Multiple sequence alignment - TraesCS7D01G090300

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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 TraesCS7D01G090300 chr7D 100.000 3273 0 0 1 3273 54318181 54321453 0.000000e+00 6045.0
1 TraesCS7D01G090300 chr7D 94.910 1886 77 7 406 2285 54335503 54337375 0.000000e+00 2933.0
2 TraesCS7D01G090300 chr7D 90.937 1942 120 18 884 2794 54353128 54355044 0.000000e+00 2560.0
3 TraesCS7D01G090300 chr7D 89.504 1372 99 16 1437 2784 54310826 54312176 0.000000e+00 1694.0
4 TraesCS7D01G090300 chr7D 95.842 505 12 4 2775 3273 54356940 54357441 0.000000e+00 808.0
5 TraesCS7D01G090300 chr7D 85.052 388 35 12 855 1227 54310434 54310813 1.110000e-99 374.0
6 TraesCS7D01G090300 chr7D 94.898 98 5 0 589 686 54310133 54310230 1.570000e-33 154.0
7 TraesCS7D01G090300 chr7A 86.826 2634 193 49 231 2793 57801743 57804293 0.000000e+00 2800.0
8 TraesCS7D01G090300 chr7A 94.891 1096 49 4 1437 2528 57864315 57865407 0.000000e+00 1707.0
9 TraesCS7D01G090300 chr7A 93.770 915 42 7 340 1247 57863232 57864138 0.000000e+00 1360.0
10 TraesCS7D01G090300 chr7A 93.878 343 14 3 1 342 57807855 57808191 8.100000e-141 510.0
11 TraesCS7D01G090300 chr7A 100.000 32 0 0 2565 2596 57865479 57865510 3.530000e-05 60.2
12 TraesCS7D01G090300 chr4A 92.100 924 64 2 1369 2284 669898117 669899039 0.000000e+00 1293.0
13 TraesCS7D01G090300 chr4A 86.233 799 49 25 463 1232 669891521 669892287 0.000000e+00 809.0
14 TraesCS7D01G090300 chr4A 84.241 514 48 11 2323 2805 669899048 669899559 1.370000e-128 470.0
15 TraesCS7D01G090300 chr4A 85.373 335 39 8 918 1247 669897696 669898025 4.050000e-89 339.0
16 TraesCS7D01G090300 chr4A 95.122 82 4 0 2899 2980 669900377 669900458 2.650000e-26 130.0
17 TraesCS7D01G090300 chrUn 92.677 874 59 3 1437 2309 49139898 49140767 0.000000e+00 1254.0
18 TraesCS7D01G090300 chrUn 92.449 874 61 3 1437 2309 49113059 49113928 0.000000e+00 1243.0
19 TraesCS7D01G090300 chrUn 92.449 874 61 3 1440 2312 384624760 384623891 0.000000e+00 1243.0
20 TraesCS7D01G090300 chrUn 85.699 944 60 34 328 1232 49112126 49113033 0.000000e+00 926.0
21 TraesCS7D01G090300 chrUn 86.233 799 49 29 463 1232 49139106 49139872 0.000000e+00 809.0
22 TraesCS7D01G090300 chrUn 85.152 660 42 25 328 967 329825441 329826064 2.770000e-175 625.0
23 TraesCS7D01G090300 chrUn 85.152 660 42 25 328 967 329829698 329829075 2.770000e-175 625.0
24 TraesCS7D01G090300 chrUn 84.749 459 35 19 801 1238 384625227 384624783 8.390000e-116 427.0
25 TraesCS7D01G090300 chr2D 92.553 282 20 1 2990 3271 516415459 516415179 1.410000e-108 403.0
26 TraesCS7D01G090300 chr5D 90.785 293 22 3 2985 3273 78808346 78808637 1.420000e-103 387.0
27 TraesCS7D01G090300 chr5B 90.323 279 25 2 2995 3273 88363764 88364040 6.670000e-97 364.0
28 TraesCS7D01G090300 chr5B 78.648 281 30 13 3001 3273 589890365 589890623 3.380000e-35 159.0
29 TraesCS7D01G090300 chr3B 89.030 237 25 1 2988 3224 17847969 17847734 3.190000e-75 292.0
30 TraesCS7D01G090300 chr3B 89.340 197 20 1 1247 1443 61788484 61788679 2.520000e-61 246.0
31 TraesCS7D01G090300 chr1B 86.131 274 26 3 2989 3254 31806691 31806422 5.350000e-73 285.0
32 TraesCS7D01G090300 chr7B 91.534 189 16 0 1247 1435 13895144 13895332 9.010000e-66 261.0
33 TraesCS7D01G090300 chr7B 90.476 189 18 0 1247 1435 354396259 354396447 1.950000e-62 250.0
34 TraesCS7D01G090300 chr5A 90.476 189 18 0 1247 1435 432109274 432109086 1.950000e-62 250.0
35 TraesCS7D01G090300 chr5A 90.476 189 18 0 1247 1435 535742191 535742003 1.950000e-62 250.0
36 TraesCS7D01G090300 chr6B 87.204 211 25 1 1247 1457 42648752 42648544 4.220000e-59 239.0
