Multiple sequence alignment - TraesCS3B01G206100

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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 TraesCS3B01G206100 chr3B 100.000 7753 0 0 1 7753 241398040 241390288 0.000000e+00 14318
1 TraesCS3B01G206100 chr3A 96.783 3481 75 12 316 3772 203659823 203656356 0.000000e+00 5773
2 TraesCS3B01G206100 chr3A 96.398 2776 61 16 4991 7753 203656365 203653616 0.000000e+00 4536
3 TraesCS3B01G206100 chr3A 97.970 197 4 0 119 315 593314290 593314094 7.450000e-90 342
4 TraesCS3B01G206100 chr3A 95.238 105 4 1 1 104 203659957 203659853 1.730000e-36 165
5 TraesCS3B01G206100 chr3D 95.900 3488 94 18 316 3770 165739105 165735634 0.000000e+00 5603
6 TraesCS3B01G206100 chr3D 91.499 2082 125 24 4991 7030 165735641 165733570 0.000000e+00 2817
7 TraesCS3B01G206100 chr3D 93.366 1221 42 19 3774 4991 112701691 112702875 0.000000e+00 1770
8 TraesCS3B01G206100 chr3D 92.857 126 1 3 1 118 165739242 165739117 8.000000e-40 176
9 TraesCS3B01G206100 chr7D 86.434 1231 101 39 3773 4991 318843146 318844322 0.000000e+00 1288
10 TraesCS3B01G206100 chr7D 86.571 767 79 16 3773 4521 268546186 268545426 0.000000e+00 824
11 TraesCS3B01G206100 chr7D 86.111 216 27 3 4800 5013 634021381 634021595 6.050000e-56 230
12 TraesCS3B01G206100 chr7D 81.028 253 46 2 4744 4995 555062714 555062463 4.740000e-47 200
13 TraesCS3B01G206100 chr6D 85.517 1229 101 41 3773 4991 27822090 27820929 0.000000e+00 1212
14 TraesCS3B01G206100 chr1D 84.900 1245 89 50 3765 4996 417199948 417201106 0.000000e+00 1166
15 TraesCS3B01G206100 chr1D 87.871 404 42 3 3773 4175 39969316 39969713 1.180000e-127 468
16 TraesCS3B01G206100 chr1D 96.954 197 5 1 119 315 254436174 254436369 5.800000e-86 329
17 TraesCS3B01G206100 chr2D 86.504 615 74 7 3773 4380 648100574 648099962 0.000000e+00 667
18 TraesCS3B01G206100 chr2D 97.462 197 5 0 119 315 638425646 638425842 3.470000e-88 337
19 TraesCS3B01G206100 chr2D 88.421 190 21 1 4803 4991 633228984 633228795 2.180000e-55 228
20 TraesCS3B01G206100 chr2D 80.292 274 49 5 4722 4991 470434448 470434720 1.320000e-47 202
21 TraesCS3B01G206100 chr7B 83.415 615 79 15 3989 4584 248533786 248533176 4.090000e-152 549
22 TraesCS3B01G206100 chr4D 85.432 405 49 6 3773 4175 369256917 369256521 5.600000e-111 412
23 TraesCS3B01G206100 chr4D 82.724 301 43 7 4694 4991 369256186 369255892 7.720000e-65 259
24 TraesCS3B01G206100 chr5D 97.462 197 5 0 119 315 512411327 512411523 3.470000e-88 337
25 TraesCS3B01G206100 chr5D 97.462 197 5 0 119 315 512418264 512418460 3.470000e-88 337
26 TraesCS3B01G206100 chr5D 97.462 197 4 1 119 315 6175776 6175581 1.250000e-87 335
27 TraesCS3B01G206100 chr5D 96.954 197 6 0 119 315 503293012 503293208 1.610000e-86 331
28 TraesCS3B01G206100 chr1B 96.954 197 6 0 119 315 542589716 542589912 1.610000e-86 331
29 TraesCS3B01G206100 chr1B 96.954 197 6 0 119 315 633708833 633709029 1.610000e-86 331
30 TraesCS3B01G206100 chr5B 85.135 296 41 3 4704 4998 52310195 52310488 4.550000e-77 300
31 TraesCS3B01G206100 chr7A 89.848 197 19 1 3773 3969 323481400 323481205 1.290000e-62 252
32 TraesCS3B01G206100 chr7A 84.656 189 25 4 4806 4991 724254241 724254054 1.330000e-42 185


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 TraesCS3B01G206100 chr3B 241390288 241398040 7752 True 14318.000000 14318 100.000000 1 7753 1 chr3B.!!$R1 7752
1 TraesCS3B01G206100 chr3A 203653616 203659957 6341 True 3491.333333 5773 96.139667 1 7753 3 chr3A.!!$R2 7752
