Multiple sequence alignment - TraesCS5A01G241400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G241400 chr5A 100.000 3228 0 0 1 3228 457098979 457102206 0.000000e+00 5962.0
1 TraesCS5A01G241400 chr5A 91.872 812 66 0 1 812 390556926 390557737 0.000000e+00 1134.0
2 TraesCS5A01G241400 chr5A 91.379 812 68 1 1 812 439808306 439809115 0.000000e+00 1110.0
3 TraesCS5A01G241400 chr5A 88.041 485 49 7 1071 1549 390558240 390558721 1.680000e-157 566.0
4 TraesCS5A01G241400 chr5A 92.289 402 21 7 2837 3228 457136754 457137155 2.170000e-156 562.0
5 TraesCS5A01G241400 chr5A 100.000 31 0 0 808 838 457099871 457099901 1.250000e-04 58.4
6 TraesCS5A01G241400 chr7B 99.506 2836 13 1 1 2836 505222346 505219512 0.000000e+00 5158.0
7 TraesCS5A01G241400 chr7B 100.000 31 0 0 808 838 505221454 505221424 1.250000e-04 58.4
8 TraesCS5A01G241400 chr3B 95.976 2187 51 20 683 2836 782172875 782170693 0.000000e+00 3517.0
9 TraesCS5A01G241400 chr3B 95.930 2187 53 19 683 2836 782255377 782253194 0.000000e+00 3513.0
10 TraesCS5A01G241400 chr3B 95.793 2187 50 20 683 2836 782297191 782295014 0.000000e+00 3491.0
11 TraesCS5A01G241400 chr3B 95.702 2187 52 20 683 2836 782213968 782211791 0.000000e+00 3480.0
12 TraesCS5A01G241400 chr3B 98.775 653 7 1 1 653 782214615 782213964 0.000000e+00 1160.0
13 TraesCS5A01G241400 chr2A 88.992 2253 164 36 626 2831 21632127 21634342 0.000000e+00 2710.0
14 TraesCS5A01G241400 chr2A 92.118 812 64 0 1 812 180214780 180213969 0.000000e+00 1146.0
15 TraesCS5A01G241400 chr2A 88.936 714 73 4 1559 2271 180213076 180212368 0.000000e+00 876.0
16 TraesCS5A01G241400 chr4A 99.503 1409 6 1 1431 2839 27194815 27193408 0.000000e+00 2562.0
17 TraesCS5A01G241400 chr4A 90.904 1825 134 17 1026 2839 698013245 698011442 0.000000e+00 2422.0
18 TraesCS5A01G241400 chr3A 99.145 1170 9 1 1670 2839 690944484 690945652 0.000000e+00 2104.0
19 TraesCS5A01G241400 chr3A 87.781 933 90 16 1 912 583077136 583078065 0.000000e+00 1070.0
20 TraesCS5A01G241400 chr3A 100.000 31 0 0 808 838 690944333 690944363 1.250000e-04 58.4
21 TraesCS5A01G241400 chr5D 99.144 1168 9 1 1673 2840 468179639 468178473 0.000000e+00 2100.0
22 TraesCS5A01G241400 chr5D 100.000 163 0 0 885 1047 468179801 468179639 5.230000e-78 302.0
23 TraesCS5A01G241400 chr5D 100.000 31 0 0 808 838 468179793 468179763 1.250000e-04 58.4
24 TraesCS5A01G241400 chr4B 99.143 1167 9 1 1670 2836 42255569 42256734 0.000000e+00 2098.0
25 TraesCS5A01G241400 chr4B 89.668 813 83 1 1 812 215014426 215013614 0.000000e+00 1035.0
26 TraesCS5A01G241400 chr4B 100.000 163 0 0 885 1047 42255410 42255572 5.230000e-78 302.0
27 TraesCS5A01G241400 chr4B 82.789 337 40 10 2885 3219 527487231 527487551 5.270000e-73 285.0
28 TraesCS5A01G241400 chr4B 82.789 337 36 11 2885 3219 527498672 527498988 6.820000e-72 281.0
29 TraesCS5A01G241400 chr4B 100.000 31 0 0 808 838 42255418 42255448 1.250000e-04 58.4
30 TraesCS5A01G241400 chr6B 91.995 812 65 0 1 812 532351343 532352154 0.000000e+00 1140.0
31 TraesCS5A01G241400 chr6B 87.835 485 50 7 1071 1549 532352527 532353008 7.820000e-156 560.0
32 TraesCS5A01G241400 chr7A 91.749 812 67 0 1 812 31808131 31808942 0.000000e+00 1129.0
33 TraesCS5A01G241400 chr6A 91.133 812 72 0 1 812 9184497 9185308 0.000000e+00 1101.0
34 TraesCS5A01G241400 chr2D 86.072 359 34 7 2885 3228 523467241 523467598 3.930000e-99 372.0
35 TraesCS5A01G241400 chr2D 85.552 353 33 9 2888 3222 263988664 263988312 1.420000e-93 353.0
36 TraesCS5A01G241400 chr2D 85.393 356 35 8 2888 3226 264008763 264008408 1.420000e-93 353.0
37 TraesCS5A01G241400 chr4D 85.319 361 36 9 2885 3228 224629189 224629549 1.100000e-94 357.0
38 TraesCS5A01G241400 chr4D 85.227 352 33 11 2885 3219 478446726 478447075 8.570000e-91 344.0
39 TraesCS5A01G241400 chr4D 85.143 350 36 10 2885 3219 478477607 478477955 8.570000e-91 344.0
40 TraesCS5A01G241400 chr4D 100.000 163 0 0 885 1047 505348908 505348746 5.230000e-78 302.0
41 TraesCS5A01G241400 chr4D 100.000 31 0 0 808 838 505348900 505348870 1.250000e-04 58.4
42 TraesCS5A01G241400 chr3D 85.387 349 34 9 2888 3219 596775601 596775253 2.380000e-91 346.0
43 TraesCS5A01G241400 chr3D 84.615 364 33 12 2885 3228 161355785 161356145 1.110000e-89 340.0
44 TraesCS5A01G241400 chr3D 100.000 31 0 0 808 838 562176192 562176162 1.250000e-04 58.4
45 TraesCS5A01G241400 chr6D 84.874 357 36 9 2888 3226 54045880 54045524 8.570000e-91 344.0
46 TraesCS5A01G241400 chr7D 100.000 163 0 0 885 1047 64826267 64826105 5.230000e-78 302.0
47 TraesCS5A01G241400 chr7D 100.000 31 0 0 808 838 64826259 64826229 1.250000e-04 58.4
48 TraesCS5A01G241400 chr1A 81.337 359 49 10 2888 3228 115074492 115074850 3.170000e-70 276.0


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 TraesCS5A01G241400 chr5A 457098979 457102206 3227 False 3010.200000 5962 100.000000 1 3228 2 chr5A.!!$F4 3227
1 TraesCS5A01G241400 chr5A 439808306 439809115 809 False 1110.000000 1110 91.379000 1 812 1 chr5A.!!$F1 811
2 TraesCS5A01G241400 chr5A 390556926 390558721 1795 False 850.000000 1134 89.956500 1 1549 2 chr5A.!!$F3 1548
3 TraesCS5A01G241400 chr7B 505219512 505222346 2834 True 2608.200000 5158 99.753000 1 2836 2 chr7B.!!$R1 2835
