Multiple sequence alignment - TraesCS3B01G350100

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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 TraesCS3B01G350100 chr3B 100.000 6697 0 0 1 6697 560115012 560121708 0.000000e+00 12368.0
1 TraesCS3B01G350100 chr3B 84.615 273 40 2 6336 6607 823775618 823775889 3.080000e-68 270.0
2 TraesCS3B01G350100 chr3B 80.226 177 26 6 4174 4348 572799468 572799299 2.540000e-24 124.0
3 TraesCS3B01G350100 chr3D 95.990 3990 81 26 2385 6334 428466962 428470912 0.000000e+00 6408.0
4 TraesCS3B01G350100 chr3D 97.692 1733 25 3 573 2291 428465232 428466963 0.000000e+00 2964.0
5 TraesCS3B01G350100 chr3D 87.967 615 36 13 1373 1984 548524712 548525291 0.000000e+00 691.0
6 TraesCS3B01G350100 chr3D 98.165 327 6 0 1 327 428464911 428465237 7.530000e-159 571.0
7 TraesCS3B01G350100 chr3D 98.374 246 4 0 327 572 268942933 268942688 3.710000e-117 433.0
8 TraesCS3B01G350100 chr3D 76.640 381 56 10 6345 6697 428471551 428471926 5.340000e-41 180.0
9 TraesCS3B01G350100 chr3D 79.532 171 29 4 4180 4348 437682177 437682011 4.240000e-22 117.0
10 TraesCS3B01G350100 chr3A 94.305 3758 135 33 2385 6080 557260555 557256815 0.000000e+00 5681.0
11 TraesCS3B01G350100 chr3A 95.439 1732 53 8 573 2291 557262272 557260554 0.000000e+00 2737.0
12 TraesCS3B01G350100 chr3A 91.867 332 19 4 1 327 557262595 557262267 2.200000e-124 457.0
13 TraesCS3B01G350100 chr3A 98.780 246 3 0 327 572 724741077 724741322 7.970000e-119 438.0
14 TraesCS3B01G350100 chr3A 87.179 117 12 2 6134 6250 557256814 557256701 5.450000e-26 130.0
15 TraesCS3B01G350100 chr3A 82.051 156 22 4 4197 4348 575614577 575614424 1.960000e-25 128.0
16 TraesCS3B01G350100 chr5D 86.407 1567 154 26 749 2291 410559239 410560770 0.000000e+00 1659.0
17 TraesCS3B01G350100 chr5D 92.230 592 28 6 1395 1984 493821226 493820651 0.000000e+00 822.0
18 TraesCS3B01G350100 chr5D 89.338 544 30 14 2458 2995 410560964 410561485 0.000000e+00 658.0
19 TraesCS3B01G350100 chr5D 83.764 542 71 11 4581 5110 30428567 30428031 1.300000e-136 497.0
20 TraesCS3B01G350100 chr5D 91.544 272 17 4 2979 3244 410561499 410561770 2.950000e-98 370.0
21 TraesCS3B01G350100 chr5D 74.570 814 151 26 1513 2281 30431297 30430495 8.440000e-79 305.0
22 TraesCS3B01G350100 chr5D 82.133 375 46 14 2401 2774 30430473 30430119 1.090000e-77 302.0
23 TraesCS3B01G350100 chr5D 83.077 195 29 4 3720 3910 30429306 30429112 2.480000e-39 174.0
24 TraesCS3B01G350100 chr6B 88.369 748 61 16 4373 5118 710649543 710648820 0.000000e+00 876.0
25 TraesCS3B01G350100 chr6B 84.924 723 53 32 2895 3568 710650786 710650071 0.000000e+00 680.0
26 TraesCS3B01G350100 chr6B 98.374 246 4 0 327 572 502312962 502312717 3.710000e-117 433.0
27 TraesCS3B01G350100 chr6B 97.984 248 5 0 325 572 502314519 502314272 1.330000e-116 431.0
28 TraesCS3B01G350100 chr6B 99.038 104 1 0 2286 2389 718346809 718346912 3.190000e-43 187.0
29 TraesCS3B01G350100 chr6B 95.726 117 1 4 2283 2395 424080495 424080611 1.150000e-42 185.0
30 TraesCS3B01G350100 chr6B 95.726 117 1 4 2283 2395 424303208 424303324 1.150000e-42 185.0
31 TraesCS3B01G350100 chr6A 88.196 754 62 15 4373 5123 612116221 612115492 0.000000e+00 874.0
32 TraesCS3B01G350100 chr6A 84.963 818 64 34 2895 3660 612117494 612116684 0.000000e+00 774.0
33 TraesCS3B01G350100 chr6A 94.915 118 3 2 2287 2404 315625263 315625377 1.480000e-41 182.0
34 TraesCS3B01G350100 chr6D 87.073 673 63 11 4373 5044 465983676 465983027 0.000000e+00 739.0
35 TraesCS3B01G350100 chr6D 87.819 509 42 10 2895 3388 465984713 465984210 4.500000e-161 579.0
36 TraesCS3B01G350100 chr6D 87.898 314 29 7 3853 4164 465983979 465983673 1.780000e-95 361.0
37 TraesCS3B01G350100 chr6D 81.609 174 24 3 4161 4334 459925973 459925808 3.260000e-28 137.0
38 TraesCS3B01G350100 chr5B 80.183 656 112 11 4468 5110 22817669 22817019 6.080000e-130 475.0
39 TraesCS3B01G350100 chr5B 80.183 656 110 10 4468 5110 22510825 22510177 2.190000e-129 473.0
40 TraesCS3B01G350100 chr5B 98.374 246 4 0 327 572 291075370 291075615 3.710000e-117 433.0
41 TraesCS3B01G350100 chr5B 97.619 252 5 1 321 572 157392980 157392730 1.330000e-116 431.0
42 TraesCS3B01G350100 chr5B 96.429 252 8 1 327 578 322909206 322909456 1.340000e-111 414.0
43 TraesCS3B01G350100 chr5B 82.952 393 54 6 2385 2774 22512641 22512259 6.430000e-90 342.0
44 TraesCS3B01G350100 chr5B 82.785 395 54 7 2385 2776 22819524 22819141 2.310000e-89 340.0
45 TraesCS3B01G350100 chr5B 76.719 640 108 21 1679 2290 22820146 22819520 1.080000e-82 318.0
46 TraesCS3B01G350100 chr5B 75.472 636 114 22 1683 2290 22513258 22512637 8.560000e-69 272.0
47 TraesCS3B01G350100 chr5B 86.585 164 19 3 3749 3910 22511397 22511235 1.920000e-40 178.0
48 TraesCS3B01G350100 chr5B 86.897 145 17 2 3749 3892 22818303 22818160 1.930000e-35 161.0
49 TraesCS3B01G350100 chr5B 81.871 171 31 0 4163 4333 515400698 515400868 1.950000e-30 145.0
