Multiple sequence alignment - TraesCS5A01G456300

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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 TraesCS5A01G456300 chr5A 100.000 3197 0 0 1 3197 636428245 636431441 0.000000e+00 5904
1 TraesCS5A01G456300 chr5A 89.779 587 42 10 7 576 129232229 129231644 0.000000e+00 736
2 TraesCS5A01G456300 chr5A 84.127 189 15 9 586 761 129231376 129231190 5.480000e-38 169
3 TraesCS5A01G456300 chr5B 84.980 1984 138 72 427 2309 639738490 639740414 0.000000e+00 1866
4 TraesCS5A01G456300 chr5B 91.395 430 33 4 12 438 639738033 639738461 1.280000e-163 586
5 TraesCS5A01G456300 chr5B 82.507 343 33 12 2820 3162 639740799 639741114 3.140000e-70 276
6 TraesCS5A01G456300 chr5B 92.000 75 6 0 2631 2705 639740644 639740718 4.360000e-19 106
7 TraesCS5A01G456300 chr5B 86.170 94 11 2 2488 2580 639740555 639740647 2.030000e-17 100
8 TraesCS5A01G456300 chr5D 88.820 966 59 21 761 1705 509232455 509233392 0.000000e+00 1140
9 TraesCS5A01G456300 chr5D 92.727 770 39 15 7 761 509231642 509232409 0.000000e+00 1096
10 TraesCS5A01G456300 chr5D 84.125 926 83 24 1909 2820 509233603 509234478 0.000000e+00 837
11 TraesCS5A01G456300 chr2D 87.898 785 57 26 7 761 287143863 287144639 0.000000e+00 889
12 TraesCS5A01G456300 chr2D 87.349 166 16 3 1971 2133 286684641 286684804 5.450000e-43 185
13 TraesCS5A01G456300 chr1A 87.659 786 60 22 7 761 505307266 505308045 0.000000e+00 880
14 TraesCS5A01G456300 chr3D 87.437 788 59 27 7 761 470482601 470483381 0.000000e+00 870


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 TraesCS5A01G456300 chr5A 636428245 636431441 3196 False 5904.000000 5904 100.000000 1 3197 1 chr5A.!!$F1 3196
1 TraesCS5A01G456300 chr5A 129231190 129232229 1039 True 452.500000 736 86.953000 7 761 2 chr5A.!!$R1 754
2 TraesCS5A01G456300 chr5B 639738033 639741114 3081 False 586.800000 1866 87.410400 12 3162 5 chr5B.!!$F1 3150
3 TraesCS5A01G456300 chr5D 509231642 509234478 2836 False 1024.333333 1140 88.557333 7 2820 3 chr5D.!!$F1 2813
4 TraesCS5A01G456300 chr2D 287143863 287144639 776 False 889.000000 889 87.898000 7 761 1 chr2D.!!$F2 754
5 TraesCS5A01G456300 chr1A 505307266 505308045 779 False 880.000000 880 87.659000 7 761 1 chr1A.!!$F1 754
6 TraesCS5A01G456300 chr3D 470482601 470483381 780 False 870.000000 870 87.437000 7 761 1 chr3D.!!$F1 754

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
995 1382 0.037326 TCTCGTTCCTTGCGCTGATT 60.037 50.0 9.73 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2714 3229 0.034896 AACGTCCATGTCAGGGTGTC 59.965 55.0 2.95 0.0 0.0 3.67 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
65 66 4.010349 ACTCCGAAGACCCATTTCATTTC 58.990 43.478 0.00 0.00 0.00 2.17
79 80 6.393171 CATTTCATTTCCTTTTCTCCCAGTC 58.607 40.000 0.00 0.00 0.00 3.51
108 109 2.229792 CTGTGCACAGTTACCCATTGT 58.770 47.619 34.04 0.00 39.09 2.71
119 120 3.339547 CCCATTGTTGTCTCGGGTT 57.660 52.632 0.00 0.00 31.80 4.11
195 196 2.522198 ATCTCCTCTGCCCTCCGTGT 62.522 60.000 0.00 0.00 0.00 4.49
231 234 6.098409 TGTGTCTCTATCCATCTTTACTTCCC 59.902 42.308 0.00 0.00 0.00 3.97
253 256 4.390603 CCGTTGATTCCGTTTATCAGTTCA 59.609 41.667 0.00 0.00 33.83 3.18
278 282 3.874543 TGTTTATGATCTGCCGCGTAATT 59.125 39.130 4.92 0.00 0.00 1.40
317 321 8.315482 TCCATTATGTTACTTAGTGTGCAGTTA 58.685 33.333 0.00 0.00 0.00 2.24
343 348 8.284945 TCTCTGAAAGCATGCTTTTTATATGT 57.715 30.769 38.45 20.05 45.16 2.29
372 380 2.363788 TTGAAGAGGACGTTCATCGG 57.636 50.000 0.00 0.00 44.69 4.18
422 472 1.303888 ATGCCCTGACAGCAACTGG 60.304 57.895 0.00 0.00 44.83 4.00
423 473 3.368571 GCCCTGACAGCAACTGGC 61.369 66.667 4.23 4.23 40.49 4.85
448 498 6.468956 CGTGACATATTTGATTACAGTTTGCC 59.531 38.462 0.00 0.00 0.00 4.52
449 499 7.538575 GTGACATATTTGATTACAGTTTGCCT 58.461 34.615 0.00 0.00 0.00 4.75
631 954 8.565896 TCTCATTGTAGATTGTTTGCAAGTAT 57.434 30.769 0.00 0.00 38.10 2.12
632 955 9.665719 TCTCATTGTAGATTGTTTGCAAGTATA 57.334 29.630 0.00 0.00 38.10 1.47
689 1015 4.910458 TTGAGTAGGAAAGAAGGAAGGG 57.090 45.455 0.00 0.00 0.00 3.95
761 1097 0.609131 TAGCAGGAAGGCAAAGCACC 60.609 55.000 0.00 0.00 35.83 5.01
796 1179 1.475280 CATCTCCCTTGGTGCAACATG 59.525 52.381 4.62 8.21 39.98 3.21
798 1181 1.702401 TCTCCCTTGGTGCAACATGTA 59.298 47.619 4.62 0.00 39.98 2.29
799 1182 1.812571 CTCCCTTGGTGCAACATGTAC 59.187 52.381 4.62 0.00 39.98 2.90
800 1183 1.423541 TCCCTTGGTGCAACATGTACT 59.576 47.619 4.62 0.00 39.98 2.73
801 1184 2.640332 TCCCTTGGTGCAACATGTACTA 59.360 45.455 4.62 0.00 39.98 1.82
816 1199 2.656432 TGTACTAGTTCCCACTACCCCT 59.344 50.000 0.00 0.00 34.06 4.79
817 1200 3.078000 TGTACTAGTTCCCACTACCCCTT 59.922 47.826 0.00 0.00 34.06 3.95
