Multiple sequence alignment - TraesCS3D01G158000

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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 TraesCS3D01G158000 chr3D 100.000 4632 0 0 3025 7656 126368474 126363843 0.000000e+00 8554.0
1 TraesCS3D01G158000 chr3D 100.000 2730 0 0 1 2730 126371498 126368769 0.000000e+00 5042.0
2 TraesCS3D01G158000 chr2A 98.340 1868 24 3 3334 5197 578392343 578390479 0.000000e+00 3271.0
3 TraesCS3D01G158000 chr2A 98.282 1863 25 3 3334 5192 421217420 421219279 0.000000e+00 3256.0
4 TraesCS3D01G158000 chr2A 98.229 1863 26 3 3334 5192 101856718 101854859 0.000000e+00 3251.0
5 TraesCS3D01G158000 chr2A 88.889 693 73 4 1 691 549795891 549795201 0.000000e+00 850.0
6 TraesCS3D01G158000 chr2A 79.310 116 20 4 2375 2489 625961578 625961690 2.290000e-10 78.7
7 TraesCS3D01G158000 chr2D 98.033 1881 30 4 3334 5210 136424945 136426822 0.000000e+00 3262.0
8 TraesCS3D01G158000 chr2D 81.579 114 19 2 2243 2356 28046908 28046797 8.180000e-15 93.5
9 TraesCS3D01G158000 chr3A 98.127 1869 26 4 3334 5196 217719196 217717331 0.000000e+00 3249.0
10 TraesCS3D01G158000 chr3A 97.871 1879 31 5 3334 5206 633851333 633853208 0.000000e+00 3240.0
11 TraesCS3D01G158000 chr3A 91.882 2094 99 24 688 2730 136532515 136530442 0.000000e+00 2859.0
12 TraesCS3D01G158000 chr3A 94.143 1622 67 13 5195 6803 136530041 136528435 0.000000e+00 2444.0
13 TraesCS3D01G158000 chr3A 92.086 695 41 8 1 690 50601309 50601994 0.000000e+00 966.0
14 TraesCS3D01G158000 chr3A 94.855 311 15 1 3025 3335 136530339 136530030 1.160000e-132 484.0
15 TraesCS3D01G158000 chr7A 98.074 1869 28 4 3334 5198 319590135 319591999 0.000000e+00 3245.0
16 TraesCS3D01G158000 chr7A 91.066 694 59 3 1 691 170251134 170250441 0.000000e+00 935.0
17 TraesCS3D01G158000 chr6A 97.927 1881 26 6 3334 5210 58017116 58015245 0.000000e+00 3245.0
18 TraesCS3D01G158000 chr6A 97.110 692 16 3 1 691 604128192 604127504 0.000000e+00 1164.0
19 TraesCS3D01G158000 chr6A 91.783 791 60 2 6870 7656 371338844 371338055 0.000000e+00 1096.0
20 TraesCS3D01G158000 chr4A 98.124 1866 27 4 3334 5195 357684241 357686102 0.000000e+00 3245.0
21 TraesCS3D01G158000 chr4A 89.542 698 66 7 3 697 15900180 15900873 0.000000e+00 878.0
22 TraesCS3D01G158000 chr4A 88.968 698 73 4 3 698 216390698 216391393 0.000000e+00 859.0
23 TraesCS3D01G158000 chr3B 93.311 2063 78 10 690 2730 180884712 180882688 0.000000e+00 2990.0
24 TraesCS3D01G158000 chr3B 96.318 869 28 3 5172 6040 180882088 180881224 0.000000e+00 1424.0
25 TraesCS3D01G158000 chr3B 96.561 756 18 4 6036 6787 180880997 180880246 0.000000e+00 1245.0
26 TraesCS3D01G158000 chr3B 91.741 787 61 1 6874 7656 418734359 418735145 0.000000e+00 1090.0
27 TraesCS3D01G158000 chr3B 91.392 790 64 1 6871 7656 670759596 670760385 0.000000e+00 1079.0
28 TraesCS3D01G158000 chr3B 91.643 694 49 8 1 691 341909524 341908837 0.000000e+00 952.0
29 TraesCS3D01G158000 chr3B 89.799 696 62 9 1 691 392637899 392638590 0.000000e+00 883.0
30 TraesCS3D01G158000 chr3B 96.863 255 4 3 3084 3335 180882310 180882057 2.550000e-114 424.0
31 TraesCS3D01G158000 chr3B 91.398 93 8 0 6778 6870 180874872 180874780 2.240000e-25 128.0
32 TraesCS3D01G158000 chr6D 92.462 796 55 2 6866 7656 413278194 413277399 0.000000e+00 1133.0
33 TraesCS3D01G158000 chr1B 92.532 790 55 1 6871 7656 611790948 611790159 0.000000e+00 1129.0
34 TraesCS3D01G158000 chr6B 91.803 793 52 5 6869 7656 151679838 151679054 0.000000e+00 1092.0
35 TraesCS3D01G158000 chr2B 91.646 790 62 1 6871 7656 30702702 30701913 0.000000e+00 1090.0
36 TraesCS3D01G158000 chr4B 91.414 792 64 1 6869 7656 182286387 182287178 0.000000e+00 1083.0
37 TraesCS3D01G158000 chr4D 91.206 796 60 7 6868 7656 127149479 127148687 0.000000e+00 1074.0
38 TraesCS3D01G158000 chr4D 77.600 250 34 15 2250 2485 483701803 483702044 1.730000e-26 132.0
39 TraesCS3D01G158000 chr4D 76.132 243 44 10 2252 2485 417622902 417623139 1.750000e-21 115.0
40 TraesCS3D01G158000 chr5A 89.001 691 67 7 6 691 151670472 151669786 0.000000e+00 846.0
