Multiple sequence alignment - TraesCS2A01G433300

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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 TraesCS2A01G433300 chr2A 100.000 3139 0 0 1 3139 686524588 686521450 0.000000e+00 5797.0
1 TraesCS2A01G433300 chr2A 97.596 2870 53 4 1 2860 686323578 686320715 0.000000e+00 4903.0
2 TraesCS2A01G433300 chr2A 98.628 1895 22 2 506 2399 686614956 686613065 0.000000e+00 3352.0
3 TraesCS2A01G433300 chr2A 96.529 1959 50 5 598 2544 686297401 686295449 0.000000e+00 3225.0
4 TraesCS2A01G433300 chr2A 93.010 515 34 2 188 700 686623037 686622523 0.000000e+00 750.0
5 TraesCS2A01G433300 chr2A 93.080 448 31 0 2413 2860 686608872 686608425 0.000000e+00 656.0
6 TraesCS2A01G433300 chr2A 93.571 420 26 1 188 606 686299389 686298970 2.660000e-175 625.0
7 TraesCS2A01G433300 chr2A 93.391 348 17 4 424 770 686623764 686623422 7.770000e-141 510.0
8 TraesCS2A01G433300 chr2A 94.014 284 17 0 2856 3139 279119078 279119361 6.220000e-117 431.0
9 TraesCS2A01G433300 chr2A 93.333 195 10 3 1 192 686623317 686623123 5.120000e-73 285.0
10 TraesCS2A01G433300 chr2A 98.925 93 1 0 100 192 686299567 686299475 1.940000e-37 167.0
11 TraesCS2A01G433300 chr2A 95.385 65 3 0 1 65 686299811 686299747 1.540000e-18 104.0
12 TraesCS2A01G433300 chr2A 84.694 98 13 2 2765 2860 72605567 72605470 2.580000e-16 97.1
13 TraesCS2A01G433300 chr2B 90.956 1548 88 23 790 2324 648931637 648930129 0.000000e+00 2036.0
14 TraesCS2A01G433300 chr2B 89.888 1335 103 26 834 2154 649370753 649369437 0.000000e+00 1688.0
15 TraesCS2A01G433300 chr2B 88.335 823 61 12 1893 2706 649192246 649191450 0.000000e+00 955.0
16 TraesCS2A01G433300 chr2B 89.474 76 7 1 751 826 649215155 649215081 9.270000e-16 95.3
17 TraesCS2A01G433300 chr2B 98.077 52 1 0 548 599 649053782 649053731 1.200000e-14 91.6
18 TraesCS2A01G433300 chr2D 89.161 1513 105 34 836 2325 543532118 543530642 0.000000e+00 1831.0
19 TraesCS2A01G433300 chr2D 87.772 1611 118 42 784 2364 543762098 543760537 0.000000e+00 1810.0
20 TraesCS2A01G433300 chr2D 88.080 1552 117 40 834 2364 543813744 543812240 0.000000e+00 1779.0
21 TraesCS2A01G433300 chr2D 86.187 1419 122 42 886 2271 543589155 543587778 0.000000e+00 1467.0
22 TraesCS2A01G433300 chr2D 94.718 284 15 0 2856 3139 396360434 396360717 2.870000e-120 442.0
23 TraesCS2A01G433300 chr2D 89.815 216 18 3 579 794 543589501 543589290 1.110000e-69 274.0
24 TraesCS2A01G433300 chr2D 89.450 218 17 3 513 730 543816142 543815931 1.430000e-68 270.0
25 TraesCS2A01G433300 chr2D 91.489 188 14 2 601 788 543532429 543532244 1.120000e-64 257.0
26 TraesCS2A01G433300 chr1A 95.423 284 12 1 2856 3139 426934892 426935174 4.770000e-123 451.0
27 TraesCS2A01G433300 chr1A 94.014 284 17 0 2856 3139 568954856 568954573 6.220000e-117 431.0
28 TraesCS2A01G433300 chr1A 77.816 293 52 11 187 473 509038593 509038308 5.380000e-38 169.0
29 TraesCS2A01G433300 chr6A 94.366 284 16 0 2856 3139 455410957 455411240 1.340000e-118 436.0
30 TraesCS2A01G433300 chr3D 94.014 284 17 0 2856 3139 537245754 537245471 6.220000e-117 431.0
31 TraesCS2A01G433300 chr4A 93.993 283 17 0 2857 3139 594838268 594837986 2.240000e-116 429.0
32 TraesCS2A01G433300 chr5A 93.662 284 18 0 2856 3139 519220923 519220640 2.890000e-115 425.0
33 TraesCS2A01G433300 chr5A 76.357 258 40 13 187 425 705150610 705150865 5.500000e-23 119.0
34 TraesCS2A01G433300 chr5A 86.316 95 12 1 2761 2854 495932349 495932443 5.540000e-18 102.0
35 TraesCS2A01G433300 chr3A 93.662 284 18 0 2856 3139 418312453 418312736 2.890000e-115 425.0
36 TraesCS2A01G433300 chr4D 86.869 99 12 1 2761 2858 129684504 129684406 3.310000e-20 110.0
37 TraesCS2A01G433300 chr6D 91.250 80 6 1 2759 2837 403665682 403665603 1.190000e-19 108.0
38 TraesCS2A01G433300 chr6D 82.653 98 14 3 2761 2855 344833431 344833528 2.010000e-12 84.2
39 TraesCS2A01G433300 chr1B 85.417 96 12 2 2766 2860 186823061 186823155 7.160000e-17 99.0
40 TraesCS2A01G433300 chr7A 84.783 92 13 1 2765 2855 264927087 264927178 1.200000e-14 91.6
41 TraesCS2A01G433300 chr7A 80.328 122 21 3 354 473 510163082 510162962 4.310000e-14 89.8
42 TraesCS2A01G433300 chr5D 72.542 295 62 17 187 473 66753103 66752820 9.330000e-11 78.7
43 TraesCS2A01G433300 chr5B 73.494 249 49 14 187 428 704304746 704304984 9.330000e-11 78.7
44 TraesCS2A01G433300 chr7D 79.464 112 16 6 355 462 143979933 143980041 4.340000e-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 TraesCS2A01G433300 chr2A 686521450 686524588 3138 True 5797.00 5797 100.000000 1 3139 1 chr2A.!!$R3 3138
1 TraesCS2A01G433300 chr2A 686320715 686323578 2863 True 4903.00 4903 97.596000 1 2860 1 chr2A.!!$R2 2859
