Multiple sequence alignment - TraesCS7D01G084700

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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 TraesCS7D01G084700 chr7D 100.000 4572 0 0 1 4572 51778469 51783040 0.000000e+00 8444.0
1 TraesCS7D01G084700 chr7D 75.391 1215 230 52 1786 2952 499886383 499887576 1.460000e-144 523.0
2 TraesCS7D01G084700 chr7D 92.248 129 10 0 1 129 206437496 206437624 2.810000e-42 183.0
3 TraesCS7D01G084700 chr4A 91.298 3252 158 60 763 3928 666148698 666151910 0.000000e+00 4322.0
4 TraesCS7D01G084700 chr4A 90.625 288 11 5 298 582 666148383 666148657 7.230000e-98 368.0
5 TraesCS7D01G084700 chr4A 88.302 265 23 5 3932 4192 666151946 666152206 1.240000e-80 311.0
6 TraesCS7D01G084700 chr4A 93.902 82 4 1 228 308 666145411 666145492 6.210000e-24 122.0
7 TraesCS7D01G084700 chr4A 100.000 33 0 0 578 610 666148666 666148698 1.370000e-05 62.1
8 TraesCS7D01G084700 chr7A 92.191 1908 84 27 776 2632 54720911 54722804 0.000000e+00 2638.0
9 TraesCS7D01G084700 chr7A 94.188 998 48 4 2650 3646 54722980 54723968 0.000000e+00 1513.0
10 TraesCS7D01G084700 chr7A 82.443 655 83 11 3934 4571 54724661 54725300 1.120000e-150 544.0
11 TraesCS7D01G084700 chr7A 77.388 712 119 28 1754 2430 565799059 565799763 7.180000e-103 385.0
12 TraesCS7D01G084700 chr7A 85.861 389 20 19 298 674 54719784 54720149 9.280000e-102 381.0
13 TraesCS7D01G084700 chr7A 91.213 239 18 2 3641 3878 54724261 54724497 5.710000e-84 322.0
14 TraesCS7D01G084700 chr7A 72.906 764 160 32 2680 3414 565800023 565800768 2.140000e-53 220.0
15 TraesCS7D01G084700 chr7A 91.667 132 11 0 1 132 115807647 115807516 2.810000e-42 183.0
16 TraesCS7D01G084700 chr7B 89.143 175 17 2 2257 2430 527858602 527858775 2.770000e-52 217.0
17 TraesCS7D01G084700 chr6D 93.600 125 8 0 1 125 367533997 367534121 2.170000e-43 187.0
18 TraesCS7D01G084700 chr4B 92.969 128 9 0 1 128 68663534 68663661 2.170000e-43 187.0
19 TraesCS7D01G084700 chr3B 92.969 128 9 0 1 128 621150080 621150207 2.170000e-43 187.0
20 TraesCS7D01G084700 chr2A 92.969 128 9 0 1 128 31878280 31878407 2.170000e-43 187.0
21 TraesCS7D01G084700 chr1B 92.969 128 9 0 1 128 118398988 118398861 2.170000e-43 187.0
22 TraesCS7D01G084700 chr2D 92.913 127 9 0 1 127 475088378 475088504 7.810000e-43 185.0
23 TraesCS7D01G084700 chrUn 84.211 190 26 3 2257 2444 35855766 35855579 1.010000e-41 182.0
24 TraesCS7D01G084700 chrUn 84.211 190 26 3 2257 2444 299959675 299959862 1.010000e-41 182.0
25 TraesCS7D01G084700 chrUn 71.810 525 113 20 2672 3178 35855337 35854830 2.890000e-22 117.0
26 TraesCS7D01G084700 chrUn 71.810 525 113 20 2672 3178 299960104 299960611 2.890000e-22 117.0
27 TraesCS7D01G084700 chr5D 90.580 138 12 1 1 137 321901954 321902091 1.010000e-41 182.0
28 TraesCS7D01G084700 chr3A 85.714 161 23 0 2277 2437 9854546 9854706 2.190000e-38 171.0
29 TraesCS7D01G084700 chr3D 73.092 524 109 18 2672 3178 4292759 4293267 1.700000e-34 158.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G084700 chr7D 51778469 51783040 4571 False 8444.00 8444 100.0000 1 4572 1 chr7D.!!$F1 4571
1 TraesCS7D01G084700 chr7D 499886383 499887576 1193 False 523.00 523 75.3910 1786 2952 1 chr7D.!!$F3 1166
2 TraesCS7D01G084700 chr4A 666145411 666152206 6795 False 1037.02 4322 92.8254 228 4192 5 chr4A.!!$F1 3964
3 TraesCS7D01G084700 chr7A 54719784 54725300 5516 False 1079.60 2638 89.1792 298 4571 5 chr7A.!!$F1 4273
4 TraesCS7D01G084700 chr7A 565799059 565800768 1709 False 302.50 385 75.1470 1754 3414 2 chr7A.!!$F2 1660

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
163 164 0.108329 AAATGCTAGTGACCCGGACG 60.108 55.0 0.73 0.0 0.00 4.79 F
211 212 0.171007 CATCGCAAATGTGGTGGACC 59.829 55.0 0.00 0.0 33.27 4.46 F
1415 5053 0.103390 TCGAGAAGCAACACCGAACA 59.897 50.0 0.00 0.0 0.00 3.18 F
1419 5057 0.240945 GAAGCAACACCGAACATGGG 59.759 55.0 0.00 0.0 0.00 4.00 F
2707 6617 0.406361 GGGGGACATGGTGGTAAACA 59.594 55.0 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 5038 0.240945 CCCATGTTCGGTGTTGCTTC 59.759 55.0 0.00 0.00 0.00 3.86 R
1477 5118 0.250513 CTCCCTGTTACCTGCAGACC 59.749 60.0 17.39 0.00 36.12 3.85 R
2707 6617 0.848735 AGCATGGCCACCATCATAGT 59.151 50.0 8.16 0.00 43.15 2.12 R
2738 6648 1.168714 GATGGTCTGTGCTTGTTCCC 58.831 55.0 0.00 0.00 0.00 3.97 R
4479 8854 0.041663 ACGGATGTTGTTTCAACGCG 60.042 50.0 3.53 3.53 0.00 6.01 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 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
26 27 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
27 28 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
28 29 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
29 30 6.152154 TGGACTACCACATACGGATGTATATG 59.848 42.308 14.23 7.16 44.82 1.78
38 39 9.599866 CACATACGGATGTATATGGACATATTT 57.400 33.333 14.23 0.00 44.82 1.40
54 55 9.817809 TGGACATATTTTAGAGTGTAGATTCAC 57.182 33.333 0.00 0.00 38.46 3.18
66 67 7.440523 AGTGTAGATTCACTCATTTTGGTTC 57.559 36.000 0.00 0.00 44.07 3.62
67 68 6.147821 AGTGTAGATTCACTCATTTTGGTTCG 59.852 38.462 0.00 0.00 44.07 3.95
68 69 5.995282 TGTAGATTCACTCATTTTGGTTCGT 59.005 36.000 0.00 0.00 0.00 3.85
69 70 7.117236 GTGTAGATTCACTCATTTTGGTTCGTA 59.883 37.037 0.00 0.00 35.68 3.43
