Multiple sequence alignment - TraesCS4B01G324100

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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 TraesCS4B01G324100 chr4B 100.000 2249 0 0 1 2249 615148735 615150983 0.000000e+00 4154.0
1 TraesCS4B01G324100 chr4B 96.818 817 26 0 1433 2249 658183701 658182885 0.000000e+00 1365.0
2 TraesCS4B01G324100 chr4B 84.384 333 37 9 918 1242 615136338 615136663 1.680000e-81 313.0
3 TraesCS4B01G324100 chr4B 91.111 180 16 0 1062 1241 615133966 615134145 6.200000e-61 244.0
4 TraesCS4B01G324100 chr5A 96.940 817 24 1 1433 2249 400784646 400783831 0.000000e+00 1369.0
5 TraesCS4B01G324100 chr5A 90.602 947 67 13 494 1429 663944540 663945475 0.000000e+00 1236.0
6 TraesCS4B01G324100 chr5A 87.773 229 28 0 1014 1242 663941430 663941658 3.680000e-68 268.0
7 TraesCS4B01G324100 chr5A 90.556 180 17 0 1062 1241 663914138 663914317 2.890000e-59 239.0
8 TraesCS4B01G324100 chr5A 88.235 204 17 2 309 511 663944327 663944524 1.040000e-58 237.0
9 TraesCS4B01G324100 chr5B 96.822 818 26 0 1432 2249 214175633 214176450 0.000000e+00 1367.0
10 TraesCS4B01G324100 chr5B 96.691 816 27 0 1433 2248 649539551 649538736 0.000000e+00 1358.0
11 TraesCS4B01G324100 chr5B 94.805 308 16 0 3 310 591487754 591487447 4.340000e-132 481.0
12 TraesCS4B01G324100 chr5B 94.137 307 14 3 1 305 27313541 27313845 4.370000e-127 464.0
13 TraesCS4B01G324100 chr2B 96.822 818 26 0 1432 2249 458237644 458238461 0.000000e+00 1367.0
14 TraesCS4B01G324100 chr2B 96.818 817 26 0 1433 2249 251121371 251122187 0.000000e+00 1365.0
15 TraesCS4B01G324100 chr2B 92.722 316 21 1 1 316 690214509 690214196 2.630000e-124 455.0
16 TraesCS4B01G324100 chr7A 96.818 817 26 0 1433 2249 697182138 697181322 0.000000e+00 1365.0
17 TraesCS4B01G324100 chr7B 96.695 817 27 0 1433 2249 28889570 28890386 0.000000e+00 1360.0
18 TraesCS4B01G324100 chr3A 95.843 842 30 4 1408 2248 215351385 215350548 0.000000e+00 1356.0
19 TraesCS4B01G324100 chr4D 90.306 949 48 22 494 1433 483971514 483972427 0.000000e+00 1203.0
20 TraesCS4B01G324100 chr4D 86.711 301 36 4 943 1242 483968179 483968476 4.630000e-87 331.0
21 TraesCS4B01G324100 chr4D 89.268 205 19 3 309 511 483971298 483971501 1.030000e-63 254.0
22 TraesCS4B01G324100 chr6B 95.752 306 12 1 1 305 545598059 545598364 2.010000e-135 492.0
23 TraesCS4B01G324100 chr3B 95.469 309 13 1 1 308 796006105 796006413 2.010000e-135 492.0
24 TraesCS4B01G324100 chr3B 89.474 57 5 1 420 475 148998294 148998238 1.110000e-08 71.3
25 TraesCS4B01G324100 chr1A 95.098 306 13 1 1 306 547342925 547342622 4.340000e-132 481.0
26 TraesCS4B01G324100 chr1A 82.540 63 11 0 410 472 577831435 577831373 3.120000e-04 56.5
27 TraesCS4B01G324100 chr2D 94.498 309 14 2 1 308 12896374 12896680 7.270000e-130 473.0
28 TraesCS4B01G324100 chr2D 94.737 304 14 1 1 304 60710431 60710732 2.610000e-129 472.0
29 TraesCS4B01G324100 chr2D 96.875 32 1 0 444 475 170610947 170610916 1.000000e-03 54.7
30 TraesCS4B01G324100 chr7D 94.444 306 14 2 1 306 630373695 630373393 3.380000e-128 468.0
31 TraesCS4B01G324100 chr5D 90.476 63 6 0 410 472 6374070 6374132 1.430000e-12 84.2
32 TraesCS4B01G324100 chr5D 100.000 31 0 0 444 474 301585292 301585322 8.680000e-05 58.4
33 TraesCS4B01G324100 chr6D 100.000 33 0 0 443 475 445975878 445975846 6.710000e-06 62.1
34 TraesCS4B01G324100 chr4A 84.375 64 7 3 409 472 146957740 146957800 2.410000e-05 60.2


