Multiple sequence alignment - TraesCS3D01G140700

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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 TraesCS3D01G140700 chr3D 100.000 4249 0 0 1 4249 102778243 102782491 0.000000e+00 7847.0
1 TraesCS3D01G140700 chr3D 94.118 204 11 1 3812 4014 102781987 102782190 4.130000e-80 309.0
2 TraesCS3D01G140700 chr3D 94.118 204 11 1 3745 3948 102782054 102782256 4.130000e-80 309.0
3 TraesCS3D01G140700 chr3D 94.536 183 8 2 1753 1935 533336751 533336931 9.000000e-72 281.0
4 TraesCS3D01G140700 chr3D 92.308 143 10 1 3878 4019 102781987 102782129 7.200000e-48 202.0
5 TraesCS3D01G140700 chr3D 92.308 143 10 1 3745 3887 102782120 102782261 7.200000e-48 202.0
6 TraesCS3D01G140700 chr3B 93.284 3529 134 38 427 3901 153606570 153610049 0.000000e+00 5108.0
7 TraesCS3D01G140700 chr3B 87.583 451 31 7 3 435 153606101 153606544 2.280000e-137 499.0
8 TraesCS3D01G140700 chr3B 80.503 318 28 16 3926 4238 153649512 153649800 3.330000e-51 213.0
9 TraesCS3D01G140700 chr3B 91.209 91 6 2 3745 3835 153609961 153610049 5.770000e-24 122.0
10 TraesCS3D01G140700 chr3B 91.667 84 5 2 3794 3877 153649512 153649593 9.650000e-22 115.0
11 TraesCS3D01G140700 chr3B 94.828 58 3 0 3778 3835 153649453 153649510 1.630000e-14 91.6
12 TraesCS3D01G140700 chr3A 91.720 3732 202 44 54 3708 553001057 552997356 0.000000e+00 5081.0
13 TraesCS3D01G140700 chr3A 85.649 439 29 11 3811 4249 552997351 552996947 8.440000e-117 431.0
14 TraesCS3D01G140700 chr3A 88.406 138 16 0 3877 4014 552997351 552997214 2.630000e-37 167.0


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 TraesCS3D01G140700 chr3D 102778243 102782491 4248 False 1773.800000 7847 94.570400 1 4249 5 chr3D.!!$F2 4248
1 TraesCS3D01G140700 chr3B 153606101 153610049 3948 False 1909.666667 5108 90.692000 3 3901 3 chr3B.!!$F1 3898
2 TraesCS3D01G140700 chr3A 552996947 553001057 4110 True 1893.000000 5081 88.591667 54 4249 3 chr3A.!!$R1 4195

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
303 360 0.247458 GATCTTGCTTTGCGCGTCTC 60.247 55.0 8.43 0.0 43.27 3.36 F
1064 1187 0.250166 ACCGTCTACACAAGGGTTGC 60.250 55.0 0.00 0.0 30.98 4.17 F
2881 3009 0.173708 CTTTCGAGAACCTCTCCCCG 59.826 60.0 0.00 0.0 40.34 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 2422 0.238289 ATTTTGAGCACTTCACGGCG 59.762 50.000 4.8 4.8 34.94 6.46 R
3052 3181 1.406614 GCTCAATCAGGGGTCTCACTG 60.407 57.143 0.0 0.0 36.07 3.66 R
4027 4186 0.247736 GCCAGGACGAACACTCTCAT 59.752 55.000 0.0 0.0 0.00 2.90 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
89 93 1.079503 GTCAGGTTCTTGATGCCGTC 58.920 55.000 0.00 0.00 0.00 4.79
101 106 2.502510 GCCGTCAGCGTGCAAATG 60.503 61.111 0.00 0.00 35.45 2.32
163 180 4.100808 TGGATTTGTCCAGTTTTTCCCTTG 59.899 41.667 0.00 0.00 34.33 3.61
164 181 3.535280 TTTGTCCAGTTTTTCCCTTGC 57.465 42.857 0.00 0.00 0.00 4.01
166 183 2.306847 TGTCCAGTTTTTCCCTTGCTC 58.693 47.619 0.00 0.00 0.00 4.26
173 203 3.066760 AGTTTTTCCCTTGCTCTTTGTCG 59.933 43.478 0.00 0.00 0.00 4.35
178 208 0.514691 CCTTGCTCTTTGTCGAGTGC 59.485 55.000 0.00 0.00 36.84 4.40
303 360 0.247458 GATCTTGCTTTGCGCGTCTC 60.247 55.000 8.43 0.00 43.27 3.36
340 397 5.101648 AGAATTGTTGCCCCATAATTTGG 57.898 39.130 0.00 0.00 46.00 3.28
342 399 1.949799 TGTTGCCCCATAATTTGGCT 58.050 45.000 0.00 0.00 44.97 4.75
396 453 4.713321 AGGAAAATCAAATGGTCTGGATGG 59.287 41.667 0.00 0.00 0.00 3.51
