Multiple sequence alignment - TraesCS6D01G301900

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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 TraesCS6D01G301900 chr6D 100.000 3440 0 0 1 3440 411471785 411468346 0.000000e+00 6353
1 TraesCS6D01G301900 chr6D 89.330 1612 163 6 814 2420 445788965 445787358 0.000000e+00 2015
2 TraesCS6D01G301900 chr6D 88.449 1593 175 9 829 2418 445964319 445965905 0.000000e+00 1914
3 TraesCS6D01G301900 chr6D 80.628 191 30 6 281 467 445963721 445963908 1.290000e-29 141
4 TraesCS6D01G301900 chr6D 84.375 128 11 3 3174 3301 411487676 411487558 2.170000e-22 117
5 TraesCS6D01G301900 chr6D 76.961 204 35 7 281 480 445978216 445978411 4.700000e-19 106
6 TraesCS6D01G301900 chr6D 84.259 108 16 1 374 480 445789369 445789262 1.690000e-18 104
7 TraesCS6D01G301900 chr6B 93.034 2584 117 31 583 3138 618670494 618667946 0.000000e+00 3716
8 TraesCS6D01G301900 chr6B 89.589 1412 136 9 809 2216 672457706 672456302 0.000000e+00 1783
9 TraesCS6D01G301900 chr6B 89.301 1374 147 0 1047 2420 672462674 672461301 0.000000e+00 1724
10 TraesCS6D01G301900 chr6B 87.222 180 12 5 3261 3440 618667809 618667641 9.740000e-46 195
11 TraesCS6D01G301900 chr6B 92.969 128 9 0 1 128 290212405 290212532 1.630000e-43 187
12 TraesCS6D01G301900 chr6B 92.969 128 9 0 1 128 688594711 688594584 1.630000e-43 187
13 TraesCS6D01G301900 chr6B 79.426 209 31 9 281 480 673875621 673875826 1.660000e-28 137
14 TraesCS6D01G301900 chr6B 95.000 80 3 1 2983 3062 618859157 618859079 1.300000e-24 124
15 TraesCS6D01G301900 chr6B 82.927 123 19 2 360 480 672493419 672493297 3.630000e-20 110
16 TraesCS6D01G301900 chr6A 97.329 1610 43 0 821 2430 556038476 556036867 0.000000e+00 2736
17 TraesCS6D01G301900 chr6A 89.764 1612 160 5 809 2419 592458969 592457362 0.000000e+00 2058
18 TraesCS6D01G301900 chr6A 88.413 1588 178 6 833 2418 592618182 592619765 0.000000e+00 1908
19 TraesCS6D01G301900 chr6A 87.626 1487 183 1 932 2418 592613354 592611869 0.000000e+00 1725
20 TraesCS6D01G301900 chr6A 90.000 510 32 13 2423 2916 556036316 556035810 2.890000e-180 641
21 TraesCS6D01G301900 chr6A 92.965 199 8 2 2944 3138 556035818 556035622 5.620000e-73 285
22 TraesCS6D01G301900 chr6A 84.351 262 21 8 583 844 556038748 556038507 4.440000e-59 239
23 TraesCS6D01G301900 chr6A 87.293 181 5 6 3260 3440 556035488 556035326 1.260000e-44 191
24 TraesCS6D01G301900 chr6A 95.181 83 4 0 480 562 556038891 556038809 7.750000e-27 132
25 TraesCS6D01G301900 chr6A 97.674 43 1 0 223 265 556039276 556039234 1.320000e-09 75
26 TraesCS6D01G301900 chr5D 98.438 128 2 0 1 128 369292981 369293108 3.450000e-55 226
27 TraesCS6D01G301900 chr7B 93.985 133 7 1 1 132 645602421 645602289 2.090000e-47 200
28 TraesCS6D01G301900 chr3B 93.798 129 8 0 1 129 786221329 786221457 9.740000e-46 195
29 TraesCS6D01G301900 chr1B 92.969 128 9 0 1 128 252161787 252161660 1.630000e-43 187
30 TraesCS6D01G301900 chr2D 92.913 127 9 0 4 130 383552246 383552120 5.860000e-43 185
31 TraesCS6D01G301900 chr3D 92.248 129 10 0 1 129 549716745 549716873 2.110000e-42 183
32 TraesCS6D01G301900 chr2B 88.276 145 15 2 1 144 769088505 769088362 4.560000e-39 172


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 TraesCS6D01G301900 chr6D 411468346 411471785 3439 True 6353.000000 6353 100.000000 1 3440 1 chr6D.!!$R1 3439
1 TraesCS6D01G301900 chr6D 445787358 445789369 2011 True 1059.500000 2015 86.794500 374 2420 2 chr6D.!!$R3 2046
2 TraesCS6D01G301900 chr6D 445963721 445965905 2184 False 1027.500000 1914 84.538500 281 2418 2 chr6D.!!$F2 2137
3 TraesCS6D01G301900 chr6B 618667641 618670494 2853 True 1955.500000 3716 90.128000 583 3440 2 chr6B.!!$R4 2857
4 TraesCS6D01G301900 chr6B 672456302 672462674 6372 True 1753.500000 1783 89.445000 809 2420 2 chr6B.!!$R5 1611
5 TraesCS6D01G301900 chr6A 592457362 592458969 1607 True 2058.000000 2058 89.764000 809 2419 1 chr6A.!!$R1 1610
6 TraesCS6D01G301900 chr6A 592618182 592619765 1583 False 1908.000000 1908 88.413000 833 2418 1 chr6A.!!$F1 1585
7 TraesCS6D01G301900 chr6A 592611869 592613354 1485 True 1725.000000 1725 87.626000 932 2418 1 chr6A.!!$R2 1486
8 TraesCS6D01G301900 chr6A 556035326 556039276 3950 True 614.142857 2736 92.113286 223 3440 7 chr6A.!!$R3 3217

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
134 135 0.179000 GACGGAGGGAGTAGTCGGTA 59.821 60.0 0.0 0.0 0.00 4.02 F
135 136 0.620556 ACGGAGGGAGTAGTCGGTAA 59.379 55.0 0.0 0.0 0.00 2.85 F
1498 5954 0.115349 AGTAGACAGCAGGGAGTGGT 59.885 55.0 0.0 0.0 37.36 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1154 5610 1.666189 GCGATACCAAGGCTTCTGTTC 59.334 52.381 0.00 0.0 0.00 3.18 R
