Multiple sequence alignment - TraesCS2D01G404400

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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 TraesCS2D01G404400 chr2D 100.000 4932 0 0 1 4932 518806041 518810972 0.000000e+00 9108.0
1 TraesCS2D01G404400 chr2D 92.216 167 11 2 2760 2926 318563734 318563898 8.250000e-58 235.0
2 TraesCS2D01G404400 chr2D 91.018 167 12 3 2767 2932 498473151 498472987 6.430000e-54 222.0
3 TraesCS2D01G404400 chr2D 91.453 117 10 0 4302 4418 95519548 95519664 1.420000e-35 161.0
4 TraesCS2D01G404400 chr2A 96.563 2764 78 10 3 2758 662965261 662968015 0.000000e+00 4562.0
5 TraesCS2D01G404400 chr2A 92.649 1374 40 10 2928 4298 662968129 662969444 0.000000e+00 1921.0
6 TraesCS2D01G404400 chr2A 87.108 574 39 18 4386 4932 662969565 662970130 7.010000e-173 617.0
7 TraesCS2D01G404400 chr2B 97.432 1830 37 5 938 2758 611063076 611064904 0.000000e+00 3110.0
8 TraesCS2D01G404400 chr2B 95.266 1204 50 5 3096 4296 611065055 611066254 0.000000e+00 1901.0
9 TraesCS2D01G404400 chr2B 95.155 743 31 1 3 745 611062025 611062762 0.000000e+00 1168.0
10 TraesCS2D01G404400 chr2B 89.838 679 56 8 2073 2749 612073306 612072639 0.000000e+00 859.0
11 TraesCS2D01G404400 chr2B 89.838 679 56 8 2073 2749 612079622 612078955 0.000000e+00 859.0
12 TraesCS2D01G404400 chr2B 88.268 537 51 6 3195 3722 612072335 612071802 2.500000e-177 632.0
13 TraesCS2D01G404400 chr2B 88.268 537 51 6 3195 3722 612078651 612078118 2.500000e-177 632.0
14 TraesCS2D01G404400 chr2B 88.866 494 41 10 4440 4929 611066307 611066790 3.290000e-166 595.0
15 TraesCS2D01G404400 chr2B 90.311 289 15 7 3789 4073 612071778 612071499 2.810000e-97 366.0
16 TraesCS2D01G404400 chr2B 90.311 289 15 7 3789 4073 612078094 612077815 2.810000e-97 366.0
17 TraesCS2D01G404400 chr2B 90.404 198 14 1 1845 2037 612073498 612073301 6.340000e-64 255.0
18 TraesCS2D01G404400 chr2B 90.404 198 14 1 1845 2037 612079814 612079617 6.340000e-64 255.0
19 TraesCS2D01G404400 chr2B 93.038 158 10 1 741 897 611062820 611062977 3.840000e-56 230.0
20 TraesCS2D01G404400 chr2B 89.655 174 15 3 2760 2932 585712655 585712484 8.310000e-53 219.0
21 TraesCS2D01G404400 chr2B 88.235 170 17 3 3097 3264 612072504 612072336 3.010000e-47 200.0
22 TraesCS2D01G404400 chr2B 88.235 170 17 3 3097 3264 612078820 612078652 3.010000e-47 200.0
23 TraesCS2D01G404400 chr2B 76.857 350 35 26 1019 1358 612080398 612080085 6.610000e-34 156.0
24 TraesCS2D01G404400 chr2B 77.492 311 32 21 1050 1358 612074043 612073769 8.550000e-33 152.0
25 TraesCS2D01G404400 chr2B 85.621 153 11 3 1573 1724 612073695 612073553 3.080000e-32 150.0
26 TraesCS2D01G404400 chr2B 85.621 153 11 3 1573 1724 612080011 612079869 3.080000e-32 150.0
27 TraesCS2D01G404400 chr2B 84.783 92 11 1 2933 3024 612072618 612072530 6.800000e-14 89.8
28 TraesCS2D01G404400 chr2B 84.783 92 11 1 2933 3024 612078934 612078846 6.800000e-14 89.8
29 TraesCS2D01G404400 chr2B 96.226 53 2 0 885 937 611062997 611063049 2.450000e-13 87.9
30 TraesCS2D01G404400 chr2B 75.172 145 25 7 4 142 612081119 612080980 1.920000e-04 58.4
31 TraesCS2D01G404400 chr7D 92.683 164 11 1 2760 2923 566026736 566026574 8.250000e-58 235.0
32 TraesCS2D01G404400 chr7D 91.463 164 13 1 2760 2923 183790423 183790261 1.790000e-54 224.0
33 TraesCS2D01G404400 chr7D 92.241 116 9 0 4302 4417 430095840 430095725 1.100000e-36 165.0
34 TraesCS2D01G404400 chr7A 91.018 167 13 2 2760 2926 652302331 652302167 1.790000e-54 224.0
35 TraesCS2D01G404400 chr3D 90.854 164 14 1 2760 2923 187836308 187836470 8.310000e-53 219.0
36 TraesCS2D01G404400 chr3D 92.105 114 9 0 4302 4415 378244629 378244516 1.420000e-35 161.0
37 TraesCS2D01G404400 chr3B 88.764 178 18 2 2760 2937 251650677 251650502 2.990000e-52 217.0
38 TraesCS2D01G404400 chr3B 92.105 114 7 2 4302 4414 543766665 543766777 5.110000e-35 159.0
39 TraesCS2D01G404400 chrUn 87.166 187 20 4 2747 2931 95767625 95767441 5.000000e-50 209.0
40 TraesCS2D01G404400 chr7B 95.413 109 5 0 4302 4410 513813820 513813928 1.820000e-39 174.0
41 TraesCS2D01G404400 chr4A 95.370 108 5 0 4302 4409 618561549 618561442 6.560000e-39 172.0
42 TraesCS2D01G404400 chr4A 92.105 114 9 0 4302 4415 714067123 714067236 1.420000e-35 161.0
43 TraesCS2D01G404400 chr4A 92.035 113 9 0 4302 4414 544199327 544199439 5.110000e-35 159.0
44 TraesCS2D01G404400 chr5B 92.593 108 8 0 4303 4410 124772398 124772505 6.610000e-34 156.0


