Multiple sequence alignment - TraesCS2B01G089400

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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 TraesCS2B01G089400 chr2B 100.000 3549 0 0 1 3549 50410203 50413751 0.000000e+00 6554.0
1 TraesCS2B01G089400 chr2B 80.682 704 121 11 1851 2551 50524181 50523490 1.880000e-147 532.0
2 TraesCS2B01G089400 chr2B 76.147 545 114 13 2019 2551 43798150 43798690 4.510000e-69 272.0
3 TraesCS2B01G089400 chr2B 96.923 130 4 0 1 130 672040567 672040696 5.970000e-53 219.0
4 TraesCS2B01G089400 chr2B 95.489 133 5 1 1 132 800377441 800377573 9.980000e-51 211.0
5 TraesCS2B01G089400 chr2B 78.632 117 19 5 1046 1159 10078181 10078068 4.910000e-09 73.1
6 TraesCS2B01G089400 chr2A 92.036 2323 97 32 700 3019 32863294 32865531 0.000000e+00 3184.0
7 TraesCS2B01G089400 chr2A 89.208 1288 123 8 1568 2851 32875893 32877168 0.000000e+00 1594.0
8 TraesCS2B01G089400 chr2A 78.716 1527 247 51 967 2452 32772982 32774471 0.000000e+00 948.0
9 TraesCS2B01G089400 chr2A 88.285 717 72 7 133 846 32816985 32817692 0.000000e+00 848.0
10 TraesCS2B01G089400 chr2A 95.356 323 13 2 928 1250 32817723 32818043 2.440000e-141 512.0
11 TraesCS2B01G089400 chr2A 86.395 441 44 6 303 741 32862840 32863266 5.360000e-128 468.0
12 TraesCS2B01G089400 chr2A 83.709 399 40 15 3098 3488 32865564 32865945 1.570000e-93 353.0
13 TraesCS2B01G089400 chr2A 73.483 1022 205 44 1012 1988 32886575 32887575 3.420000e-85 326.0
14 TraesCS2B01G089400 chr2A 75.244 614 109 27 2009 2595 32887879 32888476 5.880000e-63 252.0
15 TraesCS2B01G089400 chr2A 75.122 615 108 28 2009 2595 32928976 32929573 2.740000e-61 246.0
16 TraesCS2B01G089400 chr2A 93.662 142 7 2 1 142 565595367 565595228 9.980000e-51 211.0
17 TraesCS2B01G089400 chr2A 76.425 386 60 19 1559 1939 32821189 32821548 2.810000e-41 180.0
18 TraesCS2B01G089400 chr2A 84.795 171 21 5 2828 2997 32860753 32860919 2.190000e-37 167.0
19 TraesCS2B01G089400 chr2A 86.047 86 12 0 1903 1988 32928587 32928672 3.770000e-15 93.5
20 TraesCS2B01G089400 chr2A 77.778 99 22 0 1061 1159 1165163 1165065 1.060000e-05 62.1
21 TraesCS2B01G089400 chr2D 89.922 1419 113 14 1522 2934 30619219 30620613 0.000000e+00 1801.0
22 TraesCS2B01G089400 chr2D 93.817 372 14 4 3098 3466 30620887 30621252 5.180000e-153 551.0
23 TraesCS2B01G089400 chr2D 86.626 486 62 3 133 616 30618131 30618615 5.210000e-148 534.0
24 TraesCS2B01G089400 chr2D 86.567 335 39 3 1226 1554 30618741 30619075 7.240000e-97 364.0
25 TraesCS2B01G089400 chr2D 73.850 1109 195 60 1556 2595 30653723 30654805 1.570000e-93 353.0
26 TraesCS2B01G089400 chr2D 95.706 163 7 0 2917 3079 30620737 30620899 2.720000e-66 263.0
27 TraesCS2B01G089400 chr2D 92.920 113 8 0 950 1062 30618630 30618742 7.880000e-37 165.0
28 TraesCS2B01G089400 chr2D 96.875 32 1 0 1128 1159 1703304 1703273 2.000000e-03 54.7
29 TraesCS2B01G089400 chr6B 96.923 130 4 0 1 130 62761729 62761858 5.970000e-53 219.0
30 TraesCS2B01G089400 chr1D 96.923 130 4 0 1 130 378803721 378803592 5.970000e-53 219.0
31 TraesCS2B01G089400 chr1D 96.124 129 5 0 1 129 272313697 272313825 9.980000e-51 211.0
32 TraesCS2B01G089400 chr4B 95.489 133 5 1 1 132 328927850 328927718 9.980000e-51 211.0
33 TraesCS2B01G089400 chr4A 95.489 133 4 2 1 132 621294910 621294779 9.980000e-51 211.0
34 TraesCS2B01G089400 chr6A 94.161 137 7 1 1 136 271798009 271798145 1.290000e-49 207.0


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 TraesCS2B01G089400 chr2B 50410203 50413751 3548 False 6554.000000 6554 100.000000 1 3549 1 chr2B.!!$F2 3548
1 TraesCS2B01G089400 chr2B 50523490 50524181 691 True 532.000000 532 80.682000 1851 2551 1 chr2B.!!$R2 700
2 TraesCS2B01G089400 chr2B 43798150 43798690 540 False 272.000000 272 76.147000 2019 2551 1 chr2B.!!$F1 532
3 TraesCS2B01G089400 chr2A 32875893 32877168 1275 False 1594.000000 1594 89.208000 1568 2851 1 chr2A.!!$F2 1283
4 TraesCS2B01G089400 chr2A 32860753 32865945 5192 False 1043.000000 3184 86.733750 303 3488 4 chr2A.!!$F4 3185
5 TraesCS2B01G089400 chr2A 32772982 32774471 1489 False 948.000000 948 78.716000 967 2452 1 chr2A.!!$F1 1485
6 TraesCS2B01G089400 chr2A 32816985 32821548 4563 False 513.333333 848 86.688667 133 1939 3 chr2A.!!$F3 1806
7 TraesCS2B01G089400 chr2A 32886575 32888476 1901 False 289.000000 326 74.363500 1012 2595 2 chr2A.!!$F5 1583
8 TraesCS2B01G089400 chr2D 30618131 30621252 3121 False 613.000000 1801 90.926333 133 3466 6 chr2D.!!$F2 3333
9 TraesCS2B01G089400 chr2D 30653723 30654805 1082 False 353.000000 353 73.850000 1556 2595 1 chr2D.!!$F1 1039

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
481 2325 0.035630 GGTGGCAAGAGAGAGCACAT 60.036 55.0 0.00 0.0 0.00 3.21 F
573 2418 0.115745 AGAGGACCGGGTTCTTGGTA 59.884 55.0 9.93 0.0 38.99 3.25 F
930 2847 0.182775 ACAGTTGACAGTTCCCACCC 59.817 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 3301 1.486726 GGTGGTAGAGAATCCCACTGG 59.513 57.143 7.86 0.0 44.03 4.00 R
