Multiple sequence alignment - TraesCS1A01G058400

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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 TraesCS1A01G058400 chr1A 100.000 6781 0 0 1 6781 38734540 38727760 0.000000e+00 12523.0
1 TraesCS1A01G058400 chr1A 100.000 38 0 0 4472 4509 20031595 20031558 3.390000e-08 71.3
2 TraesCS1A01G058400 chr1D 94.718 4506 179 30 2 4477 39293366 39288890 0.000000e+00 6948.0
3 TraesCS1A01G058400 chr1D 92.775 2256 94 26 4541 6781 39288889 39286688 0.000000e+00 3199.0
4 TraesCS1A01G058400 chr1D 90.909 77 2 4 4472 4543 478184090 478184014 1.560000e-16 99.0
5 TraesCS1A01G058400 chr1B 93.257 4479 217 45 1 4447 59191871 59196296 0.000000e+00 6519.0
6 TraesCS1A01G058400 chr1B 94.319 2253 76 13 4544 6781 59196318 59198533 0.000000e+00 3404.0
7 TraesCS1A01G058400 chr7D 92.308 91 7 0 2006 2096 614168374 614168284 5.520000e-26 130.0
8 TraesCS1A01G058400 chr7A 92.308 91 7 0 2006 2096 706259399 706259309 5.520000e-26 130.0
9 TraesCS1A01G058400 chr7A 93.939 66 3 1 4475 4540 54191298 54191234 1.560000e-16 99.0
10 TraesCS1A01G058400 chr7B 91.209 91 8 0 2006 2096 705967388 705967298 2.570000e-24 124.0
11 TraesCS1A01G058400 chr7B 96.875 32 1 0 4472 4503 548471961 548471992 3.000000e-03 54.7
12 TraesCS1A01G058400 chr5B 100.000 38 0 0 4473 4510 441067883 441067846 3.390000e-08 71.3
13 TraesCS1A01G058400 chr4A 100.000 38 0 0 4472 4509 683428739 683428776 3.390000e-08 71.3
14 TraesCS1A01G058400 chr2D 88.710 62 2 2 4474 4530 628993361 628993300 3.390000e-08 71.3
15 TraesCS1A01G058400 chr3D 95.238 42 2 0 4471 4512 206968986 206968945 4.390000e-07 67.6
16 TraesCS1A01G058400 chr3D 100.000 36 0 0 4475 4510 425075676 425075641 4.390000e-07 67.6
17 TraesCS1A01G058400 chr6A 93.182 44 3 0 959 1002 617977586 617977543 1.580000e-06 65.8
18 TraesCS1A01G058400 chr5D 91.837 49 1 1 4498 4543 393754326 393754278 1.580000e-06 65.8


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 TraesCS1A01G058400 chr1A 38727760 38734540 6780 True 12523.0 12523 100.0000 1 6781 1 chr1A.!!$R2 6780
1 TraesCS1A01G058400 chr1D 39286688 39293366 6678 True 5073.5 6948 93.7465 2 6781 2 chr1D.!!$R2 6779
2 TraesCS1A01G058400 chr1B 59191871 59198533 6662 False 4961.5 6519 93.7880 1 6781 2 chr1B.!!$F1 6780

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
579 587 0.238289 AAAGGTGAATTGCGCAGACG 59.762 50.0 11.31 0.00 44.07 4.18 F
581 589 0.391661 AGGTGAATTGCGCAGACGAT 60.392 50.0 11.31 0.00 43.93 3.73 F
2204 2242 0.176680 TCTTGCTCCTCTTCATCGCC 59.823 55.0 0.00 0.00 0.00 5.54 F
2344 2382 0.396811 ACCTGAACCACCTGTACTGC 59.603 55.0 0.00 0.00 0.00 4.40 F
3471 3520 0.599728 TGGCAAAATTCTGCGTTGGC 60.600 50.0 0.00 2.19 43.60 4.52 F
4492 4542 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.0 0.00 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 2139 1.000359 GGGGTGGTTGGAGGGATTG 60.000 63.158 0.00 0.0 0.00 2.67 R
2243 2281 1.762419 CAGCATGTGCAGTGTCAAAC 58.238 50.000 7.83 0.0 45.16 2.93 R
3670 3719 1.000843 GTGAAATTGGACTGGTTGCCC 59.999 52.381 0.00 0.0 0.00 5.36 R
4315 4364 0.652592 GCTATAACTGCAGCCACACG 59.347 55.000 15.27 0.0 0.00 4.49 R
4520 4570 2.298163 ACTCCGTCCGTCAAATAAGTGT 59.702 45.455 0.00 0.0 0.00 3.55 R
6283 6364 0.179084 CAGATGCCGTCGGGTACATT 60.179 55.000 14.38 0.0 34.97 2.71 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
29 30 2.408271 TGAGCCGCAAAGATTGATCT 57.592 45.000 0.00 0.00 39.22 2.75
30 31 2.011947 TGAGCCGCAAAGATTGATCTG 58.988 47.619 0.00 0.00 37.19 2.90
35 36 3.785505 GCCGCAAAGATTGATCTGTTACG 60.786 47.826 0.00 0.00 37.19 3.18
39 40 6.019075 CCGCAAAGATTGATCTGTTACGATTA 60.019 38.462 0.00 0.00 37.19 1.75
52 53 7.655490 TCTGTTACGATTATAGCCTTAGGTTC 58.345 38.462 0.00 0.00 0.00 3.62
60 61 1.446016 AGCCTTAGGTTCAGTGGGTT 58.554 50.000 0.00 0.00 0.00 4.11
