Multiple sequence alignment - TraesCS3D01G345600

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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 TraesCS3D01G345600 chr3D 100.000 4561 0 0 1 4561 457029997 457034557 0.000000e+00 8423.0
1 TraesCS3D01G345600 chr3B 91.125 1814 75 25 1 1777 603829338 603831102 0.000000e+00 2379.0
2 TraesCS3D01G345600 chr3B 94.055 656 25 6 2319 2970 603832124 603832769 0.000000e+00 983.0
3 TraesCS3D01G345600 chr3B 91.610 584 32 10 2967 3540 603832956 603833532 0.000000e+00 791.0
4 TraesCS3D01G345600 chr3B 86.370 675 36 29 3898 4547 603834027 603834670 0.000000e+00 686.0
5 TraesCS3D01G345600 chr3B 95.000 340 10 2 3564 3900 603833530 603833865 1.120000e-145 527.0
6 TraesCS3D01G345600 chr3B 90.650 246 8 4 1983 2223 603831848 603832083 3.430000e-81 313.0
7 TraesCS3D01G345600 chr3B 100.000 35 0 0 2241 2275 603832082 603832116 1.060000e-06 65.8
8 TraesCS3D01G345600 chr3A 89.512 1802 74 38 1 1740 599895760 599897508 0.000000e+00 2174.0
9 TraesCS3D01G345600 chr3A 93.416 1291 61 15 3287 4561 599899887 599901169 0.000000e+00 1892.0
10 TraesCS3D01G345600 chr3A 90.211 807 40 16 2388 3191 599899051 599899821 0.000000e+00 1016.0
11 TraesCS3D01G345600 chr3A 90.446 157 9 2 2071 2221 599898712 599898868 7.740000e-48 202.0
12 TraesCS3D01G345600 chr4B 84.657 554 43 18 990 1540 619224842 619224328 8.750000e-142 514.0
13 TraesCS3D01G345600 chr4B 87.607 234 29 0 3288 3521 619222909 619222676 5.810000e-69 272.0
14 TraesCS3D01G345600 chr4B 81.616 359 35 9 2378 2736 619223320 619222993 7.520000e-68 268.0
15 TraesCS3D01G345600 chr1B 80.636 346 61 4 2391 2733 85432670 85433012 3.500000e-66 263.0
16 TraesCS3D01G345600 chr1D 80.347 346 62 4 2391 2733 53231524 53231866 1.630000e-64 257.0
17 TraesCS3D01G345600 chr1D 83.333 66 10 1 1794 1858 490578013 490577948 4.930000e-05 60.2
18 TraesCS3D01G345600 chr1A 80.347 346 62 4 2391 2733 53023015 53023357 1.630000e-64 257.0
19 TraesCS3D01G345600 chr1A 82.270 141 18 4 1775 1913 394878067 394878202 1.040000e-21 115.0
20 TraesCS3D01G345600 chr2D 78.756 193 30 7 2535 2723 590930810 590930625 8.020000e-23 119.0
21 TraesCS3D01G345600 chr2D 79.070 129 17 7 1787 1913 100949486 100949606 3.780000e-11 80.5
22 TraesCS3D01G345600 chr4A 83.077 130 16 3 1785 1913 703265868 703265992 3.730000e-21 113.0
23 TraesCS3D01G345600 chr7D 81.818 132 19 3 1773 1903 109301461 109301588 6.240000e-19 106.0
24 TraesCS3D01G345600 chrUn 82.203 118 13 4 1798 1913 339378004 339377893 1.350000e-15 95.3
25 TraesCS3D01G345600 chrUn 91.111 45 4 0 1860 1904 114235508 114235464 1.370000e-05 62.1
26 TraesCS3D01G345600 chr7A 83.133 83 8 4 1830 1912 342009247 342009323 2.280000e-08 71.3
27 TraesCS3D01G345600 chr6A 74.619 197 30 15 2535 2721 787461 787647 8.190000e-08 69.4
28 TraesCS3D01G345600 chr6A 89.130 46 3 1 1860 1905 50505622 50505665 6.370000e-04 56.5
29 TraesCS3D01G345600 chr6D 74.112 197 31 16 2535 2721 2107577 2107391 3.810000e-06 63.9
30 TraesCS3D01G345600 chr6D 85.000 60 8 1 1773 1832 82472744 82472802 4.930000e-05 60.2
31 TraesCS3D01G345600 chr6B 76.724 116 20 5 2535 2648 4458858 4458748 1.770000e-04 58.4
32 TraesCS3D01G345600 chr4D 90.698 43 3 1 1817 1858 507756204 507756162 6.370000e-04 56.5
33 TraesCS3D01G345600 chr2B 100.000 28 0 0 3109 3136 733963966 733963993 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G345600 chr3D 457029997 457034557 4560 False 8423.000000 8423 100.000000 1 4561 1 chr3D.!!$F1 4560
1 TraesCS3D01G345600 chr3B 603829338 603834670 5332 False 820.685714 2379 92.687143 1 4547 7 chr3B.!!$F1 4546
2 TraesCS3D01G345600 chr3A 599895760 599901169 5409 False 1321.000000 2174 90.896250 1 4561 4 chr3A.!!$F1 4560
3 TraesCS3D01G345600 chr4B 619222676 619224842 2166 True 351.333333 514 84.626667 990 3521 3 chr4B.!!$R1 2531

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