424 481 7.361799 GCTTGTTCGGGTCATAATTTTTACTCT 60.362 37.037 0.00 0.00 0.00 3.24
425 482 7.372451 TGTTCGGGTCATAATTTTTACTCTG 57.628 36.000 0.00 0.00 0.00 3.35
435 526 8.514594 TCATAATTTTTACTCTGGCAGTTTCTG 58.485 33.333 15.27 3.84 36.43 3.02
446 537 6.182627 TCTGGCAGTTTCTGTAATGATTCAT 58.817 36.000 15.27 0.00 33.43 2.57
464 555 8.667076 TGATTCATAGTATGTCCAATTGTCAG 57.333 34.615 9.94 0.00 0.00 3.51
478 569 3.799137 TTGTCAGAAAACCGCGTTATC 57.201 42.857 4.92 0.00 0.00 1.75
480 571 2.734606 TGTCAGAAAACCGCGTTATCTG 59.265 45.455 17.23 17.23 39.04 2.90
503 594 0.918258 TGCTCCATGCCTGTATTCCA 59.082 50.000 0.00 0.00 42.00 3.53
510 603 5.132502 TCCATGCCTGTATTCCACTAATTG 58.867 41.667 0.00 0.00 0.00 2.32
536 629 9.798994 GCATGAGAAGAAGTCAAATCATTATTT 57.201 29.630 0.00 0.00 35.65 1.40
665 785 0.590195 GCACCAAGTTCAGCTCACAG 59.410 55.000 0.00 0.00 0.00 3.66
759 881 4.823989 ACAAGTTTCAGGGATCTGTTTGAG 59.176 41.667 0.00 0.00 41.59 3.02
812 934 5.918608 ACACTCATCTTCTGTACAACTTGT 58.081 37.500 0.00 0.00 0.00 3.16
942 1064 3.242870 GGTTCATGCTAATCCAAGCTTCG 60.243 47.826 0.00 0.00 43.19 3.79
1064 1187 0.250166 ACCGTCTACACAAGGGTTGC 60.250 55.000 0.00 0.00 30.98 4.17
1098 1221 1.203441 ATGTGGCTCCTCTTGGCAGA 61.203 55.000 0.00 0.00 40.61 4.26
1122 1245 2.166829 GTGGAGCAGAGACTTCAGAGA 58.833 52.381 0.00 0.00 0.00 3.10
1131 1254 5.782047 CAGAGACTTCAGAGATTTGTGAGT 58.218 41.667 0.00 0.00 0.00 3.41
1142 1265 6.758886 CAGAGATTTGTGAGTATGGGTAAGTC 59.241 42.308 0.00 0.00 0.00 3.01
1178 1301 4.888038 TTGATCGAGGCAATGATGAAAG 57.112 40.909 0.00 0.00 0.00 2.62
1554 1677 3.055094 AGCGTGTGGGATCTGATAAAAGT 60.055 43.478 0.00 0.00 0.00 2.66
1830 1953 0.698238 TTGCTTCTGGGGCACATAGT 59.302 50.000 0.00 0.00 39.55 2.12
1831 1954 1.578897 TGCTTCTGGGGCACATAGTA 58.421 50.000 0.00 0.00 34.56 1.82
1841 1964 3.195825 GGGGCACATAGTAGGCTATACAG 59.804 52.174 0.00 0.00 36.24 2.74
1894 2017 1.053424 ATTTATCCGCCGGCCTAAGA 58.947 50.000 23.46 13.35 0.00 2.10
1978 2101 5.690816 CATTGTCTCATCTGCATCATAAGC 58.309 41.667 0.00 0.00 0.00 3.09
2294 2422 3.364621 CACCGTTGCTATTTTCATTGTGC 59.635 43.478 0.00 0.00 0.00 4.57
2404 2532 9.878667 TCGTTATTGATTAACCTTGTCTCATTA 57.121 29.630 0.00 0.00 37.49 1.90
2440 2568 7.926018 GGTAACTTCTGATTTCATTTTGTTGGT 59.074 33.333 0.00 0.00 0.00 3.67
2552 2680 1.228063 CTGCACAACCCAGAGCACT 60.228 57.895 0.00 0.00 31.85 4.40
2553 2681 1.512996 CTGCACAACCCAGAGCACTG 61.513 60.000 3.89 3.89 43.12 3.66
2653 2781 2.701006 CACCGCGACATTAAGCCG 59.299 61.111 8.23 0.00 0.00 5.52
2881 3009 0.173708 CTTTCGAGAACCTCTCCCCG 59.826 60.000 0.00 0.00 40.34 5.73
2923 3051 5.329623 CGTCGCGAATAACGTAAGAGTTTAG 60.330 44.000 12.06 0.00 44.60 1.85
2927 3055 7.216317 TCGCGAATAACGTAAGAGTTTAGTTAC 59.784 37.037 6.20 0.00 44.60 2.50
2974 3102 6.192234 AGAACGTAATCTGAAGATGTACGT 57.808 37.500 21.55 21.55 45.23 3.57
3029 3158 3.738982 TCAGAACAAGAAAGCGATGGAA 58.261 40.909 0.00 0.00 0.00 3.53
3052 3181 0.312102 GAAGATTATTGCCCGGCAGC 59.688 55.000 12.95 0.00 40.61 5.25
3313 3442 2.557901 GGGTATGCTCCCCTAGTCTAGG 60.558 59.091 17.97 17.97 45.81 3.02
3426 3564 3.466836 TGCATTAGTAGCTGTATGCCAC 58.533 45.455 16.40 0.00 41.98 5.01
3460 3605 8.781196 ACTTATATGTTATCTCGTTCGCTCTTA 58.219 33.333 0.00 0.00 0.00 2.10
3560 3708 8.334734 AGCCATGATTATTATCCTGCTCTTATT 58.665 33.333 0.00 0.00 0.00 1.40
3561 3709 9.618890 GCCATGATTATTATCCTGCTCTTATTA 57.381 33.333 0.00 0.00 0.00 0.98
