Multiple sequence alignment - TraesCS2B01G253600

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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 TraesCS2B01G253600 chr2B 100.000 5883 0 0 1 5883 278434641 278440523 0.000000e+00 10864.0
1 TraesCS2B01G253600 chr2B 100.000 30 0 0 2848 2877 278437440 278437411 8.240000e-04 56.5
2 TraesCS2B01G253600 chr2B 96.970 33 1 0 2771 2803 278437517 278437485 8.240000e-04 56.5
3 TraesCS2B01G253600 chr2D 94.566 2337 86 22 2892 5198 250630417 250628092 0.000000e+00 3574.0
4 TraesCS2B01G253600 chr2D 96.719 2103 46 7 749 2832 250632543 250630445 0.000000e+00 3480.0
5 TraesCS2B01G253600 chr2D 84.866 522 30 20 5311 5809 250628081 250627586 1.150000e-131 481.0
6 TraesCS2B01G253600 chr2D 93.333 120 5 3 5195 5313 617397860 617397743 2.180000e-39 174.0
7 TraesCS2B01G253600 chr2D 94.643 112 5 1 5195 5305 111321404 111321515 7.840000e-39 172.0
8 TraesCS2B01G253600 chr2D 86.585 82 5 4 4696 4777 645688631 645688556 1.050000e-12 86.1
9 TraesCS2B01G253600 chr2D 96.970 33 1 0 2845 2877 250630474 250630506 8.240000e-04 56.5
10 TraesCS2B01G253600 chr2A 96.805 1972 42 5 879 2832 249756145 249754177 0.000000e+00 3273.0
11 TraesCS2B01G253600 chr2A 95.201 1417 51 11 2892 4295 249754149 249752737 0.000000e+00 2224.0
12 TraesCS2B01G253600 chr2A 95.603 614 23 3 4587 5198 249751760 249751149 0.000000e+00 981.0
13 TraesCS2B01G253600 chr2A 88.820 322 21 5 4283 4592 249752178 249751860 1.200000e-101 381.0
14 TraesCS2B01G253600 chr2A 94.492 236 13 0 5302 5537 249751146 249750911 1.200000e-96 364.0
15 TraesCS2B01G253600 chr2A 98.529 136 1 1 753 887 249761595 249761460 7.620000e-59 239.0
16 TraesCS2B01G253600 chr2A 92.361 144 10 1 2395 2537 655039289 655039146 2.780000e-48 204.0
17 TraesCS2B01G253600 chr2A 96.970 33 1 0 2845 2877 249754206 249754238 8.240000e-04 56.5
18 TraesCS2B01G253600 chr5A 87.867 750 86 4 5 750 558314247 558313499 0.000000e+00 876.0
19 TraesCS2B01G253600 chr5A 85.515 573 80 3 180 750 601647270 601646699 3.920000e-166 595.0
20 TraesCS2B01G253600 chr5A 94.245 139 8 0 2400 2538 320214240 320214378 4.620000e-51 213.0
21 TraesCS2B01G253600 chr3B 87.166 748 84 7 5 750 772115439 772116176 0.000000e+00 839.0
22 TraesCS2B01G253600 chr3B 84.507 71 7 4 5635 5701 765127881 765127951 3.800000e-07 67.6
23 TraesCS2B01G253600 chr7A 89.828 580 52 6 175 750 576420392 576420968 0.000000e+00 737.0
24 TraesCS2B01G253600 chr7A 89.619 578 58 2 175 750 658689624 658689047 0.000000e+00 734.0
25 TraesCS2B01G253600 chr7A 88.889 171 13 6 2373 2538 451520007 451519838 7.730000e-49 206.0
26 TraesCS2B01G253600 chr1A 82.740 759 122 9 1 755 11068509 11067756 0.000000e+00 667.0
27 TraesCS2B01G253600 chr1A 96.296 108 4 0 5196 5303 584968574 584968681 1.680000e-40 178.0
28 TraesCS2B01G253600 chr1A 80.899 178 29 3 5640 5813 552982477 552982301 1.030000e-27 135.0
29 TraesCS2B01G253600 chr5D 87.219 579 65 7 175 749 200496033 200495460 0.000000e+00 651.0
30 TraesCS2B01G253600 chr4B 82.048 752 132 3 1 750 638313212 638313962 6.430000e-179 638.0
31 TraesCS2B01G253600 chr4B 80.769 156 22 7 5631 5781 619362137 619362289 1.340000e-21 115.0
32 TraesCS2B01G253600 chr5B 80.667 750 141 4 3 750 358803292 358804039 3.950000e-161 579.0
33 TraesCS2B01G253600 chr5B 96.330 109 3 1 5196 5303 165765472 165765364 1.680000e-40 178.0
34 TraesCS2B01G253600 chr5B 96.330 109 3 1 5196 5303 166157085 166156977 1.680000e-40 178.0
35 TraesCS2B01G253600 chr7B 94.203 138 8 0 2401 2538 11441307 11441170 1.660000e-50 211.0
36 TraesCS2B01G253600 chr1B 93.525 139 9 0 2400 2538 436689155 436689017 2.150000e-49 207.0
37 TraesCS2B01G253600 chr1B 94.690 113 4 2 5194 5304 113565235 113565123 2.180000e-39 174.0
38 TraesCS2B01G253600 chr6B 92.414 145 9 1 2394 2538 481857843 481857985 7.730000e-49 206.0
39 TraesCS2B01G253600 chr7D 88.095 168 14 6 2373 2535 397554881 397555047 1.670000e-45 195.0
40 TraesCS2B01G253600 chr7D 81.915 188 26 6 5629 5810 541963948 541964133 1.020000e-32 152.0
41 TraesCS2B01G253600 chr7D 88.636 44 4 1 4530 4573 634502720 634502678 1.100000e-02 52.8
42 TraesCS2B01G253600 chrUn 96.330 109 3 1 5196 5303 475962778 475962886 1.680000e-40 178.0
43 TraesCS2B01G253600 chr3D 94.828 116 3 3 5189 5303 552761268 552761381 1.680000e-40 178.0
44 TraesCS2B01G253600 chr4D 91.935 124 7 3 5195 5317 16450228 16450349 2.820000e-38 171.0
45 TraesCS2B01G253600 chr3A 82.778 180 22 6 5640 5813 497647893 497647717 1.020000e-32 152.0
46 TraesCS2B01G253600 chr4A 80.925 173 29 3 5639 5808 674434839 674435010 3.700000e-27 134.0


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 TraesCS2B01G253600 chr2B 278434641 278440523 5882 False 10864.000000 10864 100.000000 1 5883 1 chr2B.!!$F1 5882
1 TraesCS2B01G253600 chr2D 250627586 250632543 4957 True 2511.666667 3574 92.050333 749 5809 3 chr2D.!!$R3 5060
2 TraesCS2B01G253600 chr2A 249750911 249756145 5234 True 1444.600000 3273 94.184200 879 5537 5 chr2A.!!$R3 4658
3 TraesCS2B01G253600 chr5A 558313499 558314247 748 True 876.000000 876 87.867000 5 750 1 chr5A.!!$R1 745
4 TraesCS2B01G253600 chr5A 601646699 601647270 571 True 595.000000 595 85.515000 180 750 1 chr5A.!!$R2 570