50 TraesCS3B01G350100 chr4B 98.374 246 4 0 327 572 73279727 73279972 3.710000e-117 433.0
51 TraesCS3B01G350100 chr4B 99.038 104 1 0 2285 2388 538218745 538218848 3.190000e-43 187.0
52 TraesCS3B01G350100 chr4B 89.796 49 3 2 4341 4388 418510758 418510711 2.020000e-05 62.1
53 TraesCS3B01G350100 chr1B 98.374 246 4 0 327 572 57105792 57105547 3.710000e-117 433.0
54 TraesCS3B01G350100 chr1B 84.615 273 40 2 6336 6607 12756871 12757142 3.080000e-68 270.0
55 TraesCS3B01G350100 chr1B 93.023 43 2 1 4341 4382 410815267 410815309 2.020000e-05 62.1
56 TraesCS3B01G350100 chr5A 85.348 273 38 2 6336 6607 525151352 525151623 1.420000e-71 281.0
57 TraesCS3B01G350100 chr5A 84.559 272 40 2 6337 6607 529096929 529097199 1.110000e-67 268.0
58 TraesCS3B01G350100 chr5A 83.908 174 25 2 4163 4336 540276879 540277049 5.370000e-36 163.0
59 TraesCS3B01G350100 chrUn 84.982 273 39 2 6336 6607 17264493 17264764 6.620000e-70 276.0
60 TraesCS3B01G350100 chr7D 84.615 273 41 1 6335 6607 595688167 595687896 3.080000e-68 270.0
61 TraesCS3B01G350100 chr7A 84.615 273 40 2 6336 6607 721584627 721584356 3.080000e-68 270.0
62 TraesCS3B01G350100 chr7A 84.615 273 40 2 6336 6607 734933872 734933601 3.080000e-68 270.0
63 TraesCS3B01G350100 chr1A 84.307 274 41 2 6335 6607 58747646 58747918 3.980000e-67 267.0
64 TraesCS3B01G350100 chr1A 92.683 123 6 3 2278 2398 208637548 208637669 2.480000e-39 174.0
65 TraesCS3B01G350100 chr2B 98.165 109 1 1 2285 2392 397939476 397939368 8.870000e-44 189.0
66 TraesCS3B01G350100 chr2B 91.667 48 1 3 4341 4386 570832701 570832655 5.610000e-06 63.9
67 TraesCS3B01G350100 chr2B 93.023 43 2 1 4341 4382 442538019 442537977 2.020000e-05 62.1
68 TraesCS3B01G350100 chr2A 99.048 105 1 0 2289 2393 92494425 92494529 8.870000e-44 189.0
69 TraesCS3B01G350100 chr2A 81.595 163 26 4 4174 4335 692760454 692760295 1.520000e-26 132.0
70 TraesCS3B01G350100 chr7B 99.038 104 1 0 2289 2392 421056870 421056973 3.190000e-43 187.0
71 TraesCS3B01G350100 chr2D 90.000 50 2 3 4341 4389 156370267 156370220 2.020000e-05 62.1
72 TraesCS3B01G350100 chr4D 88.235 51 3 3 4341 4388 164881422 164881472 2.610000e-04 58.4
73 TraesCS3B01G350100 chr1D 85.714 56 5 2 4341 4393 38912824 38912769 1.000000e-03 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 TraesCS3B01G350100 chr3B 560115012 560121708 6696 False 12368.000000 12368 100.000000 1 6697 1 chr3B.!!$F1 6696
1 TraesCS3B01G350100 chr3D 428464911 428471926 7015 False 2530.750000 6408 92.121750 1 6697 4 chr3D.!!$F2 6696
2 TraesCS3B01G350100 chr3D 548524712 548525291 579 False 691.000000 691 87.967000 1373 1984 1 chr3D.!!$F1 611
3 TraesCS3B01G350100 chr3A 557256701 557262595 5894 True 2251.250000 5681 92.197500 1 6250 4 chr3A.!!$R2 6249
4 TraesCS3B01G350100 chr5D 410559239 410561770 2531 False 895.666667 1659 89.096333 749 3244 3 chr5D.!!$F1 2495
5 TraesCS3B01G350100 chr5D 493820651 493821226 575 True 822.000000 822 92.230000 1395 1984 1 chr5D.!!$R1 589
6 TraesCS3B01G350100 chr5D 30428031 30431297 3266 True 319.500000 497 80.886000 1513 5110 4 chr5D.!!$R2 3597
7 TraesCS3B01G350100 chr6B 710648820 710650786 1966 True 778.000000 876 86.646500 2895 5118 2 chr6B.!!$R2 2223
8 TraesCS3B01G350100 chr6B 502312717 502314519 1802 True 432.000000 433 98.179000 325 572 2 chr6B.!!$R1 247
9 TraesCS3B01G350100 chr6A 612115492 612117494 2002 True 824.000000 874 86.579500 2895 5123 2 chr6A.!!$R1 2228
10 TraesCS3B01G350100 chr6D 465983027 465984713 1686 True 559.666667 739 87.596667 2895 5044 3 chr6D.!!$R2 2149
11 TraesCS3B01G350100 chr5B 22817019 22820146 3127 True 323.500000 475 81.646000 1679 5110 4 chr5B.!!$R3 3431
12 TraesCS3B01G350100 chr5B 22510177 22513258 3081 True 316.250000 473 81.298000 1683 5110 4 chr5B.!!$R2 3427

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
565 2126 2.430610 CCCTCCTTCTAGCAGCGCT 61.431 63.158 2.64 2.64 43.41 5.92 F
1292 2871 0.536260 TTAATGCAGGGCCACATTGC 59.464 50.000 26.20 18.75 37.11 3.56 F
2304 3951 1.502039 ACATATACTCCCTCCGTCCCA 59.498 52.381 0.00 0.00 0.00 4.37 F
2307 3954 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44 F
2313 3960 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16 F
2384 4031 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85 F
4425 6486 3.888323 TGCTGGAAGTAACATTGCTTTGA 59.112 39.130 0.00 0.00 33.17 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 3937 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.0 0.00 3.85 R
2367 4014 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.0 0.00 2.44 R
4054 6045 0.788391 GTCTCGGTAACCAACAAGCG 59.212 55.000 0.00 0.0 37.92 4.68 R
4202 6262 3.883830 TGCAAAGCTTGACTTTTGGAA 57.116 38.095 0.00 0.0 46.73 3.53 R
4342 6403 6.716628 CCATTCCACAATGTAGTGCCTATAAT 59.283 38.462 0.00 0.0 38.22 1.28 R
4611 6760 1.346395 AGCGAACACCCTGTGACAATA 59.654 47.619 0.49 0.0 36.96 1.90 R
