Multiple sequence alignment - TraesCS4D01G066200

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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 TraesCS4D01G066200 chr4D 100.000 2714 0 0 1 2714 40952709 40955422 0.000000e+00 5012.0
1 TraesCS4D01G066200 chr4B 88.771 1603 68 42 568 2144 60083036 60084552 0.000000e+00 1860.0
2 TraesCS4D01G066200 chr4B 89.844 512 21 12 2220 2714 60084579 60085076 1.770000e-176 628.0
3 TraesCS4D01G066200 chr4B 82.831 332 32 16 238 557 60079156 60079474 9.570000e-70 274.0
4 TraesCS4D01G066200 chr4B 88.496 226 17 2 4 229 60078880 60079096 5.760000e-67 265.0
5 TraesCS4D01G066200 chr4B 81.121 339 28 20 238 549 60081656 60081985 3.490000e-59 239.0
6 TraesCS4D01G066200 chr4B 88.000 200 11 5 30 229 60081410 60081596 9.780000e-55 224.0
7 TraesCS4D01G066200 chr4B 81.250 80 10 4 2076 2152 20277588 20277511 2.920000e-05 60.2
8 TraesCS4D01G066200 chr4A 86.609 1501 75 60 691 2141 558651462 558650038 0.000000e+00 1543.0
9 TraesCS4D01G066200 chr4A 90.414 532 22 14 77 604 558652002 558651496 0.000000e+00 673.0
10 TraesCS4D01G066200 chr4A 93.458 428 9 7 2291 2714 558649972 558649560 3.840000e-173 617.0
11 TraesCS4D01G066200 chr4A 81.250 80 10 4 2076 2152 592547758 592547835 2.920000e-05 60.2
12 TraesCS4D01G066200 chr4A 81.250 80 10 4 2076 2152 592834128 592834205 2.920000e-05 60.2
13 TraesCS4D01G066200 chr7D 100.000 61 0 0 238 298 48275056 48274996 2.210000e-21 113.0
14 TraesCS4D01G066200 chr7D 93.750 64 2 1 232 293 513408896 513408959 8.000000e-16 95.3
15 TraesCS4D01G066200 chr2D 93.333 45 3 0 2106 2150 580191335 580191379 1.740000e-07 67.6
16 TraesCS4D01G066200 chr7B 95.000 40 1 1 2112 2151 245993865 245993827 8.110000e-06 62.1
17 TraesCS4D01G066200 chr5B 91.111 45 4 0 2106 2150 701152564 701152608 8.110000e-06 62.1
18 TraesCS4D01G066200 chr3D 93.023 43 2 1 2106 2148 567408766 567408807 8.110000e-06 62.1
19 TraesCS4D01G066200 chrUn 81.250 80 10 4 2076 2152 308089915 308089992 2.920000e-05 60.2


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 TraesCS4D01G066200 chr4D 40952709 40955422 2713 False 5012.000000 5012 100.000000 1 2714 1 chr4D.!!$F1 2713
1 TraesCS4D01G066200 chr4B 60078880 60085076 6196 False 581.666667 1860 86.510500 4 2714 6 chr4B.!!$F1 2710
2 TraesCS4D01G066200 chr4A 558649560 558652002 2442 True 944.333333 1543 90.160333 77 2714 3 chr4A.!!$R1 2637

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
996 4635 0.038159 CCTGTTCGTGTCTCCTGTCC 60.038 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 5843 0.09473 GATACAGTTGCGTTGCGTCC 59.905 55.0 0.0 0.0 0.0 4.79 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
49 50 1.413118 CCTTTTTGGTGGGAAGTGCT 58.587 50.000 0.00 0.00 0.00 4.40
56 57 1.075374 TGGTGGGAAGTGCTGCTAATT 59.925 47.619 0.00 0.00 0.00 1.40
60 61 3.507622 GTGGGAAGTGCTGCTAATTTTCT 59.492 43.478 0.00 0.00 0.00 2.52
71 72 3.947834 TGCTAATTTTCTTAGGGCAGCTC 59.052 43.478 0.00 0.00 0.00 4.09
72 73 3.002759 GCTAATTTTCTTAGGGCAGCTCG 59.997 47.826 0.00 0.00 0.00 5.03
73 74 2.789409 ATTTTCTTAGGGCAGCTCGT 57.211 45.000 0.00 0.00 0.00 4.18
74 75 3.906720 ATTTTCTTAGGGCAGCTCGTA 57.093 42.857 0.00 0.00 0.00 3.43
