Multiple sequence alignment - TraesCS1D01G191600

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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 TraesCS1D01G191600 chr1D 100.000 5990 0 0 1 5990 267374804 267380793 0.000000e+00 11062.0
1 TraesCS1D01G191600 chr1D 96.190 105 4 0 5373 5477 474916926 474916822 7.980000e-39 172.0
2 TraesCS1D01G191600 chr1D 91.228 114 8 1 5530 5643 474916814 474916703 2.890000e-33 154.0
3 TraesCS1D01G191600 chr1B 94.811 2679 102 21 1884 4551 346172764 346170112 0.000000e+00 4143.0
4 TraesCS1D01G191600 chr1B 93.002 1829 89 21 64 1882 346174637 346172838 0.000000e+00 2632.0
5 TraesCS1D01G191600 chr1B 94.239 1458 61 14 4549 5990 346170065 346168615 0.000000e+00 2206.0
6 TraesCS1D01G191600 chr1B 91.729 399 32 1 1072 1469 619096736 619097134 2.440000e-153 553.0
7 TraesCS1D01G191600 chr1B 95.706 163 7 0 1307 1469 541402235 541402397 4.600000e-66 263.0
8 TraesCS1D01G191600 chr1B 92.593 54 2 1 1245 1296 541402189 541402242 6.440000e-10 76.8
9 TraesCS1D01G191600 chr1A 95.506 1424 44 13 3133 4551 335833718 335832310 0.000000e+00 2257.0
10 TraesCS1D01G191600 chr1A 94.479 1449 73 3 4546 5990 335832266 335830821 0.000000e+00 2226.0
11 TraesCS1D01G191600 chr1A 96.256 1202 27 9 688 1882 335836399 335835209 0.000000e+00 1954.0
12 TraesCS1D01G191600 chr1A 93.910 936 38 9 1883 2813 335835144 335834223 0.000000e+00 1395.0
13 TraesCS1D01G191600 chr1A 87.944 647 54 11 64 698 335837181 335836547 0.000000e+00 741.0
14 TraesCS1D01G191600 chr1A 89.604 404 24 4 2742 3129 335834262 335833861 1.160000e-136 497.0
15 TraesCS1D01G191600 chr5A 85.839 572 66 11 1042 1602 662348008 662348575 1.440000e-165 593.0
16 TraesCS1D01G191600 chr5A 86.441 177 11 4 5468 5643 37967869 37968033 1.330000e-41 182.0
17 TraesCS1D01G191600 chr4D 85.839 572 66 12 1042 1602 481141367 481140800 1.440000e-165 593.0
18 TraesCS1D01G191600 chr4D 97.143 105 3 0 5373 5477 348307126 348307230 1.720000e-40 178.0
19 TraesCS1D01G191600 chr4D 92.105 114 9 0 5530 5643 348307238 348307351 1.730000e-35 161.0
20 TraesCS1D01G191600 chr4D 93.243 74 5 0 1 74 402018158 402018085 6.350000e-20 110.0
21 TraesCS1D01G191600 chr5B 92.481 399 29 1 1072 1469 493287066 493287464 2.420000e-158 569.0
22 TraesCS1D01G191600 chr5B 90.351 114 8 1 5530 5643 45021765 45021655 4.840000e-31 147.0
23 TraesCS1D01G191600 chr5B 97.368 38 1 0 1583 1620 364105266 364105229 1.390000e-06 65.8
24 TraesCS1D01G191600 chr5B 97.368 38 1 0 1583 1620 506503167 506503204 1.390000e-06 65.8
25 TraesCS1D01G191600 chr4B 78.715 794 151 11 3178 3962 609489051 609488267 1.150000e-141 514.0
26 TraesCS1D01G191600 chr4B 86.758 438 48 7 1173 1602 609490663 609490228 4.200000e-131 479.0
27 TraesCS1D01G191600 chr2D 90.226 399 27 2 1072 1469 69243472 69243085 1.490000e-140 510.0
28 TraesCS1D01G191600 chr2D 97.143 105 3 0 5373 5477 33946107 33946003 1.720000e-40 178.0
29 TraesCS1D01G191600 chr2D 96.190 105 4 0 5373 5477 56188904 56188800 7.980000e-39 172.0
30 TraesCS1D01G191600 chr2D 91.228 114 10 0 5530 5643 56188792 56188679 8.040000e-34 156.0