70 71 7.822334 TGTAGATTCACTCATTTTGGTTCGTAT 59.178 33.333 0.00 0.00 0.00 3.06
71 72 7.308782 AGATTCACTCATTTTGGTTCGTATC 57.691 36.000 0.00 0.00 0.00 2.24
72 73 7.106239 AGATTCACTCATTTTGGTTCGTATCT 58.894 34.615 0.00 0.00 0.00 1.98
73 74 8.258007 AGATTCACTCATTTTGGTTCGTATCTA 58.742 33.333 0.00 0.00 0.00 1.98
74 75 7.827819 TTCACTCATTTTGGTTCGTATCTAG 57.172 36.000 0.00 0.00 0.00 2.43
75 76 6.931838 TCACTCATTTTGGTTCGTATCTAGT 58.068 36.000 0.00 0.00 0.00 2.57
76 77 8.058667 TCACTCATTTTGGTTCGTATCTAGTA 57.941 34.615 0.00 0.00 0.00 1.82
77 78 8.525316 TCACTCATTTTGGTTCGTATCTAGTAA 58.475 33.333 0.00 0.00 0.00 2.24
78 79 8.592998 CACTCATTTTGGTTCGTATCTAGTAAC 58.407 37.037 0.00 0.00 0.00 2.50
79 80 8.529476 ACTCATTTTGGTTCGTATCTAGTAACT 58.471 33.333 0.00 0.00 0.00 2.24
80 81 9.367444 CTCATTTTGGTTCGTATCTAGTAACTT 57.633 33.333 0.00 0.00 0.00 2.66
81 82 9.146984 TCATTTTGGTTCGTATCTAGTAACTTG 57.853 33.333 0.00 0.00 0.00 3.16
82 83 8.932791 CATTTTGGTTCGTATCTAGTAACTTGT 58.067 33.333 0.00 0.00 0.00 3.16
83 84 8.891671 TTTTGGTTCGTATCTAGTAACTTGTT 57.108 30.769 0.00 0.00 0.00 2.83
84 85 7.878477 TTGGTTCGTATCTAGTAACTTGTTG 57.122 36.000 0.00 0.00 0.00 3.33
85 86 7.218228 TGGTTCGTATCTAGTAACTTGTTGA 57.782 36.000 0.00 0.00 0.00 3.18
86 87 7.660112 TGGTTCGTATCTAGTAACTTGTTGAA 58.340 34.615 0.00 0.00 0.00 2.69
87 88 8.143193 TGGTTCGTATCTAGTAACTTGTTGAAA 58.857 33.333 0.00 0.00 0.00 2.69
88 89 9.148104 GGTTCGTATCTAGTAACTTGTTGAAAT 57.852 33.333 0.00 0.00 0.00 2.17
116 117 9.685828 TGAAGAAAAACAAATATTTAGGAACGG 57.314 29.630 0.00 0.00 0.00 4.44
117 118 9.135843 GAAGAAAAACAAATATTTAGGAACGGG 57.864 33.333 0.00 0.00 0.00 5.28
118 119 7.608153 AGAAAAACAAATATTTAGGAACGGGG 58.392 34.615 0.00 0.00 0.00 5.73
119 120 5.925506 AAACAAATATTTAGGAACGGGGG 57.074 39.130 0.00 0.00 0.00 5.40
136 137 2.644676 GGGGGAGTAGATCTTTGTTGC 58.355 52.381 0.00 0.00 0.00 4.17
137 138 2.644676 GGGGAGTAGATCTTTGTTGCC 58.355 52.381 0.00 0.00 0.00 4.52
138 139 2.644676 GGGAGTAGATCTTTGTTGCCC 58.355 52.381 0.00 0.26 0.00 5.36
139 140 2.280628 GGAGTAGATCTTTGTTGCCCG 58.719 52.381 0.00 0.00 0.00 6.13
140 141 2.354805 GGAGTAGATCTTTGTTGCCCGT 60.355 50.000 0.00 0.00 0.00 5.28
141 142 2.930682 GAGTAGATCTTTGTTGCCCGTC 59.069 50.000 0.00 0.00 0.00 4.79
142 143 2.301870 AGTAGATCTTTGTTGCCCGTCA 59.698 45.455 0.00 0.00 0.00 4.35
143 144 2.270352 AGATCTTTGTTGCCCGTCAA 57.730 45.000 0.00 0.00 0.00 3.18
144 145 2.582052 AGATCTTTGTTGCCCGTCAAA 58.418 42.857 0.00 0.00 36.26 2.69
145 146 2.955660 AGATCTTTGTTGCCCGTCAAAA 59.044 40.909 0.00 0.00 36.26 2.44
146 147 3.383185 AGATCTTTGTTGCCCGTCAAAAA 59.617 39.130 0.00 0.00 36.26 1.94
147 148 3.810310 TCTTTGTTGCCCGTCAAAAAT 57.190 38.095 0.00 0.00 36.26 1.82
148 149 3.452474 TCTTTGTTGCCCGTCAAAAATG 58.548 40.909 0.00 0.00 36.26 2.32
149 150 1.576356 TTGTTGCCCGTCAAAAATGC 58.424 45.000 0.00 0.00 36.26 3.56
150 151 0.749649 TGTTGCCCGTCAAAAATGCT 59.250 45.000 0.00 0.00 36.26 3.79
151 152 1.957177 TGTTGCCCGTCAAAAATGCTA 59.043 42.857 0.00 0.00 36.26 3.49
152 153 2.030363 TGTTGCCCGTCAAAAATGCTAG 60.030 45.455 0.00 0.00 36.26 3.42
153 154 1.904287 TGCCCGTCAAAAATGCTAGT 58.096 45.000 0.00 0.00 0.00 2.57
154 155 1.539388 TGCCCGTCAAAAATGCTAGTG 59.461 47.619 0.00 0.00 0.00 2.74
155 156 1.810151 GCCCGTCAAAAATGCTAGTGA 59.190 47.619 0.00 0.00 0.00 3.41
156 157 2.414161 GCCCGTCAAAAATGCTAGTGAC 60.414 50.000 0.00 0.00 37.59 3.67
157 158 2.161609 CCCGTCAAAAATGCTAGTGACC 59.838 50.000 3.98 0.00 37.66 4.02
158 159 2.161609 CCGTCAAAAATGCTAGTGACCC 59.838 50.000 3.98 0.00 37.66 4.46
159 160 2.159707 CGTCAAAAATGCTAGTGACCCG 60.160 50.000 3.98 0.00 37.66 5.28
160 161 2.161609 GTCAAAAATGCTAGTGACCCGG 59.838 50.000 0.00 0.00 35.42 5.73
161 162 2.039216 TCAAAAATGCTAGTGACCCGGA 59.961 45.455 0.73 0.00 0.00 5.14
162 163 2.109425 AAAATGCTAGTGACCCGGAC 57.891 50.000 0.73 0.00 0.00 4.79
163 164 0.108329 AAATGCTAGTGACCCGGACG 60.108 55.000 0.73 0.00 0.00 4.79
164 165 2.573609 AATGCTAGTGACCCGGACGC 62.574 60.000 0.73 3.16 0.00 5.19
165 166 4.509737 GCTAGTGACCCGGACGCC 62.510 72.222 0.73 0.00 0.00 5.68
181 182 4.383861 CCGCCAGAGCTGTGCAGA 62.384 66.667 5.08 0.00 36.60 4.26
182 183 3.117171 CGCCAGAGCTGTGCAGAC 61.117 66.667 5.08 0.00 36.60 3.51
183 184 3.117171 GCCAGAGCTGTGCAGACG 61.117 66.667 5.08 0.00 35.50 4.18
184 185 3.117171 CCAGAGCTGTGCAGACGC 61.117 66.667 5.08 0.00 39.24 5.19
185 186 3.476646 CAGAGCTGTGCAGACGCG 61.477 66.667 3.53 3.53 42.97 6.01
202 203 4.573950 GCCGCCCCATCGCAAATG 62.574 66.667 0.00 0.00 0.00 2.32
203 204 3.140141 CCGCCCCATCGCAAATGT 61.140 61.111 0.00 0.00 0.00 2.71
204 205 2.102749 CGCCCCATCGCAAATGTG 59.897 61.111 0.00 0.00 0.00 3.21
205 206 2.495866 GCCCCATCGCAAATGTGG 59.504 61.111 0.00 0.00 0.00 4.17
206 207 2.350458 GCCCCATCGCAAATGTGGT 61.350 57.895 0.66 0.00 0.00 4.16
207 208 1.512230 CCCCATCGCAAATGTGGTG 59.488 57.895 0.21 0.21 36.47 4.17
210 211 3.700577 CATCGCAAATGTGGTGGAC 57.299 52.632 0.00 0.00 33.27 4.02
211 212 0.171007 CATCGCAAATGTGGTGGACC 59.829 55.000 0.00 0.00 33.27 4.46
212 213 0.965363 ATCGCAAATGTGGTGGACCC 60.965 55.000 0.00 0.00 34.29 4.46
213 214 2.635443 CGCAAATGTGGTGGACCCC 61.635 63.158 0.00 0.00 34.29 4.95
214 215 2.635443 GCAAATGTGGTGGACCCCG 61.635 63.158 0.00 0.00 34.29 5.73
