Multiple sequence alignment - TraesCS2D01G420500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G420500 chr2D 100.000 2682 0 0 849 3530 534492443 534489762 0.000000e+00 4953.0
1 TraesCS2D01G420500 chr2D 100.000 504 0 0 1 504 534493291 534492788 0.000000e+00 931.0
2 TraesCS2D01G420500 chr2B 91.899 2728 123 44 849 3530 635704661 635701986 0.000000e+00 3723.0
3 TraesCS2D01G420500 chr2B 86.585 164 9 4 352 504 635705167 635705006 6.060000e-38 169.0
4 TraesCS2D01G420500 chr2A 94.065 2140 91 14 849 2957 678018130 678015996 0.000000e+00 3216.0
5 TraesCS2D01G420500 chr2A 85.065 462 37 19 3037 3487 678015865 678015425 3.230000e-120 442.0
6 TraesCS2D01G420500 chr2A 85.455 165 8 6 351 504 678018636 678018477 1.310000e-34 158.0
7 TraesCS2D01G420500 chr2A 90.698 43 4 0 3487 3529 678015438 678015396 1.370000e-04 58.4
8 TraesCS2D01G420500 chr5D 85.750 1614 180 29 849 2426 524481274 524482873 0.000000e+00 1661.0
9 TraesCS2D01G420500 chr5B 88.783 1364 139 7 849 2208 659029436 659030789 0.000000e+00 1659.0
10 TraesCS2D01G420500 chr5B 82.463 268 33 11 2506 2772 358020404 358020658 4.590000e-54 222.0
11 TraesCS2D01G420500 chr5B 82.723 191 16 6 970 1160 664974896 664975069 1.700000e-33 154.0
12 TraesCS2D01G420500 chr5A 88.278 1365 144 9 849 2208 650671283 650672636 0.000000e+00 1620.0
13 TraesCS2D01G420500 chr3A 81.931 321 33 8 2464 2772 11823060 11822753 7.570000e-62 248.0
14 TraesCS2D01G420500 chr4D 83.955 268 29 6 2506 2772 451649612 451649358 9.790000e-61 244.0
15 TraesCS2D01G420500 chr1B 81.852 270 35 9 2504 2772 51403095 51403351 7.670000e-52 215.0
16 TraesCS2D01G420500 chr1D 80.377 265 35 7 902 1166 452336674 452336427 6.020000e-43 185.0
17 TraesCS2D01G420500 chr1D 80.534 262 34 7 902 1163 452351679 452351923 6.020000e-43 185.0


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 TraesCS2D01G420500 chr2D 534489762 534493291 3529 True 2942.0 4953 100.00000 1 3530 2 chr2D.!!$R1 3529
1 TraesCS2D01G420500 chr2B 635701986 635705167 3181 True 1946.0 3723 89.24200 352 3530 2 chr2B.!!$R1 3178
2 TraesCS2D01G420500 chr2A 678015396 678018636 3240 True 968.6 3216 88.82075 351 3529 4 chr2A.!!$R1 3178
3 TraesCS2D01G420500 chr5D 524481274 524482873 1599 False 1661.0 1661 85.75000 849 2426 1 chr5D.!!$F1 1577
4 TraesCS2D01G420500 chr5B 659029436 659030789 1353 False 1659.0 1659 88.78300 849 2208 1 chr5B.!!$F2 1359
5 TraesCS2D01G420500 chr5A 650671283 650672636 1353 False 1620.0 1620 88.27800 849 2208 1 chr5A.!!$F1 1359

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
258 259 0.038343 CCATGAACTTGTTTGGCGGG 60.038 55.000 0.00 0.00 0.00 6.13 F
442 454 0.530744 TGGCTTAGCAGTCGTGTAGG 59.469 55.000 6.53 0.00 0.00 3.18 F
456 468 4.635324 GTCGTGTAGGCTTCTAGAAGTACT 59.365 45.833 28.72 26.62 40.45 2.73 F
2224 2247 2.121564 GACATGCCGGCGATCATTGG 62.122 60.000 23.90 6.92 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1809 1.373999 GCTCACGCTGCAGAGTTCT 60.374 57.895 21.27 0.0 34.39 3.01 R
2224 2247 1.587547 GCATAGGTACAAGGCTCAGC 58.412 55.000 0.00 0.0 0.00 4.26 R
2238 2261 1.705337 CCGTGGGTTGAAGCGCATAG 61.705 60.000 11.47 0.0 33.93 2.23 R
3051 3210 0.182299 CAGGCCCCATCTTTCCTCTC 59.818 60.000 0.00 0.0 0.00 3.20 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
45 46 8.947055 ATCAAAATTTACAATAGTTCATGGGC 57.053 30.769 0.00 0.00 0.00 5.36
46 47 8.133024 TCAAAATTTACAATAGTTCATGGGCT 57.867 30.769 0.00 0.00 0.00 5.19
47 48 9.249053 TCAAAATTTACAATAGTTCATGGGCTA 57.751 29.630 0.00 0.00 0.00 3.93
48 49 9.301153 CAAAATTTACAATAGTTCATGGGCTAC 57.699 33.333 0.00 0.00 0.00 3.58
49 50 7.582667 AATTTACAATAGTTCATGGGCTACC 57.417 36.000 0.00 0.00 37.24 3.18
50 51 5.968676 TTACAATAGTTCATGGGCTACCT 57.031 39.130 0.00 0.00 37.76 3.08
51 52 7.440505 TTTACAATAGTTCATGGGCTACCTA 57.559 36.000 0.00 0.00 37.76 3.08
52 53 5.552870 ACAATAGTTCATGGGCTACCTAG 57.447 43.478 0.00 0.00 37.76 3.02
68 69 4.067972 ACCTAGCAACGTATATGGTTGG 57.932 45.455 14.18 14.18 43.77 3.77
69 70 3.707611 ACCTAGCAACGTATATGGTTGGA 59.292 43.478 20.16 0.00 43.77 3.53
70 71 4.056050 CCTAGCAACGTATATGGTTGGAC 58.944 47.826 17.79 7.07 43.77 4.02
71 72 3.620427 AGCAACGTATATGGTTGGACA 57.380 42.857 17.79 0.00 43.77 4.02
72 73 3.267483 AGCAACGTATATGGTTGGACAC 58.733 45.455 17.79 6.31 43.77 3.67
74 75 2.940410 CAACGTATATGGTTGGACACCC 59.060 50.000 11.58 0.00 46.68 4.61
75 76 2.474112 ACGTATATGGTTGGACACCCT 58.526 47.619 0.00 0.00 46.68 4.34
76 77 3.645434 ACGTATATGGTTGGACACCCTA 58.355 45.455 0.00 0.00 46.68 3.53
77 78 4.032310 ACGTATATGGTTGGACACCCTAA 58.968 43.478 0.00 0.00 46.68 2.69
78 79 4.657039 ACGTATATGGTTGGACACCCTAAT 59.343 41.667 0.00 0.00 46.68 1.73
79 80 4.994852 CGTATATGGTTGGACACCCTAATG 59.005 45.833 0.00 0.00 46.68 1.90
80 81 2.143876 ATGGTTGGACACCCTAATGC 57.856 50.000 0.00 0.00 46.68 3.56
81 82 0.774276 TGGTTGGACACCCTAATGCA 59.226 50.000 0.00 0.00 46.68 3.96
