Multiple sequence alignment - TraesCS3A01G019600

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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 TraesCS3A01G019600 chr3A 100.000 3313 0 0 1 3313 11840362 11837050 0.000000e+00 6119.0
1 TraesCS3A01G019600 chr3A 84.571 175 21 5 1054 1225 7438714 7438543 5.690000e-38 169.0
2 TraesCS3A01G019600 chr3A 81.560 141 26 0 1925 2065 7437493 7437353 2.090000e-22 117.0
3 TraesCS3A01G019600 chr3A 88.333 60 2 2 104 163 739332626 739332680 2.130000e-07 67.6
4 TraesCS3A01G019600 chr3B 89.410 1662 101 43 1271 2897 11602034 11603655 0.000000e+00 2025.0
5 TraesCS3A01G019600 chr3B 91.277 642 30 13 19 655 11600308 11600928 0.000000e+00 852.0
6 TraesCS3A01G019600 chr3B 89.494 514 36 6 767 1272 11601496 11601999 4.660000e-178 634.0
7 TraesCS3A01G019600 chr3B 84.444 135 21 0 1922 2056 5200620 5200754 2.070000e-27 134.0
8 TraesCS3A01G019600 chr3B 82.270 141 25 0 1925 2065 3635953 3635813 4.490000e-24 122.0
9 TraesCS3A01G019600 chr3B 77.419 155 25 9 3147 3297 21948227 21948375 2.120000e-12 84.2
10 TraesCS3A01G019600 chr3B 87.324 71 7 2 3244 3313 228509348 228509417 2.740000e-11 80.5
11 TraesCS3A01G019600 chr3B 88.235 68 7 1 2513 2580 775551053 775550987 2.740000e-11 80.5
12 TraesCS3A01G019600 chr3B 97.436 39 1 0 2709 2747 717662200 717662238 2.130000e-07 67.6
13 TraesCS3A01G019600 chr3D 95.814 1075 35 8 992 2065 9291547 9292612 0.000000e+00 1727.0
14 TraesCS3A01G019600 chr3D 88.746 622 50 10 2705 3313 9293406 9294020 0.000000e+00 743.0
15 TraesCS3A01G019600 chr3D 90.076 524 21 10 2156 2663 9292611 9293119 0.000000e+00 651.0
16 TraesCS3A01G019600 chr3D 84.658 365 33 13 10 371 9290337 9290681 3.170000e-90 342.0
17 TraesCS3A01G019600 chr3D 85.498 331 34 6 338 655 9290691 9291020 1.910000e-87 333.0
18 TraesCS3A01G019600 chr3D 82.540 252 17 9 767 1001 9291275 9291516 2.610000e-46 196.0
19 TraesCS3A01G019600 chr3D 83.422 187 25 5 1054 1237 1608465 1608282 5.690000e-38 169.0
20 TraesCS3A01G019600 chr3D 100.000 39 0 0 2709 2747 172019417 172019455 4.590000e-09 73.1
21 TraesCS3A01G019600 chr6D 80.952 168 29 3 3147 3313 388541702 388541867 2.680000e-26 130.0
22 TraesCS3A01G019600 chr6D 93.617 47 2 1 2612 2657 12464823 12464869 5.930000e-08 69.4
23 TraesCS3A01G019600 chr5B 86.458 96 12 1 3218 3313 596911785 596911879 1.630000e-18 104.0
24 TraesCS3A01G019600 chr5B 90.196 51 2 2 2704 2751 506972470 506972420 2.760000e-06 63.9
25 TraesCS3A01G019600 chr5D 80.000 150 17 5 2513 2657 517450461 517450602 7.570000e-17 99.0
26 TraesCS3A01G019600 chr5D 80.147 136 19 3 2527 2661 420704225 420704353 9.790000e-16 95.3
27 TraesCS3A01G019600 chr5D 92.593 54 3 1 2528 2581 507878767 507878715 3.550000e-10 76.8
28 TraesCS3A01G019600 chr2D 77.381 168 36 2 3147 3313 644770921 644770755 7.570000e-17 99.0
29 TraesCS3A01G019600 chr2D 76.389 144 24 5 2515 2657 166147125 166147259 5.930000e-08 69.4
30 TraesCS3A01G019600 chr2D 85.714 63 9 0 2519 2581 270844267 270844329 2.130000e-07 67.6
31 TraesCS3A01G019600 chr7A 82.301 113 18 2 1072 1182 306220888 306221000 2.720000e-16 97.1
32 TraesCS3A01G019600 chr7A 77.083 144 23 9 2513 2654 509653775 509653640 1.280000e-09 75.0
33 TraesCS3A01G019600 chr4A 76.220 164 33 6 3152 3313 708557658 708557499 7.620000e-12 82.4
34 TraesCS3A01G019600 chr4A 86.765 68 9 0 2513 2580 675529561 675529494 3.550000e-10 76.8
35 TraesCS3A01G019600 chr4A 78.400 125 20 4 2534 2657 540478298 540478180 1.280000e-09 75.0
36 TraesCS3A01G019600 chr4A 90.741 54 5 0 2521 2574 595574017 595574070 4.590000e-09 73.1
37 TraesCS3A01G019600 chr4A 87.302 63 3 2 104 166 649027290 649027233 2.130000e-07 67.6
38 TraesCS3A01G019600 chr4D 78.125 128 21 4 2531 2657 56696233 56696354 1.280000e-09 75.0
39 TraesCS3A01G019600 chr2B 77.083 144 23 5 2515 2657 231635949 231635815 1.280000e-09 75.0
40 TraesCS3A01G019600 chr7B 100.000 39 0 0 2709 2747 677889701 677889739 4.590000e-09 73.1
41 TraesCS3A01G019600 chr6A 100.000 39 0 0 2709 2747 127572031 127571993 4.590000e-09 73.1
42 TraesCS3A01G019600 chr6A 88.136 59 2 2 104 162 581485139 581485192 7.670000e-07 65.8
43 TraesCS3A01G019600 chr6A 96.875 32 1 0 131 162 58371424 58371455 2.000000e-03 54.7
