Multiple sequence alignment - TraesCS5D01G354800

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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 TraesCS5D01G354800 chr5D 100.000 3876 0 0 970 4845 436948959 436952834 0.000000e+00 7158.0
1 TraesCS5D01G354800 chr5D 100.000 584 0 0 1 584 436947990 436948573 0.000000e+00 1079.0
2 TraesCS5D01G354800 chr5D 92.326 417 18 12 4437 4845 59884123 59884533 9.040000e-162 580.0
3 TraesCS5D01G354800 chr5D 92.969 384 23 4 4464 4845 59940724 59940343 1.520000e-154 556.0
4 TraesCS5D01G354800 chr5D 92.267 375 26 3 4472 4845 541528058 541527686 3.320000e-146 529.0
5 TraesCS5D01G354800 chr5D 91.250 240 21 0 2698 2937 436950642 436950881 1.300000e-85 327.0
6 TraesCS5D01G354800 chr5D 91.250 240 21 0 2653 2892 436950687 436950926 1.300000e-85 327.0
7 TraesCS5D01G354800 chr5D 89.744 195 20 0 2743 2937 436950642 436950836 2.900000e-62 250.0
8 TraesCS5D01G354800 chr5D 89.744 195 20 0 2653 2847 436950732 436950926 2.900000e-62 250.0
9 TraesCS5D01G354800 chr5D 87.333 150 19 0 2788 2937 436950642 436950791 6.450000e-39 172.0
10 TraesCS5D01G354800 chr5D 87.333 150 19 0 2653 2802 436950777 436950926 6.450000e-39 172.0
11 TraesCS5D01G354800 chr5D 90.476 84 8 0 2833 2916 436950642 436950725 1.430000e-20 111.0
12 TraesCS5D01G354800 chr5D 90.476 84 8 0 2653 2736 436950822 436950905 1.430000e-20 111.0
13 TraesCS5D01G354800 chr5B 94.649 3345 128 18 970 4305 531150820 531154122 0.000000e+00 5138.0
14 TraesCS5D01G354800 chr5B 86.548 394 33 12 3 380 531150001 531150390 2.700000e-112 416.0
15 TraesCS5D01G354800 chr5B 97.585 207 5 0 378 584 531150435 531150641 5.960000e-94 355.0
16 TraesCS5D01G354800 chr5B 92.531 241 16 2 2653 2892 531152526 531152765 1.290000e-90 344.0
17 TraesCS5D01G354800 chr5B 90.871 241 20 2 2698 2937 531152481 531152720 6.050000e-84 322.0
18 TraesCS5D01G354800 chr5B 91.667 192 16 0 2656 2847 531152574 531152765 2.870000e-67 267.0
19 TraesCS5D01G354800 chr5B 88.667 150 17 0 2653 2802 531152616 531152765 2.980000e-42 183.0
20 TraesCS5D01G354800 chr5B 82.110 218 25 10 970 1176 364974028 364973814 1.790000e-39 174.0
21 TraesCS5D01G354800 chr5A 91.598 1821 137 6 2653 4472 552161204 552163009 0.000000e+00 2501.0
22 TraesCS5D01G354800 chr5A 93.191 1307 86 3 1634 2937 552160137 552161443 0.000000e+00 1917.0
23 TraesCS5D01G354800 chr5A 92.228 386 23 3 9 389 552156903 552157286 1.530000e-149 540.0
24 TraesCS5D01G354800 chr5A 91.484 364 24 5 1258 1619 552159796 552160154 1.210000e-135 494.0
25 TraesCS5D01G354800 chr5A 92.373 236 18 0 2657 2892 552161253 552161488 2.160000e-88 337.0
26 TraesCS5D01G354800 chr5A 90.336 238 21 2 2701 2937 552161162 552161398 1.310000e-80 311.0
27 TraesCS5D01G354800 chr5A 92.949 156 10 1 429 584 552157287 552157441 4.880000e-55 226.0
28 TraesCS5D01G354800 chr5A 96.226 106 4 0 1077 1182 552159472 552159577 1.790000e-39 174.0
29 TraesCS5D01G354800 chr5A 98.851 87 1 0 970 1056 552157634 552157720 6.490000e-34 156.0
30 TraesCS5D01G354800 chr5A 83.230 161 24 3 4147 4305 660831100 660831259 1.410000e-30 145.0
31 TraesCS5D01G354800 chr2D 96.277 376 7 7 4472 4845 68937256 68936886 1.150000e-170 610.0
32 TraesCS5D01G354800 chr2D 92.533 375 22 6 4472 4845 467889009 467889378 2.570000e-147 532.0
33 TraesCS5D01G354800 chr2D 91.755 376 27 4 4472 4845 6081451 6081078 2.000000e-143 520.0
34 TraesCS5D01G354800 chr2D 91.689 373 26 4 4475 4845 372514935 372514566 3.340000e-141 512.0
35 TraesCS5D01G354800 chr7D 81.184 760 129 10 3052 3803 619993595 619994348 2.500000e-167 599.0
36 TraesCS5D01G354800 chr7D 92.761 373 25 2 4472 4843 11017925 11018296 5.520000e-149 538.0
37 TraesCS5D01G354800 chr7B 80.571 736 124 15 3078 3803 716539280 716538554 2.550000e-152 549.0
38 TraesCS5D01G354800 chr7B 80.297 269 46 7 2211 2476 716595413 716595149 3.830000e-46 196.0
39 TraesCS5D01G354800 chr7B 76.331 169 36 2 2355 2521 716594883 716594717 2.400000e-13 87.9
40 TraesCS5D01G354800 chr3D 90.488 389 29 8 4459 4845 399677870 399678252 1.560000e-139 507.0
41 TraesCS5D01G354800 chr2B 83.575 207 26 7 970 1176 120178024 120178222 2.300000e-43 187.0
42 TraesCS5D01G354800 chr1B 82.609 207 27 8 970 1176 113650497 113650300 1.790000e-39 174.0
43 TraesCS5D01G354800 chr1B 85.430 151 20 2 4148 4297 507851897 507851748 6.490000e-34 156.0
44 TraesCS5D01G354800 chr4D 85.535 159 16 6 4147 4300 341693401 341693245 5.020000e-35 159.0
45 TraesCS5D01G354800 chr1D 85.443 158 17 6 4147 4301 246650131 246649977 5.020000e-35 159.0
46 TraesCS5D01G354800 chr1D 85.430 151 20 2 4148 4297 379141423 379141274 6.490000e-34 156.0
47 TraesCS5D01G354800 chr1A 84.906 159 21 3 4140 4297 459273227 459273383 1.810000e-34 158.0
48 TraesCS5D01G354800 chr1A 85.430 151 20 2 4148 4297 479836236 479836087 6.490000e-34 156.0
49 TraesCS5D01G354800 chr3A 85.526 152 18 4 4147 4296 251035764 251035913 6.490000e-34 156.0
50 TraesCS5D01G354800 chrUn 83.544 158 23 3 4146 4301 81694231 81694075 1.410000e-30 145.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G354800 chr5D 436947990 436952834 4844 False 995.700000 7158 91.760600 1 4845 10 chr5D.!!$F2 4844
1 TraesCS5D01G354800 chr5B 531150001 531154122 4121 False 1003.571429 5138 91.788286 3 4305 7 chr5B.!!$F1 4302
2 TraesCS5D01G354800 chr5A 552156903 552163009 6106 False 739.555556 2501 93.248444 9 4472 9 chr5A.!!$F2 4463
