Multiple sequence alignment - TraesCS5D01G292900

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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 TraesCS5D01G292900 chr5D 100.000 5596 0 0 1 5596 390364663 390359068 0.000000e+00 10334.0
1 TraesCS5D01G292900 chr5D 92.248 129 8 2 227 355 3237447 3237573 1.240000e-41 182.0
2 TraesCS5D01G292900 chr5B 95.005 4144 144 34 778 4893 470406297 470402189 0.000000e+00 6447.0
3 TraesCS5D01G292900 chr5B 97.462 197 5 0 5058 5254 470401837 470401641 2.500000e-88 337.0
4 TraesCS5D01G292900 chr5B 96.111 180 4 3 5240 5417 470401252 470401074 1.970000e-74 291.0
5 TraesCS5D01G292900 chr5B 96.226 106 1 2 5420 5522 470401040 470400935 2.680000e-38 171.0
6 TraesCS5D01G292900 chr5B 100.000 36 0 0 4919 4954 470402184 470402149 3.620000e-07 67.6
7 TraesCS5D01G292900 chr5B 100.000 35 0 0 5562 5596 470400937 470400903 1.300000e-06 65.8
8 TraesCS5D01G292900 chr5A 87.533 3457 221 78 2 3383 493608725 493605404 0.000000e+00 3803.0
9 TraesCS5D01G292900 chr5A 93.346 1037 44 13 3988 5015 493604720 493603700 0.000000e+00 1509.0
10 TraesCS5D01G292900 chr5A 91.297 563 39 5 3410 3963 493605342 493604781 0.000000e+00 760.0
11 TraesCS5D01G292900 chr5A 96.284 296 9 1 4959 5254 493603716 493603423 8.430000e-133 484.0
12 TraesCS5D01G292900 chr5A 94.410 161 5 3 5241 5398 493603044 493602885 1.560000e-60 244.0
13 TraesCS5D01G292900 chr5A 94.958 119 1 1 5478 5596 493602292 493602179 1.240000e-41 182.0
14 TraesCS5D01G292900 chr6A 93.548 124 6 1 227 350 42486215 42486094 3.440000e-42 183.0
15 TraesCS5D01G292900 chr3D 93.548 124 6 2 227 350 8442074 8442195 3.440000e-42 183.0
16 TraesCS5D01G292900 chr2D 93.548 124 6 2 227 350 54128220 54128099 3.440000e-42 183.0
17 TraesCS5D01G292900 chr2D 90.909 55 5 0 4695 4749 587170208 587170154 2.160000e-09 75.0
18 TraesCS5D01G292900 chr6D 92.857 126 7 1 227 352 172723254 172723377 1.240000e-41 182.0
19 TraesCS5D01G292900 chr4D 92.857 126 7 1 227 352 334733591 334733714 1.240000e-41 182.0
20 TraesCS5D01G292900 chr1D 92.857 126 7 1 227 352 197452522 197452399 1.240000e-41 182.0
21 TraesCS5D01G292900 chr1D 92.857 126 7 1 227 352 253736337 253736460 1.240000e-41 182.0
22 TraesCS5D01G292900 chr1B 88.776 98 10 1 594 691 537320845 537320749 9.850000e-23 119.0
23 TraesCS5D01G292900 chr1B 77.778 171 23 8 4901 5065 80870593 80870754 2.150000e-14 91.6
24 TraesCS5D01G292900 chr1B 83.333 90 15 0 4976 5065 80734906 80734995 3.590000e-12 84.2
25 TraesCS5D01G292900 chr7D 83.636 110 15 3 584 691 101082526 101082634 3.570000e-17 100.0
26 TraesCS5D01G292900 chr2A 83.871 93 15 0 5074 5166 706767516 706767424 7.720000e-14 89.8
27 TraesCS5D01G292900 chr2A 93.750 48 3 0 4695 4742 722056686 722056639 7.780000e-09 73.1
28 TraesCS5D01G292900 chr2A 86.792 53 7 0 626 678 75142855 75142907 6.050000e-05 60.2
