Multiple sequence alignment - TraesCS3A01G162900

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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 TraesCS3A01G162900 chr3A 100.000 3290 0 0 1 3290 165089878 165086589 0.000000e+00 6076.0
1 TraesCS3A01G162900 chr3B 92.274 2045 88 36 310 2327 214286103 214284102 0.000000e+00 2837.0
2 TraesCS3A01G162900 chr3B 88.000 225 21 5 4 223 214440501 214440278 9.060000e-66 261.0
3 TraesCS3A01G162900 chr3D 92.631 1452 55 25 306 1740 148223249 148224665 0.000000e+00 2041.0
4 TraesCS3A01G162900 chr3D 94.722 701 24 7 1791 2483 148224764 148225459 0.000000e+00 1077.0
5 TraesCS3A01G162900 chr3D 88.998 818 82 5 2481 3290 157764267 157763450 0.000000e+00 1005.0
6 TraesCS3A01G162900 chr3D 88.889 225 21 4 1 223 147967300 147967522 1.160000e-69 274.0
7 TraesCS3A01G162900 chr4D 88.753 818 84 4 2481 3290 38452613 38453430 0.000000e+00 994.0
8 TraesCS3A01G162900 chr4B 88.257 809 84 9 2489 3290 417340655 417339851 0.000000e+00 957.0
9 TraesCS3A01G162900 chr4B 79.323 266 43 9 1432 1691 380653772 380654031 3.370000e-40 176.0
10 TraesCS3A01G162900 chr7B 87.408 818 94 8 2481 3290 629014234 629015050 0.000000e+00 931.0
11 TraesCS3A01G162900 chr7B 84.483 116 13 4 72 182 518392861 518392976 3.470000e-20 110.0
12 TraesCS3A01G162900 chr7B 90.625 64 5 1 120 182 518403577 518403640 2.100000e-12 84.2
13 TraesCS3A01G162900 chr7B 90.625 64 5 1 120 182 518411685 518411748 2.100000e-12 84.2
14 TraesCS3A01G162900 chr7B 89.062 64 6 1 120 182 518395728 518395791 9.790000e-11 78.7
15 TraesCS3A01G162900 chr1B 86.414 817 99 7 2481 3288 645388164 645387351 0.000000e+00 883.0
16 TraesCS3A01G162900 chr6B 85.907 816 107 7 2483 3290 500896866 500897681 0.000000e+00 863.0
17 TraesCS3A01G162900 chr6B 86.713 143 18 1 1430 1572 134664377 134664236 1.220000e-34 158.0
18 TraesCS3A01G162900 chr6B 86.420 81 9 2 113 192 200011742 200011663 1.630000e-13 87.9
19 TraesCS3A01G162900 chr2D 85.871 821 101 11 2482 3290 9876849 9876032 0.000000e+00 859.0
20 TraesCS3A01G162900 chr2D 81.048 248 42 5 1434 1677 175331615 175331861 3.350000e-45 193.0
21 TraesCS3A01G162900 chr2D 81.208 149 16 8 1033 1177 54487979 54487839 3.470000e-20 110.0
22 TraesCS3A01G162900 chr2D 80.537 149 18 7 1033 1177 54317524 54317665 1.610000e-18 104.0
23 TraesCS3A01G162900 chr1D 84.653 821 108 10 2482 3290 491671474 491670660 0.000000e+00 802.0
24 TraesCS3A01G162900 chr1D 82.927 820 122 15 2482 3290 60170514 60171326 0.000000e+00 723.0
25 TraesCS3A01G162900 chr1D 78.238 193 27 7 45 223 435280345 435280154 3.470000e-20 110.0
26 TraesCS3A01G162900 chr2A 81.928 249 39 4 1432 1677 54882610 54882855 4.300000e-49 206.0
27 TraesCS3A01G162900 chr2A 80.321 249 42 5 1434 1677 175468037 175468283 7.250000e-42 182.0
28 TraesCS3A01G162900 chr2B 79.920 249 43 5 1434 1677 223154537 223154783 3.370000e-40 176.0
29 TraesCS3A01G162900 chr2B 81.579 152 17 7 1033 1180 85177910 85177766 7.460000e-22 115.0
30 TraesCS3A01G162900 chr2B 79.866 149 19 6 1033 1177 85074018 85074159 7.510000e-17 99.0
31 TraesCS3A01G162900 chr6D 86.577 149 19 1 1430 1578 60487531 60487384 2.630000e-36 163.0
32 TraesCS3A01G162900 chr7A 81.865 193 23 9 45 226 735449075 735449266 5.690000e-33 152.0
33 TraesCS3A01G162900 chr5D 94.872 39 1 1 343 381 476732621 476732584 3.550000e-05 60.2


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 TraesCS3A01G162900 chr3A 165086589 165089878 3289 True 6076 6076 100.0000 1 3290 1 chr3A.!!$R1 3289
1 TraesCS3A01G162900 chr3B 214284102 214286103 2001 True 2837 2837 92.2740 310 2327 1 chr3B.!!$R1 2017
2 TraesCS3A01G162900 chr3D 148223249 148225459 2210 False 1559 2041 93.6765 306 2483 2 chr3D.!!$F2 2177
3 TraesCS3A01G162900 chr3D 157763450 157764267 817 True 1005 1005 88.9980 2481 3290 1 chr3D.!!$R1 809
4 TraesCS3A01G162900 chr4D 38452613 38453430 817 False 994 994 88.7530 2481 3290 1 chr4D.!!$F1 809
5 TraesCS3A01G162900 chr4B 417339851 417340655 804 True 957 957 88.2570 2489 3290 1 chr4B.!!$R1 801
6 TraesCS3A01G162900 chr7B 629014234 629015050 816 False 931 931 87.4080 2481 3290 1 chr7B.!!$F3 809
7 TraesCS3A01G162900 chr1B 645387351 645388164 813 True 883 883 86.4140 2481 3288 1 chr1B.!!$R1 807
8 TraesCS3A01G162900 chr6B 500896866 500897681 815 False 863 863 85.9070 2483 3290 1 chr6B.!!$F1 807
9 TraesCS3A01G162900 chr2D 9876032 9876849 817 True 859 859 85.8710 2482 3290 1 chr2D.!!$R1 808
10 TraesCS3A01G162900 chr1D 491670660 491671474 814 True 802 802 84.6530 2482 3290 1 chr1D.!!$R2 808
11 TraesCS3A01G162900 chr1D 60170514 60171326 812 False 723 723 82.9270 2482 3290 1 chr1D.!!$F1 808

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
170 171 0.171903 AGTGCTCGCCAATTTCATGC 59.828 50.0 0.0 0.00 0.00 4.06 F
1080 1093 0.031314 CGGACCAGGAGATCATCGTG 59.969 60.0 0.0 2.03 42.31 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 1877 0.249155 CCGACAACCTGTGTGTACGT 60.249 55.0 0.0 0.0 41.96 3.57 R
2969 3087 0.036164 CCAAACCTCCGTGTGATCCA 59.964 55.0 0.0 0.0 27.12 3.41 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
