Multiple sequence alignment - TraesCS5B01G493600

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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 TraesCS5B01G493600 chr5B 100.000 2945 0 0 1 2945 661525938 661522994 0.000000e+00 5439
1 TraesCS5B01G493600 chr5B 88.043 1221 106 18 806 1995 661611962 661613173 0.000000e+00 1410
2 TraesCS5B01G493600 chr5D 88.687 2148 127 56 355 2418 526411953 526409838 0.000000e+00 2514
3 TraesCS5B01G493600 chr5D 84.781 1485 150 44 614 2050 526432031 526433487 0.000000e+00 1421
4 TraesCS5B01G493600 chr5D 93.607 438 25 1 1501 1935 526422496 526422933 0.000000e+00 651
5 TraesCS5B01G493600 chr5D 93.421 152 9 1 19 169 526412191 526412040 1.060000e-54 224
6 TraesCS5B01G493600 chr5A 92.108 1115 66 13 904 2016 653475404 653474310 0.000000e+00 1552
7 TraesCS5B01G493600 chr5A 86.219 1473 122 45 685 2102 653563062 653564508 0.000000e+00 1520
8 TraesCS5B01G493600 chr5A 86.553 409 27 16 301 682 653476022 653475615 2.710000e-115 425
9 TraesCS5B01G493600 chr5A 82.238 563 29 26 2417 2945 693355292 693355817 1.260000e-113 420
10 TraesCS5B01G493600 chr5A 82.398 392 35 21 2418 2801 655112344 655112709 7.930000e-81 311
11 TraesCS5B01G493600 chr5A 97.810 137 1 1 168 304 151259567 151259433 4.910000e-58 235
12 TraesCS5B01G493600 chr5A 95.918 147 3 2 168 314 422083682 422083825 4.910000e-58 235
13 TraesCS5B01G493600 chr5A 93.421 152 6 3 2267 2418 653473988 653473841 3.820000e-54 222
14 TraesCS5B01G493600 chr3A 86.441 1121 104 29 845 1949 638016646 638015558 0.000000e+00 1184
15 TraesCS5B01G493600 chr3A 96.183 131 4 1 2416 2546 660278137 660278008 2.300000e-51 213
16 TraesCS5B01G493600 chr3A 76.385 343 33 29 2583 2922 742956656 742956359 1.100000e-29 141
17 TraesCS5B01G493600 chr3D 85.918 1122 106 31 845 1949 496768607 496767521 0.000000e+00 1149
18 TraesCS5B01G493600 chr3D 95.489 532 16 3 2414 2945 19288673 19289196 0.000000e+00 843
19 TraesCS5B01G493600 chr3B 84.345 1137 115 36 845 1949 656067002 656065897 0.000000e+00 1055
20 TraesCS5B01G493600 chr3B 79.597 397 32 25 2417 2780 495276400 495276020 3.790000e-59 239
21 TraesCS5B01G493600 chr3B 96.124 129 4 1 2418 2546 113483998 113484125 2.970000e-50 209
22 TraesCS5B01G493600 chr3B 76.800 375 30 26 2581 2945 79291008 79291335 1.090000e-34 158
23 TraesCS5B01G493600 chr7A 97.757 535 12 0 2411 2945 53283828 53283294 0.000000e+00 922
24 TraesCS5B01G493600 chr7A 76.385 343 33 29 2583 2922 30925155 30925452 1.100000e-29 141
25 TraesCS5B01G493600 chr1D 95.644 528 15 3 2418 2945 398944872 398944353 0.000000e+00 841
26 TraesCS5B01G493600 chr1D 83.172 517 37 21 2418 2922 381022734 381023212 7.540000e-116 427
27 TraesCS5B01G493600 chr2D 79.418 928 140 38 1019 1943 376356683 376355804 2.510000e-170 608
28 TraesCS5B01G493600 chr2B 78.879 928 145 29 1019 1943 447825871 447824992 5.470000e-162 580
29 TraesCS5B01G493600 chr2B 97.810 137 1 1 168 304 81318938 81319072 4.910000e-58 235
30 TraesCS5B01G493600 chr7B 97.826 138 1 1 168 305 388157320 388157455 1.360000e-58 237
31 TraesCS5B01G493600 chr7B 97.810 137 1 1 168 304 44809631 44809765 4.910000e-58 235
