Multiple sequence alignment - TraesCS4B01G150800

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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 TraesCS4B01G150800 chr4B 100.000 5884 0 0 1 5884 237913465 237907582 0.000000e+00 10866.0
1 TraesCS4B01G150800 chr4B 98.669 1953 25 1 2037 3989 663890994 663889043 0.000000e+00 3461.0
2 TraesCS4B01G150800 chr4B 99.213 127 1 0 5264 5390 581163208 581163082 4.590000e-56 230.0
3 TraesCS4B01G150800 chr4B 95.455 132 6 0 5259 5390 63765827 63765696 1.660000e-50 211.0
4 TraesCS4B01G150800 chr7A 98.976 1954 20 0 2037 3990 408096550 408098503 0.000000e+00 3498.0
5 TraesCS4B01G150800 chr7A 98.872 1951 22 0 2037 3987 646732 644782 0.000000e+00 3482.0
6 TraesCS4B01G150800 chr6B 98.977 1955 18 2 2037 3991 29925406 29927358 0.000000e+00 3498.0
7 TraesCS4B01G150800 chr6B 98.565 1951 27 1 2037 3987 708526869 708528818 0.000000e+00 3446.0
8 TraesCS4B01G150800 chr2B 98.769 1950 24 0 2037 3986 748158319 748160268 0.000000e+00 3469.0
9 TraesCS4B01G150800 chr2B 98.615 1950 26 1 2037 3986 68193601 68195549 0.000000e+00 3450.0
10 TraesCS4B01G150800 chr2B 97.674 129 3 0 5262 5390 297259666 297259538 7.670000e-54 222.0
11 TraesCS4B01G150800 chr7B 98.719 1952 24 1 2037 3988 739087793 739089743 0.000000e+00 3465.0
12 TraesCS4B01G150800 chr3B 98.617 1952 25 2 2037 3988 814764420 814762471 0.000000e+00 3454.0
13 TraesCS4B01G150800 chr4A 96.135 2044 69 8 1 2040 278349192 278347155 0.000000e+00 3328.0
14 TraesCS4B01G150800 chr4A 96.779 1273 40 1 3990 5262 278347169 278345898 0.000000e+00 2122.0
15 TraesCS4B01G150800 chr4A 96.610 59 1 1 5826 5884 278345862 278345805 4.850000e-16 97.1
16 TraesCS4B01G150800 chr4D 97.707 1701 34 3 343 2040 270652956 270654654 0.000000e+00 2920.0
17 TraesCS4B01G150800 chr4D 97.807 1277 28 0 3990 5266 270654640 270655916 0.000000e+00 2204.0
18 TraesCS4B01G150800 chr4D 96.368 468 11 4 5423 5884 270656364 270656831 0.000000e+00 765.0
19 TraesCS4B01G150800 chr5B 99.231 130 1 0 5261 5390 2581776 2581647 9.860000e-58 235.0
20 TraesCS4B01G150800 chr5B 96.269 134 5 0 5261 5394 599689052 599689185 2.760000e-53 220.0
21 TraesCS4B01G150800 chr5B 95.420 131 6 0 5260 5390 318403671 318403801 5.980000e-50 209.0
22 TraesCS4B01G150800 chr5B 91.176 68 6 0 428 495 98510599 98510666 6.280000e-15 93.5
23 TraesCS4B01G150800 chr1A 99.225 129 1 0 5264 5392 23442051 23442179 3.550000e-57 233.0
24 TraesCS4B01G150800 chr1B 99.219 128 1 0 5264 5391 62060382 62060255 1.280000e-56 231.0
25 TraesCS4B01G150800 chr1B 94.737 133 7 0 5259 5391 475478921 475479053 2.150000e-49 207.0


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 TraesCS4B01G150800 chr4B 237907582 237913465 5883 True 10866.000000 10866 100.000 1 5884 1 chr4B.!!$R2 5883
1 TraesCS4B01G150800 chr4B 663889043 663890994 1951 True 3461.000000 3461 98.669 2037 3989 1 chr4B.!!$R4 1952
2 TraesCS4B01G150800 chr7A 408096550 408098503 1953 False 3498.000000 3498 98.976 2037 3990 1 chr7A.!!$F1 1953
