Multiple sequence alignment - TraesCS1A01G237300

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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 TraesCS1A01G237300 chr1A 100.000 4194 0 0 1 4194 421637006 421641199 0.000000e+00 7745
1 TraesCS1A01G237300 chr1A 97.428 3305 80 3 895 4194 425258005 425254701 0.000000e+00 5627
2 TraesCS1A01G237300 chr1A 97.089 3229 79 5 969 4194 407518165 407514949 0.000000e+00 5428
3 TraesCS1A01G237300 chr1A 97.403 2503 53 3 969 3460 406582576 406585077 0.000000e+00 4252
4 TraesCS1A01G237300 chr1A 84.063 1851 258 25 1381 3213 417389158 417387327 0.000000e+00 1749
5 TraesCS1A01G237300 chr1A 97.308 743 19 1 3452 4194 406597398 406598139 0.000000e+00 1260
6 TraesCS1A01G237300 chr1A 95.591 635 25 2 238 870 407518904 407518271 0.000000e+00 1014
7 TraesCS1A01G237300 chr1A 95.118 635 28 2 235 867 406581831 406582464 0.000000e+00 998
8 TraesCS1A01G237300 chr1A 90.447 492 34 8 895 1385 417395773 417395294 1.640000e-178 636
9 TraesCS1A01G237300 chr1A 85.780 218 16 10 586 795 425258283 425258073 2.540000e-52 217
10 TraesCS1A01G237300 chr1A 88.272 162 12 2 756 910 406582415 406582576 1.990000e-43 187
11 TraesCS1A01G237300 chr1A 86.667 165 12 3 759 916 407518320 407518159 1.550000e-39 174
12 TraesCS1A01G237300 chr1A 91.753 97 8 0 235 331 417396357 417396261 7.310000e-28 135
13 TraesCS1A01G237300 chr1A 91.753 97 8 0 235 331 425258591 425258495 7.310000e-28 135
14 TraesCS1A01G237300 chr1D 95.447 3975 161 11 235 4194 322380245 322384214 0.000000e+00 6320
15 TraesCS1A01G237300 chr1D 85.137 2624 313 47 586 3175 328446363 328443783 0.000000e+00 2614
16 TraesCS1A01G237300 chr1D 87.910 2134 224 17 965 3093 323636487 323638591 0.000000e+00 2481
17 TraesCS1A01G237300 chr1D 93.814 97 6 0 235 331 328453077 328452981 3.380000e-31 147
18 TraesCS1A01G237300 chr1B 95.944 3230 127 3 969 4194 435360632 435363861 0.000000e+00 5236
19 TraesCS1A01G237300 chr1B 88.403 1578 166 10 965 2540 435927024 435928586 0.000000e+00 1884
20 TraesCS1A01G237300 chr1B 93.371 528 27 3 342 867 435360002 435360523 0.000000e+00 774
21 TraesCS1A01G237300 chr1B 89.134 543 24 15 333 870 326928119 326927607 0.000000e+00 643
22 TraesCS1A01G237300 chr1B 93.472 337 21 1 715 1051 435808496 435808831 2.250000e-137 499
23 TraesCS1A01G237300 chr1B 88.272 162 9 4 756 910 435360474 435360632 7.160000e-43 185
24 TraesCS1A01G237300 chr1B 85.380 171 11 6 586 748 442621242 442621078 9.330000e-37 165
25 TraesCS1A01G237300 chr1B 94.737 95 5 0 239 333 435359827 435359921 9.390000e-32 148
26 TraesCS1A01G237300 chr1B 93.617 94 6 0 238 331 442621550 442621457 1.570000e-29 141
27 TraesCS1A01G237300 chr1B 89.286 84 7 2 498 579 435926188 435926271 2.060000e-18 104
28 TraesCS1A01G237300 chr3B 91.413 361 29 1 3836 4194 169901543 169901903 1.050000e-135 494
29 TraesCS1A01G237300 chr3B 89.912 228 20 3 3607 3833 169901205 169901430 1.480000e-74 291
30 TraesCS1A01G237300 chr7D 92.308 234 17 1 1 234 59987222 59987454 8.690000e-87 331


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 TraesCS1A01G237300 chr1A 421637006 421641199 4193 False 7745.000000 7745 100.000000 1 4194 1 chr1A.!!$F2 4193
1 TraesCS1A01G237300 chr1A 407514949 407518904 3955 True 2205.333333 5428 93.115667 238 4194 3 chr1A.!!$R2 3956