31 TraesCS1D01G191600 chr2D 100.000 40 0 0 940 979 427554350 427554389 2.320000e-09 75.0
32 TraesCS1D01G191600 chr7D 88.745 231 14 1 1156 1386 266895097 266894879 7.650000e-69 272.0
33 TraesCS1D01G191600 chr7D 96.154 104 4 0 5374 5477 293591676 293591779 2.870000e-38 171.0
34 TraesCS1D01G191600 chr7D 91.071 112 10 0 5530 5641 276474637 276474748 1.040000e-32 152.0
35 TraesCS1D01G191600 chr7D 97.368 38 1 0 1583 1620 587110782 587110819 1.390000e-06 65.8
36 TraesCS1D01G191600 chr5D 97.143 105 3 0 5373 5477 563593129 563593025 1.720000e-40 178.0
37 TraesCS1D01G191600 chr5D 96.190 105 4 0 5373 5477 213075030 213075134 7.980000e-39 172.0
38 TraesCS1D01G191600 chr5D 91.150 113 8 1 5531 5643 563593016 563592906 1.040000e-32 152.0
39 TraesCS1D01G191600 chr6D 90.351 114 11 0 5530 5643 263961655 263961542 3.740000e-32 150.0
40 TraesCS1D01G191600 chr2B 93.151 73 5 0 3 75 462612739 462612811 2.280000e-19 108.0


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 TraesCS1D01G191600 chr1D 267374804 267380793 5989 False 11062.000000 11062 100.000000 1 5990 1 chr1D.!!$F1 5989
1 TraesCS1D01G191600 chr1B 346168615 346174637 6022 True 2993.666667 4143 94.017333 64 5990 3 chr1B.!!$R1 5926
2 TraesCS1D01G191600 chr1A 335830821 335837181 6360 True 1511.666667 2257 92.949833 64 5990 6 chr1A.!!$R1 5926
3 TraesCS1D01G191600 chr5A 662348008 662348575 567 False 593.000000 593 85.839000 1042 1602 1 chr5A.!!$F2 560
4 TraesCS1D01G191600 chr4D 481140800 481141367 567 True 593.000000 593 85.839000 1042 1602 1 chr4D.!!$R2 560
5 TraesCS1D01G191600 chr4B 609488267 609490663 2396 True 496.500000 514 82.736500 1173 3962 2 chr4B.!!$R1 2789

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
38 39 0.037232 CTTGGTTCCACCCTCGAGTC 60.037 60.000 12.31 0.00 37.50 3.36 F
41 42 0.175989 GGTTCCACCCTCGAGTCATC 59.824 60.000 12.31 0.00 30.04 2.92 F
262 263 0.610232 GAAGGGCAGTCACCATGCTT 60.610 55.000 0.00 0.00 43.35 3.91 F
457 458 0.884704 ATTCTTCCTTGTGCGTGCGT 60.885 50.000 0.00 0.00 0.00 5.24 F
495 496 1.071699 AGCCCAAACGAGCTTTCTGTA 59.928 47.619 0.00 0.00 35.22 2.74 F
538 549 1.352622 ACAGGGTGCCAGTTTCAGGA 61.353 55.000 0.00 0.00 0.00 3.86 F
2613 2938 0.889994 TTGCTGGATGTGCATTGGAC 59.110 50.000 0.72 0.72 40.34 4.02 F
3421 3998 0.725686 CAGCAGACAGATGAAAGCCG 59.274 55.000 0.00 0.00 35.00 5.52 F
4464 5056 1.002033 GTTGTGAAGTGCTTGCTCCAG 60.002 52.381 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1914 3.740115 ACTAGCAACGAACAAGAACCAT 58.260 40.909 0.00 0.0 0.00 3.55 R
1914 2174 4.588951 ACTGCGGGATCATCTTTACTGATA 59.411 41.667 0.00 0.0 33.56 2.15 R
1931 2191 4.691860 ATCAAGAAAATTCAGACTGCGG 57.308 40.909 0.00 0.0 0.00 5.69 R
1985 2245 7.220030 TGAGTTTTTAGCTCTCAAGACAAGAT 58.780 34.615 0.00 0.0 35.65 2.40 R
2484 2809 5.276773 GCTCAAAAGATAGTCAATCAGAGCG 60.277 44.000 0.00 0.0 37.56 5.03 R
2625 2950 1.411246 CATGCTTCCATCCATTGTGGG 59.589 52.381 0.00 0.0 38.32 4.61 R
4464 5056 0.464373 TCCTGCAATGGAATCGAGCC 60.464 55.000 0.00 0.0 32.39 4.70 R
4956 5604 0.684535 TGGTGACGCCATCTTCTTCA 59.315 50.000 2.83 0.0 43.61 3.02 R
