Multiple sequence alignment - TraesCS1D01G155100

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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 TraesCS1D01G155100 chr1D 100.000 5860 0 0 1 5860 217141999 217147858 0.000000e+00 10822.0
1 TraesCS1D01G155100 chr1D 95.833 48 0 2 4866 4911 217146818 217146865 6.300000e-10 76.8
2 TraesCS1D01G155100 chr1D 95.833 48 0 2 4820 4867 217146864 217146909 6.300000e-10 76.8
3 TraesCS1D01G155100 chr1B 95.772 4920 133 14 1 4867 310926080 310930977 0.000000e+00 7864.0
4 TraesCS1D01G155100 chr1B 88.304 1026 37 32 4866 5842 310930930 310931921 0.000000e+00 1153.0
5 TraesCS1D01G155100 chr1A 91.895 2665 101 38 1 2596 278140908 278143526 0.000000e+00 3618.0
6 TraesCS1D01G155100 chr1A 91.585 2258 149 17 2612 4867 278143513 278145731 0.000000e+00 3079.0
7 TraesCS1D01G155100 chr1A 82.454 1043 64 53 4866 5842 278145684 278146673 0.000000e+00 802.0
8 TraesCS1D01G155100 chr7D 81.298 647 90 20 1025 1669 556120969 556121586 4.080000e-136 496.0
9 TraesCS1D01G155100 chr7D 86.842 76 10 0 3987 4062 556122445 556122520 1.050000e-12 86.1
10 TraesCS1D01G155100 chr7B 81.048 649 91 25 1025 1669 602938414 602939034 6.830000e-134 488.0
11 TraesCS1D01G155100 chr7B 86.842 76 10 0 3987 4062 602939910 602939985 1.050000e-12 86.1
12 TraesCS1D01G155100 chr7A 80.923 650 96 22 1025 1669 641581297 641580671 6.830000e-134 488.0
13 TraesCS1D01G155100 chr7A 88.158 76 9 0 3987 4062 641579801 641579726 2.250000e-14 91.6
14 TraesCS1D01G155100 chr6A 77.794 680 117 27 1012 1683 415907638 415906985 7.120000e-104 388.0
15 TraesCS1D01G155100 chr2D 80.583 515 87 11 1177 1682 480778479 480777969 9.210000e-103 385.0
16 TraesCS1D01G155100 chr2A 79.961 514 92 9 1177 1682 623564564 623564054 9.280000e-98 368.0
17 TraesCS1D01G155100 chr2B 80.679 471 78 10 1220 1682 563923866 563923401 2.600000e-93 353.0


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 TraesCS1D01G155100 chr1D 217141999 217147858 5859 False 3658.533333 10822 97.222000 1 5860 3 chr1D.!!$F1 5859
1 TraesCS1D01G155100 chr1B 310926080 310931921 5841 False 4508.500000 7864 92.038000 1 5842 2 chr1B.!!$F1 5841
2 TraesCS1D01G155100 chr1A 278140908 278146673 5765 False 2499.666667 3618 88.644667 1 5842 3 chr1A.!!$F1 5841
3 TraesCS1D01G155100 chr7D 556120969 556122520 1551 False 291.050000 496 84.070000 1025 4062 2 chr7D.!!$F1 3037
4 TraesCS1D01G155100 chr7B 602938414 602939985 1571 False 287.050000 488 83.945000 1025 4062 2 chr7B.!!$F1 3037
5 TraesCS1D01G155100 chr7A 641579726 641581297 1571 True 289.800000 488 84.540500 1025 4062 2 chr7A.!!$R1 3037
6 TraesCS1D01G155100 chr6A 415906985 415907638 653 True 388.000000 388 77.794000 1012 1683 1 chr6A.!!$R1 671
7 TraesCS1D01G155100 chr2D 480777969 480778479 510 True 385.000000 385 80.583000 1177 1682 1 chr2D.!!$R1 505
8 TraesCS1D01G155100 chr2A 623564054 623564564 510 True 368.000000 368 79.961000 1177 1682 1 chr2A.!!$R1 505

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
992 1024 0.879090 ATTTCGAGGCGGTGGTTTTC 59.121 50.000 0.0 0.0 0.0 2.29 F
2022 2147 1.564348 AGCTGGTTTATGGGGACGATT 59.436 47.619 0.0 0.0 0.0 3.34 F
