Multiple sequence alignment - TraesCS5D01G385800

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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 TraesCS5D01G385800 chr5D 100.000 4553 0 0 1 4553 455606000 455610552 0.000000e+00 8408
1 TraesCS5D01G385800 chr5D 95.060 1761 41 8 2054 3776 454810741 454812493 0.000000e+00 2728
2 TraesCS5D01G385800 chr5D 100.000 1037 0 0 1 1037 454836366 454837402 0.000000e+00 1916
3 TraesCS5D01G385800 chr5D 87.852 1564 70 56 2383 3893 454838300 454839796 0.000000e+00 1725
4 TraesCS5D01G385800 chr5D 94.124 902 31 7 1034 1931 454809860 454810743 0.000000e+00 1352
5 TraesCS5D01G385800 chr5D 97.017 637 18 1 1034 1670 454837629 454838264 0.000000e+00 1070
6 TraesCS5D01G385800 chr5D 92.638 163 12 0 4388 4550 22428181 22428019 7.620000e-58 235
7 TraesCS5D01G385800 chr5D 90.566 159 13 2 4393 4550 344690141 344690298 4.620000e-50 209
8 TraesCS5D01G385800 chr5D 100.000 53 0 0 985 1037 454809581 454809633 1.040000e-16 99
9 TraesCS5D01G385800 chrUn 92.563 2017 64 33 2054 4025 63664218 63666193 0.000000e+00 2815
10 TraesCS5D01G385800 chrUn 93.007 715 33 11 1034 1731 63663334 63664048 0.000000e+00 1027
11 TraesCS5D01G385800 chrUn 92.025 326 22 4 4047 4369 63666181 63666505 5.370000e-124 455
12 TraesCS5D01G385800 chrUn 90.857 175 13 3 1759 1931 63664047 63664220 9.850000e-57 231
13 TraesCS5D01G385800 chrUn 90.909 121 7 2 491 609 63662034 63662152 4.710000e-35 159
14 TraesCS5D01G385800 chr5B 90.545 1872 68 24 2054 3874 556960256 556962069 0.000000e+00 2375
15 TraesCS5D01G385800 chr5B 93.851 927 27 6 1034 1931 556959333 556960258 0.000000e+00 1369
16 TraesCS5D01G385800 chr5B 89.513 267 19 6 4063 4325 556962139 556962400 3.400000e-86 329
17 TraesCS5D01G385800 chr5B 98.496 133 2 0 1926 2058 96878939 96879071 7.620000e-58 235
18 TraesCS5D01G385800 chr5B 100.000 53 0 0 985 1037 556959054 556959106 1.040000e-16 99
19 TraesCS5D01G385800 chr5A 94.327 1040 37 9 2 1037 572349314 572350335 0.000000e+00 1574
20 TraesCS5D01G385800 chr5A 89.746 1258 75 37 2670 3895 572351667 572352902 0.000000e+00 1559
21 TraesCS5D01G385800 chr5A 83.667 949 76 22 1034 1931 572350562 572351482 0.000000e+00 821
22 TraesCS5D01G385800 chr5A 97.701 174 3 1 2054 2227 572351480 572351652 9.580000e-77 298
23 TraesCS5D01G385800 chr5A 92.157 153 9 3 1916 2066 677949641 677949490 3.570000e-51 213
24 TraesCS5D01G385800 chr2D 94.231 156 9 0 4393 4548 65640156 65640311 5.890000e-59 239
25 TraesCS5D01G385800 chr2D 93.333 150 6 4 1930 2077 100314031 100314178 7.670000e-53 219
26 TraesCS5D01G385800 chr7A 97.794 136 2 1 1926 2061 19936692 19936826 2.740000e-57 233
27 TraesCS5D01G385800 chr6D 92.121 165 12 1 4389 4553 290813548 290813385 9.850000e-57 231
28 TraesCS5D01G385800 chr6D 90.566 159 14 1 4393 4550 20358230 20358388 4.620000e-50 209
29 TraesCS5D01G385800 chr6D 88.750 160 16 1 4393 4550 388334540 388334699 1.290000e-45 195
30 TraesCS5D01G385800 chr7B 97.744 133 3 0 1927 2059 72021752 72021884 3.540000e-56 230
31 TraesCS5D01G385800 chr6B 98.462 130 2 0 1930 2059 585806339 585806468 3.540000e-56 230
32 TraesCS5D01G385800 chr4A 98.462 130 2 0 1927 2056 477881885 477881756 3.540000e-56 230
33 TraesCS5D01G385800 chr4B 97.037 135 3 1 1930 2064 580801852 580801719 4.580000e-55 226
34 TraesCS5D01G385800 chr4D 90.798 163 15 0 4388 4550 479407346 479407508 7.670000e-53 219
35 TraesCS5D01G385800 chr4D 92.157 153 9 3 1916 2066 497646673 497646522 3.570000e-51 213
36 TraesCS5D01G385800 chr1A 90.062 161 16 0 4393 4553 533262987 533262827 4.620000e-50 209
37 TraesCS5D01G385800 chr3A 88.957 163 17 1 4389 4550 588841591 588841429 2.780000e-47 200
38 TraesCS5D01G385800 chr2A 92.045 88 5 2 901 987 140514964 140515050 6.190000e-24 122


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 TraesCS5D01G385800 chr5D 455606000 455610552 4552 False 8408.000000 8408 100.000000 1 4553 1 chr5D.!!$F2 4552
1 TraesCS5D01G385800 chr5D 454836366 454839796 3430 False 1570.333333 1916 94.956333 1 3893 3 chr5D.!!$F4 3892
2 TraesCS5D01G385800 chr5D 454809581 454812493 2912 False 1393.000000 2728 96.394667 985 3776 3 chr5D.!!$F3 2791
3 TraesCS5D01G385800 chrUn 63662034 63666505 4471 False 937.400000 2815 91.872200 491 4369 5 chrUn.!!$F1 3878
4 TraesCS5D01G385800 chr5B 556959054 556962400 3346 False 1043.000000 2375 93.477250 985 4325 4 chr5B.!!$F2 3340
5 TraesCS5D01G385800 chr5A 572349314 572352902 3588 False 1063.000000 1574 91.360250 2 3895 4 chr5A.!!$F1 3893

