Multiple sequence alignment - TraesCS5D01G354700

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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 TraesCS5D01G354700 chr5D 100.000 2555 0 0 1 2555 436825154 436822600 0.000000e+00 4719
1 TraesCS5D01G354700 chr5D 88.420 829 67 16 555 1378 436349051 436349855 0.000000e+00 972
2 TraesCS5D01G354700 chr5D 89.597 769 53 17 765 1518 436578190 436578946 0.000000e+00 952
3 TraesCS5D01G354700 chr5D 85.897 702 68 24 695 1380 440375812 440375126 0.000000e+00 719
4 TraesCS5D01G354700 chr5D 87.342 158 18 2 4 159 254570170 254570327 2.020000e-41 180
5 TraesCS5D01G354700 chr5D 86.709 158 19 2 4 159 375320970 375321127 9.400000e-40 174
6 TraesCS5D01G354700 chr5D 80.488 246 29 10 2129 2357 436579644 436579887 1.220000e-38 171
7 TraesCS5D01G354700 chr5B 87.655 2098 190 45 327 2387 530974816 530972751 0.000000e+00 2375
8 TraesCS5D01G354700 chr5B 84.532 1752 174 59 665 2387 530609063 530610746 0.000000e+00 1644
9 TraesCS5D01G354700 chr5B 87.854 848 79 20 686 1518 530613201 530614039 0.000000e+00 974
10 TraesCS5D01G354700 chr5B 86.765 816 80 18 574 1378 530334070 530334868 0.000000e+00 883
11 TraesCS5D01G354700 chr5B 90.278 144 13 1 17 159 457001316 457001459 1.210000e-43 187
12 TraesCS5D01G354700 chr5B 90.278 144 13 1 17 159 703462530 703462673 1.210000e-43 187
13 TraesCS5D01G354700 chr5B 80.508 236 28 10 2138 2357 530614760 530614993 5.660000e-37 165
14 TraesCS5D01G354700 chr5B 86.792 106 10 3 2280 2384 530610753 530610855 5.780000e-22 115
15 TraesCS5D01G354700 chr5A 89.173 1173 80 24 513 1659 552078993 552077842 0.000000e+00 1419
16 TraesCS5D01G354700 chr5A 87.337 845 68 23 686 1503 551041100 551041932 0.000000e+00 931
17 TraesCS5D01G354700 chr5A 88.707 735 52 20 665 1378 550801665 550802389 0.000000e+00 869
18 TraesCS5D01G354700 chr5A 90.094 424 41 1 2133 2555 552077457 552077034 1.340000e-152 549
19 TraesCS5D01G354700 chr5A 80.147 272 29 14 2100 2346 551042458 551042729 2.020000e-41 180
20 TraesCS5D01G354700 chr2B 82.847 274 41 4 1 272 606792265 606792534 9.130000e-60 241
21 TraesCS5D01G354700 chr1D 81.743 241 41 3 35 273 485324646 485324885 5.580000e-47 198
22 TraesCS5D01G354700 chr1A 80.913 241 42 4 35 273 582508104 582508342 1.210000e-43 187
23 TraesCS5D01G354700 chr4B 89.583 144 14 1 17 159 217094593 217094736 5.620000e-42 182
24 TraesCS5D01G354700 chr6D 87.179 156 18 2 5 159 21816319 21816473 2.610000e-40 176


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 TraesCS5D01G354700 chr5D 436822600 436825154 2554 True 4719.0 4719 100.0000 1 2555 1 chr5D.!!$R1 2554
1 TraesCS5D01G354700 chr5D 436349051 436349855 804 False 972.0 972 88.4200 555 1378 1 chr5D.!!$F3 823
2 TraesCS5D01G354700 chr5D 440375126 440375812 686 True 719.0 719 85.8970 695 1380 1 chr5D.!!$R2 685
3 TraesCS5D01G354700 chr5D 436578190 436579887 1697 False 561.5 952 85.0425 765 2357 2 chr5D.!!$F4 1592
4 TraesCS5D01G354700 chr5B 530972751 530974816 2065 True 2375.0 2375 87.6550 327 2387 1 chr5B.!!$R1 2060
5 TraesCS5D01G354700 chr5B 530334070 530334868 798 False 883.0 883 86.7650 574 1378 1 chr5B.!!$F2 804
6 TraesCS5D01G354700 chr5B 530609063 530614993 5930 False 724.5 1644 84.9215 665 2387 4 chr5B.!!$F4 1722
7 TraesCS5D01G354700 chr5A 552077034 552078993 1959 True 984.0 1419 89.6335 513 2555 2 chr5A.!!$R1 2042
8 TraesCS5D01G354700 chr5A 550801665 550802389 724 False 869.0 869 88.7070 665 1378 1 chr5A.!!$F1 713
9 TraesCS5D01G354700 chr5A 551041100 551042729 1629 False 555.5 931 83.7420 686 2346 2 chr5A.!!$F2 1660

