Multiple sequence alignment - TraesCS5D01G140300

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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 TraesCS5D01G140300 chr5D 100.000 7617 0 0 1 7617 223896122 223888506 0.000000e+00 14067.0
1 TraesCS5D01G140300 chr5D 89.655 174 16 2 571 744 53869701 53869530 3.580000e-53 220.0
2 TraesCS5D01G140300 chr5A 94.627 5416 167 36 1935 7279 296474700 296469338 0.000000e+00 8275.0
3 TraesCS5D01G140300 chr5A 94.431 4256 123 49 3423 7617 296473233 296469031 0.000000e+00 6442.0
4 TraesCS5D01G140300 chr5A 92.225 1209 42 7 741 1948 296486872 296485715 0.000000e+00 1664.0
5 TraesCS5D01G140300 chr5A 90.583 223 15 6 271 493 296487299 296487083 2.690000e-74 291.0
6 TraesCS5D01G140300 chr5A 96.512 172 5 1 6 176 296487468 296487297 4.500000e-72 283.0
7 TraesCS5D01G140300 chr5A 92.000 100 6 1 175 274 51677551 51677454 1.030000e-28 139.0
8 TraesCS5D01G140300 chr5B 98.681 2880 24 7 2347 5220 247660865 247663736 0.000000e+00 5096.0
9 TraesCS5D01G140300 chr5B 98.985 2365 22 2 5253 7617 247663733 247666095 0.000000e+00 4233.0
10 TraesCS5D01G140300 chr5B 98.139 1558 18 5 800 2351 247653870 247655422 0.000000e+00 2706.0
11 TraesCS5D01G140300 chr5B 89.286 308 23 6 271 572 247653339 247653642 2.010000e-100 377.0
12 TraesCS5D01G140300 chr5B 96.552 174 6 0 3 176 247653168 247653341 9.670000e-74 289.0
13 TraesCS5D01G140300 chr6B 86.013 622 80 4 1499 2118 678885703 678885087 0.000000e+00 660.0
14 TraesCS5D01G140300 chr7A 83.906 466 62 7 1472 1936 237514494 237514041 4.220000e-117 433.0
15 TraesCS5D01G140300 chr7A 82.609 184 32 0 1704 1887 670570843 670571026 6.120000e-36 163.0
16 TraesCS5D01G140300 chr7A 83.432 169 28 0 1719 1887 670602067 670602235 2.850000e-34 158.0
17 TraesCS5D01G140300 chr4D 86.770 257 28 6 1014 1267 112588069 112588322 1.620000e-71 281.0
18 TraesCS5D01G140300 chr4D 91.124 169 15 0 566 734 433364770 433364938 5.950000e-56 230.0
19 TraesCS5D01G140300 chr4D 89.091 110 9 2 165 273 43283996 43284103 4.800000e-27 134.0
20 TraesCS5D01G140300 chr4D 76.613 248 51 6 1658 1902 487362313 487362070 6.200000e-26 130.0
21 TraesCS5D01G140300 chr4B 86.381 257 29 5 1014 1267 173035793 173036046 7.530000e-70 276.0
22 TraesCS5D01G140300 chr4A 85.944 249 29 5 1020 1265 464771514 464771269 2.110000e-65 261.0
23 TraesCS5D01G140300 chr7D 92.216 167 13 0 568 734 60706225 60706391 3.550000e-58 237.0
24 TraesCS5D01G140300 chr7D 91.228 171 15 0 566 736 147465252 147465082 4.600000e-57 233.0
25 TraesCS5D01G140300 chr7B 91.228 171 14 1 563 733 488407908 488408077 1.650000e-56 231.0
26 TraesCS5D01G140300 chr6A 92.073 164 11 1 571 734 212112699 212112860 5.950000e-56 230.0
27 TraesCS5D01G140300 chr6A 91.919 99 6 1 175 273 532902265 532902361 3.710000e-28 137.0
28 TraesCS5D01G140300 chr1D 92.025 163 13 0 571 733 311986612 311986774 5.950000e-56 230.0
29 TraesCS5D01G140300 chr2D 89.444 180 17 2 563 741 391812515 391812337 7.690000e-55 226.0
30 TraesCS5D01G140300 chr2D 92.079 101 6 1 174 274 609331813 609331911 2.870000e-29 141.0
31 TraesCS5D01G140300 chr2D 88.889 72 7 1 818 888 313635702 313635773 3.790000e-13 87.9
32 TraesCS5D01G140300 chr2D 88.732 71 5 2 750 819 639835339 639835407 4.900000e-12 84.2
33 TraesCS5D01G140300 chr6D 90.173 173 16 1 567 739 93563754 93563925 2.770000e-54 224.0