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
1084 1881 6.618287 TTTTTAAGGTATGGCTCATGATCG 57.382 37.500 0.00 0.0 0.00 3.69 F
1764 2609 2.190981 GGTAGTGCACGGATAACTTCG 58.809 52.381 12.01 0.0 0.00 3.79 F
2253 3110 0.032130 ATATGCGTACTCCTGCACCG 59.968 55.000 0.00 0.0 45.07 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 2784 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59 R
3360 4272 2.123632 AAGAGCTCAGGAGGGCCA 59.876 61.111 17.77 0.00 36.29 5.36 R
3932 4882 0.025001 CTCAATGCGGACGCGTTTAG 59.975 55.000 20.13 17.64 46.84 1.85 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
1084 1881 6.618287 TTTTTAAGGTATGGCTCATGATCG 57.382 37.500 0.00 0.00 0.00 3.69
1125 1926 6.472163 GCATTAACGCATAGCTTTGTTTGTAT 59.528 34.615 6.03 0.00 0.00 2.29
1621 2437 8.291740 TGTTGAATATGTGAACAAGTGAGATTG 58.708 33.333 0.00 0.00 36.22 2.67
1658 2493 6.873076 TCTGTGCTGATTTTGTTTTGAAGTTT 59.127 30.769 0.00 0.00 0.00 2.66
1660 2495 8.715191 TGTGCTGATTTTGTTTTGAAGTTTAT 57.285 26.923 0.00 0.00 0.00 1.40
1661 2496 8.816144 TGTGCTGATTTTGTTTTGAAGTTTATC 58.184 29.630 0.00 0.00 0.00 1.75
1663 2498 9.598517 TGCTGATTTTGTTTTGAAGTTTATCTT 57.401 25.926 0.00 0.00 39.32 2.40
1764 2609 2.190981 GGTAGTGCACGGATAACTTCG 58.809 52.381 12.01 0.00 0.00 3.79
1774 2619 2.870411 CGGATAACTTCGCCTTTTAGGG 59.130 50.000 0.00 0.00 35.37 3.53
1785 2633 4.259933 GCCTTTTAGGGAAATAAGGGGA 57.740 45.455 0.00 0.00 38.05 4.81
1789 2637 6.683537 CCTTTTAGGGAAATAAGGGGATCTT 58.316 40.000 0.00 0.00 39.40 2.40
1928 2783 5.581874 AGCAAAAACATGGAAGTTTCACTTG 59.418 36.000 0.00 0.00 38.80 3.16
1929 2784 5.351189 GCAAAAACATGGAAGTTTCACTTGT 59.649 36.000 0.00 0.00 38.80 3.16
1930 2785 6.533367 GCAAAAACATGGAAGTTTCACTTGTA 59.467 34.615 0.00 0.00 38.80 2.41
1931 2786 7.464045 GCAAAAACATGGAAGTTTCACTTGTAC 60.464 37.037 0.00 0.00 38.80 2.90
1932 2787 7.404671 AAAACATGGAAGTTTCACTTGTACT 57.595 32.000 0.00 0.00 38.80 2.73
1933 2788 6.619801 AACATGGAAGTTTCACTTGTACTC 57.380 37.500 0.00 0.00 38.80 2.59
1934 2789 5.063880 ACATGGAAGTTTCACTTGTACTCC 58.936 41.667 0.00 0.00 38.80 3.85
1935 2790 4.081322 TGGAAGTTTCACTTGTACTCCC 57.919 45.455 0.00 0.00 38.80 4.30
1936 2791 3.714798 TGGAAGTTTCACTTGTACTCCCT 59.285 43.478 0.00 0.00 38.80 4.20
1937 2792 4.202326 TGGAAGTTTCACTTGTACTCCCTC 60.202 45.833 0.00 0.00 38.80 4.30
1938 2793 4.316645 GAAGTTTCACTTGTACTCCCTCC 58.683 47.826 0.00 0.00 38.80 4.30
1939 2794 2.299297 AGTTTCACTTGTACTCCCTCCG 59.701 50.000 0.00 0.00 0.00 4.63
1940 2795 2.005370 TTCACTTGTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
1941 2796 1.542492 TCACTTGTACTCCCTCCGTC 58.458 55.000 0.00 0.00 0.00 4.79
1942 2797 0.531200 CACTTGTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
1943 2798 0.964358 ACTTGTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
1944 2799 1.664321 CTTGTACTCCCTCCGTCCGG 61.664 65.000 0.00 0.00 0.00 5.14
1945 2800 2.141011 TTGTACTCCCTCCGTCCGGA 62.141 60.000 0.00 0.00 42.90 5.14
1946 2801 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1947 2802 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
1948 2803 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1949 2804 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1950 2805 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1951 2806 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1952 2807 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1953 2808 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1954 2809 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1955 2810 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1956 2811 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1957 2812 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1958 2813 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1959 2814 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1960 2815 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1961 2816 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1962 2817 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1963 2818 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1964 2819 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1965 2820 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
1966 2821 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
1967 2822 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
1975 2830 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
