Multiple sequence alignment - TraesCS1B01G004300

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 TraesCS1B01G004300 chr1B 100.000 3405 0 0 417 3821 2558218 2554814 0.000000e+00 6288.0
1 TraesCS1B01G004300 chr1B 99.853 3407 3 2 417 3821 2614953 2611547 0.000000e+00 6263.0
2 TraesCS1B01G004300 chr1B 82.691 1375 144 49 1403 2734 169643574 169642251 0.000000e+00 1134.0
3 TraesCS1B01G004300 chr1B 100.000 316 0 0 1 316 2558634 2558319 5.500000e-163 584.0
4 TraesCS1B01G004300 chr1B 99.684 316 1 0 1 316 2619377 2619062 2.560000e-161 579.0
5 TraesCS1B01G004300 chrUn 100.000 2467 0 0 417 2883 297917714 297915248 0.000000e+00 4556.0
6 TraesCS1B01G004300 chrUn 100.000 316 0 0 1 316 323411667 323411352 5.500000e-163 584.0
7 TraesCS1B01G004300 chrUn 100.000 316 0 0 1 316 335762125 335762440 5.500000e-163 584.0
8 TraesCS1B01G004300 chr1A 84.321 1046 117 30 1403 2436 117193573 117192563 0.000000e+00 979.0
9 TraesCS1B01G004300 chr1A 88.646 229 19 5 2505 2733 117192463 117192242 4.860000e-69 272.0
10 TraesCS1B01G004300 chr1D 84.606 838 85 25 1926 2733 111010387 111009564 0.000000e+00 793.0
11 TraesCS1B01G004300 chr1D 88.608 316 33 2 1404 1716 111015672 111015357 7.750000e-102 381.0
12 TraesCS1B01G004300 chr7A 82.686 283 34 7 1847 2129 134016112 134015845 1.770000e-58 237.0
13 TraesCS1B01G004300 chr6B 84.231 260 23 5 1846 2105 444302469 444302228 1.770000e-58 237.0
14 TraesCS1B01G004300 chr4B 91.912 136 11 0 2505 2640 121936357 121936222 1.400000e-44 191.0
15 TraesCS1B01G004300 chr7D 93.671 79 5 0 184 262 563202405 563202327 6.710000e-23 119.0
16 TraesCS1B01G004300 chr4D 92.405 79 6 0 184 262 407186727 407186649 3.120000e-21 113.0
17 TraesCS1B01G004300 chr4A 76.106 226 48 6 3583 3806 38015985 38016206 3.120000e-21 113.0
18 TraesCS1B01G004300 chr4A 91.139 79 7 0 184 262 658382810 658382732 1.450000e-19 108.0
19 TraesCS1B01G004300 chr2B 91.250 80 6 1 185 263 772534642 772534563 1.450000e-19 108.0
20 TraesCS1B01G004300 chr3B 73.852 283 65 5 2127 2409 73849873 73850146 1.880000e-18 104.0
21 TraesCS1B01G004300 chr7B 89.873 79 8 0 184 262 510656667 510656589 6.750000e-18 102.0
22 TraesCS1B01G004300 chr7B 100.000 28 0 0 3483 3510 592355765 592355792 7.000000e-03 52.8
23 TraesCS1B01G004300 chr5B 89.157 83 8 1 181 263 57926375 57926456 6.750000e-18 102.0
24 TraesCS1B01G004300 chr3A 73.427 286 70 3 2124 2409 59434846 59435125 6.750000e-18 102.0
25 TraesCS1B01G004300 chr3A 92.500 40 3 0 2899 2938 329625810 329625771 1.480000e-04 58.4
26 TraesCS1B01G004300 chr2D 90.541 74 3 3 1403 1472 453570214 453570141 1.130000e-15 95.3


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 TraesCS1B01G004300 chr1B 2554814 2558634 3820 True 3436.0 6288 100.0000 1 3821 2 chr1B.!!$R4 3820
1 TraesCS1B01G004300 chr1B 2611547 2614953 3406 True 6263.0 6263 99.8530 417 3821 1 chr1B.!!$R1 3404
2 TraesCS1B01G004300 chr1B 169642251 169643574 1323 True 1134.0 1134 82.6910 1403 2734 1 chr1B.!!$R3 1331
3 TraesCS1B01G004300 chrUn 297915248 297917714 2466 True 4556.0 4556 100.0000 417 2883 1 chrUn.!!$R1 2466
4 TraesCS1B01G004300 chr1A 117192242 117193573 1331 True 625.5 979 86.4835 1403 2733 2 chr1A.!!$R1 1330
5 TraesCS1B01G004300 chr1D 111009564 111010387 823 True 793.0 793 84.6060 1926 2733 1 chr1D.!!$R1 807

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
69 70 0.103026 TCGCCGATGAGGAGTTCATG 59.897 55.0 0.0 0.0 46.51 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2921 2976 0.739462 CTTCATTGTCGCCGGTAGCA 60.739 55.0 1.9 0.0 44.04 3.49 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