34 TraesCS5D01G140300 chr3A 93.000 100 5 1 175 274 242726203 242726106 2.220000e-30 145.0
35 TraesCS5D01G140300 chr3A 88.793 116 7 5 162 274 77404915 77405027 3.710000e-28 137.0
36 TraesCS5D01G140300 chr3B 90.090 111 8 2 175 285 479298475 479298368 2.870000e-29 141.0
37 TraesCS5D01G140300 chr3B 76.378 127 19 10 1706 1826 29103322 29103201 2.970000e-04 58.4
38 TraesCS5D01G140300 chr3D 91.089 101 7 1 175 275 591877429 591877527 1.330000e-27 135.0
39 TraesCS5D01G140300 chr2B 89.091 110 10 2 175 284 716814582 716814475 1.330000e-27 135.0
40 TraesCS5D01G140300 chr2B 76.119 134 23 9 1706 1834 504300507 504300378 2.290000e-05 62.1


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 TraesCS5D01G140300 chr5D 223888506 223896122 7616 True 14067.0 14067 100.000000 1 7617 1 chr5D.!!$R2 7616
1 TraesCS5D01G140300 chr5A 296469031 296474700 5669 True 7358.5 8275 94.529000 1935 7617 2 chr5A.!!$R2 5682
2 TraesCS5D01G140300 chr5A 296485715 296487468 1753 True 746.0 1664 93.106667 6 1948 3 chr5A.!!$R3 1942
3 TraesCS5D01G140300 chr5B 247660865 247666095 5230 False 4664.5 5096 98.833000 2347 7617 2 chr5B.!!$F2 5270
4 TraesCS5D01G140300 chr5B 247653168 247655422 2254 False 1124.0 2706 94.659000 3 2351 3 chr5B.!!$F1 2348
5 TraesCS5D01G140300 chr6B 678885087 678885703 616 True 660.0 660 86.013000 1499 2118 1 chr6B.!!$R1 619

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
269 271 1.706305 ACTTAATTTGGGACGGTGGGA 59.294 47.619 0.00 0.00 0.00 4.37 F
1846 2149 1.200519 CTAACCTGGACCCGAATCCA 58.799 55.000 0.00 7.32 46.92 3.41 F
2971 3284 0.821711 GGCAAGTAACTGTGGTGGCA 60.822 55.000 0.00 0.00 35.06 4.92 F
3255 3569 3.445805 ACCAGATCGAAGGAGAGAACTTC 59.554 47.826 8.68 0.00 40.64 3.01 F
4295 4670 3.813443 AGAGTGACAAAACTGTCTGCAT 58.187 40.909 6.80 0.00 39.41 3.96 F
5251 5637 0.033781 GCCCTGCAATTTCAGCAACA 59.966 50.000 0.00 0.00 42.17 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2329 1.451028 AAGAAGCTGATGGCCTCGC 60.451 57.895 3.32 7.48 43.05 5.03 R
3823 4190 1.858091 CTTCAGGGCATGCGTACTAG 58.142 55.000 12.44 2.51 0.00 2.57 R
4295 4670 3.895656 GCATATGACCCCTAGACTGTACA 59.104 47.826 6.97 0.00 0.00 2.90 R
5177 5563 0.469892 ACAAAGTTGAGGCCAAGGGG 60.470 55.000 5.01 0.00 32.06 4.79 R
5439 5825 0.181350 AATAGCCCTACAGCCTGCAC 59.819 55.000 0.00 0.00 0.00 4.57 R
7019 7421 0.666913 CCATTACCATCAGCAGCAGC 59.333 55.000 0.00 0.00 42.56 5.25 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
85 86 9.692325 AAAGATCCTGTTTAGAGATTTAAGCAT 57.308 29.630 0.00 0.00 0.00 3.79
183 185 7.903145 ACCCAATTTTATTTTGTACTTCCTCC 58.097 34.615 0.00 0.00 0.00 4.30
184 186 7.511028 ACCCAATTTTATTTTGTACTTCCTCCA 59.489 33.333 0.00 0.00 0.00 3.86
185 187 8.539544 CCCAATTTTATTTTGTACTTCCTCCAT 58.460 33.333 0.00 0.00 0.00 3.41
186 188 9.586435 CCAATTTTATTTTGTACTTCCTCCATC 57.414 33.333 0.00 0.00 0.00 3.51
187 189 9.586435 CAATTTTATTTTGTACTTCCTCCATCC 57.414 33.333 0.00 0.00 0.00 3.51
188 190 7.712204 TTTTATTTTGTACTTCCTCCATCCC 57.288 36.000 0.00 0.00 0.00 3.85
189 191 4.946160 ATTTTGTACTTCCTCCATCCCA 57.054 40.909 0.00 0.00 0.00 4.37
190 192 4.733077 TTTTGTACTTCCTCCATCCCAA 57.267 40.909 0.00 0.00 0.00 4.12
191 193 4.733077 TTTGTACTTCCTCCATCCCAAA 57.267 40.909 0.00 0.00 0.00 3.28
192 194 4.733077 TTGTACTTCCTCCATCCCAAAA 57.267 40.909 0.00 0.00 0.00 2.44
193 195 4.946160 TGTACTTCCTCCATCCCAAAAT 57.054 40.909 0.00 0.00 0.00 1.82
