Multiple sequence alignment - TraesCS7D01G180900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G180900 chr7D 100.000 2969 0 0 1 2969 134442255 134445223 0.000000e+00 5483.0
1 TraesCS7D01G180900 chr7D 84.422 199 22 7 1122 1314 134450929 134451124 1.410000e-43 187.0
2 TraesCS7D01G180900 chr7B 89.712 1769 135 27 797 2544 96585253 96586995 0.000000e+00 2215.0
3 TraesCS7D01G180900 chr7B 88.837 430 14 10 1 413 96583384 96583796 5.720000e-137 497.0
4 TraesCS7D01G180900 chr7B 81.116 233 35 5 1114 1337 96599976 96600208 8.460000e-41 178.0
5 TraesCS7D01G180900 chr7B 78.661 239 17 11 1 237 96527402 96527608 8.640000e-26 128.0
6 TraesCS7D01G180900 chr7B 100.000 64 0 0 2902 2965 96586986 96587049 5.200000e-23 119.0
7 TraesCS7D01G180900 chr7A 90.679 1266 73 14 559 1814 133605217 133606447 0.000000e+00 1642.0
8 TraesCS7D01G180900 chr7A 89.339 741 73 5 1808 2544 133614131 133614869 0.000000e+00 926.0
9 TraesCS7D01G180900 chr7A 81.952 543 26 19 1 512 133604697 133605198 7.710000e-106 394.0
10 TraesCS7D01G180900 chr7A 82.547 212 27 8 1114 1318 133624782 133624990 8.460000e-41 178.0
11 TraesCS7D01G180900 chr7A 88.406 69 3 2 2906 2969 133614866 133614934 8.820000e-11 78.7
12 TraesCS7D01G180900 chrUn 85.635 181 19 6 2720 2895 384243767 384243589 1.820000e-42 183.0
13 TraesCS7D01G180900 chr5A 86.765 68 7 2 2753 2818 651745353 651745286 1.140000e-09 75.0


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 TraesCS7D01G180900 chr7D 134442255 134445223 2968 False 5483.000000 5483 100.000000 1 2969 1 chr7D.!!$F1 2968
1 TraesCS7D01G180900 chr7B 96583384 96587049 3665 False 943.666667 2215 92.849667 1 2965 3 chr7B.!!$F3 2964
2 TraesCS7D01G180900 chr7A 133604697 133606447 1750 False 1018.000000 1642 86.315500 1 1814 2 chr7A.!!$F2 1813
3 TraesCS7D01G180900 chr7A 133614131 133614934 803 False 502.350000 926 88.872500 1808 2969 2 chr7A.!!$F3 1161

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
690 725 0.179062 ACTCGGATCTGAGCAATGCC 60.179 55.0 28.11 0.0 39.68 4.40 F
1019 2244 0.716591 ACACTCATCCCCTACTCCCA 59.283 55.0 0.00 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 3037 0.321653 GGTAGCCATAATCCAGCCCG 60.322 60.0 0.0 0.0 0.0 6.13 R
2885 4132 0.105964 TGACGGACAGGAACTTGGTG 59.894 55.0 0.0 0.0 34.6 4.17 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
40 41 1.954382 AGTTATCTAGCGCGATCACCA 59.046 47.619 12.10 0.00 0.00 4.17
41 42 2.558795 AGTTATCTAGCGCGATCACCAT 59.441 45.455 12.10 0.00 0.00 3.55
42 43 2.917971 GTTATCTAGCGCGATCACCATC 59.082 50.000 12.10 0.00 0.00 3.51
43 44 0.244994 ATCTAGCGCGATCACCATCC 59.755 55.000 12.10 0.00 0.00 3.51
44 45 1.373497 CTAGCGCGATCACCATCCC 60.373 63.158 12.10 0.00 0.00 3.85
280 300 4.655527 GTGTCAGTGTCACCTCGG 57.344 61.111 9.09 0.00 0.00 4.63
317 337 8.801882 TCTCCCAAAATATACAAGTTTGGTAG 57.198 34.615 13.87 9.01 46.54 3.18
319 339 9.675464 CTCCCAAAATATACAAGTTTGGTAGTA 57.325 33.333 13.87 0.00 46.54 1.82
320 340 9.452287 TCCCAAAATATACAAGTTTGGTAGTAC 57.548 33.333 13.87 0.00 46.54 2.73
321 341 9.457436 CCCAAAATATACAAGTTTGGTAGTACT 57.543 33.333 13.87 0.00 46.54 2.73
326 346 9.886132 AATATACAAGTTTGGTAGTACTCCTTG 57.114 33.333 0.00 6.27 35.23 3.61
327 347 5.881923 ACAAGTTTGGTAGTACTCCTTGA 57.118 39.130 19.20 0.00 33.75 3.02
328 348 5.608449 ACAAGTTTGGTAGTACTCCTTGAC 58.392 41.667 19.20 0.00 33.75 3.18
329 349 4.886496 AGTTTGGTAGTACTCCTTGACC 57.114 45.455 0.00 1.04 0.00 4.02
330 350 4.490706 AGTTTGGTAGTACTCCTTGACCT 58.509 43.478 12.01 0.00 0.00 3.85
331 351 5.648247 AGTTTGGTAGTACTCCTTGACCTA 58.352 41.667 12.01 3.15 0.00 3.08
332 352 5.479724 AGTTTGGTAGTACTCCTTGACCTAC 59.520 44.000 12.01 9.99 0.00 3.18
333 353 4.662966 TGGTAGTACTCCTTGACCTACA 57.337 45.455 12.01 0.00 31.72 2.74
334 354 4.597004 TGGTAGTACTCCTTGACCTACAG 58.403 47.826 12.01 0.00 31.72 2.74
340 360 3.093057 ACTCCTTGACCTACAGCTACAG 58.907 50.000 0.00 0.00 0.00 2.74
389 409 1.981256 TGAGTTTGGGTTGCTCCTTC 58.019 50.000 0.00 0.00 36.25 3.46
426 457 8.980596 AGGAGAGTCATCATAATATTGATCCTC 58.019 37.037 0.00 2.66 34.09 3.71
467 498 9.703892 CATAATATGGTGGTTGTCAAAAAGAAA 57.296 29.630 0.00 0.00 0.00 2.52
470 501 4.826556 TGGTGGTTGTCAAAAAGAAAAGG 58.173 39.130 0.00 0.00 0.00 3.11
473 504 3.056465 TGGTTGTCAAAAAGAAAAGGCGT 60.056 39.130 0.00 0.00 0.00 5.68
507 538 7.915293 ATCGTCAATAACATAACCTTCACAA 57.085 32.000 0.00 0.00 0.00 3.33
533 564 9.868277 AAAAAGTGAGTGAATTTCATGTTTGTA 57.132 25.926 1.78 0.00 0.00 2.41
534 565 9.868277 AAAAGTGAGTGAATTTCATGTTTGTAA 57.132 25.926 1.78 0.00 0.00 2.41
535 566 8.856490 AAGTGAGTGAATTTCATGTTTGTAAC 57.144 30.769 1.78 0.00 0.00 2.50
536 567 7.995289 AGTGAGTGAATTTCATGTTTGTAACA 58.005 30.769 1.78 0.00 46.94 2.41
537 568 8.465999 AGTGAGTGAATTTCATGTTTGTAACAA 58.534 29.630 1.78 0.00 45.86 2.83
538 569 9.081997 GTGAGTGAATTTCATGTTTGTAACAAA 57.918 29.630 1.78 0.00 45.86 2.83
539 570 9.645059 TGAGTGAATTTCATGTTTGTAACAAAA 57.355 25.926 1.78 0.00 45.86 2.44
587 618 4.584327 ATTTAAGCAAGGTTGTGTCACC 57.416 40.909 0.00 0.00 37.04 4.02
635 667 3.242870 GGACCAATCGAGCATCACATTTC 60.243 47.826 0.00 0.00 33.17 2.17
647 679 4.092383 GCATCACATTTCAATTTGTCCAGC 59.908 41.667 0.00 0.00 0.00 4.85
651 683 1.035923 TTTCAATTTGTCCAGCCGCA 58.964 45.000 0.00 0.00 0.00 5.69
