Multiple sequence alignment - TraesCS4D01G086000

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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 TraesCS4D01G086000 chr4D 100.000 9366 0 0 1 9366 61584793 61594158 0.000000e+00 17296.0
1 TraesCS4D01G086000 chr4D 92.053 151 12 0 3385 3535 61588028 61588178 7.370000e-51 213.0
2 TraesCS4D01G086000 chr4D 92.053 151 12 0 3236 3386 61588177 61588327 7.370000e-51 213.0
3 TraesCS4D01G086000 chr4D 100.000 32 0 0 7589 7620 381882598 381882629 1.020000e-04 60.2
4 TraesCS4D01G086000 chr4B 97.660 7606 123 19 1 7590 91337552 91329986 0.000000e+00 13008.0
5 TraesCS4D01G086000 chr4B 91.832 1567 82 20 7815 9366 91329761 91328226 0.000000e+00 2143.0
6 TraesCS4D01G086000 chr4B 97.442 430 11 0 8937 9366 91228694 91228265 0.000000e+00 734.0
7 TraesCS4D01G086000 chr4B 95.706 163 4 2 7649 7808 91329987 91329825 9.330000e-65 259.0
8 TraesCS4D01G086000 chr4B 87.805 82 5 5 8608 8688 91228957 91228880 3.600000e-14 91.6
9 TraesCS4D01G086000 chr4B 100.000 34 0 0 7587 7620 670403249 670403282 7.850000e-06 63.9
10 TraesCS4D01G086000 chr4A 97.089 4432 105 10 595 5015 534782531 534786949 0.000000e+00 7448.0
11 TraesCS4D01G086000 chr4A 96.887 2506 64 10 5094 7590 534786948 534789448 0.000000e+00 4183.0
12 TraesCS4D01G086000 chr4A 91.801 744 44 14 8634 9366 534790457 534791194 0.000000e+00 1020.0
13 TraesCS4D01G086000 chr4A 89.967 608 34 4 1 605 534781782 534782365 0.000000e+00 760.0
14 TraesCS4D01G086000 chr4A 88.215 577 48 4 8024 8597 534789899 534790458 0.000000e+00 671.0
15 TraesCS4D01G086000 chr4A 97.546 163 1 2 7649 7808 534789447 534789609 9.260000e-70 276.0
16 TraesCS4D01G086000 chr4A 88.128 219 10 3 7818 8035 534789677 534789880 7.260000e-61 246.0
17 TraesCS4D01G086000 chr4A 91.558 154 12 1 3385 3537 534785171 534785324 2.650000e-50 211.0
18 TraesCS4D01G086000 chr4A 90.278 144 14 0 3243 3386 534785327 534785470 1.240000e-43 189.0
19 TraesCS4D01G086000 chr6D 93.714 175 11 0 9151 9325 358216619 358216793 7.210000e-66 263.0
20 TraesCS4D01G086000 chrUn 93.567 171 11 0 9151 9321 209272326 209272496 1.210000e-63 255.0
21 TraesCS4D01G086000 chrUn 100.000 33 0 0 7589 7621 63534417 63534385 2.820000e-05 62.1
22 TraesCS4D01G086000 chr7B 93.567 171 11 0 9151 9321 642232459 642232629 1.210000e-63 255.0
23 TraesCS4D01G086000 chr7B 100.000 32 0 0 7589 7620 334774362 334774331 1.020000e-04 60.2
24 TraesCS4D01G086000 chr3A 89.706 68 4 2 7588 7654 67912179 67912114 6.030000e-12 84.2
25 TraesCS4D01G086000 chr2A 83.333 84 3 5 7587 7660 215751277 215751195 6.070000e-07 67.6
26 TraesCS4D01G086000 chr1D 100.000 32 0 0 7589 7620 348128524 348128555 1.020000e-04 60.2
27 TraesCS4D01G086000 chr1B 100.000 32 0 0 7589 7620 465681316 465681347 1.020000e-04 60.2
28 TraesCS4D01G086000 chr1B 100.000 28 0 0 7628 7655 292204958 292204985 1.700000e-02 52.8
29 TraesCS4D01G086000 chr2D 94.737 38 0 2 7586 7621 88085394 88085357 3.650000e-04 58.4
30 TraesCS4D01G086000 chr6A 100.000 30 0 0 7628 7657 27342917 27342888 1.000000e-03 56.5
31 TraesCS4D01G086000 chr6B 96.875 32 1 0 7627 7658 277158964 277158933 5.000000e-03 54.7
32 TraesCS4D01G086000 chr5D 100.000 29 0 0 7628 7656 538166835 538166863 5.000000e-03 54.7
33 TraesCS4D01G086000 chr3B 96.970 33 0 1 7628 7660 623657626 623657657 5.000000e-03 54.7
34 TraesCS4D01G086000 chr3D 100.000 28 0 0 7628 7655 446429860 446429887 1.700000e-02 52.8
35 TraesCS4D01G086000 chr2B 96.875 32 0 1 7628 7659 488199288 488199258 1.700000e-02 52.8
36 TraesCS4D01G086000 chr1A 92.105 38 2 1 7628 7664 480430702 480430739 1.700000e-02 52.8


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 TraesCS4D01G086000 chr4D 61584793 61594158 9365 False 17296.000000 17296 100.000000 1 9366 1 chr4D.!!$F1 9365
1 TraesCS4D01G086000 chr4B 91328226 91337552 9326 True 5136.666667 13008 95.066000 1 9366 3 chr4B.!!$R2 9365
2 TraesCS4D01G086000 chr4B 91228265 91228957 692 True 412.800000 734 92.623500 8608 9366 2 chr4B.!!$R1 758
3 TraesCS4D01G086000 chr4A 534781782 534791194 9412 False 1667.111111 7448 92.385444 1 9366 9 chr4A.!!$F1 9365

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