5 TraesCS2B01G253600 chr3B 772115439 772116176 737 False 839.000000 839 87.166000 5 750 1 chr3B.!!$F2 745
6 TraesCS2B01G253600 chr7A 576420392 576420968 576 False 737.000000 737 89.828000 175 750 1 chr7A.!!$F1 575
7 TraesCS2B01G253600 chr7A 658689047 658689624 577 True 734.000000 734 89.619000 175 750 1 chr7A.!!$R2 575
8 TraesCS2B01G253600 chr1A 11067756 11068509 753 True 667.000000 667 82.740000 1 755 1 chr1A.!!$R1 754
9 TraesCS2B01G253600 chr5D 200495460 200496033 573 True 651.000000 651 87.219000 175 749 1 chr5D.!!$R1 574
10 TraesCS2B01G253600 chr4B 638313212 638313962 750 False 638.000000 638 82.048000 1 750 1 chr4B.!!$F2 749
11 TraesCS2B01G253600 chr5B 358803292 358804039 747 False 579.000000 579 80.667000 3 750 1 chr5B.!!$F1 747

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
591 594 0.165511 CTTCTGCTCGCTTTCAGCAC 59.834 55.0 0.00 0.00 42.09 4.40 F
699 702 2.365617 GGATTGCATTCGGGAGACTCTA 59.634 50.0 1.74 0.00 39.59 2.43 F
1548 1554 2.806945 TGCCCTGAAACCCTAATGAG 57.193 50.0 0.00 0.00 0.00 2.90 F
2163 2169 0.764890 TAGTTCCAGTGCTGCCTGTT 59.235 50.0 14.25 3.63 0.00 3.16 F
2847 2870 0.033405 TTAGCTGCTACTCCCTCCGT 60.033 55.0 9.27 0.00 0.00 4.69 F
2848 2871 0.033405 TAGCTGCTACTCCCTCCGTT 60.033 55.0 5.02 0.00 0.00 4.44 F
3102 3127 0.589223 CGGCGGTGCTTTGAAGTAAA 59.411 50.0 0.00 0.00 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1554 0.243636 AAAGTTGCCCTGTTATGCGC 59.756 50.000 0.0 0.0 0.00 6.09 R
2082 2088 0.850100 TGTCCAAAGAAAGGGGAGCA 59.150 50.000 0.0 0.0 0.00 4.26 R
2832 2855 1.187087 AGAAACGGAGGGAGTAGCAG 58.813 55.000 0.0 0.0 0.00 4.24 R
3587 3613 2.029666 CGAGCCCCCTTGCGATAG 59.970 66.667 0.0 0.0 36.02 2.08 R
4688 5415 1.134438 ACTCCTCCCCACAACCTTCC 61.134 60.000 0.0 0.0 0.00 3.46 R
4852 5579 2.238646 TGGTTGTCGCCTCCTGAAATAT 59.761 45.455 0.0 0.0 0.00 1.28 R
5067 5795 2.299013 CCATATGCCCTTCGTGCTACTA 59.701 50.000 0.0 0.0 0.00 1.82 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
95 96 0.186873 CTGGCATATTTGGGAGGCCT 59.813 55.000 3.86 3.86 44.85 5.19
105 106 1.288508 TGGGAGGCCTGCAATATGGT 61.289 55.000 26.95 0.00 0.00 3.55
206 207 7.687388 ACATCTATATGATCATGTTCCTGCTT 58.313 34.615 18.72 0.00 36.54 3.91
214 215 0.462759 ATGTTCCTGCTTCTAGGCGC 60.463 55.000 0.00 0.00 37.76 6.53
228 229 2.737376 GCGCGAGACCTCCGTTTT 60.737 61.111 12.10 0.00 0.00 2.43
230 231 1.372499 CGCGAGACCTCCGTTTTCA 60.372 57.895 0.00 0.00 0.00 2.69
284 285 1.908619 TGGTTGCCTTCTCTGATGCTA 59.091 47.619 0.00 0.00 0.00 3.49
286 287 2.355108 GGTTGCCTTCTCTGATGCTACA 60.355 50.000 0.00 0.00 32.35 2.74
392 393 2.829003 CGGGCGCTCTGTCTCCTA 60.829 66.667 5.36 0.00 0.00 2.94
456 457 1.911471 GGGAGGAGGGCTTCTTCAG 59.089 63.158 10.80 0.00 33.75 3.02
460 461 2.180276 GAGGAGGGCTTCTTCAGTGTA 58.820 52.381 3.79 0.00 32.43 2.90
471 472 5.645497 GCTTCTTCAGTGTATCCTTCAACAT 59.355 40.000 0.00 0.00 0.00 2.71
488 489 1.278985 ACATTGATTGCCTCTCGGTGA 59.721 47.619 0.00 0.00 0.00 4.02
591 594 0.165511 CTTCTGCTCGCTTTCAGCAC 59.834 55.000 0.00 0.00 42.09 4.40
699 702 2.365617 GGATTGCATTCGGGAGACTCTA 59.634 50.000 1.74 0.00 39.59 2.43
1383 1389 8.700439 ACTACAAGAGTAAGATATCTCCCTTC 57.300 38.462 5.51 2.46 36.27 3.46
1492 1498 6.538021 GCTTTGTGACTCATTATCTGATCTGT 59.462 38.462 0.00 0.00 32.10 3.41
1511 1517 5.908341 TCTGTCATGTGTTTGTGTAGTACA 58.092 37.500 0.00 0.00 37.56 2.90
1538 1544 4.906747 AATTTAGCCATTTGCCCTGAAA 57.093 36.364 0.00 0.00 42.71 2.69
1548 1554 2.806945 TGCCCTGAAACCCTAATGAG 57.193 50.000 0.00 0.00 0.00 2.90
1729 1735 6.727824 TTGATGTGCTTAAAAGTAGAGCTC 57.272 37.500 5.27 5.27 37.32 4.09
1807 1813 3.084536 TGTTGCTGGCATGAATTCCTA 57.915 42.857 2.27 0.00 0.00 2.94
1808 1814 3.429492 TGTTGCTGGCATGAATTCCTAA 58.571 40.909 2.27 0.00 0.00 2.69
1816 1822 3.067320 GGCATGAATTCCTAACTGCCTTC 59.933 47.826 18.29 0.00 44.47 3.46
1866 1872 7.379797 GTCTTTGATTGCTAGAACTTTGTTTCC 59.620 37.037 0.00 0.00 0.00 3.13
2163 2169 0.764890 TAGTTCCAGTGCTGCCTGTT 59.235 50.000 14.25 3.63 0.00 3.16
2200 2206 5.569059 CGTATTTGTTGTCTGGATTTCTTGC 59.431 40.000 0.00 0.00 0.00 4.01
2207 2213 4.012374 TGTCTGGATTTCTTGCATCTTCC 58.988 43.478 0.00 0.00 0.00 3.46
2412 2418 8.305317 GCTTGATTAAACGTATATACTCCCTCT 58.695 37.037 11.05 0.00 0.00 3.69
2565 2587 6.181190 AGGGAGTAGGCAGTAATTCTTTTTC 58.819 40.000 0.00 0.00 0.00 2.29
2607 2630 2.093152 CACGCCAGGTAATCGTAAACAC 59.907 50.000 0.00 0.00 34.81 3.32
2611 2634 3.749609 GCCAGGTAATCGTAAACACACTT 59.250 43.478 0.00 0.00 0.00 3.16
2612 2635 4.142966 GCCAGGTAATCGTAAACACACTTC 60.143 45.833 0.00 0.00 0.00 3.01
2709 2732 7.390162 AGAGAACTTGAAGATTTCCTCATCAAC 59.610 37.037 0.00 0.00 36.83 3.18
2842 2865 8.848474 TTATTTATCATTTAGCTGCTACTCCC 57.152 34.615 9.27 0.00 0.00 4.30
2843 2866 6.500589 TTTATCATTTAGCTGCTACTCCCT 57.499 37.500 9.27 0.00 0.00 4.20
2844 2867 4.615588 ATCATTTAGCTGCTACTCCCTC 57.384 45.455 9.27 0.00 0.00 4.30
2845 2868 2.700897 TCATTTAGCTGCTACTCCCTCC 59.299 50.000 9.27 0.00 0.00 4.30
2846 2869 1.112113 TTTAGCTGCTACTCCCTCCG 58.888 55.000 9.27 0.00 0.00 4.63
2847 2870 0.033405 TTAGCTGCTACTCCCTCCGT 60.033 55.000 9.27 0.00 0.00 4.69
2848 2871 0.033405 TAGCTGCTACTCCCTCCGTT 60.033 55.000 5.02 0.00 0.00 4.44