29 TraesCS5D01G292900 chrUn 79.688 128 21 5 594 718 281636011 281635886 2.780000e-13 87.9
30 TraesCS5D01G292900 chrUn 79.688 128 21 5 594 718 281642885 281642760 2.780000e-13 87.9
31 TraesCS5D01G292900 chrUn 79.688 128 21 5 594 718 312315869 312315744 2.780000e-13 87.9
32 TraesCS5D01G292900 chrUn 76.163 172 24 10 4901 5065 406003139 406003300 2.160000e-09 75.0
33 TraesCS5D01G292900 chr1A 82.418 91 16 0 4975 5065 124822 124732 4.650000e-11 80.5
34 TraesCS5D01G292900 chr1A 81.319 91 17 0 4975 5065 186636 186546 2.160000e-09 75.0
35 TraesCS5D01G292900 chr1A 82.143 84 15 0 4982 5065 341130 341047 7.780000e-09 73.1
36 TraesCS5D01G292900 chr2B 88.136 59 5 1 4689 4745 708990093 708990035 1.010000e-07 69.4


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 TraesCS5D01G292900 chr5D 390359068 390364663 5595 True 10334.000000 10334 100.000000 1 5596 1 chr5D.!!$R1 5595
1 TraesCS5D01G292900 chr5B 470400903 470406297 5394 True 1229.900000 6447 97.467333 778 5596 6 chr5B.!!$R1 4818
2 TraesCS5D01G292900 chr5A 493602179 493608725 6546 True 1163.666667 3803 92.971333 2 5596 6 chr5A.!!$R1 5594

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
374 378 1.202143 GGTATGCGCCAAGTGCTTAAC 60.202 52.381 4.18 0.0 40.03 2.01 F
1388 1427 0.035820 GTGGTGCGGTAGGGATTTGA 60.036 55.000 0.00 0.0 0.00 2.69 F
2141 2204 0.442310 CACAACCAATCGTGCCGTAG 59.558 55.000 0.00 0.0 0.00 3.51 F
2388 2458 0.035056 GGCACACATTAGCAGGTCCT 60.035 55.000 0.00 0.0 0.00 3.85 F
3875 3995 1.270414 ACAGTGCTCAGGGATCAGGG 61.270 60.000 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2051 0.953727 TTCACATCAACCAGCAGCAC 59.046 50.0 0.00 0.0 0.00 4.40 R
2362 2432 2.420022 CTGCTAATGTGTGCCTACAACC 59.580 50.0 0.00 0.0 38.82 3.77 R
4021 4176 1.016627 ATTCATCAATGGGACGTGCG 58.983 50.0 0.00 0.0 0.00 5.34 R
4304 4462 0.321298 GCCTCGTCCCAGCTTTGTTA 60.321 55.0 0.00 0.0 0.00 2.41 R
5417 6512 0.744874 ACCACGAGTACGATGGGATG 59.255 55.0 14.99 0.0 41.37 3.51 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
244 248 8.873215 AAAGAATATGAACTACTCCACATACG 57.127 34.615 0.00 0.00 0.00 3.06
292 296 4.943705 TGTAGATTCACTCATTTTGCTCCC 59.056 41.667 0.00 0.00 0.00 4.30
294 298 5.441718 AGATTCACTCATTTTGCTCCCTA 57.558 39.130 0.00 0.00 0.00 3.53
295 299 6.011122 AGATTCACTCATTTTGCTCCCTAT 57.989 37.500 0.00 0.00 0.00 2.57
296 300 5.826737 AGATTCACTCATTTTGCTCCCTATG 59.173 40.000 0.00 0.00 0.00 2.23
298 302 5.692115 TCACTCATTTTGCTCCCTATGTA 57.308 39.130 0.00 0.00 0.00 2.29
300 304 5.189736 TCACTCATTTTGCTCCCTATGTAGT 59.810 40.000 0.00 0.00 0.00 2.73
301 305 5.525378 CACTCATTTTGCTCCCTATGTAGTC 59.475 44.000 0.00 0.00 0.00 2.59
302 306 5.189736 ACTCATTTTGCTCCCTATGTAGTCA 59.810 40.000 0.00 0.00 0.00 3.41
303 307 6.126652 ACTCATTTTGCTCCCTATGTAGTCAT 60.127 38.462 0.00 0.00 38.00 3.06
304 308 6.662755 TCATTTTGCTCCCTATGTAGTCATT 58.337 36.000 0.00 0.00 35.70 2.57
305 309 7.118723 TCATTTTGCTCCCTATGTAGTCATTT 58.881 34.615 0.00 0.00 35.70 2.32
