Multiple sequence alignment - TraesCS5A01G109300

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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 TraesCS5A01G109300 chr5A 100.000 4334 0 0 1 4334 198653866 198649533 0.000000e+00 8004
1 TraesCS5A01G109300 chr5B 94.664 3373 99 29 624 3940 182989363 182992710 0.000000e+00 5156
2 TraesCS5A01G109300 chr5B 90.099 202 19 1 413 613 182988785 182988986 1.200000e-65 261
3 TraesCS5A01G109300 chr5B 92.035 113 5 3 1 112 182988659 182988768 5.800000e-34 156
4 TraesCS5A01G109300 chr5D 94.035 1995 44 18 625 2580 174800588 174798630 0.000000e+00 2955
5 TraesCS5A01G109300 chr5D 96.341 738 24 2 3204 3940 174796461 174795726 0.000000e+00 1210
6 TraesCS5A01G109300 chr5D 90.438 617 48 8 1 613 174801575 174800966 0.000000e+00 802
7 TraesCS5A01G109300 chr5D 98.378 370 6 0 2788 3157 174796930 174796561 0.000000e+00 651
8 TraesCS5A01G109300 chr5D 88.177 406 21 13 3939 4334 481880472 481880084 3.950000e-125 459
9 TraesCS5A01G109300 chr5D 94.505 182 7 2 2579 2757 174798580 174798399 1.190000e-70 278
10 TraesCS5A01G109300 chr7D 91.807 415 18 14 3930 4334 637191636 637192044 8.140000e-157 564
11 TraesCS5A01G109300 chr7D 92.443 397 16 13 3944 4332 231008197 231007807 4.900000e-154 555
12 TraesCS5A01G109300 chr7A 90.865 416 21 15 3930 4334 728660418 728660827 3.810000e-150 542
13 TraesCS5A01G109300 chr3A 91.542 402 17 10 3940 4334 739557681 739557290 4.930000e-149 538
14 TraesCS5A01G109300 chr4B 89.136 405 28 10 3940 4334 442960360 442960758 1.400000e-134 490
15 TraesCS5A01G109300 chr2B 91.124 338 18 9 3995 4325 5600142 5600474 8.550000e-122 448
16 TraesCS5A01G109300 chr3B 84.539 401 33 19 3940 4334 829368317 829368694 1.900000e-98 370
17 TraesCS5A01G109300 chr2D 82.673 404 36 22 3939 4334 456961898 456962275 1.160000e-85 327


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 TraesCS5A01G109300 chr5A 198649533 198653866 4333 True 8004.000000 8004 100.0000 1 4334 1 chr5A.!!$R1 4333
1 TraesCS5A01G109300 chr5B 182988659 182992710 4051 False 1857.666667 5156 92.2660 1 3940 3 chr5B.!!$F1 3939
2 TraesCS5A01G109300 chr5D 174795726 174801575 5849 True 1179.200000 2955 94.7394 1 3940 5 chr5D.!!$R2 3939

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
408 413 1.202533 CCCGTTCAACCGCATCTATCT 60.203 52.381 0.0 0.0 0.00 1.98 F
1183 1581 0.932399 CGACGACAACGGTTTCCTTT 59.068 50.000 0.0 0.0 44.46 3.11 F
1698 2102 1.153086 GCAGAGGATGGGCATCGTT 60.153 57.895 0.0 0.0 38.69 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 2102 1.056660 GGTCCTTTGTGAGGGTGAGA 58.943 55.000 0.00 0.0 46.31 3.27 R
2950 4862 0.304705 CGACGTTGCTGCTGAACTTT 59.695 50.000 0.00 0.0 0.00 2.66 R
3636 5601 1.135721 GCCTTCATGTTCTGGCATTCC 59.864 52.381 13.16 0.0 44.34 3.01 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
26 27 5.529800 TGTACTAGAGGGCAAACACTTTTTC 59.470 40.000 0.00 0.00 0.00 2.29
27 28 3.889538 ACTAGAGGGCAAACACTTTTTCC 59.110 43.478 0.00 0.00 0.00 3.13
28 29 2.039418 AGAGGGCAAACACTTTTTCCC 58.961 47.619 0.00 0.00 45.91 3.97
86 90 4.384647 GCAATACCCCAGAAATCTGAGAGT 60.385 45.833 11.94 8.21 46.59 3.24
189 194 6.773976 ATGCCGAAATCTCTCCAAATTAAA 57.226 33.333 0.00 0.00 0.00 1.52
204 209 8.795842 TCCAAATTAAATAAGATGTGTACCGT 57.204 30.769 0.00 0.00 0.00 4.83
207 212 8.670135 CAAATTAAATAAGATGTGTACCGTCCA 58.330 33.333 0.00 0.00 0.00 4.02
245 250 5.487433 TCACATGATTTAATCGGTGTGTCT 58.513 37.500 26.80 4.98 43.27 3.41
247 252 6.023435 CACATGATTTAATCGGTGTGTCTTG 58.977 40.000 23.20 8.25 40.55 3.02
298 303 5.097529 GTGACATAACGAAAGGACATACGA 58.902 41.667 0.00 0.00 0.00 3.43
304 309 2.295349 ACGAAAGGACATACGACACACT 59.705 45.455 0.00 0.00 0.00 3.55
305 310 2.915463 CGAAAGGACATACGACACACTC 59.085 50.000 0.00 0.00 0.00 3.51
306 311 3.366070 CGAAAGGACATACGACACACTCT 60.366 47.826 0.00 0.00 0.00 3.24
308 313 2.791655 AGGACATACGACACACTCTCA 58.208 47.619 0.00 0.00 0.00 3.27
325 330 6.886459 ACACTCTCATAAACCATTAGCACATT 59.114 34.615 0.00 0.00 0.00 2.71
408 413 1.202533 CCCGTTCAACCGCATCTATCT 60.203 52.381 0.00 0.00 0.00 1.98
411 416 4.307432 CCGTTCAACCGCATCTATCTAAT 58.693 43.478 0.00 0.00 0.00 1.73
412 417 4.150627 CCGTTCAACCGCATCTATCTAATG 59.849 45.833 0.00 0.00 0.00 1.90
430 435 1.913778 TGGTTCACGCCACTCTAGTA 58.086 50.000 0.00 0.00 32.81 1.82
455 460 4.492791 AGCGTTAAACATGTTTACCACC 57.507 40.909 26.72 17.05 35.05 4.61
474 479 2.038557 ACCAGACACGTTTAGCATCCTT 59.961 45.455 0.00 0.00 0.00 3.36
617 622 7.865706 AATGTCTACTGTCACTTTTTCAAGT 57.134 32.000 0.00 0.00 44.72 3.16
618 623 6.903883 TGTCTACTGTCACTTTTTCAAGTC 57.096 37.500 0.00 0.00 41.69 3.01
619 624 6.403049 TGTCTACTGTCACTTTTTCAAGTCA 58.597 36.000 0.00 0.00 41.69 3.41
620 625 6.876789 TGTCTACTGTCACTTTTTCAAGTCAA 59.123 34.615 0.00 0.00 41.69 3.18
621 626 7.389330 TGTCTACTGTCACTTTTTCAAGTCAAA 59.611 33.333 0.00 0.00 41.69 2.69
622 627 8.398665 GTCTACTGTCACTTTTTCAAGTCAAAT 58.601 33.333 0.00 0.00 41.69 2.32
689 1069 7.938140 TGTTTTTCAGGGTCTAAATATCTGG 57.062 36.000 0.00 0.00 0.00 3.86
949 1335 5.779241 TCCTCTCCACAAACCAATCTAAT 57.221 39.130 0.00 0.00 0.00 1.73
1183 1581 0.932399 CGACGACAACGGTTTCCTTT 59.068 50.000 0.00 0.00 44.46 3.11
1367 1765 4.436998 GGACCTCCTGTGTCCGCG 62.437 72.222 0.00 0.00 42.63 6.46
1698 2102 1.153086 GCAGAGGATGGGCATCGTT 60.153 57.895 0.00 0.00 38.69 3.85
