Multiple sequence alignment - TraesCS6B01G336500

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 TraesCS6B01G336500 chr6B 100.000 3062 0 0 1 3062 592466033 592462972 0.000000e+00 5655.0
1 TraesCS6B01G336500 chr6D 92.418 2717 102 46 29 2673 396012561 396009877 0.000000e+00 3781.0
2 TraesCS6B01G336500 chr6A 89.833 2872 147 58 24 2827 542432100 542429306 0.000000e+00 3552.0
3 TraesCS6B01G336500 chr1A 81.877 309 48 8 1752 2056 495192326 495192022 1.410000e-63 254.0
4 TraesCS6B01G336500 chr1A 78.761 339 52 13 1326 1663 495192933 495192614 3.090000e-50 209.0
5 TraesCS6B01G336500 chr1A 96.226 53 2 0 1177 1229 495193073 495193021 1.510000e-13 87.9
6 TraesCS6B01G336500 chr3A 81.849 292 51 2 1751 2041 594493030 594493320 8.480000e-61 244.0
7 TraesCS6B01G336500 chr3A 82.090 134 20 4 1507 1638 170659024 170659155 8.970000e-21 111.0
8 TraesCS6B01G336500 chr1D 80.938 320 52 9 1741 2056 397973297 397972983 8.480000e-61 244.0
9 TraesCS6B01G336500 chr1D 79.941 339 48 13 1326 1663 397973932 397973613 6.600000e-57 231.0
10 TraesCS6B01G336500 chr1B 81.150 313 51 8 1748 2056 533324016 533323708 8.480000e-61 244.0
11 TraesCS6B01G336500 chr1B 78.171 339 54 13 1326 1663 533324652 533324333 6.700000e-47 198.0
12 TraesCS6B01G336500 chr1B 94.340 53 3 0 1177 1229 533324803 533324751 7.040000e-12 82.4
13 TraesCS6B01G336500 chr3D 81.570 293 52 2 1750 2041 451710640 451710931 1.100000e-59 241.0
14 TraesCS6B01G336500 chr3D 81.229 293 53 2 1750 2041 451886115 451886406 5.100000e-58 235.0
15 TraesCS6B01G336500 chr3D 74.487 341 63 19 1328 1662 157443377 157443055 3.210000e-25 126.0
16 TraesCS6B01G336500 chr3D 78.481 158 31 3 1510 1665 427294637 427294481 1.940000e-17 100.0
17 TraesCS6B01G336500 chr3D 93.878 49 3 0 1177 1225 451709915 451709963 1.180000e-09 75.0
18 TraesCS6B01G336500 chr3D 93.878 49 3 0 1177 1225 451885414 451885462 1.180000e-09 75.0
19 TraesCS6B01G336500 chr3B 78.481 158 31 3 1510 1665 556959889 556959733 1.940000e-17 100.0
20 TraesCS6B01G336500 chr5B 98.113 53 1 0 1178 1230 619927323 619927271 3.250000e-15 93.5


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 TraesCS6B01G336500 chr6B 592462972 592466033 3061 True 5655.0 5655 100.0000 1 3062 1 chr6B.!!$R1 3061
1 TraesCS6B01G336500 chr6D 396009877 396012561 2684 True 3781.0 3781 92.4180 29 2673 1 chr6D.!!$R1 2644
2 TraesCS6B01G336500 chr6A 542429306 542432100 2794 True 3552.0 3552 89.8330 24 2827 1 chr6A.!!$R1 2803
3 TraesCS6B01G336500 chr1D 397972983 397973932 949 True 237.5 244 80.4395 1326 2056 2 chr1D.!!$R1 730

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
633 688 0.031994 CCCCTTCCAAACTTTGCACG 59.968 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2962 0.601046 TGCGAGTTGAAGACAGCAGG 60.601 55.0 0.0 0.0 38.59 4.85 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
130 131 8.889717 TGAAGTTAAAAATCAACGAGACTTCTT 58.110 29.630 12.37 0.00 41.22 2.52
185 200 0.035439 CTTGCCACCTACAATCCCGT 60.035 55.000 0.00 0.00 0.00 5.28
236 253 5.507985 GCATTGCAGGTTCTTGTTCTTAAGT 60.508 40.000 3.15 0.00 0.00 2.24
240 257 6.354130 TGCAGGTTCTTGTTCTTAAGTAACT 58.646 36.000 1.63 0.00 0.00 2.24
241 268 7.502696 TGCAGGTTCTTGTTCTTAAGTAACTA 58.497 34.615 1.63 2.82 0.00 2.24
253 289 7.224522 TCTTAAGTAACTAACTGACTGACCC 57.775 40.000 1.63 0.00 38.88 4.46
265 301 3.670629 CTGACCCGAGCTCCTCCCT 62.671 68.421 8.47 0.00 0.00 4.20
296 332 8.175716 CGTCCTTATTTTACTTCCAGATTTGTC 58.824 37.037 0.00 0.00 0.00 3.18
311 348 1.725641 TTGTCTATTCGCAGCCACAG 58.274 50.000 0.00 0.00 0.00 3.66
460 512 0.390860 CAATCAAAACCCAACGCCCA 59.609 50.000 0.00 0.00 0.00 5.36
576 628 2.622436 CAAGCAAGCCTACCACTCTAC 58.378 52.381 0.00 0.00 0.00 2.59
578 630 3.383698 AGCAAGCCTACCACTCTACTA 57.616 47.619 0.00 0.00 0.00 1.82
591 643 4.994852 CCACTCTACTACTAGCTAGCTCTG 59.005 50.000 23.26 17.61 0.00 3.35
594 646 5.129815 ACTCTACTACTAGCTAGCTCTGTGT 59.870 44.000 23.26 20.37 0.00 3.72
628 683 1.533033 CGGCCCCCTTCCAAACTTT 60.533 57.895 0.00 0.00 0.00 2.66
633 688 0.031994 CCCCTTCCAAACTTTGCACG 59.968 55.000 0.00 0.00 0.00 5.34
697 752 0.385390 CCAACGCCTCAGCTTTTGTT 59.615 50.000 0.00 0.00 36.60 2.83
698 753 1.600413 CCAACGCCTCAGCTTTTGTTC 60.600 52.381 0.00 0.00 36.60 3.18
728 792 0.251165 TGCTGCTTTTACCACTCCCC 60.251 55.000 0.00 0.00 0.00 4.81
797 862 2.629656 CCACCTGCGGCTTTTCCAG 61.630 63.158 0.00 0.00 34.01 3.86
943 1017 4.408821 GAGCACATCCCCACCGCA 62.409 66.667 0.00 0.00 0.00 5.69
1116 1194 4.838152 CACGGCCTGGTCCATCGG 62.838 72.222 0.00 4.03 0.00 4.18
1264 1345 5.391629 CGTCACTCACAGCATTGTAGTACTA 60.392 44.000 0.00 0.00 35.25 1.82
1288 1369 1.822990 CTTGGTGCATCTTTGATGCCT 59.177 47.619 24.05 0.00 43.94 4.75
