Multiple sequence alignment - TraesCS2A01G425900

Loading Multiple Alignment...

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 TraesCS2A01G425900 chr2A 100.000 3999 0 0 1 3999 679517106 679513108 0.000000e+00 7385.0
1 TraesCS2A01G425900 chr2A 88.889 81 7 2 1896 1974 679514404 679514324 9.150000e-17 99.0
2 TraesCS2A01G425900 chr2A 88.889 81 7 2 2703 2783 679515211 679515133 9.150000e-17 99.0
3 TraesCS2A01G425900 chr2D 94.715 1722 58 13 775 2468 536925892 536924176 0.000000e+00 2645.0
4 TraesCS2A01G425900 chr2D 95.553 742 32 1 6 747 94536692 94535952 0.000000e+00 1186.0
5 TraesCS2A01G425900 chr2D 94.943 613 26 4 2664 3273 536923851 536923241 0.000000e+00 955.0
6 TraesCS2A01G425900 chr2D 92.222 270 6 7 3670 3929 536922740 536922476 6.310000e-98 368.0
7 TraesCS2A01G425900 chr2D 91.016 256 18 3 2217 2468 536923812 536924066 1.380000e-89 340.0
8 TraesCS2A01G425900 chr2D 94.500 200 8 3 2469 2666 536924080 536923882 5.020000e-79 305.0
9 TraesCS2A01G425900 chr2D 94.000 200 8 4 2469 2666 536924162 536924359 2.340000e-77 300.0
10 TraesCS2A01G425900 chr2D 86.139 202 26 2 1970 2170 69541105 69540905 2.420000e-52 217.0
11 TraesCS2A01G425900 chr2D 77.489 231 13 13 3406 3613 536923065 536922851 7.070000e-18 102.0
12 TraesCS2A01G425900 chr2D 88.732 71 6 2 2713 2783 536924740 536924672 7.120000e-13 86.1
13 TraesCS2A01G425900 chr7D 95.850 747 31 0 1 747 180628100 180627354 0.000000e+00 1208.0
14 TraesCS2A01G425900 chr7D 95.850 747 31 0 1 747 515888606 515887860 0.000000e+00 1208.0
15 TraesCS2A01G425900 chr7D 87.019 208 26 1 1970 2176 329047509 329047302 2.400000e-57 233.0
16 TraesCS2A01G425900 chr3D 95.716 747 32 0 1 747 420652824 420652078 0.000000e+00 1203.0
17 TraesCS2A01G425900 chr3D 88.797 241 21 4 2234 2468 380956211 380955971 1.410000e-74 291.0
18 TraesCS2A01G425900 chr3D 92.935 184 8 5 2470 2651 380955958 380956138 3.060000e-66 263.0
19 TraesCS2A01G425900 chr3D 87.864 206 25 0 1967 2172 317203599 317203394 3.990000e-60 243.0
20 TraesCS2A01G425900 chr5D 95.582 747 33 0 1 747 478919079 478918333 0.000000e+00 1197.0
21 TraesCS2A01G425900 chr5D 95.206 751 32 1 1 747 454674634 454673884 0.000000e+00 1184.0
22 TraesCS2A01G425900 chr1D 95.582 747 31 1 1 747 324589897 324589153 0.000000e+00 1195.0
23 TraesCS2A01G425900 chr1D 95.448 747 34 0 1 747 211832292 211833038 0.000000e+00 1192.0
24 TraesCS2A01G425900 chr4D 95.181 747 36 0 1 747 90881404 90880658 0.000000e+00 1181.0
25 TraesCS2A01G425900 chr2B 82.017 1190 119 43 801 1926 638974418 638973260 0.000000e+00 924.0
26 TraesCS2A01G425900 chr2B 87.931 580 44 18 2700 3272 638973291 638972731 0.000000e+00 660.0
27 TraesCS2A01G425900 chr2B 89.655 261 10 4 3670 3913 638972264 638972004 2.320000e-82 316.0
28 TraesCS2A01G425900 chr2B 90.795 239 18 4 2234 2468 694890503 694890741 2.320000e-82 316.0
29 TraesCS2A01G425900 chr2B 93.158 190 7 5 2481 2666 694890743 694890556 1.420000e-69 274.0
30 TraesCS2A01G425900 chr5B 90.756 238 19 3 2234 2468 122293039 122292802 8.340000e-82 315.0
31 TraesCS2A01G425900 chr5B 88.333 240 23 3 2234 2468 541306743 541306504 2.350000e-72 283.0
32 TraesCS2A01G425900 chr5B 92.079 202 10 6 2469 2666 122292787 122292986 3.040000e-71 279.0
33 TraesCS2A01G425900 chr1B 91.026 234 17 2 2234 2463 119296746 119296513 3.000000e-81 313.0
34 TraesCS2A01G425900 chr1B 90.295 237 21 2 2234 2468 142799379 142799143 3.880000e-80 309.0
35 TraesCS2A01G425900 chr1B 92.857 196 8 5 2470 2662 142799130 142799322 3.040000e-71 279.0
36 TraesCS2A01G425900 chr4A 87.124 233 26 4 2234 2462 443377175 443377407 1.100000e-65 261.0
37 TraesCS2A01G425900 chr7B 91.579 190 10 4 2481 2666 742522934 742522747 1.430000e-64 257.0
38 TraesCS2A01G425900 chr7B 92.179 179 10 4 2470 2646 742481744 742481568 2.390000e-62 250.0
39 TraesCS2A01G425900 chr6B 92.778 180 9 3 2470 2646 34044307 34044485 1.430000e-64 257.0
40 TraesCS2A01G425900 chr6B 88.060 201 23 1 1972 2172 347751043 347750844 1.860000e-58 237.0
41 TraesCS2A01G425900 chr6B 85.990 207 27 2 1966 2172 424243303 424243507 1.870000e-53 220.0
42 TraesCS2A01G425900 chr7A 86.500 200 27 0 1966 2165 5650874 5651073 1.870000e-53 220.0
43 TraesCS2A01G425900 chr7A 85.854 205 26 2 1967 2171 504221348 504221549 8.700000e-52 215.0
44 TraesCS2A01G425900 chr5A 87.113 194 24 1 1970 2162 536817991 536818184 6.730000e-53 219.0


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 TraesCS2A01G425900 chr2A 679513108 679517106 3998 True 2527.666667 7385 92.592667 1 3999 3 chr2A.!!$R1 3998
1 TraesCS2A01G425900 chr2D 94535952 94536692 740 True 1186.000000 1186 95.553000 6 747 1 chr2D.!!$R2 741
2 TraesCS2A01G425900 chr2D 536922476 536925892 3416 True 743.516667 2645 90.433500 775 3929 6 chr2D.!!$R3 3154
3 TraesCS2A01G425900 chr2D 536923812 536924359 547 False 320.000000 340 92.508000 2217 2666 2 chr2D.!!$F1 449
4 TraesCS2A01G425900 chr7D 180627354 180628100 746 True 1208.000000 1208 95.850000 1 747 1 chr7D.!!$R1 746
5 TraesCS2A01G425900 chr7D 515887860 515888606 746 True 1208.000000 1208 95.850000 1 747 1 chr7D.!!$R3 746
6 TraesCS2A01G425900 chr3D 420652078 420652824 746 True 1203.000000 1203 95.716000 1 747 1 chr3D.!!$R3 746
