Multiple sequence alignment - TraesCS3A01G323200

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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 TraesCS3A01G323200 chr3A 100.000 5824 0 0 1 5824 567974833 567980656 0.000000e+00 10756
1 TraesCS3A01G323200 chr3A 79.159 1689 276 48 3168 4826 568020324 568021966 0.000000e+00 1099
2 TraesCS3A01G323200 chr3A 79.794 1262 228 18 1078 2318 568018372 568019627 0.000000e+00 893
3 TraesCS3A01G323200 chr3A 79.124 1255 222 30 1090 2318 568095154 568096394 0.000000e+00 830
4 TraesCS3A01G323200 chr3A 85.390 794 112 4 5033 5824 388952579 388951788 0.000000e+00 821
5 TraesCS3A01G323200 chr3D 92.014 4921 237 60 4 4858 429723273 429728103 0.000000e+00 6767
6 TraesCS3A01G323200 chr3D 84.109 1246 173 14 1078 2306 429909583 429910820 0.000000e+00 1181
7 TraesCS3A01G323200 chr3D 81.510 1444 199 38 3445 4866 429789533 429790930 0.000000e+00 1125
8 TraesCS3A01G323200 chr3D 79.110 1259 242 12 1078 2318 429786830 429788085 0.000000e+00 848
9 TraesCS3A01G323200 chr3D 78.824 1242 227 24 1090 2307 430050467 430051696 0.000000e+00 804
10 TraesCS3A01G323200 chr3D 80.894 738 137 4 5024 5759 92270733 92269998 3.910000e-161 579
11 TraesCS3A01G323200 chr3B 89.449 3213 197 62 422 3577 561970163 561973290 0.000000e+00 3925
12 TraesCS3A01G323200 chr3B 94.745 1351 40 11 3596 4922 561973384 561974727 0.000000e+00 2073
13 TraesCS3A01G323200 chr3B 81.584 1515 217 36 3361 4858 562275193 562276662 0.000000e+00 1195
14 TraesCS3A01G323200 chr3B 78.589 1247 246 12 1090 2318 562273033 562274276 0.000000e+00 804
15 TraesCS3A01G323200 chr3B 78.452 1253 234 25 1090 2318 562401824 562403064 0.000000e+00 785
16 TraesCS3A01G323200 chr3B 84.367 403 25 14 4 405 561969812 561970177 1.540000e-95 361
17 TraesCS3A01G323200 chr2B 79.197 1245 212 27 1114 2318 766231961 766233198 0.000000e+00 821
18 TraesCS3A01G323200 chr2B 83.382 692 112 3 5133 5822 534373973 534374663 6.360000e-179 638
19 TraesCS3A01G323200 chr2A 78.421 1330 226 43 1033 2318 755702977 755704289 0.000000e+00 809
20 TraesCS3A01G323200 chr2A 83.706 804 128 3 5022 5823 263217994 263218796 0.000000e+00 756
21 TraesCS3A01G323200 chr2A 79.950 798 153 5 5014 5806 771491122 771491917 1.090000e-161 580
22 TraesCS3A01G323200 chr2D 82.545 888 130 13 1451 2318 624303603 624304485 0.000000e+00 758
23 TraesCS3A01G323200 chr7D 80.693 808 143 10 5024 5824 137572461 137573262 2.980000e-172 616
24 TraesCS3A01G323200 chr7D 80.025 806 152 6 5024 5824 277447654 277448455 6.500000e-164 588
25 TraesCS3A01G323200 chr5D 79.703 808 158 4 5022 5824 193142764 193141958 3.910000e-161 579
26 TraesCS3A01G323200 chr5D 79.646 791 150 9 5024 5806 380622689 380621902 5.100000e-155 558


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 TraesCS3A01G323200 chr3A 567974833 567980656 5823 False 10756.000000 10756 100.000000 1 5824 1 chr3A.!!$F1 5823
1 TraesCS3A01G323200 chr3A 568018372 568021966 3594 False 996.000000 1099 79.476500 1078 4826 2 chr3A.!!$F3 3748
2 TraesCS3A01G323200 chr3A 568095154 568096394 1240 False 830.000000 830 79.124000 1090 2318 1 chr3A.!!$F2 1228
3 TraesCS3A01G323200 chr3A 388951788 388952579 791 True 821.000000 821 85.390000 5033 5824 1 chr3A.!!$R1 791
4 TraesCS3A01G323200 chr3D 429723273 429728103 4830 False 6767.000000 6767 92.014000 4 4858 1 chr3D.!!$F1 4854
5 TraesCS3A01G323200 chr3D 429909583 429910820 1237 False 1181.000000 1181 84.109000 1078 2306 1 chr3D.!!$F2 1228
6 TraesCS3A01G323200 chr3D 429786830 429790930 4100 False 986.500000 1125 80.310000 1078 4866 2 chr3D.!!$F4 3788
7 TraesCS3A01G323200 chr3D 430050467 430051696 1229 False 804.000000 804 78.824000 1090 2307 1 chr3D.!!$F3 1217
8 TraesCS3A01G323200 chr3D 92269998 92270733 735 True 579.000000 579 80.894000 5024 5759 1 chr3D.!!$R1 735
9 TraesCS3A01G323200 chr3B 561969812 561974727 4915 False 2119.666667 3925 89.520333 4 4922 3 chr3B.!!$F2 4918
10 TraesCS3A01G323200 chr3B 562273033 562276662 3629 False 999.500000 1195 80.086500 1090 4858 2 chr3B.!!$F3 3768
11 TraesCS3A01G323200 chr3B 562401824 562403064 1240 False 785.000000 785 78.452000 1090 2318 1 chr3B.!!$F1 1228
12 TraesCS3A01G323200 chr2B 766231961 766233198 1237 False 821.000000 821 79.197000 1114 2318 1 chr2B.!!$F2 1204
13 TraesCS3A01G323200 chr2B 534373973 534374663 690 False 638.000000 638 83.382000 5133 5822 1 chr2B.!!$F1 689
14 TraesCS3A01G323200 chr2A 755702977 755704289 1312 False 809.000000 809 78.421000 1033 2318 1 chr2A.!!$F2 1285
15 TraesCS3A01G323200 chr2A 263217994 263218796 802 False 756.000000 756 83.706000 5022 5823 1 chr2A.!!$F1 801
16 TraesCS3A01G323200 chr2A 771491122 771491917 795 False 580.000000 580 79.950000 5014 5806 1 chr2A.!!$F3 792