1589 6045 3.543680 TTTGGAGATTCGACCATCCTC 57.456 47.619 9.65 0.0 36.02 3.71 R
2700 7728 0.033781 TGCATTTTCAGGCAGCCAAC 59.966 50.000 15.80 0.0 34.58 3.77 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
56 57 8.891671 AACATTGATATCTTTTTGCACAAACT 57.108 26.923 3.98 0.00 0.00 2.66
57 58 8.524870 ACATTGATATCTTTTTGCACAAACTC 57.475 30.769 3.98 0.00 0.00 3.01
58 59 7.326789 ACATTGATATCTTTTTGCACAAACTCG 59.673 33.333 3.98 0.00 0.00 4.18
60 61 5.240623 TGATATCTTTTTGCACAAACTCGGT 59.759 36.000 3.98 0.00 0.00 4.69
61 62 3.414549 TCTTTTTGCACAAACTCGGTC 57.585 42.857 0.00 0.00 0.00 4.79
62 63 2.750166 TCTTTTTGCACAAACTCGGTCA 59.250 40.909 0.00 0.00 0.00 4.02
63 64 3.191581 TCTTTTTGCACAAACTCGGTCAA 59.808 39.130 0.00 0.00 0.00 3.18
64 65 3.577649 TTTTGCACAAACTCGGTCAAA 57.422 38.095 0.00 0.00 0.00 2.69
65 66 2.553079 TTGCACAAACTCGGTCAAAC 57.447 45.000 0.00 0.00 0.00 2.93
66 67 1.745232 TGCACAAACTCGGTCAAACT 58.255 45.000 0.00 0.00 0.00 2.66
67 68 2.088423 TGCACAAACTCGGTCAAACTT 58.912 42.857 0.00 0.00 0.00 2.66
68 69 2.490115 TGCACAAACTCGGTCAAACTTT 59.510 40.909 0.00 0.00 0.00 2.66
69 70 2.851824 GCACAAACTCGGTCAAACTTTG 59.148 45.455 0.00 0.00 0.00 2.77
70 71 3.426963 GCACAAACTCGGTCAAACTTTGA 60.427 43.478 0.00 0.00 37.33 2.69
71 72 4.342772 CACAAACTCGGTCAAACTTTGAG 58.657 43.478 4.36 0.00 41.01 3.02
72 73 4.094294 CACAAACTCGGTCAAACTTTGAGA 59.906 41.667 4.36 0.00 41.01 3.27
73 74 4.881850 ACAAACTCGGTCAAACTTTGAGAT 59.118 37.500 4.36 0.00 41.01 2.75
74 75 6.018262 CACAAACTCGGTCAAACTTTGAGATA 60.018 38.462 4.36 0.00 41.01 1.98
75 76 6.202954 ACAAACTCGGTCAAACTTTGAGATAG 59.797 38.462 4.36 5.24 41.01 2.08
77 78 5.855045 ACTCGGTCAAACTTTGAGATAGTT 58.145 37.500 4.36 0.00 41.01 2.24
78 79 6.289064 ACTCGGTCAAACTTTGAGATAGTTT 58.711 36.000 4.36 0.00 44.38 2.66
87 88 8.519799 AAACTTTGAGATAGTTTGACCTTTCA 57.480 30.769 0.00 0.00 42.54 2.69
88 89 8.519799 AACTTTGAGATAGTTTGACCTTTCAA 57.480 30.769 0.00 0.00 40.14 2.69
89 90 8.697507 ACTTTGAGATAGTTTGACCTTTCAAT 57.302 30.769 0.00 0.00 41.50 2.57
90 91 9.793259 ACTTTGAGATAGTTTGACCTTTCAATA 57.207 29.630 0.00 0.00 41.50 1.90
97 98 9.573133 GATAGTTTGACCTTTCAATAATGTTGG 57.427 33.333 0.00 0.00 41.50 3.77
98 99 7.595819 AGTTTGACCTTTCAATAATGTTGGA 57.404 32.000 0.00 0.00 41.50 3.53
99 100 8.017418 AGTTTGACCTTTCAATAATGTTGGAA 57.983 30.769 0.00 0.00 41.50 3.53
100 101 8.143835 AGTTTGACCTTTCAATAATGTTGGAAG 58.856 33.333 4.03 4.03 41.50 3.46
101 102 7.595819 TTGACCTTTCAATAATGTTGGAAGT 57.404 32.000 9.44 0.00 36.79 3.01
104 105 7.721842 TGACCTTTCAATAATGTTGGAAGTACA 59.278 33.333 9.44 6.54 34.06 2.90
107 108 8.237267 CCTTTCAATAATGTTGGAAGTACACTC 58.763 37.037 9.44 0.00 34.06 3.51
108 109 8.918202 TTTCAATAATGTTGGAAGTACACTCT 57.082 30.769 0.00 0.00 0.00 3.24
110 111 8.918202 TCAATAATGTTGGAAGTACACTCTTT 57.082 30.769 0.00 0.00 0.00 2.52
115 116 7.745620 ATGTTGGAAGTACACTCTTTAAAGG 57.254 36.000 15.13 8.48 0.00 3.11
116 117 6.891388 TGTTGGAAGTACACTCTTTAAAGGA 58.109 36.000 15.13 1.82 0.00 3.36
118 119 5.535333 TGGAAGTACACTCTTTAAAGGACG 58.465 41.667 15.13 6.90 0.00 4.79
119 120 4.928020 GGAAGTACACTCTTTAAAGGACGG 59.072 45.833 15.13 5.64 0.00 4.79
120 121 5.279156 GGAAGTACACTCTTTAAAGGACGGA 60.279 44.000 15.13 0.00 0.00 4.69
123 124 2.302157 ACACTCTTTAAAGGACGGAGGG 59.698 50.000 15.13 8.51 34.07 4.30
124 125 2.565834 CACTCTTTAAAGGACGGAGGGA 59.434 50.000 15.13 0.00 29.82 4.20
125 126 2.832733 ACTCTTTAAAGGACGGAGGGAG 59.167 50.000 15.13 4.81 0.00 4.30
126 127 2.832733 CTCTTTAAAGGACGGAGGGAGT 59.167 50.000 15.13 0.00 0.00 3.85
127 128 4.021916 CTCTTTAAAGGACGGAGGGAGTA 58.978 47.826 15.13 0.00 0.00 2.59
128 129 4.021916 TCTTTAAAGGACGGAGGGAGTAG 58.978 47.826 15.13 0.00 0.00 2.57
130 131 1.849977 AAAGGACGGAGGGAGTAGTC 58.150 55.000 0.00 0.00 0.00 2.59
131 132 0.394080 AAGGACGGAGGGAGTAGTCG 60.394 60.000 0.00 0.00 34.68 4.18
132 133 1.823041 GGACGGAGGGAGTAGTCGG 60.823 68.421 0.00 0.00 34.68 4.79
133 134 1.077858 GACGGAGGGAGTAGTCGGT 60.078 63.158 0.00 0.00 0.00 4.69
134 135 0.179000 GACGGAGGGAGTAGTCGGTA 59.821 60.000 0.00 0.00 0.00 4.02
135 136 0.620556 ACGGAGGGAGTAGTCGGTAA 59.379 55.000 0.00 0.00 0.00 2.85
136 137 1.213926 ACGGAGGGAGTAGTCGGTAAT 59.786 52.381 0.00 0.00 0.00 1.89
137 138 2.305009 CGGAGGGAGTAGTCGGTAATT 58.695 52.381 0.00 0.00 0.00 1.40
138 139 2.292845 CGGAGGGAGTAGTCGGTAATTC 59.707 54.545 0.00 0.00 0.00 2.17
139 140 3.564264 GGAGGGAGTAGTCGGTAATTCT 58.436 50.000 0.00 0.00 0.00 2.40
141 142 4.202131 GGAGGGAGTAGTCGGTAATTCTTG 60.202 50.000 0.00 0.00 0.00 3.02
