Multiple sequence alignment - TraesCS5A01G125500

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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 TraesCS5A01G125500 chr5A 100.000 8061 0 0 1 8061 275952130 275960190 0.000000e+00 14886.0
1 TraesCS5A01G125500 chr5A 92.569 794 53 4 7270 8061 680223177 680222388 0.000000e+00 1134.0
2 TraesCS5A01G125500 chr5B 96.415 2706 65 13 583 3271 226626345 226629035 0.000000e+00 4431.0
3 TraesCS5A01G125500 chr5B 92.926 2064 91 29 5241 7270 226630909 226632951 0.000000e+00 2952.0
4 TraesCS5A01G125500 chr5B 94.638 1865 54 12 3395 5242 226629033 226630868 0.000000e+00 2848.0
5 TraesCS5A01G125500 chr5B 91.231 593 38 4 1 591 226625185 226625765 0.000000e+00 795.0
6 TraesCS5A01G125500 chr5B 95.652 138 4 2 3264 3400 553351921 553352057 3.790000e-53 220.0
7 TraesCS5A01G125500 chr5B 97.778 45 0 1 5356 5400 226630994 226631037 8.670000e-10 76.8
8 TraesCS5A01G125500 chr5D 95.780 2678 72 16 599 3271 212559101 212561742 0.000000e+00 4281.0
9 TraesCS5A01G125500 chr5D 94.181 2028 77 21 5257 7270 212566738 212568738 0.000000e+00 3053.0
10 TraesCS5A01G125500 chr5D 95.610 1868 49 12 3395 5244 212561740 212563592 0.000000e+00 2964.0
11 TraesCS5A01G125500 chr5D 92.588 796 53 5 7270 8061 318337767 318336974 0.000000e+00 1138.0
12 TraesCS5A01G125500 chr5D 93.600 500 24 4 1 498 212547347 212547840 0.000000e+00 739.0
13 TraesCS5A01G125500 chr5D 95.556 135 5 1 3265 3399 381817914 381817781 1.760000e-51 215.0
14 TraesCS5A01G125500 chr5D 96.429 84 3 0 526 609 212547840 212547923 1.090000e-28 139.0
15 TraesCS5A01G125500 chr1B 93.711 795 46 3 7270 8061 683374129 683374922 0.000000e+00 1188.0
16 TraesCS5A01G125500 chr1B 92.588 796 51 7 7270 8061 324348657 324349448 0.000000e+00 1136.0
17 TraesCS5A01G125500 chr1B 95.652 138 5 1 3267 3404 676714821 676714685 3.790000e-53 220.0
18 TraesCS5A01G125500 chr1B 96.241 133 4 1 3267 3399 669583094 669582963 4.900000e-52 217.0
19 TraesCS5A01G125500 chr2D 92.625 800 55 3 7266 8061 432017091 432017890 0.000000e+00 1147.0
20 TraesCS5A01G125500 chr2A 92.821 794 54 2 7270 8061 673003422 673004214 0.000000e+00 1147.0
21 TraesCS5A01G125500 chrUn 92.491 799 55 4 7267 8061 30844544 30845341 0.000000e+00 1138.0
22 TraesCS5A01G125500 chr6A 92.588 796 53 5 7270 8061 44967004 44966211 0.000000e+00 1138.0
23 TraesCS5A01G125500 chr3D 92.443 794 56 3 7270 8061 422557213 422556422 0.000000e+00 1131.0
24 TraesCS5A01G125500 chr3D 95.556 135 5 1 3270 3404 84562610 84562743 1.760000e-51 215.0
25 TraesCS5A01G125500 chr6B 95.205 146 4 3 3253 3397 207510884 207511027 2.260000e-55 228.0
26 TraesCS5A01G125500 chr4B 96.241 133 5 0 3266 3398 68097401 68097533 1.360000e-52 219.0
27 TraesCS5A01G125500 chr4B 86.335 161 22 0 984 1144 132048224 132048384 8.310000e-40 176.0
28 TraesCS5A01G125500 chr4B 78.947 209 35 4 3451 3659 132050236 132050435 5.080000e-27 134.0
29 TraesCS5A01G125500 chr4B 79.874 159 27 5 2547 2703 132049709 132049864 2.380000e-20 111.0
30 TraesCS5A01G125500 chr2B 92.667 150 8 3 3270 3418 545760514 545760367 6.340000e-51 213.0
31 TraesCS5A01G125500 chr1A 93.056 144 8 2 3254 3397 530167093 530166952 8.200000e-50 209.0
32 TraesCS5A01G125500 chr1A 100.000 34 0 0 5454 5487 527957207 527957174 6.750000e-06 63.9
33 TraesCS5A01G125500 chr4D 76.724 348 60 15 984 1319 93604541 93604879 2.990000e-39 174.0
34 TraesCS5A01G125500 chr4D 78.947 209 35 4 3451 3659 93606377 93606576 5.080000e-27 134.0
35 TraesCS5A01G125500 chr4D 78.616 159 29 5 2547 2703 93605850 93606005 5.150000e-17 100.0
36 TraesCS5A01G125500 chr4A 85.093 161 24 0 984 1144 488257179 488257019 1.800000e-36 165.0
37 TraesCS5A01G125500 chr4A 88.991 109 12 0 3551 3659 488255253 488255145 1.410000e-27 135.0
38 TraesCS5A01G125500 chr4A 79.874 159 27 5 2547 2703 488255871 488255716 2.380000e-20 111.0


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 TraesCS5A01G125500 chr5A 275952130 275960190 8060 False 14886.000000 14886 100.000000 1 8061 1 chr5A.!!$F1 8060
1 TraesCS5A01G125500 chr5A 680222388 680223177 789 True 1134.000000 1134 92.569000 7270 8061 1 chr5A.!!$R1 791
2 TraesCS5A01G125500 chr5B 226625185 226632951 7766 False 2220.560000 4431 94.597600 1 7270 5 chr5B.!!$F2 7269
3 TraesCS5A01G125500 chr5D 212559101 212568738 9637 False 3432.666667 4281 95.190333 599 7270 3 chr5D.!!$F2 6671
4 TraesCS5A01G125500 chr5D 318336974 318337767 793 True 1138.000000 1138 92.588000 7270 8061 1 chr5D.!!$R1 791
5 TraesCS5A01G125500 chr5D 212547347 212547923 576 False 439.000000 739 95.014500 1 609 2 chr5D.!!$F1 608
6 TraesCS5A01G125500 chr1B 683374129 683374922 793 False 1188.000000 1188 93.711000 7270 8061 1 chr1B.!!$F2 791
7 TraesCS5A01G125500 chr1B 324348657 324349448 791 False 1136.000000 1136 92.588000 7270 8061 1 chr1B.!!$F1 791
8 TraesCS5A01G125500 chr2D 432017091 432017890 799 False 1147.000000 1147 92.625000 7266 8061 1 chr2D.!!$F1 795
9 TraesCS5A01G125500 chr2A 673003422 673004214 792 False 1147.000000 1147 92.821000 7270 8061 1 chr2A.!!$F1 791
