
1384 5638 1.227704 TTCGTCCGCCTTGCTTTGA 60.228 52.632 0.00 0.00 0.00 2.69
1386 5640 1.019278 TCGTCCGCCTTGCTTTGATC 61.019 55.000 0.00 0.00 0.00 2.92
1387 5641 1.425428 GTCCGCCTTGCTTTGATCG 59.575 57.895 0.00 0.00 0.00 3.69
1388 5642 1.019278 GTCCGCCTTGCTTTGATCGA 61.019 55.000 0.00 0.00 0.00 3.59
1389 5643 0.107703 TCCGCCTTGCTTTGATCGAT 60.108 50.000 0.00 0.00 0.00 3.59
1390 5644 0.734889 CCGCCTTGCTTTGATCGATT 59.265 50.000 0.00 0.00 0.00 3.34
1391 5645 1.133025 CCGCCTTGCTTTGATCGATTT 59.867 47.619 0.00 0.00 0.00 2.17
1392 5646 2.179589 CGCCTTGCTTTGATCGATTTG 58.820 47.619 0.00 0.00 0.00 2.32
1393 5647 1.922545 GCCTTGCTTTGATCGATTTGC 59.077 47.619 0.00 2.76 0.00 3.68
1394 5648 2.416431 GCCTTGCTTTGATCGATTTGCT 60.416 45.455 0.00 0.00 0.00 3.91
1395 5649 3.432782 CCTTGCTTTGATCGATTTGCTC 58.567 45.455 0.00 0.00 0.00 4.26
1487 5743 3.934962 GGAGGGGAGAGCATCGGC 61.935 72.222 0.00 0.00 42.67 5.54
1521 5777 1.444553 CAACAGAGTCCTCCGCGTC 60.445 63.158 4.92 0.00 0.00 5.19
1522 5778 2.979197 AACAGAGTCCTCCGCGTCG 61.979 63.158 4.92 0.00 0.00 5.12
1523 5779 3.432588 CAGAGTCCTCCGCGTCGT 61.433 66.667 4.92 0.00 0.00 4.34
1581 5837 2.496817 GACGCGAATCTCCTGGCT 59.503 61.111 15.93 0.00 0.00 4.75
1611 5867 2.277084 CCAATACTGGTGTTACTCGGC 58.723 52.381 0.00 0.00 38.00 5.54
1699 5955 1.009829 GAATGCGCGATCTGTTTCCT 58.990 50.000 12.10 0.00 0.00 3.36
1752 6025 1.224315 CGCCCATTCACCAGATGGA 59.776 57.895 5.72 0.00 37.66 3.41
1770 6043 0.319125 GATCGGAGCCGGTGAAGATC 60.319 60.000 9.29 9.63 40.25 2.75
1779 6052 2.190578 GTGAAGATCCCGCCCCTG 59.809 66.667 0.00 0.00 0.00 4.45
1834 6107 3.833645 CGTTCGGGATGCGAGGGA 61.834 66.667 0.00 0.00 0.00 4.20
1839 6112 4.554036 GGGATGCGAGGGAGCCAC 62.554 72.222 0.00 0.00 36.02 5.01
1840 6113 4.554036 GGATGCGAGGGAGCCACC 62.554 72.222 0.00 0.00 36.02 4.61
1841 6114 4.899239 GATGCGAGGGAGCCACCG 62.899 72.222 0.00 0.00 40.11 4.94
2088 6437 0.322816 TGCCCATTCCTGCAGAAGAC 60.323 55.000 17.39 0.00 38.07 3.01
2103 6452 3.681897 CAGAAGACCAGAAATTCGACAGG 59.318 47.826 0.00 0.00 0.00 4.00
2129 6478 3.195698 GGTCGGCGCATCCTTGTC 61.196 66.667 10.83 0.00 0.00 3.18
2218 6567 1.674962 GATTTCCACTGATGCTGCTCC 59.325 52.381 0.00 0.00 0.00 4.70
2268 6617 5.012148 ACTGTATTAACTGAGCAGAACTGGT 59.988 40.000 6.22 6.22 44.89 4.00
2397 6753 4.202357 ACTTCATTTGTACAGGCAGAGTCA 60.202 41.667 0.00 0.00 0.00 3.41
