Multiple sequence alignment - TraesCS7A01G441900

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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 TraesCS7A01G441900 chr7A 100.000 3052 0 0 1 3052 635859352 635862403 0.000000e+00 5637.0
1 TraesCS7A01G441900 chr7A 89.404 1878 119 34 298 2152 636126206 636128026 0.000000e+00 2292.0
2 TraesCS7A01G441900 chr7A 87.663 1378 110 21 794 2160 636628860 636630188 0.000000e+00 1548.0
3 TraesCS7A01G441900 chr7A 83.232 495 29 22 306 757 636628295 636628778 3.660000e-109 405.0
4 TraesCS7A01G441900 chr7A 87.330 221 20 7 2388 2605 636206655 636206870 2.350000e-61 246.0
5 TraesCS7A01G441900 chr7A 87.805 205 19 6 2282 2480 636141469 636141673 5.090000e-58 235.0
6 TraesCS7A01G441900 chr7A 85.973 221 23 7 2388 2605 636144783 636144998 2.370000e-56 230.0
7 TraesCS7A01G441900 chr7A 87.826 115 11 3 2603 2715 636141813 636141926 6.870000e-27 132.0
8 TraesCS7A01G441900 chr7A 87.143 70 5 2 12 77 636126089 636126158 3.260000e-10 76.8
9 TraesCS7A01G441900 chr7A 96.970 33 1 0 2603 2635 636145041 636145073 4.250000e-04 56.5
10 TraesCS7A01G441900 chr7A 96.970 33 1 0 2603 2635 636206913 636206945 4.250000e-04 56.5
11 TraesCS7A01G441900 chr7D 89.054 2494 195 35 298 2754 550462279 550464731 0.000000e+00 3022.0
12 TraesCS7A01G441900 chr7D 88.457 1854 109 35 312 2121 550552367 550554159 0.000000e+00 2141.0
13 TraesCS7A01G441900 chr7D 89.084 1255 90 15 912 2160 550800374 550801587 0.000000e+00 1515.0
14 TraesCS7A01G441900 chr7D 88.810 1126 91 15 298 1401 550642545 550643657 0.000000e+00 1349.0
15 TraesCS7A01G441900 chr7D 87.704 675 60 13 2100 2759 550554170 550554836 0.000000e+00 765.0
16 TraesCS7A01G441900 chr7D 92.857 252 18 0 2801 3052 550466113 550466364 1.730000e-97 366.0
17 TraesCS7A01G441900 chr7D 92.460 252 19 0 2801 3052 550555454 550555705 8.040000e-96 361.0
18 TraesCS7A01G441900 chr7D 92.941 85 5 1 2650 2733 550684711 550684795 4.130000e-24 122.0
19 TraesCS7A01G441900 chr7D 92.982 57 2 2 91 147 550462228 550462282 7.010000e-12 82.4
20 TraesCS7A01G441900 chr7D 92.982 57 2 2 91 147 550642494 550642548 7.010000e-12 82.4
21 TraesCS7A01G441900 chr7D 97.561 41 0 1 11 51 550462194 550462233 5.460000e-08 69.4
22 TraesCS7A01G441900 chr7D 97.561 41 0 1 11 51 550642460 550642499 5.460000e-08 69.4
23 TraesCS7A01G441900 chr7D 90.698 43 2 2 306 348 550799832 550799872 4.250000e-04 56.5
24 TraesCS7A01G441900 chr7B 91.472 1372 99 10 794 2160 595007243 595008601 0.000000e+00 1869.0
25 TraesCS7A01G441900 chr7B 87.881 1378 121 12 794 2160 595080361 595081703 0.000000e+00 1578.0
26 TraesCS7A01G441900 chr7B 87.038 1381 110 25 794 2160 595307144 595308469 0.000000e+00 1495.0
27 TraesCS7A01G441900 chr7B 92.355 654 45 2 1511 2159 595172829 595173482 0.000000e+00 926.0
28 TraesCS7A01G441900 chr7B 86.203 819 60 21 447 1219 595165966 595166777 0.000000e+00 837.0
29 TraesCS7A01G441900 chr7B 90.526 475 23 10 296 751 595006684 595007155 2.600000e-170 608.0
30 TraesCS7A01G441900 chr7B 86.087 345 36 10 2271 2605 595081693 595082035 8.040000e-96 361.0
31 TraesCS7A01G441900 chr7B 86.325 351 23 12 424 757 595079931 595080273 2.890000e-95 359.0
32 TraesCS7A01G441900 chr7B 92.414 145 10 1 614 757 595306704 595306848 3.990000e-49 206.0
33 TraesCS7A01G441900 chr7B 89.024 164 13 1 1298 1461 595166773 595166931 6.670000e-47 198.0
34 TraesCS7A01G441900 chr7B 81.595 163 12 10 2271 2416 595008591 595008752 5.350000e-23 119.0
35 TraesCS7A01G441900 chr7B 84.746 118 4 5 29 132 595006565 595006682 4.160000e-19 106.0
36 TraesCS7A01G441900 chr7B 78.462 130 17 4 13 134 595165655 595165781 1.170000e-09 75.0
37 TraesCS7A01G441900 chr7B 97.561 41 1 0 755 795 595306866 595306906 1.520000e-08 71.3
38 TraesCS7A01G441900 chr4B 82.415 762 97 26 1332 2075 14054982 14055724 5.550000e-177 630.0
39 TraesCS7A01G441900 chr4B 84.783 138 13 5 2333 2463 14055780 14055916 6.870000e-27 132.0
40 TraesCS7A01G441900 chr3D 86.232 138 15 4 2333 2466 551432649 551432786 2.450000e-31 147.0
41 TraesCS7A01G441900 chr6D 83.784 74 11 1 140 213 103046443 103046371 5.460000e-08 69.4
42 TraesCS7A01G441900 chr6D 97.059 34 1 0 101 134 77171810 77171843 1.180000e-04 58.4


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 TraesCS7A01G441900 chr7A 635859352 635862403 3051 False 5637.000000 5637 100.000000 1 3052 1 chr7A.!!$F1 3051
1 TraesCS7A01G441900 chr7A 636126089 636128026 1937 False 1184.400000 2292 88.273500 12 2152 2 chr7A.!!$F2 2140
2 TraesCS7A01G441900 chr7A 636628295 636630188 1893 False 976.500000 1548 85.447500 306 2160 2 chr7A.!!$F5 1854
3 TraesCS7A01G441900 chr7D 550552367 550555705 3338 False 1089.000000 2141 89.540333 312 3052 3 chr7D.!!$F3 2740
4 TraesCS7A01G441900 chr7D 550462194 550466364 4170 False 884.950000 3022 93.113500 11 3052 4 chr7D.!!$F2 3041
5 TraesCS7A01G441900 chr7D 550799832 550801587 1755 False 785.750000 1515 89.891000 306 2160 2 chr7D.!!$F5 1854