823 1206 1.016415 TCCCACTACCCCTTCTAGCT 58.984 55.000 0.00 0.00 0.00 3.32
831 1214 2.192263 ACCCCTTCTAGCTTCTTCAGG 58.808 52.381 0.00 0.00 0.00 3.86
846 1229 2.121963 AGGTGCTGTTCCCCTCCA 60.122 61.111 0.00 0.00 0.00 3.86
853 1236 1.339535 GCTGTTCCCCTCCAGAGAAAG 60.340 57.143 0.00 0.00 0.00 2.62
854 1237 2.260822 CTGTTCCCCTCCAGAGAAAGA 58.739 52.381 0.00 0.00 0.00 2.52
926 1309 3.988976 TTCCATAGCATCCTCATAGCC 57.011 47.619 0.00 0.00 0.00 3.93
939 1322 3.035173 ATAGCCGCCTGCAAGCAGA 62.035 57.895 22.76 2.52 46.30 4.26
941 1324 2.930385 TAGCCGCCTGCAAGCAGATC 62.930 60.000 22.76 12.70 46.30 2.75
955 1342 5.239351 CAAGCAGATCTGAGCAGCTATAAT 58.761 41.667 27.04 0.00 34.66 1.28
979 1366 1.583986 CCTGATCGGATCCGCTCTC 59.416 63.158 31.55 24.74 39.59 3.20
983 1370 0.386226 GATCGGATCCGCTCTCGTTC 60.386 60.000 29.62 12.24 39.59 3.95
987 1374 0.528684 GGATCCGCTCTCGTTCCTTG 60.529 60.000 0.00 0.00 34.89 3.61
988 1375 1.148759 GATCCGCTCTCGTTCCTTGC 61.149 60.000 0.00 0.00 0.00 4.01
989 1376 2.890847 ATCCGCTCTCGTTCCTTGCG 62.891 60.000 0.00 0.00 45.22 4.85
990 1377 3.843240 CGCTCTCGTTCCTTGCGC 61.843 66.667 0.00 0.00 40.15 6.09
991 1378 2.433318 GCTCTCGTTCCTTGCGCT 60.433 61.111 9.73 0.00 0.00 5.92
992 1379 2.734673 GCTCTCGTTCCTTGCGCTG 61.735 63.158 9.73 0.76 0.00 5.18
993 1380 1.080501 CTCTCGTTCCTTGCGCTGA 60.081 57.895 9.73 0.00 0.00 4.26
994 1381 0.459237 CTCTCGTTCCTTGCGCTGAT 60.459 55.000 9.73 0.00 0.00 2.90
995 1382 0.037326 TCTCGTTCCTTGCGCTGATT 60.037 50.000 9.73 0.00 0.00 2.57
996 1383 0.798776 CTCGTTCCTTGCGCTGATTT 59.201 50.000 9.73 0.00 0.00 2.17
1026 1413 0.479815 GAGGGGATTCCATGGATGCA 59.520 55.000 17.06 0.00 38.24 3.96
1041 1428 1.607628 GATGCAATCAGCCTGGATGAC 59.392 52.381 18.08 5.41 44.70 3.06
1078 1465 1.681486 CCTCGGGAGCTCCTTCTTCC 61.681 65.000 31.36 13.24 35.95 3.46
1096 1483 4.383861 TGGAGGAGTGCGCTGCTG 62.384 66.667 26.96 0.00 43.67 4.41
1098 1485 4.385405 GAGGAGTGCGCTGCTGGT 62.385 66.667 26.96 1.71 43.67 4.00
1191 1578 2.273449 CACCCTGCATCTCACCCC 59.727 66.667 0.00 0.00 0.00 4.95
1193 1580 1.997874 ACCCTGCATCTCACCCCTC 60.998 63.158 0.00 0.00 0.00 4.30
1224 1614 7.075851 TGATTGCATCCTAGATGAAGAAGAT 57.924 36.000 8.74 0.00 0.00 2.40
1241 1631 1.152610 ATGCCATGGGACCATCAGC 60.153 57.895 15.13 13.41 33.90 4.26
1259 1649 4.099170 GCAAGCTGCCTCTGCACG 62.099 66.667 12.45 0.00 44.23 5.34
1272 1662 3.515286 GCACGGCAGCAGCATGAT 61.515 61.111 2.65 0.00 44.61 2.45
1327 1717 4.521062 CGAGGCAAGGGGAGCTCG 62.521 72.222 7.83 0.00 0.00 5.03
1458 1848 1.542108 GCAGCACCTGATCATCTACCC 60.542 57.143 0.00 0.00 32.44 3.69
1591 1981 2.413142 GCTGCCACCTTCTGCATCC 61.413 63.158 0.00 0.00 36.79 3.51
1632 2037 4.298009 CAGCAGAGGAAGGTGCAG 57.702 61.111 0.00 0.00 42.47 4.41
1635 2040 1.376553 GCAGAGGAAGGTGCAGGAC 60.377 63.158 0.00 0.00 39.62 3.85
1674 2079 0.179111 TGTTCGCCGATGATGAGGTC 60.179 55.000 0.00 0.00 0.00 3.85
1696 2101 3.610242 CGATCACTCTTTCCTTCTGTTCG 59.390 47.826 0.00 0.00 0.00 3.95
1701 2106 4.025647 CACTCTTTCCTTCTGTTCGTGAAC 60.026 45.833 5.80 5.80 41.50 3.18
1705 2110 6.342906 TCTTTCCTTCTGTTCGTGAACTAAA 58.657 36.000 13.40 7.10 41.67 1.85
1707 2112 7.497909 TCTTTCCTTCTGTTCGTGAACTAAATT 59.502 33.333 13.40 0.00 41.67 1.82
1708 2113 7.562454 TTCCTTCTGTTCGTGAACTAAATTT 57.438 32.000 13.40 0.00 41.67 1.82
1710 2115 6.990349 TCCTTCTGTTCGTGAACTAAATTTCT 59.010 34.615 13.40 0.00 41.67 2.52
1711 2116 7.497909 TCCTTCTGTTCGTGAACTAAATTTCTT 59.502 33.333 13.40 0.00 41.67 2.52
1713 2118 7.780008 TCTGTTCGTGAACTAAATTTCTTCA 57.220 32.000 13.40 0.48 41.67 3.02
1714 2119 7.627340 TCTGTTCGTGAACTAAATTTCTTCAC 58.373 34.615 21.35 21.35 41.67 3.18
1715 2120 7.494625 TCTGTTCGTGAACTAAATTTCTTCACT 59.505 33.333 24.99 0.00 41.04 3.41
1716 2121 7.981142 TGTTCGTGAACTAAATTTCTTCACTT 58.019 30.769 24.99 2.58 41.04 3.16
1717 2122 8.120465 TGTTCGTGAACTAAATTTCTTCACTTC 58.880 33.333 24.99 18.72 41.04 3.01
1718 2123 8.336080 GTTCGTGAACTAAATTTCTTCACTTCT 58.664 33.333 24.99 0.00 41.04 2.85
1719 2124 9.537192 TTCGTGAACTAAATTTCTTCACTTCTA 57.463 29.630 24.99 13.66 41.04 2.10
1720 2125 8.975439 TCGTGAACTAAATTTCTTCACTTCTAC 58.025 33.333 24.99 9.99 41.04 2.59
1721 2126 8.979574 CGTGAACTAAATTTCTTCACTTCTACT 58.020 33.333 24.99 0.00 41.04 2.57
1735 2140 7.953005 TCACTTCTACTGATTGATCTTCTCT 57.047 36.000 0.00 0.00 0.00 3.10
1736 2141 8.359875 TCACTTCTACTGATTGATCTTCTCTT 57.640 34.615 0.00 0.00 0.00 2.85
1747 2153 8.163408 TGATTGATCTTCTCTTTGTTCCCTAAA 58.837 33.333 0.00 0.00 0.00 1.85
1749 2155 6.476378 TGATCTTCTCTTTGTTCCCTAAAGG 58.524 40.000 0.00 0.00 36.16 3.11
1759 2165 3.118261 TGTTCCCTAAAGGCATGCTCTAG 60.118 47.826 18.92 14.51 34.51 2.43