10 TraesCS5A01G125500 chrUn 30844544 30845341 797 False 1138.000000 1138 92.491000 7267 8061 1 chrUn.!!$F1 794
11 TraesCS5A01G125500 chr6A 44966211 44967004 793 True 1138.000000 1138 92.588000 7270 8061 1 chr6A.!!$R1 791
12 TraesCS5A01G125500 chr3D 422556422 422557213 791 True 1131.000000 1131 92.443000 7270 8061 1 chr3D.!!$R1 791

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
521 524 0.112412 GCCTCCCTTTTGTCCCAGAA 59.888 55.000 0.00 0.00 0.00 3.02 F
712 1303 0.877071 GCGCCAATATGGATCCACAG 59.123 55.000 18.99 7.08 40.96 3.66 F
1465 2063 1.355916 CCGTAGAGGCGTAGAGTGC 59.644 63.158 0.00 0.00 0.00 4.40 F
3285 3893 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30 F
3286 3894 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46 F
5185 5840 0.460987 CATGGTGTCTCGCTTCCTCC 60.461 60.000 0.00 0.00 0.00 4.30 F
5218 5873 0.323451 GGCAAGATCCGGGTTTTCCT 60.323 55.000 0.00 0.00 40.46 3.36 F
5219 5874 1.064979 GGCAAGATCCGGGTTTTCCTA 60.065 52.381 0.00 0.00 40.46 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 2226 0.971386 CAGCTCCTTGCCAACCAAAT 59.029 50.000 0.00 0.0 44.23 2.32 R
2137 2739 1.003580 TCTTTCAGATGACCCACAGCC 59.996 52.381 0.00 0.0 35.25 4.85 R
3378 3986 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.0 44.66 3.13 R
5187 5842 1.541310 ATCTTGCCGAGGACGACCAA 61.541 55.000 6.71 0.0 42.66 3.67 R
5188 5843 1.945354 GATCTTGCCGAGGACGACCA 61.945 60.000 6.71 0.0 42.66 4.02 R
6511 10356 1.088340 CAGCTCCGACATGCAGGAAG 61.088 60.000 4.84 0.0 35.90 3.46 R
6835 10684 2.921221 AGAGGGAGAAATGACTGGGAA 58.079 47.619 0.00 0.0 0.00 3.97 R
7069 10921 3.195610 CAGGATTCCCTTTTTAACTGCCC 59.804 47.826 0.00 0.0 42.02 5.36 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
33 34 2.037772 TGAAGGACAGAAAGCAGAGGTC 59.962 50.000 0.00 0.00 0.00 3.85
64 65 2.079158 TGAGTAGCAGCTTTGCATCAC 58.921 47.619 0.00 0.00 37.25 3.06
100 102 2.205307 AGCGAAGGCGATACACTTAC 57.795 50.000 0.00 0.00 46.35 2.34
107 109 1.197910 GCGATACACTTACTCGGTGC 58.802 55.000 0.00 0.00 38.14 5.01
108 110 1.836383 CGATACACTTACTCGGTGCC 58.164 55.000 0.00 0.00 38.14 5.01
136 138 5.634439 GCAAATCATATGCAACTTCAACACA 59.366 36.000 0.00 0.00 43.29 3.72
165 167 5.648178 TCCTCATGGACAATGAAACAATG 57.352 39.130 0.00 0.00 44.77 2.82
189 191 3.018856 CAAGGCTATGGCATCAAGACAA 58.981 45.455 1.65 0.00 39.98 3.18
287 289 3.004734 CCCAAAGTGTTCCACATCAGAAC 59.995 47.826 0.00 0.00 43.20 3.01
315 317 8.859236 AATCAAATATCATAGTGCATAGCTGT 57.141 30.769 0.00 0.00 0.00 4.40
316 318 9.948964 AATCAAATATCATAGTGCATAGCTGTA 57.051 29.630 0.00 0.00 0.00 2.74
520 523 1.767692 GCCTCCCTTTTGTCCCAGA 59.232 57.895 0.00 0.00 0.00 3.86
521 524 0.112412 GCCTCCCTTTTGTCCCAGAA 59.888 55.000 0.00 0.00 0.00 3.02
522 525 1.480498 GCCTCCCTTTTGTCCCAGAAA 60.480 52.381 0.00 0.00 0.00 2.52
523 526 2.957474 CCTCCCTTTTGTCCCAGAAAA 58.043 47.619 0.00 0.00 0.00 2.29
524 527 3.304829 CCTCCCTTTTGTCCCAGAAAAA 58.695 45.455 0.00 0.00 0.00 1.94
705 1296 2.099652 CTCCTCCGCGCCAATATGGA 62.100 60.000 0.00 0.00 40.96 3.41
712 1303 0.877071 GCGCCAATATGGATCCACAG 59.123 55.000 18.99 7.08 40.96 3.66
853 1444 1.691823 CCTTCCCCAACCCTCTTCC 59.308 63.158 0.00 0.00 0.00 3.46
1385 1983 4.321745 CGTTTTTGAATTGAATGCTCTCCG 59.678 41.667 0.00 0.00 0.00 4.63
1412 2010 3.965539 GATGCTCTGGCCTGCGTGT 62.966 63.158 13.72 2.76 37.74 4.49
1465 2063 1.355916 CCGTAGAGGCGTAGAGTGC 59.644 63.158 0.00 0.00 0.00 4.40
1699 2300 2.545742 GCCGAATTTGTCTTGCTTTGGT 60.546 45.455 0.00 0.00 0.00 3.67
1721 2322 4.574674 ATTTGGAGGATGTGCTTGACTA 57.425 40.909 0.00 0.00 0.00 2.59
1752 2353 7.610305 TGGACTTGGACTTTCATTAATAAGGAC 59.390 37.037 3.61 0.00 0.00 3.85
1753 2354 7.067129 GGACTTGGACTTTCATTAATAAGGACC 59.933 40.741 3.61 6.34 0.00 4.46
1780 2381 4.518970 ACGTGCAGATTTTACATTTGGAGT 59.481 37.500 0.00 0.00 0.00 3.85
1845 2446 2.226437 CCATGCTGGTGTAGTTGTGAAC 59.774 50.000 0.00 0.00 31.35 3.18
2137 2739 2.627699 GGATCTGGAGAGCTACCTGAAG 59.372 54.545 17.94 6.17 38.47 3.02
2226 2828 5.560148 ACGATTTCTGAATGATGTAAACGC 58.440 37.500 0.00 0.00 0.00 4.84
2251 2853 8.507249 GCTCTCTTATCTAAGTCTTCTCTGATC 58.493 40.741 0.00 0.00 34.93 2.92
2252 2854 9.559732 CTCTCTTATCTAAGTCTTCTCTGATCA 57.440 37.037 0.00 0.00 34.93 2.92
2306 2908 2.621338 ACAGGTTGATGCATCTACACG 58.379 47.619 32.42 25.85 34.85 4.49
2342 2947 8.980481 ATCTTAACTGGTTGGTTCCTTATATG 57.020 34.615 0.00 0.00 0.00 1.78
2718 3324 2.159379 GCTTTGAGCTGGGGATTTAACG 60.159 50.000 0.00 0.00 38.45 3.18
2906 3512 5.766150 TTGGTCAACTTTCACTATGTTGG 57.234 39.130 0.00 0.00 40.48 3.77
2950 3557 9.833917 AAGAAAATTCCCTACTTACAGTATAGC 57.166 33.333 0.00 0.00 29.08 2.97
3127 3735 2.991190 GTCGTTCGGCATTAGAACTGAA 59.009 45.455 7.37 0.00 44.08 3.02
3151 3759 3.955650 TCGGAAACTGGGAGTAGAAAG 57.044 47.619 0.00 0.00 0.00 2.62
3217 3825 6.581171 AGAAGCTAAAATTGGAAAGTGGAG 57.419 37.500 0.00 0.00 0.00 3.86
3266 3874 6.407979 GGGCCCTTTTTCAAATATGCTTATGA 60.408 38.462 17.04 0.00 0.00 2.15
3268 3876 7.172019 GGCCCTTTTTCAAATATGCTTATGATG 59.828 37.037 0.00 0.00 0.00 3.07
