Multiple sequence alignment - TraesCS3D01G481400

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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 TraesCS3D01G481400 chr3D 100.000 2933 0 0 1 2933 579428340 579431272 0.000000e+00 5417.0
1 TraesCS3D01G481400 chr3D 87.922 1540 91 45 512 2002 579502302 579500809 0.000000e+00 1725.0
2 TraesCS3D01G481400 chr3D 89.371 922 93 3 1007 1927 577892950 577893867 0.000000e+00 1155.0
3 TraesCS3D01G481400 chr3D 78.840 931 164 20 1008 1920 575737852 575736937 5.410000e-167 597.0
4 TraesCS3D01G481400 chr3D 76.667 930 185 23 1007 1920 577239467 577240380 1.220000e-133 486.0
5 TraesCS3D01G481400 chr3D 93.684 285 13 3 2652 2933 169944993 169945275 3.490000e-114 422.0
6 TraesCS3D01G481400 chr3D 85.938 320 22 12 195 503 579504504 579504197 1.310000e-83 320.0
7 TraesCS3D01G481400 chr3A 91.154 1967 74 39 449 2339 714614290 714616232 0.000000e+00 2577.0
8 TraesCS3D01G481400 chr3A 90.445 921 85 1 1007 1927 713623336 713622419 0.000000e+00 1210.0
9 TraesCS3D01G481400 chr3A 87.797 926 100 10 1007 1927 713535468 713534551 0.000000e+00 1072.0
10 TraesCS3D01G481400 chr3A 85.689 559 37 19 184 711 714607217 714607763 1.540000e-152 549.0
11 TraesCS3D01G481400 chr3A 89.655 435 19 11 9 430 714609543 714609964 5.570000e-147 531.0
12 TraesCS3D01G481400 chr3A 90.625 288 20 3 2652 2933 449338547 449338833 2.760000e-100 375.0
13 TraesCS3D01G481400 chr3B 91.224 1470 87 30 584 2041 773843317 773844756 0.000000e+00 1962.0
14 TraesCS3D01G481400 chr3B 90.659 1456 81 31 614 2041 773876866 773875438 0.000000e+00 1884.0
15 TraesCS3D01G481400 chr3B 88.580 1042 75 22 500 1505 773790102 773791135 0.000000e+00 1225.0
16 TraesCS3D01G481400 chr3B 88.829 922 98 4 1007 1927 771054049 771053132 0.000000e+00 1127.0
17 TraesCS3D01G481400 chr3B 85.139 720 42 34 97 791 773764301 773764980 0.000000e+00 676.0
18 TraesCS3D01G481400 chr3B 88.584 438 25 11 2169 2605 773875280 773874867 2.610000e-140 508.0
19 TraesCS3D01G481400 chr3B 90.604 298 10 8 2164 2461 713965600 713965321 2.130000e-101 379.0
20 TraesCS3D01G481400 chr3B 92.308 182 11 2 2 180 773842846 773843027 3.750000e-64 255.0
21 TraesCS3D01G481400 chr3B 91.758 182 12 2 2 180 773877705 773877524 1.750000e-62 250.0
22 TraesCS3D01G481400 chr3B 89.241 158 8 4 252 404 773843045 773843198 3.860000e-44 189.0
23 TraesCS3D01G481400 chr3B 88.608 158 9 4 252 404 773877491 773877338 1.800000e-42 183.0
24 TraesCS3D01G481400 chr3B 95.918 49 2 0 2603 2651 11014521 11014473 2.420000e-11 80.5
25 TraesCS3D01G481400 chrUn 92.623 1220 62 10 849 2041 41302486 41303704 0.000000e+00 1729.0
26 TraesCS3D01G481400 chrUn 83.780 783 66 35 2 757 41301727 41302475 0.000000e+00 686.0
27 TraesCS3D01G481400 chrUn 90.604 298 10 8 2164 2461 65693804 65694083 2.130000e-101 379.0
28 TraesCS3D01G481400 chrUn 89.933 298 12 8 2164 2461 41303890 41304169 4.620000e-98 368.0
29 TraesCS3D01G481400 chrUn 89.189 148 12 3 2459 2605 65704257 65704401 6.460000e-42 182.0
30 TraesCS3D01G481400 chrUn 95.745 47 2 0 2605 2651 347365946 347365992 3.130000e-10 76.8
31 TraesCS3D01G481400 chrUn 95.745 47 2 0 2605 2651 347368301 347368347 3.130000e-10 76.8
32 TraesCS3D01G481400 chrUn 95.745 47 2 0 2605 2651 446499923 446499969 3.130000e-10 76.8
33 TraesCS3D01G481400 chr1D 92.982 285 16 2 2652 2933 370709236 370709519 2.100000e-111 412.0
34 TraesCS3D01G481400 chr1D 95.276 254 10 2 2680 2933 330587961 330588212 4.550000e-108 401.0
35 TraesCS3D01G481400 chr1D 85.809 303 25 7 2647 2933 391502760 391503060 3.670000e-79 305.0
36 TraesCS3D01G481400 chr4D 94.961 258 9 2 2679 2933 353676209 353675953 4.550000e-108 401.0
37 TraesCS3D01G481400 chr4D 95.257 253 11 1 2681 2933 199405016 199404765 1.640000e-107 399.0
38 TraesCS3D01G481400 chr4D 91.837 294 10 4 2652 2933 108330372 108330081 5.890000e-107 398.0
39 TraesCS3D01G481400 chr4D 94.400 125 7 0 2450 2574 420512288 420512164 2.980000e-45 193.0
40 TraesCS3D01G481400 chr4D 93.878 49 3 0 2605 2653 59039680 59039632 1.130000e-09 75.0
41 TraesCS3D01G481400 chr2D 94.595 259 9 4 2679 2933 136791007 136790750 2.120000e-106 396.0
42 TraesCS3D01G481400 chr6D 91.289 287 19 3 2652 2933 232062918 232062633 1.270000e-103 387.0
43 TraesCS3D01G481400 chr6D 96.000 50 2 0 2602 2651 391691700 391691749 6.740000e-12 82.4
44 TraesCS3D01G481400 chr5B 90.604 298 10 8 2164 2461 15161367 15161088 2.130000e-101 379.0
45 TraesCS3D01G481400 chr2B 90.604 298 10 8 2164 2461 174350341 174350620 2.130000e-101 379.0
46 TraesCS3D01G481400 chr2B 90.604 298 10 8 2164 2461 780024314 780024593 2.130000e-101 379.0
47 TraesCS3D01G481400 chr4A 87.000 300 25 5 2647 2933 47487553 47487255 2.820000e-85 326.0
48 TraesCS3D01G481400 chr4A 92.063 126 9 1 2450 2574 43705613 43705488 3.000000e-40 176.0
49 TraesCS3D01G481400 chr4A 95.833 48 2 0 2605 2652 647353300 647353347 8.710000e-11 78.7
50 TraesCS3D01G481400 chr5A 85.430 302 26 6 2647 2931 483178829 483178529 6.150000e-77 298.0
51 TraesCS3D01G481400 chr5A 82.273 220 17 7 2645 2847 477523281 477523495 1.400000e-38 171.0
52 TraesCS3D01G481400 chr4B 92.800 125 9 0 2450 2574 517750253 517750377 6.460000e-42 182.0
53 TraesCS3D01G481400 chr5D 83.974 156 7 2 2679 2816 508756593 508756438 1.830000e-27 134.0
54 TraesCS3D01G481400 chr1A 77.059 170 35 4 1682 1849 410156421 410156588 8.650000e-16 95.3
55 TraesCS3D01G481400 chr2A 97.727 44 1 0 2607 2650 756935958 756935915 3.130000e-10 76.8
