Multiple sequence alignment - TraesCS5A01G362000

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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 TraesCS5A01G362000 chr5A 100.000 4752 0 0 1 4752 563257522 563252771 0.000000e+00 8776.0
1 TraesCS5A01G362000 chr5A 83.901 646 104 0 2473 3118 552268803 552269448 6.760000e-173 617.0
2 TraesCS5A01G362000 chr5A 79.490 863 149 15 1101 1961 552267413 552268249 5.300000e-164 588.0
3 TraesCS5A01G362000 chr5A 82.955 528 79 8 1100 1626 552298393 552298910 2.590000e-127 466.0
4 TraesCS5A01G362000 chr5D 96.315 4260 124 19 1 4240 445406852 445402606 0.000000e+00 6966.0
5 TraesCS5A01G362000 chr5D 84.877 648 89 3 2475 3116 445490906 445490262 0.000000e+00 645.0
6 TraesCS5A01G362000 chr5D 84.544 647 98 2 2473 3118 436982353 436982998 1.440000e-179 640.0
7 TraesCS5A01G362000 chr5D 80.185 863 149 12 1101 1961 436980984 436981826 1.120000e-175 627.0
8 TraesCS5A01G362000 chr5D 80.631 697 105 18 948 1636 445486178 445485504 3.280000e-141 512.0
9 TraesCS5A01G362000 chr5D 82.888 561 83 7 1076 1632 553910473 553911024 4.270000e-135 492.0
10 TraesCS5A01G362000 chr5D 83.333 540 79 8 1100 1638 437015194 437015723 5.530000e-134 488.0
11 TraesCS5A01G362000 chr5D 93.810 210 13 0 4396 4605 445400575 445400366 2.760000e-82 316.0
12 TraesCS5A01G362000 chr5D 85.000 320 37 7 3272 3584 445489986 445489671 9.930000e-82 315.0
13 TraesCS5A01G362000 chr5D 96.532 173 2 1 4230 4398 445400798 445400626 2.800000e-72 283.0
14 TraesCS5A01G362000 chr5D 87.448 239 27 2 3352 3587 553912714 553912952 6.060000e-69 272.0
15 TraesCS5A01G362000 chr5B 96.135 3312 86 10 948 4240 543246501 543243213 0.000000e+00 5369.0
16 TraesCS5A01G362000 chr5B 89.848 591 30 13 233 808 543247138 543246563 0.000000e+00 732.0
17 TraesCS5A01G362000 chr5B 85.077 650 88 3 2473 3116 543298640 543297994 0.000000e+00 654.0
18 TraesCS5A01G362000 chr5B 84.389 647 99 2 2473 3118 531193753 531194398 6.710000e-178 634.0
19 TraesCS5A01G362000 chr5B 84.154 650 80 15 1085 1727 543282521 543281888 4.070000e-170 608.0
20 TraesCS5A01G362000 chr5B 82.017 595 90 13 1110 1700 543275902 543275321 1.540000e-134 490.0
21 TraesCS5A01G362000 chr5B 83.144 528 78 8 1100 1626 531204685 531205202 5.570000e-129 472.0
22 TraesCS5A01G362000 chr5B 93.811 307 16 1 4302 4605 543241331 543241025 4.330000e-125 459.0
23 TraesCS5A01G362000 chr5B 85.811 296 36 4 3295 3584 543297743 543297448 4.620000e-80 309.0
24 TraesCS5A01G362000 chr5B 86.056 251 23 4 1 240 543248394 543248145 4.720000e-65 259.0
25 TraesCS5A01G362000 chr5B 85.714 245 32 2 3346 3587 543270125 543269881 6.100000e-64 255.0
26 TraesCS5A01G362000 chr5B 78.697 399 70 5 3195 3587 531194625 531195014 7.890000e-63 252.0
27 TraesCS5A01G362000 chr5B 88.000 100 12 0 2286 2385 531205826 531205925 8.350000e-23 119.0