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 TraesCS4B01G324100 chr4B 615148735 615150983 2248 False 4154.000000 4154 100.000000 1 2249 1 chr4B.!!$F1 2248
1 TraesCS4B01G324100 chr4B 658182885 658183701 816 True 1365.000000 1365 96.818000 1433 2249 1 chr4B.!!$R1 816
2 TraesCS4B01G324100 chr4B 615133966 615136663 2697 False 278.500000 313 87.747500 918 1242 2 chr4B.!!$F2 324
3 TraesCS4B01G324100 chr5A 400783831 400784646 815 True 1369.000000 1369 96.940000 1433 2249 1 chr5A.!!$R1 816
4 TraesCS4B01G324100 chr5A 663941430 663945475 4045 False 580.333333 1236 88.870000 309 1429 3 chr5A.!!$F2 1120
5 TraesCS4B01G324100 chr5B 214175633 214176450 817 False 1367.000000 1367 96.822000 1432 2249 1 chr5B.!!$F2 817
6 TraesCS4B01G324100 chr5B 649538736 649539551 815 True 1358.000000 1358 96.691000 1433 2248 1 chr5B.!!$R2 815
7 TraesCS4B01G324100 chr2B 458237644 458238461 817 False 1367.000000 1367 96.822000 1432 2249 1 chr2B.!!$F2 817
8 TraesCS4B01G324100 chr2B 251121371 251122187 816 False 1365.000000 1365 96.818000 1433 2249 1 chr2B.!!$F1 816
9 TraesCS4B01G324100 chr7A 697181322 697182138 816 True 1365.000000 1365 96.818000 1433 2249 1 chr7A.!!$R1 816
10 TraesCS4B01G324100 chr7B 28889570 28890386 816 False 1360.000000 1360 96.695000 1433 2249 1 chr7B.!!$F1 816
11 TraesCS4B01G324100 chr3A 215350548 215351385 837 True 1356.000000 1356 95.843000 1408 2248 1 chr3A.!!$R1 840
12 TraesCS4B01G324100 chr4D 483968179 483972427 4248 False 596.000000 1203 88.761667 309 1433 3 chr4D.!!$F1 1124

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
56 57 0.037447 GGCTTTGAGGTTGGAGCTCT 59.963 55.0 14.64 0.0 42.83 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 5241 0.59117 GCATTGTACGTGCACTTGGT 59.409 50.0 16.19 8.21 42.08 3.67 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
23 24 2.121116 CCGTCGTGGCTTCTATACAG 57.879 55.000 0.00 0.00 0.00 2.74
29 30 3.056107 TCGTGGCTTCTATACAGCTGTTT 60.056 43.478 27.06 20.10 37.43 2.83
30 31 3.062639 CGTGGCTTCTATACAGCTGTTTG 59.937 47.826 27.06 15.13 37.43 2.93
32 33 3.009723 GGCTTCTATACAGCTGTTTGCA 58.990 45.455 27.06 7.17 45.94 4.08
33 34 3.064545 GGCTTCTATACAGCTGTTTGCAG 59.935 47.826 27.06 16.14 45.94 4.41
40 41 3.132084 GCTGTTTGCAGGTTGGCT 58.868 55.556 0.00 0.00 42.78 4.75
41 42 1.442987 GCTGTTTGCAGGTTGGCTT 59.557 52.632 0.00 0.00 42.78 4.35
42 43 0.179076 GCTGTTTGCAGGTTGGCTTT 60.179 50.000 0.00 0.00 42.78 3.51
47 48 0.396974 TTGCAGGTTGGCTTTGAGGT 60.397 50.000 0.00 0.00 34.04 3.85
48 49 0.396974 TGCAGGTTGGCTTTGAGGTT 60.397 50.000 0.00 0.00 34.04 3.50
50 51 0.675633 CAGGTTGGCTTTGAGGTTGG 59.324 55.000 0.00 0.00 0.00 3.77
51 52 0.555769 AGGTTGGCTTTGAGGTTGGA 59.444 50.000 0.00 0.00 0.00 3.53
54 55 0.185901 TTGGCTTTGAGGTTGGAGCT 59.814 50.000 0.00 0.00 35.53 4.09
55 56 0.250901 TGGCTTTGAGGTTGGAGCTC 60.251 55.000 4.71 4.71 42.72 4.09
56 57 0.037447 GGCTTTGAGGTTGGAGCTCT 59.963 55.000 14.64 0.00 42.83 4.09
57 58 1.279271 GGCTTTGAGGTTGGAGCTCTA 59.721 52.381 14.64 4.15 42.83 2.43
58 59 2.092699 GGCTTTGAGGTTGGAGCTCTAT 60.093 50.000 14.64 0.00 42.83 1.98
60 61 3.539604 CTTTGAGGTTGGAGCTCTATGG 58.460 50.000 14.64 0.00 42.83 2.74
61 62 2.254152 TGAGGTTGGAGCTCTATGGT 57.746 50.000 14.64 0.00 42.83 3.55
63 64 2.111384 GAGGTTGGAGCTCTATGGTGA 58.889 52.381 14.64 0.00 39.50 4.02
64 65 2.501723 GAGGTTGGAGCTCTATGGTGAA 59.498 50.000 14.64 0.00 39.50 3.18
65 66 2.503356 AGGTTGGAGCTCTATGGTGAAG 59.497 50.000 14.64 0.00 0.00 3.02
