Multiple sequence alignment - TraesCS5B01G391000

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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 TraesCS5B01G391000 chr5B 100.000 1931 0 0 601 2531 570175876 570173946 0.000000e+00 3567.0
1 TraesCS5B01G391000 chr5B 88.856 682 52 17 861 1536 570152677 570152014 0.000000e+00 817.0
2 TraesCS5B01G391000 chr5B 100.000 276 0 0 1 276 570176476 570176201 6.250000e-141 510.0
3 TraesCS5B01G391000 chr5D 87.954 1984 160 34 604 2531 463404020 463402060 0.000000e+00 2266.0
4 TraesCS5B01G391000 chr5D 89.736 682 51 13 861 1536 463375338 463374670 0.000000e+00 854.0
5 TraesCS5B01G391000 chr5D 92.170 447 33 2 1091 1536 463357569 463357124 4.590000e-177 630.0
6 TraesCS5B01G391000 chr5D 86.607 112 11 4 25 134 127263101 127263210 1.230000e-23 121.0
7 TraesCS5B01G391000 chr5D 80.172 116 23 0 2276 2391 484283569 484283684 1.250000e-13 87.9
8 TraesCS5B01G391000 chr5D 97.674 43 1 0 3 45 116623299 116623341 9.710000e-10 75.0
9 TraesCS5B01G391000 chr5A 89.870 1155 76 22 608 1737 583628149 583627011 0.000000e+00 1447.0
10 TraesCS5B01G391000 chr5A 89.051 685 53 15 861 1536 583615738 583615067 0.000000e+00 830.0
11 TraesCS5B01G391000 chr5A 88.028 710 69 9 830 1536 583608715 583608019 0.000000e+00 826.0
12 TraesCS5B01G391000 chrUn 88.856 682 52 17 861 1536 295600358 295599695 0.000000e+00 817.0
13 TraesCS5B01G391000 chrUn 88.856 682 52 17 861 1536 310497152 310497815 0.000000e+00 817.0
14 TraesCS5B01G391000 chr7A 79.693 261 47 4 1733 1987 16160789 16161049 1.550000e-42 183.0
15 TraesCS5B01G391000 chr6B 82.160 213 37 1 1732 1944 671389815 671389604 5.560000e-42 182.0
16 TraesCS5B01G391000 chr6B 97.778 45 1 0 1 45 47254782 47254738 7.510000e-11 78.7
17 TraesCS5B01G391000 chr6B 97.778 45 0 1 1 45 20485027 20485070 2.700000e-10 76.8
18 TraesCS5B01G391000 chr3A 79.182 269 48 8 1754 2018 436414523 436414787 2.000000e-41 180.0
19 TraesCS5B01G391000 chr3A 80.435 230 41 4 1732 1958 111840099 111839871 3.350000e-39 172.0
20 TraesCS5B01G391000 chr3A 80.087 231 38 8 1733 1958 46732969 46733196 5.600000e-37 165.0
21 TraesCS5B01G391000 chr3A 82.051 195 33 2 1765 1958 739741978 739741785 5.600000e-37 165.0
22 TraesCS5B01G391000 chr6A 79.654 231 36 10 1734 1958 36071015 36071240 3.370000e-34 156.0
23 TraesCS5B01G391000 chr3D 79.386 228 42 5 1792 2017 3191475 3191251 3.370000e-34 156.0
24 TraesCS5B01G391000 chr3D 88.393 112 8 5 25 134 556068359 556068467 2.040000e-26 130.0
25 TraesCS5B01G391000 chr4D 93.548 93 6 0 42 134 20132176 20132084 3.400000e-29 139.0
26 TraesCS5B01G391000 chr4D 92.391 92 7 0 43 134 27385855 27385764 5.680000e-27 132.0
27 TraesCS5B01G391000 chr7B 94.318 88 5 0 47 134 705945516 705945429 4.390000e-28 135.0
28 TraesCS5B01G391000 chr7B 87.387 111 13 1 31 140 383509599 383509489 2.640000e-25 126.0
29 TraesCS5B01G391000 chr6D 92.553 94 6 1 42 134 16007659 16007752 1.580000e-27 134.0
30 TraesCS5B01G391000 chr6D 97.778 45 0 1 1 45 16244704 16244747 2.700000e-10 76.8
31 TraesCS5B01G391000 chr1D 92.473 93 7 0 42 134 300831792 300831884 1.580000e-27 134.0
32 TraesCS5B01G391000 chr2D 87.719 114 10 4 25 134 568270904 568271017 2.040000e-26 130.0
33 TraesCS5B01G391000 chr7D 100.000 43 0 0 1 43 506877870 506877912 2.090000e-11 80.5
34 TraesCS5B01G391000 chr7D 95.556 45 2 0 1 45 169989895 169989939 3.490000e-09 73.1
35 TraesCS5B01G391000 chr1B 97.778 45 1 0 1 45 112420556 112420512 7.510000e-11 78.7
36 TraesCS5B01G391000 chr1B 97.778 45 1 0 1 45 112440052 112440008 7.510000e-11 78.7
37 TraesCS5B01G391000 chr1B 97.778 45 0 1 1 45 112466631 112466588 2.700000e-10 76.8


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 TraesCS5B01G391000 chr5B 570173946 570176476 2530 True 2038.5 3567 100.000 1 2531 2 chr5B.!!$R2 2530
1 TraesCS5B01G391000 chr5B 570152014 570152677 663 True 817.0 817 88.856 861 1536 1 chr5B.!!$R1 675
2 TraesCS5B01G391000 chr5D 463402060 463404020 1960 True 2266.0 2266 87.954 604 2531 1 chr5D.!!$R3 1927
3 TraesCS5B01G391000 chr5D 463374670 463375338 668 True 854.0 854 89.736 861 1536 1 chr5D.!!$R2 675
4 TraesCS5B01G391000 chr5A 583627011 583628149 1138 True 1447.0 1447 89.870 608 1737 1 chr5A.!!$R3 1129
5 TraesCS5B01G391000 chr5A 583615067 583615738 671 True 830.0 830 89.051 861 1536 1 chr5A.!!$R2 675
6 TraesCS5B01G391000 chr5A 583608019 583608715 696 True 826.0 826 88.028 830 1536 1 chr5A.!!$R1 706
7 TraesCS5B01G391000 chrUn 295599695 295600358 663 True 817.0 817 88.856 861 1536 1 chrUn.!!$R1 675
8 TraesCS5B01G391000 chrUn 310497152 310497815 663 False 817.0 817 88.856 861 1536 1 chrUn.!!$F1 675

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
112 113 0.032678 CGGATCATTAGCAGACGCCT 59.967 55.0 0.0 0.0 39.83 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1817 0.038892 GCACCTGCTTGTGTTCATGG 60.039 55.0 7.79 0.0 38.52 3.66 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
47 48 9.981114 ACTTTTTCTAAAAATACATGAACTGGG 57.019 29.630 0.00 0.00 37.27 4.45
48 49 9.423061 CTTTTTCTAAAAATACATGAACTGGGG 57.577 33.333 0.00 0.00 37.27 4.96