7 TraesCS2A01G425900 chr5D 478918333 478919079 746 True 1197.000000 1197 95.582000 1 747 1 chr5D.!!$R2 746
8 TraesCS2A01G425900 chr5D 454673884 454674634 750 True 1184.000000 1184 95.206000 1 747 1 chr5D.!!$R1 746
9 TraesCS2A01G425900 chr1D 324589153 324589897 744 True 1195.000000 1195 95.582000 1 747 1 chr1D.!!$R1 746
10 TraesCS2A01G425900 chr1D 211832292 211833038 746 False 1192.000000 1192 95.448000 1 747 1 chr1D.!!$F1 746
11 TraesCS2A01G425900 chr4D 90880658 90881404 746 True 1181.000000 1181 95.181000 1 747 1 chr4D.!!$R1 746
12 TraesCS2A01G425900 chr2B 638972004 638974418 2414 True 633.333333 924 86.534333 801 3913 3 chr2B.!!$R2 3112

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
32 33 0.400815 TGGGTCTACCACAACAGGGT 60.401 55.000 0.81 0.00 46.80 4.34 F
739 746 1.411246 AGGCCATTGCATGCTGTAATG 59.589 47.619 20.33 18.87 45.82 1.90 F
2082 2161 1.431243 CTCCTACCTAGGCATCTCCCT 59.569 57.143 9.30 0.00 43.31 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1982 0.627451 AGCATCCAATCCAGAAGCCA 59.373 50.0 0.0 0.0 0.00 4.75 R
2125 2204 0.822164 TTACGGGAGGTGCTTAGAGC 59.178 55.0 0.0 0.0 42.82 4.09 R
3957 4450 0.181350 GCCCTGACCGATTCCATTCT 59.819 55.0 0.0 0.0 0.00 2.40 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
32 33 0.400815 TGGGTCTACCACAACAGGGT 60.401 55.000 0.81 0.00 46.80 4.34
50 51 5.428457 ACAGGGTCCATATGTCAGTTAATGA 59.572 40.000 1.24 0.00 34.79 2.57
59 60 7.935755 CCATATGTCAGTTAATGAAGGACAGAT 59.064 37.037 1.24 0.00 41.27 2.90
121 122 3.265737 ACATGATGGCAGTACTGGGTAAA 59.734 43.478 23.95 0.00 0.00 2.01
141 142 7.122204 GGGTAAAGCTGATTTAGTAACACCAAT 59.878 37.037 0.00 0.00 34.01 3.16
234 235 7.963532 ACTAGTTGAATAGTTCTCTTTGACCA 58.036 34.615 0.00 0.00 31.89 4.02
235 236 7.873505 ACTAGTTGAATAGTTCTCTTTGACCAC 59.126 37.037 0.00 0.00 31.89 4.16
236 237 6.591935 AGTTGAATAGTTCTCTTTGACCACA 58.408 36.000 0.00 0.00 0.00 4.17
242 243 3.138283 AGTTCTCTTTGACCACAATGGGA 59.862 43.478 0.00 0.00 43.37 4.37
255 256 4.584325 CCACAATGGGAAATAATGGATCGT 59.416 41.667 0.00 0.00 32.67 3.73
375 376 7.893124 ATACTCCGTATTTAAGAACAGAGGA 57.107 36.000 7.18 0.76 0.00 3.71
458 459 8.049117 AGAGGAAGCTTGAAATATGAACATGTA 58.951 33.333 2.10 0.00 0.00 2.29
459 460 8.757982 AGGAAGCTTGAAATATGAACATGTAT 57.242 30.769 2.10 0.00 0.00 2.29
591 598 2.313172 CGCTCACGCTCAAGTGCTT 61.313 57.895 0.00 0.00 41.61 3.91
608 615 3.194329 GTGCTTAACCTACTCCCTACGTT 59.806 47.826 0.00 0.00 0.00 3.99
621 628 1.719780 CCTACGTTCGTGAAAGACTGC 59.280 52.381 8.14 0.00 0.00 4.40
638 645 6.893958 AGACTGCACATTTAGAGATTTACG 57.106 37.500 0.00 0.00 0.00 3.18
645 652 6.966632 GCACATTTAGAGATTTACGCATTGAA 59.033 34.615 0.00 0.00 0.00 2.69
648 655 8.511321 ACATTTAGAGATTTACGCATTGAACAA 58.489 29.630 0.00 0.00 0.00 2.83
692 699 4.478206 AGTAGACTTATGTGTGCATGCT 57.522 40.909 20.33 0.00 36.58 3.79
706 713 5.066375 GTGTGCATGCTACCATTGAGATAAA 59.934 40.000 20.33 0.00 0.00 1.40
739 746 1.411246 AGGCCATTGCATGCTGTAATG 59.589 47.619 20.33 18.87 45.82 1.90
747 754 6.964807 ATTGCATGCTGTAATGAAGGATAA 57.035 33.333 20.33 0.00 31.51 1.75
748 755 6.772360 TTGCATGCTGTAATGAAGGATAAA 57.228 33.333 20.33 0.00 0.00 1.40
749 756 6.381481 TGCATGCTGTAATGAAGGATAAAG 57.619 37.500 20.33 0.00 0.00 1.85
750 757 5.218139 GCATGCTGTAATGAAGGATAAAGC 58.782 41.667 11.37 0.00 0.00 3.51
751 758 5.221106 GCATGCTGTAATGAAGGATAAAGCA 60.221 40.000 11.37 0.55 42.97 3.91
752 759 5.818136 TGCTGTAATGAAGGATAAAGCAC 57.182 39.130 0.00 0.00 34.68 4.40
753 760 4.332543 TGCTGTAATGAAGGATAAAGCACG 59.667 41.667 0.00 0.00 34.68 5.34
754 761 4.786609 GCTGTAATGAAGGATAAAGCACGC 60.787 45.833 0.00 0.00 0.00 5.34
755 762 3.308595 TGTAATGAAGGATAAAGCACGCG 59.691 43.478 3.53 3.53 0.00 6.01
756 763 2.024176 ATGAAGGATAAAGCACGCGT 57.976 45.000 5.58 5.58 0.00 6.01
757 764 2.658373 TGAAGGATAAAGCACGCGTA 57.342 45.000 13.44 0.00 0.00 4.42
758 765 2.264813 TGAAGGATAAAGCACGCGTAC 58.735 47.619 13.44 6.32 0.00 3.67
759 766 2.094390 TGAAGGATAAAGCACGCGTACT 60.094 45.455 13.44 9.50 0.00 2.73
760 767 2.667473 AGGATAAAGCACGCGTACTT 57.333 45.000 18.85 18.85 0.00 2.24
761 768 2.537401 AGGATAAAGCACGCGTACTTC 58.463 47.619 24.08 12.58 0.00 3.01
762 769 1.591619 GGATAAAGCACGCGTACTTCC 59.408 52.381 24.08 17.56 0.00 3.46
763 770 2.264813 GATAAAGCACGCGTACTTCCA 58.735 47.619 24.08 15.53 0.00 3.53
764 771 2.151881 TAAAGCACGCGTACTTCCAA 57.848 45.000 24.08 10.84 0.00 3.53
765 772 1.519408 AAAGCACGCGTACTTCCAAT 58.481 45.000 24.08 6.75 0.00 3.16
766 773 2.373540 AAGCACGCGTACTTCCAATA 57.626 45.000 18.85 0.00 0.00 1.90
767 774 1.922570 AGCACGCGTACTTCCAATAG 58.077 50.000 13.44 0.00 0.00 1.73
768 775 1.475280 AGCACGCGTACTTCCAATAGA 59.525 47.619 13.44 0.00 0.00 1.98
769 776 2.094390 AGCACGCGTACTTCCAATAGAA 60.094 45.455 13.44 0.00 0.00 2.10
770 777 2.669434 GCACGCGTACTTCCAATAGAAA 59.331 45.455 13.44 0.00 32.88 2.52
771 778 3.241995 GCACGCGTACTTCCAATAGAAAG 60.242 47.826 13.44 0.00 32.88 2.62
772 779 4.171005 CACGCGTACTTCCAATAGAAAGA 58.829 43.478 13.44 0.00 32.88 2.52
773 780 4.624024 CACGCGTACTTCCAATAGAAAGAA 59.376 41.667 13.44 0.00 32.88 2.52
774 781 4.863131 ACGCGTACTTCCAATAGAAAGAAG 59.137 41.667 11.67 0.00 42.19 2.85