2853 2876 1.275291 TGCTACTCCCTCCGTTTCTTG 59.725 52.381 0.00 0.00 0.00 3.02
2854 2877 2.007547 GCTACTCCCTCCGTTTCTTGC 61.008 57.143 0.00 0.00 0.00 4.01
2855 2878 1.550976 CTACTCCCTCCGTTTCTTGCT 59.449 52.381 0.00 0.00 0.00 3.91
2856 2879 1.640917 ACTCCCTCCGTTTCTTGCTA 58.359 50.000 0.00 0.00 0.00 3.49
2857 2880 1.975680 ACTCCCTCCGTTTCTTGCTAA 59.024 47.619 0.00 0.00 0.00 3.09
2858 2881 2.572104 ACTCCCTCCGTTTCTTGCTAAT 59.428 45.455 0.00 0.00 0.00 1.73
2859 2882 2.939103 CTCCCTCCGTTTCTTGCTAATG 59.061 50.000 0.00 0.00 0.00 1.90
2860 2883 2.569853 TCCCTCCGTTTCTTGCTAATGA 59.430 45.455 0.00 0.00 0.00 2.57
2861 2884 3.008594 TCCCTCCGTTTCTTGCTAATGAA 59.991 43.478 0.00 0.00 0.00 2.57
2862 2885 3.375299 CCCTCCGTTTCTTGCTAATGAAG 59.625 47.826 0.00 0.00 0.00 3.02
2863 2886 4.003648 CCTCCGTTTCTTGCTAATGAAGT 58.996 43.478 0.00 0.00 0.00 3.01
2864 2887 4.455877 CCTCCGTTTCTTGCTAATGAAGTT 59.544 41.667 0.00 0.00 0.00 2.66
2865 2888 5.356882 TCCGTTTCTTGCTAATGAAGTTG 57.643 39.130 0.00 0.00 0.00 3.16
2866 2889 5.060506 TCCGTTTCTTGCTAATGAAGTTGA 58.939 37.500 0.00 0.00 0.00 3.18
2867 2890 5.529430 TCCGTTTCTTGCTAATGAAGTTGAA 59.471 36.000 0.00 0.00 0.00 2.69
2868 2891 5.853282 CCGTTTCTTGCTAATGAAGTTGAAG 59.147 40.000 0.00 0.00 0.00 3.02
2869 2892 5.853282 CGTTTCTTGCTAATGAAGTTGAAGG 59.147 40.000 0.00 0.00 0.00 3.46
2870 2893 6.293407 CGTTTCTTGCTAATGAAGTTGAAGGA 60.293 38.462 0.00 0.00 0.00 3.36
2871 2894 7.573843 CGTTTCTTGCTAATGAAGTTGAAGGAT 60.574 37.037 0.00 0.00 0.00 3.24
2872 2895 6.748333 TCTTGCTAATGAAGTTGAAGGATG 57.252 37.500 0.00 0.00 0.00 3.51
2873 2896 6.475504 TCTTGCTAATGAAGTTGAAGGATGA 58.524 36.000 0.00 0.00 0.00 2.92
2874 2897 6.596888 TCTTGCTAATGAAGTTGAAGGATGAG 59.403 38.462 0.00 0.00 0.00 2.90
2875 2898 6.053632 TGCTAATGAAGTTGAAGGATGAGA 57.946 37.500 0.00 0.00 0.00 3.27
2876 2899 6.475504 TGCTAATGAAGTTGAAGGATGAGAA 58.524 36.000 0.00 0.00 0.00 2.87
2877 2900 6.942005 TGCTAATGAAGTTGAAGGATGAGAAA 59.058 34.615 0.00 0.00 0.00 2.52
2878 2901 7.613022 TGCTAATGAAGTTGAAGGATGAGAAAT 59.387 33.333 0.00 0.00 0.00 2.17
2879 2902 7.914346 GCTAATGAAGTTGAAGGATGAGAAATG 59.086 37.037 0.00 0.00 0.00 2.32
2880 2903 6.770746 ATGAAGTTGAAGGATGAGAAATGG 57.229 37.500 0.00 0.00 0.00 3.16
2881 2904 4.460382 TGAAGTTGAAGGATGAGAAATGGC 59.540 41.667 0.00 0.00 0.00 4.40
2882 2905 4.313020 AGTTGAAGGATGAGAAATGGCT 57.687 40.909 0.00 0.00 0.00 4.75
2883 2906 4.268359 AGTTGAAGGATGAGAAATGGCTC 58.732 43.478 0.00 0.00 35.46 4.70
2884 2907 4.018597 AGTTGAAGGATGAGAAATGGCTCT 60.019 41.667 0.00 0.00 35.91 4.09
2885 2908 4.581309 TGAAGGATGAGAAATGGCTCTT 57.419 40.909 0.00 0.00 35.91 2.85
2886 2909 4.927049 TGAAGGATGAGAAATGGCTCTTT 58.073 39.130 0.00 0.00 35.91 2.52
2887 2910 6.065976 TGAAGGATGAGAAATGGCTCTTTA 57.934 37.500 0.00 0.00 35.91 1.85
2888 2911 6.118170 TGAAGGATGAGAAATGGCTCTTTAG 58.882 40.000 0.00 0.00 35.91 1.85
2889 2912 5.965033 AGGATGAGAAATGGCTCTTTAGA 57.035 39.130 0.00 0.00 35.91 2.10
2890 2913 6.512514 AGGATGAGAAATGGCTCTTTAGAT 57.487 37.500 0.00 0.00 35.91 1.98
2897 2920 4.591321 AATGGCTCTTTAGATTGGGACA 57.409 40.909 0.00 0.00 0.00 4.02
2910 2933 5.538877 AGATTGGGACAGAGGGAGTATTTA 58.461 41.667 0.00 0.00 42.39 1.40
2911 2934 5.367060 AGATTGGGACAGAGGGAGTATTTAC 59.633 44.000 0.00 0.00 42.39 2.01
3049 3074 9.500864 AATTTTGTAACATTTTGCATGTTTCAC 57.499 25.926 9.31 4.05 41.81 3.18
3102 3127 0.589223 CGGCGGTGCTTTGAAGTAAA 59.411 50.000 0.00 0.00 0.00 2.01
3103 3128 1.399727 CGGCGGTGCTTTGAAGTAAAG 60.400 52.381 0.00 0.00 46.86 1.85
3161 3187 7.521529 TGAATTTGTTCTTCATCTTTCTAGCG 58.478 34.615 0.00 0.00 0.00 4.26
3393 3419 5.128827 AGTTCTGTTCTGAAACTGTAGTGGA 59.871 40.000 0.00 0.00 36.17 4.02
3441 3467 6.788598 TTTCTCTCTGCTATGTCTGAATCT 57.211 37.500 0.00 0.00 0.00 2.40
3448 3474 8.166726 TCTCTGCTATGTCTGAATCTCCTTATA 58.833 37.037 0.00 0.00 0.00 0.98
3449 3475 8.891985 TCTGCTATGTCTGAATCTCCTTATAT 57.108 34.615 0.00 0.00 0.00 0.86
3450 3476 9.319060 TCTGCTATGTCTGAATCTCCTTATATT 57.681 33.333 0.00 0.00 0.00 1.28
3495 3521 1.677576 AGTTGGCTGTTGTGACATGTG 59.322 47.619 1.15 0.00 34.72 3.21
3514 3540 5.316327 TGTGTGCATGTTGTTTTTCTACA 57.684 34.783 0.00 0.00 36.39 2.74
3587 3613 4.093998 CCACTGTGCATTATGAAGTGACTC 59.906 45.833 18.28 0.00 40.54 3.36
3707 3733 2.376518 TCAGGAGAAAATCAAGTGGGCT 59.623 45.455 0.00 0.00 0.00 5.19
4237 4275 8.716674 ATAACTAAATTATACTCCCTCCGTCA 57.283 34.615 0.00 0.00 31.28 4.35
4401 5009 2.462456 ATGCCCATGCGTAGTCATAG 57.538 50.000 0.00 0.00 41.78 2.23
4411 5019 3.611113 TGCGTAGTCATAGAAAACGAAGC 59.389 43.478 0.00 0.00 35.66 3.86
4438 5046 1.067071 CCACTGGTTTAGGAGACGGTC 60.067 57.143 0.00 0.00 0.00 4.79
4457 5077 6.640518 ACGGTCAAAAGATGATAGTGTACAT 58.359 36.000 0.00 0.00 40.97 2.29
4489 5109 9.321590 ACGATTAAAATAAAGCAAAAGTACGAC 57.678 29.630 0.00 0.00 0.00 4.34
4508 5128 1.605738 AAGGAGTGGTAGGCGTCGT 60.606 57.895 0.00 0.00 0.00 4.34
4518 5138 5.045872 GTGGTAGGCGTCGTAGAATTTTAT 58.954 41.667 0.00 0.00 39.69 1.40
4548 5168 5.411669 CGTAGTAGGTCCTTTGCAAGATTTT 59.588 40.000 0.00 0.00 0.00 1.82
4549 5169 6.072673 CGTAGTAGGTCCTTTGCAAGATTTTT 60.073 38.462 0.00 0.00 0.00 1.94