215 216 1.074072 CAAATGTGGTGGACCCCGA 59.926 57.895 0.00 0.00 34.29 5.14
216 217 0.960364 CAAATGTGGTGGACCCCGAG 60.960 60.000 0.00 0.00 34.29 4.63
217 218 1.423794 AAATGTGGTGGACCCCGAGT 61.424 55.000 0.00 0.00 34.29 4.18
218 219 0.545787 AATGTGGTGGACCCCGAGTA 60.546 55.000 0.00 0.00 34.29 2.59
219 220 0.545787 ATGTGGTGGACCCCGAGTAA 60.546 55.000 0.00 0.00 34.29 2.24
220 221 1.294459 GTGGTGGACCCCGAGTAAC 59.706 63.158 0.00 0.00 34.29 2.50
221 222 2.277591 TGGTGGACCCCGAGTAACG 61.278 63.158 0.00 0.00 42.18 3.18
222 223 2.278330 GGTGGACCCCGAGTAACGT 61.278 63.158 0.00 0.00 40.78 3.99
223 224 1.213799 GTGGACCCCGAGTAACGTC 59.786 63.158 0.00 0.00 40.78 4.34
224 225 2.334946 TGGACCCCGAGTAACGTCG 61.335 63.158 0.00 0.00 40.78 5.12
225 226 2.202531 GACCCCGAGTAACGTCGC 60.203 66.667 0.00 0.00 38.69 5.19
226 227 3.690108 GACCCCGAGTAACGTCGCC 62.690 68.421 0.00 0.00 38.69 5.54
227 228 3.751246 CCCCGAGTAACGTCGCCA 61.751 66.667 0.00 0.00 38.69 5.69
228 229 2.505557 CCCGAGTAACGTCGCCAC 60.506 66.667 0.00 0.00 38.69 5.01
229 230 2.505557 CCGAGTAACGTCGCCACC 60.506 66.667 0.00 0.00 38.69 4.61
230 231 2.872925 CGAGTAACGTCGCCACCG 60.873 66.667 0.00 0.00 37.22 4.94
231 232 2.562912 GAGTAACGTCGCCACCGA 59.437 61.111 0.00 0.00 42.01 4.69
234 235 4.424566 TAACGTCGCCACCGAGCC 62.425 66.667 0.00 0.00 45.38 4.70
300 301 3.695606 TCCACCCGCAGAGTGCTC 61.696 66.667 0.00 0.00 42.25 4.26
343 3245 3.195698 GGCACGCCAACTCCGATC 61.196 66.667 2.36 0.00 35.81 3.69
344 3246 3.195698 GCACGCCAACTCCGATCC 61.196 66.667 0.00 0.00 0.00 3.36
442 3345 1.875813 CTCAGGCGATCGTGAGCAC 60.876 63.158 19.07 1.67 44.84 4.40
537 3443 3.248446 TACGGCAGCCACCAAGACC 62.248 63.158 13.30 0.00 0.00 3.85
538 3444 4.641645 CGGCAGCCACCAAGACCA 62.642 66.667 13.30 0.00 0.00 4.02
539 3445 2.203480 GGCAGCCACCAAGACCAA 60.203 61.111 6.55 0.00 0.00 3.67
540 3446 2.564721 GGCAGCCACCAAGACCAAC 61.565 63.158 6.55 0.00 0.00 3.77
541 3447 1.827789 GCAGCCACCAAGACCAACA 60.828 57.895 0.00 0.00 0.00 3.33
542 3448 1.799258 GCAGCCACCAAGACCAACAG 61.799 60.000 0.00 0.00 0.00 3.16
543 3449 1.151450 AGCCACCAAGACCAACAGG 59.849 57.895 0.00 0.00 0.00 4.00
677 3858 4.974888 GGAGGACTAACGCGTATAAAAGAG 59.025 45.833 14.46 4.05 0.00 2.85
736 4293 8.655935 AATCCAGACCTGTCTAAAATTTTCAT 57.344 30.769 6.72 0.00 37.98 2.57
790 4370 8.696374 TGAAGAGTAGTTATCTATTTCTGGTGG 58.304 37.037 1.00 0.00 0.00 4.61
932 4515 6.128445 GGACATCCATCAATGCGAAACTATAG 60.128 42.308 0.00 0.00 35.64 1.31
980 4576 2.571653 CTCCATCCGCCCTATAAATCCA 59.428 50.000 0.00 0.00 0.00 3.41
1064 4660 1.135402 GCAAGTGGGCTTAAACATCGG 60.135 52.381 0.00 0.00 32.87 4.18
1087 4691 2.692557 ACATAATCTCACGAGCTCAGCT 59.307 45.455 15.40 0.00 43.88 4.24
1145 4749 1.744368 CTGCTCAGGTCGCAGCATT 60.744 57.895 0.00 0.00 46.98 3.56
1233 4849 4.693566 TCGATACACCCATTTCTGTTTCAC 59.306 41.667 0.00 0.00 0.00 3.18
1246 4864 2.022934 TGTTTCACAGTCTGCATGCAA 58.977 42.857 22.88 10.06 0.00 4.08
1249 4867 7.498256 CTGTTTCACAGTCTGCATGCAATGA 62.498 44.000 25.58 17.26 43.50 2.57
1250 4868 8.868439 CTGTTTCACAGTCTGCATGCAATGAA 62.868 42.308 25.58 22.15 43.50 2.57
1268 4906 2.101415 TGAATAGTGCTGCGCTATCTGT 59.899 45.455 29.64 18.05 36.33 3.41
1307 4945 2.079170 TACTGAGGATCCAGCCTGAG 57.921 55.000 15.82 0.00 43.87 3.35
1352 4990 2.884207 GCCACCGACGACGAATCC 60.884 66.667 9.28 0.00 42.66 3.01
1381 5019 1.486211 CGGGTCCAGACTGAGGTAAT 58.514 55.000 3.32 0.00 0.00 1.89
1398 5036 8.697846 TGAGGTAATGTATTTCTAACAGTTCG 57.302 34.615 0.00 0.00 0.00 3.95
1400 5038 8.928270 AGGTAATGTATTTCTAACAGTTCGAG 57.072 34.615 0.00 0.00 0.00 4.04
1407 5045 5.652744 TTTCTAACAGTTCGAGAAGCAAC 57.347 39.130 0.00 0.00 31.16 4.17
1410 5048 1.583054 ACAGTTCGAGAAGCAACACC 58.417 50.000 0.00 0.00 0.00 4.16
1411 5049 0.508641 CAGTTCGAGAAGCAACACCG 59.491 55.000 0.00 0.00 0.00 4.94
1413 5051 1.202486 AGTTCGAGAAGCAACACCGAA 60.202 47.619 0.00 0.00 36.98 4.30
1414 5052 1.214367 TTCGAGAAGCAACACCGAAC 58.786 50.000 0.00 0.00 34.83 3.95
1415 5053 0.103390 TCGAGAAGCAACACCGAACA 59.897 50.000 0.00 0.00 0.00 3.18
1416 5054 1.148310 CGAGAAGCAACACCGAACAT 58.852 50.000 0.00 0.00 0.00 2.71
1419 5057 0.240945 GAAGCAACACCGAACATGGG 59.759 55.000 0.00 0.00 0.00 4.00
1437 5075 5.946377 ACATGGGAAGTTTTAAGACATCTCC 59.054 40.000 0.00 2.19 0.00 3.71
1453 5091 7.450074 AGACATCTCCAGTTATAAACACACAA 58.550 34.615 0.00 0.00 0.00 3.33
1503 5144 2.482494 CAGGTAACAGGGAGGGAGATT 58.518 52.381 0.00 0.00 41.41 2.40
1565 5206 6.531503 AGATTTCATCGAAGAGAAGGTGTA 57.468 37.500 0.00 0.00 43.63 2.90
1611 5252 4.553330 TGAGGATTTTGGACTAGACACC 57.447 45.455 0.00 0.00 0.00 4.16
1706 5347 8.296713 TGAAAGGTTAATAACTGTGAAATCTGC 58.703 33.333 2.96 0.00 0.00 4.26
2142 5808 1.001406 ACTGTGCTACTGACAAGGCTC 59.999 52.381 0.00 0.00 0.00 4.70
2274 5961 0.580578 CATGAATGAAGAGCGAGGCG 59.419 55.000 0.00 0.00 0.00 5.52
2353 6040 4.069232 CTGCGAGGCGACCTTCCA 62.069 66.667 0.00 0.96 31.76 3.53
2471 6163 8.034058 ACATCTCTATAGTTTGTTTGTTCAGC 57.966 34.615 0.00 0.00 0.00 4.26
2619 6371 7.284261 TGAGTTTACATCCTCACATTGAAAACA 59.716 33.333 0.00 0.00 32.93 2.83
2665 6575 9.424319 CATACTTATAACTCACAAGACACAACT 57.576 33.333 0.00 0.00 0.00 3.16
2668 6578 7.653713 ACTTATAACTCACAAGACACAACTGAG 59.346 37.037 0.00 0.00 0.00 3.35
