Multiple sequence alignment - TraesCS4B01G101500

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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 TraesCS4B01G101500 chr4B 100.000 4691 0 0 1 4691 107234860 107239550 0.000000e+00 8663.0
1 TraesCS4B01G101500 chr4B 90.275 545 49 2 4148 4691 188592710 188593251 0.000000e+00 710.0
2 TraesCS4B01G101500 chr4B 88.780 508 52 4 4148 4654 402759355 402759858 6.670000e-173 617.0
3 TraesCS4B01G101500 chr4B 85.246 183 21 3 180 356 178015946 178015764 2.880000e-42 183.0
4 TraesCS4B01G101500 chr4A 96.687 3411 107 4 739 4146 512582312 512578905 0.000000e+00 5668.0
5 TraesCS4B01G101500 chr4A 96.677 331 8 2 413 740 512582724 512582394 8.870000e-152 547.0
6 TraesCS4B01G101500 chr4A 91.053 190 3 3 1 189 512582892 512582716 1.300000e-60 244.0
7 TraesCS4B01G101500 chr4A 78.889 180 33 4 182 356 129526156 129525977 2.970000e-22 117.0
8 TraesCS4B01G101500 chr4D 97.465 1223 26 3 413 1630 74845275 74846497 0.000000e+00 2082.0
9 TraesCS4B01G101500 chr4D 88.214 543 57 2 4149 4691 47690919 47691454 3.960000e-180 641.0
10 TraesCS4B01G101500 chr4D 95.855 193 4 2 1 189 74845091 74845283 4.560000e-80 309.0
11 TraesCS4B01G101500 chr4D 94.340 53 0 3 368 418 345150907 345150958 1.400000e-10 78.7
12 TraesCS4B01G101500 chr2D 89.273 550 49 7 4150 4691 641576470 641575923 0.000000e+00 680.0
13 TraesCS4B01G101500 chr2D 86.898 374 32 4 646 1018 598261326 598260969 2.030000e-108 403.0
14 TraesCS4B01G101500 chr2D 92.537 201 14 1 180 379 194818848 194819048 2.140000e-73 287.0
15 TraesCS4B01G101500 chr2D 91.707 205 14 2 182 383 315859248 315859044 9.940000e-72 281.0
16 TraesCS4B01G101500 chr2D 72.414 667 155 23 2350 3006 35782879 35783526 8.020000e-43 185.0
17 TraesCS4B01G101500 chr7B 90.157 508 36 7 4138 4644 67903506 67903012 0.000000e+00 649.0
18 TraesCS4B01G101500 chr7B 86.042 566 52 13 4148 4691 412768331 412767771 2.430000e-162 582.0
19 TraesCS4B01G101500 chr7B 100.000 46 0 0 4646 4691 67902989 67902944 8.360000e-13 86.1
20 TraesCS4B01G101500 chr3D 88.235 544 58 4 4148 4691 108025366 108025903 0.000000e+00 645.0
21 TraesCS4B01G101500 chr1D 89.841 502 43 4 4148 4645 493226518 493226021 5.120000e-179 638.0
22 TraesCS4B01G101500 chr1D 87.701 374 29 4 646 1018 71868831 71868474 2.020000e-113 420.0
23 TraesCS4B01G101500 chr1D 87.105 380 32 4 640 1018 22269122 22269485 9.390000e-112 414.0
24 TraesCS4B01G101500 chr1D 85.965 171 21 3 178 345 367002293 367002463 3.730000e-41 180.0
25 TraesCS4B01G101500 chr1D 88.462 130 10 4 413 540 22268994 22269120 8.130000e-33 152.0
26 TraesCS4B01G101500 chr1D 88.462 130 10 4 413 540 71868965 71868839 8.130000e-33 152.0
27 TraesCS4B01G101500 chr5B 88.976 508 49 4 4148 4654 28708331 28707830 5.160000e-174 621.0
28 TraesCS4B01G101500 chr3B 88.668 503 53 2 4144 4645 24269504 24270003 1.120000e-170 610.0
29 TraesCS4B01G101500 chr5D 87.701 374 29 4 646 1018 480078662 480078305 2.020000e-113 420.0
30 TraesCS4B01G101500 chr5D 93.500 200 10 2 182 378 279292871 279293070 1.280000e-75 294.0
31 TraesCS4B01G101500 chr5D 94.845 97 5 0 444 540 480078766 480078670 8.130000e-33 152.0
32 TraesCS4B01G101500 chr5D 94.231 52 1 2 367 417 364820988 364821038 1.400000e-10 78.7
33 TraesCS4B01G101500 chr5D 92.727 55 0 4 368 421 164514310 164514361 5.030000e-10 76.8
