Multiple sequence alignment - TraesCS2A01G418700

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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 TraesCS2A01G418700 chr2A 100.000 2429 0 0 1 2429 674416047 674418475 0.000000e+00 4486.0
1 TraesCS2A01G418700 chr2A 86.823 683 62 10 1027 1704 674491884 674492543 0.000000e+00 737.0
2 TraesCS2A01G418700 chr2A 77.240 413 55 21 745 1134 674491482 674491878 3.170000e-49 206.0
3 TraesCS2A01G418700 chr2D 90.181 937 65 16 1 930 529648374 529649290 0.000000e+00 1195.0
4 TraesCS2A01G418700 chr2D 92.764 539 20 4 914 1452 529650777 529651296 0.000000e+00 761.0
5 TraesCS2A01G418700 chr2D 85.714 84 11 1 2286 2368 529615330 529615413 1.200000e-13 87.9
6 TraesCS2A01G418700 chr2B 88.631 862 56 27 1 856 629655422 629656247 0.000000e+00 1011.0
7 TraesCS2A01G418700 chr2B 93.813 598 31 3 856 1452 629657695 629658287 0.000000e+00 894.0
8 TraesCS2A01G418700 chr2B 80.597 335 42 11 1756 2077 629691645 629691969 1.120000e-58 237.0
9 TraesCS2A01G418700 chr2B 90.055 181 12 5 1461 1636 629691207 629691386 1.880000e-56 230.0
10 TraesCS2A01G418700 chr1D 85.135 148 13 5 2149 2288 6311325 6311471 2.520000e-30 143.0
11 TraesCS2A01G418700 chr6B 82.558 86 7 7 439 520 711414387 711414306 4.330000e-08 69.4
12 TraesCS2A01G418700 chr6B 78.641 103 13 9 426 524 710929121 710929024 2.610000e-05 60.2
13 TraesCS2A01G418700 chr6B 78.788 99 12 9 426 520 710915560 710915467 9.380000e-05 58.4
14 TraesCS2A01G418700 chr6B 78.431 102 13 9 426 523 710942825 710942729 9.380000e-05 58.4
15 TraesCS2A01G418700 chr4A 94.595 37 1 1 2147 2182 602645257 602645221 3.370000e-04 56.5


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 TraesCS2A01G418700 chr2A 674416047 674418475 2428 False 4486.0 4486 100.0000 1 2429 1 chr2A.!!$F1 2428
1 TraesCS2A01G418700 chr2A 674491482 674492543 1061 False 471.5 737 82.0315 745 1704 2 chr2A.!!$F2 959
2 TraesCS2A01G418700 chr2D 529648374 529651296 2922 False 978.0 1195 91.4725 1 1452 2 chr2D.!!$F2 1451
3 TraesCS2A01G418700 chr2B 629655422 629658287 2865 False 952.5 1011 91.2220 1 1452 2 chr2B.!!$F1 1451
4 TraesCS2A01G418700 chr2B 629691207 629691969 762 False 233.5 237 85.3260 1461 2077 2 chr2B.!!$F2 616

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
966 3940 1.743772 CGGCTCGATTCCCTCAACAAT 60.744 52.381 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 5196 0.033011 AGCTACGAGAGGATGGGTGT 60.033 55.0 0.0 0.0 0.0 4.16 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
69 71 7.725397 AGATTGGTGGCTATATTTAGAATGCAA 59.275 33.333 0.00 0.00 0.00 4.08
189 201 9.991388 AGACATTTTCAAATTTGTGAACAATTG 57.009 25.926 17.47 3.24 37.24 2.32
197 209 9.766277 TCAAATTTGTGAACAATTGTTTAAAGC 57.234 25.926 24.02 11.92 38.56 3.51
198 210 8.723260 CAAATTTGTGAACAATTGTTTAAAGCG 58.277 29.630 24.02 13.36 38.56 4.68
199 211 6.952935 TTTGTGAACAATTGTTTAAAGCGT 57.047 29.167 24.02 0.00 38.56 5.07
200 212 5.940603 TGTGAACAATTGTTTAAAGCGTG 57.059 34.783 24.02 0.00 38.56 5.34
201 213 5.403246 TGTGAACAATTGTTTAAAGCGTGT 58.597 33.333 24.02 0.00 38.56 4.49
341 355 7.303998 GGATCATTTCTTGAAACTCTGAACAG 58.696 38.462 0.00 0.00 38.03 3.16
546 563 6.331369 TCCCAGACATTTTTAGAAAGCAAG 57.669 37.500 0.00 0.00 0.00 4.01
623 640 9.971922 CTCAGAACCATTTTTGAAACTCTTAAT 57.028 29.630 0.00 0.00 0.00 1.40
896 2365 3.118482 TCTGCTCCCAATCTCAATCTCAC 60.118 47.826 0.00 0.00 0.00 3.51
897 2366 2.208431 GCTCCCAATCTCAATCTCACG 58.792 52.381 0.00 0.00 0.00 4.35
898 2367 2.159043 GCTCCCAATCTCAATCTCACGA 60.159 50.000 0.00 0.00 0.00 4.35
899 2368 3.715495 CTCCCAATCTCAATCTCACGAG 58.285 50.000 0.00 0.00 0.00 4.18
900 2369 2.432146 TCCCAATCTCAATCTCACGAGG 59.568 50.000 0.00 0.00 0.00 4.63
902 2371 3.369892 CCCAATCTCAATCTCACGAGGTT 60.370 47.826 0.00 0.00 32.77 3.50
903 2372 4.256920 CCAATCTCAATCTCACGAGGTTT 58.743 43.478 0.00 0.00 30.07 3.27
941 3912 4.090057 GCGACACGAAAGCAGCCC 62.090 66.667 0.00 0.00 0.00 5.19
966 3940 1.743772 CGGCTCGATTCCCTCAACAAT 60.744 52.381 0.00 0.00 0.00 2.71
1024 4001 3.212685 GCAGAAGAGGATTGGATTCCAG 58.787 50.000 5.36 0.00 38.32 3.86
1094 4128 4.142881 GGAACTTCTAAACGAGATGCAACC 60.143 45.833 0.00 0.00 33.52 3.77
1135 4226 2.571548 CGGGCAGCAGAGGATTTTT 58.428 52.632 0.00 0.00 0.00 1.94
1154 4245 1.882912 TTGATCGAGCTGCAACAAGT 58.117 45.000 0.90 0.00 0.00 3.16
1379 4473 1.075836 CCACGGTGGAAATTCCCCA 59.924 57.895 22.77 0.00 40.96 4.96
1511 4627 6.183360 CGCTAGTCTTGTGAGAAATCGATTTT 60.183 38.462 23.49 13.67 32.66 1.82
1512 4628 7.522374 GCTAGTCTTGTGAGAAATCGATTTTT 58.478 34.615 23.49 18.45 32.66 1.94
1589 4707 3.305335 GGGATTGATTGTCTTTGCGTGTT 60.305 43.478 0.00 0.00 0.00 3.32
1594 4712 3.127721 TGATTGTCTTTGCGTGTTTGACA 59.872 39.130 0.00 0.00 36.10 3.58
1608 4729 6.075572 GCGTGTTTGACAAGTTTCTTTGTATC 60.076 38.462 0.00 0.00 41.15 2.24
1626 4747 1.051008 TCTCACCATCGGATCCATGG 58.949 55.000 28.02 28.02 45.74 3.66
1644 4765 4.333649 CCATGGCAAGTAATGTACTGTCTG 59.666 45.833 0.00 0.00 39.39 3.51
1653 4774 6.994221 AGTAATGTACTGTCTGCTTTGTACT 58.006 36.000 0.00 0.00 37.69 2.73
1676 4797 4.685169 ACTGACAAATTGATTAGGCACG 57.315 40.909 0.00 0.00 0.00 5.34
1692 4813 1.950472 CACGGCGTGTTGAAATCTTC 58.050 50.000 30.56 0.00 0.00 2.87
