Multiple sequence alignment - TraesCS2B01G516500

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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 TraesCS2B01G516500 chr2B 100.000 2127 0 0 1389 3515 711530630 711532756 0.000000e+00 3928.0
1 TraesCS2B01G516500 chr2B 100.000 1076 0 0 1 1076 711529242 711530317 0.000000e+00 1988.0
2 TraesCS2B01G516500 chr2A 91.909 2163 116 25 1389 3513 722817001 722819142 0.000000e+00 2970.0
3 TraesCS2B01G516500 chr2A 92.010 388 19 9 526 907 722815035 722815416 5.160000e-148 534.0
4 TraesCS2B01G516500 chr2A 86.099 446 24 20 652 1076 722816547 722816975 2.490000e-121 446.0
5 TraesCS2B01G516500 chr2A 86.650 397 33 7 96 477 722814649 722815040 4.200000e-114 422.0
6 TraesCS2B01G516500 chr2A 92.308 182 14 0 473 654 722815491 722815672 3.480000e-65 259.0
7 TraesCS2B01G516500 chr2A 84.615 117 14 1 2057 2173 691022528 691022416 2.870000e-21 113.0
8 TraesCS2B01G516500 chr2D 90.791 2150 117 34 1389 3513 588225744 588227837 0.000000e+00 2798.0
9 TraesCS2B01G516500 chr2D 90.078 383 17 8 652 1024 588225118 588225489 8.830000e-131 477.0
10 TraesCS2B01G516500 chr2D 93.103 174 11 1 483 656 588222999 588223171 1.620000e-63 254.0
11 TraesCS2B01G516500 chr2D 84.667 150 20 3 1945 2094 208608435 208608581 2.830000e-31 147.0
12 TraesCS2B01G516500 chr4D 87.830 493 36 13 2801 3284 506466314 506465837 1.100000e-154 556.0
13 TraesCS2B01G516500 chr3B 87.071 495 40 12 2801 3283 800140533 800140051 3.990000e-149 538.0
14 TraesCS2B01G516500 chr3B 78.320 738 69 41 1784 2509 800142622 800141964 3.290000e-105 392.0
15 TraesCS2B01G516500 chr4B 82.695 653 59 34 2801 3436 663865166 663864551 6.680000e-147 531.0
16 TraesCS2B01G516500 chr4B 82.695 653 59 34 2801 3436 663873200 663872585 6.680000e-147 531.0
17 TraesCS2B01G516500 chr4B 82.695 653 59 34 2801 3436 663877416 663876801 6.680000e-147 531.0
18 TraesCS2B01G516500 chr4B 82.569 654 59 35 2801 3436 663859308 663858692 3.110000e-145 525.0
19 TraesCS2B01G516500 chr4B 84.966 439 37 21 3008 3436 663870341 663869922 5.430000e-113 418.0
20 TraesCS2B01G516500 chr4B 76.790 754 97 37 1784 2521 662564857 662565548 5.580000e-93 351.0
21 TraesCS2B01G516500 chr1A 81.376 596 50 30 1890 2470 41371975 41372524 2.510000e-116 429.0
22 TraesCS2B01G516500 chr1A 80.705 596 54 31 1890 2470 42195856 42196405 1.170000e-109 407.0
23 TraesCS2B01G516500 chr1A 81.731 104 15 2 1942 2045 320508163 320508262 2.250000e-12 84.2
24 TraesCS2B01G516500 chr1D 83.946 299 34 7 2217 2515 155886256 155885972 1.240000e-69 274.0
25 TraesCS2B01G516500 chr1D 80.282 142 21 7 927 1064 41573251 41573389 2.230000e-17 100.0
26 TraesCS2B01G516500 chr7A 77.805 410 63 20 2056 2462 145760126 145760510 9.820000e-56 228.0
27 TraesCS2B01G516500 chr7A 77.340 406 60 25 2060 2460 119549385 119549763 9.890000e-51 211.0
28 TraesCS2B01G516500 chr7A 84.615 117 14 1 2057 2173 149290534 149290422 2.870000e-21 113.0
29 TraesCS2B01G516500 chr5A 80.364 275 23 21 2475 2735 702753620 702753363 2.790000e-41 180.0
30 TraesCS2B01G516500 chr5A 86.325 117 12 1 2057 2173 219650993 219650881 1.320000e-24 124.0
31 TraesCS2B01G516500 chr5A 90.741 54 3 2 2544 2596 702865484 702865432 1.750000e-08 71.3
32 TraesCS2B01G516500 chr5D 94.624 93 5 0 3 95 366060825 366060917 1.020000e-30 145.0
33 TraesCS2B01G516500 chr4A 91.398 93 8 0 3 95 684082376 684082468 1.020000e-25 128.0
34 TraesCS2B01G516500 chr7D 73.067 401 76 20 97 480 606790874 606790489 2.870000e-21 113.0


