Multiple sequence alignment - TraesCS2B01G007600

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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 TraesCS2B01G007600 chr2B 100.000 3314 0 0 1 3314 4643215 4646528 0.000000e+00 6120.0
1 TraesCS2B01G007600 chr2B 79.892 2228 408 35 1 2208 727686517 727688724 0.000000e+00 1596.0
2 TraesCS2B01G007600 chr2B 90.278 72 0 5 2856 2926 73800280 73800215 1.640000e-13 87.9
3 TraesCS2B01G007600 chr2B 92.308 52 3 1 3089 3139 464822809 464822758 4.590000e-09 73.1
4 TraesCS2B01G007600 chr2D 87.424 2314 265 16 2 2296 7970593 7972899 0.000000e+00 2638.0
5 TraesCS2B01G007600 chr2D 91.698 1867 93 26 1207 3049 8279046 8280874 0.000000e+00 2532.0
6 TraesCS2B01G007600 chr2D 80.162 2228 402 34 1 2208 598814561 598816768 0.000000e+00 1629.0
7 TraesCS2B01G007600 chr2D 95.425 153 7 0 3134 3286 7973632 7973784 9.190000e-61 244.0
8 TraesCS2B01G007600 chr2D 82.520 246 28 14 3038 3276 8280916 8281153 5.610000e-48 202.0
9 TraesCS2B01G007600 chr2D 89.831 118 10 2 2932 3047 7973370 7973487 2.060000e-32 150.0
10 TraesCS2B01G007600 chr2D 87.156 109 12 1 2637 2743 8280550 8280658 4.490000e-24 122.0
11 TraesCS2B01G007600 chr2D 95.556 45 2 0 3092 3136 135158106 135158150 4.590000e-09 73.1
12 TraesCS2B01G007600 chrUn 86.782 2315 280 16 1 2296 11753161 11750854 0.000000e+00 2556.0
13 TraesCS2B01G007600 chrUn 93.631 157 7 2 3134 3289 11748241 11748087 7.150000e-57 231.0
14 TraesCS2B01G007600 chrUn 95.000 60 2 1 2880 2939 35713295 35713353 3.520000e-15 93.5
15 TraesCS2B01G007600 chrUn 100.000 30 0 0 3018 3047 11748414 11748385 4.620000e-04 56.5
16 TraesCS2B01G007600 chr7D 80.541 2256 405 29 1 2239 555195907 555193669 0.000000e+00 1703.0
17 TraesCS2B01G007600 chr7D 79.347 2266 431 36 10 2258 20311347 20313592 0.000000e+00 1557.0
18 TraesCS2B01G007600 chr7D 79.200 2274 428 40 1 2254 20442940 20445188 0.000000e+00 1537.0
19 TraesCS2B01G007600 chr7D 94.000 50 1 2 3085 3133 6792158 6792206 1.280000e-09 75.0
20 TraesCS2B01G007600 chr7B 80.389 2264 408 31 1 2247 601114952 601117196 0.000000e+00 1688.0
21 TraesCS2B01G007600 chr7B 93.651 63 2 2 2873 2935 681769361 681769301 3.520000e-15 93.5
22 TraesCS2B01G007600 chr2A 80.053 2246 410 32 1 2227 733088263 733090489 0.000000e+00 1631.0
23 TraesCS2B01G007600 chr5B 96.552 58 1 1 2873 2930 43751666 43751722 9.790000e-16 95.3
24 TraesCS2B01G007600 chr5B 98.148 54 0 1 2873 2926 50350235 50350287 3.520000e-15 93.5
25 TraesCS2B01G007600 chr1B 93.548 62 2 2 2868 2929 498633105 498633046 1.270000e-14 91.6
26 TraesCS2B01G007600 chr6B 90.278 72 2 5 2856 2926 529709043 529709110 4.560000e-14 89.8
27 TraesCS2B01G007600 chr6B 95.556 45 2 0 3092 3136 134816415 134816459 4.590000e-09 73.1
28 TraesCS2B01G007600 chr3D 89.855 69 5 2 2859 2926 545069421 545069354 1.640000e-13 87.9
29 TraesCS2B01G007600 chr3B 89.706 68 6 1 2860 2927 101647720 101647786 5.890000e-13 86.1
30 TraesCS2B01G007600 chr3B 85.484 62 9 0 1577 1638 814451185 814451246 7.680000e-07 65.8
31 TraesCS2B01G007600 chr5D 92.308 52 3 1 3089 3139 447459634 447459583 4.590000e-09 73.1
32 TraesCS2B01G007600 chr1D 95.652 46 1 1 3089 3133 29053207 29053162 4.590000e-09 73.1
33 TraesCS2B01G007600 chr1D 95.652 46 1 1 3089 3133 70075910 70075865 4.590000e-09 73.1
34 TraesCS2B01G007600 chr1D 95.652 46 1 1 3089 3133 70373340 70373295 4.590000e-09 73.1
35 TraesCS2B01G007600 chr4A 92.157 51 3 1 3089 3138 735658398 735658448 1.650000e-08 71.3


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 TraesCS2B01G007600 chr2B 4643215 4646528 3313 False 6120.000000 6120 100.000000 1 3314 1 chr2B.!!$F1 3313
1 TraesCS2B01G007600 chr2B 727686517 727688724 2207 False 1596.000000 1596 79.892000 1 2208 1 chr2B.!!$F2 2207
2 TraesCS2B01G007600 chr2D 598814561 598816768 2207 False 1629.000000 1629 80.162000 1 2208 1 chr2D.!!$F2 2207
3 TraesCS2B01G007600 chr2D 7970593 7973784 3191 False 1010.666667 2638 90.893333 2 3286 3 chr2D.!!$F3 3284
4 TraesCS2B01G007600 chr2D 8279046 8281153 2107 False 952.000000 2532 87.124667 1207 3276 3 chr2D.!!$F4 2069
5 TraesCS2B01G007600 chrUn 11748087 11753161 5074 True 947.833333 2556 93.471000 1 3289 3 chrUn.!!$R1 3288
6 TraesCS2B01G007600 chr7D 555193669 555195907 2238 True 1703.000000 1703 80.541000 1 2239 1 chr7D.!!$R1 2238
7 TraesCS2B01G007600 chr7D 20311347 20313592 2245 False 1557.000000 1557 79.347000 10 2258 1 chr7D.!!$F2 2248
8 TraesCS2B01G007600 chr7D 20442940 20445188 2248 False 1537.000000 1537 79.200000 1 2254 1 chr7D.!!$F3 2253
9 TraesCS2B01G007600 chr7B 601114952 601117196 2244 False 1688.000000 1688 80.389000 1 2247 1 chr7B.!!$F1 2246
10 TraesCS2B01G007600 chr2A 733088263 733090489 2226 False 1631.000000 1631 80.053000 1 2227 1 chr2A.!!$F1 2226

