Multiple sequence alignment - TraesCS3B01G297500

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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 TraesCS3B01G297500 chr3B 100.000 7190 0 0 578 7767 476957330 476950141 0.000000e+00 13278.0
1 TraesCS3B01G297500 chr3B 100.000 179 0 0 1 179 476957907 476957729 1.620000e-86 331.0
2 TraesCS3B01G297500 chr3D 91.326 4669 302 38 581 5192 365923188 365918566 0.000000e+00 6283.0
3 TraesCS3B01G297500 chr3D 92.993 2155 97 21 5188 7326 365913094 365910978 0.000000e+00 3094.0
4 TraesCS3B01G297500 chr3D 95.794 428 14 1 7340 7767 365910994 365910571 0.000000e+00 688.0
5 TraesCS3B01G297500 chr3D 81.818 154 28 0 22 175 537966424 537966577 6.320000e-26 130.0
6 TraesCS3B01G297500 chr3A 91.062 1958 118 20 2176 4109 487864728 487862804 0.000000e+00 2593.0
7 TraesCS3B01G297500 chr3A 91.405 1594 98 10 4156 5712 487862798 487861207 0.000000e+00 2148.0
8 TraesCS3B01G297500 chr3A 94.093 1405 67 7 635 2036 487866119 487864728 0.000000e+00 2121.0
9 TraesCS3B01G297500 chr3A 93.735 1277 59 8 6062 7326 487860489 487859222 0.000000e+00 1895.0
10 TraesCS3B01G297500 chr3A 91.422 443 19 6 7340 7767 487859238 487858800 2.410000e-164 590.0
11 TraesCS3B01G297500 chr3A 95.429 350 12 3 5738 6085 487861210 487860863 8.810000e-154 555.0
12 TraesCS3B01G297500 chr3A 85.393 178 24 2 3 179 265175719 265175895 4.790000e-42 183.0
13 TraesCS3B01G297500 chr5B 88.953 172 14 4 1721 1889 665744634 665744465 2.840000e-49 207.0
14 TraesCS3B01G297500 chr5D 88.304 171 17 2 1721 1889 528717443 528717274 1.320000e-47 202.0
15 TraesCS3B01G297500 chr5A 88.304 171 17 2 1721 1889 656872450 656872281 1.320000e-47 202.0
16 TraesCS3B01G297500 chr4A 90.667 150 10 2 1734 1879 598724452 598724601 6.150000e-46 196.0
17 TraesCS3B01G297500 chr2D 89.375 160 12 3 1737 1891 79056319 79056160 6.150000e-46 196.0
18 TraesCS3B01G297500 chr7B 89.241 158 13 2 1736 1889 505937467 505937310 2.210000e-45 195.0
19 TraesCS3B01G297500 chr1D 87.879 165 17 2 1737 1898 289395170 289395006 2.860000e-44 191.0
20 TraesCS3B01G297500 chr2B 84.553 123 17 2 27 148 37105676 37105555 3.810000e-23 121.0
21 TraesCS3B01G297500 chr2B 82.500 80 13 1 100 179 37105480 37105402 1.400000e-07 69.4
22 TraesCS3B01G297500 chr4B 85.227 88 13 0 92 179 615146726 615146813 2.980000e-14 91.6
23 TraesCS3B01G297500 chr6B 77.778 108 22 2 581 687 423796573 423796679 1.810000e-06 65.8


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 TraesCS3B01G297500 chr3B 476950141 476957907 7766 True 6804.500000 13278 100.000000 1 7767 2 chr3B.!!$R1 7766
1 TraesCS3B01G297500 chr3D 365918566 365923188 4622 True 6283.000000 6283 91.326000 581 5192 1 chr3D.!!$R1 4611
2 TraesCS3B01G297500 chr3D 365910571 365913094 2523 True 1891.000000 3094 94.393500 5188 7767 2 chr3D.!!$R2 2579
3 TraesCS3B01G297500 chr3A 487858800 487866119 7319 True 1650.333333 2593 92.857667 635 7767 6 chr3A.!!$R1 7132

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
946 948 1.202475 TGCTCTGACGTTGTACAAGCA 60.202 47.619 8.98 10.28 36.04 3.91 F
1997 2025 0.034670 GGAATGGCTGTGAGAAGGCT 60.035 55.000 0.00 0.00 42.98 4.58 F
2105 2133 1.152631 AGGGTTTGGGGTTTGGTCG 60.153 57.895 0.00 0.00 0.00 4.79 F
2116 2144 1.865340 GGTTTGGTCGTCTTGTGAGTC 59.135 52.381 0.00 0.00 0.00 3.36 F
3305 3351 0.470766 TGTTTGACTACCCCGTGCTT 59.529 50.000 0.00 0.00 0.00 3.91 F
3361 3407 0.539438 CTTGCCAAGCAGGGGTACAA 60.539 55.000 0.00 0.00 40.61 2.41 F
5149 5236 0.035458 CCTCGTTGTCCTTTGCCTCT 59.965 55.000 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2113 0.105913 GACCAAACCCCAAACCCTCA 60.106 55.000 0.00 0.0 0.00 3.86 R
3079 3125 0.679640 TCCGCAAAATAGCACTGGGG 60.680 55.000 0.00 0.0 42.85 4.96 R
3305 3351 1.522668 CGTTGCCAGTTCCAAGATCA 58.477 50.000 0.00 0.0 0.00 2.92 R
3760 3813 2.802247 GTTTCTTGCAAGTTCAATGGCC 59.198 45.455 25.19 0.0 0.00 5.36 R
4647 4707 0.104304 ACCCCTACGACGCATTCATC 59.896 55.000 0.00 0.0 0.00 2.92 R
5294 5384 0.602638 GAACGGACATGTCTGCCACA 60.603 55.000 30.48 0.0 39.55 4.17 R
6878 7377 0.533755 AGGCAAGTGTGAGTGAGTGC 60.534 55.000 0.00 0.0 0.00 4.40 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 3.691342 TGTCCTCACCTTCGGCCG 61.691 66.667 22.12 22.12 0.00 6.13
18 19 3.379445 GTCCTCACCTTCGGCCGA 61.379 66.667 27.28 27.28 0.00 5.54
19 20 3.379445 TCCTCACCTTCGGCCGAC 61.379 66.667 31.19 0.00 0.00 4.79
20 21 4.796231 CCTCACCTTCGGCCGACG 62.796 72.222 31.19 27.09 46.11 5.12
47 48 4.154347 CCAGGCACGAGCTCCCTC 62.154 72.222 8.47 0.00 41.70 4.30
48 49 3.385384 CAGGCACGAGCTCCCTCA 61.385 66.667 8.47 0.00 41.70 3.86
49 50 3.386237 AGGCACGAGCTCCCTCAC 61.386 66.667 8.47 0.00 41.70 3.51
50 51 4.803426 GGCACGAGCTCCCTCACG 62.803 72.222 8.47 0.00 41.70 4.35