2 TraesCS2A01G433300 chr2A 686613065 686614956 1891 True 3352.00 3352 98.628000 506 2399 1 chr2A.!!$R5 1893
3 TraesCS2A01G433300 chr2A 686295449 686299811 4362 True 1030.25 3225 96.102500 1 2544 4 chr2A.!!$R6 2543
4 TraesCS2A01G433300 chr2A 686622523 686623764 1241 True 515.00 750 93.244667 1 770 3 chr2A.!!$R7 769
5 TraesCS2A01G433300 chr2B 648930129 648931637 1508 True 2036.00 2036 90.956000 790 2324 1 chr2B.!!$R1 1534
6 TraesCS2A01G433300 chr2B 649369437 649370753 1316 True 1688.00 1688 89.888000 834 2154 1 chr2B.!!$R5 1320
7 TraesCS2A01G433300 chr2B 649191450 649192246 796 True 955.00 955 88.335000 1893 2706 1 chr2B.!!$R3 813
8 TraesCS2A01G433300 chr2D 543760537 543762098 1561 True 1810.00 1810 87.772000 784 2364 1 chr2D.!!$R1 1580
9 TraesCS2A01G433300 chr2D 543530642 543532429 1787 True 1044.00 1831 90.325000 601 2325 2 chr2D.!!$R2 1724
10 TraesCS2A01G433300 chr2D 543812240 543816142 3902 True 1024.50 1779 88.765000 513 2364 2 chr2D.!!$R4 1851
11 TraesCS2A01G433300 chr2D 543587778 543589501 1723 True 870.50 1467 88.001000 579 2271 2 chr2D.!!$R3 1692

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
194 877 2.441375 TCTTGGTTGGATTGTGTGGAGA 59.559 45.455 0.0 0.0 0.0 3.71 F
317 1000 4.242475 TCTACGCTTTGTTCATTGACGAT 58.758 39.130 0.0 0.0 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 6458 2.740826 CGGCACCGTCGTTTCCAT 60.741 61.111 0.0 0.0 34.35 3.41 R
2417 6857 8.894768 ACCTATTAGCATGTGATCTACTTTTC 57.105 34.615 0.0 0.0 0.00 2.29 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
194 877 2.441375 TCTTGGTTGGATTGTGTGGAGA 59.559 45.455 0.00 0.00 0.00 3.71
265 948 4.500035 GGATCCGTGTTGATCTAGTCTTCC 60.500 50.000 0.00 0.00 40.80 3.46
269 952 4.865365 CCGTGTTGATCTAGTCTTCCTTTC 59.135 45.833 0.00 0.00 0.00 2.62
278 961 8.307483 TGATCTAGTCTTCCTTTCTGTGTTTAG 58.693 37.037 0.00 0.00 0.00 1.85
317 1000 4.242475 TCTACGCTTTGTTCATTGACGAT 58.758 39.130 0.00 0.00 0.00 3.73
2047 6458 2.501128 GCGCTATGGAGTCAGCCA 59.499 61.111 0.00 0.00 43.23 4.75
2385 6825 7.141100 TGATTAAATTTCACCTCCGAACTTC 57.859 36.000 0.00 0.00 0.00 3.01
2417 6857 3.783548 GCATTTCTTGCGTCGAGATCTTG 60.784 47.826 3.24 3.24 42.54 3.02
2418 6858 3.297830 TTTCTTGCGTCGAGATCTTGA 57.702 42.857 8.72 8.72 0.00 3.02
2434 6874 7.516470 CGAGATCTTGAAAAGTAGATCACATGC 60.516 40.741 3.60 0.00 46.34 4.06
2466 6906 1.398595 ACGAACTTACGTCCGTTTCG 58.601 50.000 18.17 18.17 43.02 3.46
2495 6935 2.368011 GGGGTTCCCTTCTCCTCCG 61.368 68.421 7.87 0.00 41.34 4.63
2532 6972 2.364961 CGGGAGGAGAGGGGAACT 59.635 66.667 0.00 0.00 0.00 3.01
2546 6986 3.116174 GGGGAACTTAGGGATCTTGTCT 58.884 50.000 0.00 0.00 0.00 3.41
2548 6988 3.775316 GGGAACTTAGGGATCTTGTCTGA 59.225 47.826 0.00 0.00 0.00 3.27
2572 7012 2.664402 TAGGGTAGTAGGGTTAGCCG 57.336 55.000 0.00 0.00 42.18 5.52
2579 7019 3.105959 AGTAGGGTTAGCCGGTTAAGA 57.894 47.619 11.43 0.00 34.97 2.10
2663 7103 2.028125 GATCCGGTTCCATCTCGGCA 62.028 60.000 0.00 0.00 43.10 5.69
2745 7185 1.304952 CGGTTTGGCTATTCCCCCA 59.695 57.895 0.00 0.00 0.00 4.96
2848 7288 8.630037 AGTTAGGAACAAGTTTTATTGAACCAG 58.370 33.333 0.00 0.00 34.24 4.00
2869 7309 2.504920 GGAGGCACCTATTTTGGCC 58.495 57.895 0.00 0.00 46.77 5.36
2875 7315 4.687901 GGCACCTATTTTGGCCATTAAT 57.312 40.909 6.09 12.49 45.70 1.40
2876 7316 4.379652 GGCACCTATTTTGGCCATTAATG 58.620 43.478 18.92 8.58 45.70 1.90
2889 7329 3.674997 CCATTAATGGCGCACTATAGGT 58.325 45.455 21.32 0.00 41.75 3.08
2890 7330 3.436704 CCATTAATGGCGCACTATAGGTG 59.563 47.826 21.32 1.66 43.83 4.00
2904 7344 6.993079 CACTATAGGTGCATCACTATTACCA 58.007 40.000 0.00 0.00 39.22 3.25
2905 7345 6.868864 CACTATAGGTGCATCACTATTACCAC 59.131 42.308 0.00 0.00 39.22 4.16
2906 7346 3.179443 AGGTGCATCACTATTACCACG 57.821 47.619 0.00 0.00 34.40 4.94
2907 7347 1.597663 GGTGCATCACTATTACCACGC 59.402 52.381 0.00 0.00 34.40 5.34
2908 7348 1.597663 GTGCATCACTATTACCACGCC 59.402 52.381 0.00 0.00 0.00 5.68
2909 7349 1.208293 TGCATCACTATTACCACGCCA 59.792 47.619 0.00 0.00 0.00 5.69
2910 7350 1.597663 GCATCACTATTACCACGCCAC 59.402 52.381 0.00 0.00 0.00 5.01
2911 7351 2.741878 GCATCACTATTACCACGCCACT 60.742 50.000 0.00 0.00 0.00 4.00
2912 7352 3.491964 GCATCACTATTACCACGCCACTA 60.492 47.826 0.00 0.00 0.00 2.74
2913 7353 4.299155 CATCACTATTACCACGCCACTAG 58.701 47.826 0.00 0.00 0.00 2.57
2914 7354 3.359033 TCACTATTACCACGCCACTAGT 58.641 45.455 0.00 0.00 0.00 2.57
2915 7355 4.525996 TCACTATTACCACGCCACTAGTA 58.474 43.478 0.00 0.00 0.00 1.82
2916 7356 4.949238 TCACTATTACCACGCCACTAGTAA 59.051 41.667 0.00 0.00 0.00 2.24
2917 7357 5.039333 CACTATTACCACGCCACTAGTAAC 58.961 45.833 0.00 0.00 0.00 2.50
