Multiple sequence alignment - TraesCS2B01G180800

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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 TraesCS2B01G180800 chr2B 100.000 5701 0 0 1 5701 154935633 154929933 0.000000e+00 10528.0
1 TraesCS2B01G180800 chr2B 89.249 493 47 6 4314 4803 154503710 154504199 3.780000e-171 612.0
2 TraesCS2B01G180800 chr2B 83.897 621 65 22 2510 3112 549346538 549345935 1.390000e-155 560.0
3 TraesCS2B01G180800 chr2B 85.888 411 41 11 5249 5655 154907219 154906822 6.830000e-114 422.0
4 TraesCS2B01G180800 chr2B 85.387 349 35 10 4850 5185 154504207 154504552 1.180000e-91 348.0
5 TraesCS2B01G180800 chr2B 91.632 239 17 3 5410 5646 154490558 154490795 1.530000e-85 327.0
6 TraesCS2B01G180800 chr2B 85.948 306 36 6 2102 2407 549346837 549346539 2.560000e-83 320.0
7 TraesCS2B01G180800 chr2B 93.571 140 7 1 1964 2103 154500509 154500646 2.080000e-49 207.0
8 TraesCS2B01G180800 chr2B 91.954 87 7 0 4229 4315 154503463 154503549 7.760000e-24 122.0
9 TraesCS2B01G180800 chr2B 83.333 120 8 5 4093 4211 154503270 154503378 3.630000e-17 100.0
10 TraesCS2B01G180800 chr2B 96.429 56 2 0 1909 1964 154933670 154933615 6.080000e-15 93.5
11 TraesCS2B01G180800 chr2B 96.429 56 2 0 1964 2019 154933725 154933670 6.080000e-15 93.5
12 TraesCS2B01G180800 chr2D 92.596 2053 116 25 3170 5204 106267837 106265803 0.000000e+00 2916.0
13 TraesCS2B01G180800 chr2D 95.403 1153 41 9 819 1964 106269063 106267916 0.000000e+00 1825.0
14 TraesCS2B01G180800 chr2D 83.985 1074 107 37 3170 4211 102944631 102945671 0.000000e+00 970.0
15 TraesCS2B01G180800 chr2D 91.410 454 31 5 4489 4940 102954065 102954512 2.920000e-172 616.0
16 TraesCS2B01G180800 chr2D 88.235 374 35 5 5276 5647 106265738 106265372 6.780000e-119 438.0
17 TraesCS2B01G180800 chr2D 83.797 395 44 6 5258 5649 102954831 102955208 1.950000e-94 357.0
18 TraesCS2B01G180800 chr2D 90.756 238 18 4 5410 5645 102944000 102944235 1.190000e-81 315.0
19 TraesCS2B01G180800 chr2D 88.672 256 24 5 5393 5645 103130165 103129912 2.000000e-79 307.0
20 TraesCS2B01G180800 chr2D 88.936 235 25 1 5407 5641 103147789 103147556 7.230000e-74 289.0
21 TraesCS2B01G180800 chr2D 86.939 245 31 1 4229 4472 102945756 102946000 2.020000e-69 274.0
22 TraesCS2B01G180800 chr2D 88.034 234 22 6 5415 5645 181440383 181440613 7.280000e-69 272.0
23 TraesCS2B01G180800 chr2D 87.946 224 25 2 5418 5641 99658527 99658748 4.380000e-66 263.0
24 TraesCS2B01G180800 chr2D 85.714 259 26 8 4935 5185 102954580 102954835 4.380000e-66 263.0
25 TraesCS2B01G180800 chr2D 97.872 141 2 1 1964 2103 106267972 106267832 5.710000e-60 243.0
26 TraesCS2B01G180800 chr2D 90.909 143 10 2 1964 2103 102944494 102944636 7.540000e-44 189.0
27 TraesCS2B01G180800 chr2D 90.826 109 3 4 713 816 106270260 106270154 7.700000e-29 139.0
28 TraesCS2B01G180800 chr2A 93.187 1277 57 20 711 1964 102683365 102682096 0.000000e+00 1849.0
29 TraesCS2B01G180800 chr2A 88.942 1040 58 22 2100 3109 691732221 691733233 0.000000e+00 1230.0
30 TraesCS2B01G180800 chr2A 87.653 980 70 28 4229 5184 102680955 102680003 0.000000e+00 1092.0
31 TraesCS2B01G180800 chr2A 85.585 992 96 26 4229 5203 102042345 102043306 0.000000e+00 996.0
32 TraesCS2B01G180800 chr2A 82.781 784 65 33 3170 3916 102035460 102036210 2.240000e-178 636.0
33 TraesCS2B01G180800 chr2A 92.444 450 26 5 3784 4226 102681472 102681024 2.240000e-178 636.0
34 TraesCS2B01G180800 chr2A 85.234 535 46 13 3171 3697 102682015 102681506 2.350000e-143 520.0
35 TraesCS2B01G180800 chr2A 87.621 412 42 5 5238 5647 102679545 102679141 2.400000e-128 470.0
36 TraesCS2B01G180800 chr2A 88.235 357 27 10 5291 5645 102043332 102043675 4.110000e-111 412.0
37 TraesCS2B01G180800 chr2A 88.312 231 25 2 5412 5641 102325475 102325246 5.630000e-70 276.0
38 TraesCS2B01G180800 chr2A 90.780 141 12 1 1964 2103 102682151 102682011 2.710000e-43 187.0
39 TraesCS2B01G180800 chr2A 89.286 140 8 2 1964 2103 102035333 102035465 9.820000e-38 169.0
40 TraesCS2B01G180800 chr2A 86.364 110 10 2 1840 1944 102035259 102035368 1.300000e-21 115.0
41 TraesCS2B01G180800 chr2A 96.721 61 2 0 3115 3175 691733267 691733327 1.010000e-17 102.0
42 TraesCS2B01G180800 chr5B 95.360 1013 44 3 2102 3112 586055899 586054888 0.000000e+00 1607.0
43 TraesCS2B01G180800 chr5B 88.154 726 71 9 1 717 508340208 508340927 0.000000e+00 850.0
44 TraesCS2B01G180800 chr5B 93.443 61 4 0 3115 3175 586054857 586054797 2.190000e-14 91.6
45 TraesCS2B01G180800 chr6A 91.325 1049 49 26 2099 3109 445970172 445971216 0.000000e+00 1395.0
46 TraesCS2B01G180800 chr6A 89.418 1049 56 28 2099 3112 479887550 479886522 0.000000e+00 1271.0
47 TraesCS2B01G180800 chr4A 90.204 735 63 9 1 729 712107986 712107255 0.000000e+00 950.0
48 TraesCS2B01G180800 chr4A 89.365 724 64 10 1 718 712456678 712457394 0.000000e+00 898.0
49 TraesCS2B01G180800 chr4A 88.842 717 70 8 1 714 743654442 743653733 0.000000e+00 872.0
50 TraesCS2B01G180800 chr4A 87.552 241 28 2 2094 2332 40247226 40247466 1.560000e-70 278.0
51 TraesCS2B01G180800 chr7B 88.707 735 73 9 1 729 726460034 726459304 0.000000e+00 889.0
52 TraesCS2B01G180800 chr6B 88.982 717 70 9 1 714 689949821 689950531 0.000000e+00 878.0
