Multiple sequence alignment - TraesCS2A01G097800

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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 TraesCS2A01G097800 chr2A 100.000 5152 0 0 1 5152 51566820 51561669 0.000000e+00 9515.0
1 TraesCS2A01G097800 chr2D 92.696 2355 103 27 2372 4665 49617862 49615516 0.000000e+00 3332.0
2 TraesCS2A01G097800 chr2D 88.505 1679 116 39 661 2292 49619511 49617863 0.000000e+00 1960.0
3 TraesCS2A01G097800 chr2D 90.421 428 25 4 4723 5150 49615522 49615111 2.710000e-152 549.0
4 TraesCS2A01G097800 chr2D 84.328 402 37 16 3 385 49620166 49619772 2.270000e-98 370.0
5 TraesCS2A01G097800 chr2B 89.568 2387 139 55 1 2292 76921324 76918953 0.000000e+00 2928.0
6 TraesCS2A01G097800 chr2B 95.796 1213 44 4 2372 3577 76918952 76917740 0.000000e+00 1951.0
7 TraesCS2A01G097800 chr2B 89.809 785 24 20 3575 4321 76917308 76916542 0.000000e+00 955.0
8 TraesCS2A01G097800 chr2B 88.918 379 23 7 4774 5152 76915626 76915267 2.830000e-122 449.0
9 TraesCS2A01G097800 chr2B 93.151 146 9 1 4678 4823 76915765 76915621 4.040000e-51 213.0
10 TraesCS2A01G097800 chr2B 92.701 137 3 3 4511 4647 76915894 76915765 1.890000e-44 191.0
11 TraesCS2A01G097800 chr6D 85.714 77 4 6 464 539 464622754 464622684 1.990000e-09 75.0
12 TraesCS2A01G097800 chr6D 97.436 39 1 0 461 499 452851699 452851661 3.330000e-07 67.6
13 TraesCS2A01G097800 chr5A 95.349 43 2 0 469 511 558167361 558167319 9.260000e-08 69.4
14 TraesCS2A01G097800 chr5D 84.848 66 7 2 469 532 441396447 441396383 4.310000e-06 63.9
15 TraesCS2A01G097800 chr3B 92.308 39 2 1 467 505 771981534 771981497 3.000000e-03 54.7
16 TraesCS2A01G097800 chr3B 92.308 39 2 1 467 505 772005516 772005479 3.000000e-03 54.7


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 TraesCS2A01G097800 chr2A 51561669 51566820 5151 True 9515.00 9515 100.000000 1 5152 1 chr2A.!!$R1 5151
1 TraesCS2A01G097800 chr2D 49615111 49620166 5055 True 1552.75 3332 88.987500 3 5150 4 chr2D.!!$R1 5147
2 TraesCS2A01G097800 chr2B 76915267 76921324 6057 True 1114.50 2928 91.657167 1 5152 6 chr2B.!!$R1 5151

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
193 203 0.033601 GAGTCAGGGAGCAGGAGAGA 60.034 60.0 0.0 0.0 0.00 3.10 F
884 1013 0.036022 GCCAGAGCCATCCATACCTC 59.964 60.0 0.0 0.0 0.00 3.85 F
1339 1483 0.319555 CAGTGTTCGGTCGGTGTCAT 60.320 55.0 0.0 0.0 0.00 3.06 F
2785 2974 0.034059 GCAGTGGTGTGTCTGTAGCT 59.966 55.0 0.0 0.0 34.57 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1461 1.372997 CACCGACCGAACACTGAGG 60.373 63.158 0.00 0.00 0.00 3.86 R
2548 2737 1.256812 GCAAGCACACCCCAATAGTT 58.743 50.000 0.00 0.00 0.00 2.24 R
3023 3220 0.396435 TCGTGTGGGCAAAGACTGAT 59.604 50.000 0.00 0.00 0.00 2.90 R
4351 5032 0.241749 ATCACGTCGACGGCAGTTTA 59.758 50.000 37.89 17.06 44.95 2.01 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
28 29 3.135712 ACAATGGGAGGCATGAACGTATA 59.864 43.478 0.00 0.00 0.00 1.47
59 60 7.120579 TGCTCTAAGTTGAGTTTGTTTTTCTGA 59.879 33.333 0.00 0.00 36.51 3.27
78 79 8.712285 TTTCTGAGTTAATTTGATAGGTACCG 57.288 34.615 6.18 0.00 0.00 4.02