2918 7358 4.706476 ACTATTACCACGCCACTAGTAACA 59.294 41.667 0.00 0.00 0.00 2.41
2919 7359 4.540359 ATTACCACGCCACTAGTAACAA 57.460 40.909 0.00 0.00 0.00 2.83
2920 7360 2.914695 ACCACGCCACTAGTAACAAA 57.085 45.000 0.00 0.00 0.00 2.83
2921 7361 3.412237 ACCACGCCACTAGTAACAAAT 57.588 42.857 0.00 0.00 0.00 2.32
2922 7362 4.540359 ACCACGCCACTAGTAACAAATA 57.460 40.909 0.00 0.00 0.00 1.40
2923 7363 4.248058 ACCACGCCACTAGTAACAAATAC 58.752 43.478 0.00 0.00 34.52 1.89
2924 7364 4.020839 ACCACGCCACTAGTAACAAATACT 60.021 41.667 0.00 0.00 46.62 2.12
2925 7365 5.185635 ACCACGCCACTAGTAACAAATACTA 59.814 40.000 0.00 0.00 43.16 1.82
2926 7366 6.101332 CCACGCCACTAGTAACAAATACTAA 58.899 40.000 0.00 0.00 44.50 2.24
2927 7367 6.759827 CCACGCCACTAGTAACAAATACTAAT 59.240 38.462 0.00 0.00 44.50 1.73
2928 7368 7.254319 CCACGCCACTAGTAACAAATACTAATG 60.254 40.741 0.00 0.00 44.50 1.90
2932 7372 6.646636 CACTAGTAACAAATACTAATGGCGC 58.353 40.000 0.00 0.00 44.50 6.53
2933 7373 6.256975 CACTAGTAACAAATACTAATGGCGCA 59.743 38.462 10.83 0.00 44.50 6.09
2934 7374 5.479716 AGTAACAAATACTAATGGCGCAC 57.520 39.130 10.83 0.00 43.16 5.34
2935 7375 3.775661 AACAAATACTAATGGCGCACC 57.224 42.857 10.83 0.00 0.00 5.01
2936 7376 2.999331 ACAAATACTAATGGCGCACCT 58.001 42.857 10.83 0.00 36.63 4.00
2937 7377 2.943033 ACAAATACTAATGGCGCACCTC 59.057 45.455 10.83 0.00 36.63 3.85
2938 7378 3.206150 CAAATACTAATGGCGCACCTCT 58.794 45.455 10.83 0.00 36.63 3.69
2939 7379 2.533266 ATACTAATGGCGCACCTCTG 57.467 50.000 10.83 0.00 36.63 3.35
2940 7380 0.464036 TACTAATGGCGCACCTCTGG 59.536 55.000 10.83 0.00 36.63 3.86
2941 7381 1.221840 CTAATGGCGCACCTCTGGT 59.778 57.895 10.83 0.00 36.63 4.00
2952 7392 1.267121 ACCTCTGGTGCGACATTAGT 58.733 50.000 0.00 0.00 32.98 2.24
2953 7393 2.453521 ACCTCTGGTGCGACATTAGTA 58.546 47.619 0.00 0.00 32.98 1.82
2954 7394 3.031736 ACCTCTGGTGCGACATTAGTAT 58.968 45.455 0.00 0.00 32.98 2.12
2955 7395 3.181475 ACCTCTGGTGCGACATTAGTATG 60.181 47.826 0.00 0.00 32.98 2.39
2956 7396 2.797156 CTCTGGTGCGACATTAGTATGC 59.203 50.000 0.00 0.00 35.03 3.14
2957 7397 1.867233 CTGGTGCGACATTAGTATGCC 59.133 52.381 0.00 0.00 35.03 4.40
2958 7398 1.208293 TGGTGCGACATTAGTATGCCA 59.792 47.619 0.00 0.00 35.03 4.92
2959 7399 1.867233 GGTGCGACATTAGTATGCCAG 59.133 52.381 0.00 0.00 35.03 4.85
2960 7400 2.483013 GGTGCGACATTAGTATGCCAGA 60.483 50.000 0.00 0.00 35.03 3.86
2961 7401 3.393800 GTGCGACATTAGTATGCCAGAT 58.606 45.455 0.00 0.00 35.03 2.90
2962 7402 4.556233 GTGCGACATTAGTATGCCAGATA 58.444 43.478 0.00 0.00 35.03 1.98
2963 7403 4.988540 GTGCGACATTAGTATGCCAGATAA 59.011 41.667 0.00 0.00 35.03 1.75
2964 7404 5.639506 GTGCGACATTAGTATGCCAGATAAT 59.360 40.000 0.00 0.00 35.03 1.28
2965 7405 6.811665 GTGCGACATTAGTATGCCAGATAATA 59.188 38.462 0.00 0.00 35.03 0.98
2966 7406 7.009631 GTGCGACATTAGTATGCCAGATAATAG 59.990 40.741 0.00 0.00 35.03 1.73
2967 7407 7.036220 GCGACATTAGTATGCCAGATAATAGT 58.964 38.462 0.00 0.00 35.03 2.12
2968 7408 7.009631 GCGACATTAGTATGCCAGATAATAGTG 59.990 40.741 0.00 0.00 35.03 2.74
2969 7409 7.489435 CGACATTAGTATGCCAGATAATAGTGG 59.511 40.741 0.00 0.00 35.03 4.00
2970 7410 8.207350 ACATTAGTATGCCAGATAATAGTGGT 57.793 34.615 0.00 0.00 36.10 4.16
2971 7411 8.097038 ACATTAGTATGCCAGATAATAGTGGTG 58.903 37.037 0.00 0.00 36.10 4.17
2972 7412 4.899502 AGTATGCCAGATAATAGTGGTGC 58.100 43.478 0.00 0.00 36.10 5.01
2973 7413 3.862877 ATGCCAGATAATAGTGGTGCA 57.137 42.857 0.00 0.00 36.10 4.57
2974 7414 2.917933 TGCCAGATAATAGTGGTGCAC 58.082 47.619 8.80 8.80 36.10 4.57
2975 7415 2.222027 GCCAGATAATAGTGGTGCACC 58.778 52.381 29.67 29.67 36.10 5.01
2976 7416 2.158755 GCCAGATAATAGTGGTGCACCT 60.159 50.000 34.75 19.61 36.10 4.00
2977 7417 3.470709 CCAGATAATAGTGGTGCACCTG 58.529 50.000 34.75 20.99 34.49 4.00
2978 7418 3.470709 CAGATAATAGTGGTGCACCTGG 58.529 50.000 34.75 9.38 34.49 4.45
2979 7419 2.158755 AGATAATAGTGGTGCACCTGGC 60.159 50.000 34.75 23.79 45.13 4.85
2997 7437 1.299541 GCAGTGCGCCATTACTATGT 58.700 50.000 4.18 0.00 32.94 2.29
2998 7438 1.261619 GCAGTGCGCCATTACTATGTC 59.738 52.381 4.18 0.00 32.94 3.06
2999 7439 1.867233 CAGTGCGCCATTACTATGTCC 59.133 52.381 4.18 0.00 0.00 4.02
3000 7440 1.484653 AGTGCGCCATTACTATGTCCA 59.515 47.619 4.18 0.00 0.00 4.02
3001 7441 2.093181 AGTGCGCCATTACTATGTCCAA 60.093 45.455 4.18 0.00 0.00 3.53
3002 7442 2.878406 GTGCGCCATTACTATGTCCAAT 59.122 45.455 4.18 0.00 0.00 3.16
3003 7443 4.062293 GTGCGCCATTACTATGTCCAATA 58.938 43.478 4.18 0.00 0.00 1.90
3004 7444 4.152402 GTGCGCCATTACTATGTCCAATAG 59.848 45.833 4.18 0.00 0.00 1.73
3005 7445 4.202315 TGCGCCATTACTATGTCCAATAGT 60.202 41.667 4.18 3.68 38.32 2.12