75 76 3.688694 TTTTCTTAGGGCAGCTCGTAA 57.311 42.857 0.00 0.00 0.00 3.18
97 98 8.875803 CGTAATAATTTACAGCAAGTAGTCCAA 58.124 33.333 0.00 0.00 38.06 3.53
123 124 4.134563 GCTCTAGTTCTGGTTTTGTGGAA 58.865 43.478 0.00 0.00 0.00 3.53
150 2651 3.195591 CTAGGCACCCGGACGATCG 62.196 68.421 14.88 14.88 0.00 3.69
256 2808 0.249868 TCTTGCTCACCAACTCACCG 60.250 55.000 0.00 0.00 0.00 4.94
311 2865 0.752743 TCAAGCACAGCAAAGGCAGT 60.753 50.000 0.00 0.00 44.61 4.40
424 2980 1.089920 GACAGGCATGAAATCGCTGT 58.910 50.000 4.84 0.00 0.00 4.40
429 2985 1.468054 GGCATGAAATCGCTGTGTTCC 60.468 52.381 0.00 0.00 0.00 3.62
433 2989 1.573829 GAAATCGCTGTGTTCCGCCA 61.574 55.000 0.00 0.00 0.00 5.69
434 2990 1.852067 AAATCGCTGTGTTCCGCCAC 61.852 55.000 0.00 0.00 35.86 5.01
439 2995 3.583276 CTGTGTTCCGCCACCGCTA 62.583 63.158 0.00 0.00 34.35 4.26
440 2996 2.125269 GTGTTCCGCCACCGCTAT 60.125 61.111 0.00 0.00 0.00 2.97
441 2997 2.171725 GTGTTCCGCCACCGCTATC 61.172 63.158 0.00 0.00 0.00 2.08
502 3083 2.035449 AGCCACGGTAAAAAGCCTTTTC 59.965 45.455 2.34 0.00 36.20 2.29
526 3108 3.951775 TCCAAAGAGAGAGAGAAGCAC 57.048 47.619 0.00 0.00 0.00 4.40
528 3110 2.605030 CAAAGAGAGAGAGAAGCACCG 58.395 52.381 0.00 0.00 0.00 4.94
530 3112 0.610509 AGAGAGAGAGAAGCACCGCA 60.611 55.000 0.00 0.00 0.00 5.69
531 3113 0.457681 GAGAGAGAGAAGCACCGCAC 60.458 60.000 0.00 0.00 0.00 5.34
604 4214 4.830826 GGTAGCCACCACAAAATATAGC 57.169 45.455 0.00 0.00 45.04 2.97
629 4239 4.171005 TGTTCTCGTGTCCGTGAATAATC 58.829 43.478 3.41 0.00 45.07 1.75
630 4240 3.060978 TCTCGTGTCCGTGAATAATCG 57.939 47.619 0.00 0.00 34.02 3.34
631 4241 2.117137 CTCGTGTCCGTGAATAATCGG 58.883 52.381 0.00 0.00 46.93 4.18
632 4242 1.202325 TCGTGTCCGTGAATAATCGGG 60.202 52.381 3.85 0.00 45.79 5.14
633 4243 1.202325 CGTGTCCGTGAATAATCGGGA 60.202 52.381 3.85 0.00 45.79 5.14
634 4244 2.199236 GTGTCCGTGAATAATCGGGAC 58.801 52.381 11.89 11.89 45.23 4.46
635 4245 1.137479 TGTCCGTGAATAATCGGGACC 59.863 52.381 14.77 0.00 44.78 4.46
636 4246 0.386476 TCCGTGAATAATCGGGACCG 59.614 55.000 3.96 3.96 45.79 4.79
637 4247 0.599204 CCGTGAATAATCGGGACCGG 60.599 60.000 11.27 0.00 42.61 5.28
638 4248 1.219522 CGTGAATAATCGGGACCGGC 61.220 60.000 11.27 0.00 40.25 6.13
639 4249 0.106149 GTGAATAATCGGGACCGGCT 59.894 55.000 11.27 0.95 40.25 5.52
640 4250 0.391597 TGAATAATCGGGACCGGCTC 59.608 55.000 11.27 0.00 40.25 4.70
641 4251 0.666577 GAATAATCGGGACCGGCTCG 60.667 60.000 11.27 11.32 43.51 5.03
642 4252 1.397390 AATAATCGGGACCGGCTCGT 61.397 55.000 16.02 2.95 42.47 4.18
643 4253 2.083835 ATAATCGGGACCGGCTCGTG 62.084 60.000 16.02 3.71 42.47 4.35
827 4437 0.543749 CCAAATTCTCTCCCTCGCCT 59.456 55.000 0.00 0.00 0.00 5.52
833 4443 3.684628 TCTCCCTCGCCTTCCCCT 61.685 66.667 0.00 0.00 0.00 4.79
834 4444 3.157949 CTCCCTCGCCTTCCCCTC 61.158 72.222 0.00 0.00 0.00 4.30
842 4452 2.764547 CCTTCCCCTCCCCGACTC 60.765 72.222 0.00 0.00 0.00 3.36
843 4453 2.364961 CTTCCCCTCCCCGACTCT 59.635 66.667 0.00 0.00 0.00 3.24
844 4454 1.758906 CTTCCCCTCCCCGACTCTC 60.759 68.421 0.00 0.00 0.00 3.20
845 4455 3.312989 TTCCCCTCCCCGACTCTCC 62.313 68.421 0.00 0.00 0.00 3.71
846 4456 4.862823 CCCCTCCCCGACTCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
