Multiple sequence alignment - TraesCS3A01G343800

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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 TraesCS3A01G343800 chr3A 100.000 2111 0 0 1 2111 593322026 593319916 0.000000e+00 3899
1 TraesCS3A01G343800 chr3A 95.665 692 14 6 177 853 393237842 393237152 0.000000e+00 1098
2 TraesCS3A01G343800 chr3A 98.929 560 5 1 177 735 435414505 435413946 0.000000e+00 1000
3 TraesCS3A01G343800 chr3B 98.362 1038 13 3 177 1212 201500088 201501123 0.000000e+00 1820
4 TraesCS3A01G343800 chr1A 99.198 998 8 0 215 1212 554471482 554470485 0.000000e+00 1799
5 TraesCS3A01G343800 chr1A 99.221 899 7 0 1213 2111 554461295 554460397 0.000000e+00 1622
6 TraesCS3A01G343800 chr1A 98.344 302 4 1 177 477 554472048 554471747 1.430000e-146 529
7 TraesCS3A01G343800 chr2D 98.888 899 10 0 1213 2111 9787973 9787075 0.000000e+00 1605
8 TraesCS3A01G343800 chr2D 99.176 364 2 1 849 1212 643860299 643860661 0.000000e+00 654
9 TraesCS3A01G343800 chr2D 96.250 240 7 2 177 414 643859887 643860126 1.960000e-105 392
10 TraesCS3A01G343800 chr2B 98.888 899 10 0 1213 2111 474903157 474902259 0.000000e+00 1605
11 TraesCS3A01G343800 chr6D 98.776 899 11 0 1213 2111 45508739 45509637 0.000000e+00 1600
12 TraesCS3A01G343800 chr6D 99.176 364 2 1 849 1212 431396950 431396588 0.000000e+00 654
13 TraesCS3A01G343800 chr6D 97.380 229 4 2 177 403 431397370 431397142 2.540000e-104 388
14 TraesCS3A01G343800 chr6D 100.000 166 0 0 1 166 108491399 108491234 7.320000e-80 307
15 TraesCS3A01G343800 chr6D 100.000 166 0 0 1 166 389251512 389251677 7.320000e-80 307
16 TraesCS3A01G343800 chr6D 100.000 166 0 0 1 166 458922149 458922314 7.320000e-80 307
17 TraesCS3A01G343800 chr6D 96.923 130 4 0 725 854 100540051 100540180 3.530000e-53 219
18 TraesCS3A01G343800 chr5D 98.554 899 13 0 1213 2111 6178135 6179033 0.000000e+00 1589
19 TraesCS3A01G343800 chr5D 97.998 899 12 1 1213 2111 503290139 503289247 0.000000e+00 1555
20 TraesCS3A01G343800 chr5D 96.222 900 32 2 1213 2111 513585573 513586471 0.000000e+00 1472
21 TraesCS3A01G343800 chr5D 99.183 367 2 1 846 1212 6217247 6216882 0.000000e+00 660
22 TraesCS3A01G343800 chr5D 97.500 240 3 3 177 414 6217656 6217418 7.010000e-110 407
23 TraesCS3A01G343800 chr5D 100.000 166 0 0 1 166 45206991 45206826 7.320000e-80 307
24 TraesCS3A01G343800 chr5D 100.000 166 0 0 1 166 503225053 503225218 7.320000e-80 307
25 TraesCS3A01G343800 chr5D 100.000 166 0 0 1 166 503235369 503235534 7.320000e-80 307
26 TraesCS3A01G343800 chr5D 100.000 166 0 0 1 166 503239619 503239784 7.320000e-80 307
27 TraesCS3A01G343800 chr4B 97.775 899 20 0 1213 2111 308680959 308681857 0.000000e+00 1550
28 TraesCS3A01G343800 chr4B 98.077 312 6 0 458 769 421404471 421404160 5.120000e-151 544
29 TraesCS3A01G343800 chr4A 96.774 899 29 0 1213 2111 309504336 309505234 0.000000e+00 1500
30 TraesCS3A01G343800 chr1D 94.581 609 24 4 177 777 244393938 244394545 0.000000e+00 933