32 TraesCS5B01G493600 chr7B 95.862 145 2 3 168 312 550398276 550398136 6.350000e-57 231
33 TraesCS5B01G493600 chr6B 97.810 137 1 1 168 304 669380278 669380412 4.910000e-58 235
34 TraesCS5B01G493600 chr6B 79.891 368 25 28 2418 2771 172766130 172765798 1.060000e-54 224
35 TraesCS5B01G493600 chr1B 97.122 139 2 1 168 306 373149613 373149477 1.760000e-57 233
36 TraesCS5B01G493600 chr1A 95.270 148 5 1 168 315 513684431 513684286 1.760000e-57 233
37 TraesCS5B01G493600 chr1A 79.459 370 29 25 2418 2770 48035907 48035568 4.940000e-53 219
38 TraesCS5B01G493600 chr4B 79.515 371 29 25 2418 2771 608780096 608780436 1.370000e-53 220
39 TraesCS5B01G493600 chr4D 83.398 259 9 15 2688 2944 503353441 503353667 2.970000e-50 209


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 TraesCS5B01G493600 chr5B 661522994 661525938 2944 True 5439 5439 100.000 1 2945 1 chr5B.!!$R1 2944
1 TraesCS5B01G493600 chr5B 661611962 661613173 1211 False 1410 1410 88.043 806 1995 1 chr5B.!!$F1 1189
2 TraesCS5B01G493600 chr5D 526432031 526433487 1456 False 1421 1421 84.781 614 2050 1 chr5D.!!$F2 1436
3 TraesCS5B01G493600 chr5D 526409838 526412191 2353 True 1369 2514 91.054 19 2418 2 chr5D.!!$R1 2399
4 TraesCS5B01G493600 chr5A 653563062 653564508 1446 False 1520 1520 86.219 685 2102 1 chr5A.!!$F2 1417
5 TraesCS5B01G493600 chr5A 653473841 653476022 2181 True 733 1552 90.694 301 2418 3 chr5A.!!$R2 2117
6 TraesCS5B01G493600 chr5A 693355292 693355817 525 False 420 420 82.238 2417 2945 1 chr5A.!!$F4 528
7 TraesCS5B01G493600 chr3A 638015558 638016646 1088 True 1184 1184 86.441 845 1949 1 chr3A.!!$R1 1104
8 TraesCS5B01G493600 chr3D 496767521 496768607 1086 True 1149 1149 85.918 845 1949 1 chr3D.!!$R1 1104
9 TraesCS5B01G493600 chr3D 19288673 19289196 523 False 843 843 95.489 2414 2945 1 chr3D.!!$F1 531
10 TraesCS5B01G493600 chr3B 656065897 656067002 1105 True 1055 1055 84.345 845 1949 1 chr3B.!!$R2 1104
11 TraesCS5B01G493600 chr7A 53283294 53283828 534 True 922 922 97.757 2411 2945 1 chr7A.!!$R1 534
12 TraesCS5B01G493600 chr1D 398944353 398944872 519 True 841 841 95.644 2418 2945 1 chr1D.!!$R1 527
13 TraesCS5B01G493600 chr2D 376355804 376356683 879 True 608 608 79.418 1019 1943 1 chr2D.!!$R1 924
14 TraesCS5B01G493600 chr2B 447824992 447825871 879 True 580 580 78.879 1019 1943 1 chr2B.!!$R1 924

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
848 982 0.030235 GGAAACGAAACAGGGTGTGC 59.97 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2190 0.832135 GATATCCGGACCCTGCCTGA 60.832 60.0 6.12 0.0 0.0 3.86 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 3.370231 CCAAAAACGCCCCTCCGG 61.370 66.667 0.00 0.00 0.00 5.14
40 41 2.426024 CAGCATGAATAAAGCACAGCCT 59.574 45.455 0.00 0.00 39.69 4.58
119 121 4.022589 ACTTTTGACACATCCTGCTGAATG 60.023 41.667 0.00 0.00 0.00 2.67
145 147 2.924290 GCATAACTGAGAACGACTGGTC 59.076 50.000 0.00 0.00 0.00 4.02
153 155 4.058124 TGAGAACGACTGGTCAAGAAATG 58.942 43.478 0.00 0.00 0.00 2.32
158 160 4.056050 ACGACTGGTCAAGAAATGTGTAC 58.944 43.478 0.00 0.00 0.00 2.90
