Multiple sequence alignment - TraesCS3A01G261900

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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 TraesCS3A01G261900 chr3A 100.000 2801 0 0 1 2801 484652042 484649242 0.000000e+00 5173
1 TraesCS3A01G261900 chr3A 80.024 826 139 15 989 1795 484999237 485000055 3.110000e-164 588
2 TraesCS3A01G261900 chr3A 79.878 820 139 17 998 1798 484643878 484643066 6.730000e-161 577
3 TraesCS3A01G261900 chr3A 84.756 164 14 6 83 235 100724668 100724831 1.340000e-33 154
4 TraesCS3A01G261900 chr3B 99.403 1005 6 0 1797 2801 816308090 816309094 0.000000e+00 1823
5 TraesCS3A01G261900 chr3B 83.202 762 101 14 989 1729 474016969 474017724 0.000000e+00 673
6 TraesCS3A01G261900 chr3B 79.979 934 142 23 893 1798 473705249 473704333 0.000000e+00 647
7 TraesCS3A01G261900 chr3B 95.556 90 3 1 597 686 473705353 473705265 2.910000e-30 143
8 TraesCS3A01G261900 chr3B 97.500 80 2 0 526 605 473707181 473707102 1.350000e-28 137
9 TraesCS3A01G261900 chr6A 99.402 1003 6 0 1799 2801 578905809 578906811 0.000000e+00 1820
10 TraesCS3A01G261900 chr6A 99.005 1005 7 1 1797 2801 598923844 598922843 0.000000e+00 1797
11 TraesCS3A01G261900 chr6A 96.552 87 3 0 1 87 59807650 59807736 8.090000e-31 145
12 TraesCS3A01G261900 chr5A 99.302 1003 7 0 1799 2801 453529009 453528007 0.000000e+00 1814
13 TraesCS3A01G261900 chr4A 99.302 1003 7 0 1799 2801 656557422 656558424 0.000000e+00 1814
14 TraesCS3A01G261900 chr1B 99.302 1003 7 0 1799 2801 675325285 675326287 0.000000e+00 1814
15 TraesCS3A01G261900 chr2B 99.302 1003 5 1 1799 2801 733174296 733173296 0.000000e+00 1812
16 TraesCS3A01G261900 chr2B 99.005 1005 10 0 1797 2801 624284776 624283772 0.000000e+00 1801
17 TraesCS3A01G261900 chr2B 81.250 304 56 1 1123 1426 784709289 784709591 7.750000e-61 244
18 TraesCS3A01G261900 chr3D 92.778 1260 73 11 541 1798 363604356 363603113 0.000000e+00 1807
19 TraesCS3A01G261900 chr3D 93.617 329 19 2 83 409 80573497 80573169 9.020000e-135 490
20 TraesCS3A01G261900 chr3D 90.728 151 5 2 600 741 363857138 363857288 2.850000e-45 193
21 TraesCS3A01G261900 chr2A 99.103 1003 9 0 1799 2801 7839332 7838330 0.000000e+00 1803
22 TraesCS3A01G261900 chr2A 80.000 210 37 2 1153 1357 775761773 775761564 1.740000e-32 150
23 TraesCS3A01G261900 chr1D 93.699 365 20 3 83 444 16969460 16969824 6.820000e-151 544
24 TraesCS3A01G261900 chr1D 92.603 365 25 2 83 445 113906049 113906413 8.890000e-145 523
25 TraesCS3A01G261900 chr1D 92.603 365 25 2 83 445 119304013 119304377 8.890000e-145 523
26 TraesCS3A01G261900 chr1D 98.851 87 1 0 1 87 119302228 119302314 3.740000e-34 156
27 TraesCS3A01G261900 chr7D 92.857 364 23 3 83 443 105200188 105199825 2.470000e-145 525
28 TraesCS3A01G261900 chr7A 91.507 365 27 4 83 443 651178223 651178587 1.500000e-137 499
29 TraesCS3A01G261900 chr7A 91.139 316 25 3 131 443 122161672 122161357 2.580000e-115 425
30 TraesCS3A01G261900 chr2D 90.164 366 31 5 83 445 480757493 480757130 3.270000e-129 472
31 TraesCS3A01G261900 chr2D 87.397 365 43 3 83 445 625191589 625191226 1.550000e-112 416
32 TraesCS3A01G261900 chr2D 97.701 87 2 0 1 87 625192197 625192111 1.740000e-32 150