1763 2169 6.158005 TCCCTAAAGGCATGCTCTAGCAAA 62.158 45.833 18.92 0.00 45.39 3.68
1765 2171 8.784876 TCCCTAAAGGCATGCTCTAGCAAATT 62.785 42.308 18.92 5.84 45.39 1.82
1766 2172 9.492039 TCCCTAAAGGCATGCTCTAGCAAATTA 62.492 40.741 18.92 6.61 45.39 1.40
1809 2215 9.707957 ACATCATTTATTATACTTGGGTCCAAA 57.292 29.630 3.87 0.00 35.33 3.28
1919 2400 8.290277 TCTATAGACTATTGAAGAGGAAAGGGT 58.710 37.037 0.00 0.00 0.00 4.34
1927 2408 5.060427 TGAAGAGGAAAGGGTGAAAATGA 57.940 39.130 0.00 0.00 0.00 2.57
1936 2417 1.620822 GGTGAAAATGACCCACTGCT 58.379 50.000 0.00 0.00 0.00 4.24
1946 2427 0.835941 ACCCACTGCTCCTGATGATC 59.164 55.000 0.00 0.00 0.00 2.92
1951 2432 3.181453 CCACTGCTCCTGATGATCTGATT 60.181 47.826 0.50 0.00 0.00 2.57
1953 2434 4.512198 CACTGCTCCTGATGATCTGATTTC 59.488 45.833 0.50 0.00 0.00 2.17
1958 2439 6.126681 TGCTCCTGATGATCTGATTTCCTTTA 60.127 38.462 0.50 0.00 0.00 1.85
1960 2441 8.099537 GCTCCTGATGATCTGATTTCCTTTATA 58.900 37.037 0.50 0.00 0.00 0.98
1961 2442 9.656040 CTCCTGATGATCTGATTTCCTTTATAG 57.344 37.037 0.50 0.00 0.00 1.31
1965 2446 7.881751 TGATGATCTGATTTCCTTTATAGCTGG 59.118 37.037 0.00 0.00 0.00 4.85
1966 2447 7.141758 TGATCTGATTTCCTTTATAGCTGGT 57.858 36.000 0.00 0.00 0.00 4.00
1967 2448 7.577303 TGATCTGATTTCCTTTATAGCTGGTT 58.423 34.615 0.00 0.00 0.00 3.67
1969 2450 7.200434 TCTGATTTCCTTTATAGCTGGTTCT 57.800 36.000 0.00 0.00 0.00 3.01
2023 2508 3.310288 GGGGGAATTTCATTTAGGGGTGA 60.310 47.826 0.00 0.00 0.00 4.02
2049 2534 0.257328 TGGCCTGGTGTTTTCTGACA 59.743 50.000 3.32 0.00 0.00 3.58
2061 2546 4.922692 TGTTTTCTGACAGTTTTGCTTGTG 59.077 37.500 1.59 0.00 0.00 3.33
2064 2549 4.782019 TCTGACAGTTTTGCTTGTGTTT 57.218 36.364 1.59 0.00 0.00 2.83
2079 2564 1.467734 GTGTTTGATCTGCTGCAGAGG 59.532 52.381 32.77 9.66 44.08 3.69
2082 2567 2.613133 GTTTGATCTGCTGCAGAGGATC 59.387 50.000 32.77 27.61 44.08 3.36
2139 2624 2.125673 GTGTCGTCGGTCATGGGG 60.126 66.667 0.00 0.00 0.00 4.96
2186 2671 3.116531 GTTCGGCGGCCACTACAC 61.117 66.667 20.71 3.62 0.00 2.90
2202 2687 2.184167 CACCGGGTTTTGACGTGCT 61.184 57.895 6.32 0.00 0.00 4.40
2203 2688 0.881159 CACCGGGTTTTGACGTGCTA 60.881 55.000 6.32 0.00 0.00 3.49
2204 2689 0.881600 ACCGGGTTTTGACGTGCTAC 60.882 55.000 6.32 0.00 0.00 3.58
2236 2721 1.480219 GAATCCGTCGACGCATCCAC 61.480 60.000 31.73 14.09 38.18 4.02
2239 2724 2.277949 CGTCGACGCATCCACGAT 60.278 61.111 26.59 0.00 38.27 3.73
2240 2725 2.286559 CGTCGACGCATCCACGATC 61.287 63.158 26.59 0.00 38.27 3.69
2242 2727 0.306840 GTCGACGCATCCACGATCTA 59.693 55.000 0.00 0.00 38.27 1.98
2243 2728 1.018910 TCGACGCATCCACGATCTAA 58.981 50.000 0.00 0.00 36.70 2.10
2248 2733 4.142966 CGACGCATCCACGATCTAATAGTA 60.143 45.833 0.00 0.00 36.70 1.82
2253 2738 7.336176 ACGCATCCACGATCTAATAGTATTAGA 59.664 37.037 27.11 27.11 34.65 2.10
2295 2780 9.638239 TGAGATTCTTTATTTACAAACATTGGC 57.362 29.630 0.00 0.00 34.12 4.52
2323 2820 1.752501 CGTAGCCTGCACGCATGTAC 61.753 60.000 10.37 3.50 31.94 2.90
2340 2837 6.702972 CATGTACATATGCTTCTACTCAGC 57.297 41.667 8.32 0.00 37.82 4.26
2341 2838 6.453943 CATGTACATATGCTTCTACTCAGCT 58.546 40.000 8.32 0.00 38.19 4.24
2342 2839 5.836347 TGTACATATGCTTCTACTCAGCTG 58.164 41.667 7.63 7.63 38.19 4.24
2343 2840 4.333913 ACATATGCTTCTACTCAGCTGG 57.666 45.455 15.13 7.28 38.19 4.85
2344 2841 3.708631 ACATATGCTTCTACTCAGCTGGT 59.291 43.478 15.13 13.13 38.19 4.00
2345 2842 4.895889 ACATATGCTTCTACTCAGCTGGTA 59.104 41.667 15.13 13.56 38.19 3.25
2346 2843 3.810310 ATGCTTCTACTCAGCTGGTAC 57.190 47.619 15.13 4.21 38.19 3.34
2353 2850 5.541953 TCTACTCAGCTGGTACGTAGATA 57.458 43.478 21.29 9.49 33.61 1.98
2358 2855 3.253432 TCAGCTGGTACGTAGATAGCATG 59.747 47.826 15.13 16.56 36.87 4.06
2405 2918 8.097038 TCCTACCAGCAGATGTGAATATTATTC 58.903 37.037 9.11 9.11 0.00 1.75
2454 2968 0.037232 CGCCTTCCCCTCCGATTATC 60.037 60.000 0.00 0.00 0.00 1.75
2474 2988 2.556534 GTACTGTACGACGAGGCAAT 57.443 50.000 0.00 0.00 0.00 3.56
2495 3009 1.474677 GGATGGTGAGGATGCTCTGTG 60.475 57.143 15.82 0.00 0.00 3.66
2505 3019 2.416431 GGATGCTCTGTGGAAATGCAAC 60.416 50.000 0.00 0.00 37.20 4.17
2512 3026 0.943835 GTGGAAATGCAACCAACGGC 60.944 55.000 11.24 0.00 37.94 5.68
2513 3027 1.112315 TGGAAATGCAACCAACGGCT 61.112 50.000 7.93 0.00 32.93 5.52
2514 3028 0.388520 GGAAATGCAACCAACGGCTC 60.389 55.000 0.00 0.00 0.00 4.70
2515 3029 0.729140 GAAATGCAACCAACGGCTCG 60.729 55.000 0.00 0.00 0.00 5.03
2517 3031 2.128853 AATGCAACCAACGGCTCGTG 62.129 55.000 0.00 0.00 39.99 4.35
2589 3104 2.674084 GGTAACCACGCGCTGGAAC 61.674 63.158 27.07 22.51 43.95 3.62
2594 3109 3.414700 CACGCGCTGGAACTGACC 61.415 66.667 5.73 0.00 0.00 4.02
2602 3117 3.426568 GGAACTGACCGCAGCTGC 61.427 66.667 29.12 29.12 46.26 5.25
