Multiple sequence alignment - TraesCS6B01G359200

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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 TraesCS6B01G359200 chr6B 100.000 2648 0 0 1 2648 630539275 630541922 0.000000e+00 4891
1 TraesCS6B01G359200 chr6B 90.030 1003 61 17 1668 2648 630594516 630595501 0.000000e+00 1262
2 TraesCS6B01G359200 chr6B 89.365 677 60 5 996 1662 630593329 630594003 0.000000e+00 841
3 TraesCS6B01G359200 chr6B 96.996 233 7 0 3 235 41421640 41421872 2.470000e-105 392
4 TraesCS6B01G359200 chr6B 96.552 232 8 0 3 234 142781466 142781697 4.130000e-103 385
5 TraesCS6B01G359200 chr6B 82.759 464 33 25 553 1000 630592832 630593264 1.160000e-98 370
6 TraesCS6B01G359200 chr6B 88.462 286 19 4 2346 2617 630949100 630949385 1.520000e-87 333
7 TraesCS6B01G359200 chr6B 77.376 442 64 21 1672 2090 630916749 630917177 2.050000e-56 230
8 TraesCS6B01G359200 chr6B 90.840 131 8 2 2196 2326 630918962 630919088 3.500000e-39 172
9 TraesCS6B01G359200 chr6A 92.515 668 41 7 995 1662 560835003 560835661 0.000000e+00 948
10 TraesCS6B01G359200 chr6A 84.453 521 35 22 782 1282 560831286 560831780 3.090000e-129 472
11 TraesCS6B01G359200 chr6A 90.260 154 10 2 553 706 560834651 560834799 2.080000e-46 196
12 TraesCS6B01G359200 chr6A 84.324 185 21 4 2203 2383 562274219 562274039 9.740000e-40 174
13 TraesCS6B01G359200 chr6A 93.333 90 3 2 782 869 560834820 560834908 2.140000e-26 130
14 TraesCS6B01G359200 chr6D 90.776 683 51 6 996 1666 418625045 418625727 0.000000e+00 902
15 TraesCS6B01G359200 chr6D 89.096 697 49 7 996 1665 418302494 418301798 0.000000e+00 841
16 TraesCS6B01G359200 chr6D 94.953 317 14 2 553 869 418302905 418302591 1.830000e-136 496
17 TraesCS6B01G359200 chr6D 82.482 548 52 8 469 992 418624476 418625003 8.700000e-120 440
18 TraesCS6B01G359200 chr1A 97.479 238 6 0 1 238 86942482 86942719 8.820000e-110 407
19 TraesCS6B01G359200 chr1B 97.845 232 5 0 3 234 109484563 109484332 4.110000e-108 401
20 TraesCS6B01G359200 chr1B 97.414 232 6 0 1 232 661466024 661466255 1.910000e-106 396
21 TraesCS6B01G359200 chr3B 97.414 232 6 0 3 234 15806077 15806308 1.910000e-106 396
22 TraesCS6B01G359200 chrUn 97.021 235 6 1 1 234 359884203 359884437 6.870000e-106 394
23 TraesCS6B01G359200 chrUn 96.596 235 7 1 1 234 8595139 8594905 3.200000e-104 388
24 TraesCS6B01G359200 chr7B 95.671 231 10 0 4 234 199291834 199291604 3.220000e-99 372


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 TraesCS6B01G359200 chr6B 630539275 630541922 2647 False 4891.000000 4891 100.000000 1 2648 1 chr6B.!!$F3 2647
1 TraesCS6B01G359200 chr6B 630592832 630595501 2669 False 824.333333 1262 87.384667 553 2648 3 chr6B.!!$F5 2095
2 TraesCS6B01G359200 chr6B 630916749 630919088 2339 False 201.000000 230 84.108000 1672 2326 2 chr6B.!!$F6 654
3 TraesCS6B01G359200 chr6A 560831286 560835661 4375 False 436.500000 948 90.140250 553 1662 4 chr6A.!!$F1 1109
4 TraesCS6B01G359200 chr6D 418624476 418625727 1251 False 671.000000 902 86.629000 469 1666 2 chr6D.!!$F1 1197
5 TraesCS6B01G359200 chr6D 418301798 418302905 1107 True 668.500000 841 92.024500 553 1665 2 chr6D.!!$R1 1112

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
875 3695 0.034574 AATCATTGGGCTGCCACGTA 60.035 50.0 22.05 2.23 0.0 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 5301 0.250338 GGATGGCCACGGTAAGGATC 60.25 60.0 8.16 0.0 0.0 3.36 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
17 18 3.637714 GTCGAAGTTCTGCCGCAA 58.362 55.556 0.56 0.00 0.00 4.85
18 19 1.938861 GTCGAAGTTCTGCCGCAAA 59.061 52.632 0.56 0.00 0.00 3.68
19 20 0.110644 GTCGAAGTTCTGCCGCAAAG 60.111 55.000 0.56 0.00 0.00 2.77
20 21 0.249699 TCGAAGTTCTGCCGCAAAGA 60.250 50.000 0.56 0.00 0.00 2.52
21 22 0.586319 CGAAGTTCTGCCGCAAAGAA 59.414 50.000 0.56 0.00 0.00 2.52
22 23 1.197721 CGAAGTTCTGCCGCAAAGAAT 59.802 47.619 0.56 0.00 36.14 2.40
23 24 2.350772 CGAAGTTCTGCCGCAAAGAATT 60.351 45.455 0.56 0.00 36.14 2.17
24 25 3.642705 GAAGTTCTGCCGCAAAGAATTT 58.357 40.909 0.00 0.00 40.26 1.82
25 26 3.733443 AGTTCTGCCGCAAAGAATTTT 57.267 38.095 0.00 0.00 35.03 1.82
26 27 4.058721 AGTTCTGCCGCAAAGAATTTTT 57.941 36.364 0.00 0.00 35.03 1.94
63 64 2.664402 ATAAATGGGCTGGCCTAGTG 57.336 50.000 21.72 0.00 36.10 2.74
64 65 0.106719 TAAATGGGCTGGCCTAGTGC 60.107 55.000 21.72 2.98 40.16 4.40
65 66 3.704231 AATGGGCTGGCCTAGTGCG 62.704 63.158 21.72 0.00 42.61 5.34
69 70 4.537433 GCTGGCCTAGTGCGGAGG 62.537 72.222 3.32 0.00 42.61 4.30
70 71 2.759973 CTGGCCTAGTGCGGAGGA 60.760 66.667 3.32 0.00 42.61 3.71
84 85 3.959991 GAGGACGGTGCTCCTTGGC 62.960 68.421 17.78 0.00 41.11 4.52