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
657 663 0.242825 CCTTCGAACTAGTGTCGCCA 59.757 55.0 17.28 9.26 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 5923 0.179108 GCCGAAGCACTATCCGTTCT 60.179 55.0 0.0 0.0 39.53 3.01 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
23 24 6.663944 GACTAAGTCTGCACCGAAAATAAT 57.336 37.500 0.00 0.00 0.00 1.28
24 25 7.766219 GACTAAGTCTGCACCGAAAATAATA 57.234 36.000 0.00 0.00 0.00 0.98
25 26 8.366671 GACTAAGTCTGCACCGAAAATAATAT 57.633 34.615 0.00 0.00 0.00 1.28
26 27 8.732746 ACTAAGTCTGCACCGAAAATAATATT 57.267 30.769 0.00 0.00 0.00 1.28
27 28 9.174166 ACTAAGTCTGCACCGAAAATAATATTT 57.826 29.630 0.00 0.00 0.00 1.40
120 121 9.772973 ATATAGCATGTTAAAATCGGAGTTACA 57.227 29.630 0.00 0.00 0.00 2.41
121 122 6.422776 AGCATGTTAAAATCGGAGTTACAG 57.577 37.500 0.00 0.00 0.00 2.74
122 123 5.938125 AGCATGTTAAAATCGGAGTTACAGT 59.062 36.000 0.00 0.00 0.00 3.55
123 124 6.430000 AGCATGTTAAAATCGGAGTTACAGTT 59.570 34.615 0.00 0.00 0.00 3.16
124 125 7.040686 AGCATGTTAAAATCGGAGTTACAGTTT 60.041 33.333 0.00 0.00 0.00 2.66
125 126 8.231837 GCATGTTAAAATCGGAGTTACAGTTTA 58.768 33.333 0.00 0.00 0.00 2.01
173 174 9.979578 AAACATTTGTTTTAGATGCATTACAGA 57.020 25.926 0.00 0.00 45.07 3.41
184 185 7.194607 AGATGCATTACAGATTGATTAACCG 57.805 36.000 0.00 0.00 0.00 4.44
185 186 6.992123 AGATGCATTACAGATTGATTAACCGA 59.008 34.615 0.00 0.00 0.00 4.69
186 187 6.993786 TGCATTACAGATTGATTAACCGAA 57.006 33.333 0.00 0.00 0.00 4.30
187 188 7.384439 TGCATTACAGATTGATTAACCGAAA 57.616 32.000 0.00 0.00 0.00 3.46
188 189 7.821652 TGCATTACAGATTGATTAACCGAAAA 58.178 30.769 0.00 0.00 0.00 2.29
189 190 8.300286 TGCATTACAGATTGATTAACCGAAAAA 58.700 29.630 0.00 0.00 0.00 1.94
190 191 9.301153 GCATTACAGATTGATTAACCGAAAAAT 57.699 29.630 0.00 0.00 0.00 1.82
197 198 9.297037 AGATTGATTAACCGAAAAATATAGGGG 57.703 33.333 0.00 0.00 0.00 4.79
198 199 9.074576 GATTGATTAACCGAAAAATATAGGGGT 57.925 33.333 0.00 0.00 0.00 4.95
199 200 8.826293 TTGATTAACCGAAAAATATAGGGGTT 57.174 30.769 0.00 0.00 40.57 4.11
200 201 8.826293 TGATTAACCGAAAAATATAGGGGTTT 57.174 30.769 0.00 0.00 38.59 3.27
201 202 9.257428 TGATTAACCGAAAAATATAGGGGTTTT 57.743 29.630 0.00 0.00 38.59 2.43
202 203 9.740239 GATTAACCGAAAAATATAGGGGTTTTC 57.260 33.333 0.00 0.00 38.59 2.29
203 204 8.882557 TTAACCGAAAAATATAGGGGTTTTCT 57.117 30.769 0.00 0.00 38.52 2.52
204 205 6.769134 ACCGAAAAATATAGGGGTTTTCTG 57.231 37.500 7.58 4.59 38.52 3.02
205 206 6.250711 ACCGAAAAATATAGGGGTTTTCTGT 58.749 36.000 7.58 5.07 38.52 3.41
206 207 6.722590 ACCGAAAAATATAGGGGTTTTCTGTT 59.277 34.615 7.58 0.00 36.13 3.16
207 208 7.889600 ACCGAAAAATATAGGGGTTTTCTGTTA 59.110 33.333 7.58 0.00 36.13 2.41
208 209 8.741841 CCGAAAAATATAGGGGTTTTCTGTTAA 58.258 33.333 7.58 0.00 38.52 2.01
247 248 9.902196 AATTCGTTTGATTTAAATAAGAACGGT 57.098 25.926 26.00 18.61 38.93 4.83
250 251 8.658609 TCGTTTGATTTAAATAAGAACGGTAGG 58.341 33.333 26.00 11.24 38.93 3.18
251 252 8.445493 CGTTTGATTTAAATAAGAACGGTAGGT 58.555 33.333 22.53 0.00 35.93 3.08
271 272 5.541098 GGTTAATTACCTCAAACGTCAGG 57.459 43.478 6.61 6.61 44.10 3.86
272 273 5.240121 GGTTAATTACCTCAAACGTCAGGA 58.760 41.667 13.64 0.09 44.10 3.86
273 274 5.878669 GGTTAATTACCTCAAACGTCAGGAT 59.121 40.000 13.64 3.03 44.10 3.24
274 275 6.373495 GGTTAATTACCTCAAACGTCAGGATT 59.627 38.462 13.64 7.43 44.10 3.01
275 276 7.413767 GGTTAATTACCTCAAACGTCAGGATTC 60.414 40.741 13.64 0.00 44.10 2.52
276 277 4.884668 TTACCTCAAACGTCAGGATTCT 57.115 40.909 13.64 0.00 33.52 2.40
277 278 3.771577 ACCTCAAACGTCAGGATTCTT 57.228 42.857 13.64 0.00 33.52 2.52