2613 3128 1.202463 CCGCAGCTGCAGATACTACTT 60.202 52.381 36.03 0.00 42.21 2.24
2614 3129 1.857217 CGCAGCTGCAGATACTACTTG 59.143 52.381 36.03 13.07 42.21 3.16
2615 3130 2.208431 GCAGCTGCAGATACTACTTGG 58.792 52.381 33.36 0.00 41.59 3.61
2616 3131 2.159043 GCAGCTGCAGATACTACTTGGA 60.159 50.000 33.36 0.00 41.59 3.53
2617 3132 3.679917 GCAGCTGCAGATACTACTTGGAA 60.680 47.826 33.36 0.00 41.59 3.53
2618 3133 4.118410 CAGCTGCAGATACTACTTGGAAG 58.882 47.826 20.43 0.00 0.00 3.46
2619 3134 2.869192 GCTGCAGATACTACTTGGAAGC 59.131 50.000 20.43 0.00 0.00 3.86
2620 3135 3.462021 CTGCAGATACTACTTGGAAGCC 58.538 50.000 8.42 0.00 0.00 4.35
2621 3136 2.837591 TGCAGATACTACTTGGAAGCCA 59.162 45.455 0.00 0.00 0.00 4.75
2622 3137 3.198872 GCAGATACTACTTGGAAGCCAC 58.801 50.000 0.00 0.00 30.78 5.01
2623 3138 3.798202 CAGATACTACTTGGAAGCCACC 58.202 50.000 0.00 0.00 30.78 4.61
2624 3139 2.431057 AGATACTACTTGGAAGCCACCG 59.569 50.000 0.00 0.00 30.78 4.94
2625 3140 0.248289 TACTACTTGGAAGCCACCGC 59.752 55.000 0.00 0.00 30.78 5.68
2626 3141 1.745489 CTACTTGGAAGCCACCGCC 60.745 63.158 0.00 0.00 30.78 6.13
2627 3142 3.599285 TACTTGGAAGCCACCGCCG 62.599 63.158 0.00 0.00 30.78 6.46
2706 3221 4.125695 GGTTCGTCGGCTAGCGGT 62.126 66.667 20.33 0.00 0.00 5.68
2707 3222 2.879462 GTTCGTCGGCTAGCGGTG 60.879 66.667 20.33 14.52 0.00 4.94
2725 3240 3.680786 CGGCGAGACACCCTGACA 61.681 66.667 0.00 0.00 0.00 3.58
2727 3242 1.448540 GGCGAGACACCCTGACATG 60.449 63.158 0.00 0.00 0.00 3.21
2742 3257 4.503910 CTGACATGGACGTTGATTCCTTA 58.496 43.478 0.00 0.00 33.84 2.69
2747 3262 4.360951 TGGACGTTGATTCCTTACCTTT 57.639 40.909 0.00 0.00 33.84 3.11
2759 3274 2.026169 CCTTACCTTTCCTCCTGTTCCC 60.026 54.545 0.00 0.00 0.00 3.97
2826 3369 4.498520 CCGTGCGCTGGATCGTCT 62.499 66.667 9.73 0.00 0.00 4.18
2851 3394 1.140407 GGCACGTCGCTGTATCTGAC 61.140 60.000 9.31 0.00 41.91 3.51
2855 3398 0.867753 CGTCGCTGTATCTGACTGGC 60.868 60.000 0.00 0.00 0.00 4.85
2857 3400 1.433471 CGCTGTATCTGACTGGCGA 59.567 57.895 9.40 0.00 46.22 5.54
2862 3405 3.242543 GCTGTATCTGACTGGCGATTTTG 60.243 47.826 0.00 0.00 0.00 2.44
2865 3408 1.896220 TCTGACTGGCGATTTTGCTT 58.104 45.000 0.00 0.00 34.52 3.91
2871 3414 1.399791 CTGGCGATTTTGCTTCCTCTC 59.600 52.381 0.00 0.00 34.52 3.20
2874 3417 2.350522 GCGATTTTGCTTCCTCTCTCA 58.649 47.619 0.00 0.00 0.00 3.27
2884 3427 4.019950 TGCTTCCTCTCTCACATGATCAAA 60.020 41.667 0.00 0.00 0.00 2.69
2885 3428 4.332268 GCTTCCTCTCTCACATGATCAAAC 59.668 45.833 0.00 0.00 0.00 2.93
2890 3433 5.350914 CCTCTCTCACATGATCAAACTTGTC 59.649 44.000 0.00 0.00 0.00 3.18
2891 3434 5.240891 TCTCTCACATGATCAAACTTGTCC 58.759 41.667 0.00 0.00 0.00 4.02
2919 3462 1.128878 CACGTCGAGATTCAGTCGTCT 59.871 52.381 0.00 0.00 38.60 4.18
2920 3463 2.347755 CACGTCGAGATTCAGTCGTCTA 59.652 50.000 0.00 0.00 38.60 2.59
2921 3464 2.348059 ACGTCGAGATTCAGTCGTCTAC 59.652 50.000 0.00 0.00 38.60 2.59
2922 3465 2.594728 CGTCGAGATTCAGTCGTCTACG 60.595 54.545 0.00 0.00 38.60 3.51
2923 3466 1.931841 TCGAGATTCAGTCGTCTACGG 59.068 52.381 2.24 0.00 38.60 4.02
2924 3467 1.003759 CGAGATTCAGTCGTCTACGGG 60.004 57.143 2.24 0.00 40.29 5.28
2925 3468 1.334243 GAGATTCAGTCGTCTACGGGG 59.666 57.143 2.24 0.00 40.29 5.73
2926 3469 0.384669 GATTCAGTCGTCTACGGGGG 59.615 60.000 2.24 0.00 40.29 5.40
2941 3484 3.276281 GGGGGTAAAAATCTGGCGT 57.724 52.632 0.00 0.00 0.00 5.68
2947 3490 2.676342 GGTAAAAATCTGGCGTCGACAT 59.324 45.455 17.16 0.00 0.00 3.06
2948 3491 3.242316 GGTAAAAATCTGGCGTCGACATC 60.242 47.826 17.16 7.27 0.00 3.06
2952 3495 1.456196 ATCTGGCGTCGACATCGGAT 61.456 55.000 17.16 17.84 40.29 4.18
2968 3511 1.072159 GATGATGGGAAGAGGCCGG 59.928 63.158 0.00 0.00 0.00 6.13
2969 3512 2.403132 GATGATGGGAAGAGGCCGGG 62.403 65.000 2.18 0.00 0.00 5.73
3002 3545 1.694018 CTGCTCTGTGACAGCGATGC 61.694 60.000 7.93 9.77 40.01 3.91
3007 3550 1.204467 TCTGTGACAGCGATGCACATA 59.796 47.619 23.87 17.20 41.21 2.29
3069 3612 5.274279 GTCCAGGGAAGAATCCAGGAAGG 62.274 56.522 9.11 0.00 46.71 3.46
3072 3615 0.464554 GGAAGAATCCAGGAAGGCGG 60.465 60.000 0.00 0.00 45.79 6.13
3074 3617 1.208165 AAGAATCCAGGAAGGCGGGT 61.208 55.000 0.00 0.00 37.29 5.28
3085 3628 0.535102 AAGGCGGGTTTGAGTGACAG 60.535 55.000 0.00 0.00 0.00 3.51
3107 3650 2.181777 GCTCGTCTGATGCCGACA 59.818 61.111 0.00 0.00 0.00 4.35
3108 3651 1.875813 GCTCGTCTGATGCCGACAG 60.876 63.158 0.00 0.00 36.80 3.51
3109 3652 1.226802 CTCGTCTGATGCCGACAGG 60.227 63.158 0.00 0.00 41.62 4.00
3110 3653 1.938657 CTCGTCTGATGCCGACAGGT 61.939 60.000 0.00 0.00 40.50 4.00
3111 3654 1.079819 CGTCTGATGCCGACAGGTT 60.080 57.895 0.00 0.00 40.50 3.50
3112 3655 0.670546 CGTCTGATGCCGACAGGTTT 60.671 55.000 0.00 0.00 40.50 3.27
3113 3656 1.523758 GTCTGATGCCGACAGGTTTT 58.476 50.000 0.00 0.00 40.50 2.43