37 TraesCS7D01G090300 chr6A 86.243 189 14 2 3085 3273 591512443 591512267 9.270000e-46 195.0
38 TraesCS7D01G090300 chr3D 91.453 117 6 2 2989 3105 388665266 388665378 1.220000e-34 158.0
39 TraesCS7D01G090300 chr2B 82.143 196 14 5 3078 3273 95790845 95791019 7.320000e-32 148.0
40 TraesCS7D01G090300 chr1D 92.857 56 3 1 2716 2771 402837827 402837773 2.710000e-11 80.5


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 TraesCS7D01G090300 chr7D 54318181 54321453 3272 False 6045.000000 6045 100.000000 1 3273 1 chr7D.!!$F1 3272
1 TraesCS7D01G090300 chr7D 54335503 54337375 1872 False 2933.000000 2933 94.910000 406 2285 1 chr7D.!!$F2 1879
2 TraesCS7D01G090300 chr7D 54353128 54357441 4313 False 1684.000000 2560 93.389500 884 3273 2 chr7D.!!$F4 2389
3 TraesCS7D01G090300 chr7D 54310133 54312176 2043 False 740.666667 1694 89.818000 589 2784 3 chr7D.!!$F3 2195
4 TraesCS7D01G090300 chr7A 57801743 57808191 6448 False 1655.000000 2800 90.352000 1 2793 2 chr7A.!!$F1 2792
5 TraesCS7D01G090300 chr7A 57863232 57865510 2278 False 1042.400000 1707 96.220333 340 2596 3 chr7A.!!$F2 2256
6 TraesCS7D01G090300 chr4A 669891521 669892287 766 False 809.000000 809 86.233000 463 1232 1 chr4A.!!$F1 769
7 TraesCS7D01G090300 chr4A 669897696 669900458 2762 False 558.000000 1293 89.209000 918 2980 4 chr4A.!!$F2 2062
8 TraesCS7D01G090300 chrUn 49112126 49113928 1802 False 1084.500000 1243 89.074000 328 2309 2 chrUn.!!$F2 1981
9 TraesCS7D01G090300 chrUn 49139106 49140767 1661 False 1031.500000 1254 89.455000 463 2309 2 chrUn.!!$F3 1846
10 TraesCS7D01G090300 chrUn 384623891 384625227 1336 True 835.000000 1243 88.599000 801 2312 2 chrUn.!!$R2 1511
11 TraesCS7D01G090300 chrUn 329825441 329826064 623 False 625.000000 625 85.152000 328 967 1 chrUn.!!$F1 639
12 TraesCS7D01G090300 chrUn 329829075 329829698 623 True 625.000000 625 85.152000 328 967 1 chrUn.!!$R1 639

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
876 959 0.102481 TAGGTCTTCGAATGCTCGCC 59.898 55.0 0.0 0.0 45.04 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 2545 0.731417 CGCTTCCAGGATGAAAGCAG 59.269 55.0 10.84 1.31 39.69 4.24 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
58 59 7.391148 AAAAAGTTCACAAGCTAGAAGTTCA 57.609 32.000 5.50 0.00 36.63 3.18
59 60 7.391148 AAAAGTTCACAAGCTAGAAGTTCAA 57.609 32.000 5.50 0.00 36.63 2.69
60 61 6.610741 AAGTTCACAAGCTAGAAGTTCAAG 57.389 37.500 5.50 0.00 33.37 3.02
61 62 5.918608 AGTTCACAAGCTAGAAGTTCAAGA 58.081 37.500 5.50 0.00 0.00 3.02
62 63 6.349300 AGTTCACAAGCTAGAAGTTCAAGAA 58.651 36.000 5.50 0.00 0.00 2.52
63 64 6.995091 AGTTCACAAGCTAGAAGTTCAAGAAT 59.005 34.615 5.50 0.00 0.00 2.40
64 65 7.500559 AGTTCACAAGCTAGAAGTTCAAGAATT 59.499 33.333 5.50 0.00 0.00 2.17
65 66 7.807977 TCACAAGCTAGAAGTTCAAGAATTT 57.192 32.000 5.50 0.00 0.00 1.82
66 67 7.642669 TCACAAGCTAGAAGTTCAAGAATTTG 58.357 34.615 5.50 4.81 35.57 2.32
67 68 7.498900 TCACAAGCTAGAAGTTCAAGAATTTGA 59.501 33.333 5.50 0.00 41.44 2.69
79 80 6.443934 TCAAGAATTTGAAAAGGTTCACGA 57.556 33.333 0.00 0.00 43.52 4.35
80 81 6.857956 TCAAGAATTTGAAAAGGTTCACGAA 58.142 32.000 0.00 0.00 43.52 3.85
81 82 7.488322 TCAAGAATTTGAAAAGGTTCACGAAT 58.512 30.769 0.00 0.00 43.52 3.34
82 83 7.978975 TCAAGAATTTGAAAAGGTTCACGAATT 59.021 29.630 0.00 0.00 43.52 2.17
83 84 8.603181 CAAGAATTTGAAAAGGTTCACGAATTT 58.397 29.630 0.00 0.00 43.52 1.82
84 85 8.130307 AGAATTTGAAAAGGTTCACGAATTTG 57.870 30.769 0.00 0.00 43.52 2.32
85 86 7.978975 AGAATTTGAAAAGGTTCACGAATTTGA 59.021 29.630 0.00 0.00 43.52 2.69