28 TraesCS5A01G362000 chr5B 87.629 97 12 0 2278 2374 543281415 543281319 3.890000e-21 113.0
29 TraesCS5A01G362000 chr5B 79.021 143 25 5 2054 2194 543281663 543281524 5.060000e-15 93.5
30 TraesCS5A01G362000 chr1D 82.045 802 132 11 2458 3250 410458693 410457895 0.000000e+00 673.0
31 TraesCS5A01G362000 chr4D 80.969 867 111 32 3161 4015 2975631 2976455 5.190000e-179 638.0
32 TraesCS5A01G362000 chr4D 79.171 893 151 23 1101 1980 1687318 1688188 1.910000e-163 586.0
33 TraesCS5A01G362000 chr4D 80.000 420 78 2 3172 3585 1689482 1689901 5.970000e-79 305.0
34 TraesCS5A01G362000 chr4D 85.542 249 32 3 3343 3587 1638580 1638828 1.700000e-64 257.0
35 TraesCS5A01G362000 chr4D 77.586 232 39 9 4210 4435 1639130 1639354 1.390000e-25 128.0
36 TraesCS5A01G362000 chr4D 92.647 68 4 1 4379 4446 2976738 2976804 3.910000e-16 97.1
37 TraesCS5A01G362000 chr1B 82.133 750 115 12 1102 1846 553015703 553014968 4.040000e-175 625.0
38 TraesCS5A01G362000 chr1B 82.862 636 107 2 2458 3092 553014263 553013629 1.920000e-158 569.0
39 TraesCS5A01G362000 chr7A 83.750 640 88 8 1085 1724 7817244 7817867 4.100000e-165 592.0
40 TraesCS5A01G362000 chr7A 89.041 73 8 0 2289 2361 7818561 7818633 1.820000e-14 91.6
41 TraesCS5A01G362000 chr3A 82.178 202 33 2 3819 4020 13553294 13553492 2.270000e-38 171.0


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 TraesCS5A01G362000 chr5A 563252771 563257522 4751 True 8776.000000 8776 100.000000 1 4752 1 chr5A.!!$R1 4751
1 TraesCS5A01G362000 chr5A 552267413 552269448 2035 False 602.500000 617 81.695500 1101 3118 2 chr5A.!!$F2 2017
2 TraesCS5A01G362000 chr5A 552298393 552298910 517 False 466.000000 466 82.955000 1100 1626 1 chr5A.!!$F1 526
3 TraesCS5A01G362000 chr5D 445400366 445406852 6486 True 2521.666667 6966 95.552333 1 4605 3 chr5D.!!$R1 4604
4 TraesCS5A01G362000 chr5D 436980984 436982998 2014 False 633.500000 640 82.364500 1101 3118 2 chr5D.!!$F2 2017
5 TraesCS5A01G362000 chr5D 445485504 445490906 5402 True 490.666667 645 83.502667 948 3584 3 chr5D.!!$R2 2636
6 TraesCS5A01G362000 chr5D 437015194 437015723 529 False 488.000000 488 83.333000 1100 1638 1 chr5D.!!$F1 538
7 TraesCS5A01G362000 chr5D 553910473 553912952 2479 False 382.000000 492 85.168000 1076 3587 2 chr5D.!!$F3 2511
8 TraesCS5A01G362000 chr5B 543241025 543248394 7369 True 1704.750000 5369 91.462500 1 4605 4 chr5B.!!$R3 4604
9 TraesCS5A01G362000 chr5B 543275321 543275902 581 True 490.000000 490 82.017000 1110 1700 1 chr5B.!!$R2 590
10 TraesCS5A01G362000 chr5B 543297448 543298640 1192 True 481.500000 654 85.444000 2473 3584 2 chr5B.!!$R5 1111
11 TraesCS5A01G362000 chr5B 531193753 531195014 1261 False 443.000000 634 81.543000 2473 3587 2 chr5B.!!$F1 1114
12 TraesCS5A01G362000 chr5B 531204685 531205925 1240 False 295.500000 472 85.572000 1100 2385 2 chr5B.!!$F2 1285
