Multiple sequence alignment - TraesCS2D01G163700

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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 TraesCS2D01G163700 chr2D 100.000 3051 0 0 1 3051 108312059 108315109 0.000000e+00 5635.0
1 TraesCS2D01G163700 chr2D 82.517 143 23 2 1234 1375 417625365 417625506 1.150000e-24 124.0
2 TraesCS2D01G163700 chr2D 88.608 79 9 0 1370 1448 417626499 417626577 2.500000e-16 97.1
3 TraesCS2D01G163700 chr2A 91.575 2896 126 53 205 3051 104449578 104452404 0.000000e+00 3888.0
4 TraesCS2D01G163700 chr2A 82.394 142 23 2 1234 1374 572487557 572487417 4.130000e-24 122.0
5 TraesCS2D01G163700 chr2B 93.622 2336 61 33 267 2571 158145614 158147892 0.000000e+00 3408.0
6 TraesCS2D01G163700 chr2B 87.619 420 41 6 2555 2968 158147934 158148348 7.650000e-131 477.0
7 TraesCS2D01G163700 chr2B 82.609 138 22 2 1239 1375 489849194 489849330 1.490000e-23 121.0
8 TraesCS2D01G163700 chr2B 97.143 35 1 0 236 270 158145559 158145593 3.290000e-05 60.2
9 TraesCS2D01G163700 chr5B 94.203 138 8 0 1238 1375 402751419 402751282 8.570000e-51 211.0
10 TraesCS2D01G163700 chr5B 90.000 80 4 4 1371 1448 266501783 266501860 1.940000e-17 100.0
11 TraesCS2D01G163700 chr5B 88.608 79 9 0 1370 1448 704916514 704916592 2.500000e-16 97.1
12 TraesCS2D01G163700 chr5B 93.750 48 2 1 2922 2968 541497474 541497521 1.520000e-08 71.3
13 TraesCS2D01G163700 chr5A 94.203 138 8 0 1238 1375 443742557 443742420 8.570000e-51 211.0
14 TraesCS2D01G163700 chr5A 85.507 138 20 0 997 1134 316085017 316085154 8.820000e-31 145.0
15 TraesCS2D01G163700 chr5A 88.608 79 9 0 1370 1448 316085399 316085477 2.500000e-16 97.1
16 TraesCS2D01G163700 chr5D 93.478 138 9 0 1238 1375 342712890 342712753 3.990000e-49 206.0
17 TraesCS2D01G163700 chr5D 85.926 135 19 0 1000 1134 238557792 238557658 8.820000e-31 145.0
18 TraesCS2D01G163700 chr5D 90.909 77 3 4 1374 1448 238557411 238557337 1.940000e-17 100.0
19 TraesCS2D01G163700 chr5D 97.619 42 1 0 2928 2969 526559562 526559603 4.220000e-09 73.1
20 TraesCS2D01G163700 chr5D 93.617 47 1 2 2923 2969 452219391 452219435 5.460000e-08 69.4
21 TraesCS2D01G163700 chr4D 91.150 113 10 0 1001 1113 107710734 107710622 1.460000e-33 154.0
22 TraesCS2D01G163700 chr4D 86.667 90 7 5 1374 1461 107710356 107710270 9.010000e-16 95.3
23 TraesCS2D01G163700 chr4B 91.150 113 10 0 1001 1113 168984879 168984991 1.460000e-33 154.0
24 TraesCS2D01G163700 chr4B 86.022 93 8 5 1371 1461 168985244 168985333 9.010000e-16 95.3
25 TraesCS2D01G163700 chr4B 92.000 50 2 2 2921 2969 620266913 620266961 5.460000e-08 69.4
26 TraesCS2D01G163700 chr4A 91.150 113 10 0 1001 1113 468603250 468603362 1.460000e-33 154.0
27 TraesCS2D01G163700 chr7A 97.674 43 1 0 2924 2966 325734256 325734298 1.170000e-09 75.0
28 TraesCS2D01G163700 chr6A 97.619 42 1 0 2928 2969 226275662 226275703 4.220000e-09 73.1
29 TraesCS2D01G163700 chr7D 92.000 50 3 1 2921 2969 544559089 544559138 5.460000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G163700 chr2D 108312059 108315109 3050 False 5635.000000 5635 100.000000 1 3051 1 chr2D.!!$F1 3050
1 TraesCS2D01G163700 chr2A 104449578 104452404 2826 False 3888.000000 3888 91.575000 205 3051 1 chr2A.!!$F1 2846
2 TraesCS2D01G163700 chr2B 158145559 158148348 2789 False 1315.066667 3408 92.794667 236 2968 3 chr2B.!!$F2 2732

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
53 54 0.035458 CAGACGAACCCTTTGGAGCT 59.965 55.0 0.0 0.0 34.81 4.09 F
54 55 0.035458 AGACGAACCCTTTGGAGCTG 59.965 55.0 0.0 0.0 34.81 4.24 F