61 62 1.780919 AGCCTTAGGTTCAGTGGGTTT 59.219 47.619 0.00 0.00 0.00 3.27
83 84 5.772393 TGGGCTTTCTAAAGGTCTTATCA 57.228 39.130 4.71 0.00 36.53 2.15
87 88 8.333235 TGGGCTTTCTAAAGGTCTTATCAATAA 58.667 33.333 4.71 0.00 36.53 1.40
149 156 2.829741 AATCAATCCGAGCTAGCTCC 57.170 50.000 33.57 18.82 39.77 4.70
166 173 1.344763 CTCCTTATCCACCCATCGTCC 59.655 57.143 0.00 0.00 0.00 4.79
217 224 7.841729 TCCATCTTCTAAGTGAGGATAAGAACT 59.158 37.037 0.00 0.00 39.14 3.01
226 233 3.383825 TGAGGATAAGAACTTAGACGGGC 59.616 47.826 0.00 0.00 0.00 6.13
230 237 5.659971 AGGATAAGAACTTAGACGGGCTTTA 59.340 40.000 0.00 0.00 0.00 1.85
234 241 2.963548 ACTTAGACGGGCTTTAGCTC 57.036 50.000 0.00 0.00 41.70 4.09
249 256 1.092921 AGCTCGCCAAACACGACAAA 61.093 50.000 0.00 0.00 35.35 2.83
253 260 0.591236 CGCCAAACACGACAAACTGG 60.591 55.000 0.00 0.00 0.00 4.00
256 263 1.202245 CCAAACACGACAAACTGGTGG 60.202 52.381 0.00 0.00 36.02 4.61
279 286 3.670625 CTGGAAAGATTGGTCCGTTACA 58.329 45.455 0.00 0.00 36.65 2.41
286 293 8.895737 GGAAAGATTGGTCCGTTACAATTATAA 58.104 33.333 0.00 0.00 37.43 0.98
291 298 6.988622 TGGTCCGTTACAATTATAACCTTG 57.011 37.500 1.12 0.00 32.36 3.61
294 301 6.114767 GTCCGTTACAATTATAACCTTGGGA 58.885 40.000 1.12 0.00 32.36 4.37
296 303 6.993902 TCCGTTACAATTATAACCTTGGGATC 59.006 38.462 1.12 0.00 32.36 3.36
298 305 7.283580 CCGTTACAATTATAACCTTGGGATCAA 59.716 37.037 1.12 0.00 32.36 2.57
303 310 6.544327 ATTATAACCTTGGGATCAATGGGA 57.456 37.500 0.00 0.00 31.75 4.37
313 320 2.843701 GATCAATGGGATCGTGCTTCT 58.156 47.619 0.00 0.00 42.81 2.85
320 327 2.569853 TGGGATCGTGCTTCTTAAAGGA 59.430 45.455 0.00 0.00 32.79 3.36
328 335 3.861840 TGCTTCTTAAAGGACAGATCGG 58.138 45.455 0.00 0.00 32.79 4.18
332 339 4.280436 TCTTAAAGGACAGATCGGCAAA 57.720 40.909 0.00 0.00 0.00 3.68
341 348 3.679389 ACAGATCGGCAAATGTCTCTTT 58.321 40.909 0.00 0.00 0.00 2.52
348 356 7.970614 AGATCGGCAAATGTCTCTTTTATTTTC 59.029 33.333 0.00 0.00 0.00 2.29
374 382 9.108284 CAAGAACATGAAAGTTTAATTGGGTTT 57.892 29.630 0.00 0.00 0.00 3.27
408 416 2.359214 CTGAGCTAGCTCGTTATCCACA 59.641 50.000 33.55 16.51 45.48 4.17
437 445 4.212214 CCTACTCAATTCGCCTCTTAATGC 59.788 45.833 0.00 0.00 0.00 3.56
450 458 5.468409 GCCTCTTAATGCTCTTCCATCTAAC 59.532 44.000 0.00 0.00 0.00 2.34
459 467 5.069648 TGCTCTTCCATCTAACTGTGGATAG 59.930 44.000 0.00 0.00 43.61 2.08
579 587 0.238289 AAAGGTGAATTGCGCAGACG 59.762 50.000 11.31 0.00 44.07 4.18
581 589 0.391661 AGGTGAATTGCGCAGACGAT 60.392 50.000 11.31 0.00 43.93 3.73
613 621 2.202797 CGCTAGCCAGTGTCGCAT 60.203 61.111 9.66 0.00 0.00 4.73
614 622 2.520039 CGCTAGCCAGTGTCGCATG 61.520 63.158 9.66 0.00 0.00 4.06
615 623 2.817423 GCTAGCCAGTGTCGCATGC 61.817 63.158 7.91 7.91 0.00 4.06
616 624 1.448365 CTAGCCAGTGTCGCATGCA 60.448 57.895 19.57 1.73 0.00 3.96
618 626 0.392863 TAGCCAGTGTCGCATGCAAT 60.393 50.000 19.57 0.00 0.00 3.56
653 661 3.247006 TGGAACGGCTCTGTATTCTTC 57.753 47.619 0.00 0.00 0.00 2.87
741 756 3.846588 AGAAATGTGGTGGTGGTCTATCT 59.153 43.478 0.00 0.00 0.00 1.98
904 922 9.705290 CCAACAAAAATACCAAATAAAGCTAGT 57.295 29.630 0.00 0.00 0.00 2.57
931 949 6.372937 GGAGACTTGAGATAACAAAAGGAAGG 59.627 42.308 0.00 0.00 0.00 3.46
1130 1151 4.747810 AGCCAAGCTTTTGTTGCATATAC 58.252 39.130 0.00 0.00 33.89 1.47
1166 1187 1.966451 CCCACCTTTCTGACACCGC 60.966 63.158 0.00 0.00 0.00 5.68
1209 1230 9.143631 CCATGTAAAATTGTTCTTCTTGAATCC 57.856 33.333 0.00 0.00 36.99 3.01
1475 1501 6.039270 TGTTCTCGTTGATTGATTGGAAGTTT 59.961 34.615 0.00 0.00 0.00 2.66
2104 2139 1.343465 CCCATATCTGGTCCGTACACC 59.657 57.143 0.00 0.00 41.37 4.16
2136 2171 0.391228 CACCCCCAAAAAGAAACCCG 59.609 55.000 0.00 0.00 0.00 5.28
2164 2200 5.614324 TTCCTCAAATATCACCGACTGAT 57.386 39.130 1.75 1.75 42.68 2.90
2168 2206 6.316140 TCCTCAAATATCACCGACTGATTTTG 59.684 38.462 15.19 15.19 40.38 2.44