874 4484 1.691434 CTCAGCCTCACCTTATCTCCC 59.309 57.143 0.00 0.00 0.00 4.30
875 4485 1.292242 TCAGCCTCACCTTATCTCCCT 59.708 52.381 0.00 0.00 0.00 4.20
877 4487 0.676736 GCCTCACCTTATCTCCCTCG 59.323 60.000 0.00 0.00 0.00 4.63
878 4488 0.676736 CCTCACCTTATCTCCCTCGC 59.323 60.000 0.00 0.00 0.00 5.03
919 4557 4.584743 CAGCTACTATCAGTATCACCACCA 59.415 45.833 0.00 0.00 29.08 4.17
922 4560 4.737855 ACTATCAGTATCACCACCACAC 57.262 45.455 0.00 0.00 0.00 3.82
978 4617 1.202348 CTGCTTCAAAACCCCGATTCC 59.798 52.381 0.00 0.00 0.00 3.01
983 4622 2.510613 TCAAAACCCCGATTCCTGTTC 58.489 47.619 0.00 0.00 0.00 3.18
985 4624 0.399075 AAACCCCGATTCCTGTTCGT 59.601 50.000 0.00 0.00 34.85 3.85
986 4625 0.321298 AACCCCGATTCCTGTTCGTG 60.321 55.000 0.00 0.00 34.85 4.35
991 4630 1.630148 CGATTCCTGTTCGTGTCTCC 58.370 55.000 0.00 0.00 32.08 3.71
992 4631 1.202582 CGATTCCTGTTCGTGTCTCCT 59.797 52.381 0.00 0.00 32.08 3.69
996 4635 0.038159 CCTGTTCGTGTCTCCTGTCC 60.038 60.000 0.00 0.00 0.00 4.02
997 4636 0.962489 CTGTTCGTGTCTCCTGTCCT 59.038 55.000 0.00 0.00 0.00 3.85
998 4637 0.959553 TGTTCGTGTCTCCTGTCCTC 59.040 55.000 0.00 0.00 0.00 3.71
1003 4642 2.760385 GTCTCCTGTCCTCCCCGG 60.760 72.222 0.00 0.00 0.00 5.73
1019 4658 2.443390 GGCCGACCCCAGTAGCTA 60.443 66.667 0.00 0.00 0.00 3.32
1020 4659 2.499827 GGCCGACCCCAGTAGCTAG 61.500 68.421 0.00 0.00 0.00 3.42
1021 4660 3.130227 CCGACCCCAGTAGCTAGC 58.870 66.667 6.62 6.62 0.00 3.42
1023 4662 1.043673 CCGACCCCAGTAGCTAGCTT 61.044 60.000 24.88 1.98 0.00 3.74
1024 4663 0.386113 CGACCCCAGTAGCTAGCTTC 59.614 60.000 24.88 18.51 0.00 3.86
1025 4664 0.386113 GACCCCAGTAGCTAGCTTCG 59.614 60.000 24.88 13.48 0.00 3.79
1026 4665 0.033405 ACCCCAGTAGCTAGCTTCGA 60.033 55.000 24.88 1.07 0.00 3.71
1053 4708 1.355381 ACATCTTGAACCAGCCCATCA 59.645 47.619 0.00 0.00 0.00 3.07
1246 4904 4.812476 CGAGGCCGCCGTCATCAA 62.812 66.667 3.05 0.00 0.00 2.57
1247 4905 2.892425 GAGGCCGCCGTCATCAAG 60.892 66.667 3.05 0.00 0.00 3.02
1248 4906 3.371097 GAGGCCGCCGTCATCAAGA 62.371 63.158 3.05 0.00 0.00 3.02
1249 4907 2.892425 GGCCGCCGTCATCAAGAG 60.892 66.667 0.00 0.00 0.00 2.85
1250 4908 3.567797 GCCGCCGTCATCAAGAGC 61.568 66.667 0.00 0.00 0.00 4.09
1349 5007 2.202932 AGCATGACGTCCATCGCC 60.203 61.111 14.12 0.00 44.19 5.54
1691 5349 2.519302 CATTGATCCGGCCCACCC 60.519 66.667 0.00 0.00 0.00 4.61
1692 5350 3.820843 ATTGATCCGGCCCACCCC 61.821 66.667 0.00 0.00 0.00 4.95
1812 5488 1.210234 CCGCCATATCTCCATGCCATA 59.790 52.381 0.00 0.00 0.00 2.74
1813 5489 2.158711 CCGCCATATCTCCATGCCATAT 60.159 50.000 0.00 0.00 0.00 1.78
1814 5490 3.548770 CGCCATATCTCCATGCCATATT 58.451 45.455 0.00 0.00 0.00 1.28
1815 5491 3.314357 CGCCATATCTCCATGCCATATTG 59.686 47.826 0.00 0.00 0.00 1.90
1816 5492 3.067742 GCCATATCTCCATGCCATATTGC 59.932 47.826 0.00 0.00 0.00 3.56
1817 5493 3.635373 CCATATCTCCATGCCATATTGCC 59.365 47.826 0.00 0.00 0.00 4.52
1818 5494 2.984435 ATCTCCATGCCATATTGCCA 57.016 45.000 0.00 0.00 0.00 4.92
1819 5495 2.984435 TCTCCATGCCATATTGCCAT 57.016 45.000 0.00 0.00 0.00 4.40
1832 5508 2.951457 TTGCCATGCATGATGAACTG 57.049 45.000 28.31 10.23 38.76 3.16
1833 5509 2.131776 TGCCATGCATGATGAACTGA 57.868 45.000 28.31 0.00 33.31 3.41
