Multiple sequence alignment - TraesCS3D01G480900

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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 TraesCS3D01G480900 chr3D 100.000 2582 0 0 1 2582 579375421 579378002 0.000000e+00 4769.0
1 TraesCS3D01G480900 chr3D 94.500 600 21 9 986 1582 579592731 579592141 0.000000e+00 915.0
2 TraesCS3D01G480900 chr3D 89.323 665 38 17 986 1639 579365715 579366357 0.000000e+00 804.0
3 TraesCS3D01G480900 chr3D 89.545 593 30 10 1003 1570 579329774 579330359 0.000000e+00 723.0
4 TraesCS3D01G480900 chr3D 79.433 141 25 3 3 142 48362427 48362290 2.110000e-16 97.1
5 TraesCS3D01G480900 chr3A 91.552 1160 27 27 653 1789 714577537 714578648 0.000000e+00 1533.0
6 TraesCS3D01G480900 chr3A 90.469 640 53 4 1 640 714576636 714577267 0.000000e+00 837.0
7 TraesCS3D01G480900 chr3A 89.457 645 33 17 986 1618 714574448 714575069 0.000000e+00 782.0
8 TraesCS3D01G480900 chr3A 90.203 592 37 13 997 1582 714650847 714650271 0.000000e+00 752.0
9 TraesCS3D01G480900 chr3A 89.116 441 21 12 1157 1570 714560223 714560663 8.190000e-145 523.0
10 TraesCS3D01G480900 chr3A 88.564 376 30 5 2209 2582 714585491 714585855 6.560000e-121 444.0
11 TraesCS3D01G480900 chr3A 81.188 202 22 7 157 344 714556108 714556307 5.760000e-32 148.0
12 TraesCS3D01G480900 chr3A 82.143 168 17 4 711 868 714566920 714567084 5.800000e-27 132.0
13 TraesCS3D01G480900 chr3A 84.000 75 7 1 1634 1708 714564701 714564770 1.660000e-07 67.6
14 TraesCS3D01G480900 chr3B 92.129 902 36 18 935 1825 773740722 773741599 0.000000e+00 1240.0
15 TraesCS3D01G480900 chr3B 92.790 638 41 3 3 640 773739577 773740209 0.000000e+00 918.0
16 TraesCS3D01G480900 chr3B 91.141 666 28 14 986 1639 773729125 773729771 0.000000e+00 874.0
17 TraesCS3D01G480900 chr3B 94.937 395 20 0 1188 1582 773907169 773906775 1.010000e-173 619.0
18 TraesCS3D01G480900 chr3B 86.157 549 46 15 2039 2582 773741637 773742160 1.340000e-157 566.0
19 TraesCS3D01G480900 chr3B 90.090 222 17 4 650 869 773740473 773740691 1.510000e-72 283.0
20 TraesCS3D01G480900 chr3B 90.647 139 7 4 986 1121 773907759 773907624 2.040000e-41 180.0
21 TraesCS3D01G480900 chr3B 82.320 181 31 1 436 616 68449170 68449349 3.440000e-34 156.0
22 TraesCS3D01G480900 chr1B 84.472 322 30 9 951 1269 378857957 378857653 1.500000e-77 300.0
23 TraesCS3D01G480900 chr2B 78.082 365 54 16 2180 2538 641871491 641871835 9.360000e-50 207.0
24 TraesCS3D01G480900 chr2B 83.684 190 27 3 428 615 219619221 219619034 2.640000e-40 176.0
25 TraesCS3D01G480900 chr2B 75.598 418 68 26 2178 2581 759745772 759745375 2.640000e-40 176.0
26 TraesCS3D01G480900 chr2B 76.606 218 37 8 2317 2530 536833446 536833239 9.770000e-20 108.0
27 TraesCS3D01G480900 chr2B 84.259 108 13 3 1888 1992 97394901 97394795 4.550000e-18 102.0
28 TraesCS3D01G480900 chr2B 84.259 108 13 3 1888 1992 492089788 492089894 4.550000e-18 102.0
29 TraesCS3D01G480900 chr2B 85.000 100 12 3 16 115 131600143 131600047 5.880000e-17 99.0
30 TraesCS3D01G480900 chr6B 77.882 321 55 10 2269 2581 480688928 480688616 4.390000e-43 185.0
31 TraesCS3D01G480900 chr6B 83.684 190 27 3 428 615 542698887 542698700 2.640000e-40 176.0
32 TraesCS3D01G480900 chr6B 86.022 93 13 0 4 96 691002561 691002653 1.630000e-17 100.0
33 TraesCS3D01G480900 chr6B 78.788 132 24 2 15 142 691003155 691003286 4.580000e-13 86.1
34 TraesCS3D01G480900 chr6A 75.177 423 78 20 2168 2578 6574576 6574983 9.500000e-40 174.0
35 TraesCS3D01G480900 chr6A 80.717 223 31 7 2180 2401 448137470 448137259 2.060000e-36 163.0
36 TraesCS3D01G480900 chr6A 82.883 111 17 1 1888 1996 14481046 14480936 5.880000e-17 99.0
37 TraesCS3D01G480900 chr7A 83.019 212 13 9 1066 1273 342810460 342810268 1.230000e-38 171.0
38 TraesCS3D01G480900 chr7A 75.723 346 61 18 2178 2517 21182880 21182552 4.450000e-33 152.0
39 TraesCS3D01G480900 chr7A 94.231 52 3 0 1323 1374 650550386 650550335 2.130000e-11 80.5
40 TraesCS3D01G480900 chr7B 76.022 367 65 17 2178 2538 131181956 131181607 4.420000e-38 169.0
41 TraesCS3D01G480900 chr7B 79.897 194 22 10 2183 2376 432942521 432942697 2.700000e-25 126.0
42 TraesCS3D01G480900 chr4D 82.199 191 32 2 424 612 127170750 127170560 2.060000e-36 163.0
43 TraesCS3D01G480900 chr4D 76.136 352 54 21 2182 2527 506886642 506886315 9.560000e-35 158.0
44 TraesCS3D01G480900 chr4D 83.962 106 13 3 1890 1992 69743657 69743553 5.880000e-17 99.0
45 TraesCS3D01G480900 chr1D 82.105 190 30 3 428 615 466375140 466375327 2.660000e-35 159.0
46 TraesCS3D01G480900 chr6D 82.386 176 30 1 428 602 447891942 447892117 4.450000e-33 152.0