1976 2831 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
1977 2832 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
1978 2833 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
1979 2834 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
1980 2835 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
1983 2838 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
1989 2844 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
2031 2886 9.657419 ACATCCCTTTTTATCAATTTTGATGAC 57.343 29.630 14.54 0.00 46.68 3.06
2032 2887 9.656040 CATCCCTTTTTATCAATTTTGATGACA 57.344 29.630 14.54 0.00 46.68 3.58
2034 2889 9.709495 TCCCTTTTTATCAATTTTGATGACAAG 57.291 29.630 14.54 13.72 46.68 3.16
2035 2890 9.492973 CCCTTTTTATCAATTTTGATGACAAGT 57.507 29.630 14.54 0.00 46.68 3.16
2043 2898 8.741101 TCAATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
2044 2899 8.572185 TCAATTTTGATGACAAGTATTTTCGGA 58.428 29.630 0.00 0.00 37.32 4.55
2045 2900 8.638565 CAATTTTGATGACAAGTATTTTCGGAC 58.361 33.333 0.00 0.00 37.32 4.79
2046 2901 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2047 2902 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2048 2903 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2049 2904 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2050 2905 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2051 2906 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2052 2907 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2253 3110 0.032130 ATATGCGTACTCCTGCACCG 59.968 55.000 0.00 0.00 45.07 4.94
2281 3138 0.833949 TGTACAGTCTGTGGTGGCAA 59.166 50.000 16.03 0.00 0.00 4.52
2317 3174 2.142292 TTTCCTGGGGAGCCTCAAGC 62.142 60.000 0.00 0.00 44.25 4.01
2423 3284 7.619512 AATTTGTTTATTGGTTCTTACCCCA 57.380 32.000 0.00 0.00 44.35 4.96
3044 3949 8.089625 TCACTTTTCTGTTCATCCATCCTATA 57.910 34.615 0.00 0.00 0.00 1.31
3360 4272 2.835431 CCAGAGGACGCGGAGGAT 60.835 66.667 12.47 0.00 0.00 3.24
3492 4404 7.783752 CATCCTTCAGATATGGCAGATGGCA 62.784 48.000 11.78 11.78 43.82 4.92
3632 4550 4.837093 TTAGGTAACCCTCTGTGATTGG 57.163 45.455 0.00 0.00 41.45 3.16
3665 4583 2.486203 TGGTTGGATTTGTATGTGCGTC 59.514 45.455 0.00 0.00 0.00 5.19
3688 4624 4.643795 TGGCACTTCCAGCATAGC 57.356 55.556 0.00 0.00 40.72 2.97
3749 4685 5.510671 CATTTACCTGTTTCACCATATCGC 58.489 41.667 0.00 0.00 0.00 4.58
3750 4686 2.779755 ACCTGTTTCACCATATCGCA 57.220 45.000 0.00 0.00 0.00 5.10
3769 4709 2.441750 GCAAGTCCTGGGGATTATACCA 59.558 50.000 0.00 0.00 32.73 3.25
3783 4723 6.979238 GGGATTATACCATTAGATGTCTACGC 59.021 42.308 0.00 0.00 0.00 4.42
3930 4880 8.687824 AGTGTTACTTTCAGAACAATGTTTTG 57.312 30.769 10.02 10.02 37.31 2.44
3932 4882 6.533367 TGTTACTTTCAGAACAATGTTTTGCC 59.467 34.615 11.27 0.00 36.22 4.52
3933 4883 5.343307 ACTTTCAGAACAATGTTTTGCCT 57.657 34.783 11.27 0.00 36.22 4.75
3934 4884 6.463995 ACTTTCAGAACAATGTTTTGCCTA 57.536 33.333 11.27 0.00 36.22 3.93
3974 4927 2.648059 GTGTAGAGATGCAGGCCAAAT 58.352 47.619 5.01 0.00 0.00 2.32
3978 4931 1.378882 GAGATGCAGGCCAAATGCGA 61.379 55.000 5.01 0.00 46.87 5.10
4019 4972 9.482627 GGATTGGTACTCTGAAACTATTATGAG 57.517 37.037 0.00 0.00 0.00 2.90
4020 4973 9.482627 GATTGGTACTCTGAAACTATTATGAGG 57.517 37.037 0.00 0.00 0.00 3.86
4021 4974 7.361457 TGGTACTCTGAAACTATTATGAGGG 57.639 40.000 0.00 0.00 0.00 4.30
4022 4975 6.183360 TGGTACTCTGAAACTATTATGAGGGC 60.183 42.308 0.00 0.00 0.00 5.19
4023 4976 5.957771 ACTCTGAAACTATTATGAGGGCA 57.042 39.130 0.00 0.00 0.00 5.36
4024 4977 5.923204 ACTCTGAAACTATTATGAGGGCAG 58.077 41.667 0.00 0.00 0.00 4.85
4025 4978 5.426833 ACTCTGAAACTATTATGAGGGCAGT 59.573 40.000 0.00 0.00 0.00 4.40
4026 4979 6.069963 ACTCTGAAACTATTATGAGGGCAGTT 60.070 38.462 0.00 0.00 0.00 3.16
4027 4980 6.721318 TCTGAAACTATTATGAGGGCAGTTT 58.279 36.000 0.00 0.00 40.99 2.66
4028 4981 7.175104 TCTGAAACTATTATGAGGGCAGTTTT 58.825 34.615 0.00 0.00 39.02 2.43
4029 4982 7.336931 TCTGAAACTATTATGAGGGCAGTTTTC 59.663 37.037 0.00 0.00 39.02 2.29
4030 4983 7.175104 TGAAACTATTATGAGGGCAGTTTTCT 58.825 34.615 0.00 0.00 39.02 2.52
4094 5048 3.248363 GTGCACATTTTCCTTTTGCCTTC 59.752 43.478 13.17 0.00 31.94 3.46
4171 5127 0.099436 GCGCCAACCATTCATCTGTC 59.901 55.000 0.00 0.00 0.00 3.51
4177 5133 2.932614 CAACCATTCATCTGTCGAGGAC 59.067 50.000 0.00 0.00 28.28 3.85
4250 5207 4.882427 TCTCGTATCCGTCTTCTCATTCTT 59.118 41.667 0.00 0.00 35.01 2.52
4263 5220 6.641314 TCTTCTCATTCTTAACGACAGTTGTC 59.359 38.462 2.16 2.16 41.35 3.18