1762 2166 5.130975 TCTCTCAATGTACATGGGTAAGCAT 59.869 40.000 9.63 0.00 0.00 3.79
1775 2179 6.909550 TGGGTAAGCATCATGTTTTTAACT 57.090 33.333 0.00 0.00 0.00 2.24
1776 2180 7.296628 TGGGTAAGCATCATGTTTTTAACTT 57.703 32.000 0.00 0.00 0.00 2.66
1777 2181 7.731054 TGGGTAAGCATCATGTTTTTAACTTT 58.269 30.769 0.00 0.00 0.00 2.66
1778 2182 7.655328 TGGGTAAGCATCATGTTTTTAACTTTG 59.345 33.333 0.00 0.00 0.00 2.77
1779 2183 7.655732 GGGTAAGCATCATGTTTTTAACTTTGT 59.344 33.333 0.00 0.00 0.00 2.83
1780 2184 9.040939 GGTAAGCATCATGTTTTTAACTTTGTT 57.959 29.630 0.00 0.00 0.00 2.83
1781 2185 9.848172 GTAAGCATCATGTTTTTAACTTTGTTG 57.152 29.630 0.00 0.00 0.00 3.33
1782 2186 7.481275 AGCATCATGTTTTTAACTTTGTTGG 57.519 32.000 0.00 0.00 0.00 3.77
1783 2187 7.047271 AGCATCATGTTTTTAACTTTGTTGGT 58.953 30.769 0.00 0.00 0.00 3.67
1784 2188 7.011295 AGCATCATGTTTTTAACTTTGTTGGTG 59.989 33.333 0.00 0.00 31.25 4.17
1785 2189 7.010923 GCATCATGTTTTTAACTTTGTTGGTGA 59.989 33.333 0.00 0.00 0.00 4.02
1786 2190 9.044150 CATCATGTTTTTAACTTTGTTGGTGAT 57.956 29.630 0.00 0.00 0.00 3.06
1808 2212 7.965107 GTGATAATTGAACTTTGTTCCTGCTAG 59.035 37.037 7.81 0.00 0.00 3.42
1870 2274 6.909895 TGTTGATAAATGTTGTGTCGTTTCTG 59.090 34.615 0.00 0.00 0.00 3.02
1872 2276 2.774439 AATGTTGTGTCGTTTCTGGC 57.226 45.000 0.00 0.00 0.00 4.85
1894 2298 1.429930 TCAGGACAAGGGCAGTACAA 58.570 50.000 0.00 0.00 0.00 2.41
2185 2594 5.985781 TGATCGCTTCAGAAAAGTTTGTAC 58.014 37.500 0.00 0.00 0.00 2.90
2194 2603 6.285990 TCAGAAAAGTTTGTACTAGACCACC 58.714 40.000 0.00 0.00 33.17 4.61
2253 2670 4.612943 TGTTACCTGAATTTTCCGCAAAC 58.387 39.130 0.00 0.00 0.00 2.93
2300 2717 8.877864 ATTTTACCAAACTGATATGTTCCTGA 57.122 30.769 0.00 0.00 0.00 3.86
2308 2725 5.911752 ACTGATATGTTCCTGATCAGACAC 58.088 41.667 24.62 18.60 46.31 3.67
2511 2928 6.780198 AGATGCCTATGGGTAAAAATCCTA 57.220 37.500 0.00 0.00 34.45 2.94
2517 2934 6.636336 GCCTATGGGTAAAAATCCTACCTTGA 60.636 42.308 0.00 0.00 39.11 3.02
2518 2935 7.351166 CCTATGGGTAAAAATCCTACCTTGAA 58.649 38.462 0.00 0.00 39.11 2.69
2526 2943 2.409064 TCCTACCTTGAACTCCACCA 57.591 50.000 0.00 0.00 0.00 4.17
2550 2967 7.094975 CCAGTAATTTTTCATGTAACCACGAGA 60.095 37.037 0.00 0.00 0.00 4.04
2568 2985 3.071479 GAGACCGGTAAAACAAGCATGA 58.929 45.455 7.34 0.00 0.00 3.07
2950 4862 0.994247 ACATCCACCTCTCCATGCAA 59.006 50.000 0.00 0.00 0.00 4.08
2968 4880 2.111756 CAAAAGTTCAGCAGCAACGTC 58.888 47.619 0.00 0.00 0.00 4.34
3113 5025 4.154918 CAGCACTTCAGAATTCCAAGGTAC 59.845 45.833 15.74 7.38 0.00 3.34
3181 5124 3.803555 GACAATATGTCTATGCTTGCGC 58.196 45.455 0.00 0.00 43.73 6.09
3395 5360 6.681777 AGATTGTTTGTCCTGTGCTATTTTC 58.318 36.000 0.00 0.00 0.00 2.29
3636 5601 1.164411 TGCCCTGCAATTACTCAACG 58.836 50.000 0.00 0.00 34.76 4.10
3760 5725 7.398618 TGGGCAGAGGAAATCACAATTAAAATA 59.601 33.333 0.00 0.00 0.00 1.40
3897 5865 3.868661 TCAATATGTTTCACCGTCCGATG 59.131 43.478 0.00 0.00 0.00 3.84
3936 5904 3.960571 AGATCTTCCAATTGTCCCACAG 58.039 45.455 4.43 0.00 0.00 3.66
3940 5908 2.342650 CCAATTGTCCCACAGGCGG 61.343 63.158 4.43 0.00 0.00 6.13
3941 5909 2.676471 AATTGTCCCACAGGCGGC 60.676 61.111 0.00 0.00 0.00 6.53
3942 5910 3.505790 AATTGTCCCACAGGCGGCA 62.506 57.895 13.08 0.00 0.00 5.69
3943 5911 2.992817 AATTGTCCCACAGGCGGCAA 62.993 55.000 13.08 0.00 0.00 4.52
3944 5912 2.992817 ATTGTCCCACAGGCGGCAAA 62.993 55.000 13.08 0.00 0.00 3.68
3945 5913 3.670377 GTCCCACAGGCGGCAAAC 61.670 66.667 13.08 0.00 0.00 2.93
3946 5914 4.966787 TCCCACAGGCGGCAAACC 62.967 66.667 13.08 0.00 0.00 3.27
3948 5916 4.974721 CCACAGGCGGCAAACCCT 62.975 66.667 13.08 0.00 0.00 4.34
3949 5917 2.033448 CACAGGCGGCAAACCCTA 59.967 61.111 13.08 0.00 0.00 3.53
3950 5918 1.378514 CACAGGCGGCAAACCCTAT 60.379 57.895 13.08 0.00 0.00 2.57
3951 5919 0.965363 CACAGGCGGCAAACCCTATT 60.965 55.000 13.08 0.00 0.00 1.73
3952 5920 0.251608 ACAGGCGGCAAACCCTATTT 60.252 50.000 13.08 0.00 0.00 1.40
3953 5921 0.173255 CAGGCGGCAAACCCTATTTG 59.827 55.000 13.08 0.00 0.00 2.32
3954 5922 0.039035 AGGCGGCAAACCCTATTTGA 59.961 50.000 13.08 0.00 0.00 2.69
3955 5923 0.172578 GGCGGCAAACCCTATTTGAC 59.827 55.000 3.07 0.00 34.19 3.18
3957 5925 3.713936 GGCAAACCCTATTTGACGC 57.286 52.632 3.62 0.00 0.00 5.19
3958 5926 1.173913 GGCAAACCCTATTTGACGCT 58.826 50.000 3.62 0.00 0.00 5.07
3959 5927 1.132453 GGCAAACCCTATTTGACGCTC 59.868 52.381 3.62 0.00 0.00 5.03
3960 5928 1.202031 GCAAACCCTATTTGACGCTCG 60.202 52.381 3.62 0.00 0.00 5.03
3961 5929 2.073816 CAAACCCTATTTGACGCTCGT 58.926 47.619 0.00 0.00 0.00 4.18
3962 5930 2.467566 AACCCTATTTGACGCTCGTT 57.532 45.000 0.00 0.00 0.00 3.85
3963 5931 3.598019 AACCCTATTTGACGCTCGTTA 57.402 42.857 0.00 0.00 0.00 3.18
3964 5932 3.160777 ACCCTATTTGACGCTCGTTAG 57.839 47.619 0.00 0.00 0.00 2.34
3965 5933 1.859080 CCCTATTTGACGCTCGTTAGC 59.141 52.381 0.00 0.00 45.86 3.09
3985 5953 1.205657 GTCAGAACGACGTGCTTTCA 58.794 50.000 5.51 0.00 34.19 2.69
3986 5954 1.071436 GTCAGAACGACGTGCTTTCAC 60.071 52.381 5.51 0.00 39.78 3.18
3987 5955 1.202371 TCAGAACGACGTGCTTTCACT 60.202 47.619 5.51 0.00 40.99 3.41
3988 5956 1.071239 CAGAACGACGTGCTTTCACTG 60.071 52.381 5.51 2.18 40.99 3.66
3989 5957 1.202371 AGAACGACGTGCTTTCACTGA 60.202 47.619 1.50 0.00 40.99 3.41
3990 5958 1.190323 GAACGACGTGCTTTCACTGAG 59.810 52.381 0.00 0.00 40.99 3.35