1440 3379 1.628340 ACCATGGGATCAAACACGAGA 59.372 47.619 18.09 0.0 0.00 4.04 R
2879 5376 1.868713 TATGTAACCAAGAGGGCGGA 58.131 50.000 0.00 0.0 42.05 5.54 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
53 54 5.806654 AGGATTGTAAAACAAATGTGGCT 57.193 34.783 0.00 0.00 41.96 4.75
55 56 5.304101 AGGATTGTAAAACAAATGTGGCTCA 59.696 36.000 0.00 0.00 41.96 4.26
56 57 5.988561 GGATTGTAAAACAAATGTGGCTCAA 59.011 36.000 0.00 0.00 41.96 3.02
57 58 6.481644 GGATTGTAAAACAAATGTGGCTCAAA 59.518 34.615 0.00 0.00 41.96 2.69
58 59 6.900568 TTGTAAAACAAATGTGGCTCAAAG 57.099 33.333 0.00 0.00 34.76 2.77
59 60 5.971763 TGTAAAACAAATGTGGCTCAAAGT 58.028 33.333 0.00 0.00 0.00 2.66
62 63 6.421377 AAAACAAATGTGGCTCAAAGTTTC 57.579 33.333 13.69 0.00 31.94 2.78
63 64 5.343307 AACAAATGTGGCTCAAAGTTTCT 57.657 34.783 0.00 0.00 0.00 2.52
64 65 4.685924 ACAAATGTGGCTCAAAGTTTCTG 58.314 39.130 0.00 0.00 0.00 3.02
65 66 4.053295 CAAATGTGGCTCAAAGTTTCTGG 58.947 43.478 0.00 0.00 0.00 3.86
66 67 1.691196 TGTGGCTCAAAGTTTCTGGG 58.309 50.000 0.00 0.00 0.00 4.45
67 68 1.214175 TGTGGCTCAAAGTTTCTGGGA 59.786 47.619 0.00 0.00 0.00 4.37
68 69 1.882623 GTGGCTCAAAGTTTCTGGGAG 59.117 52.381 0.00 0.00 0.00 4.30
69 70 1.774254 TGGCTCAAAGTTTCTGGGAGA 59.226 47.619 5.17 0.00 0.00 3.71
70 71 2.174639 TGGCTCAAAGTTTCTGGGAGAA 59.825 45.455 5.17 0.00 31.28 2.87
71 72 2.816672 GGCTCAAAGTTTCTGGGAGAAG 59.183 50.000 5.17 0.00 35.37 2.85
72 73 2.227626 GCTCAAAGTTTCTGGGAGAAGC 59.772 50.000 5.17 0.00 35.37 3.86
75 76 2.555757 CAAAGTTTCTGGGAGAAGCTGG 59.444 50.000 3.78 0.00 43.54 4.85
76 77 0.695347 AGTTTCTGGGAGAAGCTGGG 59.305 55.000 2.30 0.00 42.87 4.45
78 79 1.628846 GTTTCTGGGAGAAGCTGGGTA 59.371 52.381 0.00 0.00 35.37 3.69
79 80 1.573108 TTCTGGGAGAAGCTGGGTAG 58.427 55.000 0.00 0.00 29.50 3.18
80 81 0.325671 TCTGGGAGAAGCTGGGTAGG 60.326 60.000 0.00 0.00 0.00 3.18
81 82 1.306997 TGGGAGAAGCTGGGTAGGG 60.307 63.158 0.00 0.00 0.00 3.53
83 84 1.307084 GGAGAAGCTGGGTAGGGGT 60.307 63.158 0.00 0.00 0.00 4.95
84 85 1.338890 GGAGAAGCTGGGTAGGGGTC 61.339 65.000 0.00 0.00 0.00 4.46
85 86 1.677637 GAGAAGCTGGGTAGGGGTCG 61.678 65.000 0.00 0.00 0.00 4.79
86 87 2.687566 AAGCTGGGTAGGGGTCGG 60.688 66.667 0.00 0.00 0.00 4.79
90 91 2.041206 GCTGGGTAGGGGTCGGATTC 62.041 65.000 0.00 0.00 0.00 2.52
91 92 0.398664 CTGGGTAGGGGTCGGATTCT 60.399 60.000 0.00 0.00 0.00 2.40
92 93 0.689745 TGGGTAGGGGTCGGATTCTG 60.690 60.000 0.00 0.00 0.00 3.02
93 94 1.408453 GGGTAGGGGTCGGATTCTGG 61.408 65.000 0.00 0.00 0.00 3.86
94 95 1.408453 GGTAGGGGTCGGATTCTGGG 61.408 65.000 0.00 0.00 0.00 4.45
95 96 0.398098 GTAGGGGTCGGATTCTGGGA 60.398 60.000 0.00 0.00 0.00 4.37
96 97 0.105658 TAGGGGTCGGATTCTGGGAG 60.106 60.000 0.00 0.00 0.00 4.30
97 98 1.382695 GGGGTCGGATTCTGGGAGA 60.383 63.158 0.00 0.00 0.00 3.71
98 99 0.981277 GGGGTCGGATTCTGGGAGAA 60.981 60.000 0.00 0.00 38.78 2.87
99 100 1.132500 GGGTCGGATTCTGGGAGAAT 58.868 55.000 0.00 0.00 46.84 2.40
119 120 5.456921 AATCCCTAGATTCTGGCAAAAGA 57.543 39.130 0.00 0.00 38.36 2.52
123 124 4.397417 CCCTAGATTCTGGCAAAAGAACTG 59.603 45.833 0.00 0.00 38.95 3.16
124 125 4.397417 CCTAGATTCTGGCAAAAGAACTGG 59.603 45.833 0.00 1.96 38.95 4.00
125 126 3.160269 AGATTCTGGCAAAAGAACTGGG 58.840 45.455 0.00 0.00 38.95 4.45
126 127 1.039856 TTCTGGCAAAAGAACTGGGC 58.960 50.000 0.00 0.00 31.19 5.36
127 128 0.827507 TCTGGCAAAAGAACTGGGCC 60.828 55.000 0.00 0.00 44.82 5.80
129 130 0.480690 TGGCAAAAGAACTGGGCCTA 59.519 50.000 4.53 0.00 44.85 3.93
130 131 1.177401 GGCAAAAGAACTGGGCCTAG 58.823 55.000 15.72 15.72 41.39 3.02
131 132 1.547901 GGCAAAAGAACTGGGCCTAGT 60.548 52.381 17.38 17.38 41.39 2.57
138 139 0.252742 AACTGGGCCTAGTAGCAGGT 60.253 55.000 23.55 5.57 38.05 4.00
173 174 1.600916 GGCGGTTGCAACTTCTCCT 60.601 57.895 27.64 0.00 45.35 3.69
174 175 1.578206 GGCGGTTGCAACTTCTCCTC 61.578 60.000 27.64 9.37 45.35 3.71
179 180 0.321671 TTGCAACTTCTCCTCCGAGG 59.678 55.000 8.30 8.30 36.70 4.63
180 181 1.448717 GCAACTTCTCCTCCGAGGC 60.449 63.158 9.87 0.00 36.70 4.70
181 182 1.893919 GCAACTTCTCCTCCGAGGCT 61.894 60.000 9.87 0.00 36.70 4.58
182 183 0.610687 CAACTTCTCCTCCGAGGCTT 59.389 55.000 9.87 0.00 36.70 4.35
183 184 0.610687 AACTTCTCCTCCGAGGCTTG 59.389 55.000 9.87 2.89 36.70 4.01
188 189 1.304962 TCCTCCGAGGCTTGTGCTA 60.305 57.895 9.87 0.00 39.59 3.49
189 190 0.687757 TCCTCCGAGGCTTGTGCTAT 60.688 55.000 9.87 0.00 39.59 2.97
190 191 0.179000 CCTCCGAGGCTTGTGCTATT 59.821 55.000 0.18 0.00 39.59 1.73
193 194 1.828595 TCCGAGGCTTGTGCTATTGTA 59.171 47.619 0.12 0.00 39.59 2.41
195 196 2.351726 CCGAGGCTTGTGCTATTGTAAC 59.648 50.000 0.12 0.00 39.59 2.50
196 197 3.000041 CGAGGCTTGTGCTATTGTAACA 59.000 45.455 0.00 0.00 39.59 2.41
197 198 3.435327 CGAGGCTTGTGCTATTGTAACAA 59.565 43.478 0.00 0.00 39.59 2.83
198 199 4.669197 CGAGGCTTGTGCTATTGTAACAAC 60.669 45.833 0.00 0.00 39.59 3.32
200 201 2.908626 GCTTGTGCTATTGTAACAACGC 59.091 45.455 0.00 0.00 36.03 4.84