86 87 4.329545 GACGGTGCTCCTTGGCCA 62.330 66.667 0.00 0.00 0.00 5.36
87 88 3.842925 GACGGTGCTCCTTGGCCAA 62.843 63.158 19.25 19.25 0.00 4.52
88 89 3.365265 CGGTGCTCCTTGGCCAAC 61.365 66.667 16.05 5.34 0.00 3.77
98 99 3.899371 TGGCCAACCAGCTAGACA 58.101 55.556 0.61 0.00 42.67 3.41
100 101 0.476338 TGGCCAACCAGCTAGACAAA 59.524 50.000 0.61 0.00 42.67 2.83
102 103 1.745653 GGCCAACCAGCTAGACAAATC 59.254 52.381 0.00 0.00 35.26 2.17
108 109 1.065418 CCAGCTAGACAAATCCCGGTT 60.065 52.381 0.00 0.00 0.00 4.44
109 110 2.009774 CAGCTAGACAAATCCCGGTTG 58.990 52.381 0.00 0.36 0.00 3.77
113 114 3.694566 GCTAGACAAATCCCGGTTGAAAT 59.305 43.478 10.04 0.00 0.00 2.17
115 116 5.531287 GCTAGACAAATCCCGGTTGAAATAT 59.469 40.000 10.04 0.00 0.00 1.28
116 117 5.835113 AGACAAATCCCGGTTGAAATATG 57.165 39.130 10.04 0.00 0.00 1.78
117 118 5.261216 AGACAAATCCCGGTTGAAATATGT 58.739 37.500 10.04 0.00 0.00 2.29
118 119 5.357032 AGACAAATCCCGGTTGAAATATGTC 59.643 40.000 10.04 8.36 35.03 3.06
119 120 5.013547 ACAAATCCCGGTTGAAATATGTCA 58.986 37.500 10.04 0.00 0.00 3.58
120 121 5.478679 ACAAATCCCGGTTGAAATATGTCAA 59.521 36.000 10.04 4.07 35.14 3.18
121 122 5.835113 AATCCCGGTTGAAATATGTCAAG 57.165 39.130 8.66 0.00 38.17 3.02
122 123 3.616219 TCCCGGTTGAAATATGTCAAGG 58.384 45.455 8.66 7.62 38.17 3.61
123 124 3.009695 TCCCGGTTGAAATATGTCAAGGT 59.990 43.478 8.66 0.00 38.17 3.50
128 129 6.350110 CCGGTTGAAATATGTCAAGGTTTGAT 60.350 38.462 8.66 0.00 42.47 2.57
129 130 7.090173 CGGTTGAAATATGTCAAGGTTTGATT 58.910 34.615 8.66 0.00 42.47 2.57
130 131 7.598493 CGGTTGAAATATGTCAAGGTTTGATTT 59.402 33.333 8.66 0.00 42.47 2.17
131 132 9.921637 GGTTGAAATATGTCAAGGTTTGATTTA 57.078 29.630 8.66 0.00 42.47 1.40
135 136 9.788960 GAAATATGTCAAGGTTTGATTTAGACC 57.211 33.333 0.00 0.00 42.47 3.85
136 137 5.880054 ATGTCAAGGTTTGATTTAGACCG 57.120 39.130 0.00 0.00 42.47 4.79
137 138 4.069304 TGTCAAGGTTTGATTTAGACCGG 58.931 43.478 0.00 0.00 42.47 5.28
138 139 3.439129 GTCAAGGTTTGATTTAGACCGGG 59.561 47.826 6.32 0.00 42.47 5.73
139 140 3.328343 TCAAGGTTTGATTTAGACCGGGA 59.672 43.478 6.32 0.00 38.48 5.14
140 141 4.018779 TCAAGGTTTGATTTAGACCGGGAT 60.019 41.667 6.32 0.00 38.48 3.85
141 142 4.586306 AGGTTTGATTTAGACCGGGATT 57.414 40.909 6.32 0.00 38.48 3.01
142 143 4.270008 AGGTTTGATTTAGACCGGGATTG 58.730 43.478 6.32 0.00 38.48 2.67
144 145 3.358111 TTGATTTAGACCGGGATTGCA 57.642 42.857 6.32 0.00 0.00 4.08
145 146 3.576078 TGATTTAGACCGGGATTGCAT 57.424 42.857 6.32 0.00 0.00 3.96
146 147 4.698201 TGATTTAGACCGGGATTGCATA 57.302 40.909 6.32 0.00 0.00 3.14
147 148 4.641396 TGATTTAGACCGGGATTGCATAG 58.359 43.478 6.32 0.00 0.00 2.23
148 149 4.102524 TGATTTAGACCGGGATTGCATAGT 59.897 41.667 6.32 0.00 0.00 2.12
149 150 4.497291 TTTAGACCGGGATTGCATAGTT 57.503 40.909 6.32 0.00 0.00 2.24
151 152 1.837439 AGACCGGGATTGCATAGTTCA 59.163 47.619 6.32 0.00 0.00 3.18
152 153 2.158900 AGACCGGGATTGCATAGTTCAG 60.159 50.000 6.32 0.00 0.00 3.02
154 155 2.158900 ACCGGGATTGCATAGTTCAGAG 60.159 50.000 6.32 0.00 0.00 3.35
155 156 2.158900 CCGGGATTGCATAGTTCAGAGT 60.159 50.000 0.00 0.00 0.00 3.24
156 157 2.868583 CGGGATTGCATAGTTCAGAGTG 59.131 50.000 0.00 0.00 0.00 3.51
157 158 2.615912 GGGATTGCATAGTTCAGAGTGC 59.384 50.000 0.00 0.00 38.05 4.40
158 159 3.273434 GGATTGCATAGTTCAGAGTGCA 58.727 45.455 0.00 0.00 44.97 4.57
163 164 3.190079 GCATAGTTCAGAGTGCAATCGA 58.810 45.455 8.74 6.56 37.52 3.59
165 166 2.086054 AGTTCAGAGTGCAATCGACC 57.914 50.000 8.74 2.25 0.00 4.79
166 167 0.716108 GTTCAGAGTGCAATCGACCG 59.284 55.000 8.74 0.00 0.00 4.79
167 168 0.389817 TTCAGAGTGCAATCGACCGG 60.390 55.000 8.74 0.00 0.00 5.28
168 169 1.811266 CAGAGTGCAATCGACCGGG 60.811 63.158 8.74 0.00 0.00 5.73
169 170 1.982395 AGAGTGCAATCGACCGGGA 60.982 57.895 8.74 0.00 0.00 5.14
172 173 0.035439 AGTGCAATCGACCGGGATTT 60.035 50.000 6.32 0.00 34.50 2.17
174 175 1.087202 TGCAATCGACCGGGATTTCG 61.087 55.000 6.32 6.06 34.50 3.46
176 177 0.928229 CAATCGACCGGGATTTCGAC 59.072 55.000 16.08 0.00 46.41 4.20
177 178 0.822164 AATCGACCGGGATTTCGACT 59.178 50.000 16.08 3.70 46.41 4.18
178 179 0.822164 ATCGACCGGGATTTCGACTT 59.178 50.000 16.08 0.20 46.41 3.01
179 180 0.108992 TCGACCGGGATTTCGACTTG 60.109 55.000 10.52 0.00 39.29 3.16
180 181 1.082117 CGACCGGGATTTCGACTTGG 61.082 60.000 6.32 0.00 37.43 3.61
181 182 0.743345 GACCGGGATTTCGACTTGGG 60.743 60.000 6.32 0.00 0.00 4.12
182 183 1.451387 CCGGGATTTCGACTTGGGG 60.451 63.158 0.00 0.00 0.00 4.96
183 184 1.451387 CGGGATTTCGACTTGGGGG 60.451 63.158 0.00 0.00 0.00 5.40
184 185 1.689412 GGGATTTCGACTTGGGGGT 59.311 57.895 0.00 0.00 0.00 4.95
185 186 0.039180 GGGATTTCGACTTGGGGGTT 59.961 55.000 0.00 0.00 0.00 4.11
186 187 1.460504 GGATTTCGACTTGGGGGTTC 58.539 55.000 0.00 0.00 0.00 3.62