82 83 1.145945 TGGTTGGACACCCTAATGCAA 59.854 47.619 0.00 0.00 46.68 4.08
83 84 2.243810 GGTTGGACACCCTAATGCAAA 58.756 47.619 0.00 0.00 40.19 3.68
84 85 2.630580 GGTTGGACACCCTAATGCAAAA 59.369 45.455 0.00 0.00 40.19 2.44
85 86 3.070302 GGTTGGACACCCTAATGCAAAAA 59.930 43.478 0.00 0.00 40.19 1.94
121 122 6.611613 TCTGGTGTCAGAATCATAGTTTCT 57.388 37.500 0.00 0.00 46.08 2.52
122 123 7.718334 TCTGGTGTCAGAATCATAGTTTCTA 57.282 36.000 0.00 0.00 46.08 2.10
123 124 7.548097 TCTGGTGTCAGAATCATAGTTTCTAC 58.452 38.462 0.00 0.00 46.08 2.59
124 125 7.178451 TCTGGTGTCAGAATCATAGTTTCTACA 59.822 37.037 0.00 0.00 46.08 2.74
125 126 7.851228 TGGTGTCAGAATCATAGTTTCTACAT 58.149 34.615 0.00 0.00 32.27 2.29
126 127 7.765819 TGGTGTCAGAATCATAGTTTCTACATG 59.234 37.037 0.00 0.00 32.27 3.21
127 128 7.254590 GGTGTCAGAATCATAGTTTCTACATGC 60.255 40.741 0.00 0.00 32.27 4.06
128 129 6.476706 TGTCAGAATCATAGTTTCTACATGCG 59.523 38.462 0.00 0.00 32.27 4.73
129 130 6.697455 GTCAGAATCATAGTTTCTACATGCGA 59.303 38.462 0.00 0.00 32.27 5.10
130 131 6.920210 TCAGAATCATAGTTTCTACATGCGAG 59.080 38.462 0.00 0.00 32.27 5.03
131 132 6.920210 CAGAATCATAGTTTCTACATGCGAGA 59.080 38.462 0.00 0.00 32.27 4.04
132 133 7.114670 CAGAATCATAGTTTCTACATGCGAGAG 59.885 40.741 0.00 0.00 32.27 3.20
133 134 8.210954 AGAATCATAGTTTCTACATGCGAGAGC 61.211 40.741 0.00 0.00 43.89 4.09
147 148 3.855689 CGAGAGCAATTTTCCAATGGT 57.144 42.857 0.00 0.00 0.00 3.55
148 149 4.178545 CGAGAGCAATTTTCCAATGGTT 57.821 40.909 0.00 0.00 0.00 3.67
149 150 5.309323 CGAGAGCAATTTTCCAATGGTTA 57.691 39.130 0.00 0.00 0.00 2.85
150 151 5.708948 CGAGAGCAATTTTCCAATGGTTAA 58.291 37.500 0.00 0.00 0.00 2.01
151 152 6.332630 CGAGAGCAATTTTCCAATGGTTAAT 58.667 36.000 0.00 0.00 0.00 1.40
152 153 6.813152 CGAGAGCAATTTTCCAATGGTTAATT 59.187 34.615 0.00 4.04 0.00 1.40
153 154 7.009540 CGAGAGCAATTTTCCAATGGTTAATTC 59.990 37.037 0.00 2.42 0.00 2.17
154 155 7.105588 AGAGCAATTTTCCAATGGTTAATTCC 58.894 34.615 0.00 0.00 0.00 3.01
155 156 6.777782 AGCAATTTTCCAATGGTTAATTCCA 58.222 32.000 0.00 0.00 42.01 3.53
156 157 6.654582 AGCAATTTTCCAATGGTTAATTCCAC 59.345 34.615 0.00 0.12 40.51 4.02
157 158 6.429385 GCAATTTTCCAATGGTTAATTCCACA 59.571 34.615 0.00 0.00 40.51 4.17
158 159 7.040823 GCAATTTTCCAATGGTTAATTCCACAA 60.041 33.333 0.00 0.00 40.51 3.33
159 160 8.844244 CAATTTTCCAATGGTTAATTCCACAAA 58.156 29.630 0.00 0.00 40.51 2.83
160 161 8.986929 ATTTTCCAATGGTTAATTCCACAAAA 57.013 26.923 0.00 0.00 40.51 2.44
161 162 8.807948 TTTTCCAATGGTTAATTCCACAAAAA 57.192 26.923 0.00 0.00 40.51 1.94
162 163 7.793927 TTCCAATGGTTAATTCCACAAAAAC 57.206 32.000 0.00 0.00 40.51 2.43
163 164 6.889198 TCCAATGGTTAATTCCACAAAAACA 58.111 32.000 0.00 0.00 40.51 2.83
164 165 7.338710 TCCAATGGTTAATTCCACAAAAACAA 58.661 30.769 0.00 0.00 40.51 2.83
165 166 7.995488 TCCAATGGTTAATTCCACAAAAACAAT 59.005 29.630 0.00 0.00 40.51 2.71
166 167 8.288913 CCAATGGTTAATTCCACAAAAACAATC 58.711 33.333 0.00 0.00 40.51 2.67
167 168 8.834465 CAATGGTTAATTCCACAAAAACAATCA 58.166 29.630 0.00 0.00 40.51 2.57
168 169 7.778470 TGGTTAATTCCACAAAAACAATCAC 57.222 32.000 0.00 0.00 31.96 3.06
169 170 6.763610 TGGTTAATTCCACAAAAACAATCACC 59.236 34.615 0.00 0.00 31.96 4.02
170 171 6.989759 GGTTAATTCCACAAAAACAATCACCT 59.010 34.615 0.00 0.00 0.00 4.00
171 172 7.042119 GGTTAATTCCACAAAAACAATCACCTG 60.042 37.037 0.00 0.00 0.00 4.00
172 173 5.867903 ATTCCACAAAAACAATCACCTGA 57.132 34.783 0.00 0.00 0.00 3.86
173 174 4.647424 TCCACAAAAACAATCACCTGAC 57.353 40.909 0.00 0.00 0.00 3.51
174 175 3.383185 TCCACAAAAACAATCACCTGACC 59.617 43.478 0.00 0.00 0.00 4.02
175 176 3.371168 CACAAAAACAATCACCTGACCG 58.629 45.455 0.00 0.00 0.00 4.79
176 177 3.020984 ACAAAAACAATCACCTGACCGT 58.979 40.909 0.00 0.00 0.00 4.83
177 178 3.181491 ACAAAAACAATCACCTGACCGTG 60.181 43.478 0.00 0.00 34.93 4.94
178 179 2.631160 AAACAATCACCTGACCGTGA 57.369 45.000 0.00 0.00 46.36 4.35
179 180 2.169832 AACAATCACCTGACCGTGAG 57.830 50.000 0.00 0.00 45.55 3.51
180 181 1.048601 ACAATCACCTGACCGTGAGT 58.951 50.000 0.00 0.00 45.55 3.41
181 182 2.244695 ACAATCACCTGACCGTGAGTA 58.755 47.619 0.00 0.00 45.55 2.59
182 183 2.832129 ACAATCACCTGACCGTGAGTAT 59.168 45.455 0.00 0.00 45.55 2.12
183 184 3.260884 ACAATCACCTGACCGTGAGTATT 59.739 43.478 0.00 0.00 45.55 1.89
184 185 4.464951 ACAATCACCTGACCGTGAGTATTA 59.535 41.667 0.00 0.00 45.55 0.98
185 186 5.046878 ACAATCACCTGACCGTGAGTATTAA 60.047 40.000 0.00 0.00 45.55 1.40
186 187 5.670792 ATCACCTGACCGTGAGTATTAAA 57.329 39.130 0.00 0.00 45.55 1.52
187 188 5.471556 TCACCTGACCGTGAGTATTAAAA 57.528 39.130 0.00 0.00 37.85 1.52
188 189 5.856156 TCACCTGACCGTGAGTATTAAAAA 58.144 37.500 0.00 0.00 37.85 1.94
211 212 1.261619 GCGACTGCAACTACCATATGC 59.738 52.381 0.00 0.00 42.15 3.14
212 213 2.549926 CGACTGCAACTACCATATGCA 58.450 47.619 0.00 0.00 46.97 3.96
217 218 4.420522 TGCAACTACCATATGCATCTCA 57.579 40.909 0.19 0.00 44.52 3.27