3 TraesCS4B01G150800 chr7A 644782 646732 1950 True 3482.000000 3482 98.872 2037 3987 1 chr7A.!!$R1 1950
4 TraesCS4B01G150800 chr6B 29925406 29927358 1952 False 3498.000000 3498 98.977 2037 3991 1 chr6B.!!$F1 1954
5 TraesCS4B01G150800 chr6B 708526869 708528818 1949 False 3446.000000 3446 98.565 2037 3987 1 chr6B.!!$F2 1950
6 TraesCS4B01G150800 chr2B 748158319 748160268 1949 False 3469.000000 3469 98.769 2037 3986 1 chr2B.!!$F2 1949
7 TraesCS4B01G150800 chr2B 68193601 68195549 1948 False 3450.000000 3450 98.615 2037 3986 1 chr2B.!!$F1 1949
8 TraesCS4B01G150800 chr7B 739087793 739089743 1950 False 3465.000000 3465 98.719 2037 3988 1 chr7B.!!$F1 1951
9 TraesCS4B01G150800 chr3B 814762471 814764420 1949 True 3454.000000 3454 98.617 2037 3988 1 chr3B.!!$R1 1951
10 TraesCS4B01G150800 chr4A 278345805 278349192 3387 True 1849.033333 3328 96.508 1 5884 3 chr4A.!!$R1 5883
11 TraesCS4B01G150800 chr4D 270652956 270656831 3875 False 1963.000000 2920 97.294 343 5884 3 chr4D.!!$F1 5541

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
239 240 0.912486 ATGCTGGGGAACTAGTGGTC 59.088 55.000 0.00 0.00 41.77 4.02 F
1228 1232 1.473257 GGGATGCATACGCTCAGAACA 60.473 52.381 1.96 0.00 39.64 3.18 F
2196 2200 0.243095 GTAGACGGCGGGATATCCAC 59.757 60.000 23.27 14.03 37.91 4.02 F
3180 3184 1.552337 GTCTTCTCACCCTGATCAGCA 59.448 52.381 17.76 0.00 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 1973 2.586792 CCCTAGCAGGACAGGCAC 59.413 66.667 4.00 0.00 37.67 5.01 R
2780 2784 2.060383 TGGCCTCCGTCTCAGATGG 61.060 63.158 6.58 6.58 39.89 3.51 R
3820 3824 1.142748 CACAACCGGCTGGCAAAAA 59.857 52.632 12.89 0.00 39.70 1.94 R
5107 5113 1.668826 AACCACCAGAGATTGCCCTA 58.331 50.000 0.00 0.00 0.00 3.53 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
67 68 3.256631 AGTGCAAAGGATGTTGATGGAAC 59.743 43.478 0.00 0.00 34.84 3.62
239 240 0.912486 ATGCTGGGGAACTAGTGGTC 59.088 55.000 0.00 0.00 41.77 4.02
289 290 2.171940 GCTGTGCGCTCGTTTCTG 59.828 61.111 9.73 0.00 35.14 3.02
292 293 2.171940 GTGCGCTCGTTTCTGCTG 59.828 61.111 9.73 0.00 0.00 4.41
370 371 3.305608 GCAAACCTTTCCTCAACTCCATG 60.306 47.826 0.00 0.00 0.00 3.66
459 462 4.655921 CCACGTGGCATAACCCAT 57.344 55.556 24.02 0.00 37.20 4.00
529 532 5.806654 ACAAAAATGGGAAATGCAGTACT 57.193 34.783 0.00 0.00 0.00 2.73
697 701 9.322773 GTTAGGGAACTGAATTACCATAACTAC 57.677 37.037 0.00 0.00 45.20 2.73
721 725 5.505173 ACATGACACCTGTTTTCTCTTTG 57.495 39.130 0.00 0.00 0.00 2.77
722 726 5.192927 ACATGACACCTGTTTTCTCTTTGA 58.807 37.500 0.00 0.00 0.00 2.69
929 933 4.100035 TGATCTTACTGCCGATGAAGTGAT 59.900 41.667 0.00 0.00 0.00 3.06
1228 1232 1.473257 GGGATGCATACGCTCAGAACA 60.473 52.381 1.96 0.00 39.64 3.18
1466 1470 2.489329 GTGTGCATTCAAGTGTAGGCAT 59.511 45.455 0.72 0.00 33.43 4.40
1618 1622 2.340337 GTGCATCAAGTTTTCCCATGC 58.660 47.619 0.00 0.00 40.29 4.06
1701 1705 7.282224 GCTACAGATTGTATGACACCCAATAAA 59.718 37.037 2.32 0.00 31.66 1.40
