Multiple sequence alignment - TraesCS1A01G014000

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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 TraesCS1A01G014000 chr1A 100.000 1926 0 0 1 1926 7686641 7684716 0.000000e+00 3557.0
1 TraesCS1A01G014000 chr1A 86.564 521 53 6 934 1437 7697717 7697197 2.040000e-155 558.0
2 TraesCS1A01G014000 chr1A 100.000 134 0 0 2214 2347 7684428 7684295 5.010000e-62 248.0
3 TraesCS1A01G014000 chr1A 97.872 47 1 0 1558 1604 7697144 7697098 5.380000e-12 82.4
4 TraesCS1A01G014000 chr1D 87.014 1055 82 37 702 1726 6367635 6366606 0.000000e+00 1138.0
5 TraesCS1A01G014000 chr1D 95.501 489 17 5 1 486 224143569 224143083 0.000000e+00 776.0
6 TraesCS1A01G014000 chr1D 85.280 428 40 11 942 1351 6411352 6410930 1.000000e-113 420.0
7 TraesCS1A01G014000 chr1D 96.380 221 6 2 487 706 224142906 224142687 1.710000e-96 363.0
8 TraesCS1A01G014000 chr1D 83.158 380 47 10 983 1351 6399933 6399560 4.830000e-87 331.0
9 TraesCS1A01G014000 chr1D 94.924 197 7 3 1732 1926 4383310 4383505 2.930000e-79 305.0
10 TraesCS1A01G014000 chr1D 94.898 196 7 3 1733 1926 471092421 471092615 1.050000e-78 303.0
11 TraesCS1A01G014000 chr1D 85.811 148 11 5 1349 1486 6399512 6399365 5.230000e-32 148.0
12 TraesCS1A01G014000 chr1B 85.630 1023 96 23 737 1735 8711162 8710167 0.000000e+00 1027.0
13 TraesCS1A01G014000 chr1B 82.692 520 51 26 217 715 263932475 263932976 2.160000e-115 425.0
14 TraesCS1A01G014000 chr1B 84.091 396 31 6 978 1350 8715895 8715509 1.030000e-93 353.0
15 TraesCS1A01G014000 chr1B 79.832 357 53 12 992 1337 8658596 8658944 2.330000e-60 243.0
16 TraesCS1A01G014000 chr1B 97.761 134 3 0 2214 2347 28451844 28451711 5.040000e-57 231.0
17 TraesCS1A01G014000 chr1B 85.950 121 13 4 1587 1704 8712869 8712750 2.450000e-25 126.0
18 TraesCS1A01G014000 chr5D 95.697 488 18 3 1 486 505914871 505914385 0.000000e+00 782.0
19 TraesCS1A01G014000 chr5D 95.510 490 17 5 1 486 226734695 226734207 0.000000e+00 778.0
20 TraesCS1A01G014000 chr5D 96.413 223 6 2 487 707 447766642 447766864 1.330000e-97 366.0
21 TraesCS1A01G014000 chr4D 95.519 491 16 6 1 486 464845324 464844835 0.000000e+00 780.0
22 TraesCS1A01G014000 chr4D 95.501 489 19 3 1 486 318602139 318602627 0.000000e+00 778.0
23 TraesCS1A01G014000 chr4D 95.306 490 17 6 1 486 494482719 494482232 0.000000e+00 773.0
24 TraesCS1A01G014000 chr4D 97.761 134 3 0 2214 2347 331412932 331413065 5.040000e-57 231.0
25 TraesCS1A01G014000 chr7D 95.519 491 15 7 1 486 14186914 14186426 0.000000e+00 778.0
26 TraesCS1A01G014000 chr7D 95.102 490 20 4 1 486 497974909 497974420 0.000000e+00 769.0
27 TraesCS1A01G014000 chr7D 95.964 223 8 1 487 709 614556507 614556286 6.170000e-96 361.0
28 TraesCS1A01G014000 chr7D 97.761 134 3 0 2214 2347 15140391 15140524 5.040000e-57 231.0
29 TraesCS1A01G014000 chr3D 95.306 490 17 6 1 486 435131855 435132342 0.000000e+00 773.0
30 TraesCS1A01G014000 chr3D 95.238 231 7 3 487 713 6342156 6342386 1.710000e-96 363.0
31 TraesCS1A01G014000 chr3D 94.554 202 9 2 1726 1926 27712757 27712557 6.300000e-81 311.0
32 TraesCS1A01G014000 chr3D 97.761 134 3 0 2214 2347 593725408 593725541 5.040000e-57 231.0
33 TraesCS1A01G014000 chr7B 87.676 568 48 13 737 1293 452495642 452496198 1.970000e-180 641.0
34 TraesCS1A01G014000 chr7B 84.127 504 40 29 223 706 481816276 481816759 3.560000e-123 451.0
35 TraesCS1A01G014000 chr7B 84.182 373 32 12 985 1350 452468158 452468510 1.040000e-88 337.0
36 TraesCS1A01G014000 chr7B 83.893 149 15 6 1587 1732 452494080 452494222 1.460000e-27 134.0
37 TraesCS1A01G014000 chr2D 83.128 486 48 17 225 706 599900252 599900707 1.680000e-111 412.0
38 TraesCS1A01G014000 chr2D 96.413 223 5 3 487 706 88283495 88283717 4.770000e-97 364.0
39 TraesCS1A01G014000 chr2D 95.575 226 8 2 488 711 166854569 166854344 6.170000e-96 361.0
40 TraesCS1A01G014000 chr2D 95.455 198 8 1 1729 1926 3081807 3082003 4.870000e-82 315.0
41 TraesCS1A01G014000 chr2D 95.385 195 8 1 1733 1926 16875072 16874878 2.270000e-80 309.0
42 TraesCS1A01G014000 chr6A 96.392 194 7 0 1733 1926 46520048 46520241 1.050000e-83 320.0
43 TraesCS1A01G014000 chr6A 95.385 195 8 1 1733 1926 142778508 142778314 2.270000e-80 309.0
44 TraesCS1A01G014000 chr6A 98.485 132 2 0 2216 2347 260680223 260680092 1.400000e-57 233.0
45 TraesCS1A01G014000 chr7A 95.876 194 8 0 1733 1926 663761747 663761554 4.870000e-82 315.0
46 TraesCS1A01G014000 chr3A 94.924 197 10 0 1730 1926 572036090 572036286 2.270000e-80 309.0
47 TraesCS1A01G014000 chr3A 98.485 132 2 0 2216 2347 31053249 31053118 1.400000e-57 233.0
48 TraesCS1A01G014000 chr5A 98.507 134 2 0 2214 2347 584960694 584960827 1.080000e-58 237.0
49 TraesCS1A01G014000 chrUn 97.761 134 3 0 2214 2347 323520062 323520195 5.040000e-57 231.0
50 TraesCS1A01G014000 chr6D 97.761 134 3 0 2214 2347 47345523 47345390 5.040000e-57 231.0


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 TraesCS1A01G014000 chr1A 7684295 7686641 2346 True 1902.5 3557 100.000000 1 2347 2 chr1A.!!$R1 2346