2195 2233 7.592903 CAGTTCTTACAAATTTTCTTGCTCCTC 59.407 37.037 0.00 0.00 0.00 3.71
2204 2242 0.176680 TCTTGCTCCTCTTCATCGCC 59.823 55.000 0.00 0.00 0.00 5.54
2243 2281 1.303317 GCAGGTGTACTTGGGTGGG 60.303 63.158 0.00 0.00 0.00 4.61
2276 2314 4.590487 GCTGCTGCAAGGTACGTA 57.410 55.556 11.11 0.00 39.41 3.57
2277 2315 2.079049 GCTGCTGCAAGGTACGTAC 58.921 57.895 17.56 17.56 39.41 3.67
2293 2331 9.830294 AAGGTACGTACAAATTTAATTAAGCAC 57.170 29.630 26.02 3.60 0.00 4.40
2295 2333 7.956943 GGTACGTACAAATTTAATTAAGCACGT 59.043 33.333 26.02 18.34 41.26 4.49
2296 2334 9.950858 GTACGTACAAATTTAATTAAGCACGTA 57.049 29.630 20.67 17.00 39.36 3.57
2344 2382 0.396811 ACCTGAACCACCTGTACTGC 59.603 55.000 0.00 0.00 0.00 4.40
2348 2386 1.488812 TGAACCACCTGTACTGCAACT 59.511 47.619 0.00 0.00 0.00 3.16
2356 2394 3.134804 ACCTGTACTGCAACTCTGAAGTT 59.865 43.478 0.00 0.00 38.40 2.66
2360 2398 5.853936 TGTACTGCAACTCTGAAGTTATGT 58.146 37.500 0.00 0.00 38.40 2.29
2361 2399 5.926542 TGTACTGCAACTCTGAAGTTATGTC 59.073 40.000 0.00 0.00 38.40 3.06
2595 2633 5.756195 TGTTGAAACTGATGAACTGAAGG 57.244 39.130 0.00 0.00 0.00 3.46
2604 2642 6.171921 ACTGATGAACTGAAGGAATTCTGAG 58.828 40.000 5.23 0.00 0.00 3.35
2606 2644 6.537355 TGATGAACTGAAGGAATTCTGAGTT 58.463 36.000 5.23 2.39 33.88 3.01
2607 2645 6.652481 TGATGAACTGAAGGAATTCTGAGTTC 59.348 38.462 15.55 15.55 41.52 3.01
2608 2646 6.179906 TGAACTGAAGGAATTCTGAGTTCT 57.820 37.500 20.05 2.32 41.60 3.01
2609 2647 5.994054 TGAACTGAAGGAATTCTGAGTTCTG 59.006 40.000 20.05 15.73 41.60 3.02
2610 2648 5.815233 ACTGAAGGAATTCTGAGTTCTGA 57.185 39.130 11.90 0.00 0.00 3.27
2611 2649 5.546526 ACTGAAGGAATTCTGAGTTCTGAC 58.453 41.667 11.90 5.32 0.00 3.51
2824 2867 4.397420 ACAAATTCCCCTTTCCATTTTGC 58.603 39.130 0.00 0.00 0.00 3.68
2829 2872 1.002315 CCCCTTTCCATTTTGCACCAG 59.998 52.381 0.00 0.00 0.00 4.00
3042 3090 9.281371 TCAAAATAAGATGCATAGATCAGGAAG 57.719 33.333 0.00 0.00 0.00 3.46
3046 3094 9.451002 AATAAGATGCATAGATCAGGAAGAATG 57.549 33.333 0.00 0.00 0.00 2.67
3313 3361 1.066257 GGCGGCGATCAAATGCAAT 59.934 52.632 12.98 0.00 0.00 3.56
3331 3379 1.043673 ATGGTAGAGAGGCCGTGACC 61.044 60.000 0.00 2.55 0.00 4.02
3471 3520 0.599728 TGGCAAAATTCTGCGTTGGC 60.600 50.000 0.00 2.19 43.60 4.52
3492 3541 4.582459 GCGATTAGCTGATGAACTTGAAC 58.418 43.478 0.00 0.00 44.04 3.18
3494 3543 5.501574 GCGATTAGCTGATGAACTTGAACTC 60.502 44.000 0.00 0.00 44.04 3.01
3501 3550 6.820656 AGCTGATGAACTTGAACTCGATTATT 59.179 34.615 0.00 0.00 0.00 1.40
3710 3759 4.139786 CACTGCTGGATTTGTATGGCTAT 58.860 43.478 0.00 0.00 0.00 2.97
3771 3820 3.198635 ACCATGCTAGTGACTGCAGTATT 59.801 43.478 21.73 10.80 42.74 1.89
4035 4084 0.625683 ATGCTCCCCCTGAGATGGTT 60.626 55.000 0.00 0.00 44.42 3.67
4038 4087 2.124570 CCCCCTGAGATGGTTGCG 60.125 66.667 0.00 0.00 0.00 4.85
4243 4292 2.294233 GCCACTCTGTTTTGCAATCAGA 59.706 45.455 23.74 23.74 36.85 3.27
4314 4363 9.821662 GTACTTAGCGTCAATTAAACATTTTCT 57.178 29.630 0.00 0.00 0.00 2.52
4315 4364 8.950403 ACTTAGCGTCAATTAAACATTTTCTC 57.050 30.769 0.00 0.00 0.00 2.87
4366 4416 4.599041 CCTGATTTTCATAGTCCACCCAA 58.401 43.478 0.00 0.00 0.00 4.12
4374 4424 2.053747 TAGTCCACCCAATCCCTGTT 57.946 50.000 0.00 0.00 0.00 3.16
4441 4491 3.450817 TCTTGAGTCCTCACAAACTGTCA 59.549 43.478 0.00 0.00 39.66 3.58
4481 4531 8.936764 ACTACTAGTCATAGGATATACTCCCT 57.063 38.462 0.00 0.00 46.27 4.20
4482 4532 8.995577 ACTACTAGTCATAGGATATACTCCCTC 58.004 40.741 0.00 0.00 46.27 4.30
4483 4533 7.215743 ACTAGTCATAGGATATACTCCCTCC 57.784 44.000 0.00 0.00 46.27 4.30
4484 4534 5.118729 AGTCATAGGATATACTCCCTCCG 57.881 47.826 0.00 0.00 46.27 4.63
4485 4535 4.540906 AGTCATAGGATATACTCCCTCCGT 59.459 45.833 0.00 0.00 46.27 4.69
4486 4536 4.883006 GTCATAGGATATACTCCCTCCGTC 59.117 50.000 0.00 0.00 46.27 4.79
