Multiple sequence alignment - TraesCS3D01G163900

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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 TraesCS3D01G163900 chr3D 100.000 7151 0 0 1516 8666 135372349 135379499 0.000000e+00 13206.0
1 TraesCS3D01G163900 chr3D 100.000 1413 0 0 1 1413 135370834 135372246 0.000000e+00 2610.0
2 TraesCS3D01G163900 chr3D 84.880 291 43 1 8030 8320 449280991 449281280 8.510000e-75 292.0
3 TraesCS3D01G163900 chr3B 97.600 4791 82 13 3905 8666 193609902 193614688 0.000000e+00 8179.0
4 TraesCS3D01G163900 chr3B 97.771 1346 27 2 1516 2859 193605947 193607291 0.000000e+00 2316.0
5 TraesCS3D01G163900 chr3B 98.549 896 11 1 2850 3743 193609008 193609903 0.000000e+00 1581.0
6 TraesCS3D01G163900 chr3B 90.150 802 55 18 59 854 34213729 34212946 0.000000e+00 1022.0
7 TraesCS3D01G163900 chr3B 89.415 803 60 19 59 854 34107007 34106223 0.000000e+00 989.0
8 TraesCS3D01G163900 chr3B 96.988 498 11 2 920 1413 193605394 193605891 0.000000e+00 833.0
9 TraesCS3D01G163900 chr3B 86.102 295 40 1 8027 8320 99675563 99675857 5.050000e-82 316.0
10 TraesCS3D01G163900 chr3A 98.116 4141 48 14 3905 8028 150714093 150718220 0.000000e+00 7188.0
11 TraesCS3D01G163900 chr3A 98.296 2230 35 2 1516 3743 150711866 150714094 0.000000e+00 3904.0
12 TraesCS3D01G163900 chr3A 95.564 541 18 4 878 1413 150711271 150711810 0.000000e+00 861.0
13 TraesCS3D01G163900 chr3A 93.466 352 15 4 8322 8666 150718218 150718568 4.640000e-142 516.0
14 TraesCS3D01G163900 chr3A 90.991 111 10 0 5694 5804 130843939 130843829 5.420000e-32 150.0
15 TraesCS3D01G163900 chr5D 95.173 808 26 6 56 853 306570454 306571258 0.000000e+00 1264.0
16 TraesCS3D01G163900 chr5D 94.886 176 8 1 3735 3909 538702717 538702892 3.080000e-69 274.0
17 TraesCS3D01G163900 chr5D 77.597 308 56 5 8018 8313 290814872 290814566 3.220000e-39 174.0
18 TraesCS3D01G163900 chr5D 86.916 107 11 2 5692 5798 11305366 11305263 5.500000e-22 117.0
19 TraesCS3D01G163900 chr5D 83.810 105 16 1 5702 5805 362056147 362056043 1.990000e-16 99.0
20 TraesCS3D01G163900 chr5D 82.883 111 12 4 5701 5810 297053658 297053762 9.260000e-15 93.5
21 TraesCS3D01G163900 chr4D 94.403 804 34 10 56 853 69259239 69258441 0.000000e+00 1225.0
22 TraesCS3D01G163900 chr4D 92.963 810 42 10 56 854 465156334 465157139 0.000000e+00 1166.0
23 TraesCS3D01G163900 chr4D 86.184 304 29 3 8019 8320 358603182 358603474 5.050000e-82 316.0
24 TraesCS3D01G163900 chr4D 92.453 53 4 0 5701 5753 98453173 98453225 9.330000e-10 76.8
25 TraesCS3D01G163900 chr4D 100.000 33 0 0 5702 5734 468265272 468265240 2.610000e-05 62.1
26 TraesCS3D01G163900 chr6D 94.286 805 29 9 59 853 400782535 400783332 0.000000e+00 1216.0
27 TraesCS3D01G163900 chr6D 93.524 803 41 9 56 854 463712113 463711318 0.000000e+00 1184.0
28 TraesCS3D01G163900 chr6D 89.715 807 36 21 90 853 106950417 106951219 0.000000e+00 987.0
29 TraesCS3D01G163900 chr6D 88.514 296 32 1 8027 8320 5905866 5906161 2.980000e-94 357.0
30 TraesCS3D01G163900 chr6D 87.629 291 31 4 8029 8314 5905100 5905390 5.010000e-87 333.0
31 TraesCS3D01G163900 chr6D 97.041 169 5 0 3739 3907 406391526 406391358 1.420000e-72 285.0
32 TraesCS3D01G163900 chr6D 83.673 98 13 3 5703 5799 324520774 324520679 1.200000e-13 89.8
33 TraesCS3D01G163900 chr6D 82.474 97 12 3 5702 5798 309584394 309584485 7.210000e-11 80.5
34 TraesCS3D01G163900 chr6D 100.000 29 0 0 5702 5730 86855252 86855224 4.000000e-03 54.7
35 TraesCS3D01G163900 chr1D 90.608 905 32 17 1 854 29835197 29834295 0.000000e+00 1151.0
36 TraesCS3D01G163900 chr1D 92.390 749 36 18 1 740 307338378 307339114 0.000000e+00 1048.0
37 TraesCS3D01G163900 chr1D 94.857 175 9 0 3732 3906 81276345 81276519 3.080000e-69 274.0
38 TraesCS3D01G163900 chr1D 89.404 151 16 0 8044 8194 287465358 287465508 3.190000e-44 191.0
39 TraesCS3D01G163900 chr1D 80.583 103 19 1 5698 5800 31154864 31154763 2.590000e-10 78.7
40 TraesCS3D01G163900 chr7D 89.910 892 47 23 1 854 629617916 629617030 0.000000e+00 1109.0
41 TraesCS3D01G163900 chr7D 89.203 778 39 21 1 740 417354305 417355075 0.000000e+00 929.0