44 TraesCS3A01G019600 chr6B 86.885 61 8 0 2513 2573 716921527 716921587 5.930000e-08 69.4
45 TraesCS3A01G019600 chr1D 91.837 49 2 2 2701 2747 201519258 201519306 2.130000e-07 67.6
46 TraesCS3A01G019600 chr4B 88.889 54 4 2 2709 2760 583071727 583071780 7.670000e-07 65.8
47 TraesCS3A01G019600 chr5A 87.273 55 4 3 2714 2768 702905863 702905914 3.570000e-05 60.2
48 TraesCS3A01G019600 chr2A 85.000 60 8 1 2515 2574 184533044 184532986 3.570000e-05 60.2
49 TraesCS3A01G019600 chr2A 86.441 59 3 2 104 162 293046960 293047013 3.570000e-05 60.2


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 TraesCS3A01G019600 chr3A 11837050 11840362 3312 True 6119.000000 6119 100.000000 1 3313 1 chr3A.!!$R1 3312
1 TraesCS3A01G019600 chr3B 11600308 11603655 3347 False 1170.333333 2025 90.060333 19 2897 3 chr3B.!!$F5 2878
2 TraesCS3A01G019600 chr3D 9290337 9294020 3683 False 665.333333 1727 87.888667 10 3313 6 chr3D.!!$F2 3303

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
811 1362 0.881796 CTGTGTCCGTCTACTGCTCA 59.118 55.0 0.0 0.0 0.0 4.26 F
1013 1627 0.491371 GGAGAGATGGGGAGGGATCT 59.509 60.0 0.0 0.0 0.0 2.75 F
2111 2858 0.592637 CGAGCATTTTGACAGCACCA 59.407 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2874 0.549469 AGCAGCCATGGATCATGTCA 59.451 50.000 18.4 0.00 39.94 3.58 R
2130 2877 1.067060 CACAAGCAGCCATGGATCATG 59.933 52.381 18.4 10.28 41.10 3.07 R
3022 4055 0.179189 GTCAAAATTCTCAGCCCGCG 60.179 55.000 0.0 0.00 0.00 6.46 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
34 35 5.503683 GCTGTTGCATCTCAGTGCTAATTAG 60.504 44.000 8.20 8.20 45.27 1.73
57 58 6.809869 AGCTGTTGGCATTTTTATAATCTCC 58.190 36.000 0.00 0.00 44.79 3.71
127 128 8.789762 GGTCCTAGAGAATCAAAGTAGAGTATC 58.210 40.741 0.00 0.00 37.82 2.24
128 129 9.344772 GTCCTAGAGAATCAAAGTAGAGTATCA 57.655 37.037 0.00 0.00 35.12 2.15
129 130 9.567776 TCCTAGAGAATCAAAGTAGAGTATCAG 57.432 37.037 0.00 0.00 35.12 2.90
158 159 7.309805 GGTGAAGGAATAAAAGGCAAACAGTAT 60.310 37.037 0.00 0.00 0.00 2.12
200 201 1.662629 GTGGATGCTGAGTGATGAACG 59.337 52.381 0.00 0.00 0.00 3.95
218 222 8.192774 TGATGAACGGGTGTACTAATTAACTAG 58.807 37.037 0.00 0.00 0.00 2.57
240 244 9.244292 ACTAGACTGAATTAGAATGTCTGTACA 57.756 33.333 0.00 0.00 38.30 2.90
255 259 7.354751 TGTCTGTACATAACTACATATGGCA 57.645 36.000 7.80 0.00 37.55 4.92
480 536 3.231160 CGCATTTCTGTTAAAACGTCCC 58.769 45.455 0.00 0.00 0.00 4.46
481 537 3.304123 CGCATTTCTGTTAAAACGTCCCA 60.304 43.478 0.00 0.00 0.00 4.37
494 550 1.691976 ACGTCCCAGAGAATCAACACA 59.308 47.619 0.00 0.00 37.82 3.72
495 551 2.303022 ACGTCCCAGAGAATCAACACAT 59.697 45.455 0.00 0.00 37.82 3.21
498 554 3.686726 GTCCCAGAGAATCAACACATCAC 59.313 47.826 0.00 0.00 37.82 3.06
558 616 2.042831 GTCTGTGTGGATGCTGGGC 61.043 63.158 0.00 0.00 0.00 5.36
603 661 2.760092 TGCATCCCCTAAACATTTCTGC 59.240 45.455 0.00 0.00 0.00 4.26
658 762 2.403378 GCCCGCCGCAATTAGTTGA 61.403 57.895 1.56 0.00 37.53 3.18
715 819 1.675552 GTGACGGGTAATGAATGGGG 58.324 55.000 0.00 0.00 0.00 4.96
782 1329 4.042809 TCAATTCAGTTACCAGGACCATGT 59.957 41.667 0.00 0.00 0.00 3.21
811 1362 0.881796 CTGTGTCCGTCTACTGCTCA 59.118 55.000 0.00 0.00 0.00 4.26
839 1390 1.451387 CAACCACACCGGGATAGGC 60.451 63.158 6.32 0.00 40.22 3.93
887 1438 3.682885 TGGCAGCAACAATGGCGG 61.683 61.111 0.00 0.00 45.63 6.13
952 1516 5.228945 ACCACAAGCAGTTAGTAATCTGT 57.771 39.130 11.58 0.00 34.57 3.41
956 1520 8.537016 ACCACAAGCAGTTAGTAATCTGTATTA 58.463 33.333 11.58 0.00 34.57 0.98
975 1539 9.531412 CTGTATTATTTCTCTGTACGTAGATCG 57.469 37.037 0.00 0.00 46.00 3.69
983 1547 3.437741 TCTGTACGTAGATCGCTGACAAA 59.562 43.478 0.00 0.00 44.19 2.83
1013 1627 0.491371 GGAGAGATGGGGAGGGATCT 59.509 60.000 0.00 0.00 0.00 2.75
1020 1634 3.883549 GGGAGGGATCTGCAGGCC 61.884 72.222 15.13 15.43 32.55 5.19
1024 1638 4.115199 GGGATCTGCAGGCCGGTT 62.115 66.667 15.13 0.00 0.00 4.44
1026 1640 2.409870 GGATCTGCAGGCCGGTTTG 61.410 63.158 15.13 2.76 0.00 2.93
1255 1870 2.682269 GCCTCCACCATTCTTCTTCTCC 60.682 54.545 0.00 0.00 0.00 3.71
1276 1927 2.165998 GCTTCTTCTTCCAGCAATGGT 58.834 47.619 0.00 0.00 33.45 3.55
1301 1952 2.552373 GGACGGTTTTCTGAATCCTGGT 60.552 50.000 0.00 3.06 0.00 4.00