6 TraesCS7A01G441900 chr7D 550642460 550643657 1197 False 500.266667 1349 93.117667 11 1401 3 chr7D.!!$F4 1390
7 TraesCS7A01G441900 chr7B 595172829 595173482 653 False 926.000000 926 92.355000 1511 2159 1 chr7B.!!$F1 648
8 TraesCS7A01G441900 chr7B 595079931 595082035 2104 False 766.000000 1578 86.764333 424 2605 3 chr7B.!!$F3 2181
9 TraesCS7A01G441900 chr7B 595006565 595008752 2187 False 675.500000 1869 87.084750 29 2416 4 chr7B.!!$F2 2387
10 TraesCS7A01G441900 chr7B 595306704 595308469 1765 False 590.766667 1495 92.337667 614 2160 3 chr7B.!!$F5 1546
11 TraesCS7A01G441900 chr7B 595165655 595166931 1276 False 370.000000 837 84.563000 13 1461 3 chr7B.!!$F4 1448
12 TraesCS7A01G441900 chr4B 14054982 14055916 934 False 381.000000 630 83.599000 1332 2463 2 chr4B.!!$F1 1131

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
505 690 0.10852 TACCCCAAGATTCGTGCGTC 60.109 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 3105 0.170561 CTCTACCGTTCGACACCCTG 59.829 60.0 0.0 0.0 0.0 4.45 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
46 117 6.814954 ACTAGCTCATTCATTCCCTTCTAA 57.185 37.500 0.00 0.00 0.00 2.10
50 121 7.968014 AGCTCATTCATTCCCTTCTAATTTT 57.032 32.000 0.00 0.00 0.00 1.82
51 122 7.779073 AGCTCATTCATTCCCTTCTAATTTTG 58.221 34.615 0.00 0.00 0.00 2.44
53 124 7.704047 GCTCATTCATTCCCTTCTAATTTTGAC 59.296 37.037 0.00 0.00 0.00 3.18
54 125 8.066612 TCATTCATTCCCTTCTAATTTTGACC 57.933 34.615 0.00 0.00 0.00 4.02
55 126 6.850752 TTCATTCCCTTCTAATTTTGACCC 57.149 37.500 0.00 0.00 0.00 4.46
56 127 5.269189 TCATTCCCTTCTAATTTTGACCCC 58.731 41.667 0.00 0.00 0.00 4.95
57 128 5.016245 TCATTCCCTTCTAATTTTGACCCCT 59.984 40.000 0.00 0.00 0.00 4.79
58 129 4.586306 TCCCTTCTAATTTTGACCCCTC 57.414 45.455 0.00 0.00 0.00 4.30
59 130 3.920197 TCCCTTCTAATTTTGACCCCTCA 59.080 43.478 0.00 0.00 0.00 3.86
60 131 4.544152 TCCCTTCTAATTTTGACCCCTCAT 59.456 41.667 0.00 0.00 0.00 2.90
61 132 4.889995 CCCTTCTAATTTTGACCCCTCATC 59.110 45.833 0.00 0.00 0.00 2.92
62 133 5.340360 CCCTTCTAATTTTGACCCCTCATCT 60.340 44.000 0.00 0.00 0.00 2.90
63 134 5.825151 CCTTCTAATTTTGACCCCTCATCTC 59.175 44.000 0.00 0.00 0.00 2.75
64 135 6.353429 CCTTCTAATTTTGACCCCTCATCTCT 60.353 42.308 0.00 0.00 0.00 3.10
65 136 7.147479 CCTTCTAATTTTGACCCCTCATCTCTA 60.147 40.741 0.00 0.00 0.00 2.43
66 137 7.125792 TCTAATTTTGACCCCTCATCTCTAC 57.874 40.000 0.00 0.00 0.00 2.59
67 138 3.887621 TTTTGACCCCTCATCTCTACG 57.112 47.619 0.00 0.00 0.00 3.51
68 139 2.526888 TTGACCCCTCATCTCTACGT 57.473 50.000 0.00 0.00 0.00 3.57
69 140 2.054232 TGACCCCTCATCTCTACGTC 57.946 55.000 0.00 0.00 0.00 4.34
70 141 1.564818 TGACCCCTCATCTCTACGTCT 59.435 52.381 0.00 0.00 0.00 4.18
71 142 2.775960 TGACCCCTCATCTCTACGTCTA 59.224 50.000 0.00 0.00 0.00 2.59
72 143 3.140623 GACCCCTCATCTCTACGTCTAC 58.859 54.545 0.00 0.00 0.00 2.59
73 144 2.144730 CCCCTCATCTCTACGTCTACG 58.855 57.143 0.00 0.04 46.33 3.51
74 145 1.532007 CCCTCATCTCTACGTCTACGC 59.468 57.143 1.74 0.00 44.43 4.42
75 146 2.485903 CCTCATCTCTACGTCTACGCT 58.514 52.381 1.74 0.00 44.43 5.07
76 147 2.873472 CCTCATCTCTACGTCTACGCTT 59.127 50.000 1.74 0.00 44.43 4.68
77 148 3.312973 CCTCATCTCTACGTCTACGCTTT 59.687 47.826 1.74 0.00 44.43 3.51
78 149 4.274421 TCATCTCTACGTCTACGCTTTG 57.726 45.455 1.74 0.00 44.43 2.77
79 150 3.688185 TCATCTCTACGTCTACGCTTTGT 59.312 43.478 1.74 0.00 44.43 2.83
80 151 3.736530 TCTCTACGTCTACGCTTTGTC 57.263 47.619 1.74 0.00 44.43 3.18
81 152 3.332919 TCTCTACGTCTACGCTTTGTCT 58.667 45.455 1.74 0.00 44.43 3.41
82 153 3.750130 TCTCTACGTCTACGCTTTGTCTT 59.250 43.478 1.74 0.00 44.43 3.01
83 154 4.931601 TCTCTACGTCTACGCTTTGTCTTA 59.068 41.667 1.74 0.00 44.43 2.10
84 155 4.962693 TCTACGTCTACGCTTTGTCTTAC 58.037 43.478 1.74 0.00 44.43 2.34
85 156 3.911661 ACGTCTACGCTTTGTCTTACT 57.088 42.857 1.74 0.00 44.43 2.24
86 157 5.869344 TCTACGTCTACGCTTTGTCTTACTA 59.131 40.000 1.74 0.00 44.43 1.82
87 158 5.557891 ACGTCTACGCTTTGTCTTACTAT 57.442 39.130 1.74 0.00 44.43 2.12
88 159 6.668541 ACGTCTACGCTTTGTCTTACTATA 57.331 37.500 1.74 0.00 44.43 1.31
89 160 7.256756 ACGTCTACGCTTTGTCTTACTATAT 57.743 36.000 1.74 0.00 44.43 0.86
90 161 7.701445 ACGTCTACGCTTTGTCTTACTATATT 58.299 34.615 1.74 0.00 44.43 1.28
91 162 8.830580 ACGTCTACGCTTTGTCTTACTATATTA 58.169 33.333 1.74 0.00 44.43 0.98
92 163 9.823098 CGTCTACGCTTTGTCTTACTATATTAT 57.177 33.333 0.00 0.00 0.00 1.28
149 220 9.774413 AAAAACGCCTAGCAGTAATATATACTT 57.226 29.630 0.00 0.00 0.00 2.24
150 221 8.983307 AAACGCCTAGCAGTAATATATACTTC 57.017 34.615 0.00 0.00 0.00 3.01
151 222 7.098074 ACGCCTAGCAGTAATATATACTTCC 57.902 40.000 0.00 0.00 0.00 3.46
152 223 6.890814 ACGCCTAGCAGTAATATATACTTCCT 59.109 38.462 0.00 0.00 0.00 3.36
153 224 7.067251 ACGCCTAGCAGTAATATATACTTCCTC 59.933 40.741 0.00 0.00 0.00 3.71
154 225 7.468906 CGCCTAGCAGTAATATATACTTCCTCC 60.469 44.444 0.00 0.00 0.00 4.30
155 226 7.468906 GCCTAGCAGTAATATATACTTCCTCCG 60.469 44.444 0.00 0.00 0.00 4.63
