Multiple sequence alignment - TraesCS5A01G239200

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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 TraesCS5A01G239200 chr5A 100.000 3595 0 0 1 3595 455283117 455279523 0.000000e+00 6639
1 TraesCS5A01G239200 chr5A 98.234 906 15 1 1 905 11330522 11331427 0.000000e+00 1583
2 TraesCS5A01G239200 chr5A 97.903 906 17 2 1 904 536510329 536509424 0.000000e+00 1567
3 TraesCS5A01G239200 chrUn 98.554 899 11 2 1 898 170208121 170207224 0.000000e+00 1587
4 TraesCS5A01G239200 chr4A 98.331 899 14 1 1 898 603518377 603517479 0.000000e+00 1576
5 TraesCS5A01G239200 chr4A 98.222 900 14 2 1 898 612952488 612953387 0.000000e+00 1572
6 TraesCS5A01G239200 chr1A 98.331 899 14 1 1 898 523862935 523863833 0.000000e+00 1576
7 TraesCS5A01G239200 chr1A 98.109 899 16 1 1 898 15109782 15108884 0.000000e+00 1565
8 TraesCS5A01G239200 chr5D 87.588 1426 90 40 943 2314 354275824 354274432 0.000000e+00 1572
9 TraesCS5A01G239200 chr5D 88.613 483 13 19 3126 3595 354273569 354273116 1.890000e-152 549
10 TraesCS5A01G239200 chr5D 77.726 862 73 53 2318 3131 354274392 354273602 5.550000e-113 418
11 TraesCS5A01G239200 chr6A 98.007 903 16 2 1 902 601976711 601975810 0.000000e+00 1567
12 TraesCS5A01G239200 chr6A 98.109 899 16 1 1 898 99044607 99043709 0.000000e+00 1565
13 TraesCS5A01G239200 chr5B 87.286 1400 100 33 943 2314 418559637 418558288 0.000000e+00 1528
14 TraesCS5A01G239200 chr5B 88.152 422 21 14 3179 3595 418557362 418556965 3.250000e-130 475
15 TraesCS5A01G239200 chr5B 80.532 714 45 33 2440 3112 418558119 418557459 2.530000e-126 462


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 TraesCS5A01G239200 chr5A 455279523 455283117 3594 True 6639.000000 6639 100.000000 1 3595 1 chr5A.!!$R1 3594
1 TraesCS5A01G239200 chr5A 11330522 11331427 905 False 1583.000000 1583 98.234000 1 905 1 chr5A.!!$F1 904
2 TraesCS5A01G239200 chr5A 536509424 536510329 905 True 1567.000000 1567 97.903000 1 904 1 chr5A.!!$R2 903
3 TraesCS5A01G239200 chrUn 170207224 170208121 897 True 1587.000000 1587 98.554000 1 898 1 chrUn.!!$R1 897
4 TraesCS5A01G239200 chr4A 603517479 603518377 898 True 1576.000000 1576 98.331000 1 898 1 chr4A.!!$R1 897
5 TraesCS5A01G239200 chr4A 612952488 612953387 899 False 1572.000000 1572 98.222000 1 898 1 chr4A.!!$F1 897
6 TraesCS5A01G239200 chr1A 523862935 523863833 898 False 1576.000000 1576 98.331000 1 898 1 chr1A.!!$F1 897
7 TraesCS5A01G239200 chr1A 15108884 15109782 898 True 1565.000000 1565 98.109000 1 898 1 chr1A.!!$R1 897
8 TraesCS5A01G239200 chr5D 354273116 354275824 2708 True 846.333333 1572 84.642333 943 3595 3 chr5D.!!$R1 2652
9 TraesCS5A01G239200 chr6A 601975810 601976711 901 True 1567.000000 1567 98.007000 1 902 1 chr6A.!!$R2 901
10 TraesCS5A01G239200 chr6A 99043709 99044607 898 True 1565.000000 1565 98.109000 1 898 1 chr6A.!!$R1 897
11 TraesCS5A01G239200 chr5B 418556965 418559637 2672 True 821.666667 1528 85.323333 943 3595 3 chr5B.!!$R1 2652

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
913 916 0.547075 TAGTCTCCTCACTCCTCCCG 59.453 60.0 0.0 0.0 0.00 5.14 F
1788 1830 0.318441 TCTTCAGAACCACCTGCGAG 59.682 55.0 0.0 0.0 34.28 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 1852 0.035630 ACGGTACTACGTGCTCCTCT 60.036 55.0 0.0 0.0 46.64 3.69 R
2983 3157 0.041833 TCCCTCCCTTCTCTCCACTG 59.958 60.0 0.0 0.0 0.00 3.66 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
682 684 2.035626 CAAGCCACCAACCGGGAT 59.964 61.111 6.32 0.00 41.15 3.85
813 816 3.998672 GGCTCACGAACCGGGACA 61.999 66.667 6.32 0.00 32.99 4.02
864 867 0.912487 ACCGGGACTAATGGGCTGAA 60.912 55.000 6.32 0.00 0.00 3.02
905 908 5.105675 CCCTGTTTTCTACTAGTCTCCTCAC 60.106 48.000 0.00 0.00 0.00 3.51
906 909 5.712917 CCTGTTTTCTACTAGTCTCCTCACT 59.287 44.000 0.00 0.00 0.00 3.41
907 910 6.127842 CCTGTTTTCTACTAGTCTCCTCACTC 60.128 46.154 0.00 0.00 0.00 3.51
908 911 5.711036 TGTTTTCTACTAGTCTCCTCACTCC 59.289 44.000 0.00 0.00 0.00 3.85
909 912 5.782677 TTTCTACTAGTCTCCTCACTCCT 57.217 43.478 0.00 0.00 0.00 3.69