4333 5290 5.741510 GCAGTATAGCAGATATCGTCATCAC 59.258 44.000 0.00 0.00 0.00 3.06
4341 5298 5.410746 GCAGATATCGTCATCACCATCAATT 59.589 40.000 0.00 0.00 0.00 2.32
4349 5306 4.807304 GTCATCACCATCAATTCAATTGGC 59.193 41.667 10.30 0.00 40.61 4.52
4354 5311 1.137479 CATCAATTCAATTGGCGGGCT 59.863 47.619 10.30 0.00 40.61 5.19
4369 5326 1.828979 GGGCTCTCTAGGAGATACGG 58.171 60.000 11.19 0.00 44.45 4.02
4370 5327 1.351683 GGGCTCTCTAGGAGATACGGA 59.648 57.143 11.19 0.00 44.45 4.69
4371 5328 2.617021 GGGCTCTCTAGGAGATACGGAG 60.617 59.091 11.19 0.00 44.45 4.63
4372 5329 2.039348 GGCTCTCTAGGAGATACGGAGT 59.961 54.545 11.19 0.00 44.45 3.85
4373 5330 3.261390 GGCTCTCTAGGAGATACGGAGTA 59.739 52.174 11.19 0.00 44.35 2.59
4374 5331 4.248058 GCTCTCTAGGAGATACGGAGTAC 58.752 52.174 11.19 0.00 43.61 2.73
4375 5332 4.487948 CTCTCTAGGAGATACGGAGTACG 58.512 52.174 0.00 0.00 45.96 3.67
4376 5333 5.147208 CTCTCTAGGAGATACGGAGTACGC 61.147 54.167 0.00 0.00 45.07 4.42
4377 5334 7.517393 CTCTCTAGGAGATACGGAGTACGCA 62.517 52.000 0.00 0.00 45.07 5.24
4378 5335 8.889795 CTCTCTAGGAGATACGGAGTACGCAA 62.890 50.000 0.00 0.00 45.07 4.85
4391 5348 7.806149 CGGAGTACGCAATATCATGTATAAA 57.194 36.000 0.00 0.00 34.82 1.40
4392 5349 8.234887 CGGAGTACGCAATATCATGTATAAAA 57.765 34.615 0.00 0.00 34.82 1.52
4393 5350 8.373256 CGGAGTACGCAATATCATGTATAAAAG 58.627 37.037 0.00 0.00 34.82 2.27
4394 5351 8.169268 GGAGTACGCAATATCATGTATAAAAGC 58.831 37.037 0.00 0.00 0.00 3.51
4395 5352 8.601845 AGTACGCAATATCATGTATAAAAGCA 57.398 30.769 0.00 0.00 0.00 3.91
4396 5353 9.051679 AGTACGCAATATCATGTATAAAAGCAA 57.948 29.630 0.00 0.00 0.00 3.91
4397 5354 9.103048 GTACGCAATATCATGTATAAAAGCAAC 57.897 33.333 0.00 0.00 0.00 4.17
4398 5355 7.930217 ACGCAATATCATGTATAAAAGCAACT 58.070 30.769 0.00 0.00 0.00 3.16
4399 5356 8.070171 ACGCAATATCATGTATAAAAGCAACTC 58.930 33.333 0.00 0.00 0.00 3.01
4400 5357 7.535258 CGCAATATCATGTATAAAAGCAACTCC 59.465 37.037 0.00 0.00 0.00 3.85
4401 5358 8.352201 GCAATATCATGTATAAAAGCAACTCCA 58.648 33.333 0.00 0.00 0.00 3.86
4404 5361 6.176975 TCATGTATAAAAGCAACTCCAACG 57.823 37.500 0.00 0.00 0.00 4.10
4405 5362 5.123186 TCATGTATAAAAGCAACTCCAACGG 59.877 40.000 0.00 0.00 0.00 4.44
4406 5363 3.754323 TGTATAAAAGCAACTCCAACGGG 59.246 43.478 0.00 0.00 0.00 5.28
4407 5364 1.611519 TAAAAGCAACTCCAACGGGG 58.388 50.000 0.00 0.00 38.37 5.73
4408 5365 1.744320 AAAAGCAACTCCAACGGGGC 61.744 55.000 0.00 0.00 36.21 5.80
4411 5368 3.047877 CAACTCCAACGGGGCGAC 61.048 66.667 0.00 0.00 36.21 5.19
4426 5383 4.668118 GACCCAAACGGACGGCGA 62.668 66.667 16.62 0.00 34.64 5.54
4427 5384 3.945304 GACCCAAACGGACGGCGAT 62.945 63.158 16.62 0.00 34.64 4.58
4428 5385 2.744709 CCCAAACGGACGGCGATT 60.745 61.111 16.62 0.00 0.00 3.34
4429 5386 2.329614 CCCAAACGGACGGCGATTT 61.330 57.895 16.62 5.62 0.00 2.17
4430 5387 1.133869 CCAAACGGACGGCGATTTC 59.866 57.895 16.62 0.00 0.00 2.17
4431 5388 1.225637 CAAACGGACGGCGATTTCG 60.226 57.895 16.62 13.70 43.27 3.46
4432 5389 1.665599 AAACGGACGGCGATTTCGT 60.666 52.632 16.62 14.37 44.03 3.85
4440 5397 2.202756 GCGATTTCGTCCGCCTCT 60.203 61.111 1.55 0.00 45.06 3.69
4441 5398 1.810030 GCGATTTCGTCCGCCTCTT 60.810 57.895 1.55 0.00 45.06 2.85
4442 5399 1.999051 CGATTTCGTCCGCCTCTTG 59.001 57.895 0.00 0.00 34.11 3.02
4443 5400 0.736325 CGATTTCGTCCGCCTCTTGT 60.736 55.000 0.00 0.00 34.11 3.16
4444 5401 1.000145 GATTTCGTCCGCCTCTTGTC 59.000 55.000 0.00 0.00 0.00 3.18
4445 5402 0.391263 ATTTCGTCCGCCTCTTGTCC 60.391 55.000 0.00 0.00 0.00 4.02
4446 5403 2.758770 TTTCGTCCGCCTCTTGTCCG 62.759 60.000 0.00 0.00 0.00 4.79
4447 5404 4.052229 CGTCCGCCTCTTGTCCGT 62.052 66.667 0.00 0.00 0.00 4.69
4448 5405 2.342648 GTCCGCCTCTTGTCCGTT 59.657 61.111 0.00 0.00 0.00 4.44
4449 5406 1.301479 GTCCGCCTCTTGTCCGTTT 60.301 57.895 0.00 0.00 0.00 3.60
4450 5407 1.301401 TCCGCCTCTTGTCCGTTTG 60.301 57.895 0.00 0.00 0.00 2.93
4451 5408 2.325082 CCGCCTCTTGTCCGTTTGG 61.325 63.158 0.00 0.00 0.00 3.28
4452 5409 2.325082 CGCCTCTTGTCCGTTTGGG 61.325 63.158 0.00 0.00 35.24 4.12
4453 5410 1.228154 GCCTCTTGTCCGTTTGGGT 60.228 57.895 0.00 0.00 37.00 4.51
4454 5411 1.235281 GCCTCTTGTCCGTTTGGGTC 61.235 60.000 0.00 0.00 37.00 4.46
4455 5412 0.949105 CCTCTTGTCCGTTTGGGTCG 60.949 60.000 0.00 0.00 37.00 4.79
4457 5414 2.592287 TTGTCCGTTTGGGTCGGC 60.592 61.111 0.00 0.00 46.49 5.54
4458 5415 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
4485 5442 4.289312 GCGTCCGGCCTCTTTTAA 57.711 55.556 0.00 0.00 34.80 1.52