31 TraesCS3A01G343800 chr1D 98.901 364 3 1 849 1212 254483925 254484287 0.000000e+00 649
32 TraesCS3A01G343800 chr7B 98.305 472 6 2 479 950 300903252 300902783 0.000000e+00 826
33 TraesCS3A01G343800 chr5B 96.377 414 12 2 414 827 559429704 559430114 0.000000e+00 678
34 TraesCS3A01G343800 chrUn 99.455 367 2 0 846 1212 443804162 443803796 0.000000e+00 667
35 TraesCS3A01G343800 chrUn 99.440 357 2 0 856 1212 444441717 444442073 0.000000e+00 649
36 TraesCS3A01G343800 chrUn 100.000 166 0 0 1 166 180667053 180666888 7.320000e-80 307
37 TraesCS3A01G343800 chr6A 99.176 364 3 0 849 1212 192823179 192823542 0.000000e+00 656
38 TraesCS3A01G343800 chr6A 98.392 311 5 0 421 731 495543357 495543047 3.960000e-152 547
39 TraesCS3A01G343800 chr6B 98.188 276 4 1 710 985 204449447 204449173 4.070000e-132 481
40 TraesCS3A01G343800 chr3D 100.000 166 0 0 1 166 24164280 24164115 7.320000e-80 307
41 TraesCS3A01G343800 chr5A 91.111 225 16 3 641 862 11090770 11090993 3.400000e-78 302


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 TraesCS3A01G343800 chr3A 593319916 593322026 2110 True 3899.0 3899 100.0000 1 2111 1 chr3A.!!$R3 2110
1 TraesCS3A01G343800 chr3A 393237152 393237842 690 True 1098.0 1098 95.6650 177 853 1 chr3A.!!$R1 676
2 TraesCS3A01G343800 chr3A 435413946 435414505 559 True 1000.0 1000 98.9290 177 735 1 chr3A.!!$R2 558
3 TraesCS3A01G343800 chr3B 201500088 201501123 1035 False 1820.0 1820 98.3620 177 1212 1 chr3B.!!$F1 1035
4 TraesCS3A01G343800 chr1A 554460397 554461295 898 True 1622.0 1622 99.2210 1213 2111 1 chr1A.!!$R1 898
5 TraesCS3A01G343800 chr1A 554470485 554472048 1563 True 1164.0 1799 98.7710 177 1212 2 chr1A.!!$R2 1035
6 TraesCS3A01G343800 chr2D 9787075 9787973 898 True 1605.0 1605 98.8880 1213 2111 1 chr2D.!!$R1 898
7 TraesCS3A01G343800 chr2D 643859887 643860661 774 False 523.0 654 97.7130 177 1212 2 chr2D.!!$F1 1035
8 TraesCS3A01G343800 chr2B 474902259 474903157 898 True 1605.0 1605 98.8880 1213 2111 1 chr2B.!!$R1 898
9 TraesCS3A01G343800 chr6D 45508739 45509637 898 False 1600.0 1600 98.7760 1213 2111 1 chr6D.!!$F1 898
10 TraesCS3A01G343800 chr6D 431396588 431397370 782 True 521.0 654 98.2780 177 1212 2 chr6D.!!$R2 1035
11 TraesCS3A01G343800 chr5D 6178135 6179033 898 False 1589.0 1589 98.5540 1213 2111 1 chr5D.!!$F1 898
12 TraesCS3A01G343800 chr5D 503289247 503290139 892 True 1555.0 1555 97.9980 1213 2111 1 chr5D.!!$R2 898
13 TraesCS3A01G343800 chr5D 513585573 513586471 898 False 1472.0 1472 96.2220 1213 2111 1 chr5D.!!$F5 898
14 TraesCS3A01G343800 chr5D 6216882 6217656 774 True 533.5 660 98.3415 177 1212 2 chr5D.!!$R3 1035
15 TraesCS3A01G343800 chr4B 308680959 308681857 898 False 1550.0 1550 97.7750 1213 2111 1 chr4B.!!$F1 898
16 TraesCS3A01G343800 chr4A 309504336 309505234 898 False 1500.0 1500 96.7740 1213 2111 1 chr4A.!!$F1 898
17 TraesCS3A01G343800 chr1D 244393938 244394545 607 False 933.0 933 94.5810 177 777 1 chr1D.!!$F1 600

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