658 690 2.106938 GTCCAGCCGCATCGATCA 59.893 61.111 0.00 0.00 0.00 2.92
676 711 1.749638 ACCCTAGACAGCGACTCGG 60.750 63.158 0.00 0.00 0.00 4.63
690 725 0.179062 ACTCGGATCTGAGCAATGCC 60.179 55.000 28.11 0.00 39.68 4.40
693 728 0.745486 CGGATCTGAGCAATGCCACA 60.745 55.000 0.00 1.82 0.00 4.17
696 731 2.573369 GATCTGAGCAATGCCACATCT 58.427 47.619 0.00 0.00 0.00 2.90
706 741 4.761745 CAATGCCACATCTACGTAAATCG 58.238 43.478 0.00 0.00 46.00 3.34
727 1473 5.535333 TCGTTTTACTCCACCTAGTGAAAG 58.465 41.667 0.00 0.00 36.13 2.62
765 1655 8.328864 GGTTAATTAGAGATAGCAAGTTTCGTG 58.671 37.037 0.00 0.00 0.00 4.35
792 2017 6.907206 TTTAGTAGCACGTTTGTACTTTGT 57.093 33.333 6.56 0.00 0.00 2.83
793 2018 8.064447 CTTTAGTAGCACGTTTGTACTTTGTA 57.936 34.615 6.56 0.00 0.00 2.41
794 2019 7.627585 TTAGTAGCACGTTTGTACTTTGTAG 57.372 36.000 6.56 0.00 0.00 2.74
795 2020 4.986659 AGTAGCACGTTTGTACTTTGTAGG 59.013 41.667 0.00 0.00 0.00 3.18
998 2223 4.767255 GCACCCAGCTCCTCGTGG 62.767 72.222 0.00 0.00 41.15 4.94
1018 2243 1.123928 CACACTCATCCCCTACTCCC 58.876 60.000 0.00 0.00 0.00 4.30
1019 2244 0.716591 ACACTCATCCCCTACTCCCA 59.283 55.000 0.00 0.00 0.00 4.37
1020 2245 1.080498 ACACTCATCCCCTACTCCCAA 59.920 52.381 0.00 0.00 0.00 4.12
1047 2272 2.515523 CCCATCCTCTTGCAGCGG 60.516 66.667 0.00 0.00 0.00 5.52
1363 2592 1.298859 GACCAAGTGCACGGCTTAGG 61.299 60.000 12.01 10.50 0.00 2.69
1383 2612 1.475682 GCAGCCAGCTAGCTTTTGATT 59.524 47.619 16.46 0.00 42.61 2.57
1424 2655 4.327885 GACCGATCGATCTGGTGC 57.672 61.111 32.25 23.04 35.13 5.01
1425 2656 1.437573 GACCGATCGATCTGGTGCA 59.562 57.895 32.25 0.00 35.13 4.57
1426 2657 0.872021 GACCGATCGATCTGGTGCAC 60.872 60.000 32.25 20.58 35.13 4.57
1450 2682 2.912967 CACATGAGCGCTCAAAATCAAC 59.087 45.455 40.83 12.20 43.58 3.18
1492 2732 2.401967 GCTTGGCTAGCTGACATGG 58.598 57.895 15.72 2.23 46.77 3.66
1560 2800 5.476945 AGGCTCGTGTATTCAATTTTCCTTT 59.523 36.000 0.00 0.00 0.00 3.11
1591 2831 3.003480 GCTTAAGTAGTTGCTCACCCTG 58.997 50.000 4.02 0.00 0.00 4.45
1609 2849 9.832445 CTCACCCTGTTGTATATATTTGTACTT 57.168 33.333 0.00 0.00 0.00 2.24
1683 2923 7.870509 TGAGCTTATGATTATTTGTGAGCTT 57.129 32.000 0.00 0.00 39.15 3.74
1684 2924 7.700505 TGAGCTTATGATTATTTGTGAGCTTG 58.299 34.615 0.00 0.00 39.15 4.01
1688 2928 9.956720 GCTTATGATTATTTGTGAGCTTGTATT 57.043 29.630 0.00 0.00 0.00 1.89
1805 3047 4.431131 CTGTGGCCGGGCTGGATT 62.431 66.667 29.87 0.00 42.00 3.01
1810 3052 2.985847 GCCGGGCTGGATTATGGC 60.986 66.667 18.84 0.00 42.00 4.40
1814 3056 0.321653 CGGGCTGGATTATGGCTACC 60.322 60.000 0.00 0.00 0.00 3.18
1822 3064 3.513912 TGGATTATGGCTACCAGTATCGG 59.486 47.826 0.00 0.00 36.75 4.18
1833 3075 1.152525 AGTATCGGACTCGGCCCAT 60.153 57.895 0.00 0.00 29.95 4.00
1834 3076 1.006102 GTATCGGACTCGGCCCATG 60.006 63.158 0.00 0.00 36.95 3.66
1839 3081 1.905512 GGACTCGGCCCATGTTAGT 59.094 57.895 0.00 0.00 0.00 2.24
1899 3141 9.081997 GCCTCTCAAATATTACTCATCGAATAG 57.918 37.037 0.00 0.00 0.00 1.73
2017 3262 4.388773 GCAAGTGTTGACATACGAATGAGA 59.611 41.667 0.00 0.00 36.54 3.27
2031 3276 6.952935 ACGAATGAGACAGCTACTAAAAAG 57.047 37.500 0.00 0.00 0.00 2.27
2111 3356 2.985809 CACATTATTGCAACACCCAACG 59.014 45.455 0.00 0.00 0.00 4.10
2114 3359 3.900388 TTATTGCAACACCCAACGTAC 57.100 42.857 0.00 0.00 0.00 3.67
2119 3364 1.402613 GCAACACCCAACGTACTGTTT 59.597 47.619 0.00 0.00 39.29 2.83
2135 3380 6.471198 CGTACTGTTTCATTAGTCTATTGCGA 59.529 38.462 0.00 0.00 0.00 5.10
2145 3390 9.594478 TCATTAGTCTATTGCGATGAGTAAAAA 57.406 29.630 13.27 6.35 31.87 1.94
2156 3401 5.506832 GCGATGAGTAAAAACCATAACAACG 59.493 40.000 0.00 0.00 0.00 4.10
2157 3402 6.019152 CGATGAGTAAAAACCATAACAACGG 58.981 40.000 0.00 0.00 0.00 4.44
2159 3405 6.939132 TGAGTAAAAACCATAACAACGGAA 57.061 33.333 0.00 0.00 0.00 4.30
2263 3509 5.835113 ACCCTATTGCAATGACACAATAC 57.165 39.130 22.27 0.00 37.63 1.89
2508 3755 9.763465 GTACGCTTAGCAGAATTAAAAACATAA 57.237 29.630 4.70 0.00 0.00 1.90
2606 3853 6.408858 TTGAGATTATCAAGCTTTGTCGAC 57.591 37.500 9.11 9.11 43.09 4.20
2607 3854 4.870426 TGAGATTATCAAGCTTTGTCGACC 59.130 41.667 14.12 0.00 34.02 4.79
2608 3855 4.832248 AGATTATCAAGCTTTGTCGACCA 58.168 39.130 14.12 0.00 0.00 4.02
2609 3856 5.431765 AGATTATCAAGCTTTGTCGACCAT 58.568 37.500 14.12 0.00 0.00 3.55
2610 3857 5.882557 AGATTATCAAGCTTTGTCGACCATT 59.117 36.000 14.12 0.00 0.00 3.16
2611 3858 5.545658 TTATCAAGCTTTGTCGACCATTC 57.454 39.130 14.12 0.00 0.00 2.67
2612 3859 3.126001 TCAAGCTTTGTCGACCATTCT 57.874 42.857 14.12 2.37 0.00 2.40
2613 3860 4.265904 TCAAGCTTTGTCGACCATTCTA 57.734 40.909 14.12 0.00 0.00 2.10
2614 3861 3.994392 TCAAGCTTTGTCGACCATTCTAC 59.006 43.478 14.12 0.00 0.00 2.59
2615 3862 3.963428 AGCTTTGTCGACCATTCTACT 57.037 42.857 14.12 0.00 0.00 2.57
2616 3863 3.851098 AGCTTTGTCGACCATTCTACTC 58.149 45.455 14.12 0.00 0.00 2.59
2617 3864 3.258372 AGCTTTGTCGACCATTCTACTCA 59.742 43.478 14.12 0.00 0.00 3.41
2618 3865 3.368236 GCTTTGTCGACCATTCTACTCAC 59.632 47.826 14.12 0.00 0.00 3.51
2619 3866 2.913777 TGTCGACCATTCTACTCACG 57.086 50.000 14.12 0.00 0.00 4.35
2620 3867 2.156917 TGTCGACCATTCTACTCACGT 58.843 47.619 14.12 0.00 0.00 4.49
2621 3868 2.095415 TGTCGACCATTCTACTCACGTG 60.095 50.000 14.12 9.94 0.00 4.49