910 913 5.362105 TTCTACTAGTCTCCTCACTCCTC 57.638 47.826 0.00 0.00 0.00 3.71
911 914 3.712733 TCTACTAGTCTCCTCACTCCTCC 59.287 52.174 0.00 0.00 0.00 4.30
912 915 1.567175 ACTAGTCTCCTCACTCCTCCC 59.433 57.143 0.00 0.00 0.00 4.30
913 916 0.547075 TAGTCTCCTCACTCCTCCCG 59.453 60.000 0.00 0.00 0.00 5.14
914 917 1.755008 GTCTCCTCACTCCTCCCGG 60.755 68.421 0.00 0.00 0.00 5.73
915 918 3.151022 CTCCTCACTCCTCCCGGC 61.151 72.222 0.00 0.00 0.00 6.13
916 919 4.779733 TCCTCACTCCTCCCGGCC 62.780 72.222 0.00 0.00 0.00 6.13
940 943 4.851214 AGCCTCGCTCCCTCCCTC 62.851 72.222 0.00 0.00 30.62 4.30
1002 1005 1.079819 ATCACTCACCTCGCAACGG 60.080 57.895 0.00 0.00 0.00 4.44
1104 1114 1.601171 CCAGCAAGAGAGTCCCAGG 59.399 63.158 0.00 0.00 0.00 4.45
1108 1118 2.285743 AAGAGAGTCCCAGGGGGC 60.286 66.667 5.33 2.72 43.94 5.80
1130 1140 3.715097 AGCTGCCACTGCTCCTCC 61.715 66.667 0.00 0.00 33.52 4.30
1155 1165 2.105930 GCACTCAGGCGAGCTAGG 59.894 66.667 6.32 0.00 43.66 3.02
1192 1206 4.525949 GGTACGCGGGGAGAAGGC 62.526 72.222 12.47 0.00 0.00 4.35
1193 1207 4.525949 GTACGCGGGGAGAAGGCC 62.526 72.222 12.47 0.00 0.00 5.19
1197 1229 3.717294 GCGGGGAGAAGGCCAAGA 61.717 66.667 5.01 0.00 0.00 3.02
1642 1677 2.369532 GAGGCCCATACGGTAATTACCA 59.630 50.000 29.56 15.01 46.80 3.25
1643 1678 2.105306 AGGCCCATACGGTAATTACCAC 59.895 50.000 29.56 12.12 46.80 4.16
1644 1679 2.105306 GGCCCATACGGTAATTACCACT 59.895 50.000 29.56 18.15 46.80 4.00
1687 1729 2.943978 GCACCCAGCTCGTAGTGGT 61.944 63.158 0.00 0.00 41.15 4.16
1694 1736 3.432749 CCCAGCTCGTAGTGGTAGTAGTA 60.433 52.174 0.00 0.00 31.17 1.82
1695 1737 3.808726 CCAGCTCGTAGTGGTAGTAGTAG 59.191 52.174 0.00 0.00 0.00 2.57
1696 1738 3.248125 CAGCTCGTAGTGGTAGTAGTAGC 59.752 52.174 0.00 0.00 0.00 3.58
1714 1756 1.704010 CACACTGCATCGTACGCTG 59.296 57.895 14.50 14.50 0.00 5.18
1777 1819 6.875948 TTGACATTTTCCGAATCTTCAGAA 57.124 33.333 0.00 0.00 0.00 3.02
1786 1828 1.734465 GAATCTTCAGAACCACCTGCG 59.266 52.381 0.00 0.00 34.28 5.18
1788 1830 0.318441 TCTTCAGAACCACCTGCGAG 59.682 55.000 0.00 0.00 34.28 5.03
1789 1831 1.294659 CTTCAGAACCACCTGCGAGC 61.295 60.000 0.00 0.00 34.28 5.03
1790 1832 1.758440 TTCAGAACCACCTGCGAGCT 61.758 55.000 0.00 0.00 34.28 4.09
1802 1844 2.625906 CGAGCTCGCTCTCTCTCG 59.374 66.667 25.07 0.00 41.66 4.04
1803 1845 2.327940 GAGCTCGCTCTCTCTCGC 59.672 66.667 11.49 0.00 39.80 5.03
1827 1869 0.100861 GCAGAGGAGCACGTAGTACC 59.899 60.000 0.00 0.00 41.61 3.34
1828 1870 0.377554 CAGAGGAGCACGTAGTACCG 59.622 60.000 0.00 0.00 41.61 4.02
1831 1873 1.028868 AGGAGCACGTAGTACCGTCC 61.029 60.000 0.00 0.00 41.61 4.79
1844 1886 4.084287 AGTACCGTCCAGAGTACATTTCA 58.916 43.478 0.00 0.00 41.07 2.69
1866 1908 1.758122 GCATCCAGGGCCGGATTTT 60.758 57.895 22.05 5.44 43.58 1.82
1869 1911 0.631212 ATCCAGGGCCGGATTTTCTT 59.369 50.000 19.83 2.93 43.58 2.52
1938 1985 1.083401 GCAACAGAGCGAACGTGTG 60.083 57.895 0.00 0.00 0.00 3.82
1940 1987 2.585869 AACAGAGCGAACGTGTGCG 61.586 57.895 6.63 0.00 44.93 5.34
1960 2007 3.675790 ACACCAGCCATGCCCCAT 61.676 61.111 0.00 0.00 0.00 4.00
1961 2008 3.151710 CACCAGCCATGCCCCATG 61.152 66.667 0.00 0.00 41.10 3.66
1982 2029 3.189910 TGCATTCATCTTGCACAGAGTTC 59.810 43.478 0.00 0.00 44.73 3.01
1994 2041 1.276421 ACAGAGTTCTAGCGGCACATT 59.724 47.619 1.45 0.00 0.00 2.71
1995 2042 1.929836 CAGAGTTCTAGCGGCACATTC 59.070 52.381 1.45 0.00 0.00 2.67
1996 2043 1.550524 AGAGTTCTAGCGGCACATTCA 59.449 47.619 1.45 0.00 0.00 2.57
2006 2053 2.564771 CGGCACATTCATATCACCTGT 58.435 47.619 0.00 0.00 0.00 4.00
2012 2059 3.144506 CATTCATATCACCTGTGCTCCC 58.855 50.000 0.00 0.00 0.00 4.30
2022 2069 0.955919 CTGTGCTCCCTTCCGGTTTC 60.956 60.000 0.00 0.00 0.00 2.78
2058 2105 3.244976 CGTGCAACATTTTTCAGGATCC 58.755 45.455 2.48 2.48 35.74 3.36
2059 2106 3.588955 GTGCAACATTTTTCAGGATCCC 58.411 45.455 8.55 0.00 36.32 3.85
2125 2172 0.251121 TTCAGCAAGCGAAATGGGGA 60.251 50.000 0.00 0.00 0.00 4.81
2139 2186 0.758734 TGGGGACATGATTAGGCGAG 59.241 55.000 0.00 0.00 33.40 5.03
2144 2191 3.305471 GGGACATGATTAGGCGAGTAGTC 60.305 52.174 0.00 0.00 0.00 2.59
2149 2196 3.617284 TGATTAGGCGAGTAGTCTGTGA 58.383 45.455 0.00 0.00 35.65 3.58