2 TraesCS3B01G206100 chr3D 165733570 165739242 5672 True 2865.333333 5603 93.418667 1 7030 3 chr3D.!!$R1 7029
3 TraesCS3B01G206100 chr3D 112701691 112702875 1184 False 1770.000000 1770 93.366000 3774 4991 1 chr3D.!!$F1 1217
4 TraesCS3B01G206100 chr7D 318843146 318844322 1176 False 1288.000000 1288 86.434000 3773 4991 1 chr7D.!!$F1 1218
5 TraesCS3B01G206100 chr7D 268545426 268546186 760 True 824.000000 824 86.571000 3773 4521 1 chr7D.!!$R1 748
6 TraesCS3B01G206100 chr6D 27820929 27822090 1161 True 1212.000000 1212 85.517000 3773 4991 1 chr6D.!!$R1 1218
7 TraesCS3B01G206100 chr1D 417199948 417201106 1158 False 1166.000000 1166 84.900000 3765 4996 1 chr1D.!!$F3 1231
8 TraesCS3B01G206100 chr2D 648099962 648100574 612 True 667.000000 667 86.504000 3773 4380 1 chr2D.!!$R2 607
9 TraesCS3B01G206100 chr7B 248533176 248533786 610 True 549.000000 549 83.415000 3989 4584 1 chr7B.!!$R1 595
10 TraesCS3B01G206100 chr4D 369255892 369256917 1025 True 335.500000 412 84.078000 3773 4991 2 chr4D.!!$R1 1218

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
907 920 0.250338 AGGTTGCGAGGTGGAGAAAC 60.250 55.000 0.0 0.0 0.0 2.78 F
1666 1703 1.152652 AAACCATTCCGCCACACCA 60.153 52.632 0.0 0.0 0.0 4.17 F
3414 3454 1.722011 AAACGAGACATGGTAAGCGG 58.278 50.000 0.0 0.0 0.0 5.52 F
5147 5337 0.549950 AGGATGAGAATGGTGGGCAG 59.450 55.000 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2776 2814 2.998670 GGACTTACGGCAAACCTTAGTC 59.001 50.00 0.0 0.0 35.87 2.59 R
3459 3503 4.274147 TGGGTGCTTTGTTCTTTTCTACA 58.726 39.13 0.0 0.0 0.00 2.74 R
5225 5415 0.099436 GTCCAATGCCGCTGATCAAC 59.901 55.00 0.0 0.0 0.00 3.18 R
6944 7173 0.326618 TTTGGGGCAAAAAGGGTGGA 60.327 50.00 0.0 0.0 29.89 4.02 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
118 127 6.927936 CCTCGCTAATCTGTACTGTACTACTA 59.072 42.308 17.98 4.96 0.00 1.82
119 128 7.440556 CCTCGCTAATCTGTACTGTACTACTAA 59.559 40.741 17.98 0.00 0.00 2.24
120 129 8.722480 TCGCTAATCTGTACTGTACTACTAAA 57.278 34.615 17.98 0.00 0.00 1.85
121 130 9.334947 TCGCTAATCTGTACTGTACTACTAAAT 57.665 33.333 17.98 2.50 0.00 1.40
157 166 9.950680 GTTGTATTTTCTGGTACATCATTATGG 57.049 33.333 0.00 0.00 38.20 2.74
158 167 9.913310 TTGTATTTTCTGGTACATCATTATGGA 57.087 29.630 0.00 0.00 38.20 3.41
162 171 7.822161 TTTCTGGTACATCATTATGGATTGG 57.178 36.000 0.00 0.00 38.20 3.16
163 172 6.762077 TCTGGTACATCATTATGGATTGGA 57.238 37.500 0.00 0.00 38.20 3.53
164 173 6.533730 TCTGGTACATCATTATGGATTGGAC 58.466 40.000 0.00 0.00 38.20 4.02
165 174 6.329986 TCTGGTACATCATTATGGATTGGACT 59.670 38.462 0.00 0.00 38.20 3.85
166 175 7.512402 TCTGGTACATCATTATGGATTGGACTA 59.488 37.037 0.00 0.00 38.20 2.59
167 176 7.679783 TGGTACATCATTATGGATTGGACTAG 58.320 38.462 0.00 0.00 37.43 2.57
168 177 7.292356 TGGTACATCATTATGGATTGGACTAGT 59.708 37.037 0.00 0.00 37.43 2.57
169 178 7.819900 GGTACATCATTATGGATTGGACTAGTC 59.180 40.741 14.87 14.87 37.43 2.59
170 179 7.623999 ACATCATTATGGATTGGACTAGTCT 57.376 36.000 21.88 2.62 37.43 3.24
171 180 8.038862 ACATCATTATGGATTGGACTAGTCTT 57.961 34.615 21.88 7.91 37.43 3.01
172 181 8.497745 ACATCATTATGGATTGGACTAGTCTTT 58.502 33.333 21.88 7.56 37.43 2.52
173 182 8.997323 CATCATTATGGATTGGACTAGTCTTTC 58.003 37.037 21.88 15.04 0.00 2.62
174 183 8.324191 TCATTATGGATTGGACTAGTCTTTCT 57.676 34.615 21.88 5.30 0.00 2.52
175 184 8.424918 TCATTATGGATTGGACTAGTCTTTCTC 58.575 37.037 21.88 13.04 0.00 2.87
