Multiple sequence alignment - TraesCS5D01G526200

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 TraesCS5D01G526200 chr5D 100.000 3296 0 0 1 3296 544147968 544151263 0.000000e+00 6087.0
1 TraesCS5D01G526200 chr5D 85.206 2109 239 35 437 2492 544230877 544232965 0.000000e+00 2098.0
2 TraesCS5D01G526200 chr5D 79.654 1273 240 15 999 2263 544481609 544482870 0.000000e+00 898.0
3 TraesCS5D01G526200 chr5D 78.852 1272 252 13 999 2263 544459877 544461138 0.000000e+00 843.0
4 TraesCS5D01G526200 chr5D 81.688 557 91 6 1723 2277 543830902 543831449 1.390000e-123 453.0
5 TraesCS5D01G526200 chr5D 82.857 175 16 4 271 440 544213737 544213902 9.530000e-31 145.0
6 TraesCS5D01G526200 chr5D 81.366 161 10 5 445 605 544213961 544214101 2.690000e-21 113.0
7 TraesCS5D01G526200 chr5D 94.737 57 2 1 10 66 544230504 544230559 1.630000e-13 87.9
8 TraesCS5D01G526200 chr4A 93.401 2349 94 16 606 2917 625166661 625164337 0.000000e+00 3422.0
9 TraesCS5D01G526200 chr4A 85.701 2098 230 37 437 2492 625078200 625076131 0.000000e+00 2148.0
10 TraesCS5D01G526200 chr4A 79.826 1264 237 15 999 2253 624369657 624370911 0.000000e+00 905.0
11 TraesCS5D01G526200 chr4A 86.250 400 29 9 221 612 625167280 625166899 8.510000e-111 411.0
12 TraesCS5D01G526200 chr4A 92.754 276 9 6 3023 3296 625127560 625127294 3.990000e-104 388.0
13 TraesCS5D01G526200 chr4A 76.418 335 40 24 2785 3097 625075937 625075620 9.530000e-31 145.0
14 TraesCS5D01G526200 chr4A 89.583 96 10 0 2919 3014 625164225 625164130 4.470000e-24 122.0
15 TraesCS5D01G526200 chr5B 92.988 2125 121 10 843 2957 686200952 686203058 0.000000e+00 3073.0
16 TraesCS5D01G526200 chr5B 90.124 1367 101 14 1599 2952 686342922 686344267 0.000000e+00 1746.0
17 TraesCS5D01G526200 chr5B 86.424 1510 176 16 998 2490 686432236 686433733 0.000000e+00 1626.0
18 TraesCS5D01G526200 chr5B 82.411 1211 130 45 458 1594 686333366 686334567 0.000000e+00 979.0
19 TraesCS5D01G526200 chr5B 81.291 604 101 9 1723 2323 685657478 685656884 2.300000e-131 479.0
20 TraesCS5D01G526200 chr5B 89.180 305 7 12 3014 3296 686203545 686203845 1.120000e-94 357.0
21 TraesCS5D01G526200 chr5B 88.852 305 10 10 3014 3296 686344839 686345141 1.450000e-93 353.0
22 TraesCS5D01G526200 chr5B 83.891 329 27 11 285 605 686199946 686200256 1.160000e-74 291.0
23 TraesCS5D01G526200 chr5B 81.081 370 43 17 458 806 686430548 686430911 1.510000e-68 270.0
24 TraesCS5D01G526200 chr5B 86.335 161 18 4 65 224 605487799 605487956 4.370000e-39 172.0
25 TraesCS5D01G526200 chr5B 88.095 126 8 2 2782 2906 686433923 686434042 3.430000e-30 143.0
26 TraesCS5D01G526200 chr5B 87.500 72 7 2 2500 2570 291999079 291999149 7.580000e-12 82.4
27 TraesCS5D01G526200 chr2A 87.349 166 18 3 65 227 688585346 688585511 1.560000e-43 187.0
28 TraesCS5D01G526200 chr2A 86.420 162 20 2 65 224 722749013 722748852 3.380000e-40 176.0
29 TraesCS5D01G526200 chr6B 84.211 133 19 2 92 224 29371337 29371207 9.600000e-26 128.0
30 TraesCS5D01G526200 chr7B 93.846 65 2 2 3 66 213247965 213248028 2.710000e-16 97.1
31 TraesCS5D01G526200 chr7B 92.063 63 2 3 3 64 313691418 313691358 5.860000e-13 86.1
32 TraesCS5D01G526200 chr7A 92.308 65 3 2 3 66 251743400 251743463 1.260000e-14 91.6
33 TraesCS5D01G526200 chr7A 86.111 72 10 0 2500 2571 179531454 179531525 9.810000e-11 78.7
34 TraesCS5D01G526200 chr7D 94.737 57 2 1 9 64 13688581 13688637 1.630000e-13 87.9
35 TraesCS5D01G526200 chr7D 94.737 57 2 1 9 64 13689851 13689907 1.630000e-13 87.9
36 TraesCS5D01G526200 chr7D 94.737 57 2 1 9 64 13692393 13692449 1.630000e-13 87.9
37 TraesCS5D01G526200 chr7D 90.769 65 4 2 3 66 236640481 236640544 5.860000e-13 86.1
38 TraesCS5D01G526200 chr1B 92.063 63 3 2 3 64 636315870 636315809 1.630000e-13 87.9


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 TraesCS5D01G526200 chr5D 544147968 544151263 3295 False 6087.000000 6087 100.000000 1 3296 1 chr5D.!!$F2 3295
1 TraesCS5D01G526200 chr5D 544230504 544232965 2461 False 1092.950000 2098 89.971500 10 2492 2 chr5D.!!$F6 2482
2 TraesCS5D01G526200 chr5D 544481609 544482870 1261 False 898.000000 898 79.654000 999 2263 1 chr5D.!!$F4 1264