3991 5959 0.597637 ACGACGTGCTTTCACTGAGG 60.598 55.000 0.00 0.00 40.99 3.86
3992 5960 1.862806 GACGTGCTTTCACTGAGGC 59.137 57.895 0.00 0.73 40.99 4.70
3993 5961 1.891060 GACGTGCTTTCACTGAGGCG 61.891 60.000 0.00 0.00 40.99 5.52
3994 5962 1.664649 CGTGCTTTCACTGAGGCGA 60.665 57.895 0.00 0.00 40.99 5.54
3995 5963 1.621301 CGTGCTTTCACTGAGGCGAG 61.621 60.000 0.00 0.00 40.99 5.03
3996 5964 1.669115 TGCTTTCACTGAGGCGAGC 60.669 57.895 0.00 0.00 0.00 5.03
3997 5965 2.394563 GCTTTCACTGAGGCGAGCC 61.395 63.158 5.89 5.89 0.00 4.70
4006 5974 3.710722 AGGCGAGCCTCCTGTTGG 61.711 66.667 11.42 0.00 44.43 3.77
4007 5975 4.785453 GGCGAGCCTCCTGTTGGG 62.785 72.222 6.90 0.00 0.00 4.12
4030 5998 2.888534 CCACGTACGGGATTGGCG 60.889 66.667 21.47 0.00 0.00 5.69
4031 5999 2.125832 CACGTACGGGATTGGCGT 60.126 61.111 21.06 0.00 36.13 5.68
4032 6000 1.738830 CACGTACGGGATTGGCGTT 60.739 57.895 21.06 0.00 33.28 4.84
4033 6001 1.004679 ACGTACGGGATTGGCGTTT 60.005 52.632 21.06 0.00 31.37 3.60
4034 6002 1.293267 ACGTACGGGATTGGCGTTTG 61.293 55.000 21.06 0.00 31.37 2.93
4035 6003 1.135939 GTACGGGATTGGCGTTTGC 59.864 57.895 0.00 0.00 41.71 3.68
4036 6004 1.003112 TACGGGATTGGCGTTTGCT 60.003 52.632 0.00 0.00 42.25 3.91
4037 6005 1.302383 TACGGGATTGGCGTTTGCTG 61.302 55.000 0.00 0.00 42.25 4.41
4038 6006 2.625823 CGGGATTGGCGTTTGCTGT 61.626 57.895 0.00 0.00 42.25 4.40
4039 6007 1.665442 GGGATTGGCGTTTGCTGTT 59.335 52.632 0.00 0.00 42.25 3.16
4040 6008 0.033366 GGGATTGGCGTTTGCTGTTT 59.967 50.000 0.00 0.00 42.25 2.83
4041 6009 1.139163 GGATTGGCGTTTGCTGTTTG 58.861 50.000 0.00 0.00 42.25 2.93
4042 6010 1.269517 GGATTGGCGTTTGCTGTTTGA 60.270 47.619 0.00 0.00 42.25 2.69
4043 6011 2.610232 GGATTGGCGTTTGCTGTTTGAT 60.610 45.455 0.00 0.00 42.25 2.57
4044 6012 2.593346 TTGGCGTTTGCTGTTTGATT 57.407 40.000 0.00 0.00 42.25 2.57
4045 6013 2.132740 TGGCGTTTGCTGTTTGATTC 57.867 45.000 0.00 0.00 42.25 2.52
4046 6014 1.052287 GGCGTTTGCTGTTTGATTCG 58.948 50.000 0.00 0.00 42.25 3.34
4047 6015 1.599419 GGCGTTTGCTGTTTGATTCGT 60.599 47.619 0.00 0.00 42.25 3.85
4048 6016 2.116366 GCGTTTGCTGTTTGATTCGTT 58.884 42.857 0.00 0.00 38.39 3.85
4049 6017 2.151172 GCGTTTGCTGTTTGATTCGTTC 59.849 45.455 0.00 0.00 38.39 3.95
4050 6018 3.617669 CGTTTGCTGTTTGATTCGTTCT 58.382 40.909 0.00 0.00 0.00 3.01
4051 6019 4.035017 CGTTTGCTGTTTGATTCGTTCTT 58.965 39.130 0.00 0.00 0.00 2.52
4052 6020 4.086126 CGTTTGCTGTTTGATTCGTTCTTG 60.086 41.667 0.00 0.00 0.00 3.02
4053 6021 2.998772 TGCTGTTTGATTCGTTCTTGC 58.001 42.857 0.00 0.00 0.00 4.01
4054 6022 2.618241 TGCTGTTTGATTCGTTCTTGCT 59.382 40.909 0.00 0.00 0.00 3.91
4055 6023 2.975851 GCTGTTTGATTCGTTCTTGCTG 59.024 45.455 0.00 0.00 0.00 4.41
4056 6024 2.975851 CTGTTTGATTCGTTCTTGCTGC 59.024 45.455 0.00 0.00 0.00 5.25
4057 6025 2.618241 TGTTTGATTCGTTCTTGCTGCT 59.382 40.909 0.00 0.00 0.00 4.24
4058 6026 2.975410 TTGATTCGTTCTTGCTGCTG 57.025 45.000 0.00 0.00 0.00 4.41
4059 6027 0.518636 TGATTCGTTCTTGCTGCTGC 59.481 50.000 8.89 8.89 40.20 5.25
4060 6028 0.801251 GATTCGTTCTTGCTGCTGCT 59.199 50.000 17.00 0.00 40.48 4.24
4061 6029 1.198637 GATTCGTTCTTGCTGCTGCTT 59.801 47.619 17.00 0.00 40.48 3.91
4062 6030 0.588252 TTCGTTCTTGCTGCTGCTTC 59.412 50.000 17.00 2.33 40.48 3.86
4063 6031 1.208614 CGTTCTTGCTGCTGCTTCC 59.791 57.895 17.00 0.00 40.48 3.46
4064 6032 1.233285 CGTTCTTGCTGCTGCTTCCT 61.233 55.000 17.00 0.00 40.48 3.36
4065 6033 0.957362 GTTCTTGCTGCTGCTTCCTT 59.043 50.000 17.00 0.00 40.48 3.36
4066 6034 1.068679 GTTCTTGCTGCTGCTTCCTTC 60.069 52.381 17.00 0.14 40.48 3.46
4067 6035 0.399454 TCTTGCTGCTGCTTCCTTCT 59.601 50.000 17.00 0.00 40.48 2.85
4068 6036 0.803740 CTTGCTGCTGCTTCCTTCTC 59.196 55.000 17.00 0.00 40.48 2.87
4069 6037 0.399454 TTGCTGCTGCTTCCTTCTCT 59.601 50.000 17.00 0.00 40.48 3.10
4070 6038 1.269958 TGCTGCTGCTTCCTTCTCTA 58.730 50.000 17.00 0.00 40.48 2.43
4071 6039 1.836166 TGCTGCTGCTTCCTTCTCTAT 59.164 47.619 17.00 0.00 40.48 1.98
4072 6040 2.238144 TGCTGCTGCTTCCTTCTCTATT 59.762 45.455 17.00 0.00 40.48 1.73
4073 6041 2.871633 GCTGCTGCTTCCTTCTCTATTC 59.128 50.000 8.53 0.00 36.03 1.75
4074 6042 3.432046 GCTGCTGCTTCCTTCTCTATTCT 60.432 47.826 8.53 0.00 36.03 2.40
4075 6043 4.768583 CTGCTGCTTCCTTCTCTATTCTT 58.231 43.478 0.00 0.00 0.00 2.52
4076 6044 4.511527 TGCTGCTTCCTTCTCTATTCTTG 58.488 43.478 0.00 0.00 0.00 3.02
4077 6045 3.312146 GCTGCTTCCTTCTCTATTCTTGC 59.688 47.826 0.00 0.00 0.00 4.01
4078 6046 4.768583 CTGCTTCCTTCTCTATTCTTGCT 58.231 43.478 0.00 0.00 0.00 3.91
4079 6047 4.511527 TGCTTCCTTCTCTATTCTTGCTG 58.488 43.478 0.00 0.00 0.00 4.41
4080 6048 3.876320 GCTTCCTTCTCTATTCTTGCTGG 59.124 47.826 0.00 0.00 0.00 4.85
4081 6049 4.625083 GCTTCCTTCTCTATTCTTGCTGGT 60.625 45.833 0.00 0.00 0.00 4.00
4082 6050 5.495640 CTTCCTTCTCTATTCTTGCTGGTT 58.504 41.667 0.00 0.00 0.00 3.67
4083 6051 5.505181 TCCTTCTCTATTCTTGCTGGTTT 57.495 39.130 0.00 0.00 0.00 3.27
4084 6052 5.880901 TCCTTCTCTATTCTTGCTGGTTTT 58.119 37.500 0.00 0.00 0.00 2.43
4085 6053 6.306987 TCCTTCTCTATTCTTGCTGGTTTTT 58.693 36.000 0.00 0.00 0.00 1.94
4140 6108 4.522722 TTTTTCACTGTTTTTGTCCGGT 57.477 36.364 0.00 0.00 0.00 5.28
4141 6109 4.522722 TTTTCACTGTTTTTGTCCGGTT 57.477 36.364 0.00 0.00 0.00 4.44
4142 6110 4.522722 TTTCACTGTTTTTGTCCGGTTT 57.477 36.364 0.00 0.00 0.00 3.27
4143 6111 4.522722 TTCACTGTTTTTGTCCGGTTTT 57.477 36.364 0.00 0.00 0.00 2.43