143 144 3.132467 GGGAGTAGTCGGTAATTCTTGCT 59.868 47.826 0.00 0.00 0.00 3.91
144 145 4.113354 GGAGTAGTCGGTAATTCTTGCTG 58.887 47.826 0.00 0.00 0.00 4.41
145 146 4.381718 GGAGTAGTCGGTAATTCTTGCTGT 60.382 45.833 0.00 0.00 0.00 4.40
146 147 5.148651 AGTAGTCGGTAATTCTTGCTGTT 57.851 39.130 0.00 0.00 0.00 3.16
147 148 5.548406 AGTAGTCGGTAATTCTTGCTGTTT 58.452 37.500 0.00 0.00 0.00 2.83
187 188 8.698973 TTTTTGGGGAGTTTTTCTTTTTCTTT 57.301 26.923 0.00 0.00 0.00 2.52
188 189 8.698973 TTTTGGGGAGTTTTTCTTTTTCTTTT 57.301 26.923 0.00 0.00 0.00 2.27
189 190 8.698973 TTTGGGGAGTTTTTCTTTTTCTTTTT 57.301 26.923 0.00 0.00 0.00 1.94
190 191 7.680442 TGGGGAGTTTTTCTTTTTCTTTTTG 57.320 32.000 0.00 0.00 0.00 2.44
192 193 7.606073 TGGGGAGTTTTTCTTTTTCTTTTTGAG 59.394 33.333 0.00 0.00 0.00 3.02
193 194 7.065803 GGGGAGTTTTTCTTTTTCTTTTTGAGG 59.934 37.037 0.00 0.00 0.00 3.86
195 196 7.822334 GGAGTTTTTCTTTTTCTTTTTGAGGGA 59.178 33.333 0.00 0.00 0.00 4.20
196 197 9.383519 GAGTTTTTCTTTTTCTTTTTGAGGGAT 57.616 29.630 0.00 0.00 0.00 3.85
198 199 8.397906 GTTTTTCTTTTTCTTTTTGAGGGATGG 58.602 33.333 0.00 0.00 0.00 3.51
199 200 6.806668 TTCTTTTTCTTTTTGAGGGATGGT 57.193 33.333 0.00 0.00 0.00 3.55
200 201 7.906199 TTCTTTTTCTTTTTGAGGGATGGTA 57.094 32.000 0.00 0.00 0.00 3.25
202 203 8.491045 TCTTTTTCTTTTTGAGGGATGGTAAT 57.509 30.769 0.00 0.00 0.00 1.89
204 205 9.208022 CTTTTTCTTTTTGAGGGATGGTAATTC 57.792 33.333 0.00 0.00 0.00 2.17
205 206 8.491045 TTTTCTTTTTGAGGGATGGTAATTCT 57.509 30.769 0.00 0.00 0.00 2.40
206 207 8.491045 TTTCTTTTTGAGGGATGGTAATTCTT 57.509 30.769 0.00 0.00 0.00 2.52
207 208 7.466746 TCTTTTTGAGGGATGGTAATTCTTG 57.533 36.000 0.00 0.00 0.00 3.02
209 210 4.591321 TTGAGGGATGGTAATTCTTGCT 57.409 40.909 0.00 0.00 0.00 3.91
210 211 3.889815 TGAGGGATGGTAATTCTTGCTG 58.110 45.455 0.00 0.00 0.00 4.41
212 213 2.243221 AGGGATGGTAATTCTTGCTGCT 59.757 45.455 0.00 0.00 0.00 4.24
213 214 2.360165 GGGATGGTAATTCTTGCTGCTG 59.640 50.000 0.00 0.00 0.00 4.41
214 215 2.223665 GGATGGTAATTCTTGCTGCTGC 60.224 50.000 8.89 8.89 40.20 5.25
216 217 1.086696 GGTAATTCTTGCTGCTGCGA 58.913 50.000 11.21 8.26 43.34 5.10
227 228 0.678395 CTGCTGCGAGGTCCTATCAT 59.322 55.000 0.00 0.00 0.00 2.45
284 316 2.861006 GAGGCCGACGCTCAAAAC 59.139 61.111 0.00 0.00 34.44 2.43
296 328 2.902846 CAAAACCGACCCACGCCA 60.903 61.111 0.00 0.00 41.07 5.69
315 348 1.003718 CGAGGAAGGCGAGGGTTTT 60.004 57.895 0.00 0.00 0.00 2.43
322 355 2.556287 GCGAGGGTTTTGCTGTCG 59.444 61.111 0.00 0.00 33.06 4.35
324 357 1.860078 CGAGGGTTTTGCTGTCGAC 59.140 57.895 9.11 9.11 32.32 4.20
365 399 1.984026 CACCCATTCCAACCCCTGC 60.984 63.158 0.00 0.00 0.00 4.85
370 405 3.976701 ATTCCAACCCCTGCTCGCG 62.977 63.158 0.00 0.00 0.00 5.87
460 496 1.768684 GCGCCTGGATCCATTCCCTA 61.769 60.000 16.63 0.00 44.77 3.53
524 661 1.597663 GCGTTTGGGTCTGGAATATCG 59.402 52.381 0.00 0.00 0.00 2.92
529 666 2.039418 TGGGTCTGGAATATCGGTGAG 58.961 52.381 0.00 0.00 0.00 3.51
635 812 1.757118 TCAGGAGGTGGATGTTCGATC 59.243 52.381 0.00 0.00 0.00 3.69
651 828 2.188524 CGATCATCTCGTGGACTTGTG 58.811 52.381 0.00 0.00 42.56 3.33
652 829 2.416027 CGATCATCTCGTGGACTTGTGT 60.416 50.000 0.00 0.00 42.56 3.72
657 834 2.980568 TCTCGTGGACTTGTGTTGTTT 58.019 42.857 0.00 0.00 0.00 2.83
672 849 9.790389 CTTGTGTTGTTTTAATTGGTGTACTTA 57.210 29.630 0.00 0.00 0.00 2.24
687 864 7.981142 TGGTGTACTTATTATAGGAAATCCCC 58.019 38.462 0.00 0.00 36.42 4.81
688 865 7.797617 TGGTGTACTTATTATAGGAAATCCCCT 59.202 37.037 0.00 0.00 40.29 4.79
689 866 8.319881 GGTGTACTTATTATAGGAAATCCCCTC 58.680 40.741 0.00 0.00 37.74 4.30
690 867 8.319881 GTGTACTTATTATAGGAAATCCCCTCC 58.680 40.741 0.00 0.00 37.74 4.30
691 868 6.971932 ACTTATTATAGGAAATCCCCTCCC 57.028 41.667 0.00 0.00 37.74 4.30
692 869 5.796399 ACTTATTATAGGAAATCCCCTCCCC 59.204 44.000 0.00 0.00 37.74 4.81
693 870 2.755019 TATAGGAAATCCCCTCCCCC 57.245 55.000 0.00 0.00 37.74 5.40
694 871 0.968295 ATAGGAAATCCCCTCCCCCT 59.032 55.000 0.00 0.00 37.74 4.79
695 872 1.652726 TAGGAAATCCCCTCCCCCTA 58.347 55.000 0.00 0.00 37.74 3.53
754 950 6.979238 CGTTTGGTTAATTTTCCCTTGTAACA 59.021 34.615 0.00 0.00 0.00 2.41
790 986 8.551440 TCCATGATATAAATATTAGCCTGCAGT 58.449 33.333 13.81 0.00 0.00 4.40
818 5209 6.558771 TGGTTACTGTTCATTGTGAAGATG 57.441 37.500 0.00 0.00 37.00 2.90
831 5225 4.840271 TGTGAAGATGAGCACATGAATCT 58.160 39.130 0.00 0.00 39.86 2.40
835 5283 5.941647 TGAAGATGAGCACATGAATCTTTCA 59.058 36.000 0.00 4.29 45.01 2.69
1147 5603 3.041940 GTGTTGGCCGTGGACTCG 61.042 66.667 0.00 0.00 0.00 4.18
1154 5610 2.261671 CCGTGGACTCGACCCTTG 59.738 66.667 1.34 0.00 0.00 3.61