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 TraesCS2B01G516500 chr2B 711529242 711532756 3514 False 2958.000000 3928 100.0000 1 3515 2 chr2B.!!$F1 3514
1 TraesCS2B01G516500 chr2A 722814649 722819142 4493 False 926.200000 2970 89.7952 96 3513 5 chr2A.!!$F1 3417
2 TraesCS2B01G516500 chr2D 588222999 588227837 4838 False 1176.333333 2798 91.3240 483 3513 3 chr2D.!!$F2 3030
3 TraesCS2B01G516500 chr3B 800140051 800142622 2571 True 465.000000 538 82.6955 1784 3283 2 chr3B.!!$R1 1499
4 TraesCS2B01G516500 chr4B 663864551 663865166 615 True 531.000000 531 82.6950 2801 3436 1 chr4B.!!$R2 635
5 TraesCS2B01G516500 chr4B 663858692 663859308 616 True 525.000000 525 82.5690 2801 3436 1 chr4B.!!$R1 635
6 TraesCS2B01G516500 chr4B 663869922 663877416 7494 True 493.333333 531 83.4520 2801 3436 3 chr4B.!!$R3 635
7 TraesCS2B01G516500 chr4B 662564857 662565548 691 False 351.000000 351 76.7900 1784 2521 1 chr4B.!!$F1 737
8 TraesCS2B01G516500 chr1A 41371975 41372524 549 False 429.000000 429 81.3760 1890 2470 1 chr1A.!!$F1 580
9 TraesCS2B01G516500 chr1A 42195856 42196405 549 False 407.000000 407 80.7050 1890 2470 1 chr1A.!!$F2 580

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
312 313 0.380378 TCGAAACTTGGCTGCAACAC 59.620 50.0 0.5 0.0 0.0 3.32 F
1629 4979 0.699399 TGGGCGACTGGGGATTTTTA 59.301 50.0 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 5117 0.620556 ACACCCACATCCCATCAGAC 59.379 55.0 0.00 0.00 0.00 3.51 R
2889 11756 0.179059 AATGTGCTGACACCGTGACA 60.179 50.0 5.28 4.37 46.86 3.58 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
24 25 4.333417 GCTGAGGCCTTGAGCAAT 57.667 55.556 25.56 0.00 46.50 3.56
25 26 3.483954 GCTGAGGCCTTGAGCAATA 57.516 52.632 25.56 0.00 46.50 1.90
26 27 1.755179 GCTGAGGCCTTGAGCAATAA 58.245 50.000 25.56 0.00 46.50 1.40
27 28 1.403323 GCTGAGGCCTTGAGCAATAAC 59.597 52.381 25.56 3.64 46.50 1.89
28 29 2.715046 CTGAGGCCTTGAGCAATAACA 58.285 47.619 6.77 0.00 46.50 2.41
29 30 3.285484 CTGAGGCCTTGAGCAATAACAT 58.715 45.455 6.77 0.00 46.50 2.71
30 31 3.698040 CTGAGGCCTTGAGCAATAACATT 59.302 43.478 6.77 0.00 46.50 2.71
31 32 4.854173 TGAGGCCTTGAGCAATAACATTA 58.146 39.130 6.77 0.00 46.50 1.90
32 33 5.448654 TGAGGCCTTGAGCAATAACATTAT 58.551 37.500 6.77 0.00 46.50 1.28
33 34 6.600388 TGAGGCCTTGAGCAATAACATTATA 58.400 36.000 6.77 0.00 46.50 0.98
34 35 7.233632 TGAGGCCTTGAGCAATAACATTATAT 58.766 34.615 6.77 0.00 46.50 0.86
35 36 7.175467 TGAGGCCTTGAGCAATAACATTATATG 59.825 37.037 6.77 0.00 46.50 1.78
36 37 6.435277 AGGCCTTGAGCAATAACATTATATGG 59.565 38.462 0.00 0.00 46.50 2.74
37 38 6.209391 GGCCTTGAGCAATAACATTATATGGT 59.791 38.462 0.00 0.00 46.50 3.55
38 39 7.308435 GCCTTGAGCAATAACATTATATGGTC 58.692 38.462 13.33 13.33 42.97 4.02
39 40 7.175641 GCCTTGAGCAATAACATTATATGGTCT 59.824 37.037 17.20 0.00 42.97 3.85
40 41 8.509690 CCTTGAGCAATAACATTATATGGTCTG 58.490 37.037 17.20 13.01 33.60 3.51
41 42 9.276590 CTTGAGCAATAACATTATATGGTCTGA 57.723 33.333 17.20 10.72 33.60 3.27
42 43 9.625747 TTGAGCAATAACATTATATGGTCTGAA 57.374 29.630 17.20 8.94 33.60 3.02
43 44 9.056005 TGAGCAATAACATTATATGGTCTGAAC 57.944 33.333 17.20 0.00 33.60 3.18
44 45 8.978874 AGCAATAACATTATATGGTCTGAACA 57.021 30.769 0.00 0.00 33.60 3.18
45 46 9.578576 AGCAATAACATTATATGGTCTGAACAT 57.421 29.630 13.47 13.47 33.60 2.71
46 47 9.616634 GCAATAACATTATATGGTCTGAACATG 57.383 33.333 18.18 5.11 33.60 3.21
48 49 9.866655 AATAACATTATATGGTCTGAACATGGT 57.133 29.630 18.18 9.18 33.60 3.55
49 50 7.572523 AACATTATATGGTCTGAACATGGTG 57.427 36.000 18.18 12.52 33.60 4.17