176 185 7.733773 TTATGGATTGGACTAGTCTTTCTCA 57.266 36.000 21.88 14.81 0.00 3.27
177 186 6.821616 ATGGATTGGACTAGTCTTTCTCAT 57.178 37.500 21.88 16.16 0.00 2.90
178 187 7.921041 ATGGATTGGACTAGTCTTTCTCATA 57.079 36.000 21.88 7.91 0.00 2.15
179 188 7.353414 TGGATTGGACTAGTCTTTCTCATAG 57.647 40.000 21.88 0.00 0.00 2.23
180 189 6.183360 TGGATTGGACTAGTCTTTCTCATAGC 60.183 42.308 21.88 2.47 0.00 2.97
181 190 6.041523 GGATTGGACTAGTCTTTCTCATAGCT 59.958 42.308 21.88 0.00 0.00 3.32
182 191 7.231722 GGATTGGACTAGTCTTTCTCATAGCTA 59.768 40.741 21.88 0.00 0.00 3.32
183 192 8.719645 ATTGGACTAGTCTTTCTCATAGCTAT 57.280 34.615 21.88 0.00 0.00 2.97
184 193 8.540507 TTGGACTAGTCTTTCTCATAGCTATT 57.459 34.615 21.88 0.00 0.00 1.73
185 194 8.172352 TGGACTAGTCTTTCTCATAGCTATTC 57.828 38.462 21.88 0.36 0.00 1.75
186 195 8.001875 TGGACTAGTCTTTCTCATAGCTATTCT 58.998 37.037 21.88 0.00 0.00 2.40
187 196 8.296713 GGACTAGTCTTTCTCATAGCTATTCTG 58.703 40.741 21.88 0.00 0.00 3.02
188 197 8.988546 ACTAGTCTTTCTCATAGCTATTCTGA 57.011 34.615 2.64 0.00 0.00 3.27
189 198 9.415008 ACTAGTCTTTCTCATAGCTATTCTGAA 57.585 33.333 2.64 6.16 0.00 3.02
192 201 9.762933 AGTCTTTCTCATAGCTATTCTGAATTC 57.237 33.333 8.38 0.00 0.00 2.17
193 202 9.762933 GTCTTTCTCATAGCTATTCTGAATTCT 57.237 33.333 8.38 8.75 0.00 2.40
194 203 9.979578 TCTTTCTCATAGCTATTCTGAATTCTC 57.020 33.333 8.38 0.00 0.00 2.87
195 204 9.985730 CTTTCTCATAGCTATTCTGAATTCTCT 57.014 33.333 8.38 6.17 0.00 3.10
196 205 9.979578 TTTCTCATAGCTATTCTGAATTCTCTC 57.020 33.333 8.38 0.00 0.00 3.20
197 206 8.703378 TCTCATAGCTATTCTGAATTCTCTCA 57.297 34.615 8.38 0.00 0.00 3.27
198 207 9.311676 TCTCATAGCTATTCTGAATTCTCTCAT 57.688 33.333 8.38 0.00 0.00 2.90
199 208 9.932207 CTCATAGCTATTCTGAATTCTCTCATT 57.068 33.333 8.38 0.00 0.00 2.57
256 265 8.853126 ACCCCGTATAAAAGAAATAATTAAGGC 58.147 33.333 0.00 0.00 0.00 4.35
257 266 8.301720 CCCCGTATAAAAGAAATAATTAAGGCC 58.698 37.037 0.00 0.00 0.00 5.19
258 267 8.852135 CCCGTATAAAAGAAATAATTAAGGCCA 58.148 33.333 5.01 0.00 0.00 5.36
299 308 7.447243 AGAATAGTGAGACGTATTAAAACGC 57.553 36.000 0.00 0.00 46.71 4.84
300 309 7.031372 AGAATAGTGAGACGTATTAAAACGCA 58.969 34.615 0.00 0.00 46.71 5.24
301 310 7.543172 AGAATAGTGAGACGTATTAAAACGCAA 59.457 33.333 0.00 0.00 46.71 4.85
302 311 7.766219 ATAGTGAGACGTATTAAAACGCAAT 57.234 32.000 0.00 0.00 46.71 3.56
303 312 6.476243 AGTGAGACGTATTAAAACGCAATT 57.524 33.333 0.00 0.00 46.71 2.32
304 313 6.894828 AGTGAGACGTATTAAAACGCAATTT 58.105 32.000 0.00 0.00 46.71 1.82
305 314 6.795114 AGTGAGACGTATTAAAACGCAATTTG 59.205 34.615 0.00 0.00 46.71 2.32
306 315 5.566016 TGAGACGTATTAAAACGCAATTTGC 59.434 36.000 11.42 11.42 46.71 3.68
317 326 1.006825 GCAATTTGCGTTCCGAACCC 61.007 55.000 5.49 0.00 31.71 4.11
348 357 2.437897 CCAGCCAAGCCAGGTTCT 59.562 61.111 0.00 0.00 0.00 3.01
419 428 2.556189 TGCTGGCGTGTAAAATTGATGT 59.444 40.909 0.00 0.00 0.00 3.06
425 434 4.087930 GGCGTGTAAAATTGATGTTCGTTG 59.912 41.667 0.00 0.00 0.00 4.10
440 449 3.629438 TCGTTGATGTCACGAGTTGTA 57.371 42.857 0.00 0.00 0.00 2.41
483 492 0.771755 GATAGGGCCAAGGGGGTTAG 59.228 60.000 6.18 0.00 39.65 2.34
536 545 4.850680 ACAACCAACCAGTTTCAGAGTTA 58.149 39.130 0.00 0.00 0.00 2.24
649 658 4.504858 ACGTCACTGAGTTTGAAAGAAGT 58.495 39.130 0.00 0.00 0.00 3.01
783 796 0.963225 TGCTGCACTGCATTGAATGT 59.037 45.000 8.44 0.00 38.13 2.71
907 920 0.250338 AGGTTGCGAGGTGGAGAAAC 60.250 55.000 0.00 0.00 0.00 2.78
964 977 2.030805 CAGAGGTGAAAAAGAAAGGGCG 60.031 50.000 0.00 0.00 0.00 6.13