160 162 4.642429 GACTGGTCAAGAAATGTGTACCT 58.358 43.478 0.00 0.00 0.00 3.08
161 163 5.048846 ACTGGTCAAGAAATGTGTACCTT 57.951 39.130 0.00 0.00 0.00 3.50
162 164 6.182507 ACTGGTCAAGAAATGTGTACCTTA 57.817 37.500 0.00 0.00 0.00 2.69
163 165 6.779860 ACTGGTCAAGAAATGTGTACCTTAT 58.220 36.000 0.00 0.00 0.00 1.73
164 166 6.655003 ACTGGTCAAGAAATGTGTACCTTATG 59.345 38.462 0.00 0.00 0.00 1.90
165 167 6.774673 TGGTCAAGAAATGTGTACCTTATGA 58.225 36.000 0.00 0.00 0.00 2.15
166 168 6.653320 TGGTCAAGAAATGTGTACCTTATGAC 59.347 38.462 0.00 0.00 0.00 3.06
167 169 6.183360 GGTCAAGAAATGTGTACCTTATGACG 60.183 42.308 0.00 0.00 0.00 4.35
168 170 6.588756 GTCAAGAAATGTGTACCTTATGACGA 59.411 38.462 0.00 0.00 0.00 4.20
169 171 6.811665 TCAAGAAATGTGTACCTTATGACGAG 59.188 38.462 0.00 0.00 0.00 4.18
170 172 6.282199 AGAAATGTGTACCTTATGACGAGT 57.718 37.500 0.00 0.00 0.00 4.18
171 173 6.331061 AGAAATGTGTACCTTATGACGAGTC 58.669 40.000 0.00 0.00 0.00 3.36
172 174 5.916661 AATGTGTACCTTATGACGAGTCT 57.083 39.130 4.78 0.00 0.00 3.24
173 175 7.338703 AGAAATGTGTACCTTATGACGAGTCTA 59.661 37.037 4.78 0.00 0.00 2.59
174 176 5.808042 TGTGTACCTTATGACGAGTCTAC 57.192 43.478 4.78 0.00 0.00 2.59
175 177 5.247862 TGTGTACCTTATGACGAGTCTACA 58.752 41.667 4.78 1.51 0.00 2.74
176 178 5.706833 TGTGTACCTTATGACGAGTCTACAA 59.293 40.000 4.78 0.00 0.00 2.41
177 179 6.207221 TGTGTACCTTATGACGAGTCTACAAA 59.793 38.462 4.78 0.00 0.00 2.83
178 180 6.746364 GTGTACCTTATGACGAGTCTACAAAG 59.254 42.308 4.78 3.51 0.00 2.77
179 181 5.979288 ACCTTATGACGAGTCTACAAAGT 57.021 39.130 4.78 0.00 0.00 2.66
180 182 7.607607 TGTACCTTATGACGAGTCTACAAAGTA 59.392 37.037 4.78 0.00 0.00 2.24
181 183 7.458409 ACCTTATGACGAGTCTACAAAGTAA 57.542 36.000 4.78 0.00 0.00 2.24
182 184 8.064336 ACCTTATGACGAGTCTACAAAGTAAT 57.936 34.615 4.78 0.00 0.00 1.89
183 185 9.182214 ACCTTATGACGAGTCTACAAAGTAATA 57.818 33.333 4.78 0.00 0.00 0.98
210 212 3.067684 GGCAACTATGTTACCACACCT 57.932 47.619 0.00 0.00 35.03 4.00
211 213 4.210724 GGCAACTATGTTACCACACCTA 57.789 45.455 0.00 0.00 35.03 3.08
212 214 4.777463 GGCAACTATGTTACCACACCTAT 58.223 43.478 0.00 0.00 35.03 2.57
213 215 4.574828 GGCAACTATGTTACCACACCTATG 59.425 45.833 0.00 0.00 35.03 2.23
214 216 5.424757 GCAACTATGTTACCACACCTATGA 58.575 41.667 0.00 0.00 35.03 2.15
215 217 5.293569 GCAACTATGTTACCACACCTATGAC 59.706 44.000 0.00 0.00 35.03 3.06
216 218 6.403049 CAACTATGTTACCACACCTATGACA 58.597 40.000 0.00 0.00 35.03 3.58
217 219 5.974108 ACTATGTTACCACACCTATGACAC 58.026 41.667 0.00 0.00 35.03 3.67
218 220 5.720041 ACTATGTTACCACACCTATGACACT 59.280 40.000 0.00 0.00 35.03 3.55
219 221 6.893554 ACTATGTTACCACACCTATGACACTA 59.106 38.462 0.00 0.00 35.03 2.74
220 222 5.395682 TGTTACCACACCTATGACACTAC 57.604 43.478 0.00 0.00 0.00 2.73
221 223 4.221262 TGTTACCACACCTATGACACTACC 59.779 45.833 0.00 0.00 0.00 3.18
222 224 2.185387 ACCACACCTATGACACTACCC 58.815 52.381 0.00 0.00 0.00 3.69
223 225 2.184533 CCACACCTATGACACTACCCA 58.815 52.381 0.00 0.00 0.00 4.51
224 226 2.093658 CCACACCTATGACACTACCCAC 60.094 54.545 0.00 0.00 0.00 4.61
225 227 2.832129 CACACCTATGACACTACCCACT 59.168 50.000 0.00 0.00 0.00 4.00