156 227 7.556996 CCTAGCAGTAATATATACTTCCTCCGT 59.443 40.741 0.00 0.00 0.00 4.69
157 228 7.778185 AGCAGTAATATATACTTCCTCCGTT 57.222 36.000 0.00 0.00 0.00 4.44
158 229 7.828712 AGCAGTAATATATACTTCCTCCGTTC 58.171 38.462 0.00 0.00 0.00 3.95
159 230 7.034397 GCAGTAATATATACTTCCTCCGTTCC 58.966 42.308 0.00 0.00 0.00 3.62
160 231 7.309621 GCAGTAATATATACTTCCTCCGTTCCA 60.310 40.741 0.00 0.00 0.00 3.53
161 232 8.582437 CAGTAATATATACTTCCTCCGTTCCAA 58.418 37.037 0.00 0.00 0.00 3.53
162 233 9.151177 AGTAATATATACTTCCTCCGTTCCAAA 57.849 33.333 0.00 0.00 0.00 3.28
163 234 9.420551 GTAATATATACTTCCTCCGTTCCAAAG 57.579 37.037 0.00 0.00 0.00 2.77
164 235 5.952347 ATATACTTCCTCCGTTCCAAAGT 57.048 39.130 0.00 0.00 34.70 2.66
165 236 8.716674 ATATATACTTCCTCCGTTCCAAAGTA 57.283 34.615 0.00 0.00 36.98 2.24
166 237 5.952347 ATACTTCCTCCGTTCCAAAGTAT 57.048 39.130 0.00 0.00 37.97 2.12
167 238 8.716674 ATATACTTCCTCCGTTCCAAAGTATA 57.283 34.615 12.90 12.90 43.79 1.47
168 239 5.750352 ACTTCCTCCGTTCCAAAGTATAA 57.250 39.130 0.00 0.00 0.00 0.98
169 240 5.731591 ACTTCCTCCGTTCCAAAGTATAAG 58.268 41.667 0.00 0.00 0.00 1.73
170 241 4.748277 TCCTCCGTTCCAAAGTATAAGG 57.252 45.455 0.00 0.00 0.00 2.69
171 242 3.118519 TCCTCCGTTCCAAAGTATAAGGC 60.119 47.826 0.00 0.00 0.00 4.35
172 243 3.118371 CCTCCGTTCCAAAGTATAAGGCT 60.118 47.826 0.00 0.00 0.00 4.58
173 244 4.514401 CTCCGTTCCAAAGTATAAGGCTT 58.486 43.478 4.58 4.58 0.00 4.35
174 245 4.913784 TCCGTTCCAAAGTATAAGGCTTT 58.086 39.130 4.45 0.00 36.70 3.51
176 247 4.412207 CGTTCCAAAGTATAAGGCTTTGC 58.588 43.478 4.45 0.00 46.69 3.68
177 248 4.083003 CGTTCCAAAGTATAAGGCTTTGCA 60.083 41.667 4.45 0.00 46.69 4.08
178 249 5.563867 CGTTCCAAAGTATAAGGCTTTGCAA 60.564 40.000 4.45 0.00 46.69 4.08
179 250 6.220201 GTTCCAAAGTATAAGGCTTTGCAAA 58.780 36.000 12.14 12.14 46.69 3.68
180 251 6.024552 TCCAAAGTATAAGGCTTTGCAAAG 57.975 37.500 30.70 30.70 46.69 2.77
181 252 5.772672 TCCAAAGTATAAGGCTTTGCAAAGA 59.227 36.000 37.14 20.07 46.69 2.52
182 253 6.437162 TCCAAAGTATAAGGCTTTGCAAAGAT 59.563 34.615 37.14 24.62 46.69 2.40
183 254 7.039082 TCCAAAGTATAAGGCTTTGCAAAGATT 60.039 33.333 37.14 29.93 46.69 2.40
184 255 7.603784 CCAAAGTATAAGGCTTTGCAAAGATTT 59.396 33.333 37.14 29.20 46.69 2.17
185 256 8.650714 CAAAGTATAAGGCTTTGCAAAGATTTC 58.349 33.333 37.14 22.96 43.86 2.17
186 257 7.466746 AGTATAAGGCTTTGCAAAGATTTCA 57.533 32.000 37.14 19.74 38.28 2.69
187 258 7.315890 AGTATAAGGCTTTGCAAAGATTTCAC 58.684 34.615 37.14 26.35 38.28 3.18
188 259 4.677673 AAGGCTTTGCAAAGATTTCACT 57.322 36.364 37.14 21.65 38.28 3.41
189 260 5.789643 AAGGCTTTGCAAAGATTTCACTA 57.210 34.783 37.14 1.51 38.28 2.74
190 261 5.990120 AGGCTTTGCAAAGATTTCACTAT 57.010 34.783 37.14 12.29 38.28 2.12
191 262 5.717119 AGGCTTTGCAAAGATTTCACTATG 58.283 37.500 37.14 12.11 38.28 2.23
192 263 5.477984 AGGCTTTGCAAAGATTTCACTATGA 59.522 36.000 37.14 0.28 38.28 2.15
193 264 6.015180 AGGCTTTGCAAAGATTTCACTATGAA 60.015 34.615 37.14 0.00 38.28 2.57
194 265 6.089954 GGCTTTGCAAAGATTTCACTATGAAC 59.910 38.462 37.14 16.80 35.67 3.18
195 266 6.865205 GCTTTGCAAAGATTTCACTATGAACT 59.135 34.615 37.14 0.00 35.67 3.01
196 267 8.023128 GCTTTGCAAAGATTTCACTATGAACTA 58.977 33.333 37.14 0.00 35.67 2.24
197 268 9.334693 CTTTGCAAAGATTTCACTATGAACTAC 57.665 33.333 31.24 0.00 35.67 2.73
198 269 7.977789 TGCAAAGATTTCACTATGAACTACA 57.022 32.000 0.00 0.00 35.89 2.74
199 270 8.565896 TGCAAAGATTTCACTATGAACTACAT 57.434 30.769 0.00 0.00 35.89 2.29
200 271 9.665719 TGCAAAGATTTCACTATGAACTACATA 57.334 29.630 0.00 0.00 35.89 2.29
201 272 9.922305 GCAAAGATTTCACTATGAACTACATAC 57.078 33.333 0.00 0.00 35.89 2.39
205 276 9.737427 AGATTTCACTATGAACTACATACGAAG 57.263 33.333 0.00 0.00 35.89 3.79
206 277 9.517609 GATTTCACTATGAACTACATACGAAGT 57.482 33.333 0.00 0.00 39.67 3.01
224 295 7.485418 ACGAAGTAAAATGTGTGAATGTACA 57.515 32.000 0.00 0.00 41.94 2.90
225 296 7.349711 ACGAAGTAAAATGTGTGAATGTACAC 58.650 34.615 0.00 5.93 45.53 2.90
226 297 7.225931 ACGAAGTAAAATGTGTGAATGTACACT 59.774 33.333 0.00 0.00 45.53 3.55
254 325 6.389830 TTTTGAGCATTGTGAATGTACACT 57.610 33.333 0.00 0.00 41.01 3.55
255 326 5.611796 TTGAGCATTGTGAATGTACACTC 57.388 39.130 0.00 0.00 41.01 3.51
256 327 4.898320 TGAGCATTGTGAATGTACACTCT 58.102 39.130 5.83 0.00 41.01 3.24
257 328 6.036577 TGAGCATTGTGAATGTACACTCTA 57.963 37.500 5.83 0.00 41.01 2.43
258 329 6.463360 TGAGCATTGTGAATGTACACTCTAA 58.537 36.000 5.83 1.88 41.01 2.10
259 330 6.934083 TGAGCATTGTGAATGTACACTCTAAA 59.066 34.615 5.83 0.71 41.01 1.85
260 331 7.118245 TGAGCATTGTGAATGTACACTCTAAAG 59.882 37.037 5.83 0.31 41.01 1.85
261 332 6.936900 AGCATTGTGAATGTACACTCTAAAGT 59.063 34.615 5.83 0.00 41.01 2.66
262 333 8.094548 AGCATTGTGAATGTACACTCTAAAGTA 58.905 33.333 5.83 0.00 41.01 2.24
263 334 8.169268 GCATTGTGAATGTACACTCTAAAGTAC 58.831 37.037 5.83 0.00 41.01 2.73
375 519 1.251002 CGTAGTACGTAACGCATGCAC 59.749 52.381 19.57 7.58 36.74 4.57