47 TraesCS3D01G480900 chr6D 84.259 108 15 1 1888 1993 4511027 4510920 1.260000e-18 104.0
48 TraesCS3D01G480900 chr6D 82.022 89 13 3 2180 2268 111939271 111939186 3.560000e-09 73.1
49 TraesCS3D01G480900 chr1A 75.723 346 61 17 2186 2525 559581542 559581214 4.450000e-33 152.0
50 TraesCS3D01G480900 chr5D 81.053 190 31 4 427 613 224940962 224940775 2.070000e-31 147.0
51 TraesCS3D01G480900 chr7D 75.143 350 66 16 2186 2530 611647495 611647162 7.450000e-31 145.0
52 TraesCS3D01G480900 chr2D 85.455 110 10 4 1888 1993 626432515 626432408 2.720000e-20 110.0
53 TraesCS3D01G480900 chr2D 76.279 215 36 9 2182 2395 392553562 392553762 1.630000e-17 100.0
54 TraesCS3D01G480900 chr4A 83.193 119 16 3 1877 1992 668443942 668444059 3.510000e-19 106.0
55 TraesCS3D01G480900 chr4B 83.784 111 16 1 1888 1996 165306615 165306505 1.260000e-18 104.0
56 TraesCS3D01G480900 chr5B 81.667 120 20 1 1877 1994 538543874 538543755 5.880000e-17 99.0
57 TraesCS3D01G480900 chr5A 84.375 96 15 0 19 114 592121359 592121454 7.610000e-16 95.3


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 TraesCS3D01G480900 chr3D 579375421 579378002 2581 False 4769.000000 4769 100.000000 1 2582 1 chr3D.!!$F3 2581
1 TraesCS3D01G480900 chr3D 579592141 579592731 590 True 915.000000 915 94.500000 986 1582 1 chr3D.!!$R2 596
2 TraesCS3D01G480900 chr3D 579365715 579366357 642 False 804.000000 804 89.323000 986 1639 1 chr3D.!!$F2 653
3 TraesCS3D01G480900 chr3D 579329774 579330359 585 False 723.000000 723 89.545000 1003 1570 1 chr3D.!!$F1 567
4 TraesCS3D01G480900 chr3A 714574448 714578648 4200 False 1050.666667 1533 90.492667 1 1789 3 chr3A.!!$F4 1788
5 TraesCS3D01G480900 chr3A 714650271 714650847 576 True 752.000000 752 90.203000 997 1582 1 chr3A.!!$R1 585
6 TraesCS3D01G480900 chr3A 714556108 714560663 4555 False 335.500000 523 85.152000 157 1570 2 chr3A.!!$F2 1413
7 TraesCS3D01G480900 chr3B 773729125 773729771 646 False 874.000000 874 91.141000 986 1639 1 chr3B.!!$F2 653
8 TraesCS3D01G480900 chr3B 773739577 773742160 2583 False 751.750000 1240 90.291500 3 2582 4 chr3B.!!$F3 2579
9 TraesCS3D01G480900 chr3B 773906775 773907759 984 True 399.500000 619 92.792000 986 1582 2 chr3B.!!$R1 596

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
763 4490 0.106116 TGGCCGGGGTGTTACTTTTT 60.106 50.0 2.18 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 8362 0.035439 AATCAGAATCCGGGCACGTT 60.035 50.0 7.97 0.0 38.78 3.99 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 2215 2.760374 AGCTTCTCCACTTTTGTCTCG 58.240 47.619 0.00 0.00 0.00 4.04
36 2225 2.099098 ACTTTTGTCTCGGTTTTGCAGG 59.901 45.455 0.00 0.00 0.00 4.85
76 2265 0.741927 CCCGCGGACCGATACTTTTT 60.742 55.000 30.73 0.00 40.02 1.94
119 2308 1.062525 GGACGGATGTGATTTGCGC 59.937 57.895 0.00 0.00 0.00 6.09
120 2309 1.369091 GGACGGATGTGATTTGCGCT 61.369 55.000 9.73 0.00 0.00 5.92
148 2337 1.294068 TGGAGATGCCCTAAGTACCCT 59.706 52.381 0.00 0.00 34.97 4.34
382 2613 5.348724 AGCACTTATGTGTGTTCGTTATCTG 59.651 40.000 10.17 0.00 45.44 2.90
453 2684 5.524511 TTTAACACGATACAGACACATGC 57.475 39.130 0.00 0.00 0.00 4.06
475 2706 5.948348 GCGCTTATATATACACGCATACAC 58.052 41.667 23.71 3.65 45.25 2.90
477 2708 6.252869 GCGCTTATATATACACGCATACACTT 59.747 38.462 23.71 0.00 45.25 3.16
492 2723 9.320352 ACGCATACACTTATCAATATAAACACA 57.680 29.630 0.00 0.00 0.00 3.72
493 2724 9.580916 CGCATACACTTATCAATATAAACACAC 57.419 33.333 0.00 0.00 0.00 3.82
503 2734 7.155655 TCAATATAAACACACACATGCACAT 57.844 32.000 0.00 0.00 0.00 3.21
521 2752 2.706190 ACATCCTAACCCTATGAGCACC 59.294 50.000 0.00 0.00 0.00 5.01
526 2757 1.276622 AACCCTATGAGCACCTTCGT 58.723 50.000 0.00 0.00 0.00 3.85
528 2759 0.249073 CCCTATGAGCACCTTCGTCG 60.249 60.000 0.00 0.00 0.00 5.12
621 2852 0.319555 TTCACTGAACGCGCTAGCTT 60.320 50.000 13.93 0.00 42.32 3.74
643 2874 7.654116 AGCTTAGATATTTCTTTCCTCTAACGC 59.346 37.037 0.00 0.00 33.17 4.84
644 2875 7.358517 GCTTAGATATTTCTTTCCTCTAACGCG 60.359 40.741 3.53 3.53 33.17 6.01
645 2876 4.745620 AGATATTTCTTTCCTCTAACGCGC 59.254 41.667 5.73 0.00 0.00 6.86
647 2878 0.241749 TTCTTTCCTCTAACGCGCGA 59.758 50.000 39.36 14.99 0.00 5.87
648 2879 0.179171 TCTTTCCTCTAACGCGCGAG 60.179 55.000 39.36 24.78 0.00 5.03
716 3216 5.407691 CGGAATTGATGTGTATCTCTCCATG 59.592 44.000 0.00 0.00 34.31 3.66
718 3218 5.563876 ATTGATGTGTATCTCTCCATGCT 57.436 39.130 0.00 0.00 34.31 3.79
751 3251 2.039746 TCTCCATTTACATATGGCCGGG 59.960 50.000 2.18 2.28 43.94 5.73
752 3252 1.074727 TCCATTTACATATGGCCGGGG 59.925 52.381 2.18 3.35 43.94 5.73