306 310 8.271458 TCATTTTGCTCCCTATGTAGTCATTTA 58.729 33.333 0.00 0.00 35.70 1.40
361 365 4.213694 ACGAAGAGAGTACATAGGTATGCG 59.786 45.833 0.00 0.00 37.19 4.73
374 378 1.202143 GGTATGCGCCAAGTGCTTAAC 60.202 52.381 4.18 0.00 40.03 2.01
445 449 3.834489 ATGACTCACATCCATGGACTC 57.166 47.619 18.99 5.59 33.46 3.36
451 455 5.862845 ACTCACATCCATGGACTCATTATC 58.137 41.667 18.99 0.00 0.00 1.75
466 470 5.305386 ACTCATTATCTGGCAGCTACATGTA 59.695 40.000 10.34 5.25 0.00 2.29
469 473 7.906327 TCATTATCTGGCAGCTACATGTATAA 58.094 34.615 10.34 6.55 0.00 0.98
471 475 4.607293 TCTGGCAGCTACATGTATAAGG 57.393 45.455 10.34 0.00 0.00 2.69
472 476 3.967326 TCTGGCAGCTACATGTATAAGGT 59.033 43.478 10.34 0.00 0.00 3.50
474 478 5.600898 TCTGGCAGCTACATGTATAAGGTAA 59.399 40.000 10.34 0.00 0.00 2.85
475 479 6.270000 TCTGGCAGCTACATGTATAAGGTAAT 59.730 38.462 10.34 0.00 0.00 1.89
476 480 6.230472 TGGCAGCTACATGTATAAGGTAATG 58.770 40.000 5.91 0.00 0.00 1.90
477 481 5.122396 GGCAGCTACATGTATAAGGTAATGC 59.878 44.000 5.91 3.01 32.92 3.56
478 482 5.700832 GCAGCTACATGTATAAGGTAATGCA 59.299 40.000 5.91 0.00 33.45 3.96
479 483 6.204688 GCAGCTACATGTATAAGGTAATGCAA 59.795 38.462 5.91 0.00 33.45 4.08
480 484 7.255104 GCAGCTACATGTATAAGGTAATGCAAA 60.255 37.037 5.91 0.00 33.45 3.68
481 485 8.620416 CAGCTACATGTATAAGGTAATGCAAAA 58.380 33.333 5.91 0.00 0.00 2.44
541 545 9.592720 GACATGGTTGCATTGTTTTAAAAATAC 57.407 29.630 1.31 0.00 0.00 1.89
607 611 9.877137 GGCTTACATTTTTCAATTTTGGTAAAG 57.123 29.630 0.00 0.00 0.00 1.85
616 620 9.995003 TTTTCAATTTTGGTAAAGCACATCTAT 57.005 25.926 0.00 0.00 0.00 1.98
684 688 2.603110 CGTGAAGATTCGTGTGGGTATG 59.397 50.000 0.00 0.00 0.00 2.39
689 693 5.533154 TGAAGATTCGTGTGGGTATGTTTTT 59.467 36.000 0.00 0.00 0.00 1.94
721 725 5.648178 TTAAGTCACTAAGATGTGCCGTA 57.352 39.130 0.00 0.00 37.81 4.02
728 732 4.095932 CACTAAGATGTGCCGTAGACTACA 59.904 45.833 12.99 0.00 0.00 2.74
761 765 6.408107 AGGAAGGAGAAACTATCGGATTAC 57.592 41.667 0.00 0.00 0.00 1.89
764 768 7.728981 AGGAAGGAGAAACTATCGGATTACATA 59.271 37.037 0.00 0.00 0.00 2.29
766 770 9.194271 GAAGGAGAAACTATCGGATTACATAAC 57.806 37.037 0.00 0.00 0.00 1.89
768 772 8.142551 AGGAGAAACTATCGGATTACATAACAC 58.857 37.037 0.00 0.00 0.00 3.32
769 773 7.924412 GGAGAAACTATCGGATTACATAACACA 59.076 37.037 0.00 0.00 0.00 3.72
770 774 8.644318 AGAAACTATCGGATTACATAACACAC 57.356 34.615 0.00 0.00 0.00 3.82
771 775 7.434307 AGAAACTATCGGATTACATAACACACG 59.566 37.037 0.00 0.00 0.00 4.49
773 777 6.436261 ACTATCGGATTACATAACACACGAG 58.564 40.000 0.00 0.00 32.38 4.18
776 780 5.712004 TCGGATTACATAACACACGAGAAA 58.288 37.500 0.00 0.00 0.00 2.52
939 959 4.393062 GCCACGAAGAAATCTGATCAAAGA 59.607 41.667 0.00 0.00 0.00 2.52
1161 1186 0.744281 TCTCCGCGCATCTCATAACA 59.256 50.000 8.75 0.00 0.00 2.41
1171 1210 3.873801 GCATCTCATAACAGGTTGGTGGT 60.874 47.826 0.00 0.00 0.00 4.16