3 TraesCS5D01G526200 chr5D 544459877 544461138 1261 False 843.000000 843 78.852000 999 2263 1 chr5D.!!$F3 1264
4 TraesCS5D01G526200 chr5D 543830902 543831449 547 False 453.000000 453 81.688000 1723 2277 1 chr5D.!!$F1 554
5 TraesCS5D01G526200 chr4A 625164130 625167280 3150 True 1318.333333 3422 89.744667 221 3014 3 chr4A.!!$R3 2793
6 TraesCS5D01G526200 chr4A 625075620 625078200 2580 True 1146.500000 2148 81.059500 437 3097 2 chr4A.!!$R2 2660
7 TraesCS5D01G526200 chr4A 624369657 624370911 1254 False 905.000000 905 79.826000 999 2253 1 chr4A.!!$F1 1254
8 TraesCS5D01G526200 chr5B 686199946 686203845 3899 False 1240.333333 3073 88.686333 285 3296 3 chr5B.!!$F4 3011
9 TraesCS5D01G526200 chr5B 686342922 686345141 2219 False 1049.500000 1746 89.488000 1599 3296 2 chr5B.!!$F5 1697
10 TraesCS5D01G526200 chr5B 686333366 686334567 1201 False 979.000000 979 82.411000 458 1594 1 chr5B.!!$F3 1136
11 TraesCS5D01G526200 chr5B 686430548 686434042 3494 False 679.666667 1626 85.200000 458 2906 3 chr5B.!!$F6 2448
12 TraesCS5D01G526200 chr5B 685656884 685657478 594 True 479.000000 479 81.291000 1723 2323 1 chr5B.!!$R1 600

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
389 415 0.171007 CACATCATCCCGGTTTGTGC 59.829 55.0 0.0 0.0 32.24 4.57 F
426 459 0.673333 CGCCACAGTGCATCCTAACA 60.673 55.0 0.0 0.0 0.00 2.41 F
719 1258 0.949105 GCCGAACTGTCCACGACAAT 60.949 55.0 0.0 0.0 42.26 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 2997 0.105760 GAGAGGCTCCTGGGATGAGA 60.106 60.000 11.71 0.0 31.26 3.27 R
1301 3056 0.599204 GACGCCCACGAAAGAGTTCA 60.599 55.000 0.00 0.0 43.93 3.18 R
2624 4461 1.634753 TCGATAGACGACGAGTGCG 59.365 57.895 0.00 0.0 46.45 5.34 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
71 97 6.554334 TGTGGTCAAACTTAGAAATGCTAC 57.446 37.500 0.00 0.00 0.00 3.58
73 99 6.017440 TGTGGTCAAACTTAGAAATGCTACAC 60.017 38.462 0.00 0.00 0.00 2.90
74 100 5.472137 TGGTCAAACTTAGAAATGCTACACC 59.528 40.000 0.00 0.00 0.00 4.16
76 102 6.877322 GGTCAAACTTAGAAATGCTACACCTA 59.123 38.462 0.00 0.00 0.00 3.08
77 103 7.148457 GGTCAAACTTAGAAATGCTACACCTAC 60.148 40.741 0.00 0.00 0.00 3.18
78 104 6.588756 TCAAACTTAGAAATGCTACACCTACG 59.411 38.462 0.00 0.00 0.00 3.51
79 105 5.909621 ACTTAGAAATGCTACACCTACGA 57.090 39.130 0.00 0.00 0.00 3.43
81 107 6.875076 ACTTAGAAATGCTACACCTACGAAT 58.125 36.000 0.00 0.00 0.00 3.34
82 108 6.757010 ACTTAGAAATGCTACACCTACGAATG 59.243 38.462 0.00 0.00 0.00 2.67
83 109 4.442706 AGAAATGCTACACCTACGAATGG 58.557 43.478 0.00 0.00 0.00 3.16
84 110 3.906720 AATGCTACACCTACGAATGGT 57.093 42.857 0.00 0.00 38.53 3.55
87 113 4.804868 TGCTACACCTACGAATGGTTTA 57.195 40.909 0.00 0.00 35.28 2.01
88 114 5.149973 TGCTACACCTACGAATGGTTTAA 57.850 39.130 0.00 0.00 35.28 1.52
90 116 5.640357 TGCTACACCTACGAATGGTTTAAAG 59.360 40.000 0.00 0.00 35.28 1.85
91 117 5.640783 GCTACACCTACGAATGGTTTAAAGT 59.359 40.000 0.00 0.00 35.28 2.66
92 118 6.813152 GCTACACCTACGAATGGTTTAAAGTA 59.187 38.462 0.00 0.00 35.28 2.24
93 119 7.331687 GCTACACCTACGAATGGTTTAAAGTAA 59.668 37.037 0.00 0.00 35.28 2.24
94 120 9.374838 CTACACCTACGAATGGTTTAAAGTAAT 57.625 33.333 0.00 0.00 35.28 1.89
96 122 7.335171 ACACCTACGAATGGTTTAAAGTAATCC 59.665 37.037 0.00 0.00 35.28 3.01
97 123 7.334921 CACCTACGAATGGTTTAAAGTAATCCA 59.665 37.037 0.00 0.00 40.65 3.41
98 124 8.050930 ACCTACGAATGGTTTAAAGTAATCCAT 58.949 33.333 2.27 2.27 45.51 3.41
101 127 7.912383 ACGAATGGTTTAAAGTAATCCATACG 58.088 34.615 7.50 0.00 43.79 3.06
102 128 7.550196 ACGAATGGTTTAAAGTAATCCATACGT 59.450 33.333 7.50 0.00 43.79 3.57
103 129 7.849026 CGAATGGTTTAAAGTAATCCATACGTG 59.151 37.037 0.00 0.00 43.79 4.49
107 133 9.887629 TGGTTTAAAGTAATCCATACGTGATTA 57.112 29.630 0.00 0.02 39.62 1.75
112 138 8.873215 AAAGTAATCCATACGTGATTAGACAG 57.127 34.615 0.00 0.00 39.62 3.51
113 139 6.448006 AGTAATCCATACGTGATTAGACAGC 58.552 40.000 0.00 0.00 39.62 4.40
114 140 5.537300 AATCCATACGTGATTAGACAGCT 57.463 39.130 0.00 0.00 30.85 4.24
115 141 4.307443 TCCATACGTGATTAGACAGCTG 57.693 45.455 13.48 13.48 0.00 4.24
117 143 2.579207 TACGTGATTAGACAGCTGGC 57.421 50.000 19.93 16.91 0.00 4.85
120 146 1.661341 GTGATTAGACAGCTGGCAGG 58.339 55.000 24.55 2.59 0.00 4.85
