Multiple sequence alignment - TraesCS3A01G237900

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 TraesCS3A01G237900 chr3A 100.000 2255 0 0 1 2255 444539269 444537015 0.000000e+00 4165.0
1 TraesCS3A01G237900 chr3D 93.050 1669 72 20 604 2255 329499251 329497610 0.000000e+00 2399.0
2 TraesCS3A01G237900 chr3D 91.156 294 17 5 314 605 329499582 329499296 7.550000e-105 390.0
3 TraesCS3A01G237900 chr3B 92.597 1675 84 25 597 2253 427001776 427000124 0.000000e+00 2370.0
4 TraesCS3A01G237900 chr3B 91.400 407 28 5 199 605 427002214 427001815 3.270000e-153 551.0
5 TraesCS3A01G237900 chr3B 91.753 194 14 2 3 194 418687887 418687694 3.690000e-68 268.0
6 TraesCS3A01G237900 chr3B 90.385 52 4 1 245 295 787425860 787425911 1.450000e-07 67.6
7 TraesCS3A01G237900 chr1B 92.746 193 13 1 3 194 629686552 629686360 6.130000e-71 278.0
8 TraesCS3A01G237900 chr1B 90.674 193 17 1 3 194 671237490 671237298 2.870000e-64 255.0
9 TraesCS3A01G237900 chr1B 77.705 305 68 0 961 1265 662520779 662521083 1.060000e-43 187.0
10 TraesCS3A01G237900 chr6B 92.228 193 14 1 3 194 218979719 218979527 2.850000e-69 272.0
11 TraesCS3A01G237900 chr1A 92.228 193 14 1 3 194 571867701 571867509 2.850000e-69 272.0
12 TraesCS3A01G237900 chr1A 76.721 305 71 0 961 1265 571986945 571987249 1.070000e-38 171.0
13 TraesCS3A01G237900 chr5B 91.710 193 15 1 3 194 694229881 694229689 1.330000e-67 267.0
14 TraesCS3A01G237900 chr7B 91.192 193 16 1 3 194 384650109 384649917 6.180000e-66 261.0
15 TraesCS3A01G237900 chr7B 88.679 53 5 1 244 295 138750301 138750353 1.870000e-06 63.9
16 TraesCS3A01G237900 chr4B 90.476 189 18 0 3 191 639591569 639591381 1.340000e-62 250.0
17 TraesCS3A01G237900 chr4A 89.637 193 19 1 3 194 647255972 647255780 6.220000e-61 244.0
18 TraesCS3A01G237900 chr4A 90.741 54 5 0 244 297 485387466 485387413 3.110000e-09 73.1
19 TraesCS3A01G237900 chr1D 77.377 305 69 0 961 1265 476208177 476208481 4.950000e-42 182.0
20 TraesCS3A01G237900 chr7A 90.566 53 5 0 245 297 681767853 681767905 1.120000e-08 71.3
21 TraesCS3A01G237900 chr4D 86.667 60 4 3 244 301 22571449 22571506 1.870000e-06 63.9


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 TraesCS3A01G237900 chr3A 444537015 444539269 2254 True 4165.0 4165 100.0000 1 2255 1 chr3A.!!$R1 2254
1 TraesCS3A01G237900 chr3D 329497610 329499582 1972 True 1394.5 2399 92.1030 314 2255 2 chr3D.!!$R1 1941
2 TraesCS3A01G237900 chr3B 427000124 427002214 2090 True 1460.5 2370 91.9985 199 2253 2 chr3B.!!$R2 2054

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
90 91 0.03254 TCGATGCATCTCATGGACGG 59.967 55.0 23.73 5.68 35.41 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1938 0.458669 TATCCGGCTGACTTTCGTCC 59.541 55.0 0.0 0.0 39.47 4.79 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
22 23 5.881777 GAGAAGGACCATTTAACCTTGTC 57.118 43.478 0.00 0.00 43.21 3.18
23 24 5.313712 GAGAAGGACCATTTAACCTTGTCA 58.686 41.667 14.41 0.00 46.38 3.58
24 25 5.892348 AGAAGGACCATTTAACCTTGTCAT 58.108 37.500 0.00 0.00 42.98 3.06
25 26 7.027874 AGAAGGACCATTTAACCTTGTCATA 57.972 36.000 0.00 0.00 42.98 2.15
26 27 7.112779 AGAAGGACCATTTAACCTTGTCATAG 58.887 38.462 0.00 0.00 42.98 2.23
27 28 5.755849 AGGACCATTTAACCTTGTCATAGG 58.244 41.667 0.00 0.00 41.31 2.57
28 29 4.338400 GGACCATTTAACCTTGTCATAGGC 59.662 45.833 0.00 0.00 38.99 3.93
29 30 5.193099 ACCATTTAACCTTGTCATAGGCT 57.807 39.130 0.00 0.00 38.99 4.58
30 31 5.580022 ACCATTTAACCTTGTCATAGGCTT 58.420 37.500 0.00 0.00 38.99 4.35
31 32 6.016555 ACCATTTAACCTTGTCATAGGCTTT 58.983 36.000 0.00 0.00 38.99 3.51
32 33 6.496911 ACCATTTAACCTTGTCATAGGCTTTT 59.503 34.615 0.00 0.00 38.99 2.27
33 34 7.016170 ACCATTTAACCTTGTCATAGGCTTTTT 59.984 33.333 0.00 0.00 38.99 1.94
34 35 7.545615 CCATTTAACCTTGTCATAGGCTTTTTC 59.454 37.037 0.00 0.00 38.99 2.29
35 36 7.589958 TTTAACCTTGTCATAGGCTTTTTCA 57.410 32.000 0.00 0.00 38.99 2.69
36 37 7.589958 TTAACCTTGTCATAGGCTTTTTCAA 57.410 32.000 0.00 0.00 38.99 2.69
37 38 6.478512 AACCTTGTCATAGGCTTTTTCAAA 57.521 33.333 0.00 0.00 38.99 2.69