226 228 4.021229 CACACCTATGACACTACCCACTA 58.979 47.826 0.00 0.00 0.00 2.74
227 229 4.649674 CACACCTATGACACTACCCACTAT 59.350 45.833 0.00 0.00 0.00 2.12
228 230 4.649674 ACACCTATGACACTACCCACTATG 59.350 45.833 0.00 0.00 0.00 2.23
229 231 4.893524 CACCTATGACACTACCCACTATGA 59.106 45.833 0.00 0.00 0.00 2.15
230 232 5.362717 CACCTATGACACTACCCACTATGAA 59.637 44.000 0.00 0.00 0.00 2.57
231 233 5.598830 ACCTATGACACTACCCACTATGAAG 59.401 44.000 0.00 0.00 0.00 3.02
232 234 5.011125 CCTATGACACTACCCACTATGAAGG 59.989 48.000 0.00 0.00 0.00 3.46
233 235 3.786553 TGACACTACCCACTATGAAGGT 58.213 45.455 0.00 0.00 37.69 3.50
234 236 4.938028 TGACACTACCCACTATGAAGGTA 58.062 43.478 0.00 0.00 35.02 3.08
241 243 7.598759 CTACCCACTATGAAGGTAGTAACAT 57.401 40.000 7.19 0.00 45.39 2.71
242 244 8.701908 CTACCCACTATGAAGGTAGTAACATA 57.298 38.462 7.19 0.00 45.39 2.29
243 245 9.310449 CTACCCACTATGAAGGTAGTAACATAT 57.690 37.037 7.19 0.00 45.39 1.78
245 247 9.310449 ACCCACTATGAAGGTAGTAACATATAG 57.690 37.037 0.00 0.00 33.29 1.31
246 248 9.529823 CCCACTATGAAGGTAGTAACATATAGA 57.470 37.037 9.17 0.00 33.29 1.98
284 286 9.401058 TGTATGTTACTAGTCTAAGTTACTCCC 57.599 37.037 0.00 0.00 31.82 4.30
285 287 7.894753 ATGTTACTAGTCTAAGTTACTCCCC 57.105 40.000 0.00 0.00 31.82 4.81
286 288 6.793478 TGTTACTAGTCTAAGTTACTCCCCA 58.207 40.000 0.00 0.00 31.82 4.96
287 289 6.660949 TGTTACTAGTCTAAGTTACTCCCCAC 59.339 42.308 0.00 0.00 31.82 4.61
288 290 5.533333 ACTAGTCTAAGTTACTCCCCACT 57.467 43.478 0.00 0.00 0.00 4.00
289 291 6.649041 ACTAGTCTAAGTTACTCCCCACTA 57.351 41.667 0.00 0.00 0.00 2.74
290 292 7.223472 ACTAGTCTAAGTTACTCCCCACTAT 57.777 40.000 0.00 0.00 0.00 2.12
291 293 7.061688 ACTAGTCTAAGTTACTCCCCACTATG 58.938 42.308 0.00 0.00 0.00 2.23
292 294 6.088541 AGTCTAAGTTACTCCCCACTATGA 57.911 41.667 0.00 0.00 0.00 2.15
293 295 5.892686 AGTCTAAGTTACTCCCCACTATGAC 59.107 44.000 0.00 0.00 0.00 3.06
294 296 5.068855 GTCTAAGTTACTCCCCACTATGACC 59.931 48.000 0.00 0.00 0.00 4.02
295 297 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
296 298 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
297 299 1.789523 TACTCCCCACTATGACCAGC 58.210 55.000 0.00 0.00 0.00 4.85
298 300 0.983378 ACTCCCCACTATGACCAGCC 60.983 60.000 0.00 0.00 0.00 4.85
299 301 0.692419 CTCCCCACTATGACCAGCCT 60.692 60.000 0.00 0.00 0.00 4.58
324 326 3.064134 TGACGAAATGAACGTGCTTTCAA 59.936 39.130 14.74 2.47 43.97 2.69
332 334 7.449934 AATGAACGTGCTTTCAAACTTAAAG 57.550 32.000 0.00 0.00 38.95 1.85
346 348 2.039879 ACTTAAAGAATGTCAGGCCGGT 59.960 45.455 1.90 0.00 0.00 5.28
348 350 1.995376 AAAGAATGTCAGGCCGGTTT 58.005 45.000 1.90 0.00 0.00 3.27
349 351 1.995376 AAGAATGTCAGGCCGGTTTT 58.005 45.000 1.90 0.00 0.00 2.43
351 353 1.073923 AGAATGTCAGGCCGGTTTTCT 59.926 47.619 1.90 7.26 0.00 2.52
353 355 1.995376 ATGTCAGGCCGGTTTTCTTT 58.005 45.000 1.90 0.00 0.00 2.52
385 427 3.256383 CACCACATCATGAGGCAAAGAAA 59.744 43.478 7.40 0.00 30.80 2.52
489 542 1.084289 CTTAACCTAACCAGCCGCAC 58.916 55.000 0.00 0.00 0.00 5.34
632 708 3.800506 GTGGTATTTTAGTCGGGATCACG 59.199 47.826 12.22 12.22 0.00 4.35