1302 1953 3.307199 GGACGGTTTTCTGAATCCTGGTA 60.307 47.826 0.00 0.00 0.00 3.25
1303 1954 3.933332 GACGGTTTTCTGAATCCTGGTAG 59.067 47.826 0.00 0.00 0.00 3.18
1304 1955 3.326880 ACGGTTTTCTGAATCCTGGTAGT 59.673 43.478 0.00 0.07 0.00 2.73
1305 1956 3.684788 CGGTTTTCTGAATCCTGGTAGTG 59.315 47.826 0.00 0.00 0.00 2.74
1306 1957 4.652822 GGTTTTCTGAATCCTGGTAGTGT 58.347 43.478 0.00 0.00 0.00 3.55
1307 1958 4.695928 GGTTTTCTGAATCCTGGTAGTGTC 59.304 45.833 0.00 0.00 0.00 3.67
1308 1959 5.513267 GGTTTTCTGAATCCTGGTAGTGTCT 60.513 44.000 0.00 0.00 0.00 3.41
1309 1960 5.407407 TTTCTGAATCCTGGTAGTGTCTC 57.593 43.478 0.00 0.00 0.00 3.36
1313 1964 4.160329 TGAATCCTGGTAGTGTCTCTGTT 58.840 43.478 0.00 0.00 0.00 3.16
1317 1968 4.957296 TCCTGGTAGTGTCTCTGTTTTTC 58.043 43.478 0.00 0.00 0.00 2.29
1323 1974 6.761714 TGGTAGTGTCTCTGTTTTTCTTCTTC 59.238 38.462 0.00 0.00 0.00 2.87
1326 1977 7.546778 AGTGTCTCTGTTTTTCTTCTTCTTC 57.453 36.000 0.00 0.00 0.00 2.87
1371 2025 4.400961 ACCTTCTCGCTGCTGGCC 62.401 66.667 0.00 0.00 37.74 5.36
1452 2106 3.740397 TACCACCTGTCGCCGACG 61.740 66.667 13.18 7.39 42.01 5.12
1584 2238 4.082523 ACGGTGGTGAGCATCGGG 62.083 66.667 21.77 0.00 38.61 5.14
1692 2346 1.026718 GCCCCATCTTCAACTGGACG 61.027 60.000 0.00 0.00 34.24 4.79
1797 2451 2.725008 CGCCTCTCGGTGATCTCC 59.275 66.667 3.58 3.58 43.70 3.71
1818 2472 2.678934 ACCTGCGTCTTCGGGCTA 60.679 61.111 0.00 0.00 37.56 3.93
1848 2502 3.554692 GTCATCGCCGCCTTCACG 61.555 66.667 0.00 0.00 0.00 4.35
2075 2822 2.494918 CGGAGGGTAAGCACGGAG 59.505 66.667 0.00 0.00 0.00 4.63
2076 2823 2.050350 CGGAGGGTAAGCACGGAGA 61.050 63.158 0.00 0.00 0.00 3.71
2077 2824 1.392710 CGGAGGGTAAGCACGGAGAT 61.393 60.000 0.00 0.00 0.00 2.75
2078 2825 1.700955 GGAGGGTAAGCACGGAGATA 58.299 55.000 0.00 0.00 0.00 1.98
2079 2826 1.340568 GGAGGGTAAGCACGGAGATAC 59.659 57.143 0.00 0.00 0.00 2.24
2080 2827 2.029623 GAGGGTAAGCACGGAGATACA 58.970 52.381 0.00 0.00 0.00 2.29
2081 2828 2.429610 GAGGGTAAGCACGGAGATACAA 59.570 50.000 0.00 0.00 0.00 2.41
2082 2829 3.039011 AGGGTAAGCACGGAGATACAAT 58.961 45.455 0.00 0.00 0.00 2.71
2083 2830 3.069729 AGGGTAAGCACGGAGATACAATC 59.930 47.826 0.00 0.00 0.00 2.67
2084 2831 3.391049 GGTAAGCACGGAGATACAATCC 58.609 50.000 0.00 0.00 0.00 3.01
2085 2832 3.181469 GGTAAGCACGGAGATACAATCCA 60.181 47.826 0.00 0.00 36.57 3.41
2086 2833 2.604046 AGCACGGAGATACAATCCAC 57.396 50.000 0.00 0.00 36.57 4.02
2087 2834 1.831106 AGCACGGAGATACAATCCACA 59.169 47.619 0.00 0.00 36.57 4.17
2088 2835 2.435805 AGCACGGAGATACAATCCACAT 59.564 45.455 0.00 0.00 36.57 3.21
2089 2836 3.641436 AGCACGGAGATACAATCCACATA 59.359 43.478 0.00 0.00 36.57 2.29
2090 2837 3.741344 GCACGGAGATACAATCCACATAC 59.259 47.826 0.00 0.00 36.57 2.39
2091 2838 4.739436 GCACGGAGATACAATCCACATACA 60.739 45.833 0.00 0.00 36.57 2.29
2092 2839 4.745125 CACGGAGATACAATCCACATACAC 59.255 45.833 0.00 0.00 36.57 2.90
2093 2840 3.981416 CGGAGATACAATCCACATACACG 59.019 47.826 0.00 0.00 36.57 4.49
2094 2841 4.261447 CGGAGATACAATCCACATACACGA 60.261 45.833 0.00 0.00 36.57 4.35
2095 2842 5.223382 GGAGATACAATCCACATACACGAG 58.777 45.833 0.00 0.00 36.79 4.18
2096 2843 4.621991 AGATACAATCCACATACACGAGC 58.378 43.478 0.00 0.00 0.00 5.03
2097 2844 2.760634 ACAATCCACATACACGAGCA 57.239 45.000 0.00 0.00 0.00 4.26
2098 2845 3.266510 ACAATCCACATACACGAGCAT 57.733 42.857 0.00 0.00 0.00 3.79
2099 2846 3.609853 ACAATCCACATACACGAGCATT 58.390 40.909 0.00 0.00 0.00 3.56
2100 2847 4.009675 ACAATCCACATACACGAGCATTT 58.990 39.130 0.00 0.00 0.00 2.32
2101 2848 4.458989 ACAATCCACATACACGAGCATTTT 59.541 37.500 0.00 0.00 0.00 1.82
2102 2849 4.621068 ATCCACATACACGAGCATTTTG 57.379 40.909 0.00 0.00 0.00 2.44
2103 2850 3.669536 TCCACATACACGAGCATTTTGA 58.330 40.909 0.00 0.00 0.00 2.69
2104 2851 3.435327 TCCACATACACGAGCATTTTGAC 59.565 43.478 0.00 0.00 0.00 3.18
2105 2852 3.188254 CCACATACACGAGCATTTTGACA 59.812 43.478 0.00 0.00 0.00 3.58
2106 2853 4.397382 CACATACACGAGCATTTTGACAG 58.603 43.478 0.00 0.00 0.00 3.51
2107 2854 3.120199 ACATACACGAGCATTTTGACAGC 60.120 43.478 0.00 0.00 0.00 4.40
2108 2855 1.308047 ACACGAGCATTTTGACAGCA 58.692 45.000 0.00 0.00 0.00 4.41
2109 2856 1.002468 ACACGAGCATTTTGACAGCAC 60.002 47.619 0.00 0.00 0.00 4.40