6383 9185 0.043485 TCATAGGGGTAGGGTGTGCA 59.957 55.000 0.00 0.0 0.00 4.57 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
82 85 5.913137 TTGAATAATGCCAATCGGAAGTT 57.087 34.783 0.00 0.00 0.00 2.66
192 198 5.627182 AATTGTCAGGAGTAGATGATGCT 57.373 39.130 0.00 0.00 0.00 3.79
321 327 3.809279 CCAAGCAAACAAAAATCTGGGTC 59.191 43.478 0.00 0.00 0.00 4.46
322 328 4.440880 CAAGCAAACAAAAATCTGGGTCA 58.559 39.130 0.00 0.00 0.00 4.02
323 329 4.961438 AGCAAACAAAAATCTGGGTCAT 57.039 36.364 0.00 0.00 0.00 3.06
388 1949 9.739737 TCTTAGGGTTAATTAGAGATAAGGGTT 57.260 33.333 8.51 0.00 0.00 4.11
565 2126 2.430610 CCCTCCTTCTAGCAGCGCT 61.431 63.158 2.64 2.64 43.41 5.92
671 2232 4.332828 GAACCAAATGCACCCTTAGTACT 58.667 43.478 0.00 0.00 0.00 2.73
745 2306 7.947782 AATATTAATCTGGGGTGGAGAGTTA 57.052 36.000 0.00 0.00 0.00 2.24
862 2424 6.047231 GGTTTACGATGTCTATGCCTACTTT 58.953 40.000 0.00 0.00 0.00 2.66
1181 2746 5.398169 TGCAAATGCTAATTGGACTAAACG 58.602 37.500 6.97 0.00 42.66 3.60
1193 2758 5.142061 TGGACTAAACGCTCTGTGAAATA 57.858 39.130 0.00 0.00 0.00 1.40
1262 2841 4.642429 AGTATTAGCTCCAAATAAGCCCG 58.358 43.478 0.00 0.00 40.75 6.13
1292 2871 0.536260 TTAATGCAGGGCCACATTGC 59.464 50.000 26.20 18.75 37.11 3.56
1371 2951 5.649557 TCAACCACATTTTCAGTTTGTCAG 58.350 37.500 0.00 0.00 0.00 3.51
1374 2954 5.410067 ACCACATTTTCAGTTTGTCAGTTG 58.590 37.500 0.00 0.00 0.00 3.16
1827 3433 5.124138 ACTGTAAGGTTAGACATCTGAGACG 59.876 44.000 0.00 0.00 39.30 4.18
1845 3451 5.943416 TGAGACGTTATTCATTTTGATGGGT 59.057 36.000 0.00 0.00 0.00 4.51
2285 3932 6.910536 ATCTAGTGCACTGCAGTATTTTAC 57.089 37.500 29.57 13.53 42.51 2.01
2290 3937 9.476202 CTAGTGCACTGCAGTATTTTACATATA 57.524 33.333 29.57 1.20 42.51 0.86
2291 3938 8.142994 AGTGCACTGCAGTATTTTACATATAC 57.857 34.615 20.97 5.16 40.73 1.47
2292 3939 7.987458 AGTGCACTGCAGTATTTTACATATACT 59.013 33.333 20.97 7.19 40.73 2.12
2293 3940 8.276325 GTGCACTGCAGTATTTTACATATACTC 58.724 37.037 21.20 0.00 40.08 2.59
2294 3941 7.441157 TGCACTGCAGTATTTTACATATACTCC 59.559 37.037 21.20 0.00 36.84 3.85
2295 3942 7.095187 GCACTGCAGTATTTTACATATACTCCC 60.095 40.741 21.20 0.00 36.84 4.30
2296 3943 8.150945 CACTGCAGTATTTTACATATACTCCCT 58.849 37.037 21.20 0.00 36.84 4.20
2297 3944 8.368668 ACTGCAGTATTTTACATATACTCCCTC 58.631 37.037 20.16 0.00 36.84 4.30
2298 3945 7.676947 TGCAGTATTTTACATATACTCCCTCC 58.323 38.462 0.00 0.00 36.84 4.30
2299 3946 6.812160 GCAGTATTTTACATATACTCCCTCCG 59.188 42.308 0.00 0.00 36.84 4.63
2300 3947 7.525029 GCAGTATTTTACATATACTCCCTCCGT 60.525 40.741 0.00 0.00 36.84 4.69
2301 3948 8.027771 CAGTATTTTACATATACTCCCTCCGTC 58.972 40.741 0.00 0.00 36.84 4.79
2302 3949 5.796424 TTTTACATATACTCCCTCCGTCC 57.204 43.478 0.00 0.00 0.00 4.79
2303 3950 2.305858 ACATATACTCCCTCCGTCCC 57.694 55.000 0.00 0.00 0.00 4.46
2304 3951 1.502039 ACATATACTCCCTCCGTCCCA 59.498 52.381 0.00 0.00 0.00 4.37
2305 3952 2.090943 ACATATACTCCCTCCGTCCCAA 60.091 50.000 0.00 0.00 0.00 4.12
2306 3953 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2307 3954 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2308 3955 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2309 3956 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2310 3957 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2311 3958 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2312 3959 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2313 3960 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2314 3961 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2315 3962 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2316 3963 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2317 3964 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
2318 3965 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
2319 3966 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2320 3967 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2321 3968 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2322 3969 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
2323 3970 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
2324 3971 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2325 3972 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2326 3973 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2327 3974 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
2328 3975 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
2331 3978 8.535690 AATAAGTGTCTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
2332 3979 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
2333 3980 5.774630 AGTGTCTCAACTTTGTACTAGCTC 58.225 41.667 0.00 0.00 0.00 4.09
2334 3981 5.536916 AGTGTCTCAACTTTGTACTAGCTCT 59.463 40.000 0.00 0.00 0.00 4.09
2335 3982 6.715718 AGTGTCTCAACTTTGTACTAGCTCTA 59.284 38.462 0.00 0.00 0.00 2.43