1834 5510 2.448453 TGCCATGCATGATGAACTGAA 58.552 42.857 28.31 0.40 33.31 3.02
1835 5511 2.164827 TGCCATGCATGATGAACTGAAC 59.835 45.455 28.31 4.63 33.31 3.18
1836 5512 2.426024 GCCATGCATGATGAACTGAACT 59.574 45.455 28.31 0.00 33.31 3.01
1837 5513 3.488721 GCCATGCATGATGAACTGAACTC 60.489 47.826 28.31 0.00 33.31 3.01
1838 5514 3.945921 CCATGCATGATGAACTGAACTCT 59.054 43.478 28.31 0.00 33.31 3.24
1839 5515 5.121105 CCATGCATGATGAACTGAACTCTA 58.879 41.667 28.31 0.00 33.31 2.43
1888 5576 2.360801 ACGGCAACAGTTTTGCTATGTT 59.639 40.909 13.40 0.00 44.36 2.71
2094 5786 2.834549 CTCCCTCCGCATCCATACTAAT 59.165 50.000 0.00 0.00 0.00 1.73
2095 5787 2.832129 TCCCTCCGCATCCATACTAATC 59.168 50.000 0.00 0.00 0.00 1.75
2098 5790 3.502920 CTCCGCATCCATACTAATCGTC 58.497 50.000 0.00 0.00 0.00 4.20
2099 5791 2.888414 TCCGCATCCATACTAATCGTCA 59.112 45.455 0.00 0.00 0.00 4.35
2100 5792 2.987149 CCGCATCCATACTAATCGTCAC 59.013 50.000 0.00 0.00 0.00 3.67
2101 5793 3.552068 CCGCATCCATACTAATCGTCACA 60.552 47.826 0.00 0.00 0.00 3.58
2107 5799 2.188837 TACTAATCGTCACAGCGCTG 57.811 50.000 34.89 34.89 0.00 5.18
2144 5836 2.841988 GGATCGGAGGGAGCAGCT 60.842 66.667 0.00 0.00 30.89 4.24
2145 5837 1.531840 GGATCGGAGGGAGCAGCTA 60.532 63.158 0.00 0.00 30.89 3.32
2146 5838 1.115930 GGATCGGAGGGAGCAGCTAA 61.116 60.000 0.00 0.00 30.89 3.09
2147 5839 0.753262 GATCGGAGGGAGCAGCTAAA 59.247 55.000 0.00 0.00 0.00 1.85
2148 5840 1.346068 GATCGGAGGGAGCAGCTAAAT 59.654 52.381 0.00 0.00 0.00 1.40
2149 5841 1.204146 TCGGAGGGAGCAGCTAAATT 58.796 50.000 0.00 0.00 0.00 1.82
2150 5842 1.559682 TCGGAGGGAGCAGCTAAATTT 59.440 47.619 0.00 0.00 0.00 1.82
2151 5843 1.672881 CGGAGGGAGCAGCTAAATTTG 59.327 52.381 0.00 0.00 0.00 2.32
2152 5844 2.027385 GGAGGGAGCAGCTAAATTTGG 58.973 52.381 0.00 0.00 0.00 3.28
2153 5845 2.357154 GGAGGGAGCAGCTAAATTTGGA 60.357 50.000 5.63 0.00 0.00 3.53
2154 5846 2.685388 GAGGGAGCAGCTAAATTTGGAC 59.315 50.000 5.63 0.00 0.00 4.02
2155 5847 1.401905 GGGAGCAGCTAAATTTGGACG 59.598 52.381 5.63 0.00 0.00 4.79
2156 5848 1.202188 GGAGCAGCTAAATTTGGACGC 60.202 52.381 5.63 6.62 0.00 5.19
2157 5849 1.468520 GAGCAGCTAAATTTGGACGCA 59.531 47.619 5.63 0.00 0.00 5.24
2158 5850 1.885887 AGCAGCTAAATTTGGACGCAA 59.114 42.857 5.63 0.00 0.00 4.85
2159 5851 1.985684 GCAGCTAAATTTGGACGCAAC 59.014 47.619 5.63 0.00 0.00 4.17
2160 5852 2.241722 CAGCTAAATTTGGACGCAACG 58.758 47.619 5.63 0.00 0.00 4.10
2161 5853 0.981956 GCTAAATTTGGACGCAACGC 59.018 50.000 5.63 0.00 0.00 4.84
2162 5854 1.664588 GCTAAATTTGGACGCAACGCA 60.665 47.619 5.63 0.00 0.00 5.24
2163 5855 2.656085 CTAAATTTGGACGCAACGCAA 58.344 42.857 0.00 0.00 0.00 4.85
2164 5856 1.204792 AAATTTGGACGCAACGCAAC 58.795 45.000 0.00 0.00 0.00 4.17
2165 5857 0.383949 AATTTGGACGCAACGCAACT 59.616 45.000 0.00 0.00 0.00 3.16
2166 5858 0.317770 ATTTGGACGCAACGCAACTG 60.318 50.000 0.00 0.00 0.00 3.16
2167 5859 1.649390 TTTGGACGCAACGCAACTGT 61.649 50.000 0.00 0.00 0.00 3.55
2168 5860 0.810426 TTGGACGCAACGCAACTGTA 60.810 50.000 0.00 0.00 0.00 2.74
2169 5861 0.601576 TGGACGCAACGCAACTGTAT 60.602 50.000 0.00 0.00 0.00 2.29
2170 5862 0.094730 GGACGCAACGCAACTGTATC 59.905 55.000 0.00 0.00 0.00 2.24