13 TraesCS5A01G362000 chr5B 543281319 543282521 1202 True 271.500000 608 83.601333 1085 2374 3 chr5B.!!$R4 1289
14 TraesCS5A01G362000 chr1D 410457895 410458693 798 True 673.000000 673 82.045000 2458 3250 1 chr1D.!!$R1 792
15 TraesCS5A01G362000 chr4D 1687318 1689901 2583 False 445.500000 586 79.585500 1101 3585 2 chr4D.!!$F2 2484
16 TraesCS5A01G362000 chr4D 2975631 2976804 1173 False 367.550000 638 86.808000 3161 4446 2 chr4D.!!$F3 1285
17 TraesCS5A01G362000 chr1B 553013629 553015703 2074 True 597.000000 625 82.497500 1102 3092 2 chr1B.!!$R1 1990
18 TraesCS5A01G362000 chr7A 7817244 7818633 1389 False 341.800000 592 86.395500 1085 2361 2 chr7A.!!$F1 1276

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
32 35 0.736053 TCACCGCACAACAAACCTTC 59.264 50.000 0.00 0.0 0.00 3.46 F
673 1712 0.756903 GCGGCAGTTTAGGGGATCTA 59.243 55.000 0.00 0.0 0.00 1.98 F
1309 2395 0.250989 CCACCCTCTTTAACCGCCAA 60.251 55.000 0.00 0.0 0.00 4.52 F
1838 3077 0.322456 CCTTGAGGCCAACCATCGAA 60.322 55.000 5.01 0.0 39.06 3.71 F
2322 3882 3.566351 TCCACAAGAGTCACAGAGAAGA 58.434 45.455 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1030 2106 1.007011 CGATTCATCTCGCACGTTGAC 60.007 52.381 0.00 0.00 0.00 3.18 R
2066 3410 0.176910 TCAGGATACGGCGATGCAAA 59.823 50.000 16.62 0.00 46.39 3.68 R
2640 4580 4.683766 TTTATTTGATCTTCCCACCCCA 57.316 40.909 0.00 0.00 0.00 4.96 R
3362 5619 0.670546 CACACGCCTTCGATCACCTT 60.671 55.000 0.00 0.00 39.41 3.50 R
4321 10277 1.246649 ACAGCACCGCAATTCATGAA 58.753 45.000 11.26 11.26 0.00 2.57 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
32 35 0.736053 TCACCGCACAACAAACCTTC 59.264 50.000 0.00 0.00 0.00 3.46
34 37 1.021968 ACCGCACAACAAACCTTCTC 58.978 50.000 0.00 0.00 0.00 2.87
93 98 4.574674 TGAATAGGATTGTTGCAGGTCT 57.425 40.909 0.00 0.00 0.00 3.85
97 102 6.945435 TGAATAGGATTGTTGCAGGTCTTTTA 59.055 34.615 0.00 0.00 0.00 1.52
130 144 1.302033 CAACAGACAAGGAGGCGCT 60.302 57.895 7.64 0.00 0.00 5.92
165 179 2.287009 CGGCTGAAAGAGAAGCGTTTTT 60.287 45.455 0.00 0.00 40.46 1.94
654 1689 1.821332 GCGGCAATGAAGAGAGGGG 60.821 63.158 0.00 0.00 0.00 4.79
673 1712 0.756903 GCGGCAGTTTAGGGGATCTA 59.243 55.000 0.00 0.00 0.00 1.98
709 1750 1.136305 TCGATTCGAGTTCATCCACCC 59.864 52.381 4.29 0.00 0.00 4.61
753 1799 9.071276 CAATATCATAGTATTGCTCCACCTTTT 57.929 33.333 0.00 0.00 35.84 2.27
820 1893 7.798596 ACTGGTTTGATCTGCTTGATTATAG 57.201 36.000 0.00 0.00 35.14 1.31
931 2004 4.853007 AGAGCAAAAGATATGGTTGAGCT 58.147 39.130 0.00 0.00 0.00 4.09
972 2045 7.715249 TGATTACCATATGAAAAGTCAGTAGGC 59.285 37.037 3.65 0.00 37.14 3.93
973 2046 5.435686 ACCATATGAAAAGTCAGTAGGCA 57.564 39.130 3.65 0.00 37.14 4.75
974 2047 5.815581 ACCATATGAAAAGTCAGTAGGCAA 58.184 37.500 3.65 0.00 37.14 4.52
983 2059 3.177228 AGTCAGTAGGCAACAAGGAGAT 58.823 45.455 0.00 0.00 41.41 2.75