17 TraesCS3A01G323200 chr2D 624303603 624304485 882 False 758.000000 758 82.545000 1451 2318 1 chr2D.!!$F1 867
18 TraesCS3A01G323200 chr7D 137572461 137573262 801 False 616.000000 616 80.693000 5024 5824 1 chr7D.!!$F1 800
19 TraesCS3A01G323200 chr7D 277447654 277448455 801 False 588.000000 588 80.025000 5024 5824 1 chr7D.!!$F2 800
20 TraesCS3A01G323200 chr5D 193141958 193142764 806 True 579.000000 579 79.703000 5022 5824 1 chr5D.!!$R1 802
21 TraesCS3A01G323200 chr5D 380621902 380622689 787 True 558.000000 558 79.646000 5024 5806 1 chr5D.!!$R2 782

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
274 276 0.104304 ACGCATCCCTGTCCGTATTC 59.896 55.000 0.00 0.0 31.43 1.75 F
331 333 0.179034 AAGCAAGCTCCATCCGATCC 60.179 55.000 0.00 0.0 0.00 3.36 F
642 659 0.469331 TTGGTGGAGACGGAGACTGT 60.469 55.000 0.00 0.0 29.49 3.55 F
647 664 0.810016 GGAGACGGAGACTGTGTACC 59.190 60.000 0.00 0.0 29.49 3.34 F
730 750 0.963962 CACCATGCCAGTTGCTCTTT 59.036 50.000 0.00 0.0 42.00 2.52 F
1005 1082 1.039856 GAGAGGGAGAGAGCATGACC 58.960 60.000 0.00 0.0 0.00 4.02 F
1515 1625 1.367471 CGGCATGAAGCTCGGGATA 59.633 57.895 0.00 0.0 44.79 2.59 F
2910 3787 1.240256 GGTCGTTGGGTACAATTGCA 58.760 50.000 5.05 0.0 39.13 4.08 F
3512 4422 0.246635 CAACGGATGACTTCGACCCT 59.753 55.000 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2042 1.079819 CTGGGTGGTGTCGCAGTAG 60.080 63.158 0.00 0.0 41.40 2.57 R
2178 2312 4.388499 ATCCCGCCGCTGACGTTT 62.388 61.111 0.00 0.0 37.70 3.60 R
2500 3360 1.984026 CAATGGCCAGTGGGGGTTC 60.984 63.158 25.42 0.0 37.04 3.62 R
2529 3390 2.295629 TGATGTGATGCTCGATCCTCTC 59.704 50.000 0.00 0.0 0.00 3.20 R
2654 3531 6.550938 TGATAGCTATCAGATGGTTATGGG 57.449 41.667 28.69 0.0 37.76 4.00 R
2743 3620 0.108585 TGAGGAAAGTGGTGCCAGTC 59.891 55.000 0.00 0.0 0.00 3.51 R
3047 3925 0.114954 AGGTTGGGTGGTGATGCAAT 59.885 50.000 0.00 0.0 0.00 3.56 R
3716 4710 0.541764 TGAATTCCCCAACACCCTGC 60.542 55.000 2.27 0.0 0.00 4.85 R
4986 6035 0.042131 ACAATGGGACGGAGGGAGTA 59.958 55.000 0.00 0.0 0.00 2.59 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
41 43 3.670523 CCGCATTACATGATACTGACGAG 59.329 47.826 0.00 0.00 0.00 4.18
62 64 1.040339 AGATGCCGTCACTCCTCTCC 61.040 60.000 0.00 0.00 0.00 3.71
65 67 2.766400 GCCGTCACTCCTCTCCGAG 61.766 68.421 0.00 0.00 35.88 4.63
70 72 1.200484 GTCACTCCTCTCCGAGTTGAC 59.800 57.143 0.00 0.00 41.23 3.18
74 76 3.083293 ACTCCTCTCCGAGTTGACTTAC 58.917 50.000 0.00 0.00 40.23 2.34
86 88 3.638160 AGTTGACTTACGGACTTGTGGTA 59.362 43.478 0.00 0.00 0.00 3.25
118 120 6.382608 AGATAATAATCGTCGTGGATCACAG 58.617 40.000 0.00 0.00 37.19 3.66
150 152 4.396478 TCAACAATCAGACGGTGAACAAAA 59.604 37.500 0.00 0.00 39.19 2.44
151 153 4.552166 ACAATCAGACGGTGAACAAAAG 57.448 40.909 0.00 0.00 39.19 2.27
152 154 3.945285 ACAATCAGACGGTGAACAAAAGT 59.055 39.130 0.00 0.00 39.19 2.66
153 155 4.035208 ACAATCAGACGGTGAACAAAAGTC 59.965 41.667 0.00 0.00 39.19 3.01
154 156 3.254470 TCAGACGGTGAACAAAAGTCA 57.746 42.857 0.00 0.00 34.56 3.41
155 157 3.194861 TCAGACGGTGAACAAAAGTCAG 58.805 45.455 0.00 0.00 34.56 3.51
156 158 3.118920 TCAGACGGTGAACAAAAGTCAGA 60.119 43.478 0.00 0.00 34.56 3.27
157 159 3.809832 CAGACGGTGAACAAAAGTCAGAT 59.190 43.478 0.00 0.00 34.56 2.90
158 160 4.058817 AGACGGTGAACAAAAGTCAGATC 58.941 43.478 0.00 0.00 34.56 2.75
159 161 4.058817 GACGGTGAACAAAAGTCAGATCT 58.941 43.478 0.00 0.00 32.57 2.75
206 208 4.711949 AGCAAGCCAGCCCGTCAG 62.712 66.667 0.00 0.00 34.23 3.51
207 209 4.704833 GCAAGCCAGCCCGTCAGA 62.705 66.667 0.00 0.00 0.00 3.27
208 210 2.032528 CAAGCCAGCCCGTCAGAA 59.967 61.111 0.00 0.00 0.00 3.02
209 211 2.032681 AAGCCAGCCCGTCAGAAC 59.967 61.111 0.00 0.00 0.00 3.01
219 221 1.403514 CCCGTCAGAACTCAGAAGCTC 60.404 57.143 0.00 0.00 0.00 4.09
229 231 2.098934 ACTCAGAAGCTCGAGCACATAG 59.901 50.000 36.87 27.48 45.16 2.23
274 276 0.104304 ACGCATCCCTGTCCGTATTC 59.896 55.000 0.00 0.00 31.43 1.75
277 279 2.417719 GCATCCCTGTCCGTATTCATC 58.582 52.381 0.00 0.00 0.00 2.92
301 303 5.923665 GGTACGACATTTCAATTTTCGAGT 58.076 37.500 7.13 0.00 0.00 4.18
302 304 6.013689 GGTACGACATTTCAATTTTCGAGTC 58.986 40.000 7.13 0.00 0.00 3.36
303 305 5.666969 ACGACATTTCAATTTTCGAGTCA 57.333 34.783 7.13 0.00 0.00 3.41
304 306 5.440685 ACGACATTTCAATTTTCGAGTCAC 58.559 37.500 7.13 0.00 0.00 3.67
305 307 5.007234 ACGACATTTCAATTTTCGAGTCACA 59.993 36.000 7.13 0.00 0.00 3.58
306 308 5.906838 CGACATTTCAATTTTCGAGTCACAA 59.093 36.000 0.00 0.00 0.00 3.33
307 309 6.129717 CGACATTTCAATTTTCGAGTCACAAC 60.130 38.462 0.00 0.00 0.00 3.32
328 330 0.674581 CACAAGCAAGCTCCATCCGA 60.675 55.000 0.00 0.00 0.00 4.55
329 331 0.254178 ACAAGCAAGCTCCATCCGAT 59.746 50.000 0.00 0.00 0.00 4.18
330 332 0.942962 CAAGCAAGCTCCATCCGATC 59.057 55.000 0.00 0.00 0.00 3.69
331 333 0.179034 AAGCAAGCTCCATCCGATCC 60.179 55.000 0.00 0.00 0.00 3.36