56 TraesCS3D01G481400 chr7D 92.000 50 4 0 2602 2651 421152416 421152367 1.460000e-08 71.3
57 TraesCS3D01G481400 chr1B 92.500 40 2 1 2415 2453 475490128 475490089 4.080000e-04 56.5


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 TraesCS3D01G481400 chr3D 579428340 579431272 2932 False 5417.000000 5417 100.000000 1 2933 1 chr3D.!!$F4 2932
1 TraesCS3D01G481400 chr3D 577892950 577893867 917 False 1155.000000 1155 89.371000 1007 1927 1 chr3D.!!$F3 920
2 TraesCS3D01G481400 chr3D 579500809 579504504 3695 True 1022.500000 1725 86.930000 195 2002 2 chr3D.!!$R2 1807
3 TraesCS3D01G481400 chr3D 575736937 575737852 915 True 597.000000 597 78.840000 1008 1920 1 chr3D.!!$R1 912
4 TraesCS3D01G481400 chr3D 577239467 577240380 913 False 486.000000 486 76.667000 1007 1920 1 chr3D.!!$F2 913
5 TraesCS3D01G481400 chr3A 714614290 714616232 1942 False 2577.000000 2577 91.154000 449 2339 1 chr3A.!!$F2 1890
6 TraesCS3D01G481400 chr3A 713622419 713623336 917 True 1210.000000 1210 90.445000 1007 1927 1 chr3A.!!$R2 920
7 TraesCS3D01G481400 chr3A 713534551 713535468 917 True 1072.000000 1072 87.797000 1007 1927 1 chr3A.!!$R1 920
8 TraesCS3D01G481400 chr3A 714607217 714609964 2747 False 540.000000 549 87.672000 9 711 2 chr3A.!!$F3 702
9 TraesCS3D01G481400 chr3B 773790102 773791135 1033 False 1225.000000 1225 88.580000 500 1505 1 chr3B.!!$F2 1005
10 TraesCS3D01G481400 chr3B 771053132 771054049 917 True 1127.000000 1127 88.829000 1007 1927 1 chr3B.!!$R3 920
11 TraesCS3D01G481400 chr3B 773842846 773844756 1910 False 802.000000 1962 90.924333 2 2041 3 chr3B.!!$F3 2039
12 TraesCS3D01G481400 chr3B 773874867 773877705 2838 True 706.250000 1884 89.902250 2 2605 4 chr3B.!!$R4 2603
13 TraesCS3D01G481400 chr3B 773764301 773764980 679 False 676.000000 676 85.139000 97 791 1 chr3B.!!$F1 694
14 TraesCS3D01G481400 chrUn 41301727 41304169 2442 False 927.666667 1729 88.778667 2 2461 3 chrUn.!!$F4 2459

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
123 131 0.392336 GACCCAAATGCTGCAACCAA 59.608 50.0 6.36 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1959 5820 2.504681 GTGTGTACGTACGGGCCG 60.505 66.667 27.06 27.06 0.0 6.13 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
22 23 2.431454 CCTTCTCTTCTCTTTGTGGCC 58.569 52.381 0.00 0.00 0.00 5.36
40 41 0.745468 CCGGCCTACCTAGTGACTTC 59.255 60.000 0.00 0.00 0.00 3.01
45 47 4.505808 GGCCTACCTAGTGACTTCTTTTC 58.494 47.826 0.00 0.00 0.00 2.29
54 56 8.871125 ACCTAGTGACTTCTTTTCTAAGATTGA 58.129 33.333 0.00 0.00 40.01 2.57
89 91 4.083324 CGACTTGATGTAACCAGTTGCAAT 60.083 41.667 0.59 0.00 38.59 3.56
123 131 0.392336 GACCCAAATGCTGCAACCAA 59.608 50.000 6.36 0.00 0.00 3.67
189 202 2.038387 AAGTCATATCCAACGGGCAC 57.962 50.000 0.00 0.00 0.00 5.01
190 203 7.941101 ATGTAAGTCATATCCAACGGGCACC 62.941 48.000 0.00 0.00 39.36 5.01
225 258 0.739813 TTTTTCTCGCTCTAGCCGGC 60.740 55.000 21.89 21.89 37.91 6.13
307 343 8.975410 AGCGACACGTATTAATATAAGCAATA 57.025 30.769 0.00 0.00 0.00 1.90
308 344 9.414295 AGCGACACGTATTAATATAAGCAATAA 57.586 29.630 0.00 0.00 0.00 1.40
395 435 3.347168 GCTGCATGCACACACAGA 58.653 55.556 18.46 0.00 42.31 3.41
420 460 3.401033 TGTGTGGAATGATCAACGACT 57.599 42.857 0.00 0.00 31.55 4.18
421 461 4.529109 TGTGTGGAATGATCAACGACTA 57.471 40.909 0.00 0.00 31.55 2.59
423 463 3.865745 GTGTGGAATGATCAACGACTAGG 59.134 47.826 0.00 0.00 31.55 3.02
424 464 3.513912 TGTGGAATGATCAACGACTAGGT 59.486 43.478 0.00 0.00 31.55 3.08
447 497 4.175516 ACACAAGAAAAAGACACGTACGA 58.824 39.130 24.41 0.00 0.00 3.43
500 552 5.047188 GGTCTTGTAAGATTCAGCTAGCTC 58.953 45.833 16.15 3.60 37.39 4.09
503 555 6.420604 GTCTTGTAAGATTCAGCTAGCTCATC 59.579 42.308 16.15 18.43 37.39 2.92
505 557 5.595885 TGTAAGATTCAGCTAGCTCATCAC 58.404 41.667 25.47 18.89 0.00 3.06
508 560 3.705579 AGATTCAGCTAGCTCATCACTGT 59.294 43.478 25.47 10.10 0.00 3.55
509 561 3.516981 TTCAGCTAGCTCATCACTGTC 57.483 47.619 16.15 0.00 0.00 3.51
570 2531 1.941975 CGGAGTATTGTGCATGCATGA 59.058 47.619 30.64 15.84 0.00 3.07
612 2900 2.182842 GCATAGGCGGCCAGACTTG 61.183 63.158 23.09 11.48 40.13 3.16
714 3055 7.332182 GTCCAACAAGTTTCCAATTTTGTGTAA 59.668 33.333 0.00 0.00 34.28 2.41
715 3056 8.043710 TCCAACAAGTTTCCAATTTTGTGTAAT 58.956 29.630 0.00 0.00 34.28 1.89
814 3589 6.387220 AGGCTAGGATGACACCTAATTAACTT 59.613 38.462 0.00 0.00 41.27 2.66
816 3591 7.272978 GCTAGGATGACACCTAATTAACTTGA 58.727 38.462 0.00 0.00 41.27 3.02
829 3604 2.380064 AACTTGAAAGATGGGGTGCA 57.620 45.000 0.00 0.00 0.00 4.57
839 3619 0.397941 ATGGGGTGCACCTATCATCG 59.602 55.000 33.91 0.00 35.06 3.84
840 3620 0.689412 TGGGGTGCACCTATCATCGA 60.689 55.000 33.91 11.82 40.03 3.59
905 3857 1.210967 TCACATGCATGCATCTCTCCA 59.789 47.619 30.07 8.51 33.90 3.86
1353 5207 2.436646 CTCAACGCGGCCCTCAAT 60.437 61.111 12.47 0.00 0.00 2.57
1959 5820 2.585869 CGTCGTCCATACATGCGCC 61.586 63.158 4.18 0.00 0.00 6.53
1960 5821 2.279186 TCGTCCATACATGCGCCG 60.279 61.111 4.18 0.00 0.00 6.46
2032 5893 1.343465 AGGAGTGAAGTGTAACGTGGG 59.657 52.381 0.00 0.00 45.86 4.61
2145 6093 2.034254 CGATTCATGCAAGAGTAGTGCG 60.034 50.000 0.00 0.00 45.27 5.34
2213 6176 6.894103 AGAAGGAAATTGAGGCAGTTATGAAT 59.106 34.615 0.00 0.00 0.00 2.57
2253 6216 2.643551 CTTTATGTGCAGGGATTCCGT 58.356 47.619 0.00 0.00 38.33 4.69
2256 6219 0.107508 ATGTGCAGGGATTCCGTGAG 60.108 55.000 25.67 4.22 41.36 3.51
2257 6220 1.296715 GTGCAGGGATTCCGTGAGT 59.703 57.895 25.67 0.00 41.36 3.41
2259 6222 1.153349 GCAGGGATTCCGTGAGTCC 60.153 63.158 25.67 7.18 41.36 3.85