3576 3724 8.128322 TGCTCTTATTATAGAAGTCCCTCATC 57.872 38.462 0.00 0.00 0.00 2.92
3586 3734 6.139679 AGAAGTCCCTCATCTAGATAGAGG 57.860 45.833 27.61 27.61 46.71 3.69
3610 3758 1.743252 GAGGAAAGCCCGCTGACTG 60.743 63.158 0.00 0.00 40.87 3.51
3630 3778 1.612676 GCCAGCATTAGCATCATGGA 58.387 50.000 0.00 0.00 45.49 3.41
3631 3779 2.168496 GCCAGCATTAGCATCATGGAT 58.832 47.619 0.00 0.00 45.49 3.41
3632 3784 2.561419 GCCAGCATTAGCATCATGGATT 59.439 45.455 0.00 0.00 45.49 3.01
3685 3837 1.200716 CTTTGTTCGTCAGCATGCCAT 59.799 47.619 15.66 0.00 34.76 4.40
3693 3845 2.034104 TCAGCATGCCATTCTGACTC 57.966 50.000 15.66 0.00 34.76 3.36
3715 3867 2.362077 GTCATGGTGCTTTTGACCTGTT 59.638 45.455 0.00 0.00 34.95 3.16
3723 3875 2.767505 CTTTTGACCTGTTAGACGGCT 58.232 47.619 0.00 0.00 0.00 5.52
3759 3916 0.744414 ATTCTGTTGCGGGATGACGG 60.744 55.000 0.00 0.00 0.00 4.79
3835 3994 2.666989 GAGATGACGGCTCGGTTTC 58.333 57.895 0.00 0.00 0.00 2.78
3864 4023 5.659463 TGTTTGTTTTACTGCTGCATTTCT 58.341 33.333 1.31 0.00 0.00 2.52
3892 4051 1.511318 TTGTTGTTGCGGGATGACGG 61.511 55.000 0.00 0.00 0.00 4.79
3893 4052 1.669760 GTTGTTGCGGGATGACGGA 60.670 57.895 0.00 0.00 0.00 4.69
3901 4060 0.874607 CGGGATGACGGATCGGTTTC 60.875 60.000 7.41 7.83 30.87 2.78
3902 4061 0.177141 GGGATGACGGATCGGTTTCA 59.823 55.000 7.41 2.51 30.87 2.69
3903 4062 1.571919 GGATGACGGATCGGTTTCAG 58.428 55.000 7.41 0.00 30.87 3.02
3904 4063 1.136305 GGATGACGGATCGGTTTCAGA 59.864 52.381 7.41 0.00 30.87 3.27
3905 4064 2.224066 GGATGACGGATCGGTTTCAGAT 60.224 50.000 7.41 0.00 30.87 2.90
3906 4065 3.005472 GGATGACGGATCGGTTTCAGATA 59.995 47.826 7.41 0.00 30.87 1.98
3907 4066 4.322049 GGATGACGGATCGGTTTCAGATAT 60.322 45.833 7.41 0.00 30.87 1.63
3908 4067 3.977427 TGACGGATCGGTTTCAGATATG 58.023 45.455 7.41 0.00 0.00 1.78
3909 4068 3.383505 TGACGGATCGGTTTCAGATATGT 59.616 43.478 7.41 0.00 0.00 2.29
3910 4069 4.142026 TGACGGATCGGTTTCAGATATGTT 60.142 41.667 7.41 0.00 0.00 2.71
3911 4070 4.766375 ACGGATCGGTTTCAGATATGTTT 58.234 39.130 0.00 0.00 0.00 2.83
3912 4071 4.570772 ACGGATCGGTTTCAGATATGTTTG 59.429 41.667 0.00 0.00 0.00 2.93
3913 4072 4.570772 CGGATCGGTTTCAGATATGTTTGT 59.429 41.667 0.00 0.00 0.00 2.83
3914 4073 5.064707 CGGATCGGTTTCAGATATGTTTGTT 59.935 40.000 0.00 0.00 0.00 2.83
3915 4074 6.403200 CGGATCGGTTTCAGATATGTTTGTTT 60.403 38.462 0.00 0.00 0.00 2.83
3916 4075 7.312899 GGATCGGTTTCAGATATGTTTGTTTT 58.687 34.615 0.00 0.00 0.00 2.43
3917 4076 8.455682 GGATCGGTTTCAGATATGTTTGTTTTA 58.544 33.333 0.00 0.00 0.00 1.52
3918 4077 9.274065 GATCGGTTTCAGATATGTTTGTTTTAC 57.726 33.333 0.00 0.00 0.00 2.01
3919 4078 8.385898 TCGGTTTCAGATATGTTTGTTTTACT 57.614 30.769 0.00 0.00 0.00 2.24
3920 4079 8.286800 TCGGTTTCAGATATGTTTGTTTTACTG 58.713 33.333 0.00 0.00 0.00 2.74
3921 4080 7.060633 CGGTTTCAGATATGTTTGTTTTACTGC 59.939 37.037 0.00 0.00 0.00 4.40
3922 4081 8.082242 GGTTTCAGATATGTTTGTTTTACTGCT 58.918 33.333 0.00 0.00 0.00 4.24
3923 4082 8.905702 GTTTCAGATATGTTTGTTTTACTGCTG 58.094 33.333 0.00 0.00 0.00 4.41
3924 4083 6.611381 TCAGATATGTTTGTTTTACTGCTGC 58.389 36.000 0.00 0.00 0.00 5.25
3925 4084 6.206438 TCAGATATGTTTGTTTTACTGCTGCA 59.794 34.615 0.88 0.88 0.00 4.41
3926 4085 7.031372 CAGATATGTTTGTTTTACTGCTGCAT 58.969 34.615 1.31 0.00 0.00 3.96
3927 4086 7.543172 CAGATATGTTTGTTTTACTGCTGCATT 59.457 33.333 1.31 0.00 0.00 3.56
3928 4087 8.090214 AGATATGTTTGTTTTACTGCTGCATTT 58.910 29.630 1.31 0.00 0.00 2.32