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
944 945 0.544357 TTCATCGTGGAGAGGGGTGT 60.544 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 2433 0.029834 CAGCAAGGTGTTCAGTGCAC 59.97 55.0 9.4 9.4 39.5 4.57 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
90 91 4.946160 TCTAGTTGGGGTGGATGAAAAT 57.054 40.909 0.00 0.00 0.00 1.82
168 169 0.846015 TGATAGGAATGGGTGGGCTG 59.154 55.000 0.00 0.00 0.00 4.85
186 187 1.340889 CTGGGCAAAACAGCTTTAGCA 59.659 47.619 4.33 0.00 45.16 3.49
339 340 2.093890 TCAAACATTGCAGCGATGGAT 58.906 42.857 24.17 11.59 30.00 3.41
369 370 3.688673 GCCTTGAAGAGACATTGAAGAGG 59.311 47.826 0.00 0.00 0.00 3.69
466 467 6.362248 AGGTCACTTGTTTGTAATGGTAAGT 58.638 36.000 0.00 0.00 0.00 2.24
862 863 1.266989 GTTGTTTCCTGTACTGCAGCC 59.733 52.381 15.27 5.21 43.71 4.85
885 886 8.332487 AGCCTATTTCCAGAAGACTATCTTTTT 58.668 33.333 0.00 0.00 36.73 1.94
887 888 8.821894 CCTATTTCCAGAAGACTATCTTTTTCG 58.178 37.037 0.00 0.00 36.73 3.46
896 897 8.070769 AGAAGACTATCTTTTTCGCAGAAAAAC 58.929 33.333 18.62 11.61 38.28 2.43
897 898 7.497925 AGACTATCTTTTTCGCAGAAAAACT 57.502 32.000 18.62 13.00 45.90 2.66
944 945 0.544357 TTCATCGTGGAGAGGGGTGT 60.544 55.000 0.00 0.00 0.00 4.16
972 973 4.042187 ACATTAGAAGAAGTGGCAGAAGGT 59.958 41.667 0.00 0.00 0.00 3.50
996 997 4.351874 TCTGAAGGAGTTGGTTAACAGG 57.648 45.455 8.10 0.00 39.30 4.00
1015 1016 4.275936 ACAGGAACATGCTACAACTTGTTC 59.724 41.667 12.36 12.36 46.26 3.18
1017 1018 2.969443 ACATGCTACAACTTGTTCGC 57.031 45.000 0.00 4.57 0.00 4.70
1023 1024 2.484264 GCTACAACTTGTTCGCAGGAAT 59.516 45.455 0.00 0.00 34.05 3.01
1024 1025 3.667960 GCTACAACTTGTTCGCAGGAATG 60.668 47.826 0.00 0.00 34.05 2.67
1095 1096 2.397549 GCAGTTGATTTGTGCCAGAAC 58.602 47.619 0.00 0.00 0.00 3.01
1096 1097 2.035066 GCAGTTGATTTGTGCCAGAACT 59.965 45.455 0.00 0.00 0.00 3.01
1112 1113 6.548441 CCAGAACTATCGTTTTGGTGTTAA 57.452 37.500 10.59 0.00 45.54 2.01
1115 1116 7.749126 CCAGAACTATCGTTTTGGTGTTAAATC 59.251 37.037 10.59 0.00 45.54 2.17
1123 1124 6.488683 TCGTTTTGGTGTTAAATCTGAGGATT 59.511 34.615 0.00 0.00 43.26 3.01
1138 1139 4.886163 TGAGGATTATATATGCGGGGGTA 58.114 43.478 0.00 0.00 0.00 3.69
1146 1147 2.097110 TATGCGGGGGTACTCTTCAT 57.903 50.000 0.00 0.00 0.00 2.57
1158 1159 2.320781 ACTCTTCATAGGGATGGACGG 58.679 52.381 0.00 0.00 33.49 4.79
1159 1160 2.091278 ACTCTTCATAGGGATGGACGGA 60.091 50.000 0.00 0.00 33.49 4.69
1194 1195 8.462016 GTGCACAAACTAAAGAAGGATATTCAT 58.538 33.333 13.17 0.00 0.00 2.57
1276 1277 3.135895 GCCATTAACCCTGCTACCTCTAA 59.864 47.826 0.00 0.00 0.00 2.10
1400 1401 2.669391 GCTTGCGGGATTCAAAAGTGAG 60.669 50.000 0.00 0.00 34.49 3.51
1403 1404 2.039216 TGCGGGATTCAAAAGTGAGGTA 59.961 45.455 0.00 0.00 34.49 3.08
1410 1411 5.339200 GGATTCAAAAGTGAGGTATCTCCCA 60.339 44.000 0.00 0.00 39.23 4.37
1435 1436 5.747951 ATCCATCGAGAAGCTTTTGAATC 57.252 39.130 0.00 0.00 0.00 2.52
1731 1754 0.962489 AACACCTCCACGAGTCTCTG 59.038 55.000 0.00 0.00 0.00 3.35
1801 1824 7.067372 ACAAGAATGAAGTTCTCATGTTGAACA 59.933 33.333 24.60 0.00 46.39 3.18
1873 1896 1.553706 GACACTTTCGAGGGGGTCTA 58.446 55.000 12.76 0.00 0.00 2.59
2085 2111 0.613260 ACATGCCTAACCTGAAGCGA 59.387 50.000 0.00 0.00 0.00 4.93
2099 2125 4.037446 CCTGAAGCGACTAGAGATAAAGCT 59.963 45.833 0.00 0.00 34.70 3.74
2130 2156 1.597663 GCGACCCTGGAATCATTTACG 59.402 52.381 0.00 0.00 0.00 3.18
2305 2331 1.922220 GACGACGACGACGATGACG 60.922 63.158 25.15 14.84 42.66 4.35
2306 2332 2.271024 GACGACGACGACGATGACGA 62.271 60.000 25.15 0.00 41.06 4.20
2307 2333 1.922220 CGACGACGACGATGACGAC 60.922 63.158 15.32 1.87 41.06 4.34
2308 2334 1.579626 GACGACGACGATGACGACC 60.580 63.158 15.32 0.00 42.66 4.79
2310 2336 2.277120 GACGACGATGACGACCGG 60.277 66.667 0.00 0.00 42.66 5.28
2312 2338 2.576053 CGACGATGACGACCGGTG 60.576 66.667 14.63 7.23 42.66 4.94
2313 2339 2.872557 GACGATGACGACCGGTGA 59.127 61.111 14.63 0.00 42.66 4.02
2314 2340 1.432251 GACGATGACGACCGGTGAT 59.568 57.895 14.63 0.00 42.66 3.06
2322 2348 2.134287 CGACCGGTGATCCTCCCAT 61.134 63.158 14.63 0.00 0.00 4.00
2343 2371 6.460123 CCCATAACTTGCATGTAAGTTGATCC 60.460 42.308 37.05 2.82 46.98 3.36
2360 2388 4.278310 TGATCCCTCTCGACTGTGAAATA 58.722 43.478 0.00 0.00 0.00 1.40
2364 2392 3.181471 CCCTCTCGACTGTGAAATAGCAT 60.181 47.826 0.00 0.00 0.00 3.79
2365 2393 4.437239 CCTCTCGACTGTGAAATAGCATT 58.563 43.478 0.00 0.00 0.00 3.56
2366 2394 5.451937 CCCTCTCGACTGTGAAATAGCATTA 60.452 44.000 0.00 0.00 0.00 1.90
2367 2395 6.219473 CCTCTCGACTGTGAAATAGCATTAT 58.781 40.000 0.00 0.00 0.00 1.28
2368 2396 6.364706 CCTCTCGACTGTGAAATAGCATTATC 59.635 42.308 0.00 0.00 0.00 1.75
2369 2397 6.805713 TCTCGACTGTGAAATAGCATTATCA 58.194 36.000 0.00 0.00 0.00 2.15
2370 2398 6.920210 TCTCGACTGTGAAATAGCATTATCAG 59.080 38.462 0.00 0.00 0.00 2.90