775 832 0.825840 CCATCCGTCTCCTCTCCTCC 60.826 65.0 0.00 0.0 0.00 4.30 F
776 833 0.825840 CATCCGTCTCCTCTCCTCCC 60.826 65.0 0.00 0.0 0.00 4.30 F
970 1027 0.955428 TTCACTGTTCCATCGGCAGC 60.955 55.0 0.00 0.0 33.87 5.25 F
2315 3672 0.319641 AGAAGGCCACTTTCGTCGTC 60.320 55.0 5.01 0.0 36.97 4.20 F
2895 4729 0.787183 GAGTTGACTCAGACTTGCGC 59.213 55.0 0.00 0.0 42.42 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 3481 0.545787 AGGTCAACCGGGTACATCCA 60.546 55.000 6.32 0.0 42.08 3.41 R
2229 3524 1.275010 TGCACGTGTACATCCATCTGT 59.725 47.619 18.38 0.0 0.00 3.41 R
2831 4665 0.036010 CCGTGTGGCCAAGAGATCTT 60.036 55.000 7.24 0.0 36.45 2.40 R
3305 5343 0.319555 GCTCCACGCTCTTGTACACA 60.320 55.000 0.00 0.0 35.14 3.72 R
4516 6752 0.395173 AAGTGGTCGTGCTTTTGGGT 60.395 50.000 0.00 0.0 0.00 4.51 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
35 36 3.470567 CTCGTTCGTGCGACTGCC 61.471 66.667 0.00 0.00 41.78 4.85
74 75 8.023128 ACAACATTTAATCAAGTTTGATCCGAG 58.977 33.333 7.74 1.69 46.60 4.63
221 224 2.434359 CCACGTTTCTCCCTCCGC 60.434 66.667 0.00 0.00 0.00 5.54
223 226 4.065281 ACGTTTCTCCCTCCGCCG 62.065 66.667 0.00 0.00 0.00 6.46
225 228 4.083862 GTTTCTCCCTCCGCCGCT 62.084 66.667 0.00 0.00 0.00 5.52
226 229 3.771160 TTTCTCCCTCCGCCGCTC 61.771 66.667 0.00 0.00 0.00 5.03
385 425 2.370519 GGGCTTTAATCTCTCTCTCCCC 59.629 54.545 0.00 0.00 0.00 4.81
403 443 3.209152 TCCCCTCCTATATATACCCCTGC 59.791 52.174 0.00 0.00 0.00 4.85
437 477 1.710339 CGAAGAGTTAAGCAGCCGC 59.290 57.895 0.00 0.00 38.99 6.53
459 502 2.109126 GCGCATTCCACTCCTCCAC 61.109 63.158 0.30 0.00 0.00 4.02
463 506 1.680249 GCATTCCACTCCTCCACTTCC 60.680 57.143 0.00 0.00 0.00 3.46
479 522 2.492449 TTCCTCCAAGCTCGAGCACG 62.492 60.000 36.87 26.25 45.16 5.34
568 611 2.103042 CCCTTGTGCTGTAGCTCGC 61.103 63.158 5.38 0.00 42.66 5.03
602 649 2.607635 GTCACCGTGTGTAATGGCTATG 59.392 50.000 0.00 0.00 38.72 2.23
672 729 2.202919 TGCCATGCACGATCGAGG 60.203 61.111 24.34 14.40 31.71 4.63
775 832 0.825840 CCATCCGTCTCCTCTCCTCC 60.826 65.000 0.00 0.00 0.00 4.30
776 833 0.825840 CATCCGTCTCCTCTCCTCCC 60.826 65.000 0.00 0.00 0.00 4.30
777 834 2.014033 ATCCGTCTCCTCTCCTCCCC 62.014 65.000 0.00 0.00 0.00 4.81
778 835 2.695970 CCGTCTCCTCTCCTCCCCT 61.696 68.421 0.00 0.00 0.00 4.79
779 836 1.152839 CGTCTCCTCTCCTCCCCTC 60.153 68.421 0.00 0.00 0.00 4.30
780 837 1.231928 GTCTCCTCTCCTCCCCTCC 59.768 68.421 0.00 0.00 0.00 4.30
842 899 3.103911 GCTCCCGTCGTGTTCGTG 61.104 66.667 0.00 0.00 38.33 4.35
948 1005 1.880027 CTGTGCCCACTTTTACTCACC 59.120 52.381 0.00 0.00 0.00 4.02
964 1021 3.077359 CTCACCCTTTCACTGTTCCATC 58.923 50.000 0.00 0.00 0.00 3.51
970 1027 0.955428 TTCACTGTTCCATCGGCAGC 60.955 55.000 0.00 0.00 33.87 5.25
971 1028 1.672030 CACTGTTCCATCGGCAGCA 60.672 57.895 0.00 0.00 33.87 4.41
974 1031 2.045926 GTTCCATCGGCAGCAGGT 60.046 61.111 0.00 0.00 0.00 4.00
975 1032 2.046023 TTCCATCGGCAGCAGGTG 60.046 61.111 0.00 0.00 0.00 4.00
976 1033 3.626996 TTCCATCGGCAGCAGGTGG 62.627 63.158 18.29 18.29 0.00 4.61
1702 1956 9.965824 CTACTAGAAATTTGACAAACACCATTT 57.034 29.630 1.94 0.00 0.00 2.32
1703 1957 8.647143 ACTAGAAATTTGACAAACACCATTTG 57.353 30.769 1.94 0.00 35.64 2.32
1704 1958 8.257306 ACTAGAAATTTGACAAACACCATTTGT 58.743 29.630 1.94 4.76 44.43 2.83
1717 1973 4.869215 CACCATTTGTGTACTCATTGCAA 58.131 39.130 0.00 0.00 40.26 4.08
1777 2063 3.693085 TGACCGTCAGTATCTTGTACTCC 59.307 47.826 0.00 0.00 0.00 3.85
1780 2066 3.700038 CCGTCAGTATCTTGTACTCCCTT 59.300 47.826 0.00 0.00 0.00 3.95
1781 2067 4.159879 CCGTCAGTATCTTGTACTCCCTTT 59.840 45.833 0.00 0.00 0.00 3.11
1782 2068 5.341617 CGTCAGTATCTTGTACTCCCTTTC 58.658 45.833 0.00 0.00 0.00 2.62
1784 2070 6.350277 CGTCAGTATCTTGTACTCCCTTTCTT 60.350 42.308 0.00 0.00 0.00 2.52
1785 2071 7.387643 GTCAGTATCTTGTACTCCCTTTCTTT 58.612 38.462 0.00 0.00 0.00 2.52