29 30 0.394192 TTGTCCTGCTGTGTCTCCTG 59.606 55.000 0.00 0.00 0.00 3.86 F
116 121 1.570803 AGCACAGCTTCCTGAGATCT 58.429 50.000 0.00 0.00 41.77 2.75 F
348 355 3.244491 GGCTGGCTGACTCATTCTGATAT 60.244 47.826 0.00 0.00 0.00 1.63 F
819 1002 3.766545 TGCAATTTACCTCTCTTTGCCT 58.233 40.909 3.77 0.00 41.43 4.75 F
2302 2485 5.991328 ACAATCACTTAGTAATGCCATCG 57.009 39.130 0.00 0.00 0.00 3.84 F
2904 3087 4.362677 TGCTAGGGAAGAAGATTACACCT 58.637 43.478 0.00 0.00 0.00 4.00 F
3973 4160 3.834813 AGATTACCTTCAGAGTCTGCACA 59.165 43.478 15.72 1.03 0.00 4.57 F
4865 5060 3.305608 CCTTTGGAAGTGCAATGGTCTTC 60.306 47.826 8.71 5.64 37.44 2.87 F
5997 6200 3.096852 TCTTGCTTCACTATCTTCCCGA 58.903 45.455 0.00 0.00 0.00 5.14 F
7819 8028 0.097674 CGTGGAAGCACAAGCATAGC 59.902 55.000 0.00 0.00 45.49 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1595 1.428869 AGGAGTGCCTGAGTTTGAGT 58.571 50.000 0.00 0.00 44.90 3.41 R
1836 2019 4.015872 TGGAATACCACACCTTTGACTC 57.984 45.455 0.00 0.00 41.77 3.36 R
2302 2485 2.635427 CTGGGGCTATTCTCTCCCTTAC 59.365 54.545 0.00 0.00 40.05 2.34 R
2904 3087 6.533730 ACTCACCAGATCATTTACAAGTGAA 58.466 36.000 0.00 0.00 33.03 3.18 R
3558 3744 0.179078 CTCAGGCCTGCTTCTGCTAG 60.179 60.000 28.91 13.55 40.48 3.42 R
4843 5038 2.242043 AGACCATTGCACTTCCAAAGG 58.758 47.619 0.00 0.00 38.99 3.11 R
5997 6200 0.773644 AGTTGTCACTGGGCCTCATT 59.226 50.000 4.53 0.00 0.00 2.57 R
6294 6497 3.844211 ACTACAGTAGGCCTGATTTGGAA 59.156 43.478 17.99 0.00 44.49 3.53 R
7977 8245 0.320421 GAACGCTTCAGTGTAGGGCA 60.320 55.000 12.82 0.00 37.87 5.36 R
8929 9274 0.525882 GCCGGCGACTACTCTTTCTC 60.526 60.000 12.58 0.00 0.00 2.87 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 0.394192 TTGTCCTGCTGTGTCTCCTG 59.606 55.000 0.00 0.00 0.00 3.86
34 35 2.149578 CCTGCTGTGTCTCCTGAAAAG 58.850 52.381 0.00 0.00 0.00 2.27
35 36 2.486191 CCTGCTGTGTCTCCTGAAAAGT 60.486 50.000 0.00 0.00 0.00 2.66
36 37 3.244215 CCTGCTGTGTCTCCTGAAAAGTA 60.244 47.826 0.00 0.00 0.00 2.24
37 38 4.380531 CTGCTGTGTCTCCTGAAAAGTAA 58.619 43.478 0.00 0.00 0.00 2.24
38 39 4.776349 TGCTGTGTCTCCTGAAAAGTAAA 58.224 39.130 0.00 0.00 0.00 2.01
39 40 5.189928 TGCTGTGTCTCCTGAAAAGTAAAA 58.810 37.500 0.00 0.00 0.00 1.52
40 41 5.650266 TGCTGTGTCTCCTGAAAAGTAAAAA 59.350 36.000 0.00 0.00 0.00 1.94
41 42 5.971792 GCTGTGTCTCCTGAAAAGTAAAAAC 59.028 40.000 0.00 0.00 0.00 2.43
42 43 6.404293 GCTGTGTCTCCTGAAAAGTAAAAACA 60.404 38.462 0.00 0.00 0.00 2.83
43 44 6.848451 TGTGTCTCCTGAAAAGTAAAAACAC 58.152 36.000 0.00 0.00 35.16 3.32
48 50 6.609616 TCTCCTGAAAAGTAAAAACACCCATT 59.390 34.615 0.00 0.00 0.00 3.16
50 52 7.718525 TCCTGAAAAGTAAAAACACCCATTAC 58.281 34.615 0.00 0.00 0.00 1.89
115 120 2.399916 AAGCACAGCTTCCTGAGATC 57.600 50.000 0.00 0.00 46.77 2.75
116 121 1.570803 AGCACAGCTTCCTGAGATCT 58.429 50.000 0.00 0.00 41.77 2.75
186 191 5.046376 AGTTTTGGATCCATTGAACCCATTC 60.046 40.000 17.06 0.00 32.60 2.67
227 234 6.127168 CCAAGGTTCTGTTTTTAAAGGTTCCT 60.127 38.462 0.00 0.00 0.00 3.36
278 285 5.985530 GCTGGTTTTCTTTAAGAAATGCAGT 59.014 36.000 19.12 0.00 43.06 4.40
283 290 9.308318 GGTTTTCTTTAAGAAATGCAGTTTACA 57.692 29.630 19.12 0.00 43.06 2.41
307 314 8.784043 ACAACTTAAGAGGCAATAAAAGTACTG 58.216 33.333 10.09 0.00 0.00 2.74
348 355 3.244491 GGCTGGCTGACTCATTCTGATAT 60.244 47.826 0.00 0.00 0.00 1.63
819 1002 3.766545 TGCAATTTACCTCTCTTTGCCT 58.233 40.909 3.77 0.00 41.43 4.75
1412 1595 6.406961 CCTGTTAGCATATACAGTGTCCAAGA 60.407 42.308 0.00 0.00 40.06 3.02
2302 2485 5.991328 ACAATCACTTAGTAATGCCATCG 57.009 39.130 0.00 0.00 0.00 3.84
2652 2835 6.817765 TTTCTTGATGAACCATTACCTCAC 57.182 37.500 0.00 0.00 33.88 3.51
2904 3087 4.362677 TGCTAGGGAAGAAGATTACACCT 58.637 43.478 0.00 0.00 0.00 4.00
3145 3330 5.544650 TGTCATCACATATATGTCCTGCAG 58.455 41.667 15.60 6.78 39.39 4.41
3148 3333 6.146837 GTCATCACATATATGTCCTGCAGAAC 59.853 42.308 17.39 5.41 39.39 3.01
3204 3389 6.958192 AGGTTATACTCTTCCCTACAGTTTCA 59.042 38.462 0.00 0.00 0.00 2.69
3558 3744 5.710567 ACAAAATTAAACAGTCCTAGGCTCC 59.289 40.000 2.96 0.00 0.00 4.70
3718 3904 8.000780 AGTCTATTGTGCTTCTTTCTTTTGTT 57.999 30.769 0.00 0.00 0.00 2.83