1192 1268 0.040425 CCGGTTCTTGCCTTCGTTTG 60.040 55.0 0.0 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1196 1272 2.086869 CCACAAAGAACCATGCGATCT 58.913 47.619 0.0 0.0 0.00 2.75 R
1501 1578 2.285668 CCCTTGGAGGAGGAGGCA 60.286 66.667 0.0 0.0 37.67 4.75 R
2098 2178 0.179137 CTCCTCGCATCAGTAACGCA 60.179 55.000 0.0 0.0 0.00 5.24 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 2.437180 CTCTCGCCTGGCATGCAA 60.437 61.111 21.36 7.49 0.00 4.08
19 20 1.822613 CTCTCGCCTGGCATGCAAT 60.823 57.895 21.36 0.00 0.00 3.56
44 45 1.430632 CATGCATGCAGACGAACCC 59.569 57.895 26.69 0.00 0.00 4.11
45 46 1.028330 CATGCATGCAGACGAACCCT 61.028 55.000 26.69 2.26 0.00 4.34
46 47 0.322816 ATGCATGCAGACGAACCCTT 60.323 50.000 26.69 1.43 0.00 3.95
47 48 0.537143 TGCATGCAGACGAACCCTTT 60.537 50.000 18.46 0.00 0.00 3.11
48 49 0.109597 GCATGCAGACGAACCCTTTG 60.110 55.000 14.21 0.00 0.00 2.77
49 50 0.523072 CATGCAGACGAACCCTTTGG 59.477 55.000 0.00 0.00 37.80 3.28
50 51 0.400213 ATGCAGACGAACCCTTTGGA 59.600 50.000 0.00 0.00 34.81 3.53
51 52 0.250295 TGCAGACGAACCCTTTGGAG 60.250 55.000 0.00 0.00 34.81 3.86
52 53 1.578206 GCAGACGAACCCTTTGGAGC 61.578 60.000 0.00 0.00 34.81 4.70
53 54 0.035458 CAGACGAACCCTTTGGAGCT 59.965 55.000 0.00 0.00 34.81 4.09
54 55 0.035458 AGACGAACCCTTTGGAGCTG 59.965 55.000 0.00 0.00 34.81 4.24
55 56 0.955919 GACGAACCCTTTGGAGCTGG 60.956 60.000 0.00 0.00 34.81 4.85
56 57 1.374947 CGAACCCTTTGGAGCTGGA 59.625 57.895 0.00 0.00 34.81 3.86
57 58 0.674895 CGAACCCTTTGGAGCTGGAG 60.675 60.000 0.00 0.00 34.81 3.86
58 59 0.322906 GAACCCTTTGGAGCTGGAGG 60.323 60.000 0.00 0.00 34.81 4.30
59 60 0.772124 AACCCTTTGGAGCTGGAGGA 60.772 55.000 0.00 0.00 34.81 3.71
60 61 1.204113 ACCCTTTGGAGCTGGAGGAG 61.204 60.000 0.00 0.00 34.81 3.69
61 62 1.606531 CCTTTGGAGCTGGAGGAGG 59.393 63.158 0.00 0.00 0.00 4.30
62 63 1.204113 CCTTTGGAGCTGGAGGAGGT 61.204 60.000 0.00 0.00 34.09 3.85
63 64 0.695347 CTTTGGAGCTGGAGGAGGTT 59.305 55.000 0.00 0.00 30.42 3.50
64 65 1.074566 CTTTGGAGCTGGAGGAGGTTT 59.925 52.381 0.00 0.00 30.42 3.27
65 66 0.401738 TTGGAGCTGGAGGAGGTTTG 59.598 55.000 0.00 0.00 30.42 2.93
66 67 1.377856 GGAGCTGGAGGAGGTTTGC 60.378 63.158 0.00 0.00 30.42 3.68
67 68 1.743252 GAGCTGGAGGAGGTTTGCG 60.743 63.158 0.00 0.00 30.42 4.85
68 69 2.032681 GCTGGAGGAGGTTTGCGT 59.967 61.111 0.00 0.00 0.00 5.24
69 70 1.600916 GCTGGAGGAGGTTTGCGTT 60.601 57.895 0.00 0.00 0.00 4.84
70 71 1.856265 GCTGGAGGAGGTTTGCGTTG 61.856 60.000 0.00 0.00 0.00 4.10
71 72 1.856265 CTGGAGGAGGTTTGCGTTGC 61.856 60.000 0.00 0.00 0.00 4.17
72 73 2.556287 GAGGAGGTTTGCGTTGCG 59.444 61.111 0.00 0.00 0.00 4.85
73 74 1.959226 GAGGAGGTTTGCGTTGCGA 60.959 57.895 0.00 0.00 0.00 5.10
74 75 2.171489 GAGGAGGTTTGCGTTGCGAC 62.171 60.000 0.00 0.00 0.00 5.19
75 76 2.539338 GGAGGTTTGCGTTGCGACA 61.539 57.895 4.64 0.00 0.00 4.35
76 77 1.353804 GAGGTTTGCGTTGCGACAA 59.646 52.632 4.64 0.00 0.00 3.18
77 78 0.248296 GAGGTTTGCGTTGCGACAAA 60.248 50.000 4.64 0.00 33.42 2.83
78 79 0.524604 AGGTTTGCGTTGCGACAAAC 60.525 50.000 21.22 21.22 44.40 2.93
79 80 0.798771 GGTTTGCGTTGCGACAAACA 60.799 50.000 25.76 5.25 45.53 2.83
80 81 1.196200 GTTTGCGTTGCGACAAACAT 58.804 45.000 22.82 0.00 44.46 2.71
81 82 1.072219 GTTTGCGTTGCGACAAACATG 60.072 47.619 22.82 0.00 44.46 3.21
82 83 1.205485 TTGCGTTGCGACAAACATGC 61.205 50.000 4.64 0.00 0.00 4.06
83 84 1.370414 GCGTTGCGACAAACATGCT 60.370 52.632 4.64 0.00 0.00 3.79
84 85 0.934436 GCGTTGCGACAAACATGCTT 60.934 50.000 4.64 0.00 0.00 3.91
85 86 1.661743 GCGTTGCGACAAACATGCTTA 60.662 47.619 4.64 0.00 0.00 3.09
86 87 2.233355 CGTTGCGACAAACATGCTTAG 58.767 47.619 4.64 0.00 0.00 2.18