2622 3869 2.095364 GTCGACCATTCTACTCACGTGT 60.095 50.000 16.51 0.00 0.00 4.49
2623 3870 2.095415 TCGACCATTCTACTCACGTGTG 60.095 50.000 16.51 16.06 0.00 3.82
2624 3871 2.095415 CGACCATTCTACTCACGTGTGA 60.095 50.000 23.32 11.10 38.06 3.58
2625 3872 3.610821 CGACCATTCTACTCACGTGTGAA 60.611 47.826 23.32 18.02 39.39 3.18
2626 3873 4.304110 GACCATTCTACTCACGTGTGAAA 58.696 43.478 23.32 13.95 39.39 2.69
2627 3874 4.307432 ACCATTCTACTCACGTGTGAAAG 58.693 43.478 23.32 18.08 39.39 2.62
2628 3875 4.202223 ACCATTCTACTCACGTGTGAAAGT 60.202 41.667 23.32 17.20 39.39 2.66
2629 3876 4.750098 CCATTCTACTCACGTGTGAAAGTT 59.250 41.667 23.32 3.93 39.39 2.66
2630 3877 5.236478 CCATTCTACTCACGTGTGAAAGTTT 59.764 40.000 23.32 3.23 39.39 2.66
2631 3878 5.961395 TTCTACTCACGTGTGAAAGTTTC 57.039 39.130 23.32 8.75 39.39 2.78
2632 3879 5.001237 TCTACTCACGTGTGAAAGTTTCA 57.999 39.130 23.32 14.35 39.39 2.69
2633 3880 5.597806 TCTACTCACGTGTGAAAGTTTCAT 58.402 37.500 23.32 2.64 42.47 2.57
2634 3881 6.741109 TCTACTCACGTGTGAAAGTTTCATA 58.259 36.000 23.32 15.66 42.47 2.15
2635 3882 7.204604 TCTACTCACGTGTGAAAGTTTCATAA 58.795 34.615 23.32 10.22 42.47 1.90
2636 3883 6.671614 ACTCACGTGTGAAAGTTTCATAAA 57.328 33.333 23.32 7.86 42.47 1.40
2637 3884 6.715464 ACTCACGTGTGAAAGTTTCATAAAG 58.285 36.000 23.32 16.55 42.47 1.85
2638 3885 6.537301 ACTCACGTGTGAAAGTTTCATAAAGA 59.463 34.615 23.32 14.36 42.47 2.52
2639 3886 7.065324 ACTCACGTGTGAAAGTTTCATAAAGAA 59.935 33.333 23.32 6.13 42.47 2.52
2640 3887 7.753659 TCACGTGTGAAAGTTTCATAAAGAAA 58.246 30.769 20.72 7.49 42.47 2.52
2651 3898 5.712217 TTCATAAAGAAACGATACTGGCG 57.288 39.130 0.00 0.00 32.05 5.69
2652 3899 4.116961 TCATAAAGAAACGATACTGGCGG 58.883 43.478 0.00 0.00 0.00 6.13
2653 3900 2.467566 AAAGAAACGATACTGGCGGT 57.532 45.000 3.57 3.57 0.00 5.68
2654 3901 3.598019 AAAGAAACGATACTGGCGGTA 57.402 42.857 8.93 8.93 34.62 4.02
2655 3902 3.814005 AAGAAACGATACTGGCGGTAT 57.186 42.857 18.66 18.66 43.15 2.73
2656 3903 3.814005 AGAAACGATACTGGCGGTATT 57.186 42.857 19.51 5.14 40.82 1.89
2657 3904 4.924305 AGAAACGATACTGGCGGTATTA 57.076 40.909 19.51 0.00 40.82 0.98
2658 3905 5.464030 AGAAACGATACTGGCGGTATTAT 57.536 39.130 19.51 8.72 40.82 1.28
2659 3906 5.850614 AGAAACGATACTGGCGGTATTATT 58.149 37.500 19.51 13.71 40.82 1.40
2660 3907 5.694910 AGAAACGATACTGGCGGTATTATTG 59.305 40.000 19.51 12.32 40.82 1.90
2661 3908 3.921677 ACGATACTGGCGGTATTATTGG 58.078 45.455 19.51 9.74 40.82 3.16
2662 3909 3.322828 ACGATACTGGCGGTATTATTGGT 59.677 43.478 19.51 10.28 40.82 3.67
2663 3910 3.678072 CGATACTGGCGGTATTATTGGTG 59.322 47.826 19.51 2.06 40.82 4.17
2664 3911 4.559906 CGATACTGGCGGTATTATTGGTGA 60.560 45.833 19.51 0.00 40.82 4.02
2665 3912 3.637911 ACTGGCGGTATTATTGGTGAA 57.362 42.857 0.00 0.00 0.00 3.18
2666 3913 3.541632 ACTGGCGGTATTATTGGTGAAG 58.458 45.455 0.00 0.00 0.00 3.02
2667 3914 3.199071 ACTGGCGGTATTATTGGTGAAGA 59.801 43.478 0.00 0.00 0.00 2.87
2668 3915 4.196193 CTGGCGGTATTATTGGTGAAGAA 58.804 43.478 0.00 0.00 0.00 2.52
2669 3916 4.590918 TGGCGGTATTATTGGTGAAGAAA 58.409 39.130 0.00 0.00 0.00 2.52
2670 3917 5.010933 TGGCGGTATTATTGGTGAAGAAAA 58.989 37.500 0.00 0.00 0.00 2.29
2671 3918 5.654650 TGGCGGTATTATTGGTGAAGAAAAT 59.345 36.000 0.00 0.00 0.00 1.82
2672 3919 6.829298 TGGCGGTATTATTGGTGAAGAAAATA 59.171 34.615 0.00 0.00 0.00 1.40
2673 3920 7.136772 GGCGGTATTATTGGTGAAGAAAATAC 58.863 38.462 0.00 0.00 0.00 1.89
2674 3921 7.201750 GGCGGTATTATTGGTGAAGAAAATACA 60.202 37.037 0.00 0.00 33.51 2.29
2675 3922 8.185505 GCGGTATTATTGGTGAAGAAAATACAA 58.814 33.333 0.00 0.00 33.51 2.41
2676 3923 9.498307 CGGTATTATTGGTGAAGAAAATACAAC 57.502 33.333 0.00 0.00 33.51 3.32
2677 3924 9.797556 GGTATTATTGGTGAAGAAAATACAACC 57.202 33.333 0.00 0.00 33.51 3.77
2680 3927 5.782893 TTGGTGAAGAAAATACAACCAGG 57.217 39.130 0.00 0.00 0.00 4.45
2681 3928 4.798882 TGGTGAAGAAAATACAACCAGGT 58.201 39.130 0.00 0.00 0.00 4.00
2682 3929 4.825085 TGGTGAAGAAAATACAACCAGGTC 59.175 41.667 0.00 0.00 0.00 3.85
2683 3930 4.217767 GGTGAAGAAAATACAACCAGGTCC 59.782 45.833 0.00 0.00 0.00 4.46
2684 3931 4.217767 GTGAAGAAAATACAACCAGGTCCC 59.782 45.833 0.00 0.00 0.00 4.46
2685 3932 4.105697 TGAAGAAAATACAACCAGGTCCCT 59.894 41.667 0.00 0.00 0.00 4.20
2686 3933 5.311121 TGAAGAAAATACAACCAGGTCCCTA 59.689 40.000 0.00 0.00 0.00 3.53
2687 3934 6.011981 TGAAGAAAATACAACCAGGTCCCTAT 60.012 38.462 0.00 0.00 0.00 2.57
2688 3935 6.402981 AGAAAATACAACCAGGTCCCTATT 57.597 37.500 0.00 0.00 0.00 1.73
2689 3936 7.519347 AGAAAATACAACCAGGTCCCTATTA 57.481 36.000 0.00 0.00 0.00 0.98
2690 3937 8.114301 AGAAAATACAACCAGGTCCCTATTAT 57.886 34.615 0.00 0.00 0.00 1.28
2691 3938 8.566109 AGAAAATACAACCAGGTCCCTATTATT 58.434 33.333 0.00 0.00 0.00 1.40
2692 3939 8.762481 AAAATACAACCAGGTCCCTATTATTC 57.238 34.615 0.00 0.00 0.00 1.75
2693 3940 7.460214 AATACAACCAGGTCCCTATTATTCA 57.540 36.000 0.00 0.00 0.00 2.57
2694 3941 5.373812 ACAACCAGGTCCCTATTATTCAG 57.626 43.478 0.00 0.00 0.00 3.02
2695 3942 4.137543 CAACCAGGTCCCTATTATTCAGC 58.862 47.826 0.00 0.00 0.00 4.26
2696 3943 3.393687 ACCAGGTCCCTATTATTCAGCA 58.606 45.455 0.00 0.00 0.00 4.41
2697 3944 3.785887 ACCAGGTCCCTATTATTCAGCAA 59.214 43.478 0.00 0.00 0.00 3.91
2698 3945 4.229582 ACCAGGTCCCTATTATTCAGCAAA 59.770 41.667 0.00 0.00 0.00 3.68