376 520 1.251002 GTAGTACGTAACGCATGCACG 59.749 52.381 22.86 22.86 41.32 5.34
390 534 0.472471 TGCACGGTTTCCTTCTTCCT 59.528 50.000 0.00 0.00 0.00 3.36
440 584 5.327616 TGTACGTGATTCCCGATCTTTAA 57.672 39.130 0.00 0.00 35.69 1.52
463 634 0.247695 GTCCAGAGCGCGTAATTTGC 60.248 55.000 8.43 0.00 0.00 3.68
486 669 7.496747 TGCTTTGCTTTGTTAAGTTTCCTTAT 58.503 30.769 0.00 0.00 33.27 1.73
505 690 0.108520 TACCCCAAGATTCGTGCGTC 60.109 55.000 0.00 0.00 0.00 5.19
694 915 3.007635 GGGGAATTCGTGGTTTCTACTG 58.992 50.000 0.00 0.00 0.00 2.74
782 1072 2.995939 GTCAATCTCATCGTCAGTTGCA 59.004 45.455 0.00 0.00 0.00 4.08
807 1349 1.542915 CACTCAGGATGCCAACCAAAG 59.457 52.381 0.00 0.00 34.76 2.77
835 1384 1.837538 CGCACCATAAATACCCGGCG 61.838 60.000 0.00 0.00 37.17 6.46
964 1539 4.606210 TCGCCTTGGCTGTATATATAGGA 58.394 43.478 10.12 0.00 0.00 2.94
1092 1675 2.258897 GCCTCCGCCGCTACTATC 59.741 66.667 0.00 0.00 0.00 2.08
1148 1731 4.033776 CCAGCGGGACCACCACAT 62.034 66.667 0.00 0.00 40.22 3.21
1151 1734 3.055719 GCGGGACCACCACATGTG 61.056 66.667 19.31 19.31 45.01 3.21
1166 1749 2.811317 GTGCGCGGACCTCTTCAG 60.811 66.667 21.13 0.00 0.00 3.02
1167 1750 3.303135 TGCGCGGACCTCTTCAGT 61.303 61.111 8.83 0.00 0.00 3.41
1177 1760 3.997064 CTCTTCAGTCTGCCGCCGG 62.997 68.421 0.00 0.00 0.00 6.13
1215 1813 1.523938 GGCCACGGAGCAGTATTCC 60.524 63.158 0.00 0.00 0.00 3.01
1236 1834 2.042831 GTTCTTGGCGATGGCTGCT 61.043 57.895 0.00 0.00 39.81 4.24
1263 1861 2.815647 GCGAAGAAGGGCGTCAGG 60.816 66.667 0.00 0.00 0.00 3.86
1286 1884 1.726853 GACGGTGGTCAGGAAATGAG 58.273 55.000 0.00 0.00 42.91 2.90
1328 1926 4.210304 GCGGTCGTCGATGCTTGC 62.210 66.667 13.31 0.00 42.43 4.01
1392 1990 2.125512 GTCGACCGCATCCTGCTT 60.126 61.111 3.51 0.00 42.25 3.91
1406 2004 5.123820 GCATCCTGCTTAAACATGTAAGTCA 59.876 40.000 0.00 2.52 40.96 3.41
1467 2087 4.037446 TGCGTTTCAGGCTTTAATTTCTGT 59.963 37.500 0.00 0.00 0.00 3.41
1468 2088 4.382754 GCGTTTCAGGCTTTAATTTCTGTG 59.617 41.667 0.00 0.00 0.00 3.66
1470 2090 6.664515 CGTTTCAGGCTTTAATTTCTGTGTA 58.335 36.000 0.00 0.00 0.00 2.90
1471 2091 6.797033 CGTTTCAGGCTTTAATTTCTGTGTAG 59.203 38.462 0.00 0.00 0.00 2.74
1472 2092 7.519970 CGTTTCAGGCTTTAATTTCTGTGTAGT 60.520 37.037 0.00 0.00 0.00 2.73
1473 2093 7.817418 TTCAGGCTTTAATTTCTGTGTAGTT 57.183 32.000 0.00 0.00 0.00 2.24
1474 2094 7.817418 TCAGGCTTTAATTTCTGTGTAGTTT 57.183 32.000 0.00 0.00 0.00 2.66
1475 2095 8.232913 TCAGGCTTTAATTTCTGTGTAGTTTT 57.767 30.769 0.00 0.00 0.00 2.43
1476 2096 8.691797 TCAGGCTTTAATTTCTGTGTAGTTTTT 58.308 29.630 0.00 0.00 0.00 1.94
1477 2097 9.959749 CAGGCTTTAATTTCTGTGTAGTTTTTA 57.040 29.630 0.00 0.00 0.00 1.52
1576 2244 3.461773 CTCGACCGTGGAGGCCAT 61.462 66.667 5.01 0.00 46.52 4.40
1692 2360 4.758251 CCCAGATGTGGCGCGACA 62.758 66.667 27.45 27.45 43.44 4.35
1913 2596 0.984230 CAGTAGGAAGGTGCAAGGGA 59.016 55.000 0.00 0.00 0.00 4.20
2083 2769 8.480643 AGGAATAGTTTTAGAGTCGACATTTG 57.519 34.615 19.50 0.00 0.00 2.32
2094 2780 5.011738 AGAGTCGACATTTGGTTTCCTTCTA 59.988 40.000 19.50 0.00 0.00 2.10
2160 3021 2.404923 TCTTGTTGTTGTTGACGGGA 57.595 45.000 0.00 0.00 0.00 5.14
2161 3022 2.712709 TCTTGTTGTTGTTGACGGGAA 58.287 42.857 0.00 0.00 0.00 3.97
2162 3023 2.680841 TCTTGTTGTTGTTGACGGGAAG 59.319 45.455 0.00 0.00 0.00 3.46
2164 3025 0.736053 GTTGTTGTTGACGGGAAGCA 59.264 50.000 0.00 0.00 0.00 3.91
2166 3027 1.098712 TGTTGTTGACGGGAAGCACC 61.099 55.000 0.00 0.00 38.08 5.01
2167 3028 1.098712 GTTGTTGACGGGAAGCACCA 61.099 55.000 2.58 0.00 41.20 4.17
2168 3029 0.179004 TTGTTGACGGGAAGCACCAT 60.179 50.000 2.58 0.00 41.20 3.55
2197 3063 0.321210 CGTTGGGCCACTGACATGTA 60.321 55.000 5.23 0.00 0.00 2.29
2198 3064 1.880221 CGTTGGGCCACTGACATGTAA 60.880 52.381 5.23 0.00 0.00 2.41
2204 3070 1.089920 CCACTGACATGTAAGCCAGC 58.910 55.000 10.40 0.00 0.00 4.85
2208 3074 2.816087 ACTGACATGTAAGCCAGCTTTG 59.184 45.455 10.40 5.64 37.47 2.77
2213 3079 1.397672 TGTAAGCCAGCTTTGCAACA 58.602 45.000 10.64 5.93 37.47 3.33
2216 3082 2.356673 GCCAGCTTTGCAACAGGC 60.357 61.111 12.92 12.92 45.13 4.85
2223 3089 1.255882 CTTTGCAACAGGCCCACATA 58.744 50.000 0.00 0.00 43.89 2.29
2227 3093 1.027357 GCAACAGGCCCACATATCAG 58.973 55.000 0.00 0.00 36.11 2.90
2239 3105 4.871993 CACATATCAGTGGAAGAACAGC 57.128 45.455 0.00 0.00 35.88 4.40
2246 3112 0.179018 GTGGAAGAACAGCAGGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
2251 3117 0.249911 AGAACAGCAGGGTGTCGAAC 60.250 55.000 4.42 0.00 0.00 3.95
2253 3119 2.738521 CAGCAGGGTGTCGAACGG 60.739 66.667 0.00 0.00 0.00 4.44
2268 3134 2.807392 CGAACGGTAGAGTATCCTCCTC 59.193 54.545 0.00 0.00 38.58 3.71
2274 3140 4.548669 GGTAGAGTATCCTCCTCCTTGTT 58.451 47.826 0.00 0.00 38.58 2.83
2275 3141 4.342665 GGTAGAGTATCCTCCTCCTTGTTG 59.657 50.000 0.00 0.00 38.58 3.33
2276 3142 4.338795 AGAGTATCCTCCTCCTTGTTGA 57.661 45.455 0.00 0.00 38.58 3.18
2277 3143 4.027437 AGAGTATCCTCCTCCTTGTTGAC 58.973 47.826 0.00 0.00 38.58 3.18
2280 3147 1.376037 CCTCCTCCTTGTTGACGGC 60.376 63.158 0.00 0.00 0.00 5.68