2371 2399 6.573434 TCGACTGTGAAATAGCATTATCAGT 58.427 36.000 0.00 0.00 37.56 3.41
2401 2429 8.695456 TCACTTATATCACTCTCAGCATGTTAA 58.305 33.333 0.00 0.00 37.40 2.01
2402 2430 9.486497 CACTTATATCACTCTCAGCATGTTAAT 57.514 33.333 0.00 0.00 37.40 1.40
2407 2435 7.783090 ATCACTCTCAGCATGTTAATTAGTG 57.217 36.000 0.00 2.58 37.40 2.74
2408 2436 5.582269 TCACTCTCAGCATGTTAATTAGTGC 59.418 40.000 10.04 10.04 37.40 4.40
2409 2437 5.352293 CACTCTCAGCATGTTAATTAGTGCA 59.648 40.000 16.73 5.89 39.94 4.57
2410 2438 5.352569 ACTCTCAGCATGTTAATTAGTGCAC 59.647 40.000 9.40 9.40 39.94 4.57
2411 2439 5.491070 TCTCAGCATGTTAATTAGTGCACT 58.509 37.500 25.12 25.12 39.94 4.40
2412 2440 5.352293 TCTCAGCATGTTAATTAGTGCACTG 59.648 40.000 29.57 10.98 39.94 3.66
2471 2499 2.656560 AGATATATGCGCCTCGGTTC 57.343 50.000 4.18 0.00 0.00 3.62
2476 2504 0.885879 TATGCGCCTCGGTTCGATAT 59.114 50.000 4.18 0.00 34.61 1.63
2491 2519 4.230314 TCGATATCTGTTCTACTGCTGC 57.770 45.455 0.34 0.00 0.00 5.25
2493 2521 4.023622 TCGATATCTGTTCTACTGCTGCTC 60.024 45.833 0.00 0.00 0.00 4.26
2585 2613 3.628032 TGGCGTTGAAATAACAAGACACA 59.372 39.130 0.00 0.00 0.00 3.72
2684 2821 9.317936 TCTATTCATGTGAGCTTGTAAACTATG 57.682 33.333 0.00 0.00 0.00 2.23
2689 2826 5.109210 TGTGAGCTTGTAAACTATGATCGG 58.891 41.667 0.00 0.00 0.00 4.18
2703 2842 4.768130 ATGATCGGTACTGTCTATTCCG 57.232 45.455 0.64 0.00 42.12 4.30
2705 2844 1.027357 TCGGTACTGTCTATTCCGGC 58.973 55.000 0.00 0.00 41.27 6.13
2706 2845 0.031721 CGGTACTGTCTATTCCGGCC 59.968 60.000 0.00 0.00 37.92 6.13
2707 2846 0.031721 GGTACTGTCTATTCCGGCCG 59.968 60.000 21.04 21.04 0.00 6.13
2709 2848 0.742505 TACTGTCTATTCCGGCCGTG 59.257 55.000 26.12 15.93 0.00 4.94
2710 2849 1.883084 CTGTCTATTCCGGCCGTGC 60.883 63.158 26.12 6.15 0.00 5.34
2711 2850 2.960129 GTCTATTCCGGCCGTGCG 60.960 66.667 26.12 9.25 0.00 5.34
2712 2851 3.454573 TCTATTCCGGCCGTGCGT 61.455 61.111 26.12 9.60 0.00 5.24
2713 2852 3.261951 CTATTCCGGCCGTGCGTG 61.262 66.667 26.12 8.39 0.00 5.34
2714 2853 4.071875 TATTCCGGCCGTGCGTGT 62.072 61.111 26.12 6.18 0.00 4.49
2715 2854 3.592856 TATTCCGGCCGTGCGTGTT 62.593 57.895 26.12 3.81 0.00 3.32
2724 2863 1.727880 GCCGTGCGTGTTGAATAACTA 59.272 47.619 0.00 0.00 37.68 2.24
2734 2880 6.399564 GCGTGTTGAATAACTAAACCATTTGC 60.400 38.462 0.00 0.00 37.68 3.68
2738 2884 6.561737 TGAATAACTAAACCATTTGCGTGA 57.438 33.333 0.00 0.00 0.00 4.35
2740 2886 7.598278 TGAATAACTAAACCATTTGCGTGAAT 58.402 30.769 0.00 0.00 0.00 2.57
2741 2887 8.085296 TGAATAACTAAACCATTTGCGTGAATT 58.915 29.630 0.00 0.00 0.00 2.17
2742 2888 8.825667 AATAACTAAACCATTTGCGTGAATTT 57.174 26.923 0.00 0.00 0.00 1.82
2743 2889 6.523676 AACTAAACCATTTGCGTGAATTTG 57.476 33.333 0.00 0.00 0.00 2.32
2744 2890 5.596845 ACTAAACCATTTGCGTGAATTTGT 58.403 33.333 0.00 0.00 0.00 2.83
2745 2891 4.792528 AAACCATTTGCGTGAATTTGTG 57.207 36.364 0.00 0.00 0.00 3.33
2746 2892 2.134346 ACCATTTGCGTGAATTTGTGC 58.866 42.857 0.00 0.00 0.00 4.57
2747 2893 1.124658 CCATTTGCGTGAATTTGTGCG 59.875 47.619 0.00 0.00 0.00 5.34
2750 2896 2.804931 GCGTGAATTTGTGCGCCC 60.805 61.111 4.18 0.00 43.52 6.13
2751 2897 2.642129 CGTGAATTTGTGCGCCCA 59.358 55.556 4.18 0.00 0.00 5.36
2752 2898 1.007964 CGTGAATTTGTGCGCCCAA 60.008 52.632 4.18 1.76 0.00 4.12
2753 2899 1.274798 CGTGAATTTGTGCGCCCAAC 61.275 55.000 4.31 0.00 0.00 3.77
2754 2900 0.031994 GTGAATTTGTGCGCCCAACT 59.968 50.000 4.31 0.00 0.00 3.16
2755 2901 1.268352 GTGAATTTGTGCGCCCAACTA 59.732 47.619 4.31 0.00 0.00 2.24
2756 2902 2.094752 GTGAATTTGTGCGCCCAACTAT 60.095 45.455 4.31 0.00 0.00 2.12
2757 2903 2.560542 TGAATTTGTGCGCCCAACTATT 59.439 40.909 4.31 3.37 0.00 1.73
2758 2904 2.652941 ATTTGTGCGCCCAACTATTG 57.347 45.000 4.31 0.00 0.00 1.90
2759 2905 1.323412 TTTGTGCGCCCAACTATTGT 58.677 45.000 4.31 0.00 0.00 2.71
2760 2906 0.595588 TTGTGCGCCCAACTATTGTG 59.404 50.000 4.18 0.00 0.00 3.33
2761 2907 0.536233 TGTGCGCCCAACTATTGTGT 60.536 50.000 4.18 0.00 0.00 3.72
2762 2908 0.109781 GTGCGCCCAACTATTGTGTG 60.110 55.000 4.18 0.00 0.00 3.82
2763 2909 0.536233 TGCGCCCAACTATTGTGTGT 60.536 50.000 4.18 0.00 0.00 3.72
2764 2910 1.270893 TGCGCCCAACTATTGTGTGTA 60.271 47.619 4.18 0.00 0.00 2.90
2765 2911 2.014128 GCGCCCAACTATTGTGTGTAT 58.986 47.619 0.00 0.00 0.00 2.29
2766 2912 2.422127 GCGCCCAACTATTGTGTGTATT 59.578 45.455 0.00 0.00 0.00 1.89
2767 2913 3.486875 GCGCCCAACTATTGTGTGTATTC 60.487 47.826 0.00 0.00 0.00 1.75
2768 2914 3.938963 CGCCCAACTATTGTGTGTATTCT 59.061 43.478 0.00 0.00 0.00 2.40
2769 2915 5.113383 CGCCCAACTATTGTGTGTATTCTA 58.887 41.667 0.00 0.00 0.00 2.10
2770 2916 5.758296 CGCCCAACTATTGTGTGTATTCTAT 59.242 40.000 0.00 0.00 0.00 1.98
2771 2917 6.073765 CGCCCAACTATTGTGTGTATTCTATC 60.074 42.308 0.00 0.00 0.00 2.08
2772 2918 6.204882 GCCCAACTATTGTGTGTATTCTATCC 59.795 42.308 0.00 0.00 0.00 2.59