2260 6223 1.899437 GCAGGGATTCCGTGAGTCCA 61.899 60.000 25.67 0.00 41.36 4.02
2261 6224 0.108138 CAGGGATTCCGTGAGTCCAC 60.108 60.000 18.52 6.73 41.36 4.02
2328 6291 7.489574 GAATAGATCCAAGAAGATGTGGTTC 57.510 40.000 0.00 0.00 36.23 3.62
2333 6296 6.550854 AGATCCAAGAAGATGTGGTTCAAAAA 59.449 34.615 0.00 0.00 36.48 1.94
2334 6297 6.729690 TCCAAGAAGATGTGGTTCAAAAAT 57.270 33.333 0.00 0.00 36.23 1.82
2407 6370 7.488322 ACTGCAATTGTGTGTTACTATTTTGT 58.512 30.769 7.40 0.00 33.41 2.83
2409 6372 7.261325 TGCAATTGTGTGTTACTATTTTGTGT 58.739 30.769 7.40 0.00 33.41 3.72
2429 6392 5.980116 TGTGTGTTAAATTGTTTTCATCCGG 59.020 36.000 0.00 0.00 0.00 5.14
2504 6467 0.107703 CTCATGCAGCGAAACCCCTA 60.108 55.000 0.00 0.00 0.00 3.53
2515 6478 0.909623 AAACCCCTACGGATGGACAG 59.090 55.000 0.00 0.00 34.64 3.51
2521 6484 1.182667 CTACGGATGGACAGTGGTGA 58.817 55.000 0.00 0.00 0.00 4.02
2525 6488 1.739466 CGGATGGACAGTGGTGAATTG 59.261 52.381 0.00 0.00 0.00 2.32
2547 6510 1.676967 CTGACCAAGGCCTTCCTGC 60.677 63.158 17.29 6.12 43.40 4.85
2574 6537 4.574674 TGCAATCCTCTGTATGGAGTTT 57.425 40.909 0.00 0.00 36.99 2.66
2576 6539 5.324409 TGCAATCCTCTGTATGGAGTTTTT 58.676 37.500 0.00 0.00 36.99 1.94
2605 6568 5.059833 GGCAAATCCTCTGTATGGAGTTAG 58.940 45.833 0.00 0.00 39.48 2.34
2606 6569 5.163301 GGCAAATCCTCTGTATGGAGTTAGA 60.163 44.000 0.00 0.00 39.48 2.10
2607 6570 5.988561 GCAAATCCTCTGTATGGAGTTAGAG 59.011 44.000 0.00 0.00 39.48 2.43
2608 6571 5.799827 AATCCTCTGTATGGAGTTAGAGC 57.200 43.478 0.00 0.00 36.99 4.09
2609 6572 4.251103 TCCTCTGTATGGAGTTAGAGCA 57.749 45.455 0.00 0.00 36.27 4.26
2610 6573 4.809193 TCCTCTGTATGGAGTTAGAGCAT 58.191 43.478 0.00 0.00 36.27 3.79
2611 6574 4.830046 TCCTCTGTATGGAGTTAGAGCATC 59.170 45.833 0.00 0.00 36.27 3.91
2612 6575 6.696445 ATCCTCTGTATGGAGTTAGAGCATCT 60.696 42.308 0.00 0.00 42.68 2.90
2613 6576 8.449686 ATCCTCTGTATGGAGTTAGAGCATCTC 61.450 44.444 0.00 0.00 40.35 2.75
2622 6585 3.805267 GAGCATCTCCAACAGGCG 58.195 61.111 0.00 0.00 0.00 5.52
2623 6586 2.437359 AGCATCTCCAACAGGCGC 60.437 61.111 0.00 0.00 0.00 6.53
2624 6587 3.869272 GCATCTCCAACAGGCGCG 61.869 66.667 0.00 0.00 0.00 6.86
2625 6588 3.869272 CATCTCCAACAGGCGCGC 61.869 66.667 25.94 25.94 0.00 6.86
2626 6589 4.087892 ATCTCCAACAGGCGCGCT 62.088 61.111 32.29 14.46 0.00 5.92
2627 6590 2.721167 ATCTCCAACAGGCGCGCTA 61.721 57.895 32.29 6.91 0.00 4.26
2628 6591 2.032860 ATCTCCAACAGGCGCGCTAT 62.033 55.000 32.29 17.65 0.00 2.97
2629 6592 2.202878 TCCAACAGGCGCGCTATC 60.203 61.111 32.29 14.98 0.00 2.08
2630 6593 2.202932 CCAACAGGCGCGCTATCT 60.203 61.111 32.29 17.33 0.00 1.98
2631 6594 1.815421 CCAACAGGCGCGCTATCTT 60.815 57.895 32.29 14.08 0.00 2.40
2632 6595 0.529773 CCAACAGGCGCGCTATCTTA 60.530 55.000 32.29 0.00 0.00 2.10
2633 6596 0.855349 CAACAGGCGCGCTATCTTAG 59.145 55.000 32.29 14.67 0.00 2.18
2641 6604 3.235355 GCTATCTTAGCCGCGTGC 58.765 61.111 4.92 8.57 45.95 5.34
2665 6628 1.545841 AAAAACAATCTCGGAGGGGC 58.454 50.000 4.96 0.00 0.00 5.80
2666 6629 0.698818 AAAACAATCTCGGAGGGGCT 59.301 50.000 4.96 0.00 0.00 5.19
2667 6630 0.253327 AAACAATCTCGGAGGGGCTC 59.747 55.000 4.96 0.00 0.00 4.70
2668 6631 0.618968 AACAATCTCGGAGGGGCTCT 60.619 55.000 4.96 0.00 0.00 4.09
2669 6632 1.045911 ACAATCTCGGAGGGGCTCTC 61.046 60.000 5.60 5.60 41.71 3.20
2670 6633 1.830408 AATCTCGGAGGGGCTCTCG 60.830 63.158 8.58 4.06 43.34 4.04
2689 6652 4.181010 CCCTCCGCCATGGACCAG 62.181 72.222 18.40 6.60 43.74 4.00
2690 6653 3.083349 CCTCCGCCATGGACCAGA 61.083 66.667 18.40 4.56 43.74 3.86
2691 6654 2.503061 CTCCGCCATGGACCAGAG 59.497 66.667 18.40 10.94 43.74 3.35
2692 6655 3.083349 TCCGCCATGGACCAGAGG 61.083 66.667 18.40 10.69 43.74 3.69
2693 6656 4.181010 CCGCCATGGACCAGAGGG 62.181 72.222 18.40 10.67 42.00 4.30
2694 6657 4.181010 CGCCATGGACCAGAGGGG 62.181 72.222 18.40 15.55 44.81 4.79
2695 6658 2.692368 GCCATGGACCAGAGGGGA 60.692 66.667 18.40 0.00 41.15 4.81
2696 6659 2.308722 GCCATGGACCAGAGGGGAA 61.309 63.158 18.40 0.00 41.15 3.97
2697 6660 1.863155 GCCATGGACCAGAGGGGAAA 61.863 60.000 18.40 0.00 41.15 3.13
2698 6661 0.034089 CCATGGACCAGAGGGGAAAC 60.034 60.000 5.56 0.00 41.15 2.78
2713 6676 3.847671 GGAAACCCTTCTCCCATCTAG 57.152 52.381 0.00 0.00 0.00 2.43
2714 6677 2.439880 GGAAACCCTTCTCCCATCTAGG 59.560 54.545 0.00 0.00 37.03 3.02
2724 6687 3.654876 CCATCTAGGGGGAAGGTCA 57.345 57.895 0.00 0.00 0.00 4.02
2725 6688 1.893315 CCATCTAGGGGGAAGGTCAA 58.107 55.000 0.00 0.00 0.00 3.18
2726 6689 1.771255 CCATCTAGGGGGAAGGTCAAG 59.229 57.143 0.00 0.00 0.00 3.02
2727 6690 1.771255 CATCTAGGGGGAAGGTCAAGG 59.229 57.143 0.00 0.00 0.00 3.61
2728 6691 1.098589 TCTAGGGGGAAGGTCAAGGA 58.901 55.000 0.00 0.00 0.00 3.36
2729 6692 1.439543 TCTAGGGGGAAGGTCAAGGAA 59.560 52.381 0.00 0.00 0.00 3.36
2730 6693 1.840635 CTAGGGGGAAGGTCAAGGAAG 59.159 57.143 0.00 0.00 0.00 3.46
2731 6694 0.196118 AGGGGGAAGGTCAAGGAAGA 59.804 55.000 0.00 0.00 0.00 2.87
2732 6695 1.073098 GGGGGAAGGTCAAGGAAGAA 58.927 55.000 0.00 0.00 0.00 2.52
2733 6696 1.004862 GGGGGAAGGTCAAGGAAGAAG 59.995 57.143 0.00 0.00 0.00 2.85
2734 6697 1.985895 GGGGAAGGTCAAGGAAGAAGA 59.014 52.381 0.00 0.00 0.00 2.87
2735 6698 2.375509 GGGGAAGGTCAAGGAAGAAGAA 59.624 50.000 0.00 0.00 0.00 2.52
2736 6699 3.560239 GGGGAAGGTCAAGGAAGAAGAAG 60.560 52.174 0.00 0.00 0.00 2.85
2737 6700 3.328050 GGGAAGGTCAAGGAAGAAGAAGA 59.672 47.826 0.00 0.00 0.00 2.87
2738 6701 4.202472 GGGAAGGTCAAGGAAGAAGAAGAA 60.202 45.833 0.00 0.00 0.00 2.52