332 334 1.958205 GCAAGCTCCATCCGATCCG 60.958 63.158 0.00 0.00 0.00 4.18
344 346 1.301716 CGATCCGCCTAACCCCATG 60.302 63.158 0.00 0.00 0.00 3.66
401 403 2.259204 CGGCTAAACGTGGACCGA 59.741 61.111 12.62 0.00 46.71 4.69
418 420 5.086727 GGACCGATTTAAGCTTCGAAAAAG 58.913 41.667 0.00 0.00 37.55 2.27
420 422 4.082949 ACCGATTTAAGCTTCGAAAAAGGG 60.083 41.667 0.00 6.76 37.55 3.95
642 659 0.469331 TTGGTGGAGACGGAGACTGT 60.469 55.000 0.00 0.00 29.49 3.55
644 661 1.179814 GGTGGAGACGGAGACTGTGT 61.180 60.000 0.00 0.00 29.49 3.72
647 664 0.810016 GGAGACGGAGACTGTGTACC 59.190 60.000 0.00 0.00 29.49 3.34
675 695 3.782244 CGCGTGAAGACCAGCTGC 61.782 66.667 8.66 0.00 0.00 5.25
699 719 3.204827 CCGAATCGGGCAGCCAAG 61.205 66.667 14.91 6.81 44.15 3.61
729 749 1.530013 GCACCATGCCAGTTGCTCTT 61.530 55.000 0.00 0.00 42.00 2.85
730 750 0.963962 CACCATGCCAGTTGCTCTTT 59.036 50.000 0.00 0.00 42.00 2.52
731 751 1.342174 CACCATGCCAGTTGCTCTTTT 59.658 47.619 0.00 0.00 42.00 2.27
732 752 1.342174 ACCATGCCAGTTGCTCTTTTG 59.658 47.619 0.00 0.00 42.00 2.44
733 753 1.337447 CCATGCCAGTTGCTCTTTTGG 60.337 52.381 0.00 0.00 42.00 3.28
734 754 1.614903 CATGCCAGTTGCTCTTTTGGA 59.385 47.619 0.00 0.00 42.00 3.53
735 755 1.321474 TGCCAGTTGCTCTTTTGGAG 58.679 50.000 0.00 0.00 44.49 3.86
741 761 4.114794 CAGTTGCTCTTTTGGAGTTTTGG 58.885 43.478 0.00 0.00 43.62 3.28
757 777 2.536761 TTGGTGGTCAGTAAACGAGG 57.463 50.000 0.00 0.00 0.00 4.63
794 822 4.916041 TCAAATCCTCAAGTGGTCTCAT 57.084 40.909 0.00 0.00 0.00 2.90
860 900 2.029666 CACGCTGATCGGATCCCC 59.970 66.667 15.06 5.40 43.86 4.81
871 911 5.097948 TGATCGGATCCCCAGGAATTATTA 58.902 41.667 15.06 0.00 34.34 0.98
880 920 2.476619 CCAGGAATTATTAGTGCGAGCG 59.523 50.000 0.00 0.00 0.00 5.03
1004 1081 1.682854 CTGAGAGGGAGAGAGCATGAC 59.317 57.143 0.00 0.00 0.00 3.06
1005 1082 1.039856 GAGAGGGAGAGAGCATGACC 58.960 60.000 0.00 0.00 0.00 4.02
1323 1412 4.247380 GGCCGGCTCCTCATCCTG 62.247 72.222 28.56 0.00 0.00 3.86
1515 1625 1.367471 CGGCATGAAGCTCGGGATA 59.633 57.895 0.00 0.00 44.79 2.59
1608 1718 3.702048 TTCAAGCTCGTCCCCGGG 61.702 66.667 15.80 15.80 37.72 5.73
1728 1838 2.350522 CAGGATTTCCTCTTCACGGTG 58.649 52.381 0.56 0.56 46.65 4.94
2436 2690 8.918961 ACTCTCATTTTCTTACATCTAACTCG 57.081 34.615 0.00 0.00 0.00 4.18
2445 2699 8.462143 TTCTTACATCTAACTCGATTTGTGAC 57.538 34.615 0.00 0.00 0.00 3.67
2474 3185 3.226029 GCTTGCTAGCGTTAGAATTCG 57.774 47.619 10.82 0.00 37.71 3.34
2475 3186 2.858344 GCTTGCTAGCGTTAGAATTCGA 59.142 45.455 10.82 0.00 37.71 3.71
2500 3360 9.209175 GACCATGTATGTTAGCTAGAAATAAGG 57.791 37.037 0.00 0.00 0.00 2.69
2505 3365 8.208903 TGTATGTTAGCTAGAAATAAGGAACCC 58.791 37.037 0.00 0.00 0.00 4.11
2529 3390 2.495866 GCCATTGCGGGTCCATTG 59.504 61.111 0.00 0.00 34.06 2.82
2654 3531 4.883083 TGTGTTCTCTGTATCTTCACCAC 58.117 43.478 0.00 0.00 0.00 4.16
2656 3533 3.260884 TGTTCTCTGTATCTTCACCACCC 59.739 47.826 0.00 0.00 0.00 4.61
2814 3691 4.215827 TCTTCTGTTAGGTCGTCAGAGTTC 59.784 45.833 0.00 0.00 39.00 3.01
2903 3780 1.937546 ATCCGTCGGTCGTTGGGTAC 61.938 60.000 11.88 0.00 37.94 3.34
2910 3787 1.240256 GGTCGTTGGGTACAATTGCA 58.760 50.000 5.05 0.00 39.13 4.08
2911 3788 1.609555 GGTCGTTGGGTACAATTGCAA 59.390 47.619 5.05 0.00 39.13 4.08
2912 3789 2.034812 GGTCGTTGGGTACAATTGCAAA 59.965 45.455 1.71 0.00 39.13 3.68
2913 3790 3.305744 GGTCGTTGGGTACAATTGCAAAT 60.306 43.478 1.71 0.00 39.13 2.32
2914 3791 4.303282 GTCGTTGGGTACAATTGCAAATT 58.697 39.130 1.71 0.00 39.13 1.82
2915 3792 4.747605 GTCGTTGGGTACAATTGCAAATTT 59.252 37.500 1.71 0.00 39.13 1.82
2916 3793 4.747108 TCGTTGGGTACAATTGCAAATTTG 59.253 37.500 14.03 14.03 39.13 2.32
2917 3794 4.509600 CGTTGGGTACAATTGCAAATTTGT 59.490 37.500 19.32 19.32 39.13 2.83
2931 3808 7.526142 TGCAAATTTGTAATACCCACTGTTA 57.474 32.000 19.03 0.00 0.00 2.41
2964 3841 1.294659 CTGAGAGCACCAAACTCGCC 61.295 60.000 0.00 0.00 39.23 5.54
2973 3850 1.287425 CCAAACTCGCCGGATTACTC 58.713 55.000 5.05 0.00 0.00 2.59
3002 3879 9.099454 ACTTAGTTAAAAAGATAATCGCTGGAG 57.901 33.333 5.96 0.00 0.00 3.86
3044 3922 1.601166 AGAAACGCCACTTAACACCC 58.399 50.000 0.00 0.00 0.00 4.61
3047 3925 1.765230 AACGCCACTTAACACCCAAA 58.235 45.000 0.00 0.00 0.00 3.28
3048 3926 1.989706 ACGCCACTTAACACCCAAAT 58.010 45.000 0.00 0.00 0.00 2.32
3072 3950 1.217916 TCACCACCCAACCTGAAAGA 58.782 50.000 0.00 0.00 34.07 2.52
3098 3979 4.260139 TGGCTACAGAAAATGTCGTGTA 57.740 40.909 0.00 0.00 42.70 2.90
3125 4006 4.813027 TGGTAAACTAAGCTCAAGTACGG 58.187 43.478 2.34 0.00 0.00 4.02
3126 4007 4.281688 TGGTAAACTAAGCTCAAGTACGGT 59.718 41.667 2.34 0.00 0.00 4.83
3127 4008 4.624452 GGTAAACTAAGCTCAAGTACGGTG 59.376 45.833 2.34 0.00 0.00 4.94
3128 4009 4.332428 AAACTAAGCTCAAGTACGGTGT 57.668 40.909 2.34 0.00 0.00 4.16
