Multiple sequence alignment - TraesCS5D01G259500

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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 TraesCS5D01G259500 chr5D 100.000 4768 0 0 1 4768 365702233 365697466 0.000000e+00 8805.0
1 TraesCS5D01G259500 chr5D 84.028 144 19 3 100 239 365727485 365727628 8.320000e-28 135.0
2 TraesCS5D01G259500 chr5D 95.833 48 1 1 3814 3861 127266550 127266504 5.120000e-10 76.8
3 TraesCS5D01G259500 chr5B 92.048 4175 217 53 35 4136 432178916 432174784 0.000000e+00 5764.0
4 TraesCS5D01G259500 chr5B 88.611 360 10 9 4409 4768 432173353 432173025 4.440000e-110 409.0
5 TraesCS5D01G259500 chr5A 91.846 3385 176 45 937 4267 467384565 467381227 0.000000e+00 4630.0
6 TraesCS5D01G259500 chr5A 89.258 633 45 13 240 852 467385259 467384630 0.000000e+00 771.0
7 TraesCS5D01G259500 chr5A 94.886 176 8 1 4593 4768 467380913 467380739 1.690000e-69 274.0
8 TraesCS5D01G259500 chr5A 95.833 48 1 1 3814 3861 143026359 143026313 5.120000e-10 76.8
9 TraesCS5D01G259500 chr3A 82.494 1788 163 54 1601 3327 91473148 91471450 0.000000e+00 1430.0
10 TraesCS5D01G259500 chr3A 86.641 771 84 11 1805 2560 135988600 135989366 0.000000e+00 835.0
11 TraesCS5D01G259500 chr3A 86.494 770 86 10 1805 2560 363464116 363463351 0.000000e+00 830.0
12 TraesCS5D01G259500 chr3A 87.892 223 22 4 1308 1527 91473368 91473148 1.700000e-64 257.0
13 TraesCS5D01G259500 chr3B 86.099 1187 105 22 1601 2748 123618468 123619633 0.000000e+00 1223.0
14 TraesCS5D01G259500 chr3B 83.959 1066 132 21 1549 2594 542633135 542632089 0.000000e+00 985.0
15 TraesCS5D01G259500 chr3B 86.957 230 23 6 1302 1527 123618242 123618468 7.920000e-63 252.0
16 TraesCS5D01G259500 chr3B 92.473 93 7 0 2772 2864 123619630 123619722 2.990000e-27 134.0
17 TraesCS5D01G259500 chr2A 83.717 1216 149 25 1397 2594 748875885 748874701 0.000000e+00 1103.0
18 TraesCS5D01G259500 chr7B 82.949 1214 156 29 1396 2588 720580043 720581226 0.000000e+00 1048.0
19 TraesCS5D01G259500 chrUn 84.397 987 108 17 1624 2588 296699180 296700142 0.000000e+00 928.0
20 TraesCS5D01G259500 chr7D 84.397 987 108 17 1624 2588 623465312 623464350 0.000000e+00 928.0
21 TraesCS5D01G259500 chr1A 86.736 769 85 9 1805 2560 581265820 581265056 0.000000e+00 839.0
22 TraesCS5D01G259500 chr3D 90.737 475 42 2 2275 2748 77397172 77397645 2.420000e-177 632.0
23 TraesCS5D01G259500 chr3D 82.698 682 91 9 1656 2318 559142147 559141474 8.890000e-162 580.0
24 TraesCS5D01G259500 chr3D 86.640 247 20 6 1601 1840 77387975 77388215 1.320000e-65 261.0
25 TraesCS5D01G259500 chr3D 87.556 225 22 5 1302 1523 77387750 77387971 6.120000e-64 255.0
26 TraesCS5D01G259500 chr3D 80.872 298 27 18 3048 3327 77399210 77399495 1.740000e-49 207.0
27 TraesCS5D01G259500 chr2D 82.084 547 77 14 1396 1938 645268559 645269088 9.410000e-122 448.0


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 TraesCS5D01G259500 chr5D 365697466 365702233 4767 True 8805.000000 8805 100.000000 1 4768 1 chr5D.!!$R2 4767
1 TraesCS5D01G259500 chr5B 432173025 432178916 5891 True 3086.500000 5764 90.329500 35 4768 2 chr5B.!!$R1 4733
2 TraesCS5D01G259500 chr5A 467380739 467385259 4520 True 1891.666667 4630 91.996667 240 4768 3 chr5A.!!$R2 4528
3 TraesCS5D01G259500 chr3A 91471450 91473368 1918 True 843.500000 1430 85.193000 1308 3327 2 chr3A.!!$R2 2019
4 TraesCS5D01G259500 chr3A 135988600 135989366 766 False 835.000000 835 86.641000 1805 2560 1 chr3A.!!$F1 755
5 TraesCS5D01G259500 chr3A 363463351 363464116 765 True 830.000000 830 86.494000 1805 2560 1 chr3A.!!$R1 755
6 TraesCS5D01G259500 chr3B 542632089 542633135 1046 True 985.000000 985 83.959000 1549 2594 1 chr3B.!!$R1 1045
7 TraesCS5D01G259500 chr3B 123618242 123619722 1480 False 536.333333 1223 88.509667 1302 2864 3 chr3B.!!$F1 1562
8 TraesCS5D01G259500 chr2A 748874701 748875885 1184 True 1103.000000 1103 83.717000 1397 2594 1 chr2A.!!$R1 1197