2 TraesCS1A01G237300 chr1A 425254701 425258591 3890 True 1993.000000 5627 91.653667 235 4194 3 chr1A.!!$R4 3959
3 TraesCS1A01G237300 chr1A 406581831 406585077 3246 False 1812.333333 4252 93.597667 235 3460 3 chr1A.!!$F3 3225
4 TraesCS1A01G237300 chr1A 417387327 417389158 1831 True 1749.000000 1749 84.063000 1381 3213 1 chr1A.!!$R1 1832
5 TraesCS1A01G237300 chr1A 406597398 406598139 741 False 1260.000000 1260 97.308000 3452 4194 1 chr1A.!!$F1 742
6 TraesCS1A01G237300 chr1A 417395294 417396357 1063 True 385.500000 636 91.100000 235 1385 2 chr1A.!!$R3 1150
7 TraesCS1A01G237300 chr1D 322380245 322384214 3969 False 6320.000000 6320 95.447000 235 4194 1 chr1D.!!$F1 3959
8 TraesCS1A01G237300 chr1D 328443783 328446363 2580 True 2614.000000 2614 85.137000 586 3175 1 chr1D.!!$R1 2589
9 TraesCS1A01G237300 chr1D 323636487 323638591 2104 False 2481.000000 2481 87.910000 965 3093 1 chr1D.!!$F2 2128
10 TraesCS1A01G237300 chr1B 435359827 435363861 4034 False 1585.750000 5236 93.081000 239 4194 4 chr1B.!!$F2 3955
11 TraesCS1A01G237300 chr1B 435926188 435928586 2398 False 994.000000 1884 88.844500 498 2540 2 chr1B.!!$F3 2042
12 TraesCS1A01G237300 chr1B 326927607 326928119 512 True 643.000000 643 89.134000 333 870 1 chr1B.!!$R1 537
13 TraesCS1A01G237300 chr3B 169901205 169901903 698 False 392.500000 494 90.662500 3607 4194 2 chr3B.!!$F1 587

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
231 232 0.107945 GGCCACTCTGCTAGACTTGG 60.108 60.0 0.00 0.0 0.0 3.61 F
233 234 0.107945 CCACTCTGCTAGACTTGGCC 60.108 60.0 0.00 0.0 0.0 5.36 F
1783 2378 0.110486 AGCCGTCAAGGATGGTGTTT 59.890 50.0 6.37 0.0 45.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 2346 0.458669 GACGGCTTCATCTAACCCGA 59.541 55.000 4.24 0.0 38.39 5.14 R
2248 2849 0.768221 TCCAGAAGGGTGGTGAAGCT 60.768 55.000 0.00 0.0 38.88 3.74 R
3599 4202 1.493022 AGTGCCCAACTGAACCTAACA 59.507 47.619 0.00 0.0 37.88 2.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.867456 CGACACGCGGAATAAAAGTT 57.133 45.000 12.47 0.00 36.03 2.66
25 26 3.976468 CGACACGCGGAATAAAAGTTA 57.024 42.857 12.47 0.00 36.03 2.24
26 27 4.509915 CGACACGCGGAATAAAAGTTAT 57.490 40.909 12.47 0.00 36.03 1.89
27 28 4.260670 CGACACGCGGAATAAAAGTTATG 58.739 43.478 12.47 0.00 36.03 1.90
28 29 4.011058 ACACGCGGAATAAAAGTTATGC 57.989 40.909 12.47 0.00 0.00 3.14
29 30 3.687698 ACACGCGGAATAAAAGTTATGCT 59.312 39.130 12.47 0.00 0.00 3.79
30 31 4.155280 ACACGCGGAATAAAAGTTATGCTT 59.845 37.500 12.47 0.00 39.52 3.91
62 63 9.804758 AGTTTTTGAAACCACGAATTAAATACA 57.195 25.926 0.00 0.00 0.00 2.29
63 64 9.838163 GTTTTTGAAACCACGAATTAAATACAC 57.162 29.630 0.00 0.00 0.00 2.90
64 65 9.804758 TTTTTGAAACCACGAATTAAATACACT 57.195 25.926 0.00 0.00 0.00 3.55
89 90 5.721876 AAAATAAAATGCATGCACCGATG 57.278 34.783 25.37 0.00 0.00 3.84
90 91 2.867287 TAAAATGCATGCACCGATGG 57.133 45.000 25.37 0.00 0.00 3.51
91 92 0.176219 AAAATGCATGCACCGATGGG 59.824 50.000 25.37 0.00 40.11 4.00
92 93 0.683828 AAATGCATGCACCGATGGGA 60.684 50.000 25.37 0.00 36.97 4.37
93 94 0.468585 AATGCATGCACCGATGGGAT 60.469 50.000 25.37 0.00 36.97 3.85
94 95 1.176619 ATGCATGCACCGATGGGATG 61.177 55.000 25.37 0.00 37.18 3.51
95 96 2.558286 GCATGCACCGATGGGATGG 61.558 63.158 14.21 0.00 34.99 3.51
96 97 2.203394 ATGCACCGATGGGATGGC 60.203 61.111 0.00 1.79 36.97 4.40
97 98 2.760378 ATGCACCGATGGGATGGCT 61.760 57.895 0.00 0.00 36.97 4.75