201 202 3.488489 CTTGTGCTATTGTAACAACGCC 58.512 45.455 0.00 0.00 30.93 5.68
202 203 1.807742 TGTGCTATTGTAACAACGCCC 59.192 47.619 0.00 0.00 0.00 6.13
203 204 1.807742 GTGCTATTGTAACAACGCCCA 59.192 47.619 0.00 0.00 0.00 5.36
204 205 2.422127 GTGCTATTGTAACAACGCCCAT 59.578 45.455 0.00 0.00 0.00 4.00
206 207 2.422127 GCTATTGTAACAACGCCCATGT 59.578 45.455 0.00 0.00 0.00 3.21
207 208 3.730662 GCTATTGTAACAACGCCCATGTG 60.731 47.826 0.00 0.00 0.00 3.21
210 211 0.596082 GTAACAACGCCCATGTGCTT 59.404 50.000 0.00 0.00 0.00 3.91
211 212 0.878416 TAACAACGCCCATGTGCTTC 59.122 50.000 0.00 0.00 0.00 3.86
212 213 1.106351 AACAACGCCCATGTGCTTCA 61.106 50.000 0.00 0.00 0.00 3.02
213 214 1.210931 CAACGCCCATGTGCTTCAG 59.789 57.895 0.00 0.00 0.00 3.02
214 215 1.228245 AACGCCCATGTGCTTCAGT 60.228 52.632 0.00 0.00 0.00 3.41
215 216 1.237285 AACGCCCATGTGCTTCAGTC 61.237 55.000 0.00 0.00 0.00 3.51
216 217 1.672030 CGCCCATGTGCTTCAGTCA 60.672 57.895 0.00 0.00 0.00 3.41
218 219 1.743431 CGCCCATGTGCTTCAGTCATA 60.743 52.381 0.00 0.00 0.00 2.15
219 220 2.368439 GCCCATGTGCTTCAGTCATAA 58.632 47.619 0.00 0.00 0.00 1.90
220 221 2.754552 GCCCATGTGCTTCAGTCATAAA 59.245 45.455 0.00 0.00 0.00 1.40
221 222 3.181493 GCCCATGTGCTTCAGTCATAAAG 60.181 47.826 0.00 0.00 0.00 1.85
222 223 4.264253 CCCATGTGCTTCAGTCATAAAGA 58.736 43.478 0.00 0.00 0.00 2.52
224 225 4.334759 CCATGTGCTTCAGTCATAAAGAGG 59.665 45.833 0.00 0.00 0.00 3.69
225 226 4.623932 TGTGCTTCAGTCATAAAGAGGT 57.376 40.909 0.00 0.00 0.00 3.85
226 227 4.973168 TGTGCTTCAGTCATAAAGAGGTT 58.027 39.130 0.00 0.00 0.00 3.50
227 228 4.756642 TGTGCTTCAGTCATAAAGAGGTTG 59.243 41.667 0.00 0.00 0.00 3.77
229 230 5.932303 GTGCTTCAGTCATAAAGAGGTTGTA 59.068 40.000 0.00 0.00 0.00 2.41
230 231 6.091441 GTGCTTCAGTCATAAAGAGGTTGTAG 59.909 42.308 0.00 0.00 0.00 2.74
231 232 5.582665 GCTTCAGTCATAAAGAGGTTGTAGG 59.417 44.000 0.00 0.00 0.00 3.18
232 233 5.677319 TCAGTCATAAAGAGGTTGTAGGG 57.323 43.478 0.00 0.00 0.00 3.53
233 234 4.469945 TCAGTCATAAAGAGGTTGTAGGGG 59.530 45.833 0.00 0.00 0.00 4.79
234 235 3.780850 AGTCATAAAGAGGTTGTAGGGGG 59.219 47.826 0.00 0.00 0.00 5.40
257 258 3.622263 AGGTGGGGGAGGCCACTA 61.622 66.667 5.01 0.00 37.15 2.74
258 259 3.090532 GGTGGGGGAGGCCACTAG 61.091 72.222 5.01 0.00 37.15 2.57
260 261 2.285368 TGGGGGAGGCCACTAGTG 60.285 66.667 16.34 16.34 0.00 2.74
261 262 2.285442 GGGGGAGGCCACTAGTGT 60.285 66.667 21.18 2.97 0.00 3.55
262 263 2.670148 GGGGGAGGCCACTAGTGTG 61.670 68.421 21.18 13.48 43.45 3.82
263 264 2.269241 GGGAGGCCACTAGTGTGC 59.731 66.667 21.18 21.28 42.54 4.57
267 268 3.068881 GGCCACTAGTGTGCCTGA 58.931 61.111 31.85 0.00 42.54 3.86
268 269 1.604378 GGCCACTAGTGTGCCTGAT 59.396 57.895 31.85 0.00 42.54 2.90
269 270 0.745845 GGCCACTAGTGTGCCTGATG 60.746 60.000 31.85 14.70 42.54 3.07
280 281 2.415010 CCTGATGGCGAGAGTCGG 59.585 66.667 0.00 0.00 40.84 4.79
281 282 2.415010 CTGATGGCGAGAGTCGGG 59.585 66.667 0.00 0.00 40.84 5.14
282 283 3.144120 CTGATGGCGAGAGTCGGGG 62.144 68.421 0.00 0.00 40.84 5.73
283 284 4.593864 GATGGCGAGAGTCGGGGC 62.594 72.222 0.00 3.57 40.84 5.80
299 300 2.583472 GGCACCCCTTTCTTCCATG 58.417 57.895 0.00 0.00 0.00 3.66
300 301 1.607801 GGCACCCCTTTCTTCCATGC 61.608 60.000 0.00 0.00 0.00 4.06
301 302 0.899717 GCACCCCTTTCTTCCATGCA 60.900 55.000 0.00 0.00 0.00 3.96
302 303 1.180029 CACCCCTTTCTTCCATGCAG 58.820 55.000 0.00 0.00 0.00 4.41
303 304 0.613012 ACCCCTTTCTTCCATGCAGC 60.613 55.000 0.00 0.00 0.00 5.25
304 305 0.612732 CCCCTTTCTTCCATGCAGCA 60.613 55.000 0.00 0.00 0.00 4.41
306 307 0.172803 CCTTTCTTCCATGCAGCAGC 59.827 55.000 0.00 0.00 42.57 5.25
325 2168 1.482930 GCATCATCTCCCTCTCCCTCT 60.483 57.143 0.00 0.00 0.00 3.69
341 2184 2.636830 CCTCTTCCCTACGTCGTTAGA 58.363 52.381 1.78 0.00 0.00 2.10
365 2208 0.824109 CTATCCTTCGGTGGACAGCA 59.176 55.000 2.25 0.00 39.17 4.41
369 2212 1.672030 CTTCGGTGGACAGCATGCA 60.672 57.895 21.98 0.00 42.53 3.96
407 2251 1.202698 GCTCTGTCACAAGTTGGAGGT 60.203 52.381 7.96 0.00 0.00 3.85
454 2298 3.716539 TAGTCCAGATGCGCGGCAC 62.717 63.158 8.83 2.00 43.04 5.01
479 2323 0.952984 GTGGTGGCAAGAGAGAGCAC 60.953 60.000 0.00 0.00 0.00 4.40
481 2325 0.035630 GGTGGCAAGAGAGAGCACAT 60.036 55.000 0.00 0.00 0.00 3.21
490 2334 3.746949 GAGAGCACATGGGAGGCGG 62.747 68.421 0.00 0.00 0.00 6.13
500 2344 2.844839 GGAGGCGGGCTAGGACAT 60.845 66.667 3.20 0.00 0.00 3.06
516 2360 0.175531 ACATGCGTCCACGATGATCA 59.824 50.000 2.58 0.00 43.02 2.92
536 2380 1.203050 ACCACACAAAGATGAAGGGGG 60.203 52.381 0.00 0.00 34.43 5.40
569 2414 1.555533 GAATGAGAGGACCGGGTTCTT 59.444 52.381 9.93 0.00 0.00 2.52
573 2418 0.115745 AGAGGACCGGGTTCTTGGTA 59.884 55.000 9.93 0.00 38.99 3.25
605 2450 1.074248 GGGAGAAAGGGAAACGGCA 59.926 57.895 0.00 0.00 0.00 5.69
606 2451 0.538746 GGGAGAAAGGGAAACGGCAA 60.539 55.000 0.00 0.00 0.00 4.52
616 2461 0.385473 GAAACGGCAACATGTGTCCG 60.385 55.000 27.43 27.43 46.19 4.79