49 50 6.524101 TTCTAAAAATACATGAACTGGGGC 57.476 37.500 0.00 0.00 0.00 5.80
50 51 5.575157 TCTAAAAATACATGAACTGGGGCA 58.425 37.500 0.00 0.00 0.00 5.36
51 52 4.806640 AAAAATACATGAACTGGGGCAG 57.193 40.909 0.00 0.00 37.52 4.85
52 53 1.767759 AATACATGAACTGGGGCAGC 58.232 50.000 0.00 0.00 34.37 5.25
53 54 0.625316 ATACATGAACTGGGGCAGCA 59.375 50.000 0.00 0.00 34.37 4.41
54 55 0.625316 TACATGAACTGGGGCAGCAT 59.375 50.000 0.00 0.00 34.37 3.79
55 56 0.968901 ACATGAACTGGGGCAGCATG 60.969 55.000 0.00 0.00 37.69 4.06
66 67 2.898840 CAGCATGCTAGTGGGCCG 60.899 66.667 22.19 0.77 0.00 6.13
67 68 4.181010 AGCATGCTAGTGGGCCGG 62.181 66.667 21.21 0.00 0.00 6.13
85 86 3.277602 CCCATGCTAGCAGCGCTG 61.278 66.667 32.83 32.83 46.26 5.18
100 101 2.898840 CTGCAAGCGCCGGATCAT 60.899 61.111 5.05 0.00 37.32 2.45
101 102 2.438254 TGCAAGCGCCGGATCATT 60.438 55.556 5.05 0.00 37.32 2.57
102 103 1.153269 TGCAAGCGCCGGATCATTA 60.153 52.632 5.05 0.00 37.32 1.90
103 104 1.159713 TGCAAGCGCCGGATCATTAG 61.160 55.000 5.05 0.00 37.32 1.73
104 105 1.571460 CAAGCGCCGGATCATTAGC 59.429 57.895 5.05 0.00 0.00 3.09
105 106 1.146041 AAGCGCCGGATCATTAGCA 59.854 52.632 5.05 0.00 0.00 3.49
106 107 0.882042 AAGCGCCGGATCATTAGCAG 60.882 55.000 5.05 0.00 0.00 4.24
107 108 1.300931 GCGCCGGATCATTAGCAGA 60.301 57.895 5.05 0.00 0.00 4.26
108 109 1.560860 GCGCCGGATCATTAGCAGAC 61.561 60.000 5.05 0.00 0.00 3.51
109 110 1.278172 CGCCGGATCATTAGCAGACG 61.278 60.000 5.05 0.00 0.00 4.18
110 111 1.560860 GCCGGATCATTAGCAGACGC 61.561 60.000 5.05 0.00 38.99 5.19
111 112 0.946221 CCGGATCATTAGCAGACGCC 60.946 60.000 0.00 0.00 39.83 5.68
112 113 0.032678 CGGATCATTAGCAGACGCCT 59.967 55.000 0.00 0.00 39.83 5.52
113 114 1.506493 GGATCATTAGCAGACGCCTG 58.494 55.000 0.00 0.00 43.22 4.85
131 132 2.108566 CAGCGCTGCATAGGAGCT 59.891 61.111 26.68 0.00 40.21 4.09
132 133 1.955157 CAGCGCTGCATAGGAGCTC 60.955 63.158 26.68 4.71 37.72 4.09
133 134 2.664518 GCGCTGCATAGGAGCTCC 60.665 66.667 26.22 26.22 34.03 4.70
135 136 1.445095 CGCTGCATAGGAGCTCCTT 59.555 57.895 39.23 23.53 46.09 3.36
136 137 0.179062 CGCTGCATAGGAGCTCCTTT 60.179 55.000 39.23 28.99 46.09 3.11
137 138 1.745141 CGCTGCATAGGAGCTCCTTTT 60.745 52.381 39.23 24.27 46.09 2.27
138 139 2.373224 GCTGCATAGGAGCTCCTTTTT 58.627 47.619 39.23 21.75 46.09 1.94
158 159 5.667539 TTTTTCCCGATAAATGGAATGCA 57.332 34.783 0.00 0.00 40.22 3.96
159 160 5.667539 TTTTCCCGATAAATGGAATGCAA 57.332 34.783 0.00 0.00 40.22 4.08
160 161 4.647424 TTCCCGATAAATGGAATGCAAC 57.353 40.909 0.00 0.00 35.75 4.17
161 162 2.955660 TCCCGATAAATGGAATGCAACC 59.044 45.455 6.38 6.38 0.00 3.77
162 163 2.287547 CCCGATAAATGGAATGCAACCG 60.288 50.000 0.00 0.00 0.00 4.44
163 164 2.287547 CCGATAAATGGAATGCAACCGG 60.288 50.000 0.00 0.00 0.00 5.28
164 165 2.357637 CGATAAATGGAATGCAACCGGT 59.642 45.455 0.00 0.00 0.00 5.28
165 166 3.548014 CGATAAATGGAATGCAACCGGTC 60.548 47.826 8.04 0.00 0.00 4.79
166 167 1.626686 AAATGGAATGCAACCGGTCA 58.373 45.000 8.04 1.99 0.00 4.02
167 168 1.626686 AATGGAATGCAACCGGTCAA 58.373 45.000 8.04 0.00 0.00 3.18
168 169 1.851304 ATGGAATGCAACCGGTCAAT 58.149 45.000 8.04 0.00 0.00 2.57
169 170 1.173043 TGGAATGCAACCGGTCAATC 58.827 50.000 8.04 5.04 0.00 2.67
170 171 0.098728 GGAATGCAACCGGTCAATCG 59.901 55.000 8.04 0.00 0.00 3.34
171 172 1.083489 GAATGCAACCGGTCAATCGA 58.917 50.000 8.04 0.00 0.00 3.59
172 173 1.670811 GAATGCAACCGGTCAATCGAT 59.329 47.619 8.04 0.00 0.00 3.59
173 174 1.016627 ATGCAACCGGTCAATCGATG 58.983 50.000 8.04 0.60 0.00 3.84
174 175 0.321210 TGCAACCGGTCAATCGATGT 60.321 50.000 8.04 0.00 0.00 3.06
175 176 0.373716 GCAACCGGTCAATCGATGTC 59.626 55.000 8.04 0.00 0.00 3.06
176 177 1.720805 CAACCGGTCAATCGATGTCA 58.279 50.000 8.04 0.00 0.00 3.58
177 178 2.073056 CAACCGGTCAATCGATGTCAA 58.927 47.619 8.04 0.00 0.00 3.18
178 179 2.465860 ACCGGTCAATCGATGTCAAA 57.534 45.000 0.00 0.00 0.00 2.69
179 180 2.773487 ACCGGTCAATCGATGTCAAAA 58.227 42.857 0.00 0.00 0.00 2.44
180 181 2.742053 ACCGGTCAATCGATGTCAAAAG 59.258 45.455 0.00 0.00 0.00 2.27
181 182 3.000041 CCGGTCAATCGATGTCAAAAGA 59.000 45.455 0.00 0.00 0.00 2.52
182 183 3.435327 CCGGTCAATCGATGTCAAAAGAA 59.565 43.478 0.00 0.00 0.00 2.52
183 184 4.083537 CCGGTCAATCGATGTCAAAAGAAA 60.084 41.667 0.00 0.00 0.00 2.52
184 185 5.448438 CGGTCAATCGATGTCAAAAGAAAA 58.552 37.500 0.00 0.00 0.00 2.29
185 186 5.912396 CGGTCAATCGATGTCAAAAGAAAAA 59.088 36.000 0.00 0.00 0.00 1.94
204 205 5.508200 AAAAACACAGTCAATCGCCTTAA 57.492 34.783 0.00 0.00 0.00 1.85
205 206 5.705609 AAAACACAGTCAATCGCCTTAAT 57.294 34.783 0.00 0.00 0.00 1.40
206 207 6.811253 AAAACACAGTCAATCGCCTTAATA 57.189 33.333 0.00 0.00 0.00 0.98
207 208 6.811253 AAACACAGTCAATCGCCTTAATAA 57.189 33.333 0.00 0.00 0.00 1.40
208 209 6.811253 AACACAGTCAATCGCCTTAATAAA 57.189 33.333 0.00 0.00 0.00 1.40
209 210 7.391148 AACACAGTCAATCGCCTTAATAAAT 57.609 32.000 0.00 0.00 0.00 1.40
210 211 6.785191 ACACAGTCAATCGCCTTAATAAATG 58.215 36.000 0.00 0.00 0.00 2.32
211 212 6.597672 ACACAGTCAATCGCCTTAATAAATGA 59.402 34.615 0.00 0.00 0.00 2.57
212 213 7.120579 ACACAGTCAATCGCCTTAATAAATGAA 59.879 33.333 0.00 0.00 0.00 2.57