4487 4537 2.903375 AGGATATACTCCCTCCGTCC 57.097 55.000 0.00 0.00 46.27 4.79
4488 4538 1.358445 AGGATATACTCCCTCCGTCCC 59.642 57.143 0.00 0.00 46.27 4.46
4489 4539 1.461559 GATATACTCCCTCCGTCCCG 58.538 60.000 0.00 0.00 0.00 5.14
4490 4540 1.004044 GATATACTCCCTCCGTCCCGA 59.996 57.143 0.00 0.00 0.00 5.14
4491 4541 0.846015 TATACTCCCTCCGTCCCGAA 59.154 55.000 0.00 0.00 0.00 4.30
4492 4542 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.000 0.00 0.00 0.00 3.46
4493 4543 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
4494 4544 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
4495 4545 1.117150 CTCCCTCCGTCCCGAAATAA 58.883 55.000 0.00 0.00 0.00 1.40
4496 4546 1.068741 CTCCCTCCGTCCCGAAATAAG 59.931 57.143 0.00 0.00 0.00 1.73
4497 4547 0.828677 CCCTCCGTCCCGAAATAAGT 59.171 55.000 0.00 0.00 0.00 2.24
4498 4548 1.472728 CCCTCCGTCCCGAAATAAGTG 60.473 57.143 0.00 0.00 0.00 3.16
4499 4549 1.206371 CCTCCGTCCCGAAATAAGTGT 59.794 52.381 0.00 0.00 0.00 3.55
4500 4550 2.537401 CTCCGTCCCGAAATAAGTGTC 58.463 52.381 0.00 0.00 0.00 3.67
4501 4551 2.165845 CTCCGTCCCGAAATAAGTGTCT 59.834 50.000 0.00 0.00 0.00 3.41
4502 4552 2.165030 TCCGTCCCGAAATAAGTGTCTC 59.835 50.000 0.00 0.00 0.00 3.36
4503 4553 2.094390 CCGTCCCGAAATAAGTGTCTCA 60.094 50.000 0.00 0.00 0.00 3.27
4504 4554 3.581755 CGTCCCGAAATAAGTGTCTCAA 58.418 45.455 0.00 0.00 0.00 3.02
4505 4555 3.367025 CGTCCCGAAATAAGTGTCTCAAC 59.633 47.826 0.00 0.00 0.00 3.18
4506 4556 4.566987 GTCCCGAAATAAGTGTCTCAACT 58.433 43.478 0.00 0.00 0.00 3.16
4507 4557 4.995487 GTCCCGAAATAAGTGTCTCAACTT 59.005 41.667 0.00 0.00 42.89 2.66
4508 4558 5.469084 GTCCCGAAATAAGTGTCTCAACTTT 59.531 40.000 0.00 0.00 40.77 2.66
4509 4559 6.647895 GTCCCGAAATAAGTGTCTCAACTTTA 59.352 38.462 0.00 0.00 40.77 1.85
4510 4560 6.647895 TCCCGAAATAAGTGTCTCAACTTTAC 59.352 38.462 0.00 0.00 40.77 2.01
4511 4561 6.425721 CCCGAAATAAGTGTCTCAACTTTACA 59.574 38.462 0.00 0.00 40.77 2.41
4512 4562 7.041644 CCCGAAATAAGTGTCTCAACTTTACAA 60.042 37.037 0.00 0.00 40.77 2.41
4513 4563 8.339714 CCGAAATAAGTGTCTCAACTTTACAAA 58.660 33.333 0.00 0.00 40.77 2.83
4514 4564 9.370126 CGAAATAAGTGTCTCAACTTTACAAAG 57.630 33.333 0.13 0.13 40.77 2.77
4532 4582 9.997482 TTTACAAAGTTGAGACACTTATTTGAC 57.003 29.630 0.00 0.00 35.87 3.18
4533 4583 6.715464 ACAAAGTTGAGACACTTATTTGACG 58.285 36.000 0.00 0.00 35.87 4.35
4534 4584 5.924475 AAGTTGAGACACTTATTTGACGG 57.076 39.130 0.00 0.00 35.10 4.79
4535 4585 5.209818 AGTTGAGACACTTATTTGACGGA 57.790 39.130 0.00 0.00 0.00 4.69
4536 4586 4.989168 AGTTGAGACACTTATTTGACGGAC 59.011 41.667 0.00 0.00 0.00 4.79
4537 4587 3.571571 TGAGACACTTATTTGACGGACG 58.428 45.455 0.00 0.00 0.00 4.79
4538 4588 2.921754 GAGACACTTATTTGACGGACGG 59.078 50.000 0.00 0.00 0.00 4.79
4539 4589 2.559668 AGACACTTATTTGACGGACGGA 59.440 45.455 0.00 0.00 0.00 4.69
4679 4730 6.639279 ACGTTTTGGTGTTCTATTTTGTATGC 59.361 34.615 0.00 0.00 0.00 3.14
4680 4731 6.861055 CGTTTTGGTGTTCTATTTTGTATGCT 59.139 34.615 0.00 0.00 0.00 3.79
4681 4732 8.018520 CGTTTTGGTGTTCTATTTTGTATGCTA 58.981 33.333 0.00 0.00 0.00 3.49
4682 4733 9.855021 GTTTTGGTGTTCTATTTTGTATGCTAT 57.145 29.630 0.00 0.00 0.00 2.97
4828 4894 2.047274 GCTAGCAAGTCGGCACCA 60.047 61.111 10.63 0.00 35.83 4.17
4997 5063 5.413309 TTTTTCCTGGAAAGCAAGTTCAA 57.587 34.783 20.25 8.03 32.93 2.69
5003 5069 2.951642 TGGAAAGCAAGTTCAACTGGAG 59.048 45.455 0.00 0.00 0.00 3.86
5004 5070 2.952310 GGAAAGCAAGTTCAACTGGAGT 59.048 45.455 0.00 0.00 0.00 3.85
5005 5071 4.134563 GGAAAGCAAGTTCAACTGGAGTA 58.865 43.478 0.00 0.00 0.00 2.59
5052 5118 6.016192 TCGATCAAAGCGATAGGAATTAGACT 60.016 38.462 0.00 0.00 33.17 3.24
5053 5119 6.088749 CGATCAAAGCGATAGGAATTAGACTG 59.911 42.308 0.00 0.00 33.17 3.51
5577 5647 1.945169 CTCTGCGCTCTCTGCATCG 60.945 63.158 9.73 0.00 42.32 3.84