3929 4088 5.964887 TGTTTGTTTTACTGCTGCATTTC 57.035 34.783 1.31 0.00 0.00 2.17
3930 4089 4.808364 TGTTTGTTTTACTGCTGCATTTCC 59.192 37.500 1.31 0.00 0.00 3.13
3931 4090 3.281341 TGTTTTACTGCTGCATTTCCG 57.719 42.857 1.31 0.00 0.00 4.30
3932 4091 2.621055 TGTTTTACTGCTGCATTTCCGT 59.379 40.909 1.31 0.00 0.00 4.69
3933 4092 2.979813 GTTTTACTGCTGCATTTCCGTG 59.020 45.455 1.31 0.00 0.00 4.94
3934 4093 2.177394 TTACTGCTGCATTTCCGTGA 57.823 45.000 1.31 0.00 0.00 4.35
3935 4094 2.401583 TACTGCTGCATTTCCGTGAT 57.598 45.000 1.31 0.00 0.00 3.06
3936 4095 2.401583 ACTGCTGCATTTCCGTGATA 57.598 45.000 1.31 0.00 0.00 2.15
3937 4096 2.923121 ACTGCTGCATTTCCGTGATAT 58.077 42.857 1.31 0.00 0.00 1.63
3938 4097 3.282021 ACTGCTGCATTTCCGTGATATT 58.718 40.909 1.31 0.00 0.00 1.28
3939 4098 3.696051 ACTGCTGCATTTCCGTGATATTT 59.304 39.130 1.31 0.00 0.00 1.40
3940 4099 4.158394 ACTGCTGCATTTCCGTGATATTTT 59.842 37.500 1.31 0.00 0.00 1.82
3941 4100 4.422840 TGCTGCATTTCCGTGATATTTTG 58.577 39.130 0.00 0.00 0.00 2.44
3942 4101 4.082300 TGCTGCATTTCCGTGATATTTTGT 60.082 37.500 0.00 0.00 0.00 2.83
3943 4102 4.864247 GCTGCATTTCCGTGATATTTTGTT 59.136 37.500 0.00 0.00 0.00 2.83
3944 4103 5.220265 GCTGCATTTCCGTGATATTTTGTTG 60.220 40.000 0.00 0.00 0.00 3.33
3945 4104 5.777802 TGCATTTCCGTGATATTTTGTTGT 58.222 33.333 0.00 0.00 0.00 3.32
3946 4105 6.219473 TGCATTTCCGTGATATTTTGTTGTT 58.781 32.000 0.00 0.00 0.00 2.83
3947 4106 6.145209 TGCATTTCCGTGATATTTTGTTGTTG 59.855 34.615 0.00 0.00 0.00 3.33
3948 4107 6.524490 CATTTCCGTGATATTTTGTTGTTGC 58.476 36.000 0.00 0.00 0.00 4.17
3949 4108 3.816091 TCCGTGATATTTTGTTGTTGCG 58.184 40.909 0.00 0.00 0.00 4.85
3950 4109 2.341168 CCGTGATATTTTGTTGTTGCGC 59.659 45.455 0.00 0.00 0.00 6.09
3951 4110 2.025106 CGTGATATTTTGTTGTTGCGCG 59.975 45.455 0.00 0.00 0.00 6.86
3952 4111 3.230355 GTGATATTTTGTTGTTGCGCGA 58.770 40.909 12.10 0.00 0.00 5.87
3953 4112 3.851403 GTGATATTTTGTTGTTGCGCGAT 59.149 39.130 12.10 0.00 0.00 4.58
3954 4113 3.850837 TGATATTTTGTTGTTGCGCGATG 59.149 39.130 12.10 0.00 0.00 3.84
3955 4114 2.414058 ATTTTGTTGTTGCGCGATGA 57.586 40.000 12.10 0.00 0.00 2.92
3956 4115 1.471964 TTTTGTTGTTGCGCGATGAC 58.528 45.000 12.10 4.98 0.00 3.06
3957 4116 0.655915 TTTGTTGTTGCGCGATGACG 60.656 50.000 12.10 0.00 42.93 4.35
3958 4117 2.202171 GTTGTTGCGCGATGACGG 60.202 61.111 12.10 0.00 40.15 4.79
3959 4118 2.356433 TTGTTGCGCGATGACGGA 60.356 55.556 12.10 0.00 40.15 4.69
3960 4119 1.739929 TTGTTGCGCGATGACGGAT 60.740 52.632 12.10 0.00 40.15 4.18
3961 4120 1.692148 TTGTTGCGCGATGACGGATC 61.692 55.000 12.10 0.00 40.15 3.36
3993 4152 7.543172 CAGATATGTTTGTTTTACTGCTGCATT 59.457 33.333 1.31 0.00 0.00 3.56
3996 4155 5.659463 TGTTTGTTTTACTGCTGCATTTCT 58.341 33.333 1.31 0.00 0.00 2.52
4008 4167 6.028146 TGCTGCATTTCTGTGATATTTTGT 57.972 33.333 0.00 0.00 0.00 2.83
4010 4169 6.587226 TGCTGCATTTCTGTGATATTTTGTTC 59.413 34.615 0.00 0.00 0.00 3.18
4011 4170 6.810182 GCTGCATTTCTGTGATATTTTGTTCT 59.190 34.615 0.00 0.00 0.00 3.01
4012 4171 7.330208 GCTGCATTTCTGTGATATTTTGTTCTT 59.670 33.333 0.00 0.00 0.00 2.52
4014 4173 7.599621 TGCATTTCTGTGATATTTTGTTCTTGG 59.400 33.333 0.00 0.00 0.00 3.61
4015 4174 7.063780 GCATTTCTGTGATATTTTGTTCTTGGG 59.936 37.037 0.00 0.00 0.00 4.12
4018 4177 5.004361 TGTGATATTTTGTTCTTGGGGGA 57.996 39.130 0.00 0.00 0.00 4.81
4019 4178 5.016173 TGTGATATTTTGTTCTTGGGGGAG 58.984 41.667 0.00 0.00 0.00 4.30