38 39 6.089249 ACCTTGTCATAGGCTTTTTCAAAG 57.911 37.500 0.00 0.00 38.99 2.77
39 40 5.598417 ACCTTGTCATAGGCTTTTTCAAAGT 59.402 36.000 0.00 0.00 38.99 2.66
40 41 6.152379 CCTTGTCATAGGCTTTTTCAAAGTC 58.848 40.000 0.00 0.00 0.00 3.01
41 42 6.239008 CCTTGTCATAGGCTTTTTCAAAGTCA 60.239 38.462 0.00 0.00 0.00 3.41
42 43 6.707440 TGTCATAGGCTTTTTCAAAGTCAA 57.293 33.333 0.00 0.00 0.00 3.18
43 44 7.288810 TGTCATAGGCTTTTTCAAAGTCAAT 57.711 32.000 0.00 0.00 0.00 2.57
44 45 7.725251 TGTCATAGGCTTTTTCAAAGTCAATT 58.275 30.769 0.00 0.00 0.00 2.32
45 46 7.867403 TGTCATAGGCTTTTTCAAAGTCAATTC 59.133 33.333 0.00 0.00 0.00 2.17
46 47 8.084684 GTCATAGGCTTTTTCAAAGTCAATTCT 58.915 33.333 0.00 0.00 0.00 2.40
47 48 8.084073 TCATAGGCTTTTTCAAAGTCAATTCTG 58.916 33.333 0.00 0.00 0.00 3.02
48 49 6.469782 AGGCTTTTTCAAAGTCAATTCTGA 57.530 33.333 3.80 0.00 0.00 3.27
49 50 6.877236 AGGCTTTTTCAAAGTCAATTCTGAA 58.123 32.000 3.80 0.00 31.88 3.02
50 51 7.503549 AGGCTTTTTCAAAGTCAATTCTGAAT 58.496 30.769 3.80 0.00 31.88 2.57
51 52 8.641541 AGGCTTTTTCAAAGTCAATTCTGAATA 58.358 29.630 2.85 0.00 31.88 1.75
52 53 9.428097 GGCTTTTTCAAAGTCAATTCTGAATAT 57.572 29.630 2.85 0.00 31.88 1.28
58 59 8.498054 TCAAAGTCAATTCTGAATATCACTCC 57.502 34.615 2.85 0.00 31.88 3.85
59 60 8.102676 TCAAAGTCAATTCTGAATATCACTCCA 58.897 33.333 2.85 0.00 31.88 3.86
60 61 8.900781 CAAAGTCAATTCTGAATATCACTCCAT 58.099 33.333 2.85 0.00 31.88 3.41
61 62 9.471702 AAAGTCAATTCTGAATATCACTCCATT 57.528 29.630 2.85 0.00 31.88 3.16
62 63 8.674263 AGTCAATTCTGAATATCACTCCATTC 57.326 34.615 2.85 0.00 31.88 2.67
63 64 8.270030 AGTCAATTCTGAATATCACTCCATTCA 58.730 33.333 2.85 0.00 38.50 2.57
64 65 9.064706 GTCAATTCTGAATATCACTCCATTCAT 57.935 33.333 2.85 0.00 39.69 2.57
65 66 9.063615 TCAATTCTGAATATCACTCCATTCATG 57.936 33.333 2.85 0.00 39.69 3.07
66 67 8.847196 CAATTCTGAATATCACTCCATTCATGT 58.153 33.333 2.85 0.00 39.69 3.21
67 68 8.991783 ATTCTGAATATCACTCCATTCATGTT 57.008 30.769 0.00 0.00 39.69 2.71
68 69 8.812513 TTCTGAATATCACTCCATTCATGTTT 57.187 30.769 0.00 0.00 39.69 2.83
69 70 8.812513 TCTGAATATCACTCCATTCATGTTTT 57.187 30.769 0.00 0.00 39.69 2.43
70 71 9.246670 TCTGAATATCACTCCATTCATGTTTTT 57.753 29.630 0.00 0.00 39.69 1.94
88 89 4.621068 TTTTTCGATGCATCTCATGGAC 57.379 40.909 23.73 0.00 39.21 4.02
89 90 1.856802 TTCGATGCATCTCATGGACG 58.143 50.000 23.73 9.31 39.21 4.79
90 91 0.032540 TCGATGCATCTCATGGACGG 59.967 55.000 23.73 5.68 35.41 4.79
91 92 0.249615 CGATGCATCTCATGGACGGT 60.250 55.000 23.73 0.00 35.05 4.83
92 93 1.506493 GATGCATCTCATGGACGGTC 58.494 55.000 19.70 0.00 35.05 4.79
93 94 1.069823 GATGCATCTCATGGACGGTCT 59.930 52.381 19.70 0.00 35.05 3.85
94 95 0.461548 TGCATCTCATGGACGGTCTC 59.538 55.000 8.23 0.00 0.00 3.36
95 96 0.461548 GCATCTCATGGACGGTCTCA 59.538 55.000 8.23 5.02 0.00 3.27
96 97 1.069823 GCATCTCATGGACGGTCTCAT 59.930 52.381 8.23 7.13 0.00 2.90
97 98 2.752121 CATCTCATGGACGGTCTCATG 58.248 52.381 22.77 22.77 41.35 3.07
98 99 0.461548 TCTCATGGACGGTCTCATGC 59.538 55.000 23.43 5.02 40.20 4.06
99 100 0.176449 CTCATGGACGGTCTCATGCA 59.824 55.000 23.43 15.84 40.20 3.96
100 101 0.176449 TCATGGACGGTCTCATGCAG 59.824 55.000 23.43 9.97 40.20 4.41
101 102 0.812811 CATGGACGGTCTCATGCAGG 60.813 60.000 19.48 0.00 35.07 4.85
102 103 0.977627 ATGGACGGTCTCATGCAGGA 60.978 55.000 8.23 0.00 0.00 3.86
103 104 1.153549 GGACGGTCTCATGCAGGAC 60.154 63.158 8.23 2.75 0.00 3.85
104 105 1.608717 GGACGGTCTCATGCAGGACT 61.609 60.000 8.23 0.00 33.46 3.85
105 106 1.103803 GACGGTCTCATGCAGGACTA 58.896 55.000 0.00 0.00 33.46 2.59
106 107 0.818296 ACGGTCTCATGCAGGACTAC 59.182 55.000 0.00 0.00 33.46 2.73
107 108 1.107114 CGGTCTCATGCAGGACTACT 58.893 55.000 0.00 0.00 33.46 2.57
108 109 2.298610 CGGTCTCATGCAGGACTACTA 58.701 52.381 0.00 0.00 33.46 1.82
109 110 2.887783 CGGTCTCATGCAGGACTACTAT 59.112 50.000 0.00 0.00 33.46 2.12
110 111 4.072839 CGGTCTCATGCAGGACTACTATA 58.927 47.826 0.00 0.00 33.46 1.31
111 112 4.083217 CGGTCTCATGCAGGACTACTATAC 60.083 50.000 0.00 0.00 33.46 1.47
112 113 4.218852 GGTCTCATGCAGGACTACTATACC 59.781 50.000 0.00 0.00 33.46 2.73