121 147 1.065854 GTGATTAGACAGCTGGCAGGT 60.066 52.381 24.55 14.51 0.00 4.00
123 149 2.837591 TGATTAGACAGCTGGCAGGTTA 59.162 45.455 24.55 1.45 0.00 2.85
124 150 3.455910 TGATTAGACAGCTGGCAGGTTAT 59.544 43.478 24.55 8.30 0.00 1.89
125 151 2.988010 TAGACAGCTGGCAGGTTATG 57.012 50.000 24.55 8.76 0.00 1.90
126 152 1.279496 AGACAGCTGGCAGGTTATGA 58.721 50.000 24.55 0.00 0.00 2.15
127 153 1.842562 AGACAGCTGGCAGGTTATGAT 59.157 47.619 24.55 0.00 0.00 2.45
128 154 2.240667 AGACAGCTGGCAGGTTATGATT 59.759 45.455 24.55 0.00 0.00 2.57
129 155 2.357009 GACAGCTGGCAGGTTATGATTG 59.643 50.000 16.81 6.43 0.00 2.67
130 156 2.025981 ACAGCTGGCAGGTTATGATTGA 60.026 45.455 17.98 0.00 0.00 2.57
131 157 2.617308 CAGCTGGCAGGTTATGATTGAG 59.383 50.000 17.98 0.00 0.00 3.02
132 158 1.952296 GCTGGCAGGTTATGATTGAGG 59.048 52.381 17.64 0.00 0.00 3.86
133 159 2.684927 GCTGGCAGGTTATGATTGAGGT 60.685 50.000 17.64 0.00 0.00 3.85
134 160 3.624777 CTGGCAGGTTATGATTGAGGTT 58.375 45.455 6.61 0.00 0.00 3.50
135 161 4.780815 CTGGCAGGTTATGATTGAGGTTA 58.219 43.478 6.61 0.00 0.00 2.85
136 162 4.780815 TGGCAGGTTATGATTGAGGTTAG 58.219 43.478 0.00 0.00 0.00 2.34
137 163 4.473196 TGGCAGGTTATGATTGAGGTTAGA 59.527 41.667 0.00 0.00 0.00 2.10
138 164 5.059833 GGCAGGTTATGATTGAGGTTAGAG 58.940 45.833 0.00 0.00 0.00 2.43
139 165 5.163301 GGCAGGTTATGATTGAGGTTAGAGA 60.163 44.000 0.00 0.00 0.00 3.10
140 166 5.988561 GCAGGTTATGATTGAGGTTAGAGAG 59.011 44.000 0.00 0.00 0.00 3.20
141 167 6.183360 GCAGGTTATGATTGAGGTTAGAGAGA 60.183 42.308 0.00 0.00 0.00 3.10
142 168 7.633772 GCAGGTTATGATTGAGGTTAGAGAGAA 60.634 40.741 0.00 0.00 0.00 2.87
143 169 7.925483 CAGGTTATGATTGAGGTTAGAGAGAAG 59.075 40.741 0.00 0.00 0.00 2.85
144 170 7.070571 AGGTTATGATTGAGGTTAGAGAGAAGG 59.929 40.741 0.00 0.00 0.00 3.46
145 171 4.744795 TGATTGAGGTTAGAGAGAAGGC 57.255 45.455 0.00 0.00 0.00 4.35
146 172 3.131223 TGATTGAGGTTAGAGAGAAGGCG 59.869 47.826 0.00 0.00 0.00 5.52
147 173 1.475403 TGAGGTTAGAGAGAAGGCGG 58.525 55.000 0.00 0.00 0.00 6.13
148 174 0.747852 GAGGTTAGAGAGAAGGCGGG 59.252 60.000 0.00 0.00 0.00 6.13
149 175 1.144276 GGTTAGAGAGAAGGCGGGC 59.856 63.158 0.00 0.00 0.00 6.13
150 176 1.144276 GTTAGAGAGAAGGCGGGCC 59.856 63.158 0.18 0.18 0.00 5.80
151 177 2.064581 TTAGAGAGAAGGCGGGCCC 61.065 63.158 13.57 13.57 36.58 5.80
155 181 3.168528 GAGAAGGCGGGCCCCATA 61.169 66.667 18.66 0.00 36.58 2.74
156 182 2.694616 AGAAGGCGGGCCCCATAA 60.695 61.111 18.66 0.00 36.58 1.90
157 183 2.518587 GAAGGCGGGCCCCATAAC 60.519 66.667 18.66 1.47 36.58 1.89
158 184 3.343326 AAGGCGGGCCCCATAACA 61.343 61.111 18.66 0.00 36.58 2.41
159 185 3.655350 AAGGCGGGCCCCATAACAC 62.655 63.158 18.66 0.00 36.58 3.32
160 186 4.123545 GGCGGGCCCCATAACACT 62.124 66.667 18.66 0.00 0.00 3.55
161 187 2.044352 GCGGGCCCCATAACACTT 60.044 61.111 18.66 0.00 0.00 3.16
162 188 1.225148 GCGGGCCCCATAACACTTA 59.775 57.895 18.66 0.00 0.00 2.24
163 189 0.394625 GCGGGCCCCATAACACTTAA 60.395 55.000 18.66 0.00 0.00 1.85
164 190 1.956159 GCGGGCCCCATAACACTTAAA 60.956 52.381 18.66 0.00 0.00 1.52
165 191 2.448453 CGGGCCCCATAACACTTAAAA 58.552 47.619 18.66 0.00 0.00 1.52
166 192 3.028130 CGGGCCCCATAACACTTAAAAT 58.972 45.455 18.66 0.00 0.00 1.82
167 193 3.067601 CGGGCCCCATAACACTTAAAATC 59.932 47.826 18.66 0.00 0.00 2.17
168 194 4.027437 GGGCCCCATAACACTTAAAATCA 58.973 43.478 12.23 0.00 0.00 2.57
169 195 4.099419 GGGCCCCATAACACTTAAAATCAG 59.901 45.833 12.23 0.00 0.00 2.90
170 196 4.099419 GGCCCCATAACACTTAAAATCAGG 59.901 45.833 0.00 0.00 0.00 3.86
171 197 4.099419 GCCCCATAACACTTAAAATCAGGG 59.901 45.833 0.00 0.00 0.00 4.45
172 198 4.649218 CCCCATAACACTTAAAATCAGGGG 59.351 45.833 0.00 0.00 45.50 4.79
173 199 4.649218 CCCATAACACTTAAAATCAGGGGG 59.351 45.833 0.00 0.00 0.00 5.40
174 200 5.515106 CCATAACACTTAAAATCAGGGGGA 58.485 41.667 0.00 0.00 0.00 4.81
175 201 5.594317 CCATAACACTTAAAATCAGGGGGAG 59.406 44.000 0.00 0.00 0.00 4.30
176 202 6.423182 CATAACACTTAAAATCAGGGGGAGA 58.577 40.000 0.00 0.00 0.00 3.71
177 203 4.576330 ACACTTAAAATCAGGGGGAGAG 57.424 45.455 0.00 0.00 0.00 3.20
178 204 4.175962 ACACTTAAAATCAGGGGGAGAGA 58.824 43.478 0.00 0.00 0.00 3.10
179 205 4.601857 ACACTTAAAATCAGGGGGAGAGAA 59.398 41.667 0.00 0.00 0.00 2.87