2336 3983 7.024768 GTGTCTCAACTTTGTACTAGCTCTAG 58.975 42.308 0.00 2.55 39.04 2.43
2338 3985 7.881751 TGTCTCAACTTTGTACTAGCTCTAGTA 59.118 37.037 11.59 11.59 43.98 1.82
2362 4009 7.801716 ACAAATTTGTACTAAGCTCAAGACA 57.198 32.000 22.10 0.00 40.16 3.41
2363 4010 7.639945 ACAAATTTGTACTAAGCTCAAGACAC 58.360 34.615 22.10 2.09 40.16 3.67
2364 4011 7.499232 ACAAATTTGTACTAAGCTCAAGACACT 59.501 33.333 22.10 0.00 40.16 3.55
2365 4012 8.345565 CAAATTTGTACTAAGCTCAAGACACTT 58.654 33.333 10.15 0.00 0.00 3.16
2366 4013 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
2367 4014 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
2368 4015 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
2369 4016 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
2370 4017 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
2371 4018 8.988934 TGTACTAAGCTCAAGACACTTATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
2372 4019 7.440523 ACTAAGCTCAAGACACTTATTTTGG 57.559 36.000 3.19 0.00 0.00 3.28
2373 4020 5.712152 AAGCTCAAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
2374 4021 4.985538 AGCTCAAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
2375 4022 4.762251 AGCTCAAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
2376 4023 4.378459 GCTCAAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
2377 4024 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
2378 4025 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
2379 4026 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
2380 4027 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2381 4028 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2382 4029 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2383 4030 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2384 4031 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
4054 6045 9.419297 TGTGTGACACTTTAATCAAGTAGATAC 57.581 33.333 17.47 0.00 44.60 2.24
4200 6260 6.441274 CACAATGGAGCGCATATAGATTTTT 58.559 36.000 11.47 0.00 0.00 1.94
4253 6314 8.485578 TGACCAACTTTGTAGGGAAAAATATT 57.514 30.769 0.00 0.00 0.00 1.28
4425 6486 3.888323 TGCTGGAAGTAACATTGCTTTGA 59.112 39.130 0.00 0.00 33.17 2.69
4611 6760 8.862325 TTATGATTGTAGGACTTTGTGAATGT 57.138 30.769 0.00 0.00 0.00 2.71
4785 6936 1.801178 GGCTGCAGTTACTGACAGTTC 59.199 52.381 25.43 18.44 37.66 3.01
5169 7332 6.106003 TGGGCTATATCTATGTGTAATTGCG 58.894 40.000 0.00 0.00 0.00 4.85
5180 7343 5.431420 TGTGTAATTGCGTGACTTGAAAT 57.569 34.783 0.00 0.00 0.00 2.17
5190 7353 5.005682 TGCGTGACTTGAAATTCTGATATCG 59.994 40.000 0.00 0.00 0.00 2.92
5236 7399 0.465278 GCAGGGAGATGAGGAAAGCC 60.465 60.000 0.00 0.00 0.00 4.35
5395 7561 0.960861 TGAGCTCAGACACGGATCGT 60.961 55.000 13.74 0.00 42.36 3.73
5414 7580 7.628327 CGGATCGTTTTGATTTAACGTAAGTAC 59.372 37.037 7.83 0.00 45.18 2.73
5486 7653 5.335976 GGATCGCTTTTGTTCTTCCAGAATT 60.336 40.000 0.00 0.00 36.50 2.17
5516 7683 1.500736 CCCTCCTCCATGGGCTTAAAT 59.499 52.381 13.02 0.00 36.61 1.40
5666 7833 0.676782 GGCGCCTCAGTTACAACCAT 60.677 55.000 22.15 0.00 0.00 3.55
5718 7885 1.595382 GCAACGCCTCGGAGCATAT 60.595 57.895 0.00 0.00 32.73 1.78
5755 7923 0.040958 GCTTCTGTGCGACCACTTTG 60.041 55.000 0.00 0.00 42.54 2.77
5756 7924 1.299541 CTTCTGTGCGACCACTTTGT 58.700 50.000 0.00 0.00 42.54 2.83
5795 7964 3.710722 CTCCACGCCAGGAAGCCT 61.711 66.667 0.00 0.00 37.20 4.58
5816 7985 1.556911 GGGATGTTCAGAGAGAAGCCA 59.443 52.381 0.00 0.00 36.78 4.75
5869 8038 2.125188 GCCTCTGCAGAGCACTCC 60.125 66.667 34.09 16.80 40.75 3.85
5875 8044 2.241479 CTGCAGAGCACTCCAGGGAG 62.241 65.000 8.42 13.74 46.91 4.30
5996 8165 4.632538 AAACGAAGGGAGAAAACAACAG 57.367 40.909 0.00 0.00 0.00 3.16
6005 8174 4.875536 GGGAGAAAACAACAGCAACAAAAT 59.124 37.500 0.00 0.00 0.00 1.82
6023 8192 8.764287 CAACAAAATGGACATTTCCTTTCTTAC 58.236 33.333 10.40 0.00 43.31 2.34
6050 8219 4.385825 TGGGTTATATTGAATGCTCCGTC 58.614 43.478 0.00 0.00 0.00 4.79
6096 8265 2.536673 GGGCGTTGGTCGTCGTTTT 61.537 57.895 0.00 0.00 45.92 2.43
6097 8266 1.220817 GGGCGTTGGTCGTCGTTTTA 61.221 55.000 0.00 0.00 45.92 1.52
6098 8267 0.792031 GGCGTTGGTCGTCGTTTTAT 59.208 50.000 0.00 0.00 42.13 1.40
6099 8268 1.195222 GGCGTTGGTCGTCGTTTTATT 59.805 47.619 0.00 0.00 42.13 1.40
6109 8278 5.844396 GGTCGTCGTTTTATTTTCTCTTGTG 59.156 40.000 0.00 0.00 0.00 3.33
6133 8302 0.107508 CTGGATGGTCGCTTGGTCAT 60.108 55.000 0.00 0.00 0.00 3.06
6135 8304 0.392998 GGATGGTCGCTTGGTCATGT 60.393 55.000 0.00 0.00 0.00 3.21
6142 8311 1.001974 TCGCTTGGTCATGTTGCTACT 59.998 47.619 0.00 0.00 0.00 2.57
6148 8317 2.158827 TGGTCATGTTGCTACTGTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
6210 8379 4.022068 TGCTTAACCAAGAGGAAATGCAAG 60.022 41.667 0.00 0.00 38.69 4.01
6212 8381 5.452078 TTAACCAAGAGGAAATGCAAGTG 57.548 39.130 0.00 0.00 38.69 3.16
6278 8452 2.286935 TGAAAAGGAGGATAGCCCCT 57.713 50.000 0.00 0.00 39.77 4.79