53 TraesCS2B01G180800 chr6B 87.741 726 72 11 1 716 584113497 584114215 0.000000e+00 832.0
54 TraesCS2B01G180800 chr3B 88.649 696 72 5 1 695 767665859 767665170 0.000000e+00 841.0
55 TraesCS2B01G180800 chr3B 88.506 696 72 5 1 695 767629504 767628816 0.000000e+00 835.0
56 TraesCS2B01G180800 chr5A 86.572 633 47 18 2132 2747 282743189 282743800 0.000000e+00 664.0
57 TraesCS2B01G180800 chr5A 87.448 239 25 5 5410 5645 10860503 10860739 2.620000e-68 270.0
58 TraesCS2B01G180800 chr4D 88.000 250 27 3 2093 2340 424471817 424471569 5.590000e-75 292.0
59 TraesCS2B01G180800 chr4D 88.554 166 15 4 5494 5655 419197728 419197893 1.250000e-46 198.0
60 TraesCS2B01G180800 chr4D 96.330 109 4 0 5495 5603 326385041 326385149 4.540000e-41 180.0
61 TraesCS2B01G180800 chr4D 86.275 153 19 2 5477 5629 336842530 336842380 1.270000e-36 165.0
62 TraesCS2B01G180800 chr4B 87.200 250 30 2 2093 2340 520402244 520401995 3.360000e-72 283.0
63 TraesCS2B01G180800 chr1B 87.607 234 27 2 5413 5645 17392140 17391908 2.620000e-68 270.0
64 TraesCS2B01G180800 chr5D 85.232 237 23 10 5410 5642 13788840 13789068 3.430000e-57 233.0
65 TraesCS2B01G180800 chr5D 83.404 235 33 5 5415 5646 478156885 478156654 4.470000e-51 213.0
66 TraesCS2B01G180800 chr3D 84.681 235 32 4 5414 5646 546254138 546254370 1.240000e-56 231.0
67 TraesCS2B01G180800 chr1A 83.186 226 33 5 5414 5638 372248374 372248595 9.690000e-48 202.0
68 TraesCS2B01G180800 chr1A 85.443 158 17 4 5491 5644 552214681 552214526 5.910000e-35 159.0
69 TraesCS2B01G180800 chr1A 100.000 30 0 0 2441 2470 159167026 159166997 7.980000e-04 56.5
70 TraesCS2B01G180800 chr1D 84.772 197 23 7 5414 5607 298576179 298576371 2.100000e-44 191.0
71 TraesCS2B01G180800 chr1D 97.248 109 3 0 5490 5598 478274036 478273928 9.750000e-43 185.0
72 TraesCS2B01G180800 chr1D 85.915 142 14 5 5491 5628 461141267 461141128 4.600000e-31 147.0
73 TraesCS2B01G180800 chr6D 85.507 138 10 9 5499 5631 97353508 97353376 9.960000e-28 135.0
74 TraesCS2B01G180800 chr6D 87.387 111 11 3 5499 5607 97552776 97552667 2.160000e-24 124.0


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 TraesCS2B01G180800 chr2B 154929933 154935633 5700 True 3571.666667 10528 97.619333 1 5701 3 chr2B.!!$R2 5700
1 TraesCS2B01G180800 chr2B 549345935 549346837 902 True 440.000000 560 84.922500 2102 3112 2 chr2B.!!$R3 1010
2 TraesCS2B01G180800 chr2B 154500509 154504552 4043 False 277.800000 612 88.698800 1964 5185 5 chr2B.!!$F2 3221
3 TraesCS2B01G180800 chr2D 106265372 106270260 4888 True 1112.200000 2916 92.986400 713 5647 5 chr2D.!!$R3 4934
4 TraesCS2B01G180800 chr2D 102944000 102946000 2000 False 437.000000 970 88.147250 1964 5645 4 chr2D.!!$F3 3681
5 TraesCS2B01G180800 chr2D 102954065 102955208 1143 False 412.000000 616 86.973667 4489 5649 3 chr2D.!!$F4 1160
6 TraesCS2B01G180800 chr2A 102679141 102683365 4224 True 792.333333 1849 89.486500 711 5647 6 chr2A.!!$R2 4936
7 TraesCS2B01G180800 chr2A 102042345 102043675 1330 False 704.000000 996 86.910000 4229 5645 2 chr2A.!!$F2 1416
8 TraesCS2B01G180800 chr2A 691732221 691733327 1106 False 666.000000 1230 92.831500 2100 3175 2 chr2A.!!$F3 1075
9 TraesCS2B01G180800 chr2A 102035259 102036210 951 False 306.666667 636 86.143667 1840 3916 3 chr2A.!!$F1 2076
10 TraesCS2B01G180800 chr5B 508340208 508340927 719 False 850.000000 850 88.154000 1 717 1 chr5B.!!$F1 716
11 TraesCS2B01G180800 chr5B 586054797 586055899 1102 True 849.300000 1607 94.401500 2102 3175 2 chr5B.!!$R1 1073
12 TraesCS2B01G180800 chr6A 445970172 445971216 1044 False 1395.000000 1395 91.325000 2099 3109 1 chr6A.!!$F1 1010
13 TraesCS2B01G180800 chr6A 479886522 479887550 1028 True 1271.000000 1271 89.418000 2099 3112 1 chr6A.!!$R1 1013
14 TraesCS2B01G180800 chr4A 712107255 712107986 731 True 950.000000 950 90.204000 1 729 1 chr4A.!!$R1 728
15 TraesCS2B01G180800 chr4A 712456678 712457394 716 False 898.000000 898 89.365000 1 718 1 chr4A.!!$F2 717
16 TraesCS2B01G180800 chr4A 743653733 743654442 709 True 872.000000 872 88.842000 1 714 1 chr4A.!!$R2 713
17 TraesCS2B01G180800 chr7B 726459304 726460034 730 True 889.000000 889 88.707000 1 729 1 chr7B.!!$R1 728
18 TraesCS2B01G180800 chr6B 689949821 689950531 710 False 878.000000 878 88.982000 1 714 1 chr6B.!!$F2 713
19 TraesCS2B01G180800 chr6B 584113497 584114215 718 False 832.000000 832 87.741000 1 716 1 chr6B.!!$F1 715
20 TraesCS2B01G180800 chr3B 767665170 767665859 689 True 841.000000 841 88.649000 1 695 1 chr3B.!!$R2 694
21 TraesCS2B01G180800 chr3B 767628816 767629504 688 True 835.000000 835 88.506000 1 695 1 chr3B.!!$R1 694
22 TraesCS2B01G180800 chr5A 282743189 282743800 611 False 664.000000 664 86.572000 2132 2747 1 chr5A.!!$F2 615

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
890 2003 0.030638 CACAAACCTCAACAAGCCCG 59.969 55.000 0.00 0.0 0.00 6.13 F
1830 2964 0.034574 TTCGGGGGTCATGTCATTGG 60.035 55.000 0.00 0.0 0.00 3.16 F
1834 2968 0.323725 GGGGTCATGTCATTGGCAGT 60.324 55.000 0.00 0.0 0.00 4.40 F
2963 4276 0.677098 CGACGAGGGAGAAGTGAGGA 60.677 60.000 0.00 0.0 0.00 3.71 F
3113 4426 0.906775 GAACGGGTGGGTTCCTATGA 59.093 55.000 0.00 0.0 40.28 2.15 F