50 51 6.899089 ACATTATATGGTCTGAACATGGTGA 58.101 36.000 18.18 4.42 33.60 4.02
51 52 7.345691 ACATTATATGGTCTGAACATGGTGAA 58.654 34.615 18.18 7.06 33.60 3.18
52 53 7.500227 ACATTATATGGTCTGAACATGGTGAAG 59.500 37.037 18.18 6.42 33.60 3.02
53 54 2.566833 TGGTCTGAACATGGTGAAGG 57.433 50.000 0.00 0.00 0.00 3.46
54 55 2.054021 TGGTCTGAACATGGTGAAGGA 58.946 47.619 0.00 0.00 0.00 3.36
55 56 2.441375 TGGTCTGAACATGGTGAAGGAA 59.559 45.455 0.00 0.00 0.00 3.36
56 57 3.074390 TGGTCTGAACATGGTGAAGGAAT 59.926 43.478 0.00 0.00 0.00 3.01
57 58 4.288366 TGGTCTGAACATGGTGAAGGAATA 59.712 41.667 0.00 0.00 0.00 1.75
58 59 5.044919 TGGTCTGAACATGGTGAAGGAATAT 60.045 40.000 0.00 0.00 0.00 1.28
59 60 5.297776 GGTCTGAACATGGTGAAGGAATATG 59.702 44.000 0.00 0.00 0.00 1.78
60 61 4.883585 TCTGAACATGGTGAAGGAATATGC 59.116 41.667 0.00 0.00 0.00 3.14
61 62 3.627123 TGAACATGGTGAAGGAATATGCG 59.373 43.478 0.00 0.00 0.00 4.73
62 63 3.558931 ACATGGTGAAGGAATATGCGA 57.441 42.857 0.00 0.00 0.00 5.10
63 64 3.884895 ACATGGTGAAGGAATATGCGAA 58.115 40.909 0.00 0.00 0.00 4.70
64 65 4.269183 ACATGGTGAAGGAATATGCGAAA 58.731 39.130 0.00 0.00 0.00 3.46
65 66 4.096382 ACATGGTGAAGGAATATGCGAAAC 59.904 41.667 0.00 0.00 0.00 2.78
66 67 3.680490 TGGTGAAGGAATATGCGAAACA 58.320 40.909 0.00 0.00 0.00 2.83
67 68 4.075682 TGGTGAAGGAATATGCGAAACAA 58.924 39.130 0.00 0.00 0.00 2.83
68 69 4.704540 TGGTGAAGGAATATGCGAAACAAT 59.295 37.500 0.00 0.00 0.00 2.71
69 70 5.883115 TGGTGAAGGAATATGCGAAACAATA 59.117 36.000 0.00 0.00 0.00 1.90
70 71 6.038161 TGGTGAAGGAATATGCGAAACAATAG 59.962 38.462 0.00 0.00 0.00 1.73
71 72 6.260050 GGTGAAGGAATATGCGAAACAATAGA 59.740 38.462 0.00 0.00 0.00 1.98
72 73 7.201696 GGTGAAGGAATATGCGAAACAATAGAA 60.202 37.037 0.00 0.00 0.00 2.10
73 74 8.181573 GTGAAGGAATATGCGAAACAATAGAAA 58.818 33.333 0.00 0.00 0.00 2.52
74 75 8.735315 TGAAGGAATATGCGAAACAATAGAAAA 58.265 29.630 0.00 0.00 0.00 2.29
75 76 9.567848 GAAGGAATATGCGAAACAATAGAAAAA 57.432 29.630 0.00 0.00 0.00 1.94
76 77 9.573133 AAGGAATATGCGAAACAATAGAAAAAG 57.427 29.630 0.00 0.00 0.00 2.27
77 78 7.702348 AGGAATATGCGAAACAATAGAAAAAGC 59.298 33.333 0.00 0.00 0.00 3.51
78 79 7.487829 GGAATATGCGAAACAATAGAAAAAGCA 59.512 33.333 0.00 0.00 36.50 3.91
79 80 8.755696 AATATGCGAAACAATAGAAAAAGCAA 57.244 26.923 0.00 0.00 35.67 3.91
80 81 8.755696 ATATGCGAAACAATAGAAAAAGCAAA 57.244 26.923 0.00 0.00 35.67 3.68
81 82 6.267500 TGCGAAACAATAGAAAAAGCAAAC 57.733 33.333 0.00 0.00 0.00 2.93
82 83 5.807520 TGCGAAACAATAGAAAAAGCAAACA 59.192 32.000 0.00 0.00 0.00 2.83
83 84 6.478344 TGCGAAACAATAGAAAAAGCAAACAT 59.522 30.769 0.00 0.00 0.00 2.71
84 85 6.787043 GCGAAACAATAGAAAAAGCAAACATG 59.213 34.615 0.00 0.00 0.00 3.21
85 86 7.516627 GCGAAACAATAGAAAAAGCAAACATGT 60.517 33.333 0.00 0.00 0.00 3.21
86 87 8.327429 CGAAACAATAGAAAAAGCAAACATGTT 58.673 29.630 4.92 4.92 0.00 2.71
87 88 9.636965 GAAACAATAGAAAAAGCAAACATGTTC 57.363 29.630 12.39 0.00 0.00 3.18
88 89 7.713764 ACAATAGAAAAAGCAAACATGTTCC 57.286 32.000 12.39 6.33 0.00 3.62
89 90 7.500141 ACAATAGAAAAAGCAAACATGTTCCT 58.500 30.769 12.39 8.64 0.00 3.36
90 91 7.653311 ACAATAGAAAAAGCAAACATGTTCCTC 59.347 33.333 12.39 4.17 0.00 3.71
91 92 4.948847 AGAAAAAGCAAACATGTTCCTCC 58.051 39.130 12.39 0.83 0.00 4.30
92 93 4.405358 AGAAAAAGCAAACATGTTCCTCCA 59.595 37.500 12.39 0.00 0.00 3.86
93 94 3.733443 AAAGCAAACATGTTCCTCCAC 57.267 42.857 12.39 0.00 0.00 4.02
94 95 2.363306 AGCAAACATGTTCCTCCACA 57.637 45.000 12.39 0.00 0.00 4.17
102 103 2.325583 TGTTCCTCCACACACTTCAC 57.674 50.000 0.00 0.00 0.00 3.18