193 203 0.033601 GAGTCAGGGAGCAGGAGAGA 60.034 60.000 0.00 0.00 0.00 3.10
202 212 4.785376 AGGGAGCAGGAGAGATTTTCTTTA 59.215 41.667 0.00 0.00 35.87 1.85
669 786 2.032030 CAGGACGAAACAAAGAACGCAT 60.032 45.455 0.00 0.00 0.00 4.73
726 850 3.647771 GAGGGGGAAACGGGTGCT 61.648 66.667 0.00 0.00 0.00 4.40
884 1013 0.036022 GCCAGAGCCATCCATACCTC 59.964 60.000 0.00 0.00 0.00 3.85
886 1015 1.727062 CAGAGCCATCCATACCTCCT 58.273 55.000 0.00 0.00 0.00 3.69
936 1073 1.075600 CTCTCTCCCTCCCTCCACC 60.076 68.421 0.00 0.00 0.00 4.61
937 1074 2.443016 CTCTCCCTCCCTCCACCG 60.443 72.222 0.00 0.00 0.00 4.94
938 1075 4.075793 TCTCCCTCCCTCCACCGG 62.076 72.222 0.00 0.00 0.00 5.28
1284 1425 2.463589 TAAGCAACCACCCGCCTCTG 62.464 60.000 0.00 0.00 0.00 3.35
1291 1432 3.315949 ACCCGCCTCTGCCGTTAA 61.316 61.111 0.00 0.00 0.00 2.01
1292 1433 2.818274 CCCGCCTCTGCCGTTAAC 60.818 66.667 0.00 0.00 0.00 2.01
1306 1450 1.302993 TTAACTTCCCTGGCGTGCC 60.303 57.895 3.30 3.30 0.00 5.01
1334 1478 1.111116 TTCCTCAGTGTTCGGTCGGT 61.111 55.000 0.00 0.00 0.00 4.69
1339 1483 0.319555 CAGTGTTCGGTCGGTGTCAT 60.320 55.000 0.00 0.00 0.00 3.06
1344 1488 0.526211 TTCGGTCGGTGTCATGAGAG 59.474 55.000 0.00 0.00 0.00 3.20
1351 1495 3.189287 GTCGGTGTCATGAGAGCAAATTT 59.811 43.478 20.44 0.00 0.00 1.82
1352 1496 3.189080 TCGGTGTCATGAGAGCAAATTTG 59.811 43.478 20.44 14.03 0.00 2.32
1361 1505 3.994392 TGAGAGCAAATTTGTAGTCGTCC 59.006 43.478 19.03 9.14 0.00 4.79
1372 1521 6.769134 TTTGTAGTCGTCCTTGATGATCTA 57.231 37.500 0.00 0.00 29.93 1.98
1373 1522 6.378710 TTGTAGTCGTCCTTGATGATCTAG 57.621 41.667 0.00 0.00 29.93 2.43
1380 1529 8.478877 AGTCGTCCTTGATGATCTAGTTATTTT 58.521 33.333 3.39 0.00 29.93 1.82
1417 1584 3.641434 AGGTGTCATTAGATGCTTGCT 57.359 42.857 0.00 0.00 0.00 3.91
1423 1590 6.931281 GGTGTCATTAGATGCTTGCTTAGATA 59.069 38.462 0.00 0.00 0.00 1.98
1428 1595 9.433153 TCATTAGATGCTTGCTTAGATAGATTG 57.567 33.333 0.00 0.00 0.00 2.67
1441 1608 7.618019 TTAGATAGATTGGTTGGCTAGATGT 57.382 36.000 0.00 0.00 0.00 3.06
1459 1629 7.201600 GCTAGATGTTGAGAGTTGATTTCCTTC 60.202 40.741 0.00 0.00 0.00 3.46
1464 1634 3.190874 GAGAGTTGATTTCCTTCGCGAT 58.809 45.455 10.88 0.00 0.00 4.58
1465 1635 2.932614 AGAGTTGATTTCCTTCGCGATG 59.067 45.455 10.88 13.11 0.00 3.84
1469 1639 3.793797 TGATTTCCTTCGCGATGTCTA 57.206 42.857 10.88 0.00 0.00 2.59
1475 1645 1.134367 CCTTCGCGATGTCTACCTTCA 59.866 52.381 10.88 0.00 0.00 3.02
1489 1659 8.645814 TGTCTACCTTCAGAAGTCTGTTATTA 57.354 34.615 9.41 0.00 44.12 0.98
1493 1663 9.877178 CTACCTTCAGAAGTCTGTTATTAATGT 57.123 33.333 9.41 1.79 44.12 2.71
1495 1665 9.220767 ACCTTCAGAAGTCTGTTATTAATGTTC 57.779 33.333 9.41 0.00 44.12 3.18
1496 1666 9.219603 CCTTCAGAAGTCTGTTATTAATGTTCA 57.780 33.333 9.41 0.00 44.12 3.18
1516 1693 6.543465 TGTTCACAGAAGTTGAACAATGATCT 59.457 34.615 13.98 0.00 45.76 2.75
1517 1694 6.791887 TCACAGAAGTTGAACAATGATCTC 57.208 37.500 0.00 0.00 0.00 2.75
1609 1786 0.671781 GACAATGACGCAGCAGAGGT 60.672 55.000 0.00 0.00 0.00 3.85
1694 1872 1.026182 CGGCCTACTGCTTGCATGAA 61.026 55.000 0.00 0.00 40.92 2.57
1736 1914 3.942829 GAATGTGTCTCCAGACCATTCA 58.057 45.455 26.33 14.33 46.86 2.57
