Multiple sequence alignment - TraesCS1B01G019400

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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 TraesCS1B01G019400 chr1B 100.000 2366 0 0 1 2366 9092607 9090242 0.000000e+00 4370.0
1 TraesCS1B01G019400 chr1D 89.012 1356 84 21 256 1581 6763822 6765142 0.000000e+00 1618.0
2 TraesCS1B01G019400 chr1D 90.426 188 9 5 1 179 6763627 6763814 3.040000e-59 239.0
3 TraesCS1B01G019400 chr7B 97.704 784 16 2 1583 2366 579525715 579524934 0.000000e+00 1347.0
4 TraesCS1B01G019400 chr7B 96.667 90 3 0 1822 1911 599101200 599101111 1.460000e-32 150.0
5 TraesCS1B01G019400 chr3B 97.586 787 17 2 1581 2366 8719201 8719986 0.000000e+00 1347.0
6 TraesCS1B01G019400 chr5A 97.580 785 17 2 1583 2366 680488712 680489495 0.000000e+00 1343.0
7 TraesCS1B01G019400 chr5A 97.074 786 20 2 1583 2366 672319672 672320456 0.000000e+00 1321.0
8 TraesCS1B01G019400 chr5A 96.500 800 24 3 1569 2366 375556131 375556928 0.000000e+00 1319.0
9 TraesCS1B01G019400 chr5A 94.071 253 7 1 1583 1827 510166680 510166428 6.170000e-101 377.0
10 TraesCS1B01G019400 chr5A 96.667 90 3 0 1822 1911 706493526 706493615 1.460000e-32 150.0
11 TraesCS1B01G019400 chr1A 95.975 795 21 3 1582 2366 543472345 543473138 0.000000e+00 1280.0
12 TraesCS1B01G019400 chr1A 86.895 641 41 14 259 884 8227337 8227949 0.000000e+00 678.0
13 TraesCS1B01G019400 chr1A 85.498 462 30 10 438 884 8196325 8196764 4.640000e-122 448.0
14 TraesCS1B01G019400 chr1A 88.716 257 22 5 1331 1583 8237529 8237782 8.210000e-80 307.0
15 TraesCS1B01G019400 chr1A 92.056 214 16 1 977 1190 8197826 8198038 1.370000e-77 300.0
16 TraesCS1B01G019400 chr1A 92.056 214 16 1 977 1190 8228843 8229055 1.370000e-77 300.0
17 TraesCS1B01G019400 chr1A 93.333 180 11 1 1 179 8227140 8227319 5.010000e-67 265.0
18 TraesCS1B01G019400 chrUn 87.207 641 39 14 259 884 462550698 462550086 0.000000e+00 689.0
19 TraesCS1B01G019400 chrUn 93.676 253 7 2 1583 1827 94929542 94929291 1.030000e-98 370.0
20 TraesCS1B01G019400 chrUn 92.056 214 16 1 977 1190 453819215 453819003 1.370000e-77 300.0
21 TraesCS1B01G019400 chr6D 94.771 306 15 1 2055 2360 407182426 407182730 2.130000e-130 475.0
22 TraesCS1B01G019400 chr6D 100.000 32 0 0 1796 1827 472360898 472360929 2.540000e-05 60.2
23 TraesCS1B01G019400 chr6B 93.226 310 20 1 2055 2364 672925208 672924900 2.770000e-124 455.0
24 TraesCS1B01G019400 chr6A 92.949 312 20 1 2055 2364 74542099 74541788 9.970000e-124 453.0
25 TraesCS1B01G019400 chr6A 100.000 32 0 0 1796 1827 162419325 162419356 2.540000e-05 60.2
26 TraesCS1B01G019400 chr3A 93.676 253 8 1 1583 1827 2162935 2163187 2.870000e-99 372.0
27 TraesCS1B01G019400 chr7D 92.913 254 9 2 1582 1827 285462222 285461970 6.220000e-96 361.0
28 TraesCS1B01G019400 chr2B 96.667 90 3 0 1822 1911 12183656 12183745 1.460000e-32 150.0
29 TraesCS1B01G019400 chr7A 91.919 99 7 1 1 98 89508689 89508787 1.140000e-28 137.0


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 TraesCS1B01G019400 chr1B 9090242 9092607 2365 True 4370.000000 4370 100.000000 1 2366 1 chr1B.!!$R1 2365
1 TraesCS1B01G019400 chr1D 6763627 6765142 1515 False 928.500000 1618 89.719000 1 1581 2 chr1D.!!$F1 1580
2 TraesCS1B01G019400 chr7B 579524934 579525715 781 True 1347.000000 1347 97.704000 1583 2366 1 chr7B.!!$R1 783