3269 3877 7.712205 GCCCTTTTTCAAATATGCTTATGATGT 59.288 33.333 0.00 0.00 0.00 3.06
3275 3883 8.621532 TTCAAATATGCTTATGATGTACTCCC 57.378 34.615 0.00 0.00 0.00 4.30
3276 3884 7.977818 TCAAATATGCTTATGATGTACTCCCT 58.022 34.615 0.00 0.00 0.00 4.20
3277 3885 8.097038 TCAAATATGCTTATGATGTACTCCCTC 58.903 37.037 0.00 0.00 0.00 4.30
3278 3886 4.899352 ATGCTTATGATGTACTCCCTCC 57.101 45.455 0.00 0.00 0.00 4.30
3279 3887 2.628178 TGCTTATGATGTACTCCCTCCG 59.372 50.000 0.00 0.00 0.00 4.63
3280 3888 2.628657 GCTTATGATGTACTCCCTCCGT 59.371 50.000 0.00 0.00 0.00 4.69
3281 3889 3.305471 GCTTATGATGTACTCCCTCCGTC 60.305 52.174 0.00 0.00 0.00 4.79
3282 3890 1.705873 ATGATGTACTCCCTCCGTCC 58.294 55.000 0.00 0.00 0.00 4.79
3283 3891 0.750546 TGATGTACTCCCTCCGTCCG 60.751 60.000 0.00 0.00 0.00 4.79
3284 3892 0.465097 GATGTACTCCCTCCGTCCGA 60.465 60.000 0.00 0.00 0.00 4.55
3285 3893 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
3286 3894 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
3287 3895 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
3288 3896 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
3289 3897 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3290 3898 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3291 3899 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3292 3900 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
3293 3901 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3294 3902 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3295 3903 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3296 3904 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3297 3905 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3298 3906 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
3299 3907 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
3300 3908 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
3301 3909 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
3302 3910 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
3303 3911 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
3304 3912 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
3305 3913 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
3306 3914 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
3307 3915 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
3315 3923 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
3347 3955 9.939802 TCTAGAACTAATATACGTCTAGATGCA 57.060 33.333 12.04 0.00 32.48 3.96
3350 3958 8.679100 AGAACTAATATACGTCTAGATGCATCC 58.321 37.037 23.06 6.84 0.00 3.51
3351 3959 7.336161 ACTAATATACGTCTAGATGCATCCC 57.664 40.000 23.06 7.99 0.00 3.85
3352 3960 5.599999 AATATACGTCTAGATGCATCCCC 57.400 43.478 23.06 7.64 0.00 4.81
3353 3961 2.677542 TACGTCTAGATGCATCCCCT 57.322 50.000 23.06 7.62 0.00 4.79
3354 3962 1.794714 ACGTCTAGATGCATCCCCTT 58.205 50.000 23.06 7.24 0.00 3.95
3355 3963 2.119495 ACGTCTAGATGCATCCCCTTT 58.881 47.619 23.06 6.85 0.00 3.11
3356 3964 2.505819 ACGTCTAGATGCATCCCCTTTT 59.494 45.455 23.06 6.10 0.00 2.27
3357 3965 2.874701 CGTCTAGATGCATCCCCTTTTG 59.125 50.000 23.06 5.60 0.00 2.44
3358 3966 3.682718 CGTCTAGATGCATCCCCTTTTGT 60.683 47.826 23.06 4.58 0.00 2.83
3359 3967 4.273318 GTCTAGATGCATCCCCTTTTGTT 58.727 43.478 23.06 3.84 0.00 2.83
3360 3968 4.336713 GTCTAGATGCATCCCCTTTTGTTC 59.663 45.833 23.06 0.00 0.00 3.18
3361 3969 3.173953 AGATGCATCCCCTTTTGTTCA 57.826 42.857 23.06 0.00 0.00 3.18
3362 3970 3.716431 AGATGCATCCCCTTTTGTTCAT 58.284 40.909 23.06 0.00 0.00 2.57
3363 3971 4.098894 AGATGCATCCCCTTTTGTTCATT 58.901 39.130 23.06 0.00 0.00 2.57
3364 3972 4.533311 AGATGCATCCCCTTTTGTTCATTT 59.467 37.500 23.06 0.00 0.00 2.32
3365 3973 4.703379 TGCATCCCCTTTTGTTCATTTT 57.297 36.364 0.00 0.00 0.00 1.82
3366 3974 4.387598 TGCATCCCCTTTTGTTCATTTTG 58.612 39.130 0.00 0.00 0.00 2.44
3367 3975 4.102210 TGCATCCCCTTTTGTTCATTTTGA 59.898 37.500 0.00 0.00 0.00 2.69
3368 3976 5.221884 TGCATCCCCTTTTGTTCATTTTGAT 60.222 36.000 0.00 0.00 0.00 2.57
3369 3977 5.122711 GCATCCCCTTTTGTTCATTTTGATG 59.877 40.000 0.00 0.00 0.00 3.07
3370 3978 6.465948 CATCCCCTTTTGTTCATTTTGATGA 58.534 36.000 0.00 0.00 0.00 2.92
3371 3979 5.852827 TCCCCTTTTGTTCATTTTGATGAC 58.147 37.500 0.00 0.00 0.00 3.06
3372 3980 5.365025 TCCCCTTTTGTTCATTTTGATGACA 59.635 36.000 0.00 0.00 0.00 3.58
3373 3981 6.054295 CCCCTTTTGTTCATTTTGATGACAA 58.946 36.000 0.00 0.00 0.00 3.18
3374 3982 6.203338 CCCCTTTTGTTCATTTTGATGACAAG 59.797 38.462 0.00 0.00 37.32 3.16
3375 3983 6.762661 CCCTTTTGTTCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.32 3.16
3376 3984 7.925483 CCCTTTTGTTCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.32 2.24
3377 3985 9.480053 CCTTTTGTTCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.32 2.12
3382 3990 9.474920 TGTTCATTTTGATGACAAGTATTTTCC 57.525 29.630 0.00 0.00 37.32 3.13
3383 3991 8.638565 GTTCATTTTGATGACAAGTATTTTCCG 58.361 33.333 0.00 0.00 37.32 4.30
3384 3992 7.312154 TCATTTTGATGACAAGTATTTTCCGG 58.688 34.615 0.00 0.00 37.32 5.14
