Multiple sequence alignment - TraesCS1B01G424900

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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 TraesCS1B01G424900 chr1B 100.000 2804 0 0 1 2804 649367588 649370391 0.000000e+00 5179
1 TraesCS1B01G424900 chr1A 88.774 1550 90 41 892 2399 562784540 562786047 0.000000e+00 1821
2 TraesCS1B01G424900 chr1A 81.066 713 49 39 4 689 562783622 562784275 9.030000e-135 490
3 TraesCS1B01G424900 chr1A 80.797 276 23 13 2383 2651 562786063 562786315 3.690000e-44 189
4 TraesCS1B01G424900 chr1D 93.286 1132 44 19 867 1973 469586752 469587876 0.000000e+00 1640
5 TraesCS1B01G424900 chr1D 91.775 462 22 9 2141 2587 469588017 469588477 1.830000e-176 628
6 TraesCS1B01G424900 chr1D 82.305 616 25 31 3 597 469585837 469586389 9.150000e-125 457
7 TraesCS1B01G424900 chr1D 79.225 284 26 14 587 844 469586415 469586691 1.730000e-37 167
8 TraesCS1B01G424900 chr3A 80.478 502 80 12 1143 1633 464319835 464320329 4.410000e-98 368
9 TraesCS1B01G424900 chr3B 79.921 508 83 13 1143 1639 439333730 439333231 3.440000e-94 355
10 TraesCS1B01G424900 chr3D 79.523 503 83 14 1143 1633 340415724 340415230 9.620000e-90 340
11 TraesCS1B01G424900 chr5D 94.000 50 2 1 2755 2804 307084539 307084587 1.080000e-09 75


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 TraesCS1B01G424900 chr1B 649367588 649370391 2803 False 5179.000000 5179 100.000000 1 2804 1 chr1B.!!$F1 2803
1 TraesCS1B01G424900 chr1A 562783622 562786315 2693 False 833.333333 1821 83.545667 4 2651 3 chr1A.!!$F1 2647
2 TraesCS1B01G424900 chr1D 469585837 469588477 2640 False 723.000000 1640 86.647750 3 2587 4 chr1D.!!$F1 2584

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
953 1134 0.17902 TTCAGCACCCCACACTCTTG 60.179 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2684 2962 0.040204 AGGAAAACATGGCCTCAGGG 59.96 55.0 3.32 0.0 0.0 4.45 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
53 54 2.602211 CGCTCATCATCACAGACAGTTC 59.398 50.000 0.00 0.00 0.00 3.01
132 133 2.367202 GCTGGGCTGGGCTACACTA 61.367 63.158 0.00 0.00 0.00 2.74
135 136 1.620819 CTGGGCTGGGCTACACTATAG 59.379 57.143 0.00 0.00 0.00 1.31
206 207 0.518636 CTGTCGGTAGAACGAACGGA 59.481 55.000 0.00 0.00 45.38 4.69
207 208 0.238289 TGTCGGTAGAACGAACGGAC 59.762 55.000 0.00 6.90 45.38 4.79
208 209 0.790866 GTCGGTAGAACGAACGGACG 60.791 60.000 0.00 2.26 45.38 4.79
209 210 1.512734 CGGTAGAACGAACGGACGG 60.513 63.158 8.20 0.00 37.61 4.79
212 213 1.303236 TAGAACGAACGGACGGGGA 60.303 57.895 8.20 0.00 37.61 4.81
217 218 2.777972 CGAACGGACGGGGATGCTA 61.778 63.158 0.00 0.00 0.00 3.49
245 246 1.524863 CCAAGTCCGTCTCCGTCTGT 61.525 60.000 0.00 0.00 0.00 3.41
249 250 2.179517 CCGTCTCCGTCTGTCAGC 59.820 66.667 0.00 0.00 0.00 4.26
252 253 2.033602 TCTCCGTCTGTCAGCCGA 59.966 61.111 4.55 0.00 0.00 5.54
293 294 0.320771 TCAGTGCGCTCCCTTTTCTC 60.321 55.000 9.73 0.00 0.00 2.87
296 297 1.021920 GTGCGCTCCCTTTTCTCCTC 61.022 60.000 9.73 0.00 0.00 3.71
340 341 4.219033 GTTTCAGATCGTGCGAACAATTT 58.781 39.130 0.00 0.00 0.00 1.82
368 369 0.240945 GGAAGCGACCACAAACATGG 59.759 55.000 0.00 0.00 46.10 3.66
436 457 3.076621 GTGATCCATGTGAGAACTGCAA 58.923 45.455 0.00 0.00 0.00 4.08
480 502 4.901868 AGCATTTCTTCACATGCCATTTT 58.098 34.783 0.00 0.00 45.99 1.82
481 503 4.693566 AGCATTTCTTCACATGCCATTTTG 59.306 37.500 0.00 0.00 45.99 2.44
482 504 4.453136 GCATTTCTTCACATGCCATTTTGT 59.547 37.500 0.00 0.00 40.04 2.83
483 505 5.390145 GCATTTCTTCACATGCCATTTTGTC 60.390 40.000 0.00 0.00 40.04 3.18
500 522 1.084370 GTCTGTCACGGCCATGCTAC 61.084 60.000 2.24 0.00 0.00 3.58
524 546 1.006220 GCCGGCCCAAAGAAACAAG 60.006 57.895 18.11 0.00 0.00 3.16
533 555 2.543653 CCAAAGAAACAAGAACTGCCCG 60.544 50.000 0.00 0.00 0.00 6.13
540 582 3.976701 AAGAACTGCCCGCCCATCG 62.977 63.158 0.00 0.00 38.08 3.84
599 646 2.124819 CGCCAGCATCTGAAGGCT 60.125 61.111 10.33 6.76 44.97 4.58
600 647 1.144716 CGCCAGCATCTGAAGGCTA 59.855 57.895 6.84 0.00 41.45 3.93
602 649 1.001293 CGCCAGCATCTGAAGGCTATA 59.999 52.381 6.84 0.00 41.45 1.31
603 650 2.354503 CGCCAGCATCTGAAGGCTATAT 60.355 50.000 6.84 0.00 41.45 0.86
604 651 3.683802 GCCAGCATCTGAAGGCTATATT 58.316 45.455 6.84 0.00 41.45 1.28
605 652 4.077822 GCCAGCATCTGAAGGCTATATTT 58.922 43.478 6.84 0.00 41.45 1.40
606 653 4.522022 GCCAGCATCTGAAGGCTATATTTT 59.478 41.667 6.84 0.00 41.45 1.82
607 654 5.707298 GCCAGCATCTGAAGGCTATATTTTA 59.293 40.000 6.84 0.00 41.45 1.52