3006 7446 4.152402 GCGCCATTACTATGTCCAATAGTG 59.848 45.833 0.00 0.00 36.38 2.74
3007 7447 5.297547 CGCCATTACTATGTCCAATAGTGT 58.702 41.667 8.01 0.00 36.38 3.55
3008 7448 5.177511 CGCCATTACTATGTCCAATAGTGTG 59.822 44.000 8.01 6.89 36.38 3.82
3009 7449 5.049405 GCCATTACTATGTCCAATAGTGTGC 60.049 44.000 8.01 2.83 36.38 4.57
3010 7450 5.470098 CCATTACTATGTCCAATAGTGTGCC 59.530 44.000 8.01 0.00 36.38 5.01
3011 7451 5.685520 TTACTATGTCCAATAGTGTGCCA 57.314 39.130 8.01 0.00 36.38 4.92
3012 7452 4.778213 ACTATGTCCAATAGTGTGCCAT 57.222 40.909 0.00 0.00 33.91 4.40
3013 7453 5.116084 ACTATGTCCAATAGTGTGCCATT 57.884 39.130 0.00 0.00 33.91 3.16
3014 7454 6.247229 ACTATGTCCAATAGTGTGCCATTA 57.753 37.500 0.00 0.00 33.91 1.90
3015 7455 6.055588 ACTATGTCCAATAGTGTGCCATTAC 58.944 40.000 0.00 0.00 33.91 1.89
3016 7456 4.568072 TGTCCAATAGTGTGCCATTACT 57.432 40.909 0.00 0.00 0.00 2.24
3017 7457 5.685520 TGTCCAATAGTGTGCCATTACTA 57.314 39.130 0.00 0.00 34.23 1.82
3018 7458 6.247229 TGTCCAATAGTGTGCCATTACTAT 57.753 37.500 0.00 0.00 40.77 2.12
3019 7459 6.054941 TGTCCAATAGTGTGCCATTACTATG 58.945 40.000 5.65 0.00 39.40 2.23
3020 7460 5.049405 GTCCAATAGTGTGCCATTACTATGC 60.049 44.000 5.65 0.00 39.40 3.14
3021 7461 4.216257 CCAATAGTGTGCCATTACTATGCC 59.784 45.833 5.65 0.00 39.40 4.40
3022 7462 4.982241 ATAGTGTGCCATTACTATGCCT 57.018 40.909 4.42 0.00 38.37 4.75
3023 7463 3.652057 AGTGTGCCATTACTATGCCTT 57.348 42.857 0.00 0.00 0.00 4.35
3024 7464 3.545703 AGTGTGCCATTACTATGCCTTC 58.454 45.455 0.00 0.00 0.00 3.46
3025 7465 3.200825 AGTGTGCCATTACTATGCCTTCT 59.799 43.478 0.00 0.00 0.00 2.85
3026 7466 4.408921 AGTGTGCCATTACTATGCCTTCTA 59.591 41.667 0.00 0.00 0.00 2.10
3027 7467 4.752101 GTGTGCCATTACTATGCCTTCTAG 59.248 45.833 0.00 0.00 0.00 2.43
3028 7468 4.202357 TGTGCCATTACTATGCCTTCTAGG 60.202 45.833 0.00 0.00 38.80 3.02
3029 7469 3.327757 TGCCATTACTATGCCTTCTAGGG 59.672 47.826 0.00 0.00 35.37 3.53
3030 7470 3.307762 GCCATTACTATGCCTTCTAGGGG 60.308 52.174 0.00 0.00 35.37 4.79
3031 7471 3.264450 CCATTACTATGCCTTCTAGGGGG 59.736 52.174 5.15 2.04 35.37 5.40
3048 7488 2.227194 GGGGGCATATTTACCTTCACG 58.773 52.381 0.00 0.00 0.00 4.35
3049 7489 2.422377 GGGGGCATATTTACCTTCACGT 60.422 50.000 0.00 0.00 0.00 4.49
3050 7490 3.181452 GGGGGCATATTTACCTTCACGTA 60.181 47.826 0.00 0.00 0.00 3.57
3051 7491 4.506095 GGGGGCATATTTACCTTCACGTAT 60.506 45.833 0.00 0.00 0.00 3.06
3052 7492 4.454504 GGGGCATATTTACCTTCACGTATG 59.545 45.833 0.00 0.00 0.00 2.39
3053 7493 4.083484 GGGCATATTTACCTTCACGTATGC 60.083 45.833 4.44 4.44 42.06 3.14
3054 7494 5.030874 GCATATTTACCTTCACGTATGCC 57.969 43.478 0.00 0.00 38.79 4.40
3055 7495 4.083484 GCATATTTACCTTCACGTATGCCC 60.083 45.833 0.00 0.00 38.79 5.36
3056 7496 2.406596 TTTACCTTCACGTATGCCCC 57.593 50.000 0.00 0.00 0.00 5.80
3057 7497 0.542805 TTACCTTCACGTATGCCCCC 59.457 55.000 0.00 0.00 0.00 5.40
3058 7498 0.618107 TACCTTCACGTATGCCCCCA 60.618 55.000 0.00 0.00 0.00 4.96
3059 7499 1.301623 CCTTCACGTATGCCCCCAA 59.698 57.895 0.00 0.00 0.00 4.12
3060 7500 0.748005 CCTTCACGTATGCCCCCAAG 60.748 60.000 0.00 0.00 0.00 3.61
3061 7501 0.035439 CTTCACGTATGCCCCCAAGT 60.035 55.000 0.00 0.00 0.00 3.16
3062 7502 0.322098 TTCACGTATGCCCCCAAGTG 60.322 55.000 0.00 0.00 0.00 3.16
3063 7503 2.045340 ACGTATGCCCCCAAGTGC 60.045 61.111 0.00 0.00 0.00 4.40
3064 7504 3.202001 CGTATGCCCCCAAGTGCG 61.202 66.667 0.00 0.00 0.00 5.34
3065 7505 3.518068 GTATGCCCCCAAGTGCGC 61.518 66.667 0.00 0.00 0.00 6.09
3066 7506 4.813235 TATGCCCCCAAGTGCGCC 62.813 66.667 4.18 0.00 0.00 6.53
3070 7510 2.044451 CCCCCAAGTGCGCCATTA 60.044 61.111 4.18 0.00 0.00 1.90
3071 7511 2.414785 CCCCCAAGTGCGCCATTAC 61.415 63.158 4.18 0.00 0.00 1.89
3072 7512 1.378514 CCCCAAGTGCGCCATTACT 60.379 57.895 4.18 0.00 0.00 2.24
3073 7513 0.107410 CCCCAAGTGCGCCATTACTA 60.107 55.000 4.18 0.00 0.00 1.82
3074 7514 1.476833 CCCCAAGTGCGCCATTACTAT 60.477 52.381 4.18 0.00 0.00 2.12
3075 7515 1.603802 CCCAAGTGCGCCATTACTATG 59.396 52.381 4.18 3.24 0.00 2.23
3076 7516 1.002468 CCAAGTGCGCCATTACTATGC 60.002 52.381 4.18 0.00 0.00 3.14
3077 7517 1.002468 CAAGTGCGCCATTACTATGCC 60.002 52.381 4.18 0.00 0.00 4.40
3078 7518 0.535102 AGTGCGCCATTACTATGCCC 60.535 55.000 4.18 0.00 0.00 5.36
3079 7519 1.228124 TGCGCCATTACTATGCCCC 60.228 57.895 4.18 0.00 0.00 5.80
3080 7520 2.325082 GCGCCATTACTATGCCCCG 61.325 63.158 0.00 0.00 0.00 5.73
3081 7521 1.070786 CGCCATTACTATGCCCCGT 59.929 57.895 0.00 0.00 0.00 5.28
3082 7522 0.319083 CGCCATTACTATGCCCCGTA 59.681 55.000 0.00 0.00 0.00 4.02
3083 7523 1.270412 CGCCATTACTATGCCCCGTAA 60.270 52.381 0.00 0.00 0.00 3.18