34 TraesCS4B01G101500 chr6A 78.421 570 67 26 4148 4691 535373282 535373821 2.110000e-83 320.0
35 TraesCS4B01G101500 chr7A 78.484 488 76 15 4148 4631 237561432 237560970 4.590000e-75 292.0
36 TraesCS4B01G101500 chr7A 91.707 205 14 2 182 383 730827242 730827038 9.940000e-72 281.0
37 TraesCS4B01G101500 chr7A 77.871 479 69 21 4172 4644 609406535 609406088 3.600000e-66 263.0
38 TraesCS4B01G101500 chr7D 91.827 208 12 3 176 378 27553926 27554133 7.680000e-73 285.0
39 TraesCS4B01G101500 chr7D 87.712 236 23 6 182 414 238969228 238969460 2.150000e-68 270.0
40 TraesCS4B01G101500 chr6B 92.537 201 12 3 181 380 40710743 40710545 7.680000e-73 285.0
41 TraesCS4B01G101500 chr6B 87.624 202 22 2 182 380 715331015 715331216 1.020000e-56 231.0
42 TraesCS4B01G101500 chr6B 83.851 161 23 2 193 350 517112652 517112812 2.920000e-32 150.0
43 TraesCS4B01G101500 chr3A 91.080 213 16 3 170 380 246937069 246937280 7.680000e-73 285.0
44 TraesCS4B01G101500 chr3A 89.498 219 18 4 168 383 13847803 13847587 5.980000e-69 272.0
45 TraesCS4B01G101500 chr2A 73.412 677 150 25 2339 3006 38966833 38967488 4.720000e-55 226.0
46 TraesCS4B01G101500 chr2A 95.294 85 4 0 4607 4691 384674423 384674339 8.190000e-28 135.0
47 TraesCS4B01G101500 chr2B 72.929 676 155 23 2339 3006 58977723 58978378 4.760000e-50 209.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G101500 chr4B 107234860 107239550 4690 False 8663.00 8663 100.000000 1 4691 1 chr4B.!!$F1 4690
1 TraesCS4B01G101500 chr4B 188592710 188593251 541 False 710.00 710 90.275000 4148 4691 1 chr4B.!!$F2 543
2 TraesCS4B01G101500 chr4B 402759355 402759858 503 False 617.00 617 88.780000 4148 4654 1 chr4B.!!$F3 506
3 TraesCS4B01G101500 chr4A 512578905 512582892 3987 True 2153.00 5668 94.805667 1 4146 3 chr4A.!!$R2 4145
4 TraesCS4B01G101500 chr4D 74845091 74846497 1406 False 1195.50 2082 96.660000 1 1630 2 chr4D.!!$F3 1629
5 TraesCS4B01G101500 chr4D 47690919 47691454 535 False 641.00 641 88.214000 4149 4691 1 chr4D.!!$F1 542
6 TraesCS4B01G101500 chr2D 641575923 641576470 547 True 680.00 680 89.273000 4150 4691 1 chr2D.!!$R3 541
7 TraesCS4B01G101500 chr7B 412767771 412768331 560 True 582.00 582 86.042000 4148 4691 1 chr7B.!!$R1 543
8 TraesCS4B01G101500 chr7B 67902944 67903506 562 True 367.55 649 95.078500 4138 4691 2 chr7B.!!$R2 553
9 TraesCS4B01G101500 chr3D 108025366 108025903 537 False 645.00 645 88.235000 4148 4691 1 chr3D.!!$F1 543
10 TraesCS4B01G101500 chr5B 28707830 28708331 501 True 621.00 621 88.976000 4148 4654 1 chr5B.!!$R1 506
11 TraesCS4B01G101500 chr6A 535373282 535373821 539 False 320.00 320 78.421000 4148 4691 1 chr6A.!!$F1 543
12 TraesCS4B01G101500 chr2A 38966833 38967488 655 False 226.00 226 73.412000 2339 3006 1 chr2A.!!$F1 667
13 TraesCS4B01G101500 chr2B 58977723 58978378 655 False 209.00 209 72.929000 2339 3006 1 chr2B.!!$F1 667

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
838 930 0.250727 ACAGGGTGCAAGCGTTATGT 60.251 50.000 0.0 0.0 33.03 2.29 F
1359 1451 1.256376 CGCAAGATACTGTGTGATCGC 59.744 52.381 0.0 0.0 43.02 4.58 F
2012 2106 0.178891 AGGTCCTCCAGCCTTCAGAA 60.179 55.000 0.0 0.0 35.89 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 1790 0.539438 TGGGCCTGTTGATTGGTGAC 60.539 55.000 4.53 0.0 0.00 3.67 R
3171 3265 0.109597 GCCAGGTCAAATGCACTTCG 60.110 55.000 0.00 0.0 0.00 3.79 R
