Multiple sequence alignment - TraesCS2A01G481600

Loading Multiple Alignment...

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 TraesCS2A01G481600 chr2A 100.000 2891 0 0 1 2891 718819201 718816311 0.000000e+00 5339.0
1 TraesCS2A01G481600 chr2A 90.728 151 12 2 1 149 718884111 718883961 1.760000e-47 200.0
2 TraesCS2A01G481600 chr2A 89.933 149 14 1 312 460 718834168 718834021 1.060000e-44 191.0
3 TraesCS2A01G481600 chr2A 84.810 158 22 2 298 455 718929369 718929214 1.070000e-34 158.0
4 TraesCS2A01G481600 chr2A 84.768 151 23 0 305 455 718916971 718916821 4.990000e-33 152.0
5 TraesCS2A01G481600 chr2A 84.615 143 22 0 1 143 718838013 718837871 3.000000e-30 143.0
6 TraesCS2A01G481600 chr2A 82.667 150 24 2 1 149 718729385 718729237 6.500000e-27 132.0
7 TraesCS2A01G481600 chr2B 92.952 2029 89 24 722 2741 704411735 704409752 0.000000e+00 2905.0
8 TraesCS2A01G481600 chr2B 87.135 684 60 16 1 658 704412665 704411984 0.000000e+00 750.0
9 TraesCS2A01G481600 chr2B 89.933 149 15 0 1 149 704580131 704579983 2.940000e-45 193.0
10 TraesCS2A01G481600 chr2B 85.235 149 22 0 315 463 704426063 704425915 1.390000e-33 154.0
11 TraesCS2A01G481600 chr2B 82.530 166 28 1 291 455 704967963 704967798 8.350000e-31 145.0
12 TraesCS2A01G481600 chr2B 83.893 149 23 1 1 149 704426463 704426316 1.080000e-29 141.0
13 TraesCS2A01G481600 chr2B 84.404 109 11 4 607 709 28506405 28506297 5.100000e-18 102.0
14 TraesCS2A01G481600 chr2B 82.727 110 10 7 607 709 154226588 154226695 3.970000e-14 89.8
15 TraesCS2A01G481600 chr2D 90.440 795 65 7 1319 2112 584547556 584546772 0.000000e+00 1037.0
16 TraesCS2A01G481600 chr2D 86.201 558 46 13 1 529 584607295 584606740 2.500000e-160 575.0
17 TraesCS2A01G481600 chr2D 89.826 344 30 4 981 1324 584596646 584596308 1.230000e-118 436.0
18 TraesCS2A01G481600 chr2D 91.275 149 13 0 1 149 584657695 584657547 1.360000e-48 204.0
19 TraesCS2A01G481600 chr2D 88.732 142 15 1 1 142 584661843 584661703 3.830000e-39 172.0
20 TraesCS2A01G481600 chr2D 85.443 158 22 1 279 435 584668418 584668261 2.300000e-36 163.0
21 TraesCS2A01G481600 chr2D 85.065 154 23 0 282 435 594999110 594999263 1.070000e-34 158.0
22 TraesCS2A01G481600 chr3B 79.602 603 102 16 1109 1696 204848234 204847638 2.070000e-111 412.0
23 TraesCS2A01G481600 chr3B 78.877 374 61 12 1109 1470 469630767 469631134 1.340000e-58 237.0
24 TraesCS2A01G481600 chr3B 83.486 109 12 4 607 709 25931180 25931288 2.370000e-16 97.1
25 TraesCS2A01G481600 chr3B 83.486 109 12 5 607 709 26067065 26067173 2.370000e-16 97.1
26 TraesCS2A01G481600 chr3B 83.486 109 12 5 607 709 26256365 26256473 2.370000e-16 97.1
27 TraesCS2A01G481600 chr3D 79.496 595 101 17 1117 1696 142998114 142997526 1.250000e-108 403.0
28 TraesCS2A01G481600 chr3D 78.155 618 110 19 1109 1710 360691537 360692145 1.270000e-98 370.0
29 TraesCS2A01G481600 chr3A 78.522 582 98 14 1130 1696 162752076 162751507 9.850000e-95 357.0
30 TraesCS2A01G481600 chrUn 98.000 150 3 0 2742 2891 95083582 95083433 7.950000e-66 261.0
31 TraesCS2A01G481600 chrUn 83.486 109 12 5 607 709 437043130 437043022 2.370000e-16 97.1
32 TraesCS2A01G481600 chr6D 98.000 150 3 0 2742 2891 61038627 61038776 7.950000e-66 261.0
33 TraesCS2A01G481600 chr6D 98.000 150 3 0 2742 2891 101348987 101348838 7.950000e-66 261.0
34 TraesCS2A01G481600 chr6D 98.000 150 3 0 2742 2891 118658202 118658053 7.950000e-66 261.0
35 TraesCS2A01G481600 chr6D 98.000 150 3 0 2742 2891 150982258 150982407 7.950000e-66 261.0
36 TraesCS2A01G481600 chr6D 98.000 150 3 0 2742 2891 265255253 265255402 7.950000e-66 261.0
37 TraesCS2A01G481600 chr6D 98.000 150 3 0 2742 2891 318623443 318623592 7.950000e-66 261.0
38 TraesCS2A01G481600 chr4D 98.000 150 3 0 2742 2891 132360776 132360627 7.950000e-66 261.0
39 TraesCS2A01G481600 chr4D 98.000 150 3 0 2742 2891 429188236 429188385 7.950000e-66 261.0
40 TraesCS2A01G481600 chr4D 84.615 104 10 4 607 704 72393125 72393022 6.590000e-17 99.0
41 TraesCS2A01G481600 chr4D 82.143 112 19 1 608 719 488740954 488741064 8.530000e-16 95.3
42 TraesCS2A01G481600 chr6A 83.036 112 11 7 607 711 491022485 491022595 8.530000e-16 95.3
43 TraesCS2A01G481600 chr5B 92.308 52 2 2 2181 2232 149253635 149253684 4.000000e-09 73.1


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 TraesCS2A01G481600 chr2A 718816311 718819201 2890 True 5339.0 5339 100.0000 1 2891 1 chr2A.!!$R2 2890
1 TraesCS2A01G481600 chr2B 704409752 704412665 2913 True 1827.5 2905 90.0435 1 2741 2 chr2B.!!$R4 2740