42 TraesCS3D01G163900 chr7D 88.071 788 40 25 1 740 412389851 412390632 0.000000e+00 885.0
43 TraesCS3D01G163900 chr7D 83.206 262 12 14 1 231 108662072 108662332 2.450000e-50 211.0
44 TraesCS3D01G163900 chr2B 87.026 871 75 30 1 854 88974232 88973383 0.000000e+00 948.0
45 TraesCS3D01G163900 chr2B 96.471 170 6 0 3742 3911 174794986 174794817 1.840000e-71 281.0
46 TraesCS3D01G163900 chr2B 83.333 108 12 5 5700 5805 622914011 622914114 2.580000e-15 95.3
47 TraesCS3D01G163900 chr6B 87.960 299 32 3 8025 8320 636485830 636486127 4.980000e-92 350.0
48 TraesCS3D01G163900 chr6B 87.838 296 31 3 8027 8318 356961167 356960873 8.330000e-90 342.0
49 TraesCS3D01G163900 chr6B 83.893 298 41 5 8029 8320 184152973 184153269 2.380000e-70 278.0
50 TraesCS3D01G163900 chr2D 86.288 299 40 1 8027 8324 483630204 483630502 3.020000e-84 324.0
51 TraesCS3D01G163900 chr2D 96.450 169 6 0 3739 3907 396613796 396613964 6.620000e-71 279.0
52 TraesCS3D01G163900 chr2D 95.402 174 7 1 3733 3906 560959477 560959649 8.570000e-70 276.0
53 TraesCS3D01G163900 chr2D 81.905 210 9 6 1 181 635163151 635162942 5.420000e-32 150.0
54 TraesCS3D01G163900 chr4B 95.954 173 7 0 3742 3914 323794658 323794486 1.840000e-71 281.0
55 TraesCS3D01G163900 chr1B 97.576 165 3 1 3742 3906 515448598 515448435 1.840000e-71 281.0
56 TraesCS3D01G163900 chr7B 95.954 173 6 1 3734 3906 493508558 493508387 6.620000e-71 279.0
57 TraesCS3D01G163900 chr1A 84.739 249 35 3 8027 8273 703127 702880 6.720000e-61 246.0
58 TraesCS3D01G163900 chr1A 77.814 311 55 9 8027 8323 249384683 249384993 6.910000e-41 180.0
59 TraesCS3D01G163900 chr1A 81.416 113 18 3 8026 8137 551986761 551986871 1.200000e-13 89.8
60 TraesCS3D01G163900 chr1A 82.000 100 16 2 5701 5799 385895957 385896055 5.570000e-12 84.2
61 TraesCS3D01G163900 chr5B 81.720 279 49 2 8038 8314 77588414 77588692 1.880000e-56 231.0
62 TraesCS3D01G163900 chr5B 88.288 111 12 1 5689 5799 575975748 575975639 1.960000e-26 132.0
63 TraesCS3D01G163900 chr6A 78.896 308 50 11 8026 8320 332564764 332564459 2.470000e-45 195.0
64 TraesCS3D01G163900 chrUn 77.273 308 55 10 8027 8320 335803082 335803388 5.380000e-37 167.0
65 TraesCS3D01G163900 chrUn 83.929 112 10 6 5693 5799 42338335 42338443 5.540000e-17 100.0
66 TraesCS3D01G163900 chrUn 82.645 121 13 6 5693 5808 42530614 42530497 5.540000e-17 100.0
67 TraesCS3D01G163900 chrUn 82.645 121 13 6 5693 5808 474064267 474064150 5.540000e-17 100.0
68 TraesCS3D01G163900 chr7A 85.859 99 14 0 5700 5798 654781682 654781584 1.190000e-18 106.0


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 TraesCS3D01G163900 chr3D 135370834 135379499 8665 False 7908.00 13206 100.0000 1 8666 2 chr3D.!!$F2 8665
1 TraesCS3D01G163900 chr3B 193605394 193614688 9294 False 3227.25 8179 97.7270 920 8666 4 chr3B.!!$F2 7746
2 TraesCS3D01G163900 chr3B 34212946 34213729 783 True 1022.00 1022 90.1500 59 854 1 chr3B.!!$R2 795
3 TraesCS3D01G163900 chr3B 34106223 34107007 784 True 989.00 989 89.4150 59 854 1 chr3B.!!$R1 795
4 TraesCS3D01G163900 chr3A 150711271 150718568 7297 False 3117.25 7188 96.3605 878 8666 4 chr3A.!!$F1 7788
5 TraesCS3D01G163900 chr5D 306570454 306571258 804 False 1264.00 1264 95.1730 56 853 1 chr5D.!!$F2 797
6 TraesCS3D01G163900 chr4D 69258441 69259239 798 True 1225.00 1225 94.4030 56 853 1 chr4D.!!$R1 797
7 TraesCS3D01G163900 chr4D 465156334 465157139 805 False 1166.00 1166 92.9630 56 854 1 chr4D.!!$F3 798
8 TraesCS3D01G163900 chr6D 400782535 400783332 797 False 1216.00 1216 94.2860 59 853 1 chr6D.!!$F3 794
9 TraesCS3D01G163900 chr6D 463711318 463712113 795 True 1184.00 1184 93.5240 56 854 1 chr6D.!!$R4 798
10 TraesCS3D01G163900 chr6D 106950417 106951219 802 False 987.00 987 89.7150 90 853 1 chr6D.!!$F1 763
11 TraesCS3D01G163900 chr6D 5905100 5906161 1061 False 345.00 357 88.0715 8027 8320 2 chr6D.!!$F4 293
12 TraesCS3D01G163900 chr1D 29834295 29835197 902 True 1151.00 1151 90.6080 1 854 1 chr1D.!!$R1 853
13 TraesCS3D01G163900 chr1D 307338378 307339114 736 False 1048.00 1048 92.3900 1 740 1 chr1D.!!$F3 739