1895 2073 1.135859 CGGATTGTGCTGCTTCTCAAC 60.136 52.381 0.00 0.00 0.00 3.18
1969 2150 4.946157 CCTGTCTTTCTGCATCTTATGGTT 59.054 41.667 0.00 0.00 0.00 3.67
1973 2154 6.767902 TGTCTTTCTGCATCTTATGGTTATCC 59.232 38.462 0.00 0.00 0.00 2.59
1981 2162 7.771183 TGCATCTTATGGTTATCCTTTTTGTC 58.229 34.615 0.00 0.00 34.23 3.18
2059 2240 3.164268 AGGAATTGCCAACTGTTGCATA 58.836 40.909 14.94 8.10 40.02 3.14
2105 2286 1.027357 CCAAGCTGGGATGGAAATCG 58.973 55.000 0.00 0.00 39.12 3.34
2114 2295 2.755103 GGGATGGAAATCGTCAAAGCTT 59.245 45.455 0.00 0.00 33.11 3.74
2165 2346 3.058639 GTGATTGTCTTGGTGCTGAGAAC 60.059 47.826 0.00 0.00 0.00 3.01
2234 2415 9.823647 TCCTATCTTGATGTTTTTAGAGATGAC 57.176 33.333 0.00 0.00 0.00 3.06
2237 2418 5.874810 TCTTGATGTTTTTAGAGATGACCGG 59.125 40.000 0.00 0.00 0.00 5.28
2288 2469 6.407202 TCTAGCTTCATTTAGGAGTTTCACC 58.593 40.000 0.00 0.00 0.00 4.02
2292 2473 5.335191 GCTTCATTTAGGAGTTTCACCTGTG 60.335 44.000 0.00 0.00 38.31 3.66
2293 2474 5.304686 TCATTTAGGAGTTTCACCTGTGT 57.695 39.130 0.00 0.00 38.31 3.72
2294 2475 5.690865 TCATTTAGGAGTTTCACCTGTGTT 58.309 37.500 0.00 0.00 38.31 3.32
2295 2476 5.763204 TCATTTAGGAGTTTCACCTGTGTTC 59.237 40.000 0.00 0.00 38.31 3.18
2296 2477 5.367945 TTTAGGAGTTTCACCTGTGTTCT 57.632 39.130 0.00 0.00 38.31 3.01
2297 2478 3.933861 AGGAGTTTCACCTGTGTTCTT 57.066 42.857 0.00 0.00 36.30 2.52
2298 2479 6.488769 TTAGGAGTTTCACCTGTGTTCTTA 57.511 37.500 0.00 0.00 38.31 2.10
2299 2480 4.962155 AGGAGTTTCACCTGTGTTCTTAG 58.038 43.478 0.00 0.00 36.30 2.18
2300 2481 4.065789 GGAGTTTCACCTGTGTTCTTAGG 58.934 47.826 0.00 0.00 40.01 2.69
2301 2482 4.202326 GGAGTTTCACCTGTGTTCTTAGGA 60.202 45.833 0.00 0.00 37.52 2.94
2302 2483 5.513267 GGAGTTTCACCTGTGTTCTTAGGAT 60.513 44.000 0.00 0.00 37.52 3.24
2303 2484 5.941788 AGTTTCACCTGTGTTCTTAGGATT 58.058 37.500 0.00 0.00 37.52 3.01
2304 2485 6.365520 AGTTTCACCTGTGTTCTTAGGATTT 58.634 36.000 0.00 0.00 37.52 2.17
2305 2486 7.514721 AGTTTCACCTGTGTTCTTAGGATTTA 58.485 34.615 0.00 0.00 37.52 1.40
2306 2487 8.164070 AGTTTCACCTGTGTTCTTAGGATTTAT 58.836 33.333 0.00 0.00 37.52 1.40
2307 2488 9.444600 GTTTCACCTGTGTTCTTAGGATTTATA 57.555 33.333 0.00 0.00 37.52 0.98
2308 2489 9.667107 TTTCACCTGTGTTCTTAGGATTTATAG 57.333 33.333 0.00 0.00 37.52 1.31
2309 2490 8.375493 TCACCTGTGTTCTTAGGATTTATAGT 57.625 34.615 0.00 0.00 37.52 2.12
2310 2491 8.822805 TCACCTGTGTTCTTAGGATTTATAGTT 58.177 33.333 0.00 0.00 37.52 2.24
2311 2492 9.449719 CACCTGTGTTCTTAGGATTTATAGTTT 57.550 33.333 0.00 0.00 37.52 2.66
2355 2536 9.540538 TGAAAATTCCATCCTTTATTAAGACCA 57.459 29.630 0.00 0.00 32.92 4.02
2384 2565 6.121590 TGATTTGCCTGACTTCATGCTATTA 58.878 36.000 7.82 0.00 38.16 0.98
2400 2581 9.023962 TCATGCTATTAGATTTTGTCCTTTTGT 57.976 29.630 0.00 0.00 0.00 2.83
2443 2630 4.877823 GCCATATCAACATTGACAGACAGA 59.122 41.667 0.00 0.00 40.49 3.41
2493 2682 4.556233 TCTGTGTGGACTGTTTAATCTCG 58.444 43.478 0.00 0.00 0.00 4.04
2496 2685 3.364023 GTGTGGACTGTTTAATCTCGTCG 59.636 47.826 0.00 0.00 0.00 5.12
2508 2697 4.647291 AATCTCGTCGTGACATTTTGAC 57.353 40.909 0.00 0.00 0.00 3.18