3 TraesCS1B01G019400 chr3B 8719201 8719986 785 False 1347.000000 1347 97.586000 1581 2366 1 chr3B.!!$F1 785
4 TraesCS1B01G019400 chr5A 680488712 680489495 783 False 1343.000000 1343 97.580000 1583 2366 1 chr5A.!!$F3 783
5 TraesCS1B01G019400 chr5A 672319672 672320456 784 False 1321.000000 1321 97.074000 1583 2366 1 chr5A.!!$F2 783
6 TraesCS1B01G019400 chr5A 375556131 375556928 797 False 1319.000000 1319 96.500000 1569 2366 1 chr5A.!!$F1 797
7 TraesCS1B01G019400 chr1A 543472345 543473138 793 False 1280.000000 1280 95.975000 1582 2366 1 chr1A.!!$F2 784
8 TraesCS1B01G019400 chr1A 8227140 8229055 1915 False 414.333333 678 90.761333 1 1190 3 chr1A.!!$F4 1189
9 TraesCS1B01G019400 chr1A 8196325 8198038 1713 False 374.000000 448 88.777000 438 1190 2 chr1A.!!$F3 752
10 TraesCS1B01G019400 chrUn 462550086 462550698 612 True 689.000000 689 87.207000 259 884 1 chrUn.!!$R3 625

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
158 168 0.038435 CATGGGCGCACATTTTGACA 60.038 50.0 25.55 0.0 0.00 3.58 F
912 1955 0.242555 TATTGCAGAGTCACGTGCGA 59.757 50.0 11.67 0.0 42.96 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1154 2197 0.681564 CAGGTACCTGGAGCTCGACT 60.682 60.000 31.15 0.0 40.17 4.18 R
2320 3384 1.002624 GAATCCACGGGCTCACCAA 60.003 57.895 0.00 0.0 40.22 3.67 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
18 19 3.334078 GCCATTTCAGAACCGCATG 57.666 52.632 0.00 0.00 0.00 4.06
66 67 2.820178 TCAGAACCTCTACATGGCAGA 58.180 47.619 0.00 0.00 0.00 4.26
149 159 4.101790 CGTGGAACATGGGCGCAC 62.102 66.667 10.83 6.04 44.52 5.34
158 168 0.038435 CATGGGCGCACATTTTGACA 60.038 50.000 25.55 0.00 0.00 3.58
171 181 4.092675 ACATTTTGACAAAGTTTGCGGTTG 59.907 37.500 15.59 8.49 0.00 3.77
174 184 4.436242 TTGACAAAGTTTGCGGTTGTAA 57.564 36.364 15.59 0.00 35.67 2.41
179 189 3.349488 AAGTTTGCGGTTGTAAGCTTC 57.651 42.857 0.00 0.00 36.76 3.86
182 192 1.904287 TTGCGGTTGTAAGCTTCCAT 58.096 45.000 0.00 0.00 0.00 3.41
183 193 1.448985 TGCGGTTGTAAGCTTCCATC 58.551 50.000 0.00 0.00 0.00 3.51
184 194 0.733150 GCGGTTGTAAGCTTCCATCC 59.267 55.000 0.00 5.56 0.00 3.51
185 195 1.679032 GCGGTTGTAAGCTTCCATCCT 60.679 52.381 14.94 0.00 0.00 3.24
186 196 2.280628 CGGTTGTAAGCTTCCATCCTC 58.719 52.381 14.94 0.00 0.00 3.71
187 197 2.093447 CGGTTGTAAGCTTCCATCCTCT 60.093 50.000 14.94 0.00 0.00 3.69
188 198 3.132289 CGGTTGTAAGCTTCCATCCTCTA 59.868 47.826 14.94 0.00 0.00 2.43
189 199 4.443621 GGTTGTAAGCTTCCATCCTCTAC 58.556 47.826 0.00 0.00 0.00 2.59
190 200 4.162509 GGTTGTAAGCTTCCATCCTCTACT 59.837 45.833 0.00 0.00 0.00 2.57
191 201 5.363005 GGTTGTAAGCTTCCATCCTCTACTA 59.637 44.000 0.00 0.00 0.00 1.82
192 202 6.042208 GGTTGTAAGCTTCCATCCTCTACTAT 59.958 42.308 0.00 0.00 0.00 2.12
193 203 7.232941 GGTTGTAAGCTTCCATCCTCTACTATA 59.767 40.741 0.00 0.00 0.00 1.31
194 204 8.808092 GTTGTAAGCTTCCATCCTCTACTATAT 58.192 37.037 0.00 0.00 0.00 0.86
232 242 9.814899 GATGAAATACTATGCTATGCTATCAGT 57.185 33.333 0.00 0.00 0.00 3.41
233 243 9.814899 ATGAAATACTATGCTATGCTATCAGTC 57.185 33.333 0.00 0.00 0.00 3.51
234 244 8.806146 TGAAATACTATGCTATGCTATCAGTCA 58.194 33.333 0.00 0.00 0.00 3.41
235 245 9.645059 GAAATACTATGCTATGCTATCAGTCAA 57.355 33.333 0.00 0.00 0.00 3.18
236 246 8.994429 AATACTATGCTATGCTATCAGTCAAC 57.006 34.615 0.00 0.00 0.00 3.18
237 247 5.788450 ACTATGCTATGCTATCAGTCAACC 58.212 41.667 0.00 0.00 0.00 3.77
