Multiple sequence alignment - TraesCS4B01G125000

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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 TraesCS4B01G125000 chr4B 100.000 2336 0 0 1 2336 152082210 152079875 0.000000e+00 4314
1 TraesCS4B01G125000 chr4B 96.216 185 7 0 1 185 314784324 314784140 1.050000e-78 303
2 TraesCS4B01G125000 chr2B 92.170 2184 105 25 187 2336 746310273 746308122 0.000000e+00 3025
3 TraesCS4B01G125000 chr2B 92.590 1687 67 27 403 2058 388575614 388573955 0.000000e+00 2370
4 TraesCS4B01G125000 chr2B 84.473 921 107 21 1186 2079 270740371 270739460 0.000000e+00 876
5 TraesCS4B01G125000 chr2B 94.495 218 12 0 187 404 388575913 388575696 1.030000e-88 337
6 TraesCS4B01G125000 chr2B 88.679 265 17 6 2084 2336 654442233 654441970 6.270000e-81 311
7 TraesCS4B01G125000 chr7B 93.484 1903 72 18 474 2336 345992570 345994460 0.000000e+00 2780
8 TraesCS4B01G125000 chr7B 91.117 1227 75 12 1135 2336 20342494 20341277 0.000000e+00 1631
9 TraesCS4B01G125000 chr7B 94.798 173 9 0 13 185 355693822 355693650 1.060000e-68 270
10 TraesCS4B01G125000 chr7B 93.082 159 9 2 2180 2336 254245248 254245090 5.020000e-57 231
11 TraesCS4B01G125000 chr6B 91.320 1970 102 27 403 2336 185005813 185007749 0.000000e+00 2627
12 TraesCS4B01G125000 chr6B 89.836 1220 82 16 1142 2336 587743238 587744440 0.000000e+00 1528
13 TraesCS4B01G125000 chr6B 95.954 173 7 0 13 185 199014644 199014472 4.910000e-72 281
14 TraesCS4B01G125000 chr6B 89.394 198 7 6 2144 2327 259712543 259712740 1.080000e-58 237
15 TraesCS4B01G125000 chr6B 94.203 138 8 0 187 324 185003352 185003489 6.540000e-51 211
16 TraesCS4B01G125000 chr5B 91.163 1969 103 29 403 2336 389240269 389242201 0.000000e+00 2606
17 TraesCS4B01G125000 chr5B 89.918 1220 81 15 1142 2336 463402815 463401613 0.000000e+00 1533
18 TraesCS4B01G125000 chr5B 91.506 259 6 2 1142 1391 22033136 22032885 2.220000e-90 342
19 TraesCS4B01G125000 chr5B 94.798 173 9 0 13 185 266959333 266959505 1.060000e-68 270
20 TraesCS4B01G125000 chr5B 94.203 138 7 1 187 324 389237807 389237943 2.350000e-50 209
21 TraesCS4B01G125000 chr3B 90.835 1953 109 36 403 2336 648411656 648413557 0.000000e+00 2551
22 TraesCS4B01G125000 chr3B 91.568 1103 62 10 1249 2336 455493582 455494668 0.000000e+00 1493
23 TraesCS4B01G125000 chr3B 86.891 267 18 10 2084 2336 324231881 324231618 1.370000e-72 283
24 TraesCS4B01G125000 chr3B 94.220 173 10 0 13 185 473401648 473401820 4.950000e-67 265
25 TraesCS4B01G125000 chr3B 94.928 138 7 0 187 324 648409194 648409331 1.410000e-52 217
26 TraesCS4B01G125000 chr6A 85.591 1964 168 47 187 2074 307208980 307210904 0.000000e+00 1953
27 TraesCS4B01G125000 chr6A 85.838 1158 72 29 419 1497 233781738 233780594 0.000000e+00 1146
28 TraesCS4B01G125000 chr1A 85.487 1130 76 31 416 1497 251160894 251161983 0.000000e+00 1098
29 TraesCS4B01G125000 chr1A 94.798 173 9 0 13 185 267183323 267183151 1.060000e-68 270
30 TraesCS4B01G125000 chr3A 85.390 794 37 29 603 1321 164371029 164370240 0.000000e+00 750
31 TraesCS4B01G125000 chr3A 94.798 173 9 0 13 185 438538088 438538260 1.060000e-68 270
32 TraesCS4B01G125000 chr3A 87.054 224 14 8 2126 2336 110679408 110679187 3.000000e-59 239
33 TraesCS4B01G125000 chr7A 82.051 780 50 27 796 1497 228298295 228299062 1.200000e-162 582
34 TraesCS4B01G125000 chr7A 92.617 149 8 3 888 1035 418060152 418060298 6.540000e-51 211