3129 4010 5.458041 AAACTAAGCTCAAGTACGGTGTA 57.542 39.130 2.34 0.00 0.00 2.90
3161 4043 7.920682 ACTGGAAAAGTTCATAATTCACACAAC 59.079 33.333 0.00 0.00 34.57 3.32
3356 4266 1.226030 AAACGGCGCCAAGTAGTCAC 61.226 55.000 28.98 0.00 0.00 3.67
3512 4422 0.246635 CAACGGATGACTTCGACCCT 59.753 55.000 0.00 0.00 0.00 4.34
3530 4440 3.584406 CCTGATAGTAAGATCGGGCAG 57.416 52.381 0.00 0.00 43.76 4.85
3533 4443 1.550976 GATAGTAAGATCGGGCAGGGG 59.449 57.143 0.00 0.00 0.00 4.79
3592 4502 8.635765 AAGAAATTAAGAATCAGTTGGCACTA 57.364 30.769 0.00 0.00 0.00 2.74
3594 4533 8.103305 AGAAATTAAGAATCAGTTGGCACTAGA 58.897 33.333 0.00 0.00 0.00 2.43
3602 4541 5.584253 TCAGTTGGCACTAGATAGAGAAC 57.416 43.478 0.00 0.00 0.00 3.01
3606 4545 6.096987 CAGTTGGCACTAGATAGAGAACCTTA 59.903 42.308 0.00 0.00 0.00 2.69
3651 4645 2.301346 ACCGAATGGATCTGCATTTCC 58.699 47.619 7.89 7.89 39.21 3.13
3716 4710 7.693969 AAAGAGGTTATCCAAGAAATCAGTG 57.306 36.000 0.00 0.00 35.89 3.66
3830 4824 3.378742 ACGACGAGAGAATGCTTGTCTAT 59.621 43.478 0.00 0.00 43.91 1.98
3860 4854 1.202758 CCCAACAACAGCCTAGACACA 60.203 52.381 0.00 0.00 0.00 3.72
3897 4895 6.753279 TCAGTTCATTTTCTTTGCAGAAACAG 59.247 34.615 0.88 0.00 46.71 3.16
3942 4945 1.199789 ACATGTGCAATGTGCTTACCG 59.800 47.619 11.96 0.00 45.31 4.02
4289 5305 3.576078 TGTGAGATGGTGGTTTTCAGT 57.424 42.857 0.00 0.00 0.00 3.41
4325 5341 2.139917 GAATATGCAATGGACGGCGTA 58.860 47.619 14.74 0.00 36.09 4.42
4346 5362 7.251994 GCGTATTCTCTATGAAGTCCGATATT 58.748 38.462 0.00 0.00 38.18 1.28
4745 5777 3.071892 ACGAACCTGGAGTAAACATTGGA 59.928 43.478 0.00 0.00 0.00 3.53
4854 5886 6.089249 AGGGTAGAAATTCTTGTTGCTTTG 57.911 37.500 0.00 0.00 0.00 2.77
4879 5924 4.157656 TGGTTTGTACAGCATAGGCATTTC 59.842 41.667 0.67 0.00 44.61 2.17
4891 5940 8.725148 CAGCATAGGCATTTCTATTTTACCTAG 58.275 37.037 0.67 0.00 44.61 3.02
4897 5946 8.107095 AGGCATTTCTATTTTACCTAGTGTCAA 58.893 33.333 0.00 0.00 0.00 3.18
4909 5958 6.380079 ACCTAGTGTCAAAAGATCTTGGAT 57.620 37.500 9.17 0.00 0.00 3.41
4911 5960 7.234355 ACCTAGTGTCAAAAGATCTTGGATTT 58.766 34.615 9.17 0.00 0.00 2.17
4945 5994 9.979578 ACAAGCAATGTTTAATTACTCATCAAA 57.020 25.926 0.00 0.00 40.06 2.69
4949 5998 8.801913 GCAATGTTTAATTACTCATCAAAGAGC 58.198 33.333 0.00 0.00 39.26 4.09
4953 6002 9.719355 TGTTTAATTACTCATCAAAGAGCTACA 57.281 29.630 0.00 0.00 39.26 2.74
4958 6007 9.624373 AATTACTCATCAAAGAGCTACATCATT 57.376 29.630 0.00 0.00 39.26 2.57
4972 6021 9.979270 GAGCTACATCATTATATAAACATGTGC 57.021 33.333 21.87 20.98 0.00 4.57
4973 6022 8.659491 AGCTACATCATTATATAAACATGTGCG 58.341 33.333 21.87 16.49 31.01 5.34
4974 6023 7.426456 GCTACATCATTATATAAACATGTGCGC 59.574 37.037 21.87 19.83 0.00 6.09
4975 6024 7.439157 ACATCATTATATAAACATGTGCGCT 57.561 32.000 9.73 0.00 0.00 5.92
4976 6025 7.874940 ACATCATTATATAAACATGTGCGCTT 58.125 30.769 9.73 0.00 0.00 4.68
4977 6026 7.804600 ACATCATTATATAAACATGTGCGCTTG 59.195 33.333 9.73 11.29 0.00 4.01
4978 6027 7.258022 TCATTATATAAACATGTGCGCTTGT 57.742 32.000 9.73 12.62 34.93 3.16
4979 6028 8.371770 TCATTATATAAACATGTGCGCTTGTA 57.628 30.769 17.95 5.35 33.39 2.41
4980 6029 8.495148 TCATTATATAAACATGTGCGCTTGTAG 58.505 33.333 17.95 0.00 33.39 2.74
4981 6030 7.780008 TTATATAAACATGTGCGCTTGTAGT 57.220 32.000 17.95 11.99 33.39 2.73
4982 6031 2.686558 AAACATGTGCGCTTGTAGTG 57.313 45.000 17.95 1.57 33.39 2.74
4983 6032 1.877637 AACATGTGCGCTTGTAGTGA 58.122 45.000 17.95 0.00 33.39 3.41
4984 6033 1.877637 ACATGTGCGCTTGTAGTGAA 58.122 45.000 16.37 0.00 32.19 3.18
4985 6034 1.531149 ACATGTGCGCTTGTAGTGAAC 59.469 47.619 16.37 0.00 34.82 3.18
4986 6035 1.800586 CATGTGCGCTTGTAGTGAACT 59.199 47.619 9.73 0.00 35.29 3.01
4987 6036 2.804697 TGTGCGCTTGTAGTGAACTA 57.195 45.000 9.73 0.00 35.29 2.24
4988 6037 2.400399 TGTGCGCTTGTAGTGAACTAC 58.600 47.619 9.73 12.72 46.78 2.73
4989 6038 2.035449 TGTGCGCTTGTAGTGAACTACT 59.965 45.455 18.74 0.00 46.74 2.57
4990 6039 2.662156 GTGCGCTTGTAGTGAACTACTC 59.338 50.000 18.74 9.10 46.74 2.59
4991 6040 2.260481 GCGCTTGTAGTGAACTACTCC 58.740 52.381 18.74 8.27 46.74 3.85
4992 6041 2.877335 CGCTTGTAGTGAACTACTCCC 58.123 52.381 18.74 8.00 46.74 4.30
4993 6042 2.492484 CGCTTGTAGTGAACTACTCCCT 59.508 50.000 18.74 0.00 46.74 4.20
4994 6043 3.427773 CGCTTGTAGTGAACTACTCCCTC 60.428 52.174 18.74 5.84 46.74 4.30
4995 6044 3.119065 GCTTGTAGTGAACTACTCCCTCC 60.119 52.174 18.74 2.00 46.74 4.30
4996 6045 2.719739 TGTAGTGAACTACTCCCTCCG 58.280 52.381 18.74 0.00 46.74 4.63
4997 6046 2.040813 TGTAGTGAACTACTCCCTCCGT 59.959 50.000 18.74 0.00 46.74 4.69
4998 6047 1.836802 AGTGAACTACTCCCTCCGTC 58.163 55.000 0.00 0.00 33.17 4.79
4999 6048 0.816373 GTGAACTACTCCCTCCGTCC 59.184 60.000 0.00 0.00 0.00 4.79
5000 6049 0.324091 TGAACTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