238 248 4.694760 ATGCTATGCTATCAGTCAACCA 57.305 40.909 0.00 0.00 0.00 3.67
239 249 4.063998 TGCTATGCTATCAGTCAACCAG 57.936 45.455 0.00 0.00 0.00 4.00
240 250 3.181462 TGCTATGCTATCAGTCAACCAGG 60.181 47.826 0.00 0.00 0.00 4.45
241 251 3.181461 GCTATGCTATCAGTCAACCAGGT 60.181 47.826 0.00 0.00 0.00 4.00
242 252 4.039245 GCTATGCTATCAGTCAACCAGGTA 59.961 45.833 0.00 0.00 0.00 3.08
243 253 4.679373 ATGCTATCAGTCAACCAGGTAG 57.321 45.455 0.00 0.00 0.00 3.18
244 254 2.766263 TGCTATCAGTCAACCAGGTAGG 59.234 50.000 0.00 0.00 45.67 3.18
245 255 2.483889 GCTATCAGTCAACCAGGTAGGC 60.484 54.545 0.00 0.00 43.14 3.93
246 256 1.656587 ATCAGTCAACCAGGTAGGCA 58.343 50.000 0.00 0.00 43.14 4.75
247 257 0.685097 TCAGTCAACCAGGTAGGCAC 59.315 55.000 0.00 0.00 43.14 5.01
248 258 0.396435 CAGTCAACCAGGTAGGCACA 59.604 55.000 0.00 0.00 43.14 4.57
249 259 1.003580 CAGTCAACCAGGTAGGCACAT 59.996 52.381 0.00 0.00 43.14 3.21
250 260 1.279271 AGTCAACCAGGTAGGCACATC 59.721 52.381 0.00 0.00 43.14 3.06
251 261 1.003118 GTCAACCAGGTAGGCACATCA 59.997 52.381 0.00 0.00 43.14 3.07
252 262 1.278985 TCAACCAGGTAGGCACATCAG 59.721 52.381 0.00 0.00 43.14 2.90
253 263 1.003580 CAACCAGGTAGGCACATCAGT 59.996 52.381 0.00 0.00 43.14 3.41
254 264 1.362224 ACCAGGTAGGCACATCAGTT 58.638 50.000 0.00 0.00 43.14 3.16
289 306 8.579850 ACAGAGACATATTTTGGCAATAAGAA 57.420 30.769 0.00 0.00 34.87 2.52
291 308 8.896744 CAGAGACATATTTTGGCAATAAGAAGA 58.103 33.333 0.00 0.00 34.87 2.87
292 309 9.118300 AGAGACATATTTTGGCAATAAGAAGAG 57.882 33.333 0.00 0.00 34.87 2.85
293 310 9.113838 GAGACATATTTTGGCAATAAGAAGAGA 57.886 33.333 0.00 0.00 34.87 3.10
322 339 2.105466 GGCCAGAAGAAGAGCAGCG 61.105 63.158 0.00 0.00 0.00 5.18
354 372 3.053828 CGTGAAGGTGTACGGGGT 58.946 61.111 0.00 0.00 36.71 4.95
356 374 1.004200 GTGAAGGTGTACGGGGTGG 60.004 63.158 0.00 0.00 0.00 4.61
358 376 3.617143 GAAGGTGTACGGGGTGGCC 62.617 68.421 0.00 0.00 0.00 5.36
359 377 4.966274 AGGTGTACGGGGTGGCCA 62.966 66.667 0.00 0.00 0.00 5.36
360 378 3.956314 GGTGTACGGGGTGGCCAA 61.956 66.667 7.24 0.00 0.00 4.52
384 402 1.302949 GGAACATAGCCAGGGTGCA 59.697 57.895 0.00 0.00 0.00 4.57
455 473 4.988598 CCGCCACCGAGCACAAGT 62.989 66.667 0.00 0.00 36.29 3.16
479 497 2.846532 CCCACCTTGCCAGGAACT 59.153 61.111 11.55 0.00 44.19 3.01
495 513 6.238814 GCCAGGAACTTATGTACTCTAGACTC 60.239 46.154 0.00 0.00 34.60 3.36
517 537 5.076182 TCTCTGGCTCTTCTATGTATCCTG 58.924 45.833 0.00 0.00 0.00 3.86
518 538 4.155709 TCTGGCTCTTCTATGTATCCTGG 58.844 47.826 0.00 0.00 0.00 4.45
519 539 2.634940 TGGCTCTTCTATGTATCCTGGC 59.365 50.000 0.00 0.00 0.00 4.85
520 540 2.903135 GGCTCTTCTATGTATCCTGGCT 59.097 50.000 0.00 0.00 0.00 4.75
521 541 4.090090 GGCTCTTCTATGTATCCTGGCTA 58.910 47.826 0.00 0.00 0.00 3.93
522 542 4.081917 GGCTCTTCTATGTATCCTGGCTAC 60.082 50.000 0.75 0.75 0.00 3.58
523 543 4.770010 GCTCTTCTATGTATCCTGGCTACT 59.230 45.833 8.96 0.00 0.00 2.57
524 544 5.245075 GCTCTTCTATGTATCCTGGCTACTT 59.755 44.000 8.96 5.49 0.00 2.24
525 545 6.239458 GCTCTTCTATGTATCCTGGCTACTTT 60.239 42.308 8.96 0.41 0.00 2.66
526 546 7.055667 TCTTCTATGTATCCTGGCTACTTTG 57.944 40.000 8.96 4.49 0.00 2.77
527 547 6.611642 TCTTCTATGTATCCTGGCTACTTTGT 59.388 38.462 8.96 0.00 0.00 2.83
528 548 6.406692 TCTATGTATCCTGGCTACTTTGTC 57.593 41.667 8.96 0.00 0.00 3.18
529 549 6.136857 TCTATGTATCCTGGCTACTTTGTCT 58.863 40.000 8.96 0.00 0.00 3.41