2 TraesCS2A01G481600 chr2D 584546772 584547556 784 True 1037.0 1037 90.4400 1319 2112 1 chr2D.!!$R1 793
3 TraesCS2A01G481600 chr2D 584606740 584607295 555 True 575.0 575 86.2010 1 529 1 chr2D.!!$R3 528
4 TraesCS2A01G481600 chr3B 204847638 204848234 596 True 412.0 412 79.6020 1109 1696 1 chr3B.!!$R1 587
5 TraesCS2A01G481600 chr3D 142997526 142998114 588 True 403.0 403 79.4960 1117 1696 1 chr3D.!!$R1 579
6 TraesCS2A01G481600 chr3D 360691537 360692145 608 False 370.0 370 78.1550 1109 1710 1 chr3D.!!$F1 601
7 TraesCS2A01G481600 chr3A 162751507 162752076 569 True 357.0 357 78.5220 1130 1696 1 chr3A.!!$R1 566

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
492 520 0.179124 CCTAGCTCACCTCGCTTCAC 60.179 60.0 0.0 0.0 38.86 3.18 F
493 521 0.528017 CTAGCTCACCTCGCTTCACA 59.472 55.0 0.0 0.0 38.86 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 2113 0.108615 CCCACGTGAAGTAGGAGCAG 60.109 60.0 19.3 0.0 33.11 4.24 R
2302 2553 0.182775 ACCGAGTCCTTTTTGCTGGT 59.817 50.0 0.0 0.0 0.00 4.00 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
33 34 2.342279 CCGGAAACTGCCTCGTCA 59.658 61.111 0.00 0.00 0.00 4.35
34 35 1.079127 CCGGAAACTGCCTCGTCAT 60.079 57.895 0.00 0.00 0.00 3.06
48 49 1.202302 TCGTCATAGCTGCCTTCTTCG 60.202 52.381 0.00 0.00 0.00 3.79
53 54 0.973632 TAGCTGCCTTCTTCGTCCAA 59.026 50.000 0.00 0.00 0.00 3.53
78 79 1.123077 CACGGATGATCTCCAAGGGA 58.877 55.000 10.58 0.00 45.24 4.20
210 224 1.163554 CAAGCTTTCCTGCCTGACTC 58.836 55.000 0.00 0.00 0.00 3.36
224 242 2.932614 CCTGACTCTACCAAGCAAATCG 59.067 50.000 0.00 0.00 0.00 3.34
228 246 3.326747 ACTCTACCAAGCAAATCGTGAC 58.673 45.455 0.00 0.00 0.00 3.67
242 262 3.663464 TCGTGACGGATAGACTAAACG 57.337 47.619 4.70 7.41 0.00 3.60
274 302 4.240888 CTGCATCGAACTCTGAAGAGAAA 58.759 43.478 14.20 0.00 44.74 2.52
275 303 4.631131 TGCATCGAACTCTGAAGAGAAAA 58.369 39.130 14.20 0.00 44.74 2.29
276 304 5.056480 TGCATCGAACTCTGAAGAGAAAAA 58.944 37.500 14.20 0.00 44.74 1.94
381 409 1.153667 CCTTCTCCAGCAGCGTCTC 60.154 63.158 0.00 0.00 0.00 3.36
442 470 2.184322 GCCGTCTTCCGCATCTCA 59.816 61.111 0.00 0.00 34.38 3.27
464 492 4.457496 CCGACATCGCTGGGCAGT 62.457 66.667 0.00 0.00 38.18 4.40
492 520 0.179124 CCTAGCTCACCTCGCTTCAC 60.179 60.000 0.00 0.00 38.86 3.18
493 521 0.528017 CTAGCTCACCTCGCTTCACA 59.472 55.000 0.00 0.00 38.86 3.58
536 569 1.960689 GTATGGTTGGTTGTTGGCAGT 59.039 47.619 0.00 0.00 0.00 4.40
549 582 2.114638 GGCAGTTTGGCACACTGAA 58.885 52.632 31.93 0.83 43.90 3.02
574 607 4.038042 GTGATAGGTGCTGCATAGTACTCA 59.962 45.833 5.27 2.25 39.23 3.41
575 608 2.969628 AGGTGCTGCATAGTACTCAC 57.030 50.000 5.27 0.00 39.23 3.51
578 611 2.932614 GGTGCTGCATAGTACTCACTTG 59.067 50.000 5.27 0.00 39.23 3.16
582 615 3.619038 GCTGCATAGTACTCACTTGGTTC 59.381 47.826 0.00 0.00 36.14 3.62
625 672 9.811995 ATGAACTACTACATACGAAGCAAAATA 57.188 29.630 0.00 0.00 0.00 1.40
686 900 8.609478 TTTGTTCGTGTTGAAATCTCTAAAAC 57.391 30.769 0.00 0.00 38.60 2.43
692 906 7.908082 TCGTGTTGAAATCTCTAAAACAACTTG 59.092 33.333 0.00 0.00 38.51 3.16
708 922 5.243207 ACAACTTGTATTTAGGAACGGAGG 58.757 41.667 0.00 0.00 0.00 4.30
709 923 5.012354 ACAACTTGTATTTAGGAACGGAGGA 59.988 40.000 0.00 0.00 0.00 3.71
711 925 6.117975 ACTTGTATTTAGGAACGGAGGAAA 57.882 37.500 0.00 0.00 0.00 3.13
722 936 6.408869 AGGAACGGAGGAAATAATAAACGAA 58.591 36.000 0.00 0.00 0.00 3.85
723 937 6.314648 AGGAACGGAGGAAATAATAAACGAAC 59.685 38.462 0.00 0.00 0.00 3.95
725 939 5.410067 ACGGAGGAAATAATAAACGAACGA 58.590 37.500 0.14 0.00 0.00 3.85
726 940 6.044682 ACGGAGGAAATAATAAACGAACGAT 58.955 36.000 0.14 0.00 0.00 3.73
727 941 7.202526 ACGGAGGAAATAATAAACGAACGATA 58.797 34.615 0.14 0.00 0.00 2.92
728 942 7.706179 ACGGAGGAAATAATAAACGAACGATAA 59.294 33.333 0.14 0.00 0.00 1.75
762 993 3.131046 TGCAGATCTGAGCTATCGTTCAA 59.869 43.478 27.04 0.00 29.66 2.69
818 1051 6.349300 TCTCTATGATAAAGGTGGTTTGCTC 58.651 40.000 0.00 0.00 0.00 4.26
828 1061 2.299013 GGTGGTTTGCTCCCTAAAAAGG 59.701 50.000 0.00 0.00 0.00 3.11
838 1071 3.227614 TCCCTAAAAAGGTGGTTTGCTC 58.772 45.455 0.00 0.00 0.00 4.26
842 1075 4.099419 CCTAAAAAGGTGGTTTGCTCAGTT 59.901 41.667 0.00 0.00 0.00 3.16
850 1083 2.159448 TGGTTTGCTCAGTTGTTGTTCG 60.159 45.455 0.00 0.00 0.00 3.95
852 1085 1.745232 TTGCTCAGTTGTTGTTCGGT 58.255 45.000 0.00 0.00 0.00 4.69
914 1151 5.234466 AGCCCATTACTTATCTTGCCTAG 57.766 43.478 0.00 0.00 0.00 3.02
915 1152 3.753797 GCCCATTACTTATCTTGCCTAGC 59.246 47.826 0.00 0.00 0.00 3.42