686 791 3.527533 CATTTGGAATCCATGCACCAAG 58.472 45.455 1.39 0.00 42.16 3.61
717 822 1.079819 CTGTCGGCCTGTCATCGTT 60.080 57.895 0.00 0.00 0.00 3.85
741 846 2.247267 CGTTTGGCCGAACGTGAC 59.753 61.111 38.97 14.95 45.32 3.67
847 981 1.333619 CTGGAAACGAAACAGGGTGTG 59.666 52.381 0.00 0.00 0.00 3.82
848 982 0.030235 GGAAACGAAACAGGGTGTGC 59.970 55.000 0.00 0.00 0.00 4.57
849 983 0.736053 GAAACGAAACAGGGTGTGCA 59.264 50.000 0.00 0.00 0.00 4.57
850 984 0.454196 AAACGAAACAGGGTGTGCAC 59.546 50.000 10.75 10.75 0.00 4.57
887 1026 2.427410 CTTTGCTCGCGTTGCCAC 60.427 61.111 19.93 1.16 0.00 5.01
899 1038 1.001020 TTGCCACCCATCGCATTCT 60.001 52.632 0.00 0.00 34.35 2.40
926 1076 0.670854 GGCGTCTGGAGTTTGGAGAC 60.671 60.000 0.00 0.00 34.04 3.36
995 1213 4.492160 TCGATCGACGCACAGGCC 62.492 66.667 15.15 0.00 42.26 5.19
1184 1402 3.791586 GCTGGGCCTGGAGACCTC 61.792 72.222 12.70 0.00 0.00 3.85
1263 1484 2.931649 TTCCCCTTCCCGTCCACC 60.932 66.667 0.00 0.00 0.00 4.61
1473 1709 4.856607 GCCTCGGCCTCGTTCTCG 62.857 72.222 0.00 0.00 37.69 4.04
1647 1883 4.314440 GCCACGGTCACCTGCTCA 62.314 66.667 0.00 0.00 0.00 4.26
1782 2021 1.604915 GAGGAGCAAAGGAGGGGAC 59.395 63.158 0.00 0.00 0.00 4.46
1892 2131 4.363990 CGACCTGTGCTGCTCCGT 62.364 66.667 0.00 0.00 0.00 4.69
1949 2188 1.748122 TCGTGCTCCGGTAGAGTCC 60.748 63.158 0.00 0.00 45.21 3.85
1973 2219 1.674057 GCAGGGTCCGGATATCTGG 59.326 63.158 22.91 22.91 43.86 3.86
1977 2223 1.506418 AGGGTCCGGATATCTGGGTAA 59.494 52.381 27.12 8.42 42.72 2.85
1990 2236 3.659786 TCTGGGTAACTCGTGAAACATG 58.340 45.455 0.00 0.00 35.74 3.21
1991 2237 3.070446 TCTGGGTAACTCGTGAAACATGT 59.930 43.478 0.00 0.00 35.74 3.21
1992 2238 4.281435 TCTGGGTAACTCGTGAAACATGTA 59.719 41.667 0.00 0.00 35.74 2.29
2020 2266 8.918202 ACAACAGTTTTTCCACTAGAATATGA 57.082 30.769 0.00 0.00 33.44 2.15
2022 2268 7.617041 ACAGTTTTTCCACTAGAATATGAGC 57.383 36.000 0.00 0.00 33.44 4.26
2028 2277 9.912634 TTTTTCCACTAGAATATGAGCAAAAAG 57.087 29.630 0.00 0.00 33.44 2.27
2035 2284 8.322091 ACTAGAATATGAGCAAAAAGGTACAGT 58.678 33.333 0.00 0.00 0.00 3.55
2074 2327 2.687935 TGAAGCGGGCAAATCCTATTTC 59.312 45.455 0.00 0.00 34.39 2.17
2083 2338 6.710744 CGGGCAAATCCTATTTCTACTGTTAT 59.289 38.462 0.00 0.00 34.39 1.89
2087 2342 9.000486 GCAAATCCTATTTCTACTGTTATACCC 58.000 37.037 0.00 0.00 0.00 3.69
2164 2419 1.617850 TGGTGACAAATCCCACATTGC 59.382 47.619 0.00 0.00 37.44 3.56
2183 2482 4.344865 ACATGTGTCCCACCGGCC 62.345 66.667 0.00 0.00 32.73 6.13
2193 2492 2.589540 CACCGGCCCTCATTGCTA 59.410 61.111 0.00 0.00 0.00 3.49
2195 2494 2.592861 CCGGCCCTCATTGCTAGC 60.593 66.667 8.10 8.10 0.00 3.42
2273 2639 1.699083 TGATCCAGTGAAGACAGGCAA 59.301 47.619 0.00 0.00 0.00 4.52
2287 2653 0.680280 AGGCAAGAGCTTGGATGCAG 60.680 55.000 11.78 0.00 40.51 4.41
2322 2688 5.969423 ACTTCAATGCCAATAGTTCAATGG 58.031 37.500 0.00 0.00 37.29 3.16
2352 2718 5.068460 CACAAATCCACCCAGTTAACTCAAA 59.932 40.000 4.77 0.00 0.00 2.69
2370 2736 1.043022 AAGTTGAGCAGCCCAAAAGG 58.957 50.000 0.00 0.00 39.47 3.11
2384 2750 0.736325 AAAAGGCCTGACGACGATCG 60.736 55.000 14.88 14.88 46.93 3.69
2568 2944 3.124297 GCTCGTTTCTTTCATCTCAGGTG 59.876 47.826 0.00 0.00 0.00 4.00