14 TraesCS3D01G163900 chr7D 629617030 629617916 886 True 1109.00 1109 89.9100 1 854 1 chr7D.!!$R1 853
15 TraesCS3D01G163900 chr7D 417354305 417355075 770 False 929.00 929 89.2030 1 740 1 chr7D.!!$F3 739
16 TraesCS3D01G163900 chr7D 412389851 412390632 781 False 885.00 885 88.0710 1 740 1 chr7D.!!$F2 739
17 TraesCS3D01G163900 chr2B 88973383 88974232 849 True 948.00 948 87.0260 1 854 1 chr2B.!!$R1 853

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
856 988 0.038526 TGACCGCGGAGAGAAAAGAC 60.039 55.000 35.9 9.52 0.00 3.01 F
876 1008 0.110373 GCTGGGCGTTAGTGTTTTCG 60.110 55.000 0.0 0.00 0.00 3.46 F
1323 1459 0.620556 GGAAGGACAGGAGCATGGAA 59.379 55.000 0.0 0.00 0.00 3.53 F
2074 2212 0.852136 GCCGTGTTGTTGAATGTTGC 59.148 50.000 0.0 0.00 0.00 4.17 F
2318 2456 3.562182 TGGCGAGGTATGATCTTCTGTA 58.438 45.455 0.0 0.00 0.00 2.74 F
3747 5613 1.551883 TGGCGTTTCCTTACTACTCCC 59.448 52.381 0.0 0.00 35.26 4.30 F
3748 5614 1.829849 GGCGTTTCCTTACTACTCCCT 59.170 52.381 0.0 0.00 0.00 4.20 F
5147 7015 0.670162 CCAAGCCTGTGAAAGTGTGG 59.330 55.000 0.0 0.00 0.00 4.17 F
5734 7603 5.389830 CGATCCATATTAATTGACGCTGGTG 60.390 44.000 0.0 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2212 0.958091 TTGTGTCCTTGCGGAATTGG 59.042 50.000 0.00 0.0 42.08 3.16 R
2377 2515 9.145865 CTCAGAATACAGAAGGAAGTAAAAGTC 57.854 37.037 0.00 0.0 0.00 3.01 R
3096 4962 5.446073 GCACGAGACCTACATTAAGAAAAGC 60.446 44.000 0.00 0.0 0.00 3.51 R
3577 5443 0.038310 ACCAAGGGCCTGAGCTTTAC 59.962 55.000 6.92 0.0 39.73 2.01 R
3889 5755 0.627451 TGCTACTCCCTCCGTTCCTA 59.373 55.000 0.00 0.0 0.00 2.94 R
4959 6827 0.469070 CAGAGGATGGGAAGAGCTGG 59.531 60.000 0.00 0.0 0.00 4.85 R
6138 8008 4.973168 ACTGTCATCTTGAAACTTAGCCA 58.027 39.130 0.00 0.0 0.00 4.75 R
6993 8863 3.444916 CGTGTCGCCTGAATATACAACT 58.555 45.455 0.00 0.0 0.00 3.16 R
7843 9721 1.676006 CAGGAGGCGTGTCAAAAACTT 59.324 47.619 0.00 0.0 0.00 2.66 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
166 196 2.433664 CAGTAACCACGCGTCCCC 60.434 66.667 9.86 0.00 0.00 4.81
212 289 1.446445 CGGTTGCCATGTTGCCATG 60.446 57.895 0.00 0.00 46.65 3.66
215 292 1.149987 GTTGCCATGTTGCCATGTTG 58.850 50.000 2.81 0.00 45.83 3.33
255 362 1.888512 CTACAGTTGCCATGGTTGCTT 59.111 47.619 14.67 0.00 0.00 3.91
269 376 0.673437 TTGCTTAACTGCAGTTGCCC 59.327 50.000 36.50 24.35 44.27 5.36
539 655 1.153061 TGTGTGGGAGAGGAGACGT 59.847 57.895 0.00 0.00 0.00 4.34
642 770 4.167554 GGCAACAAATAACATGTTCGGA 57.832 40.909 15.85 0.00 38.90 4.55
676 804 0.746923 GCCATCTGCTCATGCTCACA 60.747 55.000 0.00 0.00 40.48 3.58
761 893 2.565391 TGAAAGAATGGGCAGTCGTAGA 59.435 45.455 0.00 0.00 0.00 2.59
854 986 0.790814 GTTGACCGCGGAGAGAAAAG 59.209 55.000 35.90 0.93 0.00 2.27
855 987 0.677288 TTGACCGCGGAGAGAAAAGA 59.323 50.000 35.90 3.60 0.00 2.52
856 988 0.038526 TGACCGCGGAGAGAAAAGAC 60.039 55.000 35.90 9.52 0.00 3.01
857 989 1.071567 GACCGCGGAGAGAAAAGACG 61.072 60.000 35.90 0.00 0.00 4.18
858 990 2.445438 CCGCGGAGAGAAAAGACGC 61.445 63.158 24.07 0.00 46.04 5.19
859 991 4.580835 GCGGAGAGAAAAGACGCT 57.419 55.556 0.00 0.00 46.02 5.07
860 992 2.074124 GCGGAGAGAAAAGACGCTG 58.926 57.895 0.00 0.00 46.02 5.18
861 993 1.355066 GCGGAGAGAAAAGACGCTGG 61.355 60.000 0.00 0.00 46.02 4.85
862 994 0.737715 CGGAGAGAAAAGACGCTGGG 60.738 60.000 0.00 0.00 0.00 4.45
863 995 1.021920 GGAGAGAAAAGACGCTGGGC 61.022 60.000 0.00 0.00 0.00 5.36
875 1007 3.767287 GCTGGGCGTTAGTGTTTTC 57.233 52.632 0.00 0.00 0.00 2.29
876 1008 0.110373 GCTGGGCGTTAGTGTTTTCG 60.110 55.000 0.00 0.00 0.00 3.46
1323 1459 0.620556 GGAAGGACAGGAGCATGGAA 59.379 55.000 0.00 0.00 0.00 3.53
1606 1742 4.970662 ATCCATTTCATGCACTGTGTAC 57.029 40.909 9.86 0.00 0.00 2.90
1626 1762 4.585955 ACCATATACTGCTCCGTGTAAG 57.414 45.455 0.00 0.00 0.00 2.34
1629 1765 2.846039 ATACTGCTCCGTGTAAGTCG 57.154 50.000 0.00 0.00 0.00 4.18
1658 1794 1.202842 TGGGATACTGGCTGCATGATG 60.203 52.381 0.50 0.00 0.00 3.07
1763 1901 4.518970 AGCGTGGTATCAGTGAATTTGTTT 59.481 37.500 0.00 0.00 0.00 2.83