923 1160 5.731591 ACTTATCTTGCCTAGCGTAAACTT 58.268 37.500 0.00 0.00 0.00 2.66
924 1161 5.581085 ACTTATCTTGCCTAGCGTAAACTTG 59.419 40.000 0.00 0.00 0.00 3.16
932 1169 1.495951 GCGTAAACTTGACCCGCTG 59.504 57.895 0.00 0.00 41.06 5.18
933 1170 1.495951 CGTAAACTTGACCCGCTGC 59.504 57.895 0.00 0.00 0.00 5.25
934 1171 0.949105 CGTAAACTTGACCCGCTGCT 60.949 55.000 0.00 0.00 0.00 4.24
935 1172 1.235724 GTAAACTTGACCCGCTGCTT 58.764 50.000 0.00 0.00 0.00 3.91
936 1173 1.197036 GTAAACTTGACCCGCTGCTTC 59.803 52.381 0.00 0.00 0.00 3.86
940 1177 4.742201 TGACCCGCTGCTTCGCTC 62.742 66.667 0.00 0.00 0.00 5.03
976 1213 2.069273 CATCCTCTTGACGTTGACCAC 58.931 52.381 0.00 0.00 0.00 4.16
1081 1318 1.167155 GGGCAGCAGCATGATCAGAG 61.167 60.000 2.65 0.00 44.61 3.35
1125 1362 1.454653 GCGTTTGACTACTTCGTGGTC 59.545 52.381 3.88 3.88 42.91 4.02
1697 1947 3.250323 CATCACGACCTCGCTGCG 61.250 66.667 17.25 17.25 44.43 5.18
1819 2069 4.247380 GGCCGATGCAGGGGAGAG 62.247 72.222 9.87 0.00 40.13 3.20
1862 2112 4.408821 GCCGTCCATGGGAGCACA 62.409 66.667 13.02 0.00 29.39 4.57
1863 2113 2.436646 CCGTCCATGGGAGCACAC 60.437 66.667 13.02 0.00 29.39 3.82
1897 2147 3.002656 CACGTGGGCAGATTAATTGCTAG 59.997 47.826 7.95 10.88 41.27 3.42
1908 2158 6.208007 CAGATTAATTGCTAGCCAATCCATGA 59.792 38.462 13.29 0.00 43.22 3.07
1931 2181 8.073467 TGAGTTTGGATTTGGGGAATTAATAC 57.927 34.615 0.00 0.00 0.00 1.89
1932 2182 7.125053 TGAGTTTGGATTTGGGGAATTAATACC 59.875 37.037 0.00 0.00 0.00 2.73
1939 2189 9.831682 GGATTTGGGGAATTAATACCCTATAAA 57.168 33.333 22.14 16.46 44.97 1.40
1969 2219 2.196749 CATGTGCGAGTATCACTCCAC 58.803 52.381 15.29 15.29 42.12 4.02
2036 2286 6.131544 TGAGCTTGGTTTTCTTAACAACTC 57.868 37.500 0.00 0.00 0.00 3.01
2064 2314 6.350103 TCCTATTGCGTGGTGTATTTGATTA 58.650 36.000 0.00 0.00 0.00 1.75
2136 2387 7.652909 TGCTTGAAATGATTCATTTTCGAAACT 59.347 29.630 22.14 1.81 44.70 2.66
2185 2436 3.821421 ACAATCTAGTTTAGGGCCGAG 57.179 47.619 0.00 0.00 0.00 4.63
2188 2439 4.019591 ACAATCTAGTTTAGGGCCGAGTTT 60.020 41.667 0.00 0.00 0.00 2.66
2201 2452 3.367910 GGCCGAGTTTTGATATTTTGCCA 60.368 43.478 0.00 0.00 35.30 4.92
2211 2462 9.597999 GTTTTGATATTTTGCCAAGTTCATTTC 57.402 29.630 0.00 0.00 0.00 2.17
2308 2559 0.240145 CGTCTCGTCAAGTACCAGCA 59.760 55.000 0.00 0.00 0.00 4.41
2339 2590 3.318839 TCGGTGAAAGTAAGAAACTCGGA 59.681 43.478 0.00 0.00 37.50 4.55
2343 2594 6.218746 GGTGAAAGTAAGAAACTCGGAAGTA 58.781 40.000 0.00 0.00 37.50 2.24
2377 2628 3.592059 CGAGTTCCTCCGGATAAAAACA 58.408 45.455 3.57 0.00 0.00 2.83
2406 2659 3.432335 CAGGTGGGCCCCATGGAT 61.432 66.667 22.27 0.00 35.28 3.41
2412 2665 2.203451 GGCCCCATGGATGAGCAG 60.203 66.667 15.22 0.00 0.00 4.24
2417 2670 1.890979 CCATGGATGAGCAGGCGAC 60.891 63.158 5.56 0.00 0.00 5.19
2418 2671 1.153309 CATGGATGAGCAGGCGACA 60.153 57.895 0.00 0.00 0.00 4.35
2476 2729 3.303132 GCTAATGGAAACTCGGCAATACG 60.303 47.826 0.00 0.00 0.00 3.06
2491 2744 5.559417 CGGCAATACGTGTACTTGTCTTTTT 60.559 40.000 0.00 0.00 0.00 1.94
2512 2765 1.080366 CCGAATTCGACGGGTCACA 60.080 57.895 28.76 0.00 45.65 3.58
2546 2799 4.955925 ACATGTGAAAAACAACTCGACA 57.044 36.364 0.00 0.00 43.61 4.35
2551 2804 6.862944 TGTGAAAAACAACTCGACAATTTC 57.137 33.333 0.00 0.00 35.24 2.17
2632 2886 4.084013 GCGGGGATAAACTCGACATAAATG 60.084 45.833 0.00 0.00 0.00 2.32
2636 2890 5.820947 GGGATAAACTCGACATAAATGTGGT 59.179 40.000 0.00 0.00 41.95 4.16
2642 2896 2.166870 TCGACATAAATGTGGTAGGCGT 59.833 45.455 0.00 0.00 41.95 5.68
2670 2924 1.818060 TGGCACATGTCATTAACCAGC 59.182 47.619 0.00 0.00 0.00 4.85
2671 2925 2.094675 GGCACATGTCATTAACCAGCT 58.905 47.619 0.00 0.00 0.00 4.24
2672 2926 2.159338 GGCACATGTCATTAACCAGCTG 60.159 50.000 6.78 6.78 0.00 4.24
2673 2927 2.749076 GCACATGTCATTAACCAGCTGA 59.251 45.455 17.39 0.00 0.00 4.26
2674 2928 3.379372 GCACATGTCATTAACCAGCTGAT 59.621 43.478 17.39 6.23 0.00 2.90
2675 2929 4.732647 GCACATGTCATTAACCAGCTGATG 60.733 45.833 17.39 11.10 0.00 3.07
2716 2970 2.952310 GTTCTGAAACTCAGCAAAGGGT 59.048 45.455 0.00 0.00 43.95 4.34
2735 2989 5.887754 AGGGTTAAATCTTGGTCTTAAGCA 58.112 37.500 0.00 0.00 35.65 3.91
2741 2995 4.870021 ATCTTGGTCTTAAGCAGGGAAT 57.130 40.909 0.00 0.00 33.72 3.01
2742 2996 4.222124 TCTTGGTCTTAAGCAGGGAATC 57.778 45.455 0.00 0.00 33.72 2.52
2743 2997 3.587061 TCTTGGTCTTAAGCAGGGAATCA 59.413 43.478 0.00 0.00 33.72 2.57
2744 2998 4.042809 TCTTGGTCTTAAGCAGGGAATCAA 59.957 41.667 0.00 0.00 33.72 2.57
2745 2999 4.380843 TGGTCTTAAGCAGGGAATCAAA 57.619 40.909 0.00 0.00 0.00 2.69