187 188 1.084289 GATTTCGACTTGGGGGTTCG 58.916 55.000 0.00 0.00 0.00 3.95
188 189 0.399075 ATTTCGACTTGGGGGTTCGT 59.601 50.000 0.00 0.00 0.00 3.85
190 191 0.180878 TTCGACTTGGGGGTTCGTTT 59.819 50.000 0.00 0.00 0.00 3.60
195 196 4.992511 TGGGGGTTCGTTTCGCCG 62.993 66.667 0.00 0.00 38.63 6.46
196 197 4.685467 GGGGGTTCGTTTCGCCGA 62.685 66.667 0.00 0.00 38.54 5.54
197 198 2.665854 GGGGTTCGTTTCGCCGAA 60.666 61.111 0.00 0.00 43.96 4.30
203 204 4.135570 CGTTTCGCCGAACGTCTA 57.864 55.556 0.00 0.00 45.32 2.59
204 205 1.692729 CGTTTCGCCGAACGTCTAC 59.307 57.895 0.00 0.00 45.32 2.59
205 206 1.692729 GTTTCGCCGAACGTCTACG 59.307 57.895 0.00 0.04 44.19 3.51
206 207 0.725784 GTTTCGCCGAACGTCTACGA 60.726 55.000 9.86 5.31 44.19 3.43
209 210 1.154338 CGCCGAACGTCTACGAGTT 60.154 57.895 9.86 0.00 43.02 3.01
210 211 1.124702 CGCCGAACGTCTACGAGTTC 61.125 60.000 9.86 2.88 43.02 3.01
211 212 0.110056 GCCGAACGTCTACGAGTTCA 60.110 55.000 9.86 0.00 44.94 3.18
214 215 1.465354 CGAACGTCTACGAGTTCAGGG 60.465 57.143 9.86 0.00 44.94 4.45
215 216 1.538950 GAACGTCTACGAGTTCAGGGT 59.461 52.381 9.86 0.00 44.32 4.34
216 217 1.613836 ACGTCTACGAGTTCAGGGTT 58.386 50.000 9.86 0.00 43.02 4.11
217 218 1.959282 ACGTCTACGAGTTCAGGGTTT 59.041 47.619 9.86 0.00 43.02 3.27
218 219 3.149196 ACGTCTACGAGTTCAGGGTTTA 58.851 45.455 9.86 0.00 43.02 2.01
219 220 3.569701 ACGTCTACGAGTTCAGGGTTTAA 59.430 43.478 9.86 0.00 43.02 1.52
220 221 4.037923 ACGTCTACGAGTTCAGGGTTTAAA 59.962 41.667 9.86 0.00 43.02 1.52
221 222 4.984161 CGTCTACGAGTTCAGGGTTTAAAA 59.016 41.667 0.00 0.00 43.02 1.52
222 223 5.636543 CGTCTACGAGTTCAGGGTTTAAAAT 59.363 40.000 0.00 0.00 43.02 1.82
223 224 6.400727 CGTCTACGAGTTCAGGGTTTAAAATG 60.401 42.308 0.00 0.00 43.02 2.32
224 225 5.935789 TCTACGAGTTCAGGGTTTAAAATGG 59.064 40.000 0.00 0.00 0.00 3.16
225 226 4.721132 ACGAGTTCAGGGTTTAAAATGGA 58.279 39.130 0.00 0.00 0.00 3.41
229 230 6.238925 CGAGTTCAGGGTTTAAAATGGACTTT 60.239 38.462 10.18 0.00 31.56 2.66
230 231 7.432148 AGTTCAGGGTTTAAAATGGACTTTT 57.568 32.000 5.00 0.00 40.21 2.27
231 232 7.857456 AGTTCAGGGTTTAAAATGGACTTTTT 58.143 30.769 5.00 2.24 38.09 1.94
232 233 7.985184 AGTTCAGGGTTTAAAATGGACTTTTTC 59.015 33.333 5.00 0.00 38.09 2.29
385 386 9.518906 TTTAGGGAAAAGAACGTAAAATTGAAC 57.481 29.630 0.00 0.00 0.00 3.18
386 387 7.102847 AGGGAAAAGAACGTAAAATTGAACA 57.897 32.000 0.00 0.00 0.00 3.18
387 388 7.722363 AGGGAAAAGAACGTAAAATTGAACAT 58.278 30.769 0.00 0.00 0.00 2.71
388 389 8.852135 AGGGAAAAGAACGTAAAATTGAACATA 58.148 29.630 0.00 0.00 0.00 2.29
390 391 9.887406 GGAAAAGAACGTAAAATTGAACATAGA 57.113 29.630 0.00 0.00 0.00 1.98
416 417 8.549338 ACTAATAGAGCAGTAAGAAAACAACC 57.451 34.615 0.00 0.00 0.00 3.77
420 421 3.222603 AGCAGTAAGAAAACAACCCTGG 58.777 45.455 0.00 0.00 0.00 4.45
421 422 3.117663 AGCAGTAAGAAAACAACCCTGGA 60.118 43.478 0.00 0.00 0.00 3.86
422 423 3.634910 GCAGTAAGAAAACAACCCTGGAA 59.365 43.478 0.00 0.00 0.00 3.53
423 424 4.098807 GCAGTAAGAAAACAACCCTGGAAA 59.901 41.667 0.00 0.00 0.00 3.13
424 425 5.394773 GCAGTAAGAAAACAACCCTGGAAAA 60.395 40.000 0.00 0.00 0.00 2.29
425 426 6.635755 CAGTAAGAAAACAACCCTGGAAAAA 58.364 36.000 0.00 0.00 0.00 1.94
450 451 8.432110 AACAGACACAAAAATTAAATGGAACC 57.568 30.769 0.00 0.00 0.00 3.62
451 452 6.699642 ACAGACACAAAAATTAAATGGAACCG 59.300 34.615 0.00 0.00 0.00 4.44
452 453 6.145371 CAGACACAAAAATTAAATGGAACCGG 59.855 38.462 0.00 0.00 0.00 5.28
453 454 6.041069 AGACACAAAAATTAAATGGAACCGGA 59.959 34.615 9.46 0.00 0.00 5.14
454 455 6.583562 ACACAAAAATTAAATGGAACCGGAA 58.416 32.000 9.46 0.00 0.00 4.30
456 457 6.480320 CACAAAAATTAAATGGAACCGGAACA 59.520 34.615 9.46 3.83 0.00 3.18
457 458 7.011482 CACAAAAATTAAATGGAACCGGAACAA 59.989 33.333 9.46 0.00 0.00 2.83
458 459 7.011576 ACAAAAATTAAATGGAACCGGAACAAC 59.988 33.333 9.46 0.00 0.00 3.32
459 460 5.793030 AATTAAATGGAACCGGAACAACA 57.207 34.783 9.46 0.00 0.00 3.33
460 461 5.793030 ATTAAATGGAACCGGAACAACAA 57.207 34.783 9.46 0.50 0.00 2.83
461 462 5.593679 TTAAATGGAACCGGAACAACAAA 57.406 34.783 9.46 0.00 0.00 2.83
462 463 4.473477 AAATGGAACCGGAACAACAAAA 57.527 36.364 9.46 0.00 0.00 2.44
466 467 1.132834 GAACCGGAACAACAAAACCGT 59.867 47.619 9.46 0.00 43.22 4.83
497 498 1.605500 CGTCAAATTGCCACATCGTG 58.394 50.000 0.00 0.00 0.00 4.35
541 542 2.264813 CATCGCCAAGCAAAAATCCTG 58.735 47.619 0.00 0.00 0.00 3.86
630 3444 1.579084 GGTGTTTGGTAATCGCGGCA 61.579 55.000 6.13 0.00 0.00 5.69
698 3512 2.278206 CATCGTCCTCGCCGTCAG 60.278 66.667 0.00 0.00 36.96 3.51
874 3694 1.304381 AATCATTGGGCTGCCACGT 60.304 52.632 22.05 1.73 0.00 4.49
875 3695 0.034574 AATCATTGGGCTGCCACGTA 60.035 50.000 22.05 2.23 0.00 3.57