775 782 4.267928 CGCGTACTTCCAATAGAAAGAAGG 59.732 45.833 0.00 0.00 41.06 3.46
776 783 4.034163 GCGTACTTCCAATAGAAAGAAGGC 59.966 45.833 4.23 0.00 41.06 4.35
777 784 4.571176 CGTACTTCCAATAGAAAGAAGGCC 59.429 45.833 0.00 0.00 41.06 5.19
778 785 3.969553 ACTTCCAATAGAAAGAAGGCCC 58.030 45.455 0.00 0.00 41.06 5.80
779 786 3.593780 ACTTCCAATAGAAAGAAGGCCCT 59.406 43.478 0.00 0.00 41.06 5.19
780 787 4.788617 ACTTCCAATAGAAAGAAGGCCCTA 59.211 41.667 0.00 0.00 41.06 3.53
781 788 4.772886 TCCAATAGAAAGAAGGCCCTAC 57.227 45.455 0.00 0.00 0.00 3.18
782 789 4.108570 TCCAATAGAAAGAAGGCCCTACA 58.891 43.478 0.00 0.00 0.00 2.74
837 854 1.943730 AAACCCAGCACCTCCCAACA 61.944 55.000 0.00 0.00 0.00 3.33
862 879 3.706373 GCCCAAGGAGAGACGGCA 61.706 66.667 0.00 0.00 39.50 5.69
1017 1043 1.880340 GATGGCGAAGTCTCTGCGG 60.880 63.158 0.00 0.00 32.31 5.69
1287 1313 7.875041 GCTGAGATCATTACTTCATTAGGCTTA 59.125 37.037 0.00 0.00 0.00 3.09
1303 1345 8.993121 CATTAGGCTTAAATAGTGGAGTACATG 58.007 37.037 0.00 0.00 0.00 3.21
1332 1374 3.624861 TCGATTCGTCAGGTAGGAAGTAC 59.375 47.826 5.89 0.00 35.56 2.73
1511 1557 7.432545 GCTTAGTTTGGTCTTTTTCTTCTGAAC 59.567 37.037 0.00 0.00 31.02 3.18
1674 1748 1.471119 ATCAAGCCTTGACCTGCATG 58.529 50.000 9.77 0.00 43.48 4.06
1807 1885 7.856145 TGTTTGTTTGAATTATGCCAGTTTT 57.144 28.000 0.00 0.00 0.00 2.43
1876 1955 9.494271 TGTAAATTCTAGAGTCAATATGCCATC 57.506 33.333 0.00 0.00 0.00 3.51
1903 1982 6.463995 TGTATCTTTTCTTGGCAAACTGTT 57.536 33.333 0.00 0.00 0.00 3.16
1904 1983 6.272318 TGTATCTTTTCTTGGCAAACTGTTG 58.728 36.000 0.00 0.00 37.83 3.33
2082 2161 1.431243 CTCCTACCTAGGCATCTCCCT 59.569 57.143 9.30 0.00 43.31 4.20
2125 2204 9.346725 GGTGCTTAAAGAAAGACTGATTTATTG 57.653 33.333 0.00 0.00 37.38 1.90
2201 2280 5.665916 ATTTCAATTCCATGTCACCCTTC 57.334 39.130 0.00 0.00 0.00 3.46
2232 2311 4.009675 TGTTGAGTCATGCCAGATAAACC 58.990 43.478 0.00 0.00 0.00 3.27
2255 2334 1.464997 GTTACCGACGTCTACCTTCGT 59.535 52.381 14.70 0.97 43.00 3.85
2263 2342 2.363359 ACGTCTACCTTCGTGGAGTTTT 59.637 45.455 4.38 0.00 38.85 2.43
2323 2402 2.158755 GGGGGTGTTGAGATACTCATGG 60.159 54.545 2.30 0.00 40.39 3.66
2479 2716 9.684448 CGATCAATGAACATAGTGTAGATTAGT 57.316 33.333 0.00 0.00 0.00 2.24
2571 2808 3.067833 GCTATACAAGGAAAGGATCGGC 58.932 50.000 0.00 0.00 0.00 5.54
2627 2864 5.600484 AGATTCTAGCTGCCTAAGTACATGT 59.400 40.000 2.69 2.69 0.00 3.21
2693 2965 5.069501 AGACGTCAGTAACCCAGTTTATC 57.930 43.478 19.50 0.00 0.00 1.75
2719 2991 4.796946 GCATGACAAATTGTTGGCTTCTGA 60.797 41.667 0.00 0.00 43.89 3.27
2740 3013 4.937620 TGAGATTGGATGCTTCAGTGTTAC 59.062 41.667 1.64 0.00 0.00 2.50
3119 3393 2.524306 CATTCTAGGGTGGCCAACAAA 58.476 47.619 25.24 11.31 0.00 2.83
3120 3394 2.990740 TTCTAGGGTGGCCAACAAAT 57.009 45.000 25.24 10.56 0.00 2.32
3121 3395 2.214376 TCTAGGGTGGCCAACAAATG 57.786 50.000 25.24 9.55 0.00 2.32
3122 3396 1.427368 TCTAGGGTGGCCAACAAATGT 59.573 47.619 25.24 3.45 0.00 2.71
3123 3397 2.645297 TCTAGGGTGGCCAACAAATGTA 59.355 45.455 25.24 4.53 0.00 2.29
3124 3398 1.627864 AGGGTGGCCAACAAATGTAC 58.372 50.000 25.24 2.42 0.00 2.90
3125 3399 1.146982 AGGGTGGCCAACAAATGTACT 59.853 47.619 25.24 5.22 0.00 2.73
3126 3400 1.272212 GGGTGGCCAACAAATGTACTG 59.728 52.381 25.24 0.00 0.00 2.74
3127 3401 1.272212 GGTGGCCAACAAATGTACTGG 59.728 52.381 18.33 0.77 0.00 4.00
3169 3444 2.364324 AGACGAAACTAGTGTCTGCCAA 59.636 45.455 11.33 0.00 41.21 4.52
3225 3500 3.961408 AGCTCACCTGATTACGAGGTTAT 59.039 43.478 0.00 0.00 41.31 1.89
3242 3517 4.943705 AGGTTATGCCATTGTGAACTACTG 59.056 41.667 0.00 0.00 40.61 2.74
3245 3520 0.447801 GCCATTGTGAACTACTGCCG 59.552 55.000 0.00 0.00 0.00 5.69
3246 3521 1.943968 GCCATTGTGAACTACTGCCGA 60.944 52.381 0.00 0.00 0.00 5.54
3254 3529 1.466025 AACTACTGCCGACGTCCCAA 61.466 55.000 10.58 0.00 0.00 4.12
3265 3540 4.084013 GCCGACGTCCCAAAATATAAGATG 60.084 45.833 10.58 0.00 0.00 2.90
3266 3541 5.054477 CCGACGTCCCAAAATATAAGATGT 58.946 41.667 10.58 0.00 0.00 3.06
3276 3556 8.872845 CCCAAAATATAAGATGTTTTGCAGTTC 58.127 33.333 13.07 0.00 44.74 3.01
3277 3557 9.421806 CCAAAATATAAGATGTTTTGCAGTTCA 57.578 29.630 13.07 0.00 44.74 3.18
3280 3560 8.673626 AATATAAGATGTTTTGCAGTTCAACG 57.326 30.769 0.00 0.00 33.73 4.10
3282 3562 3.952535 AGATGTTTTGCAGTTCAACGTC 58.047 40.909 11.55 11.55 36.90 4.34
3290 3570 3.215151 TGCAGTTCAACGTCCCAAAATA 58.785 40.909 0.00 0.00 0.00 1.40
3291 3571 3.823873 TGCAGTTCAACGTCCCAAAATAT 59.176 39.130 0.00 0.00 0.00 1.28
3292 3572 5.004448 TGCAGTTCAACGTCCCAAAATATA 58.996 37.500 0.00 0.00 0.00 0.86
3294 3574 6.027749 GCAGTTCAACGTCCCAAAATATAAG 58.972 40.000 0.00 0.00 0.00 1.73
3295 3575 6.128117 GCAGTTCAACGTCCCAAAATATAAGA 60.128 38.462 0.00 0.00 0.00 2.10
3296 3576 7.415206 GCAGTTCAACGTCCCAAAATATAAGAT 60.415 37.037 0.00 0.00 0.00 2.40
3297 3577 7.910162 CAGTTCAACGTCCCAAAATATAAGATG 59.090 37.037 0.00 0.00 0.00 2.90
3298 3578 7.610305 AGTTCAACGTCCCAAAATATAAGATGT 59.390 33.333 0.00 0.00 0.00 3.06
3299 3579 7.931578 TCAACGTCCCAAAATATAAGATGTT 57.068 32.000 0.00 0.00 37.20 2.71
3300 3580 9.451002 TTCAACGTCCCAAAATATAAGATGTTA 57.549 29.630 0.00 0.00 35.49 2.41
3301 3581 9.621629 TCAACGTCCCAAAATATAAGATGTTAT 57.378 29.630 0.29 0.29 35.49 1.89