1703 1707 6.603201 ACAGATTGTATGACACCCAATAAAGG 59.397 38.462 2.32 0.00 0.00 3.11
1755 1759 5.174395 AGACTCACAGATTCTCCAAATTCG 58.826 41.667 0.00 0.00 0.00 3.34
1876 1880 2.559668 ACAGTTGGCCAGATTGATGTTG 59.440 45.455 17.06 5.44 0.00 3.33
1969 1973 6.648310 AGCTGATCAGTCATCCATATTAAACG 59.352 38.462 23.38 0.00 32.98 3.60
2028 2032 7.947890 TGGAAGAATAAAGAATACCAACCAAGT 59.052 33.333 0.00 0.00 0.00 3.16
2029 2033 8.244113 GGAAGAATAAAGAATACCAACCAAGTG 58.756 37.037 0.00 0.00 0.00 3.16
2030 2034 7.703058 AGAATAAAGAATACCAACCAAGTGG 57.297 36.000 0.00 0.00 44.92 4.00
2196 2200 0.243095 GTAGACGGCGGGATATCCAC 59.757 60.000 23.27 14.03 37.91 4.02
2676 2680 6.932947 AGCTTAAACGGAAGTATAGACTTGT 58.067 36.000 7.64 0.00 46.23 3.16
2780 2784 3.859745 GCAAGTGGCTTTTTAAGTTGC 57.140 42.857 0.00 0.00 40.25 4.17
2911 2915 8.250143 AGGGTTTGATGAGAGTTAAACAAATT 57.750 30.769 0.00 0.00 35.35 1.82
3066 3070 7.040062 TGCCTATGTTGCTACTGTTTTACAATT 60.040 33.333 0.00 0.00 0.00 2.32
3067 3071 7.812669 GCCTATGTTGCTACTGTTTTACAATTT 59.187 33.333 0.00 0.00 0.00 1.82
3180 3184 1.552337 GTCTTCTCACCCTGATCAGCA 59.448 52.381 17.76 0.00 0.00 4.41
3647 3651 6.255453 CCGATCAACAAACATTCACTTTTTGT 59.745 34.615 0.00 0.00 43.61 2.83
3820 3824 7.952930 AGGATAGACATGTAGTGATCCTATTGT 59.047 37.037 20.65 5.25 43.24 2.71
4075 4081 9.613428 TTTAGAAGCTATGTATGCTAATGTTGT 57.387 29.630 0.00 0.00 40.22 3.32
4364 4370 4.115516 CACAGACCATAGCTGTACATGAC 58.884 47.826 0.00 0.00 44.28 3.06
4456 4462 2.439156 AATCGGCTGCCCTGCTTC 60.439 61.111 14.12 0.00 0.00 3.86
4466 4472 3.285484 CTGCCCTGCTTCTGATGTTAAT 58.715 45.455 0.00 0.00 0.00 1.40
4510 4516 1.067060 GCCAGTTGACCAACCAAAGTC 59.933 52.381 9.07 0.00 42.06 3.01
4533 4539 8.859090 AGTCTCTTCTCTCTGATAATAATGTGG 58.141 37.037 0.00 0.00 0.00 4.17
4551 4557 5.682234 TGTGGACAGTGATTCAGTATCAT 57.318 39.130 0.00 0.00 44.75 2.45
4613 4619 2.949447 ACCACAAGCACCTCTTCATTT 58.051 42.857 0.00 0.00 31.27 2.32
4991 4997 6.367969 GGCTTGAAATATGCAATTCATCCATC 59.632 38.462 12.06 0.23 35.63 3.51
5107 5113 4.262635 CCTGAGATTCGGGTATGTGCTATT 60.263 45.833 0.00 0.00 38.13 1.73
5141 5147 5.311121 TCTGGTGGTTTTACAGGAAGGAATA 59.689 40.000 0.00 0.00 33.19 1.75
5271 5277 3.812053 GCAATGATGACACATACTCCCTC 59.188 47.826 0.00 0.00 0.00 4.30
5272 5278 4.384056 CAATGATGACACATACTCCCTCC 58.616 47.826 0.00 0.00 0.00 4.30
5273 5279 2.031870 TGATGACACATACTCCCTCCG 58.968 52.381 0.00 0.00 0.00 4.63
5275 5281 1.471119 TGACACATACTCCCTCCGTC 58.529 55.000 0.00 0.00 0.00 4.79
5277 5283 0.040646 ACACATACTCCCTCCGTCCA 59.959 55.000 0.00 0.00 0.00 4.02
5278 5284 0.747255 CACATACTCCCTCCGTCCAG 59.253 60.000 0.00 0.00 0.00 3.86
5279 5285 0.629596 ACATACTCCCTCCGTCCAGA 59.370 55.000 0.00 0.00 0.00 3.86
5280 5286 1.006758 ACATACTCCCTCCGTCCAGAA 59.993 52.381 0.00 0.00 0.00 3.02
5284 5290 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
5285 5291 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