2739 6702 5.000591 GGAAGGTCAAGGAAGAAGAAGAAG 58.999 45.833 0.00 0.00 0.00 2.85
2740 6703 4.632327 AGGTCAAGGAAGAAGAAGAAGG 57.368 45.455 0.00 0.00 0.00 3.46
2741 6704 3.977326 AGGTCAAGGAAGAAGAAGAAGGT 59.023 43.478 0.00 0.00 0.00 3.50
2742 6705 4.068599 GGTCAAGGAAGAAGAAGAAGGTG 58.931 47.826 0.00 0.00 0.00 4.00
2743 6706 4.068599 GTCAAGGAAGAAGAAGAAGGTGG 58.931 47.826 0.00 0.00 0.00 4.61
2744 6707 3.073062 TCAAGGAAGAAGAAGAAGGTGGG 59.927 47.826 0.00 0.00 0.00 4.61
2745 6708 1.352687 AGGAAGAAGAAGAAGGTGGGC 59.647 52.381 0.00 0.00 0.00 5.36
2746 6709 1.352687 GGAAGAAGAAGAAGGTGGGCT 59.647 52.381 0.00 0.00 0.00 5.19
2747 6710 2.616765 GGAAGAAGAAGAAGGTGGGCTC 60.617 54.545 0.00 0.00 0.00 4.70
2748 6711 2.037385 AGAAGAAGAAGGTGGGCTCT 57.963 50.000 0.00 0.00 0.00 4.09
2749 6712 1.905894 AGAAGAAGAAGGTGGGCTCTC 59.094 52.381 0.00 0.00 0.00 3.20
2750 6713 1.905894 GAAGAAGAAGGTGGGCTCTCT 59.094 52.381 0.00 0.00 0.00 3.10
2751 6714 1.567357 AGAAGAAGGTGGGCTCTCTC 58.433 55.000 0.00 0.00 0.00 3.20
2752 6715 0.539518 GAAGAAGGTGGGCTCTCTCC 59.460 60.000 0.00 0.00 0.00 3.71
2753 6716 0.118144 AAGAAGGTGGGCTCTCTCCT 59.882 55.000 0.00 0.00 0.00 3.69
2754 6717 0.325203 AGAAGGTGGGCTCTCTCCTC 60.325 60.000 0.00 0.00 0.00 3.71
2755 6718 1.306568 AAGGTGGGCTCTCTCCTCC 60.307 63.158 0.00 0.00 38.00 4.30
2756 6719 1.820866 AAGGTGGGCTCTCTCCTCCT 61.821 60.000 0.00 0.00 46.70 3.69
2757 6720 1.760480 GGTGGGCTCTCTCCTCCTC 60.760 68.421 0.00 0.00 35.62 3.71
2758 6721 1.309688 GTGGGCTCTCTCCTCCTCT 59.690 63.158 0.00 0.00 0.00 3.69
2759 6722 0.755327 GTGGGCTCTCTCCTCCTCTC 60.755 65.000 0.00 0.00 0.00 3.20
2760 6723 0.923729 TGGGCTCTCTCCTCCTCTCT 60.924 60.000 0.00 0.00 0.00 3.10
2761 6724 0.178990 GGGCTCTCTCCTCCTCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
2762 6725 0.178990 GGCTCTCTCCTCCTCTCTCC 60.179 65.000 0.00 0.00 0.00 3.71
2763 6726 0.178990 GCTCTCTCCTCCTCTCTCCC 60.179 65.000 0.00 0.00 0.00 4.30
2764 6727 0.108585 CTCTCTCCTCCTCTCTCCCG 59.891 65.000 0.00 0.00 0.00 5.14
2765 6728 1.150536 CTCTCCTCCTCTCTCCCGG 59.849 68.421 0.00 0.00 0.00 5.73
2766 6729 1.619975 TCTCCTCCTCTCTCCCGGT 60.620 63.158 0.00 0.00 0.00 5.28
2767 6730 1.454847 CTCCTCCTCTCTCCCGGTG 60.455 68.421 0.00 0.00 0.00 4.94
2768 6731 2.443016 CCTCCTCTCTCCCGGTGG 60.443 72.222 0.00 0.00 0.00 4.61
2769 6732 3.151022 CTCCTCTCTCCCGGTGGC 61.151 72.222 0.00 0.00 0.00 5.01
2798 6761 3.219198 GCCGGGGCCATCATTGTC 61.219 66.667 4.39 0.00 34.56 3.18
2799 6762 2.275089 CCGGGGCCATCATTGTCA 59.725 61.111 4.39 0.00 0.00 3.58
2800 6763 2.120909 CCGGGGCCATCATTGTCAC 61.121 63.158 4.39 0.00 0.00 3.67
2801 6764 2.120909 CGGGGCCATCATTGTCACC 61.121 63.158 4.39 0.00 0.00 4.02
2802 6765 2.120909 GGGGCCATCATTGTCACCG 61.121 63.158 4.39 0.00 0.00 4.94
2803 6766 2.774799 GGGCCATCATTGTCACCGC 61.775 63.158 4.39 0.00 0.00 5.68
2804 6767 2.404789 GCCATCATTGTCACCGCG 59.595 61.111 0.00 0.00 0.00 6.46
2805 6768 2.106074 GCCATCATTGTCACCGCGA 61.106 57.895 8.23 0.00 0.00 5.87
2806 6769 1.439353 GCCATCATTGTCACCGCGAT 61.439 55.000 8.23 0.00 0.00 4.58
2807 6770 0.583438 CCATCATTGTCACCGCGATC 59.417 55.000 8.23 0.00 0.00 3.69
2808 6771 1.575244 CATCATTGTCACCGCGATCT 58.425 50.000 8.23 0.00 0.00 2.75
2809 6772 2.545742 CCATCATTGTCACCGCGATCTA 60.546 50.000 8.23 0.00 0.00 1.98
2810 6773 2.203800 TCATTGTCACCGCGATCTAC 57.796 50.000 8.23 0.15 0.00 2.59
2811 6774 1.474879 TCATTGTCACCGCGATCTACA 59.525 47.619 8.23 3.27 0.00 2.74
2812 6775 1.588404 CATTGTCACCGCGATCTACAC 59.412 52.381 8.23 0.00 0.00 2.90
2813 6776 0.108992 TTGTCACCGCGATCTACACC 60.109 55.000 8.23 0.00 0.00 4.16
2814 6777 1.245376 TGTCACCGCGATCTACACCA 61.245 55.000 8.23 0.00 0.00 4.17
2815 6778 0.108992 GTCACCGCGATCTACACCAA 60.109 55.000 8.23 0.00 0.00 3.67
2816 6779 0.604073 TCACCGCGATCTACACCAAA 59.396 50.000 8.23 0.00 0.00 3.28
2817 6780 1.001068 TCACCGCGATCTACACCAAAA 59.999 47.619 8.23 0.00 0.00 2.44
2818 6781 1.801771 CACCGCGATCTACACCAAAAA 59.198 47.619 8.23 0.00 0.00 1.94
2833 6796 2.783228 AAAAACTTCACCGCCGTCA 58.217 47.368 0.00 0.00 0.00 4.35
2834 6797 1.314730 AAAAACTTCACCGCCGTCAT 58.685 45.000 0.00 0.00 0.00 3.06
2835 6798 0.872388 AAAACTTCACCGCCGTCATC 59.128 50.000 0.00 0.00 0.00 2.92
2836 6799 0.250124 AAACTTCACCGCCGTCATCA 60.250 50.000 0.00 0.00 0.00 3.07
2837 6800 0.949105 AACTTCACCGCCGTCATCAC 60.949 55.000 0.00 0.00 0.00 3.06
2838 6801 2.047655 TTCACCGCCGTCATCACC 60.048 61.111 0.00 0.00 0.00 4.02
2839 6802 2.779951 CTTCACCGCCGTCATCACCA 62.780 60.000 0.00 0.00 0.00 4.17
2840 6803 2.358125 CACCGCCGTCATCACCAA 60.358 61.111 0.00 0.00 0.00 3.67
2841 6804 2.358247 ACCGCCGTCATCACCAAC 60.358 61.111 0.00 0.00 0.00 3.77
2842 6805 2.047274 CCGCCGTCATCACCAACT 60.047 61.111 0.00 0.00 0.00 3.16
2843 6806 2.100631 CCGCCGTCATCACCAACTC 61.101 63.158 0.00 0.00 0.00 3.01
2844 6807 1.079819 CGCCGTCATCACCAACTCT 60.080 57.895 0.00 0.00 0.00 3.24
2845 6808 0.670546 CGCCGTCATCACCAACTCTT 60.671 55.000 0.00 0.00 0.00 2.85
2846 6809 1.079503 GCCGTCATCACCAACTCTTC 58.920 55.000 0.00 0.00 0.00 2.87
2847 6810 1.726853 CCGTCATCACCAACTCTTCC 58.273 55.000 0.00 0.00 0.00 3.46
2848 6811 1.676014 CCGTCATCACCAACTCTTCCC 60.676 57.143 0.00 0.00 0.00 3.97
2849 6812 1.676014 CGTCATCACCAACTCTTCCCC 60.676 57.143 0.00 0.00 0.00 4.81
2850 6813 0.991920 TCATCACCAACTCTTCCCCC 59.008 55.000 0.00 0.00 0.00 5.40
2864 6827 3.164269 CCCCCTCTATGCAGCGGT 61.164 66.667 0.00 0.00 0.00 5.68
2865 6828 2.109799 CCCCTCTATGCAGCGGTG 59.890 66.667 10.98 10.98 0.00 4.94