2110 2857 0.593128 ACGAGCATTTTGACAGCACC 59.407 50.000 0.00 0.00 0.00 5.01
2111 2858 0.592637 CGAGCATTTTGACAGCACCA 59.407 50.000 0.00 0.00 0.00 4.17
2112 2859 1.200716 CGAGCATTTTGACAGCACCAT 59.799 47.619 0.00 0.00 0.00 3.55
2113 2860 2.352030 CGAGCATTTTGACAGCACCATT 60.352 45.455 0.00 0.00 0.00 3.16
2114 2861 2.991190 GAGCATTTTGACAGCACCATTG 59.009 45.455 0.00 0.00 0.00 2.82
2126 2873 2.693797 CACCATTGCACTTGTCTGAC 57.306 50.000 0.00 0.00 0.00 3.51
2127 2874 2.224606 CACCATTGCACTTGTCTGACT 58.775 47.619 9.51 0.00 0.00 3.41
2128 2875 2.031420 CACCATTGCACTTGTCTGACTG 60.031 50.000 9.51 4.76 0.00 3.51
2129 2876 2.158769 ACCATTGCACTTGTCTGACTGA 60.159 45.455 9.51 0.00 0.00 3.41
2130 2877 2.225019 CCATTGCACTTGTCTGACTGAC 59.775 50.000 9.51 5.57 45.54 3.51
2141 2888 3.464907 GTCTGACTGACATGATCCATGG 58.535 50.000 4.97 4.97 45.16 3.66
2146 2893 3.416253 GACATGATCCATGGCTGCT 57.584 52.632 6.96 0.00 45.62 4.24
2147 2894 1.688772 GACATGATCCATGGCTGCTT 58.311 50.000 6.96 0.00 45.62 3.91
2148 2895 1.337071 GACATGATCCATGGCTGCTTG 59.663 52.381 6.96 9.36 45.62 4.01
2149 2896 1.341679 ACATGATCCATGGCTGCTTGT 60.342 47.619 6.96 9.96 45.16 3.16
2150 2897 1.067060 CATGATCCATGGCTGCTTGTG 59.933 52.381 6.96 0.00 38.11 3.33
2151 2898 1.317431 TGATCCATGGCTGCTTGTGC 61.317 55.000 6.96 0.00 40.20 4.57
2152 2899 2.332362 GATCCATGGCTGCTTGTGCG 62.332 60.000 6.96 0.00 43.34 5.34
2153 2900 4.789075 CCATGGCTGCTTGTGCGC 62.789 66.667 0.00 0.00 43.34 6.09
2154 2901 4.045771 CATGGCTGCTTGTGCGCA 62.046 61.111 5.66 5.66 43.34 6.09
2237 2984 1.134175 GAGAAGAAGACGAGGAGCCAG 59.866 57.143 0.00 0.00 0.00 4.85
2398 3170 0.859232 CTAGTGTTTCAAGCGTGCGT 59.141 50.000 0.00 0.00 0.00 5.24
2400 3172 1.292061 AGTGTTTCAAGCGTGCGTTA 58.708 45.000 0.00 0.00 0.00 3.18
2488 3261 2.896044 GGTACCTACTGTGTATAGCCCC 59.104 54.545 4.06 0.00 0.00 5.80
2511 3284 2.029244 GTCTTCGAGTTGTGTGTGTGTG 59.971 50.000 0.00 0.00 0.00 3.82
2512 3285 1.999735 CTTCGAGTTGTGTGTGTGTGT 59.000 47.619 0.00 0.00 0.00 3.72
2583 3360 8.713708 TTGGGGTGTTCAATTTAGAATTTAGA 57.286 30.769 0.00 0.00 0.00 2.10
2584 3361 8.713708 TGGGGTGTTCAATTTAGAATTTAGAA 57.286 30.769 0.00 0.00 0.00 2.10
2585 3362 9.320295 TGGGGTGTTCAATTTAGAATTTAGAAT 57.680 29.630 0.00 0.00 0.00 2.40
2613 3390 2.239681 TGGTTTTTGTGGGGTCAACT 57.760 45.000 0.00 0.00 0.00 3.16
2624 3402 5.389520 TGTGGGGTCAACTATTTTGATGAA 58.610 37.500 0.00 0.00 0.00 2.57
2663 3441 8.804688 TGGTTCATAGTTTTTATTCGGTTTTG 57.195 30.769 0.00 0.00 0.00 2.44
2664 3442 8.414778 TGGTTCATAGTTTTTATTCGGTTTTGT 58.585 29.630 0.00 0.00 0.00 2.83
2665 3443 8.696175 GGTTCATAGTTTTTATTCGGTTTTGTG 58.304 33.333 0.00 0.00 0.00 3.33
2666 3444 9.240159 GTTCATAGTTTTTATTCGGTTTTGTGT 57.760 29.630 0.00 0.00 0.00 3.72
2667 3445 8.789881 TCATAGTTTTTATTCGGTTTTGTGTG 57.210 30.769 0.00 0.00 0.00 3.82
2668 3446 8.407064 TCATAGTTTTTATTCGGTTTTGTGTGT 58.593 29.630 0.00 0.00 0.00 3.72
2671 3449 3.992260 TTATTCGGTTTTGTGTGTGGG 57.008 42.857 0.00 0.00 0.00 4.61
2672 3450 1.770294 ATTCGGTTTTGTGTGTGGGT 58.230 45.000 0.00 0.00 0.00 4.51
2702 3480 2.224066 GGGAGTGATATCTGACCGTTGG 60.224 54.545 3.98 0.00 0.00 3.77
2703 3481 2.474816 GAGTGATATCTGACCGTTGGC 58.525 52.381 3.98 0.00 0.00 4.52
2707 3485 3.028130 TGATATCTGACCGTTGGCACTA 58.972 45.455 3.98 0.00 0.00 2.74
2747 3770 2.414559 GCTTACCACATGTGTCATGTGC 60.415 50.000 27.16 17.00 45.81 4.57
2776 3799 3.901844 ACTGTTGGCACTTAGTCTTCCTA 59.098 43.478 0.00 0.00 0.00 2.94
2860 3883 6.239600 GGCCTTTGACTAGGACATATGTATCA 60.240 42.308 8.71 5.38 43.36 2.15
2863 3886 5.984695 TGACTAGGACATATGTATCAGGC 57.015 43.478 8.71 8.49 0.00 4.85
2876 3899 0.828343 ATCAGGCCCTACTCCGTAGC 60.828 60.000 0.00 0.00 35.06 3.58
2897 3920 6.009908 AGCTATTCCCCCGTAAAGTTTTAT 57.990 37.500 0.00 0.00 0.00 1.40
2898 3921 7.140522 AGCTATTCCCCCGTAAAGTTTTATA 57.859 36.000 0.00 0.00 0.00 0.98
2900 3923 6.994496 GCTATTCCCCCGTAAAGTTTTATACT 59.006 38.462 0.00 0.00 39.32 2.12
2910 3943 7.361371 CCGTAAAGTTTTATACTGGTGAATGCA 60.361 37.037 0.00 0.00 37.12 3.96
2922 3955 2.808543 GGTGAATGCAGAAGAAAGACGT 59.191 45.455 0.00 0.00 0.00 4.34
2923 3956 3.251004 GGTGAATGCAGAAGAAAGACGTT 59.749 43.478 0.00 0.00 0.00 3.99
2924 3957 4.214437 GTGAATGCAGAAGAAAGACGTTG 58.786 43.478 0.00 0.00 0.00 4.10