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 TraesCS2D01G404400 chr2D 518806041 518810972 4931 False 9108.000000 9108 100.000000 1 4932 1 chr2D.!!$F3 4931
1 TraesCS2D01G404400 chr2A 662965261 662970130 4869 False 2366.666667 4562 92.106667 3 4932 3 chr2A.!!$F1 4929
2 TraesCS2D01G404400 chr2B 611062025 611066790 4765 False 1181.983333 3110 94.330500 3 4929 6 chr2B.!!$F1 4926
3 TraesCS2D01G404400 chr2B 612071499 612081119 9620 True 321.764706 859 86.143588 4 4073 17 chr2B.!!$R2 4069

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
392 439 1.339438 CCCTTCTCGGATGCATATGGG 60.339 57.143 0.00 0.66 33.16 4.00 F
1007 1232 0.986527 TCCACCTCACAGATGCACAT 59.013 50.000 0.00 0.00 0.00 3.21 F
1524 1791 1.003233 GCTCGCCAAGGAGTCCTTT 60.003 57.895 22.36 4.88 41.69 3.11 F
2673 2946 0.099791 ACAACTTTGAAACCACGCCG 59.900 50.000 0.00 0.00 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1786 1.221840 GGATGAGCGAGGCAAAGGA 59.778 57.895 0.0 0.0 0.0 3.36 R
2567 2840 0.977395 CAGAAAGAACTCCCCTCGGT 59.023 55.000 0.0 0.0 0.0 4.69 R
3184 3580 1.137872 GAGTCTGTGCCCCATCTAGTG 59.862 57.143 0.0 0.0 0.0 2.74 R
4392 4905 1.221021 GCTCCCTCCGTCCGAAAAT 59.779 57.895 0.0 0.0 0.0 1.82 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
57 58 2.192861 CAGTTTGCGCCCTCCAACA 61.193 57.895 4.18 0.00 0.00 3.33
332 379 1.781429 CTATATGTCGACAGTGCACGC 59.219 52.381 24.41 4.23 0.00 5.34
392 439 1.339438 CCCTTCTCGGATGCATATGGG 60.339 57.143 0.00 0.66 33.16 4.00
455 502 4.816925 GTCATAATGTTAAGGAGAGGCCAC 59.183 45.833 5.01 0.00 40.02 5.01
518 565 2.801063 CAGTTTGTGAAGTGCCACTTG 58.199 47.619 16.14 0.00 38.80 3.16
571 619 1.970640 GGCCTTGTTTTGGGATCAACT 59.029 47.619 0.00 0.00 31.78 3.16
578 626 3.772025 TGTTTTGGGATCAACTTGGTGTT 59.228 39.130 0.00 0.00 39.92 3.32
689 737 5.047802 GGATTGTTCCTTGAAGCATTCTGAA 60.048 40.000 0.00 0.00 41.68 3.02
691 739 9.134268 GGATTGTTCCTTGAAGCATTCTGAAGT 62.134 40.741 0.00 0.00 41.68 3.01
815 926 5.353394 TCAGAAACCTTGTACACTGTTCT 57.647 39.130 9.07 6.95 0.00 3.01
901 1044 7.126398 GTGAAGCTATTGTCAATTTCCGTATC 58.874 38.462 2.79 0.00 0.00 2.24
1007 1232 0.986527 TCCACCTCACAGATGCACAT 59.013 50.000 0.00 0.00 0.00 3.21
1320 1587 3.330853 GCCGCGGACGACATCATC 61.331 66.667 33.48 2.06 43.93 2.92
1524 1791 1.003233 GCTCGCCAAGGAGTCCTTT 60.003 57.895 22.36 4.88 41.69 3.11
1749 2017 6.405842 GCTTTAAAGTGATTGTATTGGAGGGG 60.406 42.308 16.38 0.00 0.00 4.79
2567 2840 5.624159 ACATCTGACTGAAAATCCAAGTCA 58.376 37.500 4.80 4.80 37.81 3.41
2673 2946 0.099791 ACAACTTTGAAACCACGCCG 59.900 50.000 0.00 0.00 0.00 6.46
2723 2996 4.956700 TCAGATACTGAGGGGTAAGACTTG 59.043 45.833 0.00 0.00 35.39 3.16
2765 3039 9.388346 TCATAAAGTTGCATTTTTGTTACTACG 57.612 29.630 6.28 0.00 0.00 3.51
2766 3040 9.176181 CATAAAGTTGCATTTTTGTTACTACGT 57.824 29.630 0.00 0.00 0.00 3.57
2767 3041 7.673810 AAAGTTGCATTTTTGTTACTACGTC 57.326 32.000 0.00 0.00 0.00 4.34
2768 3042 5.754778 AGTTGCATTTTTGTTACTACGTCC 58.245 37.500 0.00 0.00 0.00 4.79
2770 3044 3.808726 TGCATTTTTGTTACTACGTCCGT 59.191 39.130 0.00 0.00 0.00 4.69
2771 3045 4.272991 TGCATTTTTGTTACTACGTCCGTT 59.727 37.500 0.00 0.00 0.00 4.44
2772 3046 4.842376 GCATTTTTGTTACTACGTCCGTTC 59.158 41.667 0.00 0.00 0.00 3.95
2773 3047 5.376537 CATTTTTGTTACTACGTCCGTTCC 58.623 41.667 0.00 0.00 0.00 3.62
2774 3048 4.320608 TTTTGTTACTACGTCCGTTCCT 57.679 40.909 0.00 0.00 0.00 3.36
2775 3049 5.446143 TTTTGTTACTACGTCCGTTCCTA 57.554 39.130 0.00 0.00 0.00 2.94
2776 3050 5.446143 TTTGTTACTACGTCCGTTCCTAA 57.554 39.130 0.00 0.00 0.00 2.69
2777 3051 5.446143 TTGTTACTACGTCCGTTCCTAAA 57.554 39.130 0.00 0.00 0.00 1.85
2778 3052 5.643379 TGTTACTACGTCCGTTCCTAAAT 57.357 39.130 0.00 0.00 0.00 1.40
2779 3053 6.751514 TGTTACTACGTCCGTTCCTAAATA 57.248 37.500 0.00 0.00 0.00 1.40
2780 3054 7.333528 TGTTACTACGTCCGTTCCTAAATAT 57.666 36.000 0.00 0.00 0.00 1.28
2781 3055 8.445275 TGTTACTACGTCCGTTCCTAAATATA 57.555 34.615 0.00 0.00 0.00 0.86
2782 3056 8.898761 TGTTACTACGTCCGTTCCTAAATATAA 58.101 33.333 0.00 0.00 0.00 0.98
2783 3057 9.387123 GTTACTACGTCCGTTCCTAAATATAAG 57.613 37.037 0.00 0.00 0.00 1.73
2784 3058 7.573968 ACTACGTCCGTTCCTAAATATAAGT 57.426 36.000 0.00 0.00 0.00 2.24
2785 3059 7.643579 ACTACGTCCGTTCCTAAATATAAGTC 58.356 38.462 0.00 0.00 0.00 3.01
2786 3060 6.705863 ACGTCCGTTCCTAAATATAAGTCT 57.294 37.500 0.00 0.00 0.00 3.24
2787 3061 7.105241 ACGTCCGTTCCTAAATATAAGTCTT 57.895 36.000 0.00 0.00 0.00 3.01