86 87 8.485976 AATTTGAAAAGGTTCACGAATTTGAA 57.514 26.923 0.00 0.00 43.52 2.69
87 88 7.891183 TTTGAAAAGGTTCACGAATTTGAAA 57.109 28.000 0.00 0.00 43.52 2.69
88 89 7.891183 TTGAAAAGGTTCACGAATTTGAAAA 57.109 28.000 0.00 0.00 43.52 2.29
89 90 7.518731 TGAAAAGGTTCACGAATTTGAAAAG 57.481 32.000 0.00 0.00 38.88 2.27
90 91 7.316640 TGAAAAGGTTCACGAATTTGAAAAGA 58.683 30.769 0.00 0.00 38.88 2.52
91 92 7.487829 TGAAAAGGTTCACGAATTTGAAAAGAG 59.512 33.333 0.00 0.00 38.88 2.85
92 93 6.693315 AAGGTTCACGAATTTGAAAAGAGA 57.307 33.333 0.00 0.00 37.24 3.10
93 94 6.693315 AGGTTCACGAATTTGAAAAGAGAA 57.307 33.333 0.00 0.00 37.24 2.87
94 95 7.095695 AGGTTCACGAATTTGAAAAGAGAAA 57.904 32.000 0.00 0.00 37.24 2.52
95 96 7.543756 AGGTTCACGAATTTGAAAAGAGAAAA 58.456 30.769 0.00 0.00 37.24 2.29
96 97 8.032451 AGGTTCACGAATTTGAAAAGAGAAAAA 58.968 29.630 0.00 0.00 37.24 1.94
97 98 8.321005 GGTTCACGAATTTGAAAAGAGAAAAAG 58.679 33.333 0.00 0.00 37.24 2.27
98 99 8.860128 GTTCACGAATTTGAAAAGAGAAAAAGT 58.140 29.630 0.00 0.00 37.24 2.66
99 100 8.980143 TCACGAATTTGAAAAGAGAAAAAGTT 57.020 26.923 0.00 0.00 0.00 2.66
100 101 8.859156 TCACGAATTTGAAAAGAGAAAAAGTTG 58.141 29.630 0.00 0.00 0.00 3.16
101 102 8.859156 CACGAATTTGAAAAGAGAAAAAGTTGA 58.141 29.630 0.00 0.00 0.00 3.18
102 103 9.586435 ACGAATTTGAAAAGAGAAAAAGTTGAT 57.414 25.926 0.00 0.00 0.00 2.57
103 104 9.839589 CGAATTTGAAAAGAGAAAAAGTTGATG 57.160 29.630 0.00 0.00 0.00 3.07
138 139 9.764363 AATTAAGAAAATGAGAAGACCAAAACC 57.236 29.630 0.00 0.00 0.00 3.27
139 140 6.790232 AAGAAAATGAGAAGACCAAAACCA 57.210 33.333 0.00 0.00 0.00 3.67
140 141 6.149129 AGAAAATGAGAAGACCAAAACCAC 57.851 37.500 0.00 0.00 0.00 4.16
141 142 5.656416 AGAAAATGAGAAGACCAAAACCACA 59.344 36.000 0.00 0.00 0.00 4.17
142 143 4.918810 AATGAGAAGACCAAAACCACAC 57.081 40.909 0.00 0.00 0.00 3.82
143 144 3.358111 TGAGAAGACCAAAACCACACA 57.642 42.857 0.00 0.00 0.00 3.72
144 145 3.691575 TGAGAAGACCAAAACCACACAA 58.308 40.909 0.00 0.00 0.00 3.33
145 146 4.082845 TGAGAAGACCAAAACCACACAAA 58.917 39.130 0.00 0.00 0.00 2.83
146 147 4.524714 TGAGAAGACCAAAACCACACAAAA 59.475 37.500 0.00 0.00 0.00 2.44
147 148 4.816392 AGAAGACCAAAACCACACAAAAC 58.184 39.130 0.00 0.00 0.00 2.43
148 149 3.603158 AGACCAAAACCACACAAAACC 57.397 42.857 0.00 0.00 0.00 3.27
149 150 2.235155 AGACCAAAACCACACAAAACCC 59.765 45.455 0.00 0.00 0.00 4.11
150 151 1.978580 ACCAAAACCACACAAAACCCA 59.021 42.857 0.00 0.00 0.00 4.51
151 152 2.027653 ACCAAAACCACACAAAACCCAG 60.028 45.455 0.00 0.00 0.00 4.45
152 153 2.006169 CAAAACCACACAAAACCCAGC 58.994 47.619 0.00 0.00 0.00 4.85
153 154 0.539518 AAACCACACAAAACCCAGCC 59.460 50.000 0.00 0.00 0.00 4.85
154 155 1.334384 AACCACACAAAACCCAGCCC 61.334 55.000 0.00 0.00 0.00 5.19
155 156 1.760086 CCACACAAAACCCAGCCCA 60.760 57.895 0.00 0.00 0.00 5.36
156 157 1.333636 CCACACAAAACCCAGCCCAA 61.334 55.000 0.00 0.00 0.00 4.12
157 158 0.539051 CACACAAAACCCAGCCCAAA 59.461 50.000 0.00 0.00 0.00 3.28
158 159 1.065854 CACACAAAACCCAGCCCAAAA 60.066 47.619 0.00 0.00 0.00 2.44
159 160 1.630878 ACACAAAACCCAGCCCAAAAA 59.369 42.857 0.00 0.00 0.00 1.94
178 179 3.951775 AAAGGCACAGAAACAAACACA 57.048 38.095 0.00 0.00 0.00 3.72
179 180 2.939460 AGGCACAGAAACAAACACAC 57.061 45.000 0.00 0.00 0.00 3.82
180 181 2.166829 AGGCACAGAAACAAACACACA 58.833 42.857 0.00 0.00 0.00 3.72
181 182 2.094752 AGGCACAGAAACAAACACACAC 60.095 45.455 0.00 0.00 0.00 3.82
182 183 2.352225 GGCACAGAAACAAACACACACA 60.352 45.455 0.00 0.00 0.00 3.72
183 184 3.312828 GCACAGAAACAAACACACACAA 58.687 40.909 0.00 0.00 0.00 3.33
184 185 3.738282 GCACAGAAACAAACACACACAAA 59.262 39.130 0.00 0.00 0.00 2.83
