Multiple sequence alignment - TraesCS3D01G208500

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 TraesCS3D01G208500 chr3D 100.000 3573 0 0 1 3573 275638688 275635116 0.000000e+00 6599
1 TraesCS3D01G208500 chr3D 95.439 285 13 0 66 350 106316786 106316502 4.210000e-124 455
2 TraesCS3D01G208500 chr3D 95.139 288 14 0 63 350 285911919 285912206 4.210000e-124 455
3 TraesCS3D01G208500 chr3D 95.439 285 13 0 66 350 521321246 521321530 4.210000e-124 455
4 TraesCS3D01G208500 chr3A 94.208 3246 84 34 355 3554 365250100 365253287 0.000000e+00 4857
5 TraesCS3D01G208500 chr3B 94.574 2820 67 22 737 3531 362055663 362052905 0.000000e+00 4281
6 TraesCS3D01G208500 chr3B 93.052 403 17 5 355 751 362056077 362055680 2.390000e-161 579
7 TraesCS3D01G208500 chr5B 96.491 285 10 0 66 350 633283674 633283958 4.180000e-129 472
8 TraesCS3D01G208500 chr4A 95.848 289 8 3 66 350 575178755 575178467 6.990000e-127 464
9 TraesCS3D01G208500 chr5D 95.789 285 12 0 66 350 549921557 549921273 9.040000e-126 460
10 TraesCS3D01G208500 chr5D 95.156 289 14 0 64 352 260691711 260691423 1.170000e-124 457
11 TraesCS3D01G208500 chr5D 95.455 286 12 1 66 350 508089797 508089512 4.210000e-124 455
12 TraesCS3D01G208500 chr6D 95.139 288 14 0 66 353 331029951 331029664 4.210000e-124 455


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 TraesCS3D01G208500 chr3D 275635116 275638688 3572 True 6599 6599 100.000 1 3573 1 chr3D.!!$R2 3572
1 TraesCS3D01G208500 chr3A 365250100 365253287 3187 False 4857 4857 94.208 355 3554 1 chr3A.!!$F1 3199
2 TraesCS3D01G208500 chr3B 362052905 362056077 3172 True 2430 4281 93.813 355 3531 2 chr3B.!!$R1 3176

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
72 73 0.041663 CTCGCTACGCTCAGACTAGC 60.042 60.0 0.00 0.0 39.21 3.42 F
75 76 0.248702 GCTACGCTCAGACTAGCCAC 60.249 60.0 0.00 0.0 39.43 5.01 F
637 646 0.460987 GTAGCTAGCTGTGCTGTGGG 60.461 60.0 27.68 0.0 40.10 4.61 F
1213 1272 0.668706 CATCATCGGATCGGCCTCAC 60.669 60.0 0.00 0.0 0.00 3.51 F
1381 1444 0.999406 CCGGTGATGTCGTTCATGTC 59.001 55.0 0.00 0.0 36.83 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1280 1343 0.106318 AAGCCAGGATCCATCTTGCC 60.106 55.0 15.82 0.00 33.07 4.52 R
1794 1857 0.865769 CCTCGTCGTCCCTGTTTTTG 59.134 55.0 0.00 0.00 0.00 2.44 R
2389 2458 0.034767 TTTGCAGCTCCCTGATCTGG 60.035 55.0 11.58 11.58 41.77 3.86 R
2516 2585 0.688087 CCTCCTCCTAGGGTTTCGCT 60.688 60.0 9.46 0.00 35.59 4.93 R
3087 3170 0.751452 TGCATGCACAAAGAAAGGCA 59.249 45.0 18.46 0.00 41.00 4.75 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
21 22 4.415150 TCGCCGGGTACGACTCCT 62.415 66.667 2.18 0.00 44.60 3.69
22 23 3.446570 CGCCGGGTACGACTCCTT 61.447 66.667 2.18 0.00 44.60 3.36
23 24 2.493501 GCCGGGTACGACTCCTTC 59.506 66.667 2.18 0.00 44.60 3.46
24 25 3.073742 GCCGGGTACGACTCCTTCC 62.074 68.421 2.18 0.00 44.60 3.46
25 26 1.379576 CCGGGTACGACTCCTTCCT 60.380 63.158 0.00 0.00 44.60 3.36
26 27 1.664321 CCGGGTACGACTCCTTCCTG 61.664 65.000 0.00 0.00 44.60 3.86
27 28 1.664321 CGGGTACGACTCCTTCCTGG 61.664 65.000 0.00 0.00 44.60 4.45
28 29 1.516423 GGTACGACTCCTTCCTGGC 59.484 63.158 0.00 0.00 35.26 4.85
29 30 1.516423 GTACGACTCCTTCCTGGCC 59.484 63.158 0.00 0.00 35.26 5.36
30 31 1.077805 TACGACTCCTTCCTGGCCA 59.922 57.895 4.71 4.71 35.26 5.36
31 32 0.543410 TACGACTCCTTCCTGGCCAA 60.543 55.000 7.01 0.00 35.26 4.52
32 33 1.201429 ACGACTCCTTCCTGGCCAAT 61.201 55.000 7.01 0.00 35.26 3.16
33 34 0.745845 CGACTCCTTCCTGGCCAATG 60.746 60.000 7.01 0.18 35.26 2.82
34 35 1.000396 ACTCCTTCCTGGCCAATGC 60.000 57.895 7.01 0.00 35.26 3.56
60 61 4.208686 CGCCCTGGTCCTCGCTAC 62.209 72.222 0.00 0.00 0.00 3.58
61 62 4.208686 GCCCTGGTCCTCGCTACG 62.209 72.222 0.00 0.00 0.00 3.51
62 63 4.208686 CCCTGGTCCTCGCTACGC 62.209 72.222 0.00 0.00 0.00 4.42
63 64 3.141488 CCTGGTCCTCGCTACGCT 61.141 66.667 0.00 0.00 0.00 5.07
64 65 2.409651 CTGGTCCTCGCTACGCTC 59.590 66.667 0.00 0.00 0.00 5.03
65 66 2.360726 TGGTCCTCGCTACGCTCA 60.361 61.111 0.00 0.00 0.00 4.26
66 67 2.329678 CTGGTCCTCGCTACGCTCAG 62.330 65.000 0.00 0.00 0.00 3.35
67 68 2.113433 GGTCCTCGCTACGCTCAGA 61.113 63.158 0.00 0.00 0.00 3.27
68 69 1.062845 GTCCTCGCTACGCTCAGAC 59.937 63.158 0.00 0.00 0.00 3.51
69 70 1.078356 TCCTCGCTACGCTCAGACT 60.078 57.895 0.00 0.00 0.00 3.24