2788 3062 7.550712 ACGTCCGTTCCTAAATATAAGTCTTT 58.449 34.615 0.00 0.00 0.00 2.52
2789 3063 8.037166 ACGTCCGTTCCTAAATATAAGTCTTTT 58.963 33.333 0.00 0.00 0.00 2.27
2790 3064 8.876790 CGTCCGTTCCTAAATATAAGTCTTTTT 58.123 33.333 0.00 0.00 0.00 1.94
2817 3091 9.221933 AGAGATTCTAATACAGACTACATACGG 57.778 37.037 0.00 0.00 31.12 4.02
2818 3092 9.217278 GAGATTCTAATACAGACTACATACGGA 57.783 37.037 0.00 0.00 31.12 4.69
2819 3093 9.221933 AGATTCTAATACAGACTACATACGGAG 57.778 37.037 0.00 0.00 31.12 4.63
2820 3094 6.798315 TCTAATACAGACTACATACGGAGC 57.202 41.667 0.00 0.00 0.00 4.70
2821 3095 6.293698 TCTAATACAGACTACATACGGAGCA 58.706 40.000 0.00 0.00 0.00 4.26
2822 3096 5.847111 AATACAGACTACATACGGAGCAA 57.153 39.130 0.00 0.00 0.00 3.91
2823 3097 5.847111 ATACAGACTACATACGGAGCAAA 57.153 39.130 0.00 0.00 0.00 3.68
2824 3098 4.530710 ACAGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2825 3099 5.086104 ACAGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2826 3100 4.870426 ACAGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2827 3101 5.109210 CAGACTACATACGGAGCAAAATGA 58.891 41.667 0.00 0.00 0.00 2.57
2828 3102 5.233050 CAGACTACATACGGAGCAAAATGAG 59.767 44.000 0.00 0.00 0.00 2.90
2829 3103 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2830 3104 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2831 3105 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2832 3106 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2833 3107 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2834 3108 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2835 3109 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2836 3110 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2837 3111 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2838 3112 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2839 3113 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2850 3124 6.893958 AGTGAATCTACACTCTAAAATGCG 57.106 37.500 0.00 0.00 46.36 4.73
2851 3125 6.398918 AGTGAATCTACACTCTAAAATGCGT 58.601 36.000 0.00 0.00 46.36 5.24
2852 3126 6.531948 AGTGAATCTACACTCTAAAATGCGTC 59.468 38.462 0.00 0.00 46.36 5.19
2853 3127 6.531948 GTGAATCTACACTCTAAAATGCGTCT 59.468 38.462 0.00 0.00 37.73 4.18
2854 3128 7.701078 GTGAATCTACACTCTAAAATGCGTCTA 59.299 37.037 0.00 0.00 37.73 2.59
2855 3129 7.701078 TGAATCTACACTCTAAAATGCGTCTAC 59.299 37.037 0.00 0.00 0.00 2.59
2856 3130 6.505044 TCTACACTCTAAAATGCGTCTACA 57.495 37.500 0.00 0.00 0.00 2.74
2857 3131 7.096884 TCTACACTCTAAAATGCGTCTACAT 57.903 36.000 0.00 0.00 0.00 2.29
2858 3132 8.217131 TCTACACTCTAAAATGCGTCTACATA 57.783 34.615 0.00 0.00 0.00 2.29
2859 3133 8.127327 TCTACACTCTAAAATGCGTCTACATAC 58.873 37.037 0.00 0.00 0.00 2.39
2860 3134 6.627243 ACACTCTAAAATGCGTCTACATACA 58.373 36.000 0.00 0.00 0.00 2.29
2861 3135 7.265673 ACACTCTAAAATGCGTCTACATACAT 58.734 34.615 0.00 0.00 0.00 2.29
2862 3136 7.435488 ACACTCTAAAATGCGTCTACATACATC 59.565 37.037 0.00 0.00 0.00 3.06
2863 3137 6.637254 ACTCTAAAATGCGTCTACATACATCG 59.363 38.462 0.00 0.00 0.00 3.84
2864 3138 5.918576 TCTAAAATGCGTCTACATACATCGG 59.081 40.000 0.00 0.00 0.00 4.18
2865 3139 3.728076 AATGCGTCTACATACATCGGT 57.272 42.857 0.00 0.00 0.00 4.69
2866 3140 4.841443 AATGCGTCTACATACATCGGTA 57.159 40.909 0.00 0.00 0.00 4.02
2867 3141 5.386958 AATGCGTCTACATACATCGGTAT 57.613 39.130 0.00 0.00 40.86 2.73
2881 3155 6.037786 ACATCGGTATGTAGTCCCATATTG 57.962 41.667 0.00 0.00 44.66 1.90
2882 3156 5.778241 ACATCGGTATGTAGTCCCATATTGA 59.222 40.000 0.00 0.00 44.66 2.57
2883 3157 6.269077 ACATCGGTATGTAGTCCCATATTGAA 59.731 38.462 0.00 0.00 44.66 2.69
2884 3158 6.734502 TCGGTATGTAGTCCCATATTGAAA 57.265 37.500 0.00 0.00 30.47 2.69
2885 3159 7.311092 TCGGTATGTAGTCCCATATTGAAAT 57.689 36.000 0.00 0.00 30.47 2.17
2886 3160 8.425237 TCGGTATGTAGTCCCATATTGAAATA 57.575 34.615 0.00 0.00 30.47 1.40
2887 3161 9.042450 TCGGTATGTAGTCCCATATTGAAATAT 57.958 33.333 0.00 0.00 30.47 1.28
2888 3162 9.314321 CGGTATGTAGTCCCATATTGAAATATC 57.686 37.037 0.00 0.00 30.47 1.63
2896 3170 9.398921 AGTCCCATATTGAAATATCTAGAAGGT 57.601 33.333 0.00 0.00 29.35 3.50
2897 3171 9.660180 GTCCCATATTGAAATATCTAGAAGGTC 57.340 37.037 0.00 0.00 29.35 3.85
2898 3172 9.621239 TCCCATATTGAAATATCTAGAAGGTCT 57.379 33.333 0.00 0.00 29.35 3.85
2916 3190 8.422566 AGAAGGTCTTATATTTAGAAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