25 26 7.832503 AAGCTGAAATTTATCCCGAAAATTG 57.167 32.000 0.00 0.00 36.81 2.32
26 27 5.812127 AGCTGAAATTTATCCCGAAAATTGC 59.188 36.000 0.00 0.00 36.81 3.56
27 28 5.006649 GCTGAAATTTATCCCGAAAATTGCC 59.993 40.000 0.00 0.00 36.81 4.52
28 29 5.105752 TGAAATTTATCCCGAAAATTGCCG 58.894 37.500 0.00 0.00 36.81 5.69
29 30 4.729227 AATTTATCCCGAAAATTGCCGT 57.271 36.364 0.00 0.00 35.69 5.68
30 31 3.768468 TTTATCCCGAAAATTGCCGTC 57.232 42.857 0.00 0.00 0.00 4.79
31 32 1.670791 TATCCCGAAAATTGCCGTCC 58.329 50.000 0.00 0.00 0.00 4.79
32 33 0.322997 ATCCCGAAAATTGCCGTCCA 60.323 50.000 0.00 0.00 0.00 4.02
33 34 0.322997 TCCCGAAAATTGCCGTCCAT 60.323 50.000 0.00 0.00 0.00 3.41
34 35 0.179140 CCCGAAAATTGCCGTCCATG 60.179 55.000 0.00 0.00 0.00 3.66
35 36 0.179140 CCGAAAATTGCCGTCCATGG 60.179 55.000 4.97 4.97 0.00 3.66
36 37 0.179140 CGAAAATTGCCGTCCATGGG 60.179 55.000 13.02 0.00 0.00 4.00
37 38 1.181786 GAAAATTGCCGTCCATGGGA 58.818 50.000 13.02 0.00 0.00 4.37
50 51 4.473643 TGGGACAGCGAGTTTTGG 57.526 55.556 0.00 0.00 0.00 3.28
51 52 1.896660 TGGGACAGCGAGTTTTGGC 60.897 57.895 0.00 0.00 0.00 4.52
52 53 1.600916 GGGACAGCGAGTTTTGGCT 60.601 57.895 0.00 0.00 39.11 4.75
53 54 1.578206 GGGACAGCGAGTTTTGGCTC 61.578 60.000 0.00 0.00 36.10 4.70
54 55 0.603975 GGACAGCGAGTTTTGGCTCT 60.604 55.000 0.00 0.00 36.10 4.09
55 56 1.337823 GGACAGCGAGTTTTGGCTCTA 60.338 52.381 0.00 0.00 36.10 2.43
56 57 2.622436 GACAGCGAGTTTTGGCTCTAT 58.378 47.619 0.00 0.00 36.10 1.98
57 58 2.349886 GACAGCGAGTTTTGGCTCTATG 59.650 50.000 0.00 0.00 36.10 2.23
58 59 1.667724 CAGCGAGTTTTGGCTCTATGG 59.332 52.381 0.00 0.00 36.10 2.74
59 60 1.555075 AGCGAGTTTTGGCTCTATGGA 59.445 47.619 0.00 0.00 32.38 3.41
60 61 1.936547 GCGAGTTTTGGCTCTATGGAG 59.063 52.381 0.86 0.86 42.18 3.86
85 86 8.915871 GCATATGCTCTCTGAAAAACAATAAA 57.084 30.769 20.64 0.00 38.21 1.40
86 87 9.525409 GCATATGCTCTCTGAAAAACAATAAAT 57.475 29.630 20.64 0.00 38.21 1.40
158 159 4.295870 TGTTAGTGTAACAAGAGTGCTCG 58.704 43.478 0.00 0.00 44.95 5.03
159 160 1.784525 AGTGTAACAAGAGTGCTCGC 58.215 50.000 0.00 0.00 41.43 5.03
160 161 0.790814 GTGTAACAAGAGTGCTCGCC 59.209 55.000 0.00 0.00 36.32 5.54
161 162 0.391228 TGTAACAAGAGTGCTCGCCA 59.609 50.000 0.00 0.00 34.09 5.69
162 163 1.202592 TGTAACAAGAGTGCTCGCCAA 60.203 47.619 0.00 0.00 34.09 4.52
163 164 2.076863 GTAACAAGAGTGCTCGCCAAT 58.923 47.619 0.00 0.00 34.09 3.16
164 165 1.609208 AACAAGAGTGCTCGCCAATT 58.391 45.000 0.00 0.00 34.09 2.32
165 166 1.609208 ACAAGAGTGCTCGCCAATTT 58.391 45.000 0.00 0.00 34.09 1.82
166 167 1.537202 ACAAGAGTGCTCGCCAATTTC 59.463 47.619 0.00 0.00 34.09 2.17
167 168 1.536766 CAAGAGTGCTCGCCAATTTCA 59.463 47.619 0.00 0.00 34.09 2.69
168 169 2.119801 AGAGTGCTCGCCAATTTCAT 57.880 45.000 0.00 0.00 34.09 2.57
169 170 1.741706 AGAGTGCTCGCCAATTTCATG 59.258 47.619 0.00 0.00 34.09 3.07
170 171 0.171903 AGTGCTCGCCAATTTCATGC 59.828 50.000 0.00 0.00 0.00 4.06
185 186 5.694231 TTTCATGCGAAATGGGATATCAG 57.306 39.130 4.83 0.00 36.19 2.90
186 187 4.356405 TCATGCGAAATGGGATATCAGT 57.644 40.909 4.83 0.00 0.00 3.41
187 188 4.067192 TCATGCGAAATGGGATATCAGTG 58.933 43.478 4.83 0.00 0.00 3.66
188 189 2.221169 TGCGAAATGGGATATCAGTGC 58.779 47.619 4.83 0.00 0.00 4.40
189 190 1.537202 GCGAAATGGGATATCAGTGCC 59.463 52.381 4.83 0.00 0.00 5.01
190 191 2.811873 GCGAAATGGGATATCAGTGCCT 60.812 50.000 4.83 0.00 0.00 4.75
191 192 3.070018 CGAAATGGGATATCAGTGCCTC 58.930 50.000 4.83 0.00 0.00 4.70
192 193 3.494924 CGAAATGGGATATCAGTGCCTCA 60.495 47.826 4.83 0.00 0.00 3.86
193 194 3.498774 AATGGGATATCAGTGCCTCAC 57.501 47.619 4.83 0.00 34.10 3.51
194 195 2.180946 TGGGATATCAGTGCCTCACT 57.819 50.000 4.83 0.00 46.51 3.41
203 204 2.435372 AGTGCCTCACTGGAAAACAA 57.565 45.000 0.00 0.00 43.63 2.83
204 205 2.733956 AGTGCCTCACTGGAAAACAAA 58.266 42.857 0.00 0.00 43.63 2.83
205 206 3.096092 AGTGCCTCACTGGAAAACAAAA 58.904 40.909 0.00 0.00 43.63 2.44
206 207 3.706086 AGTGCCTCACTGGAAAACAAAAT 59.294 39.130 0.00 0.00 43.63 1.82
207 208 4.162131 AGTGCCTCACTGGAAAACAAAATT 59.838 37.500 0.00 0.00 43.63 1.82
208 209 5.362430 AGTGCCTCACTGGAAAACAAAATTA 59.638 36.000 0.00 0.00 43.63 1.40
209 210 6.045955 GTGCCTCACTGGAAAACAAAATTAA 58.954 36.000 0.00 0.00 38.35 1.40
210 211 6.019075 GTGCCTCACTGGAAAACAAAATTAAC 60.019 38.462 0.00 0.00 38.35 2.01
211 212 6.127196 TGCCTCACTGGAAAACAAAATTAACT 60.127 34.615 0.00 0.00 38.35 2.24
212 213 6.200854 GCCTCACTGGAAAACAAAATTAACTG 59.799 38.462 0.00 0.00 38.35 3.16
213 214 7.264947 CCTCACTGGAAAACAAAATTAACTGT 58.735 34.615 0.00 0.00 38.35 3.55
214 215 8.410141 CCTCACTGGAAAACAAAATTAACTGTA 58.590 33.333 0.00 0.00 38.35 2.74
215 216 9.233232 CTCACTGGAAAACAAAATTAACTGTAC 57.767 33.333 0.00 0.00 0.00 2.90
216 217 8.192110 TCACTGGAAAACAAAATTAACTGTACC 58.808 33.333 0.00 0.00 0.00 3.34
217 218 7.976734 CACTGGAAAACAAAATTAACTGTACCA 59.023 33.333 0.00 0.00 0.00 3.25
218 219 8.700973 ACTGGAAAACAAAATTAACTGTACCAT 58.299 29.630 0.00 0.00 0.00 3.55
219 220 9.541143 CTGGAAAACAAAATTAACTGTACCATT 57.459 29.630 0.00 0.00 0.00 3.16