1042 2118 2.029073 ACTGGGTCAACGTGCGAG 59.971 61.111 0.00 0.00 0.00 5.03
1309 2395 0.250989 CCACCCTCTTTAACCGCCAA 60.251 55.000 0.00 0.00 0.00 4.52
1809 3042 8.256605 TCTTTCTCAATCACAAGGAGAAGATAG 58.743 37.037 0.00 0.00 45.37 2.08
1838 3077 0.322456 CCTTGAGGCCAACCATCGAA 60.322 55.000 5.01 0.00 39.06 3.71
1989 3333 4.018324 GGAGAAAAGGAGAACCCACCTAAT 60.018 45.833 0.00 0.00 35.25 1.73
2065 3409 5.905331 TGAGACCTACAGGATATTTGTGGAT 59.095 40.000 1.29 0.00 38.94 3.41
2066 3410 6.386927 TGAGACCTACAGGATATTTGTGGATT 59.613 38.462 1.29 0.00 38.94 3.01
2322 3882 3.566351 TCCACAAGAGTCACAGAGAAGA 58.434 45.455 0.00 0.00 0.00 2.87
2455 4015 7.293073 AGGTATTTCTCAATGCCATACTCAAT 58.707 34.615 5.07 0.00 45.39 2.57
2618 4558 7.859875 GCAAGTTATCCTTTGCAATTCTAGATC 59.140 37.037 0.00 0.00 31.55 2.75
2640 4580 8.986991 AGATCTGGTTCTTAAGTATGTGAAGAT 58.013 33.333 1.63 3.95 0.00 2.40
3362 5619 1.550072 TGCGTGATGAGAAGATGTGGA 59.450 47.619 0.00 0.00 0.00 4.02
3938 6222 4.187694 CCAGCTGAATAACCTGAGAAGTC 58.812 47.826 17.39 0.00 0.00 3.01
3958 6244 6.241207 AGTCATTATCTCCGTGTTGTTTTG 57.759 37.500 0.00 0.00 0.00 2.44
4081 6367 5.660417 ACCTATCTCCATCTGCTATACATGG 59.340 44.000 0.00 0.00 38.83 3.66
4164 6482 6.615088 AGCTGCAAAATTACAATGTCTGTAG 58.385 36.000 1.02 0.00 41.57 2.74
4482 11104 1.067142 TGTCCGTATTGCCAGTCTGTC 60.067 52.381 0.00 0.00 0.00 3.51
4492 11114 0.109689 CCAGTCTGTCGTTCGACTCC 60.110 60.000 22.49 12.13 38.37 3.85
4540 11162 6.475076 CAGAGCTTAATACACTAGAGCTGTTG 59.525 42.308 4.71 0.00 43.22 3.33
4545 11262 7.010275 GCTTAATACACTAGAGCTGTTGGTAAC 59.990 40.741 0.00 0.00 0.00 2.50
4606 11326 4.110482 GTCGCCCTATGCCGTAATATTAG 58.890 47.826 0.00 0.00 36.24 1.73
4608 11328 4.221262 TCGCCCTATGCCGTAATATTAGTT 59.779 41.667 0.00 0.00 36.24 2.24
4609 11329 4.328983 CGCCCTATGCCGTAATATTAGTTG 59.671 45.833 0.00 0.00 36.24 3.16
4610 11330 4.094442 GCCCTATGCCGTAATATTAGTTGC 59.906 45.833 0.00 0.14 0.00 4.17
4612 11332 5.351465 CCCTATGCCGTAATATTAGTTGCTG 59.649 44.000 0.00 0.00 0.00 4.41
4613 11333 5.932303 CCTATGCCGTAATATTAGTTGCTGT 59.068 40.000 0.00 0.00 0.00 4.40
4614 11334 7.094631 CCTATGCCGTAATATTAGTTGCTGTA 58.905 38.462 0.00 0.00 0.00 2.74
4615 11335 7.275779 CCTATGCCGTAATATTAGTTGCTGTAG 59.724 40.741 0.00 6.27 0.00 2.74
4616 11336 6.151663 TGCCGTAATATTAGTTGCTGTAGA 57.848 37.500 0.00 0.00 0.00 2.59
4617 11337 6.213677 TGCCGTAATATTAGTTGCTGTAGAG 58.786 40.000 0.00 0.00 0.00 2.43
4618 11338 5.118817 GCCGTAATATTAGTTGCTGTAGAGC 59.881 44.000 4.60 4.60 46.44 4.09
4619 11339 6.448006 CCGTAATATTAGTTGCTGTAGAGCT 58.552 40.000 13.66 0.00 46.39 4.09
4620 11340 6.924060 CCGTAATATTAGTTGCTGTAGAGCTT 59.076 38.462 13.66 1.72 46.39 3.74
4623 11343 9.194271 GTAATATTAGTTGCTGTAGAGCTTACC 57.806 37.037 13.66 0.00 46.39 2.85
4625 11345 3.601443 AGTTGCTGTAGAGCTTACCAG 57.399 47.619 13.66 0.00 46.39 4.00