2917 3191 7.063934 AGGTCTTATATTTAGAAACGGAGGG 57.936 40.000 0.00 0.00 0.00 4.30
2918 3192 6.842807 AGGTCTTATATTTAGAAACGGAGGGA 59.157 38.462 0.00 0.00 0.00 4.20
2919 3193 7.015389 AGGTCTTATATTTAGAAACGGAGGGAG 59.985 40.741 0.00 0.00 0.00 4.30
2920 3194 7.201983 GGTCTTATATTTAGAAACGGAGGGAGT 60.202 40.741 0.00 0.00 0.00 3.85
2921 3195 8.854117 GTCTTATATTTAGAAACGGAGGGAGTA 58.146 37.037 0.00 0.00 0.00 2.59
2922 3196 9.597681 TCTTATATTTAGAAACGGAGGGAGTAT 57.402 33.333 0.00 0.00 0.00 2.12
2923 3197 9.857957 CTTATATTTAGAAACGGAGGGAGTATC 57.142 37.037 0.00 0.00 0.00 2.24
2924 3198 9.597681 TTATATTTAGAAACGGAGGGAGTATCT 57.402 33.333 0.00 0.00 33.73 1.98
2935 3317 5.106078 CGGAGGGAGTATCTAATAACAGAGC 60.106 48.000 0.00 0.00 33.73 4.09
2938 3320 7.238486 AGGGAGTATCTAATAACAGAGCATG 57.762 40.000 0.00 0.00 33.73 4.06
2975 3360 6.767524 ACCTCTCACAACTGATTACTAGAG 57.232 41.667 0.00 0.00 0.00 2.43
2985 3370 7.763528 ACAACTGATTACTAGAGCAGAATCTTG 59.236 37.037 3.90 1.37 32.86 3.02
3001 3396 4.543590 ATCTTGGTTCTGTTCATCTCGT 57.456 40.909 0.00 0.00 0.00 4.18
3024 3419 7.119116 TCGTCAATTGCACTGAAATATGTAGTT 59.881 33.333 0.00 0.00 0.00 2.24
3081 3476 4.646492 ACTGCTCAAAAATGGTTTCTGTCT 59.354 37.500 0.00 0.00 0.00 3.41
3082 3477 5.827797 ACTGCTCAAAAATGGTTTCTGTCTA 59.172 36.000 0.00 0.00 0.00 2.59
3083 3478 6.321181 ACTGCTCAAAAATGGTTTCTGTCTAA 59.679 34.615 0.00 0.00 0.00 2.10
3084 3479 7.106439 TGCTCAAAAATGGTTTCTGTCTAAA 57.894 32.000 0.00 0.00 0.00 1.85
3085 3480 7.551585 TGCTCAAAAATGGTTTCTGTCTAAAA 58.448 30.769 0.00 0.00 0.00 1.52
3086 3481 8.037758 TGCTCAAAAATGGTTTCTGTCTAAAAA 58.962 29.630 0.00 0.00 0.00 1.94
3087 3482 8.542953 GCTCAAAAATGGTTTCTGTCTAAAAAG 58.457 33.333 0.00 0.00 0.00 2.27
3088 3483 9.586435 CTCAAAAATGGTTTCTGTCTAAAAAGT 57.414 29.630 0.00 0.00 0.00 2.66
3089 3484 9.364989 TCAAAAATGGTTTCTGTCTAAAAAGTG 57.635 29.630 0.00 0.00 0.00 3.16
3090 3485 9.364989 CAAAAATGGTTTCTGTCTAAAAAGTGA 57.635 29.630 0.00 0.00 0.00 3.41
3091 3486 9.936759 AAAAATGGTTTCTGTCTAAAAAGTGAA 57.063 25.926 0.00 0.00 0.00 3.18
3092 3487 8.926715 AAATGGTTTCTGTCTAAAAAGTGAAC 57.073 30.769 0.00 0.00 0.00 3.18
3093 3488 6.445357 TGGTTTCTGTCTAAAAAGTGAACC 57.555 37.500 0.00 0.00 34.35 3.62
3094 3489 6.184789 TGGTTTCTGTCTAAAAAGTGAACCT 58.815 36.000 0.00 0.00 34.61 3.50
3095 3490 6.661805 TGGTTTCTGTCTAAAAAGTGAACCTT 59.338 34.615 0.00 0.00 34.61 3.50
3096 3491 6.972901 GGTTTCTGTCTAAAAAGTGAACCTTG 59.027 38.462 0.00 0.00 32.32 3.61
3097 3492 6.693315 TTCTGTCTAAAAAGTGAACCTTGG 57.307 37.500 0.00 0.00 32.32 3.61
3098 3493 5.751586 TCTGTCTAAAAAGTGAACCTTGGT 58.248 37.500 0.00 0.00 32.32 3.67
3099 3494 6.184789 TCTGTCTAAAAAGTGAACCTTGGTT 58.815 36.000 4.52 4.52 32.32 3.67
3100 3495 6.661805 TCTGTCTAAAAAGTGAACCTTGGTTT 59.338 34.615 6.49 0.00 32.32 3.27
3101 3496 6.859017 TGTCTAAAAAGTGAACCTTGGTTTC 58.141 36.000 6.49 3.98 32.32 2.78
3102 3497 6.661805 TGTCTAAAAAGTGAACCTTGGTTTCT 59.338 34.615 6.49 6.04 32.32 2.52
3103 3498 6.972901 GTCTAAAAAGTGAACCTTGGTTTCTG 59.027 38.462 6.49 0.00 32.32 3.02
3104 3499 5.738619 AAAAAGTGAACCTTGGTTTCTGT 57.261 34.783 6.49 1.84 32.32 3.41
3105 3500 4.983671 AAAGTGAACCTTGGTTTCTGTC 57.016 40.909 6.49 0.00 32.32 3.51
3113 3508 6.887545 TGAACCTTGGTTTCTGTCTAAAAAGA 59.112 34.615 6.49 0.00 0.00 2.52
3184 3580 4.180057 CAGATCCTCTACAGAGTGTTTGC 58.820 47.826 5.56 0.00 40.48 3.68
3229 3625 5.791336 TCAGTCTAGGTTCATATTCGCAT 57.209 39.130 0.00 0.00 0.00 4.73
3292 3758 2.035237 AAAGTGTTGGAGACGGCCGA 62.035 55.000 35.90 5.52 0.00 5.54
3520 3986 4.908601 TGGGAGCTTCTCTGTCATTTTA 57.091 40.909 0.00 0.00 0.00 1.52
3700 4175 6.536582 AGCAGCTCTTTGTGTATACATTACTG 59.463 38.462 9.18 10.67 36.53 2.74
4020 4498 6.182627 TGTTCAATCATACTTCTGCTTGGAT 58.817 36.000 0.00 0.00 0.00 3.41
4137 4615 1.917303 GGCATCCAAATTTGCGTAACG 59.083 47.619 12.92 0.00 39.78 3.18
4200 4698 5.593909 AGGTTGTGTTTGAGATGTTCATTCA 59.406 36.000 0.00 0.00 35.27 2.57
4227 4726 5.894393 TGTTCAAATGGGAGAAGTTGGTTAA 59.106 36.000 0.00 0.00 0.00 2.01
4280 4780 9.696917 AAAAGGAAACATGTCTGCTATTTTTAG 57.303 29.630 0.00 0.00 0.00 1.85
4281 4781 8.409358 AAGGAAACATGTCTGCTATTTTTAGT 57.591 30.769 0.00 0.00 0.00 2.24
4283 4783 8.299570 AGGAAACATGTCTGCTATTTTTAGTTG 58.700 33.333 0.00 0.00 0.00 3.16
4284 4784 8.082242 GGAAACATGTCTGCTATTTTTAGTTGT 58.918 33.333 0.00 0.00 0.00 3.32
4309 4822 9.339492 GTAATTTCTTCTTATATACTCCGTCCG 57.661 37.037 0.00 0.00 0.00 4.79