876 3696 0.464373 ATCATTGGGCTGCCACGTAG 60.464 55.000 22.05 6.04 0.00 3.51
877 3697 2.438434 ATTGGGCTGCCACGTAGC 60.438 61.111 22.05 0.00 40.44 3.58
901 3725 5.034797 CAGTTCCGGTCAAAAACTCTTTTC 58.965 41.667 0.00 0.00 32.24 2.29
905 3729 3.796717 CCGGTCAAAAACTCTTTTCTTGC 59.203 43.478 0.00 0.00 32.24 4.01
914 3738 2.291741 ACTCTTTTCTTGCGCAGGAAAG 59.708 45.455 35.82 29.41 46.43 2.62
919 3743 1.211190 CTTGCGCAGGAAAGAAGGC 59.789 57.895 15.39 0.00 37.43 4.35
923 3747 2.335712 CGCAGGAAAGAAGGCCACC 61.336 63.158 5.01 0.00 0.00 4.61
939 3763 0.389426 CACCCTTACGGACCTGTTCG 60.389 60.000 0.00 0.00 34.64 3.95
992 3829 2.514592 AATCACATCCGGCGCCAG 60.515 61.111 28.98 16.96 0.00 4.85
1141 4068 3.179265 CCGCGGCTGACAGTAACG 61.179 66.667 14.67 7.99 0.00 3.18
1145 4072 2.813908 GGCTGACAGTAACGGCGG 60.814 66.667 13.24 0.00 40.14 6.13
1204 4131 2.977178 CGCAGCTCCCTCTGAAGT 59.023 61.111 0.00 0.00 36.19 3.01
1559 4503 4.479993 GCTGTGCTGGGCTCCGAT 62.480 66.667 0.00 0.00 0.00 4.18
1662 4606 4.824166 TAAGCGCGCGAGGTCGTC 62.824 66.667 37.18 14.25 42.22 4.20
1666 4610 4.462417 CGCGCGAGGTCGTCTCTT 62.462 66.667 28.94 0.00 40.30 2.85
1667 4611 2.789917 GCGCGAGGTCGTCTCTTA 59.210 61.111 12.10 0.00 40.30 2.10
1668 4612 1.297745 GCGCGAGGTCGTCTCTTAG 60.298 63.158 12.10 0.00 40.30 2.18
1670 4614 0.026544 CGCGAGGTCGTCTCTTAGTC 59.973 60.000 0.00 0.00 40.30 2.59
1696 5148 2.832838 TGAATGGTGAGCTTCCTAGGA 58.167 47.619 7.62 7.62 0.00 2.94
1715 5167 2.544267 GGAAGTGTAATGCAGTATCCGC 59.456 50.000 0.00 0.00 0.00 5.54
1720 5172 2.296190 TGTAATGCAGTATCCGCTCGAT 59.704 45.455 0.00 0.00 34.73 3.59
1723 5175 0.030773 TGCAGTATCCGCTCGATCAC 59.969 55.000 0.00 0.00 31.92 3.06
1745 5197 2.034066 CCCGCAACATGACCACCT 59.966 61.111 0.00 0.00 0.00 4.00
1802 5254 7.959658 TCACAGGTATGAATGGAAAATGAAT 57.040 32.000 0.00 0.00 0.00 2.57
1813 5265 5.549742 TGGAAAATGAATGCAAAGACCTT 57.450 34.783 0.00 0.00 0.00 3.50
1846 5298 3.978610 AGAATACGGACTACCAAGACCT 58.021 45.455 0.00 0.00 35.64 3.85
1847 5299 3.952967 AGAATACGGACTACCAAGACCTC 59.047 47.826 0.00 0.00 35.64 3.85
1848 5300 2.134789 TACGGACTACCAAGACCTCC 57.865 55.000 0.00 0.00 35.64 4.30
1849 5301 1.807886 CGGACTACCAAGACCTCCG 59.192 63.158 0.00 0.00 38.12 4.63
1850 5302 0.679002 CGGACTACCAAGACCTCCGA 60.679 60.000 0.00 0.00 45.58 4.55
1851 5303 1.777941 GGACTACCAAGACCTCCGAT 58.222 55.000 0.00 0.00 35.02 4.18
1852 5304 1.682323 GGACTACCAAGACCTCCGATC 59.318 57.143 0.00 0.00 35.02 3.69
1853 5305 1.682323 GACTACCAAGACCTCCGATCC 59.318 57.143 0.00 0.00 0.00 3.36
1856 5308 2.544844 ACCAAGACCTCCGATCCTTA 57.455 50.000 0.00 0.00 0.00 2.69
1878 5330 1.609061 CGTGGCCATCCCTATGATCAC 60.609 57.143 9.72 0.00 34.84 3.06
1925 5381 7.442666 TCCACGCATAAAATATAGCATGTACAA 59.557 33.333 0.00 0.00 0.00 2.41
2061 5535 5.925506 TCCGAGTAAAACATCACCATCTA 57.074 39.130 0.00 0.00 0.00 1.98
2120 5600 7.719871 TGGCCATTACCTATCTCTTATACTC 57.280 40.000 0.00 0.00 0.00 2.59
2121 5601 6.668283 TGGCCATTACCTATCTCTTATACTCC 59.332 42.308 0.00 0.00 0.00 3.85
2122 5602 6.898521 GGCCATTACCTATCTCTTATACTCCT 59.101 42.308 0.00 0.00 0.00 3.69
2123 5603 8.060075 GGCCATTACCTATCTCTTATACTCCTA 58.940 40.741 0.00 0.00 0.00 2.94
2183 7360 5.164954 GGATTAAAGCGTAAAACATGGCAA 58.835 37.500 0.00 0.00 0.00 4.52
2194 7371 0.178975 ACATGGCAAAAACGGGGAGA 60.179 50.000 0.00 0.00 0.00 3.71
2236 7413 2.280592 GACCACGGCTGGACGTTT 60.281 61.111 0.00 0.00 46.25 3.60
2254 7431 3.784488 GTTTGTCAGTTAACGAGCTTCG 58.216 45.455 0.00 0.00 46.93 3.79
2321 7498 2.028930 ACTAAGCAGCTCAACTACGCTT 60.029 45.455 9.75 9.75 44.61 4.68
2342 7519 6.183359 CGCTTGTACGTACAAACTAGAGAAAG 60.183 42.308 33.77 22.05 44.67 2.62
2343 7520 6.089150 GCTTGTACGTACAAACTAGAGAAAGG 59.911 42.308 33.77 21.35 44.67 3.11
2356 7533 5.720520 ACTAGAGAAAGGGACGGACTAAAAT 59.279 40.000 0.00 0.00 0.00 1.82
2358 7535 4.530946 AGAGAAAGGGACGGACTAAAATGA 59.469 41.667 0.00 0.00 0.00 2.57
2378 7555 8.712228 AAATGACCTTCTTTGATTCTTACCTT 57.288 30.769 0.00 0.00 0.00 3.50
2380 7557 7.510549 TGACCTTCTTTGATTCTTACCTTTG 57.489 36.000 0.00 0.00 0.00 2.77
2382 7559 5.243954 ACCTTCTTTGATTCTTACCTTTGCC 59.756 40.000 0.00 0.00 0.00 4.52
2383 7560 5.336770 CCTTCTTTGATTCTTACCTTTGCCC 60.337 44.000 0.00 0.00 0.00 5.36
2384 7561 4.735369 TCTTTGATTCTTACCTTTGCCCA 58.265 39.130 0.00 0.00 0.00 5.36
2421 7602 3.769300 ACTTGTTTTGAGCTTTGGGTTCT 59.231 39.130 0.00 0.00 0.00 3.01
2430 7611 3.535561 AGCTTTGGGTTCTGATGTATCG 58.464 45.455 0.00 0.00 0.00 2.92
2437 7618 3.063997 GGGTTCTGATGTATCGCACAAAG 59.936 47.826 0.00 0.00 41.55 2.77
2438 7619 3.063997 GGTTCTGATGTATCGCACAAAGG 59.936 47.826 0.00 0.00 41.55 3.11