2773 2919 6.423905 CCCAACTATTGTGTGTATTCTATCCG 59.576 42.308 0.00 0.00 0.00 4.18
2774 2920 6.984474 CCAACTATTGTGTGTATTCTATCCGT 59.016 38.462 0.00 0.00 0.00 4.69
2775 2921 7.042725 CCAACTATTGTGTGTATTCTATCCGTG 60.043 40.741 0.00 0.00 0.00 4.94
2776 2922 7.108841 ACTATTGTGTGTATTCTATCCGTGT 57.891 36.000 0.00 0.00 0.00 4.49
2777 2923 6.978659 ACTATTGTGTGTATTCTATCCGTGTG 59.021 38.462 0.00 0.00 0.00 3.82
2778 2924 4.118093 TGTGTGTATTCTATCCGTGTGG 57.882 45.455 0.00 0.00 0.00 4.17
2779 2925 3.118920 TGTGTGTATTCTATCCGTGTGGG 60.119 47.826 0.00 0.00 35.24 4.61
2780 2926 2.159014 TGTGTATTCTATCCGTGTGGGC 60.159 50.000 0.00 0.00 35.24 5.36
2781 2927 2.102588 GTGTATTCTATCCGTGTGGGCT 59.897 50.000 0.00 0.00 35.24 5.19
2782 2928 2.769663 TGTATTCTATCCGTGTGGGCTT 59.230 45.455 0.00 0.00 35.24 4.35
2783 2929 2.332063 ATTCTATCCGTGTGGGCTTG 57.668 50.000 0.00 0.00 35.24 4.01
2784 2930 0.981183 TTCTATCCGTGTGGGCTTGT 59.019 50.000 0.00 0.00 35.24 3.16
2785 2931 1.855295 TCTATCCGTGTGGGCTTGTA 58.145 50.000 0.00 0.00 35.24 2.41
2786 2932 2.181125 TCTATCCGTGTGGGCTTGTAA 58.819 47.619 0.00 0.00 35.24 2.41
2787 2933 2.568062 TCTATCCGTGTGGGCTTGTAAA 59.432 45.455 0.00 0.00 35.24 2.01
2788 2934 1.530323 ATCCGTGTGGGCTTGTAAAC 58.470 50.000 0.00 0.00 35.24 2.01
2789 2935 0.470766 TCCGTGTGGGCTTGTAAACT 59.529 50.000 0.00 0.00 35.24 2.66
2790 2936 1.134037 TCCGTGTGGGCTTGTAAACTT 60.134 47.619 0.00 0.00 35.24 2.66
2791 2937 1.679153 CCGTGTGGGCTTGTAAACTTT 59.321 47.619 0.00 0.00 0.00 2.66
2792 2938 2.879646 CCGTGTGGGCTTGTAAACTTTA 59.120 45.455 0.00 0.00 0.00 1.85
2793 2939 3.315749 CCGTGTGGGCTTGTAAACTTTAA 59.684 43.478 0.00 0.00 0.00 1.52
2794 2940 4.022676 CCGTGTGGGCTTGTAAACTTTAAT 60.023 41.667 0.00 0.00 0.00 1.40
2795 2941 5.151389 CGTGTGGGCTTGTAAACTTTAATC 58.849 41.667 0.00 0.00 0.00 1.75
2796 2942 5.151389 GTGTGGGCTTGTAAACTTTAATCG 58.849 41.667 0.00 0.00 0.00 3.34
2797 2943 5.049267 GTGTGGGCTTGTAAACTTTAATCGA 60.049 40.000 0.00 0.00 0.00 3.59
2798 2944 5.708230 TGTGGGCTTGTAAACTTTAATCGAT 59.292 36.000 0.00 0.00 0.00 3.59
2799 2945 6.879993 TGTGGGCTTGTAAACTTTAATCGATA 59.120 34.615 0.00 0.00 0.00 2.92
2800 2946 7.148373 TGTGGGCTTGTAAACTTTAATCGATAC 60.148 37.037 0.00 0.00 0.00 2.24
2801 2947 7.065443 GTGGGCTTGTAAACTTTAATCGATACT 59.935 37.037 0.00 0.00 0.00 2.12
2802 2948 7.065324 TGGGCTTGTAAACTTTAATCGATACTG 59.935 37.037 0.00 0.00 0.00 2.74
2803 2949 7.065443 GGGCTTGTAAACTTTAATCGATACTGT 59.935 37.037 0.00 0.00 0.00 3.55
2804 2950 9.090692 GGCTTGTAAACTTTAATCGATACTGTA 57.909 33.333 0.00 0.00 0.00 2.74
2811 2957 9.661563 AAACTTTAATCGATACTGTATGTTCCA 57.338 29.630 4.79 0.00 0.00 3.53
2812 2958 8.873215 ACTTTAATCGATACTGTATGTTCCAG 57.127 34.615 4.79 0.00 36.01 3.86
2813 2959 8.475639 ACTTTAATCGATACTGTATGTTCCAGT 58.524 33.333 4.79 0.00 44.90 4.00
2814 2960 8.867112 TTTAATCGATACTGTATGTTCCAGTC 57.133 34.615 4.79 0.00 42.03 3.51
2815 2961 6.465439 AATCGATACTGTATGTTCCAGTCA 57.535 37.500 4.79 0.00 42.03 3.41
2912 3062 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2913 3063 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2914 3064 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2916 3066 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2917 3067 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2918 3068 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2919 3069 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2920 3070 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2922 3072 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2923 3073 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2926 3076 4.778958 TCTATTTTGGAACGGAGGGAGTAA 59.221 41.667 0.00 0.00 0.00 2.24
2928 3078 3.860968 TTTGGAACGGAGGGAGTAAAA 57.139 42.857 0.00 0.00 0.00 1.52
2930 3080 3.343941 TGGAACGGAGGGAGTAAAATG 57.656 47.619 0.00 0.00 0.00 2.32
2959 3123 4.171878 TGACGATGAGGAGGAATAGAGT 57.828 45.455 0.00 0.00 0.00 3.24
2966 3130 6.209589 CGATGAGGAGGAATAGAGTTCCATAA 59.790 42.308 9.29 0.00 41.00 1.90
3016 5089 5.598417 TCAGCCTAGCTATACAAATGAGTGA 59.402 40.000 0.00 0.00 36.40 3.41
3084 5225 4.194640 GCTAAGATTGCAGAATCCTGACA 58.805 43.478 0.00 0.00 43.02 3.58
3090 5231 4.890158 TTGCAGAATCCTGACAAGAGTA 57.110 40.909 0.00 0.00 43.02 2.59
3091 5232 5.426689 TTGCAGAATCCTGACAAGAGTAT 57.573 39.130 0.00 0.00 43.02 2.12
3093 5234 6.544928 TGCAGAATCCTGACAAGAGTATTA 57.455 37.500 0.00 0.00 43.02 0.98
3094 5235 6.577103 TGCAGAATCCTGACAAGAGTATTAG 58.423 40.000 0.00 0.00 43.02 1.73
3095 5236 6.381133 TGCAGAATCCTGACAAGAGTATTAGA 59.619 38.462 0.00 0.00 43.02 2.10
3096 5237 6.699642 GCAGAATCCTGACAAGAGTATTAGAC 59.300 42.308 0.00 0.00 43.02 2.59
3098 5239 8.253810 CAGAATCCTGACAAGAGTATTAGACAA 58.746 37.037 0.00 0.00 43.02 3.18