51 52 4.803426 GCACGAGCTCCCTCACGG 62.803 72.222 8.47 0.00 38.00 4.94
52 53 4.803426 CACGAGCTCCCTCACGGC 62.803 72.222 8.47 0.00 38.00 5.68
55 56 4.200283 GAGCTCCCTCACGGCGAG 62.200 72.222 16.62 5.72 41.89 5.03
75 76 3.677648 GCACCAAGCTGCCACCAG 61.678 66.667 0.00 0.00 42.13 4.00
83 84 4.960866 CTGCCACCAGCCTGTGCA 62.961 66.667 0.00 0.00 42.71 4.57
85 86 4.962836 GCCACCAGCCTGTGCACT 62.963 66.667 19.41 0.00 41.13 4.40
86 87 2.670934 CCACCAGCCTGTGCACTC 60.671 66.667 19.41 7.29 41.13 3.51
87 88 2.670934 CACCAGCCTGTGCACTCC 60.671 66.667 19.41 6.14 41.13 3.85
88 89 4.320456 ACCAGCCTGTGCACTCCG 62.320 66.667 19.41 6.22 41.13 4.63
90 91 4.694233 CAGCCTGTGCACTCCGCT 62.694 66.667 19.41 17.85 43.06 5.52
91 92 4.694233 AGCCTGTGCACTCCGCTG 62.694 66.667 19.41 1.20 43.06 5.18
93 94 4.994471 CCTGTGCACTCCGCTGCA 62.994 66.667 19.41 0.00 45.06 4.41
99 100 4.374702 CACTCCGCTGCAACGCAC 62.375 66.667 3.43 0.00 33.79 5.34
171 172 4.953868 CGACACGCCGGTCACCAA 62.954 66.667 1.90 0.00 37.66 3.67
172 173 3.041940 GACACGCCGGTCACCAAG 61.042 66.667 1.90 0.00 37.73 3.61
173 174 3.509137 GACACGCCGGTCACCAAGA 62.509 63.158 1.90 0.00 37.73 3.02
174 175 2.047274 CACGCCGGTCACCAAGAT 60.047 61.111 1.90 0.00 0.00 2.40
175 176 2.100631 CACGCCGGTCACCAAGATC 61.101 63.158 1.90 0.00 0.00 2.75
176 177 2.511600 CGCCGGTCACCAAGATCC 60.512 66.667 1.90 0.00 0.00 3.36
177 178 2.511600 GCCGGTCACCAAGATCCG 60.512 66.667 1.90 0.00 39.25 4.18
178 179 2.511600 CCGGTCACCAAGATCCGC 60.512 66.667 0.00 0.00 38.65 5.54
629 630 4.865905 AGTGTCTCTGATATGTGAGGACT 58.134 43.478 0.00 0.00 0.00 3.85
637 638 6.820335 TCTGATATGTGAGGACTTACATTGG 58.180 40.000 13.82 4.42 39.88 3.16
646 647 7.069331 TGTGAGGACTTACATTGGATTTTGTTT 59.931 33.333 0.00 0.00 0.00 2.83
657 658 9.122779 ACATTGGATTTTGTTTTTGACATCATT 57.877 25.926 0.00 0.00 38.26 2.57
658 659 9.388346 CATTGGATTTTGTTTTTGACATCATTG 57.612 29.630 0.00 0.00 38.26 2.82
674 675 9.729023 TGACATCATTGTGTAGTTAAACTTTTG 57.271 29.630 0.00 0.00 35.79 2.44
687 688 4.751767 AAACTTTTGGTGGATGCTCAAA 57.248 36.364 3.18 3.18 0.00 2.69
708 709 2.191400 TGCTTGAGTTGGGAGCTATCT 58.809 47.619 0.00 0.00 37.32 1.98
794 796 2.762745 ACTATGGTTGTGTGACGAACC 58.237 47.619 8.87 8.87 41.85 3.62
802 804 5.763698 TGGTTGTGTGACGAACCATTTATAA 59.236 36.000 13.27 0.00 45.37 0.98
803 805 6.431543 TGGTTGTGTGACGAACCATTTATAAT 59.568 34.615 13.27 0.00 45.37 1.28
817 819 6.697019 ACCATTTATAATGCGAACATGCTTTC 59.303 34.615 0.00 0.00 36.36 2.62
830 832 5.917541 ACATGCTTTCAAATTTGCAGAAG 57.082 34.783 13.54 15.92 38.87 2.85
863 865 2.949177 TCTGCTTTGCCAGAACCTAA 57.051 45.000 0.00 0.00 38.81 2.69
946 948 1.202475 TGCTCTGACGTTGTACAAGCA 60.202 47.619 8.98 10.28 36.04 3.91
1028 1030 1.257750 AAAATTCAAGCCGCCTCCCC 61.258 55.000 0.00 0.00 0.00 4.81
1397 1399 1.134759 GGTACTCCCCGCTCTTTCTTC 60.135 57.143 0.00 0.00 0.00 2.87
1480 1504 2.366916 CTCTAGCTTCAGTATGGGGTGG 59.633 54.545 0.00 0.00 36.16 4.61
1551 1575 3.131755 CCCTCAAAAAGATCAAGATGCCC 59.868 47.826 0.00 0.00 0.00 5.36
1552 1576 4.021916 CCTCAAAAAGATCAAGATGCCCT 58.978 43.478 0.00 0.00 0.00 5.19
1553 1577 4.142227 CCTCAAAAAGATCAAGATGCCCTG 60.142 45.833 0.00 0.00 0.00 4.45
1554 1578 3.194116 TCAAAAAGATCAAGATGCCCTGC 59.806 43.478 0.00 0.00 0.00 4.85
1555 1579 1.772836 AAAGATCAAGATGCCCTGCC 58.227 50.000 0.00 0.00 0.00 4.85
1568 1592 2.224843 TGCCCTGCCATAGGTGATATTG 60.225 50.000 0.00 0.00 45.80 1.90
1578 1602 6.005823 CCATAGGTGATATTGGATCAAAGCA 58.994 40.000 0.00 0.00 0.00 3.91
1743 1767 4.526262 ACATGGCTCAGTCATATACTCCTC 59.474 45.833 0.00 0.00 35.76 3.71
1748 1772 3.752665 TCAGTCATATACTCCTCCCGTC 58.247 50.000 0.00 0.00 35.76 4.79
1987 2015 4.885907 ACAGATATGAGTTTGGAATGGCTG 59.114 41.667 0.00 0.00 0.00 4.85
1997 2025 0.034670 GGAATGGCTGTGAGAAGGCT 60.035 55.000 0.00 0.00 42.98 4.58
2004 2032 3.637229 TGGCTGTGAGAAGGCTATAGTAC 59.363 47.826 0.84 0.00 42.98 2.73
2105 2133 1.152631 AGGGTTTGGGGTTTGGTCG 60.153 57.895 0.00 0.00 0.00 4.79
2116 2144 1.865340 GGTTTGGTCGTCTTGTGAGTC 59.135 52.381 0.00 0.00 0.00 3.36
2123 2151 3.298317 GTCGTCTTGTGAGTCTGTACAC 58.702 50.000 0.00 0.00 37.51 2.90
2126 2154 2.628657 GTCTTGTGAGTCTGTACACCCT 59.371 50.000 0.00 0.00 36.35 4.34
2138 2166 6.839134 AGTCTGTACACCCTCATATAATGTGA 59.161 38.462 0.00 0.00 0.00 3.58
2153 2181 9.715123 CATATAATGTGAAACGTAGAATTTGCA 57.285 29.630 0.00 0.00 42.39 4.08
2155 2183 3.867665 TGTGAAACGTAGAATTTGCACG 58.132 40.909 0.00 6.04 42.39 5.34
2174 2202 2.296190 ACGCAAAATTTTCTGGGTCTCC 59.704 45.455 0.00 0.00 33.89 3.71
2176 2204 3.756434 CGCAAAATTTTCTGGGTCTCCTA 59.244 43.478 0.00 0.00 0.00 2.94
2178 2206 5.588648 CGCAAAATTTTCTGGGTCTCCTATA 59.411 40.000 0.00 0.00 0.00 1.31