4589 5209 7.129425 TGCAAATTTAAATCCTACCAGGGTAT 58.871 34.615 0.10 0.00 35.59 2.73
4759 5486 1.269448 ACATGCGAATTCACCACCAAC 59.731 47.619 6.22 0.00 0.00 3.77
4774 5501 6.150976 TCACCACCAACTTCAGCATTTATAAG 59.849 38.462 0.00 0.00 0.00 1.73
4808 5535 9.860898 AAAGATGCTTTTCCATGTTATTAGAAC 57.139 29.630 0.00 0.00 29.68 3.01
4969 5697 0.606604 GTCACCGGAGTTTAGGAGCA 59.393 55.000 9.46 0.00 0.00 4.26
5041 5769 9.743057 CTTGTTTTTGGTATGAGATGTTACAAA 57.257 29.630 0.00 0.00 0.00 2.83
5067 5795 7.013655 AGAGATGATTTACTGCCGCATTTATTT 59.986 33.333 0.00 0.00 0.00 1.40
5076 5804 3.001838 TGCCGCATTTATTTAGTAGCACG 59.998 43.478 0.00 0.00 0.00 5.34
5096 5824 2.576615 GAAGGGCATATGGGTGACTTC 58.423 52.381 4.56 0.00 31.96 3.01
5125 5853 9.574516 ACTGTAAAGATTATGGTTCTGAAAAGT 57.425 29.630 0.00 0.00 0.00 2.66
5142 5870 3.945640 AAGTTTGGTGACCTAAGGTGT 57.054 42.857 2.11 0.00 35.25 4.16
5165 5893 3.056465 TCGCTCAGTTTGGTTTGGTTTTT 60.056 39.130 0.00 0.00 0.00 1.94
5202 5930 2.619147 GAAGGCCTTCGAAACTACTCC 58.381 52.381 29.09 3.08 0.00 3.85
5203 5931 0.903236 AGGCCTTCGAAACTACTCCC 59.097 55.000 0.00 0.00 0.00 4.30
5204 5932 0.903236 GGCCTTCGAAACTACTCCCT 59.097 55.000 0.00 0.00 0.00 4.20
5205 5933 1.134759 GGCCTTCGAAACTACTCCCTC 60.135 57.143 0.00 0.00 0.00 4.30
5206 5934 1.134759 GCCTTCGAAACTACTCCCTCC 60.135 57.143 0.00 0.00 0.00 4.30
5207 5935 2.176889 CCTTCGAAACTACTCCCTCCA 58.823 52.381 0.00 0.00 0.00 3.86
5208 5936 2.766828 CCTTCGAAACTACTCCCTCCAT 59.233 50.000 0.00 0.00 0.00 3.41
5209 5937 3.197983 CCTTCGAAACTACTCCCTCCATT 59.802 47.826 0.00 0.00 0.00 3.16
5210 5938 4.434520 CTTCGAAACTACTCCCTCCATTC 58.565 47.826 0.00 0.00 0.00 2.67
5211 5939 2.426024 TCGAAACTACTCCCTCCATTCG 59.574 50.000 0.00 0.00 39.43 3.34
5212 5940 2.481449 CGAAACTACTCCCTCCATTCGG 60.481 54.545 0.00 0.00 35.75 4.30
5213 5941 2.544844 AACTACTCCCTCCATTCGGA 57.455 50.000 0.00 0.00 39.79 4.55
5214 5942 2.544844 ACTACTCCCTCCATTCGGAA 57.455 50.000 0.00 0.00 42.21 4.30
5215 5943 3.047695 ACTACTCCCTCCATTCGGAAT 57.952 47.619 0.00 0.00 42.21 3.01
5216 5944 3.385115 ACTACTCCCTCCATTCGGAATT 58.615 45.455 0.00 0.00 42.21 2.17
5217 5945 4.553678 ACTACTCCCTCCATTCGGAATTA 58.446 43.478 0.00 0.00 42.21 1.40
5218 5946 3.840124 ACTCCCTCCATTCGGAATTAC 57.160 47.619 0.00 0.00 42.21 1.89
5219 5947 3.385115 ACTCCCTCCATTCGGAATTACT 58.615 45.455 0.00 0.00 42.21 2.24
5220 5948 3.388350 ACTCCCTCCATTCGGAATTACTC 59.612 47.826 0.00 0.00 42.21 2.59
5221 5949 2.364324 TCCCTCCATTCGGAATTACTCG 59.636 50.000 0.00 0.00 42.21 4.18
5222 5950 2.102588 CCCTCCATTCGGAATTACTCGT 59.897 50.000 0.00 0.00 42.21 4.18
5223 5951 3.381949 CCTCCATTCGGAATTACTCGTC 58.618 50.000 0.00 0.00 42.21 4.20
5224 5952 3.381949 CTCCATTCGGAATTACTCGTCC 58.618 50.000 0.00 0.00 42.21 4.79
5225 5953 2.761767 TCCATTCGGAATTACTCGTCCA 59.238 45.455 0.00 0.00 38.83 4.02
5226 5954 3.196039 TCCATTCGGAATTACTCGTCCAA 59.804 43.478 0.00 0.00 38.83 3.53
5227 5955 3.555956 CCATTCGGAATTACTCGTCCAAG 59.444 47.826 0.00 0.00 33.10 3.61
5228 5956 4.430007 CATTCGGAATTACTCGTCCAAGA 58.570 43.478 0.00 0.00 33.10 3.02
5229 5957 4.524316 TTCGGAATTACTCGTCCAAGAA 57.476 40.909 0.00 0.00 33.10 2.52
5230 5958 4.524316 TCGGAATTACTCGTCCAAGAAA 57.476 40.909 0.00 0.00 33.10 2.52
5231 5959 5.080969 TCGGAATTACTCGTCCAAGAAAT 57.919 39.130 0.00 0.00 33.10 2.17
5232 5960 4.868171 TCGGAATTACTCGTCCAAGAAATG 59.132 41.667 0.00 0.00 33.10 2.32
5233 5961 4.868171 CGGAATTACTCGTCCAAGAAATGA 59.132 41.667 0.00 0.00 33.10 2.57
5234 5962 5.350365 CGGAATTACTCGTCCAAGAAATGAA 59.650 40.000 0.00 0.00 33.10 2.57
5235 5963 6.037172 CGGAATTACTCGTCCAAGAAATGAAT 59.963 38.462 0.00 0.00 33.10 2.57
5236 5964 7.189512 GGAATTACTCGTCCAAGAAATGAATG 58.810 38.462 0.00 0.00 33.79 2.67
5237 5965 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
5238 5966 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
5239 5967 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
5240 5968 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
5241 5969 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
5242 5970 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
5243 5971 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
5244 5972 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
5245 5973 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
5246 5974 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
5247 5975 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
5291 6019 5.987777 TTTTTGTGACGAGTAATTCCGAA 57.012 34.783 0.00 0.00 0.00 4.30
5292 6020 5.585500 TTTTGTGACGAGTAATTCCGAAG 57.415 39.130 0.00 0.00 0.00 3.79
5309 6037 1.141858 GAAGGGAGGGAGTAGCCAATG 59.858 57.143 0.00 0.00 38.95 2.82
5334 6062 5.095691 ACAAATCAAACTGACGCAACTAG 57.904 39.130 0.00 0.00 0.00 2.57
5336 6064 5.050091 ACAAATCAAACTGACGCAACTAGAG 60.050 40.000 0.00 0.00 0.00 2.43
5343 6071 0.741915 GACGCAACTAGAGCCTAGCT 59.258 55.000 0.00 0.00 43.88 3.32
5382 6110 9.176181 TGTAATTTTGAATGTTAAGCGAAAGTC 57.824 29.630 0.00 0.00 0.00 3.01
5403 6131 2.261671 CGACGCCACTACAGCCTT 59.738 61.111 0.00 0.00 0.00 4.35
5410 6138 2.369394 GCCACTACAGCCTTGCTAAAT 58.631 47.619 0.00 0.00 36.40 1.40
5423 6151 8.772705 CAGCCTTGCTAAATCTAATTTCTCTAG 58.227 37.037 0.00 0.00 36.40 2.43