180 206 5.189180 CACTTAAAATCAGGGGGAGAGAAG 58.811 45.833 0.00 0.00 0.00 2.85
181 207 4.852697 ACTTAAAATCAGGGGGAGAGAAGT 59.147 41.667 0.00 0.00 0.00 3.01
182 208 6.030082 ACTTAAAATCAGGGGGAGAGAAGTA 58.970 40.000 0.00 0.00 0.00 2.24
183 209 6.678857 ACTTAAAATCAGGGGGAGAGAAGTAT 59.321 38.462 0.00 0.00 0.00 2.12
184 210 7.184753 ACTTAAAATCAGGGGGAGAGAAGTATT 59.815 37.037 0.00 0.00 0.00 1.89
185 211 8.632731 TTAAAATCAGGGGGAGAGAAGTATTA 57.367 34.615 0.00 0.00 0.00 0.98
186 212 7.525158 AAAATCAGGGGGAGAGAAGTATTAA 57.475 36.000 0.00 0.00 0.00 1.40
187 213 7.713704 AAATCAGGGGGAGAGAAGTATTAAT 57.286 36.000 0.00 0.00 0.00 1.40
188 214 6.694445 ATCAGGGGGAGAGAAGTATTAATG 57.306 41.667 0.00 0.00 0.00 1.90
189 215 4.907875 TCAGGGGGAGAGAAGTATTAATGG 59.092 45.833 0.00 0.00 0.00 3.16
190 216 4.907875 CAGGGGGAGAGAAGTATTAATGGA 59.092 45.833 0.00 0.00 0.00 3.41
191 217 5.369699 CAGGGGGAGAGAAGTATTAATGGAA 59.630 44.000 0.00 0.00 0.00 3.53
192 218 5.976870 AGGGGGAGAGAAGTATTAATGGAAA 59.023 40.000 0.00 0.00 0.00 3.13
193 219 6.101881 AGGGGGAGAGAAGTATTAATGGAAAG 59.898 42.308 0.00 0.00 0.00 2.62
194 220 6.126449 GGGGGAGAGAAGTATTAATGGAAAGT 60.126 42.308 0.00 0.00 0.00 2.66
195 221 7.347252 GGGGAGAGAAGTATTAATGGAAAGTT 58.653 38.462 0.00 0.00 0.00 2.66
196 222 7.283354 GGGGAGAGAAGTATTAATGGAAAGTTG 59.717 40.741 0.00 0.00 0.00 3.16
197 223 7.201741 GGGAGAGAAGTATTAATGGAAAGTTGC 60.202 40.741 0.00 0.00 0.00 4.17
198 224 7.336931 GGAGAGAAGTATTAATGGAAAGTTGCA 59.663 37.037 0.00 0.00 0.00 4.08
199 225 8.814038 AGAGAAGTATTAATGGAAAGTTGCAT 57.186 30.769 0.00 0.00 41.21 3.96
200 226 9.905713 AGAGAAGTATTAATGGAAAGTTGCATA 57.094 29.630 0.00 0.00 38.33 3.14
208 234 9.995003 ATTAATGGAAAGTTGCATAAAAGTTCA 57.005 25.926 0.00 0.00 38.33 3.18
209 235 7.713764 AATGGAAAGTTGCATAAAAGTTCAC 57.286 32.000 0.00 0.00 38.33 3.18
210 236 5.277825 TGGAAAGTTGCATAAAAGTTCACG 58.722 37.500 0.00 0.00 0.00 4.35
211 237 5.163602 TGGAAAGTTGCATAAAAGTTCACGT 60.164 36.000 0.00 0.00 0.00 4.49
212 238 5.746721 GGAAAGTTGCATAAAAGTTCACGTT 59.253 36.000 0.00 0.00 0.00 3.99
213 239 6.913673 GGAAAGTTGCATAAAAGTTCACGTTA 59.086 34.615 0.00 0.00 0.00 3.18
214 240 7.112984 GGAAAGTTGCATAAAAGTTCACGTTAG 59.887 37.037 0.00 0.00 0.00 2.34
215 241 6.613755 AGTTGCATAAAAGTTCACGTTAGT 57.386 33.333 0.00 0.00 0.00 2.24
216 242 6.656003 AGTTGCATAAAAGTTCACGTTAGTC 58.344 36.000 0.00 0.00 0.00 2.59
217 243 6.482308 AGTTGCATAAAAGTTCACGTTAGTCT 59.518 34.615 0.00 0.00 0.00 3.24
218 244 6.854496 TGCATAAAAGTTCACGTTAGTCTT 57.146 33.333 0.00 0.00 0.00 3.01
219 245 6.884187 TGCATAAAAGTTCACGTTAGTCTTC 58.116 36.000 0.00 0.00 0.00 2.87
220 246 6.480651 TGCATAAAAGTTCACGTTAGTCTTCA 59.519 34.615 0.00 0.00 0.00 3.02
221 247 7.172532 TGCATAAAAGTTCACGTTAGTCTTCAT 59.827 33.333 0.00 0.00 0.00 2.57
222 248 8.653338 GCATAAAAGTTCACGTTAGTCTTCATA 58.347 33.333 0.00 0.00 0.00 2.15
225 251 8.522178 AAAAGTTCACGTTAGTCTTCATAGAG 57.478 34.615 0.00 0.00 0.00 2.43
226 252 6.197364 AGTTCACGTTAGTCTTCATAGAGG 57.803 41.667 0.00 0.00 0.00 3.69
227 253 5.944599 AGTTCACGTTAGTCTTCATAGAGGA 59.055 40.000 0.00 0.00 0.00 3.71
228 254 6.603997 AGTTCACGTTAGTCTTCATAGAGGAT 59.396 38.462 0.00 0.00 0.00 3.24
229 255 7.122948 AGTTCACGTTAGTCTTCATAGAGGATT 59.877 37.037 0.00 0.00 0.00 3.01
230 256 8.404000 GTTCACGTTAGTCTTCATAGAGGATTA 58.596 37.037 0.00 0.00 0.00 1.75
231 257 8.693120 TCACGTTAGTCTTCATAGAGGATTAT 57.307 34.615 0.00 0.00 0.00 1.28
232 258 8.784994 TCACGTTAGTCTTCATAGAGGATTATC 58.215 37.037 0.00 0.00 0.00 1.75
233 259 8.024285 CACGTTAGTCTTCATAGAGGATTATCC 58.976 40.741 2.40 2.40 36.58 2.59
252 278 4.336889 TCCTTATTTATAGCGCTGCAGT 57.663 40.909 22.90 5.90 0.00 4.40
260 286 2.691409 TAGCGCTGCAGTATTTTCCT 57.309 45.000 22.90 4.16 0.00 3.36
262 288 3.199880 AGCGCTGCAGTATTTTCCTAT 57.800 42.857 10.39 0.00 0.00 2.57
265 291 5.123227 AGCGCTGCAGTATTTTCCTATAAA 58.877 37.500 10.39 0.00 0.00 1.40
379 405 1.135046 CGAGATCACGCACATCATCC 58.865 55.000 0.00 0.00 0.00 3.51
385 411 1.002624 ACGCACATCATCCCGGTTT 60.003 52.632 0.00 0.00 0.00 3.27
389 415 0.171007 CACATCATCCCGGTTTGTGC 59.829 55.000 0.00 0.00 32.24 4.57
404 430 2.391616 TGTGCACATGAGATGAGACC 57.608 50.000 17.42 0.00 0.00 3.85