41 TraesCS3D01G158000 chr7D 83.756 197 26 4 2277 2471 136694882 136695074 1.700000e-41 182.0
42 TraesCS3D01G158000 chr1A 77.689 251 43 11 2245 2485 145919520 145919273 2.880000e-29 141.0
43 TraesCS3D01G158000 chr1D 76.496 234 39 13 2252 2474 421069202 421069430 6.280000e-21 113.0
44 TraesCS3D01G158000 chr1D 89.474 76 6 2 2241 2315 337775173 337775247 2.270000e-15 95.3


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 TraesCS3D01G158000 chr3D 126363843 126371498 7655 True 6798.00 8554 100.000000 1 7656 2 chr3D.!!$R1 7655
1 TraesCS3D01G158000 chr2A 578390479 578392343 1864 True 3271.00 3271 98.340000 3334 5197 1 chr2A.!!$R3 1863
2 TraesCS3D01G158000 chr2A 421217420 421219279 1859 False 3256.00 3256 98.282000 3334 5192 1 chr2A.!!$F1 1858
3 TraesCS3D01G158000 chr2A 101854859 101856718 1859 True 3251.00 3251 98.229000 3334 5192 1 chr2A.!!$R1 1858
4 TraesCS3D01G158000 chr2A 549795201 549795891 690 True 850.00 850 88.889000 1 691 1 chr2A.!!$R2 690
5 TraesCS3D01G158000 chr2D 136424945 136426822 1877 False 3262.00 3262 98.033000 3334 5210 1 chr2D.!!$F1 1876
6 TraesCS3D01G158000 chr3A 217717331 217719196 1865 True 3249.00 3249 98.127000 3334 5196 1 chr3A.!!$R1 1862
7 TraesCS3D01G158000 chr3A 633851333 633853208 1875 False 3240.00 3240 97.871000 3334 5206 1 chr3A.!!$F2 1872
8 TraesCS3D01G158000 chr3A 136528435 136532515 4080 True 1929.00 2859 93.626667 688 6803 3 chr3A.!!$R2 6115
9 TraesCS3D01G158000 chr3A 50601309 50601994 685 False 966.00 966 92.086000 1 690 1 chr3A.!!$F1 689
10 TraesCS3D01G158000 chr7A 319590135 319591999 1864 False 3245.00 3245 98.074000 3334 5198 1 chr7A.!!$F1 1864
11 TraesCS3D01G158000 chr7A 170250441 170251134 693 True 935.00 935 91.066000 1 691 1 chr7A.!!$R1 690
12 TraesCS3D01G158000 chr6A 58015245 58017116 1871 True 3245.00 3245 97.927000 3334 5210 1 chr6A.!!$R1 1876
13 TraesCS3D01G158000 chr6A 604127504 604128192 688 True 1164.00 1164 97.110000 1 691 1 chr6A.!!$R3 690
14 TraesCS3D01G158000 chr6A 371338055 371338844 789 True 1096.00 1096 91.783000 6870 7656 1 chr6A.!!$R2 786
15 TraesCS3D01G158000 chr4A 357684241 357686102 1861 False 3245.00 3245 98.124000 3334 5195 1 chr4A.!!$F3 1861
16 TraesCS3D01G158000 chr4A 15900180 15900873 693 False 878.00 878 89.542000 3 697 1 chr4A.!!$F1 694
17 TraesCS3D01G158000 chr4A 216390698 216391393 695 False 859.00 859 88.968000 3 698 1 chr4A.!!$F2 695
18 TraesCS3D01G158000 chr3B 180880246 180884712 4466 True 1520.75 2990 95.763250 690 6787 4 chr3B.!!$R3 6097
19 TraesCS3D01G158000 chr3B 418734359 418735145 786 False 1090.00 1090 91.741000 6874 7656 1 chr3B.!!$F2 782
20 TraesCS3D01G158000 chr3B 670759596 670760385 789 False 1079.00 1079 91.392000 6871 7656 1 chr3B.!!$F3 785
21 TraesCS3D01G158000 chr3B 341908837 341909524 687 True 952.00 952 91.643000 1 691 1 chr3B.!!$R2 690
22 TraesCS3D01G158000 chr3B 392637899 392638590 691 False 883.00 883 89.799000 1 691 1 chr3B.!!$F1 690
23 TraesCS3D01G158000 chr6D 413277399 413278194 795 True 1133.00 1133 92.462000 6866 7656 1 chr6D.!!$R1 790
24 TraesCS3D01G158000 chr1B 611790159 611790948 789 True 1129.00 1129 92.532000 6871 7656 1 chr1B.!!$R1 785
25 TraesCS3D01G158000 chr6B 151679054 151679838 784 True 1092.00 1092 91.803000 6869 7656 1 chr6B.!!$R1 787
26 TraesCS3D01G158000 chr2B 30701913 30702702 789 True 1090.00 1090 91.646000 6871 7656 1 chr2B.!!$R1 785
27 TraesCS3D01G158000 chr4B 182286387 182287178 791 False 1083.00 1083 91.414000 6869 7656 1 chr4B.!!$F1 787
28 TraesCS3D01G158000 chr4D 127148687 127149479 792 True 1074.00 1074 91.206000 6868 7656 1 chr4D.!!$R1 788
29 TraesCS3D01G158000 chr5A 151669786 151670472 686 True 846.00 846 89.001000 6 691 1 chr5A.!!$R1 685

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
937 962 0.250770 GCAGTTCGTTCCCTTCCCTT 60.251 55.0 0.00 0.0 0.00 3.95 F
1270 1298 0.237498 CGAGGGTTCGTTTGCTTTCC 59.763 55.0 0.00 0.0 41.84 3.13 F
2488 2550 0.107508 CCGGACGGAGGTAGTAGTCA 60.108 60.0 4.40 0.0 37.50 3.41 F