530 550 5.700402 ATGTATCCTGGCTACTTTGTCTT 57.300 39.130 8.96 0.00 0.00 3.01
531 551 5.499004 TGTATCCTGGCTACTTTGTCTTT 57.501 39.130 8.96 0.00 0.00 2.52
532 552 5.876357 TGTATCCTGGCTACTTTGTCTTTT 58.124 37.500 8.96 0.00 0.00 2.27
533 553 7.011499 TGTATCCTGGCTACTTTGTCTTTTA 57.989 36.000 8.96 0.00 0.00 1.52
534 554 7.103641 TGTATCCTGGCTACTTTGTCTTTTAG 58.896 38.462 8.96 0.00 0.00 1.85
535 555 5.562298 TCCTGGCTACTTTGTCTTTTAGT 57.438 39.130 0.00 0.00 0.00 2.24
536 556 5.305585 TCCTGGCTACTTTGTCTTTTAGTG 58.694 41.667 0.00 0.00 0.00 2.74
537 557 5.063880 CCTGGCTACTTTGTCTTTTAGTGT 58.936 41.667 0.00 0.00 0.00 3.55
555 575 4.987832 AGTGTCTAATCAACGTCTAGCTG 58.012 43.478 0.00 0.00 0.00 4.24
559 579 6.197468 GTGTCTAATCAACGTCTAGCTGAATC 59.803 42.308 0.00 0.00 0.00 2.52
563 583 4.362932 TCAACGTCTAGCTGAATCTCAG 57.637 45.455 0.00 0.00 46.90 3.35
570 590 2.145397 AGCTGAATCTCAGTCCGGTA 57.855 50.000 0.00 0.00 45.94 4.02
591 613 4.664688 ACCAGTCAGATTTCCATCCTTT 57.335 40.909 0.00 0.00 0.00 3.11
596 618 6.989169 CCAGTCAGATTTCCATCCTTTAGTAG 59.011 42.308 0.00 0.00 0.00 2.57
606 628 6.817184 TCCATCCTTTAGTAGCATGTAAGAC 58.183 40.000 0.00 0.00 0.00 3.01
618 640 6.354794 AGCATGTAAGACCAGTTAGTAACA 57.645 37.500 15.28 0.00 0.00 2.41
640 662 1.871080 ACGATCATCGGGATTGAAGC 58.129 50.000 12.67 0.00 45.59 3.86
644 666 0.251916 TCATCGGGATTGAAGCGGTT 59.748 50.000 0.00 0.00 0.00 4.44
671 693 6.183360 ACCGGATAAAAATTCTGAATGACGAC 60.183 38.462 9.46 0.00 0.00 4.34
673 695 7.409697 CGGATAAAAATTCTGAATGACGACAT 58.590 34.615 3.22 0.00 38.50 3.06
674 696 7.374228 CGGATAAAAATTCTGAATGACGACATG 59.626 37.037 3.22 0.00 36.79 3.21
722 746 4.503910 AGCAAGGGTGTTTGTTTTTCTTC 58.496 39.130 0.00 0.00 0.00 2.87
765 789 2.416547 GCTGCTAAGTGGTACATGTGTG 59.583 50.000 9.11 0.00 44.52 3.82
770 794 1.593196 AGTGGTACATGTGTGTGTGC 58.407 50.000 9.11 0.00 44.52 4.57
836 874 3.676093 CCTCTGGGGTAAGAAACTTCAC 58.324 50.000 0.00 0.00 0.00 3.18
866 904 9.801714 CAAATTTTCTACTGAAATCAAACATGC 57.198 29.630 0.00 0.00 41.24 4.06
872 1911 7.362662 TCTACTGAAATCAAACATGCTTCAAC 58.637 34.615 0.00 0.00 0.00 3.18
888 1927 1.214175 TCAACCCTTGCTTTCTCACCA 59.786 47.619 0.00 0.00 0.00 4.17
905 1944 5.363580 TCTCACCACATATATTGCAGAGTCA 59.636 40.000 0.00 0.00 0.00 3.41
908 1947 4.141937 ACCACATATATTGCAGAGTCACGT 60.142 41.667 0.00 0.00 0.00 4.49
911 1954 1.280982 ATATTGCAGAGTCACGTGCG 58.719 50.000 11.67 0.00 42.96 5.34
912 1955 0.242555 TATTGCAGAGTCACGTGCGA 59.757 50.000 11.67 0.00 42.96 5.10
914 1957 1.008875 TTGCAGAGTCACGTGCGATC 61.009 55.000 11.67 8.47 42.96 3.69
916 1959 1.678269 GCAGAGTCACGTGCGATCAC 61.678 60.000 11.67 3.12 39.78 3.06
942 1985 1.080298 TATGCCGCAAGTACAAACCG 58.920 50.000 0.00 0.00 0.00 4.44
999 2042 0.884259 CAGCAATGGTGGACGTGTGA 60.884 55.000 4.25 0.00 0.00 3.58
1065 2108 2.369860 CCTCATGGAAATCAGGATCCGA 59.630 50.000 5.98 7.43 38.63 4.55
1143 2186 1.958288 AGAAGGTGCTGGAGGTGTAT 58.042 50.000 0.00 0.00 0.00 2.29
1154 2197 1.103803 GAGGTGTATGAGTCGAGGCA 58.896 55.000 0.00 0.00 0.00 4.75
1221 2264 2.517959 CTCAACCATGTGTCCACCATT 58.482 47.619 0.00 0.00 0.00 3.16
1234 2277 1.272425 CCACCATTTTGTGCCTAGGGA 60.272 52.381 11.72 4.36 34.85 4.20
1240 2283 3.350219 TTTTGTGCCTAGGGATCACTC 57.650 47.619 11.72 0.00 0.00 3.51
1242 2285 1.043116 TGTGCCTAGGGATCACTCCG 61.043 60.000 11.72 0.00 43.11 4.63