19 20 2.073232 AGCATTGCTCTGGAGGTGT 58.927 52.632 5.03 0.00 30.62 4.16
20 21 0.322277 AGCATTGCTCTGGAGGTGTG 60.322 55.000 5.03 0.00 30.62 3.82
21 22 1.930908 GCATTGCTCTGGAGGTGTGC 61.931 60.000 0.16 0.00 0.00 4.57
22 23 1.001641 ATTGCTCTGGAGGTGTGCC 60.002 57.895 0.00 0.00 0.00 5.01
31 32 3.330720 AGGTGTGCCTAGCCCCAC 61.331 66.667 0.00 0.00 44.90 4.61
32 33 3.646715 GGTGTGCCTAGCCCCACA 61.647 66.667 5.37 5.37 39.45 4.17
33 34 2.045926 GTGTGCCTAGCCCCACAG 60.046 66.667 8.71 0.00 42.09 3.66
34 35 3.329889 TGTGCCTAGCCCCACAGG 61.330 66.667 5.37 0.00 37.07 4.00
44 45 4.880537 CCCACAGGCGCTCGCTAG 62.881 72.222 7.64 9.19 41.60 3.42
45 46 4.880537 CCACAGGCGCTCGCTAGG 62.881 72.222 7.64 7.21 41.60 3.02
48 49 4.521062 CAGGCGCTCGCTAGGCTT 62.521 66.667 7.64 0.00 41.52 4.35
49 50 4.521062 AGGCGCTCGCTAGGCTTG 62.521 66.667 7.64 0.00 40.53 4.01
50 51 4.821589 GGCGCTCGCTAGGCTTGT 62.822 66.667 7.64 0.00 41.60 3.16
51 52 3.258290 GCGCTCGCTAGGCTTGTC 61.258 66.667 0.00 0.00 38.26 3.18
52 53 2.951745 CGCTCGCTAGGCTTGTCG 60.952 66.667 0.00 0.00 0.00 4.35
53 54 3.258290 GCTCGCTAGGCTTGTCGC 61.258 66.667 0.00 0.00 38.13 5.19
62 63 2.184322 GCTTGTCGCCGATGAGGA 59.816 61.111 0.00 0.00 45.00 3.71
63 64 1.880340 GCTTGTCGCCGATGAGGAG 60.880 63.158 0.00 0.00 45.00 3.69
64 65 1.513158 CTTGTCGCCGATGAGGAGT 59.487 57.895 0.00 0.00 45.00 3.85
65 66 0.108615 CTTGTCGCCGATGAGGAGTT 60.109 55.000 0.00 0.00 45.00 3.01
66 67 0.108804 TTGTCGCCGATGAGGAGTTC 60.109 55.000 0.00 0.00 45.00 3.01
67 68 1.248101 TGTCGCCGATGAGGAGTTCA 61.248 55.000 0.00 0.00 45.00 3.18
69 70 0.103026 TCGCCGATGAGGAGTTCATG 59.897 55.000 0.00 0.00 46.51 3.07
70 71 0.877649 CGCCGATGAGGAGTTCATGG 60.878 60.000 0.00 0.00 46.51 3.66
73 74 1.945387 CGATGAGGAGTTCATGGGTG 58.055 55.000 0.00 0.00 46.51 4.61
74 75 1.673168 GATGAGGAGTTCATGGGTGC 58.327 55.000 0.00 0.00 46.51 5.01
75 76 0.994247 ATGAGGAGTTCATGGGTGCA 59.006 50.000 0.00 0.00 44.84 4.57
76 77 0.325933 TGAGGAGTTCATGGGTGCAG 59.674 55.000 0.00 0.00 0.00 4.41
77 78 1.001641 AGGAGTTCATGGGTGCAGC 60.002 57.895 7.55 7.55 0.00 5.25
78 79 2.048603 GGAGTTCATGGGTGCAGCC 61.049 63.158 28.15 28.15 0.00 4.85
79 80 1.303561 GAGTTCATGGGTGCAGCCA 60.304 57.895 37.62 37.62 39.65 4.75
80 81 1.589716 GAGTTCATGGGTGCAGCCAC 61.590 60.000 38.27 25.23 41.32 5.01
88 89 3.271014 GTGCAGCCACCACTGATG 58.729 61.111 0.00 0.00 40.25 3.07
89 90 2.674033 TGCAGCCACCACTGATGC 60.674 61.111 0.00 0.00 40.25 3.91
90 91 2.674033 GCAGCCACCACTGATGCA 60.674 61.111 0.00 0.00 40.25 3.96
91 92 2.050350 GCAGCCACCACTGATGCAT 61.050 57.895 0.00 0.00 40.25 3.96
92 93 0.749091 GCAGCCACCACTGATGCATA 60.749 55.000 0.00 0.00 40.25 3.14
93 94 1.753930 CAGCCACCACTGATGCATAA 58.246 50.000 0.00 0.00 40.25 1.90
94 95 2.304092 CAGCCACCACTGATGCATAAT 58.696 47.619 0.00 0.00 40.25 1.28
95 96 3.479489 CAGCCACCACTGATGCATAATA 58.521 45.455 0.00 0.00 40.25 0.98
96 97 4.077108 CAGCCACCACTGATGCATAATAT 58.923 43.478 0.00 0.00 40.25 1.28
97 98 4.521639 CAGCCACCACTGATGCATAATATT 59.478 41.667 0.00 0.00 40.25 1.28
98 99 4.521639 AGCCACCACTGATGCATAATATTG 59.478 41.667 0.00 0.00 0.00 1.90
99 100 4.279169 GCCACCACTGATGCATAATATTGT 59.721 41.667 0.00 0.00 0.00 2.71
100 101 5.765176 CCACCACTGATGCATAATATTGTG 58.235 41.667 0.00 7.77 0.00 3.33
101 102 5.300034 CCACCACTGATGCATAATATTGTGT 59.700 40.000 13.03 0.00 0.00 3.72
102 103 6.432936 CACCACTGATGCATAATATTGTGTC 58.567 40.000 13.03 5.25 0.00 3.67
103 104 6.261603 CACCACTGATGCATAATATTGTGTCT 59.738 38.462 13.03 1.99 0.00 3.41