2167 2214 3.181435 TGTGAGATTGGGTGGTGATTTGA 60.181 43.478 0.00 0.00 0.00 2.69
2168 2215 3.441572 GTGAGATTGGGTGGTGATTTGAG 59.558 47.826 0.00 0.00 0.00 3.02
2169 2216 2.424956 GAGATTGGGTGGTGATTTGAGC 59.575 50.000 0.00 0.00 0.00 4.26
2173 2220 1.177401 GGGTGGTGATTTGAGCTTCC 58.823 55.000 0.00 0.00 0.00 3.46
2174 2221 1.547675 GGGTGGTGATTTGAGCTTCCA 60.548 52.381 0.00 0.00 0.00 3.53
2175 2222 1.815003 GGTGGTGATTTGAGCTTCCAG 59.185 52.381 0.00 0.00 0.00 3.86
2176 2223 1.200948 GTGGTGATTTGAGCTTCCAGC 59.799 52.381 0.00 0.00 42.84 4.85
2199 2250 0.107456 GATGTCCATCATCTGCCCGT 59.893 55.000 2.43 0.00 46.64 5.28
2203 2254 0.178767 TCCATCATCTGCCCGTTGAG 59.821 55.000 0.00 0.00 0.00 3.02
2207 2258 0.465705 TCATCTGCCCGTTGAGGATC 59.534 55.000 0.00 0.00 45.00 3.36
2212 2263 1.661821 GCCCGTTGAGGATCGATCG 60.662 63.158 18.81 9.36 45.00 3.69
2215 2266 1.065764 CGTTGAGGATCGATCGGCA 59.934 57.895 18.81 15.59 38.61 5.69
2216 2267 0.936764 CGTTGAGGATCGATCGGCAG 60.937 60.000 18.81 5.40 38.61 4.85
2218 2269 2.048690 GAGGATCGATCGGCAGGC 60.049 66.667 18.81 4.26 0.00 4.85
2220 2271 2.356793 GGATCGATCGGCAGGCAG 60.357 66.667 18.81 0.00 0.00 4.85
2232 2283 2.036256 AGGCAGCCCAACATCCAC 59.964 61.111 8.22 0.00 0.00 4.02
2261 2315 1.614903 CATTGGAGAAGCAGGCAAACA 59.385 47.619 0.00 0.00 0.00 2.83
2262 2316 1.032014 TTGGAGAAGCAGGCAAACAC 58.968 50.000 0.00 0.00 0.00 3.32
2291 2349 3.592814 CTGGAGGCCATGCATGCG 61.593 66.667 21.69 15.04 32.47 4.73
2294 2352 3.962421 GAGGCCATGCATGCGCTC 61.962 66.667 27.90 21.47 39.64 5.03
2311 2369 2.287788 CGCTCATGTGCACTTCCTTTTT 60.288 45.455 19.41 0.00 0.00 1.94
2314 2372 4.500375 GCTCATGTGCACTTCCTTTTTCTT 60.500 41.667 19.41 0.00 0.00 2.52
2315 2373 5.278463 GCTCATGTGCACTTCCTTTTTCTTA 60.278 40.000 19.41 0.00 0.00 2.10
2316 2374 6.707440 TCATGTGCACTTCCTTTTTCTTAA 57.293 33.333 19.41 0.00 0.00 1.85
2321 2416 8.785329 TGTGCACTTCCTTTTTCTTAAATTTT 57.215 26.923 19.41 0.00 0.00 1.82
2327 2422 9.161629 ACTTCCTTTTTCTTAAATTTTGGTGTG 57.838 29.630 0.00 0.00 0.00 3.82
2337 2432 4.698201 AATTTTGGTGTGGTAAAAGGGG 57.302 40.909 0.00 0.00 0.00 4.79
2348 2443 4.283467 GTGGTAAAAGGGGATTTTTGCTCT 59.717 41.667 0.00 0.00 41.40 4.09
2350 2445 5.368230 TGGTAAAAGGGGATTTTTGCTCTTT 59.632 36.000 0.00 0.00 41.40 2.52
2351 2446 6.555360 TGGTAAAAGGGGATTTTTGCTCTTTA 59.445 34.615 0.00 0.00 41.40 1.85
2352 2447 7.097192 GGTAAAAGGGGATTTTTGCTCTTTAG 58.903 38.462 0.00 0.00 41.40 1.85
2353 2448 5.551233 AAAAGGGGATTTTTGCTCTTTAGC 58.449 37.500 0.00 0.00 37.89 3.09
2364 2459 2.832563 GCTCTTTAGCTAGCTCTTGGG 58.167 52.381 23.26 13.04 45.85 4.12
2365 2460 2.169561 GCTCTTTAGCTAGCTCTTGGGT 59.830 50.000 23.26 0.00 45.85 4.51
2366 2461 3.739830 GCTCTTTAGCTAGCTCTTGGGTC 60.740 52.174 23.26 2.75 45.85 4.46
2367 2462 3.704061 CTCTTTAGCTAGCTCTTGGGTCT 59.296 47.826 23.26 0.00 0.00 3.85
2400 2495 1.377202 CGGGTGGGTGTCAAGGATG 60.377 63.158 0.00 0.00 0.00 3.51
2402 2497 1.767692 GGTGGGTGTCAAGGATGGT 59.232 57.895 0.00 0.00 0.00 3.55
2403 2498 0.112412 GGTGGGTGTCAAGGATGGTT 59.888 55.000 0.00 0.00 0.00 3.67
2405 2500 1.886542 GTGGGTGTCAAGGATGGTTTC 59.113 52.381 0.00 0.00 0.00 2.78
2406 2501 1.165270 GGGTGTCAAGGATGGTTTCG 58.835 55.000 0.00 0.00 0.00 3.46
2407 2502 0.521735 GGTGTCAAGGATGGTTTCGC 59.478 55.000 0.00 0.00 0.00 4.70
2412 2508 2.083774 TCAAGGATGGTTTCGCATGTC 58.916 47.619 0.00 0.00 0.00 3.06
2417 2513 1.004927 GATGGTTTCGCATGTCGTAGC 60.005 52.381 8.91 8.60 39.67 3.58
2423 2519 0.248498 TCGCATGTCGTAGCAGTAGC 60.248 55.000 8.91 0.00 39.32 3.58
2453 2551 6.170846 AGTAACTCCTCTCTAGTCTCTAGC 57.829 45.833 0.00 0.00 0.00 3.42
2458 2570 5.082633 TCCTCTCTAGTCTCTAGCCTAGA 57.917 47.826 0.70 0.70 37.83 2.43
2505 2623 0.532115 GGGGCCAGTTAAATGCACTG 59.468 55.000 4.39 0.00 41.29 3.66
2541 2659 1.741028 TTCCCCTCTCACATGGTGAA 58.259 50.000 0.00 0.00 42.26 3.18
2542 2660 1.971149 TCCCCTCTCACATGGTGAAT 58.029 50.000 0.00 0.00 42.26 2.57
2543 2661 2.278245 TCCCCTCTCACATGGTGAATT 58.722 47.619 0.00 0.00 42.26 2.17
2544 2662 2.025981 TCCCCTCTCACATGGTGAATTG 60.026 50.000 0.00 0.00 42.26 2.32