33 TraesCS3A01G261900 chr2D 96.552 87 3 0 1 87 44610521 44610607 8.090000e-31 145
34 TraesCS3A01G261900 chr2D 96.552 87 3 0 1 87 142437201 142437115 8.090000e-31 145
35 TraesCS3A01G261900 chr6D 98.851 87 1 0 1 87 131699625 131699711 3.740000e-34 156
36 TraesCS3A01G261900 chr6D 97.701 87 2 0 1 87 131698673 131698587 1.740000e-32 150
37 TraesCS3A01G261900 chr6D 96.552 87 3 0 1 87 397361401 397361487 8.090000e-31 145
38 TraesCS3A01G261900 chr5B 97.701 87 2 0 1 87 582884205 582884119 1.740000e-32 150


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 TraesCS3A01G261900 chr3A 484649242 484652042 2800 True 5173.0 5173 100.000000 1 2801 1 chr3A.!!$R2 2800
1 TraesCS3A01G261900 chr3A 484999237 485000055 818 False 588.0 588 80.024000 989 1795 1 chr3A.!!$F2 806
2 TraesCS3A01G261900 chr3A 484643066 484643878 812 True 577.0 577 79.878000 998 1798 1 chr3A.!!$R1 800
3 TraesCS3A01G261900 chr3B 816308090 816309094 1004 False 1823.0 1823 99.403000 1797 2801 1 chr3B.!!$F2 1004
4 TraesCS3A01G261900 chr3B 474016969 474017724 755 False 673.0 673 83.202000 989 1729 1 chr3B.!!$F1 740
5 TraesCS3A01G261900 chr3B 473704333 473707181 2848 True 309.0 647 91.011667 526 1798 3 chr3B.!!$R1 1272
6 TraesCS3A01G261900 chr6A 578905809 578906811 1002 False 1820.0 1820 99.402000 1799 2801 1 chr6A.!!$F2 1002
7 TraesCS3A01G261900 chr6A 598922843 598923844 1001 True 1797.0 1797 99.005000 1797 2801 1 chr6A.!!$R1 1004
8 TraesCS3A01G261900 chr5A 453528007 453529009 1002 True 1814.0 1814 99.302000 1799 2801 1 chr5A.!!$R1 1002
9 TraesCS3A01G261900 chr4A 656557422 656558424 1002 False 1814.0 1814 99.302000 1799 2801 1 chr4A.!!$F1 1002
10 TraesCS3A01G261900 chr1B 675325285 675326287 1002 False 1814.0 1814 99.302000 1799 2801 1 chr1B.!!$F1 1002
11 TraesCS3A01G261900 chr2B 733173296 733174296 1000 True 1812.0 1812 99.302000 1799 2801 1 chr2B.!!$R2 1002
12 TraesCS3A01G261900 chr2B 624283772 624284776 1004 True 1801.0 1801 99.005000 1797 2801 1 chr2B.!!$R1 1004
13 TraesCS3A01G261900 chr3D 363603113 363604356 1243 True 1807.0 1807 92.778000 541 1798 1 chr3D.!!$R2 1257
14 TraesCS3A01G261900 chr2A 7838330 7839332 1002 True 1803.0 1803 99.103000 1799 2801 1 chr2A.!!$R1 1002
15 TraesCS3A01G261900 chr1D 119302228 119304377 2149 False 339.5 523 95.727000 1 445 2 chr1D.!!$F3 444
16 TraesCS3A01G261900 chr2D 625191226 625192197 971 True 283.0 416 92.549000 1 445 2 chr2D.!!$R3 444

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
473 2213 0.034896 TCGAACTGCCCCAACTCTTC 59.965 55.0 0.00 0.00 0.00 2.87 F
474 2214 0.035458 CGAACTGCCCCAACTCTTCT 59.965 55.0 0.00 0.00 0.00 2.85 F
510 2250 0.036010 CGTGGAATCCTCACTTGCCT 60.036 55.0 0.00 0.00 33.31 4.75 F
1541 5061 0.040058 TTCAATCCACCTGCAGGCAT 59.960 50.0 33.06 18.81 39.32 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1319 4835 0.249489 GTCCCCGAGAATGATGGTCG 60.249 60.000 0.0 0.0 0.00 4.79 R
1675 5195 0.530650 CCGTAATCACTCGGCAGCAT 60.531 55.000 0.0 0.0 40.28 3.79 R
1773 5296 2.341101 ACTGTAGGAGCACCGTCCG 61.341 63.158 0.0 0.0 42.05 4.79 R