2746 3000 4.735369 TGGTCTTAAGCAGGGAATCAAAA 58.265 39.130 0.00 0.00 0.00 2.44
2747 3001 4.522789 TGGTCTTAAGCAGGGAATCAAAAC 59.477 41.667 0.00 0.00 0.00 2.43
2748 3002 4.082190 GGTCTTAAGCAGGGAATCAAAACC 60.082 45.833 0.00 0.00 0.00 3.27
2749 3003 3.756434 TCTTAAGCAGGGAATCAAAACCG 59.244 43.478 0.00 0.00 0.00 4.44
2750 3004 1.256812 AAGCAGGGAATCAAAACCGG 58.743 50.000 0.00 0.00 0.00 5.28
2751 3005 1.215382 GCAGGGAATCAAAACCGGC 59.785 57.895 0.00 0.00 38.23 6.13
2752 3006 1.506262 CAGGGAATCAAAACCGGCG 59.494 57.895 0.00 0.00 0.00 6.46
2753 3007 1.677633 AGGGAATCAAAACCGGCGG 60.678 57.895 27.06 27.06 0.00 6.13
2754 3008 1.676303 GGGAATCAAAACCGGCGGA 60.676 57.895 35.78 10.47 0.00 5.54
2755 3009 1.035385 GGGAATCAAAACCGGCGGAT 61.035 55.000 35.78 20.37 0.00 4.18
2756 3010 0.380733 GGAATCAAAACCGGCGGATC 59.619 55.000 35.78 16.78 0.00 3.36
2757 3011 1.379527 GAATCAAAACCGGCGGATCT 58.620 50.000 35.78 13.84 0.00 2.75
2758 3012 1.330829 GAATCAAAACCGGCGGATCTC 59.669 52.381 35.78 14.22 0.00 2.75
2759 3013 0.810031 ATCAAAACCGGCGGATCTCG 60.810 55.000 35.78 16.34 42.76 4.04
2764 3018 3.671411 CCGGCGGATCTCGGGTAG 61.671 72.222 24.41 0.00 42.32 3.18
2765 3019 3.671411 CGGCGGATCTCGGGTAGG 61.671 72.222 0.00 0.00 39.69 3.18
2766 3020 3.303928 GGCGGATCTCGGGTAGGG 61.304 72.222 5.87 0.00 39.69 3.53
2767 3021 3.303928 GCGGATCTCGGGTAGGGG 61.304 72.222 5.87 0.00 39.69 4.79
2768 3022 2.600769 CGGATCTCGGGTAGGGGG 60.601 72.222 0.00 0.00 34.75 5.40
2769 3023 2.613421 GGATCTCGGGTAGGGGGT 59.387 66.667 0.00 0.00 0.00 4.95
2770 3024 1.533513 GGATCTCGGGTAGGGGGTC 60.534 68.421 0.00 0.00 0.00 4.46
2771 3025 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
2772 3026 3.097429 ATCTCGGGTAGGGGGTCCC 62.097 68.421 0.00 0.00 45.90 4.46
2781 3035 4.717313 GGGGGTCCCGAACTGTGC 62.717 72.222 0.48 0.00 36.85 4.57
2783 3037 4.309950 GGGTCCCGAACTGTGCGT 62.310 66.667 7.51 0.00 0.00 5.24
2784 3038 2.737376 GGTCCCGAACTGTGCGTC 60.737 66.667 7.51 0.00 0.00 5.19
2785 3039 2.338984 GTCCCGAACTGTGCGTCT 59.661 61.111 7.51 0.00 0.00 4.18
2786 3040 1.582968 GTCCCGAACTGTGCGTCTA 59.417 57.895 7.51 0.00 0.00 2.59
2787 3041 0.038892 GTCCCGAACTGTGCGTCTAA 60.039 55.000 7.51 0.00 0.00 2.10
2788 3042 0.242825 TCCCGAACTGTGCGTCTAAG 59.757 55.000 7.51 0.00 0.00 2.18
2789 3043 0.736325 CCCGAACTGTGCGTCTAAGG 60.736 60.000 7.51 0.00 0.00 2.69
2790 3044 1.352156 CCGAACTGTGCGTCTAAGGC 61.352 60.000 7.51 0.00 0.00 4.35
2791 3045 1.674611 CGAACTGTGCGTCTAAGGCG 61.675 60.000 0.00 0.00 0.00 5.52
2792 3046 1.352156 GAACTGTGCGTCTAAGGCGG 61.352 60.000 0.00 0.00 0.00 6.13
2793 3047 1.812686 AACTGTGCGTCTAAGGCGGA 61.813 55.000 0.00 0.00 0.00 5.54
2794 3048 1.141881 CTGTGCGTCTAAGGCGGAT 59.858 57.895 0.00 0.00 31.50 4.18
2795 3049 1.148157 CTGTGCGTCTAAGGCGGATG 61.148 60.000 0.00 0.00 31.50 3.51
2796 3050 1.883084 GTGCGTCTAAGGCGGATGG 60.883 63.158 0.00 0.00 31.50 3.51
2797 3051 2.355986 TGCGTCTAAGGCGGATGGT 61.356 57.895 0.00 0.00 0.00 3.55
2798 3052 1.038681 TGCGTCTAAGGCGGATGGTA 61.039 55.000 0.00 0.00 0.00 3.25
2799 3053 0.103572 GCGTCTAAGGCGGATGGTAA 59.896 55.000 0.00 0.00 0.00 2.85
2800 3054 1.849097 CGTCTAAGGCGGATGGTAAC 58.151 55.000 0.00 0.00 0.00 2.50
2811 3065 3.006728 TGGTAACAGGAGGCGGGG 61.007 66.667 0.00 0.00 46.17 5.73
2812 3066 3.793888 GGTAACAGGAGGCGGGGG 61.794 72.222 0.00 0.00 0.00 5.40
2813 3067 2.686106 GTAACAGGAGGCGGGGGA 60.686 66.667 0.00 0.00 0.00 4.81
2814 3068 2.686106 TAACAGGAGGCGGGGGAC 60.686 66.667 0.00 0.00 0.00 4.46
2815 3069 3.549433 TAACAGGAGGCGGGGGACA 62.549 63.158 0.00 0.00 0.00 4.02
2818 3072 4.974438 AGGAGGCGGGGGACACAA 62.974 66.667 0.00 0.00 0.00 3.33
2819 3073 3.728373 GGAGGCGGGGGACACAAT 61.728 66.667 0.00 0.00 0.00 2.71
2820 3074 2.438434 GAGGCGGGGGACACAATG 60.438 66.667 0.00 0.00 0.00 2.82
2821 3075 3.256960 AGGCGGGGGACACAATGT 61.257 61.111 0.00 0.00 0.00 2.71
2822 3076 2.282887 GGCGGGGGACACAATGTT 60.283 61.111 0.00 0.00 0.00 2.71
2823 3077 1.906333 GGCGGGGGACACAATGTTT 60.906 57.895 0.00 0.00 0.00 2.83
2824 3078 0.609681 GGCGGGGGACACAATGTTTA 60.610 55.000 0.00 0.00 0.00 2.01
2825 3079 0.524414 GCGGGGGACACAATGTTTAC 59.476 55.000 0.00 0.00 0.00 2.01
2826 3080 1.170442 CGGGGGACACAATGTTTACC 58.830 55.000 0.00 0.00 0.00 2.85
2827 3081 1.552578 GGGGGACACAATGTTTACCC 58.447 55.000 11.42 11.42 37.95 3.69
2828 3082 1.203075 GGGGGACACAATGTTTACCCA 60.203 52.381 20.61 0.00 39.39 4.51
2829 3083 2.599677 GGGGACACAATGTTTACCCAA 58.400 47.619 14.80 0.00 38.30 4.12