278 279 4.086706 ACCTCAAACGTCAGGATTCTTT 57.913 40.909 13.64 0.00 33.52 2.52
279 280 5.223449 ACCTCAAACGTCAGGATTCTTTA 57.777 39.130 13.64 0.00 33.52 1.85
280 281 5.805728 ACCTCAAACGTCAGGATTCTTTAT 58.194 37.500 13.64 0.00 33.52 1.40
281 282 6.238648 ACCTCAAACGTCAGGATTCTTTATT 58.761 36.000 13.64 0.00 33.52 1.40
282 283 7.391620 ACCTCAAACGTCAGGATTCTTTATTA 58.608 34.615 13.64 0.00 33.52 0.98
283 284 7.881232 ACCTCAAACGTCAGGATTCTTTATTAA 59.119 33.333 13.64 0.00 33.52 1.40
284 285 8.726988 CCTCAAACGTCAGGATTCTTTATTAAA 58.273 33.333 2.61 0.00 30.32 1.52
317 318 6.973229 AAAACGGTATAGATGTAACCACAC 57.027 37.500 0.00 0.00 37.54 3.82
318 319 5.664294 AACGGTATAGATGTAACCACACA 57.336 39.130 0.00 0.00 37.54 3.72
319 320 5.664294 ACGGTATAGATGTAACCACACAA 57.336 39.130 0.00 0.00 37.54 3.33
320 321 5.413499 ACGGTATAGATGTAACCACACAAC 58.587 41.667 0.00 0.00 37.54 3.32
321 322 5.047164 ACGGTATAGATGTAACCACACAACA 60.047 40.000 0.00 0.00 37.54 3.33
322 323 5.870433 CGGTATAGATGTAACCACACAACAA 59.130 40.000 0.00 0.00 37.54 2.83
323 324 6.183360 CGGTATAGATGTAACCACACAACAAC 60.183 42.308 0.00 0.00 37.54 3.32
324 325 6.651643 GGTATAGATGTAACCACACAACAACA 59.348 38.462 0.00 0.00 37.54 3.33
325 326 4.893424 AGATGTAACCACACAACAACAC 57.107 40.909 0.00 0.00 37.54 3.32
331 332 6.787225 TGTAACCACACAACAACACTTTATC 58.213 36.000 0.00 0.00 0.00 1.75
334 335 5.646606 ACCACACAACAACACTTTATCAAC 58.353 37.500 0.00 0.00 0.00 3.18
336 337 6.127479 ACCACACAACAACACTTTATCAACAT 60.127 34.615 0.00 0.00 0.00 2.71
350 351 9.712305 ACTTTATCAACATGTATAGATGTAGCC 57.288 33.333 15.28 0.00 35.43 3.93
351 352 9.710900 CTTTATCAACATGTATAGATGTAGCCA 57.289 33.333 15.28 1.66 35.43 4.75
352 353 9.489084 TTTATCAACATGTATAGATGTAGCCAC 57.511 33.333 15.28 0.00 35.43 5.01
357 358 6.049149 ACATGTATAGATGTAGCCACACAAC 58.951 40.000 13.52 0.00 37.54 3.32
360 361 5.872617 TGTATAGATGTAGCCACACAACAAC 59.127 40.000 0.00 0.00 37.54 3.32
373 374 3.193267 ACACAACAACACTTTGCATCTGT 59.807 39.130 0.00 0.00 36.00 3.41
377 378 4.818534 ACAACACTTTGCATCTGTGTAG 57.181 40.909 16.49 3.74 43.11 2.74
382 383 3.003585 CACTTTGCATCTGTGTAGCACAA 59.996 43.478 3.51 0.00 44.08 3.33
383 384 3.251729 ACTTTGCATCTGTGTAGCACAAG 59.748 43.478 3.51 0.00 44.08 3.16
391 392 3.441922 TCTGTGTAGCACAAGTTTGCAAA 59.558 39.130 8.05 8.05 44.08 3.68
393 394 3.057245 TGTGTAGCACAAGTTTGCAAACA 60.057 39.130 36.46 16.86 45.62 2.83
406 407 5.633182 AGTTTGCAAACAAAACACTAGTGTG 59.367 36.000 36.46 18.35 46.94 3.82
407 408 5.404066 GTTTGCAAACAAAACACTAGTGTGT 59.596 36.000 32.21 21.22 46.94 3.72
408 409 6.615418 GTTTGCAAACAAAACACTAGTGTGTG 60.615 38.462 32.21 27.50 46.29 3.82
409 410 8.885557 GTTTGCAAACAAAACACTAGTGTGTGT 61.886 37.037 32.21 28.09 46.29 3.72
417 418 3.592381 CACTAGTGTGTGTGTTTCTGC 57.408 47.619 15.06 0.00 39.24 4.26
418 419 3.198068 CACTAGTGTGTGTGTTTCTGCT 58.802 45.455 15.06 0.00 39.24 4.24
419 420 3.246226 CACTAGTGTGTGTGTTTCTGCTC 59.754 47.826 15.06 0.00 39.24 4.26
420 421 2.401583 AGTGTGTGTGTTTCTGCTCA 57.598 45.000 0.00 0.00 0.00 4.26
421 422 2.283298 AGTGTGTGTGTTTCTGCTCAG 58.717 47.619 0.00 0.00 0.00 3.35
422 423 1.016627 TGTGTGTGTTTCTGCTCAGC 58.983 50.000 0.00 0.00 0.00 4.26
425 426 1.416030 TGTGTGTTTCTGCTCAGCCTA 59.584 47.619 0.00 0.00 0.00 3.93
458 459 4.747108 CGGACAAATAAACCATGTGCAAAA 59.253 37.500 0.00 0.00 35.43 2.44
504 507 1.968050 TTAGCCCGGCTTACTCAGGC 61.968 60.000 19.35 0.00 45.01 4.85
542 545 6.700960 TGTTCAAAATCCATGCAAGTAAACAG 59.299 34.615 0.00 0.00 0.00 3.16
543 546 5.782047 TCAAAATCCATGCAAGTAAACAGG 58.218 37.500 0.00 0.00 0.00 4.00