113 114 4.827835 GTCTCATGCAGGACTACTATACCA 59.172 45.833 0.00 0.00 0.00 3.25
114 115 5.478679 GTCTCATGCAGGACTACTATACCAT 59.521 44.000 0.00 0.00 0.00 3.55
115 116 5.712446 TCTCATGCAGGACTACTATACCATC 59.288 44.000 0.00 0.00 0.00 3.51
116 117 5.393866 TCATGCAGGACTACTATACCATCA 58.606 41.667 0.00 0.00 0.00 3.07
117 118 5.838521 TCATGCAGGACTACTATACCATCAA 59.161 40.000 0.00 0.00 0.00 2.57
118 119 6.326323 TCATGCAGGACTACTATACCATCAAA 59.674 38.462 0.00 0.00 0.00 2.69
119 120 6.747414 TGCAGGACTACTATACCATCAAAT 57.253 37.500 0.00 0.00 0.00 2.32
120 121 7.849322 TGCAGGACTACTATACCATCAAATA 57.151 36.000 0.00 0.00 0.00 1.40
121 122 8.435931 TGCAGGACTACTATACCATCAAATAT 57.564 34.615 0.00 0.00 0.00 1.28
122 123 9.541884 TGCAGGACTACTATACCATCAAATATA 57.458 33.333 0.00 0.00 0.00 0.86
134 135 7.530426 ACCATCAAATATATTCCTTCCTTGC 57.470 36.000 0.00 0.00 0.00 4.01
135 136 7.068702 ACCATCAAATATATTCCTTCCTTGCA 58.931 34.615 0.00 0.00 0.00 4.08
136 137 7.731688 ACCATCAAATATATTCCTTCCTTGCAT 59.268 33.333 0.00 0.00 0.00 3.96
137 138 8.033038 CCATCAAATATATTCCTTCCTTGCATG 58.967 37.037 0.00 0.00 0.00 4.06
138 139 8.799367 CATCAAATATATTCCTTCCTTGCATGA 58.201 33.333 0.00 0.00 0.00 3.07
139 140 8.765488 TCAAATATATTCCTTCCTTGCATGAA 57.235 30.769 0.00 0.08 0.00 2.57
140 141 8.632679 TCAAATATATTCCTTCCTTGCATGAAC 58.367 33.333 0.00 0.00 0.00 3.18
141 142 6.808008 ATATATTCCTTCCTTGCATGAACG 57.192 37.500 0.00 0.00 0.00 3.95
142 143 0.881118 TTCCTTCCTTGCATGAACGC 59.119 50.000 0.00 0.00 0.00 4.84
143 144 0.960364 TCCTTCCTTGCATGAACGCC 60.960 55.000 0.00 0.00 0.00 5.68
144 145 1.135315 CTTCCTTGCATGAACGCCG 59.865 57.895 0.00 0.00 0.00 6.46
145 146 1.577328 CTTCCTTGCATGAACGCCGT 61.577 55.000 0.00 0.00 0.00 5.68
146 147 1.169661 TTCCTTGCATGAACGCCGTT 61.170 50.000 0.16 0.16 0.00 4.44
147 148 1.169661 TCCTTGCATGAACGCCGTTT 61.170 50.000 3.07 0.00 0.00 3.60
148 149 1.003262 CCTTGCATGAACGCCGTTTG 61.003 55.000 3.07 0.00 0.00 2.93
149 150 0.040514 CTTGCATGAACGCCGTTTGA 60.041 50.000 3.07 0.00 0.00 2.69
150 151 0.040514 TTGCATGAACGCCGTTTGAG 60.041 50.000 3.07 0.00 0.00 3.02
151 152 0.882484 TGCATGAACGCCGTTTGAGA 60.882 50.000 3.07 0.00 0.00 3.27
152 153 0.447801 GCATGAACGCCGTTTGAGAT 59.552 50.000 3.07 0.00 0.00 2.75
153 154 1.791555 GCATGAACGCCGTTTGAGATG 60.792 52.381 3.07 5.97 0.00 2.90
154 155 1.086696 ATGAACGCCGTTTGAGATGG 58.913 50.000 3.07 0.00 37.49 3.51
160 161 2.471255 CCGTTTGAGATGGCCAGAC 58.529 57.895 13.05 8.21 0.00 3.51
161 162 0.321564 CCGTTTGAGATGGCCAGACA 60.322 55.000 13.05 8.45 0.00 3.41
162 163 1.522668 CGTTTGAGATGGCCAGACAA 58.477 50.000 13.05 14.28 0.00 3.18
163 164 1.197721 CGTTTGAGATGGCCAGACAAC 59.802 52.381 13.05 8.66 0.00 3.32
164 165 2.229792 GTTTGAGATGGCCAGACAACA 58.770 47.619 13.05 9.62 0.00 3.33
165 166 2.821969 GTTTGAGATGGCCAGACAACAT 59.178 45.455 13.05 0.00 0.00 2.71
166 167 2.118313 TGAGATGGCCAGACAACATG 57.882 50.000 13.05 0.00 0.00 3.21
167 168 1.340308 TGAGATGGCCAGACAACATGG 60.340 52.381 13.05 0.00 41.04 3.66
168 169 0.700564 AGATGGCCAGACAACATGGT 59.299 50.000 13.05 0.00 40.17 3.55
169 170 1.098050 GATGGCCAGACAACATGGTC 58.902 55.000 13.05 0.00 43.02 4.02
170 171 4.819783 GGCCAGACAACATGGTCA 57.180 55.556 0.00 0.00 42.24 4.02
171 172 2.559785 GGCCAGACAACATGGTCAG 58.440 57.895 0.00 0.00 42.24 3.51
172 173 1.589716 GGCCAGACAACATGGTCAGC 61.590 60.000 0.00 3.43 42.24 4.26
173 174 0.607489 GCCAGACAACATGGTCAGCT 60.607 55.000 0.00 0.00 40.29 4.24
174 175 1.339055 GCCAGACAACATGGTCAGCTA 60.339 52.381 0.00 0.00 40.29 3.32
175 176 2.350522 CCAGACAACATGGTCAGCTAC 58.649 52.381 0.00 0.00 40.29 3.58
187 188 2.579201 AGCTACCGCGCTGAACAT 59.421 55.556 5.61 0.00 42.32 2.71
188 189 1.813859 AGCTACCGCGCTGAACATA 59.186 52.632 5.61 0.00 42.32 2.29
189 190 0.389391 AGCTACCGCGCTGAACATAT 59.611 50.000 5.61 0.00 42.32 1.78
190 191 1.202533 AGCTACCGCGCTGAACATATT 60.203 47.619 5.61 0.00 42.32 1.28
191 192 1.070577 GCTACCGCGCTGAACATATTG 60.071 52.381 5.61 0.00 0.00 1.90
192 193 2.201732 CTACCGCGCTGAACATATTGT 58.798 47.619 5.61 0.00 0.00 2.71