68 69 1.751351 TGGAGCTCTATGGTGAAGTCG 59.249 52.381 14.64 0.00 0.00 4.18
70 71 2.025155 GAGCTCTATGGTGAAGTCGGA 58.975 52.381 6.43 0.00 0.00 4.55
72 73 1.751924 GCTCTATGGTGAAGTCGGAGT 59.248 52.381 0.00 0.00 0.00 3.85
73 74 2.223618 GCTCTATGGTGAAGTCGGAGTC 60.224 54.545 0.00 0.00 0.00 3.36
74 75 2.014857 TCTATGGTGAAGTCGGAGTCG 58.985 52.381 0.00 0.00 37.82 4.18
76 77 1.251527 ATGGTGAAGTCGGAGTCGCT 61.252 55.000 3.12 0.00 36.13 4.93
77 78 1.153997 GGTGAAGTCGGAGTCGCTC 60.154 63.158 0.00 0.00 36.13 5.03
79 80 1.964891 TGAAGTCGGAGTCGCTCGT 60.965 57.895 1.64 0.00 36.13 4.18
83 84 2.739671 TCGGAGTCGCTCGTTCGA 60.740 61.111 0.00 0.00 36.13 3.71
85 86 2.100603 GGAGTCGCTCGTTCGAGG 59.899 66.667 20.97 12.49 39.34 4.63
86 87 2.577378 GAGTCGCTCGTTCGAGGC 60.577 66.667 20.97 13.22 39.34 4.70
87 88 3.324099 GAGTCGCTCGTTCGAGGCA 62.324 63.158 20.97 5.13 39.34 4.75
88 89 2.430244 GTCGCTCGTTCGAGGCAA 60.430 61.111 20.97 0.00 39.34 4.52
109 110 0.802222 CGGTGATGACGATGACGCTT 60.802 55.000 0.00 0.00 43.96 4.68
115 116 1.801913 GACGATGACGCTTGCGACT 60.802 57.895 22.03 5.32 43.96 4.18
116 117 1.734359 GACGATGACGCTTGCGACTC 61.734 60.000 22.03 10.07 43.96 3.36
118 119 1.153745 GATGACGCTTGCGACTCCT 60.154 57.895 22.03 2.74 0.00 3.69
119 120 1.142778 GATGACGCTTGCGACTCCTC 61.143 60.000 22.03 8.64 0.00 3.71
124 125 4.116328 CTTGCGACTCCTCGGCGA 62.116 66.667 10.14 10.14 40.53 5.54
128 129 2.956964 CGACTCCTCGGCGAATGC 60.957 66.667 12.13 0.00 36.16 3.56
142 143 2.671914 GCGAATGCCATTCTTCTTTGCA 60.672 45.455 15.04 0.00 37.13 4.08
144 145 2.667473 ATGCCATTCTTCTTTGCAGC 57.333 45.000 0.00 0.00 35.10 5.25
145 146 1.624336 TGCCATTCTTCTTTGCAGCT 58.376 45.000 0.00 0.00 0.00 4.24
149 150 3.801293 GCCATTCTTCTTTGCAGCTTTGT 60.801 43.478 0.00 0.00 0.00 2.83
151 152 4.365723 CATTCTTCTTTGCAGCTTTGTGT 58.634 39.130 0.00 0.00 0.00 3.72
152 153 4.454728 TTCTTCTTTGCAGCTTTGTGTT 57.545 36.364 0.00 0.00 0.00 3.32
155 156 2.098614 TCTTTGCAGCTTTGTGTTCCA 58.901 42.857 0.00 0.00 0.00 3.53
156 157 2.694628 TCTTTGCAGCTTTGTGTTCCAT 59.305 40.909 0.00 0.00 0.00 3.41
159 160 1.337703 TGCAGCTTTGTGTTCCATGTC 59.662 47.619 0.00 0.00 0.00 3.06
161 162 1.069022 CAGCTTTGTGTTCCATGTCGG 60.069 52.381 0.00 0.00 0.00 4.79
163 164 1.334960 GCTTTGTGTTCCATGTCGGTG 60.335 52.381 0.00 0.00 35.57 4.94
165 166 1.169661 TTGTGTTCCATGTCGGTGGC 61.170 55.000 0.00 0.00 39.19 5.01
168 169 2.040544 GTTCCATGTCGGTGGCCTG 61.041 63.158 3.32 0.00 39.19 4.85
170 171 4.033776 CCATGTCGGTGGCCTGGT 62.034 66.667 3.32 0.00 31.43 4.00
173 174 3.567579 ATGTCGGTGGCCTGGTTGG 62.568 63.158 3.32 0.00 39.35 3.77
182 183 2.751436 CCTGGTTGGCCGGTGATG 60.751 66.667 1.90 0.00 39.55 3.07
183 184 3.443045 CTGGTTGGCCGGTGATGC 61.443 66.667 1.90 0.00 36.39 3.91
189 190 4.820744 GGCCGGTGATGCCCATGT 62.821 66.667 1.90 0.00 43.33 3.21
191 192 2.271821 CCGGTGATGCCCATGTCA 59.728 61.111 0.00 0.00 0.00 3.58
192 193 1.820906 CCGGTGATGCCCATGTCAG 60.821 63.158 0.00 0.00 0.00 3.51
193 194 1.820906 CGGTGATGCCCATGTCAGG 60.821 63.158 0.00 0.00 0.00 3.86
196 197 1.033746 GTGATGCCCATGTCAGGTGG 61.034 60.000 0.00 0.00 36.47 4.61
203 204 0.401738 CCATGTCAGGTGGGTTGAGT 59.598 55.000 0.00 0.00 32.98 3.41
204 205 1.202927 CCATGTCAGGTGGGTTGAGTT 60.203 52.381 0.00 0.00 32.98 3.01
205 206 1.881973 CATGTCAGGTGGGTTGAGTTG 59.118 52.381 0.00 0.00 0.00 3.16
206 207 0.916086 TGTCAGGTGGGTTGAGTTGT 59.084 50.000 0.00 0.00 0.00 3.32