3565 3656 0.243095 GCGGGAGTACTTCGACAAGT 59.757 55.0 19.25 0.0 45.39 3.16 F
4502 4602 0.336737 ACTAGGTGTGAGGAGGAGGG 59.663 60.0 0.00 0.0 0.00 4.30 F
4962 5062 0.529992 ATAGTGGACGGCTAAAGCGC 60.530 55.0 0.00 0.0 43.26 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2461 2523 0.986527 ACCTCCGTCCGGGTTTATTT 59.013 50.000 0.00 0.0 37.0 1.40 R
2681 2743 2.032799 GTGATTTTGTGCGACTTGTGGA 59.967 45.455 0.00 0.0 0.0 4.02 R
3624 3715 1.208870 CCGCACAAAACGCATGCTA 59.791 52.632 17.13 0.0 37.2 3.49 R
5246 5346 0.951040 CGCCGCTCTCCTTGAACTTT 60.951 55.000 0.00 0.0 0.0 2.66 R
5675 5776 1.882623 CCTCAACTGGAAGCTGGAAAC 59.117 52.381 0.00 0.0 37.6 2.78 R
6815 7159 0.178973 TGAGGTCTGAGGTTCGTGGA 60.179 55.000 0.00 0.0 0.0 4.02 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
138 139 6.595326 TGACAGAATAAACACATGTGATCTCC 59.405 38.462 31.94 14.98 0.00 3.71
168 169 3.083122 AGAGCATGCAACTTGATTCCT 57.917 42.857 21.98 0.00 0.00 3.36
199 200 8.424274 TGTGTGTTATGTAATGCAGAAGATAG 57.576 34.615 0.00 0.00 0.00 2.08
683 695 5.382664 TTTTCCCTACTGTTCTTTGGTCT 57.617 39.130 0.00 0.00 0.00 3.85
775 787 6.970484 TCCAGAAAAAGAAGAAGCATTGTAC 58.030 36.000 0.00 0.00 0.00 2.90
783 795 0.676782 GAAGCATTGTACGGTGGGCT 60.677 55.000 0.00 0.00 0.00 5.19
788 800 2.124507 ATTGTACGGTGGGCTGCACT 62.125 55.000 2.50 0.00 0.00 4.40
790 802 3.238497 TACGGTGGGCTGCACTGT 61.238 61.111 12.10 12.10 43.69 3.55
849 861 1.724623 CTTAACGCTCGCACTAAGCAA 59.275 47.619 0.00 0.00 46.13 3.91
859 871 2.794910 CGCACTAAGCAACGTATAGCAT 59.205 45.455 9.73 1.23 46.13 3.79
860 872 3.121328 CGCACTAAGCAACGTATAGCATC 60.121 47.826 9.73 0.00 46.13 3.91
861 873 3.184581 GCACTAAGCAACGTATAGCATCC 59.815 47.826 9.73 0.00 44.79 3.51
863 875 3.641906 ACTAAGCAACGTATAGCATCCCT 59.358 43.478 9.73 0.00 0.00 4.20
888 913 4.680171 AAAAAGAGCAACGTATAGCACC 57.320 40.909 9.73 2.29 0.00 5.01
890 915 0.815734 AGAGCAACGTATAGCACCGT 59.184 50.000 9.73 0.00 39.32 4.83
908 933 3.181443 ACCGTCCTTTGTTCTCTTCCAAT 60.181 43.478 0.00 0.00 0.00 3.16
909 934 3.437049 CCGTCCTTTGTTCTCTTCCAATC 59.563 47.826 0.00 0.00 0.00 2.67
936 961 1.375326 GCAGTTCGTTCCCTTCCCT 59.625 57.895 0.00 0.00 0.00 4.20
937 962 0.250770 GCAGTTCGTTCCCTTCCCTT 60.251 55.000 0.00 0.00 0.00 3.95
938 963 1.818131 GCAGTTCGTTCCCTTCCCTTT 60.818 52.381 0.00 0.00 0.00 3.11
939 964 2.152016 CAGTTCGTTCCCTTCCCTTTC 58.848 52.381 0.00 0.00 0.00 2.62
940 965 1.073444 AGTTCGTTCCCTTCCCTTTCC 59.927 52.381 0.00 0.00 0.00 3.13
941 966 0.402887 TTCGTTCCCTTCCCTTTCCC 59.597 55.000 0.00 0.00 0.00 3.97
1270 1298 0.237498 CGAGGGTTCGTTTGCTTTCC 59.763 55.000 0.00 0.00 41.84 3.13
1275 1303 0.596577 GTTCGTTTGCTTTCCCTCCC 59.403 55.000 0.00 0.00 0.00 4.30
1436 1464 3.259064 GCCGTGAGCTAGTGACAATTTA 58.741 45.455 0.00 0.00 38.99 1.40
1535 1563 1.675714 CGGCTTGTATCAGCTGGTCAA 60.676 52.381 15.13 14.79 41.83 3.18
1602 1630 5.762179 AGGACATCCTTGTGTTTAGATCA 57.238 39.130 0.00 0.00 46.09 2.92
1628 1656 9.942850 ATTGGTTGAGGTATAAATTCCTTTTTG 57.057 29.630 0.00 0.00 33.83 2.44
1634 1662 5.970021 AGGTATAAATTCCTTTTTGGGGCAT 59.030 36.000 0.00 0.00 36.20 4.40
1648 1677 1.202348 GGGGCATTGTTGTTAGAGTGC 59.798 52.381 0.00 0.00 0.00 4.40
1657 1686 4.755411 TGTTGTTAGAGTGCTAGTATGCC 58.245 43.478 0.00 0.00 0.00 4.40
1678 1707 2.096069 CGATTTGATGCCCTGCTATTCG 60.096 50.000 0.00 0.00 0.00 3.34
1706 1735 0.958822 AACGGTTTGAGGACATTGCC 59.041 50.000 0.00 0.00 0.00 4.52
1709 1738 1.327303 GGTTTGAGGACATTGCCACA 58.673 50.000 0.00 0.00 0.00 4.17
1753 1782 6.593770 TGGACATCAACATGTGTCATTACTAC 59.406 38.462 14.12 0.00 43.79 2.73
1906 1935 4.751767 TCCATTTTCTGTGGCTTTGTTT 57.248 36.364 0.00 0.00 36.66 2.83
2000 2029 2.202987 CATGCTCCTGCCGTCTCC 60.203 66.667 0.00 0.00 38.71 3.71
2218 2250 4.941263 TGCTATTGTAGGGCAGTTTTACAG 59.059 41.667 0.00 0.00 0.00 2.74
2242 2282 4.891992 AATGTTGACTAGTACTGGTGCT 57.108 40.909 17.50 0.00 0.00 4.40
2245 2285 5.995565 TGTTGACTAGTACTGGTGCTATT 57.004 39.130 17.50 0.00 0.00 1.73
2452 2514 7.493367 TGGTCAAAGTTTAACCCAAAATACAG 58.507 34.615 5.43 0.00 31.78 2.74