185 186 4.210120 GCACAGAAACAAACACACACAAAA 59.790 37.500 0.00 0.00 0.00 2.44
186 187 5.665232 CACAGAAACAAACACACACAAAAC 58.335 37.500 0.00 0.00 0.00 2.43
187 188 4.747605 ACAGAAACAAACACACACAAAACC 59.252 37.500 0.00 0.00 0.00 3.27
188 189 3.984633 AGAAACAAACACACACAAAACCG 59.015 39.130 0.00 0.00 0.00 4.44
189 190 2.355717 ACAAACACACACAAAACCGG 57.644 45.000 0.00 0.00 0.00 5.28
190 191 1.614413 ACAAACACACACAAAACCGGT 59.386 42.857 0.00 0.00 0.00 5.28
191 192 2.255316 CAAACACACACAAAACCGGTC 58.745 47.619 8.04 0.00 0.00 4.79
192 193 1.535833 AACACACACAAAACCGGTCA 58.464 45.000 8.04 0.00 0.00 4.02
193 194 0.806241 ACACACACAAAACCGGTCAC 59.194 50.000 8.04 0.00 0.00 3.67
194 195 0.805614 CACACACAAAACCGGTCACA 59.194 50.000 8.04 0.00 0.00 3.58
195 196 1.200252 CACACACAAAACCGGTCACAA 59.800 47.619 8.04 0.00 0.00 3.33
196 197 1.887198 ACACACAAAACCGGTCACAAA 59.113 42.857 8.04 0.00 0.00 2.83
197 198 2.296471 ACACACAAAACCGGTCACAAAA 59.704 40.909 8.04 0.00 0.00 2.44
198 199 3.243771 ACACACAAAACCGGTCACAAAAA 60.244 39.130 8.04 0.00 0.00 1.94
220 221 7.736031 AAAAAGCGAGAAGAAAACAAACTAC 57.264 32.000 0.00 0.00 0.00 2.73
221 222 6.431198 AAAGCGAGAAGAAAACAAACTACA 57.569 33.333 0.00 0.00 0.00 2.74
222 223 6.431198 AAGCGAGAAGAAAACAAACTACAA 57.569 33.333 0.00 0.00 0.00 2.41
223 224 6.431198 AGCGAGAAGAAAACAAACTACAAA 57.569 33.333 0.00 0.00 0.00 2.83
224 225 6.255950 AGCGAGAAGAAAACAAACTACAAAC 58.744 36.000 0.00 0.00 0.00 2.93
225 226 6.093633 AGCGAGAAGAAAACAAACTACAAACT 59.906 34.615 0.00 0.00 0.00 2.66
226 227 7.279313 AGCGAGAAGAAAACAAACTACAAACTA 59.721 33.333 0.00 0.00 0.00 2.24
227 228 7.372657 GCGAGAAGAAAACAAACTACAAACTAC 59.627 37.037 0.00 0.00 0.00 2.73
228 229 7.578024 CGAGAAGAAAACAAACTACAAACTACG 59.422 37.037 0.00 0.00 0.00 3.51
229 230 8.260270 AGAAGAAAACAAACTACAAACTACGT 57.740 30.769 0.00 0.00 0.00 3.57
230 231 9.369904 AGAAGAAAACAAACTACAAACTACGTA 57.630 29.630 0.00 0.00 0.00 3.57
231 232 9.413611 GAAGAAAACAAACTACAAACTACGTAC 57.586 33.333 0.00 0.00 0.00 3.67
232 233 8.707938 AGAAAACAAACTACAAACTACGTACT 57.292 30.769 0.00 0.00 0.00 2.73
233 234 8.598075 AGAAAACAAACTACAAACTACGTACTG 58.402 33.333 0.00 0.00 0.00 2.74
234 235 5.895216 ACAAACTACAAACTACGTACTGC 57.105 39.130 0.00 0.00 0.00 4.40
278 279 7.095355 GCTGAGCTTGATTTTCATGTTTTCAAT 60.095 33.333 0.00 0.00 0.00 2.57
279 280 8.301730 TGAGCTTGATTTTCATGTTTTCAATC 57.698 30.769 0.00 0.00 0.00 2.67
280 281 8.145767 TGAGCTTGATTTTCATGTTTTCAATCT 58.854 29.630 0.00 0.32 0.00 2.40
323 324 3.420893 TGATTTCCAACAGATCACACCC 58.579 45.455 0.00 0.00 0.00 4.61
324 325 1.890876 TTTCCAACAGATCACACCCG 58.109 50.000 0.00 0.00 0.00 5.28
370 373 3.378427 GGCTGTTGCTACCAAGGAATTAG 59.622 47.826 0.00 0.00 35.33 1.73
729 767 1.608590 ACGCCCTGTGAGATTGTTTTG 59.391 47.619 0.00 0.00 0.00 2.44
831 875 1.726853 ACGAAGCAAGAAAGATCGGG 58.273 50.000 0.00 0.00 37.81 5.14
872 955 1.137872 CTGGCTAGGTCTTCGAATGCT 59.862 52.381 0.00 0.00 0.00 3.79
873 956 1.137086 TGGCTAGGTCTTCGAATGCTC 59.863 52.381 0.00 0.00 0.00 4.26
874 957 1.482278 GCTAGGTCTTCGAATGCTCG 58.518 55.000 0.00 0.00 46.87 5.03
875 958 1.482278 CTAGGTCTTCGAATGCTCGC 58.518 55.000 0.00 0.00 45.04 5.03
876 959 0.102481 TAGGTCTTCGAATGCTCGCC 59.898 55.000 0.00 0.00 45.04 5.54
877 960 1.153549 GGTCTTCGAATGCTCGCCT 60.154 57.895 0.00 0.00 45.04 5.52
878 961 0.102481 GGTCTTCGAATGCTCGCCTA 59.898 55.000 0.00 0.00 45.04 3.93
879 962 1.470979 GGTCTTCGAATGCTCGCCTAA 60.471 52.381 0.00 0.00 45.04 2.69
916 1013 2.808567 GCTTCCTGCTGGAACTATAGCC 60.809 54.545 20.15 4.46 46.57 3.93
1178 1308 1.003476 CCCAAAACCCTGGCAATGC 60.003 57.895 0.00 0.00 34.88 3.56