35 TraesCS4B01G125000 chr6D 95.954 173 7 0 13 185 256248327 256248499 4.910000e-72 281
36 TraesCS4B01G125000 chr2A 94.798 173 9 0 13 185 192067114 192066942 1.060000e-68 270
37 TraesCS4B01G125000 chr5A 95.597 159 5 2 2180 2336 166878957 166878799 1.070000e-63 254
38 TraesCS4B01G125000 chr1B 88.038 209 13 5 2139 2336 429719807 429720014 1.080000e-58 237
39 TraesCS4B01G125000 chr4D 93.082 159 8 3 2180 2336 460239039 460239196 1.810000e-56 230


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 TraesCS4B01G125000 chr4B 152079875 152082210 2335 True 4314.0 4314 100.0000 1 2336 1 chr4B.!!$R1 2335
1 TraesCS4B01G125000 chr2B 746308122 746310273 2151 True 3025.0 3025 92.1700 187 2336 1 chr2B.!!$R3 2149
2 TraesCS4B01G125000 chr2B 388573955 388575913 1958 True 1353.5 2370 93.5425 187 2058 2 chr2B.!!$R4 1871
3 TraesCS4B01G125000 chr2B 270739460 270740371 911 True 876.0 876 84.4730 1186 2079 1 chr2B.!!$R1 893
4 TraesCS4B01G125000 chr7B 345992570 345994460 1890 False 2780.0 2780 93.4840 474 2336 1 chr7B.!!$F1 1862
5 TraesCS4B01G125000 chr7B 20341277 20342494 1217 True 1631.0 1631 91.1170 1135 2336 1 chr7B.!!$R1 1201
6 TraesCS4B01G125000 chr6B 587743238 587744440 1202 False 1528.0 1528 89.8360 1142 2336 1 chr6B.!!$F2 1194
7 TraesCS4B01G125000 chr6B 185003352 185007749 4397 False 1419.0 2627 92.7615 187 2336 2 chr6B.!!$F3 2149
8 TraesCS4B01G125000 chr5B 463401613 463402815 1202 True 1533.0 1533 89.9180 1142 2336 1 chr5B.!!$R2 1194
9 TraesCS4B01G125000 chr5B 389237807 389242201 4394 False 1407.5 2606 92.6830 187 2336 2 chr5B.!!$F2 2149
10 TraesCS4B01G125000 chr3B 455493582 455494668 1086 False 1493.0 1493 91.5680 1249 2336 1 chr3B.!!$F1 1087
11 TraesCS4B01G125000 chr3B 648409194 648413557 4363 False 1384.0 2551 92.8815 187 2336 2 chr3B.!!$F3 2149
12 TraesCS4B01G125000 chr6A 307208980 307210904 1924 False 1953.0 1953 85.5910 187 2074 1 chr6A.!!$F1 1887
13 TraesCS4B01G125000 chr6A 233780594 233781738 1144 True 1146.0 1146 85.8380 419 1497 1 chr6A.!!$R1 1078
14 TraesCS4B01G125000 chr1A 251160894 251161983 1089 False 1098.0 1098 85.4870 416 1497 1 chr1A.!!$F1 1081
15 TraesCS4B01G125000 chr3A 164370240 164371029 789 True 750.0 750 85.3900 603 1321 1 chr3A.!!$R2 718
16 TraesCS4B01G125000 chr7A 228298295 228299062 767 False 582.0 582 82.0510 796 1497 1 chr7A.!!$F1 701

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
152 153 0.521735 CCCACTAAGAAACAAGGCGC 59.478 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 4252 0.173029 CATTGCGCTAAATGGCACCA 59.827 50.0 9.73 0.0 39.2 4.17 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
55 56 7.749539 ATTTTTCTACAAGTTTTTCACGTGG 57.250 32.000 17.00 0.00 39.07 4.94
56 57 5.883503 TTTCTACAAGTTTTTCACGTGGT 57.116 34.783 17.00 5.37 39.07 4.16
57 58 6.981762 TTTCTACAAGTTTTTCACGTGGTA 57.018 33.333 17.00 6.30 39.07 3.25
58 59 7.556733 TTTCTACAAGTTTTTCACGTGGTAT 57.443 32.000 17.00 0.00 39.07 2.73
59 60 7.556733 TTCTACAAGTTTTTCACGTGGTATT 57.443 32.000 17.00 0.00 39.07 1.89
60 61 7.556733 TCTACAAGTTTTTCACGTGGTATTT 57.443 32.000 17.00 0.61 39.07 1.40
61 62 7.987649 TCTACAAGTTTTTCACGTGGTATTTT 58.012 30.769 17.00 1.17 39.07 1.82
62 63 9.107177 TCTACAAGTTTTTCACGTGGTATTTTA 57.893 29.630 17.00 0.00 39.07 1.52
63 64 9.377383 CTACAAGTTTTTCACGTGGTATTTTAG 57.623 33.333 17.00 3.65 39.07 1.85