2439 7620 3.610040 TCTGATGTATCGCACAAAGGT 57.390 42.857 0.00 0.00 41.55 3.50
2440 7621 3.521560 TCTGATGTATCGCACAAAGGTC 58.478 45.455 0.00 0.00 41.55 3.85
2450 7632 2.416547 CGCACAAAGGTCCAGAGTTATG 59.583 50.000 0.00 0.00 0.00 1.90
2454 7636 5.221244 GCACAAAGGTCCAGAGTTATGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
2458 7640 6.884280 AAGGTCCAGAGTTATGTTTTCTTG 57.116 37.500 0.00 0.00 0.00 3.02
2489 7684 2.254546 TTATGATGTGCACCGGATCC 57.745 50.000 15.69 0.00 0.00 3.36
2568 7763 2.555199 CCAAGTCCAATGACCTCGATC 58.445 52.381 0.00 0.00 42.81 3.69
2575 7770 5.129485 AGTCCAATGACCTCGATCTGTAAAT 59.871 40.000 0.00 0.00 42.81 1.40
2577 7772 5.817296 TCCAATGACCTCGATCTGTAAATTG 59.183 40.000 0.00 0.00 0.00 2.32
2605 7800 3.753272 GAGAGCAGTGCTTGGTTAATTGA 59.247 43.478 20.80 0.00 39.88 2.57
2640 7835 9.950680 CAAGTGAAACATAAGATTACAACTGTT 57.049 29.630 0.00 0.00 41.43 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.110644 CTTTGCGGCAGAACTTCGAC 60.111 55.000 1.67 0.00 0.00 4.20
1 2 0.249699 TCTTTGCGGCAGAACTTCGA 60.250 50.000 1.67 0.00 0.00 3.71
2 3 0.586319 TTCTTTGCGGCAGAACTTCG 59.414 50.000 1.67 0.00 0.00 3.79
3 4 2.997485 ATTCTTTGCGGCAGAACTTC 57.003 45.000 1.67 0.00 33.04 3.01
4 5 3.733443 AAATTCTTTGCGGCAGAACTT 57.267 38.095 1.67 0.00 33.04 2.66
41 42 3.706086 CACTAGGCCAGCCCATTTATTTT 59.294 43.478 5.01 0.00 36.58 1.82
43 44 2.949447 CACTAGGCCAGCCCATTTATT 58.051 47.619 5.01 0.00 36.58 1.40
44 45 1.479389 GCACTAGGCCAGCCCATTTAT 60.479 52.381 5.01 0.00 36.58 1.40
46 47 1.380380 GCACTAGGCCAGCCCATTT 60.380 57.895 5.01 0.00 36.58 2.32
48 49 4.181010 CGCACTAGGCCAGCCCAT 62.181 66.667 5.01 0.00 40.31 4.00
52 53 4.537433 CCTCCGCACTAGGCCAGC 62.537 72.222 5.01 1.94 40.31 4.85
53 54 2.759973 TCCTCCGCACTAGGCCAG 60.760 66.667 5.01 2.64 40.31 4.85
54 55 3.075005 GTCCTCCGCACTAGGCCA 61.075 66.667 5.01 0.00 40.31 5.36
55 56 4.208686 CGTCCTCCGCACTAGGCC 62.209 72.222 0.00 0.00 40.31 5.19
56 57 4.208686 CCGTCCTCCGCACTAGGC 62.209 72.222 0.00 0.00 39.90 3.93
57 58 2.754658 ACCGTCCTCCGCACTAGG 60.755 66.667 0.00 0.00 35.26 3.02
58 59 2.490217 CACCGTCCTCCGCACTAG 59.510 66.667 0.00 0.00 34.38 2.57
59 60 3.755628 GCACCGTCCTCCGCACTA 61.756 66.667 0.00 0.00 34.38 2.74
69 70 3.842925 TTGGCCAAGGAGCACCGTC 62.843 63.158 16.05 0.00 41.83 4.79
70 71 3.884774 TTGGCCAAGGAGCACCGT 61.885 61.111 16.05 0.00 41.83 4.83
71 72 3.365265 GTTGGCCAAGGAGCACCG 61.365 66.667 21.21 0.00 41.83 4.94
72 73 2.991540 GGTTGGCCAAGGAGCACC 60.992 66.667 21.21 12.92 34.09 5.01
73 74 2.203480 TGGTTGGCCAAGGAGCAC 60.203 61.111 21.21 6.41 42.83 4.40
74 75 2.115910 CTGGTTGGCCAAGGAGCA 59.884 61.111 21.21 13.33 45.51 4.26
75 76 2.484287 TAGCTGGTTGGCCAAGGAGC 62.484 60.000 29.62 29.62 45.51 4.70
76 77 0.393537 CTAGCTGGTTGGCCAAGGAG 60.394 60.000 21.21 18.25 45.51 3.69
77 78 0.840288 TCTAGCTGGTTGGCCAAGGA 60.840 55.000 21.21 7.36 45.51 3.36
78 79 0.678048 GTCTAGCTGGTTGGCCAAGG 60.678 60.000 21.21 13.30 45.51 3.61
80 81 0.476338 TTGTCTAGCTGGTTGGCCAA 59.524 50.000 16.05 16.05 45.51 4.52
82 83 1.745653 GATTTGTCTAGCTGGTTGGCC 59.254 52.381 0.00 0.00 0.00 5.36
84 85 2.369394 GGGATTTGTCTAGCTGGTTGG 58.631 52.381 0.00 0.00 0.00 3.77
85 86 2.009774 CGGGATTTGTCTAGCTGGTTG 58.990 52.381 0.00 0.00 0.00 3.77
86 87 1.065418 CCGGGATTTGTCTAGCTGGTT 60.065 52.381 0.00 0.00 0.00 3.67
87 88 0.541863 CCGGGATTTGTCTAGCTGGT 59.458 55.000 0.00 0.00 0.00 4.00
88 89 0.541863 ACCGGGATTTGTCTAGCTGG 59.458 55.000 6.32 0.00 0.00 4.85
90 91 1.906574 TCAACCGGGATTTGTCTAGCT 59.093 47.619 6.32 0.00 0.00 3.32
91 92 2.396590 TCAACCGGGATTTGTCTAGC 57.603 50.000 6.32 0.00 0.00 3.42
93 94 6.419791 ACATATTTCAACCGGGATTTGTCTA 58.580 36.000 6.32 0.00 0.00 2.59
94 95 5.261216 ACATATTTCAACCGGGATTTGTCT 58.739 37.500 6.32 0.00 0.00 3.41
95 96 5.124776 TGACATATTTCAACCGGGATTTGTC 59.875 40.000 6.32 12.13 0.00 3.18
98 99 5.127031 CCTTGACATATTTCAACCGGGATTT 59.873 40.000 6.32 0.00 32.02 2.17
100 101 4.207165 CCTTGACATATTTCAACCGGGAT 58.793 43.478 6.32 0.00 32.02 3.85
102 103 3.352648 ACCTTGACATATTTCAACCGGG 58.647 45.455 6.32 9.57 32.02 5.73
109 110 9.788960 GGTCTAAATCAAACCTTGACATATTTC 57.211 33.333 0.00 0.00 43.48 2.17
113 114 5.878116 CCGGTCTAAATCAAACCTTGACATA 59.122 40.000 0.00 0.00 43.48 2.29
115 116 4.069304 CCGGTCTAAATCAAACCTTGACA 58.931 43.478 0.00 0.00 43.48 3.58
116 117 3.439129 CCCGGTCTAAATCAAACCTTGAC 59.561 47.826 0.00 0.00 43.48 3.18
117 118 3.328343 TCCCGGTCTAAATCAAACCTTGA 59.672 43.478 0.00 0.00 45.01 3.02
118 119 3.681593 TCCCGGTCTAAATCAAACCTTG 58.318 45.455 0.00 0.00 0.00 3.61
119 120 4.586306 ATCCCGGTCTAAATCAAACCTT 57.414 40.909 0.00 0.00 0.00 3.50
120 121 4.270008 CAATCCCGGTCTAAATCAAACCT 58.730 43.478 0.00 0.00 0.00 3.50