1291 2334 1.006813 TGTAAGGGCATGGTGGGATT 58.993 50.000 0.00 0.00 0.00 3.01
1328 2371 1.606601 CGGTGAGGAGGGTGTCTGA 60.607 63.158 0.00 0.00 0.00 3.27
1329 2372 1.878656 CGGTGAGGAGGGTGTCTGAC 61.879 65.000 0.00 0.00 0.00 3.51
1339 2382 4.654262 GGAGGGTGTCTGACCTAATGAATA 59.346 45.833 5.17 0.00 45.33 1.75
1346 2389 3.949754 TCTGACCTAATGAATACGTCCGT 59.050 43.478 0.00 0.00 0.00 4.69
1354 2397 5.718649 AATGAATACGTCCGTGAAGAATG 57.281 39.130 1.98 0.00 0.00 2.67
1355 2398 4.443913 TGAATACGTCCGTGAAGAATGA 57.556 40.909 1.98 0.00 0.00 2.57
1377 2420 5.951148 TGATCTGAAATGATTTAGTTGGCCA 59.049 36.000 0.00 0.00 0.00 5.36
1381 2424 7.944061 TCTGAAATGATTTAGTTGGCCATATG 58.056 34.615 6.09 0.00 0.00 1.78
1394 2437 6.098695 AGTTGGCCATATGTTAGCATCATTTT 59.901 34.615 6.09 0.00 36.58 1.82
1395 2438 6.482898 TGGCCATATGTTAGCATCATTTTT 57.517 33.333 0.00 0.00 36.58 1.94
1437 2480 2.095461 GCAAAGGGGGAGAATGAAGTC 58.905 52.381 0.00 0.00 0.00 3.01
1444 2487 5.742743 AGGGGGAGAATGAAGTCCTATTAT 58.257 41.667 0.00 0.00 32.90 1.28
1452 2495 7.568349 AGAATGAAGTCCTATTATGTTGCTCA 58.432 34.615 0.00 0.00 0.00 4.26
1456 2499 6.100279 TGAAGTCCTATTATGTTGCTCAGGAT 59.900 38.462 0.00 0.00 0.00 3.24
1457 2500 7.290014 TGAAGTCCTATTATGTTGCTCAGGATA 59.710 37.037 0.00 0.00 0.00 2.59
1479 2522 4.553330 TGTCTTATGGGAGTTGGAAGTC 57.447 45.455 0.00 0.00 0.00 3.01
1500 2552 5.942826 AGTCCACTCTTTGATTTCCATCTTC 59.057 40.000 0.00 0.00 0.00 2.87
1515 2567 8.868522 TTTCCATCTTCTGATTTGTGATTACT 57.131 30.769 0.00 0.00 0.00 2.24
1545 2598 7.870509 AGTAACTTATCGACTATGTGTGGTA 57.129 36.000 0.00 0.00 0.00 3.25
1717 2778 4.158764 TGTCAAACCCGAAGTGTTTTGAAT 59.841 37.500 0.00 0.00 33.82 2.57
2019 3083 3.129638 GCACAACAACAACCACTCCTAAA 59.870 43.478 0.00 0.00 0.00 1.85
2320 3384 2.541466 ACTCTCCCCTCGAAACTTCAT 58.459 47.619 0.00 0.00 0.00 2.57
2324 3388 1.702957 TCCCCTCGAAACTTCATTGGT 59.297 47.619 0.00 0.00 0.00 3.67
2353 3417 4.564821 CGTGGATTCACCTTCCCTTTTCTA 60.565 45.833 0.00 0.00 40.65 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 159 4.092675 ACAACCGCAAACTTTGTCAAAATG 59.907 37.500 0.00 1.01 0.00 2.32
158 168 3.490249 GGAAGCTTACAACCGCAAACTTT 60.490 43.478 2.98 0.00 0.00 2.66
206 216 9.814899 ACTGATAGCATAGCATAGTATTTCATC 57.185 33.333 0.00 0.00 35.84 2.92
207 217 9.814899 GACTGATAGCATAGCATAGTATTTCAT 57.185 33.333 0.00 0.00 35.84 2.57
208 218 8.806146 TGACTGATAGCATAGCATAGTATTTCA 58.194 33.333 0.00 0.00 35.84 2.69
209 219 9.645059 TTGACTGATAGCATAGCATAGTATTTC 57.355 33.333 0.00 0.00 35.84 2.17
210 220 9.429359 GTTGACTGATAGCATAGCATAGTATTT 57.571 33.333 0.00 0.00 35.84 1.40
211 221 8.037758 GGTTGACTGATAGCATAGCATAGTATT 58.962 37.037 0.00 0.00 35.84 1.89
212 222 7.179160 TGGTTGACTGATAGCATAGCATAGTAT 59.821 37.037 0.00 0.00 35.84 2.12
213 223 6.493458 TGGTTGACTGATAGCATAGCATAGTA 59.507 38.462 0.00 0.00 35.84 1.82
214 224 5.305386 TGGTTGACTGATAGCATAGCATAGT 59.695 40.000 0.00 0.00 35.84 2.12
215 225 5.787380 TGGTTGACTGATAGCATAGCATAG 58.213 41.667 0.00 0.00 35.84 2.23
216 226 5.279657 CCTGGTTGACTGATAGCATAGCATA 60.280 44.000 0.00 0.00 35.84 3.14
217 227 4.504514 CCTGGTTGACTGATAGCATAGCAT 60.505 45.833 0.00 0.00 35.84 3.79
218 228 3.181462 CCTGGTTGACTGATAGCATAGCA 60.181 47.826 0.00 0.00 34.74 3.49
219 229 3.181461 ACCTGGTTGACTGATAGCATAGC 60.181 47.826 0.00 0.00 0.00 2.97