2534 2723 4.287766 ACTCCTGATTTTACAGTGGTCC 57.712 45.455 0.00 0.00 36.30 4.46
2548 2737 4.331968 CAGTGGTCCTGTGCCTAAATTTA 58.668 43.478 0.00 0.00 36.37 1.40
2558 2747 6.183360 CCTGTGCCTAAATTTAACTATTGGGG 60.183 42.308 0.00 0.00 0.00 4.96
2762 2951 3.515104 TGGTGTTGTGATGCTCAGATCTA 59.485 43.478 0.00 0.00 0.00 1.98
2785 2974 0.034059 GCAGTGGTGTGTCTGTAGCT 59.966 55.000 0.00 0.00 34.57 3.32
2791 2980 1.269998 GGTGTGTCTGTAGCTCTTCGT 59.730 52.381 0.00 0.00 0.00 3.85
2794 2983 4.380655 GGTGTGTCTGTAGCTCTTCGTAAT 60.381 45.833 0.00 0.00 0.00 1.89
2876 3072 4.019792 TCATCACTCAAGCCAGCTTTTA 57.980 40.909 1.19 0.00 33.42 1.52
2952 3149 3.570926 TCTGACAACAAGCTAGTACGG 57.429 47.619 0.00 0.00 0.00 4.02
3001 3198 9.066892 TCCAATGACTTACTCCATATTTATTGC 57.933 33.333 0.00 0.00 0.00 3.56
3572 3771 4.162509 AGCTACCCCTTTCTTGACAGTATC 59.837 45.833 0.00 0.00 0.00 2.24
3600 4233 7.394816 ACACTTTAGTTCCTACATATGCTTGT 58.605 34.615 1.58 0.00 0.00 3.16
3603 4236 9.297037 ACTTTAGTTCCTACATATGCTTGTTTT 57.703 29.630 1.58 0.00 0.00 2.43
3618 4251 5.695816 TGCTTGTTTTGCCATGTTCTAATTC 59.304 36.000 0.00 0.00 0.00 2.17
3619 4252 5.928264 GCTTGTTTTGCCATGTTCTAATTCT 59.072 36.000 0.00 0.00 0.00 2.40
3620 4253 7.090173 GCTTGTTTTGCCATGTTCTAATTCTA 58.910 34.615 0.00 0.00 0.00 2.10
3621 4254 7.598493 GCTTGTTTTGCCATGTTCTAATTCTAA 59.402 33.333 0.00 0.00 0.00 2.10
3682 4320 2.947127 AGACAGAAAAGAAGCAGGCT 57.053 45.000 0.00 0.00 0.00 4.58
3703 4341 4.651778 CTTTGGGTATCTCTTGTGTTGGA 58.348 43.478 0.00 0.00 0.00 3.53
3704 4342 3.981071 TGGGTATCTCTTGTGTTGGAG 57.019 47.619 0.00 0.00 0.00 3.86
3705 4343 3.516586 TGGGTATCTCTTGTGTTGGAGA 58.483 45.455 0.00 0.00 41.88 3.71
3706 4344 3.260884 TGGGTATCTCTTGTGTTGGAGAC 59.739 47.826 0.00 0.00 40.71 3.36
3707 4345 3.512680 GGTATCTCTTGTGTTGGAGACG 58.487 50.000 0.00 0.00 40.71 4.18
3708 4346 3.056749 GGTATCTCTTGTGTTGGAGACGT 60.057 47.826 0.00 0.00 40.71 4.34
3709 4347 2.795175 TCTCTTGTGTTGGAGACGTC 57.205 50.000 7.70 7.70 34.19 4.34
3710 4348 2.307768 TCTCTTGTGTTGGAGACGTCT 58.692 47.619 20.18 20.18 34.19 4.18
3781 4424 1.002069 TGCATTGAACAGGATCCCCT 58.998 50.000 8.55 0.00 45.74 4.79
4054 4697 2.948840 GATGGCGATGGCAGCAAAGC 62.949 60.000 2.73 0.00 43.87 3.51
4140 4810 3.737172 CGAGCGCAGGTTTTGGGG 61.737 66.667 11.47 0.00 39.88 4.96
4279 4955 5.293324 GCTTGTTTTTACCCCTCTGTTTTTG 59.707 40.000 0.00 0.00 0.00 2.44
4314 4995 1.073177 AGTAATTACACGTGCACGGC 58.927 50.000 39.21 19.09 44.95 5.68
4391 5072 2.280628 GATGGCGTAAGTTTCCTCTGG 58.719 52.381 0.00 0.00 41.68 3.86
4441 5122 5.365619 GTGTCTTCAAACTTCTGAACCCTA 58.634 41.667 0.00 0.00 32.00 3.53
4445 5126 7.394923 TGTCTTCAAACTTCTGAACCCTAAAAA 59.605 33.333 0.00 0.00 32.00 1.94
4508 5634 2.309613 CATCACCTCTCCTCTCCTGAG 58.690 57.143 0.00 0.00 39.92 3.35
4646 5785 6.140580 CGTGTTAATTAATTGGCATCGTGATG 59.859 38.462 11.05 5.48 41.60 3.07
4654 5793 3.188100 CATCGTGATGCCGTGCGT 61.188 61.111 0.00 0.00 31.39 5.24
4655 5794 2.434185 ATCGTGATGCCGTGCGTT 60.434 55.556 0.00 0.00 0.00 4.84
4656 5795 2.739704 ATCGTGATGCCGTGCGTTG 61.740 57.895 0.00 0.00 0.00 4.10
4657 5796 3.711842 CGTGATGCCGTGCGTTGT 61.712 61.111 0.00 0.00 0.00 3.32
