Multiple sequence alignment - TraesCS4A01G278400

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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 TraesCS4A01G278400 chr4A 100.000 3445 0 0 1 3445 586088244 586084800 0.000000e+00 6362
1 TraesCS4A01G278400 chr4A 90.441 136 10 2 21 156 538488667 538488799 3.530000e-40 176
2 TraesCS4A01G278400 chr4A 88.235 136 11 2 29 164 456400777 456400907 1.280000e-34 158
3 TraesCS4A01G278400 chr3B 98.722 3286 40 2 161 3445 829116452 829119736 0.000000e+00 5834
4 TraesCS4A01G278400 chr3B 98.627 3278 44 1 169 3445 813958507 813955230 0.000000e+00 5803
5 TraesCS4A01G278400 chr3B 89.855 138 9 3 29 166 452698322 452698454 4.570000e-39 172
6 TraesCS4A01G278400 chr7B 98.750 3280 40 1 167 3445 204002752 204006031 0.000000e+00 5829
7 TraesCS4A01G278400 chr3A 98.567 3280 45 2 167 3445 610424332 610421054 0.000000e+00 5795
8 TraesCS4A01G278400 chr2A 98.476 3280 49 1 167 3445 713923488 713926767 0.000000e+00 5779
9 TraesCS4A01G278400 chr2A 98.366 2631 42 1 816 3445 39363907 39361277 0.000000e+00 4619
10 TraesCS4A01G278400 chr2A 98.556 554 8 0 167 720 39364444 39363891 0.000000e+00 979
11 TraesCS4A01G278400 chr2A 90.441 136 10 2 21 156 196123148 196123016 3.530000e-40 176
12 TraesCS4A01G278400 chr7D 96.921 3053 91 3 395 3445 237548457 237551508 0.000000e+00 5114
13 TraesCS4A01G278400 chr7D 96.296 189 7 0 167 355 237548280 237548468 9.280000e-81 311
14 TraesCS4A01G278400 chr5B 97.623 2524 58 2 924 3445 599616903 599614380 0.000000e+00 4327
15 TraesCS4A01G278400 chr5B 93.088 217 11 2 165 377 531864095 531864311 7.180000e-82 315
16 TraesCS4A01G278400 chr5B 89.313 131 13 1 26 156 54827251 54827122 2.750000e-36 163
17 TraesCS4A01G278400 chr5B 91.781 73 6 0 858 930 531864453 531864525 6.080000e-18 102
18 TraesCS4A01G278400 chr3D 94.800 2519 129 2 929 3445 511280668 511278150 0.000000e+00 3925
19 TraesCS4A01G278400 chr3D 93.953 215 9 2 167 377 511281794 511281580 4.290000e-84 322
20 TraesCS4A01G278400 chr4D 98.795 166 1 1 1 166 15152336 15152500 9.350000e-76 294
21 TraesCS4A01G278400 chr4D 86.986 146 14 2 21 166 14927091 14926951 3.560000e-35 159
22 TraesCS4A01G278400 chr5D 89.706 136 13 1 21 156 51843945 51843811 4.570000e-39 172
23 TraesCS4A01G278400 chr4B 89.855 138 8 3 29 166 24768077 24767946 4.570000e-39 172


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 TraesCS4A01G278400 chr4A 586084800 586088244 3444 True 6362.0 6362 100.0000 1 3445 1 chr4A.!!$R1 3444
1 TraesCS4A01G278400 chr3B 829116452 829119736 3284 False 5834.0 5834 98.7220 161 3445 1 chr3B.!!$F2 3284
2 TraesCS4A01G278400 chr3B 813955230 813958507 3277 True 5803.0 5803 98.6270 169 3445 1 chr3B.!!$R1 3276
3 TraesCS4A01G278400 chr7B 204002752 204006031 3279 False 5829.0 5829 98.7500 167 3445 1 chr7B.!!$F1 3278
4 TraesCS4A01G278400 chr3A 610421054 610424332 3278 True 5795.0 5795 98.5670 167 3445 1 chr3A.!!$R1 3278
5 TraesCS4A01G278400 chr2A 713923488 713926767 3279 False 5779.0 5779 98.4760 167 3445 1 chr2A.!!$F1 3278
6 TraesCS4A01G278400 chr2A 39361277 39364444 3167 True 2799.0 4619 98.4610 167 3445 2 chr2A.!!$R2 3278