4310 4823 5.954296 TTCTTCTTATATACTCCGTCCGG 57.046 43.478 0.00 0.00 0.00 5.14
4316 4829 7.383102 TCTTATATACTCCGTCCGGAAATAC 57.617 40.000 5.23 0.00 44.66 1.89
4324 4837 3.700539 TCCGTCCGGAAATACTTGTCATA 59.299 43.478 5.23 0.00 42.05 2.15
4325 4838 4.049186 CCGTCCGGAAATACTTGTCATAG 58.951 47.826 5.23 0.00 37.50 2.23
4326 4839 3.489785 CGTCCGGAAATACTTGTCATAGC 59.510 47.826 5.23 0.00 0.00 2.97
4329 4842 5.527582 GTCCGGAAATACTTGTCATAGCAAT 59.472 40.000 5.23 0.00 0.00 3.56
4332 4845 6.038161 CCGGAAATACTTGTCATAGCAATGAA 59.962 38.462 0.00 0.00 43.69 2.57
4334 4847 8.773645 CGGAAATACTTGTCATAGCAATGAATA 58.226 33.333 0.00 0.00 43.69 1.75
4342 4855 9.806203 CTTGTCATAGCAATGAATAAAAATGGA 57.194 29.630 0.00 0.00 43.69 3.41
4344 4857 9.752961 TGTCATAGCAATGAATAAAAATGGATG 57.247 29.630 0.00 0.00 43.69 3.51
4345 4858 9.754382 GTCATAGCAATGAATAAAAATGGATGT 57.246 29.630 0.00 0.00 43.69 3.06
4387 4900 7.426410 TGTCTAGATACATCCATTTCTTCGAC 58.574 38.462 0.00 0.00 0.00 4.20
4388 4901 7.068226 TGTCTAGATACATCCATTTCTTCGACA 59.932 37.037 0.00 0.00 31.18 4.35
4389 4902 7.921214 GTCTAGATACATCCATTTCTTCGACAA 59.079 37.037 0.00 0.00 0.00 3.18
4390 4903 8.138074 TCTAGATACATCCATTTCTTCGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
4392 4905 7.782049 AGATACATCCATTTCTTCGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
4395 4908 7.687941 ACATCCATTTCTTCGACAAGTATTT 57.312 32.000 0.00 0.00 0.00 1.40
4397 4910 8.237267 ACATCCATTTCTTCGACAAGTATTTTC 58.763 33.333 0.00 0.00 0.00 2.29
4398 4911 6.827641 TCCATTTCTTCGACAAGTATTTTCG 58.172 36.000 0.00 0.00 0.00 3.46
4410 4947 0.462789 TATTTTCGGACGGAGGGAGC 59.537 55.000 0.00 0.00 0.00 4.70
4424 5261 3.367395 GGAGGGAGCACAAGTTTATTTGC 60.367 47.826 0.00 0.00 35.08 3.68
4436 5273 8.986847 CACAAGTTTATTTGCCATGTTTGATAA 58.013 29.630 0.00 0.00 0.00 1.75
4492 7014 1.136305 GCTGCAATGTGAGCAATCCAT 59.864 47.619 0.00 0.00 42.17 3.41
4517 7039 4.748892 TCTAGACAAAGCTTCAAGGATCG 58.251 43.478 0.00 0.00 0.00 3.69
4525 7047 2.541547 CTTCAAGGATCGGCCAGCCA 62.542 60.000 9.78 0.00 40.02 4.75
4556 7496 4.087930 GCGTTGTTGTTCATTGGTTTATCG 59.912 41.667 0.00 0.00 0.00 2.92
4575 7515 2.556189 TCGTTTGGCAGCAATTGTACAT 59.444 40.909 7.40 0.00 0.00 2.29
4590 7530 8.172484 GCAATTGTACATCTAACGACAACAATA 58.828 33.333 7.40 0.00 35.61 1.90
4697 7647 0.033405 ATCCAGATTTGCAGGCAGCT 60.033 50.000 2.86 0.00 45.94 4.24
4702 7652 1.749634 AGATTTGCAGGCAGCTCATTC 59.250 47.619 2.86 0.00 45.94 2.67
4704 7654 1.171308 TTTGCAGGCAGCTCATTCTC 58.829 50.000 2.86 0.00 45.94 2.87
4720 7670 6.462552 TCATTCTCAGAGATACCAGAACAG 57.537 41.667 0.00 0.00 0.00 3.16
4734 7684 1.004044 AGAACAGCCCACTTCCATCAG 59.996 52.381 0.00 0.00 0.00 2.90
4820 9035 7.357532 GCGAGTAAATCATGAAAAATAATGGCG 60.358 37.037 0.00 0.00 0.00 5.69
4821 9036 7.357532 CGAGTAAATCATGAAAAATAATGGCGC 60.358 37.037 0.00 0.00 0.00 6.53
4895 9366 4.142469 CCTTTCCACGTCAAACAAGACTTT 60.142 41.667 0.00 0.00 36.38 2.66
4896 9367 5.379732 TTTCCACGTCAAACAAGACTTTT 57.620 34.783 0.00 0.00 36.38 2.27
4897 9368 4.609691 TCCACGTCAAACAAGACTTTTC 57.390 40.909 0.00 0.00 36.38 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.333938 CACACTGCTTGCTGTGCC 59.666 61.111 25.16 0.00 37.68 5.01
47 48 4.410400 CGGAGGGTGTTGGAGGGC 62.410 72.222 0.00 0.00 0.00 5.19
57 58 4.528920 GAGTATATGCTATCTCGGAGGGT 58.471 47.826 4.96 0.00 0.00 4.34
185 191 0.388649 GGAACTCGATCACACGCTGT 60.389 55.000 0.00 0.00 0.00 4.40
296 343 1.745320 ATAGCTTCAGGTACCGGGCG 61.745 60.000 12.41 4.83 0.00 6.13
332 379 1.028330 ATGCAATCAGTGGGTCTGCG 61.028 55.000 0.00 0.00 43.32 5.18
392 439 3.471680 GGATGGCTTCTCATGGTCTAAC 58.528 50.000 0.00 0.00 0.00 2.34
518 565 4.761739 TGAAACATGACACTGGGAAATCTC 59.238 41.667 0.00 0.00 0.00 2.75
571 619 6.193514 TCGTAAGATATACACGAACACCAA 57.806 37.500 0.00 0.00 45.01 3.67
689 737 9.116067 TGCAGAAACTAAATTTGTTACTGTACT 57.884 29.630 0.00 0.00 0.00 2.73
691 739 9.724839 GTTGCAGAAACTAAATTTGTTACTGTA 57.275 29.630 0.00 1.72 35.75 2.74
692 740 7.704899 GGTTGCAGAAACTAAATTTGTTACTGT 59.295 33.333 0.00 0.00 38.92 3.55
841 952 5.101648 TCCTCATCACATTATTCAGTGCA 57.898 39.130 0.00 0.00 35.76 4.57
842 953 5.587844 AGTTCCTCATCACATTATTCAGTGC 59.412 40.000 0.00 0.00 35.76 4.40
844 955 7.046652 CAGAGTTCCTCATCACATTATTCAGT 58.953 38.462 0.00 0.00 32.06 3.41
882 993 6.422223 GCAGTGATACGGAAATTGACAATAG 58.578 40.000 0.00 0.00 0.00 1.73
883 994 5.006261 CGCAGTGATACGGAAATTGACAATA 59.994 40.000 0.00 0.00 0.00 1.90
