Multiple sequence alignment - TraesCS2D01G447800

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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 TraesCS2D01G447800 chr2D 100.000 4370 0 0 1 4370 557662698 557667067 0.000000e+00 8070.0
1 TraesCS2D01G447800 chr2D 85.517 290 25 7 3661 3933 557683015 557683304 1.990000e-73 287.0
2 TraesCS2D01G447800 chr2B 94.110 4058 164 32 117 4143 665667085 665671098 0.000000e+00 6100.0
3 TraesCS2D01G447800 chr2B 84.262 413 43 10 3542 3936 665857023 665857431 2.470000e-102 383.0
4 TraesCS2D01G447800 chr2A 94.787 3913 167 20 121 4016 698079974 698083866 0.000000e+00 6061.0
5 TraesCS2D01G447800 chr2A 87.018 285 25 6 3661 3933 698091628 698091912 1.180000e-80 311.0
6 TraesCS2D01G447800 chr2A 85.393 178 8 4 4015 4192 698083980 698084139 7.520000e-38 169.0
7 TraesCS2D01G447800 chr2A 85.393 178 8 4 4015 4192 698086802 698086961 7.520000e-38 169.0
8 TraesCS2D01G447800 chr7D 86.052 423 45 8 115 524 635099376 635099797 4.010000e-120 442.0
9 TraesCS2D01G447800 chr4A 83.294 425 42 12 112 524 688921096 688921503 8.930000e-97 364.0
10 TraesCS2D01G447800 chr4A 81.647 425 49 12 112 524 696397206 696397613 4.210000e-85 326.0
11 TraesCS2D01G447800 chr5B 82.824 425 44 12 112 524 380782284 380782691 1.930000e-93 353.0
12 TraesCS2D01G447800 chr3A 85.057 348 36 6 2761 3101 66226522 66226860 1.510000e-89 340.0
13 TraesCS2D01G447800 chr3B 85.784 204 23 3 2892 3095 90116923 90117120 1.230000e-50 211.0
14 TraesCS2D01G447800 chr3D 86.765 68 5 4 4256 4320 329602244 329602310 6.060000e-09 73.1


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 TraesCS2D01G447800 chr2D 557662698 557667067 4369 False 8070 8070 100.000000 1 4370 1 chr2D.!!$F1 4369
1 TraesCS2D01G447800 chr2B 665667085 665671098 4013 False 6100 6100 94.110000 117 4143 1 chr2B.!!$F1 4026
2 TraesCS2D01G447800 chr2A 698079974 698086961 6987 False 2133 6061 88.524333 121 4192 3 chr2A.!!$F2 4071

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
227 229 0.387622 TGCCGTTACGTTTCTCTCCG 60.388 55.000 3.52 0.0 0.00 4.63 F
751 780 1.222936 GTCCACCTGCATCCTGAGG 59.777 63.158 0.00 0.0 35.26 3.86 F
1269 1301 2.076100 GTGTTGGTCGATGCTGATGAA 58.924 47.619 0.00 0.0 0.00 2.57 F
2082 2114 8.261522 ACATCTATTTCTAAGGTCACCTCTTTC 58.738 37.037 0.00 0.0 30.89 2.62 F
2903 2935 0.389817 GTGGTATCGACTGCACAGCA 60.390 55.000 0.00 0.0 36.92 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1086 1118 0.325484 CAATGGGGCCCAAATCCTCA 60.325 55.000 32.57 11.03 38.67 3.86 R
2577 2609 0.385751 TCTGTACCAGCTGCGCTATC 59.614 55.000 8.66 0.00 36.40 2.08 R
2580 2612 0.742281 CAATCTGTACCAGCTGCGCT 60.742 55.000 8.66 0.00 40.77 5.92 R
3174 3206 1.001293 ACAGCGTTCATGAAGCTCTCA 59.999 47.619 21.89 0.00 39.48 3.27 R
4294 7271 0.168128 GGCTGGAAATGAAACGACCG 59.832 55.000 0.00 0.00 0.00 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
17 18 4.344865 AACCTGTCGCCGCCCAAT 62.345 61.111 0.00 0.00 0.00 3.16
18 19 4.778143 ACCTGTCGCCGCCCAATC 62.778 66.667 0.00 0.00 0.00 2.67
37 38 4.787871 GGCATCGCCTAGCTTCAT 57.212 55.556 0.00 0.00 46.69 2.57
38 39 3.012560 GGCATCGCCTAGCTTCATT 57.987 52.632 0.00 0.00 46.69 2.57
39 40 0.871057 GGCATCGCCTAGCTTCATTC 59.129 55.000 0.00 0.00 46.69 2.67
40 41 0.871057 GCATCGCCTAGCTTCATTCC 59.129 55.000 0.00 0.00 0.00 3.01
41 42 1.517242 CATCGCCTAGCTTCATTCCC 58.483 55.000 0.00 0.00 0.00 3.97
42 43 0.398318 ATCGCCTAGCTTCATTCCCC 59.602 55.000 0.00 0.00 0.00 4.81
43 44 1.227973 CGCCTAGCTTCATTCCCCC 60.228 63.158 0.00 0.00 0.00 5.40
71 72 4.194720 CCGGAGCGACCCTCGAAG 62.195 72.222 0.00 0.00 43.74 3.79
72 73 4.856607 CGGAGCGACCCTCGAAGC 62.857 72.222 0.00 0.00 43.74 3.86
73 74 4.856607 GGAGCGACCCTCGAAGCG 62.857 72.222 0.00 0.00 43.74 4.68
74 75 4.856607 GAGCGACCCTCGAAGCGG 62.857 72.222 0.00 0.00 43.74 5.52
96 97 4.292178 CGGATCTCAGGCGCCCTC 62.292 72.222 26.15 12.25 0.00 4.30
97 98 3.934962 GGATCTCAGGCGCCCTCC 61.935 72.222 26.15 17.55 0.00 4.30
98 99 2.841988 GATCTCAGGCGCCCTCCT 60.842 66.667 26.15 0.00 36.78 3.69
99 100 2.841988 ATCTCAGGCGCCCTCCTC 60.842 66.667 26.15 0.00 33.25 3.71
109 110 4.179599 CCCTCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
110 111 4.179599 CCTCCTCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
111 112 4.179599 CTCCTCCCCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
114 115 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
205 207 0.884704 TGCTCTGCTTTGTTCGGGTC 60.885 55.000 0.00 0.00 0.00 4.46
227 229 0.387622 TGCCGTTACGTTTCTCTCCG 60.388 55.000 3.52 0.00 0.00 4.63
293 295 2.258748 CTTCCTCGAGGCCTTTCCCC 62.259 65.000 27.39 0.00 34.51 4.81
335 348 1.224592 GGGCCGTCAATCAGGACAT 59.775 57.895 0.00 0.00 37.24 3.06