1498 5954 0.115349 AGTAGACAGCAGGGAGTGGT 59.885 55.000 0.00 0.00 37.36 4.16
1796 6253 2.297033 GGAAGTGCAAAGCATTGGAGAA 59.703 45.455 3.55 0.00 41.91 2.87
2053 6510 3.844211 AGGCTTCACACAAGAGGGTATTA 59.156 43.478 0.00 0.00 0.00 0.98
2298 6755 3.898509 GCCTTGGCACGTGCACAA 61.899 61.111 38.60 33.38 44.36 3.33
2309 6766 0.381801 CGTGCACAAAAGCTGGAGTT 59.618 50.000 18.64 0.00 34.99 3.01
2382 6839 3.674997 TGCCAAATCAGTTCACTACTCC 58.325 45.455 0.00 0.00 33.85 3.85
2384 6841 3.262420 CCAAATCAGTTCACTACTCCGG 58.738 50.000 0.00 0.00 33.85 5.14
2442 7457 2.159379 CGCCAAAAGGAAAGGATAGCAC 60.159 50.000 0.00 0.00 0.00 4.40
2482 7499 4.959839 TGGTTTTCCTTTAGCCTTCACTTT 59.040 37.500 0.00 0.00 41.38 2.66
2488 7505 4.289672 TCCTTTAGCCTTCACTTTGGAGAT 59.710 41.667 0.00 0.00 0.00 2.75
2489 7506 5.012893 CCTTTAGCCTTCACTTTGGAGATT 58.987 41.667 0.00 0.00 0.00 2.40
2535 7558 2.756840 TCTGATGAGTTCCAGCACTG 57.243 50.000 0.00 0.00 36.07 3.66
2624 7648 3.186702 GTAAGGTCTCCTCCTTGCATC 57.813 52.381 8.06 0.00 45.96 3.91
2646 7670 3.350833 GAGATCTCAAAACATGGCACCT 58.649 45.455 18.11 0.00 0.00 4.00
2649 7673 3.731652 TCTCAAAACATGGCACCTTTG 57.268 42.857 10.11 10.11 0.00 2.77
2650 7674 3.030291 TCTCAAAACATGGCACCTTTGT 58.970 40.909 14.03 2.32 32.00 2.83
2651 7675 3.450457 TCTCAAAACATGGCACCTTTGTT 59.550 39.130 14.03 7.73 32.00 2.83
2654 7678 5.734720 TCAAAACATGGCACCTTTGTTTTA 58.265 33.333 22.25 12.43 39.65 1.52
2656 7680 7.500992 TCAAAACATGGCACCTTTGTTTTATA 58.499 30.769 22.25 14.26 39.65 0.98
2657 7681 7.655328 TCAAAACATGGCACCTTTGTTTTATAG 59.345 33.333 22.25 14.10 39.65 1.31
2700 7728 7.315890 GGATTTTGAAAGAATACCAGGTTCTG 58.684 38.462 0.00 0.00 36.14 3.02
2709 7737 2.270986 CCAGGTTCTGTTGGCTGCC 61.271 63.158 12.87 12.87 0.00 4.85
2749 7777 6.820335 TCCTGTAATATTGTCTGGTCATCAG 58.180 40.000 0.00 0.00 44.68 2.90
2752 7780 6.582636 TGTAATATTGTCTGGTCATCAGGTC 58.417 40.000 0.00 0.00 43.53 3.85
2753 7781 5.965033 AATATTGTCTGGTCATCAGGTCT 57.035 39.130 0.00 0.00 43.53 3.85
2755 7783 3.407424 TTGTCTGGTCATCAGGTCTTG 57.593 47.619 0.00 0.00 43.53 3.02
2756 7784 1.002430 TGTCTGGTCATCAGGTCTTGC 59.998 52.381 0.00 0.00 43.53 4.01
2759 7791 2.027745 TCTGGTCATCAGGTCTTGCTTC 60.028 50.000 0.00 0.00 43.53 3.86
2769 7801 7.335422 TCATCAGGTCTTGCTTCTTTTAGATTC 59.665 37.037 0.00 0.00 0.00 2.52
2807 7839 1.198637 CTTGGCTGCTGCTTCTGTAAC 59.801 52.381 15.64 0.00 39.59 2.50
2909 7946 3.541632 AGGTGCGACTGAAAGAAAAAGA 58.458 40.909 0.00 0.00 37.43 2.52
2930 7970 1.299468 CTCCGAGAAATCGAGCCCG 60.299 63.158 0.00 0.00 34.64 6.13
2950 7990 2.668280 GCGACGCCAACAGGAACTC 61.668 63.158 9.14 0.00 34.60 3.01
2973 8013 0.591741 CGTGAGATTCCGGTCGCTAC 60.592 60.000 0.00 0.00 0.00 3.58
2974 8014 0.739561 GTGAGATTCCGGTCGCTACT 59.260 55.000 0.00 0.00 0.00 2.57
2975 8015 1.022735 TGAGATTCCGGTCGCTACTC 58.977 55.000 0.00 4.32 0.00 2.59
2976 8016 0.041135 GAGATTCCGGTCGCTACTCG 60.041 60.000 0.00 0.00 40.15 4.18
2977 8017 1.657794 GATTCCGGTCGCTACTCGC 60.658 63.158 0.00 0.00 38.27 5.03
2978 8018 2.061182 GATTCCGGTCGCTACTCGCT 62.061 60.000 0.00 0.00 38.27 4.93
2979 8019 0.816825 ATTCCGGTCGCTACTCGCTA 60.817 55.000 0.00 0.00 38.27 4.26
3138 8178 2.622436 CGGCCGAAAGAGAAGAAAGAT 58.378 47.619 24.07 0.00 0.00 2.40
3139 8179 3.430374 CCGGCCGAAAGAGAAGAAAGATA 60.430 47.826 30.73 0.00 0.00 1.98
3161 8270 5.551760 ACCTGTATTGCATTTCTCTTTCG 57.448 39.130 0.00 0.00 0.00 3.46
3165 8274 5.617609 TGTATTGCATTTCTCTTTCGTTCG 58.382 37.500 0.00 0.00 0.00 3.95
3166 8275 4.749245 ATTGCATTTCTCTTTCGTTCGT 57.251 36.364 0.00 0.00 0.00 3.85
3167 8276 4.545823 TTGCATTTCTCTTTCGTTCGTT 57.454 36.364 0.00 0.00 0.00 3.85
3168 8277 4.128554 TGCATTTCTCTTTCGTTCGTTC 57.871 40.909 0.00 0.00 0.00 3.95
3169 8278 3.146250 GCATTTCTCTTTCGTTCGTTCG 58.854 45.455 0.00 0.00 0.00 3.95
3170 8279 3.362693 GCATTTCTCTTTCGTTCGTTCGT 60.363 43.478 2.67 0.00 0.00 3.85
3171 8280 4.758561 CATTTCTCTTTCGTTCGTTCGTT 58.241 39.130 2.67 0.00 0.00 3.85
3172 8281 4.427438 TTTCTCTTTCGTTCGTTCGTTC 57.573 40.909 2.67 0.00 0.00 3.95
3173 8282 3.344904 TCTCTTTCGTTCGTTCGTTCT 57.655 42.857 2.67 0.00 0.00 3.01
3174 8283 3.699067 TCTCTTTCGTTCGTTCGTTCTT 58.301 40.909 2.67 0.00 0.00 2.52
3175 8284 4.107622 TCTCTTTCGTTCGTTCGTTCTTT 58.892 39.130 2.67 0.00 0.00 2.52
3176 8285 4.205792 TCTCTTTCGTTCGTTCGTTCTTTC 59.794 41.667 2.67 0.00 0.00 2.62
3179 8288 4.845621 TTCGTTCGTTCGTTCTTTCTTT 57.154 36.364 2.67 0.00 0.00 2.52
3193 8302 8.947115 TCGTTCTTTCTTTCTTTCTTTCTTTCT 58.053 29.630 0.00 0.00 0.00 2.52
3221 8330 2.234300 TTCCACGTTCTTCACTGGTC 57.766 50.000 0.00 0.00 0.00 4.02