4626 11346 2.900546 AGTTGCTGTAGAGCTTACCAGT 59.099 45.455 13.66 0.00 46.39 4.00
4627 11347 2.996621 GTTGCTGTAGAGCTTACCAGTG 59.003 50.000 13.66 0.00 46.39 3.66
4628 11348 1.550524 TGCTGTAGAGCTTACCAGTGG 59.449 52.381 13.66 7.91 46.39 4.00
4629 11349 1.825474 GCTGTAGAGCTTACCAGTGGA 59.175 52.381 18.40 0.00 42.52 4.02
4630 11350 2.233922 GCTGTAGAGCTTACCAGTGGAA 59.766 50.000 18.40 5.02 42.52 3.53
4631 11351 3.677424 GCTGTAGAGCTTACCAGTGGAAG 60.677 52.174 18.40 15.50 42.52 3.46
4633 11353 3.901844 TGTAGAGCTTACCAGTGGAAGTT 59.098 43.478 18.40 12.74 0.00 2.66
4666 12866 6.572167 TTGTTCATTGTGATATGCTGTTCA 57.428 33.333 0.00 0.00 0.00 3.18
4667 12867 6.185852 TGTTCATTGTGATATGCTGTTCAG 57.814 37.500 0.00 0.00 0.00 3.02
4669 12869 6.600427 TGTTCATTGTGATATGCTGTTCAGAT 59.400 34.615 3.84 0.00 0.00 2.90
4670 12870 6.613755 TCATTGTGATATGCTGTTCAGATG 57.386 37.500 3.84 0.00 0.00 2.90
4671 12871 6.350906 TCATTGTGATATGCTGTTCAGATGA 58.649 36.000 3.84 0.00 0.00 2.92
4672 12872 6.996282 TCATTGTGATATGCTGTTCAGATGAT 59.004 34.615 3.84 0.00 0.00 2.45
4673 12873 8.152246 TCATTGTGATATGCTGTTCAGATGATA 58.848 33.333 3.84 0.00 0.00 2.15
4674 12874 7.958053 TTGTGATATGCTGTTCAGATGATAG 57.042 36.000 3.84 0.00 0.00 2.08
4676 12876 7.503549 TGTGATATGCTGTTCAGATGATAGTT 58.496 34.615 3.84 0.00 0.00 2.24
4677 12877 7.989170 TGTGATATGCTGTTCAGATGATAGTTT 59.011 33.333 3.84 0.00 0.00 2.66
4678 12878 8.834465 GTGATATGCTGTTCAGATGATAGTTTT 58.166 33.333 3.84 0.00 0.00 2.43
4701 12901 8.426569 TTTTTCTTCCTTGGATCTTCATGATT 57.573 30.769 0.00 0.00 35.14 2.57
4702 12902 7.400599 TTTCTTCCTTGGATCTTCATGATTG 57.599 36.000 0.00 0.00 35.14 2.67
4703 12903 6.070951 TCTTCCTTGGATCTTCATGATTGT 57.929 37.500 0.00 0.00 35.14 2.71
4707 12907 5.884232 TCCTTGGATCTTCATGATTGTCTTG 59.116 40.000 0.00 0.00 35.14 3.02
4709 12909 6.152323 CCTTGGATCTTCATGATTGTCTTGTT 59.848 38.462 0.00 0.00 35.14 2.83
4710 12910 6.505044 TGGATCTTCATGATTGTCTTGTTG 57.495 37.500 0.00 0.00 35.14 3.33
4712 12912 6.888088 TGGATCTTCATGATTGTCTTGTTGAT 59.112 34.615 0.00 0.00 35.14 2.57
4713 12913 7.148137 TGGATCTTCATGATTGTCTTGTTGATG 60.148 37.037 0.00 0.00 35.14 3.07
4714 12914 7.148120 GGATCTTCATGATTGTCTTGTTGATGT 60.148 37.037 0.00 0.00 35.14 3.06
4715 12915 6.905578 TCTTCATGATTGTCTTGTTGATGTG 58.094 36.000 0.00 0.00 0.00 3.21
4716 12916 6.487668 TCTTCATGATTGTCTTGTTGATGTGT 59.512 34.615 0.00 0.00 0.00 3.72
4718 12918 5.764192 TCATGATTGTCTTGTTGATGTGTCA 59.236 36.000 0.00 0.00 0.00 3.58
4719 12919 6.431852 TCATGATTGTCTTGTTGATGTGTCAT 59.568 34.615 0.00 0.00 33.56 3.06
4720 12920 6.638096 TGATTGTCTTGTTGATGTGTCATT 57.362 33.333 0.00 0.00 33.56 2.57
4722 12922 7.584108 TGATTGTCTTGTTGATGTGTCATTAC 58.416 34.615 0.00 0.00 33.56 1.89
4724 12924 6.544038 TGTCTTGTTGATGTGTCATTACTG 57.456 37.500 0.00 0.00 33.56 2.74
4725 12925 5.049474 TGTCTTGTTGATGTGTCATTACTGC 60.049 40.000 0.00 0.00 33.56 4.40