3303 3583 7.871853 ACGTCCCAAAATATAAGATGTTATGC 58.128 34.615 5.40 0.00 31.04 3.14
3304 3584 7.500892 ACGTCCCAAAATATAAGATGTTATGCA 59.499 33.333 5.40 0.00 31.04 3.96
3305 3585 8.017373 CGTCCCAAAATATAAGATGTTATGCAG 58.983 37.037 5.40 0.00 31.04 4.41
3307 3587 9.420118 TCCCAAAATATAAGATGTTATGCAGTT 57.580 29.630 5.40 0.00 31.04 3.16
3308 3588 9.683069 CCCAAAATATAAGATGTTATGCAGTTC 57.317 33.333 5.40 0.00 31.04 3.01
3315 3595 6.741992 AAGATGTTATGCAGTTCAAATCGA 57.258 33.333 0.00 0.00 0.00 3.59
3316 3596 6.741992 AGATGTTATGCAGTTCAAATCGAA 57.258 33.333 0.00 0.00 0.00 3.71
3317 3597 6.779117 AGATGTTATGCAGTTCAAATCGAAG 58.221 36.000 0.00 0.00 33.09 3.79
3318 3598 5.940192 TGTTATGCAGTTCAAATCGAAGT 57.060 34.783 0.00 0.00 37.81 3.01
3319 3599 7.549134 AGATGTTATGCAGTTCAAATCGAAGTA 59.451 33.333 0.00 0.00 35.41 2.24
3320 3600 7.428282 TGTTATGCAGTTCAAATCGAAGTAA 57.572 32.000 0.00 0.00 35.41 2.24
3321 3601 7.866729 TGTTATGCAGTTCAAATCGAAGTAAA 58.133 30.769 0.00 0.00 35.41 2.01
3322 3602 8.346300 TGTTATGCAGTTCAAATCGAAGTAAAA 58.654 29.630 0.00 0.00 35.41 1.52
3323 3603 9.176181 GTTATGCAGTTCAAATCGAAGTAAAAA 57.824 29.630 0.00 0.00 35.41 1.94
3362 3673 7.674120 TGAGATGGAGTATGTCATATCTTTGG 58.326 38.462 0.00 0.00 34.45 3.28
3368 3679 6.192970 AGTATGTCATATCTTTGGAAGGGG 57.807 41.667 0.00 0.00 0.00 4.79
3369 3680 3.297134 TGTCATATCTTTGGAAGGGGC 57.703 47.619 0.00 0.00 0.00 5.80
3380 3755 3.515059 GAAGGGGCCTTACCATTCC 57.485 57.895 0.84 0.00 43.55 3.01
3381 3756 0.465642 GAAGGGGCCTTACCATTCCG 60.466 60.000 0.84 0.00 43.55 4.30
3385 3762 1.526225 GGCCTTACCATTCCGCTCC 60.526 63.158 0.00 0.00 38.86 4.70
3401 3781 3.002656 CCGCTCCTGTTGCATAACTTATG 59.997 47.826 4.61 4.61 37.68 1.90
3411 3791 2.544267 GCATAACTTATGTCGACCTGCC 59.456 50.000 14.12 0.00 38.43 4.85
3437 3820 2.105128 ATTTCTCCGGCGAGCTCG 59.895 61.111 31.37 31.37 43.27 5.03
3439 3822 2.615262 ATTTCTCCGGCGAGCTCGAC 62.615 60.000 38.74 35.62 45.58 4.20
3463 3846 1.975407 GCCTTGACACATGCCTGCT 60.975 57.895 0.00 0.00 0.00 4.24
3465 3848 0.892358 CCTTGACACATGCCTGCTGT 60.892 55.000 0.00 0.00 0.00 4.40
3475 3876 1.671979 TGCCTGCTGTTCATATGAGC 58.328 50.000 12.28 12.28 0.00 4.26
3476 3877 0.950116 GCCTGCTGTTCATATGAGCC 59.050 55.000 15.96 7.21 31.31 4.70
3484 3885 3.554934 TGTTCATATGAGCCCATGTTCC 58.445 45.455 15.96 0.00 34.31 3.62
3505 3906 4.062991 CCGTTAGGTAGCATATGGAAACC 58.937 47.826 4.56 0.00 0.00 3.27
3519 3922 1.685148 GAAACCCTGATGCAGATCCC 58.315 55.000 0.00 0.00 32.44 3.85
3520 3923 1.002069 AAACCCTGATGCAGATCCCA 58.998 50.000 0.00 0.00 32.44 4.37
3529 3932 1.977056 TGCAGATCCCAGAATGCATC 58.023 50.000 0.00 0.00 43.34 3.91
3532 3935 2.293677 GCAGATCCCAGAATGCATCAAG 59.706 50.000 0.00 0.00 38.54 3.02
3543 3946 3.846955 GCATCAAGCAGGCCAAAAT 57.153 47.368 5.01 0.00 44.79 1.82
3544 3947 2.965572 GCATCAAGCAGGCCAAAATA 57.034 45.000 5.01 0.00 44.79 1.40
3545 3948 2.543641 GCATCAAGCAGGCCAAAATAC 58.456 47.619 5.01 0.00 44.79 1.89
3546 3949 2.094078 GCATCAAGCAGGCCAAAATACA 60.094 45.455 5.01 0.00 44.79 2.29
3547 3950 3.617045 GCATCAAGCAGGCCAAAATACAA 60.617 43.478 5.01 0.00 44.79 2.41
3548 3951 4.567971 CATCAAGCAGGCCAAAATACAAA 58.432 39.130 5.01 0.00 0.00 2.83
3549 3952 4.888326 TCAAGCAGGCCAAAATACAAAT 57.112 36.364 5.01 0.00 0.00 2.32
3550 3953 5.226194 TCAAGCAGGCCAAAATACAAATT 57.774 34.783 5.01 0.00 0.00 1.82
3551 3954 5.237048 TCAAGCAGGCCAAAATACAAATTC 58.763 37.500 5.01 0.00 0.00 2.17
3552 3955 4.888326 AGCAGGCCAAAATACAAATTCA 57.112 36.364 5.01 0.00 0.00 2.57
3553 3956 4.824289 AGCAGGCCAAAATACAAATTCAG 58.176 39.130 5.01 0.00 0.00 3.02
3558 3961 5.304101 AGGCCAAAATACAAATTCAGTCACA 59.696 36.000 5.01 0.00 0.00 3.58
3603 4006 6.449698 ACAGATTGTGCTGGAAACAAAATAG 58.550 36.000 0.00 0.00 40.69 1.73
3613 4016 4.404073 TGGAAACAAAATAGCACCAGTTGT 59.596 37.500 0.00 0.00 37.44 3.32
3614 4017 5.680922 TGGAAACAAAATAGCACCAGTTGTG 60.681 40.000 0.00 0.00 42.82 3.33
3616 4019 8.765900 TGGAAACAAAATAGCACCAGTTGTGTA 61.766 37.037 0.00 0.00 42.21 2.90
3624 4027 3.915437 CACCAGTTGTGTAACCCATTC 57.085 47.619 0.00 0.00 40.26 2.67
3625 4028 2.225491 CACCAGTTGTGTAACCCATTCG 59.775 50.000 0.00 0.00 40.26 3.34
3626 4029 2.158726 ACCAGTTGTGTAACCCATTCGT 60.159 45.455 0.00 0.00 37.52 3.85
3627 4030 2.225491 CCAGTTGTGTAACCCATTCGTG 59.775 50.000 0.00 0.00 37.52 4.35
3629 4032 1.068816 GTTGTGTAACCCATTCGTGGC 60.069 52.381 0.00 0.00 34.36 5.01
3636 4091 1.626686 ACCCATTCGTGGCATTTCAA 58.373 45.000 0.00 0.00 0.00 2.69
3639 4094 2.159338 CCCATTCGTGGCATTTCAAGAG 60.159 50.000 0.00 0.00 0.00 2.85
3648 4103 2.816087 GGCATTTCAAGAGCTCAGTTCA 59.184 45.455 17.77 0.00 0.00 3.18
3650 4105 4.413087 GCATTTCAAGAGCTCAGTTCATG 58.587 43.478 17.77 12.80 0.00 3.07
3651 4106 4.674623 GCATTTCAAGAGCTCAGTTCATGG 60.675 45.833 17.77 0.00 0.00 3.66
3653 4108 3.777106 TCAAGAGCTCAGTTCATGGTT 57.223 42.857 17.77 0.00 0.00 3.67
3654 4109 4.090761 TCAAGAGCTCAGTTCATGGTTT 57.909 40.909 17.77 0.00 0.00 3.27
3656 4111 4.516698 TCAAGAGCTCAGTTCATGGTTTTC 59.483 41.667 17.77 0.00 0.00 2.29
3658 4113 5.489792 AGAGCTCAGTTCATGGTTTTCTA 57.510 39.130 17.77 0.00 0.00 2.10
3659 4114 5.869579 AGAGCTCAGTTCATGGTTTTCTAA 58.130 37.500 17.77 0.00 0.00 2.10
3660 4115 5.703130 AGAGCTCAGTTCATGGTTTTCTAAC 59.297 40.000 17.77 0.00 0.00 2.34