1707 4828 6.947464 TGAAATCTTCGTCCTTCTTATCCTT 58.053 36.000 0.00 0.00 0.00 3.36
1714 4835 8.414778 TCTTCGTCCTTCTTATCCTTCTTATTC 58.585 37.037 0.00 0.00 0.00 1.75
1723 4844 8.302515 TCTTATCCTTCTTATTCGGTGTAACT 57.697 34.615 0.00 0.00 36.74 2.24
1729 4850 6.350277 CCTTCTTATTCGGTGTAACTCACTCT 60.350 42.308 0.00 0.00 45.50 3.24
1730 4851 6.192234 TCTTATTCGGTGTAACTCACTCTC 57.808 41.667 0.00 0.00 45.50 3.20
1731 4852 5.944599 TCTTATTCGGTGTAACTCACTCTCT 59.055 40.000 0.00 0.00 45.50 3.10
1732 4853 4.705337 ATTCGGTGTAACTCACTCTCTC 57.295 45.455 0.00 0.00 45.50 3.20
1733 4854 2.434428 TCGGTGTAACTCACTCTCTCC 58.566 52.381 0.00 0.00 45.50 3.71
1734 4855 2.040012 TCGGTGTAACTCACTCTCTCCT 59.960 50.000 0.00 0.00 45.50 3.69
1737 4858 4.095185 CGGTGTAACTCACTCTCTCCTAAG 59.905 50.000 0.00 0.00 45.50 2.18
1739 4860 5.355910 GGTGTAACTCACTCTCTCCTAAGAG 59.644 48.000 0.00 0.00 44.92 2.85
1752 4873 2.685387 CTAAGAGCTACAGCCGGGCG 62.685 65.000 14.39 11.21 43.38 6.13
1754 4875 3.524606 GAGCTACAGCCGGGCGTA 61.525 66.667 14.39 16.72 43.38 4.42
1759 5048 2.143594 CTACAGCCGGGCGTATCCTC 62.144 65.000 14.39 0.00 34.39 3.71
1760 5049 2.635787 TACAGCCGGGCGTATCCTCT 62.636 60.000 14.39 0.00 34.39 3.69
1778 5067 4.063689 CCTCTGATTTTCGATGAGGATGG 58.936 47.826 0.00 0.00 45.07 3.51
1781 5070 4.080919 TCTGATTTTCGATGAGGATGGTGT 60.081 41.667 0.00 0.00 0.00 4.16
1790 5079 0.392998 GAGGATGGTGTGGACGCATT 60.393 55.000 0.00 0.00 0.00 3.56
1797 5086 1.303155 TGTGGACGCATTCATGGCA 60.303 52.632 0.00 0.00 0.00 4.92
1812 5101 4.664677 GCACGTGGTGTCGCTCCT 62.665 66.667 18.88 0.00 35.75 3.69
1813 5102 2.734723 CACGTGGTGTCGCTCCTG 60.735 66.667 7.95 0.00 0.00 3.86
1814 5103 2.910479 ACGTGGTGTCGCTCCTGA 60.910 61.111 0.00 0.00 0.00 3.86
1842 5131 0.322008 GAAGGGCCCAAGTCTGACTG 60.322 60.000 27.56 5.75 0.00 3.51
1843 5132 1.783250 AAGGGCCCAAGTCTGACTGG 61.783 60.000 27.56 13.91 0.00 4.00
1846 5145 2.046892 CCCAAGTCTGACTGGCGG 60.047 66.667 11.71 11.94 0.00 6.13
1884 5183 1.659035 GCATCCCATTTCCCTCCCCT 61.659 60.000 0.00 0.00 0.00 4.79
1886 5185 1.133356 CATCCCATTTCCCTCCCCTTC 60.133 57.143 0.00 0.00 0.00 3.46
1891 5190 2.253403 ATTTCCCTCCCCTTCGCGTC 62.253 60.000 5.77 0.00 0.00 5.19
1907 5206 2.209809 TCCCCACACACCCATCCT 59.790 61.111 0.00 0.00 0.00 3.24
1911 5210 1.219124 CCACACACCCATCCTCTCG 59.781 63.158 0.00 0.00 0.00 4.04
1917 5216 0.671251 CACCCATCCTCTCGTAGCTC 59.329 60.000 0.00 0.00 0.00 4.09
1918 5217 0.820074 ACCCATCCTCTCGTAGCTCG 60.820 60.000 0.00 0.00 41.41 5.03
1919 5218 0.820074 CCCATCCTCTCGTAGCTCGT 60.820 60.000 0.00 0.00 40.80 4.18
1920 5219 0.589223 CCATCCTCTCGTAGCTCGTC 59.411 60.000 0.00 0.00 40.80 4.20
1921 5220 0.233590 CATCCTCTCGTAGCTCGTCG 59.766 60.000 0.00 0.00 40.80 5.12
1922 5221 0.179078 ATCCTCTCGTAGCTCGTCGT 60.179 55.000 0.00 0.00 40.80 4.34
1923 5222 0.390866 TCCTCTCGTAGCTCGTCGTT 60.391 55.000 0.00 0.00 40.80 3.85
1926 5225 1.928769 CTCGTAGCTCGTCGTTCGC 60.929 63.158 0.00 0.00 40.80 4.70
1937 5236 4.749310 CGTTCGCAGCTCTGGCCT 62.749 66.667 3.32 0.00 39.73 5.19
1957 5256 1.479323 TGACAGCGGATAACCACCTAC 59.521 52.381 0.00 0.00 35.59 3.18
1963 5262 2.159254 GCGGATAACCACCTACGTTGTA 60.159 50.000 0.00 0.00 35.59 2.41
1970 5269 2.555757 ACCACCTACGTTGTACTCACTC 59.444 50.000 0.00 0.00 0.00 3.51
1980 5279 2.407428 TACTCACTCTGGAGCGCCG 61.407 63.158 2.29 0.00 38.50 6.46
2000 5301 4.334118 TGCAGATGGGCACAGCGT 62.334 61.111 0.00 0.00 39.25 5.07
2017 5318 3.751246 TGCCGCTTGGATTGCAGC 61.751 61.111 0.00 0.00 34.72 5.25
2018 5319 4.503314 GCCGCTTGGATTGCAGCC 62.503 66.667 0.97 0.97 31.82 4.85
2019 5320 3.063704 CCGCTTGGATTGCAGCCA 61.064 61.111 6.30 6.30 31.82 4.75
2027 5329 1.372087 GGATTGCAGCCACTTCCTCG 61.372 60.000 3.04 0.00 0.00 4.63
2031 5333 2.581354 CAGCCACTTCCTCGGGAG 59.419 66.667 0.00 0.00 31.21 4.30
2065 5367 1.947146 CAGGCGTCGAACACAACGA 60.947 57.895 0.00 0.00 41.29 3.85
2077 5379 0.176680 CACAACGATGGAGGAGGAGG 59.823 60.000 0.00 0.00 0.00 4.30
2078 5380 0.041238 ACAACGATGGAGGAGGAGGA 59.959 55.000 0.00 0.00 0.00 3.71
2079 5381 0.749649 CAACGATGGAGGAGGAGGAG 59.250 60.000 0.00 0.00 0.00 3.69
2080 5382 0.397816 AACGATGGAGGAGGAGGAGG 60.398 60.000 0.00 0.00 0.00 4.30
2081 5383 1.289982 ACGATGGAGGAGGAGGAGGA 61.290 60.000 0.00 0.00 0.00 3.71
2082 5384 0.539438 CGATGGAGGAGGAGGAGGAG 60.539 65.000 0.00 0.00 0.00 3.69
2083 5385 0.856982 GATGGAGGAGGAGGAGGAGA 59.143 60.000 0.00 0.00 0.00 3.71
2084 5386 1.219213 GATGGAGGAGGAGGAGGAGAA 59.781 57.143 0.00 0.00 0.00 2.87
2085 5387 1.093408 TGGAGGAGGAGGAGGAGAAA 58.907 55.000 0.00 0.00 0.00 2.52
2086 5388 1.007721 TGGAGGAGGAGGAGGAGAAAG 59.992 57.143 0.00 0.00 0.00 2.62
2087 5389 1.691163 GGAGGAGGAGGAGGAGAAAGG 60.691 61.905 0.00 0.00 0.00 3.11
2088 5390 0.341609 AGGAGGAGGAGGAGAAAGGG 59.658 60.000 0.00 0.00 0.00 3.95
2089 5391 0.692756 GGAGGAGGAGGAGAAAGGGG 60.693 65.000 0.00 0.00 0.00 4.79
2090 5392 1.307430 AGGAGGAGGAGAAAGGGGC 60.307 63.158 0.00 0.00 0.00 5.80
2091 5393 2.736826 GGAGGAGGAGAAAGGGGCG 61.737 68.421 0.00 0.00 0.00 6.13
2092 5394 2.689034 AGGAGGAGAAAGGGGCGG 60.689 66.667 0.00 0.00 0.00 6.13
2093 5395 2.687566 GGAGGAGAAAGGGGCGGA 60.688 66.667 0.00 0.00 0.00 5.54
2094 5396 2.736826 GGAGGAGAAAGGGGCGGAG 61.737 68.421 0.00 0.00 0.00 4.63
2110 5412 2.978010 AGCCAACGCTTCCGGTTG 60.978 61.111 0.00 0.00 45.55 3.77