3114 3657 1.464997 GTCTGATGCCGACAGGTTTTC 59.535 52.381 0.00 0.00 40.50 2.29
3138 3681 2.933878 TTTGAGCAACTGCCGACGGT 62.934 55.000 16.73 0.00 43.38 4.83
3139 3682 3.112709 GAGCAACTGCCGACGGTC 61.113 66.667 16.73 8.54 43.38 4.79
3154 3697 0.460987 CGGTCTCTGATTGGCACTCC 60.461 60.000 2.13 0.00 0.00 3.85
3165 3708 4.748144 GCACTCCCTGGCCCCAAG 62.748 72.222 0.00 0.00 0.00 3.61
3166 3709 2.935481 CACTCCCTGGCCCCAAGA 60.935 66.667 0.00 0.00 0.00 3.02
3167 3710 2.612115 ACTCCCTGGCCCCAAGAG 60.612 66.667 0.00 3.78 34.48 2.85
3168 3711 3.415087 CTCCCTGGCCCCAAGAGG 61.415 72.222 0.00 0.00 0.00 3.69
3179 3722 3.388552 CCCCAAGAGGCTAAATTTCCT 57.611 47.619 0.00 0.00 34.90 3.36
3180 3723 3.026694 CCCCAAGAGGCTAAATTTCCTG 58.973 50.000 3.24 0.00 31.71 3.86
3181 3724 3.564352 CCCCAAGAGGCTAAATTTCCTGT 60.564 47.826 3.24 0.00 31.71 4.00
3182 3725 4.089361 CCCAAGAGGCTAAATTTCCTGTT 58.911 43.478 3.24 3.25 36.52 3.16
3183 3726 4.528206 CCCAAGAGGCTAAATTTCCTGTTT 59.472 41.667 3.24 0.00 34.20 2.83
3184 3727 5.012046 CCCAAGAGGCTAAATTTCCTGTTTT 59.988 40.000 3.24 0.00 34.20 2.43
3185 3728 5.928264 CCAAGAGGCTAAATTTCCTGTTTTG 59.072 40.000 3.24 5.67 34.20 2.44
3186 3729 6.239289 CCAAGAGGCTAAATTTCCTGTTTTGA 60.239 38.462 3.24 0.00 34.20 2.69
3187 3730 6.332735 AGAGGCTAAATTTCCTGTTTTGAC 57.667 37.500 3.24 0.00 31.71 3.18
3188 3731 5.243954 AGAGGCTAAATTTCCTGTTTTGACC 59.756 40.000 3.24 0.00 31.71 4.02
3189 3732 4.283467 AGGCTAAATTTCCTGTTTTGACCC 59.717 41.667 0.00 0.00 0.00 4.46
3190 3733 4.283467 GGCTAAATTTCCTGTTTTGACCCT 59.717 41.667 0.00 0.00 0.00 4.34
3191 3734 5.221641 GGCTAAATTTCCTGTTTTGACCCTT 60.222 40.000 0.00 0.00 0.00 3.95
3192 3735 6.288294 GCTAAATTTCCTGTTTTGACCCTTT 58.712 36.000 0.00 0.00 0.00 3.11
3193 3736 6.765989 GCTAAATTTCCTGTTTTGACCCTTTT 59.234 34.615 0.00 0.00 0.00 2.27
3194 3737 7.042051 GCTAAATTTCCTGTTTTGACCCTTTTC 60.042 37.037 0.00 0.00 0.00 2.29
3195 3738 6.560003 AATTTCCTGTTTTGACCCTTTTCT 57.440 33.333 0.00 0.00 0.00 2.52
3196 3739 7.669089 AATTTCCTGTTTTGACCCTTTTCTA 57.331 32.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.471702 ACTTGAAAATGAGAACCATTCAGATAT 57.528 29.630 0.00 0.00 44.28 1.63
65 66 3.490348 ACAATGTGACTGGGAGAAAAGG 58.510 45.455 0.00 0.00 0.00 3.11
108 109 4.039973 AGTTGAGATTGTAACCCGAGACAA 59.960 41.667 0.00 0.00 39.74 3.18
195 196 1.123077 AGAGACACACACCAGCTGAA 58.877 50.000 17.39 0.00 0.00 3.02
231 234 5.524511 TGAACTGATAAACGGAATCAACG 57.475 39.130 0.00 0.00 33.13 4.10
253 256 2.682856 ACGCGGCAGATCATAAACAAAT 59.317 40.909 12.47 0.00 0.00 2.32
268 271 1.063027 GGGTCAAAGTAATTACGCGGC 59.937 52.381 12.47 4.31 0.00 6.53
278 282 9.220906 AGTAACATAATGGATAGGGTCAAAGTA 57.779 33.333 0.00 0.00 0.00 2.24
317 321 8.910944 ACATATAAAAAGCATGCTTTCAGAGAT 58.089 29.630 38.26 26.25 44.50 2.75
343 348 7.158697 TGAACGTCCTCTTCAAAATCAAGATA 58.841 34.615 0.00 0.00 0.00 1.98
345 350 5.364778 TGAACGTCCTCTTCAAAATCAAGA 58.635 37.500 0.00 0.00 0.00 3.02
360 368 0.464452 AGGGATTCCGATGAACGTCC 59.536 55.000 0.00 0.00 40.78 4.79
422 472 6.021468 GCAAACTGTAATCAAATATGTCACGC 60.021 38.462 0.00 0.00 0.00 5.34
423 473 6.468956 GGCAAACTGTAATCAAATATGTCACG 59.531 38.462 0.00 0.00 0.00 4.35
424 474 7.538575 AGGCAAACTGTAATCAAATATGTCAC 58.461 34.615 0.00 0.00 0.00 3.67
425 475 7.701539 AGGCAAACTGTAATCAAATATGTCA 57.298 32.000 0.00 0.00 0.00 3.58
588 911 7.884877 ACAATGAGAAAGTGATTCATACAAGGA 59.115 33.333 0.00 0.00 40.72 3.36
631 954 6.488344 TGCCGTATTTTCCTGCAATATCATTA 59.512 34.615 0.00 0.00 0.00 1.90
632 955 5.301551 TGCCGTATTTTCCTGCAATATCATT 59.698 36.000 0.00 0.00 0.00 2.57
633 956 4.826733 TGCCGTATTTTCCTGCAATATCAT 59.173 37.500 0.00 0.00 0.00 2.45
689 1015 0.761802 CCAATGGGGACTAGCTCCTC 59.238 60.000 0.00 7.54 40.62 3.71
796 1179 3.395054 AGGGGTAGTGGGAACTAGTAC 57.605 52.381 0.00 0.00 0.00 2.73
798 1181 2.386113 AGAAGGGGTAGTGGGAACTAGT 59.614 50.000 0.00 0.00 0.00 2.57
799 1182 3.117552 AGAAGGGGTAGTGGGAACTAG 57.882 52.381 0.00 0.00 0.00 2.57
800 1183 3.629282 GCTAGAAGGGGTAGTGGGAACTA 60.629 52.174 0.00 0.00 0.00 2.24
801 1184 2.893153 GCTAGAAGGGGTAGTGGGAACT 60.893 54.545 0.00 0.00 0.00 3.01
816 1199 2.634940 ACAGCACCTGAAGAAGCTAGAA 59.365 45.455 0.00 0.00 35.19 2.10
817 1200 2.251818 ACAGCACCTGAAGAAGCTAGA 58.748 47.619 0.00 0.00 35.19 2.43
823 1206 0.110486 GGGGAACAGCACCTGAAGAA 59.890 55.000 0.00 0.00 36.99 2.52
831 1214 1.194781 TCTCTGGAGGGGAACAGCAC 61.195 60.000 0.00 0.00 34.76 4.40
905 1288 3.118482 CGGCTATGAGGATGCTATGGAAT 60.118 47.826 0.00 0.00 0.00 3.01
926 1309 1.429927 CTCAGATCTGCTTGCAGGCG 61.430 60.000 18.36 10.97 34.52 5.52
939 1322 6.022315 AGGGAGTTATTATAGCTGCTCAGAT 58.978 40.000 4.91 0.00 0.00 2.90