5547 6296 6.770785 TGATAGTGGCCTAACATATTTTGGTC 59.229 38.462 3.32 0.00 0.00 4.02
5571 6320 1.202758 TCGTCACCTGCACCTCAAATT 60.203 47.619 0.00 0.00 0.00 1.82
5574 6323 2.029918 GTCACCTGCACCTCAAATTTCC 60.030 50.000 0.00 0.00 0.00 3.13
5584 6333 4.692155 CACCTCAAATTTCCCATTTTCTGC 59.308 41.667 0.00 0.00 0.00 4.26
5586 6335 3.924144 TCAAATTTCCCATTTTCTGCCG 58.076 40.909 0.00 0.00 0.00 5.69
5588 6337 2.230130 ATTTCCCATTTTCTGCCGGA 57.770 45.000 5.05 0.00 0.00 5.14
5589 6338 2.002505 TTTCCCATTTTCTGCCGGAA 57.997 45.000 5.05 0.00 0.00 4.30
5590 6339 1.253100 TTCCCATTTTCTGCCGGAAC 58.747 50.000 5.05 0.00 33.13 3.62
5591 6340 0.610785 TCCCATTTTCTGCCGGAACC 60.611 55.000 5.05 0.00 33.13 3.62
5592 6341 0.611896 CCCATTTTCTGCCGGAACCT 60.612 55.000 5.05 0.00 33.13 3.50
5593 6342 1.256812 CCATTTTCTGCCGGAACCTT 58.743 50.000 5.05 0.00 33.13 3.50
5594 6343 1.067635 CCATTTTCTGCCGGAACCTTG 60.068 52.381 5.05 0.00 33.13 3.61
5595 6344 1.885887 CATTTTCTGCCGGAACCTTGA 59.114 47.619 5.05 0.00 33.13 3.02
5596 6345 2.286365 TTTTCTGCCGGAACCTTGAT 57.714 45.000 5.05 0.00 33.13 2.57
5597 6346 3.426787 TTTTCTGCCGGAACCTTGATA 57.573 42.857 5.05 0.00 33.13 2.15
5623 6372 4.123506 GACCCTGAGCTGATAAGCTTAAC 58.876 47.826 10.85 8.63 46.36 2.01
5628 6377 4.174009 TGAGCTGATAAGCTTAACGACAC 58.826 43.478 10.85 3.67 46.36 3.67
5629 6378 3.522553 AGCTGATAAGCTTAACGACACC 58.477 45.455 10.85 1.34 43.52 4.16
5650 6410 2.167662 GACGGTTTGGGATTTGACCAT 58.832 47.619 0.00 0.00 37.93 3.55
5651 6411 1.892474 ACGGTTTGGGATTTGACCATG 59.108 47.619 0.00 0.00 37.93 3.66
5652 6412 2.166829 CGGTTTGGGATTTGACCATGA 58.833 47.619 0.00 0.00 37.93 3.07
5653 6413 2.094752 CGGTTTGGGATTTGACCATGAC 60.095 50.000 0.00 0.00 37.93 3.06
5654 6414 2.896685 GGTTTGGGATTTGACCATGACA 59.103 45.455 0.00 0.00 37.93 3.58
5655 6415 3.323403 GGTTTGGGATTTGACCATGACAA 59.677 43.478 0.00 0.00 37.93 3.18
5656 6416 4.202305 GGTTTGGGATTTGACCATGACAAA 60.202 41.667 16.09 16.09 40.62 2.83
5657 6417 5.512921 GGTTTGGGATTTGACCATGACAAAT 60.513 40.000 21.63 21.63 46.22 2.32
5659 6419 5.149973 TGGGATTTGACCATGACAAATTG 57.850 39.130 22.05 0.00 44.46 2.32
5661 6421 5.306419 TGGGATTTGACCATGACAAATTGAA 59.694 36.000 22.05 13.11 44.46 2.69
5662 6422 6.013553 TGGGATTTGACCATGACAAATTGAAT 60.014 34.615 22.05 8.95 44.46 2.57
5663 6423 7.179872 TGGGATTTGACCATGACAAATTGAATA 59.820 33.333 22.05 11.28 44.46 1.75
5664 6424 8.206189 GGGATTTGACCATGACAAATTGAATAT 58.794 33.333 22.05 7.95 44.46 1.28
5665 6425 9.603921 GGATTTGACCATGACAAATTGAATATT 57.396 29.630 22.05 0.00 44.46 1.28
5729 6489 1.747355 GCATGACAAATCCACCCTCAG 59.253 52.381 0.00 0.00 0.00 3.35
5739 6499 0.961753 CCACCCTCAGTTTGGCTTTC 59.038 55.000 0.00 0.00 0.00 2.62
5740 6500 1.691196 CACCCTCAGTTTGGCTTTCA 58.309 50.000 0.00 0.00 0.00 2.69
5741 6501 2.031120 CACCCTCAGTTTGGCTTTCAA 58.969 47.619 0.00 0.00 0.00 2.69
5778 6538 3.005791 GCTTGCCAACTAAACTTGTCCAT 59.994 43.478 0.00 0.00 0.00 3.41
5798 6558 7.084486 GTCCATCCTTGTGTCAACTAAAATTC 58.916 38.462 0.00 0.00 0.00 2.17
5862 6622 5.715434 TTTTGACCATAAAACAGTAGGGC 57.285 39.130 0.00 0.00 0.00 5.19
5863 6623 4.650972 TTGACCATAAAACAGTAGGGCT 57.349 40.909 0.00 0.00 0.00 5.19
5864 6624 4.650972 TGACCATAAAACAGTAGGGCTT 57.349 40.909 0.00 0.00 0.00 4.35
5865 6625 4.993028 TGACCATAAAACAGTAGGGCTTT 58.007 39.130 0.00 0.00 0.00 3.51
5866 6626 5.007682 TGACCATAAAACAGTAGGGCTTTC 58.992 41.667 0.00 0.00 0.00 2.62
5867 6627 4.993028 ACCATAAAACAGTAGGGCTTTCA 58.007 39.130 0.00 0.00 0.00 2.69
5868 6628 5.580022 ACCATAAAACAGTAGGGCTTTCAT 58.420 37.500 0.00 0.00 0.00 2.57
5869 6629 6.016555 ACCATAAAACAGTAGGGCTTTCATT 58.983 36.000 0.00 0.00 0.00 2.57
5870 6630 7.179269 ACCATAAAACAGTAGGGCTTTCATTA 58.821 34.615 0.00 0.00 0.00 1.90
5871 6631 7.839200 ACCATAAAACAGTAGGGCTTTCATTAT 59.161 33.333 0.00 0.00 0.00 1.28
5872 6632 9.349713 CCATAAAACAGTAGGGCTTTCATTATA 57.650 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.548214 GGAAGTCGAAAAGCCACTGTTTC 60.548 47.826 0.00 0.00 0.00 2.78
95 96 3.953612 GGTTCATTCCTCACCATATTGCA 59.046 43.478 0.00 0.00 0.00 4.08
105 106 0.321564 CGCCACAGGTTCATTCCTCA 60.322 55.000 0.00 0.00 35.37 3.86
148 149 3.352648 GTCAATGTAAGCCTTTGCCCTA 58.647 45.455 0.00 0.00 38.69 3.53
206 207 2.516460 GGAGGTCTCGCGCCTAGA 60.516 66.667 0.00 1.67 36.29 2.43
214 215 1.699343 GACTGAAAACGGAGGTCTCG 58.301 55.000 0.00 0.00 0.00 4.04
228 229 0.596577 CGGAGACCAAAGACGACTGA 59.403 55.000 0.00 0.00 0.00 3.41
230 231 1.289380 GCGGAGACCAAAGACGACT 59.711 57.895 0.00 0.00 0.00 4.18
284 285 1.668294 CCAGCTCCTTCGACACTGT 59.332 57.895 0.00 0.00 0.00 3.55
286 287 2.948720 GCCCAGCTCCTTCGACACT 61.949 63.158 0.00 0.00 0.00 3.55
410 411 2.729862 GACAGCACGTCGAAGCGT 60.730 61.111 0.00 0.00 46.88 5.07
456 457 5.126061 AGGCAATCAATGTTGAAGGATACAC 59.874 40.000 0.00 0.00 41.13 2.90
460 461 4.607239 AGAGGCAATCAATGTTGAAGGAT 58.393 39.130 0.00 0.00 41.13 3.24
488 489 0.179150 GAAGACGAGAGACGCTGCAT 60.179 55.000 0.00 0.00 46.94 3.96
591 594 1.392168 ACATTACAATGCCGACGAACG 59.608 47.619 0.00 0.00 40.04 3.95
722 725 0.038159 AGAGAGAACGTCGGCCTTTG 60.038 55.000 0.00 0.00 0.00 2.77
916 922 1.371635 CCTGCGGTTTTGCTTTCGG 60.372 57.895 0.00 0.00 35.36 4.30
