Multiple sequence alignment - TraesCS6D01G272900

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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 TraesCS6D01G272900 chr6D 100.000 5991 0 0 1 5991 381557139 381551149 0.000000e+00 11064.0
1 TraesCS6D01G272900 chr6D 97.391 115 3 0 2892 3006 381554144 381554030 4.740000e-46 196.0
2 TraesCS6D01G272900 chr6D 97.391 115 3 0 2996 3110 381554248 381554134 4.740000e-46 196.0
3 TraesCS6D01G272900 chr6D 89.524 105 9 2 1976 2080 42395956 42395854 1.350000e-26 132.0
4 TraesCS6D01G272900 chr6A 94.989 5488 147 44 1 5429 523131137 523125719 0.000000e+00 8493.0
5 TraesCS6D01G272900 chr6A 98.261 115 2 0 2996 3110 523128236 523128122 1.020000e-47 202.0
6 TraesCS6D01G272900 chr6A 95.652 115 5 0 2892 3006 523128132 523128018 1.030000e-42 185.0
7 TraesCS6D01G272900 chr6A 88.496 113 13 0 5595 5707 523070765 523070653 2.910000e-28 137.0
8 TraesCS6D01G272900 chr6A 100.000 30 0 0 2045 2074 344386894 344386923 8.390000e-04 56.5
9 TraesCS6D01G272900 chr6B 92.211 2850 116 45 2996 5805 570155161 570152378 0.000000e+00 3936.0
10 TraesCS6D01G272900 chr6B 91.178 2641 138 50 1 2605 570157982 570155401 0.000000e+00 3498.0
11 TraesCS6D01G272900 chr6B 89.524 105 9 1 1976 2080 520540078 520539976 1.350000e-26 132.0
12 TraesCS6D01G272900 chr3D 93.767 722 35 2 1138 1857 412238836 412238123 0.000000e+00 1075.0
13 TraesCS6D01G272900 chr7B 92.798 722 42 2 1138 1857 502309890 502309177 0.000000e+00 1037.0
14 TraesCS6D01G272900 chr7B 76.765 340 57 13 4374 4703 135041964 135041637 2.870000e-38 171.0
15 TraesCS6D01G272900 chr2D 91.111 720 31 14 1138 1857 180081756 180081070 0.000000e+00 944.0
16 TraesCS6D01G272900 chr5B 94.299 421 22 2 2996 3414 49504199 49504619 1.410000e-180 643.0
17 TraesCS6D01G272900 chr7D 93.602 422 24 2 2996 3414 477109838 477110259 1.420000e-175 627.0
18 TraesCS6D01G272900 chr7D 83.408 223 33 3 2136 2354 169543885 169543663 2.830000e-48 204.0
19 TraesCS6D01G272900 chr7D 76.071 280 45 13 4434 4703 169542094 169541827 6.300000e-25 126.0
20 TraesCS6D01G272900 chr7A 80.935 278 41 9 2136 2403 172242360 172242085 6.080000e-50 209.0
21 TraesCS6D01G272900 chr7A 76.833 341 55 15 4374 4703 172240675 172240348 2.870000e-38 171.0
22 TraesCS6D01G272900 chr2B 92.437 119 5 1 1901 2015 794682688 794682806 3.710000e-37 167.0
23 TraesCS6D01G272900 chr2B 94.286 35 1 1 2036 2069 794682798 794682832 1.100000e-02 52.8
24 TraesCS6D01G272900 chr3A 75.775 355 46 18 3193 3537 719769922 719770246 6.260000e-30 143.0


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 TraesCS6D01G272900 chr6D 381551149 381557139 5990 True 3818.666667 11064 98.260667 1 5991 3 chr6D.!!$R2 5990
1 TraesCS6D01G272900 chr6A 523125719 523131137 5418 True 2960.000000 8493 96.300667 1 5429 3 chr6A.!!$R2 5428
2 TraesCS6D01G272900 chr6B 570152378 570157982 5604 True 3717.000000 3936 91.694500 1 5805 2 chr6B.!!$R2 5804
3 TraesCS6D01G272900 chr3D 412238123 412238836 713 True 1075.000000 1075 93.767000 1138 1857 1 chr3D.!!$R1 719
4 TraesCS6D01G272900 chr7B 502309177 502309890 713 True 1037.000000 1037 92.798000 1138 1857 1 chr7B.!!$R2 719
5 TraesCS6D01G272900 chr2D 180081070 180081756 686 True 944.000000 944 91.111000 1138 1857 1 chr2D.!!$R1 719

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
252 256 0.034059 AGGCCATCGAATAAGCGGAG 59.966 55.000 5.01 0.00 0.00 4.63 F
598 609 0.178873 ACCACCTACATCACCACCCT 60.179 55.000 0.00 0.00 0.00 4.34 F
1455 1515 2.043752 TGGGGATCGAGCCGTACA 60.044 61.111 14.60 9.93 0.00 2.90 F
1577 1638 2.276732 TTTCTTTCTGGTGCTCCCTG 57.723 50.000 1.59 0.00 0.00 4.45 F
2903 2991 2.093711 GTGTGCCCCAAATTTACCCATC 60.094 50.000 0.00 0.00 0.00 3.51 F
3727 3821 0.381801 GCAATGGCTACAATGGACCG 59.618 55.000 0.00 0.00 36.96 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1296 1354 1.206831 GAAACCTGGAAAGCGCGTC 59.793 57.895 8.43 3.24 0.00 5.19 R
1567 1628 1.467920 CTCCAAATTCAGGGAGCACC 58.532 55.000 7.57 0.00 43.80 5.01 R
2881 2968 0.245266 GGGTAAATTTGGGGCACACG 59.755 55.000 0.00 0.00 0.00 4.49 R
3156 3244 8.076178 ACACAATATGTCAAGCACTTCTTTTAC 58.924 33.333 0.00 0.00 36.54 2.01 R
3826 3920 0.179056 TGCGGGCATAGTAAGGAAGC 60.179 55.000 0.00 0.00 0.00 3.86 R
5648 5786 0.041982 AATGGGGTTTGGGCGGTAAT 59.958 50.000 0.00 0.00 0.00 1.89 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
100 102 3.181471 ACGAGGACCAAGAAGATATGCAG 60.181 47.826 0.00 0.00 0.00 4.41
121 123 0.872388 GTGATCCCGACAAGCGTTTT 59.128 50.000 0.00 0.00 38.67 2.43
129 131 3.352652 CCGACAAGCGTTTTCGTAAAAA 58.647 40.909 12.59 0.00 46.03 1.94
182 184 1.523154 GCACCGAATCCAAGGCAACA 61.523 55.000 0.00 0.00 41.41 3.33
250 254 0.532862 ACAGGCCATCGAATAAGCGG 60.533 55.000 5.01 0.00 0.00 5.52
252 256 0.034059 AGGCCATCGAATAAGCGGAG 59.966 55.000 5.01 0.00 0.00 4.63
355 361 4.518970 TGCCCTCAAATAGACAGTTGTTTC 59.481 41.667 0.00 0.00 31.71 2.78
426 432 6.841443 ATTCAAGAATGATTAGCACTCGAG 57.159 37.500 11.84 11.84 34.96 4.04