5601 5671 2.030805 GCATTGGTCCCATAATTCTCGC 60.031 50.000 0.00 0.00 0.00 5.03
5786 5856 2.360801 TGTTTTTGCTCTACAGCCAACC 59.639 45.455 0.00 0.00 46.26 3.77
5802 5872 0.675633 AACCACCACTGCTGAATTGC 59.324 50.000 0.00 0.00 0.00 3.56
5885 5955 9.113838 CTGGTGCAAGAATATAAATACTTGAGT 57.886 33.333 0.00 0.00 41.16 3.41
5886 5956 9.109393 TGGTGCAAGAATATAAATACTTGAGTC 57.891 33.333 0.00 0.00 41.16 3.36
5887 5957 9.331282 GGTGCAAGAATATAAATACTTGAGTCT 57.669 33.333 0.00 0.00 41.16 3.24
5965 6036 9.475620 TCTACATGACTCCTAAATTCTGTAGAA 57.524 33.333 0.00 0.00 40.24 2.10
6120 6191 6.449635 ACAGATACTTCAGAAGCACTAGAG 57.550 41.667 10.33 0.00 0.00 2.43
6160 6241 5.073144 AGTTTCCTGTGTAATTTCCTCCAGA 59.927 40.000 0.00 0.00 0.00 3.86
6162 6243 4.906618 TCCTGTGTAATTTCCTCCAGAAC 58.093 43.478 0.00 0.00 32.95 3.01
6258 6339 4.261572 GCTGCAGTGATTTTGTCAGGTAAA 60.262 41.667 16.64 0.00 37.56 2.01
6283 6364 0.252057 TCTCTGTCGGGGATGGTGAA 60.252 55.000 0.00 0.00 0.00 3.18
6286 6367 1.065491 TCTGTCGGGGATGGTGAAATG 60.065 52.381 0.00 0.00 0.00 2.32
6299 6380 0.250793 TGAAATGTACCCGACGGCAT 59.749 50.000 8.86 3.82 0.00 4.40
6321 6402 2.648102 CGGCGTCGATCGAGTCAC 60.648 66.667 20.09 6.31 42.86 3.67
6384 6465 1.069049 GGCACATGTTTTTGACAGCCT 59.931 47.619 11.26 0.00 41.50 4.58
6387 6468 1.963515 ACATGTTTTTGACAGCCTCCC 59.036 47.619 0.00 0.00 42.62 4.30
6548 6634 3.454042 TGTGCGAAACAGATGAATTCG 57.546 42.857 15.83 15.83 46.36 3.34
6598 6684 7.876896 TTACTTTTGCGGGAATTATCAAAAC 57.123 32.000 0.00 0.00 35.41 2.43
6616 6702 0.930726 ACCCTTTGGTCCAAACAGGA 59.069 50.000 25.73 4.59 43.06 3.86
6631 6717 0.669625 CAGGACTCGGTTTCGTTCCC 60.670 60.000 0.00 0.00 39.08 3.97
6634 6720 1.541889 GGACTCGGTTTCGTTCCCTTT 60.542 52.381 0.00 0.00 35.26 3.11
6654 6740 6.058183 CCTTTGAGAAGAAAGAACTGGAAGA 58.942 40.000 0.00 0.00 35.30 2.87
6665 6751 0.744874 ACTGGAAGATGCATGCATGC 59.255 50.000 38.71 38.71 46.22 4.06
6683 6769 4.804108 CATGCTACTAGATCTACTGCCAC 58.196 47.826 0.00 0.00 0.00 5.01
6693 6779 0.911769 CTACTGCCACCCTCCAATCA 59.088 55.000 0.00 0.00 0.00 2.57
6722 6808 9.685828 TGATTGTATTACTTTTGTTTACTTGCC 57.314 29.630 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.840401 TCGTAACAGATCAATCTTTGCG 57.160 40.909 13.56 13.56 36.03 4.85
29 30 7.069085 ACTGAACCTAAGGCTATAATCGTAACA 59.931 37.037 0.00 0.00 0.00 2.41
30 31 7.381678 CACTGAACCTAAGGCTATAATCGTAAC 59.618 40.741 0.00 0.00 0.00 2.50
35 36 5.071923 ACCCACTGAACCTAAGGCTATAATC 59.928 44.000 0.00 0.00 0.00 1.75
39 40 2.846950 ACCCACTGAACCTAAGGCTAT 58.153 47.619 0.00 0.00 0.00 2.97
52 53 2.286365 TAGAAAGCCCAAACCCACTG 57.714 50.000 0.00 0.00 0.00 3.66
60 61 6.134535 TGATAAGACCTTTAGAAAGCCCAA 57.865 37.500 0.00 0.00 34.69 4.12
61 62 5.772393 TGATAAGACCTTTAGAAAGCCCA 57.228 39.130 0.00 0.00 34.69 5.36
99 100 9.474920 CAAACTCAATTAAGCTTCCATGTTAAA 57.525 29.630 0.00 0.00 0.00 1.52
133 140 3.367910 GGATAAGGAGCTAGCTCGGATTG 60.368 52.174 32.78 0.00 43.59 2.67
134 141 2.829120 GGATAAGGAGCTAGCTCGGATT 59.171 50.000 32.78 27.55 43.59 3.01
138 145 1.271102 GGTGGATAAGGAGCTAGCTCG 59.729 57.143 32.78 0.00 43.59 5.03
149 156 1.762957 AGTGGACGATGGGTGGATAAG 59.237 52.381 0.00 0.00 0.00 1.73
166 173 7.308782 AGAACATTAAGAGGCGAATTAAGTG 57.691 36.000 0.00 0.00 0.00 3.16
217 224 0.179119 GCGAGCTAAAGCCCGTCTAA 60.179 55.000 7.71 0.00 44.30 2.10
226 233 1.136336 GTCGTGTTTGGCGAGCTAAAG 60.136 52.381 6.85 0.00 39.14 1.85
230 237 1.092921 TTTGTCGTGTTTGGCGAGCT 61.093 50.000 0.00 0.00 39.14 4.09
234 241 0.591236 CCAGTTTGTCGTGTTTGGCG 60.591 55.000 0.00 0.00 0.00 5.69
241 248 1.525995 AGCCCACCAGTTTGTCGTG 60.526 57.895 0.00 0.00 0.00 4.35
249 256 0.779997 AATCTTTCCAGCCCACCAGT 59.220 50.000 0.00 0.00 0.00 4.00
253 260 1.177401 GACCAATCTTTCCAGCCCAC 58.823 55.000 0.00 0.00 0.00 4.61
256 263 0.322546 ACGGACCAATCTTTCCAGCC 60.323 55.000 0.00 0.00 0.00 4.85