3981 7047 1.068588 TCACTGTGTCAGCTAGCGTTT 59.931 47.619 9.55 0.0 34.37 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 3086 0.032017 ATCAGCCTACCCCGTTCTCT 60.032 55.000 0.00 0.00 0.00 3.10 R
3137 4478 0.175760 CCGATCATCAGGTGGAACGT 59.824 55.000 0.00 0.00 38.12 3.99 R
3652 5025 4.395231 TCTGACTCTACATCACACCTTACG 59.605 45.833 0.00 0.00 0.00 3.18 R
3960 7026 0.039074 ACGCTAGCTGACACAGTGAC 60.039 55.000 13.93 0.92 33.43 3.67 R
3990 7056 0.546598 ACCCCTATTGTGCCTACTGC 59.453 55.000 0.00 0.00 41.77 4.40 R
5658 9569 0.316204 GAGCACACCAGCTTTGCATT 59.684 50.000 8.61 0.00 46.75 3.56 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
54 55 0.250124 TCGTCATCAACAAAGGCGGT 60.250 50.000 0.00 0.00 0.00 5.68
481 483 5.281609 GCGTTCAGCGATTTCTTCTTTTAAG 59.718 40.000 0.00 0.00 44.77 1.85
691 710 1.226262 GATTTTAGGCGCCCCTGGA 59.774 57.895 26.15 6.15 42.90 3.86
706 725 0.538057 CTGGAGGCCAACAGCTGAAA 60.538 55.000 23.35 0.00 43.05 2.69
889 2002 1.067060 GTCACAAACCTCAACAAGCCC 59.933 52.381 0.00 0.00 0.00 5.19
890 2003 0.030638 CACAAACCTCAACAAGCCCG 59.969 55.000 0.00 0.00 0.00 6.13
891 2004 0.395173 ACAAACCTCAACAAGCCCGT 60.395 50.000 0.00 0.00 0.00 5.28
892 2005 0.310854 CAAACCTCAACAAGCCCGTC 59.689 55.000 0.00 0.00 0.00 4.79
893 2006 0.822121 AAACCTCAACAAGCCCGTCC 60.822 55.000 0.00 0.00 0.00 4.79
894 2007 2.359975 CCTCAACAAGCCCGTCCC 60.360 66.667 0.00 0.00 0.00 4.46
895 2008 2.359975 CTCAACAAGCCCGTCCCC 60.360 66.667 0.00 0.00 0.00 4.81
896 2009 2.852075 TCAACAAGCCCGTCCCCT 60.852 61.111 0.00 0.00 0.00 4.79
1261 2389 0.818296 CGTCTCCCTCAGGGTAAGTG 59.182 60.000 10.50 0.00 44.74 3.16
1602 2730 1.975407 CCCTTGGGCTGCTCACTTG 60.975 63.158 0.00 0.00 0.00 3.16
1653 2781 7.761409 TCTGTTGTTTCATATGGCTGAATTAC 58.239 34.615 2.13 0.00 35.20 1.89
1662 2790 2.408565 TGGCTGAATTACCCCTCTAGG 58.591 52.381 0.00 0.00 0.00 3.02
1676 2804 9.956558 TTACCCCTCTAGGTAATATAGTTTTGA 57.043 33.333 0.00 0.00 45.41 2.69
1783 2915 8.420222 TGGATGTGAAATAAATTGTGAGTTTGT 58.580 29.630 0.00 0.00 0.00 2.83
1830 2964 0.034574 TTCGGGGGTCATGTCATTGG 60.035 55.000 0.00 0.00 0.00 3.16
1834 2968 0.323725 GGGGTCATGTCATTGGCAGT 60.324 55.000 0.00 0.00 0.00 4.40
1910 3049 8.934023 AGGACTGGTAGATTTTGTAAATTTGA 57.066 30.769 0.00 0.00 0.00 2.69
1911 3050 9.533831 AGGACTGGTAGATTTTGTAAATTTGAT 57.466 29.630 0.00 0.00 0.00 2.57
1912 3051 9.788960 GGACTGGTAGATTTTGTAAATTTGATC 57.211 33.333 0.00 0.00 0.00 2.92
1913 3052 9.490663 GACTGGTAGATTTTGTAAATTTGATCG 57.509 33.333 0.00 0.00 0.00 3.69
1914 3053 9.226606 ACTGGTAGATTTTGTAAATTTGATCGA 57.773 29.630 0.00 0.00 0.00 3.59
1931 3070 8.662781 TTTGATCGAATTATTCAGTTCTAGGG 57.337 34.615 5.76 0.00 0.00 3.53
1932 3071 7.361457 TGATCGAATTATTCAGTTCTAGGGT 57.639 36.000 5.76 0.00 0.00 4.34
1933 3072 8.473358 TGATCGAATTATTCAGTTCTAGGGTA 57.527 34.615 5.76 0.00 0.00 3.69
1934 3073 9.090103 TGATCGAATTATTCAGTTCTAGGGTAT 57.910 33.333 5.76 0.00 0.00 2.73
1935 3074 9.360093 GATCGAATTATTCAGTTCTAGGGTATG 57.640 37.037 5.76 0.00 0.00 2.39
1936 3075 7.152645 TCGAATTATTCAGTTCTAGGGTATGC 58.847 38.462 5.76 0.00 0.00 3.14
1937 3076 7.015292 TCGAATTATTCAGTTCTAGGGTATGCT 59.985 37.037 5.76 0.00 0.00 3.79
1938 3077 7.116948 CGAATTATTCAGTTCTAGGGTATGCTG 59.883 40.741 5.76 0.00 0.00 4.41
1939 3078 7.618019 ATTATTCAGTTCTAGGGTATGCTGA 57.382 36.000 0.00 0.00 0.00 4.26
1940 3079 5.957771 ATTCAGTTCTAGGGTATGCTGAA 57.042 39.130 7.16 7.16 43.88 3.02
1941 3080 5.755409 TTCAGTTCTAGGGTATGCTGAAA 57.245 39.130 0.00 0.00 39.18 2.69
1942 3081 5.957771 TCAGTTCTAGGGTATGCTGAAAT 57.042 39.130 0.00 0.00 31.14 2.17
1943 3082 6.313519 TCAGTTCTAGGGTATGCTGAAATT 57.686 37.500 0.00 0.00 31.14 1.82
1944 3083 6.721318 TCAGTTCTAGGGTATGCTGAAATTT 58.279 36.000 0.00 0.00 31.14 1.82
1945 3084 7.175104 TCAGTTCTAGGGTATGCTGAAATTTT 58.825 34.615 0.00 0.00 31.14 1.82
1946 3085 8.325787 TCAGTTCTAGGGTATGCTGAAATTTTA 58.674 33.333 0.00 0.00 31.14 1.52
1947 3086 8.956426 CAGTTCTAGGGTATGCTGAAATTTTAA 58.044 33.333 0.00 0.00 0.00 1.52
1948 3087 9.178758 AGTTCTAGGGTATGCTGAAATTTTAAG 57.821 33.333 0.00 0.00 0.00 1.85
1949 3088 9.174166 GTTCTAGGGTATGCTGAAATTTTAAGA 57.826 33.333 0.00 0.00 0.00 2.10
1950 3089 8.964476 TCTAGGGTATGCTGAAATTTTAAGAG 57.036 34.615 0.00 0.00 0.00 2.85
1951 3090 8.768397 TCTAGGGTATGCTGAAATTTTAAGAGA 58.232 33.333 0.00 0.00 0.00 3.10
1952 3091 9.396022 CTAGGGTATGCTGAAATTTTAAGAGAA 57.604 33.333 0.00 0.00 0.00 2.87
1953 3092 8.056407 AGGGTATGCTGAAATTTTAAGAGAAC 57.944 34.615 0.00 0.00 0.00 3.01
1954 3093 6.967199 GGGTATGCTGAAATTTTAAGAGAACG 59.033 38.462 0.00 0.00 0.00 3.95
1955 3094 6.967199 GGTATGCTGAAATTTTAAGAGAACGG 59.033 38.462 0.00 0.00 0.00 4.44
1956 3095 5.371115 TGCTGAAATTTTAAGAGAACGGG 57.629 39.130 0.00 0.00 0.00 5.28
1957 3096 4.217550 TGCTGAAATTTTAAGAGAACGGGG 59.782 41.667 0.00 0.00 0.00 5.73
1958 3097 4.217767 GCTGAAATTTTAAGAGAACGGGGT 59.782 41.667 0.00 0.00 0.00 4.95
1959 3098 5.413523 GCTGAAATTTTAAGAGAACGGGGTA 59.586 40.000 0.00 0.00 0.00 3.69
1960 3099 6.403309 GCTGAAATTTTAAGAGAACGGGGTAG 60.403 42.308 0.00 0.00 0.00 3.18
1961 3100 5.941647 TGAAATTTTAAGAGAACGGGGTAGG 59.058 40.000 0.00 0.00 0.00 3.18