2866 6829 2.735772 CCCCTCTATGCAGCGGTGT 61.736 63.158 17.07 0.00 0.00 4.16
2867 6830 1.399744 CCCCTCTATGCAGCGGTGTA 61.400 60.000 17.07 12.83 0.00 2.90
2868 6831 0.464036 CCCTCTATGCAGCGGTGTAA 59.536 55.000 17.07 5.51 0.00 2.41
2869 6832 1.571919 CCTCTATGCAGCGGTGTAAC 58.428 55.000 17.07 0.00 0.00 2.50
2883 6846 2.703416 GTGTAACCCCTCTTTTACCCG 58.297 52.381 0.00 0.00 0.00 5.28
2884 6847 1.003464 TGTAACCCCTCTTTTACCCGC 59.997 52.381 0.00 0.00 0.00 6.13
2885 6848 1.280133 GTAACCCCTCTTTTACCCGCT 59.720 52.381 0.00 0.00 0.00 5.52
2886 6849 0.037734 AACCCCTCTTTTACCCGCTG 59.962 55.000 0.00 0.00 0.00 5.18
2887 6850 1.131928 ACCCCTCTTTTACCCGCTGT 61.132 55.000 0.00 0.00 0.00 4.40
2888 6851 0.906775 CCCCTCTTTTACCCGCTGTA 59.093 55.000 0.00 0.00 0.00 2.74
2889 6852 1.279846 CCCCTCTTTTACCCGCTGTAA 59.720 52.381 0.00 0.00 37.65 2.41
2890 6853 2.092592 CCCCTCTTTTACCCGCTGTAAT 60.093 50.000 0.00 0.00 39.14 1.89
2891 6854 3.135167 CCCCTCTTTTACCCGCTGTAATA 59.865 47.826 0.00 0.00 39.14 0.98
2892 6855 4.202430 CCCCTCTTTTACCCGCTGTAATAT 60.202 45.833 0.00 0.00 39.14 1.28
2893 6856 4.995487 CCCTCTTTTACCCGCTGTAATATC 59.005 45.833 0.00 0.00 39.14 1.63
2894 6857 5.221661 CCCTCTTTTACCCGCTGTAATATCT 60.222 44.000 0.00 0.00 39.14 1.98
2895 6858 6.014840 CCCTCTTTTACCCGCTGTAATATCTA 60.015 42.308 0.00 0.00 39.14 1.98
2896 6859 6.867293 CCTCTTTTACCCGCTGTAATATCTAC 59.133 42.308 0.00 0.00 39.14 2.59
2897 6860 7.255871 CCTCTTTTACCCGCTGTAATATCTACT 60.256 40.741 0.00 0.00 39.14 2.57
2898 6861 8.015185 TCTTTTACCCGCTGTAATATCTACTT 57.985 34.615 0.00 0.00 39.14 2.24
2899 6862 9.135189 TCTTTTACCCGCTGTAATATCTACTTA 57.865 33.333 0.00 0.00 39.14 2.24
2900 6863 9.754382 CTTTTACCCGCTGTAATATCTACTTAA 57.246 33.333 0.00 0.00 39.14 1.85
2902 6865 9.533253 TTTACCCGCTGTAATATCTACTTAAAC 57.467 33.333 0.00 0.00 39.14 2.01
2903 6866 7.116075 ACCCGCTGTAATATCTACTTAAACA 57.884 36.000 0.00 0.00 0.00 2.83
2904 6867 7.732996 ACCCGCTGTAATATCTACTTAAACAT 58.267 34.615 0.00 0.00 0.00 2.71
2905 6868 7.656137 ACCCGCTGTAATATCTACTTAAACATG 59.344 37.037 0.00 0.00 0.00 3.21
2906 6869 7.117812 CCCGCTGTAATATCTACTTAAACATGG 59.882 40.741 0.00 0.00 0.00 3.66
2907 6870 7.656137 CCGCTGTAATATCTACTTAAACATGGT 59.344 37.037 0.00 0.00 0.00 3.55
2908 6871 8.487970 CGCTGTAATATCTACTTAAACATGGTG 58.512 37.037 0.00 0.00 0.00 4.17
2909 6872 8.283291 GCTGTAATATCTACTTAAACATGGTGC 58.717 37.037 0.00 0.00 0.00 5.01
2910 6873 9.547753 CTGTAATATCTACTTAAACATGGTGCT 57.452 33.333 0.00 0.00 0.00 4.40
2911 6874 9.542462 TGTAATATCTACTTAAACATGGTGCTC 57.458 33.333 0.00 0.00 0.00 4.26
2912 6875 9.542462 GTAATATCTACTTAAACATGGTGCTCA 57.458 33.333 0.00 0.00 0.00 4.26
2914 6877 6.743575 ATCTACTTAAACATGGTGCTCAAC 57.256 37.500 0.00 0.00 0.00 3.18
2915 6878 3.896648 ACTTAAACATGGTGCTCAACG 57.103 42.857 0.00 0.00 0.00 4.10
2916 6879 2.031157 ACTTAAACATGGTGCTCAACGC 60.031 45.455 0.00 0.00 39.77 4.84
2917 6880 1.890876 TAAACATGGTGCTCAACGCT 58.109 45.000 0.00 0.00 40.11 5.07
2918 6881 1.890876 AAACATGGTGCTCAACGCTA 58.109 45.000 0.00 0.00 40.11 4.26
2919 6882 2.113860 AACATGGTGCTCAACGCTAT 57.886 45.000 0.00 0.00 40.11 2.97
2920 6883 2.979814 ACATGGTGCTCAACGCTATA 57.020 45.000 0.00 0.00 40.11 1.31
2921 6884 3.475566 ACATGGTGCTCAACGCTATAT 57.524 42.857 0.00 0.00 40.11 0.86
2922 6885 4.600692 ACATGGTGCTCAACGCTATATA 57.399 40.909 0.00 0.00 40.11 0.86
2923 6886 5.152623 ACATGGTGCTCAACGCTATATAT 57.847 39.130 0.00 0.00 40.11 0.86
2924 6887 5.551233 ACATGGTGCTCAACGCTATATATT 58.449 37.500 0.00 0.00 40.11 1.28
2925 6888 6.697395 ACATGGTGCTCAACGCTATATATTA 58.303 36.000 0.00 0.00 40.11 0.98
2926 6889 7.331026 ACATGGTGCTCAACGCTATATATTAT 58.669 34.615 0.00 0.00 40.11 1.28
2927 6890 7.824289 ACATGGTGCTCAACGCTATATATTATT 59.176 33.333 0.00 0.00 40.11 1.40
2928 6891 8.668353 CATGGTGCTCAACGCTATATATTATTT 58.332 33.333 0.00 0.00 40.11 1.40
2929 6892 8.251750 TGGTGCTCAACGCTATATATTATTTC 57.748 34.615 0.00 0.00 40.11 2.17
2930 6893 7.333423 TGGTGCTCAACGCTATATATTATTTCC 59.667 37.037 0.00 0.00 40.11 3.13
2931 6894 7.201617 GGTGCTCAACGCTATATATTATTTCCC 60.202 40.741 0.00 0.00 40.11 3.97
2932 6895 7.333423 GTGCTCAACGCTATATATTATTTCCCA 59.667 37.037 0.00 0.00 40.11 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.224646 GCCACAAAGAGAAGAGAAGGGT 60.225 50.000 0.00 0.00 0.00 4.34
4 5 1.270839 CCGGCCACAAAGAGAAGAGAA 60.271 52.381 2.24 0.00 0.00 2.87
22 23 1.765230 AGAAGTCACTAGGTAGGCCG 58.235 55.000 0.00 0.00 40.50 6.13
40 41 7.492994 GCTAGGTGTAGGTCAATCTTAGAAAAG 59.507 40.741 0.00 0.00 0.00 2.27
45 47 4.579340 TCGCTAGGTGTAGGTCAATCTTAG 59.421 45.833 0.00 0.00 0.00 2.18
54 56 2.211250 TCAAGTCGCTAGGTGTAGGT 57.789 50.000 0.00 0.00 0.00 3.08
89 91 1.292061 GGGTCGTGCACGCAATATTA 58.708 50.000 33.63 12.62 37.88 0.98
123 131 7.388500 CCAAATCCAATCAGTGCAAAGTAAATT 59.612 33.333 0.00 0.00 0.00 1.82
162 175 4.750098 CCGTTGGATATGACTTACATCACC 59.250 45.833 0.00 0.00 40.07 4.02
200 213 3.871594 GGCTAGAGCGAGAAAAATAAGCA 59.128 43.478 0.00 0.00 43.26 3.91
225 258 4.719997 GCGCTAGCTAGGTGTCAG 57.280 61.111 22.10 0.00 41.01 3.51
308 344 5.595133 TCCCTCAATCACGTTTAACCTTTTT 59.405 36.000 0.00 0.00 0.00 1.94
313 349 4.698304 TCATTCCCTCAATCACGTTTAACC 59.302 41.667 0.00 0.00 0.00 2.85
394 434 4.357142 GTTGATCATTCCACACATGCATC 58.643 43.478 0.00 0.00 0.00 3.91
395 435 3.181494 CGTTGATCATTCCACACATGCAT 60.181 43.478 0.00 0.00 0.00 3.96
404 444 4.707934 TGTACCTAGTCGTTGATCATTCCA 59.292 41.667 0.00 0.00 0.00 3.53