125 126 9.163894 TCACATCTCCCTCTCTCATAAATAAAT 57.836 33.333 0.00 0.00 0.00 1.40
126 127 9.790344 CACATCTCCCTCTCTCATAAATAAATT 57.210 33.333 0.00 0.00 0.00 1.82
152 153 7.522374 TGTGTGTTTAATTTTTGGCTTCAAAC 58.478 30.769 0.00 0.00 39.77 2.93
153 154 7.173218 TGTGTGTTTAATTTTTGGCTTCAAACA 59.827 29.630 0.00 0.00 39.77 2.83
154 155 8.017946 GTGTGTTTAATTTTTGGCTTCAAACAA 58.982 29.630 0.00 0.00 39.77 2.83
185 186 7.872483 AGGGTCATGTATTTTGAACAAAATGTC 59.128 33.333 25.80 20.09 46.80 3.06
199 200 9.179552 TGAACAAAATGTCTGATTACAAAATCG 57.820 29.630 0.00 0.00 43.84 3.34
246 247 7.521529 TGACGAAATCTTTGAATCAAGATCAC 58.478 34.615 0.00 0.75 0.00 3.06
247 248 6.846350 ACGAAATCTTTGAATCAAGATCACC 58.154 36.000 0.00 0.00 0.00 4.02
249 250 4.889832 ATCTTTGAATCAAGATCACCGC 57.110 40.909 0.00 0.00 0.00 5.68
259 260 4.183865 TCAAGATCACCGCTGAGTATTTG 58.816 43.478 0.00 0.00 0.00 2.32
261 262 4.471904 AGATCACCGCTGAGTATTTGAA 57.528 40.909 0.00 0.00 0.00 2.69
267 268 7.441890 TCACCGCTGAGTATTTGAAAATTAA 57.558 32.000 0.00 0.00 0.00 1.40
294 295 7.603963 TTTTTGGCCTTTTCAAACTTAACTC 57.396 32.000 3.32 0.00 34.34 3.01
303 304 7.220108 CCTTTTCAAACTTAACTCGAAACTTGG 59.780 37.037 0.00 0.00 0.00 3.61
312 313 0.380378 TCGAAACTTGGCTGCAACAC 59.620 50.000 0.50 0.00 0.00 3.32
348 349 9.730420 ATGTAATTTGTCGGTTAGAAATATTGC 57.270 29.630 0.00 0.00 31.19 3.56
350 351 7.404671 AATTTGTCGGTTAGAAATATTGCCT 57.595 32.000 0.00 0.00 31.19 4.75
351 352 6.431198 TTTGTCGGTTAGAAATATTGCCTC 57.569 37.500 0.00 0.00 0.00 4.70
352 353 5.353394 TGTCGGTTAGAAATATTGCCTCT 57.647 39.130 0.00 0.00 0.00 3.69
353 354 5.357257 TGTCGGTTAGAAATATTGCCTCTC 58.643 41.667 0.00 0.00 0.00 3.20
363 373 2.758736 ATTGCCTCTCTCTCACACAC 57.241 50.000 0.00 0.00 0.00 3.82
372 382 1.456892 TCTCACACACGTGGGTCCT 60.457 57.895 23.22 0.00 44.63 3.85
375 385 3.475494 ACACACGTGGGTCCTGCA 61.475 61.111 19.98 0.00 34.19 4.41
417 433 5.540400 TCCGAGTCTAGTTTCAAAAAGGA 57.460 39.130 0.00 0.00 0.00 3.36
422 438 7.644157 CCGAGTCTAGTTTCAAAAAGGAAAAAG 59.356 37.037 0.00 0.00 38.41 2.27
496 967 9.422196 CGATAAAAATCTAAACGGATCTGAAAC 57.578 33.333 9.00 0.00 0.00 2.78
600 1071 4.771903 TGTACAAAGTGCAAGGTTGTCTA 58.228 39.130 12.66 3.42 36.83 2.59
634 1105 8.336801 AGATATAGTCCAACTTTTGACCAAAC 57.663 34.615 0.00 0.00 0.00 2.93
635 1106 8.164070 AGATATAGTCCAACTTTTGACCAAACT 58.836 33.333 0.00 0.00 0.00 2.66
698 3997 7.805071 CACTTCTGGCTCATTACTTACTTTTTG 59.195 37.037 0.00 0.00 0.00 2.44
702 4001 8.103305 TCTGGCTCATTACTTACTTTTTGATCT 58.897 33.333 0.00 0.00 0.00 2.75
703 4002 8.044060 TGGCTCATTACTTACTTTTTGATCTG 57.956 34.615 0.00 0.00 0.00 2.90
704 4003 7.665559 TGGCTCATTACTTACTTTTTGATCTGT 59.334 33.333 0.00 0.00 0.00 3.41
705 4004 9.162764 GGCTCATTACTTACTTTTTGATCTGTA 57.837 33.333 0.00 0.00 0.00 2.74
780 4085 0.944386 ATTCGTTCGCTGTTGCAAGT 59.056 45.000 0.00 0.00 39.64 3.16
789 4094 2.018727 CTGTTGCAAGTTGGCAGCCA 62.019 55.000 11.22 11.22 45.88 4.75
822 4127 7.488322 CATTCCAAGTAAACCTTTTGAGACAA 58.512 34.615 0.00 0.00 0.00 3.18
827 4132 5.201243 AGTAAACCTTTTGAGACAAAGCCT 58.799 37.500 0.00 0.00 0.00 4.58
853 4158 2.032681 GCCCGTTCTGTGGAAGCT 59.967 61.111 0.00 0.00 31.46 3.74
932 4244 1.369321 GTGATCCGGCCATCTCTCC 59.631 63.158 2.24 0.00 0.00 3.71
937 4249 3.842923 CGGCCATCTCTCCGCTGT 61.843 66.667 2.24 0.00 39.14 4.40
1067 4401 1.982395 TGAGAGCACCCTACCACCG 60.982 63.158 0.00 0.00 0.00 4.94
1463 4798 2.637025 GCCGCGAGCAGTTTTTGA 59.363 55.556 8.23 0.00 42.97 2.69