64 65 7.197703 ACAAGTTTTTCACGTGGTATTTTAGG 58.802 34.615 17.00 1.86 39.07 2.69
65 66 5.765176 AGTTTTTCACGTGGTATTTTAGGC 58.235 37.500 17.00 0.00 0.00 3.93
66 67 5.533528 AGTTTTTCACGTGGTATTTTAGGCT 59.466 36.000 17.00 0.00 0.00 4.58
67 68 6.711645 AGTTTTTCACGTGGTATTTTAGGCTA 59.288 34.615 17.00 0.00 0.00 3.93
68 69 7.392393 AGTTTTTCACGTGGTATTTTAGGCTAT 59.608 33.333 17.00 0.00 0.00 2.97
69 70 8.667463 GTTTTTCACGTGGTATTTTAGGCTATA 58.333 33.333 17.00 0.00 0.00 1.31
70 71 8.428186 TTTTCACGTGGTATTTTAGGCTATAG 57.572 34.615 17.00 0.00 0.00 1.31
71 72 5.535333 TCACGTGGTATTTTAGGCTATAGC 58.465 41.667 16.78 16.78 41.14 2.97
72 73 5.303589 TCACGTGGTATTTTAGGCTATAGCT 59.696 40.000 23.53 12.38 41.70 3.32
73 74 5.989777 CACGTGGTATTTTAGGCTATAGCTT 59.010 40.000 23.53 19.05 41.70 3.74
74 75 5.989777 ACGTGGTATTTTAGGCTATAGCTTG 59.010 40.000 23.53 3.60 41.70 4.01
75 76 6.183360 ACGTGGTATTTTAGGCTATAGCTTGA 60.183 38.462 23.53 10.98 41.70 3.02
76 77 6.874134 CGTGGTATTTTAGGCTATAGCTTGAT 59.126 38.462 23.53 13.98 41.70 2.57
77 78 7.387948 CGTGGTATTTTAGGCTATAGCTTGATT 59.612 37.037 23.53 7.15 41.70 2.57
78 79 9.067986 GTGGTATTTTAGGCTATAGCTTGATTT 57.932 33.333 23.53 6.83 41.70 2.17
79 80 9.066892 TGGTATTTTAGGCTATAGCTTGATTTG 57.933 33.333 23.53 0.00 41.70 2.32
80 81 9.284968 GGTATTTTAGGCTATAGCTTGATTTGA 57.715 33.333 23.53 0.00 41.70 2.69
82 83 8.752005 ATTTTAGGCTATAGCTTGATTTGACA 57.248 30.769 23.53 0.00 41.70 3.58
83 84 7.553881 TTTAGGCTATAGCTTGATTTGACAC 57.446 36.000 23.53 3.12 41.70 3.67
84 85 5.365021 AGGCTATAGCTTGATTTGACACT 57.635 39.130 23.53 5.39 41.70 3.55
85 86 6.485830 AGGCTATAGCTTGATTTGACACTA 57.514 37.500 23.53 0.00 41.70 2.74
86 87 7.072263 AGGCTATAGCTTGATTTGACACTAT 57.928 36.000 23.53 0.00 41.70 2.12
87 88 7.158021 AGGCTATAGCTTGATTTGACACTATC 58.842 38.462 23.53 1.49 41.70 2.08
88 89 6.090088 GGCTATAGCTTGATTTGACACTATCG 59.910 42.308 23.53 0.00 41.70 2.92
89 90 6.642950 GCTATAGCTTGATTTGACACTATCGT 59.357 38.462 17.75 0.00 38.21 3.73
90 91 6.834959 ATAGCTTGATTTGACACTATCGTG 57.165 37.500 0.00 0.00 46.63 4.35
91 92 4.820897 AGCTTGATTTGACACTATCGTGA 58.179 39.130 4.10 0.00 43.97 4.35
92 93 5.237815 AGCTTGATTTGACACTATCGTGAA 58.762 37.500 4.10 0.00 43.97 3.18
93 94 5.349817 AGCTTGATTTGACACTATCGTGAAG 59.650 40.000 4.10 0.00 43.97 3.02
94 95 5.120830 GCTTGATTTGACACTATCGTGAAGT 59.879 40.000 4.10 0.00 43.97 3.01
96 97 4.929211 TGATTTGACACTATCGTGAAGTGG 59.071 41.667 4.10 2.80 46.97 4.00
97 98 3.313012 TTGACACTATCGTGAAGTGGG 57.687 47.619 4.10 0.00 46.97 4.61
98 99 1.548719 TGACACTATCGTGAAGTGGGG 59.451 52.381 4.10 0.00 46.97 4.96
99 100 1.549170 GACACTATCGTGAAGTGGGGT 59.451 52.381 4.10 0.00 46.97 4.95
100 101 2.756760 GACACTATCGTGAAGTGGGGTA 59.243 50.000 4.10 0.00 46.97 3.69
101 102 3.167485 ACACTATCGTGAAGTGGGGTAA 58.833 45.455 4.10 0.00 46.97 2.85
102 103 3.773119 ACACTATCGTGAAGTGGGGTAAT 59.227 43.478 4.10 0.00 46.97 1.89
103 104 4.224370 ACACTATCGTGAAGTGGGGTAATT 59.776 41.667 4.10 0.00 46.97 1.40
104 105 5.183228 CACTATCGTGAAGTGGGGTAATTT 58.817 41.667 0.00 0.00 43.97 1.82
105 106 5.646360 CACTATCGTGAAGTGGGGTAATTTT 59.354 40.000 0.00 0.00 43.97 1.82
106 107 5.878669 ACTATCGTGAAGTGGGGTAATTTTC 59.121 40.000 0.00 0.00 0.00 2.29
107 108 3.414269 TCGTGAAGTGGGGTAATTTTCC 58.586 45.455 0.00 0.00 0.00 3.13
108 109 3.150767 CGTGAAGTGGGGTAATTTTCCA 58.849 45.455 0.00 0.00 0.00 3.53
109 110 3.761752 CGTGAAGTGGGGTAATTTTCCAT 59.238 43.478 0.00 0.00 32.71 3.41