2669 6579 3.895232 ACTCACAAGACACAACTGAGT 57.105 42.857 0.00 0.00 0.00 3.41
2670 6580 4.207891 ACTCACAAGACACAACTGAGTT 57.792 40.909 0.00 0.00 32.05 3.01
2671 6581 4.579869 ACTCACAAGACACAACTGAGTTT 58.420 39.130 0.00 0.00 32.05 2.66
2672 6582 4.393062 ACTCACAAGACACAACTGAGTTTG 59.607 41.667 0.00 0.66 32.05 2.93
2707 6617 0.406361 GGGGGACATGGTGGTAAACA 59.594 55.000 0.00 0.00 0.00 2.83
2727 6637 2.057140 ACTATGATGGTGGCCATGCTA 58.943 47.619 9.72 0.00 45.26 3.49
2772 6682 4.033009 AGACCATCTACCATGTGACATCA 58.967 43.478 0.00 0.00 0.00 3.07
3017 6930 5.068329 TCGCAGATGAGAATGAGACTAATGT 59.932 40.000 0.00 0.00 0.00 2.71
3284 7205 6.515531 GCTTTGATGACATGAACCTTGAGAAA 60.516 38.462 0.00 0.00 0.00 2.52
3421 7351 4.471904 AGTATCTGGCGTGAGAATTGAA 57.528 40.909 0.00 0.00 0.00 2.69
3445 7378 7.716799 ATTTCATCCAACCAGCTAAATAACA 57.283 32.000 0.00 0.00 0.00 2.41
3446 7379 7.531857 TTTCATCCAACCAGCTAAATAACAA 57.468 32.000 0.00 0.00 0.00 2.83
3447 7380 6.509418 TCATCCAACCAGCTAAATAACAAC 57.491 37.500 0.00 0.00 0.00 3.32
3491 7424 9.692749 TTGTACTATTTGTTACAGAACTCTCAG 57.307 33.333 0.00 0.00 36.45 3.35
3493 7426 7.540474 ACTATTTGTTACAGAACTCTCAGGA 57.460 36.000 0.00 0.00 36.45 3.86
3510 7443 0.320421 GGAGTGTGTTGCCTTCGCTA 60.320 55.000 0.00 0.00 35.36 4.26
3519 7452 4.392138 GTGTTGCCTTCGCTAAGATAGTTT 59.608 41.667 0.00 0.00 34.37 2.66
3594 7528 3.865929 AAGTGGCGCGTCTGAGTGG 62.866 63.158 13.81 0.00 0.00 4.00
3722 7954 2.484241 GGGTTGTACTCGTTCAGGTGTT 60.484 50.000 0.00 0.00 0.00 3.32
3735 7974 5.220970 CGTTCAGGTGTTGTTTCAGGTTATT 60.221 40.000 0.00 0.00 0.00 1.40
3798 8037 5.527951 TCAATTTGTGACACAACATTAGGC 58.472 37.500 20.46 0.00 37.90 3.93
3802 8041 2.158682 TGTGACACAACATTAGGCCACT 60.159 45.455 5.62 0.00 0.00 4.00
3809 8048 3.521126 ACAACATTAGGCCACTCTCAGAT 59.479 43.478 5.01 0.00 0.00 2.90
3857 8097 0.736053 GTTGCAACCAAACGTCCTCA 59.264 50.000 19.15 0.00 31.68 3.86
3923 8245 8.131100 TGTAACTTACACGTATATCTTACTGGC 58.869 37.037 0.00 0.00 32.89 4.85
3928 8250 2.228343 ACGTATATCTTACTGGCCGCTC 59.772 50.000 0.00 0.00 0.00 5.03
3931 8253 2.067365 TATCTTACTGGCCGCTCAGA 57.933 50.000 13.75 0.00 38.11 3.27
3932 8254 0.749649 ATCTTACTGGCCGCTCAGAG 59.250 55.000 13.75 0.00 38.11 3.35
3940 8293 1.226435 GCCGCTCAGAGACGTGTAG 60.226 63.158 0.00 0.00 0.00 2.74
3976 8334 7.147966 GGGTATTTAAACGGAAAATGGTGATCT 60.148 37.037 0.00 0.00 0.00 2.75
3985 8343 5.261216 GGAAAATGGTGATCTAAACAGGGA 58.739 41.667 0.00 0.00 0.00 4.20
3986 8344 5.893824 GGAAAATGGTGATCTAAACAGGGAT 59.106 40.000 0.00 0.00 0.00 3.85
3995 8353 7.364762 GGTGATCTAAACAGGGATTAAGACTCA 60.365 40.741 0.00 0.00 0.00 3.41
4021 8379 2.037144 GGCCATCTTGAATGCCAGAAT 58.963 47.619 0.00 0.00 43.46 2.40
4039 8397 4.681025 CAGAATGTTTGTGTACAATGCACC 59.319 41.667 0.00 0.00 35.55 5.01
4040 8398 4.340666 AGAATGTTTGTGTACAATGCACCA 59.659 37.500 0.00 0.00 35.55 4.17
4044 8402 1.979855 TGTGTACAATGCACCAGCTT 58.020 45.000 0.00 0.00 42.74 3.74
4045 8403 3.133141 TGTGTACAATGCACCAGCTTA 57.867 42.857 0.00 0.00 42.74 3.09
4046 8404 3.481453 TGTGTACAATGCACCAGCTTAA 58.519 40.909 0.00 0.00 42.74 1.85
4122 8480 3.110705 AGTGCAGACAGATATTGAGGGT 58.889 45.455 0.00 0.00 0.00 4.34
4161 8519 1.802960 CAAACTGCTCGCATCTGTTCT 59.197 47.619 0.00 0.00 0.00 3.01
4167 8525 1.741732 GCTCGCATCTGTTCTGACCAT 60.742 52.381 0.00 0.00 0.00 3.55
4195 8553 6.072342 GGTTTAGACGTGTTTTACCATCCAAT 60.072 38.462 0.00 0.00 0.00 3.16
4196 8554 6.489127 TTAGACGTGTTTTACCATCCAATG 57.511 37.500 0.00 0.00 0.00 2.82
4202 8560 4.869861 GTGTTTTACCATCCAATGCAATCC 59.130 41.667 0.00 0.00 0.00 3.01
4208 8566 5.323382 ACCATCCAATGCAATCCTGTATA 57.677 39.130 0.00 0.00 0.00 1.47
4209 8567 5.072741 ACCATCCAATGCAATCCTGTATAC 58.927 41.667 0.00 0.00 0.00 1.47
4212 8570 6.349860 CCATCCAATGCAATCCTGTATACATG 60.350 42.308 5.91 3.74 0.00 3.21
4213 8571 5.072055 TCCAATGCAATCCTGTATACATGG 58.928 41.667 5.91 10.09 0.00 3.66
4217 8575 2.816087 GCAATCCTGTATACATGGGCTG 59.184 50.000 5.91 11.00 0.00 4.85
4239 8605 1.076332 CGTTCCGGACATCCAGAAAC 58.924 55.000 1.83 0.00 34.48 2.78
4250 8616 1.314730 TCCAGAAACCGGAAGCAAAC 58.685 50.000 9.46 0.00 0.00 2.93
4251 8617 0.040425 CCAGAAACCGGAAGCAAACG 60.040 55.000 9.46 0.00 0.00 3.60
4256 8622 4.653888 CCGGAAGCAAACGGGGGT 62.654 66.667 0.00 0.00 46.08 4.95
4257 8623 3.361977 CGGAAGCAAACGGGGGTG 61.362 66.667 0.00 0.00 0.00 4.61
4296 8671 2.358247 CCACCCCTTGTTCCGACG 60.358 66.667 0.00 0.00 0.00 5.12
4302 8677 1.374252 CCTTGTTCCGACGACCCTG 60.374 63.158 0.00 0.00 0.00 4.45
4315 8690 1.229177 ACCCTGGCCCATCCAAAAC 60.229 57.895 0.00 0.00 46.01 2.43
4326 8701 2.450476 CATCCAAAACCCTCTCCCTTG 58.550 52.381 0.00 0.00 0.00 3.61
4328 8703 0.113190 CCAAAACCCTCTCCCTTGCT 59.887 55.000 0.00 0.00 0.00 3.91
4330 8705 1.149101 AAAACCCTCTCCCTTGCTCA 58.851 50.000 0.00 0.00 0.00 4.26
4333 8708 1.153005 CCCTCTCCCTTGCTCATGC 60.153 63.158 0.00 0.00 40.20 4.06
4344 8719 3.056313 GCTCATGCACTTTCCCGCC 62.056 63.158 0.00 0.00 39.41 6.13
4345 8720 1.377725 CTCATGCACTTTCCCGCCT 60.378 57.895 0.00 0.00 0.00 5.52
4347 8722 1.973281 CATGCACTTTCCCGCCTGT 60.973 57.895 0.00 0.00 0.00 4.00
4352 8727 0.673644 CACTTTCCCGCCTGTAGTGG 60.674 60.000 0.00 0.00 46.61 4.00
4355 8730 0.834687 TTTCCCGCCTGTAGTGGTCT 60.835 55.000 0.00 0.00 45.49 3.85