1289 1370 1.927487 TGGTGCATCTTTGATGCCTT 58.073 45.000 24.05 0.00 43.94 4.35
1292 1373 2.417787 GGTGCATCTTTGATGCCTTTCC 60.418 50.000 24.05 17.76 43.94 3.13
1702 2038 3.622455 GCATTACTACCTTTGTCTGCCCT 60.622 47.826 0.00 0.00 0.00 5.19
1716 2052 0.756294 TGCCCTCGAACTGTTCAAGA 59.244 50.000 19.56 9.18 0.00 3.02
1818 2154 1.066071 GGCCACTCCTACTTCAACCTC 60.066 57.143 0.00 0.00 0.00 3.85
1821 2157 2.094649 CCACTCCTACTTCAACCTCGTC 60.095 54.545 0.00 0.00 0.00 4.20
1876 2212 3.048602 CGGTGTCCGTCAAGTCCT 58.951 61.111 0.00 0.00 42.73 3.85
1878 2214 1.292541 GGTGTCCGTCAAGTCCTCC 59.707 63.158 0.00 0.00 0.00 4.30
1968 2307 4.821589 GGCCTCTCCTTCCGCGTG 62.822 72.222 4.92 0.00 0.00 5.34
2122 2464 6.364568 TGTAGTAGTAGTGGTCAGTAGTGA 57.635 41.667 0.00 0.00 0.00 3.41
2173 2515 1.202405 GGGAAGCGCCATGGTTTTATG 60.202 52.381 14.67 0.00 38.70 1.90
2204 2546 1.153745 ACAAGCATCCGACGCTCTC 60.154 57.895 0.00 0.00 39.29 3.20
2212 2554 2.725008 CGACGCTCTCTGGGGATC 59.275 66.667 0.00 0.00 0.00 3.36
2213 2555 1.826054 CGACGCTCTCTGGGGATCT 60.826 63.158 0.00 0.00 0.00 2.75
2218 2560 1.494960 GCTCTCTGGGGATCTGAAGT 58.505 55.000 0.00 0.00 0.00 3.01
2219 2561 1.412343 GCTCTCTGGGGATCTGAAGTC 59.588 57.143 0.00 0.00 0.00 3.01
2276 2618 5.334569 GCTTTTAATTGTCTGGTTAGCGTGA 60.335 40.000 0.00 0.00 0.00 4.35
2280 2622 0.317160 TGTCTGGTTAGCGTGAGTGG 59.683 55.000 0.00 0.00 0.00 4.00
2298 2640 1.076513 TGGGTGAGTGAGTGGTAGCTA 59.923 52.381 0.00 0.00 0.00 3.32
2538 2887 5.365403 TTTGCATGTTTTACTTCCTACCG 57.635 39.130 0.00 0.00 0.00 4.02
2544 2893 4.559153 TGTTTTACTTCCTACCGTACTGC 58.441 43.478 0.00 0.00 0.00 4.40
2545 2894 4.039004 TGTTTTACTTCCTACCGTACTGCA 59.961 41.667 0.00 0.00 0.00 4.41
2550 2909 4.648651 ACTTCCTACCGTACTGCAATTTT 58.351 39.130 0.00 0.00 0.00 1.82
2557 2916 4.638304 ACCGTACTGCAATTTTACTCTGT 58.362 39.130 0.00 0.00 0.00 3.41
2564 2923 7.516198 ACTGCAATTTTACTCTGTTGAAGAT 57.484 32.000 0.00 0.00 32.66 2.40
2567 2926 8.621532 TGCAATTTTACTCTGTTGAAGATAGT 57.378 30.769 0.00 0.00 33.29 2.12
2568 2927 9.719355 TGCAATTTTACTCTGTTGAAGATAGTA 57.281 29.630 0.00 0.00 33.29 1.82
2581 2940 7.921214 TGTTGAAGATAGTATACTAGTGCTTGC 59.079 37.037 20.94 15.31 0.00 4.01
2603 2962 3.524541 CCCATCTTGCAATTTTACTGCC 58.475 45.455 0.00 0.00 39.13 4.85
2634 2993 3.664107 TCAACTCGCAAATGAGCTAACT 58.336 40.909 0.00 0.00 39.68 2.24
2645 3005 6.381801 CAAATGAGCTAACTTTCAAACGGAT 58.618 36.000 0.00 0.00 0.00 4.18
2687 3047 6.518736 GTCGATTTCTGAACATTTCGGTTTAC 59.481 38.462 0.00 0.00 37.33 2.01
2688 3048 6.425721 TCGATTTCTGAACATTTCGGTTTACT 59.574 34.615 9.74 0.00 37.33 2.24
2689 3049 6.736853 CGATTTCTGAACATTTCGGTTTACTC 59.263 38.462 0.00 0.00 37.33 2.59
2690 3050 5.934935 TTCTGAACATTTCGGTTTACTCC 57.065 39.130 0.00 0.00 37.33 3.85
2691 3051 4.320870 TCTGAACATTTCGGTTTACTCCC 58.679 43.478 0.00 0.00 37.33 4.30
2692 3052 4.069304 CTGAACATTTCGGTTTACTCCCA 58.931 43.478 0.00 0.00 0.00 4.37
2693 3053 4.658063 TGAACATTTCGGTTTACTCCCAT 58.342 39.130 0.00 0.00 0.00 4.00
2694 3054 5.806818 TGAACATTTCGGTTTACTCCCATA 58.193 37.500 0.00 0.00 0.00 2.74
2695 3055 5.878116 TGAACATTTCGGTTTACTCCCATAG 59.122 40.000 0.00 0.00 0.00 2.23
2702 3062 4.773674 TCGGTTTACTCCCATAGTTCTTGA 59.226 41.667 0.00 0.00 39.80 3.02
2717 3077 2.543687 CTTGATCGTCGGTGCGAGGT 62.544 60.000 0.00 0.00 44.43 3.85
2725 3085 2.583593 GGTGCGAGGTCGAGCATC 60.584 66.667 18.15 4.48 45.69 3.91
2727 3087 1.446099 GTGCGAGGTCGAGCATCAA 60.446 57.895 18.15 0.00 45.69 2.57
2728 3088 0.807667 GTGCGAGGTCGAGCATCAAT 60.808 55.000 18.15 0.00 45.69 2.57
2733 3093 3.611766 GCGAGGTCGAGCATCAATACATA 60.612 47.826 18.15 0.00 43.02 2.29
2744 3104 7.585210 CGAGCATCAATACATAAAACATCACTG 59.415 37.037 0.00 0.00 33.17 3.66
2765 3125 3.000727 GTCCGTTGGTCGAAGAATCAAT 58.999 45.455 0.00 0.00 39.69 2.57
2768 3128 3.435327 CCGTTGGTCGAAGAATCAATTGA 59.565 43.478 11.26 11.26 39.69 2.57
2776 3136 4.700213 TCGAAGAATCAATTGAAGAACCCC 59.300 41.667 13.09 0.00 0.00 4.95
2777 3137 4.142381 CGAAGAATCAATTGAAGAACCCCC 60.142 45.833 13.09 0.00 0.00 5.40
2819 3179 6.519679 TTTGCGAGGAGTAAGTAGTTATCA 57.480 37.500 0.00 0.00 0.00 2.15
2820 3180 5.752892 TGCGAGGAGTAAGTAGTTATCAG 57.247 43.478 0.00 0.00 0.00 2.90
2821 3181 5.191426 TGCGAGGAGTAAGTAGTTATCAGT 58.809 41.667 0.00 0.00 0.00 3.41
2822 3182 6.351711 TGCGAGGAGTAAGTAGTTATCAGTA 58.648 40.000 0.00 0.00 0.00 2.74
2824 3184 7.012138 TGCGAGGAGTAAGTAGTTATCAGTAAG 59.988 40.741 0.00 0.00 0.00 2.34
2825 3185 7.226325 GCGAGGAGTAAGTAGTTATCAGTAAGA 59.774 40.741 0.00 0.00 0.00 2.10
2828 3188 9.411189 AGGAGTAAGTAGTTATCAGTAAGAAGG 57.589 37.037 0.00 0.00 0.00 3.46
2829 3189 8.136800 GGAGTAAGTAGTTATCAGTAAGAAGGC 58.863 40.741 0.00 0.00 0.00 4.35