2714 2979 0.179043 TTAGCACCCAACGTGAAGCA 60.179 50.000 0.0 0.0 46.2 3.91 F
2716 2981 0.823356 AGCACCCAACGTGAAGCATT 60.823 50.000 0.0 0.0 46.2 3.56 F
2882 3148 1.274447 GCCGTACACAGTAGAAGGGTT 59.726 52.381 0.0 0.0 0.0 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2297 0.098552 TAAATGGTGCGCTGCATTCG 59.901 50.000 9.73 4.38 41.91 3.34 R
3447 3717 0.103208 ATAAACGGCCGAGAGAGCTG 59.897 55.000 35.90 0.00 42.55 4.24 R
4515 4791 1.138047 GACGGCCATACAACTCGTCG 61.138 60.000 2.24 0.00 40.22 5.12 R
4675 4951 3.566322 AGAAGAAGATACTATCGCGCACT 59.434 43.478 8.75 0.00 0.00 4.40 R
4866 5142 0.028110 GCATTCGATGAGGTTTCGCC 59.972 55.000 0.00 0.00 36.56 5.54 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
251 267 1.659335 CAGCACAAAAGGCAGCACG 60.659 57.895 0.00 0.00 0.00 5.34
325 341 1.548719 CAGTCATCTACGGTTGGTGGA 59.451 52.381 3.11 0.00 40.69 4.02
326 342 2.028476 CAGTCATCTACGGTTGGTGGAA 60.028 50.000 3.11 0.00 39.77 3.53
328 344 1.066430 TCATCTACGGTTGGTGGAAGC 60.066 52.381 3.11 0.00 39.77 3.86
412 428 4.052229 CACTGCAGCAGCCAAGCC 62.052 66.667 23.05 0.00 41.13 4.35
413 429 4.591399 ACTGCAGCAGCCAAGCCA 62.591 61.111 23.05 0.00 41.13 4.75
611 639 8.137437 AGGATTGGATATTTATTCTGTTTTGCG 58.863 33.333 0.00 0.00 0.00 4.85
612 640 7.920682 GGATTGGATATTTATTCTGTTTTGCGT 59.079 33.333 0.00 0.00 0.00 5.24
613 641 9.301153 GATTGGATATTTATTCTGTTTTGCGTT 57.699 29.630 0.00 0.00 0.00 4.84
614 642 8.459521 TTGGATATTTATTCTGTTTTGCGTTG 57.540 30.769 0.00 0.00 0.00 4.10
615 643 6.529829 TGGATATTTATTCTGTTTTGCGTTGC 59.470 34.615 0.00 0.00 0.00 4.17
992 1024 0.879090 ATTTCGAGGCGGTGGTTTTC 59.121 50.000 0.00 0.00 0.00 2.29
1770 1883 4.499183 ACGAGGAGAACAAGATGATGAAC 58.501 43.478 0.00 0.00 0.00 3.18
1794 1907 2.357275 CCCGCCGGTTACGTCAAA 60.357 61.111 1.90 0.00 38.78 2.69
2019 2144 2.702592 TTAGCTGGTTTATGGGGACG 57.297 50.000 0.00 0.00 0.00 4.79
2022 2147 1.564348 AGCTGGTTTATGGGGACGATT 59.436 47.619 0.00 0.00 0.00 3.34
2259 2507 1.577328 AACATGACCAGCTTTCCGCG 61.577 55.000 0.00 0.00 45.59 6.46
2262 2510 3.793144 GACCAGCTTTCCGCGCAG 61.793 66.667 8.75 0.00 45.59 5.18
2482 2744 7.004691 AGTAGTTATGGAAGAAAAGGCTTGTT 58.995 34.615 0.00 0.00 0.00 2.83
2535 2797 8.851541 AATTTGGATTATCAGTTTGCATGTTT 57.148 26.923 0.00 0.00 0.00 2.83
2659 2924 3.241067 TCTTGAATAGTACGCCACCAC 57.759 47.619 0.00 0.00 0.00 4.16
2714 2979 0.179043 TTAGCACCCAACGTGAAGCA 60.179 50.000 0.00 0.00 46.20 3.91
2716 2981 0.823356 AGCACCCAACGTGAAGCATT 60.823 50.000 0.00 0.00 46.20 3.56
2787 3052 5.351465 CGTTTAGCATGGTTAGATGTGACTT 59.649 40.000 1.12 0.00 0.00 3.01
2788 3053 6.546395 GTTTAGCATGGTTAGATGTGACTTG 58.454 40.000 1.12 0.00 0.00 3.16
2790 3055 4.655963 AGCATGGTTAGATGTGACTTGTT 58.344 39.130 0.00 0.00 0.00 2.83
2797 3062 6.371548 TGGTTAGATGTGACTTGTTTAGATGC 59.628 38.462 0.00 0.00 0.00 3.91
2882 3148 1.274447 GCCGTACACAGTAGAAGGGTT 59.726 52.381 0.00 0.00 0.00 4.11
2941 3207 7.500227 TCATCTGTCAGATTTGTTCAGTTTCTT 59.500 33.333 12.88 0.00 31.32 2.52
2950 3216 8.477256 AGATTTGTTCAGTTTCTTTCATGGAAA 58.523 29.630 0.00 0.00 0.00 3.13
2979 3245 6.014070 TCCCTGTACAAATAGTAAGAGTGCAA 60.014 38.462 0.00 0.00 33.72 4.08