399 412 4.337274 TGATTTGTACGCTAGCTGCTAGTA 59.663 41.667 31.00 18.36 40.11 1.82
433 453 6.147821 CACTGTGAATAAGTGTTCTAAGGGTG 59.852 42.308 0.32 0.00 40.17 4.61
640 660 6.368791 GTCACAGTCACATAAATCTACAGCAA 59.631 38.462 0.00 0.00 0.00 3.91
644 664 8.454106 ACAGTCACATAAATCTACAGCAAATTC 58.546 33.333 0.00 0.00 0.00 2.17
653 673 5.885230 TCTACAGCAAATTCTCACCATTG 57.115 39.130 0.00 0.00 0.00 2.82
667 687 1.995542 ACCATTGTCTCCCCAACTCAT 59.004 47.619 0.00 0.00 0.00 2.90
676 696 4.164221 GTCTCCCCAACTCATTCTGGAATA 59.836 45.833 0.00 0.00 34.35 1.75
677 697 4.164221 TCTCCCCAACTCATTCTGGAATAC 59.836 45.833 0.00 0.00 34.35 1.89
684 713 8.355169 CCCAACTCATTCTGGAATACATTTATG 58.645 37.037 0.00 0.00 34.35 1.90
722 751 9.168451 ACACATATATTTTAACCATTCACGTCA 57.832 29.630 0.00 0.00 0.00 4.35
751 780 1.222936 GTCCACCTGCATCCTGAGG 59.777 63.158 0.00 0.00 35.26 3.86
797 826 2.152016 GGTGTCTTGTTACCCTCAAGC 58.848 52.381 0.00 0.00 41.13 4.01
818 847 3.552478 GCCCTAAACTCGTACTGATAGCC 60.552 52.174 0.00 0.00 0.00 3.93
824 853 2.490903 ACTCGTACTGATAGCCGTTTGT 59.509 45.455 0.00 0.00 0.00 2.83
838 867 4.570369 AGCCGTTTGTTTTCAGGAAATTTG 59.430 37.500 0.00 0.00 0.00 2.32
845 874 9.112789 GTTTGTTTTCAGGAAATTTGAAACAAC 57.887 29.630 16.90 10.02 42.44 3.32
1086 1118 2.936498 CGTTGGCTTCGTCTCCAATAAT 59.064 45.455 7.91 0.00 43.43 1.28
1269 1301 2.076100 GTGTTGGTCGATGCTGATGAA 58.924 47.619 0.00 0.00 0.00 2.57
2082 2114 8.261522 ACATCTATTTCTAAGGTCACCTCTTTC 58.738 37.037 0.00 0.00 30.89 2.62
2577 2609 8.964476 AGTTGATACATAATGGTAGTTTGGAG 57.036 34.615 0.00 0.00 0.00 3.86
2658 2690 1.079405 CCTTTTGCATGCTGCCCAG 60.079 57.895 20.33 7.52 44.23 4.45
2903 2935 0.389817 GTGGTATCGACTGCACAGCA 60.390 55.000 0.00 0.00 36.92 4.41
3004 3036 1.600916 AGCGACAGGGTGAAAAGGC 60.601 57.895 0.00 0.00 0.00 4.35
3047 3079 4.020573 AGGTATCGACATTGACCTGAAACA 60.021 41.667 0.00 0.00 40.86 2.83
3340 3372 2.289694 CGGAAGAAGTCCTTGGATGTGT 60.290 50.000 0.00 0.00 45.36 3.72
3405 3437 4.199310 GCATCTGAAATAAGCTGGTACCA 58.801 43.478 15.39 15.39 0.00 3.25
3511 3545 4.870123 TTCATGTGCACATTTAGGCTTT 57.130 36.364 29.48 3.51 33.61 3.51
3634 3670 1.804748 GGCAGTTTCTTTCGTACCAGG 59.195 52.381 0.00 0.00 0.00 4.45
3733 3769 4.670227 GTCAAATAGACTTGTGCTGGTC 57.330 45.455 0.00 0.00 44.09 4.02
3745 3781 2.815503 TGTGCTGGTCATCATTGTCTTG 59.184 45.455 0.00 0.00 0.00 3.02
3830 3866 2.095364 AGCAGCTTCGCTTTGATGAAAG 60.095 45.455 0.00 0.00 39.99 2.62
3844 3880 7.112148 GCTTTGATGAAAGTTACTTCTTTGACG 59.888 37.037 6.52 0.00 40.77 4.35
3857 3893 2.806244 TCTTTGACGGTTAGCAAAGCTC 59.194 45.455 13.16 0.00 46.45 4.09
3862 3898 4.575885 TGACGGTTAGCAAAGCTCTAAAT 58.424 39.130 0.00 0.00 40.44 1.40
3865 3901 3.487544 CGGTTAGCAAAGCTCTAAATGCC 60.488 47.826 0.00 0.00 40.44 4.40
3866 3902 3.443681 GGTTAGCAAAGCTCTAAATGCCA 59.556 43.478 0.00 0.00 40.44 4.92
3869 3905 1.134995 GCAAAGCTCTAAATGCCACCC 60.135 52.381 0.00 0.00 32.73 4.61
3870 3906 2.450476 CAAAGCTCTAAATGCCACCCT 58.550 47.619 0.00 0.00 0.00 4.34
3871 3907 2.827921 CAAAGCTCTAAATGCCACCCTT 59.172 45.455 0.00 0.00 0.00 3.95
3872 3908 4.016444 CAAAGCTCTAAATGCCACCCTTA 58.984 43.478 0.00 0.00 0.00 2.69
3873 3909 4.316025 AAGCTCTAAATGCCACCCTTAA 57.684 40.909 0.00 0.00 0.00 1.85
3874 3910 4.526438 AGCTCTAAATGCCACCCTTAAT 57.474 40.909 0.00 0.00 0.00 1.40
3886 3922 5.656416 TGCCACCCTTAATAAATCTCTTTGG 59.344 40.000 0.00 0.00 0.00 3.28
3906 3942 9.231297 TCTTTGGTCAGATAACTTTGGAATTAG 57.769 33.333 0.00 0.00 0.00 1.73
3908 3944 9.581289 TTTGGTCAGATAACTTTGGAATTAGAA 57.419 29.630 0.00 0.00 0.00 2.10
3920 3956 9.959721 ACTTTGGAATTAGAACTTTAGCTATCA 57.040 29.630 0.00 0.00 0.00 2.15
3945 6832 8.117988 CAGACACCAAATCAATGTTTGAAAAAG 58.882 33.333 8.95 0.00 43.95 2.27
4051 7028 3.200605 TGATCAGCTTTAGGCAATGAGGA 59.799 43.478 0.00 0.00 44.79 3.71
4052 7029 3.272574 TCAGCTTTAGGCAATGAGGAG 57.727 47.619 0.00 0.00 44.79 3.69
4053 7030 2.092753 TCAGCTTTAGGCAATGAGGAGG 60.093 50.000 0.00 0.00 44.79 4.30
4055 7032 3.115390 AGCTTTAGGCAATGAGGAGGTA 58.885 45.455 0.00 0.00 44.79 3.08
4057 7034 4.166919 AGCTTTAGGCAATGAGGAGGTATT 59.833 41.667 0.00 0.00 44.79 1.89
4058 7035 4.517075 GCTTTAGGCAATGAGGAGGTATTC 59.483 45.833 0.00 0.00 41.35 1.75
4059 7036 5.688766 GCTTTAGGCAATGAGGAGGTATTCT 60.689 44.000 0.00 0.00 41.35 2.40
4060 7037 5.552870 TTAGGCAATGAGGAGGTATTCTC 57.447 43.478 0.00 0.00 41.71 2.87
4061 7038 3.387962 AGGCAATGAGGAGGTATTCTCA 58.612 45.455 0.00 0.00 44.19 3.27
4062 7039 3.390639 AGGCAATGAGGAGGTATTCTCAG 59.609 47.826 0.00 0.00 44.19 3.35
4080 7057 6.363577 TCTCAGAACTGCAACTTAGTTTTG 57.636 37.500 0.00 0.00 39.97 2.44
4112 7089 6.474140 TTTTCTGTCTAAAAGGGGAAAACC 57.526 37.500 0.00 0.00 39.11 3.27