4658 5797 2.173382 GTGATGCCGTGCGTTGTC 59.827 61.111 0.00 0.00 0.00 3.18
4659 5798 2.030412 TGATGCCGTGCGTTGTCT 59.970 55.556 0.00 0.00 0.00 3.41
4660 5799 2.027073 TGATGCCGTGCGTTGTCTC 61.027 57.895 0.00 0.00 0.00 3.36
4661 5800 2.740714 GATGCCGTGCGTTGTCTCC 61.741 63.158 0.00 0.00 0.00 3.71
4662 5801 3.529341 ATGCCGTGCGTTGTCTCCA 62.529 57.895 0.00 0.00 0.00 3.86
4663 5802 2.742372 GCCGTGCGTTGTCTCCAT 60.742 61.111 0.00 0.00 0.00 3.41
4664 5803 3.027170 GCCGTGCGTTGTCTCCATG 62.027 63.158 0.00 0.00 0.00 3.66
4665 5804 1.667830 CCGTGCGTTGTCTCCATGT 60.668 57.895 0.00 0.00 0.00 3.21
4666 5805 1.227999 CCGTGCGTTGTCTCCATGTT 61.228 55.000 0.00 0.00 0.00 2.71
4667 5806 0.586319 CGTGCGTTGTCTCCATGTTT 59.414 50.000 0.00 0.00 0.00 2.83
4668 5807 1.660052 CGTGCGTTGTCTCCATGTTTG 60.660 52.381 0.00 0.00 0.00 2.93
4669 5808 1.333619 GTGCGTTGTCTCCATGTTTGT 59.666 47.619 0.00 0.00 0.00 2.83
4670 5809 2.020720 TGCGTTGTCTCCATGTTTGTT 58.979 42.857 0.00 0.00 0.00 2.83
4671 5810 2.032799 TGCGTTGTCTCCATGTTTGTTC 59.967 45.455 0.00 0.00 0.00 3.18
4672 5811 2.290641 GCGTTGTCTCCATGTTTGTTCT 59.709 45.455 0.00 0.00 0.00 3.01
4673 5812 3.496884 GCGTTGTCTCCATGTTTGTTCTA 59.503 43.478 0.00 0.00 0.00 2.10
4674 5813 4.377431 GCGTTGTCTCCATGTTTGTTCTAG 60.377 45.833 0.00 0.00 0.00 2.43
4675 5814 4.988540 CGTTGTCTCCATGTTTGTTCTAGA 59.011 41.667 0.00 0.00 0.00 2.43
4676 5815 5.119279 CGTTGTCTCCATGTTTGTTCTAGAG 59.881 44.000 0.00 0.00 0.00 2.43
4745 5884 8.594881 AACTCAATGAGTAGTGAAGTTACTTG 57.405 34.615 17.04 0.00 42.59 3.16
4754 5893 5.500645 AGTGAAGTTACTTGTTTTGCTCC 57.499 39.130 0.93 0.00 0.00 4.70
4865 6047 5.107453 ACGATGAAGACAATCGTCAAAGAAC 60.107 40.000 5.68 0.00 46.46 3.01
4869 6051 5.757808 TGAAGACAATCGTCAAAGAACATGA 59.242 36.000 0.00 0.00 45.23 3.07
4948 6130 6.923199 ATTTCACTTTTCATGTGGGATTCT 57.077 33.333 0.00 0.00 36.21 2.40
4962 6144 3.826157 TGGGATTCTGTTTGTCATTGGAC 59.174 43.478 0.00 0.00 44.57 4.02
5061 6243 4.160252 GTGAAATTATGGAGTGCAACCCAT 59.840 41.667 20.70 20.70 45.65 4.00
5063 6245 2.142356 TTATGGAGTGCAACCCATGG 57.858 50.000 23.91 4.14 44.23 3.66
5073 6255 1.522900 CAACCCATGGTATCCCTCCT 58.477 55.000 11.73 0.00 33.12 3.69
5132 6314 3.891366 GCTCCCATTACAAAGCATATGGT 59.109 43.478 0.40 0.40 36.61 3.55
5141 6323 9.368674 CATTACAAAGCATATGGTGATTTTGAA 57.631 29.630 18.96 11.44 43.46 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.692519 ACCCTATACGTTCATGCCTCC 59.307 52.381 0.00 0.00 0.00 4.30
28 29 4.137543 CAAACTCAACTTAGAGCAACCCT 58.862 43.478 0.00 0.00 39.26 4.34
59 60 6.174760 TGCAACGGTACCTATCAAATTAACT 58.825 36.000 10.90 0.00 0.00 2.24
67 68 4.481368 AGAATTGCAACGGTACCTATCA 57.519 40.909 10.90 0.00 0.00 2.15
108 109 5.128008 TGGAGTGGGACTTTTTAAACTTTGG 59.872 40.000 0.00 0.00 0.00 3.28
225 236 9.221933 TGAAAAATATTCAAGTGTACCGTGTAT 57.778 29.630 0.00 0.00 0.00 2.29
640 757 5.183228 TCTTTGTTTCGTCCTGTTCTTCTT 58.817 37.500 0.00 0.00 0.00 2.52
646 763 2.223180 GCGTTCTTTGTTTCGTCCTGTT 60.223 45.455 0.00 0.00 0.00 3.16
648 765 1.329292 TGCGTTCTTTGTTTCGTCCTG 59.671 47.619 0.00 0.00 0.00 3.86