3973 4160 3.834813 AGATTACCTTCAGAGTCTGCACA 59.165 43.478 15.72 1.03 0.00 4.57
4865 5060 3.305608 CCTTTGGAAGTGCAATGGTCTTC 60.306 47.826 8.71 5.64 37.44 2.87
4878 5073 3.586470 TGGTCTTCTTTTTGCAGGGTA 57.414 42.857 0.00 0.00 0.00 3.69
4886 5081 6.699642 TCTTCTTTTTGCAGGGTAAAATTTCG 59.300 34.615 0.00 0.00 0.00 3.46
4942 5137 7.869016 TTCTCAAACAAAGTCTACTGATACG 57.131 36.000 0.00 0.00 0.00 3.06
5210 5405 4.265073 GCCTGACTTTCACCAGTAATGAT 58.735 43.478 0.00 0.00 0.00 2.45
5425 5627 6.560253 TTCAGGAAAGTTGAGTATTTCAGC 57.440 37.500 0.00 0.00 37.19 4.26
5526 5728 6.071952 ACCTTGGTGCTGAAAAACATATACAG 60.072 38.462 0.00 0.00 0.00 2.74
5997 6200 3.096852 TCTTGCTTCACTATCTTCCCGA 58.903 45.455 0.00 0.00 0.00 5.14
6267 6470 6.838198 CATCATTATGCATTTTTGGTCCTG 57.162 37.500 3.54 0.00 0.00 3.86
6294 6497 4.112634 TCCATGCTCTTTTTAGGGTTGT 57.887 40.909 0.00 0.00 0.00 3.32
7199 7404 5.068636 CAGAATGTAGGAATGGAGAATGGG 58.931 45.833 0.00 0.00 0.00 4.00
7320 7525 8.140628 TCTCTACATGAATCTAGCATTTGTCTC 58.859 37.037 0.00 0.00 0.00 3.36
7332 7537 5.297547 AGCATTTGTCTCGTCTTTAGAACA 58.702 37.500 0.00 0.00 0.00 3.18
7461 7666 2.033801 GTCACAACAGCTGATGCAACTT 59.966 45.455 23.35 0.00 42.74 2.66
7517 7723 3.142951 GAGCTCGACTCTTATAGGCTCA 58.857 50.000 11.33 0.00 42.62 4.26
7521 7727 4.142687 GCTCGACTCTTATAGGCTCATCTC 60.143 50.000 0.00 0.00 0.00 2.75
7542 7748 2.096069 CGAGACCTAAACGAGTCGAACA 60.096 50.000 21.50 1.99 38.08 3.18
7588 7794 4.425577 CTTGCCAAGCTCGAACTTAAAT 57.574 40.909 0.00 0.00 0.00 1.40
7589 7795 5.545658 CTTGCCAAGCTCGAACTTAAATA 57.454 39.130 0.00 0.00 0.00 1.40
7590 7796 4.939509 TGCCAAGCTCGAACTTAAATAC 57.060 40.909 0.00 0.00 0.00 1.89
7591 7797 4.575885 TGCCAAGCTCGAACTTAAATACT 58.424 39.130 0.00 0.00 0.00 2.12
7592 7798 5.726397 TGCCAAGCTCGAACTTAAATACTA 58.274 37.500 0.00 0.00 0.00 1.82
7593 7799 5.579511 TGCCAAGCTCGAACTTAAATACTAC 59.420 40.000 0.00 0.00 0.00 2.73
7594 7800 5.811100 GCCAAGCTCGAACTTAAATACTACT 59.189 40.000 0.00 0.00 0.00 2.57
7595 7801 6.019720 GCCAAGCTCGAACTTAAATACTACTC 60.020 42.308 0.00 0.00 0.00 2.59
7596 7802 7.259161 CCAAGCTCGAACTTAAATACTACTCT 58.741 38.462 0.00 0.00 0.00 3.24
7597 7803 7.221067 CCAAGCTCGAACTTAAATACTACTCTG 59.779 40.741 0.00 0.00 0.00 3.35
7598 7804 7.393841 AGCTCGAACTTAAATACTACTCTGT 57.606 36.000 0.00 0.00 0.00 3.41
7599 7805 7.474190 AGCTCGAACTTAAATACTACTCTGTC 58.526 38.462 0.00 0.00 0.00 3.51
7600 7806 6.692249 GCTCGAACTTAAATACTACTCTGTCC 59.308 42.308 0.00 0.00 0.00 4.02
7601 7807 7.093322 TCGAACTTAAATACTACTCTGTCCC 57.907 40.000 0.00 0.00 0.00 4.46
7602 7808 6.660521 TCGAACTTAAATACTACTCTGTCCCA 59.339 38.462 0.00 0.00 0.00 4.37
7603 7809 7.341256 TCGAACTTAAATACTACTCTGTCCCAT 59.659 37.037 0.00 0.00 0.00 4.00
7604 7810 8.627403 CGAACTTAAATACTACTCTGTCCCATA 58.373 37.037 0.00 0.00 0.00 2.74
7612 7818 9.656323 AATACTACTCTGTCCCATAATGTAAGA 57.344 33.333 0.00 0.00 0.00 2.10
7613 7819 7.349412 ACTACTCTGTCCCATAATGTAAGAC 57.651 40.000 0.00 0.00 0.00 3.01
7614 7820 5.263968 ACTCTGTCCCATAATGTAAGACG 57.736 43.478 0.00 0.00 0.00 4.18
7615 7821 4.710375 ACTCTGTCCCATAATGTAAGACGT 59.290 41.667 0.00 0.00 0.00 4.34
7616 7822 5.187186 ACTCTGTCCCATAATGTAAGACGTT 59.813 40.000 0.00 0.00 0.00 3.99
7617 7823 6.045072 TCTGTCCCATAATGTAAGACGTTT 57.955 37.500 0.00 0.00 0.00 3.60
7618 7824 6.469410 TCTGTCCCATAATGTAAGACGTTTT 58.531 36.000 0.00 0.00 0.00 2.43
7619 7825 6.938030 TCTGTCCCATAATGTAAGACGTTTTT 59.062 34.615 0.00 0.00 0.00 1.94
7620 7826 8.095792 TCTGTCCCATAATGTAAGACGTTTTTA 58.904 33.333 0.00 0.00 0.00 1.52
7621 7827 8.259049 TGTCCCATAATGTAAGACGTTTTTAG 57.741 34.615 0.00 0.00 0.00 1.85
7622 7828 7.148373 TGTCCCATAATGTAAGACGTTTTTAGC 60.148 37.037 0.00 0.00 0.00 3.09
7623 7829 7.065443 GTCCCATAATGTAAGACGTTTTTAGCT 59.935 37.037 0.00 0.00 0.00 3.32
7624 7830 7.608761 TCCCATAATGTAAGACGTTTTTAGCTT 59.391 33.333 0.00 0.00 0.00 3.74
7625 7831 7.696453 CCCATAATGTAAGACGTTTTTAGCTTG 59.304 37.037 0.00 0.00 0.00 4.01
7626 7832 7.218204 CCATAATGTAAGACGTTTTTAGCTTGC 59.782 37.037 0.00 0.00 0.00 4.01
7627 7833 5.941948 ATGTAAGACGTTTTTAGCTTGCT 57.058 34.783 0.00 0.00 0.00 3.91
7628 7834 7.429636 AATGTAAGACGTTTTTAGCTTGCTA 57.570 32.000 0.00 0.00 0.00 3.49