2454 5980 6.310941 TGGGAATAGGACTTCATTTCAAACA 58.689 36.000 0.0 0.0 0.00 2.83 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
63 64 1.274650 ACATCCATTCCTCCACCTCCT 60.275 52.381 0.00 0.00 0.00 3.69
134 1872 4.568956 TGATTGAGACGATGCTCTTTTGA 58.431 39.130 0.00 0.00 35.91 2.69
140 1878 5.105756 TGAGACGATGCTCTTTTGATAGACA 60.106 40.000 0.00 0.00 35.91 3.41
235 1974 4.250116 TGCTATTTGAATGCAAAACCGT 57.750 36.364 2.14 0.00 46.19 4.83
321 2061 4.571919 AGTTGCAAATTTGGACCATCATG 58.428 39.130 19.47 0.00 0.00 3.07
333 2073 5.215845 TGGACCATCATGTTAGACCATCTA 58.784 41.667 0.00 0.00 0.00 1.98
369 2109 3.451141 TTTCAAAGCTCCAAAACGCAT 57.549 38.095 0.00 0.00 0.00 4.73
405 2145 8.657729 GTTCAAATTTTACTTTTCCGGTTTTGA 58.342 29.630 0.00 0.00 0.00 2.69
432 2172 7.122055 ACCGCTAAATTTTGAACCATCTATTGA 59.878 33.333 3.69 0.00 0.00 2.57
447 2187 5.991328 TCTATTGAAGATGCTTTAAGCGG 57.009 39.130 12.54 0.00 46.26 5.52
448 2188 5.428253 TCTATTGAAGATGCTTTAAGCGGT 58.572 37.500 12.54 3.39 46.26 5.68
449 2189 5.880332 TCTATTGAAGATGCTTTAAGCGGTT 59.120 36.000 12.54 4.76 46.26 4.44
450 2190 4.419522 TTGAAGATGCTTTAAGCGGTTC 57.580 40.909 12.54 13.85 46.26 3.62
451 2191 3.674997 TGAAGATGCTTTAAGCGGTTCT 58.325 40.909 19.29 15.03 46.26 3.01
452 2192 3.436704 TGAAGATGCTTTAAGCGGTTCTG 59.563 43.478 19.29 0.00 46.26 3.02
453 2193 3.334583 AGATGCTTTAAGCGGTTCTGA 57.665 42.857 12.54 0.00 46.26 3.27
454 2194 3.878778 AGATGCTTTAAGCGGTTCTGAT 58.121 40.909 12.54 0.00 46.26 2.90
455 2195 3.873952 AGATGCTTTAAGCGGTTCTGATC 59.126 43.478 12.54 7.63 46.26 2.92
456 2196 1.999735 TGCTTTAAGCGGTTCTGATCG 59.000 47.619 12.54 0.00 46.26 3.69
457 2197 2.268298 GCTTTAAGCGGTTCTGATCGA 58.732 47.619 1.59 0.00 0.00 3.59
458 2198 2.671396 GCTTTAAGCGGTTCTGATCGAA 59.329 45.455 1.59 0.00 0.00 3.71
459 2199 5.903712 TGCTTTAAGCGGTTCTGATCGAAC 61.904 45.833 12.54 16.93 46.26 3.95
465 2205 2.768834 GTTCTGATCGAACTGCCCC 58.231 57.895 17.54 0.00 46.74 5.80
466 2206 0.036388 GTTCTGATCGAACTGCCCCA 60.036 55.000 17.54 0.00 46.74 4.96
467 2207 0.690192 TTCTGATCGAACTGCCCCAA 59.310 50.000 0.00 0.00 0.00 4.12
468 2208 0.036388 TCTGATCGAACTGCCCCAAC 60.036 55.000 0.00 0.00 0.00 3.77
469 2209 0.036010 CTGATCGAACTGCCCCAACT 60.036 55.000 0.00 0.00 0.00 3.16
470 2210 0.036388 TGATCGAACTGCCCCAACTC 60.036 55.000 0.00 0.00 0.00 3.01
471 2211 0.250513 GATCGAACTGCCCCAACTCT 59.749 55.000 0.00 0.00 0.00 3.24
472 2212 0.693049 ATCGAACTGCCCCAACTCTT 59.307 50.000 0.00 0.00 0.00 2.85
473 2213 0.034896 TCGAACTGCCCCAACTCTTC 59.965 55.000 0.00 0.00 0.00 2.87
474 2214 0.035458 CGAACTGCCCCAACTCTTCT 59.965 55.000 0.00 0.00 0.00 2.85
475 2215 1.528129 GAACTGCCCCAACTCTTCTG 58.472 55.000 0.00 0.00 0.00 3.02
476 2216 0.846693 AACTGCCCCAACTCTTCTGT 59.153 50.000 0.00 0.00 0.00 3.41
477 2217 0.109342 ACTGCCCCAACTCTTCTGTG 59.891 55.000 0.00 0.00 0.00 3.66
478 2218 0.607489 CTGCCCCAACTCTTCTGTGG 60.607 60.000 0.00 0.00 0.00 4.17
479 2219 1.973812 GCCCCAACTCTTCTGTGGC 60.974 63.158 0.00 0.00 0.00 5.01
480 2220 1.763770 CCCCAACTCTTCTGTGGCT 59.236 57.895 0.00 0.00 0.00 4.75
481 2221 0.322008 CCCCAACTCTTCTGTGGCTC 60.322 60.000 0.00 0.00 0.00 4.70
482 2222 0.689623 CCCAACTCTTCTGTGGCTCT 59.310 55.000 0.00 0.00 0.00 4.09