3083 3349 5.391416 GCTCCATGCTAGTTCTTTCAAAGTC 60.391 44.000 0.00 0.00 38.95 3.01
3134 3400 9.777297 ACCTCATAAACAAATGCAATAAAGTTT 57.223 25.926 0.00 0.87 32.20 2.66
3308 3578 3.762823 CCTCTACTTGAAAGTCCTACCGT 59.237 47.826 0.00 0.00 40.37 4.83
3343 3613 2.496070 CTGATCAGTCCCGTACTCCAAA 59.504 50.000 14.95 0.00 35.76 3.28
3447 3717 9.698309 TGCTAGCTCTATGTATCTATTGTTTTC 57.302 33.333 17.23 0.00 0.00 2.29
3500 3770 7.172361 GCTACTTCATGGAATCTTATCTCAACC 59.828 40.741 0.00 0.00 0.00 3.77
3649 3919 8.564574 TCAATTTTAGTTGGTGTTGTGATACTC 58.435 33.333 0.00 0.00 0.00 2.59
3651 3921 8.691661 ATTTTAGTTGGTGTTGTGATACTCTT 57.308 30.769 0.00 0.00 0.00 2.85
3652 3922 8.514330 TTTTAGTTGGTGTTGTGATACTCTTT 57.486 30.769 0.00 0.00 0.00 2.52
3819 4089 2.422597 TGGCTTGTGGAACTTGTATCG 58.577 47.619 0.00 0.00 38.04 2.92
4077 4353 1.688197 CTGCACCTTGGTTTGTTCCAT 59.312 47.619 0.00 0.00 37.33 3.41
4290 4566 2.775890 CAGCAGATGACTTCAAGTGGT 58.224 47.619 0.00 0.00 0.00 4.16
4435 4711 1.661463 TGAGGCTTCTGACCTTGGAT 58.339 50.000 0.00 0.00 37.77 3.41
4515 4791 4.642429 ACTTGTCTGTCTTTGGGTCATAC 58.358 43.478 0.00 0.00 0.00 2.39
4620 4896 3.434319 GCCGTCATGCACACTGGG 61.434 66.667 0.00 0.00 0.00 4.45
4679 4955 5.179368 TGCACAGTATTCTTTAACTCAGTGC 59.821 40.000 0.00 0.00 46.21 4.40
4703 4979 5.797934 CGCGATAGTATCTTCTTCTTCATCC 59.202 44.000 0.00 0.00 39.35 3.51
4726 5002 6.095300 TCCTCCAATATTGCAGTAATGTTGTG 59.905 38.462 16.07 9.83 42.80 3.33
4843 5119 2.868583 CGAAACCTCTCATCGAATGCAT 59.131 45.455 0.00 0.00 38.82 3.96
4844 5120 3.302935 CGAAACCTCTCATCGAATGCATG 60.303 47.826 0.00 0.00 38.82 4.06
4845 5121 2.251409 ACCTCTCATCGAATGCATGG 57.749 50.000 0.00 0.00 0.00 3.66
4846 5122 1.487976 ACCTCTCATCGAATGCATGGT 59.512 47.619 0.00 0.00 0.00 3.55
4847 5123 2.092753 ACCTCTCATCGAATGCATGGTT 60.093 45.455 0.00 0.00 0.00 3.67
4848 5124 2.547211 CCTCTCATCGAATGCATGGTTC 59.453 50.000 0.00 0.00 0.00 3.62
4849 5125 3.200483 CTCTCATCGAATGCATGGTTCA 58.800 45.455 0.00 0.00 0.00 3.18
4850 5126 3.200483 TCTCATCGAATGCATGGTTCAG 58.800 45.455 0.00 0.00 0.00 3.02
4851 5127 1.672363 TCATCGAATGCATGGTTCAGC 59.328 47.619 0.00 0.00 0.00 4.26
4852 5128 0.659427 ATCGAATGCATGGTTCAGCG 59.341 50.000 0.00 0.00 0.00 5.18
4853 5129 1.063006 CGAATGCATGGTTCAGCGG 59.937 57.895 0.00 0.00 0.00 5.52
4854 5130 1.434696 GAATGCATGGTTCAGCGGG 59.565 57.895 0.00 0.00 0.00 6.13
4855 5131 1.304381 AATGCATGGTTCAGCGGGT 60.304 52.632 0.00 0.00 0.00 5.28
4856 5132 1.597797 AATGCATGGTTCAGCGGGTG 61.598 55.000 0.00 0.00 0.00 4.61
4857 5133 2.672996 GCATGGTTCAGCGGGTGT 60.673 61.111 7.12 0.00 0.00 4.16
4858 5134 2.981560 GCATGGTTCAGCGGGTGTG 61.982 63.158 7.12 0.00 0.00 3.82
4859 5135 1.302431 CATGGTTCAGCGGGTGTGA 60.302 57.895 7.12 0.00 0.00 3.58
4860 5136 0.677731 CATGGTTCAGCGGGTGTGAT 60.678 55.000 7.12 0.00 0.00 3.06
4861 5137 0.908910 ATGGTTCAGCGGGTGTGATA 59.091 50.000 7.12 0.00 0.00 2.15
4862 5138 0.908910 TGGTTCAGCGGGTGTGATAT 59.091 50.000 7.12 0.00 0.00 1.63
4863 5139 1.134521 TGGTTCAGCGGGTGTGATATC 60.135 52.381 7.12 0.00 0.00 1.63
4864 5140 1.139058 GGTTCAGCGGGTGTGATATCT 59.861 52.381 7.12 0.00 0.00 1.98
4865 5141 2.420129 GGTTCAGCGGGTGTGATATCTT 60.420 50.000 7.12 0.00 0.00 2.40