110 111 4.944930 CGTGAAGTGGGGTAATTTTCCATA 59.055 41.667 0.00 0.00 32.71 2.74
111 112 5.592688 CGTGAAGTGGGGTAATTTTCCATAT 59.407 40.000 0.00 0.00 32.71 1.78
112 113 6.096282 CGTGAAGTGGGGTAATTTTCCATATT 59.904 38.462 0.00 0.00 32.71 1.28
113 114 7.264947 GTGAAGTGGGGTAATTTTCCATATTG 58.735 38.462 0.00 0.00 32.71 1.90
114 115 7.123547 GTGAAGTGGGGTAATTTTCCATATTGA 59.876 37.037 0.00 0.00 32.71 2.57
115 116 7.843760 TGAAGTGGGGTAATTTTCCATATTGAT 59.156 33.333 0.00 0.00 32.71 2.57
116 117 9.362151 GAAGTGGGGTAATTTTCCATATTGATA 57.638 33.333 0.00 0.00 32.71 2.15
117 118 9.897040 AAGTGGGGTAATTTTCCATATTGATAT 57.103 29.630 0.00 0.00 32.71 1.63
118 119 9.312904 AGTGGGGTAATTTTCCATATTGATATG 57.687 33.333 4.37 4.37 39.80 1.78
131 132 7.451501 CATATTGATATGGTTGGTATGCACA 57.548 36.000 0.00 0.00 37.16 4.57
132 133 8.058667 CATATTGATATGGTTGGTATGCACAT 57.941 34.615 0.00 0.00 37.16 3.21
133 134 6.579666 ATTGATATGGTTGGTATGCACATC 57.420 37.500 0.00 0.00 0.00 3.06
134 135 4.397420 TGATATGGTTGGTATGCACATCC 58.603 43.478 0.00 0.00 0.00 3.51
135 136 2.071778 ATGGTTGGTATGCACATCCC 57.928 50.000 0.00 0.00 0.00 3.85
136 137 0.701147 TGGTTGGTATGCACATCCCA 59.299 50.000 0.00 0.00 0.00 4.37
137 138 1.102978 GGTTGGTATGCACATCCCAC 58.897 55.000 0.00 0.00 0.00 4.61
138 139 1.340991 GGTTGGTATGCACATCCCACT 60.341 52.381 0.00 0.00 0.00 4.00
139 140 2.092646 GGTTGGTATGCACATCCCACTA 60.093 50.000 0.00 0.00 0.00 2.74
140 141 3.616219 GTTGGTATGCACATCCCACTAA 58.384 45.455 0.00 0.00 0.00 2.24
141 142 3.558931 TGGTATGCACATCCCACTAAG 57.441 47.619 0.00 0.00 0.00 2.18
142 143 3.111484 TGGTATGCACATCCCACTAAGA 58.889 45.455 0.00 0.00 0.00 2.10
143 144 3.521531 TGGTATGCACATCCCACTAAGAA 59.478 43.478 0.00 0.00 0.00 2.52
144 145 4.018870 TGGTATGCACATCCCACTAAGAAA 60.019 41.667 0.00 0.00 0.00 2.52
145 146 4.335594 GGTATGCACATCCCACTAAGAAAC 59.664 45.833 0.00 0.00 0.00 2.78
146 147 3.500448 TGCACATCCCACTAAGAAACA 57.500 42.857 0.00 0.00 0.00 2.83
147 148 3.826524 TGCACATCCCACTAAGAAACAA 58.173 40.909 0.00 0.00 0.00 2.83
148 149 3.820467 TGCACATCCCACTAAGAAACAAG 59.180 43.478 0.00 0.00 0.00 3.16
149 150 3.191371 GCACATCCCACTAAGAAACAAGG 59.809 47.826 0.00 0.00 0.00 3.61
150 151 3.191371 CACATCCCACTAAGAAACAAGGC 59.809 47.826 0.00 0.00 0.00 4.35
151 152 2.178912 TCCCACTAAGAAACAAGGCG 57.821 50.000 0.00 0.00 0.00 5.52
152 153 0.521735 CCCACTAAGAAACAAGGCGC 59.478 55.000 0.00 0.00 0.00 6.53
153 154 1.234821 CCACTAAGAAACAAGGCGCA 58.765 50.000 10.83 0.00 0.00 6.09
154 155 1.606668 CCACTAAGAAACAAGGCGCAA 59.393 47.619 10.83 0.00 0.00 4.85
155 156 2.228822 CCACTAAGAAACAAGGCGCAAT 59.771 45.455 10.83 0.00 0.00 3.56
156 157 3.438781 CCACTAAGAAACAAGGCGCAATA 59.561 43.478 10.83 0.00 0.00 1.90
157 158 4.083003 CCACTAAGAAACAAGGCGCAATAA 60.083 41.667 10.83 0.00 0.00 1.40
158 159 5.457140 CACTAAGAAACAAGGCGCAATAAA 58.543 37.500 10.83 0.00 0.00 1.40
159 160 5.918011 CACTAAGAAACAAGGCGCAATAAAA 59.082 36.000 10.83 0.00 0.00 1.52
160 161 6.088085 CACTAAGAAACAAGGCGCAATAAAAG 59.912 38.462 10.83 0.00 0.00 2.27
161 162 3.317150 AGAAACAAGGCGCAATAAAAGC 58.683 40.909 10.83 0.00 0.00 3.51
162 163 3.005791 AGAAACAAGGCGCAATAAAAGCT 59.994 39.130 10.83 0.00 0.00 3.74
163 164 2.636768 ACAAGGCGCAATAAAAGCTC 57.363 45.000 10.83 0.00 0.00 4.09
164 165 1.885887 ACAAGGCGCAATAAAAGCTCA 59.114 42.857 10.83 0.00 0.00 4.26