209 210 3.244422 TGTCAGGTGGGTTGAGTTGTATC 60.244 47.826 0.00 0.00 0.00 2.24
210 211 2.028476 TCAGGTGGGTTGAGTTGTATCG 60.028 50.000 0.00 0.00 0.00 2.92
211 212 1.278127 AGGTGGGTTGAGTTGTATCGG 59.722 52.381 0.00 0.00 0.00 4.18
214 215 3.143728 GTGGGTTGAGTTGTATCGGTTT 58.856 45.455 0.00 0.00 0.00 3.27
216 217 4.756135 GTGGGTTGAGTTGTATCGGTTTTA 59.244 41.667 0.00 0.00 0.00 1.52
217 218 4.998672 TGGGTTGAGTTGTATCGGTTTTAG 59.001 41.667 0.00 0.00 0.00 1.85
218 219 4.142752 GGGTTGAGTTGTATCGGTTTTAGC 60.143 45.833 0.00 0.00 0.00 3.09
219 220 4.142752 GGTTGAGTTGTATCGGTTTTAGCC 60.143 45.833 0.00 0.00 0.00 3.93
222 223 1.667212 GTTGTATCGGTTTTAGCCCGG 59.333 52.381 0.00 0.00 45.51 5.73
223 224 0.903942 TGTATCGGTTTTAGCCCGGT 59.096 50.000 0.00 0.00 45.51 5.28
225 226 2.290197 TGTATCGGTTTTAGCCCGGTTT 60.290 45.455 0.00 0.00 45.51 3.27
226 227 1.913778 ATCGGTTTTAGCCCGGTTTT 58.086 45.000 0.00 0.00 45.51 2.43
228 229 1.608109 TCGGTTTTAGCCCGGTTTTTC 59.392 47.619 0.00 0.00 45.51 2.29
231 232 1.030457 TTTTAGCCCGGTTTTTCGCA 58.970 45.000 0.00 0.00 0.00 5.10
232 233 1.030457 TTTAGCCCGGTTTTTCGCAA 58.970 45.000 0.00 0.00 0.00 4.85
233 234 1.030457 TTAGCCCGGTTTTTCGCAAA 58.970 45.000 0.00 0.00 0.00 3.68
234 235 1.249407 TAGCCCGGTTTTTCGCAAAT 58.751 45.000 0.00 0.00 0.00 2.32
235 236 0.391228 AGCCCGGTTTTTCGCAAATT 59.609 45.000 0.00 0.00 0.00 1.82
236 237 1.614413 AGCCCGGTTTTTCGCAAATTA 59.386 42.857 0.00 0.00 0.00 1.40
237 238 2.036089 AGCCCGGTTTTTCGCAAATTAA 59.964 40.909 0.00 0.00 0.00 1.40
239 240 2.732500 CCCGGTTTTTCGCAAATTAACC 59.267 45.455 0.00 0.00 35.91 2.85
244 245 0.959553 TTTCGCAAATTAACCGGGCA 59.040 45.000 6.32 0.00 0.00 5.36
245 246 0.959553 TTCGCAAATTAACCGGGCAA 59.040 45.000 6.32 0.00 0.00 4.52
246 247 1.178276 TCGCAAATTAACCGGGCAAT 58.822 45.000 6.32 0.96 0.00 3.56
248 249 1.923864 CGCAAATTAACCGGGCAATTC 59.076 47.619 6.32 0.00 0.00 2.17
249 250 2.416701 CGCAAATTAACCGGGCAATTCT 60.417 45.455 6.32 0.00 0.00 2.40
252 253 4.672409 CAAATTAACCGGGCAATTCTCTC 58.328 43.478 6.32 0.00 0.00 3.20
256 257 1.280457 ACCGGGCAATTCTCTCTTCT 58.720 50.000 6.32 0.00 0.00 2.85
258 259 2.284190 CCGGGCAATTCTCTCTTCTTC 58.716 52.381 0.00 0.00 0.00 2.87
259 260 2.093235 CCGGGCAATTCTCTCTTCTTCT 60.093 50.000 0.00 0.00 0.00 2.85
260 261 3.604582 CGGGCAATTCTCTCTTCTTCTT 58.395 45.455 0.00 0.00 0.00 2.52
261 262 4.383118 CCGGGCAATTCTCTCTTCTTCTTA 60.383 45.833 0.00 0.00 0.00 2.10
263 264 5.819901 CGGGCAATTCTCTCTTCTTCTTAAT 59.180 40.000 0.00 0.00 0.00 1.40
265 266 6.825721 GGGCAATTCTCTCTTCTTCTTAATCA 59.174 38.462 0.00 0.00 0.00 2.57
268 269 9.719279 GCAATTCTCTCTTCTTCTTAATCAATG 57.281 33.333 0.00 0.00 0.00 2.82
277 278 8.805175 TCTTCTTCTTAATCAATGAAAATGGCA 58.195 29.630 0.00 0.00 0.00 4.92
278 279 9.426837 CTTCTTCTTAATCAATGAAAATGGCAA 57.573 29.630 0.00 0.00 0.00 4.52
279 280 9.775854 TTCTTCTTAATCAATGAAAATGGCAAA 57.224 25.926 0.00 0.00 0.00 3.68
280 281 9.947433 TCTTCTTAATCAATGAAAATGGCAAAT 57.053 25.926 0.00 0.00 0.00 2.32
282 283 9.947433 TTCTTAATCAATGAAAATGGCAAATCT 57.053 25.926 0.00 0.00 0.00 2.40
283 284 9.947433 TCTTAATCAATGAAAATGGCAAATCTT 57.053 25.926 0.00 0.00 0.00 2.40
287 288 6.670233 TCAATGAAAATGGCAAATCTTTTGC 58.330 32.000 14.88 14.88 44.22 3.68
296 297 3.380142 GCAAATCTTTTGCCTCGTTTCA 58.620 40.909 12.74 0.00 39.38 2.69
297 298 3.801594 GCAAATCTTTTGCCTCGTTTCAA 59.198 39.130 12.74 0.00 39.38 2.69
298 299 4.269844 GCAAATCTTTTGCCTCGTTTCAAA 59.730 37.500 12.74 0.00 39.38 2.69