3 TraesCS5D01G354800 chr7D 619993595 619994348 753 False 599.000000 599 81.184000 3052 3803 1 chr7D.!!$F2 751
4 TraesCS5D01G354800 chr7B 716538554 716539280 726 True 549.000000 549 80.571000 3078 3803 1 chr7B.!!$R1 725

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
419 485 1.202533 GCCGAGCATCTACAAGGCTTA 60.203 52.381 0.00 0.00 41.21 3.09 F
1182 3165 4.032960 TGGTTTGCAGTCCATCACTAAT 57.967 40.909 7.68 0.00 32.21 1.73 F
1405 3388 0.318869 TGCTTGTGCATGCGGAAAAG 60.319 50.000 14.09 13.97 45.31 2.27 F
2910 4947 3.168035 TCCACATAAAGCCACCATGTT 57.832 42.857 0.00 0.00 30.59 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 3370 1.010419 CCTTTTCCGCATGCACAAGC 61.010 55.0 19.57 0.0 42.57 4.01 R
3088 5126 0.837691 AGTGAGCATGGTGACTCCCA 60.838 55.0 11.44 0.0 39.27 4.37 R
3232 5270 0.039618 ACGGGATGGATTTGGCAACT 59.960 50.0 0.00 0.0 37.61 3.16 R
4479 6526 0.039256 CGCACCCATGTTCACCTTTG 60.039 55.0 0.00 0.0 0.00 2.77 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
25 26 5.984695 AAAGGAAGAAGGATAAAACCAGC 57.015 39.130 0.00 0.00 0.00 4.85
118 119 4.857037 GTCGGAAATTGCAAGGTGTATTTC 59.143 41.667 4.94 8.71 0.00 2.17
182 197 1.378514 GTCCCCCAATCACGCACAT 60.379 57.895 0.00 0.00 0.00 3.21
197 214 3.504134 ACGCACATAGCTCTAGTATCCAG 59.496 47.826 0.00 0.00 42.61 3.86
218 237 5.526111 CCAGTAAAGAAAGAAACACGAGGAA 59.474 40.000 0.00 0.00 0.00 3.36
242 261 5.165676 CGCATGGTGTACTTCTTAACTACA 58.834 41.667 0.00 0.00 0.00 2.74
283 302 3.118445 TGAGTGGTCAGTGTTCAATGTCA 60.118 43.478 0.47 0.00 0.00 3.58
284 303 4.067896 GAGTGGTCAGTGTTCAATGTCAT 58.932 43.478 0.47 0.00 0.00 3.06
314 333 1.707989 TGGCCTTTGGGTCATCTGTAA 59.292 47.619 3.32 0.00 43.05 2.41
341 360 1.404391 GCCAGATTGTTCTGCTCATGG 59.596 52.381 0.00 0.00 46.76 3.66
352 371 5.819379 TGTTCTGCTCATGGATCTTGAATAC 59.181 40.000 0.00 0.00 0.00 1.89
381 400 2.677836 GGCAATTGACGAGCATCTACAA 59.322 45.455 10.34 0.00 33.89 2.41
389 455 5.822278 TGACGAGCATCTACAAGATTACTC 58.178 41.667 0.00 6.63 31.32 2.59
419 485 1.202533 GCCGAGCATCTACAAGGCTTA 60.203 52.381 0.00 0.00 41.21 3.09
1092 2889 6.070194 CCCCTTCTCTAGTGACCTCATTTAAA 60.070 42.308 0.00 0.00 0.00 1.52
1182 3165 4.032960 TGGTTTGCAGTCCATCACTAAT 57.967 40.909 7.68 0.00 32.21 1.73
1185 3168 6.894682 TGGTTTGCAGTCCATCACTAATATA 58.105 36.000 7.68 0.00 32.21 0.86
1252 3235 7.783119 TGCTAGTGAATGATACTCCCTTAGTAA 59.217 37.037 0.00 0.00 43.87 2.24
1405 3388 0.318869 TGCTTGTGCATGCGGAAAAG 60.319 50.000 14.09 13.97 45.31 2.27
1482 3466 4.876107 GGAGTCATCAATCAAATGGTACGT 59.124 41.667 0.00 0.00 0.00 3.57
1544 3529 9.515226 AATTACTTTATGTCAAAAGCTCCTACA 57.485 29.630 0.00 0.00 39.59 2.74
1709 3696 4.177165 TCGAAGCGGAGTGTGTAAATTA 57.823 40.909 0.00 0.00 0.00 1.40
1717 3705 5.675323 GCGGAGTGTGTAAATTAAACCCATC 60.675 44.000 0.00 0.00 0.00 3.51
1737 3725 9.520515 ACCCATCCAATTGTTCATAAGTATATC 57.479 33.333 4.43 0.00 0.00 1.63
1799 3788 6.823497 AGATGCAATTAAAGGCAATGCTTAT 58.177 32.000 4.82 0.00 44.20 1.73
1876 3865 9.949174 TGACATGGATATCAACAATTATTTTCG 57.051 29.630 4.83 0.00 0.00 3.46
2214 4206 4.160252 AGTTGAAGAAGAAGCAGGCAAAAA 59.840 37.500 0.00 0.00 0.00 1.94
2240 4232 4.640364 TGCAACACATAGAACAGACATGA 58.360 39.130 0.00 0.00 0.00 3.07
2485 4477 5.098663 TCTTTGTCTTATGGGGTAGAAGGT 58.901 41.667 0.00 0.00 0.00 3.50
2522 4514 4.971282 AGGAAATCTCTGTGTCATATGGGA 59.029 41.667 2.13 0.00 0.00 4.37
2533 4525 4.284490 GTGTCATATGGGATAGAAGGCAGA 59.716 45.833 2.13 0.00 0.00 4.26
2544 4536 6.042666 GGGATAGAAGGCAGAAAGAGTCTAAT 59.957 42.308 0.00 0.00 33.56 1.73
2785 4777 8.671921 CATAAAGCTACAATGTCATATGGATCC 58.328 37.037 4.20 4.20 0.00 3.36
2910 4947 3.168035 TCCACATAAAGCCACCATGTT 57.832 42.857 0.00 0.00 30.59 2.71
2931 4968 9.281371 CATGTTATATGAGTCAGGACATGAAAT 57.719 33.333 23.07 3.32 43.22 2.17
3088 5126 7.595819 TTTTCATGTTGTGGTAAAAGGAGAT 57.404 32.000 0.00 0.00 0.00 2.75
3232 5270 1.155155 GGCCCTTCTTCCCCACAAA 59.845 57.895 0.00 0.00 0.00 2.83
3849 5890 1.003118 TGCAGCAACCCGTTAGAAGAT 59.997 47.619 0.00 0.00 0.00 2.40
3930 5971 9.273016 ACATTATATGGGTGAATCTTCGTAAAG 57.727 33.333 0.00 0.00 33.60 1.85
3948 5989 4.724074 AAAGTGCATGATGGTGTTATGG 57.276 40.909 0.00 0.00 0.00 2.74
3964 6005 5.804979 GTGTTATGGAATAAATGGTGTGTGC 59.195 40.000 0.00 0.00 41.12 4.57
3965 6006 3.781079 ATGGAATAAATGGTGTGTGCG 57.219 42.857 0.00 0.00 0.00 5.34
3988 6029 4.265556 GGAAGTCGTCGTATGAACTTCATG 59.734 45.833 22.33 0.00 37.70 3.07
4012 6053 6.939730 TGATATGTGAGTAAAATGTGTGTGGT 59.060 34.615 0.00 0.00 0.00 4.16
4053 6094 5.188434 AGAACATCACCCATCTATTGTGTG 58.812 41.667 0.00 0.00 0.00 3.82
4057 6098 6.662755 ACATCACCCATCTATTGTGTGTTAT 58.337 36.000 0.00 0.00 0.00 1.89
4127 6168 9.908152 CGTACAGTATATAAAGATGACCATTCA 57.092 33.333 0.00 0.00 35.73 2.57
4168 6210 5.848921 AGCTCCCTCCATTTCAGAACTATAT 59.151 40.000 0.00 0.00 0.00 0.86
4179 6221 9.740239 CATTTCAGAACTATATGATGTTTTGGG 57.260 33.333 0.00 0.00 31.75 4.12
4193 6236 7.390027 TGATGTTTTGGGTATTTTAATGTGGG 58.610 34.615 0.00 0.00 0.00 4.61
4220 6263 6.524734 ACATACAGACTGAAATGAGTGAACA 58.475 36.000 21.47 0.00 0.00 3.18
4223 6266 6.369059 ACAGACTGAAATGAGTGAACAAAG 57.631 37.500 10.08 0.00 0.00 2.77
4226 6269 5.235186 AGACTGAAATGAGTGAACAAAGACG 59.765 40.000 0.00 0.00 0.00 4.18
4236 6279 4.336993 AGTGAACAAAGACGCCAAAACATA 59.663 37.500 0.00 0.00 0.00 2.29
4376 6423 5.885352 TCACCTTCTTCAGAACAATTTGTCA 59.115 36.000 1.83 0.00 0.00 3.58