4146 7123 6.262056 TCCCTTTTTAGAAACTGAGAACCT 57.738 37.500 0.00 0.00 0.00 3.50
4148 7125 7.808218 TCCCTTTTTAGAAACTGAGAACCTAA 58.192 34.615 0.00 0.00 0.00 2.69
4158 7135 9.020731 AGAAACTGAGAACCTAAAAACAAGAAA 57.979 29.630 0.00 0.00 0.00 2.52
4199 7176 3.166434 AACCTGGGTTGATGCGGA 58.834 55.556 4.01 0.00 36.91 5.54
4200 7177 1.002134 AACCTGGGTTGATGCGGAG 60.002 57.895 4.01 0.00 36.91 4.63
4201 7178 2.124570 CCTGGGTTGATGCGGAGG 60.125 66.667 0.00 0.00 0.00 4.30
4202 7179 2.825836 CTGGGTTGATGCGGAGGC 60.826 66.667 0.00 0.00 40.52 4.70
4203 7180 4.424711 TGGGTTGATGCGGAGGCC 62.425 66.667 0.00 0.00 38.85 5.19
4204 7181 4.424711 GGGTTGATGCGGAGGCCA 62.425 66.667 5.01 0.00 38.85 5.36
4205 7182 2.825836 GGTTGATGCGGAGGCCAG 60.826 66.667 5.01 0.00 38.85 4.85
4206 7183 2.825836 GTTGATGCGGAGGCCAGG 60.826 66.667 5.01 0.00 38.85 4.45
4207 7184 3.008517 TTGATGCGGAGGCCAGGA 61.009 61.111 5.01 0.00 38.85 3.86
4208 7185 3.035173 TTGATGCGGAGGCCAGGAG 62.035 63.158 5.01 0.00 38.85 3.69
4209 7186 4.925861 GATGCGGAGGCCAGGAGC 62.926 72.222 5.01 5.44 38.85 4.70
4212 7189 4.496336 GCGGAGGCCAGGAGCAAT 62.496 66.667 5.01 0.00 46.50 3.56
4213 7190 3.106986 GCGGAGGCCAGGAGCAATA 62.107 63.158 5.01 0.00 46.50 1.90
4214 7191 1.070445 CGGAGGCCAGGAGCAATAG 59.930 63.158 5.01 0.00 46.50 1.73
4215 7192 1.402896 CGGAGGCCAGGAGCAATAGA 61.403 60.000 5.01 0.00 46.50 1.98
4216 7193 0.839946 GGAGGCCAGGAGCAATAGAA 59.160 55.000 5.01 0.00 46.50 2.10
4217 7194 1.423161 GGAGGCCAGGAGCAATAGAAT 59.577 52.381 5.01 0.00 46.50 2.40
4218 7195 2.158549 GGAGGCCAGGAGCAATAGAATT 60.159 50.000 5.01 0.00 46.50 2.17
4219 7196 3.145286 GAGGCCAGGAGCAATAGAATTC 58.855 50.000 5.01 0.00 46.50 2.17
4220 7197 2.782341 AGGCCAGGAGCAATAGAATTCT 59.218 45.455 13.56 13.56 46.50 2.40
4221 7198 3.203934 AGGCCAGGAGCAATAGAATTCTT 59.796 43.478 14.36 0.00 46.50 2.52
4222 7199 3.567585 GGCCAGGAGCAATAGAATTCTTC 59.432 47.826 14.36 4.37 46.50 2.87
4223 7200 3.567585 GCCAGGAGCAATAGAATTCTTCC 59.432 47.826 14.36 13.69 42.97 3.46
4224 7201 4.785301 CCAGGAGCAATAGAATTCTTCCA 58.215 43.478 20.30 2.82 0.00 3.53
4225 7202 5.383476 CCAGGAGCAATAGAATTCTTCCAT 58.617 41.667 20.30 4.93 0.00 3.41
4226 7203 5.832060 CCAGGAGCAATAGAATTCTTCCATT 59.168 40.000 20.30 10.08 0.00 3.16
4227 7204 6.323225 CCAGGAGCAATAGAATTCTTCCATTT 59.677 38.462 20.30 2.80 0.00 2.32
4228 7205 7.147776 CCAGGAGCAATAGAATTCTTCCATTTT 60.148 37.037 20.30 5.00 0.00 1.82
4229 7206 7.705325 CAGGAGCAATAGAATTCTTCCATTTTG 59.295 37.037 20.30 12.90 0.00 2.44
4230 7207 7.398332 AGGAGCAATAGAATTCTTCCATTTTGT 59.602 33.333 20.30 1.63 0.00 2.83
4231 7208 7.704047 GGAGCAATAGAATTCTTCCATTTTGTC 59.296 37.037 14.36 4.17 0.00 3.18
4232 7209 8.358582 AGCAATAGAATTCTTCCATTTTGTCT 57.641 30.769 14.36 7.36 0.00 3.41
4233 7210 9.466497 AGCAATAGAATTCTTCCATTTTGTCTA 57.534 29.630 14.36 0.00 0.00 2.59
4237 7214 7.163001 AGAATTCTTCCATTTTGTCTAAGGC 57.837 36.000 0.88 0.00 0.00 4.35
4238 7215 5.921962 ATTCTTCCATTTTGTCTAAGGCC 57.078 39.130 0.00 0.00 0.00 5.19
4239 7216 4.380843 TCTTCCATTTTGTCTAAGGCCA 57.619 40.909 5.01 0.00 0.00 5.36
4240 7217 4.934356 TCTTCCATTTTGTCTAAGGCCAT 58.066 39.130 5.01 0.00 0.00 4.40
4241 7218 4.706476 TCTTCCATTTTGTCTAAGGCCATG 59.294 41.667 5.01 0.00 0.00 3.66
4242 7219 4.046286 TCCATTTTGTCTAAGGCCATGT 57.954 40.909 5.01 0.00 0.00 3.21
4243 7220 4.415596 TCCATTTTGTCTAAGGCCATGTT 58.584 39.130 5.01 0.00 0.00 2.71
4244 7221 4.837860 TCCATTTTGTCTAAGGCCATGTTT 59.162 37.500 5.01 0.00 0.00 2.83
4245 7222 4.931002 CCATTTTGTCTAAGGCCATGTTTG 59.069 41.667 5.01 0.00 0.00 2.93
4246 7223 4.599047 TTTTGTCTAAGGCCATGTTTGG 57.401 40.909 5.01 0.00 46.66 3.28
4247 7224 3.517296 TTGTCTAAGGCCATGTTTGGA 57.483 42.857 5.01 0.00 46.92 3.53
4248 7225 3.737559 TGTCTAAGGCCATGTTTGGAT 57.262 42.857 5.01 0.00 46.92 3.41
4249 7226 4.046286 TGTCTAAGGCCATGTTTGGATT 57.954 40.909 5.01 0.00 46.92 3.01
4250 7227 3.763360 TGTCTAAGGCCATGTTTGGATTG 59.237 43.478 5.01 0.00 46.92 2.67
4251 7228 2.760092 TCTAAGGCCATGTTTGGATTGC 59.240 45.455 5.01 0.00 46.92 3.56
4252 7229 1.648116 AAGGCCATGTTTGGATTGCT 58.352 45.000 5.01 0.00 46.92 3.91
4253 7230 0.899720 AGGCCATGTTTGGATTGCTG 59.100 50.000 5.01 0.00 46.92 4.41
4254 7231 0.609662 GGCCATGTTTGGATTGCTGT 59.390 50.000 0.00 0.00 46.92 4.40
4255 7232 1.002315 GGCCATGTTTGGATTGCTGTT 59.998 47.619 0.00 0.00 46.92 3.16
4256 7233 2.550639 GGCCATGTTTGGATTGCTGTTT 60.551 45.455 0.00 0.00 46.92 2.83
4257 7234 3.140623 GCCATGTTTGGATTGCTGTTTT 58.859 40.909 0.00 0.00 46.92 2.43
4258 7235 3.187022 GCCATGTTTGGATTGCTGTTTTC 59.813 43.478 0.00 0.00 46.92 2.29
4259 7236 4.634199 CCATGTTTGGATTGCTGTTTTCT 58.366 39.130 0.00 0.00 46.92 2.52