1289 1450 8.810427 TTAACTAGTTAACTTGCCGATTAATCG 58.190 33.333 27.19 27.19 38.66 3.34
1485 1687 9.868277 TTTATAGTTGATTGATTTTGCCGAATT 57.132 25.926 0.00 0.00 0.00 2.17
1594 1799 3.782443 CCCTCCCTACGCGGCTTT 61.782 66.667 12.47 0.00 0.00 3.51
1804 2009 4.636435 CCGCCCACGTCCAACCTT 62.636 66.667 0.00 0.00 37.70 3.50
1807 2012 1.373812 GCCCACGTCCAACCTTAGT 59.626 57.895 0.00 0.00 0.00 2.24
1819 2024 2.005370 ACCTTAGTGACCTCGTGGAA 57.995 50.000 11.17 0.00 37.04 3.53
2278 2486 5.004821 CGCAATCAACTACTACTAAGTGCAG 59.995 44.000 0.00 0.00 36.36 4.41
2293 2501 3.001067 CAGTGCATGCGCGTCTAG 58.999 61.111 24.54 10.34 42.97 2.43
2305 2516 3.693245 GTCTAGGACGTGCATGCG 58.307 61.111 14.09 1.59 37.94 4.73
2334 2545 3.390639 AGGATCACTCCATCTCCATTGTC 59.609 47.826 0.00 0.00 44.79 3.18
2346 2564 3.265221 TCTCCATTGTCTGCTTTCATCCT 59.735 43.478 0.00 0.00 0.00 3.24
2347 2565 3.349927 TCCATTGTCTGCTTTCATCCTG 58.650 45.455 0.00 0.00 0.00 3.86
2348 2566 2.426024 CCATTGTCTGCTTTCATCCTGG 59.574 50.000 0.00 0.00 0.00 4.45
2349 2567 3.349927 CATTGTCTGCTTTCATCCTGGA 58.650 45.455 0.00 0.00 0.00 3.86
2350 2568 3.507162 TTGTCTGCTTTCATCCTGGAA 57.493 42.857 0.00 0.00 0.00 3.53
2351 2569 3.063510 TGTCTGCTTTCATCCTGGAAG 57.936 47.619 0.00 0.00 0.00 3.46
2352 2570 1.742268 GTCTGCTTTCATCCTGGAAGC 59.258 52.381 12.29 12.29 0.00 3.86
2374 2614 3.795101 CGAGTTACCGCTGTATAGTTTGG 59.205 47.826 0.00 0.00 0.00 3.28
2375 2615 3.528532 AGTTACCGCTGTATAGTTTGGC 58.471 45.455 0.00 0.00 0.00 4.52
2986 8396 1.285962 CCTCACCCAGATGGATGGTTT 59.714 52.381 0.00 0.00 38.81 3.27
3067 8696 4.300803 ACGAGTACAAAGACGCAAACATA 58.699 39.130 0.00 0.00 0.00 2.29
3068 8697 4.149396 ACGAGTACAAAGACGCAAACATAC 59.851 41.667 0.00 0.00 0.00 2.39
3070 8699 5.163992 CGAGTACAAAGACGCAAACATACAT 60.164 40.000 0.00 0.00 0.00 2.29
3071 8700 6.165659 AGTACAAAGACGCAAACATACATC 57.834 37.500 0.00 0.00 0.00 3.06
3081 8710 4.332543 CGCAAACATACATCACAGGTACAT 59.667 41.667 0.00 0.00 0.00 2.29
3123 8765 1.021202 TCACAGAAAGCACCCAAACG 58.979 50.000 0.00 0.00 0.00 3.60
3178 8820 3.138304 TGTTCATCCTCAACCTTCAACG 58.862 45.455 0.00 0.00 0.00 4.10
3226 8868 1.871772 CAAAGGAGAGTTGCTGGCG 59.128 57.895 0.00 0.00 0.00 5.69
3243 8885 1.003355 CGAAGAAGCAAGGGCAGGA 60.003 57.895 0.00 0.00 44.61 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.391148 TGAACTTCTAGCTTGTGAACTTTTT 57.609 32.000 0.00 0.00 0.00 1.94
35 36 7.336931 TCTTGAACTTCTAGCTTGTGAACTTTT 59.663 33.333 0.00 0.00 0.00 2.27
36 37 6.823689 TCTTGAACTTCTAGCTTGTGAACTTT 59.176 34.615 0.00 0.00 0.00 2.66
37 38 6.349300 TCTTGAACTTCTAGCTTGTGAACTT 58.651 36.000 0.00 0.00 0.00 2.66
38 39 5.918608 TCTTGAACTTCTAGCTTGTGAACT 58.081 37.500 0.00 0.00 0.00 3.01
39 40 6.604735 TTCTTGAACTTCTAGCTTGTGAAC 57.395 37.500 0.00 0.00 0.00 3.18
40 41 7.807977 AATTCTTGAACTTCTAGCTTGTGAA 57.192 32.000 0.00 0.00 0.00 3.18
41 42 7.498900 TCAAATTCTTGAACTTCTAGCTTGTGA 59.501 33.333 0.00 0.00 38.65 3.58
42 43 7.642669 TCAAATTCTTGAACTTCTAGCTTGTG 58.357 34.615 0.00 0.00 38.65 3.33
43 44 7.807977 TCAAATTCTTGAACTTCTAGCTTGT 57.192 32.000 0.00 0.00 38.65 3.16
56 57 6.443934 TCGTGAACCTTTTCAAATTCTTGA 57.556 33.333 0.00 0.00 43.52 3.02
57 58 7.698836 ATTCGTGAACCTTTTCAAATTCTTG 57.301 32.000 0.00 0.00 43.52 3.02
58 59 8.603181 CAAATTCGTGAACCTTTTCAAATTCTT 58.397 29.630 0.00 0.00 43.52 2.52
59 60 7.978975 TCAAATTCGTGAACCTTTTCAAATTCT 59.021 29.630 0.00 0.00 43.52 2.40
60 61 8.125728 TCAAATTCGTGAACCTTTTCAAATTC 57.874 30.769 0.00 0.00 43.52 2.17
61 62 8.485976 TTCAAATTCGTGAACCTTTTCAAATT 57.514 26.923 0.00 0.00 43.52 1.82