669 786 3.371591 CCCGTAGCGTTAATTTGTTAGCA 59.628 43.478 0.00 0.00 0.00 3.49
715 839 2.857748 CAAACAGAAAAGCACCCGTTTC 59.142 45.455 0.00 0.00 38.98 2.78
723 847 1.134551 GTTGGCCCAAACAGAAAAGCA 60.135 47.619 0.00 0.00 0.00 3.91
726 850 2.223923 CGATGTTGGCCCAAACAGAAAA 60.224 45.455 13.50 0.00 42.99 2.29
905 1034 1.133482 GGAGAGAGGAGGAGGAGGAAG 60.133 61.905 0.00 0.00 0.00 3.46
906 1035 0.930726 GGAGAGAGGAGGAGGAGGAA 59.069 60.000 0.00 0.00 0.00 3.36
1284 1425 2.396157 CGCCAGGGAAGTTAACGGC 61.396 63.158 9.22 9.22 36.16 5.68
1286 1427 1.908066 GCACGCCAGGGAAGTTAACG 61.908 60.000 0.00 0.00 0.00 3.18
1287 1428 1.583495 GGCACGCCAGGGAAGTTAAC 61.583 60.000 2.36 0.00 35.81 2.01
1306 1450 2.386661 ACACTGAGGAATTGGTAGCG 57.613 50.000 0.00 0.00 0.00 4.26
1309 1453 2.635915 ACCGAACACTGAGGAATTGGTA 59.364 45.455 0.00 0.00 0.00 3.25
1317 1461 1.372997 CACCGACCGAACACTGAGG 60.373 63.158 0.00 0.00 0.00 3.86
1334 1478 5.120674 CGACTACAAATTTGCTCTCATGACA 59.879 40.000 18.12 0.00 0.00 3.58
1339 1483 3.994392 GGACGACTACAAATTTGCTCTCA 59.006 43.478 18.12 0.00 0.00 3.27
1344 1488 4.742438 TCAAGGACGACTACAAATTTGC 57.258 40.909 18.12 0.90 0.00 3.68
1351 1495 5.437946 ACTAGATCATCAAGGACGACTACA 58.562 41.667 0.00 0.00 0.00 2.74
1352 1496 6.380095 AACTAGATCATCAAGGACGACTAC 57.620 41.667 0.00 0.00 0.00 2.73
1380 1529 5.308497 TGACACCTAGGGAATTGACACTAAA 59.692 40.000 14.81 0.00 0.00 1.85
1382 1531 4.422057 TGACACCTAGGGAATTGACACTA 58.578 43.478 14.81 0.00 0.00 2.74
1395 1562 4.701765 AGCAAGCATCTAATGACACCTAG 58.298 43.478 0.00 0.00 0.00 3.02
1417 1584 7.618019 ACATCTAGCCAACCAATCTATCTAA 57.382 36.000 0.00 0.00 0.00 2.10
1423 1590 4.225942 TCTCAACATCTAGCCAACCAATCT 59.774 41.667 0.00 0.00 0.00 2.40
1428 1595 3.618690 ACTCTCAACATCTAGCCAACC 57.381 47.619 0.00 0.00 0.00 3.77
1441 1608 2.736721 CGCGAAGGAAATCAACTCTCAA 59.263 45.455 0.00 0.00 0.00 3.02
1459 1629 2.159366 ACTTCTGAAGGTAGACATCGCG 60.159 50.000 20.61 0.00 0.00 5.87
1464 1634 7.540474 AATAACAGACTTCTGAAGGTAGACA 57.460 36.000 20.61 3.40 46.59 3.41
1469 1639 9.220767 GAACATTAATAACAGACTTCTGAAGGT 57.779 33.333 20.61 7.11 46.59 3.50
1475 1645 9.778741 TTCTGTGAACATTAATAACAGACTTCT 57.221 29.630 16.15 0.00 45.05 2.85
1493 1663 6.767423 TGAGATCATTGTTCAACTTCTGTGAA 59.233 34.615 0.00 0.00 0.00 3.18
1495 1665 6.549912 TGAGATCATTGTTCAACTTCTGTG 57.450 37.500 0.00 0.00 0.00 3.66
1496 1666 7.572523 TTTGAGATCATTGTTCAACTTCTGT 57.427 32.000 0.00 0.00 31.11 3.41
1510 1687 5.075493 GGAGGCCACAATATTTGAGATCAT 58.925 41.667 5.01 0.00 0.00 2.45
1516 1693 4.591321 AAGAGGAGGCCACAATATTTGA 57.409 40.909 5.01 0.00 0.00 2.69
1517 1694 4.706476 TGAAAGAGGAGGCCACAATATTTG 59.294 41.667 5.01 0.00 0.00 2.32
1694 1872 8.960591 ACATTCAGCAGCTTTAGTAAATAATGT 58.039 29.630 0.00 0.00 0.00 2.71
1829 2007 2.084610 TCTTCTCCATGTCAACGCAG 57.915 50.000 0.00 0.00 0.00 5.18
1932 2110 4.963318 AAGACAGGAAAGATCACACTGA 57.037 40.909 11.89 0.00 33.57 3.41
1934 2112 5.303971 CAGAAAGACAGGAAAGATCACACT 58.696 41.667 0.00 0.00 0.00 3.55
1937 2115 4.067896 TGCAGAAAGACAGGAAAGATCAC 58.932 43.478 0.00 0.00 0.00 3.06