144 145 0.037605 AACTTTCCGCGTCGATCCTT 60.038 50.0 4.92 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1791 2.031682 CCCAACTCAAGCTGAAGAAACG 60.032 50.0 2.77 0.0 0.0 3.6 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
21 22 3.111853 TGGCAGCATCTACTAATTCGG 57.888 47.619 0.00 0.00 0.00 4.30
22 23 2.698274 TGGCAGCATCTACTAATTCGGA 59.302 45.455 0.00 0.00 0.00 4.55
23 24 3.133901 TGGCAGCATCTACTAATTCGGAA 59.866 43.478 0.00 0.00 0.00 4.30
24 25 3.495001 GGCAGCATCTACTAATTCGGAAC 59.505 47.826 0.00 0.00 0.00 3.62
25 26 4.372656 GCAGCATCTACTAATTCGGAACT 58.627 43.478 0.00 0.00 0.00 3.01
26 27 4.811557 GCAGCATCTACTAATTCGGAACTT 59.188 41.667 0.00 0.00 0.00 2.66
27 28 5.983720 GCAGCATCTACTAATTCGGAACTTA 59.016 40.000 0.00 0.00 0.00 2.24
28 29 6.479001 GCAGCATCTACTAATTCGGAACTTAA 59.521 38.462 0.00 0.00 0.00 1.85
29 30 7.171678 GCAGCATCTACTAATTCGGAACTTAAT 59.828 37.037 0.00 0.00 0.00 1.40
30 31 9.046296 CAGCATCTACTAATTCGGAACTTAATT 57.954 33.333 0.00 0.00 0.00 1.40
31 32 9.614792 AGCATCTACTAATTCGGAACTTAATTT 57.385 29.630 0.00 0.00 0.00 1.82
32 33 9.651718 GCATCTACTAATTCGGAACTTAATTTG 57.348 33.333 0.00 0.00 0.00 2.32
37 38 8.965986 ACTAATTCGGAACTTAATTTGAAAGC 57.034 30.769 0.00 0.00 0.00 3.51
38 39 8.027189 ACTAATTCGGAACTTAATTTGAAAGCC 58.973 33.333 0.00 0.00 0.00 4.35
39 40 5.776173 TTCGGAACTTAATTTGAAAGCCA 57.224 34.783 0.00 0.00 0.00 4.75
40 41 5.975693 TCGGAACTTAATTTGAAAGCCAT 57.024 34.783 0.00 0.00 0.00 4.40
41 42 7.455641 TTCGGAACTTAATTTGAAAGCCATA 57.544 32.000 0.00 0.00 0.00 2.74
42 43 7.639113 TCGGAACTTAATTTGAAAGCCATAT 57.361 32.000 0.00 0.00 0.00 1.78
43 44 8.062065 TCGGAACTTAATTTGAAAGCCATATT 57.938 30.769 0.00 0.00 32.48 1.28
44 45 8.527810 TCGGAACTTAATTTGAAAGCCATATTT 58.472 29.630 0.00 0.00 30.75 1.40
45 46 8.807581 CGGAACTTAATTTGAAAGCCATATTTC 58.192 33.333 0.00 0.00 39.22 2.17
46 47 8.807581 GGAACTTAATTTGAAAGCCATATTTCG 58.192 33.333 0.00 0.00 41.21 3.46
47 48 9.567848 GAACTTAATTTGAAAGCCATATTTCGA 57.432 29.630 0.00 0.00 41.21 3.71
48 49 8.911247 ACTTAATTTGAAAGCCATATTTCGAC 57.089 30.769 0.00 0.00 41.21 4.20
49 50 7.973944 ACTTAATTTGAAAGCCATATTTCGACC 59.026 33.333 0.00 0.00 41.21 4.79
50 51 4.712122 TTTGAAAGCCATATTTCGACCC 57.288 40.909 0.00 0.00 41.21 4.46
51 52 2.285083 TGAAAGCCATATTTCGACCCG 58.715 47.619 0.00 0.00 41.21 5.28
52 53 1.602377 GAAAGCCATATTTCGACCCGG 59.398 52.381 0.00 0.00 30.10 5.73
53 54 0.834612 AAGCCATATTTCGACCCGGA 59.165 50.000 0.73 0.00 0.00 5.14
54 55 0.106149 AGCCATATTTCGACCCGGAC 59.894 55.000 0.73 0.00 0.00 4.79
55 56 1.219522 GCCATATTTCGACCCGGACG 61.220 60.000 0.73 9.08 0.00 4.79
56 57 1.219522 CCATATTTCGACCCGGACGC 61.220 60.000 0.73 0.00 0.00 5.19
57 58 0.249322 CATATTTCGACCCGGACGCT 60.249 55.000 0.73 0.00 0.00 5.07
58 59 0.462789 ATATTTCGACCCGGACGCTT 59.537 50.000 0.73 0.00 0.00 4.68
59 60 0.247185 TATTTCGACCCGGACGCTTT 59.753 50.000 0.73 0.00 0.00 3.51
60 61 0.604511 ATTTCGACCCGGACGCTTTT 60.605 50.000 0.73 0.00 0.00 2.27
61 62 1.500512 TTTCGACCCGGACGCTTTTG 61.501 55.000 0.73 0.00 0.00 2.44