5001 6050 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
5002 6051 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
5003 6052 0.338814 ACTACTCCCTCCGTCCCATT 59.661 55.000 0.00 0.00 0.00 3.16
5004 6053 0.753262 CTACTCCCTCCGTCCCATTG 59.247 60.000 0.00 0.00 0.00 2.82
5005 6054 0.042131 TACTCCCTCCGTCCCATTGT 59.958 55.000 0.00 0.00 0.00 2.71
5006 6055 1.265454 ACTCCCTCCGTCCCATTGTC 61.265 60.000 0.00 0.00 0.00 3.18
5007 6056 0.978146 CTCCCTCCGTCCCATTGTCT 60.978 60.000 0.00 0.00 0.00 3.41
5008 6057 1.221840 CCCTCCGTCCCATTGTCTG 59.778 63.158 0.00 0.00 0.00 3.51
5009 6058 1.553690 CCCTCCGTCCCATTGTCTGT 61.554 60.000 0.00 0.00 0.00 3.41
5010 6059 0.324943 CCTCCGTCCCATTGTCTGTT 59.675 55.000 0.00 0.00 0.00 3.16
5011 6060 1.676014 CCTCCGTCCCATTGTCTGTTC 60.676 57.143 0.00 0.00 0.00 3.18
5012 6061 1.276421 CTCCGTCCCATTGTCTGTTCT 59.724 52.381 0.00 0.00 0.00 3.01
5013 6062 1.697432 TCCGTCCCATTGTCTGTTCTT 59.303 47.619 0.00 0.00 0.00 2.52
5014 6063 1.806542 CCGTCCCATTGTCTGTTCTTG 59.193 52.381 0.00 0.00 0.00 3.02
5015 6064 2.494059 CGTCCCATTGTCTGTTCTTGT 58.506 47.619 0.00 0.00 0.00 3.16
5016 6065 3.556213 CCGTCCCATTGTCTGTTCTTGTA 60.556 47.826 0.00 0.00 0.00 2.41
5017 6066 3.679980 CGTCCCATTGTCTGTTCTTGTAG 59.320 47.826 0.00 0.00 0.00 2.74
5018 6067 4.642429 GTCCCATTGTCTGTTCTTGTAGT 58.358 43.478 0.00 0.00 0.00 2.73
5019 6068 5.063880 GTCCCATTGTCTGTTCTTGTAGTT 58.936 41.667 0.00 0.00 0.00 2.24
5020 6069 5.179555 GTCCCATTGTCTGTTCTTGTAGTTC 59.820 44.000 0.00 0.00 0.00 3.01
5021 6070 5.063204 CCCATTGTCTGTTCTTGTAGTTCA 58.937 41.667 0.00 0.00 0.00 3.18
5022 6071 5.180117 CCCATTGTCTGTTCTTGTAGTTCAG 59.820 44.000 0.00 0.00 0.00 3.02
5225 6280 3.859386 GTGGAAAATCGCAAGCCATAAAG 59.141 43.478 0.00 0.00 37.18 1.85
5241 6298 6.604795 AGCCATAAAGTAGCAGTCATCAAAAT 59.395 34.615 0.00 0.00 0.00 1.82
5252 6309 1.750399 ATCAAAATCTGCGGCCGCT 60.750 52.632 45.79 27.80 42.51 5.52
5284 6341 1.128692 CGGTCCTTCGTTCTTCATTGC 59.871 52.381 0.00 0.00 0.00 3.56
5393 6450 4.145876 TGCTTCAGCTGTTAAAACATCG 57.854 40.909 14.67 0.00 42.66 3.84
5398 6455 1.196808 AGCTGTTAAAACATCGGCACG 59.803 47.619 7.89 0.00 44.07 5.34
5483 6540 2.125106 GTGCCCCTTAGCAGGTCG 60.125 66.667 0.00 0.00 45.14 4.79
5515 6572 4.951715 TGAAGCATCCACATTCAGCTTAAT 59.048 37.500 0.00 0.00 44.73 1.40
5535 6592 0.104090 AAACCCCCTAGGAGGTGTGT 60.104 55.000 16.99 1.53 39.89 3.72
5545 6602 2.065799 AGGAGGTGTGTTCCATCCTTT 58.934 47.619 0.00 0.00 37.18 3.11
5546 6603 2.162681 GGAGGTGTGTTCCATCCTTTG 58.837 52.381 0.00 0.00 34.74 2.77
5574 6631 3.578282 TCTCTTAGCATTGTGTGAGTGGA 59.422 43.478 0.00 0.00 0.00 4.02
5612 6669 4.082787 GCCATTATAACACGAATCCCCATG 60.083 45.833 0.00 0.00 0.00 3.66
5653 6713 5.047566 TGAGACTTTTCCTCATGAACCAA 57.952 39.130 0.00 0.00 35.89 3.67
5702 6762 5.069119 TCACACGGTTATAGCAATCATCTCT 59.931 40.000 0.00 0.00 0.00 3.10
5770 6830 5.677319 AGGAGTAATGATTCAAAGACCGA 57.323 39.130 0.00 0.00 0.00 4.69
5781 6841 1.878656 AAAGACCGACTCTCCCGCAG 61.879 60.000 0.00 0.00 0.00 5.18
5814 6874 6.815089 ACACATGCTTTTCTAATTGTTCCAA 58.185 32.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.123453 GCGGGTAGTTTACTTTGGTTACG 59.877 47.826 0.00 0.00 0.00 3.18
41 43 1.040339 AGAGGAGTGACGGCATCTCC 61.040 60.000 24.32 24.32 45.56 3.71
62 64 2.724690 CACAAGTCCGTAAGTCAACTCG 59.275 50.000 0.00 0.00 0.00 4.18
65 67 2.830104 ACCACAAGTCCGTAAGTCAAC 58.170 47.619 0.00 0.00 0.00 3.18
70 72 1.068055 AGCGTACCACAAGTCCGTAAG 60.068 52.381 0.00 0.00 0.00 2.34
74 76 0.241749 TGTAGCGTACCACAAGTCCG 59.758 55.000 0.00 0.00 0.00 4.79
86 88 5.624081 CACGACGATTATTATCTTGTAGCGT 59.376 40.000 0.00 0.00 0.00 5.07
88 90 6.147581 TCCACGACGATTATTATCTTGTAGC 58.852 40.000 0.00 0.00 0.00 3.58
101 103 0.246360 TGCTGTGATCCACGACGATT 59.754 50.000 0.00 0.00 37.14 3.34
102 104 0.179127 CTGCTGTGATCCACGACGAT 60.179 55.000 0.00 0.00 37.14 3.73
103 105 1.212751 CTGCTGTGATCCACGACGA 59.787 57.895 0.00 0.00 37.14 4.20
118 120 3.425359 CGTCTGATTGTTGAATGGACTGC 60.425 47.826 0.00 0.00 0.00 4.40
203 205 1.201181 GCTCGAGCTTCTGAGTTCTGA 59.799 52.381 29.88 0.00 38.21 3.27
204 206 1.067985 TGCTCGAGCTTCTGAGTTCTG 60.068 52.381 35.27 0.00 42.66 3.02
205 207 1.067915 GTGCTCGAGCTTCTGAGTTCT 60.068 52.381 35.27 0.00 42.66 3.01
206 208 1.336332 TGTGCTCGAGCTTCTGAGTTC 60.336 52.381 35.27 15.24 42.66 3.01
207 209 0.676184 TGTGCTCGAGCTTCTGAGTT 59.324 50.000 35.27 0.00 42.66 3.01
208 210 0.894141 ATGTGCTCGAGCTTCTGAGT 59.106 50.000 35.27 13.39 42.66 3.41
209 211 2.098934 ACTATGTGCTCGAGCTTCTGAG 59.901 50.000 35.27 25.73 42.66 3.35
219 221 3.664486 GCTACGTTCATACTATGTGCTCG 59.336 47.826 0.00 0.00 0.00 5.03
229 231 0.921347 CGTGGCTGCTACGTTCATAC 59.079 55.000 27.16 0.00 36.83 2.39
258 260 2.677199 CGATGAATACGGACAGGGATG 58.323 52.381 0.00 0.00 0.00 3.51