2284 3151 1.290955 CTCCTTGTTGACGGCGGTA 59.709 57.895 13.24 0.00 0.00 4.02
2307 3178 7.844779 GGTAATAGATAGGAGGATGGTTGGATA 59.155 40.741 0.00 0.00 0.00 2.59
2320 3199 9.116080 AGGATGGTTGGATAACATAGATATGAA 57.884 33.333 6.84 0.00 38.58 2.57
2370 3263 2.223711 GCTTTTTCCTTGAAGCCGTTGA 60.224 45.455 0.00 0.00 41.78 3.18
2483 3383 1.612676 GGGCGTGTCTAAGGGTTTTT 58.387 50.000 0.00 0.00 0.00 1.94
2484 3384 1.268625 GGGCGTGTCTAAGGGTTTTTG 59.731 52.381 0.00 0.00 0.00 2.44
2485 3385 1.335597 GGCGTGTCTAAGGGTTTTTGC 60.336 52.381 0.00 0.00 0.00 3.68
2486 3386 1.335496 GCGTGTCTAAGGGTTTTTGCA 59.665 47.619 0.00 0.00 0.00 4.08
2489 3389 2.691011 GTGTCTAAGGGTTTTTGCACCA 59.309 45.455 0.00 0.00 38.79 4.17
2526 3426 6.038714 GCAGGTCAAAGATAGAAATCCGATTT 59.961 38.462 6.04 6.04 31.98 2.17
2541 3441 3.386726 TCCGATTTAGATCCAACCGTCAT 59.613 43.478 0.00 0.00 0.00 3.06
2542 3442 4.585581 TCCGATTTAGATCCAACCGTCATA 59.414 41.667 0.00 0.00 0.00 2.15
2543 3443 4.923871 CCGATTTAGATCCAACCGTCATAG 59.076 45.833 0.00 0.00 0.00 2.23
2658 3559 0.396435 TTTTCTCGGCTGGCAAGAGA 59.604 50.000 11.41 11.41 39.03 3.10
2689 3590 9.344772 TGCCTAAATTCGTACAACCAAATATAT 57.655 29.630 0.00 0.00 0.00 0.86
2770 3710 4.386591 GTCCTCCGGACCCCAATA 57.613 61.111 0.00 0.00 46.19 1.90
2772 3712 0.685660 GTCCTCCGGACCCCAATATC 59.314 60.000 0.00 0.00 46.19 1.63
2773 3713 0.566176 TCCTCCGGACCCCAATATCT 59.434 55.000 0.00 0.00 0.00 1.98
2774 3714 0.687354 CCTCCGGACCCCAATATCTG 59.313 60.000 0.00 0.00 0.00 2.90
2775 3715 1.717032 CTCCGGACCCCAATATCTGA 58.283 55.000 0.00 0.00 0.00 3.27
2777 3717 0.396811 CCGGACCCCAATATCTGACC 59.603 60.000 0.00 0.00 0.00 4.02
2778 3718 0.396811 CGGACCCCAATATCTGACCC 59.603 60.000 0.00 0.00 0.00 4.46
2779 3719 0.771755 GGACCCCAATATCTGACCCC 59.228 60.000 0.00 0.00 0.00 4.95
2780 3720 1.518367 GACCCCAATATCTGACCCCA 58.482 55.000 0.00 0.00 0.00 4.96
2781 3721 1.850345 GACCCCAATATCTGACCCCAA 59.150 52.381 0.00 0.00 0.00 4.12
2783 3723 3.655777 GACCCCAATATCTGACCCCAATA 59.344 47.826 0.00 0.00 0.00 1.90
2784 3724 4.058731 ACCCCAATATCTGACCCCAATAA 58.941 43.478 0.00 0.00 0.00 1.40
2787 3727 4.832823 CCCAATATCTGACCCCAATAAACC 59.167 45.833 0.00 0.00 0.00 3.27
2788 3728 5.400189 CCCAATATCTGACCCCAATAAACCT 60.400 44.000 0.00 0.00 0.00 3.50
2789 3729 5.770162 CCAATATCTGACCCCAATAAACCTC 59.230 44.000 0.00 0.00 0.00 3.85
2790 3730 3.953542 ATCTGACCCCAATAAACCTCC 57.046 47.619 0.00 0.00 0.00 4.30
2792 3732 2.576191 TCTGACCCCAATAAACCTCCTG 59.424 50.000 0.00 0.00 0.00 3.86
2793 3733 1.005450 TGACCCCAATAAACCTCCTGC 59.995 52.381 0.00 0.00 0.00 4.85
2794 3734 1.005450 GACCCCAATAAACCTCCTGCA 59.995 52.381 0.00 0.00 0.00 4.41
2795 3735 1.431243 ACCCCAATAAACCTCCTGCAA 59.569 47.619 0.00 0.00 0.00 4.08
2796 3736 2.158234 ACCCCAATAAACCTCCTGCAAA 60.158 45.455 0.00 0.00 0.00 3.68
2798 3738 3.326297 CCCCAATAAACCTCCTGCAAAAA 59.674 43.478 0.00 0.00 0.00 1.94
2842 5142 6.567687 ATGTAATCAACGAATGGTGTGAAA 57.432 33.333 0.00 0.00 0.00 2.69
2852 5152 5.163723 ACGAATGGTGTGAAATTATCTGCAG 60.164 40.000 7.63 7.63 0.00 4.41
2870 5170 4.199310 TGCAGTATTCTCTAATTGGCACC 58.801 43.478 0.00 0.00 0.00 5.01
2899 5199 6.017605 AGAGCTTCTATTTATTTGGACATGCG 60.018 38.462 0.00 0.00 0.00 4.73
3028 5328 0.817013 AATGCAAATACGCCCACCTG 59.183 50.000 0.00 0.00 0.00 4.00
3045 5345 4.885907 CCACCTGTGATAAAGATCAGCAAT 59.114 41.667 0.00 0.00 42.87 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.695851 AATTGATTTGGTGGCGATAGATC 57.304 39.130 0.00 0.00 39.76 2.75
1 2 6.299141 AGTAATTGATTTGGTGGCGATAGAT 58.701 36.000 0.00 0.00 39.76 1.98
2 3 5.680619 AGTAATTGATTTGGTGGCGATAGA 58.319 37.500 0.00 0.00 39.76 1.98
4 5 5.468746 GCTAGTAATTGATTTGGTGGCGATA 59.531 40.000 0.00 0.00 0.00 2.92
5 6 4.275936 GCTAGTAATTGATTTGGTGGCGAT 59.724 41.667 0.00 0.00 0.00 4.58
6 7 3.625764 GCTAGTAATTGATTTGGTGGCGA 59.374 43.478 0.00 0.00 0.00 5.54
7 8 3.627577 AGCTAGTAATTGATTTGGTGGCG 59.372 43.478 0.00 0.00 0.00 5.69
8 9 4.640201 TGAGCTAGTAATTGATTTGGTGGC 59.360 41.667 0.00 0.00 0.00 5.01
9 10 6.949352 ATGAGCTAGTAATTGATTTGGTGG 57.051 37.500 0.00 0.00 0.00 4.61
46 117 3.775316 ACGTAGAGATGAGGGGTCAAAAT 59.225 43.478 0.00 0.00 0.00 1.82
50 121 1.564818 AGACGTAGAGATGAGGGGTCA 59.435 52.381 0.00 0.00 0.00 4.02
51 122 2.351706 AGACGTAGAGATGAGGGGTC 57.648 55.000 0.00 0.00 0.00 4.46
53 124 2.144730 CGTAGACGTAGAGATGAGGGG 58.855 57.143 0.00 0.00 34.11 4.79
54 125 1.532007 GCGTAGACGTAGAGATGAGGG 59.468 57.143 3.73 0.00 42.22 4.30
55 126 2.485903 AGCGTAGACGTAGAGATGAGG 58.514 52.381 3.73 0.00 42.22 3.86
56 127 4.201832 ACAAAGCGTAGACGTAGAGATGAG 60.202 45.833 3.73 0.00 42.22 2.90
57 128 3.688185 ACAAAGCGTAGACGTAGAGATGA 59.312 43.478 3.73 0.00 42.22 2.92
58 129 4.017380 ACAAAGCGTAGACGTAGAGATG 57.983 45.455 3.73 0.00 42.22 2.90
59 130 3.940221 AGACAAAGCGTAGACGTAGAGAT 59.060 43.478 3.73 0.00 42.22 2.75
60 131 3.332919 AGACAAAGCGTAGACGTAGAGA 58.667 45.455 3.73 0.00 42.22 3.10