218 219 4.779696 TGCAACTACCATATGCATCTCAA 58.220 39.130 0.19 0.00 44.52 3.02
219 220 4.818005 TGCAACTACCATATGCATCTCAAG 59.182 41.667 0.19 0.00 44.52 3.02
220 221 5.059161 GCAACTACCATATGCATCTCAAGA 58.941 41.667 0.19 0.00 39.81 3.02
221 222 5.178996 GCAACTACCATATGCATCTCAAGAG 59.821 44.000 0.19 0.00 39.81 2.85
222 223 5.480642 ACTACCATATGCATCTCAAGAGG 57.519 43.478 0.19 0.00 0.00 3.69
231 232 3.146618 CATCTCAAGAGGCAATTGCAC 57.853 47.619 30.32 22.36 44.36 4.57
232 233 1.538047 TCTCAAGAGGCAATTGCACC 58.462 50.000 30.32 20.47 44.36 5.01
233 234 0.169672 CTCAAGAGGCAATTGCACCG 59.830 55.000 30.32 16.87 44.36 4.94
234 235 1.213537 CAAGAGGCAATTGCACCGG 59.786 57.895 30.32 14.78 44.36 5.28
235 236 1.074775 AAGAGGCAATTGCACCGGA 59.925 52.632 30.32 0.00 44.36 5.14
236 237 0.962356 AAGAGGCAATTGCACCGGAG 60.962 55.000 30.32 0.00 44.36 4.63
250 251 3.935993 CGGAGGTCCATGAACTTGT 57.064 52.632 0.00 0.00 35.14 3.16
251 252 2.185004 CGGAGGTCCATGAACTTGTT 57.815 50.000 0.00 0.00 35.14 2.83
252 253 2.504367 CGGAGGTCCATGAACTTGTTT 58.496 47.619 0.00 0.00 35.14 2.83
253 254 2.226437 CGGAGGTCCATGAACTTGTTTG 59.774 50.000 0.00 0.00 35.14 2.93
254 255 2.558359 GGAGGTCCATGAACTTGTTTGG 59.442 50.000 0.00 0.00 35.64 3.28
255 256 1.963515 AGGTCCATGAACTTGTTTGGC 59.036 47.619 0.00 0.00 0.00 4.52
256 257 1.335872 GGTCCATGAACTTGTTTGGCG 60.336 52.381 0.00 0.00 0.00 5.69
257 258 0.958091 TCCATGAACTTGTTTGGCGG 59.042 50.000 0.00 0.00 0.00 6.13
258 259 0.038343 CCATGAACTTGTTTGGCGGG 60.038 55.000 0.00 0.00 0.00 6.13
259 260 0.958091 CATGAACTTGTTTGGCGGGA 59.042 50.000 0.00 0.00 0.00 5.14
260 261 1.339610 CATGAACTTGTTTGGCGGGAA 59.660 47.619 0.00 0.00 0.00 3.97
261 262 0.741915 TGAACTTGTTTGGCGGGAAC 59.258 50.000 0.00 0.00 0.00 3.62
262 263 0.741915 GAACTTGTTTGGCGGGAACA 59.258 50.000 0.00 0.00 35.36 3.18
263 264 1.339929 GAACTTGTTTGGCGGGAACAT 59.660 47.619 2.47 0.00 36.92 2.71
264 265 1.408969 ACTTGTTTGGCGGGAACATT 58.591 45.000 2.47 0.00 36.92 2.71
265 266 1.760029 ACTTGTTTGGCGGGAACATTT 59.240 42.857 2.47 0.00 36.92 2.32
266 267 2.169561 ACTTGTTTGGCGGGAACATTTT 59.830 40.909 2.47 0.00 36.92 1.82
267 268 2.990066 TGTTTGGCGGGAACATTTTT 57.010 40.000 0.00 0.00 32.44 1.94
268 269 4.141914 ACTTGTTTGGCGGGAACATTTTTA 60.142 37.500 2.47 0.00 36.92 1.52
269 270 3.983741 TGTTTGGCGGGAACATTTTTAG 58.016 40.909 0.00 0.00 32.44 1.85
270 271 3.385111 TGTTTGGCGGGAACATTTTTAGT 59.615 39.130 0.00 0.00 32.44 2.24
271 272 4.141914 TGTTTGGCGGGAACATTTTTAGTT 60.142 37.500 0.00 0.00 32.44 2.24
272 273 3.926821 TGGCGGGAACATTTTTAGTTC 57.073 42.857 0.00 0.00 43.49 3.01
273 274 2.226912 TGGCGGGAACATTTTTAGTTCG 59.773 45.455 0.00 0.00 44.78 3.95
274 275 2.227149 GGCGGGAACATTTTTAGTTCGT 59.773 45.455 0.00 0.00 44.78 3.85
275 276 3.231160 GCGGGAACATTTTTAGTTCGTG 58.769 45.455 0.00 0.00 44.78 4.35
276 277 3.058777 GCGGGAACATTTTTAGTTCGTGA 60.059 43.478 0.00 0.00 44.78 4.35
277 278 4.708601 CGGGAACATTTTTAGTTCGTGAG 58.291 43.478 0.00 0.00 44.78 3.51
278 279 4.473199 GGGAACATTTTTAGTTCGTGAGC 58.527 43.478 0.00 0.00 44.78 4.26
279 280 4.215613 GGGAACATTTTTAGTTCGTGAGCT 59.784 41.667 0.00 0.00 44.78 4.09
280 281 5.278315 GGGAACATTTTTAGTTCGTGAGCTT 60.278 40.000 0.00 0.00 44.78 3.74
281 282 5.625311 GGAACATTTTTAGTTCGTGAGCTTG 59.375 40.000 0.00 0.00 44.78 4.01
282 283 5.751243 ACATTTTTAGTTCGTGAGCTTGT 57.249 34.783 0.00 0.00 0.00 3.16
283 284 5.510671 ACATTTTTAGTTCGTGAGCTTGTG 58.489 37.500 0.00 0.00 0.00 3.33
284 285 5.295787 ACATTTTTAGTTCGTGAGCTTGTGA 59.704 36.000 0.00 0.00 0.00 3.58
285 286 5.804692 TTTTTAGTTCGTGAGCTTGTGAA 57.195 34.783 0.00 0.00 0.00 3.18
286 287 6.371809 TTTTTAGTTCGTGAGCTTGTGAAT 57.628 33.333 0.00 0.00 0.00 2.57
287 288 6.371809 TTTTAGTTCGTGAGCTTGTGAATT 57.628 33.333 0.00 0.00 0.00 2.17
288 289 5.591643 TTAGTTCGTGAGCTTGTGAATTC 57.408 39.130 0.00 0.00 0.00 2.17
289 290 3.466836 AGTTCGTGAGCTTGTGAATTCA 58.533 40.909 3.38 3.38 0.00 2.57
290 291 3.876914 AGTTCGTGAGCTTGTGAATTCAA 59.123 39.130 10.35 0.00 0.00 2.69
291 292 4.335315 AGTTCGTGAGCTTGTGAATTCAAA 59.665 37.500 10.35 0.76 0.00 2.69
292 293 4.472691 TCGTGAGCTTGTGAATTCAAAG 57.527 40.909 10.35 15.68 0.00 2.77
293 294 3.876914 TCGTGAGCTTGTGAATTCAAAGT 59.123 39.130 10.35 7.24 0.00 2.66
294 295 4.024893 TCGTGAGCTTGTGAATTCAAAGTC 60.025 41.667 10.35 14.17 0.00 3.01
295 296 4.260743 CGTGAGCTTGTGAATTCAAAGTCA 60.261 41.667 10.35 15.96 0.00 3.41
296 297 5.561532 CGTGAGCTTGTGAATTCAAAGTCAT 60.562 40.000 10.35 7.02 35.32 3.06
297 298 5.855395 GTGAGCTTGTGAATTCAAAGTCATC 59.145 40.000 10.35 13.97 35.32 2.92
298 299 5.532032 TGAGCTTGTGAATTCAAAGTCATCA 59.468 36.000 10.35 15.76 35.32 3.07
299 300 6.208007 TGAGCTTGTGAATTCAAAGTCATCAT 59.792 34.615 10.35 0.00 35.32 2.45
300 301 6.618811 AGCTTGTGAATTCAAAGTCATCATC 58.381 36.000 10.35 0.00 35.32 2.92
301 302 6.208007 AGCTTGTGAATTCAAAGTCATCATCA 59.792 34.615 10.35 0.00 35.32 3.07