1786 2072 7.546316 GTCAGTATCTTGTACTCCCTTTCTTTC 59.454 40.741 0.00 0.00 0.00 2.62
1787 2073 7.234782 TCAGTATCTTGTACTCCCTTTCTTTCA 59.765 37.037 0.00 0.00 0.00 2.69
1788 2074 8.043710 CAGTATCTTGTACTCCCTTTCTTTCAT 58.956 37.037 0.00 0.00 0.00 2.57
1792 2078 9.981460 ATCTTGTACTCCCTTTCTTTCATAAAT 57.019 29.630 0.00 0.00 0.00 1.40
1847 2275 9.725019 AATACATGAGACTGAAATAAGTGAACA 57.275 29.630 0.00 0.00 0.00 3.18
1849 2277 8.450578 ACATGAGACTGAAATAAGTGAACAAA 57.549 30.769 0.00 0.00 0.00 2.83
1850 2278 8.345565 ACATGAGACTGAAATAAGTGAACAAAC 58.654 33.333 0.00 0.00 0.00 2.93
1851 2279 7.857734 TGAGACTGAAATAAGTGAACAAACA 57.142 32.000 0.00 0.00 0.00 2.83
1852 2280 7.693952 TGAGACTGAAATAAGTGAACAAACAC 58.306 34.615 0.00 0.00 40.60 3.32
1853 2281 7.335673 TGAGACTGAAATAAGTGAACAAACACA 59.664 33.333 0.00 0.00 42.45 3.72
1854 2282 8.225603 AGACTGAAATAAGTGAACAAACACAT 57.774 30.769 0.00 0.00 42.45 3.21
1856 2284 9.944663 GACTGAAATAAGTGAACAAACACATTA 57.055 29.630 0.00 0.00 42.45 1.90
1881 2309 7.754069 ATTAAAACATGTTTGTATGCATCCG 57.246 32.000 23.93 0.00 34.06 4.18
1883 2311 5.581126 AAACATGTTTGTATGCATCCGAT 57.419 34.783 22.71 0.00 34.06 4.18
1884 2312 5.581126 AACATGTTTGTATGCATCCGATT 57.419 34.783 0.19 0.00 34.06 3.34
1885 2313 5.581126 ACATGTTTGTATGCATCCGATTT 57.419 34.783 0.19 0.00 33.16 2.17
1886 2314 6.691754 ACATGTTTGTATGCATCCGATTTA 57.308 33.333 0.19 0.00 33.16 1.40
1887 2315 6.728200 ACATGTTTGTATGCATCCGATTTAG 58.272 36.000 0.19 0.00 33.16 1.85
1888 2316 6.542005 ACATGTTTGTATGCATCCGATTTAGA 59.458 34.615 0.19 0.00 33.16 2.10
1889 2317 6.603237 TGTTTGTATGCATCCGATTTAGAG 57.397 37.500 0.19 0.00 0.00 2.43
1894 2322 7.482654 TGTATGCATCCGATTTAGAGAAAAG 57.517 36.000 0.19 0.00 0.00 2.27
1898 2326 7.539712 TGCATCCGATTTAGAGAAAAGTTAG 57.460 36.000 0.00 0.00 0.00 2.34
1899 2327 7.327975 TGCATCCGATTTAGAGAAAAGTTAGA 58.672 34.615 0.00 0.00 0.00 2.10
1900 2328 7.822334 TGCATCCGATTTAGAGAAAAGTTAGAA 59.178 33.333 0.00 0.00 0.00 2.10
1901 2329 8.117370 GCATCCGATTTAGAGAAAAGTTAGAAC 58.883 37.037 0.00 0.00 0.00 3.01
1902 2330 9.151471 CATCCGATTTAGAGAAAAGTTAGAACA 57.849 33.333 0.00 0.00 0.00 3.18
1904 2332 9.367444 TCCGATTTAGAGAAAAGTTAGAACATC 57.633 33.333 0.00 0.00 0.00 3.06
1905 2333 8.321716 CCGATTTAGAGAAAAGTTAGAACATCG 58.678 37.037 0.00 0.00 0.00 3.84
1906 2334 8.861101 CGATTTAGAGAAAAGTTAGAACATCGT 58.139 33.333 0.00 0.00 0.00 3.73
1959 2888 8.251026 TGGCTATTACATCTACATATGTACTGC 58.749 37.037 11.62 5.84 41.00 4.40
1960 2889 8.251026 GGCTATTACATCTACATATGTACTGCA 58.749 37.037 11.62 1.21 41.00 4.41
1961 2890 9.639601 GCTATTACATCTACATATGTACTGCAA 57.360 33.333 11.62 9.41 41.00 4.08
1966 2895 8.768957 ACATCTACATATGTACTGCAATCATC 57.231 34.615 11.62 0.00 38.31 2.92
1967 2896 8.370182 ACATCTACATATGTACTGCAATCATCA 58.630 33.333 11.62 0.00 38.31 3.07
1969 2898 7.955918 TCTACATATGTACTGCAATCATCAGT 58.044 34.615 11.62 1.18 45.71 3.41
1970 2899 9.077885 TCTACATATGTACTGCAATCATCAGTA 57.922 33.333 11.62 0.00 43.75 2.74
1980 2909 8.340618 ACTGCAATCATCAGTACATAAAAAGT 57.659 30.769 0.00 0.00 42.45 2.66
1981 2910 8.239314 ACTGCAATCATCAGTACATAAAAAGTG 58.761 33.333 0.00 0.00 42.45 3.16
1997 2965 9.086336 CATAAAAAGTGGTAATAGCCATTGTTG 57.914 33.333 0.00 0.00 41.08 3.33
2025 2993 6.664428 AAAAATAGGGTGTACAAGTGCAAT 57.336 33.333 0.00 0.00 0.00 3.56
2026 2994 6.664428 AAAATAGGGTGTACAAGTGCAATT 57.336 33.333 0.00 0.00 0.00 2.32
2060 3028 5.666969 TTCATTTCGTACACCTTTGTCAG 57.333 39.130 0.00 0.00 37.15 3.51
2146 3438 2.045926 GGCCGGCAAGAGTGTGAT 60.046 61.111 30.85 0.00 0.00 3.06
2221 3516 6.270064 CGGTTGACCTAAAAACAACAATTCT 58.730 36.000 0.00 0.00 43.51 2.40
2222 3517 7.419204 CGGTTGACCTAAAAACAACAATTCTA 58.581 34.615 0.00 0.00 43.51 2.10
2223 3518 7.916450 CGGTTGACCTAAAAACAACAATTCTAA 59.084 33.333 0.00 0.00 43.51 2.10
2224 3519 9.589111 GGTTGACCTAAAAACAACAATTCTAAA 57.411 29.630 0.00 0.00 43.51 1.85