4 TraesCS5A01G241400 chr3B 782170693 782172875 2182 True 3517.000000 3517 95.976000 683 2836 1 chr3B.!!$R1 2153
5 TraesCS5A01G241400 chr3B 782253194 782255377 2183 True 3513.000000 3513 95.930000 683 2836 1 chr3B.!!$R2 2153
6 TraesCS5A01G241400 chr3B 782295014 782297191 2177 True 3491.000000 3491 95.793000 683 2836 1 chr3B.!!$R3 2153
7 TraesCS5A01G241400 chr3B 782211791 782214615 2824 True 2320.000000 3480 97.238500 1 2836 2 chr3B.!!$R4 2835
8 TraesCS5A01G241400 chr2A 21632127 21634342 2215 False 2710.000000 2710 88.992000 626 2831 1 chr2A.!!$F1 2205
9 TraesCS5A01G241400 chr2A 180212368 180214780 2412 True 1011.000000 1146 90.527000 1 2271 2 chr2A.!!$R1 2270
10 TraesCS5A01G241400 chr4A 27193408 27194815 1407 True 2562.000000 2562 99.503000 1431 2839 1 chr4A.!!$R1 1408
11 TraesCS5A01G241400 chr4A 698011442 698013245 1803 True 2422.000000 2422 90.904000 1026 2839 1 chr4A.!!$R2 1813
12 TraesCS5A01G241400 chr3A 690944333 690945652 1319 False 1081.200000 2104 99.572500 808 2839 2 chr3A.!!$F2 2031
13 TraesCS5A01G241400 chr3A 583077136 583078065 929 False 1070.000000 1070 87.781000 1 912 1 chr3A.!!$F1 911
14 TraesCS5A01G241400 chr5D 468178473 468179801 1328 True 820.133333 2100 99.714667 808 2840 3 chr5D.!!$R1 2032
15 TraesCS5A01G241400 chr4B 215013614 215014426 812 True 1035.000000 1035 89.668000 1 812 1 chr4B.!!$R1 811
16 TraesCS5A01G241400 chr4B 42255410 42256734 1324 False 819.466667 2098 99.714333 808 2836 3 chr4B.!!$F3 2028
17 TraesCS5A01G241400 chr6B 532351343 532353008 1665 False 850.000000 1140 89.915000 1 1549 2 chr6B.!!$F1 1548
18 TraesCS5A01G241400 chr7A 31808131 31808942 811 False 1129.000000 1129 91.749000 1 812 1 chr7A.!!$F1 811
19 TraesCS5A01G241400 chr6A 9184497 9185308 811 False 1101.000000 1101 91.133000 1 812 1 chr6A.!!$F1 811

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
2159 2459 4.531854 TGAAACAATTCTTGGACAGTGGA 58.468 39.13 0.0 0.0 36.48 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3091 3405 1.136252 CGTGCTGAGTGAAATCCAACG 60.136 52.381 0.0 0.0 0.0 4.1 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
2159 2459 4.531854 TGAAACAATTCTTGGACAGTGGA 58.468 39.130 0.00 0.00 36.48 4.02
2840 3154 4.649218 GCACAATCCAAACATACCCCTAAT 59.351 41.667 0.00 0.00 0.00 1.73
2841 3155 5.830991 GCACAATCCAAACATACCCCTAATA 59.169 40.000 0.00 0.00 0.00 0.98
2842 3156 6.493458 GCACAATCCAAACATACCCCTAATAT 59.507 38.462 0.00 0.00 0.00 1.28
2843 3157 7.309194 GCACAATCCAAACATACCCCTAATATC 60.309 40.741 0.00 0.00 0.00 1.63
2844 3158 7.723616 CACAATCCAAACATACCCCTAATATCA 59.276 37.037 0.00 0.00 0.00 2.15
2845 3159 7.944554 ACAATCCAAACATACCCCTAATATCAG 59.055 37.037 0.00 0.00 0.00 2.90
2846 3160 7.888514 ATCCAAACATACCCCTAATATCAGA 57.111 36.000 0.00 0.00 0.00 3.27
2847 3161 7.699709 TCCAAACATACCCCTAATATCAGAA 57.300 36.000 0.00 0.00 0.00 3.02
2848 3162 7.514721 TCCAAACATACCCCTAATATCAGAAC 58.485 38.462 0.00 0.00 0.00 3.01
2849 3163 6.715264 CCAAACATACCCCTAATATCAGAACC 59.285 42.308 0.00 0.00 0.00 3.62
2850 3164 7.287061 CAAACATACCCCTAATATCAGAACCA 58.713 38.462 0.00 0.00 0.00 3.67
2851 3165 7.648177 AACATACCCCTAATATCAGAACCAT 57.352 36.000 0.00 0.00 0.00 3.55
2852 3166 7.259088 ACATACCCCTAATATCAGAACCATC 57.741 40.000 0.00 0.00 0.00 3.51
2853 3167 6.215636 ACATACCCCTAATATCAGAACCATCC 59.784 42.308 0.00 0.00 0.00 3.51
2854 3168 3.916989 ACCCCTAATATCAGAACCATCCC 59.083 47.826 0.00 0.00 0.00 3.85
2855 3169 3.267031 CCCCTAATATCAGAACCATCCCC 59.733 52.174 0.00 0.00 0.00 4.81
2856 3170 4.179133 CCCTAATATCAGAACCATCCCCT 58.821 47.826 0.00 0.00 0.00 4.79
2857 3171 5.350547 CCCTAATATCAGAACCATCCCCTA 58.649 45.833 0.00 0.00 0.00 3.53
2858 3172 5.973124 CCCTAATATCAGAACCATCCCCTAT 59.027 44.000 0.00 0.00 0.00 2.57
2859 3173 6.126652 CCCTAATATCAGAACCATCCCCTATG 60.127 46.154 0.00 0.00 35.15 2.23
2860 3174 6.445139 CCTAATATCAGAACCATCCCCTATGT 59.555 42.308 0.00 0.00 33.34 2.29
2861 3175 6.786843 AATATCAGAACCATCCCCTATGTT 57.213 37.500 0.00 0.00 33.34 2.71
2862 3176 7.888514 AATATCAGAACCATCCCCTATGTTA 57.111 36.000 0.00 0.00 33.34 2.41
2863 3177 8.468547 AATATCAGAACCATCCCCTATGTTAT 57.531 34.615 0.00 0.00 33.34 1.89
2864 3178 5.825593 TCAGAACCATCCCCTATGTTATC 57.174 43.478 0.00 0.00 33.34 1.75
2865 3179 5.476983 TCAGAACCATCCCCTATGTTATCT 58.523 41.667 0.00 0.00 33.34 1.98
2866 3180 5.911178 TCAGAACCATCCCCTATGTTATCTT 59.089 40.000 0.00 0.00 33.34 2.40
2867 3181 6.000219 CAGAACCATCCCCTATGTTATCTTG 59.000 44.000 0.00 0.00 33.34 3.02
2868 3182 5.672194 AGAACCATCCCCTATGTTATCTTGT 59.328 40.000 0.00 0.00 33.34 3.16
2869 3183 5.994416 ACCATCCCCTATGTTATCTTGTT 57.006 39.130 0.00 0.00 33.34 2.83
2870 3184 6.341408 ACCATCCCCTATGTTATCTTGTTT 57.659 37.500 0.00 0.00 33.34 2.83
2871 3185 6.129179 ACCATCCCCTATGTTATCTTGTTTG 58.871 40.000 0.00 0.00 33.34 2.93
2872 3186 6.069088 ACCATCCCCTATGTTATCTTGTTTGA 60.069 38.462 0.00 0.00 33.34 2.69
2873 3187 7.006509 CCATCCCCTATGTTATCTTGTTTGAT 58.993 38.462 0.00 0.00 33.34 2.57
2874 3188 8.163408 CCATCCCCTATGTTATCTTGTTTGATA 58.837 37.037 0.00 0.00 33.34 2.15
2875 3189 9.745018 CATCCCCTATGTTATCTTGTTTGATAT 57.255 33.333 0.00 0.00 0.00 1.63
2876 3190 9.745018 ATCCCCTATGTTATCTTGTTTGATATG 57.255 33.333 0.00 0.00 0.00 1.78