193 194 2.303163 ACCGCGCTGAACATATTGTA 57.697 45.000 5.61 0.00 0.00 2.41
194 195 1.931172 ACCGCGCTGAACATATTGTAC 59.069 47.619 5.61 0.00 0.00 2.90
195 196 1.930503 CCGCGCTGAACATATTGTACA 59.069 47.619 5.56 0.00 0.00 2.90
196 197 2.543848 CCGCGCTGAACATATTGTACAT 59.456 45.455 5.56 0.00 0.00 2.29
197 198 3.002246 CCGCGCTGAACATATTGTACATT 59.998 43.478 5.56 0.00 0.00 2.71
285 286 9.793252 ATGAGAAACATTTTGCTATACATGTTC 57.207 29.630 2.30 0.00 38.60 3.18
297 298 8.969121 TGCTATACATGTTCAACATTTTTCAG 57.031 30.769 2.30 0.00 36.53 3.02
306 307 8.410030 TGTTCAACATTTTTCAGTTTGATCAG 57.590 30.769 0.00 0.00 0.00 2.90
310 311 4.037923 ACATTTTTCAGTTTGATCAGGCGT 59.962 37.500 0.00 0.00 0.00 5.68
319 320 3.355626 TTGATCAGGCGTCGAATAGAG 57.644 47.619 0.00 0.00 0.00 2.43
404 407 1.377333 GCGGGTTCTTCTTCCCCAG 60.377 63.158 0.00 0.00 40.54 4.45
419 422 1.211457 CCCCAGTTCCTCTCCATCTTG 59.789 57.143 0.00 0.00 0.00 3.02
455 458 2.327568 CACCAAATTGCATCGAACCAC 58.672 47.619 0.00 0.00 0.00 4.16
468 471 2.557056 TCGAACCACACTACCAGAGAAG 59.443 50.000 0.00 0.00 0.00 2.85
500 503 0.388520 TGAATCGACCGACAGTGCTG 60.389 55.000 0.00 0.00 0.00 4.41
513 516 3.369381 GTGCTGACACACTGACACT 57.631 52.632 0.00 0.00 46.61 3.55
849 917 4.083057 AGCCGCAAATTCTTTCTTTCTCTC 60.083 41.667 0.00 0.00 0.00 3.20
850 918 4.083057 GCCGCAAATTCTTTCTTTCTCTCT 60.083 41.667 0.00 0.00 0.00 3.10
851 919 5.626211 CCGCAAATTCTTTCTTTCTCTCTC 58.374 41.667 0.00 0.00 0.00 3.20
852 920 5.411053 CCGCAAATTCTTTCTTTCTCTCTCT 59.589 40.000 0.00 0.00 0.00 3.10
853 921 6.402011 CCGCAAATTCTTTCTTTCTCTCTCTC 60.402 42.308 0.00 0.00 0.00 3.20
854 922 6.368516 CGCAAATTCTTTCTTTCTCTCTCTCT 59.631 38.462 0.00 0.00 0.00 3.10
855 923 7.411804 CGCAAATTCTTTCTTTCTCTCTCTCTC 60.412 40.741 0.00 0.00 0.00 3.20
856 924 7.603784 GCAAATTCTTTCTTTCTCTCTCTCTCT 59.396 37.037 0.00 0.00 0.00 3.10
857 925 9.143631 CAAATTCTTTCTTTCTCTCTCTCTCTC 57.856 37.037 0.00 0.00 0.00 3.20
858 926 8.655935 AATTCTTTCTTTCTCTCTCTCTCTCT 57.344 34.615 0.00 0.00 0.00 3.10
862 930 6.627087 TTCTTTCTCTCTCTCTCTCTCTCT 57.373 41.667 0.00 0.00 0.00 3.10
865 933 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
884 952 2.665537 CTCTCGCCATGCTCGAATAATC 59.334 50.000 9.10 0.00 35.38 1.75
893 961 4.944619 TGCTCGAATAATCTGACATCCT 57.055 40.909 0.00 0.00 0.00 3.24
908 977 4.256180 CCTATCCAGCCGGCCACC 62.256 72.222 26.15 0.00 0.00 4.61
910 979 4.815973 TATCCAGCCGGCCACCCT 62.816 66.667 26.15 7.12 0.00 4.34
913 982 4.796495 CCAGCCGGCCACCCTTAC 62.796 72.222 26.15 0.00 0.00 2.34
924 993 4.386711 GGCCACCCTTACATTATCACTAC 58.613 47.826 0.00 0.00 0.00 2.73
926 995 5.306160 GGCCACCCTTACATTATCACTACTA 59.694 44.000 0.00 0.00 0.00 1.82
934 1003 5.277857 ACATTATCACTACTACCACCTGC 57.722 43.478 0.00 0.00 0.00 4.85
935 1004 4.202121 ACATTATCACTACTACCACCTGCG 60.202 45.833 0.00 0.00 0.00 5.18
937 1006 0.251474 TCACTACTACCACCTGCGGT 60.251 55.000 0.00 0.00 43.46 5.68
938 1007 0.606604 CACTACTACCACCTGCGGTT 59.393 55.000 0.00 0.00 40.67 4.44
939 1008 1.001633 CACTACTACCACCTGCGGTTT 59.998 52.381 0.00 0.00 40.67 3.27
959 1031 2.031919 TTTGATCACCGCCGCTGT 59.968 55.556 0.00 0.00 0.00 4.40
1140 1212 4.343581 GCGATCTTGCAGGCGATA 57.656 55.556 0.16 0.00 34.15 2.92
1245 1317 2.076863 GGTTCCGCTATCACATATGGC 58.923 52.381 7.80 0.00 0.00 4.40
1273 1346 4.345257 GGTAATAGTCTCCTGAGATGGCAA 59.655 45.833 0.00 0.00 39.97 4.52
1309 1382 5.997129 TCAGAACAGTGCATAATTTGTGAGA 59.003 36.000 0.00 0.00 0.00 3.27
1311 1384 6.965500 CAGAACAGTGCATAATTTGTGAGATC 59.035 38.462 0.00 0.00 0.00 2.75
1360 1433 5.303589 TGTCAAGTTGTAACTAGGCTACTGT 59.696 40.000 2.11 0.00 38.57 3.55
1371 1444 5.542779 ACTAGGCTACTGTCAGTTTTCTTG 58.457 41.667 11.54 9.27 0.00 3.02
1385 1458 4.213482 AGTTTTCTTGCCAAAGCTACTACG 59.787 41.667 0.00 0.00 40.80 3.51
1386 1459 3.396260 TTCTTGCCAAAGCTACTACGT 57.604 42.857 0.00 0.00 40.80 3.57
1387 1460 4.524316 TTCTTGCCAAAGCTACTACGTA 57.476 40.909 0.00 0.00 40.80 3.57
1388 1461 3.841643 TCTTGCCAAAGCTACTACGTAC 58.158 45.455 0.00 0.00 40.80 3.67
1436 1509 3.244033 AGCACTGTCAATCTCAGCTAC 57.756 47.619 0.00 0.00 36.50 3.58