428 434 5.578336 TTCAAGAATGATTAGCACTCGAGTG 59.422 40.000 35.80 35.80 41.15 3.51
458 469 4.846779 AAAAGGCTTGATTCAACGCTTA 57.153 36.364 0.00 0.00 0.00 3.09
598 609 0.178873 ACCACCTACATCACCACCCT 60.179 55.000 0.00 0.00 0.00 4.34
871 909 2.921634 TCGATCTGAGACCTTTGTCG 57.078 50.000 0.00 0.00 46.51 4.35
968 1007 4.316823 TGTCGGGGGCTCCTCAGT 62.317 66.667 0.52 0.00 0.00 3.41
1024 1066 3.710722 CTGCAAGGGGAGGCGTCT 61.711 66.667 6.34 0.00 0.00 4.18
1315 1373 2.183858 GACGCGCTTTCCAGGTTTCC 62.184 60.000 5.73 0.00 0.00 3.13
1455 1515 2.043752 TGGGGATCGAGCCGTACA 60.044 61.111 14.60 9.93 0.00 2.90
1567 1628 3.234353 AGCCCCCTTTCTTTTCTTTCTG 58.766 45.455 0.00 0.00 0.00 3.02
1577 1638 2.276732 TTTCTTTCTGGTGCTCCCTG 57.723 50.000 1.59 0.00 0.00 4.45
1741 1802 5.555818 GCGATGTATTTGTTAGTTAGCCGTC 60.556 44.000 0.00 0.00 0.00 4.79
1841 1902 5.362430 GTGGGCAATTGGGTCTATAATTTGA 59.638 40.000 7.72 0.00 0.00 2.69
1858 1919 3.870723 TTGAAAGTTGTTCGATCCACG 57.129 42.857 0.00 0.00 44.09 4.94
1878 1952 8.408743 TCCACGTGGTTATTTTAAAAAGTTTG 57.591 30.769 32.74 1.59 36.34 2.93
1879 1953 8.033626 TCCACGTGGTTATTTTAAAAAGTTTGT 58.966 29.630 32.74 0.00 36.34 2.83
1880 1954 8.111224 CCACGTGGTTATTTTAAAAAGTTTGTG 58.889 33.333 26.95 8.05 0.00 3.33
1881 1955 7.632897 CACGTGGTTATTTTAAAAAGTTTGTGC 59.367 33.333 7.95 0.00 0.00 4.57
1882 1956 7.546316 ACGTGGTTATTTTAAAAAGTTTGTGCT 59.454 29.630 4.44 0.00 0.00 4.40
1883 1957 9.021863 CGTGGTTATTTTAAAAAGTTTGTGCTA 57.978 29.630 4.44 0.00 0.00 3.49
2851 2938 7.523219 CACAACACTTTTACTTGTCACTGTTA 58.477 34.615 0.00 0.00 0.00 2.41
2881 2968 3.855689 ATGCTGTCTTGCAATGTTACC 57.144 42.857 0.00 0.00 46.61 2.85
2903 2991 2.093711 GTGTGCCCCAAATTTACCCATC 60.094 50.000 0.00 0.00 0.00 3.51
3048 3136 7.494625 AGAAGTCTGACAGTTGAATTTTCGTAA 59.505 33.333 10.88 0.00 0.00 3.18
3519 3613 7.864379 TGTACCGTATAGCTAAACTTCATAAGC 59.136 37.037 0.00 0.00 35.16 3.09
3635 3729 6.646653 TCAACAGAAGATGTAAGTGCTTACTG 59.353 38.462 19.06 12.05 43.00 2.74
3650 3744 8.689251 AGTGCTTACTGTTTCTTTTCTTTTTC 57.311 30.769 0.00 0.00 0.00 2.29
3677 3771 7.721842 TGTGAGGGAAAAACATCATGTAACTTA 59.278 33.333 0.00 0.00 0.00 2.24
3678 3772 8.021396 GTGAGGGAAAAACATCATGTAACTTAC 58.979 37.037 0.00 0.00 0.00 2.34
3712 3806 4.098501 GGCAGAGTTAGCAAATAAGGCAAT 59.901 41.667 0.00 0.00 0.00 3.56
3727 3821 0.381801 GCAATGGCTACAATGGACCG 59.618 55.000 0.00 0.00 36.96 4.79
3865 3959 2.027192 CACATAGCCCACAGTTACCAGT 60.027 50.000 0.00 0.00 0.00 4.00
3887 3981 5.484290 AGTTTGTTGGATAGCTAGTACACCT 59.516 40.000 0.00 0.00 0.00 4.00
3925 4019 6.866248 AGTTGAAATTGCTGGGTAAAATAACG 59.134 34.615 0.00 0.00 0.00 3.18
3933 4027 7.733402 TGCTGGGTAAAATAACGTATTATCC 57.267 36.000 0.00 0.00 31.69 2.59
3945 4039 5.075858 ACGTATTATCCGGAAGTTCACAA 57.924 39.130 9.01 0.00 0.00 3.33
3992 4086 5.064198 CGTAATTCGGAATGGAAGCTTGTAA 59.936 40.000 2.10 0.00 35.71 2.41
3997 4091 6.861065 TCGGAATGGAAGCTTGTAAATATC 57.139 37.500 2.10 0.00 0.00 1.63
4108 4202 6.014669 TGTCCAATTTGTTTATTCTGGAAGGG 60.015 38.462 0.00 0.00 0.00 3.95
4125 4219 6.364701 TGGAAGGGTAATCCAGTATGAAATG 58.635 40.000 0.00 0.00 41.98 2.32
4173 4267 4.575885 TCTCAACTGTGTAGGTTTATGCC 58.424 43.478 0.00 0.00 0.00 4.40
4533 4634 2.042831 CCAGGAAGAAGCGCCCAAG 61.043 63.158 2.29 0.00 0.00 3.61
4750 4854 3.207669 GAATCGCCCCAGCAGCAG 61.208 66.667 0.00 0.00 39.83 4.24
4771 4875 2.255554 CAGCAGCAGCAGCAACAG 59.744 61.111 12.92 0.00 45.49 3.16
4772 4876 2.984155 AGCAGCAGCAGCAACAGG 60.984 61.111 12.92 0.00 45.49 4.00
4773 4877 3.292936 GCAGCAGCAGCAACAGGT 61.293 61.111 4.63 0.00 45.49 4.00
4774 4878 2.643272 CAGCAGCAGCAACAGGTG 59.357 61.111 3.17 0.00 45.49 4.00
4804 4908 2.491897 CCTGCAGCACAACAGGCAA 61.492 57.895 8.66 0.00 46.50 4.52
5011 5115 0.671781 CAGACAGCTAAACGCAGGCT 60.672 55.000 0.00 0.00 45.55 4.58
5013 5117 3.972227 CAGCTAAACGCAGGCTGT 58.028 55.556 17.16 0.00 45.59 4.40
5018 5122 1.663161 GCTAAACGCAGGCTGTTGTTC 60.663 52.381 21.70 10.39 38.92 3.18
5241 5345 6.493449 TGTAGATCATGAAATGCGTTTTGA 57.507 33.333 5.17 6.79 46.21 2.69
5275 5379 3.198853 TGGAATTCATCGTGTGGTGGATA 59.801 43.478 7.93 0.00 0.00 2.59
5382 5490 0.623031 TGCTCATGGTCATGGGGGTA 60.623 55.000 12.19 1.10 39.66 3.69
5383 5491 0.109342 GCTCATGGTCATGGGGGTAG 59.891 60.000 12.19 3.28 39.66 3.18
5384 5492 0.767375 CTCATGGTCATGGGGGTAGG 59.233 60.000 10.61 0.00 39.24 3.18
5385 5493 0.697511 TCATGGTCATGGGGGTAGGG 60.698 60.000 10.61 0.00 39.24 3.53
5386 5494 2.084930 ATGGTCATGGGGGTAGGGC 61.085 63.158 0.00 0.00 0.00 5.19
5439 5547 1.338655 GTGTAAAAATGTGGTGGGCGT 59.661 47.619 0.00 0.00 0.00 5.68
5532 5669 4.033894 GCATCGGCGCACTTCTAT 57.966 55.556 10.83 0.00 0.00 1.98
5536 5673 1.037493 ATCGGCGCACTTCTATGGTA 58.963 50.000 10.83 0.00 0.00 3.25
5540 5677 2.202566 GGCGCACTTCTATGGTAGTTC 58.797 52.381 10.83 0.00 0.00 3.01
5557 5694 6.373216 TGGTAGTTCCTTTCCATAATTTCACG 59.627 38.462 0.00 0.00 37.07 4.35
5586 5723 1.259609 TGCCAATGGAAAGAAGCAGG 58.740 50.000 2.05 0.00 0.00 4.85