3084 7524 2.614481 CGCCATTACTATGCCCCGTAAT 60.614 50.000 0.00 0.00 36.92 1.89
3085 7525 2.747446 GCCATTACTATGCCCCGTAATG 59.253 50.000 16.16 16.16 46.24 1.90
3086 7526 2.747446 CCATTACTATGCCCCGTAATGC 59.253 50.000 17.05 0.00 45.74 3.56
3087 7527 2.157834 TTACTATGCCCCGTAATGCG 57.842 50.000 0.00 0.00 40.95 4.73
3088 7528 0.320073 TACTATGCCCCGTAATGCGC 60.320 55.000 0.00 0.00 39.71 6.09
3089 7529 2.281208 TATGCCCCGTAATGCGCC 60.281 61.111 4.18 0.00 39.71 6.53
3090 7530 3.108288 TATGCCCCGTAATGCGCCA 62.108 57.895 4.18 0.00 39.71 5.69
3093 7533 2.502093 CCCCGTAATGCGCCACTA 59.498 61.111 4.18 0.00 39.71 2.74
3094 7534 1.594293 CCCCGTAATGCGCCACTAG 60.594 63.158 4.18 0.00 39.71 2.57
3095 7535 1.143183 CCCGTAATGCGCCACTAGT 59.857 57.895 4.18 0.00 39.71 2.57
3096 7536 0.386476 CCCGTAATGCGCCACTAGTA 59.614 55.000 4.18 0.00 39.71 1.82
3097 7537 1.000506 CCCGTAATGCGCCACTAGTAT 59.999 52.381 4.18 0.00 39.71 2.12
3098 7538 2.547218 CCCGTAATGCGCCACTAGTATT 60.547 50.000 4.18 0.00 39.71 1.89
3099 7539 3.128349 CCGTAATGCGCCACTAGTATTT 58.872 45.455 4.18 0.00 39.71 1.40
3100 7540 4.300803 CCGTAATGCGCCACTAGTATTTA 58.699 43.478 4.18 0.00 39.71 1.40
3101 7541 4.384846 CCGTAATGCGCCACTAGTATTTAG 59.615 45.833 4.18 0.00 39.71 1.85
3102 7542 4.143389 CGTAATGCGCCACTAGTATTTAGC 60.143 45.833 4.18 0.00 0.00 3.09
3103 7543 2.234300 TGCGCCACTAGTATTTAGCC 57.766 50.000 4.18 0.00 0.00 3.93
3104 7544 1.760613 TGCGCCACTAGTATTTAGCCT 59.239 47.619 4.18 0.00 0.00 4.58
3105 7545 2.169769 TGCGCCACTAGTATTTAGCCTT 59.830 45.455 4.18 0.00 0.00 4.35
3106 7546 2.544267 GCGCCACTAGTATTTAGCCTTG 59.456 50.000 0.00 0.00 0.00 3.61
3107 7547 3.131396 CGCCACTAGTATTTAGCCTTGG 58.869 50.000 0.00 0.00 0.00 3.61
3108 7548 3.431766 CGCCACTAGTATTTAGCCTTGGT 60.432 47.826 0.00 0.00 0.00 3.67
3109 7549 3.877508 GCCACTAGTATTTAGCCTTGGTG 59.122 47.826 0.00 0.00 0.00 4.17
3110 7550 3.877508 CCACTAGTATTTAGCCTTGGTGC 59.122 47.826 0.00 0.00 0.00 5.01
3111 7551 3.555956 CACTAGTATTTAGCCTTGGTGCG 59.444 47.826 0.00 0.00 36.02 5.34
3112 7552 1.379527 AGTATTTAGCCTTGGTGCGC 58.620 50.000 0.00 0.00 36.02 6.09
3113 7553 1.065418 AGTATTTAGCCTTGGTGCGCT 60.065 47.619 9.73 0.00 39.17 5.92
3114 7554 2.169769 AGTATTTAGCCTTGGTGCGCTA 59.830 45.455 9.73 0.00 36.53 4.26
3115 7555 1.379527 ATTTAGCCTTGGTGCGCTAC 58.620 50.000 9.73 5.08 37.31 3.58
3116 7556 0.323629 TTTAGCCTTGGTGCGCTACT 59.676 50.000 9.73 0.00 37.31 2.57
3117 7557 1.187974 TTAGCCTTGGTGCGCTACTA 58.812 50.000 9.73 0.00 37.31 1.82
3118 7558 1.187974 TAGCCTTGGTGCGCTACTAA 58.812 50.000 9.73 8.68 36.53 2.24
3119 7559 0.541863 AGCCTTGGTGCGCTACTAAT 59.458 50.000 9.73 0.00 36.02 1.73
3120 7560 0.657840 GCCTTGGTGCGCTACTAATG 59.342 55.000 9.73 7.82 0.00 1.90
3121 7561 0.657840 CCTTGGTGCGCTACTAATGC 59.342 55.000 9.73 0.00 0.00 3.56
3122 7562 1.656652 CTTGGTGCGCTACTAATGCT 58.343 50.000 9.73 0.00 0.00 3.79
3123 7563 1.594862 CTTGGTGCGCTACTAATGCTC 59.405 52.381 9.73 0.00 0.00 4.26
3124 7564 0.534873 TGGTGCGCTACTAATGCTCA 59.465 50.000 9.73 0.00 0.00 4.26
3125 7565 1.066502 TGGTGCGCTACTAATGCTCAA 60.067 47.619 9.73 0.00 0.00 3.02
3126 7566 1.327764 GGTGCGCTACTAATGCTCAAC 59.672 52.381 9.73 0.00 0.00 3.18
3127 7567 1.999735 GTGCGCTACTAATGCTCAACA 59.000 47.619 9.73 0.00 0.00 3.33
3128 7568 2.415168 GTGCGCTACTAATGCTCAACAA 59.585 45.455 9.73 0.00 0.00 2.83
3129 7569 2.672874 TGCGCTACTAATGCTCAACAAG 59.327 45.455 9.73 0.00 0.00 3.16
3130 7570 2.030946 GCGCTACTAATGCTCAACAAGG 59.969 50.000 0.00 0.00 0.00 3.61
3131 7571 3.262420 CGCTACTAATGCTCAACAAGGT 58.738 45.455 0.00 0.00 0.00 3.50
3132 7572 3.062639 CGCTACTAATGCTCAACAAGGTG 59.937 47.826 0.00 0.00 0.00 4.00
3133 7573 3.181506 GCTACTAATGCTCAACAAGGTGC 60.182 47.826 0.00 0.00 0.00 5.01
3134 7574 1.806542 ACTAATGCTCAACAAGGTGCG 59.193 47.619 0.00 0.00 0.00 5.34
3135 7575 0.521291 TAATGCTCAACAAGGTGCGC 59.479 50.000 0.00 0.00 0.00 6.09
3136 7576 2.146073 AATGCTCAACAAGGTGCGCC 62.146 55.000 8.71 8.71 0.00 6.53
3137 7577 3.286751 GCTCAACAAGGTGCGCCA 61.287 61.111 20.59 0.00 37.19 5.69
3138 7578 2.639286 CTCAACAAGGTGCGCCAC 59.361 61.111 20.59 2.79 37.19 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 877 4.040584 CCATGAGATCTGATGGAGACACAT 59.959 45.833 31.13 7.76 45.54 3.21
207 890 4.264083 ACACCAATCAAACCCATGAGATCT 60.264 41.667 0.00 0.00 31.76 2.75
269 952 9.956720 ATCAAAAGATCAAACTTCTAAACACAG 57.043 29.630 0.00 0.00 0.00 3.66
278 961 7.066374 AGCGTAGATCAAAAGATCAAACTTC 57.934 36.000 8.06 2.07 34.19 3.01
317 1000 3.276091 CGCGCCAGAACACAACCA 61.276 61.111 0.00 0.00 0.00 3.67
2047 6458 2.740826 CGGCACCGTCGTTTCCAT 60.741 61.111 0.00 0.00 34.35 3.41
2417 6857 8.894768 ACCTATTAGCATGTGATCTACTTTTC 57.105 34.615 0.00 0.00 0.00 2.29