7 TraesCS4A01G278400 chr7D 237548280 237551508 3228 False 2712.5 5114 96.6085 167 3445 2 chr7D.!!$F1 3278
8 TraesCS4A01G278400 chr5B 599614380 599616903 2523 True 4327.0 4327 97.6230 924 3445 1 chr5B.!!$R2 2521
9 TraesCS4A01G278400 chr3D 511278150 511281794 3644 True 2123.5 3925 94.3765 167 3445 2 chr3D.!!$R1 3278

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
59 60 0.904649 TGTAGGCAGTCAGATGGTGG 59.095 55.000 0.00 0.0 0.0 4.61 F
64 65 1.003580 GGCAGTCAGATGGTGGAAAGA 59.996 52.381 0.00 0.0 0.0 2.52 F
1517 2042 0.961019 GAACTGCAGCATTTGTGGGA 59.039 50.000 15.27 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 2021 1.068895 CCCACAAATGCTGCAGTTCAA 59.931 47.619 16.64 0.0 0.00 2.69 R
1905 2430 2.203451 GAGTATCCCCGGCCTCGA 60.203 66.667 0.00 0.0 39.00 4.04 R
3125 3651 1.176527 CAATCACCCTTGACGGCATT 58.823 50.000 0.00 0.0 33.38 3.56 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
18 19 2.163454 TGCATTTGGGGACAGAGGT 58.837 52.632 0.00 0.00 44.54 3.85
19 20 1.367346 TGCATTTGGGGACAGAGGTA 58.633 50.000 0.00 0.00 44.54 3.08
20 21 1.281867 TGCATTTGGGGACAGAGGTAG 59.718 52.381 0.00 0.00 44.54 3.18
21 22 1.282157 GCATTTGGGGACAGAGGTAGT 59.718 52.381 0.00 0.00 44.54 2.73
22 23 2.504175 GCATTTGGGGACAGAGGTAGTA 59.496 50.000 0.00 0.00 44.54 1.82
23 24 3.681874 GCATTTGGGGACAGAGGTAGTAC 60.682 52.174 0.00 0.00 44.54 2.73
24 25 2.242882 TTGGGGACAGAGGTAGTACC 57.757 55.000 11.73 11.73 44.54 3.34
25 26 1.086565 TGGGGACAGAGGTAGTACCA 58.913 55.000 21.49 0.00 42.06 3.25
26 27 1.433985 TGGGGACAGAGGTAGTACCAA 59.566 52.381 21.49 0.00 42.06 3.67
27 28 2.045326 TGGGGACAGAGGTAGTACCAAT 59.955 50.000 21.49 6.30 42.06 3.16
28 29 3.113043 GGGGACAGAGGTAGTACCAATT 58.887 50.000 21.49 0.19 42.06 2.32
29 30 4.264941 TGGGGACAGAGGTAGTACCAATTA 60.265 45.833 21.49 0.00 42.06 1.40
30 31 4.906060 GGGGACAGAGGTAGTACCAATTAT 59.094 45.833 21.49 0.00 42.06 1.28
31 32 6.080009 GGGGACAGAGGTAGTACCAATTATA 58.920 44.000 21.49 0.00 42.06 0.98
32 33 6.729569 GGGGACAGAGGTAGTACCAATTATAT 59.270 42.308 21.49 0.00 42.06 0.86
33 34 7.897565 GGGGACAGAGGTAGTACCAATTATATA 59.102 40.741 21.49 0.00 42.06 0.86
34 35 9.317827 GGGACAGAGGTAGTACCAATTATATAA 57.682 37.037 21.49 0.00 41.95 0.98
37 38 9.664777 ACAGAGGTAGTACCAATTATATAACCA 57.335 33.333 21.49 0.00 41.95 3.67
48 49 9.077885 ACCAATTATATAACCAATTGTAGGCAG 57.922 33.333 4.43 0.00 39.45 4.85
49 50 9.077885 CCAATTATATAACCAATTGTAGGCAGT 57.922 33.333 4.43 0.00 39.45 4.40
51 52 9.860650 AATTATATAACCAATTGTAGGCAGTCA 57.139 29.630 4.43 0.00 0.00 3.41
52 53 8.902540 TTATATAACCAATTGTAGGCAGTCAG 57.097 34.615 4.43 0.00 0.00 3.51
53 54 3.788227 AACCAATTGTAGGCAGTCAGA 57.212 42.857 4.43 0.00 0.00 3.27
54 55 4.307032 AACCAATTGTAGGCAGTCAGAT 57.693 40.909 4.43 0.00 0.00 2.90
55 56 3.614092 ACCAATTGTAGGCAGTCAGATG 58.386 45.455 4.43 0.00 0.00 2.90
56 57 2.947652 CCAATTGTAGGCAGTCAGATGG 59.052 50.000 4.43 0.00 0.00 3.51
57 58 3.614092 CAATTGTAGGCAGTCAGATGGT 58.386 45.455 0.00 0.00 0.00 3.55
58 59 2.768253 TTGTAGGCAGTCAGATGGTG 57.232 50.000 0.00 0.00 0.00 4.17
59 60 0.904649 TGTAGGCAGTCAGATGGTGG 59.095 55.000 0.00 0.00 0.00 4.61