7629 7835 6.219302 TGTAAGACGTTTTTAGCTTGCTAC 57.781 37.500 1.37 0.00 0.00 3.58
7630 7836 5.754406 TGTAAGACGTTTTTAGCTTGCTACA 59.246 36.000 1.37 0.00 0.00 2.74
7631 7837 5.941948 AAGACGTTTTTAGCTTGCTACAT 57.058 34.783 1.37 0.00 0.00 2.29
7632 7838 5.941948 AGACGTTTTTAGCTTGCTACATT 57.058 34.783 1.37 0.00 0.00 2.71
7633 7839 7.429636 AAGACGTTTTTAGCTTGCTACATTA 57.570 32.000 1.37 0.00 0.00 1.90
7634 7840 7.611213 AGACGTTTTTAGCTTGCTACATTAT 57.389 32.000 1.37 0.00 0.00 1.28
7635 7841 7.464358 AGACGTTTTTAGCTTGCTACATTATG 58.536 34.615 1.37 0.00 0.00 1.90
7636 7842 6.551736 ACGTTTTTAGCTTGCTACATTATGG 58.448 36.000 1.37 0.00 0.00 2.74
7637 7843 5.971202 CGTTTTTAGCTTGCTACATTATGGG 59.029 40.000 1.37 0.00 0.00 4.00
7638 7844 6.183360 CGTTTTTAGCTTGCTACATTATGGGA 60.183 38.462 1.37 0.00 0.00 4.37
7639 7845 6.693315 TTTTAGCTTGCTACATTATGGGAC 57.307 37.500 1.37 0.00 0.00 4.46
7640 7846 2.838736 AGCTTGCTACATTATGGGACG 58.161 47.619 0.00 0.00 0.00 4.79
7641 7847 1.873591 GCTTGCTACATTATGGGACGG 59.126 52.381 0.00 0.00 0.00 4.79
7642 7848 2.484770 GCTTGCTACATTATGGGACGGA 60.485 50.000 0.00 0.00 0.00 4.69
7643 7849 3.393800 CTTGCTACATTATGGGACGGAG 58.606 50.000 0.00 0.00 0.00 4.63
7644 7850 1.691976 TGCTACATTATGGGACGGAGG 59.308 52.381 0.00 0.00 0.00 4.30
7645 7851 1.002087 GCTACATTATGGGACGGAGGG 59.998 57.143 0.00 0.00 0.00 4.30
7646 7852 2.605257 CTACATTATGGGACGGAGGGA 58.395 52.381 0.00 0.00 0.00 4.20
7647 7853 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
7808 8017 2.470801 TTTTCATGCGCCGTGGAAGC 62.471 55.000 4.18 0.00 0.00 3.86
7809 8018 4.695993 TCATGCGCCGTGGAAGCA 62.696 61.111 4.18 10.97 45.46 3.91
7815 8024 3.286751 GCCGTGGAAGCACAAGCA 61.287 61.111 0.00 0.00 45.49 3.91
7818 8027 0.729116 CCGTGGAAGCACAAGCATAG 59.271 55.000 0.00 0.00 45.49 2.23
7819 8028 0.097674 CGTGGAAGCACAAGCATAGC 59.902 55.000 0.00 0.00 45.49 2.97
7821 8030 0.680921 TGGAAGCACAAGCATAGCCC 60.681 55.000 0.00 0.00 45.49 5.19
7823 8032 1.396653 GAAGCACAAGCATAGCCCAT 58.603 50.000 0.00 0.00 45.49 4.00
7838 8106 2.129607 GCCCATTTTATTGCTCATGCG 58.870 47.619 0.00 0.00 43.34 4.73
7839 8107 2.129607 CCCATTTTATTGCTCATGCGC 58.870 47.619 0.00 0.00 43.34 6.09
7938 8206 1.628846 AGTGTAAATTGACCTCGGGCT 59.371 47.619 0.00 0.00 0.00 5.19
7941 8209 2.007608 GTAAATTGACCTCGGGCTGAC 58.992 52.381 0.00 0.00 0.00 3.51
7944 8212 1.201429 ATTGACCTCGGGCTGACCTT 61.201 55.000 0.00 0.00 36.97 3.50
8039 8337 9.930693 TGGACAAAGTACTGTTTTGTTAAATTT 57.069 25.926 11.69 0.00 45.82 1.82
8078 8376 3.276857 CTGCATCATCCACAACTTAGCT 58.723 45.455 0.00 0.00 0.00 3.32
8079 8377 3.689347 TGCATCATCCACAACTTAGCTT 58.311 40.909 0.00 0.00 0.00 3.74
8080 8378 4.842574 TGCATCATCCACAACTTAGCTTA 58.157 39.130 0.00 0.00 0.00 3.09
8081 8379 5.439721 TGCATCATCCACAACTTAGCTTAT 58.560 37.500 0.00 0.00 0.00 1.73
8082 8380 6.591001 TGCATCATCCACAACTTAGCTTATA 58.409 36.000 0.00 0.00 0.00 0.98
8083 8381 7.226441 TGCATCATCCACAACTTAGCTTATAT 58.774 34.615 0.00 0.00 0.00 0.86
8084 8382 7.173735 TGCATCATCCACAACTTAGCTTATATG 59.826 37.037 0.00 0.00 0.00 1.78
8142 8440 7.760131 ATGCATATTGTTAGCATTTTGTGTC 57.240 32.000 0.00 0.00 45.98 3.67
8150 8448 3.665745 AGCATTTTGTGTCATTGACCC 57.334 42.857 14.05 3.24 0.00 4.46
8159 8457 4.661222 TGTGTCATTGACCCACATGTAAT 58.339 39.130 14.05 0.00 34.37 1.89
8166 8464 3.495331 TGACCCACATGTAATTTGCAGT 58.505 40.909 0.00 0.00 0.00 4.40
8238 8536 8.945057 TGGAAAACTGAAAAATCAAAAAGAAGG 58.055 29.630 0.00 0.00 0.00 3.46
8283 8581 8.998814 TCCCTATGTAGATATTTCTTTTGGTCA 58.001 33.333 0.00 0.00 33.17 4.02
8306 8604 1.001974 TCACCTCACAACTTCATCCGG 59.998 52.381 0.00 0.00 0.00 5.14
8385 8683 9.971922 ATCTTAATCTGGCAAGTTATAAAATGC 57.028 29.630 12.94 12.94 38.06 3.56
8393 8691 5.478407 GCAAGTTATAAAATGCCCACTGTT 58.522 37.500 11.03 0.00 32.73 3.16
8410 8708 0.110644 GTTGTTCGAGCTGCGGAAAG 60.111 55.000 10.05 0.00 41.33 2.62
8432 8730 5.415415 GCAGTTGCGAATATCAAGAGAAT 57.585 39.130 0.00 0.00 0.00 2.40
8460 8758 5.487488 AGGAACCAGTTGTCATATTAGGTCA 59.513 40.000 0.00 0.00 0.00 4.02
8518 8816 2.202298 GGCGGCATTTTCGTCACG 60.202 61.111 3.07 0.00 31.94 4.35