3713 3807 1.002502 GCCCTCGGTAAAGGCAAGT 60.003 57.895 0.00 0.0 46.34 3.16 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
182 186 8.699130 CCTGCATACACCATGATCTATCTAATA 58.301 37.037 0.00 0.00 36.69 0.98
183 187 9.526713 CTGCATACACCATGATCTATCTAATAC 57.473 37.037 0.00 0.00 36.69 1.89
184 188 9.259832 TGCATACACCATGATCTATCTAATACT 57.740 33.333 0.00 0.00 36.69 2.12
185 189 9.743057 GCATACACCATGATCTATCTAATACTC 57.257 37.037 0.00 0.00 36.69 2.59
187 191 7.726033 ACACCATGATCTATCTAATACTCCC 57.274 40.000 0.00 0.00 0.00 4.30
188 192 7.483018 ACACCATGATCTATCTAATACTCCCT 58.517 38.462 0.00 0.00 0.00 4.20
189 193 7.617723 ACACCATGATCTATCTAATACTCCCTC 59.382 40.741 0.00 0.00 0.00 4.30
190 194 7.069331 CACCATGATCTATCTAATACTCCCTCC 59.931 44.444 0.00 0.00 0.00 4.30
191 195 6.264292 CCATGATCTATCTAATACTCCCTCCG 59.736 46.154 0.00 0.00 0.00 4.63
192 196 6.390048 TGATCTATCTAATACTCCCTCCGT 57.610 41.667 0.00 0.00 0.00 4.69
193 197 6.791371 TGATCTATCTAATACTCCCTCCGTT 58.209 40.000 0.00 0.00 0.00 4.44
194 198 7.239438 TGATCTATCTAATACTCCCTCCGTTT 58.761 38.462 0.00 0.00 0.00 3.60
195 199 7.728981 TGATCTATCTAATACTCCCTCCGTTTT 59.271 37.037 0.00 0.00 0.00 2.43
196 200 7.909485 TCTATCTAATACTCCCTCCGTTTTT 57.091 36.000 0.00 0.00 0.00 1.94
197 201 9.597681 ATCTATCTAATACTCCCTCCGTTTTTA 57.402 33.333 0.00 0.00 0.00 1.52
198 202 9.597681 TCTATCTAATACTCCCTCCGTTTTTAT 57.402 33.333 0.00 0.00 0.00 1.40
203 207 9.828039 CTAATACTCCCTCCGTTTTTATTTAGT 57.172 33.333 0.00 0.00 0.00 2.24
204 208 8.728337 AATACTCCCTCCGTTTTTATTTAGTC 57.272 34.615 0.00 0.00 0.00 2.59
205 209 5.494724 ACTCCCTCCGTTTTTATTTAGTCC 58.505 41.667 0.00 0.00 0.00 3.85
206 210 4.506758 TCCCTCCGTTTTTATTTAGTCCG 58.493 43.478 0.00 0.00 0.00 4.79
207 211 4.020307 TCCCTCCGTTTTTATTTAGTCCGT 60.020 41.667 0.00 0.00 0.00 4.69
208 212 4.093850 CCCTCCGTTTTTATTTAGTCCGTG 59.906 45.833 0.00 0.00 0.00 4.94
209 213 4.692155 CCTCCGTTTTTATTTAGTCCGTGT 59.308 41.667 0.00 0.00 0.00 4.49
210 214 5.868801 CCTCCGTTTTTATTTAGTCCGTGTA 59.131 40.000 0.00 0.00 0.00 2.90
211 215 6.536224 CCTCCGTTTTTATTTAGTCCGTGTAT 59.464 38.462 0.00 0.00 0.00 2.29
212 216 7.064966 CCTCCGTTTTTATTTAGTCCGTGTATT 59.935 37.037 0.00 0.00 0.00 1.89
213 217 8.994429 TCCGTTTTTATTTAGTCCGTGTATTA 57.006 30.769 0.00 0.00 0.00 0.98
214 218 9.086336 TCCGTTTTTATTTAGTCCGTGTATTAG 57.914 33.333 0.00 0.00 0.00 1.73
215 219 7.847564 CCGTTTTTATTTAGTCCGTGTATTAGC 59.152 37.037 0.00 0.00 0.00 3.09
216 220 8.598075 CGTTTTTATTTAGTCCGTGTATTAGCT 58.402 33.333 0.00 0.00 0.00 3.32
220 224 6.920569 ATTTAGTCCGTGTATTAGCTTTGG 57.079 37.500 0.00 0.00 0.00 3.28
221 225 3.975168 AGTCCGTGTATTAGCTTTGGT 57.025 42.857 0.00 0.00 0.00 3.67
222 226 3.858247 AGTCCGTGTATTAGCTTTGGTC 58.142 45.455 0.00 0.00 0.00 4.02
223 227 3.259876 AGTCCGTGTATTAGCTTTGGTCA 59.740 43.478 0.00 0.00 0.00 4.02
224 228 3.998341 GTCCGTGTATTAGCTTTGGTCAA 59.002 43.478 0.00 0.00 0.00 3.18
225 229 4.453136 GTCCGTGTATTAGCTTTGGTCAAA 59.547 41.667 0.00 0.00 0.00 2.69
247 251 7.812309 AAAGTCAAGCTTTGTTAACTTTGAC 57.188 32.000 20.18 20.18 45.00 3.18
248 252 5.891451 AGTCAAGCTTTGTTAACTTTGACC 58.109 37.500 22.03 13.03 0.00 4.02
249 253 5.417580 AGTCAAGCTTTGTTAACTTTGACCA 59.582 36.000 22.03 0.00 0.00 4.02
250 254 6.071616 AGTCAAGCTTTGTTAACTTTGACCAA 60.072 34.615 22.03 3.76 0.00 3.67