1962 3101 3.339253 TTTTAAGAGAACGGGGTAGGC 57.661 47.619 0.00 0.00 0.00 3.93
2000 3195 7.175104 TCAGTTCTAGGGTATGCTGAAATTTT 58.825 34.615 0.00 0.00 31.14 1.82
2001 3196 8.325787 TCAGTTCTAGGGTATGCTGAAATTTTA 58.674 33.333 0.00 0.00 31.14 1.52
2002 3197 8.956426 CAGTTCTAGGGTATGCTGAAATTTTAA 58.044 33.333 0.00 0.00 0.00 1.52
2003 3198 9.178758 AGTTCTAGGGTATGCTGAAATTTTAAG 57.821 33.333 0.00 0.00 0.00 1.85
2004 3199 9.174166 GTTCTAGGGTATGCTGAAATTTTAAGA 57.826 33.333 0.00 0.00 0.00 2.10
2005 3200 8.964476 TCTAGGGTATGCTGAAATTTTAAGAG 57.036 34.615 0.00 0.00 0.00 2.85
2006 3201 8.768397 TCTAGGGTATGCTGAAATTTTAAGAGA 58.232 33.333 0.00 0.00 0.00 3.10
2007 3202 9.396022 CTAGGGTATGCTGAAATTTTAAGAGAA 57.604 33.333 0.00 0.00 0.00 2.87
2008 3203 8.829373 AGGGTATGCTGAAATTTTAAGAGAAT 57.171 30.769 0.00 0.00 0.00 2.40
2009 3204 8.689972 AGGGTATGCTGAAATTTTAAGAGAATG 58.310 33.333 0.00 0.00 0.00 2.67
2623 3859 1.832883 AAGGAAGCACACACACACAA 58.167 45.000 0.00 0.00 0.00 3.33
2958 4271 1.001887 AGAGCGACGAGGGAGAAGT 60.002 57.895 0.00 0.00 0.00 3.01
2963 4276 0.677098 CGACGAGGGAGAAGTGAGGA 60.677 60.000 0.00 0.00 0.00 3.71
2964 4277 1.099689 GACGAGGGAGAAGTGAGGAG 58.900 60.000 0.00 0.00 0.00 3.69
2970 4283 3.378399 GAGAAGTGAGGAGGCCGCC 62.378 68.421 19.43 19.43 0.00 6.13
3076 4389 2.330254 CGCATTCCGCATATTGGGT 58.670 52.632 0.00 0.00 42.60 4.51
3093 4406 1.134220 GGGTGAATATGCCGTTCCTGA 60.134 52.381 0.00 0.00 0.00 3.86
3112 4425 0.909623 AGAACGGGTGGGTTCCTATG 59.090 55.000 2.10 0.00 45.82 2.23
3113 4426 0.906775 GAACGGGTGGGTTCCTATGA 59.093 55.000 0.00 0.00 40.28 2.15
3359 4713 7.094975 GGTTGTAGTATGCATCTGTGTTGTTTA 60.095 37.037 0.19 0.00 0.00 2.01
3417 4772 5.218139 CAGTTCTTGCAAGTCAATCTTTCC 58.782 41.667 25.19 1.73 33.63 3.13
3516 4888 5.569059 GGTAAAATGTGTTCTGATTTGCTCG 59.431 40.000 0.00 0.00 0.00 5.03
3596 4968 8.296713 TGTATGTTCTGTTAGGCATTTTTCTTC 58.703 33.333 0.00 0.00 0.00 2.87
3624 4997 9.733556 TTGGTTCTGTATGTTATTGTACTTGAT 57.266 29.630 0.00 0.00 0.00 2.57
3625 4998 9.733556 TGGTTCTGTATGTTATTGTACTTGATT 57.266 29.630 0.00 0.00 0.00 2.57
3626 4999 9.988350 GGTTCTGTATGTTATTGTACTTGATTG 57.012 33.333 0.00 0.00 0.00 2.67
3729 6744 2.423538 GCTTTTGGTGTCTCGCCATATT 59.576 45.455 2.86 0.00 43.92 1.28
3730 6745 3.119495 GCTTTTGGTGTCTCGCCATATTT 60.119 43.478 2.86 0.00 43.92 1.40
3731 6746 4.662145 CTTTTGGTGTCTCGCCATATTTC 58.338 43.478 2.86 0.00 43.92 2.17
3732 6747 2.325583 TGGTGTCTCGCCATATTTCC 57.674 50.000 0.00 0.00 39.28 3.13
3733 6748 1.557371 TGGTGTCTCGCCATATTTCCA 59.443 47.619 0.00 0.00 39.28 3.53
3734 6749 2.026729 TGGTGTCTCGCCATATTTCCAA 60.027 45.455 0.00 0.00 39.28 3.53
3735 6750 3.013921 GGTGTCTCGCCATATTTCCAAA 58.986 45.455 0.00 0.00 33.65 3.28
3736 6751 3.065371 GGTGTCTCGCCATATTTCCAAAG 59.935 47.826 0.00 0.00 33.65 2.77
3737 6752 3.938963 GTGTCTCGCCATATTTCCAAAGA 59.061 43.478 0.00 0.00 0.00 2.52
3738 6753 4.034510 GTGTCTCGCCATATTTCCAAAGAG 59.965 45.833 0.00 0.00 0.00 2.85
3739 6754 3.561725 GTCTCGCCATATTTCCAAAGAGG 59.438 47.826 0.00 0.00 39.47 3.69
3761 6776 8.910944 AGAGGGCAATATATGAATTTGATATGC 58.089 33.333 0.00 0.00 0.00 3.14
3862 6896 1.774217 AAAGGAGACCCAGTGCCCA 60.774 57.895 0.00 0.00 33.88 5.36
3896 6931 9.581289 TTTTATCTCTCAGAAATTGGGTGTTTA 57.419 29.630 0.00 0.00 0.00 2.01
3981 7047 1.068588 TCACTGTGTCAGCTAGCGTTT 59.931 47.619 9.55 0.00 34.37 3.60
3990 7056 4.447724 TGTCAGCTAGCGTTTGTTCTTAAG 59.552 41.667 9.55 0.00 0.00 1.85
4100 7167 5.005779 GTGAGCACGGTCTTAATATGAACAG 59.994 44.000 0.00 0.00 0.00 3.16
4260 7432 4.471904 TTCGTCATAGGATCAGCTGTTT 57.528 40.909 14.67 2.24 0.00 2.83
4329 7663 6.041409 TGAAGAAGCTAGAGGATACCATCAAG 59.959 42.308 0.00 0.00 37.17 3.02
4372 7706 8.714179 TGTTTTATCTACGTGAAAGGTACAATG 58.286 33.333 0.00 0.00 35.89 2.82
4405 7739 9.827411 GTTATTTCTAGCTCTGGTAAAACTTTG 57.173 33.333 0.00 0.00 0.00 2.77
4461 7798 2.034558 AGTTTTTGGCCTGTCATTCGTG 59.965 45.455 3.32 0.00 0.00 4.35
4762 8116 2.806608 ATTGTTTCTGCCAGCTGTTG 57.193 45.000 13.81 0.00 0.00 3.33
4786 8140 5.497474 ACCTATGTTTCCAAGCGAATACTT 58.503 37.500 0.00 0.00 0.00 2.24
4812 8167 5.374071 ACCATCAGTAAGAAAGAAACCGTT 58.626 37.500 0.00 0.00 0.00 4.44
4858 8213 3.107402 TCTGTGCCCTATCTTCTGTCT 57.893 47.619 0.00 0.00 0.00 3.41
4933 8291 8.816640 AAATGTTTCTGTTGATGGTTTCATAC 57.183 30.769 0.00 0.00 33.34 2.39
4956 8387 2.256174 TGTAACGTAGAGCGACATTGC 58.744 47.619 0.00 0.00 44.77 3.56
4970 8401 5.121454 AGCGACATTGCTTCTTTTTCTAGAG 59.879 40.000 0.00 0.00 44.46 2.43
4971 8402 5.319931 CGACATTGCTTCTTTTTCTAGAGC 58.680 41.667 0.00 0.00 0.00 4.09
4972 8403 5.121454 CGACATTGCTTCTTTTTCTAGAGCT 59.879 40.000 0.00 0.00 0.00 4.09
4973 8404 6.251655 ACATTGCTTCTTTTTCTAGAGCTG 57.748 37.500 0.00 0.00 0.00 4.24
4974 8405 5.767168 ACATTGCTTCTTTTTCTAGAGCTGT 59.233 36.000 0.00 0.00 0.00 4.40
4977 8408 6.346477 TGCTTCTTTTTCTAGAGCTGTAGA 57.654 37.500 16.23 16.23 0.00 2.59
4998 8433 4.684703 AGAACACATCGTTGCTACTGTTAC 59.315 41.667 4.19 0.66 38.19 2.50
4999 8434 3.985008 ACACATCGTTGCTACTGTTACA 58.015 40.909 0.00 0.00 0.00 2.41
5147 8595 8.349568 AGGAAGGAAAATATGTTACAAGGTTC 57.650 34.615 0.00 0.00 0.00 3.62
5149 8597 8.459635 GGAAGGAAAATATGTTACAAGGTTCTC 58.540 37.037 0.00 0.00 0.00 2.87