121 122 3.181490 GCAATCCCGGTCTAAATCAAACC 60.181 47.826 0.00 0.00 0.00 3.27
122 123 3.442273 TGCAATCCCGGTCTAAATCAAAC 59.558 43.478 0.00 0.00 0.00 2.93
123 124 3.691575 TGCAATCCCGGTCTAAATCAAA 58.308 40.909 0.00 0.00 0.00 2.69
128 129 4.080807 TGAACTATGCAATCCCGGTCTAAA 60.081 41.667 0.00 0.00 0.00 1.85
129 130 3.452990 TGAACTATGCAATCCCGGTCTAA 59.547 43.478 0.00 0.00 0.00 2.10
130 131 3.035363 TGAACTATGCAATCCCGGTCTA 58.965 45.455 0.00 0.00 0.00 2.59
131 132 1.837439 TGAACTATGCAATCCCGGTCT 59.163 47.619 0.00 0.00 0.00 3.85
134 135 2.158900 ACTCTGAACTATGCAATCCCGG 60.159 50.000 0.00 0.00 0.00 5.73
135 136 2.868583 CACTCTGAACTATGCAATCCCG 59.131 50.000 0.00 0.00 0.00 5.14
136 137 2.615912 GCACTCTGAACTATGCAATCCC 59.384 50.000 0.00 0.00 38.00 3.85
137 138 3.273434 TGCACTCTGAACTATGCAATCC 58.727 45.455 0.00 0.00 44.72 3.01
141 142 2.931969 CGATTGCACTCTGAACTATGCA 59.068 45.455 2.32 0.00 45.94 3.96
142 143 3.000724 GTCGATTGCACTCTGAACTATGC 59.999 47.826 2.32 0.00 38.59 3.14
144 145 3.735208 CGGTCGATTGCACTCTGAACTAT 60.735 47.826 2.32 0.00 0.00 2.12
145 146 2.415491 CGGTCGATTGCACTCTGAACTA 60.415 50.000 2.32 0.00 0.00 2.24
146 147 1.670087 CGGTCGATTGCACTCTGAACT 60.670 52.381 2.32 0.00 0.00 3.01
147 148 0.716108 CGGTCGATTGCACTCTGAAC 59.284 55.000 2.32 3.67 0.00 3.18
148 149 0.389817 CCGGTCGATTGCACTCTGAA 60.390 55.000 2.32 0.00 0.00 3.02
149 150 1.215382 CCGGTCGATTGCACTCTGA 59.785 57.895 2.32 0.00 0.00 3.27
151 152 1.330655 ATCCCGGTCGATTGCACTCT 61.331 55.000 0.00 0.00 0.00 3.24
152 153 0.462047 AATCCCGGTCGATTGCACTC 60.462 55.000 0.00 0.00 31.19 3.51
154 155 0.377203 GAAATCCCGGTCGATTGCAC 59.623 55.000 6.70 0.16 32.75 4.57
155 156 1.087202 CGAAATCCCGGTCGATTGCA 61.087 55.000 6.34 0.00 39.64 4.08
156 157 0.808453 TCGAAATCCCGGTCGATTGC 60.808 55.000 10.52 6.13 41.13 3.56
157 158 0.928229 GTCGAAATCCCGGTCGATTG 59.072 55.000 16.67 2.16 46.91 2.67
158 159 0.822164 AGTCGAAATCCCGGTCGATT 59.178 50.000 16.67 10.69 46.91 3.34
159 160 0.822164 AAGTCGAAATCCCGGTCGAT 59.178 50.000 16.67 2.81 46.91 3.59
160 161 0.108992 CAAGTCGAAATCCCGGTCGA 60.109 55.000 10.52 10.52 43.61 4.20
161 162 1.082117 CCAAGTCGAAATCCCGGTCG 61.082 60.000 5.87 5.87 38.62 4.79
163 164 1.298667 CCCAAGTCGAAATCCCGGT 59.701 57.895 0.00 0.00 0.00 5.28
165 166 1.451387 CCCCCAAGTCGAAATCCCG 60.451 63.158 0.00 0.00 0.00 5.14
166 167 0.039180 AACCCCCAAGTCGAAATCCC 59.961 55.000 0.00 0.00 0.00 3.85
167 168 1.460504 GAACCCCCAAGTCGAAATCC 58.539 55.000 0.00 0.00 0.00 3.01
168 169 1.084289 CGAACCCCCAAGTCGAAATC 58.916 55.000 0.00 0.00 0.00 2.17
169 170 0.399075 ACGAACCCCCAAGTCGAAAT 59.601 50.000 0.00 0.00 0.00 2.17
172 173 0.249996 GAAACGAACCCCCAAGTCGA 60.250 55.000 0.00 0.00 0.00 4.20
174 175 1.848932 GCGAAACGAACCCCCAAGTC 61.849 60.000 0.00 0.00 0.00 3.01
175 176 1.895231 GCGAAACGAACCCCCAAGT 60.895 57.895 0.00 0.00 0.00 3.16
176 177 2.622962 GGCGAAACGAACCCCCAAG 61.623 63.158 0.00 0.00 0.00 3.61
177 178 2.595172 GGCGAAACGAACCCCCAA 60.595 61.111 0.00 0.00 0.00 4.12
178 179 4.992511 CGGCGAAACGAACCCCCA 62.993 66.667 0.00 0.00 35.47 4.96
179 180 4.685467 TCGGCGAAACGAACCCCC 62.685 66.667 7.35 0.00 40.34 5.40
180 181 2.665854 TTCGGCGAAACGAACCCC 60.666 61.111 21.53 0.00 46.68 4.95
187 188 0.725784 TCGTAGACGTTCGGCGAAAC 60.726 55.000 25.48 16.95 44.77 2.78
188 189 0.453282 CTCGTAGACGTTCGGCGAAA 60.453 55.000 25.48 5.23 44.77 3.46
190 191 1.568612 AACTCGTAGACGTTCGGCGA 61.569 55.000 4.99 4.99 44.77 5.54
195 196 1.538950 ACCCTGAACTCGTAGACGTTC 59.461 52.381 1.46 0.62 41.52 3.95
196 197 1.613836 ACCCTGAACTCGTAGACGTT 58.386 50.000 1.46 0.00 40.80 3.99
197 198 1.613836 AACCCTGAACTCGTAGACGT 58.386 50.000 1.46 0.00 40.80 4.34
198 199 2.719426 AAACCCTGAACTCGTAGACG 57.281 50.000 0.00 0.00 41.45 4.18
199 200 6.128363 CCATTTTAAACCCTGAACTCGTAGAC 60.128 42.308 0.00 0.00 0.00 2.59
200 201 5.935789 CCATTTTAAACCCTGAACTCGTAGA 59.064 40.000 0.00 0.00 0.00 2.59
203 204 4.517832 GTCCATTTTAAACCCTGAACTCGT 59.482 41.667 0.00 0.00 0.00 4.18
204 205 4.760204 AGTCCATTTTAAACCCTGAACTCG 59.240 41.667 0.00 0.00 0.00 4.18
205 206 6.650427 AAGTCCATTTTAAACCCTGAACTC 57.350 37.500 0.00 0.00 0.00 3.01
206 207 7.432148 AAAAGTCCATTTTAAACCCTGAACT 57.568 32.000 0.00 0.00 39.36 3.01
209 210 6.822442 GGAAAAAGTCCATTTTAAACCCTGA 58.178 36.000 0.00 0.00 46.97 3.86
223 224 8.953313 TCCTTCTATTTTTATCGGAAAAAGTCC 58.047 33.333 12.37 0.00 43.90 3.85
359 360 9.518906 GTTCAATTTTACGTTCTTTTCCCTAAA 57.481 29.630 0.00 0.00 0.00 1.85
360 361 8.684520 TGTTCAATTTTACGTTCTTTTCCCTAA 58.315 29.630 0.00 0.00 0.00 2.69
361 362 8.223177 TGTTCAATTTTACGTTCTTTTCCCTA 57.777 30.769 0.00 0.00 0.00 3.53