220 221 9.892130 TGGAAAACAAAATTAACTGTACCATTT 57.108 25.926 0.00 0.00 0.00 2.32
225 226 9.965824 AACAAAATTAACTGTACCATTTGAGAG 57.034 29.630 12.78 0.00 32.29 3.20
226 227 8.082242 ACAAAATTAACTGTACCATTTGAGAGC 58.918 33.333 12.78 0.00 32.29 4.09
227 228 7.759489 AAATTAACTGTACCATTTGAGAGCA 57.241 32.000 0.00 0.00 0.00 4.26
228 229 7.944729 AATTAACTGTACCATTTGAGAGCAT 57.055 32.000 0.00 0.00 0.00 3.79
229 230 6.985188 TTAACTGTACCATTTGAGAGCATC 57.015 37.500 0.00 0.00 0.00 3.91
230 231 4.558226 ACTGTACCATTTGAGAGCATCA 57.442 40.909 0.00 0.00 37.82 3.07
231 232 4.910195 ACTGTACCATTTGAGAGCATCAA 58.090 39.130 0.59 0.59 46.31 2.57
236 237 3.875369 ACCATTTGAGAGCATCAAGGGTC 60.875 47.826 17.14 0.00 46.36 4.46
237 238 3.840831 TTGAGAGCATCAAGGGTCG 57.159 52.632 0.59 0.00 43.09 4.79
238 239 0.250234 TTGAGAGCATCAAGGGTCGG 59.750 55.000 0.59 0.00 43.09 4.79
239 240 0.614697 TGAGAGCATCAAGGGTCGGA 60.615 55.000 0.00 0.00 40.14 4.55
240 241 0.537188 GAGAGCATCAAGGGTCGGAA 59.463 55.000 0.00 0.00 40.14 4.30
241 242 0.539051 AGAGCATCAAGGGTCGGAAG 59.461 55.000 0.00 0.00 40.14 3.46
242 243 0.462759 GAGCATCAAGGGTCGGAAGG 60.463 60.000 0.00 0.00 33.17 3.46
243 244 0.909610 AGCATCAAGGGTCGGAAGGA 60.910 55.000 0.00 0.00 0.00 3.36
244 245 0.744771 GCATCAAGGGTCGGAAGGAC 60.745 60.000 0.00 0.00 45.31 3.85
254 255 2.266689 GGAAGGACCGGCGCTTAA 59.733 61.111 7.64 0.00 0.00 1.85
255 256 1.153229 GGAAGGACCGGCGCTTAAT 60.153 57.895 7.64 0.00 0.00 1.40
256 257 0.746923 GGAAGGACCGGCGCTTAATT 60.747 55.000 7.64 0.00 0.00 1.40
257 258 1.092348 GAAGGACCGGCGCTTAATTT 58.908 50.000 7.64 0.00 0.00 1.82
258 259 1.471287 GAAGGACCGGCGCTTAATTTT 59.529 47.619 7.64 0.00 0.00 1.82
259 260 2.406596 AGGACCGGCGCTTAATTTTA 57.593 45.000 7.64 0.00 0.00 1.52
260 261 2.713877 AGGACCGGCGCTTAATTTTAA 58.286 42.857 7.64 0.00 0.00 1.52
261 262 2.421073 AGGACCGGCGCTTAATTTTAAC 59.579 45.455 7.64 0.00 0.00 2.01
262 263 2.421073 GGACCGGCGCTTAATTTTAACT 59.579 45.455 7.64 0.00 0.00 2.24
263 264 3.119743 GGACCGGCGCTTAATTTTAACTT 60.120 43.478 7.64 0.00 0.00 2.66
264 265 4.478699 GACCGGCGCTTAATTTTAACTTT 58.521 39.130 7.64 0.00 0.00 2.66
265 266 5.391843 GGACCGGCGCTTAATTTTAACTTTA 60.392 40.000 7.64 0.00 0.00 1.85
266 267 5.393124 ACCGGCGCTTAATTTTAACTTTAC 58.607 37.500 7.64 0.00 0.00 2.01
267 268 5.181811 ACCGGCGCTTAATTTTAACTTTACT 59.818 36.000 7.64 0.00 0.00 2.24
268 269 5.735892 CCGGCGCTTAATTTTAACTTTACTC 59.264 40.000 7.64 0.00 0.00 2.59
269 270 5.735892 CGGCGCTTAATTTTAACTTTACTCC 59.264 40.000 7.64 0.00 0.00 3.85
270 271 6.402875 CGGCGCTTAATTTTAACTTTACTCCT 60.403 38.462 7.64 0.00 0.00 3.69
271 272 6.965500 GGCGCTTAATTTTAACTTTACTCCTC 59.035 38.462 7.64 0.00 0.00 3.71
272 273 7.148289 GGCGCTTAATTTTAACTTTACTCCTCT 60.148 37.037 7.64 0.00 0.00 3.69
273 274 8.876790 GCGCTTAATTTTAACTTTACTCCTCTA 58.123 33.333 0.00 0.00 0.00 2.43
286 287 8.935741 ACTTTACTCCTCTAATACCAATAAGGG 58.064 37.037 0.00 0.00 43.89 3.95
287 288 9.155785 CTTTACTCCTCTAATACCAATAAGGGA 57.844 37.037 0.00 0.00 43.89 4.20
288 289 9.684702 TTTACTCCTCTAATACCAATAAGGGAT 57.315 33.333 0.00 0.00 45.67 3.85
289 290 7.800300 ACTCCTCTAATACCAATAAGGGATC 57.200 40.000 0.00 0.00 41.47 3.36
290 291 6.437793 ACTCCTCTAATACCAATAAGGGATCG 59.562 42.308 0.00 0.00 41.47 3.69
291 292 5.720041 TCCTCTAATACCAATAAGGGATCGG 59.280 44.000 0.00 0.00 41.47 4.18
292 293 5.416271 TCTAATACCAATAAGGGATCGGC 57.584 43.478 0.00 0.00 41.47 5.54
293 294 5.091552 TCTAATACCAATAAGGGATCGGCT 58.908 41.667 0.00 0.00 41.47 5.52
294 295 4.724279 AATACCAATAAGGGATCGGCTT 57.276 40.909 0.00 0.00 41.47 4.35
295 296 5.836024 AATACCAATAAGGGATCGGCTTA 57.164 39.130 0.00 0.00 41.47 3.09
296 297 3.771577 ACCAATAAGGGATCGGCTTAG 57.228 47.619 0.00 0.00 43.89 2.18
297 298 2.372172 ACCAATAAGGGATCGGCTTAGG 59.628 50.000 0.00 0.00 43.89 2.69
298 299 2.372172 CCAATAAGGGATCGGCTTAGGT 59.628 50.000 0.00 0.00 0.00 3.08
299 300 3.557264 CCAATAAGGGATCGGCTTAGGTC 60.557 52.174 0.00 0.00 0.00 3.85
300 301 1.713297 TAAGGGATCGGCTTAGGTCC 58.287 55.000 0.00 0.00 0.00 4.46
302 303 2.735237 GGATCGGCTTAGGTCCGG 59.265 66.667 0.00 0.00 46.43 5.14
303 304 2.132352 GGATCGGCTTAGGTCCGGT 61.132 63.158 0.00 1.24 46.43 5.28
304 305 1.683418 GGATCGGCTTAGGTCCGGTT 61.683 60.000 0.00 0.00 46.43 4.44
305 306 0.177373 GATCGGCTTAGGTCCGGTTT 59.823 55.000 0.00 0.00 46.43 3.27
306 307 1.410153 GATCGGCTTAGGTCCGGTTTA 59.590 52.381 0.00 0.00 46.43 2.01
307 308 1.265236 TCGGCTTAGGTCCGGTTTAA 58.735 50.000 0.00 0.00 46.43 1.52
308 309 1.066929 TCGGCTTAGGTCCGGTTTAAC 60.067 52.381 0.00 0.00 46.43 2.01
317 318 2.957680 GGTCCGGTTTAACCCTTCAAAA 59.042 45.455 8.72 0.00 33.75 2.44
350 351 8.848474 TTTACTTCTCTAATCAGTTTCAAGGG 57.152 34.615 0.00 0.00 0.00 3.95
379 380 7.010367 CAGCTAGAGATGCTCTTAAGTCAAAAG 59.990 40.741 1.63 0.00 41.50 2.27
425 429 5.231265 TCTGTCTTATGCACGTACAGTAG 57.769 43.478 15.76 3.58 38.88 2.57
486 491 2.337583 TGTAGCGAAGTGACAGCATTC 58.662 47.619 0.00 0.00 0.00 2.67
524 529 4.527509 ACTGTAGTTCCACATCAGTCAG 57.472 45.455 0.00 0.00 32.17 3.51