1018 1031 1.818060 CAATGGGTTTGATCAGCGGAA 59.182 47.619 0.00 0.00 37.53 4.30
1105 1118 5.055144 TGCTTGAGCTTATCTATGCTTCTG 58.945 41.667 4.44 0.00 39.91 3.02
1131 1144 2.114625 ACGGTGAGTCGTCTCCCA 59.885 61.111 7.21 0.00 39.34 4.37
1263 1280 1.372501 ACTGGCTTAGGAACATGGGT 58.627 50.000 0.00 0.00 0.00 4.51
1275 1292 9.853177 CTTAGGAACATGGGTCTTTATTTAGAT 57.147 33.333 0.00 0.00 0.00 1.98
1401 1438 7.339212 TGCTTGGCATGTAATACATAAGAAAGT 59.661 33.333 15.00 0.00 36.53 2.66
1421 1458 7.559897 AGAAAGTGTCATTTCCAAGTAAAAGGA 59.440 33.333 0.00 0.00 39.53 3.36
1480 1517 4.319549 CCTTCTTTTCGCAACCTGTAGAAC 60.320 45.833 0.00 0.00 0.00 3.01
1666 1703 1.152652 AAACCATTCCGCCACACCA 60.153 52.632 0.00 0.00 0.00 4.17
2072 2109 4.794169 ACTGTGCAAATAAACTTAAGCGG 58.206 39.130 1.29 0.00 0.00 5.52
2555 2593 8.256611 ACATATATCAGACGCATTAATGGTTC 57.743 34.615 17.02 0.00 0.00 3.62
2776 2814 7.920151 TGATGAATAACCAAATAGCCAAATTCG 59.080 33.333 0.00 0.00 0.00 3.34
3414 3454 1.722011 AAACGAGACATGGTAAGCGG 58.278 50.000 0.00 0.00 0.00 5.52
3497 3541 3.866651 CACCCAGTGAGAAATCTGGTAG 58.133 50.000 9.79 0.00 46.79 3.18
3513 3557 3.703556 CTGGTAGCTGGAGATCTCAGAAA 59.296 47.826 23.85 5.85 34.36 2.52
3672 3716 4.881273 TGCGCCTTTAATATGATGACTGTT 59.119 37.500 4.18 0.00 0.00 3.16
3762 3806 9.965902 ATACAATTTCCTCCATAATCTGTATCC 57.034 33.333 0.00 0.00 0.00 2.59
3763 3807 7.815383 ACAATTTCCTCCATAATCTGTATCCA 58.185 34.615 0.00 0.00 0.00 3.41
3764 3808 7.721399 ACAATTTCCTCCATAATCTGTATCCAC 59.279 37.037 0.00 0.00 0.00 4.02
3765 3809 7.639062 ATTTCCTCCATAATCTGTATCCACT 57.361 36.000 0.00 0.00 0.00 4.00
3766 3810 7.451731 TTTCCTCCATAATCTGTATCCACTT 57.548 36.000 0.00 0.00 0.00 3.16
3767 3811 6.672266 TCCTCCATAATCTGTATCCACTTC 57.328 41.667 0.00 0.00 0.00 3.01
3771 3815 5.665360 TCCATAATCTGTATCCACTTCCACA 59.335 40.000 0.00 0.00 0.00 4.17
3787 3831 4.572985 TCCACAGAGTGAATTGCAAAAG 57.427 40.909 1.71 0.00 35.23 2.27
3842 3886 2.949644 ACAGTTCTACAGTTTTGTGCCC 59.050 45.455 0.00 0.00 38.23 5.36
4077 4127 2.358247 GACACGGCGTTCATGGGT 60.358 61.111 11.19 3.39 0.00 4.51
4462 4528 3.282745 GACGGGAGCGAGCAACAGA 62.283 63.158 0.00 0.00 0.00 3.41
4810 4983 5.006261 TGTCTAATTGCAATCCGTTATGTCG 59.994 40.000 13.38 0.00 0.00 4.35
4881 5054 3.851976 ACGAGTGAATCAGGTGACTAC 57.148 47.619 0.00 0.00 40.21 2.73
5147 5337 0.549950 AGGATGAGAATGGTGGGCAG 59.450 55.000 0.00 0.00 0.00 4.85
5450 5640 1.687612 CCAGACAGGGGACAGCATT 59.312 57.895 0.00 0.00 0.00 3.56
5566 5756 5.889853 AGTATCATGGTGCATTTCAGTTCAT 59.110 36.000 0.00 0.00 0.00 2.57
5820 6041 1.730501 TGCAGCTGCTACACTCATTC 58.269 50.000 36.61 6.43 42.66 2.67
5852 6073 7.378966 ACCTACATTCCTATTCGTATCACATG 58.621 38.462 0.00 0.00 0.00 3.21
5952 6173 5.773575 TGTACAATCAGAGTGAAGTGTCTC 58.226 41.667 4.51 0.00 32.91 3.36
6016 6243 6.614160 CATGACAGTTTTCATGCTTATGACA 58.386 36.000 0.38 0.00 44.83 3.58
6053 6280 0.396435 AGATTGGGCAGTTGTCGACA 59.604 50.000 15.76 15.76 0.00 4.35
6167 6394 2.026356 TCTTTCGAAGATTGATGGCCCA 60.026 45.455 0.00 0.00 35.04 5.36
6335 6562 7.998964 ACTTTCTCTAATTTCACTCCCAAAGAA 59.001 33.333 0.00 0.00 0.00 2.52
6625 6852 4.096382 GGGCAGGTACAACACAGAAATATG 59.904 45.833 0.00 0.00 0.00 1.78
6684 6911 2.094700 GGGTTTGATCTTTCTTTCCCGC 60.095 50.000 0.00 0.00 0.00 6.13
6692 6919 1.332375 CTTTCTTTCCCGCGTTTGACA 59.668 47.619 4.92 0.00 0.00 3.58
6847 7074 7.528996 TTTGAAGAGATTCATCAACAACCAT 57.471 32.000 0.00 0.00 34.35 3.55