70 71 0.177373 TCCTCGCTACGCTCAGACTA 59.823 55.000 0.00 0.00 0.00 2.59
71 72 0.584396 CCTCGCTACGCTCAGACTAG 59.416 60.000 0.00 0.00 0.00 2.57
72 73 0.041663 CTCGCTACGCTCAGACTAGC 60.042 60.000 0.00 0.00 39.21 3.42
73 74 1.009449 CGCTACGCTCAGACTAGCC 60.009 63.158 0.00 0.00 39.43 3.93
74 75 1.715862 CGCTACGCTCAGACTAGCCA 61.716 60.000 0.00 0.00 39.43 4.75
75 76 0.248702 GCTACGCTCAGACTAGCCAC 60.249 60.000 0.00 0.00 39.43 5.01
76 77 1.095600 CTACGCTCAGACTAGCCACA 58.904 55.000 0.00 0.00 39.43 4.17
77 78 1.472878 CTACGCTCAGACTAGCCACAA 59.527 52.381 0.00 0.00 39.43 3.33
78 79 0.898320 ACGCTCAGACTAGCCACAAT 59.102 50.000 0.00 0.00 39.43 2.71
79 80 1.284657 CGCTCAGACTAGCCACAATG 58.715 55.000 0.00 0.00 39.43 2.82
80 81 1.661341 GCTCAGACTAGCCACAATGG 58.339 55.000 0.00 0.00 41.55 3.16
81 82 1.745141 GCTCAGACTAGCCACAATGGG 60.745 57.143 0.00 0.00 38.19 4.00
93 94 5.031066 GCCACAATGGGTAGTAACATAGA 57.969 43.478 0.00 0.00 38.19 1.98
94 95 5.057149 GCCACAATGGGTAGTAACATAGAG 58.943 45.833 0.00 0.00 38.19 2.43
95 96 5.396436 GCCACAATGGGTAGTAACATAGAGT 60.396 44.000 0.00 0.00 38.19 3.24
96 97 6.183360 GCCACAATGGGTAGTAACATAGAGTA 60.183 42.308 0.00 0.00 38.19 2.59
97 98 7.434492 CCACAATGGGTAGTAACATAGAGTAG 58.566 42.308 0.00 0.00 32.67 2.57
98 99 7.069578 CCACAATGGGTAGTAACATAGAGTAGT 59.930 40.741 0.00 0.00 32.67 2.73
99 100 9.128404 CACAATGGGTAGTAACATAGAGTAGTA 57.872 37.037 0.00 0.00 0.00 1.82
100 101 9.705103 ACAATGGGTAGTAACATAGAGTAGTAA 57.295 33.333 0.00 0.00 0.00 2.24
101 102 9.962783 CAATGGGTAGTAACATAGAGTAGTAAC 57.037 37.037 0.00 0.00 0.00 2.50
102 103 9.705103 AATGGGTAGTAACATAGAGTAGTAACA 57.295 33.333 0.00 0.00 0.00 2.41
103 104 9.878737 ATGGGTAGTAACATAGAGTAGTAACAT 57.121 33.333 0.00 0.00 0.00 2.71
104 105 9.128404 TGGGTAGTAACATAGAGTAGTAACATG 57.872 37.037 0.00 0.00 0.00 3.21
105 106 8.081025 GGGTAGTAACATAGAGTAGTAACATGC 58.919 40.741 0.00 0.00 0.00 4.06
106 107 8.081025 GGTAGTAACATAGAGTAGTAACATGCC 58.919 40.741 0.00 0.00 0.00 4.40
107 108 7.052142 AGTAACATAGAGTAGTAACATGCCC 57.948 40.000 0.00 0.00 0.00 5.36
108 109 5.950544 AACATAGAGTAGTAACATGCCCA 57.049 39.130 0.00 0.00 0.00 5.36
109 110 6.500589 AACATAGAGTAGTAACATGCCCAT 57.499 37.500 0.00 0.00 0.00 4.00
110 111 5.858381 ACATAGAGTAGTAACATGCCCATG 58.142 41.667 6.71 6.71 44.15 3.66
124 125 5.858381 CATGCCCATGTTACTACTCTATGT 58.142 41.667 0.13 0.00 34.23 2.29
125 126 5.950544 TGCCCATGTTACTACTCTATGTT 57.049 39.130 0.00 0.00 0.00 2.71
126 127 7.441836 CATGCCCATGTTACTACTCTATGTTA 58.558 38.462 0.13 0.00 34.23 2.41
127 128 6.812998 TGCCCATGTTACTACTCTATGTTAC 58.187 40.000 0.00 0.00 0.00 2.50
128 129 6.610020 TGCCCATGTTACTACTCTATGTTACT 59.390 38.462 0.00 0.00 0.00 2.24
129 130 7.781219 TGCCCATGTTACTACTCTATGTTACTA 59.219 37.037 0.00 0.00 0.00 1.82
130 131 8.081025 GCCCATGTTACTACTCTATGTTACTAC 58.919 40.741 0.00 0.00 0.00 2.73
131 132 8.574737 CCCATGTTACTACTCTATGTTACTACC 58.425 40.741 0.00 0.00 0.00 3.18
132 133 9.352191 CCATGTTACTACTCTATGTTACTACCT 57.648 37.037 0.00 0.00 0.00 3.08
142 143 8.384718 ACTCTATGTTACTACCTCTATAGTGGG 58.615 40.741 21.82 16.23 36.09 4.61
143 144 7.696981 TCTATGTTACTACCTCTATAGTGGGG 58.303 42.308 21.82 16.35 36.09 4.96
144 145 5.999987 TGTTACTACCTCTATAGTGGGGA 57.000 43.478 21.82 11.28 36.09 4.81
145 146 5.950023 TGTTACTACCTCTATAGTGGGGAG 58.050 45.833 21.82 20.04 36.09 4.30
146 147 5.434376 TGTTACTACCTCTATAGTGGGGAGT 59.566 44.000 24.72 24.72 36.09 3.85
147 148 6.621098 TGTTACTACCTCTATAGTGGGGAGTA 59.379 42.308 23.32 23.32 36.09 2.59
148 149 7.129349 TGTTACTACCTCTATAGTGGGGAGTAA 59.871 40.741 28.26 28.26 38.03 2.24
149 150 5.951204 ACTACCTCTATAGTGGGGAGTAAC 58.049 45.833 22.09 0.00 34.02 2.50
150 151 4.894252 ACCTCTATAGTGGGGAGTAACA 57.106 45.455 21.82 0.00 33.22 2.41
151 152 5.420215 ACCTCTATAGTGGGGAGTAACAT 57.580 43.478 21.82 0.00 33.22 2.71
152 153 6.541264 ACCTCTATAGTGGGGAGTAACATA 57.459 41.667 21.82 0.00 33.22 2.29
153 154 7.117331 ACCTCTATAGTGGGGAGTAACATAT 57.883 40.000 21.82 0.00 33.22 1.78
154 155 6.954684 ACCTCTATAGTGGGGAGTAACATATG 59.045 42.308 21.82 0.00 33.22 1.78
155 156 6.954684 CCTCTATAGTGGGGAGTAACATATGT 59.045 42.308 12.29 1.41 0.00 2.29
156 157 7.093727 CCTCTATAGTGGGGAGTAACATATGTG 60.094 44.444 9.63 0.00 0.00 3.21
157 158 7.302948 TCTATAGTGGGGAGTAACATATGTGT 58.697 38.462 9.63 2.63 41.28 3.72