87 88 1.978782 GTTGCGACAAACATGCTTAGC 59.021 47.619 0.00 0.00 0.00 3.09
88 89 1.233919 TGCGACAAACATGCTTAGCA 58.766 45.000 10.09 10.09 44.86 3.49
89 90 1.069296 TGCGACAAACATGCTTAGCAC 60.069 47.619 9.82 0.00 43.04 4.40
90 91 1.069296 GCGACAAACATGCTTAGCACA 60.069 47.619 9.82 0.00 43.04 4.57
91 92 2.574322 CGACAAACATGCTTAGCACAC 58.426 47.619 9.82 0.00 43.04 3.82
92 93 2.574322 GACAAACATGCTTAGCACACG 58.426 47.619 9.82 3.66 43.04 4.49
93 94 1.330306 CAAACATGCTTAGCACACGC 58.670 50.000 9.82 0.00 43.04 5.34
94 95 0.110238 AAACATGCTTAGCACACGCG 60.110 50.000 9.82 3.53 43.04 6.01
95 96 2.276868 CATGCTTAGCACACGCGC 60.277 61.111 9.82 0.00 43.04 6.86
96 97 3.499737 ATGCTTAGCACACGCGCC 61.500 61.111 9.82 0.00 43.04 6.53
109 110 4.038080 GCGCCGGGTTGGACTTTG 62.038 66.667 2.18 0.00 42.00 2.77
110 111 3.361977 CGCCGGGTTGGACTTTGG 61.362 66.667 2.18 0.00 42.00 3.28
111 112 3.680786 GCCGGGTTGGACTTTGGC 61.681 66.667 2.18 0.00 42.00 4.52
112 113 2.989253 CCGGGTTGGACTTTGGCC 60.989 66.667 0.00 0.00 42.00 5.36
113 114 3.361977 CGGGTTGGACTTTGGCCG 61.362 66.667 0.00 0.00 0.00 6.13
114 115 2.203437 GGGTTGGACTTTGGCCGT 60.203 61.111 0.00 0.00 0.00 5.68
115 116 2.561037 GGGTTGGACTTTGGCCGTG 61.561 63.158 0.00 0.00 0.00 4.94
116 117 2.561037 GGTTGGACTTTGGCCGTGG 61.561 63.158 0.00 0.00 0.00 4.94
117 118 2.909965 TTGGACTTTGGCCGTGGC 60.910 61.111 1.16 1.16 41.06 5.01
118 119 3.429372 TTGGACTTTGGCCGTGGCT 62.429 57.895 11.25 0.00 41.60 4.75
119 120 3.056328 GGACTTTGGCCGTGGCTC 61.056 66.667 11.25 0.00 41.60 4.70
120 121 3.423154 GACTTTGGCCGTGGCTCG 61.423 66.667 11.25 1.28 41.60 5.03
121 122 4.250305 ACTTTGGCCGTGGCTCGT 62.250 61.111 11.25 0.37 41.60 4.18
122 123 3.726517 CTTTGGCCGTGGCTCGTG 61.727 66.667 11.25 1.04 41.60 4.35
131 132 2.904866 TGGCTCGTGGCACCAAAC 60.905 61.111 12.86 0.99 44.10 2.93
132 133 2.594592 GGCTCGTGGCACCAAACT 60.595 61.111 12.86 0.00 44.01 2.66
133 134 1.302192 GGCTCGTGGCACCAAACTA 60.302 57.895 12.86 0.00 44.01 2.24
134 135 0.676782 GGCTCGTGGCACCAAACTAT 60.677 55.000 12.86 0.00 44.01 2.12
135 136 1.165270 GCTCGTGGCACCAAACTATT 58.835 50.000 12.86 0.00 41.35 1.73
136 137 1.539827 GCTCGTGGCACCAAACTATTT 59.460 47.619 12.86 0.00 41.35 1.40
137 138 2.414161 GCTCGTGGCACCAAACTATTTC 60.414 50.000 12.86 0.00 41.35 2.17
138 139 3.074412 CTCGTGGCACCAAACTATTTCT 58.926 45.455 12.86 0.00 0.00 2.52
139 140 3.482436 TCGTGGCACCAAACTATTTCTT 58.518 40.909 12.86 0.00 0.00 2.52
140 141 3.886505 TCGTGGCACCAAACTATTTCTTT 59.113 39.130 12.86 0.00 0.00 2.52
141 142 4.339814 TCGTGGCACCAAACTATTTCTTTT 59.660 37.500 12.86 0.00 0.00 2.27
142 143 5.047188 CGTGGCACCAAACTATTTCTTTTT 58.953 37.500 12.86 0.00 0.00 1.94
158 159 3.858886 TTTTTGAGGGATGGCACCA 57.141 47.368 8.11 0.00 0.00 4.17
159 160 2.094100 TTTTTGAGGGATGGCACCAA 57.906 45.000 8.11 0.00 0.00 3.67
160 161 2.094100 TTTTGAGGGATGGCACCAAA 57.906 45.000 8.11 3.48 0.00 3.28
161 162 1.337118 TTTGAGGGATGGCACCAAAC 58.663 50.000 8.11 0.00 0.00 2.93
162 163 0.482446 TTGAGGGATGGCACCAAACT 59.518 50.000 8.11 0.00 0.00 2.66
163 164 1.367346 TGAGGGATGGCACCAAACTA 58.633 50.000 8.11 0.00 0.00 2.24
164 165 1.922447 TGAGGGATGGCACCAAACTAT 59.078 47.619 8.11 0.00 0.00 2.12
165 166 2.311542 TGAGGGATGGCACCAAACTATT 59.688 45.455 8.11 0.00 0.00 1.73
166 167 3.525609 TGAGGGATGGCACCAAACTATTA 59.474 43.478 8.11 0.00 0.00 0.98
167 168 4.167892 TGAGGGATGGCACCAAACTATTAT 59.832 41.667 8.11 0.00 0.00 1.28
168 169 5.371176 TGAGGGATGGCACCAAACTATTATA 59.629 40.000 8.11 0.00 0.00 0.98
169 170 6.126332 TGAGGGATGGCACCAAACTATTATAA 60.126 38.462 8.11 0.00 0.00 0.98