104 105 6.484643 ACCACTGATGCATAATATTGTGTCTC 59.515 38.462 13.03 10.33 0.00 3.36
105 106 6.709397 CCACTGATGCATAATATTGTGTCTCT 59.291 38.462 13.03 0.00 0.00 3.10
106 107 7.228108 CCACTGATGCATAATATTGTGTCTCTT 59.772 37.037 13.03 0.00 0.00 2.85
107 108 8.068380 CACTGATGCATAATATTGTGTCTCTTG 58.932 37.037 13.03 9.51 0.00 3.02
108 109 7.989170 ACTGATGCATAATATTGTGTCTCTTGA 59.011 33.333 13.03 0.00 0.00 3.02
109 110 8.735692 TGATGCATAATATTGTGTCTCTTGAA 57.264 30.769 13.03 0.00 0.00 2.69
110 111 9.346005 TGATGCATAATATTGTGTCTCTTGAAT 57.654 29.630 13.03 0.00 0.00 2.57
111 112 9.823098 GATGCATAATATTGTGTCTCTTGAATC 57.177 33.333 13.03 2.18 0.00 2.52
112 113 8.735692 TGCATAATATTGTGTCTCTTGAATCA 57.264 30.769 13.03 0.00 0.00 2.57
113 114 9.176460 TGCATAATATTGTGTCTCTTGAATCAA 57.824 29.630 13.03 0.00 0.00 2.57
119 120 9.865321 ATATTGTGTCTCTTGAATCAAAATTGG 57.135 29.630 0.00 0.00 0.00 3.16
120 121 6.088016 TGTGTCTCTTGAATCAAAATTGGG 57.912 37.500 0.00 0.00 0.00 4.12
121 122 5.598005 TGTGTCTCTTGAATCAAAATTGGGT 59.402 36.000 0.00 0.00 0.00 4.51
122 123 6.775142 TGTGTCTCTTGAATCAAAATTGGGTA 59.225 34.615 0.00 0.00 0.00 3.69
123 124 7.451255 TGTGTCTCTTGAATCAAAATTGGGTAT 59.549 33.333 0.00 0.00 0.00 2.73
124 125 8.956426 GTGTCTCTTGAATCAAAATTGGGTATA 58.044 33.333 0.00 0.00 0.00 1.47
125 126 9.699410 TGTCTCTTGAATCAAAATTGGGTATAT 57.301 29.630 0.00 0.00 0.00 0.86
135 136 8.084985 TCAAAATTGGGTATATTTTCTTCCCC 57.915 34.615 0.00 0.00 37.52 4.81
136 137 7.904022 TCAAAATTGGGTATATTTTCTTCCCCT 59.096 33.333 0.00 0.00 37.52 4.79
137 138 7.914427 AAATTGGGTATATTTTCTTCCCCTC 57.086 36.000 0.00 0.00 37.52 4.30
138 139 5.397553 TTGGGTATATTTTCTTCCCCTCC 57.602 43.478 0.00 0.00 37.52 4.30
139 140 3.393278 TGGGTATATTTTCTTCCCCTCCG 59.607 47.826 0.00 0.00 37.52 4.63
140 141 3.393609 GGGTATATTTTCTTCCCCTCCGT 59.606 47.826 0.00 0.00 32.66 4.69
141 142 4.504514 GGGTATATTTTCTTCCCCTCCGTC 60.505 50.000 0.00 0.00 32.66 4.79
142 143 3.859061 ATATTTTCTTCCCCTCCGTCC 57.141 47.619 0.00 0.00 0.00 4.79
143 144 0.624254 ATTTTCTTCCCCTCCGTCCC 59.376 55.000 0.00 0.00 0.00 4.46
144 145 0.768997 TTTTCTTCCCCTCCGTCCCA 60.769 55.000 0.00 0.00 0.00 4.37
145 146 0.549169 TTTCTTCCCCTCCGTCCCAT 60.549 55.000 0.00 0.00 0.00 4.00
146 147 0.340558 TTCTTCCCCTCCGTCCCATA 59.659 55.000 0.00 0.00 0.00 2.74
147 148 0.340558 TCTTCCCCTCCGTCCCATAA 59.659 55.000 0.00 0.00 0.00 1.90
148 149 1.061657 TCTTCCCCTCCGTCCCATAAT 60.062 52.381 0.00 0.00 0.00 1.28
149 150 2.180529 TCTTCCCCTCCGTCCCATAATA 59.819 50.000 0.00 0.00 0.00 0.98
150 151 3.181399 TCTTCCCCTCCGTCCCATAATAT 60.181 47.826 0.00 0.00 0.00 1.28
151 152 3.285290 TCCCCTCCGTCCCATAATATT 57.715 47.619 0.00 0.00 0.00 1.28
152 153 4.423167 TCCCCTCCGTCCCATAATATTA 57.577 45.455 0.00 0.00 0.00 0.98
153 154 4.967871 TCCCCTCCGTCCCATAATATTAT 58.032 43.478 1.91 1.91 0.00 1.28
154 155 4.719773 TCCCCTCCGTCCCATAATATTATG 59.280 45.833 23.28 23.28 40.10 1.90
155 156 4.451900 CCCTCCGTCCCATAATATTATGC 58.548 47.826 24.38 13.33 39.30 3.14
156 157 4.119862 CCTCCGTCCCATAATATTATGCG 58.880 47.826 24.38 21.42 39.30 4.73
157 158 4.142026 CCTCCGTCCCATAATATTATGCGA 60.142 45.833 24.38 20.01 39.30 5.10
158 159 4.751060 TCCGTCCCATAATATTATGCGAC 58.249 43.478 28.30 28.30 41.84 5.19
159 160 3.869246 CCGTCCCATAATATTATGCGACC 59.131 47.826 30.09 19.89 42.06 4.79
160 161 3.550275 CGTCCCATAATATTATGCGACCG 59.450 47.826 30.09 24.32 42.06 4.79
161 162 4.675933 CGTCCCATAATATTATGCGACCGA 60.676 45.833 30.09 17.78 42.06 4.69
162 163 4.804139 GTCCCATAATATTATGCGACCGAG 59.196 45.833 28.07 15.55 40.50 4.63