5178 8626 5.560966 TTTAGGAACGGATCAAATTCTGC 57.439 39.130 0.00 0.00 0.00 4.26
5188 8636 2.300433 TCAAATTCTGCTGTGTGTGCT 58.700 42.857 0.00 0.00 0.00 4.40
5204 8652 1.108727 TGCTGCACCCAAAAGGAGTG 61.109 55.000 0.00 0.00 39.89 3.51
5206 8654 1.402787 CTGCACCCAAAAGGAGTGTT 58.597 50.000 0.00 0.00 39.89 3.32
5207 8655 1.756538 CTGCACCCAAAAGGAGTGTTT 59.243 47.619 0.00 0.00 39.89 2.83
5208 8656 2.168313 CTGCACCCAAAAGGAGTGTTTT 59.832 45.455 0.00 0.00 39.89 2.43
5209 8657 2.569404 TGCACCCAAAAGGAGTGTTTTT 59.431 40.909 0.00 0.00 39.89 1.94
5266 9120 2.952310 GGAGTTGAAAAAGTGTGAGGCT 59.048 45.455 0.00 0.00 0.00 4.58
5315 9208 0.179116 CTGTCGAGTGGGCTGATCAG 60.179 60.000 18.84 18.84 0.00 2.90
5333 9226 1.044790 AGCTGGTTGGCCCATATTGC 61.045 55.000 0.00 0.00 44.15 3.56
5342 9235 2.944129 GGCCCATATTGCCTTTCTGTA 58.056 47.619 5.88 0.00 45.70 2.74
5351 9255 4.415881 TTGCCTTTCTGTAGTTCTGTGA 57.584 40.909 0.00 0.00 0.00 3.58
5379 9283 1.207593 GTGAAGCATGTGTGACGGC 59.792 57.895 0.00 0.00 0.00 5.68
5380 9284 1.227793 TGAAGCATGTGTGACGGCA 60.228 52.632 0.00 0.00 0.00 5.69
5381 9285 1.229975 TGAAGCATGTGTGACGGCAG 61.230 55.000 0.00 0.00 0.00 4.85
5382 9286 1.227943 AAGCATGTGTGACGGCAGT 60.228 52.632 0.00 0.00 0.00 4.40
5592 9503 9.238368 ACACTAAGCAGCATACCTTAATTTTTA 57.762 29.630 0.00 0.00 0.00 1.52
5624 9535 0.253630 TCCCTGTTAGAAGGCCCCAT 60.254 55.000 0.00 0.00 35.85 4.00
5629 9540 3.628257 CCTGTTAGAAGGCCCCATCAATT 60.628 47.826 0.00 0.00 0.00 2.32
5632 9543 4.476846 TGTTAGAAGGCCCCATCAATTCTA 59.523 41.667 0.00 1.19 32.69 2.10
5672 9583 9.585099 TTAAAATAAGATAATGCAAAGCTGGTG 57.415 29.630 0.00 0.00 0.00 4.17
5673 9584 6.780457 AATAAGATAATGCAAAGCTGGTGT 57.220 33.333 0.00 0.00 0.00 4.16
5674 9585 4.445452 AAGATAATGCAAAGCTGGTGTG 57.555 40.909 0.00 0.00 0.00 3.82
5675 9586 2.165030 AGATAATGCAAAGCTGGTGTGC 59.835 45.455 14.87 14.87 38.78 4.57
5676 9587 1.619654 TAATGCAAAGCTGGTGTGCT 58.380 45.000 21.34 6.31 46.40 4.40
5677 9588 0.316204 AATGCAAAGCTGGTGTGCTC 59.684 50.000 21.34 0.00 43.24 4.26
5678 9589 0.538977 ATGCAAAGCTGGTGTGCTCT 60.539 50.000 21.34 7.56 43.24 4.09
5679 9590 0.752743 TGCAAAGCTGGTGTGCTCTT 60.753 50.000 21.34 0.00 43.24 2.85
5680 9591 0.386838 GCAAAGCTGGTGTGCTCTTT 59.613 50.000 14.49 0.00 43.24 2.52
5681 9592 1.202452 GCAAAGCTGGTGTGCTCTTTT 60.202 47.619 14.49 0.00 43.24 2.27
5682 9593 2.034558 GCAAAGCTGGTGTGCTCTTTTA 59.965 45.455 14.49 0.00 43.24 1.52
5683 9594 3.854784 GCAAAGCTGGTGTGCTCTTTTAG 60.855 47.826 14.49 0.00 43.24 1.85
5684 9595 2.191128 AGCTGGTGTGCTCTTTTAGG 57.809 50.000 0.00 0.00 39.34 2.69
5685 9596 1.168714 GCTGGTGTGCTCTTTTAGGG 58.831 55.000 0.00 0.00 0.00 3.53
5686 9597 1.545651 GCTGGTGTGCTCTTTTAGGGT 60.546 52.381 0.00 0.00 0.00 4.34
5687 9598 2.863809 CTGGTGTGCTCTTTTAGGGTT 58.136 47.619 0.00 0.00 0.00 4.11
5688 9599 2.554032 CTGGTGTGCTCTTTTAGGGTTG 59.446 50.000 0.00 0.00 0.00 3.77
5689 9600 2.173782 TGGTGTGCTCTTTTAGGGTTGA 59.826 45.455 0.00 0.00 0.00 3.18
5690 9601 3.181434 TGGTGTGCTCTTTTAGGGTTGAT 60.181 43.478 0.00 0.00 0.00 2.57
5691 9602 3.191371 GGTGTGCTCTTTTAGGGTTGATG 59.809 47.826 0.00 0.00 0.00 3.07
5692 9603 4.072131 GTGTGCTCTTTTAGGGTTGATGA 58.928 43.478 0.00 0.00 0.00 2.92
5693 9604 4.518970 GTGTGCTCTTTTAGGGTTGATGAA 59.481 41.667 0.00 0.00 0.00 2.57
5694 9605 4.518970 TGTGCTCTTTTAGGGTTGATGAAC 59.481 41.667 0.00 0.00 0.00 3.18
5695 9606 4.762251 GTGCTCTTTTAGGGTTGATGAACT 59.238 41.667 0.00 0.00 32.15 3.01
5696 9607 5.003804 TGCTCTTTTAGGGTTGATGAACTC 58.996 41.667 0.00 0.00 31.98 3.01
5697 9608 5.221925 TGCTCTTTTAGGGTTGATGAACTCT 60.222 40.000 2.14 2.14 45.46 3.24
5698 9609 5.707764 GCTCTTTTAGGGTTGATGAACTCTT 59.292 40.000 1.74 0.00 40.24 2.85
5699 9610 6.348868 GCTCTTTTAGGGTTGATGAACTCTTG 60.349 42.308 1.74 0.00 40.24 3.02
5700 9611 6.003950 TCTTTTAGGGTTGATGAACTCTTGG 58.996 40.000 1.74 0.00 40.24 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 280 1.645704 CGACTCCTCCTTCTTCGCGA 61.646 60.000 3.71 3.71 0.00 5.87
438 439 2.733671 CGAGTAGTCGCCGTCGTCA 61.734 63.158 7.09 0.00 39.88 4.35
481 483 3.158103 TCACGACGCGTTTCATAAAAC 57.842 42.857 15.53 0.00 38.32 2.43
489 498 0.231279 GACATGTTCACGACGCGTTT 59.769 50.000 15.53 0.00 38.32 3.60
579 592 1.436983 CCCCAGGCGCGTCTAATTTC 61.437 60.000 15.40 0.00 0.00 2.17
628 642 0.259356 AAAAACGACCTGGGGTGGAA 59.741 50.000 5.77 0.00 35.25 3.53
629 643 1.924352 AAAAACGACCTGGGGTGGA 59.076 52.632 5.77 0.00 35.25 4.02
630 644 4.591038 AAAAACGACCTGGGGTGG 57.409 55.556 0.00 0.00 35.25 4.61
691 710 0.319405 GCATTTTCAGCTGTTGGCCT 59.681 50.000 14.67 0.00 43.05 5.19
706 725 8.209584 ACAACATGATGAGAGTATAAGAGCATT 58.790 33.333 10.29 0.00 0.00 3.56
834 1945 9.974750 GACTAAAAGTTGCAGTAGTATCAAATC 57.025 33.333 0.00 0.00 0.00 2.17
835 1946 9.502091 TGACTAAAAGTTGCAGTAGTATCAAAT 57.498 29.630 0.00 0.00 0.00 2.32
836 1947 8.896320 TGACTAAAAGTTGCAGTAGTATCAAA 57.104 30.769 0.00 0.00 0.00 2.69
838 1949 9.502091 AAATGACTAAAAGTTGCAGTAGTATCA 57.498 29.630 0.00 0.00 0.00 2.15
839 1950 9.760660 CAAATGACTAAAAGTTGCAGTAGTATC 57.239 33.333 0.00 0.00 0.00 2.24
840 1951 8.730680 CCAAATGACTAAAAGTTGCAGTAGTAT 58.269 33.333 0.00 0.00 0.00 2.12