4144 6112 4.099380 TCACTGTTTTTGTCCGGTTTTC 57.901 40.909 0.00 0.00 0.00 2.29
4145 6113 3.506455 TCACTGTTTTTGTCCGGTTTTCA 59.494 39.130 0.00 0.00 0.00 2.69
4146 6114 3.857093 CACTGTTTTTGTCCGGTTTTCAG 59.143 43.478 0.00 5.38 0.00 3.02
4147 6115 2.857748 CTGTTTTTGTCCGGTTTTCAGC 59.142 45.455 0.00 0.00 0.00 4.26
4148 6116 2.494073 TGTTTTTGTCCGGTTTTCAGCT 59.506 40.909 0.00 0.00 0.00 4.24
4149 6117 3.113322 GTTTTTGTCCGGTTTTCAGCTC 58.887 45.455 0.00 0.00 0.00 4.09
4150 6118 2.341846 TTTGTCCGGTTTTCAGCTCT 57.658 45.000 0.00 0.00 0.00 4.09
4151 6119 2.341846 TTGTCCGGTTTTCAGCTCTT 57.658 45.000 0.00 0.00 0.00 2.85
4152 6120 2.341846 TGTCCGGTTTTCAGCTCTTT 57.658 45.000 0.00 0.00 0.00 2.52
4153 6121 2.650322 TGTCCGGTTTTCAGCTCTTTT 58.350 42.857 0.00 0.00 0.00 2.27
4154 6122 2.357637 TGTCCGGTTTTCAGCTCTTTTG 59.642 45.455 0.00 0.00 0.00 2.44
4155 6123 2.357952 GTCCGGTTTTCAGCTCTTTTGT 59.642 45.455 0.00 0.00 0.00 2.83
4156 6124 3.020984 TCCGGTTTTCAGCTCTTTTGTT 58.979 40.909 0.00 0.00 0.00 2.83
4157 6125 3.066203 TCCGGTTTTCAGCTCTTTTGTTC 59.934 43.478 0.00 0.00 0.00 3.18
4158 6126 3.372060 CGGTTTTCAGCTCTTTTGTTCC 58.628 45.455 0.00 0.00 0.00 3.62
4159 6127 3.372060 GGTTTTCAGCTCTTTTGTTCCG 58.628 45.455 0.00 0.00 0.00 4.30
4160 6128 3.372060 GTTTTCAGCTCTTTTGTTCCGG 58.628 45.455 0.00 0.00 0.00 5.14
4161 6129 2.341846 TTCAGCTCTTTTGTTCCGGT 57.658 45.000 0.00 0.00 0.00 5.28
4162 6130 2.341846 TCAGCTCTTTTGTTCCGGTT 57.658 45.000 0.00 0.00 0.00 4.44
4163 6131 2.650322 TCAGCTCTTTTGTTCCGGTTT 58.350 42.857 0.00 0.00 0.00 3.27
4164 6132 3.020984 TCAGCTCTTTTGTTCCGGTTTT 58.979 40.909 0.00 0.00 0.00 2.43
4165 6133 3.445805 TCAGCTCTTTTGTTCCGGTTTTT 59.554 39.130 0.00 0.00 0.00 1.94
4166 6134 4.641094 TCAGCTCTTTTGTTCCGGTTTTTA 59.359 37.500 0.00 0.00 0.00 1.52
4167 6135 5.300792 TCAGCTCTTTTGTTCCGGTTTTTAT 59.699 36.000 0.00 0.00 0.00 1.40
4168 6136 6.487331 TCAGCTCTTTTGTTCCGGTTTTTATA 59.513 34.615 0.00 0.00 0.00 0.98
4169 6137 7.175990 TCAGCTCTTTTGTTCCGGTTTTTATAT 59.824 33.333 0.00 0.00 0.00 0.86
4170 6138 7.812669 CAGCTCTTTTGTTCCGGTTTTTATATT 59.187 33.333 0.00 0.00 0.00 1.28
4171 6139 8.364894 AGCTCTTTTGTTCCGGTTTTTATATTT 58.635 29.630 0.00 0.00 0.00 1.40
4172 6140 8.984764 GCTCTTTTGTTCCGGTTTTTATATTTT 58.015 29.630 0.00 0.00 0.00 1.82
4196 6164 7.718334 TTTTTCTCTCTTTTGGTTCCTTTCT 57.282 32.000 0.00 0.00 0.00 2.52
4197 6165 6.944234 TTTCTCTCTTTTGGTTCCTTTCTC 57.056 37.500 0.00 0.00 0.00 2.87
4198 6166 4.974399 TCTCTCTTTTGGTTCCTTTCTCC 58.026 43.478 0.00 0.00 0.00 3.71
4199 6167 4.660771 TCTCTCTTTTGGTTCCTTTCTCCT 59.339 41.667 0.00 0.00 0.00 3.69
4200 6168 5.132816 TCTCTCTTTTGGTTCCTTTCTCCTT 59.867 40.000 0.00 0.00 0.00 3.36
4201 6169 5.766590 TCTCTTTTGGTTCCTTTCTCCTTT 58.233 37.500 0.00 0.00 0.00 3.11
4202 6170 5.828328 TCTCTTTTGGTTCCTTTCTCCTTTC 59.172 40.000 0.00 0.00 0.00 2.62
4203 6171 5.515106 TCTTTTGGTTCCTTTCTCCTTTCA 58.485 37.500 0.00 0.00 0.00 2.69
4204 6172 6.136155 TCTTTTGGTTCCTTTCTCCTTTCAT 58.864 36.000 0.00 0.00 0.00 2.57
4205 6173 6.611236 TCTTTTGGTTCCTTTCTCCTTTCATT 59.389 34.615 0.00 0.00 0.00 2.57
4206 6174 6.806668 TTTGGTTCCTTTCTCCTTTCATTT 57.193 33.333 0.00 0.00 0.00 2.32
4207 6175 6.806668 TTGGTTCCTTTCTCCTTTCATTTT 57.193 33.333 0.00 0.00 0.00 1.82
4208 6176 6.806668 TGGTTCCTTTCTCCTTTCATTTTT 57.193 33.333 0.00 0.00 0.00 1.94
4209 6177 6.816136 TGGTTCCTTTCTCCTTTCATTTTTC 58.184 36.000 0.00 0.00 0.00 2.29
4210 6178 6.611236 TGGTTCCTTTCTCCTTTCATTTTTCT 59.389 34.615 0.00 0.00 0.00 2.52
4211 6179 7.125659 TGGTTCCTTTCTCCTTTCATTTTTCTT 59.874 33.333 0.00 0.00 0.00 2.52
4212 6180 7.987458 GGTTCCTTTCTCCTTTCATTTTTCTTT 59.013 33.333 0.00 0.00 0.00 2.52
4213 6181 9.383519 GTTCCTTTCTCCTTTCATTTTTCTTTT 57.616 29.630 0.00 0.00 0.00 2.27
4252 6220 7.888250 ATTTCTGTTTCTGTTTTCCTTCTCT 57.112 32.000 0.00 0.00 0.00 3.10
4253 6221 7.703058 TTTCTGTTTCTGTTTTCCTTCTCTT 57.297 32.000 0.00 0.00 0.00 2.85
4254 6222 7.703058 TTCTGTTTCTGTTTTCCTTCTCTTT 57.297 32.000 0.00 0.00 0.00 2.52
4255 6223 8.801882 TTCTGTTTCTGTTTTCCTTCTCTTTA 57.198 30.769 0.00 0.00 0.00 1.85
4256 6224 8.980481 TCTGTTTCTGTTTTCCTTCTCTTTAT 57.020 30.769 0.00 0.00 0.00 1.40
4257 6225 9.408648 TCTGTTTCTGTTTTCCTTCTCTTTATT 57.591 29.630 0.00 0.00 0.00 1.40
4258 6226 9.455847 CTGTTTCTGTTTTCCTTCTCTTTATTG 57.544 33.333 0.00 0.00 0.00 1.90
4259 6227 7.920682 TGTTTCTGTTTTCCTTCTCTTTATTGC 59.079 33.333 0.00 0.00 0.00 3.56
4260 6228 6.241207 TCTGTTTTCCTTCTCTTTATTGCG 57.759 37.500 0.00 0.00 0.00 4.85
4261 6229 5.763204 TCTGTTTTCCTTCTCTTTATTGCGT 59.237 36.000 0.00 0.00 0.00 5.24
4262 6230 6.932400 TCTGTTTTCCTTCTCTTTATTGCGTA 59.068 34.615 0.00 0.00 0.00 4.42
4263 6231 7.606456 TCTGTTTTCCTTCTCTTTATTGCGTAT 59.394 33.333 0.00 0.00 0.00 3.06
4264 6232 8.106247 TGTTTTCCTTCTCTTTATTGCGTATT 57.894 30.769 0.00 0.00 0.00 1.89
4265 6233 9.221933 TGTTTTCCTTCTCTTTATTGCGTATTA 57.778 29.630 0.00 0.00 0.00 0.98
4280 6248 7.410800 TTGCGTATTATATAAAAGTCCACCG 57.589 36.000 0.00 0.00 0.00 4.94
4281 6249 6.514947 TGCGTATTATATAAAAGTCCACCGT 58.485 36.000 0.00 0.00 0.00 4.83
4282 6250 6.421501 TGCGTATTATATAAAAGTCCACCGTG 59.578 38.462 0.00 0.00 0.00 4.94
4283 6251 6.421801 GCGTATTATATAAAAGTCCACCGTGT 59.578 38.462 0.00 0.00 0.00 4.49
4284 6252 7.594758 GCGTATTATATAAAAGTCCACCGTGTA 59.405 37.037 0.00 0.00 0.00 2.90