251 255 6.253512 GTCAAGCTTTGTTAACTTTGACCAAG 59.746 38.462 18.66 8.41 38.64 3.61
265 269 8.664211 ACTTTGACCAAGTTTGTAAACAAAAA 57.336 26.923 9.72 0.00 43.89 1.94
266 270 9.278978 ACTTTGACCAAGTTTGTAAACAAAAAT 57.721 25.926 9.72 0.06 43.89 1.82
270 274 9.706691 TGACCAAGTTTGTAAACAAAAATTACA 57.293 25.926 9.72 0.00 46.08 2.41
381 385 9.403583 TGTTTTCTATAAACTTGGTCAAACTCT 57.596 29.630 0.00 0.00 0.00 3.24
389 393 7.759489 AAACTTGGTCAAACTCTAATATGCA 57.241 32.000 0.00 0.00 0.00 3.96
390 394 6.992063 ACTTGGTCAAACTCTAATATGCAG 57.008 37.500 0.00 0.00 0.00 4.41
391 395 6.711277 ACTTGGTCAAACTCTAATATGCAGA 58.289 36.000 0.00 0.00 0.00 4.26
392 396 6.820656 ACTTGGTCAAACTCTAATATGCAGAG 59.179 38.462 11.37 11.37 44.28 3.35
409 413 6.817765 TGCAGAGTAAATAAAAACAGAGGG 57.182 37.500 0.00 0.00 0.00 4.30
410 414 6.539173 TGCAGAGTAAATAAAAACAGAGGGA 58.461 36.000 0.00 0.00 0.00 4.20
411 415 6.655003 TGCAGAGTAAATAAAAACAGAGGGAG 59.345 38.462 0.00 0.00 0.00 4.30
412 416 6.655425 GCAGAGTAAATAAAAACAGAGGGAGT 59.345 38.462 0.00 0.00 0.00 3.85
605 611 4.765273 TGCACTGTTTCTTAAGTCTGTCA 58.235 39.130 1.63 3.94 0.00 3.58
698 706 6.663953 ACTGGCATATGTAGGTGGTATAGTAG 59.336 42.308 4.29 0.00 0.00 2.57
834 926 0.324943 ATCTACAGGGTGCAAGCGTT 59.675 50.000 0.00 0.00 33.03 4.84
838 930 0.250727 ACAGGGTGCAAGCGTTATGT 60.251 50.000 0.00 0.00 33.03 2.29
965 1057 3.764434 TGCCAGGCTGCTAGTAGTATATC 59.236 47.826 14.15 0.00 0.00 1.63
1300 1392 6.126863 TCCATCCTGATAAAAACACACTCT 57.873 37.500 0.00 0.00 0.00 3.24
1359 1451 1.256376 CGCAAGATACTGTGTGATCGC 59.744 52.381 0.00 0.00 43.02 4.58
1381 1473 1.278238 GGAGCGGTCTTTGTATGACG 58.722 55.000 15.18 0.00 35.45 4.35
1615 1707 2.094906 GCATTCAAGCTGCATGAACAGA 60.095 45.455 20.85 1.06 39.43 3.41
1632 1724 1.734465 CAGACAATGCCCTCGAGTTTC 59.266 52.381 12.31 0.22 0.00 2.78
1670 1762 5.649782 AATAATGCTGAAGTTTCACCTGG 57.350 39.130 0.00 0.00 32.90 4.45
1760 1854 4.469586 TGAACCTACCATGAATGCTACTCA 59.530 41.667 0.00 0.00 0.00 3.41
1763 1857 6.006275 ACCTACCATGAATGCTACTCAAAT 57.994 37.500 0.00 0.00 0.00 2.32
1815 1909 1.207329 AGCGGTGATGAGGAAGGTAAC 59.793 52.381 0.00 0.00 0.00 2.50
1945 2039 2.609459 CCTGATCCGAACTTCATTTCCG 59.391 50.000 0.00 0.00 0.00 4.30
1970 2064 6.597614 CACAGAACTTTAGAAGTGAAGATGC 58.402 40.000 0.00 0.00 41.91 3.91
2012 2106 0.178891 AGGTCCTCCAGCCTTCAGAA 60.179 55.000 0.00 0.00 35.89 3.02
2332 2426 5.682234 TGACTTTGGCAAGATCAGAGATA 57.318 39.130 10.45 0.00 33.72 1.98
2430 2524 7.119699 CAGGTAAAGCACATTGATACTTCTGAA 59.880 37.037 0.00 0.00 0.00 3.02
2622 2716 3.431415 AGGCAAAAATGGGAACTCCTAC 58.569 45.455 0.00 0.00 36.20 3.18
2623 2717 2.496070 GGCAAAAATGGGAACTCCTACC 59.504 50.000 0.00 0.00 36.20 3.18
2700 2794 1.762370 TGGAGCTCCGATGCAGATAAA 59.238 47.619 27.43 2.35 39.43 1.40
2753 2847 4.160439 AGTTATCTCTGATGGCTCAACGAA 59.840 41.667 0.00 0.00 0.00 3.85
2778 2872 1.663643 GATGTCATTGTTTCGCCGCTA 59.336 47.619 0.00 0.00 0.00 4.26
2814 2908 4.267690 GGCTTTGTTAGTCTTTTTGCACAC 59.732 41.667 0.00 0.00 0.00 3.82
2868 2962 5.164233 TCAAGTGAGCTACTGAGATTTTCG 58.836 41.667 0.00 0.00 40.26 3.46
2925 3019 2.281484 GTGGGCGTTGCAGAAGGA 60.281 61.111 0.00 0.00 0.00 3.36
2992 3086 4.272018 CAGCATTTCCTTCCATTACTCTCG 59.728 45.833 0.00 0.00 0.00 4.04
3054 3148 5.707298 TCCAGAATCTGAATTCCACAACTTC 59.293 40.000 12.53 0.00 41.97 3.01