941 1324 5.244851 TCAGGGAGTTATTATAGCTGCTCAG 59.755 44.000 4.91 0.00 0.00 3.35
955 1342 1.617322 CGGATCCGATCAGGGAGTTA 58.383 55.000 30.62 0.00 40.02 2.24
979 1366 1.067199 GCAAATCAGCGCAAGGAACG 61.067 55.000 11.47 0.00 38.28 3.95
989 1376 1.089481 TCCGGTCATCGCAAATCAGC 61.089 55.000 0.00 0.00 37.59 4.26
990 1377 0.933097 CTCCGGTCATCGCAAATCAG 59.067 55.000 0.00 0.00 37.59 2.90
991 1378 0.461870 CCTCCGGTCATCGCAAATCA 60.462 55.000 0.00 0.00 37.59 2.57
992 1379 1.160329 CCCTCCGGTCATCGCAAATC 61.160 60.000 0.00 0.00 37.59 2.17
993 1380 1.153168 CCCTCCGGTCATCGCAAAT 60.153 57.895 0.00 0.00 37.59 2.32
994 1381 2.267642 CCCTCCGGTCATCGCAAA 59.732 61.111 0.00 0.00 37.59 3.68
995 1382 3.781307 CCCCTCCGGTCATCGCAA 61.781 66.667 0.00 0.00 37.59 4.85
996 1383 4.770362 TCCCCTCCGGTCATCGCA 62.770 66.667 0.00 0.00 37.59 5.10
1038 1425 3.005539 GGCAGGAGCTCCCAGTCA 61.006 66.667 29.54 0.00 41.70 3.41
1041 1428 2.686470 TCAGGCAGGAGCTCCCAG 60.686 66.667 29.54 22.38 41.70 4.45
1078 1465 4.079850 AGCAGCGCACTCCTCCAG 62.080 66.667 11.47 0.00 0.00 3.86
1096 1483 0.988832 TGATCCTTACCACCACCACC 59.011 55.000 0.00 0.00 0.00 4.61
1097 1484 1.065418 CCTGATCCTTACCACCACCAC 60.065 57.143 0.00 0.00 0.00 4.16
1098 1485 1.203376 TCCTGATCCTTACCACCACCA 60.203 52.381 0.00 0.00 0.00 4.17
1224 1614 2.276409 GCTGATGGTCCCATGGCA 59.724 61.111 6.09 0.00 36.70 4.92
1259 1649 1.773054 CTCGACATCATGCTGCTGCC 61.773 60.000 13.47 0.00 38.71 4.85
1316 1706 2.136878 ATCATCGCGAGCTCCCCTT 61.137 57.895 16.66 0.00 0.00 3.95
1327 1717 1.592669 CCTCGGTCACCATCATCGC 60.593 63.158 0.00 0.00 0.00 4.58
1440 1830 1.344393 TGGGGTAGATGATCAGGTGCT 60.344 52.381 0.09 0.00 0.00 4.40
1617 2007 1.376553 GTCCTGCACCTTCCTCTGC 60.377 63.158 0.00 0.00 0.00 4.26
1621 2011 1.352622 TTGTGGTCCTGCACCTTCCT 61.353 55.000 0.00 0.00 46.98 3.36
1622 2012 0.890996 CTTGTGGTCCTGCACCTTCC 60.891 60.000 0.00 0.00 46.98 3.46
1624 2014 0.179018 GACTTGTGGTCCTGCACCTT 60.179 55.000 0.00 0.00 46.98 3.50
1635 2040 0.250901 CCTGGAACTGGGACTTGTGG 60.251 60.000 0.00 0.00 44.20 4.17
1674 2079 3.610242 CGAACAGAAGGAAAGAGTGATCG 59.390 47.826 0.00 0.00 0.00 3.69
1705 2110 9.956640 AAGATCAATCAGTAGAAGTGAAGAAAT 57.043 29.630 0.00 0.00 30.32 2.17
1707 2112 8.811017 AGAAGATCAATCAGTAGAAGTGAAGAA 58.189 33.333 0.00 0.00 30.32 2.52
1708 2113 8.359875 AGAAGATCAATCAGTAGAAGTGAAGA 57.640 34.615 0.00 0.00 30.32 2.87
1710 2115 8.359875 AGAGAAGATCAATCAGTAGAAGTGAA 57.640 34.615 0.00 0.00 30.32 3.18
1711 2116 7.953005 AGAGAAGATCAATCAGTAGAAGTGA 57.047 36.000 0.00 0.00 31.21 3.41
1713 2118 8.592809 ACAAAGAGAAGATCAATCAGTAGAAGT 58.407 33.333 0.00 0.00 0.00 3.01
1714 2119 9.434420 AACAAAGAGAAGATCAATCAGTAGAAG 57.566 33.333 0.00 0.00 0.00 2.85
1715 2120 9.429359 GAACAAAGAGAAGATCAATCAGTAGAA 57.571 33.333 0.00 0.00 0.00 2.10
1716 2121 8.037758 GGAACAAAGAGAAGATCAATCAGTAGA 58.962 37.037 0.00 0.00 0.00 2.59
1717 2122 7.279758 GGGAACAAAGAGAAGATCAATCAGTAG 59.720 40.741 0.00 0.00 0.00 2.57
1718 2123 7.038017 AGGGAACAAAGAGAAGATCAATCAGTA 60.038 37.037 0.00 0.00 0.00 2.74
1719 2124 5.942826 GGGAACAAAGAGAAGATCAATCAGT 59.057 40.000 0.00 0.00 0.00 3.41
1720 2125 6.179040 AGGGAACAAAGAGAAGATCAATCAG 58.821 40.000 0.00 0.00 0.00 2.90
1721 2126 6.131972 AGGGAACAAAGAGAAGATCAATCA 57.868 37.500 0.00 0.00 0.00 2.57
1722 2127 8.567285 TTTAGGGAACAAAGAGAAGATCAATC 57.433 34.615 0.00 0.00 0.00 2.67
1723 2128 7.613411 CCTTTAGGGAACAAAGAGAAGATCAAT 59.387 37.037 0.00 0.00 35.43 2.57
1726 2131 5.355630 GCCTTTAGGGAACAAAGAGAAGATC 59.644 44.000 0.00 0.00 35.43 2.75
1735 2140 2.825532 GAGCATGCCTTTAGGGAACAAA 59.174 45.455 15.66 0.00 39.60 2.83
1736 2141 2.041620 AGAGCATGCCTTTAGGGAACAA 59.958 45.455 15.66 0.00 39.60 2.83
1897 2354 6.261435 TCACCCTTTCCTCTTCAATAGTCTA 58.739 40.000 0.00 0.00 0.00 2.59
1898 2355 5.094387 TCACCCTTTCCTCTTCAATAGTCT 58.906 41.667 0.00 0.00 0.00 3.24
1899 2356 5.422214 TCACCCTTTCCTCTTCAATAGTC 57.578 43.478 0.00 0.00 0.00 2.59
1900 2357 5.843019 TTCACCCTTTCCTCTTCAATAGT 57.157 39.130 0.00 0.00 0.00 2.12
1901 2358 7.394359 TCATTTTCACCCTTTCCTCTTCAATAG 59.606 37.037 0.00 0.00 0.00 1.73
1902 2359 7.176690 GTCATTTTCACCCTTTCCTCTTCAATA 59.823 37.037 0.00 0.00 0.00 1.90
1903 2360 6.015095 GTCATTTTCACCCTTTCCTCTTCAAT 60.015 38.462 0.00 0.00 0.00 2.57
1904 2361 5.301805 GTCATTTTCACCCTTTCCTCTTCAA 59.698 40.000 0.00 0.00 0.00 2.69
1905 2362 4.827284 GTCATTTTCACCCTTTCCTCTTCA 59.173 41.667 0.00 0.00 0.00 3.02
1906 2363 4.218635 GGTCATTTTCACCCTTTCCTCTTC 59.781 45.833 0.00 0.00 0.00 2.87
1907 2364 4.152647 GGTCATTTTCACCCTTTCCTCTT 58.847 43.478 0.00 0.00 0.00 2.85
1908 2365 3.767711 GGTCATTTTCACCCTTTCCTCT 58.232 45.455 0.00 0.00 0.00 3.69