98 99 2.903855 GCACCGATGGGATGGCTG 60.904 66.667 0.00 0.00 36.97 4.85
99 100 2.591753 CACCGATGGGATGGCTGT 59.408 61.111 0.00 0.00 36.97 4.40
100 101 1.820906 CACCGATGGGATGGCTGTG 60.821 63.158 0.00 0.00 36.97 3.66
101 102 2.903855 CCGATGGGATGGCTGTGC 60.904 66.667 0.00 0.00 34.06 4.57
102 103 2.124612 CGATGGGATGGCTGTGCA 60.125 61.111 0.00 0.00 0.00 4.57
103 104 2.184830 CGATGGGATGGCTGTGCAG 61.185 63.158 0.00 0.00 0.00 4.41
104 105 1.225426 GATGGGATGGCTGTGCAGA 59.775 57.895 3.02 0.00 0.00 4.26
105 106 1.077212 ATGGGATGGCTGTGCAGAC 60.077 57.895 3.02 0.00 36.85 3.51
113 114 3.853831 TGGCTGTGCAGACATTTAATG 57.146 42.857 3.21 3.07 42.59 1.90
114 115 3.419943 TGGCTGTGCAGACATTTAATGA 58.580 40.909 12.28 0.00 42.59 2.57
115 116 3.191162 TGGCTGTGCAGACATTTAATGAC 59.809 43.478 12.28 5.60 42.59 3.06
116 117 3.428045 GGCTGTGCAGACATTTAATGACC 60.428 47.826 12.28 3.29 36.17 4.02
117 118 3.191162 GCTGTGCAGACATTTAATGACCA 59.809 43.478 12.28 0.00 0.00 4.02
118 119 4.321156 GCTGTGCAGACATTTAATGACCAA 60.321 41.667 12.28 0.00 0.00 3.67
119 120 5.375417 TGTGCAGACATTTAATGACCAAG 57.625 39.130 12.28 0.61 0.00 3.61
120 121 4.826733 TGTGCAGACATTTAATGACCAAGT 59.173 37.500 12.28 0.00 0.00 3.16
121 122 6.000840 TGTGCAGACATTTAATGACCAAGTA 58.999 36.000 12.28 0.00 0.00 2.24
122 123 6.488344 TGTGCAGACATTTAATGACCAAGTAA 59.512 34.615 12.28 0.00 0.00 2.24
123 124 7.013750 TGTGCAGACATTTAATGACCAAGTAAA 59.986 33.333 12.28 0.00 0.00 2.01
124 125 7.865385 GTGCAGACATTTAATGACCAAGTAAAA 59.135 33.333 12.28 0.00 0.00 1.52
125 126 8.417106 TGCAGACATTTAATGACCAAGTAAAAA 58.583 29.630 12.28 0.00 0.00 1.94
126 127 8.915654 GCAGACATTTAATGACCAAGTAAAAAG 58.084 33.333 12.28 0.00 0.00 2.27
127 128 8.915654 CAGACATTTAATGACCAAGTAAAAAGC 58.084 33.333 12.28 0.00 0.00 3.51
128 129 8.860088 AGACATTTAATGACCAAGTAAAAAGCT 58.140 29.630 12.28 0.00 0.00 3.74
129 130 9.476202 GACATTTAATGACCAAGTAAAAAGCTT 57.524 29.630 12.28 0.00 0.00 3.74
130 131 9.830975 ACATTTAATGACCAAGTAAAAAGCTTT 57.169 25.926 12.28 5.69 0.00 3.51
161 162 9.628500 ATTAGAATGGTTAATTAGGAAGGTGAC 57.372 33.333 0.00 0.00 0.00 3.67
162 163 7.027874 AGAATGGTTAATTAGGAAGGTGACA 57.972 36.000 0.00 0.00 0.00 3.58
163 164 6.884836 AGAATGGTTAATTAGGAAGGTGACAC 59.115 38.462 0.00 0.00 0.00 3.67
164 165 5.570205 TGGTTAATTAGGAAGGTGACACA 57.430 39.130 8.08 0.00 0.00 3.72
165 166 5.942961 TGGTTAATTAGGAAGGTGACACAA 58.057 37.500 8.08 0.00 0.00 3.33
166 167 6.366340 TGGTTAATTAGGAAGGTGACACAAA 58.634 36.000 8.08 0.00 0.00 2.83
167 168 6.834451 TGGTTAATTAGGAAGGTGACACAAAA 59.166 34.615 8.08 0.00 0.00 2.44
168 169 7.507616 TGGTTAATTAGGAAGGTGACACAAAAT 59.492 33.333 8.08 0.00 0.00 1.82
169 170 8.364894 GGTTAATTAGGAAGGTGACACAAAATT 58.635 33.333 8.08 6.20 0.00 1.82
170 171 9.758651 GTTAATTAGGAAGGTGACACAAAATTT 57.241 29.630 8.08 0.00 0.00 1.82
171 172 9.974980 TTAATTAGGAAGGTGACACAAAATTTC 57.025 29.630 8.08 3.26 0.00 2.17
172 173 4.937201 AGGAAGGTGACACAAAATTTCC 57.063 40.909 8.08 11.26 34.29 3.13
173 174 3.317993 AGGAAGGTGACACAAAATTTCCG 59.682 43.478 8.08 0.00 38.07 4.30
174 175 3.552068 GGAAGGTGACACAAAATTTCCGG 60.552 47.826 8.08 0.00 0.00 5.14
175 176 2.661718 AGGTGACACAAAATTTCCGGT 58.338 42.857 8.08 0.00 0.00 5.28
176 177 3.028130 AGGTGACACAAAATTTCCGGTT 58.972 40.909 8.08 0.00 0.00 4.44