4866 5142 2.602257 TCAGCGGGTGTGATATCTTG 57.398 50.000 7.12 0.00 0.00 3.02
4867 5143 1.138859 TCAGCGGGTGTGATATCTTGG 59.861 52.381 7.12 0.00 0.00 3.61
4868 5144 0.179045 AGCGGGTGTGATATCTTGGC 60.179 55.000 3.98 0.00 0.00 4.52
4869 5145 1.498865 GCGGGTGTGATATCTTGGCG 61.499 60.000 3.98 0.00 0.00 5.69
4870 5146 0.104120 CGGGTGTGATATCTTGGCGA 59.896 55.000 3.98 0.00 0.00 5.54
4871 5147 1.472552 CGGGTGTGATATCTTGGCGAA 60.473 52.381 3.98 0.00 0.00 4.70
4872 5148 2.639065 GGGTGTGATATCTTGGCGAAA 58.361 47.619 3.98 0.00 0.00 3.46
4873 5149 2.354821 GGGTGTGATATCTTGGCGAAAC 59.645 50.000 3.98 0.00 0.00 2.78
4874 5150 2.354821 GGTGTGATATCTTGGCGAAACC 59.645 50.000 3.98 0.00 39.84 3.27
4875 5151 3.270877 GTGTGATATCTTGGCGAAACCT 58.729 45.455 3.98 0.00 40.22 3.50
4876 5152 3.309954 GTGTGATATCTTGGCGAAACCTC 59.690 47.826 3.98 0.00 40.22 3.85
4877 5153 3.055458 TGTGATATCTTGGCGAAACCTCA 60.055 43.478 3.98 0.00 40.22 3.86
4878 5154 4.130118 GTGATATCTTGGCGAAACCTCAT 58.870 43.478 3.98 0.00 40.22 2.90
4879 5155 4.212214 GTGATATCTTGGCGAAACCTCATC 59.788 45.833 3.98 0.00 40.22 2.92
4880 5156 1.656652 ATCTTGGCGAAACCTCATCG 58.343 50.000 0.00 0.00 42.99 3.84
4881 5157 0.606096 TCTTGGCGAAACCTCATCGA 59.394 50.000 0.00 0.00 42.76 3.59
4882 5158 1.001520 TCTTGGCGAAACCTCATCGAA 59.998 47.619 0.00 0.00 42.76 3.71
4883 5159 2.009774 CTTGGCGAAACCTCATCGAAT 58.990 47.619 0.00 0.00 42.76 3.34
4884 5160 1.368641 TGGCGAAACCTCATCGAATG 58.631 50.000 0.00 0.00 42.76 2.67
4885 5161 0.028110 GGCGAAACCTCATCGAATGC 59.972 55.000 0.00 0.00 42.76 3.56
4886 5162 0.726827 GCGAAACCTCATCGAATGCA 59.273 50.000 0.00 0.00 42.76 3.96
4999 5276 5.284188 GCATGCGTTTTATTAGCGTTTGTTA 59.716 36.000 0.00 0.00 0.00 2.41
5040 5317 2.092838 ACTGCGTCGTCGTTAGTACTAC 59.907 50.000 0.91 0.00 39.49 2.73
5041 5318 2.065512 TGCGTCGTCGTTAGTACTACA 58.934 47.619 0.91 0.00 39.49 2.74
5042 5319 2.478514 TGCGTCGTCGTTAGTACTACAA 59.521 45.455 0.91 0.00 39.49 2.41
5043 5320 3.125146 TGCGTCGTCGTTAGTACTACAAT 59.875 43.478 0.91 0.00 39.49 2.71
5044 5321 4.328712 TGCGTCGTCGTTAGTACTACAATA 59.671 41.667 0.91 0.00 39.49 1.90
5142 5419 1.972588 AGTTAAGGGCTGGTCATCCT 58.027 50.000 0.00 0.00 34.23 3.24
5162 5439 2.970974 GCGGCTGAGTTGGAAGTGC 61.971 63.158 0.00 0.00 0.00 4.40
5163 5440 1.302033 CGGCTGAGTTGGAAGTGCT 60.302 57.895 0.00 0.00 0.00 4.40
5242 5533 8.094548 GGTCTTTGGAAATTAATTAAAGCTGGT 58.905 33.333 13.59 0.00 0.00 4.00
5319 5629 1.871039 CTTACCTTGGGACGTGTTGTG 59.129 52.381 0.00 0.00 0.00 3.33
5324 5634 2.014128 CTTGGGACGTGTTGTGTCTTT 58.986 47.619 0.00 0.00 36.58 2.52
5325 5635 2.116827 TGGGACGTGTTGTGTCTTTT 57.883 45.000 0.00 0.00 36.58 2.27
5327 5637 2.285977 GGGACGTGTTGTGTCTTTTCT 58.714 47.619 0.00 0.00 36.58 2.52
5328 5638 2.031683 GGGACGTGTTGTGTCTTTTCTG 59.968 50.000 0.00 0.00 36.58 3.02
5329 5639 2.031683 GGACGTGTTGTGTCTTTTCTGG 59.968 50.000 0.00 0.00 36.58 3.86
5330 5640 2.933906 GACGTGTTGTGTCTTTTCTGGA 59.066 45.455 0.00 0.00 33.54 3.86
5331 5641 2.676342 ACGTGTTGTGTCTTTTCTGGAC 59.324 45.455 0.00 0.00 0.00 4.02
5353 5680 4.399303 ACTGTTGTGTTCTTTTCCTGGAAG 59.601 41.667 9.42 0.00 0.00 3.46