5813 6462 0.394352 CCACTTCCATCCTTTCCCCG 60.394 60.000 0.00 0.0 0.00 5.73 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
21 22 4.672587 TCCGAGTATAAATGAGCAGCTT 57.327 40.909 0.00 0.00 0.00 3.74
22 23 4.371786 TCCGAGTATAAATGAGCAGCTTG 58.628 43.478 0.00 0.00 0.00 4.01
23 24 3.496130 CCGAGTATAAATGAGCAGCTTGG 59.504 47.826 0.00 0.00 0.00 3.61
24 25 4.122776 CGAGTATAAATGAGCAGCTTGGT 58.877 43.478 0.00 0.00 0.00 3.67
25 26 4.572389 CGAGTATAAATGAGCAGCTTGGTT 59.428 41.667 0.00 0.00 0.00 3.67
26 27 5.277058 CGAGTATAAATGAGCAGCTTGGTTC 60.277 44.000 0.00 0.00 0.00 3.62
27 28 4.884164 AGTATAAATGAGCAGCTTGGTTCC 59.116 41.667 0.00 0.00 0.00 3.62
28 29 1.999648 AAATGAGCAGCTTGGTTCCA 58.000 45.000 0.00 0.00 0.00 3.53
29 30 1.251251 AATGAGCAGCTTGGTTCCAC 58.749 50.000 0.00 0.00 0.00 4.02
30 31 0.610232 ATGAGCAGCTTGGTTCCACC 60.610 55.000 0.00 0.00 39.22 4.61
31 32 1.973812 GAGCAGCTTGGTTCCACCC 60.974 63.158 0.00 0.00 37.50 4.61
32 33 2.116125 GCAGCTTGGTTCCACCCT 59.884 61.111 0.00 0.00 37.50 4.34
33 34 1.973812 GCAGCTTGGTTCCACCCTC 60.974 63.158 0.00 0.00 37.50 4.30
34 35 1.672356 CAGCTTGGTTCCACCCTCG 60.672 63.158 0.00 0.00 37.50 4.63
35 36 1.841556 AGCTTGGTTCCACCCTCGA 60.842 57.895 0.00 0.00 37.50 4.04
36 37 1.376037 GCTTGGTTCCACCCTCGAG 60.376 63.158 5.13 5.13 37.50 4.04
37 38 2.058675 CTTGGTTCCACCCTCGAGT 58.941 57.895 12.31 0.00 37.50 4.18
38 39 0.037232 CTTGGTTCCACCCTCGAGTC 60.037 60.000 12.31 0.00 37.50 3.36
39 40 0.761323 TTGGTTCCACCCTCGAGTCA 60.761 55.000 12.31 0.00 37.50 3.41
40 41 0.544357 TGGTTCCACCCTCGAGTCAT 60.544 55.000 12.31 0.00 37.50 3.06
41 42 0.175989 GGTTCCACCCTCGAGTCATC 59.824 60.000 12.31 0.00 30.04 2.92
42 43 3.481432 GGTTCCACCCTCGAGTCATCG 62.481 61.905 12.31 0.00 40.51 3.84
55 56 3.799366 GAGTCATCGAGAGTGTAGGAGA 58.201 50.000 0.00 0.00 0.00 3.71
56 57 4.193090 GAGTCATCGAGAGTGTAGGAGAA 58.807 47.826 0.00 0.00 0.00 2.87
57 58 4.196193 AGTCATCGAGAGTGTAGGAGAAG 58.804 47.826 0.00 0.00 0.00 2.85
58 59 3.314080 GTCATCGAGAGTGTAGGAGAAGG 59.686 52.174 0.00 0.00 0.00 3.46
59 60 3.054287 TCATCGAGAGTGTAGGAGAAGGT 60.054 47.826 0.00 0.00 0.00 3.50
60 61 2.712709 TCGAGAGTGTAGGAGAAGGTG 58.287 52.381 0.00 0.00 0.00 4.00
61 62 1.746220 CGAGAGTGTAGGAGAAGGTGG 59.254 57.143 0.00 0.00 0.00 4.61
62 63 2.618302 CGAGAGTGTAGGAGAAGGTGGA 60.618 54.545 0.00 0.00 0.00 4.02
91 92 2.147387 ACAGCTCGGTTCCACCCTT 61.147 57.895 0.00 0.00 33.75 3.95
103 104 1.811266 CACCCTTGAGTCATCGGCG 60.811 63.158 0.00 0.00 0.00 6.46
142 143 3.956199 TCATTGCCTCAAATTCCATCTCC 59.044 43.478 0.00 0.00 0.00 3.71
189 190 1.103803 AGCTCAATGCCTCAATGCTG 58.896 50.000 0.00 0.00 44.23 4.41
193 194 2.693591 CTCAATGCCTCAATGCTGGATT 59.306 45.455 0.00 0.00 0.00 3.01
208 209 3.260632 GCTGGATTGGTGGTTTATTTGGT 59.739 43.478 0.00 0.00 0.00 3.67
231 232 2.036217 CACATGGTGTTTGGCTCAATGT 59.964 45.455 0.00 0.00 36.09 2.71
262 263 0.610232 GAAGGGCAGTCACCATGCTT 60.610 55.000 0.00 0.00 43.35 3.91
300 301 2.283966 AGGGCTGTAGGTGCTCGT 60.284 61.111 0.00 0.00 35.78 4.18
315 316 2.655364 CGTACCGGCGCATCTCTG 60.655 66.667 10.83 0.00 0.00 3.35
428 429 0.979665 AGCTCTAGTGCAGGCAAGAA 59.020 50.000 18.36 0.00 34.99 2.52