177 178 3.449377 AGGTGACACAAAATTTCCGGTTT 59.551 39.130 8.08 0.00 0.00 3.27
178 179 4.645588 AGGTGACACAAAATTTCCGGTTTA 59.354 37.500 8.08 0.00 0.00 2.01
179 180 4.979815 GGTGACACAAAATTTCCGGTTTAG 59.020 41.667 8.08 0.00 0.00 1.85
180 181 4.979815 GTGACACAAAATTTCCGGTTTAGG 59.020 41.667 0.00 0.00 0.00 2.69
181 182 3.985008 ACACAAAATTTCCGGTTTAGGC 58.015 40.909 0.00 0.00 0.00 3.93
182 183 3.243941 ACACAAAATTTCCGGTTTAGGCC 60.244 43.478 0.00 0.00 0.00 5.19
191 192 4.770874 GTTTAGGCCGGCCGCTCA 62.771 66.667 38.88 22.73 41.95 4.26
192 193 4.770874 TTTAGGCCGGCCGCTCAC 62.771 66.667 38.88 15.37 41.95 3.51
201 202 2.493030 GCCGCTCACGTAGGCTAA 59.507 61.111 13.90 0.00 46.83 3.09
202 203 1.589196 GCCGCTCACGTAGGCTAAG 60.589 63.158 13.90 5.89 46.83 2.18
203 204 1.589196 CCGCTCACGTAGGCTAAGC 60.589 63.158 7.40 6.62 37.70 3.09
204 205 3.999051 GCTCACGTAGGCTAAGCG 58.001 61.111 7.40 5.23 0.00 4.68
205 206 1.432251 GCTCACGTAGGCTAAGCGA 59.568 57.895 11.00 4.94 0.00 4.93
206 207 0.592754 GCTCACGTAGGCTAAGCGAG 60.593 60.000 17.58 17.58 0.00 5.03
224 225 3.774528 CAGCCGGCCACTCTGCTA 61.775 66.667 26.15 0.00 31.69 3.49
225 226 3.465403 AGCCGGCCACTCTGCTAG 61.465 66.667 26.15 0.00 30.97 3.42
226 227 3.461773 GCCGGCCACTCTGCTAGA 61.462 66.667 18.11 0.00 0.00 2.43
227 228 2.496817 CCGGCCACTCTGCTAGAC 59.503 66.667 2.24 0.00 0.00 2.59
228 229 2.055042 CCGGCCACTCTGCTAGACT 61.055 63.158 2.24 0.00 0.00 3.24
229 230 1.608717 CCGGCCACTCTGCTAGACTT 61.609 60.000 2.24 0.00 0.00 3.01
230 231 0.459237 CGGCCACTCTGCTAGACTTG 60.459 60.000 2.24 0.00 0.00 3.16
231 232 0.107945 GGCCACTCTGCTAGACTTGG 60.108 60.000 0.00 0.00 0.00 3.61
232 233 0.742635 GCCACTCTGCTAGACTTGGC 60.743 60.000 13.59 13.59 39.67 4.52
233 234 0.107945 CCACTCTGCTAGACTTGGCC 60.108 60.000 0.00 0.00 0.00 5.36
265 266 1.130054 AGGCTTTCTCTCCACCAGCA 61.130 55.000 0.00 0.00 31.71 4.41
269 270 2.575532 CTTTCTCTCCACCAGCACAAA 58.424 47.619 0.00 0.00 0.00 2.83
282 283 1.006832 GCACAAACTCGACACACACT 58.993 50.000 0.00 0.00 0.00 3.55
328 330 1.391157 TTGTGTGCTTTGCAGGGACC 61.391 55.000 9.95 0.00 40.08 4.46
389 463 2.021584 CACGCTAGCGCAACAGTCA 61.022 57.895 35.63 0.00 44.19 3.41
421 495 0.328258 CGTCCTTTCCCCTTGGTCAT 59.672 55.000 0.00 0.00 0.00 3.06
449 523 4.584518 CACCACCCACCAGCAGCA 62.585 66.667 0.00 0.00 0.00 4.41
504 625 0.247736 TTTCTCTCTTGCGGAGGCTC 59.752 55.000 5.78 5.78 42.10 4.70
561 684 1.899437 CGCCATGTAGGGGTGTCAGT 61.899 60.000 0.00 0.00 44.93 3.41
579 702 2.615447 CAGTGCATCACTTGTGTGTCTT 59.385 45.455 0.00 0.00 42.59 3.01
631 769 6.536731 GTGATTTGACTCACATATAGGCAG 57.463 41.667 0.00 0.00 44.03 4.85
790 1151 2.042259 CATTTGCTGCTCTCCGCCA 61.042 57.895 0.00 0.00 38.05 5.69
1238 1827 1.887198 CTACACTGAGGTCTTCACGGT 59.113 52.381 0.00 0.00 0.00 4.83
1239 1828 1.120530 ACACTGAGGTCTTCACGGTT 58.879 50.000 0.00 0.00 0.00 4.44
1284 1873 2.350895 CTCGCCATGGTGTCCCAA 59.649 61.111 24.28 4.31 46.04 4.12
1300 1889 2.783510 TCCCAAAGGAAGGAGTTTCTGT 59.216 45.455 0.00 0.00 40.08 3.41
1373 1962 1.827969 CCTCGGACTGGAGAAAGATGT 59.172 52.381 0.00 0.00 36.08 3.06
1476 2065 0.994247 TTGATGACAGTGGCATCCCT 59.006 50.000 31.62 2.54 41.05 4.20
1751 2346 1.831106 TGCATCCTCGGACATACTTGT 59.169 47.619 0.00 0.00 39.32 3.16
1783 2378 0.110486 AGCCGTCAAGGATGGTGTTT 59.890 50.000 6.37 0.00 45.00 2.83
1807 2402 1.893919 GCTTTCACTCTCCCTCGGCT 61.894 60.000 0.00 0.00 0.00 5.52