163 164 4.119862 CCCATAATATTATGCGACCGAGG 58.880 47.826 24.38 16.25 39.30 4.63
164 165 4.119862 CCATAATATTATGCGACCGAGGG 58.880 47.826 24.38 8.57 39.30 4.30
165 166 4.142026 CCATAATATTATGCGACCGAGGGA 60.142 45.833 24.38 0.00 39.30 4.20
166 167 3.594603 AATATTATGCGACCGAGGGAG 57.405 47.619 0.00 0.00 0.00 4.30
167 168 1.991121 TATTATGCGACCGAGGGAGT 58.009 50.000 0.00 0.00 0.00 3.85
168 169 0.389391 ATTATGCGACCGAGGGAGTG 59.611 55.000 0.00 0.00 0.00 3.51
169 170 0.681887 TTATGCGACCGAGGGAGTGA 60.682 55.000 0.00 0.00 0.00 3.41
170 171 1.381928 TATGCGACCGAGGGAGTGAC 61.382 60.000 0.00 0.00 0.00 3.67
171 172 3.063084 GCGACCGAGGGAGTGACT 61.063 66.667 0.00 0.00 0.00 3.41
172 173 1.748122 GCGACCGAGGGAGTGACTA 60.748 63.158 0.00 0.00 0.00 2.59
173 174 1.310933 GCGACCGAGGGAGTGACTAA 61.311 60.000 0.00 0.00 0.00 2.24
174 175 1.390565 CGACCGAGGGAGTGACTAAT 58.609 55.000 0.00 0.00 0.00 1.73
175 176 2.569059 CGACCGAGGGAGTGACTAATA 58.431 52.381 0.00 0.00 0.00 0.98
176 177 2.947652 CGACCGAGGGAGTGACTAATAA 59.052 50.000 0.00 0.00 0.00 1.40
177 178 3.568853 CGACCGAGGGAGTGACTAATAAT 59.431 47.826 0.00 0.00 0.00 1.28
178 179 4.556898 CGACCGAGGGAGTGACTAATAATG 60.557 50.000 0.00 0.00 0.00 1.90
179 180 4.543689 ACCGAGGGAGTGACTAATAATGA 58.456 43.478 0.00 0.00 0.00 2.57
180 181 4.585162 ACCGAGGGAGTGACTAATAATGAG 59.415 45.833 0.00 0.00 0.00 2.90
181 182 4.827835 CCGAGGGAGTGACTAATAATGAGA 59.172 45.833 0.00 0.00 0.00 3.27
182 183 5.478679 CCGAGGGAGTGACTAATAATGAGAT 59.521 44.000 0.00 0.00 0.00 2.75
183 184 6.659668 CCGAGGGAGTGACTAATAATGAGATA 59.340 42.308 0.00 0.00 0.00 1.98
184 185 7.340743 CCGAGGGAGTGACTAATAATGAGATAT 59.659 40.741 0.00 0.00 0.00 1.63
185 186 8.744652 CGAGGGAGTGACTAATAATGAGATATT 58.255 37.037 0.00 0.00 0.00 1.28
212 213 9.890629 TTATGATCCATTATAATACACCAGAGC 57.109 33.333 0.00 0.00 0.00 4.09
213 214 7.315066 TGATCCATTATAATACACCAGAGCA 57.685 36.000 0.00 0.00 0.00 4.26
214 215 7.921304 TGATCCATTATAATACACCAGAGCAT 58.079 34.615 0.00 0.00 0.00 3.79
215 216 7.825761 TGATCCATTATAATACACCAGAGCATG 59.174 37.037 0.00 0.00 0.00 4.06
216 217 7.078249 TCCATTATAATACACCAGAGCATGT 57.922 36.000 0.00 0.00 0.00 3.21
217 218 6.936335 TCCATTATAATACACCAGAGCATGTG 59.064 38.462 0.00 0.00 38.44 3.21
218 219 6.712095 CCATTATAATACACCAGAGCATGTGT 59.288 38.462 0.00 0.00 46.72 3.72
227 228 6.233434 ACACCAGAGCATGTGTATTATATGG 58.767 40.000 0.00 0.00 43.54 2.74
228 229 5.645067 CACCAGAGCATGTGTATTATATGGG 59.355 44.000 0.00 0.00 0.00 4.00
229 230 5.310594 ACCAGAGCATGTGTATTATATGGGT 59.689 40.000 0.00 0.00 0.00 4.51
230 231 5.645067 CCAGAGCATGTGTATTATATGGGTG 59.355 44.000 0.00 0.00 0.00 4.61
231 232 6.466812 CAGAGCATGTGTATTATATGGGTGA 58.533 40.000 0.00 0.00 0.00 4.02
232 233 7.108194 CAGAGCATGTGTATTATATGGGTGAT 58.892 38.462 0.00 0.00 0.00 3.06
233 234 7.279536 CAGAGCATGTGTATTATATGGGTGATC 59.720 40.741 0.00 0.00 0.00 2.92
234 235 7.181665 AGAGCATGTGTATTATATGGGTGATCT 59.818 37.037 0.00 0.00 0.00 2.75
235 236 8.379428 AGCATGTGTATTATATGGGTGATCTA 57.621 34.615 0.00 0.00 0.00 1.98
236 237 8.825774 AGCATGTGTATTATATGGGTGATCTAA 58.174 33.333 0.00 0.00 0.00 2.10
237 238 8.883731 GCATGTGTATTATATGGGTGATCTAAC 58.116 37.037 0.00 0.00 0.00 2.34
238 239 9.087424 CATGTGTATTATATGGGTGATCTAACG 57.913 37.037 0.00 0.00 0.00 3.18
239 240 7.608153 TGTGTATTATATGGGTGATCTAACGG 58.392 38.462 0.00 0.00 0.00 4.44
240 241 7.452189 TGTGTATTATATGGGTGATCTAACGGA 59.548 37.037 0.00 0.00 0.00 4.69
241 242 8.475639 GTGTATTATATGGGTGATCTAACGGAT 58.524 37.037 0.00 0.00 37.37 4.18
242 243 8.474831 TGTATTATATGGGTGATCTAACGGATG 58.525 37.037 0.00 0.00 34.33 3.51
