Multiple sequence alignment - TraesCS1A01G255400

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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 TraesCS1A01G255400 chr1A 100.000 4861 0 0 1 4861 447645004 447640144 0.000000e+00 8977.0
1 TraesCS1A01G255400 chr1D 91.430 2392 87 50 114 2453 347220089 347217764 0.000000e+00 3173.0
2 TraesCS1A01G255400 chr1D 96.934 1598 43 5 2496 4093 347217647 347216056 0.000000e+00 2675.0
3 TraesCS1A01G255400 chr1D 92.287 739 39 7 4087 4821 347216114 347215390 0.000000e+00 1033.0
4 TraesCS1A01G255400 chr1D 97.674 43 1 0 2458 2500 347217728 347217686 1.880000e-09 75.0
5 TraesCS1A01G255400 chr1B 92.012 2003 71 29 486 2452 467934456 467932507 0.000000e+00 2730.0
6 TraesCS1A01G255400 chr1B 96.934 1598 41 4 2496 4093 467932389 467930800 0.000000e+00 2673.0
7 TraesCS1A01G255400 chr1B 88.980 608 34 10 4087 4687 467930858 467930277 0.000000e+00 721.0
8 TraesCS1A01G255400 chr1B 93.559 295 16 3 114 406 467934905 467934612 2.080000e-118 436.0
9 TraesCS1A01G255400 chr1B 93.452 168 9 2 4693 4860 467927096 467926931 1.040000e-61 248.0
10 TraesCS1A01G255400 chr1B 88.406 69 4 2 422 486 467934555 467934487 4.030000e-11 80.5
11 TraesCS1A01G255400 chr1B 95.349 43 2 0 2458 2500 467932470 467932428 8.730000e-08 69.4


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 TraesCS1A01G255400 chr1A 447640144 447645004 4860 True 8977.000000 8977 100.000000 1 4861 1 chr1A.!!$R1 4860
1 TraesCS1A01G255400 chr1D 347215390 347220089 4699 True 1739.000000 3173 94.581250 114 4821 4 chr1D.!!$R1 4707
2 TraesCS1A01G255400 chr1B 467926931 467934905 7974 True 993.985714 2730 92.670286 114 4860 7 chr1B.!!$R1 4746

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
715 798 0.851332 AAAGGGGAAGGAAGGGAGGG 60.851 60.0 0.0 0.0 0.00 4.30 F
1760 1888 0.037326 TGGACGAACAGAGCATCACC 60.037 55.0 0.0 0.0 37.82 4.02 F
2331 2470 0.456221 TGCTCTAGCGAACACTAGCC 59.544 55.0 0.0 0.0 45.83 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2617 2830 0.034756 ACACTTACAGCATGCCGTCA 59.965 50.0 15.66 0.0 42.53 4.35 R
3614 3827 0.107643 TGGGCGATGTGTCTTCAACA 59.892 50.0 0.00 0.0 34.78 3.33 R
4077 4291 0.040204 CCCCTCCTTCCTTGCATTGT 59.960 55.0 0.00 0.0 0.00 2.71 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
29 30 4.600012 GTGTAGCACGCTATGATTTTGT 57.400 40.909 1.43 0.00 0.00 2.83
30 31 4.969816 GTGTAGCACGCTATGATTTTGTT 58.030 39.130 1.43 0.00 0.00 2.83
31 32 5.390613 GTGTAGCACGCTATGATTTTGTTT 58.609 37.500 1.43 0.00 0.00 2.83
32 33 6.539324 GTGTAGCACGCTATGATTTTGTTTA 58.461 36.000 1.43 0.00 0.00 2.01
33 34 6.464834 GTGTAGCACGCTATGATTTTGTTTAC 59.535 38.462 1.43 0.00 0.00 2.01
34 35 4.647964 AGCACGCTATGATTTTGTTTACG 58.352 39.130 0.00 0.00 0.00 3.18
35 36 4.153475 AGCACGCTATGATTTTGTTTACGT 59.847 37.500 0.00 0.00 0.00 3.57
36 37 5.349270 AGCACGCTATGATTTTGTTTACGTA 59.651 36.000 0.00 0.00 0.00 3.57
37 38 6.016718 GCACGCTATGATTTTGTTTACGTAA 58.983 36.000 3.29 3.29 0.00 3.18
38 39 6.022794 GCACGCTATGATTTTGTTTACGTAAC 60.023 38.462 7.70 4.36 37.26 2.50
39 40 7.231607 CACGCTATGATTTTGTTTACGTAACT 58.768 34.615 7.70 0.00 37.64 2.24
40 41 7.421613 CACGCTATGATTTTGTTTACGTAACTC 59.578 37.037 7.70 5.20 37.64 3.01
41 42 7.330208 ACGCTATGATTTTGTTTACGTAACTCT 59.670 33.333 7.70 0.00 37.64 3.24
42 43 8.166706 CGCTATGATTTTGTTTACGTAACTCTT 58.833 33.333 7.70 0.00 37.64 2.85
43 44 9.821662 GCTATGATTTTGTTTACGTAACTCTTT 57.178 29.630 7.70 0.00 37.64 2.52