2111 5413 4.700365 GCCAACGCTTCCGGTTGC 62.700 66.667 0.00 6.34 35.61 4.17
2112 5414 4.038080 CCAACGCTTCCGGTTGCC 62.038 66.667 0.00 0.00 39.22 4.52
2113 5415 4.038080 CAACGCTTCCGGTTGCCC 62.038 66.667 0.00 0.00 39.22 5.36
2114 5416 4.572571 AACGCTTCCGGTTGCCCA 62.573 61.111 0.00 0.00 39.22 5.36
2115 5417 3.860930 AACGCTTCCGGTTGCCCAT 62.861 57.895 0.00 0.00 39.22 4.00
2116 5418 3.814268 CGCTTCCGGTTGCCCATG 61.814 66.667 0.00 0.00 0.00 3.66
2117 5419 2.676471 GCTTCCGGTTGCCCATGT 60.676 61.111 0.00 0.00 0.00 3.21
2118 5420 2.700773 GCTTCCGGTTGCCCATGTC 61.701 63.158 0.00 0.00 0.00 3.06
2119 5421 2.359354 TTCCGGTTGCCCATGTCG 60.359 61.111 0.00 0.00 0.00 4.35
2120 5422 3.910914 TTCCGGTTGCCCATGTCGG 62.911 63.158 0.00 0.00 41.80 4.79
2121 5423 4.402528 CCGGTTGCCCATGTCGGA 62.403 66.667 0.00 0.00 42.94 4.55
2122 5424 2.124736 CGGTTGCCCATGTCGGAT 60.125 61.111 0.00 0.00 36.56 4.18
2123 5425 1.748879 CGGTTGCCCATGTCGGATT 60.749 57.895 0.00 0.00 36.56 3.01
2124 5426 1.312371 CGGTTGCCCATGTCGGATTT 61.312 55.000 0.00 0.00 36.56 2.17
2125 5427 0.173255 GGTTGCCCATGTCGGATTTG 59.827 55.000 0.00 0.00 36.56 2.32
2126 5428 0.173255 GTTGCCCATGTCGGATTTGG 59.827 55.000 0.00 3.00 36.56 3.28
2127 5429 0.038890 TTGCCCATGTCGGATTTGGA 59.961 50.000 9.91 0.00 36.56 3.53
2128 5430 0.038890 TGCCCATGTCGGATTTGGAA 59.961 50.000 9.91 0.00 36.56 3.53
2129 5431 0.740737 GCCCATGTCGGATTTGGAAG 59.259 55.000 9.91 0.00 36.56 3.46
2130 5432 1.681780 GCCCATGTCGGATTTGGAAGA 60.682 52.381 9.91 0.00 36.56 2.87
2131 5433 2.292267 CCCATGTCGGATTTGGAAGAG 58.708 52.381 9.91 0.00 36.56 2.85
2132 5434 1.672881 CCATGTCGGATTTGGAAGAGC 59.327 52.381 3.75 0.00 36.56 4.09
2133 5435 2.636830 CATGTCGGATTTGGAAGAGCT 58.363 47.619 0.00 0.00 0.00 4.09
2134 5436 2.859165 TGTCGGATTTGGAAGAGCTT 57.141 45.000 0.00 0.00 0.00 3.74
2135 5437 3.973206 TGTCGGATTTGGAAGAGCTTA 57.027 42.857 0.00 0.00 0.00 3.09
2136 5438 3.596214 TGTCGGATTTGGAAGAGCTTAC 58.404 45.455 0.00 0.00 0.00 2.34
2137 5439 2.937149 GTCGGATTTGGAAGAGCTTACC 59.063 50.000 0.00 0.00 0.00 2.85
2138 5440 2.093128 TCGGATTTGGAAGAGCTTACCC 60.093 50.000 0.00 0.00 0.00 3.69
2139 5441 2.355716 CGGATTTGGAAGAGCTTACCCA 60.356 50.000 0.00 0.00 0.00 4.51
2140 5442 3.697166 GGATTTGGAAGAGCTTACCCAA 58.303 45.455 9.64 9.64 36.94 4.12
2141 5443 3.696548 GGATTTGGAAGAGCTTACCCAAG 59.303 47.826 12.36 0.00 39.52 3.61
2153 5455 4.766404 CTTACCCAAGCAAAGGTGTTAG 57.234 45.455 2.10 0.00 36.88 2.34
2154 5456 1.995376 ACCCAAGCAAAGGTGTTAGG 58.005 50.000 0.00 0.00 34.20 2.69
2155 5457 1.497286 ACCCAAGCAAAGGTGTTAGGA 59.503 47.619 0.00 0.00 34.20 2.94
2156 5458 2.091555 ACCCAAGCAAAGGTGTTAGGAA 60.092 45.455 0.00 0.00 34.20 3.36
2157 5459 3.165071 CCCAAGCAAAGGTGTTAGGAAT 58.835 45.455 0.00 0.00 0.00 3.01
2158 5460 3.056607 CCCAAGCAAAGGTGTTAGGAATG 60.057 47.826 0.00 0.00 0.00 2.67
2159 5461 3.826157 CCAAGCAAAGGTGTTAGGAATGA 59.174 43.478 0.00 0.00 0.00 2.57
2160 5462 4.463891 CCAAGCAAAGGTGTTAGGAATGAT 59.536 41.667 0.00 0.00 0.00 2.45
2161 5463 5.393461 CCAAGCAAAGGTGTTAGGAATGATC 60.393 44.000 0.00 0.00 0.00 2.92
2162 5464 5.184892 AGCAAAGGTGTTAGGAATGATCT 57.815 39.130 0.00 0.00 0.00 2.75
2163 5465 5.574188 AGCAAAGGTGTTAGGAATGATCTT 58.426 37.500 0.00 0.00 0.00 2.40
2164 5466 5.416952 AGCAAAGGTGTTAGGAATGATCTTG 59.583 40.000 0.00 0.00 0.00 3.02
2165 5467 5.415701 GCAAAGGTGTTAGGAATGATCTTGA 59.584 40.000 0.00 0.00 0.00 3.02
2166 5468 6.623767 GCAAAGGTGTTAGGAATGATCTTGAC 60.624 42.308 0.00 0.00 0.00 3.18
2167 5469 5.762179 AGGTGTTAGGAATGATCTTGACA 57.238 39.130 0.00 0.00 30.25 3.58
2168 5470 6.319048 AGGTGTTAGGAATGATCTTGACAT 57.681 37.500 0.00 0.00 34.45 3.06
2169 5471 6.118170 AGGTGTTAGGAATGATCTTGACATG 58.882 40.000 0.00 0.00 34.45 3.21
2170 5472 5.220931 GGTGTTAGGAATGATCTTGACATGC 60.221 44.000 0.00 0.00 34.45 4.06
2171 5473 5.355071 GTGTTAGGAATGATCTTGACATGCA 59.645 40.000 0.00 0.00 34.45 3.96
2172 5474 5.587443 TGTTAGGAATGATCTTGACATGCAG 59.413 40.000 0.00 0.00 28.17 4.41
2173 5475 3.552875 AGGAATGATCTTGACATGCAGG 58.447 45.455 0.00 0.00 0.00 4.85
2174 5476 3.053842 AGGAATGATCTTGACATGCAGGT 60.054 43.478 2.33 2.33 0.00 4.00
2175 5477 3.066342 GGAATGATCTTGACATGCAGGTG 59.934 47.826 9.62 0.00 0.00 4.00
2176 5478 2.118313 TGATCTTGACATGCAGGTGG 57.882 50.000 9.62 0.00 0.00 4.61
2177 5479 1.340308 TGATCTTGACATGCAGGTGGG 60.340 52.381 9.62 0.00 0.00 4.61
2178 5480 0.033796 ATCTTGACATGCAGGTGGGG 60.034 55.000 9.62 0.00 0.00 4.96
2179 5481 1.679977 CTTGACATGCAGGTGGGGG 60.680 63.158 9.62 0.00 0.00 5.40
2180 5482 3.884704 TTGACATGCAGGTGGGGGC 62.885 63.158 9.62 0.00 0.00 5.80
2181 5483 4.052518 GACATGCAGGTGGGGGCT 62.053 66.667 9.62 0.00 0.00 5.19
2182 5484 2.613696 ACATGCAGGTGGGGGCTA 60.614 61.111 1.71 0.00 0.00 3.93
2183 5485 2.194056 CATGCAGGTGGGGGCTAG 59.806 66.667 0.00 0.00 0.00 3.42
2184 5486 3.813724 ATGCAGGTGGGGGCTAGC 61.814 66.667 6.04 6.04 0.00 3.42
2210 5512 3.617538 GCGTCTATGCGTGCGGTC 61.618 66.667 0.00 0.00 0.00 4.79
2211 5513 2.202557 CGTCTATGCGTGCGGTCA 60.203 61.111 0.00 0.00 0.00 4.02
2212 5514 2.224217 CGTCTATGCGTGCGGTCAG 61.224 63.158 0.00 0.00 0.00 3.51
2239 5541 4.794439 CGTCGATGTGCTGGCCGA 62.794 66.667 0.00 0.00 0.00 5.54
2240 5542 2.887568 GTCGATGTGCTGGCCGAG 60.888 66.667 0.00 0.00 0.00 4.63