753 3253 1.203001 CCATTTACATATGGCCGGGGT 60.203 52.381 2.18 0.00 38.75 4.95
758 4485 0.181824 ACATATGGCCGGGGTGTTAC 59.818 55.000 2.18 0.00 0.00 2.50
763 4490 0.106116 TGGCCGGGGTGTTACTTTTT 60.106 50.000 2.18 0.00 0.00 1.94
832 5182 3.025619 CGATTGAGCGGGCCATTC 58.974 61.111 4.39 0.03 0.00 2.67
862 5212 1.559682 ACTCCGTGTTGGGCTGAATAT 59.440 47.619 0.00 0.00 38.76 1.28
869 5219 4.016444 GTGTTGGGCTGAATATGGAAAGA 58.984 43.478 0.00 0.00 0.00 2.52
880 6350 1.303309 ATGGAAAGATAGCAGCGTGC 58.697 50.000 2.28 2.28 45.46 5.34
891 6361 4.664677 AGCGTGCGAGTCACCCAC 62.665 66.667 0.00 0.00 42.69 4.61
900 6370 1.961180 GAGTCACCCACTCCGGATGG 61.961 65.000 20.13 20.13 45.47 3.51
939 6410 1.048724 TTAGCCATCCCTGTCCTCCG 61.049 60.000 0.00 0.00 0.00 4.63
961 6438 2.790791 CCCTCTCGCCGCATCTCTT 61.791 63.158 0.00 0.00 0.00 2.85
1061 6623 0.616111 GAGGTGAAGGAGGAGCTGGA 60.616 60.000 0.00 0.00 0.00 3.86
1063 6625 1.220477 GTGAAGGAGGAGCTGGAGC 59.780 63.158 0.00 0.00 42.49 4.70
1074 6636 2.365370 CTGGAGCAGGAGGAGGCT 60.365 66.667 0.00 0.00 44.48 4.58
1677 7767 1.133482 GTCCCCACCCCATAGGATTTG 60.133 57.143 0.00 0.00 39.89 2.32
1773 7867 3.420839 AGAAAGGAAATAAATGCGCGG 57.579 42.857 8.83 0.00 0.00 6.46
1829 7923 3.274393 GCCATCAGCGGTGTAGTAG 57.726 57.895 15.22 1.82 0.00 2.57
1830 7924 0.876342 GCCATCAGCGGTGTAGTAGC 60.876 60.000 15.22 8.13 0.00 3.58
1836 7930 1.830279 AGCGGTGTAGTAGCTGTACA 58.170 50.000 0.00 1.03 40.07 2.90
1837 7931 2.165167 AGCGGTGTAGTAGCTGTACAA 58.835 47.619 11.25 0.00 40.07 2.41
1838 7932 2.163815 AGCGGTGTAGTAGCTGTACAAG 59.836 50.000 11.25 9.93 40.07 3.16
1853 7947 5.342806 TGTACAAGCAATAAGATATGCGC 57.657 39.130 0.00 0.00 46.98 6.09
1854 7948 4.813697 TGTACAAGCAATAAGATATGCGCA 59.186 37.500 14.96 14.96 46.98 6.09
1855 7949 4.214980 ACAAGCAATAAGATATGCGCAC 57.785 40.909 14.90 0.00 46.98 5.34
1856 7950 3.879295 ACAAGCAATAAGATATGCGCACT 59.121 39.130 14.90 1.56 46.98 4.40
1857 7951 4.216731 CAAGCAATAAGATATGCGCACTG 58.783 43.478 14.90 1.13 46.98 3.66
1858 7952 2.225019 AGCAATAAGATATGCGCACTGC 59.775 45.455 14.90 11.49 46.98 4.40
1881 7975 5.159209 CGTCTGTACGGAAATATCATACCC 58.841 45.833 5.82 0.00 45.50 3.69
1882 7976 5.048224 CGTCTGTACGGAAATATCATACCCT 60.048 44.000 5.82 0.00 45.50 4.34
1883 7977 6.388278 GTCTGTACGGAAATATCATACCCTC 58.612 44.000 5.82 0.00 0.00 4.30
1884 7978 6.208994 GTCTGTACGGAAATATCATACCCTCT 59.791 42.308 5.82 0.00 0.00 3.69
1885 7979 6.781014 TCTGTACGGAAATATCATACCCTCTT 59.219 38.462 0.63 0.00 0.00 2.85
1886 7980 7.289317 TCTGTACGGAAATATCATACCCTCTTT 59.711 37.037 0.63 0.00 0.00 2.52
1887 7981 7.214381 TGTACGGAAATATCATACCCTCTTTG 58.786 38.462 0.00 0.00 0.00 2.77
1888 7982 6.248569 ACGGAAATATCATACCCTCTTTGT 57.751 37.500 0.00 0.00 0.00 2.83
1889 7983 6.289064 ACGGAAATATCATACCCTCTTTGTC 58.711 40.000 0.00 0.00 0.00 3.18
1890 7984 5.701290 CGGAAATATCATACCCTCTTTGTCC 59.299 44.000 0.00 0.00 0.00 4.02
1891 7985 5.701290 GGAAATATCATACCCTCTTTGTCCG 59.299 44.000 0.00 0.00 0.00 4.79
1892 7986 6.463897 GGAAATATCATACCCTCTTTGTCCGA 60.464 42.308 0.00 0.00 0.00 4.55
1893 7987 6.494666 AATATCATACCCTCTTTGTCCGAA 57.505 37.500 0.00 0.00 0.00 4.30
1894 7988 4.837093 ATCATACCCTCTTTGTCCGAAA 57.163 40.909 0.00 0.00 0.00 3.46
1895 7989 4.627284 TCATACCCTCTTTGTCCGAAAA 57.373 40.909 0.00 0.00 0.00 2.29
1896 7990 5.174037 TCATACCCTCTTTGTCCGAAAAT 57.826 39.130 0.00 0.00 0.00 1.82
1897 7991 6.302535 TCATACCCTCTTTGTCCGAAAATA 57.697 37.500 0.00 0.00 0.00 1.40
1898 7992 6.110707 TCATACCCTCTTTGTCCGAAAATAC 58.889 40.000 0.00 0.00 0.00 1.89
1899 7993 4.635699 ACCCTCTTTGTCCGAAAATACT 57.364 40.909 0.00 0.00 0.00 2.12
1900 7994 4.981812 ACCCTCTTTGTCCGAAAATACTT 58.018 39.130 0.00 0.00 0.00 2.24
1901 7995 4.760204 ACCCTCTTTGTCCGAAAATACTTG 59.240 41.667 0.00 0.00 0.00 3.16
1902 7996 4.760204 CCCTCTTTGTCCGAAAATACTTGT 59.240 41.667 0.00 0.00 0.00 3.16
1903 7997 5.240844 CCCTCTTTGTCCGAAAATACTTGTT 59.759 40.000 0.00 0.00 0.00 2.83
1904 7998 6.142817 CCTCTTTGTCCGAAAATACTTGTTG 58.857 40.000 0.00 0.00 0.00 3.33
1905 7999 6.067263 TCTTTGTCCGAAAATACTTGTTGG 57.933 37.500 0.00 0.00 0.00 3.77
1906 8000 5.823570 TCTTTGTCCGAAAATACTTGTTGGA 59.176 36.000 0.00 0.00 0.00 3.53
1907 8001 6.319152 TCTTTGTCCGAAAATACTTGTTGGAA 59.681 34.615 0.00 0.00 0.00 3.53
1908 8002 6.452494 TTGTCCGAAAATACTTGTTGGAAA 57.548 33.333 0.00 0.00 0.00 3.13
1909 8003 6.452494 TGTCCGAAAATACTTGTTGGAAAA 57.548 33.333 0.00 0.00 0.00 2.29
1910 8004 6.864342 TGTCCGAAAATACTTGTTGGAAAAA 58.136 32.000 0.00 0.00 0.00 1.94