4020 4179 4.402474 GTGATATTTTGTTCTTGGGGGAGG 59.598 45.833 0.00 0.00 0.00 4.30
4021 4180 4.045334 TGATATTTTGTTCTTGGGGGAGGT 59.955 41.667 0.00 0.00 0.00 3.85
4022 4181 2.858787 TTTTGTTCTTGGGGGAGGTT 57.141 45.000 0.00 0.00 0.00 3.50
4023 4182 2.080654 TTTGTTCTTGGGGGAGGTTG 57.919 50.000 0.00 0.00 0.00 3.77
4024 4183 0.187361 TTGTTCTTGGGGGAGGTTGG 59.813 55.000 0.00 0.00 0.00 3.77
4025 4184 0.996762 TGTTCTTGGGGGAGGTTGGT 60.997 55.000 0.00 0.00 0.00 3.67
4026 4185 0.539669 GTTCTTGGGGGAGGTTGGTG 60.540 60.000 0.00 0.00 0.00 4.17
4027 4186 0.699577 TTCTTGGGGGAGGTTGGTGA 60.700 55.000 0.00 0.00 0.00 4.02
4028 4187 0.477597 TCTTGGGGGAGGTTGGTGAT 60.478 55.000 0.00 0.00 0.00 3.06
4029 4188 0.323725 CTTGGGGGAGGTTGGTGATG 60.324 60.000 0.00 0.00 0.00 3.07
4030 4189 0.774096 TTGGGGGAGGTTGGTGATGA 60.774 55.000 0.00 0.00 0.00 2.92
4031 4190 1.207488 TGGGGGAGGTTGGTGATGAG 61.207 60.000 0.00 0.00 0.00 2.90
4032 4191 0.914417 GGGGGAGGTTGGTGATGAGA 60.914 60.000 0.00 0.00 0.00 3.27
4051 4210 3.998672 TGTTCGTCCTGGCCGTCC 61.999 66.667 0.00 0.00 0.00 4.79
4081 4240 3.068691 CCCTGACGCGGAAGGAGA 61.069 66.667 25.79 0.00 35.40 3.71
4163 4322 4.489771 CGACCCCTGATGCCCACC 62.490 72.222 0.00 0.00 0.00 4.61
4164 4323 4.489771 GACCCCTGATGCCCACCG 62.490 72.222 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.249405 AGCAATCTAGAGCAGAGCGC 60.249 55.000 0.00 0.00 36.48 5.92
21 22 2.613133 CCAAAGCAATCTAGAGCAGAGC 59.387 50.000 6.73 2.39 36.48 4.09
50 51 0.181350 GGGTAGGAGCACAATGGGAG 59.819 60.000 0.00 0.00 0.00 4.30
89 93 2.359040 CGCACACATTTGCACGCTG 61.359 57.895 0.00 0.00 43.15 5.18
163 180 0.319900 TCTGGCACTCGACAAAGAGC 60.320 55.000 0.00 0.00 41.77 4.09
164 181 2.154854 TTCTGGCACTCGACAAAGAG 57.845 50.000 0.00 0.00 43.56 2.85
166 183 2.614057 ACTTTTCTGGCACTCGACAAAG 59.386 45.455 0.00 0.00 0.00 2.77
303 360 6.237045 GCAACAATTCTCGCGAAGAAAAATAG 60.237 38.462 19.73 13.11 46.85 1.73
340 397 1.003866 ACTTTTCACGCAACGAGAAGC 60.004 47.619 0.00 0.00 37.68 3.86
342 399 1.256895 CGACTTTTCACGCAACGAGAA 59.743 47.619 0.00 0.00 35.03 2.87
396 453 4.434713 AAATTATGACCCGAACAAGCAC 57.565 40.909 0.00 0.00 0.00 4.40
424 481 7.112122 ACTATGAATCATTACAGAAACTGCCA 58.888 34.615 0.00 0.00 34.37 4.92
425 482 7.559590 ACTATGAATCATTACAGAAACTGCC 57.440 36.000 0.00 0.00 34.37 4.85
446 537 6.370442 CGGTTTTCTGACAATTGGACATACTA 59.630 38.462 10.83 0.00 0.00 1.82
464 555 3.732943 CAGTTCAGATAACGCGGTTTTC 58.267 45.455 12.47 4.66 0.00 2.29
503 594 7.750229 TTTGACTTCTTCTCATGCAATTAGT 57.250 32.000 0.00 0.00 0.00 2.24
510 603 9.798994 AAATAATGATTTGACTTCTTCTCATGC 57.201 29.630 0.00 0.00 33.86 4.06
759 881 1.694696 AGGTCAAGGGTCTGTTCAGTC 59.305 52.381 0.00 0.00 0.00 3.51
812 934 0.757512 TTGCTGCCAAATTCTTGCCA 59.242 45.000 0.00 0.00 0.00 4.92
942 1064 6.205464 TCACAAGTGATCAGATTCCAACTTTC 59.795 38.462 0.00 0.00 34.14 2.62
1098 1221 2.496871 CTGAAGTCTCTGCTCCACATCT 59.503 50.000 0.00 0.00 0.00 2.90
1122 1245 6.013725 TCACAGACTTACCCATACTCACAAAT 60.014 38.462 0.00 0.00 0.00 2.32
1131 1254 3.181479 GCATCGTCACAGACTTACCCATA 60.181 47.826 0.00 0.00 0.00 2.74
1142 1265 1.600957 GATCAATGGGCATCGTCACAG 59.399 52.381 0.00 0.00 0.00 3.66
1830 1953 5.933617 TCGTAAAGTCCTCTGTATAGCCTA 58.066 41.667 0.00 0.00 0.00 3.93
1831 1954 4.789807 TCGTAAAGTCCTCTGTATAGCCT 58.210 43.478 0.00 0.00 0.00 4.58
1841 1964 3.982058 CGGCTTATCATCGTAAAGTCCTC 59.018 47.826 0.00 0.00 0.00 3.71