274 276 5.447846 CGAAAATTGAAATGTCGTACCGATG 59.552 40.000 0.00 0.00 38.42 3.84
277 279 4.948588 TCGAAAATTGAAATGTCGTACCG 58.051 39.130 0.00 0.00 32.02 4.02
299 301 1.672881 GCTTGCTTGTGAGTTGTGACT 59.327 47.619 0.00 0.00 39.32 3.41
300 302 1.672881 AGCTTGCTTGTGAGTTGTGAC 59.327 47.619 0.00 0.00 0.00 3.67
301 303 1.942657 GAGCTTGCTTGTGAGTTGTGA 59.057 47.619 0.00 0.00 0.00 3.58
302 304 1.002033 GGAGCTTGCTTGTGAGTTGTG 60.002 52.381 0.00 0.00 0.00 3.33
303 305 1.312815 GGAGCTTGCTTGTGAGTTGT 58.687 50.000 0.00 0.00 0.00 3.32
304 306 1.311859 TGGAGCTTGCTTGTGAGTTG 58.688 50.000 0.00 0.00 0.00 3.16
305 307 2.157738 GATGGAGCTTGCTTGTGAGTT 58.842 47.619 0.00 0.00 0.00 3.01
306 308 1.612726 GGATGGAGCTTGCTTGTGAGT 60.613 52.381 0.00 0.00 0.00 3.41
307 309 1.093159 GGATGGAGCTTGCTTGTGAG 58.907 55.000 0.00 0.00 0.00 3.51
328 330 1.056660 CTACATGGGGTTAGGCGGAT 58.943 55.000 0.00 0.00 0.00 4.18
329 331 0.031917 TCTACATGGGGTTAGGCGGA 60.032 55.000 0.00 0.00 0.00 5.54
330 332 1.056660 ATCTACATGGGGTTAGGCGG 58.943 55.000 0.00 0.00 0.00 6.13
331 333 1.270839 CCATCTACATGGGGTTAGGCG 60.271 57.143 0.00 0.00 45.63 5.52
332 334 2.568623 CCATCTACATGGGGTTAGGC 57.431 55.000 0.00 0.00 45.63 3.93
344 346 3.214250 CTCGCGGCCCTCCATCTAC 62.214 68.421 6.13 0.00 0.00 2.59
354 356 1.801512 GACATTTTTGCTCGCGGCC 60.802 57.895 6.13 0.00 40.92 6.13
382 384 3.122971 GGTCCACGTTTAGCCGGC 61.123 66.667 21.89 21.89 0.00 6.13
401 403 5.918576 CGTTTCCCTTTTTCGAAGCTTAAAT 59.081 36.000 0.00 0.00 0.00 1.40
460 462 3.041940 CGTGACCTGCCAACGGAC 61.042 66.667 0.00 0.00 0.00 4.79
461 463 3.228017 TCGTGACCTGCCAACGGA 61.228 61.111 0.00 0.00 0.00 4.69
462 464 3.041940 GTCGTGACCTGCCAACGG 61.042 66.667 0.00 0.00 0.00 4.44
463 465 3.403057 CGTCGTGACCTGCCAACG 61.403 66.667 0.00 0.00 0.00 4.10
504 506 4.101790 ATGCGCTGCGTTTTCCCG 62.102 61.111 24.04 0.00 0.00 5.14
534 536 1.041437 GACTAGGATCCCGGACCTTG 58.959 60.000 17.18 16.89 37.68 3.61
536 538 1.294426 TGGACTAGGATCCCGGACCT 61.294 60.000 8.55 11.60 38.06 3.85
539 541 0.398098 GGTTGGACTAGGATCCCGGA 60.398 60.000 8.55 0.00 38.06 5.14
549 558 2.148052 TTGGTGCGGGGTTGGACTA 61.148 57.895 0.00 0.00 0.00 2.59
699 719 4.360405 ATGGTGCCGGGGTCAACC 62.360 66.667 2.18 0.00 39.11 3.77
729 749 3.094484 ACTGACCACCAAAACTCCAAA 57.906 42.857 0.00 0.00 0.00 3.28
730 750 2.818751 ACTGACCACCAAAACTCCAA 57.181 45.000 0.00 0.00 0.00 3.53
731 751 3.935818 TTACTGACCACCAAAACTCCA 57.064 42.857 0.00 0.00 0.00 3.86
732 752 3.002965 CGTTTACTGACCACCAAAACTCC 59.997 47.826 0.00 0.00 0.00 3.85
733 753 3.872771 TCGTTTACTGACCACCAAAACTC 59.127 43.478 0.00 0.00 0.00 3.01
734 754 3.875134 CTCGTTTACTGACCACCAAAACT 59.125 43.478 0.00 0.00 0.00 2.66
735 755 3.002965 CCTCGTTTACTGACCACCAAAAC 59.997 47.826 0.00 0.00 0.00 2.43
741 761 0.971386 TCCCCTCGTTTACTGACCAC 59.029 55.000 0.00 0.00 0.00 4.16
757 777 2.607631 TTGATATCCGTTCCGTTCCC 57.392 50.000 0.00 0.00 0.00 3.97
780 800 2.507484 TGGCAAATGAGACCACTTGAG 58.493 47.619 0.00 0.00 31.69 3.02
824 852 1.134367 TGAGATGAATCGGTCGTGGAC 59.866 52.381 0.00 0.00 0.00 4.02
860 900 2.476619 CCGCTCGCACTAATAATTCCTG 59.523 50.000 0.00 0.00 0.00 3.86
895 935 0.588252 CGGGGATGATTAGCAAAGCG 59.412 55.000 0.00 0.00 0.00 4.68
901 941 0.320771 ATCGTGCGGGGATGATTAGC 60.321 55.000 0.00 0.00 0.00 3.09
1120 1200 3.041940 CGTCTGGTTGCCGGTGAC 61.042 66.667 1.90 1.49 0.00 3.67
1239 1328 4.920112 CGGTTGGCGACCCACACA 62.920 66.667 18.37 0.00 46.35 3.72
1323 1412 3.050275 GTGCTGTTCTGGCGGTCC 61.050 66.667 0.00 0.00 0.00 4.46
1515 1625 3.941657 GAGGCGCCGCTTGAAGTCT 62.942 63.158 24.06 0.00 0.00 3.24
1608 1718 3.009714 AAGAACTCCGGGAGCCCC 61.010 66.667 23.84 12.62 41.09 5.80
1728 1838 3.934391 CTCGTCGGGGCTGTTCACC 62.934 68.421 0.00 0.00 0.00 4.02
1914 2042 1.079819 CTGGGTGGTGTCGCAGTAG 60.080 63.158 0.00 0.00 41.40 2.57
2178 2312 4.388499 ATCCCGCCGCTGACGTTT 62.388 61.111 0.00 0.00 37.70 3.60
2436 2690 5.007921 AGCAAGCCAAATTTTGTCACAAATC 59.992 36.000 3.17 0.00 0.00 2.17
2440 2694 3.540314 AGCAAGCCAAATTTTGTCACA 57.460 38.095 8.26 0.00 0.00 3.58
2441 2695 3.429881 GCTAGCAAGCCAAATTTTGTCAC 59.570 43.478 10.63 0.00 43.40 3.67
2442 2696 3.652274 GCTAGCAAGCCAAATTTTGTCA 58.348 40.909 10.63 0.00 43.40 3.58
2445 2699 2.676076 ACGCTAGCAAGCCAAATTTTG 58.324 42.857 16.45 1.99 46.68 2.44
2471 3182 6.459670 TTCTAGCTAACATACATGGTCGAA 57.540 37.500 0.00 0.00 0.00 3.71
2473 3184 8.812147 TTATTTCTAGCTAACATACATGGTCG 57.188 34.615 0.00 0.00 0.00 4.79
2474 3185 9.209175 CCTTATTTCTAGCTAACATACATGGTC 57.791 37.037 0.00 0.00 0.00 4.02
2475 3186 8.934697 TCCTTATTTCTAGCTAACATACATGGT 58.065 33.333 0.00 0.00 0.00 3.55
2500 3360 1.984026 CAATGGCCAGTGGGGGTTC 60.984 63.158 25.42 0.00 37.04 3.62
2529 3390 2.295629 TGATGTGATGCTCGATCCTCTC 59.704 50.000 0.00 0.00 0.00 3.20