1911 8005 7.493367 TGTCCGAAAATACTTGTTGGAAAAAT 58.507 30.769 0.00 0.00 0.00 1.82
1912 8006 8.630917 TGTCCGAAAATACTTGTTGGAAAAATA 58.369 29.630 0.00 0.00 0.00 1.40
1913 8007 9.634163 GTCCGAAAATACTTGTTGGAAAAATAT 57.366 29.630 0.00 0.00 0.00 1.28
1986 8080 8.696374 TCTGTAACAAGTAATTCTAGATGGAGG 58.304 37.037 0.00 0.00 0.00 4.30
1987 8081 8.603898 TGTAACAAGTAATTCTAGATGGAGGA 57.396 34.615 0.00 0.00 0.00 3.71
1988 8082 9.042450 TGTAACAAGTAATTCTAGATGGAGGAA 57.958 33.333 0.00 0.00 0.00 3.36
1989 8083 9.535878 GTAACAAGTAATTCTAGATGGAGGAAG 57.464 37.037 0.00 0.00 0.00 3.46
1990 8084 7.741554 ACAAGTAATTCTAGATGGAGGAAGT 57.258 36.000 0.00 0.00 0.00 3.01
1991 8085 8.840200 ACAAGTAATTCTAGATGGAGGAAGTA 57.160 34.615 0.00 0.00 0.00 2.24
1992 8086 9.440761 ACAAGTAATTCTAGATGGAGGAAGTAT 57.559 33.333 0.00 0.00 0.00 2.12
1993 8087 9.703892 CAAGTAATTCTAGATGGAGGAAGTATG 57.296 37.037 0.00 0.00 0.00 2.39
1994 8088 9.440761 AAGTAATTCTAGATGGAGGAAGTATGT 57.559 33.333 0.00 0.00 0.00 2.29
1995 8089 8.865090 AGTAATTCTAGATGGAGGAAGTATGTG 58.135 37.037 0.00 0.00 0.00 3.21
1996 8090 5.537300 TTCTAGATGGAGGAAGTATGTGC 57.463 43.478 0.00 0.00 0.00 4.57
1997 8091 4.546674 TCTAGATGGAGGAAGTATGTGCA 58.453 43.478 0.00 0.00 0.00 4.57
1998 8092 3.550437 AGATGGAGGAAGTATGTGCAC 57.450 47.619 10.75 10.75 0.00 4.57
1999 8093 2.840038 AGATGGAGGAAGTATGTGCACA 59.160 45.455 24.08 24.08 0.00 4.57
2000 8094 3.264193 AGATGGAGGAAGTATGTGCACAA 59.736 43.478 25.72 10.60 0.00 3.33
2017 8111 7.946207 TGTGCACAATATCTTTTTGTTAAGGA 58.054 30.769 19.28 0.00 35.18 3.36
2018 8112 8.081633 TGTGCACAATATCTTTTTGTTAAGGAG 58.918 33.333 19.28 0.00 35.18 3.69
2020 8114 8.296713 TGCACAATATCTTTTTGTTAAGGAGAC 58.703 33.333 0.00 0.00 35.18 3.36
2027 8121 7.639113 TCTTTTTGTTAAGGAGACACAATGT 57.361 32.000 0.00 0.00 30.64 2.71
2037 8131 0.792640 GACACAATGTCTGTCAGCGG 59.207 55.000 1.64 0.00 43.73 5.52
2053 8147 1.696832 GCGGACTGATCCAAACTCGC 61.697 60.000 0.00 0.00 46.67 5.03
2057 8151 2.435938 TGATCCAAACTCGCCCGC 60.436 61.111 0.00 0.00 0.00 6.13
2106 8200 4.344102 TCAACCCTATCCTATCTCCAAACG 59.656 45.833 0.00 0.00 0.00 3.60
2130 8224 7.167468 ACGTCTGCACATGTTTTTCTTTAATTC 59.833 33.333 0.00 0.00 0.00 2.17
2140 8234 9.860898 ATGTTTTTCTTTAATTCCATAGCACTC 57.139 29.630 0.00 0.00 0.00 3.51
2197 8323 2.005451 GTTGCTCATGAGTTGCTCGAT 58.995 47.619 23.38 0.00 32.35 3.59
2198 8324 1.648504 TGCTCATGAGTTGCTCGATG 58.351 50.000 23.38 0.00 32.35 3.84
2199 8325 0.304098 GCTCATGAGTTGCTCGATGC 59.696 55.000 23.38 2.55 43.25 3.91
2200 8326 0.935898 CTCATGAGTTGCTCGATGCC 59.064 55.000 14.95 0.00 42.00 4.40
2201 8327 0.249955 TCATGAGTTGCTCGATGCCA 59.750 50.000 0.00 0.00 42.00 4.92
2202 8328 1.089112 CATGAGTTGCTCGATGCCAA 58.911 50.000 4.73 0.00 42.00 4.52
2203 8329 1.469703 CATGAGTTGCTCGATGCCAAA 59.530 47.619 4.73 0.00 42.00 3.28
2204 8330 1.825090 TGAGTTGCTCGATGCCAAAT 58.175 45.000 4.73 0.00 42.00 2.32
2205 8331 2.161855 TGAGTTGCTCGATGCCAAATT 58.838 42.857 4.73 0.00 42.00 1.82
2206 8332 2.557924 TGAGTTGCTCGATGCCAAATTT 59.442 40.909 4.73 0.00 42.00 1.82
2207 8333 2.919229 GAGTTGCTCGATGCCAAATTTG 59.081 45.455 11.40 11.40 42.00 2.32
2208 8334 2.297033 AGTTGCTCGATGCCAAATTTGT 59.703 40.909 16.73 0.00 42.00 2.83
2209 8335 3.059166 GTTGCTCGATGCCAAATTTGTT 58.941 40.909 16.73 1.63 42.00 2.83
2210 8336 2.674954 TGCTCGATGCCAAATTTGTTG 58.325 42.857 16.73 3.92 42.00 3.33
2211 8337 2.295629 TGCTCGATGCCAAATTTGTTGA 59.704 40.909 16.73 7.14 42.00 3.18
2212 8338 3.056678 TGCTCGATGCCAAATTTGTTGAT 60.057 39.130 16.73 5.61 42.00 2.57
2213 8339 3.305094 GCTCGATGCCAAATTTGTTGATG 59.695 43.478 16.73 2.50 35.15 3.07
2214 8340 3.252400 TCGATGCCAAATTTGTTGATGC 58.748 40.909 16.73 12.42 0.00 3.91
2215 8341 2.994578 CGATGCCAAATTTGTTGATGCA 59.005 40.909 17.54 17.54 0.00 3.96
2216 8342 3.619483 CGATGCCAAATTTGTTGATGCAT 59.381 39.130 23.33 23.33 40.37 3.96
2217 8343 4.260051 CGATGCCAAATTTGTTGATGCATC 60.260 41.667 29.91 29.91 46.14 3.91
2218 8344 4.004196 TGCCAAATTTGTTGATGCATCA 57.996 36.364 25.42 25.42 34.44 3.07
2219 8345 3.997681 TGCCAAATTTGTTGATGCATCAG 59.002 39.130 27.25 14.61 38.19 2.90
2220 8346 3.372822 GCCAAATTTGTTGATGCATCAGG 59.627 43.478 27.25 22.27 38.19 3.86
2221 8347 4.823157 CCAAATTTGTTGATGCATCAGGA 58.177 39.130 27.25 16.12 38.19 3.86
2222 8348 5.424757 CCAAATTTGTTGATGCATCAGGAT 58.575 37.500 27.25 16.93 38.19 3.24
2223 8349 6.575267 CCAAATTTGTTGATGCATCAGGATA 58.425 36.000 27.25 15.73 38.19 2.59
2224 8350 7.214381 CCAAATTTGTTGATGCATCAGGATAT 58.786 34.615 27.25 17.09 38.19 1.63
2225 8351 8.361889 CCAAATTTGTTGATGCATCAGGATATA 58.638 33.333 27.25 10.77 38.19 0.86