8543 8841 1.661112 CTTGGTAGCGCTCAAAGTAGC 59.339 52.381 16.34 5.32 39.21 3.58
8548 8846 1.719600 AGCGCTCAAAGTAGCAGAAG 58.280 50.000 2.64 0.00 42.91 2.85
8549 8847 0.096108 GCGCTCAAAGTAGCAGAAGC 59.904 55.000 0.00 0.00 42.91 3.86
8550 8848 1.432514 CGCTCAAAGTAGCAGAAGCA 58.567 50.000 0.00 0.00 45.49 3.91
8552 8850 2.030213 CGCTCAAAGTAGCAGAAGCATC 59.970 50.000 0.00 0.00 45.49 3.91
8555 8853 4.118410 CTCAAAGTAGCAGAAGCATCGAT 58.882 43.478 0.00 0.00 45.49 3.59
8561 8859 0.659957 GCAGAAGCATCGATGGGAAC 59.340 55.000 26.00 9.89 41.58 3.62
8562 8860 1.745141 GCAGAAGCATCGATGGGAACT 60.745 52.381 26.00 12.05 41.58 3.01
8577 8875 6.583806 CGATGGGAACTCAAATTTCAGAAAAG 59.416 38.462 0.00 0.00 0.00 2.27
8578 8876 5.600696 TGGGAACTCAAATTTCAGAAAAGC 58.399 37.500 0.00 0.00 0.00 3.51
8579 8877 5.128499 TGGGAACTCAAATTTCAGAAAAGCA 59.872 36.000 0.00 0.00 0.00 3.91
8584 8882 6.877236 ACTCAAATTTCAGAAAAGCAAAGGA 58.123 32.000 0.00 0.00 0.00 3.36
8589 8887 8.919661 CAAATTTCAGAAAAGCAAAGGATAGTC 58.080 33.333 0.00 0.00 0.00 2.59
8603 8901 5.934402 AGGATAGTCGATTGTTTACACCT 57.066 39.130 0.00 0.00 0.00 4.00
8605 8903 6.338937 AGGATAGTCGATTGTTTACACCTTC 58.661 40.000 0.00 0.00 0.00 3.46
8606 8904 5.231568 GGATAGTCGATTGTTTACACCTTCG 59.768 44.000 0.00 0.00 0.00 3.79
8611 8909 4.025563 TCGATTGTTTACACCTTCGTTGTG 60.026 41.667 8.15 0.00 39.63 3.33
8613 8911 4.603231 TTGTTTACACCTTCGTTGTGTC 57.397 40.909 9.86 0.00 43.15 3.67
8614 8912 3.597255 TGTTTACACCTTCGTTGTGTCA 58.403 40.909 9.86 2.13 43.15 3.58
8615 8913 4.001652 TGTTTACACCTTCGTTGTGTCAA 58.998 39.130 9.86 4.63 43.15 3.18
8616 8914 4.636648 TGTTTACACCTTCGTTGTGTCAAT 59.363 37.500 9.86 0.00 43.15 2.57
8617 8915 4.804608 TTACACCTTCGTTGTGTCAATG 57.195 40.909 9.86 0.00 43.15 2.82
8619 8917 1.333308 CACCTTCGTTGTGTCAATGCA 59.667 47.619 0.00 0.00 0.00 3.96
8620 8918 2.020720 ACCTTCGTTGTGTCAATGCAA 58.979 42.857 0.00 0.00 0.00 4.08
8621 8919 2.223479 ACCTTCGTTGTGTCAATGCAAC 60.223 45.455 0.00 0.00 40.90 4.17
8622 8920 2.384382 CTTCGTTGTGTCAATGCAACC 58.616 47.619 0.00 0.00 41.16 3.77
8624 8922 0.667993 CGTTGTGTCAATGCAACCCT 59.332 50.000 0.00 0.00 41.16 4.34
8625 8923 1.066908 CGTTGTGTCAATGCAACCCTT 59.933 47.619 0.00 0.00 41.16 3.95
8626 8924 2.742774 GTTGTGTCAATGCAACCCTTC 58.257 47.619 0.00 0.00 39.07 3.46
8627 8925 2.362077 GTTGTGTCAATGCAACCCTTCT 59.638 45.455 0.00 0.00 39.07 2.85
8640 8938 6.744112 TGCAACCCTTCTTTGTATTGTTTAG 58.256 36.000 0.00 0.00 0.00 1.85
8641 8939 6.322712 TGCAACCCTTCTTTGTATTGTTTAGT 59.677 34.615 0.00 0.00 0.00 2.24
8686 8984 4.137116 TGCTCGCAAACATAGGATAGTT 57.863 40.909 0.00 0.00 0.00 2.24
8694 8992 6.907212 CGCAAACATAGGATAGTTGATTGAAC 59.093 38.462 0.00 0.00 34.40 3.18
8702 9000 6.421485 AGGATAGTTGATTGAACAAGCTCAT 58.579 36.000 4.54 0.00 36.98 2.90
8732 9030 7.665559 AGGTTTCTAGTGCATTGTTTCTTGATA 59.334 33.333 0.00 0.00 0.00 2.15
8785 9083 3.305335 GCATTTCAGTACACACCCCTTTG 60.305 47.826 0.00 0.00 0.00 2.77
8812 9110 9.601971 GTTATTGTCGCAACTTTCTGTTAATAA 57.398 29.630 0.00 0.00 37.07 1.40
8813 9111 9.820229 TTATTGTCGCAACTTTCTGTTAATAAG 57.180 29.630 0.00 0.00 37.07 1.73
8814 9112 7.485418 TTGTCGCAACTTTCTGTTAATAAGA 57.515 32.000 0.00 0.00 37.07 2.10
8877 9191 6.534475 AATTTGTGATGATGTACAAGGCAT 57.466 33.333 0.00 4.24 37.98 4.40
8880 9217 7.643569 TTTGTGATGATGTACAAGGCATTAT 57.356 32.000 0.00 0.00 37.98 1.28
8895 9240 9.056005 ACAAGGCATTATATGTATGTACACTTG 57.944 33.333 0.00 5.15 39.30 3.16
8914 9259 5.871524 CACTTGAAAGCTAGCTACTGATTCA 59.128 40.000 19.70 19.85 0.00 2.57
8915 9260 6.538021 CACTTGAAAGCTAGCTACTGATTCAT 59.462 38.462 22.92 11.29 0.00 2.57
8928 9273 7.826252 AGCTACTGATTCATAGCAAAAAGAGAA 59.174 33.333 20.42 0.00 45.22 2.87
8929 9274 8.121708 GCTACTGATTCATAGCAAAAAGAGAAG 58.878 37.037 16.55 0.00 42.82 2.85
8931 9276 8.266392 ACTGATTCATAGCAAAAAGAGAAGAG 57.734 34.615 0.00 0.00 0.00 2.85
8935 9280 9.771915 GATTCATAGCAAAAAGAGAAGAGAAAG 57.228 33.333 0.00 0.00 0.00 2.62
9044 9392 4.814294 AACGATCGCCGCCTCACC 62.814 66.667 16.60 0.00 43.32 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.880890 AGACACAGCAGGACAATTGAAC 59.119 45.455 13.59 4.20 0.00 3.18