4385 6432 7.002816 TCAGAACAATTTGTCAATTTGCAAC 57.997 32.000 16.47 10.10 29.41 4.17
4388 6435 8.767085 CAGAACAATTTGTCAATTTGCAACTAT 58.233 29.630 16.47 0.00 29.41 2.12
4401 6448 5.845985 TTGCAACTATTGAAGAGTCTTCG 57.154 39.130 24.32 14.28 0.00 3.79
4404 6451 4.201666 GCAACTATTGAAGAGTCTTCGCTG 60.202 45.833 24.32 16.98 0.00 5.18
4426 6473 7.588854 CGCTGTATCCAACTTTCATCATTATTG 59.411 37.037 0.00 0.00 0.00 1.90
4492 6539 7.922505 TTTCGAAAATACAAAGGTGAACATG 57.077 32.000 8.44 0.00 0.00 3.21
4493 6540 6.007936 TCGAAAATACAAAGGTGAACATGG 57.992 37.500 0.00 0.00 0.00 3.66
4494 6541 5.048364 TCGAAAATACAAAGGTGAACATGGG 60.048 40.000 0.00 0.00 0.00 4.00
4495 6542 5.278758 CGAAAATACAAAGGTGAACATGGGT 60.279 40.000 0.00 0.00 0.00 4.51
4496 6543 5.467035 AAATACAAAGGTGAACATGGGTG 57.533 39.130 0.00 0.00 0.00 4.61
4497 6544 1.039856 ACAAAGGTGAACATGGGTGC 58.960 50.000 0.00 0.00 0.00 5.01
4498 6545 0.039256 CAAAGGTGAACATGGGTGCG 60.039 55.000 0.00 0.00 0.00 5.34
4499 6546 0.467290 AAAGGTGAACATGGGTGCGT 60.467 50.000 0.00 0.00 0.00 5.24
4500 6547 1.172180 AAGGTGAACATGGGTGCGTG 61.172 55.000 0.00 0.00 0.00 5.34
4501 6548 1.896660 GGTGAACATGGGTGCGTGT 60.897 57.895 0.00 0.00 0.00 4.49
4502 6549 1.282570 GTGAACATGGGTGCGTGTG 59.717 57.895 0.00 0.00 0.00 3.82
4503 6550 2.255252 GAACATGGGTGCGTGTGC 59.745 61.111 0.00 0.00 43.20 4.57
4518 6565 2.404215 GTGTGCACTCACGTGAATAGT 58.596 47.619 20.49 11.42 46.01 2.12
4519 6566 3.571571 GTGTGCACTCACGTGAATAGTA 58.428 45.455 20.49 8.82 46.01 1.82
4520 6567 3.985279 GTGTGCACTCACGTGAATAGTAA 59.015 43.478 20.49 3.59 46.01 2.24
4521 6568 4.446385 GTGTGCACTCACGTGAATAGTAAA 59.554 41.667 20.49 4.18 46.01 2.01
4522 6569 5.120208 GTGTGCACTCACGTGAATAGTAAAT 59.880 40.000 20.49 0.00 46.01 1.40
4523 6570 5.699001 TGTGCACTCACGTGAATAGTAAATT 59.301 36.000 20.49 0.00 46.01 1.82
4524 6571 6.128661 TGTGCACTCACGTGAATAGTAAATTC 60.129 38.462 20.49 4.97 46.01 2.17
4525 6572 5.929415 TGCACTCACGTGAATAGTAAATTCA 59.071 36.000 20.49 5.37 43.97 2.57
4526 6573 6.593770 TGCACTCACGTGAATAGTAAATTCAT 59.406 34.615 20.49 0.00 43.97 2.57
4527 6574 7.762159 TGCACTCACGTGAATAGTAAATTCATA 59.238 33.333 20.49 0.00 43.97 2.15
4528 6575 8.600625 GCACTCACGTGAATAGTAAATTCATAA 58.399 33.333 20.49 0.00 43.97 1.90
4575 6622 9.927668 AAAAATCTGAAATTTCACGGTATGAAT 57.072 25.926 16.91 2.57 46.80 2.57
4576 6623 9.573133 AAAATCTGAAATTTCACGGTATGAATC 57.427 29.630 16.91 0.00 46.80 2.52
4577 6624 8.511604 AATCTGAAATTTCACGGTATGAATCT 57.488 30.769 16.91 0.00 46.80 2.40
4578 6625 7.921786 TCTGAAATTTCACGGTATGAATCTT 57.078 32.000 16.91 0.00 46.80 2.40
4579 6626 9.613428 ATCTGAAATTTCACGGTATGAATCTTA 57.387 29.630 16.91 0.00 46.80 2.10
4580 6627 9.098355 TCTGAAATTTCACGGTATGAATCTTAG 57.902 33.333 16.91 2.14 46.80 2.18
4581 6628 8.786826 TGAAATTTCACGGTATGAATCTTAGT 57.213 30.769 16.91 0.00 46.80 2.24
4582 6629 8.879759 TGAAATTTCACGGTATGAATCTTAGTC 58.120 33.333 16.91 0.00 46.80 2.59
4583 6630 8.786826 AAATTTCACGGTATGAATCTTAGTCA 57.213 30.769 0.00 0.00 46.80 3.41
4584 6631 8.786826 AATTTCACGGTATGAATCTTAGTCAA 57.213 30.769 0.00 0.00 46.80 3.18
4585 6632 8.964476 ATTTCACGGTATGAATCTTAGTCAAT 57.036 30.769 0.00 0.00 46.80 2.57
4586 6633 8.420374 TTTCACGGTATGAATCTTAGTCAATC 57.580 34.615 0.00 0.00 46.80 2.67
4587 6634 7.107639 TCACGGTATGAATCTTAGTCAATCA 57.892 36.000 0.00 0.00 33.02 2.57
4588 6635 7.726216 TCACGGTATGAATCTTAGTCAATCAT 58.274 34.615 0.00 0.00 33.02 2.45
4589 6636 8.204160 TCACGGTATGAATCTTAGTCAATCATT 58.796 33.333 0.00 0.00 33.02 2.57
4590 6637 8.491152 CACGGTATGAATCTTAGTCAATCATTC 58.509 37.037 0.00 0.00 33.17 2.67
4591 6638 8.424918 ACGGTATGAATCTTAGTCAATCATTCT 58.575 33.333 0.00 0.00 33.17 2.40
4592 6639 9.914131 CGGTATGAATCTTAGTCAATCATTCTA 57.086 33.333 0.00 0.00 33.17 2.10
4598 6645 9.474920 GAATCTTAGTCAATCATTCTACTCAGG 57.525 37.037 0.00 0.00 0.00 3.86
4599 6646 7.962995 TCTTAGTCAATCATTCTACTCAGGT 57.037 36.000 0.00 0.00 0.00 4.00
4600 6647 7.776107 TCTTAGTCAATCATTCTACTCAGGTG 58.224 38.462 0.00 0.00 0.00 4.00
4601 6648 4.764172 AGTCAATCATTCTACTCAGGTGC 58.236 43.478 0.00 0.00 0.00 5.01
4602 6649 3.553511 GTCAATCATTCTACTCAGGTGCG 59.446 47.826 0.00 0.00 0.00 5.34
4603 6650 3.447229 TCAATCATTCTACTCAGGTGCGA 59.553 43.478 0.00 0.00 0.00 5.10
4604 6651 4.081697 TCAATCATTCTACTCAGGTGCGAA 60.082 41.667 0.00 0.00 0.00 4.70
4605 6652 3.510388 TCATTCTACTCAGGTGCGAAG 57.490 47.619 0.00 0.00 0.00 3.79
4606 6653 2.826128 TCATTCTACTCAGGTGCGAAGT 59.174 45.455 0.00 0.00 0.00 3.01
4607 6654 3.258372 TCATTCTACTCAGGTGCGAAGTT 59.742 43.478 0.00 0.00 0.00 2.66
4608 6655 3.746045 TTCTACTCAGGTGCGAAGTTT 57.254 42.857 0.00 0.00 0.00 2.66
4609 6656 3.299340 TCTACTCAGGTGCGAAGTTTC 57.701 47.619 0.00 0.00 0.00 2.78
4610 6657 2.626266 TCTACTCAGGTGCGAAGTTTCA 59.374 45.455 0.00 0.00 0.00 2.69
4611 6658 2.550830 ACTCAGGTGCGAAGTTTCAT 57.449 45.000 0.00 0.00 0.00 2.57
4612 6659 2.146342 ACTCAGGTGCGAAGTTTCATG 58.854 47.619 0.00 0.00 0.00 3.07
4613 6660 2.224281 ACTCAGGTGCGAAGTTTCATGA 60.224 45.455 0.00 0.00 0.00 3.07
4614 6661 3.005554 CTCAGGTGCGAAGTTTCATGAT 58.994 45.455 0.00 0.00 0.00 2.45
4615 6662 2.743664 TCAGGTGCGAAGTTTCATGATG 59.256 45.455 0.00 0.00 0.00 3.07
4616 6663 2.485426 CAGGTGCGAAGTTTCATGATGT 59.515 45.455 0.00 0.00 0.00 3.06
4617 6664 3.684305 CAGGTGCGAAGTTTCATGATGTA 59.316 43.478 0.00 0.00 0.00 2.29
4618 6665 4.333649 CAGGTGCGAAGTTTCATGATGTAT 59.666 41.667 0.00 0.00 0.00 2.29