3661 4116 5.376625 AGCTCAGTTCATGGTTTTCTAACA 58.623 37.500 0.00 0.00 35.92 2.41
3663 4118 6.072286 AGCTCAGTTCATGGTTTTCTAACATG 60.072 38.462 0.00 0.00 35.92 3.21
3664 4119 6.573664 TCAGTTCATGGTTTTCTAACATGG 57.426 37.500 0.00 0.00 35.92 3.66
3665 4120 5.048083 TCAGTTCATGGTTTTCTAACATGGC 60.048 40.000 0.00 0.00 35.92 4.40
3666 4121 4.220602 AGTTCATGGTTTTCTAACATGGCC 59.779 41.667 0.00 0.00 35.92 5.36
3692 4168 7.153315 TCTGATCTCTCATGTAAGCATCAATC 58.847 38.462 0.00 0.00 31.99 2.67
3755 4235 5.244189 TGGCTTGGGTAGTTGTGTTATTA 57.756 39.130 0.00 0.00 0.00 0.98
3787 4267 4.649088 ACGGATCGAATCTGATGTGTAA 57.351 40.909 9.69 0.00 39.01 2.41
3889 4382 2.677875 CCCCAACCTTGAGCTGGC 60.678 66.667 0.00 0.00 0.00 4.85
3929 4422 2.030805 TGTCAGTGTCACGACTCTCATG 60.031 50.000 20.72 4.52 33.38 3.07
3930 4423 1.541588 TCAGTGTCACGACTCTCATGG 59.458 52.381 0.00 0.00 33.38 3.66
3931 4424 1.541588 CAGTGTCACGACTCTCATGGA 59.458 52.381 0.00 0.00 33.38 3.41
3932 4425 2.165234 CAGTGTCACGACTCTCATGGAT 59.835 50.000 0.00 0.00 33.38 3.41
3933 4426 2.425312 AGTGTCACGACTCTCATGGATC 59.575 50.000 0.00 0.00 30.13 3.36
3934 4427 2.164422 GTGTCACGACTCTCATGGATCA 59.836 50.000 0.00 0.00 0.00 2.92
3935 4428 2.825532 TGTCACGACTCTCATGGATCAA 59.174 45.455 0.00 0.00 0.00 2.57
3936 4429 3.258123 TGTCACGACTCTCATGGATCAAA 59.742 43.478 0.00 0.00 0.00 2.69
3937 4430 4.081476 TGTCACGACTCTCATGGATCAAAT 60.081 41.667 0.00 0.00 0.00 2.32
3938 4431 4.505922 GTCACGACTCTCATGGATCAAATC 59.494 45.833 0.00 0.00 0.00 2.17
3939 4432 4.160252 TCACGACTCTCATGGATCAAATCA 59.840 41.667 0.00 0.00 0.00 2.57
3940 4433 4.507021 CACGACTCTCATGGATCAAATCAG 59.493 45.833 0.00 0.00 0.00 2.90
3941 4434 3.493877 CGACTCTCATGGATCAAATCAGC 59.506 47.826 0.00 0.00 0.00 4.26
3942 4435 3.814283 GACTCTCATGGATCAAATCAGCC 59.186 47.826 0.00 0.00 0.00 4.85
3943 4436 3.201487 ACTCTCATGGATCAAATCAGCCA 59.799 43.478 0.00 0.00 34.45 4.75
3944 4437 4.204799 CTCTCATGGATCAAATCAGCCAA 58.795 43.478 0.00 0.00 33.51 4.52
3945 4438 4.602107 TCTCATGGATCAAATCAGCCAAA 58.398 39.130 0.00 0.00 33.51 3.28
3946 4439 4.643334 TCTCATGGATCAAATCAGCCAAAG 59.357 41.667 0.00 0.00 33.51 2.77
3947 4440 4.602107 TCATGGATCAAATCAGCCAAAGA 58.398 39.130 0.00 0.00 33.51 2.52
3948 4441 5.018149 TCATGGATCAAATCAGCCAAAGAA 58.982 37.500 0.00 0.00 33.51 2.52
3949 4442 5.481122 TCATGGATCAAATCAGCCAAAGAAA 59.519 36.000 0.00 0.00 33.51 2.52
3950 4443 5.804944 TGGATCAAATCAGCCAAAGAAAA 57.195 34.783 0.00 0.00 0.00 2.29
3951 4444 6.172136 TGGATCAAATCAGCCAAAGAAAAA 57.828 33.333 0.00 0.00 0.00 1.94
3971 4464 5.582689 AAAAATGGAGAATGGAATCGGTC 57.417 39.130 0.00 0.00 0.00 4.79
3972 4465 3.931907 AATGGAGAATGGAATCGGTCA 57.068 42.857 0.00 0.00 0.00 4.02
3973 4466 2.988010 TGGAGAATGGAATCGGTCAG 57.012 50.000 0.00 0.00 0.00 3.51
3974 4467 1.486310 TGGAGAATGGAATCGGTCAGG 59.514 52.381 0.00 0.00 0.00 3.86
3975 4468 1.202698 GGAGAATGGAATCGGTCAGGG 60.203 57.143 0.00 0.00 0.00 4.45
3976 4469 0.181350 AGAATGGAATCGGTCAGGGC 59.819 55.000 0.00 0.00 0.00 5.19
3977 4470 0.819666 GAATGGAATCGGTCAGGGCC 60.820 60.000 0.00 0.00 0.00 5.80
3978 4471 1.281925 AATGGAATCGGTCAGGGCCT 61.282 55.000 0.00 0.00 0.00 5.19
3979 4472 0.399949 ATGGAATCGGTCAGGGCCTA 60.400 55.000 5.28 0.00 0.00 3.93
3980 4473 0.619255 TGGAATCGGTCAGGGCCTAA 60.619 55.000 5.28 0.00 0.00 2.69
3981 4474 0.765510 GGAATCGGTCAGGGCCTAAT 59.234 55.000 5.28 0.00 0.00 1.73
3982 4475 1.143073 GGAATCGGTCAGGGCCTAATT 59.857 52.381 5.28 1.17 0.00 1.40
3983 4476 2.370849 GGAATCGGTCAGGGCCTAATTA 59.629 50.000 5.28 0.00 0.00 1.40
3984 4477 3.009143 GGAATCGGTCAGGGCCTAATTAT 59.991 47.826 5.28 0.00 0.00 1.28
3985 4478 3.983044 ATCGGTCAGGGCCTAATTATC 57.017 47.619 5.28 0.00 0.00 1.75
3986 4479 2.684943 TCGGTCAGGGCCTAATTATCA 58.315 47.619 5.28 0.00 0.00 2.15
3987 4480 2.367567 TCGGTCAGGGCCTAATTATCAC 59.632 50.000 5.28 0.00 0.00 3.06
3988 4481 2.767505 GGTCAGGGCCTAATTATCACG 58.232 52.381 5.28 0.00 0.00 4.35
3989 4482 2.104281 GGTCAGGGCCTAATTATCACGT 59.896 50.000 5.28 0.00 0.00 4.49
3990 4483 3.391049 GTCAGGGCCTAATTATCACGTC 58.609 50.000 5.28 0.00 0.00 4.34
3991 4484 3.035363 TCAGGGCCTAATTATCACGTCA 58.965 45.455 5.28 0.00 0.00 4.35
3992 4485 3.131396 CAGGGCCTAATTATCACGTCAC 58.869 50.000 5.28 0.00 0.00 3.67
3993 4486 2.132762 GGGCCTAATTATCACGTCACG 58.867 52.381 0.84 0.00 0.00 4.35
3994 4487 2.132762 GGCCTAATTATCACGTCACGG 58.867 52.381 0.35 0.00 0.00 4.94
3995 4488 1.525619 GCCTAATTATCACGTCACGGC 59.474 52.381 0.35 0.00 0.00 5.68
3996 4489 1.784856 CCTAATTATCACGTCACGGCG 59.215 52.381 4.80 4.80 37.94 6.46
3997 4490 2.456989 CTAATTATCACGTCACGGCGT 58.543 47.619 6.77 6.77 46.88 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.125659 TCTGTCCTTCATTAACTGACATATGGA 59.874 37.037 7.80 0.00 35.59 3.41
50 51 0.108138 GCCTACGCACATCTGTCCTT 60.108 55.000 0.00 0.00 34.03 3.36
59 60 1.688422 CGCAAATACGCCTACGCACA 61.688 55.000 0.00 0.00 45.53 4.57
121 122 5.293569 GCGTATTGGTGTTACTAAATCAGCT 59.706 40.000 0.00 0.00 0.00 4.24
234 235 5.445069 TCACGATCCATTATTTCCCATTGT 58.555 37.500 0.00 0.00 0.00 2.71
235 236 5.048504 CCTCACGATCCATTATTTCCCATTG 60.049 44.000 0.00 0.00 0.00 2.82