2699 3946 4.580580 CCAGGTCCCTATTATTCAGCAAAC 59.419 45.833 0.00 0.00 0.00 2.93
2700 3947 5.192927 CAGGTCCCTATTATTCAGCAAACA 58.807 41.667 0.00 0.00 0.00 2.83
2701 3948 5.297776 CAGGTCCCTATTATTCAGCAAACAG 59.702 44.000 0.00 0.00 0.00 3.16
2702 3949 5.044846 AGGTCCCTATTATTCAGCAAACAGT 60.045 40.000 0.00 0.00 0.00 3.55
2703 3950 5.066505 GGTCCCTATTATTCAGCAAACAGTG 59.933 44.000 0.00 0.00 0.00 3.66
2721 3968 8.736742 CAAACAGTGCTTTTTAATATAGCATCG 58.263 33.333 9.11 6.87 45.61 3.84
2722 3969 7.786178 ACAGTGCTTTTTAATATAGCATCGA 57.214 32.000 9.11 0.00 45.61 3.59
2723 3970 8.383318 ACAGTGCTTTTTAATATAGCATCGAT 57.617 30.769 9.11 0.00 45.61 3.59
2724 3971 8.840321 ACAGTGCTTTTTAATATAGCATCGATT 58.160 29.630 0.00 0.00 45.61 3.34
2725 3972 9.669353 CAGTGCTTTTTAATATAGCATCGATTT 57.331 29.630 0.00 0.00 45.61 2.17
2762 4009 9.793259 TTCCTATAATACCATGGTCATTTCTTC 57.207 33.333 23.76 0.00 0.00 2.87
2763 4010 8.944138 TCCTATAATACCATGGTCATTTCTTCA 58.056 33.333 23.76 0.00 0.00 3.02
2764 4011 9.745018 CCTATAATACCATGGTCATTTCTTCAT 57.255 33.333 23.76 2.45 0.00 2.57
2767 4014 7.959658 AATACCATGGTCATTTCTTCATGAA 57.040 32.000 23.76 8.12 39.27 2.57
2769 4016 6.029346 ACCATGGTCATTTCTTCATGAAAC 57.971 37.500 13.00 3.43 46.08 2.78
2770 4017 5.776716 ACCATGGTCATTTCTTCATGAAACT 59.223 36.000 13.00 0.00 46.08 2.66
2771 4018 6.268387 ACCATGGTCATTTCTTCATGAAACTT 59.732 34.615 13.00 0.00 46.08 2.66
2772 4019 6.810182 CCATGGTCATTTCTTCATGAAACTTC 59.190 38.462 9.88 0.00 46.08 3.01
2773 4020 6.957920 TGGTCATTTCTTCATGAAACTTCA 57.042 33.333 9.88 0.00 46.08 3.02
2775 4022 8.634335 TGGTCATTTCTTCATGAAACTTCATA 57.366 30.769 9.88 0.00 45.62 2.15
2776 4023 9.246670 TGGTCATTTCTTCATGAAACTTCATAT 57.753 29.630 9.88 0.00 45.62 1.78
2777 4024 9.512435 GGTCATTTCTTCATGAAACTTCATATG 57.488 33.333 9.88 0.00 45.62 1.78
2778 4025 9.017669 GTCATTTCTTCATGAAACTTCATATGC 57.982 33.333 9.88 1.29 45.62 3.14
2779 4026 7.911727 TCATTTCTTCATGAAACTTCATATGCG 59.088 33.333 9.88 0.00 45.62 4.73
2780 4027 5.739752 TCTTCATGAAACTTCATATGCGG 57.260 39.130 9.88 0.00 45.62 5.69
2781 4028 4.576053 TCTTCATGAAACTTCATATGCGGG 59.424 41.667 9.88 0.00 45.62 6.13
2782 4029 4.149511 TCATGAAACTTCATATGCGGGA 57.850 40.909 4.66 0.00 45.62 5.14
2783 4030 4.717877 TCATGAAACTTCATATGCGGGAT 58.282 39.130 4.66 0.00 45.62 3.85
2784 4031 5.863965 TCATGAAACTTCATATGCGGGATA 58.136 37.500 4.66 0.00 45.62 2.59
2785 4032 6.475504 TCATGAAACTTCATATGCGGGATAT 58.524 36.000 4.66 0.00 45.62 1.63
2786 4033 6.372381 TCATGAAACTTCATATGCGGGATATG 59.628 38.462 19.83 19.83 45.62 1.78
2791 4038 3.782889 TCATATGCGGGATATGAGTCG 57.217 47.619 23.20 3.40 45.43 4.18
2792 4039 3.352648 TCATATGCGGGATATGAGTCGA 58.647 45.455 23.20 6.04 45.43 4.20
2793 4040 3.954258 TCATATGCGGGATATGAGTCGAT 59.046 43.478 23.20 0.00 45.43 3.59
2794 4041 4.402474 TCATATGCGGGATATGAGTCGATT 59.598 41.667 23.20 0.00 45.43 3.34
2795 4042 5.592688 TCATATGCGGGATATGAGTCGATTA 59.407 40.000 23.20 4.18 45.43 1.75
2796 4043 6.265422 TCATATGCGGGATATGAGTCGATTAT 59.735 38.462 23.20 0.00 45.43 1.28
2797 4044 4.110036 TGCGGGATATGAGTCGATTATG 57.890 45.455 0.00 0.00 0.00 1.90
2798 4045 3.509967 TGCGGGATATGAGTCGATTATGT 59.490 43.478 0.00 0.00 0.00 2.29
2799 4046 4.703093 TGCGGGATATGAGTCGATTATGTA 59.297 41.667 0.00 0.00 0.00 2.29
2800 4047 5.359860 TGCGGGATATGAGTCGATTATGTAT 59.640 40.000 0.00 0.00 0.00 2.29
2801 4048 5.687730 GCGGGATATGAGTCGATTATGTATG 59.312 44.000 0.00 0.00 0.00 2.39
2802 4049 6.680625 GCGGGATATGAGTCGATTATGTATGT 60.681 42.308 0.00 0.00 0.00 2.29
2803 4050 7.258441 CGGGATATGAGTCGATTATGTATGTT 58.742 38.462 0.00 0.00 0.00 2.71
2804 4051 8.403236 CGGGATATGAGTCGATTATGTATGTTA 58.597 37.037 0.00 0.00 0.00 2.41
2805 4052 9.517609 GGGATATGAGTCGATTATGTATGTTAC 57.482 37.037 0.00 0.00 0.00 2.50
2869 4116 8.232913 TCAAATTTACTATTCATAAGGGGTGC 57.767 34.615 0.00 0.00 0.00 5.01
2870 4117 7.836685 TCAAATTTACTATTCATAAGGGGTGCA 59.163 33.333 0.00 0.00 0.00 4.57
2871 4118 8.641541 CAAATTTACTATTCATAAGGGGTGCAT 58.358 33.333 0.00 0.00 0.00 3.96
2872 4119 7.765695 ATTTACTATTCATAAGGGGTGCATG 57.234 36.000 0.00 0.00 0.00 4.06
2873 4120 6.508030 TTACTATTCATAAGGGGTGCATGA 57.492 37.500 0.00 0.00 0.00 3.07
2874 4121 5.589367 ACTATTCATAAGGGGTGCATGAT 57.411 39.130 0.00 0.00 0.00 2.45
2875 4122 5.319453 ACTATTCATAAGGGGTGCATGATG 58.681 41.667 0.00 0.00 0.00 3.07
2876 4123 3.949586 TTCATAAGGGGTGCATGATGA 57.050 42.857 0.00 0.00 0.00 2.92
2877 4124 3.949586 TCATAAGGGGTGCATGATGAA 57.050 42.857 0.00 0.00 0.00 2.57
2878 4125 4.248174 TCATAAGGGGTGCATGATGAAA 57.752 40.909 0.00 0.00 0.00 2.69
2879 4126 3.953612 TCATAAGGGGTGCATGATGAAAC 59.046 43.478 0.00 0.00 0.00 2.78
2880 4127 2.307496 AAGGGGTGCATGATGAAACA 57.693 45.000 0.00 0.00 0.00 2.83
2881 4128 2.537633 AGGGGTGCATGATGAAACAT 57.462 45.000 0.00 0.00 0.00 2.71
2882 4129 2.381911 AGGGGTGCATGATGAAACATC 58.618 47.619 0.00 4.98 0.00 3.06
2883 4130 2.024655 AGGGGTGCATGATGAAACATCT 60.025 45.455 11.98 0.00 0.00 2.90
2884 4131 2.762327 GGGGTGCATGATGAAACATCTT 59.238 45.455 11.98 4.29 0.00 2.40
2885 4132 3.181483 GGGGTGCATGATGAAACATCTTC 60.181 47.826 11.98 3.54 0.00 2.87
2886 4133 3.444742 GGGTGCATGATGAAACATCTTCA 59.555 43.478 11.98 2.47 0.00 3.02