60 61 1.195115 GTAGGCAGTCAGATGGTGGA 58.805 55.000 0.00 0.00 0.00 4.02
61 62 1.555075 GTAGGCAGTCAGATGGTGGAA 59.445 52.381 0.00 0.00 0.00 3.53
62 63 1.067295 AGGCAGTCAGATGGTGGAAA 58.933 50.000 0.00 0.00 0.00 3.13
63 64 1.004044 AGGCAGTCAGATGGTGGAAAG 59.996 52.381 0.00 0.00 0.00 2.62
64 65 1.003580 GGCAGTCAGATGGTGGAAAGA 59.996 52.381 0.00 0.00 0.00 2.52
65 66 2.553028 GGCAGTCAGATGGTGGAAAGAA 60.553 50.000 0.00 0.00 0.00 2.52
66 67 3.350833 GCAGTCAGATGGTGGAAAGAAT 58.649 45.455 0.00 0.00 0.00 2.40
67 68 3.760684 GCAGTCAGATGGTGGAAAGAATT 59.239 43.478 0.00 0.00 0.00 2.17
68 69 4.380233 GCAGTCAGATGGTGGAAAGAATTG 60.380 45.833 0.00 0.00 0.00 2.32
69 70 4.763793 CAGTCAGATGGTGGAAAGAATTGT 59.236 41.667 0.00 0.00 0.00 2.71
70 71 5.242393 CAGTCAGATGGTGGAAAGAATTGTT 59.758 40.000 0.00 0.00 0.00 2.83
71 72 5.835280 AGTCAGATGGTGGAAAGAATTGTTT 59.165 36.000 0.00 0.00 0.00 2.83
72 73 5.922544 GTCAGATGGTGGAAAGAATTGTTTG 59.077 40.000 5.14 0.00 0.00 2.93
73 74 5.010922 TCAGATGGTGGAAAGAATTGTTTGG 59.989 40.000 5.14 0.00 0.00 3.28
74 75 5.010922 CAGATGGTGGAAAGAATTGTTTGGA 59.989 40.000 5.14 0.00 0.00 3.53
75 76 4.935352 TGGTGGAAAGAATTGTTTGGAG 57.065 40.909 5.14 0.00 0.00 3.86
76 77 3.640967 TGGTGGAAAGAATTGTTTGGAGG 59.359 43.478 5.14 0.00 0.00 4.30
77 78 3.895041 GGTGGAAAGAATTGTTTGGAGGA 59.105 43.478 5.14 0.00 0.00 3.71
78 79 4.021981 GGTGGAAAGAATTGTTTGGAGGAG 60.022 45.833 5.14 0.00 0.00 3.69
79 80 4.827284 GTGGAAAGAATTGTTTGGAGGAGA 59.173 41.667 5.14 0.00 0.00 3.71
80 81 5.301805 GTGGAAAGAATTGTTTGGAGGAGAA 59.698 40.000 5.14 0.00 0.00 2.87
81 82 5.896678 TGGAAAGAATTGTTTGGAGGAGAAA 59.103 36.000 5.14 0.00 0.00 2.52
82 83 6.382570 TGGAAAGAATTGTTTGGAGGAGAAAA 59.617 34.615 5.14 0.00 0.00 2.29
83 84 6.701841 GGAAAGAATTGTTTGGAGGAGAAAAC 59.298 38.462 5.14 0.00 36.92 2.43
84 85 7.417911 GGAAAGAATTGTTTGGAGGAGAAAACT 60.418 37.037 5.14 0.00 37.22 2.66
85 86 6.396829 AGAATTGTTTGGAGGAGAAAACTG 57.603 37.500 0.00 0.00 37.22 3.16
86 87 4.590850 ATTGTTTGGAGGAGAAAACTGC 57.409 40.909 0.00 0.00 37.22 4.40
87 88 3.011566 TGTTTGGAGGAGAAAACTGCA 57.988 42.857 0.00 0.00 37.22 4.41
88 89 3.360867 TGTTTGGAGGAGAAAACTGCAA 58.639 40.909 0.00 0.00 43.16 4.08
89 90 3.960102 TGTTTGGAGGAGAAAACTGCAAT 59.040 39.130 0.40 0.00 44.03 3.56
90 91 4.405358 TGTTTGGAGGAGAAAACTGCAATT 59.595 37.500 0.40 0.00 44.03 2.32
91 92 4.589216 TTGGAGGAGAAAACTGCAATTG 57.411 40.909 0.00 0.00 40.61 2.32
92 93 3.565307 TGGAGGAGAAAACTGCAATTGT 58.435 40.909 7.40 0.00 33.20 2.71
93 94 3.318839 TGGAGGAGAAAACTGCAATTGTG 59.681 43.478 7.40 3.29 33.20 3.33
111 112 8.188531 CAATTGTGCAAATATAAGTTGGAAGG 57.811 34.615 0.00 0.00 0.00 3.46
112 113 5.323371 TGTGCAAATATAAGTTGGAAGGC 57.677 39.130 0.00 0.00 0.00 4.35
113 114 4.769488 TGTGCAAATATAAGTTGGAAGGCA 59.231 37.500 0.00 0.00 0.00 4.75
114 115 5.244851 TGTGCAAATATAAGTTGGAAGGCAA 59.755 36.000 0.00 0.00 0.00 4.52
115 116 6.070881 TGTGCAAATATAAGTTGGAAGGCAAT 60.071 34.615 0.00 0.00 0.00 3.56
116 117 7.123397 TGTGCAAATATAAGTTGGAAGGCAATA 59.877 33.333 0.00 0.00 0.00 1.90
117 118 7.649306 GTGCAAATATAAGTTGGAAGGCAATAG 59.351 37.037 0.00 0.00 0.00 1.73