1894 2017 3.807209 GCTATTATCCCACCAGCGTCATT 60.807 47.826 0.00 0.00 0.00 2.57
2021 2144 8.865090 TGCCCAGAGATAAAATAAGAAAAACAA 58.135 29.630 0.00 0.00 0.00 2.83
2035 2158 5.086621 TGCACTATCTATGCCCAGAGATAA 58.913 41.667 12.19 0.00 40.04 1.75
2214 2339 7.732025 TCTTCTGAAGGTGTATAACAAGTTGA 58.268 34.615 16.83 0.00 0.00 3.18
2289 2417 3.947841 GCACTTCACGGCGCACAA 61.948 61.111 10.83 0.00 0.00 3.33
2290 2418 4.908687 AGCACTTCACGGCGCACA 62.909 61.111 10.83 0.00 34.54 4.57
2294 2422 0.238289 ATTTTGAGCACTTCACGGCG 59.762 50.000 4.80 4.80 34.94 6.46
2404 2532 8.474025 TGAAATCAGAAGTTACCAACAAAATGT 58.526 29.630 0.00 0.00 0.00 2.71
2440 2568 7.148407 GCTGCTACAAGCTGAATTAAGAAGTTA 60.148 37.037 9.63 0.00 41.94 2.24
2653 2781 6.432472 ACTTCTCATCAAAAAGGATGTTCTCC 59.568 38.462 0.00 0.00 44.00 3.71
2881 3009 4.242602 GCATAAGCCACCTGGACC 57.757 61.111 0.00 0.00 37.39 4.46
2902 3030 5.921784 ACTAAACTCTTACGTTATTCGCG 57.078 39.130 0.00 0.00 44.19 5.87
2923 3051 4.272748 AGAAGGCAAACTCAAACTCGTAAC 59.727 41.667 0.00 0.00 0.00 2.50
2927 3055 3.971032 AAGAAGGCAAACTCAAACTCG 57.029 42.857 0.00 0.00 0.00 4.18
2974 3102 6.688073 AAGGATTTAGTCAAGGAGAGAACA 57.312 37.500 0.00 0.00 0.00 3.18
3029 3158 1.750682 GCCGGGCAATAATCTTCAGGT 60.751 52.381 15.62 0.00 0.00 4.00
3052 3181 1.406614 GCTCAATCAGGGGTCTCACTG 60.407 57.143 0.00 0.00 36.07 3.66
3119 3248 2.543777 TCTTCTCCAGGGTTTTCACG 57.456 50.000 0.00 0.00 0.00 4.35
3255 3384 2.194271 GGTCGAAACGATGCTAGAAGG 58.806 52.381 0.00 0.00 38.42 3.46
3313 3442 4.181309 AGCTTATCATCTTACGCTAGGC 57.819 45.455 0.00 0.00 0.00 3.93
3361 3492 5.937540 CACCTAATAAACATCCGCATCCATA 59.062 40.000 0.00 0.00 0.00 2.74
3398 3529 8.134895 GGCATACAGCTACTAATGCAATAAAAA 58.865 33.333 18.00 0.00 45.13 1.94
3450 3595 2.608268 GGACAAGGAGTAAGAGCGAAC 58.392 52.381 0.00 0.00 0.00 3.95
3460 3605 0.472734 AGCAGACAGGGACAAGGAGT 60.473 55.000 0.00 0.00 0.00 3.85
3548 3696 6.625267 AGGGACTTCTATAATAAGAGCAGGA 58.375 40.000 2.34 0.00 27.25 3.86
3560 3708 8.998814 CCTCTATCTAGATGAGGGACTTCTATA 58.001 40.741 27.24 3.62 41.55 1.31
3561 3709 7.872138 CCTCTATCTAGATGAGGGACTTCTAT 58.128 42.308 27.24 1.93 41.55 1.98
3562 3710 7.265599 CCTCTATCTAGATGAGGGACTTCTA 57.734 44.000 27.24 4.12 41.55 2.10
3576 3724 2.865079 TCCTCGGCAACCTCTATCTAG 58.135 52.381 0.00 0.00 0.00 2.43
3586 3734 3.431725 CGGGCTTTCCTCGGCAAC 61.432 66.667 0.00 0.00 0.00 4.17
3605 3753 0.256752 ATGCTAATGCTGGCCAGTCA 59.743 50.000 32.81 28.68 40.48 3.41
3610 3758 0.601558 CCATGATGCTAATGCTGGCC 59.398 55.000 0.00 0.00 40.48 5.36
3614 3762 4.597004 CCCTAATCCATGATGCTAATGCT 58.403 43.478 0.00 0.00 40.48 3.79
3685 3837 0.969149 AGCACCATGACGAGTCAGAA 59.031 50.000 11.74 0.00 43.61 3.02
3693 3845 1.069022 CAGGTCAAAAGCACCATGACG 60.069 52.381 0.00 0.00 43.38 4.35
3715 3867 2.053865 CAACCGGGGTAGCCGTCTA 61.054 63.158 6.32 0.00 0.00 2.59
3723 3875 3.759618 CAGAATAAAAAGCAACCGGGGTA 59.240 43.478 6.32 0.00 0.00 3.69
3765 3922 6.377146 AGCAGTAAAACAAACATATCCCGAAT 59.623 34.615 0.00 0.00 0.00 3.34
3770 3927 5.708948 TGCAGCAGTAAAACAAACATATCC 58.291 37.500 0.00 0.00 0.00 2.59
3835 3994 4.793216 GCAGCAGTAAAACAAACATATCCG 59.207 41.667 0.00 0.00 0.00 4.18
3864 4023 3.570125 TCCCGCAACAACAAAATATCACA 59.430 39.130 0.00 0.00 0.00 3.58
3892 4051 9.274065 GTAAAACAAACATATCTGAAACCGATC 57.726 33.333 0.00 0.00 0.00 3.69
3893 4052 9.010029 AGTAAAACAAACATATCTGAAACCGAT 57.990 29.630 0.00 0.00 0.00 4.18