4726 12926 4.455533 TCTTGTTGATGTGTCATTACTGCC 59.544 41.667 0.00 0.00 33.56 4.85
4727 12927 3.081061 TGTTGATGTGTCATTACTGCCC 58.919 45.455 0.00 0.00 33.56 5.36
4728 12928 3.081061 GTTGATGTGTCATTACTGCCCA 58.919 45.455 0.00 0.00 33.56 5.36
4729 12929 3.431673 TGATGTGTCATTACTGCCCAA 57.568 42.857 0.00 0.00 0.00 4.12
4730 12930 3.760738 TGATGTGTCATTACTGCCCAAA 58.239 40.909 0.00 0.00 0.00 3.28
4732 12932 1.885887 TGTGTCATTACTGCCCAAAGC 59.114 47.619 0.00 0.00 44.14 3.51
4733 12933 1.202348 GTGTCATTACTGCCCAAAGCC 59.798 52.381 0.00 0.00 42.71 4.35
4734 12934 0.817654 GTCATTACTGCCCAAAGCCC 59.182 55.000 0.00 0.00 42.71 5.19
4735 12935 0.324275 TCATTACTGCCCAAAGCCCC 60.324 55.000 0.00 0.00 42.71 5.80
4736 12936 0.614415 CATTACTGCCCAAAGCCCCA 60.614 55.000 0.00 0.00 42.71 4.96
4737 12937 0.116143 ATTACTGCCCAAAGCCCCAA 59.884 50.000 0.00 0.00 42.71 4.12
4738 12938 0.105453 TTACTGCCCAAAGCCCCAAA 60.105 50.000 0.00 0.00 42.71 3.28
4739 12939 0.541764 TACTGCCCAAAGCCCCAAAG 60.542 55.000 0.00 0.00 42.71 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 17 1.021968 GAGAAGGTTTGTTGTGCGGT 58.978 50.000 0.00 0.00 0.00 5.68
32 35 4.156664 CTCAAACCATGTTGAGCAAGAG 57.843 45.455 11.78 0.00 45.84 2.85
93 98 9.965824 GTCTGTTGGATCTTCTTTTGATTAAAA 57.034 29.630 0.00 0.00 34.75 1.52
97 102 7.255730 CCTTGTCTGTTGGATCTTCTTTTGATT 60.256 37.037 0.00 0.00 0.00 2.57
130 144 3.289797 AGCCGACTGATCTTCTGGA 57.710 52.632 0.00 0.00 0.00 3.86
185 199 7.812669 CGAAAAATAAACCCTAGAGTGCAATTT 59.187 33.333 0.00 0.00 0.00 1.82
359 1390 5.008118 GCAGTGATTTAGGGCATCTTTCTAC 59.992 44.000 0.00 0.00 0.00 2.59
442 1473 2.515523 CCTCCCATCCGCTTGCTG 60.516 66.667 0.00 0.00 0.00 4.41
487 1519 1.151679 TCCGCCGATCTGGAGAGAT 59.848 57.895 7.64 0.00 42.02 2.75
654 1689 0.756903 TAGATCCCCTAAACTGCCGC 59.243 55.000 0.00 0.00 0.00 6.53
753 1799 8.034215 AGATGCATATTTCCAATTCGTTTTCAA 58.966 29.630 0.00 0.00 0.00 2.69
820 1893 3.747010 CAGACCTAGATGATCTGCATTGC 59.253 47.826 4.96 0.46 37.34 3.56
931 2004 4.966168 TGGTAATCACACTTAGGATGGCTA 59.034 41.667 0.00 0.00 0.00 3.93
972 2045 4.334759 CACTCCAGCATTATCTCCTTGTTG 59.665 45.833 0.00 0.00 0.00 3.33
973 2046 4.521146 CACTCCAGCATTATCTCCTTGTT 58.479 43.478 0.00 0.00 0.00 2.83
974 2047 3.118112 CCACTCCAGCATTATCTCCTTGT 60.118 47.826 0.00 0.00 0.00 3.16
983 2059 2.571653 AGCAGTAACCACTCCAGCATTA 59.428 45.455 0.00 0.00 30.46 1.90
1030 2106 1.007011 CGATTCATCTCGCACGTTGAC 60.007 52.381 0.00 0.00 0.00 3.18
1042 2118 2.611225 AAGTGAGAGGCCGATTCATC 57.389 50.000 9.57 0.00 0.00 2.92
1309 2395 3.708631 CACTACCATGATCCTGACTCCTT 59.291 47.826 0.00 0.00 0.00 3.36
1809 3042 1.600916 GCCTCAAGGTCCACCACAC 60.601 63.158 0.00 0.00 38.89 3.82
1838 3077 1.212935 AGCCACTCCTTGTGTTTGAGT 59.787 47.619 0.00 0.00 44.81 3.41
1980 3324 2.422093 GGCTCTCTTTGGATTAGGTGGG 60.422 54.545 0.00 0.00 0.00 4.61