995 1001 4.833811 CGTCCATCGCCATCTCAA 57.166 55.556 0.00 0.00 0.00 3.02
1021 1027 3.859414 GATCAGCTCCGCCTGCCT 61.859 66.667 0.00 0.00 32.87 4.75
1404 1410 6.949715 ACATATCAAATCAAAAGGGCAATGT 58.050 32.000 0.00 0.00 0.00 2.71
1511 1517 6.838612 TCAGGGCAAATGGCTAAATTAATAGT 59.161 34.615 6.93 0.00 44.01 2.12
1538 1544 2.485479 CCTGTTATGCGCTCATTAGGGT 60.485 50.000 9.73 0.00 37.95 4.34
1548 1554 0.243636 AAAGTTGCCCTGTTATGCGC 59.756 50.000 0.00 0.00 0.00 6.09
1610 1616 3.907894 TCAAAGCGTAAACATCAACCC 57.092 42.857 0.00 0.00 0.00 4.11
1816 1822 2.866762 GCTAAACTAAGTCAGATGCCCG 59.133 50.000 0.00 0.00 0.00 6.13
1866 1872 6.155910 AGGGCATACTAATGGTGATGATAGAG 59.844 42.308 0.00 0.00 33.38 2.43
1938 1944 4.238514 GGCGCTAGAATTACCTACAGATG 58.761 47.826 7.64 0.00 0.00 2.90
2008 2014 1.461127 GACTCAGCCAAAGTTAGCACG 59.539 52.381 1.11 0.00 0.00 5.34
2081 2087 1.216678 TGTCCAAAGAAAGGGGAGCAA 59.783 47.619 0.00 0.00 0.00 3.91
2082 2088 0.850100 TGTCCAAAGAAAGGGGAGCA 59.150 50.000 0.00 0.00 0.00 4.26
2163 2169 3.401182 ACAAATACGCCGTCCTAAAACA 58.599 40.909 0.00 0.00 0.00 2.83
2200 2206 3.902881 ACTAAGAGGCACTGGAAGATG 57.097 47.619 0.00 0.00 41.55 2.90
2207 2213 5.047660 ACAACTAGAGAACTAAGAGGCACTG 60.048 44.000 0.00 0.00 41.55 3.66
2312 2318 1.760192 ATGAAGTTCCTGCAGCCATC 58.240 50.000 8.66 1.50 0.00 3.51
2315 2321 3.019564 ACATAATGAAGTTCCTGCAGCC 58.980 45.455 8.66 0.00 0.00 4.85
2505 2511 9.355215 GATATTTCAATACAGACTACATACGGG 57.645 37.037 0.00 0.00 0.00 5.28
2565 2587 6.346439 GCGTGAAACATAGCTCATATCAGAAG 60.346 42.308 0.00 0.00 35.74 2.85
2629 2652 6.784969 AGCTGATCATATGGAAGTACCTAAGT 59.215 38.462 2.13 0.00 39.86 2.24
2709 2732 2.095008 ACTCACTGAGTACATGCACTCG 60.095 50.000 18.97 15.74 46.60 4.18
2832 2855 1.187087 AGAAACGGAGGGAGTAGCAG 58.813 55.000 0.00 0.00 0.00 4.24
2833 2856 1.275291 CAAGAAACGGAGGGAGTAGCA 59.725 52.381 0.00 0.00 0.00 3.49
2834 2857 2.007547 GCAAGAAACGGAGGGAGTAGC 61.008 57.143 0.00 0.00 0.00 3.58
2835 2858 1.550976 AGCAAGAAACGGAGGGAGTAG 59.449 52.381 0.00 0.00 0.00 2.57
2836 2859 1.640917 AGCAAGAAACGGAGGGAGTA 58.359 50.000 0.00 0.00 0.00 2.59
2837 2860 1.640917 TAGCAAGAAACGGAGGGAGT 58.359 50.000 0.00 0.00 0.00 3.85
2838 2861 2.762535 TTAGCAAGAAACGGAGGGAG 57.237 50.000 0.00 0.00 0.00 4.30
2841 2864 4.003648 ACTTCATTAGCAAGAAACGGAGG 58.996 43.478 0.00 0.00 0.00 4.30
2842 2865 5.179368 TCAACTTCATTAGCAAGAAACGGAG 59.821 40.000 0.00 0.00 0.00 4.63
2843 2866 5.060506 TCAACTTCATTAGCAAGAAACGGA 58.939 37.500 0.00 0.00 0.00 4.69
2844 2867 5.356882 TCAACTTCATTAGCAAGAAACGG 57.643 39.130 0.00 0.00 0.00 4.44
2845 2868 5.853282 CCTTCAACTTCATTAGCAAGAAACG 59.147 40.000 0.00 0.00 0.00 3.60
2846 2869 6.970484 TCCTTCAACTTCATTAGCAAGAAAC 58.030 36.000 0.00 0.00 0.00 2.78
2847 2870 7.448161 TCATCCTTCAACTTCATTAGCAAGAAA 59.552 33.333 0.00 0.00 0.00 2.52
2848 2871 6.942005 TCATCCTTCAACTTCATTAGCAAGAA 59.058 34.615 0.00 0.00 0.00 2.52
2853 2876 6.992063 TTCTCATCCTTCAACTTCATTAGC 57.008 37.500 0.00 0.00 0.00 3.09
2854 2877 8.404000 CCATTTCTCATCCTTCAACTTCATTAG 58.596 37.037 0.00 0.00 0.00 1.73
2855 2878 7.148018 GCCATTTCTCATCCTTCAACTTCATTA 60.148 37.037 0.00 0.00 0.00 1.90
2856 2879 6.350780 GCCATTTCTCATCCTTCAACTTCATT 60.351 38.462 0.00 0.00 0.00 2.57
2857 2880 5.126707 GCCATTTCTCATCCTTCAACTTCAT 59.873 40.000 0.00 0.00 0.00 2.57
2858 2881 4.460382 GCCATTTCTCATCCTTCAACTTCA 59.540 41.667 0.00 0.00 0.00 3.02
2859 2882 4.704057 AGCCATTTCTCATCCTTCAACTTC 59.296 41.667 0.00 0.00 0.00 3.01
2860 2883 4.670765 AGCCATTTCTCATCCTTCAACTT 58.329 39.130 0.00 0.00 0.00 2.66
2861 2884 4.018597 AGAGCCATTTCTCATCCTTCAACT 60.019 41.667 0.00 0.00 35.59 3.16
2862 2885 4.268359 AGAGCCATTTCTCATCCTTCAAC 58.732 43.478 0.00 0.00 35.59 3.18
2863 2886 4.581309 AGAGCCATTTCTCATCCTTCAA 57.419 40.909 0.00 0.00 35.59 2.69
2864 2887 4.581309 AAGAGCCATTTCTCATCCTTCA 57.419 40.909 0.00 0.00 35.59 3.02
2865 2888 6.352516 TCTAAAGAGCCATTTCTCATCCTTC 58.647 40.000 0.00 0.00 35.59 3.46
2866 2889 6.319048 TCTAAAGAGCCATTTCTCATCCTT 57.681 37.500 0.00 0.00 35.59 3.36
2867 2890 5.965033 TCTAAAGAGCCATTTCTCATCCT 57.035 39.130 0.00 0.00 35.59 3.24
2868 2891 6.016443 CCAATCTAAAGAGCCATTTCTCATCC 60.016 42.308 0.00 0.00 35.59 3.51
2869 2892 6.016443 CCCAATCTAAAGAGCCATTTCTCATC 60.016 42.308 0.00 0.00 35.59 2.92
2870 2893 5.832060 CCCAATCTAAAGAGCCATTTCTCAT 59.168 40.000 0.00 0.00 35.59 2.90
2871 2894 5.044919 TCCCAATCTAAAGAGCCATTTCTCA 60.045 40.000 0.00 0.00 35.59 3.27
2872 2895 5.298026 GTCCCAATCTAAAGAGCCATTTCTC 59.702 44.000 0.00 0.00 0.00 2.87
2873 2896 5.196695 GTCCCAATCTAAAGAGCCATTTCT 58.803 41.667 0.00 0.00 0.00 2.52
2874 2897 4.949856 TGTCCCAATCTAAAGAGCCATTTC 59.050 41.667 0.00 0.00 0.00 2.17
2875 2898 4.934356 TGTCCCAATCTAAAGAGCCATTT 58.066 39.130 0.00 0.00 0.00 2.32
2876 2899 4.228210 TCTGTCCCAATCTAAAGAGCCATT 59.772 41.667 0.00 0.00 0.00 3.16
2877 2900 3.782523 TCTGTCCCAATCTAAAGAGCCAT 59.217 43.478 0.00 0.00 0.00 4.40
2878 2901 3.181329 TCTGTCCCAATCTAAAGAGCCA 58.819 45.455 0.00 0.00 0.00 4.75
2879 2902 3.432890 CCTCTGTCCCAATCTAAAGAGCC 60.433 52.174 0.00 0.00 31.76 4.70
2880 2903 3.432890 CCCTCTGTCCCAATCTAAAGAGC 60.433 52.174 0.00 0.00 31.76 4.09