5629 5767 6.685116 ATCTCTAGGATAAACAGTGAAGCTGC 60.685 42.308 0.00 0.00 39.72 5.25
5648 5786 1.295357 CCATGCACTACGTTTGGCGA 61.295 55.000 0.00 0.00 44.77 5.54
5694 5832 4.020128 ACCTCACTCATTTACTGTCCCTTC 60.020 45.833 0.00 0.00 0.00 3.46
5779 5917 4.278513 CAACCCTTGCCCCGTCCA 62.279 66.667 0.00 0.00 0.00 4.02
5788 5926 3.090219 GCCCCGTCCACGATAAGCT 62.090 63.158 0.00 0.00 43.02 3.74
5789 5927 1.741327 GCCCCGTCCACGATAAGCTA 61.741 60.000 0.00 0.00 43.02 3.32
5790 5928 0.314302 CCCCGTCCACGATAAGCTAG 59.686 60.000 0.00 0.00 43.02 3.42
5791 5929 0.318784 CCCGTCCACGATAAGCTAGC 60.319 60.000 6.62 6.62 43.02 3.42
5794 5932 0.033642 GTCCACGATAAGCTAGCCCC 59.966 60.000 12.13 0.00 0.00 5.80
5795 5933 0.397957 TCCACGATAAGCTAGCCCCA 60.398 55.000 12.13 0.00 0.00 4.96
5797 5935 0.249911 CACGATAAGCTAGCCCCACC 60.250 60.000 12.13 0.00 0.00 4.61
5798 5936 0.689745 ACGATAAGCTAGCCCCACCA 60.690 55.000 12.13 0.00 0.00 4.17
5799 5937 0.034059 CGATAAGCTAGCCCCACCAG 59.966 60.000 12.13 0.00 0.00 4.00
5800 5938 0.250510 GATAAGCTAGCCCCACCAGC 60.251 60.000 12.13 0.00 35.49 4.85
5801 5939 0.988145 ATAAGCTAGCCCCACCAGCA 60.988 55.000 12.13 0.00 37.78 4.41
5802 5940 1.910580 TAAGCTAGCCCCACCAGCAC 61.911 60.000 12.13 0.00 37.78 4.40
5803 5941 3.721706 GCTAGCCCCACCAGCACT 61.722 66.667 2.29 0.00 35.35 4.40
5804 5942 2.270205 CTAGCCCCACCAGCACTG 59.730 66.667 0.00 0.00 0.00 3.66
5817 5955 3.114616 CACTGGCTCGACGGCTTG 61.115 66.667 7.98 4.66 39.32 4.01
5818 5956 3.303135 ACTGGCTCGACGGCTTGA 61.303 61.111 7.98 0.00 39.32 3.02
5819 5957 2.185350 CTGGCTCGACGGCTTGAT 59.815 61.111 7.98 0.00 39.32 2.57
5820 5958 2.125552 TGGCTCGACGGCTTGATG 60.126 61.111 7.98 0.00 39.32 3.07
5821 5959 3.567797 GGCTCGACGGCTTGATGC 61.568 66.667 7.98 0.00 41.94 3.91
5822 5960 3.918220 GCTCGACGGCTTGATGCG 61.918 66.667 0.00 0.00 44.05 4.73
5823 5961 2.202610 CTCGACGGCTTGATGCGA 60.203 61.111 0.00 0.00 44.05 5.10
5824 5962 1.589993 CTCGACGGCTTGATGCGAT 60.590 57.895 0.00 0.00 44.05 4.58
5825 5963 1.815212 CTCGACGGCTTGATGCGATG 61.815 60.000 0.00 0.00 44.05 3.84
5826 5964 2.167219 CGACGGCTTGATGCGATGT 61.167 57.895 0.00 0.00 44.05 3.06
5827 5965 1.638467 GACGGCTTGATGCGATGTC 59.362 57.895 0.00 0.00 44.05 3.06
5828 5966 1.766143 GACGGCTTGATGCGATGTCC 61.766 60.000 0.00 0.00 44.05 4.02
5829 5967 1.815003 CGGCTTGATGCGATGTCCA 60.815 57.895 0.00 0.00 44.05 4.02
5830 5968 1.723870 GGCTTGATGCGATGTCCAC 59.276 57.895 0.00 0.00 44.05 4.02
5831 5969 1.026182 GGCTTGATGCGATGTCCACA 61.026 55.000 0.00 0.00 44.05 4.17
5832 5970 1.019673 GCTTGATGCGATGTCCACAT 58.980 50.000 0.00 0.00 39.70 3.21
5833 5971 1.003116 GCTTGATGCGATGTCCACATC 60.003 52.381 9.33 9.33 46.93 3.06
5841 5979 2.309528 GATGTCCACATCGCTACCAA 57.690 50.000 3.96 0.00 42.66 3.67
5842 5980 2.627945 GATGTCCACATCGCTACCAAA 58.372 47.619 3.96 0.00 42.66 3.28
5843 5981 2.093306 TGTCCACATCGCTACCAAAG 57.907 50.000 0.00 0.00 0.00 2.77
5844 5982 1.621317 TGTCCACATCGCTACCAAAGA 59.379 47.619 0.00 0.00 0.00 2.52
5845 5983 2.000447 GTCCACATCGCTACCAAAGAC 59.000 52.381 0.00 0.00 0.00 3.01
5846 5984 1.621317 TCCACATCGCTACCAAAGACA 59.379 47.619 0.00 0.00 0.00 3.41
5847 5985 2.236146 TCCACATCGCTACCAAAGACAT 59.764 45.455 0.00 0.00 0.00 3.06
5848 5986 3.449377 TCCACATCGCTACCAAAGACATA 59.551 43.478 0.00 0.00 0.00 2.29
5849 5987 4.100963 TCCACATCGCTACCAAAGACATAT 59.899 41.667 0.00 0.00 0.00 1.78
5850 5988 4.212004 CCACATCGCTACCAAAGACATATG 59.788 45.833 0.00 0.00 0.00 1.78
5851 5989 5.049828 CACATCGCTACCAAAGACATATGA 58.950 41.667 10.38 0.00 0.00 2.15
5852 5990 5.050490 ACATCGCTACCAAAGACATATGAC 58.950 41.667 10.38 2.89 0.00 3.06
5853 5991 3.702330 TCGCTACCAAAGACATATGACG 58.298 45.455 10.38 0.00 0.00 4.35
5854 5992 3.129813 TCGCTACCAAAGACATATGACGT 59.870 43.478 10.38 0.00 0.00 4.34
5855 5993 3.242944 CGCTACCAAAGACATATGACGTG 59.757 47.826 10.38 7.25 0.00 4.49
5856 5994 4.181578 GCTACCAAAGACATATGACGTGT 58.818 43.478 10.38 3.85 0.00 4.49
5857 5995 4.630069 GCTACCAAAGACATATGACGTGTT 59.370 41.667 10.38 0.00 0.00 3.32
5858 5996 5.121768 GCTACCAAAGACATATGACGTGTTT 59.878 40.000 10.38 0.00 30.65 2.83
5859 5997 5.356882 ACCAAAGACATATGACGTGTTTG 57.643 39.130 10.38 9.95 43.52 2.93
5861 5999 5.356882 CAAAGACATATGACGTGTTTGGT 57.643 39.130 10.38 0.00 41.46 3.67
5862 6000 6.474819 CAAAGACATATGACGTGTTTGGTA 57.525 37.500 10.38 0.00 41.46 3.25
5863 6001 6.534059 CAAAGACATATGACGTGTTTGGTAG 58.466 40.000 10.38 0.00 41.46 3.18
5864 6002 4.755411 AGACATATGACGTGTTTGGTAGG 58.245 43.478 10.38 0.00 0.00 3.18
5865 6003 3.267483 ACATATGACGTGTTTGGTAGGC 58.733 45.455 10.38 0.00 0.00 3.93
5866 6004 3.055385 ACATATGACGTGTTTGGTAGGCT 60.055 43.478 10.38 0.00 0.00 4.58
5867 6005 1.808411 ATGACGTGTTTGGTAGGCTG 58.192 50.000 0.00 0.00 0.00 4.85
5868 6006 0.882927 TGACGTGTTTGGTAGGCTGC 60.883 55.000 0.00 0.00 0.00 5.25
5869 6007 0.882927 GACGTGTTTGGTAGGCTGCA 60.883 55.000 4.64 0.00 0.00 4.41
5870 6008 0.250727 ACGTGTTTGGTAGGCTGCAT 60.251 50.000 4.64 0.00 0.00 3.96
5871 6009 0.447801 CGTGTTTGGTAGGCTGCATC 59.552 55.000 4.64 0.00 0.00 3.91