4358 8733 2.507102 CGCCTGTAGTGGTCTGCG 60.507 66.667 0.00 0.00 35.81 5.18
4367 8742 4.435436 TGGTCTGCGCCGCTACAG 62.435 66.667 11.67 0.00 35.15 2.74
4400 8775 1.455217 ATTCATGCTGGCCCAGAGC 60.455 57.895 16.85 6.61 42.60 4.09
4401 8776 3.982316 TTCATGCTGGCCCAGAGCG 62.982 63.158 16.85 0.67 45.17 5.03
4434 8809 4.621068 TCATTGGAATCGACATTGAAGC 57.379 40.909 0.00 0.00 0.00 3.86
4479 8854 1.375098 GCTGCATGTGCCTTCTCTCC 61.375 60.000 2.07 0.00 41.18 3.71
4480 8855 1.078918 TGCATGTGCCTTCTCTCCG 60.079 57.895 2.07 0.00 41.18 4.63
4481 8856 2.467826 GCATGTGCCTTCTCTCCGC 61.468 63.158 0.00 0.00 34.31 5.54
4482 8857 2.169789 CATGTGCCTTCTCTCCGCG 61.170 63.158 0.00 0.00 0.00 6.46
4483 8858 2.650116 ATGTGCCTTCTCTCCGCGT 61.650 57.895 4.92 0.00 0.00 6.01
4484 8859 2.048127 GTGCCTTCTCTCCGCGTT 60.048 61.111 4.92 0.00 0.00 4.84
4485 8860 2.048222 TGCCTTCTCTCCGCGTTG 60.048 61.111 4.92 0.00 0.00 4.10
4486 8861 2.261671 GCCTTCTCTCCGCGTTGA 59.738 61.111 4.92 1.24 0.00 3.18
4487 8862 1.374252 GCCTTCTCTCCGCGTTGAA 60.374 57.895 4.92 2.85 0.00 2.69
4488 8863 0.949105 GCCTTCTCTCCGCGTTGAAA 60.949 55.000 4.92 0.20 0.00 2.69
4489 8864 0.790814 CCTTCTCTCCGCGTTGAAAC 59.209 55.000 4.92 0.00 0.00 2.78
4490 8865 1.497991 CTTCTCTCCGCGTTGAAACA 58.502 50.000 4.92 0.00 0.00 2.83
4499 8874 1.670326 GCGTTGAAACAACATCCGTC 58.330 50.000 13.62 0.00 0.00 4.79
4502 8877 1.600485 GTTGAAACAACATCCGTCCGT 59.400 47.619 9.32 0.00 0.00 4.69
4526 8901 3.542648 GCCTGTCTACCTCCATAAAACC 58.457 50.000 0.00 0.00 0.00 3.27
4528 8903 4.566907 GCCTGTCTACCTCCATAAAACCAA 60.567 45.833 0.00 0.00 0.00 3.67
4531 8906 5.310451 TGTCTACCTCCATAAAACCAACAC 58.690 41.667 0.00 0.00 0.00 3.32
4539 8914 3.364964 CCATAAAACCAACACGTCTGCTC 60.365 47.826 0.00 0.00 0.00 4.26
4549 8924 1.135257 CACGTCTGCTCAGGAACCTAG 60.135 57.143 0.00 0.00 0.00 3.02
4550 8925 1.178276 CGTCTGCTCAGGAACCTAGT 58.822 55.000 0.00 0.00 0.00 2.57
4559 8934 0.178903 AGGAACCTAGTCTGGCACCA 60.179 55.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2 3 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
3 4 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
5 6 6.561614 CATATACATCCGTATGTGGTAGTCC 58.438 44.000 3.56 0.00 45.99 3.85
12 13 9.599866 AAATATGTCCATATACATCCGTATGTG 57.400 33.333 3.56 3.22 45.99 3.21
28 29 9.817809 GTGAATCTACACTCTAAAATATGTCCA 57.182 33.333 0.00 0.00 37.73 4.02
43 44 6.073222 ACGAACCAAAATGAGTGAATCTACAC 60.073 38.462 0.00 0.00 40.60 2.90
44 45 5.995282 ACGAACCAAAATGAGTGAATCTACA 59.005 36.000 0.00 0.00 0.00 2.74
45 46 6.481954 ACGAACCAAAATGAGTGAATCTAC 57.518 37.500 0.00 0.00 0.00 2.59
46 47 8.258007 AGATACGAACCAAAATGAGTGAATCTA 58.742 33.333 0.00 0.00 0.00 1.98
47 48 7.106239 AGATACGAACCAAAATGAGTGAATCT 58.894 34.615 0.00 0.00 0.00 2.40
48 49 7.308782 AGATACGAACCAAAATGAGTGAATC 57.691 36.000 0.00 0.00 0.00 2.52
49 50 8.041323 ACTAGATACGAACCAAAATGAGTGAAT 58.959 33.333 0.00 0.00 0.00 2.57
50 51 7.383687 ACTAGATACGAACCAAAATGAGTGAA 58.616 34.615 0.00 0.00 0.00 3.18
51 52 6.931838 ACTAGATACGAACCAAAATGAGTGA 58.068 36.000 0.00 0.00 0.00 3.41
52 53 8.592998 GTTACTAGATACGAACCAAAATGAGTG 58.407 37.037 0.00 0.00 0.00 3.51
53 54 8.529476 AGTTACTAGATACGAACCAAAATGAGT 58.471 33.333 0.00 0.00 0.00 3.41
54 55 8.928270 AGTTACTAGATACGAACCAAAATGAG 57.072 34.615 0.00 0.00 0.00 2.90
55 56 9.146984 CAAGTTACTAGATACGAACCAAAATGA 57.853 33.333 0.00 0.00 0.00 2.57
56 57 8.932791 ACAAGTTACTAGATACGAACCAAAATG 58.067 33.333 0.00 0.00 0.00 2.32
57 58 9.498176 AACAAGTTACTAGATACGAACCAAAAT 57.502 29.630 0.00 0.00 0.00 1.82
58 59 8.767085 CAACAAGTTACTAGATACGAACCAAAA 58.233 33.333 0.00 0.00 0.00 2.44
59 60 8.143193 TCAACAAGTTACTAGATACGAACCAAA 58.857 33.333 0.00 0.00 0.00 3.28
60 61 7.660112 TCAACAAGTTACTAGATACGAACCAA 58.340 34.615 0.00 0.00 0.00 3.67
61 62 7.218228 TCAACAAGTTACTAGATACGAACCA 57.782 36.000 0.00 0.00 0.00 3.67
62 63 8.524870 TTTCAACAAGTTACTAGATACGAACC 57.475 34.615 0.00 0.00 0.00 3.62
90 91 9.685828 CCGTTCCTAAATATTTGTTTTTCTTCA 57.314 29.630 11.05 0.00 0.00 3.02
91 92 9.135843 CCCGTTCCTAAATATTTGTTTTTCTTC 57.864 33.333 11.05 0.00 0.00 2.87
92 93 8.092068 CCCCGTTCCTAAATATTTGTTTTTCTT 58.908 33.333 11.05 0.00 0.00 2.52
93 94 7.310175 CCCCCGTTCCTAAATATTTGTTTTTCT 60.310 37.037 11.05 0.00 0.00 2.52
94 95 6.814644 CCCCCGTTCCTAAATATTTGTTTTTC 59.185 38.462 11.05 0.00 0.00 2.29
95 96 6.703319 CCCCCGTTCCTAAATATTTGTTTTT 58.297 36.000 11.05 0.00 0.00 1.94
96 97 6.288941 CCCCCGTTCCTAAATATTTGTTTT 57.711 37.500 11.05 0.00 0.00 2.43
97 98 5.925506 CCCCCGTTCCTAAATATTTGTTT 57.074 39.130 11.05 0.00 0.00 2.83
116 117 2.644676 GCAACAAAGATCTACTCCCCC 58.355 52.381 0.00 0.00 0.00 5.40
117 118 2.644676 GGCAACAAAGATCTACTCCCC 58.355 52.381 0.00 0.00 0.00 4.81
118 119 2.644676 GGGCAACAAAGATCTACTCCC 58.355 52.381 0.00 0.00 39.74 4.30
119 120 2.280628 CGGGCAACAAAGATCTACTCC 58.719 52.381 0.00 0.00 39.74 3.85
120 121 2.930682 GACGGGCAACAAAGATCTACTC 59.069 50.000 0.00 0.00 39.74 2.59
121 122 2.301870 TGACGGGCAACAAAGATCTACT 59.698 45.455 0.00 0.00 39.74 2.57
122 123 2.695359 TGACGGGCAACAAAGATCTAC 58.305 47.619 0.00 0.00 39.74 2.59
123 124 3.410631 TTGACGGGCAACAAAGATCTA 57.589 42.857 0.00 0.00 39.74 1.98