4285 6253 9.630098 CGTATTATATAAAAGTCCACCGTGTAT 57.370 33.333 0.00 0.00 0.00 2.29
4289 6257 9.762933 TTATATAAAAGTCCACCGTGTATTACC 57.237 33.333 0.00 0.00 0.00 2.85
4290 6258 4.354893 AAAAGTCCACCGTGTATTACCA 57.645 40.909 0.00 0.00 0.00 3.25
4291 6259 4.354893 AAAGTCCACCGTGTATTACCAA 57.645 40.909 0.00 0.00 0.00 3.67
4292 6260 4.354893 AAGTCCACCGTGTATTACCAAA 57.645 40.909 0.00 0.00 0.00 3.28
4293 6261 4.354893 AGTCCACCGTGTATTACCAAAA 57.645 40.909 0.00 0.00 0.00 2.44
4294 6262 4.913784 AGTCCACCGTGTATTACCAAAAT 58.086 39.130 0.00 0.00 0.00 1.82
4295 6263 4.939439 AGTCCACCGTGTATTACCAAAATC 59.061 41.667 0.00 0.00 0.00 2.17
4296 6264 4.939439 GTCCACCGTGTATTACCAAAATCT 59.061 41.667 0.00 0.00 0.00 2.40
4297 6265 5.413523 GTCCACCGTGTATTACCAAAATCTT 59.586 40.000 0.00 0.00 0.00 2.40
4298 6266 5.644636 TCCACCGTGTATTACCAAAATCTTC 59.355 40.000 0.00 0.00 0.00 2.87
4299 6267 5.413213 CCACCGTGTATTACCAAAATCTTCA 59.587 40.000 0.00 0.00 0.00 3.02
4300 6268 6.094881 CCACCGTGTATTACCAAAATCTTCAT 59.905 38.462 0.00 0.00 0.00 2.57
4301 6269 7.186804 CACCGTGTATTACCAAAATCTTCATC 58.813 38.462 0.00 0.00 0.00 2.92
4302 6270 6.036735 ACCGTGTATTACCAAAATCTTCATCG 59.963 38.462 0.00 0.00 0.00 3.84
4303 6271 6.036735 CCGTGTATTACCAAAATCTTCATCGT 59.963 38.462 0.00 0.00 0.00 3.73
4304 6272 7.223193 CCGTGTATTACCAAAATCTTCATCGTA 59.777 37.037 0.00 0.00 0.00 3.43
4305 6273 8.054236 CGTGTATTACCAAAATCTTCATCGTAC 58.946 37.037 0.00 0.00 0.00 3.67
4306 6274 9.095065 GTGTATTACCAAAATCTTCATCGTACT 57.905 33.333 0.00 0.00 0.00 2.73
4311 6279 9.932207 TTACCAAAATCTTCATCGTACTAAGAA 57.068 29.630 0.00 0.00 33.26 2.52
4312 6280 8.842358 ACCAAAATCTTCATCGTACTAAGAAA 57.158 30.769 0.00 0.00 33.26 2.52
4313 6281 9.280174 ACCAAAATCTTCATCGTACTAAGAAAA 57.720 29.630 0.00 0.00 33.26 2.29
4319 6287 9.653287 ATCTTCATCGTACTAAGAAAATGTTCA 57.347 29.630 0.00 0.00 36.09 3.18
4320 6288 9.653287 TCTTCATCGTACTAAGAAAATGTTCAT 57.347 29.630 0.00 0.00 36.09 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.654091 TTGTTTGCAAGAAAGAAGAGGG 57.346 40.909 0.00 0.00 0.00 4.30
53 57 9.193806 GATTTCTGGGGTATTGCAATGATATAT 57.806 33.333 22.27 0.00 0.00 0.86
147 151 5.163519 CGGCATAGGAAAAGGACATTTTGAT 60.164 40.000 1.97 0.00 41.24 2.57
148 152 4.157656 CGGCATAGGAAAAGGACATTTTGA 59.842 41.667 1.97 0.00 41.24 2.69
149 153 4.157656 TCGGCATAGGAAAAGGACATTTTG 59.842 41.667 1.97 0.00 41.24 2.44
150 154 4.340617 TCGGCATAGGAAAAGGACATTTT 58.659 39.130 0.00 0.00 43.88 1.82
151 155 3.963129 TCGGCATAGGAAAAGGACATTT 58.037 40.909 0.00 0.00 0.00 2.32
189 194 5.416271 AAGTTGGACGGTACACATCTTAT 57.584 39.130 0.00 0.00 0.00 1.73
239 244 4.395959 AGAAACTCGTTACCAAGACACA 57.604 40.909 0.00 0.00 0.00 3.72
245 250 7.972832 ATTCATGTAAGAAACTCGTTACCAA 57.027 32.000 0.00 0.00 0.00 3.67
274 279 4.860352 CGTATGTCCTTTCGTTATGTCACA 59.140 41.667 0.00 0.00 0.00 3.58
282 287 3.054878 GTGTGTCGTATGTCCTTTCGTT 58.945 45.455 0.00 0.00 0.00 3.85
284 289 2.915463 GAGTGTGTCGTATGTCCTTTCG 59.085 50.000 0.00 0.00 0.00 3.46
298 303 5.643777 GTGCTAATGGTTTATGAGAGTGTGT 59.356 40.000 0.00 0.00 0.00 3.72
304 309 7.701539 ACAAATGTGCTAATGGTTTATGAGA 57.298 32.000 0.00 0.00 0.00 3.27
305 310 9.669353 GATACAAATGTGCTAATGGTTTATGAG 57.331 33.333 0.00 0.00 0.00 2.90
306 311 9.407380 AGATACAAATGTGCTAATGGTTTATGA 57.593 29.630 0.00 0.00 0.00 2.15
369 374 9.621629 TGAACGGGTGAAATCTATTGTATATTT 57.378 29.630 0.00 0.00 0.00 1.40
370 375 9.621629 TTGAACGGGTGAAATCTATTGTATATT 57.378 29.630 0.00 0.00 0.00 1.28
380 385 1.519408 CGGTTGAACGGGTGAAATCT 58.481 50.000 0.00 0.00 0.00 2.40
384 389 1.228003 ATGCGGTTGAACGGGTGAA 60.228 52.632 5.04 0.00 0.00 3.18
408 413 2.829720 ACTAGAGTGGCGTGAACCATTA 59.170 45.455 0.00 0.00 43.01 1.90
411 416 1.913778 TACTAGAGTGGCGTGAACCA 58.086 50.000 0.00 0.00 37.38 3.67
412 417 3.521947 AATACTAGAGTGGCGTGAACC 57.478 47.619 0.00 0.00 0.00 3.62
430 435 7.085746 GGTGGTAAACATGTTTAACGCTAAAT 58.914 34.615 38.71 15.73 46.66 1.40
455 460 3.325870 TGAAGGATGCTAAACGTGTCTG 58.674 45.455 0.00 0.00 0.00 3.51
609 614 9.616156 TGTACCACTTAGTATTTGACTTGAAAA 57.384 29.630 0.00 0.00 39.81 2.29
613 618 7.063544 GCTCTGTACCACTTAGTATTTGACTTG 59.936 40.741 0.00 0.00 39.81 3.16
614 619 7.038941 AGCTCTGTACCACTTAGTATTTGACTT 60.039 37.037 0.00 0.00 39.81 3.01
615 620 6.437793 AGCTCTGTACCACTTAGTATTTGACT 59.562 38.462 0.00 0.00 42.69 3.41
617 622 6.852420 AGCTCTGTACCACTTAGTATTTGA 57.148 37.500 0.00 0.00 0.00 2.69
618 623 7.819900 AGAAAGCTCTGTACCACTTAGTATTTG 59.180 37.037 0.00 0.00 0.00 2.32
619 624 7.819900 CAGAAAGCTCTGTACCACTTAGTATTT 59.180 37.037 0.00 0.00 43.64 1.40
620 625 7.324178 CAGAAAGCTCTGTACCACTTAGTATT 58.676 38.462 0.00 0.00 43.64 1.89
621 626 6.127310 CCAGAAAGCTCTGTACCACTTAGTAT 60.127 42.308 2.63 0.00 46.71 2.12
622 627 5.185249 CCAGAAAGCTCTGTACCACTTAGTA 59.815 44.000 2.63 0.00 46.71 1.82
684 1058 8.801882 TCCGATTTTCTATTTTAACACCAGAT 57.198 30.769 0.00 0.00 0.00 2.90
689 1069 8.635983 GCACTTTCCGATTTTCTATTTTAACAC 58.364 33.333 0.00 0.00 0.00 3.32
949 1335 5.222233 TGAGAAAATCAGTGGGGGAATTGTA 60.222 40.000 0.00 0.00 32.77 2.41
1183 1581 3.015145 GCTGGCCTTCCTGGGGTA 61.015 66.667 3.32 0.00 36.00 3.69
1338 1736 4.988716 AGGTCCCAGTCGTCGCCA 62.989 66.667 0.00 0.00 0.00 5.69
1698 2102 1.056660 GGTCCTTTGTGAGGGTGAGA 58.943 55.000 0.00 0.00 46.31 3.27