165 166 2.493278 ACAAGGCGCAATAAAAGCTCAT 59.507 40.909 10.83 0.00 0.00 2.90
166 167 3.056607 ACAAGGCGCAATAAAAGCTCATT 60.057 39.130 10.83 0.00 0.00 2.57
167 168 3.874392 AGGCGCAATAAAAGCTCATTT 57.126 38.095 10.83 0.00 0.00 2.32
168 169 4.192429 AGGCGCAATAAAAGCTCATTTT 57.808 36.364 10.83 0.00 43.54 1.82
169 170 4.176271 AGGCGCAATAAAAGCTCATTTTC 58.824 39.130 10.83 0.00 41.40 2.29
170 171 3.306973 GGCGCAATAAAAGCTCATTTTCC 59.693 43.478 10.83 0.00 41.40 3.13
171 172 3.925913 GCGCAATAAAAGCTCATTTTCCA 59.074 39.130 0.30 0.00 41.40 3.53
172 173 4.567959 GCGCAATAAAAGCTCATTTTCCAT 59.432 37.500 0.30 0.00 41.40 3.41
173 174 5.063817 GCGCAATAAAAGCTCATTTTCCATT 59.936 36.000 0.30 0.00 41.40 3.16
174 175 6.699063 CGCAATAAAAGCTCATTTTCCATTC 58.301 36.000 0.00 0.00 41.40 2.67
175 176 6.532657 CGCAATAAAAGCTCATTTTCCATTCT 59.467 34.615 0.00 0.00 41.40 2.40
176 177 7.463648 CGCAATAAAAGCTCATTTTCCATTCTG 60.464 37.037 0.00 0.00 41.40 3.02
177 178 7.675637 GCAATAAAAGCTCATTTTCCATTCTGC 60.676 37.037 0.00 0.00 41.40 4.26
178 179 4.877378 AAAGCTCATTTTCCATTCTGCA 57.123 36.364 0.00 0.00 0.00 4.41
179 180 4.877378 AAGCTCATTTTCCATTCTGCAA 57.123 36.364 0.00 0.00 0.00 4.08
180 181 4.877378 AGCTCATTTTCCATTCTGCAAA 57.123 36.364 0.00 0.00 0.00 3.68
181 182 5.217978 AGCTCATTTTCCATTCTGCAAAA 57.782 34.783 0.00 0.00 0.00 2.44
182 183 5.235516 AGCTCATTTTCCATTCTGCAAAAG 58.764 37.500 0.00 0.00 0.00 2.27
183 184 4.992951 GCTCATTTTCCATTCTGCAAAAGT 59.007 37.500 0.00 0.00 0.00 2.66
184 185 5.467735 GCTCATTTTCCATTCTGCAAAAGTT 59.532 36.000 0.00 0.00 0.00 2.66
185 186 6.565247 GCTCATTTTCCATTCTGCAAAAGTTG 60.565 38.462 0.00 0.00 0.00 3.16
190 191 7.678947 TTTCCATTCTGCAAAAGTTGAAAAA 57.321 28.000 0.00 0.00 0.00 1.94
219 220 2.878580 TGCAAAGCACAAGTTCTGTTG 58.121 42.857 0.00 0.00 35.47 3.33
387 2560 7.377766 TGTCTTTAGGAATTTGCATCAGTAC 57.622 36.000 0.00 0.00 0.00 2.73
723 2981 4.122776 CCAGATGTTGCACATAGGAGTAC 58.877 47.826 11.47 0.00 39.27 2.73
738 2996 7.730784 ACATAGGAGTACTGTGGAGCTAATAAT 59.269 37.037 0.00 0.00 42.10 1.28
771 3029 6.987386 TCTGAGCTAGCCTACTATTTCAATC 58.013 40.000 12.13 0.00 0.00 2.67
810 3068 6.332630 ACAAATCTCAGTGTTTGTTTTCAGG 58.667 36.000 4.88 0.00 43.80 3.86
903 3214 1.989620 CCTCAAGCCTTGGCTCTCT 59.010 57.895 15.10 0.00 0.00 3.10
1095 3430 3.712016 TGCCAAGTAGCCAATTAGACA 57.288 42.857 0.00 0.00 0.00 3.41
1438 3827 4.808077 CAGGATGAGTATGTCAACATGC 57.192 45.455 5.89 4.57 39.69 4.06
1466 3855 2.972625 TGACGTTGGCCTTCTTCTATG 58.027 47.619 3.32 0.00 0.00 2.23
1548 3938 6.881065 TCTTGGATGGTTACTCATTTCTCTTG 59.119 38.462 0.00 0.00 0.00 3.02
1586 3977 6.601741 AAACAATTGCATTTTCGTTGATGT 57.398 29.167 5.05 0.00 0.00 3.06
1588 3979 5.531634 ACAATTGCATTTTCGTTGATGTCT 58.468 33.333 5.05 0.00 0.00 3.41
1751 4144 7.656412 TGCATTTTATGTGAGCTTAAACAGAA 58.344 30.769 0.00 0.00 0.00 3.02
1799 4192 7.298507 TCTTACCGTATGTATTTGCTCAAAC 57.701 36.000 0.00 0.00 32.51 2.93
1800 4193 6.874664 TCTTACCGTATGTATTTGCTCAAACA 59.125 34.615 0.00 0.00 32.51 2.83
1856 4252 7.666623 CAAGTACATGGTTTTAAATGGGACTT 58.333 34.615 0.00 0.00 35.85 3.01
2048 4454 4.312443 ACTATTTTCATCGACAACACGGT 58.688 39.130 0.00 0.00 0.00 4.83
2076 4482 1.078214 TCTCTGCTCCATTTGGCGG 60.078 57.895 0.00 0.00 36.28 6.13
2096 4502 2.351726 GGAACGCATAAGAAATCGCACT 59.648 45.455 0.00 0.00 0.00 4.40
2130 4536 1.065709 GGAAACGCCTCTATCACCCAA 60.066 52.381 0.00 0.00 0.00 4.12