5432 5788 0.969894 GCTATAGGCGTGACCCATCT 59.030 55.000 1.04 0.00 40.58 2.90
5433 5789 1.337260 GCTATAGGCGTGACCCATCTG 60.337 57.143 1.04 0.00 40.58 2.90
5434 5790 1.273606 CTATAGGCGTGACCCATCTGG 59.726 57.143 0.00 0.00 40.58 3.86
5437 5793 4.408821 GCGTGACCCATCTGGCCA 62.409 66.667 4.71 4.71 37.83 5.36
5438 5794 2.591753 CGTGACCCATCTGGCCAT 59.408 61.111 5.51 0.00 37.83 4.40
5439 5795 1.524621 CGTGACCCATCTGGCCATC 60.525 63.158 5.51 0.00 37.83 3.51
5441 5797 1.308128 TGACCCATCTGGCCATCCT 60.308 57.895 5.51 0.00 37.83 3.24
5528 5894 8.346300 ACCCTACTTTTTGTTTTGTTTTGTTTG 58.654 29.630 0.00 0.00 0.00 2.93
5529 5895 7.324856 CCCTACTTTTTGTTTTGTTTTGTTTGC 59.675 33.333 0.00 0.00 0.00 3.68
5582 5949 1.438222 GCCGTGACGCGAGAAAAAC 60.438 57.895 15.93 0.06 44.77 2.43
5604 5971 0.179097 GCGCGAGGAGGAAGAGAAAT 60.179 55.000 12.10 0.00 0.00 2.17
5645 6013 3.066190 CTGGACACGCCTACCGGA 61.066 66.667 9.46 0.00 42.52 5.14
5648 6016 2.585247 GACACGCCTACCGGATGC 60.585 66.667 9.46 6.49 42.52 3.91
5668 6036 3.701040 TGCTTAATTGGATTGGAGGCTTC 59.299 43.478 0.00 0.00 0.00 3.86
5677 6045 1.492133 TTGGAGGCTTCTGGGTCTGG 61.492 60.000 0.00 0.00 0.00 3.86
5695 6063 3.114616 CAGGCTGCAAGGTCGTCG 61.115 66.667 0.00 0.00 0.00 5.12
5709 6077 0.740149 TCGTCGTAGTGTGGTGTTGT 59.260 50.000 0.00 0.00 0.00 3.32
5722 6090 0.584876 GTGTTGTTGCTACACCGTCC 59.415 55.000 0.00 0.00 39.93 4.79
5729 6097 0.540133 TGCTACACCGTCCTGTGGTA 60.540 55.000 0.00 0.00 40.62 3.25
5737 6105 1.532604 CGTCCTGTGGTAGCCTGTCA 61.533 60.000 0.00 0.00 0.00 3.58
5738 6106 0.037232 GTCCTGTGGTAGCCTGTCAC 60.037 60.000 0.00 0.00 0.00 3.67
5739 6107 1.079819 CCTGTGGTAGCCTGTCACG 60.080 63.158 0.00 0.00 34.43 4.35
5740 6108 1.738099 CTGTGGTAGCCTGTCACGC 60.738 63.158 0.00 0.00 34.43 5.34
5741 6109 2.159819 CTGTGGTAGCCTGTCACGCT 62.160 60.000 1.85 1.85 40.45 5.07
5767 6135 0.103026 GGGACGGTACCGGTTATGAC 59.897 60.000 35.86 17.43 44.69 3.06
5842 6210 2.235898 TGTCCGTGATGATGACCATGAA 59.764 45.455 0.00 0.00 35.17 2.57
5843 6211 2.868583 GTCCGTGATGATGACCATGAAG 59.131 50.000 0.00 0.00 35.17 3.02
5844 6212 1.600957 CCGTGATGATGACCATGAAGC 59.399 52.381 0.00 0.00 35.17 3.86
5845 6213 1.600957 CGTGATGATGACCATGAAGCC 59.399 52.381 0.00 0.00 35.17 4.35
5846 6214 1.600957 GTGATGATGACCATGAAGCCG 59.399 52.381 0.00 0.00 35.17 5.52
5847 6215 1.233019 GATGATGACCATGAAGCCGG 58.767 55.000 0.00 0.00 35.17 6.13
5848 6216 0.820891 ATGATGACCATGAAGCCGGC 60.821 55.000 21.89 21.89 33.39 6.13
5849 6217 2.124151 ATGACCATGAAGCCGGCC 60.124 61.111 26.15 9.73 0.00 6.13
5850 6218 3.721370 ATGACCATGAAGCCGGCCC 62.721 63.158 26.15 16.67 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 193 1.218316 GTAGGGAGTGGCGACAAGG 59.782 63.158 0.00 0.00 46.06 3.61
251 267 1.064017 TGATAAAGGATGTGGGGCCAC 60.064 52.381 4.39 0.00 46.33 5.01
262 278 0.108520 GGCGTGTCGGTGATAAAGGA 60.109 55.000 0.00 0.00 0.00 3.36
298 314 0.976073 CCGTAGATGACTGGTGGGGT 60.976 60.000 0.00 0.00 0.00 4.95
412 428 2.564975 CTCGCTTGGCTTGGCTTG 59.435 61.111 0.00 0.00 0.00 4.01
413 429 3.368571 GCTCGCTTGGCTTGGCTT 61.369 61.111 0.00 0.00 0.00 4.35
521 537 2.684735 GGAGGACGAGGAGGGAGT 59.315 66.667 0.00 0.00 0.00 3.85