2830 3084 2.560981 GGGGACACAATGTTTACCCAAG 59.439 50.000 14.80 0.00 38.30 3.61
2831 3085 3.227614 GGGACACAATGTTTACCCAAGT 58.772 45.455 12.30 0.00 37.50 3.16
2832 3086 3.639561 GGGACACAATGTTTACCCAAGTT 59.360 43.478 12.30 0.00 37.50 2.66
2833 3087 4.261867 GGGACACAATGTTTACCCAAGTTC 60.262 45.833 12.30 0.00 37.50 3.01
2834 3088 4.533222 GACACAATGTTTACCCAAGTTCG 58.467 43.478 0.00 0.00 0.00 3.95
2835 3089 3.316868 ACACAATGTTTACCCAAGTTCGG 59.683 43.478 0.00 0.00 0.00 4.30
2842 3096 3.330720 CCCAAGTTCGGGCCCTCT 61.331 66.667 22.43 12.68 40.07 3.69
2843 3097 2.269241 CCAAGTTCGGGCCCTCTC 59.731 66.667 22.43 9.57 0.00 3.20
2844 3098 2.125512 CAAGTTCGGGCCCTCTCG 60.126 66.667 22.43 6.49 0.00 4.04
2845 3099 2.283676 AAGTTCGGGCCCTCTCGA 60.284 61.111 22.43 9.26 0.00 4.04
2846 3100 1.686110 AAGTTCGGGCCCTCTCGAT 60.686 57.895 22.43 0.00 35.25 3.59
2847 3101 1.961180 AAGTTCGGGCCCTCTCGATG 61.961 60.000 22.43 1.43 35.25 3.84
2848 3102 3.154473 TTCGGGCCCTCTCGATGG 61.154 66.667 22.43 0.54 35.25 3.51
2849 3103 3.672338 TTCGGGCCCTCTCGATGGA 62.672 63.158 22.43 3.53 35.25 3.41
2850 3104 3.610669 CGGGCCCTCTCGATGGAG 61.611 72.222 22.43 0.00 41.89 3.86
2859 3113 2.826725 CCTCTCGATGGAGGTAATACCC 59.173 54.545 11.66 0.00 45.65 3.69
2860 3114 3.500654 CCTCTCGATGGAGGTAATACCCT 60.501 52.174 11.66 0.00 45.65 4.34
2861 3115 4.263816 CCTCTCGATGGAGGTAATACCCTA 60.264 50.000 11.66 0.00 45.65 3.53
2862 3116 4.660168 TCTCGATGGAGGTAATACCCTAC 58.340 47.826 5.71 0.00 39.75 3.18
2863 3117 4.353191 TCTCGATGGAGGTAATACCCTACT 59.647 45.833 5.71 0.00 39.75 2.57
2864 3118 5.070823 TCGATGGAGGTAATACCCTACTT 57.929 43.478 5.71 0.00 39.75 2.24
2865 3119 6.044754 TCTCGATGGAGGTAATACCCTACTTA 59.955 42.308 5.71 0.00 39.75 2.24
2866 3120 6.006449 TCGATGGAGGTAATACCCTACTTAC 58.994 44.000 5.71 0.00 39.75 2.34
2867 3121 6.008960 CGATGGAGGTAATACCCTACTTACT 58.991 44.000 5.71 0.00 39.75 2.24
2868 3122 7.017551 TCGATGGAGGTAATACCCTACTTACTA 59.982 40.741 5.71 0.00 39.75 1.82
2869 3123 7.120432 CGATGGAGGTAATACCCTACTTACTAC 59.880 44.444 5.71 0.00 39.75 2.73
2870 3124 7.471610 TGGAGGTAATACCCTACTTACTACT 57.528 40.000 5.71 0.00 39.75 2.57
2871 3125 7.887032 TGGAGGTAATACCCTACTTACTACTT 58.113 38.462 5.71 0.00 39.75 2.24
2872 3126 7.781693 TGGAGGTAATACCCTACTTACTACTTG 59.218 40.741 5.71 0.00 39.75 3.16
2873 3127 8.001292 GGAGGTAATACCCTACTTACTACTTGA 58.999 40.741 5.71 0.00 39.75 3.02
2874 3128 9.585369 GAGGTAATACCCTACTTACTACTTGAT 57.415 37.037 5.71 0.00 39.75 2.57
2875 3129 9.948747 AGGTAATACCCTACTTACTACTTGATT 57.051 33.333 5.71 0.00 39.75 2.57
2876 3130 9.978044 GGTAATACCCTACTTACTACTTGATTG 57.022 37.037 0.00 0.00 30.04 2.67
2880 3134 9.884814 ATACCCTACTTACTACTTGATTGATCT 57.115 33.333 0.00 0.00 0.00 2.75
2881 3135 8.611051 ACCCTACTTACTACTTGATTGATCTT 57.389 34.615 0.00 0.00 0.00 2.40
2882 3136 8.478877 ACCCTACTTACTACTTGATTGATCTTG 58.521 37.037 0.00 0.00 0.00 3.02
2883 3137 8.696374 CCCTACTTACTACTTGATTGATCTTGA 58.304 37.037 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.434359 GACGAGGCAGTTTCCGGG 60.434 66.667 0.00 0.00 0.00 5.73
27 28 2.468831 GAAGAAGGCAGCTATGACGAG 58.531 52.381 0.00 0.00 40.55 4.18
33 34 1.195115 TGGACGAAGAAGGCAGCTAT 58.805 50.000 0.00 0.00 0.00 2.97
34 35 0.973632 TTGGACGAAGAAGGCAGCTA 59.026 50.000 0.00 0.00 0.00 3.32
78 79 2.555547 GGACTTGCAAGCGCTTGGT 61.556 57.895 41.83 33.05 40.74 3.67
145 146 8.939201 TTAGCTTTGATCTCAGTTCTAAGATG 57.061 34.615 10.16 0.00 29.79 2.90
172 186 4.630111 CTTGCCAAGCCTTTGAAAACATA 58.370 39.130 0.00 0.00 36.36 2.29
210 224 1.393539 CCGTCACGATTTGCTTGGTAG 59.606 52.381 0.00 0.00 0.00 3.18
224 242 3.624861 TCCTCGTTTAGTCTATCCGTCAC 59.375 47.826 0.00 0.00 0.00 3.67
228 246 5.272397 GTTCTTCCTCGTTTAGTCTATCCG 58.728 45.833 0.00 0.00 0.00 4.18
242 262 2.003301 GTTCGATGCAGGTTCTTCCTC 58.997 52.381 0.00 0.00 46.24 3.71
254 274 5.597813 TTTTTCTCTTCAGAGTTCGATGC 57.402 39.130 3.73 0.00 42.60 3.91
463 491 1.346068 GGTGAGCTAGGGGATCATCAC 59.654 57.143 0.00 0.00 42.56 3.06
464 492 1.221523 AGGTGAGCTAGGGGATCATCA 59.778 52.381 0.00 0.00 43.28 3.07
492 520 1.219522 GGAACGACCTCACAACCGTG 61.220 60.000 0.00 0.00 45.08 4.94
493 521 1.068585 GGAACGACCTCACAACCGT 59.931 57.895 0.00 0.00 36.77 4.83
536 569 3.820467 CCTATCACTTTCAGTGTGCCAAA 59.180 43.478 3.87 0.00 46.03 3.28
544 577 2.038952 TGCAGCACCTATCACTTTCAGT 59.961 45.455 0.00 0.00 0.00 3.41
545 578 2.703416 TGCAGCACCTATCACTTTCAG 58.297 47.619 0.00 0.00 0.00 3.02