29 30 8.360325 CCAAGTAATGGGTGTTTTTACTTTTC 57.640 34.615 4.93 0.00 46.27 2.29
48 50 5.508280 ACATAAACTAGCCCAACCAAGTA 57.492 39.130 0.00 0.00 0.00 2.24
50 52 5.497474 AGTACATAAACTAGCCCAACCAAG 58.503 41.667 0.00 0.00 0.00 3.61
81 83 6.882656 AGCTGTGCTTAGAGAAAGAATGATA 58.117 36.000 0.00 0.00 33.89 2.15
283 290 9.220767 CTCAGTACTTTTATTGCCTCTTAAGTT 57.779 33.333 1.63 0.00 0.00 2.66
307 314 0.240945 CACGCACCAACAATTCCCTC 59.759 55.000 0.00 0.00 0.00 4.30
348 355 1.452110 CCAACATCACCAAGATCGCA 58.548 50.000 0.00 0.00 33.72 5.10
386 393 2.859165 TCCTTCTGGTTTGCTCGATT 57.141 45.000 0.00 0.00 34.23 3.34
819 1002 3.760738 TGCACAAACAGACCCATGAATA 58.239 40.909 0.00 0.00 0.00 1.75
898 1081 7.399478 AGTCTGGATATCTGAATAGCATGATCA 59.601 37.037 0.00 0.00 0.00 2.92
1412 1595 1.428869 AGGAGTGCCTGAGTTTGAGT 58.571 50.000 0.00 0.00 44.90 3.41
1836 2019 4.015872 TGGAATACCACACCTTTGACTC 57.984 45.455 0.00 0.00 41.77 3.36
2302 2485 2.635427 CTGGGGCTATTCTCTCCCTTAC 59.365 54.545 0.00 0.00 40.05 2.34
2904 3087 6.533730 ACTCACCAGATCATTTACAAGTGAA 58.466 36.000 0.00 0.00 33.03 3.18
3145 3330 8.398665 AGAAAACATAGTCAAACAAGACAGTTC 58.601 33.333 0.00 0.00 40.98 3.01
3148 3333 9.013490 CAAAGAAAACATAGTCAAACAAGACAG 57.987 33.333 0.00 0.00 40.98 3.51
3204 3389 8.567948 CAGACAAAACATAAACCTAACACTCAT 58.432 33.333 0.00 0.00 0.00 2.90
3470 3655 2.753055 TTTTGATGGTCGATCGGTCA 57.247 45.000 16.41 13.94 33.17 4.02
3558 3744 0.179078 CTCAGGCCTGCTTCTGCTAG 60.179 60.000 28.91 13.55 40.48 3.42
3604 3790 8.224025 TCTCTCCTATTCTCTATGTCATCAGTT 58.776 37.037 0.00 0.00 0.00 3.16
4099 4286 7.810282 TCATATTCATGTTGGGTTTGTTTAACG 59.190 33.333 0.00 0.00 34.21 3.18
4505 4700 7.337436 TCAATATGACACTGAATGATTCTTGCA 59.663 33.333 6.73 6.78 0.00 4.08
4843 5038 2.242043 AGACCATTGCACTTCCAAAGG 58.758 47.619 0.00 0.00 38.99 3.11
4849 5044 4.209911 GCAAAAAGAAGACCATTGCACTTC 59.790 41.667 6.01 6.01 44.29 3.01
4865 5060 4.749598 AGCGAAATTTTACCCTGCAAAAAG 59.250 37.500 0.00 0.00 0.00 2.27
4942 5137 7.372451 TGCAGTATAACACAAAAGTATCACC 57.628 36.000 0.00 0.00 0.00 4.02
5025 5220 9.606631 CCCTAGCTTACTTCATTTGATATATCC 57.393 37.037 10.25 0.00 0.00 2.59
5425 5627 6.129115 GCAATTAATAATAATGGCACGCACAG 60.129 38.462 5.20 0.00 44.60 3.66
5526 5728 7.801716 TGTAGGCAAGTGGTTGATATAAATC 57.198 36.000 0.00 0.00 35.46 2.17
5997 6200 0.773644 AGTTGTCACTGGGCCTCATT 59.226 50.000 4.53 0.00 0.00 2.57
6079 6282 8.677148 TTAATTATAGGCTTTTGCTCAGTAGG 57.323 34.615 0.00 0.00 46.54 3.18
6294 6497 3.844211 ACTACAGTAGGCCTGATTTGGAA 59.156 43.478 17.99 0.00 44.49 3.53
7461 7666 5.376625 ACAGCCTTCAGTGTCAATTTCTTA 58.623 37.500 0.00 0.00 0.00 2.10
7521 7727 2.096069 TGTTCGACTCGTTTAGGTCTCG 60.096 50.000 0.00 0.00 0.00 4.04
7597 7803 7.065443 AGCTAAAAACGTCTTACATTATGGGAC 59.935 37.037 0.00 1.75 0.00 4.46
7598 7804 7.107542 AGCTAAAAACGTCTTACATTATGGGA 58.892 34.615 0.00 0.00 0.00 4.37
7599 7805 7.316544 AGCTAAAAACGTCTTACATTATGGG 57.683 36.000 0.00 0.00 0.00 4.00
7600 7806 7.218204 GCAAGCTAAAAACGTCTTACATTATGG 59.782 37.037 0.00 0.00 0.00 2.74
7601 7807 7.962918 AGCAAGCTAAAAACGTCTTACATTATG 59.037 33.333 0.00 0.00 0.00 1.90
7602 7808 8.040716 AGCAAGCTAAAAACGTCTTACATTAT 57.959 30.769 0.00 0.00 0.00 1.28
7603 7809 7.429636 AGCAAGCTAAAAACGTCTTACATTA 57.570 32.000 0.00 0.00 0.00 1.90
7604 7810 6.313744 AGCAAGCTAAAAACGTCTTACATT 57.686 33.333 0.00 0.00 0.00 2.71
7605 7811 5.941948 AGCAAGCTAAAAACGTCTTACAT 57.058 34.783 0.00 0.00 0.00 2.29
7606 7812 5.754406 TGTAGCAAGCTAAAAACGTCTTACA 59.246 36.000 2.92 0.00 0.00 2.41
7607 7813 6.219302 TGTAGCAAGCTAAAAACGTCTTAC 57.781 37.500 2.92 0.00 0.00 2.34
7608 7814 7.429636 AATGTAGCAAGCTAAAAACGTCTTA 57.570 32.000 2.92 0.00 0.00 2.10
7609 7815 5.941948 ATGTAGCAAGCTAAAAACGTCTT 57.058 34.783 2.92 0.00 0.00 3.01
7610 7816 5.941948 AATGTAGCAAGCTAAAAACGTCT 57.058 34.783 2.92 0.00 0.00 4.18
7611 7817 6.687105 CCATAATGTAGCAAGCTAAAAACGTC 59.313 38.462 2.92 0.00 0.00 4.34
7612 7818 6.404293 CCCATAATGTAGCAAGCTAAAAACGT 60.404 38.462 2.92 0.00 0.00 3.99
7613 7819 5.971202 CCCATAATGTAGCAAGCTAAAAACG 59.029 40.000 2.92 0.00 0.00 3.60
7614 7820 6.972901 GTCCCATAATGTAGCAAGCTAAAAAC 59.027 38.462 2.92 0.00 0.00 2.43