3115 3209 6.096705 CCAAATTTGGGCTATCTACAATGACA 59.903 38.462 26.87 0.00 44.70 3.58
3132 3226 4.753516 TGACACTGATACATTCCCGAAT 57.246 40.909 0.00 0.00 0.00 3.34
3181 3275 1.305201 ACAACCGTTCGAAGTGCATT 58.695 45.000 0.00 0.00 0.00 3.56
3261 3355 0.472044 TACCTGTGAGCTGTGGCAAA 59.528 50.000 0.00 0.00 41.70 3.68
3280 3374 5.220397 GGCAAATTTAAAATACGAAGCTGGC 60.220 40.000 0.00 0.00 0.00 4.85
3366 3460 4.479158 ACTGGCAGGTTAAAATTCTTCCA 58.521 39.130 20.34 0.00 0.00 3.53
3369 3463 6.126911 ACTGGCAGGTTAAAATTCTTCCAAAA 60.127 34.615 20.34 0.00 0.00 2.44
3481 3575 1.002576 TCGTCGAGTGCAGTAAACGAA 60.003 47.619 21.88 10.47 36.34 3.85
3534 3628 1.394917 GGCTATGTCGCTGTGTTCAAG 59.605 52.381 0.00 0.00 0.00 3.02
3585 3679 3.445987 ACCTAGGAAAGAGAACCTGAGG 58.554 50.000 17.98 0.00 37.68 3.86
3630 3724 1.814793 GTCTCACAAAGGAGGAAGGC 58.185 55.000 0.00 0.00 35.58 4.35
3697 3791 4.299155 TGGCGATTTTCTATAGAAGAGCG 58.701 43.478 29.08 29.08 46.29 5.03
3713 3807 1.976474 GCGCCCCCTTGAATTGACA 60.976 57.895 0.00 0.00 0.00 3.58
3723 3817 4.280677 CCCTTGAATTGACACTTGCCTTTA 59.719 41.667 0.00 0.00 0.00 1.85
3751 3845 3.371595 GGCAGCAAGAGGGAATTAACCTA 60.372 47.826 1.35 0.00 38.79 3.08
3808 3902 2.299013 TGAACCTAGGGCGCAGTATATG 59.701 50.000 14.81 0.00 0.00 1.78
3829 3923 2.093890 CTGGCTAAATGTGACCATGCA 58.906 47.619 0.00 0.00 0.00 3.96
3863 3957 6.637657 TCTTTCGGGGTCTCTTAATTTAGTC 58.362 40.000 0.00 0.00 0.00 2.59
3876 3970 7.446769 TCTTAATTTAGTCAGTACTGTTGGCA 58.553 34.615 21.99 6.08 36.36 4.92
3924 4019 2.164219 CAGTGAAGCAAGTGGTGTTTGT 59.836 45.455 0.00 0.00 29.63 2.83
3929 4024 2.387757 AGCAAGTGGTGTTTGTTGGAT 58.612 42.857 0.00 0.00 0.00 3.41
3932 4027 2.071778 AGTGGTGTTTGTTGGATGCT 57.928 45.000 0.00 0.00 0.00 3.79
4018 4113 9.841295 ATAATATTCCTGGTTACGTATTTGTGT 57.159 29.630 0.00 0.00 0.00 3.72
4022 4117 6.283544 TCCTGGTTACGTATTTGTGTCATA 57.716 37.500 0.00 0.00 0.00 2.15
4043 4138 1.682854 CTTGTGTGCCAGTCCAAATGT 59.317 47.619 0.00 0.00 0.00 2.71
4053 4148 3.753272 CCAGTCCAAATGTAGGTGTGAAG 59.247 47.826 0.00 0.00 0.00 3.02
4059 4154 5.763204 TCCAAATGTAGGTGTGAAGTTCTTC 59.237 40.000 4.17 5.70 0.00 2.87
4067 4162 2.540101 GTGTGAAGTTCTTCCACAGTCG 59.460 50.000 19.24 0.00 40.90 4.18
4084 4179 1.202582 GTCGGCATGTAGTCAGTCAGT 59.797 52.381 0.00 0.00 0.00 3.41
4333 4432 4.593157 TGCACGTGTATTTGAACTGAAAC 58.407 39.130 18.38 0.00 0.00 2.78
4377 4480 4.082523 CAGGAAGGCCGGCGAGAA 62.083 66.667 22.54 0.00 39.96 2.87
4390 4493 0.460284 GCGAGAATCCACGTGTCCAT 60.460 55.000 15.65 0.15 0.00 3.41
4571 4681 1.277273 GTAGTTCGGGGGTAGCTGTTT 59.723 52.381 0.00 0.00 0.00 2.83
4580 4690 3.315949 TAGCTGTTTCGGCGGGGT 61.316 61.111 7.21 1.06 41.21 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 186 5.494724 GGACTAAATAAAAACGGAGGGAGT 58.505 41.667 0.00 0.00 0.00 3.85
183 187 4.569564 CGGACTAAATAAAAACGGAGGGAG 59.430 45.833 0.00 0.00 0.00 4.30
184 188 4.020307 ACGGACTAAATAAAAACGGAGGGA 60.020 41.667 0.00 0.00 0.00 4.20
185 189 4.093850 CACGGACTAAATAAAAACGGAGGG 59.906 45.833 0.00 0.00 0.00 4.30
186 190 4.692155 ACACGGACTAAATAAAAACGGAGG 59.308 41.667 0.00 0.00 0.00 4.30
187 191 5.851047 ACACGGACTAAATAAAAACGGAG 57.149 39.130 0.00 0.00 0.00 4.63
188 192 7.903995 AATACACGGACTAAATAAAAACGGA 57.096 32.000 0.00 0.00 0.00 4.69
189 193 7.847564 GCTAATACACGGACTAAATAAAAACGG 59.152 37.037 0.00 0.00 0.00 4.44