1 TraesCS1A01G014000 chr1A 7697098 7697717 619 True 320.2 558 92.218000 934 1604 2 chr1A.!!$R2 670
2 TraesCS1A01G014000 chr1D 6366606 6367635 1029 True 1138.0 1138 87.014000 702 1726 1 chr1D.!!$R1 1024
3 TraesCS1A01G014000 chr1D 224142687 224143569 882 True 569.5 776 95.940500 1 706 2 chr1D.!!$R4 705
4 TraesCS1A01G014000 chr1D 6399365 6399933 568 True 239.5 331 84.484500 983 1486 2 chr1D.!!$R3 503
5 TraesCS1A01G014000 chr1B 8710167 8715895 5728 True 502.0 1027 85.223667 737 1735 3 chr1B.!!$R2 998
6 TraesCS1A01G014000 chr1B 263932475 263932976 501 False 425.0 425 82.692000 217 715 1 chr1B.!!$F2 498
7 TraesCS1A01G014000 chr7B 452494080 452496198 2118 False 387.5 641 85.784500 737 1732 2 chr7B.!!$F3 995

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
962 4997 0.108233 GCAGCAGCAGTAGAGAGCTT 60.108 55.0 0.0 0.0 39.5 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 6012 0.249573 TTCGTGTCTCAAACCGGGAC 60.25 55.0 6.32 3.26 0.0 4.46 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
111 113 7.272515 CGGGTACACAAAAATGTTTCATGTATC 59.727 37.037 0.00 5.20 32.17 2.24
212 214 5.195001 TGGTTGCTCTTTTTGTATGGAAC 57.805 39.130 0.00 0.00 0.00 3.62
486 490 8.907222 AATCCATGCTTAACACTTTTTGAAAT 57.093 26.923 0.00 0.00 0.00 2.17
644 824 5.270853 GCCGACGCTGTATTATTTTTGAAT 58.729 37.500 0.00 0.00 0.00 2.57
816 4847 8.177119 AGAGATGAAGACTATGAACTATGGAC 57.823 38.462 0.00 0.00 0.00 4.02
845 4876 7.365652 GGACTTTTTCCATTCTAGTCAGGGATA 60.366 40.741 0.00 0.00 45.10 2.59
861 4892 6.039829 GTCAGGGATATTTTTAGGGCTTTCTG 59.960 42.308 0.00 0.00 0.00 3.02
892 4923 2.032681 AAGCTCACAAGGGACGCC 59.967 61.111 0.00 0.00 0.00 5.68
893 4924 3.553095 AAGCTCACAAGGGACGCCC 62.553 63.158 6.80 6.80 45.90 6.13
962 4997 0.108233 GCAGCAGCAGTAGAGAGCTT 60.108 55.000 0.00 0.00 39.50 3.74
976 5011 4.965814 AGAGAGCTTTGATTTGACACTCA 58.034 39.130 0.00 0.00 0.00 3.41
1108 5171 2.835431 CCTCCCACCGATCGAGCT 60.835 66.667 18.66 0.00 0.00 4.09
1130 5193 8.511604 AGCTGCTGTAAACTGTAATTAATCAT 57.488 30.769 0.00 0.00 0.00 2.45
1131 5194 9.613428 AGCTGCTGTAAACTGTAATTAATCATA 57.387 29.630 0.00 0.00 0.00 2.15
1179 5247 0.816825 CATTGCAGAGATGGGGACGG 60.817 60.000 0.00 0.00 0.00 4.79
1386 5511 7.393515 AGAAATAAAGTAGCTCCATCGGTTTTT 59.606 33.333 0.00 0.00 0.00 1.94
1410 5543 4.038042 CCTCTTCATCTTCATGCATGCATT 59.962 41.667 30.32 13.29 33.90 3.56
1431 5564 4.764679 TCATGCATGTTGTTTAGGTGAC 57.235 40.909 25.43 0.00 0.00 3.67
1437 5570 3.646611 TGTTGTTTAGGTGACGATCGA 57.353 42.857 24.34 0.00 0.00 3.59
1449 5582 2.261586 CGATCGATCCTGGCTCCGA 61.262 63.158 19.51 7.20 35.43 4.55
1497 5630 9.820725 TTTGTGCGGTTAATGTATACTAGTAAT 57.179 29.630 6.70 0.00 0.00 1.89
1543 5676 3.431572 GCTTCTCTGTGTTGTGATCTGTC 59.568 47.826 0.00 0.00 0.00 3.51
1548 5681 4.769688 TCTGTGTTGTGATCTGTCTTGTT 58.230 39.130 0.00 0.00 0.00 2.83
1550 5683 5.294306 TCTGTGTTGTGATCTGTCTTGTTTC 59.706 40.000 0.00 0.00 0.00 2.78
1552 5685 6.345298 TGTGTTGTGATCTGTCTTGTTTCTA 58.655 36.000 0.00 0.00 0.00 2.10
1572 5705 7.809546 TTCTATATGTTGTGTTGTGTTGGAA 57.190 32.000 0.00 0.00 0.00 3.53
1621 5761 6.894339 TTTTTCCAAAAGGACCAGATCTAC 57.106 37.500 0.00 0.00 0.00 2.59
1626 5766 4.113354 CAAAAGGACCAGATCTACTACGC 58.887 47.826 0.00 0.00 0.00 4.42
1629 5769 4.434545 AGGACCAGATCTACTACGCTAA 57.565 45.455 0.00 0.00 0.00 3.09
1646 5786 3.541632 GCTAAAGATTCACCGGATTCCA 58.458 45.455 9.46 0.00 0.00 3.53
1696 5838 7.823745 AAATATATCAAGTTCCATGGACACC 57.176 36.000 15.91 5.49 0.00 4.16
1697 5839 2.113860 ATCAAGTTCCATGGACACCG 57.886 50.000 15.91 10.12 0.00 4.94
1705 5848 1.484653 TCCATGGACACCGAATCGAAT 59.515 47.619 11.44 0.00 0.00 3.34
1710 5853 1.404986 GGACACCGAATCGAATGACCA 60.405 52.381 17.65 0.00 32.10 4.02
1726 5869 1.026718 ACCATTGCTGCCGCTAGAAC 61.027 55.000 0.70 0.00 36.97 3.01
1735 5878 3.285371 CGCTAGAACGGGACCACT 58.715 61.111 0.00 0.00 0.00 4.00
1736 5879 2.485677 CGCTAGAACGGGACCACTA 58.514 57.895 0.00 0.00 0.00 2.74
1737 5880 0.381089 CGCTAGAACGGGACCACTAG 59.619 60.000 0.00 0.00 36.44 2.57
1738 5881 1.472188 GCTAGAACGGGACCACTAGT 58.528 55.000 0.00 0.00 35.96 2.57
1739 5882 2.648059 GCTAGAACGGGACCACTAGTA 58.352 52.381 0.00 0.00 35.96 1.82
1740 5883 2.617774 GCTAGAACGGGACCACTAGTAG 59.382 54.545 0.00 0.00 35.96 2.57
1741 5884 3.683847 GCTAGAACGGGACCACTAGTAGA 60.684 52.174 3.59 0.00 35.96 2.59
1742 5885 3.446442 AGAACGGGACCACTAGTAGAA 57.554 47.619 3.59 0.00 0.00 2.10
1743 5886 3.771216 AGAACGGGACCACTAGTAGAAA 58.229 45.455 3.59 0.00 0.00 2.52
1744 5887 4.154942 AGAACGGGACCACTAGTAGAAAA 58.845 43.478 3.59 0.00 0.00 2.29
1745 5888 3.949842 ACGGGACCACTAGTAGAAAAC 57.050 47.619 3.59 0.00 0.00 2.43
1746 5889 3.233507 ACGGGACCACTAGTAGAAAACA 58.766 45.455 3.59 0.00 0.00 2.83
1747 5890 3.257624 ACGGGACCACTAGTAGAAAACAG 59.742 47.826 3.59 0.00 0.00 3.16
1748 5891 3.368116 CGGGACCACTAGTAGAAAACAGG 60.368 52.174 3.59 0.00 0.00 4.00
1749 5892 3.055312 GGGACCACTAGTAGAAAACAGGG 60.055 52.174 3.59 0.00 0.00 4.45