2402 3003 1.338136 GGTGTCCGTCCATCTCCCAT 61.338 60.000 0.00 0.00 0.00 4.00
2410 3011 1.153369 CCATCTCCCATTGTCGCGT 60.153 57.895 5.77 0.00 0.00 6.01
2492 3093 0.680921 CCCGGGCTCAACATCATTGT 60.681 55.000 8.08 0.00 37.82 2.71
2541 3142 3.017048 TCTGGGCCATTCAACATTAGG 57.983 47.619 6.72 0.00 0.00 2.69
2549 3150 4.796606 CCATTCAACATTAGGTCAGGGAT 58.203 43.478 0.00 0.00 0.00 3.85
2699 3300 0.179062 ATCTTGGACGAGCAGCATCC 60.179 55.000 0.00 0.00 0.00 3.51
2910 3511 1.732259 GCACAGTTGAACTACCCATCG 59.268 52.381 0.00 0.00 0.00 3.84
2984 3585 1.830477 TGTGGGGCCAATAAATTCAGC 59.170 47.619 4.39 0.00 0.00 4.26
3202 3805 6.042638 TCTCCTCTGTTGTAATCAGGAAAG 57.957 41.667 0.00 0.00 34.15 2.62
3256 3859 6.027749 GCGCATGTAATATTGTAATTAGGGC 58.972 40.000 0.30 0.00 0.00 5.19
3355 3958 7.327032 GCTGTCACAATTCTTTTCTGAATTACC 59.673 37.037 0.00 0.00 42.63 2.85
3599 4202 9.862149 TTTCCTCTAAGTTAGTTCCTTTCAATT 57.138 29.630 9.71 0.00 0.00 2.32
3600 4203 8.848474 TCCTCTAAGTTAGTTCCTTTCAATTG 57.152 34.615 9.71 0.00 0.00 2.32
3751 4354 4.503714 TCTCCCTGTGTTTCTTTTCTGT 57.496 40.909 0.00 0.00 0.00 3.41
3816 4513 9.952188 AAGCTAAATTGAGTCTTGACTTTTAAC 57.048 29.630 4.67 2.78 0.00 2.01
3869 4582 7.125536 ACAGTTTAAACCTATTAGTTCGTGC 57.874 36.000 14.72 0.00 0.00 5.34
3876 4589 5.909621 ACCTATTAGTTCGTGCTGTAAGA 57.090 39.130 0.00 0.00 34.07 2.10
3927 4640 6.961554 GCTTGTACTATTAGTTGTGCATGTTC 59.038 38.462 0.85 0.00 0.00 3.18
4034 4749 2.283966 CCTCCAGGTCCAGGTCGT 60.284 66.667 0.00 0.00 0.00 4.34
4104 4819 5.097742 TCCGAAATCCTTCATCTTTGCTA 57.902 39.130 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.867456 AACTTTTATTCCGCGTGTCG 57.133 45.000 4.92 0.00 38.08 4.35
7 8 3.687698 AGCATAACTTTTATTCCGCGTGT 59.312 39.130 4.92 0.00 0.00 4.49
9 10 4.957759 AAGCATAACTTTTATTCCGCGT 57.042 36.364 4.92 0.00 33.71 6.01
36 37 9.804758 TGTATTTAATTCGTGGTTTCAAAAACT 57.195 25.926 2.90 0.00 0.00 2.66
37 38 9.838163 GTGTATTTAATTCGTGGTTTCAAAAAC 57.162 29.630 0.00 0.00 0.00 2.43
38 39 9.804758 AGTGTATTTAATTCGTGGTTTCAAAAA 57.195 25.926 0.00 0.00 0.00 1.94
66 67 5.064962 CCATCGGTGCATGCATTTTATTTTT 59.935 36.000 25.64 0.00 0.00 1.94
67 68 4.571580 CCATCGGTGCATGCATTTTATTTT 59.428 37.500 25.64 0.96 0.00 1.82
68 69 4.121317 CCATCGGTGCATGCATTTTATTT 58.879 39.130 25.64 2.65 0.00 1.40
69 70 3.493002 CCCATCGGTGCATGCATTTTATT 60.493 43.478 25.64 4.33 0.00 1.40
70 71 2.036217 CCCATCGGTGCATGCATTTTAT 59.964 45.455 25.64 12.34 0.00 1.40
71 72 1.408340 CCCATCGGTGCATGCATTTTA 59.592 47.619 25.64 10.46 0.00 1.52
72 73 0.176219 CCCATCGGTGCATGCATTTT 59.824 50.000 25.64 6.61 0.00 1.82
73 74 0.683828 TCCCATCGGTGCATGCATTT 60.684 50.000 25.64 6.23 0.00 2.32
74 75 0.468585 ATCCCATCGGTGCATGCATT 60.469 50.000 25.64 6.62 0.00 3.56
75 76 1.152138 ATCCCATCGGTGCATGCAT 59.848 52.632 25.64 4.32 0.00 3.96
76 77 1.824760 CATCCCATCGGTGCATGCA 60.825 57.895 18.46 18.46 0.00 3.96
77 78 2.558286 CCATCCCATCGGTGCATGC 61.558 63.158 11.82 11.82 0.00 4.06
78 79 2.558286 GCCATCCCATCGGTGCATG 61.558 63.158 0.00 0.00 0.00 4.06
79 80 2.203394 GCCATCCCATCGGTGCAT 60.203 61.111 0.00 0.00 0.00 3.96
80 81 3.410628 AGCCATCCCATCGGTGCA 61.411 61.111 0.00 0.00 0.00 4.57
81 82 2.903855 CAGCCATCCCATCGGTGC 60.904 66.667 0.00 0.00 0.00 5.01
82 83 1.820906 CACAGCCATCCCATCGGTG 60.821 63.158 0.00 0.00 0.00 4.94