611 639 1.215014 GCCGGTCAAAGCAAAGCAAC 61.215 55.000 1.90 0.00 0.00 4.17
612 640 1.067250 GCCGGTCAAAGCAAAGCAA 59.933 52.632 1.90 0.00 0.00 3.91
613 641 2.727544 GCCGGTCAAAGCAAAGCA 59.272 55.556 1.90 0.00 0.00 3.91
614 642 2.429069 CGCCGGTCAAAGCAAAGC 60.429 61.111 1.90 0.00 0.00 3.51
615 643 2.429069 GCGCCGGTCAAAGCAAAG 60.429 61.111 1.90 0.00 0.00 2.77
992 1024 0.176680 CACCTCCTTCATCTCCACCG 59.823 60.000 0.00 0.00 0.00 4.94
1794 1907 2.121506 TTCACCTTCCCCCTGCCT 60.122 61.111 0.00 0.00 0.00 4.75
2001 2126 1.868713 TCGTCCCCATAAACCAGCTA 58.131 50.000 0.00 0.00 0.00 3.32
2019 2144 2.095212 GGCAACCTGAACCGAAGAAATC 60.095 50.000 0.00 0.00 0.00 2.17
2022 2147 3.015516 GGCAACCTGAACCGAAGAA 57.984 52.632 0.00 0.00 0.00 2.52
2169 2294 0.815213 ATGGTGCGCTGCATTCGTAT 60.815 50.000 9.73 0.00 41.91 3.06
2172 2297 0.098552 TAAATGGTGCGCTGCATTCG 59.901 50.000 9.73 4.38 41.91 3.34
2451 2713 8.476447 GCCTTTTCTTCCATAACTACTAGTACT 58.524 37.037 0.00 0.00 0.00 2.73
2452 2714 8.476447 AGCCTTTTCTTCCATAACTACTAGTAC 58.524 37.037 0.00 0.00 0.00 2.73
2453 2715 8.605325 AGCCTTTTCTTCCATAACTACTAGTA 57.395 34.615 1.89 1.89 0.00 1.82
2454 2716 7.497773 AGCCTTTTCTTCCATAACTACTAGT 57.502 36.000 0.00 0.00 0.00 2.57
2455 2717 7.824779 ACAAGCCTTTTCTTCCATAACTACTAG 59.175 37.037 0.00 0.00 0.00 2.57
2456 2718 7.686434 ACAAGCCTTTTCTTCCATAACTACTA 58.314 34.615 0.00 0.00 0.00 1.82
2482 2744 3.072476 ACCAGCAAAGCTACTAAAGGACA 59.928 43.478 0.00 0.00 36.40 4.02
2535 2797 7.952671 TGACAAAGAAGAGAGCTACTTAGAAA 58.047 34.615 5.76 0.00 0.00 2.52
2669 2934 3.366679 CCAAACATCAAGCTGTGACATCC 60.367 47.826 0.00 0.00 39.72 3.51
2670 2935 3.254166 ACCAAACATCAAGCTGTGACATC 59.746 43.478 0.00 0.00 39.72 3.06
2787 3052 5.874810 AGACAAATAGCTTCGCATCTAAACA 59.125 36.000 0.00 0.00 0.00 2.83
2788 3053 6.351327 AGACAAATAGCTTCGCATCTAAAC 57.649 37.500 0.00 0.00 0.00 2.01
2790 3055 8.662781 AATTAGACAAATAGCTTCGCATCTAA 57.337 30.769 0.00 1.64 0.00 2.10
2841 3106 6.374333 ACGGCATTTCATTAGATTTGTGTACT 59.626 34.615 0.00 0.00 0.00 2.73
2950 3216 8.041323 CACTCTTACTATTTGTACAGGGACAAT 58.959 37.037 0.00 0.00 39.04 2.71
2979 3245 4.277476 AGACTCCGATCTCAATTCTCTGT 58.723 43.478 0.00 0.00 0.00 3.41
3083 3349 7.169140 GTGCCAGTAAGAATTTGGTTGTAAAAG 59.831 37.037 0.00 0.00 34.43 2.27
3134 3400 4.225042 AGGAACATGCAGTATTCTACACCA 59.775 41.667 0.00 0.00 0.00 4.17
3225 3495 8.501580 CATGGATCATTGTCATACTACATGAAC 58.498 37.037 0.00 0.00 35.30 3.18
3226 3496 8.212995 ACATGGATCATTGTCATACTACATGAA 58.787 33.333 0.00 0.00 36.44 2.57
3227 3497 7.738847 ACATGGATCATTGTCATACTACATGA 58.261 34.615 0.00 0.00 36.44 3.07
3241 3511 7.975616 GCACAAACAGTTTATACATGGATCATT 59.024 33.333 0.00 0.00 0.00 2.57
3308 3578 7.500992 GGGACTGATCAGATAAGACAAATGTA 58.499 38.462 29.27 0.00 0.00 2.29
3447 3717 0.103208 ATAAACGGCCGAGAGAGCTG 59.897 55.000 35.90 0.00 42.55 4.24
3500 3770 7.281040 TCCTACGTAGGTGGATAACATAAAG 57.719 40.000 34.80 9.32 44.02 1.85
3649 3919 6.363357 GGTGCTTGTAGAACTAAAATGCAAAG 59.637 38.462 0.00 0.00 0.00 2.77
3651 3921 5.300539 TGGTGCTTGTAGAACTAAAATGCAA 59.699 36.000 0.00 0.00 0.00 4.08
3652 3922 4.824537 TGGTGCTTGTAGAACTAAAATGCA 59.175 37.500 0.00 0.00 0.00 3.96