62 63 8.485976 TTTCAAATTCGTGAACCTTTTCAAAT 57.514 26.923 0.00 0.00 43.52 2.32
63 64 7.891183 TTTCAAATTCGTGAACCTTTTCAAA 57.109 28.000 0.00 0.00 43.52 2.69
64 65 7.815068 TCTTTTCAAATTCGTGAACCTTTTCAA 59.185 29.630 0.00 0.00 43.52 2.69
65 66 7.316640 TCTTTTCAAATTCGTGAACCTTTTCA 58.683 30.769 0.00 0.00 39.55 2.69
66 67 7.700656 TCTCTTTTCAAATTCGTGAACCTTTTC 59.299 33.333 0.00 0.00 37.24 2.29
67 68 7.543756 TCTCTTTTCAAATTCGTGAACCTTTT 58.456 30.769 0.00 0.00 37.24 2.27
68 69 7.095695 TCTCTTTTCAAATTCGTGAACCTTT 57.904 32.000 0.00 0.00 37.24 3.11
69 70 6.693315 TCTCTTTTCAAATTCGTGAACCTT 57.307 33.333 0.00 0.00 37.24 3.50
70 71 6.693315 TTCTCTTTTCAAATTCGTGAACCT 57.307 33.333 0.00 0.00 37.24 3.50
71 72 7.749539 TTTTCTCTTTTCAAATTCGTGAACC 57.250 32.000 0.00 0.00 37.24 3.62
72 73 8.860128 ACTTTTTCTCTTTTCAAATTCGTGAAC 58.140 29.630 0.00 0.00 37.24 3.18
73 74 8.980143 ACTTTTTCTCTTTTCAAATTCGTGAA 57.020 26.923 0.00 0.00 35.72 3.18
74 75 8.859156 CAACTTTTTCTCTTTTCAAATTCGTGA 58.141 29.630 0.00 0.00 0.00 4.35
75 76 8.859156 TCAACTTTTTCTCTTTTCAAATTCGTG 58.141 29.630 0.00 0.00 0.00 4.35
76 77 8.980143 TCAACTTTTTCTCTTTTCAAATTCGT 57.020 26.923 0.00 0.00 0.00 3.85
77 78 9.839589 CATCAACTTTTTCTCTTTTCAAATTCG 57.160 29.630 0.00 0.00 0.00 3.34
112 113 9.764363 GGTTTTGGTCTTCTCATTTTCTTAATT 57.236 29.630 0.00 0.00 0.00 1.40
113 114 8.923270 TGGTTTTGGTCTTCTCATTTTCTTAAT 58.077 29.630 0.00 0.00 0.00 1.40
114 115 8.194769 GTGGTTTTGGTCTTCTCATTTTCTTAA 58.805 33.333 0.00 0.00 0.00 1.85
115 116 7.340743 TGTGGTTTTGGTCTTCTCATTTTCTTA 59.659 33.333 0.00 0.00 0.00 2.10
116 117 6.154363 TGTGGTTTTGGTCTTCTCATTTTCTT 59.846 34.615 0.00 0.00 0.00 2.52
117 118 5.656416 TGTGGTTTTGGTCTTCTCATTTTCT 59.344 36.000 0.00 0.00 0.00 2.52
118 119 5.748630 GTGTGGTTTTGGTCTTCTCATTTTC 59.251 40.000 0.00 0.00 0.00 2.29
119 120 5.186797 TGTGTGGTTTTGGTCTTCTCATTTT 59.813 36.000 0.00 0.00 0.00 1.82
120 121 4.709397 TGTGTGGTTTTGGTCTTCTCATTT 59.291 37.500 0.00 0.00 0.00 2.32
121 122 4.277476 TGTGTGGTTTTGGTCTTCTCATT 58.723 39.130 0.00 0.00 0.00 2.57
122 123 3.897239 TGTGTGGTTTTGGTCTTCTCAT 58.103 40.909 0.00 0.00 0.00 2.90
123 124 3.358111 TGTGTGGTTTTGGTCTTCTCA 57.642 42.857 0.00 0.00 0.00 3.27
124 125 4.712122 TTTGTGTGGTTTTGGTCTTCTC 57.288 40.909 0.00 0.00 0.00 2.87
125 126 4.322424 GGTTTTGTGTGGTTTTGGTCTTCT 60.322 41.667 0.00 0.00 0.00 2.85
126 127 3.930229 GGTTTTGTGTGGTTTTGGTCTTC 59.070 43.478 0.00 0.00 0.00 2.87
127 128 3.307129 GGGTTTTGTGTGGTTTTGGTCTT 60.307 43.478 0.00 0.00 0.00 3.01
128 129 2.235155 GGGTTTTGTGTGGTTTTGGTCT 59.765 45.455 0.00 0.00 0.00 3.85
129 130 2.028020 TGGGTTTTGTGTGGTTTTGGTC 60.028 45.455 0.00 0.00 0.00 4.02
130 131 1.978580 TGGGTTTTGTGTGGTTTTGGT 59.021 42.857 0.00 0.00 0.00 3.67
131 132 2.626840 CTGGGTTTTGTGTGGTTTTGG 58.373 47.619 0.00 0.00 0.00 3.28
132 133 2.006169 GCTGGGTTTTGTGTGGTTTTG 58.994 47.619 0.00 0.00 0.00 2.44
133 134 1.065782 GGCTGGGTTTTGTGTGGTTTT 60.066 47.619 0.00 0.00 0.00 2.43
134 135 0.539518 GGCTGGGTTTTGTGTGGTTT 59.460 50.000 0.00 0.00 0.00 3.27
135 136 1.334384 GGGCTGGGTTTTGTGTGGTT 61.334 55.000 0.00 0.00 0.00 3.67
136 137 1.760480 GGGCTGGGTTTTGTGTGGT 60.760 57.895 0.00 0.00 0.00 4.16
137 138 1.333636 TTGGGCTGGGTTTTGTGTGG 61.334 55.000 0.00 0.00 0.00 4.17
138 139 0.539051 TTTGGGCTGGGTTTTGTGTG 59.461 50.000 0.00 0.00 0.00 3.82
139 140 1.280457 TTTTGGGCTGGGTTTTGTGT 58.720 45.000 0.00 0.00 0.00 3.72
140 141 2.409948 TTTTTGGGCTGGGTTTTGTG 57.590 45.000 0.00 0.00 0.00 3.33
156 157 4.450757 GTGTGTTTGTTTCTGTGCCTTTTT 59.549 37.500 0.00 0.00 0.00 1.94
157 158 3.993736 GTGTGTTTGTTTCTGTGCCTTTT 59.006 39.130 0.00 0.00 0.00 2.27