3385 3993 6.885952 TTTTGATGACAAGTATTTTCCGGA 57.114 33.333 0.00 0.00 37.32 5.14
3386 3994 5.873179 TTGATGACAAGTATTTTCCGGAC 57.127 39.130 1.83 0.00 0.00 4.79
3387 3995 3.930229 TGATGACAAGTATTTTCCGGACG 59.070 43.478 1.83 0.00 0.00 4.79
3388 3996 2.690786 TGACAAGTATTTTCCGGACGG 58.309 47.619 1.83 3.96 0.00 4.79
3389 3997 2.299582 TGACAAGTATTTTCCGGACGGA 59.700 45.455 1.83 9.76 43.52 4.69
3390 3998 2.928116 GACAAGTATTTTCCGGACGGAG 59.072 50.000 13.64 2.43 46.06 4.63
3391 3999 2.277084 CAAGTATTTTCCGGACGGAGG 58.723 52.381 13.64 0.00 46.06 4.30
3392 4000 0.828677 AGTATTTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3393 4001 0.826062 GTATTTTCCGGACGGAGGGA 59.174 55.000 13.64 4.60 46.06 4.20
3419 4027 4.575885 TGTGCTTAGACATCCAACTAACC 58.424 43.478 0.00 0.00 0.00 2.85
3449 4057 4.908601 TTCAATAGGTGAAGCTCCTTGA 57.091 40.909 0.00 0.00 41.47 3.02
3515 4123 5.756195 TTCAACAAGGATCAGTGTTTCAG 57.244 39.130 9.81 1.84 35.81 3.02
3874 4483 2.682352 TGTGACCATGTTGATATTGGCG 59.318 45.455 0.00 0.00 33.66 5.69
3875 4484 2.942376 GTGACCATGTTGATATTGGCGA 59.058 45.455 0.00 0.00 33.66 5.54
3876 4485 2.942376 TGACCATGTTGATATTGGCGAC 59.058 45.455 0.00 0.00 33.66 5.19
3877 4486 3.206150 GACCATGTTGATATTGGCGACT 58.794 45.455 0.00 0.00 33.66 4.18
3878 4487 4.141824 TGACCATGTTGATATTGGCGACTA 60.142 41.667 0.00 0.00 33.66 2.59
3879 4488 4.973168 ACCATGTTGATATTGGCGACTAT 58.027 39.130 0.00 0.00 33.66 2.12
3880 4489 4.756642 ACCATGTTGATATTGGCGACTATG 59.243 41.667 0.00 0.00 33.66 2.23
3947 4556 9.020813 GGTTGAAGTAATTTTTCAAGACAGTTC 57.979 33.333 14.51 0.62 43.11 3.01
4218 4827 6.770785 TGTTAACCAATATAGGGTCAATCAGC 59.229 38.462 2.48 0.00 37.77 4.26
4224 4834 5.848286 ATATAGGGTCAATCAGCATGGAA 57.152 39.130 0.00 0.00 36.16 3.53
4232 4842 6.268566 GGTCAATCAGCATGGAATTTTACTC 58.731 40.000 0.00 0.00 36.16 2.59
4272 4882 8.306313 TGTATGGTCTCTCTTGTGTGTATTAT 57.694 34.615 0.00 0.00 0.00 1.28
4286 4896 6.539103 TGTGTGTATTATTTGCGTTAGCCATA 59.461 34.615 0.00 0.00 44.33 2.74
4482 5092 8.072567 GGAGCTTGTCATATACATCAATGTTTC 58.927 37.037 0.20 0.00 41.97 2.78
4525 5135 7.613801 TGTCTAGGCACCACATGTATTTATTTT 59.386 33.333 0.00 0.00 0.00 1.82
4571 5198 8.786826 TGTTGTTCAACTATAATTACAGGGAG 57.213 34.615 15.18 0.00 0.00 4.30
4572 5199 8.380099 TGTTGTTCAACTATAATTACAGGGAGT 58.620 33.333 15.18 0.00 0.00 3.85
4573 5200 9.880157 GTTGTTCAACTATAATTACAGGGAGTA 57.120 33.333 8.23 0.00 0.00 2.59
4676 5307 4.330074 GTGCGCTATTGACAGTTATCAGTT 59.670 41.667 9.73 0.00 0.00 3.16
4735 5366 6.214615 TGGAAGTGATACTGAATCCCAACTTA 59.785 38.462 0.00 0.00 31.76 2.24
4782 5413 4.009370 AGCCCTTCAGAACAACTTAGAC 57.991 45.455 0.00 0.00 0.00 2.59
4917 5548 6.010850 TCTACACTATCTTGTCCAGACAGTT 58.989 40.000 0.09 0.00 35.57 3.16
4995 5626 3.900966 TGGTGATGACTGGATTCAGAG 57.099 47.619 8.39 0.00 43.49 3.35
5077 5708 2.818921 AGTGCTTCAGATCTGGAGACT 58.181 47.619 31.70 25.61 38.49 3.24
5185 5840 0.460987 CATGGTGTCTCGCTTCCTCC 60.461 60.000 0.00 0.00 0.00 4.30
5186 5841 1.617947 ATGGTGTCTCGCTTCCTCCC 61.618 60.000 0.00 0.00 0.00 4.30
5187 5842 1.985116 GGTGTCTCGCTTCCTCCCT 60.985 63.158 0.00 0.00 0.00 4.20
5188 5843 1.545706 GGTGTCTCGCTTCCTCCCTT 61.546 60.000 0.00 0.00 0.00 3.95
5218 5873 0.323451 GGCAAGATCCGGGTTTTCCT 60.323 55.000 0.00 0.00 40.46 3.36
5219 5874 1.064979 GGCAAGATCCGGGTTTTCCTA 60.065 52.381 0.00 0.00 40.46 2.94
5229 5884 2.548493 CGGGTTTTCCTAGTCGGTTCAA 60.548 50.000 0.00 0.00 40.46 2.69
5293 9081 2.746277 CCCTCGTGGCCTTTTCCG 60.746 66.667 3.32 0.00 0.00 4.30
5332 9120 4.736896 GGTCTGACGGTGTCGGGC 62.737 72.222 5.97 3.96 42.20 6.13
5333 9121 3.681835 GTCTGACGGTGTCGGGCT 61.682 66.667 3.21 0.00 40.06 5.19
5334 9122 3.680786 TCTGACGGTGTCGGGCTG 61.681 66.667 5.97 0.00 39.23 4.85
5335 9123 4.742201 CTGACGGTGTCGGGCTGG 62.742 72.222 0.00 0.00 41.39 4.85
5355 9143 3.064324 GCCTTGGCGCTTGGTGAT 61.064 61.111 7.64 0.00 0.00 3.06
5356 9144 2.879907 CCTTGGCGCTTGGTGATG 59.120 61.111 7.64 0.00 0.00 3.07
5357 9145 1.973281 CCTTGGCGCTTGGTGATGT 60.973 57.895 7.64 0.00 0.00 3.06
5358 9146 1.503542 CTTGGCGCTTGGTGATGTC 59.496 57.895 7.64 0.00 0.00 3.06
5359 9147 2.244436 CTTGGCGCTTGGTGATGTCG 62.244 60.000 7.64 0.00 0.00 4.35
5360 9148 2.742372 GGCGCTTGGTGATGTCGT 60.742 61.111 7.64 0.00 0.00 4.34
5361 9149 2.476051 GCGCTTGGTGATGTCGTG 59.524 61.111 0.00 0.00 0.00 4.35
5362 9150 2.476051 CGCTTGGTGATGTCGTGC 59.524 61.111 0.00 0.00 0.00 5.34
5409 9247 2.258726 GCCTGTGGTGGTTTCGTCC 61.259 63.158 0.00 0.00 0.00 4.79
5419 9257 2.662527 TTTCGTCCGTTCGGTGCC 60.663 61.111 11.04 0.62 0.00 5.01
5494 9332 4.286297 TGTAGCTTGCTAATGTTCAGGT 57.714 40.909 3.72 0.00 0.00 4.00
5539 9383 6.657117 TCTTGCCTTGTTATGTATTGCTGTTA 59.343 34.615 0.00 0.00 0.00 2.41
5572 9416 4.283212 TGGGATTTGTTTTGGTCATCTTCC 59.717 41.667 0.00 0.00 0.00 3.46
5596 9440 3.840831 TGGATTGCCAAGTCTCGAG 57.159 52.632 5.93 5.93 42.49 4.04
5598 9442 2.176045 TGGATTGCCAAGTCTCGAGTA 58.824 47.619 13.13 0.00 42.49 2.59
5670 9514 3.821841 CCTTTCTTTGGCGTTGTATCAC 58.178 45.455 0.00 0.00 0.00 3.06