549 582 4.651503 AGTACTATGCAGCACCTATCACTT 59.348 41.667 0.00 0.00 0.00 3.16
555 588 3.632333 AGTGAGTACTATGCAGCACCTA 58.368 45.455 0.00 0.00 34.74 3.08
557 590 2.932614 CAAGTGAGTACTATGCAGCACC 59.067 50.000 0.00 0.00 35.69 5.01
595 628 8.797266 TGCTTCGTATGTAGTAGTTCATATTG 57.203 34.615 0.81 0.00 0.00 1.90
605 652 9.642327 TTCACTTATTTTGCTTCGTATGTAGTA 57.358 29.630 0.00 0.00 0.00 1.82
606 653 8.542497 TTCACTTATTTTGCTTCGTATGTAGT 57.458 30.769 0.00 0.00 0.00 2.73
607 654 9.638300 GATTCACTTATTTTGCTTCGTATGTAG 57.362 33.333 0.00 0.00 0.00 2.74
608 655 9.378551 AGATTCACTTATTTTGCTTCGTATGTA 57.621 29.630 0.00 0.00 0.00 2.29
659 706 9.796120 TTTTAGAGATTTCAACACGAACAAAAT 57.204 25.926 0.00 0.00 31.73 1.82
660 707 9.068008 GTTTTAGAGATTTCAACACGAACAAAA 57.932 29.630 0.00 0.00 31.73 2.44
661 708 8.237949 TGTTTTAGAGATTTCAACACGAACAAA 58.762 29.630 0.00 0.00 31.73 2.83
662 709 7.753659 TGTTTTAGAGATTTCAACACGAACAA 58.246 30.769 0.00 0.00 31.73 2.83
664 711 7.908601 AGTTGTTTTAGAGATTTCAACACGAAC 59.091 33.333 0.00 0.00 37.97 3.95
665 712 7.981142 AGTTGTTTTAGAGATTTCAACACGAA 58.019 30.769 0.00 0.00 37.97 3.85
666 713 7.548196 AGTTGTTTTAGAGATTTCAACACGA 57.452 32.000 0.00 0.00 37.97 4.35
667 714 7.696453 ACAAGTTGTTTTAGAGATTTCAACACG 59.304 33.333 1.64 0.00 37.97 4.49
668 715 8.911247 ACAAGTTGTTTTAGAGATTTCAACAC 57.089 30.769 1.64 0.00 37.97 3.32
680 894 8.776470 TCCGTTCCTAAATACAAGTTGTTTTAG 58.224 33.333 25.03 25.03 34.52 1.85
686 900 5.484715 TCCTCCGTTCCTAAATACAAGTTG 58.515 41.667 0.00 0.00 0.00 3.16
703 917 5.954434 TCGTTCGTTTATTATTTCCTCCG 57.046 39.130 0.00 0.00 0.00 4.63
762 993 1.603802 CACAACCGAGACAAGTTGCAT 59.396 47.619 1.81 0.00 45.79 3.96
818 1051 2.962421 TGAGCAAACCACCTTTTTAGGG 59.038 45.455 0.00 0.00 0.00 3.53
828 1061 2.939460 ACAACAACTGAGCAAACCAC 57.061 45.000 0.00 0.00 0.00 4.16
838 1071 8.789881 TTGAATAATTAACCGAACAACAACTG 57.210 30.769 0.00 0.00 0.00 3.16
885 1118 8.856103 GGCAAGATAAGTAATGGGCTAATAAAA 58.144 33.333 0.00 0.00 0.00 1.52
907 1144 2.419667 GGTCAAGTTTACGCTAGGCAA 58.580 47.619 0.00 0.00 0.00 4.52
915 1152 0.949105 AGCAGCGGGTCAAGTTTACG 60.949 55.000 0.00 0.00 0.00 3.18
933 1170 0.452184 TACTCAGGAAGCGAGCGAAG 59.548 55.000 0.00 0.00 33.58 3.79
934 1171 0.452184 CTACTCAGGAAGCGAGCGAA 59.548 55.000 0.00 0.00 33.58 4.70
935 1172 0.677098 ACTACTCAGGAAGCGAGCGA 60.677 55.000 0.00 0.00 33.58 4.93
936 1173 1.015109 TACTACTCAGGAAGCGAGCG 58.985 55.000 0.00 0.00 33.58 5.03
940 1177 2.952978 AGGATGTACTACTCAGGAAGCG 59.047 50.000 0.00 0.00 0.00 4.68
1100 1337 0.438830 GAAGTAGTCAAACGCCTGCG 59.561 55.000 10.40 10.40 46.03 5.18
1101 1338 0.438830 CGAAGTAGTCAAACGCCTGC 59.561 55.000 0.00 0.00 0.00 4.85
1125 1362 1.352404 CGTCGCCTCGAAGTCTAGG 59.648 63.158 0.00 0.00 37.72 3.02
1671 1921 2.459442 GGTCGTGATGCTGAGCTGC 61.459 63.158 5.83 0.00 0.00 5.25
1704 1954 2.230750 AGTTACAGTTACCTGAGGCGAC 59.769 50.000 0.00 0.00 41.50 5.19
1819 2069 0.390209 TTACCGCAACCGTAGAAGCC 60.390 55.000 0.00 0.00 0.00 4.35
1861 2111 1.670087 CCACGTGAAGTAGGAGCAGTG 60.670 57.143 19.30 0.00 0.00 3.66
1862 2112 0.603569 CCACGTGAAGTAGGAGCAGT 59.396 55.000 19.30 0.00 0.00 4.40
1863 2113 0.108615 CCCACGTGAAGTAGGAGCAG 60.109 60.000 19.30 0.00 33.11 4.24
1908 2158 6.385759 GGGTATTAATTCCCCAAATCCAAACT 59.614 38.462 17.34 0.00 38.37 2.66
1931 2181 6.346279 CGCACATGTACGTGTAATTTATAGGG 60.346 42.308 20.05 9.87 39.19 3.53
1932 2182 6.418523 TCGCACATGTACGTGTAATTTATAGG 59.581 38.462 20.05 6.26 39.19 2.57
1939 2189 3.226346 ACTCGCACATGTACGTGTAAT 57.774 42.857 21.18 1.10 39.19 1.89
1940 2190 2.710220 ACTCGCACATGTACGTGTAA 57.290 45.000 21.18 8.37 39.19 2.41
1941 2191 3.374678 TGATACTCGCACATGTACGTGTA 59.625 43.478 26.58 26.58 40.94 2.90
1943 2193 2.530297 GTGATACTCGCACATGTACGTG 59.470 50.000 17.60 17.14 40.00 4.49
1944 2194 2.422479 AGTGATACTCGCACATGTACGT 59.578 45.455 17.60 2.73 38.70 3.57
1945 2195 3.036633 GAGTGATACTCGCACATGTACG 58.963 50.000 12.37 12.37 35.28 3.67
1946 2196 3.181490 TGGAGTGATACTCGCACATGTAC 60.181 47.826 0.00 0.00 45.96 2.90
1969 2219 6.038603 TGTGTTGACAAGAGAAATCAAAGAGG 59.961 38.462 0.00 0.00 34.28 3.69
2036 2286 1.651987 ACACCACGCAATAGGATTCG 58.348 50.000 0.00 0.00 0.00 3.34
2136 2387 6.663093 AGTGGAACATGCAATTTTCTACCATA 59.337 34.615 14.31 0.00 43.05 2.74
2177 2428 3.119137 GCAAAATATCAAAACTCGGCCCT 60.119 43.478 0.00 0.00 0.00 5.19
2185 2436 9.597999 GAAATGAACTTGGCAAAATATCAAAAC 57.402 29.630 0.00 0.00 0.00 2.43
2188 2439 9.153721 GATGAAATGAACTTGGCAAAATATCAA 57.846 29.630 0.00 0.00 0.00 2.57