608 655 6.207417 GCCAGCATCTGAAGGCTATATTTTAA 59.793 38.462 6.84 0.00 41.45 1.52
610 657 8.632679 CCAGCATCTGAAGGCTATATTTTAAAA 58.367 33.333 2.51 2.51 41.45 1.52
621 702 9.899661 AGGCTATATTTTAAAATTGTTTTCCCC 57.100 29.630 18.14 8.68 34.19 4.81
689 799 7.566858 GTGTACTTCACAATTATTTTGCCAG 57.433 36.000 0.00 0.00 45.51 4.85
709 819 3.779759 AGAGTCGATCTGCATCTTGAAC 58.220 45.455 0.00 0.00 36.69 3.18
710 820 2.533535 GAGTCGATCTGCATCTTGAACG 59.466 50.000 0.00 0.00 0.00 3.95
711 821 2.164422 AGTCGATCTGCATCTTGAACGA 59.836 45.455 2.57 2.57 35.69 3.85
712 822 3.119291 GTCGATCTGCATCTTGAACGAT 58.881 45.455 8.81 0.00 39.07 3.73
716 826 3.997319 TCTGCATCTTGAACGATTTCG 57.003 42.857 0.00 0.00 46.33 3.46
717 827 2.094258 TCTGCATCTTGAACGATTTCGC 59.906 45.455 0.00 0.00 44.43 4.70
723 842 1.195448 CTTGAACGATTTCGCAGCTGT 59.805 47.619 16.64 0.00 44.43 4.40
725 844 0.790207 GAACGATTTCGCAGCTGTGA 59.210 50.000 25.69 25.69 44.43 3.58
727 846 1.002366 ACGATTTCGCAGCTGTGATC 58.998 50.000 29.33 22.64 44.43 2.92
836 969 2.025898 TCGTGTCGGTAGCCATATCAA 58.974 47.619 0.00 0.00 0.00 2.57
846 994 1.280710 AGCCATATCAACCGGTCAACA 59.719 47.619 8.04 0.00 0.00 3.33
848 996 2.939640 GCCATATCAACCGGTCAACACT 60.940 50.000 8.04 0.00 0.00 3.55
849 997 3.680475 GCCATATCAACCGGTCAACACTA 60.680 47.826 8.04 0.00 0.00 2.74
854 1002 2.105134 TCAACCGGTCAACACTAACCAT 59.895 45.455 8.04 0.00 35.13 3.55
859 1007 2.028476 CGGTCAACACTAACCATCCAGA 60.028 50.000 0.00 0.00 35.13 3.86
864 1012 4.836175 TCAACACTAACCATCCAGACTGTA 59.164 41.667 0.93 0.00 0.00 2.74
885 1063 1.457455 CACACAGGCCCAAAACCCT 60.457 57.895 0.00 0.00 0.00 4.34
888 1066 1.152546 ACAGGCCCAAAACCCTCAC 60.153 57.895 0.00 0.00 0.00 3.51
953 1134 0.179020 TTCAGCACCCCACACTCTTG 60.179 55.000 0.00 0.00 0.00 3.02
1020 1204 4.838486 GCGTCGTCCAGGAGAGCG 62.838 72.222 0.00 0.00 0.00 5.03
1359 1546 2.262915 CAGGACCAGGTGACGCTC 59.737 66.667 0.00 0.00 0.00 5.03
1506 1693 2.737376 GCCGTCAACGTCTCCACC 60.737 66.667 1.48 0.00 37.74 4.61
1814 2001 5.107298 CGTGCCTCTTGTAAGAAGAAGAAAG 60.107 44.000 0.00 0.00 34.83 2.62
1815 2002 5.760743 GTGCCTCTTGTAAGAAGAAGAAAGT 59.239 40.000 0.00 0.00 34.83 2.66
1816 2003 5.760253 TGCCTCTTGTAAGAAGAAGAAAGTG 59.240 40.000 0.00 0.00 34.83 3.16
1817 2004 5.334491 GCCTCTTGTAAGAAGAAGAAAGTGC 60.334 44.000 0.00 0.00 34.83 4.40
1821 2008 5.196341 TGTAAGAAGAAGAAAGTGCGAGA 57.804 39.130 0.00 0.00 0.00 4.04
1832 2025 2.064434 AGTGCGAGAGAGGATCATGA 57.936 50.000 0.00 0.00 37.82 3.07
1836 2029 2.030451 TGCGAGAGAGGATCATGATTCG 60.030 50.000 17.00 17.00 37.82 3.34
1902 2099 4.989168 GCGTGGATTTGGATAGGTTACTAG 59.011 45.833 0.00 0.00 31.54 2.57
1904 2101 6.579865 CGTGGATTTGGATAGGTTACTAGTT 58.420 40.000 0.00 0.00 31.54 2.24
1905 2102 6.700520 CGTGGATTTGGATAGGTTACTAGTTC 59.299 42.308 0.00 0.00 31.54 3.01
1906 2103 6.990939 GTGGATTTGGATAGGTTACTAGTTCC 59.009 42.308 0.00 4.63 31.65 3.62
1907 2104 6.906901 TGGATTTGGATAGGTTACTAGTTCCT 59.093 38.462 18.77 18.77 32.08 3.36
1909 2106 5.609533 TTGGATAGGTTACTAGTTCCTGC 57.390 43.478 21.86 15.64 32.08 4.85
1910 2107 4.616553 TGGATAGGTTACTAGTTCCTGCA 58.383 43.478 21.86 10.83 32.08 4.41
1913 2111 6.842280 TGGATAGGTTACTAGTTCCTGCATTA 59.158 38.462 21.86 8.37 32.08 1.90
1923 2121 0.329261 TCCTGCATTAGTGGCTGCTT 59.671 50.000 0.00 0.00 39.16 3.91
1931 2129 3.601443 TTAGTGGCTGCTTCTTCTCTC 57.399 47.619 0.00 0.00 0.00 3.20
1932 2130 1.643310 AGTGGCTGCTTCTTCTCTCT 58.357 50.000 0.00 0.00 0.00 3.10
1933 2131 1.550072 AGTGGCTGCTTCTTCTCTCTC 59.450 52.381 0.00 0.00 0.00 3.20
1936 2134 2.636893 TGGCTGCTTCTTCTCTCTCTTT 59.363 45.455 0.00 0.00 0.00 2.52
1973 2172 7.763985 TGTCCATTTTTGTTCTCTTTCTTTTCC 59.236 33.333 0.00 0.00 0.00 3.13
1976 2175 7.439356 CCATTTTTGTTCTCTTTCTTTTCCTCC 59.561 37.037 0.00 0.00 0.00 4.30
1978 2177 4.100279 TGTTCTCTTTCTTTTCCTCCCC 57.900 45.455 0.00 0.00 0.00 4.81
1983 2182 3.823304 CTCTTTCTTTTCCTCCCCTGTTG 59.177 47.826 0.00 0.00 0.00 3.33
1984 2183 3.461831 TCTTTCTTTTCCTCCCCTGTTGA 59.538 43.478 0.00 0.00 0.00 3.18
1993 2212 0.918983 TCCCCTGTTGATGGGCTAAG 59.081 55.000 0.00 0.00 43.26 2.18
2001 2220 5.455183 CCTGTTGATGGGCTAAGATGTGATA 60.455 44.000 0.00 0.00 0.00 2.15
2003 2222 6.057533 TGTTGATGGGCTAAGATGTGATAAG 58.942 40.000 0.00 0.00 0.00 1.73
2009 2228 6.291377 TGGGCTAAGATGTGATAAGATGTTC 58.709 40.000 0.00 0.00 0.00 3.18
2023 2242 5.695851 AAGATGTTCCACTGTTGAATCAC 57.304 39.130 0.00 0.00 0.00 3.06
2025 2244 2.217750 TGTTCCACTGTTGAATCACGG 58.782 47.619 0.00 0.00 0.00 4.94