1320 1587 2.511600 GGCTCCCGGTTGATCACG 60.512 66.667 0.00 0.00 0.00 4.35
1377 1644 3.833645 TCGGTGAGGGAATCCGCG 61.834 66.667 0.00 0.00 43.35 6.46
1519 1786 1.221840 GGATGAGCGAGGCAAAGGA 59.778 57.895 0.00 0.00 0.00 3.36
2061 2334 2.167662 TCAGACTGCCGTAATGTCTCA 58.832 47.619 0.00 0.00 38.80 3.27
2388 2661 2.838637 TTTTCAGAACCCCAAGTGGT 57.161 45.000 0.00 0.00 41.55 4.16
2567 2840 0.977395 CAGAAAGAACTCCCCTCGGT 59.023 55.000 0.00 0.00 0.00 4.69
2694 2967 3.791320 ACCCCTCAGTATCTGAAGAACA 58.209 45.455 1.22 0.00 40.18 3.18
2761 3035 7.869800 AGACTTATATTTAGGAACGGACGTAG 58.130 38.462 0.00 0.00 0.00 3.51
2763 3037 6.705863 AGACTTATATTTAGGAACGGACGT 57.294 37.500 0.00 0.00 0.00 4.34
2764 3038 7.998753 AAAGACTTATATTTAGGAACGGACG 57.001 36.000 0.00 0.00 0.00 4.79
2791 3065 9.221933 CCGTATGTAGTCTGTATTAGAATCTCT 57.778 37.037 0.00 0.00 37.12 3.10
2792 3066 9.217278 TCCGTATGTAGTCTGTATTAGAATCTC 57.783 37.037 0.00 0.00 37.12 2.75
2793 3067 9.221933 CTCCGTATGTAGTCTGTATTAGAATCT 57.778 37.037 0.00 0.00 37.12 2.40
2794 3068 7.964011 GCTCCGTATGTAGTCTGTATTAGAATC 59.036 40.741 0.00 0.00 37.12 2.52
2795 3069 7.447545 TGCTCCGTATGTAGTCTGTATTAGAAT 59.552 37.037 0.00 0.00 37.12 2.40
2796 3070 6.769341 TGCTCCGTATGTAGTCTGTATTAGAA 59.231 38.462 0.00 0.00 37.12 2.10
2797 3071 6.293698 TGCTCCGTATGTAGTCTGTATTAGA 58.706 40.000 0.00 0.00 0.00 2.10
2798 3072 6.555812 TGCTCCGTATGTAGTCTGTATTAG 57.444 41.667 0.00 0.00 0.00 1.73
2799 3073 6.947644 TTGCTCCGTATGTAGTCTGTATTA 57.052 37.500 0.00 0.00 0.00 0.98
2800 3074 5.847111 TTGCTCCGTATGTAGTCTGTATT 57.153 39.130 0.00 0.00 0.00 1.89
2801 3075 5.847111 TTTGCTCCGTATGTAGTCTGTAT 57.153 39.130 0.00 0.00 0.00 2.29
2802 3076 5.648178 TTTTGCTCCGTATGTAGTCTGTA 57.352 39.130 0.00 0.00 0.00 2.74
2803 3077 4.530710 TTTTGCTCCGTATGTAGTCTGT 57.469 40.909 0.00 0.00 0.00 3.41
2804 3078 5.109210 TCATTTTGCTCCGTATGTAGTCTG 58.891 41.667 0.00 0.00 0.00 3.51
2805 3079 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
2806 3080 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2807 3081 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2808 3082 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2809 3083 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2810 3084 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2811 3085 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2812 3086 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2813 3087 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2814 3088 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2815 3089 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2816 3090 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2817 3091 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2828 3102 6.531948 AGACGCATTTTAGAGTGTAGATTCAC 59.468 38.462 0.00 0.00 38.46 3.18
2829 3103 6.631016 AGACGCATTTTAGAGTGTAGATTCA 58.369 36.000 0.00 0.00 0.00 2.57
2830 3104 7.701078 TGTAGACGCATTTTAGAGTGTAGATTC 59.299 37.037 0.00 0.00 0.00 2.52
2831 3105 7.544622 TGTAGACGCATTTTAGAGTGTAGATT 58.455 34.615 0.00 0.00 0.00 2.40
2832 3106 7.096884 TGTAGACGCATTTTAGAGTGTAGAT 57.903 36.000 0.00 0.00 0.00 1.98
2833 3107 6.505044 TGTAGACGCATTTTAGAGTGTAGA 57.495 37.500 0.00 0.00 0.00 2.59
2834 3108 7.913821 TGTATGTAGACGCATTTTAGAGTGTAG 59.086 37.037 0.00 0.00 0.00 2.74
2835 3109 7.764331 TGTATGTAGACGCATTTTAGAGTGTA 58.236 34.615 0.00 0.00 0.00 2.90
2836 3110 6.627243 TGTATGTAGACGCATTTTAGAGTGT 58.373 36.000 0.00 0.00 0.00 3.55
2837 3111 7.357613 CGATGTATGTAGACGCATTTTAGAGTG 60.358 40.741 0.00 0.00 0.00 3.51
2838 3112 6.637254 CGATGTATGTAGACGCATTTTAGAGT 59.363 38.462 0.00 0.00 0.00 3.24
2839 3113 6.088217 CCGATGTATGTAGACGCATTTTAGAG 59.912 42.308 0.00 0.00 0.00 2.43
2840 3114 5.918576 CCGATGTATGTAGACGCATTTTAGA 59.081 40.000 0.00 0.00 0.00 2.10
2841 3115 5.690409 ACCGATGTATGTAGACGCATTTTAG 59.310 40.000 0.00 0.00 0.00 1.85
2842 3116 5.593968 ACCGATGTATGTAGACGCATTTTA 58.406 37.500 0.00 0.00 0.00 1.52
2843 3117 4.439057 ACCGATGTATGTAGACGCATTTT 58.561 39.130 0.00 0.00 0.00 1.82
2844 3118 4.054780 ACCGATGTATGTAGACGCATTT 57.945 40.909 0.00 0.00 0.00 2.32
2845 3119 3.728076 ACCGATGTATGTAGACGCATT 57.272 42.857 0.00 0.00 0.00 3.56
2846 3120 4.733850 CATACCGATGTATGTAGACGCAT 58.266 43.478 4.86 0.00 46.11 4.73
2847 3121 4.155310 CATACCGATGTATGTAGACGCA 57.845 45.455 4.86 0.00 46.11 5.24
2856 3130 7.618117 TCAATATGGGACTACATACCGATGTAT 59.382 37.037 0.00 0.00 45.42 2.29