279 286 6.932753 TCCCATTGATCCCAAGGTTATAATT 58.067 36.000 0.00 0.00 35.48 1.40
286 293 1.143684 CGATCCCATTGATCCCAAGGT 59.856 52.381 0.00 0.00 46.06 3.50
291 298 0.109342 AGCACGATCCCATTGATCCC 59.891 55.000 0.00 0.00 46.06 3.85
294 301 3.287867 AAGAAGCACGATCCCATTGAT 57.712 42.857 0.00 0.00 36.01 2.57
296 303 4.201950 CCTTTAAGAAGCACGATCCCATTG 60.202 45.833 0.00 0.00 0.00 2.82
298 305 3.199946 TCCTTTAAGAAGCACGATCCCAT 59.800 43.478 0.00 0.00 0.00 4.00
303 310 4.537135 TCTGTCCTTTAAGAAGCACGAT 57.463 40.909 0.00 0.00 0.00 3.73
306 313 3.619038 CCGATCTGTCCTTTAAGAAGCAC 59.381 47.826 0.00 0.00 0.00 4.40
312 319 4.396166 ACATTTGCCGATCTGTCCTTTAAG 59.604 41.667 0.00 0.00 0.00 1.85
313 320 4.331968 ACATTTGCCGATCTGTCCTTTAA 58.668 39.130 0.00 0.00 0.00 1.52
320 327 3.340814 AAGAGACATTTGCCGATCTGT 57.659 42.857 0.00 0.00 0.00 3.41
325 332 6.976088 TGAAAATAAAAGAGACATTTGCCGA 58.024 32.000 0.00 0.00 0.00 5.54
348 356 8.661352 AACCCAATTAAACTTTCATGTTCTTG 57.339 30.769 0.00 0.00 0.00 3.02
374 382 6.338214 AGCTAGCTCAGATCGATTTATTCA 57.662 37.500 12.68 0.00 0.00 2.57
408 416 1.571919 GCGAATTGAGTAGGCGATGT 58.428 50.000 0.00 0.00 0.00 3.06
450 458 2.033049 CCGTCTACGTTCCTATCCACAG 59.967 54.545 0.00 0.00 37.74 3.66
459 467 1.150827 CCAAAACCCGTCTACGTTCC 58.849 55.000 0.00 0.00 37.74 3.62
590 598 1.924320 GACACTGGCTAGCGACGAGT 61.924 60.000 9.00 5.13 0.00 4.18
620 628 1.491670 CGTTCCATGCGGATACTCTG 58.508 55.000 0.00 0.00 42.41 3.35
621 629 3.967886 CGTTCCATGCGGATACTCT 57.032 52.632 0.00 0.00 42.41 3.24
638 646 4.582701 AGATGAGAAGAATACAGAGCCG 57.417 45.455 0.00 0.00 0.00 5.52
699 708 9.087424 CATTTCTACGATTCTATTGAACACTCA 57.913 33.333 0.00 0.00 34.71 3.41
715 724 1.695242 ACCACCACCACATTTCTACGA 59.305 47.619 0.00 0.00 0.00 3.43
741 756 3.162666 AGGACAGTCGATTGGTCTTACA 58.837 45.455 12.90 0.00 0.00 2.41
904 922 7.792364 TCCTTTTGTTATCTCAAGTCTCCTA 57.208 36.000 0.00 0.00 0.00 2.94
905 923 6.688073 TCCTTTTGTTATCTCAAGTCTCCT 57.312 37.500 0.00 0.00 0.00 3.69
906 924 6.372937 CCTTCCTTTTGTTATCTCAAGTCTCC 59.627 42.308 0.00 0.00 0.00 3.71
1130 1151 1.539157 GGAGCTTTTGGAGTGAAGGG 58.461 55.000 0.00 0.00 0.00 3.95
1184 1205 9.918630 AGGATTCAAGAAGAACAATTTTACATG 57.081 29.630 0.00 0.00 39.49 3.21
1209 1230 1.068250 GGCCGCTAGCTAACCTCAG 59.932 63.158 13.93 0.00 43.05 3.35
1475 1501 1.596934 GCCGAGATCACCACTTCCA 59.403 57.895 0.00 0.00 0.00 3.53
2104 2139 1.000359 GGGGTGGTTGGAGGGATTG 60.000 63.158 0.00 0.00 0.00 2.67
2158 2194 8.579682 AATTTGTAAGAACTGCAAAATCAGTC 57.420 30.769 0.00 0.00 45.77 3.51
2164 2200 8.174422 GCAAGAAAATTTGTAAGAACTGCAAAA 58.826 29.630 0.00 0.00 36.00 2.44
2168 2206 6.144563 GGAGCAAGAAAATTTGTAAGAACTGC 59.855 38.462 0.00 0.00 0.00 4.40
2243 2281 1.762419 CAGCATGTGCAGTGTCAAAC 58.238 50.000 7.83 0.00 45.16 2.93
2274 2312 7.478044 TGCGTACGTGCTTAATTAAATTTGTAC 59.522 33.333 17.90 14.42 35.36 2.90
2275 2313 7.516481 TGCGTACGTGCTTAATTAAATTTGTA 58.484 30.769 17.90 0.00 35.36 2.41
2276 2314 6.372185 TGCGTACGTGCTTAATTAAATTTGT 58.628 32.000 17.90 0.00 35.36 2.83
2277 2315 6.521821 ACTGCGTACGTGCTTAATTAAATTTG 59.478 34.615 17.90 0.00 35.36 2.32
2293 2331 5.231357 ACATCACAATTATGTACTGCGTACG 59.769 40.000 11.84 11.84 41.41 3.67
2295 2333 6.334202 TCACATCACAATTATGTACTGCGTA 58.666 36.000 0.00 0.00 37.82 4.42
2296 2334 5.175127 TCACATCACAATTATGTACTGCGT 58.825 37.500 0.00 0.00 37.82 5.24
2333 2371 2.820059 TCAGAGTTGCAGTACAGGTG 57.180 50.000 0.00 0.00 0.00 4.00
2344 2382 5.788450 AGTGGAGACATAACTTCAGAGTTG 58.212 41.667 2.25 0.00 43.37 3.16
2348 2386 5.080337 ACAGAGTGGAGACATAACTTCAGA 58.920 41.667 0.00 0.00 46.14 3.27
2356 2394 6.166279 GTGAAATGAACAGAGTGGAGACATA 58.834 40.000 0.00 0.00 46.14 2.29
2360 2398 3.554960 CGGTGAAATGAACAGAGTGGAGA 60.555 47.826 0.00 0.00 0.00 3.71