660 2505 0.391263 GACCGGCCAAAGACGAGATT 60.391 55.000 0.00 0.00 0.00 2.40
709 2623 5.801947 CCTCACAAAGTCACAAGAAAACTTG 59.198 40.000 8.18 8.18 39.98 3.16
720 2634 6.096673 ACAAGAAAACTTGGTTGTGAAGTT 57.903 33.333 13.25 0.00 43.88 2.66
721 2635 5.925969 ACAAGAAAACTTGGTTGTGAAGTTG 59.074 36.000 13.25 0.00 41.71 3.16
837 2754 3.491104 GGGCGTACTCTCAAATAGTCCAG 60.491 52.174 0.00 0.00 0.00 3.86
854 2771 0.602106 CAGAGACACAGGCCACACAG 60.602 60.000 5.01 0.00 0.00 3.66
861 2778 4.334118 AGGCCACACAGCGCATCA 62.334 61.111 11.47 0.00 0.00 3.07
925 2842 2.548920 CCTCTCCACAGTTGACAGTTCC 60.549 54.545 0.00 0.00 0.00 3.62
927 2844 1.140852 CTCCACAGTTGACAGTTCCCA 59.859 52.381 0.00 0.00 0.00 4.37
928 2845 1.134220 TCCACAGTTGACAGTTCCCAC 60.134 52.381 0.00 0.00 0.00 4.61
929 2846 1.308998 CACAGTTGACAGTTCCCACC 58.691 55.000 0.00 0.00 0.00 4.61
930 2847 0.182775 ACAGTTGACAGTTCCCACCC 59.817 55.000 0.00 0.00 0.00 4.61
931 2848 0.537371 CAGTTGACAGTTCCCACCCC 60.537 60.000 0.00 0.00 0.00 4.95
932 2849 1.228459 GTTGACAGTTCCCACCCCC 60.228 63.158 0.00 0.00 0.00 5.40
933 2850 1.698116 TTGACAGTTCCCACCCCCA 60.698 57.895 0.00 0.00 0.00 4.96
934 2851 2.002018 TTGACAGTTCCCACCCCCAC 62.002 60.000 0.00 0.00 0.00 4.61
935 2852 2.038762 ACAGTTCCCACCCCCACT 60.039 61.111 0.00 0.00 0.00 4.00
966 2883 4.282195 TCTCTCTCTCCACTTCCAAAACTC 59.718 45.833 0.00 0.00 0.00 3.01
987 2904 3.241530 AGGTCTTCACAGGCGGCA 61.242 61.111 13.08 0.00 0.00 5.69
1048 2965 1.654954 AATACTCGCCGACGTGCTCT 61.655 55.000 0.00 0.00 41.18 4.09
1356 3289 6.503560 TGGGAGGATTATTACGTGGTTAAT 57.496 37.500 0.00 0.00 0.00 1.40
1368 3301 2.403586 GTTAATCCAGCCACGCGC 59.596 61.111 5.73 0.00 37.98 6.86
1422 3361 5.220873 CGTGTTCGAGGAGATAGATGAAGAA 60.221 44.000 0.00 0.00 39.71 2.52
1440 3379 7.558161 TGAAGAACTCAAATGCGAATATCAT 57.442 32.000 0.00 0.00 0.00 2.45
1780 3945 6.201044 CGTAATGAGGTACCTAATTGCTCTTG 59.799 42.308 28.70 14.17 30.34 3.02
1894 4063 7.273320 CAGGATCTGCTTGTCAAATGATAAT 57.727 36.000 0.00 0.00 0.00 1.28
1895 4064 8.387190 CAGGATCTGCTTGTCAAATGATAATA 57.613 34.615 0.00 0.00 0.00 0.98
1896 4065 8.843262 CAGGATCTGCTTGTCAAATGATAATAA 58.157 33.333 0.00 0.00 0.00 1.40
1991 4160 0.850784 AGGGGTGTACCTTGCAACTT 59.149 50.000 0.00 0.00 37.69 2.66
2017 4472 9.683069 TCTACTTTTAAAACGTCTCGTCTTATT 57.317 29.630 0.00 0.00 39.99 1.40
2207 4676 3.531538 GACGACTTGGAATGGCTAATGA 58.468 45.455 0.00 0.00 0.00 2.57
2414 4905 4.424842 AGGGTTGGCCTATCATTTGAAAA 58.575 39.130 3.32 0.00 34.45 2.29
2452 4943 5.411669 GGATCTTGGCTATTTATACCCAACG 59.588 44.000 0.00 0.00 33.99 4.10
2635 5131 3.778265 ACTCATGTTTATGGCCTGGTTT 58.222 40.909 3.32 0.00 34.97 3.27
2643 5139 5.941647 TGTTTATGGCCTGGTTTAGTCTTAC 59.058 40.000 3.32 0.00 0.00 2.34
2644 5140 5.765576 TTATGGCCTGGTTTAGTCTTACA 57.234 39.130 3.32 0.00 0.00 2.41
2720 5216 2.806244 GCTGTTGTACGGACATGAAACT 59.194 45.455 0.00 0.00 34.86 2.66
2726 5222 4.699637 TGTACGGACATGAAACTTCAAGT 58.300 39.130 0.00 0.20 41.28 3.16
2879 5376 7.201732 CCAATATTTCACTCAGCGGTATCTTTT 60.202 37.037 0.00 0.00 0.00 2.27
2894 5391 1.700739 TCTTTTCCGCCCTCTTGGTTA 59.299 47.619 0.00 0.00 36.04 2.85
2898 5395 1.868713 TCCGCCCTCTTGGTTACATA 58.131 50.000 0.00 0.00 36.04 2.29
2902 5421 2.290641 CGCCCTCTTGGTTACATATTGC 59.709 50.000 0.00 0.00 36.04 3.56
2909 5428 6.375455 CCTCTTGGTTACATATTGCTGTTTCT 59.625 38.462 0.00 0.00 0.00 2.52
2962 5598 3.603965 TTTTCCTTACTTTGGGCTCCA 57.396 42.857 0.00 0.00 0.00 3.86
3068 5704 1.696336 GGGATGATGGCAGCTCTAAGA 59.304 52.381 3.69 0.00 0.00 2.10
3069 5705 2.105477 GGGATGATGGCAGCTCTAAGAA 59.895 50.000 3.69 0.00 0.00 2.52
3070 5706 3.434167 GGGATGATGGCAGCTCTAAGAAA 60.434 47.826 3.69 0.00 0.00 2.52
3071 5707 4.202441 GGATGATGGCAGCTCTAAGAAAA 58.798 43.478 3.69 0.00 0.00 2.29
3073 5709 5.278364 GGATGATGGCAGCTCTAAGAAAATG 60.278 44.000 3.69 0.00 0.00 2.32
3075 5711 5.012239 TGATGGCAGCTCTAAGAAAATGTT 58.988 37.500 3.69 0.00 0.00 2.71
3077 5713 5.789643 TGGCAGCTCTAAGAAAATGTTTT 57.210 34.783 0.00 0.00 0.00 2.43
3078 5714 6.160576 TGGCAGCTCTAAGAAAATGTTTTT 57.839 33.333 0.00 0.00 0.00 1.94
3080 5716 7.145323 TGGCAGCTCTAAGAAAATGTTTTTAC 58.855 34.615 0.00 0.00 0.00 2.01
3082 5718 6.856426 GCAGCTCTAAGAAAATGTTTTTACGT 59.144 34.615 0.00 0.00 0.00 3.57
3084 5720 7.534239 CAGCTCTAAGAAAATGTTTTTACGTCC 59.466 37.037 0.00 0.00 0.00 4.79
3085 5721 6.800408 GCTCTAAGAAAATGTTTTTACGTCCC 59.200 38.462 0.00 0.00 0.00 4.46
3086 5722 7.520937 GCTCTAAGAAAATGTTTTTACGTCCCA 60.521 37.037 0.00 0.00 0.00 4.37
3087 5723 7.641760 TCTAAGAAAATGTTTTTACGTCCCAC 58.358 34.615 0.00 0.00 0.00 4.61
3088 5724 5.838531 AGAAAATGTTTTTACGTCCCACA 57.161 34.783 0.00 0.00 0.00 4.17
3204 5934 1.804396 TTGCCGTGGTGGAAATGCTG 61.804 55.000 0.00 0.00 42.00 4.41
3238 5968 2.226013 ACTGGAAAGGGAGGGAAGAGAT 60.226 50.000 0.00 0.00 0.00 2.75
3326 7113 5.466058 CAGACAGCATTTCTATTAGCCTCTG 59.534 44.000 0.00 0.00 0.00 3.35
3376 7164 3.334691 AGCTTGCGACTTTAGCATGTAA 58.665 40.909 0.00 0.00 44.74 2.41