1764 1902 4.616802 GCGTGGTATCAGTGAATTTGTTTG 59.383 41.667 0.00 0.00 0.00 2.93
1766 1904 5.851177 CGTGGTATCAGTGAATTTGTTTGTC 59.149 40.000 0.00 0.00 0.00 3.18
2017 2155 8.135382 ACTTTACACACTTGGTCTATCTGTAT 57.865 34.615 0.00 0.00 0.00 2.29
2074 2212 0.852136 GCCGTGTTGTTGAATGTTGC 59.148 50.000 0.00 0.00 0.00 4.17
2318 2456 3.562182 TGGCGAGGTATGATCTTCTGTA 58.438 45.455 0.00 0.00 0.00 2.74
2377 2515 4.398247 GCTTACACAAGAAGCTCGAATTG 58.602 43.478 0.19 0.00 44.83 2.32
2516 2654 6.089551 CCTTCATCGCTAAAATGTAGTATCCG 59.910 42.308 0.00 0.00 0.00 4.18
3577 5443 8.156820 AGAAATTAAAGGAAAATTTGACCCTGG 58.843 33.333 9.98 0.00 36.82 4.45
3652 5518 2.398588 TGGGAACTCTGTGAAGACTGT 58.601 47.619 0.00 0.00 0.00 3.55
3669 5535 4.160626 AGACTGTAGCTGGTAGAATGGTTC 59.839 45.833 0.00 0.00 0.00 3.62
3694 5560 6.611381 GTGCTGATTGCTAAACTATTGAACA 58.389 36.000 0.00 0.00 43.37 3.18
3741 5607 1.679032 GGCTCATGGCGTTTCCTTACT 60.679 52.381 0.00 0.00 42.94 2.24
3742 5608 2.419574 GGCTCATGGCGTTTCCTTACTA 60.420 50.000 0.00 0.00 42.94 1.82
3743 5609 2.608090 GCTCATGGCGTTTCCTTACTAC 59.392 50.000 0.00 0.00 35.26 2.73
3744 5610 3.679083 GCTCATGGCGTTTCCTTACTACT 60.679 47.826 0.00 0.00 35.26 2.57
3745 5611 4.113354 CTCATGGCGTTTCCTTACTACTC 58.887 47.826 0.00 0.00 35.26 2.59
3746 5612 3.118884 TCATGGCGTTTCCTTACTACTCC 60.119 47.826 0.00 0.00 35.26 3.85
3747 5613 1.551883 TGGCGTTTCCTTACTACTCCC 59.448 52.381 0.00 0.00 35.26 4.30
3748 5614 1.829849 GGCGTTTCCTTACTACTCCCT 59.170 52.381 0.00 0.00 0.00 4.20
3749 5615 2.159128 GGCGTTTCCTTACTACTCCCTC 60.159 54.545 0.00 0.00 0.00 4.30
3750 5616 2.159128 GCGTTTCCTTACTACTCCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
3751 5617 2.098770 CGTTTCCTTACTACTCCCTCCG 59.901 54.545 0.00 0.00 0.00 4.63
3752 5618 3.095332 GTTTCCTTACTACTCCCTCCGT 58.905 50.000 0.00 0.00 0.00 4.69
3753 5619 3.463048 TTCCTTACTACTCCCTCCGTT 57.537 47.619 0.00 0.00 0.00 4.44
3754 5620 3.010200 TCCTTACTACTCCCTCCGTTC 57.990 52.381 0.00 0.00 0.00 3.95
3755 5621 2.030371 CCTTACTACTCCCTCCGTTCC 58.970 57.143 0.00 0.00 0.00 3.62
3756 5622 2.357986 CCTTACTACTCCCTCCGTTCCT 60.358 54.545 0.00 0.00 0.00 3.36
3757 5623 3.117738 CCTTACTACTCCCTCCGTTCCTA 60.118 52.174 0.00 0.00 0.00 2.94
3758 5624 4.530875 CTTACTACTCCCTCCGTTCCTAA 58.469 47.826 0.00 0.00 0.00 2.69
3759 5625 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3760 5626 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3761 5627 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3762 5628 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3763 5629 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
3764 5630 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3765 5631 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3766 5632 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3767 5633 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3768 5634 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3769 5635 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3770 5636 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3771 5637 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
3772 5638 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
3846 5712 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3847 5713 6.471146 AGTGTAGATTCACTCATTTTGCTCT 58.529 36.000 0.00 0.00 44.07 4.09
3848 5714 6.370994 AGTGTAGATTCACTCATTTTGCTCTG 59.629 38.462 0.00 0.00 44.07 3.35
3849 5715 6.148480 GTGTAGATTCACTCATTTTGCTCTGT 59.852 38.462 0.00 0.00 35.68 3.41
3850 5716 7.331934 GTGTAGATTCACTCATTTTGCTCTGTA 59.668 37.037 0.00 0.00 35.68 2.74
3851 5717 8.043113 TGTAGATTCACTCATTTTGCTCTGTAT 58.957 33.333 0.00 0.00 0.00 2.29
3852 5718 7.317842 AGATTCACTCATTTTGCTCTGTATG 57.682 36.000 0.00 0.00 0.00 2.39
3853 5719 6.883217 AGATTCACTCATTTTGCTCTGTATGT 59.117 34.615 0.00 0.00 0.00 2.29
3854 5720 8.043113 AGATTCACTCATTTTGCTCTGTATGTA 58.957 33.333 0.00 0.00 0.00 2.29
3855 5721 7.601073 TTCACTCATTTTGCTCTGTATGTAG 57.399 36.000 0.00 0.00 0.00 2.74
3856 5722 6.701340 TCACTCATTTTGCTCTGTATGTAGT 58.299 36.000 0.00 0.00 0.00 2.73