483 2223 1.610102 CCCAACTCTTCTGTGGCTCTG 60.610 57.143 0.00 0.00 0.00 3.35
484 2224 1.071385 CCAACTCTTCTGTGGCTCTGT 59.929 52.381 0.00 0.00 0.00 3.41
485 2225 2.141517 CAACTCTTCTGTGGCTCTGTG 58.858 52.381 0.00 0.00 0.00 3.66
486 2226 1.709578 ACTCTTCTGTGGCTCTGTGA 58.290 50.000 0.00 0.00 0.00 3.58
487 2227 1.617850 ACTCTTCTGTGGCTCTGTGAG 59.382 52.381 12.95 12.95 0.00 3.51
488 2228 1.617850 CTCTTCTGTGGCTCTGTGAGT 59.382 52.381 0.00 0.00 31.39 3.41
489 2229 2.822561 CTCTTCTGTGGCTCTGTGAGTA 59.177 50.000 0.00 0.00 31.39 2.59
490 2230 2.558795 TCTTCTGTGGCTCTGTGAGTAC 59.441 50.000 0.00 0.00 31.39 2.73
491 2231 1.257743 TCTGTGGCTCTGTGAGTACC 58.742 55.000 0.00 0.00 31.39 3.34
492 2232 0.109086 CTGTGGCTCTGTGAGTACCG 60.109 60.000 0.00 0.00 31.39 4.02
493 2233 0.826256 TGTGGCTCTGTGAGTACCGT 60.826 55.000 0.00 0.00 31.39 4.83
494 2234 0.388649 GTGGCTCTGTGAGTACCGTG 60.389 60.000 0.00 0.00 31.39 4.94
495 2235 1.215647 GGCTCTGTGAGTACCGTGG 59.784 63.158 0.00 0.00 31.39 4.94
496 2236 1.248785 GGCTCTGTGAGTACCGTGGA 61.249 60.000 0.00 0.00 31.39 4.02
497 2237 0.601558 GCTCTGTGAGTACCGTGGAA 59.398 55.000 0.00 0.00 31.39 3.53
498 2238 1.204941 GCTCTGTGAGTACCGTGGAAT 59.795 52.381 0.00 0.00 31.39 3.01
499 2239 2.735762 GCTCTGTGAGTACCGTGGAATC 60.736 54.545 0.00 0.00 31.39 2.52
500 2240 1.822990 TCTGTGAGTACCGTGGAATCC 59.177 52.381 0.00 0.00 0.00 3.01
501 2241 1.825474 CTGTGAGTACCGTGGAATCCT 59.175 52.381 0.00 0.00 0.00 3.24
502 2242 1.822990 TGTGAGTACCGTGGAATCCTC 59.177 52.381 0.00 0.00 0.00 3.71
503 2243 1.822990 GTGAGTACCGTGGAATCCTCA 59.177 52.381 0.00 0.00 0.00 3.86
504 2244 1.822990 TGAGTACCGTGGAATCCTCAC 59.177 52.381 0.00 0.00 0.00 3.51
505 2245 2.100989 GAGTACCGTGGAATCCTCACT 58.899 52.381 0.00 0.00 33.31 3.41
506 2246 2.496470 GAGTACCGTGGAATCCTCACTT 59.504 50.000 0.00 0.00 33.31 3.16
507 2247 2.233922 AGTACCGTGGAATCCTCACTTG 59.766 50.000 0.00 0.00 33.31 3.16
508 2248 0.321653 ACCGTGGAATCCTCACTTGC 60.322 55.000 0.00 0.00 33.31 4.01
509 2249 1.026718 CCGTGGAATCCTCACTTGCC 61.027 60.000 0.00 0.00 33.31 4.52
510 2250 0.036010 CGTGGAATCCTCACTTGCCT 60.036 55.000 0.00 0.00 33.31 4.75
511 2251 1.611673 CGTGGAATCCTCACTTGCCTT 60.612 52.381 0.00 0.00 33.31 4.35
512 2252 1.815003 GTGGAATCCTCACTTGCCTTG 59.185 52.381 0.00 0.00 32.78 3.61
513 2253 0.813821 GGAATCCTCACTTGCCTTGC 59.186 55.000 0.00 0.00 0.00 4.01
514 2254 0.813821 GAATCCTCACTTGCCTTGCC 59.186 55.000 0.00 0.00 0.00 4.52
515 2255 0.613012 AATCCTCACTTGCCTTGCCC 60.613 55.000 0.00 0.00 0.00 5.36
516 2256 2.826777 ATCCTCACTTGCCTTGCCCG 62.827 60.000 0.00 0.00 0.00 6.13
517 2257 2.281761 CTCACTTGCCTTGCCCGT 60.282 61.111 0.00 0.00 0.00 5.28
518 2258 2.281484 TCACTTGCCTTGCCCGTC 60.281 61.111 0.00 0.00 0.00 4.79
519 2259 2.594303 CACTTGCCTTGCCCGTCA 60.594 61.111 0.00 0.00 0.00 4.35
520 2260 2.192861 CACTTGCCTTGCCCGTCAA 61.193 57.895 0.00 0.00 0.00 3.18
521 2261 1.454847 ACTTGCCTTGCCCGTCAAA 60.455 52.632 0.00 0.00 33.65 2.69
522 2262 1.040339 ACTTGCCTTGCCCGTCAAAA 61.040 50.000 0.00 0.00 33.65 2.44
523 2263 0.103937 CTTGCCTTGCCCGTCAAAAA 59.896 50.000 0.00 0.00 33.65 1.94
714 4211 4.248842 CCTGTGGTGGGCGTGTGA 62.249 66.667 0.00 0.00 0.00 3.58