4486 5443 2.547026 GCGTCCGGCCTCTTTTAAA 58.453 52.632 0.00 0.00 34.80 1.52
4487 5444 1.092348 GCGTCCGGCCTCTTTTAAAT 58.908 50.000 0.00 0.00 34.80 1.40
4488 5445 1.471287 GCGTCCGGCCTCTTTTAAATT 59.529 47.619 0.00 0.00 34.80 1.82
4489 5446 2.094906 GCGTCCGGCCTCTTTTAAATTT 60.095 45.455 0.00 0.00 34.80 1.82
4490 5447 3.498082 CGTCCGGCCTCTTTTAAATTTG 58.502 45.455 0.00 0.00 0.00 2.32
4491 5448 3.672241 CGTCCGGCCTCTTTTAAATTTGG 60.672 47.826 0.00 0.00 0.00 3.28
4492 5449 2.829120 TCCGGCCTCTTTTAAATTTGGG 59.171 45.455 0.00 0.00 0.00 4.12
4493 5450 2.565391 CCGGCCTCTTTTAAATTTGGGT 59.435 45.455 0.00 0.00 0.00 4.51
4494 5451 3.368013 CCGGCCTCTTTTAAATTTGGGTC 60.368 47.826 0.00 0.00 0.00 4.46
4495 5452 3.672241 CGGCCTCTTTTAAATTTGGGTCG 60.672 47.826 0.00 8.70 34.34 4.79
4496 5453 3.368013 GGCCTCTTTTAAATTTGGGTCGG 60.368 47.826 0.00 0.00 0.00 4.79
4497 5454 3.845178 CCTCTTTTAAATTTGGGTCGGC 58.155 45.455 0.00 0.00 0.00 5.54
4498 5455 3.257127 CCTCTTTTAAATTTGGGTCGGCA 59.743 43.478 0.00 0.00 0.00 5.69
4499 5456 4.485163 CTCTTTTAAATTTGGGTCGGCAG 58.515 43.478 0.00 0.00 0.00 4.85
4500 5457 3.257127 TCTTTTAAATTTGGGTCGGCAGG 59.743 43.478 0.00 0.00 0.00 4.85
4501 5458 1.551452 TTAAATTTGGGTCGGCAGGG 58.449 50.000 0.00 0.00 0.00 4.45
4502 5459 0.968393 TAAATTTGGGTCGGCAGGGC 60.968 55.000 0.00 0.00 0.00 5.19
4523 5480 3.732892 CAACGCGCCGACCCATTT 61.733 61.111 5.73 0.00 0.00 2.32
4524 5481 3.428282 AACGCGCCGACCCATTTC 61.428 61.111 5.73 0.00 0.00 2.17
4525 5482 4.690719 ACGCGCCGACCCATTTCA 62.691 61.111 5.73 0.00 0.00 2.69
4526 5483 3.202001 CGCGCCGACCCATTTCAT 61.202 61.111 0.00 0.00 0.00 2.57
4527 5484 2.408835 GCGCCGACCCATTTCATG 59.591 61.111 0.00 0.00 0.00 3.07
4528 5485 2.406616 GCGCCGACCCATTTCATGT 61.407 57.895 0.00 0.00 0.00 3.21
4529 5486 1.721487 CGCCGACCCATTTCATGTC 59.279 57.895 0.00 0.00 0.00 3.06
4530 5487 1.714899 CGCCGACCCATTTCATGTCC 61.715 60.000 0.00 0.00 0.00 4.02
4531 5488 1.714899 GCCGACCCATTTCATGTCCG 61.715 60.000 0.00 0.00 0.00 4.79
4532 5489 1.714899 CCGACCCATTTCATGTCCGC 61.715 60.000 0.00 0.00 0.00 5.54
4533 5490 1.721487 GACCCATTTCATGTCCGCG 59.279 57.895 0.00 0.00 0.00 6.46
4534 5491 2.322999 GACCCATTTCATGTCCGCGC 62.323 60.000 0.00 0.00 0.00 6.86
4535 5492 2.023181 CCATTTCATGTCCGCGCG 59.977 61.111 25.67 25.67 0.00 6.86
4536 5493 2.648724 CATTTCATGTCCGCGCGC 60.649 61.111 27.36 23.91 0.00 6.86
4537 5494 3.124270 ATTTCATGTCCGCGCGCA 61.124 55.556 32.61 19.15 0.00 6.09
4538 5495 2.685829 ATTTCATGTCCGCGCGCAA 61.686 52.632 32.61 16.17 0.00 4.85
4539 5496 1.992233 ATTTCATGTCCGCGCGCAAT 61.992 50.000 32.61 17.17 0.00 3.56
4540 5497 2.193865 TTTCATGTCCGCGCGCAATT 62.194 50.000 32.61 7.59 0.00 2.32
4541 5498 2.193865 TTCATGTCCGCGCGCAATTT 62.194 50.000 32.61 8.40 0.00 1.82
4542 5499 1.801113 CATGTCCGCGCGCAATTTT 60.801 52.632 32.61 9.62 0.00 1.82
4543 5500 1.080839 ATGTCCGCGCGCAATTTTT 60.081 47.368 32.61 7.81 0.00 1.94
4544 5501 0.169230 ATGTCCGCGCGCAATTTTTA 59.831 45.000 32.61 10.32 0.00 1.52
4545 5502 0.453615 TGTCCGCGCGCAATTTTTAG 60.454 50.000 32.61 11.84 0.00 1.85
4546 5503 0.179210 GTCCGCGCGCAATTTTTAGA 60.179 50.000 32.61 10.17 0.00 2.10
4547 5504 0.517755 TCCGCGCGCAATTTTTAGAA 59.482 45.000 32.61 0.00 0.00 2.10
4548 5505 1.069159 TCCGCGCGCAATTTTTAGAAA 60.069 42.857 32.61 0.71 0.00 2.52
4549 5506 1.716581 CCGCGCGCAATTTTTAGAAAA 59.283 42.857 32.61 0.00 0.00 2.29
4550 5507 2.344142 CCGCGCGCAATTTTTAGAAAAT 59.656 40.909 32.61 0.00 0.00 1.82
4551 5508 3.324432 CGCGCGCAATTTTTAGAAAATG 58.676 40.909 32.61 4.31 0.00 2.32
4552 5509 3.658695 GCGCGCAATTTTTAGAAAATGG 58.341 40.909 29.10 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1084 1881 6.580476 CGTTAATGCACTCAAATGGAAAAAC 58.420 36.000 0.00 0.00 0.00 2.43
1125 1926 6.009589 TCATGAGGAAAGCTTTAACCAATGA 58.990 36.000 20.22 20.22 0.00 2.57
1252 2062 7.805163 TCCTCATGTATACCATCTTCACAAAT 58.195 34.615 0.00 0.00 0.00 2.32
1440 2256 2.815503 TGCCATGTCTGAGTGTGAAATG 59.184 45.455 0.00 0.00 0.00 2.32
1621 2437 2.102084 TCAGCACAGATACCAGATCAGC 59.898 50.000 0.00 0.00 0.00 4.26
1738 2583 5.736813 AGTTATCCGTGCACTACCAATAAA 58.263 37.500 16.19 0.00 0.00 1.40
1739 2584 5.347620 AGTTATCCGTGCACTACCAATAA 57.652 39.130 16.19 8.37 0.00 1.40
1764 2609 4.259933 TCCCCTTATTTCCCTAAAAGGC 57.740 45.455 0.00 0.00 32.73 4.35
1801 2649 3.557228 TTTTTCATTGGCAGCTTGGTT 57.443 38.095 0.00 0.00 0.00 3.67
1840 2693 7.613022 AGACCATGTCAATTGACTGAAATACAT 59.387 33.333 32.57 17.03 44.99 2.29