2182 2210 9.681062 CAAAATTTTCTGGGTCTCCTATAGTTA 57.319 33.333 0.00 0.00 0.00 2.24
2246 2274 3.396260 TCTACGAACAAAGGTGGGAAG 57.604 47.619 0.00 0.00 0.00 3.46
2298 2330 8.944029 TCCATTACTACTACGAGATTAGCATAC 58.056 37.037 0.00 0.00 0.00 2.39
2360 2392 9.599866 CTTGTATCAAGGTAGATGAACATGTTA 57.400 33.333 11.95 0.61 0.00 2.41
2429 2462 8.470805 TGAGAAGAAGAAAACTCTATTCGCTAT 58.529 33.333 0.00 0.00 32.04 2.97
2487 2521 4.957759 ATGTTGTAAAATACCCTCGTGC 57.042 40.909 0.00 0.00 0.00 5.34
2489 2523 3.075884 GTTGTAAAATACCCTCGTGCCA 58.924 45.455 0.00 0.00 0.00 4.92
2595 2629 6.558771 TCTGAAGATCTCGCAAATTTTCAA 57.441 33.333 0.00 0.00 29.86 2.69
2690 2725 8.996024 TCTTGTATAGAAAAATCACATGACGA 57.004 30.769 0.00 0.00 0.00 4.20
2801 2836 9.704098 GTGCAAATTATAAAGTGTTAGCTCTAC 57.296 33.333 0.00 0.00 0.00 2.59
2906 2943 9.506018 TGTATTATAGACATAGTGCATGCATTT 57.494 29.630 25.64 17.53 38.29 2.32
2976 3022 7.234782 TCCTCAAACTTAGAATCTGGAGTACAA 59.765 37.037 0.00 0.00 0.00 2.41
3008 3054 6.780522 ACTCACACCAAAACCCACTTATTTAT 59.219 34.615 0.00 0.00 0.00 1.40
3093 3139 4.668138 TTAAGGTCCCCAGTGCTATTTT 57.332 40.909 0.00 0.00 0.00 1.82
3111 3157 5.862924 ATTTTGCGGAGTATATCGAATGG 57.137 39.130 0.00 0.00 0.00 3.16
3305 3351 0.470766 TGTTTGACTACCCCGTGCTT 59.529 50.000 0.00 0.00 0.00 3.91
3361 3407 0.539438 CTTGCCAAGCAGGGGTACAA 60.539 55.000 0.00 0.00 40.61 2.41
3571 3624 8.354426 ACTTTCTAAGAACTGAACAGACTACTC 58.646 37.037 8.87 0.00 0.00 2.59
3583 3636 3.028850 CAGACTACTCCCGAAATACCCA 58.971 50.000 0.00 0.00 0.00 4.51
3661 3714 1.069049 GCCACTGTCAATGCCAAAGTT 59.931 47.619 0.00 0.00 0.00 2.66
3674 3727 3.450457 TGCCAAAGTTGCCCTTATTATGG 59.550 43.478 0.00 0.00 32.61 2.74
3698 3751 7.977293 TGGATTTTGAAGATCATATGTTTGCAG 59.023 33.333 1.90 0.00 0.00 4.41
3715 3768 7.939782 TGTTTGCAGAAGAATGAATAGTTTCA 58.060 30.769 0.00 0.00 45.57 2.69
3716 3769 8.412456 TGTTTGCAGAAGAATGAATAGTTTCAA 58.588 29.630 0.00 0.00 44.70 2.69
3968 4022 7.495934 ACATGTTGTTACATATTCTGTAGCCTC 59.504 37.037 0.00 0.00 43.07 4.70
3972 4026 8.391106 GTTGTTACATATTCTGTAGCCTCAAAG 58.609 37.037 0.00 0.00 41.30 2.77
3982 4036 2.091852 AGCCTCAAAGAGAAAGAGCG 57.908 50.000 0.00 0.00 0.00 5.03
4013 4067 7.815068 ACAACAATAGCTACTTTCACTAGTCTG 59.185 37.037 0.00 0.00 0.00 3.51
4061 4115 5.692814 CATCTTTGCATCTTGTCGAAAAGA 58.307 37.500 20.11 20.11 40.36 2.52
4071 4125 6.249035 TCTTGTCGAAAAGAACAAACACTT 57.751 33.333 15.82 0.00 33.25 3.16
4072 4126 7.367159 TCTTGTCGAAAAGAACAAACACTTA 57.633 32.000 15.82 0.00 33.25 2.24
4073 4127 7.238571 TCTTGTCGAAAAGAACAAACACTTAC 58.761 34.615 15.82 0.00 33.25 2.34
4198 4257 7.870954 TGTATACTATTTTTCCGTCATAGCAGG 59.129 37.037 4.17 0.00 0.00 4.85
4202 4261 4.546829 TTTTTCCGTCATAGCAGGTACT 57.453 40.909 0.00 0.00 43.88 2.73
4213 4272 7.309255 CGTCATAGCAGGTACTATATCCAGTTT 60.309 40.741 0.00 0.00 36.02 2.66
4249 4308 3.259374 TCAACAAAAAGTGCAGTTTCCCA 59.741 39.130 19.51 0.00 0.00 4.37
4515 4575 6.494893 TCTTAGCACAACCAATTGACATAC 57.505 37.500 7.12 0.00 39.30 2.39
4525 4585 5.984725 ACCAATTGACATACGACATAGGAA 58.015 37.500 7.12 0.00 0.00 3.36
4569 4629 7.543756 TCAAAGACATATGACATAGTCGTGAA 58.456 34.615 10.38 9.23 34.95 3.18
4609 4669 5.204292 TGCCATAGGATATAGCAGTAGGAG 58.796 45.833 0.00 0.00 0.00 3.69
4628 4688 1.453015 AAGCAACACTTCACCGGCA 60.453 52.632 0.00 0.00 30.77 5.69
4647 4707 3.305608 GGCATTTTCTGAAGTGGAAGTGG 60.306 47.826 6.89 0.00 0.00 4.00
4672 4732 1.405872 TGCGTCGTAGGGGTTATCAT 58.594 50.000 0.00 0.00 0.00 2.45
4679 4739 4.458642 GTCGTAGGGGTTATCATAGTCCTC 59.541 50.000 0.00 0.00 0.00 3.71
4682 4742 3.924922 AGGGGTTATCATAGTCCTCGTT 58.075 45.455 0.00 0.00 0.00 3.85
4686 4746 3.317430 GGTTATCATAGTCCTCGTTCGGT 59.683 47.826 0.00 0.00 0.00 4.69
4717 4777 1.355796 CGACGCGGGCTTGTTCATTA 61.356 55.000 12.47 0.00 0.00 1.90
4756 4840 4.916314 GCCTCGATCCCCTCCCGA 62.916 72.222 0.00 0.00 0.00 5.14
4817 4901 1.611673 CCTTCGTGGTCAAGGAGCATT 60.612 52.381 1.15 0.00 42.94 3.56
4883 4967 2.125350 GTGCTGGAGCGGAGAAGG 60.125 66.667 0.00 0.00 45.83 3.46
4885 4969 1.687146 TGCTGGAGCGGAGAAGGAT 60.687 57.895 0.00 0.00 45.83 3.24
4887 4971 1.227497 CTGGAGCGGAGAAGGATGC 60.227 63.158 0.00 0.00 0.00 3.91
4888 4972 2.279784 GGAGCGGAGAAGGATGCG 60.280 66.667 0.00 0.00 37.05 4.73
4889 4973 2.496817 GAGCGGAGAAGGATGCGT 59.503 61.111 0.00 0.00 36.29 5.24
4892 4976 2.798689 CGGAGAAGGATGCGTCGA 59.201 61.111 0.00 0.00 0.00 4.20
4944 5031 3.736224 CAGCAGGAGGGCCATGGT 61.736 66.667 14.67 4.07 36.29 3.55
5149 5236 0.035458 CCTCGTTGTCCTTTGCCTCT 59.965 55.000 0.00 0.00 0.00 3.69
5161 5248 3.604582 CTTTGCCTCTAAGAGTTCCCAG 58.395 50.000 0.00 0.00 0.00 4.45
5236 5323 2.094234 GGAGAGCTGAGGAAAGTGAGTC 60.094 54.545 0.00 0.00 0.00 3.36