9 TraesCS5D01G259500 chr7B 720580043 720581226 1183 False 1048.000000 1048 82.949000 1396 2588 1 chr7B.!!$F1 1192
10 TraesCS5D01G259500 chrUn 296699180 296700142 962 False 928.000000 928 84.397000 1624 2588 1 chrUn.!!$F1 964
11 TraesCS5D01G259500 chr7D 623464350 623465312 962 True 928.000000 928 84.397000 1624 2588 1 chr7D.!!$R1 964
12 TraesCS5D01G259500 chr1A 581265056 581265820 764 True 839.000000 839 86.736000 1805 2560 1 chr1A.!!$R1 755
13 TraesCS5D01G259500 chr3D 559141474 559142147 673 True 580.000000 580 82.698000 1656 2318 1 chr3D.!!$R1 662
14 TraesCS5D01G259500 chr3D 77397172 77399495 2323 False 419.500000 632 85.804500 2275 3327 2 chr3D.!!$F2 1052
15 TraesCS5D01G259500 chr2D 645268559 645269088 529 False 448.000000 448 82.084000 1396 1938 1 chr2D.!!$F1 542

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
268 282 0.040514 TGCGAAACCAAATGTCTGCG 60.041 50.0 0.00 0.0 0.00 5.18 F
854 889 0.335361 AAGGAGGCGAGGACTAGGAA 59.665 55.0 0.00 0.0 0.00 3.36 F
1343 1415 0.340208 TCCCCTCCTCTTCCCTTCTC 59.660 60.0 0.00 0.0 0.00 2.87 F
3084 4593 0.546122 TTGAAGGCCATCGCAGGTAT 59.454 50.0 5.01 0.0 36.38 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 1592 0.748005 AATGCGGAATCCTTGGACCG 60.748 55.000 12.58 12.58 46.74 4.79 R
2357 2501 2.852449 TCAAAATTGACACGGCACCTA 58.148 42.857 0.00 0.00 31.01 3.08 R
3225 4745 2.285977 GGGCAGGTAATAGGTGTTTCG 58.714 52.381 0.00 0.00 0.00 3.46 R
4598 7360 0.105224 TTCCTTCCTCACGACGCAAA 59.895 50.000 0.00 0.00 0.00 3.68 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
20 21 1.842562 AGAGGAGATGGGAATGTGTGG 59.157 52.381 0.00 0.00 0.00 4.17
21 22 0.921896 AGGAGATGGGAATGTGTGGG 59.078 55.000 0.00 0.00 0.00 4.61
22 23 0.625849 GGAGATGGGAATGTGTGGGT 59.374 55.000 0.00 0.00 0.00 4.51
23 24 1.005924 GGAGATGGGAATGTGTGGGTT 59.994 52.381 0.00 0.00 0.00 4.11
24 25 2.094675 GAGATGGGAATGTGTGGGTTG 58.905 52.381 0.00 0.00 0.00 3.77
25 26 1.185315 GATGGGAATGTGTGGGTTGG 58.815 55.000 0.00 0.00 0.00 3.77
26 27 0.252193 ATGGGAATGTGTGGGTTGGG 60.252 55.000 0.00 0.00 0.00 4.12
27 28 2.282783 GGGAATGTGTGGGTTGGGC 61.283 63.158 0.00 0.00 0.00 5.36
28 29 2.282783 GGAATGTGTGGGTTGGGCC 61.283 63.158 0.00 0.00 0.00 5.80
88 89 0.179225 CCACATTAGCACGTCAACGC 60.179 55.000 1.81 0.00 44.43 4.84
89 90 0.516322 CACATTAGCACGTCAACGCG 60.516 55.000 3.53 3.53 44.43 6.01
90 91 1.058748 CATTAGCACGTCAACGCGG 59.941 57.895 12.47 0.00 44.43 6.46
126 139 0.389948 CTGGTGTCTCCCGTGTAAGC 60.390 60.000 0.00 0.00 34.77 3.09
185 198 9.410556 ACCAGATTTGAATATTTTCTGAAAACG 57.589 29.630 17.06 0.00 36.72 3.60
188 201 9.846248 AGATTTGAATATTTTCTGAAAACGAGG 57.154 29.630 17.06 0.00 32.37 4.63
195 208 9.626045 AATATTTTCTGAAAACGAGGTCAATTC 57.374 29.630 17.06 0.00 32.37 2.17
196 209 5.432885 TTTCTGAAAACGAGGTCAATTCC 57.567 39.130 0.00 0.00 0.00 3.01
198 211 2.147958 TGAAAACGAGGTCAATTCCGG 58.852 47.619 0.00 0.00 0.00 5.14
203 216 3.067684 ACGAGGTCAATTCCGGATTTT 57.932 42.857 4.15 0.00 0.00 1.82
204 217 2.747446 ACGAGGTCAATTCCGGATTTTG 59.253 45.455 17.43 17.43 0.00 2.44
206 219 3.190535 CGAGGTCAATTCCGGATTTTGTT 59.809 43.478 20.85 11.86 0.00 2.83
207 220 4.393680 CGAGGTCAATTCCGGATTTTGTTA 59.606 41.667 20.85 6.34 0.00 2.41
208 221 5.447279 CGAGGTCAATTCCGGATTTTGTTAG 60.447 44.000 20.85 7.12 0.00 2.34
209 222 4.157840 AGGTCAATTCCGGATTTTGTTAGC 59.842 41.667 20.85 14.68 0.00 3.09
210 223 4.082463 GGTCAATTCCGGATTTTGTTAGCA 60.082 41.667 20.85 5.21 0.00 3.49
211 224 4.857037 GTCAATTCCGGATTTTGTTAGCAC 59.143 41.667 20.85 11.66 0.00 4.40
225 239 6.872670 TTGTTAGCACAAAAGGTTAAAACG 57.127 33.333 0.00 0.00 40.10 3.60
226 240 5.341617 TGTTAGCACAAAAGGTTAAAACGG 58.658 37.500 0.00 0.00 0.00 4.44
268 282 0.040514 TGCGAAACCAAATGTCTGCG 60.041 50.000 0.00 0.00 0.00 5.18
276 290 1.466167 CCAAATGTCTGCGAGTTCCTG 59.534 52.381 0.00 0.00 0.00 3.86
282 296 2.560981 TGTCTGCGAGTTCCTGTCAATA 59.439 45.455 0.00 0.00 0.00 1.90
297 318 8.561738 TCCTGTCAATACTTTAATTTCTGTCC 57.438 34.615 0.00 0.00 0.00 4.02