2608 2990 3.099267 CGCTGATCGTTCCTAATTCCT 57.901 47.619 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.605710 CTTTATTCATGCTGCCCGGAG 59.394 52.381 0.73 0.00 0.00 4.63
13 14 1.679139 CTTTATTCATGCTGCCCGGA 58.321 50.000 0.73 0.00 0.00 5.14
14 15 0.031178 GCTTTATTCATGCTGCCCGG 59.969 55.000 0.00 0.00 0.00 5.73
15 16 0.740149 TGCTTTATTCATGCTGCCCG 59.260 50.000 0.00 0.00 0.00 6.13
16 17 1.477700 TGTGCTTTATTCATGCTGCCC 59.522 47.619 0.00 0.00 0.00 5.36
17 18 2.805845 CTGTGCTTTATTCATGCTGCC 58.194 47.619 0.00 0.00 0.00 4.85
21 22 3.629398 AGTAGGCTGTGCTTTATTCATGC 59.371 43.478 0.00 0.00 0.00 4.06
40 41 5.660460 AGCACATTCATGTATCGTTGAGTA 58.340 37.500 0.00 0.00 39.39 2.59
84 86 5.520632 TGTGTCAAAAGTTCGAGAGACTAG 58.479 41.667 0.00 0.00 41.84 2.57
85 87 5.509716 TGTGTCAAAAGTTCGAGAGACTA 57.490 39.130 0.00 0.00 41.84 2.59
119 121 4.560819 CAGTCGTTCTCAGTTATGCTCTTC 59.439 45.833 0.00 0.00 0.00 2.87
145 147 6.590292 ACTCGTCATAAGGTACACATTTCTTG 59.410 38.462 0.00 0.00 0.00 3.02
153 155 5.808042 TGTAGACTCGTCATAAGGTACAC 57.192 43.478 0.00 0.00 0.00 2.90
199 201 4.382362 GGGTAGTGTCATAGGTGTGGTAAC 60.382 50.000 0.00 0.00 0.00 2.50
200 202 3.770933 GGGTAGTGTCATAGGTGTGGTAA 59.229 47.826 0.00 0.00 0.00 2.85
201 203 3.245694 TGGGTAGTGTCATAGGTGTGGTA 60.246 47.826 0.00 0.00 0.00 3.25
202 204 2.185387 GGGTAGTGTCATAGGTGTGGT 58.815 52.381 0.00 0.00 0.00 4.16
203 205 2.093658 GTGGGTAGTGTCATAGGTGTGG 60.094 54.545 0.00 0.00 0.00 4.17
204 206 2.832129 AGTGGGTAGTGTCATAGGTGTG 59.168 50.000 0.00 0.00 0.00 3.82
205 207 3.185880 AGTGGGTAGTGTCATAGGTGT 57.814 47.619 0.00 0.00 0.00 4.16
206 208 4.893524 TCATAGTGGGTAGTGTCATAGGTG 59.106 45.833 0.00 0.00 0.00 4.00
207 209 5.138758 TCATAGTGGGTAGTGTCATAGGT 57.861 43.478 0.00 0.00 0.00 3.08
208 210 5.011125 CCTTCATAGTGGGTAGTGTCATAGG 59.989 48.000 0.00 0.00 0.00 2.57
209 211 5.598830 ACCTTCATAGTGGGTAGTGTCATAG 59.401 44.000 0.00 0.00 0.00 2.23
210 212 5.525484 ACCTTCATAGTGGGTAGTGTCATA 58.475 41.667 0.00 0.00 0.00 2.15
211 213 4.362677 ACCTTCATAGTGGGTAGTGTCAT 58.637 43.478 0.00 0.00 0.00 3.06
212 214 3.786553 ACCTTCATAGTGGGTAGTGTCA 58.213 45.455 0.00 0.00 0.00 3.58
213 215 5.517322 CTACCTTCATAGTGGGTAGTGTC 57.483 47.826 9.46 0.00 44.30 3.67
219 221 9.310449 CTATATGTTACTACCTTCATAGTGGGT 57.690 37.037 0.00 0.00 36.09 4.51
220 222 9.529823 TCTATATGTTACTACCTTCATAGTGGG 57.470 37.037 0.00 0.00 36.09 4.61
258 260 9.401058 GGGAGTAACTTAGACTAGTAACATACA 57.599 37.037 0.00 0.00 0.00 2.29
259 261 8.845227 GGGGAGTAACTTAGACTAGTAACATAC 58.155 40.741 0.00 0.00 0.00 2.39
260 262 8.560039 TGGGGAGTAACTTAGACTAGTAACATA 58.440 37.037 0.00 0.00 0.00 2.29
261 263 7.341512 GTGGGGAGTAACTTAGACTAGTAACAT 59.658 40.741 0.00 0.00 0.00 2.71
262 264 6.660949 GTGGGGAGTAACTTAGACTAGTAACA 59.339 42.308 0.00 0.00 0.00 2.41
263 265 6.889177 AGTGGGGAGTAACTTAGACTAGTAAC 59.111 42.308 0.00 0.00 0.00 2.50
264 266 7.037342 AGTGGGGAGTAACTTAGACTAGTAA 57.963 40.000 0.00 0.00 0.00 2.24
265 267 6.649041 AGTGGGGAGTAACTTAGACTAGTA 57.351 41.667 0.00 0.00 0.00 1.82
266 268 5.533333 AGTGGGGAGTAACTTAGACTAGT 57.467 43.478 0.00 0.00 0.00 2.57