4260 7237 5.058490 CCATGTTTGGATTGCTGTTTTCTT 58.942 37.500 0.00 0.00 46.92 2.52
4261 7238 5.528320 CCATGTTTGGATTGCTGTTTTCTTT 59.472 36.000 0.00 0.00 46.92 2.52
4262 7239 6.293027 CCATGTTTGGATTGCTGTTTTCTTTC 60.293 38.462 0.00 0.00 46.92 2.62
4263 7240 5.728471 TGTTTGGATTGCTGTTTTCTTTCA 58.272 33.333 0.00 0.00 0.00 2.69
4264 7241 6.169094 TGTTTGGATTGCTGTTTTCTTTCAA 58.831 32.000 0.00 0.00 0.00 2.69
4265 7242 6.652481 TGTTTGGATTGCTGTTTTCTTTCAAA 59.348 30.769 0.00 0.00 0.00 2.69
4266 7243 7.336427 TGTTTGGATTGCTGTTTTCTTTCAAAT 59.664 29.630 0.00 0.00 0.00 2.32
4267 7244 8.825745 GTTTGGATTGCTGTTTTCTTTCAAATA 58.174 29.630 0.00 0.00 0.00 1.40
4268 7245 7.945033 TGGATTGCTGTTTTCTTTCAAATAC 57.055 32.000 0.00 0.00 0.00 1.89
4269 7246 6.928492 TGGATTGCTGTTTTCTTTCAAATACC 59.072 34.615 0.00 0.00 0.00 2.73
4270 7247 6.368791 GGATTGCTGTTTTCTTTCAAATACCC 59.631 38.462 0.00 0.00 0.00 3.69
4271 7248 6.478512 TTGCTGTTTTCTTTCAAATACCCT 57.521 33.333 0.00 0.00 0.00 4.34
4272 7249 6.478512 TGCTGTTTTCTTTCAAATACCCTT 57.521 33.333 0.00 0.00 0.00 3.95
4273 7250 6.279882 TGCTGTTTTCTTTCAAATACCCTTG 58.720 36.000 0.00 0.00 0.00 3.61
4274 7251 6.127196 TGCTGTTTTCTTTCAAATACCCTTGT 60.127 34.615 0.00 0.00 0.00 3.16
4275 7252 7.068839 TGCTGTTTTCTTTCAAATACCCTTGTA 59.931 33.333 0.00 0.00 0.00 2.41
4276 7253 7.923878 GCTGTTTTCTTTCAAATACCCTTGTAA 59.076 33.333 0.00 0.00 0.00 2.41
4277 7254 9.810545 CTGTTTTCTTTCAAATACCCTTGTAAA 57.189 29.630 0.00 0.00 0.00 2.01
4300 7277 3.669686 CAGGTCTCTGTCGGTCGT 58.330 61.111 0.00 0.00 36.30 4.34
4301 7278 1.957562 CAGGTCTCTGTCGGTCGTT 59.042 57.895 0.00 0.00 36.30 3.85
4302 7279 0.314302 CAGGTCTCTGTCGGTCGTTT 59.686 55.000 0.00 0.00 36.30 3.60
4303 7280 0.597072 AGGTCTCTGTCGGTCGTTTC 59.403 55.000 0.00 0.00 0.00 2.78
4304 7281 0.313043 GGTCTCTGTCGGTCGTTTCA 59.687 55.000 0.00 0.00 0.00 2.69
4305 7282 1.067776 GGTCTCTGTCGGTCGTTTCAT 60.068 52.381 0.00 0.00 0.00 2.57
4306 7283 2.609737 GGTCTCTGTCGGTCGTTTCATT 60.610 50.000 0.00 0.00 0.00 2.57
4307 7284 3.057734 GTCTCTGTCGGTCGTTTCATTT 58.942 45.455 0.00 0.00 0.00 2.32
4308 7285 3.121445 GTCTCTGTCGGTCGTTTCATTTC 59.879 47.826 0.00 0.00 0.00 2.17
4309 7286 2.409975 TCTGTCGGTCGTTTCATTTCC 58.590 47.619 0.00 0.00 0.00 3.13
4310 7287 2.139917 CTGTCGGTCGTTTCATTTCCA 58.860 47.619 0.00 0.00 0.00 3.53
4311 7288 2.139917 TGTCGGTCGTTTCATTTCCAG 58.860 47.619 0.00 0.00 0.00 3.86
4312 7289 1.136057 GTCGGTCGTTTCATTTCCAGC 60.136 52.381 0.00 0.00 0.00 4.85
4313 7290 0.168128 CGGTCGTTTCATTTCCAGCC 59.832 55.000 0.00 0.00 0.00 4.85
4314 7291 1.243902 GGTCGTTTCATTTCCAGCCA 58.756 50.000 0.00 0.00 0.00 4.75
4315 7292 1.200020 GGTCGTTTCATTTCCAGCCAG 59.800 52.381 0.00 0.00 0.00 4.85
4316 7293 2.151202 GTCGTTTCATTTCCAGCCAGA 58.849 47.619 0.00 0.00 0.00 3.86
4317 7294 2.552315 GTCGTTTCATTTCCAGCCAGAA 59.448 45.455 0.00 0.00 0.00 3.02
4318 7295 3.004315 GTCGTTTCATTTCCAGCCAGAAA 59.996 43.478 1.60 1.60 39.92 2.52
4319 7296 3.826157 TCGTTTCATTTCCAGCCAGAAAT 59.174 39.130 5.87 5.87 45.21 2.17
4320 7297 5.007034 TCGTTTCATTTCCAGCCAGAAATA 58.993 37.500 10.34 0.00 43.06 1.40
4321 7298 5.095490 CGTTTCATTTCCAGCCAGAAATAC 58.905 41.667 10.34 6.02 43.06 1.89
4322 7299 5.410924 GTTTCATTTCCAGCCAGAAATACC 58.589 41.667 10.34 0.00 43.06 2.73
4323 7300 4.591321 TCATTTCCAGCCAGAAATACCT 57.409 40.909 10.34 0.00 43.06 3.08
4324 7301 4.526970 TCATTTCCAGCCAGAAATACCTC 58.473 43.478 10.34 0.00 43.06 3.85
4325 7302 4.018506 TCATTTCCAGCCAGAAATACCTCA 60.019 41.667 10.34 0.00 43.06 3.86
4326 7303 3.350219 TTCCAGCCAGAAATACCTCAC 57.650 47.619 0.00 0.00 0.00 3.51
4327 7304 2.265367 TCCAGCCAGAAATACCTCACA 58.735 47.619 0.00 0.00 0.00 3.58
4328 7305 2.237143 TCCAGCCAGAAATACCTCACAG 59.763 50.000 0.00 0.00 0.00 3.66
4329 7306 2.012673 CAGCCAGAAATACCTCACAGC 58.987 52.381 0.00 0.00 0.00 4.40
4330 7307 1.065126 AGCCAGAAATACCTCACAGCC 60.065 52.381 0.00 0.00 0.00 4.85
4331 7308 2.019156 GCCAGAAATACCTCACAGCCC 61.019 57.143 0.00 0.00 0.00 5.19
4332 7309 1.656652 CAGAAATACCTCACAGCCCG 58.343 55.000 0.00 0.00 0.00 6.13
4333 7310 1.066143 CAGAAATACCTCACAGCCCGT 60.066 52.381 0.00 0.00 0.00 5.28
4334 7311 1.207329 AGAAATACCTCACAGCCCGTC 59.793 52.381 0.00 0.00 0.00 4.79
4335 7312 0.981183 AAATACCTCACAGCCCGTCA 59.019 50.000 0.00 0.00 0.00 4.35
4336 7313 0.981183 AATACCTCACAGCCCGTCAA 59.019 50.000 0.00 0.00 0.00 3.18
4337 7314 0.537188 ATACCTCACAGCCCGTCAAG 59.463 55.000 0.00 0.00 0.00 3.02
4338 7315 0.830444 TACCTCACAGCCCGTCAAGT 60.830 55.000 0.00 0.00 0.00 3.16
4339 7316 1.071471 CCTCACAGCCCGTCAAGTT 59.929 57.895 0.00 0.00 0.00 2.66
4340 7317 0.320374 CCTCACAGCCCGTCAAGTTA 59.680 55.000 0.00 0.00 0.00 2.24