6958 7187 2.928801 ACATTTCCACCCTTTTTGCC 57.071 45.000 0.00 0.00 0.00 4.52
7041 7270 7.365741 ACAAAGTCTAAGAATCAAATGTGCAG 58.634 34.615 0.00 0.00 0.00 4.41
7053 7282 1.592400 ATGTGCAGACAGTGGCATGC 61.592 55.000 9.90 9.90 42.75 4.06
7056 7285 0.253894 TGCAGACAGTGGCATGCTAT 59.746 50.000 18.92 0.00 39.42 2.97
7057 7286 1.340308 TGCAGACAGTGGCATGCTATT 60.340 47.619 18.92 5.22 39.42 1.73
7074 7303 8.965172 GCATGCTATTGAGAATTACAGAAAATG 58.035 33.333 11.37 0.00 0.00 2.32
7097 7326 1.005294 ACAACGTAGCGGCAAGTACG 61.005 55.000 15.81 15.81 45.96 3.67
7129 7358 2.566724 GCCCTGGATTTTGATTGTCCAA 59.433 45.455 0.00 0.00 41.21 3.53
7217 7446 5.745294 GGAAGCGTGTATATTTGTCGTTAGA 59.255 40.000 0.00 0.00 0.00 2.10
7220 7449 7.766219 AGCGTGTATATTTGTCGTTAGAAAT 57.234 32.000 0.00 0.00 33.49 2.17
7275 7504 2.563086 CTTGGCGCCACGAAATCGAC 62.563 60.000 32.95 0.00 43.02 4.20
7408 7641 1.675641 ACATTGCTCCACCGAAGCC 60.676 57.895 0.00 0.00 39.05 4.35
7409 7642 1.675310 CATTGCTCCACCGAAGCCA 60.675 57.895 0.00 0.00 39.05 4.75
7410 7643 1.675641 ATTGCTCCACCGAAGCCAC 60.676 57.895 0.00 0.00 39.05 5.01
7411 7644 4.680237 TGCTCCACCGAAGCCACG 62.680 66.667 0.00 0.00 39.05 4.94
7413 7646 4.379243 CTCCACCGAAGCCACGCT 62.379 66.667 0.00 0.00 42.56 5.07
7414 7647 4.680237 TCCACCGAAGCCACGCTG 62.680 66.667 0.00 0.00 39.62 5.18
7419 7652 4.081030 CGAAGCCACGCTGCAGTG 62.081 66.667 25.37 25.37 39.62 3.66
7507 7745 2.746277 GGCGCATCGGAAGTTGGT 60.746 61.111 10.83 0.00 0.00 3.67
7602 7841 3.567797 GATGCCAAGAGGACGCGC 61.568 66.667 5.73 0.00 36.89 6.86
7623 7862 0.992431 ATGGCTGCTCCCTCTCCATT 60.992 55.000 0.00 0.00 34.09 3.16
7638 7877 0.758734 CCATTCTCCCTACCGCATGA 59.241 55.000 0.00 0.00 0.00 3.07
7663 7905 0.395448 TTCATCCAATGGCCGCATCA 60.395 50.000 0.00 0.00 0.00 3.07
7683 7925 2.781431 ATTTCCACGCCCAAGTCCCC 62.781 60.000 0.00 0.00 0.00 4.81
7748 7990 4.352009 TCTACCCCGTAATACTTGGACAA 58.648 43.478 2.71 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 3.014304 ACAGTACAGATTAGCGAGGGA 57.986 47.619 0.00 0.00 0.00 4.20
93 94 5.759273 AGTAGTACAGTACAGATTAGCGAGG 59.241 44.000 13.37 0.00 0.00 4.63
131 140 9.950680 CCATAATGATGTACCAGAAAATACAAC 57.049 33.333 0.00 0.00 35.05 3.32
132 141 9.913310 TCCATAATGATGTACCAGAAAATACAA 57.087 29.630 0.00 0.00 35.05 2.41
136 145 8.863086 CCAATCCATAATGATGTACCAGAAAAT 58.137 33.333 0.00 0.00 0.00 1.82
137 146 8.058235 TCCAATCCATAATGATGTACCAGAAAA 58.942 33.333 0.00 0.00 0.00 2.29
138 147 7.502226 GTCCAATCCATAATGATGTACCAGAAA 59.498 37.037 0.00 0.00 0.00 2.52
139 148 6.998074 GTCCAATCCATAATGATGTACCAGAA 59.002 38.462 0.00 0.00 0.00 3.02
140 149 6.329986 AGTCCAATCCATAATGATGTACCAGA 59.670 38.462 0.00 0.00 0.00 3.86
141 150 6.537355 AGTCCAATCCATAATGATGTACCAG 58.463 40.000 0.00 0.00 0.00 4.00
142 151 6.514012 AGTCCAATCCATAATGATGTACCA 57.486 37.500 0.00 0.00 0.00 3.25
143 152 7.680730 ACTAGTCCAATCCATAATGATGTACC 58.319 38.462 0.00 0.00 0.00 3.34
144 153 8.589338 AGACTAGTCCAATCCATAATGATGTAC 58.411 37.037 19.38 0.00 0.00 2.90
145 154 8.727100 AGACTAGTCCAATCCATAATGATGTA 57.273 34.615 19.38 0.00 0.00 2.29
146 155 7.623999 AGACTAGTCCAATCCATAATGATGT 57.376 36.000 19.38 0.00 0.00 3.06
147 156 8.915057 AAAGACTAGTCCAATCCATAATGATG 57.085 34.615 19.38 0.00 0.00 3.07
148 157 8.943085 AGAAAGACTAGTCCAATCCATAATGAT 58.057 33.333 19.38 0.00 0.00 2.45
149 158 8.324191 AGAAAGACTAGTCCAATCCATAATGA 57.676 34.615 19.38 0.00 0.00 2.57
150 159 8.206867 TGAGAAAGACTAGTCCAATCCATAATG 58.793 37.037 19.38 0.00 0.00 1.90