426 459 0.673333 CGCCACAGTGCATCCTAACA 60.673 55.000 0.00 0.00 0.00 2.41
440 513 3.325870 TCCTAACATTTGACGACTGCAG 58.674 45.455 13.48 13.48 0.00 4.41
443 516 1.597742 ACATTTGACGACTGCAGCTT 58.402 45.000 15.27 0.00 0.00 3.74
454 533 4.283403 GCAGCTTTGGCCGCACAA 62.283 61.111 0.00 0.00 41.15 3.33
478 557 4.406648 TCACTGAACTAGGCATATGTGG 57.593 45.455 4.29 0.00 0.00 4.17
581 674 1.496060 TTGATGGACTATGGCGGAGT 58.504 50.000 0.00 0.00 0.00 3.85
582 675 1.040646 TGATGGACTATGGCGGAGTC 58.959 55.000 9.48 9.48 42.24 3.36
620 1158 2.631418 TGCTGTACTACACGAGCTTC 57.369 50.000 0.00 0.00 34.39 3.86
642 1180 1.298340 CCATGCCACCCACGAGTAA 59.702 57.895 0.00 0.00 0.00 2.24
684 1222 1.482177 CCAGGGGGAAACATCCACAAA 60.482 52.381 0.00 0.00 34.04 2.83
699 1237 4.009675 TCCACAAACATTGATGGACTAGC 58.990 43.478 9.06 0.00 36.56 3.42
719 1258 0.949105 GCCGAACTGTCCACGACAAT 60.949 55.000 0.00 0.00 42.26 2.71
735 1274 5.926542 CACGACAATTAGAGTTGAGAAGGAA 59.073 40.000 0.00 0.00 33.37 3.36
800 1344 4.359706 GCAGACAACTACAAAAACCAAGG 58.640 43.478 0.00 0.00 0.00 3.61
835 2563 6.071503 GGCCACGGACTAATAATAGTACTGAT 60.072 42.308 5.39 0.00 42.47 2.90
1244 2999 4.008933 GCGTGGCCTCACAGGTCT 62.009 66.667 3.32 0.00 41.63 3.85
1554 3309 4.717629 TTGCCGCCGTCTCTGTCG 62.718 66.667 0.00 0.00 0.00 4.35
1856 3611 2.922740 AGTTTGTTACGGCTCAAGGA 57.077 45.000 0.00 0.00 0.00 3.36
1857 3612 2.767505 AGTTTGTTACGGCTCAAGGAG 58.232 47.619 0.00 0.00 0.00 3.69
2331 4140 6.085555 GGATCGATTCCATCTACAAGTACA 57.914 41.667 0.00 0.00 44.74 2.90
2337 4146 7.285629 TCGATTCCATCTACAAGTACAAGATCT 59.714 37.037 0.00 0.00 0.00 2.75
2624 4461 9.307121 CCTATCATGAGAATTATATCCAACGAC 57.693 37.037 0.09 0.00 0.00 4.34
2690 4527 9.769093 GTGGTTATTGTTATTAGATGTGTGAAC 57.231 33.333 0.00 0.00 0.00 3.18
2952 4936 1.269831 GCACTCGACCTGACTTTGACT 60.270 52.381 0.00 0.00 0.00 3.41
2957 4941 1.802069 GACCTGACTTTGACTGGCTC 58.198 55.000 0.00 0.00 0.00 4.70
2968 4958 1.299541 GACTGGCTCTCTCTCTCTCG 58.700 60.000 0.00 0.00 0.00 4.04
2970 4960 1.490490 ACTGGCTCTCTCTCTCTCGAT 59.510 52.381 0.00 0.00 0.00 3.59
2972 4962 1.768275 TGGCTCTCTCTCTCTCGATCT 59.232 52.381 0.00 0.00 0.00 2.75
3138 5655 1.746171 CGTACATCCTCCTCCTCGTGA 60.746 57.143 0.00 0.00 0.00 4.35
3142 5659 2.432510 ACATCCTCCTCCTCGTGAATTC 59.567 50.000 0.00 0.00 0.00 2.17
3143 5660 2.534042 TCCTCCTCCTCGTGAATTCT 57.466 50.000 7.05 0.00 0.00 2.40
3144 5661 2.379972 TCCTCCTCCTCGTGAATTCTC 58.620 52.381 7.05 1.90 0.00 2.87
3216 5735 5.502089 AAAATTTCTCCCATGATGGCAAA 57.498 34.783 5.79 5.03 35.79 3.68
3218 5737 5.703730 AATTTCTCCCATGATGGCAAATT 57.296 34.783 5.79 12.33 35.79 1.82
3219 5738 4.741321 TTTCTCCCATGATGGCAAATTC 57.259 40.909 5.79 0.00 35.79 2.17
3220 5739 3.675348 TCTCCCATGATGGCAAATTCT 57.325 42.857 5.79 0.00 35.79 2.40
3221 5740 3.559069 TCTCCCATGATGGCAAATTCTC 58.441 45.455 5.79 0.00 35.79 2.87
3222 5741 2.626743 CTCCCATGATGGCAAATTCTCC 59.373 50.000 5.79 0.00 35.79 3.71
3261 5780 1.751927 CACTTGCATGAGCCCCCTC 60.752 63.158 6.60 0.00 41.13 4.30
3263 5782 4.113815 TTGCATGAGCCCCCTCCG 62.114 66.667 0.00 0.00 41.13 4.63
3266 5785 3.866582 CATGAGCCCCCTCCGGAC 61.867 72.222 0.00 0.00 37.29 4.79
3267 5786 4.414956 ATGAGCCCCCTCCGGACA 62.415 66.667 0.00 0.00 37.29 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 92 3.688694 AAACCATTCGTAGGTGTAGCA 57.311 42.857 0.00 0.00 39.86 3.49
67 93 5.640783 ACTTTAAACCATTCGTAGGTGTAGC 59.359 40.000 0.00 0.00 39.86 3.58
68 94 8.761575 TTACTTTAAACCATTCGTAGGTGTAG 57.238 34.615 0.00 0.00 39.86 2.74
70 96 7.335171 GGATTACTTTAAACCATTCGTAGGTGT 59.665 37.037 0.00 0.00 39.86 4.16
71 97 7.334921 TGGATTACTTTAAACCATTCGTAGGTG 59.665 37.037 0.00 0.00 39.86 4.00
73 99 7.852971 TGGATTACTTTAAACCATTCGTAGG 57.147 36.000 0.00 0.00 35.93 3.18
76 102 7.912383 CGTATGGATTACTTTAAACCATTCGT 58.088 34.615 18.09 4.07 45.57 3.85
78 104 8.885722 TCACGTATGGATTACTTTAAACCATTC 58.114 33.333 11.62 7.19 45.57 2.67
79 105 8.795842 TCACGTATGGATTACTTTAAACCATT 57.204 30.769 11.62 0.00 45.57 3.16
81 107 8.795842 AATCACGTATGGATTACTTTAAACCA 57.204 30.769 0.00 0.00 43.47 3.67
87 113 7.438459 GCTGTCTAATCACGTATGGATTACTTT 59.562 37.037 3.41 0.00 36.45 2.66