2877 3191 8.723365 TCCCCTATGTTATCTTGTTTGATATGT 58.277 33.333 0.00 0.00 0.00 2.29
2878 3192 9.354673 CCCCTATGTTATCTTGTTTGATATGTT 57.645 33.333 0.00 0.00 0.00 2.71
2887 3201 8.585471 ATCTTGTTTGATATGTTTGATGAGGT 57.415 30.769 0.00 0.00 0.00 3.85
2888 3202 7.819644 TCTTGTTTGATATGTTTGATGAGGTG 58.180 34.615 0.00 0.00 0.00 4.00
2889 3203 5.953183 TGTTTGATATGTTTGATGAGGTGC 58.047 37.500 0.00 0.00 0.00 5.01
2890 3204 5.476254 TGTTTGATATGTTTGATGAGGTGCA 59.524 36.000 0.00 0.00 0.00 4.57
2891 3205 6.015603 TGTTTGATATGTTTGATGAGGTGCAA 60.016 34.615 0.00 0.00 0.00 4.08
2892 3206 6.778834 TTGATATGTTTGATGAGGTGCAAT 57.221 33.333 0.00 0.00 0.00 3.56
2893 3207 7.878547 TTGATATGTTTGATGAGGTGCAATA 57.121 32.000 0.00 0.00 0.00 1.90
2894 3208 8.467963 TTGATATGTTTGATGAGGTGCAATAT 57.532 30.769 0.00 0.00 0.00 1.28
2895 3209 8.102800 TGATATGTTTGATGAGGTGCAATATC 57.897 34.615 0.00 0.00 0.00 1.63
2896 3210 7.940688 TGATATGTTTGATGAGGTGCAATATCT 59.059 33.333 0.00 0.00 0.00 1.98
2897 3211 8.701908 ATATGTTTGATGAGGTGCAATATCTT 57.298 30.769 0.00 0.00 0.00 2.40
2898 3212 6.839124 TGTTTGATGAGGTGCAATATCTTT 57.161 33.333 0.00 0.00 0.00 2.52
2899 3213 7.230849 TGTTTGATGAGGTGCAATATCTTTT 57.769 32.000 0.00 0.00 0.00 2.27
2900 3214 8.347004 TGTTTGATGAGGTGCAATATCTTTTA 57.653 30.769 0.00 0.00 0.00 1.52
2901 3215 8.970020 TGTTTGATGAGGTGCAATATCTTTTAT 58.030 29.630 0.00 0.00 0.00 1.40
2902 3216 9.807649 GTTTGATGAGGTGCAATATCTTTTATT 57.192 29.630 0.00 0.00 0.00 1.40
2920 3234 8.682710 TCTTTTATTTTAGTATGGGTCACATGC 58.317 33.333 0.00 0.00 40.82 4.06
2921 3235 7.946381 TTTATTTTAGTATGGGTCACATGCA 57.054 32.000 5.92 0.00 43.72 3.96
2922 3236 8.532186 TTTATTTTAGTATGGGTCACATGCAT 57.468 30.769 5.92 0.00 43.72 3.96
2923 3237 9.634021 TTTATTTTAGTATGGGTCACATGCATA 57.366 29.630 5.92 0.00 43.72 3.14
2924 3238 9.806448 TTATTTTAGTATGGGTCACATGCATAT 57.194 29.630 5.92 0.00 43.72 1.78
2926 3240 9.979897 ATTTTAGTATGGGTCACATGCATATAT 57.020 29.630 5.92 0.00 43.72 0.86
2927 3241 9.806448 TTTTAGTATGGGTCACATGCATATATT 57.194 29.630 5.92 0.00 43.72 1.28
2928 3242 9.448438 TTTAGTATGGGTCACATGCATATATTC 57.552 33.333 5.92 0.00 43.72 1.75
2929 3243 7.262990 AGTATGGGTCACATGCATATATTCT 57.737 36.000 5.92 0.00 43.72 2.40
2930 3244 8.379428 AGTATGGGTCACATGCATATATTCTA 57.621 34.615 5.92 0.00 43.72 2.10
2931 3245 8.825774 AGTATGGGTCACATGCATATATTCTAA 58.174 33.333 5.92 0.00 43.72 2.10
2932 3246 7.928307 ATGGGTCACATGCATATATTCTAAC 57.072 36.000 0.00 0.00 38.70 2.34
2933 3247 6.237901 TGGGTCACATGCATATATTCTAACC 58.762 40.000 0.00 0.00 0.00 2.85
2934 3248 6.183361 TGGGTCACATGCATATATTCTAACCA 60.183 38.462 0.00 0.00 0.00 3.67
2935 3249 6.886459 GGGTCACATGCATATATTCTAACCAT 59.114 38.462 0.00 0.00 0.00 3.55
2936 3250 7.066284 GGGTCACATGCATATATTCTAACCATC 59.934 40.741 0.00 0.00 0.00 3.51
2937 3251 7.607607 GGTCACATGCATATATTCTAACCATCA 59.392 37.037 0.00 0.00 0.00 3.07
2938 3252 8.663025 GTCACATGCATATATTCTAACCATCAG 58.337 37.037 0.00 0.00 0.00 2.90
2939 3253 8.377799 TCACATGCATATATTCTAACCATCAGT 58.622 33.333 0.00 0.00 0.00 3.41
2940 3254 8.448615 CACATGCATATATTCTAACCATCAGTG 58.551 37.037 0.00 0.00 0.00 3.66
2954 3268 3.930336 CATCAGTGGACAGTACATGTGT 58.070 45.455 9.11 0.00 44.17 3.72
2955 3269 3.385193 TCAGTGGACAGTACATGTGTG 57.615 47.619 9.11 8.54 44.17 3.82
2956 3270 2.698274 TCAGTGGACAGTACATGTGTGT 59.302 45.455 9.11 11.95 44.17 3.72
2957 3271 3.133901 TCAGTGGACAGTACATGTGTGTT 59.866 43.478 9.11 0.00 44.17 3.32
2958 3272 3.248363 CAGTGGACAGTACATGTGTGTTG 59.752 47.826 9.11 3.74 44.17 3.33
2959 3273 2.032030 GTGGACAGTACATGTGTGTTGC 60.032 50.000 9.11 1.43 44.17 4.17
2960 3274 2.217750 GGACAGTACATGTGTGTTGCA 58.782 47.619 9.11 0.00 44.17 4.08
2961 3275 2.813754 GGACAGTACATGTGTGTTGCAT 59.186 45.455 9.11 0.00 44.17 3.96
2962 3276 4.000325 GGACAGTACATGTGTGTTGCATA 59.000 43.478 9.11 0.00 44.17 3.14
2963 3277 4.093408 GGACAGTACATGTGTGTTGCATAG 59.907 45.833 9.11 0.00 44.17 2.23
2964 3278 4.893608 ACAGTACATGTGTGTTGCATAGA 58.106 39.130 9.11 0.00 41.91 1.98
2965 3279 4.931601 ACAGTACATGTGTGTTGCATAGAG 59.068 41.667 9.11 0.00 41.91 2.43
2966 3280 3.935203 AGTACATGTGTGTTGCATAGAGC 59.065 43.478 9.11 0.00 40.91 4.09
2967 3281 2.086869 ACATGTGTGTTGCATAGAGCC 58.913 47.619 0.00 0.00 44.83 4.70
2968 3282 2.290514 ACATGTGTGTTGCATAGAGCCT 60.291 45.455 0.00 0.00 44.83 4.58
2969 3283 2.099141 TGTGTGTTGCATAGAGCCTC 57.901 50.000 0.00 0.00 44.83 4.70
2970 3284 1.625315 TGTGTGTTGCATAGAGCCTCT 59.375 47.619 0.00 0.00 44.83 3.69
2971 3285 2.831526 TGTGTGTTGCATAGAGCCTCTA 59.168 45.455 3.46 3.46 44.83 2.43
2972 3286 3.190874 GTGTGTTGCATAGAGCCTCTAC 58.809 50.000 2.96 0.00 44.83 2.59
2973 3287 2.831526 TGTGTTGCATAGAGCCTCTACA 59.168 45.455 2.96 0.00 44.83 2.74
2974 3288 3.190874 GTGTTGCATAGAGCCTCTACAC 58.809 50.000 2.96 6.29 44.83 2.90
2975 3289 3.099905 TGTTGCATAGAGCCTCTACACT 58.900 45.455 2.96 0.00 44.83 3.55
2976 3290 3.131223 TGTTGCATAGAGCCTCTACACTC 59.869 47.826 2.96 0.00 44.83 3.51
2977 3291 3.304911 TGCATAGAGCCTCTACACTCT 57.695 47.619 2.96 0.00 45.15 3.24
2978 3292 4.439253 TGCATAGAGCCTCTACACTCTA 57.561 45.455 2.96 2.49 46.57 2.43
2979 3293 4.393834 TGCATAGAGCCTCTACACTCTAG 58.606 47.826 2.96 0.00 45.93 2.43