3819 4089 3.788937 CAAATGGATTGGTGGAATGCTC 58.211 45.455 0.00 0.00 33.62 4.26
4098 4374 1.602327 AAGACGGGGTTAGAGCGTCC 61.602 60.000 0.00 0.00 0.00 4.79
4311 4587 2.169769 TGAACTATTTCCAGTAGCCCCG 59.830 50.000 0.00 0.00 0.00 5.73
4435 4711 2.598394 GCAGTGCCCAGCTTCCAA 60.598 61.111 2.85 0.00 0.00 3.53
4515 4791 1.138047 GACGGCCATACAACTCGTCG 61.138 60.000 2.24 0.00 40.22 5.12
4675 4951 3.566322 AGAAGAAGATACTATCGCGCACT 59.434 43.478 8.75 0.00 0.00 4.40
4676 4952 3.891324 AGAAGAAGATACTATCGCGCAC 58.109 45.455 8.75 0.00 0.00 5.34
4679 4955 5.797934 GGATGAAGAAGAAGATACTATCGCG 59.202 44.000 0.00 0.00 0.00 5.87
4843 5119 0.908910 ATATCACACCCGCTGAACCA 59.091 50.000 0.00 0.00 0.00 3.67
4844 5120 1.139058 AGATATCACACCCGCTGAACC 59.861 52.381 5.32 0.00 0.00 3.62
4845 5121 2.604046 AGATATCACACCCGCTGAAC 57.396 50.000 5.32 0.00 0.00 3.18
4846 5122 2.419990 CCAAGATATCACACCCGCTGAA 60.420 50.000 5.32 0.00 0.00 3.02
4847 5123 1.138859 CCAAGATATCACACCCGCTGA 59.861 52.381 5.32 0.00 0.00 4.26
4848 5124 1.586422 CCAAGATATCACACCCGCTG 58.414 55.000 5.32 0.00 0.00 5.18
4849 5125 0.179045 GCCAAGATATCACACCCGCT 60.179 55.000 5.32 0.00 0.00 5.52
4850 5126 1.498865 CGCCAAGATATCACACCCGC 61.499 60.000 5.32 0.00 0.00 6.13
4851 5127 0.104120 TCGCCAAGATATCACACCCG 59.896 55.000 5.32 1.41 0.00 5.28
4852 5128 2.325583 TTCGCCAAGATATCACACCC 57.674 50.000 5.32 0.00 0.00 4.61
4853 5129 2.354821 GGTTTCGCCAAGATATCACACC 59.645 50.000 5.32 0.00 37.17 4.16
4854 5130 3.270877 AGGTTTCGCCAAGATATCACAC 58.729 45.455 5.32 0.00 40.61 3.82
4855 5131 3.055458 TGAGGTTTCGCCAAGATATCACA 60.055 43.478 5.32 0.00 40.61 3.58
4856 5132 3.531538 TGAGGTTTCGCCAAGATATCAC 58.468 45.455 5.32 0.00 40.61 3.06
4857 5133 3.904800 TGAGGTTTCGCCAAGATATCA 57.095 42.857 5.32 0.00 40.61 2.15
4858 5134 3.430218 CGATGAGGTTTCGCCAAGATATC 59.570 47.826 0.00 0.00 40.61 1.63
4859 5135 3.069586 TCGATGAGGTTTCGCCAAGATAT 59.930 43.478 0.00 0.00 40.61 1.63
4860 5136 2.429250 TCGATGAGGTTTCGCCAAGATA 59.571 45.455 0.00 0.00 40.61 1.98
4861 5137 1.207089 TCGATGAGGTTTCGCCAAGAT 59.793 47.619 0.00 0.00 40.61 2.40
4862 5138 0.606096 TCGATGAGGTTTCGCCAAGA 59.394 50.000 0.00 0.00 40.61 3.02
4863 5139 1.438651 TTCGATGAGGTTTCGCCAAG 58.561 50.000 0.00 0.00 40.61 3.61
4864 5140 1.737236 CATTCGATGAGGTTTCGCCAA 59.263 47.619 0.00 0.00 40.61 4.52
4865 5141 1.368641 CATTCGATGAGGTTTCGCCA 58.631 50.000 0.00 0.00 40.61 5.69
4866 5142 0.028110 GCATTCGATGAGGTTTCGCC 59.972 55.000 0.00 0.00 36.56 5.54
4867 5143 0.726827 TGCATTCGATGAGGTTTCGC 59.273 50.000 0.00 0.00 36.56 4.70
4868 5144 2.286595 CCATGCATTCGATGAGGTTTCG 60.287 50.000 0.00 0.00 37.94 3.46
4869 5145 2.684881 ACCATGCATTCGATGAGGTTTC 59.315 45.455 0.00 0.00 30.66 2.78
4870 5146 2.726821 ACCATGCATTCGATGAGGTTT 58.273 42.857 0.00 0.00 30.66 3.27
4871 5147 2.425143 ACCATGCATTCGATGAGGTT 57.575 45.000 0.00 0.00 30.66 3.50
4872 5148 2.292267 GAACCATGCATTCGATGAGGT 58.708 47.619 0.00 0.00 34.42 3.85
4873 5149 2.289820 CTGAACCATGCATTCGATGAGG 59.710 50.000 0.00 0.00 0.00 3.86
4874 5150 2.286831 GCTGAACCATGCATTCGATGAG 60.287 50.000 0.00 0.00 0.00 2.90