842 1953 6.770785 TCCAAATGACTAAAAGTTGCAGTAGT 59.229 34.615 0.00 0.00 0.00 2.73
843 1954 7.078228 GTCCAAATGACTAAAAGTTGCAGTAG 58.922 38.462 0.00 0.00 41.03 2.57
844 1955 6.293190 CGTCCAAATGACTAAAAGTTGCAGTA 60.293 38.462 0.00 0.00 42.13 2.74
845 1956 5.505654 CGTCCAAATGACTAAAAGTTGCAGT 60.506 40.000 0.00 0.00 42.13 4.40
846 1957 4.911610 CGTCCAAATGACTAAAAGTTGCAG 59.088 41.667 0.00 0.00 42.13 4.41
847 1958 4.336993 ACGTCCAAATGACTAAAAGTTGCA 59.663 37.500 0.00 0.00 42.13 4.08
889 2002 2.764547 GGAGGGGAGAAGGGGACG 60.765 72.222 0.00 0.00 0.00 4.79
890 2003 1.383386 GAGGAGGGGAGAAGGGGAC 60.383 68.421 0.00 0.00 0.00 4.46
891 2004 2.647949 GGAGGAGGGGAGAAGGGGA 61.648 68.421 0.00 0.00 0.00 4.81
892 2005 2.040359 GGAGGAGGGGAGAAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
893 2006 2.040359 GGGAGGAGGGGAGAAGGG 60.040 72.222 0.00 0.00 0.00 3.95
894 2007 2.040359 GGGGAGGAGGGGAGAAGG 60.040 72.222 0.00 0.00 0.00 3.46
895 2008 0.766288 GATGGGGAGGAGGGGAGAAG 60.766 65.000 0.00 0.00 0.00 2.85
896 2009 1.318380 GATGGGGAGGAGGGGAGAA 59.682 63.158 0.00 0.00 0.00 2.87
979 2107 3.935024 CGGAGATCGGAGTGGGAA 58.065 61.111 0.00 0.00 34.75 3.97
1464 2592 2.515901 GGTGGCTTGTGGTCAGGT 59.484 61.111 0.00 0.00 0.00 4.00
1628 2756 6.839124 AATTCAGCCATATGAAACAACAGA 57.161 33.333 3.65 0.00 42.21 3.41
1629 2757 6.974622 GGTAATTCAGCCATATGAAACAACAG 59.025 38.462 3.65 0.00 42.21 3.16
1653 2781 7.291651 TGGTCAAAACTATATTACCTAGAGGGG 59.708 40.741 0.00 0.00 40.27 4.79
1676 2804 7.977853 GCAAATTCAATAGAATGAATCACTGGT 59.022 33.333 3.26 0.00 46.57 4.00
1725 2853 4.201990 CGTGGGTGACAGGTAGAGTATAAC 60.202 50.000 0.00 0.00 0.00 1.89
1783 2915 3.351794 TCATAATAACCCAACCACGCA 57.648 42.857 0.00 0.00 0.00 5.24
1830 2964 1.583404 CGAACTTGCAAACAACACTGC 59.417 47.619 0.00 0.00 39.09 4.40
1834 2968 2.486203 ACAGACGAACTTGCAAACAACA 59.514 40.909 0.00 0.00 0.00 3.33
1908 3047 7.361457 ACCCTAGAACTGAATAATTCGATCA 57.639 36.000 0.00 0.00 0.00 2.92
1909 3048 9.360093 CATACCCTAGAACTGAATAATTCGATC 57.640 37.037 0.00 0.00 0.00 3.69
1910 3049 7.819900 GCATACCCTAGAACTGAATAATTCGAT 59.180 37.037 0.00 0.00 0.00 3.59
1911 3050 7.015292 AGCATACCCTAGAACTGAATAATTCGA 59.985 37.037 0.00 0.00 0.00 3.71
1912 3051 7.116948 CAGCATACCCTAGAACTGAATAATTCG 59.883 40.741 0.00 0.00 0.00 3.34
1913 3052 8.150945 TCAGCATACCCTAGAACTGAATAATTC 58.849 37.037 0.00 0.00 31.60 2.17
1914 3053 8.034313 TCAGCATACCCTAGAACTGAATAATT 57.966 34.615 0.00 0.00 31.60 1.40
1915 3054 7.618019 TCAGCATACCCTAGAACTGAATAAT 57.382 36.000 0.00 0.00 31.60 1.28
1916 3055 7.432148 TTCAGCATACCCTAGAACTGAATAA 57.568 36.000 0.00 0.00 38.76 1.40
1917 3056 7.432148 TTTCAGCATACCCTAGAACTGAATA 57.568 36.000 4.29 0.00 42.04 1.75
1918 3057 5.957771 TTCAGCATACCCTAGAACTGAAT 57.042 39.130 0.00 0.00 38.76 2.57
1919 3058 5.755409 TTTCAGCATACCCTAGAACTGAA 57.245 39.130 0.00 0.00 41.11 3.02
1920 3059 5.957771 ATTTCAGCATACCCTAGAACTGA 57.042 39.130 0.00 0.00 32.62 3.41
1921 3060 7.396540 AAAATTTCAGCATACCCTAGAACTG 57.603 36.000 0.00 0.00 0.00 3.16
1922 3061 9.178758 CTTAAAATTTCAGCATACCCTAGAACT 57.821 33.333 0.00 0.00 0.00 3.01
1923 3062 9.174166 TCTTAAAATTTCAGCATACCCTAGAAC 57.826 33.333 0.00 0.00 0.00 3.01
1924 3063 9.396022 CTCTTAAAATTTCAGCATACCCTAGAA 57.604 33.333 0.00 0.00 0.00 2.10
1925 3064 8.768397 TCTCTTAAAATTTCAGCATACCCTAGA 58.232 33.333 0.00 0.00 0.00 2.43
1926 3065 8.964476 TCTCTTAAAATTTCAGCATACCCTAG 57.036 34.615 0.00 0.00 0.00 3.02
1927 3066 9.174166 GTTCTCTTAAAATTTCAGCATACCCTA 57.826 33.333 0.00 0.00 0.00 3.53
1928 3067 7.148239 CGTTCTCTTAAAATTTCAGCATACCCT 60.148 37.037 0.00 0.00 0.00 4.34
1929 3068 6.967199 CGTTCTCTTAAAATTTCAGCATACCC 59.033 38.462 0.00 0.00 0.00 3.69
1930 3069 6.967199 CCGTTCTCTTAAAATTTCAGCATACC 59.033 38.462 0.00 0.00 0.00 2.73
1931 3070 6.967199 CCCGTTCTCTTAAAATTTCAGCATAC 59.033 38.462 0.00 0.00 0.00 2.39
1932 3071 6.094881 CCCCGTTCTCTTAAAATTTCAGCATA 59.905 38.462 0.00 0.00 0.00 3.14
1933 3072 5.105756 CCCCGTTCTCTTAAAATTTCAGCAT 60.106 40.000 0.00 0.00 0.00 3.79
1934 3073 4.217550 CCCCGTTCTCTTAAAATTTCAGCA 59.782 41.667 0.00 0.00 0.00 4.41
1935 3074 4.217767 ACCCCGTTCTCTTAAAATTTCAGC 59.782 41.667 0.00 0.00 0.00 4.26
1936 3075 5.959618 ACCCCGTTCTCTTAAAATTTCAG 57.040 39.130 0.00 0.00 0.00 3.02
1937 3076 5.941647 CCTACCCCGTTCTCTTAAAATTTCA 59.058 40.000 0.00 0.00 0.00 2.69
1938 3077 5.163683 GCCTACCCCGTTCTCTTAAAATTTC 60.164 44.000 0.00 0.00 0.00 2.17
1939 3078 4.703575 GCCTACCCCGTTCTCTTAAAATTT 59.296 41.667 0.00 0.00 0.00 1.82
1940 3079 4.018688 AGCCTACCCCGTTCTCTTAAAATT 60.019 41.667 0.00 0.00 0.00 1.82
1941 3080 3.522343 AGCCTACCCCGTTCTCTTAAAAT 59.478 43.478 0.00 0.00 0.00 1.82
1942 3081 2.908351 AGCCTACCCCGTTCTCTTAAAA 59.092 45.455 0.00 0.00 0.00 1.52
1943 3082 2.235402 CAGCCTACCCCGTTCTCTTAAA 59.765 50.000 0.00 0.00 0.00 1.52
1944 3083 1.829222 CAGCCTACCCCGTTCTCTTAA 59.171 52.381 0.00 0.00 0.00 1.85
1945 3084 1.006281 TCAGCCTACCCCGTTCTCTTA 59.994 52.381 0.00 0.00 0.00 2.10
1946 3085 0.252103 TCAGCCTACCCCGTTCTCTT 60.252 55.000 0.00 0.00 0.00 2.85
1947 3086 0.032017 ATCAGCCTACCCCGTTCTCT 60.032 55.000 0.00 0.00 0.00 3.10
1948 3087 0.831307 AATCAGCCTACCCCGTTCTC 59.169 55.000 0.00 0.00 0.00 2.87