1866 2720 6.183360 GGAAAGTTTTGGTCCAATGTACTTGA 60.183 38.462 19.75 0.00 36.97 3.02
1868 2722 5.897250 AGGAAAGTTTTGGTCCAATGTACTT 59.103 36.000 4.80 12.19 33.57 2.24
1928 2783 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
1929 2784 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1930 2785 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1931 2786 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1932 2787 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1933 2788 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1934 2789 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1935 2790 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1936 2791 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1937 2792 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1938 2793 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1939 2794 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1940 2795 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
1941 2796 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
1942 2797 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
1949 2804 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
1950 2805 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
1951 2806 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
1952 2807 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
1953 2808 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
1954 2809 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
1957 2812 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
1963 2818 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
2005 2860 9.657419 GTCATCAAAATTGATAAAAAGGGATGT 57.343 29.630 8.24 0.00 45.62 3.06
2006 2861 9.656040 TGTCATCAAAATTGATAAAAAGGGATG 57.344 29.630 8.24 0.00 45.62 3.51
2008 2863 9.709495 CTTGTCATCAAAATTGATAAAAAGGGA 57.291 29.630 8.24 0.00 45.62 4.20
2009 2864 9.492973 ACTTGTCATCAAAATTGATAAAAAGGG 57.507 29.630 11.98 0.00 45.62 3.95
2018 2873 8.572185 TCCGAAAATACTTGTCATCAAAATTGA 58.428 29.630 0.00 0.00 42.14 2.57
2019 2874 8.638565 GTCCGAAAATACTTGTCATCAAAATTG 58.361 33.333 0.00 0.00 32.87 2.32
2020 2875 7.537306 CGTCCGAAAATACTTGTCATCAAAATT 59.463 33.333 0.00 0.00 32.87 1.82
2021 2876 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2022 2877 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2023 2878 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2024 2879 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2025 2880 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2026 2881 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2027 2882 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2028 2883 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2029 2884 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2030 2885 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2031 2886 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2032 2887 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2033 2888 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2034 2889 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2035 2890 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2036 2891 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2037 2892 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
2038 2893 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
2039 2894 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
2040 2895 0.477204 ATCATACTCCCTCCGTCCGA 59.523 55.000 0.00 0.00 0.00 4.55
2041 2896 1.329256 AATCATACTCCCTCCGTCCG 58.671 55.000 0.00 0.00 0.00 4.79
2042 2897 4.527038 TGAATAATCATACTCCCTCCGTCC 59.473 45.833 0.00 0.00 0.00 4.79
2043 2898 5.723672 TGAATAATCATACTCCCTCCGTC 57.276 43.478 0.00 0.00 0.00 4.79
2044 2899 5.602978 AGTTGAATAATCATACTCCCTCCGT 59.397 40.000 0.00 0.00 34.96 4.69
2045 2900 5.928839 CAGTTGAATAATCATACTCCCTCCG 59.071 44.000 0.00 0.00 34.96 4.63
2046 2901 7.067496 TCAGTTGAATAATCATACTCCCTCC 57.933 40.000 0.00 0.00 34.96 4.30
2131 2988 4.323417 ACGCCATCATGAAACTAAACAGA 58.677 39.130 0.00 0.00 0.00 3.41
2232 3089 1.068588 GGTGCAGGAGTACGCATATCA 59.931 52.381 0.00 0.00 40.89 2.15
2253 3110 1.344763 ACAGACTGTACAGGCTTGGTC 59.655 52.381 29.19 14.91 46.84 4.02
2281 3138 1.703513 GAAACCTACCTCACCCTGGTT 59.296 52.381 0.00 0.00 42.09 3.67
2351 3208 9.836864 ATTGTATTCTTAGAGTCACATAATGCA 57.163 29.630 0.00 0.00 0.00 3.96
2512 3376 5.721232 ACAACCAACCTAGATTCTAGAACG 58.279 41.667 20.14 7.84 0.00 3.95