332 353 9.750125 AATAAAATTCTCTCGGAAATAAATGGC 57.250 29.630 0.00 0.00 37.49 4.40
527 550 1.257750 CCCCTGATGACAGACGACCA 61.258 60.000 0.00 0.00 46.03 4.02
529 552 0.603065 CCTGATGACAGACGACCACA 59.397 55.000 0.00 0.00 46.03 4.17
664 687 1.000739 TCCATAGACCCCGTCCGTT 59.999 57.895 0.00 0.00 32.18 4.44
696 719 2.527123 TTGTACGGACAGCCCCCA 60.527 61.111 0.00 0.00 36.76 4.96
810 841 4.308458 CGAACACGCCACCCCTCA 62.308 66.667 0.00 0.00 0.00 3.86
835 870 1.771073 CGCGAGCACAGGTTTTGACA 61.771 55.000 0.00 0.00 0.00 3.58
852 887 0.684805 ACAAGGAGGCGAGGACTAGG 60.685 60.000 0.00 0.00 0.00 3.02
854 889 0.335361 AAGGAGGCGAGGACTAGGAA 59.665 55.000 0.00 0.00 0.00 3.36
856 891 1.737201 GAGGCGAGGACTAGGAAGC 59.263 63.158 0.00 0.00 0.00 3.86
857 892 2.065906 GAGGCGAGGACTAGGAAGCG 62.066 65.000 0.00 0.00 0.00 4.68
858 893 2.278923 GCGAGGACTAGGAAGCGC 60.279 66.667 0.00 0.00 37.60 5.92
859 894 3.064987 GCGAGGACTAGGAAGCGCA 62.065 63.158 11.47 0.00 43.45 6.09
860 895 1.064946 CGAGGACTAGGAAGCGCAG 59.935 63.158 11.47 0.00 0.00 5.18
861 896 1.658686 CGAGGACTAGGAAGCGCAGT 61.659 60.000 11.47 2.88 0.00 4.40
862 897 0.533032 GAGGACTAGGAAGCGCAGTT 59.467 55.000 11.47 0.00 0.00 3.16
864 899 1.751924 AGGACTAGGAAGCGCAGTTAG 59.248 52.381 11.47 8.39 0.00 2.34
865 900 1.202428 GGACTAGGAAGCGCAGTTAGG 60.202 57.143 11.47 0.00 0.00 2.69
866 901 1.749634 GACTAGGAAGCGCAGTTAGGA 59.250 52.381 11.47 0.00 0.00 2.94
867 902 1.751924 ACTAGGAAGCGCAGTTAGGAG 59.248 52.381 11.47 0.00 0.00 3.69
871 906 1.202359 GGAAGCGCAGTTAGGAGAGAG 60.202 57.143 11.47 0.00 0.00 3.20
887 940 1.884926 GAGAGGGCTTTGATCGCGG 60.885 63.158 6.13 0.00 0.00 6.46
888 941 2.186903 GAGGGCTTTGATCGCGGA 59.813 61.111 6.13 0.00 0.00 5.54
890 943 1.002624 AGGGCTTTGATCGCGGAAA 60.003 52.632 6.13 2.36 0.00 3.13
891 944 0.608035 AGGGCTTTGATCGCGGAAAA 60.608 50.000 6.13 3.90 0.00 2.29
910 963 3.808834 AAAACCTTCCGGAATCTTCCT 57.191 42.857 19.21 0.00 45.33 3.36
911 964 2.789409 AACCTTCCGGAATCTTCCTG 57.211 50.000 19.21 3.66 45.33 3.86
992 1056 2.346365 GGGGGTTTCTTCTCGCGT 59.654 61.111 5.77 0.00 0.00 6.01
1304 1376 3.573491 GCCCAAGCGTATGTCGGC 61.573 66.667 0.00 0.00 40.26 5.54
1342 1414 0.341609 CTCCCCTCCTCTTCCCTTCT 59.658 60.000 0.00 0.00 0.00 2.85
1343 1415 0.340208 TCCCCTCCTCTTCCCTTCTC 59.660 60.000 0.00 0.00 0.00 2.87
1345 1417 1.045911 CCCTCCTCTTCCCTTCTCCG 61.046 65.000 0.00 0.00 0.00 4.63
1507 1592 3.461061 TCAGCTCATGTCCGATCAATTC 58.539 45.455 0.00 0.00 0.00 2.17
1565 1650 4.102524 ACTTCCATGGCTCGATTAACCATA 59.897 41.667 6.96 0.00 42.31 2.74
1584 1669 2.734723 CGTGTCTCCTGTGCGGTG 60.735 66.667 0.00 0.00 0.00 4.94
1799 1912 1.142474 GCCATTGCTGCTGTTCAAAC 58.858 50.000 0.00 0.00 33.53 2.93
1826 1939 5.598005 TGAAACTGAACCATGAAAGTTCCAT 59.402 36.000 9.84 0.00 42.41 3.41
1831 1944 4.653341 TGAACCATGAAAGTTCCATTGGTT 59.347 37.500 16.68 16.68 42.41 3.67
1962 2088 6.583806 CCACTGCAATTCTTAACAATTCAGTC 59.416 38.462 13.24 0.00 34.91 3.51
1968 2096 7.523709 GCAATTCTTAACAATTCAGTCAAGGGA 60.524 37.037 0.00 0.00 0.00 4.20
2199 2339 4.789012 TTTGCATCTCCCATTTCTTGTC 57.211 40.909 0.00 0.00 0.00 3.18
2204 2344 4.159135 GCATCTCCCATTTCTTGTCATGTT 59.841 41.667 0.00 0.00 0.00 2.71
2224 2366 9.571816 TCATGTTTCTAAATCATATGCATACCA 57.428 29.630 8.99 0.00 0.00 3.25
2357 2501 4.664688 ACCCATGGAGATTCAGAAACTT 57.335 40.909 15.22 0.00 0.00 2.66
2580 2773 4.872124 GCATCCCATCCAAATTTTCTCAAC 59.128 41.667 0.00 0.00 0.00 3.18
2594 2787 9.533253 AAATTTTCTCAACATGTTTTAGACCTG 57.467 29.630 16.44 2.36 0.00 4.00
2861 3054 3.969117 TCAACATCTTCAACACAGCAC 57.031 42.857 0.00 0.00 0.00 4.40
2862 3055 3.544684 TCAACATCTTCAACACAGCACT 58.455 40.909 0.00 0.00 0.00 4.40
2863 3056 3.313249 TCAACATCTTCAACACAGCACTG 59.687 43.478 0.00 0.00 0.00 3.66
2864 3057 1.605710 ACATCTTCAACACAGCACTGC 59.394 47.619 0.00 0.00 0.00 4.40
2865 3058 1.605232 CATCTTCAACACAGCACTGCA 59.395 47.619 3.30 0.00 0.00 4.41