194 196 6.395780 TTGTACTTCCTCCATCCCAAAATA 57.604 37.500 0.00 0.00 0.00 1.40
195 197 6.590656 TGTACTTCCTCCATCCCAAAATAT 57.409 37.500 0.00 0.00 0.00 1.28
196 198 7.699709 TGTACTTCCTCCATCCCAAAATATA 57.300 36.000 0.00 0.00 0.00 0.86
197 199 8.108378 TGTACTTCCTCCATCCCAAAATATAA 57.892 34.615 0.00 0.00 0.00 0.98
198 200 8.217799 TGTACTTCCTCCATCCCAAAATATAAG 58.782 37.037 0.00 0.00 0.00 1.73
199 201 7.226059 ACTTCCTCCATCCCAAAATATAAGT 57.774 36.000 0.00 0.00 0.00 2.24
200 202 7.062957 ACTTCCTCCATCCCAAAATATAAGTG 58.937 38.462 0.00 0.00 0.00 3.16
201 203 6.840090 TCCTCCATCCCAAAATATAAGTGA 57.160 37.500 0.00 0.00 0.00 3.41
202 204 6.601332 TCCTCCATCCCAAAATATAAGTGAC 58.399 40.000 0.00 0.00 0.00 3.67
203 205 6.389869 TCCTCCATCCCAAAATATAAGTGACT 59.610 38.462 0.00 0.00 0.00 3.41
204 206 6.712547 CCTCCATCCCAAAATATAAGTGACTC 59.287 42.308 0.00 0.00 0.00 3.36
205 207 7.206789 TCCATCCCAAAATATAAGTGACTCA 57.793 36.000 0.00 0.00 0.00 3.41
206 208 7.638444 TCCATCCCAAAATATAAGTGACTCAA 58.362 34.615 0.00 0.00 0.00 3.02
207 209 7.556275 TCCATCCCAAAATATAAGTGACTCAAC 59.444 37.037 0.00 0.00 0.00 3.18
208 210 7.557719 CCATCCCAAAATATAAGTGACTCAACT 59.442 37.037 0.00 0.00 0.00 3.16
209 211 8.960591 CATCCCAAAATATAAGTGACTCAACTT 58.039 33.333 0.00 0.00 42.89 2.66
210 212 8.934023 TCCCAAAATATAAGTGACTCAACTTT 57.066 30.769 0.00 0.00 40.77 2.66
211 213 8.792633 TCCCAAAATATAAGTGACTCAACTTTG 58.207 33.333 0.00 0.00 40.77 2.77
212 214 8.576442 CCCAAAATATAAGTGACTCAACTTTGT 58.424 33.333 0.00 0.00 40.77 2.83
223 225 9.174166 AGTGACTCAACTTTGTACTAATTTTGT 57.826 29.630 0.00 0.00 0.00 2.83
249 251 8.015185 ACTAAACCTAGTACAAAGTTGAGTCA 57.985 34.615 6.24 0.00 36.56 3.41
250 252 7.924947 ACTAAACCTAGTACAAAGTTGAGTCAC 59.075 37.037 0.00 0.00 36.56 3.67
251 253 6.481434 AACCTAGTACAAAGTTGAGTCACT 57.519 37.500 0.00 0.00 0.00 3.41
252 254 6.481434 ACCTAGTACAAAGTTGAGTCACTT 57.519 37.500 0.00 0.00 38.74 3.16
253 255 7.592885 ACCTAGTACAAAGTTGAGTCACTTA 57.407 36.000 0.00 0.00 35.87 2.24
254 256 8.015185 ACCTAGTACAAAGTTGAGTCACTTAA 57.985 34.615 0.00 0.00 35.87 1.85
255 257 8.648693 ACCTAGTACAAAGTTGAGTCACTTAAT 58.351 33.333 0.00 0.00 35.87 1.40
256 258 9.490379 CCTAGTACAAAGTTGAGTCACTTAATT 57.510 33.333 0.00 0.00 35.87 1.40
259 261 8.621286 AGTACAAAGTTGAGTCACTTAATTTGG 58.379 33.333 16.35 5.04 35.87 3.28
260 262 6.805713 ACAAAGTTGAGTCACTTAATTTGGG 58.194 36.000 16.35 4.33 35.87 4.12
261 263 6.605594 ACAAAGTTGAGTCACTTAATTTGGGA 59.394 34.615 16.35 0.00 35.87 4.37
262 264 6.635030 AAGTTGAGTCACTTAATTTGGGAC 57.365 37.500 0.00 5.66 35.10 4.46
263 265 4.755123 AGTTGAGTCACTTAATTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
264 266 3.670625 TGAGTCACTTAATTTGGGACGG 58.329 45.455 7.56 0.00 33.84 4.79
265 267 3.071892 TGAGTCACTTAATTTGGGACGGT 59.928 43.478 7.56 0.00 33.84 4.83
266 268 3.408634 AGTCACTTAATTTGGGACGGTG 58.591 45.455 7.56 0.00 33.84 4.94
267 269 2.486592 GTCACTTAATTTGGGACGGTGG 59.513 50.000 0.00 0.00 0.00 4.61
268 270 1.816224 CACTTAATTTGGGACGGTGGG 59.184 52.381 0.00 0.00 0.00 4.61
269 271 1.706305 ACTTAATTTGGGACGGTGGGA 59.294 47.619 0.00 0.00 0.00 4.37
305 307 8.713708 TGATATTTTTCCTTTTGTCTTACCCA 57.286 30.769 0.00 0.00 0.00 4.51
316 318 4.137116 TGTCTTACCCATATGTCACTGC 57.863 45.455 1.24 0.00 0.00 4.40
342 344 4.868067 TCTCCTCGTCCGAATTTATTAGC 58.132 43.478 0.00 0.00 0.00 3.09