2654 3531 6.550938 TGATAGCTATCAGATGGTTATGGG 57.449 41.667 28.69 0.00 37.76 4.00
2656 3533 7.063898 CGGTTTGATAGCTATCAGATGGTTATG 59.936 40.741 29.98 14.19 42.99 1.90
2743 3620 0.108585 TGAGGAAAGTGGTGCCAGTC 59.891 55.000 0.00 0.00 0.00 3.51
2773 3650 6.091437 CAGAAGAGCTGGATTCAAATTGAAC 58.909 40.000 10.91 5.33 38.90 3.18
2814 3691 0.670546 ACTGTTTCATCGACTGGCCG 60.671 55.000 0.00 0.00 0.00 6.13
2903 3780 7.387397 ACAGTGGGTATTACAAATTTGCAATTG 59.613 33.333 19.21 13.34 0.00 2.32
2949 3826 3.423154 CCGGCGAGTTTGGTGCTC 61.423 66.667 9.30 0.00 0.00 4.26
3044 3922 2.415776 GTTGGGTGGTGATGCAATTTG 58.584 47.619 0.00 0.00 0.00 2.32
3047 3925 0.114954 AGGTTGGGTGGTGATGCAAT 59.885 50.000 0.00 0.00 0.00 3.56
3048 3926 0.827089 CAGGTTGGGTGGTGATGCAA 60.827 55.000 0.00 0.00 0.00 4.08
3072 3950 3.935203 CGACATTTTCTGTAGCCATGTCT 59.065 43.478 8.52 0.00 41.02 3.41
3098 3979 8.136165 CGTACTTGAGCTTAGTTTACCATATCT 58.864 37.037 7.62 0.00 0.00 1.98
3123 4004 2.536761 TTTCCAGTCCAAGTACACCG 57.463 50.000 0.00 0.00 0.00 4.94
3125 4006 4.879545 TGAACTTTTCCAGTCCAAGTACAC 59.120 41.667 0.00 0.00 32.94 2.90
3126 4007 5.105567 TGAACTTTTCCAGTCCAAGTACA 57.894 39.130 0.00 0.00 32.94 2.90
3127 4008 7.739498 TTATGAACTTTTCCAGTCCAAGTAC 57.261 36.000 0.00 0.00 32.94 2.73
3128 4009 8.934023 AATTATGAACTTTTCCAGTCCAAGTA 57.066 30.769 0.00 0.00 32.94 2.24
3129 4010 7.505585 TGAATTATGAACTTTTCCAGTCCAAGT 59.494 33.333 0.00 0.00 32.94 3.16
3161 4043 4.598257 CCGGTCTAACACTGGCTG 57.402 61.111 0.00 0.00 45.12 4.85
3344 4254 1.344942 CGTCGCTGTGACTACTTGGC 61.345 60.000 18.17 0.00 45.87 4.52
3512 4422 2.248248 CCCTGCCCGATCTTACTATCA 58.752 52.381 0.00 0.00 0.00 2.15
3533 4443 4.202430 ACCATATAGACGGAACCAAATCCC 60.202 45.833 0.00 0.00 36.00 3.85
3572 4482 8.928448 TCTATCTAGTGCCAACTGATTCTTAAT 58.072 33.333 0.00 0.00 37.19 1.40
3574 4484 7.780271 TCTCTATCTAGTGCCAACTGATTCTTA 59.220 37.037 0.00 0.00 37.19 2.10
3576 4486 6.132658 TCTCTATCTAGTGCCAACTGATTCT 58.867 40.000 0.00 0.00 37.19 2.40
3577 4487 6.398234 TCTCTATCTAGTGCCAACTGATTC 57.602 41.667 0.00 0.00 37.19 2.52
3578 4488 6.407525 GGTTCTCTATCTAGTGCCAACTGATT 60.408 42.308 0.00 0.00 37.19 2.57
3579 4489 5.069781 GGTTCTCTATCTAGTGCCAACTGAT 59.930 44.000 0.00 0.00 37.19 2.90
3580 4490 4.402793 GGTTCTCTATCTAGTGCCAACTGA 59.597 45.833 0.00 0.00 37.19 3.41
3584 4494 7.676683 AATAAGGTTCTCTATCTAGTGCCAA 57.323 36.000 0.00 0.00 0.00 4.52
3585 4495 8.958060 ATAATAAGGTTCTCTATCTAGTGCCA 57.042 34.615 0.00 0.00 0.00 4.92
3621 4567 6.998074 TGCAGATCCATTCGGTTAAAATCTAT 59.002 34.615 0.00 0.00 0.00 1.98
3651 4645 2.490903 CCTCAAGTTTTCCCTGCTCATG 59.509 50.000 0.00 0.00 0.00 3.07
3716 4710 0.541764 TGAATTCCCCAACACCCTGC 60.542 55.000 2.27 0.00 0.00 4.85
3830 4824 1.955778 CTGTTGTTGGGCATGAACTCA 59.044 47.619 0.00 0.00 0.00 3.41
3897 4895 2.485814 CCCAGCACAAGAAGTTAGAAGC 59.514 50.000 0.00 0.00 0.00 3.86
4081 5084 2.736144 ACACATTGCTTGCCTTCATG 57.264 45.000 0.00 0.00 0.00 3.07
4132 5135 2.202610 CTCGCGATGCCGAAGTCA 60.203 61.111 10.36 0.00 36.72 3.41
4289 5305 4.503817 GCATATTCTGGAGACATGTAGCCA 60.504 45.833 15.97 15.97 41.51 4.75
4346 5362 3.833650 TCACCAGGACACCGAAACTATAA 59.166 43.478 0.00 0.00 0.00 0.98
4745 5777 4.322080 TTCAGTGTCAGACGTGATCTTT 57.678 40.909 0.00 0.00 34.41 2.52
4826 5858 8.422577 AGCAACAAGAATTTCTACCCTTAATT 57.577 30.769 0.00 0.00 0.00 1.40
4827 5859 8.422577 AAGCAACAAGAATTTCTACCCTTAAT 57.577 30.769 0.00 0.00 0.00 1.40
4828 5860 7.833285 AAGCAACAAGAATTTCTACCCTTAA 57.167 32.000 0.00 0.00 0.00 1.85
4829 5861 7.286775 ACAAAGCAACAAGAATTTCTACCCTTA 59.713 33.333 0.00 0.00 0.00 2.69
4854 5886 2.817258 TGCCTATGCTGTACAAACCAAC 59.183 45.455 0.00 0.00 38.71 3.77
4923 5972 8.801913 GCTCTTTGATGAGTAATTAAACATTGC 58.198 33.333 6.96 0.00 36.51 3.56
4927 5976 9.719355 TGTAGCTCTTTGATGAGTAATTAAACA 57.281 29.630 0.00 0.00 36.51 2.83
4932 5981 9.624373 AATGATGTAGCTCTTTGATGAGTAATT 57.376 29.630 0.00 0.00 36.51 1.40
4946 5995 9.979270 GCACATGTTTATATAATGATGTAGCTC 57.021 33.333 14.84 6.23 0.00 4.09
4947 5996 8.659491 CGCACATGTTTATATAATGATGTAGCT 58.341 33.333 21.04 0.00 0.00 3.32
4948 5997 7.426456 GCGCACATGTTTATATAATGATGTAGC 59.574 37.037 0.30 16.90 0.00 3.58
4949 5998 8.659491 AGCGCACATGTTTATATAATGATGTAG 58.341 33.333 11.47 13.35 0.00 2.74
4950 5999 8.546597 AGCGCACATGTTTATATAATGATGTA 57.453 30.769 11.47 0.00 0.00 2.29
4951 6000 7.439157 AGCGCACATGTTTATATAATGATGT 57.561 32.000 11.47 11.49 0.00 3.06
4952 6001 7.804600 ACAAGCGCACATGTTTATATAATGATG 59.195 33.333 11.47 10.58 0.00 3.07
4953 6002 7.874940 ACAAGCGCACATGTTTATATAATGAT 58.125 30.769 11.47 0.00 0.00 2.45
4954 6003 7.258022 ACAAGCGCACATGTTTATATAATGA 57.742 32.000 11.47 0.00 0.00 2.57
4955 6004 8.282592 ACTACAAGCGCACATGTTTATATAATG 58.717 33.333 11.47 0.00 0.00 1.90