3857 5723 6.813649 TCACTCATTTTGCTCTGTATGTAGTC 59.186 38.462 0.00 0.00 0.00 2.59
3858 5724 6.591448 CACTCATTTTGCTCTGTATGTAGTCA 59.409 38.462 0.00 0.00 0.00 3.41
3859 5725 6.591834 ACTCATTTTGCTCTGTATGTAGTCAC 59.408 38.462 0.00 0.00 0.00 3.67
3860 5726 6.701340 TCATTTTGCTCTGTATGTAGTCACT 58.299 36.000 0.00 0.00 0.00 3.41
3861 5727 6.813649 TCATTTTGCTCTGTATGTAGTCACTC 59.186 38.462 0.00 0.00 0.00 3.51
3862 5728 4.720649 TTGCTCTGTATGTAGTCACTCC 57.279 45.455 0.00 0.00 0.00 3.85
3863 5729 3.969553 TGCTCTGTATGTAGTCACTCCT 58.030 45.455 0.00 0.00 0.00 3.69
3864 5730 4.344978 TGCTCTGTATGTAGTCACTCCTT 58.655 43.478 0.00 0.00 0.00 3.36
3865 5731 4.158579 TGCTCTGTATGTAGTCACTCCTTG 59.841 45.833 0.00 0.00 0.00 3.61
3866 5732 4.399618 GCTCTGTATGTAGTCACTCCTTGA 59.600 45.833 0.00 0.00 0.00 3.02
3867 5733 5.105716 GCTCTGTATGTAGTCACTCCTTGAA 60.106 44.000 0.00 0.00 35.39 2.69
3868 5734 6.572509 GCTCTGTATGTAGTCACTCCTTGAAA 60.573 42.308 0.00 0.00 35.39 2.69
3869 5735 7.482169 TCTGTATGTAGTCACTCCTTGAAAT 57.518 36.000 0.00 0.00 35.39 2.17
3870 5736 7.548097 TCTGTATGTAGTCACTCCTTGAAATC 58.452 38.462 0.00 0.00 35.39 2.17
3871 5737 7.397476 TCTGTATGTAGTCACTCCTTGAAATCT 59.603 37.037 0.00 0.00 35.39 2.40
3872 5738 7.907389 TGTATGTAGTCACTCCTTGAAATCTT 58.093 34.615 0.00 0.00 35.39 2.40
3873 5739 8.375506 TGTATGTAGTCACTCCTTGAAATCTTT 58.624 33.333 0.00 0.00 35.39 2.52
3874 5740 9.871238 GTATGTAGTCACTCCTTGAAATCTTTA 57.129 33.333 0.00 0.00 35.39 1.85
3876 5742 8.190326 TGTAGTCACTCCTTGAAATCTTTAGA 57.810 34.615 0.00 0.00 35.39 2.10
3877 5743 8.647796 TGTAGTCACTCCTTGAAATCTTTAGAA 58.352 33.333 0.00 0.00 35.39 2.10
3878 5744 9.490379 GTAGTCACTCCTTGAAATCTTTAGAAA 57.510 33.333 0.00 0.00 35.39 2.52
3879 5745 8.614469 AGTCACTCCTTGAAATCTTTAGAAAG 57.386 34.615 0.00 0.00 35.39 2.62
3880 5746 8.432805 AGTCACTCCTTGAAATCTTTAGAAAGA 58.567 33.333 7.15 7.15 41.72 2.52
3881 5747 8.499967 GTCACTCCTTGAAATCTTTAGAAAGAC 58.500 37.037 6.85 0.00 40.95 3.01
3882 5748 8.210946 TCACTCCTTGAAATCTTTAGAAAGACA 58.789 33.333 6.85 0.00 46.80 3.41
3883 5749 8.840321 CACTCCTTGAAATCTTTAGAAAGACAA 58.160 33.333 6.85 6.61 46.80 3.18
3884 5750 9.408648 ACTCCTTGAAATCTTTAGAAAGACAAA 57.591 29.630 6.85 0.22 46.80 2.83
3898 5764 9.947433 TTAGAAAGACAAATATTTAGGAACGGA 57.053 29.630 0.00 0.00 0.00 4.69
3899 5765 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3900 5766 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3901 5767 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3902 5768 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3903 5769 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4515 6382 4.824289 ACATTTTTCCAATGACTGCATCC 58.176 39.130 1.59 0.00 32.35 3.51
4885 6753 3.662759 TTTCCCTCCTTTGTGACACTT 57.337 42.857 7.20 0.00 0.00 3.16
4959 6827 4.396790 TCACGTCTTAATTTTGTATGCCCC 59.603 41.667 0.00 0.00 0.00 5.80
5147 7015 0.670162 CCAAGCCTGTGAAAGTGTGG 59.330 55.000 0.00 0.00 0.00 4.17
5338 7206 5.711506 TCTTCTCTGGCAATTTAATGCTTGA 59.288 36.000 1.33 0.41 45.68 3.02
5734 7603 5.389830 CGATCCATATTAATTGACGCTGGTG 60.390 44.000 0.00 0.00 0.00 4.17
5817 7686 7.407337 GGAGTACTATTTATTTTGCAGGTTCG 58.593 38.462 0.00 0.00 0.00 3.95
5823 7692 9.174166 ACTATTTATTTTGCAGGTTCGACTTAT 57.826 29.630 0.00 0.00 0.00 1.73
6138 8008 9.713684 TGATATTTTAGATGAACAGGGGAATTT 57.286 29.630 0.00 0.00 0.00 1.82
6139 8009 9.971922 GATATTTTAGATGAACAGGGGAATTTG 57.028 33.333 0.00 0.00 0.00 2.32
7139 9009 5.005299 GTGCGCACAATAATTACCCATTTTC 59.995 40.000 34.52 0.04 0.00 2.29
7173 9043 3.458044 TGACCTCTGTCCATAGTGTCT 57.542 47.619 0.00 0.00 41.01 3.41
7234 9104 7.307694 CAACAGCACTAAATTAGATCTTGCAA 58.692 34.615 14.07 0.00 0.00 4.08
7482 9356 0.984230 TGACCCACTTTAGCCAGAGG 59.016 55.000 0.00 0.00 0.00 3.69
7581 9455 4.481112 GATTTGCCCGTGCTGCCG 62.481 66.667 0.00 0.00 38.71 5.69
7762 9640 1.269517 CCGAGGATTCTCAGCTGTAGC 60.270 57.143 14.67 3.34 39.95 3.58
7843 9721 1.681793 GGCTCTCGCTGTCATACCTTA 59.318 52.381 0.00 0.00 36.09 2.69