1565 4907 4.059459 CGTGCGTGCGTTGGTCTC 62.059 66.667 0.00 0.00 0.00 3.36
1581 4928 3.197766 TGGTCTCGCTATTTGGTTCTGAT 59.802 43.478 0.00 0.00 0.00 2.90
1629 4979 0.699399 TGGGCGACTGGGGATTTTTA 59.301 50.000 0.00 0.00 0.00 1.52
1903 5281 2.063266 CAACTAAAAGCTCCACGCGTA 58.937 47.619 13.44 0.00 45.59 4.42
2178 5583 1.227350 CTTGATCGGCCAGCGATGA 60.227 57.895 0.06 0.00 0.00 2.92
2487 5905 2.112297 GTCCTCCACAACGCCCAA 59.888 61.111 0.00 0.00 0.00 4.12
2528 6345 3.102276 GCGAATAGTCAGTCGAGTTCAG 58.898 50.000 0.00 0.00 44.71 3.02
2639 6464 4.227538 CTGTTTCTTCTGCATGCTTTCTG 58.772 43.478 20.33 5.65 0.00 3.02
2641 6466 2.195741 TCTTCTGCATGCTTTCTGCT 57.804 45.000 20.33 0.00 43.37 4.24
2642 6467 1.810755 TCTTCTGCATGCTTTCTGCTG 59.189 47.619 20.33 0.00 43.37 4.41
2735 6560 1.202580 GCTCGTATGAATCTGCCACCT 60.203 52.381 0.00 0.00 0.00 4.00
2736 6561 2.477825 CTCGTATGAATCTGCCACCTG 58.522 52.381 0.00 0.00 0.00 4.00
2886 11753 2.744202 GTGTGATGCTTTCCTGTCGAAT 59.256 45.455 0.00 0.00 0.00 3.34
2889 11756 2.271800 GATGCTTTCCTGTCGAATCGT 58.728 47.619 1.52 0.00 0.00 3.73
2890 11757 1.428448 TGCTTTCCTGTCGAATCGTG 58.572 50.000 1.52 0.00 0.00 4.35
2891 11758 1.270094 TGCTTTCCTGTCGAATCGTGT 60.270 47.619 1.52 0.00 0.00 4.49
2892 11759 1.390463 GCTTTCCTGTCGAATCGTGTC 59.610 52.381 1.52 0.00 0.00 3.67
2893 11760 2.672714 CTTTCCTGTCGAATCGTGTCA 58.327 47.619 1.52 0.53 0.00 3.58
2894 11761 2.060326 TTCCTGTCGAATCGTGTCAC 57.940 50.000 1.52 0.00 0.00 3.67
2895 11762 0.109919 TCCTGTCGAATCGTGTCACG 60.110 55.000 19.38 19.38 44.19 4.35
2896 11763 1.071019 CCTGTCGAATCGTGTCACGG 61.071 60.000 24.33 9.11 42.81 4.94
2951 11818 7.500227 GTCTCAATCTGGGAACATAAATCATGA 59.500 37.037 0.00 0.00 41.51 3.07
2960 14489 7.987458 TGGGAACATAAATCATGAGACTAGTTC 59.013 37.037 17.74 17.74 38.10 3.01
3354 14916 5.541953 ACATGATATCAGTAGCAGCAAGA 57.458 39.130 11.78 0.00 28.40 3.02
3379 14943 8.546083 AGATATGTCACTTGAGGAGTATTTCT 57.454 34.615 0.00 0.00 36.65 2.52
3448 15016 7.388460 AGAAATTAAGAAGGTGAGCAATCAG 57.612 36.000 0.00 0.00 0.00 2.90
3485 15053 8.686334 AGTAATCAACTGATGAAACACTTGTTT 58.314 29.630 7.06 7.06 43.10 2.83
3514 15082 9.832445 AGCCTTCTTCACTAAATAAAATATCGA 57.168 29.630 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.403323 GTTATTGCTCAAGGCCTCAGC 59.597 52.381 24.03 24.03 40.92 4.26
8 9 2.715046 TGTTATTGCTCAAGGCCTCAG 58.285 47.619 5.23 6.50 40.92 3.35
9 10 2.877097 TGTTATTGCTCAAGGCCTCA 57.123 45.000 5.23 0.00 40.92 3.86
10 11 7.362401 CCATATAATGTTATTGCTCAAGGCCTC 60.362 40.741 5.23 0.00 40.92 4.70
11 12 6.435277 CCATATAATGTTATTGCTCAAGGCCT 59.565 38.462 0.00 0.00 40.92 5.19
12 13 6.209391 ACCATATAATGTTATTGCTCAAGGCC 59.791 38.462 0.00 0.00 40.92 5.19
13 14 7.175641 AGACCATATAATGTTATTGCTCAAGGC 59.824 37.037 0.00 0.00 42.22 4.35
14 15 8.509690 CAGACCATATAATGTTATTGCTCAAGG 58.490 37.037 0.00 0.00 0.00 3.61
15 16 9.276590 TCAGACCATATAATGTTATTGCTCAAG 57.723 33.333 0.00 0.00 0.00 3.02
16 17 9.625747 TTCAGACCATATAATGTTATTGCTCAA 57.374 29.630 0.00 0.00 0.00 3.02
17 18 9.056005 GTTCAGACCATATAATGTTATTGCTCA 57.944 33.333 0.00 0.00 0.00 4.26
18 19 9.056005 TGTTCAGACCATATAATGTTATTGCTC 57.944 33.333 0.00 0.00 0.00 4.26
19 20 8.978874 TGTTCAGACCATATAATGTTATTGCT 57.021 30.769 0.00 0.00 0.00 3.91
20 21 9.616634 CATGTTCAGACCATATAATGTTATTGC 57.383 33.333 0.00 0.00 0.00 3.56
22 23 9.866655 ACCATGTTCAGACCATATAATGTTATT 57.133 29.630 0.00 0.00 0.00 1.40
23 24 9.288576 CACCATGTTCAGACCATATAATGTTAT 57.711 33.333 0.00 0.00 0.00 1.89
24 25 8.490311 TCACCATGTTCAGACCATATAATGTTA 58.510 33.333 0.00 0.00 0.00 2.41