2029 2248 0.586319 CACTGTTGAATCACGGCGTT 59.414 50.000 11.19 0.00 0.00 4.84
2030 2249 1.795872 CACTGTTGAATCACGGCGTTA 59.204 47.619 11.19 1.73 0.00 3.18
2031 2250 2.222213 CACTGTTGAATCACGGCGTTAA 59.778 45.455 11.19 1.00 0.00 2.01
2032 2251 3.071479 ACTGTTGAATCACGGCGTTAAT 58.929 40.909 11.19 3.98 0.00 1.40
2033 2252 3.500680 ACTGTTGAATCACGGCGTTAATT 59.499 39.130 11.19 13.67 0.00 1.40
2034 2253 4.023536 ACTGTTGAATCACGGCGTTAATTT 60.024 37.500 11.19 0.94 0.00 1.82
2051 2270 9.687717 GCGTTAATTTGTTGGATGATTAAATTG 57.312 29.630 0.00 0.00 34.12 2.32
2052 2271 9.687717 CGTTAATTTGTTGGATGATTAAATTGC 57.312 29.630 0.00 0.00 34.12 3.56
2056 2275 7.655236 TTTGTTGGATGATTAAATTGCACTG 57.345 32.000 0.00 0.00 0.00 3.66
2057 2276 5.170021 TGTTGGATGATTAAATTGCACTGC 58.830 37.500 0.00 0.00 0.00 4.40
2058 2277 5.047164 TGTTGGATGATTAAATTGCACTGCT 60.047 36.000 1.98 0.00 0.00 4.24
2060 2279 6.964807 TGGATGATTAAATTGCACTGCTAT 57.035 33.333 1.98 0.00 0.00 2.97
2061 2280 8.352201 GTTGGATGATTAAATTGCACTGCTATA 58.648 33.333 1.98 0.00 0.00 1.31
2062 2281 8.640063 TGGATGATTAAATTGCACTGCTATAT 57.360 30.769 1.98 0.00 0.00 0.86
2063 2282 9.081204 TGGATGATTAAATTGCACTGCTATATT 57.919 29.630 1.98 1.47 0.00 1.28
2064 2283 9.918630 GGATGATTAAATTGCACTGCTATATTT 57.081 29.630 1.98 8.17 0.00 1.40
2071 2290 8.867112 AAATTGCACTGCTATATTTGATCTTG 57.133 30.769 1.98 0.00 0.00 3.02
2072 2291 6.381481 TTGCACTGCTATATTTGATCTTGG 57.619 37.500 1.98 0.00 0.00 3.61
2073 2292 4.276678 TGCACTGCTATATTTGATCTTGGC 59.723 41.667 1.98 0.00 0.00 4.52
2074 2293 4.518211 GCACTGCTATATTTGATCTTGGCT 59.482 41.667 0.00 0.00 0.00 4.75
2077 2296 6.933521 CACTGCTATATTTGATCTTGGCTAGT 59.066 38.462 0.00 0.00 0.00 2.57
2079 2298 7.659390 ACTGCTATATTTGATCTTGGCTAGTTC 59.341 37.037 0.00 0.00 0.00 3.01
2080 2299 7.508687 TGCTATATTTGATCTTGGCTAGTTCA 58.491 34.615 5.75 5.75 32.13 3.18
2081 2300 7.442364 TGCTATATTTGATCTTGGCTAGTTCAC 59.558 37.037 8.84 0.00 33.40 3.18
2103 2325 8.521170 TCACTAGCAGCTAAGTTATCTTCTAA 57.479 34.615 3.09 0.00 35.36 2.10
2105 2327 9.026074 CACTAGCAGCTAAGTTATCTTCTAAAC 57.974 37.037 3.09 0.00 35.36 2.01
2107 2329 7.835634 AGCAGCTAAGTTATCTTCTAAACAC 57.164 36.000 0.00 0.00 35.36 3.32
2108 2330 7.616313 AGCAGCTAAGTTATCTTCTAAACACT 58.384 34.615 0.00 0.00 35.36 3.55
2110 2332 7.545965 GCAGCTAAGTTATCTTCTAAACACTCA 59.454 37.037 0.00 0.00 35.36 3.41
2112 2334 9.810545 AGCTAAGTTATCTTCTAAACACTCATC 57.189 33.333 0.00 0.00 35.36 2.92
2113 2335 8.747666 GCTAAGTTATCTTCTAAACACTCATCG 58.252 37.037 0.00 0.00 35.36 3.84
2114 2336 9.790389 CTAAGTTATCTTCTAAACACTCATCGT 57.210 33.333 0.00 0.00 35.36 3.73
2116 2338 9.570488 AAGTTATCTTCTAAACACTCATCGTAC 57.430 33.333 0.00 0.00 0.00 3.67
2117 2339 8.737175 AGTTATCTTCTAAACACTCATCGTACA 58.263 33.333 0.00 0.00 0.00 2.90
2118 2340 9.517609 GTTATCTTCTAAACACTCATCGTACAT 57.482 33.333 0.00 0.00 0.00 2.29
2119 2341 7.993821 ATCTTCTAAACACTCATCGTACATG 57.006 36.000 0.00 0.00 0.00 3.21
2120 2342 6.920817 TCTTCTAAACACTCATCGTACATGT 58.079 36.000 2.69 2.69 0.00 3.21
2121 2343 8.047413 TCTTCTAAACACTCATCGTACATGTA 57.953 34.615 0.08 0.08 0.00 2.29
2123 2345 9.946165 CTTCTAAACACTCATCGTACATGTATA 57.054 33.333 9.18 0.96 0.00 1.47
2125 2347 9.893305 TCTAAACACTCATCGTACATGTATATG 57.107 33.333 18.37 18.37 40.24 1.78
2194 2416 2.191786 TACTCCCACGGGGCAACATG 62.192 60.000 0.00 0.00 43.94 3.21
2271 2493 8.924511 AGACTGTAAAGGAAAATGAGATTTGA 57.075 30.769 0.00 0.00 31.77 2.69
2426 2687 2.427506 GACTGGACAAACTAAGCCTGG 58.572 52.381 0.00 0.00 0.00 4.45
2493 2767 1.135960 TGGTTGGATCCTGTGTGTGA 58.864 50.000 14.23 0.00 0.00 3.58
2525 2799 2.366640 ATCACGGGCTAGCTCTCTTA 57.633 50.000 13.91 0.00 0.00 2.10
2528 2802 3.031736 TCACGGGCTAGCTCTCTTATTT 58.968 45.455 13.91 0.00 0.00 1.40
2530 2804 3.804873 CACGGGCTAGCTCTCTTATTTTC 59.195 47.826 13.91 0.00 0.00 2.29
2531 2805 3.053455 CGGGCTAGCTCTCTTATTTTCG 58.947 50.000 13.91 0.00 0.00 3.46
2532 2806 3.491104 CGGGCTAGCTCTCTTATTTTCGT 60.491 47.826 13.91 0.00 0.00 3.85
2535 2809 5.006844 GGGCTAGCTCTCTTATTTTCGTTTC 59.993 44.000 15.72 0.00 0.00 2.78
2537 2811 6.237969 GGCTAGCTCTCTTATTTTCGTTTCTG 60.238 42.308 15.72 0.00 0.00 3.02
2538 2812 5.538067 AGCTCTCTTATTTTCGTTTCTGC 57.462 39.130 0.00 0.00 0.00 4.26
2539 2813 4.997395 AGCTCTCTTATTTTCGTTTCTGCA 59.003 37.500 0.00 0.00 0.00 4.41
2540 2814 5.470098 AGCTCTCTTATTTTCGTTTCTGCAA 59.530 36.000 0.00 0.00 0.00 4.08
2591 2866 4.806247 CCTAGTGTAAATGCAGCTACAGTC 59.194 45.833 17.31 6.19 34.35 3.51