2830 3190 8.009622 AGTAAGTAGTTATCAGTAAGAAGGCC 57.990 38.462 0.00 0.00 0.00 5.19
2831 3191 5.873146 AGTAGTTATCAGTAAGAAGGCCC 57.127 43.478 0.00 0.00 0.00 5.80
2832 3192 3.821421 AGTTATCAGTAAGAAGGCCCG 57.179 47.619 0.00 0.00 0.00 6.13
2833 3193 2.158943 AGTTATCAGTAAGAAGGCCCGC 60.159 50.000 0.00 0.00 0.00 6.13
2834 3194 0.387929 TATCAGTAAGAAGGCCCGCG 59.612 55.000 0.00 0.00 0.00 6.46
2835 3195 1.327690 ATCAGTAAGAAGGCCCGCGA 61.328 55.000 8.23 0.00 0.00 5.87
2836 3196 1.519455 CAGTAAGAAGGCCCGCGAG 60.519 63.158 8.23 0.00 0.00 5.03
2848 3208 3.592070 CGCGAGGAGTTCTCCAGA 58.408 61.111 19.28 0.00 39.30 3.86
2849 3209 1.137825 CGCGAGGAGTTCTCCAGAC 59.862 63.158 19.28 10.03 39.30 3.51
2850 3210 1.587043 CGCGAGGAGTTCTCCAGACA 61.587 60.000 19.28 0.00 39.30 3.41
2851 3211 0.109039 GCGAGGAGTTCTCCAGACAC 60.109 60.000 19.28 6.00 39.30 3.67
2852 3212 1.248486 CGAGGAGTTCTCCAGACACA 58.752 55.000 19.28 0.00 39.30 3.72
2853 3213 1.613925 CGAGGAGTTCTCCAGACACAA 59.386 52.381 19.28 0.00 39.30 3.33
2854 3214 2.035961 CGAGGAGTTCTCCAGACACAAA 59.964 50.000 19.28 0.00 39.30 2.83
2855 3215 3.492656 CGAGGAGTTCTCCAGACACAAAA 60.493 47.826 19.28 0.00 39.30 2.44
2856 3216 3.809905 AGGAGTTCTCCAGACACAAAAC 58.190 45.455 19.28 0.00 0.00 2.43
2857 3217 2.544267 GGAGTTCTCCAGACACAAAACG 59.456 50.000 13.31 0.00 0.00 3.60
2858 3218 3.454375 GAGTTCTCCAGACACAAAACGA 58.546 45.455 0.00 0.00 0.00 3.85
2859 3219 3.458189 AGTTCTCCAGACACAAAACGAG 58.542 45.455 0.00 0.00 0.00 4.18
2860 3220 3.132289 AGTTCTCCAGACACAAAACGAGA 59.868 43.478 0.00 0.00 0.00 4.04
2861 3221 3.812156 TCTCCAGACACAAAACGAGAA 57.188 42.857 0.00 0.00 0.00 2.87
2862 3222 3.717707 TCTCCAGACACAAAACGAGAAG 58.282 45.455 0.00 0.00 0.00 2.85
2863 3223 3.132289 TCTCCAGACACAAAACGAGAAGT 59.868 43.478 0.00 0.00 0.00 3.01
2864 3224 3.194861 TCCAGACACAAAACGAGAAGTG 58.805 45.455 0.00 0.00 37.95 3.16
2865 3225 3.118920 TCCAGACACAAAACGAGAAGTGA 60.119 43.478 0.00 0.00 35.97 3.41
2866 3226 3.246226 CCAGACACAAAACGAGAAGTGAG 59.754 47.826 0.00 0.00 35.97 3.51
2867 3227 3.246226 CAGACACAAAACGAGAAGTGAGG 59.754 47.826 0.00 0.00 35.97 3.86
2868 3228 1.940613 ACACAAAACGAGAAGTGAGGC 59.059 47.619 0.00 0.00 35.97 4.70
2869 3229 2.213499 CACAAAACGAGAAGTGAGGCT 58.787 47.619 0.00 0.00 33.99 4.58
2870 3230 2.614057 CACAAAACGAGAAGTGAGGCTT 59.386 45.455 0.00 0.00 40.76 4.35
2885 3245 3.010200 AGGCTTCCCTCATGAACAATC 57.990 47.619 0.00 0.00 36.46 2.67
2886 3246 2.309755 AGGCTTCCCTCATGAACAATCA 59.690 45.455 0.00 0.00 36.46 2.57
2887 3247 3.091545 GGCTTCCCTCATGAACAATCAA 58.908 45.455 0.00 0.00 39.49 2.57
2888 3248 3.119352 GGCTTCCCTCATGAACAATCAAC 60.119 47.826 0.00 0.00 39.49 3.18
2889 3249 3.507233 GCTTCCCTCATGAACAATCAACA 59.493 43.478 0.00 0.00 39.49 3.33
2890 3250 4.159135 GCTTCCCTCATGAACAATCAACAT 59.841 41.667 0.00 0.00 39.49 2.71
2891 3251 5.357878 GCTTCCCTCATGAACAATCAACATA 59.642 40.000 0.00 0.00 39.49 2.29
2892 3252 6.127647 GCTTCCCTCATGAACAATCAACATAA 60.128 38.462 0.00 0.00 39.49 1.90
2893 3253 7.395190 TTCCCTCATGAACAATCAACATAAG 57.605 36.000 0.00 0.00 39.49 1.73
2894 3254 6.720309 TCCCTCATGAACAATCAACATAAGA 58.280 36.000 0.00 0.00 39.49 2.10
2895 3255 6.825213 TCCCTCATGAACAATCAACATAAGAG 59.175 38.462 0.00 0.00 39.49 2.85
2896 3256 6.459298 CCCTCATGAACAATCAACATAAGAGC 60.459 42.308 0.00 0.00 39.49 4.09
2897 3257 6.094464 CCTCATGAACAATCAACATAAGAGCA 59.906 38.462 0.00 0.00 39.49 4.26
2898 3258 7.201794 CCTCATGAACAATCAACATAAGAGCAT 60.202 37.037 0.00 0.00 39.49 3.79
2899 3259 7.700505 TCATGAACAATCAACATAAGAGCATC 58.299 34.615 0.00 0.00 39.49 3.91
2900 3260 7.555195 TCATGAACAATCAACATAAGAGCATCT 59.445 33.333 0.00 0.00 44.06 2.90
2901 3261 8.833493 CATGAACAATCAACATAAGAGCATCTA 58.167 33.333 0.00 0.00 42.08 1.98
2902 3262 8.201554 TGAACAATCAACATAAGAGCATCTAC 57.798 34.615 0.00 0.00 37.20 2.59
2903 3263 7.280876 TGAACAATCAACATAAGAGCATCTACC 59.719 37.037 0.00 0.00 37.20 3.18
2912 3272 1.291132 GAGCATCTACCTCAAACGCC 58.709 55.000 0.00 0.00 0.00 5.68
2913 3273 0.107654 AGCATCTACCTCAAACGCCC 60.108 55.000 0.00 0.00 0.00 6.13
2914 3274 0.107654 GCATCTACCTCAAACGCCCT 60.108 55.000 0.00 0.00 0.00 5.19
2915 3275 1.656652 CATCTACCTCAAACGCCCTG 58.343 55.000 0.00 0.00 0.00 4.45
2916 3276 1.066143 CATCTACCTCAAACGCCCTGT 60.066 52.381 0.00 0.00 0.00 4.00
2917 3277 0.606604 TCTACCTCAAACGCCCTGTC 59.393 55.000 0.00 0.00 0.00 3.51
2918 3278 0.320374 CTACCTCAAACGCCCTGTCA 59.680 55.000 0.00 0.00 0.00 3.58
2919 3279 0.981183 TACCTCAAACGCCCTGTCAT 59.019 50.000 0.00 0.00 0.00 3.06
2920 3280 0.606401 ACCTCAAACGCCCTGTCATG 60.606 55.000 0.00 0.00 0.00 3.07
2921 3281 0.321564 CCTCAAACGCCCTGTCATGA 60.322 55.000 0.00 0.00 0.00 3.07