118 119 7.559533 TGCAAATATAAGTTGGAAGGCAATAGA 59.440 33.333 0.00 0.00 0.00 1.98
119 120 8.413229 GCAAATATAAGTTGGAAGGCAATAGAA 58.587 33.333 0.00 0.00 0.00 2.10
120 121 9.736023 CAAATATAAGTTGGAAGGCAATAGAAC 57.264 33.333 0.00 0.00 0.00 3.01
121 122 9.474313 AAATATAAGTTGGAAGGCAATAGAACA 57.526 29.630 0.00 0.00 0.00 3.18
122 123 8.682936 ATATAAGTTGGAAGGCAATAGAACAG 57.317 34.615 0.00 0.00 0.00 3.16
123 124 4.373156 AGTTGGAAGGCAATAGAACAGT 57.627 40.909 0.00 0.00 0.00 3.55
124 125 4.074970 AGTTGGAAGGCAATAGAACAGTG 58.925 43.478 0.00 0.00 0.00 3.66
125 126 3.788227 TGGAAGGCAATAGAACAGTGT 57.212 42.857 0.00 0.00 0.00 3.55
126 127 3.411446 TGGAAGGCAATAGAACAGTGTG 58.589 45.455 0.00 0.00 0.00 3.82
127 128 2.162408 GGAAGGCAATAGAACAGTGTGC 59.838 50.000 0.00 0.00 34.42 4.57
128 129 2.566833 AGGCAATAGAACAGTGTGCA 57.433 45.000 3.49 0.00 36.93 4.57
129 130 2.862541 AGGCAATAGAACAGTGTGCAA 58.137 42.857 3.49 0.00 36.93 4.08
130 131 3.221771 AGGCAATAGAACAGTGTGCAAA 58.778 40.909 3.49 0.00 36.93 3.68
131 132 3.636300 AGGCAATAGAACAGTGTGCAAAA 59.364 39.130 3.49 0.00 36.93 2.44
132 133 4.099266 AGGCAATAGAACAGTGTGCAAAAA 59.901 37.500 3.49 0.00 36.93 1.94
133 134 4.445385 GGCAATAGAACAGTGTGCAAAAAG 59.555 41.667 3.49 0.00 36.93 2.27
134 135 5.280945 GCAATAGAACAGTGTGCAAAAAGA 58.719 37.500 3.49 0.00 35.28 2.52
135 136 5.400485 GCAATAGAACAGTGTGCAAAAAGAG 59.600 40.000 3.49 0.00 35.28 2.85
136 137 6.498304 CAATAGAACAGTGTGCAAAAAGAGT 58.502 36.000 3.49 0.00 0.00 3.24
137 138 6.699575 ATAGAACAGTGTGCAAAAAGAGTT 57.300 33.333 3.49 0.00 0.00 3.01
138 139 7.801716 ATAGAACAGTGTGCAAAAAGAGTTA 57.198 32.000 3.49 0.00 0.00 2.24
139 140 5.880341 AGAACAGTGTGCAAAAAGAGTTAC 58.120 37.500 3.49 0.00 0.00 2.50
140 141 4.632538 ACAGTGTGCAAAAAGAGTTACC 57.367 40.909 0.00 0.00 0.00 2.85
141 142 3.064820 ACAGTGTGCAAAAAGAGTTACCG 59.935 43.478 0.00 0.00 0.00 4.02
142 143 3.311322 CAGTGTGCAAAAAGAGTTACCGA 59.689 43.478 0.00 0.00 0.00 4.69
143 144 3.942748 AGTGTGCAAAAAGAGTTACCGAA 59.057 39.130 0.00 0.00 0.00 4.30
144 145 4.578928 AGTGTGCAAAAAGAGTTACCGAAT 59.421 37.500 0.00 0.00 0.00 3.34
145 146 5.067283 AGTGTGCAAAAAGAGTTACCGAATT 59.933 36.000 0.00 0.00 0.00 2.17
146 147 5.398416 GTGTGCAAAAAGAGTTACCGAATTC 59.602 40.000 0.00 0.00 0.00 2.17
147 148 5.066634 TGTGCAAAAAGAGTTACCGAATTCA 59.933 36.000 6.22 0.00 0.00 2.57
148 149 5.974751 GTGCAAAAAGAGTTACCGAATTCAA 59.025 36.000 6.22 0.00 0.00 2.69
149 150 6.640907 GTGCAAAAAGAGTTACCGAATTCAAT 59.359 34.615 6.22 0.00 0.00 2.57
150 151 7.169140 GTGCAAAAAGAGTTACCGAATTCAATT 59.831 33.333 6.22 0.00 0.00 2.32
151 152 7.381139 TGCAAAAAGAGTTACCGAATTCAATTC 59.619 33.333 6.22 0.00 35.94 2.17
152 153 7.381139 GCAAAAAGAGTTACCGAATTCAATTCA 59.619 33.333 10.76 0.00 39.22 2.57
153 154 8.690840 CAAAAAGAGTTACCGAATTCAATTCAC 58.309 33.333 10.76 1.01 39.22 3.18
154 155 7.745620 AAAGAGTTACCGAATTCAATTCACT 57.254 32.000 10.76 5.82 39.22 3.41
155 156 8.842358 AAAGAGTTACCGAATTCAATTCACTA 57.158 30.769 10.76 0.00 39.22 2.74
156 157 8.480643 AAGAGTTACCGAATTCAATTCACTAG 57.519 34.615 10.76 0.00 39.22 2.57
157 158 7.042335 AGAGTTACCGAATTCAATTCACTAGG 58.958 38.462 10.76 5.70 39.22 3.02