1775 2179 9.092876 GAACAAAGTTCAATTATCACCAACAAA 57.907 29.630 5.09 0.00 0.00 2.83
1776 2180 7.708752 GGAACAAAGTTCAATTATCACCAACAA 59.291 33.333 11.51 0.00 0.00 2.83
1777 2181 7.069331 AGGAACAAAGTTCAATTATCACCAACA 59.931 33.333 11.51 0.00 0.00 3.33
1778 2182 7.382218 CAGGAACAAAGTTCAATTATCACCAAC 59.618 37.037 11.51 0.00 0.00 3.77
1779 2183 7.432869 CAGGAACAAAGTTCAATTATCACCAA 58.567 34.615 11.51 0.00 0.00 3.67
1780 2184 6.516527 GCAGGAACAAAGTTCAATTATCACCA 60.517 38.462 11.51 0.00 0.00 4.17
1781 2185 5.863935 GCAGGAACAAAGTTCAATTATCACC 59.136 40.000 11.51 0.00 0.00 4.02
1782 2186 6.681777 AGCAGGAACAAAGTTCAATTATCAC 58.318 36.000 11.51 0.00 0.00 3.06
1783 2187 6.899393 AGCAGGAACAAAGTTCAATTATCA 57.101 33.333 11.51 0.00 0.00 2.15
1784 2188 8.045176 ACTAGCAGGAACAAAGTTCAATTATC 57.955 34.615 11.51 0.00 0.00 1.75
1785 2189 8.299570 CAACTAGCAGGAACAAAGTTCAATTAT 58.700 33.333 11.51 0.00 0.00 1.28
1786 2190 7.284489 ACAACTAGCAGGAACAAAGTTCAATTA 59.716 33.333 11.51 0.00 0.00 1.40
1787 2191 6.096846 ACAACTAGCAGGAACAAAGTTCAATT 59.903 34.615 11.51 0.00 0.00 2.32
1788 2192 5.594317 ACAACTAGCAGGAACAAAGTTCAAT 59.406 36.000 11.51 0.00 0.00 2.57
1789 2193 4.947388 ACAACTAGCAGGAACAAAGTTCAA 59.053 37.500 11.51 0.00 0.00 2.69
1790 2194 4.523083 ACAACTAGCAGGAACAAAGTTCA 58.477 39.130 11.51 0.00 0.00 3.18
1791 2195 5.500645 AACAACTAGCAGGAACAAAGTTC 57.499 39.130 1.37 1.37 0.00 3.01
1792 2196 5.914898 AAACAACTAGCAGGAACAAAGTT 57.085 34.783 0.00 0.00 0.00 2.66
1793 2197 5.914898 AAAACAACTAGCAGGAACAAAGT 57.085 34.783 0.00 0.00 0.00 2.66
1850 2254 4.518970 AGCCAGAAACGACACAACATTTAT 59.481 37.500 0.00 0.00 0.00 1.40
1870 2274 1.228552 TGCCCTTGTCCTGAAAGCC 60.229 57.895 0.00 0.00 0.00 4.35
1872 2276 2.224523 TGTACTGCCCTTGTCCTGAAAG 60.225 50.000 0.00 0.00 0.00 2.62
1894 2298 4.502087 GCCCTCAAGCTTTCAATCAGTTTT 60.502 41.667 0.00 0.00 0.00 2.43
2113 2522 7.844779 TCTCTGGACCCAAATAGACTAACTTAT 59.155 37.037 0.00 0.00 0.00 1.73
2185 2594 2.232452 CAGACAAGTGGAGGTGGTCTAG 59.768 54.545 0.00 0.00 36.74 2.43
2194 2603 4.543692 CTGCAAAATTCAGACAAGTGGAG 58.456 43.478 0.00 0.00 33.54 3.86
2300 2717 9.155975 GTAGATTGTGAGTTAATTGTGTCTGAT 57.844 33.333 0.00 0.00 0.00 2.90
2511 2928 4.724279 AATTACTGGTGGAGTTCAAGGT 57.276 40.909 0.00 0.00 35.96 3.50
2517 2934 6.976934 ACATGAAAAATTACTGGTGGAGTT 57.023 33.333 0.00 0.00 35.96 3.01
2518 2935 7.039993 GGTTACATGAAAAATTACTGGTGGAGT 60.040 37.037 0.00 0.00 38.88 3.85
2526 2943 7.094933 GGTCTCGTGGTTACATGAAAAATTACT 60.095 37.037 0.00 0.00 41.81 2.24
2550 2967 5.968528 TTAATCATGCTTGTTTTACCGGT 57.031 34.783 13.98 13.98 0.00 5.28
2816 4728 6.047870 AGCAGATAAGCTCATGAGTTTACAG 58.952 40.000 27.85 21.37 42.18 2.74
2950 4862 0.304705 CGACGTTGCTGCTGAACTTT 59.695 50.000 0.00 0.00 0.00 2.66
2968 4880 2.069273 ACTTTCAGGCATTTCTCGACG 58.931 47.619 0.00 0.00 0.00 5.12
3113 5025 7.041167 TGACTCTGTTTTGGTTGAGATGTTATG 60.041 37.037 0.00 0.00 0.00 1.90
3181 5124 5.413833 ACATCAACAAAATGGCTCAGTAGAG 59.586 40.000 0.00 0.00 44.96 2.43
3383 5348 5.801350 TTGAATCCGAGAAAATAGCACAG 57.199 39.130 0.00 0.00 0.00 3.66
3395 5360 6.374333 TCACTTTTATCCCTTTTGAATCCGAG 59.626 38.462 0.00 0.00 0.00 4.63
3629 5594 1.202758 TGTTCTGGCATTCCGTTGAGT 60.203 47.619 0.00 0.00 34.14 3.41
3636 5601 1.135721 GCCTTCATGTTCTGGCATTCC 59.864 52.381 13.16 0.00 44.34 3.01
3737 5702 8.250332 TGGTATTTTAATTGTGATTTCCTCTGC 58.750 33.333 0.00 0.00 0.00 4.26
3760 5725 8.447833 CGTTCATGTTGTGTTAACTATAATGGT 58.552 33.333 7.22 0.00 0.00 3.55
3769 5734 3.002862 TGCTCCGTTCATGTTGTGTTAAC 59.997 43.478 0.00 0.00 0.00 2.01
3897 5865 9.213799 GGAAGATCTAGAATGTCCAATTATGTC 57.786 37.037 12.00 0.00 0.00 3.06
3910 5878 6.069440 TGTGGGACAATTGGAAGATCTAGAAT 60.069 38.462 10.83 0.00 44.16 2.40
3936 5904 0.172578 GTCAAATAGGGTTTGCCGCC 59.827 55.000 0.00 0.00 34.97 6.13
3940 5908 1.202031 CGAGCGTCAAATAGGGTTTGC 60.202 52.381 0.00 0.00 0.00 3.68
3941 5909 2.073816 ACGAGCGTCAAATAGGGTTTG 58.926 47.619 0.00 0.00 0.00 2.93
3942 5910 2.467566 ACGAGCGTCAAATAGGGTTT 57.532 45.000 0.00 0.00 0.00 3.27
3943 5911 2.467566 AACGAGCGTCAAATAGGGTT 57.532 45.000 0.00 0.00 0.00 4.11
3944 5912 2.737679 GCTAACGAGCGTCAAATAGGGT 60.738 50.000 0.00 0.00 39.39 4.34
3945 5913 1.859080 GCTAACGAGCGTCAAATAGGG 59.141 52.381 0.00 0.00 39.39 3.53
3966 5934 1.071436 GTGAAAGCACGTCGTTCTGAC 60.071 52.381 0.00 0.00 44.53 3.51
3967 5935 1.205657 GTGAAAGCACGTCGTTCTGA 58.794 50.000 0.00 0.00 34.94 3.27
3968 5936 3.710233 GTGAAAGCACGTCGTTCTG 57.290 52.632 0.00 0.00 34.94 3.02
3977 5945 1.905922 GCTCGCCTCAGTGAAAGCAC 61.906 60.000 13.59 0.00 45.49 4.40
3978 5946 1.669115 GCTCGCCTCAGTGAAAGCA 60.669 57.895 13.59 2.60 30.51 3.91
3979 5947 2.394563 GGCTCGCCTCAGTGAAAGC 61.395 63.158 0.00 4.99 30.51 3.51
3980 5948 1.294780 AGGCTCGCCTCAGTGAAAG 59.705 57.895 4.23 0.00 44.43 2.62
3981 5949 3.471620 AGGCTCGCCTCAGTGAAA 58.528 55.556 4.23 0.00 44.43 2.69
3990 5958 4.785453 CCCAACAGGAGGCTCGCC 62.785 72.222 8.69 0.00 38.24 5.54
4013 5981 2.888534 CGCCAATCCCGTACGTGG 60.889 66.667 15.21 15.72 0.00 4.94
4014 5982 1.293267 AAACGCCAATCCCGTACGTG 61.293 55.000 15.21 2.17 38.06 4.49
4015 5983 1.004679 AAACGCCAATCCCGTACGT 60.005 52.632 15.21 0.00 38.06 3.57
4016 5984 1.422269 CAAACGCCAATCCCGTACG 59.578 57.895 8.69 8.69 38.06 3.67