2922 3282 1.522668 CTCAAACGCCCTGTCATGAA 58.477 50.000 0.00 0.00 0.00 2.57
2923 3283 1.879380 CTCAAACGCCCTGTCATGAAA 59.121 47.619 0.00 0.00 0.00 2.69
2924 3284 2.489329 CTCAAACGCCCTGTCATGAAAT 59.511 45.455 0.00 0.00 0.00 2.17
2925 3285 2.890311 TCAAACGCCCTGTCATGAAATT 59.110 40.909 0.00 0.00 0.00 1.82
2926 3286 3.320541 TCAAACGCCCTGTCATGAAATTT 59.679 39.130 0.00 0.00 0.00 1.82
2927 3287 4.057432 CAAACGCCCTGTCATGAAATTTT 58.943 39.130 0.00 0.00 0.00 1.82
2928 3288 3.302365 ACGCCCTGTCATGAAATTTTG 57.698 42.857 0.00 0.00 0.00 2.44
2929 3289 2.890311 ACGCCCTGTCATGAAATTTTGA 59.110 40.909 0.00 0.00 0.00 2.69
2930 3290 3.244976 CGCCCTGTCATGAAATTTTGAC 58.755 45.455 13.74 13.74 42.05 3.18
2939 3299 8.620116 TGTCATGAAATTTTGACATAGACAGA 57.380 30.769 17.73 0.00 45.35 3.41
2940 3300 8.506437 TGTCATGAAATTTTGACATAGACAGAC 58.494 33.333 17.73 9.05 45.35 3.51
2941 3301 7.689812 GTCATGAAATTTTGACATAGACAGACG 59.310 37.037 15.15 0.00 41.48 4.18
2942 3302 7.602265 TCATGAAATTTTGACATAGACAGACGA 59.398 33.333 0.00 0.00 0.00 4.20
2943 3303 7.117241 TGAAATTTTGACATAGACAGACGAC 57.883 36.000 0.00 0.00 0.00 4.34
2944 3304 6.704050 TGAAATTTTGACATAGACAGACGACA 59.296 34.615 0.00 0.00 0.00 4.35
2945 3305 6.712241 AATTTTGACATAGACAGACGACAG 57.288 37.500 0.00 0.00 0.00 3.51
2946 3306 5.447624 TTTTGACATAGACAGACGACAGA 57.552 39.130 0.00 0.00 0.00 3.41
2947 3307 4.421033 TTGACATAGACAGACGACAGAC 57.579 45.455 0.00 0.00 0.00 3.51
2959 3319 0.778815 CGACAGACGTCTCAAACAGC 59.221 55.000 16.96 0.00 40.23 4.40
2960 3320 1.140816 GACAGACGTCTCAAACAGCC 58.859 55.000 16.96 0.00 39.22 4.85
2961 3321 0.249911 ACAGACGTCTCAAACAGCCC 60.250 55.000 16.96 0.00 0.00 5.19
2962 3322 1.006102 AGACGTCTCAAACAGCCCG 60.006 57.895 13.58 0.00 0.00 6.13
2963 3323 1.006571 GACGTCTCAAACAGCCCGA 60.007 57.895 8.70 0.00 0.00 5.14
2964 3324 0.389948 GACGTCTCAAACAGCCCGAT 60.390 55.000 8.70 0.00 0.00 4.18
2965 3325 0.034896 ACGTCTCAAACAGCCCGATT 59.965 50.000 0.00 0.00 0.00 3.34
2966 3326 1.156736 CGTCTCAAACAGCCCGATTT 58.843 50.000 0.00 0.00 0.00 2.17
2967 3327 1.535462 CGTCTCAAACAGCCCGATTTT 59.465 47.619 0.00 0.00 0.00 1.82
2968 3328 2.665519 CGTCTCAAACAGCCCGATTTTG 60.666 50.000 0.00 0.00 0.00 2.44
2969 3329 2.552315 GTCTCAAACAGCCCGATTTTGA 59.448 45.455 0.00 0.00 37.00 2.69
2970 3330 2.552315 TCTCAAACAGCCCGATTTTGAC 59.448 45.455 0.00 0.00 34.96 3.18
2971 3331 2.293122 CTCAAACAGCCCGATTTTGACA 59.707 45.455 0.00 0.00 34.96 3.58
2972 3332 2.890311 TCAAACAGCCCGATTTTGACAT 59.110 40.909 0.00 0.00 34.96 3.06
2973 3333 4.075682 TCAAACAGCCCGATTTTGACATA 58.924 39.130 0.00 0.00 34.96 2.29
2974 3334 4.155826 TCAAACAGCCCGATTTTGACATAG 59.844 41.667 0.00 0.00 34.96 2.23
2975 3335 3.627395 ACAGCCCGATTTTGACATAGA 57.373 42.857 0.00 0.00 0.00 1.98
2976 3336 3.270877 ACAGCCCGATTTTGACATAGAC 58.729 45.455 0.00 0.00 0.00 2.59
2977 3337 2.285220 CAGCCCGATTTTGACATAGACG 59.715 50.000 0.00 0.00 0.00 4.18
2978 3338 2.167693 AGCCCGATTTTGACATAGACGA 59.832 45.455 0.00 0.00 0.00 4.20
2979 3339 2.284417 GCCCGATTTTGACATAGACGAC 59.716 50.000 0.00 0.00 0.00 4.34
2980 3340 3.517602 CCCGATTTTGACATAGACGACA 58.482 45.455 0.00 0.00 0.00 4.35
2981 3341 3.551890 CCCGATTTTGACATAGACGACAG 59.448 47.826 0.00 0.00 0.00 3.51
2982 3342 4.421058 CCGATTTTGACATAGACGACAGA 58.579 43.478 0.00 0.00 0.00 3.41
2983 3343 4.265556 CCGATTTTGACATAGACGACAGAC 59.734 45.833 0.00 0.00 0.00 3.51
2995 3355 0.778815 CGACAGACGTCTCAAACAGC 59.221 55.000 16.96 0.00 40.23 4.40
2996 3356 1.140816 GACAGACGTCTCAAACAGCC 58.859 55.000 16.96 0.00 39.22 4.85
2997 3357 0.597637 ACAGACGTCTCAAACAGCCG 60.598 55.000 16.96 3.49 0.00 5.52
2998 3358 1.006102 AGACGTCTCAAACAGCCGG 60.006 57.895 13.58 0.00 0.00 6.13
2999 3359 2.027625 GACGTCTCAAACAGCCGGG 61.028 63.158 8.70 0.00 0.00 5.73
3000 3360 3.423154 CGTCTCAAACAGCCGGGC 61.423 66.667 12.11 12.11 0.00 6.13
3001 3361 2.032681 GTCTCAAACAGCCGGGCT 59.967 61.111 17.69 17.69 40.77 5.19
3014 3374 2.997897 GGGCTGACCGACACCTCT 60.998 66.667 0.00 0.00 36.48 3.69
3015 3375 2.584391 GGGCTGACCGACACCTCTT 61.584 63.158 0.00 0.00 36.48 2.85
3016 3376 1.374758 GGCTGACCGACACCTCTTG 60.375 63.158 0.00 0.00 0.00 3.02
3017 3377 1.367840 GCTGACCGACACCTCTTGT 59.632 57.895 0.00 0.00 43.10 3.16
3018 3378 0.601558 GCTGACCGACACCTCTTGTA 59.398 55.000 0.00 0.00 39.17 2.41
3019 3379 1.204941 GCTGACCGACACCTCTTGTAT 59.795 52.381 0.00 0.00 39.17 2.29
3020 3380 2.353803 GCTGACCGACACCTCTTGTATT 60.354 50.000 0.00 0.00 39.17 1.89
3021 3381 3.254060 CTGACCGACACCTCTTGTATTG 58.746 50.000 0.00 0.00 39.17 1.90
3022 3382 2.631062 TGACCGACACCTCTTGTATTGT 59.369 45.455 0.00 0.00 39.17 2.71
3023 3383 2.993899 GACCGACACCTCTTGTATTGTG 59.006 50.000 0.00 0.00 39.17 3.33