432 433 4.133078 GCTCTAGTGCAGGCAAGAATAAT 58.867 43.478 11.82 0.00 0.00 1.28
447 448 7.263496 GCAAGAATAATGCTGAATTCTTCCTT 58.737 34.615 7.05 1.02 45.02 3.36
450 451 7.769220 AGAATAATGCTGAATTCTTCCTTGTG 58.231 34.615 7.05 0.00 38.93 3.33
457 458 0.884704 ATTCTTCCTTGTGCGTGCGT 60.885 50.000 0.00 0.00 0.00 5.24
460 461 2.430080 CTTCCTTGTGCGTGCGTCAC 62.430 60.000 10.51 10.51 35.14 3.67
474 475 1.990799 CGTCACGTAAGCAATCCTGA 58.009 50.000 0.00 0.00 45.62 3.86
495 496 1.071699 AGCCCAAACGAGCTTTCTGTA 59.928 47.619 0.00 0.00 35.22 2.74
506 507 4.151689 CGAGCTTTCTGTAAAAATCGGTCA 59.848 41.667 0.00 0.00 32.80 4.02
538 549 1.352622 ACAGGGTGCCAGTTTCAGGA 61.353 55.000 0.00 0.00 0.00 3.86
551 562 7.070074 TGCCAGTTTCAGGAATTTTAAGGTTAA 59.930 33.333 0.00 0.00 0.00 2.01
594 605 6.015504 CGTACGAATTCAAGGTTGATTTCAG 58.984 40.000 10.44 15.79 42.91 3.02
826 997 2.821366 CGAGCAAGCGCATTCCCT 60.821 61.111 11.47 0.00 42.27 4.20
898 1071 2.223923 CGGAGCACCAAAATCCAAAACA 60.224 45.455 0.00 0.00 35.59 2.83
1009 1185 2.339556 GGCCCTAACATGTTGCGCA 61.340 57.895 21.42 5.66 0.00 6.09
1101 1277 3.003763 AACTGCCTCGAGGACCCC 61.004 66.667 35.69 17.45 37.39 4.95
1707 1889 8.579682 AGCTTACTTTTCTGCTGTTAATTTTG 57.420 30.769 0.00 0.00 34.19 2.44
1727 1909 7.596749 TTTTGTAGCTCTAGCATTGTTCTAC 57.403 36.000 4.54 0.00 45.16 2.59
1728 1910 6.531503 TTGTAGCTCTAGCATTGTTCTACT 57.468 37.500 4.54 0.00 45.16 2.57
1729 1911 6.531503 TGTAGCTCTAGCATTGTTCTACTT 57.468 37.500 4.54 0.00 45.16 2.24
1730 1912 6.565234 TGTAGCTCTAGCATTGTTCTACTTC 58.435 40.000 4.54 0.00 45.16 3.01
1731 1913 5.930837 AGCTCTAGCATTGTTCTACTTCT 57.069 39.130 4.54 0.00 45.16 2.85
1732 1914 7.556635 TGTAGCTCTAGCATTGTTCTACTTCTA 59.443 37.037 4.54 0.00 45.16 2.10
1769 1951 3.131400 TGCTAGTTTGGGTGGTTTTGAAC 59.869 43.478 0.00 0.00 0.00 3.18
1814 1996 4.556501 CGCTAACTTCCAGCATTTGTTTCA 60.557 41.667 0.00 0.00 39.04 2.69
1815 1997 5.473039 GCTAACTTCCAGCATTTGTTTCAT 58.527 37.500 0.00 0.00 38.93 2.57
1872 2060 2.691011 GTCTTCTACCCTCCTGCTAGTG 59.309 54.545 0.00 0.00 0.00 2.74
1914 2174 7.793927 GCTAAAGCAACTCCTCAATATAAGT 57.206 36.000 0.00 0.00 41.59 2.24
1985 2245 4.141620 GCCCTTTTAGGAGTGATCTGATCA 60.142 45.833 16.06 16.06 37.67 2.92
2042 2302 6.691754 TTTTTCACAACAAGCTATCTGACA 57.308 33.333 0.00 0.00 0.00 3.58
2044 2305 6.882610 TTTCACAACAAGCTATCTGACAAT 57.117 33.333 0.00 0.00 0.00 2.71
2417 2742 7.773690 TGGTAAGATAGTTGCTTCCTATTTTCC 59.226 37.037 0.00 0.00 0.00 3.13
2435 2760 6.664428 TTTTCCTATTTCTGTTTCCCCTTG 57.336 37.500 0.00 0.00 0.00 3.61
2483 2808 9.817809 CTGGTTTTCTTAGTTCATAGTATAGCA 57.182 33.333 0.00 0.00 0.00 3.49
2484 2809 9.595823 TGGTTTTCTTAGTTCATAGTATAGCAC 57.404 33.333 0.00 0.00 0.00 4.40
2613 2938 0.889994 TTGCTGGATGTGCATTGGAC 59.110 50.000 0.72 0.72 40.34 4.02
2709 3036 4.880696 CCAAAGGGCTGTTTGAAATGAAAA 59.119 37.500 12.56 0.00 39.40 2.29
2722 3049 9.384682 GTTTGAAATGAAAAACAGCCAAATATG 57.615 29.630 0.00 0.00 36.50 1.78
3092 3518 7.584122 ATGGTCACTATACTATGAACTTCGT 57.416 36.000 0.00 0.00 33.47 3.85
3388 3965 1.247567 AATGAACACTCTTTGCGGGG 58.752 50.000 0.00 0.00 0.00 5.73