158 159 4.487714 AGTGGGGAGTAACATATGTGTG 57.512 45.455 9.63 0.00 38.92 3.82
159 160 3.199946 AGTGGGGAGTAACATATGTGTGG 59.800 47.826 9.63 0.00 38.92 4.17
160 161 3.054655 GTGGGGAGTAACATATGTGTGGT 60.055 47.826 9.63 0.00 38.92 4.16
161 162 4.162698 GTGGGGAGTAACATATGTGTGGTA 59.837 45.833 9.63 0.00 38.92 3.25
162 163 4.783763 TGGGGAGTAACATATGTGTGGTAA 59.216 41.667 9.63 0.00 38.92 2.85
163 164 5.121105 GGGGAGTAACATATGTGTGGTAAC 58.879 45.833 9.63 1.91 38.92 2.50
176 177 1.598882 TGGTAACATGCAACGCTTCA 58.401 45.000 0.00 0.00 46.17 3.02
177 178 2.158559 TGGTAACATGCAACGCTTCAT 58.841 42.857 0.00 0.00 46.17 2.57
178 179 2.556189 TGGTAACATGCAACGCTTCATT 59.444 40.909 0.00 0.00 46.17 2.57
179 180 3.005261 TGGTAACATGCAACGCTTCATTT 59.995 39.130 0.00 0.00 46.17 2.32
180 181 4.216472 TGGTAACATGCAACGCTTCATTTA 59.784 37.500 0.00 0.00 46.17 1.40
181 182 5.105957 TGGTAACATGCAACGCTTCATTTAT 60.106 36.000 0.00 0.00 46.17 1.40
182 183 5.804979 GGTAACATGCAACGCTTCATTTATT 59.195 36.000 0.00 0.00 0.00 1.40
183 184 6.970043 GGTAACATGCAACGCTTCATTTATTA 59.030 34.615 0.00 0.00 0.00 0.98
184 185 7.165812 GGTAACATGCAACGCTTCATTTATTAG 59.834 37.037 0.00 0.00 0.00 1.73
185 186 5.581605 ACATGCAACGCTTCATTTATTAGG 58.418 37.500 0.00 0.00 0.00 2.69
186 187 4.027572 TGCAACGCTTCATTTATTAGGC 57.972 40.909 0.00 0.00 0.00 3.93
187 188 3.694072 TGCAACGCTTCATTTATTAGGCT 59.306 39.130 0.00 0.00 0.00 4.58
188 189 4.878971 TGCAACGCTTCATTTATTAGGCTA 59.121 37.500 0.00 0.00 0.00 3.93
189 190 5.530915 TGCAACGCTTCATTTATTAGGCTAT 59.469 36.000 0.00 0.00 0.00 2.97
190 191 6.708502 TGCAACGCTTCATTTATTAGGCTATA 59.291 34.615 0.00 0.00 0.00 1.31
191 192 7.227711 TGCAACGCTTCATTTATTAGGCTATAA 59.772 33.333 0.00 0.00 0.00 0.98
192 193 8.073768 GCAACGCTTCATTTATTAGGCTATAAA 58.926 33.333 0.00 3.68 35.20 1.40
193 194 9.382244 CAACGCTTCATTTATTAGGCTATAAAC 57.618 33.333 0.00 0.00 33.96 2.01
194 195 8.904099 ACGCTTCATTTATTAGGCTATAAACT 57.096 30.769 0.00 0.00 33.96 2.66
195 196 8.989980 ACGCTTCATTTATTAGGCTATAAACTC 58.010 33.333 0.00 0.00 33.96 3.01
196 197 8.988934 CGCTTCATTTATTAGGCTATAAACTCA 58.011 33.333 0.00 0.00 33.96 3.41
216 217 9.671279 AAACTCATCTTGTATTGATATGTGTGA 57.329 29.630 0.00 0.00 0.00 3.58
217 218 9.842775 AACTCATCTTGTATTGATATGTGTGAT 57.157 29.630 0.00 0.00 0.00 3.06
218 219 9.269453 ACTCATCTTGTATTGATATGTGTGATG 57.731 33.333 0.00 0.00 0.00 3.07
219 220 9.269453 CTCATCTTGTATTGATATGTGTGATGT 57.731 33.333 0.00 0.00 32.21 3.06
220 221 9.617523 TCATCTTGTATTGATATGTGTGATGTT 57.382 29.630 0.00 0.00 32.21 2.71
225 226 9.883142 TTGTATTGATATGTGTGATGTTACTCA 57.117 29.630 0.00 0.00 0.00 3.41
235 236 8.803397 TGTGTGATGTTACTCATACTAGTAGT 57.197 34.615 8.85 8.14 37.92 2.73
236 237 9.895138 TGTGTGATGTTACTCATACTAGTAGTA 57.105 33.333 12.38 12.38 37.92 1.82
257 258 9.570488 GTAGTAACTAGCTATGTTACCATATGC 57.430 37.037 25.92 15.95 46.31 3.14
258 259 7.612677 AGTAACTAGCTATGTTACCATATGCC 58.387 38.462 25.92 11.54 46.31 4.40
259 260 6.688073 AACTAGCTATGTTACCATATGCCT 57.312 37.500 0.00 0.00 33.18 4.75
260 261 6.287589 ACTAGCTATGTTACCATATGCCTC 57.712 41.667 0.00 0.00 33.18 4.70
261 262 6.019748 ACTAGCTATGTTACCATATGCCTCT 58.980 40.000 0.00 0.00 33.18 3.69
262 263 5.413309 AGCTATGTTACCATATGCCTCTC 57.587 43.478 0.00 0.00 33.18 3.20
263 264 5.090139 AGCTATGTTACCATATGCCTCTCT 58.910 41.667 0.00 0.00 33.18 3.10
264 265 5.545723 AGCTATGTTACCATATGCCTCTCTT 59.454 40.000 0.00 0.00 33.18 2.85
265 266 6.043706 AGCTATGTTACCATATGCCTCTCTTT 59.956 38.462 0.00 0.00 33.18 2.52
266 267 6.370166 GCTATGTTACCATATGCCTCTCTTTC 59.630 42.308 0.00 0.00 33.18 2.62
267 268 5.957771 TGTTACCATATGCCTCTCTTTCT 57.042 39.130 0.00 0.00 0.00 2.52
268 269 6.313519 TGTTACCATATGCCTCTCTTTCTT 57.686 37.500 0.00 0.00 0.00 2.52
269 270 6.349300 TGTTACCATATGCCTCTCTTTCTTC 58.651 40.000 0.00 0.00 0.00 2.87
270 271 6.070251 TGTTACCATATGCCTCTCTTTCTTCA 60.070 38.462 0.00 0.00 0.00 3.02
271 272 5.643421 ACCATATGCCTCTCTTTCTTCAT 57.357 39.130 0.00 0.00 0.00 2.57
272 273 6.011122 ACCATATGCCTCTCTTTCTTCATT 57.989 37.500 0.00 0.00 0.00 2.57
273 274 6.430007 ACCATATGCCTCTCTTTCTTCATTT 58.570 36.000 0.00 0.00 0.00 2.32
274 275 7.577303 ACCATATGCCTCTCTTTCTTCATTTA 58.423 34.615 0.00 0.00 0.00 1.40