4619 6666 4.943705 AGGTGCGAAGTTTCATGATGTATT 59.056 37.500 0.00 0.00 0.00 1.89
4620 6667 5.030295 GGTGCGAAGTTTCATGATGTATTG 58.970 41.667 0.00 0.00 0.00 1.90
4621 6668 5.163764 GGTGCGAAGTTTCATGATGTATTGA 60.164 40.000 0.00 0.00 0.00 2.57
4622 6669 5.734498 GTGCGAAGTTTCATGATGTATTGAC 59.266 40.000 0.00 0.00 0.00 3.18
4623 6670 5.411053 TGCGAAGTTTCATGATGTATTGACA 59.589 36.000 0.00 0.00 40.72 3.58
4624 6671 5.734498 GCGAAGTTTCATGATGTATTGACAC 59.266 40.000 0.00 0.00 38.76 3.67
4625 6672 6.250819 CGAAGTTTCATGATGTATTGACACC 58.749 40.000 0.00 0.00 38.76 4.16
4626 6673 6.515272 AAGTTTCATGATGTATTGACACCC 57.485 37.500 0.00 0.00 38.76 4.61
4627 6674 5.569355 AGTTTCATGATGTATTGACACCCA 58.431 37.500 0.00 0.00 38.76 4.51
4628 6675 6.189859 AGTTTCATGATGTATTGACACCCAT 58.810 36.000 0.00 0.00 38.76 4.00
4629 6676 6.095860 AGTTTCATGATGTATTGACACCCATG 59.904 38.462 0.00 12.46 43.94 3.66
4630 6677 4.463070 TCATGATGTATTGACACCCATGG 58.537 43.478 4.14 4.14 43.39 3.66
4631 6678 4.079844 TCATGATGTATTGACACCCATGGT 60.080 41.667 11.73 0.00 43.39 3.55
4632 6679 5.131809 TCATGATGTATTGACACCCATGGTA 59.868 40.000 11.73 0.00 43.39 3.25
4633 6680 5.645056 TGATGTATTGACACCCATGGTAT 57.355 39.130 11.73 0.00 38.76 2.73
4634 6681 6.012337 TGATGTATTGACACCCATGGTATT 57.988 37.500 11.73 0.00 38.76 1.89
4635 6682 6.061441 TGATGTATTGACACCCATGGTATTC 58.939 40.000 11.73 3.90 38.76 1.75
4636 6683 5.708736 TGTATTGACACCCATGGTATTCT 57.291 39.130 11.73 0.00 32.11 2.40
4637 6684 6.073447 TGTATTGACACCCATGGTATTCTT 57.927 37.500 11.73 0.00 32.11 2.52
4638 6685 7.201702 TGTATTGACACCCATGGTATTCTTA 57.798 36.000 11.73 0.00 32.11 2.10
4639 6686 7.279615 TGTATTGACACCCATGGTATTCTTAG 58.720 38.462 11.73 0.00 32.11 2.18
4640 6687 5.772393 TTGACACCCATGGTATTCTTAGT 57.228 39.130 11.73 0.00 32.11 2.24
4641 6688 5.097742 TGACACCCATGGTATTCTTAGTG 57.902 43.478 11.73 11.15 32.11 2.74
4642 6689 4.780554 TGACACCCATGGTATTCTTAGTGA 59.219 41.667 17.12 0.00 32.11 3.41
4643 6690 5.249622 TGACACCCATGGTATTCTTAGTGAA 59.750 40.000 17.12 5.46 34.39 3.18
4644 6691 5.745227 ACACCCATGGTATTCTTAGTGAAG 58.255 41.667 17.12 0.00 33.70 3.02
4645 6692 5.487488 ACACCCATGGTATTCTTAGTGAAGA 59.513 40.000 17.12 0.00 35.30 2.87
4646 6693 6.012858 ACACCCATGGTATTCTTAGTGAAGAA 60.013 38.462 17.12 2.80 44.02 2.52
4647 6694 6.884295 CACCCATGGTATTCTTAGTGAAGAAA 59.116 38.462 11.73 0.00 43.53 2.52
4648 6695 7.393234 CACCCATGGTATTCTTAGTGAAGAAAA 59.607 37.037 11.73 0.00 43.53 2.29
4658 6705 8.948853 TTCTTAGTGAAGAAAATACAAATGCG 57.051 30.769 0.00 0.00 46.44 4.73
4659 6706 8.317891 TCTTAGTGAAGAAAATACAAATGCGA 57.682 30.769 0.00 0.00 38.80 5.10
4660 6707 8.227791 TCTTAGTGAAGAAAATACAAATGCGAC 58.772 33.333 0.00 0.00 38.80 5.19
4661 6708 5.699839 AGTGAAGAAAATACAAATGCGACC 58.300 37.500 0.00 0.00 0.00 4.79
4662 6709 5.240623 AGTGAAGAAAATACAAATGCGACCA 59.759 36.000 0.00 0.00 0.00 4.02
4663 6710 6.071952 AGTGAAGAAAATACAAATGCGACCAT 60.072 34.615 0.00 0.00 0.00 3.55
4664 6711 7.120579 AGTGAAGAAAATACAAATGCGACCATA 59.879 33.333 0.00 0.00 0.00 2.74
4665 6712 7.218204 GTGAAGAAAATACAAATGCGACCATAC 59.782 37.037 0.00 0.00 0.00 2.39
4666 6713 7.120579 TGAAGAAAATACAAATGCGACCATACT 59.879 33.333 0.00 0.00 0.00 2.12
4667 6714 8.500753 AAGAAAATACAAATGCGACCATACTA 57.499 30.769 0.00 0.00 0.00 1.82
4668 6715 8.677148 AGAAAATACAAATGCGACCATACTAT 57.323 30.769 0.00 0.00 0.00 2.12
4669 6716 9.120538 AGAAAATACAAATGCGACCATACTATT 57.879 29.630 0.00 0.00 0.00 1.73
4670 6717 9.382244 GAAAATACAAATGCGACCATACTATTC 57.618 33.333 0.00 0.00 0.00 1.75
4671 6718 8.445275 AAATACAAATGCGACCATACTATTCA 57.555 30.769 0.00 0.00 0.00 2.57
4672 6719 8.621532 AATACAAATGCGACCATACTATTCAT 57.378 30.769 0.00 0.00 0.00 2.57
4673 6720 6.942532 ACAAATGCGACCATACTATTCATT 57.057 33.333 0.00 0.00 0.00 2.57
4674 6721 9.719355 ATACAAATGCGACCATACTATTCATTA 57.281 29.630 0.00 0.00 0.00 1.90
4675 6722 8.445275 ACAAATGCGACCATACTATTCATTAA 57.555 30.769 0.00 0.00 0.00 1.40
4676 6723 8.898761 ACAAATGCGACCATACTATTCATTAAA 58.101 29.630 0.00 0.00 0.00 1.52
4677 6724 9.897744 CAAATGCGACCATACTATTCATTAAAT 57.102 29.630 0.00 0.00 0.00 1.40
4715 6762 8.816640 ATAGCTTCGATTTTTGTCATTTTTGT 57.183 26.923 0.00 0.00 0.00 2.83
4716 6763 7.165427 AGCTTCGATTTTTGTCATTTTTGTC 57.835 32.000 0.00 0.00 0.00 3.18
4717 6764 6.200854 AGCTTCGATTTTTGTCATTTTTGTCC 59.799 34.615 0.00 0.00 0.00 4.02
4718 6765 6.019156 GCTTCGATTTTTGTCATTTTTGTCCA 60.019 34.615 0.00 0.00 0.00 4.02
4719 6766 7.462109 TTCGATTTTTGTCATTTTTGTCCAG 57.538 32.000 0.00 0.00 0.00 3.86
4720 6767 6.800543 TCGATTTTTGTCATTTTTGTCCAGA 58.199 32.000 0.00 0.00 0.00 3.86
4721 6768 7.432869 TCGATTTTTGTCATTTTTGTCCAGAT 58.567 30.769 0.00 0.00 0.00 2.90
4722 6769 7.925483 TCGATTTTTGTCATTTTTGTCCAGATT 59.075 29.630 0.00 0.00 0.00 2.40
4723 6770 9.190858 CGATTTTTGTCATTTTTGTCCAGATTA 57.809 29.630 0.00 0.00 0.00 1.75
4725 6772 7.945033 TTTTGTCATTTTTGTCCAGATTAGC 57.055 32.000 0.00 0.00 0.00 3.09
4726 6773 6.647334 TTGTCATTTTTGTCCAGATTAGCA 57.353 33.333 0.00 0.00 0.00 3.49
4727 6774 6.012658 TGTCATTTTTGTCCAGATTAGCAC 57.987 37.500 0.00 0.00 0.00 4.40
4728 6775 5.088739 GTCATTTTTGTCCAGATTAGCACG 58.911 41.667 0.00 0.00 0.00 5.34
4729 6776 4.155826 TCATTTTTGTCCAGATTAGCACGG 59.844 41.667 0.00 0.00 0.00 4.94
4730 6777 3.410631 TTTTGTCCAGATTAGCACGGA 57.589 42.857 0.00 0.00 0.00 4.69
4731 6778 3.627395 TTTGTCCAGATTAGCACGGAT 57.373 42.857 0.00 0.00 0.00 4.18