3099 5240 8.816894 AGAATCCTGACAAGAGTATTAGACAAA 58.183 33.333 0.00 0.00 0.00 2.83
3100 5241 8.779354 AATCCTGACAAGAGTATTAGACAAAC 57.221 34.615 0.00 0.00 0.00 2.93
3101 5242 6.698380 TCCTGACAAGAGTATTAGACAAACC 58.302 40.000 0.00 0.00 0.00 3.27
3102 5243 6.497259 TCCTGACAAGAGTATTAGACAAACCT 59.503 38.462 0.00 0.00 0.00 3.50
3104 5245 8.311836 CCTGACAAGAGTATTAGACAAACCTAA 58.688 37.037 0.00 0.00 33.65 2.69
3105 5246 9.360093 CTGACAAGAGTATTAGACAAACCTAAG 57.640 37.037 0.00 0.00 32.75 2.18
3107 5248 9.924650 GACAAGAGTATTAGACAAACCTAAGAA 57.075 33.333 0.00 0.00 32.75 2.52
3127 5268 2.215942 AAGAATTTTGGGACGGAGGG 57.784 50.000 0.00 0.00 0.00 4.30
3128 5269 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3129 5270 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3132 5273 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
3289 5432 8.604035 CATTACAAGATACATGTATATTCCGCC 58.396 37.037 20.18 6.56 33.55 6.13
3290 5433 6.360370 ACAAGATACATGTATATTCCGCCT 57.640 37.500 20.18 8.57 0.00 5.52
3291 5434 6.769512 ACAAGATACATGTATATTCCGCCTT 58.230 36.000 20.18 13.36 0.00 4.35
3292 5435 7.224297 ACAAGATACATGTATATTCCGCCTTT 58.776 34.615 20.18 6.47 0.00 3.11
3293 5436 7.719633 ACAAGATACATGTATATTCCGCCTTTT 59.280 33.333 20.18 8.00 0.00 2.27
3294 5437 8.567948 CAAGATACATGTATATTCCGCCTTTTT 58.432 33.333 20.18 0.00 0.00 1.94
3295 5438 9.787435 AAGATACATGTATATTCCGCCTTTTTA 57.213 29.630 18.28 0.00 0.00 1.52
3296 5439 9.787435 AGATACATGTATATTCCGCCTTTTTAA 57.213 29.630 18.28 0.00 0.00 1.52
3300 5443 8.962679 ACATGTATATTCCGCCTTTTTAAAAGA 58.037 29.630 17.91 0.00 0.00 2.52
3301 5444 9.965824 CATGTATATTCCGCCTTTTTAAAAGAT 57.034 29.630 17.91 6.44 0.00 2.40
3302 5445 9.965824 ATGTATATTCCGCCTTTTTAAAAGATG 57.034 29.630 17.91 9.74 0.00 2.90
3303 5446 9.179909 TGTATATTCCGCCTTTTTAAAAGATGA 57.820 29.630 17.91 8.70 0.00 2.92
3304 5447 9.447040 GTATATTCCGCCTTTTTAAAAGATGAC 57.553 33.333 17.91 4.77 0.00 3.06
3305 5448 4.413495 TCCGCCTTTTTAAAAGATGACG 57.587 40.909 17.91 14.32 0.00 4.35
3306 5449 2.914838 CCGCCTTTTTAAAAGATGACGC 59.085 45.455 17.91 11.21 0.00 5.19
3307 5450 2.588106 CGCCTTTTTAAAAGATGACGCG 59.412 45.455 17.91 17.93 0.00 6.01
3308 5451 2.341464 GCCTTTTTAAAAGATGACGCGC 59.659 45.455 17.91 7.72 0.00 6.86
3309 5452 3.560503 CCTTTTTAAAAGATGACGCGCA 58.439 40.909 17.91 5.73 0.00 6.09
3310 5453 3.978217 CCTTTTTAAAAGATGACGCGCAA 59.022 39.130 17.91 0.00 0.00 4.85
3311 5454 4.442733 CCTTTTTAAAAGATGACGCGCAAA 59.557 37.500 17.91 0.00 0.00 3.68
3312 5455 5.118510 CCTTTTTAAAAGATGACGCGCAAAT 59.881 36.000 17.91 0.00 0.00 2.32
3313 5456 6.306837 CCTTTTTAAAAGATGACGCGCAAATA 59.693 34.615 17.91 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 4.985538 ACCATTGCTCAAGTTTTCCTCTA 58.014 39.130 0.00 0.00 0.00 2.43
168 169 2.029110 TGATGCTAAAGCTGTTTTGCCC 60.029 45.455 3.26 0.00 41.90 5.36
186 187 9.653516 TCTCTCTCTTTCCTATAGACATTTGAT 57.346 33.333 0.00 0.00 0.00 2.57
292 293 7.286546 TGGACCACTGACTTCATTTTTGAATAA 59.713 33.333 0.00 0.00 0.00 1.40
301 302 4.371624 TTGATGGACCACTGACTTCATT 57.628 40.909 0.00 0.00 0.00 2.57
304 305 3.476552 TGTTTGATGGACCACTGACTTC 58.523 45.455 0.00 0.00 0.00 3.01
339 340 4.890158 TGTCTCTTCAAGGCTTGTGATA 57.110 40.909 25.39 14.67 0.00 2.15
466 467 6.402442 CGTGTTGTGATTATCAATCTGCTTCA 60.402 38.462 0.00 0.00 38.72 3.02
862 863 8.331742 GCGAAAAAGATAGTCTTCTGGAAATAG 58.668 37.037 0.00 0.00 35.27 1.73
885 886 2.798283 CCGTACAAGAGTTTTTCTGCGA 59.202 45.455 0.00 0.00 35.91 5.10
887 888 4.547406 AACCGTACAAGAGTTTTTCTGC 57.453 40.909 0.00 0.00 35.91 4.26
896 897 2.805845 CCGTCCATAACCGTACAAGAG 58.194 52.381 0.00 0.00 0.00 2.85
897 898 1.135024 GCCGTCCATAACCGTACAAGA 60.135 52.381 0.00 0.00 0.00 3.02
944 945 4.905429 TGCCACTTCTTCTAATGTGCTTA 58.095 39.130 0.00 0.00 0.00 3.09
972 973 6.271391 TCCTGTTAACCAACTCCTTCAGATAA 59.729 38.462 2.48 0.00 35.56 1.75
996 997 3.226347 GCGAACAAGTTGTAGCATGTTC 58.774 45.455 23.37 10.36 45.04 3.18
1017 1018 4.209538 TCATCCTACCAAATGCATTCCTG 58.790 43.478 13.38 8.28 0.00 3.86
1023 1024 6.436847 TGAATCTTTTCATCCTACCAAATGCA 59.563 34.615 0.00 0.00 36.94 3.96
1024 1025 6.866480 TGAATCTTTTCATCCTACCAAATGC 58.134 36.000 0.00 0.00 36.94 3.56
1095 1096 7.333423 TCCTCAGATTTAACACCAAAACGATAG 59.667 37.037 0.00 0.00 46.19 2.08
1096 1097 7.162761 TCCTCAGATTTAACACCAAAACGATA 58.837 34.615 0.00 0.00 0.00 2.92
1112 1113 5.072329 CCCCCGCATATATAATCCTCAGATT 59.928 44.000 0.00 0.00 44.95 2.40
1115 1116 3.711704 ACCCCCGCATATATAATCCTCAG 59.288 47.826 0.00 0.00 0.00 3.35
1123 1124 4.938028 TGAAGAGTACCCCCGCATATATA 58.062 43.478 0.00 0.00 0.00 0.86
1127 1128 2.097110 ATGAAGAGTACCCCCGCATA 57.903 50.000 0.00 0.00 0.00 3.14
1131 1132 1.133262 TCCCTATGAAGAGTACCCCCG 60.133 57.143 0.00 0.00 0.00 5.73
1138 1139 2.091278 TCCGTCCATCCCTATGAAGAGT 60.091 50.000 0.00 0.00 34.84 3.24