1302 1341 2.271173 CTGTAAGTTCCCCCGCCC 59.729 66.667 0.00 0.00 0.00 6.13
1350 1389 1.551019 GGGACTAGGGTTTGTCGGCT 61.551 60.000 0.00 0.00 34.31 5.52
1377 1416 4.624364 TGTGGCTCTGTGGTGCGG 62.624 66.667 0.00 0.00 33.30 5.69
1388 1427 0.035820 GTGGTGCGGTAGGGATTTGA 60.036 55.000 0.00 0.00 0.00 2.69
1438 1477 1.880027 GCCTCACTTCGTTGATTTGGT 59.120 47.619 0.00 0.00 0.00 3.67
1451 1490 3.917300 TGATTTGGTTAGGGTTTGGTGT 58.083 40.909 0.00 0.00 0.00 4.16
1478 1518 2.356741 GGTCTCGGATTGAATTTGGGGA 60.357 50.000 0.00 0.00 0.00 4.81
1592 1650 4.931002 ACATAAACATGAAACATGCCTTGC 59.069 37.500 0.00 0.00 0.00 4.01
1694 1752 4.375313 AGTAGAGGATTGGTTTGGGAGAT 58.625 43.478 0.00 0.00 0.00 2.75
1706 1764 6.552008 TGGTTTGGGAGATAGAAAGATGTTT 58.448 36.000 0.00 0.00 0.00 2.83
1798 1859 1.607628 GCTTCTATGCTGGCATTCAGG 59.392 52.381 13.39 2.93 43.54 3.86
1885 1946 2.314122 GTCTGTCGTAACGTCTGTTCC 58.686 52.381 0.00 0.00 39.54 3.62
1894 1955 3.314541 AACGTCTGTTCCTACCATGAC 57.685 47.619 0.00 0.00 30.83 3.06
1997 2059 2.253452 GTTTGCTCCGTGCTGCTG 59.747 61.111 0.00 0.00 43.37 4.41
2018 2081 7.613585 TGCTGGTTGATGTGAAAATTGATAAT 58.386 30.769 0.00 0.00 0.00 1.28
2054 2117 1.405821 CACCGTCTGGAGTAGGACATC 59.594 57.143 0.00 0.00 39.21 3.06
2077 2140 9.093970 CATCTAACACAAAATGATGCAATGAAT 57.906 29.630 0.00 0.00 0.00 2.57
2078 2141 8.692110 TCTAACACAAAATGATGCAATGAATC 57.308 30.769 0.00 0.00 0.00 2.52
2079 2142 8.305317 TCTAACACAAAATGATGCAATGAATCA 58.695 29.630 6.34 6.34 38.37 2.57
2084 2147 8.611757 CACAAAATGATGCAATGAATCAATGAT 58.388 29.630 8.15 0.00 37.58 2.45
2119 2182 9.075678 AGATGTCTTCATTTGATTGAGAGTTTT 57.924 29.630 0.00 0.00 34.06 2.43
2132 2195 8.514594 TGATTGAGAGTTTTATCACAACCAATC 58.485 33.333 0.00 0.00 37.63 2.67
2141 2204 0.442310 CACAACCAATCGTGCCGTAG 59.558 55.000 0.00 0.00 0.00 3.51
2152 2215 1.924524 CGTGCCGTAGTTATGTTCCAG 59.075 52.381 0.00 0.00 0.00 3.86
2276 2342 4.131596 TGCTTAATGTTAGGCGGTAATCC 58.868 43.478 3.01 0.00 38.44 3.01
2362 2432 5.437289 TGAGTGAAAGCAAATGTTGTAGG 57.563 39.130 0.00 0.00 0.00 3.18
2388 2458 0.035056 GGCACACATTAGCAGGTCCT 60.035 55.000 0.00 0.00 0.00 3.85
2912 2989 3.857549 TCTTCATCTCAGTTCCAGACG 57.142 47.619 0.00 0.00 0.00 4.18
2933 3010 2.736670 AAACCCAGAACAACTGCTCT 57.263 45.000 0.00 0.00 44.52 4.09
3062 3139 5.762711 TGCTGAAAATCAGTACACTGCTTAA 59.237 36.000 8.97 0.00 45.94 1.85
3268 3345 7.799784 TGTTTACCGTAGATTTTAGCAACTTC 58.200 34.615 0.00 0.00 0.00 3.01
3361 3438 3.330198 TCCTATCCATTGCCTCCTCAAT 58.670 45.455 0.00 0.00 37.16 2.57
3404 3516 5.123227 TCCTTGGCAATGTAGTACTAATGC 58.877 41.667 20.33 20.33 0.00 3.56
3467 3584 7.099120 AGAAATGGTATTTCATTGCCACTTTC 58.901 34.615 14.56 0.00 37.42 2.62
3480 3597 3.585289 TGCCACTTTCTACACCTGGAATA 59.415 43.478 0.00 0.00 0.00 1.75
3672 3792 3.576982 CTCCAACACCCTGTACTACAAGA 59.423 47.826 0.00 0.00 0.00 3.02