151 160 8.324191 TGAGAAAGACTAGTCCAATCCATAAT 57.676 34.615 19.38 0.00 0.00 1.28
152 161 7.733773 TGAGAAAGACTAGTCCAATCCATAA 57.266 36.000 19.38 0.00 0.00 1.90
153 162 7.921041 ATGAGAAAGACTAGTCCAATCCATA 57.079 36.000 19.38 5.47 0.00 2.74
154 163 6.821616 ATGAGAAAGACTAGTCCAATCCAT 57.178 37.500 19.38 13.88 0.00 3.41
155 164 6.183360 GCTATGAGAAAGACTAGTCCAATCCA 60.183 42.308 19.38 12.31 0.00 3.41
156 165 6.041523 AGCTATGAGAAAGACTAGTCCAATCC 59.958 42.308 19.38 7.17 0.00 3.01
157 166 7.049799 AGCTATGAGAAAGACTAGTCCAATC 57.950 40.000 19.38 14.30 0.00 2.67
158 167 8.719645 ATAGCTATGAGAAAGACTAGTCCAAT 57.280 34.615 19.38 5.83 0.00 3.16
159 168 8.540507 AATAGCTATGAGAAAGACTAGTCCAA 57.459 34.615 19.38 0.00 0.00 3.53
160 169 8.001875 AGAATAGCTATGAGAAAGACTAGTCCA 58.998 37.037 19.38 10.02 0.00 4.02
161 170 8.296713 CAGAATAGCTATGAGAAAGACTAGTCC 58.703 40.741 19.38 4.40 0.00 3.85
162 171 9.062524 TCAGAATAGCTATGAGAAAGACTAGTC 57.937 37.037 15.41 15.41 0.00 2.59
163 172 8.988546 TCAGAATAGCTATGAGAAAGACTAGT 57.011 34.615 7.09 0.00 0.00 2.57
166 175 9.762933 GAATTCAGAATAGCTATGAGAAAGACT 57.237 33.333 7.09 0.00 0.00 3.24
167 176 9.762933 AGAATTCAGAATAGCTATGAGAAAGAC 57.237 33.333 7.09 7.76 0.00 3.01
168 177 9.979578 GAGAATTCAGAATAGCTATGAGAAAGA 57.020 33.333 7.09 0.00 0.00 2.52
169 178 9.985730 AGAGAATTCAGAATAGCTATGAGAAAG 57.014 33.333 7.09 0.00 0.00 2.62
170 179 9.979578 GAGAGAATTCAGAATAGCTATGAGAAA 57.020 33.333 7.09 0.95 0.00 2.52
171 180 9.140874 TGAGAGAATTCAGAATAGCTATGAGAA 57.859 33.333 7.09 11.80 0.00 2.87
172 181 8.703378 TGAGAGAATTCAGAATAGCTATGAGA 57.297 34.615 7.09 3.06 0.00 3.27
173 182 9.932207 AATGAGAGAATTCAGAATAGCTATGAG 57.068 33.333 7.09 0.52 0.00 2.90
230 239 8.853126 GCCTTAATTATTTCTTTTATACGGGGT 58.147 33.333 0.00 0.00 0.00 4.95
231 240 8.301720 GGCCTTAATTATTTCTTTTATACGGGG 58.698 37.037 0.00 0.00 0.00 5.73
232 241 8.852135 TGGCCTTAATTATTTCTTTTATACGGG 58.148 33.333 3.32 0.00 0.00 5.28
273 282 9.013490 GCGTTTTAATACGTCTCACTATTCTAA 57.987 33.333 17.71 0.00 43.22 2.10
274 283 8.183536 TGCGTTTTAATACGTCTCACTATTCTA 58.816 33.333 17.71 0.00 43.22 2.10
275 284 7.031372 TGCGTTTTAATACGTCTCACTATTCT 58.969 34.615 17.71 0.00 43.22 2.40
276 285 7.213252 TGCGTTTTAATACGTCTCACTATTC 57.787 36.000 17.71 0.78 43.22 1.75
277 286 7.585286 TTGCGTTTTAATACGTCTCACTATT 57.415 32.000 17.71 0.00 43.22 1.73
278 287 7.766219 ATTGCGTTTTAATACGTCTCACTAT 57.234 32.000 17.71 3.25 43.22 2.12
279 288 7.585286 AATTGCGTTTTAATACGTCTCACTA 57.415 32.000 17.71 1.28 43.22 2.74
280 289 6.476243 AATTGCGTTTTAATACGTCTCACT 57.524 33.333 17.71 2.13 43.22 3.41
281 290 6.450667 GCAAATTGCGTTTTAATACGTCTCAC 60.451 38.462 17.71 3.82 43.22 3.51
282 291 5.566016 GCAAATTGCGTTTTAATACGTCTCA 59.434 36.000 17.71 6.71 43.22 3.27
283 292 5.993552 GCAAATTGCGTTTTAATACGTCTC 58.006 37.500 17.71 4.45 43.22 3.36
284 293 5.985526 GCAAATTGCGTTTTAATACGTCT 57.014 34.783 17.71 2.93 43.22 4.18
307 316 2.037381 AGAGAAGTGAAGGGTTCGGAAC 59.963 50.000 12.41 12.41 0.00 3.62
308 317 2.326428 AGAGAAGTGAAGGGTTCGGAA 58.674 47.619 0.00 0.00 0.00 4.30
309 318 2.011122 AGAGAAGTGAAGGGTTCGGA 57.989 50.000 0.00 0.00 0.00 4.55
310 319 2.613223 GGAAGAGAAGTGAAGGGTTCGG 60.613 54.545 0.00 0.00 0.00 4.30
311 320 2.613223 GGGAAGAGAAGTGAAGGGTTCG 60.613 54.545 0.00 0.00 0.00 3.95
312 321 2.372172 TGGGAAGAGAAGTGAAGGGTTC 59.628 50.000 0.00 0.00 0.00 3.62
313 322 2.373502 CTGGGAAGAGAAGTGAAGGGTT 59.626 50.000 0.00 0.00 0.00 4.11