4875 5151 1.672363 GCTGAACCATGCATTCGATGA 59.328 47.619 0.00 0.00 0.00 2.92
4876 5152 1.596220 CGCTGAACCATGCATTCGATG 60.596 52.381 0.00 0.00 0.00 3.84
4877 5153 0.659427 CGCTGAACCATGCATTCGAT 59.341 50.000 0.00 0.00 0.00 3.59
4878 5154 1.368345 CCGCTGAACCATGCATTCGA 61.368 55.000 0.00 0.00 0.00 3.71
4879 5155 1.063006 CCGCTGAACCATGCATTCG 59.937 57.895 0.00 0.00 0.00 3.34
4880 5156 1.315257 ACCCGCTGAACCATGCATTC 61.315 55.000 0.00 0.00 0.00 2.67
4881 5157 1.304381 ACCCGCTGAACCATGCATT 60.304 52.632 0.00 0.00 0.00 3.56
4882 5158 2.048023 CACCCGCTGAACCATGCAT 61.048 57.895 0.00 0.00 0.00 3.96
4883 5159 2.672651 CACCCGCTGAACCATGCA 60.673 61.111 0.00 0.00 0.00 3.96
4884 5160 2.672996 ACACCCGCTGAACCATGC 60.673 61.111 0.00 0.00 0.00 4.06
4885 5161 0.677731 ATCACACCCGCTGAACCATG 60.678 55.000 0.00 0.00 0.00 3.66
4886 5162 0.908910 TATCACACCCGCTGAACCAT 59.091 50.000 0.00 0.00 0.00 3.55
4970 5246 6.474819 ACGCTAATAAAACGCATGCATATA 57.525 33.333 19.57 5.25 0.00 0.86
5142 5419 2.032528 CTTCCAACTCAGCCGCCA 59.967 61.111 0.00 0.00 0.00 5.69
5162 5439 3.612860 CCGTCCAAGAGTTCGTTGATAAG 59.387 47.826 0.00 0.00 0.00 1.73
5163 5440 3.256383 TCCGTCCAAGAGTTCGTTGATAA 59.744 43.478 0.00 0.00 0.00 1.75
5242 5533 0.991146 TTTCATCTACCCAGGCAGCA 59.009 50.000 0.00 0.00 0.00 4.41
5319 5629 4.636206 AGAACACAACAGTCCAGAAAAGAC 59.364 41.667 0.00 0.00 34.31 3.01
5324 5634 4.398044 GGAAAAGAACACAACAGTCCAGAA 59.602 41.667 0.00 0.00 0.00 3.02
5325 5635 3.945285 GGAAAAGAACACAACAGTCCAGA 59.055 43.478 0.00 0.00 0.00 3.86
5327 5637 3.694072 CAGGAAAAGAACACAACAGTCCA 59.306 43.478 0.00 0.00 0.00 4.02
5328 5638 3.066760 CCAGGAAAAGAACACAACAGTCC 59.933 47.826 0.00 0.00 0.00 3.85
5329 5639 3.945285 TCCAGGAAAAGAACACAACAGTC 59.055 43.478 0.00 0.00 0.00 3.51
5330 5640 3.963129 TCCAGGAAAAGAACACAACAGT 58.037 40.909 0.00 0.00 0.00 3.55
5331 5641 4.202050 CCTTCCAGGAAAAGAACACAACAG 60.202 45.833 2.72 0.00 37.67 3.16
5353 5680 2.038837 CCGGGAAGACCTTTTCGCC 61.039 63.158 0.00 0.00 36.87 5.54
5479 5835 3.765026 GTGTCTCTCTCACGGAAAGATC 58.235 50.000 0.00 0.00 0.00 2.75
5645 6013 3.919834 AGCCTCCAATCCAATTAAGCAT 58.080 40.909 0.00 0.00 0.00 3.79
5648 6016 4.340381 CCAGAAGCCTCCAATCCAATTAAG 59.660 45.833 0.00 0.00 0.00 1.85
5677 6045 3.426568 GACGACCTTGCAGCCTGC 61.427 66.667 10.45 10.45 45.29 4.85
5688 6056 0.031178 AACACCACACTACGACGACC 59.969 55.000 0.00 0.00 0.00 4.79
5695 6063 3.001939 GTGTAGCAACAACACCACACTAC 59.998 47.826 0.00 0.00 41.10 2.73
5709 6077 1.369692 CCACAGGACGGTGTAGCAA 59.630 57.895 2.17 0.00 37.06 3.91
5722 6090 1.738099 GCGTGACAGGCTACCACAG 60.738 63.158 12.78 10.56 0.00 3.66
5740 6108 1.502163 CGGTACCGTCCCTAGCGTAG 61.502 65.000 26.39 0.00 31.89 3.51
5741 6109 1.523711 CGGTACCGTCCCTAGCGTA 60.524 63.158 26.39 0.00 31.89 4.42
5767 6135 2.095161 GCTCAACCTAGGACGATATCGG 60.095 54.545 27.58 12.01 44.95 4.18
5771 6139 3.014304 ACAGCTCAACCTAGGACGATA 57.986 47.619 17.98 0.00 0.00 2.92
5772 6140 1.853963 ACAGCTCAACCTAGGACGAT 58.146 50.000 17.98 0.00 0.00 3.73
5773 6141 1.629043 AACAGCTCAACCTAGGACGA 58.371 50.000 17.98 10.21 0.00 4.20


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

AutoCloner maintained by Alex Coulton.