2487 2549 0.817229 CCCGGACGGAGGTAGTAGTC 60.817 65.000 13.13 0.00 37.50 2.59
2488 2550 0.107508 CCGGACGGAGGTAGTAGTCA 60.108 60.000 4.40 0.00 37.50 3.41
2515 2577 4.080299 AGGTCTTCATGATTGTTAGGGGTC 60.080 45.833 0.00 0.00 0.00 4.46
2528 2590 4.022068 TGTTAGGGGTCGTTACTGTAGTTG 60.022 45.833 0.00 0.00 0.00 3.16
2654 2716 7.963532 ACCTTGGAGATATGATACGTTGTAAT 58.036 34.615 0.00 0.00 0.00 1.89
2681 2743 5.772672 CACAGCTCCTTATAGGATGTCTACT 59.227 44.000 0.00 0.00 44.81 2.57
2710 2772 0.584396 GCACAAAATCACACCGTCGA 59.416 50.000 0.00 0.00 0.00 4.20
3051 3113 8.704234 GTCGAATACACAATATCCAATTCTCTC 58.296 37.037 0.00 0.00 0.00 3.20
3056 3118 6.950842 ACACAATATCCAATTCTCTCTCACA 58.049 36.000 0.00 0.00 0.00 3.58
3070 3132 3.377172 TCTCTCACATGCTGCATCATTTG 59.623 43.478 13.10 9.83 0.00 2.32
3072 3134 3.119637 TCTCACATGCTGCATCATTTGTG 60.120 43.478 21.29 21.29 0.00 3.33
3073 3135 2.559231 TCACATGCTGCATCATTTGTGT 59.441 40.909 24.36 13.27 0.00 3.72
3336 3425 8.800370 ATTTTTATTTTGGTTGAGTTGTTGGT 57.200 26.923 0.00 0.00 0.00 3.67
3565 3656 0.243095 GCGGGAGTACTTCGACAAGT 59.757 55.000 19.25 0.00 45.39 3.16
3624 3715 2.494073 GGACGACTCCTTTGATGAGACT 59.506 50.000 0.00 0.00 33.07 3.24
3656 3747 2.125106 GCGGCGAATCCAGGAGTT 60.125 61.111 12.98 0.00 34.01 3.01
4080 4175 5.068198 GGACTTGCATATGGTGTTCATTGAT 59.932 40.000 4.56 0.00 37.30 2.57
4388 4483 3.974757 CGATAGTCGGACGGGGGC 61.975 72.222 1.89 0.00 36.00 5.80
4449 4546 4.161001 TCGAAAGGGTTTAGGCTTAGTAGG 59.839 45.833 0.00 0.00 0.00 3.18
4502 4602 0.336737 ACTAGGTGTGAGGAGGAGGG 59.663 60.000 0.00 0.00 0.00 4.30
4667 4767 1.268079 TCTCTGTGACAAGAGAGTGCG 59.732 52.381 9.61 0.00 46.13 5.34
4962 5062 0.529992 ATAGTGGACGGCTAAAGCGC 60.530 55.000 0.00 0.00 43.26 5.92
5024 5124 1.553706 TGGGAGGAGTCCGTTAAGAC 58.446 55.000 2.76 0.00 45.05 3.01
5110 5210 0.681887 CCATGTGCCAGAGCCATGAA 60.682 55.000 14.22 0.00 44.14 2.57
5198 5298 5.109210 TGTTGTTGTTGTTGTTGTTGTTGA 58.891 33.333 0.00 0.00 0.00 3.18
5199 5299 5.233050 TGTTGTTGTTGTTGTTGTTGTTGAG 59.767 36.000 0.00 0.00 0.00 3.02
5200 5300 4.938080 TGTTGTTGTTGTTGTTGTTGAGT 58.062 34.783 0.00 0.00 0.00 3.41
5202 5302 5.233050 TGTTGTTGTTGTTGTTGTTGAGTTG 59.767 36.000 0.00 0.00 0.00 3.16
5203 5303 4.938080 TGTTGTTGTTGTTGTTGAGTTGT 58.062 34.783 0.00 0.00 0.00 3.32
5331 5432 8.276325 CGTTATGTGAGGCAGTCTAAATTATTC 58.724 37.037 0.00 0.00 0.00 1.75
5523 5624 6.740110 ACTCTTTACATGCGGTATCTTCTAG 58.260 40.000 0.00 0.00 0.00 2.43
5782 5883 6.131961 AGGGAGAAGTAATATGCAATTTGCT 58.868 36.000 21.19 10.06 45.31 3.91
5874 5975 6.821665 GCTGTCAACCAACCTGAAATATAGTA 59.178 38.462 0.00 0.00 0.00 1.82
5875 5976 7.201617 GCTGTCAACCAACCTGAAATATAGTAC 60.202 40.741 0.00 0.00 0.00 2.73
5927 6028 4.626287 GCTCAACCCAGTCCAAATCTGATA 60.626 45.833 0.00 0.00 35.20 2.15
6210 6544 2.923655 CGTGTACAGCACTGTCCTAATG 59.076 50.000 6.56 0.00 45.57 1.90
6213 6547 5.475719 GTGTACAGCACTGTCCTAATGTTA 58.524 41.667 6.56 0.00 43.74 2.41
6310 6647 6.040391 TGGGTTTAGCCTCATAATGTATTTGC 59.960 38.462 0.00 0.00 37.43 3.68
6422 6761 9.658799 CCAATGGATCTTTATATGTAGGTAGTG 57.341 37.037 0.00 0.00 0.00 2.74
6467 6807 1.515736 GCAGAATCAGCGCCTTTGC 60.516 57.895 2.29 2.17 0.00 3.68
6536 6876 4.405680 TCGAAGCAGAATTGGAGGATAAGA 59.594 41.667 0.00 0.00 0.00 2.10
6735 7075 5.676552 TGGCCTATCAACGTGTAATGTATT 58.323 37.500 3.32 0.00 32.67 1.89
6737 7077 5.756347 GGCCTATCAACGTGTAATGTATTCA 59.244 40.000 0.00 0.00 32.67 2.57
6738 7078 6.073765 GGCCTATCAACGTGTAATGTATTCAG 60.074 42.308 0.00 0.00 32.67 3.02
6739 7079 6.073765 GCCTATCAACGTGTAATGTATTCAGG 60.074 42.308 0.00 0.00 32.67 3.86
6803 7147 7.834181 ACTAATATGTGTGCCAGGAACTTTTAT 59.166 33.333 0.00 0.00 34.60 1.40
6804 7148 6.699575 ATATGTGTGCCAGGAACTTTTATC 57.300 37.500 0.00 0.00 34.60 1.75
6805 7149 4.098914 TGTGTGCCAGGAACTTTTATCT 57.901 40.909 0.00 0.00 34.60 1.98
6806 7150 3.820467 TGTGTGCCAGGAACTTTTATCTG 59.180 43.478 0.00 0.00 34.60 2.90
6807 7151 3.821033 GTGTGCCAGGAACTTTTATCTGT 59.179 43.478 0.00 0.00 34.60 3.41
6808 7152 4.278419 GTGTGCCAGGAACTTTTATCTGTT 59.722 41.667 0.00 0.00 34.60 3.16