5872 6010 0.811281 GTGTTTGGTAGGCTGCATCC 59.189 55.000 4.64 0.00 0.00 3.51
5873 6011 0.676466 TGTTTGGTAGGCTGCATCCG 60.676 55.000 4.64 0.00 0.00 4.18
5874 6012 0.676782 GTTTGGTAGGCTGCATCCGT 60.677 55.000 4.64 0.00 0.00 4.69
5875 6013 0.392461 TTTGGTAGGCTGCATCCGTC 60.392 55.000 4.64 0.00 0.00 4.79
5876 6014 2.109181 GGTAGGCTGCATCCGTCC 59.891 66.667 4.64 4.25 0.00 4.79
5877 6015 2.109181 GTAGGCTGCATCCGTCCC 59.891 66.667 0.50 0.00 0.00 4.46
5878 6016 2.364973 TAGGCTGCATCCGTCCCA 60.365 61.111 0.50 0.00 0.00 4.37
5879 6017 1.992834 TAGGCTGCATCCGTCCCAA 60.993 57.895 0.50 0.00 0.00 4.12
5880 6018 2.252072 TAGGCTGCATCCGTCCCAAC 62.252 60.000 0.50 0.00 0.00 3.77
5881 6019 3.134127 GCTGCATCCGTCCCAACC 61.134 66.667 0.00 0.00 0.00 3.77
5882 6020 2.350895 CTGCATCCGTCCCAACCA 59.649 61.111 0.00 0.00 0.00 3.67
5883 6021 1.303236 CTGCATCCGTCCCAACCAA 60.303 57.895 0.00 0.00 0.00 3.67
5884 6022 1.303236 TGCATCCGTCCCAACCAAG 60.303 57.895 0.00 0.00 0.00 3.61
5885 6023 2.700773 GCATCCGTCCCAACCAAGC 61.701 63.158 0.00 0.00 0.00 4.01
5886 6024 2.046285 CATCCGTCCCAACCAAGCC 61.046 63.158 0.00 0.00 0.00 4.35
5887 6025 2.534396 ATCCGTCCCAACCAAGCCA 61.534 57.895 0.00 0.00 0.00 4.75
5888 6026 1.863155 ATCCGTCCCAACCAAGCCAT 61.863 55.000 0.00 0.00 0.00 4.40
5889 6027 2.342650 CCGTCCCAACCAAGCCATG 61.343 63.158 0.00 0.00 0.00 3.66
5890 6028 1.603455 CGTCCCAACCAAGCCATGT 60.603 57.895 0.00 0.00 0.00 3.21
5891 6029 1.586154 CGTCCCAACCAAGCCATGTC 61.586 60.000 0.00 0.00 0.00 3.06
5892 6030 1.303236 TCCCAACCAAGCCATGTCG 60.303 57.895 0.00 0.00 0.00 4.35
5893 6031 1.303236 CCCAACCAAGCCATGTCGA 60.303 57.895 0.00 0.00 0.00 4.20
5894 6032 0.680921 CCCAACCAAGCCATGTCGAT 60.681 55.000 0.00 0.00 0.00 3.59
5895 6033 0.452987 CCAACCAAGCCATGTCGATG 59.547 55.000 0.00 0.00 0.00 3.84
5896 6034 0.179156 CAACCAAGCCATGTCGATGC 60.179 55.000 0.00 0.00 0.00 3.91
5897 6035 0.608856 AACCAAGCCATGTCGATGCA 60.609 50.000 0.00 0.00 0.00 3.96
5898 6036 0.608856 ACCAAGCCATGTCGATGCAA 60.609 50.000 0.00 0.00 0.00 4.08
5899 6037 0.527113 CCAAGCCATGTCGATGCAAA 59.473 50.000 0.00 0.00 0.00 3.68
5900 6038 1.621107 CAAGCCATGTCGATGCAAAC 58.379 50.000 0.00 0.00 0.00 2.93
5901 6039 1.200716 CAAGCCATGTCGATGCAAACT 59.799 47.619 0.00 0.00 0.00 2.66
5902 6040 1.538047 AGCCATGTCGATGCAAACTT 58.462 45.000 0.00 0.00 0.00 2.66
5903 6041 1.200716 AGCCATGTCGATGCAAACTTG 59.799 47.619 0.00 0.00 0.00 3.16
5916 6054 1.868498 CAAACTTGCATGCTTGGTTGG 59.132 47.619 23.86 16.98 0.00 3.77
5917 6055 0.249996 AACTTGCATGCTTGGTTGGC 60.250 50.000 20.33 0.00 0.00 4.52
5918 6056 1.117142 ACTTGCATGCTTGGTTGGCT 61.117 50.000 20.33 0.00 0.00 4.75
5919 6057 0.669318 CTTGCATGCTTGGTTGGCTG 60.669 55.000 20.33 0.00 0.00 4.85
5920 6058 2.102109 TTGCATGCTTGGTTGGCTGG 62.102 55.000 20.33 0.00 0.00 4.85
5921 6059 2.975536 CATGCTTGGTTGGCTGGG 59.024 61.111 0.00 0.00 0.00 4.45
5922 6060 2.999063 ATGCTTGGTTGGCTGGGC 60.999 61.111 0.00 0.00 0.00 5.36
5923 6061 3.534704 ATGCTTGGTTGGCTGGGCT 62.535 57.895 0.00 0.00 0.00 5.19
5924 6062 3.688159 GCTTGGTTGGCTGGGCTG 61.688 66.667 0.00 0.00 0.00 4.85
5925 6063 3.688159 CTTGGTTGGCTGGGCTGC 61.688 66.667 0.00 0.00 0.00 5.25
5926 6064 4.536526 TTGGTTGGCTGGGCTGCA 62.537 61.111 0.50 0.00 34.04 4.41
5929 6067 4.982701 GTTGGCTGGGCTGCACCT 62.983 66.667 0.00 0.00 39.10 4.00
5930 6068 4.980702 TTGGCTGGGCTGCACCTG 62.981 66.667 0.00 4.64 39.10 4.00
5932 6070 4.437587 GGCTGGGCTGCACCTGAT 62.438 66.667 14.86 0.00 39.10 2.90
5933 6071 2.362120 GCTGGGCTGCACCTGATT 60.362 61.111 14.86 0.00 39.10 2.57
5934 6072 2.413142 GCTGGGCTGCACCTGATTC 61.413 63.158 14.86 0.00 39.10 2.52
5935 6073 2.046023 TGGGCTGCACCTGATTCG 60.046 61.111 0.00 0.00 39.10 3.34
5936 6074 2.045926 GGGCTGCACCTGATTCGT 60.046 61.111 0.50 0.00 39.10 3.85
5937 6075 2.401766 GGGCTGCACCTGATTCGTG 61.402 63.158 0.50 0.00 39.10 4.35
5938 6076 2.401766 GGCTGCACCTGATTCGTGG 61.402 63.158 0.50 0.00 34.51 4.94
5939 6077 1.375908 GCTGCACCTGATTCGTGGA 60.376 57.895 0.00 0.00 0.00 4.02
5940 6078 1.639298 GCTGCACCTGATTCGTGGAC 61.639 60.000 0.00 0.00 0.00 4.02
5941 6079 1.003839 TGCACCTGATTCGTGGACC 60.004 57.895 3.02 0.00 0.00 4.46
5942 6080 2.100631 GCACCTGATTCGTGGACCG 61.101 63.158 3.02 0.00 38.13 4.79
5943 6081 2.100631 CACCTGATTCGTGGACCGC 61.101 63.158 0.00 0.00 36.19 5.68
5944 6082 2.264480 CCTGATTCGTGGACCGCA 59.736 61.111 5.75 0.00 36.19 5.69
5945 6083 1.811266 CCTGATTCGTGGACCGCAG 60.811 63.158 5.75 0.00 36.19 5.18
5946 6084 1.215382 CTGATTCGTGGACCGCAGA 59.785 57.895 5.75 0.71 36.19 4.26
5947 6085 0.389817 CTGATTCGTGGACCGCAGAA 60.390 55.000 5.75 9.87 36.19 3.02
5948 6086 0.669318 TGATTCGTGGACCGCAGAAC 60.669 55.000 5.75 5.82 36.19 3.01
5949 6087 1.359459 GATTCGTGGACCGCAGAACC 61.359 60.000 5.75 0.00 36.19 3.62
5950 6088 3.851845 TTCGTGGACCGCAGAACCG 62.852 63.158 5.75 0.00 36.19 4.44
5952 6090 4.980805 GTGGACCGCAGAACCGCA 62.981 66.667 0.00 0.00 34.76 5.69
5953 6091 4.243008 TGGACCGCAGAACCGCAA 62.243 61.111 0.00 0.00 0.00 4.85