1989 3333 3.584406 TCTCAATCTTGGCTCTCTTTGGA 59.416 43.478 0.00 0.00 0.00 3.53
2065 3409 1.013596 CAGGATACGGCGATGCAAAA 58.986 50.000 16.62 0.00 46.39 2.44
2066 3410 0.176910 TCAGGATACGGCGATGCAAA 59.823 50.000 16.62 0.00 46.39 3.68
2618 4558 6.540189 CCCATCTTCACATACTTAAGAACCAG 59.460 42.308 10.09 0.00 33.26 4.00
2640 4580 4.683766 TTTATTTGATCTTCCCACCCCA 57.316 40.909 0.00 0.00 0.00 4.96
3362 5619 0.670546 CACACGCCTTCGATCACCTT 60.671 55.000 0.00 0.00 39.41 3.50
3587 5853 3.575256 TCATTTCTCAAACAATGGCTGCT 59.425 39.130 0.00 0.00 32.17 4.24
3588 5854 3.916761 TCATTTCTCAAACAATGGCTGC 58.083 40.909 0.00 0.00 32.17 5.25
3768 6044 3.515602 ATATCTCCAAACCTGGCATCC 57.484 47.619 0.00 0.00 43.17 3.51
3938 6222 6.893759 TGTACAAAACAACACGGAGATAATG 58.106 36.000 0.00 0.00 34.29 1.90
3958 6244 5.428253 ACACACAGGATTATCACCATGTAC 58.572 41.667 0.00 0.00 31.18 2.90
4105 6391 5.603813 ACAAACAGACTGGTAGGTAAGGTAA 59.396 40.000 7.51 0.00 0.00 2.85
4106 6392 5.011329 CACAAACAGACTGGTAGGTAAGGTA 59.989 44.000 7.51 0.00 0.00 3.08
4107 6393 3.971971 ACAAACAGACTGGTAGGTAAGGT 59.028 43.478 7.51 0.00 0.00 3.50
4108 6394 4.202326 ACACAAACAGACTGGTAGGTAAGG 60.202 45.833 7.51 0.00 0.00 2.69
4109 6395 4.750098 CACACAAACAGACTGGTAGGTAAG 59.250 45.833 7.51 0.00 0.00 2.34
4164 6482 6.659668 TCTGGCATCCATACTATACTACAGAC 59.340 42.308 0.00 0.00 30.82 3.51
4321 10277 1.246649 ACAGCACCGCAATTCATGAA 58.753 45.000 11.26 11.26 0.00 2.57
4492 11114 3.492421 AAATACCACAGCTGCAAATCG 57.508 42.857 15.27 0.00 0.00 3.34
4540 11162 6.770746 TGTAGAGATGAACTGGTAGTTACC 57.229 41.667 1.25 1.25 46.62 2.85
4545 11262 5.605534 CCCATTGTAGAGATGAACTGGTAG 58.394 45.833 0.00 0.00 0.00 3.18
4550 11267 4.458397 CATGCCCATTGTAGAGATGAACT 58.542 43.478 0.00 0.00 0.00 3.01
4610 11330 3.511934 ACTTCCACTGGTAAGCTCTACAG 59.488 47.826 9.23 9.23 37.01 2.74
4612 11332 4.221041 AGAACTTCCACTGGTAAGCTCTAC 59.779 45.833 9.61 0.00 28.83 2.59
4613 11333 4.220821 CAGAACTTCCACTGGTAAGCTCTA 59.779 45.833 10.43 0.00 29.38 2.43
4614 11334 3.007398 CAGAACTTCCACTGGTAAGCTCT 59.993 47.826 0.00 2.04 30.24 4.09
4615 11335 3.244249 ACAGAACTTCCACTGGTAAGCTC 60.244 47.826 0.00 0.00 38.30 4.09
4616 11336 2.706190 ACAGAACTTCCACTGGTAAGCT 59.294 45.455 0.00 0.00 38.30 3.74
4617 11337 3.067833 GACAGAACTTCCACTGGTAAGC 58.932 50.000 0.00 0.00 38.30 3.09
4618 11338 4.608948 AGACAGAACTTCCACTGGTAAG 57.391 45.455 0.00 0.93 38.30 2.34
4619 11339 5.367945 AAAGACAGAACTTCCACTGGTAA 57.632 39.130 0.00 0.00 38.30 2.85
4620 11340 5.367945 AAAAGACAGAACTTCCACTGGTA 57.632 39.130 0.00 0.00 38.30 3.25
4646 12846 6.824704 TCATCTGAACAGCATATCACAATGAA 59.175 34.615 0.00 0.00 0.00 2.57
4647 12847 6.350906 TCATCTGAACAGCATATCACAATGA 58.649 36.000 0.00 0.00 0.00 2.57
4648 12848 6.613755 TCATCTGAACAGCATATCACAATG 57.386 37.500 0.00 0.00 0.00 2.82