3222 8331 1.116308 TCCACGTTCTTCACTGGTCA 58.884 50.000 0.00 0.00 0.00 4.02
3223 8332 1.483004 TCCACGTTCTTCACTGGTCAA 59.517 47.619 0.00 0.00 0.00 3.18
3224 8333 2.104111 TCCACGTTCTTCACTGGTCAAT 59.896 45.455 0.00 0.00 0.00 2.57
3225 8334 2.878406 CCACGTTCTTCACTGGTCAATT 59.122 45.455 0.00 0.00 0.00 2.32
3226 8335 3.315191 CCACGTTCTTCACTGGTCAATTT 59.685 43.478 0.00 0.00 0.00 1.82
3227 8336 4.527564 CACGTTCTTCACTGGTCAATTTC 58.472 43.478 0.00 0.00 0.00 2.17
3228 8337 3.247648 ACGTTCTTCACTGGTCAATTTCG 59.752 43.478 0.00 0.00 0.00 3.46
3229 8338 3.493129 CGTTCTTCACTGGTCAATTTCGA 59.507 43.478 0.00 0.00 0.00 3.71
3230 8339 4.152402 CGTTCTTCACTGGTCAATTTCGAT 59.848 41.667 0.00 0.00 0.00 3.59
3231 8340 5.334105 CGTTCTTCACTGGTCAATTTCGATT 60.334 40.000 0.00 0.00 0.00 3.34
3232 8341 6.128661 CGTTCTTCACTGGTCAATTTCGATTA 60.129 38.462 0.00 0.00 0.00 1.75
3233 8342 6.968131 TCTTCACTGGTCAATTTCGATTAG 57.032 37.500 0.00 0.00 0.00 1.73
3234 8343 6.464222 TCTTCACTGGTCAATTTCGATTAGT 58.536 36.000 0.00 0.00 0.00 2.24
3235 8344 6.934645 TCTTCACTGGTCAATTTCGATTAGTT 59.065 34.615 0.00 0.00 0.00 2.24
3236 8345 8.092068 TCTTCACTGGTCAATTTCGATTAGTTA 58.908 33.333 0.00 0.00 0.00 2.24
3237 8346 8.610248 TTCACTGGTCAATTTCGATTAGTTAA 57.390 30.769 0.00 0.00 0.00 2.01
3238 8347 8.025243 TCACTGGTCAATTTCGATTAGTTAAC 57.975 34.615 0.00 0.00 0.00 2.01
3239 8348 7.876068 TCACTGGTCAATTTCGATTAGTTAACT 59.124 33.333 13.68 13.68 0.00 2.24
3240 8349 8.504005 CACTGGTCAATTTCGATTAGTTAACTT 58.496 33.333 14.49 0.00 0.00 2.66
3241 8350 9.063615 ACTGGTCAATTTCGATTAGTTAACTTT 57.936 29.630 14.49 1.69 0.00 2.66
3242 8351 9.893305 CTGGTCAATTTCGATTAGTTAACTTTT 57.107 29.630 14.49 1.30 0.00 2.27
3293 8402 5.669477 AGTTAACTGGCAGCAAAATCAAAA 58.331 33.333 15.89 0.00 0.00 2.44
3386 8495 6.607689 TGCATTCAAAGATTCGTCGTTTAAT 58.392 32.000 0.00 0.00 0.00 1.40
3388 8497 8.394877 TGCATTCAAAGATTCGTCGTTTAATAT 58.605 29.630 0.00 0.00 0.00 1.28
3389 8498 9.858247 GCATTCAAAGATTCGTCGTTTAATATA 57.142 29.630 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.328845 AGTTTGTGCAAAAAGATATCAATGTTT 57.671 25.926 1.16 0.00 30.27 2.83
31 32 8.891671 AGTTTGTGCAAAAAGATATCAATGTT 57.108 26.923 1.16 0.00 31.33 2.71
32 33 7.326789 CGAGTTTGTGCAAAAAGATATCAATGT 59.673 33.333 1.16 0.00 31.33 2.71
33 34 7.201376 CCGAGTTTGTGCAAAAAGATATCAATG 60.201 37.037 1.16 0.00 31.33 2.82
34 35 6.808212 CCGAGTTTGTGCAAAAAGATATCAAT 59.192 34.615 1.16 0.00 31.33 2.57
35 36 6.148948 CCGAGTTTGTGCAAAAAGATATCAA 58.851 36.000 1.16 0.00 31.33 2.57
38 39 5.240623 TGACCGAGTTTGTGCAAAAAGATAT 59.759 36.000 1.16 0.00 31.33 1.63
39 40 4.576873 TGACCGAGTTTGTGCAAAAAGATA 59.423 37.500 1.16 0.00 31.33 1.98
40 41 3.380004 TGACCGAGTTTGTGCAAAAAGAT 59.620 39.130 1.16 0.00 31.33 2.40
41 42 2.750166 TGACCGAGTTTGTGCAAAAAGA 59.250 40.909 1.16 0.00 31.33 2.52
42 43 3.143807 TGACCGAGTTTGTGCAAAAAG 57.856 42.857 1.16 0.00 31.33 2.27
43 44 3.577649 TTGACCGAGTTTGTGCAAAAA 57.422 38.095 0.00 0.00 31.33 1.94
44 45 3.057174 AGTTTGACCGAGTTTGTGCAAAA 60.057 39.130 0.00 0.00 31.33 2.44
45 46 2.490115 AGTTTGACCGAGTTTGTGCAAA 59.510 40.909 0.00 0.00 0.00 3.68
46 47 2.088423 AGTTTGACCGAGTTTGTGCAA 58.912 42.857 0.00 0.00 0.00 4.08
47 48 1.745232 AGTTTGACCGAGTTTGTGCA 58.255 45.000 0.00 0.00 0.00 4.57
48 49 2.844122 AAGTTTGACCGAGTTTGTGC 57.156 45.000 0.00 0.00 0.00 4.57
50 51 4.258543 TCTCAAAGTTTGACCGAGTTTGT 58.741 39.130 14.35 0.00 38.17 2.83
51 52 4.875544 TCTCAAAGTTTGACCGAGTTTG 57.124 40.909 14.35 2.86 38.28 2.93
52 53 6.289064 ACTATCTCAAAGTTTGACCGAGTTT 58.711 36.000 14.35 0.45 35.46 2.66
54 55 5.470047 ACTATCTCAAAGTTTGACCGAGT 57.530 39.130 14.35 13.26 35.46 4.18
62 63 8.519799 TGAAAGGTCAAACTATCTCAAAGTTT 57.480 30.769 0.00 0.00 45.64 2.66
63 64 8.519799 TTGAAAGGTCAAACTATCTCAAAGTT 57.480 30.769 0.00 0.00 40.87 2.66
64 65 8.697507 ATTGAAAGGTCAAACTATCTCAAAGT 57.302 30.769 0.00 0.00 46.66 2.66
68 69 9.739276 ACATTATTGAAAGGTCAAACTATCTCA 57.261 29.630 0.00 0.00 46.66 3.27
71 72 9.573133 CCAACATTATTGAAAGGTCAAACTATC 57.427 33.333 0.00 0.00 46.66 2.08
72 73 9.308000 TCCAACATTATTGAAAGGTCAAACTAT 57.692 29.630 0.00 0.00 46.66 2.12
73 74 8.698973 TCCAACATTATTGAAAGGTCAAACTA 57.301 30.769 0.00 0.00 46.66 2.24
74 75 7.595819 TCCAACATTATTGAAAGGTCAAACT 57.404 32.000 0.00 0.00 46.66 2.66
75 76 7.926018 ACTTCCAACATTATTGAAAGGTCAAAC 59.074 33.333 0.00 0.00 46.66 2.93
78 79 7.721842 TGTACTTCCAACATTATTGAAAGGTCA 59.278 33.333 0.00 0.00 0.00 4.02
79 80 8.021396 GTGTACTTCCAACATTATTGAAAGGTC 58.979 37.037 0.00 0.00 0.00 3.85
81 82 8.110860 AGTGTACTTCCAACATTATTGAAAGG 57.889 34.615 0.00 0.00 0.00 3.11