314 323 1.981495 CTGGGAAGAGAAGTGAAGGGT 59.019 52.381 0.00 0.00 0.00 4.34
317 326 1.349026 TGGCTGGGAAGAGAAGTGAAG 59.651 52.381 0.00 0.00 0.00 3.02
419 428 2.816689 ACAACTCGTGACATCAACGAA 58.183 42.857 0.05 0.00 35.40 3.85
425 434 3.299340 ACAGGTACAACTCGTGACATC 57.701 47.619 0.00 0.00 0.00 3.06
440 449 4.082571 GCAGATGATTTTGTGCTAACAGGT 60.083 41.667 0.00 0.00 37.67 4.00
483 492 7.484140 ACTTTGATCTCTTGAAAAAGTTCACC 58.516 34.615 0.00 0.00 43.52 4.02
649 658 6.438186 TGATTTACATGCATATCTCCCTCA 57.562 37.500 0.00 0.00 0.00 3.86
783 796 3.088532 GCTCACCCACACCATTAATTGA 58.911 45.455 0.00 0.00 0.00 2.57
907 920 0.972134 TTCTGTCTGGTGCTCTCTGG 59.028 55.000 0.00 0.00 0.00 3.86
964 977 4.499865 GCTCCCCTTGTTTTGTTCTCTTTC 60.500 45.833 0.00 0.00 0.00 2.62
1018 1031 3.812167 GCCAAGATCTTGAAGAACACCCT 60.812 47.826 32.49 0.00 42.93 4.34
1105 1118 0.232303 CGACTCACCGTGCAGTTTTC 59.768 55.000 0.00 0.00 0.00 2.29
1281 1298 8.798859 AGAAATAGATGACAACAAATGTAGCT 57.201 30.769 0.00 0.00 44.12 3.32
1349 1383 1.299541 CAACGACAGAGTGCCACTTT 58.700 50.000 0.00 0.00 0.00 2.66
1401 1438 6.310941 TCCATCCTTTTACTTGGAAATGACA 58.689 36.000 0.00 0.00 35.38 3.58
1421 1458 4.901250 AGATTCCACACCTTGTTTTTCCAT 59.099 37.500 0.00 0.00 0.00 3.41
1666 1703 2.939298 CGGAGGGGAGGGAGATCT 59.061 66.667 0.00 0.00 0.00 2.75
2095 2132 7.969536 ATCGATGTTTCCTATTCAGGTTATG 57.030 36.000 0.00 0.00 43.18 1.90
2533 2571 7.004555 AGGAACCATTAATGCGTCTGATATA 57.995 36.000 10.11 0.00 0.00 0.86
2555 2593 6.283694 TCTGCTAGCTATAATGTTGTTGAGG 58.716 40.000 17.23 0.00 0.00 3.86
2745 2783 7.944061 TGGCTATTTGGTTATTCATCATTCTG 58.056 34.615 0.00 0.00 0.00 3.02
2776 2814 2.998670 GGACTTACGGCAAACCTTAGTC 59.001 50.000 0.00 0.00 35.87 2.59
2816 2854 5.104859 TGCAATGGTTAATGAATTCTGCCAT 60.105 36.000 7.05 9.75 36.89 4.40
3046 3086 7.640597 ATTGGTTACAAACTTATAAGGCCTC 57.359 36.000 16.73 0.00 40.55 4.70
3459 3503 4.274147 TGGGTGCTTTGTTCTTTTCTACA 58.726 39.130 0.00 0.00 0.00 2.74
3497 3541 4.575645 CCTGAAATTTCTGAGATCTCCAGC 59.424 45.833 22.50 0.00 0.00 4.85
3692 3736 4.021192 CCAAAACCAACTACATTCAGCCAT 60.021 41.667 0.00 0.00 0.00 4.40
3762 3806 2.880268 TGCAATTCACTCTGTGGAAGTG 59.120 45.455 0.00 0.00 33.87 3.16
3763 3807 3.213206 TGCAATTCACTCTGTGGAAGT 57.787 42.857 0.00 0.00 33.87 3.01
3764 3808 4.572985 TTTGCAATTCACTCTGTGGAAG 57.427 40.909 0.00 0.00 33.87 3.46
3765 3809 4.644234 TCTTTTGCAATTCACTCTGTGGAA 59.356 37.500 0.00 0.00 33.87 3.53
3766 3810 4.036734 GTCTTTTGCAATTCACTCTGTGGA 59.963 41.667 0.00 0.00 33.87 4.02
3767 3811 4.202040 TGTCTTTTGCAATTCACTCTGTGG 60.202 41.667 0.00 0.00 33.87 4.17
3771 3815 4.756642 TCGATGTCTTTTGCAATTCACTCT 59.243 37.500 0.00 0.00 0.00 3.24
3787 3831 3.126831 CCTAGCCTTCAATGTCGATGTC 58.873 50.000 0.00 0.00 0.00 3.06
3842 3886 4.871933 AGCCTTGGAATTAGTGGTTTTG 57.128 40.909 0.00 0.00 0.00 2.44
4571 4664 4.079850 CCACCGCTGCTGCTCTCT 62.080 66.667 14.03 0.00 36.97 3.10
4590 4683 4.527583 CTGCTCTCTCCCGCCTGC 62.528 72.222 0.00 0.00 0.00 4.85
4591 4684 3.073735 ACTGCTCTCTCCCGCCTG 61.074 66.667 0.00 0.00 0.00 4.85
4592 4685 3.073735 CACTGCTCTCTCCCGCCT 61.074 66.667 0.00 0.00 0.00 5.52
4753 4926 4.342092 GGACTACATTGCAAAAGGGCATAT 59.658 41.667 1.71 0.00 44.48 1.78
4810 4983 1.212751 GAAAAGGGTGATGTGGCGC 59.787 57.895 0.00 0.00 0.00 6.53
4902 5090 4.156008 GTGCCAAAATCACTAATTCCGAGT 59.844 41.667 0.00 0.00 0.00 4.18
4905 5093 4.433186 TGTGCCAAAATCACTAATTCCG 57.567 40.909 0.00 0.00 35.58 4.30