158 159 6.708285 AGTTACCGAATTCAATTCACTAGGT 58.292 36.000 10.76 10.90 39.22 3.08
159 160 7.166167 AGTTACCGAATTCAATTCACTAGGTT 58.834 34.615 10.76 0.00 39.22 3.50
160 161 8.316214 AGTTACCGAATTCAATTCACTAGGTTA 58.684 33.333 10.76 1.01 39.22 2.85
161 162 9.106070 GTTACCGAATTCAATTCACTAGGTTAT 57.894 33.333 10.76 0.00 39.22 1.89
1020 1545 3.334881 ACATGGGAGAAAATCAGGGACTT 59.665 43.478 0.00 0.00 34.60 3.01
1063 1588 1.552337 CTGAGCTCCTAACAGCCAAGA 59.448 52.381 12.15 0.00 40.65 3.02
1163 1688 8.088365 AAATGAAATTAAGCTGGAAGGTGTTAC 58.912 33.333 0.00 0.00 39.24 2.50
1379 1904 2.977772 ATCTCAACTGCTACTGAGGC 57.022 50.000 8.87 0.00 39.67 4.70
1496 2021 7.094205 GGAAAATTCTGTGATGGAGTATGTTGT 60.094 37.037 0.00 0.00 0.00 3.32
1517 2042 0.961019 GAACTGCAGCATTTGTGGGA 59.039 50.000 15.27 0.00 0.00 4.37
1841 2366 4.380867 GGGTCATTTGATTCGTTCTTGCAT 60.381 41.667 0.00 0.00 0.00 3.96
1871 2396 1.303317 GGAACATGCGTGGAAGGGT 60.303 57.895 11.36 0.00 0.00 4.34
1905 2430 1.894699 GAGGTGGATTAAGGGGAGGT 58.105 55.000 0.00 0.00 0.00 3.85
2036 2561 7.460402 AGGTGATAAGGATCATGAGGATTGTAT 59.540 37.037 0.09 0.00 43.95 2.29
2125 2650 4.097437 CACAAAGATCACATCCTGATTGGG 59.903 45.833 0.00 0.00 39.96 4.12
2182 2707 5.472148 GCACATCAATGGAATTTGAGTCAA 58.528 37.500 0.08 0.08 38.90 3.18
2353 2878 3.066621 GTCAATGAGTGCTTTGGTTGACA 59.933 43.478 15.14 0.00 42.84 3.58
2527 3052 5.011023 ACAATGATGGGAGAAAAGGAAACAC 59.989 40.000 0.00 0.00 0.00 3.32
2591 3117 7.546250 TGAGAAGATGAGTAAAGTCTTTCCT 57.454 36.000 0.00 0.00 32.67 3.36
2767 3293 8.190326 TCTCTAAGTGGAATGAAGTACTTTGA 57.810 34.615 10.02 0.00 35.26 2.69
3051 3577 0.400213 TTTGGAGGTTGCTCGGTCAT 59.600 50.000 0.00 0.00 0.00 3.06
3068 3594 8.721478 GCTCGGTCATTAATGTATACAATGAAT 58.279 33.333 16.61 10.78 39.63 2.57
3125 3651 2.766263 AGCTACATTCCTCATCAACCGA 59.234 45.455 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.281867 CTACCTCTGTCCCCAAATGCA 59.718 52.381 0.00 0.00 0.00 3.96
1 2 1.282157 ACTACCTCTGTCCCCAAATGC 59.718 52.381 0.00 0.00 0.00 3.56
2 3 3.118371 GGTACTACCTCTGTCCCCAAATG 60.118 52.174 0.00 0.00 34.73 2.32
3 4 3.113043 GGTACTACCTCTGTCCCCAAAT 58.887 50.000 0.00 0.00 34.73 2.32
4 5 2.158127 TGGTACTACCTCTGTCCCCAAA 60.158 50.000 6.79 0.00 39.58 3.28
5 6 1.433985 TGGTACTACCTCTGTCCCCAA 59.566 52.381 6.79 0.00 39.58 4.12
6 7 1.086565 TGGTACTACCTCTGTCCCCA 58.913 55.000 6.79 0.00 39.58 4.96
7 8 2.242882 TTGGTACTACCTCTGTCCCC 57.757 55.000 6.79 0.00 39.58 4.81
8 9 7.793948 ATATAATTGGTACTACCTCTGTCCC 57.206 40.000 6.79 0.00 39.58 4.46
11 12 9.664777 TGGTTATATAATTGGTACTACCTCTGT 57.335 33.333 6.79 0.00 39.58 3.41
22 23 9.077885 CTGCCTACAATTGGTTATATAATTGGT 57.922 33.333 10.83 3.43 44.51 3.67
23 24 9.077885 ACTGCCTACAATTGGTTATATAATTGG 57.922 33.333 10.83 0.00 44.51 3.16
25 26 9.860650 TGACTGCCTACAATTGGTTATATAATT 57.139 29.630 10.83 0.00 0.00 1.40
26 27 9.507329 CTGACTGCCTACAATTGGTTATATAAT 57.493 33.333 10.83 0.00 0.00 1.28
27 28 8.710239 TCTGACTGCCTACAATTGGTTATATAA 58.290 33.333 10.83 0.00 0.00 0.98
28 29 8.257602 TCTGACTGCCTACAATTGGTTATATA 57.742 34.615 10.83 0.00 0.00 0.86