2176 5868 2.161410 GCAACGCAACTGTATCAATCCA 59.839 45.455 0.00 0.00 0.00 3.41
2179 5871 1.004610 CGCAACTGTATCAATCCAGCG 60.005 52.381 0.00 0.00 36.62 5.18
2186 5878 3.381045 TGTATCAATCCAGCGACGAATC 58.619 45.455 0.00 0.00 0.00 2.52
2206 5898 4.322080 TCCGAGTATGAAATAGCTGGTG 57.678 45.455 0.00 0.00 0.00 4.17
2207 5899 2.802816 CCGAGTATGAAATAGCTGGTGC 59.197 50.000 0.00 0.00 40.05 5.01
2218 5910 4.711949 CTGGTGCTTGCGAGGCCT 62.712 66.667 3.86 3.86 0.00 5.19
2228 5920 0.972983 TGCGAGGCCTAGAGCTTTCT 60.973 55.000 18.16 0.00 43.05 2.52
2234 5926 2.630580 AGGCCTAGAGCTTTCTTATCCG 59.369 50.000 1.29 0.00 43.05 4.18
2257 5949 2.340078 GGCGCTGCCTATCGATGA 59.660 61.111 8.54 0.00 46.69 2.92
2258 5950 1.079543 GGCGCTGCCTATCGATGAT 60.080 57.895 8.54 0.00 46.69 2.45
2259 5951 0.671781 GGCGCTGCCTATCGATGATT 60.672 55.000 8.54 0.00 46.69 2.57
2260 5952 1.404181 GGCGCTGCCTATCGATGATTA 60.404 52.381 8.54 0.00 46.69 1.75
2261 5953 1.923204 GCGCTGCCTATCGATGATTAG 59.077 52.381 8.54 2.86 0.00 1.73
2275 5967 7.502120 TCGATGATTAGTAGTAGTAACACCC 57.498 40.000 0.00 0.00 0.00 4.61
2277 5969 7.776969 TCGATGATTAGTAGTAGTAACACCCTT 59.223 37.037 0.00 0.00 0.00 3.95
2278 5970 8.074972 CGATGATTAGTAGTAGTAACACCCTTC 58.925 40.741 0.00 0.00 0.00 3.46
2442 6152 1.555075 TGCCGAAGAACTGGAGCTTAT 59.445 47.619 0.00 0.00 0.00 1.73
2443 6153 2.764010 TGCCGAAGAACTGGAGCTTATA 59.236 45.455 0.00 0.00 0.00 0.98
2444 6154 3.124560 GCCGAAGAACTGGAGCTTATAC 58.875 50.000 0.00 0.00 0.00 1.47
2445 6155 3.181474 GCCGAAGAACTGGAGCTTATACT 60.181 47.826 0.00 0.00 0.00 2.12
2446 6156 4.612943 CCGAAGAACTGGAGCTTATACTC 58.387 47.826 0.00 0.00 35.86 2.59
2477 6187 3.296709 ATGGTGCAGACGGACGGAC 62.297 63.158 0.00 0.00 33.50 4.79
2481 6191 4.773117 GCAGACGGACGGACGGAC 62.773 72.222 6.00 0.32 38.39 4.79
2482 6192 4.456253 CAGACGGACGGACGGACG 62.456 72.222 6.00 8.35 38.39 4.79
2699 6414 2.159517 GCCGGTGAATGAGATTGTTGAC 60.160 50.000 1.90 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.790765 AAGAAAATTAGCAGCACTTCCC 57.209 40.909 0.00 0.00 0.00 3.97
49 50 3.947834 GAGCTGCCCTAAGAAAATTAGCA 59.052 43.478 0.00 0.00 32.64 3.49
56 57 3.906720 ATTACGAGCTGCCCTAAGAAA 57.093 42.857 0.00 0.00 0.00 2.52
60 61 6.584488 TGTAAATTATTACGAGCTGCCCTAA 58.416 36.000 0.00 0.00 43.59 2.69
71 72 8.415192 TGGACTACTTGCTGTAAATTATTACG 57.585 34.615 0.00 0.00 43.59 3.18
72 73 9.983804 GTTGGACTACTTGCTGTAAATTATTAC 57.016 33.333 0.00 0.00 41.50 1.89
73 74 9.169592 GGTTGGACTACTTGCTGTAAATTATTA 57.830 33.333 0.00 0.00 0.00 0.98
74 75 7.668052 TGGTTGGACTACTTGCTGTAAATTATT 59.332 33.333 0.00 0.00 0.00 1.40
75 76 7.172342 TGGTTGGACTACTTGCTGTAAATTAT 58.828 34.615 0.00 0.00 0.00 1.28
123 124 1.120530 CGGGTGCCTAGATACTGGTT 58.879 55.000 0.00 0.00 0.00 3.67
311 2865 2.777094 TGTGCATTTGTGCTAGCAGTA 58.223 42.857 20.03 7.67 37.72 2.74
424 2980 2.185867 GATAGCGGTGGCGGAACA 59.814 61.111 0.00 0.00 46.35 3.18
604 4214 0.038618 TCACGGACACGAGAACATGG 60.039 55.000 0.00 0.00 44.60 3.66
702 4312 3.771160 ATGTGGTCCCCGCGTCTC 61.771 66.667 4.92 0.00 36.72 3.36
703 4313 4.082523 CATGTGGTCCCCGCGTCT 62.083 66.667 4.92 0.00 36.72 4.18
713 4323 2.669569 GTGCGCTGGTCATGTGGT 60.670 61.111 9.73 0.00 0.00 4.16