2887 4134 4.418392 GGTGCATGATGAAACATCTTCAC 58.582 43.478 11.98 14.04 0.00 3.18
2888 4135 4.418392 GTGCATGATGAAACATCTTCACC 58.582 43.478 11.98 0.00 0.00 4.02
2889 4136 4.080687 TGCATGATGAAACATCTTCACCA 58.919 39.130 11.98 0.00 0.00 4.17
2890 4137 4.523558 TGCATGATGAAACATCTTCACCAA 59.476 37.500 11.98 0.00 0.00 3.67
2891 4138 5.100259 GCATGATGAAACATCTTCACCAAG 58.900 41.667 11.98 0.00 0.00 3.61
2892 4139 5.336213 GCATGATGAAACATCTTCACCAAGT 60.336 40.000 11.98 0.00 0.00 3.16
2893 4140 6.684686 CATGATGAAACATCTTCACCAAGTT 58.315 36.000 11.98 0.00 0.00 2.66
2894 4141 6.317789 TGATGAAACATCTTCACCAAGTTC 57.682 37.500 11.98 0.00 0.00 3.01
2895 4142 5.241506 TGATGAAACATCTTCACCAAGTTCC 59.758 40.000 11.98 0.00 0.00 3.62
2896 4143 4.792068 TGAAACATCTTCACCAAGTTCCT 58.208 39.130 0.00 0.00 0.00 3.36
2897 4144 4.580167 TGAAACATCTTCACCAAGTTCCTG 59.420 41.667 0.00 0.00 0.00 3.86
2898 4145 3.864789 ACATCTTCACCAAGTTCCTGT 57.135 42.857 0.00 0.00 0.00 4.00
2899 4146 3.744660 ACATCTTCACCAAGTTCCTGTC 58.255 45.455 0.00 0.00 0.00 3.51
2900 4147 2.930826 TCTTCACCAAGTTCCTGTCC 57.069 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.417339 TGGTGATCGCGCTAGATAAC 57.583 50.000 5.56 4.97 32.39 1.89
40 41 1.439353 GCGTGAATGCGTGATGGGAT 61.439 55.000 0.00 0.00 0.00 3.85
41 42 2.106074 GCGTGAATGCGTGATGGGA 61.106 57.895 0.00 0.00 0.00 4.37
42 43 2.404789 GCGTGAATGCGTGATGGG 59.595 61.111 0.00 0.00 0.00 4.00
43 44 2.404789 GGCGTGAATGCGTGATGG 59.595 61.111 0.00 0.00 35.06 3.51
44 45 2.021793 CGGCGTGAATGCGTGATG 59.978 61.111 0.00 0.00 35.06 3.07
194 197 4.580580 AGCGAAATATCTTTGTCCCATTCC 59.419 41.667 0.00 0.00 0.00 3.01
280 300 1.827399 TTGGGAGAACCTGACTCGGC 61.827 60.000 0.00 0.00 41.11 5.54
317 337 4.015084 TGTAGCTGTAGGTCAAGGAGTAC 58.985 47.826 0.00 0.00 0.00 2.73
319 339 3.093057 CTGTAGCTGTAGGTCAAGGAGT 58.907 50.000 0.00 0.00 0.00 3.85
320 340 2.428890 CCTGTAGCTGTAGGTCAAGGAG 59.571 54.545 9.33 0.00 32.88 3.69
321 341 2.457598 CCTGTAGCTGTAGGTCAAGGA 58.542 52.381 9.33 0.00 32.88 3.36
323 343 1.134670 GGCCTGTAGCTGTAGGTCAAG 60.135 57.143 15.44 0.00 43.05 3.02
324 344 0.902531 GGCCTGTAGCTGTAGGTCAA 59.097 55.000 15.44 0.00 43.05 3.18
325 345 0.041238 AGGCCTGTAGCTGTAGGTCA 59.959 55.000 20.54 0.88 41.16 4.02
326 346 0.747852 GAGGCCTGTAGCTGTAGGTC 59.252 60.000 12.00 13.18 43.05 3.85
327 347 0.336737 AGAGGCCTGTAGCTGTAGGT 59.663 55.000 12.00 1.51 43.05 3.08
328 348 1.036707 GAGAGGCCTGTAGCTGTAGG 58.963 60.000 12.00 12.41 43.05 3.18
329 349 0.665835 CGAGAGGCCTGTAGCTGTAG 59.334 60.000 12.00 0.00 43.05 2.74
330 350 1.384989 GCGAGAGGCCTGTAGCTGTA 61.385 60.000 25.02 0.00 43.05 2.74
331 351 2.716017 GCGAGAGGCCTGTAGCTGT 61.716 63.158 25.02 0.00 43.05 4.40
332 352 2.105930 GCGAGAGGCCTGTAGCTG 59.894 66.667 25.02 7.10 43.05 4.24
358 378 6.208644 CAACCCAAACTCAAACTCAATAGTG 58.791 40.000 0.00 0.00 35.62 2.74
389 409 2.451490 TGACTCTCCTAGACTTGCTGG 58.549 52.381 0.00 0.00 0.00 4.85
455 486 7.036220 TGAATTTACGCCTTTTCTTTTTGACA 58.964 30.769 0.00 0.00 0.00 3.58
464 495 5.628134 ACGATTCTGAATTTACGCCTTTTC 58.372 37.500 4.11 0.00 0.00 2.29
467 498 4.250464 TGACGATTCTGAATTTACGCCTT 58.750 39.130 4.11 0.00 0.00 4.35
468 499 3.857052 TGACGATTCTGAATTTACGCCT 58.143 40.909 4.11 0.00 0.00 5.52
470 501 7.177407 TGTTATTGACGATTCTGAATTTACGC 58.823 34.615 4.11 2.02 0.00 4.42
507 538 8.776376 ACAAACATGAAATTCACTCACTTTTT 57.224 26.923 0.00 0.00 0.00 1.94
512 543 8.627487 TTGTTACAAACATGAAATTCACTCAC 57.373 30.769 0.00 0.00 41.79 3.51
560 591 9.685828 GTGACACAACCTTGCTTAAATTAATAA 57.314 29.630 0.00 0.00 0.00 1.40
561 592 8.301002 GGTGACACAACCTTGCTTAAATTAATA 58.699 33.333 8.08 0.00 37.24 0.98
562 593 7.151976 GGTGACACAACCTTGCTTAAATTAAT 58.848 34.615 8.08 0.00 37.24 1.40
563 594 6.508777 GGTGACACAACCTTGCTTAAATTAA 58.491 36.000 8.08 0.00 37.24 1.40
564 595 6.079424 GGTGACACAACCTTGCTTAAATTA 57.921 37.500 8.08 0.00 37.24 1.40
576 607 1.029681 GGGTGAAAGGTGACACAACC 58.970 55.000 8.08 6.52 40.85 3.77
613 645 1.959042 ATGTGATGCTCGATTGGTCC 58.041 50.000 0.00 0.00 0.00 4.46
617 649 6.309494 ACAAATTGAAATGTGATGCTCGATTG 59.691 34.615 0.00 0.00 0.00 2.67
622 654 5.472148 TGGACAAATTGAAATGTGATGCTC 58.528 37.500 0.00 0.00 0.00 4.26
635 667 0.523968 CGATGCGGCTGGACAAATTG 60.524 55.000 0.00 0.00 0.00 2.32
647 679 0.039074 GTCTAGGGTGATCGATGCGG 60.039 60.000 0.54 0.00 0.00 5.69
651 683 0.955178 CGCTGTCTAGGGTGATCGAT 59.045 55.000 0.00 0.00 32.59 3.59
658 690 1.749638 CCGAGTCGCTGTCTAGGGT 60.750 63.158 7.12 0.00 38.02 4.34
676 711 2.573369 AGATGTGGCATTGCTCAGATC 58.427 47.619 20.06 20.06 33.39 2.75
706 741 6.285990 TGACTTTCACTAGGTGGAGTAAAAC 58.714 40.000 0.00 0.00 33.26 2.43
740 1625 8.328864 CCACGAAACTTGCTATCTCTAATTAAC 58.671 37.037 0.00 0.00 0.00 2.01
753 1638 1.880027 CTAAAGCCCACGAAACTTGCT 59.120 47.619 0.00 0.00 0.00 3.91
783 2008 7.308348 GCAAAAATGCTAGACCTACAAAGTACA 60.308 37.037 0.00 0.00 0.00 2.90
787 2012 6.259550 AGCAAAAATGCTAGACCTACAAAG 57.740 37.500 0.67 0.00 44.28 2.77
790 2015 3.932710 CGAGCAAAAATGCTAGACCTACA 59.067 43.478 2.89 0.00 46.36 2.74
791 2016 4.181578 TCGAGCAAAAATGCTAGACCTAC 58.818 43.478 9.15 0.00 46.36 3.18
792 2017 4.465632 TCGAGCAAAAATGCTAGACCTA 57.534 40.909 9.15 0.00 46.36 3.08
793 2018 3.334583 TCGAGCAAAAATGCTAGACCT 57.665 42.857 9.15 0.00 46.36 3.85