406 446 5.647589 TGTGTACCTAGTCGTTGATCATTC 58.352 41.667 0.00 0.00 0.00 2.67
420 460 5.663456 ACGTGTCTTTTTCTTGTGTACCTA 58.337 37.500 0.00 0.00 0.00 3.08
421 461 4.510571 ACGTGTCTTTTTCTTGTGTACCT 58.489 39.130 0.00 0.00 0.00 3.08
423 463 5.229887 TCGTACGTGTCTTTTTCTTGTGTAC 59.770 40.000 16.05 0.00 0.00 2.90
424 464 5.339177 TCGTACGTGTCTTTTTCTTGTGTA 58.661 37.500 16.05 0.00 0.00 2.90
447 497 2.233676 TGCTCACATGATTGGTCGTACT 59.766 45.455 0.00 0.00 0.00 2.73
500 552 7.968246 AGATCGAATTTAAGTTGACAGTGATG 58.032 34.615 0.00 0.00 0.00 3.07
503 555 7.351414 TGAGATCGAATTTAAGTTGACAGTG 57.649 36.000 0.00 0.00 0.00 3.66
505 557 7.515841 CGGATGAGATCGAATTTAAGTTGACAG 60.516 40.741 0.00 0.00 0.00 3.51
508 560 5.234329 GCGGATGAGATCGAATTTAAGTTGA 59.766 40.000 0.00 0.00 0.00 3.18
509 561 5.435557 GCGGATGAGATCGAATTTAAGTTG 58.564 41.667 0.00 0.00 0.00 3.16
612 2900 5.432885 TCTTGAAAAATCTTTCGTGGACC 57.567 39.130 0.00 0.00 43.40 4.46
715 3056 8.447833 CGTGCCAGATTTTCACTTATAGTTTTA 58.552 33.333 0.00 0.00 0.00 1.52
718 3059 6.170506 TCGTGCCAGATTTTCACTTATAGTT 58.829 36.000 0.00 0.00 0.00 2.24
719 3060 5.730550 TCGTGCCAGATTTTCACTTATAGT 58.269 37.500 0.00 0.00 0.00 2.12
720 3061 6.851222 ATCGTGCCAGATTTTCACTTATAG 57.149 37.500 0.00 0.00 0.00 1.31
726 3109 2.677836 TGCTATCGTGCCAGATTTTCAC 59.322 45.455 0.00 0.00 32.39 3.18
814 3589 1.367346 TAGGTGCACCCCATCTTTCA 58.633 50.000 32.29 3.60 36.07 2.69
816 3591 1.922447 TGATAGGTGCACCCCATCTTT 59.078 47.619 32.38 18.99 36.07 2.52
829 3604 3.441922 CCATCTCATCGTCGATGATAGGT 59.558 47.826 32.10 18.67 46.16 3.08
839 3619 4.039245 TCCTTATTCCACCATCTCATCGTC 59.961 45.833 0.00 0.00 0.00 4.20
840 3620 3.967326 TCCTTATTCCACCATCTCATCGT 59.033 43.478 0.00 0.00 0.00 3.73
925 3893 2.146146 TTGCTCTCCCTGCTGCCATT 62.146 55.000 0.00 0.00 0.00 3.16
928 3896 2.034687 TTTGCTCTCCCTGCTGCC 59.965 61.111 0.00 0.00 0.00 4.85
1959 5820 2.504681 GTGTGTACGTACGGGCCG 60.505 66.667 27.06 27.06 0.00 6.13
1960 5821 2.504681 CGTGTGTACGTACGGGCC 60.505 66.667 21.06 7.17 44.99 5.80
2118 6066 4.871993 ACTCTTGCATGAATCGATGTTC 57.128 40.909 0.00 0.00 0.00 3.18
2253 6216 0.249155 GACGTGTTTCCGTGGACTCA 60.249 55.000 0.00 0.00 41.98 3.41
2256 6219 0.942884 GGAGACGTGTTTCCGTGGAC 60.943 60.000 0.00 0.00 41.98 4.02
2257 6220 1.364901 GGAGACGTGTTTCCGTGGA 59.635 57.895 0.00 0.00 41.98 4.02
2259 6222 1.068417 TGGGAGACGTGTTTCCGTG 59.932 57.895 0.00 0.00 41.98 4.94
2260 6223 1.068585 GTGGGAGACGTGTTTCCGT 59.931 57.895 0.00 0.00 45.18 4.69
2261 6224 0.944311 CAGTGGGAGACGTGTTTCCG 60.944 60.000 0.00 0.00 34.90 4.30
2262 6225 0.391597 TCAGTGGGAGACGTGTTTCC 59.608 55.000 0.00 1.05 33.43 3.13
2263 6226 2.135933 CTTCAGTGGGAGACGTGTTTC 58.864 52.381 0.00 0.00 0.00 2.78
2264 6227 1.202651 CCTTCAGTGGGAGACGTGTTT 60.203 52.381 0.00 0.00 0.00 2.83
2265 6228 0.393077 CCTTCAGTGGGAGACGTGTT 59.607 55.000 0.00 0.00 0.00 3.32
2266 6229 0.469331 TCCTTCAGTGGGAGACGTGT 60.469 55.000 0.00 0.00 0.00 4.49
2267 6230 0.679505 TTCCTTCAGTGGGAGACGTG 59.320 55.000 0.00 0.00 34.06 4.49
2268 6231 0.680061 GTTCCTTCAGTGGGAGACGT 59.320 55.000 0.00 0.00 34.06 4.34
2407 6370 4.985409 GCCGGATGAAAACAATTTAACACA 59.015 37.500 5.05 0.00 0.00 3.72
2409 6372 5.221342 ACAGCCGGATGAAAACAATTTAACA 60.221 36.000 29.47 0.00 0.00 2.41
2418 6381 5.034797 GCTAATTTACAGCCGGATGAAAAC 58.965 41.667 29.47 9.78 32.68 2.43
2429 6392 8.122952 ACAATTACAGAATCGCTAATTTACAGC 58.877 33.333 0.00 0.00 35.61 4.40
2504 6467 0.984230 ATTCACCACTGTCCATCCGT 59.016 50.000 0.00 0.00 0.00 4.69
2515 6478 1.680735 TGGTCAGCAACAATTCACCAC 59.319 47.619 0.00 0.00 0.00 4.16
2521 6484 0.681175 GGCCTTGGTCAGCAACAATT 59.319 50.000 0.00 0.00 0.00 2.32
2525 6488 1.527433 GGAAGGCCTTGGTCAGCAAC 61.527 60.000 26.25 4.40 0.00 4.17
2547 6510 6.046290 TCCATACAGAGGATTGCATCTATG 57.954 41.667 0.00 0.00 32.55 2.23
2576 6539 1.327303 ACAGAGGATTTGCCGCAAAA 58.673 45.000 21.80 6.54 43.43 2.44
2581 6544 2.158900 ACTCCATACAGAGGATTTGCCG 60.159 50.000 0.00 0.00 43.43 5.69
2582 6545 3.567478 ACTCCATACAGAGGATTTGCC 57.433 47.619 0.00 0.00 38.26 4.52
2584 6547 5.988561 GCTCTAACTCCATACAGAGGATTTG 59.011 44.000 0.00 0.00 38.26 2.32
2588 6551 4.251103 TGCTCTAACTCCATACAGAGGA 57.749 45.455 0.00 0.00 38.26 3.71
2589 6552 4.832266 AGATGCTCTAACTCCATACAGAGG 59.168 45.833 0.00 0.00 38.26 3.69
2590 6553 5.048083 GGAGATGCTCTAACTCCATACAGAG 60.048 48.000 0.00 0.00 46.42 3.35
2605 6568 2.467826 GCGCCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 34.95 4.26
2606 6569 2.437359 GCGCCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 34.95 3.79
2607 6570 3.869272 CGCGCCTGTTGGAGATGC 61.869 66.667 0.00 0.00 34.95 3.91
2608 6571 2.906182 TAGCGCGCCTGTTGGAGATG 62.906 60.000 30.33 0.00 34.95 2.90
2609 6572 2.032860 ATAGCGCGCCTGTTGGAGAT 62.033 55.000 30.33 7.53 34.95 2.75
2610 6573 2.629050 GATAGCGCGCCTGTTGGAGA 62.629 60.000 30.33 1.89 34.95 3.71
2611 6574 2.202932 ATAGCGCGCCTGTTGGAG 60.203 61.111 30.33 0.00 36.16 3.86
2612 6575 2.202878 GATAGCGCGCCTGTTGGA 60.203 61.111 30.33 4.67 34.57 3.53
2613 6576 0.529773 TAAGATAGCGCGCCTGTTGG 60.530 55.000 30.33 0.00 0.00 3.77
2614 6577 0.855349 CTAAGATAGCGCGCCTGTTG 59.145 55.000 30.33 8.63 0.00 3.33
2615 6578 0.876342 GCTAAGATAGCGCGCCTGTT 60.876 55.000 30.33 21.83 42.62 3.16
2616 6579 1.300233 GCTAAGATAGCGCGCCTGT 60.300 57.895 30.33 14.54 42.62 4.00
2617 6580 3.543548 GCTAAGATAGCGCGCCTG 58.456 61.111 30.33 11.09 42.62 4.85
2646 6609 1.075536 AGCCCCTCCGAGATTGTTTTT 59.924 47.619 0.00 0.00 0.00 1.94