1969 2150 9.098355 CAAGATCTACAATCGACAAAAAGGATA 57.902 33.333 0.00 0.00 0.00 2.59
1973 2154 7.237173 GGACAAGATCTACAATCGACAAAAAG 58.763 38.462 0.00 0.00 0.00 2.27
1981 2162 3.819564 TGGGGACAAGATCTACAATCG 57.180 47.619 0.00 0.00 37.44 3.34
2059 2240 1.672881 GCTCTTGAGTGTTGCACTTGT 59.327 47.619 3.16 0.00 45.44 3.16
2114 2295 7.473735 TTGTGGGATATTGCTTGTTTTATCA 57.526 32.000 0.00 0.00 0.00 2.15
2234 2415 2.287915 CACAAACAAAGACAGTCTCCGG 59.712 50.000 2.72 0.00 0.00 5.14
2237 2418 4.946784 ACACACAAACAAAGACAGTCTC 57.053 40.909 2.72 0.00 0.00 3.36
2329 2510 9.540538 TGGTCTTAATAAAGGATGGAATTTTCA 57.459 29.630 0.00 0.00 33.22 2.69
2345 2526 9.639563 TCAGGCAAATCATATTTGGTCTTAATA 57.360 29.630 12.82 0.00 0.00 0.98
2346 2527 8.416329 GTCAGGCAAATCATATTTGGTCTTAAT 58.584 33.333 12.82 0.00 0.00 1.40
2347 2528 7.615365 AGTCAGGCAAATCATATTTGGTCTTAA 59.385 33.333 12.82 0.00 0.00 1.85
2348 2529 7.118723 AGTCAGGCAAATCATATTTGGTCTTA 58.881 34.615 12.82 0.00 0.00 2.10
2349 2530 5.954150 AGTCAGGCAAATCATATTTGGTCTT 59.046 36.000 12.82 0.00 0.00 3.01
2350 2531 5.513233 AGTCAGGCAAATCATATTTGGTCT 58.487 37.500 12.82 0.57 0.00 3.85
2351 2532 5.841957 AGTCAGGCAAATCATATTTGGTC 57.158 39.130 12.82 0.00 0.00 4.02
2352 2533 5.716228 TGAAGTCAGGCAAATCATATTTGGT 59.284 36.000 12.82 0.00 0.00 3.67
2353 2534 6.211587 TGAAGTCAGGCAAATCATATTTGG 57.788 37.500 12.82 0.00 0.00 3.28
2354 2535 7.694388 CATGAAGTCAGGCAAATCATATTTG 57.306 36.000 7.80 7.80 0.00 2.32
2367 2548 8.218338 ACAAAATCTAATAGCATGAAGTCAGG 57.782 34.615 0.00 0.00 0.00 3.86
2368 2549 8.341173 GGACAAAATCTAATAGCATGAAGTCAG 58.659 37.037 0.00 0.00 0.00 3.51
2369 2550 8.049117 AGGACAAAATCTAATAGCATGAAGTCA 58.951 33.333 0.00 0.00 0.00 3.41
2370 2551 8.443953 AGGACAAAATCTAATAGCATGAAGTC 57.556 34.615 0.00 0.00 0.00 3.01
2384 2565 5.893824 AGGACAAGACAAAAGGACAAAATCT 59.106 36.000 0.00 0.00 0.00 2.40
2400 2581 2.553028 GCTTCCATGGAACAGGACAAGA 60.553 50.000 23.63 0.00 46.40 3.02
2443 2630 4.454728 AGGTGCGTGCATGAAAATAAAT 57.545 36.364 10.93 0.00 0.00 1.40
2454 2641 2.621055 ACAGAAAATTTAGGTGCGTGCA 59.379 40.909 0.00 0.00 0.00 4.57
2493 2682 5.333111 GGAGTAGTTGTCAAAATGTCACGAC 60.333 44.000 0.00 0.00 0.00 4.34
2496 2685 5.758296 TCAGGAGTAGTTGTCAAAATGTCAC 59.242 40.000 0.00 0.00 0.00 3.67
2508 2697 6.231211 ACCACTGTAAAATCAGGAGTAGTTG 58.769 40.000 0.00 0.00 39.48 3.16
2534 2723 6.379988 ACCCCAATAGTTAAATTTAGGCACAG 59.620 38.462 0.00 0.00 0.00 3.66
2548 2737 1.256812 GCAAGCACACCCCAATAGTT 58.743 50.000 0.00 0.00 0.00 2.24
2785 2974 6.481976 TCTCAACTCTTTTGCAATTACGAAGA 59.518 34.615 0.00 5.12 0.00 2.87
2791 2980 7.448161 TCCATCTTCTCAACTCTTTTGCAATTA 59.552 33.333 0.00 0.00 0.00 1.40
2794 2983 5.009010 GTCCATCTTCTCAACTCTTTTGCAA 59.991 40.000 0.00 0.00 0.00 4.08
2952 3149 8.100791 TGGATAATGCATTTCCAGGTATACTAC 58.899 37.037 26.22 8.19 34.65 2.73
3001 3198 8.975410 TGATGATTTCTTTAACTGCAAGAATG 57.025 30.769 0.00 0.00 39.46 2.67
3023 3220 0.396435 TCGTGTGGGCAAAGACTGAT 59.604 50.000 0.00 0.00 0.00 2.90
3324 3522 7.987458 TCACTTCCATCTTCTGTGATAATTACC 59.013 37.037 0.00 0.00 33.45 2.85
3572 3771 7.727181 AGCATATGTAGGAACTAAAGTGTAGG 58.273 38.462 4.29 0.00 45.48 3.18