5237 5324 1.543802 AGAGCTGAGGAAAGTGAGTCG 59.456 52.381 0.00 0.00 0.00 4.18
5238 5325 1.542030 GAGCTGAGGAAAGTGAGTCGA 59.458 52.381 0.00 0.00 0.00 4.20
5239 5326 2.165437 GAGCTGAGGAAAGTGAGTCGAT 59.835 50.000 0.00 0.00 0.00 3.59
5242 5329 3.124297 GCTGAGGAAAGTGAGTCGATTTG 59.876 47.826 0.00 0.00 0.00 2.32
5246 5333 1.468914 GAAAGTGAGTCGATTTGGGGC 59.531 52.381 0.00 0.00 0.00 5.80
5247 5334 0.693049 AAGTGAGTCGATTTGGGGCT 59.307 50.000 0.00 0.00 0.00 5.19
5248 5335 0.036010 AGTGAGTCGATTTGGGGCTG 60.036 55.000 0.00 0.00 0.00 4.85
5250 5337 1.198094 TGAGTCGATTTGGGGCTGGA 61.198 55.000 0.00 0.00 0.00 3.86
5251 5338 0.744771 GAGTCGATTTGGGGCTGGAC 60.745 60.000 0.00 0.00 0.00 4.02
5289 5379 2.007576 GGATAGGCCCAGGTTTGGT 58.992 57.895 0.00 0.00 43.40 3.67
5294 5384 1.142688 AGGCCCAGGTTTGGTCTGAT 61.143 55.000 0.00 0.00 43.40 2.90
5300 5390 0.478072 AGGTTTGGTCTGATGTGGCA 59.522 50.000 0.00 0.00 0.00 4.92
5312 5402 0.036732 ATGTGGCAGACATGTCCGTT 59.963 50.000 22.21 0.74 44.12 4.44
5448 5543 1.313091 GGACGAATGGGGCAGGTTTC 61.313 60.000 0.00 0.00 0.00 2.78
5457 5552 4.035102 GCAGGTTTCGGGAGGGCT 62.035 66.667 0.00 0.00 0.00 5.19
5491 5586 8.006298 TGCCCTTATCAAATGGTTATTAAGTG 57.994 34.615 0.00 0.00 0.00 3.16
5582 5677 6.284459 ACTTGAGACAAAGTTAGACAGGAAG 58.716 40.000 0.00 0.00 37.05 3.46
5656 5751 0.039527 GGCCGTGCAAAAAGGTACAG 60.040 55.000 0.00 0.00 0.00 2.74
5725 5821 3.372060 CTTTTCGCTTTTGTCCACTTCC 58.628 45.455 0.00 0.00 0.00 3.46
5733 5829 4.156008 GCTTTTGTCCACTTCCGTGATTAT 59.844 41.667 0.00 0.00 43.97 1.28
5735 5831 4.819105 TTGTCCACTTCCGTGATTATCT 57.181 40.909 0.00 0.00 43.97 1.98
5793 5889 9.605275 TCTGTGAGATTTGATTATCTAACAAGG 57.395 33.333 5.56 0.00 42.68 3.61
5825 5921 9.079833 CAAATTTTGCATACTAGAGTTGGAATG 57.920 33.333 0.00 0.00 0.00 2.67
6002 6098 2.086054 AGCCGAGTTTCACTGCTTAG 57.914 50.000 0.00 0.00 24.43 2.18
6059 6155 7.168637 CCAGTGAGTTATATTTCATTGCAATGC 59.831 37.037 30.57 15.98 36.36 3.56
6060 6156 7.703197 CAGTGAGTTATATTTCATTGCAATGCA 59.297 33.333 30.57 20.33 36.36 3.96
6116 6610 2.414161 GCGGTTCCAATACACAAGAAGC 60.414 50.000 0.00 0.00 34.29 3.86
6119 6613 3.191371 GGTTCCAATACACAAGAAGCCTG 59.809 47.826 0.00 0.00 32.07 4.85
6140 6634 9.819267 AGCCTGTGTTAAAGATATCTTAAGTAC 57.181 33.333 18.23 14.63 34.61 2.73
6189 6683 9.337396 TGAGTTAACATTGTTCTCTTTATGTGT 57.663 29.630 8.61 0.00 31.98 3.72
6300 6796 6.073548 CGTGCAAACTCTCTGAAACTCTTATT 60.074 38.462 0.00 0.00 0.00 1.40
6420 6916 2.011222 TCGGTATGCGGAAATTTGGTC 58.989 47.619 0.00 0.00 0.00 4.02
6575 7071 3.149981 GTGAAAGGCCAGCTTAAGAGTT 58.850 45.455 5.01 0.00 0.00 3.01
6579 7075 4.855715 AAGGCCAGCTTAAGAGTTTTTC 57.144 40.909 5.01 0.00 0.00 2.29
6596 7092 8.180317 GAGTTTTTCTCTCTATGTTGTAGCTC 57.820 38.462 0.00 0.00 39.86 4.09
6727 7223 1.002792 GCAAACGAACAAGAGGGACAC 60.003 52.381 0.00 0.00 0.00 3.67
6759 7255 8.810427 ACTGTATTATTTATGTAACCGTGAACG 58.190 33.333 0.00 0.00 39.44 3.95
6778 7276 5.184864 TGAACGTTTGCCCATTTTCATAGAT 59.815 36.000 0.46 0.00 0.00 1.98
6786 7284 6.439487 TGCCCATTTTCATAGATTTTCCCTA 58.561 36.000 0.00 0.00 0.00 3.53
6806 7304 5.393962 CCTACTTTTTCCAAAGAGAATGCG 58.606 41.667 1.73 0.00 41.97 4.73
6821 7319 1.303091 ATGCGGACGTTTTAGTGCCC 61.303 55.000 0.00 0.00 0.00 5.36
6831 7329 0.035739 TTTAGTGCCCGGTGTCTTCC 59.964 55.000 0.00 0.00 0.00 3.46
6832 7330 1.122632 TTAGTGCCCGGTGTCTTCCA 61.123 55.000 0.00 0.00 0.00 3.53
6836 7334 0.907704 TGCCCGGTGTCTTCCATAGT 60.908 55.000 0.00 0.00 0.00 2.12
6878 7377 3.581755 CCATGAATGTTGGAAAGCTGTG 58.418 45.455 0.00 0.00 36.26 3.66
6988 7489 6.223852 AGTCAAGTGTGTTGTTCCTAGTATG 58.776 40.000 0.00 0.00 0.00 2.39
7057 7561 8.985315 ATTTTGCATCTTCTGTATCCTATGAA 57.015 30.769 0.00 0.00 0.00 2.57
7058 7562 8.985315 TTTTGCATCTTCTGTATCCTATGAAT 57.015 30.769 0.00 0.00 0.00 2.57
7060 7564 7.307131 TGCATCTTCTGTATCCTATGAATGA 57.693 36.000 0.00 0.00 0.00 2.57
7067 7571 5.069119 TCTGTATCCTATGAATGACAGCGTT 59.931 40.000 0.00 0.00 33.28 4.84
7074 7578 2.621338 TGAATGACAGCGTTGATCTCC 58.379 47.619 6.16 0.00 0.00 3.71
7080 7584 1.207329 ACAGCGTTGATCTCCCTAACC 59.793 52.381 6.16 0.00 0.00 2.85
7108 7615 8.781196 CATCCAATGAGACTAATATTTGACAGG 58.219 37.037 3.83 1.58 0.00 4.00
7127 7634 1.212195 GGACCTAACCACCATTCTCCC 59.788 57.143 0.00 0.00 0.00 4.30
7179 7686 4.681978 GTTGAGGTGGCGTCGGCT 62.682 66.667 20.29 0.00 39.81 5.52
7223 7730 3.170717 TCCTACAGGTTCTGTAACTGGG 58.829 50.000 4.34 6.90 44.80 4.45
7225 7732 0.400594 ACAGGTTCTGTAACTGGGGC 59.599 55.000 4.34 0.00 43.46 5.80
7283 7790 6.881065 TCTTACATTCTGATTGAAACTGAGGG 59.119 38.462 6.56 0.00 38.29 4.30
7317 7826 3.452627 GACTGGACATGGGTAAGACAGAT 59.547 47.826 0.00 0.00 0.00 2.90
7322 7831 4.080863 GGACATGGGTAAGACAGATCTGTT 60.081 45.833 28.46 16.66 45.05 3.16