2226 8352 9.923143 CAAATTTGTTGATGCATCAGGATATAT 57.077 29.630 27.25 14.94 38.19 0.86
2230 8356 9.797642 TTTGTTGATGCATCAGGATATATAACT 57.202 29.630 27.25 0.00 38.19 2.24
2231 8357 9.440773 TTGTTGATGCATCAGGATATATAACTC 57.559 33.333 27.25 2.56 38.19 3.01
2232 8358 8.596293 TGTTGATGCATCAGGATATATAACTCA 58.404 33.333 27.25 6.66 38.19 3.41
2233 8359 9.610705 GTTGATGCATCAGGATATATAACTCAT 57.389 33.333 27.25 0.00 38.19 2.90
2234 8360 9.828039 TTGATGCATCAGGATATATAACTCATC 57.172 33.333 27.25 0.00 38.19 2.92
2235 8361 8.139989 TGATGCATCAGGATATATAACTCATCG 58.860 37.037 25.42 0.00 32.11 3.84
2236 8362 7.645058 TGCATCAGGATATATAACTCATCGA 57.355 36.000 0.00 0.00 0.00 3.59
2237 8363 8.066612 TGCATCAGGATATATAACTCATCGAA 57.933 34.615 0.00 0.00 0.00 3.71
2244 8370 1.935933 ATAACTCATCGAACGTGCCC 58.064 50.000 0.00 0.00 0.00 5.36
2261 8387 2.099405 GCCCGGATTCTGATTTGGAAA 58.901 47.619 0.73 0.00 0.00 3.13
2268 8394 5.981315 CGGATTCTGATTTGGAAATTGGATG 59.019 40.000 0.00 0.00 0.00 3.51
2269 8395 6.406177 CGGATTCTGATTTGGAAATTGGATGT 60.406 38.462 0.00 0.00 0.00 3.06
2270 8396 7.333323 GGATTCTGATTTGGAAATTGGATGTT 58.667 34.615 0.00 0.00 0.00 2.71
2271 8397 7.279313 GGATTCTGATTTGGAAATTGGATGTTG 59.721 37.037 0.00 0.00 0.00 3.33
2272 8398 6.040209 TCTGATTTGGAAATTGGATGTTGG 57.960 37.500 0.00 0.00 0.00 3.77
2273 8399 5.779260 TCTGATTTGGAAATTGGATGTTGGA 59.221 36.000 0.00 0.00 0.00 3.53
2274 8400 6.441284 TCTGATTTGGAAATTGGATGTTGGAT 59.559 34.615 0.00 0.00 0.00 3.41
2281 8407 6.207221 TGGAAATTGGATGTTGGATATGATCG 59.793 38.462 0.00 0.00 0.00 3.69
2287 8413 6.633856 TGGATGTTGGATATGATCGTCTATG 58.366 40.000 0.00 0.00 0.00 2.23
2321 8447 4.473520 CTCCGGCGCCACCTTCAT 62.474 66.667 28.98 0.00 35.61 2.57
2335 8461 2.169352 ACCTTCATCCTCATCCTTCACG 59.831 50.000 0.00 0.00 0.00 4.35
2344 8470 3.558829 CCTCATCCTTCACGATCATGTTG 59.441 47.826 0.00 0.00 0.00 3.33
2372 8498 1.159285 CGCACAACATGTCATCACCT 58.841 50.000 0.00 0.00 0.00 4.00
2387 8513 1.557832 TCACCTCCCATAAGTTTCCGG 59.442 52.381 0.00 0.00 0.00 5.14
2400 8526 7.668052 CCATAAGTTTCCGGATCCCATATTTTA 59.332 37.037 4.15 0.00 0.00 1.52
2402 8528 9.822727 ATAAGTTTCCGGATCCCATATTTTAAT 57.177 29.630 4.15 0.00 0.00 1.40
2403 8529 8.547481 AAGTTTCCGGATCCCATATTTTAATT 57.453 30.769 4.15 0.00 0.00 1.40
2404 8530 8.547481 AGTTTCCGGATCCCATATTTTAATTT 57.453 30.769 4.15 0.00 0.00 1.82
2405 8531 8.421002 AGTTTCCGGATCCCATATTTTAATTTG 58.579 33.333 4.15 0.00 0.00 2.32
2450 8576 2.163010 CAGGCTTGGAGCACTACAAATG 59.837 50.000 2.04 0.00 44.75 2.32
2476 8602 5.600484 CCTCTCCACATCCTTACTAACTCAT 59.400 44.000 0.00 0.00 0.00 2.90
2480 8606 6.640518 TCCACATCCTTACTAACTCATTGTC 58.359 40.000 0.00 0.00 0.00 3.18
2483 8609 7.607991 CCACATCCTTACTAACTCATTGTCTTT 59.392 37.037 0.00 0.00 0.00 2.52
2531 8657 9.344772 GACTAACTAGGTAAGAGATGATCTTCA 57.655 37.037 10.90 0.00 45.50 3.02
2556 8682 7.971168 CACGAAGGAGGATATATAGATGTTGTC 59.029 40.741 0.00 0.00 0.00 3.18
2557 8683 7.670140 ACGAAGGAGGATATATAGATGTTGTCA 59.330 37.037 0.00 0.00 0.00 3.58
2562 8688 8.037758 GGAGGATATATAGATGTTGTCAACCAG 58.962 40.741 13.13 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.181483 ACAAAAGTGGAGAAGCTTTGCAG 60.181 43.478 0.00 0.00 35.40 4.41
11 12 3.792124 GCAAAACCGAGACAAAAGTGGAG 60.792 47.826 0.00 0.00 0.00 3.86
12 13 2.098443 GCAAAACCGAGACAAAAGTGGA 59.902 45.455 0.00 0.00 0.00 4.02
26 2215 1.269448 TGCGATTTCTCCTGCAAAACC 59.731 47.619 0.00 0.00 33.80 3.27
36 2225 1.215655 CGGTCCGGATGCGATTTCTC 61.216 60.000 7.81 0.00 0.00 2.87
119 2308 1.821332 GGCATCTCCAAGGCGGAAG 60.821 63.158 0.00 0.00 45.75 3.46
120 2309 2.272146 GGCATCTCCAAGGCGGAA 59.728 61.111 0.00 0.00 45.75 4.30
382 2613 7.103641 TCCCGCAAAAGAGATATATAATGGTC 58.896 38.462 0.00 0.00 0.00 4.02
453 2684 7.736031 AAGTGTATGCGTGTATATATAAGCG 57.264 36.000 11.54 10.91 0.00 4.68
475 2706 9.225201 GTGCATGTGTGTGTTTATATTGATAAG 57.775 33.333 0.00 0.00 0.00 1.73
477 2708 8.273780 TGTGCATGTGTGTGTTTATATTGATA 57.726 30.769 0.00 0.00 0.00 2.15
481 2712 6.377996 AGGATGTGCATGTGTGTGTTTATATT 59.622 34.615 0.00 0.00 0.00 1.28
492 2723 1.635487 AGGGTTAGGATGTGCATGTGT 59.365 47.619 0.00 0.00 0.00 3.72
493 2724 2.425143 AGGGTTAGGATGTGCATGTG 57.575 50.000 0.00 0.00 0.00 3.21
503 2734 2.868964 AGGTGCTCATAGGGTTAGGA 57.131 50.000 0.00 0.00 0.00 2.94
528 2759 2.234908 AGATAATATGCCGGCTCAGTCC 59.765 50.000 29.70 11.28 0.00 3.85
603 2834 0.524414 TAAGCTAGCGCGTTCAGTGA 59.476 50.000 9.55 0.00 42.32 3.41
621 2852 5.919141 GCGCGTTAGAGGAAAGAAATATCTA 59.081 40.000 8.43 0.00 33.77 1.98