2415 6771 3.935203 AGTCAGTGATATTGGAAAGTGCG 59.065 43.478 0.00 0.00 0.00 5.34
2425 6781 1.578206 GGAAAGTGCGAGCAAGGGTC 61.578 60.000 0.00 0.00 0.00 4.46
2432 6788 0.741221 GCGAGCAAGGGTCTTACTGG 60.741 60.000 0.00 0.00 0.00 4.00
2433 6789 0.741221 CGAGCAAGGGTCTTACTGGC 60.741 60.000 0.00 0.00 35.06 4.85
2454 6810 4.357142 GCTATCTCGACACGGTTGATAAA 58.643 43.478 0.00 0.00 0.00 1.40
2463 6819 7.863666 TCGACACGGTTGATAAATTAAAAAGT 58.136 30.769 0.00 0.00 0.00 2.66
2466 6822 7.430441 ACACGGTTGATAAATTAAAAAGTGCT 58.570 30.769 0.00 0.00 0.00 4.40
2547 6903 2.095110 CGATGAATTGCTTCACAAGGCA 60.095 45.455 0.00 0.00 43.92 4.75
2608 6964 1.526575 ATGCAGGTTCAGTTTGCCCG 61.527 55.000 0.00 0.00 37.03 6.13
2767 7123 3.406764 AGCGAAAGATTCTGCTGAAAGT 58.593 40.909 10.27 0.00 37.84 2.66
2812 7168 3.629855 TCTCTCTTCCTACGCTCATTGAG 59.370 47.826 9.40 9.40 0.00 3.02
2855 7211 6.402011 GCTCTCAAAGTTAGCTCAGAAATCAC 60.402 42.308 0.00 0.00 33.40 3.06
2931 7287 5.051816 ACAAGTTTCAAATTGCCTGACATG 58.948 37.500 0.00 0.00 37.49 3.21
2942 7298 1.154282 CTGACATGCTTGCAGTGCG 60.154 57.895 11.20 0.00 0.00 5.34
2952 7308 0.536233 TTGCAGTGCGGTGTTACCAT 60.536 50.000 11.20 0.00 38.47 3.55
3170 7526 4.518970 TCTTGACTTTTGACCACATAAGGC 59.481 41.667 0.00 0.00 41.32 4.35
3227 7583 7.284489 AGCTGACTATTTGTTCAACAGGTAAAA 59.716 33.333 0.00 0.00 33.88 1.52
3730 8088 7.469594 CGCTCTCTAATACACACCAAATACCTA 60.470 40.741 0.00 0.00 0.00 3.08
4042 8400 8.928733 GCAATTTGACATTGTACTTGATGAAAT 58.071 29.630 0.00 5.48 0.00 2.17
4587 8945 2.235650 CTGGTCTCTGAAATCTCTGGCA 59.764 50.000 0.00 0.00 0.00 4.92
4934 9293 0.460722 GCACAATGCATGCCCACATA 59.539 50.000 16.68 0.00 44.26 2.29
4950 9309 4.199310 CCACATATCGTCCAGTTTCCATT 58.801 43.478 0.00 0.00 0.00 3.16
4991 9350 6.994421 ATTTGCCCTTTCCTTCTCTTTTTA 57.006 33.333 0.00 0.00 0.00 1.52
5165 9524 7.197071 ACTTTCAATGCGATGTGTACTTTAA 57.803 32.000 0.00 0.00 0.00 1.52
5312 9673 4.153986 CCGATAACGAGTTACGCGATAAT 58.846 43.478 15.93 5.22 46.94 1.28
5549 9910 3.091545 AGGTGCAATTGTATCAAGTGGG 58.908 45.455 9.58 0.00 0.00 4.61
5761 10122 3.317430 AGCTAGGCTTTGATAATGCTTGC 59.683 43.478 0.00 0.00 33.89 4.01
5779 10140 2.466846 TGCCTCAGCAGTATTAGTGGA 58.533 47.619 0.85 0.00 46.52 4.02
5780 10141 3.041211 TGCCTCAGCAGTATTAGTGGAT 58.959 45.455 0.85 0.00 46.52 3.41
5781 10142 3.070159 TGCCTCAGCAGTATTAGTGGATC 59.930 47.826 0.85 0.00 46.52 3.36