158 159 3.006323 TGTGTGTTTGTTTCTGTGCCTTT 59.994 39.130 0.00 0.00 0.00 3.11
159 160 2.560542 TGTGTGTTTGTTTCTGTGCCTT 59.439 40.909 0.00 0.00 0.00 4.35
160 161 2.094752 GTGTGTGTTTGTTTCTGTGCCT 60.095 45.455 0.00 0.00 0.00 4.75
161 162 2.258755 GTGTGTGTTTGTTTCTGTGCC 58.741 47.619 0.00 0.00 0.00 5.01
162 163 2.940147 TGTGTGTGTTTGTTTCTGTGC 58.060 42.857 0.00 0.00 0.00 4.57
163 164 5.332959 GGTTTTGTGTGTGTTTGTTTCTGTG 60.333 40.000 0.00 0.00 0.00 3.66
164 165 4.747605 GGTTTTGTGTGTGTTTGTTTCTGT 59.252 37.500 0.00 0.00 0.00 3.41
165 166 4.143431 CGGTTTTGTGTGTGTTTGTTTCTG 60.143 41.667 0.00 0.00 0.00 3.02
166 167 3.984633 CGGTTTTGTGTGTGTTTGTTTCT 59.015 39.130 0.00 0.00 0.00 2.52
167 168 3.122111 CCGGTTTTGTGTGTGTTTGTTTC 59.878 43.478 0.00 0.00 0.00 2.78
168 169 3.060602 CCGGTTTTGTGTGTGTTTGTTT 58.939 40.909 0.00 0.00 0.00 2.83
169 170 2.036089 ACCGGTTTTGTGTGTGTTTGTT 59.964 40.909 0.00 0.00 0.00 2.83
170 171 1.614413 ACCGGTTTTGTGTGTGTTTGT 59.386 42.857 0.00 0.00 0.00 2.83
171 172 2.255316 GACCGGTTTTGTGTGTGTTTG 58.745 47.619 9.42 0.00 0.00 2.93
172 173 1.887198 TGACCGGTTTTGTGTGTGTTT 59.113 42.857 9.42 0.00 0.00 2.83
173 174 1.200484 GTGACCGGTTTTGTGTGTGTT 59.800 47.619 9.42 0.00 0.00 3.32
174 175 0.806241 GTGACCGGTTTTGTGTGTGT 59.194 50.000 9.42 0.00 0.00 3.72
175 176 0.805614 TGTGACCGGTTTTGTGTGTG 59.194 50.000 9.42 0.00 0.00 3.82
176 177 1.535833 TTGTGACCGGTTTTGTGTGT 58.464 45.000 9.42 0.00 0.00 3.72
177 178 2.638556 TTTGTGACCGGTTTTGTGTG 57.361 45.000 9.42 0.00 0.00 3.82
178 179 3.662247 TTTTTGTGACCGGTTTTGTGT 57.338 38.095 9.42 0.00 0.00 3.72
196 197 7.309920 TGTAGTTTGTTTTCTTCTCGCTTTTT 58.690 30.769 0.00 0.00 0.00 1.94
197 198 6.848451 TGTAGTTTGTTTTCTTCTCGCTTTT 58.152 32.000 0.00 0.00 0.00 2.27
198 199 6.431198 TGTAGTTTGTTTTCTTCTCGCTTT 57.569 33.333 0.00 0.00 0.00 3.51
199 200 6.431198 TTGTAGTTTGTTTTCTTCTCGCTT 57.569 33.333 0.00 0.00 0.00 4.68
200 201 6.093633 AGTTTGTAGTTTGTTTTCTTCTCGCT 59.906 34.615 0.00 0.00 0.00 4.93
201 202 6.255950 AGTTTGTAGTTTGTTTTCTTCTCGC 58.744 36.000 0.00 0.00 0.00 5.03
202 203 7.578024 CGTAGTTTGTAGTTTGTTTTCTTCTCG 59.422 37.037 0.00 0.00 0.00 4.04
203 204 8.385858 ACGTAGTTTGTAGTTTGTTTTCTTCTC 58.614 33.333 0.00 0.00 37.78 2.87
204 205 8.260270 ACGTAGTTTGTAGTTTGTTTTCTTCT 57.740 30.769 0.00 0.00 37.78 2.85
205 206 9.413611 GTACGTAGTTTGTAGTTTGTTTTCTTC 57.586 33.333 0.00 0.00 37.78 2.87
206 207 9.154847 AGTACGTAGTTTGTAGTTTGTTTTCTT 57.845 29.630 0.00 0.00 37.78 2.52
207 208 8.598075 CAGTACGTAGTTTGTAGTTTGTTTTCT 58.402 33.333 0.00 0.00 37.78 2.52
208 209 7.371615 GCAGTACGTAGTTTGTAGTTTGTTTTC 59.628 37.037 0.00 0.00 37.78 2.29
209 210 7.148440 TGCAGTACGTAGTTTGTAGTTTGTTTT 60.148 33.333 0.00 0.00 37.78 2.43
210 211 6.313411 TGCAGTACGTAGTTTGTAGTTTGTTT 59.687 34.615 0.00 0.00 37.78 2.83
211 212 5.811613 TGCAGTACGTAGTTTGTAGTTTGTT 59.188 36.000 0.00 0.00 37.78 2.83
212 213 5.350633 TGCAGTACGTAGTTTGTAGTTTGT 58.649 37.500 0.00 0.00 37.78 2.83
213 214 5.893512 TGCAGTACGTAGTTTGTAGTTTG 57.106 39.130 0.00 0.00 37.78 2.93
214 215 8.592105 TTTATGCAGTACGTAGTTTGTAGTTT 57.408 30.769 0.00 0.00 37.78 2.66
215 216 8.767478 ATTTATGCAGTACGTAGTTTGTAGTT 57.233 30.769 0.00 0.00 37.78 2.24
216 217 8.653338 CAATTTATGCAGTACGTAGTTTGTAGT 58.347 33.333 0.00 0.00 37.78 2.73
217 218 8.114290 CCAATTTATGCAGTACGTAGTTTGTAG 58.886 37.037 0.00 0.00 37.78 2.74
218 219 7.413219 GCCAATTTATGCAGTACGTAGTTTGTA 60.413 37.037 0.00 0.00 37.78 2.41
219 220 6.622028 GCCAATTTATGCAGTACGTAGTTTGT 60.622 38.462 0.00 0.00 37.78 2.83
220 221 5.737290 GCCAATTTATGCAGTACGTAGTTTG 59.263 40.000 0.00 1.31 37.78 2.93