3435 8014 5.048434 GCCTGCCCTCTGTTTTCATTATATC 60.048 44.000 0.00 0.00 0.00 1.63
3439 8018 6.547141 TGCCCTCTGTTTTCATTATATCCTTG 59.453 38.462 0.00 0.00 0.00 3.61
3491 8070 7.397892 TTTTAAGGTAATTCGCATTGATGGA 57.602 32.000 0.00 0.00 0.00 3.41
3492 8071 7.581213 TTTAAGGTAATTCGCATTGATGGAT 57.419 32.000 0.00 0.00 0.00 3.41
3493 8072 7.581213 TTAAGGTAATTCGCATTGATGGATT 57.419 32.000 0.00 0.00 0.00 3.01
3494 8073 5.695851 AGGTAATTCGCATTGATGGATTC 57.304 39.130 0.00 0.00 0.00 2.52
3496 8075 4.278170 GGTAATTCGCATTGATGGATTCCA 59.722 41.667 8.08 8.08 38.19 3.53
3497 8076 5.221224 GGTAATTCGCATTGATGGATTCCAA 60.221 40.000 9.98 0.00 36.95 3.53
3499 8078 3.003394 TCGCATTGATGGATTCCAACT 57.997 42.857 9.98 0.00 36.95 3.16
3500 8079 4.149511 TCGCATTGATGGATTCCAACTA 57.850 40.909 9.98 4.44 36.95 2.24
3501 8080 4.717877 TCGCATTGATGGATTCCAACTAT 58.282 39.130 9.98 6.78 36.95 2.12
3502 8081 5.863965 TCGCATTGATGGATTCCAACTATA 58.136 37.500 9.98 0.00 36.95 1.31
3503 8082 5.934043 TCGCATTGATGGATTCCAACTATAG 59.066 40.000 9.98 7.41 36.95 1.31
3504 8083 5.122869 CGCATTGATGGATTCCAACTATAGG 59.877 44.000 9.98 0.64 36.95 2.57
3506 8085 5.912149 TTGATGGATTCCAACTATAGGCT 57.088 39.130 9.98 0.00 36.95 4.58
3507 8086 5.233083 TGATGGATTCCAACTATAGGCTG 57.767 43.478 9.98 1.04 36.95 4.85
3508 8087 4.907269 TGATGGATTCCAACTATAGGCTGA 59.093 41.667 9.98 0.00 36.95 4.26
3510 8089 4.556697 TGGATTCCAACTATAGGCTGAGA 58.443 43.478 1.94 0.00 0.00 3.27
3511 8090 4.345257 TGGATTCCAACTATAGGCTGAGAC 59.655 45.833 1.94 0.00 0.00 3.36
3512 8091 4.591072 GGATTCCAACTATAGGCTGAGACT 59.409 45.833 4.43 0.00 0.00 3.24
3513 8092 5.279256 GGATTCCAACTATAGGCTGAGACTC 60.279 48.000 4.43 0.00 0.00 3.36
3515 8094 4.873010 TCCAACTATAGGCTGAGACTCTT 58.127 43.478 4.43 0.00 0.00 2.85
3516 8095 4.646945 TCCAACTATAGGCTGAGACTCTTG 59.353 45.833 4.43 0.00 0.00 3.02
3517 8096 4.646945 CCAACTATAGGCTGAGACTCTTGA 59.353 45.833 4.43 0.00 0.00 3.02
3518 8097 5.221224 CCAACTATAGGCTGAGACTCTTGAG 60.221 48.000 4.43 0.00 0.00 3.02
3519 8098 3.888930 ACTATAGGCTGAGACTCTTGAGC 59.111 47.826 4.43 4.42 0.00 4.26
3520 8099 2.222227 TAGGCTGAGACTCTTGAGCA 57.778 50.000 13.53 0.00 32.83 4.26
3521 8100 1.570803 AGGCTGAGACTCTTGAGCAT 58.429 50.000 13.53 5.34 32.83 3.79
3522 8101 1.207570 AGGCTGAGACTCTTGAGCATG 59.792 52.381 13.53 0.00 32.83 4.06
3523 8102 1.066286 GGCTGAGACTCTTGAGCATGT 60.066 52.381 13.53 0.00 32.83 3.21
3524 8103 2.167281 GGCTGAGACTCTTGAGCATGTA 59.833 50.000 13.53 0.00 32.83 2.29
3526 8105 4.248859 GCTGAGACTCTTGAGCATGTAAA 58.751 43.478 3.68 0.00 0.00 2.01
3527 8106 4.692625 GCTGAGACTCTTGAGCATGTAAAA 59.307 41.667 3.68 0.00 0.00 1.52
3528 8107 5.180117 GCTGAGACTCTTGAGCATGTAAAAA 59.820 40.000 3.68 0.00 0.00 1.94
3529 8108 6.545504 TGAGACTCTTGAGCATGTAAAAAC 57.454 37.500 3.68 0.00 0.00 2.43
3530 8109 6.054941 TGAGACTCTTGAGCATGTAAAAACA 58.945 36.000 3.68 0.00 0.00 2.83
3531 8110 6.017934 TGAGACTCTTGAGCATGTAAAAACAC 60.018 38.462 3.68 0.00 0.00 3.32
3532 8111 6.058183 AGACTCTTGAGCATGTAAAAACACT 58.942 36.000 0.00 0.00 0.00 3.55
3535 8114 6.318648 ACTCTTGAGCATGTAAAAACACTTGA 59.681 34.615 0.00 0.00 0.00 3.02
3536 8115 7.094508 TCTTGAGCATGTAAAAACACTTGAA 57.905 32.000 0.00 0.00 0.00 2.69
3537 8116 6.972328 TCTTGAGCATGTAAAAACACTTGAAC 59.028 34.615 0.00 0.00 0.00 3.18
3538 8117 6.201226 TGAGCATGTAAAAACACTTGAACA 57.799 33.333 0.00 0.00 0.00 3.18
3540 8119 7.264221 TGAGCATGTAAAAACACTTGAACATT 58.736 30.769 0.00 0.00 0.00 2.71
3541 8120 7.222417 TGAGCATGTAAAAACACTTGAACATTG 59.778 33.333 0.00 0.00 0.00 2.82
3542 8121 7.264221 AGCATGTAAAAACACTTGAACATTGA 58.736 30.769 0.00 0.00 0.00 2.57
3543 8122 7.436080 AGCATGTAAAAACACTTGAACATTGAG 59.564 33.333 0.00 0.00 0.00 3.02
3544 8123 7.434897 GCATGTAAAAACACTTGAACATTGAGA 59.565 33.333 0.00 0.00 0.00 3.27
3545 8124 9.467258 CATGTAAAAACACTTGAACATTGAGAT 57.533 29.630 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.682710 GCCACATTTGTTTTACAATCCTATCTA 58.317 33.333 0.00 0.00 38.00 1.98
28 29 7.547227 AGCCACATTTGTTTTACAATCCTATC 58.453 34.615 0.00 0.00 38.00 2.08
32 33 5.537188 TGAGCCACATTTGTTTTACAATCC 58.463 37.500 0.00 0.00 38.00 3.01
33 34 7.224557 ACTTTGAGCCACATTTGTTTTACAATC 59.775 33.333 0.00 0.00 38.00 2.67
34 35 7.047271 ACTTTGAGCCACATTTGTTTTACAAT 58.953 30.769 0.00 0.00 38.00 2.71
35 36 6.402222 ACTTTGAGCCACATTTGTTTTACAA 58.598 32.000 0.00 0.00 36.11 2.41
36 37 5.971763 ACTTTGAGCCACATTTGTTTTACA 58.028 33.333 0.00 0.00 0.00 2.41
37 38 6.902224 AACTTTGAGCCACATTTGTTTTAC 57.098 33.333 0.00 0.00 0.00 2.01
39 40 6.092533 CAGAAACTTTGAGCCACATTTGTTTT 59.907 34.615 0.00 0.00 31.42 2.43
41 42 5.111293 CAGAAACTTTGAGCCACATTTGTT 58.889 37.500 0.00 0.00 0.00 2.83
42 43 4.441913 CCAGAAACTTTGAGCCACATTTGT 60.442 41.667 0.00 0.00 0.00 2.83
43 44 4.053295 CCAGAAACTTTGAGCCACATTTG 58.947 43.478 0.00 0.00 0.00 2.32
44 45 3.070015 CCCAGAAACTTTGAGCCACATTT 59.930 43.478 0.00 0.00 0.00 2.32