1750 5893 3.597255 GACCACTAGTAGAAAACAGGGC 58.403 50.000 3.59 0.00 0.00 5.19
1751 5894 3.248888 ACCACTAGTAGAAAACAGGGCT 58.751 45.455 3.59 0.00 0.00 5.19
1752 5895 3.651423 ACCACTAGTAGAAAACAGGGCTT 59.349 43.478 3.59 0.00 0.00 4.35
1753 5896 4.104261 ACCACTAGTAGAAAACAGGGCTTT 59.896 41.667 3.59 0.00 0.00 3.51
1754 5897 4.695928 CCACTAGTAGAAAACAGGGCTTTC 59.304 45.833 3.59 0.00 33.75 2.62
1755 5898 4.389077 CACTAGTAGAAAACAGGGCTTTCG 59.611 45.833 3.59 0.00 37.76 3.46
1756 5899 3.487120 AGTAGAAAACAGGGCTTTCGT 57.513 42.857 0.00 0.00 37.76 3.85
1757 5900 3.816994 AGTAGAAAACAGGGCTTTCGTT 58.183 40.909 0.00 0.00 37.76 3.85
1758 5901 3.813724 AGTAGAAAACAGGGCTTTCGTTC 59.186 43.478 0.00 0.00 37.76 3.95
1759 5902 2.650322 AGAAAACAGGGCTTTCGTTCA 58.350 42.857 0.00 0.00 37.76 3.18
1760 5903 2.618709 AGAAAACAGGGCTTTCGTTCAG 59.381 45.455 0.00 0.00 37.76 3.02
1761 5904 2.341846 AAACAGGGCTTTCGTTCAGA 57.658 45.000 0.00 0.00 0.00 3.27
1762 5905 1.594331 AACAGGGCTTTCGTTCAGAC 58.406 50.000 0.00 0.00 0.00 3.51
1763 5906 0.250338 ACAGGGCTTTCGTTCAGACC 60.250 55.000 0.00 0.00 40.26 3.85
1764 5907 0.250295 CAGGGCTTTCGTTCAGACCA 60.250 55.000 6.02 0.00 42.86 4.02
1765 5908 0.035458 AGGGCTTTCGTTCAGACCAG 59.965 55.000 6.02 0.00 42.86 4.00
1766 5909 0.034896 GGGCTTTCGTTCAGACCAGA 59.965 55.000 0.00 0.00 39.62 3.86
1767 5910 1.339151 GGGCTTTCGTTCAGACCAGAT 60.339 52.381 0.00 0.00 39.62 2.90
1768 5911 2.093658 GGGCTTTCGTTCAGACCAGATA 60.094 50.000 0.00 0.00 39.62 1.98
1769 5912 3.596214 GGCTTTCGTTCAGACCAGATAA 58.404 45.455 0.00 0.00 0.00 1.75
1770 5913 3.619038 GGCTTTCGTTCAGACCAGATAAG 59.381 47.826 0.00 0.00 0.00 1.73
1771 5914 3.062774 GCTTTCGTTCAGACCAGATAAGC 59.937 47.826 0.00 0.00 0.00 3.09
1772 5915 2.961526 TCGTTCAGACCAGATAAGCC 57.038 50.000 0.00 0.00 0.00 4.35
1773 5916 1.480954 TCGTTCAGACCAGATAAGCCC 59.519 52.381 0.00 0.00 0.00 5.19
1774 5917 1.207089 CGTTCAGACCAGATAAGCCCA 59.793 52.381 0.00 0.00 0.00 5.36
1775 5918 2.158900 CGTTCAGACCAGATAAGCCCAT 60.159 50.000 0.00 0.00 0.00 4.00
1776 5919 3.682718 CGTTCAGACCAGATAAGCCCATT 60.683 47.826 0.00 0.00 0.00 3.16
1777 5920 4.442893 CGTTCAGACCAGATAAGCCCATTA 60.443 45.833 0.00 0.00 0.00 1.90
1778 5921 4.963318 TCAGACCAGATAAGCCCATTAG 57.037 45.455 0.00 0.00 0.00 1.73
1779 5922 4.298626 TCAGACCAGATAAGCCCATTAGT 58.701 43.478 0.00 0.00 0.00 2.24
1780 5923 4.345257 TCAGACCAGATAAGCCCATTAGTC 59.655 45.833 0.00 0.00 0.00 2.59
1781 5924 3.648545 AGACCAGATAAGCCCATTAGTCC 59.351 47.826 0.00 0.00 0.00 3.85
1782 5925 3.648545 GACCAGATAAGCCCATTAGTCCT 59.351 47.826 0.00 0.00 0.00 3.85
1783 5926 3.392616 ACCAGATAAGCCCATTAGTCCTG 59.607 47.826 0.00 0.00 0.00 3.86
1784 5927 3.244700 CCAGATAAGCCCATTAGTCCTGG 60.245 52.174 0.00 0.00 35.21 4.45
1785 5928 3.392616 CAGATAAGCCCATTAGTCCTGGT 59.607 47.826 0.00 0.00 31.44 4.00
1786 5929 4.047883 AGATAAGCCCATTAGTCCTGGTT 58.952 43.478 0.00 0.00 31.44 3.67
1787 5930 2.808906 AAGCCCATTAGTCCTGGTTC 57.191 50.000 0.00 0.00 31.44 3.62
1788 5931 1.668826 AGCCCATTAGTCCTGGTTCA 58.331 50.000 0.00 0.00 31.44 3.18
1789 5932 1.992557 AGCCCATTAGTCCTGGTTCAA 59.007 47.619 0.00 0.00 31.44 2.69
1790 5933 2.582636 AGCCCATTAGTCCTGGTTCAAT 59.417 45.455 0.00 0.00 31.44 2.57
1791 5934 2.952310 GCCCATTAGTCCTGGTTCAATC 59.048 50.000 0.00 0.00 31.44 2.67
1792 5935 3.624707 GCCCATTAGTCCTGGTTCAATCA 60.625 47.826 0.00 0.00 31.44 2.57
1793 5936 3.947834 CCCATTAGTCCTGGTTCAATCAC 59.052 47.826 0.00 0.00 31.44 3.06
1794 5937 3.623060 CCATTAGTCCTGGTTCAATCACG 59.377 47.826 0.00 0.00 0.00 4.35
1795 5938 4.503910 CATTAGTCCTGGTTCAATCACGA 58.496 43.478 0.00 0.00 0.00 4.35
1796 5939 4.610605 TTAGTCCTGGTTCAATCACGAA 57.389 40.909 0.00 0.00 0.00 3.85
1797 5940 2.767505 AGTCCTGGTTCAATCACGAAC 58.232 47.619 0.00 0.00 43.75 3.95
1802 5945 3.220447 GTTCAATCACGAACCGGGA 57.780 52.632 6.32 0.00 45.56 5.14
1803 5946 0.794473 GTTCAATCACGAACCGGGAC 59.206 55.000 6.32 0.00 43.84 4.46
1804 5947 0.682852 TTCAATCACGAACCGGGACT 59.317 50.000 6.32 0.00 43.84 3.85
1805 5948 1.548081 TCAATCACGAACCGGGACTA 58.452 50.000 6.32 0.00 43.84 2.59
1806 5949 1.894466 TCAATCACGAACCGGGACTAA 59.106 47.619 6.32 0.00 43.84 2.24
1807 5950 2.498481 TCAATCACGAACCGGGACTAAT 59.502 45.455 6.32 0.00 43.84 1.73
1808 5951 2.596904 ATCACGAACCGGGACTAATG 57.403 50.000 6.32 0.00 43.84 1.90
1809 5952 1.259609 TCACGAACCGGGACTAATGT 58.740 50.000 6.32 0.00 32.99 2.71
1810 5953 1.067425 TCACGAACCGGGACTAATGTG 60.067 52.381 6.32 4.66 32.99 3.21
1811 5954 1.067425 CACGAACCGGGACTAATGTGA 60.067 52.381 6.32 0.00 28.17 3.58
1812 5955 1.203994 ACGAACCGGGACTAATGTGAG 59.796 52.381 6.32 0.00 0.00 3.51
1813 5956 1.653151 GAACCGGGACTAATGTGAGC 58.347 55.000 6.32 0.00 0.00 4.26
1814 5957 0.981183 AACCGGGACTAATGTGAGCA 59.019 50.000 6.32 0.00 0.00 4.26
1815 5958 1.204146 ACCGGGACTAATGTGAGCAT 58.796 50.000 6.32 0.00 36.80 3.79
1816 5959 1.559682 ACCGGGACTAATGTGAGCATT 59.440 47.619 6.32 0.00 46.14 3.56
1817 5960 1.942657 CCGGGACTAATGTGAGCATTG 59.057 52.381 0.00 0.00 44.32 2.82