62 63 3.419759 CGACCCGGACGCTTTTGG 61.420 66.667 0.73 0.00 0.00 3.28
64 65 3.540367 GACCCGGACGCTTTTGGGA 62.540 63.158 0.73 0.00 44.88 4.37
65 66 2.045340 CCCGGACGCTTTTGGGAT 60.045 61.111 0.73 0.00 44.88 3.85
66 67 2.406616 CCCGGACGCTTTTGGGATG 61.407 63.158 0.73 0.00 44.88 3.51
67 68 2.485122 CGGACGCTTTTGGGATGC 59.515 61.111 0.00 0.00 36.14 3.91
68 69 2.040544 CGGACGCTTTTGGGATGCT 61.041 57.895 0.00 0.00 36.14 3.79
69 70 1.586154 CGGACGCTTTTGGGATGCTT 61.586 55.000 0.00 0.00 36.14 3.91
70 71 0.171231 GGACGCTTTTGGGATGCTTC 59.829 55.000 0.00 0.00 36.14 3.86
71 72 1.168714 GACGCTTTTGGGATGCTTCT 58.831 50.000 0.00 0.00 36.14 2.85
72 73 2.356135 GACGCTTTTGGGATGCTTCTA 58.644 47.619 0.00 0.00 36.14 2.10
73 74 2.747446 GACGCTTTTGGGATGCTTCTAA 59.253 45.455 0.00 0.00 36.14 2.10
74 75 3.356290 ACGCTTTTGGGATGCTTCTAAT 58.644 40.909 0.00 0.00 36.14 1.73
75 76 4.523083 ACGCTTTTGGGATGCTTCTAATA 58.477 39.130 0.00 0.00 36.14 0.98
76 77 4.947388 ACGCTTTTGGGATGCTTCTAATAA 59.053 37.500 0.00 0.00 36.14 1.40
77 78 5.163652 ACGCTTTTGGGATGCTTCTAATAAC 60.164 40.000 0.00 0.00 36.14 1.89
78 79 5.592054 GCTTTTGGGATGCTTCTAATAACC 58.408 41.667 0.00 0.00 0.00 2.85
79 80 5.127031 GCTTTTGGGATGCTTCTAATAACCA 59.873 40.000 0.00 0.00 0.00 3.67
80 81 6.350949 GCTTTTGGGATGCTTCTAATAACCAA 60.351 38.462 0.00 0.00 35.17 3.67
81 82 6.524101 TTTGGGATGCTTCTAATAACCAAC 57.476 37.500 0.00 0.00 36.57 3.77
82 83 4.196193 TGGGATGCTTCTAATAACCAACG 58.804 43.478 0.00 0.00 0.00 4.10
83 84 4.080807 TGGGATGCTTCTAATAACCAACGA 60.081 41.667 0.00 0.00 0.00 3.85
84 85 4.879545 GGGATGCTTCTAATAACCAACGAA 59.120 41.667 0.00 0.00 0.00 3.85
85 86 5.531287 GGGATGCTTCTAATAACCAACGAAT 59.469 40.000 0.00 0.00 0.00 3.34
86 87 6.430451 GGATGCTTCTAATAACCAACGAATG 58.570 40.000 0.00 0.00 0.00 2.67
94 95 4.557942 CCAACGAATGGCAAGTGC 57.442 55.556 0.00 0.00 43.80 4.40
95 96 1.959085 CCAACGAATGGCAAGTGCT 59.041 52.632 2.85 0.00 43.80 4.40
96 97 0.109597 CCAACGAATGGCAAGTGCTC 60.110 55.000 2.85 0.00 43.80 4.26
97 98 0.877071 CAACGAATGGCAAGTGCTCT 59.123 50.000 2.85 0.00 41.70 4.09
98 99 1.267806 CAACGAATGGCAAGTGCTCTT 59.732 47.619 2.85 0.00 41.70 2.85
99 100 1.160137 ACGAATGGCAAGTGCTCTTC 58.840 50.000 2.85 5.91 41.70 2.87
100 101 0.449388 CGAATGGCAAGTGCTCTTCC 59.551 55.000 2.85 4.38 41.70 3.46
101 102 1.831580 GAATGGCAAGTGCTCTTCCT 58.168 50.000 2.85 1.07 41.70 3.36
102 103 2.165998 GAATGGCAAGTGCTCTTCCTT 58.834 47.619 2.85 8.19 41.70 3.36
103 104 1.542492 ATGGCAAGTGCTCTTCCTTG 58.458 50.000 2.85 0.00 40.77 3.61
104 105 0.183492 TGGCAAGTGCTCTTCCTTGT 59.817 50.000 2.85 0.00 40.13 3.16
105 106 1.322442 GGCAAGTGCTCTTCCTTGTT 58.678 50.000 2.85 0.00 40.13 2.83
106 107 1.683385 GGCAAGTGCTCTTCCTTGTTT 59.317 47.619 2.85 0.00 40.13 2.83
107 108 2.884639 GGCAAGTGCTCTTCCTTGTTTA 59.115 45.455 2.85 0.00 40.13 2.01
108 109 3.057946 GGCAAGTGCTCTTCCTTGTTTAG 60.058 47.826 2.85 0.00 40.13 1.85
109 110 3.815401 GCAAGTGCTCTTCCTTGTTTAGA 59.185 43.478 0.00 0.00 40.13 2.10