25 26 7.345691 TCACCATGTTCAGACCATATAATGTT 58.654 34.615 0.00 0.00 0.00 2.71
26 27 6.899089 TCACCATGTTCAGACCATATAATGT 58.101 36.000 0.00 0.00 0.00 2.71
27 28 7.040892 CCTTCACCATGTTCAGACCATATAATG 60.041 40.741 0.00 0.00 0.00 1.90
28 29 7.000472 CCTTCACCATGTTCAGACCATATAAT 59.000 38.462 0.00 0.00 0.00 1.28
29 30 6.157820 TCCTTCACCATGTTCAGACCATATAA 59.842 38.462 0.00 0.00 0.00 0.98
30 31 5.665360 TCCTTCACCATGTTCAGACCATATA 59.335 40.000 0.00 0.00 0.00 0.86
31 32 4.474651 TCCTTCACCATGTTCAGACCATAT 59.525 41.667 0.00 0.00 0.00 1.78
32 33 3.843619 TCCTTCACCATGTTCAGACCATA 59.156 43.478 0.00 0.00 0.00 2.74
33 34 2.644299 TCCTTCACCATGTTCAGACCAT 59.356 45.455 0.00 0.00 0.00 3.55
34 35 2.054021 TCCTTCACCATGTTCAGACCA 58.946 47.619 0.00 0.00 0.00 4.02
35 36 2.859165 TCCTTCACCATGTTCAGACC 57.141 50.000 0.00 0.00 0.00 3.85
36 37 5.220931 GCATATTCCTTCACCATGTTCAGAC 60.221 44.000 0.00 0.00 0.00 3.51
37 38 4.883585 GCATATTCCTTCACCATGTTCAGA 59.116 41.667 0.00 0.00 0.00 3.27
38 39 4.260907 CGCATATTCCTTCACCATGTTCAG 60.261 45.833 0.00 0.00 0.00 3.02
39 40 3.627123 CGCATATTCCTTCACCATGTTCA 59.373 43.478 0.00 0.00 0.00 3.18
40 41 3.876914 TCGCATATTCCTTCACCATGTTC 59.123 43.478 0.00 0.00 0.00 3.18
41 42 3.884895 TCGCATATTCCTTCACCATGTT 58.115 40.909 0.00 0.00 0.00 2.71
42 43 3.558931 TCGCATATTCCTTCACCATGT 57.441 42.857 0.00 0.00 0.00 3.21
43 44 4.096231 TGTTTCGCATATTCCTTCACCATG 59.904 41.667 0.00 0.00 0.00 3.66
44 45 4.269183 TGTTTCGCATATTCCTTCACCAT 58.731 39.130 0.00 0.00 0.00 3.55
45 46 3.680490 TGTTTCGCATATTCCTTCACCA 58.320 40.909 0.00 0.00 0.00 4.17
46 47 4.695217 TTGTTTCGCATATTCCTTCACC 57.305 40.909 0.00 0.00 0.00 4.02
47 48 7.246674 TCTATTGTTTCGCATATTCCTTCAC 57.753 36.000 0.00 0.00 0.00 3.18
48 49 7.857734 TTCTATTGTTTCGCATATTCCTTCA 57.142 32.000 0.00 0.00 0.00 3.02
49 50 9.567848 TTTTTCTATTGTTTCGCATATTCCTTC 57.432 29.630 0.00 0.00 0.00 3.46
50 51 9.573133 CTTTTTCTATTGTTTCGCATATTCCTT 57.427 29.630 0.00 0.00 0.00 3.36
51 52 7.702348 GCTTTTTCTATTGTTTCGCATATTCCT 59.298 33.333 0.00 0.00 0.00 3.36
52 53 7.487829 TGCTTTTTCTATTGTTTCGCATATTCC 59.512 33.333 0.00 0.00 0.00 3.01
53 54 8.393395 TGCTTTTTCTATTGTTTCGCATATTC 57.607 30.769 0.00 0.00 0.00 1.75
54 55 8.755696 TTGCTTTTTCTATTGTTTCGCATATT 57.244 26.923 0.00 0.00 0.00 1.28
55 56 8.647226 GTTTGCTTTTTCTATTGTTTCGCATAT 58.353 29.630 0.00 0.00 0.00 1.78
56 57 7.649705 TGTTTGCTTTTTCTATTGTTTCGCATA 59.350 29.630 0.00 0.00 0.00 3.14
57 58 6.478344 TGTTTGCTTTTTCTATTGTTTCGCAT 59.522 30.769 0.00 0.00 0.00 4.73
58 59 5.807520 TGTTTGCTTTTTCTATTGTTTCGCA 59.192 32.000 0.00 0.00 0.00 5.10
59 60 6.267500 TGTTTGCTTTTTCTATTGTTTCGC 57.733 33.333 0.00 0.00 0.00 4.70
60 61 7.840489 ACATGTTTGCTTTTTCTATTGTTTCG 58.160 30.769 0.00 0.00 0.00 3.46
61 62 9.636965 GAACATGTTTGCTTTTTCTATTGTTTC 57.363 29.630 13.36 0.00 0.00 2.78
62 63 8.611757 GGAACATGTTTGCTTTTTCTATTGTTT 58.388 29.630 13.36 0.00 0.00 2.83
63 64 7.986889 AGGAACATGTTTGCTTTTTCTATTGTT 59.013 29.630 13.36 0.00 0.00 2.83
64 65 7.500141 AGGAACATGTTTGCTTTTTCTATTGT 58.500 30.769 13.36 0.00 0.00 2.71
65 66 7.116805 GGAGGAACATGTTTGCTTTTTCTATTG 59.883 37.037 13.36 0.00 0.00 1.90
66 67 7.154656 GGAGGAACATGTTTGCTTTTTCTATT 58.845 34.615 13.36 0.00 0.00 1.73
67 68 6.267471 TGGAGGAACATGTTTGCTTTTTCTAT 59.733 34.615 13.36 0.00 0.00 1.98
68 69 5.596361 TGGAGGAACATGTTTGCTTTTTCTA 59.404 36.000 13.36 0.00 0.00 2.10
69 70 4.405358 TGGAGGAACATGTTTGCTTTTTCT 59.595 37.500 13.36 0.00 0.00 2.52