2418 6858 9.686683 AAACCTATTAGCATGTGATCTACTTTT 57.313 29.630 0.00 0.00 0.00 2.27
2460 6900 2.549282 CAGGTTCACCGCGAAACG 59.451 61.111 8.23 0.00 46.70 3.60
2481 6921 1.990060 CCAGCGGAGGAGAAGGGAA 60.990 63.158 0.00 0.00 0.00 3.97
2532 6972 6.726299 CCCTATACATCAGACAAGATCCCTAA 59.274 42.308 0.00 0.00 0.00 2.69
2546 6986 6.251471 GCTAACCCTACTACCCTATACATCA 58.749 44.000 0.00 0.00 0.00 3.07
2548 6988 5.587861 GGCTAACCCTACTACCCTATACAT 58.412 45.833 0.00 0.00 0.00 2.29
2579 7019 2.995872 GCCGGACGAAGAGCACTCT 61.996 63.158 5.05 0.00 42.75 3.24
2706 7146 3.314331 CTCCACAGGAGCACCGGT 61.314 66.667 0.00 0.00 43.29 5.28
2728 7168 1.704641 GATGGGGGAATAGCCAAACC 58.295 55.000 0.00 0.00 38.95 3.27
2784 7224 7.278461 TCTGCTACTATACTGTTTCATCCTC 57.722 40.000 0.00 0.00 0.00 3.71
2835 7275 5.007682 GTGCCTCCTACTGGTTCAATAAAA 58.992 41.667 0.00 0.00 34.23 1.52
2839 7279 1.282157 GGTGCCTCCTACTGGTTCAAT 59.718 52.381 0.00 0.00 34.23 2.57
2868 7308 3.436704 CACCTATAGTGCGCCATTAATGG 59.563 47.826 27.35 27.35 44.70 3.16
2869 7309 4.668576 CACCTATAGTGCGCCATTAATG 57.331 45.455 4.18 8.58 40.28 1.90
2881 7321 6.294564 CGTGGTAATAGTGATGCACCTATAGT 60.295 42.308 0.00 0.00 34.49 2.12
2882 7322 6.093404 CGTGGTAATAGTGATGCACCTATAG 58.907 44.000 0.00 0.00 34.49 1.31
2883 7323 5.566032 GCGTGGTAATAGTGATGCACCTATA 60.566 44.000 0.00 0.00 34.49 1.31
2884 7324 4.799586 GCGTGGTAATAGTGATGCACCTAT 60.800 45.833 0.00 0.00 34.49 2.57
2885 7325 3.491964 GCGTGGTAATAGTGATGCACCTA 60.492 47.826 0.00 0.00 34.49 3.08
2886 7326 2.741878 GCGTGGTAATAGTGATGCACCT 60.742 50.000 0.00 0.00 34.49 4.00
2887 7327 1.597663 GCGTGGTAATAGTGATGCACC 59.402 52.381 0.00 0.00 34.49 5.01
2888 7328 1.597663 GGCGTGGTAATAGTGATGCAC 59.402 52.381 0.00 0.00 34.10 4.57
2889 7329 1.208293 TGGCGTGGTAATAGTGATGCA 59.792 47.619 0.00 0.00 0.00 3.96
2890 7330 1.597663 GTGGCGTGGTAATAGTGATGC 59.402 52.381 0.00 0.00 0.00 3.91
2891 7331 3.179443 AGTGGCGTGGTAATAGTGATG 57.821 47.619 0.00 0.00 0.00 3.07
2892 7332 3.958798 ACTAGTGGCGTGGTAATAGTGAT 59.041 43.478 0.00 0.00 0.00 3.06
2893 7333 3.359033 ACTAGTGGCGTGGTAATAGTGA 58.641 45.455 0.00 0.00 0.00 3.41
2894 7334 3.795623 ACTAGTGGCGTGGTAATAGTG 57.204 47.619 0.00 0.00 0.00 2.74
2895 7335 4.706476 TGTTACTAGTGGCGTGGTAATAGT 59.294 41.667 5.39 0.00 33.04 2.12
2896 7336 5.252969 TGTTACTAGTGGCGTGGTAATAG 57.747 43.478 5.39 0.00 0.00 1.73
2897 7337 5.657826 TTGTTACTAGTGGCGTGGTAATA 57.342 39.130 5.39 0.00 0.00 0.98
2898 7338 4.540359 TTGTTACTAGTGGCGTGGTAAT 57.460 40.909 5.39 0.00 0.00 1.89
2899 7339 4.333913 TTTGTTACTAGTGGCGTGGTAA 57.666 40.909 5.39 0.00 0.00 2.85
2900 7340 4.540359 ATTTGTTACTAGTGGCGTGGTA 57.460 40.909 5.39 0.00 0.00 3.25
2901 7341 2.914695 TTTGTTACTAGTGGCGTGGT 57.085 45.000 5.39 0.00 0.00 4.16
2902 7342 4.501071 AGTATTTGTTACTAGTGGCGTGG 58.499 43.478 5.39 0.00 39.44 4.94
2903 7343 7.618442 CATTAGTATTTGTTACTAGTGGCGTG 58.382 38.462 5.39 0.00 42.82 5.34
2904 7344 7.766219 CATTAGTATTTGTTACTAGTGGCGT 57.234 36.000 5.39 0.00 42.82 5.68
2908 7348 6.256975 TGCGCCATTAGTATTTGTTACTAGTG 59.743 38.462 4.18 7.81 44.61 2.74
2909 7349 6.257193 GTGCGCCATTAGTATTTGTTACTAGT 59.743 38.462 4.18 0.00 42.83 2.57
2910 7350 6.292703 GGTGCGCCATTAGTATTTGTTACTAG 60.293 42.308 12.58 0.00 38.35 2.57
2911 7351 5.524646 GGTGCGCCATTAGTATTTGTTACTA 59.475 40.000 12.58 0.00 37.25 1.82
2912 7352 4.334481 GGTGCGCCATTAGTATTTGTTACT 59.666 41.667 12.58 0.00 38.53 2.24
2913 7353 4.334481 AGGTGCGCCATTAGTATTTGTTAC 59.666 41.667 20.59 0.00 37.19 2.50
2914 7354 4.519213 AGGTGCGCCATTAGTATTTGTTA 58.481 39.130 20.59 0.00 37.19 2.41
2915 7355 3.352648 AGGTGCGCCATTAGTATTTGTT 58.647 40.909 20.59 0.00 37.19 2.83
2916 7356 2.943033 GAGGTGCGCCATTAGTATTTGT 59.057 45.455 20.59 0.00 37.19 2.83
2917 7357 3.002656 CAGAGGTGCGCCATTAGTATTTG 59.997 47.826 20.59 0.00 37.19 2.32
2918 7358 3.206150 CAGAGGTGCGCCATTAGTATTT 58.794 45.455 20.59 0.00 37.19 1.40
2919 7359 2.485479 CCAGAGGTGCGCCATTAGTATT 60.485 50.000 20.59 0.00 37.19 1.89
2920 7360 1.070758 CCAGAGGTGCGCCATTAGTAT 59.929 52.381 20.59 0.00 37.19 2.12
2921 7361 0.464036 CCAGAGGTGCGCCATTAGTA 59.536 55.000 20.59 0.00 37.19 1.82
2922 7362 1.221840 CCAGAGGTGCGCCATTAGT 59.778 57.895 20.59 0.00 37.19 2.24
2923 7363 1.221840 ACCAGAGGTGCGCCATTAG 59.778 57.895 20.59 6.97 32.98 1.73
2924 7364 3.399046 ACCAGAGGTGCGCCATTA 58.601 55.556 20.59 0.00 32.98 1.90
2933 7373 1.267121 ACTAATGTCGCACCAGAGGT 58.733 50.000 0.00 0.00 35.62 3.85
2934 7374 3.384668 CATACTAATGTCGCACCAGAGG 58.615 50.000 0.00 0.00 0.00 3.69
2935 7375 2.797156 GCATACTAATGTCGCACCAGAG 59.203 50.000 0.00 0.00 35.38 3.35