612 621 1.737793 CGCTGAAAAGGGCGTAAATCT 59.262 47.619 0.00 0.00 45.34 2.40
632 641 1.923356 TGAAGAGGTTTGGCCCATTC 58.077 50.000 0.00 0.00 38.26 2.67
693 702 0.179140 GTTACGCGTAATCACCCGGA 60.179 55.000 32.03 6.19 30.12 5.14
710 719 1.648467 GGAAGCTTGACGTGCCATCC 61.648 60.000 2.10 0.00 32.46 3.51
847 856 0.389948 CTTGGCTACCCTGACGACAC 60.390 60.000 0.00 0.00 0.00 3.67
848 857 1.116536 TTGGCTACCCTGACGACACA 61.117 55.000 0.00 0.00 0.00 3.72
893 902 1.458064 GTAACTTACGCGTGTGCATGT 59.542 47.619 24.59 7.26 42.97 3.21
894 903 1.785768 AACTTACGCGTGTGCATGTA 58.214 45.000 24.59 0.00 42.97 2.29
895 904 2.004583 ACTTACGCGTGTGCATGTAT 57.995 45.000 24.59 0.00 42.97 2.29
896 905 3.153676 ACTTACGCGTGTGCATGTATA 57.846 42.857 24.59 0.00 42.97 1.47
897 906 3.713288 ACTTACGCGTGTGCATGTATAT 58.287 40.909 24.59 0.00 42.97 0.86
898 907 4.862350 ACTTACGCGTGTGCATGTATATA 58.138 39.130 24.59 0.00 42.97 0.86
951 960 3.051392 GCGTTCCCAAATCAGGCCG 62.051 63.158 0.00 0.00 0.00 6.13
953 962 1.241315 CGTTCCCAAATCAGGCCGTT 61.241 55.000 0.00 0.00 0.00 4.44
969 978 1.401931 CCGTTTCTTCTTCGTCGGCTA 60.402 52.381 0.00 0.00 0.00 3.93
971 980 2.669364 GTTTCTTCTTCGTCGGCTACA 58.331 47.619 0.00 0.00 0.00 2.74
984 997 2.352457 CTACACGAGCTAGCGCGG 60.352 66.667 37.52 28.77 43.22 6.46
985 998 2.820619 CTACACGAGCTAGCGCGGA 61.821 63.158 37.52 23.81 43.22 5.54
986 999 2.119147 CTACACGAGCTAGCGCGGAT 62.119 60.000 37.52 28.18 43.22 4.18
987 1000 2.114331 TACACGAGCTAGCGCGGATC 62.114 60.000 37.52 16.95 43.22 3.36
1080 1093 0.031314 CGGACCAGGAGATCATCGTG 59.969 60.000 0.00 2.03 42.31 4.35
1223 1240 3.566853 CGTAGCCACGCCATGCAG 61.567 66.667 0.00 0.00 42.05 4.41
1318 1339 0.317938 GCCGACCAGCTATCTACACG 60.318 60.000 0.00 0.00 0.00 4.49
1319 1340 1.022735 CCGACCAGCTATCTACACGT 58.977 55.000 0.00 0.00 0.00 4.49
1320 1341 2.216046 CCGACCAGCTATCTACACGTA 58.784 52.381 0.00 0.00 0.00 3.57
1321 1342 2.032204 CCGACCAGCTATCTACACGTAC 60.032 54.545 0.00 0.00 0.00 3.67
1362 1391 2.103373 TCGATCCTGGAACAAGAGAGG 58.897 52.381 0.00 0.00 38.70 3.69
1364 1393 2.697751 CGATCCTGGAACAAGAGAGGAT 59.302 50.000 0.00 0.00 46.11 3.24
1368 1397 6.209589 CGATCCTGGAACAAGAGAGGATTATA 59.790 42.308 0.00 0.00 43.95 0.98
1373 1402 8.145122 CCTGGAACAAGAGAGGATTATAGTAAC 58.855 40.741 0.00 0.00 38.70 2.50
1374 1403 8.603898 TGGAACAAGAGAGGATTATAGTAACA 57.396 34.615 0.00 0.00 31.92 2.41
1379 1408 9.256228 ACAAGAGAGGATTATAGTAACACTGAA 57.744 33.333 0.00 0.00 0.00 3.02
1419 1453 5.609423 TGGATGGAAGTTTGACAATTTTGG 58.391 37.500 0.00 0.00 0.00 3.28
1420 1454 4.996758 GGATGGAAGTTTGACAATTTTGGG 59.003 41.667 0.00 0.00 0.00 4.12
1421 1455 5.454613 GGATGGAAGTTTGACAATTTTGGGT 60.455 40.000 0.00 0.00 0.00 4.51
1422 1456 5.428184 TGGAAGTTTGACAATTTTGGGTT 57.572 34.783 0.00 0.00 0.00 4.11
1423 1457 5.181748 TGGAAGTTTGACAATTTTGGGTTG 58.818 37.500 0.00 0.00 0.00 3.77
1480 1514 1.302511 TGGTTCTTCTTCAGCCCGC 60.303 57.895 0.00 0.00 0.00 6.13
1626 1660 0.312416 CGCTCGTCTTCTATCAGGGG 59.688 60.000 0.00 0.00 0.00 4.79
1677 1711 1.447838 CATGCACGAGTACCGCCTT 60.448 57.895 0.00 0.00 43.32 4.35
1691 1725 4.796231 CCTTCTCCACGCCGACGG 62.796 72.222 10.29 10.29 46.04 4.79
1757 1850 4.622456 CAAACCCCACACGCGTGC 62.622 66.667 37.35 0.00 42.17 5.34
1771 1864 0.772926 GCGTGCGTCGATGAATCTAG 59.227 55.000 9.31 0.00 42.86 2.43
1772 1865 1.860399 GCGTGCGTCGATGAATCTAGT 60.860 52.381 9.31 0.00 42.86 2.57
1773 1866 2.601504 GCGTGCGTCGATGAATCTAGTA 60.602 50.000 9.31 0.00 42.86 1.82
1775 1868 4.219802 CGTGCGTCGATGAATCTAGTATT 58.780 43.478 9.31 0.00 42.86 1.89
1777 1870 6.022208 CGTGCGTCGATGAATCTAGTATTAT 58.978 40.000 9.31 0.00 42.86 1.28
1779 1872 7.851472 CGTGCGTCGATGAATCTAGTATTATAT 59.149 37.037 9.31 0.00 42.86 0.86
1782 1875 9.303941 GCGTCGATGAATCTAGTATTATATACG 57.696 37.037 9.31 0.00 0.00 3.06
1902 2002 4.856801 GCGCCGGACATGGATGGT 62.857 66.667 5.05 0.00 0.00 3.55
1955 2055 2.158813 AGGCAATTGATAGTACCACCGG 60.159 50.000 10.34 0.00 0.00 5.28
2328 2428 3.069289 CACGAGGTATATGCATGCACAT 58.931 45.455 25.37 20.84 0.00 3.21
2329 2429 3.069289 ACGAGGTATATGCATGCACATG 58.931 45.455 25.37 7.13 41.60 3.21
2343 2443 3.135414 GCACATGCACGTAATCAACAT 57.865 42.857 0.00 0.00 41.59 2.71
2358 2458 1.790043 CAACATTCGACAGTGTGCGTA 59.210 47.619 0.00 0.00 0.00 4.42
2450 2550 2.682856 TCCACACTTGCAGAACAACTTC 59.317 45.455 0.00 0.00 33.68 3.01
2471 2571 8.430801 ACTTCATTTATTCTCTATCACTGCAC 57.569 34.615 0.00 0.00 0.00 4.57
2472 2572 8.263640 ACTTCATTTATTCTCTATCACTGCACT 58.736 33.333 0.00 0.00 0.00 4.40
2527 2629 0.614979 TCCTCCACTTCTTCCCCTCG 60.615 60.000 0.00 0.00 0.00 4.63
2743 2859 1.659794 GTGGCTGCGTTGGATTTGT 59.340 52.632 0.00 0.00 0.00 2.83
2754 2870 0.762418 TGGATTTGTCTGGTGGTCGT 59.238 50.000 0.00 0.00 0.00 4.34
2761 2877 3.941188 CTGGTGGTCGTGGGTGCT 61.941 66.667 0.00 0.00 0.00 4.40
2862 2978 1.137086 CACGTCGGATCCTTGGATTCT 59.863 52.381 10.75 0.00 0.00 2.40
2878 2994 3.068873 GGATTCTGCGTCTGGAGTTCTAT 59.931 47.826 0.00 0.00 34.70 1.98
2882 2998 3.119459 TCTGCGTCTGGAGTTCTATGTTC 60.119 47.826 0.00 0.00 34.70 3.18