170 171 6.068670 AGGGATGGCACCAAACTATTATAAC 58.931 40.000 8.11 0.00 0.00 1.89
171 172 5.048991 GGGATGGCACCAAACTATTATAACG 60.049 44.000 8.11 0.00 0.00 3.18
172 173 5.529800 GGATGGCACCAAACTATTATAACGT 59.470 40.000 0.00 0.00 0.00 3.99
173 174 5.804692 TGGCACCAAACTATTATAACGTG 57.195 39.130 0.00 0.00 0.00 4.49
174 175 4.095185 TGGCACCAAACTATTATAACGTGC 59.905 41.667 0.00 0.00 43.49 5.34
175 176 4.095185 GGCACCAAACTATTATAACGTGCA 59.905 41.667 10.58 0.00 45.45 4.57
176 177 5.263185 GCACCAAACTATTATAACGTGCAG 58.737 41.667 0.00 0.00 43.64 4.41
177 178 5.163794 GCACCAAACTATTATAACGTGCAGT 60.164 40.000 0.00 0.00 43.64 4.40
178 179 6.247903 CACCAAACTATTATAACGTGCAGTG 58.752 40.000 0.00 0.00 0.00 3.66
179 180 5.935789 ACCAAACTATTATAACGTGCAGTGT 59.064 36.000 0.00 0.00 0.00 3.55
180 181 6.128391 ACCAAACTATTATAACGTGCAGTGTG 60.128 38.462 0.00 0.00 0.00 3.82
181 182 6.091577 CCAAACTATTATAACGTGCAGTGTGA 59.908 38.462 0.00 0.00 0.00 3.58
182 183 7.201609 CCAAACTATTATAACGTGCAGTGTGAT 60.202 37.037 0.00 0.00 0.00 3.06
183 184 7.843490 AACTATTATAACGTGCAGTGTGATT 57.157 32.000 0.00 0.00 0.00 2.57
184 185 7.234187 ACTATTATAACGTGCAGTGTGATTG 57.766 36.000 0.00 0.00 0.00 2.67
185 186 6.816640 ACTATTATAACGTGCAGTGTGATTGT 59.183 34.615 0.00 0.00 0.00 2.71
186 187 5.933187 TTATAACGTGCAGTGTGATTGTT 57.067 34.783 0.00 0.00 0.00 2.83
187 188 4.829064 ATAACGTGCAGTGTGATTGTTT 57.171 36.364 0.00 0.00 0.00 2.83
188 189 3.502191 AACGTGCAGTGTGATTGTTTT 57.498 38.095 0.00 0.00 0.00 2.43
189 190 3.065019 ACGTGCAGTGTGATTGTTTTC 57.935 42.857 0.00 0.00 0.00 2.29
190 191 2.036217 CGTGCAGTGTGATTGTTTTCG 58.964 47.619 0.00 0.00 0.00 3.46
191 192 2.384382 GTGCAGTGTGATTGTTTTCGG 58.616 47.619 0.00 0.00 0.00 4.30
192 193 2.032799 GTGCAGTGTGATTGTTTTCGGA 59.967 45.455 0.00 0.00 0.00 4.55
193 194 2.884012 TGCAGTGTGATTGTTTTCGGAT 59.116 40.909 0.00 0.00 0.00 4.18
194 195 3.317711 TGCAGTGTGATTGTTTTCGGATT 59.682 39.130 0.00 0.00 0.00 3.01
195 196 4.202101 TGCAGTGTGATTGTTTTCGGATTT 60.202 37.500 0.00 0.00 0.00 2.17
196 197 4.744631 GCAGTGTGATTGTTTTCGGATTTT 59.255 37.500 0.00 0.00 0.00 1.82
197 198 5.234116 GCAGTGTGATTGTTTTCGGATTTTT 59.766 36.000 0.00 0.00 0.00 1.94
449 483 1.305297 CTGGCCCCTTTCCCTTTCC 60.305 63.158 0.00 0.00 0.00 3.13
469 503 3.108289 CTGTCTCTGCACGCACCG 61.108 66.667 0.00 0.00 0.00 4.94
520 559 0.914644 CCTCAAGGAAGGAGCCATGA 59.085 55.000 0.00 0.00 38.87 3.07
522 561 0.620556 TCAAGGAAGGAGCCATGACC 59.379 55.000 0.00 0.00 31.26 4.02
1192 1268 0.040425 CCGGTTCTTGCCTTCGTTTG 60.040 55.000 0.00 0.00 0.00 2.93
1193 1269 0.661020 CGGTTCTTGCCTTCGTTTGT 59.339 50.000 0.00 0.00 0.00 2.83
1194 1270 1.868498 CGGTTCTTGCCTTCGTTTGTA 59.132 47.619 0.00 0.00 0.00 2.41
1195 1271 2.349155 CGGTTCTTGCCTTCGTTTGTAC 60.349 50.000 0.00 0.00 0.00 2.90
1196 1272 2.614983 GGTTCTTGCCTTCGTTTGTACA 59.385 45.455 0.00 0.00 0.00 2.90
1209 1286 3.483574 CGTTTGTACAGATCGCATGGTTC 60.484 47.826 0.00 0.00 0.00 3.62
1297 1374 3.246112 ACCAACTACCTGCGCCCA 61.246 61.111 4.18 0.00 0.00 5.36
2074 2154 1.086696 CTCCACCGTGCCAAGTTATG 58.913 55.000 0.00 0.00 0.00 1.90
2097 2177 1.404843 GTCGATGTTCCCCTAGCTCT 58.595 55.000 0.00 0.00 0.00 4.09
2098 2178 1.757699 GTCGATGTTCCCCTAGCTCTT 59.242 52.381 0.00 0.00 0.00 2.85
2111 2191 1.363744 AGCTCTTGCGTTACTGATGC 58.636 50.000 0.00 0.00 45.42 3.91
2208 2288 2.005451 CAATCAGCTTCCTTGGTCTCG 58.995 52.381 0.00 0.00 0.00 4.04
2268 2350 1.351350 GAAGGGAGGTTGTGGTAGCTT 59.649 52.381 0.00 0.00 0.00 3.74
2312 2394 5.577164 GCTGTAACTGTGACTTGGTACTATG 59.423 44.000 0.00 0.00 0.00 2.23
2313 2395 6.659745 TGTAACTGTGACTTGGTACTATGT 57.340 37.500 0.00 0.00 0.00 2.29