1949 3088 0.541863 CAATCAGCCTACCCCGTTCT 59.458 55.000 0.00 0.00 0.00 3.01
1950 3089 0.539986 TCAATCAGCCTACCCCGTTC 59.460 55.000 0.00 0.00 0.00 3.95
1951 3090 0.988832 TTCAATCAGCCTACCCCGTT 59.011 50.000 0.00 0.00 0.00 4.44
1952 3091 1.213296 ATTCAATCAGCCTACCCCGT 58.787 50.000 0.00 0.00 0.00 5.28
1953 3092 2.348411 AATTCAATCAGCCTACCCCG 57.652 50.000 0.00 0.00 0.00 5.73
1954 3093 5.385198 TGAATAATTCAATCAGCCTACCCC 58.615 41.667 0.00 0.00 36.59 4.95
1955 3094 6.064717 ACTGAATAATTCAATCAGCCTACCC 58.935 40.000 12.48 0.00 43.41 3.69
1956 3095 7.500559 AGAACTGAATAATTCAATCAGCCTACC 59.499 37.037 12.48 2.25 43.41 3.18
1957 3096 8.443953 AGAACTGAATAATTCAATCAGCCTAC 57.556 34.615 12.48 5.04 43.41 3.18
1958 3097 9.770097 CTAGAACTGAATAATTCAATCAGCCTA 57.230 33.333 12.48 12.30 43.41 3.93
1959 3098 7.718753 CCTAGAACTGAATAATTCAATCAGCCT 59.281 37.037 12.48 11.97 43.41 4.58
1960 3099 7.040823 CCCTAGAACTGAATAATTCAATCAGCC 60.041 40.741 12.48 7.16 43.41 4.85
1961 3100 7.500559 ACCCTAGAACTGAATAATTCAATCAGC 59.499 37.037 12.48 1.85 43.41 4.26
1962 3101 8.970859 ACCCTAGAACTGAATAATTCAATCAG 57.029 34.615 11.46 11.46 44.77 2.90
2000 3195 2.172717 GCAAGCCTACCCCATTCTCTTA 59.827 50.000 0.00 0.00 0.00 2.10
2001 3196 1.064389 GCAAGCCTACCCCATTCTCTT 60.064 52.381 0.00 0.00 0.00 2.85
2002 3197 0.548510 GCAAGCCTACCCCATTCTCT 59.451 55.000 0.00 0.00 0.00 3.10
2003 3198 0.255890 TGCAAGCCTACCCCATTCTC 59.744 55.000 0.00 0.00 0.00 2.87
2004 3199 0.257039 CTGCAAGCCTACCCCATTCT 59.743 55.000 0.00 0.00 0.00 2.40
2005 3200 2.799176 CTGCAAGCCTACCCCATTC 58.201 57.895 0.00 0.00 0.00 2.67
2499 3735 2.596923 TGAACCGGCTGCAATGCA 60.597 55.556 7.99 7.99 36.92 3.96
2586 3822 7.147915 TGCTTCCTTTCTGAATTTTAACACTGT 60.148 33.333 0.00 0.00 0.00 3.55
2623 3859 1.603802 CAGAAGCCGATGTGTTGTGTT 59.396 47.619 0.00 0.00 0.00 3.32
2970 4283 1.141881 CCAACTCCGACCTCCATCG 59.858 63.158 0.00 0.00 41.89 3.84
3041 4354 2.103538 GCTCGTACCGCCGAATCA 59.896 61.111 0.00 0.00 36.24 2.57
3076 4389 3.531538 GTTCTCAGGAACGGCATATTCA 58.468 45.455 0.00 0.00 41.70 2.57
3093 4406 0.909623 CATAGGAACCCACCCGTTCT 59.090 55.000 1.88 0.00 41.58 3.01
3112 4425 1.405661 GGTCCGTTCTGTTCCTGGATC 60.406 57.143 0.00 0.00 0.00 3.36
3113 4426 0.613777 GGTCCGTTCTGTTCCTGGAT 59.386 55.000 0.00 0.00 0.00 3.41
3137 4478 0.175760 CCGATCATCAGGTGGAACGT 59.824 55.000 0.00 0.00 38.12 3.99
3417 4772 6.595326 TCTTCTCCAAACACACTAATATGCAG 59.405 38.462 0.00 0.00 0.00 4.41
3516 4888 8.084590 ACATACTCTTGTACAAGTAACAAAGC 57.915 34.615 29.83 0.00 39.38 3.51
3596 4968 8.450964 CAAGTACAATAACATACAGAACCAAGG 58.549 37.037 0.00 0.00 0.00 3.61
3652 5025 4.395231 TCTGACTCTACATCACACCTTACG 59.605 45.833 0.00 0.00 0.00 3.18
3665 6678 6.260870 TGTTCAGTGAGAATCTGACTCTAC 57.739 41.667 0.00 2.09 40.90 2.59
3729 6744 8.423349 CAAATTCATATATTGCCCTCTTTGGAA 58.577 33.333 0.00 0.00 38.35 3.53
3730 6745 7.784073 TCAAATTCATATATTGCCCTCTTTGGA 59.216 33.333 0.00 0.00 38.35 3.53
3731 6746 7.954835 TCAAATTCATATATTGCCCTCTTTGG 58.045 34.615 0.00 0.00 0.00 3.28
3735 6750 8.910944 GCATATCAAATTCATATATTGCCCTCT 58.089 33.333 0.00 0.00 0.00 3.69
3736 6751 7.859377 CGCATATCAAATTCATATATTGCCCTC 59.141 37.037 0.00 0.00 0.00 4.30
3737 6752 7.557358 TCGCATATCAAATTCATATATTGCCCT 59.443 33.333 0.00 0.00 0.00 5.19
3738 6753 7.706159 TCGCATATCAAATTCATATATTGCCC 58.294 34.615 0.00 0.00 0.00 5.36
3739 6754 9.740239 AATCGCATATCAAATTCATATATTGCC 57.260 29.630 0.00 0.00 0.00 4.52
3788 6803 5.997129 TGTGCTTATGTTGAAGAACTGATGA 59.003 36.000 0.00 0.00 36.13 2.92
3789 6804 6.245115 TGTGCTTATGTTGAAGAACTGATG 57.755 37.500 0.00 0.00 36.13 3.07
3790 6805 8.743085 ATATGTGCTTATGTTGAAGAACTGAT 57.257 30.769 0.00 0.00 36.13 2.90
3791 6806 8.565896 AATATGTGCTTATGTTGAAGAACTGA 57.434 30.769 0.00 0.00 36.13 3.41
3792 6807 9.630098 AAAATATGTGCTTATGTTGAAGAACTG 57.370 29.630 0.00 0.00 36.13 3.16
3793 6808 9.846248 GAAAATATGTGCTTATGTTGAAGAACT 57.154 29.630 0.00 0.00 36.13 3.01
3794 6809 9.624697 TGAAAATATGTGCTTATGTTGAAGAAC 57.375 29.630 0.00 0.00 35.75 3.01
3835 6869 1.704628 TGGGTCTCCTTTCTGCATTCA 59.295 47.619 0.00 0.00 0.00 2.57
3896 6931 3.077359 GGACAATGTTGCAGAAGCTACT 58.923 45.455 0.00 0.00 45.02 2.57
3956 7022 2.611473 GCTAGCTGACACAGTGACACAT 60.611 50.000 7.81 0.00 33.43 3.21
3960 7026 0.039074 ACGCTAGCTGACACAGTGAC 60.039 55.000 13.93 0.92 33.43 3.67
3981 7047 3.762407 TGTGCCTACTGCTTAAGAACA 57.238 42.857 6.67 0.00 42.00 3.18
3990 7056 0.546598 ACCCCTATTGTGCCTACTGC 59.453 55.000 0.00 0.00 41.77 4.40
4100 7167 8.132362 TGGTGACTTAACAATGTTAATGTGTTC 58.868 33.333 17.63 10.34 36.83 3.18
4211 7314 8.400947 CAATATAGGAGTTATAACATGCCATGC 58.599 37.037 17.65 1.41 0.00 4.06
4214 7317 9.860650 AAACAATATAGGAGTTATAACATGCCA 57.139 29.630 17.65 7.33 0.00 4.92
4245 7416 6.548622 ACAAATGCATAAACAGCTGATCCTAT 59.451 34.615 23.35 8.12 0.00 2.57
4260 7432 8.518702 TGCAACAAGTAAGAATACAAATGCATA 58.481 29.630 0.00 0.00 36.05 3.14
4372 7706 3.559242 CAGAGCTAGAAATAACAGGCAGC 59.441 47.826 0.00 0.00 0.00 5.25
4461 7798 7.108194 ACCAGTGCCTTAAAAATACTAGGTAC 58.892 38.462 0.00 0.00 41.82 3.34
4762 8116 5.116882 AGTATTCGCTTGGAAACATAGGTC 58.883 41.667 0.00 0.00 42.32 3.85