2857 3131 6.949463 TCAATATGGGACTACATACCGATGTA 59.051 38.462 0.00 0.00 44.77 2.29
2859 3133 6.280855 TCAATATGGGACTACATACCGATG 57.719 41.667 0.00 0.00 36.26 3.84
2860 3134 6.928348 TTCAATATGGGACTACATACCGAT 57.072 37.500 0.00 0.00 36.26 4.18
2861 3135 6.734502 TTTCAATATGGGACTACATACCGA 57.265 37.500 0.00 0.00 36.26 4.69
2862 3136 9.314321 GATATTTCAATATGGGACTACATACCG 57.686 37.037 0.00 0.00 36.26 4.02
2870 3144 9.398921 ACCTTCTAGATATTTCAATATGGGACT 57.601 33.333 0.00 0.00 31.96 3.85
2871 3145 9.660180 GACCTTCTAGATATTTCAATATGGGAC 57.340 37.037 0.00 0.00 31.96 4.46
2872 3146 9.621239 AGACCTTCTAGATATTTCAATATGGGA 57.379 33.333 0.00 0.00 31.96 4.37
2890 3164 8.422566 CCTCCGTTTCTAAATATAAGACCTTCT 58.577 37.037 0.00 0.00 0.00 2.85
2891 3165 7.656542 CCCTCCGTTTCTAAATATAAGACCTTC 59.343 40.741 0.00 0.00 0.00 3.46
2892 3166 7.346436 TCCCTCCGTTTCTAAATATAAGACCTT 59.654 37.037 0.00 0.00 0.00 3.50
2893 3167 6.842807 TCCCTCCGTTTCTAAATATAAGACCT 59.157 38.462 0.00 0.00 0.00 3.85
2894 3168 7.059202 TCCCTCCGTTTCTAAATATAAGACC 57.941 40.000 0.00 0.00 0.00 3.85
2895 3169 7.724287 ACTCCCTCCGTTTCTAAATATAAGAC 58.276 38.462 0.00 0.00 0.00 3.01
2896 3170 7.909485 ACTCCCTCCGTTTCTAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2897 3171 9.857957 GATACTCCCTCCGTTTCTAAATATAAG 57.142 37.037 0.00 0.00 0.00 1.73
2898 3172 9.597681 AGATACTCCCTCCGTTTCTAAATATAA 57.402 33.333 0.00 0.00 0.00 0.98
2900 3174 9.597681 TTAGATACTCCCTCCGTTTCTAAATAT 57.402 33.333 0.00 0.00 34.36 1.28
2901 3175 9.597681 ATTAGATACTCCCTCCGTTTCTAAATA 57.402 33.333 0.00 0.00 37.95 1.40
2902 3176 7.909485 TTAGATACTCCCTCCGTTTCTAAAT 57.091 36.000 0.00 0.00 34.36 1.40
2903 3177 7.909485 ATTAGATACTCCCTCCGTTTCTAAA 57.091 36.000 0.00 0.00 37.95 1.85
2904 3178 8.854117 GTTATTAGATACTCCCTCCGTTTCTAA 58.146 37.037 0.00 0.00 38.41 2.10
2905 3179 8.000709 TGTTATTAGATACTCCCTCCGTTTCTA 58.999 37.037 0.00 0.00 0.00 2.10
2906 3180 6.837568 TGTTATTAGATACTCCCTCCGTTTCT 59.162 38.462 0.00 0.00 0.00 2.52
2907 3181 7.014038 TCTGTTATTAGATACTCCCTCCGTTTC 59.986 40.741 0.00 0.00 0.00 2.78
2908 3182 6.837568 TCTGTTATTAGATACTCCCTCCGTTT 59.162 38.462 0.00 0.00 0.00 3.60
2909 3183 6.371278 TCTGTTATTAGATACTCCCTCCGTT 58.629 40.000 0.00 0.00 0.00 4.44
2910 3184 5.950023 TCTGTTATTAGATACTCCCTCCGT 58.050 41.667 0.00 0.00 0.00 4.69
2911 3185 5.106078 GCTCTGTTATTAGATACTCCCTCCG 60.106 48.000 0.00 0.00 0.00 4.63
2912 3186 5.775701 TGCTCTGTTATTAGATACTCCCTCC 59.224 44.000 0.00 0.00 0.00 4.30
2913 3187 6.902771 TGCTCTGTTATTAGATACTCCCTC 57.097 41.667 0.00 0.00 0.00 4.30
2914 3188 6.784969 ACATGCTCTGTTATTAGATACTCCCT 59.215 38.462 0.00 0.00 32.90 4.20
2915 3189 6.998802 ACATGCTCTGTTATTAGATACTCCC 58.001 40.000 0.00 0.00 32.90 4.30
2916 3190 9.632807 CTTACATGCTCTGTTATTAGATACTCC 57.367 37.037 0.00 0.00 39.39 3.85
2917 3191 9.632807 CCTTACATGCTCTGTTATTAGATACTC 57.367 37.037 0.00 0.00 39.39 2.59
2918 3192 9.148879 ACCTTACATGCTCTGTTATTAGATACT 57.851 33.333 0.00 0.00 39.39 2.12
2922 3196 9.982651 GAATACCTTACATGCTCTGTTATTAGA 57.017 33.333 0.00 0.00 39.39 2.10
2923 3197 9.764363 TGAATACCTTACATGCTCTGTTATTAG 57.236 33.333 0.00 0.00 39.39 1.73
2925 3199 9.632638 ATTGAATACCTTACATGCTCTGTTATT 57.367 29.630 0.00 0.00 39.39 1.40
2985 3370 4.670221 GCAATTGACGAGATGAACAGAACC 60.670 45.833 10.34 0.00 0.00 3.62
2996 3391 5.643348 ACATATTTCAGTGCAATTGACGAGA 59.357 36.000 10.34 6.01 29.78 4.04
3001 3396 9.979578 AAAAACTACATATTTCAGTGCAATTGA 57.020 25.926 10.34 0.00 0.00 2.57
3024 3419 7.987750 TGGTACAACTACAGCATGAATAAAA 57.012 32.000 0.00 0.00 34.82 1.52
3081 3476 6.661805 AGACAGAAACCAAGGTTCACTTTTTA 59.338 34.615 4.73 0.00 37.29 1.52
3082 3477 5.480422 AGACAGAAACCAAGGTTCACTTTTT 59.520 36.000 4.73 0.00 37.29 1.94
3083 3478 5.016831 AGACAGAAACCAAGGTTCACTTTT 58.983 37.500 4.73 0.00 37.29 2.27
3084 3479 4.600062 AGACAGAAACCAAGGTTCACTTT 58.400 39.130 4.73 1.84 37.29 2.66
3085 3480 4.236527 AGACAGAAACCAAGGTTCACTT 57.763 40.909 4.73 0.00 41.00 3.16
3086 3481 3.933861 AGACAGAAACCAAGGTTCACT 57.066 42.857 4.73 5.52 37.35 3.41
3087 3482 6.445357 TTTTAGACAGAAACCAAGGTTCAC 57.555 37.500 4.73 3.32 37.35 3.18
3088 3483 6.887545 TCTTTTTAGACAGAAACCAAGGTTCA 59.112 34.615 4.73 0.00 37.35 3.18
3089 3484 7.282450 TCTCTTTTTAGACAGAAACCAAGGTTC 59.718 37.037 4.73 0.00 37.35 3.62
3090 3485 7.116736 TCTCTTTTTAGACAGAAACCAAGGTT 58.883 34.615 0.00 0.00 40.45 3.50