362 363 7.102847 TGTTCAATTTTACGTTCTTTTCCCT 57.897 32.000 0.00 0.00 0.00 4.20
388 389 9.998106 TTGTTTTCTTACTGCTCTATTAGTTCT 57.002 29.630 0.00 0.00 0.00 3.01
390 391 9.000486 GGTTGTTTTCTTACTGCTCTATTAGTT 58.000 33.333 0.00 0.00 0.00 2.24
391 392 7.606839 GGGTTGTTTTCTTACTGCTCTATTAGT 59.393 37.037 0.00 0.00 0.00 2.24
393 394 7.606456 CAGGGTTGTTTTCTTACTGCTCTATTA 59.394 37.037 0.00 0.00 0.00 0.98
394 395 6.431234 CAGGGTTGTTTTCTTACTGCTCTATT 59.569 38.462 0.00 0.00 0.00 1.73
395 396 5.940470 CAGGGTTGTTTTCTTACTGCTCTAT 59.060 40.000 0.00 0.00 0.00 1.98
396 397 5.305585 CAGGGTTGTTTTCTTACTGCTCTA 58.694 41.667 0.00 0.00 0.00 2.43
397 398 4.137543 CAGGGTTGTTTTCTTACTGCTCT 58.862 43.478 0.00 0.00 0.00 4.09
399 400 3.117663 TCCAGGGTTGTTTTCTTACTGCT 60.118 43.478 0.00 0.00 0.00 4.24
400 401 3.219281 TCCAGGGTTGTTTTCTTACTGC 58.781 45.455 0.00 0.00 0.00 4.40
401 402 5.845391 TTTCCAGGGTTGTTTTCTTACTG 57.155 39.130 0.00 0.00 0.00 2.74
402 403 6.860790 TTTTTCCAGGGTTGTTTTCTTACT 57.139 33.333 0.00 0.00 0.00 2.24
424 425 8.888716 GGTTCCATTTAATTTTTGTGTCTGTTT 58.111 29.630 0.00 0.00 0.00 2.83
425 426 7.223777 CGGTTCCATTTAATTTTTGTGTCTGTT 59.776 33.333 0.00 0.00 0.00 3.16
426 427 6.699642 CGGTTCCATTTAATTTTTGTGTCTGT 59.300 34.615 0.00 0.00 0.00 3.41
427 428 6.145371 CCGGTTCCATTTAATTTTTGTGTCTG 59.855 38.462 0.00 0.00 0.00 3.51
428 429 6.041069 TCCGGTTCCATTTAATTTTTGTGTCT 59.959 34.615 0.00 0.00 0.00 3.41
429 430 6.217294 TCCGGTTCCATTTAATTTTTGTGTC 58.783 36.000 0.00 0.00 0.00 3.67
430 431 6.163135 TCCGGTTCCATTTAATTTTTGTGT 57.837 33.333 0.00 0.00 0.00 3.72
431 432 6.480320 TGTTCCGGTTCCATTTAATTTTTGTG 59.520 34.615 0.00 0.00 0.00 3.33
432 433 6.583562 TGTTCCGGTTCCATTTAATTTTTGT 58.416 32.000 0.00 0.00 0.00 2.83
433 434 7.011482 TGTTGTTCCGGTTCCATTTAATTTTTG 59.989 33.333 0.00 0.00 0.00 2.44
434 435 7.048512 TGTTGTTCCGGTTCCATTTAATTTTT 58.951 30.769 0.00 0.00 0.00 1.94
435 436 6.583562 TGTTGTTCCGGTTCCATTTAATTTT 58.416 32.000 0.00 0.00 0.00 1.82
437 438 5.793030 TGTTGTTCCGGTTCCATTTAATT 57.207 34.783 0.00 0.00 0.00 1.40
438 439 5.793030 TTGTTGTTCCGGTTCCATTTAAT 57.207 34.783 0.00 0.00 0.00 1.40
439 440 5.593679 TTTGTTGTTCCGGTTCCATTTAA 57.406 34.783 0.00 0.00 0.00 1.52
440 441 5.349809 GTTTTGTTGTTCCGGTTCCATTTA 58.650 37.500 0.00 0.00 0.00 1.40
441 442 4.185394 GTTTTGTTGTTCCGGTTCCATTT 58.815 39.130 0.00 0.00 0.00 2.32
442 443 3.431068 GGTTTTGTTGTTCCGGTTCCATT 60.431 43.478 0.00 0.00 0.00 3.16
443 444 2.101750 GGTTTTGTTGTTCCGGTTCCAT 59.898 45.455 0.00 0.00 0.00 3.41
444 445 1.477295 GGTTTTGTTGTTCCGGTTCCA 59.523 47.619 0.00 0.00 0.00 3.53
445 446 1.534385 CGGTTTTGTTGTTCCGGTTCC 60.534 52.381 0.00 0.00 39.41 3.62
446 447 1.132834 ACGGTTTTGTTGTTCCGGTTC 59.867 47.619 0.00 0.00 46.06 3.62
447 448 1.132834 GACGGTTTTGTTGTTCCGGTT 59.867 47.619 0.00 0.00 46.06 4.44
448 449 0.734309 GACGGTTTTGTTGTTCCGGT 59.266 50.000 0.00 0.00 46.06 5.28
449 450 0.029700 GGACGGTTTTGTTGTTCCGG 59.970 55.000 0.00 0.00 46.06 5.14
450 451 0.316360 CGGACGGTTTTGTTGTTCCG 60.316 55.000 0.00 0.00 46.98 4.30
451 452 0.734309 ACGGACGGTTTTGTTGTTCC 59.266 50.000 0.00 0.00 0.00 3.62
452 453 1.817609 CACGGACGGTTTTGTTGTTC 58.182 50.000 0.00 0.00 0.00 3.18
453 454 0.179158 GCACGGACGGTTTTGTTGTT 60.179 50.000 0.00 0.00 0.00 2.83
454 455 1.430228 GCACGGACGGTTTTGTTGT 59.570 52.632 0.00 0.00 0.00 3.32
456 457 2.483197 GGGCACGGACGGTTTTGTT 61.483 57.895 0.00 0.00 0.00 2.83
457 458 2.903350 GGGCACGGACGGTTTTGT 60.903 61.111 0.00 0.00 0.00 2.83
458 459 4.020378 CGGGCACGGACGGTTTTG 62.020 66.667 0.00 0.00 36.18 2.44
497 498 2.866156 TGCTTGCTTATCTCATACACGC 59.134 45.455 0.00 0.00 0.00 5.34
541 542 5.507315 CCAGAAATGTGGCGGTATTTTATCC 60.507 44.000 0.00 0.00 0.00 2.59
579 3393 1.154836 GTTGCAGACGAACGAAGCG 60.155 57.895 0.14 0.00 0.00 4.68
630 3444 1.862123 CGCGTTGTCAGCAGTCATT 59.138 52.632 0.00 0.00 34.19 2.57
670 3484 3.649073 CGAGGACGATGGCAATATACAA 58.351 45.455 0.00 0.00 42.66 2.41
874 3694 2.158726 AGTTTTTGACCGGAACTGGCTA 60.159 45.455 9.46 0.00 32.73 3.93
875 3695 1.029681 GTTTTTGACCGGAACTGGCT 58.970 50.000 9.46 0.00 0.00 4.75
876 3696 1.001706 GAGTTTTTGACCGGAACTGGC 60.002 52.381 9.46 0.00 34.02 4.85
877 3697 2.572290 AGAGTTTTTGACCGGAACTGG 58.428 47.619 9.46 0.00 34.02 4.00
878 3698 4.632538 AAAGAGTTTTTGACCGGAACTG 57.367 40.909 9.46 0.00 34.02 3.16
901 3725 1.211190 GCCTTCTTTCCTGCGCAAG 59.789 57.895 13.05 5.31 43.44 4.01
905 3729 2.335712 GGTGGCCTTCTTTCCTGCG 61.336 63.158 3.32 0.00 0.00 5.18
955 3786 0.038166 GGAGTGGAAATGGTGCCTGA 59.962 55.000 0.00 0.00 0.00 3.86
962 3793 3.382546 GGATGTGATTGGAGTGGAAATGG 59.617 47.826 0.00 0.00 0.00 3.16
969 3800 1.431488 CGCCGGATGTGATTGGAGTG 61.431 60.000 5.05 0.00 0.00 3.51