302 303 6.864685 GCTTGTGAATTCAAAGTCATCATCAA 59.135 34.615 10.35 5.30 35.32 2.57
303 304 7.383029 GCTTGTGAATTCAAAGTCATCATCAAA 59.617 33.333 10.35 0.00 35.32 2.69
304 305 8.578308 TTGTGAATTCAAAGTCATCATCAAAC 57.422 30.769 10.35 0.00 35.32 2.93
305 306 7.944061 TGTGAATTCAAAGTCATCATCAAACT 58.056 30.769 10.35 0.00 35.32 2.66
306 307 8.415553 TGTGAATTCAAAGTCATCATCAAACTT 58.584 29.630 10.35 0.00 35.32 2.66
307 308 8.697067 GTGAATTCAAAGTCATCATCAAACTTG 58.303 33.333 10.35 0.00 35.32 3.16
308 309 7.383029 TGAATTCAAAGTCATCATCAAACTTGC 59.617 33.333 5.45 0.00 33.68 4.01
309 310 5.771153 TCAAAGTCATCATCAAACTTGCA 57.229 34.783 0.00 0.00 33.68 4.08
310 311 6.146601 TCAAAGTCATCATCAAACTTGCAA 57.853 33.333 0.00 0.00 33.68 4.08
311 312 6.571605 TCAAAGTCATCATCAAACTTGCAAA 58.428 32.000 0.00 0.00 33.68 3.68
312 313 7.040494 TCAAAGTCATCATCAAACTTGCAAAA 58.960 30.769 0.00 0.00 33.68 2.44
313 314 7.548427 TCAAAGTCATCATCAAACTTGCAAAAA 59.452 29.630 0.00 0.00 33.68 1.94
400 401 4.093011 AGTAGACAGACCTTCAGCTCAAT 58.907 43.478 0.00 0.00 0.00 2.57
428 429 2.653726 TGCAATATTGGACGATGGCTT 58.346 42.857 17.02 0.00 0.00 4.35
442 454 0.530744 TGGCTTAGCAGTCGTGTAGG 59.469 55.000 6.53 0.00 0.00 3.18
456 468 4.635324 GTCGTGTAGGCTTCTAGAAGTACT 59.365 45.833 28.72 26.62 40.45 2.73
457 469 5.814705 GTCGTGTAGGCTTCTAGAAGTACTA 59.185 44.000 28.72 25.78 40.45 1.82
460 472 7.655328 TCGTGTAGGCTTCTAGAAGTACTATAC 59.345 40.741 30.04 30.04 40.45 1.47
461 473 7.440556 CGTGTAGGCTTCTAGAAGTACTATACA 59.559 40.741 33.41 27.25 39.26 2.29
462 474 8.776470 GTGTAGGCTTCTAGAAGTACTATACAG 58.224 40.741 32.02 14.50 39.20 2.74
463 475 8.492782 TGTAGGCTTCTAGAAGTACTATACAGT 58.507 37.037 28.72 10.70 40.45 3.55
2040 2062 4.936575 GGTTCCCCGTTTCCCTTT 57.063 55.556 0.00 0.00 0.00 3.11
2224 2247 2.121564 GACATGCCGGCGATCATTGG 62.122 60.000 23.90 6.92 0.00 3.16
2337 2395 3.599338 CTTAGATTGAGACGACGACGAG 58.401 50.000 15.32 0.00 42.66 4.18
2448 2513 4.499040 CGAATCAGTTGTTGTTTTGTGACC 59.501 41.667 0.00 0.00 0.00 4.02
2533 2609 9.976776 TCCAATTAAACCAAGTGTATAATACCA 57.023 29.630 0.00 0.00 30.13 3.25
2630 2707 0.532862 CTGTTGCGTGTTGGAGGTCT 60.533 55.000 0.00 0.00 0.00 3.85
2666 2743 3.562557 CAGTACCGCAGTAGGTTGTTTTT 59.437 43.478 0.00 0.00 43.00 1.94
2708 2785 1.749983 GCTAGGGAGGTGTACGCTAGT 60.750 57.143 6.35 0.00 45.88 2.57
2789 2866 4.080243 CCTACTGACTACTGAGAGGAGGAA 60.080 50.000 0.00 0.00 0.00 3.36
2790 2867 4.390129 ACTGACTACTGAGAGGAGGAAA 57.610 45.455 0.00 0.00 0.00 3.13
2791 2868 4.340617 ACTGACTACTGAGAGGAGGAAAG 58.659 47.826 0.00 0.00 0.00 2.62
2792 2869 3.699038 CTGACTACTGAGAGGAGGAAAGG 59.301 52.174 0.00 0.00 0.00 3.11
2793 2870 3.333980 TGACTACTGAGAGGAGGAAAGGA 59.666 47.826 0.00 0.00 0.00 3.36
2810 2887 3.806949 AGGAAATGGGTCAAGCTTGTA 57.193 42.857 25.19 10.13 0.00 2.41
2847 2938 1.986413 CTACAGGTTGGCAGAGGCT 59.014 57.895 0.00 0.00 40.87 4.58
2938 3029 0.460284 CCCTTTCCTGACCGTGATCG 60.460 60.000 0.00 0.00 0.00 3.69
2977 3093 2.485814 CTCCCTTGCTGTAACTTTCTGC 59.514 50.000 0.00 0.00 0.00 4.26
2979 3095 2.485814 CCCTTGCTGTAACTTTCTGCTC 59.514 50.000 0.00 0.00 0.00 4.26
2989 3105 7.058023 TGTAACTTTCTGCTCTACCAGTAAA 57.942 36.000 0.00 0.00 34.47 2.01
2992 3151 9.649167 GTAACTTTCTGCTCTACCAGTAAATAA 57.351 33.333 0.00 0.00 34.47 1.40
3045 3204 5.296531 TCGTTCCAGGGTAACAAAAGTAAAC 59.703 40.000 0.00 0.00 39.74 2.01
3046 3205 5.066246 CGTTCCAGGGTAACAAAAGTAAACA 59.934 40.000 0.00 0.00 39.74 2.83
3051 3210 8.035984 TCCAGGGTAACAAAAGTAAACAAAAAG 58.964 33.333 0.00 0.00 39.74 2.27
3098 3262 2.128771 AACACACAAACAGTCTGGCT 57.871 45.000 4.53 0.00 0.00 4.75
3106 3270 2.664402 AACAGTCTGGCTGGTTCATT 57.336 45.000 14.56 0.00 43.98 2.57
3107 3271 2.508526 AACAGTCTGGCTGGTTCATTC 58.491 47.619 14.56 0.00 43.98 2.67
3109 3273 2.719739 CAGTCTGGCTGGTTCATTCAT 58.280 47.619 0.16 0.00 41.42 2.57
3110 3274 2.422479 CAGTCTGGCTGGTTCATTCATG 59.578 50.000 0.16 0.00 41.42 3.07
3111 3275 2.306805 AGTCTGGCTGGTTCATTCATGA 59.693 45.455 0.00 0.00 34.44 3.07
3112 3276 3.084039 GTCTGGCTGGTTCATTCATGAA 58.916 45.455 11.26 11.26 43.94 2.57
3146 3310 0.108329 ATTTGGGCGTACCGTCTGAG 60.108 55.000 0.00 0.00 44.64 3.35
3155 3319 2.541556 GTACCGTCTGAGGAGCATTTC 58.458 52.381 0.00 0.00 34.73 2.17
3211 3375 3.586100 GCATTATGATCCATGCATGCA 57.414 42.857 25.04 25.04 44.49 3.96
3212 3376 4.123497 GCATTATGATCCATGCATGCAT 57.877 40.909 27.46 27.46 44.49 3.96
3267 3431 3.619233 GTTGACAACAACGCAATAGGT 57.381 42.857 13.52 0.00 45.06 3.08
3268 3432 4.735662 GTTGACAACAACGCAATAGGTA 57.264 40.909 13.52 0.00 45.06 3.08
3269 3433 5.291293 GTTGACAACAACGCAATAGGTAT 57.709 39.130 13.52 0.00 45.06 2.73
3292 3456 3.049674 CATGACGCGCAGTTGGGT 61.050 61.111 5.73 0.00 37.78 4.51
3347 3512 0.394352 GTGGTAGGGGCAGGTCATTG 60.394 60.000 0.00 0.00 0.00 2.82
3348 3513 1.453928 GGTAGGGGCAGGTCATTGC 60.454 63.158 0.00 0.00 43.34 3.56
3349 3514 1.609783 GTAGGGGCAGGTCATTGCT 59.390 57.895 0.00 0.00 43.57 3.91