2236 3531 8.647143 ACAACAATTCTAAAAACAACAGATGG 57.353 30.769 0.00 0.00 0.00 3.51
2237 3532 8.474025 ACAACAATTCTAAAAACAACAGATGGA 58.526 29.630 0.00 0.00 0.00 3.41
2238 3533 9.480053 CAACAATTCTAAAAACAACAGATGGAT 57.520 29.630 0.00 0.00 0.00 3.41
2239 3534 9.480053 AACAATTCTAAAAACAACAGATGGATG 57.520 29.630 0.00 0.00 0.00 3.51
2280 3579 6.207810 ACTGTTTTGGTTGTACTTCAAAGACA 59.792 34.615 0.00 8.39 37.81 3.41
2284 3583 7.548196 TTTGGTTGTACTTCAAAGACAGTAG 57.452 36.000 0.00 0.00 37.81 2.57
2285 3584 5.054477 TGGTTGTACTTCAAAGACAGTAGC 58.946 41.667 0.00 0.00 37.81 3.58
2300 3657 5.986135 AGACAGTAGCACAAGTTAACAGAAG 59.014 40.000 8.61 0.00 0.00 2.85
2313 3670 0.600255 ACAGAAGGCCACTTTCGTCG 60.600 55.000 5.01 0.00 36.97 5.12
2315 3672 0.319641 AGAAGGCCACTTTCGTCGTC 60.320 55.000 5.01 0.00 36.97 4.20
2330 3687 2.285141 CGTCGTCTACGTCTAGCTTGAG 60.285 54.545 0.00 0.00 46.72 3.02
2335 3692 4.554200 CGTCTACGTCTAGCTTGAGAAAAC 59.446 45.833 0.00 0.00 34.11 2.43
2336 3693 4.858140 GTCTACGTCTAGCTTGAGAAAACC 59.142 45.833 0.00 0.00 0.00 3.27
2364 3753 3.671256 CGTACACGTACTCTCACTGATG 58.329 50.000 5.84 0.00 34.04 3.07
2386 4215 4.575645 TGTGATATGTATGCATGTGTGTGG 59.424 41.667 10.16 0.00 36.58 4.17
2738 4570 5.138276 GGCGACCAGATCCAGGTATATATA 58.862 45.833 7.39 0.00 40.09 0.86
2788 4620 2.311450 CATGCATGCAAGCGTCTATC 57.689 50.000 26.68 0.00 37.31 2.08
2789 4621 1.069432 CATGCATGCAAGCGTCTATCC 60.069 52.381 26.68 0.00 37.31 2.59
2792 4624 1.069432 GCATGCAAGCGTCTATCCATG 60.069 52.381 14.21 0.00 34.68 3.66
2816 4648 2.025418 GCCGTTCGGCTTCGAGAAA 61.025 57.895 25.91 0.00 46.99 2.52
2821 4655 2.285950 CGTTCGGCTTCGAGAAACAAAA 60.286 45.455 0.00 0.00 44.25 2.44
2831 4665 2.477375 CGAGAAACAAAACCGATCGGAA 59.523 45.455 39.55 0.00 38.96 4.30
2832 4666 3.059461 CGAGAAACAAAACCGATCGGAAA 60.059 43.478 39.55 0.00 38.96 3.13
2853 4687 2.507110 ATCTCTTGGCCACACGGTCG 62.507 60.000 3.88 0.00 41.18 4.79
2866 4700 3.372822 CACACGGTCGGCAGTTAAATAAT 59.627 43.478 0.00 0.00 0.00 1.28
2868 4702 3.869246 CACGGTCGGCAGTTAAATAATCT 59.131 43.478 0.00 0.00 0.00 2.40
2874 4708 4.879545 TCGGCAGTTAAATAATCTGTTCCC 59.120 41.667 0.00 0.00 0.00 3.97
2893 4727 1.423395 CGGAGTTGACTCAGACTTGC 58.577 55.000 12.76 0.00 44.60 4.01
2894 4728 1.423395 GGAGTTGACTCAGACTTGCG 58.577 55.000 12.76 0.00 44.60 4.85
2895 4729 0.787183 GAGTTGACTCAGACTTGCGC 59.213 55.000 0.00 0.00 42.42 6.09
2896 4730 0.941463 AGTTGACTCAGACTTGCGCG 60.941 55.000 0.00 0.00 0.00 6.86
2897 4731 2.310233 TTGACTCAGACTTGCGCGC 61.310 57.895 27.26 27.26 0.00 6.86
2898 4732 2.734723 GACTCAGACTTGCGCGCA 60.735 61.111 33.09 33.09 0.00 6.09
2899 4733 2.724708 GACTCAGACTTGCGCGCAG 61.725 63.158 34.25 27.70 0.00 5.18
2978 5003 2.210116 ACGCCGATTATTGTGATCACC 58.790 47.619 22.85 5.48 0.00 4.02
2981 5006 2.143122 CCGATTATTGTGATCACCCCG 58.857 52.381 22.85 15.05 0.00 5.73
2990 5015 1.145377 GATCACCCCGTTACGGCAT 59.855 57.895 19.48 5.15 46.86 4.40
2994 5019 3.871574 CCCCGTTACGGCATTGCG 61.872 66.667 19.48 3.24 46.86 4.85
3027 5052 5.190992 TGTCTTCTGAAGCAACTACGTAA 57.809 39.130 12.54 0.00 0.00 3.18
3158 5183 5.705441 ACGGACAATTAATTCATCGGCATAT 59.295 36.000 14.14 0.00 0.00 1.78
3159 5184 6.876789 ACGGACAATTAATTCATCGGCATATA 59.123 34.615 14.14 0.00 0.00 0.86
3160 5185 7.064609 ACGGACAATTAATTCATCGGCATATAG 59.935 37.037 14.14 0.00 0.00 1.31
3161 5186 7.189512 GGACAATTAATTCATCGGCATATAGC 58.810 38.462 0.00 0.00 44.65 2.97
3162 5187 7.066284 GGACAATTAATTCATCGGCATATAGCT 59.934 37.037 0.00 0.00 44.79 3.32
3163 5188 9.098355 GACAATTAATTCATCGGCATATAGCTA 57.902 33.333 0.00 0.00 44.79 3.32
3178 5215 1.945387 AGCTAGACATTCCATGTGCG 58.055 50.000 0.00 0.00 45.03 5.34
3198 5235 2.300433 GTGAGCCATGAACCATGCATA 58.700 47.619 0.00 0.00 40.20 3.14
3199 5236 2.889045 GTGAGCCATGAACCATGCATAT 59.111 45.455 0.00 0.00 40.20 1.78
3210 5248 2.097954 ACCATGCATATTGTCAGCAACG 59.902 45.455 0.00 0.00 42.15 4.10