1545 1618 1.144057 GCACTCCCAGGATACGGTG 59.856 63.158 0.00 0.60 46.39 4.94
1673 1748 4.202223 CCACACACTACTGTCCTACAAAGT 60.202 45.833 0.00 0.00 0.00 2.66
1704 1779 4.380974 GCAGAAGAAGCGAAATTGTTCAAG 59.619 41.667 7.66 2.74 35.49 3.02
1715 1790 6.524586 GCGAAATTGTTCAAGAGGAAGTTATG 59.475 38.462 0.00 0.00 35.82 1.90
1742 1817 6.376581 CAGCAAAGAGAAATTCCCTAATGTCT 59.623 38.462 0.00 0.00 41.56 3.41
1768 1843 3.610040 TGGACAAGCAATAGACACGAT 57.390 42.857 0.00 0.00 0.00 3.73
1794 1869 0.178981 ACAGAACCACCAGCTTGCAT 60.179 50.000 0.00 0.00 0.00 3.96
1822 1897 9.355215 GCAAAATGATGGATATGATGAGAAATC 57.645 33.333 0.00 0.00 0.00 2.17
1847 1922 5.933790 TGCTTTTGTATAAAGTTGCTACCG 58.066 37.500 0.00 0.00 0.00 4.02
1973 2049 6.825213 GGATATATCAAGCCATATCAAGTGCA 59.175 38.462 14.60 0.00 36.33 4.57
1974 2050 7.501559 GGATATATCAAGCCATATCAAGTGCAT 59.498 37.037 14.60 0.00 36.33 3.96
1975 2051 4.848562 ATCAAGCCATATCAAGTGCATG 57.151 40.909 0.00 0.00 0.00 4.06
1976 2052 2.359848 TCAAGCCATATCAAGTGCATGC 59.640 45.455 11.82 11.82 0.00 4.06
1981 2057 2.355444 CCATATCAAGTGCATGCGACAA 59.645 45.455 14.09 0.00 0.00 3.18
1983 2059 0.806868 ATCAAGTGCATGCGACAAGG 59.193 50.000 14.09 6.40 0.00 3.61
2051 2127 7.882179 ACAAATTGTCTATCACCAACCTTAAC 58.118 34.615 0.00 0.00 0.00 2.01
2092 2168 1.814169 GCTAGTACCTTGCCACCGC 60.814 63.158 0.00 0.00 0.00 5.68
2226 2302 3.341823 AGCAGCACCTTGAATCAACTAG 58.658 45.455 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.313712 TGACAAGGTTAAATGGTCCTTCTC 58.686 41.667 0.00 0.00 39.22 2.87
1 2 5.319043 TGACAAGGTTAAATGGTCCTTCT 57.681 39.130 0.00 0.00 39.22 2.85
2 3 6.318900 CCTATGACAAGGTTAAATGGTCCTTC 59.681 42.308 0.00 0.00 39.22 3.46
3 4 6.187682 CCTATGACAAGGTTAAATGGTCCTT 58.812 40.000 0.00 0.00 41.53 3.36
4 5 5.755849 CCTATGACAAGGTTAAATGGTCCT 58.244 41.667 0.00 0.00 31.46 3.85
5 6 4.338400 GCCTATGACAAGGTTAAATGGTCC 59.662 45.833 5.82 0.00 39.02 4.46
6 7 5.193679 AGCCTATGACAAGGTTAAATGGTC 58.806 41.667 5.82 0.00 39.02 4.02
7 8 5.193099 AGCCTATGACAAGGTTAAATGGT 57.807 39.130 5.82 0.00 39.02 3.55
8 9 6.530019 AAAGCCTATGACAAGGTTAAATGG 57.470 37.500 5.82 0.00 39.02 3.16
9 10 8.087750 TGAAAAAGCCTATGACAAGGTTAAATG 58.912 33.333 5.82 0.00 39.02 2.32
10 11 8.189119 TGAAAAAGCCTATGACAAGGTTAAAT 57.811 30.769 5.82 0.00 39.02 1.40
11 12 7.589958 TGAAAAAGCCTATGACAAGGTTAAA 57.410 32.000 5.82 0.00 39.02 1.52
12 13 7.589958 TTGAAAAAGCCTATGACAAGGTTAA 57.410 32.000 5.82 0.00 39.02 2.01
13 14 7.286775 ACTTTGAAAAAGCCTATGACAAGGTTA 59.713 33.333 0.00 0.00 39.02 2.85
14 15 6.098266 ACTTTGAAAAAGCCTATGACAAGGTT 59.902 34.615 0.00 0.00 39.02 3.50
15 16 5.598417 ACTTTGAAAAAGCCTATGACAAGGT 59.402 36.000 0.00 0.00 39.02 3.50
16 17 6.089249 ACTTTGAAAAAGCCTATGACAAGG 57.911 37.500 0.00 0.00 39.87 3.61
17 18 6.738114 TGACTTTGAAAAAGCCTATGACAAG 58.262 36.000 0.00 0.00 0.00 3.16
18 19 6.707440 TGACTTTGAAAAAGCCTATGACAA 57.293 33.333 0.00 0.00 0.00 3.18
19 20 6.707440 TTGACTTTGAAAAAGCCTATGACA 57.293 33.333 0.00 0.00 0.00 3.58
20 21 8.084684 AGAATTGACTTTGAAAAAGCCTATGAC 58.915 33.333 0.00 0.00 0.00 3.06
21 22 8.084073 CAGAATTGACTTTGAAAAAGCCTATGA 58.916 33.333 0.00 0.00 0.00 2.15
22 23 8.084073 TCAGAATTGACTTTGAAAAAGCCTATG 58.916 33.333 0.00 0.00 0.00 2.23
23 24 8.181904 TCAGAATTGACTTTGAAAAAGCCTAT 57.818 30.769 0.00 0.00 0.00 2.57
24 25 7.581213 TCAGAATTGACTTTGAAAAAGCCTA 57.419 32.000 0.00 0.00 0.00 3.93
25 26 6.469782 TCAGAATTGACTTTGAAAAAGCCT 57.530 33.333 0.00 0.00 0.00 4.58
26 27 7.719778 ATTCAGAATTGACTTTGAAAAAGCC 57.280 32.000 0.00 0.00 33.71 4.35
32 33 8.950210 GGAGTGATATTCAGAATTGACTTTGAA 58.050 33.333 0.00 0.00 34.42 2.69
33 34 8.102676 TGGAGTGATATTCAGAATTGACTTTGA 58.897 33.333 0.00 0.00 31.71 2.69
34 35 8.272545 TGGAGTGATATTCAGAATTGACTTTG 57.727 34.615 0.00 0.00 31.71 2.77
35 36 9.471702 AATGGAGTGATATTCAGAATTGACTTT 57.528 29.630 0.00 0.00 31.71 2.66
36 37 9.118300 GAATGGAGTGATATTCAGAATTGACTT 57.882 33.333 0.00 0.00 31.71 3.01
37 38 8.270030 TGAATGGAGTGATATTCAGAATTGACT 58.730 33.333 0.00 1.40 31.71 3.41