45 46 2.629617 CCCAGAAACTTTGAGCCACATT 59.370 45.455 0.00 0.00 0.00 2.71
48 49 1.882623 CTCCCAGAAACTTTGAGCCAC 59.117 52.381 0.00 0.00 0.00 5.01
50 51 2.568623 TCTCCCAGAAACTTTGAGCC 57.431 50.000 0.00 0.00 0.00 4.70
51 52 2.227626 GCTTCTCCCAGAAACTTTGAGC 59.772 50.000 0.00 0.00 33.19 4.26
53 54 3.480470 CAGCTTCTCCCAGAAACTTTGA 58.520 45.455 0.00 0.00 33.19 2.69
55 56 2.489802 CCCAGCTTCTCCCAGAAACTTT 60.490 50.000 0.00 0.00 33.19 2.66
56 57 1.074566 CCCAGCTTCTCCCAGAAACTT 59.925 52.381 0.00 0.00 33.19 2.66
57 58 0.695347 CCCAGCTTCTCCCAGAAACT 59.305 55.000 0.00 0.00 33.19 2.66
58 59 0.402121 ACCCAGCTTCTCCCAGAAAC 59.598 55.000 0.00 0.00 33.19 2.78
59 60 1.909302 CTACCCAGCTTCTCCCAGAAA 59.091 52.381 0.00 0.00 33.19 2.52
62 63 1.341156 CCCTACCCAGCTTCTCCCAG 61.341 65.000 0.00 0.00 0.00 4.45
63 64 1.306997 CCCTACCCAGCTTCTCCCA 60.307 63.158 0.00 0.00 0.00 4.37
64 65 2.073101 CCCCTACCCAGCTTCTCCC 61.073 68.421 0.00 0.00 0.00 4.30
65 66 1.307084 ACCCCTACCCAGCTTCTCC 60.307 63.158 0.00 0.00 0.00 3.71
66 67 1.677637 CGACCCCTACCCAGCTTCTC 61.678 65.000 0.00 0.00 0.00 2.87
67 68 1.686110 CGACCCCTACCCAGCTTCT 60.686 63.158 0.00 0.00 0.00 2.85
68 69 2.732619 CCGACCCCTACCCAGCTTC 61.733 68.421 0.00 0.00 0.00 3.86
69 70 2.547123 ATCCGACCCCTACCCAGCTT 62.547 60.000 0.00 0.00 0.00 3.74
70 71 2.547123 AATCCGACCCCTACCCAGCT 62.547 60.000 0.00 0.00 0.00 4.24
71 72 2.041206 GAATCCGACCCCTACCCAGC 62.041 65.000 0.00 0.00 0.00 4.85
72 73 0.398664 AGAATCCGACCCCTACCCAG 60.399 60.000 0.00 0.00 0.00 4.45
75 76 1.408453 CCCAGAATCCGACCCCTACC 61.408 65.000 0.00 0.00 0.00 3.18
76 77 0.398098 TCCCAGAATCCGACCCCTAC 60.398 60.000 0.00 0.00 0.00 3.18
78 79 1.383248 CTCCCAGAATCCGACCCCT 60.383 63.158 0.00 0.00 0.00 4.79
79 80 0.981277 TTCTCCCAGAATCCGACCCC 60.981 60.000 0.00 0.00 0.00 4.95
80 81 1.132500 ATTCTCCCAGAATCCGACCC 58.868 55.000 0.00 0.00 40.75 4.46
97 98 5.456921 TCTTTTGCCAGAATCTAGGGATT 57.543 39.130 0.00 0.00 43.99 3.01
98 99 5.044550 AGTTCTTTTGCCAGAATCTAGGGAT 60.045 40.000 0.00 0.00 35.23 3.85
99 100 4.289672 AGTTCTTTTGCCAGAATCTAGGGA 59.710 41.667 0.00 0.00 35.23 4.20
100 101 4.397417 CAGTTCTTTTGCCAGAATCTAGGG 59.603 45.833 0.00 0.00 35.23 3.53
101 102 4.397417 CCAGTTCTTTTGCCAGAATCTAGG 59.603 45.833 0.00 0.00 35.23 3.02
102 103 4.397417 CCCAGTTCTTTTGCCAGAATCTAG 59.603 45.833 0.00 0.00 35.23 2.43
103 104 4.335416 CCCAGTTCTTTTGCCAGAATCTA 58.665 43.478 0.00 0.00 35.23 1.98
105 106 2.353109 GCCCAGTTCTTTTGCCAGAATC 60.353 50.000 0.00 0.00 35.23 2.52
106 107 1.620323 GCCCAGTTCTTTTGCCAGAAT 59.380 47.619 0.00 0.00 35.23 2.40
107 108 1.039856 GCCCAGTTCTTTTGCCAGAA 58.960 50.000 0.00 0.00 0.00 3.02
109 110 0.829182 AGGCCCAGTTCTTTTGCCAG 60.829 55.000 0.00 0.00 44.60 4.85
110 111 0.480690 TAGGCCCAGTTCTTTTGCCA 59.519 50.000 0.00 0.00 44.60 4.92
111 112 1.177401 CTAGGCCCAGTTCTTTTGCC 58.823 55.000 0.00 0.00 42.48 4.52
112 113 1.911057 ACTAGGCCCAGTTCTTTTGC 58.089 50.000 0.00 0.00 0.00 3.68
113 114 3.010420 GCTACTAGGCCCAGTTCTTTTG 58.990 50.000 9.77 0.00 0.00 2.44
114 115 2.642807 TGCTACTAGGCCCAGTTCTTTT 59.357 45.455 9.77 0.00 0.00 2.27
115 116 2.237392 CTGCTACTAGGCCCAGTTCTTT 59.763 50.000 9.77 0.00 0.00 2.52
116 117 1.834263 CTGCTACTAGGCCCAGTTCTT 59.166 52.381 9.77 0.00 0.00 2.52
117 118 1.490574 CTGCTACTAGGCCCAGTTCT 58.509 55.000 9.77 0.00 0.00 3.01
118 119 0.466124 CCTGCTACTAGGCCCAGTTC 59.534 60.000 9.77 2.72 0.00 3.01
119 120 0.252742 ACCTGCTACTAGGCCCAGTT 60.253 55.000 9.77 0.00 41.75 3.16
123 124 3.130227 CGACCTGCTACTAGGCCC 58.870 66.667 0.00 0.00 41.75 5.80
124 125 2.356818 CTGCGACCTGCTACTAGGCC 62.357 65.000 0.00 0.00 46.63 5.19
125 126 1.066587 CTGCGACCTGCTACTAGGC 59.933 63.158 0.00 0.00 46.63 3.93
126 127 1.066587 GCTGCGACCTGCTACTAGG 59.933 63.158 0.00 0.00 46.63 3.02
127 128 0.030101 GAGCTGCGACCTGCTACTAG 59.970 60.000 0.00 0.00 44.92 2.57
129 130 2.716017 GGAGCTGCGACCTGCTACT 61.716 63.158 0.00 0.00 44.92 2.57
130 131 2.202810 GGAGCTGCGACCTGCTAC 60.203 66.667 0.00 0.00 44.92 3.58
131 132 3.826754 CGGAGCTGCGACCTGCTA 61.827 66.667 24.56 0.00 44.92 3.49
165 166 0.543174 ACAAGCCTCGGAGGAGAAGT 60.543 55.000 27.95 15.62 43.27 3.01
173 174 0.613260 ACAATAGCACAAGCCTCGGA 59.387 50.000 0.00 0.00 43.56 4.55
174 175 2.309528 TACAATAGCACAAGCCTCGG 57.690 50.000 0.00 0.00 43.56 4.63
179 180 2.908626 GCGTTGTTACAATAGCACAAGC 59.091 45.455 18.40 0.00 42.56 4.01
180 181 3.488489 GGCGTTGTTACAATAGCACAAG 58.512 45.455 22.38 0.00 31.10 3.16
181 182 2.226912 GGGCGTTGTTACAATAGCACAA 59.773 45.455 22.38 0.00 0.00 3.33
182 183 1.807742 GGGCGTTGTTACAATAGCACA 59.192 47.619 22.38 0.00 0.00 4.57
183 184 1.807742 TGGGCGTTGTTACAATAGCAC 59.192 47.619 22.38 20.63 0.00 4.40
188 189 1.067915 GCACATGGGCGTTGTTACAAT 60.068 47.619 3.02 0.00 0.00 2.71
189 190 0.312416 GCACATGGGCGTTGTTACAA 59.688 50.000 3.02 0.00 0.00 2.41
190 191 0.536233 AGCACATGGGCGTTGTTACA 60.536 50.000 15.67 0.00 39.27 2.41
193 194 1.106351 TGAAGCACATGGGCGTTGTT 61.106 50.000 15.67 2.47 39.27 2.83