593 598 6.038603 CCATATCAATTGATCGTGGAAACAGT 59.961 38.462 30.76 9.75 40.23 3.55
616 621 5.918011 GTGAAATACGCTTTCCAAATTGTCA 59.082 36.000 8.18 0.00 0.00 3.58
651 657 1.719780 GTTCACGCCTTCGAACTAGTG 59.280 52.381 13.03 13.03 38.76 2.74
657 663 0.242825 CCTTCGAACTAGTGTCGCCA 59.757 55.000 17.28 9.26 0.00 5.69
661 667 1.445582 GAACTAGTGTCGCCACGGG 60.446 63.158 0.00 0.00 46.56 5.28
846 868 4.455606 CTCAGAAAAGAAACACACCTCCT 58.544 43.478 0.00 0.00 0.00 3.69
857 879 3.374402 ACCTCCTCGCCACGTCAG 61.374 66.667 0.00 0.00 0.00 3.51
911 935 2.708593 ATCGATCCCCATCCGACGGA 62.709 60.000 20.85 20.85 35.02 4.69
961 988 4.740822 CCCGCCCCCAAACCTGAG 62.741 72.222 0.00 0.00 0.00 3.35
1093 1146 3.661648 GGCAAGGGAGGCAAGGGA 61.662 66.667 0.00 0.00 0.00 4.20
1210 5382 2.125512 GTGAAGCGCATCTCGGGT 60.126 61.111 14.40 0.00 38.94 5.28
1388 5560 3.866582 GCTAGGCCGCCACCAGAT 61.867 66.667 13.15 0.00 0.00 2.90
1389 5561 2.911143 CTAGGCCGCCACCAGATT 59.089 61.111 13.15 0.00 0.00 2.40
1398 5579 0.761802 GCCACCAGATTAGCTAGCCT 59.238 55.000 12.13 0.00 0.00 4.58
1484 5670 9.525409 CTGTAGAATGGAATTGAATGGAAATTC 57.475 33.333 0.00 0.00 41.35 2.17
1542 5765 0.469070 CCCCATTCTCTGGCTCTCAG 59.531 60.000 0.00 0.00 44.46 3.35
1579 5802 0.808060 CGGTTGTTGGTTTTGGTGCC 60.808 55.000 0.00 0.00 0.00 5.01
1587 5810 0.948623 GGTTTTGGTGCCCGCAATTC 60.949 55.000 0.00 0.00 0.00 2.17
1603 5826 3.056891 GCAATTCGAACCATCCCTTCAAA 60.057 43.478 0.00 0.00 0.00 2.69
1665 5888 1.400494 CCCAATTCCAAATCCGTCGAC 59.600 52.381 5.18 5.18 0.00 4.20
1670 5894 5.176958 CCAATTCCAAATCCGTCGACTATAC 59.823 44.000 14.70 0.00 0.00 1.47
1671 5896 5.786264 ATTCCAAATCCGTCGACTATACT 57.214 39.130 14.70 0.00 0.00 2.12
1683 5908 1.136305 GACTATACTTGCAGGCACCGA 59.864 52.381 0.00 0.00 0.00 4.69
1690 5915 4.101448 GCAGGCACCGATCCACCT 62.101 66.667 0.00 0.00 0.00 4.00
1693 5918 4.530857 GGCACCGATCCACCTCCG 62.531 72.222 0.00 0.00 0.00 4.63
1695 5920 2.978824 CACCGATCCACCTCCGTT 59.021 61.111 0.00 0.00 0.00 4.44
1698 5923 2.264480 CGATCCACCTCCGTTGCA 59.736 61.111 0.00 0.00 0.00 4.08
1716 5941 1.560923 CAGAACGGATAGTGCTTCGG 58.439 55.000 0.00 0.00 36.30 4.30
1742 5967 4.227134 CAGCGGCGGCAGAGGTAT 62.227 66.667 19.21 0.00 43.41 2.73
1793 6020 0.607217 TTCGTCGAGCACCTGAGGTA 60.607 55.000 2.59 0.00 32.11 3.08
1794 6021 0.607217 TCGTCGAGCACCTGAGGTAA 60.607 55.000 2.59 0.00 32.11 2.85
1816 6043 0.534203 TGTGTTTTCCTGGTCGCCTC 60.534 55.000 0.00 0.00 0.00 4.70
1824 6051 1.014564 CCTGGTCGCCTCGTCTTTTC 61.015 60.000 0.00 0.00 0.00 2.29
1826 6053 0.105224 TGGTCGCCTCGTCTTTTCAA 59.895 50.000 0.00 0.00 0.00 2.69
1842 6069 7.099120 GTCTTTTCAAGGCATTAATGTTCCAT 58.901 34.615 16.61 1.05 32.07 3.41
1856 6091 0.986527 TTCCATGCCTCTGCTTCTGA 59.013 50.000 0.00 0.00 38.71 3.27
1874 6117 3.883744 AAGCAGGTCTCGTTGCCGG 62.884 63.158 0.00 0.00 41.17 6.13
1878 6121 2.432628 GGTCTCGTTGCCGGTGAG 60.433 66.667 1.90 6.06 33.95 3.51
1888 6131 0.888619 TGCCGGTGAGAACAGAGTAG 59.111 55.000 1.90 0.00 0.00 2.57
1958 6310 0.030908 GAGCGATCTCTTGGTACCCG 59.969 60.000 10.07 4.70 36.42 5.28
1963 6315 2.376109 GATCTCTTGGTACCCGTCTGA 58.624 52.381 10.07 1.85 0.00 3.27
1998 6356 5.301805 TCTGTTGTCTTCCCAAATTTTCTCC 59.698 40.000 0.00 0.00 0.00 3.71
2005 6363 5.948162 TCTTCCCAAATTTTCTCCTGATCAG 59.052 40.000 16.24 16.24 0.00 2.90
2012 6375 3.795688 TTTCTCCTGATCAGTGGCTTT 57.204 42.857 21.11 0.00 0.00 3.51
2022 6389 2.436417 TCAGTGGCTTTCATGGCTTAC 58.564 47.619 0.00 0.00 0.00 2.34
2180 6646 5.192522 AGTGGATTTTGACTACCTGATCCAT 59.807 40.000 6.20 0.00 43.32 3.41