38 39 8.442632 TGAATGGAGTGATATTCAGAATTGAC 57.557 34.615 0.00 0.00 31.71 3.18
39 40 9.063615 CATGAATGGAGTGATATTCAGAATTGA 57.936 33.333 0.00 0.00 36.61 2.57
40 41 8.847196 ACATGAATGGAGTGATATTCAGAATTG 58.153 33.333 0.00 0.00 36.61 2.32
41 42 8.991783 ACATGAATGGAGTGATATTCAGAATT 57.008 30.769 0.00 0.00 36.61 2.17
42 43 8.991783 AACATGAATGGAGTGATATTCAGAAT 57.008 30.769 0.00 0.20 36.61 2.40
43 44 8.812513 AAACATGAATGGAGTGATATTCAGAA 57.187 30.769 0.00 0.00 36.61 3.02
44 45 8.812513 AAAACATGAATGGAGTGATATTCAGA 57.187 30.769 0.00 0.00 36.61 3.27
67 68 3.063861 CGTCCATGAGATGCATCGAAAAA 59.936 43.478 20.67 6.66 34.15 1.94
68 69 2.609002 CGTCCATGAGATGCATCGAAAA 59.391 45.455 20.67 8.40 34.15 2.29
69 70 2.204237 CGTCCATGAGATGCATCGAAA 58.796 47.619 20.67 10.86 34.15 3.46
70 71 1.538849 CCGTCCATGAGATGCATCGAA 60.539 52.381 20.67 13.36 34.15 3.71
71 72 0.032540 CCGTCCATGAGATGCATCGA 59.967 55.000 20.67 12.10 34.15 3.59
72 73 0.249615 ACCGTCCATGAGATGCATCG 60.250 55.000 20.67 7.09 34.15 3.84
73 74 1.069823 AGACCGTCCATGAGATGCATC 59.930 52.381 19.37 19.37 34.15 3.91
74 75 1.069823 GAGACCGTCCATGAGATGCAT 59.930 52.381 0.00 0.00 37.85 3.96
75 76 0.461548 GAGACCGTCCATGAGATGCA 59.538 55.000 0.00 0.00 0.00 3.96
76 77 0.461548 TGAGACCGTCCATGAGATGC 59.538 55.000 0.00 0.00 0.00 3.91
77 78 2.752121 CATGAGACCGTCCATGAGATG 58.248 52.381 18.14 0.00 41.88 2.90
78 79 1.069823 GCATGAGACCGTCCATGAGAT 59.930 52.381 23.42 0.00 41.88 2.75
79 80 0.461548 GCATGAGACCGTCCATGAGA 59.538 55.000 23.42 0.00 41.88 3.27
80 81 0.176449 TGCATGAGACCGTCCATGAG 59.824 55.000 23.42 7.88 41.88 2.90
81 82 0.176449 CTGCATGAGACCGTCCATGA 59.824 55.000 23.42 13.19 41.88 3.07
82 83 0.812811 CCTGCATGAGACCGTCCATG 60.813 60.000 18.44 18.44 42.13 3.66
83 84 0.977627 TCCTGCATGAGACCGTCCAT 60.978 55.000 0.00 0.00 0.00 3.41
84 85 1.609210 TCCTGCATGAGACCGTCCA 60.609 57.895 0.00 0.00 0.00 4.02
85 86 1.153549 GTCCTGCATGAGACCGTCC 60.154 63.158 0.00 0.00 0.00 4.79
86 87 1.103803 TAGTCCTGCATGAGACCGTC 58.896 55.000 0.00 0.00 33.29 4.79
87 88 0.818296 GTAGTCCTGCATGAGACCGT 59.182 55.000 0.00 0.00 33.29 4.83
88 89 1.107114 AGTAGTCCTGCATGAGACCG 58.893 55.000 0.00 0.00 33.29 4.79
89 90 4.218852 GGTATAGTAGTCCTGCATGAGACC 59.781 50.000 0.00 0.00 33.29 3.85
90 91 4.827835 TGGTATAGTAGTCCTGCATGAGAC 59.172 45.833 0.00 0.00 0.00 3.36
91 92 5.061721 TGGTATAGTAGTCCTGCATGAGA 57.938 43.478 0.00 0.00 0.00 3.27
92 93 5.478332 TGATGGTATAGTAGTCCTGCATGAG 59.522 44.000 0.00 0.00 0.00 2.90
93 94 5.393866 TGATGGTATAGTAGTCCTGCATGA 58.606 41.667 0.00 0.00 0.00 3.07
94 95 5.728637 TGATGGTATAGTAGTCCTGCATG 57.271 43.478 0.00 0.00 0.00 4.06
95 96 6.747414 TTTGATGGTATAGTAGTCCTGCAT 57.253 37.500 0.00 0.00 0.00 3.96
96 97 6.747414 ATTTGATGGTATAGTAGTCCTGCA 57.253 37.500 0.00 0.00 0.00 4.41
108 109 9.247861 GCAAGGAAGGAATATATTTGATGGTAT 57.752 33.333 0.00 0.00 0.00 2.73
109 110 8.224025 TGCAAGGAAGGAATATATTTGATGGTA 58.776 33.333 0.00 0.00 0.00 3.25
110 111 7.068702 TGCAAGGAAGGAATATATTTGATGGT 58.931 34.615 0.00 0.00 0.00 3.55
111 112 7.528996 TGCAAGGAAGGAATATATTTGATGG 57.471 36.000 0.00 0.00 0.00 3.51
112 113 8.799367 TCATGCAAGGAAGGAATATATTTGATG 58.201 33.333 0.00 0.28 0.00 3.07
113 114 8.945195 TCATGCAAGGAAGGAATATATTTGAT 57.055 30.769 0.00 0.00 0.00 2.57
114 115 8.632679 GTTCATGCAAGGAAGGAATATATTTGA 58.367 33.333 0.00 0.00 37.27 2.69
115 116 7.592533 CGTTCATGCAAGGAAGGAATATATTTG 59.407 37.037 15.19 0.00 44.28 2.32
116 117 7.651808 CGTTCATGCAAGGAAGGAATATATTT 58.348 34.615 15.19 0.00 44.28 1.40
117 118 6.294176 GCGTTCATGCAAGGAAGGAATATATT 60.294 38.462 21.25 0.00 44.28 1.28
118 119 5.182001 GCGTTCATGCAAGGAAGGAATATAT 59.818 40.000 21.25 0.00 44.28 0.86
119 120 4.515191 GCGTTCATGCAAGGAAGGAATATA 59.485 41.667 21.25 0.00 44.28 0.86
120 121 3.316308 GCGTTCATGCAAGGAAGGAATAT 59.684 43.478 21.25 0.00 44.28 1.28
121 122 2.682856 GCGTTCATGCAAGGAAGGAATA 59.317 45.455 21.25 0.00 44.28 1.75
122 123 1.474077 GCGTTCATGCAAGGAAGGAAT 59.526 47.619 21.25 0.00 44.28 3.01
123 124 0.881118 GCGTTCATGCAAGGAAGGAA 59.119 50.000 21.25 4.82 44.28 3.36