2241 5543 3.381983 TCGATGTGCTGGCCGAGT 61.382 61.111 0.00 0.00 0.00 4.18
2242 5544 2.887568 CGATGTGCTGGCCGAGTC 60.888 66.667 0.00 0.00 0.00 3.36
2243 5545 2.581354 GATGTGCTGGCCGAGTCT 59.419 61.111 0.00 0.00 0.00 3.24
2244 5546 1.520342 GATGTGCTGGCCGAGTCTC 60.520 63.158 0.00 0.00 0.00 3.36
2245 5547 2.914777 GATGTGCTGGCCGAGTCTCC 62.915 65.000 0.00 0.00 0.00 3.71
2246 5548 3.695606 GTGCTGGCCGAGTCTCCA 61.696 66.667 0.00 1.72 0.00 3.86
2253 5555 2.125350 CCGAGTCTCCAGGCAAGC 60.125 66.667 0.00 0.00 0.00 4.01
2254 5556 2.659016 CGAGTCTCCAGGCAAGCA 59.341 61.111 0.00 0.00 0.00 3.91
2255 5557 1.220206 CGAGTCTCCAGGCAAGCAT 59.780 57.895 0.00 0.00 0.00 3.79
2256 5558 0.392193 CGAGTCTCCAGGCAAGCATT 60.392 55.000 0.00 0.00 0.00 3.56
2257 5559 1.831580 GAGTCTCCAGGCAAGCATTT 58.168 50.000 0.00 0.00 0.00 2.32
2258 5560 2.165998 GAGTCTCCAGGCAAGCATTTT 58.834 47.619 0.00 0.00 0.00 1.82
2259 5561 1.891150 AGTCTCCAGGCAAGCATTTTG 59.109 47.619 0.00 0.00 0.00 2.44
2260 5562 1.067354 GTCTCCAGGCAAGCATTTTGG 60.067 52.381 0.00 0.00 0.00 3.28
2261 5563 0.248289 CTCCAGGCAAGCATTTTGGG 59.752 55.000 0.00 0.00 0.00 4.12
2262 5564 1.376295 CCAGGCAAGCATTTTGGGC 60.376 57.895 0.00 0.00 0.00 5.36
2263 5565 1.371932 CAGGCAAGCATTTTGGGCA 59.628 52.632 0.00 0.00 0.00 5.36
2264 5566 0.672401 CAGGCAAGCATTTTGGGCAG 60.672 55.000 0.00 0.00 0.00 4.85
2265 5567 2.036571 GGCAAGCATTTTGGGCAGC 61.037 57.895 0.00 0.00 34.94 5.25
2266 5568 2.385091 GCAAGCATTTTGGGCAGCG 61.385 57.895 0.00 0.00 0.00 5.18
2267 5569 1.738830 CAAGCATTTTGGGCAGCGG 60.739 57.895 0.00 0.00 0.00 5.52
2268 5570 1.907807 AAGCATTTTGGGCAGCGGA 60.908 52.632 0.00 0.00 0.00 5.54
2269 5571 2.125952 GCATTTTGGGCAGCGGAC 60.126 61.111 0.00 0.00 0.00 4.79
2270 5572 2.179018 CATTTTGGGCAGCGGACG 59.821 61.111 0.00 0.00 0.00 4.79
2271 5573 2.282180 ATTTTGGGCAGCGGACGT 60.282 55.556 0.00 0.00 0.00 4.34
2272 5574 2.625823 ATTTTGGGCAGCGGACGTG 61.626 57.895 0.00 0.00 0.00 4.49
2282 5584 3.995669 CGGACGTGCAACCGTGTG 61.996 66.667 16.58 2.76 41.98 3.82
2283 5585 2.893404 GGACGTGCAACCGTGTGT 60.893 61.111 7.13 0.00 41.98 3.72
2284 5586 2.323105 GACGTGCAACCGTGTGTG 59.677 61.111 7.13 0.00 41.98 3.82
2285 5587 3.163110 GACGTGCAACCGTGTGTGG 62.163 63.158 7.13 0.00 41.98 4.17
2286 5588 4.605967 CGTGCAACCGTGTGTGGC 62.606 66.667 0.00 0.00 44.85 5.01
2287 5589 3.209097 GTGCAACCGTGTGTGGCT 61.209 61.111 0.00 0.00 44.88 4.75
2288 5590 2.899838 TGCAACCGTGTGTGGCTC 60.900 61.111 0.00 0.00 44.88 4.70
2289 5591 2.591715 GCAACCGTGTGTGGCTCT 60.592 61.111 0.00 0.00 41.06 4.09
2290 5592 1.301401 GCAACCGTGTGTGGCTCTA 60.301 57.895 0.00 0.00 41.06 2.43
2291 5593 1.291877 GCAACCGTGTGTGGCTCTAG 61.292 60.000 0.00 0.00 41.06 2.43
2292 5594 0.670546 CAACCGTGTGTGGCTCTAGG 60.671 60.000 0.00 0.00 0.00 3.02
2293 5595 2.125512 CCGTGTGTGGCTCTAGGC 60.126 66.667 0.00 0.00 41.50 3.93
2294 5596 2.507102 CGTGTGTGGCTCTAGGCG 60.507 66.667 0.00 0.00 44.42 5.52
2295 5597 2.125512 GTGTGTGGCTCTAGGCGG 60.126 66.667 0.00 0.00 44.42 6.13
2296 5598 2.283604 TGTGTGGCTCTAGGCGGA 60.284 61.111 0.00 0.00 44.42 5.54
2297 5599 2.351244 TGTGTGGCTCTAGGCGGAG 61.351 63.158 6.24 6.24 44.42 4.63
2310 5612 4.742201 CGGAGCCACTGTCCACCG 62.742 72.222 0.00 0.00 33.14 4.94
2345 5647 2.933666 CGCAGCTATGACATGCCG 59.066 61.111 0.00 0.00 36.60 5.69
2346 5648 1.884464 CGCAGCTATGACATGCCGT 60.884 57.895 0.00 0.00 36.60 5.68
2347 5649 1.645455 GCAGCTATGACATGCCGTG 59.355 57.895 0.00 0.00 33.81 4.94
2348 5650 1.645455 CAGCTATGACATGCCGTGC 59.355 57.895 0.00 0.00 0.00 5.34
2349 5651 1.884464 AGCTATGACATGCCGTGCG 60.884 57.895 0.00 0.00 0.00 5.34
2350 5652 2.628106 CTATGACATGCCGTGCGC 59.372 61.111 0.00 0.00 38.31 6.09
2360 5662 4.459331 CCGTGCGCATTTCGGTGG 62.459 66.667 25.00 10.68 39.51 4.61
2361 5663 3.722295 CGTGCGCATTTCGGTGGT 61.722 61.111 15.91 0.00 38.94 4.16
2362 5664 2.642700 GTGCGCATTTCGGTGGTT 59.357 55.556 15.91 0.00 38.94 3.67
2363 5665 1.442017 GTGCGCATTTCGGTGGTTC 60.442 57.895 15.91 0.00 38.94 3.62
2364 5666 2.178273 GCGCATTTCGGTGGTTCC 59.822 61.111 0.30 0.00 38.94 3.62
2373 5675 3.850508 GGTGGTTCCGCTGGTTTT 58.149 55.556 2.41 0.00 0.00 2.43
2374 5676 1.362355 GGTGGTTCCGCTGGTTTTG 59.638 57.895 2.41 0.00 0.00 2.44
2375 5677 1.299850 GTGGTTCCGCTGGTTTTGC 60.300 57.895 0.00 0.00 0.00 3.68
2376 5678 1.454847 TGGTTCCGCTGGTTTTGCT 60.455 52.632 0.00 0.00 0.00 3.91
2377 5679 1.007387 GGTTCCGCTGGTTTTGCTG 60.007 57.895 0.00 0.00 0.00 4.41
2378 5680 1.661509 GTTCCGCTGGTTTTGCTGC 60.662 57.895 0.00 0.00 0.00 5.25
2379 5681 2.855514 TTCCGCTGGTTTTGCTGCC 61.856 57.895 0.00 0.00 0.00 4.85
2380 5682 4.705519 CCGCTGGTTTTGCTGCCG 62.706 66.667 0.00 0.00 0.00 5.69
2381 5683 3.964875 CGCTGGTTTTGCTGCCGT 61.965 61.111 0.00 0.00 0.00 5.68
2382 5684 2.355009 GCTGGTTTTGCTGCCGTG 60.355 61.111 0.00 0.00 0.00 4.94
2383 5685 2.355009 CTGGTTTTGCTGCCGTGC 60.355 61.111 0.00 0.00 0.00 5.34
2384 5686 3.846602 CTGGTTTTGCTGCCGTGCC 62.847 63.158 0.00 0.00 0.00 5.01
2385 5687 4.999939 GGTTTTGCTGCCGTGCCG 63.000 66.667 0.00 0.00 0.00 5.69
2407 5709 4.312052 TGGCGTATCCAAGGTTGC 57.688 55.556 0.00 0.00 43.21 4.17
2408 5710 1.376848 TGGCGTATCCAAGGTTGCA 59.623 52.632 0.00 0.00 43.21 4.08
2409 5711 0.034574 TGGCGTATCCAAGGTTGCAT 60.035 50.000 0.00 0.00 43.21 3.96