2545 2663 2.372264 CCCTCTCACATGGTGAATTGG 58.628 52.381 0.00 3.47 42.26 3.16
2546 2664 2.291153 CCCTCTCACATGGTGAATTGGT 60.291 50.000 0.00 0.00 42.26 3.67
2547 2665 2.751259 CCTCTCACATGGTGAATTGGTG 59.249 50.000 0.00 0.00 42.26 4.17
2548 2666 3.559811 CCTCTCACATGGTGAATTGGTGA 60.560 47.826 0.00 0.00 42.26 4.02
2570 2688 0.609131 GATGGTGTGGTGGTCCTTGG 60.609 60.000 0.00 0.00 34.23 3.61
2571 2689 1.360393 ATGGTGTGGTGGTCCTTGGT 61.360 55.000 0.00 0.00 34.23 3.67
2574 2692 1.101049 GTGTGGTGGTCCTTGGTGTG 61.101 60.000 0.00 0.00 34.23 3.82
2577 2695 0.694783 TGGTGGTCCTTGGTGTGGTA 60.695 55.000 0.00 0.00 34.23 3.25
2611 2732 1.447838 GCTGGTTGTGCGCTAGCTA 60.448 57.895 13.93 0.00 45.42 3.32
2678 2800 0.811616 CGCTTTGAATCCCTCCCTCG 60.812 60.000 0.00 0.00 0.00 4.63
2680 2802 0.464554 CTTTGAATCCCTCCCTCGCC 60.465 60.000 0.00 0.00 0.00 5.54
2688 2810 3.584052 CTCCCTCGCCCGTCTACG 61.584 72.222 0.00 0.00 39.44 3.51
2789 2937 0.775861 GCATGTCCGTTTTTGAACGC 59.224 50.000 6.19 0.00 44.18 4.84
2791 2939 0.938713 ATGTCCGTTTTTGAACGCGA 59.061 45.000 15.93 3.20 44.18 5.87
2792 2940 0.302288 TGTCCGTTTTTGAACGCGAG 59.698 50.000 15.93 0.00 44.18 5.03
2794 2942 0.810823 TCCGTTTTTGAACGCGAGGT 60.811 50.000 15.93 0.00 44.18 3.85
2795 2943 0.860533 CCGTTTTTGAACGCGAGGTA 59.139 50.000 15.93 0.00 44.18 3.08
2796 2944 1.261089 CCGTTTTTGAACGCGAGGTAA 59.739 47.619 15.93 0.00 44.18 2.85
2797 2945 2.286301 CCGTTTTTGAACGCGAGGTAAA 60.286 45.455 15.93 5.79 44.18 2.01
2800 2948 2.604969 TTTGAACGCGAGGTAAATGC 57.395 45.000 15.93 0.00 0.00 3.56
2849 3001 1.153549 GAGCTGGCCCGTTACAGAG 60.154 63.158 0.00 0.00 36.86 3.35
2851 3003 2.656069 GCTGGCCCGTTACAGAGGA 61.656 63.158 0.00 0.00 36.86 3.71
2852 3004 1.980052 CTGGCCCGTTACAGAGGAA 59.020 57.895 0.00 0.00 36.86 3.36
2853 3005 0.108138 CTGGCCCGTTACAGAGGAAG 60.108 60.000 0.00 0.00 36.86 3.46
2854 3006 0.543410 TGGCCCGTTACAGAGGAAGA 60.543 55.000 0.00 0.00 0.00 2.87
2855 3007 0.831307 GGCCCGTTACAGAGGAAGAT 59.169 55.000 0.00 0.00 0.00 2.40
2856 3008 1.209747 GGCCCGTTACAGAGGAAGATT 59.790 52.381 0.00 0.00 0.00 2.40
2857 3009 2.552031 GCCCGTTACAGAGGAAGATTC 58.448 52.381 0.00 0.00 0.00 2.52
2858 3010 2.093658 GCCCGTTACAGAGGAAGATTCA 60.094 50.000 0.00 0.00 0.00 2.57
2859 3011 3.618997 GCCCGTTACAGAGGAAGATTCAA 60.619 47.826 0.00 0.00 0.00 2.69
2860 3012 4.575885 CCCGTTACAGAGGAAGATTCAAA 58.424 43.478 0.00 0.00 0.00 2.69
2861 3013 5.001232 CCCGTTACAGAGGAAGATTCAAAA 58.999 41.667 0.00 0.00 0.00 2.44
2862 3014 5.648092 CCCGTTACAGAGGAAGATTCAAAAT 59.352 40.000 0.00 0.00 0.00 1.82
2863 3015 6.821665 CCCGTTACAGAGGAAGATTCAAAATA 59.178 38.462 0.00 0.00 0.00 1.40
2867 3019 9.660180 GTTACAGAGGAAGATTCAAAATAGAGT 57.340 33.333 0.00 0.00 0.00 3.24
2887 3039 7.653767 AGAGTTTCAAAATACTCCAACGTAG 57.346 36.000 0.00 0.00 41.31 3.51
2888 3040 7.215085 AGAGTTTCAAAATACTCCAACGTAGT 58.785 34.615 0.00 0.00 42.07 2.73
2890 3042 9.148104 GAGTTTCAAAATACTCCAACGTAGTAT 57.852 33.333 4.04 4.04 40.96 2.12
2918 3080 0.611062 TGGAGTGGTACTGAGACCGG 60.611 60.000 0.00 0.00 42.99 5.28
2962 3132 3.151554 GGATTTGTTAACAACCCGTCCT 58.848 45.455 20.43 0.40 35.28 3.85
2990 3164 4.421515 CTGGGCTGGGCAGTGGAG 62.422 72.222 0.00 0.00 0.00 3.86
2991 3165 4.980592 TGGGCTGGGCAGTGGAGA 62.981 66.667 0.00 0.00 0.00 3.71
2992 3166 4.106925 GGGCTGGGCAGTGGAGAG 62.107 72.222 0.00 0.00 0.00 3.20
2993 3167 3.005539 GGCTGGGCAGTGGAGAGA 61.006 66.667 0.00 0.00 0.00 3.10
2994 3168 2.596851 GGCTGGGCAGTGGAGAGAA 61.597 63.158 0.00 0.00 0.00 2.87
2995 3169 1.078567 GCTGGGCAGTGGAGAGAAG 60.079 63.158 0.00 0.00 0.00 2.85
2996 3170 1.601171 CTGGGCAGTGGAGAGAAGG 59.399 63.158 0.00 0.00 0.00 3.46
2997 3171 1.908340 CTGGGCAGTGGAGAGAAGGG 61.908 65.000 0.00 0.00 0.00 3.95
2998 3172 1.613630 GGGCAGTGGAGAGAAGGGA 60.614 63.158 0.00 0.00 0.00 4.20
2999 3173 1.621672 GGGCAGTGGAGAGAAGGGAG 61.622 65.000 0.00 0.00 0.00 4.30
3000 3174 1.621672 GGCAGTGGAGAGAAGGGAGG 61.622 65.000 0.00 0.00 0.00 4.30
3001 3175 1.621672 GCAGTGGAGAGAAGGGAGGG 61.622 65.000 0.00 0.00 0.00 4.30
3002 3176 0.041833 CAGTGGAGAGAAGGGAGGGA 59.958 60.000 0.00 0.00 0.00 4.20