4956 6005 8.282592 CACTACAAGCGCACATGTTTATATAAT 58.717 33.333 11.47 0.00 0.00 1.28
4957 6006 7.492994 TCACTACAAGCGCACATGTTTATATAA 59.507 33.333 11.47 0.00 0.00 0.98
4958 6007 6.981559 TCACTACAAGCGCACATGTTTATATA 59.018 34.615 11.47 0.00 0.00 0.86
4959 6008 5.815222 TCACTACAAGCGCACATGTTTATAT 59.185 36.000 11.47 0.00 0.00 0.86
4960 6009 5.172205 TCACTACAAGCGCACATGTTTATA 58.828 37.500 11.47 0.00 0.00 0.98
4961 6010 4.000325 TCACTACAAGCGCACATGTTTAT 59.000 39.130 11.47 0.00 0.00 1.40
4962 6011 3.394719 TCACTACAAGCGCACATGTTTA 58.605 40.909 11.47 0.00 0.00 2.01
4963 6012 2.217750 TCACTACAAGCGCACATGTTT 58.782 42.857 11.47 0.00 0.00 2.83
4964 6013 1.877637 TCACTACAAGCGCACATGTT 58.122 45.000 11.47 0.00 0.00 2.71
4965 6014 1.531149 GTTCACTACAAGCGCACATGT 59.469 47.619 11.47 14.37 0.00 3.21
4966 6015 1.800586 AGTTCACTACAAGCGCACATG 59.199 47.619 11.47 8.37 0.00 3.21
4967 6016 2.169832 AGTTCACTACAAGCGCACAT 57.830 45.000 11.47 0.00 0.00 3.21
4968 6017 2.400399 GTAGTTCACTACAAGCGCACA 58.600 47.619 11.47 0.00 46.08 4.57
4977 6026 2.682352 GACGGAGGGAGTAGTTCACTAC 59.318 54.545 8.82 8.82 40.54 2.73
4978 6027 2.356535 GGACGGAGGGAGTAGTTCACTA 60.357 54.545 0.00 0.00 40.54 2.74
4979 6028 1.616456 GGACGGAGGGAGTAGTTCACT 60.616 57.143 0.00 0.00 44.17 3.41
4980 6029 0.816373 GGACGGAGGGAGTAGTTCAC 59.184 60.000 0.00 0.00 0.00 3.18
4981 6030 0.324091 GGGACGGAGGGAGTAGTTCA 60.324 60.000 0.00 0.00 0.00 3.18
4982 6031 0.324091 TGGGACGGAGGGAGTAGTTC 60.324 60.000 0.00 0.00 0.00 3.01
4983 6032 0.338814 ATGGGACGGAGGGAGTAGTT 59.661 55.000 0.00 0.00 0.00 2.24
4984 6033 0.338814 AATGGGACGGAGGGAGTAGT 59.661 55.000 0.00 0.00 0.00 2.73
4985 6034 0.753262 CAATGGGACGGAGGGAGTAG 59.247 60.000 0.00 0.00 0.00 2.57
4986 6035 0.042131 ACAATGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59
4987 6036 1.229529 ACAATGGGACGGAGGGAGT 60.230 57.895 0.00 0.00 0.00 3.85
4988 6037 0.978146 AGACAATGGGACGGAGGGAG 60.978 60.000 0.00 0.00 0.00 4.30
4989 6038 1.080354 AGACAATGGGACGGAGGGA 59.920 57.895 0.00 0.00 0.00 4.20
4990 6039 1.221840 CAGACAATGGGACGGAGGG 59.778 63.158 0.00 0.00 0.00 4.30
4991 6040 0.324943 AACAGACAATGGGACGGAGG 59.675 55.000 0.00 0.00 0.00 4.30
4992 6041 1.276421 AGAACAGACAATGGGACGGAG 59.724 52.381 0.00 0.00 0.00 4.63
4993 6042 1.348064 AGAACAGACAATGGGACGGA 58.652 50.000 0.00 0.00 0.00 4.69
4994 6043 1.806542 CAAGAACAGACAATGGGACGG 59.193 52.381 0.00 0.00 0.00 4.79
4995 6044 2.494059 ACAAGAACAGACAATGGGACG 58.506 47.619 0.00 0.00 0.00 4.79
4996 6045 4.642429 ACTACAAGAACAGACAATGGGAC 58.358 43.478 0.00 0.00 0.00 4.46
4997 6046 4.974645 ACTACAAGAACAGACAATGGGA 57.025 40.909 0.00 0.00 0.00 4.37
4998 6047 5.063204 TGAACTACAAGAACAGACAATGGG 58.937 41.667 0.00 0.00 0.00 4.00
4999 6048 5.760253 ACTGAACTACAAGAACAGACAATGG 59.240 40.000 0.00 0.00 33.53 3.16
5000 6049 6.851222 ACTGAACTACAAGAACAGACAATG 57.149 37.500 0.00 0.00 33.53 2.82
5001 6050 7.865706 AAACTGAACTACAAGAACAGACAAT 57.134 32.000 0.00 0.00 33.53 2.71
5002 6051 7.681939 AAAACTGAACTACAAGAACAGACAA 57.318 32.000 0.00 0.00 33.53 3.18
5003 6052 7.681939 AAAAACTGAACTACAAGAACAGACA 57.318 32.000 0.00 0.00 33.53 3.41
5099 6148 5.540337 AGCGATTGGATAGAAGAACCTATGA 59.460 40.000 0.00 0.00 30.03 2.15
5109 6158 3.186909 CGTGACAAGCGATTGGATAGAA 58.813 45.455 18.84 0.00 0.00 2.10
5204 6254 3.509575 ACTTTATGGCTTGCGATTTTCCA 59.490 39.130 0.00 0.00 0.00 3.53
5264 6321 1.128692 GCAATGAAGAACGAAGGACCG 59.871 52.381 0.00 0.00 0.00 4.79
5265 6322 1.128692 CGCAATGAAGAACGAAGGACC 59.871 52.381 0.00 0.00 0.00 4.46
5284 6341 8.393366 ACTCTGACAATATGAAATTCATTGACG 58.607 33.333 14.15 3.73 38.26 4.35
5312 6369 4.021456 ACGGGATGCAATCGTCTCATTATA 60.021 41.667 6.54 0.00 46.86 0.98
5393 6450 1.337635 TGGAAAATTGAATGGCGTGCC 60.338 47.619 3.30 3.30 0.00 5.01
5398 6455 5.106197 GGTGGAAATTGGAAAATTGAATGGC 60.106 40.000 0.00 0.00 0.00 4.40
5483 6540 4.707030 TGTGGATGCTTCATTTGATCAC 57.293 40.909 0.00 0.00 0.00 3.06
5515 6572 1.152701 ACACACCTCCTAGGGGGTTTA 59.847 52.381 32.26 0.00 45.32 2.01
5555 6612 3.402110 TGTCCACTCACACAATGCTAAG 58.598 45.455 0.00 0.00 0.00 2.18
5564 6621 7.273381 GCAAATTATGTTAATGTCCACTCACAC 59.727 37.037 0.00 0.00 0.00 3.82
5612 6669 1.737793 CAAGAGGCGTACCAAACATCC 59.262 52.381 0.00 0.00 39.06 3.51
5615 6672 1.689813 TCTCAAGAGGCGTACCAAACA 59.310 47.619 0.00 0.00 39.06 2.83
5678 6738 5.069119 AGAGATGATTGCTATAACCGTGTGA 59.931 40.000 0.00 0.00 0.00 3.58
5682 6742 4.278669 ACGAGAGATGATTGCTATAACCGT 59.721 41.667 0.00 0.00 0.00 4.83
5702 6762 1.974265 TGGGTTTTCAGAATGCACGA 58.026 45.000 0.00 0.00 34.76 4.35
5770 6830 0.904865 TGTTGATCCTGCGGGAGAGT 60.905 55.000 21.28 2.52 45.86 3.24
5781 6841 4.874970 AGAAAAGCATGTGTTGTTGATCC 58.125 39.130 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.