124 125 0.960364 GGCGTTCATGCAAGGAAGGA 60.960 55.000 21.25 0.00 44.28 3.36
125 126 1.508088 GGCGTTCATGCAAGGAAGG 59.492 57.895 15.70 15.70 44.34 3.46
126 127 1.135315 CGGCGTTCATGCAAGGAAG 59.865 57.895 0.00 0.00 37.27 3.46
127 128 1.169661 AACGGCGTTCATGCAAGGAA 61.170 50.000 21.19 0.00 32.22 3.36
128 129 1.169661 AAACGGCGTTCATGCAAGGA 61.170 50.000 26.96 0.00 36.28 3.36
129 130 1.003262 CAAACGGCGTTCATGCAAGG 61.003 55.000 26.96 4.70 36.28 3.61
130 131 0.040514 TCAAACGGCGTTCATGCAAG 60.041 50.000 26.96 9.93 36.28 4.01
131 132 0.040514 CTCAAACGGCGTTCATGCAA 60.041 50.000 26.96 5.76 36.28 4.08
132 133 0.882484 TCTCAAACGGCGTTCATGCA 60.882 50.000 26.96 8.58 36.28 3.96
133 134 0.447801 ATCTCAAACGGCGTTCATGC 59.552 50.000 26.96 0.00 0.00 4.06
134 135 1.202065 CCATCTCAAACGGCGTTCATG 60.202 52.381 26.96 20.94 0.00 3.07
135 136 1.086696 CCATCTCAAACGGCGTTCAT 58.913 50.000 26.96 8.66 0.00 2.57
136 137 1.573829 GCCATCTCAAACGGCGTTCA 61.574 55.000 26.96 14.56 35.79 3.18
137 138 1.134694 GCCATCTCAAACGGCGTTC 59.865 57.895 26.96 6.92 35.79 3.95
138 139 3.263941 GCCATCTCAAACGGCGTT 58.736 55.556 21.19 21.19 35.79 4.84
141 142 1.377202 TCTGGCCATCTCAAACGGC 60.377 57.895 5.51 0.00 45.47 5.68
142 143 0.321564 TGTCTGGCCATCTCAAACGG 60.322 55.000 5.51 0.00 0.00 4.44
143 144 1.197721 GTTGTCTGGCCATCTCAAACG 59.802 52.381 5.51 0.00 0.00 3.60
144 145 2.229792 TGTTGTCTGGCCATCTCAAAC 58.770 47.619 5.51 7.89 0.00 2.93
145 146 2.655090 TGTTGTCTGGCCATCTCAAA 57.345 45.000 5.51 0.00 0.00 2.69
146 147 2.439409 CATGTTGTCTGGCCATCTCAA 58.561 47.619 5.51 9.60 0.00 3.02
147 148 1.340308 CCATGTTGTCTGGCCATCTCA 60.340 52.381 5.51 2.85 0.00 3.27
148 149 1.340405 ACCATGTTGTCTGGCCATCTC 60.340 52.381 5.51 0.00 37.27 2.75
149 150 0.700564 ACCATGTTGTCTGGCCATCT 59.299 50.000 5.51 0.00 37.27 2.90
150 151 1.098050 GACCATGTTGTCTGGCCATC 58.902 55.000 5.51 3.08 37.27 3.51
151 152 0.405198 TGACCATGTTGTCTGGCCAT 59.595 50.000 5.51 0.00 37.27 4.40
152 153 0.250858 CTGACCATGTTGTCTGGCCA 60.251 55.000 4.71 4.71 37.27 5.36
153 154 1.589716 GCTGACCATGTTGTCTGGCC 61.590 60.000 0.00 0.00 37.27 5.36
154 155 0.607489 AGCTGACCATGTTGTCTGGC 60.607 55.000 9.78 10.01 37.27 4.85
155 156 2.350522 GTAGCTGACCATGTTGTCTGG 58.649 52.381 0.00 0.00 39.80 3.86
171 172 1.070577 CAATATGTTCAGCGCGGTAGC 60.071 52.381 11.92 4.64 40.74 3.58
172 173 2.201732 ACAATATGTTCAGCGCGGTAG 58.798 47.619 11.92 5.90 0.00 3.18
173 174 2.303163 ACAATATGTTCAGCGCGGTA 57.697 45.000 11.92 0.00 0.00 4.02
174 175 1.931172 GTACAATATGTTCAGCGCGGT 59.069 47.619 4.23 4.23 0.00 5.68
175 176 1.930503 TGTACAATATGTTCAGCGCGG 59.069 47.619 8.83 0.00 0.00 6.46
176 177 3.859745 ATGTACAATATGTTCAGCGCG 57.140 42.857 0.00 0.00 31.35 6.86
177 178 6.869421 AAAAATGTACAATATGTTCAGCGC 57.131 33.333 0.00 0.00 31.35 5.92
251 252 6.785191 AGCAAAATGTTTCTCATGTATACGG 58.215 36.000 0.00 0.00 36.81 4.02
260 261 8.791675 TGAACATGTATAGCAAAATGTTTCTCA 58.208 29.630 0.00 0.00 41.91 3.27
281 282 7.492020 CCTGATCAAACTGAAAAATGTTGAACA 59.508 33.333 0.00 0.00 0.00 3.18
285 286 5.107760 CGCCTGATCAAACTGAAAAATGTTG 60.108 40.000 0.00 0.00 0.00 3.33
297 298 3.444916 TCTATTCGACGCCTGATCAAAC 58.555 45.455 0.00 0.00 0.00 2.93
301 302 1.068194 CCCTCTATTCGACGCCTGATC 60.068 57.143 0.00 0.00 0.00 2.92
306 307 0.311477 GAGACCCTCTATTCGACGCC 59.689 60.000 0.00 0.00 0.00 5.68
310 311 3.815962 CGATCAAGAGACCCTCTATTCGA 59.184 47.826 13.23 0.00 40.28 3.71
319 320 0.036388 TGCAACCGATCAAGAGACCC 60.036 55.000 0.00 0.00 0.00 4.46
349 352 3.242518 CTTCGACGCTTGATCACACTTA 58.757 45.455 0.00 0.00 0.00 2.24
352 355 0.716108 CCTTCGACGCTTGATCACAC 59.284 55.000 0.00 0.00 0.00 3.82
404 407 2.499289 TCAGAGCAAGATGGAGAGGAAC 59.501 50.000 0.00 0.00 0.00 3.62
419 422 1.208052 TGGTGGCTACAGAATCAGAGC 59.792 52.381 1.52 0.00 0.00 4.09
455 458 4.999950 ACTCAATTTGCTTCTCTGGTAGTG 59.000 41.667 0.00 0.00 0.00 2.74
468 471 4.346129 GGTCGATTCATGACTCAATTTGC 58.654 43.478 12.93 0.00 36.58 3.68
500 503 0.753262 AGGACCAGTGTCAGTGTGTC 59.247 55.000 15.56 15.56 43.65 3.67