2866 3059 1.748950 TCTTCAACACAGCACTGCAA 58.251 45.000 3.30 0.00 0.00 4.08
2867 3060 1.672363 TCTTCAACACAGCACTGCAAG 59.328 47.619 3.30 0.00 42.29 4.01
3084 4593 0.546122 TTGAAGGCCATCGCAGGTAT 59.454 50.000 5.01 0.00 36.38 2.73
3087 4597 1.604278 GAAGGCCATCGCAGGTATTTC 59.396 52.381 5.01 0.00 36.38 2.17
3089 4599 2.047061 AGGCCATCGCAGGTATTTCTA 58.953 47.619 5.01 0.00 36.38 2.10
3100 4610 5.584649 CGCAGGTATTTCTATCAAGTTCCAA 59.415 40.000 0.00 0.00 0.00 3.53
3175 4685 8.802267 CATAGAAGTTTGTCCCTTGGAATAAAA 58.198 33.333 0.00 0.00 31.38 1.52
3278 4803 5.221067 GCTGCATGATCTCAATGTTCTCAAT 60.221 40.000 0.00 0.00 0.00 2.57
3282 4807 7.078851 GCATGATCTCAATGTTCTCAATCATC 58.921 38.462 0.00 0.00 31.78 2.92
3305 4833 6.625267 TCCTTATAGGAGTAGCAGGATTCTT 58.375 40.000 0.00 0.00 40.06 2.52
3338 4866 8.981647 CCCAACTTTTAGAATGTTTCATTTCAG 58.018 33.333 0.00 0.00 0.00 3.02
3342 4870 9.533253 ACTTTTAGAATGTTTCATTTCAGTTGG 57.467 29.630 0.00 0.00 0.00 3.77
3360 4888 7.402054 TCAGTTGGGTGATAATAGTCAAATGT 58.598 34.615 0.00 0.00 33.68 2.71
3363 4891 7.770897 AGTTGGGTGATAATAGTCAAATGTCTC 59.229 37.037 0.00 0.00 0.00 3.36
3364 4892 7.194112 TGGGTGATAATAGTCAAATGTCTCA 57.806 36.000 0.00 0.00 0.00 3.27
3578 5109 4.756502 ACCGGAAACTTATAGTTGAGCTC 58.243 43.478 9.46 6.82 38.66 4.09
3612 5143 0.537143 AAACGGCACATTGAGCTGGA 60.537 50.000 17.48 0.00 42.62 3.86
3716 5247 5.212745 CCCAAGGAAGAGGACTACTTCTAT 58.787 45.833 0.00 0.00 42.07 1.98
3719 5250 4.219919 AGGAAGAGGACTACTTCTATGCC 58.780 47.826 0.00 0.00 42.07 4.40
3746 5277 0.467844 ATGAGTGCTTGCACCAACCA 60.468 50.000 20.39 13.91 0.00 3.67
3782 5313 7.068348 TCAGCTTTATGATACCCTCGGATATAC 59.932 40.741 0.00 0.00 0.00 1.47
3802 5333 2.158623 ACACACATTCTTTCCAGAGCCA 60.159 45.455 0.00 0.00 0.00 4.75
3887 5424 2.664081 GGGACAGGCACCTGAGAGG 61.664 68.421 23.30 0.00 46.30 3.69
4010 5550 5.610398 TGTGTTGTACATATGAGCATAGGG 58.390 41.667 10.38 0.15 33.42 3.53
4011 5551 4.452455 GTGTTGTACATATGAGCATAGGGC 59.548 45.833 10.38 1.09 45.30 5.19
4024 5564 4.902443 GCATAGGGCTTAGAAGAAAACC 57.098 45.455 0.00 0.00 40.25 3.27
4090 5631 7.549615 GCATGTGATGTGATGCATATATACT 57.450 36.000 0.00 0.00 43.75 2.12
4091 5632 7.628235 GCATGTGATGTGATGCATATATACTC 58.372 38.462 0.00 0.00 43.75 2.59
4092 5633 7.516312 GCATGTGATGTGATGCATATATACTCG 60.516 40.741 0.00 0.00 43.75 4.18
4099 5640 8.911247 TGTGATGCATATATACTCGTACATTC 57.089 34.615 0.00 0.00 0.00 2.67
4108 5649 3.526931 ACTCGTACATTCTGATGGTGG 57.473 47.619 0.00 0.00 37.60 4.61
4119 5660 0.036732 TGATGGTGGTGGTCAGAAGC 59.963 55.000 0.00 0.00 0.00 3.86
4124 5665 1.623811 GGTGGTGGTCAGAAGCTCTTA 59.376 52.381 0.00 0.00 0.00 2.10
4137 5678 5.289675 CAGAAGCTCTTATTCCGTTGTACAG 59.710 44.000 0.00 0.00 0.00 2.74
4139 5764 5.401531 AGCTCTTATTCCGTTGTACAGAA 57.598 39.130 0.00 0.00 0.00 3.02
4192 5821 2.812011 GTGTTTAGTTCTGGGCGTGATT 59.188 45.455 0.00 0.00 0.00 2.57
4205 5834 3.978855 GGGCGTGATTTTTGTTACTGAAC 59.021 43.478 0.00 0.00 36.00 3.18
4244 6917 2.419574 GCTCGGTTTCTGCCCAAGTATA 60.420 50.000 0.00 0.00 0.00 1.47
4259 6932 6.879458 GCCCAAGTATATTGATTTAGATCCGT 59.121 38.462 0.00 0.00 0.00 4.69
4260 6933 7.148407 GCCCAAGTATATTGATTTAGATCCGTG 60.148 40.741 0.00 0.00 0.00 4.94
4274 6947 4.533815 AGATCCGTGTGGTCAGATACTTA 58.466 43.478 0.00 0.00 36.30 2.24
4275 6948 4.338682 AGATCCGTGTGGTCAGATACTTAC 59.661 45.833 0.00 0.00 36.30 2.34
4276 6949 2.421073 TCCGTGTGGTCAGATACTTACG 59.579 50.000 0.00 0.00 36.30 3.18
4319 7080 9.169468 GCCACGAATTATTGTTAATTGATACTG 57.831 33.333 0.00 0.00 37.98 2.74
4341 7102 6.260271 ACTGCTACTGGTAGAAGAAAAACAAC 59.740 38.462 19.37 0.00 40.58 3.32
4344 7105 3.314357 ACTGGTAGAAGAAAAACAACGGC 59.686 43.478 0.00 0.00 0.00 5.68
4346 7107 2.619646 GGTAGAAGAAAAACAACGGCCA 59.380 45.455 2.24 0.00 0.00 5.36
4349 7110 3.020984 AGAAGAAAAACAACGGCCAGAA 58.979 40.909 2.24 0.00 0.00 3.02
4376 7138 6.650120 AGGTATTGAGACCGTGTTAATTGAT 58.350 36.000 0.00 0.00 44.88 2.57
4398 7160 4.724399 TGTCTAAAATGACAGGCCAAAGA 58.276 39.130 5.01 0.00 41.43 2.52