6809 7153 4.892934 TGTGCCAGGAACTTTTATCTGTTT 59.107 37.500 0.00 0.00 34.60 2.83
6810 7154 5.362430 TGTGCCAGGAACTTTTATCTGTTTT 59.638 36.000 0.00 0.00 34.60 2.43
6811 7155 6.547880 TGTGCCAGGAACTTTTATCTGTTTTA 59.452 34.615 0.00 0.00 34.60 1.52
6812 7156 7.232534 TGTGCCAGGAACTTTTATCTGTTTTAT 59.767 33.333 0.00 0.00 34.60 1.40
6813 7157 7.755373 GTGCCAGGAACTTTTATCTGTTTTATC 59.245 37.037 0.00 0.00 34.60 1.75
6814 7158 7.669722 TGCCAGGAACTTTTATCTGTTTTATCT 59.330 33.333 0.00 0.00 34.60 1.98
6815 7159 8.523658 GCCAGGAACTTTTATCTGTTTTATCTT 58.476 33.333 0.00 0.00 34.60 2.40
6818 7162 9.807921 AGGAACTTTTATCTGTTTTATCTTCCA 57.192 29.630 0.00 0.00 27.25 3.53
6819 7163 9.841880 GGAACTTTTATCTGTTTTATCTTCCAC 57.158 33.333 0.00 0.00 0.00 4.02
6820 7164 9.543018 GAACTTTTATCTGTTTTATCTTCCACG 57.457 33.333 0.00 0.00 0.00 4.94
6821 7165 8.842358 ACTTTTATCTGTTTTATCTTCCACGA 57.158 30.769 0.00 0.00 0.00 4.35
6822 7166 9.280174 ACTTTTATCTGTTTTATCTTCCACGAA 57.720 29.630 0.00 0.00 0.00 3.85
6823 7167 9.543018 CTTTTATCTGTTTTATCTTCCACGAAC 57.457 33.333 0.00 0.00 0.00 3.95
6824 7168 7.605410 TTATCTGTTTTATCTTCCACGAACC 57.395 36.000 0.00 0.00 0.00 3.62
6825 7169 5.223449 TCTGTTTTATCTTCCACGAACCT 57.777 39.130 0.00 0.00 0.00 3.50
6826 7170 5.235516 TCTGTTTTATCTTCCACGAACCTC 58.764 41.667 0.00 0.00 0.00 3.85
6827 7171 4.963373 TGTTTTATCTTCCACGAACCTCA 58.037 39.130 0.00 0.00 0.00 3.86
6828 7172 4.994852 TGTTTTATCTTCCACGAACCTCAG 59.005 41.667 0.00 0.00 0.00 3.35
6829 7173 5.221561 TGTTTTATCTTCCACGAACCTCAGA 60.222 40.000 0.00 0.00 0.00 3.27
6830 7174 4.451629 TTATCTTCCACGAACCTCAGAC 57.548 45.455 0.00 0.00 0.00 3.51
6831 7175 0.966920 TCTTCCACGAACCTCAGACC 59.033 55.000 0.00 0.00 0.00 3.85
6832 7176 0.969894 CTTCCACGAACCTCAGACCT 59.030 55.000 0.00 0.00 0.00 3.85
6833 7177 0.966920 TTCCACGAACCTCAGACCTC 59.033 55.000 0.00 0.00 0.00 3.85
6834 7178 0.178973 TCCACGAACCTCAGACCTCA 60.179 55.000 0.00 0.00 0.00 3.86
6835 7179 0.244994 CCACGAACCTCAGACCTCAG 59.755 60.000 0.00 0.00 0.00 3.35
6836 7180 1.248486 CACGAACCTCAGACCTCAGA 58.752 55.000 0.00 0.00 0.00 3.27
6837 7181 1.201181 CACGAACCTCAGACCTCAGAG 59.799 57.143 0.00 0.00 0.00 3.35
6838 7182 1.202952 ACGAACCTCAGACCTCAGAGT 60.203 52.381 0.00 0.00 0.00 3.24
6839 7183 1.470890 CGAACCTCAGACCTCAGAGTC 59.529 57.143 0.00 0.00 37.01 3.36
6847 7191 3.799432 AGACCTCAGAGTCTGTACTGT 57.201 47.619 19.53 12.05 45.41 3.55
6848 7192 4.107127 AGACCTCAGAGTCTGTACTGTT 57.893 45.455 19.53 0.20 45.41 3.16
6849 7193 4.475345 AGACCTCAGAGTCTGTACTGTTT 58.525 43.478 19.53 5.85 45.41 2.83
6850 7194 4.279671 AGACCTCAGAGTCTGTACTGTTTG 59.720 45.833 19.53 3.86 45.41 2.93
6851 7195 4.215908 ACCTCAGAGTCTGTACTGTTTGA 58.784 43.478 19.53 0.00 35.56 2.69
6852 7196 4.649674 ACCTCAGAGTCTGTACTGTTTGAA 59.350 41.667 19.53 0.00 35.56 2.69
6853 7197 5.221342 ACCTCAGAGTCTGTACTGTTTGAAG 60.221 44.000 19.53 5.71 35.56 3.02
6854 7198 4.621991 TCAGAGTCTGTACTGTTTGAAGC 58.378 43.478 19.53 0.00 35.56 3.86
6855 7199 4.099419 TCAGAGTCTGTACTGTTTGAAGCA 59.901 41.667 19.53 0.00 35.56 3.91
6856 7200 4.210120 CAGAGTCTGTACTGTTTGAAGCAC 59.790 45.833 12.28 0.00 35.56 4.40
6857 7201 4.119862 GAGTCTGTACTGTTTGAAGCACA 58.880 43.478 0.00 0.00 35.56 4.57
6858 7202 4.708177 AGTCTGTACTGTTTGAAGCACAT 58.292 39.130 0.00 0.00 33.57 3.21
6859 7203 4.512944 AGTCTGTACTGTTTGAAGCACATG 59.487 41.667 0.00 0.00 33.57 3.21
6860 7204 3.814842 TCTGTACTGTTTGAAGCACATGG 59.185 43.478 0.00 0.00 0.00 3.66
6861 7205 2.293122 TGTACTGTTTGAAGCACATGGC 59.707 45.455 0.00 0.00 45.30 4.40
6945 7289 9.814899 TGTTTGTGAGAAACATTACAATTTCAT 57.185 25.926 3.58 0.00 38.99 2.57
6971 7315 2.087646 GGCTCCTCAAACCAATCTGAC 58.912 52.381 0.00 0.00 0.00 3.51
6978 7323 3.057019 TCAAACCAATCTGACGTCGAAG 58.943 45.455 11.62 3.63 0.00 3.79
7033 7379 8.988934 TGCTATTTTATTTGCCTCTCTATTACG 58.011 33.333 0.00 0.00 0.00 3.18
7054 7400 6.332504 ACGATGTTCGAATTTAGTCATGAC 57.667 37.500 18.47 18.47 43.74 3.06
7170 7516 7.932491 CCAGATTGTCAGAGTTGATGATTAGAT 59.068 37.037 0.00 0.00 35.39 1.98