2410 5712 0.381801 GGCGTATCCAAGGTTGCATG 59.618 55.000 0.00 0.00 34.01 4.06
2411 5713 0.381801 GCGTATCCAAGGTTGCATGG 59.618 55.000 0.00 0.00 38.09 3.66
2412 5714 1.750193 CGTATCCAAGGTTGCATGGT 58.250 50.000 4.04 0.00 37.94 3.55
2413 5715 1.670811 CGTATCCAAGGTTGCATGGTC 59.329 52.381 4.04 0.00 37.94 4.02
2414 5716 2.024414 GTATCCAAGGTTGCATGGTCC 58.976 52.381 4.04 0.00 37.94 4.46
2415 5717 0.409092 ATCCAAGGTTGCATGGTCCA 59.591 50.000 4.04 0.00 37.94 4.02
2416 5718 0.251297 TCCAAGGTTGCATGGTCCAG 60.251 55.000 4.04 0.00 37.94 3.86
2417 5719 0.540365 CCAAGGTTGCATGGTCCAGT 60.540 55.000 0.00 0.00 31.84 4.00
2418 5720 1.331214 CAAGGTTGCATGGTCCAGTT 58.669 50.000 0.00 0.00 0.00 3.16
2419 5721 1.270550 CAAGGTTGCATGGTCCAGTTC 59.729 52.381 0.00 0.00 0.00 3.01
2420 5722 0.478072 AGGTTGCATGGTCCAGTTCA 59.522 50.000 0.00 0.00 0.00 3.18
2421 5723 1.076024 AGGTTGCATGGTCCAGTTCAT 59.924 47.619 0.00 0.00 0.00 2.57
2422 5724 1.895131 GGTTGCATGGTCCAGTTCATT 59.105 47.619 0.00 0.00 0.00 2.57
2423 5725 2.299867 GGTTGCATGGTCCAGTTCATTT 59.700 45.455 0.00 0.00 0.00 2.32
2424 5726 3.578688 GTTGCATGGTCCAGTTCATTTC 58.421 45.455 0.00 0.00 0.00 2.17
2425 5727 2.874014 TGCATGGTCCAGTTCATTTCA 58.126 42.857 0.00 0.00 0.00 2.69
2426 5728 3.229293 TGCATGGTCCAGTTCATTTCAA 58.771 40.909 0.00 0.00 0.00 2.69
2427 5729 3.640498 TGCATGGTCCAGTTCATTTCAAA 59.360 39.130 0.00 0.00 0.00 2.69
2428 5730 4.100653 TGCATGGTCCAGTTCATTTCAAAA 59.899 37.500 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.515502 ACCAATCTCATCTTTCGAGTGGA 59.484 43.478 11.34 0.00 43.49 4.02
69 71 9.701098 TTTTGTCGTTGATAGTTCTTACATACT 57.299 29.630 0.00 0.00 0.00 2.12
159 163 9.814899 TGTTCACAAATTTGAAAATGTCTATGT 57.185 25.926 24.64 0.00 37.24 2.29
163 167 9.991388 CAATTGTTCACAAATTTGAAAATGTCT 57.009 25.926 24.64 0.00 39.55 3.41
325 339 8.915871 TTTCAAATTCTGTTCAGAGTTTCAAG 57.084 30.769 16.46 9.11 0.00 3.02
758 778 0.971386 CAGGCTTTTCCTTGCACCAT 59.029 50.000 0.00 0.00 44.75 3.55
812 832 0.970640 TTCCCGTTTCCGACATGAGA 59.029 50.000 0.00 0.00 35.63 3.27
896 2365 5.333513 CACTAGTAGCTGACTAAAACCTCG 58.666 45.833 0.00 0.00 40.23 4.63
897 2366 5.103687 GCACTAGTAGCTGACTAAAACCTC 58.896 45.833 0.00 0.00 40.23 3.85
898 2367 4.380655 CGCACTAGTAGCTGACTAAAACCT 60.381 45.833 13.14 0.00 40.23 3.50
899 2368 3.858238 CGCACTAGTAGCTGACTAAAACC 59.142 47.826 13.14 0.00 40.23 3.27
900 2369 4.483311 ACGCACTAGTAGCTGACTAAAAC 58.517 43.478 13.14 0.00 40.23 2.43
902 2371 5.481200 CTACGCACTAGTAGCTGACTAAA 57.519 43.478 13.14 0.00 40.23 1.85
966 3940 4.502962 CTGCTTTTGTTTTCCCTGTTTGA 58.497 39.130 0.00 0.00 0.00 2.69
1024 4001 1.136500 GTACTCCTGTTCCATCCCGAC 59.864 57.143 0.00 0.00 0.00 4.79
1041 4075 1.447314 CGGCTGGAACGGGAAGTAC 60.447 63.158 0.00 0.00 33.56 2.73
1082 4116 0.179100 CTCATCCGGTTGCATCTCGT 60.179 55.000 7.70 0.00 0.00 4.18
1135 4226 1.532437 CACTTGTTGCAGCTCGATCAA 59.468 47.619 1.17 0.00 0.00 2.57
1231 4325 3.842923 CGGCAGCTCCTCCATCGT 61.843 66.667 0.00 0.00 0.00 3.73
1272 4366 3.118261 TCATGTGCTCCAGGTAAGAATCC 60.118 47.826 0.00 0.00 0.00 3.01
1379 4473 4.148825 GATCCGCCCGCTGACACT 62.149 66.667 0.00 0.00 0.00 3.55
1418 4515 7.280205 ACAAATTACAAGAACCCTAGATTAGCG 59.720 37.037 0.00 0.00 0.00 4.26
1419 4516 8.507524 ACAAATTACAAGAACCCTAGATTAGC 57.492 34.615 0.00 0.00 0.00 3.09
1458 4555 7.571613 GCCAACTGTCGTGTTAAATACAATACA 60.572 37.037 0.00 0.00 38.80 2.29
1459 4556 6.739550 GCCAACTGTCGTGTTAAATACAATAC 59.260 38.462 0.00 0.00 38.80 1.89
1470 4567 2.244651 GCGAGCCAACTGTCGTGTT 61.245 57.895 0.00 0.00 38.48 3.32
1471 4568 1.802337 TAGCGAGCCAACTGTCGTGT 61.802 55.000 0.00 0.00 38.48 4.49
1472 4569 1.073216 CTAGCGAGCCAACTGTCGTG 61.073 60.000 0.00 0.00 38.48 4.35
1473 4570 1.213013 CTAGCGAGCCAACTGTCGT 59.787 57.895 0.00 0.00 38.48 4.34
1513 4629 9.480538 GCAACTAAACAAATCGATCGTTATAAA 57.519 29.630 15.94 0.00 0.00 1.40
1514 4630 8.875803 AGCAACTAAACAAATCGATCGTTATAA 58.124 29.630 15.94 0.00 0.00 0.98
1515 4631 8.415192 AGCAACTAAACAAATCGATCGTTATA 57.585 30.769 15.94 0.00 0.00 0.98
1516 4632 7.303634 AGCAACTAAACAAATCGATCGTTAT 57.696 32.000 15.94 0.00 0.00 1.89
1517 4633 6.715344 AGCAACTAAACAAATCGATCGTTA 57.285 33.333 15.94 4.30 0.00 3.18
1518 4634 5.607119 AGCAACTAAACAAATCGATCGTT 57.393 34.783 15.94 3.47 0.00 3.85
1519 4635 5.408604 AGAAGCAACTAAACAAATCGATCGT 59.591 36.000 15.94 0.00 0.00 3.73
1520 4636 5.858475 AGAAGCAACTAAACAAATCGATCG 58.142 37.500 9.36 9.36 0.00 3.69
1589 4707 6.826231 TGGTGAGATACAAAGAAACTTGTCAA 59.174 34.615 0.00 0.00 40.08 3.18
1594 4712 5.643777 CCGATGGTGAGATACAAAGAAACTT 59.356 40.000 0.00 0.00 0.00 2.66
1608 4729 0.604780 GCCATGGATCCGATGGTGAG 60.605 60.000 28.94 14.50 42.25 3.51
1626 4747 5.049405 ACAAAGCAGACAGTACATTACTTGC 60.049 40.000 0.00 1.78 39.27 4.01
1653 4774 5.123186 CCGTGCCTAATCAATTTGTCAGTAA 59.877 40.000 0.00 0.00 0.00 2.24
1676 4797 1.136057 GGACGAAGATTTCAACACGCC 60.136 52.381 0.00 0.00 0.00 5.68
1692 4813 5.921408 CCGAATAAGAAGGATAAGAAGGACG 59.079 44.000 0.00 0.00 0.00 4.79
1729 4850 1.681538 CGGCTGTAGCTCTTAGGAGA 58.318 55.000 5.96 0.00 41.86 3.71
1730 4851 0.671251 CCGGCTGTAGCTCTTAGGAG 59.329 60.000 3.63 0.00 41.70 3.69
1731 4852 0.755698 CCCGGCTGTAGCTCTTAGGA 60.756 60.000 0.00 0.00 41.70 2.94