3603 4236 7.109501 TGCTTAGTTAGAATTAGAACATGGCA 58.890 34.615 0.00 0.00 0.00 4.92
3621 4254 8.813951 AGGTCTACAGTTTATAACTTGCTTAGT 58.186 33.333 0.00 0.00 40.46 2.24
3626 4259 6.872020 TGACAGGTCTACAGTTTATAACTTGC 59.128 38.462 0.65 0.00 40.46 4.01
3682 4320 4.349636 TCTCCAACACAAGAGATACCCAAA 59.650 41.667 0.00 0.00 34.23 3.28
3703 4341 7.254353 GCAACTTGAAAGTTAACTTAGACGTCT 60.254 37.037 23.66 23.66 46.89 4.18
3704 4342 6.844779 GCAACTTGAAAGTTAACTTAGACGTC 59.155 38.462 20.83 14.28 46.89 4.34
3705 4343 6.314400 TGCAACTTGAAAGTTAACTTAGACGT 59.686 34.615 20.83 12.85 46.89 4.34
3706 4344 6.711579 TGCAACTTGAAAGTTAACTTAGACG 58.288 36.000 20.83 12.28 46.89 4.18
4054 4697 3.248446 TTGGGTTCTTCGCCCTCGG 62.248 63.158 1.85 0.00 46.22 4.63
4058 4701 2.361230 CCCTTGGGTTCTTCGCCC 60.361 66.667 0.00 0.00 46.26 6.13
4118 4761 1.075542 CAAAACCTGCGCTCGTCATA 58.924 50.000 9.73 0.00 0.00 2.15
4140 4810 6.757947 TGTAATACAACCTACTAATTCGCACC 59.242 38.462 0.00 0.00 0.00 5.01
4314 4995 5.201713 TGTACTCTCTTTGACAGTCCAAG 57.798 43.478 7.90 7.90 0.00 3.61
4349 5030 1.468127 TCACGTCGACGGCAGTTTATA 59.532 47.619 37.89 11.36 44.95 0.98
4351 5032 0.241749 ATCACGTCGACGGCAGTTTA 59.758 50.000 37.89 17.06 44.95 2.01
4358 5039 2.230940 GCCATCATCACGTCGACGG 61.231 63.158 37.89 26.87 44.95 4.79
4391 5072 3.166679 TGTAGGTTGCCCCCAAAATTAC 58.833 45.455 0.00 0.00 31.68 1.89
4445 5126 1.741706 CTGACAGGCGAATGCAATCTT 59.258 47.619 0.00 0.00 45.35 2.40
4457 5138 3.426568 GTGGCTTCGCTGACAGGC 61.427 66.667 4.26 0.00 36.13 4.85
4467 5148 2.960170 CTGCTTGGCTGTGGCTTC 59.040 61.111 0.00 0.00 38.73 3.86
4474 5155 2.340328 TGATGCTGCTGCTTGGCTG 61.340 57.895 17.00 0.00 40.48 4.85
4508 5634 0.250901 ACCCATTGGCTGACACTGAC 60.251 55.000 1.92 0.00 31.88 3.51
4598 5737 6.090493 ACGCTTTAAACTTACTTTCGATCTCC 59.910 38.462 0.00 0.00 0.00 3.71
4656 5795 5.407407 TCCTCTAGAACAAACATGGAGAC 57.593 43.478 0.00 0.00 0.00 3.36
4669 5808 5.437060 AGCAACAAAAGTGTTCCTCTAGAA 58.563 37.500 0.00 0.00 45.00 2.10
4670 5809 5.036117 AGCAACAAAAGTGTTCCTCTAGA 57.964 39.130 0.00 0.00 45.00 2.43
4671 5810 5.349824 GAGCAACAAAAGTGTTCCTCTAG 57.650 43.478 3.75 0.00 45.52 2.43
4675 5814 5.047377 TGAAAAGAGCAACAAAAGTGTTCCT 60.047 36.000 0.00 0.00 45.00 3.36
4676 5815 5.167845 TGAAAAGAGCAACAAAAGTGTTCC 58.832 37.500 0.00 0.00 45.00 3.62
4696 5835 6.723298 ACACATTTACAAGTGGGATTTGAA 57.277 33.333 0.00 0.00 39.99 2.69
4745 5884 0.872388 ATCACGAACCGGAGCAAAAC 59.128 50.000 9.46 0.00 0.00 2.43
4754 5893 3.319972 TCCTTATAGGGAATCACGAACCG 59.680 47.826 0.06 0.00 35.59 4.44
4865 6047 4.159321 TCCACTAGCTCTTGAGTCTTCATG 59.841 45.833 0.00 0.00 32.27 3.07
4968 6150 1.069775 GGTCCCCACCTACCAAGAAA 58.930 55.000 0.00 0.00 40.00 2.52
4992 6174 3.009695 ACGGAAATTTCATGGTAGGTGGA 59.990 43.478 19.49 0.00 0.00 4.02
5063 6245 6.295916 CCATATTTGGAGTACAGGAGGGATAC 60.296 46.154 0.00 0.00 46.92 2.24
5120 6302 6.875195 ACCTTTCAAAATCACCATATGCTTTG 59.125 34.615 0.00 2.41 34.53 2.77
5124 6306 7.649306 GTCATACCTTTCAAAATCACCATATGC 59.351 37.037 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.