3213 5251 4.023792 CCATGCATATTGTCAGCAACGTAT 60.024 41.667 0.00 0.00 42.15 3.06
3215 5253 5.651172 TGCATATTGTCAGCAACGTATAC 57.349 39.130 0.00 0.00 37.44 1.47
3232 5270 4.034394 CGTATACACACTGCTCCGTACTTA 59.966 45.833 3.32 0.00 0.00 2.24
3240 5278 2.980476 CTGCTCCGTACTTATATGTGCG 59.020 50.000 18.24 18.24 43.66 5.34
3242 5280 3.067040 TGCTCCGTACTTATATGTGCGAA 59.933 43.478 24.16 8.96 46.13 4.70
3245 5283 5.512082 GCTCCGTACTTATATGTGCGAATAG 59.488 44.000 24.16 18.90 46.13 1.73
3285 5323 7.589958 ATTTGTTGGTGTAACTAATTGTGGA 57.410 32.000 0.00 0.00 40.26 4.02
3305 5343 4.141551 TGGATGCAGATATTGAGCAACTCT 60.142 41.667 0.00 0.00 42.15 3.24
3404 5442 1.115930 AAGGCGATGTCCCGATAGCT 61.116 55.000 0.00 0.00 0.00 3.32
3744 5785 8.771920 ATCGAAATTAATGGACGATATGCTAA 57.228 30.769 17.04 0.00 40.90 3.09
3746 5787 8.085909 TCGAAATTAATGGACGATATGCTAAGA 58.914 33.333 0.00 0.00 0.00 2.10
3862 5906 1.068434 TCGAGAACCGCATCATGCATA 59.932 47.619 11.00 0.00 45.36 3.14
3863 5907 2.071540 CGAGAACCGCATCATGCATAT 58.928 47.619 11.00 0.00 45.36 1.78
3864 5908 2.093310 CGAGAACCGCATCATGCATATC 59.907 50.000 11.00 3.96 45.36 1.63
3865 5909 3.069289 GAGAACCGCATCATGCATATCA 58.931 45.455 11.00 0.00 45.36 2.15
3930 6138 3.993081 CCGAGCTTCACATCTGGAATATC 59.007 47.826 0.00 0.00 0.00 1.63
4135 6358 1.202806 TCCAAACCAACTGCTCTGAGG 60.203 52.381 6.83 0.00 0.00 3.86
4200 6425 6.317789 CACACATGGACTACAGTGAAAAAT 57.682 37.500 0.00 0.00 34.45 1.82
4488 6721 2.867429 CTAAAGTTGGGCAGCAAATCG 58.133 47.619 0.00 0.00 0.00 3.34
4508 6744 0.949105 GGCCACAACACGTACAGAGG 60.949 60.000 0.00 0.00 0.00 3.69
4514 6750 4.274950 CCACAACACGTACAGAGGAAAAAT 59.725 41.667 0.00 0.00 0.00 1.82
4516 6752 5.007234 CACAACACGTACAGAGGAAAAATGA 59.993 40.000 0.00 0.00 0.00 2.57
4539 6775 0.102300 AAAAGCACGACCACTTTGCC 59.898 50.000 0.00 0.00 36.28 4.52
4543 6779 1.227823 CACGACCACTTTGCCTGGA 60.228 57.895 0.00 0.00 32.55 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.082756 GCACGAACGAGCCAAACAG 60.083 57.895 5.43 0.00 0.00 3.16
35 36 0.586319 ATGTTGTTCAACTCACGGCG 59.414 50.000 4.80 4.80 0.00 6.46
385 425 4.145807 CTCGGCAGGGGTATATATAGGAG 58.854 52.174 0.00 0.00 0.00 3.69
443 483 1.680249 GGAAGTGGAGGAGTGGAATGC 60.680 57.143 0.00 0.00 0.00 3.56
452 492 0.178891 AGCTTGGAGGAAGTGGAGGA 60.179 55.000 0.00 0.00 33.73 3.71
453 493 0.251634 GAGCTTGGAGGAAGTGGAGG 59.748 60.000 0.00 0.00 33.73 4.30
459 502 0.739112 GTGCTCGAGCTTGGAGGAAG 60.739 60.000 35.27 0.00 42.66 3.46
463 506 1.803519 GTCGTGCTCGAGCTTGGAG 60.804 63.158 35.27 21.42 46.96 3.86
479 522 0.524816 TTAAGCCGCGATCGAGTGTC 60.525 55.000 21.57 7.08 38.10 3.67
521 564 3.873910 AGCTAGGAAAGGTACGTACGTA 58.126 45.455 23.60 23.60 32.98 3.57
522 565 2.716217 AGCTAGGAAAGGTACGTACGT 58.284 47.619 25.98 25.98 32.98 3.57
568 611 1.810532 GGTGACTAGCAGGAGGACG 59.189 63.158 0.00 0.00 0.00 4.79
602 649 1.434696 CTTGATGGTTCATGGCGCC 59.565 57.895 22.73 22.73 0.00 6.53
672 729 2.175322 GTCTCGTGGACGGTCGAC 59.825 66.667 7.13 7.13 40.29 4.20
700 757 1.871080 CTCATGGGAATGCTACGGAC 58.129 55.000 0.00 0.00 0.00 4.79
775 832 1.972660 GATGAACCACGAGGGGAGGG 61.973 65.000 3.29 0.00 42.91 4.30
776 833 1.264749 TGATGAACCACGAGGGGAGG 61.265 60.000 3.29 0.00 42.91 4.30
777 834 0.108138 GTGATGAACCACGAGGGGAG 60.108 60.000 3.29 0.00 42.91 4.30
778 835 0.544357 AGTGATGAACCACGAGGGGA 60.544 55.000 3.29 0.00 42.91 4.81
779 836 0.108138 GAGTGATGAACCACGAGGGG 60.108 60.000 3.29 0.00 42.91 4.79
780 837 0.458543 CGAGTGATGAACCACGAGGG 60.459 60.000 3.29 0.00 41.67 4.30
820 877 1.146358 GAACACGACGGGAGCATAGC 61.146 60.000 2.90 0.00 0.00 2.97
821 878 0.866061 CGAACACGACGGGAGCATAG 60.866 60.000 2.90 0.00 0.00 2.23
822 879 1.138036 CGAACACGACGGGAGCATA 59.862 57.895 2.90 0.00 0.00 3.14
823 880 2.126071 CGAACACGACGGGAGCAT 60.126 61.111 2.90 0.00 0.00 3.79