640 2871 3.030308 CGATATTGCCTCGCGCGT 61.030 61.111 30.98 12.06 42.08 6.01
645 2876 2.423926 AGTAGTGCGATATTGCCTCG 57.576 50.000 12.54 0.00 39.11 4.63
647 2878 5.470098 CCAATTAAGTAGTGCGATATTGCCT 59.530 40.000 12.54 10.99 0.00 4.75
648 2879 5.238650 ACCAATTAAGTAGTGCGATATTGCC 59.761 40.000 12.54 4.11 0.00 4.52
693 3193 5.180868 GCATGGAGAGATACACATCAATTCC 59.819 44.000 0.00 0.00 33.21 3.01
703 3203 7.342026 TCACTAACTAAAGCATGGAGAGATACA 59.658 37.037 0.00 0.00 0.00 2.29
716 3216 8.718102 TGTAAATGGAGATCACTAACTAAAGC 57.282 34.615 0.00 0.00 0.00 3.51
769 4496 2.112815 CGCCGGATCTTTTGTCCCC 61.113 63.158 5.05 0.00 31.87 4.81
862 5212 1.083806 CGCACGCTGCTATCTTTCCA 61.084 55.000 0.00 0.00 42.25 3.53
869 5219 1.517257 GTGACTCGCACGCTGCTAT 60.517 57.895 0.00 0.00 42.25 2.97
891 6361 3.009115 ACCCACCACCATCCGGAG 61.009 66.667 11.34 0.00 35.59 4.63
900 6370 2.067365 AAAAAGAGGACACCCACCAC 57.933 50.000 0.00 0.00 33.88 4.16
961 6438 1.891919 GCTCGGCAACCACAAGACA 60.892 57.895 0.00 0.00 0.00 3.41
1061 6623 2.365370 CCTCAGCCTCCTCCTGCT 60.365 66.667 0.00 0.00 38.67 4.24
1063 6625 1.001503 ACTCCTCAGCCTCCTCCTG 59.998 63.158 0.00 0.00 0.00 3.86
1074 6636 2.687805 CGGCTCGAACGACTCCTCA 61.688 63.158 3.30 0.00 0.00 3.86
1587 7670 2.599677 CCTACTGAGTACTGATCCCCC 58.400 57.143 0.00 0.00 0.00 5.40
1665 7755 1.405105 CGCAACACCAAATCCTATGGG 59.595 52.381 0.00 0.00 42.48 4.00
1666 7756 2.091541 ACGCAACACCAAATCCTATGG 58.908 47.619 0.00 0.00 43.84 2.74
1667 7757 3.848272 AACGCAACACCAAATCCTATG 57.152 42.857 0.00 0.00 0.00 2.23
1668 7758 4.079253 AGAAACGCAACACCAAATCCTAT 58.921 39.130 0.00 0.00 0.00 2.57
1677 7767 0.100503 AGCACAAGAAACGCAACACC 59.899 50.000 0.00 0.00 0.00 4.16
1746 7840 6.188175 CGCATTTATTTCCTTTCTTCTCTCG 58.812 40.000 0.00 0.00 0.00 4.04
1773 7867 4.279922 ACCAACCCAACTGCTTTATTACAC 59.720 41.667 0.00 0.00 0.00 2.90
1830 7924 5.050159 TGCGCATATCTTATTGCTTGTACAG 60.050 40.000 5.66 0.00 36.71 2.74
1832 7926 5.050091 AGTGCGCATATCTTATTGCTTGTAC 60.050 40.000 15.91 0.00 36.71 2.90
1834 7928 3.879295 AGTGCGCATATCTTATTGCTTGT 59.121 39.130 15.91 0.00 36.71 3.16
1835 7929 4.216731 CAGTGCGCATATCTTATTGCTTG 58.783 43.478 15.91 0.00 36.71 4.01
1836 7930 3.304257 GCAGTGCGCATATCTTATTGCTT 60.304 43.478 15.91 0.00 41.79 3.91
1837 7931 2.225019 GCAGTGCGCATATCTTATTGCT 59.775 45.455 15.91 0.00 41.79 3.91
1838 7932 2.578495 GCAGTGCGCATATCTTATTGC 58.422 47.619 15.91 10.03 41.79 3.56
1859 7953 6.208994 AGAGGGTATGATATTTCCGTACAGAC 59.791 42.308 0.00 0.00 0.00 3.51
1860 7954 6.312529 AGAGGGTATGATATTTCCGTACAGA 58.687 40.000 0.00 0.00 0.00 3.41
1861 7955 6.591750 AGAGGGTATGATATTTCCGTACAG 57.408 41.667 0.00 0.00 0.00 2.74
1862 7956 6.989155 AAGAGGGTATGATATTTCCGTACA 57.011 37.500 0.00 0.00 0.00 2.90
1863 7957 7.215085 ACAAAGAGGGTATGATATTTCCGTAC 58.785 38.462 0.00 0.00 0.00 3.67
1864 7958 7.369551 ACAAAGAGGGTATGATATTTCCGTA 57.630 36.000 0.00 0.00 0.00 4.02
1865 7959 6.248569 ACAAAGAGGGTATGATATTTCCGT 57.751 37.500 0.00 0.00 0.00 4.69
1866 7960 5.701290 GGACAAAGAGGGTATGATATTTCCG 59.299 44.000 0.00 0.00 0.00 4.30
1867 7961 5.701290 CGGACAAAGAGGGTATGATATTTCC 59.299 44.000 0.00 0.00 0.00 3.13
1868 7962 6.522054 TCGGACAAAGAGGGTATGATATTTC 58.478 40.000 0.00 0.00 0.00 2.17
1869 7963 6.494666 TCGGACAAAGAGGGTATGATATTT 57.505 37.500 0.00 0.00 0.00 1.40
1870 7964 6.494666 TTCGGACAAAGAGGGTATGATATT 57.505 37.500 0.00 0.00 0.00 1.28
1871 7965 6.494666 TTTCGGACAAAGAGGGTATGATAT 57.505 37.500 0.00 0.00 0.00 1.63
1872 7966 5.943349 TTTCGGACAAAGAGGGTATGATA 57.057 39.130 0.00 0.00 0.00 2.15
1873 7967 4.837093 TTTCGGACAAAGAGGGTATGAT 57.163 40.909 0.00 0.00 0.00 2.45
1874 7968 4.627284 TTTTCGGACAAAGAGGGTATGA 57.373 40.909 0.00 0.00 0.00 2.15
1875 7969 6.113411 AGTATTTTCGGACAAAGAGGGTATG 58.887 40.000 0.00 0.00 0.00 2.39
1876 7970 6.309389 AGTATTTTCGGACAAAGAGGGTAT 57.691 37.500 0.00 0.00 0.00 2.73
1877 7971 5.750352 AGTATTTTCGGACAAAGAGGGTA 57.250 39.130 0.00 0.00 0.00 3.69
1878 7972 4.635699 AGTATTTTCGGACAAAGAGGGT 57.364 40.909 0.00 0.00 0.00 4.34
1879 7973 4.760204 ACAAGTATTTTCGGACAAAGAGGG 59.240 41.667 0.00 0.00 0.00 4.30
1880 7974 5.941948 ACAAGTATTTTCGGACAAAGAGG 57.058 39.130 0.00 0.00 0.00 3.69
1881 7975 6.017440 TCCAACAAGTATTTTCGGACAAAGAG 60.017 38.462 0.00 0.00 0.00 2.85
1882 7976 5.823570 TCCAACAAGTATTTTCGGACAAAGA 59.176 36.000 0.00 0.00 0.00 2.52
1883 7977 6.067263 TCCAACAAGTATTTTCGGACAAAG 57.933 37.500 0.00 0.00 0.00 2.77
1884 7978 6.452494 TTCCAACAAGTATTTTCGGACAAA 57.548 33.333 0.00 0.00 0.00 2.83
1885 7979 6.452494 TTTCCAACAAGTATTTTCGGACAA 57.548 33.333 0.00 0.00 0.00 3.18