1818 5961 1.942657 CGGGACTAATGTGAGCATTGG 59.057 52.381 3.39 3.10 44.32 3.16
1823 5966 1.942657 CTAATGTGAGCATTGGTCCCG 59.057 52.381 12.99 0.00 44.32 5.14
1824 5967 0.680921 AATGTGAGCATTGGTCCCGG 60.681 55.000 12.99 0.00 43.12 5.73
1825 5968 1.852157 ATGTGAGCATTGGTCCCGGT 61.852 55.000 12.99 0.00 29.54 5.28
1826 5969 1.303317 GTGAGCATTGGTCCCGGTT 60.303 57.895 12.99 0.00 0.00 4.44
1827 5970 1.002624 TGAGCATTGGTCCCGGTTC 60.003 57.895 12.99 0.00 0.00 3.62
1828 5971 2.046314 AGCATTGGTCCCGGTTCG 60.046 61.111 0.00 0.00 0.00 3.95
1829 5972 2.359478 GCATTGGTCCCGGTTCGT 60.359 61.111 0.00 0.00 0.00 3.85
1830 5973 2.686816 GCATTGGTCCCGGTTCGTG 61.687 63.158 0.00 0.00 0.00 4.35
1831 5974 2.359478 ATTGGTCCCGGTTCGTGC 60.359 61.111 0.00 0.00 0.00 5.34
1832 5975 4.973055 TTGGTCCCGGTTCGTGCG 62.973 66.667 0.00 0.00 0.00 5.34
1835 5978 4.424566 GTCCCGGTTCGTGCGCTA 62.425 66.667 9.73 0.00 0.00 4.26
1836 5979 3.682885 TCCCGGTTCGTGCGCTAA 61.683 61.111 9.73 0.00 0.00 3.09
1837 5980 2.739287 CCCGGTTCGTGCGCTAAA 60.739 61.111 9.73 0.00 0.00 1.85
1838 5981 2.736682 CCCGGTTCGTGCGCTAAAG 61.737 63.158 9.73 0.00 0.00 1.85
1839 5982 2.736682 CCGGTTCGTGCGCTAAAGG 61.737 63.158 9.73 4.27 0.00 3.11
1840 5983 2.479198 GGTTCGTGCGCTAAAGGC 59.521 61.111 9.73 0.00 37.64 4.35
1841 5984 2.322081 GGTTCGTGCGCTAAAGGCA 61.322 57.895 9.73 0.00 41.91 4.75
1842 5985 1.644786 GGTTCGTGCGCTAAAGGCAT 61.645 55.000 9.73 0.00 43.19 4.40
1843 5986 0.168128 GTTCGTGCGCTAAAGGCATT 59.832 50.000 9.73 0.00 43.19 3.56
1844 5987 1.395608 GTTCGTGCGCTAAAGGCATTA 59.604 47.619 9.73 0.00 43.19 1.90
1845 5988 1.286501 TCGTGCGCTAAAGGCATTAG 58.713 50.000 9.73 5.16 43.19 1.73
1846 5989 1.006832 CGTGCGCTAAAGGCATTAGT 58.993 50.000 9.73 0.00 43.19 2.24
1847 5990 1.004927 CGTGCGCTAAAGGCATTAGTC 60.005 52.381 9.73 4.65 43.19 2.59
1848 5991 1.330829 GTGCGCTAAAGGCATTAGTCC 59.669 52.381 9.73 3.68 43.19 3.85
1849 5992 0.945099 GCGCTAAAGGCATTAGTCCC 59.055 55.000 10.80 0.00 42.58 4.46
1850 5993 1.217882 CGCTAAAGGCATTAGTCCCG 58.782 55.000 10.80 3.12 42.58 5.14
1851 5994 1.594331 GCTAAAGGCATTAGTCCCGG 58.406 55.000 10.80 0.00 42.58 5.73
1852 5995 1.134189 GCTAAAGGCATTAGTCCCGGT 60.134 52.381 10.80 0.00 42.58 5.28
1853 5996 2.682858 GCTAAAGGCATTAGTCCCGGTT 60.683 50.000 10.80 0.00 42.58 4.44
1854 5997 2.124277 AAAGGCATTAGTCCCGGTTC 57.876 50.000 0.00 0.00 0.00 3.62
1855 5998 0.988832 AAGGCATTAGTCCCGGTTCA 59.011 50.000 0.00 0.00 0.00 3.18
1856 5999 0.988832 AGGCATTAGTCCCGGTTCAA 59.011 50.000 0.00 0.00 0.00 2.69
1857 6000 1.353022 AGGCATTAGTCCCGGTTCAAA 59.647 47.619 0.00 0.00 0.00 2.69
1858 6001 2.025321 AGGCATTAGTCCCGGTTCAAAT 60.025 45.455 0.00 0.00 0.00 2.32
1859 6002 2.099098 GGCATTAGTCCCGGTTCAAATG 59.901 50.000 0.00 6.59 0.00 2.32
1860 6003 3.013921 GCATTAGTCCCGGTTCAAATGA 58.986 45.455 16.56 0.00 0.00 2.57
1861 6004 3.065371 GCATTAGTCCCGGTTCAAATGAG 59.935 47.826 16.56 0.00 0.00 2.90
1862 6005 2.396590 TAGTCCCGGTTCAAATGAGC 57.603 50.000 0.00 0.00 0.00 4.26
1863 6006 0.400213 AGTCCCGGTTCAAATGAGCA 59.600 50.000 0.00 0.00 0.00 4.26
1864 6007 1.004745 AGTCCCGGTTCAAATGAGCAT 59.995 47.619 0.00 0.00 0.00 3.79
1865 6008 1.818674 GTCCCGGTTCAAATGAGCATT 59.181 47.619 0.00 0.00 0.00 3.56
1866 6009 2.231235 GTCCCGGTTCAAATGAGCATTT 59.769 45.455 0.00 2.74 41.33 2.32
1867 6010 2.896685 TCCCGGTTCAAATGAGCATTTT 59.103 40.909 0.00 0.00 38.84 1.82
1868 6011 4.082463 GTCCCGGTTCAAATGAGCATTTTA 60.082 41.667 0.00 0.00 38.84 1.52
1869 6012 4.157656 TCCCGGTTCAAATGAGCATTTTAG 59.842 41.667 0.00 0.00 38.84 1.85
1870 6013 4.082245 CCCGGTTCAAATGAGCATTTTAGT 60.082 41.667 0.00 0.00 38.84 2.24
1871 6014 5.095490 CCGGTTCAAATGAGCATTTTAGTC 58.905 41.667 5.75 0.00 38.84 2.59
1872 6015 5.095490 CGGTTCAAATGAGCATTTTAGTCC 58.905 41.667 5.75 6.11 38.84 3.85
1873 6016 5.410924 GGTTCAAATGAGCATTTTAGTCCC 58.589 41.667 5.75 0.14 38.84 4.46
1874 6017 4.963276 TCAAATGAGCATTTTAGTCCCG 57.037 40.909 5.75 0.00 38.84 5.14
1875 6018 3.694072 TCAAATGAGCATTTTAGTCCCGG 59.306 43.478 5.75 0.00 38.84 5.73
1876 6019 3.366052 AATGAGCATTTTAGTCCCGGT 57.634 42.857 0.00 0.00 0.00 5.28
1877 6020 2.871096 TGAGCATTTTAGTCCCGGTT 57.129 45.000 0.00 0.00 0.00 4.44
1878 6021 3.149005 TGAGCATTTTAGTCCCGGTTT 57.851 42.857 0.00 0.00 0.00 3.27
1879 6022 2.817258 TGAGCATTTTAGTCCCGGTTTG 59.183 45.455 0.00 0.00 0.00 2.93
1880 6023 3.078837 GAGCATTTTAGTCCCGGTTTGA 58.921 45.455 0.00 0.00 0.00 2.69
1881 6024 3.081804 AGCATTTTAGTCCCGGTTTGAG 58.918 45.455 0.00 0.00 0.00 3.02
1882 6025 3.078837 GCATTTTAGTCCCGGTTTGAGA 58.921 45.455 0.00 0.00 0.00 3.27
1883 6026 3.119955 GCATTTTAGTCCCGGTTTGAGAC 60.120 47.826 0.00 0.00 0.00 3.36
1884 6027 3.842007 TTTTAGTCCCGGTTTGAGACA 57.158 42.857 9.96 0.00 32.82 3.41
1885 6028 2.825861 TTAGTCCCGGTTTGAGACAC 57.174 50.000 9.96 0.00 32.82 3.67
1886 6029 0.599558 TAGTCCCGGTTTGAGACACG 59.400 55.000 9.96 0.00 32.82 4.49
1887 6030 1.111116 AGTCCCGGTTTGAGACACGA 61.111 55.000 9.96 0.00 32.82 4.35