2132 4538 0.252197 AACGCCTCTATCACCCAACC 59.748 55.000 0.00 0.00 0.00 3.77
2137 4543 2.196595 CCTCTATCACCCAACCAAGGA 58.803 52.381 0.00 0.00 0.00 3.36
2172 4578 2.862597 AGGAAGGGGATAGACAGTCTCT 59.137 50.000 6.27 0.00 0.00 3.10
2264 4681 5.905913 ACATATGGGCTATCCTAATACCTCC 59.094 44.000 7.80 0.00 36.20 4.30
2271 4688 5.273208 GCTATCCTAATACCTCCTGATCCA 58.727 45.833 0.00 0.00 0.00 3.41
2297 4714 9.719355 ATATATCTCCGTATATGCACAACAAAA 57.281 29.630 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.291664 CCACGTGAAAAACTTGTAGAAAAATTA 57.708 29.630 19.30 0.00 0.00 1.40
30 31 7.815549 ACCACGTGAAAAACTTGTAGAAAAATT 59.184 29.630 19.30 0.00 0.00 1.82
31 32 7.317390 ACCACGTGAAAAACTTGTAGAAAAAT 58.683 30.769 19.30 0.00 0.00 1.82
32 33 6.679843 ACCACGTGAAAAACTTGTAGAAAAA 58.320 32.000 19.30 0.00 0.00 1.94
33 34 6.256912 ACCACGTGAAAAACTTGTAGAAAA 57.743 33.333 19.30 0.00 0.00 2.29
34 35 5.883503 ACCACGTGAAAAACTTGTAGAAA 57.116 34.783 19.30 0.00 0.00 2.52
35 36 7.556733 AATACCACGTGAAAAACTTGTAGAA 57.443 32.000 19.30 0.00 0.00 2.10
36 37 7.556733 AAATACCACGTGAAAAACTTGTAGA 57.443 32.000 19.30 0.00 0.00 2.59
37 38 9.377383 CTAAAATACCACGTGAAAAACTTGTAG 57.623 33.333 19.30 6.60 0.00 2.74
38 39 8.344098 CCTAAAATACCACGTGAAAAACTTGTA 58.656 33.333 19.30 8.29 0.00 2.41
39 40 7.197703 CCTAAAATACCACGTGAAAAACTTGT 58.802 34.615 19.30 6.07 0.00 3.16
40 41 6.143278 GCCTAAAATACCACGTGAAAAACTTG 59.857 38.462 19.30 0.00 0.00 3.16
41 42 6.040054 AGCCTAAAATACCACGTGAAAAACTT 59.960 34.615 19.30 5.61 0.00 2.66
42 43 5.533528 AGCCTAAAATACCACGTGAAAAACT 59.466 36.000 19.30 0.00 0.00 2.66
43 44 5.765176 AGCCTAAAATACCACGTGAAAAAC 58.235 37.500 19.30 0.00 0.00 2.43
44 45 7.690952 ATAGCCTAAAATACCACGTGAAAAA 57.309 32.000 19.30 0.00 0.00 1.94
45 46 7.011669 GCTATAGCCTAAAATACCACGTGAAAA 59.988 37.037 19.30 1.55 34.31 2.29
46 47 6.480981 GCTATAGCCTAAAATACCACGTGAAA 59.519 38.462 19.30 4.48 34.31 2.69
47 48 5.987347 GCTATAGCCTAAAATACCACGTGAA 59.013 40.000 19.30 4.90 34.31 3.18
48 49 5.303589 AGCTATAGCCTAAAATACCACGTGA 59.696 40.000 21.17 0.00 43.38 4.35
49 50 5.539048 AGCTATAGCCTAAAATACCACGTG 58.461 41.667 21.17 9.08 43.38 4.49
50 51 5.803237 AGCTATAGCCTAAAATACCACGT 57.197 39.130 21.17 0.00 43.38 4.49
51 52 6.220930 TCAAGCTATAGCCTAAAATACCACG 58.779 40.000 21.17 0.00 43.38 4.94
52 53 8.622948 AATCAAGCTATAGCCTAAAATACCAC 57.377 34.615 21.17 0.00 43.38 4.16
53 54 9.066892 CAAATCAAGCTATAGCCTAAAATACCA 57.933 33.333 21.17 0.00 43.38 3.25
54 55 9.284968 TCAAATCAAGCTATAGCCTAAAATACC 57.715 33.333 21.17 0.00 43.38 2.73
56 57 9.845740 TGTCAAATCAAGCTATAGCCTAAAATA 57.154 29.630 21.17 0.90 43.38 1.40
57 58 8.624776 GTGTCAAATCAAGCTATAGCCTAAAAT 58.375 33.333 21.17 5.60 43.38 1.82
58 59 7.829211 AGTGTCAAATCAAGCTATAGCCTAAAA 59.171 33.333 21.17 3.41 43.38 1.52
59 60 7.338710 AGTGTCAAATCAAGCTATAGCCTAAA 58.661 34.615 21.17 5.21 43.38 1.85
60 61 6.889198 AGTGTCAAATCAAGCTATAGCCTAA 58.111 36.000 21.17 7.03 43.38 2.69
61 62 6.485830 AGTGTCAAATCAAGCTATAGCCTA 57.514 37.500 21.17 7.39 43.38 3.93
62 63 5.365021 AGTGTCAAATCAAGCTATAGCCT 57.635 39.130 21.17 5.42 43.38 4.58
63 64 6.090088 CGATAGTGTCAAATCAAGCTATAGCC 59.910 42.308 21.17 3.64 43.38 3.93
64 65 7.043454 CGATAGTGTCAAATCAAGCTATAGC 57.957 40.000 17.33 17.33 42.49 2.97
83 84 5.296035 GGAAAATTACCCCACTTCACGATAG 59.704 44.000 0.00 0.00 46.19 2.08
84 85 5.187687 GGAAAATTACCCCACTTCACGATA 58.812 41.667 0.00 0.00 0.00 2.92