4907 5095 7.224557 ACAGTTTTGTGCCAAAATCACTAATTC 59.775 33.333 13.75 2.02 35.83 2.17
5225 5415 0.099436 GTCCAATGCCGCTGATCAAC 59.901 55.000 0.00 0.00 0.00 3.18
5450 5640 0.697658 TGATTCCATGGTGGCAGTGA 59.302 50.000 12.58 0.00 37.47 3.41
5528 5718 8.458843 GCACCATGATACTTGTAAACTGTAATT 58.541 33.333 0.00 0.00 0.00 1.40
5566 5756 6.883756 TGAAATGCACTACCATCATACTTTCA 59.116 34.615 0.00 0.00 0.00 2.69
5688 5909 1.615392 CTTGGGAAGTTGGCTCCAAAG 59.385 52.381 2.45 0.00 38.60 2.77
5820 6041 4.680110 CGAATAGGAATGTAGGTAGTTGCG 59.320 45.833 0.00 0.00 0.00 4.85
5918 6139 8.559536 TCACTCTGATTGTACAATTGAACTTTC 58.440 33.333 21.63 8.39 0.00 2.62
5920 6141 8.450578 TTCACTCTGATTGTACAATTGAACTT 57.549 30.769 21.63 0.00 0.00 2.66
5941 6162 6.907748 GCTTAAGTTTTTCTGAGACACTTCAC 59.092 38.462 4.02 0.00 0.00 3.18
5952 6173 7.820648 AGTGGACATATGCTTAAGTTTTTCTG 58.179 34.615 1.58 0.00 0.00 3.02
6167 6394 5.020132 AGAACTAGATTGCCAGTAGACAGT 58.980 41.667 0.00 0.00 0.00 3.55
6317 6544 5.076873 CCACCTTCTTTGGGAGTGAAATTA 58.923 41.667 0.00 0.00 0.00 1.40
6320 6547 2.512056 TCCACCTTCTTTGGGAGTGAAA 59.488 45.455 0.00 0.00 34.56 2.69
6335 6562 6.351286 GCAGTTTTTCCATTGAATATCCACCT 60.351 38.462 0.00 0.00 0.00 4.00
6684 6911 3.242837 CCCATGTATCTGCATGTCAAACG 60.243 47.826 7.36 0.00 43.33 3.60
6692 6919 3.713248 TCTTCACTCCCATGTATCTGCAT 59.287 43.478 0.00 0.00 0.00 3.96
6847 7074 3.938963 ACAACTGACGCTTCTTTCTTTGA 59.061 39.130 0.00 0.00 0.00 2.69
6935 7164 5.126779 GGCAAAAAGGGTGGAAATGTAAAA 58.873 37.500 0.00 0.00 0.00 1.52
6944 7173 0.326618 TTTGGGGCAAAAAGGGTGGA 60.327 50.000 0.00 0.00 29.89 4.02
6958 7187 6.153340 TGCTTTATTTCAGAAGATCCTTTGGG 59.847 38.462 0.00 0.00 0.00 4.12
7041 7270 2.910199 TCTCAATAGCATGCCACTGTC 58.090 47.619 15.66 0.00 0.00 3.51
7074 7303 1.997606 ACTTGCCGCTACGTTGTAATC 59.002 47.619 0.00 0.00 0.00 1.75
7162 7391 8.899771 TCTCAACTGATATGATACGTTCTTGTA 58.100 33.333 0.00 0.00 0.00 2.41
7217 7446 8.706322 ATGAGGTACACACTTCCTTTTTATTT 57.294 30.769 0.00 0.00 29.85 1.40
7220 7449 6.833041 TGATGAGGTACACACTTCCTTTTTA 58.167 36.000 0.00 0.00 29.85 1.52
7295 7524 4.718774 TCTCCTTCCTGTCATAGATTTGCT 59.281 41.667 0.00 0.00 0.00 3.91
7411 7644 4.457496 TAGCTCCGCCACTGCAGC 62.457 66.667 15.27 0.00 37.32 5.25
7412 7645 2.510238 GTAGCTCCGCCACTGCAG 60.510 66.667 13.48 13.48 37.32 4.41
7413 7646 3.300934 CTGTAGCTCCGCCACTGCA 62.301 63.158 0.00 0.00 37.32 4.41
7414 7647 2.510238 CTGTAGCTCCGCCACTGC 60.510 66.667 0.00 0.00 0.00 4.40
7415 7648 1.153745 GTCTGTAGCTCCGCCACTG 60.154 63.158 0.00 0.00 0.00 3.66
7416 7649 2.701780 CGTCTGTAGCTCCGCCACT 61.702 63.158 0.00 0.00 0.00 4.00
7417 7650 2.202623 CGTCTGTAGCTCCGCCAC 60.203 66.667 0.00 0.00 0.00 5.01
7418 7651 3.449227 CCGTCTGTAGCTCCGCCA 61.449 66.667 0.00 0.00 0.00 5.69
7419 7652 2.017559 ATTCCGTCTGTAGCTCCGCC 62.018 60.000 0.00 0.00 0.00 6.13
7420 7653 0.179108 AATTCCGTCTGTAGCTCCGC 60.179 55.000 0.00 0.00 0.00 5.54
7602 7841 2.509916 GAGAGGGAGCAGCCATGG 59.490 66.667 7.63 7.63 38.95 3.66
7623 7862 1.412710 GAACATCATGCGGTAGGGAGA 59.587 52.381 0.00 0.00 0.00 3.71
7638 7877 2.026641 CGGCCATTGGATGAAGAACAT 58.973 47.619 6.95 0.00 42.47 2.71
7663 7905 0.898326 GGGACTTGGGCGTGGAAATT 60.898 55.000 0.00 0.00 0.00 1.82
7683 7925 1.270094 GGGTTTTTCTTGCGGGAAAGG 60.270 52.381 4.54 0.00 36.69 3.11
7684 7926 1.410882 TGGGTTTTTCTTGCGGGAAAG 59.589 47.619 4.54 0.00 36.69 2.62


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

AutoCloner maintained by Alex Coulton.