2185 6651 5.359194 TTTGACTACCTGATCCATCTTCC 57.641 43.478 0.00 0.00 0.00 3.46
2207 6673 4.097892 CCTGAATTACAATAACCAGTGGCC 59.902 45.833 9.78 0.00 0.00 5.36
2324 6806 3.877559 TCATGTTAGGATGTGCAAGGAG 58.122 45.455 0.00 0.00 0.00 3.69
2362 6844 1.069668 GCTGGAATGGATTGGATTGGC 59.930 52.381 0.00 0.00 0.00 4.52
2363 6845 2.674420 CTGGAATGGATTGGATTGGCT 58.326 47.619 0.00 0.00 0.00 4.75
2368 6850 4.405358 GGAATGGATTGGATTGGCTTGTAA 59.595 41.667 0.00 0.00 0.00 2.41
2396 6878 7.867445 ATTTCAGTTGTTTACCTTAAATGCG 57.133 32.000 0.00 0.00 0.00 4.73
2397 6879 6.380095 TTCAGTTGTTTACCTTAAATGCGT 57.620 33.333 0.00 0.00 0.00 5.24
2411 6893 3.609103 AATGCGTATTCTTCATTCCGC 57.391 42.857 0.00 0.00 41.34 5.54
2425 6907 1.834188 TTCCGCTCCCCAATTTCTTC 58.166 50.000 0.00 0.00 0.00 2.87
2426 6908 0.392461 TCCGCTCCCCAATTTCTTCG 60.392 55.000 0.00 0.00 0.00 3.79
2429 6911 1.676014 CGCTCCCCAATTTCTTCGTCT 60.676 52.381 0.00 0.00 0.00 4.18
2433 6915 2.162681 CCCCAATTTCTTCGTCTGCTT 58.837 47.619 0.00 0.00 0.00 3.91
2436 6918 4.501400 CCCCAATTTCTTCGTCTGCTTTTT 60.501 41.667 0.00 0.00 0.00 1.94
2440 6922 3.338818 TTCTTCGTCTGCTTTTTGCTG 57.661 42.857 0.00 0.00 43.37 4.41
2459 6942 5.255687 TGCTGTGGTCTTTGATCATGTTAT 58.744 37.500 0.00 0.00 0.00 1.89
2475 6958 5.942826 TCATGTTATTGTGTTAGGATGCACA 59.057 36.000 0.00 0.00 42.95 4.57
2488 6971 1.945394 GATGCACAATGGACTGGCTAG 59.055 52.381 0.00 0.00 0.00 3.42
2502 6985 1.687494 GGCTAGTGCTTGTTCGCTCG 61.687 60.000 0.00 0.00 39.59 5.03
2509 6992 1.009829 GCTTGTTCGCTCGAATGGAT 58.990 50.000 8.01 0.00 36.45 3.41
2515 6998 2.614057 GTTCGCTCGAATGGATTGGATT 59.386 45.455 8.01 0.00 36.45 3.01
2516 6999 2.212652 TCGCTCGAATGGATTGGATTG 58.787 47.619 0.00 0.00 0.00 2.67
2528 7011 4.017591 TGGATTGGATTGGGTTGTAGTGAT 60.018 41.667 0.00 0.00 0.00 3.06
2545 7028 3.008813 AGTGATTGTCAGGCTCTGTTGAT 59.991 43.478 2.68 0.00 32.61 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.663944 ATTATTTTCGGTGCAGACTTAGTC 57.336 37.500 3.85 3.85 0.00 2.59
1 2 8.732746 AATATTATTTTCGGTGCAGACTTAGT 57.267 30.769 0.00 0.00 0.00 2.24
94 95 9.772973 TGTAACTCCGATTTTAACATGCTATAT 57.227 29.630 0.00 0.00 0.00 0.86
95 96 9.256477 CTGTAACTCCGATTTTAACATGCTATA 57.744 33.333 0.00 0.00 0.00 1.31
96 97 7.769044 ACTGTAACTCCGATTTTAACATGCTAT 59.231 33.333 0.00 0.00 0.00 2.97
97 98 7.101054 ACTGTAACTCCGATTTTAACATGCTA 58.899 34.615 0.00 0.00 0.00 3.49
98 99 5.938125 ACTGTAACTCCGATTTTAACATGCT 59.062 36.000 0.00 0.00 0.00 3.79
99 100 6.178239 ACTGTAACTCCGATTTTAACATGC 57.822 37.500 0.00 0.00 0.00 4.06
158 159 8.773645 CGGTTAATCAATCTGTAATGCATCTAA 58.226 33.333 0.00 0.00 0.00 2.10
159 160 8.147704 TCGGTTAATCAATCTGTAATGCATCTA 58.852 33.333 0.00 0.00 0.00 1.98
160 161 6.992123 TCGGTTAATCAATCTGTAATGCATCT 59.008 34.615 0.00 0.00 0.00 2.90
161 162 7.189693 TCGGTTAATCAATCTGTAATGCATC 57.810 36.000 0.00 0.00 0.00 3.91
162 163 7.566760 TTCGGTTAATCAATCTGTAATGCAT 57.433 32.000 0.00 0.00 0.00 3.96
163 164 6.993786 TTCGGTTAATCAATCTGTAATGCA 57.006 33.333 0.00 0.00 0.00 3.96
164 165 8.682128 TTTTTCGGTTAATCAATCTGTAATGC 57.318 30.769 0.00 0.00 0.00 3.56
171 172 9.297037 CCCCTATATTTTTCGGTTAATCAATCT 57.703 33.333 0.00 0.00 0.00 2.40
172 173 9.074576 ACCCCTATATTTTTCGGTTAATCAATC 57.925 33.333 0.00 0.00 0.00 2.67
173 174 9.429109 AACCCCTATATTTTTCGGTTAATCAAT 57.571 29.630 0.00 0.00 31.93 2.57
174 175 8.826293 AACCCCTATATTTTTCGGTTAATCAA 57.174 30.769 0.00 0.00 31.93 2.57
175 176 8.826293 AAACCCCTATATTTTTCGGTTAATCA 57.174 30.769 0.00 0.00 33.33 2.57
176 177 9.740239 GAAAACCCCTATATTTTTCGGTTAATC 57.260 33.333 0.00 0.00 33.33 1.75