2956 3989 1.165270 AGGACTTGCGTGTTATTGCC 58.835 50.000 0.00 0.00 0.00 4.52
2972 4005 7.062255 GTGTTATTGCCATAAAGAAGTTCTTGC 59.938 37.037 18.70 16.75 36.71 4.01
2998 4031 6.884832 AGGATTGGTTTCATCTAATACGTGA 58.115 36.000 0.00 0.00 0.00 4.35
3002 4035 7.972832 TTGGTTTCATCTAATACGTGACTTT 57.027 32.000 0.00 0.00 0.00 2.66
3013 4046 1.281656 GTGACTTTGGCGTTTCCGG 59.718 57.895 0.00 0.00 37.80 5.14
3022 4055 1.577922 GCGTTTCCGGAAAAGGGAC 59.422 57.895 34.00 21.47 34.13 4.46
3024 4057 1.577922 GTTTCCGGAAAAGGGACGC 59.422 57.895 30.49 13.03 32.05 5.19
3053 4087 6.129179 TGAGAATTTTGACTTTTGAGGACCT 58.871 36.000 0.00 0.00 0.00 3.85
3067 4101 5.497464 TGAGGACCTTGTTTGATCATGTA 57.503 39.130 0.00 0.00 0.00 2.29
3078 4112 5.012046 TGTTTGATCATGTAGTCACAGTCCT 59.988 40.000 0.00 0.00 38.30 3.85
3080 4114 6.850752 TTGATCATGTAGTCACAGTCCTAA 57.149 37.500 0.00 0.00 38.30 2.69
3081 4115 6.208988 TGATCATGTAGTCACAGTCCTAAC 57.791 41.667 0.00 0.00 38.30 2.34
3082 4116 5.952347 TGATCATGTAGTCACAGTCCTAACT 59.048 40.000 0.00 0.00 38.30 2.24
3083 4117 5.899120 TCATGTAGTCACAGTCCTAACTC 57.101 43.478 0.00 0.00 38.30 3.01
3084 4118 4.705507 TCATGTAGTCACAGTCCTAACTCC 59.294 45.833 0.00 0.00 38.30 3.85
3085 4119 4.383931 TGTAGTCACAGTCCTAACTCCT 57.616 45.455 0.00 0.00 31.71 3.69
3086 4120 5.509832 TGTAGTCACAGTCCTAACTCCTA 57.490 43.478 0.00 0.00 31.71 2.94
3087 4121 5.884322 TGTAGTCACAGTCCTAACTCCTAA 58.116 41.667 0.00 0.00 31.71 2.69
3097 4131 4.217118 GTCCTAACTCCTAAGTCGTGTCAA 59.783 45.833 0.00 0.00 33.48 3.18
3106 4140 4.024302 CCTAAGTCGTGTCAAAAGTTTCCC 60.024 45.833 0.00 0.00 0.00 3.97
3108 4142 4.411256 AGTCGTGTCAAAAGTTTCCCTA 57.589 40.909 0.00 0.00 0.00 3.53
3110 4144 5.374071 AGTCGTGTCAAAAGTTTCCCTATT 58.626 37.500 0.00 0.00 0.00 1.73
3126 4160 4.766404 CCTATTAATGGGACGGAAATGC 57.234 45.455 12.37 0.00 0.00 3.56
3134 4168 0.472471 GGACGGAAATGCATAGGGGA 59.528 55.000 0.00 0.00 0.00 4.81
3161 4195 2.308039 GCGGCTCGTTTTGTCTCGT 61.308 57.895 0.00 0.00 0.00 4.18
3166 4200 2.223377 GGCTCGTTTTGTCTCGTGATTT 59.777 45.455 0.00 0.00 0.00 2.17
3168 4202 3.218398 CTCGTTTTGTCTCGTGATTTGC 58.782 45.455 0.00 0.00 0.00 3.68
3176 4210 1.992667 TCTCGTGATTTGCGCAGTAAG 59.007 47.619 11.31 3.02 31.13 2.34
3189 4223 2.674177 CGCAGTAAGTCAATCCCGAACT 60.674 50.000 0.00 0.00 0.00 3.01
3197 4231 2.094182 GTCAATCCCGAACTAGAGCACA 60.094 50.000 0.00 0.00 0.00 4.57
3205 4239 4.935808 CCCGAACTAGAGCACAGTAAAAAT 59.064 41.667 0.00 0.00 0.00 1.82
3206 4240 6.071221 TCCCGAACTAGAGCACAGTAAAAATA 60.071 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.337889 GCAACAGCAGCGACGTCA 61.338 61.111 17.16 0.00 0.00 4.35
1 2 2.554365 GATGCAACAGCAGCGACGTC 62.554 60.000 5.18 5.18 42.36 4.34
2 3 2.666190 ATGCAACAGCAGCGACGT 60.666 55.556 0.00 0.00 42.36 4.34
3 4 2.097160 GATGCAACAGCAGCGACG 59.903 61.111 0.00 0.00 42.36 5.12
7 8 0.168348 CACTGAGATGCAACAGCAGC 59.832 55.000 14.03 0.00 44.61 5.25
8 9 0.168348 GCACTGAGATGCAACAGCAG 59.832 55.000 15.43 14.21 45.39 4.24
34 35 6.698766 CAGGAGATTATAAAAATGCCAACAGC 59.301 38.462 0.00 0.00 44.14 4.40
42 43 7.502226 TGTGGCCTACAGGAGATTATAAAAATG 59.498 37.037 3.32 0.00 37.39 2.32
44 45 6.964464 TGTGGCCTACAGGAGATTATAAAAA 58.036 36.000 3.32 0.00 37.39 1.94
127 128 3.119352 GCCTTTTATTCCTTCACCAGCTG 60.119 47.826 6.78 6.78 0.00 4.24
128 129 3.092301 GCCTTTTATTCCTTCACCAGCT 58.908 45.455 0.00 0.00 0.00 4.24
129 130 2.825532 TGCCTTTTATTCCTTCACCAGC 59.174 45.455 0.00 0.00 0.00 4.85
240 244 9.578576 AATTCAGTCATTGCCATATGTAGTTAT 57.421 29.630 1.24 0.00 0.00 1.89
241 245 8.978874 AATTCAGTCATTGCCATATGTAGTTA 57.021 30.769 1.24 0.00 0.00 2.24
242 246 7.886629 AATTCAGTCATTGCCATATGTAGTT 57.113 32.000 1.24 0.00 0.00 2.24
243 247 8.432013 TCTAATTCAGTCATTGCCATATGTAGT 58.568 33.333 1.24 0.00 0.00 2.73
244 248 8.837788 TCTAATTCAGTCATTGCCATATGTAG 57.162 34.615 1.24 0.00 0.00 2.74
245 249 9.797642 ATTCTAATTCAGTCATTGCCATATGTA 57.202 29.630 1.24 0.00 0.00 2.29
246 250 8.573885 CATTCTAATTCAGTCATTGCCATATGT 58.426 33.333 1.24 0.00 0.00 2.29
247 251 8.573885 ACATTCTAATTCAGTCATTGCCATATG 58.426 33.333 0.00 0.00 0.00 1.78
253 257 9.869844 GTACATACATTCTAATTCAGTCATTGC 57.130 33.333 0.00 0.00 0.00 3.56