2314 2396 7.058023 TGTAACTGTGACTTGGTACTATGTT 57.942 36.000 0.00 0.00 0.00 2.71
2315 2397 8.180706 TGTAACTGTGACTTGGTACTATGTTA 57.819 34.615 0.00 0.00 0.00 2.41
2316 2398 8.809066 TGTAACTGTGACTTGGTACTATGTTAT 58.191 33.333 0.00 0.00 0.00 1.89
2451 2536 8.898761 CACTAATTAACCAGTATGCCAAATACA 58.101 33.333 0.00 0.00 31.97 2.29
2473 2558 6.821031 CAGGTACCTGTCATATACTCCTAC 57.179 45.833 30.57 0.00 39.10 3.18
2474 2559 6.544650 CAGGTACCTGTCATATACTCCTACT 58.455 44.000 30.57 0.00 39.10 2.57
2475 2560 7.687388 CAGGTACCTGTCATATACTCCTACTA 58.313 42.308 30.57 0.00 39.10 1.82
2476 2561 8.330247 CAGGTACCTGTCATATACTCCTACTAT 58.670 40.741 30.57 0.00 39.10 2.12
2477 2562 9.571823 AGGTACCTGTCATATACTCCTACTATA 57.428 37.037 15.42 0.00 0.00 1.31
2521 2606 7.406104 AGTAGGTTGATTAATCTTTGGAGCTT 58.594 34.615 16.24 0.00 0.00 3.74
2542 2627 5.858581 GCTTTTTCATGGTCAGTATGTCAAC 59.141 40.000 0.00 0.00 37.40 3.18
2645 2788 9.113838 AGTTATGCCAGTAAGTTGATTAATCAG 57.886 33.333 17.28 5.62 38.19 2.90
2674 2818 7.532199 TCTGACTTTAAGGGGGAAATAGTTTT 58.468 34.615 0.00 0.00 0.00 2.43
2756 2906 2.723273 GATTTGTCCCTCGGGTGATTT 58.277 47.619 1.18 0.00 36.47 2.17
2758 2908 0.768622 TTGTCCCTCGGGTGATTTGT 59.231 50.000 1.18 0.00 36.47 2.83
2763 2913 1.026718 CCTCGGGTGATTTGTGGAGC 61.027 60.000 0.00 0.00 0.00 4.70
2785 2935 5.954150 AGCTGGTACCAATTGATCAAATCTT 59.046 36.000 17.11 0.00 0.00 2.40
2802 2952 7.725251 TCAAATCTTAAATTTGACTTGGTGCT 58.275 30.769 15.67 0.00 41.46 4.40
2853 3003 7.358931 CGTCTAAAGCTGTTCAAGATTTCGTAA 60.359 37.037 0.00 0.00 40.47 3.18
3031 3183 9.436957 ACATTGACCATAAAGTAGTTAACTCTG 57.563 33.333 12.39 1.91 37.50 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.822613 ATTGCATGCCAGGCGAGAG 60.823 57.895 16.68 0.00 0.00 3.20
2 3 2.116533 CATTGCATGCCAGGCGAGA 61.117 57.895 16.68 0.00 0.00 4.04
3 4 2.411701 CATTGCATGCCAGGCGAG 59.588 61.111 16.68 2.33 0.00 5.03
26 27 1.028330 AGGGTTCGTCTGCATGCATG 61.028 55.000 22.97 22.70 0.00 4.06
27 28 0.322816 AAGGGTTCGTCTGCATGCAT 60.323 50.000 22.97 0.00 0.00 3.96
28 29 0.537143 AAAGGGTTCGTCTGCATGCA 60.537 50.000 21.29 21.29 0.00 3.96
29 30 0.109597 CAAAGGGTTCGTCTGCATGC 60.110 55.000 11.82 11.82 0.00 4.06
30 31 0.523072 CCAAAGGGTTCGTCTGCATG 59.477 55.000 0.00 0.00 0.00 4.06
31 32 0.400213 TCCAAAGGGTTCGTCTGCAT 59.600 50.000 0.00 0.00 34.93 3.96
32 33 0.250295 CTCCAAAGGGTTCGTCTGCA 60.250 55.000 0.00 0.00 34.93 4.41
33 34 1.578206 GCTCCAAAGGGTTCGTCTGC 61.578 60.000 0.00 0.00 34.93 4.26
34 35 0.035458 AGCTCCAAAGGGTTCGTCTG 59.965 55.000 0.00 0.00 34.93 3.51
35 36 0.035458 CAGCTCCAAAGGGTTCGTCT 59.965 55.000 0.00 0.00 34.93 4.18
36 37 0.955919 CCAGCTCCAAAGGGTTCGTC 60.956 60.000 0.00 0.00 34.93 4.20
37 38 1.073199 CCAGCTCCAAAGGGTTCGT 59.927 57.895 0.00 0.00 34.93 3.85
38 39 0.674895 CTCCAGCTCCAAAGGGTTCG 60.675 60.000 0.00 0.00 34.93 3.95
39 40 0.322906 CCTCCAGCTCCAAAGGGTTC 60.323 60.000 0.00 0.00 34.93 3.62
40 41 0.772124 TCCTCCAGCTCCAAAGGGTT 60.772 55.000 0.00 0.00 34.93 4.11
41 42 1.151810 TCCTCCAGCTCCAAAGGGT 60.152 57.895 0.00 0.00 34.93 4.34
42 43 1.606531 CTCCTCCAGCTCCAAAGGG 59.393 63.158 0.00 0.00 0.00 3.95
43 44 1.204113 ACCTCCTCCAGCTCCAAAGG 61.204 60.000 0.00 0.00 0.00 3.11
44 45 0.695347 AACCTCCTCCAGCTCCAAAG 59.305 55.000 0.00 0.00 0.00 2.77
45 46 1.149101 AAACCTCCTCCAGCTCCAAA 58.851 50.000 0.00 0.00 0.00 3.28
46 47 0.401738 CAAACCTCCTCCAGCTCCAA 59.598 55.000 0.00 0.00 0.00 3.53
47 48 2.069776 CAAACCTCCTCCAGCTCCA 58.930 57.895 0.00 0.00 0.00 3.86
48 49 1.377856 GCAAACCTCCTCCAGCTCC 60.378 63.158 0.00 0.00 0.00 4.70