299 300 5.220567 GCAAATCTTTTGCCTCGTTTCAAAA 60.221 36.000 12.74 9.63 39.13 2.44
359 3729 8.612145 ACTATAAATTCAAGAACTTGTAGGGGT 58.388 33.333 13.15 2.43 41.16 4.95
364 3734 3.650942 TCAAGAACTTGTAGGGGTCACAT 59.349 43.478 13.15 0.00 41.16 3.21
414 3785 9.897744 CTTGAGAGCTGTGATATTTTTAAAACA 57.102 29.630 0.00 0.00 0.00 2.83
426 3797 9.305925 GATATTTTTAAAACAAGATCAGCCAGG 57.694 33.333 0.00 0.00 0.00 4.45
428 3799 6.723298 TTTTAAAACAAGATCAGCCAGGAA 57.277 33.333 0.00 0.00 0.00 3.36
433 3804 2.776536 ACAAGATCAGCCAGGAATAGCT 59.223 45.455 0.00 0.00 0.00 3.32
440 3811 2.103771 CAGCCAGGAATAGCTCTTAGCA 59.896 50.000 0.00 0.00 45.56 3.49
441 3812 2.774234 AGCCAGGAATAGCTCTTAGCAA 59.226 45.455 0.00 0.00 45.56 3.91
576 3980 3.896648 AAATGGTCAAAGTGTAGCACG 57.103 42.857 0.00 0.00 39.64 5.34
589 3993 1.325943 GTAGCACGCATCTCAAAGCTC 59.674 52.381 0.00 0.00 33.83 4.09
611 4016 1.369091 CCCGACGCTGGATTCTTTGG 61.369 60.000 0.00 0.00 0.00 3.28
616 4021 1.608590 ACGCTGGATTCTTTGGTGTTG 59.391 47.619 0.00 0.00 0.00 3.33
678 4083 1.484227 CGGCCGAATCGATGCGTTTA 61.484 55.000 24.07 0.00 0.00 2.01
683 4088 3.722082 GCCGAATCGATGCGTTTATGATC 60.722 47.826 23.79 0.81 0.00 2.92
742 4148 4.063230 CGGTCGTCGTCGTCGTCA 62.063 66.667 11.41 0.00 38.33 4.35
759 4169 2.277084 GTCACAGACCACGTGAGTTTT 58.723 47.619 19.30 3.52 46.40 2.43
767 4177 4.117685 GACCACGTGAGTTTTCTTGTAGT 58.882 43.478 19.30 0.41 46.40 2.73
804 4214 2.010497 GGATCGACCTTTGGCTCTTTC 58.990 52.381 0.00 0.00 35.41 2.62
808 4218 1.813862 CGACCTTTGGCTCTTTCCACA 60.814 52.381 0.00 0.00 35.50 4.17
816 4229 3.450904 TGGCTCTTTCCACATACTACCT 58.549 45.455 0.00 0.00 0.00 3.08
822 4235 6.323225 GCTCTTTCCACATACTACCTACCTAA 59.677 42.308 0.00 0.00 0.00 2.69
861 4274 3.065655 CGCCTTTTTCATTTGGATGCAA 58.934 40.909 0.00 0.00 33.14 4.08
924 4338 1.144969 GCGCCGCTACATTATAAGCA 58.855 50.000 0.00 0.00 38.70 3.91
929 4343 2.480419 CCGCTACATTATAAGCAGGTGC 59.520 50.000 0.00 0.00 38.70 5.01
939 4355 3.279116 GCAGGTGCGCTCACACAA 61.279 61.111 9.73 0.00 44.87 3.33
940 4356 2.633657 CAGGTGCGCTCACACAAC 59.366 61.111 9.73 0.00 44.87 3.32
941 4357 1.889105 CAGGTGCGCTCACACAACT 60.889 57.895 9.73 0.00 44.87 3.16
991 4407 5.292834 CCTGATACACTCATAACAAGCAGTG 59.707 44.000 0.00 0.00 41.77 3.66
1341 4769 4.335874 CACCTCTGTGCGTCTATAGTAGTT 59.664 45.833 0.00 0.00 35.31 2.24
1342 4770 5.526479 CACCTCTGTGCGTCTATAGTAGTTA 59.474 44.000 0.00 0.00 35.31 2.24
1343 4771 5.759273 ACCTCTGTGCGTCTATAGTAGTTAG 59.241 44.000 0.00 0.00 0.00 2.34
1344 4772 5.334260 CCTCTGTGCGTCTATAGTAGTTAGC 60.334 48.000 0.00 0.00 0.00 3.09
1391 4823 1.271488 TGTCTGTCATGGCATGCTGAA 60.271 47.619 22.56 13.09 0.00 3.02
1412 4844 2.032680 TGGGTATAAGAAACGCAGGC 57.967 50.000 0.00 0.00 35.18 4.85
1415 4847 2.158943 GGGTATAAGAAACGCAGGCTCT 60.159 50.000 0.00 0.00 0.00 4.09
1480 4912 4.773149 ACGGGGCCACATTAATTTTAAGAA 59.227 37.500 5.46 0.00 0.00 2.52
1657 5089 6.363626 CCATCTATTTCACAGATACACGCTAC 59.636 42.308 0.00 0.00 31.48 3.58
1702 5134 6.320164 TGTGTATTATATTTGCCACCAGAACC 59.680 38.462 0.00 0.00 0.00 3.62
1822 5254 1.080366 CCGCTACCAAGTGCACGTA 60.080 57.895 12.01 7.04 31.50 3.57
2065 5498 9.798885 CACTAAGCAGCGATAAATCTAAATAAC 57.201 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.159226 ACAGCTGTATAGAAGCCACGAC 60.159 50.000 20.16 0.00 41.82 4.34
15 16 3.981071 ACCTGCAAACAGCTGTATAGA 57.019 42.857 22.01 4.06 45.94 1.98
19 20 1.317613 CCAACCTGCAAACAGCTGTA 58.682 50.000 22.01 2.85 45.94 2.74