236 237 5.072741 CCTCACGATCCATTATTTCCCATT 58.927 41.667 0.00 0.00 0.00 3.16
242 243 5.131142 AGGAAGTCCTCACGATCCATTATTT 59.869 40.000 0.00 0.00 44.77 1.40
364 365 5.072464 AGAGTAAAAGCCTTCCTCTGTTCTT 59.928 40.000 1.73 0.00 31.55 2.52
365 366 4.595350 AGAGTAAAAGCCTTCCTCTGTTCT 59.405 41.667 1.73 0.00 31.55 3.01
375 376 6.884836 CCCAAATAGTACAGAGTAAAAGCCTT 59.115 38.462 0.00 0.00 0.00 4.35
458 459 1.487137 GGGGCTTACTCCCTCCCATAT 60.487 57.143 0.00 0.00 45.80 1.78
459 460 0.104620 GGGGCTTACTCCCTCCCATA 60.105 60.000 0.00 0.00 45.80 2.74
591 598 3.009723 CACGAACGTAGGGAGTAGGTTA 58.990 50.000 0.00 0.00 39.34 2.85
608 615 4.627058 TCTAAATGTGCAGTCTTTCACGA 58.373 39.130 0.00 0.00 36.06 4.35
621 628 7.962373 TGTTCAATGCGTAAATCTCTAAATGTG 59.038 33.333 0.00 0.00 0.00 3.21
673 680 4.161377 TGGTAGCATGCACACATAAGTCTA 59.839 41.667 21.98 0.00 33.67 2.59
706 713 6.052405 TGCAATGGCCTTCATTTAATCTTT 57.948 33.333 3.32 0.00 43.04 2.52
739 746 2.537401 AGTACGCGTGCTTTATCCTTC 58.463 47.619 24.67 0.00 0.00 3.46
747 754 2.094390 TCTATTGGAAGTACGCGTGCTT 60.094 45.455 37.06 37.06 38.22 3.91
748 755 1.475280 TCTATTGGAAGTACGCGTGCT 59.525 47.619 24.67 24.67 0.00 4.40
749 756 1.917273 TCTATTGGAAGTACGCGTGC 58.083 50.000 24.59 22.34 0.00 5.34
750 757 4.171005 TCTTTCTATTGGAAGTACGCGTG 58.829 43.478 24.59 0.00 35.16 5.34
751 758 4.445452 TCTTTCTATTGGAAGTACGCGT 57.555 40.909 19.17 19.17 35.16 6.01
752 759 4.267928 CCTTCTTTCTATTGGAAGTACGCG 59.732 45.833 3.53 3.53 35.90 6.01
753 760 4.034163 GCCTTCTTTCTATTGGAAGTACGC 59.966 45.833 0.00 0.00 35.90 4.42
754 761 4.571176 GGCCTTCTTTCTATTGGAAGTACG 59.429 45.833 0.00 0.00 35.90 3.67
755 762 4.882427 GGGCCTTCTTTCTATTGGAAGTAC 59.118 45.833 0.84 0.00 35.90 2.73
756 763 4.788617 AGGGCCTTCTTTCTATTGGAAGTA 59.211 41.667 0.00 0.00 35.90 2.24
757 764 3.593780 AGGGCCTTCTTTCTATTGGAAGT 59.406 43.478 0.00 0.00 35.90 3.01
758 765 4.242336 AGGGCCTTCTTTCTATTGGAAG 57.758 45.455 0.00 0.00 36.99 3.46
759 766 4.538490 TGTAGGGCCTTCTTTCTATTGGAA 59.462 41.667 13.45 0.00 0.00 3.53
760 767 4.108570 TGTAGGGCCTTCTTTCTATTGGA 58.891 43.478 13.45 0.00 0.00 3.53
761 768 4.455606 CTGTAGGGCCTTCTTTCTATTGG 58.544 47.826 13.45 0.00 0.00 3.16
762 769 3.879892 GCTGTAGGGCCTTCTTTCTATTG 59.120 47.826 13.45 0.00 0.00 1.90
763 770 4.157849 GCTGTAGGGCCTTCTTTCTATT 57.842 45.455 13.45 0.00 0.00 1.73
764 771 3.847671 GCTGTAGGGCCTTCTTTCTAT 57.152 47.619 13.45 0.00 0.00 1.98
776 783 2.664402 ATAATTGCCAGGCTGTAGGG 57.336 50.000 14.15 0.00 0.00 3.53
777 784 5.824624 CCATATATAATTGCCAGGCTGTAGG 59.175 44.000 14.15 0.00 0.00 3.18
778 785 5.824624 CCCATATATAATTGCCAGGCTGTAG 59.175 44.000 14.15 0.00 0.00 2.74
779 786 5.754782 CCCATATATAATTGCCAGGCTGTA 58.245 41.667 14.15 2.26 0.00 2.74
780 787 4.603131 CCCATATATAATTGCCAGGCTGT 58.397 43.478 14.15 0.00 0.00 4.40
781 788 3.382546 GCCCATATATAATTGCCAGGCTG 59.617 47.826 14.15 7.75 35.00 4.85
782 789 3.270433 AGCCCATATATAATTGCCAGGCT 59.730 43.478 14.15 0.00 43.21 4.58
811 818 2.557056 GGAGGTGCTGGGTTTAAACTTC 59.443 50.000 17.50 10.86 0.00 3.01
837 854 2.147433 CTCTCCTTGGGCTGGGCTTT 62.147 60.000 0.00 0.00 0.00 3.51
862 879 1.270465 CGGTTCTTGTAGGAACGGGTT 60.270 52.381 6.56 0.00 44.45 4.11
1017 1043 2.815647 CGCTTCTCCCGCTTGGAC 60.816 66.667 0.00 0.00 38.61 4.02
1287 1313 7.338703 TCGAGTTACTCATGTACTCCACTATTT 59.661 37.037 13.14 0.00 0.00 1.40
1291 1317 4.586884 TCGAGTTACTCATGTACTCCACT 58.413 43.478 13.14 1.49 0.00 4.00
1303 1345 3.761311 ACCTGACGAATCGAGTTACTC 57.239 47.619 10.55 1.64 0.00 2.59
1332 1374 2.864343 CCCACTACGAGCTAATTTTCCG 59.136 50.000 0.00 0.00 0.00 4.30
1674 1748 5.926542 GCAAAATCTTCAGTTAAAAGGACCC 59.073 40.000 0.00 0.00 0.00 4.46
1876 1955 3.829886 TGCCAAGAAAAGATACAAGCG 57.170 42.857 0.00 0.00 0.00 4.68
1903 1982 0.627451 AGCATCCAATCCAGAAGCCA 59.373 50.000 0.00 0.00 0.00 4.75
1904 1983 1.680207 GAAGCATCCAATCCAGAAGCC 59.320 52.381 0.00 0.00 0.00 4.35
2125 2204 0.822164 TTACGGGAGGTGCTTAGAGC 59.178 55.000 0.00 0.00 42.82 4.09
2191 2270 5.888724 TCAACAAAAATACAGAAGGGTGACA 59.111 36.000 0.00 0.00 0.00 3.58
2201 2280 5.771469 TGGCATGACTCAACAAAAATACAG 58.229 37.500 0.00 0.00 0.00 2.74
2255 2334 2.104792 CAGAGACTGGACCAAAACTCCA 59.895 50.000 14.57 0.00 36.34 3.86
2263 2342 1.530655 TGACGCAGAGACTGGACCA 60.531 57.895 0.00 0.00 31.21 4.02
2479 2716 6.229733 TGGCATACGATCAATGAACATATCA 58.770 36.000 8.80 0.00 43.67 2.15
2516 2753 5.163301 TGAGATATCCTTGCCCTTGTACTTC 60.163 44.000 0.00 0.00 0.00 3.01
2517 2754 4.721776 TGAGATATCCTTGCCCTTGTACTT 59.278 41.667 0.00 0.00 0.00 2.24
2571 2808 6.879276 TGTTTCCTAGTCTACGGATATCTG 57.121 41.667 10.14 10.14 0.00 2.90
2607 2844 4.278310 TCACATGTACTTAGGCAGCTAGA 58.722 43.478 0.00 0.00 0.00 2.43
2627 2864 3.706594 GGGGTGTTGAGATACTCTGATCA 59.293 47.826 0.00 0.00 0.00 2.92
2693 2965 2.070783 GCCAACAATTTGTCATGCCAG 58.929 47.619 1.83 0.00 0.00 4.85
2719 2991 4.910195 TGTAACACTGAAGCATCCAATCT 58.090 39.130 0.00 0.00 0.00 2.40
2763 3036 2.525368 ACCTAAAAGGGTTGGCATGTC 58.475 47.619 0.00 0.00 40.58 3.06
3119 3393 5.069119 TGCTCGTTGAGATATTCCAGTACAT 59.931 40.000 0.00 0.00 0.00 2.29
3120 3394 4.401202 TGCTCGTTGAGATATTCCAGTACA 59.599 41.667 0.00 0.00 0.00 2.90