2944 3060 2.278854 GCTCTTTCATCTCTGCAGGTC 58.721 52.381 15.13 0.00 0.00 3.85
2956 3072 1.296715 GCAGGTCTCGGTTCATGGT 59.703 57.895 0.00 0.00 0.00 3.55
2969 3087 3.214328 GTTCATGGTTATTGCCGGATCT 58.786 45.455 5.05 0.00 0.00 2.75
3007 3126 2.089638 TGGTGGTATAGGATGGGACCAT 60.090 50.000 2.93 2.93 43.61 3.55
3102 3223 1.324740 CCGTGGTCCGTCCTATCCAA 61.325 60.000 0.00 0.00 37.07 3.53
3141 3262 4.830826 ACGAAAGTCAAAAATCCAGTCC 57.169 40.909 0.00 0.00 44.19 3.85
3189 3311 1.496060 TGTATTCTCCATGGAGGCGT 58.504 50.000 35.95 24.75 42.20 5.68
3207 3329 0.031616 GTCATCTGGGGAGGACCTCT 60.032 60.000 20.97 0.00 44.50 3.69
3261 3383 2.427320 GTGTGGCTCCAGCAGTGA 59.573 61.111 0.03 0.00 44.36 3.41
3262 3384 1.002868 GTGTGGCTCCAGCAGTGAT 60.003 57.895 0.03 0.00 44.36 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.148423 GCAATTTTCGGGATAAATTTCAGCTTT 60.148 33.333 0.00 0.00 34.01 3.51
3 4 5.006649 GGCAATTTTCGGGATAAATTTCAGC 59.993 40.000 0.00 0.00 34.01 4.26
4 5 5.231991 CGGCAATTTTCGGGATAAATTTCAG 59.768 40.000 0.00 0.00 34.01 3.02
5 6 5.105752 CGGCAATTTTCGGGATAAATTTCA 58.894 37.500 0.00 0.00 34.01 2.69
6 7 5.106442 ACGGCAATTTTCGGGATAAATTTC 58.894 37.500 0.00 0.00 34.01 2.17
7 8 5.079689 ACGGCAATTTTCGGGATAAATTT 57.920 34.783 0.00 0.00 34.01 1.82
8 9 4.440940 GGACGGCAATTTTCGGGATAAATT 60.441 41.667 0.00 0.00 36.03 1.82
9 10 3.067601 GGACGGCAATTTTCGGGATAAAT 59.932 43.478 0.00 0.00 0.00 1.40
10 11 2.424246 GGACGGCAATTTTCGGGATAAA 59.576 45.455 0.00 0.00 0.00 1.40
11 12 2.018515 GGACGGCAATTTTCGGGATAA 58.981 47.619 0.00 0.00 0.00 1.75
12 13 1.065345 TGGACGGCAATTTTCGGGATA 60.065 47.619 0.00 0.00 0.00 2.59
13 14 0.322997 TGGACGGCAATTTTCGGGAT 60.323 50.000 0.00 0.00 0.00 3.85
14 15 0.322997 ATGGACGGCAATTTTCGGGA 60.323 50.000 0.00 0.00 0.00 5.14
15 16 0.179140 CATGGACGGCAATTTTCGGG 60.179 55.000 0.00 0.00 0.00 5.14
16 17 0.179140 CCATGGACGGCAATTTTCGG 60.179 55.000 5.56 0.00 0.00 4.30
17 18 0.179140 CCCATGGACGGCAATTTTCG 60.179 55.000 15.22 0.00 0.00 3.46
18 19 1.135112 GTCCCATGGACGGCAATTTTC 60.135 52.381 15.22 0.00 43.14 2.29
19 20 0.894835 GTCCCATGGACGGCAATTTT 59.105 50.000 15.22 0.00 43.14 1.82
20 21 2.578683 GTCCCATGGACGGCAATTT 58.421 52.632 15.22 0.00 43.14 1.82
21 22 4.337013 GTCCCATGGACGGCAATT 57.663 55.556 15.22 0.00 43.14 2.32
29 30 0.400213 AAAACTCGCTGTCCCATGGA 59.600 50.000 15.22 0.00 0.00 3.41
30 31 0.523072 CAAAACTCGCTGTCCCATGG 59.477 55.000 4.14 4.14 0.00 3.66
31 32 0.523072 CCAAAACTCGCTGTCCCATG 59.477 55.000 0.00 0.00 0.00 3.66
32 33 1.244019 GCCAAAACTCGCTGTCCCAT 61.244 55.000 0.00 0.00 0.00 4.00
33 34 1.896660 GCCAAAACTCGCTGTCCCA 60.897 57.895 0.00 0.00 0.00 4.37
34 35 1.578206 GAGCCAAAACTCGCTGTCCC 61.578 60.000 0.00 0.00 34.84 4.46
35 36 0.603975 AGAGCCAAAACTCGCTGTCC 60.604 55.000 0.00 0.00 41.77 4.02
36 37 2.080286 TAGAGCCAAAACTCGCTGTC 57.920 50.000 0.00 0.00 41.77 3.51
37 38 2.350522 CATAGAGCCAAAACTCGCTGT 58.649 47.619 0.00 0.00 41.77 4.40
38 39 1.667724 CCATAGAGCCAAAACTCGCTG 59.332 52.381 0.00 0.00 41.77 5.18
39 40 1.555075 TCCATAGAGCCAAAACTCGCT 59.445 47.619 0.00 0.00 41.77 4.93
40 41 1.936547 CTCCATAGAGCCAAAACTCGC 59.063 52.381 0.00 0.00 41.77 5.03
60 61 8.915871 TTTATTGTTTTTCAGAGAGCATATGC 57.084 30.769 20.36 20.36 42.49 3.14
125 126 9.990360 TCTTGTTACACTAACATGAACATCTAA 57.010 29.630 0.00 0.00 46.89 2.10
126 127 9.639601 CTCTTGTTACACTAACATGAACATCTA 57.360 33.333 0.00 0.00 46.89 1.98
127 128 8.150945 ACTCTTGTTACACTAACATGAACATCT 58.849 33.333 0.00 0.00 46.89 2.90
128 129 8.223769 CACTCTTGTTACACTAACATGAACATC 58.776 37.037 0.00 0.00 46.89 3.06
129 130 7.307989 GCACTCTTGTTACACTAACATGAACAT 60.308 37.037 0.00 0.00 46.89 2.71
130 131 6.018262 GCACTCTTGTTACACTAACATGAACA 60.018 38.462 0.00 0.00 46.89 3.18
131 132 6.202954 AGCACTCTTGTTACACTAACATGAAC 59.797 38.462 0.00 0.00 46.89 3.18
132 133 6.288294 AGCACTCTTGTTACACTAACATGAA 58.712 36.000 0.00 0.00 46.89 2.57
133 134 5.853936 AGCACTCTTGTTACACTAACATGA 58.146 37.500 0.00 9.25 46.89 3.07
134 135 5.164051 CGAGCACTCTTGTTACACTAACATG 60.164 44.000 0.00 0.00 46.89 3.21
135 136 4.923871 CGAGCACTCTTGTTACACTAACAT 59.076 41.667 0.00 0.00 46.89 2.71
136 137 4.295870 CGAGCACTCTTGTTACACTAACA 58.704 43.478 0.00 0.00 46.13 2.41
137 138 3.121445 GCGAGCACTCTTGTTACACTAAC 59.879 47.826 0.00 0.00 39.11 2.34
138 139 3.314553 GCGAGCACTCTTGTTACACTAA 58.685 45.455 0.00 0.00 0.00 2.24
139 140 2.352421 GGCGAGCACTCTTGTTACACTA 60.352 50.000 0.00 0.00 0.00 2.74
140 141 1.605712 GGCGAGCACTCTTGTTACACT 60.606 52.381 0.00 0.00 0.00 3.55
141 142 0.790814 GGCGAGCACTCTTGTTACAC 59.209 55.000 0.00 0.00 0.00 2.90
142 143 0.391228 TGGCGAGCACTCTTGTTACA 59.609 50.000 0.00 0.00 0.00 2.41
143 144 1.508632 TTGGCGAGCACTCTTGTTAC 58.491 50.000 0.00 0.00 0.00 2.50
144 145 2.472695 ATTGGCGAGCACTCTTGTTA 57.527 45.000 0.00 0.00 0.00 2.41
145 146 1.609208 AATTGGCGAGCACTCTTGTT 58.391 45.000 0.00 0.00 0.00 2.83
146 147 1.537202 GAAATTGGCGAGCACTCTTGT 59.463 47.619 0.00 0.00 0.00 3.16
147 148 1.536766 TGAAATTGGCGAGCACTCTTG 59.463 47.619 0.00 0.00 0.00 3.02