579 712 8.885494 TCTAGACGTATTTTAGTACTCTCTCC 57.115 38.462 0.00 0.00 0.00 3.71
580 713 6.601741 AGACGTATTTTAGTACTCTCTCCG 57.398 41.667 0.00 0.00 0.00 4.63
581 714 6.112058 AGACGTATTTTAGTACTCTCTCCGT 58.888 40.000 0.00 2.26 0.00 4.69
582 715 6.597280 AGACGTATTTTAGTACTCTCTCCGTT 59.403 38.462 0.00 0.00 0.00 4.44
583 716 7.120432 AGACGTATTTTAGTACTCTCTCCGTTT 59.880 37.037 0.00 0.00 0.00 3.60
584 717 7.247019 ACGTATTTTAGTACTCTCTCCGTTTC 58.753 38.462 0.00 0.00 0.00 2.78
585 718 7.120432 ACGTATTTTAGTACTCTCTCCGTTTCT 59.880 37.037 0.00 0.00 0.00 2.52
586 719 8.607459 CGTATTTTAGTACTCTCTCCGTTTCTA 58.393 37.037 0.00 0.00 0.00 2.10
597 730 9.411189 ACTCTCTCCGTTTCTAAATATAAGTCT 57.589 33.333 0.00 0.00 0.00 3.24
620 753 9.827411 GTCTTTGTAGAAATTTCACTATGAACC 57.173 33.333 19.99 6.84 31.84 3.62
621 754 9.567776 TCTTTGTAGAAATTTCACTATGAACCA 57.432 29.630 19.99 0.96 35.89 3.67
622 755 9.612620 CTTTGTAGAAATTTCACTATGAACCAC 57.387 33.333 19.99 3.25 35.89 4.16
623 756 8.684386 TTGTAGAAATTTCACTATGAACCACA 57.316 30.769 19.99 5.40 35.89 4.17
624 757 8.862325 TGTAGAAATTTCACTATGAACCACAT 57.138 30.769 19.99 0.00 35.89 3.21
625 758 9.952030 TGTAGAAATTTCACTATGAACCACATA 57.048 29.630 19.99 0.00 35.89 2.29
627 760 7.974675 AGAAATTTCACTATGAACCACATACG 58.025 34.615 19.99 0.00 35.89 3.06
628 761 7.822334 AGAAATTTCACTATGAACCACATACGA 59.178 33.333 19.99 0.00 35.89 3.43
629 762 7.915293 AATTTCACTATGAACCACATACGAA 57.085 32.000 0.00 0.00 35.89 3.85
630 763 8.506168 AATTTCACTATGAACCACATACGAAT 57.494 30.769 0.00 0.00 35.89 3.34
631 764 6.902224 TTCACTATGAACCACATACGAATG 57.098 37.500 0.00 0.00 40.07 2.67
632 765 6.403049 TTCACTATGAACCACATACGAATGT 58.597 36.000 0.00 0.00 37.91 2.71
633 766 7.102847 TCACTATGAACCACATACGAATGTA 57.897 36.000 0.00 0.00 44.70 2.29
634 767 7.722363 TCACTATGAACCACATACGAATGTAT 58.278 34.615 0.00 0.00 44.70 2.29
635 768 8.852135 TCACTATGAACCACATACGAATGTATA 58.148 33.333 0.00 0.00 44.70 1.47
636 769 9.639601 CACTATGAACCACATACGAATGTATAT 57.360 33.333 0.00 0.00 44.70 0.86
642 775 9.755064 GAACCACATACGAATGTATATAAATGC 57.245 33.333 0.00 0.00 44.70 3.56
643 776 8.840833 ACCACATACGAATGTATATAAATGCA 57.159 30.769 0.00 0.00 44.70 3.96
644 777 9.448438 ACCACATACGAATGTATATAAATGCAT 57.552 29.630 0.00 0.00 44.70 3.96
673 806 7.934855 AGTGTAGATTCATTCATTTTGCTCT 57.065 32.000 0.00 0.00 0.00 4.09
674 807 7.759465 AGTGTAGATTCATTCATTTTGCTCTG 58.241 34.615 0.00 0.00 0.00 3.35
675 808 7.392673 AGTGTAGATTCATTCATTTTGCTCTGT 59.607 33.333 0.00 0.00 0.00 3.41
676 809 8.668353 GTGTAGATTCATTCATTTTGCTCTGTA 58.332 33.333 0.00 0.00 0.00 2.74
677 810 9.399797 TGTAGATTCATTCATTTTGCTCTGTAT 57.600 29.630 0.00 0.00 0.00 2.29
684 817 9.494271 TCATTCATTTTGCTCTGTATATAGTCC 57.506 33.333 0.00 0.00 0.00 3.85
685 818 9.276590 CATTCATTTTGCTCTGTATATAGTCCA 57.723 33.333 0.00 0.00 0.00 4.02
687 820 9.494271 TTCATTTTGCTCTGTATATAGTCCATC 57.506 33.333 0.00 0.00 0.00 3.51
688 821 8.874156 TCATTTTGCTCTGTATATAGTCCATCT 58.126 33.333 0.00 0.00 0.00 2.90
689 822 9.499479 CATTTTGCTCTGTATATAGTCCATCTT 57.501 33.333 0.00 0.00 0.00 2.40
709 842 8.600449 CATCTTATGGAATCTCTACAAAGACC 57.400 38.462 0.00 0.00 0.00 3.85
710 843 7.979786 TCTTATGGAATCTCTACAAAGACCT 57.020 36.000 0.00 0.00 0.00 3.85
711 844 9.661954 ATCTTATGGAATCTCTACAAAGACCTA 57.338 33.333 0.00 0.00 0.00 3.08