3421 3998 0.725686 CAGCAGACAGATGAAAGCCG 59.274 55.000 0.00 0.00 35.00 5.52
3831 4411 1.892209 CTTTGTCGTTGCCCTAAGGT 58.108 50.000 0.00 0.00 34.57 3.50
3985 4568 1.203075 AGTCGGGTTTCCTCTGTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
3986 4569 1.202817 GTCGGGTTTCCTCTGTCTCTC 59.797 57.143 0.00 0.00 0.00 3.20
4001 4586 1.568597 TCTCTCTCCCTCTCCCTCTTG 59.431 57.143 0.00 0.00 0.00 3.02
4015 4600 4.985538 TCCCTCTTGTTTCTATGCTGTTT 58.014 39.130 0.00 0.00 0.00 2.83
4195 4783 9.029368 TGAAGATATGGTGAGAGGTGAATATAG 57.971 37.037 0.00 0.00 0.00 1.31
4238 4826 2.380084 TATGCACCGGTGTTCTTCTC 57.620 50.000 33.92 16.89 0.00 2.87
4247 4835 3.005554 CGGTGTTCTTCTCTGCATGAAT 58.994 45.455 0.00 0.00 0.00 2.57
4256 4844 3.870274 TCTCTGCATGAATCTCTTGGTG 58.130 45.455 0.00 0.00 0.00 4.17
4359 4951 4.843728 ACCAACTTGATTCCACGATATGT 58.156 39.130 0.00 0.00 0.00 2.29
4364 4956 7.910162 CCAACTTGATTCCACGATATGTTTAAG 59.090 37.037 0.00 0.00 0.00 1.85
4367 4959 9.396022 ACTTGATTCCACGATATGTTTAAGATT 57.604 29.630 0.00 0.00 0.00 2.40
4411 5003 5.738225 CGTACTACTCTTCCGTTTGATCTTC 59.262 44.000 0.00 0.00 0.00 2.87
4414 5006 6.391537 ACTACTCTTCCGTTTGATCTTCTTC 58.608 40.000 0.00 0.00 0.00 2.87
4417 5009 5.698545 ACTCTTCCGTTTGATCTTCTTCTTG 59.301 40.000 0.00 0.00 0.00 3.02
4419 5011 5.696724 TCTTCCGTTTGATCTTCTTCTTGTC 59.303 40.000 0.00 0.00 0.00 3.18
4420 5012 3.987868 TCCGTTTGATCTTCTTCTTGTCG 59.012 43.478 0.00 0.00 0.00 4.35
4421 5013 3.741344 CCGTTTGATCTTCTTCTTGTCGT 59.259 43.478 0.00 0.00 0.00 4.34
4422 5014 4.211374 CCGTTTGATCTTCTTCTTGTCGTT 59.789 41.667 0.00 0.00 0.00 3.85
4423 5015 5.133264 CGTTTGATCTTCTTCTTGTCGTTG 58.867 41.667 0.00 0.00 0.00 4.10
4424 5016 5.051039 CGTTTGATCTTCTTCTTGTCGTTGA 60.051 40.000 0.00 0.00 0.00 3.18
4425 5017 6.358762 GTTTGATCTTCTTCTTGTCGTTGAG 58.641 40.000 0.00 0.00 0.00 3.02
4426 5018 5.453567 TGATCTTCTTCTTGTCGTTGAGA 57.546 39.130 0.00 0.00 0.00 3.27
4427 5019 5.842907 TGATCTTCTTCTTGTCGTTGAGAA 58.157 37.500 0.00 0.00 0.00 2.87
4428 5020 6.459066 TGATCTTCTTCTTGTCGTTGAGAAT 58.541 36.000 0.00 0.00 31.97 2.40
4429 5021 6.931281 TGATCTTCTTCTTGTCGTTGAGAATT 59.069 34.615 0.00 0.00 31.97 2.17
4430 5022 7.442364 TGATCTTCTTCTTGTCGTTGAGAATTT 59.558 33.333 0.00 0.00 31.97 1.82
4431 5023 8.833231 ATCTTCTTCTTGTCGTTGAGAATTTA 57.167 30.769 0.00 0.00 31.97 1.40
4464 5056 1.002033 GTTGTGAAGTGCTTGCTCCAG 60.002 52.381 0.00 0.00 0.00 3.86
4532 5124 8.585471 ATCACTGATTTGTTCTTACATTCCAT 57.415 30.769 0.00 0.00 33.44 3.41
4607 5247 2.762360 CGGAGCTCGTATTTGCCAA 58.238 52.632 7.83 0.00 0.00 4.52
4672 5312 1.985473 ACTGGAATGCTGCAAACTGA 58.015 45.000 6.36 0.00 0.00 3.41
4683 5323 1.955778 TGCAAACTGATCAACCACAGG 59.044 47.619 0.00 0.00 38.30 4.00
4701 5341 1.133792 AGGAATCCTTTGGTATGCCCG 60.134 52.381 0.00 0.00 35.15 6.13
4707 5347 3.547746 TCCTTTGGTATGCCCGTTTATC 58.452 45.455 0.00 0.00 35.15 1.75
4716 5356 3.916359 TGCCCGTTTATCTATCACCAA 57.084 42.857 0.00 0.00 0.00 3.67
4732 5372 9.183368 TCTATCACCAATTTATGCACATAACAA 57.817 29.630 2.59 0.00 33.40 2.83
4768 5410 2.124570 ATGCACATCTGTCCCCGC 60.125 61.111 0.00 0.00 0.00 6.13