7860 9738 3.314357 ACCTTAAGTTTTTGACACGCCTC 59.686 43.478 0.97 0.00 0.00 4.70
8028 9920 7.741027 TCGAGTAGACTGGTTATATGTAAGG 57.259 40.000 0.00 0.00 0.00 2.69
8108 10000 9.547279 AGATAAAATTTCTATGGAACCCTTTGT 57.453 29.630 0.00 0.00 0.00 2.83
8126 10018 7.147391 ACCCTTTGTTTTGTAGGAATGGATTTT 60.147 33.333 0.00 0.00 0.00 1.82
8230 10125 7.934855 ATCCTATGCATTAAATGACATCTCC 57.065 36.000 3.54 0.00 32.25 3.71
8320 10985 2.025321 TCCTATGAACCAAAGAAGGCCC 60.025 50.000 0.00 0.00 0.00 5.80
8326 10991 1.115326 ACCAAAGAAGGCCCAAGTGC 61.115 55.000 0.00 0.00 0.00 4.40
8332 10997 1.228675 AAGGCCCAAGTGCTTCCTG 60.229 57.895 0.00 0.00 0.00 3.86
8364 11029 2.496817 CTGTCCTACTGGAGCGGC 59.503 66.667 0.00 0.00 44.16 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 171 4.639824 GTGGTTACTGACACGCGA 57.360 55.556 15.93 0.00 0.00 5.87
166 196 3.585990 GACCATGGCAATCGCGGG 61.586 66.667 13.04 0.00 39.92 6.13
191 222 1.365633 GGCAACATGGCAACCGAAA 59.634 52.632 0.00 0.00 43.14 3.46
212 289 0.383231 AGCAACTGCAGTTCAGCAAC 59.617 50.000 31.69 17.85 46.76 4.17
215 292 0.664761 TTCAGCAACTGCAGTTCAGC 59.335 50.000 28.97 27.45 46.76 4.26
255 362 2.027192 CCTAAGAGGGCAACTGCAGTTA 60.027 50.000 30.67 12.58 44.36 2.24
269 376 0.895530 TCCGGCACTTGACCTAAGAG 59.104 55.000 0.00 0.00 39.76 2.85
539 655 2.751036 CACCATCGCCCACATGCA 60.751 61.111 0.00 0.00 0.00 3.96
629 757 8.095169 ACTCTCTTTTTACTCCGAACATGTTAT 58.905 33.333 11.95 0.00 0.00 1.89
642 770 4.457257 GCAGATGGCAACTCTCTTTTTACT 59.543 41.667 0.00 0.00 43.97 2.24
761 893 2.065799 ACCACTTCTGTTCCCCATCTT 58.934 47.619 0.00 0.00 0.00 2.40
793 925 3.044305 GAAACTGCTGTCGCGCCT 61.044 61.111 0.00 0.00 39.65 5.52
857 989 0.110373 CGAAAACACTAACGCCCAGC 60.110 55.000 0.00 0.00 0.00 4.85
858 990 1.223187 ACGAAAACACTAACGCCCAG 58.777 50.000 0.00 0.00 0.00 4.45
859 991 1.666054 AACGAAAACACTAACGCCCA 58.334 45.000 0.00 0.00 0.00 5.36
860 992 3.876242 TTAACGAAAACACTAACGCCC 57.124 42.857 0.00 0.00 0.00 6.13
861 993 7.834821 TTTTATTAACGAAAACACTAACGCC 57.165 32.000 0.00 0.00 0.00 5.68
862 994 7.884222 GCATTTTATTAACGAAAACACTAACGC 59.116 33.333 0.00 0.00 0.00 4.84
863 995 8.360132 GGCATTTTATTAACGAAAACACTAACG 58.640 33.333 0.00 0.00 0.00 3.18
864 996 9.401873 AGGCATTTTATTAACGAAAACACTAAC 57.598 29.630 0.00 0.00 0.00 2.34
867 999 9.968870 TTTAGGCATTTTATTAACGAAAACACT 57.031 25.926 0.00 2.76 0.00 3.55
1035 1168 1.604915 GGTTTGGGAGAGAGGGAGC 59.395 63.158 0.00 0.00 0.00 4.70
1263 1399 1.665679 CGCATCTTATTGAACGCCACT 59.334 47.619 0.00 0.00 0.00 4.00
1323 1459 2.032681 GCCCTGCGGTTCTTGAGT 59.967 61.111 0.00 0.00 0.00 3.41
1606 1742 4.547532 GACTTACACGGAGCAGTATATGG 58.452 47.826 0.00 0.00 0.00 2.74
1626 1762 1.141019 TATCCCAACTGCGCTCGAC 59.859 57.895 9.73 0.00 0.00 4.20
1629 1765 0.811616 CCAGTATCCCAACTGCGCTC 60.812 60.000 9.73 0.00 44.56 5.03
1658 1794 2.289195 TGTTCCCTGACACCGACATTAC 60.289 50.000 0.00 0.00 0.00 1.89
1763 1901 1.202371 GCATGTTACGATCTCCCGACA 60.202 52.381 0.00 0.00 0.00 4.35
1764 1902 1.067212 AGCATGTTACGATCTCCCGAC 59.933 52.381 0.00 0.00 0.00 4.79
1766 1904 1.860950 CAAGCATGTTACGATCTCCCG 59.139 52.381 0.00 0.00 0.00 5.14
1837 1975 1.549037 GCCCATTACAACCAGTTGGGA 60.549 52.381 14.62 3.43 46.98 4.37
2074 2212 0.958091 TTGTGTCCTTGCGGAATTGG 59.042 50.000 0.00 0.00 42.08 3.16
2377 2515 9.145865 CTCAGAATACAGAAGGAAGTAAAAGTC 57.854 37.037 0.00 0.00 0.00 3.01
3096 4962 5.446073 GCACGAGACCTACATTAAGAAAAGC 60.446 44.000 0.00 0.00 0.00 3.51
3577 5443 0.038310 ACCAAGGGCCTGAGCTTTAC 59.962 55.000 6.92 0.00 39.73 2.01
3652 5518 2.418197 GCACGAACCATTCTACCAGCTA 60.418 50.000 0.00 0.00 0.00 3.32
3741 5607 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3742 5608 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3743 5609 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3744 5610 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3745 5611 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3746 5612 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
3775 5641 9.354673 CCATATGTGGTAGTCCATTTAAAATCT 57.645 33.333 0.00 0.00 46.20 2.40