83 84 8.918202 AGAGTGTACTTCCAACATTATTGAAA 57.082 30.769 0.00 0.00 0.00 2.69
84 85 8.918202 AAGAGTGTACTTCCAACATTATTGAA 57.082 30.769 0.00 0.00 0.00 2.69
85 86 8.918202 AAAGAGTGTACTTCCAACATTATTGA 57.082 30.769 0.00 0.00 0.00 2.57
89 90 9.280174 CCTTTAAAGAGTGTACTTCCAACATTA 57.720 33.333 16.98 0.00 0.00 1.90
90 91 7.996644 TCCTTTAAAGAGTGTACTTCCAACATT 59.003 33.333 16.98 0.00 0.00 2.71
91 92 7.444487 GTCCTTTAAAGAGTGTACTTCCAACAT 59.556 37.037 16.98 0.00 0.00 2.71
95 96 5.510179 CCGTCCTTTAAAGAGTGTACTTCCA 60.510 44.000 16.98 0.00 0.00 3.53
97 98 5.776744 TCCGTCCTTTAAAGAGTGTACTTC 58.223 41.667 16.98 0.00 0.00 3.01
98 99 5.279356 CCTCCGTCCTTTAAAGAGTGTACTT 60.279 44.000 16.98 0.00 0.00 2.24
99 100 4.220163 CCTCCGTCCTTTAAAGAGTGTACT 59.780 45.833 16.98 0.00 0.00 2.73
100 101 4.492611 CCTCCGTCCTTTAAAGAGTGTAC 58.507 47.826 16.98 5.84 0.00 2.90
101 102 3.512724 CCCTCCGTCCTTTAAAGAGTGTA 59.487 47.826 16.98 0.00 0.00 2.90
104 105 2.832733 CTCCCTCCGTCCTTTAAAGAGT 59.167 50.000 16.98 0.00 0.00 3.24
107 108 3.768215 ACTACTCCCTCCGTCCTTTAAAG 59.232 47.826 8.32 8.32 0.00 1.85
108 109 3.766051 GACTACTCCCTCCGTCCTTTAAA 59.234 47.826 0.00 0.00 0.00 1.52
110 111 2.681976 CGACTACTCCCTCCGTCCTTTA 60.682 54.545 0.00 0.00 0.00 1.85
111 112 1.849977 GACTACTCCCTCCGTCCTTT 58.150 55.000 0.00 0.00 0.00 3.11
113 114 1.224039 CGACTACTCCCTCCGTCCT 59.776 63.158 0.00 0.00 0.00 3.85
114 115 1.823041 CCGACTACTCCCTCCGTCC 60.823 68.421 0.00 0.00 0.00 4.79
115 116 0.179000 TACCGACTACTCCCTCCGTC 59.821 60.000 0.00 0.00 0.00 4.79
116 117 0.620556 TTACCGACTACTCCCTCCGT 59.379 55.000 0.00 0.00 0.00 4.69
118 119 3.564264 AGAATTACCGACTACTCCCTCC 58.436 50.000 0.00 0.00 0.00 4.30
119 120 4.737055 GCAAGAATTACCGACTACTCCCTC 60.737 50.000 0.00 0.00 0.00 4.30
120 121 3.132467 GCAAGAATTACCGACTACTCCCT 59.868 47.826 0.00 0.00 0.00 4.20
123 124 4.745649 ACAGCAAGAATTACCGACTACTC 58.254 43.478 0.00 0.00 0.00 2.59
124 125 4.803098 ACAGCAAGAATTACCGACTACT 57.197 40.909 0.00 0.00 0.00 2.57
125 126 5.857822 AAACAGCAAGAATTACCGACTAC 57.142 39.130 0.00 0.00 0.00 2.73
126 127 6.870971 AAAAACAGCAAGAATTACCGACTA 57.129 33.333 0.00 0.00 0.00 2.59
127 128 5.767816 AAAAACAGCAAGAATTACCGACT 57.232 34.783 0.00 0.00 0.00 4.18
162 163 8.698973 AAAGAAAAAGAAAAACTCCCCAAAAA 57.301 26.923 0.00 0.00 0.00 1.94
163 164 8.698973 AAAAGAAAAAGAAAAACTCCCCAAAA 57.301 26.923 0.00 0.00 0.00 2.44
164 165 8.572185 CAAAAAGAAAAAGAAAAACTCCCCAAA 58.428 29.630 0.00 0.00 0.00 3.28
166 167 7.454225 TCAAAAAGAAAAAGAAAAACTCCCCA 58.546 30.769 0.00 0.00 0.00 4.96
167 168 7.065803 CCTCAAAAAGAAAAAGAAAAACTCCCC 59.934 37.037 0.00 0.00 0.00 4.81
168 169 7.065803 CCCTCAAAAAGAAAAAGAAAAACTCCC 59.934 37.037 0.00 0.00 0.00 4.30
169 170 7.822334 TCCCTCAAAAAGAAAAAGAAAAACTCC 59.178 33.333 0.00 0.00 0.00 3.85
170 171 8.771920 TCCCTCAAAAAGAAAAAGAAAAACTC 57.228 30.769 0.00 0.00 0.00 3.01
172 173 8.397906 CCATCCCTCAAAAAGAAAAAGAAAAAC 58.602 33.333 0.00 0.00 0.00 2.43
174 175 7.629157 ACCATCCCTCAAAAAGAAAAAGAAAA 58.371 30.769 0.00 0.00 0.00 2.29
176 177 6.806668 ACCATCCCTCAAAAAGAAAAAGAA 57.193 33.333 0.00 0.00 0.00 2.52
177 178 7.906199 TTACCATCCCTCAAAAAGAAAAAGA 57.094 32.000 0.00 0.00 0.00 2.52
178 179 9.208022 GAATTACCATCCCTCAAAAAGAAAAAG 57.792 33.333 0.00 0.00 0.00 2.27
180 181 8.491045 AGAATTACCATCCCTCAAAAAGAAAA 57.509 30.769 0.00 0.00 0.00 2.29
181 182 8.367156 CAAGAATTACCATCCCTCAAAAAGAAA 58.633 33.333 0.00 0.00 0.00 2.52
182 183 7.525360 GCAAGAATTACCATCCCTCAAAAAGAA 60.525 37.037 0.00 0.00 0.00 2.52
183 184 6.071391 GCAAGAATTACCATCCCTCAAAAAGA 60.071 38.462 0.00 0.00 0.00 2.52
184 185 6.071165 AGCAAGAATTACCATCCCTCAAAAAG 60.071 38.462 0.00 0.00 0.00 2.27
185 186 5.779771 AGCAAGAATTACCATCCCTCAAAAA 59.220 36.000 0.00 0.00 0.00 1.94
186 187 5.185635 CAGCAAGAATTACCATCCCTCAAAA 59.814 40.000 0.00 0.00 0.00 2.44
187 188 4.706476 CAGCAAGAATTACCATCCCTCAAA 59.294 41.667 0.00 0.00 0.00 2.69
188 189 4.272489 CAGCAAGAATTACCATCCCTCAA 58.728 43.478 0.00 0.00 0.00 3.02
189 190 3.889815 CAGCAAGAATTACCATCCCTCA 58.110 45.455 0.00 0.00 0.00 3.86
190 191 2.620585 GCAGCAAGAATTACCATCCCTC 59.379 50.000 0.00 0.00 0.00 4.30
192 193 2.360165 CAGCAGCAAGAATTACCATCCC 59.640 50.000 0.00 0.00 0.00 3.85
193 194 2.223665 GCAGCAGCAAGAATTACCATCC 60.224 50.000 0.00 0.00 41.58 3.51
195 196 1.402968 CGCAGCAGCAAGAATTACCAT 59.597 47.619 0.82 0.00 42.27 3.55
196 197 0.804364 CGCAGCAGCAAGAATTACCA 59.196 50.000 0.82 0.00 42.27 3.25
198 199 1.063174 CCTCGCAGCAGCAAGAATTAC 59.937 52.381 0.82 0.00 42.27 1.89
199 200 1.339055 ACCTCGCAGCAGCAAGAATTA 60.339 47.619 0.82 0.00 42.27 1.40