712 845 9.661954 TCTTATGGAATCTCTACAAAGACCTAT 57.338 33.333 0.00 0.00 0.00 2.57
737 870 9.978044 ATATTTAGGAACGAAGGAAGTATGTAC 57.022 33.333 0.00 0.00 0.00 2.90
738 871 7.472334 TTTAGGAACGAAGGAAGTATGTACT 57.528 36.000 0.00 0.00 38.39 2.73
739 872 8.579850 TTTAGGAACGAAGGAAGTATGTACTA 57.420 34.615 0.00 0.00 34.99 1.82
1370 1671 2.861375 CTCGTTAGCGTGCTAGAGC 58.139 57.895 1.39 0.00 39.49 4.09
1391 1692 1.496429 CCAATTGGGCTGGGATAGACT 59.504 52.381 17.36 0.00 33.66 3.24
1392 1693 2.091665 CCAATTGGGCTGGGATAGACTT 60.092 50.000 17.36 0.00 33.66 3.01
1639 1942 1.656587 TAAGGATCCCTGCACACACT 58.343 50.000 8.55 0.00 32.13 3.55
1846 2149 1.200519 CTAACCTGGACCCGAATCCA 58.799 55.000 0.00 7.32 46.92 3.41
2019 2329 2.190578 GGCCGGATGGTGAGAAGG 59.809 66.667 5.05 0.00 37.67 3.46
2345 2658 6.726258 TGTATGTACTGAAGTTCAATGCTG 57.274 37.500 7.06 0.00 0.00 4.41
2971 3284 0.821711 GGCAAGTAACTGTGGTGGCA 60.822 55.000 0.00 0.00 35.06 4.92
3255 3569 3.445805 ACCAGATCGAAGGAGAGAACTTC 59.554 47.826 8.68 0.00 40.64 3.01
3415 3755 9.926158 AATTATGTAAATGAACAACAGCATTGA 57.074 25.926 7.65 0.00 35.11 2.57
3416 3756 8.741101 TTATGTAAATGAACAACAGCATTGAC 57.259 30.769 7.65 0.00 36.71 3.18
3417 3757 6.389830 TGTAAATGAACAACAGCATTGACT 57.610 33.333 7.65 0.00 36.98 3.41
3418 3758 6.207928 TGTAAATGAACAACAGCATTGACTG 58.792 36.000 7.65 6.56 43.59 3.51
3823 4190 5.995897 AGGTCAATGAGTTACTGGTTAACAC 59.004 40.000 8.10 0.00 42.45 3.32
3829 4196 9.136952 CAATGAGTTACTGGTTAACACTAGTAC 57.863 37.037 8.10 7.72 44.33 2.73
4295 4670 3.813443 AGAGTGACAAAACTGTCTGCAT 58.187 40.909 6.80 0.00 39.41 3.96
4349 4733 7.606456 GTGTCTCTCTTCACAAATGGGTATTAA 59.394 37.037 0.00 0.00 35.04 1.40
5251 5637 0.033781 GCCCTGCAATTTCAGCAACA 59.966 50.000 0.00 0.00 42.17 3.33
5439 5825 4.319261 CCGTGATCAATGTGTCATGCTATG 60.319 45.833 0.00 0.00 31.54 2.23
6111 6502 2.353704 CCTGACCACTTGCGTCTCATAA 60.354 50.000 0.00 0.00 0.00 1.90
6358 6753 2.988493 CCTGTTGGATTTTTCACATGCG 59.012 45.455 0.00 0.00 34.57 4.73
6638 7040 0.108520 GCTGCATGTGTTTCCATGGG 60.109 55.000 13.02 0.00 42.01 4.00
6907 7309 3.126001 TGGTCTGCTTGTCTTGGTTAG 57.874 47.619 0.00 0.00 0.00 2.34
7019 7421 0.827089 TGCTGTTGTCCATGGGGTTG 60.827 55.000 13.02 0.00 34.93 3.77
7608 8010 7.336931 TCTTGGTGTCTAAATTTAGATCAAGGC 59.663 37.037 33.60 22.91 41.43 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.970553 ATATCAATTGATGCACATAGTCCTATT 57.029 29.630 27.59 1.72 36.05 1.73
66 67 6.111768 ACGCATGCTTAAATCTCTAAACAG 57.888 37.500 17.13 0.00 0.00 3.16
173 175 8.218488 ACTTATATTTTGGGATGGAGGAAGTAC 58.782 37.037 0.00 0.00 0.00 2.73
174 176 8.217799 CACTTATATTTTGGGATGGAGGAAGTA 58.782 37.037 0.00 0.00 0.00 2.24
175 177 7.062957 CACTTATATTTTGGGATGGAGGAAGT 58.937 38.462 0.00 0.00 0.00 3.01
176 178 7.229506 GTCACTTATATTTTGGGATGGAGGAAG 59.770 40.741 0.00 0.00 0.00 3.46
177 179 7.060421 GTCACTTATATTTTGGGATGGAGGAA 58.940 38.462 0.00 0.00 0.00 3.36
178 180 6.389869 AGTCACTTATATTTTGGGATGGAGGA 59.610 38.462 0.00 0.00 0.00 3.71
179 181 6.605119 AGTCACTTATATTTTGGGATGGAGG 58.395 40.000 0.00 0.00 0.00 4.30
180 182 7.282585 TGAGTCACTTATATTTTGGGATGGAG 58.717 38.462 0.00 0.00 0.00 3.86
181 183 7.206789 TGAGTCACTTATATTTTGGGATGGA 57.793 36.000 0.00 0.00 0.00 3.41
182 184 7.557719 AGTTGAGTCACTTATATTTTGGGATGG 59.442 37.037 0.00 0.00 0.00 3.51
183 185 8.511604 AGTTGAGTCACTTATATTTTGGGATG 57.488 34.615 0.00 0.00 0.00 3.51