47 48 9.279904 TGATTTTGTTTACGTAACTCTTTTGTG 57.720 29.630 7.70 0.00 37.64 3.33
48 49 8.623310 ATTTTGTTTACGTAACTCTTTTGTGG 57.377 30.769 7.70 0.00 37.64 4.17
49 50 6.740411 TTGTTTACGTAACTCTTTTGTGGT 57.260 33.333 7.70 0.00 37.64 4.16
50 51 6.109320 TGTTTACGTAACTCTTTTGTGGTG 57.891 37.500 7.70 0.00 37.64 4.17
51 52 5.873712 TGTTTACGTAACTCTTTTGTGGTGA 59.126 36.000 7.70 0.00 37.64 4.02
52 53 6.370994 TGTTTACGTAACTCTTTTGTGGTGAA 59.629 34.615 7.70 0.00 37.64 3.18
53 54 7.066043 TGTTTACGTAACTCTTTTGTGGTGAAT 59.934 33.333 7.70 0.00 37.64 2.57
54 55 5.418310 ACGTAACTCTTTTGTGGTGAATG 57.582 39.130 0.00 0.00 0.00 2.67
55 56 5.120399 ACGTAACTCTTTTGTGGTGAATGA 58.880 37.500 0.00 0.00 0.00 2.57
56 57 5.763204 ACGTAACTCTTTTGTGGTGAATGAT 59.237 36.000 0.00 0.00 0.00 2.45
57 58 6.262273 ACGTAACTCTTTTGTGGTGAATGATT 59.738 34.615 0.00 0.00 0.00 2.57
58 59 7.138736 CGTAACTCTTTTGTGGTGAATGATTT 58.861 34.615 0.00 0.00 0.00 2.17
59 60 7.647715 CGTAACTCTTTTGTGGTGAATGATTTT 59.352 33.333 0.00 0.00 0.00 1.82
60 61 9.313118 GTAACTCTTTTGTGGTGAATGATTTTT 57.687 29.630 0.00 0.00 0.00 1.94
84 85 7.862741 TTTTAATCTGACAGTGTGTAGTACG 57.137 36.000 0.00 0.00 0.00 3.67
85 86 2.983402 TCTGACAGTGTGTAGTACGC 57.017 50.000 0.00 6.91 40.13 4.42
98 99 2.205307 AGTACGCTACGATTCTTGGC 57.795 50.000 0.00 0.00 0.00 4.52
99 100 1.202382 AGTACGCTACGATTCTTGGCC 60.202 52.381 0.00 0.00 0.00 5.36
100 101 1.108776 TACGCTACGATTCTTGGCCT 58.891 50.000 3.32 0.00 0.00 5.19
101 102 1.108776 ACGCTACGATTCTTGGCCTA 58.891 50.000 3.32 0.00 0.00 3.93
102 103 1.687123 ACGCTACGATTCTTGGCCTAT 59.313 47.619 3.32 0.00 0.00 2.57
103 104 2.889045 ACGCTACGATTCTTGGCCTATA 59.111 45.455 3.32 0.00 0.00 1.31
104 105 3.510360 ACGCTACGATTCTTGGCCTATAT 59.490 43.478 3.32 0.00 0.00 0.86
105 106 4.021368 ACGCTACGATTCTTGGCCTATATT 60.021 41.667 3.32 0.00 0.00 1.28
106 107 4.929808 CGCTACGATTCTTGGCCTATATTT 59.070 41.667 3.32 0.00 0.00 1.40
107 108 6.097356 CGCTACGATTCTTGGCCTATATTTA 58.903 40.000 3.32 0.00 0.00 1.40
108 109 6.757010 CGCTACGATTCTTGGCCTATATTTAT 59.243 38.462 3.32 0.00 0.00 1.40
109 110 7.277981 CGCTACGATTCTTGGCCTATATTTATT 59.722 37.037 3.32 0.00 0.00 1.40
110 111 8.947115 GCTACGATTCTTGGCCTATATTTATTT 58.053 33.333 3.32 0.00 0.00 1.40
112 113 8.336801 ACGATTCTTGGCCTATATTTATTTCC 57.663 34.615 3.32 0.00 0.00 3.13
149 151 3.435671 CCTCACCCTCACGTGTAAAAATC 59.564 47.826 16.51 0.00 35.18 2.17
258 261 0.956633 GAAAACAGGAAACGGACCCC 59.043 55.000 0.00 0.00 0.00 4.95
562 641 4.502645 CGCGATTAAAATCAAAATCCACCC 59.497 41.667 0.00 0.00 35.11 4.61
705 788 3.788766 CGACGCGCAAAGGGGAAG 61.789 66.667 5.73 0.00 37.07 3.46
706 789 3.431725 GACGCGCAAAGGGGAAGG 61.432 66.667 5.73 0.00 37.07 3.46
711 794 1.678970 CGCAAAGGGGAAGGAAGGG 60.679 63.158 0.00 0.00 0.00 3.95
715 798 0.851332 AAAGGGGAAGGAAGGGAGGG 60.851 60.000 0.00 0.00 0.00 4.30
767 850 3.827898 GACGACGCTGGGAGGAGG 61.828 72.222 0.00 0.00 0.00 4.30
768 851 4.361971 ACGACGCTGGGAGGAGGA 62.362 66.667 0.00 0.00 0.00 3.71
769 852 3.522731 CGACGCTGGGAGGAGGAG 61.523 72.222 0.00 0.00 0.00 3.69
770 853 3.844090 GACGCTGGGAGGAGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
818 901 4.697756 TTGCCAGCGACGGAAGGG 62.698 66.667 0.00 0.00 0.00 3.95
823 906 4.377760 AGCGACGGAAGGGAGGGA 62.378 66.667 0.00 0.00 0.00 4.20
824 907 3.839432 GCGACGGAAGGGAGGGAG 61.839 72.222 0.00 0.00 0.00 4.30
825 908 3.148279 CGACGGAAGGGAGGGAGG 61.148 72.222 0.00 0.00 0.00 4.30