1919 2400 1.425066 AGGAGCAGTGGGTCATTTTCA 59.575 47.619 0.00 0.00 43.32 2.69
1927 2408 0.835941 GATCATCAGGAGCAGTGGGT 59.164 55.000 0.00 0.00 0.00 4.51
1936 2417 8.099537 GCTATAAAGGAAATCAGATCATCAGGA 58.900 37.037 0.00 0.00 0.00 3.86
1946 2427 7.201767 CCAAGAACCAGCTATAAAGGAAATCAG 60.202 40.741 0.00 0.00 0.00 2.90
1951 2432 5.772393 TCCAAGAACCAGCTATAAAGGAA 57.228 39.130 0.00 0.00 0.00 3.36
1953 2434 6.360618 AGATTCCAAGAACCAGCTATAAAGG 58.639 40.000 0.00 0.00 0.00 3.11
1958 2439 3.950395 GCAAGATTCCAAGAACCAGCTAT 59.050 43.478 0.00 0.00 0.00 2.97
1960 2441 2.165998 GCAAGATTCCAAGAACCAGCT 58.834 47.619 0.00 0.00 0.00 4.24
1961 2442 1.888512 TGCAAGATTCCAAGAACCAGC 59.111 47.619 0.00 0.00 0.00 4.85
1965 2446 7.859875 GCTAATCTATTGCAAGATTCCAAGAAC 59.140 37.037 15.31 0.00 43.52 3.01
1966 2447 7.013655 GGCTAATCTATTGCAAGATTCCAAGAA 59.986 37.037 15.31 0.00 43.52 2.52
1967 2448 6.488006 GGCTAATCTATTGCAAGATTCCAAGA 59.512 38.462 15.31 0.00 43.52 3.02
1969 2450 6.367983 AGGCTAATCTATTGCAAGATTCCAA 58.632 36.000 15.31 0.63 43.52 3.53
2001 2485 3.038280 CACCCCTAAATGAAATTCCCCC 58.962 50.000 0.00 0.00 33.67 5.40
2003 2487 6.367374 TTTTCACCCCTAAATGAAATTCCC 57.633 37.500 0.62 0.00 42.72 3.97
2049 2534 4.114794 GCAGATCAAACACAAGCAAAACT 58.885 39.130 0.00 0.00 0.00 2.66
2061 2546 2.105006 TCCTCTGCAGCAGATCAAAC 57.895 50.000 25.59 0.00 39.92 2.93
2064 2549 0.757512 GGATCCTCTGCAGCAGATCA 59.242 55.000 30.58 14.99 39.92 2.92
2186 2671 1.864176 GTAGCACGTCAAAACCCGG 59.136 57.895 0.00 0.00 0.00 5.73
2202 2687 4.197750 ACGGATTCTAGAAGCTTCTCGTA 58.802 43.478 31.67 19.65 38.70 3.43
2203 2688 3.018149 ACGGATTCTAGAAGCTTCTCGT 58.982 45.455 31.67 27.54 38.70 4.18
2204 2689 3.623863 GACGGATTCTAGAAGCTTCTCG 58.376 50.000 31.67 26.92 38.70 4.04
2205 2690 3.312973 TCGACGGATTCTAGAAGCTTCTC 59.687 47.826 31.67 17.12 38.70 2.87
2323 2820 4.333913 ACCAGCTGAGTAGAAGCATATG 57.666 45.455 17.39 0.00 43.37 1.78
2332 2829 4.152759 GCTATCTACGTACCAGCTGAGTAG 59.847 50.000 17.39 20.27 36.91 2.57
2334 2831 2.879646 GCTATCTACGTACCAGCTGAGT 59.120 50.000 17.39 13.96 0.00 3.41
2335 2832 2.879026 TGCTATCTACGTACCAGCTGAG 59.121 50.000 17.39 8.04 33.38 3.35
2336 2833 2.927028 TGCTATCTACGTACCAGCTGA 58.073 47.619 17.39 0.00 33.38 4.26
2338 2835 3.487372 TCATGCTATCTACGTACCAGCT 58.513 45.455 15.48 0.00 33.38 4.24
2340 2837 4.083217 GGACTCATGCTATCTACGTACCAG 60.083 50.000 0.00 0.00 0.00 4.00
2341 2838 3.819337 GGACTCATGCTATCTACGTACCA 59.181 47.826 0.00 0.00 0.00 3.25
2342 2839 3.819337 TGGACTCATGCTATCTACGTACC 59.181 47.826 0.00 0.00 0.00 3.34
2343 2840 4.515944 AGTGGACTCATGCTATCTACGTAC 59.484 45.833 0.00 0.00 0.00 3.67
2344 2841 4.515567 CAGTGGACTCATGCTATCTACGTA 59.484 45.833 0.00 0.00 0.00 3.57
2345 2842 3.316588 CAGTGGACTCATGCTATCTACGT 59.683 47.826 0.00 0.00 0.00 3.57
2346 2843 3.316588 ACAGTGGACTCATGCTATCTACG 59.683 47.826 0.00 0.00 0.00 3.51
2353 2850 1.627329 ACATGACAGTGGACTCATGCT 59.373 47.619 17.65 6.74 42.46 3.79
2358 2855 4.631813 GGAAATGTACATGACAGTGGACTC 59.368 45.833 9.63 0.00 42.79 3.36
2405 2918 1.135689 CGCGGAGAAAATCAAACCCAG 60.136 52.381 0.00 0.00 0.00 4.45
2470 2984 0.672342 GCATCCTCACCATCCATTGC 59.328 55.000 0.00 0.00 0.00 3.56
2472 2986 2.133520 AGAGCATCCTCACCATCCATT 58.866 47.619 0.00 0.00 40.68 3.16
2474 2988 0.835276 CAGAGCATCCTCACCATCCA 59.165 55.000 0.00 0.00 40.68 3.41
2495 3009 0.388520 GAGCCGTTGGTTGCATTTCC 60.389 55.000 0.00 0.00 0.00 3.13
2525 3040 3.877559 TGAATCCTCTTTGTCATCGCAT 58.122 40.909 0.00 0.00 0.00 4.73
2540 3055 0.865769 AGTGACGTGCGTTTGAATCC 59.134 50.000 0.00 0.00 0.00 3.01
2594 3109 1.857217 CAAGTAGTATCTGCAGCTGCG 59.143 52.381 32.11 25.46 45.83 5.18
2602 3117 3.738281 CGGTGGCTTCCAAGTAGTATCTG 60.738 52.174 0.00 0.00 34.18 2.90
2713 3228 0.832135 ACGTCCATGTCAGGGTGTCT 60.832 55.000 2.95 0.00 0.00 3.41
2714 3229 0.034896 AACGTCCATGTCAGGGTGTC 59.965 55.000 2.95 0.00 0.00 3.67
2715 3230 0.250295 CAACGTCCATGTCAGGGTGT 60.250 55.000 2.95 0.98 0.00 4.16
2721 3236 3.417069 AAGGAATCAACGTCCATGTCA 57.583 42.857 0.00 0.00 37.65 3.58
2725 3240 4.569719 AAGGTAAGGAATCAACGTCCAT 57.430 40.909 0.00 0.00 37.65 3.41
2727 3242 3.688185 GGAAAGGTAAGGAATCAACGTCC 59.312 47.826 0.00 0.00 35.17 4.79
2742 3257 2.067197 CGGGAACAGGAGGAAAGGT 58.933 57.895 0.00 0.00 0.00 3.50
2764 3279 2.723746 CATATGCCGTTGCCTGCC 59.276 61.111 0.00 0.00 36.33 4.85
2765 3280 2.026590 GCATATGCCGTTGCCTGC 59.973 61.111 17.26 0.00 36.33 4.85
2766 3281 1.357690 CTGCATATGCCGTTGCCTG 59.642 57.895 24.54 1.70 41.18 4.85
2767 3282 0.680921 AACTGCATATGCCGTTGCCT 60.681 50.000 29.47 11.57 44.69 4.75
2776 3291 1.168407 CCTCCGGGCAACTGCATATG 61.168 60.000 0.00 0.00 44.36 1.78