1732 4853 1.742768 CCCGGCTGTAGCTCTTAGG 59.257 63.158 0.00 0.93 41.70 2.69
1733 4854 1.068250 GCCCGGCTGTAGCTCTTAG 59.932 63.158 0.71 0.00 41.70 2.18
1734 4855 2.782222 CGCCCGGCTGTAGCTCTTA 61.782 63.158 8.05 0.00 41.70 2.10
1737 4858 2.750715 GATACGCCCGGCTGTAGCTC 62.751 65.000 17.04 9.40 41.70 4.09
1739 4860 2.355956 GATACGCCCGGCTGTAGC 60.356 66.667 8.05 10.41 41.14 3.58
1743 4864 3.227276 AGAGGATACGCCCGGCTG 61.227 66.667 8.05 3.74 46.39 4.85
1744 4865 3.227276 CAGAGGATACGCCCGGCT 61.227 66.667 8.05 0.00 46.39 5.52
1759 5048 4.034858 CACACCATCCTCATCGAAAATCAG 59.965 45.833 0.00 0.00 0.00 2.90
1760 5049 3.940852 CACACCATCCTCATCGAAAATCA 59.059 43.478 0.00 0.00 0.00 2.57
1775 5064 1.097232 CATGAATGCGTCCACACCAT 58.903 50.000 0.00 0.00 0.00 3.55
1776 5065 0.959867 CCATGAATGCGTCCACACCA 60.960 55.000 0.00 0.00 0.00 4.17
1778 5067 1.137404 GCCATGAATGCGTCCACAC 59.863 57.895 0.00 0.00 0.00 3.82
1781 5070 2.397754 CGTGCCATGAATGCGTCCA 61.398 57.895 0.00 0.00 0.00 4.02
1790 5079 2.356913 CGACACCACGTGCCATGA 60.357 61.111 10.91 0.00 36.98 3.07
1797 5086 2.910479 TCAGGAGCGACACCACGT 60.910 61.111 0.00 0.00 35.59 4.49
1823 5112 0.322008 CAGTCAGACTTGGGCCCTTC 60.322 60.000 25.70 16.60 0.00 3.46
1824 5113 1.763770 CAGTCAGACTTGGGCCCTT 59.236 57.895 25.70 7.15 0.00 3.95
1833 5122 2.031163 GTTGCCGCCAGTCAGACT 59.969 61.111 0.00 0.00 0.00 3.24
1843 5132 3.352990 TAGGATTGGGGGTTGCCGC 62.353 63.158 0.00 0.00 35.60 6.53
1846 5145 1.455773 GGCTAGGATTGGGGGTTGC 60.456 63.158 0.00 0.00 0.00 4.17
1854 5153 0.037303 ATGGGATGCGGCTAGGATTG 59.963 55.000 0.00 0.00 0.00 2.67
1857 5156 0.108585 GAAATGGGATGCGGCTAGGA 59.891 55.000 0.00 0.00 0.00 2.94
1884 5183 4.612412 GGTGTGTGGGGACGCGAA 62.612 66.667 15.93 0.00 46.31 4.70
1891 5190 1.915078 GAGAGGATGGGTGTGTGGGG 61.915 65.000 0.00 0.00 0.00 4.96
1892 5191 1.604378 GAGAGGATGGGTGTGTGGG 59.396 63.158 0.00 0.00 0.00 4.61
1897 5196 0.033011 AGCTACGAGAGGATGGGTGT 60.033 55.000 0.00 0.00 0.00 4.16
1898 5197 0.671251 GAGCTACGAGAGGATGGGTG 59.329 60.000 0.00 0.00 0.00 4.61
1907 5206 1.706301 CGAACGACGAGCTACGAGA 59.294 57.895 0.00 0.00 45.77 4.04
1911 5210 2.497928 GCTGCGAACGACGAGCTAC 61.498 63.158 0.00 0.00 45.77 3.58
1917 5216 3.175240 CCAGAGCTGCGAACGACG 61.175 66.667 0.00 0.00 45.66 5.12
1918 5217 3.482783 GCCAGAGCTGCGAACGAC 61.483 66.667 0.00 0.00 35.50 4.34
1919 5218 4.742201 GGCCAGAGCTGCGAACGA 62.742 66.667 0.00 0.00 39.73 3.85
1920 5219 4.749310 AGGCCAGAGCTGCGAACG 62.749 66.667 5.01 0.00 39.73 3.95
1921 5220 3.123620 CAGGCCAGAGCTGCGAAC 61.124 66.667 5.01 0.00 39.73 3.95
1922 5221 3.313524 TCAGGCCAGAGCTGCGAA 61.314 61.111 5.01 0.00 39.73 4.70
1923 5222 4.074526 GTCAGGCCAGAGCTGCGA 62.075 66.667 5.01 0.00 39.73 5.10
1926 5225 2.436292 GCTGTCAGGCCAGAGCTG 60.436 66.667 5.01 3.07 39.73 4.24
1937 5236 1.479323 GTAGGTGGTTATCCGCTGTCA 59.521 52.381 3.47 0.00 43.20 3.58
1957 5256 1.729472 CGCTCCAGAGTGAGTACAACG 60.729 57.143 1.90 0.00 41.24 4.10
1963 5262 3.753434 CGGCGCTCCAGAGTGAGT 61.753 66.667 7.64 0.00 41.24 3.41
1980 5279 3.138798 CTGTGCCCATCTGCAGCC 61.139 66.667 9.47 0.00 43.02 4.85
2003 5304 1.870055 AAGTGGCTGCAATCCAAGCG 61.870 55.000 8.75 0.00 35.01 4.68
2017 5318 1.324005 GGAGACTCCCGAGGAAGTGG 61.324 65.000 10.74 0.00 0.00 4.00
2018 5319 0.612174 TGGAGACTCCCGAGGAAGTG 60.612 60.000 19.11 0.00 35.03 3.16
2019 5320 0.323908 CTGGAGACTCCCGAGGAAGT 60.324 60.000 19.11 0.00 35.03 3.01
2065 5367 1.324014 TTCTCCTCCTCCTCCTCCAT 58.676 55.000 0.00 0.00 0.00 3.41
2077 5379 2.904131 CTCCGCCCCTTTCTCCTC 59.096 66.667 0.00 0.00 0.00 3.71
2078 5380 3.403558 GCTCCGCCCCTTTCTCCT 61.404 66.667 0.00 0.00 0.00 3.69
2079 5381 4.491409 GGCTCCGCCCCTTTCTCC 62.491 72.222 0.00 0.00 44.06 3.71
2094 5396 4.700365 GCAACCGGAAGCGTTGGC 62.700 66.667 9.46 0.00 40.37 4.52
2095 5397 4.038080 GGCAACCGGAAGCGTTGG 62.038 66.667 9.46 0.00 40.37 3.77
2107 5409 0.173255 CCAAATCCGACATGGGCAAC 59.827 55.000 0.00 0.00 38.76 4.17
2108 5410 0.038890 TCCAAATCCGACATGGGCAA 59.961 50.000 0.00 0.00 38.76 4.52
2109 5411 0.038890 TTCCAAATCCGACATGGGCA 59.961 50.000 0.00 0.00 38.76 5.36
2110 5412 0.740737 CTTCCAAATCCGACATGGGC 59.259 55.000 0.00 0.00 38.76 5.36
2111 5413 2.292267 CTCTTCCAAATCCGACATGGG 58.708 52.381 0.00 0.00 38.76 4.00
2112 5414 1.672881 GCTCTTCCAAATCCGACATGG 59.327 52.381 0.00 0.00 40.09 3.66
2113 5415 2.636830 AGCTCTTCCAAATCCGACATG 58.363 47.619 0.00 0.00 0.00 3.21
2114 5416 3.356529 AAGCTCTTCCAAATCCGACAT 57.643 42.857 0.00 0.00 0.00 3.06
2115 5417 2.859165 AAGCTCTTCCAAATCCGACA 57.141 45.000 0.00 0.00 0.00 4.35
2116 5418 2.937149 GGTAAGCTCTTCCAAATCCGAC 59.063 50.000 0.00 0.00 0.00 4.79
2117 5419 2.093128 GGGTAAGCTCTTCCAAATCCGA 60.093 50.000 0.00 0.00 0.00 4.55
2118 5420 2.289565 GGGTAAGCTCTTCCAAATCCG 58.710 52.381 0.00 0.00 0.00 4.18
2119 5421 3.366052 TGGGTAAGCTCTTCCAAATCC 57.634 47.619 0.00 0.00 0.00 3.01
2120 5422 4.972514 CTTGGGTAAGCTCTTCCAAATC 57.027 45.455 13.30 0.00 38.60 2.17
2132 5434 3.506067 CCTAACACCTTTGCTTGGGTAAG 59.494 47.826 0.00 0.00 34.07 2.34
2133 5435 3.138653 TCCTAACACCTTTGCTTGGGTAA 59.861 43.478 0.00 0.00 34.07 2.85
2134 5436 2.712087 TCCTAACACCTTTGCTTGGGTA 59.288 45.455 0.00 0.00 34.07 3.69
2135 5437 1.497286 TCCTAACACCTTTGCTTGGGT 59.503 47.619 0.00 0.00 36.07 4.51