794 2019 4.333926 AGATTCGAGCAAAAATGCTAGACC 59.666 41.667 12.20 8.21 46.36 3.85
795 2020 5.476752 AGATTCGAGCAAAAATGCTAGAC 57.523 39.130 12.20 3.94 46.36 2.59
954 2179 3.538346 CGCTTTTATATACGCGCGG 57.462 52.632 35.22 16.31 39.11 6.46
960 2185 3.186613 GCTCTGTGCCCGCTTTTATATAC 59.813 47.826 0.00 0.00 35.15 1.47
998 2223 0.466124 GGAGTAGGGGATGAGTGTGC 59.534 60.000 0.00 0.00 0.00 4.57
1018 2243 1.452108 GGATGGGAGGAAGGCGTTG 60.452 63.158 0.00 0.00 0.00 4.10
1019 2244 1.616628 AGGATGGGAGGAAGGCGTT 60.617 57.895 0.00 0.00 0.00 4.84
1020 2245 2.041265 AGGATGGGAGGAAGGCGT 59.959 61.111 0.00 0.00 0.00 5.68
1047 2272 3.365265 CGGTTGCTTGGGTGAGGC 61.365 66.667 0.00 0.00 0.00 4.70
1201 2430 3.677648 CCGGTCCTTGTCCGTCGT 61.678 66.667 0.00 0.00 45.63 4.34
1203 2432 4.754667 GGCCGGTCCTTGTCCGTC 62.755 72.222 1.90 0.00 45.63 4.79
1363 2592 1.101331 ATCAAAAGCTAGCTGGCTGC 58.899 50.000 26.51 8.47 42.24 5.25
1432 2664 2.161855 TGGTTGATTTTGAGCGCTCAT 58.838 42.857 38.40 25.46 39.64 2.90
1492 2732 2.269172 GCTCCAGCTTACCGAGTTTAC 58.731 52.381 0.00 0.00 38.21 2.01
1560 2800 0.988832 CTACTTAAGCCACCCACCCA 59.011 55.000 1.29 0.00 0.00 4.51
1609 2849 2.582052 GTGGACACACCCAAGAATTGA 58.418 47.619 0.00 0.00 45.03 2.57
1688 2928 6.542370 GGCTGGTCATGCTTAGATTAGTAAAA 59.458 38.462 0.00 0.00 0.00 1.52
1788 3030 2.343475 ATAATCCAGCCCGGCCACAG 62.343 60.000 5.55 0.00 33.14 3.66
1795 3037 0.321653 GGTAGCCATAATCCAGCCCG 60.322 60.000 0.00 0.00 0.00 6.13
1805 3047 3.418995 GAGTCCGATACTGGTAGCCATA 58.581 50.000 0.00 0.00 39.07 2.74
1810 3052 0.592148 GCCGAGTCCGATACTGGTAG 59.408 60.000 0.00 0.00 39.07 3.18
1814 3056 1.464376 ATGGGCCGAGTCCGATACTG 61.464 60.000 0.00 0.00 39.07 2.74
1822 3064 1.369625 CAACTAACATGGGCCGAGTC 58.630 55.000 0.00 0.00 0.00 3.36
1833 3075 7.539436 TCTTACAACACATTTTGCAACTAACA 58.461 30.769 0.00 0.00 0.00 2.41
1834 3076 7.979115 TCTTACAACACATTTTGCAACTAAC 57.021 32.000 0.00 0.00 0.00 2.34
1839 3081 7.871973 AGCAATATCTTACAACACATTTTGCAA 59.128 29.630 0.00 0.00 36.33 4.08
1926 3168 7.443259 AATGCCCAATCTTTTCATCTTTTTG 57.557 32.000 0.00 0.00 0.00 2.44
1930 3172 9.743581 AATTTTAATGCCCAATCTTTTCATCTT 57.256 25.926 0.00 0.00 0.00 2.40
2111 3356 7.751047 TCGCAATAGACTAATGAAACAGTAC 57.249 36.000 1.52 0.00 0.00 2.73
2114 3359 7.223582 ACTCATCGCAATAGACTAATGAAACAG 59.776 37.037 1.52 0.00 0.00 3.16
2119 3364 9.594478 TTTTTACTCATCGCAATAGACTAATGA 57.406 29.630 1.52 0.00 0.00 2.57
2135 3380 7.513371 TTCCGTTGTTATGGTTTTTACTCAT 57.487 32.000 0.00 0.00 0.00 2.90
2219 3465 9.705290 AGGGTTAAAATTGTGCTTTATAACAAG 57.295 29.630 0.00 0.00 39.50 3.16
2224 3470 9.810545 GCAATAGGGTTAAAATTGTGCTTTATA 57.189 29.630 0.00 0.00 33.96 0.98
2480 3727 7.812648 TGTTTTTAATTCTGCTAAGCGTACAT 58.187 30.769 0.00 0.00 0.00 2.29
2576 3823 9.985730 ACAAAGCTTGATAATCTCAAAATTTCA 57.014 25.926 0.00 0.00 43.20 2.69
2578 3825 9.132521 CGACAAAGCTTGATAATCTCAAAATTT 57.867 29.630 0.00 0.00 43.20 1.82
2579 3826 8.514594 TCGACAAAGCTTGATAATCTCAAAATT 58.485 29.630 0.00 0.00 43.20 1.82
2580 3827 7.965107 GTCGACAAAGCTTGATAATCTCAAAAT 59.035 33.333 11.55 0.00 43.20 1.82
2581 3828 7.298122 GTCGACAAAGCTTGATAATCTCAAAA 58.702 34.615 11.55 0.00 43.20 2.44
2582 3829 6.128282 GGTCGACAAAGCTTGATAATCTCAAA 60.128 38.462 18.91 0.00 43.20 2.69
2583 3830 5.351465 GGTCGACAAAGCTTGATAATCTCAA 59.649 40.000 18.91 0.00 41.61 3.02
2584 3831 4.870426 GGTCGACAAAGCTTGATAATCTCA 59.130 41.667 18.91 0.00 0.00 3.27
2585 3832 4.870426 TGGTCGACAAAGCTTGATAATCTC 59.130 41.667 18.91 0.00 0.00 2.75
2586 3833 4.832248 TGGTCGACAAAGCTTGATAATCT 58.168 39.130 18.91 0.00 0.00 2.40
2587 3834 5.741388 ATGGTCGACAAAGCTTGATAATC 57.259 39.130 18.91 0.00 0.00 1.75
2588 3835 5.882557 AGAATGGTCGACAAAGCTTGATAAT 59.117 36.000 18.91 0.00 0.00 1.28
2589 3836 5.245531 AGAATGGTCGACAAAGCTTGATAA 58.754 37.500 18.91 0.00 0.00 1.75
2590 3837 4.832248 AGAATGGTCGACAAAGCTTGATA 58.168 39.130 18.91 0.00 0.00 2.15
2591 3838 3.679389 AGAATGGTCGACAAAGCTTGAT 58.321 40.909 18.91 0.00 0.00 2.57
2592 3839 3.126001 AGAATGGTCGACAAAGCTTGA 57.874 42.857 18.91 0.00 0.00 3.02
2593 3840 3.997021 AGTAGAATGGTCGACAAAGCTTG 59.003 43.478 18.91 0.00 32.20 4.01
2594 3841 4.246458 GAGTAGAATGGTCGACAAAGCTT 58.754 43.478 18.91 0.00 32.20 3.74
2595 3842 3.258372 TGAGTAGAATGGTCGACAAAGCT 59.742 43.478 18.91 10.30 32.20 3.74
2596 3843 3.368236 GTGAGTAGAATGGTCGACAAAGC 59.632 47.826 18.91 2.41 32.20 3.51
2597 3844 3.608506 CGTGAGTAGAATGGTCGACAAAG 59.391 47.826 18.91 0.00 32.20 2.77
2598 3845 3.005050 ACGTGAGTAGAATGGTCGACAAA 59.995 43.478 18.91 5.15 46.88 2.83
2599 3846 2.555325 ACGTGAGTAGAATGGTCGACAA 59.445 45.455 18.91 6.46 46.88 3.18
2600 3847 2.156917 ACGTGAGTAGAATGGTCGACA 58.843 47.619 18.91 3.91 46.88 4.35
2601 3848 2.915738 ACGTGAGTAGAATGGTCGAC 57.084 50.000 7.13 7.13 46.88 4.20
2606 3853 8.843676 TGAAACTTTCACACGTGAGTAGAATGG 61.844 40.741 25.01 15.85 41.13 3.16
2607 3854 6.019075 TGAAACTTTCACACGTGAGTAGAATG 60.019 38.462 25.01 20.65 41.13 2.67
2608 3855 6.046593 TGAAACTTTCACACGTGAGTAGAAT 58.953 36.000 25.01 10.24 41.13 2.40
2609 3856 5.412640 TGAAACTTTCACACGTGAGTAGAA 58.587 37.500 25.01 16.47 41.13 2.10
2610 3857 5.001237 TGAAACTTTCACACGTGAGTAGA 57.999 39.130 25.01 11.34 41.13 2.59