4341 7318 1.429463 CTCACAGCCCGTCAAGTTAC 58.571 55.000 0.00 0.00 0.00 2.50
4342 7319 0.319211 TCACAGCCCGTCAAGTTACG 60.319 55.000 0.00 0.00 42.49 3.18
4343 7320 1.666872 ACAGCCCGTCAAGTTACGC 60.667 57.895 0.00 0.00 41.51 4.42
4344 7321 2.047560 AGCCCGTCAAGTTACGCC 60.048 61.111 0.00 0.00 41.51 5.68
4345 7322 2.047560 GCCCGTCAAGTTACGCCT 60.048 61.111 0.00 0.00 41.51 5.52
4346 7323 2.388232 GCCCGTCAAGTTACGCCTG 61.388 63.158 0.00 0.00 41.51 4.85
4347 7324 2.388232 CCCGTCAAGTTACGCCTGC 61.388 63.158 0.00 0.00 41.51 4.85
4348 7325 1.666553 CCGTCAAGTTACGCCTGCA 60.667 57.895 0.00 0.00 41.51 4.41
4349 7326 1.225376 CCGTCAAGTTACGCCTGCAA 61.225 55.000 0.00 0.00 41.51 4.08
4350 7327 0.584396 CGTCAAGTTACGCCTGCAAA 59.416 50.000 0.00 0.00 35.87 3.68
4351 7328 1.196808 CGTCAAGTTACGCCTGCAAAT 59.803 47.619 0.00 0.00 35.87 2.32
4352 7329 2.350388 CGTCAAGTTACGCCTGCAAATT 60.350 45.455 0.00 0.00 35.87 1.82
4353 7330 3.120477 CGTCAAGTTACGCCTGCAAATTA 60.120 43.478 0.00 0.00 35.87 1.40
4354 7331 4.611807 CGTCAAGTTACGCCTGCAAATTAA 60.612 41.667 0.00 0.00 35.87 1.40
4355 7332 5.216648 GTCAAGTTACGCCTGCAAATTAAA 58.783 37.500 0.00 0.00 0.00 1.52
4356 7333 5.861787 GTCAAGTTACGCCTGCAAATTAAAT 59.138 36.000 0.00 0.00 0.00 1.40
4357 7334 7.024768 GTCAAGTTACGCCTGCAAATTAAATA 58.975 34.615 0.00 0.00 0.00 1.40
4358 7335 7.007995 GTCAAGTTACGCCTGCAAATTAAATAC 59.992 37.037 0.00 0.00 0.00 1.89
4359 7336 5.886992 AGTTACGCCTGCAAATTAAATACC 58.113 37.500 0.00 0.00 0.00 2.73
4360 7337 3.793797 ACGCCTGCAAATTAAATACCC 57.206 42.857 0.00 0.00 0.00 3.69
4361 7338 3.093057 ACGCCTGCAAATTAAATACCCA 58.907 40.909 0.00 0.00 0.00 4.51
4362 7339 3.119280 ACGCCTGCAAATTAAATACCCAC 60.119 43.478 0.00 0.00 0.00 4.61
4363 7340 3.443976 GCCTGCAAATTAAATACCCACG 58.556 45.455 0.00 0.00 0.00 4.94
4364 7341 3.119280 GCCTGCAAATTAAATACCCACGT 60.119 43.478 0.00 0.00 0.00 4.49
4365 7342 4.096682 GCCTGCAAATTAAATACCCACGTA 59.903 41.667 0.00 0.00 0.00 3.57
4366 7343 5.221165 GCCTGCAAATTAAATACCCACGTAT 60.221 40.000 0.00 0.00 36.72 3.06
4367 7344 6.681865 GCCTGCAAATTAAATACCCACGTATT 60.682 38.462 0.00 0.00 45.25 1.89
4368 7345 7.468906 GCCTGCAAATTAAATACCCACGTATTA 60.469 37.037 0.00 0.00 43.05 0.98
4369 7346 8.407064 CCTGCAAATTAAATACCCACGTATTAA 58.593 33.333 0.00 0.00 43.05 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.344865 ATTGGGCGGCGACAGGTT 62.345 61.111 17.61 0.00 0.00 3.50
1 2 4.778143 GATTGGGCGGCGACAGGT 62.778 66.667 17.61 0.00 0.00 4.00
21 22 0.871057 GGAATGAAGCTAGGCGATGC 59.129 55.000 0.00 0.00 0.00 3.91
22 23 1.517242 GGGAATGAAGCTAGGCGATG 58.483 55.000 0.00 0.00 0.00 3.84
23 24 0.398318 GGGGAATGAAGCTAGGCGAT 59.602 55.000 0.00 0.00 0.00 4.58
24 25 1.696097 GGGGGAATGAAGCTAGGCGA 61.696 60.000 0.00 0.00 0.00 5.54
25 26 1.227973 GGGGGAATGAAGCTAGGCG 60.228 63.158 0.00 0.00 0.00 5.52
26 27 4.909678 GGGGGAATGAAGCTAGGC 57.090 61.111 0.00 0.00 0.00 3.93
54 55 4.194720 CTTCGAGGGTCGCTCCGG 62.195 72.222 11.06 0.00 40.21 5.14
55 56 4.856607 GCTTCGAGGGTCGCTCCG 62.857 72.222 11.06 6.83 40.21 4.63
56 57 4.856607 CGCTTCGAGGGTCGCTCC 62.857 72.222 11.06 0.00 40.21 4.70
57 58 4.856607 CCGCTTCGAGGGTCGCTC 62.857 72.222 6.84 6.84 40.21 5.03
79 80 4.292178 GAGGGCGCCTGAGATCCG 62.292 72.222 28.56 0.00 31.76 4.18
80 81 3.934962 GGAGGGCGCCTGAGATCC 61.935 72.222 28.56 20.67 31.76 3.36
81 82 2.841988 AGGAGGGCGCCTGAGATC 60.842 66.667 28.56 15.90 36.76 2.75
82 83 2.841988 GAGGAGGGCGCCTGAGAT 60.842 66.667 28.56 9.03 38.73 2.75
92 93 4.179599 GAGGGGAGGGGAGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
93 94 4.179599 GGAGGGGAGGGGAGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
94 95 4.179599 GGGAGGGGAGGGGAGGAG 62.180 77.778 0.00 0.00 0.00 3.69
97 98 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
102 103 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
107 108 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
205 207 1.719780 GAGAGAAACGTAACGGCAGTG 59.280 52.381 0.00 0.00 0.00 3.66
227 229 1.978712 GCGGCGAAGAAAAGTAGGCC 61.979 60.000 12.98 0.00 37.21 5.19
259 261 1.403687 GGAAGAGGGATCTGGTCGGG 61.404 65.000 0.00 0.00 0.00 5.14
309 311 0.529992 GATTGACGGCCCTAGGAACG 60.530 60.000 11.48 16.47 0.00 3.95
310 312 0.539986 TGATTGACGGCCCTAGGAAC 59.460 55.000 11.48 1.15 0.00 3.62
311 313 0.830648 CTGATTGACGGCCCTAGGAA 59.169 55.000 11.48 0.00 0.00 3.36
312 314 1.048724 CCTGATTGACGGCCCTAGGA 61.049 60.000 11.48 0.00 0.00 2.94
313 315 1.048724 TCCTGATTGACGGCCCTAGG 61.049 60.000 0.06 0.06 0.00 3.02
314 316 0.105039 GTCCTGATTGACGGCCCTAG 59.895 60.000 0.00 0.00 0.00 3.02
315 317 0.616395 TGTCCTGATTGACGGCCCTA 60.616 55.000 0.00 0.00 38.11 3.53
316 318 1.274703 ATGTCCTGATTGACGGCCCT 61.275 55.000 0.00 0.00 38.11 5.19