184 186 9.533831 AAAGTTGAGTCACTTATATTTTGGGAT 57.466 29.630 0.00 0.00 35.87 3.85
185 187 8.792633 CAAAGTTGAGTCACTTATATTTTGGGA 58.207 33.333 0.00 0.00 35.87 4.37
186 188 8.576442 ACAAAGTTGAGTCACTTATATTTTGGG 58.424 33.333 11.91 0.00 35.87 4.12
197 199 9.174166 ACAAAATTAGTACAAAGTTGAGTCACT 57.826 29.630 0.00 0.00 0.00 3.41
223 225 9.135189 TGACTCAACTTTGTACTAGGTTTAGTA 57.865 33.333 15.38 5.84 40.55 1.82
224 226 7.924947 GTGACTCAACTTTGTACTAGGTTTAGT 59.075 37.037 15.35 15.35 42.66 2.24
225 227 8.142551 AGTGACTCAACTTTGTACTAGGTTTAG 58.857 37.037 10.44 10.44 0.00 1.85
226 228 8.015185 AGTGACTCAACTTTGTACTAGGTTTA 57.985 34.615 2.19 0.00 0.00 2.01
227 229 6.885922 AGTGACTCAACTTTGTACTAGGTTT 58.114 36.000 2.19 0.00 0.00 3.27
228 230 6.481434 AGTGACTCAACTTTGTACTAGGTT 57.519 37.500 0.00 0.00 0.00 3.50
229 231 6.481434 AAGTGACTCAACTTTGTACTAGGT 57.519 37.500 0.00 0.00 37.05 3.08
230 232 9.490379 AATTAAGTGACTCAACTTTGTACTAGG 57.510 33.333 0.00 0.00 40.77 3.02
233 235 8.621286 CCAAATTAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
234 236 7.860872 CCCAAATTAAGTGACTCAACTTTGTAC 59.139 37.037 8.71 0.00 40.77 2.90
235 237 7.776030 TCCCAAATTAAGTGACTCAACTTTGTA 59.224 33.333 8.71 0.00 40.77 2.41
236 238 6.605594 TCCCAAATTAAGTGACTCAACTTTGT 59.394 34.615 8.71 0.00 40.77 2.83
237 239 6.918022 GTCCCAAATTAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
238 240 6.238648 CGTCCCAAATTAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
239 241 5.238650 CGTCCCAAATTAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
240 242 4.755123 CGTCCCAAATTAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
241 243 4.083484 CCGTCCCAAATTAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
242 244 4.069304 CCGTCCCAAATTAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
243 245 3.071892 ACCGTCCCAAATTAAGTGACTCA 59.928 43.478 0.00 0.00 0.00 3.41
244 246 3.435671 CACCGTCCCAAATTAAGTGACTC 59.564 47.826 0.00 0.00 0.00 3.36
245 247 3.408634 CACCGTCCCAAATTAAGTGACT 58.591 45.455 0.00 0.00 0.00 3.41
246 248 2.486592 CCACCGTCCCAAATTAAGTGAC 59.513 50.000 0.00 0.00 0.00 3.67
247 249 2.553466 CCCACCGTCCCAAATTAAGTGA 60.553 50.000 0.00 0.00 0.00 3.41
248 250 1.816224 CCCACCGTCCCAAATTAAGTG 59.184 52.381 0.00 0.00 0.00 3.16
249 251 1.706305 TCCCACCGTCCCAAATTAAGT 59.294 47.619 0.00 0.00 0.00 2.24
250 252 2.290705 ACTCCCACCGTCCCAAATTAAG 60.291 50.000 0.00 0.00 0.00 1.85
251 253 1.706305 ACTCCCACCGTCCCAAATTAA 59.294 47.619 0.00 0.00 0.00 1.40
252 254 1.364269 ACTCCCACCGTCCCAAATTA 58.636 50.000 0.00 0.00 0.00 1.40
253 255 1.364269 TACTCCCACCGTCCCAAATT 58.636 50.000 0.00 0.00 0.00 1.82
254 256 1.591768 ATACTCCCACCGTCCCAAAT 58.408 50.000 0.00 0.00 0.00 2.32
255 257 2.250921 TATACTCCCACCGTCCCAAA 57.749 50.000 0.00 0.00 0.00 3.28
256 258 2.482414 ATATACTCCCACCGTCCCAA 57.518 50.000 0.00 0.00 0.00 4.12
257 259 2.448194 AGTATATACTCCCACCGTCCCA 59.552 50.000 9.71 0.00 0.00 4.37
258 260 3.166560 AGTATATACTCCCACCGTCCC 57.833 52.381 9.71 0.00 0.00 4.46
259 261 4.586001 TCAAAGTATATACTCCCACCGTCC 59.414 45.833 15.72 0.00 34.99 4.79
260 262 5.779529 TCAAAGTATATACTCCCACCGTC 57.220 43.478 15.72 0.00 34.99 4.79
261 263 8.431910 AATATCAAAGTATATACTCCCACCGT 57.568 34.615 15.72 0.00 34.99 4.83
262 264 9.720769 AAAATATCAAAGTATATACTCCCACCG 57.279 33.333 15.72 2.22 34.99 4.94