49 50 1.743252 CGCAAACCTCCTCCAGCTC 60.743 63.158 0.00 0.00 0.00 4.09
50 51 2.056906 AACGCAAACCTCCTCCAGCT 62.057 55.000 0.00 0.00 0.00 4.24
51 52 1.600916 AACGCAAACCTCCTCCAGC 60.601 57.895 0.00 0.00 0.00 4.85
52 53 1.856265 GCAACGCAAACCTCCTCCAG 61.856 60.000 0.00 0.00 0.00 3.86
53 54 1.896660 GCAACGCAAACCTCCTCCA 60.897 57.895 0.00 0.00 0.00 3.86
54 55 2.954611 GCAACGCAAACCTCCTCC 59.045 61.111 0.00 0.00 0.00 4.30
55 56 1.959226 TCGCAACGCAAACCTCCTC 60.959 57.895 0.00 0.00 0.00 3.71
56 57 2.110213 TCGCAACGCAAACCTCCT 59.890 55.556 0.00 0.00 0.00 3.69
57 58 2.054140 TTGTCGCAACGCAAACCTCC 62.054 55.000 0.00 0.00 0.00 4.30
58 59 0.248296 TTTGTCGCAACGCAAACCTC 60.248 50.000 5.80 0.00 31.95 3.85
59 60 0.524604 GTTTGTCGCAACGCAAACCT 60.525 50.000 19.62 0.00 42.14 3.50
60 61 0.798771 TGTTTGTCGCAACGCAAACC 60.799 50.000 23.63 13.90 44.46 3.27
61 62 1.072219 CATGTTTGTCGCAACGCAAAC 60.072 47.619 21.68 21.68 44.84 2.93
62 63 1.195347 CATGTTTGTCGCAACGCAAA 58.805 45.000 5.80 5.80 33.42 3.68
63 64 1.205485 GCATGTTTGTCGCAACGCAA 61.205 50.000 0.00 0.00 0.00 4.85
64 65 1.656875 GCATGTTTGTCGCAACGCA 60.657 52.632 0.00 0.00 0.00 5.24
65 66 0.934436 AAGCATGTTTGTCGCAACGC 60.934 50.000 0.00 0.00 0.00 4.84
66 67 2.233355 CTAAGCATGTTTGTCGCAACG 58.767 47.619 4.89 0.00 0.00 4.10
67 68 1.978782 GCTAAGCATGTTTGTCGCAAC 59.021 47.619 4.89 0.00 0.00 4.17
68 69 1.606189 TGCTAAGCATGTTTGTCGCAA 59.394 42.857 4.89 0.00 31.71 4.85
69 70 1.069296 GTGCTAAGCATGTTTGTCGCA 60.069 47.619 4.89 8.11 41.91 5.10
70 71 1.069296 TGTGCTAAGCATGTTTGTCGC 60.069 47.619 4.89 5.71 41.91 5.19
71 72 2.574322 GTGTGCTAAGCATGTTTGTCG 58.426 47.619 4.89 0.00 41.91 4.35
72 73 2.574322 CGTGTGCTAAGCATGTTTGTC 58.426 47.619 4.89 0.00 41.91 3.18
73 74 1.334960 GCGTGTGCTAAGCATGTTTGT 60.335 47.619 4.89 0.00 41.91 2.83
74 75 1.330306 GCGTGTGCTAAGCATGTTTG 58.670 50.000 4.89 0.00 41.91 2.93
75 76 0.110238 CGCGTGTGCTAAGCATGTTT 60.110 50.000 0.00 0.00 41.91 2.83
76 77 1.497278 CGCGTGTGCTAAGCATGTT 59.503 52.632 0.00 0.00 41.91 2.71
77 78 3.027170 GCGCGTGTGCTAAGCATGT 62.027 57.895 8.43 0.00 41.91 3.21
78 79 2.276868 GCGCGTGTGCTAAGCATG 60.277 61.111 8.43 0.00 41.91 4.06
79 80 3.499737 GGCGCGTGTGCTAAGCAT 61.500 61.111 8.43 0.00 41.91 3.79
92 93 4.038080 CAAAGTCCAACCCGGCGC 62.038 66.667 0.00 0.00 33.14 6.53
93 94 3.361977 CCAAAGTCCAACCCGGCG 61.362 66.667 0.00 0.00 33.14 6.46
94 95 3.680786 GCCAAAGTCCAACCCGGC 61.681 66.667 0.00 0.00 33.14 6.13
95 96 2.989253 GGCCAAAGTCCAACCCGG 60.989 66.667 0.00 0.00 0.00 5.73
96 97 3.361977 CGGCCAAAGTCCAACCCG 61.362 66.667 2.24 0.00 0.00 5.28
97 98 2.203437 ACGGCCAAAGTCCAACCC 60.203 61.111 2.24 0.00 0.00 4.11
98 99 2.561037 CCACGGCCAAAGTCCAACC 61.561 63.158 2.24 0.00 0.00 3.77
99 100 3.039134 CCACGGCCAAAGTCCAAC 58.961 61.111 2.24 0.00 0.00 3.77
100 101 2.909965 GCCACGGCCAAAGTCCAA 60.910 61.111 2.24 0.00 34.56 3.53
101 102 3.842925 GAGCCACGGCCAAAGTCCA 62.843 63.158 2.24 0.00 43.17 4.02
102 103 3.056328 GAGCCACGGCCAAAGTCC 61.056 66.667 2.24 0.00 43.17 3.85
103 104 3.423154 CGAGCCACGGCCAAAGTC 61.423 66.667 2.24 0.00 43.17 3.01
113 114 2.904866 TTTGGTGCCACGAGCCAC 60.905 61.111 0.00 0.00 42.71 5.01
114 115 2.046009 TAGTTTGGTGCCACGAGCCA 62.046 55.000 0.00 0.00 42.71 4.75
115 116 0.676782 ATAGTTTGGTGCCACGAGCC 60.677 55.000 0.00 0.00 42.71 4.70
116 117 1.165270 AATAGTTTGGTGCCACGAGC 58.835 50.000 0.00 0.00 44.14 5.03
117 118 3.074412 AGAAATAGTTTGGTGCCACGAG 58.926 45.455 0.00 0.00 0.00 4.18
118 119 3.134574 AGAAATAGTTTGGTGCCACGA 57.865 42.857 0.00 0.00 0.00 4.35
119 120 3.915437 AAGAAATAGTTTGGTGCCACG 57.085 42.857 0.00 0.00 0.00 4.94