5954 6092 2.975799 GGACCGCAGAACCGCAAA 60.976 61.111 0.00 0.00 0.00 3.68
5955 6093 2.556287 GACCGCAGAACCGCAAAG 59.444 61.111 0.00 0.00 0.00 2.77
5956 6094 3.595108 GACCGCAGAACCGCAAAGC 62.595 63.158 0.00 0.00 0.00 3.51
5957 6095 3.659092 CCGCAGAACCGCAAAGCA 61.659 61.111 0.00 0.00 0.00 3.91
5958 6096 2.427410 CGCAGAACCGCAAAGCAC 60.427 61.111 0.00 0.00 0.00 4.40
5959 6097 2.896801 CGCAGAACCGCAAAGCACT 61.897 57.895 0.00 0.00 0.00 4.40
5960 6098 1.360192 GCAGAACCGCAAAGCACTT 59.640 52.632 0.00 0.00 0.00 3.16
5961 6099 0.661483 GCAGAACCGCAAAGCACTTC 60.661 55.000 0.00 0.00 0.00 3.01
5962 6100 0.947244 CAGAACCGCAAAGCACTTCT 59.053 50.000 0.00 0.00 0.00 2.85
5963 6101 0.947244 AGAACCGCAAAGCACTTCTG 59.053 50.000 0.00 0.00 0.00 3.02
5964 6102 0.040067 GAACCGCAAAGCACTTCTGG 60.040 55.000 0.00 0.00 0.00 3.86
5965 6103 1.455383 AACCGCAAAGCACTTCTGGG 61.455 55.000 0.00 3.10 0.00 4.45
5966 6104 2.256461 CGCAAAGCACTTCTGGGC 59.744 61.111 0.00 0.00 0.00 5.36
5967 6105 2.653115 GCAAAGCACTTCTGGGCC 59.347 61.111 0.00 0.00 0.00 5.80
5968 6106 1.905354 GCAAAGCACTTCTGGGCCT 60.905 57.895 4.53 0.00 0.00 5.19
5969 6107 1.962144 CAAAGCACTTCTGGGCCTG 59.038 57.895 4.53 4.06 0.00 4.85
5970 6108 1.228675 AAAGCACTTCTGGGCCTGG 60.229 57.895 10.79 0.45 0.00 4.45
5971 6109 3.875510 AAGCACTTCTGGGCCTGGC 62.876 63.158 11.05 11.05 0.00 4.85
5972 6110 4.357279 GCACTTCTGGGCCTGGCT 62.357 66.667 19.68 0.00 0.00 4.75
5973 6111 2.360852 CACTTCTGGGCCTGGCTG 60.361 66.667 19.68 9.40 0.00 4.85
5974 6112 2.530151 ACTTCTGGGCCTGGCTGA 60.530 61.111 19.68 11.61 0.00 4.26
5975 6113 2.271497 CTTCTGGGCCTGGCTGAG 59.729 66.667 19.68 14.20 0.00 3.35
5976 6114 3.333219 TTCTGGGCCTGGCTGAGG 61.333 66.667 19.68 6.87 46.13 3.86
5982 6120 4.432741 GCCTGGCTGAGGGGGAAC 62.433 72.222 12.43 0.00 43.07 3.62
5983 6121 2.612115 CCTGGCTGAGGGGGAACT 60.612 66.667 0.00 0.00 38.36 3.01
5984 6122 2.673523 CTGGCTGAGGGGGAACTG 59.326 66.667 0.00 0.00 0.00 3.16
5985 6123 2.121963 TGGCTGAGGGGGAACTGT 60.122 61.111 0.00 0.00 0.00 3.55
5986 6124 2.190488 CTGGCTGAGGGGGAACTGTC 62.190 65.000 0.00 0.00 0.00 3.51
5987 6125 2.266055 GCTGAGGGGGAACTGTCG 59.734 66.667 0.00 0.00 0.00 4.35
5988 6126 2.283529 GCTGAGGGGGAACTGTCGA 61.284 63.158 0.00 0.00 0.00 4.20
5989 6127 1.827399 GCTGAGGGGGAACTGTCGAA 61.827 60.000 0.00 0.00 0.00 3.71
5990 6128 0.905357 CTGAGGGGGAACTGTCGAAT 59.095 55.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.722700 AGCATGTGACGCCCACCC 62.723 66.667 6.15 0.00 45.09 4.61
71 72 3.005472 TCTTCTTGGTCCTCGTGTTGTAG 59.995 47.826 0.00 0.00 0.00 2.74
73 74 1.760613 TCTTCTTGGTCCTCGTGTTGT 59.239 47.619 0.00 0.00 0.00 3.32
100 102 3.554692 CGCTTGTCGGGATCACGC 61.555 66.667 13.88 8.73 33.78 5.34
129 131 3.769300 GGATGTATTTTGGAGGGCAACTT 59.231 43.478 0.00 0.00 0.00 2.66
130 132 3.245586 TGGATGTATTTTGGAGGGCAACT 60.246 43.478 0.00 0.00 0.00 3.16
131 133 3.096092 TGGATGTATTTTGGAGGGCAAC 58.904 45.455 0.00 0.00 0.00 4.17
132 134 3.464720 TGGATGTATTTTGGAGGGCAA 57.535 42.857 0.00 0.00 0.00 4.52
133 135 3.364549 CTTGGATGTATTTTGGAGGGCA 58.635 45.455 0.00 0.00 0.00 5.36
134 136 2.695147 CCTTGGATGTATTTTGGAGGGC 59.305 50.000 0.00 0.00 0.00 5.19
136 138 2.695147 GGCCTTGGATGTATTTTGGAGG 59.305 50.000 0.00 0.00 0.00 4.30
138 140 3.627237 GGAGGCCTTGGATGTATTTTGGA 60.627 47.826 6.77 0.00 0.00 3.53
139 141 2.695147 GGAGGCCTTGGATGTATTTTGG 59.305 50.000 6.77 0.00 0.00 3.28
140 142 3.635591 AGGAGGCCTTGGATGTATTTTG 58.364 45.455 6.77 0.00 0.00 2.44
141 143 4.689983 GCTAGGAGGCCTTGGATGTATTTT 60.690 45.833 6.77 0.00 34.61 1.82
142 144 3.181439 GCTAGGAGGCCTTGGATGTATTT 60.181 47.826 6.77 0.00 34.61 1.40
143 145 2.373502 GCTAGGAGGCCTTGGATGTATT 59.626 50.000 6.77 0.00 34.61 1.89
147 149 0.179034 GTGCTAGGAGGCCTTGGATG 60.179 60.000 6.77 0.00 34.61 3.51
215 218 6.271488 TGGCCTGTATCTTCAAAAATCTTG 57.729 37.500 3.32 0.00 0.00 3.02
234 238 0.033504 TCTCCGCTTATTCGATGGCC 59.966 55.000 0.00 0.00 0.00 5.36
275 279 6.986424 TGCATTGTATCTTAAGTCGTATCG 57.014 37.500 1.63 0.00 0.00 2.92
360 366 6.382869 CCAACTCTCTATTGGGCATTTTAG 57.617 41.667 0.00 0.00 42.57 1.85
438 449 4.846779 TTAAGCGTTGAATCAAGCCTTT 57.153 36.364 11.57 5.70 0.00 3.11
439 450 6.699575 ATATTAAGCGTTGAATCAAGCCTT 57.300 33.333 11.73 11.47 0.00 4.35
440 451 6.511767 CGAATATTAAGCGTTGAATCAAGCCT 60.512 38.462 11.73 2.63 0.00 4.58
454 465 6.401153 CGCTAAATCTCCACCGAATATTAAGC 60.401 42.308 0.00 0.00 0.00 3.09
458 469 5.209818 TCGCTAAATCTCCACCGAATATT 57.790 39.130 0.00 0.00 0.00 1.28
598 609 2.355837 GGCGTTCACGTGCAGAGA 60.356 61.111 11.67 0.00 42.22 3.10
670 696 1.735571 GCTCTACGGAATTTTTCGGCA 59.264 47.619 0.00 0.00 33.74 5.69
731 768 4.410743 GTTTCGCCTGGCTGCTGC 62.411 66.667 17.92 7.10 38.76 5.25
732 769 2.974489 CTGTTTCGCCTGGCTGCTG 61.974 63.158 17.92 0.47 0.00 4.41
864 902 0.243636 GCCATTTGGGGACGACAAAG 59.756 55.000 0.00 0.00 40.70 2.77
871 909 4.759205 AGGCGGCCATTTGGGGAC 62.759 66.667 23.09 0.00 37.04 4.46
1274 1320 4.521062 CGCAGGCGAAGAGAGGGG 62.521 72.222 8.15 0.00 42.83 4.79