110 111 4.457257 GCAAGTGCTCTTCCTTGTTTAGAT 59.543 41.667 0.00 0.00 40.13 1.98
111 112 5.391416 GCAAGTGCTCTTCCTTGTTTAGATC 60.391 44.000 0.00 0.00 40.13 2.75
112 113 4.837972 AGTGCTCTTCCTTGTTTAGATCC 58.162 43.478 0.00 0.00 0.00 3.36
113 114 4.534103 AGTGCTCTTCCTTGTTTAGATCCT 59.466 41.667 0.00 0.00 0.00 3.24
114 115 5.721960 AGTGCTCTTCCTTGTTTAGATCCTA 59.278 40.000 0.00 0.00 0.00 2.94
115 116 6.385467 AGTGCTCTTCCTTGTTTAGATCCTAT 59.615 38.462 0.00 0.00 0.00 2.57
116 117 7.051000 GTGCTCTTCCTTGTTTAGATCCTATT 58.949 38.462 0.00 0.00 0.00 1.73
117 118 7.554476 GTGCTCTTCCTTGTTTAGATCCTATTT 59.446 37.037 0.00 0.00 0.00 1.40
118 119 7.770897 TGCTCTTCCTTGTTTAGATCCTATTTC 59.229 37.037 0.00 0.00 0.00 2.17
119 120 7.770897 GCTCTTCCTTGTTTAGATCCTATTTCA 59.229 37.037 0.00 0.00 0.00 2.69
120 121 9.672673 CTCTTCCTTGTTTAGATCCTATTTCAA 57.327 33.333 0.00 0.00 0.00 2.69
123 124 8.662781 TCCTTGTTTAGATCCTATTTCAATCG 57.337 34.615 0.00 0.00 0.00 3.34
124 125 7.715249 TCCTTGTTTAGATCCTATTTCAATCGG 59.285 37.037 0.00 0.00 0.00 4.18
125 126 7.715249 CCTTGTTTAGATCCTATTTCAATCGGA 59.285 37.037 0.00 0.00 35.10 4.55
126 127 9.109393 CTTGTTTAGATCCTATTTCAATCGGAA 57.891 33.333 0.00 0.00 34.41 4.30
127 128 8.433421 TGTTTAGATCCTATTTCAATCGGAAC 57.567 34.615 0.00 0.00 34.41 3.62
128 129 8.265055 TGTTTAGATCCTATTTCAATCGGAACT 58.735 33.333 7.68 7.68 37.25 3.01
129 130 9.110502 GTTTAGATCCTATTTCAATCGGAACTT 57.889 33.333 7.82 0.00 35.76 2.66
130 131 9.681062 TTTAGATCCTATTTCAATCGGAACTTT 57.319 29.630 7.82 0.00 35.76 2.66
131 132 7.793927 AGATCCTATTTCAATCGGAACTTTC 57.206 36.000 0.00 0.00 31.99 2.62
132 133 6.768381 AGATCCTATTTCAATCGGAACTTTCC 59.232 38.462 0.00 0.00 44.05 3.13
140 141 4.180496 GGAACTTTCCGCGTCGAT 57.820 55.556 4.92 0.00 37.65 3.59
141 142 1.996755 GGAACTTTCCGCGTCGATC 59.003 57.895 4.92 0.00 37.65 3.69
142 143 1.419107 GGAACTTTCCGCGTCGATCC 61.419 60.000 4.92 1.01 37.65 3.36
143 144 0.458025 GAACTTTCCGCGTCGATCCT 60.458 55.000 4.92 0.00 0.00 3.24
144 145 0.037605 AACTTTCCGCGTCGATCCTT 60.038 50.000 4.92 0.00 0.00 3.36
145 146 0.037605 ACTTTCCGCGTCGATCCTTT 60.038 50.000 4.92 0.00 0.00 3.11
146 147 1.076332 CTTTCCGCGTCGATCCTTTT 58.924 50.000 4.92 0.00 0.00 2.27
147 148 1.463444 CTTTCCGCGTCGATCCTTTTT 59.537 47.619 4.92 0.00 0.00 1.94
172 173 9.540431 TTTATTACGTCTTGTTTTTATTACGCC 57.460 29.630 0.00 0.00 33.87 5.68
173 174 4.408993 ACGTCTTGTTTTTATTACGCCC 57.591 40.909 0.00 0.00 33.87 6.13
174 175 3.814283 ACGTCTTGTTTTTATTACGCCCA 59.186 39.130 0.00 0.00 33.87 5.36
175 176 4.456566 ACGTCTTGTTTTTATTACGCCCAT 59.543 37.500 0.00 0.00 33.87 4.00
176 177 5.642919 ACGTCTTGTTTTTATTACGCCCATA 59.357 36.000 0.00 0.00 33.87 2.74
177 178 6.149142 ACGTCTTGTTTTTATTACGCCCATAA 59.851 34.615 0.00 0.00 33.87 1.90
178 179 7.022384 CGTCTTGTTTTTATTACGCCCATAAA 58.978 34.615 0.00 0.00 0.00 1.40
179 180 7.537991 CGTCTTGTTTTTATTACGCCCATAAAA 59.462 33.333 3.92 3.92 35.31 1.52
180 181 8.856247 GTCTTGTTTTTATTACGCCCATAAAAG 58.144 33.333 6.94 0.00 37.38 2.27