190 194 8.598075 AGCTAATACACGGACTAAATAAAAACG 58.402 33.333 0.00 0.00 0.00 3.60
194 198 8.885722 CCAAAGCTAATACACGGACTAAATAAA 58.114 33.333 0.00 0.00 0.00 1.40
195 199 8.042515 ACCAAAGCTAATACACGGACTAAATAA 58.957 33.333 0.00 0.00 0.00 1.40
196 200 7.558604 ACCAAAGCTAATACACGGACTAAATA 58.441 34.615 0.00 0.00 0.00 1.40
197 201 6.412214 ACCAAAGCTAATACACGGACTAAAT 58.588 36.000 0.00 0.00 0.00 1.40
198 202 5.797051 ACCAAAGCTAATACACGGACTAAA 58.203 37.500 0.00 0.00 0.00 1.85
199 203 5.047164 TGACCAAAGCTAATACACGGACTAA 60.047 40.000 0.00 0.00 0.00 2.24
200 204 4.463539 TGACCAAAGCTAATACACGGACTA 59.536 41.667 0.00 0.00 0.00 2.59
201 205 3.259876 TGACCAAAGCTAATACACGGACT 59.740 43.478 0.00 0.00 0.00 3.85
202 206 3.592059 TGACCAAAGCTAATACACGGAC 58.408 45.455 0.00 0.00 0.00 4.79
203 207 3.965379 TGACCAAAGCTAATACACGGA 57.035 42.857 0.00 0.00 0.00 4.69
204 208 4.969816 CTTTGACCAAAGCTAATACACGG 58.030 43.478 9.25 0.00 40.94 4.94
224 228 6.071616 TGGTCAAAGTTAACAAAGCTTGACTT 60.072 34.615 22.50 3.36 41.70 3.01
225 229 5.417580 TGGTCAAAGTTAACAAAGCTTGACT 59.582 36.000 22.50 0.00 0.00 3.41
226 230 5.646606 TGGTCAAAGTTAACAAAGCTTGAC 58.353 37.500 18.93 18.93 0.00 3.18
227 231 5.906113 TGGTCAAAGTTAACAAAGCTTGA 57.094 34.783 8.61 5.83 0.00 3.02
228 232 6.573617 CTTGGTCAAAGTTAACAAAGCTTG 57.426 37.500 8.61 0.00 0.00 4.01
244 248 9.706691 TGTAATTTTTGTTTACAAACTTGGTCA 57.293 25.926 7.51 2.22 44.56 4.02
355 359 9.403583 AGAGTTTGACCAAGTTTATAGAAAACA 57.596 29.630 3.70 0.00 32.81 2.83
363 367 9.461312 TGCATATTAGAGTTTGACCAAGTTTAT 57.539 29.630 0.00 0.00 0.00 1.40
364 368 8.856153 TGCATATTAGAGTTTGACCAAGTTTA 57.144 30.769 0.00 0.00 0.00 2.01
365 369 7.665559 TCTGCATATTAGAGTTTGACCAAGTTT 59.334 33.333 0.00 0.00 0.00 2.66
366 370 7.168219 TCTGCATATTAGAGTTTGACCAAGTT 58.832 34.615 0.00 0.00 0.00 2.66
367 371 6.711277 TCTGCATATTAGAGTTTGACCAAGT 58.289 36.000 0.00 0.00 0.00 3.16
368 372 7.244166 CTCTGCATATTAGAGTTTGACCAAG 57.756 40.000 5.84 0.00 37.48 3.61
383 387 9.125026 CCCTCTGTTTTTATTTACTCTGCATAT 57.875 33.333 0.00 0.00 0.00 1.78
384 388 8.325787 TCCCTCTGTTTTTATTTACTCTGCATA 58.674 33.333 0.00 0.00 0.00 3.14
385 389 7.175104 TCCCTCTGTTTTTATTTACTCTGCAT 58.825 34.615 0.00 0.00 0.00 3.96
386 390 6.539173 TCCCTCTGTTTTTATTTACTCTGCA 58.461 36.000 0.00 0.00 0.00 4.41
387 391 6.655425 ACTCCCTCTGTTTTTATTTACTCTGC 59.345 38.462 0.00 0.00 0.00 4.26
388 392 9.892130 ATACTCCCTCTGTTTTTATTTACTCTG 57.108 33.333 0.00 0.00 0.00 3.35
394 398 9.059023 AGGTAGATACTCCCTCTGTTTTTATTT 57.941 33.333 0.00 0.00 0.00 1.40
395 399 8.625467 AGGTAGATACTCCCTCTGTTTTTATT 57.375 34.615 0.00 0.00 0.00 1.40
396 400 8.625467 AAGGTAGATACTCCCTCTGTTTTTAT 57.375 34.615 0.00 0.00 0.00 1.40
397 401 8.319146 CAAAGGTAGATACTCCCTCTGTTTTTA 58.681 37.037 0.00 0.00 0.00 1.52
398 402 6.954352 AAGGTAGATACTCCCTCTGTTTTT 57.046 37.500 0.00 0.00 0.00 1.94
399 403 6.296489 CCAAAGGTAGATACTCCCTCTGTTTT 60.296 42.308 0.00 0.00 0.00 2.43
400 404 5.189934 CCAAAGGTAGATACTCCCTCTGTTT 59.810 44.000 0.00 0.00 0.00 2.83
401 405 4.717280 CCAAAGGTAGATACTCCCTCTGTT 59.283 45.833 0.00 0.00 0.00 3.16
402 406 4.264895 ACCAAAGGTAGATACTCCCTCTGT 60.265 45.833 0.00 0.00 32.11 3.41
403 407 4.290942 ACCAAAGGTAGATACTCCCTCTG 58.709 47.826 0.00 0.00 32.11 3.35
404 408 4.628661 ACCAAAGGTAGATACTCCCTCT 57.371 45.455 0.00 0.00 32.11 3.69