5287 5293 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
5288 5294 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
5290 5296 3.056107 CCTCCGTCCAGAAATACTTGTCA 60.056 47.826 0.00 0.00 0.00 3.58
5291 5297 4.383118 CCTCCGTCCAGAAATACTTGTCAT 60.383 45.833 0.00 0.00 0.00 3.06
5292 5298 4.755411 TCCGTCCAGAAATACTTGTCATC 58.245 43.478 0.00 0.00 0.00 2.92
5293 5299 4.221924 TCCGTCCAGAAATACTTGTCATCA 59.778 41.667 0.00 0.00 0.00 3.07
5295 5301 5.411361 CCGTCCAGAAATACTTGTCATCAAA 59.589 40.000 0.00 0.00 32.87 2.69
5297 5303 7.362056 CCGTCCAGAAATACTTGTCATCAAAAT 60.362 37.037 0.00 0.00 32.87 1.82
5298 5304 7.482743 CGTCCAGAAATACTTGTCATCAAAATG 59.517 37.037 0.00 0.00 32.87 2.32
5299 5305 7.756722 GTCCAGAAATACTTGTCATCAAAATGG 59.243 37.037 0.00 0.00 33.42 3.16
5300 5306 7.669304 TCCAGAAATACTTGTCATCAAAATGGA 59.331 33.333 0.00 0.00 33.42 3.41
5301 5307 8.472413 CCAGAAATACTTGTCATCAAAATGGAT 58.528 33.333 0.00 0.00 33.42 3.41
5307 5313 7.636150 ACTTGTCATCAAAATGGATAGAAGG 57.364 36.000 0.00 0.00 33.42 3.46
5308 5314 6.604795 ACTTGTCATCAAAATGGATAGAAGGG 59.395 38.462 0.00 0.00 33.42 3.95
5309 5315 5.448654 TGTCATCAAAATGGATAGAAGGGG 58.551 41.667 0.00 0.00 33.42 4.79
5310 5316 5.193527 TGTCATCAAAATGGATAGAAGGGGA 59.806 40.000 0.00 0.00 33.42 4.81
5311 5317 6.126097 TGTCATCAAAATGGATAGAAGGGGAT 60.126 38.462 0.00 0.00 33.42 3.85
5312 5318 6.208204 GTCATCAAAATGGATAGAAGGGGATG 59.792 42.308 0.00 0.00 33.42 3.51
5313 5319 5.732331 TCAAAATGGATAGAAGGGGATGT 57.268 39.130 0.00 0.00 0.00 3.06
5314 5320 6.840090 TCAAAATGGATAGAAGGGGATGTA 57.160 37.500 0.00 0.00 0.00 2.29
5315 5321 7.406620 TCAAAATGGATAGAAGGGGATGTAT 57.593 36.000 0.00 0.00 0.00 2.29
5316 5322 7.461749 TCAAAATGGATAGAAGGGGATGTATC 58.538 38.462 0.00 0.00 0.00 2.24
5317 5323 7.295672 TCAAAATGGATAGAAGGGGATGTATCT 59.704 37.037 0.00 0.00 0.00 1.98
5318 5324 8.605947 CAAAATGGATAGAAGGGGATGTATCTA 58.394 37.037 0.00 0.00 0.00 1.98
5319 5325 7.986553 AATGGATAGAAGGGGATGTATCTAG 57.013 40.000 0.00 0.00 0.00 2.43
5320 5326 6.736561 TGGATAGAAGGGGATGTATCTAGA 57.263 41.667 0.00 0.00 0.00 2.43
5321 5327 7.304054 TGGATAGAAGGGGATGTATCTAGAT 57.696 40.000 10.73 10.73 0.00 1.98
5322 5328 7.128751 TGGATAGAAGGGGATGTATCTAGATG 58.871 42.308 15.79 0.00 0.00 2.90
5323 5329 6.041523 GGATAGAAGGGGATGTATCTAGATGC 59.958 46.154 15.79 14.54 0.00 3.91
5324 5330 4.756564 AGAAGGGGATGTATCTAGATGCA 58.243 43.478 23.38 23.38 37.79 3.96
5325 5331 5.348833 AGAAGGGGATGTATCTAGATGCAT 58.651 41.667 29.54 29.54 44.84 3.96
5326 5332 5.789575 AGAAGGGGATGTATCTAGATGCATT 59.210 40.000 29.66 18.35 42.77 3.56
5327 5333 6.274200 AGAAGGGGATGTATCTAGATGCATTT 59.726 38.462 29.66 21.84 42.77 2.32
5328 5334 6.460103 AGGGGATGTATCTAGATGCATTTT 57.540 37.500 29.66 14.70 42.77 1.82
5329 5335 7.574021 AGGGGATGTATCTAGATGCATTTTA 57.426 36.000 29.66 8.65 42.77 1.52
5330 5336 7.628234 AGGGGATGTATCTAGATGCATTTTAG 58.372 38.462 29.66 6.74 42.77 1.85
5331 5337 7.238514 AGGGGATGTATCTAGATGCATTTTAGT 59.761 37.037 29.66 13.41 42.77 2.24