6285 8459 2.184565 AGGAGGATAGCCCCTGGAAATA 59.815 50.000 6.28 0.00 36.49 1.40
6302 8476 8.417884 CCTGGAAATAAAAGTTGTGGAGTTTTA 58.582 33.333 0.00 2.39 43.60 1.52
6315 8489 8.377681 GTTGTGGAGTTTTAAAGTTAACAAAGC 58.622 33.333 8.61 2.33 0.00 3.51
6326 8500 4.718961 AGTTAACAAAGCCATCACTCACT 58.281 39.130 8.61 0.00 0.00 3.41
6327 8501 5.133221 AGTTAACAAAGCCATCACTCACTT 58.867 37.500 8.61 0.00 0.00 3.16
6334 8508 1.300971 CCATCACTCACTTGTGCCGG 61.301 60.000 0.00 0.00 37.81 6.13
6336 8510 2.395988 ATCACTCACTTGTGCCGGCA 62.396 55.000 29.03 29.03 37.81 5.69
6337 8511 2.186160 CACTCACTTGTGCCGGCAA 61.186 57.895 34.66 16.92 0.00 4.52
6342 8516 3.289834 CTTGTGCCGGCAAGTGCT 61.290 61.111 34.66 0.00 40.52 4.40
6343 8517 3.259425 CTTGTGCCGGCAAGTGCTC 62.259 63.158 34.66 18.73 40.52 4.26
6349 9151 1.097547 GCCGGCAAGTGCTCATACAT 61.098 55.000 24.80 0.00 41.70 2.29
6351 9153 1.867233 CCGGCAAGTGCTCATACATAC 59.133 52.381 2.85 0.00 41.70 2.39
6353 9155 1.261619 GGCAAGTGCTCATACATACGC 59.738 52.381 2.85 0.00 41.70 4.42
6358 9160 5.151389 CAAGTGCTCATACATACGCGTATA 58.849 41.667 29.79 17.16 30.83 1.47
6361 9163 4.320164 GTGCTCATACATACGCGTATACAC 59.680 45.833 29.79 21.88 30.83 2.90
6363 9165 4.787083 GCTCATACATACGCGTATACACTC 59.213 45.833 29.79 12.89 30.83 3.51
6365 9167 6.490566 TCATACATACGCGTATACACTCAT 57.509 37.500 29.79 14.02 30.83 2.90
6368 9170 3.819337 ACATACGCGTATACACTCATCCT 59.181 43.478 29.79 2.97 0.00 3.24
6375 9177 6.093404 CGCGTATACACTCATCCTTATGAAT 58.907 40.000 0.00 0.00 41.57 2.57
6376 9178 7.094506 ACGCGTATACACTCATCCTTATGAATA 60.095 37.037 11.67 0.00 41.57 1.75
6397 9199 1.378514 CACATGCACACCCTACCCC 60.379 63.158 0.00 0.00 0.00 4.95
6399 9201 0.252974 ACATGCACACCCTACCCCTA 60.253 55.000 0.00 0.00 0.00 3.53
6407 9209 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
6411 9213 1.341531 CTACCCCTATGAGCACCTTCG 59.658 57.143 0.00 0.00 0.00 3.79
6421 9223 1.132262 GAGCACCTTCGAGAGACTGAG 59.868 57.143 0.00 0.00 41.84 3.35
6422 9224 0.457681 GCACCTTCGAGAGACTGAGC 60.458 60.000 0.00 0.00 41.84 4.26
6423 9225 0.172352 CACCTTCGAGAGACTGAGCC 59.828 60.000 0.00 0.00 41.84 4.70
6424 9226 1.309499 ACCTTCGAGAGACTGAGCCG 61.309 60.000 0.00 0.00 41.84 5.52
6432 9234 0.676184 GAGACTGAGCCGGCATATCA 59.324 55.000 31.54 22.44 0.00 2.15
6460 9262 7.482169 TGAGATTTATGAAGTCACTGTAGGT 57.518 36.000 0.00 0.00 0.00 3.08
6461 9263 7.323420 TGAGATTTATGAAGTCACTGTAGGTG 58.677 38.462 0.00 0.00 46.60 4.00
6465 9267 2.047061 TGAAGTCACTGTAGGTGCCTT 58.953 47.619 0.00 0.00 45.26 4.35
6468 9270 1.768870 AGTCACTGTAGGTGCCTTGTT 59.231 47.619 0.00 0.00 44.98 2.83
6471 9273 1.873591 CACTGTAGGTGCCTTGTTGTC 59.126 52.381 0.00 0.00 39.22 3.18
6474 9276 1.346395 TGTAGGTGCCTTGTTGTCGAT 59.654 47.619 0.00 0.00 0.00 3.59
6475 9277 2.563620 TGTAGGTGCCTTGTTGTCGATA 59.436 45.455 0.00 0.00 0.00 2.92
6481 9283 2.037902 TGCCTTGTTGTCGATAGGAACA 59.962 45.455 0.00 0.00 37.17 3.18
6483 9285 3.063997 GCCTTGTTGTCGATAGGAACATG 59.936 47.826 0.00 0.00 38.21 3.21
6486 9288 4.801330 TGTTGTCGATAGGAACATGTCT 57.199 40.909 0.00 0.00 35.07 3.41
6488 9290 6.275494 TGTTGTCGATAGGAACATGTCTTA 57.725 37.500 0.00 0.00 35.07 2.10
6492 9294 5.362717 TGTCGATAGGAACATGTCTTACCAT 59.637 40.000 0.00 0.00 0.00 3.55
6498 9300 9.125026 GATAGGAACATGTCTTACCATTGAAAT 57.875 33.333 0.00 0.00 0.00 2.17
6499 9301 7.396540 AGGAACATGTCTTACCATTGAAATC 57.603 36.000 0.00 0.00 0.00 2.17
6505 9307 8.956426 ACATGTCTTACCATTGAAATCGTAATT 58.044 29.630 0.00 0.00 0.00 1.40
6507 9309 7.247728 TGTCTTACCATTGAAATCGTAATTGC 58.752 34.615 0.00 0.00 0.00 3.56
6510 9312 4.997565 ACCATTGAAATCGTAATTGCTGG 58.002 39.130 0.00 0.00 0.00 4.85
6516 9318 6.507958 TGAAATCGTAATTGCTGGAAATCA 57.492 33.333 0.00 0.00 0.00 2.57
6554 9356 1.901591 AATGTGAGCACCAGGACTTG 58.098 50.000 0.00 0.00 0.00 3.16
6556 9358 0.836606 TGTGAGCACCAGGACTTGAA 59.163 50.000 0.00 0.00 0.00 2.69
6559 9361 0.951040 GAGCACCAGGACTTGAACCG 60.951 60.000 0.00 0.00 0.00 4.44
6560 9362 1.227853 GCACCAGGACTTGAACCGT 60.228 57.895 0.00 0.00 0.00 4.83
6562 9364 0.884704 CACCAGGACTTGAACCGTGG 60.885 60.000 0.00 0.00 34.39 4.94
6563 9365 1.342672 ACCAGGACTTGAACCGTGGT 61.343 55.000 0.00 0.00 35.63 4.16
6565 9367 0.884704 CAGGACTTGAACCGTGGTGG 60.885 60.000 0.00 0.00 46.41 4.61
6566 9368 1.599797 GGACTTGAACCGTGGTGGG 60.600 63.158 0.00 0.00 44.64 4.61
6567 9369 2.203294 ACTTGAACCGTGGTGGGC 60.203 61.111 0.00 0.00 44.64 5.36
6568 9370 2.113139 CTTGAACCGTGGTGGGCT 59.887 61.111 0.00 0.00 44.64 5.19
6569 9371 2.203280 TTGAACCGTGGTGGGCTG 60.203 61.111 0.00 0.00 44.64 4.85
6590 9392 4.668636 TGGGGTTACCATTGTCCTTTTAG 58.331 43.478 2.98 0.00 46.80 1.85
6592 9394 4.341487 GGGTTACCATTGTCCTTTTAGCT 58.659 43.478 2.98 0.00 36.50 3.32
6600 9402 6.152831 ACCATTGTCCTTTTAGCTATTCAACC 59.847 38.462 0.00 0.00 0.00 3.77
6609 9411 7.175990 CCTTTTAGCTATTCAACCACAGGTAAA 59.824 37.037 0.00 0.00 38.50 2.01