3776 5642 9.349713 TCCATATGTGGTAGTCCATTTAAAATC 57.650 33.333 8.51 0.00 46.20 2.17
3777 5643 9.881773 ATCCATATGTGGTAGTCCATTTAAAAT 57.118 29.630 8.51 0.00 46.20 1.82
3778 5644 9.130661 CATCCATATGTGGTAGTCCATTTAAAA 57.869 33.333 8.51 0.00 46.20 1.52
3779 5645 8.278639 ACATCCATATGTGGTAGTCCATTTAAA 58.721 33.333 8.51 0.00 44.79 1.52
3780 5646 7.811282 ACATCCATATGTGGTAGTCCATTTAA 58.189 34.615 8.51 0.00 44.79 1.52
3781 5647 7.387265 ACATCCATATGTGGTAGTCCATTTA 57.613 36.000 8.51 0.00 44.79 1.40
3782 5648 6.266131 ACATCCATATGTGGTAGTCCATTT 57.734 37.500 8.51 0.00 44.79 2.32
3783 5649 5.912149 ACATCCATATGTGGTAGTCCATT 57.088 39.130 8.51 0.00 44.79 3.16
3784 5650 8.860517 ATATACATCCATATGTGGTAGTCCAT 57.139 34.615 8.51 3.29 45.99 3.41
3785 5651 9.421399 CTATATACATCCATATGTGGTAGTCCA 57.579 37.037 8.51 1.36 45.99 4.02
3786 5652 9.642343 TCTATATACATCCATATGTGGTAGTCC 57.358 37.037 8.51 0.00 45.99 3.85
3788 5654 9.990868 TGTCTATATACATCCATATGTGGTAGT 57.009 33.333 8.51 10.44 45.99 2.73
3824 5690 6.148480 ACAGAGCAAAATGAGTGAATCTACAC 59.852 38.462 0.00 0.00 40.60 2.90
3825 5691 6.233434 ACAGAGCAAAATGAGTGAATCTACA 58.767 36.000 0.00 0.00 0.00 2.74
3826 5692 6.734104 ACAGAGCAAAATGAGTGAATCTAC 57.266 37.500 0.00 0.00 0.00 2.59
3827 5693 8.043113 ACATACAGAGCAAAATGAGTGAATCTA 58.957 33.333 0.00 0.00 0.00 1.98
3828 5694 6.883217 ACATACAGAGCAAAATGAGTGAATCT 59.117 34.615 0.00 0.00 0.00 2.40
3829 5695 7.081526 ACATACAGAGCAAAATGAGTGAATC 57.918 36.000 0.00 0.00 0.00 2.52
3830 5696 7.826252 ACTACATACAGAGCAAAATGAGTGAAT 59.174 33.333 0.00 0.00 0.00 2.57
3831 5697 7.161404 ACTACATACAGAGCAAAATGAGTGAA 58.839 34.615 0.00 0.00 0.00 3.18
3832 5698 6.701340 ACTACATACAGAGCAAAATGAGTGA 58.299 36.000 0.00 0.00 0.00 3.41
3833 5699 6.591448 TGACTACATACAGAGCAAAATGAGTG 59.409 38.462 0.00 0.00 0.00 3.51
3834 5700 6.591834 GTGACTACATACAGAGCAAAATGAGT 59.408 38.462 0.00 0.00 0.00 3.41
3835 5701 6.815641 AGTGACTACATACAGAGCAAAATGAG 59.184 38.462 0.00 0.00 0.00 2.90
3836 5702 6.701340 AGTGACTACATACAGAGCAAAATGA 58.299 36.000 0.00 0.00 0.00 2.57
3837 5703 6.036517 GGAGTGACTACATACAGAGCAAAATG 59.963 42.308 0.00 0.00 0.00 2.32
3838 5704 6.070538 AGGAGTGACTACATACAGAGCAAAAT 60.071 38.462 0.00 0.00 0.00 1.82
3839 5705 5.246203 AGGAGTGACTACATACAGAGCAAAA 59.754 40.000 0.00 0.00 0.00 2.44
3840 5706 4.772624 AGGAGTGACTACATACAGAGCAAA 59.227 41.667 0.00 0.00 0.00 3.68
3841 5707 4.344978 AGGAGTGACTACATACAGAGCAA 58.655 43.478 0.00 0.00 0.00 3.91
3842 5708 3.969553 AGGAGTGACTACATACAGAGCA 58.030 45.455 0.00 0.00 0.00 4.26
3843 5709 4.399618 TCAAGGAGTGACTACATACAGAGC 59.600 45.833 0.00 0.00 0.00 4.09
3844 5710 6.516739 TTCAAGGAGTGACTACATACAGAG 57.483 41.667 0.00 0.00 35.39 3.35
3845 5711 6.911250 TTTCAAGGAGTGACTACATACAGA 57.089 37.500 0.00 0.00 35.39 3.41
3846 5712 7.551585 AGATTTCAAGGAGTGACTACATACAG 58.448 38.462 0.00 0.00 35.39 2.74
3847 5713 7.482169 AGATTTCAAGGAGTGACTACATACA 57.518 36.000 0.00 0.00 35.39 2.29
3848 5714 8.779354 AAAGATTTCAAGGAGTGACTACATAC 57.221 34.615 0.00 0.00 35.39 2.39
3850 5716 8.816894 TCTAAAGATTTCAAGGAGTGACTACAT 58.183 33.333 0.00 0.00 35.39 2.29
3851 5717 8.190326 TCTAAAGATTTCAAGGAGTGACTACA 57.810 34.615 0.00 0.00 35.39 2.74
3852 5718 9.490379 TTTCTAAAGATTTCAAGGAGTGACTAC 57.510 33.333 0.00 0.00 35.39 2.73
3853 5719 9.712305 CTTTCTAAAGATTTCAAGGAGTGACTA 57.288 33.333 0.00 0.00 38.28 2.59
3854 5720 8.432805 TCTTTCTAAAGATTTCAAGGAGTGACT 58.567 33.333 1.00 0.00 39.95 3.41
3855 5721 8.499967 GTCTTTCTAAAGATTTCAAGGAGTGAC 58.500 37.037 8.31 0.00 45.83 3.67
3856 5722 8.210946 TGTCTTTCTAAAGATTTCAAGGAGTGA 58.789 33.333 8.31 0.00 45.83 3.41
3857 5723 8.383318 TGTCTTTCTAAAGATTTCAAGGAGTG 57.617 34.615 8.31 0.00 45.83 3.51
3858 5724 8.980481 TTGTCTTTCTAAAGATTTCAAGGAGT 57.020 30.769 8.31 0.00 45.83 3.85
3872 5738 9.947433 TCCGTTCCTAAATATTTGTCTTTCTAA 57.053 29.630 11.05 0.00 0.00 2.10