2713 3610 5.985530 TGAATAGAAATCATGCACGAGTAGG 59.014 40.000 0.00 0.00 0.00 3.18
3268 4177 5.048434 GGAAGTGAGGAGACAAAAAGGAATG 60.048 44.000 0.00 0.00 0.00 2.67
3360 4272 2.123632 AAGAGCTCAGGAGGGCCA 59.876 61.111 17.77 0.00 36.29 5.36
3492 4404 5.462240 TCCTCATCATGGTAGATGTTCTCT 58.538 41.667 0.00 0.00 44.46 3.10
3574 4489 5.248380 AGGTATTATCTTGCCTCCATTCC 57.752 43.478 0.00 0.00 0.00 3.01
3688 4624 5.977725 CGACAGGTAGTCTAATTGGTATGTG 59.022 44.000 0.00 0.00 45.32 3.21
3749 4685 5.324832 AATGGTATAATCCCCAGGACTTG 57.675 43.478 0.00 0.00 32.98 3.16
3750 4686 6.399013 TCTAATGGTATAATCCCCAGGACTT 58.601 40.000 0.00 0.00 32.98 3.01
3769 4709 7.255520 CCCAACTTACTAGCGTAGACATCTAAT 60.256 40.741 0.00 0.00 0.00 1.73
3783 4723 2.359900 CAGCCTTGCCCAACTTACTAG 58.640 52.381 0.00 0.00 0.00 2.57
3835 4783 3.306973 GCAACAAGAAAGAAACCTGCAAC 59.693 43.478 0.00 0.00 0.00 4.17
3842 4790 4.201676 CCCGTTTTGCAACAAGAAAGAAAC 60.202 41.667 0.00 0.00 32.54 2.78
3847 4797 2.231478 TGACCCGTTTTGCAACAAGAAA 59.769 40.909 0.00 0.00 32.54 2.52
3850 4800 1.535860 CCTGACCCGTTTTGCAACAAG 60.536 52.381 0.00 0.00 32.54 3.16
3929 4879 3.943479 ATGCGGACGCGTTTAGGCA 62.943 57.895 22.83 22.83 45.51 4.75
3930 4880 2.746803 AATGCGGACGCGTTTAGGC 61.747 57.895 15.53 15.13 46.84 3.93
3932 4882 0.025001 CTCAATGCGGACGCGTTTAG 59.975 55.000 20.13 17.64 46.84 1.85
3933 4883 0.668096 ACTCAATGCGGACGCGTTTA 60.668 50.000 20.13 12.54 46.84 2.01
3934 4884 1.897398 GACTCAATGCGGACGCGTTT 61.897 55.000 20.13 9.77 46.84 3.60
3940 4890 1.135489 TCTACACGACTCAATGCGGAC 60.135 52.381 0.00 0.00 0.00 4.79
3974 4927 3.080319 TCCATGAACAAACATCATCGCA 58.920 40.909 0.00 0.00 35.38 5.10
3978 4931 6.664816 AGTACCAATCCATGAACAAACATCAT 59.335 34.615 0.00 0.00 38.02 2.45
4042 4995 5.906073 GCATACACTGCCCTCATAATTTTT 58.094 37.500 0.00 0.00 45.66 1.94
4043 4996 5.520376 GCATACACTGCCCTCATAATTTT 57.480 39.130 0.00 0.00 45.66 1.82
4059 5012 2.033294 TGCACGCTTGGGCATACA 59.967 55.556 0.00 0.00 38.60 2.29
4062 5015 1.818959 AAATGTGCACGCTTGGGCAT 61.819 50.000 13.13 0.00 42.75 4.40
4094 5048 0.886490 GGTTGTGCTGGTGAGGTCAG 60.886 60.000 0.00 0.00 35.49 3.51
4171 5127 2.434884 ATTGCACGGCTGTCCTCG 60.435 61.111 0.00 0.00 0.00 4.63
4263 5220 5.718146 AGCTTGATGGTATGAGATGTATCG 58.282 41.667 0.00 0.00 0.00 2.92
4333 5290 1.807377 GCCCGCCAATTGAATTGATGG 60.807 52.381 18.82 17.48 42.83 3.51
4341 5298 0.465705 CTAGAGAGCCCGCCAATTGA 59.534 55.000 7.12 0.00 0.00 2.57
4349 5306 1.444836 CGTATCTCCTAGAGAGCCCG 58.555 60.000 0.32 0.00 42.26 6.13
4354 5311 3.305950 GCGTACTCCGTATCTCCTAGAGA 60.306 52.174 0.00 0.00 40.01 3.10
4369 5326 8.708742 TGCTTTTATACATGATATTGCGTACTC 58.291 33.333 0.00 0.00 0.00 2.59
4370 5327 8.601845 TGCTTTTATACATGATATTGCGTACT 57.398 30.769 0.00 0.00 0.00 2.73
4371 5328 9.103048 GTTGCTTTTATACATGATATTGCGTAC 57.897 33.333 0.00 0.00 0.00 3.67
4372 5329 9.051679 AGTTGCTTTTATACATGATATTGCGTA 57.948 29.630 0.00 0.00 0.00 4.42
4373 5330 7.930217 AGTTGCTTTTATACATGATATTGCGT 58.070 30.769 0.00 0.00 0.00 5.24
4374 5331 7.535258 GGAGTTGCTTTTATACATGATATTGCG 59.465 37.037 0.00 0.00 0.00 4.85
4375 5332 8.352201 TGGAGTTGCTTTTATACATGATATTGC 58.648 33.333 0.00 0.00 0.00 3.56
4378 5335 8.559536 CGTTGGAGTTGCTTTTATACATGATAT 58.440 33.333 0.00 0.00 0.00 1.63
4379 5336 7.011950 CCGTTGGAGTTGCTTTTATACATGATA 59.988 37.037 0.00 0.00 0.00 2.15
4380 5337 6.183360 CCGTTGGAGTTGCTTTTATACATGAT 60.183 38.462 0.00 0.00 0.00 2.45
4381 5338 5.123186 CCGTTGGAGTTGCTTTTATACATGA 59.877 40.000 0.00 0.00 0.00 3.07
4382 5339 5.331902 CCGTTGGAGTTGCTTTTATACATG 58.668 41.667 0.00 0.00 0.00 3.21
4383 5340 4.398044 CCCGTTGGAGTTGCTTTTATACAT 59.602 41.667 0.00 0.00 0.00 2.29
4384 5341 3.754323 CCCGTTGGAGTTGCTTTTATACA 59.246 43.478 0.00 0.00 0.00 2.29
4385 5342 3.128068 CCCCGTTGGAGTTGCTTTTATAC 59.872 47.826 0.00 0.00 35.39 1.47
4386 5343 3.349022 CCCCGTTGGAGTTGCTTTTATA 58.651 45.455 0.00 0.00 35.39 0.98
4387 5344 2.167662 CCCCGTTGGAGTTGCTTTTAT 58.832 47.619 0.00 0.00 35.39 1.40
4388 5345 1.611519 CCCCGTTGGAGTTGCTTTTA 58.388 50.000 0.00 0.00 35.39 1.52
4389 5346 1.744320 GCCCCGTTGGAGTTGCTTTT 61.744 55.000 0.00 0.00 35.39 2.27
4390 5347 2.200337 GCCCCGTTGGAGTTGCTTT 61.200 57.895 0.00 0.00 35.39 3.51
4391 5348 2.597510 GCCCCGTTGGAGTTGCTT 60.598 61.111 0.00 0.00 35.39 3.91
4394 5351 3.047877 GTCGCCCCGTTGGAGTTG 61.048 66.667 0.00 0.00 35.07 3.16
4395 5352 4.324991 GGTCGCCCCGTTGGAGTT 62.325 66.667 0.00 0.00 35.07 3.01