827 4437 2.363361 GAGAGTCGGGGAGGGGAA 59.637 66.667 0.00 0.00 0.00 3.97
846 4456 2.066999 GTGAGGCTGAGGTAGGGGG 61.067 68.421 0.00 0.00 0.00 5.40
857 4467 1.755977 CGAGGGAGATAAGGTGAGGCT 60.756 57.143 0.00 0.00 0.00 4.58
896 4507 4.584743 TGGTGGTGATACTGATAGTAGCTG 59.415 45.833 0.00 0.00 37.91 4.24
948 4586 2.952310 GTTTTGAAGCAGGAGTGGAGTT 59.048 45.455 0.00 0.00 0.00 3.01
949 4587 2.576615 GTTTTGAAGCAGGAGTGGAGT 58.423 47.619 0.00 0.00 0.00 3.85
950 4588 1.882623 GGTTTTGAAGCAGGAGTGGAG 59.117 52.381 0.00 0.00 0.00 3.86
951 4589 1.478654 GGGTTTTGAAGCAGGAGTGGA 60.479 52.381 0.00 0.00 0.00 4.02
952 4590 0.961753 GGGTTTTGAAGCAGGAGTGG 59.038 55.000 0.00 0.00 0.00 4.00
978 4617 0.962489 AGGACAGGAGACACGAACAG 59.038 55.000 0.00 0.00 0.00 3.16
983 4622 2.352032 GGGGAGGACAGGAGACACG 61.352 68.421 0.00 0.00 0.00 4.49
985 4624 2.037367 CGGGGAGGACAGGAGACA 59.963 66.667 0.00 0.00 0.00 3.41
986 4625 2.760385 CCGGGGAGGACAGGAGAC 60.760 72.222 0.00 0.00 45.00 3.36
1003 4642 3.130227 CTAGCTACTGGGGTCGGC 58.870 66.667 0.00 0.00 0.00 5.54
1012 4651 4.082190 TGTTCATTGTCGAAGCTAGCTACT 60.082 41.667 19.70 2.33 0.00 2.57
1013 4652 4.174009 TGTTCATTGTCGAAGCTAGCTAC 58.826 43.478 19.70 13.49 0.00 3.58
1014 4653 4.450082 TGTTCATTGTCGAAGCTAGCTA 57.550 40.909 19.70 0.40 0.00 3.32
1015 4654 3.319137 TGTTCATTGTCGAAGCTAGCT 57.681 42.857 12.68 12.68 0.00 3.32
1016 4655 3.868077 AGATGTTCATTGTCGAAGCTAGC 59.132 43.478 6.62 6.62 0.00 3.42
1017 4656 5.578336 TCAAGATGTTCATTGTCGAAGCTAG 59.422 40.000 0.00 0.00 0.00 3.42
1018 4657 5.478407 TCAAGATGTTCATTGTCGAAGCTA 58.522 37.500 0.00 0.00 0.00 3.32
1019 4658 4.318332 TCAAGATGTTCATTGTCGAAGCT 58.682 39.130 0.00 0.00 0.00 3.74
1020 4659 4.668576 TCAAGATGTTCATTGTCGAAGC 57.331 40.909 0.00 0.00 0.00 3.86
1021 4660 5.049474 TGGTTCAAGATGTTCATTGTCGAAG 60.049 40.000 0.00 0.00 0.00 3.79
1023 4662 4.384940 TGGTTCAAGATGTTCATTGTCGA 58.615 39.130 0.00 0.00 0.00 4.20
1024 4663 4.715896 CTGGTTCAAGATGTTCATTGTCG 58.284 43.478 0.00 0.00 0.00 4.35
1025 4664 4.479619 GCTGGTTCAAGATGTTCATTGTC 58.520 43.478 0.00 0.00 0.00 3.18
1026 4665 3.256631 GGCTGGTTCAAGATGTTCATTGT 59.743 43.478 0.00 0.00 0.00 2.71
1242 4900 2.202851 CTGCTCCGCGCTCTTGAT 60.203 61.111 5.56 0.00 40.11 2.57
1691 5349 6.125029 GGTATAATTGATGGATGGATGGAGG 58.875 44.000 0.00 0.00 0.00 4.30
1692 5350 6.125029 GGGTATAATTGATGGATGGATGGAG 58.875 44.000 0.00 0.00 0.00 3.86
1753 5413 4.389576 CAAGCACGGCGAAGTGGC 62.390 66.667 16.62 9.02 42.09 5.01
1754 5414 2.954753 GACAAGCACGGCGAAGTGG 61.955 63.158 16.62 2.12 42.09 4.00
1755 5415 2.551270 GACAAGCACGGCGAAGTG 59.449 61.111 16.62 8.50 44.47 3.16
1778 5438 2.158959 GGCGGACGACGTGAATGAG 61.159 63.158 4.58 0.00 46.52 2.90
1812 5488 3.028130 TCAGTTCATCATGCATGGCAAT 58.972 40.909 25.97 10.10 43.62 3.56
1813 5489 2.448453 TCAGTTCATCATGCATGGCAA 58.552 42.857 25.97 13.29 43.62 4.52
1814 5490 2.131776 TCAGTTCATCATGCATGGCA 57.868 45.000 25.97 8.77 44.86 4.92
1815 5491 2.426024 AGTTCAGTTCATCATGCATGGC 59.574 45.455 25.97 11.43 32.64 4.40
1816 5492 3.945921 AGAGTTCAGTTCATCATGCATGG 59.054 43.478 25.97 11.53 32.64 3.66
1817 5493 6.862711 ATAGAGTTCAGTTCATCATGCATG 57.137 37.500 21.07 21.07 0.00 4.06