7221 7567 4.307032 AGGCCAAATTTGAGAGCTAAGA 57.693 40.909 19.86 0.00 0.00 2.10
7260 7606 5.105310 ACATCCACGCAGTAGTCTATCTTTT 60.105 40.000 0.00 0.00 41.61 2.27
7324 7670 2.029307 GCCCTCATCGTACCCTCCAC 62.029 65.000 0.00 0.00 0.00 4.02
7325 7671 0.397254 CCCTCATCGTACCCTCCACT 60.397 60.000 0.00 0.00 0.00 4.00
7327 7673 2.491086 CCCTCATCGTACCCTCCACTAT 60.491 54.545 0.00 0.00 0.00 2.12
7362 7708 1.531149 AGGCGTCAACATTGAGTTTCG 59.469 47.619 0.00 0.00 38.74 3.46
7371 7717 1.000385 CATTGAGTTTCGCAAAGCCCA 60.000 47.619 0.00 0.00 0.00 5.36
7463 7810 5.549228 TGTAAGAGCTATGATCCCCATTGAT 59.451 40.000 0.00 0.00 36.71 2.57
7467 7814 5.369110 AGAGCTATGATCCCCATTGATATCC 59.631 44.000 0.00 0.00 36.71 2.59
7522 7873 4.489737 TCCGTCTTTCCCACCATAGATAT 58.510 43.478 0.00 0.00 0.00 1.63
7612 7963 7.878644 GGAAGGAGTAATAGGTATTCCAATGTC 59.121 40.741 0.00 0.00 40.35 3.06
7615 7966 7.569111 AGGAGTAATAGGTATTCCAATGTCACT 59.431 37.037 0.00 0.00 40.35 3.41
7643 7994 2.417933 GCACGATCAATCTCACAAGCTT 59.582 45.455 0.00 0.00 0.00 3.74
7645 7996 4.093408 GCACGATCAATCTCACAAGCTTTA 59.907 41.667 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.248363 TGAAAGTGTCAACAGCATCTTCG 59.752 43.478 0.00 0.00 31.51 3.79
138 139 3.681897 AGTTGCATGCTCTTTCGAGTTAG 59.318 43.478 20.33 0.00 39.53 2.34
168 169 7.327214 TCTGCATTACATAACACACATGTAGA 58.673 34.615 0.00 0.00 39.40 2.59
199 200 1.276705 GGAGGTGAGTTCTGTCTTCCC 59.723 57.143 0.00 0.00 0.00 3.97
641 653 1.909700 AACCCTACTGTGTGGCATTG 58.090 50.000 0.00 0.00 0.00 2.82
664 676 6.503560 TTTTAGACCAAAGAACAGTAGGGA 57.496 37.500 0.00 0.00 0.00 4.20
761 773 1.737793 CCCACCGTACAATGCTTCTTC 59.262 52.381 0.00 0.00 0.00 2.87
767 779 3.051392 GCAGCCCACCGTACAATGC 62.051 63.158 0.00 0.00 0.00 3.56
775 787 2.906897 AAACAGTGCAGCCCACCG 60.907 61.111 0.00 0.00 45.83 4.94
788 800 3.283684 CTGAACGGCCCGCAAACA 61.284 61.111 1.23 0.00 0.00 2.83
843 855 5.794726 TTAGGGATGCTATACGTTGCTTA 57.205 39.130 0.00 0.00 0.00 3.09
874 899 0.179119 AGGACGGTGCTATACGTTGC 60.179 55.000 0.00 0.00 44.24 4.17
875 900 2.288961 AAGGACGGTGCTATACGTTG 57.711 50.000 1.54 0.00 44.24 4.10
878 903 2.288961 ACAAAGGACGGTGCTATACG 57.711 50.000 1.54 0.00 0.00 3.06
880 905 3.767673 AGAGAACAAAGGACGGTGCTATA 59.232 43.478 1.54 0.00 0.00 1.31
882 907 1.968493 AGAGAACAAAGGACGGTGCTA 59.032 47.619 1.54 0.00 0.00 3.49
888 913 4.319177 AGATTGGAAGAGAACAAAGGACG 58.681 43.478 0.00 0.00 0.00 4.79
890 915 5.545723 AGAGAGATTGGAAGAGAACAAAGGA 59.454 40.000 0.00 0.00 0.00 3.36
908 933 3.131396 GGAACGAACTGCAAAAGAGAGA 58.869 45.455 0.00 0.00 0.00 3.10
909 934 2.224314 GGGAACGAACTGCAAAAGAGAG 59.776 50.000 0.00 0.00 0.00 3.20
1270 1298 2.786495 CCGTCATGGTCTCGGGAGG 61.786 68.421 0.00 0.00 40.49 4.30
1275 1303 2.579787 GTCGCCGTCATGGTCTCG 60.580 66.667 0.00 0.00 41.21 4.04
1436 1464 4.537688 TCTCCTCCTGAAATGTCCAGAAAT 59.462 41.667 0.00 0.00 33.65 2.17
1476 1504 7.041780 ACAATTAGCTCGGATTTAAGCAGTATG 60.042 37.037 0.00 0.00 41.06 2.39
1535 1563 4.063335 CCATCTGGCTCACCCTCT 57.937 61.111 0.00 0.00 33.59 3.69
1602 1630 9.942850 CAAAAAGGAATTTATACCTCAACCAAT 57.057 29.630 0.00 0.00 35.25 3.16
1628 1656 1.202348 GCACTCTAACAACAATGCCCC 59.798 52.381 0.00 0.00 0.00 5.80
1634 1662 5.175859 GGCATACTAGCACTCTAACAACAA 58.824 41.667 0.00 0.00 35.83 2.83
1648 1677 2.744202 GGGCATCAAATCGGCATACTAG 59.256 50.000 0.00 0.00 0.00 2.57
1657 1686 2.096069 CGAATAGCAGGGCATCAAATCG 60.096 50.000 0.00 0.00 0.00 3.34
1678 1707 1.200020 CCTCAAACCGTTCCTGCAATC 59.800 52.381 0.00 0.00 0.00 2.67
1706 1735 1.079266 GGAGCCTCTCAGCTGTGTG 60.079 63.158 14.67 12.07 45.15 3.82
1709 1738 0.913451 AATGGGAGCCTCTCAGCTGT 60.913 55.000 14.67 0.00 45.15 4.40
1753 1782 9.409949 CGTAAAAGAAGCTATTGAATTTAGTCG 57.590 33.333 0.00 0.00 0.00 4.18
2000 2029 6.706270 AGTGTAAGGTATCACAGTCAAACTTG 59.294 38.462 0.00 0.00 37.07 3.16
2218 2250 4.567159 GCACCAGTACTAGTCAACATTAGC 59.433 45.833 0.00 0.00 0.00 3.09
2242 2282 4.147321 GGACGGAGGGAGTATGTGTAATA 58.853 47.826 0.00 0.00 0.00 0.98