1146 1147 1.062428 ACCAATCTCCGTCCATCCCTA 60.062 52.381 0.00 0.00 0.00 3.53
1158 1159 6.426937 TCTTTAGTTTGTGCACTACCAATCTC 59.573 38.462 19.41 0.00 0.00 2.75
1159 1160 6.296026 TCTTTAGTTTGTGCACTACCAATCT 58.704 36.000 19.41 10.44 0.00 2.40
1194 1195 7.994911 AGTCCATGTATGCTAGAAAATGAATGA 59.005 33.333 0.00 0.00 0.00 2.57
1197 1198 7.011389 CGAAGTCCATGTATGCTAGAAAATGAA 59.989 37.037 0.00 0.00 0.00 2.57
1209 1210 6.668541 ATGAAAGTTCGAAGTCCATGTATG 57.331 37.500 15.71 0.00 0.00 2.39
1400 1401 4.040461 TCTCGATGGATTTTGGGAGATACC 59.960 45.833 0.00 0.00 38.08 2.73
1403 1404 4.712476 CTTCTCGATGGATTTTGGGAGAT 58.288 43.478 0.00 0.00 31.33 2.75
1410 1411 5.964958 TCAAAAGCTTCTCGATGGATTTT 57.035 34.783 0.00 0.00 0.00 1.82
1435 1436 1.414181 ACAGAGGTCCAGTGTCAACAG 59.586 52.381 0.00 0.00 0.00 3.16
1731 1754 2.340337 GACAAAAATGGCATCTGCACC 58.660 47.619 0.00 0.00 44.36 5.01
1801 1824 2.042843 CAGGCTAGTCGGGAGGGT 60.043 66.667 0.00 0.00 0.00 4.34
1860 1883 1.296984 AGAGAGTAGACCCCCTCGAA 58.703 55.000 0.00 0.00 32.88 3.71
1873 1896 2.224402 GCTCCACACCTTGAAAGAGAGT 60.224 50.000 0.00 0.00 0.00 3.24
2085 2111 4.547671 TGGCACCTAGCTTTATCTCTAGT 58.452 43.478 0.00 0.00 44.79 2.57
2099 2125 3.792736 GGGTCGCCATGGCACCTA 61.793 66.667 36.19 20.64 40.01 3.08
2130 2156 1.821216 TGCTGTTTAGGCTGCCTAAC 58.179 50.000 34.51 27.78 44.64 2.34
2305 2331 1.070289 GTTATGGGAGGATCACCGGTC 59.930 57.143 2.59 0.00 38.18 4.79
2306 2332 1.129058 GTTATGGGAGGATCACCGGT 58.871 55.000 0.00 0.00 38.18 5.28
2307 2333 1.424638 AGTTATGGGAGGATCACCGG 58.575 55.000 0.00 0.00 38.18 5.28
2308 2334 2.838736 CAAGTTATGGGAGGATCACCG 58.161 52.381 0.00 0.00 38.18 4.94
2310 2336 3.281727 TGCAAGTTATGGGAGGATCAC 57.718 47.619 0.00 0.00 40.71 3.06
2312 2338 3.825328 ACATGCAAGTTATGGGAGGATC 58.175 45.455 0.00 0.00 0.00 3.36
2313 2339 3.959495 ACATGCAAGTTATGGGAGGAT 57.041 42.857 0.00 0.00 0.00 3.24
2314 2340 4.227300 ACTTACATGCAAGTTATGGGAGGA 59.773 41.667 5.44 0.00 35.16 3.71
2322 2348 5.815581 AGGGATCAACTTACATGCAAGTTA 58.184 37.500 20.97 11.69 44.86 2.24
2343 2371 3.510388 TGCTATTTCACAGTCGAGAGG 57.490 47.619 0.00 0.00 0.00 3.69
2368 2396 9.190858 GCTGAGAGTGATATAAGTGATAAACTG 57.809 37.037 0.00 0.00 39.81 3.16
2369 2397 8.918116 TGCTGAGAGTGATATAAGTGATAAACT 58.082 33.333 0.00 0.00 42.60 2.66
2370 2398 9.703892 ATGCTGAGAGTGATATAAGTGATAAAC 57.296 33.333 0.00 0.00 0.00 2.01
2371 2399 9.702494 CATGCTGAGAGTGATATAAGTGATAAA 57.298 33.333 0.00 0.00 0.00 1.40
2382 2410 7.439356 GCACTAATTAACATGCTGAGAGTGATA 59.561 37.037 14.79 0.00 34.98 2.15
2401 2429 2.554032 GCAAGGTGTTCAGTGCACTAAT 59.446 45.455 21.20 0.00 36.97 1.73
2402 2430 1.946768 GCAAGGTGTTCAGTGCACTAA 59.053 47.619 21.20 0.57 36.97 2.24
2403 2431 1.140852 AGCAAGGTGTTCAGTGCACTA 59.859 47.619 21.20 1.09 39.50 2.74
2404 2432 0.107017 AGCAAGGTGTTCAGTGCACT 60.107 50.000 15.25 15.25 39.50 4.40
2405 2433 0.029834 CAGCAAGGTGTTCAGTGCAC 59.970 55.000 9.40 9.40 39.50 4.57
2406 2434 1.102809 CCAGCAAGGTGTTCAGTGCA 61.103 55.000 0.00 0.00 39.50 4.57
2407 2435 1.656441 CCAGCAAGGTGTTCAGTGC 59.344 57.895 0.00 0.00 37.26 4.40
2471 2499 4.023279 AGAGCAGCAGTAGAACAGATATCG 60.023 45.833 0.00 0.00 0.00 2.92
2476 2504 3.421844 TGTAGAGCAGCAGTAGAACAGA 58.578 45.455 0.00 0.00 0.00 3.41
2491 2519 0.901124 AGCAGCCCAGTCTTGTAGAG 59.099 55.000 0.00 0.00 0.00 2.43
2493 2521 4.881019 ATATAGCAGCCCAGTCTTGTAG 57.119 45.455 0.00 0.00 0.00 2.74
2585 2613 4.798433 TTGCGACACAAGCAGGAT 57.202 50.000 0.00 0.00 46.01 3.24
2612 2641 2.669364 ACGCGTAAAAAGTGATCGAGT 58.331 42.857 11.67 0.00 0.00 4.18
2665 2802 5.755375 CCGATCATAGTTTACAAGCTCACAT 59.245 40.000 0.00 0.00 0.00 3.21
2684 2821 2.351544 GCCGGAATAGACAGTACCGATC 60.352 54.545 5.05 0.00 45.31 3.69
2689 2826 0.743097 ACGGCCGGAATAGACAGTAC 59.257 55.000 31.76 0.00 0.00 2.73
2703 2842 0.453782 GTTATTCAACACGCACGGCC 60.454 55.000 0.00 0.00 34.60 6.13
2705 2844 4.145997 GTTTAGTTATTCAACACGCACGG 58.854 43.478 0.00 0.00 37.10 4.94
2706 2845 4.145997 GGTTTAGTTATTCAACACGCACG 58.854 43.478 0.00 0.00 37.10 5.34
2707 2846 5.098218 TGGTTTAGTTATTCAACACGCAC 57.902 39.130 0.00 0.00 37.10 5.34
2709 2848 6.399564 GCAAATGGTTTAGTTATTCAACACGC 60.400 38.462 0.00 0.00 37.10 5.34
2710 2849 6.183359 CGCAAATGGTTTAGTTATTCAACACG 60.183 38.462 0.00 0.00 37.10 4.49
2711 2850 6.639279 ACGCAAATGGTTTAGTTATTCAACAC 59.361 34.615 0.00 0.00 37.10 3.32
2712 2851 6.638873 CACGCAAATGGTTTAGTTATTCAACA 59.361 34.615 0.00 0.00 37.10 3.33
2713 2852 6.858993 TCACGCAAATGGTTTAGTTATTCAAC 59.141 34.615 0.00 0.00 34.67 3.18
2714 2853 6.971602 TCACGCAAATGGTTTAGTTATTCAA 58.028 32.000 0.00 0.00 0.00 2.69
2715 2854 6.561737 TCACGCAAATGGTTTAGTTATTCA 57.438 33.333 0.00 0.00 0.00 2.57
2716 2855 8.460831 AATTCACGCAAATGGTTTAGTTATTC 57.539 30.769 0.00 0.00 0.00 1.75