220 230 4.679373 ACCTGGTTGACTGATAGCATAG 57.321 45.455 0.00 0.00 0.00 2.23
221 231 4.588951 CCTACCTGGTTGACTGATAGCATA 59.411 45.833 3.84 0.00 0.00 3.14
222 232 3.389329 CCTACCTGGTTGACTGATAGCAT 59.611 47.826 3.84 0.00 0.00 3.79
223 233 2.766263 CCTACCTGGTTGACTGATAGCA 59.234 50.000 3.84 0.00 0.00 3.49
224 234 2.483889 GCCTACCTGGTTGACTGATAGC 60.484 54.545 3.84 0.00 38.35 2.97
225 235 2.766263 TGCCTACCTGGTTGACTGATAG 59.234 50.000 3.84 0.00 38.35 2.08
226 236 2.500098 GTGCCTACCTGGTTGACTGATA 59.500 50.000 3.84 0.00 38.35 2.15
227 237 1.279271 GTGCCTACCTGGTTGACTGAT 59.721 52.381 3.84 0.00 38.35 2.90
228 238 0.685097 GTGCCTACCTGGTTGACTGA 59.315 55.000 3.84 0.00 38.35 3.41
229 239 0.396435 TGTGCCTACCTGGTTGACTG 59.604 55.000 3.84 0.00 38.35 3.51
230 240 1.279271 GATGTGCCTACCTGGTTGACT 59.721 52.381 3.84 0.00 38.35 3.41
231 241 1.003118 TGATGTGCCTACCTGGTTGAC 59.997 52.381 3.84 0.00 38.35 3.18
232 242 1.278985 CTGATGTGCCTACCTGGTTGA 59.721 52.381 3.84 0.00 38.35 3.18
233 243 1.003580 ACTGATGTGCCTACCTGGTTG 59.996 52.381 3.84 2.21 38.35 3.77
234 244 1.362224 ACTGATGTGCCTACCTGGTT 58.638 50.000 3.84 0.00 38.35 3.67
235 245 1.003580 CAACTGATGTGCCTACCTGGT 59.996 52.381 4.05 4.05 38.35 4.00
236 246 1.278985 TCAACTGATGTGCCTACCTGG 59.721 52.381 0.00 0.00 39.35 4.45
237 247 2.625737 CTCAACTGATGTGCCTACCTG 58.374 52.381 0.00 0.00 0.00 4.00
238 248 1.556911 CCTCAACTGATGTGCCTACCT 59.443 52.381 0.00 0.00 0.00 3.08
239 249 1.279271 ACCTCAACTGATGTGCCTACC 59.721 52.381 0.00 0.00 0.00 3.18
240 250 2.028112 TCACCTCAACTGATGTGCCTAC 60.028 50.000 9.50 0.00 39.50 3.18
241 251 2.256306 TCACCTCAACTGATGTGCCTA 58.744 47.619 9.50 0.00 39.50 3.93
242 252 1.059098 TCACCTCAACTGATGTGCCT 58.941 50.000 9.50 0.00 39.50 4.75
243 253 1.808945 CTTCACCTCAACTGATGTGCC 59.191 52.381 9.50 0.00 39.50 5.01
244 254 2.481952 GTCTTCACCTCAACTGATGTGC 59.518 50.000 9.50 0.00 39.50 4.57
245 255 3.732212 TGTCTTCACCTCAACTGATGTG 58.268 45.455 8.37 8.37 40.52 3.21
246 256 3.643320 TCTGTCTTCACCTCAACTGATGT 59.357 43.478 0.00 0.00 0.00 3.06
247 257 4.021632 TCTCTGTCTTCACCTCAACTGATG 60.022 45.833 0.00 0.00 0.00 3.07
248 258 4.021544 GTCTCTGTCTTCACCTCAACTGAT 60.022 45.833 0.00 0.00 0.00 2.90
249 259 3.319405 GTCTCTGTCTTCACCTCAACTGA 59.681 47.826 0.00 0.00 0.00 3.41
250 260 3.068732 TGTCTCTGTCTTCACCTCAACTG 59.931 47.826 0.00 0.00 0.00 3.16
251 261 3.300388 TGTCTCTGTCTTCACCTCAACT 58.700 45.455 0.00 0.00 0.00 3.16
252 262 3.735237 TGTCTCTGTCTTCACCTCAAC 57.265 47.619 0.00 0.00 0.00 3.18
253 263 6.611613 AATATGTCTCTGTCTTCACCTCAA 57.388 37.500 0.00 0.00 0.00 3.02
254 264 6.611613 AAATATGTCTCTGTCTTCACCTCA 57.388 37.500 0.00 0.00 0.00 3.86
289 306 4.083862 GCCGGCCGGTTTCTCTCT 62.084 66.667 42.53 0.00 37.65 3.10
358 376 3.012518 CCTGGCTATGTTCCAAGACTTG 58.987 50.000 8.31 8.31 32.41 3.16
359 377 2.025887 CCCTGGCTATGTTCCAAGACTT 60.026 50.000 0.00 0.00 32.41 3.01
360 378 1.561542 CCCTGGCTATGTTCCAAGACT 59.438 52.381 0.00 0.00 32.41 3.24
440 458 4.030452 GCACTTGTGCTCGGTGGC 62.030 66.667 17.36 0.00 0.00 5.01
443 461 4.643387 GGGGCACTTGTGCTCGGT 62.643 66.667 22.55 0.00 35.80 4.69
479 497 6.100569 AGAGCCAGAGAGTCTAGAGTACATAA 59.899 42.308 0.00 0.00 0.00 1.90
495 513 4.220382 CCAGGATACATAGAAGAGCCAGAG 59.780 50.000 0.00 0.00 41.41 3.35
517 537 7.958053 TTAGACACTAAAAGACAAAGTAGCC 57.042 36.000 0.00 0.00 0.00 3.93