140 141 2.094100 TTGGTGCCATCCCTCAAAAA 57.906 45.000 0.00 0.00 0.00 1.94
141 142 1.691434 GTTTGGTGCCATCCCTCAAAA 59.309 47.619 0.00 0.00 0.00 2.44
142 143 1.133199 AGTTTGGTGCCATCCCTCAAA 60.133 47.619 0.00 0.00 0.00 2.69
143 144 0.482446 AGTTTGGTGCCATCCCTCAA 59.518 50.000 0.00 0.00 0.00 3.02
144 145 1.367346 TAGTTTGGTGCCATCCCTCA 58.633 50.000 0.00 0.00 0.00 3.86
145 146 2.736670 ATAGTTTGGTGCCATCCCTC 57.263 50.000 0.00 0.00 0.00 4.30
146 147 4.814224 ATAATAGTTTGGTGCCATCCCT 57.186 40.909 0.00 0.00 0.00 4.20
147 148 5.048991 CGTTATAATAGTTTGGTGCCATCCC 60.049 44.000 0.00 0.00 0.00 3.85
148 149 5.529800 ACGTTATAATAGTTTGGTGCCATCC 59.470 40.000 0.00 0.00 0.00 3.51
149 150 6.427150 CACGTTATAATAGTTTGGTGCCATC 58.573 40.000 0.00 0.00 0.00 3.51
150 151 5.220970 GCACGTTATAATAGTTTGGTGCCAT 60.221 40.000 1.64 0.00 42.58 4.40
151 152 4.095185 GCACGTTATAATAGTTTGGTGCCA 59.905 41.667 1.64 0.00 42.58 4.92
152 153 4.095185 TGCACGTTATAATAGTTTGGTGCC 59.905 41.667 9.92 0.00 46.47 5.01
154 155 6.128391 ACACTGCACGTTATAATAGTTTGGTG 60.128 38.462 0.00 4.24 0.00 4.17
155 156 5.935789 ACACTGCACGTTATAATAGTTTGGT 59.064 36.000 0.00 0.00 0.00 3.67
156 157 6.091577 TCACACTGCACGTTATAATAGTTTGG 59.908 38.462 0.00 0.00 0.00 3.28
157 158 7.056002 TCACACTGCACGTTATAATAGTTTG 57.944 36.000 0.00 0.00 0.00 2.93
158 159 7.843490 ATCACACTGCACGTTATAATAGTTT 57.157 32.000 0.00 0.00 0.00 2.66
159 160 7.333423 ACAATCACACTGCACGTTATAATAGTT 59.667 33.333 0.00 0.00 0.00 2.24
160 161 6.816640 ACAATCACACTGCACGTTATAATAGT 59.183 34.615 0.00 0.00 0.00 2.12
161 162 7.234187 ACAATCACACTGCACGTTATAATAG 57.766 36.000 0.00 0.00 0.00 1.73
162 163 7.603963 AACAATCACACTGCACGTTATAATA 57.396 32.000 0.00 0.00 0.00 0.98
163 164 6.494893 AACAATCACACTGCACGTTATAAT 57.505 33.333 0.00 0.00 0.00 1.28
164 165 5.933187 AACAATCACACTGCACGTTATAA 57.067 34.783 0.00 0.00 0.00 0.98
165 166 5.933187 AAACAATCACACTGCACGTTATA 57.067 34.783 0.00 0.00 0.00 0.98
166 167 4.829064 AAACAATCACACTGCACGTTAT 57.171 36.364 0.00 0.00 0.00 1.89
167 168 4.593157 GAAAACAATCACACTGCACGTTA 58.407 39.130 0.00 0.00 0.00 3.18
168 169 3.434637 GAAAACAATCACACTGCACGTT 58.565 40.909 0.00 0.00 0.00 3.99
169 170 2.538737 CGAAAACAATCACACTGCACGT 60.539 45.455 0.00 0.00 0.00 4.49
170 171 2.036217 CGAAAACAATCACACTGCACG 58.964 47.619 0.00 0.00 0.00 5.34
171 172 2.032799 TCCGAAAACAATCACACTGCAC 59.967 45.455 0.00 0.00 0.00 4.57
172 173 2.293170 TCCGAAAACAATCACACTGCA 58.707 42.857 0.00 0.00 0.00 4.41
173 174 3.559238 ATCCGAAAACAATCACACTGC 57.441 42.857 0.00 0.00 0.00 4.40
174 175 6.826893 AAAAATCCGAAAACAATCACACTG 57.173 33.333 0.00 0.00 0.00 3.66
304 329 3.014036 CCGCGTGCATTAATCGCT 58.986 55.556 15.37 0.00 46.31 4.93
449 483 4.007644 TGCGTGCAGAGACAGGGG 62.008 66.667 0.00 0.00 0.00 4.79
469 503 0.757561 GAGAGAGGGTAGGGAGGTGC 60.758 65.000 0.00 0.00 0.00 5.01
471 505 2.137702 GTAGAGAGAGGGTAGGGAGGT 58.862 57.143 0.00 0.00 0.00 3.85
479 513 4.468153 GGAGTCAAAATGTAGAGAGAGGGT 59.532 45.833 0.00 0.00 0.00 4.34
520 559 0.033796 TACTACTGTAGCCTGCGGGT 60.034 55.000 14.55 8.99 37.19 5.28
522 561 1.390565 AGTACTACTGTAGCCTGCGG 58.609 55.000 14.55 0.00 0.00 5.69
549 588 1.611519 GATACCGAGACAGCTAGCCT 58.388 55.000 12.13 0.51 0.00 4.58
758 812 2.280797 GACGAAGGCTGTGGTGCA 60.281 61.111 0.00 0.00 34.04 4.57
866 930 2.312390 GGGGACAAGGAGTCTAGCTAG 58.688 57.143 15.01 15.01 46.72 3.42
867 931 1.409802 CGGGGACAAGGAGTCTAGCTA 60.410 57.143 0.00 0.00 46.72 3.32
868 932 0.684805 CGGGGACAAGGAGTCTAGCT 60.685 60.000 0.00 0.00 46.72 3.32
869 933 1.817209 CGGGGACAAGGAGTCTAGC 59.183 63.158 0.00 0.00 46.72 3.42