85 86 4.014406 GGAAAATTACCCCACTTCACGAT 58.986 43.478 0.00 0.00 0.00 3.73
86 87 3.181442 TGGAAAATTACCCCACTTCACGA 60.181 43.478 0.00 0.00 0.00 4.35
87 88 3.150767 TGGAAAATTACCCCACTTCACG 58.849 45.455 0.00 0.00 0.00 4.35
88 89 7.123547 TCAATATGGAAAATTACCCCACTTCAC 59.876 37.037 0.00 0.00 32.07 3.18
89 90 7.185565 TCAATATGGAAAATTACCCCACTTCA 58.814 34.615 0.00 0.00 32.07 3.02
90 91 7.654022 TCAATATGGAAAATTACCCCACTTC 57.346 36.000 0.00 0.00 32.07 3.01
91 92 9.897040 ATATCAATATGGAAAATTACCCCACTT 57.103 29.630 0.00 0.00 32.07 3.16
92 93 9.312904 CATATCAATATGGAAAATTACCCCACT 57.687 33.333 2.60 0.00 37.16 4.00
107 108 7.451501 TGTGCATACCAACCATATCAATATG 57.548 36.000 0.00 3.45 39.80 1.78
108 109 7.340232 GGATGTGCATACCAACCATATCAATAT 59.660 37.037 0.00 0.00 31.30 1.28
109 110 6.658816 GGATGTGCATACCAACCATATCAATA 59.341 38.462 0.00 0.00 31.30 1.90
110 111 5.477984 GGATGTGCATACCAACCATATCAAT 59.522 40.000 0.00 0.00 31.30 2.57
111 112 4.826733 GGATGTGCATACCAACCATATCAA 59.173 41.667 0.00 0.00 31.30 2.57
112 113 4.397420 GGATGTGCATACCAACCATATCA 58.603 43.478 0.00 0.00 31.30 2.15
113 114 3.758554 GGGATGTGCATACCAACCATATC 59.241 47.826 8.50 0.00 41.64 1.63
114 115 3.766545 GGGATGTGCATACCAACCATAT 58.233 45.455 8.50 0.00 41.64 1.78
115 116 3.222173 GGGATGTGCATACCAACCATA 57.778 47.619 8.50 0.00 41.64 2.74
116 117 2.071778 GGGATGTGCATACCAACCAT 57.928 50.000 8.50 0.00 41.64 3.55
117 118 3.586843 GGGATGTGCATACCAACCA 57.413 52.632 8.50 0.00 41.64 3.67
122 123 3.838244 TCTTAGTGGGATGTGCATACC 57.162 47.619 6.48 6.48 42.39 2.73
123 124 4.941263 TGTTTCTTAGTGGGATGTGCATAC 59.059 41.667 0.00 0.00 0.00 2.39
124 125 5.172687 TGTTTCTTAGTGGGATGTGCATA 57.827 39.130 0.00 0.00 0.00 3.14
125 126 4.032960 TGTTTCTTAGTGGGATGTGCAT 57.967 40.909 0.00 0.00 0.00 3.96
126 127 3.500448 TGTTTCTTAGTGGGATGTGCA 57.500 42.857 0.00 0.00 0.00 4.57
127 128 3.191371 CCTTGTTTCTTAGTGGGATGTGC 59.809 47.826 0.00 0.00 0.00 4.57
128 129 3.191371 GCCTTGTTTCTTAGTGGGATGTG 59.809 47.826 0.00 0.00 0.00 3.21
129 130 3.421844 GCCTTGTTTCTTAGTGGGATGT 58.578 45.455 0.00 0.00 0.00 3.06
130 131 2.420022 CGCCTTGTTTCTTAGTGGGATG 59.580 50.000 0.00 0.00 0.00 3.51
131 132 2.711542 CGCCTTGTTTCTTAGTGGGAT 58.288 47.619 0.00 0.00 0.00 3.85
132 133 1.880646 GCGCCTTGTTTCTTAGTGGGA 60.881 52.381 0.00 0.00 0.00 4.37
133 134 0.521735 GCGCCTTGTTTCTTAGTGGG 59.478 55.000 0.00 0.00 0.00 4.61
134 135 1.234821 TGCGCCTTGTTTCTTAGTGG 58.765 50.000 4.18 0.00 0.00 4.00
135 136 3.559238 ATTGCGCCTTGTTTCTTAGTG 57.441 42.857 4.18 0.00 0.00 2.74
136 137 5.699097 TTTATTGCGCCTTGTTTCTTAGT 57.301 34.783 4.18 0.00 0.00 2.24
137 138 5.060940 GCTTTTATTGCGCCTTGTTTCTTAG 59.939 40.000 4.18 0.00 0.00 2.18
138 139 4.920927 GCTTTTATTGCGCCTTGTTTCTTA 59.079 37.500 4.18 0.00 0.00 2.10
139 140 3.740832 GCTTTTATTGCGCCTTGTTTCTT 59.259 39.130 4.18 0.00 0.00 2.52
140 141 3.005791 AGCTTTTATTGCGCCTTGTTTCT 59.994 39.130 4.18 0.00 35.28 2.52
141 142 3.317150 AGCTTTTATTGCGCCTTGTTTC 58.683 40.909 4.18 0.00 35.28 2.78
142 143 3.243704 TGAGCTTTTATTGCGCCTTGTTT 60.244 39.130 4.18 0.00 35.28 2.83
143 144 2.295909 TGAGCTTTTATTGCGCCTTGTT 59.704 40.909 4.18 0.00 35.28 2.83
144 145 1.885887 TGAGCTTTTATTGCGCCTTGT 59.114 42.857 4.18 0.00 35.28 3.16
145 146 2.634982 TGAGCTTTTATTGCGCCTTG 57.365 45.000 4.18 0.00 35.28 3.61
146 147 3.874392 AATGAGCTTTTATTGCGCCTT 57.126 38.095 4.18 0.00 35.28 4.35