3901 4060 6.380995 TGCAGCAGTAAAACAAACATATCTG 58.619 36.000 0.00 0.00 0.00 2.90
3902 4061 6.573664 TGCAGCAGTAAAACAAACATATCT 57.426 33.333 0.00 0.00 0.00 1.98
3903 4062 7.816945 AATGCAGCAGTAAAACAAACATATC 57.183 32.000 0.00 0.00 0.00 1.63
3904 4063 7.331687 GGAAATGCAGCAGTAAAACAAACATAT 59.668 33.333 0.00 0.00 0.00 1.78
3905 4064 6.644592 GGAAATGCAGCAGTAAAACAAACATA 59.355 34.615 0.00 0.00 0.00 2.29
3906 4065 5.466393 GGAAATGCAGCAGTAAAACAAACAT 59.534 36.000 0.00 0.00 0.00 2.71
3907 4066 4.808364 GGAAATGCAGCAGTAAAACAAACA 59.192 37.500 0.00 0.00 0.00 2.83
3908 4067 4.085107 CGGAAATGCAGCAGTAAAACAAAC 60.085 41.667 0.00 0.00 0.00 2.93
3909 4068 4.047822 CGGAAATGCAGCAGTAAAACAAA 58.952 39.130 0.00 0.00 0.00 2.83
3910 4069 3.067461 ACGGAAATGCAGCAGTAAAACAA 59.933 39.130 0.00 0.00 0.00 2.83
3911 4070 2.621055 ACGGAAATGCAGCAGTAAAACA 59.379 40.909 0.00 0.00 0.00 2.83
3912 4071 2.979813 CACGGAAATGCAGCAGTAAAAC 59.020 45.455 0.00 0.00 0.00 2.43
3913 4072 2.881513 TCACGGAAATGCAGCAGTAAAA 59.118 40.909 0.00 0.00 0.00 1.52
3914 4073 2.499197 TCACGGAAATGCAGCAGTAAA 58.501 42.857 0.00 0.00 0.00 2.01
3915 4074 2.177394 TCACGGAAATGCAGCAGTAA 57.823 45.000 0.00 0.00 0.00 2.24
3916 4075 2.401583 ATCACGGAAATGCAGCAGTA 57.598 45.000 0.00 0.00 0.00 2.74
3917 4076 2.401583 TATCACGGAAATGCAGCAGT 57.598 45.000 0.00 0.00 0.00 4.40
3918 4077 3.976793 AATATCACGGAAATGCAGCAG 57.023 42.857 0.00 0.00 0.00 4.24
3919 4078 4.082300 ACAAAATATCACGGAAATGCAGCA 60.082 37.500 0.00 0.00 0.00 4.41
3920 4079 4.423732 ACAAAATATCACGGAAATGCAGC 58.576 39.130 0.00 0.00 0.00 5.25
3921 4080 5.863397 ACAACAAAATATCACGGAAATGCAG 59.137 36.000 0.00 0.00 0.00 4.41
3922 4081 5.777802 ACAACAAAATATCACGGAAATGCA 58.222 33.333 0.00 0.00 0.00 3.96
3923 4082 6.524490 CAACAACAAAATATCACGGAAATGC 58.476 36.000 0.00 0.00 0.00 3.56
3924 4083 6.524490 GCAACAACAAAATATCACGGAAATG 58.476 36.000 0.00 0.00 0.00 2.32
3925 4084 5.344665 CGCAACAACAAAATATCACGGAAAT 59.655 36.000 0.00 0.00 0.00 2.17
3926 4085 4.677378 CGCAACAACAAAATATCACGGAAA 59.323 37.500 0.00 0.00 0.00 3.13
3927 4086 4.222886 CGCAACAACAAAATATCACGGAA 58.777 39.130 0.00 0.00 0.00 4.30
3928 4087 3.816091 CGCAACAACAAAATATCACGGA 58.184 40.909 0.00 0.00 0.00 4.69
3929 4088 2.341168 GCGCAACAACAAAATATCACGG 59.659 45.455 0.30 0.00 0.00 4.94
3930 4089 2.025106 CGCGCAACAACAAAATATCACG 59.975 45.455 8.75 0.00 0.00 4.35
3931 4090 3.230355 TCGCGCAACAACAAAATATCAC 58.770 40.909 8.75 0.00 0.00 3.06
3932 4091 3.544356 TCGCGCAACAACAAAATATCA 57.456 38.095 8.75 0.00 0.00 2.15
3933 4092 4.028509 GTCATCGCGCAACAACAAAATATC 60.029 41.667 8.75 0.00 0.00 1.63
3934 4093 3.851403 GTCATCGCGCAACAACAAAATAT 59.149 39.130 8.75 0.00 0.00 1.28
3935 4094 3.230355 GTCATCGCGCAACAACAAAATA 58.770 40.909 8.75 0.00 0.00 1.40
3936 4095 2.050691 GTCATCGCGCAACAACAAAAT 58.949 42.857 8.75 0.00 0.00 1.82
3937 4096 1.471964 GTCATCGCGCAACAACAAAA 58.528 45.000 8.75 0.00 0.00 2.44
3938 4097 0.655915 CGTCATCGCGCAACAACAAA 60.656 50.000 8.75 0.00 0.00 2.83
3939 4098 1.083080 CGTCATCGCGCAACAACAA 60.083 52.632 8.75 0.00 0.00 2.83
3940 4099 2.548787 CGTCATCGCGCAACAACA 59.451 55.556 8.75 0.00 0.00 3.33
3941 4100 1.966493 ATCCGTCATCGCGCAACAAC 61.966 55.000 8.75 0.00 35.54 3.32
3942 4101 1.692148 GATCCGTCATCGCGCAACAA 61.692 55.000 8.75 0.00 35.54 2.83
3943 4102 2.125713 ATCCGTCATCGCGCAACA 60.126 55.556 8.75 0.00 35.54 3.33
3944 4103 2.621000 GATCCGTCATCGCGCAAC 59.379 61.111 8.75 0.00 35.54 4.17