6624 9452 8.387813 ACCACAGGTAAATTTAATGGAGTTCTA 58.612 33.333 18.77 0.00 32.11 2.10
6646 9474 7.402862 TCTATTTAAGGAAAACCAAGGGAGAG 58.597 38.462 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 56 6.942005 TCCGATTGGCATTATTCAATCTGTAT 59.058 34.615 12.30 0.00 44.04 2.29
321 327 5.529791 CCCATTACGTACTCTAACAGGATG 58.470 45.833 0.00 0.00 46.00 3.51
322 328 4.038883 GCCCATTACGTACTCTAACAGGAT 59.961 45.833 0.00 0.00 0.00 3.24
323 329 3.382546 GCCCATTACGTACTCTAACAGGA 59.617 47.826 0.00 0.00 0.00 3.86
388 1949 0.771127 ACTTGACCCCTAAGCAAGCA 59.229 50.000 0.00 0.00 41.97 3.91
544 2105 2.107953 CTGCTAGAAGGAGGGCGC 59.892 66.667 0.00 0.00 29.18 6.53
565 2126 6.199376 TGAGAGGTGGTTAGGATGTGTTATA 58.801 40.000 0.00 0.00 0.00 0.98
671 2232 0.251608 TCCTCGTGTCCAGATGTCCA 60.252 55.000 0.00 0.00 0.00 4.02
745 2306 4.956075 ACACAGAAACAGTCTCCCAAAATT 59.044 37.500 0.00 0.00 32.70 1.82
1181 2746 4.697352 AGGTCACAATGTATTTCACAGAGC 59.303 41.667 0.00 0.00 41.51 4.09
1193 2758 2.224606 CAGCTTCACAGGTCACAATGT 58.775 47.619 0.00 0.00 0.00 2.71
1262 2841 3.674410 GCCCTGCATTAAGAGCTTGTTTC 60.674 47.826 0.00 0.00 0.00 2.78
1292 2871 8.285394 AGCAACAACATATCGCTTATTAGATTG 58.715 33.333 0.00 0.00 0.00 2.67
1371 2951 6.223852 TCTACTTCTCCAGAACACATTCAAC 58.776 40.000 0.00 0.00 37.29 3.18
1374 2954 6.274157 TCTCTACTTCTCCAGAACACATTC 57.726 41.667 0.00 0.00 34.78 2.67
2285 3932 2.304221 TGGGACGGAGGGAGTATATG 57.696 55.000 0.00 0.00 0.00 1.78
2290 3937 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2291 3938 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2292 3939 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2293 3940 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2294 3941 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2295 3942 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
2296 3943 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
2297 3944 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
2298 3945 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
2299 3946 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2300 3947 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
2301 3948 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
2302 3949 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
2305 3952 8.989980 GCTAGTACAAAGTTGAGACACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
2306 3953 8.368668 AGCTAGTACAAAGTTGAGACACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
2307 3954 7.897864 AGCTAGTACAAAGTTGAGACACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
2308 3955 7.230913 AGAGCTAGTACAAAGTTGAGACACTTA 59.769 37.037 0.00 0.00 35.87 2.24
2309 3956 6.041069 AGAGCTAGTACAAAGTTGAGACACTT 59.959 38.462 0.00 0.00 38.74 3.16
2310 3957 5.536916 AGAGCTAGTACAAAGTTGAGACACT 59.463 40.000 0.00 0.00 0.00 3.55
2311 3958 5.774630 AGAGCTAGTACAAAGTTGAGACAC 58.225 41.667 0.00 0.00 0.00 3.67
2312 3959 6.715718 ACTAGAGCTAGTACAAAGTTGAGACA 59.284 38.462 8.35 0.00 43.98 3.41
2313 3960 7.148355 ACTAGAGCTAGTACAAAGTTGAGAC 57.852 40.000 8.35 0.00 43.98 3.36
2337 3984 8.770828 GTGTCTTGAGCTTAGTACAAATTTGTA 58.229 33.333 23.91 23.91 42.35 2.41
2338 3985 7.499232 AGTGTCTTGAGCTTAGTACAAATTTGT 59.501 33.333 25.99 25.99 44.86 2.83
2339 3986 7.865707 AGTGTCTTGAGCTTAGTACAAATTTG 58.134 34.615 16.67 16.67 0.00 2.32
2340 3987 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
2341 3988 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
2342 3989 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
2343 3990 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
2344 3991 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
2345 3992 8.988934 CAAAATAAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
2346 3993 8.443937 CCAAAATAAGTGTCTTGAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
2347 3994 7.606456 CCCAAAATAAGTGTCTTGAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
2348 3995 6.431234 CCCAAAATAAGTGTCTTGAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
2349 3996 6.655003 TCCCAAAATAAGTGTCTTGAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
2350 3997 6.430000 GTCCCAAAATAAGTGTCTTGAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
2351 3998 5.241728 GTCCCAAAATAAGTGTCTTGAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
2352 3999 4.762251 GTCCCAAAATAAGTGTCTTGAGCT 59.238 41.667 0.00 0.00 0.00 4.09
2353 4000 4.378459 CGTCCCAAAATAAGTGTCTTGAGC 60.378 45.833 0.00 0.00 0.00 4.26
2354 4001 4.154195 CCGTCCCAAAATAAGTGTCTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
2355 4002 4.069304 CCGTCCCAAAATAAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
2356 4003 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
2357 4004 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