2201 2452 3.274288 GAGCTCCCGATGAAATGAACTT 58.726 45.455 0.87 0.00 0.00 2.66
2211 2462 2.125147 TTTGCCGAGCTCCCGATG 60.125 61.111 8.47 0.00 0.00 3.84
2262 2513 6.248569 AGTTTCCCAAGTTTCTTCTCACTA 57.751 37.500 0.00 0.00 0.00 2.74
2302 2553 0.182775 ACCGAGTCCTTTTTGCTGGT 59.817 50.000 0.00 0.00 0.00 4.00
2308 2559 5.677567 TCTTACTTTCACCGAGTCCTTTTT 58.322 37.500 0.00 0.00 0.00 1.94
2339 2590 2.963782 ACTCGGTGAACTTGAGGTACTT 59.036 45.455 0.00 0.00 41.55 2.24
2343 2594 1.070289 GGAACTCGGTGAACTTGAGGT 59.930 52.381 7.72 2.12 34.03 3.85
2377 2628 1.829533 CCACCTGCCAGTGTTTGCT 60.830 57.895 2.90 0.00 35.93 3.91
2399 2652 1.890979 GTCGCCTGCTCATCCATGG 60.891 63.158 4.97 4.97 0.00 3.66
2406 2659 1.597854 CACCTTTGTCGCCTGCTCA 60.598 57.895 0.00 0.00 0.00 4.26
2412 2665 0.889186 ACCATCACACCTTTGTCGCC 60.889 55.000 0.00 0.00 31.66 5.54
2417 2670 2.276732 AGTCCACCATCACACCTTTG 57.723 50.000 0.00 0.00 0.00 2.77
2418 2671 3.330701 ACATAGTCCACCATCACACCTTT 59.669 43.478 0.00 0.00 0.00 3.11
2491 2744 0.887247 TGACCCGTCGAATTCGGTAA 59.113 50.000 26.47 7.88 45.63 2.85
2611 2865 5.238650 CCACATTTATGTCGAGTTTATCCCC 59.761 44.000 0.00 0.00 39.39 4.81
2642 2896 1.451207 GACATGTGCCATGCGGGTA 60.451 57.895 1.15 0.00 39.65 3.69
2655 2909 4.563337 CCATCAGCTGGTTAATGACATG 57.437 45.455 15.13 6.57 40.49 3.21
2667 2921 3.165606 GGAGACCAACCATCAGCTG 57.834 57.895 7.63 7.63 0.00 4.24
2678 2932 7.364762 GTTTCAGAACTCATTATAGGGAGACCA 60.365 40.741 9.07 0.00 42.32 4.02
2679 2933 6.987404 GTTTCAGAACTCATTATAGGGAGACC 59.013 42.308 9.07 0.00 41.07 3.85
2716 2970 6.134535 TCCCTGCTTAAGACCAAGATTTAA 57.865 37.500 6.67 0.00 0.00 1.52
2735 2989 1.677633 CCGCCGGTTTTGATTCCCT 60.678 57.895 1.90 0.00 0.00 4.20
2741 2995 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.00 0.00 2.69
2742 2996 2.461110 CCGAGATCCGCCGGTTTTG 61.461 63.158 1.63 0.00 40.78 2.44
2743 2997 2.125269 CCGAGATCCGCCGGTTTT 60.125 61.111 1.63 0.00 40.78 2.43
2744 2998 4.157120 CCCGAGATCCGCCGGTTT 62.157 66.667 1.63 0.00 43.93 3.27
2746 3000 4.511246 TACCCGAGATCCGCCGGT 62.511 66.667 1.63 11.60 43.93 5.28
2747 3001 3.671411 CTACCCGAGATCCGCCGG 61.671 72.222 0.00 0.00 44.94 6.13
2748 3002 3.671411 CCTACCCGAGATCCGCCG 61.671 72.222 0.00 0.00 36.84 6.46
2749 3003 3.303928 CCCTACCCGAGATCCGCC 61.304 72.222 0.00 0.00 36.84 6.13
2750 3004 3.303928 CCCCTACCCGAGATCCGC 61.304 72.222 0.00 0.00 36.84 5.54
2751 3005 2.600769 CCCCCTACCCGAGATCCG 60.601 72.222 0.00 0.00 38.18 4.18
2752 3006 1.533513 GACCCCCTACCCGAGATCC 60.534 68.421 0.00 0.00 0.00 3.36
2753 3007 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.00 0.00 2.75
2754 3008 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.00 0.00 2.75
2755 3009 3.759101 GGGACCCCCTACCCGAGA 61.759 72.222 0.00 0.00 41.34 4.04
2759 3013 3.085947 GTTCGGGACCCCCTACCC 61.086 72.222 4.46 0.00 42.67 3.69
2760 3014 2.040114 AGTTCGGGACCCCCTACC 59.960 66.667 4.46 0.00 42.67 3.18
2761 3015 1.611556 ACAGTTCGGGACCCCCTAC 60.612 63.158 4.46 0.29 42.67 3.18
2762 3016 1.611261 CACAGTTCGGGACCCCCTA 60.611 63.158 4.46 0.00 42.67 3.53
2763 3017 2.928396 CACAGTTCGGGACCCCCT 60.928 66.667 4.46 0.00 42.67 4.79
2764 3018 4.717313 GCACAGTTCGGGACCCCC 62.717 72.222 4.46 0.00 41.09 5.40
2766 3020 4.309950 ACGCACAGTTCGGGACCC 62.310 66.667 0.00 0.00 0.00 4.46
2767 3021 1.870055 TAGACGCACAGTTCGGGACC 61.870 60.000 0.00 0.00 0.00 4.46
2768 3022 0.038892 TTAGACGCACAGTTCGGGAC 60.039 55.000 0.00 0.00 0.00 4.46
2769 3023 0.242825 CTTAGACGCACAGTTCGGGA 59.757 55.000 0.00 0.00 0.00 5.14
2770 3024 0.736325 CCTTAGACGCACAGTTCGGG 60.736 60.000 0.00 0.00 0.00 5.14
2771 3025 1.352156 GCCTTAGACGCACAGTTCGG 61.352 60.000 0.00 0.00 0.00 4.30
2772 3026 1.674611 CGCCTTAGACGCACAGTTCG 61.675 60.000 0.00 0.00 0.00 3.95
2773 3027 1.352156 CCGCCTTAGACGCACAGTTC 61.352 60.000 0.00 0.00 0.00 3.01
2774 3028 1.374252 CCGCCTTAGACGCACAGTT 60.374 57.895 0.00 0.00 0.00 3.16
2775 3029 1.605058 ATCCGCCTTAGACGCACAGT 61.605 55.000 0.00 0.00 0.00 3.55
2776 3030 1.141881 ATCCGCCTTAGACGCACAG 59.858 57.895 0.00 0.00 0.00 3.66
2777 3031 1.153647 CATCCGCCTTAGACGCACA 60.154 57.895 0.00 0.00 0.00 4.57
2778 3032 1.883084 CCATCCGCCTTAGACGCAC 60.883 63.158 0.00 0.00 0.00 5.34
2779 3033 1.038681 TACCATCCGCCTTAGACGCA 61.039 55.000 0.00 0.00 0.00 5.24
2780 3034 0.103572 TTACCATCCGCCTTAGACGC 59.896 55.000 0.00 0.00 0.00 5.19
2781 3035 1.135527 TGTTACCATCCGCCTTAGACG 59.864 52.381 0.00 0.00 0.00 4.18