4650 12850 7.503549 ACTATCATCTGAACAGCATATCACAA 58.496 34.615 0.00 0.00 0.00 3.33
4651 12851 7.059202 ACTATCATCTGAACAGCATATCACA 57.941 36.000 0.00 0.00 0.00 3.58
4652 12852 7.959689 AACTATCATCTGAACAGCATATCAC 57.040 36.000 0.00 0.00 0.00 3.06
4653 12853 8.969260 AAAACTATCATCTGAACAGCATATCA 57.031 30.769 0.00 0.00 0.00 2.15
4676 12876 8.308931 CAATCATGAAGATCCAAGGAAGAAAAA 58.691 33.333 0.00 0.00 35.39 1.94
4677 12877 7.452501 ACAATCATGAAGATCCAAGGAAGAAAA 59.547 33.333 0.00 0.00 35.39 2.29
4678 12878 6.950041 ACAATCATGAAGATCCAAGGAAGAAA 59.050 34.615 0.00 0.00 35.39 2.52
4681 12881 6.120905 AGACAATCATGAAGATCCAAGGAAG 58.879 40.000 0.00 0.00 35.39 3.46
4683 12883 5.705397 AGACAATCATGAAGATCCAAGGA 57.295 39.130 0.00 0.00 35.39 3.36
4684 12884 5.651139 ACAAGACAATCATGAAGATCCAAGG 59.349 40.000 0.00 0.00 35.39 3.61
4685 12885 6.754702 ACAAGACAATCATGAAGATCCAAG 57.245 37.500 0.00 0.00 35.39 3.61
4686 12886 6.716173 TCAACAAGACAATCATGAAGATCCAA 59.284 34.615 0.00 0.00 35.39 3.53
4687 12887 6.240145 TCAACAAGACAATCATGAAGATCCA 58.760 36.000 0.00 0.00 35.39 3.41
4691 12891 6.487668 ACACATCAACAAGACAATCATGAAGA 59.512 34.615 0.00 0.00 0.00 2.87
4694 12894 5.764192 TGACACATCAACAAGACAATCATGA 59.236 36.000 0.00 0.00 0.00 3.07
4695 12895 6.004408 TGACACATCAACAAGACAATCATG 57.996 37.500 0.00 0.00 0.00 3.07
4696 12896 6.829229 ATGACACATCAACAAGACAATCAT 57.171 33.333 0.00 0.00 38.69 2.45
4697 12897 6.638096 AATGACACATCAACAAGACAATCA 57.362 33.333 0.00 0.00 38.69 2.57
4698 12898 7.747799 CAGTAATGACACATCAACAAGACAATC 59.252 37.037 0.00 0.00 38.69 2.67
4701 12901 5.049474 GCAGTAATGACACATCAACAAGACA 60.049 40.000 0.00 0.00 38.69 3.41
4702 12902 5.385617 GCAGTAATGACACATCAACAAGAC 58.614 41.667 0.00 0.00 38.69 3.01
4703 12903 4.455533 GGCAGTAATGACACATCAACAAGA 59.544 41.667 0.00 0.00 38.69 3.02
4707 12907 3.081061 TGGGCAGTAATGACACATCAAC 58.919 45.455 0.00 0.00 38.69 3.18
4709 12909 3.431673 TTGGGCAGTAATGACACATCA 57.568 42.857 0.00 0.00 39.83 3.07
4710 12910 3.428045 GCTTTGGGCAGTAATGACACATC 60.428 47.826 0.00 0.00 41.35 3.06
4712 12912 1.885887 GCTTTGGGCAGTAATGACACA 59.114 47.619 0.00 0.00 41.35 3.72
4713 12913 1.202348 GGCTTTGGGCAGTAATGACAC 59.798 52.381 0.00 0.00 44.01 3.67
4714 12914 1.544724 GGCTTTGGGCAGTAATGACA 58.455 50.000 0.00 0.00 44.01 3.58
4715 12915 0.817654 GGGCTTTGGGCAGTAATGAC 59.182 55.000 0.00 0.00 44.01 3.06
4716 12916 0.324275 GGGGCTTTGGGCAGTAATGA 60.324 55.000 0.00 0.00 44.01 2.57
4718 12918 0.116143 TTGGGGCTTTGGGCAGTAAT 59.884 50.000 0.00 0.00 44.01 1.89
4719 12919 0.105453 TTTGGGGCTTTGGGCAGTAA 60.105 50.000 0.00 0.00 44.01 2.24
4720 12920 0.541764 CTTTGGGGCTTTGGGCAGTA 60.542 55.000 0.00 0.00 44.01 2.74
4722 12922 2.586293 CCTTTGGGGCTTTGGGCAG 61.586 63.158 0.00 0.00 44.01 4.85


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

AutoCloner maintained by Alex Coulton.