1888 6031 0.249573 GTCCCGGTTTGAGACACGAA 60.250 55.000 0.00 0.00 0.00 3.85
1889 6032 0.249573 TCCCGGTTTGAGACACGAAC 60.250 55.000 0.00 0.00 40.95 3.95
1893 6036 2.231820 GTTTGAGACACGAACCGGG 58.768 57.895 6.32 0.00 37.02 5.73
1894 6037 0.249573 GTTTGAGACACGAACCGGGA 60.250 55.000 6.32 0.00 37.02 5.14
1895 6038 0.249573 TTTGAGACACGAACCGGGAC 60.250 55.000 6.32 0.00 32.98 4.46
1896 6039 1.111116 TTGAGACACGAACCGGGACT 61.111 55.000 6.32 0.00 38.03 3.85
1897 6040 0.250858 TGAGACACGAACCGGGACTA 60.251 55.000 6.32 0.00 35.29 2.59
1898 6041 0.883833 GAGACACGAACCGGGACTAA 59.116 55.000 6.32 0.00 35.29 2.24
1899 6042 1.270550 GAGACACGAACCGGGACTAAA 59.729 52.381 6.32 0.00 35.29 1.85
1900 6043 1.271656 AGACACGAACCGGGACTAAAG 59.728 52.381 6.32 0.00 33.23 1.85
1901 6044 0.319405 ACACGAACCGGGACTAAAGG 59.681 55.000 6.32 0.00 32.98 3.11
1902 6045 0.390735 CACGAACCGGGACTAAAGGG 60.391 60.000 6.32 0.00 28.17 3.95
1903 6046 0.833409 ACGAACCGGGACTAAAGGGT 60.833 55.000 6.32 0.00 0.00 4.34
1904 6047 0.390735 CGAACCGGGACTAAAGGGTG 60.391 60.000 6.32 0.00 31.96 4.61
1905 6048 0.689055 GAACCGGGACTAAAGGGTGT 59.311 55.000 6.32 0.00 31.96 4.16
1906 6049 0.399075 AACCGGGACTAAAGGGTGTG 59.601 55.000 6.32 0.00 31.96 3.82
1907 6050 0.472352 ACCGGGACTAAAGGGTGTGA 60.472 55.000 6.32 0.00 0.00 3.58
1908 6051 0.909623 CCGGGACTAAAGGGTGTGAT 59.090 55.000 0.00 0.00 0.00 3.06
1909 6052 1.406887 CCGGGACTAAAGGGTGTGATG 60.407 57.143 0.00 0.00 0.00 3.07
1910 6053 1.751437 GGGACTAAAGGGTGTGATGC 58.249 55.000 0.00 0.00 0.00 3.91
1911 6054 1.682087 GGGACTAAAGGGTGTGATGCC 60.682 57.143 0.00 0.00 0.00 4.40
1912 6055 1.682087 GGACTAAAGGGTGTGATGCCC 60.682 57.143 0.00 0.00 46.43 5.36
1918 6061 3.978876 GGGTGTGATGCCCTTTAGT 57.021 52.632 0.00 0.00 42.81 2.24
1919 6062 1.751437 GGGTGTGATGCCCTTTAGTC 58.249 55.000 0.00 0.00 42.81 2.59
1920 6063 1.682087 GGGTGTGATGCCCTTTAGTCC 60.682 57.143 0.00 0.00 42.81 3.85
1921 6064 1.682087 GGTGTGATGCCCTTTAGTCCC 60.682 57.143 0.00 0.00 0.00 4.46
1922 6065 0.251916 TGTGATGCCCTTTAGTCCCG 59.748 55.000 0.00 0.00 0.00 5.14
1923 6066 0.463833 GTGATGCCCTTTAGTCCCGG 60.464 60.000 0.00 0.00 0.00 5.73
1924 6067 0.912487 TGATGCCCTTTAGTCCCGGT 60.912 55.000 0.00 0.00 0.00 5.28
1925 6068 0.255033 GATGCCCTTTAGTCCCGGTT 59.745 55.000 0.00 0.00 0.00 4.44
2285 6428 9.530633 AAATCCTTCGAGATGTAGTTATGTTAC 57.469 33.333 0.00 0.00 0.00 2.50
2286 6429 7.876936 TCCTTCGAGATGTAGTTATGTTACT 57.123 36.000 0.00 0.00 0.00 2.24
2287 6430 8.969260 TCCTTCGAGATGTAGTTATGTTACTA 57.031 34.615 0.00 0.00 0.00 1.82
2288 6431 8.834465 TCCTTCGAGATGTAGTTATGTTACTAC 58.166 37.037 6.92 6.92 46.85 2.73
2337 6480 7.798596 AACATAAATTTGGACATGTTTTGCA 57.201 28.000 10.06 0.00 38.18 4.08
2338 6481 7.798596 ACATAAATTTGGACATGTTTTGCAA 57.201 28.000 0.00 0.00 0.00 4.08
2339 6482 8.218338 ACATAAATTTGGACATGTTTTGCAAA 57.782 26.923 8.05 8.05 0.00 3.68
2340 6483 8.680903 ACATAAATTTGGACATGTTTTGCAAAA 58.319 25.926 20.46 20.46 0.00 2.44
2341 6484 9.512435 CATAAATTTGGACATGTTTTGCAAAAA 57.488 25.926 25.40 15.82 0.00 1.94
2342 6485 9.733219 ATAAATTTGGACATGTTTTGCAAAAAG 57.267 25.926 25.40 19.30 0.00 2.27
2343 6486 6.756299 ATTTGGACATGTTTTGCAAAAAGT 57.244 29.167 25.40 22.02 0.00 2.66
2344 6487 5.542616 TTGGACATGTTTTGCAAAAAGTG 57.457 34.783 25.40 25.05 0.00 3.16
2345 6488 4.573900 TGGACATGTTTTGCAAAAAGTGT 58.426 34.783 28.99 28.99 33.32 3.55
2346 6489 5.724328 TGGACATGTTTTGCAAAAAGTGTA 58.276 33.333 28.81 18.78 31.84 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 89 7.272515 CCGATACATGAAACATTTTTGTGTACC 59.727 37.037 0.00 0.00 30.80 3.34
111 113 4.477302 ACACGTTTAACCTTTCATTCCG 57.523 40.909 0.00 0.00 0.00 4.30
464 468 7.439056 ACTGATTTCAAAAAGTGTTAAGCATGG 59.561 33.333 0.00 0.00 0.00 3.66
486 490 3.625897 CCACTGTGGGCCGACTGA 61.626 66.667 27.42 4.81 32.67 3.41
572 752 2.110967 CACAGCAGGCCGATTGGAG 61.111 63.158 1.98 0.00 37.49 3.86
797 4828 6.926272 GTCCATGTCCATAGTTCATAGTCTTC 59.074 42.308 0.00 0.00 0.00 2.87
798 4829 6.613271 AGTCCATGTCCATAGTTCATAGTCTT 59.387 38.462 0.00 0.00 0.00 3.01
830 4861 7.295911 AGCCCTAAAAATATCCCTGACTAGAAT 59.704 37.037 0.00 0.00 0.00 2.40
840 4871 4.039245 GCCAGAAAGCCCTAAAAATATCCC 59.961 45.833 0.00 0.00 0.00 3.85
845 4876 4.281657 CCTAGCCAGAAAGCCCTAAAAAT 58.718 43.478 0.00 0.00 0.00 1.82
921 4956 2.334023 GATGAGGGGAGCTACCATCTT 58.666 52.381 29.03 23.34 41.69 2.40
962 4997 5.125356 TGCTCTCTTTGAGTGTCAAATCAA 58.875 37.500 2.67 0.00 44.37 2.57
976 5011 3.070734 TCTCTTCTGCACTTGCTCTCTTT 59.929 43.478 2.33 0.00 42.66 2.52
1032 5075 4.361971 AGGACGAGGAGGACGGCA 62.362 66.667 0.00 0.00 40.86 5.69
1045 5103 2.766400 CGACGAGGAGGAGCAGGAC 61.766 68.421 0.00 0.00 0.00 3.85
1081 5144 1.925972 GGTGGGAGGGAGGAAGCTT 60.926 63.158 0.00 0.00 0.00 3.74
1108 5171 8.836413 GCCTATGATTAATTACAGTTTACAGCA 58.164 33.333 0.00 0.00 0.00 4.41
1130 5193 5.474189 ACCACAAAAAGTAATTAAGCGCCTA 59.526 36.000 2.29 0.00 0.00 3.93
1131 5194 4.279922 ACCACAAAAAGTAATTAAGCGCCT 59.720 37.500 2.29 0.00 0.00 5.52