124 125 2.270352 TTGACGGGCAACAAAGATCT 57.730 45.000 0.00 0.00 39.74 2.75
125 126 3.363341 TTTTGACGGGCAACAAAGATC 57.637 42.857 0.00 0.00 37.32 2.75
126 127 3.810310 TTTTTGACGGGCAACAAAGAT 57.190 38.095 0.00 0.00 37.32 2.40
127 128 3.452474 CATTTTTGACGGGCAACAAAGA 58.548 40.909 0.00 0.00 37.32 2.52
128 129 2.032979 GCATTTTTGACGGGCAACAAAG 60.033 45.455 0.00 0.00 37.32 2.77
129 130 1.936547 GCATTTTTGACGGGCAACAAA 59.063 42.857 0.00 1.16 35.91 2.83
130 131 1.137872 AGCATTTTTGACGGGCAACAA 59.862 42.857 0.00 0.00 35.91 2.83
131 132 0.749649 AGCATTTTTGACGGGCAACA 59.250 45.000 0.00 0.00 35.91 3.33
132 133 2.030274 ACTAGCATTTTTGACGGGCAAC 60.030 45.455 0.00 0.00 35.91 4.17
133 134 2.030363 CACTAGCATTTTTGACGGGCAA 60.030 45.455 0.00 0.00 33.88 4.52
134 135 1.539388 CACTAGCATTTTTGACGGGCA 59.461 47.619 0.00 0.00 0.00 5.36
135 136 1.810151 TCACTAGCATTTTTGACGGGC 59.190 47.619 0.00 0.00 0.00 6.13
136 137 2.161609 GGTCACTAGCATTTTTGACGGG 59.838 50.000 0.00 0.00 39.46 5.28
137 138 2.161609 GGGTCACTAGCATTTTTGACGG 59.838 50.000 0.00 0.00 39.46 4.79
138 139 2.159707 CGGGTCACTAGCATTTTTGACG 60.160 50.000 0.00 0.00 39.46 4.35
139 140 2.161609 CCGGGTCACTAGCATTTTTGAC 59.838 50.000 0.00 1.30 38.11 3.18
140 141 2.039216 TCCGGGTCACTAGCATTTTTGA 59.961 45.455 0.00 0.00 0.00 2.69
141 142 2.161609 GTCCGGGTCACTAGCATTTTTG 59.838 50.000 0.00 0.00 0.00 2.44
142 143 2.433436 GTCCGGGTCACTAGCATTTTT 58.567 47.619 0.00 0.00 0.00 1.94
143 144 1.674817 CGTCCGGGTCACTAGCATTTT 60.675 52.381 0.00 0.00 0.00 1.82
144 145 0.108329 CGTCCGGGTCACTAGCATTT 60.108 55.000 0.00 0.00 0.00 2.32
145 146 1.515954 CGTCCGGGTCACTAGCATT 59.484 57.895 0.00 0.00 0.00 3.56
146 147 3.077519 GCGTCCGGGTCACTAGCAT 62.078 63.158 0.00 0.00 0.00 3.79
147 148 3.755628 GCGTCCGGGTCACTAGCA 61.756 66.667 0.00 0.00 0.00 3.49
148 149 4.509737 GGCGTCCGGGTCACTAGC 62.510 72.222 0.00 0.00 0.00 3.42
149 150 4.189188 CGGCGTCCGGGTCACTAG 62.189 72.222 0.00 0.00 44.15 2.57
164 165 4.383861 TCTGCACAGCTCTGGCGG 62.384 66.667 10.80 10.80 44.37 6.13
165 166 3.117171 GTCTGCACAGCTCTGGCG 61.117 66.667 1.66 0.00 44.37 5.69
166 167 3.117171 CGTCTGCACAGCTCTGGC 61.117 66.667 1.66 3.14 39.06 4.85
167 168 3.117171 GCGTCTGCACAGCTCTGG 61.117 66.667 1.66 0.00 42.15 3.86
168 169 3.476646 CGCGTCTGCACAGCTCTG 61.477 66.667 0.00 0.00 42.97 3.35
185 186 4.573950 CATTTGCGATGGGGCGGC 62.574 66.667 0.00 0.00 35.06 6.53
186 187 3.140141 ACATTTGCGATGGGGCGG 61.140 61.111 5.08 0.00 35.06 6.13
187 188 2.102749 CACATTTGCGATGGGGCG 59.897 61.111 5.08 0.00 35.06 6.13
188 189 2.350458 ACCACATTTGCGATGGGGC 61.350 57.895 18.29 0.00 46.34 5.80
190 191 0.964860 TCCACCACATTTGCGATGGG 60.965 55.000 5.08 0.55 37.86 4.00
191 192 0.171007 GTCCACCACATTTGCGATGG 59.829 55.000 5.08 0.00 39.57 3.51
192 193 0.171007 GGTCCACCACATTTGCGATG 59.829 55.000 0.00 0.00 35.64 3.84
193 194 0.965363 GGGTCCACCACATTTGCGAT 60.965 55.000 0.00 0.00 39.85 4.58
194 195 1.602323 GGGTCCACCACATTTGCGA 60.602 57.895 0.00 0.00 39.85 5.10
195 196 2.635443 GGGGTCCACCACATTTGCG 61.635 63.158 0.00 0.00 42.91 4.85
196 197 2.635443 CGGGGTCCACCACATTTGC 61.635 63.158 0.00 0.00 40.22 3.68
197 198 0.960364 CTCGGGGTCCACCACATTTG 60.960 60.000 0.00 0.00 40.22 2.32
198 199 1.378762 CTCGGGGTCCACCACATTT 59.621 57.895 0.00 0.00 40.22 2.32
199 200 0.545787 TACTCGGGGTCCACCACATT 60.546 55.000 0.00 0.00 40.22 2.71
200 201 0.545787 TTACTCGGGGTCCACCACAT 60.546 55.000 0.00 0.00 40.22 3.21
201 202 1.152290 TTACTCGGGGTCCACCACA 60.152 57.895 0.00 0.00 40.22 4.17
202 203 1.294459 GTTACTCGGGGTCCACCAC 59.706 63.158 0.00 0.00 42.91 4.16
203 204 2.277591 CGTTACTCGGGGTCCACCA 61.278 63.158 0.00 0.00 42.91 4.17
204 205 2.218037 GACGTTACTCGGGGTCCACC 62.218 65.000 0.00 0.00 44.69 4.61
205 206 1.213799 GACGTTACTCGGGGTCCAC 59.786 63.158 0.00 0.00 44.69 4.02
206 207 2.334946 CGACGTTACTCGGGGTCCA 61.335 63.158 0.00 0.00 44.69 4.02
207 208 2.486966 CGACGTTACTCGGGGTCC 59.513 66.667 0.00 0.00 44.69 4.46
208 209 2.202531 GCGACGTTACTCGGGGTC 60.203 66.667 0.00 0.00 44.69 4.46
209 210 3.752339 GGCGACGTTACTCGGGGT 61.752 66.667 0.00 0.00 44.69 4.95
210 211 3.751246 TGGCGACGTTACTCGGGG 61.751 66.667 0.00 0.00 44.69 5.73
211 212 2.505557 GTGGCGACGTTACTCGGG 60.506 66.667 0.00 0.00 44.69 5.14
212 213 2.505557 GGTGGCGACGTTACTCGG 60.506 66.667 0.00 0.00 44.69 4.63
213 214 2.872925 CGGTGGCGACGTTACTCG 60.873 66.667 0.00 0.00 46.00 4.18
214 215 1.513586 CTCGGTGGCGACGTTACTC 60.514 63.158 0.00 0.00 0.00 2.59
215 216 2.564975 CTCGGTGGCGACGTTACT 59.435 61.111 0.00 0.00 0.00 2.24
216 217 3.177249 GCTCGGTGGCGACGTTAC 61.177 66.667 0.00 0.00 0.00 2.50
217 218 4.424566 GGCTCGGTGGCGACGTTA 62.425 66.667 0.00 0.00 0.00 3.18
250 251 2.514824 GGGCTTCTCGCATGGGTC 60.515 66.667 9.86 0.00 41.67 4.46
300 301 1.675641 GTGCTGGTGTAGGCCCTTG 60.676 63.158 0.00 0.00 0.00 3.61
340 3242 3.122369 CCAGATTTGGGGCAGGATC 57.878 57.895 0.00 0.00 41.05 3.36
442 3345 3.900855 CTGCTAGCAGCCTGGTTG 58.099 61.111 30.62 6.87 41.51 3.77
523 3429 1.799258 CTGTTGGTCTTGGTGGCTGC 61.799 60.000 0.00 0.00 0.00 5.25
537 3443 2.727544 CGGGGTTGTTGCCTGTTG 59.272 61.111 0.00 0.00 0.00 3.33
538 3444 3.223589 GCGGGGTTGTTGCCTGTT 61.224 61.111 0.00 0.00 0.00 3.16
539 3445 4.514585 TGCGGGGTTGTTGCCTGT 62.515 61.111 0.00 0.00 0.00 4.00