405 409 4.683671 GCAACCAAAGGTAGATACTCCCTC 60.684 50.000 0.00 0.00 33.12 4.30
406 410 3.200165 GCAACCAAAGGTAGATACTCCCT 59.800 47.826 0.00 0.00 33.12 4.20
407 411 3.200165 AGCAACCAAAGGTAGATACTCCC 59.800 47.826 0.00 0.00 33.12 4.30
408 412 4.489306 AGCAACCAAAGGTAGATACTCC 57.511 45.455 0.00 0.00 33.12 3.85
409 413 6.706716 GGAATAGCAACCAAAGGTAGATACTC 59.293 42.308 0.00 0.00 33.12 2.59
410 414 6.157994 TGGAATAGCAACCAAAGGTAGATACT 59.842 38.462 0.00 0.00 33.12 2.12
411 415 6.354130 TGGAATAGCAACCAAAGGTAGATAC 58.646 40.000 0.00 0.00 33.12 2.24
412 416 6.569127 TGGAATAGCAACCAAAGGTAGATA 57.431 37.500 0.00 0.00 33.12 1.98
521 527 3.057526 GGCCTAAACTTGTGACCAACATC 60.058 47.826 0.00 0.00 38.99 3.06
698 706 7.859377 CACAACAAGGATTATATGCAGATGAAC 59.141 37.037 3.54 0.00 0.00 3.18
910 1002 7.094377 TGCTCCAAATAACAGGTTTCTAATGAC 60.094 37.037 0.00 0.00 0.00 3.06
965 1057 2.825861 ATTGCCACAAAAGCCTTCAG 57.174 45.000 0.00 0.00 0.00 3.02
1300 1392 0.761187 AGAGCAACTTCAGCACCAGA 59.239 50.000 0.00 0.00 0.00 3.86
1359 1451 0.999406 CATACAAAGACCGCTCCGTG 59.001 55.000 0.00 0.00 0.00 4.94
1381 1473 2.284190 GGAAGCATACTGCCTTCTGAC 58.716 52.381 0.00 0.00 46.52 3.51
1573 1665 5.347342 TGCAAAGAACAATTTACCACAGTG 58.653 37.500 0.00 0.00 0.00 3.66
1615 1707 0.693049 AGGAAACTCGAGGGCATTGT 59.307 50.000 18.41 0.00 32.90 2.71
1696 1790 0.539438 TGGGCCTGTTGATTGGTGAC 60.539 55.000 4.53 0.00 0.00 3.67
1763 1857 8.102676 TGTCAATCCTTTCTCTATGTTCATCAA 58.897 33.333 0.00 0.00 0.00 2.57
1815 1909 3.018598 TCGCTTCTTGTCTCTGAACAG 57.981 47.619 0.00 0.00 0.00 3.16
1945 2039 6.597614 CATCTTCACTTCTAAAGTTCTGTGC 58.402 40.000 0.00 0.00 40.46 4.57
1970 2064 6.381481 TTGCAATATTTGGCACTAGAGATG 57.619 37.500 0.00 0.00 40.23 2.90
2012 2106 9.118300 CATCATCTTGCTTTCTCTTACCTAATT 57.882 33.333 0.00 0.00 0.00 1.40
2124 2218 4.143263 GCAACAGCAGCATTGTCATTAAAC 60.143 41.667 10.28 0.00 0.00 2.01
2126 2220 3.256383 AGCAACAGCAGCATTGTCATTAA 59.744 39.130 10.28 0.00 0.00 1.40
2184 2278 1.207791 CTCCACCTTGGCTATCCACT 58.792 55.000 0.00 0.00 43.33 4.00
2332 2426 6.839124 TTGATCAACTGCAATCAGGTTTAT 57.161 33.333 3.38 0.00 44.54 1.40
2430 2524 3.944015 GCCATGTCAGCTGAACTCTTAAT 59.056 43.478 20.19 1.06 0.00 1.40
2622 2716 8.004801 ACCTCACCCTTATTAGGATTTATTTGG 58.995 37.037 0.00 0.00 45.05 3.28
2623 2717 8.996651 ACCTCACCCTTATTAGGATTTATTTG 57.003 34.615 0.00 0.00 45.05 2.32
2700 2794 6.238869 CGACATCATATCCATAGGATCGACAT 60.239 42.308 1.05 0.00 42.11 3.06
2753 2847 2.830772 CGAAACAATGACATCGCCAT 57.169 45.000 0.00 0.00 0.00 4.40
2778 2872 6.012745 ACTAACAAAGCCTTCAATCCTCATT 58.987 36.000 0.00 0.00 0.00 2.57
2805 2899 1.669604 TGTCCTTAGCGTGTGCAAAA 58.330 45.000 0.00 0.00 46.23 2.44
2814 2908 1.992170 AGTAGCGTTTGTCCTTAGCG 58.008 50.000 0.00 0.00 0.00 4.26
2868 2962 6.260271 GTGTTCTATAAAAGGGGATACAGTGC 59.740 42.308 0.00 0.00 39.74 4.40
2925 3019 2.906389 TGCTGTATCCAGTTCCAGAAGT 59.094 45.455 0.00 0.00 41.02 3.01
2992 3086 3.444388 AGTTCCGAAGACATGTAGGAGTC 59.556 47.826 0.00 3.89 35.02 3.36
3054 3148 1.067846 TCACATGACCGGTCTTCTTCG 60.068 52.381 33.39 17.96 0.00 3.79
3103 3197 7.220030 GGGAATGTATCAGTGTCATTGTAGAT 58.780 38.462 12.68 0.00 32.90 1.98
3132 3226 0.767998 TGCTCACCCAACCATACACA 59.232 50.000 0.00 0.00 0.00 3.72
3141 3235 2.727123 TCTCAACTTTGCTCACCCAA 57.273 45.000 0.00 0.00 0.00 4.12