5792 9636 7.658525 ATGTTATTTTGCCCTGACAATGATA 57.341 32.000 0.00 0.00 0.00 2.15
6020 9865 5.292101 GGTGATTGATTCCGTTTACTCTGAG 59.708 44.000 2.45 2.45 0.00 3.35
6031 9876 6.925165 TCCGTTTACTCTGAGTTCGTTATTTT 59.075 34.615 16.53 0.00 0.00 1.82
6045 9890 5.790593 TCGTTATTTTAGGCTGTTCAGACT 58.209 37.500 12.96 12.96 0.00 3.24
6165 10010 4.261825 GCCATGGTAGCTTGTTGTGTTAAA 60.262 41.667 14.67 0.00 0.00 1.52
6257 10102 8.836268 TTTCAATATGCAATTTGAAGAGCTTT 57.164 26.923 20.16 0.00 41.42 3.51
6364 10209 4.084693 GCCTATATGTCCTTCGTTAAACGC 60.085 45.833 0.00 0.00 42.21 4.84
6496 10341 2.093106 GTAGGAAAGAGAGGTGCGAGA 58.907 52.381 0.00 0.00 0.00 4.04
6511 10356 7.815068 AGAGGTGCGAGAATATTGTATGTTATC 59.185 37.037 0.00 0.00 0.00 1.75
6607 10453 4.830826 AACAAAGAAAGAAACCCTAGCG 57.169 40.909 0.00 0.00 0.00 4.26
6643 10489 1.221021 GACCCCAGAACCTTAGCCG 59.779 63.158 0.00 0.00 0.00 5.52
6656 10502 6.492429 AGAACCTTAGCCGTGTATATGATACA 59.508 38.462 0.00 0.00 0.00 2.29
6658 10504 7.949690 ACCTTAGCCGTGTATATGATACATA 57.050 36.000 2.81 0.00 0.00 2.29
6693 10542 5.495640 TCAAAATGGAGGCAAAAGTTTTGT 58.504 33.333 25.20 10.17 37.63 2.83
6781 10630 4.524802 TCCATTTTCCCATCTGCTACAT 57.475 40.909 0.00 0.00 0.00 2.29
6835 10684 1.315257 GCAGCCCAATCATCGTTGGT 61.315 55.000 5.09 0.00 45.78 3.67
6972 10824 6.219417 TGTTGAAAATGAAAAGAAGCCTCA 57.781 33.333 0.00 0.00 0.00 3.86
7069 10921 0.613777 AGAAGAAGTAAGCACCGGGG 59.386 55.000 6.32 0.84 0.00 5.73
7095 10947 5.163612 GCAGTTAAAAAGGGAATCCTGCTAG 60.164 44.000 0.00 0.00 44.07 3.42
7230 11082 7.872138 ACATCCCAGAGAGGATAATACAAAAA 58.128 34.615 0.00 0.00 45.21 1.94
7316 11168 9.760077 ACTACGAGATTTAATCCGAATAAACAT 57.240 29.630 17.75 1.84 0.00 2.71
7391 11243 7.733969 AGCATAGTAGATGAACAGATCACATT 58.266 34.615 0.00 0.00 41.93 2.71
7437 11289 2.981898 TCTACCACGATCTCGAACAGA 58.018 47.619 6.60 1.06 43.02 3.41
7448 11300 6.127703 ACGATCTCGAACAGAAAGGATAGAAA 60.128 38.462 6.60 0.00 43.02 2.52
7455 11307 8.258007 TCGAACAGAAAGGATAGAAACACATAT 58.742 33.333 0.00 0.00 0.00 1.78
7579 11431 2.355126 CAGCAGTCGCGTGAGTGT 60.355 61.111 29.09 16.42 45.59 3.55
7598 11450 1.970640 GTGCTCCCCAAAAACCTGATT 59.029 47.619 0.00 0.00 0.00 2.57
7603 11455 1.351076 CCCAAAAACCTGATTGCCCT 58.649 50.000 0.00 0.00 0.00 5.19
7635 11487 2.240162 GATCACGAGAGGCGGGGTTT 62.240 60.000 0.00 0.00 45.52 3.27
7650 11502 1.600916 GTTTCGGAGGCCTGCTGTT 60.601 57.895 23.05 0.00 0.00 3.16
7652 11504 3.589654 TTCGGAGGCCTGCTGTTCG 62.590 63.158 23.05 6.21 0.00 3.95
7660 11512 1.371183 CCTGCTGTTCGTTCTCCCA 59.629 57.895 0.00 0.00 0.00 4.37
7669 11521 2.031163 GTTCTCCCAGTGCACGCT 59.969 61.111 12.01 0.00 0.00 5.07
7690 11542 3.715834 CTGAAAGGAGGGATGGAGAAGAT 59.284 47.826 0.00 0.00 0.00 2.40
7699 11551 3.359950 GGATGGAGAAGATTTGCTTGGT 58.640 45.455 0.00 0.00 36.83 3.67
7815 11667 3.471354 GGGAGTAAACCCCATGTCG 57.529 57.895 0.00 0.00 43.81 4.35
7863 11715 4.083908 GGAAACGGTTCAGTAATTAACGCA 60.084 41.667 16.38 0.00 35.25 5.24
7923 11776 6.210385 TCCCAAGCAGCAAAAATATAGACAAA 59.790 34.615 0.00 0.00 0.00 2.83
7941 11794 3.244700 ACAAAGTGCATAGCTCTGTCCTT 60.245 43.478 0.00 0.00 32.56 3.36
7951 11804 1.304962 TCTGTCCTTGGCTCGGCTA 60.305 57.895 0.00 0.00 0.00 3.93
8014 11880 0.251209 AGGAGCACGTGTAGGTCTCA 60.251 55.000 18.38 0.00 34.14 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.037772 GACCTCTGCTTTCTGTCCTTCA 59.962 50.000 0.00 0.00 0.00 3.02
33 34 5.114785 AGCTGCTACTCACTGATATAACG 57.885 43.478 0.00 0.00 0.00 3.18
64 65 5.221048 CCTTCGCTTTATCATTTAAGGGTGG 60.221 44.000 0.00 0.00 36.19 4.61
126 128 5.304686 TGAGGAAGGTTATGTGTTGAAGT 57.695 39.130 0.00 0.00 0.00 3.01
189 191 7.739444 TCCCAGTGTCCTATATTGGATCTTATT 59.261 37.037 9.20 0.00 38.52 1.40
287 289 9.163899 AGCTATGCACTATGATATTTGATTCTG 57.836 33.333 0.00 0.00 0.00 3.02
315 317 0.253160 AGATGGTGGGCTTCCTGGTA 60.253 55.000 0.00 0.00 0.00 3.25
316 318 0.253160 TAGATGGTGGGCTTCCTGGT 60.253 55.000 0.00 0.00 0.00 4.00
698 1289 3.434167 GGTCTGTGCTGTGGATCCATATT 60.434 47.826 19.62 0.00 0.00 1.28
705 1296 2.665000 CCGGTCTGTGCTGTGGAT 59.335 61.111 0.00 0.00 0.00 3.41
712 1303 3.825160 TTGGTCTGCCGGTCTGTGC 62.825 63.158 1.90 0.00 37.67 4.57
853 1444 3.819188 GGGAATGCTGCCGAGAAG 58.181 61.111 0.00 0.00 0.00 2.85
1385 1983 1.086634 GCCAGAGCATCGTTGAGGAC 61.087 60.000 0.00 0.00 42.67 3.85
1626 2226 0.971386 CAGCTCCTTGCCAACCAAAT 59.029 50.000 0.00 0.00 44.23 2.32
1662 2262 2.439104 GGCGCTCTCAATCCCCTCT 61.439 63.158 7.64 0.00 0.00 3.69
1699 2300 4.574674 AGTCAAGCACATCCTCCAAATA 57.425 40.909 0.00 0.00 0.00 1.40
1721 2322 7.654022 TTAATGAAAGTCCAAGTCCAAAACT 57.346 32.000 0.00 0.00 41.10 2.66
1752 2353 2.339418 TGTAAAATCTGCACGTACCGG 58.661 47.619 0.00 0.00 0.00 5.28
1753 2354 4.593597 AATGTAAAATCTGCACGTACCG 57.406 40.909 0.00 0.00 0.00 4.02
1780 2381 9.890629 ATCTATTATCTATGCGCCTTTAATCAA 57.109 29.630 4.18 0.00 0.00 2.57
1845 2446 6.437928 TGCTAGTAAACAAGAACAAATGCAG 58.562 36.000 0.00 0.00 0.00 4.41