148 149 1.896220 TGAAATTGGCGAGCACTCTT 58.104 45.000 0.00 0.00 0.00 2.85
149 150 1.741706 CATGAAATTGGCGAGCACTCT 59.258 47.619 0.00 0.00 0.00 3.24
150 151 1.796617 GCATGAAATTGGCGAGCACTC 60.797 52.381 0.00 0.00 0.00 3.51
151 152 0.171903 GCATGAAATTGGCGAGCACT 59.828 50.000 0.00 0.00 0.00 4.40
152 153 2.657336 GCATGAAATTGGCGAGCAC 58.343 52.632 0.00 0.00 0.00 4.40
164 165 4.516321 CACTGATATCCCATTTCGCATGAA 59.484 41.667 0.00 0.00 0.00 2.57
165 166 4.067192 CACTGATATCCCATTTCGCATGA 58.933 43.478 0.00 0.00 0.00 3.07
166 167 3.365666 GCACTGATATCCCATTTCGCATG 60.366 47.826 0.00 0.00 0.00 4.06
167 168 2.816087 GCACTGATATCCCATTTCGCAT 59.184 45.455 0.00 0.00 0.00 4.73
168 169 2.221169 GCACTGATATCCCATTTCGCA 58.779 47.619 0.00 0.00 0.00 5.10
169 170 1.537202 GGCACTGATATCCCATTTCGC 59.463 52.381 0.00 0.00 0.00 4.70
170 171 3.070018 GAGGCACTGATATCCCATTTCG 58.930 50.000 0.00 0.00 41.55 3.46
171 172 3.817647 GTGAGGCACTGATATCCCATTTC 59.182 47.826 0.00 0.00 41.55 2.17
172 173 3.461085 AGTGAGGCACTGATATCCCATTT 59.539 43.478 0.00 0.00 43.63 2.32
173 174 3.051581 AGTGAGGCACTGATATCCCATT 58.948 45.455 0.00 0.00 43.63 3.16
174 175 2.699160 AGTGAGGCACTGATATCCCAT 58.301 47.619 0.00 0.00 43.63 4.00
175 176 2.180946 AGTGAGGCACTGATATCCCA 57.819 50.000 0.00 0.00 43.63 4.37
184 185 2.435372 TTGTTTTCCAGTGAGGCACT 57.565 45.000 0.00 0.00 46.51 4.40
185 186 3.518634 TTTTGTTTTCCAGTGAGGCAC 57.481 42.857 0.00 0.00 37.29 5.01
186 187 4.751767 AATTTTGTTTTCCAGTGAGGCA 57.248 36.364 0.00 0.00 37.29 4.75
187 188 6.200854 CAGTTAATTTTGTTTTCCAGTGAGGC 59.799 38.462 0.00 0.00 37.29 4.70
188 189 7.264947 ACAGTTAATTTTGTTTTCCAGTGAGG 58.735 34.615 0.00 0.00 39.47 3.86
189 190 9.233232 GTACAGTTAATTTTGTTTTCCAGTGAG 57.767 33.333 0.00 0.00 0.00 3.51
190 191 8.192110 GGTACAGTTAATTTTGTTTTCCAGTGA 58.808 33.333 0.00 0.00 0.00 3.41
191 192 7.976734 TGGTACAGTTAATTTTGTTTTCCAGTG 59.023 33.333 0.00 0.00 0.00 3.66
192 193 8.068892 TGGTACAGTTAATTTTGTTTTCCAGT 57.931 30.769 0.00 0.00 0.00 4.00
209 210 4.910195 TTGATGCTCTCAAATGGTACAGT 58.090 39.130 0.00 0.00 39.77 3.55
210 211 4.334759 CCTTGATGCTCTCAAATGGTACAG 59.665 45.833 0.00 0.00 43.20 2.74
211 212 4.264253 CCTTGATGCTCTCAAATGGTACA 58.736 43.478 0.00 0.00 43.20 2.90
212 213 3.629398 CCCTTGATGCTCTCAAATGGTAC 59.371 47.826 4.28 0.00 43.20 3.34
213 214 3.266772 ACCCTTGATGCTCTCAAATGGTA 59.733 43.478 15.54 0.00 42.76 3.25
214 215 2.042162 ACCCTTGATGCTCTCAAATGGT 59.958 45.455 13.17 13.17 43.20 3.55
215 216 2.686915 GACCCTTGATGCTCTCAAATGG 59.313 50.000 12.33 12.33 43.20 3.16
216 217 2.353889 CGACCCTTGATGCTCTCAAATG 59.646 50.000 4.28 1.87 43.20 2.32
217 218 2.636830 CGACCCTTGATGCTCTCAAAT 58.363 47.619 4.28 0.00 43.20 2.32
218 219 1.339055 CCGACCCTTGATGCTCTCAAA 60.339 52.381 4.28 0.00 43.20 2.69
219 220 0.250234 CCGACCCTTGATGCTCTCAA 59.750 55.000 2.92 2.92 41.61 3.02
220 221 0.614697 TCCGACCCTTGATGCTCTCA 60.615 55.000 0.00 0.00 0.00 3.27
221 222 0.537188 TTCCGACCCTTGATGCTCTC 59.463 55.000 0.00 0.00 0.00 3.20
222 223 0.539051 CTTCCGACCCTTGATGCTCT 59.461 55.000 0.00 0.00 0.00 4.09
223 224 0.462759 CCTTCCGACCCTTGATGCTC 60.463 60.000 0.00 0.00 0.00 4.26
224 225 0.909610 TCCTTCCGACCCTTGATGCT 60.910 55.000 0.00 0.00 0.00 3.79
225 226 0.744771 GTCCTTCCGACCCTTGATGC 60.745 60.000 0.00 0.00 35.23 3.91
226 227 3.460648 GTCCTTCCGACCCTTGATG 57.539 57.895 0.00 0.00 35.23 3.07
237 238 0.746923 AATTAAGCGCCGGTCCTTCC 60.747 55.000 2.29 0.00 0.00 3.46
238 239 1.092348 AAATTAAGCGCCGGTCCTTC 58.908 50.000 2.29 0.00 0.00 3.46
239 240 1.541379 AAAATTAAGCGCCGGTCCTT 58.459 45.000 2.29 8.66 0.00 3.36
240 241 2.406596 TAAAATTAAGCGCCGGTCCT 57.593 45.000 2.29 0.00 0.00 3.85
241 242 2.421073 AGTTAAAATTAAGCGCCGGTCC 59.579 45.455 2.29 0.00 0.00 4.46
242 243 3.752412 AGTTAAAATTAAGCGCCGGTC 57.248 42.857 2.29 0.00 0.00 4.79
243 244 4.508461 AAAGTTAAAATTAAGCGCCGGT 57.492 36.364 2.29 0.00 0.00 5.28
244 245 5.633927 AGTAAAGTTAAAATTAAGCGCCGG 58.366 37.500 2.29 0.00 0.00 6.13
245 246 5.735892 GGAGTAAAGTTAAAATTAAGCGCCG 59.264 40.000 2.29 0.00 0.00 6.46
246 247 6.849502 AGGAGTAAAGTTAAAATTAAGCGCC 58.150 36.000 2.29 0.00 0.00 6.53
247 248 7.749808 AGAGGAGTAAAGTTAAAATTAAGCGC 58.250 34.615 0.00 0.00 0.00 5.92
260 261 8.935741 CCCTTATTGGTATTAGAGGAGTAAAGT 58.064 37.037 0.00 0.00 0.00 2.66
261 262 9.155785 TCCCTTATTGGTATTAGAGGAGTAAAG 57.844 37.037 0.00 0.00 0.00 1.85
262 263 9.684702 ATCCCTTATTGGTATTAGAGGAGTAAA 57.315 33.333 0.00 0.00 0.00 2.01
263 264 9.322769 GATCCCTTATTGGTATTAGAGGAGTAA 57.677 37.037 0.00 0.00 0.00 2.24
264 265 7.614583 CGATCCCTTATTGGTATTAGAGGAGTA 59.385 40.741 0.00 0.00 0.00 2.59
265 266 6.437793 CGATCCCTTATTGGTATTAGAGGAGT 59.562 42.308 0.00 0.00 0.00 3.85
266 267 6.127310 CCGATCCCTTATTGGTATTAGAGGAG 60.127 46.154 0.00 0.00 34.67 3.69
267 268 5.720041 CCGATCCCTTATTGGTATTAGAGGA 59.280 44.000 0.00 0.00 34.67 3.71
268 269 5.627040 GCCGATCCCTTATTGGTATTAGAGG 60.627 48.000 0.00 0.00 40.92 3.69
269 270 5.187967 AGCCGATCCCTTATTGGTATTAGAG 59.812 44.000 0.00 0.00 40.92 2.43