2717 2856 8.707839 CAAATTCACGCAAATGGTTTAGTTATT 58.292 29.630 0.00 0.00 0.00 1.40
2724 2863 3.002144 GCACAAATTCACGCAAATGGTTT 59.998 39.130 0.00 0.00 0.00 3.27
2734 2880 1.007964 TTGGGCGCACAAATTCACG 60.008 52.632 25.47 0.00 0.00 4.35
2738 2884 2.298729 ACAATAGTTGGGCGCACAAATT 59.701 40.909 31.52 22.43 34.12 1.82
2740 2886 1.000827 CACAATAGTTGGGCGCACAAA 60.001 47.619 29.48 13.85 34.12 2.83
2741 2887 0.595588 CACAATAGTTGGGCGCACAA 59.404 50.000 23.74 23.74 34.12 3.33
2742 2888 0.536233 ACACAATAGTTGGGCGCACA 60.536 50.000 9.15 9.15 37.68 4.57
2743 2889 0.109781 CACACAATAGTTGGGCGCAC 60.110 55.000 10.83 6.04 37.68 5.34
2744 2890 0.536233 ACACACAATAGTTGGGCGCA 60.536 50.000 10.83 0.00 37.68 6.09
2745 2891 1.444836 TACACACAATAGTTGGGCGC 58.555 50.000 0.00 0.00 37.68 6.53
2746 2892 3.938963 AGAATACACACAATAGTTGGGCG 59.061 43.478 0.00 0.00 37.68 6.13
2747 2893 6.204882 GGATAGAATACACACAATAGTTGGGC 59.795 42.308 0.00 0.00 37.68 5.36
2748 2894 6.423905 CGGATAGAATACACACAATAGTTGGG 59.576 42.308 0.00 0.00 40.79 4.12
2749 2895 6.984474 ACGGATAGAATACACACAATAGTTGG 59.016 38.462 0.00 0.00 34.12 3.77
2750 2896 7.491372 ACACGGATAGAATACACACAATAGTTG 59.509 37.037 0.00 0.00 0.00 3.16
2751 2897 7.491372 CACACGGATAGAATACACACAATAGTT 59.509 37.037 0.00 0.00 0.00 2.24
2752 2898 6.978659 CACACGGATAGAATACACACAATAGT 59.021 38.462 0.00 0.00 0.00 2.12
2753 2899 6.420903 CCACACGGATAGAATACACACAATAG 59.579 42.308 0.00 0.00 0.00 1.73
2754 2900 6.277605 CCACACGGATAGAATACACACAATA 58.722 40.000 0.00 0.00 0.00 1.90
2755 2901 5.116180 CCACACGGATAGAATACACACAAT 58.884 41.667 0.00 0.00 0.00 2.71
2756 2902 4.500127 CCACACGGATAGAATACACACAA 58.500 43.478 0.00 0.00 0.00 3.33
2757 2903 3.118920 CCCACACGGATAGAATACACACA 60.119 47.826 0.00 0.00 0.00 3.72
2758 2904 3.454375 CCCACACGGATAGAATACACAC 58.546 50.000 0.00 0.00 0.00 3.82
2759 2905 2.159014 GCCCACACGGATAGAATACACA 60.159 50.000 0.00 0.00 0.00 3.72
2760 2906 2.102588 AGCCCACACGGATAGAATACAC 59.897 50.000 0.00 0.00 0.00 2.90
2761 2907 2.394632 AGCCCACACGGATAGAATACA 58.605 47.619 0.00 0.00 0.00 2.29
2762 2908 3.131396 CAAGCCCACACGGATAGAATAC 58.869 50.000 0.00 0.00 0.00 1.89
2763 2909 2.769663 ACAAGCCCACACGGATAGAATA 59.230 45.455 0.00 0.00 0.00 1.75
2764 2910 1.559682 ACAAGCCCACACGGATAGAAT 59.440 47.619 0.00 0.00 0.00 2.40
2765 2911 0.981183 ACAAGCCCACACGGATAGAA 59.019 50.000 0.00 0.00 0.00 2.10
2766 2912 1.855295 TACAAGCCCACACGGATAGA 58.145 50.000 0.00 0.00 0.00 1.98
2767 2913 2.676342 GTTTACAAGCCCACACGGATAG 59.324 50.000 0.00 0.00 0.00 2.08
2768 2914 2.303600 AGTTTACAAGCCCACACGGATA 59.696 45.455 0.00 0.00 0.00 2.59
2769 2915 1.073284 AGTTTACAAGCCCACACGGAT 59.927 47.619 0.00 0.00 0.00 4.18
2770 2916 0.470766 AGTTTACAAGCCCACACGGA 59.529 50.000 0.00 0.00 0.00 4.69
2771 2917 1.314730 AAGTTTACAAGCCCACACGG 58.685 50.000 0.00 0.00 0.00 4.94
2772 2918 4.555348 TTAAAGTTTACAAGCCCACACG 57.445 40.909 0.00 0.00 0.00 4.49
2773 2919 5.049267 TCGATTAAAGTTTACAAGCCCACAC 60.049 40.000 0.00 0.00 0.00 3.82
2774 2920 5.064558 TCGATTAAAGTTTACAAGCCCACA 58.935 37.500 0.00 0.00 0.00 4.17
2775 2921 5.616488 TCGATTAAAGTTTACAAGCCCAC 57.384 39.130 0.00 0.00 0.00 4.61
2776 2922 7.065324 CAGTATCGATTAAAGTTTACAAGCCCA 59.935 37.037 1.71 0.00 0.00 5.36
2777 2923 7.065443 ACAGTATCGATTAAAGTTTACAAGCCC 59.935 37.037 1.71 0.00 0.00 5.19
2778 2924 7.971455 ACAGTATCGATTAAAGTTTACAAGCC 58.029 34.615 1.71 0.00 0.00 4.35
2785 2931 9.661563 TGGAACATACAGTATCGATTAAAGTTT 57.338 29.630 1.71 0.00 0.00 2.66
2786 2932 9.314321 CTGGAACATACAGTATCGATTAAAGTT 57.686 33.333 1.71 0.20 38.20 2.66
2787 2933 8.475639 ACTGGAACATACAGTATCGATTAAAGT 58.524 33.333 1.71 0.38 46.62 2.66
2788 2934 8.873215 ACTGGAACATACAGTATCGATTAAAG 57.127 34.615 1.71 0.00 46.62 1.85
2800 2946 2.941064 CAGGCATGACTGGAACATACAG 59.059 50.000 21.76 0.00 38.20 2.74
2801 2947 2.305635 ACAGGCATGACTGGAACATACA 59.694 45.455 31.68 0.00 42.75 2.29
2802 2948 2.991250 ACAGGCATGACTGGAACATAC 58.009 47.619 31.68 0.00 42.75 2.39
2803 2949 3.719268 AACAGGCATGACTGGAACATA 57.281 42.857 31.68 0.00 42.75 2.29
2804 2950 2.592102 AACAGGCATGACTGGAACAT 57.408 45.000 31.68 8.25 42.75 2.71
2805 2951 3.500448 TTAACAGGCATGACTGGAACA 57.500 42.857 31.68 11.22 42.75 3.18
2806 2952 6.509418 TTATTTAACAGGCATGACTGGAAC 57.491 37.500 31.68 0.00 42.75 3.62
2807 2953 7.716799 ATTTATTTAACAGGCATGACTGGAA 57.283 32.000 31.68 21.69 42.75 3.53
2808 2954 8.815565 TTATTTATTTAACAGGCATGACTGGA 57.184 30.769 31.68 16.98 42.75 3.86
2809 2955 9.301153 GTTTATTTATTTAACAGGCATGACTGG 57.699 33.333 31.68 14.37 42.75 4.00
2810 2956 9.301153 GGTTTATTTATTTAACAGGCATGACTG 57.699 33.333 27.47 27.47 44.03 3.51
2811 2957 9.030452 TGGTTTATTTATTTAACAGGCATGACT 57.970 29.630 4.84 0.00 0.00 3.41