7323 7832 4.836825 ACATGGGTAAGACAGATCTGTTG 58.163 43.478 28.46 20.95 45.05 3.33
7324 7833 4.287067 ACATGGGTAAGACAGATCTGTTGT 59.713 41.667 28.46 21.56 45.05 3.32
7325 7834 4.974645 TGGGTAAGACAGATCTGTTGTT 57.025 40.909 28.46 24.35 45.05 2.83
7326 7835 5.304686 TGGGTAAGACAGATCTGTTGTTT 57.695 39.130 28.46 22.66 45.05 2.83
7327 7836 5.063204 TGGGTAAGACAGATCTGTTGTTTG 58.937 41.667 28.46 1.86 45.05 2.93
7328 7837 5.063880 GGGTAAGACAGATCTGTTGTTTGT 58.936 41.667 28.46 12.90 45.05 2.83
7329 7838 5.531287 GGGTAAGACAGATCTGTTGTTTGTT 59.469 40.000 28.46 16.45 45.05 2.83
7330 7839 6.293462 GGGTAAGACAGATCTGTTGTTTGTTC 60.293 42.308 28.46 13.50 45.05 3.18
7331 7840 6.260050 GGTAAGACAGATCTGTTGTTTGTTCA 59.740 38.462 28.46 8.19 45.05 3.18
7332 7841 6.757897 AAGACAGATCTGTTGTTTGTTCAA 57.242 33.333 28.46 0.00 45.05 2.69
7333 7842 6.757897 AGACAGATCTGTTGTTTGTTCAAA 57.242 33.333 28.46 0.00 45.05 2.69
7334 7843 7.156876 AGACAGATCTGTTGTTTGTTCAAAA 57.843 32.000 28.46 0.00 45.05 2.44
7335 7844 7.601856 AGACAGATCTGTTGTTTGTTCAAAAA 58.398 30.769 28.46 0.00 45.05 1.94
7357 7866 2.348411 AAAGACAGACCTGGTGTTGG 57.652 50.000 2.82 0.00 34.19 3.77
7508 8017 5.982890 TTCAGGGCAAGAAAATAGAAAGG 57.017 39.130 0.00 0.00 0.00 3.11
7514 8023 6.659668 AGGGCAAGAAAATAGAAAGGTCTAAC 59.340 38.462 0.00 0.00 39.81 2.34
7566 8075 1.066858 CAGTGCCATCGAGTACACCTT 60.067 52.381 9.97 0.00 33.46 3.50
7637 8146 3.713858 TCAACTGAAGGTGCATGTTTG 57.286 42.857 0.00 0.00 0.00 2.93
7660 8169 3.625764 GGAACAAATATGCGCTAGTTGGA 59.374 43.478 21.89 0.00 39.22 3.53
7668 8177 1.717937 CGCTAGTTGGATGCAGCAC 59.282 57.895 3.51 0.00 33.55 4.40
7692 8216 5.006746 CGAGCATGGAAGGTTTACATTCTAC 59.993 44.000 7.15 0.00 36.91 2.59
7693 8217 4.876107 AGCATGGAAGGTTTACATTCTACG 59.124 41.667 7.15 0.00 36.91 3.51
7694 8218 4.634443 GCATGGAAGGTTTACATTCTACGT 59.366 41.667 7.15 0.00 36.91 3.57
7695 8219 5.813672 GCATGGAAGGTTTACATTCTACGTA 59.186 40.000 7.15 0.00 36.91 3.57
7696 8220 6.482308 GCATGGAAGGTTTACATTCTACGTAT 59.518 38.462 7.15 0.00 36.91 3.06
7697 8221 7.654520 GCATGGAAGGTTTACATTCTACGTATA 59.345 37.037 7.15 0.00 36.91 1.47
7698 8222 9.706691 CATGGAAGGTTTACATTCTACGTATAT 57.293 33.333 7.15 0.00 36.91 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.803426 CGTGAGGGAGCTCGTGCC 62.803 72.222 7.83 3.27 40.80 5.01
45 46 4.803426 GGTGCTCCTCGCCGTGAG 62.803 72.222 1.65 1.65 44.83 3.51
58 59 3.677648 CTGGTGGCAGCTTGGTGC 61.678 66.667 18.53 15.41 43.19 5.01
59 60 3.677648 GCTGGTGGCAGCTTGGTG 61.678 66.667 18.53 4.35 44.31 4.17
60 61 4.982701 GGCTGGTGGCAGCTTGGT 62.983 66.667 18.53 0.00 46.69 3.67
61 62 4.673375 AGGCTGGTGGCAGCTTGG 62.673 66.667 18.53 9.08 46.69 3.61
62 63 3.371063 CAGGCTGGTGGCAGCTTG 61.371 66.667 18.53 11.54 46.10 4.01
63 64 3.894638 ACAGGCTGGTGGCAGCTT 61.895 61.111 20.34 0.00 46.69 3.74
64 65 4.655647 CACAGGCTGGTGGCAGCT 62.656 66.667 20.34 0.00 46.69 4.24
66 67 4.960866 TGCACAGGCTGGTGGCAG 62.961 66.667 20.34 2.44 44.01 4.85
68 69 4.962836 AGTGCACAGGCTGGTGGC 62.963 66.667 21.04 18.72 41.91 5.01
69 70 2.670934 GAGTGCACAGGCTGGTGG 60.671 66.667 21.04 9.03 41.91 4.61
70 71 2.670934 GGAGTGCACAGGCTGGTG 60.671 66.667 21.04 15.02 41.91 4.17
71 72 4.320456 CGGAGTGCACAGGCTGGT 62.320 66.667 21.04 1.28 41.91 4.00
82 83 4.374702 GTGCGTTGCAGCGGAGTG 62.375 66.667 24.49 0.00 40.08 3.51
154 155 4.953868 TTGGTGACCGGCGTGTCG 62.954 66.667 18.81 2.16 38.11 4.35
155 156 2.781595 ATCTTGGTGACCGGCGTGTC 62.782 60.000 17.77 17.77 35.77 3.67
156 157 2.781595 GATCTTGGTGACCGGCGTGT 62.782 60.000 6.01 2.99 0.00 4.49
157 158 2.047274 ATCTTGGTGACCGGCGTG 60.047 61.111 6.01 0.00 0.00 5.34
158 159 2.264794 GATCTTGGTGACCGGCGT 59.735 61.111 6.01 0.00 0.00 5.68
159 160 2.511600 GGATCTTGGTGACCGGCG 60.512 66.667 0.00 0.00 0.00 6.46
160 161 2.511600 CGGATCTTGGTGACCGGC 60.512 66.667 0.00 0.00 41.41 6.13
161 162 2.511600 GCGGATCTTGGTGACCGG 60.512 66.667 0.00 0.00 44.61 5.28
578 579 2.872557 CATGAGCCACAGCAACGG 59.127 61.111 0.00 0.00 43.56 4.44
579 580 2.177531 GCATGAGCCACAGCAACG 59.822 61.111 0.00 0.00 43.56 4.10
629 630 9.605275 TGATGTCAAAAACAAAATCCAATGTAA 57.395 25.926 0.00 0.00 42.37 2.41
657 658 6.460399 GCATCCACCAAAAGTTTAACTACACA 60.460 38.462 0.00 0.00 0.00 3.72
658 659 5.918576 GCATCCACCAAAAGTTTAACTACAC 59.081 40.000 0.00 0.00 0.00 2.90
674 675 1.820519 TCAAGCATTTGAGCATCCACC 59.179 47.619 0.00 0.00 38.37 4.61
687 688 2.776536 AGATAGCTCCCAACTCAAGCAT 59.223 45.455 0.00 0.00 38.51 3.79
767 768 3.362831 GTCACACAACCATAGTTCGTACG 59.637 47.826 9.53 9.53 32.45 3.67
794 796 7.682593 TGAAAGCATGTTCGCATTATAAATG 57.317 32.000 0.00 0.00 35.23 2.32
802 804 4.377635 GCAAATTTGAAAGCATGTTCGCAT 60.378 37.500 22.31 0.00 38.60 4.73