518 538 9.204570 TGATTAGACACTAAAAGACAAAGTAGC 57.795 33.333 0.00 0.00 0.00 3.58
521 541 8.548721 CGTTGATTAGACACTAAAAGACAAAGT 58.451 33.333 0.00 0.00 0.00 2.66
522 542 8.548721 ACGTTGATTAGACACTAAAAGACAAAG 58.451 33.333 0.00 0.00 0.00 2.77
523 543 8.428186 ACGTTGATTAGACACTAAAAGACAAA 57.572 30.769 0.00 0.00 0.00 2.83
524 544 7.924412 AGACGTTGATTAGACACTAAAAGACAA 59.076 33.333 0.00 0.00 0.00 3.18
525 545 7.431249 AGACGTTGATTAGACACTAAAAGACA 58.569 34.615 0.00 0.00 0.00 3.41
526 546 7.870588 AGACGTTGATTAGACACTAAAAGAC 57.129 36.000 0.00 0.00 0.00 3.01
527 547 7.754027 GCTAGACGTTGATTAGACACTAAAAGA 59.246 37.037 0.00 0.00 0.00 2.52
528 548 7.755822 AGCTAGACGTTGATTAGACACTAAAAG 59.244 37.037 0.00 0.00 0.00 2.27
529 549 7.541091 CAGCTAGACGTTGATTAGACACTAAAA 59.459 37.037 0.00 0.00 0.00 1.52
530 550 7.027760 CAGCTAGACGTTGATTAGACACTAAA 58.972 38.462 0.00 0.00 0.00 1.85
531 551 6.373495 TCAGCTAGACGTTGATTAGACACTAA 59.627 38.462 0.00 0.00 0.00 2.24
532 552 5.878669 TCAGCTAGACGTTGATTAGACACTA 59.121 40.000 0.00 0.00 0.00 2.74
533 553 4.700692 TCAGCTAGACGTTGATTAGACACT 59.299 41.667 0.00 0.00 0.00 3.55
534 554 4.982999 TCAGCTAGACGTTGATTAGACAC 58.017 43.478 0.00 0.00 0.00 3.67
535 555 5.638596 TTCAGCTAGACGTTGATTAGACA 57.361 39.130 0.00 0.00 32.65 3.41
536 556 6.500041 AGATTCAGCTAGACGTTGATTAGAC 58.500 40.000 0.00 0.00 32.65 2.59
537 557 6.318900 TGAGATTCAGCTAGACGTTGATTAGA 59.681 38.462 0.00 0.00 32.65 2.10
555 575 2.099427 GACTGGTACCGGACTGAGATTC 59.901 54.545 27.93 7.81 0.00 2.52
559 579 0.811915 CTGACTGGTACCGGACTGAG 59.188 60.000 27.93 11.49 0.00 3.35
563 583 2.418334 GGAAATCTGACTGGTACCGGAC 60.418 54.545 27.93 21.32 0.00 4.79
570 590 4.664688 AAAGGATGGAAATCTGACTGGT 57.335 40.909 0.00 0.00 0.00 4.00
591 613 8.680903 GTTACTAACTGGTCTTACATGCTACTA 58.319 37.037 0.00 0.00 0.00 1.82
596 618 5.929992 TGTGTTACTAACTGGTCTTACATGC 59.070 40.000 0.00 0.00 0.00 4.06
606 628 5.004440 CGATGATCGTTGTGTTACTAACTGG 59.996 44.000 6.68 0.00 34.72 4.00
618 640 2.979814 TCAATCCCGATGATCGTTGT 57.020 45.000 14.27 0.00 38.40 3.32
644 666 6.183360 CGTCATTCAGAATTTTTATCCGGTCA 60.183 38.462 0.00 0.00 0.00 4.02
658 680 3.317603 TCAGCATGTCGTCATTCAGAA 57.682 42.857 0.00 0.00 37.40 3.02
659 681 3.317603 TTCAGCATGTCGTCATTCAGA 57.682 42.857 0.00 0.00 37.40 3.27
722 746 5.075670 CTAATCAGCAACATCAACGCTAG 57.924 43.478 0.00 0.00 33.82 3.42
765 789 4.266265 GCTGTGAAAAGAGAAAAAGCACAC 59.734 41.667 0.00 0.00 32.17 3.82
770 794 5.400485 CGAATGGCTGTGAAAAGAGAAAAAG 59.600 40.000 0.00 0.00 0.00 2.27
836 874 8.420189 GTTTGATTTCAGTAGAAAATTTGCTCG 58.580 33.333 0.59 0.00 46.06 5.03
866 904 2.294512 GGTGAGAAAGCAAGGGTTGAAG 59.705 50.000 0.00 0.00 0.00 3.02
872 1911 1.915141 ATGTGGTGAGAAAGCAAGGG 58.085 50.000 0.00 0.00 38.21 3.95
888 1927 3.804325 GCACGTGACTCTGCAATATATGT 59.196 43.478 22.23 0.00 33.31 2.29
908 1947 1.597195 GGCATACATTTCGTGATCGCA 59.403 47.619 7.12 0.00 36.96 5.10
911 1954 1.597195 TGCGGCATACATTTCGTGATC 59.403 47.619 0.00 0.00 0.00 2.92
912 1955 1.662517 TGCGGCATACATTTCGTGAT 58.337 45.000 0.00 0.00 0.00 3.06
914 1957 1.130373 ACTTGCGGCATACATTTCGTG 59.870 47.619 2.28 0.00 0.00 4.35
916 1959 2.350192 TGTACTTGCGGCATACATTTCG 59.650 45.455 11.35 0.00 0.00 3.46
917 1960 4.349663 TTGTACTTGCGGCATACATTTC 57.650 40.909 15.04 0.26 0.00 2.17
918 1961 4.481463 GTTTGTACTTGCGGCATACATTT 58.519 39.130 15.04 0.00 0.00 2.32