2592 2867 3.600388 AGTGTAAATGCAGCTACAGTCC 58.400 45.455 10.18 1.43 27.60 3.85
2593 2868 3.261897 AGTGTAAATGCAGCTACAGTCCT 59.738 43.478 10.18 3.34 27.60 3.85
2594 2869 3.619038 GTGTAAATGCAGCTACAGTCCTC 59.381 47.826 10.18 0.00 0.00 3.71
2595 2870 2.409948 AAATGCAGCTACAGTCCTCC 57.590 50.000 0.00 0.00 0.00 4.30
2596 2871 1.577736 AATGCAGCTACAGTCCTCCT 58.422 50.000 0.00 0.00 0.00 3.69
2597 2872 2.461300 ATGCAGCTACAGTCCTCCTA 57.539 50.000 0.00 0.00 0.00 2.94
2598 2873 1.769026 TGCAGCTACAGTCCTCCTAG 58.231 55.000 0.00 0.00 0.00 3.02
2599 2874 1.006043 TGCAGCTACAGTCCTCCTAGT 59.994 52.381 0.00 0.00 0.00 2.57
2600 2875 1.407258 GCAGCTACAGTCCTCCTAGTG 59.593 57.143 0.00 0.00 0.00 2.74
2601 2876 2.729194 CAGCTACAGTCCTCCTAGTGT 58.271 52.381 0.00 0.00 36.92 3.55
2602 2877 3.887352 CAGCTACAGTCCTCCTAGTGTA 58.113 50.000 0.00 0.00 34.82 2.90
2618 2896 5.185249 CCTAGTGTAACAGAGCTGTAAAGGA 59.815 44.000 3.21 0.00 44.13 3.36
2622 2900 4.530553 TGTAACAGAGCTGTAAAGGATGGA 59.469 41.667 3.21 0.00 44.13 3.41
2651 2929 3.594603 AAATAGACGGACACACCTGAG 57.405 47.619 0.00 0.00 36.31 3.35
2652 2930 1.475403 ATAGACGGACACACCTGAGG 58.525 55.000 0.00 0.00 36.31 3.86
2653 2931 1.248785 TAGACGGACACACCTGAGGC 61.249 60.000 0.00 0.00 36.31 4.70
2654 2932 3.591254 GACGGACACACCTGAGGCC 62.591 68.421 0.00 0.00 36.31 5.19
2655 2933 3.625897 CGGACACACCTGAGGCCA 61.626 66.667 5.01 0.00 36.31 5.36
2656 2934 2.959484 CGGACACACCTGAGGCCAT 61.959 63.158 5.01 0.00 36.31 4.40
2657 2935 1.377725 GGACACACCTGAGGCCATG 60.378 63.158 5.01 0.00 35.41 3.66
2658 2936 2.034687 ACACACCTGAGGCCATGC 59.965 61.111 5.01 0.00 0.00 4.06
2659 2937 2.353958 CACACCTGAGGCCATGCT 59.646 61.111 5.01 0.00 0.00 3.79
2660 2938 1.748122 CACACCTGAGGCCATGCTC 60.748 63.158 5.01 0.00 0.00 4.26
2661 2939 2.124403 CACCTGAGGCCATGCTCC 60.124 66.667 5.01 0.00 0.00 4.70
2662 2940 2.611800 ACCTGAGGCCATGCTCCA 60.612 61.111 5.01 0.00 0.00 3.86
2663 2941 2.124403 CCTGAGGCCATGCTCCAC 60.124 66.667 5.01 0.03 0.00 4.02
2664 2942 2.677289 CCTGAGGCCATGCTCCACT 61.677 63.158 5.01 0.00 0.00 4.00
2665 2943 1.153208 CTGAGGCCATGCTCCACTC 60.153 63.158 5.01 0.00 0.00 3.51
2666 2944 1.907222 CTGAGGCCATGCTCCACTCA 61.907 60.000 5.01 0.00 36.78 3.41
2667 2945 1.300963 GAGGCCATGCTCCACTCAA 59.699 57.895 5.01 0.00 0.00 3.02
2668 2946 0.322816 GAGGCCATGCTCCACTCAAA 60.323 55.000 5.01 0.00 0.00 2.69
2669 2947 0.112995 AGGCCATGCTCCACTCAAAA 59.887 50.000 5.01 0.00 0.00 2.44
2670 2948 0.968405 GGCCATGCTCCACTCAAAAA 59.032 50.000 0.00 0.00 0.00 1.94
2694 2972 1.872773 AAAAACAAACCCTGAGGCCA 58.127 45.000 5.01 0.00 36.11 5.36
2695 2973 2.101640 AAAACAAACCCTGAGGCCAT 57.898 45.000 5.01 0.00 36.11 4.40
2696 2974 1.341080 AAACAAACCCTGAGGCCATG 58.659 50.000 5.01 0.00 36.11 3.66
2697 2975 0.188342 AACAAACCCTGAGGCCATGT 59.812 50.000 5.01 0.00 36.11 3.21
2698 2976 0.188342 ACAAACCCTGAGGCCATGTT 59.812 50.000 5.01 0.00 36.11 2.71
2699 2977 1.341080 CAAACCCTGAGGCCATGTTT 58.659 50.000 5.01 3.87 36.11 2.83
2700 2978 1.693606 CAAACCCTGAGGCCATGTTTT 59.306 47.619 5.01 0.00 36.11 2.43
2701 2979 1.632589 AACCCTGAGGCCATGTTTTC 58.367 50.000 5.01 0.00 36.11 2.29
2702 2980 0.251787 ACCCTGAGGCCATGTTTTCC 60.252 55.000 5.01 0.00 36.11 3.13
2703 2981 0.040204 CCCTGAGGCCATGTTTTCCT 59.960 55.000 5.01 0.00 0.00 3.36
2704 2982 1.467920 CCTGAGGCCATGTTTTCCTC 58.532 55.000 5.01 11.42 45.02 3.71
2736 3014 3.818295 AAACCCTAAAGGCATGTACCA 57.182 42.857 0.00 0.00 40.58 3.25
2737 3015 3.818295 AACCCTAAAGGCATGTACCAA 57.182 42.857 0.00 0.00 40.58 3.67
2738 3016 4.331159 AACCCTAAAGGCATGTACCAAT 57.669 40.909 0.00 0.00 40.58 3.16
2739 3017 3.631250 ACCCTAAAGGCATGTACCAATG 58.369 45.455 0.00 0.00 40.58 2.82
2740 3018 2.958355 CCCTAAAGGCATGTACCAATGG 59.042 50.000 0.00 0.00 0.00 3.16
2741 3019 3.627237 CCCTAAAGGCATGTACCAATGGT 60.627 47.826 10.81 10.81 40.16 3.55
2742 3020 4.385865 CCCTAAAGGCATGTACCAATGGTA 60.386 45.833 8.27 8.27 37.09 3.25
2757 3035 1.866015 TGGTACTCCATCTGTCCAGG 58.134 55.000 0.00 0.00 39.03 4.45
2758 3036 1.078823 TGGTACTCCATCTGTCCAGGT 59.921 52.381 0.00 0.00 39.03 4.00
2759 3037 2.188817 GGTACTCCATCTGTCCAGGTT 58.811 52.381 0.00 0.00 0.00 3.50
2760 3038 2.572104 GGTACTCCATCTGTCCAGGTTT 59.428 50.000 0.00 0.00 0.00 3.27
2761 3039 3.773119 GGTACTCCATCTGTCCAGGTTTA 59.227 47.826 0.00 0.00 0.00 2.01
2762 3040 4.409247 GGTACTCCATCTGTCCAGGTTTAT 59.591 45.833 0.00 0.00 0.00 1.40
2763 3041 5.104485 GGTACTCCATCTGTCCAGGTTTATT 60.104 44.000 0.00 0.00 0.00 1.40