5782 10143 3.070159 GCCTCAGCAGTATTAGTGGATCA 59.930 47.826 0.00 0.00 39.53 2.92
5783 10144 4.262808 GCCTCAGCAGTATTAGTGGATCAT 60.263 45.833 0.00 0.00 39.53 2.45
5784 10145 5.236282 CCTCAGCAGTATTAGTGGATCATG 58.764 45.833 0.00 0.00 0.00 3.07
5785 10146 4.635223 TCAGCAGTATTAGTGGATCATGC 58.365 43.478 0.00 0.00 0.00 4.06
5786 10147 4.346127 TCAGCAGTATTAGTGGATCATGCT 59.654 41.667 0.00 0.00 43.14 3.79
5787 10148 4.689812 CAGCAGTATTAGTGGATCATGCTC 59.310 45.833 0.00 0.00 40.58 4.26
5788 10149 4.592351 AGCAGTATTAGTGGATCATGCTCT 59.408 41.667 0.00 0.00 38.30 4.09
5789 10150 5.777223 AGCAGTATTAGTGGATCATGCTCTA 59.223 40.000 0.00 0.00 38.30 2.43
5790 10151 6.440010 AGCAGTATTAGTGGATCATGCTCTAT 59.560 38.462 0.00 0.00 38.30 1.98
5791 10152 7.038445 AGCAGTATTAGTGGATCATGCTCTATT 60.038 37.037 0.00 0.00 38.30 1.73
5792 10153 7.064371 GCAGTATTAGTGGATCATGCTCTATTG 59.936 40.741 0.00 0.00 0.00 1.90
5793 10154 7.548427 CAGTATTAGTGGATCATGCTCTATTGG 59.452 40.741 0.00 0.00 0.00 3.16
5794 10155 3.784511 AGTGGATCATGCTCTATTGGG 57.215 47.619 0.00 0.00 0.00 4.12
5795 10156 2.374504 AGTGGATCATGCTCTATTGGGG 59.625 50.000 0.00 0.00 0.00 4.96
5796 10157 2.373169 GTGGATCATGCTCTATTGGGGA 59.627 50.000 0.00 0.00 0.00 4.81
5797 10158 2.641321 TGGATCATGCTCTATTGGGGAG 59.359 50.000 0.00 0.00 0.00 4.30
5798 10159 2.026449 GGATCATGCTCTATTGGGGAGG 60.026 54.545 0.00 0.00 0.00 4.30
5799 10160 1.438469 TCATGCTCTATTGGGGAGGG 58.562 55.000 0.00 0.00 0.00 4.30
5800 10161 0.403271 CATGCTCTATTGGGGAGGGG 59.597 60.000 0.00 0.00 0.00 4.79
5801 10162 0.773700 ATGCTCTATTGGGGAGGGGG 60.774 60.000 0.00 0.00 0.00 5.40
5821 10437 5.446260 GGGGGACTGGATCTAGTTTTTAA 57.554 43.478 13.51 0.00 0.00 1.52
5979 10660 1.007387 GCCCAGTTCCGTTGCAAAG 60.007 57.895 0.00 2.09 0.00 2.77
6155 10836 3.388024 AGTACACTCCAGAAGCACTTGAA 59.612 43.478 0.00 0.00 0.00 2.69
6186 10867 8.514594 CACTTGGTAATCTATTTGCAAAGAAGA 58.485 33.333 22.31 22.31 35.25 2.87
6194 10875 7.994425 TCTATTTGCAAAGAAGATACCACAA 57.006 32.000 18.19 0.00 0.00 3.33
6221 10902 0.767375 ACTGGGACACTGATTGCACT 59.233 50.000 0.00 0.00 0.00 4.40
6339 11057 2.672996 GGCGGTGGCAGTTGTGAT 60.673 61.111 0.00 0.00 42.47 3.06
6528 11251 6.480524 TGTCTACATTCACTGCATGTTAAC 57.519 37.500 0.00 0.00 36.28 2.01
6539 11262 4.212636 ACTGCATGTTAACGTTGGAGTTAC 59.787 41.667 21.80 0.30 36.44 2.50