61 132 3.743567 AGACAAAGCGTAGACGTAGAG 57.256 47.619 3.73 0.00 42.22 2.43
62 133 4.692625 AGTAAGACAAAGCGTAGACGTAGA 59.307 41.667 3.73 0.00 42.22 2.59
63 134 4.967437 AGTAAGACAAAGCGTAGACGTAG 58.033 43.478 3.73 0.00 42.22 3.51
64 135 6.668541 ATAGTAAGACAAAGCGTAGACGTA 57.331 37.500 3.73 0.00 42.22 3.57
65 136 3.911661 AGTAAGACAAAGCGTAGACGT 57.088 42.857 3.73 0.00 42.22 4.34
66 137 9.823098 ATAATATAGTAAGACAAAGCGTAGACG 57.177 33.333 0.00 0.00 43.27 4.18
90 161 9.273016 GCTAGCTGTAGATGGTTGATAAAAATA 57.727 33.333 7.70 0.00 0.00 1.40
91 162 7.229506 GGCTAGCTGTAGATGGTTGATAAAAAT 59.770 37.037 15.72 0.00 0.00 1.82
92 163 6.542370 GGCTAGCTGTAGATGGTTGATAAAAA 59.458 38.462 15.72 0.00 0.00 1.94
93 164 6.055588 GGCTAGCTGTAGATGGTTGATAAAA 58.944 40.000 15.72 0.00 0.00 1.52
94 165 5.130311 TGGCTAGCTGTAGATGGTTGATAAA 59.870 40.000 15.72 0.00 0.00 1.40
95 166 4.653801 TGGCTAGCTGTAGATGGTTGATAA 59.346 41.667 15.72 0.00 0.00 1.75
96 167 4.223144 TGGCTAGCTGTAGATGGTTGATA 58.777 43.478 15.72 0.00 0.00 2.15
97 168 3.041211 TGGCTAGCTGTAGATGGTTGAT 58.959 45.455 15.72 0.00 0.00 2.57
134 205 7.034397 GGAACGGAGGAAGTATATATTACTGC 58.966 42.308 0.00 0.00 0.00 4.40
135 206 8.118976 TGGAACGGAGGAAGTATATATTACTG 57.881 38.462 0.00 0.00 0.00 2.74
136 207 8.716674 TTGGAACGGAGGAAGTATATATTACT 57.283 34.615 0.00 0.00 0.00 2.24
137 208 9.420551 CTTTGGAACGGAGGAAGTATATATTAC 57.579 37.037 0.00 0.00 0.00 1.89
138 209 9.151177 ACTTTGGAACGGAGGAAGTATATATTA 57.849 33.333 0.00 0.00 0.00 0.98
139 210 8.030913 ACTTTGGAACGGAGGAAGTATATATT 57.969 34.615 0.00 0.00 0.00 1.28
141 212 8.716674 ATACTTTGGAACGGAGGAAGTATATA 57.283 34.615 5.52 0.00 40.08 0.86
142 213 5.952347 ACTTTGGAACGGAGGAAGTATAT 57.048 39.130 0.00 0.00 0.00 0.86
143 214 8.537728 TTATACTTTGGAACGGAGGAAGTATA 57.462 34.615 9.14 9.14 41.33 1.47
144 215 5.952347 ATACTTTGGAACGGAGGAAGTAT 57.048 39.130 0.00 0.00 38.20 2.12
145 216 6.127253 CCTTATACTTTGGAACGGAGGAAGTA 60.127 42.308 0.00 0.00 37.26 2.24
146 217 5.338137 CCTTATACTTTGGAACGGAGGAAGT 60.338 44.000 0.00 0.00 35.07 3.01
147 218 5.116882 CCTTATACTTTGGAACGGAGGAAG 58.883 45.833 0.00 0.00 0.00 3.46
148 219 4.624604 GCCTTATACTTTGGAACGGAGGAA 60.625 45.833 0.00 0.00 0.00 3.36
149 220 3.118519 GCCTTATACTTTGGAACGGAGGA 60.119 47.826 0.00 0.00 0.00 3.71
150 221 3.118371 AGCCTTATACTTTGGAACGGAGG 60.118 47.826 0.00 0.00 0.00 4.30
151 222 4.138487 AGCCTTATACTTTGGAACGGAG 57.862 45.455 0.00 0.00 0.00 4.63
152 223 4.563140 AAGCCTTATACTTTGGAACGGA 57.437 40.909 0.00 0.00 0.00 4.69
153 224 4.981794 CAAAGCCTTATACTTTGGAACGG 58.018 43.478 8.08 0.00 46.58 4.44
160 231 8.367156 TGAAATCTTTGCAAAGCCTTATACTTT 58.633 29.630 30.35 18.10 37.85 2.66
161 232 7.814587 GTGAAATCTTTGCAAAGCCTTATACTT 59.185 33.333 30.35 11.40 35.99 2.24
162 233 7.177392 AGTGAAATCTTTGCAAAGCCTTATACT 59.823 33.333 30.35 24.56 35.99 2.12
163 234 7.315890 AGTGAAATCTTTGCAAAGCCTTATAC 58.684 34.615 30.35 23.28 35.99 1.47
164 235 7.466746 AGTGAAATCTTTGCAAAGCCTTATA 57.533 32.000 30.35 15.23 35.99 0.98
165 236 6.350629 AGTGAAATCTTTGCAAAGCCTTAT 57.649 33.333 30.35 17.72 35.99 1.73
166 237 5.789643 AGTGAAATCTTTGCAAAGCCTTA 57.210 34.783 30.35 16.28 35.99 2.69
167 238 4.677673 AGTGAAATCTTTGCAAAGCCTT 57.322 36.364 30.35 24.31 35.99 4.35
168 239 5.477984 TCATAGTGAAATCTTTGCAAAGCCT 59.522 36.000 30.35 18.70 35.99 4.58
169 240 5.713025 TCATAGTGAAATCTTTGCAAAGCC 58.287 37.500 30.35 19.49 35.99 4.35
170 241 6.865205 AGTTCATAGTGAAATCTTTGCAAAGC 59.135 34.615 30.35 18.41 38.22 3.51
171 242 9.334693 GTAGTTCATAGTGAAATCTTTGCAAAG 57.665 33.333 29.53 29.53 38.22 2.77
172 243 8.845227 TGTAGTTCATAGTGAAATCTTTGCAAA 58.155 29.630 12.14 12.14 38.22 3.68
173 244 8.389779 TGTAGTTCATAGTGAAATCTTTGCAA 57.610 30.769 0.00 0.00 38.22 4.08
174 245 7.977789 TGTAGTTCATAGTGAAATCTTTGCA 57.022 32.000 0.00 0.00 38.22 4.08
175 246 9.922305 GTATGTAGTTCATAGTGAAATCTTTGC 57.078 33.333 0.00 0.00 38.22 3.68
179 250 9.737427 CTTCGTATGTAGTTCATAGTGAAATCT 57.263 33.333 0.00 0.00 38.22 2.40
180 251 9.517609 ACTTCGTATGTAGTTCATAGTGAAATC 57.482 33.333 0.00 0.00 38.22 2.17
189 260 9.431887 ACACATTTTACTTCGTATGTAGTTCAT 57.568 29.630 0.00 0.00 40.25 2.57
190 261 8.705134 CACACATTTTACTTCGTATGTAGTTCA 58.295 33.333 0.00 0.00 30.53 3.18
191 262 8.918658 TCACACATTTTACTTCGTATGTAGTTC 58.081 33.333 0.00 0.00 30.53 3.01
192 263 8.821147 TCACACATTTTACTTCGTATGTAGTT 57.179 30.769 0.00 0.00 30.53 2.24
193 264 8.821147 TTCACACATTTTACTTCGTATGTAGT 57.179 30.769 0.00 0.00 30.53 2.73
194 265 9.689075 CATTCACACATTTTACTTCGTATGTAG 57.311 33.333 0.00 0.00 30.53 2.74
195 266 9.210329 ACATTCACACATTTTACTTCGTATGTA 57.790 29.630 0.00 0.00 30.53 2.29
196 267 8.094798 ACATTCACACATTTTACTTCGTATGT 57.905 30.769 0.00 0.00 0.00 2.29
197 268 9.472995 GTACATTCACACATTTTACTTCGTATG 57.527 33.333 0.00 0.00 0.00 2.39
198 269 9.210329 TGTACATTCACACATTTTACTTCGTAT 57.790 29.630 0.00 0.00 0.00 3.06
199 270 8.489559 GTGTACATTCACACATTTTACTTCGTA 58.510 33.333 0.00 0.00 46.55 3.43