2037 2639 8.329203 TGCAAATAAAAGTTCCAAACAAAGTT 57.671 26.923 0.00 0.00 0.00 2.66
2137 2739 1.003580 TCTTTCAGATGACCCACAGCC 59.996 52.381 0.00 0.00 35.25 4.85
2226 2828 9.559732 TGATCAGAGAAGACTTAGATAAGAGAG 57.440 37.037 6.61 0.00 37.08 3.20
2251 2853 3.441572 ACCGCTTGAATTCTTCCTCAATG 59.558 43.478 7.05 0.00 31.40 2.82
2252 2854 3.690460 ACCGCTTGAATTCTTCCTCAAT 58.310 40.909 7.05 0.00 31.40 2.57
2277 2879 2.741517 TGCATCAACCTGTATGTTGTCG 59.258 45.455 4.07 0.00 44.66 4.35
2306 2908 6.587608 CCAACCAGTTAAGATTTCAGAAATGC 59.412 38.462 13.38 5.37 0.00 3.56
2342 2947 3.503748 ACAGCAATTGTTCCTCTAGCAAC 59.496 43.478 7.40 0.00 36.31 4.17
2950 3557 8.993121 CCAATAAGTATGGCAGAGTAATGTAAG 58.007 37.037 0.00 0.00 0.00 2.34
3127 3735 3.709587 TCTACTCCCAGTTTCCGAAGAT 58.290 45.455 0.00 0.00 0.00 2.40
3151 3759 9.601217 TTCTTTCTACATCATCTTTACTAAGCC 57.399 33.333 0.00 0.00 0.00 4.35
3266 3874 0.033796 TTCGGACGGAGGGAGTACAT 60.034 55.000 0.00 0.00 0.00 2.29
3268 3876 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
3269 3877 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
3270 3878 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
3271 3879 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
3272 3880 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
3273 3881 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3274 3882 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3275 3883 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3276 3884 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3277 3885 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
3278 3886 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
3279 3887 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
3280 3888 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
3281 3889 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
3282 3890 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
3289 3897 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
3321 3929 9.939802 TGCATCTAGACGTATATTAGTTCTAGA 57.060 33.333 8.64 8.64 38.94 2.43
3324 3932 8.679100 GGATGCATCTAGACGTATATTAGTTCT 58.321 37.037 25.28 0.00 0.00 3.01
3325 3933 7.916450 GGGATGCATCTAGACGTATATTAGTTC 59.084 40.741 25.28 2.81 0.00 3.01
3326 3934 7.147880 GGGGATGCATCTAGACGTATATTAGTT 60.148 40.741 25.28 0.00 0.00 2.24
3327 3935 6.321690 GGGGATGCATCTAGACGTATATTAGT 59.678 42.308 25.28 0.00 0.00 2.24
3328 3936 6.547880 AGGGGATGCATCTAGACGTATATTAG 59.452 42.308 25.28 0.00 0.00 1.73
3329 3937 6.432581 AGGGGATGCATCTAGACGTATATTA 58.567 40.000 25.28 0.00 0.00 0.98
3330 3938 5.273208 AGGGGATGCATCTAGACGTATATT 58.727 41.667 25.28 0.00 0.00 1.28
3331 3939 4.873010 AGGGGATGCATCTAGACGTATAT 58.127 43.478 25.28 0.00 0.00 0.86
3332 3940 4.317530 AGGGGATGCATCTAGACGTATA 57.682 45.455 25.28 0.00 0.00 1.47
3333 3941 3.176924 AGGGGATGCATCTAGACGTAT 57.823 47.619 25.28 0.00 0.00 3.06
3334 3942 2.677542 AGGGGATGCATCTAGACGTA 57.322 50.000 25.28 0.00 0.00 3.57
3335 3943 1.794714 AAGGGGATGCATCTAGACGT 58.205 50.000 25.28 12.28 0.00 4.34
3336 3944 2.874701 CAAAAGGGGATGCATCTAGACG 59.125 50.000 25.28 5.79 0.00 4.18
3337 3945 3.891049 ACAAAAGGGGATGCATCTAGAC 58.109 45.455 25.28 13.29 0.00 2.59
3338 3946 4.018506 TGAACAAAAGGGGATGCATCTAGA 60.019 41.667 25.28 0.00 0.00 2.43
3339 3947 4.272489 TGAACAAAAGGGGATGCATCTAG 58.728 43.478 25.28 10.37 0.00 2.43
3340 3948 4.314522 TGAACAAAAGGGGATGCATCTA 57.685 40.909 25.28 0.00 0.00 1.98
3341 3949 3.173953 TGAACAAAAGGGGATGCATCT 57.826 42.857 25.28 3.74 0.00 2.90
3342 3950 4.476628 AATGAACAAAAGGGGATGCATC 57.523 40.909 18.81 18.81 0.00 3.91
3343 3951 4.914177 AAATGAACAAAAGGGGATGCAT 57.086 36.364 0.00 0.00 0.00 3.96
3344 3952 4.102210 TCAAAATGAACAAAAGGGGATGCA 59.898 37.500 0.00 0.00 0.00 3.96
3345 3953 4.640364 TCAAAATGAACAAAAGGGGATGC 58.360 39.130 0.00 0.00 0.00 3.91
3346 3954 6.369615 GTCATCAAAATGAACAAAAGGGGATG 59.630 38.462 0.00 0.00 43.42 3.51
3347 3955 6.043012 TGTCATCAAAATGAACAAAAGGGGAT 59.957 34.615 0.00 0.00 43.42 3.85
3348 3956 5.365025 TGTCATCAAAATGAACAAAAGGGGA 59.635 36.000 0.00 0.00 43.42 4.81
3349 3957 5.609423 TGTCATCAAAATGAACAAAAGGGG 58.391 37.500 0.00 0.00 43.42 4.79
3350 3958 6.762661 ACTTGTCATCAAAATGAACAAAAGGG 59.237 34.615 0.87 0.00 43.42 3.95
3351 3959 7.775397 ACTTGTCATCAAAATGAACAAAAGG 57.225 32.000 0.87 0.00 43.42 3.11
3356 3964 9.474920 GGAAAATACTTGTCATCAAAATGAACA 57.525 29.630 0.00 0.00 43.42 3.18
3357 3965 8.638565 CGGAAAATACTTGTCATCAAAATGAAC 58.361 33.333 0.00 0.00 43.42 3.18
3358 3966 7.812191 CCGGAAAATACTTGTCATCAAAATGAA 59.188 33.333 0.00 0.00 43.42 2.57
3359 3967 7.175816 TCCGGAAAATACTTGTCATCAAAATGA 59.824 33.333 0.00 0.00 39.63 2.57
3360 3968 7.273381 GTCCGGAAAATACTTGTCATCAAAATG 59.727 37.037 5.23 0.00 32.87 2.32
3361 3969 7.312899 GTCCGGAAAATACTTGTCATCAAAAT 58.687 34.615 5.23 0.00 32.87 1.82
3362 3970 6.566942 CGTCCGGAAAATACTTGTCATCAAAA 60.567 38.462 5.23 0.00 32.87 2.44
3363 3971 5.106869 CGTCCGGAAAATACTTGTCATCAAA 60.107 40.000 5.23 0.00 32.87 2.69
3364 3972 4.390603 CGTCCGGAAAATACTTGTCATCAA 59.609 41.667 5.23 0.00 0.00 2.57