4399 7161 5.136828 TGTCTAAAATGACAGGCCAAAGAA 58.863 37.500 5.01 0.00 41.43 2.52
4400 7162 5.241506 TGTCTAAAATGACAGGCCAAAGAAG 59.758 40.000 5.01 0.00 41.43 2.85
4401 7163 4.766891 TCTAAAATGACAGGCCAAAGAAGG 59.233 41.667 5.01 0.00 0.00 3.46
4402 7164 2.978156 AATGACAGGCCAAAGAAGGA 57.022 45.000 5.01 0.00 0.00 3.36
4403 7165 2.503895 ATGACAGGCCAAAGAAGGAG 57.496 50.000 5.01 0.00 0.00 3.69
4404 7166 0.401738 TGACAGGCCAAAGAAGGAGG 59.598 55.000 5.01 0.00 0.00 4.30
4423 7185 0.947180 GCGGGTGCTACGACTTTTGA 60.947 55.000 0.00 0.00 38.39 2.69
4459 7221 6.707608 CCATGCTGATCTGTTTTAGTAGCATA 59.292 38.462 10.08 0.00 42.17 3.14
4460 7222 7.095313 CCATGCTGATCTGTTTTAGTAGCATAG 60.095 40.741 10.08 1.75 42.17 2.23
4461 7223 5.755375 TGCTGATCTGTTTTAGTAGCATAGC 59.245 40.000 1.27 0.00 35.60 2.97
4462 7224 5.755375 GCTGATCTGTTTTAGTAGCATAGCA 59.245 40.000 1.27 0.00 32.90 3.49
4463 7225 6.426328 GCTGATCTGTTTTAGTAGCATAGCAT 59.574 38.462 1.27 0.00 32.90 3.79
4464 7226 7.570875 GCTGATCTGTTTTAGTAGCATAGCATG 60.571 40.741 1.27 0.00 32.90 4.06
4465 7227 7.500141 TGATCTGTTTTAGTAGCATAGCATGA 58.500 34.615 0.00 0.00 0.00 3.07
4466 7228 8.152898 TGATCTGTTTTAGTAGCATAGCATGAT 58.847 33.333 0.00 0.00 0.00 2.45
4519 7281 4.162690 GGCCGCCTCAATCGTCCT 62.163 66.667 0.71 0.00 0.00 3.85
4520 7282 2.586357 GCCGCCTCAATCGTCCTC 60.586 66.667 0.00 0.00 0.00 3.71
4521 7283 2.107141 CCGCCTCAATCGTCCTCC 59.893 66.667 0.00 0.00 0.00 4.30
4589 7351 1.125566 GTGCGTGCGGTTTTCTACTAC 59.874 52.381 0.00 0.00 0.00 2.73
4598 7360 3.427233 CGGTTTTCTACTACTAGCAGCGT 60.427 47.826 0.00 0.00 0.00 5.07
4635 7397 0.249322 AACGATCCAGCCCGTATTCG 60.249 55.000 0.00 0.00 38.13 3.34
4659 7421 0.529992 AGCGCCGATACCAAAGCTAC 60.530 55.000 2.29 0.00 32.73 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.842562 CCACACATTCCCATCTCCTCT 59.157 52.381 0.00 0.00 0.00 3.69
1 2 1.133976 CCCACACATTCCCATCTCCTC 60.134 57.143 0.00 0.00 0.00 3.71
2 3 0.921896 CCCACACATTCCCATCTCCT 59.078 55.000 0.00 0.00 0.00 3.69
3 4 0.625849 ACCCACACATTCCCATCTCC 59.374 55.000 0.00 0.00 0.00 3.71
4 5 2.094675 CAACCCACACATTCCCATCTC 58.905 52.381 0.00 0.00 0.00 2.75
5 6 1.272648 CCAACCCACACATTCCCATCT 60.273 52.381 0.00 0.00 0.00 2.90
6 7 1.185315 CCAACCCACACATTCCCATC 58.815 55.000 0.00 0.00 0.00 3.51
7 8 0.252193 CCCAACCCACACATTCCCAT 60.252 55.000 0.00 0.00 0.00 4.00
8 9 1.154921 CCCAACCCACACATTCCCA 59.845 57.895 0.00 0.00 0.00 4.37
9 10 2.282783 GCCCAACCCACACATTCCC 61.283 63.158 0.00 0.00 0.00 3.97
10 11 2.282783 GGCCCAACCCACACATTCC 61.283 63.158 0.00 0.00 0.00 3.01
11 12 3.376546 GGCCCAACCCACACATTC 58.623 61.111 0.00 0.00 0.00 2.67
67 68 0.871722 GTTGACGTGCTAATGTGGCA 59.128 50.000 0.00 0.00 37.36 4.92
68 69 0.179225 CGTTGACGTGCTAATGTGGC 60.179 55.000 0.00 0.00 34.11 5.01
69 70 0.179225 GCGTTGACGTGCTAATGTGG 60.179 55.000 0.00 0.00 42.22 4.17
70 71 0.516322 CGCGTTGACGTGCTAATGTG 60.516 55.000 0.00 0.00 43.06 3.21
71 72 1.779061 CGCGTTGACGTGCTAATGT 59.221 52.632 0.00 0.00 43.06 2.71
72 73 4.624747 CGCGTTGACGTGCTAATG 57.375 55.556 0.00 0.00 43.06 1.90
100 101 2.122954 GGAGACACCAGGGTCCCT 59.877 66.667 3.85 3.85 38.59 4.20
102 103 3.391382 CGGGAGACACCAGGGTCC 61.391 72.222 0.00 0.00 41.20 4.46
103 104 2.603776 ACGGGAGACACCAGGGTC 60.604 66.667 0.00 0.00 41.20 4.46
104 105 2.923035 CACGGGAGACACCAGGGT 60.923 66.667 0.00 0.00 41.20 4.34
105 106 1.189524 TTACACGGGAGACACCAGGG 61.190 60.000 0.00 0.00 42.87 4.45
106 107 0.246635 CTTACACGGGAGACACCAGG 59.753 60.000 0.00 0.00 41.20 4.45
107 108 0.389948 GCTTACACGGGAGACACCAG 60.390 60.000 0.00 0.00 41.20 4.00
108 109 0.830444 AGCTTACACGGGAGACACCA 60.830 55.000 0.00 0.00 41.20 4.17
159 172 9.410556 CGTTTTCAGAAAATATTCAAATCTGGT 57.589 29.630 11.54 0.00 38.39 4.00
160 173 9.624697 TCGTTTTCAGAAAATATTCAAATCTGG 57.375 29.630 11.54 5.06 38.39 3.86
165 178 8.625651 TGACCTCGTTTTCAGAAAATATTCAAA 58.374 29.630 11.54 0.00 38.06 2.69