3024 3384 1.732259 CCGACACCTCTTGTATTGTGC 59.268 52.381 0.00 0.00 39.17 4.57
3025 3385 1.390123 CGACACCTCTTGTATTGTGCG 59.610 52.381 0.00 0.00 39.17 5.34
3026 3386 1.128692 GACACCTCTTGTATTGTGCGC 59.871 52.381 0.00 0.00 39.17 6.09
3027 3387 0.095245 CACCTCTTGTATTGTGCGCG 59.905 55.000 0.00 0.00 0.00 6.86
3028 3388 0.037697 ACCTCTTGTATTGTGCGCGA 60.038 50.000 12.10 0.00 0.00 5.87
3029 3389 0.370273 CCTCTTGTATTGTGCGCGAC 59.630 55.000 12.10 5.96 0.00 5.19
3030 3390 1.350193 CTCTTGTATTGTGCGCGACT 58.650 50.000 12.10 0.00 0.00 4.18
3031 3391 1.059692 CTCTTGTATTGTGCGCGACTG 59.940 52.381 12.10 0.00 0.00 3.51
3032 3392 0.519175 CTTGTATTGTGCGCGACTGC 60.519 55.000 12.10 0.00 37.91 4.40
3033 3393 1.906994 TTGTATTGTGCGCGACTGCC 61.907 55.000 12.10 0.00 38.08 4.85
3034 3394 2.047750 TATTGTGCGCGACTGCCA 60.048 55.556 12.10 0.00 38.08 4.92
3035 3395 2.387445 TATTGTGCGCGACTGCCAC 61.387 57.895 12.10 8.80 40.51 5.01
3037 3397 4.986645 TGTGCGCGACTGCCACAT 62.987 61.111 12.10 0.00 43.01 3.21
3038 3398 4.152625 GTGCGCGACTGCCACATC 62.153 66.667 12.10 0.00 40.12 3.06
3041 3401 4.794439 CGCGACTGCCACATCGGA 62.794 66.667 0.00 0.00 38.78 4.55
3042 3402 2.202932 GCGACTGCCACATCGGAT 60.203 61.111 0.00 0.00 38.78 4.18
3043 3403 2.240500 GCGACTGCCACATCGGATC 61.241 63.158 0.00 0.00 38.78 3.36
3044 3404 1.592669 CGACTGCCACATCGGATCC 60.593 63.158 0.00 0.00 36.56 3.36
3045 3405 1.592669 GACTGCCACATCGGATCCG 60.593 63.158 28.62 28.62 36.56 4.18
3054 3414 2.196776 TCGGATCCGACCCTACCC 59.803 66.667 32.59 0.00 44.01 3.69
3055 3415 2.123597 CGGATCCGACCCTACCCA 60.124 66.667 30.62 0.00 42.83 4.51
3056 3416 1.759299 CGGATCCGACCCTACCCAA 60.759 63.158 30.62 0.00 42.83 4.12
3057 3417 1.332144 CGGATCCGACCCTACCCAAA 61.332 60.000 30.62 0.00 42.83 3.28
3058 3418 1.137697 GGATCCGACCCTACCCAAAT 58.862 55.000 0.00 0.00 0.00 2.32
3059 3419 2.332117 GGATCCGACCCTACCCAAATA 58.668 52.381 0.00 0.00 0.00 1.40
3060 3420 2.910977 GGATCCGACCCTACCCAAATAT 59.089 50.000 0.00 0.00 0.00 1.28
3061 3421 4.098894 GGATCCGACCCTACCCAAATATA 58.901 47.826 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.581289 TTGATTTGGATGTTCCCGTAAATATAT 57.419 29.630 0.00 0.00 35.03 0.86
19 20 8.982091 TTGATTTGGATGTTCCCGTAAATATA 57.018 30.769 0.00 0.00 35.03 0.86
20 21 7.889873 TTGATTTGGATGTTCCCGTAAATAT 57.110 32.000 0.00 0.00 35.03 1.28
21 22 7.612244 TCTTTGATTTGGATGTTCCCGTAAATA 59.388 33.333 0.00 0.00 35.03 1.40
22 23 6.435904 TCTTTGATTTGGATGTTCCCGTAAAT 59.564 34.615 0.00 0.00 35.03 1.40
23 24 5.770663 TCTTTGATTTGGATGTTCCCGTAAA 59.229 36.000 0.00 0.00 35.03 2.01
24 25 5.317808 TCTTTGATTTGGATGTTCCCGTAA 58.682 37.500 0.00 0.00 35.03 3.18
25 26 4.912586 TCTTTGATTTGGATGTTCCCGTA 58.087 39.130 0.00 0.00 35.03 4.02
26 27 3.761897 TCTTTGATTTGGATGTTCCCGT 58.238 40.909 0.00 0.00 35.03 5.28
130 131 4.952460 AGCAAAGGTTTCTACAAGTACGA 58.048 39.130 0.00 0.00 0.00 3.43
162 177 0.392461 GATTGTAGGTGGCAAGCGGA 60.392 55.000 0.00 0.00 0.00 5.54
236 253 2.490903 GCTCGGGTCAGTCAGTTAGTTA 59.509 50.000 0.00 0.00 0.00 2.24
240 257 1.174783 GAGCTCGGGTCAGTCAGTTA 58.825 55.000 0.00 0.00 0.00 2.24
241 268 1.536943 GGAGCTCGGGTCAGTCAGTT 61.537 60.000 7.83 0.00 0.00 3.16
248 275 2.314215 TAGGGAGGAGCTCGGGTCA 61.314 63.158 7.83 0.00 0.00 4.02
265 301 4.081752 TGGAAGTAAAATAAGGACGCCGTA 60.082 41.667 0.00 0.00 0.00 4.02
296 332 0.804364 TTTGCTGTGGCTGCGAATAG 59.196 50.000 0.00 0.00 39.59 1.73
311 348 0.874175 GGTTTTGCTCCGGTGTTTGC 60.874 55.000 0.00 0.12 0.00 3.68
465 517 1.571215 AATTTCCGTCGAACGTGCCC 61.571 55.000 0.00 0.00 40.58 5.36
576 628 2.685388 TGCACACAGAGCTAGCTAGTAG 59.315 50.000 19.38 15.14 0.00 2.57
578 630 1.550327 TGCACACAGAGCTAGCTAGT 58.450 50.000 19.38 16.60 0.00 2.57
919 988 3.415087 GGGATGTGCTCTGGGGCT 61.415 66.667 0.00 0.00 0.00 5.19
922 991 2.273449 GTGGGGATGTGCTCTGGG 59.727 66.667 0.00 0.00 0.00 4.45
926 1000 4.408821 TGCGGTGGGGATGTGCTC 62.409 66.667 0.00 0.00 0.00 4.26
1264 1345 4.501071 GCATCAAAGATGCACCAAGAAAT 58.499 39.130 22.96 0.00 44.00 2.17
1288 1369 1.302993 GTAAGCACCGGCAGGGAAA 60.303 57.895 8.08 0.00 44.61 3.13
1289 1370 2.349755 GTAAGCACCGGCAGGGAA 59.650 61.111 8.08 0.00 44.61 3.97
1666 1747 1.066430 GTAATGCGTGACAGAAGGGGA 60.066 52.381 0.00 0.00 0.00 4.81
1702 2038 4.142249 TGTCAACTCTCTTGAACAGTTCGA 60.142 41.667 8.80 5.93 0.00 3.71
1716 2052 3.967886 CACCGTCAGTGTCAACTCT 57.032 52.632 0.00 0.00 41.93 3.24
1993 2332 1.375523 GGACGGCGTTGTTGGAGAT 60.376 57.895 16.19 0.00 0.00 2.75
2064 2406 1.228063 GCGGATGGATGATGCAGGT 60.228 57.895 0.00 0.00 0.00 4.00
2067 2409 2.281002 CGGCGGATGGATGATGCA 60.281 61.111 0.00 0.00 0.00 3.96
2122 2464 1.035932 ATCGGGAGGTTGACGACGAT 61.036 55.000 0.00 0.00 39.64 3.73