2764 3042 6.099269 GGTACTCCATCTGTCCAGGTTTATTA 59.901 42.308 0.00 0.00 0.00 0.98
2765 3043 6.240549 ACTCCATCTGTCCAGGTTTATTAG 57.759 41.667 0.00 0.00 0.00 1.73
2766 3044 5.964477 ACTCCATCTGTCCAGGTTTATTAGA 59.036 40.000 0.00 0.00 0.00 2.10
2767 3045 6.127026 ACTCCATCTGTCCAGGTTTATTAGAC 60.127 42.308 0.00 0.00 0.00 2.59
2768 3046 5.130477 TCCATCTGTCCAGGTTTATTAGACC 59.870 44.000 0.00 0.00 37.44 3.85
2769 3047 5.368989 CATCTGTCCAGGTTTATTAGACCC 58.631 45.833 0.00 0.00 37.93 4.46
2770 3048 3.778629 TCTGTCCAGGTTTATTAGACCCC 59.221 47.826 0.00 0.00 37.93 4.95
2771 3049 2.848071 TGTCCAGGTTTATTAGACCCCC 59.152 50.000 0.00 0.00 37.93 5.40
2772 3050 3.120898 GTCCAGGTTTATTAGACCCCCT 58.879 50.000 0.00 0.00 37.93 4.79
2773 3051 3.136077 GTCCAGGTTTATTAGACCCCCTC 59.864 52.174 0.00 0.00 37.93 4.30
2774 3052 3.014807 TCCAGGTTTATTAGACCCCCTCT 59.985 47.826 0.00 0.00 37.93 3.69
2775 3053 3.786450 CCAGGTTTATTAGACCCCCTCTT 59.214 47.826 0.00 0.00 37.93 2.85
2776 3054 4.973211 CCAGGTTTATTAGACCCCCTCTTA 59.027 45.833 0.00 0.00 37.93 2.10
2777 3055 5.611408 CCAGGTTTATTAGACCCCCTCTTAT 59.389 44.000 0.00 0.00 37.93 1.73
2778 3056 6.102762 CCAGGTTTATTAGACCCCCTCTTATT 59.897 42.308 0.00 0.00 37.93 1.40
2779 3057 7.367459 CCAGGTTTATTAGACCCCCTCTTATTT 60.367 40.741 0.00 0.00 37.93 1.40
2780 3058 8.059461 CAGGTTTATTAGACCCCCTCTTATTTT 58.941 37.037 0.00 0.00 37.93 1.82
2781 3059 8.059461 AGGTTTATTAGACCCCCTCTTATTTTG 58.941 37.037 0.00 0.00 37.93 2.44
2782 3060 8.057011 GGTTTATTAGACCCCCTCTTATTTTGA 58.943 37.037 0.00 0.00 0.00 2.69
2783 3061 9.121658 GTTTATTAGACCCCCTCTTATTTTGAG 57.878 37.037 0.00 0.00 0.00 3.02
2784 3062 3.653835 AGACCCCCTCTTATTTTGAGC 57.346 47.619 0.00 0.00 0.00 4.26
2785 3063 3.193782 AGACCCCCTCTTATTTTGAGCT 58.806 45.455 0.00 0.00 0.00 4.09
2786 3064 4.371681 AGACCCCCTCTTATTTTGAGCTA 58.628 43.478 0.00 0.00 0.00 3.32
2787 3065 4.788617 AGACCCCCTCTTATTTTGAGCTAA 59.211 41.667 0.00 0.00 0.00 3.09
2788 3066 5.253096 AGACCCCCTCTTATTTTGAGCTAAA 59.747 40.000 0.00 0.00 0.00 1.85
2789 3067 6.068794 AGACCCCCTCTTATTTTGAGCTAAAT 60.069 38.462 0.39 0.39 0.00 1.40
2790 3068 6.503041 ACCCCCTCTTATTTTGAGCTAAATT 58.497 36.000 0.00 0.00 0.00 1.82
2791 3069 6.959954 ACCCCCTCTTATTTTGAGCTAAATTT 59.040 34.615 0.00 0.00 0.00 1.82
2792 3070 7.457852 ACCCCCTCTTATTTTGAGCTAAATTTT 59.542 33.333 0.00 0.00 0.00 1.82
2793 3071 7.765819 CCCCCTCTTATTTTGAGCTAAATTTTG 59.234 37.037 0.00 0.00 0.00 2.44
2794 3072 8.531146 CCCCTCTTATTTTGAGCTAAATTTTGA 58.469 33.333 3.69 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.474570 GGAGCAGGATGGAGCCGT 61.475 66.667 0.00 0.00 35.86 5.68
1 2 3.457625 CTGGAGCAGGATGGAGCCG 62.458 68.421 0.00 0.00 35.86 5.52
29 30 3.382865 ACTGTCTGTGATGATGAGCGTAT 59.617 43.478 0.00 0.00 0.00 3.06
53 54 1.890979 GGCCTGTGATCTGCATCGG 60.891 63.158 0.00 0.00 0.00 4.18
117 118 1.896465 CTCTATAGTGTAGCCCAGCCC 59.104 57.143 0.00 0.00 0.00 5.19
118 119 1.273886 GCTCTATAGTGTAGCCCAGCC 59.726 57.143 0.00 0.00 0.00 4.85
119 120 2.029470 CAGCTCTATAGTGTAGCCCAGC 60.029 54.545 8.00 3.58 36.92 4.85
120 121 2.029470 GCAGCTCTATAGTGTAGCCCAG 60.029 54.545 8.00 1.84 36.92 4.45
121 122 1.964223 GCAGCTCTATAGTGTAGCCCA 59.036 52.381 8.00 0.00 36.92 5.36
122 123 2.243810 AGCAGCTCTATAGTGTAGCCC 58.756 52.381 8.00 1.67 36.92 5.19
123 124 4.303282 GAAAGCAGCTCTATAGTGTAGCC 58.697 47.826 0.00 0.00 36.92 3.93
124 125 3.978217 CGAAAGCAGCTCTATAGTGTAGC 59.022 47.826 0.00 4.17 36.48 3.58
206 207 3.227276 CTCCGCTAGCATCCCCGT 61.227 66.667 16.45 0.00 0.00 5.28
217 218 4.379243 CGGACTTGGTGCTCCGCT 62.379 66.667 0.00 0.00 42.86 5.52
234 235 2.179517 CGGCTGACAGACGGAGAC 59.820 66.667 23.44 0.00 44.58 3.36
245 246 3.230976 TGGCTAGATTCTATTCGGCTGA 58.769 45.455 0.00 0.00 0.00 4.26
249 250 5.541845 TGAACATGGCTAGATTCTATTCGG 58.458 41.667 0.00 0.00 0.00 4.30
252 253 7.129457 TGACTGAACATGGCTAGATTCTATT 57.871 36.000 0.00 0.00 0.00 1.73
318 319 2.941891 TTGTTCGCACGATCTGAAAC 57.058 45.000 0.00 0.00 0.00 2.78
340 341 2.401766 GGTCGCTTCCTACGGTCGA 61.402 63.158 0.00 0.00 0.00 4.20
343 344 1.466025 TTGTGGTCGCTTCCTACGGT 61.466 55.000 0.00 0.00 0.00 4.83
344 345 0.320073 TTTGTGGTCGCTTCCTACGG 60.320 55.000 0.00 0.00 0.00 4.02
368 369 1.937391 CCGCTGCTGCTATTGCTAC 59.063 57.895 14.03 0.00 40.48 3.58
385 386 2.360852 ACATGGACTGCTGCTGCC 60.361 61.111 13.47 9.27 38.71 4.85
386 387 1.645704 CTCACATGGACTGCTGCTGC 61.646 60.000 8.89 8.89 40.20 5.25