317 319 0.815615 GATGTCCTGATTGACGGCCC 60.816 60.000 0.00 0.00 38.11 5.80
318 320 1.154205 CGATGTCCTGATTGACGGCC 61.154 60.000 0.00 0.00 38.11 6.13
319 321 1.766143 GCGATGTCCTGATTGACGGC 61.766 60.000 0.00 0.00 38.11 5.68
399 412 8.627208 AACACTTATTCACAGTGAAATCTGAT 57.373 30.769 19.92 5.14 43.90 2.90
420 440 2.543777 TCTGTGCACCCTTAGAACAC 57.456 50.000 15.69 0.00 0.00 3.32
433 453 0.601311 ACGAGGTTGAGCTTCTGTGC 60.601 55.000 0.00 0.00 0.00 4.57
512 532 2.420058 GCACCCATGCCTACTAGTTT 57.580 50.000 0.00 0.00 46.97 2.66
540 560 6.654582 GGTTGAAAAATATCAATGGCAACCTT 59.345 34.615 0.20 0.00 46.33 3.50
613 633 6.035435 GCTGTAGATTTATGTGACTGTGACTG 59.965 42.308 0.00 0.00 0.00 3.51
640 660 2.649312 TGGGGAGACAATGGTGAGAATT 59.351 45.455 0.00 0.00 0.00 2.17
644 664 1.352352 AGTTGGGGAGACAATGGTGAG 59.648 52.381 0.00 0.00 32.24 3.51
653 673 1.909302 TCCAGAATGAGTTGGGGAGAC 59.091 52.381 0.00 0.00 39.69 3.36
667 687 9.967451 TCTGTTAACCATAAATGTATTCCAGAA 57.033 29.630 2.48 0.00 0.00 3.02
676 696 7.994425 TGTGTGATCTGTTAACCATAAATGT 57.006 32.000 2.48 0.00 0.00 2.71
726 755 3.939837 ATGCAGGTGGACGCAGACG 62.940 63.158 0.00 0.00 42.37 4.18
727 756 2.046892 ATGCAGGTGGACGCAGAC 60.047 61.111 0.00 0.00 42.37 3.51
728 757 2.265739 GATGCAGGTGGACGCAGA 59.734 61.111 0.00 0.00 42.37 4.26
729 758 2.821366 GGATGCAGGTGGACGCAG 60.821 66.667 0.00 0.00 42.37 5.18
730 759 3.321648 AGGATGCAGGTGGACGCA 61.322 61.111 0.00 0.00 43.45 5.24
731 760 2.821366 CAGGATGCAGGTGGACGC 60.821 66.667 0.00 0.00 0.00 5.19
732 761 1.153489 CTCAGGATGCAGGTGGACG 60.153 63.158 0.00 0.00 34.76 4.79
733 762 1.222936 CCTCAGGATGCAGGTGGAC 59.777 63.158 0.00 0.00 34.76 4.02
737 766 3.005539 ACGCCTCAGGATGCAGGT 61.006 61.111 0.00 0.00 36.29 4.00
751 780 1.750399 ATGGTGGATGCCTTGACGC 60.750 57.895 0.00 0.00 0.00 5.19
765 794 8.875954 GGGTAACAAGACACCAAAATACATGGT 61.876 40.741 0.00 0.00 46.55 3.55
783 812 3.396611 AGTTTAGGGCTTGAGGGTAACAA 59.603 43.478 0.00 0.00 39.74 2.83
797 826 3.304525 CGGCTATCAGTACGAGTTTAGGG 60.305 52.174 0.00 0.00 0.00 3.53
818 847 7.513968 TGTTTCAAATTTCCTGAAAACAAACG 58.486 30.769 5.56 0.00 42.73 3.60
824 853 6.878389 AGCAGTTGTTTCAAATTTCCTGAAAA 59.122 30.769 5.56 0.00 42.73 2.29
845 874 4.925646 GGAGAAGCCAAAAATAACAAGCAG 59.074 41.667 0.00 0.00 36.34 4.24
874 903 9.696917 AGGAAATTAACAATTCACAAACTGATC 57.303 29.630 0.00 0.00 0.00 2.92
1086 1118 0.325484 CAATGGGGCCCAAATCCTCA 60.325 55.000 32.57 11.03 38.67 3.86
2082 2114 2.069273 CGTGCAAACTGTTCCTCTAGG 58.931 52.381 0.00 0.00 0.00 3.02
2577 2609 0.385751 TCTGTACCAGCTGCGCTATC 59.614 55.000 8.66 0.00 36.40 2.08
2580 2612 0.742281 CAATCTGTACCAGCTGCGCT 60.742 55.000 8.66 0.00 40.77 5.92
2658 2690 2.225727 CCGTTTAGGAAGTCCACAAAGC 59.774 50.000 0.00 0.00 45.00 3.51
3047 3079 4.345257 TGTCTTCTGCAAACTCCTCTAACT 59.655 41.667 0.00 0.00 0.00 2.24
3113 3145 6.817765 TCTCGACAAGGCAATCTTTAAAAT 57.182 33.333 0.00 0.00 32.41 1.82
3174 3206 1.001293 ACAGCGTTCATGAAGCTCTCA 59.999 47.619 21.89 0.00 39.48 3.27
3340 3372 7.040409 GCTAAAATCCTTCAACCTTCTCTTCAA 60.040 37.037 0.00 0.00 0.00 2.69
3405 3437 9.343539 AGAAGCAAATTTAAGTTCTACTCAACT 57.656 29.630 6.95 0.00 38.30 3.16
3689 3725 4.274459 CAGCTTTCTTCACAGTTACTGCTT 59.726 41.667 12.80 0.00 34.37 3.91
3724 3760 2.815503 CAAGACAATGATGACCAGCACA 59.184 45.455 0.00 0.00 0.00 4.57
3733 3769 6.809689 TCTTTAAGCAATGCAAGACAATGATG 59.190 34.615 8.35 0.00 30.03 3.07
3745 3781 5.406477 CCAAGGTTTTCTCTTTAAGCAATGC 59.594 40.000 0.00 0.00 0.00 3.56
3817 3853 7.112148 GTCAAAGAAGTAACTTTCATCAAAGCG 59.888 37.037 0.00 0.00 42.66 4.68
3830 3866 5.662211 TTGCTAACCGTCAAAGAAGTAAC 57.338 39.130 0.00 0.00 0.00 2.50
3844 3880 3.443681 TGGCATTTAGAGCTTTGCTAACC 59.556 43.478 0.00 0.00 39.88 2.85
3854 3890 6.709018 TTTATTAAGGGTGGCATTTAGAGC 57.291 37.500 0.00 0.00 0.00 4.09
3857 3893 8.697507 AGAGATTTATTAAGGGTGGCATTTAG 57.302 34.615 0.00 0.00 0.00 1.85
3862 3898 5.656416 CCAAAGAGATTTATTAAGGGTGGCA 59.344 40.000 0.00 0.00 0.00 4.92
3865 3901 7.829211 TCTGACCAAAGAGATTTATTAAGGGTG 59.171 37.037 0.00 0.00 0.00 4.61
3866 3902 7.928873 TCTGACCAAAGAGATTTATTAAGGGT 58.071 34.615 0.00 0.00 0.00 4.34
3874 3910 9.231297 CCAAAGTTATCTGACCAAAGAGATTTA 57.769 33.333 0.00 0.00 31.29 1.40
3906 3942 7.334421 TGATTTGGTGTCTGATAGCTAAAGTTC 59.666 37.037 0.00 0.00 0.00 3.01
3908 3944 6.711277 TGATTTGGTGTCTGATAGCTAAAGT 58.289 36.000 0.00 0.00 0.00 2.66
3917 3953 6.653526 TCAAACATTGATTTGGTGTCTGAT 57.346 33.333 10.01 0.00 39.57 2.90
3920 3956 8.040132 TCTTTTTCAAACATTGATTTGGTGTCT 58.960 29.630 10.01 0.00 39.84 3.41
3922 3958 8.558973 TTCTTTTTCAAACATTGATTTGGTGT 57.441 26.923 10.01 0.00 39.84 4.16