4786 8140 5.468746 CGGTTTCTTTCTTACTGATGGTTCA 59.531 40.000 0.00 0.00 0.00 3.18
4812 8167 6.124340 AGGCATTTCACAAGTATGATGATCA 58.876 36.000 0.00 0.00 0.00 2.92
4903 8261 5.702865 ACCATCAACAGAAACATTTCATCG 58.297 37.500 7.10 0.00 39.61 3.84
4905 8263 7.499292 TGAAACCATCAACAGAAACATTTCAT 58.501 30.769 7.10 0.00 35.91 2.57
4933 8291 2.447089 TGTCGCTCTACGTTACATCG 57.553 50.000 0.00 0.00 44.19 3.84
4956 8387 7.653713 TGTGTTCTACAGCTCTAGAAAAAGAAG 59.346 37.037 12.40 0.00 35.07 2.85
4959 8390 7.201393 CGATGTGTTCTACAGCTCTAGAAAAAG 60.201 40.741 12.40 0.00 43.39 2.27
4960 8391 6.586463 CGATGTGTTCTACAGCTCTAGAAAAA 59.414 38.462 12.40 2.85 43.39 1.94
4965 8396 4.624336 ACGATGTGTTCTACAGCTCTAG 57.376 45.455 0.00 0.00 43.39 2.43
4966 8397 4.733850 CAACGATGTGTTCTACAGCTCTA 58.266 43.478 0.00 0.00 43.39 2.43
4967 8398 3.579709 CAACGATGTGTTCTACAGCTCT 58.420 45.455 0.00 0.00 43.39 4.09
4970 8401 2.069273 AGCAACGATGTGTTCTACAGC 58.931 47.619 0.00 0.00 43.80 4.40
4971 8402 4.324669 CAGTAGCAACGATGTGTTCTACAG 59.675 45.833 9.61 0.78 43.80 2.74
4972 8403 4.234574 CAGTAGCAACGATGTGTTCTACA 58.765 43.478 9.61 0.00 44.87 2.74
4973 8404 4.235360 ACAGTAGCAACGATGTGTTCTAC 58.765 43.478 0.00 0.00 39.29 2.59
4974 8405 4.514781 ACAGTAGCAACGATGTGTTCTA 57.485 40.909 0.00 0.00 39.29 2.10
4977 8408 4.373527 TGTAACAGTAGCAACGATGTGTT 58.626 39.130 5.08 5.08 43.09 3.32
4998 8433 4.989168 ACTCGCTAAAAGGAACAGTACTTG 59.011 41.667 0.00 0.00 0.00 3.16
4999 8434 4.989168 CACTCGCTAAAAGGAACAGTACTT 59.011 41.667 0.00 0.00 0.00 2.24
5188 8636 1.859302 AAACACTCCTTTTGGGTGCA 58.141 45.000 0.00 0.00 41.44 4.57
5252 9106 1.142262 ACCCGTAGCCTCACACTTTTT 59.858 47.619 0.00 0.00 0.00 1.94
5254 9108 0.320697 GACCCGTAGCCTCACACTTT 59.679 55.000 0.00 0.00 0.00 2.66
5266 9120 2.589157 CCAGCCCAACAGACCCGTA 61.589 63.158 0.00 0.00 0.00 4.02
5298 9191 4.823276 CTGATCAGCCCACTCGAC 57.177 61.111 10.38 0.00 0.00 4.20
5333 9226 4.264460 AGCTCACAGAACTACAGAAAGG 57.736 45.455 0.00 0.00 0.00 3.11
5337 9230 3.070159 AGCAAAGCTCACAGAACTACAGA 59.930 43.478 0.00 0.00 30.62 3.41
5342 9235 1.133976 ACCAGCAAAGCTCACAGAACT 60.134 47.619 0.00 0.00 36.40 3.01
5373 9277 2.142357 CTTCCACTCGACTGCCGTCA 62.142 60.000 9.06 0.00 40.23 4.35
5379 9283 1.153939 CGCCTCTTCCACTCGACTG 60.154 63.158 0.00 0.00 0.00 3.51
5380 9284 2.344203 CCGCCTCTTCCACTCGACT 61.344 63.158 0.00 0.00 0.00 4.18
5381 9285 2.182030 CCGCCTCTTCCACTCGAC 59.818 66.667 0.00 0.00 0.00 4.20
5382 9286 2.035155 TCCGCCTCTTCCACTCGA 59.965 61.111 0.00 0.00 0.00 4.04
5383 9287 2.492090 CTCCGCCTCTTCCACTCG 59.508 66.667 0.00 0.00 0.00 4.18
5403 9312 2.031420 GGTGGGACTAAACGAAAACAGC 60.031 50.000 0.00 0.00 0.00 4.40
5459 9370 6.406400 GCTAGCACCACATCCTCTTATATAGG 60.406 46.154 10.63 0.00 35.26 2.57
5612 9523 5.725551 TTTAGAATTGATGGGGCCTTCTA 57.274 39.130 0.84 4.98 0.00 2.10
5648 9559 7.546667 CACACCAGCTTTGCATTATCTTATTTT 59.453 33.333 0.00 0.00 0.00 1.82
5650 9561 6.567050 CACACCAGCTTTGCATTATCTTATT 58.433 36.000 0.00 0.00 0.00 1.40
5651 9562 5.450965 GCACACCAGCTTTGCATTATCTTAT 60.451 40.000 0.00 0.00 36.22 1.73
5652 9563 4.142403 GCACACCAGCTTTGCATTATCTTA 60.142 41.667 0.00 0.00 36.22 2.10
5653 9564 3.367703 GCACACCAGCTTTGCATTATCTT 60.368 43.478 0.00 0.00 36.22 2.40
5654 9565 2.165030 GCACACCAGCTTTGCATTATCT 59.835 45.455 0.00 0.00 36.22 1.98
5655 9566 2.165030 AGCACACCAGCTTTGCATTATC 59.835 45.455 8.61 0.00 43.70 1.75
5656 9567 2.165030 GAGCACACCAGCTTTGCATTAT 59.835 45.455 8.61 0.00 46.75 1.28
5657 9568 1.541147 GAGCACACCAGCTTTGCATTA 59.459 47.619 8.61 0.00 46.75 1.90
5658 9569 0.316204 GAGCACACCAGCTTTGCATT 59.684 50.000 8.61 0.00 46.75 3.56
5659 9570 0.538977 AGAGCACACCAGCTTTGCAT 60.539 50.000 8.61 0.00 46.75 3.96
5660 9571 0.752743 AAGAGCACACCAGCTTTGCA 60.753 50.000 8.61 0.00 46.75 4.08
5661 9572 0.386838 AAAGAGCACACCAGCTTTGC 59.613 50.000 0.00 0.00 46.75 3.68
5662 9573 2.877043 AAAAGAGCACACCAGCTTTG 57.123 45.000 0.00 0.00 46.75 2.77
5663 9574 2.887152 CCTAAAAGAGCACACCAGCTTT 59.113 45.455 0.00 0.00 46.75 3.51
5664 9575 2.508526 CCTAAAAGAGCACACCAGCTT 58.491 47.619 0.00 0.00 46.75 3.74
5666 9577 1.168714 CCCTAAAAGAGCACACCAGC 58.831 55.000 0.00 0.00 0.00 4.85
5667 9578 2.554032 CAACCCTAAAAGAGCACACCAG 59.446 50.000 0.00 0.00 0.00 4.00
5668 9579 2.173782 TCAACCCTAAAAGAGCACACCA 59.826 45.455 0.00 0.00 0.00 4.17
5669 9580 2.858745 TCAACCCTAAAAGAGCACACC 58.141 47.619 0.00 0.00 0.00 4.16
5670 9581 4.072131 TCATCAACCCTAAAAGAGCACAC 58.928 43.478 0.00 0.00 0.00 3.82
5671 9582 4.365514 TCATCAACCCTAAAAGAGCACA 57.634 40.909 0.00 0.00 0.00 4.57
5672 9583 4.762251 AGTTCATCAACCCTAAAAGAGCAC 59.238 41.667 0.00 0.00 32.22 4.40
5673 9584 4.985538 AGTTCATCAACCCTAAAAGAGCA 58.014 39.130 0.00 0.00 32.22 4.26
5674 9585 5.249420 AGAGTTCATCAACCCTAAAAGAGC 58.751 41.667 0.00 0.00 32.22 4.09
5675 9586 6.150140 CCAAGAGTTCATCAACCCTAAAAGAG 59.850 42.308 0.00 0.00 32.22 2.85
5676 9587 6.003950 CCAAGAGTTCATCAACCCTAAAAGA 58.996 40.000 0.00 0.00 32.22 2.52
5677 9588 6.259550 CCAAGAGTTCATCAACCCTAAAAG 57.740 41.667 0.00 0.00 32.22 2.27


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

AutoCloner maintained by Alex Coulton.