3168 3262 2.350772 CCAGGTCAAATGCACTTCGAAC 60.351 50.000 0.00 0.00 0.00 3.95
3171 3265 0.109597 GCCAGGTCAAATGCACTTCG 60.110 55.000 0.00 0.00 0.00 3.79
3213 3307 2.116125 AACCACAGCTTCCCCTGC 59.884 61.111 0.00 0.00 36.29 4.85
3218 3312 2.991540 GCCCCAACCACAGCTTCC 60.992 66.667 0.00 0.00 0.00 3.46
3225 3319 1.173913 GTACATTCTGCCCCAACCAC 58.826 55.000 0.00 0.00 0.00 4.16
3261 3355 5.102313 GCTTGCCAGCTTCGTATTTTAAAT 58.898 37.500 1.78 0.00 43.51 1.40
3295 3389 2.118403 TGAGAGAAGGGGTGGTTTCT 57.882 50.000 0.00 0.00 36.41 2.52
3366 3460 1.407618 GCCCAAACTTCACCGACTTTT 59.592 47.619 0.00 0.00 0.00 2.27
3369 3463 1.228154 GGCCCAAACTTCACCGACT 60.228 57.895 0.00 0.00 0.00 4.18
3585 3679 5.567138 ATGATGGAATTCGGTGAGAAAAC 57.433 39.130 0.00 0.00 42.91 2.43
3697 3791 1.273327 CAAGTGTCAATTCAAGGGGGC 59.727 52.381 0.00 0.00 0.00 5.80
3713 3807 1.002502 GCCCTCGGTAAAGGCAAGT 60.003 57.895 0.00 0.00 46.34 3.16
3723 3817 3.710722 CCTCTTGCTGCCCTCGGT 61.711 66.667 0.00 0.00 0.00 4.69
3760 3854 6.750039 GCACAAAACACAAAACACTGTATAGT 59.250 34.615 0.00 0.00 37.75 2.12
3768 3862 3.321497 TCAGGCACAAAACACAAAACAC 58.679 40.909 0.00 0.00 0.00 3.32
3771 3865 3.007398 AGGTTCAGGCACAAAACACAAAA 59.993 39.130 0.00 0.00 0.00 2.44
3772 3866 2.564947 AGGTTCAGGCACAAAACACAAA 59.435 40.909 0.00 0.00 0.00 2.83
3808 3902 1.202336 GCATGGTCACATTTAGCCAGC 60.202 52.381 0.00 0.00 34.35 4.85
3809 3903 2.093890 TGCATGGTCACATTTAGCCAG 58.906 47.619 0.00 0.00 34.35 4.85
3829 3923 3.009143 AGACCCCGAAAGAAACTTAGCAT 59.991 43.478 0.00 0.00 0.00 3.79
3876 3970 7.552687 TGAGTTACTTTCAGTTCAACAATGACT 59.447 33.333 0.00 0.00 34.61 3.41
3881 3975 6.653320 ACTGTGAGTTACTTTCAGTTCAACAA 59.347 34.615 14.13 0.00 36.17 2.83
3899 3993 1.600957 CACCACTTGCTTCACTGTGAG 59.399 52.381 10.77 6.72 32.72 3.51
3900 3994 1.065491 ACACCACTTGCTTCACTGTGA 60.065 47.619 6.36 6.36 32.72 3.58
3901 3995 1.382522 ACACCACTTGCTTCACTGTG 58.617 50.000 0.17 0.17 0.00 3.66
3902 3996 2.128771 AACACCACTTGCTTCACTGT 57.871 45.000 0.00 0.00 0.00 3.55
3932 4027 1.685803 CCATGGCCCAACAGCTTCATA 60.686 52.381 0.00 0.00 0.00 2.15
3969 4064 5.295950 TGAAGCAAACAACAACAATATGGG 58.704 37.500 0.00 0.00 0.00 4.00
4018 4113 1.696884 TGGACTGGCACACAAGTATGA 59.303 47.619 0.00 0.00 0.00 2.15
4022 4117 1.682854 CATTTGGACTGGCACACAAGT 59.317 47.619 0.00 0.00 0.00 3.16
4043 4138 3.709653 ACTGTGGAAGAACTTCACACCTA 59.290 43.478 21.28 11.21 41.20 3.08
4053 4148 0.798776 CATGCCGACTGTGGAAGAAC 59.201 55.000 0.00 0.00 0.00 3.01
4059 4154 0.246360 TGACTACATGCCGACTGTGG 59.754 55.000 0.00 0.00 0.00 4.17
4067 4162 2.611518 GTCACTGACTGACTACATGCC 58.388 52.381 1.58 0.00 45.38 4.40
4084 4179 0.392461 GTGCCCAATCTTAGCGGTCA 60.392 55.000 0.00 0.00 0.00 4.02
4089 4184 2.162681 ACAAGTGTGCCCAATCTTAGC 58.837 47.619 0.00 0.00 0.00 3.09
4146 4241 2.328099 GCCCGTTGGAGTTGCTCTG 61.328 63.158 0.00 0.00 0.00 3.35
4241 4336 2.036006 GCATACGCCGACCCAAACA 61.036 57.895 0.00 0.00 0.00 2.83
4305 4404 6.203915 TCAGTTCAAATACACGTGCATAGTTT 59.796 34.615 17.22 6.91 0.00 2.66
4306 4405 5.699001 TCAGTTCAAATACACGTGCATAGTT 59.301 36.000 17.22 4.16 0.00 2.24
4377 4480 4.623932 ATGCTAATATGGACACGTGGAT 57.376 40.909 21.57 11.03 0.00 3.41
4463 4567 3.417224 CCGAGGACGACGACGACA 61.417 66.667 15.32 0.00 42.66 4.35
4556 4666 2.652095 CCGAAACAGCTACCCCCGA 61.652 63.158 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.