3003 3177 0.338120 AGTGGAGAGAAGGGAGGGAG 59.662 60.000 0.00 0.00 0.00 4.30
3042 3216 0.366871 GCACTGTCGTGTAATGCTCG 59.633 55.000 0.00 0.00 43.16 5.03
3083 3257 3.503363 GCGATCACCAGCACAGCC 61.503 66.667 0.00 0.00 0.00 4.85
3093 3268 4.830046 TCACCAGCACAGCCTTAAATTTAA 59.170 37.500 10.16 10.16 0.00 1.52
3099 3274 4.805719 GCACAGCCTTAAATTTAATGAGGC 59.194 41.667 23.42 23.42 40.90 4.70
3112 3287 1.186200 ATGAGGCGACTTAGCTGTCA 58.814 50.000 0.00 0.00 44.43 3.58
3113 3288 0.966179 TGAGGCGACTTAGCTGTCAA 59.034 50.000 0.00 0.00 44.43 3.18
3117 3292 0.299003 GCGACTTAGCTGTCAATCGC 59.701 55.000 14.06 14.06 46.68 4.58
3162 3384 2.134346 CGGACAAAAACAAATGCCTGG 58.866 47.619 0.00 0.00 0.00 4.45
3165 3387 1.490069 ACAAAAACAAATGCCTGGCCT 59.510 42.857 17.53 2.69 0.00 5.19
3166 3388 1.874872 CAAAAACAAATGCCTGGCCTG 59.125 47.619 17.53 13.12 0.00 4.85
3167 3389 0.397564 AAAACAAATGCCTGGCCTGG 59.602 50.000 23.89 23.89 0.00 4.45
3235 3457 3.419580 AGATTCATGGCGGGGGCA 61.420 61.111 0.00 0.00 43.52 5.36
3410 3653 2.615227 ATCTGATTCTGGGCCGGTGC 62.615 60.000 13.14 3.64 0.00 5.01
3445 3688 0.460109 TAGTACAGGCGCATGCAGTG 60.460 55.000 23.75 13.50 45.35 3.66
3458 3701 2.981909 CAGTGGTGCAGTGCAGGG 60.982 66.667 20.42 2.43 40.08 4.45
3459 3702 4.962836 AGTGGTGCAGTGCAGGGC 62.963 66.667 20.42 11.19 40.08 5.19
3461 3704 4.960866 TGGTGCAGTGCAGGGCAG 62.961 66.667 20.42 0.00 40.08 4.85
3561 3804 1.153628 CGTGTGTACTGGCTAGGGC 60.154 63.158 0.85 0.00 37.82 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
567 569 2.610694 GCGCAAGAGCAGAGCACAA 61.611 57.895 0.30 0.00 42.27 3.33
682 684 2.440147 CTGGCCCACCACCATTGA 59.560 61.111 0.00 0.00 42.67 2.57
710 712 1.616091 GGGACGAACCGGGACCAATA 61.616 60.000 6.32 0.00 40.11 1.90
813 816 2.445525 ACCGGGACTAATATGGGCATTT 59.554 45.455 6.32 0.00 0.00 2.32
864 867 2.590092 GCTATGGTTCAGGCCGGT 59.410 61.111 1.90 0.00 0.00 5.28
873 876 4.929146 AGTAGAAAACAGGGCTATGGTT 57.071 40.909 0.00 0.00 0.00 3.67
923 926 4.851214 GAGGGAGGGAGCGAGGCT 62.851 72.222 0.00 0.00 43.88 4.58
925 928 3.151022 GTGAGGGAGGGAGCGAGG 61.151 72.222 0.00 0.00 0.00 4.63
926 929 2.043450 AGTGAGGGAGGGAGCGAG 60.043 66.667 0.00 0.00 0.00 5.03
927 930 2.043852 GAGTGAGGGAGGGAGCGA 60.044 66.667 0.00 0.00 0.00 4.93
928 931 3.151022 GGAGTGAGGGAGGGAGCG 61.151 72.222 0.00 0.00 0.00 5.03
929 932 2.766229 GGGAGTGAGGGAGGGAGC 60.766 72.222 0.00 0.00 0.00 4.70
930 933 2.041405 GGGGAGTGAGGGAGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
931 934 2.257541 GATGGGGAGTGAGGGAGGGA 62.258 65.000 0.00 0.00 0.00 4.20
932 935 1.768077 GATGGGGAGTGAGGGAGGG 60.768 68.421 0.00 0.00 0.00 4.30
933 936 1.768077 GGATGGGGAGTGAGGGAGG 60.768 68.421 0.00 0.00 0.00 4.30
934 937 1.768077 GGGATGGGGAGTGAGGGAG 60.768 68.421 0.00 0.00 0.00 4.30
935 938 2.372688 GGGATGGGGAGTGAGGGA 59.627 66.667 0.00 0.00 0.00 4.20
936 939 3.164269 CGGGATGGGGAGTGAGGG 61.164 72.222 0.00 0.00 0.00 4.30
937 940 2.946988 TAGCGGGATGGGGAGTGAGG 62.947 65.000 0.00 0.00 0.00 3.86
938 941 0.833834 ATAGCGGGATGGGGAGTGAG 60.834 60.000 0.00 0.00 0.00 3.51
939 942 0.485543 TATAGCGGGATGGGGAGTGA 59.514 55.000 0.00 0.00 0.00 3.41
940 943 1.573108 ATATAGCGGGATGGGGAGTG 58.427 55.000 0.00 0.00 0.00 3.51
941 944 3.105283 GTTATATAGCGGGATGGGGAGT 58.895 50.000 0.00 0.00 0.00 3.85
1002 1005 1.090052 GGATGTACTTGGCGCTGGTC 61.090 60.000 7.64 0.00 0.00 4.02
1087 1097 1.601171 CCCTGGGACTCTCTTGCTG 59.399 63.158 7.01 0.00 0.00 4.41
1108 1118 4.694233 AGCAGTGGCAGCTGGTCG 62.694 66.667 17.12 0.00 42.76 4.79
1130 1140 2.790791 CGCCTGAGTGCCTCTAGGG 61.791 68.421 15.50 0.00 32.99 3.53
1192 1206 1.216710 GTCCTCACGAGCCTCTTGG 59.783 63.158 0.00 0.00 0.00 3.61
1193 1207 0.318441 TTGTCCTCACGAGCCTCTTG 59.682 55.000 0.00 0.00 0.00 3.02
1194 1208 1.066573 CATTGTCCTCACGAGCCTCTT 60.067 52.381 0.00 0.00 0.00 2.85
1195 1209 0.534412 CATTGTCCTCACGAGCCTCT 59.466 55.000 0.00 0.00 0.00 3.69
1197 1229 1.078848 GCATTGTCCTCACGAGCCT 60.079 57.895 0.00 0.00 0.00 4.58
1201 1233 1.026182 GCCATGCATTGTCCTCACGA 61.026 55.000 0.00 0.00 0.00 4.35
1687 1729 3.014623 ACGATGCAGTGTGCTACTACTA 58.985 45.455 0.00 0.00 45.31 1.82