1386 5511 3.211865 GCATGCATGAAGATGAAGAGGA 58.788 45.455 30.64 0.00 0.00 3.71
1410 5543 3.188254 CGTCACCTAAACAACATGCATGA 59.812 43.478 32.75 8.53 0.00 3.07
1431 5564 2.256764 CGGAGCCAGGATCGATCG 59.743 66.667 18.81 9.36 0.00 3.69
1437 5570 1.827399 AAACACGTCGGAGCCAGGAT 61.827 55.000 0.00 0.00 0.00 3.24
1449 5582 0.383949 AATTGAAGCCGCAAACACGT 59.616 45.000 0.00 0.00 0.00 4.49
1497 5630 2.112029 GCATCAGTGGCATGCATCA 58.888 52.632 21.36 6.25 45.19 3.07
1543 5676 8.957028 CAACACAACACAACATATAGAAACAAG 58.043 33.333 0.00 0.00 0.00 3.16
1548 5681 7.809546 TTCCAACACAACACAACATATAGAA 57.190 32.000 0.00 0.00 0.00 2.10
1550 5683 7.815641 TGATTCCAACACAACACAACATATAG 58.184 34.615 0.00 0.00 0.00 1.31
1552 5685 6.265196 ACTGATTCCAACACAACACAACATAT 59.735 34.615 0.00 0.00 0.00 1.78
1572 5705 4.040952 AGACAAGCCAACTAACTGACTGAT 59.959 41.667 0.00 0.00 0.00 2.90
1604 5744 4.113354 GCGTAGTAGATCTGGTCCTTTTG 58.887 47.826 5.18 0.00 0.00 2.44
1610 5750 6.563222 ATCTTTAGCGTAGTAGATCTGGTC 57.437 41.667 5.18 0.00 0.00 4.02
1611 5751 6.546403 TGAATCTTTAGCGTAGTAGATCTGGT 59.454 38.462 5.18 0.00 0.00 4.00
1612 5752 6.858993 GTGAATCTTTAGCGTAGTAGATCTGG 59.141 42.308 5.18 0.00 0.00 3.86
1621 5761 3.431922 TCCGGTGAATCTTTAGCGTAG 57.568 47.619 0.00 0.00 36.18 3.51
1626 5766 6.288294 TGTATGGAATCCGGTGAATCTTTAG 58.712 40.000 0.00 0.00 0.00 1.85
1629 5769 4.771114 TGTATGGAATCCGGTGAATCTT 57.229 40.909 0.00 0.00 0.00 2.40
1671 5813 7.659799 CGGTGTCCATGGAACTTGATATATTTA 59.340 37.037 18.20 0.00 0.00 1.40
1683 5825 1.006832 CGATTCGGTGTCCATGGAAC 58.993 55.000 18.20 16.15 0.00 3.62
1684 5826 0.899019 TCGATTCGGTGTCCATGGAA 59.101 50.000 18.20 4.13 0.00 3.53
1694 5836 1.670811 GCAATGGTCATTCGATTCGGT 59.329 47.619 6.18 0.00 0.00 4.69
1695 5837 1.942657 AGCAATGGTCATTCGATTCGG 59.057 47.619 6.18 0.00 0.00 4.30
1696 5838 2.852143 GCAGCAATGGTCATTCGATTCG 60.852 50.000 0.00 0.00 0.00 3.34
1697 5839 2.542411 GGCAGCAATGGTCATTCGATTC 60.542 50.000 0.00 0.00 0.00 2.52
1726 5869 3.368116 CCTGTTTTCTACTAGTGGTCCCG 60.368 52.174 5.39 0.00 0.00 5.14
1728 5871 3.619242 GCCCTGTTTTCTACTAGTGGTCC 60.619 52.174 5.39 0.00 0.00 4.46
1732 5875 4.389077 CGAAAGCCCTGTTTTCTACTAGTG 59.611 45.833 5.39 0.00 32.09 2.74
1735 5878 4.612264 ACGAAAGCCCTGTTTTCTACTA 57.388 40.909 0.00 0.00 32.09 1.82
1736 5879 3.487120 ACGAAAGCCCTGTTTTCTACT 57.513 42.857 0.00 0.00 32.09 2.57
1737 5880 3.562557 TGAACGAAAGCCCTGTTTTCTAC 59.437 43.478 0.00 0.00 32.09 2.59
1738 5881 3.811083 TGAACGAAAGCCCTGTTTTCTA 58.189 40.909 0.00 0.00 32.09 2.10
1739 5882 2.618709 CTGAACGAAAGCCCTGTTTTCT 59.381 45.455 0.00 0.00 32.09 2.52
1740 5883 2.616842 TCTGAACGAAAGCCCTGTTTTC 59.383 45.455 0.00 0.00 31.18 2.29
1741 5884 2.357952 GTCTGAACGAAAGCCCTGTTTT 59.642 45.455 0.00 0.00 0.00 2.43
1742 5885 1.947456 GTCTGAACGAAAGCCCTGTTT 59.053 47.619 0.00 0.00 0.00 2.83
1743 5886 1.594331 GTCTGAACGAAAGCCCTGTT 58.406 50.000 0.00 0.00 0.00 3.16
1744 5887 0.250338 GGTCTGAACGAAAGCCCTGT 60.250 55.000 0.00 0.00 0.00 4.00
1745 5888 0.250295 TGGTCTGAACGAAAGCCCTG 60.250 55.000 0.00 0.00 0.00 4.45
1746 5889 0.035458 CTGGTCTGAACGAAAGCCCT 59.965 55.000 0.00 0.00 0.00 5.19
1747 5890 0.034896 TCTGGTCTGAACGAAAGCCC 59.965 55.000 0.00 0.00 0.00 5.19
1748 5891 2.100605 ATCTGGTCTGAACGAAAGCC 57.899 50.000 0.00 0.00 0.00 4.35
1749 5892 3.062774 GCTTATCTGGTCTGAACGAAAGC 59.937 47.826 0.00 5.71 0.00 3.51
1750 5893 3.619038 GGCTTATCTGGTCTGAACGAAAG 59.381 47.826 0.00 0.00 0.00 2.62
1751 5894 3.596214 GGCTTATCTGGTCTGAACGAAA 58.404 45.455 0.00 0.00 0.00 3.46
1752 5895 2.093658 GGGCTTATCTGGTCTGAACGAA 60.094 50.000 0.00 0.00 0.00 3.85
1753 5896 1.480954 GGGCTTATCTGGTCTGAACGA 59.519 52.381 0.00 0.00 0.00 3.85
1754 5897 1.207089 TGGGCTTATCTGGTCTGAACG 59.793 52.381 0.00 0.00 0.00 3.95
1755 5898 3.567478 ATGGGCTTATCTGGTCTGAAC 57.433 47.619 0.00 0.00 0.00 3.18
1756 5899 4.721776 ACTAATGGGCTTATCTGGTCTGAA 59.278 41.667 0.00 0.00 0.00 3.02
1757 5900 4.298626 ACTAATGGGCTTATCTGGTCTGA 58.701 43.478 0.00 0.00 0.00 3.27
1758 5901 4.503991 GGACTAATGGGCTTATCTGGTCTG 60.504 50.000 0.00 0.00 0.00 3.51
1759 5902 3.648545 GGACTAATGGGCTTATCTGGTCT 59.351 47.826 0.00 0.00 0.00 3.85
1760 5903 3.648545 AGGACTAATGGGCTTATCTGGTC 59.351 47.826 0.00 0.00 0.00 4.02
1761 5904 3.392616 CAGGACTAATGGGCTTATCTGGT 59.607 47.826 0.00 0.00 0.00 4.00
1762 5905 3.244700 CCAGGACTAATGGGCTTATCTGG 60.245 52.174 0.00 0.00 33.94 3.86
1763 5906 3.392616 ACCAGGACTAATGGGCTTATCTG 59.607 47.826 0.00 0.00 42.48 2.90
1764 5907 3.669949 ACCAGGACTAATGGGCTTATCT 58.330 45.455 0.00 0.00 42.48 1.98
1765 5908 4.141482 TGAACCAGGACTAATGGGCTTATC 60.141 45.833 0.00 0.00 42.48 1.75
1766 5909 3.785887 TGAACCAGGACTAATGGGCTTAT 59.214 43.478 0.00 0.00 42.48 1.73
1767 5910 3.186283 TGAACCAGGACTAATGGGCTTA 58.814 45.455 0.00 0.00 42.48 3.09
1768 5911 1.992557 TGAACCAGGACTAATGGGCTT 59.007 47.619 0.00 0.00 42.48 4.35
1769 5912 1.668826 TGAACCAGGACTAATGGGCT 58.331 50.000 0.00 0.00 42.48 5.19
1770 5913 2.507407 TTGAACCAGGACTAATGGGC 57.493 50.000 0.00 0.00 42.48 5.36