3747 3867 3.479489 ACCGACTTCCGTATTTGGTTTT 58.521 40.909 0.00 0.00 36.31 2.43
3748 3868 3.251487 ACCGACTTCCGTATTTGGTTTTG 59.749 43.478 0.00 0.00 36.31 2.44
3781 3901 3.462483 TCCTGTTTAGCGTGTTCTGAA 57.538 42.857 0.00 0.00 0.00 3.02
3783 3903 3.131396 CCTGTTTAGCGTGTTCTGAACT 58.869 45.455 20.18 3.92 34.73 3.01
3789 3909 6.259167 TGTTTAGCGTGTTCTGAACTTGTATT 59.741 34.615 20.18 5.40 34.73 1.89
3821 3941 3.108376 AGGGAAAGGATGTGTCTACTCC 58.892 50.000 0.00 0.00 0.00 3.85
3845 3965 2.575735 TGATGCTGTTGGGTCCTATGAA 59.424 45.455 0.00 0.00 0.00 2.57
3875 3995 1.270414 ACAGTGCTCAGGGATCAGGG 61.270 60.000 0.00 0.00 0.00 4.45
3969 4103 9.952188 GAGTAAGCCCTCACATTTTTATATTTC 57.048 33.333 0.00 0.00 0.00 2.17
4008 4163 5.718146 TCACAGATCTCTTGCTGACTAAAG 58.282 41.667 0.00 0.00 36.07 1.85
4021 4176 6.381465 GCTGACTAAAGCAAGCAAATTTAC 57.619 37.500 0.00 0.00 43.01 2.01
4067 4222 7.445945 GTGATTATAATAGTGCCTCAGAGGTT 58.554 38.462 18.37 6.42 37.80 3.50
4068 4223 7.600752 GTGATTATAATAGTGCCTCAGAGGTTC 59.399 40.741 18.37 11.03 37.80 3.62
4085 4243 7.124448 TCAGAGGTTCCTAAGAATCTTCCTTAC 59.876 40.741 0.00 0.00 43.75 2.34
4091 4249 9.886132 GTTCCTAAGAATCTTCCTTACAATGTA 57.114 33.333 0.00 0.00 33.67 2.29
4230 4388 4.067896 AGAGATCATCGTTTGTTGCTGTT 58.932 39.130 0.00 0.00 0.00 3.16
4263 4421 4.184629 CCACTGTACTAATCTGCTGAACC 58.815 47.826 0.00 0.00 0.00 3.62
4265 4423 5.127194 CCACTGTACTAATCTGCTGAACCTA 59.873 44.000 0.00 0.00 0.00 3.08
4304 4462 5.491982 GACAAGGTGGAGATTGTAGTCATT 58.508 41.667 0.00 0.00 39.66 2.57
4319 4477 3.074412 AGTCATTAACAAAGCTGGGACG 58.926 45.455 0.00 0.00 0.00 4.79
4428 4586 4.502282 CAGAGCTGCTACTTGATAGAAACG 59.498 45.833 0.15 0.00 31.83 3.60
4769 4930 1.283029 CCAATCTGATGGGTGGTGAGT 59.717 52.381 2.65 0.00 36.79 3.41
4770 4931 2.291153 CCAATCTGATGGGTGGTGAGTT 60.291 50.000 2.65 0.00 36.79 3.01
4771 4932 3.424703 CAATCTGATGGGTGGTGAGTTT 58.575 45.455 0.00 0.00 0.00 2.66
4808 4969 4.962836 ACCGGTGGAGGTCGTCGT 62.963 66.667 6.12 0.00 41.46 4.34
4809 4970 4.112341 CCGGTGGAGGTCGTCGTC 62.112 72.222 0.00 0.00 0.00 4.20
4810 4971 4.456253 CGGTGGAGGTCGTCGTCG 62.456 72.222 0.00 0.00 38.55 5.12
4905 5069 1.754803 TGCCTAGTCCTAATCACACCG 59.245 52.381 0.00 0.00 0.00 4.94
4955 5119 5.174943 GCGAAACAGGGTTCTTTTATGTTTG 59.825 40.000 6.36 1.72 42.44 2.93
4956 5120 6.270064 CGAAACAGGGTTCTTTTATGTTTGT 58.730 36.000 6.36 0.00 42.44 2.83
4980 5175 3.184541 CGTTAGACATACAAGGTTCGGG 58.815 50.000 0.00 0.00 0.00 5.14
4985 5180 1.337447 ACATACAAGGTTCGGGTGTCG 60.337 52.381 0.00 0.00 40.90 4.35
5210 5599 0.111639 TTAGGCTTTGGGGTGTCACC 59.888 55.000 14.13 14.13 37.60 4.02
5298 6091 1.464997 GAGAAACACCAATGAGACCGC 59.535 52.381 0.00 0.00 0.00 5.68
5322 6118 0.460811 TCTATCGTGCTGCAAGGCTG 60.461 55.000 15.31 6.11 0.00 4.85
5417 6512 0.237498 CTCGCCACCGAAAGAAAACC 59.763 55.000 0.00 0.00 43.87 3.27
5459 6585 1.619669 ATCCAGTGAACCCCCTCCC 60.620 63.158 0.00 0.00 0.00 4.30