3091 3486 6.659824 TCTCTTTTTAGACAGAAACCAAGGT 58.340 36.000 0.00 0.00 0.00 3.50
3092 3487 7.418408 GTTCTCTTTTTAGACAGAAACCAAGG 58.582 38.462 0.00 0.00 0.00 3.61
3093 3488 7.283354 AGGTTCTCTTTTTAGACAGAAACCAAG 59.717 37.037 12.05 0.00 33.71 3.61
3094 3489 7.116736 AGGTTCTCTTTTTAGACAGAAACCAA 58.883 34.615 12.05 0.00 33.71 3.67
3095 3490 6.659824 AGGTTCTCTTTTTAGACAGAAACCA 58.340 36.000 12.05 0.00 33.71 3.67
3096 3491 7.067129 ACAAGGTTCTCTTTTTAGACAGAAACC 59.933 37.037 0.00 0.00 33.71 3.27
3097 3492 7.986562 ACAAGGTTCTCTTTTTAGACAGAAAC 58.013 34.615 0.00 0.00 33.46 2.78
3098 3493 9.847224 ATACAAGGTTCTCTTTTTAGACAGAAA 57.153 29.630 0.00 0.00 32.41 2.52
3099 3494 9.273016 CATACAAGGTTCTCTTTTTAGACAGAA 57.727 33.333 0.00 0.00 32.41 3.02
3100 3495 8.429641 ACATACAAGGTTCTCTTTTTAGACAGA 58.570 33.333 0.00 0.00 32.41 3.41
3101 3496 8.608844 ACATACAAGGTTCTCTTTTTAGACAG 57.391 34.615 0.00 0.00 32.41 3.51
3102 3497 8.836413 CAACATACAAGGTTCTCTTTTTAGACA 58.164 33.333 0.00 0.00 32.41 3.41
3103 3498 7.803659 GCAACATACAAGGTTCTCTTTTTAGAC 59.196 37.037 0.00 0.00 32.41 2.59
3104 3499 7.500892 TGCAACATACAAGGTTCTCTTTTTAGA 59.499 33.333 0.00 0.00 32.41 2.10
3105 3500 7.648142 TGCAACATACAAGGTTCTCTTTTTAG 58.352 34.615 0.00 0.00 32.41 1.85
3113 3508 3.508845 ACCTGCAACATACAAGGTTCT 57.491 42.857 0.00 0.00 0.00 3.01
3184 3580 1.137872 GAGTCTGTGCCCCATCTAGTG 59.862 57.143 0.00 0.00 0.00 2.74
3684 4159 4.106909 CCGCGACAGTAATGTATACACAA 58.893 43.478 8.23 0.00 38.42 3.33
3700 4175 4.899239 ATAGCCTGCTGCCGCGAC 62.899 66.667 8.23 0.00 42.71 5.19
4020 4498 4.978099 GAGAGGCTCCATCCAAATGAATA 58.022 43.478 11.71 0.00 34.61 1.75
4200 4698 5.366477 ACCAACTTCTCCCATTTGAACATTT 59.634 36.000 0.00 0.00 0.00 2.32
4227 4726 3.820557 ACTAAAGTTCATGCACACCAGT 58.179 40.909 0.00 0.00 0.00 4.00
4308 4821 6.603237 TCATTGCTATGACAAGTATTTCCG 57.397 37.500 6.75 0.00 35.87 4.30
4316 4829 9.806203 TCCATTTTTATTCATTGCTATGACAAG 57.194 29.630 10.48 0.00 40.42 3.16
4377 4890 6.400727 CGTCCGAAAATACTTGTCGAAGAAAT 60.401 38.462 1.13 0.00 39.69 2.17
4383 4896 2.228582 TCCGTCCGAAAATACTTGTCGA 59.771 45.455 1.13 0.00 36.92 4.20
4384 4897 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
4385 4898 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4387 4900 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4388 4901 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
4389 4902 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
4390 4903 1.805495 GCTCCCTCCGTCCGAAAATAC 60.805 57.143 0.00 0.00 0.00 1.89
4392 4905 1.221021 GCTCCCTCCGTCCGAAAAT 59.779 57.895 0.00 0.00 0.00 1.82
4395 4908 3.379445 GTGCTCCCTCCGTCCGAA 61.379 66.667 0.00 0.00 0.00 4.30
4397 4910 3.649277 CTTGTGCTCCCTCCGTCCG 62.649 68.421 0.00 0.00 0.00 4.79
4398 4911 2.113243 AACTTGTGCTCCCTCCGTCC 62.113 60.000 0.00 0.00 0.00 4.79
4410 4947 6.841443 TCAAACATGGCAAATAAACTTGTG 57.159 33.333 0.00 0.00 0.00 3.33
4424 5261 5.672503 TGGCCAATCAATTATCAAACATGG 58.327 37.500 0.61 0.00 0.00 3.66
4436 5273 4.829872 ACACAATTCATGGCCAATCAAT 57.170 36.364 10.96 5.34 0.00 2.57
4489 7011 7.050377 TCCTTGAAGCTTTGTCTAGATAATGG 58.950 38.462 14.34 7.48 0.00 3.16
4492 7014 6.980978 CGATCCTTGAAGCTTTGTCTAGATAA 59.019 38.462 0.00 0.00 0.00 1.75
4517 7039 1.446618 CGCAAAGAAATGGCTGGCC 60.447 57.895 4.43 4.43 0.00 5.36
4525 7047 5.006552 CCAATGAACAACAACGCAAAGAAAT 59.993 36.000 0.00 0.00 0.00 2.17
4556 7496 4.178545 AGATGTACAATTGCTGCCAAAC 57.821 40.909 5.05 0.00 34.05 2.93
4575 7515 6.254804 CACGATTGGATATTGTTGTCGTTAGA 59.745 38.462 0.00 0.00 38.59 2.10
4697 7647 5.163468 GCTGTTCTGGTATCTCTGAGAATGA 60.163 44.000 12.00 3.37 0.00 2.57
4702 7652 2.102252 GGGCTGTTCTGGTATCTCTGAG 59.898 54.545 0.00 0.00 0.00 3.35
4704 7654 1.833630 TGGGCTGTTCTGGTATCTCTG 59.166 52.381 0.00 0.00 0.00 3.35
4720 7670 0.253044 TGCTACTGATGGAAGTGGGC 59.747 55.000 0.00 0.00 33.65 5.36
4778 8993 4.147219 ACTCGCAAAGCATTTTACACTC 57.853 40.909 0.00 0.00 35.03 3.51
4820 9035 1.377856 GTTTCTCTCCCAGGCAGGC 60.378 63.158 0.00 0.00 35.39 4.85
4821 9036 1.484240 CTAGTTTCTCTCCCAGGCAGG 59.516 57.143 0.00 0.00 37.03 4.85
4895 9366 6.062258 ACCTCGGATTTATCCTTTTCTGAA 57.938 37.500 7.16 0.00 44.93 3.02
4896 9367 5.693769 ACCTCGGATTTATCCTTTTCTGA 57.306 39.130 7.16 0.00 44.93 3.27
4897 9368 6.346096 TGTACCTCGGATTTATCCTTTTCTG 58.654 40.000 7.16 0.00 44.93 3.02


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

AutoCloner maintained by Alex Coulton.