275 276 8.223330 ACCATATGCCTCTCTTTCTTCATTTAT 58.777 33.333 0.00 0.00 0.00 1.40
276 277 9.075678 CCATATGCCTCTCTTTCTTCATTTATT 57.924 33.333 0.00 0.00 0.00 1.40
277 278 9.894783 CATATGCCTCTCTTTCTTCATTTATTG 57.105 33.333 0.00 0.00 0.00 1.90
278 279 6.199937 TGCCTCTCTTTCTTCATTTATTGC 57.800 37.500 0.00 0.00 0.00 3.56
279 280 5.948162 TGCCTCTCTTTCTTCATTTATTGCT 59.052 36.000 0.00 0.00 0.00 3.91
280 281 6.435277 TGCCTCTCTTTCTTCATTTATTGCTT 59.565 34.615 0.00 0.00 0.00 3.91
281 282 6.750963 GCCTCTCTTTCTTCATTTATTGCTTG 59.249 38.462 0.00 0.00 0.00 4.01
282 283 7.576477 GCCTCTCTTTCTTCATTTATTGCTTGT 60.576 37.037 0.00 0.00 0.00 3.16
283 284 7.967303 CCTCTCTTTCTTCATTTATTGCTTGTC 59.033 37.037 0.00 0.00 0.00 3.18
284 285 8.394971 TCTCTTTCTTCATTTATTGCTTGTCA 57.605 30.769 0.00 0.00 0.00 3.58
285 286 8.292448 TCTCTTTCTTCATTTATTGCTTGTCAC 58.708 33.333 0.00 0.00 0.00 3.67
286 287 7.939782 TCTTTCTTCATTTATTGCTTGTCACA 58.060 30.769 0.00 0.00 0.00 3.58
287 288 8.579006 TCTTTCTTCATTTATTGCTTGTCACAT 58.421 29.630 0.00 0.00 0.00 3.21
288 289 9.199982 CTTTCTTCATTTATTGCTTGTCACATT 57.800 29.630 0.00 0.00 0.00 2.71
334 335 9.680315 GTGTGATGTTACTATCTATGTTACTCC 57.320 37.037 0.00 0.00 0.00 3.85
335 336 8.857098 TGTGATGTTACTATCTATGTTACTCCC 58.143 37.037 0.00 0.00 0.00 4.30
336 337 8.857098 GTGATGTTACTATCTATGTTACTCCCA 58.143 37.037 0.00 0.00 0.00 4.37
337 338 9.078990 TGATGTTACTATCTATGTTACTCCCAG 57.921 37.037 0.00 0.00 0.00 4.45
338 339 9.080097 GATGTTACTATCTATGTTACTCCCAGT 57.920 37.037 0.00 0.00 0.00 4.00
339 340 8.234136 TGTTACTATCTATGTTACTCCCAGTG 57.766 38.462 0.00 0.00 0.00 3.66
340 341 7.837689 TGTTACTATCTATGTTACTCCCAGTGT 59.162 37.037 0.00 0.00 0.00 3.55
341 342 6.716934 ACTATCTATGTTACTCCCAGTGTG 57.283 41.667 0.00 0.00 0.00 3.82
342 343 5.598830 ACTATCTATGTTACTCCCAGTGTGG 59.401 44.000 0.00 0.00 37.25 4.17
353 354 0.608640 CCAGTGTGGGTAGTCTCACC 59.391 60.000 0.00 0.00 37.91 4.02
366 367 0.674581 TCTCACCGCATGCTTCCTTG 60.675 55.000 17.13 5.41 0.00 3.61
377 378 0.951040 GCTTCCTTGTGACTGACCCG 60.951 60.000 0.00 0.00 0.00 5.28
402 403 1.814394 CTAAAACCCGGCAACTTACCC 59.186 52.381 0.00 0.00 0.00 3.69
587 596 7.143340 CCACACAATCAAGAGCATTAATATGG 58.857 38.462 0.00 0.00 32.15 2.74
637 646 0.460987 GTAGCTAGCTGTGCTGTGGG 60.461 60.000 27.68 0.00 40.10 4.61
721 737 3.758425 TGAGGTAGTGTGCTGTGTAGTA 58.242 45.455 0.00 0.00 0.00 1.82
722 738 4.146564 TGAGGTAGTGTGCTGTGTAGTAA 58.853 43.478 0.00 0.00 0.00 2.24
723 739 4.022589 TGAGGTAGTGTGCTGTGTAGTAAC 60.023 45.833 0.00 0.00 0.00 2.50
724 740 3.893200 AGGTAGTGTGCTGTGTAGTAACA 59.107 43.478 0.00 0.00 0.00 2.41
726 742 4.684703 GGTAGTGTGCTGTGTAGTAACAAG 59.315 45.833 0.00 0.00 37.36 3.16
729 745 5.287226 AGTGTGCTGTGTAGTAACAAGTAC 58.713 41.667 0.00 0.00 37.36 2.73
1027 1083 4.287067 TCCCTCTGTTGCTCCAATATATCC 59.713 45.833 0.00 0.00 0.00 2.59
1057 1113 1.414181 CTAGCCTACCATCACCACCAG 59.586 57.143 0.00 0.00 0.00 4.00
1063 1122 1.379443 CCATCACCACCAGCAGCAT 60.379 57.895 0.00 0.00 0.00 3.79
1104 1163 0.833949 CCCCTCTTCCTCAGCTTACC 59.166 60.000 0.00 0.00 0.00 2.85
1138 1197 1.088306 TAAAGGTACGCGCCATTTGG 58.912 50.000 16.19 0.00 38.53 3.28
1199 1258 3.379372 GGTAGTTGCATGTGCTTCATCAT 59.621 43.478 6.55 0.00 42.66 2.45
1200 1259 3.777465 AGTTGCATGTGCTTCATCATC 57.223 42.857 6.55 0.00 42.66 2.92
1201 1260 2.096980 AGTTGCATGTGCTTCATCATCG 59.903 45.455 6.55 0.00 42.66 3.84
1213 1272 0.668706 CATCATCGGATCGGCCTCAC 60.669 60.000 0.00 0.00 0.00 3.51
1278 1341 9.088512 CATATCCGATTTCTTATTAGTAGGTGC 57.911 37.037 0.00 0.00 0.00 5.01
1279 1342 6.726490 TCCGATTTCTTATTAGTAGGTGCT 57.274 37.500 0.00 0.00 0.00 4.40
1280 1343 6.513180 TCCGATTTCTTATTAGTAGGTGCTG 58.487 40.000 0.00 0.00 0.00 4.41
1376 1439 3.186047 CGGCCGGTGATGTCGTTC 61.186 66.667 20.10 0.00 0.00 3.95
1381 1444 0.999406 CCGGTGATGTCGTTCATGTC 59.001 55.000 0.00 0.00 36.83 3.06
1638 1701 2.903855 CGTGATGGGGATGCCTGC 60.904 66.667 2.19 0.00 0.00 4.85
1799 1862 2.647875 CCACATCGGCGGCAAAAA 59.352 55.556 10.53 0.00 0.00 1.94
1934 2003 1.548357 GGAGAACCCTCTCTGCAGCA 61.548 60.000 9.47 0.00 46.45 4.41
2389 2458 1.219393 CCTCCGCTTCCTCAAGTCC 59.781 63.158 0.00 0.00 31.45 3.85
2755 2833 7.213678 TCACCTTTCTTCTTCTTCTTCTTCTC 58.786 38.462 0.00 0.00 0.00 2.87
2769 2847 5.151454 TCTTCTTCTCCTTCTCCTTCTGTT 58.849 41.667 0.00 0.00 0.00 3.16