177 178 9.483489 AGAAAACCCCTATATTTTTCGGTTAAT 57.517 29.630 0.00 0.00 41.88 1.40
178 179 8.741841 CAGAAAACCCCTATATTTTTCGGTTAA 58.258 33.333 0.00 0.00 41.88 2.01
179 180 7.889600 ACAGAAAACCCCTATATTTTTCGGTTA 59.110 33.333 8.58 0.00 41.68 2.85
180 181 6.722590 ACAGAAAACCCCTATATTTTTCGGTT 59.277 34.615 8.58 0.00 41.68 4.44
181 182 6.250711 ACAGAAAACCCCTATATTTTTCGGT 58.749 36.000 8.58 8.58 41.88 4.69
182 183 6.769134 ACAGAAAACCCCTATATTTTTCGG 57.231 37.500 7.65 7.65 41.88 4.30
221 222 9.902196 ACCGTTCTTATTTAAATCAAACGAATT 57.098 25.926 27.08 16.42 40.10 2.17
224 225 8.658609 CCTACCGTTCTTATTTAAATCAAACGA 58.341 33.333 27.08 16.27 40.10 3.85
225 226 8.445493 ACCTACCGTTCTTATTTAAATCAAACG 58.555 33.333 22.72 22.72 38.12 3.60
250 251 6.980051 ATCCTGACGTTTGAGGTAATTAAC 57.020 37.500 8.57 0.00 0.00 2.01
251 252 7.391620 AGAATCCTGACGTTTGAGGTAATTAA 58.608 34.615 8.57 0.00 0.00 1.40
252 253 6.942976 AGAATCCTGACGTTTGAGGTAATTA 58.057 36.000 8.57 0.00 0.00 1.40
253 254 5.805728 AGAATCCTGACGTTTGAGGTAATT 58.194 37.500 8.57 3.56 0.00 1.40
254 255 5.422214 AGAATCCTGACGTTTGAGGTAAT 57.578 39.130 8.57 0.00 0.00 1.89
255 256 4.884668 AGAATCCTGACGTTTGAGGTAA 57.115 40.909 8.57 0.00 0.00 2.85
256 257 4.884668 AAGAATCCTGACGTTTGAGGTA 57.115 40.909 8.57 0.00 0.00 3.08
257 258 3.771577 AAGAATCCTGACGTTTGAGGT 57.228 42.857 8.57 0.00 0.00 3.85
258 259 6.743575 AATAAAGAATCCTGACGTTTGAGG 57.256 37.500 0.00 0.00 0.00 3.86
293 294 6.935771 TGTGTGGTTACATCTATACCGTTTTT 59.064 34.615 0.00 0.00 39.39 1.94
294 295 6.465948 TGTGTGGTTACATCTATACCGTTTT 58.534 36.000 0.00 0.00 39.39 2.43
295 296 6.040209 TGTGTGGTTACATCTATACCGTTT 57.960 37.500 0.00 0.00 39.39 3.60
296 297 5.664294 TGTGTGGTTACATCTATACCGTT 57.336 39.130 0.00 0.00 39.39 4.44
297 298 5.047164 TGTTGTGTGGTTACATCTATACCGT 60.047 40.000 0.00 0.00 39.39 4.83
298 299 5.412640 TGTTGTGTGGTTACATCTATACCG 58.587 41.667 0.00 0.00 39.39 4.02
299 300 6.651643 TGTTGTTGTGTGGTTACATCTATACC 59.348 38.462 0.00 0.00 39.39 2.73
300 301 7.386848 AGTGTTGTTGTGTGGTTACATCTATAC 59.613 37.037 0.00 0.00 39.39 1.47
301 302 7.446769 AGTGTTGTTGTGTGGTTACATCTATA 58.553 34.615 0.00 0.00 39.39 1.31
302 303 6.296026 AGTGTTGTTGTGTGGTTACATCTAT 58.704 36.000 0.00 0.00 39.39 1.98
303 304 5.676552 AGTGTTGTTGTGTGGTTACATCTA 58.323 37.500 0.00 0.00 39.39 1.98
304 305 4.523083 AGTGTTGTTGTGTGGTTACATCT 58.477 39.130 0.00 0.00 39.39 2.90
305 306 4.893424 AGTGTTGTTGTGTGGTTACATC 57.107 40.909 0.00 0.00 39.39 3.06
306 307 5.652994 AAAGTGTTGTTGTGTGGTTACAT 57.347 34.783 0.00 0.00 39.39 2.29
307 308 6.374613 TGATAAAGTGTTGTTGTGTGGTTACA 59.625 34.615 0.00 0.00 0.00 2.41
308 309 6.787225 TGATAAAGTGTTGTTGTGTGGTTAC 58.213 36.000 0.00 0.00 0.00 2.50
309 310 7.094334 TGTTGATAAAGTGTTGTTGTGTGGTTA 60.094 33.333 0.00 0.00 0.00 2.85
310 311 5.906113 TGATAAAGTGTTGTTGTGTGGTT 57.094 34.783 0.00 0.00 0.00 3.67
311 312 5.184096 TGTTGATAAAGTGTTGTTGTGTGGT 59.816 36.000 0.00 0.00 0.00 4.16
312 313 5.645624 TGTTGATAAAGTGTTGTTGTGTGG 58.354 37.500 0.00 0.00 0.00 4.17
313 314 6.751425 ACATGTTGATAAAGTGTTGTTGTGTG 59.249 34.615 0.00 0.00 0.00 3.82
314 315 6.862209 ACATGTTGATAAAGTGTTGTTGTGT 58.138 32.000 0.00 0.00 0.00 3.72
324 325 9.712305 GGCTACATCTATACATGTTGATAAAGT 57.288 33.333 2.30 3.82 38.07 2.66
325 326 9.710900 TGGCTACATCTATACATGTTGATAAAG 57.289 33.333 2.30 7.79 38.07 1.85
331 332 6.048509 TGTGTGGCTACATCTATACATGTTG 58.951 40.000 6.06 0.00 39.39 3.33
334 335 6.048509 TGTTGTGTGGCTACATCTATACATG 58.951 40.000 6.06 0.00 39.39 3.21
336 337 5.669164 TGTTGTGTGGCTACATCTATACA 57.331 39.130 6.06 4.19 39.39 2.29