147 148 3.874392 AAATGAGCTTTTATTGCGCCT 57.126 38.095 4.18 0.00 35.28 5.52
148 149 3.306973 GGAAAATGAGCTTTTATTGCGCC 59.693 43.478 4.18 0.00 37.18 6.53
149 150 3.925913 TGGAAAATGAGCTTTTATTGCGC 59.074 39.130 0.00 0.00 37.18 6.09
150 151 6.532657 AGAATGGAAAATGAGCTTTTATTGCG 59.467 34.615 0.00 0.00 37.18 4.85
151 152 7.675637 GCAGAATGGAAAATGAGCTTTTATTGC 60.676 37.037 0.00 0.00 35.05 3.56
152 153 7.332430 TGCAGAATGGAAAATGAGCTTTTATTG 59.668 33.333 0.00 0.00 35.05 1.90
153 154 7.388437 TGCAGAATGGAAAATGAGCTTTTATT 58.612 30.769 0.00 0.00 35.05 1.40
154 155 6.938507 TGCAGAATGGAAAATGAGCTTTTAT 58.061 32.000 0.00 0.00 35.05 1.40
155 156 6.343716 TGCAGAATGGAAAATGAGCTTTTA 57.656 33.333 0.00 0.00 35.05 1.52
156 157 5.217978 TGCAGAATGGAAAATGAGCTTTT 57.782 34.783 0.00 0.00 36.73 2.27
157 158 4.877378 TGCAGAATGGAAAATGAGCTTT 57.123 36.364 0.00 0.00 35.86 3.51
158 159 4.877378 TTGCAGAATGGAAAATGAGCTT 57.123 36.364 0.00 0.00 45.87 3.74
190 191 6.762661 AGAACTTGTGCTTTGCAAATACAATT 59.237 30.769 27.85 23.08 41.47 2.32
219 220 6.094881 TGACTGGCAATAAAAATAGTAGCCAC 59.905 38.462 0.00 0.00 44.89 5.01
242 243 7.979786 AGAGAAGGTTGAAGATATAGGTTGA 57.020 36.000 0.00 0.00 0.00 3.18
284 285 5.598417 AGTATTTTGAAGGCAACCAAGAACT 59.402 36.000 0.00 0.00 32.79 3.01
738 2996 7.366847 AGTAGGCTAGCTCAGATTCAAATAA 57.633 36.000 15.72 0.00 0.00 1.40
771 3029 8.571336 ACTGAGATTTGTAATTTTTGACCTCAG 58.429 33.333 0.00 0.00 45.38 3.35
810 3068 4.019771 AGGAGAAGGGAAGAAGATTGACAC 60.020 45.833 0.00 0.00 0.00 3.67
903 3214 7.994425 TGAAGACTGCATTTTCCAGTAAATA 57.006 32.000 0.00 0.00 43.17 1.40
1438 3827 0.535102 AGGCCAACGTCAAGGAACAG 60.535 55.000 5.01 0.00 0.00 3.16
1466 3855 4.142513 GGAGGAGAATTGCATGTGAACTTC 60.143 45.833 0.00 0.00 0.00 3.01
1527 3917 4.336713 GGCAAGAGAAATGAGTAACCATCC 59.663 45.833 0.00 0.00 0.00 3.51
1548 3938 5.665232 CAATTGTTTTGATACAACAACGGC 58.335 37.500 0.00 0.00 44.76 5.68
1586 3977 2.291209 TGAAAATGAGCCCAAGCAGA 57.709 45.000 0.00 0.00 43.56 4.26
1588 3979 1.619827 CCTTGAAAATGAGCCCAAGCA 59.380 47.619 0.00 0.00 43.56 3.91
1827 4223 7.033185 CCCATTTAAAACCATGTACTTGCTAC 58.967 38.462 3.24 0.00 0.00 3.58
1856 4252 0.173029 CATTGCGCTAAATGGCACCA 59.827 50.000 9.73 0.00 39.20 4.17
1970 4373 6.290605 TGTAGAAAGCCCGTATATTAAACCC 58.709 40.000 0.00 0.00 0.00 4.11
1982 4387 3.865745 CAGTACTCATTGTAGAAAGCCCG 59.134 47.826 0.00 0.00 0.00 6.13
2045 4451 1.359459 GCAGAGACCCGCTAAAACCG 61.359 60.000 0.00 0.00 0.00 4.44
2048 4454 0.249398 GGAGCAGAGACCCGCTAAAA 59.751 55.000 0.00 0.00 38.99 1.52
2076 4482 3.345714 CAGTGCGATTTCTTATGCGTTC 58.654 45.455 0.00 0.00 0.00 3.95
2081 4487 2.285220 CCGACCAGTGCGATTTCTTATG 59.715 50.000 0.00 0.00 0.00 1.90
2096 4502 2.809307 TTTCCTCAACCGCCGACCA 61.809 57.895 0.00 0.00 0.00 4.02
2122 4528 1.821666 CGGTTTCCTTGGTTGGGTGAT 60.822 52.381 0.00 0.00 0.00 3.06
2130 4536 3.570912 TTCTTTCTCGGTTTCCTTGGT 57.429 42.857 0.00 0.00 0.00 3.67
2132 4538 4.134563 TCCTTTCTTTCTCGGTTTCCTTG 58.865 43.478 0.00 0.00 0.00 3.61
2137 4543 3.487372 CCCTTCCTTTCTTTCTCGGTTT 58.513 45.455 0.00 0.00 0.00 3.27
2172 4578 3.800261 GCTGAATATGAAGCGGTCTAGCA 60.800 47.826 0.00 0.00 40.15 3.49
2264 4681 8.026026 GTGCATATACGGAGATATATGGATCAG 58.974 40.741 12.44 0.00 43.49 2.90
2271 4688 9.719355 TTTTGTTGTGCATATACGGAGATATAT 57.281 29.630 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.