826 909 2.363361 GACGGAAGGGAGGGAGGA 59.637 66.667 0.00 0.00 0.00 3.71
827 910 1.758906 GACGGAAGGGAGGGAGGAG 60.759 68.421 0.00 0.00 0.00 3.69
828 911 2.226149 GACGGAAGGGAGGGAGGAGA 62.226 65.000 0.00 0.00 0.00 3.71
923 1006 2.115427 CCTCTTCCTCTTCCTCTTCCC 58.885 57.143 0.00 0.00 0.00 3.97
1203 1309 2.754658 GCCGAGGAGGAGGACGAA 60.755 66.667 0.00 0.00 45.00 3.85
1285 1391 1.606885 CTTCGGCAAGGGGGTACGTA 61.607 60.000 0.00 0.00 0.00 3.57
1287 1393 2.353610 CGGCAAGGGGGTACGTACT 61.354 63.158 24.07 2.40 0.00 2.73
1473 1599 4.660938 GACAGGTGGGTGGGTGGC 62.661 72.222 0.00 0.00 0.00 5.01
1526 1653 4.770010 TGGTTGGACACCCATTTAAATCTC 59.230 41.667 0.00 0.00 46.68 2.75
1700 1828 0.323725 AGCACAGCCAGGTTTATGGG 60.324 55.000 0.00 0.00 40.97 4.00
1753 1881 2.996621 GTGAGGATTTGGACGAACAGAG 59.003 50.000 0.00 0.00 0.00 3.35
1760 1888 0.037326 TGGACGAACAGAGCATCACC 60.037 55.000 0.00 0.00 37.82 4.02
1761 1889 0.741221 GGACGAACAGAGCATCACCC 60.741 60.000 0.00 0.00 37.82 4.61
1808 1940 9.579932 AGTTTGGATTTAGAGTTCTTCATTTCT 57.420 29.630 0.00 0.00 0.00 2.52
1823 1955 6.934645 TCTTCATTTCTGGTTTCTAATCGTGT 59.065 34.615 0.00 0.00 0.00 4.49
1838 1970 0.464373 CGTGTGCAGGGCATTATCCT 60.464 55.000 0.00 0.00 41.91 3.24
1859 1991 2.203788 TGGGACGAGCAGAACCCT 60.204 61.111 0.00 0.00 39.36 4.34
1953 2085 8.816894 AGGTACAACAAGAGATTTCAGATCTTA 58.183 33.333 0.00 0.00 32.16 2.10
1969 2101 5.623264 CAGATCTTACTCAGAAACGATAGCG 59.377 44.000 0.00 0.00 38.20 4.26
1982 2114 1.135972 CGATAGCGCTTTGTTGTTGCT 60.136 47.619 18.68 0.00 39.59 3.91
2157 2289 2.523245 TGTTGGCAGCATCCATTGTTA 58.477 42.857 0.00 0.00 35.77 2.41
2159 2291 3.130869 TGTTGGCAGCATCCATTGTTATC 59.869 43.478 0.00 0.00 35.77 1.75
2266 2400 1.205417 GGCTTTATGCATGTGGCTTGT 59.795 47.619 10.16 0.00 45.15 3.16
2331 2470 0.456221 TGCTCTAGCGAACACTAGCC 59.544 55.000 0.00 0.00 45.83 3.93
2393 2532 5.757886 TGACGAAATTTCACAGGACAATTC 58.242 37.500 17.99 0.00 0.00 2.17
2453 2592 8.784994 TGTTAAAATTCAAATAGACTTACGGCA 58.215 29.630 0.00 0.00 0.00 5.69
2466 2636 9.772973 ATAGACTTACGGCATATTGTTATTTGA 57.227 29.630 0.00 0.00 0.00 2.69
2617 2830 3.167485 TGGAACCACACGGACTTACTAT 58.833 45.455 0.00 0.00 35.59 2.12
2658 2871 8.548721 AGTGTTGACTTGAACTCGTAAAATTAG 58.451 33.333 0.00 0.00 0.00 1.73
2896 3109 6.240145 TGATCACTTTGAAATGTCATGGAGA 58.760 36.000 0.00 0.00 32.48 3.71
3115 3328 1.374252 CGTCCTTGGAGTTCACCCG 60.374 63.158 0.00 0.00 0.00 5.28
3169 3382 4.383602 CGGCACCCTCAAAACGCG 62.384 66.667 3.53 3.53 0.00 6.01
3290 3503 5.121768 ACCTTACAATTCATTACTCGTGCAC 59.878 40.000 6.82 6.82 0.00 4.57
3511 3724 6.312529 TCTTACTGGAACGACATATATCCCT 58.687 40.000 0.00 0.00 0.00 4.20
3520 3733 7.284716 GGAACGACATATATCCCTTTCCTTTTT 59.715 37.037 9.89 0.00 0.00 1.94
3561 3774 8.143193 ACAGTTATGCATGAATTTCTTGTTTCA 58.857 29.630 10.16 4.56 36.38 2.69
3565 3778 6.831727 TGCATGAATTTCTTGTTTCAACAG 57.168 33.333 12.33 0.00 40.50 3.16
3584 3797 9.661563 TTCAACAGTACTAACCAAATTCGATAT 57.338 29.630 0.00 0.00 0.00 1.63
3827 4041 5.125097 CAGAAAGCATGCATTTAGGAAGAGT 59.875 40.000 21.98 0.00 0.00 3.24
3849 4063 1.540267 CCCTACCATGCCAAACGAAA 58.460 50.000 0.00 0.00 0.00 3.46
3887 4101 9.549078 AAGATTAAACTAAGCATTCTAGGTAGC 57.451 33.333 0.00 0.00 0.00 3.58
4024 4238 1.472082 CAAATGGCACGCTTGATACCA 59.528 47.619 0.00 0.00 34.28 3.25
4056 4270 2.174685 AGGAGGGGTTTTGCAACTTT 57.825 45.000 0.00 0.00 32.90 2.66
4057 4271 2.039418 AGGAGGGGTTTTGCAACTTTC 58.961 47.619 0.00 0.00 32.90 2.62