243 244 7.733773 ATTATATGGGTGATCTAACGGATGA 57.266 36.000 0.00 0.00 34.33 2.92
244 245 5.667539 ATATGGGTGATCTAACGGATGAG 57.332 43.478 0.00 0.00 34.33 2.90
245 246 3.026707 TGGGTGATCTAACGGATGAGA 57.973 47.619 0.00 0.00 34.33 3.27
246 247 2.693591 TGGGTGATCTAACGGATGAGAC 59.306 50.000 0.00 0.00 34.33 3.36
247 248 2.959707 GGGTGATCTAACGGATGAGACT 59.040 50.000 0.00 0.00 34.33 3.24
248 249 4.142790 GGGTGATCTAACGGATGAGACTA 58.857 47.826 0.00 0.00 34.33 2.59
249 250 4.583489 GGGTGATCTAACGGATGAGACTAA 59.417 45.833 0.00 0.00 34.33 2.24
250 251 5.507650 GGGTGATCTAACGGATGAGACTAAC 60.508 48.000 0.00 0.00 34.33 2.34
251 252 5.299782 GGTGATCTAACGGATGAGACTAACT 59.700 44.000 0.00 0.00 34.33 2.24
252 253 6.202937 GTGATCTAACGGATGAGACTAACTG 58.797 44.000 0.00 0.00 34.33 3.16
253 254 5.299531 TGATCTAACGGATGAGACTAACTGG 59.700 44.000 0.00 0.00 34.33 4.00
254 255 3.952323 TCTAACGGATGAGACTAACTGGG 59.048 47.826 0.00 0.00 0.00 4.45
255 256 0.824759 ACGGATGAGACTAACTGGGC 59.175 55.000 0.00 0.00 0.00 5.36
256 257 1.115467 CGGATGAGACTAACTGGGCT 58.885 55.000 0.00 0.00 0.00 5.19
257 258 1.482593 CGGATGAGACTAACTGGGCTT 59.517 52.381 0.00 0.00 0.00 4.35
258 259 2.093447 CGGATGAGACTAACTGGGCTTT 60.093 50.000 0.00 0.00 0.00 3.51
259 260 3.619979 CGGATGAGACTAACTGGGCTTTT 60.620 47.826 0.00 0.00 0.00 2.27
260 261 4.336280 GGATGAGACTAACTGGGCTTTTT 58.664 43.478 0.00 0.00 0.00 1.94
315 316 8.753497 ATTTGTAAGGGGAATCTAATCAGTTC 57.247 34.615 0.00 0.00 0.00 3.01
2883 2938 0.101759 CGTCGCTCCTTCCCGAAATA 59.898 55.000 0.00 0.00 35.00 1.40
3415 3470 3.307480 GCTATCCAACACGGGCCTATATT 60.307 47.826 0.84 0.00 34.36 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.322277 CACACCTCCAGAGCAATGCT 60.322 55.000 7.79 7.79 43.88 3.79
2 3 1.930908 GCACACCTCCAGAGCAATGC 61.931 60.000 0.00 0.00 0.00 3.56
3 4 1.310933 GGCACACCTCCAGAGCAATG 61.311 60.000 0.00 0.00 0.00 2.82
4 5 1.001641 GGCACACCTCCAGAGCAAT 60.002 57.895 0.00 0.00 0.00 3.56
5 6 0.835971 TAGGCACACCTCCAGAGCAA 60.836 55.000 0.00 0.00 46.34 3.91
6 7 1.229177 TAGGCACACCTCCAGAGCA 60.229 57.895 0.00 0.00 46.34 4.26
7 8 1.519719 CTAGGCACACCTCCAGAGC 59.480 63.158 0.00 0.00 46.34 4.09
8 9 1.519719 GCTAGGCACACCTCCAGAG 59.480 63.158 0.00 0.00 46.34 3.35
9 10 1.990060 GGCTAGGCACACCTCCAGA 60.990 63.158 12.16 0.00 46.34 3.86
10 11 2.586792 GGCTAGGCACACCTCCAG 59.413 66.667 12.16 0.00 46.34 3.86
11 12 3.009115 GGGCTAGGCACACCTCCA 61.009 66.667 19.14 0.00 46.34 3.86
12 13 3.798511 GGGGCTAGGCACACCTCC 61.799 72.222 19.14 4.91 46.34 4.30
13 14 3.009115 TGGGGCTAGGCACACCTC 61.009 66.667 18.79 0.00 46.34 3.85
15 16 3.628646 CTGTGGGGCTAGGCACACC 62.629 68.421 39.43 25.59 37.23 4.16
16 17 2.045926 CTGTGGGGCTAGGCACAC 60.046 66.667 37.46 37.46 38.05 3.82
17 18 3.329889 CCTGTGGGGCTAGGCACA 61.330 66.667 18.79 18.79 30.93 4.57
27 28 4.880537 CTAGCGAGCGCCTGTGGG 62.881 72.222 11.66 0.00 43.17 4.61
28 29 4.880537 CCTAGCGAGCGCCTGTGG 62.881 72.222 11.66 5.10 43.17 4.17
31 32 4.521062 AAGCCTAGCGAGCGCCTG 62.521 66.667 11.66 0.00 43.17 4.85
32 33 4.521062 CAAGCCTAGCGAGCGCCT 62.521 66.667 11.66 0.00 43.17 5.52
33 34 4.821589 ACAAGCCTAGCGAGCGCC 62.822 66.667 11.66 0.00 43.17 6.53
34 35 3.258290 GACAAGCCTAGCGAGCGC 61.258 66.667 6.78 6.78 42.33 5.92
35 36 2.951745 CGACAAGCCTAGCGAGCG 60.952 66.667 0.00 0.00 34.64 5.03
36 37 3.258290 GCGACAAGCCTAGCGAGC 61.258 66.667 0.00 0.00 40.81 5.03
46 47 0.108615 AACTCCTCATCGGCGACAAG 60.109 55.000 13.76 12.72 0.00 3.16
47 48 0.108804 GAACTCCTCATCGGCGACAA 60.109 55.000 13.76 1.58 0.00 3.18