5519 6828 2.540265 ACTCGGGCATGAGATCAATC 57.460 50.000 12.27 0.00 39.35 2.67
5520 6829 1.764723 ACTCGGGCATGAGATCAATCA 59.235 47.619 12.27 0.00 39.35 2.57
5521 6830 2.171237 ACTCGGGCATGAGATCAATCAA 59.829 45.455 12.27 0.00 39.35 2.57
5544 6853 2.874086 TCAATAGAGCACGCCATGAATG 59.126 45.455 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.951642 TCTTTTGACAAGGCTTCCACAG 59.048 45.455 0.00 0.00 0.00 3.66
178 180 8.250143 ACATCCTTTTAACTGAGGTTCATTTT 57.750 30.769 0.00 0.00 36.92 1.82
221 225 6.776116 TCCGTATGTGGAGTAGTTCATATTCT 59.224 38.462 0.00 0.00 33.05 2.40
222 226 6.978338 TCCGTATGTGGAGTAGTTCATATTC 58.022 40.000 0.00 0.00 33.05 1.75
314 318 8.879759 CGTGCCTAAATATTTGTCTTTCTAGAA 58.120 33.333 11.05 0.00 30.65 2.10
324 328 6.407202 ACTCTCTTCGTGCCTAAATATTTGT 58.593 36.000 11.05 0.00 0.00 2.83
374 378 6.878923 TCTGTTGTTAAGGATAATCCAGTGTG 59.121 38.462 0.00 0.00 39.61 3.82
445 449 7.279536 CCTTATACATGTAGCTGCCAGATAATG 59.720 40.741 11.91 3.51 0.00 1.90
451 455 4.342862 ACCTTATACATGTAGCTGCCAG 57.657 45.455 11.91 0.00 0.00 4.85
493 497 3.501062 CACATCTGCAAGTGTGAGTCATT 59.499 43.478 20.72 0.00 43.73 2.57
558 562 5.997746 CCGATGCTATCCTCATTTCCTAAAA 59.002 40.000 0.00 0.00 0.00 1.52
577 581 7.095271 ACCAAAATTGAAAAATGTAAGCCGATG 60.095 33.333 0.00 0.00 0.00 3.84
580 584 6.538189 ACCAAAATTGAAAAATGTAAGCCG 57.462 33.333 0.00 0.00 0.00 5.52
649 653 7.332430 ACGAATCTTCACGTAAAATCAATGGTA 59.668 33.333 0.00 0.00 40.92 3.25
650 654 6.148811 ACGAATCTTCACGTAAAATCAATGGT 59.851 34.615 0.00 0.00 40.92 3.55
659 663 3.061322 CCCACACGAATCTTCACGTAAA 58.939 45.455 0.00 0.00 40.76 2.01
689 693 9.890629 ACATCTTAGTGACTTAATTAGCATCAA 57.109 29.630 0.00 0.00 0.00 2.57
690 694 9.317936 CACATCTTAGTGACTTAATTAGCATCA 57.682 33.333 0.00 0.00 42.05 3.07
692 696 7.227512 GGCACATCTTAGTGACTTAATTAGCAT 59.772 37.037 0.00 0.00 44.26 3.79
707 711 4.895224 TGTAGTCTACGGCACATCTTAG 57.105 45.455 5.55 0.00 0.00 2.18
736 740 5.538849 ATCCGATAGTTTCTCCTTCCTTC 57.461 43.478 0.00 0.00 0.00 3.46
776 780 6.016108 TCCCCGACAGAAAATATTTCGTTTTT 60.016 34.615 0.10 0.00 0.00 1.94
939 959 0.832135 TGTGTCTCGCTTCCTTCCCT 60.832 55.000 0.00 0.00 0.00 4.20
1109 1129 3.787001 GACGAAGGGCCAGAGGGG 61.787 72.222 6.18 0.00 40.85 4.79
1161 1186 1.455587 CCTGCACAACCACCAACCT 60.456 57.895 0.00 0.00 0.00 3.50
1377 1416 4.887655 CCACCAAGGTATTCAAATCCCTAC 59.112 45.833 0.00 0.00 0.00 3.18
1388 1427 1.831736 CGACCTCTCCACCAAGGTATT 59.168 52.381 0.00 0.00 45.93 1.89
1438 1477 2.245287 ACCTCCAAACACCAAACCCTAA 59.755 45.455 0.00 0.00 0.00 2.69
1451 1490 4.301072 AATTCAATCCGAGACCTCCAAA 57.699 40.909 0.00 0.00 0.00 3.28
1478 1518 6.445357 AACTCATGAACGTTTAGGTGTTTT 57.555 33.333 16.15 0.24 0.00 2.43
1550 1608 4.920640 TGTCGTCTCTCCATAGAAATCC 57.079 45.455 0.00 0.00 0.00 3.01
1592 1650 4.969484 AGTGAGGGTACACAAACTAAAGG 58.031 43.478 0.00 0.00 42.45 3.11