803 805 3.059733 GCAAATTTGAAAGCATGTTCGCA 60.060 39.130 22.31 0.00 0.00 5.10
817 819 6.128849 CCGGTAAAATGTCTTCTGCAAATTTG 60.129 38.462 14.03 14.03 0.00 2.32
830 832 4.662145 CAAAGCAGATCCGGTAAAATGTC 58.338 43.478 0.00 0.00 0.00 3.06
946 948 1.001393 ACGGCGGAATGGAATGGTT 60.001 52.632 13.24 0.00 0.00 3.67
1028 1030 0.390735 CCGGGGTTAGAACTTGGACG 60.391 60.000 0.00 0.00 0.00 4.79
1068 1070 2.917751 GGATCGGGCGGGAGATCA 60.918 66.667 7.59 0.00 43.61 2.92
1397 1399 6.399249 CGTTTCAAACTCAGCTAATTTGCATG 60.399 38.462 14.27 9.22 34.09 4.06
1480 1504 2.866156 TGCATCGCATACTCTTAACAGC 59.134 45.455 0.00 0.00 31.71 4.40
1551 1575 5.169992 TGATCCAATATCACCTATGGCAG 57.830 43.478 0.00 0.00 0.00 4.85
1552 1576 5.581350 TTGATCCAATATCACCTATGGCA 57.419 39.130 0.00 0.00 0.00 4.92
1553 1577 5.105997 GCTTTGATCCAATATCACCTATGGC 60.106 44.000 0.00 0.00 0.00 4.40
1554 1578 6.005823 TGCTTTGATCCAATATCACCTATGG 58.994 40.000 0.00 0.00 0.00 2.74
1555 1579 6.713903 AGTGCTTTGATCCAATATCACCTATG 59.286 38.462 0.00 0.00 0.00 2.23
1568 1592 9.780413 CTTTAAATTTCTCTAGTGCTTTGATCC 57.220 33.333 0.00 0.00 0.00 3.36
1634 1658 3.181507 CCATTTGCAACGAGTCATGGTAG 60.182 47.826 14.79 0.00 0.00 3.18
1699 1723 1.821936 CAAGCCCTGCACCAAAACA 59.178 52.632 0.00 0.00 0.00 2.83
1730 1754 2.557490 GTGGACGGGAGGAGTATATGAC 59.443 54.545 0.00 0.00 0.00 3.06
1743 1767 6.693315 AAACATCTTATATTTGTGGACGGG 57.307 37.500 0.00 0.00 0.00 5.28
1945 1973 6.505044 TCTGTGATAGTTTAGTCGTGCTTA 57.495 37.500 0.00 0.00 0.00 3.09
1987 2015 9.575783 GCTATTTATGTACTATAGCCTTCTCAC 57.424 37.037 0.00 0.00 40.38 3.51
2065 2093 6.284459 CCTCACATCAGGGAATAACTCTAAC 58.716 44.000 0.00 0.00 0.00 2.34
2085 2113 0.105913 GACCAAACCCCAAACCCTCA 60.106 55.000 0.00 0.00 0.00 3.86
2095 2123 1.226746 CTCACAAGACGACCAAACCC 58.773 55.000 0.00 0.00 0.00 4.11
2105 2133 2.628657 AGGGTGTACAGACTCACAAGAC 59.371 50.000 0.00 0.00 36.43 3.01
2116 2144 7.042725 CGTTTCACATTATATGAGGGTGTACAG 60.043 40.741 0.00 0.00 0.00 2.74
2123 2151 8.833231 ATTCTACGTTTCACATTATATGAGGG 57.167 34.615 0.00 0.00 0.00 4.30
2126 2154 9.929722 GCAAATTCTACGTTTCACATTATATGA 57.070 29.630 0.00 0.00 0.00 2.15
2138 2166 3.341857 TTGCGTGCAAATTCTACGTTT 57.658 38.095 4.52 0.00 39.79 3.60
2153 2181 2.296190 GGAGACCCAGAAAATTTTGCGT 59.704 45.455 8.47 0.00 0.00 5.24
2155 2183 5.921962 ATAGGAGACCCAGAAAATTTTGC 57.078 39.130 8.47 0.42 33.88 3.68
2167 2195 8.476447 GGTAAGCATAATAACTATAGGAGACCC 58.524 40.741 4.43 0.00 0.00 4.46
2182 2210 9.519191 TGCATAATGTAGAATGGTAAGCATAAT 57.481 29.630 0.00 0.00 0.00 1.28
2220 2248 4.561938 CCCACCTTTGTTCGTAGATGTACA 60.562 45.833 0.00 0.00 35.04 2.90
2224 2252 3.328382 TCCCACCTTTGTTCGTAGATG 57.672 47.619 0.00 0.00 35.04 2.90
2226 2254 2.701951 ACTTCCCACCTTTGTTCGTAGA 59.298 45.455 0.00 0.00 0.00 2.59
2230 2258 2.294074 TGAACTTCCCACCTTTGTTCG 58.706 47.619 0.00 0.00 39.61 3.95
2276 2308 6.400409 CGCGTATGCTAATCTCGTAGTAGTAA 60.400 42.308 5.20 0.00 39.65 2.24
2277 2309 5.061435 CGCGTATGCTAATCTCGTAGTAGTA 59.939 44.000 5.20 0.00 39.65 1.82
2298 2330 8.289440 TGTTATATTTTAGGTCTGAATACGCG 57.711 34.615 3.53 3.53 0.00 6.01
2332 2364 7.766278 ACATGTTCATCTACCTTGATACAAGAC 59.234 37.037 12.25 2.08 0.00 3.01
2341 2373 7.864108 TTGGATAACATGTTCATCTACCTTG 57.136 36.000 15.85 0.00 0.00 3.61
2406 2438 8.865590 AGATAGCGAATAGAGTTTTCTTCTTC 57.134 34.615 0.00 0.00 34.79 2.87
2463 2497 5.571357 GCACGAGGGTATTTTACAACATTTG 59.429 40.000 0.00 0.00 0.00 2.32
2471 2505 1.662122 CGTGGCACGAGGGTATTTTAC 59.338 52.381 34.85 0.00 46.05 2.01
2483 2517 1.299850 TCAGAACTGTCGTGGCACG 60.300 57.895 32.75 32.75 44.19 5.34
2487 2521 2.821546 TCTTTGTCAGAACTGTCGTGG 58.178 47.619 1.73 0.00 0.00 4.94
2489 2523 4.051922 GTCATCTTTGTCAGAACTGTCGT 58.948 43.478 1.73 0.00 34.16 4.34
2492 2526 4.422073 TGGTCATCTTTGTCAGAACTGT 57.578 40.909 1.73 0.00 34.16 3.55
2595 2629 2.360350 CCAGCATGCCCGTGTTCT 60.360 61.111 15.66 0.00 31.97 3.01
2720 2755 7.932335 ACATCGTAAAACCAATTAGTGACAAA 58.068 30.769 0.00 0.00 0.00 2.83
2860 2896 4.122776 ACAGATGATCAACGGCTTCATAC 58.877 43.478 0.00 0.00 30.48 2.39
2906 2943 2.094390 GCATGCTCAATGGCTCTTTTCA 60.094 45.455 11.37 0.00 36.71 2.69
2976 3022 1.029408 TTTTGGTGTGAGTGCGTGCT 61.029 50.000 0.00 0.00 0.00 4.40
3079 3125 0.679640 TCCGCAAAATAGCACTGGGG 60.680 55.000 0.00 0.00 42.85 4.96
3093 3139 3.319689 TCAACCATTCGATATACTCCGCA 59.680 43.478 0.00 0.00 0.00 5.69
3111 3157 9.422196 GTAGCGACAAATAATGAATAACTCAAC 57.578 33.333 0.00 0.00 37.67 3.18
3305 3351 1.522668 CGTTGCCAGTTCCAAGATCA 58.477 50.000 0.00 0.00 0.00 2.92
3562 3615 3.028850 TGGGTATTTCGGGAGTAGTCTG 58.971 50.000 0.00 0.00 0.00 3.51
3571 3624 3.560636 ACTGAGAATGGGTATTTCGGG 57.439 47.619 0.00 0.00 0.00 5.14