2358 4005 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2359 4006 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2360 4007 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2361 4008 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2362 4009 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2363 4010 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2364 4011 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2365 4012 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2366 4013 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2367 4014 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2368 4015 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2369 4016 3.339713 AATATACTCCCTCCGTCCCAA 57.660 47.619 0.00 0.00 0.00 4.12
2370 4017 4.687262 ATAATATACTCCCTCCGTCCCA 57.313 45.455 0.00 0.00 0.00 4.37
2371 4018 4.382793 GCAATAATATACTCCCTCCGTCCC 60.383 50.000 0.00 0.00 0.00 4.46
2372 4019 4.222145 TGCAATAATATACTCCCTCCGTCC 59.778 45.833 0.00 0.00 0.00 4.79
2373 4020 5.401531 TGCAATAATATACTCCCTCCGTC 57.598 43.478 0.00 0.00 0.00 4.79
2374 4021 5.734720 CATGCAATAATATACTCCCTCCGT 58.265 41.667 0.00 0.00 0.00 4.69
2375 4022 4.572389 GCATGCAATAATATACTCCCTCCG 59.428 45.833 14.21 0.00 0.00 4.63
2376 4023 4.572389 CGCATGCAATAATATACTCCCTCC 59.428 45.833 19.57 0.00 0.00 4.30
2377 4024 4.034510 GCGCATGCAATAATATACTCCCTC 59.965 45.833 19.57 0.00 42.15 4.30
2378 4025 3.941483 GCGCATGCAATAATATACTCCCT 59.059 43.478 19.57 0.00 42.15 4.20
2379 4026 3.941483 AGCGCATGCAATAATATACTCCC 59.059 43.478 19.57 0.00 46.23 4.30
2380 4027 6.662414 TTAGCGCATGCAATAATATACTCC 57.338 37.500 19.57 0.00 46.23 3.85
2381 4028 8.136057 AGATTAGCGCATGCAATAATATACTC 57.864 34.615 19.57 9.33 46.23 2.59
2382 4029 8.498054 AAGATTAGCGCATGCAATAATATACT 57.502 30.769 19.57 11.00 46.23 2.12
2383 4030 9.214953 GAAAGATTAGCGCATGCAATAATATAC 57.785 33.333 19.57 11.44 46.23 1.47
2384 4031 9.166173 AGAAAGATTAGCGCATGCAATAATATA 57.834 29.630 19.57 0.00 46.23 0.86
4054 6045 0.788391 GTCTCGGTAACCAACAAGCG 59.212 55.000 0.00 0.00 37.92 4.68
4094 6136 8.836268 AACACCATACGTTCTCAAAAGTTATA 57.164 30.769 0.00 0.00 0.00 0.98
4095 6137 7.739498 AACACCATACGTTCTCAAAAGTTAT 57.261 32.000 0.00 0.00 0.00 1.89
4096 6138 7.556733 AAACACCATACGTTCTCAAAAGTTA 57.443 32.000 0.00 0.00 0.00 2.24
4200 6260 4.573900 TGCAAAGCTTGACTTTTGGAAAA 58.426 34.783 0.00 0.00 46.73 2.29
4201 6261 4.199432 TGCAAAGCTTGACTTTTGGAAA 57.801 36.364 0.00 0.00 46.73 3.13
4202 6262 3.883830 TGCAAAGCTTGACTTTTGGAA 57.116 38.095 0.00 0.00 46.73 3.53
4203 6263 3.883830 TTGCAAAGCTTGACTTTTGGA 57.116 38.095 0.00 0.00 46.73 3.53
4342 6403 6.716628 CCATTCCACAATGTAGTGCCTATAAT 59.283 38.462 0.00 0.00 38.22 1.28
4611 6760 1.346395 AGCGAACACCCTGTGACAATA 59.654 47.619 0.49 0.00 36.96 1.90
4785 6936 6.417635 TGCAAGTTCAAGAAAAATAAAGCTCG 59.582 34.615 0.00 0.00 0.00 5.03
5169 7332 7.525688 TCACGATATCAGAATTTCAAGTCAC 57.474 36.000 3.12 0.00 0.00 3.67
5180 7343 8.337532 CAAAAGCATGTATTCACGATATCAGAA 58.662 33.333 3.12 6.78 0.00 3.02
5190 7353 4.168760 GACCTGCAAAAGCATGTATTCAC 58.831 43.478 0.00 0.00 0.00 3.18
5371 7537 1.153958 CGTGTCTGAGCTCATCGCA 60.154 57.895 18.63 13.34 42.61 5.10
5414 7580 1.450312 GTGGTGCCAGGGAAGATCG 60.450 63.158 0.00 0.00 0.00 3.69
5516 7683 1.971505 CTATGGAGGTGAAGGCGGCA 61.972 60.000 13.08 0.00 0.00 5.69
5718 7885 2.916703 ACCGGCCTTGCATTGCAA 60.917 55.556 21.97 21.97 46.80 4.08
5795 7964 1.556911 GGCTTCTCTCTGAACATCCCA 59.443 52.381 0.00 0.00 0.00 4.37
5869 8038 1.227943 CACACACCCACACTCCCTG 60.228 63.158 0.00 0.00 0.00 4.45
5875 8044 2.113139 CCCTCCACACACCCACAC 59.887 66.667 0.00 0.00 0.00 3.82
5876 8045 2.004120 AACCCTCCACACACCCACA 61.004 57.895 0.00 0.00 0.00 4.17
6023 8192 6.147821 CGGAGCATTCAATATAACCCAAGTAG 59.852 42.308 0.00 0.00 0.00 2.57
6050 8219 2.166254 AGCCCAACACAAAACTGTTCAG 59.834 45.455 0.00 0.00 31.73 3.02
6096 8265 6.830324 CCATCCAGAATCCACAAGAGAAAATA 59.170 38.462 0.00 0.00 0.00 1.40
6097 8266 5.655532 CCATCCAGAATCCACAAGAGAAAAT 59.344 40.000 0.00 0.00 0.00 1.82
6098 8267 5.012239 CCATCCAGAATCCACAAGAGAAAA 58.988 41.667 0.00 0.00 0.00 2.29
6099 8268 4.043310 ACCATCCAGAATCCACAAGAGAAA 59.957 41.667 0.00 0.00 0.00 2.52
6109 8278 1.303309 CAAGCGACCATCCAGAATCC 58.697 55.000 0.00 0.00 0.00 3.01
6133 8302 3.275617 AAGGAACACACAGTAGCAACA 57.724 42.857 0.00 0.00 0.00 3.33
6135 8304 3.134985 TGGTAAGGAACACACAGTAGCAA 59.865 43.478 0.00 0.00 0.00 3.91
6142 8311 4.974645 ATCTTCTGGTAAGGAACACACA 57.025 40.909 0.00 0.00 0.00 3.72
6148 8317 6.271391 TGAACACCTAATCTTCTGGTAAGGAA 59.729 38.462 0.00 0.00 32.13 3.36
6212 8381 9.278734 GCAAGAGAAAATAGTAACAGTATTTGC 57.721 33.333 0.90 0.00 34.79 3.68
6285 8459 9.984190 TGTTAACTTTAAAACTCCACAACTTTT 57.016 25.926 7.22 0.00 0.00 2.27
6302 8476 5.594317 AGTGAGTGATGGCTTTGTTAACTTT 59.406 36.000 7.22 0.00 0.00 2.66
6315 8489 1.300971 CCGGCACAAGTGAGTGATGG 61.301 60.000 4.04 0.00 42.05 3.51