716 4213 2.515057 TGTGGTGGGCGTGTGAAC 60.515 61.111 0.00 0.00 0.00 3.18
733 4230 4.629634 TGTGAACGTGAATATGTGATGACC 59.370 41.667 0.00 0.00 0.00 4.02
734 4231 3.862845 TGAACGTGAATATGTGATGACCG 59.137 43.478 0.00 0.00 0.00 4.79
738 4235 4.202111 ACGTGAATATGTGATGACCGATGA 60.202 41.667 0.00 0.00 0.00 2.92
741 4238 6.400409 CGTGAATATGTGATGACCGATGATTC 60.400 42.308 0.00 0.00 0.00 2.52
743 4240 7.118825 GTGAATATGTGATGACCGATGATTCAT 59.881 37.037 0.00 0.00 34.39 2.57
744 4241 8.313292 TGAATATGTGATGACCGATGATTCATA 58.687 33.333 0.00 0.00 32.43 2.15
745 4242 8.484641 AATATGTGATGACCGATGATTCATAC 57.515 34.615 0.00 0.00 32.43 2.39
746 4243 5.535753 TGTGATGACCGATGATTCATACT 57.464 39.130 0.00 0.00 32.43 2.12
747 4244 6.648879 TGTGATGACCGATGATTCATACTA 57.351 37.500 0.00 0.00 32.43 1.82
748 4245 6.681777 TGTGATGACCGATGATTCATACTAG 58.318 40.000 0.00 0.00 32.43 2.57
749 4246 6.265422 TGTGATGACCGATGATTCATACTAGT 59.735 38.462 0.00 0.00 32.43 2.57
750 4247 7.447238 TGTGATGACCGATGATTCATACTAGTA 59.553 37.037 4.77 4.77 32.43 1.82
751 4248 8.462811 GTGATGACCGATGATTCATACTAGTAT 58.537 37.037 9.71 9.71 32.43 2.12
755 4252 7.665974 TGACCGATGATTCATACTAGTATGTCT 59.334 37.037 32.16 23.47 42.57 3.41
791 4288 2.030007 ACACATCTTTTGGCATTGACCG 60.030 45.455 0.00 0.00 0.00 4.79
927 4424 4.640771 ATATACGGCCACATTCCTCAAT 57.359 40.909 2.24 0.00 0.00 2.57
934 4431 4.498009 CGGCCACATTCCTCAATATCAAAC 60.498 45.833 2.24 0.00 0.00 2.93
935 4432 4.498009 GGCCACATTCCTCAATATCAAACG 60.498 45.833 0.00 0.00 0.00 3.60
958 4455 3.542875 CGCGTGCATAATCAGAGTTGAAG 60.543 47.826 0.00 0.00 36.78 3.02
1023 4530 0.687354 CTCACCTACCACACCAGCTT 59.313 55.000 0.00 0.00 0.00 3.74
1059 4566 0.732880 CCGTTCATGTCTTCGTCGCT 60.733 55.000 0.00 0.00 0.00 4.93
1075 4582 3.001358 GCTTCCCATGGCTCCCCTT 62.001 63.158 6.09 0.00 0.00 3.95
1077 4584 0.926293 CTTCCCATGGCTCCCCTTTA 59.074 55.000 6.09 0.00 0.00 1.85
1158 4665 7.072030 GCGTTGACATCAAATATCCATTCTAC 58.928 38.462 0.00 0.00 37.63 2.59
1161 4668 9.778741 GTTGACATCAAATATCCATTCTACCTA 57.221 33.333 0.00 0.00 37.63 3.08
1173 4680 6.177610 TCCATTCTACCTATCAAACACAACC 58.822 40.000 0.00 0.00 0.00 3.77
1197 4704 1.408266 GCAACCCCCGATTACACATCT 60.408 52.381 0.00 0.00 0.00 2.90
1206 4713 5.069251 CCCCGATTACACATCTTACTTCTCT 59.931 44.000 0.00 0.00 0.00 3.10
1318 4834 5.068234 TCGGAACATCTTCTACGACAATT 57.932 39.130 0.00 0.00 0.00 2.32
1319 4835 5.100259 TCGGAACATCTTCTACGACAATTC 58.900 41.667 0.00 0.00 0.00 2.17
1396 4915 1.206578 CACAACGTGTCATTCGGCC 59.793 57.895 0.00 0.00 0.00 6.13
1487 5006 1.134280 CGATCACCTGCCTCCTGATTT 60.134 52.381 0.00 0.00 0.00 2.17
1492 5011 0.253044 CCTGCCTCCTGATTTTCCGA 59.747 55.000 0.00 0.00 0.00 4.55
1493 5012 1.373570 CTGCCTCCTGATTTTCCGAC 58.626 55.000 0.00 0.00 0.00 4.79
1498 5017 3.265791 CCTCCTGATTTTCCGACAGAAG 58.734 50.000 0.00 0.00 35.40 2.85
1500 5020 4.383552 CCTCCTGATTTTCCGACAGAAGAT 60.384 45.833 0.00 0.00 35.40 2.40
1503 5023 6.003950 TCCTGATTTTCCGACAGAAGATTTT 58.996 36.000 0.00 0.00 35.40 1.82
1510 5030 5.405935 TCCGACAGAAGATTTTCAGATCA 57.594 39.130 0.00 0.00 35.70 2.92