70 71 4.507756 GTGGAGGAACATGTTTGCTTTTTC 59.492 41.667 13.36 0.00 0.00 2.29
71 72 4.081198 TGTGGAGGAACATGTTTGCTTTTT 60.081 37.500 13.36 0.00 0.00 1.94
72 73 3.450457 TGTGGAGGAACATGTTTGCTTTT 59.550 39.130 13.36 0.00 0.00 2.27
73 74 3.030291 TGTGGAGGAACATGTTTGCTTT 58.970 40.909 13.36 0.00 0.00 3.51
74 75 2.362077 GTGTGGAGGAACATGTTTGCTT 59.638 45.455 13.36 0.00 31.49 3.91
75 76 1.956477 GTGTGGAGGAACATGTTTGCT 59.044 47.619 13.36 7.13 31.49 3.91
76 77 1.680735 TGTGTGGAGGAACATGTTTGC 59.319 47.619 13.36 3.57 31.49 3.68
77 78 2.951642 AGTGTGTGGAGGAACATGTTTG 59.048 45.455 13.36 0.00 31.49 2.93
78 79 3.297134 AGTGTGTGGAGGAACATGTTT 57.703 42.857 13.36 0.00 31.49 2.83
79 80 3.214328 GAAGTGTGTGGAGGAACATGTT 58.786 45.455 11.78 11.78 31.49 2.71
80 81 2.172505 TGAAGTGTGTGGAGGAACATGT 59.827 45.455 0.00 0.00 31.49 3.21
81 82 2.549754 GTGAAGTGTGTGGAGGAACATG 59.450 50.000 0.00 0.00 31.49 3.21
82 83 2.172505 TGTGAAGTGTGTGGAGGAACAT 59.827 45.455 0.00 0.00 31.49 2.71
83 84 1.557371 TGTGAAGTGTGTGGAGGAACA 59.443 47.619 0.00 0.00 0.00 3.18
84 85 2.325583 TGTGAAGTGTGTGGAGGAAC 57.674 50.000 0.00 0.00 0.00 3.62
85 86 2.705658 AGATGTGAAGTGTGTGGAGGAA 59.294 45.455 0.00 0.00 0.00 3.36
86 87 2.300152 GAGATGTGAAGTGTGTGGAGGA 59.700 50.000 0.00 0.00 0.00 3.71
87 88 2.613977 GGAGATGTGAAGTGTGTGGAGG 60.614 54.545 0.00 0.00 0.00 4.30
88 89 2.613977 GGGAGATGTGAAGTGTGTGGAG 60.614 54.545 0.00 0.00 0.00 3.86
89 90 1.347707 GGGAGATGTGAAGTGTGTGGA 59.652 52.381 0.00 0.00 0.00 4.02
90 91 1.349026 AGGGAGATGTGAAGTGTGTGG 59.651 52.381 0.00 0.00 0.00 4.17
91 92 2.301296 AGAGGGAGATGTGAAGTGTGTG 59.699 50.000 0.00 0.00 0.00 3.82
92 93 2.564947 GAGAGGGAGATGTGAAGTGTGT 59.435 50.000 0.00 0.00 0.00 3.72
93 94 2.830923 AGAGAGGGAGATGTGAAGTGTG 59.169 50.000 0.00 0.00 0.00 3.82
94 95 3.096092 GAGAGAGGGAGATGTGAAGTGT 58.904 50.000 0.00 0.00 0.00 3.55
125 126 7.672983 TGAAGCCAAAAATTAAACACACAAA 57.327 28.000 0.00 0.00 0.00 2.83
126 127 7.672983 TTGAAGCCAAAAATTAAACACACAA 57.327 28.000 0.00 0.00 0.00 3.33
129 130 7.672983 TGTTTGAAGCCAAAAATTAAACACA 57.327 28.000 0.00 0.00 43.18 3.72
157 158 9.054922 CATTTTGTTCAAAATACATGACCCTTT 57.945 29.630 18.82 0.00 31.67 3.11
158 159 8.210265 ACATTTTGTTCAAAATACATGACCCTT 58.790 29.630 18.82 0.00 31.67 3.95
159 160 7.734942 ACATTTTGTTCAAAATACATGACCCT 58.265 30.769 18.82 0.00 31.67 4.34
160 161 7.872483 AGACATTTTGTTCAAAATACATGACCC 59.128 33.333 18.82 7.54 31.67 4.46
193 194 7.320399 ACAAAGAAGGAAGTCAAAACGATTTT 58.680 30.769 0.00 0.00 0.00 1.82
194 195 6.863275 ACAAAGAAGGAAGTCAAAACGATTT 58.137 32.000 0.00 0.00 0.00 2.17
199 200 7.410407 CGTCAAAACAAAGAAGGAAGTCAAAAC 60.410 37.037 0.00 0.00 0.00 2.43
215 216 8.694975 TTGATTCAAAGATTTCGTCAAAACAA 57.305 26.923 0.00 0.00 0.00 2.83
267 268 9.845740 AGTTAAGTTTGAAAAGGCCAAAAATAT 57.154 25.926 5.01 0.00 35.57 1.28
284 285 4.497507 GCAGCCAAGTTTCGAGTTAAGTTT 60.498 41.667 0.00 0.00 0.00 2.66
294 295 0.381801 AGTGTTGCAGCCAAGTTTCG 59.618 50.000 0.00 0.00 0.00 3.46
303 304 5.046910 ACATAATGTGTAAGTGTTGCAGC 57.953 39.130 0.00 0.00 39.91 5.25
337 338 6.381133 TGTGTGAGAGAGAGGCAATATTTCTA 59.619 38.462 0.00 0.00 0.00 2.10
347 348 1.960612 ACGTGTGTGAGAGAGAGGC 59.039 57.895 0.00 0.00 0.00 4.70
363 373 3.434319 GTGCATGCAGGACCCACG 61.434 66.667 23.41 0.00 31.47 4.94
375 385 2.495155 TGTACTGGAAGCATGTGCAT 57.505 45.000 7.83 0.00 45.16 3.96
388 398 5.562506 TGAAACTAGACTCGGATGTACTG 57.437 43.478 0.00 0.00 0.00 2.74
471 487 9.717892 GGTTTCAGATCCGTTTAGATTTTTATC 57.282 33.333 0.00 0.00 0.00 1.75