387 388 0.321387 ACTCACATGGACTGCTGCTG 60.321 55.000 4.89 4.89 0.00 4.41
436 457 4.016706 CGGGGTGAAAGAGGCCGT 62.017 66.667 0.00 0.00 0.00 5.68
480 502 1.540435 TAGCATGGCCGTGACAGACA 61.540 55.000 29.54 2.94 0.00 3.41
481 503 1.084370 GTAGCATGGCCGTGACAGAC 61.084 60.000 29.54 14.98 0.00 3.51
482 504 1.218047 GTAGCATGGCCGTGACAGA 59.782 57.895 29.54 6.78 0.00 3.41
483 505 1.815421 GGTAGCATGGCCGTGACAG 60.815 63.158 29.54 1.84 0.00 3.51
556 598 0.108804 CCAATCTGCTGCAGCTTTGG 60.109 55.000 33.64 33.64 42.66 3.28
610 657 9.429109 TCTTTAGAAAAAGTAGGGGAAAACAAT 57.571 29.630 0.00 0.00 42.36 2.71
611 658 8.826293 TCTTTAGAAAAAGTAGGGGAAAACAA 57.174 30.769 0.00 0.00 42.36 2.83
612 659 8.276477 TCTCTTTAGAAAAAGTAGGGGAAAACA 58.724 33.333 0.00 0.00 42.36 2.83
613 660 8.687292 TCTCTTTAGAAAAAGTAGGGGAAAAC 57.313 34.615 0.00 0.00 42.36 2.43
614 661 9.350951 CTTCTCTTTAGAAAAAGTAGGGGAAAA 57.649 33.333 0.00 0.00 41.19 2.29
615 662 8.720537 TCTTCTCTTTAGAAAAAGTAGGGGAAA 58.279 33.333 0.00 0.00 41.19 3.13
619 700 9.726438 TTGATCTTCTCTTTAGAAAAAGTAGGG 57.274 33.333 0.00 0.00 41.19 3.53
689 799 2.533535 CGTTCAAGATGCAGATCGACTC 59.466 50.000 0.00 0.00 33.34 3.36
705 815 0.512518 CACAGCTGCGAAATCGTTCA 59.487 50.000 15.27 0.00 42.22 3.18
706 816 0.790207 TCACAGCTGCGAAATCGTTC 59.210 50.000 15.27 0.00 42.22 3.95
709 819 1.001624 TGATCACAGCTGCGAAATCG 58.998 50.000 15.27 0.00 43.27 3.34
710 820 2.733820 CTGATCACAGCTGCGAAATC 57.266 50.000 15.27 11.86 37.33 2.17
737 856 7.309255 GCGATCCTCAGATTATACTAACCAGAA 60.309 40.741 0.00 0.00 30.90 3.02
746 865 3.502920 CCGTGCGATCCTCAGATTATAC 58.497 50.000 0.00 0.00 30.90 1.47
836 969 1.002773 GGATGGTTAGTGTTGACCGGT 59.997 52.381 6.92 6.92 38.81 5.28
846 994 5.483937 TGTGATTACAGTCTGGATGGTTAGT 59.516 40.000 4.53 0.00 31.91 2.24
848 996 5.247337 TGTGTGATTACAGTCTGGATGGTTA 59.753 40.000 4.53 0.00 37.52 2.85
849 997 4.041567 TGTGTGATTACAGTCTGGATGGTT 59.958 41.667 4.53 0.00 37.52 3.67
854 1002 2.028112 GCCTGTGTGATTACAGTCTGGA 60.028 50.000 4.53 0.00 45.12 3.86
859 1007 1.064003 TGGGCCTGTGTGATTACAGT 58.936 50.000 4.53 0.00 45.12 3.55
864 1012 1.047801 GGTTTTGGGCCTGTGTGATT 58.952 50.000 4.53 0.00 0.00 2.57
874 1052 1.606601 GGAGGTGAGGGTTTTGGGC 60.607 63.158 0.00 0.00 0.00 5.36
875 1053 0.409484 ATGGAGGTGAGGGTTTTGGG 59.591 55.000 0.00 0.00 0.00 4.12
885 1063 1.385915 GGGATGGGGATGGAGGTGA 60.386 63.158 0.00 0.00 0.00 4.02
888 1066 2.038438 TGGGGATGGGGATGGAGG 60.038 66.667 0.00 0.00 0.00 4.30
942 1120 1.277557 AGCTTAGCTCAAGAGTGTGGG 59.722 52.381 0.00 0.00 36.22 4.61
1020 1204 4.479993 ACCGCCAGCAGGATGAGC 62.480 66.667 0.00 0.00 39.69 4.26
1506 1693 2.125673 GTGGTGTGGACGATCCCG 60.126 66.667 0.00 0.00 35.03 5.14
1814 2001 3.316283 GAATCATGATCCTCTCTCGCAC 58.684 50.000 9.06 0.00 0.00 5.34
1815 2002 2.030451 CGAATCATGATCCTCTCTCGCA 60.030 50.000 9.06 0.00 0.00 5.10
1816 2003 2.030363 ACGAATCATGATCCTCTCTCGC 60.030 50.000 19.87 0.00 0.00 5.03
1817 2004 3.251972 TCACGAATCATGATCCTCTCTCG 59.748 47.826 18.83 18.83 0.00 4.04
1821 2008 3.320541 GGTCTCACGAATCATGATCCTCT 59.679 47.826 9.06 0.00 0.00 3.69
1832 2025 1.064208 CGATCTGTCGGTCTCACGAAT 59.936 52.381 0.00 0.00 45.38 3.34
1881 2078 6.990939 GGAACTAGTAACCTATCCAAATCCAC 59.009 42.308 0.00 0.00 0.00 4.02
1902 2099 0.453390 GCAGCCACTAATGCAGGAAC 59.547 55.000 0.00 0.00 42.11 3.62
1904 2101 0.329261 AAGCAGCCACTAATGCAGGA 59.671 50.000 0.00 0.00 45.01 3.86
1905 2102 0.737219 GAAGCAGCCACTAATGCAGG 59.263 55.000 0.00 0.00 45.01 4.85
1906 2103 1.747709 AGAAGCAGCCACTAATGCAG 58.252 50.000 0.00 0.00 45.01 4.41
1907 2104 2.086869 GAAGAAGCAGCCACTAATGCA 58.913 47.619 0.00 0.00 45.01 3.96
1909 2106 3.870419 GAGAGAAGAAGCAGCCACTAATG 59.130 47.826 0.00 0.00 0.00 1.90
1910 2107 3.774216 AGAGAGAAGAAGCAGCCACTAAT 59.226 43.478 0.00 0.00 0.00 1.73
1913 2111 1.550072 GAGAGAGAAGAAGCAGCCACT 59.450 52.381 0.00 0.00 0.00 4.00
1950 2148 7.439356 GGAGGAAAAGAAAGAGAACAAAAATGG 59.561 37.037 0.00 0.00 0.00 3.16
1957 2156 3.722101 AGGGGAGGAAAAGAAAGAGAACA 59.278 43.478 0.00 0.00 0.00 3.18
1958 2157 4.075682 CAGGGGAGGAAAAGAAAGAGAAC 58.924 47.826 0.00 0.00 0.00 3.01
1960 2159 3.327439 ACAGGGGAGGAAAAGAAAGAGA 58.673 45.455 0.00 0.00 0.00 3.10
1967 2166 2.450476 CCATCAACAGGGGAGGAAAAG 58.550 52.381 0.00 0.00 0.00 2.27
1978 2177 3.877559 TCACATCTTAGCCCATCAACAG 58.122 45.455 0.00 0.00 0.00 3.16
1983 2182 6.471146 ACATCTTATCACATCTTAGCCCATC 58.529 40.000 0.00 0.00 0.00 3.51
1984 2183 6.445451 ACATCTTATCACATCTTAGCCCAT 57.555 37.500 0.00 0.00 0.00 4.00