2647 6610 0.698818 AGCCCCTCCGAGATTGTTTT 59.301 50.000 0.00 0.00 0.00 2.43
2648 6611 0.253327 GAGCCCCTCCGAGATTGTTT 59.747 55.000 0.00 0.00 0.00 2.83
2649 6612 0.618968 AGAGCCCCTCCGAGATTGTT 60.619 55.000 0.00 0.00 0.00 2.83
2650 6613 1.002274 AGAGCCCCTCCGAGATTGT 59.998 57.895 0.00 0.00 0.00 2.71
2651 6614 1.745264 GAGAGCCCCTCCGAGATTG 59.255 63.158 0.00 0.00 35.87 2.67
2652 6615 1.830408 CGAGAGCCCCTCCGAGATT 60.830 63.158 0.00 0.00 38.71 2.40
2653 6616 2.203422 CGAGAGCCCCTCCGAGAT 60.203 66.667 0.00 0.00 38.71 2.75
2675 6638 3.083349 CCTCTGGTCCATGGCGGA 61.083 66.667 6.96 3.64 43.61 5.54
2676 6639 4.181010 CCCTCTGGTCCATGGCGG 62.181 72.222 6.96 0.00 0.00 6.13
2677 6640 4.181010 CCCCTCTGGTCCATGGCG 62.181 72.222 6.96 0.00 0.00 5.69
2678 6641 1.863155 TTTCCCCTCTGGTCCATGGC 61.863 60.000 6.96 1.78 34.77 4.40
2679 6642 0.034089 GTTTCCCCTCTGGTCCATGG 60.034 60.000 4.97 4.97 34.77 3.66
2680 6643 0.034089 GGTTTCCCCTCTGGTCCATG 60.034 60.000 0.00 0.00 34.77 3.66
2681 6644 2.398919 GGTTTCCCCTCTGGTCCAT 58.601 57.895 0.00 0.00 34.77 3.41
2682 6645 3.916184 GGTTTCCCCTCTGGTCCA 58.084 61.111 0.00 0.00 34.77 4.02
2693 6656 2.439880 CCTAGATGGGAGAAGGGTTTCC 59.560 54.545 0.00 0.00 33.64 3.13
2694 6657 3.847671 CCTAGATGGGAGAAGGGTTTC 57.152 52.381 0.00 0.00 0.00 2.78
2706 6669 1.771255 CTTGACCTTCCCCCTAGATGG 59.229 57.143 0.00 0.00 37.16 3.51
2707 6670 1.771255 CCTTGACCTTCCCCCTAGATG 59.229 57.143 0.00 0.00 0.00 2.90
2708 6671 1.657162 TCCTTGACCTTCCCCCTAGAT 59.343 52.381 0.00 0.00 0.00 1.98
2709 6672 1.098589 TCCTTGACCTTCCCCCTAGA 58.901 55.000 0.00 0.00 0.00 2.43
2710 6673 1.840635 CTTCCTTGACCTTCCCCCTAG 59.159 57.143 0.00 0.00 0.00 3.02
2711 6674 1.439543 TCTTCCTTGACCTTCCCCCTA 59.560 52.381 0.00 0.00 0.00 3.53
2712 6675 0.196118 TCTTCCTTGACCTTCCCCCT 59.804 55.000 0.00 0.00 0.00 4.79
2713 6676 1.004862 CTTCTTCCTTGACCTTCCCCC 59.995 57.143 0.00 0.00 0.00 5.40
2714 6677 1.985895 TCTTCTTCCTTGACCTTCCCC 59.014 52.381 0.00 0.00 0.00 4.81
2715 6678 3.328050 TCTTCTTCTTCCTTGACCTTCCC 59.672 47.826 0.00 0.00 0.00 3.97
2716 6679 4.625607 TCTTCTTCTTCCTTGACCTTCC 57.374 45.455 0.00 0.00 0.00 3.46
2717 6680 5.000591 CCTTCTTCTTCTTCCTTGACCTTC 58.999 45.833 0.00 0.00 0.00 3.46
2718 6681 4.413851 ACCTTCTTCTTCTTCCTTGACCTT 59.586 41.667 0.00 0.00 0.00 3.50
2719 6682 3.977326 ACCTTCTTCTTCTTCCTTGACCT 59.023 43.478 0.00 0.00 0.00 3.85
2720 6683 4.068599 CACCTTCTTCTTCTTCCTTGACC 58.931 47.826 0.00 0.00 0.00 4.02
2721 6684 4.068599 CCACCTTCTTCTTCTTCCTTGAC 58.931 47.826 0.00 0.00 0.00 3.18
2722 6685 3.073062 CCCACCTTCTTCTTCTTCCTTGA 59.927 47.826 0.00 0.00 0.00 3.02
2723 6686 3.416156 CCCACCTTCTTCTTCTTCCTTG 58.584 50.000 0.00 0.00 0.00 3.61
2724 6687 2.224892 GCCCACCTTCTTCTTCTTCCTT 60.225 50.000 0.00 0.00 0.00 3.36
2725 6688 1.352687 GCCCACCTTCTTCTTCTTCCT 59.647 52.381 0.00 0.00 0.00 3.36
2726 6689 1.352687 AGCCCACCTTCTTCTTCTTCC 59.647 52.381 0.00 0.00 0.00 3.46
2727 6690 2.304470 AGAGCCCACCTTCTTCTTCTTC 59.696 50.000 0.00 0.00 0.00 2.87
2728 6691 2.304470 GAGAGCCCACCTTCTTCTTCTT 59.696 50.000 0.00 0.00 0.00 2.52
2729 6692 1.905894 GAGAGCCCACCTTCTTCTTCT 59.094 52.381 0.00 0.00 0.00 2.85
2730 6693 1.905894 AGAGAGCCCACCTTCTTCTTC 59.094 52.381 0.00 0.00 0.00 2.87
2731 6694 1.905894 GAGAGAGCCCACCTTCTTCTT 59.094 52.381 0.00 0.00 0.00 2.52
2732 6695 1.567357 GAGAGAGCCCACCTTCTTCT 58.433 55.000 0.00 0.00 0.00 2.85
2733 6696 0.539518 GGAGAGAGCCCACCTTCTTC 59.460 60.000 0.00 0.00 0.00 2.87
2734 6697 0.118144 AGGAGAGAGCCCACCTTCTT 59.882 55.000 0.00 0.00 0.00 2.52
2735 6698 0.325203 GAGGAGAGAGCCCACCTTCT 60.325 60.000 0.00 0.00 32.53 2.85
2736 6699 1.334384 GGAGGAGAGAGCCCACCTTC 61.334 65.000 0.00 0.00 32.53 3.46
2737 6700 1.306568 GGAGGAGAGAGCCCACCTT 60.307 63.158 0.00 0.00 32.53 3.50
2738 6701 2.236959 GAGGAGGAGAGAGCCCACCT 62.237 65.000 0.00 0.00 37.74 4.00
2739 6702 1.760480 GAGGAGGAGAGAGCCCACC 60.760 68.421 0.00 0.00 0.00 4.61
2740 6703 0.755327 GAGAGGAGGAGAGAGCCCAC 60.755 65.000 0.00 0.00 0.00 4.61
2741 6704 0.923729 AGAGAGGAGGAGAGAGCCCA 60.924 60.000 0.00 0.00 0.00 5.36
2742 6705 0.178990 GAGAGAGGAGGAGAGAGCCC 60.179 65.000 0.00 0.00 0.00 5.19
2743 6706 0.178990 GGAGAGAGGAGGAGAGAGCC 60.179 65.000 0.00 0.00 0.00 4.70
2744 6707 0.178990 GGGAGAGAGGAGGAGAGAGC 60.179 65.000 0.00 0.00 0.00 4.09
2745 6708 0.108585 CGGGAGAGAGGAGGAGAGAG 59.891 65.000 0.00 0.00 0.00 3.20
2746 6709 1.349542 CCGGGAGAGAGGAGGAGAGA 61.350 65.000 0.00 0.00 0.00 3.10
2747 6710 1.150536 CCGGGAGAGAGGAGGAGAG 59.849 68.421 0.00 0.00 0.00 3.20
2748 6711 1.619975 ACCGGGAGAGAGGAGGAGA 60.620 63.158 6.32 0.00 0.00 3.71
2749 6712 1.454847 CACCGGGAGAGAGGAGGAG 60.455 68.421 6.32 0.00 0.00 3.69
2750 6713 2.684104 CACCGGGAGAGAGGAGGA 59.316 66.667 6.32 0.00 0.00 3.71
2751 6714 2.443016 CCACCGGGAGAGAGGAGG 60.443 72.222 6.32 0.00 35.59 4.30
2752 6715 3.151022 GCCACCGGGAGAGAGGAG 61.151 72.222 6.32 0.00 35.59 3.69
2781 6744 3.219198 GACAATGATGGCCCCGGC 61.219 66.667 0.00 0.00 41.06 6.13
2782 6745 2.120909 GTGACAATGATGGCCCCGG 61.121 63.158 0.00 0.00 31.48 5.73
2783 6746 2.120909 GGTGACAATGATGGCCCCG 61.121 63.158 0.00 0.00 31.48 5.73
2784 6747 2.120909 CGGTGACAATGATGGCCCC 61.121 63.158 0.00 0.00 31.48 5.80
2785 6748 2.774799 GCGGTGACAATGATGGCCC 61.775 63.158 0.00 0.00 31.48 5.80
2786 6749 2.800736 GCGGTGACAATGATGGCC 59.199 61.111 0.00 0.00 31.48 5.36
2787 6750 1.439353 ATCGCGGTGACAATGATGGC 61.439 55.000 6.13 0.00 34.00 4.40