2611 3858 5.907197 ATGAAACTTTCACACGTGAGTAG 57.093 39.130 25.01 17.46 42.92 2.57
2612 3859 7.707464 TCTTTATGAAACTTTCACACGTGAGTA 59.293 33.333 25.01 5.18 42.92 2.59
2613 3860 6.537301 TCTTTATGAAACTTTCACACGTGAGT 59.463 34.615 25.01 12.44 43.48 3.41
2614 3861 6.943981 TCTTTATGAAACTTTCACACGTGAG 58.056 36.000 25.01 15.63 43.48 3.51
2615 3862 6.912203 TCTTTATGAAACTTTCACACGTGA 57.088 33.333 25.01 0.00 43.48 4.35
2616 3863 7.962934 TTTCTTTATGAAACTTTCACACGTG 57.037 32.000 15.48 15.48 43.48 4.49
2628 3875 5.064198 CCGCCAGTATCGTTTCTTTATGAAA 59.936 40.000 0.00 0.00 41.85 2.69
2629 3876 4.569162 CCGCCAGTATCGTTTCTTTATGAA 59.431 41.667 0.00 0.00 0.00 2.57
2630 3877 4.116961 CCGCCAGTATCGTTTCTTTATGA 58.883 43.478 0.00 0.00 0.00 2.15
2631 3878 3.869246 ACCGCCAGTATCGTTTCTTTATG 59.131 43.478 0.00 0.00 0.00 1.90
2632 3879 4.133013 ACCGCCAGTATCGTTTCTTTAT 57.867 40.909 0.00 0.00 0.00 1.40
2633 3880 3.598019 ACCGCCAGTATCGTTTCTTTA 57.402 42.857 0.00 0.00 0.00 1.85
2634 3881 2.467566 ACCGCCAGTATCGTTTCTTT 57.532 45.000 0.00 0.00 0.00 2.52
2635 3882 3.814005 ATACCGCCAGTATCGTTTCTT 57.186 42.857 0.00 0.00 37.01 2.52
2636 3883 3.814005 AATACCGCCAGTATCGTTTCT 57.186 42.857 0.00 0.00 40.98 2.52
2637 3884 5.107220 CCAATAATACCGCCAGTATCGTTTC 60.107 44.000 0.00 0.00 40.98 2.78
2638 3885 4.753107 CCAATAATACCGCCAGTATCGTTT 59.247 41.667 0.00 0.00 40.98 3.60
2639 3886 4.202284 ACCAATAATACCGCCAGTATCGTT 60.202 41.667 0.00 0.00 40.98 3.85
2640 3887 3.322828 ACCAATAATACCGCCAGTATCGT 59.677 43.478 0.00 0.00 40.98 3.73
2641 3888 3.678072 CACCAATAATACCGCCAGTATCG 59.322 47.826 0.00 0.00 40.98 2.92
2642 3889 4.890088 TCACCAATAATACCGCCAGTATC 58.110 43.478 0.00 0.00 40.98 2.24
2643 3890 4.967084 TCACCAATAATACCGCCAGTAT 57.033 40.909 0.00 0.00 43.85 2.12
2644 3891 4.406326 TCTTCACCAATAATACCGCCAGTA 59.594 41.667 0.00 0.00 34.76 2.74
2645 3892 3.199071 TCTTCACCAATAATACCGCCAGT 59.801 43.478 0.00 0.00 0.00 4.00
2646 3893 3.804036 TCTTCACCAATAATACCGCCAG 58.196 45.455 0.00 0.00 0.00 4.85
2647 3894 3.916359 TCTTCACCAATAATACCGCCA 57.084 42.857 0.00 0.00 0.00 5.69
2648 3895 5.570234 TTTTCTTCACCAATAATACCGCC 57.430 39.130 0.00 0.00 0.00 6.13
2649 3896 7.699566 TGTATTTTCTTCACCAATAATACCGC 58.300 34.615 0.00 0.00 30.99 5.68
2650 3897 9.498307 GTTGTATTTTCTTCACCAATAATACCG 57.502 33.333 0.00 0.00 30.99 4.02
2651 3898 9.797556 GGTTGTATTTTCTTCACCAATAATACC 57.202 33.333 0.00 0.00 30.99 2.73
2654 3901 8.531146 CCTGGTTGTATTTTCTTCACCAATAAT 58.469 33.333 0.00 0.00 0.00 1.28
2655 3902 7.507616 ACCTGGTTGTATTTTCTTCACCAATAA 59.492 33.333 0.00 0.00 0.00 1.40
2656 3903 7.007723 ACCTGGTTGTATTTTCTTCACCAATA 58.992 34.615 0.00 0.00 0.00 1.90
2657 3904 5.838521 ACCTGGTTGTATTTTCTTCACCAAT 59.161 36.000 0.00 0.00 0.00 3.16
2658 3905 5.205056 ACCTGGTTGTATTTTCTTCACCAA 58.795 37.500 0.00 0.00 0.00 3.67
2659 3906 4.798882 ACCTGGTTGTATTTTCTTCACCA 58.201 39.130 0.00 0.00 0.00 4.17
2660 3907 4.217767 GGACCTGGTTGTATTTTCTTCACC 59.782 45.833 0.00 0.00 0.00 4.02
2661 3908 4.217767 GGGACCTGGTTGTATTTTCTTCAC 59.782 45.833 0.00 0.00 0.00 3.18
2662 3909 4.105697 AGGGACCTGGTTGTATTTTCTTCA 59.894 41.667 0.00 0.00 0.00 3.02
2663 3910 4.663334 AGGGACCTGGTTGTATTTTCTTC 58.337 43.478 0.00 0.00 0.00 2.87
2664 3911 4.741928 AGGGACCTGGTTGTATTTTCTT 57.258 40.909 0.00 0.00 0.00 2.52
2665 3912 6.402981 AATAGGGACCTGGTTGTATTTTCT 57.597 37.500 0.00 0.00 0.00 2.52
2666 3913 8.762481 AATAATAGGGACCTGGTTGTATTTTC 57.238 34.615 0.00 0.00 0.00 2.29
2667 3914 8.340757 TGAATAATAGGGACCTGGTTGTATTTT 58.659 33.333 0.00 0.00 0.00 1.82
2668 3915 7.878495 TGAATAATAGGGACCTGGTTGTATTT 58.122 34.615 0.00 0.00 0.00 1.40
2669 3916 7.460214 TGAATAATAGGGACCTGGTTGTATT 57.540 36.000 0.00 7.52 0.00 1.89
2670 3917 6.465894 GCTGAATAATAGGGACCTGGTTGTAT 60.466 42.308 0.00 0.00 0.00 2.29
2671 3918 5.163237 GCTGAATAATAGGGACCTGGTTGTA 60.163 44.000 0.00 0.00 0.00 2.41
2672 3919 4.385310 GCTGAATAATAGGGACCTGGTTGT 60.385 45.833 0.00 0.00 0.00 3.32
2673 3920 4.137543 GCTGAATAATAGGGACCTGGTTG 58.862 47.826 0.00 0.00 0.00 3.77
2674 3921 3.785887 TGCTGAATAATAGGGACCTGGTT 59.214 43.478 0.00 0.00 0.00 3.67
2675 3922 3.393687 TGCTGAATAATAGGGACCTGGT 58.606 45.455 0.00 0.00 0.00 4.00
2676 3923 4.437682 TTGCTGAATAATAGGGACCTGG 57.562 45.455 0.00 0.00 0.00 4.45
2677 3924 5.192927 TGTTTGCTGAATAATAGGGACCTG 58.807 41.667 0.00 0.00 0.00 4.00
2678 3925 5.044846 ACTGTTTGCTGAATAATAGGGACCT 60.045 40.000 0.00 0.00 0.00 3.85
2679 3926 5.066505 CACTGTTTGCTGAATAATAGGGACC 59.933 44.000 0.00 0.00 0.00 4.46
2680 3927 6.124088 CACTGTTTGCTGAATAATAGGGAC 57.876 41.667 0.00 0.00 0.00 4.46
2736 3983 9.793259 GAAGAAATGACCATGGTATTATAGGAA 57.207 33.333 19.80 0.00 0.00 3.36
2737 3984 8.944138 TGAAGAAATGACCATGGTATTATAGGA 58.056 33.333 19.80 0.00 0.00 2.94
2738 3985 9.745018 ATGAAGAAATGACCATGGTATTATAGG 57.255 33.333 19.80 0.00 0.00 2.57
2741 3988 9.645128 TTCATGAAGAAATGACCATGGTATTAT 57.355 29.630 19.80 10.12 36.31 1.28
2742 3989 9.473007 TTTCATGAAGAAATGACCATGGTATTA 57.527 29.630 19.80 7.96 41.17 0.98
2743 3990 7.959658 TTCATGAAGAAATGACCATGGTATT 57.040 32.000 19.80 13.48 36.31 1.89
2744 3991 7.959658 TTTCATGAAGAAATGACCATGGTAT 57.040 32.000 19.80 9.11 41.17 2.73