48 49 1.248101 TGAACTCCTCATCGGCGACA 61.248 55.000 13.76 0.00 0.00 4.35
49 50 0.103208 ATGAACTCCTCATCGGCGAC 59.897 55.000 13.76 0.00 41.13 5.19
50 51 0.103026 CATGAACTCCTCATCGGCGA 59.897 55.000 13.87 13.87 43.28 5.54
51 52 0.877649 CCATGAACTCCTCATCGGCG 60.878 60.000 0.00 0.00 43.28 6.46
52 53 0.533755 CCCATGAACTCCTCATCGGC 60.534 60.000 0.00 0.00 43.28 5.54
53 54 0.833287 ACCCATGAACTCCTCATCGG 59.167 55.000 0.00 0.00 45.68 4.18
54 55 1.945387 CACCCATGAACTCCTCATCG 58.055 55.000 0.00 0.00 43.28 3.84
55 56 1.065199 TGCACCCATGAACTCCTCATC 60.065 52.381 0.00 0.00 43.28 2.92
56 57 0.994247 TGCACCCATGAACTCCTCAT 59.006 50.000 0.00 0.00 46.25 2.90
57 58 0.325933 CTGCACCCATGAACTCCTCA 59.674 55.000 0.00 0.00 38.81 3.86
58 59 1.028868 GCTGCACCCATGAACTCCTC 61.029 60.000 0.00 0.00 0.00 3.71
59 60 1.001641 GCTGCACCCATGAACTCCT 60.002 57.895 0.00 0.00 0.00 3.69
60 61 2.048603 GGCTGCACCCATGAACTCC 61.049 63.158 0.50 0.00 0.00 3.85
61 62 1.303561 TGGCTGCACCCATGAACTC 60.304 57.895 0.50 0.00 37.83 3.01
62 63 1.604593 GTGGCTGCACCCATGAACT 60.605 57.895 3.54 0.00 37.20 3.01
63 64 2.639327 GGTGGCTGCACCCATGAAC 61.639 63.158 3.54 0.00 39.27 3.18
64 65 2.283101 GGTGGCTGCACCCATGAA 60.283 61.111 3.54 0.00 39.27 2.57
65 66 3.578286 TGGTGGCTGCACCCATGA 61.578 61.111 3.54 0.00 44.38 3.07
66 67 3.376078 GTGGTGGCTGCACCCATG 61.376 66.667 3.54 0.00 44.38 3.66
67 68 3.583380 AGTGGTGGCTGCACCCAT 61.583 61.111 3.54 2.30 44.38 4.00
68 69 4.584518 CAGTGGTGGCTGCACCCA 62.585 66.667 15.42 11.05 44.38 4.51
69 70 3.574074 ATCAGTGGTGGCTGCACCC 62.574 63.158 15.42 8.83 44.38 4.61
70 71 2.034687 ATCAGTGGTGGCTGCACC 59.965 61.111 12.44 12.44 45.20 5.01
71 72 2.986306 GCATCAGTGGTGGCTGCAC 61.986 63.158 5.34 0.00 36.49 4.57
72 73 2.674033 GCATCAGTGGTGGCTGCA 60.674 61.111 5.34 0.00 36.49 4.41
73 74 0.749091 TATGCATCAGTGGTGGCTGC 60.749 55.000 0.19 0.00 36.49 5.25
74 75 1.753930 TTATGCATCAGTGGTGGCTG 58.246 50.000 0.19 0.00 37.81 4.85
75 76 2.742428 ATTATGCATCAGTGGTGGCT 57.258 45.000 0.19 0.00 0.00 4.75
76 77 4.279169 ACAATATTATGCATCAGTGGTGGC 59.721 41.667 0.19 0.03 0.00 5.01
77 78 5.300034 ACACAATATTATGCATCAGTGGTGG 59.700 40.000 0.19 0.00 0.00 4.61
78 79 6.261603 AGACACAATATTATGCATCAGTGGTG 59.738 38.462 0.19 8.97 0.00 4.17
79 80 6.359804 AGACACAATATTATGCATCAGTGGT 58.640 36.000 0.19 0.44 0.00 4.16
80 81 6.709397 AGAGACACAATATTATGCATCAGTGG 59.291 38.462 0.19 0.00 0.00 4.00
81 82 7.725818 AGAGACACAATATTATGCATCAGTG 57.274 36.000 0.19 6.98 0.00 3.66
82 83 7.989170 TCAAGAGACACAATATTATGCATCAGT 59.011 33.333 0.19 0.00 0.00 3.41
83 84 8.374327 TCAAGAGACACAATATTATGCATCAG 57.626 34.615 0.19 0.00 0.00 2.90
84 85 8.735692 TTCAAGAGACACAATATTATGCATCA 57.264 30.769 0.19 0.00 0.00 3.07
85 86 9.823098 GATTCAAGAGACACAATATTATGCATC 57.177 33.333 0.19 0.00 0.00 3.91
86 87 9.346005 TGATTCAAGAGACACAATATTATGCAT 57.654 29.630 3.79 3.79 0.00 3.96
87 88 8.735692 TGATTCAAGAGACACAATATTATGCA 57.264 30.769 0.00 0.00 0.00 3.96
93 94 9.865321 CCAATTTTGATTCAAGAGACACAATAT 57.135 29.630 0.00 0.00 0.00 1.28
94 95 8.306038 CCCAATTTTGATTCAAGAGACACAATA 58.694 33.333 0.00 0.00 0.00 1.90
95 96 7.156673 CCCAATTTTGATTCAAGAGACACAAT 58.843 34.615 0.00 0.00 0.00 2.71
96 97 6.098124 ACCCAATTTTGATTCAAGAGACACAA 59.902 34.615 0.00 0.00 0.00 3.33
97 98 5.598005 ACCCAATTTTGATTCAAGAGACACA 59.402 36.000 0.00 0.00 0.00 3.72
98 99 6.089249 ACCCAATTTTGATTCAAGAGACAC 57.911 37.500 0.00 0.00 0.00 3.67
99 100 9.699410 ATATACCCAATTTTGATTCAAGAGACA 57.301 29.630 0.00 0.00 0.00 3.41
109 110 8.713971 GGGGAAGAAAATATACCCAATTTTGAT 58.286 33.333 0.00 0.00 42.03 2.57