1818 5494 9.650539 GTATATAGAGTTCAGTTCATCATGCAT 57.349 33.333 0.00 0.00 0.00 3.96
1819 5495 8.641541 TGTATATAGAGTTCAGTTCATCATGCA 58.358 33.333 0.00 0.00 0.00 3.96
1832 5508 8.410673 TCCATCTTGGTCTGTATATAGAGTTC 57.589 38.462 6.78 2.56 39.03 3.01
1833 5509 8.964533 ATCCATCTTGGTCTGTATATAGAGTT 57.035 34.615 6.78 0.00 39.03 3.01
1834 5510 7.338196 CGATCCATCTTGGTCTGTATATAGAGT 59.662 40.741 6.78 0.00 39.03 3.24
1835 5511 7.554476 TCGATCCATCTTGGTCTGTATATAGAG 59.446 40.741 0.00 0.35 39.03 2.43
1836 5512 7.337184 GTCGATCCATCTTGGTCTGTATATAGA 59.663 40.741 0.00 0.00 39.03 1.98
1837 5513 7.476667 GTCGATCCATCTTGGTCTGTATATAG 58.523 42.308 0.00 0.00 39.03 1.31
1838 5514 6.093633 CGTCGATCCATCTTGGTCTGTATATA 59.906 42.308 0.00 0.00 39.03 0.86
1839 5515 5.106118 CGTCGATCCATCTTGGTCTGTATAT 60.106 44.000 0.00 0.00 39.03 0.86
1888 5576 4.575236 TGCCTCACAATTTACAACAACGTA 59.425 37.500 0.00 0.00 0.00 3.57
1993 5685 2.568062 TGTAACCCTGAACCTCGCATAA 59.432 45.455 0.00 0.00 0.00 1.90
2094 5786 0.733909 CAGATTCAGCGCTGTGACGA 60.734 55.000 34.70 14.63 34.06 4.20
2095 5787 1.706301 CAGATTCAGCGCTGTGACG 59.294 57.895 34.70 17.75 0.00 4.35
2107 5799 7.176075 CGATCCATATTAATTGTCGCAGATTC 58.824 38.462 0.00 0.00 40.67 2.52
2144 5836 2.033550 AGTTGCGTTGCGTCCAAATTTA 59.966 40.909 0.00 0.00 31.68 1.40
2145 5837 1.202359 AGTTGCGTTGCGTCCAAATTT 60.202 42.857 0.00 0.00 31.68 1.82
2146 5838 0.383949 AGTTGCGTTGCGTCCAAATT 59.616 45.000 0.00 0.00 31.68 1.82
2147 5839 0.317770 CAGTTGCGTTGCGTCCAAAT 60.318 50.000 0.00 0.00 31.68 2.32
2148 5840 1.063327 CAGTTGCGTTGCGTCCAAA 59.937 52.632 0.00 0.00 31.68 3.28
2149 5841 0.810426 TACAGTTGCGTTGCGTCCAA 60.810 50.000 0.00 0.00 0.00 3.53
2150 5842 0.601576 ATACAGTTGCGTTGCGTCCA 60.602 50.000 0.00 0.00 0.00 4.02
2151 5843 0.094730 GATACAGTTGCGTTGCGTCC 59.905 55.000 0.00 0.00 0.00 4.79
2152 5844 0.787787 TGATACAGTTGCGTTGCGTC 59.212 50.000 0.00 0.00 0.00 5.19
2153 5845 1.222300 TTGATACAGTTGCGTTGCGT 58.778 45.000 0.00 0.00 0.00 5.24
2154 5846 2.430956 GATTGATACAGTTGCGTTGCG 58.569 47.619 0.00 0.00 0.00 4.85
2155 5847 2.161410 TGGATTGATACAGTTGCGTTGC 59.839 45.455 0.00 0.00 0.00 4.17
2156 5848 3.728864 GCTGGATTGATACAGTTGCGTTG 60.729 47.826 5.18 0.00 40.95 4.10
2157 5849 2.420022 GCTGGATTGATACAGTTGCGTT 59.580 45.455 5.18 0.00 40.95 4.84
2158 5850 2.009774 GCTGGATTGATACAGTTGCGT 58.990 47.619 5.18 0.00 40.95 5.24
2159 5851 1.004610 CGCTGGATTGATACAGTTGCG 60.005 52.381 5.18 0.19 40.95 4.85
2160 5852 2.030946 GTCGCTGGATTGATACAGTTGC 59.969 50.000 5.18 0.00 40.95 4.17
2161 5853 2.282555 CGTCGCTGGATTGATACAGTTG 59.717 50.000 5.18 0.00 40.95 3.16
2162 5854 2.165641 TCGTCGCTGGATTGATACAGTT 59.834 45.455 5.18 0.00 40.95 3.16
2163 5855 1.749063 TCGTCGCTGGATTGATACAGT 59.251 47.619 5.18 0.00 40.95 3.55
2164 5856 2.492019 TCGTCGCTGGATTGATACAG 57.508 50.000 0.00 0.00 41.81 2.74
2165 5857 2.951457 TTCGTCGCTGGATTGATACA 57.049 45.000 0.00 0.00 0.00 2.29
2166 5858 2.731976 GGATTCGTCGCTGGATTGATAC 59.268 50.000 0.00 0.00 0.00 2.24
2167 5859 2.607038 CGGATTCGTCGCTGGATTGATA 60.607 50.000 0.00 0.00 0.00 2.15
2168 5860 1.869754 CGGATTCGTCGCTGGATTGAT 60.870 52.381 0.00 0.00 0.00 2.57
2169 5861 0.527600 CGGATTCGTCGCTGGATTGA 60.528 55.000 0.00 0.00 0.00 2.57