29 30 7.136822 TCTGACTGCCTACAATTGGTTATAT 57.863 36.000 10.83 0.00 0.00 0.86
30 31 6.553953 TCTGACTGCCTACAATTGGTTATA 57.446 37.500 10.83 0.00 0.00 0.98
31 32 5.435686 TCTGACTGCCTACAATTGGTTAT 57.564 39.130 10.83 0.00 0.00 1.89
32 33 4.901197 TCTGACTGCCTACAATTGGTTA 57.099 40.909 10.83 0.00 0.00 2.85
33 34 3.788227 TCTGACTGCCTACAATTGGTT 57.212 42.857 10.83 0.00 0.00 3.67
34 35 3.614092 CATCTGACTGCCTACAATTGGT 58.386 45.455 10.83 0.00 0.00 3.67
35 36 2.947652 CCATCTGACTGCCTACAATTGG 59.052 50.000 10.83 0.00 0.00 3.16
36 37 3.376234 CACCATCTGACTGCCTACAATTG 59.624 47.826 3.24 3.24 0.00 2.32
37 38 3.614092 CACCATCTGACTGCCTACAATT 58.386 45.455 0.00 0.00 0.00 2.32
38 39 2.092753 CCACCATCTGACTGCCTACAAT 60.093 50.000 0.00 0.00 0.00 2.71
39 40 1.278985 CCACCATCTGACTGCCTACAA 59.721 52.381 0.00 0.00 0.00 2.41
40 41 0.904649 CCACCATCTGACTGCCTACA 59.095 55.000 0.00 0.00 0.00 2.74
41 42 1.195115 TCCACCATCTGACTGCCTAC 58.805 55.000 0.00 0.00 0.00 3.18
42 43 1.951209 TTCCACCATCTGACTGCCTA 58.049 50.000 0.00 0.00 0.00 3.93
43 44 1.004044 CTTTCCACCATCTGACTGCCT 59.996 52.381 0.00 0.00 0.00 4.75
44 45 1.003580 TCTTTCCACCATCTGACTGCC 59.996 52.381 0.00 0.00 0.00 4.85
45 46 2.479566 TCTTTCCACCATCTGACTGC 57.520 50.000 0.00 0.00 0.00 4.40
46 47 4.763793 ACAATTCTTTCCACCATCTGACTG 59.236 41.667 0.00 0.00 0.00 3.51
47 48 4.990526 ACAATTCTTTCCACCATCTGACT 58.009 39.130 0.00 0.00 0.00 3.41
48 49 5.712152 AACAATTCTTTCCACCATCTGAC 57.288 39.130 0.00 0.00 0.00 3.51
49 50 5.010922 CCAAACAATTCTTTCCACCATCTGA 59.989 40.000 0.00 0.00 0.00 3.27
50 51 5.010922 TCCAAACAATTCTTTCCACCATCTG 59.989 40.000 0.00 0.00 0.00 2.90
51 52 5.147032 TCCAAACAATTCTTTCCACCATCT 58.853 37.500 0.00 0.00 0.00 2.90
52 53 5.467035 TCCAAACAATTCTTTCCACCATC 57.533 39.130 0.00 0.00 0.00 3.51
53 54 4.284234 CCTCCAAACAATTCTTTCCACCAT 59.716 41.667 0.00 0.00 0.00 3.55
54 55 3.640967 CCTCCAAACAATTCTTTCCACCA 59.359 43.478 0.00 0.00 0.00 4.17
55 56 3.895041 TCCTCCAAACAATTCTTTCCACC 59.105 43.478 0.00 0.00 0.00 4.61
56 57 4.827284 TCTCCTCCAAACAATTCTTTCCAC 59.173 41.667 0.00 0.00 0.00 4.02
57 58 5.060427 TCTCCTCCAAACAATTCTTTCCA 57.940 39.130 0.00 0.00 0.00 3.53
58 59 6.405278 TTTCTCCTCCAAACAATTCTTTCC 57.595 37.500 0.00 0.00 0.00 3.13
59 60 7.436376 CAGTTTTCTCCTCCAAACAATTCTTTC 59.564 37.037 0.00 0.00 35.66 2.62
60 61 7.267857 CAGTTTTCTCCTCCAAACAATTCTTT 58.732 34.615 0.00 0.00 35.66 2.52
61 62 6.683861 GCAGTTTTCTCCTCCAAACAATTCTT 60.684 38.462 0.00 0.00 35.66 2.52
62 63 5.221322 GCAGTTTTCTCCTCCAAACAATTCT 60.221 40.000 0.00 0.00 35.66 2.40
63 64 4.984785 GCAGTTTTCTCCTCCAAACAATTC 59.015 41.667 0.00 0.00 35.66 2.17
64 65 4.405358 TGCAGTTTTCTCCTCCAAACAATT 59.595 37.500 0.00 0.00 35.66 2.32
65 66 3.960102 TGCAGTTTTCTCCTCCAAACAAT 59.040 39.130 0.00 0.00 35.66 2.71
66 67 3.360867 TGCAGTTTTCTCCTCCAAACAA 58.639 40.909 0.00 0.00 35.66 2.83
67 68 3.011566 TGCAGTTTTCTCCTCCAAACA 57.988 42.857 0.00 0.00 35.66 2.83
68 69 4.590850 ATTGCAGTTTTCTCCTCCAAAC 57.409 40.909 0.00 0.00 33.75 2.93
69 70 4.405358 ACAATTGCAGTTTTCTCCTCCAAA 59.595 37.500 5.05 0.00 0.00 3.28
70 71 3.960102 ACAATTGCAGTTTTCTCCTCCAA 59.040 39.130 5.05 0.00 0.00 3.53