4828 5472 2.027469 GGACCCGTTAATGTTCTGGACT 60.027 50.000 0.00 0.00 0.00 3.85
4841 5485 4.597507 TGTTCTGGACTAGGAATTTCCACT 59.402 41.667 17.57 0.41 39.61 4.00
4997 5645 3.379372 AGGTGGCTCGATTGATCAAAATG 59.621 43.478 13.09 5.46 0.00 2.32
5023 5671 3.526931 TCCATCTGCTTTAGGAGAACG 57.473 47.619 5.04 0.46 45.49 3.95
5025 5674 3.131223 TCCATCTGCTTTAGGAGAACGAG 59.869 47.826 5.04 0.00 45.49 4.18
5140 5789 2.240667 ACCTATTGCAGAGACCTTGCAT 59.759 45.455 0.32 0.00 38.43 3.96
5212 5861 1.767289 AGTGTCGACAACAAGCGTAG 58.233 50.000 21.95 0.00 40.31 3.51
5279 5928 5.012328 ACTTGTTATCCTTGTCGATCTCC 57.988 43.478 0.00 0.00 0.00 3.71
5953 6611 3.443925 CGACGAGCTGCTCTCCCA 61.444 66.667 25.59 0.00 38.62 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.371786 CAAGCTGCTCATTTATACTCGGA 58.628 43.478 1.00 0.00 0.00 4.55
1 2 3.496130 CCAAGCTGCTCATTTATACTCGG 59.504 47.826 1.00 0.00 0.00 4.63
6 7 4.640201 GTGGAACCAAGCTGCTCATTTATA 59.360 41.667 1.00 0.00 0.00 0.98
7 8 3.445096 GTGGAACCAAGCTGCTCATTTAT 59.555 43.478 1.00 0.00 0.00 1.40
8 9 2.819608 GTGGAACCAAGCTGCTCATTTA 59.180 45.455 1.00 0.00 0.00 1.40
9 10 1.615392 GTGGAACCAAGCTGCTCATTT 59.385 47.619 1.00 0.00 0.00 2.32
10 11 1.251251 GTGGAACCAAGCTGCTCATT 58.749 50.000 1.00 0.00 0.00 2.57
11 12 2.952714 GTGGAACCAAGCTGCTCAT 58.047 52.632 1.00 0.00 0.00 2.90
12 13 4.481195 GTGGAACCAAGCTGCTCA 57.519 55.556 1.00 0.00 0.00 4.26
23 24 3.742983 GATGACTCGAGGGTGGAAC 57.257 57.895 18.41 0.00 0.00 3.62
33 34 2.542178 CTCCTACACTCTCGATGACTCG 59.458 54.545 0.00 0.00 46.41 4.18
34 35 3.799366 TCTCCTACACTCTCGATGACTC 58.201 50.000 0.00 0.00 0.00 3.36
35 36 3.916359 TCTCCTACACTCTCGATGACT 57.084 47.619 0.00 0.00 0.00 3.41
36 37 3.314080 CCTTCTCCTACACTCTCGATGAC 59.686 52.174 0.00 0.00 0.00 3.06
37 38 3.054287 ACCTTCTCCTACACTCTCGATGA 60.054 47.826 0.00 0.00 0.00 2.92
38 39 3.066064 CACCTTCTCCTACACTCTCGATG 59.934 52.174 0.00 0.00 0.00 3.84
39 40 3.283751 CACCTTCTCCTACACTCTCGAT 58.716 50.000 0.00 0.00 0.00 3.59
40 41 2.618302 CCACCTTCTCCTACACTCTCGA 60.618 54.545 0.00 0.00 0.00 4.04
41 42 1.746220 CCACCTTCTCCTACACTCTCG 59.254 57.143 0.00 0.00 0.00 4.04
42 43 3.020984 CTCCACCTTCTCCTACACTCTC 58.979 54.545 0.00 0.00 0.00 3.20
43 44 2.650322 TCTCCACCTTCTCCTACACTCT 59.350 50.000 0.00 0.00 0.00 3.24
44 45 3.088789 TCTCCACCTTCTCCTACACTC 57.911 52.381 0.00 0.00 0.00 3.51
45 46 3.011821 TCATCTCCACCTTCTCCTACACT 59.988 47.826 0.00 0.00 0.00 3.55
46 47 3.366396 TCATCTCCACCTTCTCCTACAC 58.634 50.000 0.00 0.00 0.00 2.90
47 48 3.636679 CTCATCTCCACCTTCTCCTACA 58.363 50.000 0.00 0.00 0.00 2.74
48 49 2.364002 GCTCATCTCCACCTTCTCCTAC 59.636 54.545 0.00 0.00 0.00 3.18
49 50 2.246067 AGCTCATCTCCACCTTCTCCTA 59.754 50.000 0.00 0.00 0.00 2.94
50 51 1.008206 AGCTCATCTCCACCTTCTCCT 59.992 52.381 0.00 0.00 0.00 3.69
51 52 1.412343 GAGCTCATCTCCACCTTCTCC 59.588 57.143 9.40 0.00 35.77 3.71
52 53 2.888834 GAGCTCATCTCCACCTTCTC 57.111 55.000 9.40 0.00 35.77 2.87
91 92 2.954684 AAAGCCCGCCGATGACTCA 61.955 57.895 0.00 0.00 0.00 3.41
115 116 3.256383 TGGAATTTGAGGCAATGACACAG 59.744 43.478 0.00 0.00 0.00 3.66