20 21 2.019897 GCCAACCTGCAAACAGCTGT 62.020 55.000 15.25 15.25 45.94 4.40
21 22 1.300388 GCCAACCTGCAAACAGCTG 60.300 57.895 13.48 13.48 45.94 4.24
22 23 1.044790 AAGCCAACCTGCAAACAGCT 61.045 50.000 0.00 0.00 45.94 4.24
23 24 0.179076 AAAGCCAACCTGCAAACAGC 60.179 50.000 0.00 0.00 43.02 4.40
29 30 0.396974 AACCTCAAAGCCAACCTGCA 60.397 50.000 0.00 0.00 0.00 4.41
30 31 0.032540 CAACCTCAAAGCCAACCTGC 59.967 55.000 0.00 0.00 0.00 4.85
32 33 0.555769 TCCAACCTCAAAGCCAACCT 59.444 50.000 0.00 0.00 0.00 3.50
33 34 0.961753 CTCCAACCTCAAAGCCAACC 59.038 55.000 0.00 0.00 0.00 3.77
35 36 0.185901 AGCTCCAACCTCAAAGCCAA 59.814 50.000 0.00 0.00 35.32 4.52
38 39 2.770164 TAGAGCTCCAACCTCAAAGC 57.230 50.000 10.93 0.00 34.95 3.51
40 41 2.912956 ACCATAGAGCTCCAACCTCAAA 59.087 45.455 10.93 0.00 0.00 2.69
41 42 2.237143 CACCATAGAGCTCCAACCTCAA 59.763 50.000 10.93 0.00 0.00 3.02
42 43 1.833630 CACCATAGAGCTCCAACCTCA 59.166 52.381 10.93 0.00 0.00 3.86
47 48 2.166459 CGACTTCACCATAGAGCTCCAA 59.834 50.000 10.93 0.00 0.00 3.53
48 49 1.751351 CGACTTCACCATAGAGCTCCA 59.249 52.381 10.93 0.00 0.00 3.86
50 51 2.025155 TCCGACTTCACCATAGAGCTC 58.975 52.381 5.27 5.27 0.00 4.09
51 52 2.028130 CTCCGACTTCACCATAGAGCT 58.972 52.381 0.00 0.00 0.00 4.09
54 55 2.014857 CGACTCCGACTTCACCATAGA 58.985 52.381 0.00 0.00 38.22 1.98
55 56 1.534175 GCGACTCCGACTTCACCATAG 60.534 57.143 0.00 0.00 38.22 2.23
56 57 0.454600 GCGACTCCGACTTCACCATA 59.545 55.000 0.00 0.00 38.22 2.74
57 58 1.215647 GCGACTCCGACTTCACCAT 59.784 57.895 0.00 0.00 38.22 3.55
58 59 1.863662 GAGCGACTCCGACTTCACCA 61.864 60.000 0.00 0.00 38.22 4.17
60 61 1.512310 CGAGCGACTCCGACTTCAC 60.512 63.158 0.00 0.00 38.22 3.18
61 62 1.512996 AACGAGCGACTCCGACTTCA 61.513 55.000 0.00 0.00 38.22 3.02
63 64 1.209640 GAACGAGCGACTCCGACTT 59.790 57.895 0.00 0.00 38.22 3.01
64 65 2.868920 GAACGAGCGACTCCGACT 59.131 61.111 0.00 0.00 38.22 4.18
65 66 2.573689 CGAACGAGCGACTCCGAC 60.574 66.667 0.00 0.00 38.22 4.79
68 69 2.100603 CCTCGAACGAGCGACTCC 59.899 66.667 17.21 0.00 40.69 3.85
70 71 2.214181 ATTGCCTCGAACGAGCGACT 62.214 55.000 17.21 1.29 40.69 4.18
72 73 1.516386 GATTGCCTCGAACGAGCGA 60.516 57.895 17.21 12.84 40.69 4.93
73 74 2.998667 GATTGCCTCGAACGAGCG 59.001 61.111 17.21 11.97 40.69 5.03
83 84 0.465705 ATCGTCATCACCGATTGCCT 59.534 50.000 0.00 0.00 42.00 4.75
85 86 1.258982 GTCATCGTCATCACCGATTGC 59.741 52.381 0.00 0.00 42.75 3.56
86 87 1.518515 CGTCATCGTCATCACCGATTG 59.481 52.381 0.00 0.00 42.75 2.67
87 88 1.840181 CGTCATCGTCATCACCGATT 58.160 50.000 0.00 0.00 42.75 3.34
88 89 0.595053 GCGTCATCGTCATCACCGAT 60.595 55.000 0.00 0.00 45.31 4.18
91 92 0.647410 CAAGCGTCATCGTCATCACC 59.353 55.000 0.00 0.00 39.49 4.02
92 93 0.025513 GCAAGCGTCATCGTCATCAC 59.974 55.000 0.00 0.00 39.49 3.06
94 95 1.139816 TCGCAAGCGTCATCGTCATC 61.140 55.000 14.57 0.00 40.74 2.92
95 96 1.153842 TCGCAAGCGTCATCGTCAT 60.154 52.632 14.57 0.00 40.74 3.06
98 99 1.801913 GAGTCGCAAGCGTCATCGT 60.802 57.895 14.57 0.00 40.74 3.73
104 105 4.421479 CCGAGGAGTCGCAAGCGT 62.421 66.667 14.57 0.00 45.41 5.07
109 110 3.449227 ATTCGCCGAGGAGTCGCA 61.449 61.111 0.00 0.00 45.41 5.10
122 123 3.176708 CTGCAAAGAAGAATGGCATTCG 58.823 45.455 28.96 17.41 43.92 3.34
123 124 2.928116 GCTGCAAAGAAGAATGGCATTC 59.072 45.455 28.54 28.54 39.56 2.67
124 125 2.565834 AGCTGCAAAGAAGAATGGCATT 59.434 40.909 13.54 13.54 33.50 3.56