1541 5061 0.040058 TTCAATCCACCTGCAGGCAT 59.960 50.000 33.06 18.81 39.32 4.40
1584 5104 3.584406 TGTTCACCTCTGAGGATGACAAT 59.416 43.478 29.71 2.61 37.67 2.71
1608 5128 1.404391 TCTCGAGAGTACGAATTGGCC 59.596 52.381 12.08 0.00 41.67 5.36
1633 5153 2.190313 GCAGCCGGATGGTCATCA 59.810 61.111 23.25 0.00 39.54 3.07
1636 5156 0.179037 CAGCCGGATGGTCATCATGT 60.179 55.000 13.14 0.00 39.54 3.21
1678 5198 1.376942 AGCAGTGGTCAGCTCATGC 60.377 57.895 0.00 0.00 36.00 4.06
1739 5262 4.604976 GAGTTGAAATGGCATATGAGCAC 58.395 43.478 6.97 0.00 35.83 4.40
1773 5296 1.593750 CCTGTGCGAGCTATCTGGC 60.594 63.158 0.00 0.00 43.31 4.85
1912 5435 9.892130 AAGGAATATTACAAGGAGTTTGAGTAG 57.108 33.333 0.00 0.00 39.21 2.57
2454 5980 5.337169 GCACTCACAAGAGAGGAATTAGACT 60.337 44.000 0.00 0.00 44.98 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 1823 8.981724 AGTTTTTCGCCCTAGAAATTAAAATC 57.018 30.769 0.00 0.00 39.52 2.17
140 1878 8.355169 GTGCATCACCATCATAGTATCAAATTT 58.645 33.333 0.00 0.00 0.00 1.82
222 1961 0.313672 TCAGCCACGGTTTTGCATTC 59.686 50.000 0.00 0.00 0.00 2.67
235 1974 1.414866 TACCAGCCACTGTTCAGCCA 61.415 55.000 0.00 0.00 0.00 4.75
376 2116 6.822442 ACCGGAAAAGTAAAATTTGAACCAT 58.178 32.000 9.46 0.00 0.00 3.55
377 2117 6.223351 ACCGGAAAAGTAAAATTTGAACCA 57.777 33.333 9.46 0.00 0.00 3.67
381 2121 8.657729 GTTCAAAACCGGAAAAGTAAAATTTGA 58.342 29.630 9.46 6.12 33.79 2.69
405 2145 5.722021 AGATGGTTCAAAATTTAGCGGTT 57.278 34.783 0.00 0.00 0.00 4.44
432 2172 3.674997 TCAGAACCGCTTAAAGCATCTT 58.325 40.909 0.00 0.00 42.58 2.40
448 2188 0.690192 TTGGGGCAGTTCGATCAGAA 59.310 50.000 0.00 0.00 36.31 3.02
449 2189 0.036388 GTTGGGGCAGTTCGATCAGA 60.036 55.000 0.00 0.00 0.00 3.27
450 2190 0.036010 AGTTGGGGCAGTTCGATCAG 60.036 55.000 0.00 0.00 0.00 2.90
451 2191 0.036388 GAGTTGGGGCAGTTCGATCA 60.036 55.000 0.00 0.00 0.00 2.92
452 2192 0.250513 AGAGTTGGGGCAGTTCGATC 59.749 55.000 0.00 0.00 0.00 3.69
453 2193 0.693049 AAGAGTTGGGGCAGTTCGAT 59.307 50.000 0.00 0.00 0.00 3.59
454 2194 0.034896 GAAGAGTTGGGGCAGTTCGA 59.965 55.000 0.00 0.00 0.00 3.71
455 2195 0.035458 AGAAGAGTTGGGGCAGTTCG 59.965 55.000 0.00 0.00 0.00 3.95
456 2196 1.202818 ACAGAAGAGTTGGGGCAGTTC 60.203 52.381 0.00 0.00 0.00 3.01
457 2197 0.846693 ACAGAAGAGTTGGGGCAGTT 59.153 50.000 0.00 0.00 0.00 3.16
458 2198 0.109342 CACAGAAGAGTTGGGGCAGT 59.891 55.000 0.00 0.00 0.00 4.40
459 2199 0.607489 CCACAGAAGAGTTGGGGCAG 60.607 60.000 0.00 0.00 31.22 4.85
460 2200 1.455849 CCACAGAAGAGTTGGGGCA 59.544 57.895 0.00 0.00 31.22 5.36
461 2201 4.404691 CCACAGAAGAGTTGGGGC 57.595 61.111 0.00 0.00 31.22 5.80
462 2202 0.322008 GAGCCACAGAAGAGTTGGGG 60.322 60.000 0.00 0.00 42.22 4.96
463 2203 0.689623 AGAGCCACAGAAGAGTTGGG 59.310 55.000 0.00 0.00 0.00 4.12
464 2204 1.071385 ACAGAGCCACAGAAGAGTTGG 59.929 52.381 0.00 0.00 0.00 3.77
465 2205 2.141517 CACAGAGCCACAGAAGAGTTG 58.858 52.381 0.00 0.00 0.00 3.16
466 2206 2.036992 CTCACAGAGCCACAGAAGAGTT 59.963 50.000 0.00 0.00 0.00 3.01
467 2207 1.617850 CTCACAGAGCCACAGAAGAGT 59.382 52.381 0.00 0.00 0.00 3.24
468 2208 1.617850 ACTCACAGAGCCACAGAAGAG 59.382 52.381 0.00 0.00 32.04 2.85
469 2209 1.709578 ACTCACAGAGCCACAGAAGA 58.290 50.000 0.00 0.00 32.04 2.87