2980 3294 4.103311 TGCATAGAGCCTCTACACTCTAGA 59.897 45.833 2.96 0.00 45.93 2.43
2981 3295 5.222027 TGCATAGAGCCTCTACACTCTAGAT 60.222 44.000 2.96 0.00 45.93 1.98
2982 3296 6.013293 TGCATAGAGCCTCTACACTCTAGATA 60.013 42.308 2.96 0.00 45.93 1.98
2983 3297 7.054124 GCATAGAGCCTCTACACTCTAGATAT 58.946 42.308 2.96 0.00 45.93 1.63
2984 3298 7.012327 GCATAGAGCCTCTACACTCTAGATATG 59.988 44.444 2.96 0.00 45.93 1.78
2985 3299 6.448369 AGAGCCTCTACACTCTAGATATGT 57.552 41.667 12.89 12.89 41.44 2.29
2986 3300 7.562259 AGAGCCTCTACACTCTAGATATGTA 57.438 40.000 13.58 13.58 41.44 2.29
2987 3301 7.620880 AGAGCCTCTACACTCTAGATATGTAG 58.379 42.308 25.17 25.17 44.73 2.74
3033 3347 8.546597 ACACACATTAATTTTCTTTTATGGGC 57.453 30.769 0.00 0.00 0.00 5.36
3034 3348 8.153550 ACACACATTAATTTTCTTTTATGGGCA 58.846 29.630 0.00 0.00 0.00 5.36
3035 3349 9.165035 CACACATTAATTTTCTTTTATGGGCAT 57.835 29.630 0.00 0.00 0.00 4.40
3051 3365 9.469807 TTTATGGGCATATTTTATTTAAGTGCG 57.530 29.630 0.00 0.00 32.23 5.34
3052 3366 6.701145 TGGGCATATTTTATTTAAGTGCGA 57.299 33.333 0.00 0.00 32.23 5.10
3053 3367 7.101652 TGGGCATATTTTATTTAAGTGCGAA 57.898 32.000 0.00 0.00 32.23 4.70
3054 3368 7.721402 TGGGCATATTTTATTTAAGTGCGAAT 58.279 30.769 0.00 0.00 32.23 3.34
3055 3369 7.865385 TGGGCATATTTTATTTAAGTGCGAATC 59.135 33.333 0.00 0.00 32.23 2.52
3056 3370 7.060633 GGGCATATTTTATTTAAGTGCGAATCG 59.939 37.037 0.00 0.00 32.23 3.34
3057 3371 7.801315 GGCATATTTTATTTAAGTGCGAATCGA 59.199 33.333 6.91 0.00 32.23 3.59
3058 3372 8.831372 GCATATTTTATTTAAGTGCGAATCGAG 58.169 33.333 6.91 0.00 0.00 4.04
3061 3375 6.954616 TTTATTTAAGTGCGAATCGAGACA 57.045 33.333 6.91 0.00 0.00 3.41
3062 3376 6.954616 TTATTTAAGTGCGAATCGAGACAA 57.045 33.333 6.91 0.00 0.00 3.18
3063 3377 4.640805 TTTAAGTGCGAATCGAGACAAC 57.359 40.909 6.91 0.00 0.00 3.32
3064 3378 2.440539 AAGTGCGAATCGAGACAACT 57.559 45.000 6.91 0.00 0.00 3.16
3065 3379 3.570926 AAGTGCGAATCGAGACAACTA 57.429 42.857 6.91 0.00 0.00 2.24
3066 3380 3.138205 AGTGCGAATCGAGACAACTAG 57.862 47.619 6.91 0.00 0.00 2.57
3067 3381 2.488545 AGTGCGAATCGAGACAACTAGT 59.511 45.455 6.91 0.00 0.00 2.57
3068 3382 3.688185 AGTGCGAATCGAGACAACTAGTA 59.312 43.478 6.91 0.00 0.00 1.82
3069 3383 4.335874 AGTGCGAATCGAGACAACTAGTAT 59.664 41.667 6.91 0.00 0.00 2.12
3070 3384 5.035443 GTGCGAATCGAGACAACTAGTATT 58.965 41.667 6.91 0.00 0.00 1.89
3071 3385 5.515626 GTGCGAATCGAGACAACTAGTATTT 59.484 40.000 6.91 0.00 0.00 1.40
3072 3386 6.034683 GTGCGAATCGAGACAACTAGTATTTT 59.965 38.462 6.91 0.00 0.00 1.82
3073 3387 6.252869 TGCGAATCGAGACAACTAGTATTTTC 59.747 38.462 6.91 0.00 0.00 2.29
3074 3388 6.252869 GCGAATCGAGACAACTAGTATTTTCA 59.747 38.462 6.91 0.00 0.00 2.69
3075 3389 7.043325 GCGAATCGAGACAACTAGTATTTTCAT 60.043 37.037 6.91 0.00 0.00 2.57
3076 3390 8.808529 CGAATCGAGACAACTAGTATTTTCATT 58.191 33.333 0.00 0.00 0.00 2.57
3093 3407 8.948631 ATTTTCATTATCTCATGTCTACACGT 57.051 30.769 0.00 0.00 0.00 4.49
3094 3408 8.771920 TTTTCATTATCTCATGTCTACACGTT 57.228 30.769 0.00 0.00 0.00 3.99
3095 3409 7.755582 TTCATTATCTCATGTCTACACGTTG 57.244 36.000 0.00 0.00 0.00 4.10
3096 3410 6.273071 TCATTATCTCATGTCTACACGTTGG 58.727 40.000 0.00 0.00 0.00 3.77
3097 3411 5.907866 TTATCTCATGTCTACACGTTGGA 57.092 39.130 0.00 0.00 0.00 3.53
3098 3412 6.465439 TTATCTCATGTCTACACGTTGGAT 57.535 37.500 0.00 0.00 0.00 3.41
3099 3413 4.801330 TCTCATGTCTACACGTTGGATT 57.199 40.909 0.00 0.00 0.00 3.01
3100 3414 5.147330 TCTCATGTCTACACGTTGGATTT 57.853 39.130 0.00 0.00 0.00 2.17
3101 3415 5.168569 TCTCATGTCTACACGTTGGATTTC 58.831 41.667 0.00 0.00 0.00 2.17
3102 3416 4.888917 TCATGTCTACACGTTGGATTTCA 58.111 39.130 0.00 0.00 0.00 2.69
3103 3417 4.688879 TCATGTCTACACGTTGGATTTCAC 59.311 41.667 0.00 0.00 0.00 3.18
3104 3418 4.330944 TGTCTACACGTTGGATTTCACT 57.669 40.909 0.00 0.00 0.00 3.41
3105 3419 4.304110 TGTCTACACGTTGGATTTCACTC 58.696 43.478 0.00 0.00 0.00 3.51
3106 3420 4.202172 TGTCTACACGTTGGATTTCACTCA 60.202 41.667 0.00 0.00 0.00 3.41
3107 3421 4.386049 GTCTACACGTTGGATTTCACTCAG 59.614 45.833 0.00 0.00 0.00 3.35
3108 3422 1.873591 ACACGTTGGATTTCACTCAGC 59.126 47.619 0.00 0.00 0.00 4.26
3109 3423 1.872952 CACGTTGGATTTCACTCAGCA 59.127 47.619 0.00 0.00 0.00 4.41
3110 3424 1.873591 ACGTTGGATTTCACTCAGCAC 59.126 47.619 0.00 0.00 0.00 4.40
3111 3425 1.136252 CGTTGGATTTCACTCAGCACG 60.136 52.381 0.00 0.00 0.00 5.34
3112 3426 1.873591 GTTGGATTTCACTCAGCACGT 59.126 47.619 0.00 0.00 0.00 4.49
3113 3427 2.254546 TGGATTTCACTCAGCACGTT 57.745 45.000 0.00 0.00 0.00 3.99
3114 3428 2.143122 TGGATTTCACTCAGCACGTTC 58.857 47.619 0.00 0.00 0.00 3.95
3115 3429 2.224281 TGGATTTCACTCAGCACGTTCT 60.224 45.455 0.00 0.00 0.00 3.01
3116 3430 3.006430 TGGATTTCACTCAGCACGTTCTA 59.994 43.478 0.00 0.00 0.00 2.10
3117 3431 4.184629 GGATTTCACTCAGCACGTTCTAT 58.815 43.478 0.00 0.00 0.00 1.98
3118 3432 5.105513 TGGATTTCACTCAGCACGTTCTATA 60.106 40.000 0.00 0.00 0.00 1.31
3119 3433 5.986135 GGATTTCACTCAGCACGTTCTATAT 59.014 40.000 0.00 0.00 0.00 0.86
3120 3434 6.074088 GGATTTCACTCAGCACGTTCTATATG 60.074 42.308 0.00 0.00 0.00 1.78
3121 3435 3.706698 TCACTCAGCACGTTCTATATGC 58.293 45.455 0.00 0.00 39.74 3.14
3122 3436 3.130340 TCACTCAGCACGTTCTATATGCA 59.870 43.478 0.00 0.00 41.97 3.96