2361 2399 2.738846 CGGTGAAATGAACAGAGTGGAG 59.261 50.000 0.00 0.00 0.00 3.86
2604 2642 4.946784 ACAACAACAACAGAGTCAGAAC 57.053 40.909 0.00 0.00 0.00 3.01
2606 2644 4.323417 ACAACAACAACAACAGAGTCAGA 58.677 39.130 0.00 0.00 0.00 3.27
2607 2645 4.685169 ACAACAACAACAACAGAGTCAG 57.315 40.909 0.00 0.00 0.00 3.51
2608 2646 5.218885 CAAACAACAACAACAACAGAGTCA 58.781 37.500 0.00 0.00 0.00 3.41
2609 2647 4.621034 CCAAACAACAACAACAACAGAGTC 59.379 41.667 0.00 0.00 0.00 3.36
2610 2648 4.038642 ACCAAACAACAACAACAACAGAGT 59.961 37.500 0.00 0.00 0.00 3.24
2611 2649 4.385447 CACCAAACAACAACAACAACAGAG 59.615 41.667 0.00 0.00 0.00 3.35
2613 2651 3.431572 CCACCAAACAACAACAACAACAG 59.568 43.478 0.00 0.00 0.00 3.16
2824 2867 9.398170 CATGAAGTAAGAAATGTAAAACTGGTG 57.602 33.333 0.00 0.00 0.00 4.17
2829 2872 8.863049 CATGCCATGAAGTAAGAAATGTAAAAC 58.137 33.333 0.00 0.00 0.00 2.43
3017 3062 9.281371 TCTTCCTGATCTATGCATCTTATTTTG 57.719 33.333 0.19 0.00 0.00 2.44
3042 3090 9.331282 ACTGCCTACTACTATTTCATTTCATTC 57.669 33.333 0.00 0.00 0.00 2.67
3046 3094 7.272978 TCCACTGCCTACTACTATTTCATTTC 58.727 38.462 0.00 0.00 0.00 2.17
3313 3361 1.681327 GGTCACGGCCTCTCTACCA 60.681 63.158 0.00 0.00 0.00 3.25
3331 3379 2.383527 GGTGCTCGGCTCGAAGTTG 61.384 63.158 0.00 0.00 34.74 3.16
3471 3520 5.276114 CGAGTTCAAGTTCATCAGCTAATCG 60.276 44.000 0.00 0.00 0.00 3.34
3492 3541 3.123621 GCCTGCCAATCGTAATAATCGAG 59.876 47.826 0.00 0.00 40.57 4.04
3494 3543 2.159841 CGCCTGCCAATCGTAATAATCG 60.160 50.000 0.00 0.00 0.00 3.34
3501 3550 2.310327 ATCTGCGCCTGCCAATCGTA 62.310 55.000 4.18 0.00 41.78 3.43
3616 3665 3.239449 TGGTCTCTTTAGTTCAGAGCCA 58.761 45.455 8.25 8.25 39.88 4.75
3670 3719 1.000843 GTGAAATTGGACTGGTTGCCC 59.999 52.381 0.00 0.00 0.00 5.36
3771 3820 9.715121 AAAAAGACTTTGTTACGATAGGACATA 57.285 29.630 0.06 0.00 43.77 2.29
3863 3912 1.607148 GGTGAATATAGTTTGGGCGGC 59.393 52.381 0.00 0.00 0.00 6.53
3873 3922 8.492673 AACATGTTACTGTGTGGTGAATATAG 57.507 34.615 9.97 0.00 0.00 1.31
3990 4039 4.457603 ACCTGCATAACACGCAAAAGATTA 59.542 37.500 0.00 0.00 39.30 1.75
4050 4099 1.957765 GCTCGGTCAGAAGGGGGTAC 61.958 65.000 0.00 0.00 0.00 3.34
4243 4292 0.689055 TCAGTCTGCATCAGCCAGTT 59.311 50.000 0.00 0.00 41.13 3.16
4314 4363 1.739035 GCTATAACTGCAGCCACACGA 60.739 52.381 15.27 0.00 0.00 4.35
4315 4364 0.652592 GCTATAACTGCAGCCACACG 59.347 55.000 15.27 0.00 0.00 4.49
4366 4416 3.242867 TGACTCTGAACTCAACAGGGAT 58.757 45.455 0.00 0.00 38.01 3.85
4374 4424 7.093333 TGCTAGGAATTAATGACTCTGAACTCA 60.093 37.037 0.00 0.00 0.00 3.41
4483 4533 6.304286 AAGTTGAGACACTTATTTCGGGACG 61.304 44.000 0.00 0.00 44.44 4.79
4484 4534 4.566987 AGTTGAGACACTTATTTCGGGAC 58.433 43.478 0.00 0.00 0.00 4.46
4485 4535 4.884668 AGTTGAGACACTTATTTCGGGA 57.115 40.909 0.00 0.00 0.00 5.14
4486 4536 5.941948 AAAGTTGAGACACTTATTTCGGG 57.058 39.130 0.00 0.00 35.87 5.14
4487 4537 7.416154 TGTAAAGTTGAGACACTTATTTCGG 57.584 36.000 0.00 0.00 35.87 4.30
4488 4538 9.370126 CTTTGTAAAGTTGAGACACTTATTTCG 57.630 33.333 0.00 0.00 35.87 3.46
4506 4556 9.997482 GTCAAATAAGTGTCTCAACTTTGTAAA 57.003 29.630 0.00 0.00 40.77 2.01
4507 4557 8.332464 CGTCAAATAAGTGTCTCAACTTTGTAA 58.668 33.333 0.00 0.00 40.77 2.41
4508 4558 7.042321 CCGTCAAATAAGTGTCTCAACTTTGTA 60.042 37.037 0.00 0.00 40.77 2.41
4509 4559 6.238374 CCGTCAAATAAGTGTCTCAACTTTGT 60.238 38.462 0.00 0.00 40.77 2.83
4510 4560 6.018262 TCCGTCAAATAAGTGTCTCAACTTTG 60.018 38.462 0.00 0.00 40.77 2.77
4511 4561 6.018180 GTCCGTCAAATAAGTGTCTCAACTTT 60.018 38.462 0.00 0.00 40.77 2.66
4512 4562 5.465724 GTCCGTCAAATAAGTGTCTCAACTT 59.534 40.000 0.00 0.00 42.89 2.66
4513 4563 4.989168 GTCCGTCAAATAAGTGTCTCAACT 59.011 41.667 0.00 0.00 0.00 3.16
4514 4564 4.143389 CGTCCGTCAAATAAGTGTCTCAAC 60.143 45.833 0.00 0.00 0.00 3.18
4515 4565 3.985279 CGTCCGTCAAATAAGTGTCTCAA 59.015 43.478 0.00 0.00 0.00 3.02