4058 4272 2.039418 GGAGGGGTTTTGCAACTTTCT 58.961 47.619 0.00 0.00 32.90 2.52
4059 4273 2.434336 GGAGGGGTTTTGCAACTTTCTT 59.566 45.455 0.00 0.00 32.90 2.52
4060 4274 3.118408 GGAGGGGTTTTGCAACTTTCTTT 60.118 43.478 0.00 0.00 32.90 2.52
4061 4275 4.119862 GAGGGGTTTTGCAACTTTCTTTC 58.880 43.478 0.00 0.00 32.90 2.62
4062 4276 3.118408 AGGGGTTTTGCAACTTTCTTTCC 60.118 43.478 0.00 0.00 32.90 3.13
4063 4277 2.863740 GGGTTTTGCAACTTTCTTTCCG 59.136 45.455 0.00 0.00 32.90 4.30
4064 4278 2.284150 GGTTTTGCAACTTTCTTTCCGC 59.716 45.455 0.00 0.00 32.90 5.54
4065 4279 3.186909 GTTTTGCAACTTTCTTTCCGCT 58.813 40.909 0.00 0.00 0.00 5.52
4066 4280 2.490328 TTGCAACTTTCTTTCCGCTG 57.510 45.000 0.00 0.00 0.00 5.18
4067 4281 0.030638 TGCAACTTTCTTTCCGCTGC 59.969 50.000 0.00 0.00 0.00 5.25
4068 4282 0.664466 GCAACTTTCTTTCCGCTGCC 60.664 55.000 0.00 0.00 0.00 4.85
4069 4283 0.039165 CAACTTTCTTTCCGCTGCCC 60.039 55.000 0.00 0.00 0.00 5.36
4070 4284 0.178990 AACTTTCTTTCCGCTGCCCT 60.179 50.000 0.00 0.00 0.00 5.19
4071 4285 0.606673 ACTTTCTTTCCGCTGCCCTC 60.607 55.000 0.00 0.00 0.00 4.30
4072 4286 0.606401 CTTTCTTTCCGCTGCCCTCA 60.606 55.000 0.00 0.00 0.00 3.86
4073 4287 0.889186 TTTCTTTCCGCTGCCCTCAC 60.889 55.000 0.00 0.00 0.00 3.51
4074 4288 3.121030 CTTTCCGCTGCCCTCACG 61.121 66.667 0.00 0.00 0.00 4.35
4094 4308 0.529378 GCACAATGCAAGGAAGGAGG 59.471 55.000 0.00 0.00 44.26 4.30
4095 4309 1.180029 CACAATGCAAGGAAGGAGGG 58.820 55.000 0.00 0.00 0.00 4.30
4096 4310 0.040204 ACAATGCAAGGAAGGAGGGG 59.960 55.000 0.00 0.00 0.00 4.79
4097 4311 0.040204 CAATGCAAGGAAGGAGGGGT 59.960 55.000 0.00 0.00 0.00 4.95
4098 4312 0.786435 AATGCAAGGAAGGAGGGGTT 59.214 50.000 0.00 0.00 0.00 4.11
4099 4313 0.786435 ATGCAAGGAAGGAGGGGTTT 59.214 50.000 0.00 0.00 0.00 3.27
4100 4314 0.560688 TGCAAGGAAGGAGGGGTTTT 59.439 50.000 0.00 0.00 0.00 2.43
4101 4315 0.969149 GCAAGGAAGGAGGGGTTTTG 59.031 55.000 0.00 0.00 0.00 2.44
4102 4316 0.969149 CAAGGAAGGAGGGGTTTTGC 59.031 55.000 0.00 0.00 0.00 3.68
4103 4317 0.560688 AAGGAAGGAGGGGTTTTGCA 59.439 50.000 0.00 0.00 0.00 4.08
4104 4318 0.560688 AGGAAGGAGGGGTTTTGCAA 59.439 50.000 0.00 0.00 0.00 4.08
4105 4319 0.679505 GGAAGGAGGGGTTTTGCAAC 59.320 55.000 0.00 0.00 0.00 4.17
4106 4320 1.704641 GAAGGAGGGGTTTTGCAACT 58.295 50.000 0.00 0.00 32.90 3.16
4107 4321 2.039418 GAAGGAGGGGTTTTGCAACTT 58.961 47.619 0.00 0.00 32.90 2.66
4113 4327 1.939934 GGGGTTTTGCAACTTGCTTTC 59.060 47.619 14.78 3.48 45.31 2.62
4126 4340 2.750888 GCTTTCCGCTGCCCTTACG 61.751 63.158 0.00 0.00 35.14 3.18
4155 4369 3.758554 TGCAAGGAAGGAAGCTTGTAATC 59.241 43.478 2.10 0.00 0.00 1.75
4227 4441 6.068670 GGGGCTTGTACATATTAAGGATTGT 58.931 40.000 0.00 0.00 0.00 2.71
4228 4442 7.147284 TGGGGCTTGTACATATTAAGGATTGTA 60.147 37.037 0.00 0.00 0.00 2.41
4229 4443 7.888546 GGGGCTTGTACATATTAAGGATTGTAT 59.111 37.037 0.00 0.00 0.00 2.29
4230 4444 8.947115 GGGCTTGTACATATTAAGGATTGTATC 58.053 37.037 0.00 0.00 0.00 2.24
4231 4445 9.726438 GGCTTGTACATATTAAGGATTGTATCT 57.274 33.333 0.00 0.00 0.00 1.98
4247 4461 8.960591 GGATTGTATCTAAATTGTATCCATGGG 58.039 37.037 13.02 0.00 32.48 4.00
4263 4477 4.475381 TCCATGGGGCTACTTTGTATGTTA 59.525 41.667 13.02 0.00 0.00 2.41
4301 4515 3.432749 GGAAGAGCTGGTCTATGATTGCA 60.433 47.826 10.13 0.00 32.65 4.08
4315 4529 4.717233 TGATTGCACTGTTTGTTTCAGT 57.283 36.364 0.00 0.00 45.43 3.41
4374 4588 4.262891 TGGATCTCTGGAGTCTTCTGAT 57.737 45.455 0.00 0.00 0.00 2.90
4382 4596 5.761205 TCTGGAGTCTTCTGATAAGCTAGT 58.239 41.667 0.00 0.00 0.00 2.57