110 111 7.904022 AGGGGAAGAAAATATACCCAATTTTGA 59.096 33.333 0.00 0.00 42.03 2.69
111 112 8.089625 AGGGGAAGAAAATATACCCAATTTTG 57.910 34.615 0.00 0.00 42.03 2.44
112 113 7.347222 GGAGGGGAAGAAAATATACCCAATTTT 59.653 37.037 0.00 0.00 42.03 1.82
113 114 6.844388 GGAGGGGAAGAAAATATACCCAATTT 59.156 38.462 0.00 0.00 42.03 1.82
114 115 6.382087 GGAGGGGAAGAAAATATACCCAATT 58.618 40.000 0.00 0.00 42.03 2.32
115 116 5.457633 CGGAGGGGAAGAAAATATACCCAAT 60.458 44.000 0.00 0.00 42.03 3.16
116 117 4.141344 CGGAGGGGAAGAAAATATACCCAA 60.141 45.833 0.00 0.00 42.03 4.12
117 118 3.393278 CGGAGGGGAAGAAAATATACCCA 59.607 47.826 0.00 0.00 42.03 4.51
118 119 3.393609 ACGGAGGGGAAGAAAATATACCC 59.606 47.826 0.00 0.00 39.79 3.69
119 120 4.504514 GGACGGAGGGGAAGAAAATATACC 60.505 50.000 0.00 0.00 0.00 2.73
120 121 4.504514 GGGACGGAGGGGAAGAAAATATAC 60.505 50.000 0.00 0.00 0.00 1.47
121 122 3.649502 GGGACGGAGGGGAAGAAAATATA 59.350 47.826 0.00 0.00 0.00 0.86
122 123 2.442126 GGGACGGAGGGGAAGAAAATAT 59.558 50.000 0.00 0.00 0.00 1.28
123 124 1.841919 GGGACGGAGGGGAAGAAAATA 59.158 52.381 0.00 0.00 0.00 1.40
124 125 0.624254 GGGACGGAGGGGAAGAAAAT 59.376 55.000 0.00 0.00 0.00 1.82
125 126 0.768997 TGGGACGGAGGGGAAGAAAA 60.769 55.000 0.00 0.00 0.00 2.29
126 127 0.549169 ATGGGACGGAGGGGAAGAAA 60.549 55.000 0.00 0.00 0.00 2.52
127 128 0.340558 TATGGGACGGAGGGGAAGAA 59.659 55.000 0.00 0.00 0.00 2.52
128 129 0.340558 TTATGGGACGGAGGGGAAGA 59.659 55.000 0.00 0.00 0.00 2.87
129 130 1.435256 ATTATGGGACGGAGGGGAAG 58.565 55.000 0.00 0.00 0.00 3.46
130 131 2.799282 TATTATGGGACGGAGGGGAA 57.201 50.000 0.00 0.00 0.00 3.97
131 132 3.285290 AATATTATGGGACGGAGGGGA 57.715 47.619 0.00 0.00 0.00 4.81
132 133 4.686122 GCATAATATTATGGGACGGAGGGG 60.686 50.000 28.45 7.00 40.61 4.79
133 134 4.451900 GCATAATATTATGGGACGGAGGG 58.548 47.826 28.45 7.42 40.61 4.30
142 143 4.119862 CCCTCGGTCGCATAATATTATGG 58.880 47.826 28.45 20.60 40.61 2.74
143 144 5.006153 TCCCTCGGTCGCATAATATTATG 57.994 43.478 25.10 25.10 42.61 1.90
144 145 4.710375 ACTCCCTCGGTCGCATAATATTAT 59.290 41.667 1.91 1.91 0.00 1.28
145 146 4.082408 CACTCCCTCGGTCGCATAATATTA 60.082 45.833 0.00 0.00 0.00 0.98
146 147 2.897969 ACTCCCTCGGTCGCATAATATT 59.102 45.455 0.00 0.00 0.00 1.28
147 148 2.231478 CACTCCCTCGGTCGCATAATAT 59.769 50.000 0.00 0.00 0.00 1.28
148 149 1.611977 CACTCCCTCGGTCGCATAATA 59.388 52.381 0.00 0.00 0.00 0.98
149 150 0.389391 CACTCCCTCGGTCGCATAAT 59.611 55.000 0.00 0.00 0.00 1.28
150 151 0.681887 TCACTCCCTCGGTCGCATAA 60.682 55.000 0.00 0.00 0.00 1.90
151 152 1.077285 TCACTCCCTCGGTCGCATA 60.077 57.895 0.00 0.00 0.00 3.14
152 153 2.362503 TCACTCCCTCGGTCGCAT 60.363 61.111 0.00 0.00 0.00 4.73
153 154 2.473891 TAGTCACTCCCTCGGTCGCA 62.474 60.000 0.00 0.00 0.00 5.10
154 155 1.310933 TTAGTCACTCCCTCGGTCGC 61.311 60.000 0.00 0.00 0.00 5.19
155 156 1.390565 ATTAGTCACTCCCTCGGTCG 58.609 55.000 0.00 0.00 0.00 4.79
156 157 4.583489 TCATTATTAGTCACTCCCTCGGTC 59.417 45.833 0.00 0.00 0.00 4.79
157 158 4.543689 TCATTATTAGTCACTCCCTCGGT 58.456 43.478 0.00 0.00 0.00 4.69
158 159 4.827835 TCTCATTATTAGTCACTCCCTCGG 59.172 45.833 0.00 0.00 0.00 4.63
159 160 6.582677 ATCTCATTATTAGTCACTCCCTCG 57.417 41.667 0.00 0.00 0.00 4.63
186 187 9.890629 GCTCTGGTGTATTATAATGGATCATAA 57.109 33.333 8.28 0.00 0.00 1.90
187 188 9.045745 TGCTCTGGTGTATTATAATGGATCATA 57.954 33.333 8.28 0.00 0.00 2.15
188 189 7.921304 TGCTCTGGTGTATTATAATGGATCAT 58.079 34.615 8.28 0.00 0.00 2.45
189 190 7.315066 TGCTCTGGTGTATTATAATGGATCA 57.685 36.000 8.28 0.52 0.00 2.92