470 2210 2.353208 GGTACTCACAGAGCCACAGAAG 60.353 54.545 0.00 0.00 32.04 2.85
471 2211 1.618837 GGTACTCACAGAGCCACAGAA 59.381 52.381 0.00 0.00 32.04 3.02
472 2212 1.257743 GGTACTCACAGAGCCACAGA 58.742 55.000 0.00 0.00 32.04 3.41
473 2213 0.109086 CGGTACTCACAGAGCCACAG 60.109 60.000 0.00 0.00 32.04 3.66
474 2214 0.826256 ACGGTACTCACAGAGCCACA 60.826 55.000 0.00 0.00 32.04 4.17
475 2215 0.388649 CACGGTACTCACAGAGCCAC 60.389 60.000 0.00 0.00 32.04 5.01
476 2216 1.532604 CCACGGTACTCACAGAGCCA 61.533 60.000 0.00 0.00 32.04 4.75
477 2217 1.215647 CCACGGTACTCACAGAGCC 59.784 63.158 0.00 0.00 32.04 4.70
478 2218 0.601558 TTCCACGGTACTCACAGAGC 59.398 55.000 0.00 0.00 32.04 4.09
479 2219 2.159226 GGATTCCACGGTACTCACAGAG 60.159 54.545 0.00 0.00 35.52 3.35
480 2220 1.822990 GGATTCCACGGTACTCACAGA 59.177 52.381 0.00 0.00 0.00 3.41
481 2221 1.825474 AGGATTCCACGGTACTCACAG 59.175 52.381 5.29 0.00 0.00 3.66
482 2222 1.822990 GAGGATTCCACGGTACTCACA 59.177 52.381 5.29 0.00 0.00 3.58
483 2223 1.822990 TGAGGATTCCACGGTACTCAC 59.177 52.381 5.29 0.00 30.75 3.51
484 2224 1.822990 GTGAGGATTCCACGGTACTCA 59.177 52.381 5.29 0.00 33.05 3.41
485 2225 2.100989 AGTGAGGATTCCACGGTACTC 58.899 52.381 5.29 0.00 39.38 2.59
486 2226 2.233305 AGTGAGGATTCCACGGTACT 57.767 50.000 5.29 0.00 39.38 2.73
487 2227 2.618053 CAAGTGAGGATTCCACGGTAC 58.382 52.381 5.29 0.00 39.38 3.34
488 2228 1.066430 GCAAGTGAGGATTCCACGGTA 60.066 52.381 5.29 0.00 39.38 4.02
489 2229 0.321653 GCAAGTGAGGATTCCACGGT 60.322 55.000 5.29 0.00 39.38 4.83
490 2230 1.026718 GGCAAGTGAGGATTCCACGG 61.027 60.000 5.29 0.00 39.38 4.94
491 2231 0.036010 AGGCAAGTGAGGATTCCACG 60.036 55.000 5.29 0.00 39.38 4.94
492 2232 1.815003 CAAGGCAAGTGAGGATTCCAC 59.185 52.381 5.29 0.00 34.89 4.02
493 2233 1.887956 GCAAGGCAAGTGAGGATTCCA 60.888 52.381 5.29 0.00 0.00 3.53
494 2234 0.813821 GCAAGGCAAGTGAGGATTCC 59.186 55.000 0.00 0.00 0.00 3.01
495 2235 0.813821 GGCAAGGCAAGTGAGGATTC 59.186 55.000 0.00 0.00 0.00 2.52
496 2236 0.613012 GGGCAAGGCAAGTGAGGATT 60.613 55.000 0.00 0.00 0.00 3.01
497 2237 1.000396 GGGCAAGGCAAGTGAGGAT 60.000 57.895 0.00 0.00 0.00 3.24
498 2238 2.436109 GGGCAAGGCAAGTGAGGA 59.564 61.111 0.00 0.00 0.00 3.71
499 2239 3.058160 CGGGCAAGGCAAGTGAGG 61.058 66.667 0.00 0.00 0.00 3.86
500 2240 2.281761 ACGGGCAAGGCAAGTGAG 60.282 61.111 0.00 0.00 0.00 3.51
501 2241 2.281484 GACGGGCAAGGCAAGTGA 60.281 61.111 0.00 0.00 0.00 3.41
502 2242 1.733402 TTTGACGGGCAAGGCAAGTG 61.733 55.000 0.00 0.00 40.66 3.16
503 2243 1.040339 TTTTGACGGGCAAGGCAAGT 61.040 50.000 0.00 0.00 40.66 3.16
504 2244 0.103937 TTTTTGACGGGCAAGGCAAG 59.896 50.000 0.00 0.00 40.66 4.01
505 2245 2.202866 TTTTTGACGGGCAAGGCAA 58.797 47.368 0.00 0.00 37.87 4.52
506 2246 3.941081 TTTTTGACGGGCAAGGCA 58.059 50.000 0.00 0.00 37.87 4.75
645 4142 4.304939 CAGCTCTCTGCATGATTCGATAA 58.695 43.478 0.00 0.00 45.94 1.75
714 4211 4.118093 TCGGTCATCACATATTCACGTT 57.882 40.909 0.00 0.00 0.00 3.99
716 4213 4.298332 TCATCGGTCATCACATATTCACG 58.702 43.478 0.00 0.00 0.00 4.35
733 4230 8.642885 GCAAAGACATACTAGTATGAATCATCG 58.357 37.037 37.75 23.18 44.22 3.84