919 1962 3.119637 GGTTTGTACTTGCGGCATACATT 60.120 43.478 15.04 0.00 0.00 2.71
942 1985 2.731374 CCGATCCCGAGAAGCTCC 59.269 66.667 0.00 0.00 38.22 4.70
955 1998 2.270205 CAGCTCCTGGTTGCCGAT 59.730 61.111 9.92 0.00 0.00 4.18
999 2042 1.994463 GTGAGCCTCCACCTCCATT 59.006 57.895 0.00 0.00 0.00 3.16
1143 2186 2.691771 GCTCGACTGCCTCGACTCA 61.692 63.158 0.00 0.00 46.75 3.41
1154 2197 0.681564 CAGGTACCTGGAGCTCGACT 60.682 60.000 31.15 0.00 40.17 4.18
1221 2264 1.559682 GGAGTGATCCCTAGGCACAAA 59.440 52.381 17.22 0.00 35.08 2.83
1234 2277 2.217510 ACTGACCTGTACGGAGTGAT 57.782 50.000 2.31 0.00 45.73 3.06
1240 2283 1.135746 GTCGAGAACTGACCTGTACGG 60.136 57.143 0.00 0.00 39.35 4.02
1242 2285 1.728502 GCGTCGAGAACTGACCTGTAC 60.729 57.143 0.00 0.00 32.68 2.90
1275 2318 1.686800 GCAATCCCACCATGCCCTT 60.687 57.895 0.00 0.00 34.03 3.95
1328 2371 4.400251 TCTTCACGGACGTATTCATTAGGT 59.600 41.667 0.00 0.00 0.00 3.08
1329 2372 4.928601 TCTTCACGGACGTATTCATTAGG 58.071 43.478 0.00 0.00 0.00 2.69
1339 2382 2.492088 TCAGATCATTCTTCACGGACGT 59.508 45.455 0.00 0.00 0.00 4.34
1354 2397 6.455360 TGGCCAACTAAATCATTTCAGATC 57.545 37.500 0.61 0.00 0.00 2.75
1355 2398 8.582437 CATATGGCCAACTAAATCATTTCAGAT 58.418 33.333 10.96 0.00 0.00 2.90
1396 2439 4.583907 TGCCATCAAGACTCACATGAAAAA 59.416 37.500 0.00 0.00 30.07 1.94
1397 2440 4.143543 TGCCATCAAGACTCACATGAAAA 58.856 39.130 0.00 0.00 30.07 2.29
1405 2448 1.272092 CCCCTTTGCCATCAAGACTCA 60.272 52.381 0.00 0.00 33.12 3.41
1411 2454 0.783206 TTCTCCCCCTTTGCCATCAA 59.217 50.000 0.00 0.00 0.00 2.57
1417 2460 2.095461 GACTTCATTCTCCCCCTTTGC 58.905 52.381 0.00 0.00 0.00 3.68
1437 2480 7.619050 AGACATATCCTGAGCAACATAATAGG 58.381 38.462 0.00 0.00 0.00 2.57
1444 2487 5.455183 CCCATAAGACATATCCTGAGCAACA 60.455 44.000 0.00 0.00 0.00 3.33
1452 2495 5.476983 TCCAACTCCCATAAGACATATCCT 58.523 41.667 0.00 0.00 0.00 3.24
1456 2499 5.130477 GGACTTCCAACTCCCATAAGACATA 59.870 44.000 0.00 0.00 35.64 2.29
1457 2500 4.080299 GGACTTCCAACTCCCATAAGACAT 60.080 45.833 0.00 0.00 35.64 3.06
1479 2522 5.942236 TCAGAAGATGGAAATCAAAGAGTGG 59.058 40.000 0.00 0.00 0.00 4.00
1520 2572 7.870509 ACCACACATAGTCGATAAGTTACTA 57.129 36.000 0.00 0.00 0.00 1.82
1522 2574 9.525409 AAATACCACACATAGTCGATAAGTTAC 57.475 33.333 0.00 0.00 0.00 2.50
1529 2581 4.127171 GCCAAATACCACACATAGTCGAT 58.873 43.478 0.00 0.00 0.00 3.59
1531 2583 3.531538 AGCCAAATACCACACATAGTCG 58.468 45.455 0.00 0.00 0.00 4.18
1532 2584 4.438744 GCAAGCCAAATACCACACATAGTC 60.439 45.833 0.00 0.00 0.00 2.59
1533 2585 3.443681 GCAAGCCAAATACCACACATAGT 59.556 43.478 0.00 0.00 0.00 2.12
1534 2586 3.696051 AGCAAGCCAAATACCACACATAG 59.304 43.478 0.00 0.00 0.00 2.23
1535 2587 3.696045 AGCAAGCCAAATACCACACATA 58.304 40.909 0.00 0.00 0.00 2.29
1545 2598 4.697352 CACAAGTAGAGTAGCAAGCCAAAT 59.303 41.667 0.00 0.00 0.00 2.32
1717 2778 3.225940 TGGCACATTGTCCAAATACACA 58.774 40.909 5.75 0.00 0.00 3.72
2091 3155 8.704668 GGTCAAAATCATACCCCTCAATTAAAT 58.295 33.333 0.00 0.00 0.00 1.40
2209 3273 3.430453 GTCTCAACCATCCATTCCCAAA 58.570 45.455 0.00 0.00 0.00 3.28
2320 3384 1.002624 GAATCCACGGGCTCACCAA 60.003 57.895 0.00 0.00 40.22 3.67
2324 3388 1.488705 AAGGTGAATCCACGGGCTCA 61.489 55.000 0.00 0.00 44.09 4.26


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

AutoCloner maintained by Alex Coulton.