480 536 5.233050 GGATACGTGATGTGTTGATTCTCTG 59.767 44.000 0.00 0.00 0.00 3.35
481 537 5.352284 GGATACGTGATGTGTTGATTCTCT 58.648 41.667 0.00 0.00 0.00 3.10
558 616 2.287188 GCATTGGTGCCATGTTCTATCG 60.287 50.000 0.00 0.00 45.76 2.92
583 641 3.026694 AGCAGAAATGTTTAGGGGATGC 58.973 45.455 0.00 0.00 0.00 3.91
584 642 3.181483 GCAGCAGAAATGTTTAGGGGATG 60.181 47.826 0.00 0.00 0.00 3.51
585 643 3.026694 GCAGCAGAAATGTTTAGGGGAT 58.973 45.455 0.00 0.00 0.00 3.85
586 644 2.041620 AGCAGCAGAAATGTTTAGGGGA 59.958 45.455 0.00 0.00 0.00 4.81
587 645 2.165030 CAGCAGCAGAAATGTTTAGGGG 59.835 50.000 0.00 0.00 0.00 4.79
603 661 4.333649 TCGCCTTAATTTGATTCTCAGCAG 59.666 41.667 0.00 0.00 0.00 4.24
655 729 1.204704 AGCGATCGATCAACACCTCAA 59.795 47.619 24.40 0.00 0.00 3.02
658 762 0.807667 GCAGCGATCGATCAACACCT 60.808 55.000 24.40 9.42 0.00 4.00
660 764 0.299895 CAGCAGCGATCGATCAACAC 59.700 55.000 24.40 11.13 0.00 3.32
782 1329 1.816835 GACGGACACAGGACAGACATA 59.183 52.381 0.00 0.00 0.00 2.29
811 1362 0.182775 GGTGTGGTTGTCCTGTCCTT 59.817 55.000 0.00 0.00 34.23 3.36
839 1390 3.465403 CTCCGGTGGCCTCTCCTG 61.465 72.222 3.32 0.69 35.26 3.86
853 1404 1.890979 CACTGGCGCATCATCCTCC 60.891 63.158 10.83 0.00 0.00 4.30
854 1405 1.890979 CCACTGGCGCATCATCCTC 60.891 63.158 10.83 0.00 0.00 3.71
855 1406 2.191375 CCACTGGCGCATCATCCT 59.809 61.111 10.83 0.00 0.00 3.24
867 1418 1.373748 GCCATTGTTGCTGCCACTG 60.374 57.895 5.42 0.00 0.00 3.66
887 1438 3.118371 GGTGCAGGGGTATATATAGTGGC 60.118 52.174 0.00 0.00 0.00 5.01
952 1516 8.228464 CAGCGATCTACGTACAGAGAAATAATA 58.772 37.037 0.00 0.00 44.60 0.98
956 1520 4.575236 TCAGCGATCTACGTACAGAGAAAT 59.425 41.667 0.00 0.00 44.60 2.17
975 1539 4.081420 TCTCCCTCTCTACAATTTGTCAGC 60.081 45.833 5.07 0.00 0.00 4.26
983 1547 3.439260 CCCCATCTCTCCCTCTCTACAAT 60.439 52.174 0.00 0.00 0.00 2.71
1255 1870 1.131883 CCATTGCTGGAAGAAGAAGCG 59.868 52.381 0.00 0.00 46.37 4.68
1276 1927 2.500229 GATTCAGAAAACCGTCCACCA 58.500 47.619 0.00 0.00 0.00 4.17
1301 1952 8.478877 AGAAGAAGAAGAAAAACAGAGACACTA 58.521 33.333 0.00 0.00 0.00 2.74
1302 1953 7.334858 AGAAGAAGAAGAAAAACAGAGACACT 58.665 34.615 0.00 0.00 0.00 3.55
1303 1954 7.546778 AGAAGAAGAAGAAAAACAGAGACAC 57.453 36.000 0.00 0.00 0.00 3.67
1304 1955 8.043710 AGAAGAAGAAGAAGAAAAACAGAGACA 58.956 33.333 0.00 0.00 0.00 3.41
1305 1956 8.432110 AGAAGAAGAAGAAGAAAAACAGAGAC 57.568 34.615 0.00 0.00 0.00 3.36
1306 1957 9.103861 GAAGAAGAAGAAGAAGAAAAACAGAGA 57.896 33.333 0.00 0.00 0.00 3.10
1307 1958 8.887717 TGAAGAAGAAGAAGAAGAAAAACAGAG 58.112 33.333 0.00 0.00 0.00 3.35
1308 1959 8.792830 TGAAGAAGAAGAAGAAGAAAAACAGA 57.207 30.769 0.00 0.00 0.00 3.41
1309 1960 8.127954 CCTGAAGAAGAAGAAGAAGAAAAACAG 58.872 37.037 0.00 0.00 0.00 3.16
1692 2346 2.510238 ATGAAGACGCAGCCGAGC 60.510 61.111 0.00 0.00 38.29 5.03
1791 2445 1.040339 AGACGCAGGTGAGGGAGATC 61.040 60.000 0.00 0.00 0.00 2.75
1797 2451 2.125912 CCGAAGACGCAGGTGAGG 60.126 66.667 0.00 0.00 38.29 3.86
1818 2472 0.811915 CGATGACGAGGAACTGGAGT 59.188 55.000 0.00 0.00 41.55 3.85
1848 2502 3.151022 CGGCTCAGGTCCTCCTCC 61.151 72.222 0.00 0.00 43.07 4.30
1989 2643 2.743928 GTCTGCACGGGCTGGAAG 60.744 66.667 17.05 2.04 41.91 3.46
2065 2812 3.449377 TGTGGATTGTATCTCCGTGCTTA 59.551 43.478 0.00 0.00 35.41 3.09
2066 2813 2.236146 TGTGGATTGTATCTCCGTGCTT 59.764 45.455 0.00 0.00 35.41 3.91
2067 2814 1.831106 TGTGGATTGTATCTCCGTGCT 59.169 47.619 0.00 0.00 35.41 4.40
2068 2815 2.309528 TGTGGATTGTATCTCCGTGC 57.690 50.000 0.00 0.00 35.41 5.34
2069 2816 4.745125 GTGTATGTGGATTGTATCTCCGTG 59.255 45.833 0.00 0.00 35.41 4.94
2070 2817 4.499188 CGTGTATGTGGATTGTATCTCCGT 60.499 45.833 0.00 0.00 35.41 4.69
2071 2818 3.981416 CGTGTATGTGGATTGTATCTCCG 59.019 47.826 0.00 0.00 35.41 4.63
2072 2819 5.196341 TCGTGTATGTGGATTGTATCTCC 57.804 43.478 0.00 0.00 0.00 3.71
2073 2820 4.681942 GCTCGTGTATGTGGATTGTATCTC 59.318 45.833 0.00 0.00 0.00 2.75
2074 2821 4.099419 TGCTCGTGTATGTGGATTGTATCT 59.901 41.667 0.00 0.00 0.00 1.98
2075 2822 4.368315 TGCTCGTGTATGTGGATTGTATC 58.632 43.478 0.00 0.00 0.00 2.24
2076 2823 4.400529 TGCTCGTGTATGTGGATTGTAT 57.599 40.909 0.00 0.00 0.00 2.29
2077 2824 3.878160 TGCTCGTGTATGTGGATTGTA 57.122 42.857 0.00 0.00 0.00 2.41