83 84 2.591753 CACAGCCATCCCATCGGT 59.408 61.111 0.00 0.00 0.00 4.69
84 85 2.903855 GCACAGCCATCCCATCGG 60.904 66.667 0.00 0.00 0.00 4.18
85 86 2.124612 TGCACAGCCATCCCATCG 60.125 61.111 0.00 0.00 0.00 3.84
86 87 1.099879 GTCTGCACAGCCATCCCATC 61.100 60.000 0.00 0.00 0.00 3.51
87 88 1.077212 GTCTGCACAGCCATCCCAT 60.077 57.895 0.00 0.00 0.00 4.00
88 89 1.855441 ATGTCTGCACAGCCATCCCA 61.855 55.000 0.00 0.00 35.41 4.37
89 90 0.682209 AATGTCTGCACAGCCATCCC 60.682 55.000 0.00 0.00 35.41 3.85
90 91 1.180029 AAATGTCTGCACAGCCATCC 58.820 50.000 0.00 0.00 35.41 3.51
91 92 4.096833 TCATTAAATGTCTGCACAGCCATC 59.903 41.667 0.00 0.00 35.41 3.51
92 93 4.018490 TCATTAAATGTCTGCACAGCCAT 58.982 39.130 0.00 0.00 35.41 4.40
93 94 3.191162 GTCATTAAATGTCTGCACAGCCA 59.809 43.478 0.00 0.00 35.41 4.75
94 95 3.428045 GGTCATTAAATGTCTGCACAGCC 60.428 47.826 0.00 0.00 35.41 4.85
95 96 3.191162 TGGTCATTAAATGTCTGCACAGC 59.809 43.478 0.00 0.00 35.41 4.40
96 97 5.048504 ACTTGGTCATTAAATGTCTGCACAG 60.049 40.000 0.00 0.00 35.41 3.66
97 98 4.826733 ACTTGGTCATTAAATGTCTGCACA 59.173 37.500 0.00 0.00 36.78 4.57
98 99 5.376854 ACTTGGTCATTAAATGTCTGCAC 57.623 39.130 0.00 0.00 0.00 4.57
99 100 7.517614 TTTACTTGGTCATTAAATGTCTGCA 57.482 32.000 0.00 0.00 0.00 4.41
100 101 8.810652 TTTTTACTTGGTCATTAAATGTCTGC 57.189 30.769 0.00 0.00 0.00 4.26
101 102 8.915654 GCTTTTTACTTGGTCATTAAATGTCTG 58.084 33.333 0.00 0.00 0.00 3.51
102 103 8.860088 AGCTTTTTACTTGGTCATTAAATGTCT 58.140 29.630 0.00 0.00 0.00 3.41
103 104 9.476202 AAGCTTTTTACTTGGTCATTAAATGTC 57.524 29.630 0.00 0.00 0.00 3.06
104 105 9.830975 AAAGCTTTTTACTTGGTCATTAAATGT 57.169 25.926 5.69 0.00 0.00 2.71
135 136 9.628500 GTCACCTTCCTAATTAACCATTCTAAT 57.372 33.333 0.00 0.00 0.00 1.73
136 137 8.607713 TGTCACCTTCCTAATTAACCATTCTAA 58.392 33.333 0.00 0.00 0.00 2.10
137 138 8.044908 GTGTCACCTTCCTAATTAACCATTCTA 58.955 37.037 0.00 0.00 0.00 2.10
138 139 6.884836 GTGTCACCTTCCTAATTAACCATTCT 59.115 38.462 0.00 0.00 0.00 2.40
139 140 6.657541 TGTGTCACCTTCCTAATTAACCATTC 59.342 38.462 0.00 0.00 0.00 2.67
140 141 6.548321 TGTGTCACCTTCCTAATTAACCATT 58.452 36.000 0.00 0.00 0.00 3.16
141 142 6.134535 TGTGTCACCTTCCTAATTAACCAT 57.865 37.500 0.00 0.00 0.00 3.55
142 143 5.570205 TGTGTCACCTTCCTAATTAACCA 57.430 39.130 0.00 0.00 0.00 3.67
143 144 6.887626 TTTGTGTCACCTTCCTAATTAACC 57.112 37.500 0.00 0.00 0.00 2.85
144 145 9.758651 AAATTTTGTGTCACCTTCCTAATTAAC 57.241 29.630 0.00 0.00 0.00 2.01
145 146 9.974980 GAAATTTTGTGTCACCTTCCTAATTAA 57.025 29.630 0.00 0.00 0.00 1.40
146 147 8.581578 GGAAATTTTGTGTCACCTTCCTAATTA 58.418 33.333 0.00 0.00 0.00 1.40
147 148 7.441836 GGAAATTTTGTGTCACCTTCCTAATT 58.558 34.615 0.00 0.00 0.00 1.40
148 149 6.294508 CGGAAATTTTGTGTCACCTTCCTAAT 60.295 38.462 0.00 0.00 30.76 1.73
149 150 5.009210 CGGAAATTTTGTGTCACCTTCCTAA 59.991 40.000 0.00 0.00 30.76 2.69
150 151 4.517453 CGGAAATTTTGTGTCACCTTCCTA 59.483 41.667 0.00 0.00 30.76 2.94
151 152 3.317993 CGGAAATTTTGTGTCACCTTCCT 59.682 43.478 0.00 0.00 30.76 3.36
152 153 3.552068 CCGGAAATTTTGTGTCACCTTCC 60.552 47.826 0.00 4.57 0.00 3.46
153 154 3.067601 ACCGGAAATTTTGTGTCACCTTC 59.932 43.478 9.46 0.00 0.00 3.46
154 155 3.028130 ACCGGAAATTTTGTGTCACCTT 58.972 40.909 9.46 0.00 0.00 3.50
155 156 2.661718 ACCGGAAATTTTGTGTCACCT 58.338 42.857 9.46 0.00 0.00 4.00