2788 6751 0.583438 GATCGCGGTGACAATGATGG 59.417 55.000 6.13 0.00 0.00 3.51
2789 6752 1.575244 AGATCGCGGTGACAATGATG 58.425 50.000 6.13 0.00 0.00 3.07
2790 6753 2.100749 TGTAGATCGCGGTGACAATGAT 59.899 45.455 6.13 0.00 0.00 2.45
2791 6754 1.474879 TGTAGATCGCGGTGACAATGA 59.525 47.619 6.13 0.00 0.00 2.57
2792 6755 1.588404 GTGTAGATCGCGGTGACAATG 59.412 52.381 6.13 0.00 0.00 2.82
2793 6756 1.470979 GGTGTAGATCGCGGTGACAAT 60.471 52.381 6.13 0.00 0.00 2.71
2794 6757 0.108992 GGTGTAGATCGCGGTGACAA 60.109 55.000 6.13 0.00 0.00 3.18
2795 6758 1.245376 TGGTGTAGATCGCGGTGACA 61.245 55.000 6.13 2.32 0.00 3.58
2796 6759 0.108992 TTGGTGTAGATCGCGGTGAC 60.109 55.000 6.13 0.00 0.00 3.67
2797 6760 0.604073 TTTGGTGTAGATCGCGGTGA 59.396 50.000 6.13 0.00 0.00 4.02
2798 6761 1.434555 TTTTGGTGTAGATCGCGGTG 58.565 50.000 6.13 0.00 0.00 4.94
2799 6762 2.172851 TTTTTGGTGTAGATCGCGGT 57.827 45.000 6.13 0.00 0.00 5.68
2815 6778 1.265905 GATGACGGCGGTGAAGTTTTT 59.734 47.619 13.24 0.00 0.00 1.94
2816 6779 0.872388 GATGACGGCGGTGAAGTTTT 59.128 50.000 13.24 0.00 0.00 2.43
2817 6780 0.250124 TGATGACGGCGGTGAAGTTT 60.250 50.000 13.24 0.00 0.00 2.66
2818 6781 0.949105 GTGATGACGGCGGTGAAGTT 60.949 55.000 13.24 0.00 0.00 2.66
2819 6782 1.374252 GTGATGACGGCGGTGAAGT 60.374 57.895 13.24 0.00 0.00 3.01
2820 6783 2.100631 GGTGATGACGGCGGTGAAG 61.101 63.158 13.24 0.00 0.00 3.02
2821 6784 2.047655 GGTGATGACGGCGGTGAA 60.048 61.111 13.24 0.00 0.00 3.18
2822 6785 2.873525 TTGGTGATGACGGCGGTGA 61.874 57.895 13.24 0.00 0.00 4.02
2823 6786 2.358125 TTGGTGATGACGGCGGTG 60.358 61.111 13.24 0.00 0.00 4.94
2824 6787 2.358247 GTTGGTGATGACGGCGGT 60.358 61.111 13.24 0.00 0.00 5.68
2825 6788 2.047274 AGTTGGTGATGACGGCGG 60.047 61.111 13.24 0.00 0.00 6.13
2826 6789 0.670546 AAGAGTTGGTGATGACGGCG 60.671 55.000 4.80 4.80 0.00 6.46
2827 6790 1.079503 GAAGAGTTGGTGATGACGGC 58.920 55.000 0.00 0.00 0.00 5.68
2828 6791 1.676014 GGGAAGAGTTGGTGATGACGG 60.676 57.143 0.00 0.00 0.00 4.79
2829 6792 1.676014 GGGGAAGAGTTGGTGATGACG 60.676 57.143 0.00 0.00 0.00 4.35
2830 6793 1.340114 GGGGGAAGAGTTGGTGATGAC 60.340 57.143 0.00 0.00 0.00 3.06
2831 6794 0.991920 GGGGGAAGAGTTGGTGATGA 59.008 55.000 0.00 0.00 0.00 2.92
2832 6795 3.577389 GGGGGAAGAGTTGGTGATG 57.423 57.895 0.00 0.00 0.00 3.07
2847 6810 3.164269 ACCGCTGCATAGAGGGGG 61.164 66.667 10.88 7.89 46.98 5.40
2848 6811 2.109799 CACCGCTGCATAGAGGGG 59.890 66.667 0.00 5.36 46.98 4.79
2849 6812 0.464036 TTACACCGCTGCATAGAGGG 59.536 55.000 0.00 0.00 46.98 4.30
2851 6814 1.571919 GGTTACACCGCTGCATAGAG 58.428 55.000 0.00 0.00 0.00 2.43
2852 6815 0.177141 GGGTTACACCGCTGCATAGA 59.823 55.000 0.00 0.00 39.83 1.98
2853 6816 0.814010 GGGGTTACACCGCTGCATAG 60.814 60.000 0.00 0.00 46.55 2.23
2854 6817 1.222387 GGGGTTACACCGCTGCATA 59.778 57.895 0.00 0.00 46.55 3.14
2855 6818 2.045340 GGGGTTACACCGCTGCAT 60.045 61.111 0.00 0.00 46.55 3.96
2861 6824 2.616256 GGGTAAAAGAGGGGTTACACCG 60.616 54.545 0.00 0.00 39.83 4.94
2862 6825 2.616256 CGGGTAAAAGAGGGGTTACACC 60.616 54.545 0.00 0.00 37.60 4.16
2863 6826 2.703416 CGGGTAAAAGAGGGGTTACAC 58.297 52.381 0.00 0.00 32.83 2.90
2864 6827 1.003464 GCGGGTAAAAGAGGGGTTACA 59.997 52.381 0.00 0.00 32.83 2.41
2865 6828 1.280133 AGCGGGTAAAAGAGGGGTTAC 59.720 52.381 0.00 0.00 0.00 2.50
2866 6829 1.279846 CAGCGGGTAAAAGAGGGGTTA 59.720 52.381 0.00 0.00 0.00 2.85
2867 6830 0.037734 CAGCGGGTAAAAGAGGGGTT 59.962 55.000 0.00 0.00 0.00 4.11
2868 6831 1.131928 ACAGCGGGTAAAAGAGGGGT 61.132 55.000 0.00 0.00 0.00 4.95
2869 6832 0.906775 TACAGCGGGTAAAAGAGGGG 59.093 55.000 0.00 0.00 0.00 4.79
2870 6833 2.773993 TTACAGCGGGTAAAAGAGGG 57.226 50.000 2.11 0.00 38.98 4.30
2871 6834 5.855045 AGATATTACAGCGGGTAAAAGAGG 58.145 41.667 7.87 0.00 44.70 3.69
2872 6835 7.659186 AGTAGATATTACAGCGGGTAAAAGAG 58.341 38.462 7.87 0.00 44.70 2.85
2873 6836 7.592885 AGTAGATATTACAGCGGGTAAAAGA 57.407 36.000 7.87 0.00 44.70 2.52
2874 6837 9.754382 TTAAGTAGATATTACAGCGGGTAAAAG 57.246 33.333 7.87 0.00 44.70 2.27
2876 6839 9.533253 GTTTAAGTAGATATTACAGCGGGTAAA 57.467 33.333 7.87 0.45 44.70 2.01
2877 6840 8.694540 TGTTTAAGTAGATATTACAGCGGGTAA 58.305 33.333 6.50 6.50 45.55 2.85
2878 6841 8.236585 TGTTTAAGTAGATATTACAGCGGGTA 57.763 34.615 0.00 0.00 0.00 3.69
2879 6842 7.116075 TGTTTAAGTAGATATTACAGCGGGT 57.884 36.000 0.00 0.00 0.00 5.28
2880 6843 7.117812 CCATGTTTAAGTAGATATTACAGCGGG 59.882 40.741 0.00 0.00 0.00 6.13
2881 6844 7.656137 ACCATGTTTAAGTAGATATTACAGCGG 59.344 37.037 0.00 0.00 0.00 5.52
2882 6845 8.487970 CACCATGTTTAAGTAGATATTACAGCG 58.512 37.037 0.00 0.00 0.00 5.18
2883 6846 8.283291 GCACCATGTTTAAGTAGATATTACAGC 58.717 37.037 0.00 0.00 0.00 4.40
2884 6847 9.547753 AGCACCATGTTTAAGTAGATATTACAG 57.452 33.333 0.00 0.00 0.00 2.74
2885 6848 9.542462 GAGCACCATGTTTAAGTAGATATTACA 57.458 33.333 0.00 0.00 0.00 2.41
2886 6849 9.542462 TGAGCACCATGTTTAAGTAGATATTAC 57.458 33.333 0.00 0.00 0.00 1.89
2888 6851 8.893727 GTTGAGCACCATGTTTAAGTAGATATT 58.106 33.333 0.00 0.00 0.00 1.28
2889 6852 7.224753 CGTTGAGCACCATGTTTAAGTAGATAT 59.775 37.037 0.00 0.00 0.00 1.63
2890 6853 6.533723 CGTTGAGCACCATGTTTAAGTAGATA 59.466 38.462 0.00 0.00 0.00 1.98
2891 6854 5.351465 CGTTGAGCACCATGTTTAAGTAGAT 59.649 40.000 0.00 0.00 0.00 1.98
2892 6855 4.688879 CGTTGAGCACCATGTTTAAGTAGA 59.311 41.667 0.00 0.00 0.00 2.59
2893 6856 4.957971 CGTTGAGCACCATGTTTAAGTAG 58.042 43.478 0.00 0.00 0.00 2.57
2895 6858 3.896648 CGTTGAGCACCATGTTTAAGT 57.103 42.857 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.