3123 3437 4.053983 CACTCAGCACGTTCTATATGCAT 58.946 43.478 3.79 3.79 41.97 3.96
3124 3438 4.509230 CACTCAGCACGTTCTATATGCATT 59.491 41.667 3.54 0.00 41.97 3.56
3125 3439 5.691754 CACTCAGCACGTTCTATATGCATTA 59.308 40.000 3.54 0.00 41.97 1.90
3126 3440 5.923114 ACTCAGCACGTTCTATATGCATTAG 59.077 40.000 3.54 7.02 41.97 1.73
3127 3441 6.084326 TCAGCACGTTCTATATGCATTAGA 57.916 37.500 3.54 9.31 41.97 2.10
3128 3442 6.152379 TCAGCACGTTCTATATGCATTAGAG 58.848 40.000 3.54 0.00 41.97 2.43
3129 3443 5.923114 CAGCACGTTCTATATGCATTAGAGT 59.077 40.000 3.54 5.04 41.97 3.24
3130 3444 7.040686 TCAGCACGTTCTATATGCATTAGAGTA 60.041 37.037 3.54 0.00 41.97 2.59
3131 3445 7.757173 CAGCACGTTCTATATGCATTAGAGTAT 59.243 37.037 3.54 0.00 41.97 2.12
3132 3446 8.957466 AGCACGTTCTATATGCATTAGAGTATA 58.043 33.333 3.54 0.00 41.97 1.47
3133 3447 9.737427 GCACGTTCTATATGCATTAGAGTATAT 57.263 33.333 3.54 0.00 39.23 0.86
3182 3496 7.454553 TGTATATAACATTTGTACCCCCTGT 57.545 36.000 0.00 0.00 31.43 4.00
3183 3497 7.874252 TGTATATAACATTTGTACCCCCTGTT 58.126 34.615 0.00 0.00 31.43 3.16
3184 3498 8.337739 TGTATATAACATTTGTACCCCCTGTTT 58.662 33.333 5.79 0.05 31.43 2.83
3185 3499 5.993748 ATAACATTTGTACCCCCTGTTTG 57.006 39.130 5.79 0.00 32.66 2.93
3186 3500 3.322191 ACATTTGTACCCCCTGTTTGT 57.678 42.857 0.00 0.00 0.00 2.83
3187 3501 4.456662 ACATTTGTACCCCCTGTTTGTA 57.543 40.909 0.00 0.00 0.00 2.41
3188 3502 5.005628 ACATTTGTACCCCCTGTTTGTAT 57.994 39.130 0.00 0.00 0.00 2.29
3189 3503 5.399113 ACATTTGTACCCCCTGTTTGTATT 58.601 37.500 0.00 0.00 0.00 1.89
3190 3504 6.553857 ACATTTGTACCCCCTGTTTGTATTA 58.446 36.000 0.00 0.00 0.00 0.98
3191 3505 6.434965 ACATTTGTACCCCCTGTTTGTATTAC 59.565 38.462 0.00 0.00 0.00 1.89
3192 3506 5.846528 TTGTACCCCCTGTTTGTATTACT 57.153 39.130 0.00 0.00 0.00 2.24
3193 3507 6.949117 TTGTACCCCCTGTTTGTATTACTA 57.051 37.500 0.00 0.00 0.00 1.82
3194 3508 7.513560 TTGTACCCCCTGTTTGTATTACTAT 57.486 36.000 0.00 0.00 0.00 2.12
3195 3509 7.513560 TGTACCCCCTGTTTGTATTACTATT 57.486 36.000 0.00 0.00 0.00 1.73
3196 3510 7.340256 TGTACCCCCTGTTTGTATTACTATTG 58.660 38.462 0.00 0.00 0.00 1.90
3197 3511 6.645884 ACCCCCTGTTTGTATTACTATTGA 57.354 37.500 0.00 0.00 0.00 2.57
3198 3512 6.420638 ACCCCCTGTTTGTATTACTATTGAC 58.579 40.000 0.00 0.00 0.00 3.18
3199 3513 5.526111 CCCCCTGTTTGTATTACTATTGACG 59.474 44.000 0.00 0.00 0.00 4.35
3200 3514 6.110707 CCCCTGTTTGTATTACTATTGACGT 58.889 40.000 0.00 0.00 0.00 4.34
3201 3515 6.036735 CCCCTGTTTGTATTACTATTGACGTG 59.963 42.308 0.00 0.00 0.00 4.49
3202 3516 6.814644 CCCTGTTTGTATTACTATTGACGTGA 59.185 38.462 0.00 0.00 0.00 4.35
3203 3517 7.201496 CCCTGTTTGTATTACTATTGACGTGAC 60.201 40.741 0.00 0.00 0.00 3.67
3204 3518 7.329962 CCTGTTTGTATTACTATTGACGTGACA 59.670 37.037 0.00 0.00 0.00 3.58
3205 3519 8.766000 TGTTTGTATTACTATTGACGTGACAT 57.234 30.769 0.00 0.00 0.00 3.06
3206 3520 9.857957 TGTTTGTATTACTATTGACGTGACATA 57.142 29.630 0.00 0.00 0.00 2.29
3208 3522 8.570096 TTGTATTACTATTGACGTGACATAGC 57.430 34.615 0.00 0.00 0.00 2.97
3209 3523 7.708998 TGTATTACTATTGACGTGACATAGCA 58.291 34.615 0.00 0.00 0.00 3.49
3210 3524 8.357402 TGTATTACTATTGACGTGACATAGCAT 58.643 33.333 0.00 0.00 0.00 3.79
3211 3525 7.643528 ATTACTATTGACGTGACATAGCATG 57.356 36.000 0.00 0.00 0.00 4.06
3212 3526 3.804325 ACTATTGACGTGACATAGCATGC 59.196 43.478 10.51 10.51 0.00 4.06
3213 3527 2.091852 TTGACGTGACATAGCATGCA 57.908 45.000 21.98 6.36 0.00 3.96
3214 3528 2.314323 TGACGTGACATAGCATGCAT 57.686 45.000 21.98 8.63 0.00 3.96
3215 3529 1.935199 TGACGTGACATAGCATGCATG 59.065 47.619 22.70 22.70 32.96 4.06
3216 3530 1.935873 GACGTGACATAGCATGCATGT 59.064 47.619 26.79 25.70 39.31 3.21
3221 3535 2.291365 GACATAGCATGCATGTCCACA 58.709 47.619 31.65 9.06 44.25 4.17
3222 3536 2.684374 GACATAGCATGCATGTCCACAA 59.316 45.455 31.65 7.72 44.25 3.33
3223 3537 3.293337 ACATAGCATGCATGTCCACAAT 58.707 40.909 26.79 9.53 30.82 2.71
3224 3538 3.067601 ACATAGCATGCATGTCCACAATG 59.932 43.478 26.79 20.35 30.82 2.82
3225 3539 1.552578 AGCATGCATGTCCACAATGT 58.447 45.000 26.79 0.54 0.00 2.71
3226 3540 2.725637 AGCATGCATGTCCACAATGTA 58.274 42.857 26.79 0.00 0.00 2.29
3227 3541 3.090790 AGCATGCATGTCCACAATGTAA 58.909 40.909 26.79 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
713 715 0.036388 GCCTCTTCATCACGAACCCA 60.036 55.000 0.00 0.00 0.00 4.51
2159 2459 2.364002 GAGGCTCGAAGAAGCTAAGGAT 59.636 50.000 0.00 0.00 34.09 3.24
2840 3154 7.256399 AGATAACATAGGGGATGGTTCTGATA 58.744 38.462 0.00 0.00 40.18 2.15
2841 3155 6.094302 AGATAACATAGGGGATGGTTCTGAT 58.906 40.000 0.00 0.00 40.18 2.90
2842 3156 5.476983 AGATAACATAGGGGATGGTTCTGA 58.523 41.667 0.00 0.00 40.18 3.27
2843 3157 5.832539 AGATAACATAGGGGATGGTTCTG 57.167 43.478 0.00 0.00 40.18 3.02
2844 3158 5.672194 ACAAGATAACATAGGGGATGGTTCT 59.328 40.000 0.00 0.00 40.18 3.01
2845 3159 5.941788 ACAAGATAACATAGGGGATGGTTC 58.058 41.667 0.00 0.00 40.18 3.62
2846 3160 5.994416 ACAAGATAACATAGGGGATGGTT 57.006 39.130 0.00 0.00 40.18 3.67
2847 3161 5.994416 AACAAGATAACATAGGGGATGGT 57.006 39.130 0.00 0.00 40.18 3.55
2848 3162 6.364701 TCAAACAAGATAACATAGGGGATGG 58.635 40.000 0.00 0.00 40.18 3.51
2849 3163 9.745018 ATATCAAACAAGATAACATAGGGGATG 57.255 33.333 0.00 0.00 35.72 3.51