195 196 1.210931 CTGAAGCACATGGGCGTTG 59.789 57.895 15.67 4.85 39.27 4.10
196 197 1.228245 ACTGAAGCACATGGGCGTT 60.228 52.632 15.67 9.37 39.27 4.84
197 198 1.672356 GACTGAAGCACATGGGCGT 60.672 57.895 15.67 12.28 39.27 5.68
198 199 1.028330 ATGACTGAAGCACATGGGCG 61.028 55.000 15.67 2.12 39.27 6.13
200 201 4.264253 TCTTTATGACTGAAGCACATGGG 58.736 43.478 0.00 0.00 0.00 4.00
201 202 4.334759 CCTCTTTATGACTGAAGCACATGG 59.665 45.833 0.00 0.00 0.00 3.66
202 203 4.940046 ACCTCTTTATGACTGAAGCACATG 59.060 41.667 0.00 0.00 0.00 3.21
203 204 5.171339 ACCTCTTTATGACTGAAGCACAT 57.829 39.130 0.00 0.00 0.00 3.21
204 205 4.623932 ACCTCTTTATGACTGAAGCACA 57.376 40.909 0.00 0.00 0.00 4.57
206 207 4.973168 ACAACCTCTTTATGACTGAAGCA 58.027 39.130 0.00 0.00 0.00 3.91
207 208 5.582665 CCTACAACCTCTTTATGACTGAAGC 59.417 44.000 0.00 0.00 0.00 3.86
210 211 4.469945 CCCCTACAACCTCTTTATGACTGA 59.530 45.833 0.00 0.00 0.00 3.41
211 212 4.384208 CCCCCTACAACCTCTTTATGACTG 60.384 50.000 0.00 0.00 0.00 3.51
212 213 3.780850 CCCCCTACAACCTCTTTATGACT 59.219 47.826 0.00 0.00 0.00 3.41
213 214 4.152284 CCCCCTACAACCTCTTTATGAC 57.848 50.000 0.00 0.00 0.00 3.06
243 244 2.285368 CACTAGTGGCCTCCCCCA 60.285 66.667 15.49 0.00 0.00 4.96
244 245 2.285442 ACACTAGTGGCCTCCCCC 60.285 66.667 26.12 0.00 34.19 5.40
245 246 2.990479 CACACTAGTGGCCTCCCC 59.010 66.667 26.12 0.00 42.13 4.81
246 247 2.269241 GCACACTAGTGGCCTCCC 59.731 66.667 26.12 4.66 45.98 4.30
263 264 2.415010 CCGACTCTCGCCATCAGG 59.585 66.667 0.00 0.00 38.82 3.86
265 266 3.147595 CCCCGACTCTCGCCATCA 61.148 66.667 0.00 0.00 38.82 3.07
266 267 4.593864 GCCCCGACTCTCGCCATC 62.594 72.222 0.00 0.00 38.82 3.51
280 281 0.972471 CATGGAAGAAAGGGGTGCCC 60.972 60.000 0.00 0.00 45.90 5.36
281 282 1.607801 GCATGGAAGAAAGGGGTGCC 61.608 60.000 0.00 0.00 0.00 5.01
282 283 0.899717 TGCATGGAAGAAAGGGGTGC 60.900 55.000 0.00 0.00 0.00 5.01
283 284 1.180029 CTGCATGGAAGAAAGGGGTG 58.820 55.000 0.00 0.00 0.00 4.61
284 285 0.613012 GCTGCATGGAAGAAAGGGGT 60.613 55.000 0.00 0.00 0.00 4.95
287 288 0.172803 GCTGCTGCATGGAAGAAAGG 59.827 55.000 11.11 0.00 39.41 3.11
289 290 3.039452 TGCTGCTGCATGGAAGAAA 57.961 47.368 14.93 0.00 45.31 2.52
290 291 4.826248 TGCTGCTGCATGGAAGAA 57.174 50.000 14.93 0.00 45.31 2.52
299 300 0.885596 GAGGGAGATGATGCTGCTGC 60.886 60.000 8.89 8.89 40.20 5.25
300 301 0.759959 AGAGGGAGATGATGCTGCTG 59.240 55.000 0.00 0.00 0.00 4.41
301 302 1.050204 GAGAGGGAGATGATGCTGCT 58.950 55.000 0.00 0.00 0.00 4.24
302 303 0.035176 GGAGAGGGAGATGATGCTGC 59.965 60.000 0.00 0.00 0.00 5.25
303 304 0.686224 GGGAGAGGGAGATGATGCTG 59.314 60.000 0.00 0.00 0.00 4.41
304 305 0.567182 AGGGAGAGGGAGATGATGCT 59.433 55.000 0.00 0.00 0.00 3.79
306 307 2.700353 AGAGGGAGAGGGAGATGATG 57.300 55.000 0.00 0.00 0.00 3.07
325 2168 4.521146 AGAAGATCTAACGACGTAGGGAA 58.479 43.478 0.00 0.00 0.00 3.97
365 2208 2.045634 ATGCTGCTCCACGTGCAT 60.046 55.556 10.91 6.49 39.86 3.96
369 2212 2.046892 GACCATGCTGCTCCACGT 60.047 61.111 0.00 0.00 0.00 4.49
407 2251 0.586319 GCAACGCTGCTACAGTTTCA 59.414 50.000 2.93 0.00 45.74 2.69
429 2273 1.421410 CGCATCTGGACTACCGCAAC 61.421 60.000 0.00 0.00 39.42 4.17
454 2298 0.178992 TCTCTTGCCACCACAAAGGG 60.179 55.000 0.00 0.00 43.89 3.95
479 2323 3.946201 CCTAGCCCGCCTCCCATG 61.946 72.222 0.00 0.00 0.00 3.66
499 2343 0.530650 GGTGATCATCGTGGACGCAT 60.531 55.000 0.00 0.00 39.60 4.73
500 2344 1.153647 GGTGATCATCGTGGACGCA 60.154 57.895 0.00 0.00 39.60 5.24
508 2352 3.934579 TCATCTTTGTGTGGTGATCATCG 59.065 43.478 0.00 0.00 0.00 3.84
516 2360 1.203050 CCCCCTTCATCTTTGTGTGGT 60.203 52.381 0.00 0.00 0.00 4.16
536 2380 4.656112 TCCTCTCATTCCCATCTAACTTCC 59.344 45.833 0.00 0.00 0.00 3.46
537 2381 5.454045 GGTCCTCTCATTCCCATCTAACTTC 60.454 48.000 0.00 0.00 0.00 3.01
542 2386 2.598565 CGGTCCTCTCATTCCCATCTA 58.401 52.381 0.00 0.00 0.00 1.98
552 2396 1.192146 CCAAGAACCCGGTCCTCTCA 61.192 60.000 0.00 0.00 0.00 3.27
569 2414 3.958798 CTCCCTTTCCTTATCGTCTACCA 59.041 47.826 0.00 0.00 0.00 3.25
573 2418 4.162509 CCTTTCTCCCTTTCCTTATCGTCT 59.837 45.833 0.00 0.00 0.00 4.18
605 2450 1.100463 TGTTGCTGCGGACACATGTT 61.100 50.000 0.00 0.00 0.00 2.71
606 2451 0.890542 ATGTTGCTGCGGACACATGT 60.891 50.000 10.25 0.00 0.00 3.21
616 2461 2.429571 CACGTGCCATGTTGCTGC 60.430 61.111 0.82 0.00 0.00 5.25
709 2623 6.526674 CACAACTAAGTTTCAACTTCACAACC 59.473 38.462 8.22 0.00 45.65 3.77
837 2754 1.963338 GCTGTGTGGCCTGTGTCTC 60.963 63.158 3.32 0.00 0.00 3.36
861 2778 2.224066 GGGTGCTACGCATTAGACATCT 60.224 50.000 0.00 0.00 41.91 2.90
887 2804 4.883354 GCAGGCGGCTAGGGCAAT 62.883 66.667 12.74 0.00 40.87 3.56
925 2842 0.686112 GAGAGAGAGAGTGGGGGTGG 60.686 65.000 0.00 0.00 0.00 4.61
927 2844 0.629058 GAGAGAGAGAGAGTGGGGGT 59.371 60.000 0.00 0.00 0.00 4.95
928 2845 0.926293 AGAGAGAGAGAGAGTGGGGG 59.074 60.000 0.00 0.00 0.00 5.40
929 2846 1.846439 AGAGAGAGAGAGAGAGTGGGG 59.154 57.143 0.00 0.00 0.00 4.96