1295 1353 2.494504 GAAACCTGGAAAGCGCGTCG 62.495 60.000 8.43 0.00 0.00 5.12
1296 1354 1.206831 GAAACCTGGAAAGCGCGTC 59.793 57.895 8.43 3.24 0.00 5.19
1297 1355 2.258726 GGAAACCTGGAAAGCGCGT 61.259 57.895 8.43 0.00 0.00 6.01
1298 1356 1.966451 AGGAAACCTGGAAAGCGCG 60.966 57.895 0.00 0.00 29.57 6.86
1299 1357 4.081050 AGGAAACCTGGAAAGCGC 57.919 55.556 0.00 0.00 29.57 5.92
1315 1373 2.489938 TGAGGAAAACCCCGATTCAG 57.510 50.000 0.00 0.00 34.66 3.02
1567 1628 1.467920 CTCCAAATTCAGGGAGCACC 58.532 55.000 7.57 0.00 43.80 5.01
1577 1638 7.501844 AGGCACTAACTAGATACTCCAAATTC 58.498 38.462 0.00 0.00 36.02 2.17
1741 1802 2.376956 TGAAAAACGTCGCAATTTCGG 58.623 42.857 0.00 0.00 35.15 4.30
1841 1902 1.871039 CCACGTGGATCGAACAACTTT 59.129 47.619 31.31 0.00 42.86 2.66
2214 2300 4.402616 TCCCTTTGGATGGTTCATCTTT 57.597 40.909 7.68 0.00 40.39 2.52
2637 2724 2.432146 TCTCACAGTTGTGCTCTTCTGT 59.568 45.455 7.38 9.38 45.25 3.41
2728 2815 9.322776 CGTTTAATGATTCTTATATGCAGCTTC 57.677 33.333 0.00 0.00 0.00 3.86
2753 2840 4.991687 AGTTAGAAAAGCAGAGAGGTTTCG 59.008 41.667 0.00 0.00 46.52 3.46
2881 2968 0.245266 GGGTAAATTTGGGGCACACG 59.755 55.000 0.00 0.00 0.00 4.49
2903 2991 8.253810 TGTCAGACTTCTCATTAAGTTAGATGG 58.746 37.037 1.31 0.00 39.78 3.51
3066 3154 8.974060 AAGTAACTCAGTTAATTTGAAGGTCA 57.026 30.769 4.39 0.00 33.49 4.02
3156 3244 8.076178 ACACAATATGTCAAGCACTTCTTTTAC 58.924 33.333 0.00 0.00 36.54 2.01
3519 3613 9.240303 AGCAGTGCTACTCCTGTAAAGATACAG 62.240 44.444 18.11 8.65 46.45 2.74
3635 3729 6.863275 TCCCTCACAGAAAAAGAAAAGAAAC 58.137 36.000 0.00 0.00 0.00 2.78
3650 3744 6.207417 AGTTACATGATGTTTTTCCCTCACAG 59.793 38.462 2.29 0.00 0.00 3.66
3712 3806 1.298340 CCACGGTCCATTGTAGCCA 59.702 57.895 0.00 0.00 0.00 4.75
3727 3821 4.426313 GGGGTACAGCAGGCCCAC 62.426 72.222 0.00 0.00 44.07 4.61
3751 3845 3.354467 TGGCAACATATTCATGTGCTGA 58.646 40.909 2.72 0.00 44.83 4.26
3826 3920 0.179056 TGCGGGCATAGTAAGGAAGC 60.179 55.000 0.00 0.00 0.00 3.86
3865 3959 5.247564 ACAGGTGTACTAGCTATCCAACAAA 59.752 40.000 0.00 0.00 34.81 2.83
3887 3981 6.430925 AGCAATTTCAACTAGAATGCTGTACA 59.569 34.615 0.00 0.00 45.87 2.90
3925 4019 5.527582 AGCATTGTGAACTTCCGGATAATAC 59.472 40.000 4.15 2.04 0.00 1.89
3933 4027 2.699954 AGGTAGCATTGTGAACTTCCG 58.300 47.619 0.00 0.00 0.00 4.30
3957 4051 4.789012 TCCGAATTACGTTAACTGGTCT 57.211 40.909 3.71 0.00 40.78 3.85
3997 4091 7.985184 TGGGCAATTCTAATAGTGTAAGTGTAG 59.015 37.037 0.00 0.00 0.00 2.74
4013 4107 6.183360 GCTTCTGATTAAGATTGGGCAATTCT 60.183 38.462 0.00 0.00 33.93 2.40
4153 4247 4.359434 TGGCATAAACCTACACAGTTGA 57.641 40.909 0.00 0.00 0.00 3.18
4206 4300 8.457261 ACTGCACAAAAAGAAAATGCAAATAAA 58.543 25.926 0.00 0.00 45.08 1.40
4456 4557 0.755686 CTCCTCCGATTAGCTTGCCT 59.244 55.000 0.00 0.00 0.00 4.75
4533 4634 1.369091 CTGCTGGTAATGGTGGACGC 61.369 60.000 0.00 0.00 0.00 5.19
4804 4908 4.815973 TGCGGCCCCAGGGAGTAT 62.816 66.667 7.25 0.00 37.50 2.12
5011 5115 3.662759 ACTGGGAAAGGAAGAACAACA 57.337 42.857 0.00 0.00 0.00 3.33
5012 5116 4.885325 TGTAACTGGGAAAGGAAGAACAAC 59.115 41.667 0.00 0.00 0.00 3.32
5013 5117 5.118729 TGTAACTGGGAAAGGAAGAACAA 57.881 39.130 0.00 0.00 0.00 2.83
5018 5122 4.034285 ACCATGTAACTGGGAAAGGAAG 57.966 45.455 0.00 0.00 40.85 3.46
5225 5329 5.164031 CCAACAGATCAAAACGCATTTCATG 60.164 40.000 0.00 0.00 0.00 3.07
5226 5330 4.925054 CCAACAGATCAAAACGCATTTCAT 59.075 37.500 0.00 0.00 0.00 2.57
5227 5331 4.202101 ACCAACAGATCAAAACGCATTTCA 60.202 37.500 0.00 0.00 0.00 2.69
5234 5338 2.226437 CCAGGACCAACAGATCAAAACG 59.774 50.000 0.00 0.00 0.00 3.60
5241 5345 4.530875 GATGAATTCCAGGACCAACAGAT 58.469 43.478 2.27 0.00 0.00 2.90
5439 5547 1.229975 CGTGGCAGCATGTGACTGAA 61.230 55.000 3.29 0.00 39.31 3.02
5496 5633 0.673644 CGTACTGCCTTGTCCCCTTG 60.674 60.000 0.00 0.00 0.00 3.61
5498 5635 2.955881 GCGTACTGCCTTGTCCCCT 61.956 63.158 0.00 0.00 37.76 4.79
5532 5669 6.373216 CGTGAAATTATGGAAAGGAACTACCA 59.627 38.462 0.00 0.00 45.58 3.25
5540 5677 3.126171 TCGTGCGTGAAATTATGGAAAGG 59.874 43.478 0.00 0.00 0.00 3.11
5557 5694 2.404789 CATTGGCATCGGTCGTGC 59.595 61.111 0.00 8.58 41.78 5.34
5629 5767 1.134487 CGCCAAACGTAGTGCATGG 59.866 57.895 0.00 0.00 45.00 3.66
5648 5786 0.041982 AATGGGGTTTGGGCGGTAAT 59.958 50.000 0.00 0.00 0.00 1.89
5716 5854 1.202817 TCAGTGCAACCGAAGCGTATA 59.797 47.619 0.00 0.00 37.80 1.47
5726 5864 1.001641 AGAGGCCATCAGTGCAACC 60.002 57.895 5.01 0.00 37.80 3.77
5779 5917 0.689745 TGGTGGGGCTAGCTTATCGT 60.690 55.000 15.72 0.00 0.00 3.73
5788 5926 3.329889 CCAGTGCTGGTGGGGCTA 61.330 66.667 9.96 0.00 45.53 3.93
5800 5938 2.842394 ATCAAGCCGTCGAGCCAGTG 62.842 60.000 0.00 0.00 0.00 3.66
5801 5939 2.650116 ATCAAGCCGTCGAGCCAGT 61.650 57.895 0.00 0.00 0.00 4.00
5802 5940 2.169789 CATCAAGCCGTCGAGCCAG 61.170 63.158 0.00 0.00 0.00 4.85
5803 5941 2.125552 CATCAAGCCGTCGAGCCA 60.126 61.111 0.00 0.00 0.00 4.75
5804 5942 3.567797 GCATCAAGCCGTCGAGCC 61.568 66.667 0.00 0.00 37.23 4.70
5805 5943 3.918220 CGCATCAAGCCGTCGAGC 61.918 66.667 0.00 0.00 41.38 5.03