2850 3164 9.745018 CATATCAAACAAGATAACATAGGGGAT 57.255 33.333 0.00 0.00 34.42 3.85
2851 3165 8.723365 ACATATCAAACAAGATAACATAGGGGA 58.277 33.333 0.00 0.00 34.42 4.81
2852 3166 8.924511 ACATATCAAACAAGATAACATAGGGG 57.075 34.615 0.00 0.00 34.42 4.79
2861 3175 9.685276 ACCTCATCAAACATATCAAACAAGATA 57.315 29.630 0.00 0.00 35.16 1.98
2862 3176 8.464404 CACCTCATCAAACATATCAAACAAGAT 58.536 33.333 0.00 0.00 0.00 2.40
2863 3177 7.575532 GCACCTCATCAAACATATCAAACAAGA 60.576 37.037 0.00 0.00 0.00 3.02
2864 3178 6.529125 GCACCTCATCAAACATATCAAACAAG 59.471 38.462 0.00 0.00 0.00 3.16
2865 3179 6.015603 TGCACCTCATCAAACATATCAAACAA 60.016 34.615 0.00 0.00 0.00 2.83
2866 3180 5.476254 TGCACCTCATCAAACATATCAAACA 59.524 36.000 0.00 0.00 0.00 2.83
2867 3181 5.953183 TGCACCTCATCAAACATATCAAAC 58.047 37.500 0.00 0.00 0.00 2.93
2868 3182 6.587206 TTGCACCTCATCAAACATATCAAA 57.413 33.333 0.00 0.00 0.00 2.69
2869 3183 6.778834 ATTGCACCTCATCAAACATATCAA 57.221 33.333 0.00 0.00 0.00 2.57
2870 3184 7.940688 AGATATTGCACCTCATCAAACATATCA 59.059 33.333 8.52 0.00 0.00 2.15
2871 3185 8.332996 AGATATTGCACCTCATCAAACATATC 57.667 34.615 0.00 0.00 0.00 1.63
2872 3186 8.701908 AAGATATTGCACCTCATCAAACATAT 57.298 30.769 0.00 0.00 0.00 1.78
2873 3187 8.523915 AAAGATATTGCACCTCATCAAACATA 57.476 30.769 0.00 0.00 0.00 2.29
2874 3188 7.414222 AAAGATATTGCACCTCATCAAACAT 57.586 32.000 0.00 0.00 0.00 2.71
2875 3189 6.839124 AAAGATATTGCACCTCATCAAACA 57.161 33.333 0.00 0.00 0.00 2.83
2876 3190 9.807649 AATAAAAGATATTGCACCTCATCAAAC 57.192 29.630 0.00 0.00 0.00 2.93
2894 3208 8.682710 GCATGTGACCCATACTAAAATAAAAGA 58.317 33.333 0.00 0.00 30.71 2.52
2895 3209 8.465999 TGCATGTGACCCATACTAAAATAAAAG 58.534 33.333 0.00 0.00 30.71 2.27
2896 3210 8.354711 TGCATGTGACCCATACTAAAATAAAA 57.645 30.769 0.00 0.00 30.71 1.52
2897 3211 7.946381 TGCATGTGACCCATACTAAAATAAA 57.054 32.000 0.00 0.00 30.71 1.40
2898 3212 9.806448 ATATGCATGTGACCCATACTAAAATAA 57.194 29.630 10.16 0.00 30.71 1.40
2900 3214 9.979897 ATATATGCATGTGACCCATACTAAAAT 57.020 29.630 10.16 0.00 30.71 1.82
2901 3215 9.806448 AATATATGCATGTGACCCATACTAAAA 57.194 29.630 10.16 0.00 30.71 1.52
2902 3216 9.448438 GAATATATGCATGTGACCCATACTAAA 57.552 33.333 10.16 0.00 30.71 1.85
2903 3217 8.825774 AGAATATATGCATGTGACCCATACTAA 58.174 33.333 10.16 0.00 30.71 2.24
2904 3218 8.379428 AGAATATATGCATGTGACCCATACTA 57.621 34.615 10.16 0.00 30.71 1.82
2905 3219 7.262990 AGAATATATGCATGTGACCCATACT 57.737 36.000 10.16 0.00 30.71 2.12
2906 3220 8.883731 GTTAGAATATATGCATGTGACCCATAC 58.116 37.037 10.16 0.00 30.71 2.39
2907 3221 8.046708 GGTTAGAATATATGCATGTGACCCATA 58.953 37.037 10.16 0.00 30.71 2.74
2908 3222 6.886459 GGTTAGAATATATGCATGTGACCCAT 59.114 38.462 10.16 0.00 0.00 4.00
2909 3223 6.183361 TGGTTAGAATATATGCATGTGACCCA 60.183 38.462 10.16 1.57 0.00 4.51
2910 3224 6.237901 TGGTTAGAATATATGCATGTGACCC 58.762 40.000 10.16 0.00 0.00 4.46
2911 3225 7.607607 TGATGGTTAGAATATATGCATGTGACC 59.392 37.037 10.16 6.65 0.00 4.02
2912 3226 8.552083 TGATGGTTAGAATATATGCATGTGAC 57.448 34.615 10.16 0.00 0.00 3.67
2913 3227 8.377799 ACTGATGGTTAGAATATATGCATGTGA 58.622 33.333 10.16 0.00 0.00 3.58
2914 3228 8.448615 CACTGATGGTTAGAATATATGCATGTG 58.551 37.037 10.16 0.00 0.00 3.21
2915 3229 7.609146 CCACTGATGGTTAGAATATATGCATGT 59.391 37.037 10.16 5.06 41.64 3.21
2916 3230 7.982224 CCACTGATGGTTAGAATATATGCATG 58.018 38.462 10.16 0.00 41.64 4.06
2932 3246 7.760788 ACACACATGTACTGTCCACTGATGG 62.761 48.000 0.00 0.00 42.04 3.51
2933 3247 3.681417 CACACATGTACTGTCCACTGATG 59.319 47.826 0.00 0.00 35.29 3.07
2934 3248 3.324846 ACACACATGTACTGTCCACTGAT 59.675 43.478 0.00 0.00 37.26 2.90
2935 3249 2.698274 ACACACATGTACTGTCCACTGA 59.302 45.455 0.00 0.00 37.26 3.41
2936 3250 3.111853 ACACACATGTACTGTCCACTG 57.888 47.619 0.00 0.00 37.26 3.66
2937 3251 3.466836 CAACACACATGTACTGTCCACT 58.533 45.455 0.00 0.00 38.45 4.00
2938 3252 2.032030 GCAACACACATGTACTGTCCAC 60.032 50.000 0.00 0.00 38.45 4.02
2939 3253 2.217750 GCAACACACATGTACTGTCCA 58.782 47.619 0.00 0.00 38.45 4.02
2940 3254 2.217750 TGCAACACACATGTACTGTCC 58.782 47.619 0.00 0.00 38.45 4.02
2941 3255 4.929211 TCTATGCAACACACATGTACTGTC 59.071 41.667 0.00 0.00 38.45 3.51
2942 3256 4.893608 TCTATGCAACACACATGTACTGT 58.106 39.130 0.00 0.00 38.45 3.55
2943 3257 4.201753 GCTCTATGCAACACACATGTACTG 60.202 45.833 0.00 0.00 38.45 2.74
2944 3258 3.935203 GCTCTATGCAACACACATGTACT 59.065 43.478 0.00 0.00 38.45 2.73
2945 3259 3.063997 GGCTCTATGCAACACACATGTAC 59.936 47.826 0.00 0.00 45.15 2.90
2946 3260 3.055167 AGGCTCTATGCAACACACATGTA 60.055 43.478 0.00 0.00 45.15 2.29
2947 3261 2.086869 GGCTCTATGCAACACACATGT 58.913 47.619 0.00 0.00 45.15 3.21
2948 3262 2.353889 GAGGCTCTATGCAACACACATG 59.646 50.000 7.40 0.00 45.15 3.21
2949 3263 2.238144 AGAGGCTCTATGCAACACACAT 59.762 45.455 17.09 0.00 45.15 3.21
2950 3264 1.625315 AGAGGCTCTATGCAACACACA 59.375 47.619 17.09 0.00 45.15 3.72
2951 3265 2.393271 AGAGGCTCTATGCAACACAC 57.607 50.000 17.09 0.00 45.15 3.82
2952 3266 2.831526 TGTAGAGGCTCTATGCAACACA 59.168 45.455 25.93 17.23 45.15 3.72
2953 3267 3.118956 AGTGTAGAGGCTCTATGCAACAC 60.119 47.826 28.08 28.08 45.15 3.32