2245 2285 1.748244 CGGACGGAGGGAGTATGTGTA 60.748 57.143 0.00 0.00 0.00 2.90
2461 2523 0.986527 ACCTCCGTCCGGGTTTATTT 59.013 50.000 0.00 0.00 37.00 1.40
2487 2549 6.039047 CCCTAACAATCATGAAGACCTTGATG 59.961 42.308 11.90 3.32 38.97 3.07
2488 2550 6.125029 CCCTAACAATCATGAAGACCTTGAT 58.875 40.000 11.90 4.03 40.22 2.57
2515 2577 7.806149 TGTCATCATAACAACTACAGTAACG 57.194 36.000 0.00 0.00 0.00 3.18
2574 2636 9.823647 TGTTTGGCAACTAGAAAAATTTAATGA 57.176 25.926 0.00 0.00 33.58 2.57
2654 2716 2.174685 TCCTATAAGGAGCTGTGGCA 57.825 50.000 0.00 0.00 40.06 4.92
2681 2743 2.032799 GTGATTTTGTGCGACTTGTGGA 59.967 45.455 0.00 0.00 0.00 4.02
3051 3113 3.179048 CACAAATGATGCAGCATGTGAG 58.821 45.455 35.48 26.17 35.88 3.51
3056 3118 4.569162 GCAATAACACAAATGATGCAGCAT 59.431 37.500 12.63 12.63 32.80 3.79
3070 3132 6.095377 AGCAGAAAATAAGCAGCAATAACAC 58.905 36.000 0.00 0.00 0.00 3.32
3072 3134 7.586714 AAAGCAGAAAATAAGCAGCAATAAC 57.413 32.000 0.00 0.00 0.00 1.89
3073 3135 7.656948 ACAAAAGCAGAAAATAAGCAGCAATAA 59.343 29.630 0.00 0.00 0.00 1.40
3255 3344 5.246307 ACTTGGCACTTAATGTAGTCTTCC 58.754 41.667 0.00 0.00 0.00 3.46
3336 3425 3.354678 GCTTTGCGGCCTTCTTCA 58.645 55.556 0.00 0.00 0.00 3.02
3565 3656 4.043310 ACTCTCATTCTCCCCATTGAACAA 59.957 41.667 0.00 0.00 0.00 2.83
3624 3715 1.208870 CCGCACAAAACGCATGCTA 59.791 52.632 17.13 0.00 37.20 3.49
3656 3747 4.447138 TTTAAAGCCTCCTTGACCTCAA 57.553 40.909 0.00 0.00 0.00 3.02
4080 4175 6.770286 ATCTTATCATAGGCCTTCTCCAAA 57.230 37.500 12.58 0.00 0.00 3.28
4388 4483 9.535878 GTCTCCATAACTCTAACTTCCTATTTG 57.464 37.037 0.00 0.00 0.00 2.32
4449 4546 5.220416 GCACATCATGTACTCGGTTTTAGTC 60.220 44.000 0.00 0.00 0.00 2.59
4606 4706 1.672881 CTTCATCCATCCGGCTTTGAC 59.327 52.381 0.00 0.00 0.00 3.18
4667 4767 5.592054 AGAACTTGCCTTTTAGCTTTTGTC 58.408 37.500 0.00 0.00 0.00 3.18
4962 5062 1.554392 CTCTCTTGACATTCTCCGCG 58.446 55.000 0.00 0.00 0.00 6.46
5024 5124 4.406972 TGATACTCCAATCCTTCAGGTCTG 59.593 45.833 0.00 0.00 36.34 3.51
5110 5210 4.985538 ACCCATAATATCTCGCAACCAAT 58.014 39.130 0.00 0.00 0.00 3.16
5198 5298 7.944729 ATTCTAGCATTACCATTCAACAACT 57.055 32.000 0.00 0.00 0.00 3.16
5199 5299 8.863049 CAAATTCTAGCATTACCATTCAACAAC 58.137 33.333 0.00 0.00 0.00 3.32
5200 5300 8.584157 ACAAATTCTAGCATTACCATTCAACAA 58.416 29.630 0.00 0.00 0.00 2.83
5245 5345 1.239347 GCCGCTCTCCTTGAACTTTT 58.761 50.000 0.00 0.00 0.00 2.27
5246 5346 0.951040 CGCCGCTCTCCTTGAACTTT 60.951 55.000 0.00 0.00 0.00 2.66
5331 5432 4.843220 ACATTTGTTCCTGCTTTCTGAG 57.157 40.909 0.00 0.00 0.00 3.35
5523 5624 7.492344 CCAATTTGGATTGCTTCATAAACCTAC 59.508 37.037 10.03 0.00 40.96 3.18
5672 5773 2.172505 TCAACTGGAAGCTGGAAACTCA 59.827 45.455 0.00 0.00 37.60 3.41
5675 5776 1.882623 CCTCAACTGGAAGCTGGAAAC 59.117 52.381 0.00 0.00 37.60 2.78
5727 5828 4.125703 AGAGAGCACACACAGAAAGAAAG 58.874 43.478 0.00 0.00 0.00 2.62
5734 5835 5.722021 TGTATAAAGAGAGCACACACAGA 57.278 39.130 0.00 0.00 0.00 3.41
5739 5840 6.265649 TCTCCCTATGTATAAAGAGAGCACAC 59.734 42.308 0.00 0.00 0.00 3.82
5782 5883 6.889198 AGCTTTGCATATAACTGAACTCCTA 58.111 36.000 0.00 0.00 0.00 2.94
5874 5975 5.308014 TGTTCAGATATGTGCAAGACTTGT 58.692 37.500 16.39 0.00 0.00 3.16
5875 5976 5.868043 TGTTCAGATATGTGCAAGACTTG 57.132 39.130 11.02 11.02 0.00 3.16
5927 6028 3.328535 AGATTTGGGAACTTGGGTTGT 57.671 42.857 0.00 0.00 35.58 3.32
6213 6547 9.528018 CCATGGAAAATATTTTACAGCGTAAAT 57.472 29.630 25.87 9.10 43.66 1.40
6310 6647 7.275920 AGTATGTAGGGCACAGAAATCTAAAG 58.724 38.462 0.00 0.00 41.51 1.85
6467 6807 5.830000 TCTTCTTCATCAGCCAATGAATG 57.170 39.130 10.75 6.74 42.97 2.67
6536 6876 4.401022 TCTTCAACATGCACAGGAGAAAT 58.599 39.130 0.00 0.00 0.00 2.17
6735 7075 8.533569 TCATGTCACTCATATTAGTTACCTGA 57.466 34.615 5.67 5.67 34.67 3.86
6737 7077 8.982723 AGTTCATGTCACTCATATTAGTTACCT 58.017 33.333 0.00 0.00 34.67 3.08
6738 7078 9.601217 AAGTTCATGTCACTCATATTAGTTACC 57.399 33.333 0.00 0.00 34.67 2.85
6803 7147 5.221561 TGAGGTTCGTGGAAGATAAAACAGA 60.222 40.000 0.00 0.00 0.00 3.41
6804 7148 4.994852 TGAGGTTCGTGGAAGATAAAACAG 59.005 41.667 0.00 0.00 0.00 3.16