71 72 3.318839 CACAATTGCAGTTTTCTCCTCCA 59.681 43.478 5.05 0.00 0.00 3.86
72 73 3.905784 CACAATTGCAGTTTTCTCCTCC 58.094 45.455 5.05 0.00 0.00 4.30
86 87 7.201548 GCCTTCCAACTTATATTTGCACAATTG 60.202 37.037 3.24 3.24 0.00 2.32
87 88 6.818142 GCCTTCCAACTTATATTTGCACAATT 59.182 34.615 0.00 0.00 0.00 2.32
88 89 6.070881 TGCCTTCCAACTTATATTTGCACAAT 60.071 34.615 0.00 0.00 0.00 2.71
89 90 5.244851 TGCCTTCCAACTTATATTTGCACAA 59.755 36.000 0.00 0.00 0.00 3.33
90 91 4.769488 TGCCTTCCAACTTATATTTGCACA 59.231 37.500 0.00 0.00 0.00 4.57
91 92 5.323371 TGCCTTCCAACTTATATTTGCAC 57.677 39.130 0.00 0.00 0.00 4.57
92 93 5.991933 TTGCCTTCCAACTTATATTTGCA 57.008 34.783 0.00 0.00 0.00 4.08
93 94 7.940850 TCTATTGCCTTCCAACTTATATTTGC 58.059 34.615 0.00 0.00 35.99 3.68
94 95 9.736023 GTTCTATTGCCTTCCAACTTATATTTG 57.264 33.333 0.00 0.00 35.99 2.32
95 96 9.474313 TGTTCTATTGCCTTCCAACTTATATTT 57.526 29.630 0.00 0.00 35.99 1.40
96 97 9.125026 CTGTTCTATTGCCTTCCAACTTATATT 57.875 33.333 0.00 0.00 35.99 1.28
97 98 8.275040 ACTGTTCTATTGCCTTCCAACTTATAT 58.725 33.333 0.00 0.00 35.99 0.86
98 99 7.552687 CACTGTTCTATTGCCTTCCAACTTATA 59.447 37.037 0.00 0.00 35.99 0.98
99 100 6.375455 CACTGTTCTATTGCCTTCCAACTTAT 59.625 38.462 0.00 0.00 35.99 1.73
100 101 5.705441 CACTGTTCTATTGCCTTCCAACTTA 59.295 40.000 0.00 0.00 35.99 2.24
101 102 4.520492 CACTGTTCTATTGCCTTCCAACTT 59.480 41.667 0.00 0.00 35.99 2.66
102 103 4.074970 CACTGTTCTATTGCCTTCCAACT 58.925 43.478 0.00 0.00 35.99 3.16
103 104 3.821033 ACACTGTTCTATTGCCTTCCAAC 59.179 43.478 0.00 0.00 35.99 3.77
104 105 3.820467 CACACTGTTCTATTGCCTTCCAA 59.180 43.478 0.00 0.00 37.94 3.53
105 106 3.411446 CACACTGTTCTATTGCCTTCCA 58.589 45.455 0.00 0.00 0.00 3.53
106 107 2.162408 GCACACTGTTCTATTGCCTTCC 59.838 50.000 0.00 0.00 0.00 3.46
107 108 2.813754 TGCACACTGTTCTATTGCCTTC 59.186 45.455 0.00 0.00 31.94 3.46
108 109 2.862541 TGCACACTGTTCTATTGCCTT 58.137 42.857 0.00 0.00 31.94 4.35
109 110 2.566833 TGCACACTGTTCTATTGCCT 57.433 45.000 0.00 0.00 31.94 4.75
110 111 3.641437 TTTGCACACTGTTCTATTGCC 57.359 42.857 0.00 0.00 31.94 4.52
111 112 5.280945 TCTTTTTGCACACTGTTCTATTGC 58.719 37.500 0.00 0.00 0.00 3.56
112 113 6.498304 ACTCTTTTTGCACACTGTTCTATTG 58.502 36.000 0.00 0.00 0.00 1.90
113 114 6.699575 ACTCTTTTTGCACACTGTTCTATT 57.300 33.333 0.00 0.00 0.00 1.73
114 115 6.699575 AACTCTTTTTGCACACTGTTCTAT 57.300 33.333 0.00 0.00 0.00 1.98
115 116 6.037830 GGTAACTCTTTTTGCACACTGTTCTA 59.962 38.462 0.00 0.00 0.00 2.10
116 117 5.163652 GGTAACTCTTTTTGCACACTGTTCT 60.164 40.000 0.00 0.00 0.00 3.01
117 118 5.034797 GGTAACTCTTTTTGCACACTGTTC 58.965 41.667 0.00 0.00 0.00 3.18
118 119 4.438200 CGGTAACTCTTTTTGCACACTGTT 60.438 41.667 0.00 0.00 0.00 3.16
119 120 3.064820 CGGTAACTCTTTTTGCACACTGT 59.935 43.478 0.00 0.00 0.00 3.55
120 121 3.311322 TCGGTAACTCTTTTTGCACACTG 59.689 43.478 0.00 0.00 0.00 3.66
121 122 3.537580 TCGGTAACTCTTTTTGCACACT 58.462 40.909 0.00 0.00 0.00 3.55
122 123 3.955771 TCGGTAACTCTTTTTGCACAC 57.044 42.857 0.00 0.00 0.00 3.82
123 124 5.066634 TGAATTCGGTAACTCTTTTTGCACA 59.933 36.000 0.04 0.00 0.00 4.57