213 214 7.429340 CACAGTCAATCGCCTTAATAAATGAAC 59.571 37.037 0.00 0.00 0.00 3.18
214 215 7.120579 ACAGTCAATCGCCTTAATAAATGAACA 59.879 33.333 0.00 0.00 0.00 3.18
215 216 7.967854 CAGTCAATCGCCTTAATAAATGAACAA 59.032 33.333 0.00 0.00 0.00 2.83
216 217 8.519526 AGTCAATCGCCTTAATAAATGAACAAA 58.480 29.630 0.00 0.00 0.00 2.83
217 218 9.134734 GTCAATCGCCTTAATAAATGAACAAAA 57.865 29.630 0.00 0.00 0.00 2.44
218 219 9.698309 TCAATCGCCTTAATAAATGAACAAAAA 57.302 25.926 0.00 0.00 0.00 1.94
236 237 3.857638 AAAAACACCGGTCGATTGC 57.142 47.368 2.59 0.00 0.00 3.56
237 238 0.312729 AAAAACACCGGTCGATTGCC 59.687 50.000 2.59 0.00 0.00 4.52
245 246 3.857038 GTCGATTGCCGCCCCCTA 61.857 66.667 0.00 0.00 38.37 3.53
246 247 2.847234 TCGATTGCCGCCCCCTAT 60.847 61.111 0.00 0.00 38.37 2.57
247 248 2.113139 CGATTGCCGCCCCCTATT 59.887 61.111 0.00 0.00 0.00 1.73
248 249 2.260869 CGATTGCCGCCCCCTATTG 61.261 63.158 0.00 0.00 0.00 1.90
249 250 2.521708 ATTGCCGCCCCCTATTGC 60.522 61.111 0.00 0.00 0.00 3.56
250 251 4.832088 TTGCCGCCCCCTATTGCC 62.832 66.667 0.00 0.00 0.00 4.52
253 254 4.586235 CCGCCCCCTATTGCCAGG 62.586 72.222 0.00 0.00 35.26 4.45
254 255 3.488569 CGCCCCCTATTGCCAGGA 61.489 66.667 0.00 0.00 38.00 3.86
255 256 2.517919 GCCCCCTATTGCCAGGAG 59.482 66.667 0.00 0.00 38.00 3.69
256 257 2.386935 GCCCCCTATTGCCAGGAGT 61.387 63.158 0.00 0.00 38.00 3.85
257 258 1.839894 CCCCCTATTGCCAGGAGTC 59.160 63.158 0.00 0.00 38.00 3.36
258 259 1.709994 CCCCCTATTGCCAGGAGTCC 61.710 65.000 0.00 0.00 38.00 3.85
259 260 0.695803 CCCCTATTGCCAGGAGTCCT 60.696 60.000 5.62 5.62 38.00 3.85
260 261 0.761802 CCCTATTGCCAGGAGTCCTC 59.238 60.000 9.36 0.00 38.00 3.71
261 262 0.390860 CCTATTGCCAGGAGTCCTCG 59.609 60.000 9.36 3.49 38.00 4.63
262 263 1.115467 CTATTGCCAGGAGTCCTCGT 58.885 55.000 9.36 0.00 0.00 4.18
263 264 0.824109 TATTGCCAGGAGTCCTCGTG 59.176 55.000 9.36 9.47 43.03 4.35
264 265 2.527951 ATTGCCAGGAGTCCTCGTGC 62.528 60.000 9.36 12.98 42.32 5.34
265 266 3.695606 GCCAGGAGTCCTCGTGCA 61.696 66.667 9.36 0.00 42.32 4.57
266 267 3.059982 CCAGGAGTCCTCGTGCAA 58.940 61.111 9.36 0.00 42.32 4.08
267 268 1.371183 CCAGGAGTCCTCGTGCAAA 59.629 57.895 9.36 0.00 42.32 3.68
268 269 0.951040 CCAGGAGTCCTCGTGCAAAC 60.951 60.000 9.36 0.00 42.32 2.93
269 270 0.951040 CAGGAGTCCTCGTGCAAACC 60.951 60.000 9.36 0.00 38.41 3.27
270 271 1.122019 AGGAGTCCTCGTGCAAACCT 61.122 55.000 5.62 0.00 0.00 3.50
271 272 0.250338 GGAGTCCTCGTGCAAACCTT 60.250 55.000 0.41 0.00 0.00 3.50
272 273 1.149148 GAGTCCTCGTGCAAACCTTC 58.851 55.000 0.00 0.00 0.00 3.46
273 274 0.759346 AGTCCTCGTGCAAACCTTCT 59.241 50.000 0.00 0.00 0.00 2.85
274 275 1.968493 AGTCCTCGTGCAAACCTTCTA 59.032 47.619 0.00 0.00 0.00 2.10
275 276 2.028930 AGTCCTCGTGCAAACCTTCTAG 60.029 50.000 0.00 0.00 0.00 2.43
654 662 3.285484 TCGGTCATACCTTCACCTACTC 58.715 50.000 0.00 0.00 35.66 2.59
730 741 2.548057 CTCTCTCTCTCTCACGCATACC 59.452 54.545 0.00 0.00 0.00 2.73
809 820 6.711645 ACACGGCCAGAAATACTAAACTAAAA 59.288 34.615 2.24 0.00 0.00 1.52
819 830 8.999905 AAATACTAAACTAAAAACTGGGGACA 57.000 30.769 0.00 0.00 39.59 4.02
833 844 1.152830 GGACAGGCCACCCAGAAAA 59.847 57.895 5.01 0.00 36.34 2.29
857 868 0.476771 AAGGACCCAACAACCACGAT 59.523 50.000 0.00 0.00 0.00 3.73
875 886 3.181483 ACGATTCGCCGTTAAATAGACCT 60.181 43.478 5.86 0.00 40.17 3.85
880 891 5.368256 TCGCCGTTAAATAGACCTATCTC 57.632 43.478 0.00 0.00 36.29 2.75
881 892 5.068636 TCGCCGTTAAATAGACCTATCTCT 58.931 41.667 0.00 0.00 36.29 3.10
882 893 5.048921 TCGCCGTTAAATAGACCTATCTCTG 60.049 44.000 0.00 0.00 36.29 3.35
883 894 5.048921 CGCCGTTAAATAGACCTATCTCTGA 60.049 44.000 0.00 0.00 36.29 3.27
884 895 6.514541 CGCCGTTAAATAGACCTATCTCTGAA 60.515 42.308 0.00 0.00 36.29 3.02
900 911 1.267806 CTGAACTGCACCATTGGACAC 59.732 52.381 10.37 0.00 0.00 3.67
908 919 2.503331 CACCATTGGACACACAAGCTA 58.497 47.619 10.37 0.00 33.23 3.32
919 930 1.676006 ACACAAGCTACACAAACCTGC 59.324 47.619 0.00 0.00 0.00 4.85
920 931 1.675483 CACAAGCTACACAAACCTGCA 59.325 47.619 0.00 0.00 0.00 4.41
974 987 3.843422 TCAAACCACCAACATCCATTCT 58.157 40.909 0.00 0.00 0.00 2.40
1555 1580 1.523154 GCATCCTTGTTTCGTGCCCA 61.523 55.000 0.00 0.00 0.00 5.36
1565 1590 1.466025 TTCGTGCCCAGTCGGTACTT 61.466 55.000 0.00 0.00 44.68 2.24
1573 1598 3.618019 GCCCAGTCGGTACTTTGATTGTA 60.618 47.826 0.00 0.00 31.97 2.41
1574 1599 3.930848 CCCAGTCGGTACTTTGATTGTAC 59.069 47.826 0.00 0.00 39.43 2.90
1575 1600 4.322499 CCCAGTCGGTACTTTGATTGTACT 60.322 45.833 0.00 0.00 39.89 2.73
1576 1601 4.625742 CCAGTCGGTACTTTGATTGTACTG 59.374 45.833 6.54 6.54 44.34 2.74
1594 1619 8.836268 TTGTACTGTAATTCGTTAACTGGATT 57.164 30.769 3.71 6.62 0.00 3.01
1595 1620 9.926158 TTGTACTGTAATTCGTTAACTGGATTA 57.074 29.630 3.71 5.72 0.00 1.75
1602 1627 9.874215 GTAATTCGTTAACTGGATTAATAAGCC 57.126 33.333 0.00 0.00 35.23 4.35
1603 1628 8.747538 AATTCGTTAACTGGATTAATAAGCCT 57.252 30.769 8.86 0.00 37.96 4.58
1604 1629 7.548196 TTCGTTAACTGGATTAATAAGCCTG 57.452 36.000 11.75 11.75 41.11 4.85
1658 1689 5.916883 CCAATAGCTTATTTGCATTTCGAGG 59.083 40.000 0.00 0.00 34.99 4.63