6805 7149 4.963373 TGAGGTTCGTGGAAGATAAAACA 58.037 39.130 0.00 0.00 0.00 2.83
6806 7150 5.120363 GTCTGAGGTTCGTGGAAGATAAAAC 59.880 44.000 0.00 0.00 0.00 2.43
6807 7151 5.235516 GTCTGAGGTTCGTGGAAGATAAAA 58.764 41.667 0.00 0.00 0.00 1.52
6808 7152 4.322499 GGTCTGAGGTTCGTGGAAGATAAA 60.322 45.833 0.00 0.00 0.00 1.40
6809 7153 3.194968 GGTCTGAGGTTCGTGGAAGATAA 59.805 47.826 0.00 0.00 0.00 1.75
6810 7154 2.758979 GGTCTGAGGTTCGTGGAAGATA 59.241 50.000 0.00 0.00 0.00 1.98
6811 7155 1.550976 GGTCTGAGGTTCGTGGAAGAT 59.449 52.381 0.00 0.00 0.00 2.40
6812 7156 0.966920 GGTCTGAGGTTCGTGGAAGA 59.033 55.000 0.00 0.00 0.00 2.87
6813 7157 0.969894 AGGTCTGAGGTTCGTGGAAG 59.030 55.000 0.00 0.00 0.00 3.46
6814 7158 0.966920 GAGGTCTGAGGTTCGTGGAA 59.033 55.000 0.00 0.00 0.00 3.53
6815 7159 0.178973 TGAGGTCTGAGGTTCGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
6816 7160 0.244994 CTGAGGTCTGAGGTTCGTGG 59.755 60.000 0.00 0.00 0.00 4.94
6817 7161 1.201181 CTCTGAGGTCTGAGGTTCGTG 59.799 57.143 6.08 0.00 38.00 4.35
6818 7162 1.202952 ACTCTGAGGTCTGAGGTTCGT 60.203 52.381 15.79 0.00 43.52 3.85
6819 7163 1.470890 GACTCTGAGGTCTGAGGTTCG 59.529 57.143 15.79 0.00 43.52 3.95
6820 7164 2.802719 AGACTCTGAGGTCTGAGGTTC 58.197 52.381 15.79 7.34 43.89 3.62
6821 7165 2.990740 AGACTCTGAGGTCTGAGGTT 57.009 50.000 15.79 3.65 43.89 3.50
6827 7171 3.799432 ACAGTACAGACTCTGAGGTCT 57.201 47.619 13.25 6.77 46.14 3.85
6828 7172 4.278669 TCAAACAGTACAGACTCTGAGGTC 59.721 45.833 13.25 4.59 35.18 3.85
6829 7173 4.215908 TCAAACAGTACAGACTCTGAGGT 58.784 43.478 13.25 0.02 35.18 3.85
6830 7174 4.855715 TCAAACAGTACAGACTCTGAGG 57.144 45.455 13.25 2.00 35.18 3.86
6831 7175 4.683781 GCTTCAAACAGTACAGACTCTGAG 59.316 45.833 13.25 2.45 35.18 3.35
6832 7176 4.099419 TGCTTCAAACAGTACAGACTCTGA 59.901 41.667 13.25 0.00 35.18 3.27
6833 7177 4.210120 GTGCTTCAAACAGTACAGACTCTG 59.790 45.833 4.36 4.36 37.52 3.35
6834 7178 4.141937 TGTGCTTCAAACAGTACAGACTCT 60.142 41.667 0.00 0.00 34.79 3.24
6835 7179 4.119862 TGTGCTTCAAACAGTACAGACTC 58.880 43.478 0.00 0.00 34.79 3.36
6836 7180 4.137116 TGTGCTTCAAACAGTACAGACT 57.863 40.909 0.00 0.00 34.79 3.24
6837 7181 4.319766 CCATGTGCTTCAAACAGTACAGAC 60.320 45.833 0.00 0.00 41.92 3.51
6838 7182 3.814842 CCATGTGCTTCAAACAGTACAGA 59.185 43.478 0.00 0.00 41.92 3.41
6839 7183 3.610114 GCCATGTGCTTCAAACAGTACAG 60.610 47.826 0.00 0.00 41.92 2.74
6840 7184 2.293122 GCCATGTGCTTCAAACAGTACA 59.707 45.455 0.00 0.00 42.68 2.90
6841 7185 2.933769 GCCATGTGCTTCAAACAGTAC 58.066 47.619 0.00 0.00 36.87 2.73
6919 7263 9.814899 ATGAAATTGTAATGTTTCTCACAAACA 57.185 25.926 2.55 2.55 43.33 2.83
6945 7289 6.069673 TCAGATTGGTTTGAGGAGCCTATTAA 60.070 38.462 0.00 0.00 0.00 1.40
7012 7358 8.958119 ACATCGTAATAGAGAGGCAAATAAAA 57.042 30.769 0.00 0.00 0.00 1.52
7033 7379 8.948853 TTTTGTCATGACTAAATTCGAACATC 57.051 30.769 25.15 0.00 32.70 3.06
7076 7422 1.645034 CGGCAATCTTCGATGACTGT 58.355 50.000 10.84 0.00 0.00 3.55
7182 7528 2.165641 GCCTAAATTTAGCGCAAAGGGT 59.834 45.455 23.00 0.00 31.52 4.34
7221 7567 1.211457 GGATGTTCTCATGGCAGAGGT 59.789 52.381 12.09 0.55 36.30 3.85
7260 7606 6.772716 GGTAGATTTATTGCAGGAGGAAATGA 59.227 38.462 0.00 0.00 0.00 2.57
7324 7670 3.310774 CGCCTCTTTTGACCATGACATAG 59.689 47.826 0.00 0.00 0.00 2.23
7325 7671 3.270027 CGCCTCTTTTGACCATGACATA 58.730 45.455 0.00 0.00 0.00 2.29
7327 7673 1.202758 ACGCCTCTTTTGACCATGACA 60.203 47.619 0.00 0.00 0.00 3.58
7362 7708 0.255890 TGTCCTCCTATGGGCTTTGC 59.744 55.000 0.00 0.00 31.91 3.68
7371 7717 1.215423 GGGTTGGCAATGTCCTCCTAT 59.785 52.381 1.92 0.00 0.00 2.57
7406 7753 2.336945 ATGCATCATCTTCGAAGGCA 57.663 45.000 24.37 23.31 34.89 4.75
7463 7810 3.520290 ACTCAAAATGCGACTCGGATA 57.480 42.857 5.82 0.00 36.82 2.59
7467 7814 5.281376 CACAATTAACTCAAAATGCGACTCG 59.719 40.000 0.00 0.00 0.00 4.18
7612 7963 2.084610 TTGATCGTGCTGGAGAAGTG 57.915 50.000 0.00 0.00 0.00 3.16
7615 7966 2.497273 TGAGATTGATCGTGCTGGAGAA 59.503 45.455 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.