3945 6832 5.236047 GCATGACTGACACTGATAGGATTTC 59.764 44.000 0.00 0.00 0.00 2.17
3950 6837 3.455327 CTGCATGACTGACACTGATAGG 58.545 50.000 0.00 0.00 0.00 2.57
4051 7028 4.899352 AGTTGCAGTTCTGAGAATACCT 57.101 40.909 0.00 0.00 0.00 3.08
4052 7029 6.166982 ACTAAGTTGCAGTTCTGAGAATACC 58.833 40.000 0.00 0.00 0.00 2.73
4053 7030 7.659652 AACTAAGTTGCAGTTCTGAGAATAC 57.340 36.000 0.00 0.00 30.36 1.89
4055 7032 7.420800 CAAAACTAAGTTGCAGTTCTGAGAAT 58.579 34.615 0.00 0.00 35.19 2.40
4057 7034 6.363577 CAAAACTAAGTTGCAGTTCTGAGA 57.636 37.500 3.84 0.00 35.19 3.27
4112 7089 5.193099 TCTAAAAAGGGAAATCAGGAGGG 57.807 43.478 0.00 0.00 0.00 4.30
4166 7143 3.333804 CAGGTTGCCTGTGTTTGTTTTT 58.666 40.909 6.99 0.00 45.82 1.94
4192 7169 4.925861 GCTCCTGGCCTCCGCATC 62.926 72.222 3.32 0.00 36.38 3.91
4195 7172 3.106986 TATTGCTCCTGGCCTCCGC 62.107 63.158 3.32 1.79 40.92 5.54
4196 7173 1.070445 CTATTGCTCCTGGCCTCCG 59.930 63.158 3.32 0.00 40.92 4.63
4197 7174 0.839946 TTCTATTGCTCCTGGCCTCC 59.160 55.000 3.32 0.00 40.92 4.30
4198 7175 2.947127 ATTCTATTGCTCCTGGCCTC 57.053 50.000 3.32 0.00 40.92 4.70
4199 7176 2.782341 AGAATTCTATTGCTCCTGGCCT 59.218 45.455 6.06 0.00 40.92 5.19
4200 7177 3.220674 AGAATTCTATTGCTCCTGGCC 57.779 47.619 6.06 0.00 40.92 5.36
4201 7178 3.567585 GGAAGAATTCTATTGCTCCTGGC 59.432 47.826 8.75 0.00 46.56 4.85
4202 7179 4.785301 TGGAAGAATTCTATTGCTCCTGG 58.215 43.478 19.26 0.00 46.56 4.45
4212 7189 7.339466 GGCCTTAGACAAAATGGAAGAATTCTA 59.661 37.037 8.75 0.00 46.56 2.10
4213 7190 6.153510 GGCCTTAGACAAAATGGAAGAATTCT 59.846 38.462 0.88 0.88 46.56 2.40
4214 7191 6.071391 TGGCCTTAGACAAAATGGAAGAATTC 60.071 38.462 3.32 0.00 46.67 2.17
4215 7192 5.779771 TGGCCTTAGACAAAATGGAAGAATT 59.220 36.000 3.32 0.00 0.00 2.17
4216 7193 5.332743 TGGCCTTAGACAAAATGGAAGAAT 58.667 37.500 3.32 0.00 0.00 2.40
4217 7194 4.735369 TGGCCTTAGACAAAATGGAAGAA 58.265 39.130 3.32 0.00 0.00 2.52
4218 7195 4.380843 TGGCCTTAGACAAAATGGAAGA 57.619 40.909 3.32 0.00 0.00 2.87
4219 7196 4.463891 ACATGGCCTTAGACAAAATGGAAG 59.536 41.667 3.32 0.00 0.00 3.46
4220 7197 4.415596 ACATGGCCTTAGACAAAATGGAA 58.584 39.130 3.32 0.00 0.00 3.53
4221 7198 4.046286 ACATGGCCTTAGACAAAATGGA 57.954 40.909 3.32 0.00 0.00 3.41
4222 7199 4.806640 AACATGGCCTTAGACAAAATGG 57.193 40.909 3.32 0.00 0.00 3.16
4223 7200 4.931002 CCAAACATGGCCTTAGACAAAATG 59.069 41.667 3.32 0.00 0.00 2.32
4224 7201 4.837860 TCCAAACATGGCCTTAGACAAAAT 59.162 37.500 3.32 0.00 0.00 1.82
4225 7202 4.219115 TCCAAACATGGCCTTAGACAAAA 58.781 39.130 3.32 0.00 0.00 2.44
4226 7203 3.838565 TCCAAACATGGCCTTAGACAAA 58.161 40.909 3.32 0.00 0.00 2.83
4227 7204 3.517296 TCCAAACATGGCCTTAGACAA 57.483 42.857 3.32 0.00 0.00 3.18
4228 7205 3.737559 ATCCAAACATGGCCTTAGACA 57.262 42.857 3.32 0.00 0.00 3.41
4229 7206 3.429410 GCAATCCAAACATGGCCTTAGAC 60.429 47.826 3.32 0.00 0.00 2.59
4230 7207 2.760092 GCAATCCAAACATGGCCTTAGA 59.240 45.455 3.32 0.00 0.00 2.10
4231 7208 2.762327 AGCAATCCAAACATGGCCTTAG 59.238 45.455 3.32 0.00 0.00 2.18
4232 7209 2.496871 CAGCAATCCAAACATGGCCTTA 59.503 45.455 3.32 0.00 0.00 2.69
4233 7210 1.276989 CAGCAATCCAAACATGGCCTT 59.723 47.619 3.32 0.00 0.00 4.35
4234 7211 0.899720 CAGCAATCCAAACATGGCCT 59.100 50.000 3.32 0.00 0.00 5.19
4235 7212 0.609662 ACAGCAATCCAAACATGGCC 59.390 50.000 0.00 0.00 0.00 5.36
4236 7213 2.460757 AACAGCAATCCAAACATGGC 57.539 45.000 0.00 0.00 0.00 4.40
4237 7214 4.634199 AGAAAACAGCAATCCAAACATGG 58.366 39.130 0.00 0.00 0.00 3.66
4238 7215 6.258287 TGAAAGAAAACAGCAATCCAAACATG 59.742 34.615 0.00 0.00 0.00 3.21
4239 7216 6.347696 TGAAAGAAAACAGCAATCCAAACAT 58.652 32.000 0.00 0.00 0.00 2.71
4240 7217 5.728471 TGAAAGAAAACAGCAATCCAAACA 58.272 33.333 0.00 0.00 0.00 2.83
4241 7218 6.660887 TTGAAAGAAAACAGCAATCCAAAC 57.339 33.333 0.00 0.00 0.00 2.93
4242 7219 7.862512 ATTTGAAAGAAAACAGCAATCCAAA 57.137 28.000 0.00 0.00 0.00 3.28
4243 7220 7.440856 GGTATTTGAAAGAAAACAGCAATCCAA 59.559 33.333 0.00 0.00 0.00 3.53
4244 7221 6.928492 GGTATTTGAAAGAAAACAGCAATCCA 59.072 34.615 0.00 0.00 0.00 3.41
4245 7222 6.368791 GGGTATTTGAAAGAAAACAGCAATCC 59.631 38.462 0.00 0.00 0.00 3.01
4246 7223 7.154656 AGGGTATTTGAAAGAAAACAGCAATC 58.845 34.615 0.00 0.00 0.00 2.67
4247 7224 7.066307 AGGGTATTTGAAAGAAAACAGCAAT 57.934 32.000 0.00 0.00 0.00 3.56
4248 7225 6.478512 AGGGTATTTGAAAGAAAACAGCAA 57.521 33.333 0.00 0.00 0.00 3.91
4249 7226 6.127196 ACAAGGGTATTTGAAAGAAAACAGCA 60.127 34.615 0.00 0.00 0.00 4.41
4250 7227 6.280643 ACAAGGGTATTTGAAAGAAAACAGC 58.719 36.000 0.00 0.00 0.00 4.40
4251 7228 9.810545 TTTACAAGGGTATTTGAAAGAAAACAG 57.189 29.630 0.00 0.00 0.00 3.16
4283 7260 0.314302 AAACGACCGACAGAGACCTG 59.686 55.000 0.00 0.00 45.76 4.00