3365 3973 3.930229 CGTCCGGAAAATACTTGTCATCA 59.070 43.478 5.23 0.00 0.00 3.07
3366 3974 3.308866 CCGTCCGGAAAATACTTGTCATC 59.691 47.826 5.23 0.00 37.50 2.92
3367 3975 3.055675 TCCGTCCGGAAAATACTTGTCAT 60.056 43.478 5.23 0.00 42.05 3.06
3368 3976 2.299582 TCCGTCCGGAAAATACTTGTCA 59.700 45.455 5.23 0.00 42.05 3.58
3369 3977 2.928116 CTCCGTCCGGAAAATACTTGTC 59.072 50.000 5.23 0.00 44.66 3.18
3370 3978 2.354403 CCTCCGTCCGGAAAATACTTGT 60.354 50.000 5.23 0.00 44.66 3.16
3371 3979 2.277084 CCTCCGTCCGGAAAATACTTG 58.723 52.381 5.23 0.00 44.66 3.16
3372 3980 1.208776 CCCTCCGTCCGGAAAATACTT 59.791 52.381 5.23 0.00 44.66 2.24
3373 3981 0.828677 CCCTCCGTCCGGAAAATACT 59.171 55.000 5.23 0.00 44.66 2.12
3374 3982 0.826062 TCCCTCCGTCCGGAAAATAC 59.174 55.000 5.23 0.00 44.66 1.89
3375 3983 1.117150 CTCCCTCCGTCCGGAAAATA 58.883 55.000 5.23 0.00 44.66 1.40
3376 3984 0.908180 ACTCCCTCCGTCCGGAAAAT 60.908 55.000 5.23 0.00 44.66 1.82
3377 3985 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
3378 3986 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3379 3987 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
3380 3988 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
3381 3989 1.455217 ACATACTCCCTCCGTCCGG 60.455 63.158 0.00 0.00 0.00 5.14
3382 3990 1.734137 CACATACTCCCTCCGTCCG 59.266 63.158 0.00 0.00 0.00 4.79
3383 3991 1.043673 AGCACATACTCCCTCCGTCC 61.044 60.000 0.00 0.00 0.00 4.79
3384 3992 0.824759 AAGCACATACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
3385 3993 2.032620 CTAAGCACATACTCCCTCCGT 58.967 52.381 0.00 0.00 0.00 4.69
3386 3994 2.034812 GTCTAAGCACATACTCCCTCCG 59.965 54.545 0.00 0.00 0.00 4.63
3387 3995 3.031736 TGTCTAAGCACATACTCCCTCC 58.968 50.000 0.00 0.00 0.00 4.30
3388 3996 4.262249 GGATGTCTAAGCACATACTCCCTC 60.262 50.000 0.00 0.00 37.11 4.30
3389 3997 3.643792 GGATGTCTAAGCACATACTCCCT 59.356 47.826 0.00 0.00 37.11 4.20
3390 3998 3.388024 TGGATGTCTAAGCACATACTCCC 59.612 47.826 0.00 0.00 38.33 4.30
3391 3999 4.672587 TGGATGTCTAAGCACATACTCC 57.327 45.455 0.00 0.00 38.33 3.85
3392 4000 5.665459 AGTTGGATGTCTAAGCACATACTC 58.335 41.667 0.00 0.00 38.33 2.59
3393 4001 5.683876 AGTTGGATGTCTAAGCACATACT 57.316 39.130 0.00 0.00 38.33 2.12
3449 4057 6.980593 TCATCACAAATTTTTCGTTCTCCAT 58.019 32.000 0.00 0.00 0.00 3.41
3515 4123 0.108585 TCCAGTTCCTGCCAGTTCAC 59.891 55.000 0.00 0.00 0.00 3.18
3538 4146 4.752101 GCTGAGAAGAGTTTTAGCAACAGA 59.248 41.667 0.00 0.00 0.00 3.41
3741 4349 6.313905 GCTAGAAATGTTGCGTATATATGGCT 59.686 38.462 4.14 0.00 0.00 4.75
3862 4471 5.295787 TGTTTCCATAGTCGCCAATATCAAC 59.704 40.000 0.00 0.00 0.00 3.18
3863 4472 5.432645 TGTTTCCATAGTCGCCAATATCAA 58.567 37.500 0.00 0.00 0.00 2.57
3874 4483 3.617263 CAGGCGTTACTGTTTCCATAGTC 59.383 47.826 0.00 0.00 33.81 2.59
3875 4484 3.596214 CAGGCGTTACTGTTTCCATAGT 58.404 45.455 0.00 0.00 33.81 2.12
3876 4485 2.351726 GCAGGCGTTACTGTTTCCATAG 59.648 50.000 5.94 0.00 40.59 2.23
3877 4486 2.352388 GCAGGCGTTACTGTTTCCATA 58.648 47.619 5.94 0.00 40.59 2.74
3878 4487 1.165270 GCAGGCGTTACTGTTTCCAT 58.835 50.000 5.94 0.00 40.59 3.41
3879 4488 0.887387 GGCAGGCGTTACTGTTTCCA 60.887 55.000 5.94 0.00 40.59 3.53
3880 4489 0.605589 AGGCAGGCGTTACTGTTTCC 60.606 55.000 5.94 0.35 40.59 3.13
3947 4556 1.279152 CTCACGCATCTCAGAGCAAG 58.721 55.000 0.00 0.00 0.00 4.01
3954 4563 2.125391 GCAGCCTCACGCATCTCA 60.125 61.111 0.00 0.00 41.38 3.27
4044 4653 6.335471 TGGACGTTAGTCTTTGAAGTATCA 57.665 37.500 0.00 0.00 46.29 2.15
4200 4809 5.563592 TCCATGCTGATTGACCCTATATTG 58.436 41.667 0.00 0.00 0.00 1.90
4232 4842 9.442047 AGAGACCATACATCTCAAAAGTTAAAG 57.558 33.333 4.92 0.00 44.34 1.85
4272 4882 3.127895 GGACAACATATGGCTAACGCAAA 59.872 43.478 7.80 0.00 37.17 3.68
4286 4896 6.819284 ACAAAATGTGAATTCAGGACAACAT 58.181 32.000 8.80 4.79 0.00 2.71
4482 5092 3.412386 AGACACGGAAAGAAGAAATGGG 58.588 45.455 0.00 0.00 0.00 4.00
4630 5258 3.976793 ATCAGTTAGCATGCCATTTCG 57.023 42.857 15.66 0.00 0.00 3.46
4735 5366 7.264221 TGCATTATCTTTGTCAAAACAACTGT 58.736 30.769 0.00 0.00 44.90 3.55
4782 5413 4.081309 TCCTTGTACTGGTTAGATTTCCCG 60.081 45.833 0.00 0.00 0.00 5.14
4935 5566 6.064060 TCTGACCTTGTGATGAGACAAAAAT 58.936 36.000 0.00 0.00 35.44 1.82
4954 5585 5.415415 CAAGTATATGCTTGGCTTCTGAC 57.585 43.478 21.93 0.00 41.41 3.51
4995 5626 4.041740 TGCTGTACAATCCTACGATGTC 57.958 45.455 0.00 0.00 0.00 3.06
5185 5840 3.234630 TTGCCGAGGACGACCAAGG 62.235 63.158 6.71 9.81 42.66 3.61
5186 5841 1.738099 CTTGCCGAGGACGACCAAG 60.738 63.158 6.71 0.00 42.66 3.61
5187 5842 1.541310 ATCTTGCCGAGGACGACCAA 61.541 55.000 6.71 0.00 42.66 3.67
5188 5843 1.945354 GATCTTGCCGAGGACGACCA 61.945 60.000 6.71 0.00 42.66 4.02
5338 9126 3.064324 ATCACCAAGCGCCAAGGC 61.064 61.111 2.29 0.00 37.85 4.35
5339 9127 1.926511 GACATCACCAAGCGCCAAGG 61.927 60.000 2.29 6.26 0.00 3.61
5340 9128 1.503542 GACATCACCAAGCGCCAAG 59.496 57.895 2.29 0.00 0.00 3.61
5341 9129 2.324330 CGACATCACCAAGCGCCAA 61.324 57.895 2.29 0.00 0.00 4.52