267 269 7.229106 GTCATAGTGGGGAGTAACTTAGACTAG 59.771 44.444 0.00 0.00 31.58 2.57
268 270 7.059156 GTCATAGTGGGGAGTAACTTAGACTA 58.941 42.308 0.00 0.00 31.58 2.59
269 271 5.892686 GTCATAGTGGGGAGTAACTTAGACT 59.107 44.000 0.00 0.00 31.58 3.24
270 272 5.068855 GGTCATAGTGGGGAGTAACTTAGAC 59.931 48.000 0.00 0.00 32.58 2.59
271 273 5.206587 GGTCATAGTGGGGAGTAACTTAGA 58.793 45.833 0.00 0.00 0.00 2.10
272 274 4.960469 TGGTCATAGTGGGGAGTAACTTAG 59.040 45.833 0.00 0.00 0.00 2.18
273 275 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
274 276 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
275 277 3.375699 CTGGTCATAGTGGGGAGTAACT 58.624 50.000 0.00 0.00 0.00 2.24
276 278 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
277 279 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
278 280 1.691482 GGCTGGTCATAGTGGGGAGTA 60.691 57.143 0.00 0.00 0.00 2.59
279 281 0.983378 GGCTGGTCATAGTGGGGAGT 60.983 60.000 0.00 0.00 0.00 3.85
280 282 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
281 283 0.253160 AAGGCTGGTCATAGTGGGGA 60.253 55.000 0.00 0.00 0.00 4.81
282 284 1.507140 TAAGGCTGGTCATAGTGGGG 58.493 55.000 0.00 0.00 0.00 4.96
283 285 2.705658 TCATAAGGCTGGTCATAGTGGG 59.294 50.000 0.00 0.00 0.00 4.61
284 286 3.733337 GTCATAAGGCTGGTCATAGTGG 58.267 50.000 0.00 0.00 0.00 4.00
285 287 3.068165 TCGTCATAAGGCTGGTCATAGTG 59.932 47.826 0.00 0.00 0.00 2.74
286 288 3.296854 TCGTCATAAGGCTGGTCATAGT 58.703 45.455 0.00 0.00 0.00 2.12
287 289 4.322080 TTCGTCATAAGGCTGGTCATAG 57.678 45.455 0.00 0.00 0.00 2.23
288 290 4.746535 TTTCGTCATAAGGCTGGTCATA 57.253 40.909 0.00 0.00 0.00 2.15
289 291 3.627395 TTTCGTCATAAGGCTGGTCAT 57.373 42.857 0.00 0.00 0.00 3.06
290 292 3.055458 TCATTTCGTCATAAGGCTGGTCA 60.055 43.478 0.00 0.00 0.00 4.02
291 293 3.531538 TCATTTCGTCATAAGGCTGGTC 58.468 45.455 0.00 0.00 0.00 4.02
292 294 3.627395 TCATTTCGTCATAAGGCTGGT 57.373 42.857 0.00 0.00 0.00 4.00
293 295 3.242413 CGTTCATTTCGTCATAAGGCTGG 60.242 47.826 0.00 0.00 0.00 4.85
294 296 3.370978 ACGTTCATTTCGTCATAAGGCTG 59.629 43.478 0.00 0.00 36.85 4.85
295 297 3.370978 CACGTTCATTTCGTCATAAGGCT 59.629 43.478 0.00 0.00 39.55 4.58
296 298 3.670203 CACGTTCATTTCGTCATAAGGC 58.330 45.455 0.00 0.00 39.55 4.35
297 299 3.370978 AGCACGTTCATTTCGTCATAAGG 59.629 43.478 0.00 0.00 39.55 2.69
298 300 4.584029 AGCACGTTCATTTCGTCATAAG 57.416 40.909 0.00 0.00 39.55 1.73
299 301 5.050023 TGAAAGCACGTTCATTTCGTCATAA 60.050 36.000 10.58 0.00 39.55 1.90
324 326 3.081804 CCGGCCTGACATTCTTTAAGTT 58.918 45.455 0.00 0.00 0.00 2.66
332 334 1.534729 AGAAAACCGGCCTGACATTC 58.465 50.000 0.00 2.49 0.00 2.67
348 350 2.946329 TGTGGTGCGCTTTTCTAAAGAA 59.054 40.909 9.73 0.00 0.00 2.52
349 351 2.566913 TGTGGTGCGCTTTTCTAAAGA 58.433 42.857 9.73 0.00 0.00 2.52
351 353 2.881513 TGATGTGGTGCGCTTTTCTAAA 59.118 40.909 9.73 0.00 0.00 1.85
353 355 2.177394 TGATGTGGTGCGCTTTTCTA 57.823 45.000 9.73 0.00 0.00 2.10
385 427 1.968017 CGATGCATTGGCCGGCTAT 60.968 57.895 28.56 17.37 40.13 2.97
515 583 1.663445 GCTATACAGTACAGCGGCTCG 60.663 57.143 0.00 0.00 0.00 5.03