1673 1704 6.128553 GCATTTCGAGGGTATGTGTATATGTG 60.129 42.308 0.00 0.00 0.00 3.21
1681 1712 6.542370 AGGGTATGTGTATATGTGTTTTGAGC 59.458 38.462 0.00 0.00 0.00 4.26
1722 1753 6.780198 AATAATGGATTCCCCTAACTAGCA 57.220 37.500 0.00 0.00 35.38 3.49
1725 1756 3.460825 TGGATTCCCCTAACTAGCAACT 58.539 45.455 0.00 0.00 35.38 3.16
1731 1762 2.618045 CCCCTAACTAGCAACTGTTGGG 60.618 54.545 21.01 11.24 42.18 4.12
1758 1789 5.471556 TTAACCCAGTACAATCGAAGTCA 57.528 39.130 0.00 0.00 0.00 3.41
1762 1793 3.172050 CCAGTACAATCGAAGTCACTCG 58.828 50.000 0.00 0.00 40.25 4.18
1783 1814 3.796717 CGCATACACGAACATACACTCAT 59.203 43.478 0.00 0.00 34.06 2.90
1786 1817 5.276868 GCATACACGAACATACACTCATTCC 60.277 44.000 0.00 0.00 0.00 3.01
1787 1818 3.596214 ACACGAACATACACTCATTCCC 58.404 45.455 0.00 0.00 0.00 3.97
1794 1825 5.178096 ACATACACTCATTCCCATGAACA 57.822 39.130 0.00 0.00 39.04 3.18
1797 1828 3.831323 ACACTCATTCCCATGAACACAA 58.169 40.909 0.00 0.00 39.04 3.33
1801 1832 2.821378 TCATTCCCATGAACACAAGCAG 59.179 45.455 0.00 0.00 36.41 4.24
1804 1835 0.599558 CCCATGAACACAAGCAGGTG 59.400 55.000 6.26 6.26 44.35 4.00
1807 1838 0.670162 ATGAACACAAGCAGGTGCAC 59.330 50.000 8.80 8.80 45.16 4.57
1813 1844 0.474184 ACAAGCAGGTGCACCTTACT 59.526 50.000 36.06 30.26 46.09 2.24
1825 1856 2.432510 GCACCTTACTCCTATGAGCACT 59.567 50.000 0.00 0.00 42.74 4.40
1839 1870 0.600557 AGCACTTCCGAGACACTGAG 59.399 55.000 0.00 0.00 0.00 3.35
1852 1883 2.042831 ACTGAGCCGGCAAAGCATC 61.043 57.895 31.54 16.99 0.00 3.91
1864 1895 5.450965 CCGGCAAAGCATCTTGAGATTTTAT 60.451 40.000 0.00 0.00 31.21 1.40
1865 1896 5.457799 CGGCAAAGCATCTTGAGATTTTATG 59.542 40.000 0.00 0.00 31.21 1.90
1874 1905 6.968131 TCTTGAGATTTTATGAAGTCACCG 57.032 37.500 0.00 0.00 0.00 4.94
1879 1910 4.943705 AGATTTTATGAAGTCACCGCATGT 59.056 37.500 0.00 0.00 0.00 3.21
1884 1915 1.639298 GAAGTCACCGCATGTGCCTC 61.639 60.000 0.00 0.00 45.03 4.70
1914 1945 0.966920 GGAACGTCTCCTTCCACTGA 59.033 55.000 8.87 0.00 41.61 3.41
1916 1947 2.405172 GAACGTCTCCTTCCACTGAAC 58.595 52.381 0.00 0.00 0.00 3.18
1920 1951 2.545113 CGTCTCCTTCCACTGAACGAAA 60.545 50.000 0.00 0.00 0.00 3.46
1935 1966 0.097674 CGAAAATCGCCAGAAGCCTG 59.902 55.000 0.00 0.00 38.78 4.85
1944 1976 2.669391 CGCCAGAAGCCTGAAACAAATC 60.669 50.000 0.00 0.00 43.02 2.17
1945 1977 2.353109 GCCAGAAGCCTGAAACAAATCC 60.353 50.000 0.00 0.00 43.02 3.01
1947 1979 3.321682 CCAGAAGCCTGAAACAAATCCAA 59.678 43.478 0.00 0.00 43.02 3.53
1950 1982 5.993441 CAGAAGCCTGAAACAAATCCAAAAT 59.007 36.000 0.00 0.00 43.02 1.82
1958 1990 6.597614 TGAAACAAATCCAAAATTAATGCGC 58.402 32.000 0.00 0.00 0.00 6.09
1959 1991 6.203530 TGAAACAAATCCAAAATTAATGCGCA 59.796 30.769 14.96 14.96 0.00 6.09
1960 1992 6.740411 AACAAATCCAAAATTAATGCGCAT 57.260 29.167 19.28 19.28 0.00 4.73
1964 1996 7.710044 ACAAATCCAAAATTAATGCGCATATCA 59.290 29.630 25.61 11.02 0.00 2.15
1977 2009 5.809464 TGCGCATATCAATGTCAAGTTTAG 58.191 37.500 5.66 0.00 35.38 1.85
1978 2010 5.584251 TGCGCATATCAATGTCAAGTTTAGA 59.416 36.000 5.66 0.00 35.38 2.10
1981 2013 6.907212 CGCATATCAATGTCAAGTTTAGAACC 59.093 38.462 0.00 0.00 35.38 3.62
1985 2017 9.739276 ATATCAATGTCAAGTTTAGAACCTGAA 57.261 29.630 0.00 0.00 33.92 3.02
2007 2040 0.181350 CAGGTGGGCTAGGGATTCAC 59.819 60.000 0.00 0.00 0.00 3.18
2015 2048 1.414550 GCTAGGGATTCACTGTCCTCC 59.585 57.143 0.00 0.00 36.00 4.30
2018 2051 3.715648 AGGGATTCACTGTCCTCCTAT 57.284 47.619 0.00 0.00 36.00 2.57
2020 2053 3.051803 AGGGATTCACTGTCCTCCTATCA 60.052 47.826 0.00 0.00 36.00 2.15
2021 2054 3.070302 GGGATTCACTGTCCTCCTATCAC 59.930 52.174 0.00 0.00 36.00 3.06
2022 2055 3.706594 GGATTCACTGTCCTCCTATCACA 59.293 47.826 0.00 0.00 32.85 3.58
2023 2056 4.162320 GGATTCACTGTCCTCCTATCACAA 59.838 45.833 0.00 0.00 32.85 3.33
2046 2088 4.457949 AGTTGGTTCACGATTATTGGGTTC 59.542 41.667 0.00 0.00 0.00 3.62
2047 2089 4.295141 TGGTTCACGATTATTGGGTTCT 57.705 40.909 0.00 0.00 0.00 3.01
2048 2090 5.423704 TGGTTCACGATTATTGGGTTCTA 57.576 39.130 0.00 0.00 0.00 2.10
2049 2091 5.996644 TGGTTCACGATTATTGGGTTCTAT 58.003 37.500 0.00 0.00 0.00 1.98
2112 2180 8.815565 TCTTCTCTCTATTCATTACAGTGAGT 57.184 34.615 0.00 0.00 33.64 3.41
2142 2210 3.746492 CCACTAGTTATAGCGGCCAAATC 59.254 47.826 2.24 0.00 31.66 2.17
2149 2217 0.179094 TAGCGGCCAAATCTGTACCG 60.179 55.000 2.24 0.00 41.18 4.02
2157 2225 0.107897 AAATCTGTACCGCGGCATGA 60.108 50.000 28.58 18.66 0.00 3.07
2159 2227 1.676678 ATCTGTACCGCGGCATGACT 61.677 55.000 28.58 7.06 0.00 3.41
2180 2248 1.490490 GGCCTCTTGATGACCATGGTA 59.510 52.381 19.80 6.95 0.00 3.25
2195 2263 3.754965 CATGGTAATGGTCTATGGTGGG 58.245 50.000 0.00 0.00 0.00 4.61
2197 2265 3.465832 TGGTAATGGTCTATGGTGGGAA 58.534 45.455 0.00 0.00 0.00 3.97
2198 2266 4.051478 TGGTAATGGTCTATGGTGGGAAT 58.949 43.478 0.00 0.00 0.00 3.01
2199 2267 4.104102 TGGTAATGGTCTATGGTGGGAATC 59.896 45.833 0.00 0.00 0.00 2.52
2204 2272 1.760613 GTCTATGGTGGGAATCCGTCA 59.239 52.381 0.00 0.00 35.24 4.35
2253 2321 1.564622 CGTGAAGCACAGACAACCG 59.435 57.895 0.00 0.00 33.40 4.44
2256 2324 2.954753 GAAGCACAGACAACCGCGG 61.955 63.158 26.86 26.86 0.00 6.46