2770 2848 6.315714 TCTTCTTCTCCTTCTCCTTCTGTTA 58.684 40.000 0.00 0.00 0.00 2.41
2771 2849 6.435904 TCTTCTTCTCCTTCTCCTTCTGTTAG 59.564 42.308 0.00 0.00 0.00 2.34
2772 2850 5.893500 TCTTCTCCTTCTCCTTCTGTTAGA 58.106 41.667 0.00 0.00 0.00 2.10
2964 3047 1.934525 TGTAGACGCGTGAAAGCAAAA 59.065 42.857 20.70 0.00 36.85 2.44
3058 3141 7.621428 ACATCATCATGACAACTTTCTAAGG 57.379 36.000 0.00 0.00 33.72 2.69
3143 3227 2.336478 CCGGGATCGATCGAGGAGG 61.336 68.421 24.91 18.33 39.00 4.30
3310 3397 2.279252 AGACGTGTGGTGTCGTGC 60.279 61.111 0.00 0.00 41.24 5.34
3535 3634 3.195610 TGATGAGATGCTGTCGTAACCTT 59.804 43.478 0.00 0.00 0.00 3.50
3545 3644 4.451096 GCTGTCGTAACCTTTGAATCTTGA 59.549 41.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.925630 AAGGAGTCGTACCCGGCGA 62.926 63.158 9.30 0.00 45.26 5.54
5 6 3.407046 GAAGGAGTCGTACCCGGCG 62.407 68.421 0.00 0.00 45.26 6.46
6 7 2.493501 GAAGGAGTCGTACCCGGC 59.506 66.667 0.00 0.00 39.53 6.13
7 8 1.379576 AGGAAGGAGTCGTACCCGG 60.380 63.158 0.00 0.00 33.95 5.73
8 9 1.664321 CCAGGAAGGAGTCGTACCCG 61.664 65.000 0.00 0.00 41.22 5.28
9 10 1.957765 GCCAGGAAGGAGTCGTACCC 61.958 65.000 0.00 0.00 41.22 3.69
10 11 1.516423 GCCAGGAAGGAGTCGTACC 59.484 63.158 0.00 0.00 41.22 3.34
11 12 1.255667 TGGCCAGGAAGGAGTCGTAC 61.256 60.000 0.00 0.00 41.22 3.67
12 13 0.543410 TTGGCCAGGAAGGAGTCGTA 60.543 55.000 5.11 0.00 41.22 3.43
13 14 1.201429 ATTGGCCAGGAAGGAGTCGT 61.201 55.000 5.11 0.00 41.22 4.34
14 15 0.745845 CATTGGCCAGGAAGGAGTCG 60.746 60.000 5.11 0.00 41.22 4.18
15 16 1.034292 GCATTGGCCAGGAAGGAGTC 61.034 60.000 5.11 0.00 41.22 3.36
16 17 1.000396 GCATTGGCCAGGAAGGAGT 60.000 57.895 5.11 0.00 41.22 3.85
17 18 3.930504 GCATTGGCCAGGAAGGAG 58.069 61.111 5.11 0.00 41.22 3.69
43 44 4.208686 GTAGCGAGGACCAGGGCG 62.209 72.222 0.00 0.00 0.00 6.13
44 45 4.208686 CGTAGCGAGGACCAGGGC 62.209 72.222 0.00 0.00 0.00 5.19
57 58 1.095600 TGTGGCTAGTCTGAGCGTAG 58.904 55.000 0.00 0.00 43.83 3.51
58 59 1.541379 TTGTGGCTAGTCTGAGCGTA 58.459 50.000 0.00 0.00 43.83 4.42
59 60 0.898320 ATTGTGGCTAGTCTGAGCGT 59.102 50.000 0.00 0.00 43.83 5.07
60 61 1.284657 CATTGTGGCTAGTCTGAGCG 58.715 55.000 0.00 0.00 43.83 5.03
61 62 1.661341 CCATTGTGGCTAGTCTGAGC 58.339 55.000 0.00 0.00 42.05 4.26
62 63 1.556911 ACCCATTGTGGCTAGTCTGAG 59.443 52.381 0.00 0.00 35.79 3.35
63 64 1.656587 ACCCATTGTGGCTAGTCTGA 58.343 50.000 0.00 0.00 35.79 3.27
64 65 2.501723 ACTACCCATTGTGGCTAGTCTG 59.498 50.000 0.00 0.00 35.79 3.51
65 66 2.834113 ACTACCCATTGTGGCTAGTCT 58.166 47.619 0.00 0.00 35.79 3.24
66 67 4.081309 TGTTACTACCCATTGTGGCTAGTC 60.081 45.833 7.13 0.00 35.79 2.59
67 68 3.841845 TGTTACTACCCATTGTGGCTAGT 59.158 43.478 8.55 8.55 35.79 2.57
68 69 4.481368 TGTTACTACCCATTGTGGCTAG 57.519 45.455 0.00 0.00 35.79 3.42
69 70 5.900699 TCTATGTTACTACCCATTGTGGCTA 59.099 40.000 0.00 0.00 35.79 3.93
70 71 4.719773 TCTATGTTACTACCCATTGTGGCT 59.280 41.667 0.00 0.00 35.79 4.75
71 72 5.031066 TCTATGTTACTACCCATTGTGGC 57.969 43.478 0.00 0.00 35.79 5.01
72 73 6.235231 ACTCTATGTTACTACCCATTGTGG 57.765 41.667 0.00 0.00 37.25 4.17
73 74 8.008513 ACTACTCTATGTTACTACCCATTGTG 57.991 38.462 0.00 0.00 0.00 3.33
74 75 9.705103 TTACTACTCTATGTTACTACCCATTGT 57.295 33.333 0.00 0.00 0.00 2.71
75 76 9.962783 GTTACTACTCTATGTTACTACCCATTG 57.037 37.037 0.00 0.00 0.00 2.82
76 77 9.705103 TGTTACTACTCTATGTTACTACCCATT 57.295 33.333 0.00 0.00 0.00 3.16
77 78 9.878737 ATGTTACTACTCTATGTTACTACCCAT 57.121 33.333 0.00 0.00 0.00 4.00
78 79 9.128404 CATGTTACTACTCTATGTTACTACCCA 57.872 37.037 0.00 0.00 0.00 4.51
79 80 8.081025 GCATGTTACTACTCTATGTTACTACCC 58.919 40.741 0.00 0.00 0.00 3.69
80 81 8.081025 GGCATGTTACTACTCTATGTTACTACC 58.919 40.741 0.00 0.00 0.00 3.18
81 82 8.081025 GGGCATGTTACTACTCTATGTTACTAC 58.919 40.741 0.00 0.00 0.00 2.73
82 83 7.781219 TGGGCATGTTACTACTCTATGTTACTA 59.219 37.037 0.00 0.00 0.00 1.82
83 84 6.610020 TGGGCATGTTACTACTCTATGTTACT 59.390 38.462 0.00 0.00 0.00 2.24
84 85 6.812998 TGGGCATGTTACTACTCTATGTTAC 58.187 40.000 0.00 0.00 0.00 2.50
85 86 7.441836 CATGGGCATGTTACTACTCTATGTTA 58.558 38.462 0.00 0.00 34.23 2.41
86 87 5.950544 TGGGCATGTTACTACTCTATGTT 57.049 39.130 0.00 0.00 0.00 2.71
87 88 5.858381 CATGGGCATGTTACTACTCTATGT 58.142 41.667 0.00 0.00 34.23 2.29