2078 2825 2.760634 TGCTCGTGTATGTGGATTGT 57.239 45.000 0.00 0.00 0.00 2.71
2079 2826 4.621068 AAATGCTCGTGTATGTGGATTG 57.379 40.909 0.00 0.00 0.00 2.67
2080 2827 4.699735 TCAAAATGCTCGTGTATGTGGATT 59.300 37.500 0.00 0.00 0.00 3.01
2081 2828 4.094887 GTCAAAATGCTCGTGTATGTGGAT 59.905 41.667 0.00 0.00 0.00 3.41
2082 2829 3.435327 GTCAAAATGCTCGTGTATGTGGA 59.565 43.478 0.00 0.00 0.00 4.02
2083 2830 3.188254 TGTCAAAATGCTCGTGTATGTGG 59.812 43.478 0.00 0.00 0.00 4.17
2084 2831 4.397382 CTGTCAAAATGCTCGTGTATGTG 58.603 43.478 0.00 0.00 0.00 3.21
2085 2832 3.120199 GCTGTCAAAATGCTCGTGTATGT 60.120 43.478 0.00 0.00 0.00 2.29
2086 2833 3.120234 TGCTGTCAAAATGCTCGTGTATG 60.120 43.478 0.00 0.00 0.00 2.39
2087 2834 3.073678 TGCTGTCAAAATGCTCGTGTAT 58.926 40.909 0.00 0.00 0.00 2.29
2088 2835 2.223144 GTGCTGTCAAAATGCTCGTGTA 59.777 45.455 0.00 0.00 0.00 2.90
2089 2836 1.002468 GTGCTGTCAAAATGCTCGTGT 60.002 47.619 0.00 0.00 0.00 4.49
2090 2837 1.664016 GGTGCTGTCAAAATGCTCGTG 60.664 52.381 0.00 0.00 0.00 4.35
2091 2838 0.593128 GGTGCTGTCAAAATGCTCGT 59.407 50.000 0.00 0.00 0.00 4.18
2092 2839 0.592637 TGGTGCTGTCAAAATGCTCG 59.407 50.000 0.00 0.00 0.00 5.03
2093 2840 2.991190 CAATGGTGCTGTCAAAATGCTC 59.009 45.455 0.00 0.00 0.00 4.26
2094 2841 3.034721 CAATGGTGCTGTCAAAATGCT 57.965 42.857 0.00 0.00 0.00 3.79
2107 2854 2.031420 CAGTCAGACAAGTGCAATGGTG 60.031 50.000 0.00 0.00 0.00 4.17
2108 2855 2.158769 TCAGTCAGACAAGTGCAATGGT 60.159 45.455 2.66 0.00 0.00 3.55
2109 2856 2.225019 GTCAGTCAGACAAGTGCAATGG 59.775 50.000 2.66 0.00 46.77 3.16
2110 2857 3.532892 GTCAGTCAGACAAGTGCAATG 57.467 47.619 2.66 0.00 46.77 2.82
2121 2868 2.158856 GCCATGGATCATGTCAGTCAGA 60.159 50.000 18.40 0.00 39.94 3.27
2122 2869 2.158798 AGCCATGGATCATGTCAGTCAG 60.159 50.000 18.40 0.00 39.94 3.51
2123 2870 1.841919 AGCCATGGATCATGTCAGTCA 59.158 47.619 18.40 0.00 39.94 3.41
2124 2871 2.219458 CAGCCATGGATCATGTCAGTC 58.781 52.381 18.40 0.00 39.94 3.51
2125 2872 1.749635 GCAGCCATGGATCATGTCAGT 60.750 52.381 18.40 0.00 39.94 3.41
2126 2873 0.952280 GCAGCCATGGATCATGTCAG 59.048 55.000 18.40 0.00 39.94 3.51
2127 2874 0.549469 AGCAGCCATGGATCATGTCA 59.451 50.000 18.40 0.00 39.94 3.58
2128 2875 1.337071 CAAGCAGCCATGGATCATGTC 59.663 52.381 18.40 4.76 39.94 3.06
2129 2876 1.341679 ACAAGCAGCCATGGATCATGT 60.342 47.619 18.40 10.98 39.94 3.21
2130 2877 1.067060 CACAAGCAGCCATGGATCATG 59.933 52.381 18.40 10.28 41.10 3.07
2131 2878 1.399714 CACAAGCAGCCATGGATCAT 58.600 50.000 18.40 0.00 0.00 2.45
2132 2879 1.317431 GCACAAGCAGCCATGGATCA 61.317 55.000 18.40 0.00 41.58 2.92
2133 2880 1.436336 GCACAAGCAGCCATGGATC 59.564 57.895 18.40 3.39 41.58 3.36
2134 2881 2.412323 CGCACAAGCAGCCATGGAT 61.412 57.895 18.40 6.18 42.27 3.41
2135 2882 3.057548 CGCACAAGCAGCCATGGA 61.058 61.111 18.40 0.00 42.27 3.41
2136 2883 4.789075 GCGCACAAGCAGCCATGG 62.789 66.667 7.63 7.63 42.27 3.66
2137 2884 4.045771 TGCGCACAAGCAGCCATG 62.046 61.111 5.66 0.00 42.92 3.66
2143 2890 1.371337 GATGATCCTGCGCACAAGCA 61.371 55.000 5.66 6.87 45.96 3.91
2144 2891 1.354506 GATGATCCTGCGCACAAGC 59.645 57.895 5.66 0.00 37.71 4.01
2145 2892 1.640069 CGATGATCCTGCGCACAAG 59.360 57.895 5.66 0.00 0.00 3.16
2146 2893 1.815003 CCGATGATCCTGCGCACAA 60.815 57.895 5.66 0.00 0.00 3.33
2147 2894 2.202919 CCGATGATCCTGCGCACA 60.203 61.111 5.66 2.63 0.00 4.57
2148 2895 3.643978 GCCGATGATCCTGCGCAC 61.644 66.667 5.66 0.00 0.00 5.34
2153 2900 4.592192 ACCGCGCCGATGATCCTG 62.592 66.667 0.00 0.00 0.00 3.86
2154 2901 4.592192 CACCGCGCCGATGATCCT 62.592 66.667 0.00 0.00 0.00 3.24
2237 2984 3.917760 CTCGCCATCTCCGGGTCC 61.918 72.222 0.00 0.00 0.00 4.46
2330 3093 3.506398 TCAGTACACACATCTCCAAGGA 58.494 45.455 0.00 0.00 0.00 3.36
2398 3170 5.562307 CGAGTCTTCTTCTTCTTGGTCGTAA 60.562 44.000 0.00 0.00 0.00 3.18
2400 3172 3.304794 CGAGTCTTCTTCTTCTTGGTCGT 60.305 47.826 0.00 0.00 0.00 4.34
2488 3261 2.282555 CACACACACAACTCGAAGACAG 59.717 50.000 0.00 0.00 0.00 3.51
2581 3358 6.770303 CCCACAAAAACCATAAACCAAATTCT 59.230 34.615 0.00 0.00 0.00 2.40
2582 3359 6.016693 CCCCACAAAAACCATAAACCAAATTC 60.017 38.462 0.00 0.00 0.00 2.17
2583 3360 5.830457 CCCCACAAAAACCATAAACCAAATT 59.170 36.000 0.00 0.00 0.00 1.82