2261 2329 1.153628 ACAGACAACCGCGGCTATC 60.154 57.895 28.58 19.84 0.00 2.08
2280 2349 6.090129 GCTATCGAAGATATGTCCTCAAGAC 58.910 44.000 0.00 0.00 45.12 3.01
2287 2356 6.365970 AGATATGTCCTCAAGACTGTGTTT 57.634 37.500 0.00 0.00 46.46 2.83
2289 2358 2.917933 TGTCCTCAAGACTGTGTTTGG 58.082 47.619 0.00 0.00 46.46 3.28
2291 2360 3.054728 TGTCCTCAAGACTGTGTTTGGAA 60.055 43.478 9.65 1.52 46.46 3.53
2305 2374 4.013050 TGTTTGGAACACACTTCATGTCA 58.987 39.130 0.00 0.00 40.64 3.58
2307 2376 2.849942 TGGAACACACTTCATGTCAGG 58.150 47.619 0.00 0.00 40.64 3.86
2313 2382 1.774254 ACACTTCATGTCAGGGGTGAA 59.226 47.619 14.77 3.33 36.54 3.18
2328 2397 2.361119 GGGTGAAAACCCTTGTTCTGAC 59.639 50.000 6.68 0.00 46.39 3.51
2342 2411 3.146847 GTTCTGACCTTTACTGGTTGGG 58.853 50.000 0.00 0.00 41.00 4.12
2345 2414 3.203487 TCTGACCTTTACTGGTTGGGTTT 59.797 43.478 0.00 0.00 41.00 3.27
2347 2416 4.721132 TGACCTTTACTGGTTGGGTTTAG 58.279 43.478 0.00 0.00 41.00 1.85
2351 2420 6.855667 ACCTTTACTGGTTGGGTTTAGTAAT 58.144 36.000 0.00 0.00 36.89 1.89
2358 2427 8.257602 ACTGGTTGGGTTTAGTAATGAAAAAT 57.742 30.769 0.00 0.00 0.00 1.82
2364 2433 8.263854 TGGGTTTAGTAATGAAAAATTTGGGA 57.736 30.769 0.00 0.00 0.00 4.37
2383 2452 6.494893 TGGGACATTATTTTCTTGAAGACG 57.505 37.500 0.00 0.00 0.00 4.18
2388 2457 7.534239 GGACATTATTTTCTTGAAGACGTTGTC 59.466 37.037 0.00 3.37 0.00 3.18
2391 2460 7.780008 TTATTTTCTTGAAGACGTTGTCTCA 57.220 32.000 0.00 0.00 42.59 3.27
2396 2465 1.792367 TGAAGACGTTGTCTCATTGCG 59.208 47.619 0.00 0.00 42.59 4.85
2426 2495 2.036733 CACCTTAGTTGGTTGGTCTCGA 59.963 50.000 0.00 0.00 38.45 4.04
2429 2498 3.318017 CTTAGTTGGTTGGTCTCGACTG 58.682 50.000 0.00 0.00 0.00 3.51
2433 2502 0.673985 TGGTTGGTCTCGACTGTCAG 59.326 55.000 8.73 0.00 0.00 3.51
2464 2533 6.760440 ATCCTTATCTTGGTCATCATGAGT 57.240 37.500 0.09 0.00 33.81 3.41
2468 2537 3.354948 TCTTGGTCATCATGAGTTGGG 57.645 47.619 0.09 0.00 0.00 4.12
2504 2573 1.276421 GTGAGCAAGTCTAGCCCTTCA 59.724 52.381 0.00 0.00 0.00 3.02
2520 2589 2.653890 CTTCATGAAGGTGTTGTTGCG 58.346 47.619 25.14 0.00 34.87 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.981114 CCCAGTTCATGTATTTTTAGAAAAAGT 57.019 29.630 6.36 0.00 40.78 2.66
22 23 9.423061 CCCCAGTTCATGTATTTTTAGAAAAAG 57.577 33.333 6.36 0.00 40.78 2.27
23 24 7.875554 GCCCCAGTTCATGTATTTTTAGAAAAA 59.124 33.333 2.82 2.82 41.59 1.94
24 25 7.015682 TGCCCCAGTTCATGTATTTTTAGAAAA 59.984 33.333 0.00 0.00 0.00 2.29
25 26 6.495181 TGCCCCAGTTCATGTATTTTTAGAAA 59.505 34.615 0.00 0.00 0.00 2.52
26 27 6.013379 TGCCCCAGTTCATGTATTTTTAGAA 58.987 36.000 0.00 0.00 0.00 2.10
27 28 5.575157 TGCCCCAGTTCATGTATTTTTAGA 58.425 37.500 0.00 0.00 0.00 2.10
28 29 5.679638 GCTGCCCCAGTTCATGTATTTTTAG 60.680 44.000 0.00 0.00 33.43 1.85
29 30 4.159506 GCTGCCCCAGTTCATGTATTTTTA 59.840 41.667 0.00 0.00 33.43 1.52
30 31 3.055891 GCTGCCCCAGTTCATGTATTTTT 60.056 43.478 0.00 0.00 33.43 1.94
31 32 2.497273 GCTGCCCCAGTTCATGTATTTT 59.503 45.455 0.00 0.00 33.43 1.82
32 33 2.102578 GCTGCCCCAGTTCATGTATTT 58.897 47.619 0.00 0.00 33.43 1.40
33 34 1.005805 TGCTGCCCCAGTTCATGTATT 59.994 47.619 0.00 0.00 33.43 1.89
34 35 0.625316 TGCTGCCCCAGTTCATGTAT 59.375 50.000 0.00 0.00 33.43 2.29
35 36 0.625316 ATGCTGCCCCAGTTCATGTA 59.375 50.000 0.00 0.00 33.43 2.29
36 37 0.968901 CATGCTGCCCCAGTTCATGT 60.969 55.000 0.00 0.00 31.83 3.21
37 38 1.813859 CATGCTGCCCCAGTTCATG 59.186 57.895 0.00 0.00 33.43 3.07
38 39 2.056223 GCATGCTGCCCCAGTTCAT 61.056 57.895 11.37 0.00 37.42 2.57
39 40 1.851065 TAGCATGCTGCCCCAGTTCA 61.851 55.000 30.42 2.54 46.52 3.18
40 41 1.077501 TAGCATGCTGCCCCAGTTC 60.078 57.895 30.42 0.00 46.52 3.01
41 42 1.077212 CTAGCATGCTGCCCCAGTT 60.077 57.895 30.42 2.70 46.52 3.16
42 43 2.304056 ACTAGCATGCTGCCCCAGT 61.304 57.895 30.42 21.18 46.52 4.00
43 44 1.822613 CACTAGCATGCTGCCCCAG 60.823 63.158 30.42 20.49 46.52 4.45
44 45 2.273123 CACTAGCATGCTGCCCCA 59.727 61.111 30.42 8.82 46.52 4.96
45 46 2.517875 CCACTAGCATGCTGCCCC 60.518 66.667 30.42 0.00 46.52 5.80
46 47 2.517875 CCCACTAGCATGCTGCCC 60.518 66.667 30.42 0.00 46.52 5.36
47 48 3.214845 GCCCACTAGCATGCTGCC 61.215 66.667 30.42 7.77 46.52 4.85
48 49 3.214845 GGCCCACTAGCATGCTGC 61.215 66.667 30.42 22.78 45.46 5.25
49 50 2.898840 CGGCCCACTAGCATGCTG 60.899 66.667 30.42 20.80 0.00 4.41
50 51 4.181010 CCGGCCCACTAGCATGCT 62.181 66.667 25.99 25.99 0.00 3.79
68 69 3.277602 CAGCGCTGCTAGCATGGG 61.278 66.667 26.68 19.72 42.58 4.00
83 84 1.159713 TAATGATCCGGCGCTTGCAG 61.160 55.000 7.64 0.00 41.71 4.41
84 85 1.153269 TAATGATCCGGCGCTTGCA 60.153 52.632 7.64 0.00 41.71 4.08
85 86 1.571460 CTAATGATCCGGCGCTTGC 59.429 57.895 7.64 0.00 38.11 4.01
86 87 1.159713 TGCTAATGATCCGGCGCTTG 61.160 55.000 7.64 0.00 0.00 4.01
87 88 0.882042 CTGCTAATGATCCGGCGCTT 60.882 55.000 7.64 0.00 0.00 4.68
88 89 1.301244 CTGCTAATGATCCGGCGCT 60.301 57.895 7.64 0.00 0.00 5.92
89 90 1.300931 TCTGCTAATGATCCGGCGC 60.301 57.895 0.00 0.00 0.00 6.53
90 91 1.278172 CGTCTGCTAATGATCCGGCG 61.278 60.000 0.00 0.00 0.00 6.46
91 92 1.560860 GCGTCTGCTAATGATCCGGC 61.561 60.000 0.00 0.00 38.39 6.13