1694 1736 2.094659 GCGTACGATGCAGTGTGCT 61.095 57.895 21.65 0.00 45.31 4.40
1695 1737 2.094659 AGCGTACGATGCAGTGTGC 61.095 57.895 21.65 0.00 45.29 4.57
1696 1738 1.008875 ACAGCGTACGATGCAGTGTG 61.009 55.000 31.46 8.32 34.49 3.82
1714 1756 4.498009 GGACAATGCATACCACTATTGCAC 60.498 45.833 0.00 0.00 38.37 4.57
1786 1828 2.327940 GCGAGAGAGAGCGAGCTC 59.672 66.667 16.63 16.63 43.03 4.09
1806 1848 1.989966 TACTACGTGCTCCTCTGCGC 61.990 60.000 0.00 0.00 39.78 6.09
1807 1849 0.248134 GTACTACGTGCTCCTCTGCG 60.248 60.000 0.00 0.00 35.36 5.18
1808 1850 0.100861 GGTACTACGTGCTCCTCTGC 59.899 60.000 0.00 0.00 0.00 4.26
1809 1851 0.377554 CGGTACTACGTGCTCCTCTG 59.622 60.000 0.00 0.00 0.00 3.35
1810 1852 0.035630 ACGGTACTACGTGCTCCTCT 60.036 55.000 0.00 0.00 46.64 3.69
1812 1854 4.730487 ACGGTACTACGTGCTCCT 57.270 55.556 0.00 0.00 46.64 3.69
1827 1869 3.553511 GCAGATGAAATGTACTCTGGACG 59.446 47.826 8.98 0.00 36.48 4.79
1828 1870 4.507710 TGCAGATGAAATGTACTCTGGAC 58.492 43.478 8.98 0.00 36.48 4.02
1831 1873 5.121105 TGGATGCAGATGAAATGTACTCTG 58.879 41.667 0.00 3.76 38.49 3.35
1844 1886 3.882326 CCGGCCCTGGATGCAGAT 61.882 66.667 16.85 0.00 0.00 2.90
1866 1908 1.933021 TCCGGCTCCAGACTTTAAGA 58.067 50.000 0.00 0.00 0.00 2.10
1869 1911 4.081642 GCATATATCCGGCTCCAGACTTTA 60.082 45.833 0.00 0.00 0.00 1.85
1954 2001 0.249741 GCAAGATGAATGCATGGGGC 60.250 55.000 0.00 0.00 43.29 5.80
1955 2002 3.980583 GCAAGATGAATGCATGGGG 57.019 52.632 0.00 0.00 43.29 4.96
1961 2008 3.439476 AGAACTCTGTGCAAGATGAATGC 59.561 43.478 0.00 0.00 44.08 3.56
1965 2012 3.674410 CGCTAGAACTCTGTGCAAGATGA 60.674 47.826 0.00 0.00 33.29 2.92
1982 2029 2.738846 GGTGATATGAATGTGCCGCTAG 59.261 50.000 0.00 0.00 0.00 3.42
1994 2041 2.180946 AGGGAGCACAGGTGATATGA 57.819 50.000 3.10 0.00 0.00 2.15
1995 2042 2.486191 GGAAGGGAGCACAGGTGATATG 60.486 54.545 3.10 0.00 0.00 1.78
1996 2043 1.771255 GGAAGGGAGCACAGGTGATAT 59.229 52.381 3.10 0.00 0.00 1.63
2012 2059 0.868406 GCTGTCACTGAAACCGGAAG 59.132 55.000 9.46 2.17 0.00 3.46
2022 2069 1.368019 CACGCGTTTGCTGTCACTG 60.368 57.895 10.22 0.00 39.65 3.66
2065 2112 4.680237 TGTCTCGTGCCGCCTTGG 62.680 66.667 0.00 0.00 42.50 3.61
2068 2115 4.363990 CACTGTCTCGTGCCGCCT 62.364 66.667 0.00 0.00 0.00 5.52
2071 2118 2.375766 GCTTCACTGTCTCGTGCCG 61.376 63.158 0.00 0.00 34.92 5.69
2110 2157 0.179129 CATGTCCCCATTTCGCTTGC 60.179 55.000 0.00 0.00 0.00 4.01
2118 2165 1.774254 TCGCCTAATCATGTCCCCATT 59.226 47.619 0.00 0.00 0.00 3.16
2120 2167 0.758734 CTCGCCTAATCATGTCCCCA 59.241 55.000 0.00 0.00 0.00 4.96
2125 2172 3.954904 ACAGACTACTCGCCTAATCATGT 59.045 43.478 0.00 0.00 0.00 3.21
2130 2177 3.887352 TCTCACAGACTACTCGCCTAAT 58.113 45.455 0.00 0.00 0.00 1.73
2137 2184 3.118956 CCACCCAATCTCACAGACTACTC 60.119 52.174 0.00 0.00 0.00 2.59
2139 2186 2.567615 ACCACCCAATCTCACAGACTAC 59.432 50.000 0.00 0.00 0.00 2.73
2144 2191 2.795231 ATCACCACCCAATCTCACAG 57.205 50.000 0.00 0.00 0.00 3.66
2149 2196 2.042162 AGCTCAAATCACCACCCAATCT 59.958 45.455 0.00 0.00 0.00 2.40
2169 2216 3.349927 TGATGGACATCAAAGCTGGAAG 58.650 45.455 12.27 0.00 44.14 3.46
2182 2231 0.392863 CAACGGGCAGATGATGGACA 60.393 55.000 0.00 0.00 0.00 4.02
2194 2243 1.661821 CGATCGATCCTCAACGGGC 60.662 63.158 19.51 0.00 0.00 6.13
2199 2250 1.742146 CCTGCCGATCGATCCTCAA 59.258 57.895 18.66 2.54 0.00 3.02
2203 2254 2.356793 CTGCCTGCCGATCGATCC 60.357 66.667 18.66 7.25 0.00 3.36
2215 2266 2.036256 GTGGATGTTGGGCTGCCT 59.964 61.111 19.68 0.00 0.00 4.75
2216 2267 3.070576 GGTGGATGTTGGGCTGCC 61.071 66.667 11.05 11.05 0.00 4.85
2218 2269 2.345760 GCTGGTGGATGTTGGGCTG 61.346 63.158 0.00 0.00 0.00 4.85
2220 2271 3.443045 CGCTGGTGGATGTTGGGC 61.443 66.667 0.00 0.00 0.00 5.36
2232 2283 0.731417 CTTCTCCAATGAAGCGCTGG 59.269 55.000 12.58 8.83 37.27 4.85
2291 2349 3.005155 AGAAAAAGGAAGTGCACATGAGC 59.995 43.478 21.04 8.32 0.00 4.26
2292 2350 4.843220 AGAAAAAGGAAGTGCACATGAG 57.157 40.909 21.04 0.00 0.00 2.90
2293 2351 6.707440 TTAAGAAAAAGGAAGTGCACATGA 57.293 33.333 21.04 0.00 0.00 3.07
2294 2352 7.951530 ATTTAAGAAAAAGGAAGTGCACATG 57.048 32.000 21.04 0.00 0.00 3.21