3350 3515 0.749454 GTAGGGGCAGGTCATTGCTG 60.749 60.000 0.00 0.00 43.57 4.41
3424 3598 3.890527 ACATGGCATGTTCTCTCCC 57.109 52.632 26.78 0.00 41.63 4.30
3425 3599 1.293062 ACATGGCATGTTCTCTCCCT 58.707 50.000 26.78 1.23 41.63 4.20
3474 3648 1.457009 CCTTCCCTCGGATCGACCTC 61.457 65.000 0.00 0.00 36.31 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.761689 AGCCCATGAACTATTGTAAATTTTGAT 58.238 29.630 0.00 0.00 0.00 2.57
21 22 8.133024 AGCCCATGAACTATTGTAAATTTTGA 57.867 30.769 0.00 0.00 0.00 2.69
22 23 9.301153 GTAGCCCATGAACTATTGTAAATTTTG 57.699 33.333 0.00 0.00 0.00 2.44
23 24 8.474831 GGTAGCCCATGAACTATTGTAAATTTT 58.525 33.333 0.00 0.00 0.00 1.82
24 25 7.839200 AGGTAGCCCATGAACTATTGTAAATTT 59.161 33.333 0.00 0.00 0.00 1.82
25 26 7.354312 AGGTAGCCCATGAACTATTGTAAATT 58.646 34.615 0.00 0.00 0.00 1.82
26 27 6.911308 AGGTAGCCCATGAACTATTGTAAAT 58.089 36.000 0.00 0.00 0.00 1.40
27 28 6.321821 AGGTAGCCCATGAACTATTGTAAA 57.678 37.500 0.00 0.00 0.00 2.01
28 29 5.968676 AGGTAGCCCATGAACTATTGTAA 57.031 39.130 0.00 0.00 0.00 2.41
29 30 5.011738 GCTAGGTAGCCCATGAACTATTGTA 59.988 44.000 0.00 0.00 43.39 2.41
30 31 4.202367 GCTAGGTAGCCCATGAACTATTGT 60.202 45.833 0.00 0.00 43.39 2.71
31 32 4.319177 GCTAGGTAGCCCATGAACTATTG 58.681 47.826 0.00 0.00 43.39 1.90
32 33 4.625607 GCTAGGTAGCCCATGAACTATT 57.374 45.455 0.00 0.00 43.39 1.73
45 46 5.010314 TCCAACCATATACGTTGCTAGGTAG 59.990 44.000 0.00 0.00 39.42 3.18
46 47 4.894705 TCCAACCATATACGTTGCTAGGTA 59.105 41.667 0.00 3.30 39.42 3.08
47 48 3.707611 TCCAACCATATACGTTGCTAGGT 59.292 43.478 0.00 0.00 39.42 3.08
48 49 4.056050 GTCCAACCATATACGTTGCTAGG 58.944 47.826 0.00 0.00 39.42 3.02
49 50 4.506654 GTGTCCAACCATATACGTTGCTAG 59.493 45.833 0.00 0.00 39.42 3.42
50 51 4.435425 GTGTCCAACCATATACGTTGCTA 58.565 43.478 0.00 0.00 39.42 3.49
51 52 3.267483 GTGTCCAACCATATACGTTGCT 58.733 45.455 0.00 0.00 39.42 3.91
52 53 3.668596 GTGTCCAACCATATACGTTGC 57.331 47.619 0.00 0.00 39.42 4.17
64 65 4.329462 TTTTTGCATTAGGGTGTCCAAC 57.671 40.909 0.00 0.00 34.83 3.77
98 99 6.611613 AGAAACTATGATTCTGACACCAGA 57.388 37.500 0.00 0.00 46.95 3.86
99 100 7.323420 TGTAGAAACTATGATTCTGACACCAG 58.677 38.462 0.00 0.00 37.67 4.00
100 101 7.239763 TGTAGAAACTATGATTCTGACACCA 57.760 36.000 0.00 0.00 37.67 4.17
101 102 7.254590 GCATGTAGAAACTATGATTCTGACACC 60.255 40.741 0.00 0.00 37.67 4.16
102 103 7.515841 CGCATGTAGAAACTATGATTCTGACAC 60.516 40.741 0.00 0.00 37.67 3.67
103 104 6.476706 CGCATGTAGAAACTATGATTCTGACA 59.523 38.462 0.00 1.59 37.67 3.58
104 105 6.697455 TCGCATGTAGAAACTATGATTCTGAC 59.303 38.462 0.00 0.00 37.67 3.51
105 106 6.805713 TCGCATGTAGAAACTATGATTCTGA 58.194 36.000 0.00 0.00 37.67 3.27
106 107 6.920210 TCTCGCATGTAGAAACTATGATTCTG 59.080 38.462 0.00 0.00 37.67 3.02
107 108 7.043961 TCTCGCATGTAGAAACTATGATTCT 57.956 36.000 0.00 0.00 40.18 2.40
108 109 6.128956 GCTCTCGCATGTAGAAACTATGATTC 60.129 42.308 0.00 0.00 35.78 2.52
109 110 5.694006 GCTCTCGCATGTAGAAACTATGATT 59.306 40.000 0.00 0.00 35.78 2.57
110 111 5.221322 TGCTCTCGCATGTAGAAACTATGAT 60.221 40.000 0.00 0.00 42.25 2.45
111 112 4.097892 TGCTCTCGCATGTAGAAACTATGA 59.902 41.667 0.00 0.00 42.25 2.15
112 113 4.363138 TGCTCTCGCATGTAGAAACTATG 58.637 43.478 0.00 0.00 42.25 2.23
113 114 4.655762 TGCTCTCGCATGTAGAAACTAT 57.344 40.909 0.00 0.00 42.25 2.12
125 126 2.094597 CCATTGGAAAATTGCTCTCGCA 60.095 45.455 0.00 0.00 46.24 5.10
126 127 2.094545 ACCATTGGAAAATTGCTCTCGC 60.095 45.455 10.37 0.00 0.00 5.03
127 128 3.855689 ACCATTGGAAAATTGCTCTCG 57.144 42.857 10.37 0.00 0.00 4.04
128 129 7.278646 GGAATTAACCATTGGAAAATTGCTCTC 59.721 37.037 20.63 10.52 31.79 3.20
129 130 7.105588 GGAATTAACCATTGGAAAATTGCTCT 58.894 34.615 20.63 4.72 31.79 4.09
130 131 6.878389 TGGAATTAACCATTGGAAAATTGCTC 59.122 34.615 24.38 13.33 33.68 4.26
131 132 6.654582 GTGGAATTAACCATTGGAAAATTGCT 59.345 34.615 24.38 8.01 42.17 3.91
132 133 6.429385 TGTGGAATTAACCATTGGAAAATTGC 59.571 34.615 20.88 20.88 42.17 3.56
133 134 7.976135 TGTGGAATTAACCATTGGAAAATTG 57.024 32.000 18.36 0.00 42.17 2.32
134 135 8.986929 TTTGTGGAATTAACCATTGGAAAATT 57.013 26.923 10.37 13.55 42.17 1.82
135 136 8.986929 TTTTGTGGAATTAACCATTGGAAAAT 57.013 26.923 10.37 5.64 42.17 1.82
136 137 8.678199 GTTTTTGTGGAATTAACCATTGGAAAA 58.322 29.630 10.37 3.34 42.17 2.29
137 138 7.829211 TGTTTTTGTGGAATTAACCATTGGAAA 59.171 29.630 10.37 3.72 42.17 3.13
138 139 7.338710 TGTTTTTGTGGAATTAACCATTGGAA 58.661 30.769 10.37 0.00 42.17 3.53
139 140 6.889198 TGTTTTTGTGGAATTAACCATTGGA 58.111 32.000 10.37 0.00 42.17 3.53
140 141 7.559590 TTGTTTTTGTGGAATTAACCATTGG 57.440 32.000 0.00 0.00 42.17 3.16
141 142 8.834465 TGATTGTTTTTGTGGAATTAACCATTG 58.166 29.630 0.00 0.00 42.17 2.82
142 143 8.835439 GTGATTGTTTTTGTGGAATTAACCATT 58.165 29.630 0.00 0.00 42.17 3.16
143 144 7.443879 GGTGATTGTTTTTGTGGAATTAACCAT 59.556 33.333 0.00 0.00 42.17 3.55