5332 5338 7.885399 GGGGATGTATCTAGATGCATTTTAGTT 59.115 37.037 29.66 12.78 42.77 2.24
5333 5339 8.940952 GGGATGTATCTAGATGCATTTTAGTTC 58.059 37.037 29.66 18.97 42.77 3.01
5334 5340 9.717942 GGATGTATCTAGATGCATTTTAGTTCT 57.282 33.333 29.66 11.50 42.77 3.01
5376 5382 8.915871 ATCCATTTTGATGACAACTATTTTCG 57.084 30.769 0.00 0.00 35.63 3.46
5377 5383 7.312154 TCCATTTTGATGACAACTATTTTCGG 58.688 34.615 0.00 0.00 35.63 4.30
5378 5384 7.175816 TCCATTTTGATGACAACTATTTTCGGA 59.824 33.333 0.00 0.00 35.63 4.55
5379 5385 7.273381 CCATTTTGATGACAACTATTTTCGGAC 59.727 37.037 0.00 0.00 35.63 4.79
5380 5386 5.524511 TTGATGACAACTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
5381 5387 3.930229 TGATGACAACTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
5382 5388 3.663995 TGACAACTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
5383 5389 3.581755 TGACAACTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
5384 5390 2.928116 GACAACTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
5385 5391 2.277084 CAACTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5386 5392 1.856629 ACTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
5387 5393 1.755380 ACTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
5388 5394 1.755380 CTATTTTCGGACGGAGGGAGT 59.245 52.381 0.00 0.00 0.00 3.85
5389 5395 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
5390 5396 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
5391 5397 0.967380 TTTCGGACGGAGGGAGTACC 60.967 60.000 0.00 0.00 40.67 3.34
5392 5398 2.044650 CGGACGGAGGGAGTACCA 60.045 66.667 0.00 0.00 43.89 3.25
5393 5399 2.119655 CGGACGGAGGGAGTACCAG 61.120 68.421 0.00 0.00 43.89 4.00
5394 5400 2.424733 GGACGGAGGGAGTACCAGC 61.425 68.421 0.00 0.00 43.89 4.85
5395 5401 1.380112 GACGGAGGGAGTACCAGCT 60.380 63.158 0.00 0.00 43.89 4.24
5396 5402 0.106819 GACGGAGGGAGTACCAGCTA 60.107 60.000 0.00 0.00 43.89 3.32
5397 5403 0.556747 ACGGAGGGAGTACCAGCTAT 59.443 55.000 0.00 0.00 43.89 2.97
5422 5428 3.503748 GCTATTTGCTGGTCTGAACAACT 59.496 43.478 0.00 0.00 38.95 3.16
5474 5890 2.623535 CATGATTGCACCCAAATGTGG 58.376 47.619 0.00 0.00 45.53 4.17
5511 5927 7.996644 GGTAATTATTACTGATGGTGGAAGGAA 59.003 37.037 13.86 0.00 36.39 3.36
5593 6011 8.553459 AGAAGTGGTACTTATCAAGATGTTTG 57.447 34.615 0.00 0.00 38.80 2.93
5594 6012 8.375506 AGAAGTGGTACTTATCAAGATGTTTGA 58.624 33.333 0.00 0.00 38.80 2.69
5628 6046 8.535335 ACTCCATAGAAATATCGAATATGCAGT 58.465 33.333 0.00 0.00 0.00 4.40
5698 6116 6.408858 TTGCTCGTTTGATTAGATTCAGAC 57.591 37.500 0.00 0.00 0.00 3.51
5712 6130 4.394300 AGATTCAGACGCAGGAAGAAAATG 59.606 41.667 0.00 0.00 0.00 2.32
5748 6166 2.092968 TCTGGCGCCATAGTTTGAATCT 60.093 45.455 32.87 0.00 0.00 2.40
5758 6176 9.520204 CGCCATAGTTTGAATCTTGATTTATTT 57.480 29.630 0.00 0.00 0.00 1.40
5808 6230 7.557724 AGAGAAGGCCTATTAGTTACAGAAAC 58.442 38.462 5.16 0.00 38.46 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 1.550072 CCAAAAGGTGCCTTGGGTATG 59.450 52.381 4.00 0.38 38.77 2.39