3951 4110 2.579207 TCTGAAACCGATCCGTCATC 57.421 50.000 0.00 0.00 0.00 2.92
3952 4111 4.039245 ACATATCTGAAACCGATCCGTCAT 59.961 41.667 0.00 0.00 0.00 3.06
3953 4112 3.383505 ACATATCTGAAACCGATCCGTCA 59.616 43.478 0.00 0.00 0.00 4.35
3954 4113 3.978687 ACATATCTGAAACCGATCCGTC 58.021 45.455 0.00 0.00 0.00 4.79
3955 4114 4.402056 AACATATCTGAAACCGATCCGT 57.598 40.909 0.00 0.00 0.00 4.69
3956 4115 4.570772 ACAAACATATCTGAAACCGATCCG 59.429 41.667 0.00 0.00 0.00 4.18
3957 4116 6.436843 AACAAACATATCTGAAACCGATCC 57.563 37.500 0.00 0.00 0.00 3.36
3958 4117 9.274065 GTAAAACAAACATATCTGAAACCGATC 57.726 33.333 0.00 0.00 0.00 3.69
3959 4118 9.010029 AGTAAAACAAACATATCTGAAACCGAT 57.990 29.630 0.00 0.00 0.00 4.18
3960 4119 8.286800 CAGTAAAACAAACATATCTGAAACCGA 58.713 33.333 0.00 0.00 0.00 4.69
3961 4120 7.060633 GCAGTAAAACAAACATATCTGAAACCG 59.939 37.037 0.00 0.00 0.00 4.44
3962 4121 8.082242 AGCAGTAAAACAAACATATCTGAAACC 58.918 33.333 0.00 0.00 0.00 3.27
3963 4122 8.905702 CAGCAGTAAAACAAACATATCTGAAAC 58.094 33.333 0.00 0.00 0.00 2.78
3964 4123 7.594758 GCAGCAGTAAAACAAACATATCTGAAA 59.405 33.333 0.00 0.00 0.00 2.69
3965 4124 7.083858 GCAGCAGTAAAACAAACATATCTGAA 58.916 34.615 0.00 0.00 0.00 3.02
3966 4125 6.206438 TGCAGCAGTAAAACAAACATATCTGA 59.794 34.615 0.00 0.00 0.00 3.27
3967 4126 6.380995 TGCAGCAGTAAAACAAACATATCTG 58.619 36.000 0.00 0.00 0.00 2.90
3993 4152 5.480073 CCCCCAAGAACAAAATATCACAGAA 59.520 40.000 0.00 0.00 0.00 3.02
3996 4155 5.004361 TCCCCCAAGAACAAAATATCACA 57.996 39.130 0.00 0.00 0.00 3.58
4008 4167 0.699577 TCACCAACCTCCCCCAAGAA 60.700 55.000 0.00 0.00 0.00 2.52
4010 4169 0.323725 CATCACCAACCTCCCCCAAG 60.324 60.000 0.00 0.00 0.00 3.61
4011 4170 0.774096 TCATCACCAACCTCCCCCAA 60.774 55.000 0.00 0.00 0.00 4.12
4012 4171 1.151699 TCATCACCAACCTCCCCCA 60.152 57.895 0.00 0.00 0.00 4.96
4014 4173 0.543749 CTCTCATCACCAACCTCCCC 59.456 60.000 0.00 0.00 0.00 4.81
4015 4174 1.065854 CACTCTCATCACCAACCTCCC 60.066 57.143 0.00 0.00 0.00 4.30
4018 4177 2.289072 CGAACACTCTCATCACCAACCT 60.289 50.000 0.00 0.00 0.00 3.50
4019 4178 2.069273 CGAACACTCTCATCACCAACC 58.931 52.381 0.00 0.00 0.00 3.77
4020 4179 2.731976 GACGAACACTCTCATCACCAAC 59.268 50.000 0.00 0.00 0.00 3.77
4021 4180 2.288825 GGACGAACACTCTCATCACCAA 60.289 50.000 0.00 0.00 0.00 3.67
4022 4181 1.272490 GGACGAACACTCTCATCACCA 59.728 52.381 0.00 0.00 0.00 4.17
4023 4182 1.546476 AGGACGAACACTCTCATCACC 59.454 52.381 0.00 0.00 0.00 4.02
4024 4183 2.600731 CAGGACGAACACTCTCATCAC 58.399 52.381 0.00 0.00 0.00 3.06
4025 4184 1.546029 CCAGGACGAACACTCTCATCA 59.454 52.381 0.00 0.00 0.00 3.07
4026 4185 1.737363 GCCAGGACGAACACTCTCATC 60.737 57.143 0.00 0.00 0.00 2.92
4027 4186 0.247736 GCCAGGACGAACACTCTCAT 59.752 55.000 0.00 0.00 0.00 2.90
4028 4187 1.666011 GCCAGGACGAACACTCTCA 59.334 57.895 0.00 0.00 0.00 3.27
4029 4188 1.079750 GGCCAGGACGAACACTCTC 60.080 63.158 0.00 0.00 0.00 3.20
4030 4189 2.932234 CGGCCAGGACGAACACTCT 61.932 63.158 10.09 0.00 35.20 3.24
4031 4190 2.432628 CGGCCAGGACGAACACTC 60.433 66.667 10.09 0.00 35.20 3.51
4032 4191 3.222354 GACGGCCAGGACGAACACT 62.222 63.158 25.69 0.00 35.20 3.55
4079 4238 2.120718 AACGTCCAGGCCCTCTCT 59.879 61.111 0.00 0.00 0.00 3.10
4081 4240 2.147387 AACAACGTCCAGGCCCTCT 61.147 57.895 0.00 0.00 0.00 3.69
4147 4306 4.489771 CGGTGGGCATCAGGGGTC 62.490 72.222 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.