5806 5944 1.589993 ATCGCATCAAGCCGTCGAG 60.590 57.895 0.00 0.00 41.38 4.04
5807 5945 1.878069 CATCGCATCAAGCCGTCGA 60.878 57.895 0.00 0.00 41.38 4.20
5808 5946 2.082437 GACATCGCATCAAGCCGTCG 62.082 60.000 0.00 0.00 41.38 5.12
5809 5947 1.638467 GACATCGCATCAAGCCGTC 59.362 57.895 0.00 0.00 41.38 4.79
5810 5948 1.815421 GGACATCGCATCAAGCCGT 60.815 57.895 0.00 0.00 41.38 5.68
5811 5949 1.815003 TGGACATCGCATCAAGCCG 60.815 57.895 0.00 0.00 41.38 5.52
5812 5950 1.026182 TGTGGACATCGCATCAAGCC 61.026 55.000 0.00 0.00 41.38 4.35
5813 5951 1.019673 ATGTGGACATCGCATCAAGC 58.980 50.000 0.00 0.00 42.41 4.01
5822 5960 2.309528 TTGGTAGCGATGTGGACATC 57.690 50.000 9.37 9.37 46.93 3.06
5823 5961 2.236146 TCTTTGGTAGCGATGTGGACAT 59.764 45.455 0.00 0.00 39.70 3.06
5824 5962 1.621317 TCTTTGGTAGCGATGTGGACA 59.379 47.619 0.00 0.00 0.00 4.02
5825 5963 2.000447 GTCTTTGGTAGCGATGTGGAC 59.000 52.381 0.00 0.00 0.00 4.02
5826 5964 1.621317 TGTCTTTGGTAGCGATGTGGA 59.379 47.619 0.00 0.00 0.00 4.02
5827 5965 2.093306 TGTCTTTGGTAGCGATGTGG 57.907 50.000 0.00 0.00 0.00 4.17
5828 5966 5.049828 TCATATGTCTTTGGTAGCGATGTG 58.950 41.667 1.90 0.00 0.00 3.21
5829 5967 5.050490 GTCATATGTCTTTGGTAGCGATGT 58.950 41.667 1.90 0.00 0.00 3.06
5830 5968 4.148871 CGTCATATGTCTTTGGTAGCGATG 59.851 45.833 1.90 0.00 0.00 3.84
5831 5969 4.202121 ACGTCATATGTCTTTGGTAGCGAT 60.202 41.667 1.90 0.00 0.00 4.58
5832 5970 3.129813 ACGTCATATGTCTTTGGTAGCGA 59.870 43.478 1.90 0.00 0.00 4.93
5833 5971 3.242944 CACGTCATATGTCTTTGGTAGCG 59.757 47.826 1.90 0.00 0.00 4.26
5834 5972 4.181578 ACACGTCATATGTCTTTGGTAGC 58.818 43.478 1.90 0.00 0.00 3.58
5835 5973 6.402118 CCAAACACGTCATATGTCTTTGGTAG 60.402 42.308 16.87 0.00 34.96 3.18
5836 5974 5.410132 CCAAACACGTCATATGTCTTTGGTA 59.590 40.000 16.87 0.00 34.96 3.25
5837 5975 4.215399 CCAAACACGTCATATGTCTTTGGT 59.785 41.667 16.87 4.48 34.96 3.67
5838 5976 4.215399 ACCAAACACGTCATATGTCTTTGG 59.785 41.667 20.49 20.49 41.06 3.28
5839 5977 5.356882 ACCAAACACGTCATATGTCTTTG 57.643 39.130 1.90 4.74 0.00 2.77
5840 5978 5.642063 CCTACCAAACACGTCATATGTCTTT 59.358 40.000 1.90 0.00 0.00 2.52
5841 5979 5.175859 CCTACCAAACACGTCATATGTCTT 58.824 41.667 1.90 0.00 0.00 3.01
5842 5980 4.755411 CCTACCAAACACGTCATATGTCT 58.245 43.478 1.90 0.00 0.00 3.41
5843 5981 3.308866 GCCTACCAAACACGTCATATGTC 59.691 47.826 1.90 0.00 0.00 3.06
5844 5982 3.055385 AGCCTACCAAACACGTCATATGT 60.055 43.478 1.90 0.00 0.00 2.29
5845 5983 3.309682 CAGCCTACCAAACACGTCATATG 59.690 47.826 0.00 0.00 0.00 1.78
5846 5984 3.531538 CAGCCTACCAAACACGTCATAT 58.468 45.455 0.00 0.00 0.00 1.78
5847 5985 2.933492 GCAGCCTACCAAACACGTCATA 60.933 50.000 0.00 0.00 0.00 2.15
5848 5986 1.808411 CAGCCTACCAAACACGTCAT 58.192 50.000 0.00 0.00 0.00 3.06
5849 5987 0.882927 GCAGCCTACCAAACACGTCA 60.883 55.000 0.00 0.00 0.00 4.35
5850 5988 0.882927 TGCAGCCTACCAAACACGTC 60.883 55.000 0.00 0.00 0.00 4.34
5851 5989 0.250727 ATGCAGCCTACCAAACACGT 60.251 50.000 0.00 0.00 0.00 4.49
5852 5990 0.447801 GATGCAGCCTACCAAACACG 59.552 55.000 0.00 0.00 0.00 4.49
5853 5991 0.811281 GGATGCAGCCTACCAAACAC 59.189 55.000 15.35 0.00 0.00 3.32
5854 5992 0.676466 CGGATGCAGCCTACCAAACA 60.676 55.000 20.58 0.00 0.00 2.83
5855 5993 0.676782 ACGGATGCAGCCTACCAAAC 60.677 55.000 20.58 0.00 0.00 2.93
5856 5994 0.392461 GACGGATGCAGCCTACCAAA 60.392 55.000 20.58 0.00 0.00 3.28
5857 5995 1.220749 GACGGATGCAGCCTACCAA 59.779 57.895 20.58 0.00 0.00 3.67
5858 5996 2.731571 GGACGGATGCAGCCTACCA 61.732 63.158 20.58 0.00 0.00 3.25
5859 5997 2.109181 GGACGGATGCAGCCTACC 59.891 66.667 20.58 17.59 0.00 3.18
5860 5998 2.109181 GGGACGGATGCAGCCTAC 59.891 66.667 20.58 12.35 0.00 3.18
5861 5999 1.992834 TTGGGACGGATGCAGCCTA 60.993 57.895 20.58 0.00 0.00 3.93
5862 6000 3.329889 TTGGGACGGATGCAGCCT 61.330 61.111 20.58 6.00 0.00 4.58
5863 6001 3.134127 GTTGGGACGGATGCAGCC 61.134 66.667 12.07 12.07 0.00 4.85
5864 6002 3.134127 GGTTGGGACGGATGCAGC 61.134 66.667 0.00 0.00 0.00 5.25
5865 6003 1.303236 TTGGTTGGGACGGATGCAG 60.303 57.895 0.00 0.00 0.00 4.41
5866 6004 1.303236 CTTGGTTGGGACGGATGCA 60.303 57.895 0.00 0.00 0.00 3.96
5867 6005 2.700773 GCTTGGTTGGGACGGATGC 61.701 63.158 0.00 0.00 0.00 3.91
5868 6006 2.046285 GGCTTGGTTGGGACGGATG 61.046 63.158 0.00 0.00 0.00 3.51
5869 6007 1.863155 ATGGCTTGGTTGGGACGGAT 61.863 55.000 0.00 0.00 0.00 4.18
5870 6008 2.534396 ATGGCTTGGTTGGGACGGA 61.534 57.895 0.00 0.00 0.00 4.69
5871 6009 2.035626 ATGGCTTGGTTGGGACGG 59.964 61.111 0.00 0.00 0.00 4.79
5872 6010 1.586154 GACATGGCTTGGTTGGGACG 61.586 60.000 5.31 0.00 0.00 4.79
5873 6011 1.586154 CGACATGGCTTGGTTGGGAC 61.586 60.000 0.00 0.00 0.00 4.46
5874 6012 1.303236 CGACATGGCTTGGTTGGGA 60.303 57.895 0.00 0.00 0.00 4.37
5875 6013 0.680921 ATCGACATGGCTTGGTTGGG 60.681 55.000 0.00 0.00 0.00 4.12
5876 6014 0.452987 CATCGACATGGCTTGGTTGG 59.547 55.000 0.00 0.00 0.00 3.77
5877 6015 0.179156 GCATCGACATGGCTTGGTTG 60.179 55.000 0.00 0.00 0.00 3.77