2302 2360 8.611757 CCACACCAAAATTTAAGAAAAAGGAAG 58.388 33.333 0.00 0.00 0.00 3.46
2311 2369 7.419172 CCCCTTTTACCACACCAAAATTTAAGA 60.419 37.037 0.00 0.00 0.00 2.10
2314 2372 5.903589 TCCCCTTTTACCACACCAAAATTTA 59.096 36.000 0.00 0.00 0.00 1.40
2315 2373 4.722279 TCCCCTTTTACCACACCAAAATTT 59.278 37.500 0.00 0.00 0.00 1.82
2316 2374 4.299485 TCCCCTTTTACCACACCAAAATT 58.701 39.130 0.00 0.00 0.00 1.82
2321 2416 3.621682 AAATCCCCTTTTACCACACCA 57.378 42.857 0.00 0.00 0.00 4.17
2327 2422 5.483685 AAGAGCAAAAATCCCCTTTTACC 57.516 39.130 0.00 0.00 36.01 2.85
2348 2443 2.501723 CCAGACCCAAGAGCTAGCTAAA 59.498 50.000 19.38 0.00 0.00 1.85
2350 2445 1.007238 ACCAGACCCAAGAGCTAGCTA 59.993 52.381 19.38 0.00 0.00 3.32
2351 2446 0.252467 ACCAGACCCAAGAGCTAGCT 60.252 55.000 19.45 19.45 0.00 3.32
2352 2447 0.176910 GACCAGACCCAAGAGCTAGC 59.823 60.000 6.62 6.62 0.00 3.42
2353 2448 1.480137 CAGACCAGACCCAAGAGCTAG 59.520 57.143 0.00 0.00 0.00 3.42
2363 2458 2.567049 CGACGACCAGACCAGACC 59.433 66.667 0.00 0.00 0.00 3.85
2364 2459 2.567049 CCGACGACCAGACCAGAC 59.433 66.667 0.00 0.00 0.00 3.51
2365 2460 3.371063 GCCGACGACCAGACCAGA 61.371 66.667 0.00 0.00 0.00 3.86
2366 2461 4.778415 CGCCGACGACCAGACCAG 62.778 72.222 0.00 0.00 43.93 4.00
2389 2484 1.234821 TGCGAAACCATCCTTGACAC 58.765 50.000 0.00 0.00 0.00 3.67
2391 2486 1.812571 ACATGCGAAACCATCCTTGAC 59.187 47.619 0.00 0.00 0.00 3.18
2392 2487 2.083774 GACATGCGAAACCATCCTTGA 58.916 47.619 0.00 0.00 0.00 3.02
2393 2488 1.202065 CGACATGCGAAACCATCCTTG 60.202 52.381 3.85 0.00 44.57 3.61
2394 2489 1.086696 CGACATGCGAAACCATCCTT 58.913 50.000 3.85 0.00 44.57 3.36
2395 2490 0.036388 ACGACATGCGAAACCATCCT 60.036 50.000 14.88 0.00 44.57 3.24
2397 2492 1.004927 GCTACGACATGCGAAACCATC 60.005 52.381 14.88 0.00 44.57 3.51
2400 2495 0.370273 CTGCTACGACATGCGAAACC 59.630 55.000 14.88 3.21 44.57 3.27
2402 2497 2.526077 CTACTGCTACGACATGCGAAA 58.474 47.619 14.88 3.74 44.57 3.46
2403 2498 1.797713 GCTACTGCTACGACATGCGAA 60.798 52.381 14.88 0.00 38.76 4.70
2405 2500 1.532343 CGCTACTGCTACGACATGCG 61.532 60.000 7.79 7.79 40.90 4.73
2406 2501 1.209275 CCGCTACTGCTACGACATGC 61.209 60.000 0.00 0.00 36.97 4.06
2407 2502 0.100682 ACCGCTACTGCTACGACATG 59.899 55.000 0.00 0.00 36.97 3.21
2412 2508 1.269166 CTTTGACCGCTACTGCTACG 58.731 55.000 0.00 0.00 36.97 3.51
2417 2513 3.056749 AGGAGTTACTTTGACCGCTACTG 60.057 47.826 0.00 0.00 0.00 2.74
2423 2519 4.701171 ACTAGAGAGGAGTTACTTTGACCG 59.299 45.833 0.00 0.00 0.00 4.79
2453 2551 3.834489 ACATTCAGAGCCACATCTAGG 57.166 47.619 0.00 0.00 0.00 3.02
2458 2570 5.163723 CGATACAAAACATTCAGAGCCACAT 60.164 40.000 0.00 0.00 0.00 3.21
2522 2640 1.741028 TTCACCATGTGAGAGGGGAA 58.259 50.000 0.00 0.00 44.70 3.97
2525 2643 2.291153 ACCAATTCACCATGTGAGAGGG 60.291 50.000 12.88 10.49 43.69 4.30
2526 2644 2.751259 CACCAATTCACCATGTGAGAGG 59.249 50.000 0.00 4.14 43.69 3.69
2527 2645 3.678289 TCACCAATTCACCATGTGAGAG 58.322 45.455 0.00 0.00 43.69 3.20
2528 2646 3.786368 TCACCAATTCACCATGTGAGA 57.214 42.857 0.00 0.00 43.69 3.27
2529 2647 3.129813 CCATCACCAATTCACCATGTGAG 59.870 47.826 0.00 0.00 43.69 3.51
2530 2648 3.090790 CCATCACCAATTCACCATGTGA 58.909 45.455 0.00 0.00 41.09 3.58
2531 2649 3.090790 TCCATCACCAATTCACCATGTG 58.909 45.455 0.00 0.00 34.45 3.21
2541 2659 1.358787 ACCACACCATCCATCACCAAT 59.641 47.619 0.00 0.00 0.00 3.16
2542 2660 0.776810 ACCACACCATCCATCACCAA 59.223 50.000 0.00 0.00 0.00 3.67
2543 2661 0.038021 CACCACACCATCCATCACCA 59.962 55.000 0.00 0.00 0.00 4.17
2544 2662 0.680921 CCACCACACCATCCATCACC 60.681 60.000 0.00 0.00 0.00 4.02
2545 2663 0.038166 ACCACCACACCATCCATCAC 59.962 55.000 0.00 0.00 0.00 3.06
2546 2664 0.327924 GACCACCACACCATCCATCA 59.672 55.000 0.00 0.00 0.00 3.07
2547 2665 0.394352 GGACCACCACACCATCCATC 60.394 60.000 0.00 0.00 35.97 3.51
2548 2666 0.846427 AGGACCACCACACCATCCAT 60.846 55.000 0.00 0.00 38.94 3.41
2570 2688 5.220491 GCACGTACTACTACTACTACCACAC 60.220 48.000 0.00 0.00 0.00 3.82
2571 2689 4.870426 GCACGTACTACTACTACTACCACA 59.130 45.833 0.00 0.00 0.00 4.17
2574 2692 4.509600 CCAGCACGTACTACTACTACTACC 59.490 50.000 0.00 0.00 0.00 3.18