5342 9130 2.741985 CGACATCACCAAGCGCCA 60.742 61.111 2.29 0.00 0.00 5.69
5343 9131 2.742372 ACGACATCACCAAGCGCC 60.742 61.111 2.29 0.00 0.00 6.53
5344 9132 2.476051 CACGACATCACCAAGCGC 59.524 61.111 0.00 0.00 0.00 5.92
5345 9133 2.476051 GCACGACATCACCAAGCG 59.524 61.111 0.00 0.00 0.00 4.68
5346 9134 0.391130 TAGGCACGACATCACCAAGC 60.391 55.000 0.00 0.00 0.00 4.01
5347 9135 1.066858 ACTAGGCACGACATCACCAAG 60.067 52.381 0.00 0.00 0.00 3.61
5348 9136 0.973632 ACTAGGCACGACATCACCAA 59.026 50.000 0.00 0.00 0.00 3.67
5349 9137 0.530744 GACTAGGCACGACATCACCA 59.469 55.000 0.00 0.00 0.00 4.17
5350 9138 0.818296 AGACTAGGCACGACATCACC 59.182 55.000 0.00 0.00 0.00 4.02
5351 9139 1.532090 CGAGACTAGGCACGACATCAC 60.532 57.143 10.17 0.00 0.00 3.06
5352 9140 0.733150 CGAGACTAGGCACGACATCA 59.267 55.000 10.17 0.00 0.00 3.07
5353 9141 0.733729 ACGAGACTAGGCACGACATC 59.266 55.000 22.76 0.00 0.00 3.06
5354 9142 0.452184 CACGAGACTAGGCACGACAT 59.548 55.000 22.76 0.00 0.00 3.06
5355 9143 1.873863 CACGAGACTAGGCACGACA 59.126 57.895 22.76 0.00 0.00 4.35
5356 9144 1.514443 GCACGAGACTAGGCACGAC 60.514 63.158 22.76 9.73 0.00 4.34
5357 9145 1.313091 ATGCACGAGACTAGGCACGA 61.313 55.000 22.76 0.00 39.34 4.35
5358 9146 1.139734 ATGCACGAGACTAGGCACG 59.860 57.895 14.29 14.29 39.34 5.34
5359 9147 0.108615 ACATGCACGAGACTAGGCAC 60.109 55.000 0.00 0.00 39.34 5.01
5360 9148 0.108662 CACATGCACGAGACTAGGCA 60.109 55.000 0.00 0.00 41.00 4.75
5361 9149 0.807667 CCACATGCACGAGACTAGGC 60.808 60.000 0.00 0.00 0.00 3.93
5362 9150 0.532573 ACCACATGCACGAGACTAGG 59.467 55.000 0.00 0.00 0.00 3.02
5409 9247 2.954753 GAAGCACAGGCACCGAACG 61.955 63.158 0.00 0.00 44.61 3.95
5494 9332 0.400213 AGGAACATCCGCCACAAGAA 59.600 50.000 0.00 0.00 42.75 2.52
5539 9383 8.664669 ACCAAAACAAATCCCAACTAATCTAT 57.335 30.769 0.00 0.00 0.00 1.98
5572 9416 1.635663 GACTTGGCAATCCACGACCG 61.636 60.000 0.00 0.00 43.33 4.79
5596 9440 6.861144 ACTAAAACGACCTAAGGATCACTAC 58.139 40.000 0.00 0.00 0.00 2.73
5598 9442 5.997384 ACTAAAACGACCTAAGGATCACT 57.003 39.130 0.00 0.00 0.00 3.41
5670 9514 9.288576 TGCATGTATATTCATTAAGGAAGAAGG 57.711 33.333 8.68 0.00 0.00 3.46
5792 9636 4.328536 TGTGCCCAACGACAAAATATAGT 58.671 39.130 0.00 0.00 0.00 2.12
6020 9865 6.147328 AGTCTGAACAGCCTAAAATAACGAAC 59.853 38.462 0.00 0.00 0.00 3.95
6031 9876 2.041755 TGGAGAGAGTCTGAACAGCCTA 59.958 50.000 0.00 0.00 0.00 3.93
6045 9890 2.877300 GCTGGCAACTTGAATGGAGAGA 60.877 50.000 0.00 0.00 37.61 3.10
6257 10102 3.691118 GTCCATAGAGATTGCTTTGCACA 59.309 43.478 0.00 0.00 38.71 4.57
6364 10209 8.201464 AGAAAAAGTTGGTTAACATACCCAAAG 58.799 33.333 8.10 0.00 39.79 2.77
6496 10341 9.578576 ACATGCAGGAAGATAACATACAATATT 57.421 29.630 4.84 0.00 0.00 1.28
6511 10356 1.088340 CAGCTCCGACATGCAGGAAG 61.088 60.000 4.84 0.00 35.90 3.46
6607 10453 5.163499 TGGGGTCAAAGTCAAACACAATTAC 60.163 40.000 0.00 0.00 0.00 1.89
6672 10521 5.744171 AGACAAAACTTTTGCCTCCATTTT 58.256 33.333 13.22 0.00 0.00 1.82
6676 10525 3.360867 TGAGACAAAACTTTTGCCTCCA 58.639 40.909 21.22 11.09 0.00 3.86
6715 10564 5.589050 ACCAAGAAAACCACAACTCTCTTAC 59.411 40.000 0.00 0.00 0.00 2.34
6727 10576 7.123547 AGAGACATTGTAAAACCAAGAAAACCA 59.876 33.333 0.00 0.00 0.00 3.67
6835 10684 2.921221 AGAGGGAGAAATGACTGGGAA 58.079 47.619 0.00 0.00 0.00 3.97
6972 10824 9.071276 CATCTGGCTGGTATTTCAAGTATTTAT 57.929 33.333 0.00 0.00 0.00 1.40
7069 10921 3.195610 CAGGATTCCCTTTTTAACTGCCC 59.804 47.826 0.00 0.00 42.02 5.36
7075 10927 7.266905 ACTACTAGCAGGATTCCCTTTTTAA 57.733 36.000 0.00 0.00 42.02 1.52
7095 10947 6.846325 ACAGAAGTTTGCTACAAGAACTAC 57.154 37.500 0.00 0.00 33.54 2.73
7235 11087 6.714810 TGGTAAATTCTGTTCAGCTTGTACAT 59.285 34.615 0.00 0.00 27.53 2.29
7241 11093 4.773323 GCTGGTAAATTCTGTTCAGCTT 57.227 40.909 0.00 0.00 42.77 3.74
7391 11243 6.553953 TCATGTTTCTAGTATGTGCCCTAA 57.446 37.500 0.00 0.00 0.00 2.69
7482 11334 0.605319 ACATGGGCGACAACGTCAAT 60.605 50.000 0.00 0.00 46.58 2.57
7579 11431 1.969923 CAATCAGGTTTTTGGGGAGCA 59.030 47.619 0.00 0.00 0.00 4.26
7598 11450 1.987855 CCTGTACGGGAGAAGGGCA 60.988 63.158 16.40 0.00 0.00 5.36
7603 11455 1.100510 CGTGATCCTGTACGGGAGAA 58.899 55.000 27.05 15.58 38.92 2.87
7635 11487 4.069232 CGAACAGCAGGCCTCCGA 62.069 66.667 0.00 0.00 0.00 4.55
7650 11502 2.338620 CGTGCACTGGGAGAACGA 59.661 61.111 16.19 0.00 36.38 3.85
7652 11504 2.031163 AGCGTGCACTGGGAGAAC 59.969 61.111 16.19 0.00 0.00 3.01
7660 11512 1.302033 CCTCCTTTCAGCGTGCACT 60.302 57.895 16.19 0.00 0.00 4.40
7669 11521 3.205519 TCTTCTCCATCCCTCCTTTCA 57.794 47.619 0.00 0.00 0.00 2.69
7699 11551 1.368345 CGTTCCAGATCATTGCGCCA 61.368 55.000 4.18 0.00 0.00 5.69
7815 11667 3.861840 TCTTTTGGATCATGACGACTCC 58.138 45.455 0.00 1.16 0.00 3.85
7923 11776 1.209019 CCAAGGACAGAGCTATGCACT 59.791 52.381 8.60 3.77 0.00 4.40
7941 11794 2.504032 CGGGATTTAGCCGAGCCA 59.496 61.111 0.00 0.00 0.00 4.75
7993 11850 1.136984 GACCTACACGTGCTCCTCG 59.863 63.158 17.22 0.00 0.00 4.63
8014 11880 5.104610 ACCACTTGTATGAGCATGAGAAGAT 60.105 40.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.