4732 6779 2.602257 TGTCCAGATTAGCACGGATG 57.398 50.000 0.00 0.00 0.00 3.51
4733 6780 1.831106 TGTCCAGATTAGCACGGATGT 59.169 47.619 0.00 0.00 0.00 3.06
4749 6796 5.519722 ACGGATGTGATTTCTTTGTGAAAC 58.480 37.500 0.00 0.00 46.08 2.78
4750 6797 4.917415 CGGATGTGATTTCTTTGTGAAACC 59.083 41.667 0.00 0.00 46.08 3.27
4751 6798 5.278463 CGGATGTGATTTCTTTGTGAAACCT 60.278 40.000 0.00 0.00 46.08 3.50
4752 6799 6.152379 GGATGTGATTTCTTTGTGAAACCTC 58.848 40.000 0.00 0.00 46.08 3.85
4753 6800 6.239008 GGATGTGATTTCTTTGTGAAACCTCA 60.239 38.462 0.00 0.00 46.08 3.86
4754 6801 6.713762 TGTGATTTCTTTGTGAAACCTCAT 57.286 33.333 0.00 0.00 46.08 2.90
4755 6802 7.815840 TGTGATTTCTTTGTGAAACCTCATA 57.184 32.000 0.00 0.00 46.08 2.15
4756 6803 8.408043 TGTGATTTCTTTGTGAAACCTCATAT 57.592 30.769 0.00 0.00 46.08 1.78
4757 6804 9.513906 TGTGATTTCTTTGTGAAACCTCATATA 57.486 29.630 0.00 0.00 46.08 0.86
4758 6805 9.774742 GTGATTTCTTTGTGAAACCTCATATAC 57.225 33.333 0.00 0.00 46.08 1.47
4759 6806 8.664798 TGATTTCTTTGTGAAACCTCATATACG 58.335 33.333 0.00 0.00 46.08 3.06
4760 6807 8.786826 ATTTCTTTGTGAAACCTCATATACGA 57.213 30.769 0.00 0.00 46.08 3.43
4761 6808 7.827819 TTCTTTGTGAAACCTCATATACGAG 57.172 36.000 0.00 0.00 34.36 4.18
4762 6809 6.931838 TCTTTGTGAAACCTCATATACGAGT 58.068 36.000 0.00 0.00 34.36 4.18
4763 6810 8.058667 TCTTTGTGAAACCTCATATACGAGTA 57.941 34.615 0.00 0.00 34.36 2.59
4764 6811 8.692710 TCTTTGTGAAACCTCATATACGAGTAT 58.307 33.333 0.00 1.16 34.36 2.12
4765 6812 9.961265 CTTTGTGAAACCTCATATACGAGTATA 57.039 33.333 5.54 5.54 34.36 1.47
4766 6813 9.740239 TTTGTGAAACCTCATATACGAGTATAC 57.260 33.333 5.22 0.00 34.36 1.47
4767 6814 7.879070 TGTGAAACCTCATATACGAGTATACC 58.121 38.462 5.22 0.00 34.36 2.73
4768 6815 7.020010 GTGAAACCTCATATACGAGTATACCG 58.980 42.308 10.87 10.87 33.05 4.02
4769 6816 6.149973 TGAAACCTCATATACGAGTATACCGG 59.850 42.308 0.00 0.00 31.52 5.28
4770 6817 5.171339 ACCTCATATACGAGTATACCGGT 57.829 43.478 13.98 13.98 31.52 5.28
4771 6818 5.564550 ACCTCATATACGAGTATACCGGTT 58.435 41.667 15.04 3.05 31.52 4.44
4772 6819 5.413833 ACCTCATATACGAGTATACCGGTTG 59.586 44.000 15.04 0.00 31.52 3.77
4773 6820 5.645067 CCTCATATACGAGTATACCGGTTGA 59.355 44.000 15.04 4.51 31.52 3.18
4774 6821 6.402983 CCTCATATACGAGTATACCGGTTGAC 60.403 46.154 15.04 11.82 31.52 3.18
4775 6822 6.233434 TCATATACGAGTATACCGGTTGACT 58.767 40.000 15.04 17.09 31.52 3.41
4776 6823 7.386059 TCATATACGAGTATACCGGTTGACTA 58.614 38.462 15.04 2.04 31.52 2.59
4777 6824 8.043113 TCATATACGAGTATACCGGTTGACTAT 58.957 37.037 15.04 10.74 31.52 2.12
4778 6825 4.825546 ACGAGTATACCGGTTGACTATG 57.174 45.455 15.04 14.36 0.00 2.23
4779 6826 4.202441 ACGAGTATACCGGTTGACTATGT 58.798 43.478 15.04 14.98 0.00 2.29
4780 6827 5.368145 ACGAGTATACCGGTTGACTATGTA 58.632 41.667 15.04 0.00 0.00 2.29
4781 6828 6.000219 ACGAGTATACCGGTTGACTATGTAT 59.000 40.000 15.04 0.00 0.00 2.29
4782 6829 7.161404 ACGAGTATACCGGTTGACTATGTATA 58.839 38.462 15.04 0.00 0.00 1.47
4783 6830 7.826252 ACGAGTATACCGGTTGACTATGTATAT 59.174 37.037 15.04 0.00 29.87 0.86
4784 6831 8.671921 CGAGTATACCGGTTGACTATGTATATT 58.328 37.037 15.04 0.00 29.87 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.849518 AGAGCTGGTTTTATCCTTCTTCC 58.150 43.478 0.00 0.00 0.00 3.46
25 26 3.555139 GCTGCAGTACAAGCATAGAAGAG 59.445 47.826 16.64 2.32 41.82 2.85
118 119 6.416750 GGTGAAAATCTTGACTTAACCAAACG 59.583 38.462 0.00 0.00 0.00 3.60
171 178 7.692415 TGGATACTAGAGCTATGTGCGTGATT 61.692 42.308 0.00 0.00 42.49 2.57
182 197 9.696572 TTCTTTCTTTACTGGATACTAGAGCTA 57.303 33.333 0.00 0.00 37.61 3.32
197 214 5.429615 CGTTCCTCGTGTTTCTTTCTTTAC 58.570 41.667 0.00 0.00 34.52 2.01
218 237 4.267349 AGTTAAGAAGTACACCATGCGT 57.733 40.909 0.00 0.00 0.00 5.24
242 261 4.012374 CTCAGCCATTCACATAACACCTT 58.988 43.478 0.00 0.00 0.00 3.50
275 294 4.754618 GGCCAACGTATGATATGACATTGA 59.245 41.667 0.00 0.00 0.00 2.57
278 297 4.623932 AGGCCAACGTATGATATGACAT 57.376 40.909 5.01 0.00 0.00 3.06
283 302 3.117663 ACCCAAAGGCCAACGTATGATAT 60.118 43.478 5.01 0.00 36.11 1.63
284 303 2.240160 ACCCAAAGGCCAACGTATGATA 59.760 45.455 5.01 0.00 36.11 2.15
341 360 4.517285 TGCCAGGTTGAGTATTCAAGATC 58.483 43.478 0.16 0.00 43.66 2.75
352 371 1.466167 CTCGTCAATTGCCAGGTTGAG 59.534 52.381 0.00 0.00 35.22 3.02
381 400 3.260884 TCGGCCACAAGAAAGAGTAATCT 59.739 43.478 2.24 0.00 0.00 2.40
389 455 0.449388 GATGCTCGGCCACAAGAAAG 59.551 55.000 2.24 0.00 0.00 2.62
1070 1136 8.043710 ACCATTTAAATGAGGTCACTAGAGAAG 58.956 37.037 26.32 8.59 38.70 2.85
1092 2889 5.244755 GCCACCAATAATTGTCAAAACCAT 58.755 37.500 0.00 0.00 0.00 3.55
1215 3198 9.277783 GTATCATTCACTAGCACAAAAGGATAT 57.722 33.333 0.00 0.00 28.99 1.63
1216 3199 8.486210 AGTATCATTCACTAGCACAAAAGGATA 58.514 33.333 0.00 0.00 0.00 2.59
1217 3200 7.341805 AGTATCATTCACTAGCACAAAAGGAT 58.658 34.615 0.00 0.00 0.00 3.24
1218 3201 6.711277 AGTATCATTCACTAGCACAAAAGGA 58.289 36.000 0.00 0.00 0.00 3.36
1387 3370 1.010419 CCTTTTCCGCATGCACAAGC 61.010 55.000 19.57 0.00 42.57 4.01
1405 3388 3.683365 TGTAACGGTTTAGAAGGGTCC 57.317 47.619 0.00 0.00 0.00 4.46
1461 3445 6.206634 ACAAACGTACCATTTGATTGATGACT 59.793 34.615 19.16 0.00 39.01 3.41
1482 3466 9.190858 CGTATTGAGATGGAAATTTTGAACAAA 57.809 29.630 0.00 0.00 0.00 2.83
1544 3529 5.047092 CCATCAATCAAAGGTAAGTTTGGCT 60.047 40.000 0.00 0.00 37.89 4.75
1709 3696 6.933514 ACTTATGAACAATTGGATGGGTTT 57.066 33.333 10.83 0.00 0.00 3.27