6564 11287 6.583806 CGAAATCTTTCATTGTTTCTCCAAGG 59.416 38.462 3.77 0.00 37.01 3.61
6648 11371 7.767198 GGTTGTTAACTGCATAATCTACCTGTA 59.233 37.037 7.22 0.00 0.00 2.74
6655 11378 7.796054 ACTGCATAATCTACCTGTAAACTGAT 58.204 34.615 0.00 0.00 0.00 2.90
6656 11379 7.712639 ACTGCATAATCTACCTGTAAACTGATG 59.287 37.037 0.00 0.00 0.00 3.07
6671 11399 3.987745 ACTGATGTGAGATACCTGACCT 58.012 45.455 0.00 0.00 0.00 3.85
6835 11565 1.062488 AGCCCCCATACATGACCCTC 61.062 60.000 0.00 0.00 0.00 4.30
6855 11585 6.702329 CCCTCATGGTTAGCTAGTAATAAGG 58.298 44.000 0.00 0.00 0.00 2.69
6883 11613 5.106317 CCGTTGTGGCTGAAAAATGTAGTAT 60.106 40.000 0.00 0.00 0.00 2.12
6922 11652 9.355215 GAGTCGAATGTACTCTTATTTTTCAGA 57.645 33.333 0.00 0.00 40.21 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.107177 CTTGCATGTTGAGAGAAATATCTTACT 57.893 33.333 0.00 0.00 35.54 2.24
1 2 7.854916 GCTTGCATGTTGAGAGAAATATCTTAC 59.145 37.037 1.14 0.00 35.54 2.34
79 80 2.289569 TGGAACCTTTTTCATGCATGGC 60.290 45.455 25.97 5.17 0.00 4.40
94 95 5.209818 TGGTCGTATATTGAGATGGAACC 57.790 43.478 0.00 0.00 0.00 3.62
112 113 2.166254 CCCTTGGTTTGTATGCATGGTC 59.834 50.000 10.16 0.33 0.00 4.02
148 149 2.627945 CGCTAGGCAATTGTGTCCTAA 58.372 47.619 7.40 0.00 34.88 2.69
267 3083 0.890996 GCCCCTCACAACTTCCACAG 60.891 60.000 0.00 0.00 0.00 3.66
322 3138 2.285083 ACTGTGCTAGCGTTTTTGTGA 58.715 42.857 10.77 0.00 0.00 3.58
439 3255 0.041400 CACAACTTTCACGCGCATGA 60.041 50.000 0.05 0.05 0.00 3.07
444 3260 1.136690 TCTAGCACAACTTTCACGCG 58.863 50.000 3.53 3.53 0.00 6.01
463 3279 1.068610 CACGCATCACCATCGGTTTTT 60.069 47.619 0.00 0.00 31.02 1.94
504 3320 5.758924 AGACTTTATTTTGCCAACGTTCTC 58.241 37.500 0.00 0.00 0.00 2.87
524 3340 8.709386 ACGATGCTTATCATTATCCATAAGAC 57.291 34.615 0.00 0.00 35.41 3.01
532 3348 8.851960 TTACCGATACGATGCTTATCATTATC 57.148 34.615 0.00 0.00 35.05 1.75
547 3363 9.872757 AATGTAATTAAAGCATTTACCGATACG 57.127 29.630 0.00 0.00 40.86 3.06
566 3382 5.245751 TGCCTGTTGGATGTTTCAATGTAAT 59.754 36.000 0.00 0.00 34.57 1.89
621 3437 2.867472 CCATCGGTTTCCACGTGC 59.133 61.111 10.91 0.00 0.00 5.34
624 3440 0.390603 TAGTGCCATCGGTTTCCACG 60.391 55.000 0.00 0.00 0.00 4.94
634 3450 0.875908 TCGATGCGCTTAGTGCCATC 60.876 55.000 15.51 15.30 41.57 3.51
648 3464 3.195002 AACCGCGTGCCATCGATG 61.195 61.111 18.76 18.76 0.00 3.84