92 93 0.946221 GGCGTCTGCTAATGATCCGG 60.946 60.000 0.00 0.00 42.25 5.14
93 94 0.032678 AGGCGTCTGCTAATGATCCG 59.967 55.000 0.00 0.00 42.25 4.18
94 95 1.506493 CAGGCGTCTGCTAATGATCC 58.494 55.000 3.01 0.00 42.25 3.36
114 115 1.955157 GAGCTCCTATGCAGCGCTG 60.955 63.158 32.83 32.83 42.14 5.18
115 116 2.420890 GAGCTCCTATGCAGCGCT 59.579 61.111 2.64 2.64 42.14 5.92
116 117 2.664518 GGAGCTCCTATGCAGCGC 60.665 66.667 26.25 0.00 42.14 5.92
117 118 3.136750 AGGAGCTCCTATGCAGCG 58.863 61.111 34.40 0.00 46.48 5.18
136 137 5.667539 TGCATTCCATTTATCGGGAAAAA 57.332 34.783 0.00 0.00 45.63 1.94
137 138 5.415221 GTTGCATTCCATTTATCGGGAAAA 58.585 37.500 0.00 0.00 45.63 2.29
138 139 4.142049 GGTTGCATTCCATTTATCGGGAAA 60.142 41.667 0.00 0.00 45.63 3.13
139 140 3.383185 GGTTGCATTCCATTTATCGGGAA 59.617 43.478 0.00 0.00 46.48 3.97
140 141 2.955660 GGTTGCATTCCATTTATCGGGA 59.044 45.455 0.00 0.00 0.00 5.14
141 142 2.287547 CGGTTGCATTCCATTTATCGGG 60.288 50.000 8.76 0.00 0.00 5.14
142 143 2.287547 CCGGTTGCATTCCATTTATCGG 60.288 50.000 0.00 0.00 0.00 4.18
143 144 2.357637 ACCGGTTGCATTCCATTTATCG 59.642 45.455 0.00 0.00 0.00 2.92
144 145 3.380004 TGACCGGTTGCATTCCATTTATC 59.620 43.478 9.42 0.00 0.00 1.75
145 146 3.360867 TGACCGGTTGCATTCCATTTAT 58.639 40.909 9.42 0.00 0.00 1.40
146 147 2.796557 TGACCGGTTGCATTCCATTTA 58.203 42.857 9.42 0.00 0.00 1.40
147 148 1.626686 TGACCGGTTGCATTCCATTT 58.373 45.000 9.42 0.00 0.00 2.32
148 149 1.626686 TTGACCGGTTGCATTCCATT 58.373 45.000 9.42 0.00 0.00 3.16
149 150 1.750778 GATTGACCGGTTGCATTCCAT 59.249 47.619 9.42 0.00 0.00 3.41
150 151 1.173043 GATTGACCGGTTGCATTCCA 58.827 50.000 9.42 0.00 0.00 3.53
151 152 0.098728 CGATTGACCGGTTGCATTCC 59.901 55.000 9.42 0.00 0.00 3.01
152 153 1.083489 TCGATTGACCGGTTGCATTC 58.917 50.000 9.42 8.28 0.00 2.67
153 154 1.401552 CATCGATTGACCGGTTGCATT 59.598 47.619 9.42 0.00 0.00 3.56
154 155 1.016627 CATCGATTGACCGGTTGCAT 58.983 50.000 9.42 0.24 0.00 3.96
155 156 0.321210 ACATCGATTGACCGGTTGCA 60.321 50.000 9.42 0.00 0.00 4.08
156 157 0.373716 GACATCGATTGACCGGTTGC 59.626 55.000 9.42 0.00 0.00 4.17
157 158 1.720805 TGACATCGATTGACCGGTTG 58.279 50.000 9.42 3.04 0.00 3.77
158 159 2.465860 TTGACATCGATTGACCGGTT 57.534 45.000 9.42 0.00 0.00 4.44
159 160 2.465860 TTTGACATCGATTGACCGGT 57.534 45.000 6.92 6.92 0.00 5.28
160 161 3.000041 TCTTTTGACATCGATTGACCGG 59.000 45.455 0.00 0.00 0.00 5.28
161 162 4.661993 TTCTTTTGACATCGATTGACCG 57.338 40.909 0.00 0.00 0.00 4.79
182 183 5.508200 TTAAGGCGATTGACTGTGTTTTT 57.492 34.783 0.00 0.00 29.56 1.94
183 184 5.705609 ATTAAGGCGATTGACTGTGTTTT 57.294 34.783 0.00 0.00 29.56 2.43
184 185 6.811253 TTATTAAGGCGATTGACTGTGTTT 57.189 33.333 0.00 0.00 29.56 2.83
185 186 6.811253 TTTATTAAGGCGATTGACTGTGTT 57.189 33.333 0.00 0.00 29.56 3.32
186 187 6.597672 TCATTTATTAAGGCGATTGACTGTGT 59.402 34.615 0.00 0.00 29.56 3.72
187 188 7.015226 TCATTTATTAAGGCGATTGACTGTG 57.985 36.000 0.00 0.00 29.56 3.66
188 189 7.120579 TGTTCATTTATTAAGGCGATTGACTGT 59.879 33.333 0.00 0.00 29.56 3.55
189 190 7.471721 TGTTCATTTATTAAGGCGATTGACTG 58.528 34.615 0.00 0.00 29.56 3.51
190 191 7.624360 TGTTCATTTATTAAGGCGATTGACT 57.376 32.000 0.00 0.00 31.31 3.41
191 192 8.682128 TTTGTTCATTTATTAAGGCGATTGAC 57.318 30.769 0.00 0.00 0.00 3.18
192 193 9.698309 TTTTTGTTCATTTATTAAGGCGATTGA 57.302 25.926 0.00 0.00 0.00 2.57
218 219 0.312729 GGCAATCGACCGGTGTTTTT 59.687 50.000 14.63 0.00 0.00 1.94
219 220 1.953772 GGCAATCGACCGGTGTTTT 59.046 52.632 14.63 0.00 0.00 2.43
220 221 3.663202 GGCAATCGACCGGTGTTT 58.337 55.556 14.63 3.04 0.00 2.83
229 230 2.448582 AATAGGGGGCGGCAATCGA 61.449 57.895 12.47 0.00 42.43 3.59
230 231 2.113139 AATAGGGGGCGGCAATCG 59.887 61.111 12.47 0.00 42.76 3.34
231 232 2.564721 GCAATAGGGGGCGGCAATC 61.565 63.158 12.47 0.00 0.00 2.67
232 233 2.521708 GCAATAGGGGGCGGCAAT 60.522 61.111 12.47 0.00 0.00 3.56
233 234 4.832088 GGCAATAGGGGGCGGCAA 62.832 66.667 12.47 0.00 0.00 4.52
236 237 4.586235 CCTGGCAATAGGGGGCGG 62.586 72.222 0.00 0.00 34.06 6.13
237 238 3.482232 CTCCTGGCAATAGGGGGCG 62.482 68.421 0.00 0.00 38.42 6.13
238 239 2.344878 GACTCCTGGCAATAGGGGGC 62.345 65.000 5.85 0.00 42.97 5.80
239 240 1.709994 GGACTCCTGGCAATAGGGGG 61.710 65.000 5.85 0.00 42.97 5.40
240 241 0.695803 AGGACTCCTGGCAATAGGGG 60.696 60.000 0.00 0.00 44.32 4.79
241 242 0.761802 GAGGACTCCTGGCAATAGGG 59.238 60.000 0.93 0.00 38.42 3.53
242 243 0.390860 CGAGGACTCCTGGCAATAGG 59.609 60.000 0.93 0.00 39.29 2.57
243 244 1.115467 ACGAGGACTCCTGGCAATAG 58.885 55.000 0.93 0.00 32.43 1.73
244 245 0.824109 CACGAGGACTCCTGGCAATA 59.176 55.000 0.93 0.00 32.43 1.90
245 246 1.599047 CACGAGGACTCCTGGCAAT 59.401 57.895 0.93 0.00 32.43 3.56
246 247 3.059982 CACGAGGACTCCTGGCAA 58.940 61.111 0.93 0.00 32.43 4.52
247 248 3.695606 GCACGAGGACTCCTGGCA 61.696 66.667 0.93 0.00 32.43 4.92
248 249 2.731691 TTTGCACGAGGACTCCTGGC 62.732 60.000 0.93 4.27 32.43 4.85
249 250 0.951040 GTTTGCACGAGGACTCCTGG 60.951 60.000 0.93 3.60 35.43 4.45
250 251 0.951040 GGTTTGCACGAGGACTCCTG 60.951 60.000 0.93 0.00 31.76 3.86
251 252 1.122019 AGGTTTGCACGAGGACTCCT 61.122 55.000 0.00 0.00 36.03 3.69