4466 4680 3.825328 ACAGCTTGTTGTGATTCTCCTT 58.175 40.909 0.00 0.00 0.00 3.36
4545 4759 0.595825 GCTGCTGCTGTTGTTTGGTC 60.596 55.000 8.53 0.00 36.03 4.02
4548 4762 0.312102 GCTGCTGTTGTTTGGTCTCC 59.688 55.000 0.00 0.00 0.00 3.71
4555 4769 3.947834 CTGTTGTTTGGTCTCCACTTCTT 59.052 43.478 0.00 0.00 30.78 2.52
4565 4779 5.123936 GGTCTCCACTTCTTGTTTGTAGTT 58.876 41.667 0.00 0.00 0.00 2.24
4573 4787 7.228706 CCACTTCTTGTTTGTAGTTATTGTCCT 59.771 37.037 0.00 0.00 0.00 3.85
4581 4795 2.762535 AGTTATTGTCCTGTGACGGG 57.237 50.000 3.42 3.42 44.86 5.28
4600 4818 1.073284 GGGAACTGGCCTAGTGTTTCA 59.927 52.381 3.32 0.00 40.26 2.69
4601 4819 2.488347 GGGAACTGGCCTAGTGTTTCAA 60.488 50.000 3.32 0.00 40.26 2.69
4613 4831 6.638468 GCCTAGTGTTTCAAATCTGTTTCAAG 59.362 38.462 0.00 0.00 0.00 3.02
4625 4846 9.888878 CAAATCTGTTTCAAGCATATACATAGG 57.111 33.333 0.00 0.00 0.00 2.57
4634 4855 6.936335 TCAAGCATATACATAGGTGTTGGATG 59.064 38.462 0.00 0.00 39.77 3.51
4730 8126 5.997746 ACTTGCACTAGTCTGCTTTAATGAA 59.002 36.000 6.85 0.00 38.07 2.57
4731 8127 6.486657 ACTTGCACTAGTCTGCTTTAATGAAA 59.513 34.615 6.85 0.00 38.07 2.69
4732 8128 6.241207 TGCACTAGTCTGCTTTAATGAAAC 57.759 37.500 6.85 0.00 38.07 2.78
4735 8131 5.705441 CACTAGTCTGCTTTAATGAAACCCA 59.295 40.000 0.00 0.00 0.00 4.51
4860 8256 8.134895 TCAGATTAAAGAAATCAAAACAAGCGT 58.865 29.630 1.01 0.00 45.58 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.600012 ACAAAATCATAGCGTGCTACAC 57.400 40.909 3.26 0.00 0.00 2.90
9 10 5.621197 AAACAAAATCATAGCGTGCTACA 57.379 34.783 3.26 0.00 0.00 2.74
10 11 5.671140 CGTAAACAAAATCATAGCGTGCTAC 59.329 40.000 3.26 0.00 0.00 3.58
11 12 5.349270 ACGTAAACAAAATCATAGCGTGCTA 59.651 36.000 3.73 3.73 0.00 3.49
12 13 4.153475 ACGTAAACAAAATCATAGCGTGCT 59.847 37.500 0.00 0.00 0.00 4.40
13 14 4.399978 ACGTAAACAAAATCATAGCGTGC 58.600 39.130 0.00 0.00 0.00 5.34
14 15 7.231607 AGTTACGTAAACAAAATCATAGCGTG 58.768 34.615 10.11 0.00 40.83 5.34
15 16 7.330208 AGAGTTACGTAAACAAAATCATAGCGT 59.670 33.333 10.11 0.00 40.83 5.07
16 17 7.672738 AGAGTTACGTAAACAAAATCATAGCG 58.327 34.615 10.11 0.00 40.83 4.26
17 18 9.821662 AAAGAGTTACGTAAACAAAATCATAGC 57.178 29.630 10.11 0.00 40.83 2.97
21 22 9.279904 CACAAAAGAGTTACGTAAACAAAATCA 57.720 29.630 10.11 0.00 40.83 2.57
22 23 8.739461 CCACAAAAGAGTTACGTAAACAAAATC 58.261 33.333 10.11 0.00 40.83 2.17
23 24 8.245491 ACCACAAAAGAGTTACGTAAACAAAAT 58.755 29.630 10.11 0.00 40.83 1.82
24 25 7.537991 CACCACAAAAGAGTTACGTAAACAAAA 59.462 33.333 10.11 0.00 40.83 2.44
25 26 7.022384 CACCACAAAAGAGTTACGTAAACAAA 58.978 34.615 10.11 0.00 40.83 2.83
26 27 6.370994 TCACCACAAAAGAGTTACGTAAACAA 59.629 34.615 10.11 0.00 40.83 2.83
27 28 5.873712 TCACCACAAAAGAGTTACGTAAACA 59.126 36.000 10.11 0.00 40.83 2.83
28 29 6.348621 TCACCACAAAAGAGTTACGTAAAC 57.651 37.500 10.11 7.56 38.46 2.01
29 30 6.981762 TTCACCACAAAAGAGTTACGTAAA 57.018 33.333 10.11 0.00 0.00 2.01
30 31 6.762187 TCATTCACCACAAAAGAGTTACGTAA 59.238 34.615 3.29 3.29 0.00 3.18
31 32 6.282167 TCATTCACCACAAAAGAGTTACGTA 58.718 36.000 0.00 0.00 0.00 3.57
32 33 5.120399 TCATTCACCACAAAAGAGTTACGT 58.880 37.500 0.00 0.00 0.00 3.57
33 34 5.666969 TCATTCACCACAAAAGAGTTACG 57.333 39.130 0.00 0.00 0.00 3.18
34 35 8.871686 AAAATCATTCACCACAAAAGAGTTAC 57.128 30.769 0.00 0.00 0.00 2.50
59 60 7.095940 GCGTACTACACACTGTCAGATTAAAAA 60.096 37.037 6.91 0.00 0.00 1.94
60 61 6.364165 GCGTACTACACACTGTCAGATTAAAA 59.636 38.462 6.91 0.00 0.00 1.52