124 125 5.516090 TGAATTCGGTAACTCTTTTTGCAC 58.484 37.500 0.04 0.00 0.00 4.57
125 126 5.759506 TGAATTCGGTAACTCTTTTTGCA 57.240 34.783 0.04 0.00 0.00 4.08
126 127 7.381139 TGAATTGAATTCGGTAACTCTTTTTGC 59.619 33.333 12.72 0.00 42.15 3.68
127 128 8.690840 GTGAATTGAATTCGGTAACTCTTTTTG 58.309 33.333 12.72 0.00 42.15 2.44
128 129 8.630037 AGTGAATTGAATTCGGTAACTCTTTTT 58.370 29.630 12.72 0.00 42.15 1.94
129 130 8.166422 AGTGAATTGAATTCGGTAACTCTTTT 57.834 30.769 12.72 0.00 42.15 2.27
130 131 7.745620 AGTGAATTGAATTCGGTAACTCTTT 57.254 32.000 12.72 0.00 42.15 2.52
131 132 7.549488 CCTAGTGAATTGAATTCGGTAACTCTT 59.451 37.037 12.72 0.00 42.15 2.85
132 133 7.042335 CCTAGTGAATTGAATTCGGTAACTCT 58.958 38.462 12.72 5.58 42.15 3.24
133 134 6.817140 ACCTAGTGAATTGAATTCGGTAACTC 59.183 38.462 12.72 0.00 42.15 3.01
134 135 6.708285 ACCTAGTGAATTGAATTCGGTAACT 58.292 36.000 12.72 12.13 42.15 2.24
135 136 6.980051 ACCTAGTGAATTGAATTCGGTAAC 57.020 37.500 12.72 5.84 42.15 2.50
149 150 9.621629 CAACCCAACATTATATAACCTAGTGAA 57.378 33.333 0.00 0.00 0.00 3.18
150 151 8.774183 ACAACCCAACATTATATAACCTAGTGA 58.226 33.333 0.00 0.00 0.00 3.41
151 152 8.974060 ACAACCCAACATTATATAACCTAGTG 57.026 34.615 0.00 0.00 0.00 2.74
161 162 9.907229 TTCACACATATACAACCCAACATTATA 57.093 29.630 0.00 0.00 0.00 0.98
162 163 8.815565 TTCACACATATACAACCCAACATTAT 57.184 30.769 0.00 0.00 0.00 1.28
163 164 8.815565 ATTCACACATATACAACCCAACATTA 57.184 30.769 0.00 0.00 0.00 1.90
164 165 7.615365 AGATTCACACATATACAACCCAACATT 59.385 33.333 0.00 0.00 0.00 2.71
165 166 7.067372 CAGATTCACACATATACAACCCAACAT 59.933 37.037 0.00 0.00 0.00 2.71
368 373 2.197324 GCCAACAACCACCCTGGA 59.803 61.111 0.00 0.00 40.96 3.86
677 970 3.063485 GTTCTCAGTCTTTCTCCAGCAC 58.937 50.000 0.00 0.00 0.00 4.40
720 1013 2.281070 CTCTGCCGCACCAACAGT 60.281 61.111 0.00 0.00 33.12 3.55
1020 1545 4.756135 GCCAATTTTTCAATTGCCTTCTCA 59.244 37.500 0.00 0.00 45.63 3.27
1063 1588 1.719529 AGAGATGCTGCAGCTCCTAT 58.280 50.000 35.98 26.26 46.56 2.57
1163 1688 5.801350 TCTTGACCAGCTCAAATAATTCG 57.199 39.130 0.00 0.00 38.47 3.34
1379 1904 4.342092 ACAGTTTTGAGAGGGTTTTCCATG 59.658 41.667 0.00 0.00 42.91 3.66
1496 2021 1.068895 CCCACAAATGCTGCAGTTCAA 59.931 47.619 16.64 0.00 0.00 2.69
1871 2396 3.139584 TCCACCTCGGTTATATCCTCTCA 59.860 47.826 0.00 0.00 35.57 3.27
1905 2430 2.203451 GAGTATCCCCGGCCTCGA 60.203 66.667 0.00 0.00 39.00 4.04
2125 2650 3.695830 TGATGCCCCCGAATCTAATAC 57.304 47.619 0.00 0.00 0.00 1.89
2182 2707 6.218195 ACATGTGGGTGGATATGGAATATT 57.782 37.500 0.00 0.00 40.26 1.28
2353 2878 8.730680 GTCAACTATTACTCAACAATCCACATT 58.269 33.333 0.00 0.00 0.00 2.71
2365 2890 8.418662 ACATAAATAGCGGTCAACTATTACTCA 58.581 33.333 0.00 0.00 38.96 3.41
2527 3052 5.185454 TCTACAATGGTGAAGCATTACCTG 58.815 41.667 7.37 0.00 37.84 4.00
2591 3117 1.988846 TCCACCCCACACATTACATCA 59.011 47.619 0.00 0.00 0.00 3.07
3068 3594 3.030291 ACTCCACAAGAATTTTGGCACA 58.970 40.909 0.00 0.00 0.00 4.57
3125 3651 1.176527 CAATCACCCTTGACGGCATT 58.823 50.000 0.00 0.00 33.38 3.56


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

AutoCloner maintained by Alex Coulton.