3121 3395 4.740695 GTGCTCGTTGAGATATTCCAGTAC 59.259 45.833 0.00 0.00 0.00 2.73
3122 3396 4.645136 AGTGCTCGTTGAGATATTCCAGTA 59.355 41.667 0.00 0.00 0.00 2.74
3123 3397 3.449018 AGTGCTCGTTGAGATATTCCAGT 59.551 43.478 0.00 0.00 0.00 4.00
3124 3398 4.047822 GAGTGCTCGTTGAGATATTCCAG 58.952 47.826 0.00 0.00 0.00 3.86
3125 3399 3.489229 CGAGTGCTCGTTGAGATATTCCA 60.489 47.826 12.87 0.00 46.99 3.53
3126 3400 3.046390 CGAGTGCTCGTTGAGATATTCC 58.954 50.000 12.87 0.00 46.99 3.01
3147 3422 2.030185 TGGCAGACACTAGTTTCGTCTC 60.030 50.000 10.56 6.93 37.92 3.36
3149 3424 2.433868 TGGCAGACACTAGTTTCGTC 57.566 50.000 3.43 3.79 0.00 4.20
3156 3431 3.931468 CAGATGAACTTGGCAGACACTAG 59.069 47.826 0.00 0.00 0.00 2.57
3169 3444 4.706842 AGTGGGTACAAACAGATGAACT 57.293 40.909 0.00 0.00 0.00 3.01
3225 3500 1.533625 GGCAGTAGTTCACAATGGCA 58.466 50.000 0.00 0.00 36.53 4.92
3242 3517 3.460103 TCTTATATTTTGGGACGTCGGC 58.540 45.455 9.92 0.00 0.00 5.54
3245 3520 7.220108 GCAAAACATCTTATATTTTGGGACGTC 59.780 37.037 7.13 7.13 41.51 4.34
3246 3521 7.033185 GCAAAACATCTTATATTTTGGGACGT 58.967 34.615 9.88 0.00 41.51 4.34
3254 3529 9.128107 CGTTGAACTGCAAAACATCTTATATTT 57.872 29.630 0.00 0.00 38.44 1.40
3265 3540 1.133407 TGGGACGTTGAACTGCAAAAC 59.867 47.619 0.00 0.00 38.44 2.43
3266 3541 1.464734 TGGGACGTTGAACTGCAAAA 58.535 45.000 0.00 0.00 38.44 2.44
3276 3556 9.663904 CATAACATCTTATATTTTGGGACGTTG 57.336 33.333 0.00 0.00 0.00 4.10
3277 3557 8.349983 GCATAACATCTTATATTTTGGGACGTT 58.650 33.333 0.00 0.00 0.00 3.99
3279 3559 7.870826 TGCATAACATCTTATATTTTGGGACG 58.129 34.615 0.00 0.00 0.00 4.79
3280 3560 8.850156 ACTGCATAACATCTTATATTTTGGGAC 58.150 33.333 0.00 0.00 0.00 4.46
3282 3562 9.683069 GAACTGCATAACATCTTATATTTTGGG 57.317 33.333 0.00 0.00 0.00 4.12
3290 3570 8.437360 TCGATTTGAACTGCATAACATCTTAT 57.563 30.769 0.00 0.00 0.00 1.73
3291 3571 7.841915 TCGATTTGAACTGCATAACATCTTA 57.158 32.000 0.00 0.00 0.00 2.10
3292 3572 6.741992 TCGATTTGAACTGCATAACATCTT 57.258 33.333 0.00 0.00 0.00 2.40
3294 3574 6.546395 ACTTCGATTTGAACTGCATAACATC 58.454 36.000 0.00 0.00 31.87 3.06
3295 3575 6.500684 ACTTCGATTTGAACTGCATAACAT 57.499 33.333 0.00 0.00 31.87 2.71
3296 3576 5.940192 ACTTCGATTTGAACTGCATAACA 57.060 34.783 0.00 0.00 31.87 2.41
3297 3577 8.722342 TTTTACTTCGATTTGAACTGCATAAC 57.278 30.769 0.00 0.00 31.87 1.89
3336 3616 8.152898 CCAAAGATATGACATACTCCATCTCAA 58.847 37.037 0.00 0.00 0.00 3.02
3339 3619 7.862274 TCCAAAGATATGACATACTCCATCT 57.138 36.000 0.00 0.00 0.00 2.90
3342 3622 6.183361 CCCTTCCAAAGATATGACATACTCCA 60.183 42.308 0.00 0.00 0.00 3.86
3347 3627 4.202567 GGCCCCTTCCAAAGATATGACATA 60.203 45.833 0.00 0.00 0.00 2.29
3348 3628 3.437052 GGCCCCTTCCAAAGATATGACAT 60.437 47.826 0.00 0.00 0.00 3.06
3359 3670 1.006639 GAATGGTAAGGCCCCTTCCAA 59.993 52.381 16.68 0.00 37.07 3.53
3362 3673 0.465642 CGGAATGGTAAGGCCCCTTC 60.466 60.000 0.00 0.00 37.47 3.46
3368 3679 0.815615 CAGGAGCGGAATGGTAAGGC 60.816 60.000 0.00 0.00 0.00 4.35
3369 3680 0.541863 ACAGGAGCGGAATGGTAAGG 59.458 55.000 0.00 0.00 0.00 2.69
3380 3755 3.623060 ACATAAGTTATGCAACAGGAGCG 59.377 43.478 20.52 0.00 39.79 5.03
3381 3756 4.260375 CGACATAAGTTATGCAACAGGAGC 60.260 45.833 20.52 0.00 39.79 4.70
3385 3762 4.870426 AGGTCGACATAAGTTATGCAACAG 59.130 41.667 20.52 9.24 39.79 3.16
3401 3781 1.521681 GGCATACAGGCAGGTCGAC 60.522 63.158 7.13 7.13 43.51 4.20
3437 3820 1.808945 CATGTGTCAAGGCTGGAAGTC 59.191 52.381 0.00 0.00 40.46 3.01
3439 3822 0.524862 GCATGTGTCAAGGCTGGAAG 59.475 55.000 0.00 0.00 0.00 3.46
3463 3846 3.554934 GGAACATGGGCTCATATGAACA 58.445 45.455 6.90 6.85 31.33 3.18
3465 3848 2.172505 ACGGAACATGGGCTCATATGAA 59.827 45.455 6.90 0.00 31.33 2.57
3475 3876 1.208535 TGCTACCTAACGGAACATGGG 59.791 52.381 0.00 0.00 0.00 4.00
3476 3877 2.684001 TGCTACCTAACGGAACATGG 57.316 50.000 0.00 0.00 0.00 3.66
3484 3885 4.062991 GGGTTTCCATATGCTACCTAACG 58.937 47.826 14.79 0.00 0.00 3.18
3505 3906 2.505405 CATTCTGGGATCTGCATCAGG 58.495 52.381 0.00 0.00 31.51 3.86
3529 3932 4.996122 TGAATTTGTATTTTGGCCTGCTTG 59.004 37.500 3.32 0.00 0.00 4.01
3532 3935 4.568956 ACTGAATTTGTATTTTGGCCTGC 58.431 39.130 3.32 0.00 0.00 4.85
3534 3937 5.304101 TGTGACTGAATTTGTATTTTGGCCT 59.696 36.000 3.32 0.00 0.00 5.19
3535 3938 5.537188 TGTGACTGAATTTGTATTTTGGCC 58.463 37.500 0.00 0.00 0.00 5.36
3537 3940 8.815141 TGATTGTGACTGAATTTGTATTTTGG 57.185 30.769 0.00 0.00 0.00 3.28
3542 3945 9.896645 AGTAGATGATTGTGACTGAATTTGTAT 57.103 29.630 0.00 0.00 0.00 2.29
3543 3946 9.371136 GAGTAGATGATTGTGACTGAATTTGTA 57.629 33.333 0.00 0.00 0.00 2.41
3544 3947 7.879677 TGAGTAGATGATTGTGACTGAATTTGT 59.120 33.333 0.00 0.00 0.00 2.83
3545 3948 8.260270 TGAGTAGATGATTGTGACTGAATTTG 57.740 34.615 0.00 0.00 0.00 2.32
3546 3949 8.890718 CATGAGTAGATGATTGTGACTGAATTT 58.109 33.333 0.00 0.00 0.00 1.82
3547 3950 8.045507 ACATGAGTAGATGATTGTGACTGAATT 58.954 33.333 0.00 0.00 0.00 2.17
3548 3951 7.494952 CACATGAGTAGATGATTGTGACTGAAT 59.505 37.037 0.00 0.00 37.28 2.57
3549 3952 6.815142 CACATGAGTAGATGATTGTGACTGAA 59.185 38.462 0.00 0.00 37.28 3.02
3550 3953 6.335777 CACATGAGTAGATGATTGTGACTGA 58.664 40.000 0.00 0.00 37.28 3.41
3551 3954 5.006455 GCACATGAGTAGATGATTGTGACTG 59.994 44.000 0.00 0.00 37.28 3.51