144 145 6.763610 GGTGATTGTTTTTGTGGAATTAACCA 59.236 34.615 0.00 0.00 37.63 3.67
145 146 6.989759 AGGTGATTGTTTTTGTGGAATTAACC 59.010 34.615 0.00 0.00 0.00 2.85
146 147 7.708752 TCAGGTGATTGTTTTTGTGGAATTAAC 59.291 33.333 0.00 0.00 0.00 2.01
147 148 7.708752 GTCAGGTGATTGTTTTTGTGGAATTAA 59.291 33.333 0.00 0.00 0.00 1.40
148 149 7.206687 GTCAGGTGATTGTTTTTGTGGAATTA 58.793 34.615 0.00 0.00 0.00 1.40
149 150 6.048509 GTCAGGTGATTGTTTTTGTGGAATT 58.951 36.000 0.00 0.00 0.00 2.17
150 151 5.453198 GGTCAGGTGATTGTTTTTGTGGAAT 60.453 40.000 0.00 0.00 0.00 3.01
151 152 4.142049 GGTCAGGTGATTGTTTTTGTGGAA 60.142 41.667 0.00 0.00 0.00 3.53
152 153 3.383185 GGTCAGGTGATTGTTTTTGTGGA 59.617 43.478 0.00 0.00 0.00 4.02
153 154 3.716601 GGTCAGGTGATTGTTTTTGTGG 58.283 45.455 0.00 0.00 0.00 4.17
154 155 3.181491 ACGGTCAGGTGATTGTTTTTGTG 60.181 43.478 0.00 0.00 0.00 3.33
155 156 3.020984 ACGGTCAGGTGATTGTTTTTGT 58.979 40.909 0.00 0.00 0.00 2.83
156 157 3.066064 TCACGGTCAGGTGATTGTTTTTG 59.934 43.478 0.00 0.00 41.76 2.44
157 158 3.283751 TCACGGTCAGGTGATTGTTTTT 58.716 40.909 0.00 0.00 41.76 1.94
158 159 2.878406 CTCACGGTCAGGTGATTGTTTT 59.122 45.455 0.00 0.00 45.23 2.43
159 160 2.158813 ACTCACGGTCAGGTGATTGTTT 60.159 45.455 0.00 0.00 45.23 2.83
160 161 1.416401 ACTCACGGTCAGGTGATTGTT 59.584 47.619 0.00 0.00 45.23 2.83
161 162 1.048601 ACTCACGGTCAGGTGATTGT 58.951 50.000 0.00 0.00 45.23 2.71
162 163 3.526931 ATACTCACGGTCAGGTGATTG 57.473 47.619 0.00 0.00 45.23 2.67
163 164 5.670792 TTAATACTCACGGTCAGGTGATT 57.329 39.130 0.00 0.00 45.23 2.57
164 165 5.670792 TTTAATACTCACGGTCAGGTGAT 57.329 39.130 0.00 0.00 45.23 3.06
165 166 5.471556 TTTTAATACTCACGGTCAGGTGA 57.528 39.130 0.00 0.00 44.25 4.02
191 192 1.261619 GCATATGGTAGTTGCAGTCGC 59.738 52.381 4.56 0.00 36.40 5.19
192 193 2.549926 TGCATATGGTAGTTGCAGTCG 58.450 47.619 4.56 0.00 41.18 4.18
197 198 5.059161 TCTTGAGATGCATATGGTAGTTGC 58.941 41.667 0.00 0.00 36.91 4.17
198 199 5.699915 CCTCTTGAGATGCATATGGTAGTTG 59.300 44.000 0.00 0.00 0.00 3.16
199 200 5.744300 GCCTCTTGAGATGCATATGGTAGTT 60.744 44.000 0.00 0.00 36.03 2.24
200 201 4.262808 GCCTCTTGAGATGCATATGGTAGT 60.263 45.833 0.00 0.00 36.03 2.73
201 202 4.252073 GCCTCTTGAGATGCATATGGTAG 58.748 47.826 0.00 0.00 36.03 3.18
202 203 3.647590 TGCCTCTTGAGATGCATATGGTA 59.352 43.478 0.00 0.00 40.01 3.25
203 204 2.440627 TGCCTCTTGAGATGCATATGGT 59.559 45.455 0.00 0.00 40.01 3.55
204 205 3.136009 TGCCTCTTGAGATGCATATGG 57.864 47.619 0.00 0.00 40.01 2.74
205 206 5.461526 CAATTGCCTCTTGAGATGCATATG 58.538 41.667 10.96 0.00 43.33 1.78
206 207 4.022242 GCAATTGCCTCTTGAGATGCATAT 60.022 41.667 20.06 0.00 43.33 1.78
207 208 3.317149 GCAATTGCCTCTTGAGATGCATA 59.683 43.478 20.06 4.45 43.33 3.14
208 209 2.100916 GCAATTGCCTCTTGAGATGCAT 59.899 45.455 20.06 0.00 43.33 3.96
209 210 1.475280 GCAATTGCCTCTTGAGATGCA 59.525 47.619 20.06 6.84 42.45 3.96
210 211 1.475280 TGCAATTGCCTCTTGAGATGC 59.525 47.619 26.94 0.00 41.18 3.91
211 212 2.159282 GGTGCAATTGCCTCTTGAGATG 60.159 50.000 26.94 0.00 41.18 2.90
212 213 2.097825 GGTGCAATTGCCTCTTGAGAT 58.902 47.619 26.94 0.00 41.18 2.75
213 214 1.538047 GGTGCAATTGCCTCTTGAGA 58.462 50.000 26.94 3.21 41.18 3.27
214 215 0.169672 CGGTGCAATTGCCTCTTGAG 59.830 55.000 26.94 8.13 41.18 3.02
215 216 1.243342 CCGGTGCAATTGCCTCTTGA 61.243 55.000 26.94 4.79 41.18 3.02
216 217 1.213537 CCGGTGCAATTGCCTCTTG 59.786 57.895 26.94 15.19 41.18 3.02
217 218 0.962356 CTCCGGTGCAATTGCCTCTT 60.962 55.000 26.94 0.00 41.18 2.85
218 219 1.377725 CTCCGGTGCAATTGCCTCT 60.378 57.895 26.94 0.00 41.18 3.69
219 220 2.409870 CCTCCGGTGCAATTGCCTC 61.410 63.158 26.94 18.85 41.18 4.70
220 221 2.361610 CCTCCGGTGCAATTGCCT 60.362 61.111 26.94 0.00 41.18 4.75
221 222 2.676471 ACCTCCGGTGCAATTGCC 60.676 61.111 26.94 17.54 41.18 4.52
222 223 2.700773 GGACCTCCGGTGCAATTGC 61.701 63.158 23.69 23.69 43.66 3.56
223 224 3.590824 GGACCTCCGGTGCAATTG 58.409 61.111 0.00 0.00 43.66 2.32
228 229 1.745489 GTTCATGGACCTCCGGTGC 60.745 63.158 0.00 0.00 44.48 5.01
229 230 0.324943 AAGTTCATGGACCTCCGGTG 59.675 55.000 0.00 0.00 35.25 4.94
230 231 0.324943 CAAGTTCATGGACCTCCGGT 59.675 55.000 0.00 0.00 39.44 5.28
231 232 0.324943 ACAAGTTCATGGACCTCCGG 59.675 55.000 0.00 0.00 39.43 5.14
232 233 2.185004 AACAAGTTCATGGACCTCCG 57.815 50.000 0.00 0.00 39.43 4.63
233 234 2.558359 CCAAACAAGTTCATGGACCTCC 59.442 50.000 0.00 0.00 34.82 4.30
234 235 2.029918 GCCAAACAAGTTCATGGACCTC 60.030 50.000 0.00 0.00 34.82 3.85
235 236 1.963515 GCCAAACAAGTTCATGGACCT 59.036 47.619 0.00 0.00 34.82 3.85
236 237 1.335872 CGCCAAACAAGTTCATGGACC 60.336 52.381 0.00 0.00 34.82 4.46
237 238 1.335872 CCGCCAAACAAGTTCATGGAC 60.336 52.381 7.64 0.00 34.82 4.02
238 239 0.958091 CCGCCAAACAAGTTCATGGA 59.042 50.000 7.64 0.00 34.82 3.41
239 240 0.038343 CCCGCCAAACAAGTTCATGG 60.038 55.000 0.00 0.35 36.00 3.66