101 102 5.858381 ACATAGAGTAGTAACATGGGCATG 58.142 41.667 0.00 0.00 44.15 4.06
102 103 6.500589 AACATAGAGTAGTAACATGGGCAT 57.499 37.500 0.00 0.00 0.00 4.40
103 104 5.950544 AACATAGAGTAGTAACATGGGCA 57.049 39.130 0.00 0.00 0.00 5.36
104 105 7.052142 AGTAACATAGAGTAGTAACATGGGC 57.948 40.000 0.00 0.00 0.00 5.36
105 106 8.574737 GGTAGTAACATAGAGTAGTAACATGGG 58.425 40.741 0.00 0.00 0.00 4.00
106 107 9.352191 AGGTAGTAACATAGAGTAGTAACATGG 57.648 37.037 0.00 0.00 0.00 3.66
116 117 8.384718 CCCACTATAGAGGTAGTAACATAGAGT 58.615 40.741 14.29 0.00 33.29 3.24
117 118 7.830201 CCCCACTATAGAGGTAGTAACATAGAG 59.170 44.444 14.29 0.00 33.29 2.43
118 119 7.518653 TCCCCACTATAGAGGTAGTAACATAGA 59.481 40.741 14.29 0.00 33.29 1.98
119 120 7.696981 TCCCCACTATAGAGGTAGTAACATAG 58.303 42.308 14.29 0.00 33.29 2.23
120 121 7.296628 ACTCCCCACTATAGAGGTAGTAACATA 59.703 40.741 14.29 0.00 33.29 2.29
121 122 6.104392 ACTCCCCACTATAGAGGTAGTAACAT 59.896 42.308 14.29 0.00 33.29 2.71
122 123 5.434376 ACTCCCCACTATAGAGGTAGTAACA 59.566 44.000 14.29 0.00 33.29 2.41
123 124 5.951204 ACTCCCCACTATAGAGGTAGTAAC 58.049 45.833 14.29 0.00 33.29 2.50
124 125 7.129349 TGTTACTCCCCACTATAGAGGTAGTAA 59.871 40.741 23.15 23.15 33.91 2.24
125 126 6.621098 TGTTACTCCCCACTATAGAGGTAGTA 59.379 42.308 17.42 17.42 33.29 1.82
126 127 5.434376 TGTTACTCCCCACTATAGAGGTAGT 59.566 44.000 18.82 18.82 35.34 2.73
127 128 5.950023 TGTTACTCCCCACTATAGAGGTAG 58.050 45.833 14.29 12.87 31.70 3.18
128 129 5.999987 TGTTACTCCCCACTATAGAGGTA 57.000 43.478 14.29 2.62 31.70 3.08
129 130 4.894252 TGTTACTCCCCACTATAGAGGT 57.106 45.455 14.29 0.00 31.70 3.85
130 131 6.954684 ACATATGTTACTCCCCACTATAGAGG 59.045 42.308 6.78 8.10 31.70 3.69
131 132 7.451877 ACACATATGTTACTCCCCACTATAGAG 59.548 40.741 5.37 0.00 34.46 2.43
132 133 7.232737 CACACATATGTTACTCCCCACTATAGA 59.767 40.741 5.37 0.00 36.72 1.98
133 134 7.378966 CACACATATGTTACTCCCCACTATAG 58.621 42.308 5.37 0.00 36.72 1.31
134 135 6.269077 CCACACATATGTTACTCCCCACTATA 59.731 42.308 5.37 0.00 36.72 1.31
135 136 5.071788 CCACACATATGTTACTCCCCACTAT 59.928 44.000 5.37 0.00 36.72 2.12
136 137 4.407621 CCACACATATGTTACTCCCCACTA 59.592 45.833 5.37 0.00 36.72 2.74
137 138 3.199946 CCACACATATGTTACTCCCCACT 59.800 47.826 5.37 0.00 36.72 4.00
138 139 3.054655 ACCACACATATGTTACTCCCCAC 60.055 47.826 5.37 0.00 36.72 4.61
139 140 3.186283 ACCACACATATGTTACTCCCCA 58.814 45.455 5.37 0.00 36.72 4.96
140 141 3.926058 ACCACACATATGTTACTCCCC 57.074 47.619 5.37 0.00 36.72 4.81
141 142 5.736813 TGTTACCACACATATGTTACTCCC 58.263 41.667 5.37 0.00 36.72 4.30
142 143 6.238374 GCATGTTACCACACATATGTTACTCC 60.238 42.308 5.37 0.00 36.72 3.85
143 144 6.315144 TGCATGTTACCACACATATGTTACTC 59.685 38.462 5.37 0.00 36.72 2.59
144 145 6.176896 TGCATGTTACCACACATATGTTACT 58.823 36.000 5.37 0.00 36.72 2.24
145 146 6.429791 TGCATGTTACCACACATATGTTAC 57.570 37.500 5.37 0.00 36.72 2.50
146 147 6.402658 CGTTGCATGTTACCACACATATGTTA 60.403 38.462 5.37 0.00 36.72 2.41
147 148 5.618863 CGTTGCATGTTACCACACATATGTT 60.619 40.000 5.37 0.00 36.72 2.71
148 149 4.142708 CGTTGCATGTTACCACACATATGT 60.143 41.667 1.41 1.41 40.80 2.29
149 150 4.341935 CGTTGCATGTTACCACACATATG 58.658 43.478 0.00 0.00 35.51 1.78
150 151 3.181501 GCGTTGCATGTTACCACACATAT 60.182 43.478 0.00 0.00 35.51 1.78
151 152 2.160615 GCGTTGCATGTTACCACACATA 59.839 45.455 0.00 0.00 35.51 2.29
152 153 1.068610 GCGTTGCATGTTACCACACAT 60.069 47.619 0.00 0.00 37.93 3.21
153 154 0.309302 GCGTTGCATGTTACCACACA 59.691 50.000 0.00 0.00 35.03 3.72
154 155 0.591170 AGCGTTGCATGTTACCACAC 59.409 50.000 0.00 0.00 35.03 3.82
155 156 1.265635 GAAGCGTTGCATGTTACCACA 59.734 47.619 0.00 0.00 37.31 4.17
156 157 1.265635 TGAAGCGTTGCATGTTACCAC 59.734 47.619 0.00 0.00 0.00 4.16
157 158 1.598882 TGAAGCGTTGCATGTTACCA 58.401 45.000 0.00 0.00 0.00 3.25
158 159 2.919666 ATGAAGCGTTGCATGTTACC 57.080 45.000 0.00 0.00 0.00 2.85
159 160 6.869421 AATAAATGAAGCGTTGCATGTTAC 57.131 33.333 0.00 0.00 0.00 2.50
160 161 7.192913 CCTAATAAATGAAGCGTTGCATGTTA 58.807 34.615 0.00 0.00 0.00 2.41
161 162 6.035843 CCTAATAAATGAAGCGTTGCATGTT 58.964 36.000 0.00 0.00 0.00 2.71
162 163 5.581605 CCTAATAAATGAAGCGTTGCATGT 58.418 37.500 0.00 0.00 0.00 3.21
163 164 4.442073 GCCTAATAAATGAAGCGTTGCATG 59.558 41.667 0.00 0.00 0.00 4.06