4516 4566 3.571571 CGTCCGTCAAATAAGTGTCTCA 58.428 45.455 0.00 0.00 0.00 3.27
4517 4567 2.921754 CCGTCCGTCAAATAAGTGTCTC 59.078 50.000 0.00 0.00 0.00 3.36
4518 4568 2.559668 TCCGTCCGTCAAATAAGTGTCT 59.440 45.455 0.00 0.00 0.00 3.41
4519 4569 2.921754 CTCCGTCCGTCAAATAAGTGTC 59.078 50.000 0.00 0.00 0.00 3.67
4520 4570 2.298163 ACTCCGTCCGTCAAATAAGTGT 59.702 45.455 0.00 0.00 0.00 3.55
4521 4571 2.955614 ACTCCGTCCGTCAAATAAGTG 58.044 47.619 0.00 0.00 0.00 3.16
4522 4572 4.996788 ATACTCCGTCCGTCAAATAAGT 57.003 40.909 0.00 0.00 0.00 2.24
4523 4573 7.814642 ACTATATACTCCGTCCGTCAAATAAG 58.185 38.462 0.00 0.00 0.00 1.73
4524 4574 7.750229 ACTATATACTCCGTCCGTCAAATAA 57.250 36.000 0.00 0.00 0.00 1.40
4526 4576 7.934855 ATACTATATACTCCGTCCGTCAAAT 57.065 36.000 0.00 0.00 0.00 2.32
4527 4577 8.846943 TTATACTATATACTCCGTCCGTCAAA 57.153 34.615 0.00 0.00 0.00 2.69
4528 4578 8.846943 TTTATACTATATACTCCGTCCGTCAA 57.153 34.615 0.00 0.00 0.00 3.18
4532 4582 9.823098 GCATATTTATACTATATACTCCGTCCG 57.177 37.037 0.00 0.00 0.00 4.79
4780 4846 4.006319 GCTTCCAAGTAAAGCTGTGAGAT 58.994 43.478 0.00 0.00 44.53 2.75
4781 4847 3.403038 GCTTCCAAGTAAAGCTGTGAGA 58.597 45.455 0.00 0.00 44.53 3.27
4849 4915 6.566197 TTTTCAAAACAAATGGCAAACTGT 57.434 29.167 0.00 0.00 0.00 3.55
4997 5063 5.134679 AGGTGAGGTAGATATGTACTCCAGT 59.865 44.000 9.66 0.00 0.00 4.00
5003 5069 8.021973 CGACATAAAGGTGAGGTAGATATGTAC 58.978 40.741 1.36 1.36 33.87 2.90
5004 5070 7.940688 TCGACATAAAGGTGAGGTAGATATGTA 59.059 37.037 0.00 0.00 33.87 2.29
5005 5071 6.776116 TCGACATAAAGGTGAGGTAGATATGT 59.224 38.462 0.00 0.00 35.76 2.29
5490 5560 4.649267 TCCAATCCACTACATGAAACCA 57.351 40.909 0.00 0.00 0.00 3.67
5577 5647 1.000274 GAATTATGGGACCAATGCGCC 60.000 52.381 4.18 0.00 0.00 6.53
5601 5671 4.642437 TGAGCTGAGGTTAGTATCTGACAG 59.358 45.833 0.00 0.00 0.00 3.51
5786 5856 0.956633 AGTGCAATTCAGCAGTGGTG 59.043 50.000 16.28 16.28 45.90 4.17
5802 5872 3.609373 CAGTGCAAGAACAAACAACAGTG 59.391 43.478 0.00 0.00 0.00 3.66
5965 6036 7.995488 ACATTTCTAGGCATACTTTCTAGCAAT 59.005 33.333 0.00 0.00 30.92 3.56
5968 6039 6.986817 TGACATTTCTAGGCATACTTTCTAGC 59.013 38.462 0.00 0.00 32.72 3.42
5972 6043 9.937175 GTAATTGACATTTCTAGGCATACTTTC 57.063 33.333 0.00 0.00 0.00 2.62
6012 6083 8.743085 TTCAGAGAGATATTTTTCCATTGGAG 57.257 34.615 5.36 0.00 31.21 3.86
6120 6191 3.437049 GGAAACTGTCATAGTCCAACTGC 59.563 47.826 0.00 0.00 39.18 4.40
6147 6228 8.576442 GTTCTGAATTTGTTCTGGAGGAAATTA 58.424 33.333 0.00 0.00 35.51 1.40
6153 6234 4.823989 ACAGTTCTGAATTTGTTCTGGAGG 59.176 41.667 6.83 0.00 0.00 4.30
6160 6241 7.601856 TGTCTTCAAACAGTTCTGAATTTGTT 58.398 30.769 13.89 13.89 35.43 2.83
6162 6243 7.675270 CTGTCTTCAAACAGTTCTGAATTTG 57.325 36.000 6.83 8.09 41.43 2.32
6258 6339 1.065854 CATCCCCGACAGAGAAGCTTT 60.066 52.381 0.00 0.00 0.00 3.51
6283 6364 0.179084 CAGATGCCGTCGGGTACATT 60.179 55.000 14.38 0.00 34.97 2.71
6286 6367 1.226888 GACAGATGCCGTCGGGTAC 60.227 63.158 14.38 0.00 34.97 3.34
6384 6465 5.536538 CAGTGATCTTACTACTGCATAGGGA 59.463 44.000 0.00 0.00 35.87 4.20
6562 6648 4.502645 CCGCAAAAGTAAACTTGTTTCCTG 59.497 41.667 1.72 0.00 36.12 3.86
6598 6684 3.839979 TCCTGTTTGGACCAAAGGG 57.160 52.632 20.14 22.00 40.56 3.95
6613 6699 0.830866 AGGGAACGAAACCGAGTCCT 60.831 55.000 0.00 0.00 36.10 3.85
6616 6702 1.139455 TCAAAGGGAACGAAACCGAGT 59.861 47.619 0.00 0.00 0.00 4.18
6631 6717 7.583230 CATCTTCCAGTTCTTTCTTCTCAAAG 58.417 38.462 0.00 0.00 35.06 2.77
6634 6720 4.999950 GCATCTTCCAGTTCTTTCTTCTCA 59.000 41.667 0.00 0.00 0.00 3.27
6665 6751 4.076394 GAGGGTGGCAGTAGATCTAGTAG 58.924 52.174 9.80 6.28 0.00 2.57
6706 6792 6.622896 GCATATCGAGGCAAGTAAACAAAAGT 60.623 38.462 0.00 0.00 30.94 2.66


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

AutoCloner maintained by Alex Coulton.