577 1112 2.771372 TGGTAGCTGTGAATAGCCATCA 59.229 45.455 0.00 0.00 44.76 3.07
1236 1791 4.034048 CGGTTAGCAGTCACCATTGAATAC 59.966 45.833 0.00 0.00 31.90 1.89
1846 2401 3.222603 CCCCCTAAAGCGAAATAAGCAT 58.777 45.455 0.00 0.00 37.01 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.133901 TCCGAATTAGTAGATGCTGCCAA 59.866 43.478 0.00 0.00 0.00 4.52
1 2 2.698274 TCCGAATTAGTAGATGCTGCCA 59.302 45.455 0.00 0.00 0.00 4.92
2 3 3.386768 TCCGAATTAGTAGATGCTGCC 57.613 47.619 0.00 0.00 0.00 4.85
4 5 8.594881 ATTAAGTTCCGAATTAGTAGATGCTG 57.405 34.615 0.00 0.00 0.00 4.41
5 6 9.614792 AAATTAAGTTCCGAATTAGTAGATGCT 57.385 29.630 0.00 0.00 0.00 3.79
6 7 9.651718 CAAATTAAGTTCCGAATTAGTAGATGC 57.348 33.333 0.00 0.00 0.00 3.91
12 13 8.027189 GGCTTTCAAATTAAGTTCCGAATTAGT 58.973 33.333 0.00 0.00 0.00 2.24
13 14 8.026607 TGGCTTTCAAATTAAGTTCCGAATTAG 58.973 33.333 0.00 0.00 0.00 1.73
14 15 7.887381 TGGCTTTCAAATTAAGTTCCGAATTA 58.113 30.769 0.00 0.00 0.00 1.40
15 16 6.754193 TGGCTTTCAAATTAAGTTCCGAATT 58.246 32.000 0.00 0.00 0.00 2.17
16 17 6.339587 TGGCTTTCAAATTAAGTTCCGAAT 57.660 33.333 0.00 0.00 0.00 3.34
17 18 5.776173 TGGCTTTCAAATTAAGTTCCGAA 57.224 34.783 0.00 0.00 0.00 4.30
18 19 5.975693 ATGGCTTTCAAATTAAGTTCCGA 57.024 34.783 0.00 0.00 0.00 4.55
19 20 8.702163 AAATATGGCTTTCAAATTAAGTTCCG 57.298 30.769 0.00 0.00 0.00 4.30
20 21 8.807581 CGAAATATGGCTTTCAAATTAAGTTCC 58.192 33.333 0.00 0.00 35.32 3.62
21 22 9.567848 TCGAAATATGGCTTTCAAATTAAGTTC 57.432 29.630 0.00 0.00 35.32 3.01
22 23 9.353999 GTCGAAATATGGCTTTCAAATTAAGTT 57.646 29.630 0.00 0.00 35.32 2.66
23 24 7.973944 GGTCGAAATATGGCTTTCAAATTAAGT 59.026 33.333 0.00 0.00 35.32 2.24
24 25 7.435192 GGGTCGAAATATGGCTTTCAAATTAAG 59.565 37.037 0.00 0.00 35.32 1.85
25 26 7.262048 GGGTCGAAATATGGCTTTCAAATTAA 58.738 34.615 0.00 0.00 35.32 1.40
26 27 6.459024 CGGGTCGAAATATGGCTTTCAAATTA 60.459 38.462 0.00 0.00 35.32 1.40
27 28 5.660460 GGGTCGAAATATGGCTTTCAAATT 58.340 37.500 0.00 0.00 35.32 1.82
28 29 4.202010 CGGGTCGAAATATGGCTTTCAAAT 60.202 41.667 0.00 0.00 35.32 2.32
29 30 3.127895 CGGGTCGAAATATGGCTTTCAAA 59.872 43.478 0.00 0.00 35.32 2.69
30 31 2.680841 CGGGTCGAAATATGGCTTTCAA 59.319 45.455 0.00 0.00 35.32 2.69
31 32 2.285083 CGGGTCGAAATATGGCTTTCA 58.715 47.619 0.00 0.00 35.32 2.69
32 33 1.602377 CCGGGTCGAAATATGGCTTTC 59.398 52.381 0.00 0.00 32.84 2.62
33 34 1.210967 TCCGGGTCGAAATATGGCTTT 59.789 47.619 0.00 0.00 0.00 3.51
34 35 0.834612 TCCGGGTCGAAATATGGCTT 59.165 50.000 0.00 0.00 0.00 4.35
35 36 0.106149 GTCCGGGTCGAAATATGGCT 59.894 55.000 0.00 0.00 0.00 4.75
36 37 1.219522 CGTCCGGGTCGAAATATGGC 61.220 60.000 7.97 0.00 0.00 4.40
37 38 1.219522 GCGTCCGGGTCGAAATATGG 61.220 60.000 17.64 0.00 0.00 2.74
38 39 0.249322 AGCGTCCGGGTCGAAATATG 60.249 55.000 17.64 0.00 0.00 1.78
39 40 0.462789 AAGCGTCCGGGTCGAAATAT 59.537 50.000 17.64 0.00 0.00 1.28
40 41 0.247185 AAAGCGTCCGGGTCGAAATA 59.753 50.000 17.64 0.00 0.00 1.40
41 42 0.604511 AAAAGCGTCCGGGTCGAAAT 60.605 50.000 17.64 0.00 0.00 2.17