164 165 4.339247 AGCCTAATAAATGAAGCGTTGCAT 59.661 37.500 0.00 0.00 0.00 3.96
165 166 3.694072 AGCCTAATAAATGAAGCGTTGCA 59.306 39.130 0.00 0.00 0.00 4.08
166 167 4.292977 AGCCTAATAAATGAAGCGTTGC 57.707 40.909 0.00 0.00 0.00 4.17
167 168 9.382244 GTTTATAGCCTAATAAATGAAGCGTTG 57.618 33.333 1.27 0.00 34.67 4.10
168 169 9.338622 AGTTTATAGCCTAATAAATGAAGCGTT 57.661 29.630 1.27 0.00 34.67 4.84
169 170 8.904099 AGTTTATAGCCTAATAAATGAAGCGT 57.096 30.769 1.27 0.00 34.67 5.07
170 171 8.988934 TGAGTTTATAGCCTAATAAATGAAGCG 58.011 33.333 1.27 0.00 34.67 4.68
190 191 9.671279 TCACACATATCAATACAAGATGAGTTT 57.329 29.630 0.00 0.00 0.00 2.66
191 192 9.842775 ATCACACATATCAATACAAGATGAGTT 57.157 29.630 0.00 0.00 0.00 3.01
192 193 9.269453 CATCACACATATCAATACAAGATGAGT 57.731 33.333 0.00 0.00 32.98 3.41
193 194 9.269453 ACATCACACATATCAATACAAGATGAG 57.731 33.333 0.00 0.00 34.73 2.90
194 195 9.617523 AACATCACACATATCAATACAAGATGA 57.382 29.630 0.00 0.00 34.73 2.92
199 200 9.883142 TGAGTAACATCACACATATCAATACAA 57.117 29.630 0.00 0.00 0.00 2.41
209 210 9.409918 ACTACTAGTATGAGTAACATCACACAT 57.590 33.333 2.33 0.00 40.07 3.21
210 211 8.803397 ACTACTAGTATGAGTAACATCACACA 57.197 34.615 2.33 0.00 40.07 3.72
246 247 6.349300 TGAAGAAAGAGAGGCATATGGTAAC 58.651 40.000 4.56 0.00 0.00 2.50
247 248 6.560003 TGAAGAAAGAGAGGCATATGGTAA 57.440 37.500 4.56 0.00 0.00 2.85
248 249 6.753913 ATGAAGAAAGAGAGGCATATGGTA 57.246 37.500 4.56 0.00 0.00 3.25
249 250 5.643421 ATGAAGAAAGAGAGGCATATGGT 57.357 39.130 4.56 0.00 0.00 3.55
250 251 6.956202 AAATGAAGAAAGAGAGGCATATGG 57.044 37.500 4.56 0.00 0.00 2.74
251 252 9.894783 CAATAAATGAAGAAAGAGAGGCATATG 57.105 33.333 0.00 0.00 0.00 1.78
252 253 8.574737 GCAATAAATGAAGAAAGAGAGGCATAT 58.425 33.333 0.00 0.00 0.00 1.78
253 254 7.776969 AGCAATAAATGAAGAAAGAGAGGCATA 59.223 33.333 0.00 0.00 0.00 3.14
254 255 6.606395 AGCAATAAATGAAGAAAGAGAGGCAT 59.394 34.615 0.00 0.00 0.00 4.40
255 256 5.948162 AGCAATAAATGAAGAAAGAGAGGCA 59.052 36.000 0.00 0.00 0.00 4.75
256 257 6.448207 AGCAATAAATGAAGAAAGAGAGGC 57.552 37.500 0.00 0.00 0.00 4.70
257 258 7.824672 ACAAGCAATAAATGAAGAAAGAGAGG 58.175 34.615 0.00 0.00 0.00 3.69
258 259 8.509690 TGACAAGCAATAAATGAAGAAAGAGAG 58.490 33.333 0.00 0.00 0.00 3.20
259 260 8.292448 GTGACAAGCAATAAATGAAGAAAGAGA 58.708 33.333 0.00 0.00 0.00 3.10
260 261 8.077991 TGTGACAAGCAATAAATGAAGAAAGAG 58.922 33.333 0.00 0.00 0.00 2.85
261 262 7.939782 TGTGACAAGCAATAAATGAAGAAAGA 58.060 30.769 0.00 0.00 0.00 2.52
262 263 8.752766 ATGTGACAAGCAATAAATGAAGAAAG 57.247 30.769 0.00 0.00 0.00 2.62
308 309 9.680315 GGAGTAACATAGATAGTAACATCACAC 57.320 37.037 0.00 0.00 0.00 3.82
309 310 8.857098 GGGAGTAACATAGATAGTAACATCACA 58.143 37.037 0.00 0.00 0.00 3.58
310 311 8.857098 TGGGAGTAACATAGATAGTAACATCAC 58.143 37.037 0.00 0.00 0.00 3.06
311 312 9.078990 CTGGGAGTAACATAGATAGTAACATCA 57.921 37.037 0.00 0.00 0.00 3.07
312 313 9.080097 ACTGGGAGTAACATAGATAGTAACATC 57.920 37.037 0.00 0.00 0.00 3.06
313 314 8.861086 CACTGGGAGTAACATAGATAGTAACAT 58.139 37.037 0.00 0.00 0.00 2.71
314 315 7.837689 ACACTGGGAGTAACATAGATAGTAACA 59.162 37.037 0.00 0.00 0.00 2.41
315 316 8.136165 CACACTGGGAGTAACATAGATAGTAAC 58.864 40.741 0.00 0.00 0.00 2.50
316 317 7.287005 CCACACTGGGAGTAACATAGATAGTAA 59.713 40.741 0.00 0.00 32.67 2.24
317 318 6.776116 CCACACTGGGAGTAACATAGATAGTA 59.224 42.308 0.00 0.00 32.67 1.82
318 319 5.598830 CCACACTGGGAGTAACATAGATAGT 59.401 44.000 0.00 0.00 32.67 2.12
319 320 6.090483 CCACACTGGGAGTAACATAGATAG 57.910 45.833 0.00 0.00 32.67 2.08
334 335 0.608640 GGTGAGACTACCCACACTGG 59.391 60.000 0.00 0.00 37.25 4.00
335 336 0.243907 CGGTGAGACTACCCACACTG 59.756 60.000 0.00 0.00 37.44 3.66
336 337 1.533469 GCGGTGAGACTACCCACACT 61.533 60.000 0.00 0.00 37.44 3.55
337 338 1.080025 GCGGTGAGACTACCCACAC 60.080 63.158 0.00 0.00 37.44 3.82
338 339 0.902984 ATGCGGTGAGACTACCCACA 60.903 55.000 0.00 0.00 37.44 4.17
339 340 0.460284 CATGCGGTGAGACTACCCAC 60.460 60.000 0.00 0.00 37.44 4.61
340 341 1.897423 CATGCGGTGAGACTACCCA 59.103 57.895 0.00 0.00 37.44 4.51
341 342 1.521681 GCATGCGGTGAGACTACCC 60.522 63.158 0.00 0.00 37.44 3.69
342 343 0.108138 AAGCATGCGGTGAGACTACC 60.108 55.000 13.01 0.00 37.37 3.18
343 344 1.281899 GAAGCATGCGGTGAGACTAC 58.718 55.000 13.01 0.00 0.00 2.73