1771 5914 3.947834 GTGATTGAACCAGGACTAATGGG 59.052 47.826 0.00 0.00 42.48 4.00
1772 5915 3.623060 CGTGATTGAACCAGGACTAATGG 59.377 47.826 0.00 0.00 43.87 3.16
1773 5916 4.503910 TCGTGATTGAACCAGGACTAATG 58.496 43.478 0.00 0.00 0.00 1.90
1774 5917 4.819105 TCGTGATTGAACCAGGACTAAT 57.181 40.909 0.00 0.00 0.00 1.73
1775 5918 4.312443 GTTCGTGATTGAACCAGGACTAA 58.688 43.478 0.00 0.00 41.88 2.24
1776 5919 3.921677 GTTCGTGATTGAACCAGGACTA 58.078 45.455 0.00 0.00 41.88 2.59
1777 5920 2.767505 GTTCGTGATTGAACCAGGACT 58.232 47.619 0.00 0.00 41.88 3.85
1784 5927 0.794473 GTCCCGGTTCGTGATTGAAC 59.206 55.000 0.00 0.00 45.91 3.18
1785 5928 0.682852 AGTCCCGGTTCGTGATTGAA 59.317 50.000 0.00 0.00 0.00 2.69
1786 5929 1.548081 TAGTCCCGGTTCGTGATTGA 58.452 50.000 0.00 0.00 0.00 2.57
1787 5930 2.373540 TTAGTCCCGGTTCGTGATTG 57.626 50.000 0.00 0.00 0.00 2.67
1788 5931 2.235402 ACATTAGTCCCGGTTCGTGATT 59.765 45.455 0.00 0.00 0.00 2.57
1789 5932 1.829222 ACATTAGTCCCGGTTCGTGAT 59.171 47.619 0.00 0.00 0.00 3.06
1790 5933 1.067425 CACATTAGTCCCGGTTCGTGA 60.067 52.381 0.00 0.00 0.00 4.35
1791 5934 1.067425 TCACATTAGTCCCGGTTCGTG 60.067 52.381 0.00 0.00 0.00 4.35
1792 5935 1.203994 CTCACATTAGTCCCGGTTCGT 59.796 52.381 0.00 0.00 0.00 3.85
1793 5936 1.922570 CTCACATTAGTCCCGGTTCG 58.077 55.000 0.00 0.00 0.00 3.95
1794 5937 1.066430 TGCTCACATTAGTCCCGGTTC 60.066 52.381 0.00 0.00 0.00 3.62
1795 5938 0.981183 TGCTCACATTAGTCCCGGTT 59.019 50.000 0.00 0.00 0.00 4.44
1796 5939 1.204146 ATGCTCACATTAGTCCCGGT 58.796 50.000 0.00 0.00 30.07 5.28
1797 5940 1.942657 CAATGCTCACATTAGTCCCGG 59.057 52.381 0.00 0.00 44.83 5.73
1798 5941 1.942657 CCAATGCTCACATTAGTCCCG 59.057 52.381 0.00 0.00 44.83 5.14
1799 5942 2.945668 GACCAATGCTCACATTAGTCCC 59.054 50.000 6.20 0.00 44.37 4.46
1802 5945 2.680805 CGGGACCAATGCTCACATTAGT 60.681 50.000 0.00 0.00 44.83 2.24
1803 5946 1.942657 CGGGACCAATGCTCACATTAG 59.057 52.381 0.00 0.00 44.83 1.73
1804 5947 1.408127 CCGGGACCAATGCTCACATTA 60.408 52.381 0.00 0.00 44.83 1.90
1806 5949 1.077501 CCGGGACCAATGCTCACAT 60.078 57.895 0.00 0.00 38.49 3.21
1807 5950 2.063015 AACCGGGACCAATGCTCACA 62.063 55.000 6.32 0.00 0.00 3.58
1808 5951 1.303317 AACCGGGACCAATGCTCAC 60.303 57.895 6.32 0.00 0.00 3.51
1809 5952 1.002624 GAACCGGGACCAATGCTCA 60.003 57.895 6.32 0.00 0.00 4.26
1810 5953 2.106683 CGAACCGGGACCAATGCTC 61.107 63.158 6.32 0.00 0.00 4.26
1811 5954 2.046314 CGAACCGGGACCAATGCT 60.046 61.111 6.32 0.00 0.00 3.79
1812 5955 2.359478 ACGAACCGGGACCAATGC 60.359 61.111 6.32 0.00 0.00 3.56
1813 5956 2.686816 GCACGAACCGGGACCAATG 61.687 63.158 6.32 0.00 28.17 2.82
1814 5957 2.359478 GCACGAACCGGGACCAAT 60.359 61.111 6.32 0.00 28.17 3.16
1815 5958 4.973055 CGCACGAACCGGGACCAA 62.973 66.667 6.32 0.00 28.17 3.67
1818 5961 3.919973 TTAGCGCACGAACCGGGAC 62.920 63.158 11.47 0.00 28.17 4.46
1819 5962 3.223710 TTTAGCGCACGAACCGGGA 62.224 57.895 11.47 0.00 28.17 5.14
1820 5963 2.736682 CTTTAGCGCACGAACCGGG 61.737 63.158 11.47 0.00 0.00 5.73
1821 5964 2.736682 CCTTTAGCGCACGAACCGG 61.737 63.158 11.47 0.00 0.00 5.28
1822 5965 2.776072 CCTTTAGCGCACGAACCG 59.224 61.111 11.47 0.00 0.00 4.44
1823 5966 2.479198 GCCTTTAGCGCACGAACC 59.521 61.111 11.47 0.00 0.00 3.62
1832 5975 1.134189 ACCGGGACTAATGCCTTTAGC 60.134 52.381 6.32 0.00 40.94 3.09
1833 5976 3.203716 GAACCGGGACTAATGCCTTTAG 58.796 50.000 6.32 2.80 42.62 1.85
1834 5977 2.572556 TGAACCGGGACTAATGCCTTTA 59.427 45.455 6.32 0.00 33.05 1.85
1835 5978 1.353022 TGAACCGGGACTAATGCCTTT 59.647 47.619 6.32 0.00 33.05 3.11
1836 5979 0.988832 TGAACCGGGACTAATGCCTT 59.011 50.000 6.32 0.00 33.05 4.35
1837 5980 0.988832 TTGAACCGGGACTAATGCCT 59.011 50.000 6.32 0.00 33.05 4.75
1838 5981 1.828979 TTTGAACCGGGACTAATGCC 58.171 50.000 6.32 0.00 0.00 4.40
1839 5982 3.013921 TCATTTGAACCGGGACTAATGC 58.986 45.455 21.82 0.00 32.50 3.56
1840 5983 3.065371 GCTCATTTGAACCGGGACTAATG 59.935 47.826 21.15 21.15 33.24 1.90
1841 5984 3.279434 GCTCATTTGAACCGGGACTAAT 58.721 45.455 6.32 5.23 0.00 1.73
1842 5985 2.039216 TGCTCATTTGAACCGGGACTAA 59.961 45.455 6.32 2.80 0.00 2.24
1843 5986 1.626321 TGCTCATTTGAACCGGGACTA 59.374 47.619 6.32 0.00 0.00 2.59
1844 5987 0.400213 TGCTCATTTGAACCGGGACT 59.600 50.000 6.32 0.00 0.00 3.85
1845 5988 1.463674 ATGCTCATTTGAACCGGGAC 58.536 50.000 6.32 0.00 0.00 4.46
1846 5989 2.214376 AATGCTCATTTGAACCGGGA 57.786 45.000 6.32 0.00 0.00 5.14
1847 5990 3.317603 AAAATGCTCATTTGAACCGGG 57.682 42.857 6.32 0.00 40.57 5.73
1848 5991 5.059404 ACTAAAATGCTCATTTGAACCGG 57.941 39.130 0.00 0.00 40.57 5.28
1849 5992 5.095490 GGACTAAAATGCTCATTTGAACCG 58.905 41.667 8.43 0.35 40.57 4.44
1850 5993 5.410924 GGGACTAAAATGCTCATTTGAACC 58.589 41.667 8.43 9.40 40.57 3.62
1851 5994 5.095490 CGGGACTAAAATGCTCATTTGAAC 58.905 41.667 8.43 2.47 40.57 3.18
1852 5995 4.157656 CCGGGACTAAAATGCTCATTTGAA 59.842 41.667 8.43 0.86 40.57 2.69
1853 5996 3.694072 CCGGGACTAAAATGCTCATTTGA 59.306 43.478 8.43 0.96 40.57 2.69