252 253 0.250338 AAGGTTTGCACGAGGACTCC 60.250 55.000 0.00 0.00 0.00 3.85
253 254 1.149148 GAAGGTTTGCACGAGGACTC 58.851 55.000 0.00 0.00 0.00 3.36
254 255 0.759346 AGAAGGTTTGCACGAGGACT 59.241 50.000 0.00 0.00 0.00 3.85
255 256 2.338500 CTAGAAGGTTTGCACGAGGAC 58.662 52.381 0.00 0.00 0.00 3.85
256 257 2.743636 CTAGAAGGTTTGCACGAGGA 57.256 50.000 0.00 0.00 0.00 3.71
600 601 0.393537 AGTTAGGTGATGCAGGCTGC 60.394 55.000 31.91 31.91 45.29 5.25
601 602 2.988010 TAGTTAGGTGATGCAGGCTG 57.012 50.000 10.94 10.94 0.00 4.85
602 603 3.007398 GCTATAGTTAGGTGATGCAGGCT 59.993 47.826 0.84 0.00 0.00 4.58
654 662 1.795768 TGAACAGTAAGAAGCTGCGG 58.204 50.000 0.00 0.00 37.47 5.69
730 741 4.794248 TCACATTCGTCTTGTTCTTGTG 57.206 40.909 0.00 0.00 35.49 3.33
809 820 3.580319 GGTGGCCTGTCCCCAGTT 61.580 66.667 3.32 0.00 36.95 3.16
819 830 0.482446 TGACATTTTCTGGGTGGCCT 59.518 50.000 3.32 0.00 0.00 5.19
820 831 1.273327 CTTGACATTTTCTGGGTGGCC 59.727 52.381 0.00 0.00 0.00 5.36
821 832 1.273327 CCTTGACATTTTCTGGGTGGC 59.727 52.381 0.00 0.00 0.00 5.01
822 833 2.558359 GTCCTTGACATTTTCTGGGTGG 59.442 50.000 0.00 0.00 32.09 4.61
824 835 2.490902 GGGTCCTTGACATTTTCTGGGT 60.491 50.000 0.00 0.00 33.68 4.51
825 836 2.171003 GGGTCCTTGACATTTTCTGGG 58.829 52.381 0.00 0.00 33.68 4.45
833 844 1.216678 TGGTTGTTGGGTCCTTGACAT 59.783 47.619 0.00 0.00 33.68 3.06
857 868 5.533903 AGAGATAGGTCTATTTAACGGCGAA 59.466 40.000 16.62 0.00 33.97 4.70
875 886 3.519107 TCCAATGGTGCAGTTCAGAGATA 59.481 43.478 0.00 0.00 0.00 1.98
880 891 1.267806 GTGTCCAATGGTGCAGTTCAG 59.732 52.381 0.00 0.00 0.00 3.02
881 892 1.317613 GTGTCCAATGGTGCAGTTCA 58.682 50.000 0.00 0.00 0.00 3.18
882 893 1.001378 GTGTGTCCAATGGTGCAGTTC 60.001 52.381 0.00 0.00 0.00 3.01
883 894 1.032014 GTGTGTCCAATGGTGCAGTT 58.968 50.000 0.00 0.00 0.00 3.16
884 895 0.106769 TGTGTGTCCAATGGTGCAGT 60.107 50.000 0.00 0.00 0.00 4.40
900 911 1.675483 TGCAGGTTTGTGTAGCTTGTG 59.325 47.619 0.00 0.00 0.00 3.33
908 919 1.103398 GGAGCTGTGCAGGTTTGTGT 61.103 55.000 5.34 0.00 39.57 3.72
919 930 0.891373 TCTTCTTCCGAGGAGCTGTG 59.109 55.000 0.00 0.00 0.00 3.66
920 931 1.633774 TTCTTCTTCCGAGGAGCTGT 58.366 50.000 0.00 0.00 0.00 4.40
1263 1288 1.695893 CGCTGACGTACATGCCTTGG 61.696 60.000 0.00 0.00 33.53 3.61
1299 1324 1.897137 CATGGCCATGAGCAGCGAT 60.897 57.895 37.84 0.02 46.50 4.58
1555 1580 5.464030 ACAGTACAATCAAAGTACCGACT 57.536 39.130 0.00 0.00 42.09 4.18
1565 1590 8.714179 CCAGTTAACGAATTACAGTACAATCAA 58.286 33.333 0.00 0.00 0.00 2.57
1576 1601 9.874215 GGCTTATTAATCCAGTTAACGAATTAC 57.126 33.333 0.00 0.00 35.23 1.89
1586 1611 6.152831 GGAACAACAGGCTTATTAATCCAGTT 59.847 38.462 0.00 2.32 31.07 3.16
1587 1612 5.652452 GGAACAACAGGCTTATTAATCCAGT 59.348 40.000 0.00 0.00 0.00 4.00
1588 1613 5.652014 TGGAACAACAGGCTTATTAATCCAG 59.348 40.000 0.00 0.00 31.92 3.86
1589 1614 5.575157 TGGAACAACAGGCTTATTAATCCA 58.425 37.500 0.00 8.84 31.92 3.41
1658 1689 7.279981 TCAGCTCAAAACACATATACACATACC 59.720 37.037 0.00 0.00 0.00 2.73
1673 1704 9.651913 TTATTTCCCAATAAATCAGCTCAAAAC 57.348 29.630 0.00 0.00 32.79 2.43
1691 1722 8.812972 GTTAGGGGAATCCATTATTTATTTCCC 58.187 37.037 9.56 9.56 45.55 3.97
1740 1771 3.512680 GAGTGACTTCGATTGTACTGGG 58.487 50.000 0.00 0.00 0.00 4.45
1741 1772 3.172050 CGAGTGACTTCGATTGTACTGG 58.828 50.000 0.00 0.00 43.03 4.00
1750 1781 1.465187 CGTGTATGCGAGTGACTTCGA 60.465 52.381 8.26 0.00 43.03 3.71
1752 1783 2.257974 TCGTGTATGCGAGTGACTTC 57.742 50.000 0.00 0.00 35.83 3.01
1758 1789 3.119602 AGTGTATGTTCGTGTATGCGAGT 60.120 43.478 0.00 0.00 42.10 4.18
1762 1793 5.276868 GGAATGAGTGTATGTTCGTGTATGC 60.277 44.000 0.00 0.00 0.00 3.14
1783 1814 1.133513 ACCTGCTTGTGTTCATGGGAA 60.134 47.619 0.00 0.00 0.00 3.97
1786 1817 0.038892 GCACCTGCTTGTGTTCATGG 60.039 55.000 7.79 0.00 38.52 3.66
1787 1818 0.669619 TGCACCTGCTTGTGTTCATG 59.330 50.000 7.79 0.00 42.66 3.07
1801 1832 2.483889 GCTCATAGGAGTAAGGTGCACC 60.484 54.545 29.22 29.22 43.37 5.01
1804 1835 2.432510 AGTGCTCATAGGAGTAAGGTGC 59.567 50.000 6.23 0.00 43.37 5.01
1807 1838 3.243569 CGGAAGTGCTCATAGGAGTAAGG 60.244 52.174 6.23 0.00 43.37 2.69
1809 1840 3.628008 TCGGAAGTGCTCATAGGAGTAA 58.372 45.455 6.23 0.00 43.37 2.24
1813 1844 2.025155 GTCTCGGAAGTGCTCATAGGA 58.975 52.381 0.00 0.00 0.00 2.94
1825 1856 2.636412 CCGGCTCAGTGTCTCGGAA 61.636 63.158 12.82 0.00 42.94 4.30
1839 1870 1.138247 CTCAAGATGCTTTGCCGGC 59.862 57.895 22.73 22.73 0.00 6.13
1852 1883 5.122239 TGCGGTGACTTCATAAAATCTCAAG 59.878 40.000 0.00 0.00 0.00 3.02
1874 1905 3.857854 CGACTGCGAGGCACATGC 61.858 66.667 0.00 0.00 40.82 4.06
1884 1915 4.695231 ACGTTCCCGTCGACTGCG 62.695 66.667 14.70 12.25 46.28 5.18
1900 1931 2.814280 TTCGTTCAGTGGAAGGAGAC 57.186 50.000 0.00 0.00 45.50 3.36
1907 1938 1.153353 GGCGATTTTCGTTCAGTGGA 58.847 50.000 0.00 0.00 42.81 4.02
1908 1939 0.871722 TGGCGATTTTCGTTCAGTGG 59.128 50.000 0.00 0.00 42.81 4.00
1911 1942 2.726066 GCTTCTGGCGATTTTCGTTCAG 60.726 50.000 12.63 12.63 42.81 3.02
1914 1945 0.521735 GGCTTCTGGCGATTTTCGTT 59.478 50.000 0.00 0.00 42.81 3.85
1916 1947 0.097674 CAGGCTTCTGGCGATTTTCG 59.902 55.000 0.00 0.00 43.89 3.46