520 588 3.908978 CGAATGAGCTATACAGTACAGCG 59.091 47.826 5.17 0.00 40.29 5.18
649 725 1.826385 AATGGAAAGAGCCGGTTGAG 58.174 50.000 1.90 0.00 0.00 3.02
698 803 1.532604 AACGATGACAGGCCGACAGA 61.533 55.000 0.00 0.00 0.00 3.41
717 822 0.664224 GTTCGGCCAAACGGAAAGAA 59.336 50.000 2.24 0.00 39.09 2.52
795 905 2.357034 TTGGCGCCTTCGTGTCTC 60.357 61.111 29.70 0.00 38.14 3.36
847 981 1.650238 GTTTTATAGGCGCGCGTGC 60.650 57.895 35.15 35.15 37.91 5.34
848 982 0.095589 TTGTTTTATAGGCGCGCGTG 59.904 50.000 34.10 16.86 0.00 5.34
849 983 0.095762 GTTGTTTTATAGGCGCGCGT 59.904 50.000 32.35 30.14 0.00 6.01
850 984 0.372334 AGTTGTTTTATAGGCGCGCG 59.628 50.000 28.44 28.44 0.00 6.86
887 1026 2.974698 GCGGGAGAATGCGATGGG 60.975 66.667 0.00 0.00 0.00 4.00
926 1076 1.630148 GGAGGTCGATCGAACAACAG 58.370 55.000 32.96 0.00 33.52 3.16
997 1215 2.736682 CCGTGGTCGTCGGCATTTC 61.737 63.158 0.00 0.00 41.48 2.17
1263 1484 1.450312 GGCATCCGTGGAAGTGGAG 60.450 63.158 0.00 0.00 37.76 3.86
1741 1980 4.161295 CTCCATCGCGGCCTCCAA 62.161 66.667 6.13 0.00 33.14 3.53
1782 2021 2.867109 TGGCCTCCTCTCTTTCTTTG 57.133 50.000 3.32 0.00 0.00 2.77
1950 2189 1.122019 ATATCCGGACCCTGCCTGAC 61.122 60.000 6.12 0.00 0.00 3.51
1951 2190 0.832135 GATATCCGGACCCTGCCTGA 60.832 60.000 6.12 0.00 0.00 3.86
1952 2191 0.833834 AGATATCCGGACCCTGCCTG 60.834 60.000 6.12 0.00 0.00 4.85
1973 2219 6.151691 TGTACTACATGTTTCACGAGTTACC 58.848 40.000 2.30 0.00 0.00 2.85
1977 2223 5.593968 TGTTGTACTACATGTTTCACGAGT 58.406 37.500 2.30 2.42 0.00 4.18
1990 2236 8.652810 TTCTAGTGGAAAAACTGTTGTACTAC 57.347 34.615 0.05 0.05 0.00 2.73
2018 2264 5.592282 TCAAATCACTGTACCTTTTTGCTCA 59.408 36.000 0.00 0.00 0.00 4.26
2020 2266 5.594317 AGTCAAATCACTGTACCTTTTTGCT 59.406 36.000 0.00 0.00 0.00 3.91
2022 2268 5.687285 GCAGTCAAATCACTGTACCTTTTTG 59.313 40.000 2.73 0.00 44.98 2.44
2028 2277 3.433615 GTCAGCAGTCAAATCACTGTACC 59.566 47.826 2.73 0.00 44.98 3.34
2045 2294 3.426568 GCCCGCTTCACTGTCAGC 61.427 66.667 0.00 0.00 0.00 4.26
2074 2327 7.478520 CCTGAATTTTCGGGTATAACAGTAG 57.521 40.000 9.61 0.00 46.49 2.57
2087 2342 1.267806 ACTGTGCTGCCTGAATTTTCG 59.732 47.619 0.00 0.00 0.00 3.46
2136 2391 2.943033 GGGATTTGTCACCAATAGTCGG 59.057 50.000 0.00 0.00 0.00 4.79
2195 2494 3.188786 GTGGGCGTCAGCTTAGCG 61.189 66.667 0.00 0.00 44.37 4.26
2246 2572 4.635223 TGTCTTCACTGGATCAAGTTCAG 58.365 43.478 0.00 0.00 34.91 3.02
2273 2639 1.220206 CGTCCTGCATCCAAGCTCT 59.780 57.895 0.00 0.00 34.99 4.09
2287 2653 2.413453 GCATTGAAGTCTGAGTTCGTCC 59.587 50.000 17.77 5.38 30.24 4.79
2322 2688 1.608590 CTGGGTGGATTTGTGTGTCAC 59.391 52.381 0.00 0.00 34.56 3.67
2352 2718 2.737503 CCTTTTGGGCTGCTCAACT 58.262 52.632 15.73 0.00 35.46 3.16
2370 2736 2.351336 ATTCCCGATCGTCGTCAGGC 62.351 60.000 15.09 0.00 38.40 4.85
2384 2750 5.810074 GTGTAAATTTGGTGTGCATATTCCC 59.190 40.000 0.00 0.00 0.00 3.97
2428 2794 2.121689 ACCCTGGCCACCCTACAA 60.122 61.111 0.00 0.00 0.00 2.41
2568 2944 2.724690 CGTACATACAGATAACAGGCGC 59.275 50.000 0.00 0.00 0.00 6.53
2771 3153 1.663702 CGCGGTTCCTTCGTTGACT 60.664 57.895 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.