1886 7980 6.452494 TTTTCCAACAAGTATTTTCGGACA 57.548 33.333 0.00 0.00 0.00 4.02
1887 7981 7.940178 ATTTTTCCAACAAGTATTTTCGGAC 57.060 32.000 0.00 0.00 0.00 4.79
1960 8054 8.696374 CCTCCATCTAGAATTACTTGTTACAGA 58.304 37.037 0.00 0.00 0.00 3.41
1961 8055 8.696374 TCCTCCATCTAGAATTACTTGTTACAG 58.304 37.037 0.00 0.00 0.00 2.74
1962 8056 8.603898 TCCTCCATCTAGAATTACTTGTTACA 57.396 34.615 0.00 0.00 0.00 2.41
1963 8057 9.535878 CTTCCTCCATCTAGAATTACTTGTTAC 57.464 37.037 0.00 0.00 0.00 2.50
1964 8058 9.268282 ACTTCCTCCATCTAGAATTACTTGTTA 57.732 33.333 0.00 0.00 0.00 2.41
1965 8059 8.152023 ACTTCCTCCATCTAGAATTACTTGTT 57.848 34.615 0.00 0.00 0.00 2.83
1966 8060 7.741554 ACTTCCTCCATCTAGAATTACTTGT 57.258 36.000 0.00 0.00 0.00 3.16
1967 8061 9.703892 CATACTTCCTCCATCTAGAATTACTTG 57.296 37.037 0.00 0.00 0.00 3.16
1968 8062 9.440761 ACATACTTCCTCCATCTAGAATTACTT 57.559 33.333 0.00 0.00 0.00 2.24
1969 8063 8.865090 CACATACTTCCTCCATCTAGAATTACT 58.135 37.037 0.00 0.00 0.00 2.24
1970 8064 7.600752 GCACATACTTCCTCCATCTAGAATTAC 59.399 40.741 0.00 0.00 0.00 1.89
1971 8065 7.290014 TGCACATACTTCCTCCATCTAGAATTA 59.710 37.037 0.00 0.00 0.00 1.40
1972 8066 6.100279 TGCACATACTTCCTCCATCTAGAATT 59.900 38.462 0.00 0.00 0.00 2.17
1973 8067 5.604231 TGCACATACTTCCTCCATCTAGAAT 59.396 40.000 0.00 0.00 0.00 2.40
1974 8068 4.962362 TGCACATACTTCCTCCATCTAGAA 59.038 41.667 0.00 0.00 0.00 2.10
1975 8069 4.342378 GTGCACATACTTCCTCCATCTAGA 59.658 45.833 13.17 0.00 0.00 2.43
1976 8070 4.100035 TGTGCACATACTTCCTCCATCTAG 59.900 45.833 17.42 0.00 0.00 2.43
1977 8071 4.030216 TGTGCACATACTTCCTCCATCTA 58.970 43.478 17.42 0.00 0.00 1.98
1978 8072 2.840038 TGTGCACATACTTCCTCCATCT 59.160 45.455 17.42 0.00 0.00 2.90
1979 8073 3.266510 TGTGCACATACTTCCTCCATC 57.733 47.619 17.42 0.00 0.00 3.51
1980 8074 3.719268 TTGTGCACATACTTCCTCCAT 57.281 42.857 22.39 0.00 0.00 3.41
1981 8075 3.719268 ATTGTGCACATACTTCCTCCA 57.281 42.857 22.39 1.00 0.00 3.86
1982 8076 5.615289 AGATATTGTGCACATACTTCCTCC 58.385 41.667 22.39 3.61 0.00 4.30
1983 8077 7.559590 AAAGATATTGTGCACATACTTCCTC 57.440 36.000 22.39 10.56 0.00 3.71
1984 8078 7.944729 AAAAGATATTGTGCACATACTTCCT 57.055 32.000 22.39 10.39 0.00 3.36
1985 8079 8.028938 ACAAAAAGATATTGTGCACATACTTCC 58.971 33.333 22.39 8.23 39.43 3.46
1986 8080 8.970691 ACAAAAAGATATTGTGCACATACTTC 57.029 30.769 22.39 14.80 39.43 3.01
1990 8084 9.853555 CCTTAACAAAAAGATATTGTGCACATA 57.146 29.630 22.39 14.96 39.98 2.29
1991 8085 8.584157 TCCTTAACAAAAAGATATTGTGCACAT 58.416 29.630 22.39 13.21 39.98 3.21
1992 8086 7.946207 TCCTTAACAAAAAGATATTGTGCACA 58.054 30.769 17.42 17.42 39.98 4.57
1993 8087 8.296713 TCTCCTTAACAAAAAGATATTGTGCAC 58.703 33.333 10.75 10.75 39.98 4.57
1994 8088 8.296713 GTCTCCTTAACAAAAAGATATTGTGCA 58.703 33.333 0.00 0.00 39.98 4.57
1995 8089 8.296713 TGTCTCCTTAACAAAAAGATATTGTGC 58.703 33.333 0.00 0.00 39.98 4.57
1996 8090 9.612620 GTGTCTCCTTAACAAAAAGATATTGTG 57.387 33.333 0.00 0.00 39.98 3.33
1997 8091 9.349713 TGTGTCTCCTTAACAAAAAGATATTGT 57.650 29.630 0.00 0.00 42.56 2.71
2018 8112 5.954639 AGTCCGCTGACAGACATTGTGTC 62.955 52.174 11.07 1.94 44.33 3.67
2020 8114 0.792640 GTCCGCTGACAGACATTGTG 59.207 55.000 6.65 0.00 41.05 3.33
2024 8118 2.658548 TCAGTCCGCTGACAGACAT 58.341 52.632 11.07 0.00 45.94 3.06
2025 8119 4.174305 TCAGTCCGCTGACAGACA 57.826 55.556 11.07 0.00 45.94 3.41
2036 8130 0.744771 GGGCGAGTTTGGATCAGTCC 60.745 60.000 0.00 0.00 45.31 3.85
2037 8131 1.084370 CGGGCGAGTTTGGATCAGTC 61.084 60.000 0.00 0.00 0.00 3.51
2106 8200 7.437862 TGGAATTAAAGAAAAACATGTGCAGAC 59.562 33.333 0.00 0.00 0.00 3.51
2156 8250 9.890629 AGCAACATAGTTAGATTGTAAGATTCA 57.109 29.630 0.00 0.00 0.00 2.57
2178 8304 2.004733 CATCGAGCAACTCATGAGCAA 58.995 47.619 22.83 1.04 0.00 3.91
2197 8323 3.997681 CTGATGCATCAACAAATTTGGCA 59.002 39.130 28.39 19.41 36.18 4.92
2198 8324 3.372822 CCTGATGCATCAACAAATTTGGC 59.627 43.478 28.39 14.77 36.18 4.52
2199 8325 4.823157 TCCTGATGCATCAACAAATTTGG 58.177 39.130 28.39 22.16 36.18 3.28
2200 8326 9.923143 ATATATCCTGATGCATCAACAAATTTG 57.077 29.630 28.39 16.67 36.18 2.32
2204 8330 9.797642 AGTTATATATCCTGATGCATCAACAAA 57.202 29.630 28.39 15.61 36.18 2.83
2205 8331 9.440773 GAGTTATATATCCTGATGCATCAACAA 57.559 33.333 28.39 17.25 36.18 2.83
2206 8332 8.596293 TGAGTTATATATCCTGATGCATCAACA 58.404 33.333 28.39 18.39 36.18 3.33
2207 8333 9.610705 ATGAGTTATATATCCTGATGCATCAAC 57.389 33.333 28.39 19.65 36.18 3.18
2208 8334 9.828039 GATGAGTTATATATCCTGATGCATCAA 57.172 33.333 28.39 16.51 36.18 2.57