734 4231 9.481340 TGCAAAGACATACTAGTATGAATCATC 57.519 33.333 37.75 26.83 44.22 2.92
738 4235 9.672673 AAAGTGCAAAGACATACTAGTATGAAT 57.327 29.630 37.75 25.81 44.22 2.57
741 4238 7.182761 GCAAAGTGCAAAGACATACTAGTATG 58.817 38.462 32.20 32.20 44.26 2.39
743 4240 6.721571 GCAAAGTGCAAAGACATACTAGTA 57.278 37.500 4.77 4.77 44.26 1.82
744 4241 5.613358 GCAAAGTGCAAAGACATACTAGT 57.387 39.130 0.00 0.00 44.26 2.57
775 4272 0.825425 TGCCGGTCAATGCCAAAAGA 60.825 50.000 1.90 0.00 0.00 2.52
927 4424 1.000145 TTATGCACGCGCGTTTGATA 59.000 45.000 35.90 24.36 42.97 2.15
934 4431 1.200103 CTCTGATTATGCACGCGCG 59.800 57.895 30.96 30.96 42.97 6.86
935 4432 0.652592 AACTCTGATTATGCACGCGC 59.347 50.000 5.73 0.00 39.24 6.86
958 4455 3.776616 AGACTAATCTGGCTGCTGC 57.223 52.632 7.10 7.10 32.29 5.25
1023 4530 1.076632 GGCGAGGAAGAGGAGGAGA 60.077 63.158 0.00 0.00 0.00 3.71
1059 4566 0.629058 GTAAAGGGGAGCCATGGGAA 59.371 55.000 15.13 0.00 0.00 3.97
1075 4582 1.684983 GTAGGTGCTAGATGGCGGTAA 59.315 52.381 0.00 0.00 34.52 2.85
1077 4584 0.686441 TGTAGGTGCTAGATGGCGGT 60.686 55.000 0.00 0.00 34.52 5.68
1158 4665 2.890311 TGCTTGGGTTGTGTTTGATAGG 59.110 45.455 0.00 0.00 0.00 2.57
1161 4668 2.158971 GGTTGCTTGGGTTGTGTTTGAT 60.159 45.455 0.00 0.00 0.00 2.57
1173 4680 0.322997 TGTAATCGGGGGTTGCTTGG 60.323 55.000 0.00 0.00 0.00 3.61
1197 4704 2.353406 GGTGTAGCCGCAAGAGAAGTAA 60.353 50.000 0.00 0.00 43.02 2.24
1263 4770 2.990066 ATTGATCGAGTGGAAGGACC 57.010 50.000 0.00 0.00 39.54 4.46
1264 4771 4.386867 TGTATTGATCGAGTGGAAGGAC 57.613 45.455 0.00 0.00 0.00 3.85
1318 4834 0.396556 TCCCCGAGAATGATGGTCGA 60.397 55.000 0.00 0.00 35.70 4.20
1319 4835 0.249489 GTCCCCGAGAATGATGGTCG 60.249 60.000 0.00 0.00 0.00 4.79
1320 4836 0.830648 TGTCCCCGAGAATGATGGTC 59.169 55.000 0.00 0.00 0.00 4.02
1396 4915 1.359848 GTGTATTCCAGCCACTCGTG 58.640 55.000 0.00 0.00 0.00 4.35
1487 5006 5.793817 TGATCTGAAAATCTTCTGTCGGAA 58.206 37.500 0.00 0.00 33.46 4.30
1492 5011 5.766670 TGCAGTTGATCTGAAAATCTTCTGT 59.233 36.000 0.00 0.00 46.27 3.41
1493 5012 6.250344 TGCAGTTGATCTGAAAATCTTCTG 57.750 37.500 0.00 0.00 46.27 3.02
1498 5017 5.166398 CCCTTTGCAGTTGATCTGAAAATC 58.834 41.667 0.00 0.00 46.80 2.17
1500 5020 3.960102 ACCCTTTGCAGTTGATCTGAAAA 59.040 39.130 0.00 0.00 46.15 2.29
1503 5023 2.957402 ACCCTTTGCAGTTGATCTGA 57.043 45.000 0.00 0.00 46.27 3.27
1510 5030 2.365293 GTGGATTGAACCCTTTGCAGTT 59.635 45.455 0.00 0.00 0.00 3.16
1541 5061 2.105821 ACGAAGGAAACACCATCTCCAA 59.894 45.455 0.00 0.00 42.04 3.53
1584 5104 4.482386 CCAATTCGTACTCTCGAGAAACA 58.518 43.478 17.36 1.23 40.86 2.83
1608 5128 4.827087 ATCCGGCTGCAGTGCTCG 62.827 66.667 17.60 16.30 0.00 5.03
1636 5156 9.042008 GCTCAATAGAACATCTTTATTTACCGA 57.958 33.333 0.00 0.00 0.00 4.69
1675 5195 0.530650 CCGTAATCACTCGGCAGCAT 60.531 55.000 0.00 0.00 40.28 3.79
1773 5296 2.341101 ACTGTAGGAGCACCGTCCG 61.341 63.158 0.00 0.00 42.05 4.79
1912 5435 4.625607 TCTCAAACTCCTTTCCTTCTCC 57.374 45.455 0.00 0.00 0.00 3.71
2454 5980 6.310941 TGGGAATAGGACTTCATTTCAAACA 58.689 36.000 0.00 0.00 0.00 2.83
2773 6299 9.753674 AGGTCAAGAAAACTCAATATGGAATTA 57.246 29.630 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.