4017 5985 1.135939 GCAAACGCCAATCCCGTAC 59.864 57.895 0.00 0.00 38.06 3.67
4018 5986 1.003112 AGCAAACGCCAATCCCGTA 60.003 52.632 0.00 0.00 38.06 4.02
4019 5987 2.282180 AGCAAACGCCAATCCCGT 60.282 55.556 0.00 0.00 41.24 5.28
4020 5988 2.141122 AACAGCAAACGCCAATCCCG 62.141 55.000 0.00 0.00 0.00 5.14
4021 5989 0.033366 AAACAGCAAACGCCAATCCC 59.967 50.000 0.00 0.00 0.00 3.85
4022 5990 1.139163 CAAACAGCAAACGCCAATCC 58.861 50.000 0.00 0.00 0.00 3.01
4023 5991 2.132740 TCAAACAGCAAACGCCAATC 57.867 45.000 0.00 0.00 0.00 2.67
4024 5992 2.818130 ATCAAACAGCAAACGCCAAT 57.182 40.000 0.00 0.00 0.00 3.16
4025 5993 2.468831 GAATCAAACAGCAAACGCCAA 58.531 42.857 0.00 0.00 0.00 4.52
4026 5994 1.599171 CGAATCAAACAGCAAACGCCA 60.599 47.619 0.00 0.00 0.00 5.69
4027 5995 1.052287 CGAATCAAACAGCAAACGCC 58.948 50.000 0.00 0.00 0.00 5.68
4028 5996 1.753956 ACGAATCAAACAGCAAACGC 58.246 45.000 0.00 0.00 0.00 4.84
4029 5997 3.617669 AGAACGAATCAAACAGCAAACG 58.382 40.909 0.00 0.00 0.00 3.60
4030 5998 4.317348 GCAAGAACGAATCAAACAGCAAAC 60.317 41.667 0.00 0.00 0.00 2.93
4031 5999 3.796178 GCAAGAACGAATCAAACAGCAAA 59.204 39.130 0.00 0.00 0.00 3.68
4032 6000 3.066621 AGCAAGAACGAATCAAACAGCAA 59.933 39.130 0.00 0.00 0.00 3.91
4033 6001 2.618241 AGCAAGAACGAATCAAACAGCA 59.382 40.909 0.00 0.00 0.00 4.41
4034 6002 2.975851 CAGCAAGAACGAATCAAACAGC 59.024 45.455 0.00 0.00 0.00 4.40
4035 6003 2.975851 GCAGCAAGAACGAATCAAACAG 59.024 45.455 0.00 0.00 0.00 3.16
4036 6004 2.618241 AGCAGCAAGAACGAATCAAACA 59.382 40.909 0.00 0.00 0.00 2.83
4037 6005 2.975851 CAGCAGCAAGAACGAATCAAAC 59.024 45.455 0.00 0.00 0.00 2.93
4038 6006 2.605338 GCAGCAGCAAGAACGAATCAAA 60.605 45.455 0.00 0.00 41.58 2.69
4039 6007 1.069022 GCAGCAGCAAGAACGAATCAA 60.069 47.619 0.00 0.00 41.58 2.57
4040 6008 0.518636 GCAGCAGCAAGAACGAATCA 59.481 50.000 0.00 0.00 41.58 2.57
4041 6009 0.801251 AGCAGCAGCAAGAACGAATC 59.199 50.000 3.17 0.00 45.49 2.52
4042 6010 1.198637 GAAGCAGCAGCAAGAACGAAT 59.801 47.619 3.17 0.00 45.49 3.34
4043 6011 0.588252 GAAGCAGCAGCAAGAACGAA 59.412 50.000 3.17 0.00 45.49 3.85
4044 6012 1.230635 GGAAGCAGCAGCAAGAACGA 61.231 55.000 3.17 0.00 45.49 3.85
4045 6013 1.208614 GGAAGCAGCAGCAAGAACG 59.791 57.895 3.17 0.00 45.49 3.95
4046 6014 0.957362 AAGGAAGCAGCAGCAAGAAC 59.043 50.000 3.17 0.00 45.49 3.01
4047 6015 1.202855 AGAAGGAAGCAGCAGCAAGAA 60.203 47.619 3.17 0.00 45.49 2.52
4048 6016 0.399454 AGAAGGAAGCAGCAGCAAGA 59.601 50.000 3.17 0.00 45.49 3.02
4049 6017 0.803740 GAGAAGGAAGCAGCAGCAAG 59.196 55.000 3.17 0.00 45.49 4.01
4050 6018 0.399454 AGAGAAGGAAGCAGCAGCAA 59.601 50.000 3.17 0.00 45.49 3.91
4051 6019 1.269958 TAGAGAAGGAAGCAGCAGCA 58.730 50.000 3.17 0.00 45.49 4.41
4052 6020 2.618442 ATAGAGAAGGAAGCAGCAGC 57.382 50.000 0.00 0.00 42.56 5.25
4053 6021 4.405116 AGAATAGAGAAGGAAGCAGCAG 57.595 45.455 0.00 0.00 0.00 4.24
4054 6022 4.511527 CAAGAATAGAGAAGGAAGCAGCA 58.488 43.478 0.00 0.00 0.00 4.41
4055 6023 3.312146 GCAAGAATAGAGAAGGAAGCAGC 59.688 47.826 0.00 0.00 0.00 5.25
4056 6024 4.571580 CAGCAAGAATAGAGAAGGAAGCAG 59.428 45.833 0.00 0.00 0.00 4.24
4057 6025 4.511527 CAGCAAGAATAGAGAAGGAAGCA 58.488 43.478 0.00 0.00 0.00 3.91
4058 6026 3.876320 CCAGCAAGAATAGAGAAGGAAGC 59.124 47.826 0.00 0.00 0.00 3.86
4059 6027 5.096443 ACCAGCAAGAATAGAGAAGGAAG 57.904 43.478 0.00 0.00 0.00 3.46
4060 6028 5.505181 AACCAGCAAGAATAGAGAAGGAA 57.495 39.130 0.00 0.00 0.00 3.36
4061 6029 5.505181 AAACCAGCAAGAATAGAGAAGGA 57.495 39.130 0.00 0.00 0.00 3.36
4062 6030 6.581171 AAAAACCAGCAAGAATAGAGAAGG 57.419 37.500 0.00 0.00 0.00 3.46
4119 6087 4.522722 ACCGGACAAAAACAGTGAAAAA 57.477 36.364 9.46 0.00 0.00 1.94
4120 6088 4.522722 AACCGGACAAAAACAGTGAAAA 57.477 36.364 9.46 0.00 0.00 2.29
4121 6089 4.522722 AAACCGGACAAAAACAGTGAAA 57.477 36.364 9.46 0.00 0.00 2.69
4122 6090 4.022242 TGAAAACCGGACAAAAACAGTGAA 60.022 37.500 9.46 0.00 0.00 3.18
4123 6091 3.506455 TGAAAACCGGACAAAAACAGTGA 59.494 39.130 9.46 0.00 0.00 3.41
4124 6092 3.839293 TGAAAACCGGACAAAAACAGTG 58.161 40.909 9.46 0.00 0.00 3.66
4125 6093 3.674955 GCTGAAAACCGGACAAAAACAGT 60.675 43.478 9.46 0.00 0.00 3.55
4126 6094 2.857748 GCTGAAAACCGGACAAAAACAG 59.142 45.455 9.46 9.19 0.00 3.16
4127 6095 2.494073 AGCTGAAAACCGGACAAAAACA 59.506 40.909 9.46 0.00 0.00 2.83
4128 6096 3.113322 GAGCTGAAAACCGGACAAAAAC 58.887 45.455 9.46 0.00 0.00 2.43
4129 6097 3.020984 AGAGCTGAAAACCGGACAAAAA 58.979 40.909 9.46 0.00 0.00 1.94
4130 6098 2.650322 AGAGCTGAAAACCGGACAAAA 58.350 42.857 9.46 0.00 0.00 2.44
4131 6099 2.341846 AGAGCTGAAAACCGGACAAA 57.658 45.000 9.46 0.00 0.00 2.83
4132 6100 2.341846 AAGAGCTGAAAACCGGACAA 57.658 45.000 9.46 0.00 0.00 3.18
4133 6101 2.341846 AAAGAGCTGAAAACCGGACA 57.658 45.000 9.46 1.56 0.00 4.02
4134 6102 2.357952 ACAAAAGAGCTGAAAACCGGAC 59.642 45.455 9.46 0.00 0.00 4.79
4135 6103 2.650322 ACAAAAGAGCTGAAAACCGGA 58.350 42.857 9.46 0.00 0.00 5.14
4136 6104 3.372060 GAACAAAAGAGCTGAAAACCGG 58.628 45.455 0.00 0.00 0.00 5.28
4137 6105 3.372060 GGAACAAAAGAGCTGAAAACCG 58.628 45.455 0.00 0.00 0.00 4.44
4138 6106 3.372060 CGGAACAAAAGAGCTGAAAACC 58.628 45.455 0.00 0.00 0.00 3.27
4139 6107 3.181490 ACCGGAACAAAAGAGCTGAAAAC 60.181 43.478 9.46 0.00 0.00 2.43
4140 6108 3.020984 ACCGGAACAAAAGAGCTGAAAA 58.979 40.909 9.46 0.00 0.00 2.29
4141 6109 2.650322 ACCGGAACAAAAGAGCTGAAA 58.350 42.857 9.46 0.00 0.00 2.69