6326 8500 3.286751 GAGCACTTGCCGGCACAA 61.287 61.111 32.95 15.86 43.38 3.33
6327 8501 2.462125 TATGAGCACTTGCCGGCACA 62.462 55.000 32.95 23.44 43.38 4.57
6334 8508 1.071239 CGCGTATGTATGAGCACTTGC 60.071 52.381 0.00 0.00 42.49 4.01
6336 8510 2.579207 ACGCGTATGTATGAGCACTT 57.421 45.000 11.67 0.00 0.00 3.16
6337 8511 3.917329 ATACGCGTATGTATGAGCACT 57.083 42.857 29.77 2.68 33.86 4.40
6340 8514 4.720090 AGTGTATACGCGTATGTATGAGC 58.280 43.478 35.61 19.72 35.85 4.26
6342 8516 5.927954 TGAGTGTATACGCGTATGTATGA 57.072 39.130 35.61 17.13 35.85 2.15
6343 8517 5.737757 GGATGAGTGTATACGCGTATGTATG 59.262 44.000 35.61 0.00 35.85 2.39
6349 9151 5.702209 TCATAAGGATGAGTGTATACGCGTA 59.298 40.000 22.94 22.94 37.15 4.42
6351 9153 5.043189 TCATAAGGATGAGTGTATACGCG 57.957 43.478 3.53 3.53 37.15 6.01
6358 9160 9.716531 CATGTGTATATTCATAAGGATGAGTGT 57.283 33.333 0.00 0.00 43.03 3.55
6361 9163 8.663025 GTGCATGTGTATATTCATAAGGATGAG 58.337 37.037 0.00 0.00 43.03 2.90
6363 9165 8.232513 GTGTGCATGTGTATATTCATAAGGATG 58.767 37.037 0.00 0.00 0.00 3.51
6365 9167 6.710295 GGTGTGCATGTGTATATTCATAAGGA 59.290 38.462 0.00 0.00 0.00 3.36
6368 9170 6.600388 AGGGTGTGCATGTGTATATTCATAA 58.400 36.000 0.00 0.00 0.00 1.90
6375 9177 2.436542 GGGTAGGGTGTGCATGTGTATA 59.563 50.000 0.00 0.00 0.00 1.47
6376 9178 1.211949 GGGTAGGGTGTGCATGTGTAT 59.788 52.381 0.00 0.00 0.00 2.29
6379 9181 1.378514 GGGGTAGGGTGTGCATGTG 60.379 63.158 0.00 0.00 0.00 3.21
6383 9185 0.043485 TCATAGGGGTAGGGTGTGCA 59.957 55.000 0.00 0.00 0.00 4.57
6397 9199 2.948979 AGTCTCTCGAAGGTGCTCATAG 59.051 50.000 0.00 0.00 0.00 2.23
6399 9201 1.476085 CAGTCTCTCGAAGGTGCTCAT 59.524 52.381 0.00 0.00 0.00 2.90
6407 9209 1.431440 CCGGCTCAGTCTCTCGAAG 59.569 63.158 0.00 0.00 0.00 3.79
6411 9213 0.965439 ATATGCCGGCTCAGTCTCTC 59.035 55.000 29.70 0.00 0.00 3.20
6421 9223 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
6422 9224 6.820152 TCATAAATCTCAAGATGATATGCCGG 59.180 38.462 0.00 0.00 36.32 6.13
6423 9225 7.838771 TCATAAATCTCAAGATGATATGCCG 57.161 36.000 15.00 0.00 36.32 5.69
6424 9226 9.228949 ACTTCATAAATCTCAAGATGATATGCC 57.771 33.333 15.00 0.00 36.32 4.40
6432 9234 9.814899 CTACAGTGACTTCATAAATCTCAAGAT 57.185 33.333 0.00 0.00 36.07 2.40
6454 9256 0.753867 TCGACAACAAGGCACCTACA 59.246 50.000 0.00 0.00 0.00 2.74
6460 9262 2.037902 TGTTCCTATCGACAACAAGGCA 59.962 45.455 0.00 0.00 0.00 4.75
6461 9263 2.695359 TGTTCCTATCGACAACAAGGC 58.305 47.619 0.00 0.00 0.00 4.35
6465 9267 4.801330 AGACATGTTCCTATCGACAACA 57.199 40.909 0.00 0.00 34.61 3.33
6468 9270 4.707934 TGGTAAGACATGTTCCTATCGACA 59.292 41.667 0.00 0.00 0.00 4.35
6471 9273 6.280643 TCAATGGTAAGACATGTTCCTATCG 58.719 40.000 0.00 0.00 0.00 2.92
6474 9276 7.279981 CGATTTCAATGGTAAGACATGTTCCTA 59.720 37.037 0.00 0.00 0.00 2.94
6475 9277 6.094048 CGATTTCAATGGTAAGACATGTTCCT 59.906 38.462 0.00 0.00 0.00 3.36
6481 9283 7.915397 GCAATTACGATTTCAATGGTAAGACAT 59.085 33.333 11.35 0.00 40.98 3.06
6483 9285 7.429340 CAGCAATTACGATTTCAATGGTAAGAC 59.571 37.037 11.35 5.32 40.98 3.01
6486 9288 6.375736 TCCAGCAATTACGATTTCAATGGTAA 59.624 34.615 8.91 8.91 41.57 2.85
6488 9290 4.704540 TCCAGCAATTACGATTTCAATGGT 59.295 37.500 0.00 0.00 0.00 3.55
6492 9294 6.918626 TGATTTCCAGCAATTACGATTTCAA 58.081 32.000 0.00 0.00 0.00 2.69
6498 9300 6.507958 TTTCATGATTTCCAGCAATTACGA 57.492 33.333 0.00 0.00 0.00 3.43
6499 9301 8.854979 TTATTTCATGATTTCCAGCAATTACG 57.145 30.769 0.00 0.00 0.00 3.18
6505 9307 9.631257 TCTAGATTTATTTCATGATTTCCAGCA 57.369 29.630 0.00 0.00 0.00 4.41
6539 9341 0.108585 GGTTCAAGTCCTGGTGCTCA 59.891 55.000 0.00 0.00 0.00 4.26
6545 9347 0.884704 CACCACGGTTCAAGTCCTGG 60.885 60.000 0.00 0.00 33.05 4.45
6559 9361 2.035155 GTAACCCCAGCCCACCAC 59.965 66.667 0.00 0.00 0.00 4.16
6560 9362 3.261677 GGTAACCCCAGCCCACCA 61.262 66.667 0.00 0.00 0.00 4.17
6569 9371 3.446161 GCTAAAAGGACAATGGTAACCCC 59.554 47.826 0.00 0.00 0.00 4.95
6573 9375 8.736244 GTTGAATAGCTAAAAGGACAATGGTAA 58.264 33.333 0.00 0.00 0.00 2.85
6579 9381 6.065374 TGTGGTTGAATAGCTAAAAGGACAA 58.935 36.000 0.00 0.00 0.00 3.18
6585 9387 8.644374 ATTTACCTGTGGTTGAATAGCTAAAA 57.356 30.769 0.00 0.00 37.09 1.52
6587 9389 8.644374 AAATTTACCTGTGGTTGAATAGCTAA 57.356 30.769 0.00 0.00 37.09 3.09
6590 9392 9.301153 CATTAAATTTACCTGTGGTTGAATAGC 57.699 33.333 0.00 0.00 37.09 2.97
6592 9394 9.535170 TCCATTAAATTTACCTGTGGTTGAATA 57.465 29.630 0.00 0.00 37.09 1.75
6624 9452 6.214177 TCTCTCCCTTGGTTTTCCTTAAAT 57.786 37.500 0.00 0.00 41.38 1.40
6630 9458 3.223674 TGTTCTCTCCCTTGGTTTTCC 57.776 47.619 0.00 0.00 41.14 3.13
6635 9463 2.241176 TGTTGTTGTTCTCTCCCTTGGT 59.759 45.455 0.00 0.00 0.00 3.67
6637 9465 4.981806 TTTGTTGTTGTTCTCTCCCTTG 57.018 40.909 0.00 0.00 0.00 3.61
6646 9474 6.590234 AGGATATCCCTTTTGTTGTTGTTC 57.410 37.500 18.56 0.00 44.85 3.18


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

AutoCloner maintained by Alex Coulton.