3552 3955 5.114780 GCACATGAGTAGATGATTGTGACT 58.885 41.667 0.00 0.00 37.28 3.41
3553 3956 4.872124 TGCACATGAGTAGATGATTGTGAC 59.128 41.667 0.00 0.00 37.28 3.67
3558 3961 5.247862 TGTTGTGCACATGAGTAGATGATT 58.752 37.500 22.39 0.00 0.00 2.57
3591 3994 4.744631 CACAACTGGTGCTATTTTGTTTCC 59.255 41.667 0.00 0.00 41.36 3.13
3620 4023 2.163010 AGCTCTTGAAATGCCACGAATG 59.837 45.455 0.00 0.00 0.00 2.67
3621 4024 2.421424 GAGCTCTTGAAATGCCACGAAT 59.579 45.455 6.43 0.00 0.00 3.34
3622 4025 1.806542 GAGCTCTTGAAATGCCACGAA 59.193 47.619 6.43 0.00 0.00 3.85
3623 4026 1.270785 TGAGCTCTTGAAATGCCACGA 60.271 47.619 16.19 0.00 0.00 4.35
3624 4027 1.129998 CTGAGCTCTTGAAATGCCACG 59.870 52.381 16.19 0.00 0.00 4.94
3625 4028 2.157738 ACTGAGCTCTTGAAATGCCAC 58.842 47.619 16.19 0.00 0.00 5.01
3626 4029 2.574006 ACTGAGCTCTTGAAATGCCA 57.426 45.000 16.19 0.00 0.00 4.92
3627 4030 2.816087 TGAACTGAGCTCTTGAAATGCC 59.184 45.455 16.19 0.00 0.00 4.40
3629 4032 4.458295 ACCATGAACTGAGCTCTTGAAATG 59.542 41.667 16.19 12.64 0.00 2.32
3636 4091 4.363991 AGAAAACCATGAACTGAGCTCT 57.636 40.909 16.19 0.00 0.00 4.09
3639 4094 5.689383 TGTTAGAAAACCATGAACTGAGC 57.311 39.130 0.00 0.00 34.49 4.26
3648 4103 4.019174 CAGAGGCCATGTTAGAAAACCAT 58.981 43.478 5.01 0.00 34.49 3.55
3650 4105 3.686016 TCAGAGGCCATGTTAGAAAACC 58.314 45.455 5.01 0.00 34.49 3.27
3651 4106 5.189180 AGATCAGAGGCCATGTTAGAAAAC 58.811 41.667 5.01 0.00 36.07 2.43
3653 4108 4.718774 AGAGATCAGAGGCCATGTTAGAAA 59.281 41.667 5.01 0.00 0.00 2.52
3654 4109 4.293494 AGAGATCAGAGGCCATGTTAGAA 58.707 43.478 5.01 0.00 0.00 2.10
3656 4111 3.640498 TGAGAGATCAGAGGCCATGTTAG 59.360 47.826 5.01 0.00 0.00 2.34
3658 4113 2.475155 TGAGAGATCAGAGGCCATGTT 58.525 47.619 5.01 0.00 0.00 2.71
3659 4114 2.171568 TGAGAGATCAGAGGCCATGT 57.828 50.000 5.01 0.00 0.00 3.21
3660 4115 2.369203 ACATGAGAGATCAGAGGCCATG 59.631 50.000 5.01 2.98 36.81 3.66
3661 4116 2.692024 ACATGAGAGATCAGAGGCCAT 58.308 47.619 5.01 0.00 0.00 4.40
3663 4118 3.554752 GCTTACATGAGAGATCAGAGGCC 60.555 52.174 0.00 0.00 0.00 5.19
3664 4119 3.069300 TGCTTACATGAGAGATCAGAGGC 59.931 47.826 0.00 0.00 0.00 4.70
3665 4120 4.933505 TGCTTACATGAGAGATCAGAGG 57.066 45.455 0.00 0.00 0.00 3.69
3666 4121 6.086785 TGATGCTTACATGAGAGATCAGAG 57.913 41.667 0.00 0.00 36.35 3.35
3692 4168 3.595819 GGCTGCTTAAGGCCACTG 58.404 61.111 15.56 0.00 46.84 3.66
3755 4235 8.208718 TCAGATTCGATCCGTTTAATTCAAAT 57.791 30.769 0.00 0.00 0.00 2.32
3774 4254 8.877864 TCAACCCTATTTTTACACATCAGATT 57.122 30.769 0.00 0.00 0.00 2.40
3787 4267 5.221441 GCCAAGAACAACTCAACCCTATTTT 60.221 40.000 0.00 0.00 0.00 1.82
3889 4382 2.092212 ACATTGGAGATGCCCTAACCAG 60.092 50.000 0.00 0.00 34.97 4.00
3949 4442 5.016173 TGACCGATTCCATTCTCCATTTTT 58.984 37.500 0.00 0.00 0.00 1.94
3950 4443 4.599041 TGACCGATTCCATTCTCCATTTT 58.401 39.130 0.00 0.00 0.00 1.82
3951 4444 4.202441 CTGACCGATTCCATTCTCCATTT 58.798 43.478 0.00 0.00 0.00 2.32
3952 4445 3.434167 CCTGACCGATTCCATTCTCCATT 60.434 47.826 0.00 0.00 0.00 3.16
3953 4446 2.105477 CCTGACCGATTCCATTCTCCAT 59.895 50.000 0.00 0.00 0.00 3.41
3954 4447 1.486310 CCTGACCGATTCCATTCTCCA 59.514 52.381 0.00 0.00 0.00 3.86
3955 4448 1.202698 CCCTGACCGATTCCATTCTCC 60.203 57.143 0.00 0.00 0.00 3.71
3956 4449 1.811941 GCCCTGACCGATTCCATTCTC 60.812 57.143 0.00 0.00 0.00 2.87
3957 4450 0.181350 GCCCTGACCGATTCCATTCT 59.819 55.000 0.00 0.00 0.00 2.40
3958 4451 0.819666 GGCCCTGACCGATTCCATTC 60.820 60.000 0.00 0.00 0.00 2.67
3959 4452 1.227383 GGCCCTGACCGATTCCATT 59.773 57.895 0.00 0.00 0.00 3.16
3960 4453 0.399949 TAGGCCCTGACCGATTCCAT 60.400 55.000 0.00 0.00 33.69 3.41
3961 4454 0.619255 TTAGGCCCTGACCGATTCCA 60.619 55.000 0.00 0.00 33.69 3.53
3962 4455 0.765510 ATTAGGCCCTGACCGATTCC 59.234 55.000 0.00 0.00 33.69 3.01
3963 4456 2.640316 AATTAGGCCCTGACCGATTC 57.360 50.000 0.00 0.00 33.69 2.52
3964 4457 3.650942 TGATAATTAGGCCCTGACCGATT 59.349 43.478 0.00 0.00 33.69 3.34
3965 4458 3.008049 GTGATAATTAGGCCCTGACCGAT 59.992 47.826 0.00 0.00 33.69 4.18
3966 4459 2.367567 GTGATAATTAGGCCCTGACCGA 59.632 50.000 0.00 0.00 33.69 4.69
3967 4460 2.767505 GTGATAATTAGGCCCTGACCG 58.232 52.381 0.00 0.00 33.69 4.79
3968 4461 2.104281 ACGTGATAATTAGGCCCTGACC 59.896 50.000 0.00 0.00 0.00 4.02
3969 4462 3.181469 TGACGTGATAATTAGGCCCTGAC 60.181 47.826 0.00 0.00 0.00 3.51
3970 4463 3.035363 TGACGTGATAATTAGGCCCTGA 58.965 45.455 0.00 0.00 0.00 3.86
3971 4464 3.131396 GTGACGTGATAATTAGGCCCTG 58.869 50.000 0.00 0.00 0.00 4.45
3972 4465 2.223971 CGTGACGTGATAATTAGGCCCT 60.224 50.000 0.00 0.00 0.00 5.19
3973 4466 2.132762 CGTGACGTGATAATTAGGCCC 58.867 52.381 0.00 0.00 0.00 5.80
3974 4467 2.132762 CCGTGACGTGATAATTAGGCC 58.867 52.381 3.64 0.00 0.00 5.19
3975 4468 1.525619 GCCGTGACGTGATAATTAGGC 59.474 52.381 3.64 0.00 35.00 3.93
3976 4469 1.784856 CGCCGTGACGTGATAATTAGG 59.215 52.381 3.64 0.00 0.00 2.69
3977 4470 2.456989 ACGCCGTGACGTGATAATTAG 58.543 47.619 3.64 0.00 46.28 1.73
3978 4471 2.565210 ACGCCGTGACGTGATAATTA 57.435 45.000 3.64 0.00 46.28 1.40
3979 4472 3.429043 ACGCCGTGACGTGATAATT 57.571 47.368 3.64 0.00 46.28 1.40


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

AutoCloner maintained by Alex Coulton.