348 349 0.998669 GCAAAGTGTTGTTGTGTGGC 59.001 50.000 0.00 0.00 37.06 5.01
349 350 2.360553 TGCAAAGTGTTGTTGTGTGG 57.639 45.000 0.00 0.00 37.06 4.17
350 351 3.548668 CAGATGCAAAGTGTTGTTGTGTG 59.451 43.478 0.00 0.00 37.06 3.82
351 352 3.193267 ACAGATGCAAAGTGTTGTTGTGT 59.807 39.130 0.00 0.00 37.06 3.72
352 353 3.548668 CACAGATGCAAAGTGTTGTTGTG 59.451 43.478 0.00 0.00 37.06 3.33
357 358 3.003585 TGCTACACAGATGCAAAGTGTTG 59.996 43.478 21.82 20.31 43.40 3.33
360 361 2.549329 TGTGCTACACAGATGCAAAGTG 59.451 45.455 13.06 13.06 39.62 3.16
373 374 3.857549 TGTTTGCAAACTTGTGCTACA 57.142 38.095 35.09 15.82 45.17 2.74
377 378 3.905416 GTGTTTTGTTTGCAAACTTGTGC 59.095 39.130 35.09 23.12 43.47 4.57
382 383 5.633182 CACACTAGTGTTTTGTTTGCAAACT 59.367 36.000 35.09 20.24 42.83 2.66
383 384 5.842377 CACACTAGTGTTTTGTTTGCAAAC 58.158 37.500 30.95 30.95 42.83 2.93
406 407 2.072298 CTAGGCTGAGCAGAAACACAC 58.928 52.381 6.82 0.00 0.00 3.82
407 408 1.970640 TCTAGGCTGAGCAGAAACACA 59.029 47.619 6.82 0.00 0.00 3.72
408 409 2.232452 TCTCTAGGCTGAGCAGAAACAC 59.768 50.000 6.82 0.00 34.29 3.32
409 410 2.495270 CTCTCTAGGCTGAGCAGAAACA 59.505 50.000 6.82 0.00 34.29 2.83
410 411 2.159114 CCTCTCTAGGCTGAGCAGAAAC 60.159 54.545 6.82 0.00 35.64 2.78
411 412 2.106566 CCTCTCTAGGCTGAGCAGAAA 58.893 52.381 6.82 0.00 35.64 2.52
412 413 1.286257 TCCTCTCTAGGCTGAGCAGAA 59.714 52.381 6.82 0.00 43.31 3.02
413 414 0.922626 TCCTCTCTAGGCTGAGCAGA 59.077 55.000 6.82 0.00 43.31 4.26
414 415 1.682854 CTTCCTCTCTAGGCTGAGCAG 59.317 57.143 6.82 0.00 43.31 4.24
415 416 1.774110 CTTCCTCTCTAGGCTGAGCA 58.226 55.000 6.82 0.00 43.31 4.26
416 417 0.389025 GCTTCCTCTCTAGGCTGAGC 59.611 60.000 0.00 0.00 43.31 4.26
417 418 0.667993 CGCTTCCTCTCTAGGCTGAG 59.332 60.000 0.00 2.26 43.31 3.35
418 419 0.753479 CCGCTTCCTCTCTAGGCTGA 60.753 60.000 0.00 0.00 43.31 4.26
419 420 0.753479 TCCGCTTCCTCTCTAGGCTG 60.753 60.000 0.00 0.00 43.31 4.85
420 421 0.753848 GTCCGCTTCCTCTCTAGGCT 60.754 60.000 0.00 0.00 43.31 4.58
421 422 1.038130 TGTCCGCTTCCTCTCTAGGC 61.038 60.000 0.00 0.00 43.31 3.93
422 423 1.475403 TTGTCCGCTTCCTCTCTAGG 58.525 55.000 0.00 0.00 45.21 3.02
425 426 4.254492 GTTTATTTGTCCGCTTCCTCTCT 58.746 43.478 0.00 0.00 0.00 3.10
433 434 2.094752 GCACATGGTTTATTTGTCCGCT 60.095 45.455 0.00 0.00 0.00 5.52
436 437 5.525378 TGTTTTGCACATGGTTTATTTGTCC 59.475 36.000 0.00 0.00 0.00 4.02
468 471 6.103997 CGGGCTAACTGAATACAAGTAGAAA 58.896 40.000 0.00 0.00 0.00 2.52
484 487 0.179081 CCTGAGTAAGCCGGGCTAAC 60.179 60.000 24.16 13.90 38.25 2.34
504 507 7.377398 TGGATTTTGAACACTTTGTATCATGG 58.623 34.615 0.00 0.00 0.00 3.66
507 510 6.867816 GCATGGATTTTGAACACTTTGTATCA 59.132 34.615 0.00 0.00 0.00 2.15
542 545 3.082548 GTTTCTTTCACCTAGAAGGCCC 58.917 50.000 0.00 0.00 39.63 5.80
543 546 3.502595 GTGTTTCTTTCACCTAGAAGGCC 59.497 47.826 0.00 0.00 39.63 5.19
569 573 6.908820 CACTGTTTCCACGATCAATTGATATG 59.091 38.462 20.75 19.66 34.37 1.78
593 598 6.078202 TGACAATTTGGAAAGCGTATTTCA 57.922 33.333 14.46 0.00 0.00 2.69
616 621 2.030893 CGTGAACTCATGTTGTTGCCAT 60.031 45.455 10.54 0.00 36.39 4.40
634 640 1.337821 GACACTAGTTCGAAGGCGTG 58.662 55.000 15.19 15.19 38.98 5.34
676 682 1.452108 GGAATTCTGGCCGGTGGAG 60.452 63.158 12.43 0.00 0.00 3.86
961 988 1.610886 GGCGAGGTGGATTTATAGCCC 60.611 57.143 0.00 0.00 37.54 5.19
1267 5439 2.646719 GTGTAGGTGACGGCGTCA 59.353 61.111 36.29 36.29 40.50 4.35
1386 5558 3.257127 CCCTAGACACAGGCTAGCTAATC 59.743 52.174 15.72 5.85 35.19 1.75
1387 5559 3.235200 CCCTAGACACAGGCTAGCTAAT 58.765 50.000 15.72 0.00 35.19 1.73