221 222 5.446741 CGCCAATTTATGCAGTACGTAGTTT 60.447 40.000 0.00 0.00 37.78 2.66
222 223 4.033587 CGCCAATTTATGCAGTACGTAGTT 59.966 41.667 0.00 0.00 37.78 2.24
224 225 3.554324 ACGCCAATTTATGCAGTACGTAG 59.446 43.478 0.00 0.00 0.00 3.51
225 226 3.523547 ACGCCAATTTATGCAGTACGTA 58.476 40.909 0.00 0.00 0.00 3.57
226 227 2.352388 ACGCCAATTTATGCAGTACGT 58.648 42.857 0.00 0.00 0.00 3.57
227 228 3.097910 CAACGCCAATTTATGCAGTACG 58.902 45.455 0.00 0.00 0.00 3.67
228 229 4.349663 TCAACGCCAATTTATGCAGTAC 57.650 40.909 0.00 0.00 0.00 2.73
229 230 4.260579 CGATCAACGCCAATTTATGCAGTA 60.261 41.667 0.00 0.00 34.51 2.74
230 231 3.487376 CGATCAACGCCAATTTATGCAGT 60.487 43.478 0.00 0.00 34.51 4.40
231 232 3.038017 CGATCAACGCCAATTTATGCAG 58.962 45.455 0.00 0.00 34.51 4.41
232 233 3.063670 CGATCAACGCCAATTTATGCA 57.936 42.857 0.00 0.00 34.51 3.96
257 258 8.225777 GGAAGATTGAAAACATGAAAATCAAGC 58.774 33.333 0.00 7.48 36.84 4.01
312 313 2.159296 TCGATGTAACGGGTGTGATCTG 60.159 50.000 0.00 0.00 0.00 2.90
316 317 1.819903 TGATCGATGTAACGGGTGTGA 59.180 47.619 0.54 0.00 0.00 3.58
317 318 2.287393 TGATCGATGTAACGGGTGTG 57.713 50.000 0.54 0.00 0.00 3.82
323 324 5.109662 ACAGGTAGATGATCGATGTAACG 57.890 43.478 0.54 0.00 0.00 3.18
324 325 7.085116 CCTAACAGGTAGATGATCGATGTAAC 58.915 42.308 0.54 0.00 30.50 2.50
370 373 5.485662 AATTTCCTGCGAGCATTAACTAC 57.514 39.130 0.00 0.00 0.00 2.73
729 767 2.597510 GACAACCCAGTGGCACCC 60.598 66.667 15.27 0.00 33.59 4.61
875 958 5.269505 AGCTGCTTATATAGGCGATTAGG 57.730 43.478 11.75 0.55 0.00 2.69
876 959 5.751028 GGAAGCTGCTTATATAGGCGATTAG 59.249 44.000 15.95 5.21 0.00 1.73
877 960 5.422331 AGGAAGCTGCTTATATAGGCGATTA 59.578 40.000 15.95 0.00 0.00 1.75
878 961 4.223923 AGGAAGCTGCTTATATAGGCGATT 59.776 41.667 15.95 10.92 0.00 3.34
879 962 3.772025 AGGAAGCTGCTTATATAGGCGAT 59.228 43.478 15.95 3.53 0.00 4.58
1289 1450 3.733024 CTCGATGATCCTACGAGTAGC 57.267 52.381 18.44 0.00 45.23 3.58
1594 1799 1.066422 GATGGCGTCGATCAGCTCA 59.934 57.895 0.00 7.10 0.00 4.26
1804 2009 1.629043 AGCTTTCCACGAGGTCACTA 58.371 50.000 0.00 0.00 35.89 2.74
1807 2012 1.134220 ACAAAGCTTTCCACGAGGTCA 60.134 47.619 9.23 0.00 35.89 4.02
1819 2024 1.172812 GGCCCTTGACGACAAAGCTT 61.173 55.000 17.20 0.00 36.35 3.74
1993 2198 4.353437 GTCGGGTCGTTGTCGCCT 62.353 66.667 0.00 0.00 36.96 5.52
1998 2203 2.567497 ATCACCGTCGGGTCGTTGT 61.567 57.895 17.28 0.00 46.01 3.32
2278 2486 2.202743 TCCTAGACGCGCATGCAC 60.203 61.111 19.57 7.15 42.97 4.57
2293 2501 4.088762 CACCACGCATGCACGTCC 62.089 66.667 19.57 0.00 46.34 4.79
2334 2545 0.731417 CGCTTCCAGGATGAAAGCAG 59.269 55.000 10.84 1.31 39.69 4.24
2352 2570 3.795101 CCAAACTATACAGCGGTAACTCG 59.205 47.826 0.00 0.00 32.19 4.18
2367 2587 4.155280 GGATGCTAAAAGAACGCCAAACTA 59.845 41.667 0.00 0.00 0.00 2.24
2374 2614 4.558538 ATGATGGATGCTAAAAGAACGC 57.441 40.909 0.00 0.00 0.00 4.84
2375 2615 5.883661 ACAATGATGGATGCTAAAAGAACG 58.116 37.500 0.00 0.00 0.00 3.95
2418 2662 3.725010 CGTTGGCGAGAATTGAACTAAGC 60.725 47.826 0.00 0.00 41.33 3.09
3081 8710 1.053424 GGTGGGACAACTGTACTGGA 58.947 55.000 4.66 0.00 46.61 3.86
3123 8765 5.344933 GGACTTTTATGCGATTTTGGTGTTC 59.655 40.000 0.00 0.00 0.00 3.18
3178 8820 1.152383 GGCAGAGATTACGGCGGTTC 61.152 60.000 13.24 4.77 32.23 3.62
3222 8864 2.672996 GCCCTTGCTTCTTCGCCA 60.673 61.111 0.00 0.00 33.53 5.69
3226 8868 1.311651 GCTCCTGCCCTTGCTTCTTC 61.312 60.000 0.00 0.00 38.71 2.87
3243 8885 1.973281 CCTTTGTGGCGATGGTGCT 60.973 57.895 0.00 0.00 34.52 4.40


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

AutoCloner maintained by Alex Coulton.