524 527 0.181350 GATTGAGGGTTGAGGCGGAT 59.819 55.000 0.00 0.00 0.00 4.18
527 530 1.019673 CATGATTGAGGGTTGAGGCG 58.980 55.000 0.00 0.00 0.00 5.52
786 849 0.976073 TTAAGAGGGCTCAGGGACGG 60.976 60.000 0.00 0.00 0.00 4.79
849 917 2.546795 GGCGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
850 918 1.412710 GGCGAGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
851 919 1.138859 TGGCGAGAGAGAGAGAGAGAG 59.861 57.143 0.00 0.00 0.00 3.20
852 920 1.199615 TGGCGAGAGAGAGAGAGAGA 58.800 55.000 0.00 0.00 0.00 3.10
853 921 1.875514 CATGGCGAGAGAGAGAGAGAG 59.124 57.143 0.00 0.00 0.00 3.20
854 922 1.965935 CATGGCGAGAGAGAGAGAGA 58.034 55.000 0.00 0.00 0.00 3.10
855 923 0.311790 GCATGGCGAGAGAGAGAGAG 59.688 60.000 0.00 0.00 0.00 3.20
856 924 0.106769 AGCATGGCGAGAGAGAGAGA 60.107 55.000 0.00 0.00 0.00 3.10
857 925 0.311790 GAGCATGGCGAGAGAGAGAG 59.688 60.000 0.00 0.00 0.00 3.20
858 926 1.443322 CGAGCATGGCGAGAGAGAGA 61.443 60.000 0.00 0.00 0.00 3.10
862 930 1.318576 TATTCGAGCATGGCGAGAGA 58.681 50.000 0.00 0.00 39.14 3.10
865 933 2.411069 CAGATTATTCGAGCATGGCGAG 59.589 50.000 0.00 0.00 39.14 5.03
884 952 0.319728 CCGGCTGGATAGGATGTCAG 59.680 60.000 5.28 0.00 37.49 3.51
893 961 2.900269 TAAGGGTGGCCGGCTGGATA 62.900 60.000 28.56 9.62 37.49 2.59
908 977 7.434492 CAGGTGGTAGTAGTGATAATGTAAGG 58.566 42.308 0.00 0.00 0.00 2.69
910 979 6.460537 CGCAGGTGGTAGTAGTGATAATGTAA 60.461 42.308 0.00 0.00 0.00 2.41
913 982 4.299155 CGCAGGTGGTAGTAGTGATAATG 58.701 47.826 0.00 0.00 0.00 1.90
935 1004 1.401018 CGGCGGTGATCAAAGAAAACC 60.401 52.381 0.00 0.00 0.00 3.27
937 1006 0.239879 GCGGCGGTGATCAAAGAAAA 59.760 50.000 9.78 0.00 0.00 2.29
938 1007 0.605319 AGCGGCGGTGATCAAAGAAA 60.605 50.000 12.25 0.00 0.00 2.52
939 1008 1.003839 AGCGGCGGTGATCAAAGAA 60.004 52.632 12.25 0.00 0.00 2.52
959 1031 1.654954 GCGGCGACTGAAGAGTAGGA 61.655 60.000 12.98 0.00 30.16 2.94
1083 1155 4.484872 GCGGCCTCCAAGTACCCC 62.485 72.222 0.00 0.00 0.00 4.95
1137 1209 4.074970 GGGATGTGGTGTCCAATGATATC 58.925 47.826 0.00 0.00 37.49 1.63
1139 1211 2.849318 TGGGATGTGGTGTCCAATGATA 59.151 45.455 0.00 0.00 37.49 2.15
1140 1212 1.640149 TGGGATGTGGTGTCCAATGAT 59.360 47.619 0.00 0.00 37.49 2.45
1176 1248 4.810790 ACAAAGACGAGTTCCTCATACTG 58.189 43.478 0.00 0.00 0.00 2.74
1218 1290 2.094182 TGTGATAGCGGAACCAGAAGTC 60.094 50.000 0.00 0.00 0.00 3.01
1273 1346 4.702131 GCACTGTTCTGAATTCCTTATGGT 59.298 41.667 2.27 0.00 34.23 3.55
1333 1406 5.291905 AGCCTAGTTACAACTTGACAAGT 57.708 39.130 15.23 15.23 45.46 3.16
1360 1433 4.207165 AGTAGCTTTGGCAAGAAAACTGA 58.793 39.130 0.00 0.00 41.70 3.41
1545 1618 4.142381 GCAAGGTCATTAACTGGAATGGAC 60.142 45.833 5.16 0.00 37.41 4.02
1673 1748 2.503331 TCGCTTCTTCTGCAATTCCAA 58.497 42.857 0.00 0.00 0.00 3.53
1704 1779 3.347216 TCTTTGCTGGCATAACTTCCTC 58.653 45.455 0.00 0.00 0.00 3.71
1715 1790 2.174360 AGGGAATTTCTCTTTGCTGGC 58.826 47.619 0.00 0.00 0.00 4.85
1768 1843 4.634012 AGCTGGTGGTTCTGTATGTTAA 57.366 40.909 0.00 0.00 0.00 2.01
1794 1869 7.826918 TCTCATCATATCCATCATTTTGCAA 57.173 32.000 0.00 0.00 0.00 4.08
1822 1897 6.468956 CGGTAGCAACTTTATACAAAAGCATG 59.531 38.462 0.00 0.00 0.00 4.06
1858 1933 1.204312 GCTGACTTTCGTCCAACGC 59.796 57.895 0.00 0.00 42.21 4.84
1863 1938 0.458669 TATCCGGCTGACTTTCGTCC 59.541 55.000 0.00 0.00 39.47 4.79
1876 1951 4.511826 GTCATTCTGCCTTTAGTTATCCGG 59.488 45.833 0.00 0.00 0.00 5.14
1973 2049 1.079127 CGGAAGTCCCTTGTCGCAT 60.079 57.895 0.00 0.00 0.00 4.73
1974 2050 2.342279 CGGAAGTCCCTTGTCGCA 59.658 61.111 0.00 0.00 0.00 5.10
1975 2051 3.119096 GCGGAAGTCCCTTGTCGC 61.119 66.667 0.00 0.00 36.33 5.19
1976 2052 1.446272 GAGCGGAAGTCCCTTGTCG 60.446 63.158 0.00 0.00 0.00 4.35
1981 2057 0.610687 CTTGAAGAGCGGAAGTCCCT 59.389 55.000 0.00 0.00 0.00 4.20
1983 2059 3.528597 ATACTTGAAGAGCGGAAGTCC 57.471 47.619 0.00 0.00 32.27 3.85
2051 2127 3.192001 ACAATGCAATGCTACTCAACTGG 59.808 43.478 6.82 0.00 0.00 4.00
2115 2191 2.812358 TATGTAGCCGCGTTGATCAT 57.188 45.000 4.92 5.87 0.00 2.45


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

AutoCloner maintained by Alex Coulton.