3661 3714 7.784073 TGATCTTCAAAATCCATAATAAGGGCA 59.216 33.333 0.00 0.00 0.00 5.36
3674 3727 9.577110 TTCTGCAAACATATGATCTTCAAAATC 57.423 29.630 10.38 0.00 0.00 2.17
3715 3768 9.546428 CCTGTTAAATCTGAAAACCTGAAAATT 57.454 29.630 0.00 0.00 0.00 1.82
3716 3769 8.923270 TCCTGTTAAATCTGAAAACCTGAAAAT 58.077 29.630 0.00 0.00 0.00 1.82
3760 3813 2.802247 GTTTCTTGCAAGTTCAATGGCC 59.198 45.455 25.19 0.00 0.00 5.36
3885 3939 6.474751 ACAAAGTGTAGACTTCGTAGACAAAC 59.525 38.462 5.63 0.00 41.87 2.93
3949 4003 8.198109 TCTCTTTGAGGCTACAGAATATGTAAC 58.802 37.037 0.00 0.00 43.78 2.50
3968 4022 5.177511 TGTTGTCATACGCTCTTTCTCTTTG 59.822 40.000 0.00 0.00 0.00 2.77
3972 4026 5.786401 ATTGTTGTCATACGCTCTTTCTC 57.214 39.130 0.00 0.00 0.00 2.87
3982 4036 8.480643 AGTGAAAGTAGCTATTGTTGTCATAC 57.519 34.615 0.00 0.00 0.00 2.39
4013 4067 3.373439 TCTCGTTTAGCTAAGACTCGTCC 59.627 47.826 6.24 0.00 0.00 4.79
4054 4108 9.931210 ATTCTTAGTAAGTGTTTGTTCTTTTCG 57.069 29.630 9.71 0.00 0.00 3.46
4133 4191 8.458573 TGGTCTTTCATGCTTTTACTTTTAGA 57.541 30.769 0.00 0.00 0.00 2.10
4198 4257 5.914033 TCTGCCACAAACTGGATATAGTAC 58.086 41.667 0.00 0.00 43.95 2.73
4202 4261 7.517320 ACATTATCTGCCACAAACTGGATATA 58.483 34.615 0.00 0.00 43.95 0.86
4213 4272 5.781210 TTTTGTTGACATTATCTGCCACA 57.219 34.783 0.00 0.00 0.00 4.17
4249 4308 5.198602 AGGGCTGAATACATTTTCTTCCT 57.801 39.130 0.00 0.00 0.00 3.36
4333 4392 8.807948 ACATGCAAACTACCACTAGATATTTT 57.192 30.769 0.00 0.00 0.00 1.82
4394 4453 3.004629 TGCATGGCAAGTACAAAGTTGAG 59.995 43.478 0.00 0.00 38.14 3.02
4515 4575 7.359262 TGTTGTATGAACTTTTCCTATGTCG 57.641 36.000 0.00 0.00 0.00 4.35
4555 4615 4.434520 TGTGTTGTTTCACGACTATGTCA 58.565 39.130 0.00 0.00 40.74 3.58
4563 4623 6.377780 CATTGGAATATGTGTTGTTTCACGA 58.622 36.000 0.00 0.00 40.74 4.35
4569 4629 5.680594 ATGGCATTGGAATATGTGTTGTT 57.319 34.783 0.00 0.00 0.00 2.83
4628 4688 5.634118 TCATCCACTTCCACTTCAGAAAAT 58.366 37.500 0.00 0.00 0.00 1.82
4647 4707 0.104304 ACCCCTACGACGCATTCATC 59.896 55.000 0.00 0.00 0.00 2.92
4679 4739 2.125912 CAGAGCCCTCACCGAACG 60.126 66.667 0.00 0.00 0.00 3.95
4700 4760 1.644786 GCTAATGAACAAGCCCGCGT 61.645 55.000 4.92 0.00 32.40 6.01
4817 4901 2.220586 TGGTCCACGGCATCCTTCA 61.221 57.895 0.00 0.00 0.00 3.02
4880 4964 2.103143 CTCGCTCGACGCATCCTT 59.897 61.111 7.47 0.00 43.23 3.36
4887 4971 4.753877 TGTTCGGCTCGCTCGACG 62.754 66.667 2.75 0.00 45.62 5.12
4888 4972 3.173240 GTGTTCGGCTCGCTCGAC 61.173 66.667 2.75 1.09 36.30 4.20
4889 4973 3.666253 TGTGTTCGGCTCGCTCGA 61.666 61.111 0.00 0.00 34.62 4.04
4892 4976 2.356313 CAGTGTGTTCGGCTCGCT 60.356 61.111 0.00 0.00 32.35 4.93
4952 5039 2.741092 GGTGGTCAAGCTCGTCCA 59.259 61.111 0.00 0.00 0.00 4.02
5079 5166 1.326213 CCGAGGCTGTCTGTCATCCT 61.326 60.000 0.00 0.00 44.27 3.24
5083 5170 2.203640 ACCCGAGGCTGTCTGTCA 60.204 61.111 0.00 0.00 0.00 3.58
5136 5223 3.008049 GGAACTCTTAGAGGCAAAGGACA 59.992 47.826 14.24 0.00 33.35 4.02
5142 5229 2.567615 GACTGGGAACTCTTAGAGGCAA 59.432 50.000 14.24 0.00 33.35 4.52
5149 5236 1.480954 GGCATCGACTGGGAACTCTTA 59.519 52.381 0.00 0.00 0.00 2.10
5193 5280 1.526917 CCGCCTCCATCCACCATTC 60.527 63.158 0.00 0.00 0.00 2.67
5194 5281 2.597340 CCGCCTCCATCCACCATT 59.403 61.111 0.00 0.00 0.00 3.16
5236 5323 1.185315 AAATGTCCAGCCCCAAATCG 58.815 50.000 0.00 0.00 0.00 3.34
5237 5324 3.701205 AAAAATGTCCAGCCCCAAATC 57.299 42.857 0.00 0.00 0.00 2.17
5289 5379 1.065926 GGACATGTCTGCCACATCAGA 60.066 52.381 24.50 0.00 44.60 3.27
5294 5384 0.602638 GAACGGACATGTCTGCCACA 60.603 55.000 30.48 0.00 39.55 4.17
5300 5390 1.296715 GGGCTGAACGGACATGTCT 59.703 57.895 24.50 5.76 0.00 3.41
5312 5402 1.151810 GGGGAGGATATGGGGCTGA 60.152 63.158 0.00 0.00 0.00 4.26
5364 5454 2.821969 CAAACCTCTCCATTTGTCTGGG 59.178 50.000 0.00 0.00 36.89 4.45
5448 5543 1.152440 ATCTCCTACAGCCCTCCCG 60.152 63.158 0.00 0.00 0.00 5.14
5457 5552 5.456619 CCATTTGATAAGGGCATCTCCTACA 60.457 44.000 0.00 0.00 35.80 2.74
5491 5586 5.049954 TCGTCAAAACACCATAACTGTAAGC 60.050 40.000 0.00 0.00 37.60 3.09
5540 5635 2.735151 AGTACATCATCGACCTGGTGA 58.265 47.619 2.82 2.46 31.49 4.02
5656 5751 2.422832 AGAATGACCGAGTCGTAGTTCC 59.577 50.000 12.31 0.00 34.95 3.62
5725 5821 4.357018 TCCGCAGCTATAGATAATCACG 57.643 45.455 3.21 0.00 0.00 4.35
5733 5829 9.502091 AACAATATTTAATTCCGCAGCTATAGA 57.498 29.630 3.21 0.00 0.00 1.98
5735 5831 9.278978 TCAACAATATTTAATTCCGCAGCTATA 57.721 29.630 0.00 0.00 0.00 1.31
5793 5889 8.045176 ACTCTAGTATGCAAAATTTGAAGGTC 57.955 34.615 10.26 0.00 0.00 3.85
5825 5921 4.759183 CCTAATGCTTCCAGATTTCTAGCC 59.241 45.833 0.00 0.00 0.00 3.93
6002 6098 2.443887 AAATCAACATGGTGTGCTGC 57.556 45.000 11.27 0.00 0.00 5.25