270 271 5.091552 AGCCGATCCCTTATTGGTATTAGA 58.908 41.667 0.00 0.00 40.92 2.10
271 272 5.422214 AGCCGATCCCTTATTGGTATTAG 57.578 43.478 0.00 0.00 40.92 1.73
272 273 5.836024 AAGCCGATCCCTTATTGGTATTA 57.164 39.130 0.00 0.00 40.92 0.98
273 274 4.724279 AAGCCGATCCCTTATTGGTATT 57.276 40.909 0.00 0.00 40.92 1.89
274 275 4.225267 CCTAAGCCGATCCCTTATTGGTAT 59.775 45.833 2.09 0.00 40.92 2.73
275 276 3.581332 CCTAAGCCGATCCCTTATTGGTA 59.419 47.826 2.09 0.00 40.92 3.25
276 277 2.372172 CCTAAGCCGATCCCTTATTGGT 59.628 50.000 2.09 0.00 40.92 3.67
277 278 2.372172 ACCTAAGCCGATCCCTTATTGG 59.628 50.000 2.09 3.90 41.68 3.16
278 279 3.557264 GGACCTAAGCCGATCCCTTATTG 60.557 52.174 2.09 0.93 0.00 1.90
279 280 2.638363 GGACCTAAGCCGATCCCTTATT 59.362 50.000 2.09 0.00 0.00 1.40
280 281 2.258109 GGACCTAAGCCGATCCCTTAT 58.742 52.381 2.09 0.00 0.00 1.73
281 282 1.713297 GGACCTAAGCCGATCCCTTA 58.287 55.000 0.00 0.00 0.00 2.69
282 283 2.529312 GGACCTAAGCCGATCCCTT 58.471 57.895 0.00 0.00 0.00 3.95
283 284 4.297207 GGACCTAAGCCGATCCCT 57.703 61.111 0.00 0.00 0.00 4.20
290 291 1.679944 GGGTTAAACCGGACCTAAGCC 60.680 57.143 9.46 16.73 39.83 4.35
291 292 1.280133 AGGGTTAAACCGGACCTAAGC 59.720 52.381 9.46 11.63 39.83 3.09
292 293 3.008266 TGAAGGGTTAAACCGGACCTAAG 59.992 47.826 9.46 0.00 39.83 2.18
293 294 2.978278 TGAAGGGTTAAACCGGACCTAA 59.022 45.455 9.46 0.00 39.83 2.69
294 295 2.618794 TGAAGGGTTAAACCGGACCTA 58.381 47.619 9.46 0.00 39.83 3.08
295 296 1.437397 TGAAGGGTTAAACCGGACCT 58.563 50.000 9.46 2.34 39.83 3.85
296 297 2.275134 TTGAAGGGTTAAACCGGACC 57.725 50.000 9.46 4.59 39.83 4.46
297 298 3.633525 ACTTTTGAAGGGTTAAACCGGAC 59.366 43.478 9.46 0.00 39.83 4.79
298 299 3.633065 CACTTTTGAAGGGTTAAACCGGA 59.367 43.478 9.46 0.00 39.83 5.14
299 300 3.633065 TCACTTTTGAAGGGTTAAACCGG 59.367 43.478 3.26 0.00 39.83 5.28
300 301 4.904253 TCACTTTTGAAGGGTTAAACCG 57.096 40.909 3.26 0.00 39.83 4.44
301 302 6.216801 AGTTCACTTTTGAAGGGTTAAACC 57.783 37.500 0.00 0.00 42.60 3.27
338 339 4.096681 TCTAGCTGATCCCTTGAAACTGA 58.903 43.478 0.00 0.00 0.00 3.41
399 403 5.756347 ACTGTACGTGCATAAGACAGAAAAA 59.244 36.000 20.92 0.00 39.94 1.94
400 404 5.294356 ACTGTACGTGCATAAGACAGAAAA 58.706 37.500 20.92 0.00 39.94 2.29
425 429 2.342910 TCTTCGTCAGCTTTCGTACC 57.657 50.000 7.10 0.00 0.00 3.34
458 463 0.859232 CACTTCGCTACAGCAAACGT 59.141 50.000 1.61 0.00 42.21 3.99
459 464 1.136611 GTCACTTCGCTACAGCAAACG 60.137 52.381 1.61 0.00 42.21 3.60
460 465 1.864711 TGTCACTTCGCTACAGCAAAC 59.135 47.619 1.61 0.00 42.21 2.93
461 466 2.135139 CTGTCACTTCGCTACAGCAAA 58.865 47.619 1.61 0.00 42.21 3.68
482 487 7.875971 ACAGTTTTACTCAGGCTTAAAGAATG 58.124 34.615 0.00 0.00 0.00 2.67
486 491 7.964604 ACTACAGTTTTACTCAGGCTTAAAG 57.035 36.000 0.00 0.00 0.00 1.85
544 549 2.006169 TGTGTTTATGCGTGCATCGAT 58.994 42.857 11.16 0.00 42.86 3.59
545 550 1.433534 TGTGTTTATGCGTGCATCGA 58.566 45.000 11.16 0.00 42.86 3.59
546 551 2.239751 TTGTGTTTATGCGTGCATCG 57.760 45.000 11.16 0.00 43.12 3.84
547 552 4.858692 AGATTTTGTGTTTATGCGTGCATC 59.141 37.500 11.16 0.00 37.82 3.91
612 621 2.247358 GAATGGGCCAAACCTCTTCAA 58.753 47.619 11.89 0.00 39.10 2.69
632 641 1.066858 AGCCGCATATTGATACTCCCG 60.067 52.381 0.00 0.00 0.00 5.14
641 650 3.539253 GCTTGACAGCCGCATATTG 57.461 52.632 0.00 0.00 40.61 1.90
688 697 3.423154 GCACGTCAAGCTTCCGGG 61.423 66.667 16.79 14.47 0.00 5.73
693 702 2.034879 CGGATGGCACGTCAAGCTT 61.035 57.895 0.00 0.00 0.00 3.74
710 719 0.030908 GATTAGCCTCCCTGACGTCG 59.969 60.000 11.62 5.76 0.00 5.12
817 826 2.360165 GGGTAGCCAAGCAATGAGATTG 59.640 50.000 5.96 0.00 43.13 2.67
847 856 2.523015 CTAAGTAACCGTACGTGCCTG 58.477 52.381 15.21 0.29 35.20 4.85
848 857 1.135286 GCTAAGTAACCGTACGTGCCT 60.135 52.381 15.21 1.39 35.20 4.75
951 960 2.407696 GTGTAGCCGACGAAGAAGAAAC 59.592 50.000 0.00 0.00 0.00 2.78
953 962 1.400629 CGTGTAGCCGACGAAGAAGAA 60.401 52.381 0.00 0.00 39.21 2.52
969 978 3.471244 GATCCGCGCTAGCTCGTGT 62.471 63.158 24.06 12.97 42.32 4.49
971 980 4.315122 CGATCCGCGCTAGCTCGT 62.315 66.667 24.06 8.12 42.32 4.18
1080 1093 1.903183 ACCTTCCTCTTGAGGTAGCAC 59.097 52.381 15.44 0.00 32.13 4.40
1223 1240 4.880886 AGAAACAAAACTTTGCATTGGC 57.119 36.364 2.07 0.00 41.79 4.52
1330 1351 6.437162 TGTTCCAGGATCGATGATGATACATA 59.563 38.462 0.54 0.00 31.13 2.29
1337 1358 4.056740 CTCTTGTTCCAGGATCGATGATG 58.943 47.826 0.54 0.45 0.00 3.07
1338 1359 3.963374 TCTCTTGTTCCAGGATCGATGAT 59.037 43.478 0.54 0.00 0.00 2.45
1339 1360 3.365472 TCTCTTGTTCCAGGATCGATGA 58.635 45.455 0.54 0.00 0.00 2.92
1340 1361 3.492309 CCTCTCTTGTTCCAGGATCGATG 60.492 52.174 0.54 0.00 0.00 3.84
1341 1362 2.697751 CCTCTCTTGTTCCAGGATCGAT 59.302 50.000 0.00 0.00 0.00 3.59
1342 1363 2.103373 CCTCTCTTGTTCCAGGATCGA 58.897 52.381 0.00 0.00 0.00 3.59
1343 1364 2.103373 TCCTCTCTTGTTCCAGGATCG 58.897 52.381 0.00 0.00 29.57 3.69
1344 1365 4.769345 AATCCTCTCTTGTTCCAGGATC 57.231 45.455 0.00 0.00 43.74 3.36
1345 1366 7.079048 ACTATAATCCTCTCTTGTTCCAGGAT 58.921 38.462 0.00 0.00 46.02 3.24