919 983 2.138453 AAAGAAAGGGACCGAGGGGC 62.138 60.000 0.00 0.00 36.48 5.80
926 990 4.072839 ACGATGAAAGAAAGAAAGGGACC 58.927 43.478 0.00 0.00 0.00 4.46
988 1052 2.202797 CCCCATGCTCACGTCTCG 60.203 66.667 0.00 0.00 0.00 4.04
1139 1203 2.322355 AGAAGATGGATGGAAGCGTG 57.678 50.000 0.00 0.00 0.00 5.34
1140 1204 2.503356 AGAAGAAGATGGATGGAAGCGT 59.497 45.455 0.00 0.00 0.00 5.07
1141 1205 3.191078 AGAAGAAGATGGATGGAAGCG 57.809 47.619 0.00 0.00 0.00 4.68
1142 1206 4.779696 AGAAGAAGAAGATGGATGGAAGC 58.220 43.478 0.00 0.00 0.00 3.86
1143 1207 6.652053 AGAAGAAGAAGAAGATGGATGGAAG 58.348 40.000 0.00 0.00 0.00 3.46
1144 1208 6.633325 AGAAGAAGAAGAAGATGGATGGAA 57.367 37.500 0.00 0.00 0.00 3.53
1192 1268 3.684788 ACAAAGAACCATGCGATCTGTAC 59.315 43.478 0.00 0.00 0.00 2.90
1193 1269 3.684305 CACAAAGAACCATGCGATCTGTA 59.316 43.478 0.00 0.00 0.00 2.74
1194 1270 2.485426 CACAAAGAACCATGCGATCTGT 59.515 45.455 0.00 0.00 0.00 3.41
1195 1271 2.159476 CCACAAAGAACCATGCGATCTG 60.159 50.000 0.00 0.00 0.00 2.90
1196 1272 2.086869 CCACAAAGAACCATGCGATCT 58.913 47.619 0.00 0.00 0.00 2.75
1297 1374 4.408821 TTGCCGCGCTTGATCCCT 62.409 61.111 5.56 0.00 0.00 4.20
1501 1578 2.285668 CCCTTGGAGGAGGAGGCA 60.286 66.667 0.00 0.00 37.67 4.75
1726 1803 4.367023 GTGAGCACGTACGGCCCA 62.367 66.667 21.06 13.91 0.00 5.36
2074 2154 1.202545 GCTAGGGGAACATCGACCTTC 60.203 57.143 0.00 0.00 34.59 3.46
2097 2177 0.245266 TCCTCGCATCAGTAACGCAA 59.755 50.000 0.00 0.00 0.00 4.85
2098 2178 0.179137 CTCCTCGCATCAGTAACGCA 60.179 55.000 0.00 0.00 0.00 5.24
2111 2191 0.249447 TGCAGTGAACACACTCCTCG 60.249 55.000 7.68 0.00 42.09 4.63
2208 2288 8.494016 AAACTATGCAGATCCTAAGTAAACAC 57.506 34.615 0.00 0.00 0.00 3.32
2268 2350 5.046591 ACAGCAGTAAATAACAGGAGCACTA 60.047 40.000 0.00 0.00 0.00 2.74
2312 2394 4.882842 ACCCAAAACCCATGAACATAAC 57.117 40.909 0.00 0.00 0.00 1.89
2313 2395 5.896073 AAACCCAAAACCCATGAACATAA 57.104 34.783 0.00 0.00 0.00 1.90
2314 2396 5.131142 ACAAAACCCAAAACCCATGAACATA 59.869 36.000 0.00 0.00 0.00 2.29
2315 2397 4.080072 ACAAAACCCAAAACCCATGAACAT 60.080 37.500 0.00 0.00 0.00 2.71
2316 2398 3.264450 ACAAAACCCAAAACCCATGAACA 59.736 39.130 0.00 0.00 0.00 3.18
2451 2536 6.783517 AGTAGGAGTATATGACAGGTACCT 57.216 41.667 9.21 9.21 0.00 3.08
2499 2584 7.544804 AAAAGCTCCAAAGATTAATCAACCT 57.455 32.000 17.56 1.54 29.07 3.50
2500 2585 7.872483 TGAAAAAGCTCCAAAGATTAATCAACC 59.128 33.333 17.56 0.00 29.07 3.77
2501 2586 8.816640 TGAAAAAGCTCCAAAGATTAATCAAC 57.183 30.769 17.56 0.00 29.07 3.18
2502 2587 9.426837 CATGAAAAAGCTCCAAAGATTAATCAA 57.573 29.630 17.56 0.00 32.68 2.57
2521 2606 7.450074 AGTAGTTGACATACTGACCATGAAAA 58.550 34.615 0.00 0.00 32.27 2.29
2542 2627 5.934625 GGTGGAAATATATGACAGGCAGTAG 59.065 44.000 0.00 0.00 0.00 2.57
2591 2734 8.341173 GTGATACATATATACGGCAGGTAGTAC 58.659 40.741 0.00 0.00 33.84 2.73
2594 2737 7.569639 AGTGATACATATATACGGCAGGTAG 57.430 40.000 0.00 0.00 33.84 3.18
2645 2788 4.772886 TTCCCCCTTAAAGTCAGATAGC 57.227 45.455 0.00 0.00 0.00 2.97
2756 2906 1.702401 TCAATTGGTACCAGCTCCACA 59.298 47.619 15.65 0.00 33.12 4.17
2758 2908 2.575735 TGATCAATTGGTACCAGCTCCA 59.424 45.455 15.65 7.13 0.00 3.86
2785 2935 9.606631 AAAAATACAAGCACCAAGTCAAATTTA 57.393 25.926 0.00 0.00 0.00 1.40
2802 2952 7.483375 CGCCGAATCAATTGTAGAAAAATACAA 59.517 33.333 5.13 2.13 46.60 2.41
2969 3121 3.481453 TGCAGATCTAGATACGCTCACT 58.519 45.455 20.69 5.08 0.00 3.41
2973 3125 3.119531 GCTCATGCAGATCTAGATACGCT 60.120 47.826 20.69 6.93 39.41 5.07


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

AutoCloner maintained by Alex Coulton.