2577 2695 4.213564 ACCAGCACGTACTACTACTACT 57.786 45.455 0.00 0.00 0.00 2.57
2611 2732 2.648059 GTAGCAGACAAGCATGGGAAT 58.352 47.619 0.00 0.00 36.85 3.01
2653 2774 2.121538 GGGATTCAAAGCGAGGGCC 61.122 63.158 0.00 0.00 41.24 5.80
2654 2775 1.077429 AGGGATTCAAAGCGAGGGC 60.077 57.895 0.00 0.00 40.37 5.19
2678 2800 2.194271 CAGAGATTTTCGTAGACGGGC 58.806 52.381 1.67 0.00 40.29 6.13
2680 2802 1.846782 CGCAGAGATTTTCGTAGACGG 59.153 52.381 1.67 0.00 40.29 4.79
2688 2810 0.179179 GGCTGCACGCAGAGATTTTC 60.179 55.000 22.81 2.80 46.30 2.29
2708 2830 2.867647 GCAAAGGCTTCATTGAACCCAC 60.868 50.000 12.25 0.00 36.96 4.61
2800 2948 1.138036 CTGGTTCCGTGCATGCATG 59.862 57.895 29.36 29.36 0.00 4.06
2858 3010 9.893305 CGTTGGAGTATTTTGAAACTCTATTTT 57.107 29.630 2.82 0.00 41.53 1.82
2859 3011 9.063615 ACGTTGGAGTATTTTGAAACTCTATTT 57.936 29.630 2.82 0.00 41.53 1.40
2860 3012 8.617290 ACGTTGGAGTATTTTGAAACTCTATT 57.383 30.769 2.82 0.00 41.53 1.73
2861 3013 9.367444 CTACGTTGGAGTATTTTGAAACTCTAT 57.633 33.333 0.00 0.00 41.53 1.98
2862 3014 8.362639 ACTACGTTGGAGTATTTTGAAACTCTA 58.637 33.333 0.00 0.00 41.53 2.43
2863 3015 7.215085 ACTACGTTGGAGTATTTTGAAACTCT 58.785 34.615 0.00 0.00 41.53 3.24
2887 3039 8.059798 TCAGTACCACTCCACTTTACTTATAC 57.940 38.462 0.00 0.00 0.00 1.47
2888 3040 8.111545 TCTCAGTACCACTCCACTTTACTTATA 58.888 37.037 0.00 0.00 0.00 0.98
2890 3042 6.208204 GTCTCAGTACCACTCCACTTTACTTA 59.792 42.308 0.00 0.00 0.00 2.24
2891 3043 5.010820 GTCTCAGTACCACTCCACTTTACTT 59.989 44.000 0.00 0.00 0.00 2.24
2896 3058 2.249139 GGTCTCAGTACCACTCCACTT 58.751 52.381 0.00 0.00 39.50 3.16
2918 3080 2.124942 CTTTGGAGGAGAGCGGCC 60.125 66.667 0.00 0.00 0.00 6.13
2977 3151 1.078567 CTTCTCTCCACTGCCCAGC 60.079 63.158 0.00 0.00 0.00 4.85
2980 3154 1.613630 TCCCTTCTCTCCACTGCCC 60.614 63.158 0.00 0.00 0.00 5.36
2981 3155 1.621672 CCTCCCTTCTCTCCACTGCC 61.622 65.000 0.00 0.00 0.00 4.85
2982 3156 1.621672 CCCTCCCTTCTCTCCACTGC 61.622 65.000 0.00 0.00 0.00 4.40
2983 3157 0.041833 TCCCTCCCTTCTCTCCACTG 59.958 60.000 0.00 0.00 0.00 3.66
2984 3158 0.338120 CTCCCTCCCTTCTCTCCACT 59.662 60.000 0.00 0.00 0.00 4.00
2985 3159 0.689412 CCTCCCTCCCTTCTCTCCAC 60.689 65.000 0.00 0.00 0.00 4.02
2986 3160 1.706575 CCTCCCTCCCTTCTCTCCA 59.293 63.158 0.00 0.00 0.00 3.86
2987 3161 1.074850 CCCTCCCTCCCTTCTCTCC 60.075 68.421 0.00 0.00 0.00 3.71
2988 3162 1.074850 CCCCTCCCTCCCTTCTCTC 60.075 68.421 0.00 0.00 0.00 3.20
2989 3163 2.652113 CCCCCTCCCTCCCTTCTCT 61.652 68.421 0.00 0.00 0.00 3.10
2990 3164 2.040359 CCCCCTCCCTCCCTTCTC 60.040 72.222 0.00 0.00 0.00 2.87
2991 3165 4.439901 GCCCCCTCCCTCCCTTCT 62.440 72.222 0.00 0.00 0.00 2.85
2995 3169 4.583442 CTAGGCCCCCTCCCTCCC 62.583 77.778 0.00 0.00 34.61 4.30
2997 3171 4.499116 TGCTAGGCCCCCTCCCTC 62.499 72.222 0.00 0.00 34.61 4.30
2998 3172 4.825679 GTGCTAGGCCCCCTCCCT 62.826 72.222 0.00 0.00 34.61 4.20
3000 3174 2.774351 ATGTGCTAGGCCCCCTCC 60.774 66.667 0.00 0.00 34.61 4.30
3001 3175 1.763546 GAGATGTGCTAGGCCCCCTC 61.764 65.000 0.00 0.00 34.61 4.30
3002 3176 1.768077 GAGATGTGCTAGGCCCCCT 60.768 63.158 0.00 0.00 37.71 4.79
3003 3177 2.823758 GGAGATGTGCTAGGCCCCC 61.824 68.421 0.00 0.00 0.00 5.40
3083 3257 7.852945 CAGCTAAGTCGCCTCATTAAATTTAAG 59.147 37.037 15.45 8.41 0.00 1.85
3093 3268 1.186200 TGACAGCTAAGTCGCCTCAT 58.814 50.000 0.00 0.00 41.41 2.90
3099 3274 1.585668 CAGCGATTGACAGCTAAGTCG 59.414 52.381 0.00 0.00 42.52 4.18
3177 3399 2.907897 CTACTACTGTGCCGGGCAGC 62.908 65.000 24.58 17.39 40.08 5.25
3301 3528 4.034258 CGATCCATGCATGCCCGC 62.034 66.667 21.69 8.81 0.00 6.13
3365 3596 4.883354 GCCCCGCCATCTCTTGGG 62.883 72.222 0.00 0.00 46.55 4.12
3393 3636 2.825836 GCACCGGCCCAGAATCAG 60.826 66.667 0.00 0.00 0.00 2.90
3394 3637 4.776322 CGCACCGGCCCAGAATCA 62.776 66.667 0.00 0.00 36.38 2.57
3395 3638 4.778143 ACGCACCGGCCCAGAATC 62.778 66.667 0.00 0.00 36.38 2.52
3410 3653 2.716828 CTAACCACGCAGTCGCACG 61.717 63.158 0.00 0.00 41.61 5.34
3536 3779 3.035503 CAGTACACACGCAGCGCA 61.036 61.111 16.61 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.