88 114 6.924060 GCTGTCTAATCACGTATGGATTACTT 59.076 38.462 3.41 0.00 36.45 2.24
90 116 6.363626 CAGCTGTCTAATCACGTATGGATTAC 59.636 42.308 5.25 0.00 36.45 1.89
91 117 6.447162 CAGCTGTCTAATCACGTATGGATTA 58.553 40.000 5.25 6.64 36.45 1.75
92 118 5.292765 CAGCTGTCTAATCACGTATGGATT 58.707 41.667 5.25 5.13 38.46 3.01
93 119 4.262207 CCAGCTGTCTAATCACGTATGGAT 60.262 45.833 13.81 0.00 0.00 3.41
94 120 3.068165 CCAGCTGTCTAATCACGTATGGA 59.932 47.826 13.81 0.00 0.00 3.41
96 122 2.797156 GCCAGCTGTCTAATCACGTATG 59.203 50.000 13.81 0.00 0.00 2.39
97 123 2.430694 TGCCAGCTGTCTAATCACGTAT 59.569 45.455 13.81 0.00 0.00 3.06
98 124 1.822371 TGCCAGCTGTCTAATCACGTA 59.178 47.619 13.81 0.00 0.00 3.57
100 126 1.284657 CTGCCAGCTGTCTAATCACG 58.715 55.000 13.81 0.00 0.00 4.35
101 127 1.065854 ACCTGCCAGCTGTCTAATCAC 60.066 52.381 13.81 0.00 0.00 3.06
102 128 1.279496 ACCTGCCAGCTGTCTAATCA 58.721 50.000 13.81 0.00 0.00 2.57
103 129 2.409948 AACCTGCCAGCTGTCTAATC 57.590 50.000 13.81 0.00 0.00 1.75
107 133 1.279496 TCATAACCTGCCAGCTGTCT 58.721 50.000 13.81 0.00 0.00 3.41
109 135 2.025981 TCAATCATAACCTGCCAGCTGT 60.026 45.455 13.81 0.00 0.00 4.40
110 136 2.617308 CTCAATCATAACCTGCCAGCTG 59.383 50.000 6.78 6.78 0.00 4.24
111 137 2.422519 CCTCAATCATAACCTGCCAGCT 60.423 50.000 0.00 0.00 0.00 4.24
112 138 1.952296 CCTCAATCATAACCTGCCAGC 59.048 52.381 0.00 0.00 0.00 4.85
113 139 3.287867 ACCTCAATCATAACCTGCCAG 57.712 47.619 0.00 0.00 0.00 4.85
114 140 3.737559 AACCTCAATCATAACCTGCCA 57.262 42.857 0.00 0.00 0.00 4.92
115 141 5.036117 TCTAACCTCAATCATAACCTGCC 57.964 43.478 0.00 0.00 0.00 4.85
117 143 7.353414 TCTCTCTAACCTCAATCATAACCTG 57.647 40.000 0.00 0.00 0.00 4.00
120 146 6.704050 GCCTTCTCTCTAACCTCAATCATAAC 59.296 42.308 0.00 0.00 0.00 1.89
121 147 6.461648 CGCCTTCTCTCTAACCTCAATCATAA 60.462 42.308 0.00 0.00 0.00 1.90
123 149 4.202202 CGCCTTCTCTCTAACCTCAATCAT 60.202 45.833 0.00 0.00 0.00 2.45
124 150 3.131223 CGCCTTCTCTCTAACCTCAATCA 59.869 47.826 0.00 0.00 0.00 2.57
125 151 3.491792 CCGCCTTCTCTCTAACCTCAATC 60.492 52.174 0.00 0.00 0.00 2.67
126 152 2.432510 CCGCCTTCTCTCTAACCTCAAT 59.567 50.000 0.00 0.00 0.00 2.57
127 153 1.825474 CCGCCTTCTCTCTAACCTCAA 59.175 52.381 0.00 0.00 0.00 3.02
128 154 1.475403 CCGCCTTCTCTCTAACCTCA 58.525 55.000 0.00 0.00 0.00 3.86
129 155 0.747852 CCCGCCTTCTCTCTAACCTC 59.252 60.000 0.00 0.00 0.00 3.85
130 156 1.331399 GCCCGCCTTCTCTCTAACCT 61.331 60.000 0.00 0.00 0.00 3.50
131 157 1.144276 GCCCGCCTTCTCTCTAACC 59.856 63.158 0.00 0.00 0.00 2.85
132 158 1.144276 GGCCCGCCTTCTCTCTAAC 59.856 63.158 0.00 0.00 0.00 2.34
133 159 2.064581 GGGCCCGCCTTCTCTCTAA 61.065 63.158 5.69 0.00 36.10 2.10
134 160 2.444140 GGGCCCGCCTTCTCTCTA 60.444 66.667 5.69 0.00 36.10 2.43
137 163 3.714078 TATGGGGCCCGCCTTCTCT 62.714 63.158 19.83 0.00 36.10 3.10
138 164 2.752807 TTATGGGGCCCGCCTTCTC 61.753 63.158 19.83 0.00 36.10 2.87
139 165 2.694616 TTATGGGGCCCGCCTTCT 60.695 61.111 19.83 0.26 36.10 2.85
140 166 2.518587 GTTATGGGGCCCGCCTTC 60.519 66.667 19.83 0.88 36.10 3.46
141 167 3.343326 TGTTATGGGGCCCGCCTT 61.343 61.111 19.83 5.16 36.10 4.35
142 168 4.123545 GTGTTATGGGGCCCGCCT 62.124 66.667 19.83 7.78 36.10 5.52
143 169 2.273588 TAAGTGTTATGGGGCCCGCC 62.274 60.000 19.83 2.70 0.00 6.13
144 170 0.394625 TTAAGTGTTATGGGGCCCGC 60.395 55.000 19.83 9.75 0.00 6.13
145 171 2.131776 TTTAAGTGTTATGGGGCCCG 57.868 50.000 19.83 0.00 0.00 6.13
146 172 4.027437 TGATTTTAAGTGTTATGGGGCCC 58.973 43.478 18.17 18.17 0.00 5.80
147 173 4.099419 CCTGATTTTAAGTGTTATGGGGCC 59.901 45.833 0.00 0.00 0.00 5.80
148 174 4.099419 CCCTGATTTTAAGTGTTATGGGGC 59.901 45.833 0.00 0.00 0.00 5.80
149 175 4.649218 CCCCTGATTTTAAGTGTTATGGGG 59.351 45.833 0.00 0.00 43.65 4.96
150 176 4.649218 CCCCCTGATTTTAAGTGTTATGGG 59.351 45.833 0.00 0.00 0.00 4.00
151 177 5.515106 TCCCCCTGATTTTAAGTGTTATGG 58.485 41.667 0.00 0.00 0.00 2.74
152 178 6.423182 TCTCCCCCTGATTTTAAGTGTTATG 58.577 40.000 0.00 0.00 0.00 1.90
153 179 6.447084 TCTCTCCCCCTGATTTTAAGTGTTAT 59.553 38.462 0.00 0.00 0.00 1.89
154 180 5.788533 TCTCTCCCCCTGATTTTAAGTGTTA 59.211 40.000 0.00 0.00 0.00 2.41
155 181 4.601857 TCTCTCCCCCTGATTTTAAGTGTT 59.398 41.667 0.00 0.00 0.00 3.32