2204 2546 1.067821 GCTACGACTTCAGATCCCCAG 59.932 57.143 0.00 0.00 0.00 4.45
2212 2554 3.851976 AACTACCTGCTACGACTTCAG 57.148 47.619 0.00 0.00 0.00 3.02
2213 2555 3.693085 CCTAACTACCTGCTACGACTTCA 59.307 47.826 0.00 0.00 0.00 3.02
2218 2560 1.064166 AGGCCTAACTACCTGCTACGA 60.064 52.381 1.29 0.00 34.07 3.43
2219 2561 1.400737 AGGCCTAACTACCTGCTACG 58.599 55.000 1.29 0.00 34.07 3.51
2276 2618 1.633774 CTACCACTCACTCACCCACT 58.366 55.000 0.00 0.00 0.00 4.00
2280 2622 3.851098 CTTTAGCTACCACTCACTCACC 58.149 50.000 0.00 0.00 0.00 4.02
2298 2640 4.321230 CCTCGTTCAAATGCTTTAGGCTTT 60.321 41.667 0.00 0.00 42.39 3.51
2535 2884 4.638304 ACAGAGTAAAATTGCAGTACGGT 58.362 39.130 0.00 0.00 0.00 4.83
2538 2887 7.861630 TCTTCAACAGAGTAAAATTGCAGTAC 58.138 34.615 0.00 0.00 0.00 2.73
2557 2916 7.434492 GGCAAGCACTAGTATACTATCTTCAA 58.566 38.462 12.98 0.00 0.00 2.69
2564 2923 3.918566 TGGGGCAAGCACTAGTATACTA 58.081 45.455 12.05 12.05 0.00 1.82
2567 2926 3.587498 AGATGGGGCAAGCACTAGTATA 58.413 45.455 0.00 0.00 0.00 1.47
2568 2927 2.412591 AGATGGGGCAAGCACTAGTAT 58.587 47.619 0.00 0.00 0.00 2.12
2569 2928 1.879575 AGATGGGGCAAGCACTAGTA 58.120 50.000 0.00 0.00 0.00 1.82
2570 2929 0.995024 AAGATGGGGCAAGCACTAGT 59.005 50.000 0.00 0.00 0.00 2.57
2581 2940 3.524541 GCAGTAAAATTGCAAGATGGGG 58.475 45.455 4.94 0.00 41.17 4.96
2603 2962 0.601046 TGCGAGTTGAAGACAGCAGG 60.601 55.000 0.00 0.00 38.59 4.85
2634 2993 5.957842 AAGTTATCTGCATCCGTTTGAAA 57.042 34.783 0.00 0.00 0.00 2.69
2645 3005 4.265904 TCGACCAGAAAAGTTATCTGCA 57.734 40.909 0.00 0.00 42.36 4.41
2687 3047 3.551046 CCGACGATCAAGAACTATGGGAG 60.551 52.174 0.00 0.00 0.00 4.30
2688 3048 2.361119 CCGACGATCAAGAACTATGGGA 59.639 50.000 0.00 0.00 0.00 4.37
2689 3049 2.100916 ACCGACGATCAAGAACTATGGG 59.899 50.000 0.00 0.00 0.00 4.00
2690 3050 3.116300 CACCGACGATCAAGAACTATGG 58.884 50.000 0.00 0.00 0.00 2.74
2691 3051 2.535984 GCACCGACGATCAAGAACTATG 59.464 50.000 0.00 0.00 0.00 2.23
2692 3052 2.794981 CGCACCGACGATCAAGAACTAT 60.795 50.000 0.00 0.00 34.06 2.12
2693 3053 1.466866 CGCACCGACGATCAAGAACTA 60.467 52.381 0.00 0.00 34.06 2.24
2694 3054 0.732880 CGCACCGACGATCAAGAACT 60.733 55.000 0.00 0.00 34.06 3.01
2695 3055 0.731514 TCGCACCGACGATCAAGAAC 60.732 55.000 0.00 0.00 37.09 3.01
2702 3062 4.175489 CGACCTCGCACCGACGAT 62.175 66.667 0.00 0.00 42.02 3.73
2717 3077 7.495606 AGTGATGTTTTATGTATTGATGCTCGA 59.504 33.333 0.00 0.00 0.00 4.04
2725 3085 7.072177 ACGGACAGTGATGTTTTATGTATTG 57.928 36.000 0.00 0.00 0.00 1.90
2727 3087 6.093495 CCAACGGACAGTGATGTTTTATGTAT 59.907 38.462 0.00 0.00 0.00 2.29
2728 3088 5.410132 CCAACGGACAGTGATGTTTTATGTA 59.590 40.000 0.00 0.00 0.00 2.29
2733 3093 2.616842 GACCAACGGACAGTGATGTTTT 59.383 45.455 0.00 0.00 0.00 2.43
2744 3104 2.074547 TGATTCTTCGACCAACGGAC 57.925 50.000 0.00 0.00 42.82 4.79
2802 3162 9.411189 CCTTCTTACTGATAACTACTTACTCCT 57.589 37.037 0.00 0.00 0.00 3.69
2805 3165 7.069702 GGGCCTTCTTACTGATAACTACTTACT 59.930 40.741 0.84 0.00 0.00 2.24
2806 3166 7.208777 GGGCCTTCTTACTGATAACTACTTAC 58.791 42.308 0.84 0.00 0.00 2.34
2819 3179 2.722201 CCTCGCGGGCCTTCTTACT 61.722 63.158 6.13 0.00 0.00 2.24
2820 3180 2.202892 CCTCGCGGGCCTTCTTAC 60.203 66.667 6.13 0.00 0.00 2.34
2821 3181 2.363276 TCCTCGCGGGCCTTCTTA 60.363 61.111 6.13 0.00 34.39 2.10
2822 3182 3.775654 CTCCTCGCGGGCCTTCTT 61.776 66.667 6.13 0.00 34.39 2.52
2824 3184 4.083862 AACTCCTCGCGGGCCTTC 62.084 66.667 6.13 0.00 34.39 3.46
2825 3185 4.083862 GAACTCCTCGCGGGCCTT 62.084 66.667 6.13 0.95 34.39 4.35
2827 3187 4.516195 GAGAACTCCTCGCGGGCC 62.516 72.222 6.13 0.00 34.39 5.80
2828 3188 4.516195 GGAGAACTCCTCGCGGGC 62.516 72.222 6.13 0.00 46.16 6.13
2837 3197 3.454375 TCGTTTTGTGTCTGGAGAACTC 58.546 45.455 0.00 0.00 0.00 3.01
2838 3198 3.132289 TCTCGTTTTGTGTCTGGAGAACT 59.868 43.478 0.00 0.00 0.00 3.01
2839 3199 3.454375 TCTCGTTTTGTGTCTGGAGAAC 58.546 45.455 0.00 0.00 0.00 3.01
2840 3200 3.812156 TCTCGTTTTGTGTCTGGAGAA 57.188 42.857 0.00 0.00 0.00 2.87
2841 3201 3.132289 ACTTCTCGTTTTGTGTCTGGAGA 59.868 43.478 0.00 0.00 0.00 3.71
2842 3202 3.246226 CACTTCTCGTTTTGTGTCTGGAG 59.754 47.826 0.00 0.00 0.00 3.86
2843 3203 3.118920 TCACTTCTCGTTTTGTGTCTGGA 60.119 43.478 0.00 0.00 0.00 3.86
2844 3204 3.194861 TCACTTCTCGTTTTGTGTCTGG 58.805 45.455 0.00 0.00 0.00 3.86
2845 3205 3.246226 CCTCACTTCTCGTTTTGTGTCTG 59.754 47.826 0.00 0.00 0.00 3.51
2846 3206 3.458189 CCTCACTTCTCGTTTTGTGTCT 58.542 45.455 0.00 0.00 0.00 3.41
2847 3207 2.032808 GCCTCACTTCTCGTTTTGTGTC 60.033 50.000 0.00 0.00 0.00 3.67
2848 3208 1.940613 GCCTCACTTCTCGTTTTGTGT 59.059 47.619 0.00 0.00 0.00 3.72
2849 3209 2.213499 AGCCTCACTTCTCGTTTTGTG 58.787 47.619 0.00 0.00 0.00 3.33