42 43 1.227615 AAAAGCGTCCGGGTCGAAA 60.228 52.632 17.64 0.00 0.00 3.46
43 44 1.957186 CAAAAGCGTCCGGGTCGAA 60.957 57.895 17.64 0.00 0.00 3.71
44 45 2.356553 CAAAAGCGTCCGGGTCGA 60.357 61.111 17.64 0.00 0.00 4.20
45 46 3.419759 CCAAAAGCGTCCGGGTCG 61.420 66.667 9.35 9.35 0.00 4.79
46 47 2.814913 ATCCCAAAAGCGTCCGGGTC 62.815 60.000 0.00 0.00 39.87 4.46
47 48 2.902457 ATCCCAAAAGCGTCCGGGT 61.902 57.895 0.00 0.00 39.87 5.28
48 49 2.045340 ATCCCAAAAGCGTCCGGG 60.045 61.111 0.00 0.45 40.32 5.73
49 50 3.051392 GCATCCCAAAAGCGTCCGG 62.051 63.158 0.00 0.00 0.00 5.14
50 51 1.586154 AAGCATCCCAAAAGCGTCCG 61.586 55.000 0.00 0.00 0.00 4.79
51 52 0.171231 GAAGCATCCCAAAAGCGTCC 59.829 55.000 0.00 0.00 31.93 4.79
52 53 1.168714 AGAAGCATCCCAAAAGCGTC 58.831 50.000 0.00 0.00 37.10 5.19
53 54 2.489938 TAGAAGCATCCCAAAAGCGT 57.510 45.000 0.00 0.00 0.00 5.07
54 55 5.273944 GTTATTAGAAGCATCCCAAAAGCG 58.726 41.667 0.00 0.00 0.00 4.68
55 56 5.127031 TGGTTATTAGAAGCATCCCAAAAGC 59.873 40.000 0.00 0.00 0.00 3.51
56 57 6.773976 TGGTTATTAGAAGCATCCCAAAAG 57.226 37.500 0.00 0.00 0.00 2.27
57 58 6.349777 CGTTGGTTATTAGAAGCATCCCAAAA 60.350 38.462 0.00 0.00 32.94 2.44
58 59 5.124776 CGTTGGTTATTAGAAGCATCCCAAA 59.875 40.000 0.00 0.00 32.94 3.28
59 60 4.638421 CGTTGGTTATTAGAAGCATCCCAA 59.362 41.667 0.00 0.00 0.00 4.12
60 61 4.080807 TCGTTGGTTATTAGAAGCATCCCA 60.081 41.667 0.00 0.00 0.00 4.37
61 62 4.448210 TCGTTGGTTATTAGAAGCATCCC 58.552 43.478 0.00 0.00 0.00 3.85
62 63 6.430451 CATTCGTTGGTTATTAGAAGCATCC 58.570 40.000 0.00 0.00 0.00 3.51
63 64 6.430451 CCATTCGTTGGTTATTAGAAGCATC 58.570 40.000 0.00 0.00 40.99 3.91
64 65 6.377327 CCATTCGTTGGTTATTAGAAGCAT 57.623 37.500 0.00 0.00 40.99 3.79
65 66 5.811399 CCATTCGTTGGTTATTAGAAGCA 57.189 39.130 0.00 0.00 40.99 3.91
77 78 5.742791 GAAGAGCACTTGCCATTCGTTGG 62.743 52.174 0.00 3.21 41.54 3.77
78 79 0.877071 AGAGCACTTGCCATTCGTTG 59.123 50.000 0.00 0.00 43.38 4.10
79 80 1.537202 GAAGAGCACTTGCCATTCGTT 59.463 47.619 0.00 0.00 43.38 3.85
80 81 1.160137 GAAGAGCACTTGCCATTCGT 58.840 50.000 0.00 0.00 43.38 3.85
81 82 0.449388 GGAAGAGCACTTGCCATTCG 59.551 55.000 0.00 0.00 43.38 3.34
82 83 1.831580 AGGAAGAGCACTTGCCATTC 58.168 50.000 11.57 2.79 43.80 2.67
83 84 1.891150 CAAGGAAGAGCACTTGCCATT 59.109 47.619 11.57 0.00 43.80 3.16
84 85 1.202976 ACAAGGAAGAGCACTTGCCAT 60.203 47.619 11.57 0.00 46.03 4.40
85 86 0.183492 ACAAGGAAGAGCACTTGCCA 59.817 50.000 11.57 0.00 46.03 4.92
86 87 1.322442 AACAAGGAAGAGCACTTGCC 58.678 50.000 11.57 7.79 46.03 4.52
87 88 3.815401 TCTAAACAAGGAAGAGCACTTGC 59.185 43.478 7.31 7.31 46.03 4.01
89 90 5.013599 AGGATCTAAACAAGGAAGAGCACTT 59.986 40.000 0.00 0.00 39.24 3.16
90 91 4.534103 AGGATCTAAACAAGGAAGAGCACT 59.466 41.667 0.00 0.00 0.00 4.40
91 92 4.837972 AGGATCTAAACAAGGAAGAGCAC 58.162 43.478 0.00 0.00 0.00 4.40
92 93 6.814954 ATAGGATCTAAACAAGGAAGAGCA 57.185 37.500 0.00 0.00 0.00 4.26
93 94 7.770897 TGAAATAGGATCTAAACAAGGAAGAGC 59.229 37.037 0.00 0.00 0.00 4.09
94 95 9.672673 TTGAAATAGGATCTAAACAAGGAAGAG 57.327 33.333 0.00 0.00 0.00 2.85