826 883 2.014554 CACACGAACACGACGGGAG 61.015 63.158 2.90 0.00 37.60 4.30
842 899 2.651137 GCACATGCACGCAAAGCAC 61.651 57.895 0.00 0.00 45.95 4.40
900 957 2.655364 CCCGACGACTATGCGCAG 60.655 66.667 18.32 5.51 33.86 5.18
901 958 2.997075 AACCCGACGACTATGCGCA 61.997 57.895 14.96 14.96 33.86 6.09
902 959 2.202703 AACCCGACGACTATGCGC 60.203 61.111 0.00 0.00 33.86 6.09
903 960 2.514013 GCAACCCGACGACTATGCG 61.514 63.158 0.00 0.00 37.29 4.73
1669 1919 9.827411 GTTTGTCAAATTTCTAGTAGGATCAAC 57.173 33.333 0.40 0.00 0.00 3.18
1702 1956 3.769739 AGGAGTTGCAATGAGTACACA 57.230 42.857 0.59 0.00 0.00 3.72
1703 1957 7.549488 AGTTTATAGGAGTTGCAATGAGTACAC 59.451 37.037 0.59 0.00 0.00 2.90
1704 1958 7.620880 AGTTTATAGGAGTTGCAATGAGTACA 58.379 34.615 0.59 0.00 0.00 2.90
1747 2033 5.061920 AGATACTGACGGTCAAAGTTCTC 57.938 43.478 12.54 8.06 0.00 2.87
1759 2045 4.985538 AAGGGAGTACAAGATACTGACG 57.014 45.455 0.00 0.00 0.00 4.35
1821 2249 9.725019 TGTTCACTTATTTCAGTCTCATGTATT 57.275 29.630 0.00 0.00 0.00 1.89
1825 2253 8.344831 TGTTTGTTCACTTATTTCAGTCTCATG 58.655 33.333 0.00 0.00 0.00 3.07
1826 2254 8.345565 GTGTTTGTTCACTTATTTCAGTCTCAT 58.654 33.333 0.00 0.00 35.68 2.90
1830 2258 8.856490 AATGTGTTTGTTCACTTATTTCAGTC 57.144 30.769 0.00 0.00 38.90 3.51
1856 2284 8.031864 TCGGATGCATACAAACATGTTTTAATT 58.968 29.630 21.10 8.59 0.00 1.40
1857 2285 7.542890 TCGGATGCATACAAACATGTTTTAAT 58.457 30.769 21.10 13.98 0.00 1.40
1859 2287 6.502136 TCGGATGCATACAAACATGTTTTA 57.498 33.333 21.10 15.87 0.00 1.52
1862 2290 5.581126 AATCGGATGCATACAAACATGTT 57.419 34.783 10.18 4.92 0.00 2.71
1863 2291 5.581126 AAATCGGATGCATACAAACATGT 57.419 34.783 10.18 0.00 0.00 3.21
1864 2292 6.958255 TCTAAATCGGATGCATACAAACATG 58.042 36.000 10.18 0.00 0.00 3.21
1865 2293 6.992123 TCTCTAAATCGGATGCATACAAACAT 59.008 34.615 10.18 0.00 0.00 2.71
1866 2294 6.345298 TCTCTAAATCGGATGCATACAAACA 58.655 36.000 10.18 0.00 0.00 2.83
1867 2295 6.844696 TCTCTAAATCGGATGCATACAAAC 57.155 37.500 10.18 0.00 0.00 2.93
1868 2296 7.857734 TTTCTCTAAATCGGATGCATACAAA 57.142 32.000 10.18 0.00 0.00 2.83
1869 2297 7.552687 ACTTTTCTCTAAATCGGATGCATACAA 59.447 33.333 10.18 0.00 0.00 2.41
1872 2300 9.261180 CTAACTTTTCTCTAAATCGGATGCATA 57.739 33.333 0.00 0.00 0.00 3.14
1873 2301 7.987458 TCTAACTTTTCTCTAAATCGGATGCAT 59.013 33.333 0.00 0.00 0.00 3.96
1874 2302 7.327975 TCTAACTTTTCTCTAAATCGGATGCA 58.672 34.615 0.00 0.00 0.00 3.96
1875 2303 7.772332 TCTAACTTTTCTCTAAATCGGATGC 57.228 36.000 0.00 0.00 0.00 3.91
1876 2304 9.151471 TGTTCTAACTTTTCTCTAAATCGGATG 57.849 33.333 0.00 0.00 0.00 3.51
1877 2305 9.892130 ATGTTCTAACTTTTCTCTAAATCGGAT 57.108 29.630 0.00 0.00 0.00 4.18
1933 2361 8.251026 GCAGTACATATGTAGATGTAATAGCCA 58.749 37.037 15.93 0.00 42.48 4.75
1934 2362 8.251026 TGCAGTACATATGTAGATGTAATAGCC 58.749 37.037 15.93 0.25 42.48 3.93
1935 2363 9.639601 TTGCAGTACATATGTAGATGTAATAGC 57.360 33.333 15.93 9.63 42.48 2.97
1940 2368 9.860898 GATGATTGCAGTACATATGTAGATGTA 57.139 33.333 15.93 13.67 40.54 2.29
1941 2369 8.370182 TGATGATTGCAGTACATATGTAGATGT 58.630 33.333 15.93 3.20 42.68 3.06
1944 2372 7.955918 ACTGATGATTGCAGTACATATGTAGA 58.044 34.615 15.93 0.00 44.27 2.59
1965 2894 8.322828 TGGCTATTACCACTTTTTATGTACTGA 58.677 33.333 0.00 0.00 33.75 3.41
1966 2895 8.500753 TGGCTATTACCACTTTTTATGTACTG 57.499 34.615 0.00 0.00 33.75 2.74
1967 2896 9.695155 AATGGCTATTACCACTTTTTATGTACT 57.305 29.630 0.00 0.00 44.17 2.73
1969 2898 9.469097 ACAATGGCTATTACCACTTTTTATGTA 57.531 29.630 0.00 0.00 44.17 2.29
1970 2899 8.361169 ACAATGGCTATTACCACTTTTTATGT 57.639 30.769 0.00 0.00 44.17 2.29
1971 2900 9.086336 CAACAATGGCTATTACCACTTTTTATG 57.914 33.333 0.00 0.00 44.17 1.90
1972 2901 7.763985 GCAACAATGGCTATTACCACTTTTTAT 59.236 33.333 0.00 0.00 44.17 1.40
1973 2902 7.039363 AGCAACAATGGCTATTACCACTTTTTA 60.039 33.333 0.00 0.00 44.17 1.52
1974 2903 5.931724 GCAACAATGGCTATTACCACTTTTT 59.068 36.000 0.00 0.00 44.17 1.94