2936 7376 2.483013 GGCATACTAATGTCGCACCAGA 60.483 50.000 0.00 0.00 35.38 3.86
2937 7377 1.867233 GGCATACTAATGTCGCACCAG 59.133 52.381 0.00 0.00 35.38 4.00
2938 7378 1.208293 TGGCATACTAATGTCGCACCA 59.792 47.619 0.00 0.00 40.81 4.17
2939 7379 1.867233 CTGGCATACTAATGTCGCACC 59.133 52.381 0.00 0.00 40.81 5.01
2940 7380 2.821546 TCTGGCATACTAATGTCGCAC 58.178 47.619 0.00 0.00 40.81 5.34
2941 7381 3.751479 ATCTGGCATACTAATGTCGCA 57.249 42.857 0.00 0.00 40.81 5.10
2942 7382 7.009631 CACTATTATCTGGCATACTAATGTCGC 59.990 40.741 0.00 0.00 40.81 5.19
2943 7383 7.489435 CCACTATTATCTGGCATACTAATGTCG 59.511 40.741 0.00 0.00 40.81 4.35
2944 7384 8.314751 ACCACTATTATCTGGCATACTAATGTC 58.685 37.037 0.00 0.00 38.26 3.06
2945 7385 8.097038 CACCACTATTATCTGGCATACTAATGT 58.903 37.037 0.00 0.00 35.38 2.71
2946 7386 7.065085 GCACCACTATTATCTGGCATACTAATG 59.935 40.741 0.00 0.00 36.09 1.90
2947 7387 7.106239 GCACCACTATTATCTGGCATACTAAT 58.894 38.462 0.00 0.00 0.00 1.73
2948 7388 6.042666 TGCACCACTATTATCTGGCATACTAA 59.957 38.462 0.00 0.00 0.00 2.24
2949 7389 5.542251 TGCACCACTATTATCTGGCATACTA 59.458 40.000 0.00 0.00 0.00 1.82
2950 7390 4.347876 TGCACCACTATTATCTGGCATACT 59.652 41.667 0.00 0.00 0.00 2.12
2951 7391 4.452455 GTGCACCACTATTATCTGGCATAC 59.548 45.833 5.22 0.00 32.16 2.39
2952 7392 4.504864 GGTGCACCACTATTATCTGGCATA 60.505 45.833 31.23 0.00 34.40 3.14
2953 7393 3.480470 GTGCACCACTATTATCTGGCAT 58.520 45.455 5.22 0.00 32.16 4.40
2954 7394 2.421388 GGTGCACCACTATTATCTGGCA 60.421 50.000 31.23 0.00 34.40 4.92
2955 7395 2.158755 AGGTGCACCACTATTATCTGGC 60.159 50.000 36.39 5.24 38.89 4.85
2956 7396 3.470709 CAGGTGCACCACTATTATCTGG 58.529 50.000 36.39 7.76 38.89 3.86
2957 7397 3.470709 CCAGGTGCACCACTATTATCTG 58.529 50.000 36.39 21.64 38.89 2.90
2958 7398 2.158755 GCCAGGTGCACCACTATTATCT 60.159 50.000 36.39 10.81 40.77 1.98
2959 7399 2.222027 GCCAGGTGCACCACTATTATC 58.778 52.381 36.39 12.89 40.77 1.75
2960 7400 2.348411 GCCAGGTGCACCACTATTAT 57.652 50.000 36.39 12.43 40.77 1.28
2961 7401 3.873781 GCCAGGTGCACCACTATTA 57.126 52.632 36.39 0.00 40.77 0.98
2962 7402 4.743018 GCCAGGTGCACCACTATT 57.257 55.556 36.39 14.05 40.77 1.73
2978 7418 1.261619 GACATAGTAATGGCGCACTGC 59.738 52.381 10.83 0.00 45.38 4.40
2979 7419 1.867233 GGACATAGTAATGGCGCACTG 59.133 52.381 10.83 0.00 42.67 3.66
2980 7420 1.484653 TGGACATAGTAATGGCGCACT 59.515 47.619 10.83 6.53 42.67 4.40
2981 7421 1.948104 TGGACATAGTAATGGCGCAC 58.052 50.000 10.83 0.00 42.67 5.34
2982 7422 2.700722 TTGGACATAGTAATGGCGCA 57.299 45.000 10.83 0.00 42.67 6.09
2983 7423 4.152402 CACTATTGGACATAGTAATGGCGC 59.848 45.833 0.00 0.00 42.67 6.53
2984 7424 5.177511 CACACTATTGGACATAGTAATGGCG 59.822 44.000 0.00 0.00 42.67 5.69
2985 7425 5.049405 GCACACTATTGGACATAGTAATGGC 60.049 44.000 0.00 0.00 40.80 4.40
2986 7426 5.470098 GGCACACTATTGGACATAGTAATGG 59.530 44.000 0.00 0.00 37.43 3.16
2987 7427 6.054941 TGGCACACTATTGGACATAGTAATG 58.945 40.000 0.00 0.00 39.17 1.90
2988 7428 6.247229 TGGCACACTATTGGACATAGTAAT 57.753 37.500 0.00 0.00 33.45 1.89
2989 7429 5.685520 TGGCACACTATTGGACATAGTAA 57.314 39.130 0.00 0.00 33.45 2.24
3009 7449 3.264450 CCCCCTAGAAGGCATAGTAATGG 59.736 52.174 0.00 0.00 32.73 3.16
3010 7450 4.559862 CCCCCTAGAAGGCATAGTAATG 57.440 50.000 0.00 0.00 32.73 1.90
3028 7468 2.227194 CGTGAAGGTAAATATGCCCCC 58.773 52.381 0.00 0.00 30.28 5.40
3029 7469 2.927028 ACGTGAAGGTAAATATGCCCC 58.073 47.619 0.00 0.00 30.28 5.80
3030 7470 4.083484 GCATACGTGAAGGTAAATATGCCC 60.083 45.833 0.00 0.00 39.19 5.36
3031 7471 5.030874 GCATACGTGAAGGTAAATATGCC 57.969 43.478 0.00 0.00 39.19 4.40
3032 7472 4.083484 GGGCATACGTGAAGGTAAATATGC 60.083 45.833 0.00 0.62 42.60 3.14
3033 7473 4.454504 GGGGCATACGTGAAGGTAAATATG 59.545 45.833 0.00 0.00 0.00 1.78
3034 7474 4.506095 GGGGGCATACGTGAAGGTAAATAT 60.506 45.833 0.00 0.00 0.00 1.28
3035 7475 3.181452 GGGGGCATACGTGAAGGTAAATA 60.181 47.826 0.00 0.00 0.00 1.40
3036 7476 2.422377 GGGGGCATACGTGAAGGTAAAT 60.422 50.000 0.00 0.00 0.00 1.40
3037 7477 1.065272 GGGGGCATACGTGAAGGTAAA 60.065 52.381 0.00 0.00 0.00 2.01
3038 7478 0.542805 GGGGGCATACGTGAAGGTAA 59.457 55.000 0.00 0.00 0.00 2.85
3039 7479 0.618107 TGGGGGCATACGTGAAGGTA 60.618 55.000 0.00 0.00 0.00 3.08
3040 7480 1.493854 TTGGGGGCATACGTGAAGGT 61.494 55.000 0.00 0.00 0.00 3.50
3041 7481 0.748005 CTTGGGGGCATACGTGAAGG 60.748 60.000 0.00 0.00 0.00 3.46
3042 7482 0.035439 ACTTGGGGGCATACGTGAAG 60.035 55.000 0.00 0.00 0.00 3.02
3043 7483 0.322098 CACTTGGGGGCATACGTGAA 60.322 55.000 0.00 0.00 0.00 3.18
3044 7484 1.298340 CACTTGGGGGCATACGTGA 59.702 57.895 0.00 0.00 0.00 4.35
3045 7485 2.406616 GCACTTGGGGGCATACGTG 61.407 63.158 0.00 0.00 0.00 4.49