4409 5366 3.945304 ATCGCCGTCCGTTTGGGTC 62.945 63.158 0.00 0.00 38.35 4.46
4410 5367 3.540367 AATCGCCGTCCGTTTGGGT 62.540 57.895 0.00 0.00 38.35 4.51
4411 5368 2.248274 GAAATCGCCGTCCGTTTGGG 62.248 60.000 0.00 0.00 38.35 4.12
4412 5369 1.133869 GAAATCGCCGTCCGTTTGG 59.866 57.895 0.00 0.00 38.35 3.28
4413 5370 1.225637 CGAAATCGCCGTCCGTTTG 60.226 57.895 0.00 0.00 38.35 2.93
4414 5371 1.665599 ACGAAATCGCCGTCCGTTT 60.666 52.632 2.15 0.00 44.43 3.60
4415 5372 2.048877 ACGAAATCGCCGTCCGTT 60.049 55.556 2.15 0.00 44.43 4.44
4424 5381 0.736325 ACAAGAGGCGGACGAAATCG 60.736 55.000 0.48 0.48 46.33 3.34
4425 5382 1.000145 GACAAGAGGCGGACGAAATC 59.000 55.000 0.00 0.00 0.00 2.17
4426 5383 0.391263 GGACAAGAGGCGGACGAAAT 60.391 55.000 0.00 0.00 0.00 2.17
4427 5384 1.005394 GGACAAGAGGCGGACGAAA 60.005 57.895 0.00 0.00 0.00 3.46
4428 5385 2.654877 GGACAAGAGGCGGACGAA 59.345 61.111 0.00 0.00 0.00 3.85
4429 5386 3.744719 CGGACAAGAGGCGGACGA 61.745 66.667 0.00 0.00 0.00 4.20
4430 5387 3.569049 AACGGACAAGAGGCGGACG 62.569 63.158 0.00 0.00 0.00 4.79
4431 5388 1.301479 AAACGGACAAGAGGCGGAC 60.301 57.895 0.00 0.00 0.00 4.79
4432 5389 1.301401 CAAACGGACAAGAGGCGGA 60.301 57.895 0.00 0.00 0.00 5.54
4433 5390 2.325082 CCAAACGGACAAGAGGCGG 61.325 63.158 0.00 0.00 0.00 6.13
4434 5391 2.325082 CCCAAACGGACAAGAGGCG 61.325 63.158 0.00 0.00 0.00 5.52
4435 5392 1.228154 ACCCAAACGGACAAGAGGC 60.228 57.895 0.00 0.00 34.64 4.70
4436 5393 0.949105 CGACCCAAACGGACAAGAGG 60.949 60.000 0.00 0.00 34.64 3.69
4437 5394 2.528797 CGACCCAAACGGACAAGAG 58.471 57.895 0.00 0.00 34.64 2.85
4438 5395 4.762825 CGACCCAAACGGACAAGA 57.237 55.556 0.00 0.00 34.64 3.02
4468 5425 1.092348 ATTTAAAAGAGGCCGGACGC 58.908 50.000 5.05 3.00 0.00 5.19
4469 5426 3.498082 CAAATTTAAAAGAGGCCGGACG 58.502 45.455 5.05 0.00 0.00 4.79
4470 5427 3.368013 CCCAAATTTAAAAGAGGCCGGAC 60.368 47.826 5.05 0.00 0.00 4.79
4471 5428 2.829120 CCCAAATTTAAAAGAGGCCGGA 59.171 45.455 5.05 0.00 0.00 5.14
4472 5429 2.565391 ACCCAAATTTAAAAGAGGCCGG 59.435 45.455 0.00 0.00 0.00 6.13
4473 5430 3.672241 CGACCCAAATTTAAAAGAGGCCG 60.672 47.826 0.00 0.00 0.00 6.13
4474 5431 3.368013 CCGACCCAAATTTAAAAGAGGCC 60.368 47.826 0.00 0.00 0.00 5.19
4475 5432 3.845178 CCGACCCAAATTTAAAAGAGGC 58.155 45.455 0.00 0.00 0.00 4.70
4476 5433 3.257127 TGCCGACCCAAATTTAAAAGAGG 59.743 43.478 0.00 0.00 0.00 3.69
4477 5434 4.485163 CTGCCGACCCAAATTTAAAAGAG 58.515 43.478 0.00 0.00 0.00 2.85
4478 5435 3.257127 CCTGCCGACCCAAATTTAAAAGA 59.743 43.478 0.00 0.00 0.00 2.52
4479 5436 3.584834 CCTGCCGACCCAAATTTAAAAG 58.415 45.455 0.00 0.00 0.00 2.27
4480 5437 2.300437 CCCTGCCGACCCAAATTTAAAA 59.700 45.455 0.00 0.00 0.00 1.52
4481 5438 1.896465 CCCTGCCGACCCAAATTTAAA 59.104 47.619 0.00 0.00 0.00 1.52
4482 5439 1.551452 CCCTGCCGACCCAAATTTAA 58.449 50.000 0.00 0.00 0.00 1.52
4483 5440 0.968393 GCCCTGCCGACCCAAATTTA 60.968 55.000 0.00 0.00 0.00 1.40
4484 5441 2.282783 GCCCTGCCGACCCAAATTT 61.283 57.895 0.00 0.00 0.00 1.82
4485 5442 2.679996 GCCCTGCCGACCCAAATT 60.680 61.111 0.00 0.00 0.00 1.82
4506 5463 3.661025 GAAATGGGTCGGCGCGTTG 62.661 63.158 12.62 0.00 36.96 4.10
4507 5464 3.428282 GAAATGGGTCGGCGCGTT 61.428 61.111 8.43 5.61 38.23 4.84
4508 5465 3.969250 ATGAAATGGGTCGGCGCGT 62.969 57.895 8.43 0.00 0.00 6.01
4509 5466 3.202001 ATGAAATGGGTCGGCGCG 61.202 61.111 0.00 0.00 0.00 6.86
4510 5467 2.408835 CATGAAATGGGTCGGCGC 59.591 61.111 0.00 0.00 41.79 6.53
4520 5477 1.992233 ATTGCGCGCGGACATGAAAT 61.992 50.000 33.06 15.39 0.00 2.17
4521 5478 2.193865 AATTGCGCGCGGACATGAAA 62.194 50.000 33.06 13.44 0.00 2.69
4522 5479 2.193865 AAATTGCGCGCGGACATGAA 62.194 50.000 33.06 14.30 0.00 2.57
4523 5480 2.193865 AAAATTGCGCGCGGACATGA 62.194 50.000 33.06 14.75 0.00 3.07
4524 5481 1.343510 AAAAATTGCGCGCGGACATG 61.344 50.000 33.06 1.90 0.00 3.21
4525 5482 0.169230 TAAAAATTGCGCGCGGACAT 59.831 45.000 33.06 20.88 0.00 3.06
4526 5483 0.453615 CTAAAAATTGCGCGCGGACA 60.454 50.000 33.06 19.45 0.00 4.02
4527 5484 0.179210 TCTAAAAATTGCGCGCGGAC 60.179 50.000 33.06 16.69 0.00 4.79
4528 5485 0.517755 TTCTAAAAATTGCGCGCGGA 59.482 45.000 33.06 28.65 0.00 5.54
4529 5486 1.332178 TTTCTAAAAATTGCGCGCGG 58.668 45.000 33.06 13.66 0.00 6.46
4530 5487 3.324432 CATTTTCTAAAAATTGCGCGCG 58.676 40.909 28.44 28.44 0.00 6.86
4531 5488 3.658695 CCATTTTCTAAAAATTGCGCGC 58.341 40.909 27.26 27.26 0.00 6.86


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

AutoCloner maintained by Alex Coulton.