200 201 0.607489 ACCTCGCAGCAGCAAGAATT 60.607 50.000 0.82 0.00 42.27 2.17
202 203 1.669115 GACCTCGCAGCAGCAAGAA 60.669 57.895 0.82 0.00 42.27 2.52
204 205 2.230994 TAGGACCTCGCAGCAGCAAG 62.231 60.000 0.00 0.00 42.27 4.01
205 206 1.617018 ATAGGACCTCGCAGCAGCAA 61.617 55.000 0.00 0.00 42.27 3.91
206 207 2.021068 GATAGGACCTCGCAGCAGCA 62.021 60.000 0.00 0.00 42.27 4.41
207 208 1.300542 GATAGGACCTCGCAGCAGC 60.301 63.158 0.00 0.00 37.42 5.25
209 210 0.676184 GATGATAGGACCTCGCAGCA 59.324 55.000 0.00 0.00 0.00 4.41
210 211 0.676184 TGATGATAGGACCTCGCAGC 59.324 55.000 0.00 0.52 0.00 5.25
212 213 2.362397 GACTTGATGATAGGACCTCGCA 59.638 50.000 0.00 0.00 0.00 5.10
213 214 2.605823 CGACTTGATGATAGGACCTCGC 60.606 54.545 0.00 0.00 0.00 5.03
214 215 2.030717 CCGACTTGATGATAGGACCTCG 60.031 54.545 0.00 0.00 0.00 4.63
216 217 2.320781 CCCGACTTGATGATAGGACCT 58.679 52.381 0.00 0.00 0.00 3.85
217 218 1.270358 GCCCGACTTGATGATAGGACC 60.270 57.143 0.00 0.00 0.00 4.46
218 219 1.270358 GGCCCGACTTGATGATAGGAC 60.270 57.143 0.00 0.00 0.00 3.85
266 298 2.736995 TTTTGAGCGTCGGCCTCG 60.737 61.111 11.87 11.87 41.24 4.63
274 306 1.890510 GTGGGTCGGTTTTGAGCGT 60.891 57.895 0.00 0.00 37.24 5.07
296 328 1.765597 AAAACCCTCGCCTTCCTCGT 61.766 55.000 0.00 0.00 0.00 4.18
342 376 1.000359 GGTTGGAATGGGTGGGGAG 60.000 63.158 0.00 0.00 0.00 4.30
410 446 2.156051 GAGCCGACGAACCAGGAAGT 62.156 60.000 0.00 0.00 0.00 3.01
460 496 1.813513 CAATGTTGCTCGAGAAGGGT 58.186 50.000 18.75 0.00 0.00 4.34
524 661 5.542251 AGGCTATTTCCTCTAGAATCTCACC 59.458 44.000 0.00 0.00 33.44 4.02
529 666 5.816955 ACCAGGCTATTTCCTCTAGAATC 57.183 43.478 0.00 0.00 33.25 2.52
635 812 2.483876 ACAACACAAGTCCACGAGATG 58.516 47.619 0.00 0.00 0.00 2.90
672 849 3.150781 AGGGGGAGGGGATTTCCTATAAT 59.849 47.826 0.00 0.00 37.25 1.28
674 851 2.179248 AGGGGGAGGGGATTTCCTATA 58.821 52.381 0.00 0.00 37.25 1.31
675 852 0.968295 AGGGGGAGGGGATTTCCTAT 59.032 55.000 0.00 0.00 37.25 2.57
676 853 1.224905 GTAGGGGGAGGGGATTTCCTA 59.775 57.143 0.00 0.00 37.25 2.94
678 855 1.066585 GGTAGGGGGAGGGGATTTCC 61.067 65.000 0.00 0.00 0.00 3.13
680 857 1.007037 GGGTAGGGGGAGGGGATTT 59.993 63.158 0.00 0.00 0.00 2.17
685 862 4.837421 GTGGGGGTAGGGGGAGGG 62.837 77.778 0.00 0.00 0.00 4.30
692 869 3.470888 CTGCTCGGTGGGGGTAGG 61.471 72.222 0.00 0.00 0.00 3.18
693 870 4.162690 GCTGCTCGGTGGGGGTAG 62.163 72.222 0.00 0.00 0.00 3.18
811 1007 5.941647 TGAAAGATTCATGTGCTCATCTTCA 59.058 36.000 0.00 0.00 34.08 3.02
818 5209 5.159209 CCAGTTTGAAAGATTCATGTGCTC 58.841 41.667 0.00 0.00 39.84 4.26
1101 5557 4.056125 CTGTGCTCCGCCTCGACA 62.056 66.667 0.00 0.00 0.00 4.35
1147 5603 1.882623 CAAGGCTTCTGTTCAAGGGTC 59.117 52.381 0.00 0.00 0.00 4.46
1154 5610 1.666189 GCGATACCAAGGCTTCTGTTC 59.334 52.381 0.00 0.00 0.00 3.18
1589 6045 3.543680 TTTGGAGATTCGACCATCCTC 57.456 47.619 9.65 0.00 36.02 3.71
1796 6253 7.696017 ACCAATAACATACTCCAGGTAAAGTT 58.304 34.615 0.00 0.00 36.94 2.66
2053 6510 4.067896 GGACATGATTGGATGAGCGTTAT 58.932 43.478 0.00 0.00 0.00 1.89
2298 6755 1.271054 ACGATCAGCAACTCCAGCTTT 60.271 47.619 0.00 0.00 41.14 3.51
2309 6766 1.270305 GGCAGCCTATAACGATCAGCA 60.270 52.381 3.29 0.00 0.00 4.41
2464 7481 4.104102 TCTCCAAAGTGAAGGCTAAAGGAA 59.896 41.667 0.00 0.00 0.00 3.36
2482 7499 5.809001 ACAGATACAGCTTCAAAATCTCCA 58.191 37.500 0.00 0.00 0.00 3.86
2488 7505 8.169977 AGAAAATGACAGATACAGCTTCAAAA 57.830 30.769 0.00 0.00 0.00 2.44
2489 7506 7.663081 AGAGAAAATGACAGATACAGCTTCAAA 59.337 33.333 0.00 0.00 0.00 2.69
2535 7558 5.748152 CGGACTCATCAGAAGAAGAAATCTC 59.252 44.000 0.00 0.00 37.42 2.75
2624 7648 2.096496 GGTGCCATGTTTTGAGATCTCG 59.904 50.000 17.76 2.18 0.00 4.04
2646 7670 6.601613 CCCCATCACAGCTACTATAAAACAAA 59.398 38.462 0.00 0.00 0.00 2.83
2649 7673 5.681639 ACCCCATCACAGCTACTATAAAAC 58.318 41.667 0.00 0.00 0.00 2.43
2650 7674 5.968676 ACCCCATCACAGCTACTATAAAA 57.031 39.130 0.00 0.00 0.00 1.52
2651 7675 5.452776 CGAACCCCATCACAGCTACTATAAA 60.453 44.000 0.00 0.00 0.00 1.40
2654 7678 2.365617 CGAACCCCATCACAGCTACTAT 59.634 50.000 0.00 0.00 0.00 2.12
2656 7680 0.537188 CGAACCCCATCACAGCTACT 59.463 55.000 0.00 0.00 0.00 2.57
2657 7681 0.462047 CCGAACCCCATCACAGCTAC 60.462 60.000 0.00 0.00 0.00 3.58
2700 7728 0.033781 TGCATTTTCAGGCAGCCAAC 59.966 50.000 15.80 0.00 34.58 3.77
2709 7737 3.293311 CAGGAACACCTGCATTTTCAG 57.707 47.619 3.31 0.00 43.51 3.02
2749 7777 9.943163 GATTATGAATCTAAAAGAAGCAAGACC 57.057 33.333 0.00 0.00 35.02 3.85
2769 7801 7.139392 CAGCCAAGATCACAAAGATGATTATG 58.861 38.462 0.00 0.00 39.48 1.90
2807 7839 3.146104 ACAAGGGACAAATGAGTCTGG 57.854 47.619 0.00 0.00 38.57 3.86