344 345 0.175760 GGAAGCATGCGGTGAGACTA 59.824 55.000 13.01 0.00 0.00 2.59
345 346 1.078848 GGAAGCATGCGGTGAGACT 60.079 57.895 13.01 0.00 0.00 3.24
346 347 0.674895 AAGGAAGCATGCGGTGAGAC 60.675 55.000 13.01 0.00 0.00 3.36
347 348 0.674581 CAAGGAAGCATGCGGTGAGA 60.675 55.000 13.01 0.00 0.00 3.27
348 349 0.957395 ACAAGGAAGCATGCGGTGAG 60.957 55.000 13.01 4.83 0.00 3.51
349 350 1.073025 ACAAGGAAGCATGCGGTGA 59.927 52.632 13.01 0.00 0.00 4.02
350 351 1.210931 CACAAGGAAGCATGCGGTG 59.789 57.895 13.01 10.98 0.00 4.94
351 352 1.073025 TCACAAGGAAGCATGCGGT 59.927 52.632 13.01 4.02 0.00 5.68
352 353 0.957395 AGTCACAAGGAAGCATGCGG 60.957 55.000 13.01 1.65 0.00 5.69
353 354 0.167470 CAGTCACAAGGAAGCATGCG 59.833 55.000 13.01 0.00 0.00 4.73
366 367 4.153655 GGTTTTAGAATTCGGGTCAGTCAC 59.846 45.833 0.00 0.00 0.00 3.67
377 378 4.514781 AAGTTGCCGGGTTTTAGAATTC 57.485 40.909 2.18 0.00 0.00 2.17
587 596 5.730296 ATCACTCACTATGGTATGCCTAC 57.270 43.478 0.16 0.00 35.27 3.18
791 843 3.552273 GCAGGCCAAAGAATAGATGCATG 60.552 47.826 2.46 0.00 34.03 4.06
792 844 2.626743 GCAGGCCAAAGAATAGATGCAT 59.373 45.455 5.01 0.00 32.79 3.96
793 845 2.026641 GCAGGCCAAAGAATAGATGCA 58.973 47.619 5.01 0.00 32.79 3.96
794 846 1.339291 GGCAGGCCAAAGAATAGATGC 59.661 52.381 5.01 0.77 35.81 3.91
877 929 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
878 930 1.375396 AGCGTGTGTGTGTGTGTGT 60.375 52.632 0.00 0.00 0.00 3.72
998 1054 1.615384 GGAGCAACAGAGGGAGCATTT 60.615 52.381 0.00 0.00 0.00 2.32
1027 1083 0.179134 GGTAGGCTAGCTCGTGTGTG 60.179 60.000 15.72 0.00 0.00 3.82
1057 1113 2.202440 CGCTGTTGCTGATGCTGC 60.202 61.111 0.00 0.00 40.48 5.25
1063 1122 2.357881 CTCTGCCGCTGTTGCTGA 60.358 61.111 0.00 0.00 36.97 4.26
1104 1163 6.056428 GTACCTTTAATTAATGGGACGCAG 57.944 41.667 22.97 6.14 35.45 5.18
1199 1258 2.678580 TGTGTGAGGCCGATCCGA 60.679 61.111 0.00 0.00 40.77 4.55
1200 1259 2.021068 ATCTGTGTGAGGCCGATCCG 62.021 60.000 0.00 0.00 40.77 4.18
1201 1260 0.249657 GATCTGTGTGAGGCCGATCC 60.250 60.000 0.00 0.00 0.00 3.36
1213 1272 1.001487 CTAGCGAGGCTCTGATCTGTG 60.001 57.143 13.50 0.00 40.44 3.66
1278 1341 0.822532 GCCAGGATCCATCTTGCCAG 60.823 60.000 15.82 0.00 33.07 4.85
1279 1342 1.228228 GCCAGGATCCATCTTGCCA 59.772 57.895 15.82 0.00 33.07 4.92
1280 1343 0.106318 AAGCCAGGATCCATCTTGCC 60.106 55.000 15.82 0.00 33.07 4.52
1376 1439 2.509336 GCTCCCGTCCACGACATG 60.509 66.667 0.00 0.00 43.02 3.21
1438 1501 2.586079 AGTTCCATGATCGCGGCG 60.586 61.111 17.70 17.70 0.00 6.46
1453 1516 2.937689 ACCTGGATGCCCTGCAGT 60.938 61.111 13.81 0.00 43.65 4.40
1783 1846 1.003262 CTGTTTTTGCCGCCGATGTG 61.003 55.000 0.00 0.00 0.00 3.21
1794 1857 0.865769 CCTCGTCGTCCCTGTTTTTG 59.134 55.000 0.00 0.00 0.00 2.44
1797 1860 2.342648 GCCTCGTCGTCCCTGTTT 59.657 61.111 0.00 0.00 0.00 2.83
1799 1862 3.374402 CTGCCTCGTCGTCCCTGT 61.374 66.667 0.00 0.00 0.00 4.00
1934 2003 2.264794 GTTGGTGGACGCGAGGAT 59.735 61.111 15.93 0.00 0.00 3.24
2003 2072 4.373116 GGTGCGCTTGGAGGACGA 62.373 66.667 9.73 0.00 0.00 4.20
2236 2305 3.823330 GTCTGCGGGTCGGACGAT 61.823 66.667 1.43 0.00 40.88 3.73
2389 2458 0.034767 TTTGCAGCTCCCTGATCTGG 60.035 55.000 11.58 11.58 41.77 3.86
2516 2585 0.688087 CCTCCTCCTAGGGTTTCGCT 60.688 60.000 9.46 0.00 35.59 4.93
2755 2833 6.882656 TCATCAATCTAACAGAAGGAGAAGG 58.117 40.000 0.00 0.00 0.00 3.46
2769 2847 8.398878 TGCATGCAGAATTATTCATCAATCTA 57.601 30.769 18.46 0.00 0.00 1.98
2770 2848 7.284919 TGCATGCAGAATTATTCATCAATCT 57.715 32.000 18.46 0.00 0.00 2.40
2771 2849 7.953393 CATGCATGCAGAATTATTCATCAATC 58.047 34.615 26.69 2.41 0.00 2.67
2772 2850 7.889589 CATGCATGCAGAATTATTCATCAAT 57.110 32.000 26.69 0.00 0.00 2.57
3058 3141 4.893424 TTCAAAGAGGCCATAATTACGC 57.107 40.909 5.01 0.00 0.00 4.42
3087 3170 0.751452 TGCATGCACAAAGAAAGGCA 59.249 45.000 18.46 0.00 41.00 4.75
3143 3227 3.425162 TTTGCCCTCTCTTCTTCCTTC 57.575 47.619 0.00 0.00 0.00 3.46
3264 3351 9.214957 TCGATCATATACAACTCAAACAGTTTT 57.785 29.630 0.00 0.00 43.38 2.43
3265 3352 8.771920 TCGATCATATACAACTCAAACAGTTT 57.228 30.769 0.00 0.00 43.38 2.66
3282 3369 1.947456 CCACACGTCTCCTCGATCATA 59.053 52.381 0.00 0.00 34.70 2.15
3310 3397 3.417224 CATCGGCATCGGCATCGG 61.417 66.667 0.00 0.00 43.71 4.18


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

AutoCloner maintained by Alex Coulton.