2136 5438 2.286365 TCCTAACACCTTTGCTTGGG 57.714 50.000 0.00 0.00 0.00 4.12
2137 5439 3.826157 TCATTCCTAACACCTTTGCTTGG 59.174 43.478 0.00 0.00 0.00 3.61
2138 5440 5.416952 AGATCATTCCTAACACCTTTGCTTG 59.583 40.000 0.00 0.00 0.00 4.01
2139 5441 5.574188 AGATCATTCCTAACACCTTTGCTT 58.426 37.500 0.00 0.00 0.00 3.91
2140 5442 5.184892 AGATCATTCCTAACACCTTTGCT 57.815 39.130 0.00 0.00 0.00 3.91
2141 5443 5.415701 TCAAGATCATTCCTAACACCTTTGC 59.584 40.000 0.00 0.00 0.00 3.68
2142 5444 6.430925 TGTCAAGATCATTCCTAACACCTTTG 59.569 38.462 0.00 0.00 0.00 2.77
2143 5445 6.542821 TGTCAAGATCATTCCTAACACCTTT 58.457 36.000 0.00 0.00 0.00 3.11
2144 5446 6.126863 TGTCAAGATCATTCCTAACACCTT 57.873 37.500 0.00 0.00 0.00 3.50
2145 5447 5.762179 TGTCAAGATCATTCCTAACACCT 57.238 39.130 0.00 0.00 0.00 4.00
2146 5448 5.220931 GCATGTCAAGATCATTCCTAACACC 60.221 44.000 0.00 0.00 0.00 4.16
2147 5449 5.355071 TGCATGTCAAGATCATTCCTAACAC 59.645 40.000 0.00 0.00 0.00 3.32
2148 5450 5.499313 TGCATGTCAAGATCATTCCTAACA 58.501 37.500 0.00 0.00 0.00 2.41
2149 5451 5.008415 CCTGCATGTCAAGATCATTCCTAAC 59.992 44.000 0.00 0.00 0.00 2.34
2150 5452 5.128205 CCTGCATGTCAAGATCATTCCTAA 58.872 41.667 0.00 0.00 0.00 2.69
2151 5453 4.164796 ACCTGCATGTCAAGATCATTCCTA 59.835 41.667 0.00 0.00 0.00 2.94
2152 5454 3.053842 ACCTGCATGTCAAGATCATTCCT 60.054 43.478 0.00 0.00 0.00 3.36
2153 5455 3.066342 CACCTGCATGTCAAGATCATTCC 59.934 47.826 0.00 0.00 0.00 3.01
2154 5456 3.066342 CCACCTGCATGTCAAGATCATTC 59.934 47.826 0.00 0.00 0.00 2.67
2155 5457 3.021695 CCACCTGCATGTCAAGATCATT 58.978 45.455 0.00 0.00 0.00 2.57
2156 5458 2.651455 CCACCTGCATGTCAAGATCAT 58.349 47.619 0.00 0.00 0.00 2.45
2157 5459 1.340308 CCCACCTGCATGTCAAGATCA 60.340 52.381 0.00 0.00 0.00 2.92
2158 5460 1.386533 CCCACCTGCATGTCAAGATC 58.613 55.000 0.00 0.00 0.00 2.75
2159 5461 0.033796 CCCCACCTGCATGTCAAGAT 60.034 55.000 0.00 0.00 0.00 2.40
2160 5462 1.379916 CCCCACCTGCATGTCAAGA 59.620 57.895 0.00 0.00 0.00 3.02
2161 5463 1.679977 CCCCCACCTGCATGTCAAG 60.680 63.158 0.00 0.00 0.00 3.02
2162 5464 2.440147 CCCCCACCTGCATGTCAA 59.560 61.111 0.00 0.00 0.00 3.18
2163 5465 4.365111 GCCCCCACCTGCATGTCA 62.365 66.667 0.00 0.00 0.00 3.58
2164 5466 2.615227 CTAGCCCCCACCTGCATGTC 62.615 65.000 0.00 0.00 0.00 3.06
2165 5467 2.613696 TAGCCCCCACCTGCATGT 60.614 61.111 0.00 0.00 0.00 3.21
2166 5468 2.194056 CTAGCCCCCACCTGCATG 59.806 66.667 0.00 0.00 0.00 4.06
2167 5469 3.813724 GCTAGCCCCCACCTGCAT 61.814 66.667 2.29 0.00 0.00 3.96
2193 5495 3.617538 GACCGCACGCATAGACGC 61.618 66.667 0.00 0.00 36.19 5.19
2194 5496 2.202557 TGACCGCACGCATAGACG 60.203 61.111 0.00 0.00 39.50 4.18
2195 5497 2.517450 GCTGACCGCACGCATAGAC 61.517 63.158 0.00 0.00 38.92 2.59
2196 5498 2.202743 GCTGACCGCACGCATAGA 60.203 61.111 0.00 0.00 38.92 1.98
2197 5499 2.202797 AGCTGACCGCACGCATAG 60.203 61.111 0.00 0.00 42.61 2.23
2198 5500 2.509111 CAGCTGACCGCACGCATA 60.509 61.111 8.42 0.00 42.61 3.14
2204 5506 4.994471 CTGTGCCAGCTGACCGCA 62.994 66.667 17.39 13.99 42.61 5.69
2213 5515 2.433145 ACATCGACGCTGTGCCAG 60.433 61.111 3.11 0.00 34.12 4.85
2214 5516 2.738139 CACATCGACGCTGTGCCA 60.738 61.111 17.73 0.00 37.76 4.92
2222 5524 4.794439 TCGGCCAGCACATCGACG 62.794 66.667 2.24 0.00 0.00 5.12
2223 5525 2.887568 CTCGGCCAGCACATCGAC 60.888 66.667 2.24 0.00 0.00 4.20
2224 5526 3.356639 GACTCGGCCAGCACATCGA 62.357 63.158 2.24 0.00 0.00 3.59
2225 5527 2.887568 GACTCGGCCAGCACATCG 60.888 66.667 2.24 0.00 0.00 3.84
2226 5528 1.520342 GAGACTCGGCCAGCACATC 60.520 63.158 2.24 0.00 0.00 3.06
2227 5529 2.581354 GAGACTCGGCCAGCACAT 59.419 61.111 2.24 0.00 0.00 3.21
2228 5530 3.695606 GGAGACTCGGCCAGCACA 61.696 66.667 2.24 0.00 0.00 4.57
2229 5531 3.655810 CTGGAGACTCGGCCAGCAC 62.656 68.421 2.24 0.00 44.53 4.40
2230 5532 3.385384 CTGGAGACTCGGCCAGCA 61.385 66.667 2.24 0.00 44.53 4.41
2234 5536 3.672295 CTTGCCTGGAGACTCGGCC 62.672 68.421 16.14 0.00 43.90 6.13
2235 5537 2.125350 CTTGCCTGGAGACTCGGC 60.125 66.667 12.97 12.97 44.50 5.54
2236 5538 2.125350 GCTTGCCTGGAGACTCGG 60.125 66.667 0.00 0.00 0.00 4.63
2237 5539 0.392193 AATGCTTGCCTGGAGACTCG 60.392 55.000 0.00 0.00 0.00 4.18
2238 5540 1.831580 AAATGCTTGCCTGGAGACTC 58.168 50.000 0.00 0.00 0.00 3.36
2239 5541 1.891150 CAAAATGCTTGCCTGGAGACT 59.109 47.619 0.00 0.00 0.00 3.24
2240 5542 1.067354 CCAAAATGCTTGCCTGGAGAC 60.067 52.381 0.00 0.00 0.00 3.36
2241 5543 1.259609 CCAAAATGCTTGCCTGGAGA 58.740 50.000 0.00 0.00 0.00 3.71
2242 5544 0.248289 CCCAAAATGCTTGCCTGGAG 59.752 55.000 0.00 0.00 0.00 3.86
2243 5545 1.829523 GCCCAAAATGCTTGCCTGGA 61.830 55.000 0.00 0.00 0.00 3.86
2244 5546 1.376295 GCCCAAAATGCTTGCCTGG 60.376 57.895 0.00 0.00 0.00 4.45
2245 5547 0.672401 CTGCCCAAAATGCTTGCCTG 60.672 55.000 0.00 0.00 0.00 4.85
2246 5548 1.675219 CTGCCCAAAATGCTTGCCT 59.325 52.632 0.00 0.00 0.00 4.75
2247 5549 2.036571 GCTGCCCAAAATGCTTGCC 61.037 57.895 0.00 0.00 0.00 4.52
2248 5550 2.385091 CGCTGCCCAAAATGCTTGC 61.385 57.895 0.00 0.00 0.00 4.01
2249 5551 1.738830 CCGCTGCCCAAAATGCTTG 60.739 57.895 0.00 0.00 0.00 4.01
2250 5552 1.907807 TCCGCTGCCCAAAATGCTT 60.908 52.632 0.00 0.00 0.00 3.91
2251 5553 2.283101 TCCGCTGCCCAAAATGCT 60.283 55.556 0.00 0.00 0.00 3.79