661 3477 0.368907 CACTTACGATTCCGCAACCG 59.631 55.000 0.00 0.00 39.95 4.44
667 3483 5.907197 ATCTTATTGCACTTACGATTCCG 57.093 39.130 0.00 0.00 42.50 4.30
672 3488 6.037726 TCGCTAAATCTTATTGCACTTACGA 58.962 36.000 0.00 0.00 0.00 3.43
781 3597 4.584029 AATCTTCATTGTTGCGTCGTAG 57.416 40.909 0.00 0.00 0.00 3.51
814 3630 2.956333 GCATAAATAAACCGCCCCTCTT 59.044 45.455 0.00 0.00 0.00 2.85
815 3631 2.174854 AGCATAAATAAACCGCCCCTCT 59.825 45.455 0.00 0.00 0.00 3.69
816 3632 2.552743 GAGCATAAATAAACCGCCCCTC 59.447 50.000 0.00 0.00 0.00 4.30
817 3633 2.174854 AGAGCATAAATAAACCGCCCCT 59.825 45.455 0.00 0.00 0.00 4.79
818 3634 2.552743 GAGAGCATAAATAAACCGCCCC 59.447 50.000 0.00 0.00 0.00 5.80
854 5075 3.028130 CCCCTTCCTCTCAGACTCTTAC 58.972 54.545 0.00 0.00 0.00 2.34
860 5081 2.726351 CGCCCCCTTCCTCTCAGAC 61.726 68.421 0.00 0.00 0.00 3.51
920 5164 9.686683 AAACAAGCAGAGGAAAATATATGTAGT 57.313 29.630 0.00 0.00 0.00 2.73
923 5167 8.470002 GGAAAACAAGCAGAGGAAAATATATGT 58.530 33.333 0.00 0.00 0.00 2.29
924 5168 7.922811 GGGAAAACAAGCAGAGGAAAATATATG 59.077 37.037 0.00 0.00 0.00 1.78
925 5169 7.841222 AGGGAAAACAAGCAGAGGAAAATATAT 59.159 33.333 0.00 0.00 0.00 0.86
926 5170 7.182060 AGGGAAAACAAGCAGAGGAAAATATA 58.818 34.615 0.00 0.00 0.00 0.86
927 5171 6.019108 AGGGAAAACAAGCAGAGGAAAATAT 58.981 36.000 0.00 0.00 0.00 1.28
928 5172 5.393866 AGGGAAAACAAGCAGAGGAAAATA 58.606 37.500 0.00 0.00 0.00 1.40
929 5173 4.226384 AGGGAAAACAAGCAGAGGAAAAT 58.774 39.130 0.00 0.00 0.00 1.82
930 5174 3.642141 AGGGAAAACAAGCAGAGGAAAA 58.358 40.909 0.00 0.00 0.00 2.29
931 5175 3.312736 AGGGAAAACAAGCAGAGGAAA 57.687 42.857 0.00 0.00 0.00 3.13
932 5176 3.312736 AAGGGAAAACAAGCAGAGGAA 57.687 42.857 0.00 0.00 0.00 3.36
933 5177 3.312736 AAAGGGAAAACAAGCAGAGGA 57.687 42.857 0.00 0.00 0.00 3.71
934 5178 4.406648 AAAAAGGGAAAACAAGCAGAGG 57.593 40.909 0.00 0.00 0.00 3.69
935 5179 6.149129 AGTAAAAAGGGAAAACAAGCAGAG 57.851 37.500 0.00 0.00 0.00 3.35
936 5180 6.379988 AGAAGTAAAAAGGGAAAACAAGCAGA 59.620 34.615 0.00 0.00 0.00 4.26
937 5181 6.573434 AGAAGTAAAAAGGGAAAACAAGCAG 58.427 36.000 0.00 0.00 0.00 4.24
938 5182 6.538945 AGAAGTAAAAAGGGAAAACAAGCA 57.461 33.333 0.00 0.00 0.00 3.91
939 5183 7.265673 AGAAGAAGTAAAAAGGGAAAACAAGC 58.734 34.615 0.00 0.00 0.00 4.01
940 5184 9.302345 GAAGAAGAAGTAAAAAGGGAAAACAAG 57.698 33.333 0.00 0.00 0.00 3.16