2815 7849 4.190772 CAAAGCACAAACAAGGGACAAAT 58.809 39.130 0.00 0.00 0.00 2.32
2882 7919 2.826128 TCTTTCAGTCGCACCTACAGAT 59.174 45.455 0.00 0.00 0.00 2.90
2885 7922 3.462483 TTTCTTTCAGTCGCACCTACA 57.538 42.857 0.00 0.00 0.00 2.74
2887 7924 4.699637 TCTTTTTCTTTCAGTCGCACCTA 58.300 39.130 0.00 0.00 0.00 3.08
2894 7931 6.258068 TCTCGGAGTTTCTTTTTCTTTCAGTC 59.742 38.462 4.69 0.00 0.00 3.51
2909 7946 1.405661 GGGCTCGATTTCTCGGAGTTT 60.406 52.381 4.69 0.00 45.10 2.66
2930 7970 2.970324 TTCCTGTTGGCGTCGCAC 60.970 61.111 20.50 10.20 0.00 5.34
2944 7984 1.137282 GGAATCTCACGGAGGAGTTCC 59.863 57.143 13.69 13.69 43.04 3.62
2973 8013 1.330655 TGGCTTCCCTTCCTAGCGAG 61.331 60.000 0.00 0.00 35.77 5.03
2974 8014 0.907704 TTGGCTTCCCTTCCTAGCGA 60.908 55.000 0.00 0.00 35.77 4.93
2975 8015 0.462759 CTTGGCTTCCCTTCCTAGCG 60.463 60.000 0.00 0.00 35.77 4.26
2976 8016 0.912486 TCTTGGCTTCCCTTCCTAGC 59.088 55.000 0.00 0.00 0.00 3.42
2977 8017 3.721087 TTTCTTGGCTTCCCTTCCTAG 57.279 47.619 0.00 0.00 0.00 3.02
2978 8018 3.333680 ACATTTCTTGGCTTCCCTTCCTA 59.666 43.478 0.00 0.00 0.00 2.94
2979 8019 2.110721 ACATTTCTTGGCTTCCCTTCCT 59.889 45.455 0.00 0.00 0.00 3.36
3138 8178 6.170506 ACGAAAGAGAAATGCAATACAGGTA 58.829 36.000 0.00 0.00 0.00 3.08
3139 8179 5.003804 ACGAAAGAGAAATGCAATACAGGT 58.996 37.500 0.00 0.00 0.00 4.00
3161 8270 6.476051 AGAAAGAAAGAAAGAACGAACGAAC 58.524 36.000 0.14 0.00 0.00 3.95
3165 8274 8.897457 AAGAAAGAAAGAAAGAAAGAACGAAC 57.103 30.769 0.00 0.00 0.00 3.95
3166 8275 9.556030 GAAAGAAAGAAAGAAAGAAAGAACGAA 57.444 29.630 0.00 0.00 0.00 3.85
3167 8276 8.947115 AGAAAGAAAGAAAGAAAGAAAGAACGA 58.053 29.630 0.00 0.00 0.00 3.85
3168 8277 9.561270 AAGAAAGAAAGAAAGAAAGAAAGAACG 57.439 29.630 0.00 0.00 0.00 3.95
3170 8279 9.358872 GCAAGAAAGAAAGAAAGAAAGAAAGAA 57.641 29.630 0.00 0.00 0.00 2.52
3171 8280 8.522830 TGCAAGAAAGAAAGAAAGAAAGAAAGA 58.477 29.630 0.00 0.00 0.00 2.52
3172 8281 8.693542 TGCAAGAAAGAAAGAAAGAAAGAAAG 57.306 30.769 0.00 0.00 0.00 2.62
3173 8282 7.276438 GCTGCAAGAAAGAAAGAAAGAAAGAAA 59.724 33.333 0.00 0.00 34.07 2.52
3174 8283 6.753744 GCTGCAAGAAAGAAAGAAAGAAAGAA 59.246 34.615 0.00 0.00 34.07 2.52
3175 8284 6.268566 GCTGCAAGAAAGAAAGAAAGAAAGA 58.731 36.000 0.00 0.00 34.07 2.52
3176 8285 5.172771 CGCTGCAAGAAAGAAAGAAAGAAAG 59.827 40.000 0.00 0.00 34.07 2.62
3179 8288 3.627577 ACGCTGCAAGAAAGAAAGAAAGA 59.372 39.130 0.00 0.00 34.07 2.52
3193 8302 1.092921 AGAACGTGGAAACGCTGCAA 61.093 50.000 0.00 0.00 39.21 4.08
3244 8353 3.000724 CGAAATTGTGCCGCAAAGAAAAA 59.999 39.130 0.00 0.00 40.91 1.94
3245 8354 2.537625 CGAAATTGTGCCGCAAAGAAAA 59.462 40.909 0.00 0.00 40.91 2.29
3246 8355 2.123342 CGAAATTGTGCCGCAAAGAAA 58.877 42.857 0.00 0.00 40.91 2.52
3247 8356 1.335182 TCGAAATTGTGCCGCAAAGAA 59.665 42.857 0.00 0.00 40.91 2.52
3248 8357 0.947960 TCGAAATTGTGCCGCAAAGA 59.052 45.000 0.00 0.00 40.91 2.52
3249 8358 1.981254 ATCGAAATTGTGCCGCAAAG 58.019 45.000 0.00 0.00 40.91 2.77
3250 8359 2.430546 AATCGAAATTGTGCCGCAAA 57.569 40.000 0.00 0.00 40.91 3.68
3251 8360 2.486203 ACTAATCGAAATTGTGCCGCAA 59.514 40.909 0.00 0.00 41.89 4.85
3252 8361 2.080693 ACTAATCGAAATTGTGCCGCA 58.919 42.857 0.00 0.00 0.00 5.69
3253 8362 2.825086 ACTAATCGAAATTGTGCCGC 57.175 45.000 0.00 0.00 0.00 6.53
3254 8363 5.732647 CAGTTAACTAATCGAAATTGTGCCG 59.267 40.000 8.04 0.00 0.00 5.69
3255 8364 6.027749 CCAGTTAACTAATCGAAATTGTGCC 58.972 40.000 8.04 0.00 0.00 5.01
3256 8365 5.511729 GCCAGTTAACTAATCGAAATTGTGC 59.488 40.000 8.04 0.00 0.00 4.57
3257 8366 6.607689 TGCCAGTTAACTAATCGAAATTGTG 58.392 36.000 8.04 0.00 0.00 3.33
3258 8367 6.622896 GCTGCCAGTTAACTAATCGAAATTGT 60.623 38.462 8.04 0.00 0.00 2.71
3293 8402 1.067212 CCGATCACGCCTAGCTTTAGT 59.933 52.381 0.00 0.00 38.29 2.24
3393 8502 9.570488 CCAAAGTACTACTACTTTCATCAGTAC 57.430 37.037 0.00 0.00 46.16 2.73
3394 8503 9.305555 ACCAAAGTACTACTACTTTCATCAGTA 57.694 33.333 0.00 0.00 46.16 2.74
3399 8508 9.433153 GCTTAACCAAAGTACTACTACTTTCAT 57.567 33.333 0.00 0.00 46.16 2.57
3400 8509 7.596248 CGCTTAACCAAAGTACTACTACTTTCA 59.404 37.037 0.00 0.00 46.16 2.69
3401 8510 7.062722 CCGCTTAACCAAAGTACTACTACTTTC 59.937 40.741 0.00 0.00 46.16 2.62
3403 8512 6.015095 ACCGCTTAACCAAAGTACTACTACTT 60.015 38.462 0.00 0.00 43.87 2.24
3404 8513 5.478332 ACCGCTTAACCAAAGTACTACTACT 59.522 40.000 0.00 0.00 37.53 2.57
3405 8514 5.714047 ACCGCTTAACCAAAGTACTACTAC 58.286 41.667 0.00 0.00 37.53 2.73
3406 8515 5.982890 ACCGCTTAACCAAAGTACTACTA 57.017 39.130 0.00 0.00 37.53 1.82


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

AutoCloner maintained by Alex Coulton.