477 493 5.080969 TCGGTTTCAGATCCGTTTAGATT 57.919 39.130 12.38 0.00 45.88 2.40
485 956 0.249398 AGGGTTCGGTTTCAGATCCG 59.751 55.000 7.90 7.90 46.93 4.18
501 972 0.825840 TGGCCCGAACAGAAAAAGGG 60.826 55.000 0.00 0.00 44.72 3.95
600 1071 7.944729 AAGTTGGACTATATCTTTTGTGCAT 57.055 32.000 0.00 0.00 31.40 3.96
634 1105 5.435291 AGATGAAAAGGTAATGAGCCAGAG 58.565 41.667 0.00 0.00 0.00 3.35
635 1106 5.441718 AGATGAAAAGGTAATGAGCCAGA 57.558 39.130 0.00 0.00 0.00 3.86
728 4027 6.528537 ACTCTGCTGCCTATATTAGATGAG 57.471 41.667 0.00 0.00 0.00 2.90
780 4085 0.469070 ATGCAAGTTTTGGCTGCCAA 59.531 45.000 29.24 29.24 42.29 4.52
789 4094 6.233905 AGGTTTACTTGGAATGCAAGTTTT 57.766 33.333 24.25 3.49 42.25 2.43
827 4132 2.203938 AGAACGGGCCTCCTTCCA 60.204 61.111 0.84 0.00 0.00 3.53
932 4244 1.639298 GCAGCAAGGGTAGAACAGCG 61.639 60.000 0.00 0.00 0.00 5.18
937 4249 1.362224 AGGAAGCAGCAAGGGTAGAA 58.638 50.000 0.00 0.00 0.00 2.10
1055 4389 3.396570 GGGGTCGGTGGTAGGGTG 61.397 72.222 0.00 0.00 0.00 4.61
1443 4778 3.236618 AAAAACTGCTCGCGGCGAC 62.237 57.895 22.69 17.98 45.43 5.19
1565 4907 4.393062 ACAACTCATCAGAACCAAATAGCG 59.607 41.667 0.00 0.00 0.00 4.26
1581 4928 1.760613 AGGGAACAGACGAACAACTCA 59.239 47.619 0.00 0.00 0.00 3.41
1629 4979 6.641161 AATCTCCCCAAGCCAAAAATAAAT 57.359 33.333 0.00 0.00 0.00 1.40
1767 5117 0.620556 ACACCCACATCCCATCAGAC 59.379 55.000 0.00 0.00 0.00 3.51
1815 5176 1.305201 TCAGCGAGGGAACAAAACAC 58.695 50.000 0.00 0.00 0.00 3.32
1903 5281 1.006220 TCGTCGTTGCTCTGCACAT 60.006 52.632 0.00 0.00 38.71 3.21
2178 5583 1.918293 TTCATGTCTCCGGCCAGGT 60.918 57.895 2.24 0.00 41.99 4.00
2300 5710 2.233007 CTTGCTGCGGCGAGTTTCTC 62.233 60.000 24.58 0.00 43.20 2.87
2487 5905 0.908198 GGATGTGGAAGAGCTGGAGT 59.092 55.000 0.00 0.00 0.00 3.85
2528 6345 1.066908 AGCTAGCTGATCGAAGCAGAC 59.933 52.381 18.57 11.78 46.08 3.51
2617 6442 4.227538 CAGAAAGCATGCAGAAGAAACAG 58.772 43.478 21.98 0.00 0.00 3.16
2735 6560 0.181114 AGAAGTGGCAACTCACTGCA 59.819 50.000 0.00 0.00 46.17 4.41
2736 6561 0.590195 CAGAAGTGGCAACTCACTGC 59.410 55.000 13.13 3.61 46.17 4.40
2865 11732 1.795768 TCGACAGGAAAGCATCACAC 58.204 50.000 0.00 0.00 0.00 3.82
2886 11753 2.027024 GCTGACACCGTGACACGA 59.973 61.111 28.83 7.84 46.05 4.35
2889 11756 0.179059 AATGTGCTGACACCGTGACA 60.179 50.000 5.28 4.37 46.86 3.58
2890 11757 0.512952 GAATGTGCTGACACCGTGAC 59.487 55.000 5.28 0.00 46.86 3.67
2891 11758 0.392706 AGAATGTGCTGACACCGTGA 59.607 50.000 5.28 0.00 46.86 4.35
2892 11759 0.792640 GAGAATGTGCTGACACCGTG 59.207 55.000 0.00 0.00 46.86 4.94
2893 11760 0.392706 TGAGAATGTGCTGACACCGT 59.607 50.000 0.00 0.00 46.86 4.83
2894 11761 1.195448 GTTGAGAATGTGCTGACACCG 59.805 52.381 0.00 0.00 46.86 4.94
2895 11762 1.537202 GGTTGAGAATGTGCTGACACC 59.463 52.381 0.00 0.00 46.86 4.16
2960 14489 5.758296 ACATAACAAAGTACCACTGTCTGTG 59.242 40.000 2.97 2.97 45.80 3.66
2999 14533 3.786635 ACCAAACATAACTTGCGCAAAA 58.213 36.364 25.01 12.89 0.00 2.44
3004 14538 6.550843 TCATCAATACCAAACATAACTTGCG 58.449 36.000 0.00 0.00 0.00 4.85
3156 14693 8.734386 GGAAATGACAATGATGATAAGTATCCC 58.266 37.037 0.00 0.00 31.71 3.85
3333 14895 5.780984 TCTCTTGCTGCTACTGATATCATG 58.219 41.667 5.72 3.43 0.00 3.07
3354 14916 8.546083 AGAAATACTCCTCAAGTGACATATCT 57.454 34.615 0.00 0.00 39.11 1.98
3423 14991 7.066284 GCTGATTGCTCACCTTCTTAATTTCTA 59.934 37.037 0.00 0.00 38.95 2.10
3448 15016 4.691860 AGTTGATTACTGTTGCATCAGC 57.308 40.909 21.97 7.25 38.84 4.26


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

AutoCloner maintained by Alex Coulton.