941 5185 8.808092 TGAAGAAGAAGTAAAAAGGGAAAACAA 58.192 29.630 0.00 0.00 0.00 2.83
1346 5600 2.802414 AACGAACGTACCTCGCGC 60.802 61.111 0.00 0.00 44.19 6.86
1372 5626 2.179589 CAAATCGATCAAAGCAAGGCG 58.820 47.619 0.00 0.00 0.00 5.52
1373 5627 1.922545 GCAAATCGATCAAAGCAAGGC 59.077 47.619 0.00 0.00 0.00 4.35
1521 5777 1.680105 CCCGTCGAACCGATCAAACG 61.680 60.000 0.00 0.00 38.42 3.60
1522 5778 1.963190 GCCCGTCGAACCGATCAAAC 61.963 60.000 0.00 0.00 38.42 2.93
1523 5779 1.738830 GCCCGTCGAACCGATCAAA 60.739 57.895 0.00 0.00 38.42 2.69
1594 5850 0.179119 GCGCCGAGTAACACCAGTAT 60.179 55.000 0.00 0.00 0.00 2.12
1611 5867 3.849951 ACATACCTGGGCCTCGCG 61.850 66.667 4.53 0.00 0.00 5.87
1699 5955 4.892291 GGGGCCGGTGGGGAGATA 62.892 72.222 1.90 0.00 38.47 1.98
1743 6016 2.502492 CGGCTCCGATCCATCTGGT 61.502 63.158 1.35 0.00 42.83 4.00
1752 6025 1.742768 GATCTTCACCGGCTCCGAT 59.257 57.895 10.28 0.00 42.83 4.18
1834 6107 3.165160 AAGCACGACTTCGGTGGCT 62.165 57.895 3.30 6.28 43.40 4.75
1855 6201 2.626840 CAAACCTAGAGAAGCAGGAGC 58.373 52.381 0.00 0.00 42.56 4.70
1857 6203 1.066858 CGCAAACCTAGAGAAGCAGGA 60.067 52.381 0.00 0.00 35.76 3.86
2043 6392 4.726416 GTCAGTTAACCATGACATTGCAG 58.274 43.478 18.29 0.00 44.21 4.41
2114 6463 1.741401 CAAGACAAGGATGCGCCGA 60.741 57.895 4.18 0.00 43.43 5.54
2129 6478 9.829507 AAGACTAGATCCTATCACAAATTCAAG 57.170 33.333 0.00 0.00 0.00 3.02
2168 6517 5.453903 CCAAATGTTCCACCATAACCAAACA 60.454 40.000 0.00 0.00 0.00 2.83
2218 6567 3.845178 TGTTAGACCACGCATACAGAAG 58.155 45.455 0.00 0.00 0.00 2.85
2268 6617 7.532199 ACCCCTGTTTCTCTAAAATAAAAGGA 58.468 34.615 0.00 0.00 0.00 3.36
2359 6715 8.856490 ACAAATGAAGTTCAGTGAAACATTAC 57.144 30.769 22.53 7.98 41.43 1.89
2397 6753 2.939103 GCTCGCACTTTCCAATATCACT 59.061 45.455 0.00 0.00 0.00 3.41
2415 6771 0.615850 AGCCAGTAAGACCCTTGCTC 59.384 55.000 0.00 0.00 0.00 4.26
2425 6781 2.287069 CCGTGTCGAGATAGCCAGTAAG 60.287 54.545 0.00 0.00 0.00 2.34
2432 6788 2.493713 ATCAACCGTGTCGAGATAGC 57.506 50.000 0.00 0.00 0.00 2.97
2433 6789 8.570096 TTAATTTATCAACCGTGTCGAGATAG 57.430 34.615 0.00 0.00 0.00 2.08
2454 6810 6.772716 TGAAGAAGTCCTCAGCACTTTTTAAT 59.227 34.615 0.00 0.00 34.10 1.40
2463 6819 2.700371 TGAAGTGAAGAAGTCCTCAGCA 59.300 45.455 0.00 0.00 0.00 4.41
2466 6822 7.303182 TCTATTTGAAGTGAAGAAGTCCTCA 57.697 36.000 0.00 0.00 0.00 3.86
2547 6903 1.627329 TCATTCTCCAACTCAGCAGCT 59.373 47.619 0.00 0.00 0.00 4.24