6059 6155 7.175347 ACCTATCCTGTATGTGCATATACTG 57.825 40.000 27.36 25.81 35.16 2.74
6060 6156 7.798710 AACCTATCCTGTATGTGCATATACT 57.201 36.000 27.36 14.24 35.16 2.12
6300 6796 4.283978 TCAATTCTACGGGACTGGTGTAAA 59.716 41.667 0.00 0.00 0.00 2.01
6420 6916 1.510383 CTCTGTCTGCGTCCTCCTG 59.490 63.158 0.00 0.00 0.00 3.86
6575 7071 7.671302 ACAAGAGCTACAACATAGAGAGAAAA 58.329 34.615 0.00 0.00 0.00 2.29
6594 7090 7.226325 CCTGAGGATAAAATTGAGCTACAAGAG 59.774 40.741 0.00 0.00 42.02 2.85
6595 7091 7.050377 CCTGAGGATAAAATTGAGCTACAAGA 58.950 38.462 0.00 0.00 42.02 3.02
6596 7092 6.825721 ACCTGAGGATAAAATTGAGCTACAAG 59.174 38.462 4.99 0.00 42.02 3.16
6701 7197 3.120199 CCCTCTTGTTCGTTTGCACTATG 60.120 47.826 0.00 0.00 0.00 2.23
6702 7198 3.074412 CCCTCTTGTTCGTTTGCACTAT 58.926 45.455 0.00 0.00 0.00 2.12
6708 7204 1.260561 CGTGTCCCTCTTGTTCGTTTG 59.739 52.381 0.00 0.00 0.00 2.93
6718 7214 2.217510 ACAGTACATCGTGTCCCTCT 57.782 50.000 0.00 0.00 0.00 3.69
6759 7255 6.316140 GGGAAAATCTATGAAAATGGGCAAAC 59.684 38.462 0.00 0.00 0.00 2.93
6778 7276 7.964666 TTCTCTTTGGAAAAAGTAGGGAAAA 57.035 32.000 0.00 0.00 0.00 2.29
6786 7284 3.888930 TCCGCATTCTCTTTGGAAAAAGT 59.111 39.130 0.00 0.00 0.00 2.66
6806 7304 1.301953 ACCGGGCACTAAAACGTCC 60.302 57.895 6.32 0.00 0.00 4.79
6831 7329 5.990996 AGTGAAAATTTTGTGCCCAACTATG 59.009 36.000 8.47 0.00 0.00 2.23
6832 7330 5.990996 CAGTGAAAATTTTGTGCCCAACTAT 59.009 36.000 8.47 0.00 0.00 2.12
6836 7334 2.941720 GCAGTGAAAATTTTGTGCCCAA 59.058 40.909 8.47 0.00 0.00 4.12
6878 7377 0.533755 AGGCAAGTGTGAGTGAGTGC 60.534 55.000 0.00 0.00 0.00 4.40
6988 7489 4.449743 TCCGTAGAATTGTACACAAAGCAC 59.550 41.667 12.72 0.00 39.55 4.40
7057 7561 1.198713 AGGGAGATCAACGCTGTCAT 58.801 50.000 8.26 0.00 0.00 3.06
7058 7562 1.847328 TAGGGAGATCAACGCTGTCA 58.153 50.000 15.76 0.00 32.98 3.58
7060 7564 1.207329 GGTTAGGGAGATCAACGCTGT 59.793 52.381 15.76 0.00 32.98 4.40
7067 7571 3.706389 TGGATGAGGTTAGGGAGATCA 57.294 47.619 0.00 0.00 0.00 2.92
7108 7615 2.092914 CAGGGAGAATGGTGGTTAGGTC 60.093 54.545 0.00 0.00 0.00 3.85
7179 7686 1.534959 AGGACTCACAGAGCCTGCA 60.535 57.895 8.52 0.00 35.82 4.41
7258 7765 6.881065 CCCTCAGTTTCAATCAGAATGTAAGA 59.119 38.462 0.00 0.00 35.83 2.10
7283 7790 5.694910 CCCATGTCCAGTCACGTATATAAAC 59.305 44.000 0.00 0.00 0.00 2.01
7336 7845 3.023832 CCAACACCAGGTCTGTCTTTTT 58.976 45.455 0.00 0.00 0.00 1.94
7337 7846 2.654863 CCAACACCAGGTCTGTCTTTT 58.345 47.619 0.00 0.00 0.00 2.27
7338 7847 1.750682 GCCAACACCAGGTCTGTCTTT 60.751 52.381 0.00 0.00 0.00 2.52
7339 7848 0.179018 GCCAACACCAGGTCTGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
7340 7849 1.056700 AGCCAACACCAGGTCTGTCT 61.057 55.000 0.00 0.00 0.00 3.41
7341 7850 0.886490 CAGCCAACACCAGGTCTGTC 60.886 60.000 0.00 0.00 0.00 3.51
7342 7851 1.149174 CAGCCAACACCAGGTCTGT 59.851 57.895 0.00 0.00 0.00 3.41
7343 7852 0.396435 TACAGCCAACACCAGGTCTG 59.604 55.000 4.07 4.07 36.78 3.51
7344 7853 0.396811 GTACAGCCAACACCAGGTCT 59.603 55.000 0.00 0.00 0.00 3.85
7345 7854 0.605589 GGTACAGCCAACACCAGGTC 60.606 60.000 0.00 0.00 37.17 3.85
7346 7855 1.454539 GGTACAGCCAACACCAGGT 59.545 57.895 0.00 0.00 37.17 4.00
7347 7856 1.671054 CGGTACAGCCAACACCAGG 60.671 63.158 0.00 0.00 36.97 4.45
7348 7857 0.036388 ATCGGTACAGCCAACACCAG 60.036 55.000 0.00 0.00 36.97 4.00
7349 7858 0.321210 CATCGGTACAGCCAACACCA 60.321 55.000 0.00 0.00 36.97 4.17
7350 7859 1.024579 CCATCGGTACAGCCAACACC 61.025 60.000 0.00 0.00 36.97 4.16
7357 7866 0.940126 CATTGCTCCATCGGTACAGC 59.060 55.000 0.00 0.00 0.00 4.40
7413 7922 1.689813 TGTTCAGAACAGCCGGAGTTA 59.310 47.619 12.24 0.00 36.25 2.24
7508 8017 6.407202 ACTGAATCATGTAACCTGGTTAGAC 58.593 40.000 19.25 12.04 0.00 2.59
7514 8023 5.350504 AGAGACTGAATCATGTAACCTGG 57.649 43.478 0.00 0.00 0.00 4.45
7637 8146 3.243068 CCAACTAGCGCATATTTGTTCCC 60.243 47.826 11.47 0.00 0.00 3.97
7644 8153 2.810274 CTGCATCCAACTAGCGCATATT 59.190 45.455 11.47 0.00 31.10 1.28
7652 8161 1.284657 CTCGTGCTGCATCCAACTAG 58.715 55.000 5.27 0.00 0.00 2.57
7668 8177 3.941483 AGAATGTAAACCTTCCATGCTCG 59.059 43.478 0.00 0.00 0.00 5.03
7692 8216 3.168963 CCATCGCCGTAAGTGATATACG 58.831 50.000 0.00 0.00 44.03 3.06
7693 8217 2.921754 GCCATCGCCGTAAGTGATATAC 59.078 50.000 0.00 0.00 44.03 1.47
7694 8218 2.559231 TGCCATCGCCGTAAGTGATATA 59.441 45.455 0.00 0.00 44.03 0.86
7695 8219 1.343142 TGCCATCGCCGTAAGTGATAT 59.657 47.619 0.00 0.00 44.03 1.63
7696 8220 0.747852 TGCCATCGCCGTAAGTGATA 59.252 50.000 0.00 0.00 44.03 2.15
7697 8221 0.107897 TTGCCATCGCCGTAAGTGAT 60.108 50.000 0.00 0.00 46.87 3.06
7698 8222 0.107897 ATTGCCATCGCCGTAAGTGA 60.108 50.000 0.00 0.00 39.91 3.41


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

AutoCloner maintained by Alex Coulton.