1388 5560 2.024273 ACCCTAGACACAGGCTAGCTAA 60.024 50.000 15.72 0.00 35.19 3.09
1389 5561 1.569548 ACCCTAGACACAGGCTAGCTA 59.430 52.381 15.72 0.00 35.19 3.32
1398 5579 0.963962 GACCACGAACCCTAGACACA 59.036 55.000 0.00 0.00 0.00 3.72
1484 5670 8.180267 CAGCAGATTTCAAGGATAAACTAGTTG 58.820 37.037 9.34 0.00 0.00 3.16
1542 5765 4.425577 ACCGATTTGAGCACAGAAAATC 57.574 40.909 0.00 0.00 37.09 2.17
1579 5802 0.748005 AGGGATGGTTCGAATTGCGG 60.748 55.000 0.00 0.00 41.33 5.69
1587 5810 4.485163 GAACAATTTGAAGGGATGGTTCG 58.515 43.478 2.79 0.00 29.36 3.95
1665 5888 2.408050 GATCGGTGCCTGCAAGTATAG 58.592 52.381 0.00 0.00 0.00 1.31
1670 5894 2.046023 TGGATCGGTGCCTGCAAG 60.046 61.111 0.00 0.00 0.00 4.01
1671 5896 2.359850 GTGGATCGGTGCCTGCAA 60.360 61.111 0.00 0.00 0.00 4.08
1683 5908 0.321653 GTTCTGCAACGGAGGTGGAT 60.322 55.000 0.00 0.00 0.00 3.41
1693 5918 1.726853 AGCACTATCCGTTCTGCAAC 58.273 50.000 0.00 0.00 31.71 4.17
1695 5920 1.735700 CGAAGCACTATCCGTTCTGCA 60.736 52.381 0.00 0.00 31.71 4.41
1698 5923 0.179108 GCCGAAGCACTATCCGTTCT 60.179 55.000 0.00 0.00 39.53 3.01
1753 5978 0.759959 TTGCTGAACGGGAACAGGTA 59.240 50.000 0.00 0.00 35.05 3.08
1793 6020 1.404035 GCGACCAGGAAAACACAACTT 59.596 47.619 0.00 0.00 0.00 2.66
1794 6021 1.021968 GCGACCAGGAAAACACAACT 58.978 50.000 0.00 0.00 0.00 3.16
1874 6117 2.165437 CTGCCTCCTACTCTGTTCTCAC 59.835 54.545 0.00 0.00 0.00 3.51
1878 6121 1.205893 CACCTGCCTCCTACTCTGTTC 59.794 57.143 0.00 0.00 0.00 3.18
1888 6131 2.512515 GCACGATCACCTGCCTCC 60.513 66.667 0.00 0.00 0.00 4.30
1958 6310 3.618690 ACAGAGGCAGGTAAATCAGAC 57.381 47.619 0.00 0.00 0.00 3.51
1963 6315 4.327680 GAAGACAACAGAGGCAGGTAAAT 58.672 43.478 0.00 0.00 0.00 1.40
1998 6356 1.404391 GCCATGAAAGCCACTGATCAG 59.596 52.381 21.37 21.37 0.00 2.90
2005 6363 1.544724 TGGTAAGCCATGAAAGCCAC 58.455 50.000 0.00 0.00 40.46 5.01
2022 6389 5.474532 TCAGAGGAACAGATTTTTCATGTGG 59.525 40.000 0.00 0.00 31.13 4.17
2180 6646 6.884295 CCACTGGTTATTGTAATTCAGGAAGA 59.116 38.462 0.00 0.00 0.00 2.87
2185 6651 4.704540 TGGCCACTGGTTATTGTAATTCAG 59.295 41.667 0.00 0.00 0.00 3.02
2324 6806 0.387750 GCAAACAAGCAGTAGCCAGC 60.388 55.000 0.00 0.00 43.56 4.85
2362 6844 9.965824 AGGTAAACAACTGAAATTCATTACAAG 57.034 29.630 14.51 0.00 0.00 3.16
2389 6871 4.814234 AGCGGAATGAAGAATACGCATTTA 59.186 37.500 9.53 0.00 43.41 1.40
2390 6872 3.627577 AGCGGAATGAAGAATACGCATTT 59.372 39.130 9.53 0.00 43.41 2.32
2396 6878 2.158813 TGGGGAGCGGAATGAAGAATAC 60.159 50.000 0.00 0.00 0.00 1.89
2397 6879 2.123589 TGGGGAGCGGAATGAAGAATA 58.876 47.619 0.00 0.00 0.00 1.75
2411 6893 1.740025 GCAGACGAAGAAATTGGGGAG 59.260 52.381 0.00 0.00 0.00 4.30
2433 6915 4.341806 ACATGATCAAAGACCACAGCAAAA 59.658 37.500 0.00 0.00 0.00 2.44
2436 6918 3.144657 ACATGATCAAAGACCACAGCA 57.855 42.857 0.00 0.00 0.00 4.41
2440 6922 6.913170 ACACAATAACATGATCAAAGACCAC 58.087 36.000 0.00 0.00 0.00 4.16
2475 6958 1.352352 ACAAGCACTAGCCAGTCCATT 59.648 47.619 0.00 0.00 43.56 3.16
2479 6962 1.071605 CGAACAAGCACTAGCCAGTC 58.928 55.000 0.00 0.00 43.56 3.51
2488 6971 0.179215 CCATTCGAGCGAACAAGCAC 60.179 55.000 7.54 0.00 40.15 4.40
2502 6985 4.956075 ACTACAACCCAATCCAATCCATTC 59.044 41.667 0.00 0.00 0.00 2.67
2509 6992 4.735369 ACAATCACTACAACCCAATCCAA 58.265 39.130 0.00 0.00 0.00 3.53
2515 6998 2.552155 GCCTGACAATCACTACAACCCA 60.552 50.000 0.00 0.00 0.00 4.51
2516 6999 2.084546 GCCTGACAATCACTACAACCC 58.915 52.381 0.00 0.00 0.00 4.11
2528 7011 3.578282 TGTAGATCAACAGAGCCTGACAA 59.422 43.478 8.91 0.00 35.18 3.18


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

AutoCloner maintained by Alex Coulton.