97 98 9.109393 CGATTGAAATAGGATCTAAACAAGGAA 57.891 33.333 0.00 0.00 0.00 3.36
98 99 7.715249 CCGATTGAAATAGGATCTAAACAAGGA 59.285 37.037 0.00 0.00 33.52 3.36
99 100 7.715249 TCCGATTGAAATAGGATCTAAACAAGG 59.285 37.037 1.18 0.00 35.61 3.61
100 101 8.662781 TCCGATTGAAATAGGATCTAAACAAG 57.337 34.615 1.18 0.00 35.61 3.16
101 102 8.889717 GTTCCGATTGAAATAGGATCTAAACAA 58.110 33.333 5.81 0.00 39.46 2.83
102 103 8.265055 AGTTCCGATTGAAATAGGATCTAAACA 58.735 33.333 11.76 0.00 39.46 2.83
103 104 8.664211 AGTTCCGATTGAAATAGGATCTAAAC 57.336 34.615 11.76 5.41 39.46 2.01
104 105 9.681062 AAAGTTCCGATTGAAATAGGATCTAAA 57.319 29.630 13.10 0.00 38.48 1.85
105 106 9.326413 GAAAGTTCCGATTGAAATAGGATCTAA 57.674 33.333 13.10 0.00 38.48 2.10
106 107 7.931948 GGAAAGTTCCGATTGAAATAGGATCTA 59.068 37.037 13.10 0.00 38.48 1.98
107 108 6.768381 GGAAAGTTCCGATTGAAATAGGATCT 59.232 38.462 5.81 7.57 40.03 2.75
108 109 6.960468 GGAAAGTTCCGATTGAAATAGGATC 58.040 40.000 5.81 5.67 39.46 3.36
109 110 6.944234 GGAAAGTTCCGATTGAAATAGGAT 57.056 37.500 5.81 0.00 39.46 3.24
123 124 1.419107 GGATCGACGCGGAAAGTTCC 61.419 60.000 12.47 8.70 44.05 3.62
124 125 0.458025 AGGATCGACGCGGAAAGTTC 60.458 55.000 12.47 0.00 0.00 3.01
125 126 0.037605 AAGGATCGACGCGGAAAGTT 60.038 50.000 12.47 0.00 0.00 2.66
126 127 0.037605 AAAGGATCGACGCGGAAAGT 60.038 50.000 12.47 0.00 0.00 2.66
127 128 1.076332 AAAAGGATCGACGCGGAAAG 58.924 50.000 12.47 0.00 0.00 2.62
128 129 1.515081 AAAAAGGATCGACGCGGAAA 58.485 45.000 12.47 0.00 0.00 3.13
129 130 3.220447 AAAAAGGATCGACGCGGAA 57.780 47.368 12.47 0.00 0.00 4.30
146 147 9.540431 GGCGTAATAAAAACAAGACGTAATAAA 57.460 29.630 0.00 0.00 33.05 1.40
147 148 8.174422 GGGCGTAATAAAAACAAGACGTAATAA 58.826 33.333 0.00 0.00 33.05 1.40
148 149 7.332926 TGGGCGTAATAAAAACAAGACGTAATA 59.667 33.333 0.00 0.00 33.05 0.98
149 150 6.149142 TGGGCGTAATAAAAACAAGACGTAAT 59.851 34.615 0.00 0.00 33.05 1.89
150 151 5.468072 TGGGCGTAATAAAAACAAGACGTAA 59.532 36.000 0.00 0.00 33.05 3.18
151 152 4.993584 TGGGCGTAATAAAAACAAGACGTA 59.006 37.500 0.00 0.00 33.05 3.57
152 153 3.814283 TGGGCGTAATAAAAACAAGACGT 59.186 39.130 0.00 0.00 33.05 4.34
153 154 4.407496 TGGGCGTAATAAAAACAAGACG 57.593 40.909 0.00 0.00 0.00 4.18
154 155 8.745464 TTTTATGGGCGTAATAAAAACAAGAC 57.255 30.769 8.18 0.00 36.83 3.01
155 156 8.794553 TCTTTTATGGGCGTAATAAAAACAAGA 58.205 29.630 10.57 4.59 38.40 3.02
156 157 8.973835 TCTTTTATGGGCGTAATAAAAACAAG 57.026 30.769 10.57 2.99 38.40 3.16
157 158 9.760077 TTTCTTTTATGGGCGTAATAAAAACAA 57.240 25.926 10.57 6.09 38.40 2.83
158 159 9.760077 TTTTCTTTTATGGGCGTAATAAAAACA 57.240 25.926 10.57 0.00 38.40 2.83
1224 1779 5.088739 GCTGAAGAAACGTATTCAATGGTG 58.911 41.667 10.74 2.67 34.66 4.17
1236 1791 2.031682 CCCAACTCAAGCTGAAGAAACG 60.032 50.000 2.77 0.00 0.00 3.60
1846 2401 3.780294 TCTGGCCTATTGCTCTTTCCTTA 59.220 43.478 3.32 0.00 40.92 2.69


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

AutoCloner maintained by Alex Coulton.