4284 7261 0.597072 GAAACGACCGACAGAGACCT 59.403 55.000 0.00 0.00 0.00 3.85
4285 7262 0.313043 TGAAACGACCGACAGAGACC 59.687 55.000 0.00 0.00 0.00 3.85
4286 7263 2.349297 ATGAAACGACCGACAGAGAC 57.651 50.000 0.00 0.00 0.00 3.36
4287 7264 3.314553 GAAATGAAACGACCGACAGAGA 58.685 45.455 0.00 0.00 0.00 3.10
4288 7265 2.412089 GGAAATGAAACGACCGACAGAG 59.588 50.000 0.00 0.00 0.00 3.35
4289 7266 2.224090 TGGAAATGAAACGACCGACAGA 60.224 45.455 0.00 0.00 0.00 3.41
4290 7267 2.139917 TGGAAATGAAACGACCGACAG 58.860 47.619 0.00 0.00 0.00 3.51
4291 7268 2.139917 CTGGAAATGAAACGACCGACA 58.860 47.619 0.00 0.00 0.00 4.35
4292 7269 1.136057 GCTGGAAATGAAACGACCGAC 60.136 52.381 0.00 0.00 0.00 4.79
4293 7270 1.153353 GCTGGAAATGAAACGACCGA 58.847 50.000 0.00 0.00 0.00 4.69
4294 7271 0.168128 GGCTGGAAATGAAACGACCG 59.832 55.000 0.00 0.00 0.00 4.79
4295 7272 1.200020 CTGGCTGGAAATGAAACGACC 59.800 52.381 0.00 0.00 0.00 4.79
4296 7273 2.151202 TCTGGCTGGAAATGAAACGAC 58.849 47.619 0.00 0.00 0.00 4.34
4297 7274 2.559698 TCTGGCTGGAAATGAAACGA 57.440 45.000 0.00 0.00 0.00 3.85
4298 7275 3.641437 TTTCTGGCTGGAAATGAAACG 57.359 42.857 2.99 0.00 31.29 3.60
4299 7276 5.185828 AGGTATTTCTGGCTGGAAATGAAAC 59.814 40.000 20.61 14.18 43.22 2.78
4300 7277 5.332743 AGGTATTTCTGGCTGGAAATGAAA 58.667 37.500 20.61 0.00 43.22 2.69
4301 7278 4.934356 AGGTATTTCTGGCTGGAAATGAA 58.066 39.130 20.61 6.92 43.22 2.57
4302 7279 4.018506 TGAGGTATTTCTGGCTGGAAATGA 60.019 41.667 20.61 8.90 43.22 2.57
4303 7280 4.096984 GTGAGGTATTTCTGGCTGGAAATG 59.903 45.833 20.61 0.00 43.22 2.32
4304 7281 4.263905 TGTGAGGTATTTCTGGCTGGAAAT 60.264 41.667 17.72 17.72 44.76 2.17
4305 7282 3.073798 TGTGAGGTATTTCTGGCTGGAAA 59.926 43.478 8.19 8.19 39.16 3.13
4306 7283 2.642311 TGTGAGGTATTTCTGGCTGGAA 59.358 45.455 0.00 0.00 0.00 3.53
4307 7284 2.237143 CTGTGAGGTATTTCTGGCTGGA 59.763 50.000 0.00 0.00 0.00 3.86
4308 7285 2.636830 CTGTGAGGTATTTCTGGCTGG 58.363 52.381 0.00 0.00 0.00 4.85
4309 7286 2.012673 GCTGTGAGGTATTTCTGGCTG 58.987 52.381 0.00 0.00 0.00 4.85
4310 7287 1.065126 GGCTGTGAGGTATTTCTGGCT 60.065 52.381 0.00 0.00 0.00 4.75
4311 7288 1.383523 GGCTGTGAGGTATTTCTGGC 58.616 55.000 0.00 0.00 0.00 4.85
4312 7289 1.743772 CGGGCTGTGAGGTATTTCTGG 60.744 57.143 0.00 0.00 0.00 3.86
4313 7290 1.066143 ACGGGCTGTGAGGTATTTCTG 60.066 52.381 0.00 0.00 0.00 3.02
4314 7291 1.207329 GACGGGCTGTGAGGTATTTCT 59.793 52.381 2.25 0.00 0.00 2.52
4315 7292 1.066430 TGACGGGCTGTGAGGTATTTC 60.066 52.381 2.25 0.00 0.00 2.17
4316 7293 0.981183 TGACGGGCTGTGAGGTATTT 59.019 50.000 2.25 0.00 0.00 1.40
4317 7294 0.981183 TTGACGGGCTGTGAGGTATT 59.019 50.000 2.25 0.00 0.00 1.89
4318 7295 0.537188 CTTGACGGGCTGTGAGGTAT 59.463 55.000 2.25 0.00 0.00 2.73
4319 7296 0.830444 ACTTGACGGGCTGTGAGGTA 60.830 55.000 2.25 0.00 0.00 3.08
4320 7297 1.696097 AACTTGACGGGCTGTGAGGT 61.696 55.000 2.25 0.00 0.00 3.85
4321 7298 0.320374 TAACTTGACGGGCTGTGAGG 59.680 55.000 2.25 0.00 0.00 3.86
4322 7299 1.429463 GTAACTTGACGGGCTGTGAG 58.571 55.000 2.25 4.15 0.00 3.51
4323 7300 0.319211 CGTAACTTGACGGGCTGTGA 60.319 55.000 2.25 0.00 39.19 3.58
4324 7301 1.897398 GCGTAACTTGACGGGCTGTG 61.897 60.000 2.25 0.00 43.13 3.66
4325 7302 1.666872 GCGTAACTTGACGGGCTGT 60.667 57.895 0.00 0.00 43.13 4.40
4326 7303 2.388232 GGCGTAACTTGACGGGCTG 61.388 63.158 0.00 0.00 43.13 4.85
4327 7304 2.047560 GGCGTAACTTGACGGGCT 60.048 61.111 0.00 0.00 43.13 5.19
4328 7305 2.047560 AGGCGTAACTTGACGGGC 60.048 61.111 0.00 0.00 43.13 6.13
4329 7306 2.388232 GCAGGCGTAACTTGACGGG 61.388 63.158 0.00 0.00 43.13 5.28
4330 7307 1.225376 TTGCAGGCGTAACTTGACGG 61.225 55.000 0.00 0.00 43.13 4.79
4331 7308 0.584396 TTTGCAGGCGTAACTTGACG 59.416 50.000 0.00 0.00 45.70 4.35
4332 7309 2.989422 ATTTGCAGGCGTAACTTGAC 57.011 45.000 0.00 0.00 0.00 3.18
4333 7310 5.440234 TTTAATTTGCAGGCGTAACTTGA 57.560 34.783 0.00 0.00 0.00 3.02
4334 7311 6.252655 GGTATTTAATTTGCAGGCGTAACTTG 59.747 38.462 0.00 0.00 0.00 3.16
4335 7312 6.327154 GGTATTTAATTTGCAGGCGTAACTT 58.673 36.000 0.00 0.00 0.00 2.66
4336 7313 5.163591 GGGTATTTAATTTGCAGGCGTAACT 60.164 40.000 0.00 0.00 0.00 2.24
4337 7314 5.038683 GGGTATTTAATTTGCAGGCGTAAC 58.961 41.667 0.00 0.00 0.00 2.50
4338 7315 4.705507 TGGGTATTTAATTTGCAGGCGTAA 59.294 37.500 0.00 0.00 0.00 3.18
4339 7316 4.096682 GTGGGTATTTAATTTGCAGGCGTA 59.903 41.667 0.00 0.00 0.00 4.42
4340 7317 3.093057 TGGGTATTTAATTTGCAGGCGT 58.907 40.909 0.00 0.00 0.00 5.68
4341 7318 3.443976 GTGGGTATTTAATTTGCAGGCG 58.556 45.455 0.00 0.00 0.00 5.52
4342 7319 3.119280 ACGTGGGTATTTAATTTGCAGGC 60.119 43.478 0.00 0.00 0.00 4.85
4343 7320 4.712122 ACGTGGGTATTTAATTTGCAGG 57.288 40.909 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.