992 3829 1.067821 CGAGGTCCTCCATGAGCTTAC 59.932 57.143 13.54 0.00 42.81 2.34
1185 4112 3.306595 CTTCAGAGGGAGCTGCGCA 62.307 63.158 10.98 10.98 35.86 6.09
1321 4248 2.435059 GAAGTCCCTGTGCCTCGC 60.435 66.667 0.00 0.00 0.00 5.03
1480 4424 1.938657 CTCCTGCTCGCCTTCTTCGA 61.939 60.000 0.00 0.00 34.52 3.71
1626 4570 5.528870 GCTTAAAAGCCAAAGCAGACTAAA 58.471 37.500 3.22 0.00 45.89 1.85
1629 4573 3.650070 GCTTAAAAGCCAAAGCAGACT 57.350 42.857 3.22 0.00 45.89 3.24
1662 4606 6.036953 GCTCACCATTCAAATCAGACTAAGAG 59.963 42.308 0.00 0.00 0.00 2.85
1666 4610 5.426689 AGCTCACCATTCAAATCAGACTA 57.573 39.130 0.00 0.00 0.00 2.59
1667 4611 4.298103 AGCTCACCATTCAAATCAGACT 57.702 40.909 0.00 0.00 0.00 3.24
1668 4612 4.142513 GGAAGCTCACCATTCAAATCAGAC 60.143 45.833 5.21 0.00 0.00 3.51
1670 4614 4.015084 AGGAAGCTCACCATTCAAATCAG 58.985 43.478 11.59 0.00 0.00 2.90
1696 5148 3.458189 GAGCGGATACTGCATTACACTT 58.542 45.455 5.39 0.00 38.34 3.16
1703 5155 0.961753 TGATCGAGCGGATACTGCAT 59.038 50.000 0.00 0.00 38.34 3.96
1715 5167 1.672854 TTGCGGGGGTAGTGATCGAG 61.673 60.000 0.00 0.00 0.00 4.04
1720 5172 1.195442 TCATGTTGCGGGGGTAGTGA 61.195 55.000 0.00 0.00 0.00 3.41
1723 5175 1.451387 GGTCATGTTGCGGGGGTAG 60.451 63.158 0.00 0.00 0.00 3.18
1745 5197 0.756294 ATGGTGTCGTCCAAGTGACA 59.244 50.000 1.64 0.00 44.71 3.58
1802 5254 1.305201 GTGTTCGGAAGGTCTTTGCA 58.695 50.000 0.00 0.00 0.00 4.08
1813 5265 2.746904 TCCGTATTCTAACGTGTTCGGA 59.253 45.455 6.83 6.83 41.27 4.55
1846 5298 2.428925 GGCCACGGTAAGGATCGGA 61.429 63.158 0.00 0.00 31.62 4.55
1847 5299 2.040009 ATGGCCACGGTAAGGATCGG 62.040 60.000 8.16 0.00 31.62 4.18
1848 5300 0.600255 GATGGCCACGGTAAGGATCG 60.600 60.000 8.16 0.00 34.43 3.69
1849 5301 0.250338 GGATGGCCACGGTAAGGATC 60.250 60.000 8.16 0.00 0.00 3.36
1850 5302 1.705997 GGGATGGCCACGGTAAGGAT 61.706 60.000 8.16 0.00 35.15 3.24
1851 5303 2.372074 GGGATGGCCACGGTAAGGA 61.372 63.158 8.16 0.00 35.15 3.36
1852 5304 1.052124 TAGGGATGGCCACGGTAAGG 61.052 60.000 8.16 0.00 35.15 2.69
1853 5305 1.056660 ATAGGGATGGCCACGGTAAG 58.943 55.000 8.16 0.00 35.15 2.34
1856 5308 0.768221 ATCATAGGGATGGCCACGGT 60.768 55.000 8.16 0.00 34.06 4.83
1878 5330 6.470235 GTGGACTTGCAAAATCTCATAAATCG 59.530 38.462 0.00 0.00 0.00 3.34
1925 5381 3.906720 AGTGATAACGCCCATGTACTT 57.093 42.857 0.00 0.00 0.00 2.24
1978 5442 1.133598 CCCTCATGTAGTTGCGACGTA 59.866 52.381 0.00 0.00 0.00 3.57
1993 5457 0.409876 AGAGAGTGTAGGTGCCCTCA 59.590 55.000 0.00 0.00 34.61 3.86
2029 5493 6.316640 TGATGTTTTACTCGGAAGAAAACACA 59.683 34.615 22.19 19.24 45.52 3.72
2061 5535 4.553330 ATCAAAGTATCAAGGACCACGT 57.447 40.909 0.00 0.00 0.00 4.49
2123 5603 9.525826 TCTTGCCTTTAGTTAACTACTACTAGT 57.474 33.333 14.96 0.00 39.05 2.57
2183 7360 2.346365 GGCTCGTCTCCCCGTTTT 59.654 61.111 0.00 0.00 0.00 2.43
2216 7393 3.374402 CGTCCAGCCGTGGTCTCT 61.374 66.667 0.00 0.00 45.28 3.10
2228 7405 3.117794 CTCGTTAACTGACAAACGTCCA 58.882 45.455 9.92 0.00 46.41 4.02
2254 7431 7.975750 AGCAAATAAAAGTAACTAGCTAGTGC 58.024 34.615 26.70 20.85 36.50 4.40
2321 7498 5.769662 TCCCTTTCTCTAGTTTGTACGTACA 59.230 40.000 24.10 24.10 0.00 2.90
2342 7519 3.055312 AGAAGGTCATTTTAGTCCGTCCC 60.055 47.826 0.00 0.00 0.00 4.46
2343 7520 4.203654 AGAAGGTCATTTTAGTCCGTCC 57.796 45.455 0.00 0.00 0.00 4.79
2356 7533 6.016276 GCAAAGGTAAGAATCAAAGAAGGTCA 60.016 38.462 0.00 0.00 0.00 4.02
2358 7535 5.243954 GGCAAAGGTAAGAATCAAAGAAGGT 59.756 40.000 0.00 0.00 0.00 3.50
2421 7602 2.027653 TGGACCTTTGTGCGATACATCA 60.028 45.455 0.00 0.00 39.48 3.07
2430 7611 3.412386 ACATAACTCTGGACCTTTGTGC 58.588 45.455 0.00 0.00 0.00 4.57
2437 7618 6.431234 ACATCAAGAAAACATAACTCTGGACC 59.569 38.462 0.00 0.00 0.00 4.46
2438 7619 7.440523 ACATCAAGAAAACATAACTCTGGAC 57.559 36.000 0.00 0.00 0.00 4.02
2439 7620 9.166173 CATACATCAAGAAAACATAACTCTGGA 57.834 33.333 0.00 0.00 0.00 3.86
2440 7621 7.912250 GCATACATCAAGAAAACATAACTCTGG 59.088 37.037 0.00 0.00 0.00 3.86
2454 7636 7.863877 GCACATCATAAAATGCATACATCAAGA 59.136 33.333 0.00 0.00 38.00 3.02
2471 7653 1.423584 AGGATCCGGTGCACATCATA 58.576 50.000 20.43 0.00 0.00 2.15
2472 7654 0.548031 AAGGATCCGGTGCACATCAT 59.452 50.000 20.43 8.10 0.00 2.45
2473 7655 0.327924 AAAGGATCCGGTGCACATCA 59.672 50.000 20.43 0.68 0.00 3.07
2489 7684 7.877612 ACAAATGATTTACTTAGGGGCAAAAAG 59.122 33.333 0.00 0.00 0.00 2.27
2568 7763 4.634883 ACTGCTCTCATGCTCAATTTACAG 59.365 41.667 0.00 0.00 0.00 2.74
2575 7770 0.323957 AGCACTGCTCTCATGCTCAA 59.676 50.000 0.00 0.00 46.68 3.02
2577 7772 4.937193 AGCACTGCTCTCATGCTC 57.063 55.556 0.00 0.00 46.68 4.26


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

AutoCloner maintained by Alex Coulton.