156 157 3.446310 AACCGGAAATTTTGTGTCACC 57.554 42.857 9.46 0.00 0.00 4.02
157 158 4.979815 CCTAAACCGGAAATTTTGTGTCAC 59.020 41.667 9.46 0.00 0.00 3.67
158 159 4.500035 GCCTAAACCGGAAATTTTGTGTCA 60.500 41.667 9.46 0.00 0.00 3.58
159 160 3.985279 GCCTAAACCGGAAATTTTGTGTC 59.015 43.478 9.46 0.00 0.00 3.67
160 161 3.243941 GGCCTAAACCGGAAATTTTGTGT 60.244 43.478 9.46 0.00 0.00 3.72
161 162 3.322369 GGCCTAAACCGGAAATTTTGTG 58.678 45.455 9.46 0.00 0.00 3.33
162 163 3.671008 GGCCTAAACCGGAAATTTTGT 57.329 42.857 9.46 0.00 0.00 2.83
174 175 4.770874 TGAGCGGCCGGCCTAAAC 62.771 66.667 41.01 27.82 45.17 2.01
175 176 4.770874 GTGAGCGGCCGGCCTAAA 62.771 66.667 41.01 22.16 45.17 1.85
185 186 1.589196 GCTTAGCCTACGTGAGCGG 60.589 63.158 0.00 0.00 43.45 5.52
186 187 3.999051 GCTTAGCCTACGTGAGCG 58.001 61.111 0.00 0.00 44.93 5.03
187 188 0.592754 CTCGCTTAGCCTACGTGAGC 60.593 60.000 5.94 0.00 0.00 4.26
188 189 0.592754 GCTCGCTTAGCCTACGTGAG 60.593 60.000 12.94 12.94 46.25 3.51
189 190 1.432251 GCTCGCTTAGCCTACGTGA 59.568 57.895 0.00 0.00 46.25 4.35
190 191 3.999051 GCTCGCTTAGCCTACGTG 58.001 61.111 0.00 0.00 46.25 4.49
207 208 3.729965 CTAGCAGAGTGGCCGGCTG 62.730 68.421 28.56 17.67 38.05 4.85
208 209 3.465403 CTAGCAGAGTGGCCGGCT 61.465 66.667 28.56 6.33 40.51 5.52
209 210 3.461773 TCTAGCAGAGTGGCCGGC 61.462 66.667 21.18 21.18 0.00 6.13
210 211 1.608717 AAGTCTAGCAGAGTGGCCGG 61.609 60.000 0.00 0.00 0.00 6.13
211 212 0.459237 CAAGTCTAGCAGAGTGGCCG 60.459 60.000 0.00 0.00 0.00 6.13
212 213 0.107945 CCAAGTCTAGCAGAGTGGCC 60.108 60.000 0.00 0.00 0.00 5.36
213 214 0.742635 GCCAAGTCTAGCAGAGTGGC 60.743 60.000 17.39 17.39 44.50 5.01
214 215 0.107945 GGCCAAGTCTAGCAGAGTGG 60.108 60.000 0.00 9.60 34.99 4.00
215 216 0.901124 AGGCCAAGTCTAGCAGAGTG 59.099 55.000 5.01 0.00 0.00 3.51
216 217 1.277557 CAAGGCCAAGTCTAGCAGAGT 59.722 52.381 5.01 0.00 0.00 3.24
217 218 1.277557 ACAAGGCCAAGTCTAGCAGAG 59.722 52.381 5.01 0.00 0.00 3.35
218 219 1.352083 ACAAGGCCAAGTCTAGCAGA 58.648 50.000 5.01 0.00 0.00 4.26
219 220 2.191128 AACAAGGCCAAGTCTAGCAG 57.809 50.000 5.01 0.00 0.00 4.24
220 221 2.229792 CAAACAAGGCCAAGTCTAGCA 58.770 47.619 5.01 0.00 0.00 3.49
221 222 2.230660 ACAAACAAGGCCAAGTCTAGC 58.769 47.619 5.01 0.00 0.00 3.42
222 223 4.499696 CCAAACAAACAAGGCCAAGTCTAG 60.500 45.833 5.01 0.00 0.00 2.43
223 224 3.383185 CCAAACAAACAAGGCCAAGTCTA 59.617 43.478 5.01 0.00 0.00 2.59
224 225 2.168313 CCAAACAAACAAGGCCAAGTCT 59.832 45.455 5.01 0.00 0.00 3.24
225 226 2.167487 TCCAAACAAACAAGGCCAAGTC 59.833 45.455 5.01 0.00 0.00 3.01
226 227 2.168313 CTCCAAACAAACAAGGCCAAGT 59.832 45.455 5.01 0.00 0.00 3.16
227 228 2.483538 CCTCCAAACAAACAAGGCCAAG 60.484 50.000 5.01 0.00 0.00 3.61
228 229 1.484240 CCTCCAAACAAACAAGGCCAA 59.516 47.619 5.01 0.00 0.00 4.52
229 230 1.118838 CCTCCAAACAAACAAGGCCA 58.881 50.000 5.01 0.00 0.00 5.36
230 231 0.249868 GCCTCCAAACAAACAAGGCC 60.250 55.000 0.00 0.00 45.45 5.19
231 232 3.289128 GCCTCCAAACAAACAAGGC 57.711 52.632 0.00 0.00 45.11 4.35
232 233 3.132824 AGAAAGCCTCCAAACAAACAAGG 59.867 43.478 0.00 0.00 0.00 3.61
233 234 4.098501 AGAGAAAGCCTCCAAACAAACAAG 59.901 41.667 0.00 0.00 42.97 3.16
265 266 3.444916 CACTAGTGTGTGTCGAGTTTGT 58.555 45.455 15.06 0.00 39.24 2.83
282 283 6.015350 GGCAAGGCTATACTTCATAGACACTA 60.015 42.308 0.26 0.00 46.53 2.74
296 297 1.681780 GCACACAAGGGCAAGGCTATA 60.682 52.381 0.00 0.00 0.00 1.31