120 121 3.956199 GGAGATGGAATTTGAGGCAATGA 59.044 43.478 0.00 0.00 0.00 2.57
142 143 3.668386 GGCGAAAGACAAGGTGGG 58.332 61.111 0.00 0.00 40.66 4.61
189 190 5.244178 TGTGTACCAAATAAACCACCAATCC 59.756 40.000 0.00 0.00 0.00 3.01
193 194 4.524714 CCATGTGTACCAAATAAACCACCA 59.475 41.667 0.00 0.00 0.00 4.17
208 209 2.647683 TGAGCCAAACACCATGTGTA 57.352 45.000 0.00 0.00 46.79 2.90
231 232 2.678934 CCCTTCCGTCGGAGTGGA 60.679 66.667 27.02 9.55 31.85 4.02
262 263 1.153568 GCAGTCGGCATGCTACTGA 60.154 57.895 36.46 21.44 42.59 3.41
300 301 4.221422 GGCAGAGATGCGCCGGTA 62.221 66.667 4.18 0.00 38.82 4.02
332 333 2.582498 CGTTAGGGAGAAGCGCGG 60.582 66.667 8.83 0.00 34.07 6.46
343 344 5.521010 TCGACACTTTTATATTGCCGTTAGG 59.479 40.000 0.00 0.00 41.62 2.69
345 346 5.005971 GCTCGACACTTTTATATTGCCGTTA 59.994 40.000 0.00 0.00 0.00 3.18
443 444 2.964925 GTGACGCACGCACAAGGA 60.965 61.111 11.04 0.00 36.31 3.36
457 458 2.346803 GCTTCAGGATTGCTTACGTGA 58.653 47.619 0.00 0.00 0.00 4.35
460 461 1.017387 GGGCTTCAGGATTGCTTACG 58.983 55.000 0.00 0.00 0.00 3.18
495 496 6.374613 GTCCTTTCTAATCCTGACCGATTTTT 59.625 38.462 0.00 0.00 34.35 1.94
506 507 2.239907 GCACCCTGTCCTTTCTAATCCT 59.760 50.000 0.00 0.00 0.00 3.24
551 562 7.516144 CGTACGCGAAGTTTGAATCAAACCT 62.516 44.000 28.84 20.07 45.90 3.50
664 676 6.037172 CCGTCGATGGATTCAAGAGTAAAAAT 59.963 38.462 19.48 0.00 0.00 1.82
669 681 2.223735 GCCGTCGATGGATTCAAGAGTA 60.224 50.000 28.06 0.00 0.00 2.59
797 968 1.284982 CTTGCTCGTCAACGGTCTGG 61.285 60.000 2.31 0.00 40.29 3.86
826 997 0.172127 GCACGAGCAGAGATGAGTGA 59.828 55.000 0.00 0.00 41.58 3.41
917 1090 1.472878 CTCCGCTACAGTCTACAGCAA 59.527 52.381 5.87 0.00 34.94 3.91
996 1172 2.685829 CGGGCTGCGCAACATGTTA 61.686 57.895 13.05 0.00 0.00 2.41
1707 1889 6.801575 AGAAGTAGAACAATGCTAGAGCTAC 58.198 40.000 2.72 0.00 42.66 3.58
1727 1909 4.452455 AGCAACGAACAAGAACCATAGAAG 59.548 41.667 0.00 0.00 0.00 2.85
1728 1910 4.385825 AGCAACGAACAAGAACCATAGAA 58.614 39.130 0.00 0.00 0.00 2.10
1729 1911 4.002906 AGCAACGAACAAGAACCATAGA 57.997 40.909 0.00 0.00 0.00 1.98
1730 1912 4.929808 ACTAGCAACGAACAAGAACCATAG 59.070 41.667 0.00 0.00 0.00 2.23
1731 1913 4.890088 ACTAGCAACGAACAAGAACCATA 58.110 39.130 0.00 0.00 0.00 2.74
1732 1914 3.740115 ACTAGCAACGAACAAGAACCAT 58.260 40.909 0.00 0.00 0.00 3.55
1769 1951 8.186178 AGCGAACAATTAGTTACTATGAAGTG 57.814 34.615 0.61 0.00 41.51 3.16
1914 2174 4.588951 ACTGCGGGATCATCTTTACTGATA 59.411 41.667 0.00 0.00 33.56 2.15
1931 2191 4.691860 ATCAAGAAAATTCAGACTGCGG 57.308 40.909 0.00 0.00 0.00 5.69
1932 2192 7.639072 CAGAATATCAAGAAAATTCAGACTGCG 59.361 37.037 0.00 0.00 33.06 5.18
1933 2193 8.457261 ACAGAATATCAAGAAAATTCAGACTGC 58.543 33.333 0.00 0.00 33.06 4.40
1985 2245 7.220030 TGAGTTTTTAGCTCTCAAGACAAGAT 58.780 34.615 0.00 0.00 35.65 2.40
2150 2411 7.567994 TGGTACATACTTACATGGGGTACAATA 59.432 37.037 0.00 0.00 33.22 1.90
2417 2742 7.547227 CCAAATACAAGGGGAAACAGAAATAG 58.453 38.462 0.00 0.00 0.00 1.73
2483 2808 5.724328 TCAAAAGATAGTCAATCAGAGCGT 58.276 37.500 0.00 0.00 37.03 5.07
2484 2809 5.276773 GCTCAAAAGATAGTCAATCAGAGCG 60.277 44.000 0.00 0.00 37.56 5.03