1799 3788 3.536570 TCATTGAATCGCCGGTATCAAA 58.463 40.909 1.90 0.00 35.62 2.69
1876 3865 3.365969 GCAGTACATGTGGTTAACTTGGC 60.366 47.826 9.11 0.62 38.07 4.52
2214 4206 6.389830 TGTCTGTTCTATGTGTTGCAAATT 57.610 33.333 0.00 0.00 0.00 1.82
2485 4477 4.175962 AGATTTCCTTTAGGACACCCTCA 58.824 43.478 0.00 0.00 45.39 3.86
2522 4514 6.613271 TCCATTAGACTCTTTCTGCCTTCTAT 59.387 38.462 0.00 0.00 35.55 1.98
2533 4525 4.042187 ACAGGTGCTTCCATTAGACTCTTT 59.958 41.667 1.79 0.00 39.02 2.52
2544 4536 3.355378 CCATATGAAACAGGTGCTTCCA 58.645 45.455 3.65 0.00 39.02 3.53
2650 4642 2.190538 TGTGGATCCTCTGCATCTTGA 58.809 47.619 14.23 0.00 0.00 3.02
2785 4777 3.251479 TGTGGATCCTCTTCATGTTCG 57.749 47.619 14.23 0.00 0.00 3.95
2910 4947 7.616528 TCCATTTCATGTCCTGACTCATATA 57.383 36.000 0.00 0.00 32.17 0.86
2931 4968 9.010029 GTCCTGTTAAAAATGTCTTTAGATCCA 57.990 33.333 0.00 0.00 0.00 3.41
3076 5114 3.370633 GGTGACTCCCATCTCCTTTTACC 60.371 52.174 0.00 0.00 30.89 2.85
3088 5126 0.837691 AGTGAGCATGGTGACTCCCA 60.838 55.000 11.44 0.00 39.27 4.37
3232 5270 0.039618 ACGGGATGGATTTGGCAACT 59.960 50.000 0.00 0.00 37.61 3.16
3849 5890 4.522689 ACAGGTGCACGTGCGTCA 62.523 61.111 33.17 15.59 45.83 4.35
3930 5971 4.924305 ATTCCATAACACCATCATGCAC 57.076 40.909 0.00 0.00 0.00 4.57
3948 5989 3.190535 ACTTCCGCACACACCATTTATTC 59.809 43.478 0.00 0.00 0.00 1.75
3964 6005 2.539346 AGTTCATACGACGACTTCCG 57.461 50.000 0.00 0.00 45.44 4.30
3965 6006 3.829948 TGAAGTTCATACGACGACTTCC 58.170 45.455 18.28 6.47 44.50 3.46
3988 6029 7.094805 ACACCACACACATTTTACTCACATATC 60.095 37.037 0.00 0.00 0.00 1.63
4012 6053 4.216472 TGTTCTTACAACAACTGCAACACA 59.784 37.500 0.00 0.00 0.00 3.72
4076 6117 9.265901 CGGAAAGACATTTCATAGATTACTCAT 57.734 33.333 3.41 0.00 45.59 2.90
4142 6184 3.075134 AGTTCTGAAATGGAGGGAGCTTT 59.925 43.478 0.00 0.00 0.00 3.51
4144 6186 2.273619 AGTTCTGAAATGGAGGGAGCT 58.726 47.619 0.00 0.00 0.00 4.09
4145 6187 2.797177 AGTTCTGAAATGGAGGGAGC 57.203 50.000 0.00 0.00 0.00 4.70
4147 6189 7.293299 ACATCATATAGTTCTGAAATGGAGGGA 59.707 37.037 0.00 0.00 0.00 4.20
4149 6191 8.915057 AACATCATATAGTTCTGAAATGGAGG 57.085 34.615 0.00 0.00 0.00 4.30
4152 6194 9.740239 CCAAAACATCATATAGTTCTGAAATGG 57.260 33.333 0.00 0.00 0.00 3.16
4153 6195 9.740239 CCCAAAACATCATATAGTTCTGAAATG 57.260 33.333 0.00 0.00 0.00 2.32
4154 6196 9.479549 ACCCAAAACATCATATAGTTCTGAAAT 57.520 29.630 0.00 0.00 0.00 2.17
4155 6197 8.877864 ACCCAAAACATCATATAGTTCTGAAA 57.122 30.769 0.00 0.00 0.00 2.69
4168 6210 7.390027 CCCACATTAAAATACCCAAAACATCA 58.610 34.615 0.00 0.00 0.00 3.07
4177 6219 6.773685 TGTATGTAGCCCACATTAAAATACCC 59.226 38.462 6.84 0.00 46.01 3.69
4179 6221 8.557029 GTCTGTATGTAGCCCACATTAAAATAC 58.443 37.037 6.84 0.07 46.01 1.89
4182 6224 6.597672 CAGTCTGTATGTAGCCCACATTAAAA 59.402 38.462 6.84 0.00 46.01 1.52
4189 6232 3.887621 TTCAGTCTGTATGTAGCCCAC 57.112 47.619 0.00 0.00 0.00 4.61
4193 6236 6.333416 TCACTCATTTCAGTCTGTATGTAGC 58.667 40.000 13.61 0.00 0.00 3.58
4202 6245 5.235186 CGTCTTTGTTCACTCATTTCAGTCT 59.765 40.000 0.00 0.00 0.00 3.24
4220 6263 9.332502 TGTATACATATATGTTTTGGCGTCTTT 57.667 29.630 22.90 0.00 41.97 2.52
4223 6266 8.388103 GGATGTATACATATATGTTTTGGCGTC 58.612 37.037 22.90 16.86 41.97 5.19
4288 6335 9.989869 GCAAAACTGTTTAGAATATACTCCTTC 57.010 33.333 6.16 0.00 0.00 3.46
4354 6401 6.773976 TTGACAAATTGTTCTGAAGAAGGT 57.226 33.333 0.00 4.40 34.27 3.50
4357 6404 7.548427 TGCAAATTGACAAATTGTTCTGAAGAA 59.452 29.630 15.57 2.25 36.11 2.52
4359 6406 7.236674 TGCAAATTGACAAATTGTTCTGAAG 57.763 32.000 15.57 0.00 36.11 3.02
4376 6423 7.301054 CGAAGACTCTTCAATAGTTGCAAATT 58.699 34.615 17.23 0.00 0.00 1.82
4385 6432 5.918011 GGATACAGCGAAGACTCTTCAATAG 59.082 44.000 17.23 7.51 0.00 1.73
4388 6435 3.509967 TGGATACAGCGAAGACTCTTCAA 59.490 43.478 17.23 0.00 46.17 2.69
4404 6451 9.941664 CTCACAATAATGATGAAAGTTGGATAC 57.058 33.333 0.00 0.00 0.00 2.24
4472 6519 5.925969 CACCCATGTTCACCTTTGTATTTTC 59.074 40.000 0.00 0.00 0.00 2.29
4473 6520 5.741673 GCACCCATGTTCACCTTTGTATTTT 60.742 40.000 0.00 0.00 0.00 1.82
4474 6521 4.262420 GCACCCATGTTCACCTTTGTATTT 60.262 41.667 0.00 0.00 0.00 1.40
4475 6522 3.258123 GCACCCATGTTCACCTTTGTATT 59.742 43.478 0.00 0.00 0.00 1.89
4476 6523 2.825532 GCACCCATGTTCACCTTTGTAT 59.174 45.455 0.00 0.00 0.00 2.29
4477 6524 2.235016 GCACCCATGTTCACCTTTGTA 58.765 47.619 0.00 0.00 0.00 2.41
4478 6525 1.039856 GCACCCATGTTCACCTTTGT 58.960 50.000 0.00 0.00 0.00 2.83
4479 6526 0.039256 CGCACCCATGTTCACCTTTG 60.039 55.000 0.00 0.00 0.00 2.77
4480 6527 0.467290 ACGCACCCATGTTCACCTTT 60.467 50.000 0.00 0.00 0.00 3.11
4481 6528 1.150536 ACGCACCCATGTTCACCTT 59.849 52.632 0.00 0.00 0.00 3.50
4482 6529 1.600636 CACGCACCCATGTTCACCT 60.601 57.895 0.00 0.00 0.00 4.00
4483 6530 1.896660 ACACGCACCCATGTTCACC 60.897 57.895 0.00 0.00 0.00 4.02
4484 6531 1.282570 CACACGCACCCATGTTCAC 59.717 57.895 0.00 0.00 0.00 3.18
4485 6532 2.551006 GCACACGCACCCATGTTCA 61.551 57.895 0.00 0.00 38.36 3.18
4486 6533 2.255252 GCACACGCACCCATGTTC 59.745 61.111 0.00 0.00 38.36 3.18
4487 6534 2.518112 TGCACACGCACCCATGTT 60.518 55.556 0.00 0.00 45.36 2.71
4563 6610 7.107639 TGATTGACTAAGATTCATACCGTGA 57.892 36.000 0.00 0.00 34.25 4.35
4564 6611 7.953158 ATGATTGACTAAGATTCATACCGTG 57.047 36.000 0.00 0.00 0.00 4.94
4565 6612 8.424918 AGAATGATTGACTAAGATTCATACCGT 58.575 33.333 0.00 0.00 0.00 4.83