2608 6964 3.621558 AGAAGTATGGGCCTAAGCAAAC 58.378 45.455 4.53 0.00 42.56 2.93
2767 7123 2.361104 GCACCCGGATTTGGCTGA 60.361 61.111 0.73 0.00 0.00 4.26
2855 7211 3.320541 TGTTTATGGCAACCAAGTTGGAG 59.679 43.478 28.80 19.66 42.99 3.86
2931 7287 1.082104 GTAACACCGCACTGCAAGC 60.082 57.895 1.11 0.85 37.60 4.01
2952 7308 7.122138 TGGGCAAGCAAATCATGAAATATAA 57.878 32.000 0.00 0.00 0.00 0.98
3098 7454 5.585047 GGATCCAGTGAGTAATTTTAGCGTT 59.415 40.000 6.95 0.00 0.00 4.84
3170 7526 6.449698 AGCAAACATCATTTTACAGTCCAAG 58.550 36.000 0.00 0.00 0.00 3.61
3227 7583 3.364964 CGCGTTCACTAGGAAAAAGCAAT 60.365 43.478 0.00 0.00 37.23 3.56
3730 8088 8.546597 AACGGCAATTTTCTTTAAATTAGCAT 57.453 26.923 0.00 0.00 43.00 3.79
3742 8100 3.130633 GGCTTGAAAACGGCAATTTTCT 58.869 40.909 19.50 0.00 45.12 2.52
3750 8108 0.316841 TGGATTGGCTTGAAAACGGC 59.683 50.000 0.00 0.00 0.00 5.68
3813 8171 2.093783 GTCGTTCGCCAACCTAAATCTG 59.906 50.000 0.00 0.00 0.00 2.90
4496 8854 5.541953 TTAGTGATGACAGATAGCTGCAT 57.458 39.130 8.16 12.28 46.26 3.96
4507 8865 6.466812 TGAAAGATCAGCTTTAGTGATGACA 58.533 36.000 0.00 0.00 46.52 3.58
4587 8945 5.510861 GGTTGGTCTCTACGGCATGTATAAT 60.511 44.000 0.00 0.00 31.20 1.28
4598 8956 6.446781 TTTACATCTAGGTTGGTCTCTACG 57.553 41.667 0.00 0.00 0.00 3.51
4710 9068 6.671190 TGTGTTTCTCTCATTGTATGCTTTG 58.329 36.000 0.00 0.00 0.00 2.77
4934 9293 5.253330 ACATGTTAATGGAAACTGGACGAT 58.747 37.500 0.00 0.00 38.19 3.73
4950 9309 7.233757 AGGGCAAATAGGTAAACAAACATGTTA 59.766 33.333 12.39 0.00 0.00 2.41
4991 9350 6.891908 AGACAATCCAATACCTGCAGTTAATT 59.108 34.615 13.81 6.30 0.00 1.40
5297 9658 5.629097 AGGATAAGATTATCGCGTAACTCG 58.371 41.667 5.77 0.00 40.30 4.18
5644 10005 2.647683 TTCACCACAACAGTATGCCA 57.352 45.000 0.00 0.00 42.53 4.92
5761 10122 4.944619 TGATCCACTAATACTGCTGAGG 57.055 45.455 0.00 0.00 0.00 3.86
5779 10140 1.991070 CCCTCCCCAATAGAGCATGAT 59.009 52.381 0.00 0.00 0.00 2.45
5780 10141 1.438469 CCCTCCCCAATAGAGCATGA 58.562 55.000 0.00 0.00 0.00 3.07
5781 10142 0.403271 CCCCTCCCCAATAGAGCATG 59.597 60.000 0.00 0.00 0.00 4.06
5782 10143 0.773700 CCCCCTCCCCAATAGAGCAT 60.774 60.000 0.00 0.00 0.00 3.79
5783 10144 1.385915 CCCCCTCCCCAATAGAGCA 60.386 63.158 0.00 0.00 0.00 4.26
5784 10145 3.581372 CCCCCTCCCCAATAGAGC 58.419 66.667 0.00 0.00 0.00 4.09
5799 10160 5.446260 TTAAAAACTAGATCCAGTCCCCC 57.554 43.478 0.00 0.00 0.00 5.40