3873 5739 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3874 5740 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3875 5741 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3876 5742 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3877 5743 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3878 5744 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3879 5745 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3880 5746 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3881 5747 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3882 5748 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3883 5749 5.011840 GCTACTCCCTCCGTTCCTAAATATT 59.988 44.000 0.00 0.00 0.00 1.28
3884 5750 4.527427 GCTACTCCCTCCGTTCCTAAATAT 59.473 45.833 0.00 0.00 0.00 1.28
3885 5751 3.893813 GCTACTCCCTCCGTTCCTAAATA 59.106 47.826 0.00 0.00 0.00 1.40
3886 5752 2.699321 GCTACTCCCTCCGTTCCTAAAT 59.301 50.000 0.00 0.00 0.00 1.40
3887 5753 2.105766 GCTACTCCCTCCGTTCCTAAA 58.894 52.381 0.00 0.00 0.00 1.85
3888 5754 1.006281 TGCTACTCCCTCCGTTCCTAA 59.994 52.381 0.00 0.00 0.00 2.69
3889 5755 0.627451 TGCTACTCCCTCCGTTCCTA 59.373 55.000 0.00 0.00 0.00 2.94
3890 5756 0.971447 GTGCTACTCCCTCCGTTCCT 60.971 60.000 0.00 0.00 0.00 3.36
3891 5757 1.255667 TGTGCTACTCCCTCCGTTCC 61.256 60.000 0.00 0.00 0.00 3.62
3892 5758 0.824759 ATGTGCTACTCCCTCCGTTC 59.175 55.000 0.00 0.00 0.00 3.95
3893 5759 2.154567 TATGTGCTACTCCCTCCGTT 57.845 50.000 0.00 0.00 0.00 4.44
3894 5760 1.964223 CATATGTGCTACTCCCTCCGT 59.036 52.381 0.00 0.00 0.00 4.69
3895 5761 1.964223 ACATATGTGCTACTCCCTCCG 59.036 52.381 7.78 0.00 0.00 4.63
3896 5762 3.733337 CAACATATGTGCTACTCCCTCC 58.267 50.000 9.63 0.00 0.00 4.30
3897 5763 3.134458 GCAACATATGTGCTACTCCCTC 58.866 50.000 9.63 0.00 0.00 4.30
3898 5764 2.774234 AGCAACATATGTGCTACTCCCT 59.226 45.455 22.94 5.87 37.11 4.20
3899 5765 3.199880 AGCAACATATGTGCTACTCCC 57.800 47.619 22.94 3.70 37.11 4.30
3900 5766 6.293626 CCATTAAGCAACATATGTGCTACTCC 60.294 42.308 23.88 5.35 38.01 3.85
3901 5767 6.293626 CCCATTAAGCAACATATGTGCTACTC 60.294 42.308 23.88 7.02 38.01 2.59
3902 5768 5.532406 CCCATTAAGCAACATATGTGCTACT 59.468 40.000 23.88 16.00 38.01 2.57
3903 5769 5.299279 ACCCATTAAGCAACATATGTGCTAC 59.701 40.000 23.88 10.13 38.01 3.58
4515 6382 6.802608 AGCATGGATGAATAAACATTCACAG 58.197 36.000 2.35 0.00 42.57 3.66
4885 6753 4.892934 AGGAACTTCCATGTTTTTACTGCA 59.107 37.500 10.57 0.00 39.61 4.41
4959 6827 0.469070 CAGAGGATGGGAAGAGCTGG 59.531 60.000 0.00 0.00 0.00 4.85
6138 8008 4.973168 ACTGTCATCTTGAAACTTAGCCA 58.027 39.130 0.00 0.00 0.00 4.75
6139 8009 6.166982 ACTACTGTCATCTTGAAACTTAGCC 58.833 40.000 0.00 0.00 0.00 3.93
6993 8863 3.444916 CGTGTCGCCTGAATATACAACT 58.555 45.455 0.00 0.00 0.00 3.16
7139 9009 4.714308 ACAGAGGTCAAGAGAAATAGGAGG 59.286 45.833 0.00 0.00 0.00 4.30
7173 9043 7.540400 CACATTAATTAAACGTGAAGAATGCCA 59.460 33.333 19.20 0.00 0.00 4.92
7482 9356 5.526479 GTCAAAGACCGGGATTTTAGGATAC 59.474 44.000 6.32 0.00 0.00 2.24
7722 9599 6.325919 TCGGGTTAAAATCATATGCCAATC 57.674 37.500 0.00 0.00 0.00 2.67
7762 9640 4.708177 CAATGTATCAGGTCTACAAGGGG 58.292 47.826 0.00 0.00 33.12 4.79
7843 9721 1.676006 CAGGAGGCGTGTCAAAAACTT 59.324 47.619 0.00 0.00 0.00 2.66
7860 9738 3.378427 TCGGATGACATATATCTCGCAGG 59.622 47.826 0.00 0.00 0.00 4.85
7988 9880 6.428771 GTCTACTCGAATTCTAGCTCATACCT 59.571 42.308 6.89 0.00 0.00 3.08
7989 9881 6.428771 AGTCTACTCGAATTCTAGCTCATACC 59.571 42.308 6.89 0.00 0.00 2.73
8005 9897 6.380190 GCCTTACATATAACCAGTCTACTCG 58.620 44.000 0.00 0.00 0.00 4.18
8028 9920 2.579410 TCCTACAAACCAAAGGAGGC 57.421 50.000 0.00 0.00 34.46 4.70
8100 9992 4.810345 TCCATTCCTACAAAACAAAGGGT 58.190 39.130 0.00 0.00 0.00 4.34
8294 10194 5.994668 GCCTTCTTTGGTTCATAGGATAGAG 59.005 44.000 0.00 0.00 0.00 2.43
8332 10997 2.825836 CAGGGGCGACATTCCAGC 60.826 66.667 0.00 0.00 0.00 4.85
8342 11007 2.363795 TCCAGTAGGACAGGGGCG 60.364 66.667 0.00 0.00 39.61 6.13
8364 11029 1.138859 TGGTTGGGATGAGATGCTACG 59.861 52.381 0.00 0.00 0.00 3.51
8378 11043 5.175859 AGTTTCAGTATATCACGTGGTTGG 58.824 41.667 17.00 0.00 0.00 3.77
8602 11280 3.070987 TACGGGGGAGGAGGAGAGC 62.071 68.421 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.