540 3446 3.222855 TTGCGGGGTTGTTGCCTG 61.223 61.111 0.00 0.00 0.00 4.85
541 3447 3.223589 GTTGCGGGGTTGTTGCCT 61.224 61.111 0.00 0.00 0.00 4.75
542 3448 3.532155 TGTTGCGGGGTTGTTGCC 61.532 61.111 0.00 0.00 0.00 4.52
543 3449 2.279186 GTGTTGCGGGGTTGTTGC 60.279 61.111 0.00 0.00 0.00 4.17
647 3566 2.002509 GCGTTAGTCCTCCCGTCCTC 62.003 65.000 0.00 0.00 0.00 3.71
693 3874 3.539756 GATTCTCGCTCGAATGAATTGC 58.460 45.455 7.76 0.00 33.96 3.56
697 3878 2.427095 TCTGGATTCTCGCTCGAATGAA 59.573 45.455 2.55 0.00 33.96 2.57
700 3881 1.067821 GGTCTGGATTCTCGCTCGAAT 59.932 52.381 0.00 0.00 36.38 3.34
750 4307 3.403038 ACTCTTCAAGTCCCACGAAATG 58.597 45.455 0.00 0.00 30.02 2.32
790 4370 7.384439 GCTGGAGCTAATTTATTCCTAATCC 57.616 40.000 0.00 0.00 38.21 3.01
875 4458 3.082579 GCGGAGGCAGGTCACCTAG 62.083 68.421 0.00 0.00 37.77 3.02
932 4515 8.372521 CACCTAAATCGTTGCATTATTGTTTTC 58.627 33.333 0.00 0.00 0.00 2.29
980 4576 1.003355 CCTGTGACGACTTGGCCAT 60.003 57.895 6.09 0.00 0.00 4.40
1064 4660 3.637432 CTGAGCTCGTGAGATTATGTCC 58.363 50.000 9.64 0.00 40.84 4.02
1087 4691 1.613317 ATCGGATCCGTCTGCCACAA 61.613 55.000 32.15 11.42 40.74 3.33
1145 4749 3.392616 GAGGATATTCTTGCCCCTGAAGA 59.607 47.826 0.00 0.00 0.00 2.87
1233 4849 4.598062 CACTATTCATTGCATGCAGACTG 58.402 43.478 21.50 18.51 0.00 3.51
1256 4874 3.190327 AGAGCACTATACAGATAGCGCAG 59.810 47.826 11.47 0.00 43.38 5.18
1258 4876 3.840890 AGAGCACTATACAGATAGCGC 57.159 47.619 0.00 0.00 41.93 5.92
1259 4877 4.216472 TCCAAGAGCACTATACAGATAGCG 59.784 45.833 0.00 0.00 39.00 4.26
1260 4878 5.475220 TCTCCAAGAGCACTATACAGATAGC 59.525 44.000 0.00 0.00 39.00 2.97
1268 4906 7.290813 TCAGTATCTTCTCCAAGAGCACTATA 58.709 38.462 0.00 0.00 42.13 1.31
1307 4945 0.892063 AGAGGAAGAGCTTCGTGACC 59.108 55.000 9.85 0.00 40.37 4.02
1381 5019 6.452242 TGCTTCTCGAACTGTTAGAAATACA 58.548 36.000 4.92 3.07 0.00 2.29
1398 5036 1.197721 CCATGTTCGGTGTTGCTTCTC 59.802 52.381 0.00 0.00 0.00 2.87
1400 5038 0.240945 CCCATGTTCGGTGTTGCTTC 59.759 55.000 0.00 0.00 0.00 3.86
1407 5045 4.517453 TCTTAAAACTTCCCATGTTCGGTG 59.483 41.667 0.00 0.00 0.00 4.94
1410 5048 5.682943 TGTCTTAAAACTTCCCATGTTCG 57.317 39.130 0.00 0.00 0.00 3.95
1411 5049 7.362142 GGAGATGTCTTAAAACTTCCCATGTTC 60.362 40.741 0.00 0.00 0.00 3.18
1413 5051 5.946377 GGAGATGTCTTAAAACTTCCCATGT 59.054 40.000 0.00 0.00 0.00 3.21
1414 5052 5.945784 TGGAGATGTCTTAAAACTTCCCATG 59.054 40.000 0.00 0.00 0.00 3.66
1415 5053 6.139679 TGGAGATGTCTTAAAACTTCCCAT 57.860 37.500 0.00 0.00 0.00 4.00
1416 5054 5.073144 ACTGGAGATGTCTTAAAACTTCCCA 59.927 40.000 0.00 5.50 0.00 4.37
1477 5118 0.250513 CTCCCTGTTACCTGCAGACC 59.749 60.000 17.39 0.00 36.12 3.85
1503 5144 5.192927 TGCTTTTCTCTGAGAACTTGGAAA 58.807 37.500 19.17 9.24 33.26 3.13
1611 5252 0.947244 ACACTTCTTTCAGCTTGGCG 59.053 50.000 0.00 0.00 0.00 5.69
1706 5347 5.794687 TGGTAAGAACATGTATGCTTTCG 57.205 39.130 0.00 0.00 0.00 3.46
1953 5603 9.173021 TCAAGTCAGTTAATCACTTTTGAGAAA 57.827 29.630 0.00 0.00 34.35 2.52
1958 5608 7.166473 GCTGTTCAAGTCAGTTAATCACTTTTG 59.834 37.037 0.00 0.00 35.60 2.44
2142 5808 4.401925 AGTTCCTTCATGGTTTTCCTCTG 58.598 43.478 0.00 0.00 41.38 3.35
2219 5885 5.054477 ACGTGTTACTACTGTTGCAGAAAT 58.946 37.500 2.91 0.00 35.18 2.17
2287 5974 3.930848 CCTTGGTGAACACGTAGGTATTC 59.069 47.826 0.00 0.00 31.74 1.75
2353 6040 2.815308 GGCCGGATGATGACGACT 59.185 61.111 5.05 0.00 0.00 4.18
2458 6150 5.126222 TGTCACCATAAGCTGAACAAACAAA 59.874 36.000 0.00 0.00 0.00 2.83
2471 6163 6.500684 AATGCAAGTTAGTGTCACCATAAG 57.499 37.500 0.00 0.00 0.00 1.73
2647 6550 5.339008 ACTCAGTTGTGTCTTGTGAGTTA 57.661 39.130 0.00 0.00 44.25 2.24
2665 6575 3.888930 GGAATCTGTCCAAACCAAACTCA 59.111 43.478 0.00 0.00 46.97 3.41
2707 6617 0.848735 AGCATGGCCACCATCATAGT 59.151 50.000 8.16 0.00 43.15 2.12
2727 6637 2.738213 CTTGTTCCCCTGAGTGCGCT 62.738 60.000 9.73 0.00 0.00 5.92
2738 6648 1.168714 GATGGTCTGTGCTTGTTCCC 58.831 55.000 0.00 0.00 0.00 3.97
2772 6682 2.124151 GCCGGGTTGCTCATGGAT 60.124 61.111 2.18 0.00 0.00 3.41
2953 6866 6.868339 CCAATTTCAAATCTAAATATCGGCCC 59.132 38.462 0.00 0.00 0.00 5.80
3017 6930 5.559770 TCAAGCTCAATCATAGGACAAACA 58.440 37.500 0.00 0.00 0.00 2.83
3284 7205 1.919600 GCTCCATGGCCTTCCTCAGT 61.920 60.000 6.96 0.00 0.00 3.41
3421 7351 7.716799 TGTTATTTAGCTGGTTGGATGAAAT 57.283 32.000 0.00 0.00 0.00 2.17
3482 7415 5.373203 AGGCAACACACTCCTGAGAGTTC 62.373 52.174 0.22 0.00 46.66 3.01
3491 7424 0.320421 TAGCGAAGGCAACACACTCC 60.320 55.000 0.00 0.00 43.41 3.85
3493 7426 1.070134 TCTTAGCGAAGGCAACACACT 59.930 47.619 6.73 0.00 43.41 3.55
3501 7434 6.258068 ACATACAAAACTATCTTAGCGAAGGC 59.742 38.462 6.73 0.00 40.37 4.35
3722 7954 3.243569 CGTTTGGCCAATAACCTGAAACA 60.244 43.478 21.26 0.00 0.00 2.83
3735 7974 1.670949 TTCAAAGCAGCGTTTGGCCA 61.671 50.000 0.00 0.00 45.17 5.36
3798 8037 5.976458 AGCTTTTCTCTTATCTGAGAGTGG 58.024 41.667 2.23 0.00 43.05 4.00
3802 8041 5.395103 GCCTGAGCTTTTCTCTTATCTGAGA 60.395 44.000 0.00 0.00 42.38 3.27
3809 8048 2.037251 ACGTGCCTGAGCTTTTCTCTTA 59.963 45.455 0.00 0.00 42.38 2.10
3851 8091 4.065110 AGCACGGCTTTTGAGGAC 57.935 55.556 0.00 0.00 33.89 3.85
3923 8245 0.522180 AACTACACGTCTCTGAGCGG 59.478 55.000 19.94 13.45 0.00 5.52