3046 7486 2.045340 GCACTTGGGGGCATACGT 60.045 61.111 0.00 0.00 0.00 3.57
3047 7487 3.202001 CGCACTTGGGGGCATACG 61.202 66.667 0.00 0.00 0.00 3.06
3048 7488 3.518068 GCGCACTTGGGGGCATAC 61.518 66.667 0.30 0.00 45.15 2.39
3053 7493 2.044451 TAATGGCGCACTTGGGGG 60.044 61.111 10.83 0.00 0.00 5.40
3054 7494 0.107410 TAGTAATGGCGCACTTGGGG 60.107 55.000 10.83 0.00 0.00 4.96
3055 7495 1.603802 CATAGTAATGGCGCACTTGGG 59.396 52.381 10.83 0.00 0.00 4.12
3056 7496 1.002468 GCATAGTAATGGCGCACTTGG 60.002 52.381 10.83 0.90 33.38 3.61
3057 7497 2.389713 GCATAGTAATGGCGCACTTG 57.610 50.000 10.83 6.58 33.38 3.16
3067 7507 2.695359 CGCATTACGGGGCATAGTAAT 58.305 47.619 5.91 5.91 42.33 1.89
3068 7508 1.874739 GCGCATTACGGGGCATAGTAA 60.875 52.381 0.30 2.17 45.15 2.24
3069 7509 0.320073 GCGCATTACGGGGCATAGTA 60.320 55.000 0.30 0.00 45.15 1.82
3070 7510 1.597027 GCGCATTACGGGGCATAGT 60.597 57.895 0.30 0.00 45.15 2.12
3071 7511 3.253955 GCGCATTACGGGGCATAG 58.746 61.111 0.30 0.00 45.15 2.23
3076 7516 1.594293 CTAGTGGCGCATTACGGGG 60.594 63.158 10.83 0.00 43.93 5.73
3077 7517 0.386476 TACTAGTGGCGCATTACGGG 59.614 55.000 10.83 6.13 43.93 5.28
3078 7518 2.433868 ATACTAGTGGCGCATTACGG 57.566 50.000 10.83 6.47 43.93 4.02
3080 7520 4.151867 GGCTAAATACTAGTGGCGCATTAC 59.848 45.833 10.83 5.01 0.00 1.89
3081 7521 4.039973 AGGCTAAATACTAGTGGCGCATTA 59.960 41.667 10.83 0.00 0.00 1.90
3082 7522 3.139077 GGCTAAATACTAGTGGCGCATT 58.861 45.455 10.83 0.00 0.00 3.56
3083 7523 2.368875 AGGCTAAATACTAGTGGCGCAT 59.631 45.455 10.83 0.00 0.00 4.73
3084 7524 1.760613 AGGCTAAATACTAGTGGCGCA 59.239 47.619 10.83 0.00 0.00 6.09
3085 7525 2.528041 AGGCTAAATACTAGTGGCGC 57.472 50.000 5.39 0.00 0.00 6.53
3086 7526 3.131396 CCAAGGCTAAATACTAGTGGCG 58.869 50.000 5.39 0.00 0.00 5.69
3087 7527 3.877508 CACCAAGGCTAAATACTAGTGGC 59.122 47.826 5.39 0.09 0.00 5.01
3088 7528 3.877508 GCACCAAGGCTAAATACTAGTGG 59.122 47.826 5.39 0.00 0.00 4.00
3089 7529 3.555956 CGCACCAAGGCTAAATACTAGTG 59.444 47.826 5.39 0.00 0.00 2.74
3090 7530 3.793559 CGCACCAAGGCTAAATACTAGT 58.206 45.455 0.00 0.00 0.00 2.57
3091 7531 2.544267 GCGCACCAAGGCTAAATACTAG 59.456 50.000 0.30 0.00 0.00 2.57
3092 7532 2.169769 AGCGCACCAAGGCTAAATACTA 59.830 45.455 11.47 0.00 37.83 1.82
3093 7533 1.065418 AGCGCACCAAGGCTAAATACT 60.065 47.619 11.47 0.00 37.83 2.12
3094 7534 1.379527 AGCGCACCAAGGCTAAATAC 58.620 50.000 11.47 0.00 37.83 1.89
3095 7535 2.169769 AGTAGCGCACCAAGGCTAAATA 59.830 45.455 11.47 0.00 42.85 1.40
3096 7536 1.065418 AGTAGCGCACCAAGGCTAAAT 60.065 47.619 11.47 0.00 42.85 1.40
3097 7537 0.323629 AGTAGCGCACCAAGGCTAAA 59.676 50.000 11.47 0.00 42.85 1.85
3098 7538 1.187974 TAGTAGCGCACCAAGGCTAA 58.812 50.000 11.47 0.00 42.85 3.09
3099 7539 1.187974 TTAGTAGCGCACCAAGGCTA 58.812 50.000 11.47 0.00 40.58 3.93
3100 7540 0.541863 ATTAGTAGCGCACCAAGGCT 59.458 50.000 11.47 0.00 43.12 4.58
3101 7541 0.657840 CATTAGTAGCGCACCAAGGC 59.342 55.000 11.47 0.00 0.00 4.35
3102 7542 0.657840 GCATTAGTAGCGCACCAAGG 59.342 55.000 11.47 4.35 0.00 3.61
3103 7543 1.594862 GAGCATTAGTAGCGCACCAAG 59.405 52.381 11.47 0.00 37.01 3.61
3104 7544 1.066502 TGAGCATTAGTAGCGCACCAA 60.067 47.619 11.47 1.44 36.88 3.67
3105 7545 0.534873 TGAGCATTAGTAGCGCACCA 59.465 50.000 11.47 0.00 36.88 4.17
3106 7546 1.327764 GTTGAGCATTAGTAGCGCACC 59.672 52.381 11.47 0.00 41.41 5.01
3107 7547 1.999735 TGTTGAGCATTAGTAGCGCAC 59.000 47.619 11.47 5.97 41.41 5.34
3108 7548 2.378445 TGTTGAGCATTAGTAGCGCA 57.622 45.000 11.47 0.00 40.01 6.09
3109 7549 2.030946 CCTTGTTGAGCATTAGTAGCGC 59.969 50.000 0.00 0.00 37.01 5.92
3110 7550 3.062639 CACCTTGTTGAGCATTAGTAGCG 59.937 47.826 0.00 0.00 37.01 4.26
3111 7551 3.181506 GCACCTTGTTGAGCATTAGTAGC 60.182 47.826 0.00 0.00 0.00 3.58
3112 7552 3.062639 CGCACCTTGTTGAGCATTAGTAG 59.937 47.826 0.00 0.00 0.00 2.57
3113 7553 3.000041 CGCACCTTGTTGAGCATTAGTA 59.000 45.455 0.00 0.00 0.00 1.82
3114 7554 1.806542 CGCACCTTGTTGAGCATTAGT 59.193 47.619 0.00 0.00 0.00 2.24
3115 7555 1.466360 GCGCACCTTGTTGAGCATTAG 60.466 52.381 0.30 0.00 41.51 1.73
3116 7556 0.521291 GCGCACCTTGTTGAGCATTA 59.479 50.000 0.30 0.00 41.51 1.90
3117 7557 1.286880 GCGCACCTTGTTGAGCATT 59.713 52.632 0.30 0.00 41.51 3.56
3118 7558 2.629656 GGCGCACCTTGTTGAGCAT 61.630 57.895 10.83 0.00 43.47 3.79
3119 7559 3.286751 GGCGCACCTTGTTGAGCA 61.287 61.111 10.83 0.00 43.47 4.26
3120 7560 3.286751 TGGCGCACCTTGTTGAGC 61.287 61.111 10.83 0.00 41.19 4.26
3121 7561 2.639286 GTGGCGCACCTTGTTGAG 59.361 61.111 10.83 0.00 36.63 3.02


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

AutoCloner maintained by Alex Coulton.