2170 5862 0.527600 TCGGATTCGTCGCTGGATTG 60.528 55.000 0.00 0.00 37.69 2.67
2176 5868 1.306148 TCATACTCGGATTCGTCGCT 58.694 50.000 0.00 0.00 37.69 4.93
2179 5871 5.343593 CAGCTATTTCATACTCGGATTCGTC 59.656 44.000 0.00 0.00 37.69 4.20
2186 5878 2.802816 GCACCAGCTATTTCATACTCGG 59.197 50.000 0.00 0.00 37.91 4.63
2206 5898 2.585791 AAGCTCTAGGCCTCGCAAGC 62.586 60.000 9.68 14.50 43.05 4.01
2207 5899 0.107945 AAAGCTCTAGGCCTCGCAAG 60.108 55.000 9.68 0.00 43.05 4.01
2208 5900 0.108138 GAAAGCTCTAGGCCTCGCAA 60.108 55.000 9.68 0.00 43.05 4.85
2209 5901 0.972983 AGAAAGCTCTAGGCCTCGCA 60.973 55.000 9.68 0.00 43.05 5.10
2210 5902 0.176910 AAGAAAGCTCTAGGCCTCGC 59.823 55.000 9.68 11.43 43.05 5.03
2211 5903 3.305744 GGATAAGAAAGCTCTAGGCCTCG 60.306 52.174 9.68 1.83 43.05 4.63
2212 5904 3.305744 CGGATAAGAAAGCTCTAGGCCTC 60.306 52.174 9.68 0.00 43.05 4.70
2213 5905 2.630580 CGGATAAGAAAGCTCTAGGCCT 59.369 50.000 11.78 11.78 43.05 5.19
2214 5906 2.365941 ACGGATAAGAAAGCTCTAGGCC 59.634 50.000 0.00 0.00 43.05 5.19
2215 5907 3.737032 ACGGATAAGAAAGCTCTAGGC 57.263 47.619 0.00 0.00 42.19 3.93
2216 5908 5.956642 GGATACGGATAAGAAAGCTCTAGG 58.043 45.833 0.00 0.00 0.00 3.02
2252 5944 7.507733 AGGGTGTTACTACTACTAATCATCG 57.492 40.000 0.00 0.00 0.00 3.84
2253 5945 9.134055 AGAAGGGTGTTACTACTACTAATCATC 57.866 37.037 0.00 0.00 0.00 2.92
2254 5946 9.490083 AAGAAGGGTGTTACTACTACTAATCAT 57.510 33.333 0.00 0.00 0.00 2.45
2255 5947 8.746530 CAAGAAGGGTGTTACTACTACTAATCA 58.253 37.037 0.00 0.00 0.00 2.57
2256 5948 8.196103 CCAAGAAGGGTGTTACTACTACTAATC 58.804 40.741 0.00 0.00 0.00 1.75
2257 5949 7.677319 ACCAAGAAGGGTGTTACTACTACTAAT 59.323 37.037 0.00 0.00 43.89 1.73
2258 5950 7.012607 ACCAAGAAGGGTGTTACTACTACTAA 58.987 38.462 0.00 0.00 43.89 2.24
2259 5951 6.555711 ACCAAGAAGGGTGTTACTACTACTA 58.444 40.000 0.00 0.00 43.89 1.82
2260 5952 5.400870 ACCAAGAAGGGTGTTACTACTACT 58.599 41.667 0.00 0.00 43.89 2.57
2261 5953 5.735285 ACCAAGAAGGGTGTTACTACTAC 57.265 43.478 0.00 0.00 43.89 2.73
2274 5966 2.027561 TCGGTATCACCAACCAAGAAGG 60.028 50.000 0.00 0.00 38.47 3.46
2275 5967 3.000727 GTCGGTATCACCAACCAAGAAG 58.999 50.000 0.00 0.00 38.47 2.85
2277 5969 1.067425 CGTCGGTATCACCAACCAAGA 60.067 52.381 0.00 0.00 38.47 3.02
2278 5970 1.355971 CGTCGGTATCACCAACCAAG 58.644 55.000 0.00 0.00 38.47 3.61
2442 6152 0.670706 CATCGCAGCTGCTAGGAGTA 59.329 55.000 34.22 12.34 39.32 2.59
2443 6153 1.440893 CATCGCAGCTGCTAGGAGT 59.559 57.895 34.22 7.71 39.32 3.85
2444 6154 1.300775 CCATCGCAGCTGCTAGGAG 60.301 63.158 34.22 19.56 39.32 3.69
2445 6155 2.060383 ACCATCGCAGCTGCTAGGA 61.060 57.895 33.57 25.85 39.32 2.94
2446 6156 1.886313 CACCATCGCAGCTGCTAGG 60.886 63.158 34.22 30.90 39.32 3.02
2447 6157 2.532256 GCACCATCGCAGCTGCTAG 61.532 63.158 34.22 22.84 39.32 3.42
2477 6187 3.900892 CTGACCGATCCCCGTCCG 61.901 72.222 0.00 0.00 36.31 4.79
2478 6188 3.537874 CCTGACCGATCCCCGTCC 61.538 72.222 0.00 0.00 36.31 4.79
2480 6190 4.070265 TCCCTGACCGATCCCCGT 62.070 66.667 0.00 0.00 36.31 5.28
2481 6191 3.537874 GTCCCTGACCGATCCCCG 61.538 72.222 0.00 0.00 38.18 5.73
2482 6192 3.537874 CGTCCCTGACCGATCCCC 61.538 72.222 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.