190 191 7.826252 ACATGCTCTGGTGTATTATAATGGATC 59.174 37.037 8.28 0.00 0.00 3.36
191 192 7.609146 CACATGCTCTGGTGTATTATAATGGAT 59.391 37.037 8.28 0.00 0.00 3.41
192 193 6.936335 CACATGCTCTGGTGTATTATAATGGA 59.064 38.462 8.28 0.00 0.00 3.41
193 194 6.712095 ACACATGCTCTGGTGTATTATAATGG 59.288 38.462 8.28 0.00 45.77 3.16
194 195 7.734924 ACACATGCTCTGGTGTATTATAATG 57.265 36.000 8.28 0.00 45.77 1.90
204 205 5.645067 CCCATATAATACACATGCTCTGGTG 59.355 44.000 0.00 0.00 40.78 4.17
205 206 5.310594 ACCCATATAATACACATGCTCTGGT 59.689 40.000 0.00 0.00 0.00 4.00
206 207 5.645067 CACCCATATAATACACATGCTCTGG 59.355 44.000 0.00 0.00 0.00 3.86
207 208 6.466812 TCACCCATATAATACACATGCTCTG 58.533 40.000 0.00 0.00 0.00 3.35
208 209 6.686484 TCACCCATATAATACACATGCTCT 57.314 37.500 0.00 0.00 0.00 4.09
209 210 7.334090 AGATCACCCATATAATACACATGCTC 58.666 38.462 0.00 0.00 0.00 4.26
210 211 7.262990 AGATCACCCATATAATACACATGCT 57.737 36.000 0.00 0.00 0.00 3.79
211 212 8.883731 GTTAGATCACCCATATAATACACATGC 58.116 37.037 0.00 0.00 0.00 4.06
212 213 9.087424 CGTTAGATCACCCATATAATACACATG 57.913 37.037 0.00 0.00 0.00 3.21
213 214 8.258007 CCGTTAGATCACCCATATAATACACAT 58.742 37.037 0.00 0.00 0.00 3.21
214 215 7.452189 TCCGTTAGATCACCCATATAATACACA 59.548 37.037 0.00 0.00 0.00 3.72
215 216 7.833786 TCCGTTAGATCACCCATATAATACAC 58.166 38.462 0.00 0.00 0.00 2.90
216 217 8.474831 CATCCGTTAGATCACCCATATAATACA 58.525 37.037 0.00 0.00 30.59 2.29
217 218 8.692710 TCATCCGTTAGATCACCCATATAATAC 58.307 37.037 0.00 0.00 30.59 1.89
218 219 8.832458 TCATCCGTTAGATCACCCATATAATA 57.168 34.615 0.00 0.00 30.59 0.98
219 220 7.619698 TCTCATCCGTTAGATCACCCATATAAT 59.380 37.037 0.00 0.00 30.59 1.28
220 221 6.951778 TCTCATCCGTTAGATCACCCATATAA 59.048 38.462 0.00 0.00 30.59 0.98
221 222 6.377429 GTCTCATCCGTTAGATCACCCATATA 59.623 42.308 0.00 0.00 30.59 0.86
222 223 5.186021 GTCTCATCCGTTAGATCACCCATAT 59.814 44.000 0.00 0.00 30.59 1.78
223 224 4.523173 GTCTCATCCGTTAGATCACCCATA 59.477 45.833 0.00 0.00 30.59 2.74
224 225 3.322254 GTCTCATCCGTTAGATCACCCAT 59.678 47.826 0.00 0.00 30.59 4.00
225 226 2.693591 GTCTCATCCGTTAGATCACCCA 59.306 50.000 0.00 0.00 30.59 4.51
226 227 2.959707 AGTCTCATCCGTTAGATCACCC 59.040 50.000 0.00 0.00 30.59 4.61
227 228 5.299782 AGTTAGTCTCATCCGTTAGATCACC 59.700 44.000 0.00 0.00 30.59 4.02
228 229 6.202937 CAGTTAGTCTCATCCGTTAGATCAC 58.797 44.000 0.00 0.00 30.59 3.06
229 230 5.299531 CCAGTTAGTCTCATCCGTTAGATCA 59.700 44.000 0.00 0.00 30.59 2.92
230 231 5.278561 CCCAGTTAGTCTCATCCGTTAGATC 60.279 48.000 0.00 0.00 30.59 2.75
231 232 4.585162 CCCAGTTAGTCTCATCCGTTAGAT 59.415 45.833 0.00 0.00 34.66 1.98
232 233 3.952323 CCCAGTTAGTCTCATCCGTTAGA 59.048 47.826 0.00 0.00 0.00 2.10
233 234 3.491104 GCCCAGTTAGTCTCATCCGTTAG 60.491 52.174 0.00 0.00 0.00 2.34
234 235 2.429610 GCCCAGTTAGTCTCATCCGTTA 59.570 50.000 0.00 0.00 0.00 3.18
235 236 1.207329 GCCCAGTTAGTCTCATCCGTT 59.793 52.381 0.00 0.00 0.00 4.44
236 237 0.824759 GCCCAGTTAGTCTCATCCGT 59.175 55.000 0.00 0.00 0.00 4.69
237 238 1.115467 AGCCCAGTTAGTCTCATCCG 58.885 55.000 0.00 0.00 0.00 4.18
238 239 3.636153 AAAGCCCAGTTAGTCTCATCC 57.364 47.619 0.00 0.00 0.00 3.51
289 290 9.847224 GAACTGATTAGATTCCCCTTACAAATA 57.153 33.333 0.00 0.00 0.00 1.40
290 291 8.753497 GAACTGATTAGATTCCCCTTACAAAT 57.247 34.615 0.00 0.00 0.00 2.32
2921 2976 0.739462 CTTCATTGTCGCCGGTAGCA 60.739 55.000 1.90 0.00 44.04 3.49
3415 3470 1.080366 CGAAACGGTCGGTGGATCA 60.080 57.895 3.07 0.00 46.45 2.92


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

AutoCloner maintained by Alex Coulton.