2844 3387 3.266510 AGCAAAATCGCCAGTCAGATA 57.733 42.857 0.00 0.00 0.00 1.98
2845 3388 2.119801 AGCAAAATCGCCAGTCAGAT 57.880 45.000 0.00 0.00 0.00 2.90
2847 3390 1.135575 GGAAGCAAAATCGCCAGTCAG 60.136 52.381 0.00 0.00 0.00 3.51
2851 3394 1.399791 GAGAGGAAGCAAAATCGCCAG 59.600 52.381 0.00 0.00 0.00 4.85
2855 3398 3.329386 TGTGAGAGAGGAAGCAAAATCG 58.671 45.455 0.00 0.00 0.00 3.34
2857 3400 4.914983 TCATGTGAGAGAGGAAGCAAAAT 58.085 39.130 0.00 0.00 0.00 1.82
2862 3405 3.815856 TGATCATGTGAGAGAGGAAGC 57.184 47.619 0.00 0.00 0.00 3.86
2865 3408 5.012458 ACAAGTTTGATCATGTGAGAGAGGA 59.988 40.000 0.00 0.00 0.00 3.71
2871 3414 3.125829 CCGGACAAGTTTGATCATGTGAG 59.874 47.826 4.44 0.00 0.00 3.51
2874 3417 3.417069 TCCGGACAAGTTTGATCATGT 57.583 42.857 0.00 0.00 0.00 3.21
2884 3427 0.462789 ACGTGTTCTTCCGGACAAGT 59.537 50.000 1.83 5.04 0.00 3.16
2885 3428 1.137513 GACGTGTTCTTCCGGACAAG 58.862 55.000 1.83 4.29 0.00 3.16
2890 3433 0.170561 ATCTCGACGTGTTCTTCCGG 59.829 55.000 0.00 0.00 0.00 5.14
2891 3434 1.912110 GAATCTCGACGTGTTCTTCCG 59.088 52.381 0.00 0.00 0.00 4.30
2923 3466 1.100510 GACGCCAGATTTTTACCCCC 58.899 55.000 0.00 0.00 0.00 5.40
2924 3467 0.730840 CGACGCCAGATTTTTACCCC 59.269 55.000 0.00 0.00 0.00 4.95
2925 3468 1.395954 GTCGACGCCAGATTTTTACCC 59.604 52.381 0.00 0.00 0.00 3.69
2926 3469 2.070783 TGTCGACGCCAGATTTTTACC 58.929 47.619 11.62 0.00 0.00 2.85
2927 3470 3.541516 CGATGTCGACGCCAGATTTTTAC 60.542 47.826 11.62 0.00 43.02 2.01
2928 3471 2.601314 CGATGTCGACGCCAGATTTTTA 59.399 45.455 11.62 0.00 43.02 1.52
2929 3472 1.393539 CGATGTCGACGCCAGATTTTT 59.606 47.619 11.62 0.00 43.02 1.94
2930 3473 0.999406 CGATGTCGACGCCAGATTTT 59.001 50.000 11.62 0.00 43.02 1.82
2931 3474 0.806102 CCGATGTCGACGCCAGATTT 60.806 55.000 11.62 0.00 43.02 2.17
2932 3475 1.226974 CCGATGTCGACGCCAGATT 60.227 57.895 11.62 0.00 43.02 2.40
2933 3476 1.456196 ATCCGATGTCGACGCCAGAT 61.456 55.000 11.62 8.00 43.02 2.90
2934 3477 2.119029 ATCCGATGTCGACGCCAGA 61.119 57.895 11.62 5.86 43.02 3.86
2935 3478 1.946156 CATCCGATGTCGACGCCAG 60.946 63.158 11.62 2.18 43.02 4.85
2936 3479 1.734388 ATCATCCGATGTCGACGCCA 61.734 55.000 11.62 0.00 43.02 5.69
2937 3480 1.007271 ATCATCCGATGTCGACGCC 60.007 57.895 11.62 3.96 43.02 5.68
2941 3484 1.341209 CTTCCCATCATCCGATGTCGA 59.659 52.381 8.24 0.00 46.54 4.20
2947 3490 1.410850 GGCCTCTTCCCATCATCCGA 61.411 60.000 0.00 0.00 0.00 4.55
2948 3491 1.072159 GGCCTCTTCCCATCATCCG 59.928 63.158 0.00 0.00 0.00 4.18
2952 3495 3.089874 CCCGGCCTCTTCCCATCA 61.090 66.667 0.00 0.00 0.00 3.07
3002 3545 1.070758 CCCTTCCTCCGGATGTATGTG 59.929 57.143 3.57 0.00 0.00 3.21
3007 3550 0.983378 CCTTCCCTTCCTCCGGATGT 60.983 60.000 3.57 0.00 0.00 3.06
3018 3561 2.203743 ACCCGTCGTCCTTCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
3021 3564 0.036671 AAATCACCCGTCGTCCTTCC 60.037 55.000 0.00 0.00 0.00 3.46
3069 3612 1.941812 CACTGTCACTCAAACCCGC 59.058 57.895 0.00 0.00 0.00 6.13
3072 3615 0.308993 GCAGCACTGTCACTCAAACC 59.691 55.000 0.00 0.00 0.00 3.27
3074 3617 1.586422 GAGCAGCACTGTCACTCAAA 58.414 50.000 0.00 0.00 0.00 2.69
3085 3628 2.459442 GGCATCAGACGAGCAGCAC 61.459 63.158 0.00 0.00 0.00 4.40
3123 3666 3.575351 GAGACCGTCGGCAGTTGCT 62.575 63.158 12.28 0.00 41.70 3.91
3124 3667 3.112709 GAGACCGTCGGCAGTTGC 61.113 66.667 12.28 0.00 41.14 4.17
3125 3668 1.734477 CAGAGACCGTCGGCAGTTG 60.734 63.158 12.28 1.46 0.00 3.16
3126 3669 1.251527 ATCAGAGACCGTCGGCAGTT 61.252 55.000 12.28 0.00 0.00 3.16
3127 3670 1.251527 AATCAGAGACCGTCGGCAGT 61.252 55.000 12.28 0.00 0.00 4.40
3128 3671 0.803768 CAATCAGAGACCGTCGGCAG 60.804 60.000 12.28 0.00 0.00 4.85
3138 3681 0.907486 CAGGGAGTGCCAATCAGAGA 59.093 55.000 2.50 0.00 35.15 3.10
3139 3682 0.107312 CCAGGGAGTGCCAATCAGAG 60.107 60.000 2.50 0.00 35.15 3.35
3162 3705 6.642540 GTCAAAACAGGAAATTTAGCCTCTTG 59.357 38.462 0.00 0.00 30.41 3.02
3163 3706 6.239317 GGTCAAAACAGGAAATTTAGCCTCTT 60.239 38.462 0.00 0.00 30.41 2.85
3164 3707 5.243954 GGTCAAAACAGGAAATTTAGCCTCT 59.756 40.000 0.00 0.00 30.41 3.69
3165 3708 5.470368 GGTCAAAACAGGAAATTTAGCCTC 58.530 41.667 0.00 0.00 30.41 4.70
3166 3709 4.283467 GGGTCAAAACAGGAAATTTAGCCT 59.717 41.667 0.00 0.00 33.99 4.58
3167 3710 4.283467 AGGGTCAAAACAGGAAATTTAGCC 59.717 41.667 0.00 0.00 0.00 3.93
3168 3711 5.468540 AGGGTCAAAACAGGAAATTTAGC 57.531 39.130 0.00 0.00 0.00 3.09
3169 3712 8.204160 AGAAAAGGGTCAAAACAGGAAATTTAG 58.796 33.333 0.00 0.00 0.00 1.85
3170 3713 8.084985 AGAAAAGGGTCAAAACAGGAAATTTA 57.915 30.769 0.00 0.00 0.00 1.40
3171 3714 6.957631 AGAAAAGGGTCAAAACAGGAAATTT 58.042 32.000 0.00 0.00 0.00 1.82
3172 3715 6.560003 AGAAAAGGGTCAAAACAGGAAATT 57.440 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.