1798 1859 8.709386 TTGAGATAAAGCTCATTGTAGACTTC 57.291 34.615 0.00 0.00 43.84 3.01
1885 1946 5.707298 AGAACCAAATTGTCTGTCATGGTAG 59.293 40.000 0.00 0.00 36.34 3.18
1894 1955 8.764287 GGAACAAAAATAGAACCAAATTGTCTG 58.236 33.333 0.00 0.00 0.00 3.51
1989 2051 0.953727 TTCACATCAACCAGCAGCAC 59.046 50.000 0.00 0.00 0.00 4.40
1997 2059 9.807649 AGCTTATTATCAATTTTCACATCAACC 57.192 29.630 0.00 0.00 0.00 3.77
2018 2081 4.060205 GACGGTGTAAACCAGAAAGCTTA 58.940 43.478 0.00 0.00 0.00 3.09
2027 2090 1.416243 ACTCCAGACGGTGTAAACCA 58.584 50.000 2.20 0.00 37.24 3.67
2054 2117 8.468720 TGATTCATTGCATCATTTTGTGTTAG 57.531 30.769 0.00 0.00 0.00 2.34
2077 2140 7.717875 TGAAGACATCTATTGCATCATCATTGA 59.282 33.333 0.00 0.00 36.00 2.57
2078 2141 7.871853 TGAAGACATCTATTGCATCATCATTG 58.128 34.615 0.00 0.00 0.00 2.82
2079 2142 8.637196 ATGAAGACATCTATTGCATCATCATT 57.363 30.769 0.00 0.00 29.98 2.57
2084 2147 7.868906 TCAAATGAAGACATCTATTGCATCA 57.131 32.000 0.00 0.00 35.50 3.07
2141 2204 3.127030 GCAAGGCTGTACTGGAACATAAC 59.873 47.826 1.65 0.00 38.20 1.89
2152 2215 3.941483 ACATCACAATAGCAAGGCTGTAC 59.059 43.478 0.07 0.00 40.10 2.90
2362 2432 2.420022 CTGCTAATGTGTGCCTACAACC 59.580 50.000 0.00 0.00 38.82 3.77
2912 2989 2.952310 AGAGCAGTTGTTCTGGGTTTTC 59.048 45.455 0.00 0.00 43.78 2.29
3062 3139 6.229936 ACCACGTGTCCTACAAATATATGT 57.770 37.500 15.65 0.00 37.32 2.29
3125 3202 9.167239 GTACTAGCACTACGACACAATAATAAG 57.833 37.037 0.00 0.00 0.00 1.73
3132 3209 3.148412 TGGTACTAGCACTACGACACAA 58.852 45.455 0.00 0.00 0.00 3.33
3141 3218 4.243793 AGAGACTGATGGTACTAGCACT 57.756 45.455 0.00 0.00 0.00 4.40
3268 3345 3.181506 GCCTCAAACGGAAGCTCATAAAG 60.182 47.826 0.00 0.00 29.97 1.85
3361 3438 3.446873 GGAGAAGAGAACAGAGAGCATGA 59.553 47.826 0.00 0.00 0.00 3.07
3404 3516 1.202440 AGTTGTTGCATTGCCACACAG 60.202 47.619 14.51 0.00 34.01 3.66
3447 3559 6.007076 TGTAGAAAGTGGCAATGAAATACCA 58.993 36.000 0.00 0.00 30.91 3.25
3449 3561 6.151144 AGGTGTAGAAAGTGGCAATGAAATAC 59.849 38.462 0.00 0.00 0.00 1.89
3452 3569 4.278170 CAGGTGTAGAAAGTGGCAATGAAA 59.722 41.667 0.00 0.00 0.00 2.69
3467 3584 3.055819 ACTGCAGTGTATTCCAGGTGTAG 60.056 47.826 20.97 0.00 31.15 2.74
3672 3792 7.141758 TGAAAGCATAGTATGGGAAGAATCT 57.858 36.000 12.07 0.00 0.00 2.40
3747 3867 6.147164 CGCTAAACAGGAAAATCTAACTGACA 59.853 38.462 0.00 0.00 35.08 3.58
3748 3868 6.147328 ACGCTAAACAGGAAAATCTAACTGAC 59.853 38.462 0.00 0.00 35.08 3.51
3781 3901 6.308015 TCCCTGCACAAGTATAATACAAGT 57.692 37.500 0.00 0.00 0.00 3.16
3783 3903 6.601613 CCTTTCCCTGCACAAGTATAATACAA 59.398 38.462 0.00 0.00 0.00 2.41
3789 3909 4.227300 ACATCCTTTCCCTGCACAAGTATA 59.773 41.667 0.00 0.00 0.00 1.47
3821 3941 4.040829 TCATAGGACCCAACAGCATCATAG 59.959 45.833 0.00 0.00 0.00 2.23
3875 3995 3.201290 CACTGGCATGATCAAGGTAGAC 58.799 50.000 0.00 0.00 0.00 2.59
3969 4103 6.762187 AGATCTGTGATTTGATAGCAGACAAG 59.238 38.462 0.00 0.00 38.74 3.16