1976 2905 4.772100 AGCAACAATGGCTATTACCACTTT 59.228 37.500 0.00 0.00 44.17 2.66
1977 2906 4.344104 AGCAACAATGGCTATTACCACTT 58.656 39.130 0.00 0.00 44.17 3.16
1978 2907 3.968265 AGCAACAATGGCTATTACCACT 58.032 40.909 0.00 0.00 44.17 4.00
1980 2909 6.842437 TTTAAGCAACAATGGCTATTACCA 57.158 33.333 0.00 0.00 45.82 3.25
2015 2983 6.655078 ATCTCCTTTTGTAATTGCACTTGT 57.345 33.333 0.00 0.00 0.00 3.16
2017 2985 7.288810 TGAATCTCCTTTTGTAATTGCACTT 57.711 32.000 0.00 0.00 0.00 3.16
2018 2986 6.899393 TGAATCTCCTTTTGTAATTGCACT 57.101 33.333 0.00 0.00 0.00 4.40
2019 2987 8.538409 AAATGAATCTCCTTTTGTAATTGCAC 57.462 30.769 0.00 0.00 0.00 4.57
2020 2988 7.541783 CGAAATGAATCTCCTTTTGTAATTGCA 59.458 33.333 0.00 0.00 0.00 4.08
2021 2989 7.542130 ACGAAATGAATCTCCTTTTGTAATTGC 59.458 33.333 0.00 0.00 30.28 3.56
2022 2990 8.970691 ACGAAATGAATCTCCTTTTGTAATTG 57.029 30.769 0.00 0.00 30.28 2.32
2024 2992 9.226606 TGTACGAAATGAATCTCCTTTTGTAAT 57.773 29.630 0.00 0.00 34.72 1.89
2025 2993 8.500773 GTGTACGAAATGAATCTCCTTTTGTAA 58.499 33.333 0.00 0.00 34.72 2.41
2026 2994 7.118680 GGTGTACGAAATGAATCTCCTTTTGTA 59.881 37.037 0.00 2.26 32.99 2.41
2048 3016 7.013655 GGATTTCATATATGCTGACAAAGGTGT 59.986 37.037 7.92 0.00 42.10 4.16
2060 3028 4.911610 GCACGTGTTGGATTTCATATATGC 59.088 41.667 18.38 0.00 0.00 3.14
2146 3438 3.263170 TGGCAAGCTTGGAATAGTAGTCA 59.737 43.478 27.10 3.13 0.00 3.41
2187 3481 0.545787 AGGTCAACCGGGTACATCCA 60.546 55.000 6.32 0.00 42.08 3.41
2221 3516 6.483974 ACGTGTACATCCATCTGTTGTTTTTA 59.516 34.615 0.00 0.00 0.00 1.52
2222 3517 5.298276 ACGTGTACATCCATCTGTTGTTTTT 59.702 36.000 0.00 0.00 0.00 1.94
2223 3518 4.819630 ACGTGTACATCCATCTGTTGTTTT 59.180 37.500 0.00 0.00 0.00 2.43
2224 3519 4.213270 CACGTGTACATCCATCTGTTGTTT 59.787 41.667 7.58 0.00 0.00 2.83
2225 3520 3.745975 CACGTGTACATCCATCTGTTGTT 59.254 43.478 7.58 0.00 0.00 2.83
2226 3521 3.325870 CACGTGTACATCCATCTGTTGT 58.674 45.455 7.58 0.00 0.00 3.32
2227 3522 2.094258 GCACGTGTACATCCATCTGTTG 59.906 50.000 18.38 0.00 0.00 3.33
2228 3523 2.289382 TGCACGTGTACATCCATCTGTT 60.289 45.455 18.38 0.00 0.00 3.16
2229 3524 1.275010 TGCACGTGTACATCCATCTGT 59.725 47.619 18.38 0.00 0.00 3.41
2230 3525 1.929169 CTGCACGTGTACATCCATCTG 59.071 52.381 18.38 0.00 0.00 2.90
2231 3526 1.824852 TCTGCACGTGTACATCCATCT 59.175 47.619 18.38 0.00 0.00 2.90
2232 3527 2.293677 TCTGCACGTGTACATCCATC 57.706 50.000 18.38 0.00 0.00 3.51
2233 3528 2.760634 TTCTGCACGTGTACATCCAT 57.239 45.000 18.38 0.00 0.00 3.41
2234 3529 2.028567 TGATTCTGCACGTGTACATCCA 60.029 45.455 18.38 4.22 0.00 3.41
2235 3530 2.348666 GTGATTCTGCACGTGTACATCC 59.651 50.000 18.38 0.00 0.00 3.51
2236 3531 3.061295 CAGTGATTCTGCACGTGTACATC 59.939 47.826 18.38 14.45 43.42 3.06
2237 3532 2.995939 CAGTGATTCTGCACGTGTACAT 59.004 45.455 18.38 5.34 43.42 2.29
2238 3533 2.403259 CAGTGATTCTGCACGTGTACA 58.597 47.619 18.38 6.55 43.42 2.90
2280 3579 4.065789 GCCTTCTGTTAACTTGTGCTACT 58.934 43.478 7.22 0.00 0.00 2.57
2284 3583 1.953686 TGGCCTTCTGTTAACTTGTGC 59.046 47.619 3.32 3.51 0.00 4.57
2285 3584 3.214328 AGTGGCCTTCTGTTAACTTGTG 58.786 45.455 3.32 0.00 0.00 3.33
2313 3670 4.858140 GGTTTTCTCAAGCTAGACGTAGAC 59.142 45.833 0.00 0.00 0.00 2.59
2315 3672 4.174762 GGGTTTTCTCAAGCTAGACGTAG 58.825 47.826 0.00 0.00 0.00 3.51
2330 3687 1.451651 CGTGTACGTGTACGGGTTTTC 59.548 52.381 15.78 0.00 44.95 2.29
2363 3752 4.575645 CCACACACATGCATACATATCACA 59.424 41.667 0.00 0.00 33.67 3.58
2364 3753 4.576053 ACCACACACATGCATACATATCAC 59.424 41.667 0.00 0.00 33.67 3.06
2386 4215 2.358737 CCGACACCTCCCTGCAAC 60.359 66.667 0.00 0.00 0.00 4.17
2738 4570 7.041576 TGCAGACTAATTATACGTACGATGAGT 60.042 37.037 24.41 13.12 0.00 3.41
2786 4618 1.717791 CGAACGGCACATGCATGGAT 61.718 55.000 29.41 7.86 44.36 3.41
2788 4620 2.100797 CGAACGGCACATGCATGG 59.899 61.111 29.41 19.00 44.36 3.66