2209 8335 8.139989 CGATGAGTTATATATCCTGATGCATCA 58.860 37.037 27.10 27.10 35.16 3.07
2210 8336 8.355913 TCGATGAGTTATATATCCTGATGCATC 58.644 37.037 20.14 20.14 0.00 3.91
2211 8337 8.242729 TCGATGAGTTATATATCCTGATGCAT 57.757 34.615 0.00 0.00 0.00 3.96
2212 8338 7.645058 TCGATGAGTTATATATCCTGATGCA 57.355 36.000 0.00 0.00 0.00 3.96
2213 8339 7.166638 CGTTCGATGAGTTATATATCCTGATGC 59.833 40.741 0.00 0.00 0.00 3.91
2214 8340 8.184848 ACGTTCGATGAGTTATATATCCTGATG 58.815 37.037 0.00 0.00 0.00 3.07
2215 8341 8.184848 CACGTTCGATGAGTTATATATCCTGAT 58.815 37.037 0.00 0.00 0.00 2.90
2216 8342 7.527457 CACGTTCGATGAGTTATATATCCTGA 58.473 38.462 0.00 0.00 0.00 3.86
2217 8343 6.251589 GCACGTTCGATGAGTTATATATCCTG 59.748 42.308 0.00 0.00 0.00 3.86
2218 8344 6.323266 GCACGTTCGATGAGTTATATATCCT 58.677 40.000 0.00 0.00 0.00 3.24
2219 8345 5.515626 GGCACGTTCGATGAGTTATATATCC 59.484 44.000 0.00 0.00 0.00 2.59
2220 8346 5.515626 GGGCACGTTCGATGAGTTATATATC 59.484 44.000 0.00 0.00 0.00 1.63
2221 8347 5.408356 GGGCACGTTCGATGAGTTATATAT 58.592 41.667 0.00 0.00 0.00 0.86
2222 8348 4.614306 CGGGCACGTTCGATGAGTTATATA 60.614 45.833 0.00 0.00 34.81 0.86
2223 8349 3.650139 GGGCACGTTCGATGAGTTATAT 58.350 45.455 0.00 0.00 0.00 0.86
2224 8350 2.542205 CGGGCACGTTCGATGAGTTATA 60.542 50.000 0.00 0.00 34.81 0.98
2225 8351 1.801395 CGGGCACGTTCGATGAGTTAT 60.801 52.381 0.00 0.00 34.81 1.89
2226 8352 0.457166 CGGGCACGTTCGATGAGTTA 60.457 55.000 0.00 0.00 34.81 2.24
2227 8353 1.736645 CGGGCACGTTCGATGAGTT 60.737 57.895 0.00 0.00 34.81 3.01
2228 8354 2.126071 CGGGCACGTTCGATGAGT 60.126 61.111 0.00 0.00 34.81 3.41
2229 8355 2.629050 ATCCGGGCACGTTCGATGAG 62.629 60.000 7.97 0.00 38.78 2.90
2230 8356 2.233605 AATCCGGGCACGTTCGATGA 62.234 55.000 7.97 0.00 38.78 2.92
2231 8357 1.762222 GAATCCGGGCACGTTCGATG 61.762 60.000 7.97 0.00 38.78 3.84
2232 8358 1.520787 GAATCCGGGCACGTTCGAT 60.521 57.895 7.97 0.00 38.78 3.59
2233 8359 2.125832 GAATCCGGGCACGTTCGA 60.126 61.111 7.97 0.00 38.78 3.71
2234 8360 2.125673 AGAATCCGGGCACGTTCG 60.126 61.111 7.97 0.00 38.78 3.95
2235 8361 0.462047 ATCAGAATCCGGGCACGTTC 60.462 55.000 7.97 5.46 38.78 3.95
2236 8362 0.035439 AATCAGAATCCGGGCACGTT 60.035 50.000 7.97 0.00 38.78 3.99
2237 8363 0.035439 AAATCAGAATCCGGGCACGT 60.035 50.000 7.97 0.00 38.78 4.49
2244 8370 5.581126 TCCAATTTCCAAATCAGAATCCG 57.419 39.130 0.00 0.00 0.00 4.18
2261 8387 6.119240 AGACGATCATATCCAACATCCAAT 57.881 37.500 0.00 0.00 0.00 3.16
2268 8394 7.371159 TGAGAACATAGACGATCATATCCAAC 58.629 38.462 0.00 0.00 0.00 3.77
2269 8395 7.524717 TGAGAACATAGACGATCATATCCAA 57.475 36.000 0.00 0.00 0.00 3.53
2270 8396 7.524717 TTGAGAACATAGACGATCATATCCA 57.475 36.000 0.00 0.00 0.00 3.41
2271 8397 8.994429 ATTTGAGAACATAGACGATCATATCC 57.006 34.615 0.00 0.00 0.00 2.59
2273 8399 9.429359 GGAATTTGAGAACATAGACGATCATAT 57.571 33.333 0.00 0.00 0.00 1.78
2274 8400 8.421002 TGGAATTTGAGAACATAGACGATCATA 58.579 33.333 0.00 0.00 0.00 2.15
2281 8407 6.410540 AGGTCTGGAATTTGAGAACATAGAC 58.589 40.000 5.72 0.00 33.22 2.59
2287 8413 3.003480 CGGAGGTCTGGAATTTGAGAAC 58.997 50.000 0.00 0.00 0.00 3.01
2319 8445 3.740631 TGATCGTGAAGGATGAGGATG 57.259 47.619 0.00 0.00 0.00 3.51
2321 8447 3.033909 ACATGATCGTGAAGGATGAGGA 58.966 45.455 21.75 0.00 0.00 3.71
2352 8478 0.874390 GGTGATGACATGTTGTGCGT 59.126 50.000 0.00 0.00 0.00 5.24
2354 8480 1.470098 GGAGGTGATGACATGTTGTGC 59.530 52.381 0.00 0.00 0.00 4.57
2372 8498 1.772453 GGGATCCGGAAACTTATGGGA 59.228 52.381 9.01 0.00 0.00 4.37
2387 8513 6.762333 AGCCTGCAAATTAAAATATGGGATC 58.238 36.000 0.00 0.00 0.00 3.36
2400 8526 1.896220 TGTTCGAGAGCCTGCAAATT 58.104 45.000 0.00 0.00 0.00 1.82
2402 8528 0.944386 GTTGTTCGAGAGCCTGCAAA 59.056 50.000 0.00 0.00 0.00 3.68
2403 8529 0.106708 AGTTGTTCGAGAGCCTGCAA 59.893 50.000 0.00 0.00 0.00 4.08
2404 8530 0.106708 AAGTTGTTCGAGAGCCTGCA 59.893 50.000 0.00 0.00 0.00 4.41
2405 8531 0.793250 GAAGTTGTTCGAGAGCCTGC 59.207 55.000 0.00 0.00 0.00 4.85
2450 8576 4.957327 AGTTAGTAAGGATGTGGAGAGGAC 59.043 45.833 0.00 0.00 0.00 3.85
2483 8609 0.823356 AAAAGAGCTCGCTTTGCCCA 60.823 50.000 8.37 0.00 38.08 5.36
2513 8639 5.068460 CCTTCGTGAAGATCATCTCTTACCT 59.932 44.000 11.11 0.00 44.42 3.08
2515 8641 6.137794 TCCTTCGTGAAGATCATCTCTTAC 57.862 41.667 11.11 0.00 44.42 2.34
2531 8657 7.670140 TGACAACATCTATATATCCTCCTTCGT 59.330 37.037 0.00 0.00 0.00 3.85
2556 8682 2.826428 ACATGCGCTACTATCTGGTTG 58.174 47.619 9.73 0.00 0.00 3.77
2557 8683 3.543680 AACATGCGCTACTATCTGGTT 57.456 42.857 9.73 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.