200 271 7.349711 GTGTACATTCACACATTTTACTTCGT 58.650 34.615 0.00 0.00 46.55 3.85
201 272 7.760750 GTGTACATTCACACATTTTACTTCG 57.239 36.000 0.00 0.00 46.55 3.79
230 301 6.804677 AGTGTACATTCACAATGCTCAAAAA 58.195 32.000 0.00 0.00 42.69 1.94
231 302 6.262944 AGAGTGTACATTCACAATGCTCAAAA 59.737 34.615 19.24 0.00 42.69 2.44
232 303 5.764686 AGAGTGTACATTCACAATGCTCAAA 59.235 36.000 19.24 0.00 42.69 2.69
233 304 5.308014 AGAGTGTACATTCACAATGCTCAA 58.692 37.500 19.24 0.00 42.69 3.02
234 305 4.898320 AGAGTGTACATTCACAATGCTCA 58.102 39.130 19.24 0.00 42.69 4.26
235 306 6.968131 TTAGAGTGTACATTCACAATGCTC 57.032 37.500 19.24 8.39 42.69 4.26
236 307 6.936900 ACTTTAGAGTGTACATTCACAATGCT 59.063 34.615 19.24 0.00 40.37 3.79
237 308 7.133891 ACTTTAGAGTGTACATTCACAATGC 57.866 36.000 19.24 0.00 40.37 3.56
238 309 9.203421 TGTACTTTAGAGTGTACATTCACAATG 57.797 33.333 19.24 15.27 42.49 2.82
269 340 9.292195 TCCATCTGTTCTACATACGAATGTATA 57.708 33.333 0.00 0.00 45.33 1.47
270 341 8.178313 TCCATCTGTTCTACATACGAATGTAT 57.822 34.615 0.00 0.00 45.33 2.29
271 342 7.284716 ACTCCATCTGTTCTACATACGAATGTA 59.715 37.037 0.00 0.00 44.66 2.29
273 344 6.507900 ACTCCATCTGTTCTACATACGAATG 58.492 40.000 0.00 0.00 39.17 2.67
274 345 6.716934 ACTCCATCTGTTCTACATACGAAT 57.283 37.500 0.00 0.00 0.00 3.34
275 346 7.818997 ATACTCCATCTGTTCTACATACGAA 57.181 36.000 0.00 0.00 0.00 3.85
276 347 9.163899 GATATACTCCATCTGTTCTACATACGA 57.836 37.037 0.00 0.00 0.00 3.43
277 348 9.168451 AGATATACTCCATCTGTTCTACATACG 57.832 37.037 0.00 0.00 31.49 3.06
280 351 9.241919 CTGAGATATACTCCATCTGTTCTACAT 57.758 37.037 0.00 0.00 44.34 2.29
281 352 7.175816 GCTGAGATATACTCCATCTGTTCTACA 59.824 40.741 0.00 0.00 44.34 2.74
282 353 7.175816 TGCTGAGATATACTCCATCTGTTCTAC 59.824 40.741 0.00 0.00 44.34 2.59
283 354 7.175816 GTGCTGAGATATACTCCATCTGTTCTA 59.824 40.741 0.00 0.00 44.34 2.10
284 355 6.015519 GTGCTGAGATATACTCCATCTGTTCT 60.016 42.308 0.00 0.00 44.34 3.01
285 356 6.155827 GTGCTGAGATATACTCCATCTGTTC 58.844 44.000 0.00 0.00 44.34 3.18
286 357 5.600069 TGTGCTGAGATATACTCCATCTGTT 59.400 40.000 0.00 0.00 44.34 3.16
287 358 5.143369 TGTGCTGAGATATACTCCATCTGT 58.857 41.667 0.00 0.00 44.34 3.41
288 359 5.718724 TGTGCTGAGATATACTCCATCTG 57.281 43.478 0.00 0.00 44.34 2.90
289 360 6.931790 AATGTGCTGAGATATACTCCATCT 57.068 37.500 0.00 0.00 44.34 2.90
290 361 9.149225 CTTTAATGTGCTGAGATATACTCCATC 57.851 37.037 0.00 0.00 44.34 3.51
291 362 8.654997 ACTTTAATGTGCTGAGATATACTCCAT 58.345 33.333 0.00 0.00 44.34 3.41
292 363 8.023021 ACTTTAATGTGCTGAGATATACTCCA 57.977 34.615 0.00 0.00 44.34 3.86
293 364 9.413048 GTACTTTAATGTGCTGAGATATACTCC 57.587 37.037 4.33 0.00 44.34 3.85
294 365 9.119329 CGTACTTTAATGTGCTGAGATATACTC 57.881 37.037 4.33 0.00 45.11 2.59
375 519 2.561478 TTCCAGGAAGAAGGAAACCG 57.439 50.000 0.00 0.00 40.76 4.44
376 520 3.056536 GCAATTCCAGGAAGAAGGAAACC 60.057 47.826 8.20 0.00 46.17 3.27
390 534 1.005450 GGTTACTGGAGGGCAATTCCA 59.995 52.381 4.82 4.82 42.30 3.53
440 584 0.246635 ATTACGCGCTCTGGACTTGT 59.753 50.000 5.73 0.00 0.00 3.16
486 669 0.108520 GACGCACGAATCTTGGGGTA 60.109 55.000 8.52 0.00 0.00 3.69
505 690 2.005451 CGTTGAGCCTTTGATCTCTGG 58.995 52.381 0.00 0.00 0.00 3.86
694 915 6.030228 CGTTTCAATCTCTCCCTAAATTTGC 58.970 40.000 0.00 0.00 0.00 3.68
753 975 0.533755 GATGAGATTGACCGGCCCTG 60.534 60.000 0.00 0.00 0.00 4.45
782 1072 2.356535 GGTTGGCATCCTGAGTGAGAAT 60.357 50.000 7.36 0.00 0.00 2.40
835 1384 2.109181 GTCCGTAGATGGCAGGCC 59.891 66.667 2.62 2.62 0.00 5.19
889 1453 1.658717 GTGAGGTCATCGATCGGCG 60.659 63.158 16.41 0.00 42.69 6.46
1146 1729 2.434884 AAGAGGTCCGCGCACATG 60.435 61.111 8.75 0.00 0.00 3.21
1147 1730 2.125512 GAAGAGGTCCGCGCACAT 60.126 61.111 8.75 0.00 0.00 3.21
1148 1731 3.573772 CTGAAGAGGTCCGCGCACA 62.574 63.158 8.75 0.00 0.00 4.57
1151 1734 2.507324 GACTGAAGAGGTCCGCGC 60.507 66.667 0.00 0.00 0.00 6.86
1177 1760 3.295462 CGTCGTCGTCATCGTCGC 61.295 66.667 0.00 0.00 44.86 5.19
1215 1813 1.448540 AGCCATCGCCAAGAACTCG 60.449 57.895 0.00 0.00 34.57 4.18
1239 1837 1.709147 CGCCCTTCTTCGCCAGATTG 61.709 60.000 0.00 0.00 0.00 2.67
1240 1838 1.450312 CGCCCTTCTTCGCCAGATT 60.450 57.895 0.00 0.00 0.00 2.40
1274 1872 3.988379 TGTTTGTGCTCATTTCCTGAC 57.012 42.857 0.00 0.00 0.00 3.51
1286 1884 2.010817 CGCTTCCGCTTGTTTGTGC 61.011 57.895 0.00 0.00 0.00 4.57
1310 1908 3.554692 CAAGCATCGACGACCGCC 61.555 66.667 15.40 0.00 38.37 6.13
1406 2004 1.338973 GGCGATTTGATCATGGCATGT 59.661 47.619 25.62 13.94 29.82 3.21
1467 2087 6.219473 TCGACCACGGTTAATAAAAACTACA 58.781 36.000 0.00 0.00 40.21 2.74
1468 2088 6.704512 TCGACCACGGTTAATAAAAACTAC 57.295 37.500 0.00 0.00 40.21 2.73
1470 2090 5.933463 TCATCGACCACGGTTAATAAAAACT 59.067 36.000 0.00 0.00 40.21 2.66
1471 2091 6.168164 TCATCGACCACGGTTAATAAAAAC 57.832 37.500 0.00 0.00 40.21 2.43
1472 2092 6.675971 GCATCATCGACCACGGTTAATAAAAA 60.676 38.462 0.00 0.00 40.21 1.94