2789 4621 2.100797 CCGAACGGCACATGCATG 59.899 61.111 25.09 25.09 44.36 4.06
2831 4665 0.036010 CCGTGTGGCCAAGAGATCTT 60.036 55.000 7.24 0.00 36.45 2.40
2832 4666 1.194781 ACCGTGTGGCCAAGAGATCT 61.195 55.000 7.24 0.00 39.70 2.75
2853 4687 4.036380 CCGGGAACAGATTATTTAACTGCC 59.964 45.833 0.00 0.00 35.38 4.85
2866 4700 0.966920 GAGTCAACTCCGGGAACAGA 59.033 55.000 0.00 0.00 37.02 3.41
2868 4702 0.679505 CTGAGTCAACTCCGGGAACA 59.320 55.000 0.00 0.00 42.20 3.18
2874 4708 1.423395 GCAAGTCTGAGTCAACTCCG 58.577 55.000 7.66 1.69 42.20 4.63
2897 4731 4.172512 AGCTCTCATGCCGGGCTG 62.173 66.667 21.46 15.39 31.68 4.85
2898 4732 3.859414 GAGCTCTCATGCCGGGCT 61.859 66.667 21.46 8.69 35.86 5.19
2981 5006 1.007114 GTACGTACGCAATGCCGTAAC 60.007 52.381 16.72 7.64 44.25 2.50
2990 5015 4.207635 CAGAAGACAAAAGTACGTACGCAA 59.792 41.667 19.49 0.03 0.00 4.85
2994 5019 5.461078 TGCTTCAGAAGACAAAAGTACGTAC 59.539 40.000 18.10 18.10 0.00 3.67
3027 5052 1.005569 TGAGTGTATGTCCGAGGGAGT 59.994 52.381 0.00 0.00 29.39 3.85
3082 5107 4.764679 TGTTGTTCGGTACTACGTACAT 57.235 40.909 6.51 0.00 42.24 2.29
3124 5149 2.198906 AATTGTCCGTGCCGTGCATG 62.199 55.000 10.15 10.15 44.25 4.06
3125 5150 0.675208 TAATTGTCCGTGCCGTGCAT 60.675 50.000 1.90 0.00 41.91 3.96
3126 5151 0.885150 TTAATTGTCCGTGCCGTGCA 60.885 50.000 0.00 0.00 35.60 4.57
3178 5215 1.108776 ATGCATGGTTCATGGCTCAC 58.891 50.000 0.00 0.00 41.64 3.51
3191 5228 3.409851 ACGTTGCTGACAATATGCATG 57.590 42.857 10.16 0.00 38.27 4.06
3194 5231 5.006261 TGTGTATACGTTGCTGACAATATGC 59.994 40.000 0.00 0.00 38.27 3.14
3198 5235 4.388773 CAGTGTGTATACGTTGCTGACAAT 59.611 41.667 0.00 0.00 38.27 2.71
3199 5236 3.738791 CAGTGTGTATACGTTGCTGACAA 59.261 43.478 0.00 0.00 0.00 3.18
3210 5248 4.367386 AAGTACGGAGCAGTGTGTATAC 57.633 45.455 0.00 0.00 0.00 1.47
3213 5251 5.591472 ACATATAAGTACGGAGCAGTGTGTA 59.409 40.000 0.00 0.00 0.00 2.90
3215 5253 4.740205 CACATATAAGTACGGAGCAGTGTG 59.260 45.833 0.00 0.00 0.00 3.82
3232 5270 5.811100 CAGCTCATGATCTATTCGCACATAT 59.189 40.000 0.00 0.00 0.00 1.78
3285 5323 4.575236 CACAGAGTTGCTCAATATCTGCAT 59.425 41.667 19.11 6.48 39.01 3.96
3305 5343 0.319555 GCTCCACGCTCTTGTACACA 60.320 55.000 0.00 0.00 35.14 3.72
3392 5430 3.224324 GCCGGAGCTATCGGGACA 61.224 66.667 23.81 0.00 46.34 4.02
3565 5603 5.317733 TGCAAGACCCGGTTAATTAATTG 57.682 39.130 11.05 1.64 0.00 2.32
3862 5906 4.460034 TGCATGGAAAGCGCATATATTGAT 59.540 37.500 11.47 0.00 33.85 2.57
3863 5907 3.819902 TGCATGGAAAGCGCATATATTGA 59.180 39.130 11.47 0.00 33.85 2.57
3864 5908 4.163458 TGCATGGAAAGCGCATATATTG 57.837 40.909 11.47 1.18 33.85 1.90
3865 5909 4.740268 CATGCATGGAAAGCGCATATATT 58.260 39.130 19.40 0.00 44.30 1.28
3930 6138 7.814587 TGCTTATATTCGGTGATATCTCAAGTG 59.185 37.037 3.98 0.00 31.85 3.16
3965 6173 2.515523 AAGCTAGCGCCCATGCAG 60.516 61.111 9.55 0.00 37.32 4.41
3966 6174 2.514592 GAAGCTAGCGCCCATGCA 60.515 61.111 9.55 0.00 37.32 3.96
3980 6194 0.512952 CGTCCGCTTCCAACTTGAAG 59.487 55.000 0.00 0.00 43.71 3.02
4012 6226 3.195698 GGCTGGCGTGACGGAATC 61.196 66.667 7.25 0.00 0.00 2.52
4035 6249 5.295045 TGAACAGATATGTGATGTGCATGTC 59.705 40.000 6.90 0.00 35.56 3.06
4038 6252 6.117488 TCTTGAACAGATATGTGATGTGCAT 58.883 36.000 6.90 0.00 32.57 3.96
4135 6358 5.858581 GTGGAAAGTTAGATTGAACATGCAC 59.141 40.000 0.00 0.00 34.85 4.57
4186 6411 7.280356 ACAGGTCACTAATTTTTCACTGTAGT 58.720 34.615 0.00 0.00 35.17 2.73
4488 6721 0.949105 CTCTGTACGTGTTGTGGCCC 60.949 60.000 0.00 0.00 0.00 5.80
4508 6744 3.489416 GTCGTGCTTTTGGGTCATTTTTC 59.511 43.478 0.00 0.00 0.00 2.29
4514 6750 1.098712 GTGGTCGTGCTTTTGGGTCA 61.099 55.000 0.00 0.00 0.00 4.02
4516 6752 0.395173 AAGTGGTCGTGCTTTTGGGT 60.395 50.000 0.00 0.00 0.00 4.51
4539 6775 1.332195 TCATCGTAGGCAGGATCCAG 58.668 55.000 15.82 7.25 0.00 3.86


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

AutoCloner maintained by Alex Coulton.