2252 5554 2.125952 GTCCGCTGCCCAAAATGC 60.126 61.111 0.00 0.00 0.00 3.56
2253 5555 2.179018 CGTCCGCTGCCCAAAATG 59.821 61.111 0.00 0.00 0.00 2.32
2254 5556 2.282180 ACGTCCGCTGCCCAAAAT 60.282 55.556 0.00 0.00 0.00 1.82
2255 5557 3.283684 CACGTCCGCTGCCCAAAA 61.284 61.111 0.00 0.00 0.00 2.44
2265 5567 3.995669 CACACGGTTGCACGTCCG 61.996 66.667 18.46 18.46 46.75 4.79
2266 5568 2.893404 ACACACGGTTGCACGTCC 60.893 61.111 0.00 0.00 46.75 4.79
2267 5569 2.323105 CACACACGGTTGCACGTC 59.677 61.111 0.00 0.00 46.75 4.34
2269 5571 4.605967 GCCACACACGGTTGCACG 62.606 66.667 0.00 0.00 38.03 5.34
2270 5572 3.181169 GAGCCACACACGGTTGCAC 62.181 63.158 0.00 0.00 40.48 4.57
2271 5573 2.034048 TAGAGCCACACACGGTTGCA 62.034 55.000 0.00 0.00 40.48 4.08
2272 5574 1.291877 CTAGAGCCACACACGGTTGC 61.292 60.000 0.00 0.00 38.39 4.17
2273 5575 0.670546 CCTAGAGCCACACACGGTTG 60.671 60.000 0.00 0.00 0.00 3.77
2274 5576 1.671742 CCTAGAGCCACACACGGTT 59.328 57.895 0.00 0.00 0.00 4.44
2275 5577 2.943978 GCCTAGAGCCACACACGGT 61.944 63.158 0.00 0.00 34.35 4.83
2276 5578 2.125512 GCCTAGAGCCACACACGG 60.126 66.667 0.00 0.00 34.35 4.94
2277 5579 2.507102 CGCCTAGAGCCACACACG 60.507 66.667 0.00 0.00 38.78 4.49
2278 5580 2.125512 CCGCCTAGAGCCACACAC 60.126 66.667 0.00 0.00 38.78 3.82
2279 5581 2.283604 TCCGCCTAGAGCCACACA 60.284 61.111 0.00 0.00 38.78 3.72
2280 5582 2.496817 CTCCGCCTAGAGCCACAC 59.503 66.667 0.00 0.00 38.78 3.82
2293 5595 4.742201 CGGTGGACAGTGGCTCCG 62.742 72.222 15.99 15.99 0.00 4.63
2317 5619 0.318529 ATAGCTGCGCTCTCATGTCG 60.319 55.000 9.73 0.00 40.44 4.35
2318 5620 1.138337 CATAGCTGCGCTCTCATGTC 58.862 55.000 9.73 0.00 40.44 3.06
2319 5621 0.749049 TCATAGCTGCGCTCTCATGT 59.251 50.000 9.73 0.00 40.44 3.21
2320 5622 1.138337 GTCATAGCTGCGCTCTCATG 58.862 55.000 9.73 7.59 40.44 3.07
2321 5623 0.749049 TGTCATAGCTGCGCTCTCAT 59.251 50.000 9.73 0.00 40.44 2.90
2322 5624 0.749049 ATGTCATAGCTGCGCTCTCA 59.251 50.000 9.73 0.51 40.44 3.27
2323 5625 1.138337 CATGTCATAGCTGCGCTCTC 58.862 55.000 9.73 0.00 40.44 3.20
2324 5626 0.879400 GCATGTCATAGCTGCGCTCT 60.879 55.000 9.73 8.56 40.44 4.09
2325 5627 1.568514 GCATGTCATAGCTGCGCTC 59.431 57.895 9.73 0.00 40.44 5.03
2326 5628 1.890979 GGCATGTCATAGCTGCGCT 60.891 57.895 9.73 8.09 43.41 5.92
2327 5629 2.635899 GGCATGTCATAGCTGCGC 59.364 61.111 0.00 0.00 36.76 6.09
2328 5630 1.884464 ACGGCATGTCATAGCTGCG 60.884 57.895 13.01 8.92 40.76 5.18
2329 5631 1.645455 CACGGCATGTCATAGCTGC 59.355 57.895 13.01 0.00 40.76 5.25
2330 5632 1.645455 GCACGGCATGTCATAGCTG 59.355 57.895 0.00 12.02 42.73 4.24
2331 5633 1.884464 CGCACGGCATGTCATAGCT 60.884 57.895 0.00 0.00 0.00 3.32
2332 5634 2.628106 CGCACGGCATGTCATAGC 59.372 61.111 0.00 0.00 0.00 2.97
2333 5635 2.628106 GCGCACGGCATGTCATAG 59.372 61.111 0.30 0.00 42.87 2.23
2344 5646 3.248630 AACCACCGAAATGCGCACG 62.249 57.895 14.90 12.82 39.11 5.34
2345 5647 1.442017 GAACCACCGAAATGCGCAC 60.442 57.895 14.90 0.00 39.11 5.34
2346 5648 2.622011 GGAACCACCGAAATGCGCA 61.622 57.895 14.96 14.96 39.11 6.09
2347 5649 2.178273 GGAACCACCGAAATGCGC 59.822 61.111 0.00 0.00 39.11 6.09
2356 5658 1.362355 CAAAACCAGCGGAACCACC 59.638 57.895 1.50 0.00 0.00 4.61
2357 5659 1.299850 GCAAAACCAGCGGAACCAC 60.300 57.895 1.50 0.00 0.00 4.16
2358 5660 1.454847 AGCAAAACCAGCGGAACCA 60.455 52.632 1.50 0.00 37.01 3.67
2359 5661 1.007387 CAGCAAAACCAGCGGAACC 60.007 57.895 1.50 0.00 37.01 3.62
2360 5662 1.661509 GCAGCAAAACCAGCGGAAC 60.662 57.895 1.50 0.00 37.01 3.62
2361 5663 2.727544 GCAGCAAAACCAGCGGAA 59.272 55.556 1.50 0.00 37.01 4.30
2362 5664 3.294493 GGCAGCAAAACCAGCGGA 61.294 61.111 0.00 0.00 37.01 5.54
2363 5665 4.705519 CGGCAGCAAAACCAGCGG 62.706 66.667 0.00 0.00 37.01 5.52
2364 5666 3.964875 ACGGCAGCAAAACCAGCG 61.965 61.111 0.00 0.00 37.01 5.18
2365 5667 2.355009 CACGGCAGCAAAACCAGC 60.355 61.111 0.00 0.00 0.00 4.85
2366 5668 2.355009 GCACGGCAGCAAAACCAG 60.355 61.111 0.00 0.00 0.00 4.00
2367 5669 3.910490 GGCACGGCAGCAAAACCA 61.910 61.111 0.00 0.00 35.83 3.67
2391 5693 0.381801 CATGCAACCTTGGATACGCC 59.618 55.000 0.00 0.00 37.10 5.68
2392 5694 0.381801 CCATGCAACCTTGGATACGC 59.618 55.000 0.00 0.00 37.10 4.42
2393 5695 1.670811 GACCATGCAACCTTGGATACG 59.329 52.381 11.04 0.00 37.10 3.06
2394 5696 2.024414 GGACCATGCAACCTTGGATAC 58.976 52.381 11.04 2.49 37.10 2.24
2395 5697 1.638070 TGGACCATGCAACCTTGGATA 59.362 47.619 11.04 0.00 37.10 2.59
2396 5698 0.409092 TGGACCATGCAACCTTGGAT 59.591 50.000 11.04 0.00 40.00 3.41
2397 5699 0.251297 CTGGACCATGCAACCTTGGA 60.251 55.000 11.04 0.00 39.07 3.53
2398 5700 0.540365 ACTGGACCATGCAACCTTGG 60.540 55.000 2.41 2.41 40.97 3.61
2399 5701 1.270550 GAACTGGACCATGCAACCTTG 59.729 52.381 0.00 0.00 0.00 3.61
2400 5702 1.133513 TGAACTGGACCATGCAACCTT 60.134 47.619 0.00 0.00 0.00 3.50
2401 5703 0.478072 TGAACTGGACCATGCAACCT 59.522 50.000 0.00 0.00 0.00 3.50
2402 5704 1.549203 ATGAACTGGACCATGCAACC 58.451 50.000 0.00 0.00 0.00 3.77
2403 5705 3.005684 TGAAATGAACTGGACCATGCAAC 59.994 43.478 0.00 0.00 0.00 4.17
2404 5706 3.229293 TGAAATGAACTGGACCATGCAA 58.771 40.909 0.00 0.00 0.00 4.08
2405 5707 2.874014 TGAAATGAACTGGACCATGCA 58.126 42.857 0.00 0.00 0.00 3.96
2406 5708 3.940209 TTGAAATGAACTGGACCATGC 57.060 42.857 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.