2812 2958 9.816354 ATGGTTTATTTATTTAACAGGCATGAC 57.184 29.630 4.84 0.00 0.00 3.06
2886 3036 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2887 3037 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2894 3044 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2895 3045 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2902 3052 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2903 3053 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2904 3054 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2905 3055 5.502089 TTTACTCCCTCCGTTCCAAAATA 57.498 39.130 0.00 0.00 0.00 1.40
2906 3056 4.376225 TTTACTCCCTCCGTTCCAAAAT 57.624 40.909 0.00 0.00 0.00 1.82
2907 3057 3.860968 TTTACTCCCTCCGTTCCAAAA 57.139 42.857 0.00 0.00 0.00 2.44
2908 3058 3.860968 TTTTACTCCCTCCGTTCCAAA 57.139 42.857 0.00 0.00 0.00 3.28
2910 3060 2.026636 CCATTTTACTCCCTCCGTTCCA 60.027 50.000 0.00 0.00 0.00 3.53
2912 3062 2.014857 GCCATTTTACTCCCTCCGTTC 58.985 52.381 0.00 0.00 0.00 3.95
2913 3063 1.353022 TGCCATTTTACTCCCTCCGTT 59.647 47.619 0.00 0.00 0.00 4.44
2914 3064 0.988832 TGCCATTTTACTCCCTCCGT 59.011 50.000 0.00 0.00 0.00 4.69
2916 3066 3.631250 TCAATGCCATTTTACTCCCTCC 58.369 45.455 0.00 0.00 0.00 4.30
2917 3067 4.889409 TCATCAATGCCATTTTACTCCCTC 59.111 41.667 0.00 0.00 0.00 4.30
2918 3068 4.646492 GTCATCAATGCCATTTTACTCCCT 59.354 41.667 0.00 0.00 0.00 4.20
2919 3069 4.498009 CGTCATCAATGCCATTTTACTCCC 60.498 45.833 0.00 0.00 0.00 4.30
2920 3070 4.335315 TCGTCATCAATGCCATTTTACTCC 59.665 41.667 0.00 0.00 0.00 3.85
2922 3072 5.589855 TCATCGTCATCAATGCCATTTTACT 59.410 36.000 0.00 0.00 0.00 2.24
2923 3073 5.820131 TCATCGTCATCAATGCCATTTTAC 58.180 37.500 0.00 0.00 0.00 2.01
2926 3076 3.317149 CCTCATCGTCATCAATGCCATTT 59.683 43.478 0.00 0.00 0.00 2.32
2928 3078 2.105306 TCCTCATCGTCATCAATGCCAT 59.895 45.455 0.00 0.00 0.00 4.40
2930 3080 2.141517 CTCCTCATCGTCATCAATGCC 58.858 52.381 0.00 0.00 0.00 4.40
2959 3123 8.843885 TTCACATGAAAATTGCAATTATGGAA 57.156 26.923 26.00 22.61 41.38 3.53
2988 3152 5.366768 TCATTTGTATAGCTAGGCTGAAGGT 59.633 40.000 0.00 0.00 40.10 3.50
3093 5234 8.204160 CCCAAAATTCTTTTCTTAGGTTTGTCT 58.796 33.333 0.00 0.00 0.00 3.41
3094 5235 8.201464 TCCCAAAATTCTTTTCTTAGGTTTGTC 58.799 33.333 0.00 0.00 0.00 3.18
3095 5236 7.985184 GTCCCAAAATTCTTTTCTTAGGTTTGT 59.015 33.333 0.00 0.00 0.00 2.83
3096 5237 7.169140 CGTCCCAAAATTCTTTTCTTAGGTTTG 59.831 37.037 0.00 0.00 0.00 2.93
3098 5239 6.239204 CCGTCCCAAAATTCTTTTCTTAGGTT 60.239 38.462 0.00 0.00 0.00 3.50
3099 5240 5.243060 CCGTCCCAAAATTCTTTTCTTAGGT 59.757 40.000 0.00 0.00 0.00 3.08
3100 5241 5.475564 TCCGTCCCAAAATTCTTTTCTTAGG 59.524 40.000 0.00 0.00 0.00 2.69
3101 5242 6.349363 CCTCCGTCCCAAAATTCTTTTCTTAG 60.349 42.308 0.00 0.00 0.00 2.18
3102 5243 5.475564 CCTCCGTCCCAAAATTCTTTTCTTA 59.524 40.000 0.00 0.00 0.00 2.10
3104 5245 3.826729 CCTCCGTCCCAAAATTCTTTTCT 59.173 43.478 0.00 0.00 0.00 2.52
3105 5246 3.056821 CCCTCCGTCCCAAAATTCTTTTC 60.057 47.826 0.00 0.00 0.00 2.29
3107 5248 2.109304 TCCCTCCGTCCCAAAATTCTTT 59.891 45.455 0.00 0.00 0.00 2.52
3108 5249 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3109 5250 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3110 5251 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3112 5253 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3113 5254 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3114 5255 1.252904 CGTACTCCCTCCGTCCCAAA 61.253 60.000 0.00 0.00 0.00 3.28
3115 5256 1.679977 CGTACTCCCTCCGTCCCAA 60.680 63.158 0.00 0.00 0.00 4.12
3116 5257 1.561769 TACGTACTCCCTCCGTCCCA 61.562 60.000 0.00 0.00 36.12 4.37
3117 5258 0.817229 CTACGTACTCCCTCCGTCCC 60.817 65.000 0.00 0.00 36.12 4.46
3118 5259 0.107459 ACTACGTACTCCCTCCGTCC 60.107 60.000 0.00 0.00 36.12 4.79
3119 5260 2.604046 TACTACGTACTCCCTCCGTC 57.396 55.000 0.00 0.00 36.12 4.79
3120 5261 2.435805 TGATACTACGTACTCCCTCCGT 59.564 50.000 0.00 0.00 38.53 4.69
3121 5262 3.117491 TGATACTACGTACTCCCTCCG 57.883 52.381 0.00 0.00 0.00 4.63
3122 5263 4.459330 ACTTGATACTACGTACTCCCTCC 58.541 47.826 0.00 0.00 0.00 4.30
3123 5264 6.540189 TGTAACTTGATACTACGTACTCCCTC 59.460 42.308 0.00 0.00 0.00 4.30
3124 5265 6.418101 TGTAACTTGATACTACGTACTCCCT 58.582 40.000 0.00 0.00 0.00 4.20
3125 5266 6.540189 TCTGTAACTTGATACTACGTACTCCC 59.460 42.308 0.00 0.00 0.00 4.30
3126 5267 7.545362 TCTGTAACTTGATACTACGTACTCC 57.455 40.000 0.00 0.00 0.00 3.85
3129 5270 9.875675 CCTATTCTGTAACTTGATACTACGTAC 57.124 37.037 0.00 0.00 0.00 3.67
3132 5273 8.618677 TGTCCTATTCTGTAACTTGATACTACG 58.381 37.037 0.00 0.00 0.00 3.51
3286 5429 2.588106 CGCGTCATCTTTTAAAAAGGCG 59.412 45.455 17.62 17.62 0.00 5.52
3289 5432 5.553692 TTTGCGCGTCATCTTTTAAAAAG 57.446 34.783 8.43 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.