61 62 5.860182 GCGTACTACACACTGTCAGATTAAA 59.140 40.000 6.91 0.00 0.00 1.52
62 63 5.182570 AGCGTACTACACACTGTCAGATTAA 59.817 40.000 6.91 0.00 0.00 1.40
63 64 4.698780 AGCGTACTACACACTGTCAGATTA 59.301 41.667 6.91 0.00 0.00 1.75
64 65 3.506455 AGCGTACTACACACTGTCAGATT 59.494 43.478 6.91 0.00 0.00 2.40
65 66 3.082548 AGCGTACTACACACTGTCAGAT 58.917 45.455 6.91 0.00 0.00 2.90
66 67 2.501261 AGCGTACTACACACTGTCAGA 58.499 47.619 6.91 0.00 0.00 3.27
67 68 2.991434 AGCGTACTACACACTGTCAG 57.009 50.000 0.00 0.00 0.00 3.51
68 69 3.818961 GTAGCGTACTACACACTGTCA 57.181 47.619 0.00 0.00 46.80 3.58
77 78 3.041492 GCCAAGAATCGTAGCGTACTAC 58.959 50.000 0.00 0.00 44.57 2.73
78 79 2.033801 GGCCAAGAATCGTAGCGTACTA 59.966 50.000 0.00 0.00 0.00 1.82
79 80 1.202382 GGCCAAGAATCGTAGCGTACT 60.202 52.381 0.00 0.00 0.00 2.73
80 81 1.202382 AGGCCAAGAATCGTAGCGTAC 60.202 52.381 5.01 0.00 0.00 3.67
81 82 1.108776 AGGCCAAGAATCGTAGCGTA 58.891 50.000 5.01 0.00 0.00 4.42
82 83 1.108776 TAGGCCAAGAATCGTAGCGT 58.891 50.000 5.01 0.00 0.00 5.07
83 84 2.440539 ATAGGCCAAGAATCGTAGCG 57.559 50.000 5.01 0.00 0.00 4.26
84 85 8.494016 AATAAATATAGGCCAAGAATCGTAGC 57.506 34.615 5.01 0.00 0.00 3.58
86 87 9.444600 GGAAATAAATATAGGCCAAGAATCGTA 57.555 33.333 5.01 0.00 0.00 3.43
87 88 7.942341 TGGAAATAAATATAGGCCAAGAATCGT 59.058 33.333 5.01 0.00 0.00 3.73
88 89 8.335532 TGGAAATAAATATAGGCCAAGAATCG 57.664 34.615 5.01 0.00 0.00 3.34
94 95 9.930158 AACTACTTGGAAATAAATATAGGCCAA 57.070 29.630 5.01 0.00 33.37 4.52
95 96 9.349713 CAACTACTTGGAAATAAATATAGGCCA 57.650 33.333 5.01 0.00 0.00 5.36
96 97 9.350951 ACAACTACTTGGAAATAAATATAGGCC 57.649 33.333 0.00 0.00 0.00 5.19
102 103 9.169592 GGCAGTACAACTACTTGGAAATAAATA 57.830 33.333 0.00 0.00 30.03 1.40
103 104 7.888546 AGGCAGTACAACTACTTGGAAATAAAT 59.111 33.333 0.00 0.00 30.03 1.40
104 105 7.228590 AGGCAGTACAACTACTTGGAAATAAA 58.771 34.615 0.00 0.00 30.03 1.40
105 106 6.775708 AGGCAGTACAACTACTTGGAAATAA 58.224 36.000 0.00 0.00 30.03 1.40
106 107 6.014070 TGAGGCAGTACAACTACTTGGAAATA 60.014 38.462 0.00 0.00 30.03 1.40
107 108 5.221843 TGAGGCAGTACAACTACTTGGAAAT 60.222 40.000 0.00 0.00 30.03 2.17
108 109 4.101898 TGAGGCAGTACAACTACTTGGAAA 59.898 41.667 0.00 0.00 30.03 3.13
109 110 3.644265 TGAGGCAGTACAACTACTTGGAA 59.356 43.478 0.00 0.00 30.03 3.53
110 111 3.006537 GTGAGGCAGTACAACTACTTGGA 59.993 47.826 0.00 0.00 30.03 3.53
111 112 3.326747 GTGAGGCAGTACAACTACTTGG 58.673 50.000 0.00 0.00 30.03 3.61
112 113 3.326747 GGTGAGGCAGTACAACTACTTG 58.673 50.000 0.00 0.00 30.03 3.16
149 151 1.012086 TCGGTAGAGTCACGAATCCG 58.988 55.000 0.00 0.00 42.50 4.18
258 261 3.783362 TTTGTGTGGCGGGGACAGG 62.783 63.158 0.00 0.00 0.00 4.00
550 629 1.673009 GGACGCGGGTGGATTTTGA 60.673 57.895 10.96 0.00 0.00 2.69
551 630 2.874751 GGACGCGGGTGGATTTTG 59.125 61.111 10.96 0.00 0.00 2.44
552 631 2.744709 CGGACGCGGGTGGATTTT 60.745 61.111 10.96 0.00 0.00 1.82
553 632 3.697747 TCGGACGCGGGTGGATTT 61.698 61.111 10.96 0.00 0.00 2.17
554 633 4.446413 GTCGGACGCGGGTGGATT 62.446 66.667 10.96 0.00 0.00 3.01
600 683 2.434185 CGATGTGTGTGACGGGGG 60.434 66.667 0.00 0.00 0.00 5.40
601 684 1.736645 GACGATGTGTGTGACGGGG 60.737 63.158 0.00 0.00 0.00 5.73
698 781 2.461637 CCCTCCCTTCCTTCCCCT 59.538 66.667 0.00 0.00 0.00 4.79
702 785 2.687566 TCCGCCCTCCCTTCCTTC 60.688 66.667 0.00 0.00 0.00 3.46
703 786 3.009714 GTCCGCCCTCCCTTCCTT 61.010 66.667 0.00 0.00 0.00 3.36
711 794 4.493747 CGTTCTCCGTCCGCCCTC 62.494 72.222 0.00 0.00 0.00 4.30