2881 2904 4.033709 TCCCTCTGTCCCAATCTAAAGAG 58.966 47.826 0.00 0.00 0.00 2.85
2882 2905 4.033709 CTCCCTCTGTCCCAATCTAAAGA 58.966 47.826 0.00 0.00 0.00 2.52
2883 2906 3.777522 ACTCCCTCTGTCCCAATCTAAAG 59.222 47.826 0.00 0.00 0.00 1.85
2884 2907 3.803340 ACTCCCTCTGTCCCAATCTAAA 58.197 45.455 0.00 0.00 0.00 1.85
2885 2908 3.491766 ACTCCCTCTGTCCCAATCTAA 57.508 47.619 0.00 0.00 0.00 2.10
2886 2909 4.834406 ATACTCCCTCTGTCCCAATCTA 57.166 45.455 0.00 0.00 0.00 1.98
2887 2910 3.715648 ATACTCCCTCTGTCCCAATCT 57.284 47.619 0.00 0.00 0.00 2.40
2888 2911 4.779993 AAATACTCCCTCTGTCCCAATC 57.220 45.455 0.00 0.00 0.00 2.67
2889 2912 5.289510 AGTAAATACTCCCTCTGTCCCAAT 58.710 41.667 0.00 0.00 0.00 3.16
2890 2913 4.695606 AGTAAATACTCCCTCTGTCCCAA 58.304 43.478 0.00 0.00 0.00 4.12
3049 3074 3.452627 ACTTGCCTCTGACAATACCCTAG 59.547 47.826 0.00 0.00 0.00 3.02
3102 3127 9.715119 TGTAACATATATAGGCTCCATATGTCT 57.285 33.333 23.51 18.09 42.31 3.41
3188 3214 4.624024 CAGCTGCAAATTGTACCTGAAATG 59.376 41.667 0.00 0.00 0.00 2.32
3294 3320 6.373495 TCACATTTCTTGAACAGATGGAGATG 59.627 38.462 0.00 0.00 0.00 2.90
3449 3475 9.295825 TGACAAAAGCTTATCTCCTTCATAAAA 57.704 29.630 0.00 0.00 0.00 1.52
3450 3476 8.862325 TGACAAAAGCTTATCTCCTTCATAAA 57.138 30.769 0.00 0.00 0.00 1.40
3587 3613 2.029666 CGAGCCCCCTTGCGATAG 59.970 66.667 0.00 0.00 36.02 2.08
3636 3662 3.634448 CCCAACCTGTGAAATGTACACAA 59.366 43.478 0.00 0.00 45.49 3.33
3683 3709 4.381292 GCCCACTTGATTTTCTCCTGAATG 60.381 45.833 0.00 0.00 31.56 2.67
3707 3733 8.219546 TCTTGTTCAATTCACTTGTTGTATCA 57.780 30.769 0.00 0.00 36.20 2.15
3885 3911 9.368416 ACAGCAGAATGAATAGTAGGAACTATA 57.632 33.333 0.00 0.00 42.31 1.31
3889 3915 8.894768 AATACAGCAGAATGAATAGTAGGAAC 57.105 34.615 0.00 0.00 39.69 3.62
3890 3916 9.905713 AAAATACAGCAGAATGAATAGTAGGAA 57.094 29.630 0.00 0.00 39.69 3.36
3891 3917 9.905713 AAAAATACAGCAGAATGAATAGTAGGA 57.094 29.630 0.00 0.00 39.69 2.94
4147 4185 5.779241 AAATTCCCAAGTGACCTCTGATA 57.221 39.130 0.00 0.00 0.00 2.15
4411 5019 3.000727 CTCCTAAACCAGTGGCTTAACG 58.999 50.000 9.78 1.08 0.00 3.18
4438 5046 9.926751 GTCAATCATGTACACTATCATCTTTTG 57.073 33.333 0.00 0.00 0.00 2.44
4483 5103 1.135170 GCCTACCACTCCTTGTCGTAC 60.135 57.143 0.00 0.00 0.00 3.67
4486 5106 1.153823 CGCCTACCACTCCTTGTCG 60.154 63.158 0.00 0.00 0.00 4.35
4489 5109 1.153823 CGACGCCTACCACTCCTTG 60.154 63.158 0.00 0.00 0.00 3.61
4508 5128 8.297470 ACCTACTACGGTCACATAAAATTCTA 57.703 34.615 0.00 0.00 29.14 2.10
4534 5154 6.738114 TGTCTCACTAAAAATCTTGCAAAGG 58.262 36.000 0.00 0.00 46.24 3.11
4581 5201 8.840321 CAATCAACTTACTAATGAATACCCTGG 58.160 37.037 0.00 0.00 0.00 4.45
4584 5204 7.352739 CGCAATCAACTTACTAATGAATACCC 58.647 38.462 0.00 0.00 0.00 3.69
4589 5209 4.697828 TGCCGCAATCAACTTACTAATGAA 59.302 37.500 0.00 0.00 0.00 2.57
4688 5415 1.134438 ACTCCTCCCCACAACCTTCC 61.134 60.000 0.00 0.00 0.00 3.46
4852 5579 2.238646 TGGTTGTCGCCTCCTGAAATAT 59.761 45.455 0.00 0.00 0.00 1.28
4879 5606 6.456501 AGGTGTGATACTTCAGTCAAACTAC 58.543 40.000 0.00 0.00 33.90 2.73
5041 5769 2.988010 TGCGGCAGTAAATCATCTCT 57.012 45.000 0.00 0.00 0.00 3.10
5067 5795 2.299013 CCATATGCCCTTCGTGCTACTA 59.701 50.000 0.00 0.00 0.00 1.82
5076 5804 2.576615 GAAGTCACCCATATGCCCTTC 58.423 52.381 0.00 0.60 0.00 3.46
5096 5824 5.580691 TCAGAACCATAATCTTTACAGTGCG 59.419 40.000 0.00 0.00 0.00 5.34
5125 5853 2.841215 CGAACACCTTAGGTCACCAAA 58.159 47.619 0.00 0.00 31.02 3.28
5142 5870 1.757682 ACCAAACCAAACTGAGCGAA 58.242 45.000 0.00 0.00 0.00 4.70
5165 5893 2.494059 CTTCGGGTCAGAGAGCAAAAA 58.506 47.619 0.00 0.00 0.00 1.94
5168 5896 1.975327 CCTTCGGGTCAGAGAGCAA 59.025 57.895 0.00 0.00 0.00 3.91
5169 5897 2.650116 GCCTTCGGGTCAGAGAGCA 61.650 63.158 0.00 0.00 37.45 4.26
5191 5919 2.481449 CCGAATGGAGGGAGTAGTTTCG 60.481 54.545 0.00 0.00 37.49 3.46
5204 5932 2.761767 TGGACGAGTAATTCCGAATGGA 59.238 45.455 0.00 0.00 44.61 3.41
5205 5933 3.173668 TGGACGAGTAATTCCGAATGG 57.826 47.619 0.00 0.00 0.00 3.16
5206 5934 4.430007 TCTTGGACGAGTAATTCCGAATG 58.570 43.478 0.00 0.00 0.00 2.67
5207 5935 4.730949 TCTTGGACGAGTAATTCCGAAT 57.269 40.909 0.00 0.00 0.00 3.34
5208 5936 4.524316 TTCTTGGACGAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
5209 5937 4.524316 TTTCTTGGACGAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
5210 5938 4.868171 TCATTTCTTGGACGAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
5211 5939 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
5212 5940 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
5213 5941 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
5214 5942 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
5215 5943 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
5216 5944 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
5217 5945 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
5218 5946 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
5219 5947 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
5220 5948 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
5221 5949 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