305 307 3.818210 CGAGGAGAGTAGCAGTGACATAT 59.182 47.826 0.00 0.00 0.00 1.78
316 318 5.692613 ATAAATTCGGACGAGGAGAGTAG 57.307 43.478 0.00 0.00 0.00 2.57
443 446 7.568199 AAATTAGACCGTGGGAAATCTATTG 57.432 36.000 0.00 0.00 0.00 1.90
444 447 8.466798 CAAAAATTAGACCGTGGGAAATCTATT 58.533 33.333 0.00 0.00 0.00 1.73
445 448 7.614192 ACAAAAATTAGACCGTGGGAAATCTAT 59.386 33.333 0.00 0.00 0.00 1.98
446 449 6.943718 ACAAAAATTAGACCGTGGGAAATCTA 59.056 34.615 0.00 0.00 0.00 1.98
594 727 9.827411 GGTTCATAGTGAAATTTCTACAAAGAC 57.173 33.333 18.64 7.04 38.22 3.01
595 728 9.567776 TGGTTCATAGTGAAATTTCTACAAAGA 57.432 29.630 18.64 7.52 38.22 2.52
596 729 9.612620 GTGGTTCATAGTGAAATTTCTACAAAG 57.387 33.333 18.64 5.49 38.22 2.77
597 730 9.126151 TGTGGTTCATAGTGAAATTTCTACAAA 57.874 29.630 18.64 8.40 38.22 2.83
598 731 8.684386 TGTGGTTCATAGTGAAATTTCTACAA 57.316 30.769 18.64 3.14 38.22 2.41
599 732 8.862325 ATGTGGTTCATAGTGAAATTTCTACA 57.138 30.769 18.64 4.82 38.22 2.74
601 734 9.093970 CGTATGTGGTTCATAGTGAAATTTCTA 57.906 33.333 18.64 4.82 38.22 2.10
602 735 7.822334 TCGTATGTGGTTCATAGTGAAATTTCT 59.178 33.333 18.64 2.61 38.22 2.52
603 736 7.970384 TCGTATGTGGTTCATAGTGAAATTTC 58.030 34.615 11.41 11.41 38.22 2.17
604 737 7.915293 TCGTATGTGGTTCATAGTGAAATTT 57.085 32.000 0.00 0.00 38.22 1.82
605 738 7.915293 TTCGTATGTGGTTCATAGTGAAATT 57.085 32.000 0.00 0.00 38.22 1.82
606 739 7.552687 ACATTCGTATGTGGTTCATAGTGAAAT 59.447 33.333 6.89 0.00 43.29 2.17
607 740 6.876789 ACATTCGTATGTGGTTCATAGTGAAA 59.123 34.615 6.89 0.00 43.29 2.69
608 741 6.403049 ACATTCGTATGTGGTTCATAGTGAA 58.597 36.000 6.89 0.00 43.29 3.18
609 742 5.972935 ACATTCGTATGTGGTTCATAGTGA 58.027 37.500 6.89 0.00 43.29 3.41
610 743 7.946655 ATACATTCGTATGTGGTTCATAGTG 57.053 36.000 16.91 0.00 44.56 2.74
616 749 9.755064 GCATTTATATACATTCGTATGTGGTTC 57.245 33.333 16.91 0.00 44.56 3.62
617 750 9.278978 TGCATTTATATACATTCGTATGTGGTT 57.721 29.630 16.91 5.39 44.56 3.67
618 751 8.840833 TGCATTTATATACATTCGTATGTGGT 57.159 30.769 16.91 8.59 44.56 4.16
647 780 9.453572 AGAGCAAAATGAATGAATCTACACTTA 57.546 29.630 0.00 0.00 0.00 2.24
648 781 8.242053 CAGAGCAAAATGAATGAATCTACACTT 58.758 33.333 0.00 0.00 0.00 3.16
649 782 7.392673 ACAGAGCAAAATGAATGAATCTACACT 59.607 33.333 0.00 0.00 0.00 3.55
650 783 7.533426 ACAGAGCAAAATGAATGAATCTACAC 58.467 34.615 0.00 0.00 0.00 2.90
651 784 7.692460 ACAGAGCAAAATGAATGAATCTACA 57.308 32.000 0.00 0.00 0.00 2.74
658 791 9.494271 GGACTATATACAGAGCAAAATGAATGA 57.506 33.333 0.00 0.00 0.00 2.57
659 792 9.276590 TGGACTATATACAGAGCAAAATGAATG 57.723 33.333 0.00 0.00 0.00 2.67
661 794 9.494271 GATGGACTATATACAGAGCAAAATGAA 57.506 33.333 0.00 0.00 0.00 2.57
662 795 8.874156 AGATGGACTATATACAGAGCAAAATGA 58.126 33.333 0.00 0.00 0.00 2.57
663 796 9.499479 AAGATGGACTATATACAGAGCAAAATG 57.501 33.333 0.00 0.00 0.00 2.32
684 817 8.428063 AGGTCTTTGTAGAGATTCCATAAGATG 58.572 37.037 0.00 0.00 0.00 2.90
685 818 8.560124 AGGTCTTTGTAGAGATTCCATAAGAT 57.440 34.615 0.00 0.00 0.00 2.40
686 819 7.979786 AGGTCTTTGTAGAGATTCCATAAGA 57.020 36.000 0.00 0.00 0.00 2.10
711 844 9.978044 GTACATACTTCCTTCGTTCCTAAATAT 57.022 33.333 0.00 0.00 0.00 1.28
712 845 9.193806 AGTACATACTTCCTTCGTTCCTAAATA 57.806 33.333 0.00 0.00 31.13 1.40
713 846 8.075761 AGTACATACTTCCTTCGTTCCTAAAT 57.924 34.615 0.00 0.00 31.13 1.40