128 129 3.739300 CACAAAGCTGCAAAGAAGAATGG 59.261 43.478 1.02 0.00 0.00 3.16
129 130 4.365723 ACACAAAGCTGCAAAGAAGAATG 58.634 39.130 1.02 0.00 0.00 2.67
131 132 4.423732 GAACACAAAGCTGCAAAGAAGAA 58.576 39.130 1.02 0.00 0.00 2.52
132 133 3.181487 GGAACACAAAGCTGCAAAGAAGA 60.181 43.478 1.02 0.00 0.00 2.87
134 135 2.495270 TGGAACACAAAGCTGCAAAGAA 59.505 40.909 1.02 0.00 0.00 2.52
135 136 2.098614 TGGAACACAAAGCTGCAAAGA 58.901 42.857 1.02 0.00 0.00 2.52
136 137 2.582728 TGGAACACAAAGCTGCAAAG 57.417 45.000 1.02 0.00 0.00 2.77
151 152 2.350895 CAGGCCACCGACATGGAA 59.649 61.111 5.01 0.00 43.02 3.53
152 153 3.716195 CCAGGCCACCGACATGGA 61.716 66.667 5.01 0.00 43.02 3.41
155 156 2.034066 CAACCAGGCCACCGACAT 59.966 61.111 5.01 0.00 0.00 3.06
156 157 4.263572 CCAACCAGGCCACCGACA 62.264 66.667 5.01 0.00 0.00 4.35
165 166 2.751436 CATCACCGGCCAACCAGG 60.751 66.667 0.00 0.00 41.84 4.45
173 174 3.211963 GACATGGGCATCACCGGC 61.212 66.667 0.00 0.00 40.62 6.13
174 175 1.820906 CTGACATGGGCATCACCGG 60.821 63.158 0.00 0.00 40.62 5.28
176 177 1.033746 CACCTGACATGGGCATCACC 61.034 60.000 0.00 0.00 37.93 4.02
178 179 1.303948 CCACCTGACATGGGCATCA 59.696 57.895 0.00 0.00 33.18 3.07
179 180 4.247781 CCACCTGACATGGGCATC 57.752 61.111 0.00 0.00 33.18 3.91
185 186 1.881973 CAACTCAACCCACCTGACATG 59.118 52.381 0.00 0.00 0.00 3.21
187 188 0.916086 ACAACTCAACCCACCTGACA 59.084 50.000 0.00 0.00 0.00 3.58
189 190 2.028476 CGATACAACTCAACCCACCTGA 60.028 50.000 0.00 0.00 0.00 3.86
191 192 1.278127 CCGATACAACTCAACCCACCT 59.722 52.381 0.00 0.00 0.00 4.00
192 193 1.002773 ACCGATACAACTCAACCCACC 59.997 52.381 0.00 0.00 0.00 4.61
193 194 2.467566 ACCGATACAACTCAACCCAC 57.532 50.000 0.00 0.00 0.00 4.61
196 197 4.142752 GGCTAAAACCGATACAACTCAACC 60.143 45.833 0.00 0.00 0.00 3.77
197 198 4.142752 GGGCTAAAACCGATACAACTCAAC 60.143 45.833 0.00 0.00 0.00 3.18
210 211 1.931709 GCGAAAAACCGGGCTAAAACC 60.932 52.381 6.32 0.00 0.00 3.27
211 212 1.269154 TGCGAAAAACCGGGCTAAAAC 60.269 47.619 6.32 0.00 0.00 2.43
214 215 1.030457 TTTGCGAAAAACCGGGCTAA 58.970 45.000 6.32 0.00 0.00 3.09
216 217 0.391228 AATTTGCGAAAAACCGGGCT 59.609 45.000 6.32 0.00 0.00 5.19
217 218 2.067414 TAATTTGCGAAAAACCGGGC 57.933 45.000 6.32 0.00 0.00 6.13
218 219 2.732500 GGTTAATTTGCGAAAAACCGGG 59.267 45.455 6.32 0.00 30.18 5.73
219 220 2.405690 CGGTTAATTTGCGAAAAACCGG 59.594 45.455 30.84 20.15 45.28 5.28
222 223 2.156117 GCCCGGTTAATTTGCGAAAAAC 59.844 45.455 0.00 6.70 0.00 2.43
223 224 2.223971 TGCCCGGTTAATTTGCGAAAAA 60.224 40.909 0.00 0.00 0.00 1.94
225 226 0.959553 TGCCCGGTTAATTTGCGAAA 59.040 45.000 0.00 0.00 0.00 3.46
226 227 0.959553 TTGCCCGGTTAATTTGCGAA 59.040 45.000 0.00 0.00 0.00 4.70
228 229 1.923864 GAATTGCCCGGTTAATTTGCG 59.076 47.619 12.67 0.00 0.00 4.85
231 232 4.600062 AGAGAGAATTGCCCGGTTAATTT 58.400 39.130 12.67 5.37 0.00 1.82
232 233 4.236527 AGAGAGAATTGCCCGGTTAATT 57.763 40.909 11.61 11.61 0.00 1.40
233 234 3.933861 AGAGAGAATTGCCCGGTTAAT 57.066 42.857 0.00 0.00 0.00 1.40
234 235 3.263425 AGAAGAGAGAATTGCCCGGTTAA 59.737 43.478 0.00 0.00 0.00 2.01
235 236 2.838202 AGAAGAGAGAATTGCCCGGTTA 59.162 45.455 0.00 0.00 0.00 2.85
236 237 1.630878 AGAAGAGAGAATTGCCCGGTT 59.369 47.619 0.00 0.00 0.00 4.44
237 238 1.280457 AGAAGAGAGAATTGCCCGGT 58.720 50.000 0.00 0.00 0.00 5.28
239 240 3.258971 AGAAGAAGAGAGAATTGCCCG 57.741 47.619 0.00 0.00 0.00 6.13
240 241 6.825721 TGATTAAGAAGAAGAGAGAATTGCCC 59.174 38.462 0.00 0.00 0.00 5.36