2850 3210 2.622064 AGCCTCACTTCTCGTTTTGT 57.378 45.000 0.00 0.00 0.00 2.83
2864 3224 2.496899 TTGTTCATGAGGGAAGCCTC 57.503 50.000 0.00 0.00 37.35 4.70
2865 3225 2.309755 TGATTGTTCATGAGGGAAGCCT 59.690 45.455 0.00 0.00 0.00 4.58
2866 3226 2.726821 TGATTGTTCATGAGGGAAGCC 58.273 47.619 0.00 0.00 0.00 4.35
2867 3227 3.507233 TGTTGATTGTTCATGAGGGAAGC 59.493 43.478 0.00 0.00 0.00 3.86
2868 3228 5.909621 ATGTTGATTGTTCATGAGGGAAG 57.090 39.130 0.00 0.00 0.00 3.46
2869 3229 7.174413 TCTTATGTTGATTGTTCATGAGGGAA 58.826 34.615 0.00 0.00 0.00 3.97
2870 3230 6.720309 TCTTATGTTGATTGTTCATGAGGGA 58.280 36.000 0.00 0.00 0.00 4.20
2871 3231 6.459298 GCTCTTATGTTGATTGTTCATGAGGG 60.459 42.308 0.00 0.00 31.65 4.30
2872 3232 6.094464 TGCTCTTATGTTGATTGTTCATGAGG 59.906 38.462 0.00 0.00 0.00 3.86
2873 3233 7.080353 TGCTCTTATGTTGATTGTTCATGAG 57.920 36.000 0.00 0.00 0.00 2.90
2874 3234 7.555195 AGATGCTCTTATGTTGATTGTTCATGA 59.445 33.333 0.00 0.00 0.00 3.07
2875 3235 7.704271 AGATGCTCTTATGTTGATTGTTCATG 58.296 34.615 0.00 0.00 0.00 3.07
2876 3236 7.876936 AGATGCTCTTATGTTGATTGTTCAT 57.123 32.000 0.00 0.00 0.00 2.57
2877 3237 7.280876 GGTAGATGCTCTTATGTTGATTGTTCA 59.719 37.037 0.00 0.00 0.00 3.18
2878 3238 7.497249 AGGTAGATGCTCTTATGTTGATTGTTC 59.503 37.037 0.00 0.00 0.00 3.18
2879 3239 7.341805 AGGTAGATGCTCTTATGTTGATTGTT 58.658 34.615 0.00 0.00 0.00 2.83
2880 3240 6.893583 AGGTAGATGCTCTTATGTTGATTGT 58.106 36.000 0.00 0.00 0.00 2.71
2881 3241 6.988580 TGAGGTAGATGCTCTTATGTTGATTG 59.011 38.462 0.00 0.00 0.00 2.67
2882 3242 7.129457 TGAGGTAGATGCTCTTATGTTGATT 57.871 36.000 0.00 0.00 0.00 2.57
2883 3243 6.737720 TGAGGTAGATGCTCTTATGTTGAT 57.262 37.500 0.00 0.00 0.00 2.57
2884 3244 6.544928 TTGAGGTAGATGCTCTTATGTTGA 57.455 37.500 0.00 0.00 0.00 3.18
2885 3245 6.237942 CGTTTGAGGTAGATGCTCTTATGTTG 60.238 42.308 0.00 0.00 0.00 3.33
2886 3246 5.812642 CGTTTGAGGTAGATGCTCTTATGTT 59.187 40.000 0.00 0.00 0.00 2.71
2887 3247 5.352284 CGTTTGAGGTAGATGCTCTTATGT 58.648 41.667 0.00 0.00 0.00 2.29
2888 3248 4.210120 GCGTTTGAGGTAGATGCTCTTATG 59.790 45.833 0.00 0.00 0.00 1.90
2889 3249 4.372656 GCGTTTGAGGTAGATGCTCTTAT 58.627 43.478 0.00 0.00 0.00 1.73
2890 3250 3.430374 GGCGTTTGAGGTAGATGCTCTTA 60.430 47.826 0.00 0.00 0.00 2.10
2891 3251 2.622436 GCGTTTGAGGTAGATGCTCTT 58.378 47.619 0.00 0.00 0.00 2.85
2892 3252 1.134670 GGCGTTTGAGGTAGATGCTCT 60.135 52.381 0.00 0.00 0.00 4.09
2893 3253 1.291132 GGCGTTTGAGGTAGATGCTC 58.709 55.000 0.00 0.00 0.00 4.26
2894 3254 0.107654 GGGCGTTTGAGGTAGATGCT 60.108 55.000 0.00 0.00 0.00 3.79
2895 3255 0.107654 AGGGCGTTTGAGGTAGATGC 60.108 55.000 0.00 0.00 0.00 3.91
2896 3256 1.066143 ACAGGGCGTTTGAGGTAGATG 60.066 52.381 0.00 0.00 0.00 2.90
2897 3257 1.207329 GACAGGGCGTTTGAGGTAGAT 59.793 52.381 0.00 0.00 0.00 1.98
2898 3258 0.606604 GACAGGGCGTTTGAGGTAGA 59.393 55.000 0.00 0.00 0.00 2.59
2899 3259 0.320374 TGACAGGGCGTTTGAGGTAG 59.680 55.000 0.00 0.00 0.00 3.18
2900 3260 0.981183 ATGACAGGGCGTTTGAGGTA 59.019 50.000 0.00 0.00 0.00 3.08
2901 3261 0.606401 CATGACAGGGCGTTTGAGGT 60.606 55.000 0.00 0.00 0.00 3.85
2902 3262 0.321564 TCATGACAGGGCGTTTGAGG 60.322 55.000 0.00 0.00 0.00 3.86
2903 3263 1.522668 TTCATGACAGGGCGTTTGAG 58.477 50.000 0.00 0.00 0.00 3.02
2904 3264 1.974265 TTTCATGACAGGGCGTTTGA 58.026 45.000 0.00 0.00 0.00 2.69
2905 3265 3.302365 AATTTCATGACAGGGCGTTTG 57.698 42.857 0.00 0.00 0.00 2.93
2906 3266 4.057432 CAAAATTTCATGACAGGGCGTTT 58.943 39.130 0.00 0.00 0.00 3.60
2907 3267 3.320541 TCAAAATTTCATGACAGGGCGTT 59.679 39.130 0.00 0.00 0.00 4.84
2908 3268 2.890311 TCAAAATTTCATGACAGGGCGT 59.110 40.909 0.00 0.00 0.00 5.68
2909 3269 3.244976 GTCAAAATTTCATGACAGGGCG 58.755 45.455 15.15 0.00 44.19 6.13
2915 3275 7.689812 CGTCTGTCTATGTCAAAATTTCATGAC 59.310 37.037 13.74 13.74 44.84 3.06
2916 3276 7.602265 TCGTCTGTCTATGTCAAAATTTCATGA 59.398 33.333 0.00 0.00 0.00 3.07
2917 3277 7.689812 GTCGTCTGTCTATGTCAAAATTTCATG 59.310 37.037 0.00 0.00 0.00 3.07
2918 3278 7.387673 TGTCGTCTGTCTATGTCAAAATTTCAT 59.612 33.333 0.00 0.00 0.00 2.57
2919 3279 6.704050 TGTCGTCTGTCTATGTCAAAATTTCA 59.296 34.615 0.00 0.00 0.00 2.69
2920 3280 7.116376 TCTGTCGTCTGTCTATGTCAAAATTTC 59.884 37.037 0.00 0.00 0.00 2.17
2921 3281 6.929049 TCTGTCGTCTGTCTATGTCAAAATTT 59.071 34.615 0.00 0.00 0.00 1.82
2922 3282 6.366332 GTCTGTCGTCTGTCTATGTCAAAATT 59.634 38.462 0.00 0.00 0.00 1.82
2923 3283 5.864474 GTCTGTCGTCTGTCTATGTCAAAAT 59.136 40.000 0.00 0.00 0.00 1.82
2924 3284 5.220381 GTCTGTCGTCTGTCTATGTCAAAA 58.780 41.667 0.00 0.00 0.00 2.44
2925 3285 4.612939 CGTCTGTCGTCTGTCTATGTCAAA 60.613 45.833 0.00 0.00 34.52 2.69
2926 3286 3.120304 CGTCTGTCGTCTGTCTATGTCAA 60.120 47.826 0.00 0.00 34.52 3.18