328 330 1.392589 ATCAAAATAGCGGGGCACTG 58.607 50.000 0.00 0.00 0.00 3.66
389 463 1.233285 AAGGACGACGCTACGTGTCT 61.233 55.000 9.53 4.95 46.52 3.41
421 495 2.114411 GGTGGTGGCGGAAGGAAA 59.886 61.111 0.00 0.00 0.00 3.13
449 523 6.355747 CATCTATGGAAAAAGAGGAAGCTCT 58.644 40.000 0.00 0.00 34.76 4.09
579 702 3.068881 CGGTTCCTCTTGGCAGGA 58.931 61.111 0.00 0.00 41.16 3.86
631 769 1.300542 GCACGCCTAGATGCTCCTC 60.301 63.158 6.40 0.00 38.84 3.71
698 838 2.195567 GGGCAGAGCACAAGCACAA 61.196 57.895 1.60 0.00 45.49 3.33
790 1151 3.506743 TGGTGGTGGTGGTGGCAT 61.507 61.111 0.00 0.00 0.00 4.40
1051 1640 1.442526 CCTAGGTCGTCGCATACCGT 61.443 60.000 0.00 0.00 40.88 4.83
1132 1721 2.031163 GTGGTCGTCCTTGCTGCT 59.969 61.111 0.00 0.00 34.23 4.24
1138 1727 4.003788 CCAGCGGTGGTCGTCCTT 62.004 66.667 25.51 0.00 39.30 3.36
1190 1779 3.838271 GGCGTGGCTCATCGGAGA 61.838 66.667 0.00 0.00 44.26 3.71
1257 1846 1.215382 CATGGCGAGGTCGTCTTCA 59.785 57.895 5.47 0.00 45.41 3.02
1284 1873 1.202940 GCCCACAGAAACTCCTTCCTT 60.203 52.381 0.00 0.00 34.21 3.36
1300 1889 1.002624 GATGGTCTGGAAACGCCCA 60.003 57.895 0.00 0.00 34.97 5.36
1373 1962 4.631740 TGTCCCTCCACAGCCCGA 62.632 66.667 0.00 0.00 0.00 5.14
1403 1992 1.619332 GGACCCCGATTATGACTCCTC 59.381 57.143 0.00 0.00 0.00 3.71
1751 2346 0.458669 GACGGCTTCATCTAACCCGA 59.541 55.000 4.24 0.00 38.39 5.14
2248 2849 0.768221 TCCAGAAGGGTGGTGAAGCT 60.768 55.000 0.00 0.00 38.88 3.74
2402 3003 1.640428 GGATGAGAATGACGCGACAA 58.360 50.000 15.93 0.00 0.00 3.18
2410 3011 1.441729 GACCGCGGGATGAGAATGA 59.558 57.895 31.76 0.00 0.00 2.57
2492 3093 1.902918 GTGAGTGGTGGCCATGCAA 60.903 57.895 9.72 0.00 35.28 4.08
2541 3142 2.894126 AGTCGACATGGATATCCCTGAC 59.106 50.000 27.88 21.67 35.54 3.51
2549 3150 3.733443 CATGTGGAGTCGACATGGATA 57.267 47.619 30.32 2.28 44.68 2.59
2699 3300 3.261951 CATACGCGGTTGCCCTCG 61.262 66.667 12.47 0.00 44.51 4.63
2910 3511 2.028112 TGTCCTGAGTGGCACTGTTATC 60.028 50.000 27.45 11.03 35.26 1.75
2984 3585 4.446371 GGAACCTCCATCTTCTGTGTATG 58.554 47.826 0.00 0.00 36.28 2.39
3284 3887 6.819284 ACATCAATTATTTTACAGGCATGGG 58.181 36.000 2.31 0.00 0.00 4.00
3355 3958 8.940768 TGTTGATAAGTTGGGAAAAAGAAAAG 57.059 30.769 0.00 0.00 0.00 2.27
3361 3964 8.887717 CAAACATTGTTGATAAGTTGGGAAAAA 58.112 29.630 2.13 0.00 0.00 1.94
3582 4185 8.762481 AACCTAACAATTGAAAGGAACTAACT 57.238 30.769 26.86 8.91 38.49 2.24
3583 4186 8.626526 TGAACCTAACAATTGAAAGGAACTAAC 58.373 33.333 26.86 15.38 38.49 2.34
3599 4202 1.493022 AGTGCCCAACTGAACCTAACA 59.507 47.619 0.00 0.00 37.88 2.41
3600 4203 2.271944 AGTGCCCAACTGAACCTAAC 57.728 50.000 0.00 0.00 37.88 2.34
3711 4314 5.093457 GGAGAAAAACCAATTTAGCTACGC 58.907 41.667 0.00 0.00 0.00 4.42
3751 4354 4.862018 CGAACTGCAAAAGACAAAAAGGAA 59.138 37.500 0.00 0.00 0.00 3.36
3816 4513 8.673626 ATTACTGCAACGATGTATTTTTCTTG 57.326 30.769 0.00 0.00 0.00 3.02
3869 4582 9.295214 CTGACTCACTAATACATGTTCTTACAG 57.705 37.037 2.30 2.39 37.77 2.74
3900 4613 6.655003 ACATGCACAACTAATAGTACAAGCTT 59.345 34.615 0.00 0.00 0.00 3.74
3927 4640 1.536073 TTGAGACAGGGGAGTGAGCG 61.536 60.000 0.00 0.00 0.00 5.03
4034 4749 2.009681 TGTAGCACCACTGAGGAGAA 57.990 50.000 0.00 0.00 41.22 2.87
4104 4819 7.114849 TGGGAAAATATAGGGGAATAGCATT 57.885 36.000 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.