3928 8250 5.634020 CCCTTCTAAAAACTACACGTCTCTG 59.366 44.000 0.00 0.00 0.00 3.35
3931 8253 5.541953 ACCCTTCTAAAAACTACACGTCT 57.458 39.130 0.00 0.00 0.00 4.18
3932 8254 7.895975 AATACCCTTCTAAAAACTACACGTC 57.104 36.000 0.00 0.00 0.00 4.34
3940 8293 9.964303 TTTCCGTTTAAATACCCTTCTAAAAAC 57.036 29.630 0.00 0.00 0.00 2.43
3961 8319 4.096382 CCCTGTTTAGATCACCATTTTCCG 59.904 45.833 0.00 0.00 0.00 4.30
3976 8334 5.497474 GCCTTGAGTCTTAATCCCTGTTTA 58.503 41.667 0.00 0.00 0.00 2.01
3985 8343 0.107165 GGCCCGCCTTGAGTCTTAAT 60.107 55.000 0.00 0.00 0.00 1.40
3986 8344 1.298667 GGCCCGCCTTGAGTCTTAA 59.701 57.895 0.00 0.00 0.00 1.85
3995 8353 1.039233 CATTCAAGATGGCCCGCCTT 61.039 55.000 7.35 0.00 36.94 4.35
4021 8379 2.223688 GCTGGTGCATTGTACACAAACA 60.224 45.455 7.21 0.00 39.87 2.83
4046 8404 9.244292 GGGTCCTTTTAATGTTCTCTCTTTTAT 57.756 33.333 0.00 0.00 0.00 1.40
4133 8491 1.347817 GCGAGCAGTTTGAGAGTCCG 61.348 60.000 0.00 0.00 0.00 4.79
4167 8525 4.511527 TGGTAAAACACGTCTAAACCACA 58.488 39.130 2.98 0.00 30.84 4.17
4174 8532 4.393680 GCATTGGATGGTAAAACACGTCTA 59.606 41.667 0.00 0.00 0.00 2.59
4195 8553 2.442878 AGCCCATGTATACAGGATTGCA 59.557 45.455 18.73 0.00 0.00 4.08
4196 8554 2.816087 CAGCCCATGTATACAGGATTGC 59.184 50.000 18.73 16.29 0.00 3.56
4202 8560 0.603707 CGGCCAGCCCATGTATACAG 60.604 60.000 11.91 3.82 0.00 2.74
4208 8566 4.740822 GGAACGGCCAGCCCATGT 62.741 66.667 2.24 0.00 36.34 3.21
4234 8592 1.170290 CCCGTTTGCTTCCGGTTTCT 61.170 55.000 0.00 0.00 42.67 2.52
4235 8593 1.284715 CCCGTTTGCTTCCGGTTTC 59.715 57.895 0.00 0.00 42.67 2.78
4239 8605 4.653888 ACCCCCGTTTGCTTCCGG 62.654 66.667 0.00 0.00 43.82 5.14
4273 8639 4.280019 AACAAGGGGTGGCCGGAC 62.280 66.667 5.05 0.56 0.00 4.79
4274 8640 3.961414 GAACAAGGGGTGGCCGGA 61.961 66.667 5.05 0.00 0.00 5.14
4277 8643 3.961414 TCGGAACAAGGGGTGGCC 61.961 66.667 0.00 0.00 0.00 5.36
4278 8644 2.671963 GTCGGAACAAGGGGTGGC 60.672 66.667 0.00 0.00 0.00 5.01
4286 8661 2.738480 CCAGGGTCGTCGGAACAA 59.262 61.111 0.00 0.00 0.00 2.83
4302 8677 0.684479 GAGAGGGTTTTGGATGGGCC 60.684 60.000 0.00 0.00 37.10 5.80
4315 8690 1.153005 GCATGAGCAAGGGAGAGGG 60.153 63.158 0.00 0.00 41.58 4.30
4326 8701 2.486966 GCGGGAAAGTGCATGAGC 59.513 61.111 0.00 0.00 42.57 4.26
4328 8703 1.675310 CAGGCGGGAAAGTGCATGA 60.675 57.895 0.00 0.00 45.03 3.07
4330 8705 0.392998 CTACAGGCGGGAAAGTGCAT 60.393 55.000 0.00 0.00 0.00 3.96
4333 8708 0.673644 CCACTACAGGCGGGAAAGTG 60.674 60.000 9.07 9.07 37.81 3.16
4344 8719 2.507102 CGGCGCAGACCACTACAG 60.507 66.667 10.83 0.00 0.00 2.74
4345 8720 4.735132 GCGGCGCAGACCACTACA 62.735 66.667 29.21 0.00 0.00 2.74
4347 8722 2.752640 TAGCGGCGCAGACCACTA 60.753 61.111 35.02 12.89 0.00 2.74
4400 8775 1.135315 CAATGAAAGCTCACGCCCG 59.865 57.895 0.00 0.00 36.60 6.13
4401 8776 0.960364 TCCAATGAAAGCTCACGCCC 60.960 55.000 0.00 0.00 36.60 6.13
4403 8778 2.789092 CGATTCCAATGAAAGCTCACGC 60.789 50.000 0.00 0.00 33.30 5.34
4404 8779 2.672874 TCGATTCCAATGAAAGCTCACG 59.327 45.455 0.00 0.00 33.30 4.35
4406 8781 3.673902 TGTCGATTCCAATGAAAGCTCA 58.326 40.909 0.00 0.00 33.32 4.26
4409 8784 4.985413 TCAATGTCGATTCCAATGAAAGC 58.015 39.130 0.00 0.00 33.32 3.51
4416 8791 1.737236 CCGCTTCAATGTCGATTCCAA 59.263 47.619 0.00 0.00 0.00 3.53
4456 8831 3.352338 GAAGGCACATGCAGCAGGC 62.352 63.158 7.05 7.45 44.36 4.85
4458 8833 0.677098 AGAGAAGGCACATGCAGCAG 60.677 55.000 12.17 0.00 44.36 4.24
4459 8834 0.675837 GAGAGAAGGCACATGCAGCA 60.676 55.000 12.17 0.00 44.36 4.41
4461 8836 1.088340 CGGAGAGAAGGCACATGCAG 61.088 60.000 6.15 0.00 44.36 4.41
4470 8845 0.790814 GTTTCAACGCGGAGAGAAGG 59.209 55.000 12.47 0.00 0.00 3.46
4471 8846 1.497991 TGTTTCAACGCGGAGAGAAG 58.502 50.000 12.47 0.00 0.00 2.85
4479 8854 0.041663 ACGGATGTTGTTTCAACGCG 60.042 50.000 3.53 3.53 0.00 6.01
4480 8855 1.662026 GGACGGATGTTGTTTCAACGC 60.662 52.381 7.87 3.38 0.00 4.84
4481 8856 1.397945 CGGACGGATGTTGTTTCAACG 60.398 52.381 7.87 0.00 0.00 4.10
4482 8857 1.600485 ACGGACGGATGTTGTTTCAAC 59.400 47.619 5.78 5.78 0.00 3.18
4483 8858 1.868498 GACGGACGGATGTTGTTTCAA 59.132 47.619 0.00 0.00 0.00 2.69
4484 8859 1.504359 GACGGACGGATGTTGTTTCA 58.496 50.000 0.00 0.00 0.00 2.69
4485 8860 0.794473 GGACGGACGGATGTTGTTTC 59.206 55.000 0.00 0.00 0.00 2.78
4486 8861 0.947180 CGGACGGACGGATGTTGTTT 60.947 55.000 0.00 0.00 0.00 2.83
4487 8862 1.373748 CGGACGGACGGATGTTGTT 60.374 57.895 0.00 0.00 0.00 2.83
4488 8863 2.260434 CGGACGGACGGATGTTGT 59.740 61.111 0.00 0.00 0.00 3.32
4489 8864 3.186047 GCGGACGGACGGATGTTG 61.186 66.667 3.28 0.00 0.00 3.33
4490 8865 4.446413 GGCGGACGGACGGATGTT 62.446 66.667 3.28 0.00 0.00 2.71
4499 8874 2.754658 AGGTAGACAGGCGGACGG 60.755 66.667 0.00 0.00 0.00 4.79
4502 8877 0.554305 TATGGAGGTAGACAGGCGGA 59.446 55.000 0.00 0.00 0.00 5.54
4508 8883 5.310451 GTGTTGGTTTTATGGAGGTAGACA 58.690 41.667 0.00 0.00 0.00 3.41
4510 8885 4.040706 ACGTGTTGGTTTTATGGAGGTAGA 59.959 41.667 0.00 0.00 0.00 2.59
4526 8901 0.861837 GTTCCTGAGCAGACGTGTTG 59.138 55.000 0.00 0.00 0.00 3.33
4528 8903 1.115930 AGGTTCCTGAGCAGACGTGT 61.116 55.000 0.00 0.00 0.00 4.49
4531 8906 1.133407 GACTAGGTTCCTGAGCAGACG 59.867 57.143 1.12 0.00 0.00 4.18
4539 8914 0.250513 GGTGCCAGACTAGGTTCCTG 59.749 60.000 1.12 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.