2584 3361 5.103898 ACCCCACAAAAACCATAAACCAAAT 60.104 36.000 0.00 0.00 0.00 2.32
2585 3362 4.227527 ACCCCACAAAAACCATAAACCAAA 59.772 37.500 0.00 0.00 0.00 3.28
2586 3363 3.780850 ACCCCACAAAAACCATAAACCAA 59.219 39.130 0.00 0.00 0.00 3.67
2587 3364 3.385115 ACCCCACAAAAACCATAAACCA 58.615 40.909 0.00 0.00 0.00 3.67
2596 3373 6.342111 TCAAAATAGTTGACCCCACAAAAAC 58.658 36.000 0.00 0.00 0.00 2.43
2601 3378 4.991776 TCATCAAAATAGTTGACCCCACA 58.008 39.130 0.00 0.00 0.00 4.17
2603 3380 5.640147 ACTTCATCAAAATAGTTGACCCCA 58.360 37.500 0.00 0.00 0.00 4.96
2604 3381 6.590234 AACTTCATCAAAATAGTTGACCCC 57.410 37.500 0.00 0.00 30.17 4.95
2633 3411 9.634163 ACCGAATAAAAACTATGAACCAAATTC 57.366 29.630 0.00 0.00 37.88 2.17
2663 3441 3.966543 CCCTCCCCACCCACACAC 61.967 72.222 0.00 0.00 0.00 3.82
2683 3461 2.159099 TGCCAACGGTCAGATATCACTC 60.159 50.000 5.32 0.00 0.00 3.51
2684 3462 1.831106 TGCCAACGGTCAGATATCACT 59.169 47.619 5.32 0.00 0.00 3.41
2685 3463 1.933853 GTGCCAACGGTCAGATATCAC 59.066 52.381 5.32 0.00 0.00 3.06
2687 3465 2.604046 AGTGCCAACGGTCAGATATC 57.396 50.000 0.00 0.00 0.00 1.63
2688 3466 4.689612 AATAGTGCCAACGGTCAGATAT 57.310 40.909 0.00 0.00 0.00 1.63
2689 3467 4.481368 AAATAGTGCCAACGGTCAGATA 57.519 40.909 0.00 0.00 0.00 1.98
2693 3471 5.968528 ATTAAAAATAGTGCCAACGGTCA 57.031 34.783 0.00 0.00 0.00 4.02
2697 3475 7.169982 TCCAAACAATTAAAAATAGTGCCAACG 59.830 33.333 0.00 0.00 0.00 4.10
2702 3480 8.720562 AGCAATCCAAACAATTAAAAATAGTGC 58.279 29.630 0.00 0.00 0.00 4.40
2707 3485 9.566432 TGGTAAGCAATCCAAACAATTAAAAAT 57.434 25.926 0.00 0.00 0.00 1.82
2747 3770 1.959042 AAGTGCCAACAGTGAGACAG 58.041 50.000 0.00 0.00 0.00 3.51
2832 3855 1.440618 TGTCCTAGTCAAAGGCCCAA 58.559 50.000 0.00 0.00 36.51 4.12
2876 3899 7.443272 CCAGTATAAAACTTTACGGGGGAATAG 59.557 40.741 0.00 0.00 35.76 1.73
2897 3920 4.997395 GTCTTTCTTCTGCATTCACCAGTA 59.003 41.667 0.00 0.00 0.00 2.74
2898 3921 3.817647 GTCTTTCTTCTGCATTCACCAGT 59.182 43.478 0.00 0.00 0.00 4.00
2900 3923 2.807967 CGTCTTTCTTCTGCATTCACCA 59.192 45.455 0.00 0.00 0.00 4.17
2910 3943 5.368989 AGGAAACATCAACGTCTTTCTTCT 58.631 37.500 0.00 0.00 0.00 2.85
2956 3989 6.810182 CCAATCCTTGCAAGAACTTCTTTATG 59.190 38.462 28.05 6.32 33.78 1.90
2972 4005 7.279981 TCACGTATTAGATGAAACCAATCCTTG 59.720 37.037 0.00 0.00 0.00 3.61
2994 4027 4.914291 GGAAACGCCAAAGTCACG 57.086 55.556 0.00 0.00 36.34 4.35
3013 4046 3.431725 CAGCCCGCGTCCCTTTTC 61.432 66.667 4.92 0.00 0.00 2.29
3022 4055 0.179189 GTCAAAATTCTCAGCCCGCG 60.179 55.000 0.00 0.00 0.00 6.46
3024 4057 3.923017 AAAGTCAAAATTCTCAGCCCG 57.077 42.857 0.00 0.00 0.00 6.13
3053 4087 5.700832 GGACTGTGACTACATGATCAAACAA 59.299 40.000 0.00 0.00 35.97 2.83
3067 4101 5.000570 ACTTAGGAGTTAGGACTGTGACT 57.999 43.478 0.00 0.00 35.88 3.41
3078 4112 6.152932 ACTTTTGACACGACTTAGGAGTTA 57.847 37.500 0.00 0.00 35.88 2.24
3080 4114 4.667519 ACTTTTGACACGACTTAGGAGT 57.332 40.909 0.00 0.00 39.32 3.85
3081 4115 5.050295 GGAAACTTTTGACACGACTTAGGAG 60.050 44.000 0.00 0.00 0.00 3.69
3082 4116 4.812626 GGAAACTTTTGACACGACTTAGGA 59.187 41.667 0.00 0.00 0.00 2.94
3083 4117 4.024302 GGGAAACTTTTGACACGACTTAGG 60.024 45.833 0.00 0.00 0.00 2.69
3084 4118 4.814771 AGGGAAACTTTTGACACGACTTAG 59.185 41.667 0.00 0.00 0.00 2.18
3085 4119 4.773013 AGGGAAACTTTTGACACGACTTA 58.227 39.130 0.00 0.00 0.00 2.24
3086 4120 3.617284 AGGGAAACTTTTGACACGACTT 58.383 40.909 0.00 0.00 0.00 3.01
3087 4121 3.277142 AGGGAAACTTTTGACACGACT 57.723 42.857 0.00 0.00 0.00 4.18
3106 4140 5.964958 ATGCATTTCCGTCCCATTAATAG 57.035 39.130 0.00 0.00 0.00 1.73
3108 4142 4.766891 CCTATGCATTTCCGTCCCATTAAT 59.233 41.667 3.54 0.00 0.00 1.40
3110 4144 3.497763 CCCTATGCATTTCCGTCCCATTA 60.498 47.826 3.54 0.00 0.00 1.90
3118 4152 1.597742 CACTCCCCTATGCATTTCCG 58.402 55.000 3.54 0.00 0.00 4.30
3126 4160 1.227380 GCACTCGCACTCCCCTATG 60.227 63.158 0.00 0.00 38.36 2.23
3161 4195 3.126858 GGATTGACTTACTGCGCAAATCA 59.873 43.478 22.97 14.76 0.00 2.57
3166 4200 0.739462 CGGGATTGACTTACTGCGCA 60.739 55.000 10.98 10.98 0.00 6.09
3168 4202 1.659098 GTTCGGGATTGACTTACTGCG 59.341 52.381 0.00 0.00 0.00 5.18
3176 4210 2.094182 TGTGCTCTAGTTCGGGATTGAC 60.094 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.