786 869 4.705519 CAAGGCAAACCGCTGGCG 62.706 66.667 8.08 8.08 46.09 5.69
818 901 0.478507 CTCCTCTCCTCTCCTCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
823 906 2.587060 TCTCTCTCCTCTCCTCTCCT 57.413 55.000 0.00 0.00 0.00 3.69
824 907 4.993705 TTATCTCTCTCCTCTCCTCTCC 57.006 50.000 0.00 0.00 0.00 3.71
825 908 5.238650 CGTTTTATCTCTCTCCTCTCCTCTC 59.761 48.000 0.00 0.00 0.00 3.20
826 909 5.104277 TCGTTTTATCTCTCTCCTCTCCTCT 60.104 44.000 0.00 0.00 0.00 3.69
827 910 5.127491 TCGTTTTATCTCTCTCCTCTCCTC 58.873 45.833 0.00 0.00 0.00 3.71
828 911 5.118729 TCGTTTTATCTCTCTCCTCTCCT 57.881 43.478 0.00 0.00 0.00 3.69
1185 1291 4.816984 TCGTCCTCCTCCTCGGCC 62.817 72.222 0.00 0.00 0.00 6.13
1285 1391 4.388499 CGCCCGCCACAGGTAAGT 62.388 66.667 0.00 0.00 0.00 2.24
1331 1447 1.375551 AAAAACAGGAACGCGTGAGT 58.624 45.000 14.98 6.40 34.18 3.41
1514 1640 5.346281 GGATAGCTCGTCGAGATTTAAATGG 59.654 44.000 26.11 0.00 28.73 3.16
1526 1653 2.311462 CGAATTCAGGATAGCTCGTCG 58.689 52.381 6.22 0.00 0.00 5.12
1753 1881 0.820891 CCATAGTGCCAGGGTGATGC 60.821 60.000 0.00 0.00 0.00 3.91
1808 1940 2.422597 CCTGCACACGATTAGAAACCA 58.577 47.619 0.00 0.00 0.00 3.67
1838 1970 1.069090 GTTCTGCTCGTCCCACACA 59.931 57.895 0.00 0.00 0.00 3.72
1859 1991 2.043551 TGCCCCACAAAGTGCACA 60.044 55.556 21.04 0.00 31.34 4.57
1953 2085 2.656560 AAGCGCTATCGTTTCTGAGT 57.343 45.000 12.05 0.00 33.95 3.41
1969 2101 2.094099 CACCAACAAGCAACAACAAAGC 59.906 45.455 0.00 0.00 0.00 3.51
1982 2114 4.022416 GCATGAACATTCTACCACCAACAA 60.022 41.667 0.00 0.00 0.00 2.83
2203 2335 8.456471 CAATCAAACAGAGATGCTCATTTTAGA 58.544 33.333 0.00 0.00 32.06 2.10
2245 2377 0.457035 AAGCCACATGCATAAAGCCG 59.543 50.000 0.00 0.00 44.83 5.52
2453 2592 8.778059 TGGACCCTTACTCTCAAATAACAATAT 58.222 33.333 0.00 0.00 0.00 1.28
2455 2594 7.027874 TGGACCCTTACTCTCAAATAACAAT 57.972 36.000 0.00 0.00 0.00 2.71
2456 2595 6.442541 TGGACCCTTACTCTCAAATAACAA 57.557 37.500 0.00 0.00 0.00 2.83
2466 2636 4.832823 CCAAAATTGTTGGACCCTTACTCT 59.167 41.667 0.00 0.00 42.06 3.24
2617 2830 0.034756 ACACTTACAGCATGCCGTCA 59.965 50.000 15.66 0.00 42.53 4.35
2896 3109 8.151596 TCAACTAAACCAGAAAAACCAACTTTT 58.848 29.630 0.00 0.00 33.13 2.27
3010 3223 0.771127 TGGGAAAGGTCTTGAGGGTG 59.229 55.000 0.00 0.00 0.00 4.61
3275 3488 6.947903 TTAATAACGTGCACGAGTAATGAA 57.052 33.333 42.94 24.25 43.02 2.57
3282 3495 5.950965 AGAAGATTAATAACGTGCACGAG 57.049 39.130 42.94 18.23 43.02 4.18
3469 3682 6.701841 CAGTAAGAACTTCACAGCAAGACTTA 59.298 38.462 0.00 0.00 31.97 2.24
3552 3765 7.925043 TTTGGTTAGTACTGTTGAAACAAGA 57.075 32.000 5.39 0.00 38.66 3.02
3584 3797 7.147983 CCCAGGTTATCGTCCATTTGAATTTAA 60.148 37.037 0.00 0.00 0.00 1.52
3614 3827 0.107643 TGGGCGATGTGTCTTCAACA 59.892 50.000 0.00 0.00 34.78 3.33
3827 4041 1.694856 GTTTGGCATGGTAGGGGGA 59.305 57.895 0.00 0.00 0.00 4.81
3887 4101 2.880890 CCACCTTGTTTCTTCCTCACTG 59.119 50.000 0.00 0.00 0.00 3.66
4024 4238 1.489560 CCCTCCTTCCAAGAACCGGT 61.490 60.000 0.00 0.00 0.00 5.28
4056 4270 2.347490 GTGAGGGCAGCGGAAAGA 59.653 61.111 0.00 0.00 0.00 2.52
4057 4271 3.121030 CGTGAGGGCAGCGGAAAG 61.121 66.667 0.00 0.00 0.00 2.62
4069 4283 1.210931 CCTTGCATTGTGCCGTGAG 59.789 57.895 0.00 0.00 44.23 3.51
4070 4284 0.821301 TTCCTTGCATTGTGCCGTGA 60.821 50.000 0.00 0.00 44.23 4.35
4071 4285 0.387622 CTTCCTTGCATTGTGCCGTG 60.388 55.000 0.00 0.00 44.23 4.94
4072 4286 1.526575 CCTTCCTTGCATTGTGCCGT 61.527 55.000 0.00 0.00 44.23 5.68