4142 6110 2.341846 ACCGGAACAAAAGAGCTGAA 57.658 45.000 9.46 0.00 0.00 3.02
4143 6111 2.341846 AACCGGAACAAAAGAGCTGA 57.658 45.000 9.46 0.00 0.00 4.26
4144 6112 3.436700 AAAACCGGAACAAAAGAGCTG 57.563 42.857 9.46 0.00 0.00 4.24
4145 6113 5.784578 ATAAAAACCGGAACAAAAGAGCT 57.215 34.783 9.46 0.00 0.00 4.09
4146 6114 8.528917 AAATATAAAAACCGGAACAAAAGAGC 57.471 30.769 9.46 0.00 0.00 4.09
4172 6140 7.147897 GGAGAAAGGAACCAAAAGAGAGAAAAA 60.148 37.037 0.00 0.00 0.00 1.94
4173 6141 6.321435 GGAGAAAGGAACCAAAAGAGAGAAAA 59.679 38.462 0.00 0.00 0.00 2.29
4174 6142 5.828328 GGAGAAAGGAACCAAAAGAGAGAAA 59.172 40.000 0.00 0.00 0.00 2.52
4175 6143 5.132816 AGGAGAAAGGAACCAAAAGAGAGAA 59.867 40.000 0.00 0.00 0.00 2.87
4176 6144 4.660771 AGGAGAAAGGAACCAAAAGAGAGA 59.339 41.667 0.00 0.00 0.00 3.10
4177 6145 4.979335 AGGAGAAAGGAACCAAAAGAGAG 58.021 43.478 0.00 0.00 0.00 3.20
4178 6146 5.388599 AAGGAGAAAGGAACCAAAAGAGA 57.611 39.130 0.00 0.00 0.00 3.10
4179 6147 5.594317 TGAAAGGAGAAAGGAACCAAAAGAG 59.406 40.000 0.00 0.00 0.00 2.85
4180 6148 5.515106 TGAAAGGAGAAAGGAACCAAAAGA 58.485 37.500 0.00 0.00 0.00 2.52
4181 6149 5.852282 TGAAAGGAGAAAGGAACCAAAAG 57.148 39.130 0.00 0.00 0.00 2.27
4182 6150 6.806668 AATGAAAGGAGAAAGGAACCAAAA 57.193 33.333 0.00 0.00 0.00 2.44
4183 6151 6.806668 AAATGAAAGGAGAAAGGAACCAAA 57.193 33.333 0.00 0.00 0.00 3.28
4184 6152 6.806668 AAAATGAAAGGAGAAAGGAACCAA 57.193 33.333 0.00 0.00 0.00 3.67
4185 6153 6.611236 AGAAAAATGAAAGGAGAAAGGAACCA 59.389 34.615 0.00 0.00 0.00 3.67
4186 6154 7.055667 AGAAAAATGAAAGGAGAAAGGAACC 57.944 36.000 0.00 0.00 0.00 3.62
4187 6155 8.948631 AAAGAAAAATGAAAGGAGAAAGGAAC 57.051 30.769 0.00 0.00 0.00 3.62
4226 6194 9.408648 AGAGAAGGAAAACAGAAACAGAAATAA 57.591 29.630 0.00 0.00 0.00 1.40
4227 6195 8.980481 AGAGAAGGAAAACAGAAACAGAAATA 57.020 30.769 0.00 0.00 0.00 1.40
4228 6196 7.888250 AGAGAAGGAAAACAGAAACAGAAAT 57.112 32.000 0.00 0.00 0.00 2.17
4229 6197 7.703058 AAGAGAAGGAAAACAGAAACAGAAA 57.297 32.000 0.00 0.00 0.00 2.52
4230 6198 7.703058 AAAGAGAAGGAAAACAGAAACAGAA 57.297 32.000 0.00 0.00 0.00 3.02
4231 6199 8.980481 ATAAAGAGAAGGAAAACAGAAACAGA 57.020 30.769 0.00 0.00 0.00 3.41
4232 6200 9.455847 CAATAAAGAGAAGGAAAACAGAAACAG 57.544 33.333 0.00 0.00 0.00 3.16
4233 6201 7.920682 GCAATAAAGAGAAGGAAAACAGAAACA 59.079 33.333 0.00 0.00 0.00 2.83
4234 6202 7.113544 CGCAATAAAGAGAAGGAAAACAGAAAC 59.886 37.037 0.00 0.00 0.00 2.78
4235 6203 7.138736 CGCAATAAAGAGAAGGAAAACAGAAA 58.861 34.615 0.00 0.00 0.00 2.52
4236 6204 6.262273 ACGCAATAAAGAGAAGGAAAACAGAA 59.738 34.615 0.00 0.00 0.00 3.02
4237 6205 5.763204 ACGCAATAAAGAGAAGGAAAACAGA 59.237 36.000 0.00 0.00 0.00 3.41
4238 6206 6.002062 ACGCAATAAAGAGAAGGAAAACAG 57.998 37.500 0.00 0.00 0.00 3.16
4239 6207 7.681939 ATACGCAATAAAGAGAAGGAAAACA 57.318 32.000 0.00 0.00 0.00 2.83
4254 6222 9.142515 CGGTGGACTTTTATATAATACGCAATA 57.857 33.333 0.00 0.00 0.00 1.90
4255 6223 7.658575 ACGGTGGACTTTTATATAATACGCAAT 59.341 33.333 0.00 0.00 0.00 3.56
4256 6224 6.985645 ACGGTGGACTTTTATATAATACGCAA 59.014 34.615 0.00 0.00 0.00 4.85
4257 6225 6.421501 CACGGTGGACTTTTATATAATACGCA 59.578 38.462 0.00 0.00 0.00 5.24
4258 6226 6.421801 ACACGGTGGACTTTTATATAATACGC 59.578 38.462 13.48 0.00 0.00 4.42
4259 6227 7.935338 ACACGGTGGACTTTTATATAATACG 57.065 36.000 13.48 0.00 0.00 3.06
4263 6231 9.762933 GGTAATACACGGTGGACTTTTATATAA 57.237 33.333 13.48 0.00 0.00 0.98
4264 6232 8.922237 TGGTAATACACGGTGGACTTTTATATA 58.078 33.333 13.48 0.00 0.00 0.86
4265 6233 7.794041 TGGTAATACACGGTGGACTTTTATAT 58.206 34.615 13.48 0.00 0.00 0.86
4266 6234 7.180322 TGGTAATACACGGTGGACTTTTATA 57.820 36.000 13.48 0.00 0.00 0.98
4267 6235 6.052405 TGGTAATACACGGTGGACTTTTAT 57.948 37.500 13.48 0.00 0.00 1.40
4268 6236 5.480642 TGGTAATACACGGTGGACTTTTA 57.519 39.130 13.48 0.00 0.00 1.52
4269 6237 4.354893 TGGTAATACACGGTGGACTTTT 57.645 40.909 13.48 0.00 0.00 2.27
4270 6238 4.354893 TTGGTAATACACGGTGGACTTT 57.645 40.909 13.48 0.00 0.00 2.66
4271 6239 4.354893 TTTGGTAATACACGGTGGACTT 57.645 40.909 13.48 5.35 0.00 3.01
4272 6240 4.354893 TTTTGGTAATACACGGTGGACT 57.645 40.909 13.48 0.00 0.00 3.85
4273 6241 4.939439 AGATTTTGGTAATACACGGTGGAC 59.061 41.667 13.48 4.83 0.00 4.02
4274 6242 5.168647 AGATTTTGGTAATACACGGTGGA 57.831 39.130 13.48 3.76 0.00 4.02
4275 6243 5.413213 TGAAGATTTTGGTAATACACGGTGG 59.587 40.000 13.48 0.00 0.00 4.61
4276 6244 6.489127 TGAAGATTTTGGTAATACACGGTG 57.511 37.500 6.58 6.58 0.00 4.94
4277 6245 6.036735 CGATGAAGATTTTGGTAATACACGGT 59.963 38.462 0.00 0.00 0.00 4.83
4278 6246 6.036735 ACGATGAAGATTTTGGTAATACACGG 59.963 38.462 0.00 0.00 0.00 4.94
4279 6247 7.000575 ACGATGAAGATTTTGGTAATACACG 57.999 36.000 0.00 0.00 0.00 4.49
4280 6248 9.095065 AGTACGATGAAGATTTTGGTAATACAC 57.905 33.333 0.00 0.00 0.00 2.90
4285 6253 9.932207 TTCTTAGTACGATGAAGATTTTGGTAA 57.068 29.630 0.00 0.00 0.00 2.85
4286 6254 9.932207 TTTCTTAGTACGATGAAGATTTTGGTA 57.068 29.630 4.85 0.00 0.00 3.25
4287 6255 8.842358 TTTCTTAGTACGATGAAGATTTTGGT 57.158 30.769 4.85 0.00 0.00 3.67
4293 6261 9.653287 TGAACATTTTCTTAGTACGATGAAGAT 57.347 29.630 4.85 3.93 32.36 2.40
4294 6262 9.653287 ATGAACATTTTCTTAGTACGATGAAGA 57.347 29.630 4.85 2.00 32.36 2.87


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

AutoCloner maintained by Alex Coulton.