5878 6016 0.608856 TGCATCGACATGGCTTGGTT 60.609 50.000 0.00 0.00 0.00 3.67
5879 6017 0.608856 TTGCATCGACATGGCTTGGT 60.609 50.000 0.00 0.00 0.00 3.67
5880 6018 0.527113 TTTGCATCGACATGGCTTGG 59.473 50.000 0.00 0.00 0.00 3.61
5881 6019 1.200716 AGTTTGCATCGACATGGCTTG 59.799 47.619 0.00 0.00 0.00 4.01
5882 6020 1.538047 AGTTTGCATCGACATGGCTT 58.462 45.000 0.00 0.00 0.00 4.35
5883 6021 1.200716 CAAGTTTGCATCGACATGGCT 59.799 47.619 0.00 0.00 0.00 4.75
5884 6022 1.621107 CAAGTTTGCATCGACATGGC 58.379 50.000 0.00 0.00 0.00 4.40
5896 6034 1.868498 CCAACCAAGCATGCAAGTTTG 59.132 47.619 21.98 14.97 0.00 2.93
5897 6035 1.811176 GCCAACCAAGCATGCAAGTTT 60.811 47.619 21.98 1.65 0.00 2.66
5898 6036 0.249996 GCCAACCAAGCATGCAAGTT 60.250 50.000 21.98 16.47 0.00 2.66
5899 6037 1.117142 AGCCAACCAAGCATGCAAGT 61.117 50.000 21.98 11.00 0.00 3.16
5900 6038 0.669318 CAGCCAACCAAGCATGCAAG 60.669 55.000 21.98 11.51 0.00 4.01
5901 6039 1.368209 CAGCCAACCAAGCATGCAA 59.632 52.632 21.98 0.00 0.00 4.08
5902 6040 2.575893 CCAGCCAACCAAGCATGCA 61.576 57.895 21.98 0.00 0.00 3.96
5903 6041 2.263540 CCAGCCAACCAAGCATGC 59.736 61.111 10.51 10.51 0.00 4.06
5904 6042 2.975536 CCCAGCCAACCAAGCATG 59.024 61.111 0.00 0.00 0.00 4.06
5905 6043 2.999063 GCCCAGCCAACCAAGCAT 60.999 61.111 0.00 0.00 0.00 3.79
5906 6044 4.223125 AGCCCAGCCAACCAAGCA 62.223 61.111 0.00 0.00 0.00 3.91
5907 6045 3.688159 CAGCCCAGCCAACCAAGC 61.688 66.667 0.00 0.00 0.00 4.01
5908 6046 3.688159 GCAGCCCAGCCAACCAAG 61.688 66.667 0.00 0.00 0.00 3.61
5909 6047 4.536526 TGCAGCCCAGCCAACCAA 62.537 61.111 0.00 0.00 0.00 3.67
5912 6050 4.982701 AGGTGCAGCCCAGCCAAC 62.983 66.667 13.29 0.00 42.90 3.77
5913 6051 4.980702 CAGGTGCAGCCCAGCCAA 62.981 66.667 13.29 0.00 42.90 4.52
5915 6053 3.951769 AATCAGGTGCAGCCCAGCC 62.952 63.158 13.29 0.00 42.90 4.85
5916 6054 2.362120 AATCAGGTGCAGCCCAGC 60.362 61.111 13.29 0.00 42.22 4.85
5917 6055 2.110967 CGAATCAGGTGCAGCCCAG 61.111 63.158 13.29 3.11 38.26 4.45
5918 6056 2.046023 CGAATCAGGTGCAGCCCA 60.046 61.111 13.29 0.00 38.26 5.36
5919 6057 2.045926 ACGAATCAGGTGCAGCCC 60.046 61.111 13.29 0.00 38.26 5.19
5920 6058 2.401766 CCACGAATCAGGTGCAGCC 61.402 63.158 13.29 4.65 34.08 4.85
5921 6059 1.375908 TCCACGAATCAGGTGCAGC 60.376 57.895 8.11 8.11 34.08 5.25
5922 6060 1.021390 GGTCCACGAATCAGGTGCAG 61.021 60.000 0.00 0.00 34.08 4.41
5923 6061 1.003839 GGTCCACGAATCAGGTGCA 60.004 57.895 0.00 0.00 34.08 4.57
5924 6062 3.890674 GGTCCACGAATCAGGTGC 58.109 61.111 0.00 0.00 34.08 5.01
5935 6073 4.980805 TGCGGTTCTGCGGTCCAC 62.981 66.667 9.40 1.78 37.81 4.02
5936 6074 3.758973 TTTGCGGTTCTGCGGTCCA 62.759 57.895 9.40 0.00 37.81 4.02
5937 6075 2.966309 CTTTGCGGTTCTGCGGTCC 61.966 63.158 0.00 0.00 37.81 4.46
5938 6076 2.556287 CTTTGCGGTTCTGCGGTC 59.444 61.111 0.00 0.00 37.81 4.79
5939 6077 3.660111 GCTTTGCGGTTCTGCGGT 61.660 61.111 0.00 0.00 37.81 5.68
5940 6078 3.659092 TGCTTTGCGGTTCTGCGG 61.659 61.111 0.00 0.00 37.81 5.69
5941 6079 2.392613 AAGTGCTTTGCGGTTCTGCG 62.393 55.000 0.00 0.00 37.81 5.18
5942 6080 0.661483 GAAGTGCTTTGCGGTTCTGC 60.661 55.000 0.00 0.00 0.00 4.26
5943 6081 0.947244 AGAAGTGCTTTGCGGTTCTG 59.053 50.000 5.72 0.00 33.78 3.02
5944 6082 0.947244 CAGAAGTGCTTTGCGGTTCT 59.053 50.000 0.00 0.00 34.83 3.01
5945 6083 0.040067 CCAGAAGTGCTTTGCGGTTC 60.040 55.000 0.00 0.00 0.00 3.62
5946 6084 1.455383 CCCAGAAGTGCTTTGCGGTT 61.455 55.000 0.00 0.00 0.00 4.44
5947 6085 1.898574 CCCAGAAGTGCTTTGCGGT 60.899 57.895 0.00 0.00 0.00 5.68
5948 6086 2.956987 CCCAGAAGTGCTTTGCGG 59.043 61.111 0.00 0.00 0.00 5.69
5949 6087 2.256461 GCCCAGAAGTGCTTTGCG 59.744 61.111 0.00 0.00 0.00 4.85
5950 6088 1.905354 AGGCCCAGAAGTGCTTTGC 60.905 57.895 0.00 0.00 0.00 3.68
5951 6089 1.530013 CCAGGCCCAGAAGTGCTTTG 61.530 60.000 0.00 0.00 0.00 2.77
5952 6090 1.228675 CCAGGCCCAGAAGTGCTTT 60.229 57.895 0.00 0.00 0.00 3.51
5953 6091 2.437897 CCAGGCCCAGAAGTGCTT 59.562 61.111 0.00 0.00 0.00 3.91
5954 6092 4.357279 GCCAGGCCCAGAAGTGCT 62.357 66.667 0.00 0.00 0.00 4.40
5955 6093 4.357279 AGCCAGGCCCAGAAGTGC 62.357 66.667 8.22 0.00 0.00 4.40
5956 6094 2.360852 CAGCCAGGCCCAGAAGTG 60.361 66.667 8.22 0.00 0.00 3.16
5957 6095 2.530151 TCAGCCAGGCCCAGAAGT 60.530 61.111 8.22 0.00 0.00 3.01
5958 6096 2.271497 CTCAGCCAGGCCCAGAAG 59.729 66.667 8.22 0.00 0.00 2.85
5959 6097 3.333219 CCTCAGCCAGGCCCAGAA 61.333 66.667 8.22 0.00 34.56 3.02
5965 6103 4.432741 GTTCCCCCTCAGCCAGGC 62.433 72.222 1.84 1.84 41.80 4.85
5966 6104 2.612115 AGTTCCCCCTCAGCCAGG 60.612 66.667 0.00 0.00 43.01 4.45
5967 6105 2.190488 GACAGTTCCCCCTCAGCCAG 62.190 65.000 0.00 0.00 0.00 4.85
5968 6106 2.121963 ACAGTTCCCCCTCAGCCA 60.122 61.111 0.00 0.00 0.00 4.75
5969 6107 2.671682 GACAGTTCCCCCTCAGCC 59.328 66.667 0.00 0.00 0.00 4.85
5970 6108 1.827399 TTCGACAGTTCCCCCTCAGC 61.827 60.000 0.00 0.00 0.00 4.26
5971 6109 0.905357 ATTCGACAGTTCCCCCTCAG 59.095 55.000 0.00 0.00 0.00 3.35
5972 6110 3.082619 ATTCGACAGTTCCCCCTCA 57.917 52.632 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.