240 241 0.958091 TCCCGCCAAACAAGTTCATG 59.042 50.000 0.00 0.00 0.00 3.07
241 242 1.339929 GTTCCCGCCAAACAAGTTCAT 59.660 47.619 0.00 0.00 0.00 2.57
242 243 0.741915 GTTCCCGCCAAACAAGTTCA 59.258 50.000 0.00 0.00 0.00 3.18
243 244 0.741915 TGTTCCCGCCAAACAAGTTC 59.258 50.000 0.00 0.00 33.86 3.01
244 245 1.408969 ATGTTCCCGCCAAACAAGTT 58.591 45.000 0.00 0.00 39.84 2.66
245 246 1.408969 AATGTTCCCGCCAAACAAGT 58.591 45.000 0.00 0.00 39.84 3.16
246 247 2.524569 AAATGTTCCCGCCAAACAAG 57.475 45.000 0.00 0.00 39.84 3.16
247 248 2.990066 AAAATGTTCCCGCCAAACAA 57.010 40.000 0.00 0.00 39.84 2.83
248 249 2.990066 AAAAATGTTCCCGCCAAACA 57.010 40.000 0.00 0.00 40.63 2.83
249 250 3.985008 ACTAAAAATGTTCCCGCCAAAC 58.015 40.909 0.00 0.00 0.00 2.93
250 251 4.623002 GAACTAAAAATGTTCCCGCCAAA 58.377 39.130 0.00 0.00 38.19 3.28
251 252 3.304794 CGAACTAAAAATGTTCCCGCCAA 60.305 43.478 0.00 0.00 40.26 4.52
252 253 2.226912 CGAACTAAAAATGTTCCCGCCA 59.773 45.455 0.00 0.00 40.26 5.69
253 254 2.227149 ACGAACTAAAAATGTTCCCGCC 59.773 45.455 0.00 0.00 40.26 6.13
254 255 3.058777 TCACGAACTAAAAATGTTCCCGC 60.059 43.478 0.00 0.00 40.26 6.13
255 256 4.708601 CTCACGAACTAAAAATGTTCCCG 58.291 43.478 0.00 0.00 40.26 5.14
256 257 4.215613 AGCTCACGAACTAAAAATGTTCCC 59.784 41.667 0.00 0.00 40.26 3.97
257 258 5.358298 AGCTCACGAACTAAAAATGTTCC 57.642 39.130 0.00 0.00 40.26 3.62
258 259 6.140737 CACAAGCTCACGAACTAAAAATGTTC 59.859 38.462 0.00 0.00 40.05 3.18
259 260 5.971202 CACAAGCTCACGAACTAAAAATGTT 59.029 36.000 0.00 0.00 0.00 2.71
260 261 5.295787 TCACAAGCTCACGAACTAAAAATGT 59.704 36.000 0.00 0.00 0.00 2.71
261 262 5.747565 TCACAAGCTCACGAACTAAAAATG 58.252 37.500 0.00 0.00 0.00 2.32
262 263 6.371809 TTCACAAGCTCACGAACTAAAAAT 57.628 33.333 0.00 0.00 0.00 1.82
263 264 5.804692 TTCACAAGCTCACGAACTAAAAA 57.195 34.783 0.00 0.00 0.00 1.94
264 265 6.037720 TGAATTCACAAGCTCACGAACTAAAA 59.962 34.615 3.38 0.00 0.00 1.52
265 266 5.525745 TGAATTCACAAGCTCACGAACTAAA 59.474 36.000 3.38 0.00 0.00 1.85
266 267 5.053811 TGAATTCACAAGCTCACGAACTAA 58.946 37.500 3.38 0.00 0.00 2.24
267 268 4.627058 TGAATTCACAAGCTCACGAACTA 58.373 39.130 3.38 0.00 0.00 2.24
268 269 3.466836 TGAATTCACAAGCTCACGAACT 58.533 40.909 3.38 0.00 0.00 3.01
269 270 3.878086 TGAATTCACAAGCTCACGAAC 57.122 42.857 3.38 0.00 0.00 3.95
270 271 4.335315 ACTTTGAATTCACAAGCTCACGAA 59.665 37.500 20.72 6.17 0.00 3.85
271 272 3.876914 ACTTTGAATTCACAAGCTCACGA 59.123 39.130 20.72 0.00 0.00 4.35
272 273 4.214437 GACTTTGAATTCACAAGCTCACG 58.786 43.478 20.72 4.06 0.00 4.35
273 274 5.173774 TGACTTTGAATTCACAAGCTCAC 57.826 39.130 20.72 14.03 0.00 3.51
274 275 5.532032 TGATGACTTTGAATTCACAAGCTCA 59.468 36.000 20.72 20.71 0.00 4.26
275 276 6.005583 TGATGACTTTGAATTCACAAGCTC 57.994 37.500 20.72 17.87 0.00 4.09
276 277 6.208007 TGATGATGACTTTGAATTCACAAGCT 59.792 34.615 20.72 13.02 0.00 3.74
277 278 6.384224 TGATGATGACTTTGAATTCACAAGC 58.616 36.000 20.72 16.18 0.00 4.01
278 279 8.697067 GTTTGATGATGACTTTGAATTCACAAG 58.303 33.333 19.86 19.86 0.00 3.16
279 280 8.415553 AGTTTGATGATGACTTTGAATTCACAA 58.584 29.630 7.89 2.30 0.00 3.33
280 281 7.944061 AGTTTGATGATGACTTTGAATTCACA 58.056 30.769 7.89 3.11 0.00 3.58
281 282 8.697067 CAAGTTTGATGATGACTTTGAATTCAC 58.303 33.333 7.89 0.00 31.63 3.18
282 283 7.383029 GCAAGTTTGATGATGACTTTGAATTCA 59.617 33.333 3.38 3.38 31.63 2.57
283 284 7.383029 TGCAAGTTTGATGATGACTTTGAATTC 59.617 33.333 0.00 0.00 31.63 2.17
284 285 7.211573 TGCAAGTTTGATGATGACTTTGAATT 58.788 30.769 0.00 0.00 31.63 2.17
285 286 6.751157 TGCAAGTTTGATGATGACTTTGAAT 58.249 32.000 0.00 0.00 31.63 2.57
286 287 6.146601 TGCAAGTTTGATGATGACTTTGAA 57.853 33.333 0.00 0.00 31.63 2.69
287 288 5.771153 TGCAAGTTTGATGATGACTTTGA 57.229 34.783 0.00 0.00 31.63 2.69
288 289 6.831727 TTTGCAAGTTTGATGATGACTTTG 57.168 33.333 0.00 0.00 31.63 2.77
289 290 7.846644 TTTTTGCAAGTTTGATGATGACTTT 57.153 28.000 0.00 0.00 31.63 2.66
329 330 9.729281 TCCTAACCGAATTATGTAAACTCTTTT 57.271 29.630 0.00 0.00 0.00 2.27
330 331 9.159364 GTCCTAACCGAATTATGTAAACTCTTT 57.841 33.333 0.00 0.00 0.00 2.52
331 332 7.767659 GGTCCTAACCGAATTATGTAAACTCTT 59.232 37.037 0.00 0.00 35.36 2.85
332 333 7.270779 GGTCCTAACCGAATTATGTAAACTCT 58.729 38.462 0.00 0.00 35.36 3.24
333 334 7.474398 GGTCCTAACCGAATTATGTAAACTC 57.526 40.000 0.00 0.00 35.36 3.01
348 349 1.203287 GTCAGTACGTGGGTCCTAACC 59.797 57.143 0.00 0.00 45.65 2.85
349 350 1.888512 TGTCAGTACGTGGGTCCTAAC 59.111 52.381 0.00 0.00 0.00 2.34
400 401 4.512484 TCGTCCAATATTGCATTCAGACA 58.488 39.130 10.11 0.69 0.00 3.41
428 429 1.835494 AGAAGCCTACACGACTGCTA 58.165 50.000 0.00 0.00 32.82 3.49
456 468 5.773680 GGAGCCAACCACTCTATACTGTATA 59.226 44.000 7.28 7.28 34.46 1.47
457 469 4.589374 GGAGCCAACCACTCTATACTGTAT 59.411 45.833 5.53 5.53 34.46 2.29
460 472 2.223829 CGGAGCCAACCACTCTATACTG 60.224 54.545 0.00 0.00 34.46 2.74
461 473 2.032620 CGGAGCCAACCACTCTATACT 58.967 52.381 0.00 0.00 34.46 2.12