4073 4287 1.213537 CCTTCCTTGCATTGTGCCG 59.786 57.895 0.00 0.00 44.23 5.69
4074 4288 0.529378 CTCCTTCCTTGCATTGTGCC 59.471 55.000 0.00 0.00 44.23 5.01
4075 4289 0.529378 CCTCCTTCCTTGCATTGTGC 59.471 55.000 0.00 0.00 45.29 4.57
4076 4290 1.180029 CCCTCCTTCCTTGCATTGTG 58.820 55.000 0.00 0.00 0.00 3.33
4077 4291 0.040204 CCCCTCCTTCCTTGCATTGT 59.960 55.000 0.00 0.00 0.00 2.71
4078 4292 0.040204 ACCCCTCCTTCCTTGCATTG 59.960 55.000 0.00 0.00 0.00 2.82
4079 4293 0.786435 AACCCCTCCTTCCTTGCATT 59.214 50.000 0.00 0.00 0.00 3.56
4080 4294 0.786435 AAACCCCTCCTTCCTTGCAT 59.214 50.000 0.00 0.00 0.00 3.96
4081 4295 0.560688 AAAACCCCTCCTTCCTTGCA 59.439 50.000 0.00 0.00 0.00 4.08
4082 4296 0.969149 CAAAACCCCTCCTTCCTTGC 59.031 55.000 0.00 0.00 0.00 4.01
4083 4297 0.969149 GCAAAACCCCTCCTTCCTTG 59.031 55.000 0.00 0.00 0.00 3.61
4084 4298 0.560688 TGCAAAACCCCTCCTTCCTT 59.439 50.000 0.00 0.00 0.00 3.36
4085 4299 0.560688 TTGCAAAACCCCTCCTTCCT 59.439 50.000 0.00 0.00 0.00 3.36
4086 4300 0.679505 GTTGCAAAACCCCTCCTTCC 59.320 55.000 0.00 0.00 0.00 3.46
4087 4301 1.704641 AGTTGCAAAACCCCTCCTTC 58.295 50.000 0.00 0.00 0.00 3.46
4088 4302 1.762370 CAAGTTGCAAAACCCCTCCTT 59.238 47.619 0.00 0.00 0.00 3.36
4089 4303 1.413118 CAAGTTGCAAAACCCCTCCT 58.587 50.000 0.00 0.00 0.00 3.69
4090 4304 0.249868 GCAAGTTGCAAAACCCCTCC 60.250 55.000 22.90 0.00 44.26 4.30
4091 4305 3.289128 GCAAGTTGCAAAACCCCTC 57.711 52.632 22.90 0.00 44.26 4.30
4126 4340 0.968405 TTCCTTCCTTGCATTGTGCC 59.032 50.000 0.00 0.00 44.23 5.01
4155 4369 1.751351 TGATCTGTAACCTCCTGCTCG 59.249 52.381 0.00 0.00 0.00 5.03
4238 4452 4.663120 ACATACAAAGTAGCCCCATGGATA 59.337 41.667 15.22 0.00 0.00 2.59
4247 4461 5.221048 CCATTGCCTAACATACAAAGTAGCC 60.221 44.000 0.00 0.00 0.00 3.93
4263 4477 1.613437 CTTCCGTCAAAACCATTGCCT 59.387 47.619 0.00 0.00 0.00 4.75
4315 4529 5.867903 ACCCAATTCAAATGACAAACTCA 57.132 34.783 0.00 0.00 0.00 3.41
4374 4588 7.149202 ACCATGGATAATTTGGACTAGCTTA 57.851 36.000 21.47 0.00 34.52 3.09
4382 4596 6.015918 AGTCAACAACCATGGATAATTTGGA 58.984 36.000 21.47 3.01 34.52 3.53
4456 4670 5.249163 TCACAAGAGGATCAAAGGAGAATCA 59.751 40.000 0.00 0.00 37.82 2.57
4545 4759 8.154649 ACAATAACTACAAACAAGAAGTGGAG 57.845 34.615 0.00 0.00 0.00 3.86
4548 4762 8.070171 CAGGACAATAACTACAAACAAGAAGTG 58.930 37.037 0.00 0.00 0.00 3.16
4555 4769 5.464057 CGTCACAGGACAATAACTACAAACA 59.536 40.000 0.00 0.00 44.54 2.83
4565 4779 1.276989 GTTCCCCGTCACAGGACAATA 59.723 52.381 0.00 0.00 44.54 1.90
4573 4787 3.948719 GGCCAGTTCCCCGTCACA 61.949 66.667 0.00 0.00 0.00 3.58
4581 4795 2.561478 TGAAACACTAGGCCAGTTCC 57.439 50.000 5.01 0.00 34.26 3.62
4591 4809 7.094508 TGCTTGAAACAGATTTGAAACACTA 57.905 32.000 0.00 0.00 0.00 2.74
4600 4818 9.632638 ACCTATGTATATGCTTGAAACAGATTT 57.367 29.630 0.00 0.00 0.00 2.17
4601 4819 9.060347 CACCTATGTATATGCTTGAAACAGATT 57.940 33.333 0.00 0.00 0.00 2.40
4613 4831 8.792830 AATACATCCAACACCTATGTATATGC 57.207 34.615 7.42 0.00 42.91 3.14
4659 4880 2.047274 CTCGAACCACGCACCCAT 60.047 61.111 0.00 0.00 42.26 4.00
4730 8126 0.251033 GCCGGTCCTACTTTTGGGTT 60.251 55.000 1.90 0.00 0.00 4.11
4731 8127 1.131928 AGCCGGTCCTACTTTTGGGT 61.132 55.000 1.90 0.00 0.00 4.51
4732 8128 0.392595 GAGCCGGTCCTACTTTTGGG 60.393 60.000 1.90 0.00 0.00 4.12
4735 8131 1.190178 ACGGAGCCGGTCCTACTTTT 61.190 55.000 14.60 0.00 44.35 2.27


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

AutoCloner maintained by Alex Coulton.