1993 2212 6.595326 TCAACAGTGGAACATCTTATCACATC 59.405 38.462 0.00 0.00 44.52 3.06
2001 2220 4.214119 CGTGATTCAACAGTGGAACATCTT 59.786 41.667 0.00 0.00 44.52 2.40
2003 2222 3.120199 CCGTGATTCAACAGTGGAACATC 60.120 47.826 0.00 0.00 44.52 3.06
2009 2228 1.227999 ACGCCGTGATTCAACAGTGG 61.228 55.000 0.00 0.00 0.00 4.00
2023 2242 3.479505 TCATCCAACAAATTAACGCCG 57.520 42.857 0.00 0.00 0.00 6.46
2025 2244 9.687717 CAATTTAATCATCCAACAAATTAACGC 57.312 29.630 0.00 0.00 29.98 4.84
2029 2248 9.941325 AGTGCAATTTAATCATCCAACAAATTA 57.059 25.926 0.00 0.00 29.98 1.40
2030 2249 8.723311 CAGTGCAATTTAATCATCCAACAAATT 58.277 29.630 0.00 0.00 30.89 1.82
2031 2250 7.148373 GCAGTGCAATTTAATCATCCAACAAAT 60.148 33.333 11.09 0.00 0.00 2.32
2032 2251 6.147492 GCAGTGCAATTTAATCATCCAACAAA 59.853 34.615 11.09 0.00 0.00 2.83
2033 2252 5.638657 GCAGTGCAATTTAATCATCCAACAA 59.361 36.000 11.09 0.00 0.00 2.83
2034 2253 5.047164 AGCAGTGCAATTTAATCATCCAACA 60.047 36.000 19.20 0.00 0.00 3.33
2051 2270 4.518211 AGCCAAGATCAAATATAGCAGTGC 59.482 41.667 7.13 7.13 0.00 4.40
2052 2271 6.933521 ACTAGCCAAGATCAAATATAGCAGTG 59.066 38.462 0.00 0.00 0.00 3.66
2056 2275 7.659390 AGTGAACTAGCCAAGATCAAATATAGC 59.341 37.037 0.00 0.00 38.59 2.97
2073 2292 7.936584 AGATAACTTAGCTGCTAGTGAACTAG 58.063 38.462 9.62 12.30 46.63 2.57
2074 2293 7.883391 AGATAACTTAGCTGCTAGTGAACTA 57.117 36.000 9.62 1.47 0.00 2.24
2077 2296 7.411486 AGAAGATAACTTAGCTGCTAGTGAA 57.589 36.000 9.62 0.00 36.39 3.18
2079 2298 9.026074 GTTTAGAAGATAACTTAGCTGCTAGTG 57.974 37.037 9.62 9.41 34.05 2.74
2080 2299 8.750298 TGTTTAGAAGATAACTTAGCTGCTAGT 58.250 33.333 9.62 7.58 34.05 2.57
2081 2300 9.026074 GTGTTTAGAAGATAACTTAGCTGCTAG 57.974 37.037 9.62 6.98 34.05 3.42
2086 2305 9.810545 GATGAGTGTTTAGAAGATAACTTAGCT 57.189 33.333 0.00 0.00 36.39 3.32
2088 2307 9.790389 ACGATGAGTGTTTAGAAGATAACTTAG 57.210 33.333 0.00 0.00 36.39 2.18
2127 2349 2.367567 ACCGGATTCTGTGTACAACTGT 59.632 45.455 9.46 0.00 0.00 3.55
2128 2350 3.040147 ACCGGATTCTGTGTACAACTG 57.960 47.619 9.46 0.00 0.00 3.16
2129 2351 3.181458 ACAACCGGATTCTGTGTACAACT 60.181 43.478 9.46 0.00 0.00 3.16
2130 2352 3.135994 ACAACCGGATTCTGTGTACAAC 58.864 45.455 9.46 0.00 0.00 3.32
2131 2353 3.395639 GACAACCGGATTCTGTGTACAA 58.604 45.455 9.46 0.00 0.00 2.41
2132 2354 2.608506 CGACAACCGGATTCTGTGTACA 60.609 50.000 9.46 0.00 33.91 2.90
2133 2355 1.990563 CGACAACCGGATTCTGTGTAC 59.009 52.381 9.46 0.00 33.91 2.90
2134 2356 2.357327 CGACAACCGGATTCTGTGTA 57.643 50.000 9.46 0.00 33.91 2.90
2135 2357 3.210857 CGACAACCGGATTCTGTGT 57.789 52.632 9.46 1.57 33.91 3.72
2194 2416 6.401047 GGCTTCACTTTTTCAACAACAGAAAC 60.401 38.462 0.00 0.00 34.94 2.78
2337 2563 3.306088 GCTACTGACACCAAGTTGCTCTA 60.306 47.826 0.00 0.00 33.04 2.43
2426 2687 5.303971 CCCATCTTCTGATCCAGATACAAC 58.696 45.833 0.00 0.00 40.39 3.32
2493 2767 3.117888 AGCCCGTGATAGAATTCATTGGT 60.118 43.478 8.44 0.00 0.00 3.67
2525 2799 6.074034 CCCGTTATTTTTGCAGAAACGAAAAT 60.074 34.615 12.66 10.76 44.11 1.82
2528 2802 4.291783 CCCGTTATTTTTGCAGAAACGAA 58.708 39.130 12.66 4.93 44.11 3.85
2530 2804 2.407026 GCCCGTTATTTTTGCAGAAACG 59.593 45.455 4.29 5.21 41.79 3.60
2531 2805 3.649073 AGCCCGTTATTTTTGCAGAAAC 58.351 40.909 4.29 0.00 0.00 2.78
2532 2806 4.617298 GCTAGCCCGTTATTTTTGCAGAAA 60.617 41.667 2.29 4.71 0.00 2.52
2535 2809 2.423538 AGCTAGCCCGTTATTTTTGCAG 59.576 45.455 12.13 0.00 0.00 4.41
2537 2811 2.422127 TGAGCTAGCCCGTTATTTTTGC 59.578 45.455 12.13 0.00 0.00 3.68
2538 2812 4.278678 CTGAGCTAGCCCGTTATTTTTG 57.721 45.455 12.13 0.00 0.00 2.44
2591 2866 3.093057 ACAGCTCTGTTACACTAGGAGG 58.907 50.000 0.00 0.00 41.83 4.30
2592 2867 5.899120 TTACAGCTCTGTTACACTAGGAG 57.101 43.478 7.92 0.00 41.83 3.69
2593 2868 5.185249 CCTTTACAGCTCTGTTACACTAGGA 59.815 44.000 7.92 0.00 41.83 2.94
2594 2869 5.185249 TCCTTTACAGCTCTGTTACACTAGG 59.815 44.000 7.92 3.50 41.83 3.02
2595 2870 6.268825 TCCTTTACAGCTCTGTTACACTAG 57.731 41.667 7.92 0.00 41.83 2.57
2596 2871 6.351033 CCATCCTTTACAGCTCTGTTACACTA 60.351 42.308 7.92 0.00 41.83 2.74
2597 2872 5.482908 CATCCTTTACAGCTCTGTTACACT 58.517 41.667 7.92 0.00 41.83 3.55
2598 2873 4.631813 CCATCCTTTACAGCTCTGTTACAC 59.368 45.833 7.92 0.00 41.83 2.90
2599 2874 4.530553 TCCATCCTTTACAGCTCTGTTACA 59.469 41.667 7.92 0.00 41.83 2.41
2600 2875 4.870991 GTCCATCCTTTACAGCTCTGTTAC 59.129 45.833 7.92 0.00 41.83 2.50
2601 2876 4.777896 AGTCCATCCTTTACAGCTCTGTTA 59.222 41.667 7.92 0.00 41.83 2.41