2954 3268 3.099905 AGTGTAGAGGCTCTATGCAACA 58.900 45.455 25.93 18.61 45.15 3.33
2955 3269 3.383185 AGAGTGTAGAGGCTCTATGCAAC 59.617 47.826 25.93 19.92 45.15 4.17
2956 3270 3.636679 AGAGTGTAGAGGCTCTATGCAA 58.363 45.455 25.93 10.60 45.15 4.08
2957 3271 3.304911 AGAGTGTAGAGGCTCTATGCA 57.695 47.619 25.93 17.46 45.15 3.96
2958 3272 4.647611 TCTAGAGTGTAGAGGCTCTATGC 58.352 47.826 25.93 20.15 41.68 3.14
2959 3273 8.046708 ACATATCTAGAGTGTAGAGGCTCTATG 58.953 40.741 25.93 17.96 41.68 2.23
2960 3274 8.158025 ACATATCTAGAGTGTAGAGGCTCTAT 57.842 38.462 25.93 11.50 41.68 1.98
2961 3275 7.562259 ACATATCTAGAGTGTAGAGGCTCTA 57.438 40.000 20.11 20.11 41.70 2.43
2962 3276 6.448369 ACATATCTAGAGTGTAGAGGCTCT 57.552 41.667 22.48 22.48 43.63 4.09
2963 3277 7.617225 TCTACATATCTAGAGTGTAGAGGCTC 58.383 42.308 29.16 6.34 45.49 4.70
2964 3278 7.562259 TCTACATATCTAGAGTGTAGAGGCT 57.438 40.000 29.16 0.00 45.49 4.58
3007 3321 9.646427 GCCCATAAAAGAAAATTAATGTGTGTA 57.354 29.630 0.00 0.00 0.00 2.90
3008 3322 8.153550 TGCCCATAAAAGAAAATTAATGTGTGT 58.846 29.630 0.00 0.00 0.00 3.72
3009 3323 8.545229 TGCCCATAAAAGAAAATTAATGTGTG 57.455 30.769 0.00 0.00 0.00 3.82
3025 3339 9.469807 CGCACTTAAATAAAATATGCCCATAAA 57.530 29.630 0.00 0.00 0.00 1.40
3026 3340 8.851145 TCGCACTTAAATAAAATATGCCCATAA 58.149 29.630 0.00 0.00 0.00 1.90
3027 3341 8.397575 TCGCACTTAAATAAAATATGCCCATA 57.602 30.769 0.00 0.00 0.00 2.74
3028 3342 7.283625 TCGCACTTAAATAAAATATGCCCAT 57.716 32.000 0.00 0.00 0.00 4.00
3029 3343 6.701145 TCGCACTTAAATAAAATATGCCCA 57.299 33.333 0.00 0.00 0.00 5.36
3030 3344 7.060633 CGATTCGCACTTAAATAAAATATGCCC 59.939 37.037 0.00 0.00 0.00 5.36
3031 3345 7.801315 TCGATTCGCACTTAAATAAAATATGCC 59.199 33.333 0.00 0.00 0.00 4.40
3032 3346 8.708075 TCGATTCGCACTTAAATAAAATATGC 57.292 30.769 0.00 0.00 0.00 3.14
3035 3349 9.089601 TGTCTCGATTCGCACTTAAATAAAATA 57.910 29.630 0.00 0.00 0.00 1.40
3036 3350 7.970384 TGTCTCGATTCGCACTTAAATAAAAT 58.030 30.769 0.00 0.00 0.00 1.82
3037 3351 7.354025 TGTCTCGATTCGCACTTAAATAAAA 57.646 32.000 0.00 0.00 0.00 1.52
3038 3352 6.954616 TGTCTCGATTCGCACTTAAATAAA 57.045 33.333 0.00 0.00 0.00 1.40
3039 3353 6.588756 AGTTGTCTCGATTCGCACTTAAATAA 59.411 34.615 0.00 0.00 0.00 1.40
3040 3354 6.097356 AGTTGTCTCGATTCGCACTTAAATA 58.903 36.000 0.00 0.00 0.00 1.40
3041 3355 4.929808 AGTTGTCTCGATTCGCACTTAAAT 59.070 37.500 0.00 0.00 0.00 1.40
3042 3356 4.304110 AGTTGTCTCGATTCGCACTTAAA 58.696 39.130 0.00 0.00 0.00 1.52
3043 3357 3.909430 AGTTGTCTCGATTCGCACTTAA 58.091 40.909 0.00 0.00 0.00 1.85
3044 3358 3.570926 AGTTGTCTCGATTCGCACTTA 57.429 42.857 0.00 0.00 0.00 2.24
3045 3359 2.440539 AGTTGTCTCGATTCGCACTT 57.559 45.000 0.00 0.00 0.00 3.16
3046 3360 2.488545 ACTAGTTGTCTCGATTCGCACT 59.511 45.455 0.00 1.32 0.00 4.40
3047 3361 2.864968 ACTAGTTGTCTCGATTCGCAC 58.135 47.619 0.00 1.26 0.00 5.34
3048 3362 4.895224 ATACTAGTTGTCTCGATTCGCA 57.105 40.909 0.00 0.00 0.00 5.10
3049 3363 6.252869 TGAAAATACTAGTTGTCTCGATTCGC 59.747 38.462 0.00 0.00 0.00 4.70
3050 3364 7.736031 TGAAAATACTAGTTGTCTCGATTCG 57.264 36.000 0.00 0.00 0.00 3.34
3068 3382 8.948631 ACGTGTAGACATGAGATAATGAAAAT 57.051 30.769 8.84 0.00 36.72 1.82
3069 3383 8.655970 CAACGTGTAGACATGAGATAATGAAAA 58.344 33.333 8.84 0.00 36.72 2.29
3070 3384 7.277760 CCAACGTGTAGACATGAGATAATGAAA 59.722 37.037 8.84 0.00 36.72 2.69
3071 3385 6.756542 CCAACGTGTAGACATGAGATAATGAA 59.243 38.462 8.84 0.00 36.72 2.57
3072 3386 6.096282 TCCAACGTGTAGACATGAGATAATGA 59.904 38.462 8.84 0.00 36.72 2.57
3073 3387 6.273071 TCCAACGTGTAGACATGAGATAATG 58.727 40.000 8.84 0.00 36.72 1.90
3074 3388 6.465439 TCCAACGTGTAGACATGAGATAAT 57.535 37.500 8.84 0.00 36.72 1.28
3075 3389 5.907866 TCCAACGTGTAGACATGAGATAA 57.092 39.130 8.84 0.00 36.72 1.75
3076 3390 6.465439 AATCCAACGTGTAGACATGAGATA 57.535 37.500 8.84 0.00 36.72 1.98
3077 3391 5.344743 AATCCAACGTGTAGACATGAGAT 57.655 39.130 8.84 5.29 36.72 2.75
3078 3392 4.801330 AATCCAACGTGTAGACATGAGA 57.199 40.909 8.84 3.35 36.72 3.27
3079 3393 4.929211 TGAAATCCAACGTGTAGACATGAG 59.071 41.667 8.84 1.39 36.72 2.90
3080 3394 4.688879 GTGAAATCCAACGTGTAGACATGA 59.311 41.667 8.84 0.00 36.72 3.07
3081 3395 4.690748 AGTGAAATCCAACGTGTAGACATG 59.309 41.667 0.00 0.22 38.76 3.21
3082 3396 4.894784 AGTGAAATCCAACGTGTAGACAT 58.105 39.130 0.00 0.00 0.00 3.06
3083 3397 4.202172 TGAGTGAAATCCAACGTGTAGACA 60.202 41.667 0.00 0.00 0.00 3.41
3084 3398 4.304110 TGAGTGAAATCCAACGTGTAGAC 58.696 43.478 0.00 0.00 0.00 2.59
3085 3399 4.556233 CTGAGTGAAATCCAACGTGTAGA 58.444 43.478 0.00 0.00 0.00 2.59
3086 3400 3.123621 GCTGAGTGAAATCCAACGTGTAG 59.876 47.826 0.00 0.00 0.00 2.74
3087 3401 3.064207 GCTGAGTGAAATCCAACGTGTA 58.936 45.455 0.00 0.00 0.00 2.90
3088 3402 1.873591 GCTGAGTGAAATCCAACGTGT 59.126 47.619 0.00 0.00 0.00 4.49
3089 3403 1.872952 TGCTGAGTGAAATCCAACGTG 59.127 47.619 0.00 0.00 0.00 4.49
3090 3404 1.873591 GTGCTGAGTGAAATCCAACGT 59.126 47.619 0.00 0.00 0.00 3.99
3091 3405 1.136252 CGTGCTGAGTGAAATCCAACG 60.136 52.381 0.00 0.00 0.00 4.10
3092 3406 1.873591 ACGTGCTGAGTGAAATCCAAC 59.126 47.619 0.00 0.00 0.00 3.77
3093 3407 2.254546 ACGTGCTGAGTGAAATCCAA 57.745 45.000 0.00 0.00 0.00 3.53
3094 3408 2.143122 GAACGTGCTGAGTGAAATCCA 58.857 47.619 0.00 0.00 0.00 3.41