5800 10161 7.770366 TTTTTAAAAACTAGATCCAGTCCCC 57.230 36.000 9.31 0.00 0.00 4.81
5850 10466 8.783660 TGATACCTCTGTCCATAGAACTAAAT 57.216 34.615 0.00 0.00 0.00 1.40
5905 10583 3.990469 GCTGAGGATGTACATTATCCACG 59.010 47.826 10.30 4.78 45.28 4.94
6155 10836 7.283625 TGCAAATAGATTACCAAGTGTTTGT 57.716 32.000 0.00 0.00 32.21 2.83
6186 10867 4.080526 GTCCCAGTTCACCTATTGTGGTAT 60.081 45.833 0.00 0.00 45.48 2.73
6194 10875 2.902608 TCAGTGTCCCAGTTCACCTAT 58.097 47.619 0.00 0.00 35.45 2.57
6236 10917 5.248477 TGACAGGAAGCTTCTAACTTACCAT 59.752 40.000 25.05 0.19 0.00 3.55
6237 10918 4.591498 TGACAGGAAGCTTCTAACTTACCA 59.409 41.667 25.05 10.18 0.00 3.25
6238 10919 5.148651 TGACAGGAAGCTTCTAACTTACC 57.851 43.478 25.05 7.41 0.00 2.85
6299 10980 1.748244 CGCCACCACCTCATCATCATT 60.748 52.381 0.00 0.00 0.00 2.57
6339 11057 5.746721 CGGAACACTCGTAATATTGTGATCA 59.253 40.000 9.85 0.00 35.08 2.92
6386 11104 4.508662 AGCCATTGTAGAGAACTTGTAGC 58.491 43.478 0.00 0.00 0.00 3.58
6392 11110 8.870075 AGAAAATTTAGCCATTGTAGAGAACT 57.130 30.769 0.00 0.00 0.00 3.01
6528 11251 5.585500 TGAAAGATTTCGTAACTCCAACG 57.415 39.130 1.18 0.00 40.01 4.10
6539 11262 6.583806 CCTTGGAGAAACAATGAAAGATTTCG 59.416 38.462 1.18 0.00 40.01 3.46
6564 11287 2.262423 ACTTGGTCTGAACCTCAAGC 57.738 50.000 0.00 0.00 46.60 4.01
6622 11345 6.598064 ACAGGTAGATTATGCAGTTAACAACC 59.402 38.462 8.61 0.00 0.00 3.77
6628 11351 8.755028 TCAGTTTACAGGTAGATTATGCAGTTA 58.245 33.333 0.00 0.00 0.00 2.24
6648 11371 4.780021 AGGTCAGGTATCTCACATCAGTTT 59.220 41.667 0.00 0.00 0.00 2.66
6655 11378 4.895889 CCTCATAAGGTCAGGTATCTCACA 59.104 45.833 0.00 0.00 37.94 3.58
6656 11379 5.461032 CCTCATAAGGTCAGGTATCTCAC 57.539 47.826 0.00 0.00 37.94 3.51
6671 11399 2.038952 ACTGCAGAGCAACACCTCATAA 59.961 45.455 23.35 0.00 38.41 1.90
6779 11508 4.553678 AGAATTTCCTTGCATCCATGGAT 58.446 39.130 22.15 22.15 42.75 3.41
6835 11565 7.974501 CGGATACCTTATTACTAGCTAACCATG 59.025 40.741 0.00 0.00 0.00 3.66
6840 11570 8.355169 CACAACGGATACCTTATTACTAGCTAA 58.645 37.037 0.00 0.00 0.00 3.09
6855 11585 3.907894 TTTTTCAGCCACAACGGATAC 57.092 42.857 0.00 0.00 36.56 2.24
6883 11613 6.252967 ACATTCGACTCATTTGCAAATACA 57.747 33.333 23.69 12.67 0.00 2.29
6922 11652 4.085357 TGCCATGAGTGAGTTGTAGTTT 57.915 40.909 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.