2756 4003 6.404623 CCCGCATATGAAGTTTCATGAAGAAA 60.405 38.462 15.72 0.00 46.68 2.52
2757 4004 5.066375 CCCGCATATGAAGTTTCATGAAGAA 59.934 40.000 15.72 0.00 46.68 2.52
2758 4005 4.576053 CCCGCATATGAAGTTTCATGAAGA 59.424 41.667 15.72 0.00 46.68 2.87
2759 4006 4.576053 TCCCGCATATGAAGTTTCATGAAG 59.424 41.667 15.72 7.74 46.68 3.02
2760 4007 4.522114 TCCCGCATATGAAGTTTCATGAA 58.478 39.130 15.72 3.38 46.68 2.57
2761 4008 4.149511 TCCCGCATATGAAGTTTCATGA 57.850 40.909 15.72 0.00 46.68 3.07
2762 4009 6.549061 CATATCCCGCATATGAAGTTTCATG 58.451 40.000 15.72 4.72 45.33 3.07
2763 4010 6.748333 CATATCCCGCATATGAAGTTTCAT 57.252 37.500 6.97 11.69 45.33 2.57
2772 4019 3.782889 TCGACTCATATCCCGCATATG 57.217 47.619 0.00 0.00 44.26 1.78
2773 4020 6.040955 ACATAATCGACTCATATCCCGCATAT 59.959 38.462 0.00 0.00 0.00 1.78
2774 4021 5.359860 ACATAATCGACTCATATCCCGCATA 59.640 40.000 0.00 0.00 0.00 3.14
2775 4022 4.160439 ACATAATCGACTCATATCCCGCAT 59.840 41.667 0.00 0.00 0.00 4.73
2776 4023 3.509967 ACATAATCGACTCATATCCCGCA 59.490 43.478 0.00 0.00 0.00 5.69
2777 4024 4.111375 ACATAATCGACTCATATCCCGC 57.889 45.455 0.00 0.00 0.00 6.13
2778 4025 6.796426 ACATACATAATCGACTCATATCCCG 58.204 40.000 0.00 0.00 0.00 5.14
2779 4026 9.517609 GTAACATACATAATCGACTCATATCCC 57.482 37.037 0.00 0.00 0.00 3.85
2843 4090 8.691797 GCACCCCTTATGAATAGTAAATTTGAA 58.308 33.333 0.00 0.00 0.00 2.69
2844 4091 7.836685 TGCACCCCTTATGAATAGTAAATTTGA 59.163 33.333 0.00 0.00 0.00 2.69
2845 4092 8.006298 TGCACCCCTTATGAATAGTAAATTTG 57.994 34.615 0.00 0.00 0.00 2.32
2846 4093 8.641541 CATGCACCCCTTATGAATAGTAAATTT 58.358 33.333 0.00 0.00 0.00 1.82
2847 4094 8.004215 TCATGCACCCCTTATGAATAGTAAATT 58.996 33.333 0.00 0.00 0.00 1.82
2848 4095 7.526041 TCATGCACCCCTTATGAATAGTAAAT 58.474 34.615 0.00 0.00 0.00 1.40
2849 4096 6.905736 TCATGCACCCCTTATGAATAGTAAA 58.094 36.000 0.00 0.00 0.00 2.01
2850 4097 6.508030 TCATGCACCCCTTATGAATAGTAA 57.492 37.500 0.00 0.00 0.00 2.24
2851 4098 6.272090 TCATCATGCACCCCTTATGAATAGTA 59.728 38.462 0.00 0.00 34.80 1.82
2852 4099 5.073554 TCATCATGCACCCCTTATGAATAGT 59.926 40.000 0.00 0.00 34.80 2.12
2853 4100 5.563592 TCATCATGCACCCCTTATGAATAG 58.436 41.667 0.00 0.00 34.80 1.73
2854 4101 5.581350 TCATCATGCACCCCTTATGAATA 57.419 39.130 0.00 0.00 34.80 1.75
2855 4102 4.458256 TCATCATGCACCCCTTATGAAT 57.542 40.909 0.00 0.00 34.80 2.57
2856 4103 3.949586 TCATCATGCACCCCTTATGAA 57.050 42.857 0.00 0.00 34.80 2.57
2857 4104 3.949586 TTCATCATGCACCCCTTATGA 57.050 42.857 0.00 0.00 35.52 2.15
2858 4105 3.700539 TGTTTCATCATGCACCCCTTATG 59.299 43.478 0.00 0.00 0.00 1.90
2859 4106 3.979911 TGTTTCATCATGCACCCCTTAT 58.020 40.909 0.00 0.00 0.00 1.73
2860 4107 3.448093 TGTTTCATCATGCACCCCTTA 57.552 42.857 0.00 0.00 0.00 2.69
2861 4108 2.307496 TGTTTCATCATGCACCCCTT 57.693 45.000 0.00 0.00 0.00 3.95
2862 4109 2.024655 AGATGTTTCATCATGCACCCCT 60.025 45.455 11.47 0.00 0.00 4.79
2863 4110 2.381911 AGATGTTTCATCATGCACCCC 58.618 47.619 11.47 0.00 0.00 4.95
2864 4111 3.444742 TGAAGATGTTTCATCATGCACCC 59.555 43.478 11.47 0.00 0.00 4.61
2865 4112 4.418392 GTGAAGATGTTTCATCATGCACC 58.582 43.478 11.47 0.84 32.66 5.01
2866 4113 4.082625 TGGTGAAGATGTTTCATCATGCAC 60.083 41.667 11.47 13.41 34.88 4.57
2867 4114 4.080687 TGGTGAAGATGTTTCATCATGCA 58.919 39.130 11.47 0.00 34.88 3.96
2868 4115 4.707030 TGGTGAAGATGTTTCATCATGC 57.293 40.909 11.47 2.37 34.88 4.06
2869 4116 6.263516 ACTTGGTGAAGATGTTTCATCATG 57.736 37.500 11.47 11.98 39.08 3.07
2870 4117 6.071728 GGAACTTGGTGAAGATGTTTCATCAT 60.072 38.462 11.47 0.42 39.08 2.45
2871 4118 5.241506 GGAACTTGGTGAAGATGTTTCATCA 59.758 40.000 11.47 0.00 37.73 3.07
2872 4119 5.474876 AGGAACTTGGTGAAGATGTTTCATC 59.525 40.000 1.98 1.98 27.25 2.92
2873 4120 5.242393 CAGGAACTTGGTGAAGATGTTTCAT 59.758 40.000 0.00 0.00 34.60 2.57
2874 4121 4.580167 CAGGAACTTGGTGAAGATGTTTCA 59.420 41.667 0.00 0.00 34.60 2.69
2875 4122 4.580580 ACAGGAACTTGGTGAAGATGTTTC 59.419 41.667 0.00 0.00 34.60 2.78
2876 4123 4.536765 ACAGGAACTTGGTGAAGATGTTT 58.463 39.130 0.00 0.00 34.60 2.83
2877 4124 4.137543 GACAGGAACTTGGTGAAGATGTT 58.862 43.478 0.00 0.00 34.60 2.71
2878 4125 3.496870 GGACAGGAACTTGGTGAAGATGT 60.497 47.826 0.00 0.00 34.60 3.06
2879 4126 3.077359 GGACAGGAACTTGGTGAAGATG 58.923 50.000 0.00 0.00 34.60 2.90
2880 4127 2.289694 CGGACAGGAACTTGGTGAAGAT 60.290 50.000 0.00 0.00 34.60 2.40
2881 4128 1.070134 CGGACAGGAACTTGGTGAAGA 59.930 52.381 0.00 0.00 34.60 2.87
2882 4129 1.202651 ACGGACAGGAACTTGGTGAAG 60.203 52.381 0.00 0.00 34.60 3.02
2883 4130 0.834612 ACGGACAGGAACTTGGTGAA 59.165 50.000 0.00 0.00 34.60 3.18
2884 4131 0.391597 GACGGACAGGAACTTGGTGA 59.608 55.000 0.00 0.00 34.60 4.02
2885 4132 0.105964 TGACGGACAGGAACTTGGTG 59.894 55.000 0.00 0.00 34.60 4.17
2886 4133 0.834612 TTGACGGACAGGAACTTGGT 59.165 50.000 0.00 0.00 34.60 3.67
2887 4134 2.185004 ATTGACGGACAGGAACTTGG 57.815 50.000 0.00 0.00 34.60 3.61
2888 4135 7.434492 AGTATATATTGACGGACAGGAACTTG 58.566 38.462 0.00 0.00 34.60 3.16
2889 4136 7.598759 AGTATATATTGACGGACAGGAACTT 57.401 36.000 0.00 0.00 34.60 2.66
2890 4137 7.598759 AAGTATATATTGACGGACAGGAACT 57.401 36.000 0.00 0.00 43.88 3.01
2891 4138 9.754382 TTAAAGTATATATTGACGGACAGGAAC 57.246 33.333 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.