2782 3036 2.483188 CCTGTTACCATCCGCCTTAGAC 60.483 54.545 0.00 0.00 0.00 2.59
2783 3037 1.760613 CCTGTTACCATCCGCCTTAGA 59.239 52.381 0.00 0.00 0.00 2.10
2784 3038 1.760613 TCCTGTTACCATCCGCCTTAG 59.239 52.381 0.00 0.00 0.00 2.18
2785 3039 1.760613 CTCCTGTTACCATCCGCCTTA 59.239 52.381 0.00 0.00 0.00 2.69
2786 3040 0.541863 CTCCTGTTACCATCCGCCTT 59.458 55.000 0.00 0.00 0.00 4.35
2787 3041 1.338136 CCTCCTGTTACCATCCGCCT 61.338 60.000 0.00 0.00 0.00 5.52
2788 3042 1.146263 CCTCCTGTTACCATCCGCC 59.854 63.158 0.00 0.00 0.00 6.13
2789 3043 1.523938 GCCTCCTGTTACCATCCGC 60.524 63.158 0.00 0.00 0.00 5.54
2790 3044 1.227263 CGCCTCCTGTTACCATCCG 60.227 63.158 0.00 0.00 0.00 4.18
2791 3045 1.146263 CCGCCTCCTGTTACCATCC 59.854 63.158 0.00 0.00 0.00 3.51
2792 3046 1.146263 CCCGCCTCCTGTTACCATC 59.854 63.158 0.00 0.00 0.00 3.51
2793 3047 2.375345 CCCCGCCTCCTGTTACCAT 61.375 63.158 0.00 0.00 0.00 3.55
2794 3048 3.006728 CCCCGCCTCCTGTTACCA 61.007 66.667 0.00 0.00 0.00 3.25
2795 3049 3.793888 CCCCCGCCTCCTGTTACC 61.794 72.222 0.00 0.00 0.00 2.85
2796 3050 2.686106 TCCCCCGCCTCCTGTTAC 60.686 66.667 0.00 0.00 0.00 2.50
2797 3051 2.686106 GTCCCCCGCCTCCTGTTA 60.686 66.667 0.00 0.00 0.00 2.41
2798 3052 4.974438 TGTCCCCCGCCTCCTGTT 62.974 66.667 0.00 0.00 0.00 3.16
2801 3055 4.974438 TTGTGTCCCCCGCCTCCT 62.974 66.667 0.00 0.00 0.00 3.69
2802 3056 3.728373 ATTGTGTCCCCCGCCTCC 61.728 66.667 0.00 0.00 0.00 4.30
2803 3057 2.438434 CATTGTGTCCCCCGCCTC 60.438 66.667 0.00 0.00 0.00 4.70
2804 3058 2.366153 AAACATTGTGTCCCCCGCCT 62.366 55.000 0.00 0.00 0.00 5.52
2805 3059 0.609681 TAAACATTGTGTCCCCCGCC 60.610 55.000 0.00 0.00 0.00 6.13
2806 3060 0.524414 GTAAACATTGTGTCCCCCGC 59.476 55.000 0.00 0.00 0.00 6.13
2807 3061 1.170442 GGTAAACATTGTGTCCCCCG 58.830 55.000 0.00 0.00 0.00 5.73
2808 3062 1.203075 TGGGTAAACATTGTGTCCCCC 60.203 52.381 5.22 6.45 33.96 5.40
2809 3063 2.296073 TGGGTAAACATTGTGTCCCC 57.704 50.000 16.40 10.25 34.88 4.81
2810 3064 3.227614 ACTTGGGTAAACATTGTGTCCC 58.772 45.455 13.79 13.79 35.85 4.46
2811 3065 4.555906 CGAACTTGGGTAAACATTGTGTCC 60.556 45.833 0.00 0.00 0.00 4.02
2812 3066 4.533222 CGAACTTGGGTAAACATTGTGTC 58.467 43.478 0.00 0.00 0.00 3.67
2813 3067 3.316868 CCGAACTTGGGTAAACATTGTGT 59.683 43.478 0.00 0.00 0.00 3.72
2814 3068 3.305064 CCCGAACTTGGGTAAACATTGTG 60.305 47.826 0.00 0.00 44.76 3.33
2815 3069 2.888414 CCCGAACTTGGGTAAACATTGT 59.112 45.455 0.00 0.00 44.76 2.71
2816 3070 3.569250 CCCGAACTTGGGTAAACATTG 57.431 47.619 0.00 0.00 44.76 2.82
2826 3080 2.269241 GAGAGGGCCCGAACTTGG 59.731 66.667 18.44 0.00 0.00 3.61
2827 3081 1.961180 ATCGAGAGGGCCCGAACTTG 61.961 60.000 18.44 19.84 38.36 3.16
2828 3082 1.686110 ATCGAGAGGGCCCGAACTT 60.686 57.895 18.44 0.00 38.36 2.66
2829 3083 2.042843 ATCGAGAGGGCCCGAACT 60.043 61.111 18.44 17.42 38.36 3.01
2830 3084 2.107141 CATCGAGAGGGCCCGAAC 59.893 66.667 18.44 12.45 38.36 3.95
2831 3085 3.154473 CCATCGAGAGGGCCCGAA 61.154 66.667 18.44 1.01 38.36 4.30
2832 3086 4.137615 TCCATCGAGAGGGCCCGA 62.138 66.667 18.44 10.63 39.25 5.14
2833 3087 3.610669 CTCCATCGAGAGGGCCCG 61.611 72.222 18.44 4.06 38.52 6.13
2839 3093 3.768878 AGGGTATTACCTCCATCGAGAG 58.231 50.000 12.54 0.00 38.52 3.20
2840 3094 3.897657 AGGGTATTACCTCCATCGAGA 57.102 47.619 12.54 0.00 38.52 4.04
2841 3095 4.664392 AGTAGGGTATTACCTCCATCGAG 58.336 47.826 12.54 0.00 42.09 4.04
2842 3096 4.736611 AGTAGGGTATTACCTCCATCGA 57.263 45.455 12.54 0.00 42.09 3.59
2843 3097 6.008960 AGTAAGTAGGGTATTACCTCCATCG 58.991 44.000 12.54 0.00 42.09 3.84
2844 3098 8.169393 AGTAGTAAGTAGGGTATTACCTCCATC 58.831 40.741 12.54 0.00 42.09 3.51
2845 3099 8.066552 AGTAGTAAGTAGGGTATTACCTCCAT 57.933 38.462 12.54 0.29 42.09 3.41
2846 3100 7.471610 AGTAGTAAGTAGGGTATTACCTCCA 57.528 40.000 12.54 0.00 42.09 3.86
2847 3101 8.001292 TCAAGTAGTAAGTAGGGTATTACCTCC 58.999 40.741 12.54 0.00 42.09 4.30
2848 3102 8.986929 TCAAGTAGTAAGTAGGGTATTACCTC 57.013 38.462 12.54 3.41 42.09 3.85
2849 3103 9.948747 AATCAAGTAGTAAGTAGGGTATTACCT 57.051 33.333 12.54 2.07 44.75 3.08
2850 3104 9.978044 CAATCAAGTAGTAAGTAGGGTATTACC 57.022 37.037 4.11 4.11 37.60 2.85
2854 3108 9.884814 AGATCAATCAAGTAGTAAGTAGGGTAT 57.115 33.333 0.00 0.00 0.00 2.73
2855 3109 9.710818 AAGATCAATCAAGTAGTAAGTAGGGTA 57.289 33.333 0.00 0.00 0.00 3.69
2856 3110 8.478877 CAAGATCAATCAAGTAGTAAGTAGGGT 58.521 37.037 0.00 0.00 0.00 4.34
2857 3111 8.696374 TCAAGATCAATCAAGTAGTAAGTAGGG 58.304 37.037 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.