1854 5997 3.443681 ACCGGGACTAAAATGCTCATTTG 59.556 43.478 6.32 0.94 40.57 2.32
1855 5998 3.697166 ACCGGGACTAAAATGCTCATTT 58.303 40.909 6.32 2.24 42.35 2.32
1856 5999 3.366052 ACCGGGACTAAAATGCTCATT 57.634 42.857 6.32 0.00 0.00 2.57
1857 6000 3.366052 AACCGGGACTAAAATGCTCAT 57.634 42.857 6.32 0.00 0.00 2.90
1858 6001 2.817258 CAAACCGGGACTAAAATGCTCA 59.183 45.455 6.32 0.00 0.00 4.26
1859 6002 3.078837 TCAAACCGGGACTAAAATGCTC 58.921 45.455 6.32 0.00 0.00 4.26
1860 6003 3.081804 CTCAAACCGGGACTAAAATGCT 58.918 45.455 6.32 0.00 0.00 3.79
1861 6004 3.078837 TCTCAAACCGGGACTAAAATGC 58.921 45.455 6.32 0.00 0.00 3.56
1862 6005 4.069304 TGTCTCAAACCGGGACTAAAATG 58.931 43.478 6.32 0.00 0.00 2.32
1863 6006 4.070009 GTGTCTCAAACCGGGACTAAAAT 58.930 43.478 6.32 0.00 0.00 1.82
1864 6007 3.469739 GTGTCTCAAACCGGGACTAAAA 58.530 45.455 6.32 0.00 0.00 1.52
1865 6008 2.546373 CGTGTCTCAAACCGGGACTAAA 60.546 50.000 6.32 0.00 0.00 1.85
1866 6009 1.000060 CGTGTCTCAAACCGGGACTAA 60.000 52.381 6.32 0.00 0.00 2.24
1867 6010 0.599558 CGTGTCTCAAACCGGGACTA 59.400 55.000 6.32 0.00 0.00 2.59
1868 6011 1.111116 TCGTGTCTCAAACCGGGACT 61.111 55.000 6.32 0.00 0.00 3.85
1869 6012 0.249573 TTCGTGTCTCAAACCGGGAC 60.250 55.000 6.32 3.26 0.00 4.46
1870 6013 0.249573 GTTCGTGTCTCAAACCGGGA 60.250 55.000 6.32 0.00 0.00 5.14
1871 6014 1.226030 GGTTCGTGTCTCAAACCGGG 61.226 60.000 6.32 0.00 33.68 5.73
1872 6015 2.231820 GGTTCGTGTCTCAAACCGG 58.768 57.895 0.00 0.00 33.68 5.28
1874 6017 1.226030 CCCGGTTCGTGTCTCAAACC 61.226 60.000 0.00 0.00 39.25 3.27
1875 6018 0.249573 TCCCGGTTCGTGTCTCAAAC 60.250 55.000 0.00 0.00 0.00 2.93
1876 6019 0.249573 GTCCCGGTTCGTGTCTCAAA 60.250 55.000 0.00 0.00 0.00 2.69
1877 6020 1.111116 AGTCCCGGTTCGTGTCTCAA 61.111 55.000 0.00 0.00 0.00 3.02
1878 6021 0.250858 TAGTCCCGGTTCGTGTCTCA 60.251 55.000 0.00 0.00 0.00 3.27
1879 6022 0.883833 TTAGTCCCGGTTCGTGTCTC 59.116 55.000 0.00 0.00 0.00 3.36
1880 6023 1.271656 CTTTAGTCCCGGTTCGTGTCT 59.728 52.381 0.00 0.00 0.00 3.41
1881 6024 1.670967 CCTTTAGTCCCGGTTCGTGTC 60.671 57.143 0.00 0.00 0.00 3.67
1882 6025 0.319405 CCTTTAGTCCCGGTTCGTGT 59.681 55.000 0.00 0.00 0.00 4.49
1883 6026 0.390735 CCCTTTAGTCCCGGTTCGTG 60.391 60.000 0.00 0.00 0.00 4.35
1884 6027 0.833409 ACCCTTTAGTCCCGGTTCGT 60.833 55.000 0.00 0.00 0.00 3.85
1885 6028 0.390735 CACCCTTTAGTCCCGGTTCG 60.391 60.000 0.00 0.00 0.00 3.95
1886 6029 0.689055 ACACCCTTTAGTCCCGGTTC 59.311 55.000 0.00 0.00 0.00 3.62
1887 6030 0.399075 CACACCCTTTAGTCCCGGTT 59.601 55.000 0.00 0.00 0.00 4.44
1888 6031 0.472352 TCACACCCTTTAGTCCCGGT 60.472 55.000 0.00 0.00 0.00 5.28
1889 6032 0.909623 ATCACACCCTTTAGTCCCGG 59.090 55.000 0.00 0.00 0.00 5.73
1890 6033 2.012051 GCATCACACCCTTTAGTCCCG 61.012 57.143 0.00 0.00 0.00 5.14
1891 6034 1.682087 GGCATCACACCCTTTAGTCCC 60.682 57.143 0.00 0.00 0.00 4.46
1892 6035 1.682087 GGGCATCACACCCTTTAGTCC 60.682 57.143 0.00 0.00 44.68 3.85
1893 6036 1.751437 GGGCATCACACCCTTTAGTC 58.249 55.000 0.00 0.00 44.68 2.59
1894 6037 3.978876 GGGCATCACACCCTTTAGT 57.021 52.632 0.00 0.00 44.68 2.24
1901 6044 1.682087 GGGACTAAAGGGCATCACACC 60.682 57.143 0.00 0.00 0.00 4.16
1902 6045 1.751437 GGGACTAAAGGGCATCACAC 58.249 55.000 0.00 0.00 0.00 3.82
1903 6046 0.251916 CGGGACTAAAGGGCATCACA 59.748 55.000 0.00 0.00 0.00 3.58
1904 6047 0.463833 CCGGGACTAAAGGGCATCAC 60.464 60.000 0.00 0.00 0.00 3.06
1905 6048 0.912487 ACCGGGACTAAAGGGCATCA 60.912 55.000 6.32 0.00 0.00 3.07
1906 6049 0.255033 AACCGGGACTAAAGGGCATC 59.745 55.000 6.32 0.00 0.00 3.91
1907 6050 2.394514 AACCGGGACTAAAGGGCAT 58.605 52.632 6.32 0.00 0.00 4.40
1908 6051 3.910039 AACCGGGACTAAAGGGCA 58.090 55.556 6.32 0.00 0.00 5.36
2259 6402 9.530633 GTAACATAACTACATCTCGAAGGATTT 57.469 33.333 0.00 0.00 0.00 2.17
2260 6403 8.915036 AGTAACATAACTACATCTCGAAGGATT 58.085 33.333 0.00 0.00 0.00 3.01
2261 6404 8.466617 AGTAACATAACTACATCTCGAAGGAT 57.533 34.615 0.00 0.00 0.00 3.24
2262 6405 7.876936 AGTAACATAACTACATCTCGAAGGA 57.123 36.000 0.00 0.00 0.00 3.36
2313 6456 7.798596 TGCAAAACATGTCCAAATTTATGTT 57.201 28.000 10.06 10.06 43.40 2.71
2314 6457 7.798596 TTGCAAAACATGTCCAAATTTATGT 57.201 28.000 0.00 0.00 35.43 2.29
2315 6458 9.512435 TTTTTGCAAAACATGTCCAAATTTATG 57.488 25.926 23.79 0.00 0.00 1.90
2316 6459 9.733219 CTTTTTGCAAAACATGTCCAAATTTAT 57.267 25.926 23.79 0.00 0.00 1.40
2317 6460 8.734386 ACTTTTTGCAAAACATGTCCAAATTTA 58.266 25.926 23.79 3.76 0.00 1.40
2318 6461 7.541437 CACTTTTTGCAAAACATGTCCAAATTT 59.459 29.630 23.79 0.00 0.00 1.82
2319 6462 7.028361 CACTTTTTGCAAAACATGTCCAAATT 58.972 30.769 23.79 0.00 0.00 1.82
2320 6463 6.150809 ACACTTTTTGCAAAACATGTCCAAAT 59.849 30.769 23.79 5.87 0.00 2.32
2321 6464 5.471456 ACACTTTTTGCAAAACATGTCCAAA 59.529 32.000 23.79 5.61 0.00 3.28
2322 6465 4.999950 ACACTTTTTGCAAAACATGTCCAA 59.000 33.333 23.79 6.32 0.00 3.53
2323 6466 4.573900 ACACTTTTTGCAAAACATGTCCA 58.426 34.783 23.79 7.05 0.00 4.02


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

AutoCloner maintained by Alex Coulton.