140 141 7.280205 CACTTACCAAGAGTATATTCCAACACC 59.720 40.741 0.00 0.00 0.00 4.16
259 260 1.673923 CGCACAGCTTCATCTCAGGAA 60.674 52.381 0.00 0.00 0.00 3.36
459 462 1.302511 GGAAAGACTGGGCAAGCGA 60.303 57.895 0.00 0.00 0.00 4.93
594 598 5.496556 CCCCTCATAACTGTTACATGTGAA 58.503 41.667 9.11 0.00 0.00 3.18
697 701 3.393800 AGAGAAAACAGGTGTCATGTCG 58.606 45.455 0.00 0.00 0.00 4.35
929 933 5.070001 CACCAAGATTTTCTTCACCTGGTA 58.930 41.667 0.00 0.00 33.78 3.25
1203 1207 3.324846 TCTGAGCGTATGCATCCCTTAAT 59.675 43.478 10.11 0.00 46.23 1.40
1204 1208 2.698274 TCTGAGCGTATGCATCCCTTAA 59.302 45.455 10.11 0.00 46.23 1.85
1466 1470 3.652869 AGGAGTTCCAGGTTGATTGAAGA 59.347 43.478 0.28 0.00 38.89 2.87
1582 1586 9.287373 ACTTGATGCACCATTTGATTTTAATTT 57.713 25.926 0.00 0.00 0.00 1.82
1618 1622 9.787532 TTTTCTCTTGAAAATTACTGTTGACTG 57.212 29.630 0.49 0.00 44.39 3.51
1755 1759 9.922305 CCGTCTGACTTATTAAATTCATTCTTC 57.078 33.333 6.21 0.00 0.00 2.87
1876 1880 5.353678 CAGCAAGCCCTGATCTATTATTAGC 59.646 44.000 0.00 0.00 34.77 3.09
1969 1973 2.586792 CCCTAGCAGGACAGGCAC 59.413 66.667 4.00 0.00 37.67 5.01
2028 2032 8.258007 TGTGTGTTTGGAAATAATGTTAAACCA 58.742 29.630 0.00 0.00 0.00 3.67
2029 2033 8.649973 TGTGTGTTTGGAAATAATGTTAAACC 57.350 30.769 0.00 0.00 0.00 3.27
2031 2035 9.319143 CCTTGTGTGTTTGGAAATAATGTTAAA 57.681 29.630 0.00 0.00 0.00 1.52
2032 2036 7.928706 CCCTTGTGTGTTTGGAAATAATGTTAA 59.071 33.333 0.00 0.00 0.00 2.01
2033 2037 7.437748 CCCTTGTGTGTTTGGAAATAATGTTA 58.562 34.615 0.00 0.00 0.00 2.41
2034 2038 6.287525 CCCTTGTGTGTTTGGAAATAATGTT 58.712 36.000 0.00 0.00 0.00 2.71
2035 2039 5.221621 CCCCTTGTGTGTTTGGAAATAATGT 60.222 40.000 0.00 0.00 0.00 2.71
2676 2680 5.221722 GGTCTGCAGATAATATCCCACTTCA 60.222 44.000 21.47 0.00 0.00 3.02
2780 2784 2.060383 TGGCCTCCGTCTCAGATGG 61.060 63.158 6.58 6.58 39.89 3.51
3066 3070 6.889722 CCTAAAGTTGATATTGAGGGGAACAA 59.110 38.462 0.00 0.00 0.00 2.83
3067 3071 6.423182 CCTAAAGTTGATATTGAGGGGAACA 58.577 40.000 0.00 0.00 0.00 3.18
3180 3184 5.411669 CCGTTCTTAGTAAGTTTCCAATGCT 59.588 40.000 9.71 0.00 0.00 3.79
3356 3360 4.074259 GGACCTACCCAATTACGTTTTGT 58.926 43.478 0.00 0.00 0.00 2.83
3647 3651 1.760613 CGTGGCCCTGAAGATAACCTA 59.239 52.381 0.00 0.00 0.00 3.08
3820 3824 1.142748 CACAACCGGCTGGCAAAAA 59.857 52.632 12.89 0.00 39.70 1.94
3991 3997 5.461032 TTCCACATCCAATGTTAAACCAC 57.539 39.130 0.00 0.00 42.70 4.16
3992 3998 4.021544 GCTTCCACATCCAATGTTAAACCA 60.022 41.667 0.00 0.00 42.70 3.67
4063 4069 8.807948 ACTAATAGTTTCCACAACATTAGCAT 57.192 30.769 12.16 0.00 31.78 3.79
4075 4081 8.660295 TTCAGGAAGACTACTAATAGTTTCCA 57.340 34.615 18.51 2.47 43.00 3.53
4364 4370 3.728076 TTCCGAGAAGATGATAACCGG 57.272 47.619 0.00 0.00 37.08 5.28
4423 4429 5.123186 CAGCCGATTGGTTTTGTATCACTAA 59.877 40.000 0.00 0.00 37.67 2.24
4456 4462 7.720442 TCTGTCATCACTCCTATTAACATCAG 58.280 38.462 0.00 0.00 0.00 2.90