156 182 4.175962 TCTCTCCCCCTGATTTTAAGTGT 58.824 43.478 0.00 0.00 0.00 3.55
157 183 4.844349 TCTCTCCCCCTGATTTTAAGTG 57.156 45.455 0.00 0.00 0.00 3.16
158 184 4.852697 ACTTCTCTCCCCCTGATTTTAAGT 59.147 41.667 0.00 0.00 0.00 2.24
159 185 5.443230 ACTTCTCTCCCCCTGATTTTAAG 57.557 43.478 0.00 0.00 0.00 1.85
160 186 7.525158 AATACTTCTCTCCCCCTGATTTTAA 57.475 36.000 0.00 0.00 0.00 1.52
161 187 8.632731 TTAATACTTCTCTCCCCCTGATTTTA 57.367 34.615 0.00 0.00 0.00 1.52
162 188 7.525158 TTAATACTTCTCTCCCCCTGATTTT 57.475 36.000 0.00 0.00 0.00 1.82
163 189 7.421853 CCATTAATACTTCTCTCCCCCTGATTT 60.422 40.741 0.00 0.00 0.00 2.17
164 190 6.044871 CCATTAATACTTCTCTCCCCCTGATT 59.955 42.308 0.00 0.00 0.00 2.57
165 191 5.549619 CCATTAATACTTCTCTCCCCCTGAT 59.450 44.000 0.00 0.00 0.00 2.90
166 192 4.907875 CCATTAATACTTCTCTCCCCCTGA 59.092 45.833 0.00 0.00 0.00 3.86
167 193 4.907875 TCCATTAATACTTCTCTCCCCCTG 59.092 45.833 0.00 0.00 0.00 4.45
168 194 5.171541 TCCATTAATACTTCTCTCCCCCT 57.828 43.478 0.00 0.00 0.00 4.79
169 195 5.906772 TTCCATTAATACTTCTCTCCCCC 57.093 43.478 0.00 0.00 0.00 5.40
170 196 6.901300 ACTTTCCATTAATACTTCTCTCCCC 58.099 40.000 0.00 0.00 0.00 4.81
171 197 7.201741 GCAACTTTCCATTAATACTTCTCTCCC 60.202 40.741 0.00 0.00 0.00 4.30
172 198 7.336931 TGCAACTTTCCATTAATACTTCTCTCC 59.663 37.037 0.00 0.00 0.00 3.71
173 199 8.268850 TGCAACTTTCCATTAATACTTCTCTC 57.731 34.615 0.00 0.00 0.00 3.20
174 200 8.814038 ATGCAACTTTCCATTAATACTTCTCT 57.186 30.769 0.00 0.00 0.00 3.10
182 208 9.995003 TGAACTTTTATGCAACTTTCCATTAAT 57.005 25.926 0.00 0.00 0.00 1.40
183 209 9.255304 GTGAACTTTTATGCAACTTTCCATTAA 57.745 29.630 0.00 0.00 0.00 1.40
184 210 7.593273 CGTGAACTTTTATGCAACTTTCCATTA 59.407 33.333 0.00 0.00 0.00 1.90
185 211 6.420604 CGTGAACTTTTATGCAACTTTCCATT 59.579 34.615 0.00 0.00 0.00 3.16
186 212 5.920273 CGTGAACTTTTATGCAACTTTCCAT 59.080 36.000 0.00 0.00 0.00 3.41
187 213 5.163602 ACGTGAACTTTTATGCAACTTTCCA 60.164 36.000 0.00 0.00 0.00 3.53
188 214 5.278604 ACGTGAACTTTTATGCAACTTTCC 58.721 37.500 0.00 0.00 0.00 3.13
189 215 6.806120 AACGTGAACTTTTATGCAACTTTC 57.194 33.333 0.00 0.00 0.00 2.62
190 216 7.477494 ACTAACGTGAACTTTTATGCAACTTT 58.523 30.769 0.00 0.00 0.00 2.66
191 217 7.012044 AGACTAACGTGAACTTTTATGCAACTT 59.988 33.333 0.00 0.00 0.00 2.66
192 218 6.482308 AGACTAACGTGAACTTTTATGCAACT 59.518 34.615 0.00 0.00 0.00 3.16
193 219 6.656003 AGACTAACGTGAACTTTTATGCAAC 58.344 36.000 0.00 0.00 0.00 4.17
194 220 6.854496 AGACTAACGTGAACTTTTATGCAA 57.146 33.333 0.00 0.00 0.00 4.08
195 221 6.480651 TGAAGACTAACGTGAACTTTTATGCA 59.519 34.615 0.00 0.00 0.00 3.96
196 222 6.884187 TGAAGACTAACGTGAACTTTTATGC 58.116 36.000 0.00 0.00 0.00 3.14
199 225 9.622004 CTCTATGAAGACTAACGTGAACTTTTA 57.378 33.333 0.00 0.00 0.00 1.52
200 226 7.599245 CCTCTATGAAGACTAACGTGAACTTTT 59.401 37.037 0.00 0.00 0.00 2.27
201 227 7.039923 TCCTCTATGAAGACTAACGTGAACTTT 60.040 37.037 0.00 0.00 0.00 2.66
202 228 6.433404 TCCTCTATGAAGACTAACGTGAACTT 59.567 38.462 0.00 0.00 0.00 2.66
203 229 5.944599 TCCTCTATGAAGACTAACGTGAACT 59.055 40.000 0.00 0.00 0.00 3.01
204 230 6.192234 TCCTCTATGAAGACTAACGTGAAC 57.808 41.667 0.00 0.00 0.00 3.18
205 231 7.406031 AATCCTCTATGAAGACTAACGTGAA 57.594 36.000 0.00 0.00 0.00 3.18
206 232 8.693120 ATAATCCTCTATGAAGACTAACGTGA 57.307 34.615 0.00 0.00 0.00 4.35
207 233 8.024285 GGATAATCCTCTATGAAGACTAACGTG 58.976 40.741 0.00 0.00 32.53 4.49
208 234 7.945664 AGGATAATCCTCTATGAAGACTAACGT 59.054 37.037 0.00 0.00 45.66 3.99
209 235 8.343168 AGGATAATCCTCTATGAAGACTAACG 57.657 38.462 0.00 0.00 45.66 3.18
225 251 6.538742 TGCAGCGCTATAAATAAGGATAATCC 59.461 38.462 10.99 0.00 36.58 3.01
226 252 7.278868 ACTGCAGCGCTATAAATAAGGATAATC 59.721 37.037 15.27 0.00 0.00 1.75
227 253 7.106239 ACTGCAGCGCTATAAATAAGGATAAT 58.894 34.615 15.27 0.00 0.00 1.28
228 254 6.464222 ACTGCAGCGCTATAAATAAGGATAA 58.536 36.000 15.27 0.00 0.00 1.75
229 255 6.037786 ACTGCAGCGCTATAAATAAGGATA 57.962 37.500 15.27 0.00 0.00 2.59
230 256 4.899502 ACTGCAGCGCTATAAATAAGGAT 58.100 39.130 15.27 0.00 0.00 3.24
231 257 4.336889 ACTGCAGCGCTATAAATAAGGA 57.663 40.909 15.27 0.00 0.00 3.36