2625 2950 1.411246 CATGCTTCCATCCATTGTGGG 59.589 52.381 0.00 0.00 38.32 4.61
2754 3143 8.797438 GGAAAGAAACTGAATCTCAAATAAGGT 58.203 33.333 0.00 0.00 0.00 3.50
2863 3285 2.229792 TCTGCAATTGGTGAACTGGAC 58.770 47.619 7.72 0.00 0.00 4.02
3092 3518 5.064707 GCGGTAAAACATGCTCTTATCTTGA 59.935 40.000 0.00 0.00 0.00 3.02
3388 3965 2.482374 GCTGTTCACCATCGCAGC 59.518 61.111 0.00 0.00 45.70 5.25
3421 3998 6.651643 TCTCTTGTCACACTCTAGAGTTAGTC 59.348 42.308 23.01 15.12 40.20 2.59
3704 4284 5.707764 AGAAGACCTGAGCTTATTTTTGGAC 59.292 40.000 0.00 0.00 0.00 4.02
3831 4411 6.884295 ACATGAAAACCCGAATTATCTCTTGA 59.116 34.615 0.00 0.00 0.00 3.02
3985 4568 2.112691 AGAAACAAGAGGGAGAGGGAGA 59.887 50.000 0.00 0.00 0.00 3.71
3986 4569 2.545810 AGAAACAAGAGGGAGAGGGAG 58.454 52.381 0.00 0.00 0.00 4.30
4001 4586 5.705905 ACAGGTTAGGAAACAGCATAGAAAC 59.294 40.000 0.00 0.00 37.34 2.78
4142 4730 4.879598 ACGAGTACTAACTGAAAAGGGTG 58.120 43.478 0.00 0.00 35.56 4.61
4206 4794 6.015772 ACACCGGTGCATAATCTTTTAACTTT 60.016 34.615 34.26 5.09 0.00 2.66
4209 4797 5.305139 ACACCGGTGCATAATCTTTTAAC 57.695 39.130 34.26 0.00 0.00 2.01
4238 4826 5.578005 AAATCACCAAGAGATTCATGCAG 57.422 39.130 0.00 0.00 34.78 4.41
4247 4835 7.394077 TCATTGCATCTAAAAATCACCAAGAGA 59.606 33.333 0.00 0.00 0.00 3.10
4371 4963 9.567776 AGAGTAGTACGAGATACACTAGTAGTA 57.432 37.037 1.57 1.31 39.68 1.82
4372 4964 8.463930 AGAGTAGTACGAGATACACTAGTAGT 57.536 38.462 0.00 0.00 41.11 2.73
4373 4965 9.398170 GAAGAGTAGTACGAGATACACTAGTAG 57.602 40.741 0.00 0.00 37.38 2.57
4387 4979 5.232610 AGATCAAACGGAAGAGTAGTACG 57.767 43.478 0.00 0.00 0.00 3.67
4430 5022 9.502091 AGCACTTCACAACTATTCAAAGTAATA 57.498 29.630 0.00 0.00 0.00 0.98
4431 5023 8.396272 AGCACTTCACAACTATTCAAAGTAAT 57.604 30.769 0.00 0.00 0.00 1.89
4464 5056 0.464373 TCCTGCAATGGAATCGAGCC 60.464 55.000 0.00 0.00 32.39 4.70
4532 5124 9.629649 AGGGAGTTAAATATTATACAGGGATCA 57.370 33.333 0.00 0.00 0.00 2.92
4607 5247 3.355378 TCCCAAACATCGAAAGCATGAT 58.645 40.909 0.00 0.00 0.00 2.45
4683 5323 2.052782 ACGGGCATACCAAAGGATTC 57.947 50.000 0.00 0.00 40.22 2.52
4707 5347 9.236691 GTTGTTATGTGCATAAATTGGTGATAG 57.763 33.333 6.24 0.00 35.30 2.08
4768 5410 9.965824 AAAATAAAGATTCGCTATTACCATTGG 57.034 29.630 0.00 0.00 0.00 3.16
4828 5472 3.266772 AGTCATGGCAGTGGAAATTCCTA 59.733 43.478 13.78 0.00 37.46 2.94
4956 5604 0.684535 TGGTGACGCCATCTTCTTCA 59.315 50.000 2.83 0.00 43.61 3.02
4997 5645 2.439507 TCCTAAAGCAGATGGATGGGTC 59.560 50.000 0.00 0.00 0.00 4.46
5140 5789 2.499197 TGAAACAATTCGCAGTGGCTA 58.501 42.857 0.00 0.00 38.46 3.93
5212 5861 5.904362 ATTTTCTCCACTGGAAATAGCAC 57.096 39.130 0.00 0.00 33.51 4.40
5279 5928 2.581354 CCGGAGCTGTGGAAGGAG 59.419 66.667 0.00 0.00 0.00 3.69
5779 6428 4.717629 CCAAGCGACGACGAGCCA 62.718 66.667 12.29 0.00 42.66 4.75
5813 6462 0.394352 CCACTTCCATCCTTTCCCCG 60.394 60.000 0.00 0.00 0.00 5.73
5816 6465 1.354368 TCCACCACTTCCATCCTTTCC 59.646 52.381 0.00 0.00 0.00 3.13
5953 6611 2.748388 AGGCTATTACCACGAGGAAGT 58.252 47.619 5.68 0.00 38.69 3.01


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

AutoCloner maintained by Alex Coulton.