171 184 7.572353 CGGAATTGACCTCGTTTTCAGAAAATA 60.572 37.037 11.54 3.05 32.22 1.40
172 185 6.447162 GGAATTGACCTCGTTTTCAGAAAAT 58.553 36.000 11.54 0.00 32.22 1.82
185 198 4.783764 AACAAAATCCGGAATTGACCTC 57.216 40.909 29.62 0.00 0.00 3.85
188 201 4.857037 GTGCTAACAAAATCCGGAATTGAC 59.143 41.667 29.62 17.82 0.00 3.18
203 216 5.125097 TCCGTTTTAACCTTTTGTGCTAACA 59.875 36.000 0.00 0.00 0.00 2.41
204 217 5.580661 TCCGTTTTAACCTTTTGTGCTAAC 58.419 37.500 0.00 0.00 0.00 2.34
206 219 5.831702 TTCCGTTTTAACCTTTTGTGCTA 57.168 34.783 0.00 0.00 0.00 3.49
207 220 4.722361 TTCCGTTTTAACCTTTTGTGCT 57.278 36.364 0.00 0.00 0.00 4.40
208 221 5.977171 ATTTCCGTTTTAACCTTTTGTGC 57.023 34.783 0.00 0.00 0.00 4.57
209 222 8.231161 ACAAAATTTCCGTTTTAACCTTTTGTG 58.769 29.630 8.71 0.00 41.42 3.33
210 223 8.325421 ACAAAATTTCCGTTTTAACCTTTTGT 57.675 26.923 0.00 0.00 39.44 2.83
211 224 7.906010 GGACAAAATTTCCGTTTTAACCTTTTG 59.094 33.333 0.00 0.00 37.98 2.44
225 239 7.436376 GCATATCAAAGCTAGGACAAAATTTCC 59.564 37.037 0.00 0.00 0.00 3.13
226 240 7.166473 CGCATATCAAAGCTAGGACAAAATTTC 59.834 37.037 0.00 0.00 0.00 2.17
276 290 8.739972 ACCATGGACAGAAATTAAAGTATTGAC 58.260 33.333 21.47 0.00 0.00 3.18
282 296 9.975218 ATTAGTACCATGGACAGAAATTAAAGT 57.025 29.630 21.47 0.00 0.00 2.66
297 318 9.542462 TTCCGAGAGAATTTTATTAGTACCATG 57.458 33.333 0.00 0.00 0.00 3.66
331 352 2.681848 TCTGAGGTTGTAGTACTAGCGC 59.318 50.000 1.87 0.00 0.00 5.92
332 353 4.959596 TTCTGAGGTTGTAGTACTAGCG 57.040 45.455 1.87 0.00 0.00 4.26
492 515 3.357079 GGTGCTTCGTGTGGCTGG 61.357 66.667 0.00 0.00 0.00 4.85
696 719 3.800685 TACGCACACGGCAGCAAGT 62.801 57.895 0.00 0.00 46.04 3.16
742 767 2.203015 AGGCGCGTGTCAAAGTGT 60.203 55.556 8.43 0.00 0.00 3.55
744 769 3.036084 CGAGGCGCGTGTCAAAGT 61.036 61.111 7.63 0.00 34.64 2.66
781 812 4.728102 TGTTCGTACTGCCGGCGG 62.728 66.667 33.73 33.73 0.00 6.13
795 826 4.619227 CGTGAGGGGTGGCGTGTT 62.619 66.667 0.00 0.00 0.00 3.32
820 855 2.301346 CTCCTTGTCAAAACCTGTGCT 58.699 47.619 0.00 0.00 0.00 4.40
821 856 1.338020 CCTCCTTGTCAAAACCTGTGC 59.662 52.381 0.00 0.00 0.00 4.57
831 866 0.039180 TAGTCCTCGCCTCCTTGTCA 59.961 55.000 0.00 0.00 0.00 3.58
835 870 0.335361 TTCCTAGTCCTCGCCTCCTT 59.665 55.000 0.00 0.00 0.00 3.36
852 887 1.746220 TCTCTCTCCTAACTGCGCTTC 59.254 52.381 9.73 0.00 0.00 3.86
854 889 1.388547 CTCTCTCTCCTAACTGCGCT 58.611 55.000 9.73 0.00 0.00 5.92
856 891 1.028905 CCCTCTCTCTCCTAACTGCG 58.971 60.000 0.00 0.00 0.00 5.18
857 892 0.750249 GCCCTCTCTCTCCTAACTGC 59.250 60.000 0.00 0.00 0.00 4.40
858 893 2.452600 AGCCCTCTCTCTCCTAACTG 57.547 55.000 0.00 0.00 0.00 3.16
859 894 3.103742 CAAAGCCCTCTCTCTCCTAACT 58.896 50.000 0.00 0.00 0.00 2.24
860 895 3.100671 TCAAAGCCCTCTCTCTCCTAAC 58.899 50.000 0.00 0.00 0.00 2.34
861 896 3.474798 TCAAAGCCCTCTCTCTCCTAA 57.525 47.619 0.00 0.00 0.00 2.69
862 897 3.571590 GATCAAAGCCCTCTCTCTCCTA 58.428 50.000 0.00 0.00 0.00 2.94
864 899 1.068434 CGATCAAAGCCCTCTCTCTCC 59.932 57.143 0.00 0.00 0.00 3.71
865 900 1.537990 GCGATCAAAGCCCTCTCTCTC 60.538 57.143 0.00 0.00 0.00 3.20
866 901 0.463620 GCGATCAAAGCCCTCTCTCT 59.536 55.000 0.00 0.00 0.00 3.10
867 902 0.873743 CGCGATCAAAGCCCTCTCTC 60.874 60.000 0.00 0.00 0.00 3.20
871 906 1.024579 TTTCCGCGATCAAAGCCCTC 61.025 55.000 8.23 0.00 0.00 4.30
901 954 2.611292 CGTCTGAATGGCAGGAAGATTC 59.389 50.000 0.00 0.00 44.98 2.52
902 955 2.636830 CGTCTGAATGGCAGGAAGATT 58.363 47.619 0.00 0.00 44.98 2.40
903 956 1.134280 CCGTCTGAATGGCAGGAAGAT 60.134 52.381 0.00 0.00 44.98 2.40
904 957 0.250234 CCGTCTGAATGGCAGGAAGA 59.750 55.000 0.00 0.00 44.98 2.87
905 958 2.772739 CCGTCTGAATGGCAGGAAG 58.227 57.895 0.00 0.00 44.98 3.46
1304 1376 1.815003 AGCAAAAGAAGCAGGAATCGG 59.185 47.619 0.00 0.00 0.00 4.18
1342 1414 1.068588 CGCAGATGATTCCTAACCGGA 59.931 52.381 9.46 0.00 41.06 5.14
1343 1415 1.068588 TCGCAGATGATTCCTAACCGG 59.931 52.381 0.00 0.00 0.00 5.28
1345 1417 4.380531 TGATTCGCAGATGATTCCTAACC 58.619 43.478 0.00 0.00 35.04 2.85