232 258 6.727824 AATACTGCAGCGCTATAAATAAGG 57.272 37.500 15.27 0.00 0.00 2.69
233 259 7.746475 GGAAAATACTGCAGCGCTATAAATAAG 59.254 37.037 15.27 2.55 0.00 1.73
282 308 6.570672 TTCTTACGCCGACTGATTATATCT 57.429 37.500 0.00 0.00 0.00 1.98
368 394 1.305219 ACAAACCGGGATGATGTGCG 61.305 55.000 14.83 0.00 0.00 5.34
379 405 1.135603 CATCTCATGTGCACAAACCGG 60.136 52.381 25.72 12.30 0.00 5.28
385 411 1.624813 TGGTCTCATCTCATGTGCACA 59.375 47.619 24.08 24.08 0.00 4.57
389 415 1.568606 CGCTGGTCTCATCTCATGTG 58.431 55.000 0.00 0.00 0.00 3.21
404 430 2.857575 TAGGATGCACTGTGGCGCTG 62.858 60.000 7.64 3.19 36.28 5.18
426 459 1.267806 CCAAAGCTGCAGTCGTCAAAT 59.732 47.619 16.64 0.00 0.00 2.32
440 513 1.153958 GATCTTGTGCGGCCAAAGC 60.154 57.895 2.24 0.00 38.76 3.51
443 516 1.073025 AGTGATCTTGTGCGGCCAA 59.927 52.632 2.24 0.47 0.00 4.52
454 533 5.221601 CCACATATGCCTAGTTCAGTGATCT 60.222 44.000 8.71 8.71 0.00 2.75
478 557 2.391389 GCACAGGTACGGCTCTTGC 61.391 63.158 0.00 0.00 38.76 4.01
581 674 1.451567 CTAGACGAGGACAGCGGGA 60.452 63.158 0.00 0.00 0.00 5.14
582 675 1.313812 AACTAGACGAGGACAGCGGG 61.314 60.000 0.00 0.00 0.00 6.13
583 676 0.179161 CAACTAGACGAGGACAGCGG 60.179 60.000 0.00 0.00 0.00 5.52
584 677 0.798771 GCAACTAGACGAGGACAGCG 60.799 60.000 0.00 0.00 0.00 5.18
585 678 0.528470 AGCAACTAGACGAGGACAGC 59.472 55.000 0.00 0.00 0.00 4.40
642 1180 1.916181 ACCTAGGGCAATGCTACTGTT 59.084 47.619 14.81 0.00 0.00 3.16
684 1222 0.530650 CGGCGCTAGTCCATCAATGT 60.531 55.000 7.64 0.00 0.00 2.71
699 1237 3.103911 GTCGTGGACAGTTCGGCG 61.104 66.667 0.00 0.00 32.09 6.46
719 1258 5.419471 GGCTAGTCTTCCTTCTCAACTCTAA 59.581 44.000 0.00 0.00 0.00 2.10
735 1274 0.743688 CGACTCATGCTGGCTAGTCT 59.256 55.000 0.00 0.00 36.94 3.24
800 1344 0.039527 GTCCGTGGCCACAATTCAAC 60.040 55.000 34.16 17.78 0.00 3.18
1239 2994 1.383803 GGCTCCTGGGATGAGACCT 60.384 63.158 0.00 0.00 31.28 3.85
1242 2997 0.105760 GAGAGGCTCCTGGGATGAGA 60.106 60.000 11.71 0.00 31.26 3.27
1244 2999 1.146774 CTAGAGAGGCTCCTGGGATGA 59.853 57.143 11.71 0.00 0.00 2.92
1301 3056 0.599204 GACGCCCACGAAAGAGTTCA 60.599 55.000 0.00 0.00 43.93 3.18
1421 3176 1.963515 ACAAATCCAACAAGGTGAGGC 59.036 47.619 0.00 0.00 39.02 4.70
1500 3255 2.268076 GGAGTGTGCGGCCAAATGT 61.268 57.895 2.24 0.00 0.00 2.71
1554 3309 7.264817 GAGCTCACGGAGAGATGATAGTGAC 62.265 52.000 9.40 0.00 44.50 3.67
1709 3464 2.037772 AGGTTGAGCGACTTGAGTTCAT 59.962 45.455 0.00 0.00 0.00 2.57
2226 4030 3.962063 TCCCAGATACCGTATTGTTGCTA 59.038 43.478 0.00 0.00 0.00 3.49
2331 4140 5.187381 TCTCTTTGATGTGCTCTGAGATCTT 59.813 40.000 9.28 0.00 0.00 2.40
2337 4146 3.366781 CGACTCTCTTTGATGTGCTCTGA 60.367 47.826 0.00 0.00 0.00 3.27
2624 4461 1.634753 TCGATAGACGACGAGTGCG 59.365 57.895 0.00 0.00 46.45 5.34
2690 4527 4.510167 AGTAAGGGATCATTCAACAGGG 57.490 45.455 0.00 0.00 0.00 4.45
2762 4599 4.037446 TCCGCAAAGAATAAGCTGTTGTTT 59.963 37.500 0.00 0.00 0.00 2.83
2968 4958 3.442273 AGTCAAAGTCAGGTCGAGAGATC 59.558 47.826 0.00 0.00 45.19 2.75
2970 4960 2.554462 CAGTCAAAGTCAGGTCGAGAGA 59.446 50.000 0.00 0.00 38.16 3.10
2972 4962 1.613925 CCAGTCAAAGTCAGGTCGAGA 59.386 52.381 0.00 0.00 0.00 4.04
3138 5655 5.722263 CATGTCACAGACAGAGAGAGAATT 58.278 41.667 6.01 0.00 46.04 2.17
3142 5659 2.230750 TGCATGTCACAGACAGAGAGAG 59.769 50.000 6.01 0.00 46.04 3.20
3143 5660 2.242043 TGCATGTCACAGACAGAGAGA 58.758 47.619 6.01 0.00 46.04 3.10
3144 5661 2.738013 TGCATGTCACAGACAGAGAG 57.262 50.000 6.01 0.00 46.04 3.20
3216 5735 8.727100 AGGAAAGGAATAAAAACAAGGAGAAT 57.273 30.769 0.00 0.00 0.00 2.40
3218 5737 7.782644 TGAAGGAAAGGAATAAAAACAAGGAGA 59.217 33.333 0.00 0.00 0.00 3.71
3219 5738 7.867909 GTGAAGGAAAGGAATAAAAACAAGGAG 59.132 37.037 0.00 0.00 0.00 3.69
3220 5739 7.563556 AGTGAAGGAAAGGAATAAAAACAAGGA 59.436 33.333 0.00 0.00 0.00 3.36
3221 5740 7.726216 AGTGAAGGAAAGGAATAAAAACAAGG 58.274 34.615 0.00 0.00 0.00 3.61
3222 5741 9.034544 CAAGTGAAGGAAAGGAATAAAAACAAG 57.965 33.333 0.00 0.00 0.00 3.16
3261 5780 2.261172 CTGCATGCATGTGTGTCCGG 62.261 60.000 26.79 10.89 0.00 5.14
3263 5782 1.153901 GCTGCATGCATGTGTGTCC 60.154 57.895 26.79 10.36 42.31 4.02


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

AutoCloner maintained by Alex Coulton.