4566 6613 8.824159 AGAATGATTGACTAAGATTCATACCG 57.176 34.615 0.00 0.00 0.00 4.02
4572 6619 9.474920 CCTGAGTAGAATGATTGACTAAGATTC 57.525 37.037 3.70 0.00 0.00 2.52
4573 6620 8.986991 ACCTGAGTAGAATGATTGACTAAGATT 58.013 33.333 3.70 0.00 0.00 2.40
4574 6621 8.420222 CACCTGAGTAGAATGATTGACTAAGAT 58.580 37.037 3.70 0.00 0.00 2.40
4575 6622 7.631594 GCACCTGAGTAGAATGATTGACTAAGA 60.632 40.741 3.70 0.00 0.00 2.10
4576 6623 6.478344 GCACCTGAGTAGAATGATTGACTAAG 59.522 42.308 0.00 0.00 0.00 2.18
4577 6624 6.341316 GCACCTGAGTAGAATGATTGACTAA 58.659 40.000 0.00 0.00 0.00 2.24
4578 6625 5.450550 CGCACCTGAGTAGAATGATTGACTA 60.451 44.000 0.00 0.00 0.00 2.59
4579 6626 4.679106 CGCACCTGAGTAGAATGATTGACT 60.679 45.833 0.00 0.00 0.00 3.41
4580 6627 3.553511 CGCACCTGAGTAGAATGATTGAC 59.446 47.826 0.00 0.00 0.00 3.18
4581 6628 3.447229 TCGCACCTGAGTAGAATGATTGA 59.553 43.478 0.00 0.00 0.00 2.57
4582 6629 3.785486 TCGCACCTGAGTAGAATGATTG 58.215 45.455 0.00 0.00 0.00 2.67
4583 6630 4.081420 ACTTCGCACCTGAGTAGAATGATT 60.081 41.667 0.00 0.00 0.00 2.57
4584 6631 3.449018 ACTTCGCACCTGAGTAGAATGAT 59.551 43.478 0.00 0.00 0.00 2.45
4585 6632 2.826128 ACTTCGCACCTGAGTAGAATGA 59.174 45.455 0.00 0.00 0.00 2.57
4586 6633 3.238108 ACTTCGCACCTGAGTAGAATG 57.762 47.619 0.00 0.00 0.00 2.67
4587 6634 3.963428 AACTTCGCACCTGAGTAGAAT 57.037 42.857 0.00 0.00 0.00 2.40
4588 6635 3.069016 TGAAACTTCGCACCTGAGTAGAA 59.931 43.478 0.00 0.00 0.00 2.10
4589 6636 2.626266 TGAAACTTCGCACCTGAGTAGA 59.374 45.455 0.00 0.00 0.00 2.59
4590 6637 3.026630 TGAAACTTCGCACCTGAGTAG 57.973 47.619 0.00 0.00 0.00 2.57
4591 6638 3.006430 TCATGAAACTTCGCACCTGAGTA 59.994 43.478 0.00 0.00 0.00 2.59
4592 6639 2.146342 CATGAAACTTCGCACCTGAGT 58.854 47.619 0.00 0.00 0.00 3.41
4593 6640 2.416747 TCATGAAACTTCGCACCTGAG 58.583 47.619 0.00 0.00 0.00 3.35
4594 6641 2.542020 TCATGAAACTTCGCACCTGA 57.458 45.000 0.00 0.00 0.00 3.86
4595 6642 2.485426 ACATCATGAAACTTCGCACCTG 59.515 45.455 0.00 0.00 0.00 4.00
4596 6643 2.783135 ACATCATGAAACTTCGCACCT 58.217 42.857 0.00 0.00 0.00 4.00
4597 6644 4.882671 ATACATCATGAAACTTCGCACC 57.117 40.909 0.00 0.00 0.00 5.01
4598 6645 5.734498 GTCAATACATCATGAAACTTCGCAC 59.266 40.000 0.00 0.00 0.00 5.34
4599 6646 5.411053 TGTCAATACATCATGAAACTTCGCA 59.589 36.000 0.00 0.00 0.00 5.10
4600 6647 5.734498 GTGTCAATACATCATGAAACTTCGC 59.266 40.000 0.00 0.00 38.08 4.70
4601 6648 6.250819 GGTGTCAATACATCATGAAACTTCG 58.749 40.000 0.00 0.00 36.67 3.79
4602 6649 6.150976 TGGGTGTCAATACATCATGAAACTTC 59.849 38.462 0.00 0.00 38.58 3.01
4603 6650 6.009589 TGGGTGTCAATACATCATGAAACTT 58.990 36.000 0.00 0.00 38.58 2.66
4604 6651 5.569355 TGGGTGTCAATACATCATGAAACT 58.431 37.500 0.00 0.00 38.58 2.66
4605 6652 5.895636 TGGGTGTCAATACATCATGAAAC 57.104 39.130 0.00 0.00 38.58 2.78
4606 6653 5.360429 CCATGGGTGTCAATACATCATGAAA 59.640 40.000 2.85 0.00 44.28 2.69
4607 6654 4.888823 CCATGGGTGTCAATACATCATGAA 59.111 41.667 2.85 0.00 44.28 2.57
4608 6655 4.079844 ACCATGGGTGTCAATACATCATGA 60.080 41.667 18.09 0.00 44.28 3.07
4609 6656 4.209538 ACCATGGGTGTCAATACATCATG 58.790 43.478 18.09 13.25 42.90 3.07
4610 6657 4.524802 ACCATGGGTGTCAATACATCAT 57.475 40.909 18.09 0.00 38.58 2.45
4611 6658 5.645056 ATACCATGGGTGTCAATACATCA 57.355 39.130 18.09 0.00 38.58 3.07
4612 6659 6.299141 AGAATACCATGGGTGTCAATACATC 58.701 40.000 18.09 0.46 38.08 3.06
4613 6660 6.266131 AGAATACCATGGGTGTCAATACAT 57.734 37.500 18.09 0.00 38.08 2.29
4614 6661 5.708736 AGAATACCATGGGTGTCAATACA 57.291 39.130 18.09 0.00 36.19 2.29
4615 6662 7.226720 CACTAAGAATACCATGGGTGTCAATAC 59.773 40.741 18.09 0.00 36.19 1.89
4616 6663 7.126573 TCACTAAGAATACCATGGGTGTCAATA 59.873 37.037 18.09 0.00 36.19 1.90
4617 6664 6.069673 TCACTAAGAATACCATGGGTGTCAAT 60.070 38.462 18.09 5.69 36.19 2.57
4618 6665 5.249622 TCACTAAGAATACCATGGGTGTCAA 59.750 40.000 18.09 1.84 36.19 3.18
4619 6666 4.780554 TCACTAAGAATACCATGGGTGTCA 59.219 41.667 18.09 0.00 36.19 3.58
4620 6667 5.353394 TCACTAAGAATACCATGGGTGTC 57.647 43.478 18.09 9.62 36.19 3.67
4621 6668 5.487488 TCTTCACTAAGAATACCATGGGTGT 59.513 40.000 18.09 0.00 38.81 4.16
4622 6669 5.989477 TCTTCACTAAGAATACCATGGGTG 58.011 41.667 18.09 11.64 38.81 4.61
4623 6670 6.636454 TTCTTCACTAAGAATACCATGGGT 57.364 37.500 18.09 4.30 44.85 4.51
4634 6681 8.227791 GTCGCATTTGTATTTTCTTCACTAAGA 58.772 33.333 0.00 0.00 40.03 2.10
4635 6682 7.481798 GGTCGCATTTGTATTTTCTTCACTAAG 59.518 37.037 0.00 0.00 0.00 2.18
4636 6683 7.041030 TGGTCGCATTTGTATTTTCTTCACTAA 60.041 33.333 0.00 0.00 0.00 2.24
4637 6684 6.428465 TGGTCGCATTTGTATTTTCTTCACTA 59.572 34.615 0.00 0.00 0.00 2.74
4638 6685 5.240623 TGGTCGCATTTGTATTTTCTTCACT 59.759 36.000 0.00 0.00 0.00 3.41
4639 6686 5.457140 TGGTCGCATTTGTATTTTCTTCAC 58.543 37.500 0.00 0.00 0.00 3.18
4640 6687 5.697473 TGGTCGCATTTGTATTTTCTTCA 57.303 34.783 0.00 0.00 0.00 3.02
4641 6688 7.472543 AGTATGGTCGCATTTGTATTTTCTTC 58.527 34.615 0.00 0.00 0.00 2.87
4642 6689 7.391148 AGTATGGTCGCATTTGTATTTTCTT 57.609 32.000 0.00 0.00 0.00 2.52
4643 6690 8.677148 ATAGTATGGTCGCATTTGTATTTTCT 57.323 30.769 0.00 0.00 0.00 2.52
4644 6691 9.382244 GAATAGTATGGTCGCATTTGTATTTTC 57.618 33.333 0.00 0.00 0.00 2.29
4645 6692 8.898761 TGAATAGTATGGTCGCATTTGTATTTT 58.101 29.630 0.00 0.00 0.00 1.82
4646 6693 8.445275 TGAATAGTATGGTCGCATTTGTATTT 57.555 30.769 0.00 0.00 0.00 1.40
4647 6694 8.621532 ATGAATAGTATGGTCGCATTTGTATT 57.378 30.769 0.00 0.00 0.00 1.89