4008 4163 1.382088 GACGTGCGTAAATTTGCTTGC 59.618 47.619 0.00 0.04 0.00 4.01
4015 4170 2.428491 TCAATGGGACGTGCGTAAATT 58.572 42.857 0.00 0.00 0.00 1.82
4016 4171 2.102070 TCAATGGGACGTGCGTAAAT 57.898 45.000 0.00 0.00 0.00 1.40
4021 4176 1.016627 ATTCATCAATGGGACGTGCG 58.983 50.000 0.00 0.00 0.00 5.34
4042 4197 6.998802 ACCTCTGAGGCACTATTATAATCAC 58.001 40.000 23.43 0.00 41.55 3.06
4043 4198 7.256332 GGAACCTCTGAGGCACTATTATAATCA 60.256 40.741 23.43 0.00 41.55 2.57
4068 4223 8.778358 GCATACATTGTAAGGAAGATTCTTAGG 58.222 37.037 0.00 0.00 0.00 2.69
4230 4388 9.325198 CAGATTAGTACAGTGGCAAATGTATAA 57.675 33.333 4.44 5.58 34.60 0.98
4263 4421 3.897239 TGTCCCCCTGCATTATTTGTAG 58.103 45.455 0.00 0.00 37.76 2.74
4265 4423 2.917713 TGTCCCCCTGCATTATTTGT 57.082 45.000 0.00 0.00 0.00 2.83
4304 4462 0.321298 GCCTCGTCCCAGCTTTGTTA 60.321 55.000 0.00 0.00 0.00 2.41
4428 4586 3.504524 AAGCAAAGCAAGCACGGGC 62.505 57.895 0.00 0.00 41.61 6.13
4566 4724 7.488471 CGATGAGAGTATTTATTCCGGGTAATC 59.512 40.741 0.00 0.00 0.00 1.75
4569 4727 5.184479 CCGATGAGAGTATTTATTCCGGGTA 59.816 44.000 0.00 0.00 0.00 3.69
4574 4732 4.254492 GCCCCGATGAGAGTATTTATTCC 58.746 47.826 0.00 0.00 0.00 3.01
4612 4770 9.923143 ACTGTTTTTAGGTATCCAAATTTTAGC 57.077 29.630 0.00 0.00 0.00 3.09
4648 4809 4.439837 GCTACCTAAAACCTACTCTCCACG 60.440 50.000 0.00 0.00 0.00 4.94
4764 4925 8.926715 AGGTCAAAATCAAACTTAAAACTCAC 57.073 30.769 0.00 0.00 0.00 3.51
4769 4930 6.975772 CGGTGAGGTCAAAATCAAACTTAAAA 59.024 34.615 0.00 0.00 0.00 1.52
4770 4931 6.460399 CCGGTGAGGTCAAAATCAAACTTAAA 60.460 38.462 0.00 0.00 34.51 1.52
4771 4932 5.009210 CCGGTGAGGTCAAAATCAAACTTAA 59.991 40.000 0.00 0.00 34.51 1.85
4905 5069 1.333435 CCGACGGTAAACAGTTGCAAC 60.333 52.381 22.17 22.17 0.00 4.17
4955 5119 2.872370 ACCTTGTATGTCTAACGCGAC 58.128 47.619 15.93 0.00 34.52 5.19
4956 5120 3.504863 GAACCTTGTATGTCTAACGCGA 58.495 45.455 15.93 0.00 0.00 5.87
4980 5175 1.736032 CGAGAAATCCTGACCCGACAC 60.736 57.143 0.00 0.00 0.00 3.67
4985 5180 3.194968 TGTCTAACGAGAAATCCTGACCC 59.805 47.826 0.00 0.00 31.96 4.46
5250 5639 8.345565 ACATTTCAGACATGTTCAGTTAAACTC 58.654 33.333 0.00 0.00 30.22 3.01
5298 6091 1.153597 TTGCAGCACGATAGATGCGG 61.154 55.000 0.00 2.57 44.22 5.69
5322 6118 1.541588 GCCATGTCCAACTTCAGTTCC 59.458 52.381 0.00 0.00 35.83 3.62
5417 6512 0.744874 ACCACGAGTACGATGGGATG 59.255 55.000 14.99 0.00 41.37 3.51
5459 6585 2.124403 GCTCTGCCATGGTGGAGG 60.124 66.667 26.03 14.62 40.96 4.30
5519 6828 3.313249 TCATGGCGTGCTCTATTGATTTG 59.687 43.478 0.65 0.00 0.00 2.32
5520 6829 3.544684 TCATGGCGTGCTCTATTGATTT 58.455 40.909 0.65 0.00 0.00 2.17
5521 6830 3.198409 TCATGGCGTGCTCTATTGATT 57.802 42.857 0.65 0.00 0.00 2.57
5544 6853 4.203077 CAGTTGCGTAATTTGCTTTTTGC 58.797 39.130 4.31 0.00 43.25 3.68


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

AutoCloner maintained by Alex Coulton.