1473 2093 5.220700 GCATCATCGACCACGGTTAATAAAA 60.221 40.000 0.00 0.00 40.21 1.52
1474 2094 4.271533 GCATCATCGACCACGGTTAATAAA 59.728 41.667 0.00 0.00 40.21 1.40
1475 2095 3.805422 GCATCATCGACCACGGTTAATAA 59.195 43.478 0.00 0.00 40.21 1.40
1476 2096 3.181474 TGCATCATCGACCACGGTTAATA 60.181 43.478 0.00 0.00 40.21 0.98
1477 2097 2.210116 GCATCATCGACCACGGTTAAT 58.790 47.619 0.00 0.00 40.21 1.40
1509 2177 0.541063 TCCGCCAGAGTAGTCCACAA 60.541 55.000 0.00 0.00 0.00 3.33
1553 2221 1.352404 CTCCACGGTCGAGACGATC 59.648 63.158 15.40 0.00 38.42 3.69
1600 2268 1.586564 CGCTCAATCTCGTCGTCCC 60.587 63.158 0.00 0.00 0.00 4.46
1692 2360 2.507102 CTCGTTGGACTGCGCGAT 60.507 61.111 12.10 0.00 32.79 4.58
1894 2577 0.984230 TCCCTTGCACCTTCCTACTG 59.016 55.000 0.00 0.00 0.00 2.74
2083 2769 9.421806 GACTCTAGTAAGTTTTAGAAGGAAACC 57.578 37.037 0.00 0.00 37.64 3.27
2094 2780 8.713737 AACAAAAGTCGACTCTAGTAAGTTTT 57.286 30.769 20.33 9.31 31.83 2.43
2145 2866 0.736053 TGCTTCCCGTCAACAACAAC 59.264 50.000 0.00 0.00 0.00 3.32
2148 3002 1.098712 TGGTGCTTCCCGTCAACAAC 61.099 55.000 0.00 0.00 34.77 3.32
2175 3041 2.978010 GTCAGTGGCCCAACGTGG 60.978 66.667 0.00 0.00 37.25 4.94
2176 3042 1.600636 ATGTCAGTGGCCCAACGTG 60.601 57.895 0.00 0.00 0.00 4.49
2178 3044 0.321210 TACATGTCAGTGGCCCAACG 60.321 55.000 0.00 0.00 0.00 4.10
2186 3052 2.105006 AGCTGGCTTACATGTCAGTG 57.895 50.000 0.00 0.00 41.33 3.66
2187 3053 2.816087 CAAAGCTGGCTTACATGTCAGT 59.184 45.455 0.00 0.00 41.33 3.41
2197 3063 1.744014 CCTGTTGCAAAGCTGGCTT 59.256 52.632 0.00 1.60 37.98 4.35
2198 3064 2.864471 GCCTGTTGCAAAGCTGGCT 61.864 57.895 22.80 0.00 43.48 4.75
2204 3070 1.255882 TATGTGGGCCTGTTGCAAAG 58.744 50.000 4.53 0.97 43.89 2.77
2208 3074 1.027357 CTGATATGTGGGCCTGTTGC 58.973 55.000 4.53 0.00 40.16 4.17
2223 3089 1.004044 CCCTGCTGTTCTTCCACTGAT 59.996 52.381 0.00 0.00 0.00 2.90
2227 3093 0.179018 ACACCCTGCTGTTCTTCCAC 60.179 55.000 0.00 0.00 0.00 4.02
2231 3097 0.468226 TTCGACACCCTGCTGTTCTT 59.532 50.000 0.00 0.00 0.00 2.52
2237 3103 1.874345 CTACCGTTCGACACCCTGCT 61.874 60.000 0.00 0.00 0.00 4.24
2238 3104 1.445582 CTACCGTTCGACACCCTGC 60.446 63.158 0.00 0.00 0.00 4.85
2239 3105 0.170561 CTCTACCGTTCGACACCCTG 59.829 60.000 0.00 0.00 0.00 4.45
2268 3134 1.931172 CTATTACCGCCGTCAACAAGG 59.069 52.381 0.00 0.00 0.00 3.61
2274 3140 3.079578 CTCCTATCTATTACCGCCGTCA 58.920 50.000 0.00 0.00 0.00 4.35
2275 3141 2.422832 CCTCCTATCTATTACCGCCGTC 59.577 54.545 0.00 0.00 0.00 4.79
2276 3142 2.040813 TCCTCCTATCTATTACCGCCGT 59.959 50.000 0.00 0.00 0.00 5.68
2277 3143 2.719739 TCCTCCTATCTATTACCGCCG 58.280 52.381 0.00 0.00 0.00 6.46
2280 3147 5.105310 CCAACCATCCTCCTATCTATTACCG 60.105 48.000 0.00 0.00 0.00 4.02
2284 3151 7.739444 TGTTATCCAACCATCCTCCTATCTATT 59.261 37.037 0.00 0.00 33.41 1.73
2359 3252 4.037327 TGAACAATTGATTCAACGGCTTCA 59.963 37.500 13.59 4.66 33.16 3.02
2489 3389 0.842030 TGACCTGCTTCACCATCCCT 60.842 55.000 0.00 0.00 0.00 4.20
2526 3426 4.822350 CACTCTCTATGACGGTTGGATCTA 59.178 45.833 0.00 0.00 0.00 1.98
2574 3475 0.544223 AACCAACCTTTTGCCAACCC 59.456 50.000 0.00 0.00 0.00 4.11
2638 3539 0.519077 CTCTTGCCAGCCGAGAAAAC 59.481 55.000 1.09 0.00 33.54 2.43
2658 3559 4.157105 GGTTGTACGAATTTAGGCACCAAT 59.843 41.667 0.00 0.00 0.00 3.16
2757 3697 1.420430 GTCAGATATTGGGGTCCGGA 58.580 55.000 0.00 0.00 0.00 5.14
2758 3698 0.396811 GGTCAGATATTGGGGTCCGG 59.603 60.000 0.00 0.00 0.00 5.14
2759 3699 0.396811 GGGTCAGATATTGGGGTCCG 59.603 60.000 0.00 0.00 0.00 4.79
2761 3701 1.518367 TGGGGTCAGATATTGGGGTC 58.482 55.000 0.00 0.00 0.00 4.46
2763 3703 4.740154 TTATTGGGGTCAGATATTGGGG 57.260 45.455 0.00 0.00 0.00 4.96
2766 3706 5.770162 GGAGGTTTATTGGGGTCAGATATTG 59.230 44.000 0.00 0.00 0.00 1.90
2767 3707 5.676811 AGGAGGTTTATTGGGGTCAGATATT 59.323 40.000 0.00 0.00 0.00 1.28
2768 3708 5.073691 CAGGAGGTTTATTGGGGTCAGATAT 59.926 44.000 0.00 0.00 0.00 1.63
2769 3709 4.412199 CAGGAGGTTTATTGGGGTCAGATA 59.588 45.833 0.00 0.00 0.00 1.98
2770 3710 3.203040 CAGGAGGTTTATTGGGGTCAGAT 59.797 47.826 0.00 0.00 0.00 2.90
2772 3712 2.945890 GCAGGAGGTTTATTGGGGTCAG 60.946 54.545 0.00 0.00 0.00 3.51
2773 3713 1.005450 GCAGGAGGTTTATTGGGGTCA 59.995 52.381 0.00 0.00 0.00 4.02
2774 3714 1.005450 TGCAGGAGGTTTATTGGGGTC 59.995 52.381 0.00 0.00 0.00 4.46
2775 3715 1.080638 TGCAGGAGGTTTATTGGGGT 58.919 50.000 0.00 0.00 0.00 4.95
2777 3717 4.615588 TTTTTGCAGGAGGTTTATTGGG 57.384 40.909 0.00 0.00 0.00 4.12
2821 5121 9.221775 GATAATTTCACACCATTCGTTGATTAC 57.778 33.333 0.00 0.00 0.00 1.89
2842 5142 8.159447 TGCCAATTAGAGAATACTGCAGATAAT 58.841 33.333 23.35 7.94 0.00 1.28
2899 5199 5.818136 TTAAATGCCAGATTACTGTCAGC 57.182 39.130 0.00 0.00 42.05 4.26
2949 5249 7.174946 GTCCTATTGTGTTTCCTCAAGATTCAA 59.825 37.037 0.00 0.00 0.00 2.69
3010 5310 0.323360 ACAGGTGGGCGTATTTGCAT 60.323 50.000 0.00 0.00 36.28 3.96


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

AutoCloner maintained by Alex Coulton.