1920 1951 1.168714 GTTTCAGGCTTCTGGCGATT 58.831 50.000 0.00 0.00 44.18 3.34
1935 1966 6.597614 TGCGCATTAATTTTGGATTTGTTTC 58.402 32.000 5.66 0.00 0.00 2.78
1944 1976 7.169476 TGACATTGATATGCGCATTAATTTTGG 59.831 33.333 30.42 15.44 35.03 3.28
1945 1977 8.063339 TGACATTGATATGCGCATTAATTTTG 57.937 30.769 30.42 20.00 35.03 2.44
1947 1979 7.922278 ACTTGACATTGATATGCGCATTAATTT 59.078 29.630 30.42 18.29 35.03 1.82
1950 1982 6.375945 ACTTGACATTGATATGCGCATTAA 57.624 33.333 30.42 20.61 35.03 1.40
1958 1990 9.166173 TCAGGTTCTAAACTTGACATTGATATG 57.834 33.333 1.03 0.00 41.79 1.78
1959 1991 9.739276 TTCAGGTTCTAAACTTGACATTGATAT 57.261 29.630 4.37 0.00 45.59 1.63
1960 1992 8.999431 GTTCAGGTTCTAAACTTGACATTGATA 58.001 33.333 4.37 0.00 45.59 2.15
1964 1996 5.535030 GGGTTCAGGTTCTAAACTTGACATT 59.465 40.000 4.37 0.00 45.59 2.71
1998 2030 3.051803 TGATAGGAGGACAGTGAATCCCT 60.052 47.826 0.00 0.66 36.86 4.20
2000 2032 3.706594 TGTGATAGGAGGACAGTGAATCC 59.293 47.826 0.00 0.77 36.38 3.01
2007 2040 3.261897 ACCAACTTGTGATAGGAGGACAG 59.738 47.826 0.00 0.00 0.00 3.51
2015 2048 5.862924 AATCGTGAACCAACTTGTGATAG 57.137 39.130 0.00 0.00 0.00 2.08
2018 2051 5.049060 CCAATAATCGTGAACCAACTTGTGA 60.049 40.000 0.00 0.00 0.00 3.58
2020 2053 4.217550 CCCAATAATCGTGAACCAACTTGT 59.782 41.667 0.00 0.00 0.00 3.16
2021 2054 4.217550 ACCCAATAATCGTGAACCAACTTG 59.782 41.667 0.00 0.00 0.00 3.16
2022 2055 4.403734 ACCCAATAATCGTGAACCAACTT 58.596 39.130 0.00 0.00 0.00 2.66
2023 2056 4.028993 ACCCAATAATCGTGAACCAACT 57.971 40.909 0.00 0.00 0.00 3.16
2046 2088 7.761249 GGAGAAATTGTTTGGTTTCATCCATAG 59.239 37.037 0.00 0.00 36.92 2.23
2047 2089 7.310361 GGGAGAAATTGTTTGGTTTCATCCATA 60.310 37.037 13.27 0.00 36.92 2.74
2048 2090 6.466812 GGAGAAATTGTTTGGTTTCATCCAT 58.533 36.000 0.00 0.00 36.92 3.41
2049 2091 5.221621 GGGAGAAATTGTTTGGTTTCATCCA 60.222 40.000 13.27 0.00 36.92 3.41
2126 2194 3.497262 GGTACAGATTTGGCCGCTATAAC 59.503 47.826 0.00 0.00 0.00 1.89
2142 2210 2.167219 CAGTCATGCCGCGGTACAG 61.167 63.158 28.70 18.74 0.00 2.74
2157 2225 1.064906 CATGGTCATCAAGAGGCCAGT 60.065 52.381 5.01 0.00 32.28 4.00
2159 2227 0.256752 CCATGGTCATCAAGAGGCCA 59.743 55.000 5.01 0.00 0.00 5.36
2180 2248 2.106511 CGGATTCCCACCATAGACCATT 59.893 50.000 0.00 0.00 0.00 3.16
2191 2259 0.320374 TGAGTGTGACGGATTCCCAC 59.680 55.000 5.42 5.42 0.00 4.61
2192 2260 1.207089 GATGAGTGTGACGGATTCCCA 59.793 52.381 0.00 0.00 0.00 4.37
2195 2263 1.929836 GCAGATGAGTGTGACGGATTC 59.070 52.381 0.00 0.00 0.00 2.52
2197 2265 1.189752 AGCAGATGAGTGTGACGGAT 58.810 50.000 0.00 0.00 0.00 4.18
2198 2266 1.745653 CTAGCAGATGAGTGTGACGGA 59.254 52.381 0.00 0.00 0.00 4.69
2199 2267 1.800655 GCTAGCAGATGAGTGTGACGG 60.801 57.143 10.63 0.00 0.00 4.79
2204 2272 4.823276 GCGCTAGCAGATGAGTGT 57.177 55.556 16.45 0.00 44.35 3.55
2231 2299 1.159713 TTGTCTGTGCTTCACGCCAG 61.160 55.000 0.00 0.00 37.14 4.85
2233 2301 1.279840 GTTGTCTGTGCTTCACGCC 59.720 57.895 0.00 0.00 37.14 5.68
2235 2303 1.564622 CGGTTGTCTGTGCTTCACG 59.435 57.895 0.00 0.00 37.14 4.35
2245 2313 1.940883 TTCGATAGCCGCGGTTGTCT 61.941 55.000 29.97 20.08 38.37 3.41
2253 2321 2.164624 AGGACATATCTTCGATAGCCGC 59.835 50.000 0.00 0.00 38.37 6.53
2256 2324 6.072175 AGTCTTGAGGACATATCTTCGATAGC 60.072 42.308 0.00 0.00 46.72 2.97
2261 2329 5.039984 CACAGTCTTGAGGACATATCTTCG 58.960 45.833 0.00 0.00 46.72 3.79
2287 2356 2.487086 CCCTGACATGAAGTGTGTTCCA 60.487 50.000 0.00 0.00 42.36 3.53
2289 2358 2.154462 CCCCTGACATGAAGTGTGTTC 58.846 52.381 0.00 0.00 42.36 3.18
2291 2360 1.140312 ACCCCTGACATGAAGTGTGT 58.860 50.000 0.00 0.00 42.36 3.72
2313 2382 4.887655 CAGTAAAGGTCAGAACAAGGGTTT 59.112 41.667 0.00 0.00 37.36 3.27
2318 2387 4.275936 CCAACCAGTAAAGGTCAGAACAAG 59.724 45.833 0.00 0.00 42.25 3.16
2328 2397 6.943718 TCATTACTAAACCCAACCAGTAAAGG 59.056 38.462 0.00 0.00 37.12 3.11
2358 2427 7.013846 ACGTCTTCAAGAAAATAATGTCCCAAA 59.986 33.333 0.00 0.00 0.00 3.28
2364 2433 8.154649 AGACAACGTCTTCAAGAAAATAATGT 57.845 30.769 0.00 0.00 40.28 2.71
2383 2452 3.262420 AGTACATCCGCAATGAGACAAC 58.738 45.455 3.24 0.00 38.83 3.32
2388 2457 2.159043 AGGTGAGTACATCCGCAATGAG 60.159 50.000 3.24 0.00 38.83 2.90
2391 2460 3.451178 ACTAAGGTGAGTACATCCGCAAT 59.549 43.478 0.00 0.00 0.00 3.56
2396 2465 4.820894 ACCAACTAAGGTGAGTACATCC 57.179 45.455 0.00 0.00 41.30 3.51
2426 2495 9.388506 CAAGATAAGGATTTTCATACTGACAGT 57.611 33.333 13.68 13.68 0.00 3.55
2429 2498 8.738645 ACCAAGATAAGGATTTTCATACTGAC 57.261 34.615 0.00 0.00 0.00 3.51
2433 2502 9.342308 TGATGACCAAGATAAGGATTTTCATAC 57.658 33.333 0.00 0.00 0.00 2.39
2438 2507 8.057623 ACTCATGATGACCAAGATAAGGATTTT 58.942 33.333 0.00 0.00 0.00 1.82
2443 2512 5.530171 CCAACTCATGATGACCAAGATAAGG 59.470 44.000 0.00 0.00 0.00 2.69
2450 2519 1.075212 TGCCCAACTCATGATGACCAA 59.925 47.619 0.00 0.00 0.00 3.67
2460 2529 1.374125 CGTCGTCATGCCCAACTCA 60.374 57.895 0.00 0.00 0.00 3.41
2464 2533 2.358125 CACCGTCGTCATGCCCAA 60.358 61.111 0.00 0.00 0.00 4.12
2504 2573 1.608590 CTTCCGCAACAACACCTTCAT 59.391 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.