1347 1368 6.739331 ACTATAATCCTCTCTTGTTCCAGG 57.261 41.667 0.00 0.00 0.00 4.45
1349 1370 8.475639 GTGTTACTATAATCCTCTCTTGTTCCA 58.524 37.037 0.00 0.00 0.00 3.53
1373 1402 9.498176 TCCATTCATCAGTATATTCATTCAGTG 57.502 33.333 0.00 0.00 0.00 3.66
1379 1408 9.682465 CTTCCATCCATTCATCAGTATATTCAT 57.318 33.333 0.00 0.00 0.00 2.57
1393 1422 7.095102 CCAAAATTGTCAAACTTCCATCCATTC 60.095 37.037 0.00 0.00 0.00 2.67
1419 1453 3.364441 TCTGCATGCACGCCAACC 61.364 61.111 18.46 0.00 0.00 3.77
1420 1454 2.126734 GTCTGCATGCACGCCAAC 60.127 61.111 18.46 6.48 0.00 3.77
1421 1455 2.132517 CTTGTCTGCATGCACGCCAA 62.133 55.000 18.46 17.27 0.00 4.52
1422 1456 2.594013 TTGTCTGCATGCACGCCA 60.594 55.556 18.46 10.64 0.00 5.69
1423 1457 2.177531 CTTGTCTGCATGCACGCC 59.822 61.111 18.46 7.91 0.00 5.68
1452 1486 0.905337 AGAAGAACCACTCCCCCTCG 60.905 60.000 0.00 0.00 0.00 4.63
1480 1514 4.462280 GGGGTACTTGCGGTCCCG 62.462 72.222 0.24 0.24 43.09 5.14
1527 1561 2.070650 GGCCTTCCAGTACCCCGAT 61.071 63.158 0.00 0.00 0.00 4.18
1771 1864 8.495949 ACCTGTGTGTACGTACGTATATAATAC 58.504 37.037 29.05 21.46 32.82 1.89
1772 1865 8.601845 ACCTGTGTGTACGTACGTATATAATA 57.398 34.615 29.05 16.15 32.82 0.98
1773 1866 7.496529 ACCTGTGTGTACGTACGTATATAAT 57.503 36.000 29.05 10.03 32.82 1.28
1775 1868 6.315144 ACAACCTGTGTGTACGTACGTATATA 59.685 38.462 29.05 22.06 39.72 0.86
1777 1870 4.454161 ACAACCTGTGTGTACGTACGTATA 59.546 41.667 29.05 24.16 39.72 1.47
1779 1872 2.616376 ACAACCTGTGTGTACGTACGTA 59.384 45.455 23.60 23.60 39.72 3.57
1781 1874 2.046313 GACAACCTGTGTGTACGTACG 58.954 52.381 20.18 15.01 41.96 3.67
1782 1875 2.046313 CGACAACCTGTGTGTACGTAC 58.954 52.381 18.90 18.90 41.96 3.67
1784 1877 0.249155 CCGACAACCTGTGTGTACGT 60.249 55.000 0.00 0.00 41.96 3.57
1785 1878 0.249155 ACCGACAACCTGTGTGTACG 60.249 55.000 0.00 0.00 41.96 3.67
1786 1879 1.202440 TGACCGACAACCTGTGTGTAC 60.202 52.381 0.00 0.00 41.96 2.90
1787 1880 1.112950 TGACCGACAACCTGTGTGTA 58.887 50.000 0.00 0.00 41.96 2.90
1788 1881 0.250793 TTGACCGACAACCTGTGTGT 59.749 50.000 0.00 0.00 41.96 3.72
1789 1882 3.073086 TTGACCGACAACCTGTGTG 57.927 52.632 0.00 0.00 41.96 3.82
1793 1886 7.308348 AATGTAATTAAGTTGACCGACAACCTG 60.308 37.037 17.19 0.00 46.71 4.00
1794 1887 6.713450 AATGTAATTAAGTTGACCGACAACCT 59.287 34.615 17.19 10.31 46.71 3.50
1819 1912 1.065491 CAGCTGCACCCAACATAGGTA 60.065 52.381 0.00 0.00 35.24 3.08
1820 1913 0.322816 CAGCTGCACCCAACATAGGT 60.323 55.000 0.00 0.00 38.48 3.08
1821 1914 1.033746 CCAGCTGCACCCAACATAGG 61.034 60.000 8.66 0.00 0.00 2.57
1920 2020 3.050275 GCCTGAACCTCCGTGTGC 61.050 66.667 0.00 0.00 0.00 4.57
1924 2024 0.400213 TCAATTGCCTGAACCTCCGT 59.600 50.000 0.00 0.00 0.00 4.69
2328 2428 3.060602 TGTCGAATGTTGATTACGTGCA 58.939 40.909 0.00 0.00 0.00 4.57
2329 2429 3.122948 ACTGTCGAATGTTGATTACGTGC 59.877 43.478 0.00 0.00 0.00 5.34
2330 2430 4.149922 ACACTGTCGAATGTTGATTACGTG 59.850 41.667 0.00 0.00 0.00 4.49
2331 2431 4.149922 CACACTGTCGAATGTTGATTACGT 59.850 41.667 0.00 0.00 0.00 3.57
2339 2439 1.790623 GTACGCACACTGTCGAATGTT 59.209 47.619 7.68 0.00 0.00 2.71
2343 2443 3.352554 TTAAGTACGCACACTGTCGAA 57.647 42.857 7.68 0.00 0.00 3.71
2358 2458 3.814005 ATCGTGGCTACCGAATTAAGT 57.186 42.857 0.00 0.00 37.93 2.24
2450 2550 7.642978 GCAAAGTGCAGTGATAGAGAATAAATG 59.357 37.037 0.00 0.00 44.26 2.32
2471 2571 1.541588 GGCTAGGGTTTCACAGCAAAG 59.458 52.381 0.00 0.00 35.69 2.77
2472 2572 1.616159 GGCTAGGGTTTCACAGCAAA 58.384 50.000 0.00 0.00 35.69 3.68
2514 2615 2.647158 GGCGACGAGGGGAAGAAGT 61.647 63.158 0.00 0.00 0.00 3.01
2578 2683 3.003763 GGTGAGGAGAAGCCCCGT 61.004 66.667 0.00 0.00 37.37 5.28
2743 2859 3.936203 GCACCCACGACCACCAGA 61.936 66.667 0.00 0.00 0.00 3.86
2754 2870 2.934932 TGGATCTGGCAGCACCCA 60.935 61.111 20.82 18.07 37.83 4.51
2761 2877 1.976404 GGATCTGATCTGGATCTGGCA 59.024 52.381 16.61 0.00 39.41 4.92
2792 2908 0.094730 GCCGACGGATTTCAAAGACG 59.905 55.000 20.50 0.00 0.00 4.18
2853 2969 1.066573 ACTCCAGACGCAGAATCCAAG 60.067 52.381 0.00 0.00 0.00 3.61
2862 2978 2.415491 CGAACATAGAACTCCAGACGCA 60.415 50.000 0.00 0.00 0.00 5.24
2878 2994 0.316204 GGACCGAGAAGAACCGAACA 59.684 55.000 0.00 0.00 0.00 3.18
2882 2998 0.966370 AGGAGGACCGAGAAGAACCG 60.966 60.000 0.00 0.00 41.83 4.44
2944 3060 1.330521 CGGCAATAACCATGAACCGAG 59.669 52.381 0.00 0.00 41.61 4.63
2956 3072 2.437651 TGTGATCCAGATCCGGCAATAA 59.562 45.455 0.00 0.00 37.02 1.40
2969 3087 0.036164 CCAAACCTCCGTGTGATCCA 59.964 55.000 0.00 0.00 27.12 3.41
3007 3126 3.637769 ACAAGCCAACCAAAGTTTCCTA 58.362 40.909 0.00 0.00 32.45 2.94
3086 3207 0.979187 GGGTTGGATAGGACGGACCA 60.979 60.000 0.00 0.00 42.04 4.02
3168 3290 2.158900 ACGCCTCCATGGAGAATACAAG 60.159 50.000 38.37 22.32 44.53 3.16
3189 3311 0.719015 AAGAGGTCCTCCCCAGATGA 59.281 55.000 15.72 0.00 0.00 2.92
3207 3329 1.056660 GGCATCTCTCCCCCGAATAA 58.943 55.000 0.00 0.00 0.00 1.40
3261 3383 1.304381 GCCACCACCACACCATCAT 60.304 57.895 0.00 0.00 0.00 2.45
3262 3384 1.130678 TAGCCACCACCACACCATCA 61.131 55.000 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.