4648 6695 8.621532 AATGAATAGTATGGTCGCATTTGTAT 57.378 30.769 0.00 0.00 0.00 2.29
4649 6696 9.549078 TTAATGAATAGTATGGTCGCATTTGTA 57.451 29.630 0.00 0.00 0.00 2.41
4650 6697 6.942532 AATGAATAGTATGGTCGCATTTGT 57.057 33.333 0.00 0.00 0.00 2.83
4651 6698 9.897744 ATTTAATGAATAGTATGGTCGCATTTG 57.102 29.630 0.00 0.00 0.00 2.32
4689 6736 9.906660 ACAAAAATGACAAAAATCGAAGCTATA 57.093 25.926 0.00 0.00 0.00 1.31
4690 6737 8.816640 ACAAAAATGACAAAAATCGAAGCTAT 57.183 26.923 0.00 0.00 0.00 2.97
4691 6738 7.381139 GGACAAAAATGACAAAAATCGAAGCTA 59.619 33.333 0.00 0.00 0.00 3.32
4692 6739 6.200854 GGACAAAAATGACAAAAATCGAAGCT 59.799 34.615 0.00 0.00 0.00 3.74
4693 6740 6.019156 TGGACAAAAATGACAAAAATCGAAGC 60.019 34.615 0.00 0.00 0.00 3.86
4694 6741 7.434897 TCTGGACAAAAATGACAAAAATCGAAG 59.565 33.333 0.00 0.00 0.00 3.79
4695 6742 7.261325 TCTGGACAAAAATGACAAAAATCGAA 58.739 30.769 0.00 0.00 0.00 3.71
4696 6743 6.800543 TCTGGACAAAAATGACAAAAATCGA 58.199 32.000 0.00 0.00 0.00 3.59
4697 6744 7.642071 ATCTGGACAAAAATGACAAAAATCG 57.358 32.000 0.00 0.00 0.00 3.34
4699 6746 8.992073 GCTAATCTGGACAAAAATGACAAAAAT 58.008 29.630 0.00 0.00 0.00 1.82
4700 6747 7.984050 TGCTAATCTGGACAAAAATGACAAAAA 59.016 29.630 0.00 0.00 0.00 1.94
4701 6748 7.437862 GTGCTAATCTGGACAAAAATGACAAAA 59.562 33.333 0.00 0.00 0.00 2.44
4702 6749 6.922957 GTGCTAATCTGGACAAAAATGACAAA 59.077 34.615 0.00 0.00 0.00 2.83
4703 6750 6.446318 GTGCTAATCTGGACAAAAATGACAA 58.554 36.000 0.00 0.00 0.00 3.18
4704 6751 5.334802 CGTGCTAATCTGGACAAAAATGACA 60.335 40.000 0.00 0.00 0.00 3.58
4705 6752 5.088739 CGTGCTAATCTGGACAAAAATGAC 58.911 41.667 0.00 0.00 0.00 3.06
4706 6753 4.155826 CCGTGCTAATCTGGACAAAAATGA 59.844 41.667 0.00 0.00 0.00 2.57
4707 6754 4.155826 TCCGTGCTAATCTGGACAAAAATG 59.844 41.667 0.00 0.00 0.00 2.32
4708 6755 4.331968 TCCGTGCTAATCTGGACAAAAAT 58.668 39.130 0.00 0.00 0.00 1.82
4709 6756 3.745799 TCCGTGCTAATCTGGACAAAAA 58.254 40.909 0.00 0.00 0.00 1.94
4710 6757 3.410631 TCCGTGCTAATCTGGACAAAA 57.589 42.857 0.00 0.00 0.00 2.44
4711 6758 3.270027 CATCCGTGCTAATCTGGACAAA 58.730 45.455 0.00 0.00 32.33 2.83
4712 6759 2.236146 ACATCCGTGCTAATCTGGACAA 59.764 45.455 0.00 0.00 32.33 3.18
4713 6760 1.831106 ACATCCGTGCTAATCTGGACA 59.169 47.619 0.00 0.00 32.33 4.02
4714 6761 2.159099 TCACATCCGTGCTAATCTGGAC 60.159 50.000 0.00 0.00 43.28 4.02
4715 6762 2.107366 TCACATCCGTGCTAATCTGGA 58.893 47.619 0.00 0.00 43.28 3.86
4716 6763 2.602257 TCACATCCGTGCTAATCTGG 57.398 50.000 0.00 0.00 43.28 3.86
4717 6764 4.813161 AGAAATCACATCCGTGCTAATCTG 59.187 41.667 0.00 0.00 43.28 2.90
4718 6765 5.028549 AGAAATCACATCCGTGCTAATCT 57.971 39.130 0.00 0.00 43.28 2.40
4719 6766 5.741388 AAGAAATCACATCCGTGCTAATC 57.259 39.130 0.00 0.00 43.28 1.75
4720 6767 5.415701 ACAAAGAAATCACATCCGTGCTAAT 59.584 36.000 0.00 0.00 43.28 1.73
4721 6768 4.759693 ACAAAGAAATCACATCCGTGCTAA 59.240 37.500 0.00 0.00 43.28 3.09
4722 6769 4.154015 CACAAAGAAATCACATCCGTGCTA 59.846 41.667 0.00 0.00 43.28 3.49
4723 6770 3.058016 CACAAAGAAATCACATCCGTGCT 60.058 43.478 0.00 0.00 43.28 4.40
4724 6771 3.058293 TCACAAAGAAATCACATCCGTGC 60.058 43.478 0.00 0.00 43.28 5.34
4725 6772 4.747540 TCACAAAGAAATCACATCCGTG 57.252 40.909 0.00 0.00 45.08 4.94
4726 6773 5.766150 TTTCACAAAGAAATCACATCCGT 57.234 34.783 0.00 0.00 41.17 4.69
4730 6777 7.294017 ATGAGGTTTCACAAAGAAATCACAT 57.706 32.000 7.60 7.60 46.59 3.21
4736 6783 7.876068 ACTCGTATATGAGGTTTCACAAAGAAA 59.124 33.333 22.92 0.00 40.79 2.52
4737 6784 7.383687 ACTCGTATATGAGGTTTCACAAAGAA 58.616 34.615 22.92 0.00 40.39 2.52
4738 6785 6.931838 ACTCGTATATGAGGTTTCACAAAGA 58.068 36.000 22.92 0.00 40.39 2.52
4739 6786 8.873215 ATACTCGTATATGAGGTTTCACAAAG 57.127 34.615 22.92 0.00 40.39 2.77
4740 6787 9.740239 GTATACTCGTATATGAGGTTTCACAAA 57.260 33.333 22.92 1.39 40.39 2.83
4741 6788 8.355169 GGTATACTCGTATATGAGGTTTCACAA 58.645 37.037 22.92 2.26 40.39 3.33
4742 6789 7.308169 CGGTATACTCGTATATGAGGTTTCACA 60.308 40.741 22.92 3.13 40.39 3.58
4743 6790 7.020010 CGGTATACTCGTATATGAGGTTTCAC 58.980 42.308 22.92 13.51 40.39 3.18
4744 6791 6.149973 CCGGTATACTCGTATATGAGGTTTCA 59.850 42.308 22.92 6.07 40.39 2.69
4745 6792 6.150140 ACCGGTATACTCGTATATGAGGTTTC 59.850 42.308 22.92 11.92 40.39 2.78
4746 6793 6.006449 ACCGGTATACTCGTATATGAGGTTT 58.994 40.000 22.92 11.35 40.39 3.27
4747 6794 5.564550 ACCGGTATACTCGTATATGAGGTT 58.435 41.667 22.92 13.43 40.39 3.50
4748 6795 5.171339 ACCGGTATACTCGTATATGAGGT 57.829 43.478 22.92 14.59 40.39 3.85
4749 6796 5.645067 TCAACCGGTATACTCGTATATGAGG 59.355 44.000 22.92 9.19 40.39 3.86
4750 6797 6.370994 AGTCAACCGGTATACTCGTATATGAG 59.629 42.308 18.61 18.61 41.86 2.90
4751 6798 6.233434 AGTCAACCGGTATACTCGTATATGA 58.767 40.000 8.00 0.00 31.45 2.15
4752 6799 6.492007 AGTCAACCGGTATACTCGTATATG 57.508 41.667 8.00 0.00 31.45 1.78
4753 6800 7.826252 ACATAGTCAACCGGTATACTCGTATAT 59.174 37.037 21.47 9.48 31.45 0.86
4754 6801 7.161404 ACATAGTCAACCGGTATACTCGTATA 58.839 38.462 21.47 7.79 0.00 1.47
4755 6802 6.000219 ACATAGTCAACCGGTATACTCGTAT 59.000 40.000 21.47 10.08 0.00 3.06
4756 6803 5.368145 ACATAGTCAACCGGTATACTCGTA 58.632 41.667 21.47 8.41 0.00 3.43
4757 6804 4.202441 ACATAGTCAACCGGTATACTCGT 58.798 43.478 21.47 17.27 0.00 4.18
4758 6805 4.825546 ACATAGTCAACCGGTATACTCG 57.174 45.455 21.47 16.75 0.00 4.18


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

AutoCloner maintained by Alex Coulton.