714 847 7.472334 AGTACATACTTCCTTCGTTCCTAAA 57.528 36.000 0.00 0.00 31.13 1.85
715 848 8.757982 ATAGTACATACTTCCTTCGTTCCTAA 57.242 34.615 0.00 0.00 37.73 2.69
717 850 8.937207 ATATAGTACATACTTCCTTCGTTCCT 57.063 34.615 0.00 0.00 37.73 3.36
718 851 9.623350 GAATATAGTACATACTTCCTTCGTTCC 57.377 37.037 0.00 0.00 37.73 3.62
720 853 9.962783 GTGAATATAGTACATACTTCCTTCGTT 57.037 33.333 0.00 0.00 37.73 3.85
721 854 9.352191 AGTGAATATAGTACATACTTCCTTCGT 57.648 33.333 0.00 0.00 37.73 3.85
722 855 9.828852 GAGTGAATATAGTACATACTTCCTTCG 57.171 37.037 0.00 0.00 37.73 3.79
1391 1692 9.882996 CTATATTTCTCAAATTCGCAATGCTAA 57.117 29.630 2.94 0.00 32.38 3.09
1392 1693 8.506437 CCTATATTTCTCAAATTCGCAATGCTA 58.494 33.333 2.94 0.00 32.38 3.49
1639 1942 2.237643 TGGCTGCAATTGTTAGCTTCA 58.762 42.857 25.47 17.61 37.58 3.02
1846 2149 2.071844 CTACGTCGATGGGATGCGGT 62.072 60.000 9.90 0.00 34.88 5.68
2019 2329 1.451028 AAGAAGCTGATGGCCTCGC 60.451 57.895 3.32 7.48 43.05 5.03
2345 2658 1.153353 CCCCACACACACGTTATGTC 58.847 55.000 0.00 0.00 40.64 3.06
2532 2845 2.238521 AGTTGCCGATCACCAAATTGT 58.761 42.857 0.00 0.00 0.00 2.71
3255 3569 7.255381 CCCTGCAATATCAAAATAAGTCTGGAG 60.255 40.741 0.00 0.00 0.00 3.86
3402 3742 3.772932 CAACACAGTCAATGCTGTTGTT 58.227 40.909 10.50 11.16 46.45 2.83
3403 3743 2.754552 ACAACACAGTCAATGCTGTTGT 59.245 40.909 15.72 15.72 46.45 3.32
3404 3744 3.425577 ACAACACAGTCAATGCTGTTG 57.574 42.857 14.77 14.77 46.45 3.33
3405 3745 5.574891 TTTACAACACAGTCAATGCTGTT 57.425 34.783 7.42 0.00 46.45 3.16
3407 3747 5.761003 TCATTTACAACACAGTCAATGCTG 58.239 37.500 3.74 3.74 41.92 4.41
3408 3748 6.183360 TGTTCATTTACAACACAGTCAATGCT 60.183 34.615 0.00 0.00 34.62 3.79
3409 3749 5.976534 TGTTCATTTACAACACAGTCAATGC 59.023 36.000 0.00 0.00 34.62 3.56
3410 3750 7.984002 TTGTTCATTTACAACACAGTCAATG 57.016 32.000 0.00 0.00 35.47 2.82
3421 3761 6.696583 CAGTCAATGCTGTTGTTCATTTACAA 59.303 34.615 0.00 0.00 35.75 2.41
3422 3762 6.183360 ACAGTCAATGCTGTTGTTCATTTACA 60.183 34.615 4.86 0.00 46.45 2.41
3423 3763 6.142798 CACAGTCAATGCTGTTGTTCATTTAC 59.857 38.462 7.42 0.00 46.45 2.01
3424 3764 6.183360 ACACAGTCAATGCTGTTGTTCATTTA 60.183 34.615 7.42 0.00 46.45 1.40
3425 3765 5.045215 CACAGTCAATGCTGTTGTTCATTT 58.955 37.500 7.42 0.00 46.45 2.32
3426 3766 4.098349 ACACAGTCAATGCTGTTGTTCATT 59.902 37.500 7.42 0.00 46.45 2.57
3427 3767 3.633525 ACACAGTCAATGCTGTTGTTCAT 59.366 39.130 7.42 0.00 46.45 2.57
3428 3768 3.016031 ACACAGTCAATGCTGTTGTTCA 58.984 40.909 7.42 0.00 46.45 3.18
3429 3769 3.698029 ACACAGTCAATGCTGTTGTTC 57.302 42.857 7.42 0.00 46.45 3.18
3823 4190 1.858091 CTTCAGGGCATGCGTACTAG 58.142 55.000 12.44 2.51 0.00 2.57
4295 4670 3.895656 GCATATGACCCCTAGACTGTACA 59.104 47.826 6.97 0.00 0.00 2.90
5177 5563 0.469892 ACAAAGTTGAGGCCAAGGGG 60.470 55.000 5.01 0.00 32.06 4.79
5439 5825 0.181350 AATAGCCCTACAGCCTGCAC 59.819 55.000 0.00 0.00 0.00 4.57
6638 7040 2.222027 ACAGCTTGCTACACCTTTCAC 58.778 47.619 0.00 0.00 0.00 3.18
6879 7281 1.748493 GACAAGCAGACCAAACCACAA 59.252 47.619 0.00 0.00 0.00 3.33
7011 7413 2.509931 ATCAGCAGCAGCAACCCCAT 62.510 55.000 3.17 0.00 45.49 4.00
7019 7421 0.666913 CCATTACCATCAGCAGCAGC 59.333 55.000 0.00 0.00 42.56 5.25
7323 7725 8.887264 AGTAAAAACCCAAATATATGGACACA 57.113 30.769 0.00 0.00 43.54 3.72


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

AutoCloner maintained by Alex Coulton.