7615 7821 6.183360 CGTCCCATAATGTAGCAAGCTAAAAA 60.183 38.462 2.92 0.00 0.00 1.94
7616 7822 5.295787 CGTCCCATAATGTAGCAAGCTAAAA 59.704 40.000 2.92 0.00 0.00 1.52
7617 7823 4.814234 CGTCCCATAATGTAGCAAGCTAAA 59.186 41.667 2.92 0.00 0.00 1.85
7618 7824 4.377021 CGTCCCATAATGTAGCAAGCTAA 58.623 43.478 2.92 0.00 0.00 3.09
7619 7825 3.244078 CCGTCCCATAATGTAGCAAGCTA 60.244 47.826 0.00 0.00 0.00 3.32
7620 7826 2.485479 CCGTCCCATAATGTAGCAAGCT 60.485 50.000 0.00 0.00 0.00 3.74
7621 7827 1.873591 CCGTCCCATAATGTAGCAAGC 59.126 52.381 0.00 0.00 0.00 4.01
7622 7828 3.393800 CTCCGTCCCATAATGTAGCAAG 58.606 50.000 0.00 0.00 0.00 4.01
7623 7829 2.104111 CCTCCGTCCCATAATGTAGCAA 59.896 50.000 0.00 0.00 0.00 3.91
7624 7830 1.691976 CCTCCGTCCCATAATGTAGCA 59.308 52.381 0.00 0.00 0.00 3.49
7625 7831 1.002087 CCCTCCGTCCCATAATGTAGC 59.998 57.143 0.00 0.00 0.00 3.58
7626 7832 2.563179 CTCCCTCCGTCCCATAATGTAG 59.437 54.545 0.00 0.00 0.00 2.74
7627 7833 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
7628 7834 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
7629 7835 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
7630 7836 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
7631 7837 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
7632 7838 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
7633 7839 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
7634 7840 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
7635 7841 0.324091 TGAACTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
7636 7842 1.104630 CTGAACTACTCCCTCCGTCC 58.895 60.000 0.00 0.00 0.00 4.79
7637 7843 1.836802 ACTGAACTACTCCCTCCGTC 58.163 55.000 0.00 0.00 0.00 4.79
7638 7844 3.354467 CTTACTGAACTACTCCCTCCGT 58.646 50.000 0.00 0.00 0.00 4.69
7639 7845 2.688958 CCTTACTGAACTACTCCCTCCG 59.311 54.545 0.00 0.00 0.00 4.63
7640 7846 2.431419 GCCTTACTGAACTACTCCCTCC 59.569 54.545 0.00 0.00 0.00 4.30
7641 7847 3.367321 AGCCTTACTGAACTACTCCCTC 58.633 50.000 0.00 0.00 0.00 4.30
7642 7848 3.367321 GAGCCTTACTGAACTACTCCCT 58.633 50.000 0.00 0.00 0.00 4.20
7643 7849 2.099427 CGAGCCTTACTGAACTACTCCC 59.901 54.545 0.00 0.00 0.00 4.30
7644 7850 2.099427 CCGAGCCTTACTGAACTACTCC 59.901 54.545 0.00 0.00 0.00 3.85
7645 7851 2.754002 ACCGAGCCTTACTGAACTACTC 59.246 50.000 0.00 0.00 0.00 2.59
7646 7852 2.805194 ACCGAGCCTTACTGAACTACT 58.195 47.619 0.00 0.00 0.00 2.57
7647 7853 3.944015 TCTACCGAGCCTTACTGAACTAC 59.056 47.826 0.00 0.00 0.00 2.73
7808 8017 4.508861 GCAATAAAATGGGCTATGCTTGTG 59.491 41.667 0.00 0.00 0.00 3.33
7809 8018 4.406649 AGCAATAAAATGGGCTATGCTTGT 59.593 37.500 0.00 0.00 34.25 3.16
7812 8021 4.217510 TGAGCAATAAAATGGGCTATGCT 58.782 39.130 0.00 0.00 36.59 3.79
7815 8024 4.321452 CGCATGAGCAATAAAATGGGCTAT 60.321 41.667 0.00 0.00 42.27 2.97
7818 8027 2.129607 CGCATGAGCAATAAAATGGGC 58.870 47.619 0.00 0.00 42.27 5.36
7819 8028 2.129607 GCGCATGAGCAATAAAATGGG 58.870 47.619 17.16 0.00 42.27 4.00
7821 8030 3.441163 ACAGCGCATGAGCAATAAAATG 58.559 40.909 23.73 12.92 42.27 2.32
7823 8032 3.487376 GCTACAGCGCATGAGCAATAAAA 60.487 43.478 23.73 1.92 42.27 1.52
7839 8107 2.391616 TGTGAGGCTGAATGCTACAG 57.608 50.000 0.00 0.00 42.39 2.74
7858 8126 9.793252 CAAGCAAATTACATTTAGTAGATGCTT 57.207 29.630 13.52 13.52 46.64 3.91
7938 8206 3.118775 CGAGTGAATACATCCCAAGGTCA 60.119 47.826 0.00 0.00 0.00 4.02
7941 8209 3.722147 CTCGAGTGAATACATCCCAAGG 58.278 50.000 3.62 0.00 0.00 3.61
7944 8212 2.388735 AGCTCGAGTGAATACATCCCA 58.611 47.619 15.13 0.00 0.00 4.37
7977 8245 0.320421 GAACGCTTCAGTGTAGGGCA 60.320 55.000 12.82 0.00 37.87 5.36
8039 8337 7.801104 TGATGCAGGAGAATACTACCAAAATA 58.199 34.615 0.00 0.00 0.00 1.40
8142 8440 4.818642 TGCAAATTACATGTGGGTCAATG 58.181 39.130 9.11 0.00 0.00 2.82
8150 8448 4.669965 CGGAGACACTGCAAATTACATGTG 60.670 45.833 9.11 0.00 0.00 3.21
8159 8457 1.040646 AGACTCGGAGACACTGCAAA 58.959 50.000 12.86 0.00 0.00 3.68
8238 8536 3.251004 GGGATTACGATCAATGCACCTTC 59.749 47.826 0.00 0.00 33.77 3.46
8283 8581 3.368843 CGGATGAAGTTGTGAGGTGAGAT 60.369 47.826 0.00 0.00 0.00 2.75
8306 8604 1.978782 CGCAAAGAGAAATCGCCAAAC 59.021 47.619 0.00 0.00 0.00 2.93