4466 4472 1.683385 CCGCATCTGTCATCACTCCTA 59.317 52.381 0.00 0.00 0.00 2.94
4510 4516 8.637099 TGTCCACATTATTATCAGAGAGAAGAG 58.363 37.037 0.00 0.00 0.00 2.85
4533 4539 8.114201 ATCACCACATGATACTGAATCACTGTC 61.114 40.741 0.00 0.00 46.80 3.51
4613 4619 7.117397 ACTGTATACTAGAAGACTTGGTAGCA 58.883 38.462 4.17 0.00 0.00 3.49
4941 4947 9.689501 CCATACCACCCTTCTTTTAAATAGTTA 57.310 33.333 0.00 0.00 0.00 2.24
5107 5113 1.668826 AACCACCAGAGATTGCCCTA 58.331 50.000 0.00 0.00 0.00 3.53
5141 5147 4.273148 CTACAGAAGGGTGTAGTTTGCT 57.727 45.455 3.34 0.00 43.39 3.91
5268 5274 3.056107 TGACAAGTATTTCTGGACGGAGG 60.056 47.826 0.00 0.00 0.00 4.30
5271 5277 4.503910 TGATGACAAGTATTTCTGGACGG 58.496 43.478 0.00 0.00 0.00 4.79
5272 5278 6.480524 TTTGATGACAAGTATTTCTGGACG 57.519 37.500 0.00 0.00 37.32 4.79
5273 5279 7.756722 CCATTTTGATGACAAGTATTTCTGGAC 59.243 37.037 0.00 0.00 37.32 4.02
5275 5281 7.829725 TCCATTTTGATGACAAGTATTTCTGG 58.170 34.615 0.00 0.00 37.32 3.86
5284 5290 6.040166 CCCCTTCTATCCATTTTGATGACAAG 59.960 42.308 0.00 0.00 37.32 3.16
5285 5291 5.893255 CCCCTTCTATCCATTTTGATGACAA 59.107 40.000 0.00 0.00 0.00 3.18
5287 5293 5.694995 TCCCCTTCTATCCATTTTGATGAC 58.305 41.667 0.00 0.00 0.00 3.06
5288 5294 5.992564 TCCCCTTCTATCCATTTTGATGA 57.007 39.130 0.00 0.00 0.00 2.92
5290 5296 6.285329 ACATCCCCTTCTATCCATTTTGAT 57.715 37.500 0.00 0.00 0.00 2.57
5291 5297 5.732331 ACATCCCCTTCTATCCATTTTGA 57.268 39.130 0.00 0.00 0.00 2.69
5292 5298 7.465116 AGATACATCCCCTTCTATCCATTTTG 58.535 38.462 0.00 0.00 0.00 2.44
5293 5299 7.654287 AGATACATCCCCTTCTATCCATTTT 57.346 36.000 0.00 0.00 0.00 1.82
5295 5301 7.723382 TCTAGATACATCCCCTTCTATCCATT 58.277 38.462 0.00 0.00 0.00 3.16
5297 5303 6.736561 TCTAGATACATCCCCTTCTATCCA 57.263 41.667 0.00 0.00 0.00 3.41
5298 5304 6.041523 GCATCTAGATACATCCCCTTCTATCC 59.958 46.154 4.54 0.00 0.00 2.59
5299 5305 6.609212 TGCATCTAGATACATCCCCTTCTATC 59.391 42.308 4.54 0.00 0.00 2.08
5300 5306 6.506661 TGCATCTAGATACATCCCCTTCTAT 58.493 40.000 4.54 0.00 0.00 1.98
5301 5307 5.903923 TGCATCTAGATACATCCCCTTCTA 58.096 41.667 4.54 0.00 0.00 2.10
5302 5308 4.756564 TGCATCTAGATACATCCCCTTCT 58.243 43.478 4.54 0.00 0.00 2.85
5303 5309 5.690464 ATGCATCTAGATACATCCCCTTC 57.310 43.478 12.00 0.00 0.00 3.46
5304 5310 6.460103 AAATGCATCTAGATACATCCCCTT 57.540 37.500 17.09 6.79 0.00 3.95
5305 5311 6.460103 AAAATGCATCTAGATACATCCCCT 57.540 37.500 17.09 1.19 0.00 4.79
5306 5312 7.398024 ACTAAAATGCATCTAGATACATCCCC 58.602 38.462 17.09 0.00 0.00 4.81
5307 5313 8.854614 AACTAAAATGCATCTAGATACATCCC 57.145 34.615 17.09 0.00 0.00 3.85
5308 5314 9.717942 AGAACTAAAATGCATCTAGATACATCC 57.282 33.333 17.09 3.81 0.00 3.51
5351 5357 7.975616 CCGAAAATAGTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 35.20 3.41
5352 5358 7.175816 TCCGAAAATAGTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 35.20 3.41
5353 5359 7.273381 GTCCGAAAATAGTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 35.20 3.16