1507 1592 0.748005 AATGCGGAATCCTTGGACCG 60.748 55.000 12.58 12.58 46.74 4.79
1565 1650 2.029073 CCGCACAGGAGACACGTT 59.971 61.111 0.00 0.00 45.00 3.99
1584 1669 7.878547 ACAGGGTTAGAATCAGTAGTAGTAC 57.121 40.000 0.00 0.00 0.00 2.73
1799 1912 5.505173 ACTTTCATGGTTCAGTTTCAGTG 57.495 39.130 0.00 0.00 0.00 3.66
1826 1939 9.506018 CACCATATCACATATCTGATTAACCAA 57.494 33.333 0.00 0.00 32.86 3.67
1831 1944 7.178451 ACCGTCACCATATCACATATCTGATTA 59.822 37.037 0.00 0.00 32.86 1.75
1968 2096 6.012745 ACAGAAAAGGATAAGACAAAGGCAT 58.987 36.000 0.00 0.00 0.00 4.40
2163 2302 7.231317 GGGAGATGCAAATAAACCTGATTATGA 59.769 37.037 0.00 0.00 0.00 2.15
2177 2316 4.773674 TGACAAGAAATGGGAGATGCAAAT 59.226 37.500 0.00 0.00 0.00 2.32
2357 2501 2.852449 TCAAAATTGACACGGCACCTA 58.148 42.857 0.00 0.00 31.01 3.08
2580 2773 7.490962 TTGTCAACTACAGGTCTAAAACATG 57.509 36.000 0.00 0.00 45.14 3.21
2614 2807 3.260884 AGCGTATCTTCCAAGTTCAAGGA 59.739 43.478 0.00 0.00 0.00 3.36
3084 4593 5.773176 GGGAAAGGTTGGAACTTGATAGAAA 59.227 40.000 0.00 0.00 0.00 2.52
3087 4597 4.923415 AGGGAAAGGTTGGAACTTGATAG 58.077 43.478 0.00 0.00 0.00 2.08
3089 4599 3.897505 CAAGGGAAAGGTTGGAACTTGAT 59.102 43.478 0.00 0.00 36.79 2.57
3100 4610 4.141251 AGTGTCACATAACAAGGGAAAGGT 60.141 41.667 5.62 0.00 0.00 3.50
3225 4745 2.285977 GGGCAGGTAATAGGTGTTTCG 58.714 52.381 0.00 0.00 0.00 3.46
3278 4803 5.600669 TCCTGCTACTCCTATAAGGATGA 57.399 43.478 0.00 0.00 44.81 2.92
3282 4807 6.926630 AAGAATCCTGCTACTCCTATAAGG 57.073 41.667 0.00 0.00 36.46 2.69
3303 4831 7.272244 ACATTCTAAAAGTTGGGGTTTGAAAG 58.728 34.615 0.00 0.00 0.00 2.62
3305 4833 6.800072 ACATTCTAAAAGTTGGGGTTTGAA 57.200 33.333 0.00 0.00 0.00 2.69
3338 4866 7.552687 TGAGACATTTGACTATTATCACCCAAC 59.447 37.037 0.00 0.00 0.00 3.77
3342 4870 9.774742 GTTTTGAGACATTTGACTATTATCACC 57.225 33.333 0.00 0.00 0.00 4.02
3360 4888 7.063191 CACAACACAATTGTTCATGTTTTGAGA 59.937 33.333 8.77 0.00 44.57 3.27
3363 4891 6.829703 ACACAACACAATTGTTCATGTTTTG 58.170 32.000 8.77 14.60 44.57 2.44
3364 4892 8.715191 ATACACAACACAATTGTTCATGTTTT 57.285 26.923 8.77 0.50 44.57 2.43
3485 5016 7.242783 ACAAAACAACAGTTGAATGAAAATGC 58.757 30.769 20.56 0.00 0.00 3.56
3578 5109 2.471749 GCCGTTTTTGTACTCATCGACG 60.472 50.000 0.00 0.00 0.00 5.12
3612 5143 1.827969 CACAGAGGAGGAGAAATCGGT 59.172 52.381 0.00 0.00 0.00 4.69
3686 5217 2.131854 TCCTCTTCCTTGGGTTTGTCA 58.868 47.619 0.00 0.00 0.00 3.58
3716 5247 0.622136 AGCACTCATGAGGATTGGCA 59.378 50.000 26.08 0.00 0.00 4.92
3719 5250 2.089201 TGCAAGCACTCATGAGGATTG 58.911 47.619 26.08 25.61 32.26 2.67
3773 5304 6.097696 TCTGGAAAGAATGTGTGTATATCCGA 59.902 38.462 0.00 0.00 0.00 4.55
3782 5313 2.507484 TGGCTCTGGAAAGAATGTGTG 58.493 47.619 0.00 0.00 0.00 3.82
3812 5348 6.115446 TGCCTACTCAAGAAATGTAATCCAG 58.885 40.000 0.00 0.00 0.00 3.86
3887 5424 5.186992 ACCTAACAAAAGGCACCATTTATCC 59.813 40.000 0.00 0.00 40.62 2.59
3951 5488 4.378046 GCTTATTCCGACAACAACAACGAT 60.378 41.667 0.00 0.00 0.00 3.73
4010 5550 2.289547 TGCGTGTGGTTTTCTTCTAAGC 59.710 45.455 0.00 0.00 0.00 3.09
4011 5551 3.603857 CGTGCGTGTGGTTTTCTTCTAAG 60.604 47.826 0.00 0.00 0.00 2.18
4024 5564 3.345808 CCCCAACTCGTGCGTGTG 61.346 66.667 0.05 0.00 0.00 3.82
4042 5582 3.751698 AGCTCAATACAGAAACCGAAACC 59.248 43.478 0.00 0.00 0.00 3.27
4043 5583 5.147162 CAAGCTCAATACAGAAACCGAAAC 58.853 41.667 0.00 0.00 0.00 2.78
4087 5628 4.021229 ACCACCATCAGAATGTACGAGTA 58.979 43.478 0.00 0.00 37.40 2.59
4089 5630 3.190079 CACCACCATCAGAATGTACGAG 58.810 50.000 0.00 0.00 37.40 4.18
4090 5631 2.093711 CCACCACCATCAGAATGTACGA 60.094 50.000 0.00 0.00 37.40 3.43
4091 5632 2.279741 CCACCACCATCAGAATGTACG 58.720 52.381 0.00 0.00 37.40 3.67
4092 5633 3.270877 GACCACCACCATCAGAATGTAC 58.729 50.000 0.00 0.00 37.40 2.90
4099 5640 1.947678 GCTTCTGACCACCACCATCAG 60.948 57.143 0.00 0.00 41.06 2.90
4108 5649 3.190874 CGGAATAAGAGCTTCTGACCAC 58.809 50.000 0.00 0.00 31.85 4.16