3095 3409 2.417719 AGAACGTGCTGAGTGAAATCC 58.582 47.619 0.00 0.00 0.00 3.01
3096 3410 6.563010 GCATATAGAACGTGCTGAGTGAAATC 60.563 42.308 6.22 0.00 36.02 2.17
3097 3411 5.235186 GCATATAGAACGTGCTGAGTGAAAT 59.765 40.000 6.22 0.00 36.02 2.17
3098 3412 4.566759 GCATATAGAACGTGCTGAGTGAAA 59.433 41.667 6.22 0.00 36.02 2.69
3099 3413 4.112634 GCATATAGAACGTGCTGAGTGAA 58.887 43.478 6.22 0.00 36.02 3.18
3100 3414 3.130340 TGCATATAGAACGTGCTGAGTGA 59.870 43.478 6.22 0.00 39.52 3.41
3101 3415 3.447742 TGCATATAGAACGTGCTGAGTG 58.552 45.455 6.22 2.92 39.52 3.51
3102 3416 3.801114 TGCATATAGAACGTGCTGAGT 57.199 42.857 6.22 0.00 39.52 3.41
3103 3417 6.152379 TCTAATGCATATAGAACGTGCTGAG 58.848 40.000 6.22 0.00 39.52 3.35
3104 3418 6.084326 TCTAATGCATATAGAACGTGCTGA 57.916 37.500 6.22 0.00 39.52 4.26
3105 3419 5.923114 ACTCTAATGCATATAGAACGTGCTG 59.077 40.000 6.22 0.00 39.52 4.41
3106 3420 6.090483 ACTCTAATGCATATAGAACGTGCT 57.910 37.500 0.00 0.00 39.52 4.40
3107 3421 9.737427 ATATACTCTAATGCATATAGAACGTGC 57.263 33.333 0.00 0.00 39.26 5.34
3152 3466 9.654663 GGGGTACAAATGTTATATACATCTCTC 57.345 37.037 0.00 0.00 46.75 3.20
3153 3467 8.603304 GGGGGTACAAATGTTATATACATCTCT 58.397 37.037 0.00 0.00 46.75 3.10
3154 3468 8.603304 AGGGGGTACAAATGTTATATACATCTC 58.397 37.037 0.00 0.00 46.75 2.75
3155 3469 8.383175 CAGGGGGTACAAATGTTATATACATCT 58.617 37.037 0.00 0.00 46.75 2.90
3156 3470 8.161425 ACAGGGGGTACAAATGTTATATACATC 58.839 37.037 0.00 0.00 46.75 3.06
3158 3472 7.454553 ACAGGGGGTACAAATGTTATATACA 57.545 36.000 0.00 0.00 41.97 2.29
3159 3473 8.626526 CAAACAGGGGGTACAAATGTTATATAC 58.373 37.037 0.00 0.00 33.17 1.47
3160 3474 8.337739 ACAAACAGGGGGTACAAATGTTATATA 58.662 33.333 0.00 0.00 33.17 0.86
3161 3475 7.186268 ACAAACAGGGGGTACAAATGTTATAT 58.814 34.615 0.00 0.00 33.17 0.86
3162 3476 6.553857 ACAAACAGGGGGTACAAATGTTATA 58.446 36.000 0.00 0.00 33.17 0.98
3163 3477 5.399113 ACAAACAGGGGGTACAAATGTTAT 58.601 37.500 0.00 0.00 33.17 1.89
3164 3478 4.805744 ACAAACAGGGGGTACAAATGTTA 58.194 39.130 0.00 0.00 33.17 2.41
3165 3479 3.648739 ACAAACAGGGGGTACAAATGTT 58.351 40.909 0.00 0.00 35.70 2.71
3166 3480 3.322191 ACAAACAGGGGGTACAAATGT 57.678 42.857 0.00 0.00 0.00 2.71
3167 3481 5.993748 AATACAAACAGGGGGTACAAATG 57.006 39.130 0.00 0.00 0.00 2.32
3168 3482 6.796648 AGTAATACAAACAGGGGGTACAAAT 58.203 36.000 0.00 0.00 0.00 2.32
3169 3483 6.203526 AGTAATACAAACAGGGGGTACAAA 57.796 37.500 0.00 0.00 0.00 2.83
3170 3484 5.846528 AGTAATACAAACAGGGGGTACAA 57.153 39.130 0.00 0.00 0.00 2.41
3171 3485 7.182387 TCAATAGTAATACAAACAGGGGGTACA 59.818 37.037 0.00 0.00 0.00 2.90
3172 3486 7.496920 GTCAATAGTAATACAAACAGGGGGTAC 59.503 40.741 0.00 0.00 0.00 3.34
3173 3487 7.567458 GTCAATAGTAATACAAACAGGGGGTA 58.433 38.462 0.00 0.00 0.00 3.69
3174 3488 6.420638 GTCAATAGTAATACAAACAGGGGGT 58.579 40.000 0.00 0.00 0.00 4.95
3175 3489 5.526111 CGTCAATAGTAATACAAACAGGGGG 59.474 44.000 0.00 0.00 0.00 5.40
3176 3490 6.036735 CACGTCAATAGTAATACAAACAGGGG 59.963 42.308 0.00 0.00 0.00 4.79
3177 3491 6.814644 TCACGTCAATAGTAATACAAACAGGG 59.185 38.462 0.00 0.00 0.00 4.45
3178 3492 7.329962 TGTCACGTCAATAGTAATACAAACAGG 59.670 37.037 0.00 0.00 0.00 4.00
3179 3493 8.234887 TGTCACGTCAATAGTAATACAAACAG 57.765 34.615 0.00 0.00 0.00 3.16
3180 3494 8.766000 ATGTCACGTCAATAGTAATACAAACA 57.234 30.769 0.00 0.00 0.00 2.83
3182 3496 9.027129 GCTATGTCACGTCAATAGTAATACAAA 57.973 33.333 9.31 0.00 0.00 2.83
3183 3497 8.192110 TGCTATGTCACGTCAATAGTAATACAA 58.808 33.333 9.31 0.00 0.00 2.41
3184 3498 7.708998 TGCTATGTCACGTCAATAGTAATACA 58.291 34.615 9.31 0.00 0.00 2.29
3185 3499 8.639428 CATGCTATGTCACGTCAATAGTAATAC 58.361 37.037 9.31 0.00 0.00 1.89
3186 3500 7.328493 GCATGCTATGTCACGTCAATAGTAATA 59.672 37.037 11.37 0.00 0.00 0.98
3187 3501 6.146184 GCATGCTATGTCACGTCAATAGTAAT 59.854 38.462 11.37 3.52 0.00 1.89
3188 3502 5.462068 GCATGCTATGTCACGTCAATAGTAA 59.538 40.000 11.37 1.88 0.00 2.24
3189 3503 4.982295 GCATGCTATGTCACGTCAATAGTA 59.018 41.667 11.37 6.34 0.00 1.82
3190 3504 3.804325 GCATGCTATGTCACGTCAATAGT 59.196 43.478 11.37 0.00 0.00 2.12
3191 3505 3.803778 TGCATGCTATGTCACGTCAATAG 59.196 43.478 20.33 0.00 0.00 1.73
3192 3506 3.791245 TGCATGCTATGTCACGTCAATA 58.209 40.909 20.33 0.00 0.00 1.90
3193 3507 2.631267 TGCATGCTATGTCACGTCAAT 58.369 42.857 20.33 0.00 0.00 2.57
3194 3508 2.091852 TGCATGCTATGTCACGTCAA 57.908 45.000 20.33 0.00 0.00 3.18
3195 3509 1.935199 CATGCATGCTATGTCACGTCA 59.065 47.619 20.33 0.00 0.00 4.35
3196 3510 1.935873 ACATGCATGCTATGTCACGTC 59.064 47.619 26.53 0.00 33.72 4.34
3197 3511 2.028420 ACATGCATGCTATGTCACGT 57.972 45.000 26.53 0.00 33.72 4.49
3202 3516 2.423446 TGTGGACATGCATGCTATGT 57.577 45.000 26.53 25.70 41.21 2.29
3203 3517 3.067601 ACATTGTGGACATGCATGCTATG 59.932 43.478 26.53 21.18 0.00 2.23
3204 3518 3.293337 ACATTGTGGACATGCATGCTAT 58.707 40.909 26.53 7.36 0.00 2.97
3205 3519 2.725637 ACATTGTGGACATGCATGCTA 58.274 42.857 26.53 14.05 0.00 3.49
3206 3520 1.552578 ACATTGTGGACATGCATGCT 58.447 45.000 26.53 13.62 0.00 3.79
3207 3521 3.507103 TTACATTGTGGACATGCATGC 57.493 42.857 26.53 18.01 0.00 4.06


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

AutoCloner maintained by Alex Coulton.