462 474 2.510768 CGGAGCCAACCACTCTATAC 57.489 55.000 0.00 0.00 34.46 1.47
1787 1809 1.373999 GCTCACGCTGCAGAGTTCT 60.374 57.895 21.27 0.00 34.39 3.01
2224 2247 1.587547 GCATAGGTACAAGGCTCAGC 58.412 55.000 0.00 0.00 0.00 4.26
2238 2261 1.705337 CCGTGGGTTGAAGCGCATAG 61.705 60.000 11.47 0.00 33.93 2.23
2337 2395 2.224305 ACCACACTCACTAAAGCACTCC 60.224 50.000 0.00 0.00 0.00 3.85
2448 2513 3.374058 AGAGGTGTTTTGTTCGTCAGTTG 59.626 43.478 0.00 0.00 0.00 3.16
2533 2609 4.704833 ATGTCGCAGTTGCCGGCT 62.705 61.111 29.70 3.84 37.91 5.52
2630 2707 0.318441 GTACTGCTGACTGCTGACCA 59.682 55.000 16.27 0.00 42.27 4.02
2648 2725 1.679153 CCAAAAACAACCTACTGCGGT 59.321 47.619 2.42 2.42 39.48 5.68
2650 2727 2.542824 CCACCAAAAACAACCTACTGCG 60.543 50.000 0.00 0.00 0.00 5.18
2666 2743 4.188462 CAATCAGCTCGTAATAACCACCA 58.812 43.478 0.00 0.00 0.00 4.17
2708 2785 1.576577 ATCAGTGATGAGCCTGTCCA 58.423 50.000 4.39 0.00 0.00 4.02
2789 2866 2.962859 ACAAGCTTGACCCATTTCCTT 58.037 42.857 32.50 2.52 0.00 3.36
2790 2867 2.683211 ACAAGCTTGACCCATTTCCT 57.317 45.000 32.50 3.08 0.00 3.36
2791 2868 3.421844 ACTACAAGCTTGACCCATTTCC 58.578 45.455 32.50 0.00 0.00 3.13
2792 2869 4.278419 ACAACTACAAGCTTGACCCATTTC 59.722 41.667 32.50 0.00 0.00 2.17
2793 2870 4.037923 CACAACTACAAGCTTGACCCATTT 59.962 41.667 32.50 10.97 0.00 2.32
2826 2905 1.195115 CCTCTGCCAACCTGTAGCTA 58.805 55.000 0.00 0.00 0.00 3.32
2827 2906 1.986413 CCTCTGCCAACCTGTAGCT 59.014 57.895 0.00 0.00 0.00 3.32
2847 2938 6.245408 ACTCCCATCTTTACAAGTTATTGCA 58.755 36.000 0.00 0.00 40.27 4.08
2938 3029 0.250166 AGAACAGTTGTGGTACCGGC 60.250 55.000 7.57 3.24 0.00 6.13
2977 3093 7.923414 AAGGCTTGTTTATTTACTGGTAGAG 57.077 36.000 0.00 0.00 0.00 2.43
2979 3095 9.836076 GTTAAAGGCTTGTTTATTTACTGGTAG 57.164 33.333 0.00 0.00 0.00 3.18
2989 3105 4.530161 TGGCATGGTTAAAGGCTTGTTTAT 59.470 37.500 0.00 0.00 0.00 1.40
2992 3151 2.299867 CTGGCATGGTTAAAGGCTTGTT 59.700 45.455 0.00 0.00 0.00 2.83
3045 3204 3.194329 GCCCCATCTTTCCTCTCTTTTTG 59.806 47.826 0.00 0.00 0.00 2.44
3046 3205 3.435275 GCCCCATCTTTCCTCTCTTTTT 58.565 45.455 0.00 0.00 0.00 1.94
3051 3210 0.182299 CAGGCCCCATCTTTCCTCTC 59.818 60.000 0.00 0.00 0.00 3.20
3106 3270 7.148137 CCAAATCTGAATCTGACATGTTCATGA 60.148 37.037 17.96 0.00 32.17 3.07
3107 3271 6.972901 CCAAATCTGAATCTGACATGTTCATG 59.027 38.462 0.00 10.72 32.17 3.07
3109 3273 5.416639 CCCAAATCTGAATCTGACATGTTCA 59.583 40.000 0.00 0.00 0.00 3.18
3110 3274 5.678107 GCCCAAATCTGAATCTGACATGTTC 60.678 44.000 0.00 0.00 0.00 3.18
3111 3275 4.159135 GCCCAAATCTGAATCTGACATGTT 59.841 41.667 0.00 0.00 0.00 2.71
3112 3276 3.698040 GCCCAAATCTGAATCTGACATGT 59.302 43.478 0.00 0.00 0.00 3.21
3113 3277 3.242969 CGCCCAAATCTGAATCTGACATG 60.243 47.826 0.00 0.00 0.00 3.21
3114 3278 2.947652 CGCCCAAATCTGAATCTGACAT 59.052 45.455 0.00 0.00 0.00 3.06
3115 3279 2.290260 ACGCCCAAATCTGAATCTGACA 60.290 45.455 0.00 0.00 0.00 3.58
3211 3375 3.418995 GAGACCAGGATTATGCATGCAT 58.581 45.455 33.92 33.92 40.19 3.96
3212 3376 2.487805 GGAGACCAGGATTATGCATGCA 60.488 50.000 25.04 25.04 0.00 3.96
3213 3377 2.157738 GGAGACCAGGATTATGCATGC 58.842 52.381 11.82 11.82 0.00 4.06
3214 3378 3.497103 TGGAGACCAGGATTATGCATG 57.503 47.619 10.16 0.00 0.00 4.06
3263 3427 1.581934 GCGTCATGCAGCAATACCTA 58.418 50.000 0.00 0.00 45.45 3.08
3264 3428 1.431488 CGCGTCATGCAGCAATACCT 61.431 55.000 0.00 0.00 46.97 3.08
3265 3429 1.010797 CGCGTCATGCAGCAATACC 60.011 57.895 0.00 0.00 46.97 2.73
3266 3430 1.652329 GCGCGTCATGCAGCAATAC 60.652 57.895 8.43 0.00 46.97 1.89
3267 3431 2.105466 TGCGCGTCATGCAGCAATA 61.105 52.632 8.43 0.00 45.37 1.90
3268 3432 3.433453 TGCGCGTCATGCAGCAAT 61.433 55.556 8.43 0.00 45.37 3.56
3274 3438 4.465512 CCCAACTGCGCGTCATGC 62.466 66.667 8.43 0.00 41.47 4.06
3275 3439 3.049674 ACCCAACTGCGCGTCATG 61.050 61.111 8.43 1.96 0.00 3.07
3276 3440 3.049674 CACCCAACTGCGCGTCAT 61.050 61.111 8.43 0.00 0.00 3.06
3292 3456 0.620030 CAGGTCCATCCATGTGACCA 59.380 55.000 20.45 0.00 44.03 4.02
3347 3512 4.496336 ATTCCCCTCGCAGCCAGC 62.496 66.667 0.00 0.00 40.87 4.85
3348 3513 2.335092 ATCATTCCCCTCGCAGCCAG 62.335 60.000 0.00 0.00 0.00 4.85
3349 3514 2.329539 GATCATTCCCCTCGCAGCCA 62.330 60.000 0.00 0.00 0.00 4.75
3350 3515 1.599240 GATCATTCCCCTCGCAGCC 60.599 63.158 0.00 0.00 0.00 4.85
3392 3558 1.690219 CCATGTTCTCCTCTCCCCGG 61.690 65.000 0.00 0.00 0.00 5.73
3393 3559 1.826024 CCATGTTCTCCTCTCCCCG 59.174 63.158 0.00 0.00 0.00 5.73
3421 3595 6.281190 TCATTCTCTAATCTACAGGAGGGA 57.719 41.667 0.00 0.00 0.00 4.20
3422 3596 6.574073 GCATCATTCTCTAATCTACAGGAGGG 60.574 46.154 0.00 0.00 0.00 4.30
3423 3597 6.397272 GCATCATTCTCTAATCTACAGGAGG 58.603 44.000 0.00 0.00 0.00 4.30
3424 3598 6.014755 TGGCATCATTCTCTAATCTACAGGAG 60.015 42.308 0.00 0.00 0.00 3.69
3425 3599 5.840693 TGGCATCATTCTCTAATCTACAGGA 59.159 40.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.