4137 5678 7.153985 TCAGTTCAACCAAATCATCCAAATTC 58.846 34.615 0.00 0.00 0.00 2.17
4139 5764 6.669125 TCAGTTCAACCAAATCATCCAAAT 57.331 33.333 0.00 0.00 0.00 2.32
4223 6896 0.321298 TACTTGGGCAGAAACCGAGC 60.321 55.000 0.00 0.00 42.28 5.03
4225 6898 4.080807 TCAATATACTTGGGCAGAAACCGA 60.081 41.667 0.00 0.00 0.00 4.69
4244 6917 5.097742 TGACCACACGGATCTAAATCAAT 57.902 39.130 0.00 0.00 35.59 2.57
4259 6932 6.693466 TCATTTTCGTAAGTATCTGACCACA 58.307 36.000 0.00 0.00 39.48 4.17
4260 6933 7.772332 ATCATTTTCGTAAGTATCTGACCAC 57.228 36.000 0.00 0.00 39.48 4.16
4274 6947 5.227152 GTGGCCAAAGTTTATCATTTTCGT 58.773 37.500 7.24 0.00 0.00 3.85
4275 6948 4.323336 CGTGGCCAAAGTTTATCATTTTCG 59.677 41.667 7.24 0.00 0.00 3.46
4276 6949 5.465935 TCGTGGCCAAAGTTTATCATTTTC 58.534 37.500 7.24 0.00 0.00 2.29
4288 7017 7.543868 TCAATTAACAATAATTCGTGGCCAAAG 59.456 33.333 7.24 4.75 39.21 2.77
4290 7019 6.925211 TCAATTAACAATAATTCGTGGCCAA 58.075 32.000 7.24 0.00 39.21 4.52
4292 7021 8.349983 AGTATCAATTAACAATAATTCGTGGCC 58.650 33.333 0.00 0.00 39.21 5.36
4319 7080 5.333875 CCGTTGTTTTTCTTCTACCAGTAGC 60.334 44.000 0.00 0.00 33.32 3.58
4325 7086 2.619646 TGGCCGTTGTTTTTCTTCTACC 59.380 45.455 0.00 0.00 0.00 3.18
4341 7102 2.693591 TCTCAATACCTACTTCTGGCCG 59.306 50.000 0.00 0.00 0.00 6.13
4344 7105 3.700038 ACGGTCTCAATACCTACTTCTGG 59.300 47.826 0.00 0.00 37.39 3.86
4346 7107 4.342359 ACACGGTCTCAATACCTACTTCT 58.658 43.478 0.00 0.00 37.39 2.85
4349 7110 6.786967 ATTAACACGGTCTCAATACCTACT 57.213 37.500 0.00 0.00 37.39 2.57
4376 7138 4.724399 TCTTTGGCCTGTCATTTTAGACA 58.276 39.130 3.32 0.00 45.64 3.41
4389 7151 2.352805 CGCCTCCTTCTTTGGCCT 59.647 61.111 3.32 0.00 43.42 5.19
4392 7154 1.675641 CACCCGCCTCCTTCTTTGG 60.676 63.158 0.00 0.00 0.00 3.28
4394 7156 1.198759 TAGCACCCGCCTCCTTCTTT 61.199 55.000 0.00 0.00 39.83 2.52
4395 7157 1.612442 TAGCACCCGCCTCCTTCTT 60.612 57.895 0.00 0.00 39.83 2.52
4396 7158 2.038975 TAGCACCCGCCTCCTTCT 59.961 61.111 0.00 0.00 39.83 2.85
4397 7159 2.187163 GTAGCACCCGCCTCCTTC 59.813 66.667 0.00 0.00 39.83 3.46
4398 7160 3.771160 CGTAGCACCCGCCTCCTT 61.771 66.667 0.00 0.00 39.83 3.36
4399 7161 4.753662 TCGTAGCACCCGCCTCCT 62.754 66.667 0.00 0.00 39.83 3.69
4400 7162 4.509737 GTCGTAGCACCCGCCTCC 62.510 72.222 0.00 0.00 39.83 4.30
4401 7163 2.502692 AAAGTCGTAGCACCCGCCTC 62.503 60.000 0.00 0.00 39.83 4.70
4402 7164 2.108278 AAAAGTCGTAGCACCCGCCT 62.108 55.000 0.00 0.00 39.83 5.52
4403 7165 1.670083 AAAAGTCGTAGCACCCGCC 60.670 57.895 0.00 0.00 39.83 6.13
4404 7166 0.947180 TCAAAAGTCGTAGCACCCGC 60.947 55.000 0.00 0.00 38.99 6.13
4407 7169 3.303791 CCAAGTTCAAAAGTCGTAGCACC 60.304 47.826 0.00 0.00 0.00 5.01
4459 7221 5.010314 TCAGCTTCTGAACAAAAATCATGCT 59.990 36.000 0.00 0.00 37.57 3.79
4460 7222 5.224888 TCAGCTTCTGAACAAAAATCATGC 58.775 37.500 0.00 0.00 37.57 4.06
4461 7223 6.250739 CGATCAGCTTCTGAACAAAAATCATG 59.749 38.462 0.27 0.00 44.04 3.07
4462 7224 6.149973 TCGATCAGCTTCTGAACAAAAATCAT 59.850 34.615 0.27 0.00 44.04 2.45
4463 7225 5.469760 TCGATCAGCTTCTGAACAAAAATCA 59.530 36.000 0.27 0.00 44.04 2.57
4464 7226 5.931532 TCGATCAGCTTCTGAACAAAAATC 58.068 37.500 0.27 0.00 44.04 2.17
4465 7227 5.106396 CCTCGATCAGCTTCTGAACAAAAAT 60.106 40.000 0.27 0.00 44.04 1.82
4466 7228 4.214119 CCTCGATCAGCTTCTGAACAAAAA 59.786 41.667 0.27 0.00 44.04 1.94
4519 7281 1.742146 CATTGCGGATCGAGGAGGA 59.258 57.895 0.00 0.00 0.00 3.71
4520 7282 1.958205 GCATTGCGGATCGAGGAGG 60.958 63.158 0.00 0.00 0.00 4.30
4521 7283 3.635204 GCATTGCGGATCGAGGAG 58.365 61.111 0.00 0.00 0.00 3.69
4577 7339 4.107363 ACGCTGCTAGTAGTAGAAAACC 57.893 45.455 18.39 0.31 28.61 3.27
4598 7360 0.105224 TTCCTTCCTCACGACGCAAA 59.895 50.000 0.00 0.00 0.00 3.68
4635 7397 4.830765 TGGTATCGGCGCTGCACC 62.831 66.667 24.95 24.95 0.00 5.01
4649 7411 1.374252 CGACGCAGGTAGCTTTGGT 60.374 57.895 0.00 0.00 42.61 3.67


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

AutoCloner maintained by Alex Coulton.