8371 8669 6.454795 ACAACAGTGGGCATTTTATAACTTG 58.545 36.000 0.00 0.00 0.00 3.16
8385 8683 1.845809 GCAGCTCGAACAACAGTGGG 61.846 60.000 0.00 0.00 0.00 4.61
8393 8691 2.317609 GCTTTCCGCAGCTCGAACA 61.318 57.895 7.07 0.00 41.67 3.18
8410 8708 4.864916 TTCTCTTGATATTCGCAACTGC 57.135 40.909 0.00 0.00 37.78 4.40
8418 8716 6.319658 TGGTTCCTTGCATTCTCTTGATATTC 59.680 38.462 0.00 0.00 0.00 1.75
8423 8721 3.181440 ACTGGTTCCTTGCATTCTCTTGA 60.181 43.478 0.00 0.00 0.00 3.02
8432 8730 2.363306 ATGACAACTGGTTCCTTGCA 57.637 45.000 0.00 0.00 0.00 4.08
8518 8816 2.886124 GAGCGCTACCAAGCCGTC 60.886 66.667 11.50 0.00 46.68 4.79
8522 8820 1.661112 CTACTTTGAGCGCTACCAAGC 59.339 52.381 11.50 0.00 45.86 4.01
8531 8829 1.432514 TGCTTCTGCTACTTTGAGCG 58.567 50.000 0.00 0.00 45.99 5.03
8543 8841 2.208431 GAGTTCCCATCGATGCTTCTG 58.792 52.381 20.25 5.77 0.00 3.02
8548 8846 4.142403 TGAAATTTGAGTTCCCATCGATGC 60.142 41.667 20.25 6.26 0.00 3.91
8549 8847 5.355071 TCTGAAATTTGAGTTCCCATCGATG 59.645 40.000 18.76 18.76 0.00 3.84
8550 8848 5.500234 TCTGAAATTTGAGTTCCCATCGAT 58.500 37.500 4.52 0.00 0.00 3.59
8552 8850 5.627499 TTCTGAAATTTGAGTTCCCATCG 57.373 39.130 4.52 0.00 0.00 3.84
8555 8853 5.128499 TGCTTTTCTGAAATTTGAGTTCCCA 59.872 36.000 3.31 0.00 0.00 4.37
8561 8859 7.958053 ATCCTTTGCTTTTCTGAAATTTGAG 57.042 32.000 3.31 0.00 0.00 3.02
8562 8860 8.641541 ACTATCCTTTGCTTTTCTGAAATTTGA 58.358 29.630 3.31 0.00 0.00 2.69
8577 8875 6.248631 GTGTAAACAATCGACTATCCTTTGC 58.751 40.000 0.00 0.00 0.00 3.68
8578 8876 6.594159 AGGTGTAAACAATCGACTATCCTTTG 59.406 38.462 0.00 0.00 0.00 2.77
8579 8877 6.708285 AGGTGTAAACAATCGACTATCCTTT 58.292 36.000 0.00 0.00 0.00 3.11
8584 8882 5.717119 ACGAAGGTGTAAACAATCGACTAT 58.283 37.500 14.46 0.00 34.74 2.12
8589 8887 4.208355 CACAACGAAGGTGTAAACAATCG 58.792 43.478 7.85 7.85 35.90 3.34
8603 8901 1.066303 GGGTTGCATTGACACAACGAA 59.934 47.619 0.00 0.00 45.62 3.85
8605 8903 0.667993 AGGGTTGCATTGACACAACG 59.332 50.000 0.00 0.00 45.62 4.10
8606 8904 2.362077 AGAAGGGTTGCATTGACACAAC 59.638 45.455 0.00 0.00 44.29 3.32
8611 8909 3.733443 ACAAAGAAGGGTTGCATTGAC 57.267 42.857 0.00 0.00 0.00 3.18
8612 8910 5.304101 ACAATACAAAGAAGGGTTGCATTGA 59.696 36.000 14.10 0.00 40.12 2.57
8613 8911 5.540911 ACAATACAAAGAAGGGTTGCATTG 58.459 37.500 8.03 8.03 42.02 2.82
8614 8912 5.806654 ACAATACAAAGAAGGGTTGCATT 57.193 34.783 0.00 0.00 0.00 3.56
8615 8913 5.806654 AACAATACAAAGAAGGGTTGCAT 57.193 34.783 0.00 0.00 0.00 3.96
8616 8914 5.606348 AAACAATACAAAGAAGGGTTGCA 57.394 34.783 0.00 0.00 0.00 4.08
8617 8915 6.745116 ACTAAACAATACAAAGAAGGGTTGC 58.255 36.000 0.00 0.00 0.00 4.17
8640 8938 4.685628 CACTGGGCACATCAAAATGTTTAC 59.314 41.667 0.00 0.00 43.74 2.01
8641 8939 4.343526 ACACTGGGCACATCAAAATGTTTA 59.656 37.500 0.00 0.00 43.74 2.01
8686 8984 5.809001 ACCTAGAATGAGCTTGTTCAATCA 58.191 37.500 12.70 0.00 30.95 2.57
8694 8992 5.293079 GCACTAGAAACCTAGAATGAGCTTG 59.707 44.000 0.00 0.00 37.61 4.01
8702 9000 7.224297 AGAAACAATGCACTAGAAACCTAGAA 58.776 34.615 0.00 0.00 37.61 2.10
8785 9083 4.483476 ACAGAAAGTTGCGACAATAACC 57.517 40.909 6.90 0.00 0.00 2.85
8812 9110 8.980481 TTTGTATTCTCTTGGTTCTTTCTTCT 57.020 30.769 0.00 0.00 0.00 2.85
8813 9111 8.841300 ACTTTGTATTCTCTTGGTTCTTTCTTC 58.159 33.333 0.00 0.00 0.00 2.87
8814 9112 8.624776 CACTTTGTATTCTCTTGGTTCTTTCTT 58.375 33.333 0.00 0.00 0.00 2.52
8855 9169 6.534475 AATGCCTTGTACATCATCACAAAT 57.466 33.333 0.00 0.00 34.43 2.32
8880 9217 7.782049 AGCTAGCTTTCAAGTGTACATACATA 58.218 34.615 12.68 0.00 38.63 2.29
8895 9240 6.219473 TGCTATGAATCAGTAGCTAGCTTTC 58.781 40.000 24.88 19.52 42.86 2.62
8914 9259 9.651913 CTACTCTTTCTCTTCTCTTTTTGCTAT 57.348 33.333 0.00 0.00 0.00 2.97
8915 9260 8.643324 ACTACTCTTTCTCTTCTCTTTTTGCTA 58.357 33.333 0.00 0.00 0.00 3.49
8928 9273 1.096416 CCGGCGACTACTCTTTCTCT 58.904 55.000 9.30 0.00 0.00 3.10
8929 9274 0.525882 GCCGGCGACTACTCTTTCTC 60.526 60.000 12.58 0.00 0.00 2.87
8931 9276 0.737219 TAGCCGGCGACTACTCTTTC 59.263 55.000 23.20 0.00 0.00 2.62
8935 9280 2.327244 CGTAGCCGGCGACTACTC 59.673 66.667 32.50 10.77 38.27 2.59


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

AutoCloner maintained by Alex Coulton.