5269 5997 5.049954 CCTTCGGAATTACTCGTCACAAAAA 60.050 40.000 0.00 0.00 0.00 1.94
5270 5998 4.449743 CCTTCGGAATTACTCGTCACAAAA 59.550 41.667 0.00 0.00 0.00 2.44
5271 5999 3.991773 CCTTCGGAATTACTCGTCACAAA 59.008 43.478 0.00 0.00 0.00 2.83
5272 6000 3.581755 CCTTCGGAATTACTCGTCACAA 58.418 45.455 0.00 0.00 0.00 3.33
5273 6001 2.094390 CCCTTCGGAATTACTCGTCACA 60.094 50.000 0.00 0.00 0.00 3.58
5274 6002 2.165030 TCCCTTCGGAATTACTCGTCAC 59.835 50.000 0.00 0.00 34.19 3.67
5275 6003 2.426024 CTCCCTTCGGAATTACTCGTCA 59.574 50.000 0.00 0.00 37.86 4.35
5276 6004 2.223758 CCTCCCTTCGGAATTACTCGTC 60.224 54.545 0.00 0.00 37.86 4.20
5277 6005 1.755380 CCTCCCTTCGGAATTACTCGT 59.245 52.381 0.00 0.00 37.86 4.18
5278 6006 1.068741 CCCTCCCTTCGGAATTACTCG 59.931 57.143 0.00 0.00 37.86 4.18
5279 6007 2.365941 CTCCCTCCCTTCGGAATTACTC 59.634 54.545 0.00 0.00 37.86 2.59
5280 6008 2.292984 ACTCCCTCCCTTCGGAATTACT 60.293 50.000 0.00 0.00 37.86 2.24
5281 6009 2.117051 ACTCCCTCCCTTCGGAATTAC 58.883 52.381 0.00 0.00 37.86 1.89
5282 6010 2.563039 ACTCCCTCCCTTCGGAATTA 57.437 50.000 0.00 0.00 37.86 1.40
5283 6011 2.399580 CTACTCCCTCCCTTCGGAATT 58.600 52.381 0.00 0.00 37.86 2.17
5284 6012 2.035331 GCTACTCCCTCCCTTCGGAAT 61.035 57.143 0.00 0.00 37.86 3.01
5285 6013 0.686769 GCTACTCCCTCCCTTCGGAA 60.687 60.000 0.00 0.00 37.86 4.30
5286 6014 1.076192 GCTACTCCCTCCCTTCGGA 60.076 63.158 0.00 0.00 36.45 4.55
5287 6015 2.134933 GGCTACTCCCTCCCTTCGG 61.135 68.421 0.00 0.00 0.00 4.30
5288 6016 0.976073 TTGGCTACTCCCTCCCTTCG 60.976 60.000 0.00 0.00 0.00 3.79
5289 6017 1.141858 CATTGGCTACTCCCTCCCTTC 59.858 57.143 0.00 0.00 0.00 3.46
5290 6018 1.216990 CATTGGCTACTCCCTCCCTT 58.783 55.000 0.00 0.00 0.00 3.95
5291 6019 0.695803 CCATTGGCTACTCCCTCCCT 60.696 60.000 0.00 0.00 0.00 4.20
5292 6020 0.988678 ACCATTGGCTACTCCCTCCC 60.989 60.000 1.54 0.00 0.00 4.30
5293 6021 1.416772 GTACCATTGGCTACTCCCTCC 59.583 57.143 1.54 0.00 0.00 4.30
5294 6022 2.116238 TGTACCATTGGCTACTCCCTC 58.884 52.381 1.54 0.00 0.00 4.30
5295 6023 2.263895 TGTACCATTGGCTACTCCCT 57.736 50.000 1.54 0.00 0.00 4.20
5296 6024 3.359695 TTTGTACCATTGGCTACTCCC 57.640 47.619 1.54 0.00 0.00 4.30
5297 6025 4.523083 TGATTTGTACCATTGGCTACTCC 58.477 43.478 1.54 0.00 0.00 3.85
5298 6026 6.151144 AGTTTGATTTGTACCATTGGCTACTC 59.849 38.462 1.54 0.77 0.00 2.59
5299 6027 6.010219 AGTTTGATTTGTACCATTGGCTACT 58.990 36.000 1.54 0.00 0.00 2.57
5300 6028 6.072175 TCAGTTTGATTTGTACCATTGGCTAC 60.072 38.462 1.54 5.66 0.00 3.58
5309 6037 3.889196 TGCGTCAGTTTGATTTGTACC 57.111 42.857 0.00 0.00 0.00 3.34
5382 6110 1.801913 GCTGTAGTGGCGTCGTCAG 60.802 63.158 0.00 0.00 0.00 3.51
5423 6151 7.417612 AGGCAATACGATGTCATATTCAAAAC 58.582 34.615 0.00 0.00 0.00 2.43
5547 6296 3.036084 GGTGCAGGTGACGACACG 61.036 66.667 11.73 0.56 46.77 4.49
5571 6320 1.253100 GTTCCGGCAGAAAATGGGAA 58.747 50.000 0.00 0.00 35.85 3.97
5574 6323 1.067635 CAAGGTTCCGGCAGAAAATGG 60.068 52.381 0.00 0.00 35.85 3.16
5584 6333 2.629051 GGTCAACTATCAAGGTTCCGG 58.371 52.381 0.00 0.00 0.00 5.14
5586 6335 3.263425 TCAGGGTCAACTATCAAGGTTCC 59.737 47.826 0.00 0.00 0.00 3.62
5588 6337 3.307762 GCTCAGGGTCAACTATCAAGGTT 60.308 47.826 0.00 0.00 0.00 3.50
5589 6338 2.237392 GCTCAGGGTCAACTATCAAGGT 59.763 50.000 0.00 0.00 0.00 3.50
5590 6339 2.503356 AGCTCAGGGTCAACTATCAAGG 59.497 50.000 0.00 0.00 0.00 3.61
5591 6340 3.196469 TCAGCTCAGGGTCAACTATCAAG 59.804 47.826 0.00 0.00 0.00 3.02
5592 6341 3.173151 TCAGCTCAGGGTCAACTATCAA 58.827 45.455 0.00 0.00 0.00 2.57
5593 6342 2.820178 TCAGCTCAGGGTCAACTATCA 58.180 47.619 0.00 0.00 0.00 2.15
5594 6343 5.537188 CTTATCAGCTCAGGGTCAACTATC 58.463 45.833 0.00 0.00 0.00 2.08
5595 6344 4.202305 GCTTATCAGCTCAGGGTCAACTAT 60.202 45.833 0.00 0.00 43.51 2.12
5596 6345 3.133003 GCTTATCAGCTCAGGGTCAACTA 59.867 47.826 0.00 0.00 43.51 2.24
5597 6346 2.093235 GCTTATCAGCTCAGGGTCAACT 60.093 50.000 0.00 0.00 43.51 3.16
5623 6372 2.775032 ATCCCAAACCGTCGGTGTCG 62.775 60.000 19.67 4.67 35.34 4.35
5628 6377 0.519961 GTCAAATCCCAAACCGTCGG 59.480 55.000 10.48 10.48 0.00 4.79
5629 6378 0.519961 GGTCAAATCCCAAACCGTCG 59.480 55.000 0.00 0.00 0.00 5.12
5683 6443 9.148104 CTTACCTACTAAACTTGTCATGGTAAC 57.852 37.037 0.00 0.00 34.88 2.50
5684 6444 7.820872 GCTTACCTACTAAACTTGTCATGGTAA 59.179 37.037 0.00 0.00 36.49 2.85
5685 6445 7.038870 TGCTTACCTACTAAACTTGTCATGGTA 60.039 37.037 0.00 0.00 0.00 3.25
5703 6463 3.356290 GGTGGATTTGTCATGCTTACCT 58.644 45.455 0.00 0.00 0.00 3.08
5778 6538 5.450453 TGGGAATTTTAGTTGACACAAGGA 58.550 37.500 0.00 0.00 0.00 3.36
5839 6599 5.836358 AGCCCTACTGTTTTATGGTCAAAAA 59.164 36.000 0.00 0.00 0.00 1.94
5840 6600 5.390387 AGCCCTACTGTTTTATGGTCAAAA 58.610 37.500 0.00 0.00 0.00 2.44
5841 6601 4.993028 AGCCCTACTGTTTTATGGTCAAA 58.007 39.130 0.00 0.00 0.00 2.69
5842 6602 4.650972 AGCCCTACTGTTTTATGGTCAA 57.349 40.909 0.00 0.00 0.00 3.18
5843 6603 4.650972 AAGCCCTACTGTTTTATGGTCA 57.349 40.909 0.00 0.00 0.00 4.02
5844 6604 5.007682 TGAAAGCCCTACTGTTTTATGGTC 58.992 41.667 0.00 0.00 0.00 4.02
5845 6605 4.993028 TGAAAGCCCTACTGTTTTATGGT 58.007 39.130 0.00 0.00 0.00 3.55
5846 6606 6.530019 AATGAAAGCCCTACTGTTTTATGG 57.470 37.500 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.