2602 2877 3.584848 AGTCCATCCTTTACAGCTCTGTT 59.415 43.478 7.92 0.00 41.83 3.16
2622 2900 4.525487 TGTGTCCGTCTATTTAGTGGAAGT 59.475 41.667 3.88 0.00 33.25 3.01
2631 2909 2.233922 CCTCAGGTGTGTCCGTCTATTT 59.766 50.000 0.00 0.00 41.99 1.40
2638 2916 2.959484 ATGGCCTCAGGTGTGTCCG 61.959 63.158 3.32 0.00 41.99 4.79
2651 2929 0.968405 TTTTTGAGTGGAGCATGGCC 59.032 50.000 0.00 0.00 0.00 5.36
2675 2953 1.872773 TGGCCTCAGGGTTTGTTTTT 58.127 45.000 3.32 0.00 34.45 1.94
2676 2954 1.693606 CATGGCCTCAGGGTTTGTTTT 59.306 47.619 3.32 0.00 34.45 2.43
2677 2955 1.341080 CATGGCCTCAGGGTTTGTTT 58.659 50.000 3.32 0.00 34.45 2.83
2678 2956 0.188342 ACATGGCCTCAGGGTTTGTT 59.812 50.000 3.32 0.00 34.45 2.83
2679 2957 0.188342 AACATGGCCTCAGGGTTTGT 59.812 50.000 3.32 0.00 34.45 2.83
2680 2958 1.341080 AAACATGGCCTCAGGGTTTG 58.659 50.000 3.32 0.00 29.42 2.93
2681 2959 1.970640 GAAAACATGGCCTCAGGGTTT 59.029 47.619 3.32 0.00 45.70 3.27
2682 2960 1.632589 GAAAACATGGCCTCAGGGTT 58.367 50.000 3.32 0.00 35.99 4.11
2683 2961 0.251787 GGAAAACATGGCCTCAGGGT 60.252 55.000 3.32 0.00 34.45 4.34
2684 2962 0.040204 AGGAAAACATGGCCTCAGGG 59.960 55.000 3.32 0.00 0.00 4.45
2685 2963 1.467920 GAGGAAAACATGGCCTCAGG 58.532 55.000 16.50 0.00 45.89 3.86
2688 2966 3.653344 GTTTTGAGGAAAACATGGCCTC 58.347 45.455 3.32 15.24 46.97 4.70
2689 2967 3.751479 GTTTTGAGGAAAACATGGCCT 57.249 42.857 3.32 0.00 46.97 5.19
2714 2992 4.484912 TGGTACATGCCTTTAGGGTTTTT 58.515 39.130 0.00 0.00 37.43 1.94
2715 2993 4.120946 TGGTACATGCCTTTAGGGTTTT 57.879 40.909 0.00 0.00 37.43 2.43
2716 2994 3.818295 TGGTACATGCCTTTAGGGTTT 57.182 42.857 0.00 0.00 37.43 3.27
2717 2995 3.818295 TTGGTACATGCCTTTAGGGTT 57.182 42.857 0.00 0.00 39.30 4.11
2718 2996 3.627237 CCATTGGTACATGCCTTTAGGGT 60.627 47.826 0.00 0.00 39.30 4.34
2719 2997 2.958355 CCATTGGTACATGCCTTTAGGG 59.042 50.000 0.00 0.00 39.30 3.53
2720 2998 3.631250 ACCATTGGTACATGCCTTTAGG 58.369 45.455 6.54 0.00 39.30 2.69
2739 3017 1.867363 ACCTGGACAGATGGAGTACC 58.133 55.000 0.00 0.00 0.00 3.34
2740 3018 3.983044 AAACCTGGACAGATGGAGTAC 57.017 47.619 0.00 0.00 0.00 2.73
2741 3019 7.069578 GTCTAATAAACCTGGACAGATGGAGTA 59.930 40.741 0.00 0.00 0.00 2.59
2742 3020 5.964477 TCTAATAAACCTGGACAGATGGAGT 59.036 40.000 0.00 0.00 0.00 3.85
2743 3021 6.284459 GTCTAATAAACCTGGACAGATGGAG 58.716 44.000 0.00 0.00 0.00 3.86
2744 3022 5.130477 GGTCTAATAAACCTGGACAGATGGA 59.870 44.000 0.00 0.00 33.78 3.41
2745 3023 5.368989 GGTCTAATAAACCTGGACAGATGG 58.631 45.833 0.00 0.00 33.78 3.51
2746 3024 5.368989 GGGTCTAATAAACCTGGACAGATG 58.631 45.833 0.00 0.00 36.97 2.90
2747 3025 4.412528 GGGGTCTAATAAACCTGGACAGAT 59.587 45.833 0.00 0.00 36.97 2.90
2748 3026 3.778629 GGGGTCTAATAAACCTGGACAGA 59.221 47.826 0.00 0.00 36.97 3.41
2749 3027 3.118000 GGGGGTCTAATAAACCTGGACAG 60.118 52.174 0.00 0.00 36.97 3.51
2750 3028 2.848071 GGGGGTCTAATAAACCTGGACA 59.152 50.000 0.00 0.00 36.97 4.02
2751 3029 3.120898 AGGGGGTCTAATAAACCTGGAC 58.879 50.000 0.00 0.00 36.97 4.02
2752 3030 3.014807 AGAGGGGGTCTAATAAACCTGGA 59.985 47.826 0.00 0.00 36.97 3.86
2753 3031 3.394645 AGAGGGGGTCTAATAAACCTGG 58.605 50.000 0.00 0.00 36.97 4.45
2754 3032 6.765355 ATAAGAGGGGGTCTAATAAACCTG 57.235 41.667 0.00 0.00 36.97 4.00
2755 3033 7.782695 AAATAAGAGGGGGTCTAATAAACCT 57.217 36.000 0.00 0.00 36.97 3.50
2756 3034 8.057011 TCAAAATAAGAGGGGGTCTAATAAACC 58.943 37.037 0.00 0.00 32.65 3.27
2757 3035 9.121658 CTCAAAATAAGAGGGGGTCTAATAAAC 57.878 37.037 0.00 0.00 32.65 2.01
2758 3036 7.778382 GCTCAAAATAAGAGGGGGTCTAATAAA 59.222 37.037 0.00 0.00 32.65 1.40
2759 3037 7.128883 AGCTCAAAATAAGAGGGGGTCTAATAA 59.871 37.037 0.00 0.00 32.65 1.40
2760 3038 6.619852 AGCTCAAAATAAGAGGGGGTCTAATA 59.380 38.462 0.00 0.00 32.65 0.98
2761 3039 5.433381 AGCTCAAAATAAGAGGGGGTCTAAT 59.567 40.000 0.00 0.00 32.65 1.73
2762 3040 4.788617 AGCTCAAAATAAGAGGGGGTCTAA 59.211 41.667 0.00 0.00 32.65 2.10
2763 3041 4.371681 AGCTCAAAATAAGAGGGGGTCTA 58.628 43.478 0.00 0.00 32.65 2.59
2764 3042 3.193782 AGCTCAAAATAAGAGGGGGTCT 58.806 45.455 0.00 0.00 36.94 3.85
2765 3043 3.653835 AGCTCAAAATAAGAGGGGGTC 57.346 47.619 0.00 0.00 33.72 4.46
2766 3044 5.530176 TTTAGCTCAAAATAAGAGGGGGT 57.470 39.130 0.00 0.00 33.72 4.95
2767 3045 7.423844 AAATTTAGCTCAAAATAAGAGGGGG 57.576 36.000 0.00 0.00 33.72 5.40
2768 3046 8.531146 TCAAAATTTAGCTCAAAATAAGAGGGG 58.469 33.333 0.00 0.00 33.72 4.79


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

AutoCloner maintained by Alex Coulton.