2927 3287 2.415512 CGTCTGTCGTCTGTCTATGTCA 59.584 50.000 0.00 0.00 34.52 3.58
2928 3288 3.040990 CGTCTGTCGTCTGTCTATGTC 57.959 52.381 0.00 0.00 34.52 3.06
2941 3301 1.140816 GGCTGTTTGAGACGTCTGTC 58.859 55.000 25.58 10.58 45.86 3.51
2942 3302 0.249911 GGGCTGTTTGAGACGTCTGT 60.250 55.000 25.58 0.00 0.00 3.41
2943 3303 1.284982 CGGGCTGTTTGAGACGTCTG 61.285 60.000 25.58 8.49 0.00 3.51
2944 3304 1.006102 CGGGCTGTTTGAGACGTCT 60.006 57.895 20.18 20.18 0.00 4.18
2945 3305 0.389948 ATCGGGCTGTTTGAGACGTC 60.390 55.000 7.70 7.70 0.00 4.34
2946 3306 0.034896 AATCGGGCTGTTTGAGACGT 59.965 50.000 0.00 0.00 0.00 4.34
2947 3307 1.156736 AAATCGGGCTGTTTGAGACG 58.843 50.000 0.00 0.00 0.00 4.18
2948 3308 2.552315 TCAAAATCGGGCTGTTTGAGAC 59.448 45.455 7.74 0.00 36.58 3.36
2949 3309 2.552315 GTCAAAATCGGGCTGTTTGAGA 59.448 45.455 11.20 1.29 40.82 3.27
2950 3310 2.293122 TGTCAAAATCGGGCTGTTTGAG 59.707 45.455 11.20 0.00 40.82 3.02
2951 3311 2.302260 TGTCAAAATCGGGCTGTTTGA 58.698 42.857 7.74 7.74 38.57 2.69
2952 3312 2.791383 TGTCAAAATCGGGCTGTTTG 57.209 45.000 3.64 3.64 34.29 2.93
2953 3313 4.156008 GTCTATGTCAAAATCGGGCTGTTT 59.844 41.667 0.00 0.00 0.00 2.83
2954 3314 3.689649 GTCTATGTCAAAATCGGGCTGTT 59.310 43.478 0.00 0.00 0.00 3.16
2955 3315 3.270877 GTCTATGTCAAAATCGGGCTGT 58.729 45.455 0.00 0.00 0.00 4.40
2956 3316 2.285220 CGTCTATGTCAAAATCGGGCTG 59.715 50.000 0.00 0.00 0.00 4.85
2957 3317 2.167693 TCGTCTATGTCAAAATCGGGCT 59.832 45.455 0.00 0.00 0.00 5.19
2958 3318 2.284417 GTCGTCTATGTCAAAATCGGGC 59.716 50.000 0.00 0.00 0.00 6.13
2959 3319 3.517602 TGTCGTCTATGTCAAAATCGGG 58.482 45.455 0.00 0.00 0.00 5.14
2960 3320 4.265556 GTCTGTCGTCTATGTCAAAATCGG 59.734 45.833 0.00 0.00 0.00 4.18
2961 3321 4.028429 CGTCTGTCGTCTATGTCAAAATCG 60.028 45.833 0.00 0.00 34.52 3.34
2962 3322 5.362987 CGTCTGTCGTCTATGTCAAAATC 57.637 43.478 0.00 0.00 34.52 2.17
2977 3337 1.140816 GGCTGTTTGAGACGTCTGTC 58.859 55.000 25.58 10.58 45.86 3.51
2978 3338 3.290776 GGCTGTTTGAGACGTCTGT 57.709 52.632 25.58 0.00 0.00 3.41
2984 3344 2.032681 AGCCCGGCTGTTTGAGAC 59.967 61.111 12.38 0.00 37.57 3.36
2997 3357 2.584391 AAGAGGTGTCGGTCAGCCC 61.584 63.158 0.95 0.00 44.62 5.19
2998 3358 1.374758 CAAGAGGTGTCGGTCAGCC 60.375 63.158 0.95 0.00 44.62 4.85
2999 3359 0.601558 TACAAGAGGTGTCGGTCAGC 59.398 55.000 0.00 0.00 41.98 4.26
3000 3360 3.254060 CAATACAAGAGGTGTCGGTCAG 58.746 50.000 0.00 0.00 41.98 3.51
3001 3361 2.631062 ACAATACAAGAGGTGTCGGTCA 59.369 45.455 0.00 0.00 41.98 4.02
3002 3362 2.993899 CACAATACAAGAGGTGTCGGTC 59.006 50.000 0.00 0.00 41.98 4.79
3003 3363 2.870435 GCACAATACAAGAGGTGTCGGT 60.870 50.000 0.00 0.00 41.98 4.69
3004 3364 1.732259 GCACAATACAAGAGGTGTCGG 59.268 52.381 0.00 0.00 41.98 4.79
3005 3365 1.390123 CGCACAATACAAGAGGTGTCG 59.610 52.381 0.00 0.00 41.98 4.35
3006 3366 1.128692 GCGCACAATACAAGAGGTGTC 59.871 52.381 0.30 0.00 41.98 3.67
3007 3367 1.156736 GCGCACAATACAAGAGGTGT 58.843 50.000 0.30 0.00 44.82 4.16
3008 3368 0.095245 CGCGCACAATACAAGAGGTG 59.905 55.000 8.75 0.00 0.00 4.00
3009 3369 0.037697 TCGCGCACAATACAAGAGGT 60.038 50.000 8.75 0.00 0.00 3.85
3010 3370 0.370273 GTCGCGCACAATACAAGAGG 59.630 55.000 8.75 0.00 0.00 3.69
3011 3371 1.059692 CAGTCGCGCACAATACAAGAG 59.940 52.381 8.75 0.00 0.00 2.85
3012 3372 1.067693 CAGTCGCGCACAATACAAGA 58.932 50.000 8.75 0.00 0.00 3.02
3013 3373 0.519175 GCAGTCGCGCACAATACAAG 60.519 55.000 8.75 0.00 0.00 3.16
3014 3374 1.495509 GCAGTCGCGCACAATACAA 59.504 52.632 8.75 0.00 0.00 2.41
3015 3375 2.387445 GGCAGTCGCGCACAATACA 61.387 57.895 8.75 0.00 39.92 2.29
3016 3376 2.387445 TGGCAGTCGCGCACAATAC 61.387 57.895 8.75 0.00 39.92 1.89
3017 3377 2.047750 TGGCAGTCGCGCACAATA 60.048 55.556 8.75 0.00 39.92 1.90
3018 3378 3.726517 GTGGCAGTCGCGCACAAT 61.727 61.111 8.75 0.00 38.46 2.71
3020 3380 4.986645 ATGTGGCAGTCGCGCACA 62.987 61.111 16.79 16.79 46.37 4.57
3021 3381 4.152625 GATGTGGCAGTCGCGCAC 62.153 66.667 8.75 3.70 39.92 5.34
3024 3384 4.794439 TCCGATGTGGCAGTCGCG 62.794 66.667 14.69 0.00 39.92 5.87
3025 3385 2.202932 ATCCGATGTGGCAGTCGC 60.203 61.111 14.69 0.00 37.80 5.19
3026 3386 1.592669 GGATCCGATGTGGCAGTCG 60.593 63.158 13.53 13.53 37.80 4.18
3027 3387 1.592669 CGGATCCGATGTGGCAGTC 60.593 63.158 30.62 0.00 42.83 3.51
3028 3388 2.058001 TCGGATCCGATGTGGCAGT 61.058 57.895 32.59 0.00 44.01 4.40
3029 3389 2.814604 TCGGATCCGATGTGGCAG 59.185 61.111 32.59 1.58 44.01 4.85
3037 3397 2.196776 GGGTAGGGTCGGATCCGA 59.803 66.667 32.59 32.59 46.87 4.55
3038 3398 1.332144 TTTGGGTAGGGTCGGATCCG 61.332 60.000 28.62 28.62 41.35 4.18
3039 3399 1.137697 ATTTGGGTAGGGTCGGATCC 58.862 55.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.