5354 5360 7.007367 CGTCCGAAAATAGTTGTCATCAAAATG 59.993 37.037 0.00 0.00 35.20 2.32
5355 5361 7.021196 CGTCCGAAAATAGTTGTCATCAAAAT 58.979 34.615 0.00 0.00 35.20 1.82
5356 5362 6.367421 CGTCCGAAAATAGTTGTCATCAAAA 58.633 36.000 0.00 0.00 35.20 2.44
5357 5363 5.106869 CCGTCCGAAAATAGTTGTCATCAAA 60.107 40.000 0.00 0.00 35.20 2.69
5358 5364 4.390603 CCGTCCGAAAATAGTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
5359 5365 3.930229 CCGTCCGAAAATAGTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
5360 5366 4.178540 TCCGTCCGAAAATAGTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
5361 5367 4.181578 CTCCGTCCGAAAATAGTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
5362 5368 3.581755 CTCCGTCCGAAAATAGTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
5363 5369 2.928116 CCTCCGTCCGAAAATAGTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5364 5370 2.354403 CCCTCCGTCCGAAAATAGTTGT 60.354 50.000 0.00 0.00 0.00 3.32
5365 5371 2.093869 TCCCTCCGTCCGAAAATAGTTG 60.094 50.000 0.00 0.00 0.00 3.16
5366 5372 2.167900 CTCCCTCCGTCCGAAAATAGTT 59.832 50.000 0.00 0.00 0.00 2.24
5367 5373 1.755380 CTCCCTCCGTCCGAAAATAGT 59.245 52.381 0.00 0.00 0.00 2.12
5368 5374 1.755380 ACTCCCTCCGTCCGAAAATAG 59.245 52.381 0.00 0.00 0.00 1.73
5369 5375 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
5370 5376 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
5371 5377 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
5372 5378 0.967380 GGTACTCCCTCCGTCCGAAA 60.967 60.000 0.00 0.00 0.00 3.46
5373 5379 1.379044 GGTACTCCCTCCGTCCGAA 60.379 63.158 0.00 0.00 0.00 4.30
5374 5380 2.273449 GGTACTCCCTCCGTCCGA 59.727 66.667 0.00 0.00 0.00 4.55
5375 5381 2.044650 TGGTACTCCCTCCGTCCG 60.045 66.667 0.00 0.00 0.00 4.79
5376 5382 2.424733 GCTGGTACTCCCTCCGTCC 61.425 68.421 0.00 0.00 0.00 4.79
5377 5383 0.106819 TAGCTGGTACTCCCTCCGTC 60.107 60.000 0.00 0.00 0.00 4.79
5378 5384 0.556747 ATAGCTGGTACTCCCTCCGT 59.443 55.000 0.00 0.00 0.00 4.69
5379 5385 1.705873 AATAGCTGGTACTCCCTCCG 58.294 55.000 0.00 0.00 0.00 4.63
5380 5386 2.485657 GCAAATAGCTGGTACTCCCTCC 60.486 54.545 0.00 0.00 41.15 4.30
5381 5387 2.839975 GCAAATAGCTGGTACTCCCTC 58.160 52.381 0.00 0.00 41.15 4.30
5406 5412 2.023673 CCAAAGTTGTTCAGACCAGCA 58.976 47.619 0.00 0.00 0.00 4.41
5422 5428 0.482446 ACCCCTCACAGATTGCCAAA 59.518 50.000 0.00 0.00 0.00 3.28
5521 5939 7.447374 AAAACAACTTCGTCATATGATTCCA 57.553 32.000 9.02 0.00 0.00 3.53
5522 5940 7.807907 ACAAAAACAACTTCGTCATATGATTCC 59.192 33.333 9.02 0.00 0.00 3.01
5628 6046 6.268158 TGGTAAATCGTATGCCTATACCTTCA 59.732 38.462 0.00 0.00 36.60 3.02
5698 6116 4.201851 CCATCACTACATTTTCTTCCTGCG 60.202 45.833 0.00 0.00 0.00 5.18
5712 6130 0.755686 CCAGAGAGCCCCATCACTAC 59.244 60.000 0.00 0.00 0.00 2.73
5808 6230 2.223829 CCTGTACATCGGTAGAAGGCAG 60.224 54.545 0.00 0.00 31.33 4.85


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

AutoCloner maintained by Alex Coulton.