930 2847 2.774234 AGAGAGAGAGAGAGAGAGTGGG 59.226 54.545 0.00 0.00 0.00 4.61
931 2848 3.181461 GGAGAGAGAGAGAGAGAGAGTGG 60.181 56.522 0.00 0.00 0.00 4.00
932 2849 3.452264 TGGAGAGAGAGAGAGAGAGAGTG 59.548 52.174 0.00 0.00 0.00 3.51
933 2850 3.452627 GTGGAGAGAGAGAGAGAGAGAGT 59.547 52.174 0.00 0.00 0.00 3.24
934 2851 3.708631 AGTGGAGAGAGAGAGAGAGAGAG 59.291 52.174 0.00 0.00 0.00 3.20
935 2852 3.724478 AGTGGAGAGAGAGAGAGAGAGA 58.276 50.000 0.00 0.00 0.00 3.10
966 2883 2.352805 GCCTGTGAAGACCTGGGG 59.647 66.667 0.00 0.00 0.00 4.96
987 2904 0.179062 GATCCATCTCGCTGCAAGGT 60.179 55.000 0.00 0.00 0.00 3.50
1368 3301 1.486726 GGTGGTAGAGAATCCCACTGG 59.513 57.143 7.86 0.00 44.03 4.00
1422 3361 5.176406 CACGAGATGATATTCGCATTTGAGT 59.824 40.000 0.00 0.00 40.32 3.41
1440 3379 1.628340 ACCATGGGATCAAACACGAGA 59.372 47.619 18.09 0.00 0.00 4.04
1894 4063 7.753630 TGGGTGGTTTAATTACTTGGTACTTA 58.246 34.615 0.00 0.00 0.00 2.24
1895 4064 6.612741 TGGGTGGTTTAATTACTTGGTACTT 58.387 36.000 0.00 0.00 0.00 2.24
1896 4065 6.203526 TGGGTGGTTTAATTACTTGGTACT 57.796 37.500 0.00 0.00 0.00 2.73
1991 4160 9.683069 AATAAGACGAGACGTTTTAAAAGTAGA 57.317 29.630 0.00 0.00 41.37 2.59
2017 4472 2.445145 TGATTCCTCAAGGACCCAAACA 59.555 45.455 0.00 0.00 45.39 2.83
2207 4676 7.267857 CCAGAGTTCAACTCCAATTTCTTTTT 58.732 34.615 14.27 0.00 46.18 1.94
2366 4838 5.358725 TGCACATTGATACATGCAGAAAGAT 59.641 36.000 0.00 0.00 42.92 2.40
2414 4905 5.541484 AGCCAAGATCCTGAAACTTTGAATT 59.459 36.000 0.00 0.00 0.00 2.17
2452 4943 3.256136 CCCCCGATACTAGATGACAAGTC 59.744 52.174 0.00 0.00 0.00 3.01
2879 5376 1.868713 TATGTAACCAAGAGGGCGGA 58.131 50.000 0.00 0.00 42.05 5.54
2882 5379 3.316308 CAGCAATATGTAACCAAGAGGGC 59.684 47.826 0.00 0.00 42.05 5.19
2885 5382 7.383102 AGAAACAGCAATATGTAACCAAGAG 57.617 36.000 0.00 0.00 31.70 2.85
2894 5391 6.839124 TTGATTGGAGAAACAGCAATATGT 57.161 33.333 0.00 0.00 33.96 2.29
2962 5598 4.282496 AGTAACACAGTATAGGCAGAGCT 58.718 43.478 0.00 0.00 0.00 4.09
3068 5704 7.668525 TTTTTGTGGGACGTAAAAACATTTT 57.331 28.000 2.57 0.00 33.26 1.82
3118 5847 9.869757 AAATAAGCCAAAATTACATAACCAGAC 57.130 29.630 0.00 0.00 0.00 3.51
3204 5934 2.125753 CCAGTCAGCCTCGCTCAC 60.126 66.667 0.00 0.00 36.40 3.51
3326 7113 0.790814 CAGTTTCCCGAACTTCTCGC 59.209 55.000 0.00 0.00 46.34 5.03
3346 7133 1.038130 AGTCGCAAGCTACTCCCGAT 61.038 55.000 0.00 0.00 37.18 4.18
3466 8045 8.006298 TCCATCAATGCGAATTACCTTAAAAT 57.994 30.769 0.00 0.00 0.00 1.82
3481 8060 5.105997 GCCTATAGTTGGAATCCATCAATGC 60.106 44.000 12.40 2.74 31.53 3.56
3483 8062 6.044754 TCAGCCTATAGTTGGAATCCATCAAT 59.955 38.462 12.40 4.89 31.53 2.57
3484 8063 5.369404 TCAGCCTATAGTTGGAATCCATCAA 59.631 40.000 12.40 0.00 31.53 2.57
3486 8065 5.247110 TCTCAGCCTATAGTTGGAATCCATC 59.753 44.000 1.39 1.84 31.53 3.51
3487 8066 5.012561 GTCTCAGCCTATAGTTGGAATCCAT 59.987 44.000 1.39 0.00 31.53 3.41
3488 8067 4.345257 GTCTCAGCCTATAGTTGGAATCCA 59.655 45.833 0.00 0.00 0.00 3.41
3491 8070 5.463154 AGAGTCTCAGCCTATAGTTGGAAT 58.537 41.667 1.94 0.00 0.00 3.01
3492 8071 4.873010 AGAGTCTCAGCCTATAGTTGGAA 58.127 43.478 1.94 0.00 0.00 3.53
3493 8072 4.528076 AGAGTCTCAGCCTATAGTTGGA 57.472 45.455 1.94 0.00 0.00 3.53
3494 8073 4.646945 TCAAGAGTCTCAGCCTATAGTTGG 59.353 45.833 1.94 0.00 0.00 3.77
3496 8075 4.340950 GCTCAAGAGTCTCAGCCTATAGTT 59.659 45.833 11.48 0.00 0.00 2.24
3497 8076 3.888930 GCTCAAGAGTCTCAGCCTATAGT 59.111 47.826 11.48 0.00 0.00 2.12
3499 8078 3.903467 TGCTCAAGAGTCTCAGCCTATA 58.097 45.455 17.42 1.18 0.00 1.31
3500 8079 2.744760 TGCTCAAGAGTCTCAGCCTAT 58.255 47.619 17.42 0.00 0.00 2.57
3501 8080 2.222227 TGCTCAAGAGTCTCAGCCTA 57.778 50.000 17.42 2.06 0.00 3.93
3502 8081 1.207570 CATGCTCAAGAGTCTCAGCCT 59.792 52.381 17.42 8.28 0.00 4.58
3503 8082 1.066286 ACATGCTCAAGAGTCTCAGCC 60.066 52.381 17.42 4.80 0.00 4.85
3504 8083 2.383368 ACATGCTCAAGAGTCTCAGC 57.617 50.000 14.54 14.54 0.00 4.26
3506 8085 6.017934 GTGTTTTTACATGCTCAAGAGTCTCA 60.018 38.462 1.94 0.00 0.00 3.27
3507 8086 6.203723 AGTGTTTTTACATGCTCAAGAGTCTC 59.796 38.462 0.00 0.00 0.00 3.36
3508 8087 6.058183 AGTGTTTTTACATGCTCAAGAGTCT 58.942 36.000 0.00 0.00 0.00 3.24
3510 8089 6.318648 TCAAGTGTTTTTACATGCTCAAGAGT 59.681 34.615 0.00 0.00 0.00 3.24
3511 8090 6.728200 TCAAGTGTTTTTACATGCTCAAGAG 58.272 36.000 0.00 0.00 0.00 2.85
3512 8091 6.691754 TCAAGTGTTTTTACATGCTCAAGA 57.308 33.333 0.00 0.00 0.00 3.02
3513 8092 6.751425 TGTTCAAGTGTTTTTACATGCTCAAG 59.249 34.615 0.00 0.00 0.00 3.02
3515 8094 6.201226 TGTTCAAGTGTTTTTACATGCTCA 57.799 33.333 0.00 0.00 0.00 4.26
3516 8095 7.434897 TCAATGTTCAAGTGTTTTTACATGCTC 59.565 33.333 0.00 0.00 0.00 4.26
3517 8096 7.264221 TCAATGTTCAAGTGTTTTTACATGCT 58.736 30.769 0.00 0.00 0.00 3.79
3518 8097 7.434897 TCTCAATGTTCAAGTGTTTTTACATGC 59.565 33.333 0.00 0.00 0.00 4.06
3519 8098 8.854979 TCTCAATGTTCAAGTGTTTTTACATG 57.145 30.769 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.