241 242 7.856145 TGATTAAGAAGAAGAGAGAATTGCC 57.144 36.000 0.00 0.00 0.00 4.52
252 253 8.991243 TGCCATTTTCATTGATTAAGAAGAAG 57.009 30.769 0.00 0.00 0.00 2.85
256 257 9.947433 AGATTTGCCATTTTCATTGATTAAGAA 57.053 25.926 0.00 0.00 0.00 2.52
261 262 7.810759 GCAAAAGATTTGCCATTTTCATTGATT 59.189 29.630 15.12 0.00 39.38 2.57
263 264 6.670233 GCAAAAGATTTGCCATTTTCATTGA 58.330 32.000 15.12 0.00 39.38 2.57
275 276 3.380142 TGAAACGAGGCAAAAGATTTGC 58.620 40.909 17.18 17.18 44.22 3.68
277 278 6.976636 TTTTTGAAACGAGGCAAAAGATTT 57.023 29.167 11.51 0.00 42.71 2.17
304 305 6.650390 AGTCTTGCTTCATTTGTTGTTGTTTT 59.350 30.769 0.00 0.00 0.00 2.43
305 306 6.165577 AGTCTTGCTTCATTTGTTGTTGTTT 58.834 32.000 0.00 0.00 0.00 2.83
306 307 5.723295 AGTCTTGCTTCATTTGTTGTTGTT 58.277 33.333 0.00 0.00 0.00 2.83
307 308 5.329035 AGTCTTGCTTCATTTGTTGTTGT 57.671 34.783 0.00 0.00 0.00 3.32
308 309 7.754069 TTTAGTCTTGCTTCATTTGTTGTTG 57.246 32.000 0.00 0.00 0.00 3.33
309 310 8.034804 AGTTTTAGTCTTGCTTCATTTGTTGTT 58.965 29.630 0.00 0.00 0.00 2.83
310 311 7.547227 AGTTTTAGTCTTGCTTCATTTGTTGT 58.453 30.769 0.00 0.00 0.00 3.32
311 312 7.992180 AGTTTTAGTCTTGCTTCATTTGTTG 57.008 32.000 0.00 0.00 0.00 3.33
359 3729 0.109532 TTTTCCAGCGGTCCATGTGA 59.890 50.000 0.00 0.00 0.00 3.58
381 3751 4.623932 ATCACAGCTCTCAAGGTACAAA 57.376 40.909 0.00 0.00 0.00 2.83
414 3785 3.316501 AGAGCTATTCCTGGCTGATCTT 58.683 45.455 0.00 0.00 39.63 2.40
553 3957 5.619086 GCGTGCTACACTTTGACCATTTATT 60.619 40.000 0.00 0.00 31.34 1.40
564 3968 2.455674 TGAGATGCGTGCTACACTTT 57.544 45.000 0.00 0.00 31.34 2.66
576 3980 2.476320 GGGGCGAGCTTTGAGATGC 61.476 63.158 0.00 0.00 0.00 3.91
611 4016 2.359478 CCACCCGGTAGGCAACAC 60.359 66.667 0.00 0.00 40.58 3.32
665 4070 4.318760 CGGTTGATCATAAACGCATCGATT 60.319 41.667 0.00 0.00 33.66 3.34
678 4083 2.586079 CGGCGAGCGGTTGATCAT 60.586 61.111 0.00 0.00 0.00 2.45
726 4132 2.498466 GTGACGACGACGACGACC 60.498 66.667 25.15 15.92 42.66 4.79
742 4148 2.936498 CAAGAAAACTCACGTGGTCTGT 59.064 45.455 17.00 7.12 0.00 3.41
759 4169 3.490249 CGACGCCATGGATTACTACAAGA 60.490 47.826 18.40 0.00 0.00 3.02
804 4214 5.227908 CGCAATTAGGTAGGTAGTATGTGG 58.772 45.833 0.00 0.00 0.00 4.17
808 4218 3.899360 TGCCGCAATTAGGTAGGTAGTAT 59.101 43.478 0.00 0.00 0.00 2.12
816 4229 4.884744 ACAAATATGTGCCGCAATTAGGTA 59.115 37.500 0.00 0.00 38.69 3.08
822 4235 1.533756 GCGACAAATATGTGCCGCAAT 60.534 47.619 20.15 0.00 46.28 3.56
861 4274 1.959226 AAACCGAACGCGATGCAGT 60.959 52.632 15.93 0.00 40.82 4.40
906 4320 1.726791 CCTGCTTATAATGTAGCGGCG 59.273 52.381 0.51 0.51 41.41 6.46
913 4327 2.332063 AGCGCACCTGCTTATAATGT 57.668 45.000 11.47 0.00 44.46 2.71
924 4338 0.319900 CTAGTTGTGTGAGCGCACCT 60.320 55.000 18.33 9.93 44.51 4.00
929 4343 0.668706 AGCTGCTAGTTGTGTGAGCG 60.669 55.000 0.00 0.00 39.14 5.03
938 4354 1.484240 GGAGTGATGGAGCTGCTAGTT 59.516 52.381 6.82 0.00 0.00 2.24
939 4355 1.118838 GGAGTGATGGAGCTGCTAGT 58.881 55.000 6.82 0.00 0.00 2.57
940 4356 1.117994 TGGAGTGATGGAGCTGCTAG 58.882 55.000 6.82 0.00 0.00 3.42
941 4357 0.826715 GTGGAGTGATGGAGCTGCTA 59.173 55.000 6.82 0.00 0.00 3.49
991 4407 0.319125 GAAGCCTCCATCGACCGATC 60.319 60.000 1.46 0.00 31.62 3.69
1062 4486 4.523282 GGGCCTCCCATCTCCCCT 62.523 72.222 0.84 0.00 44.65 4.79
1242 4666 2.683362 GAGGCAATAGGTTGGTTACTGC 59.317 50.000 0.00 0.00 35.83 4.40
1305 4733 4.711949 AGGTGCGAGCAAGCCAGG 62.712 66.667 0.00 0.00 36.02 4.45
1331 4759 6.694877 TGGACACAGTGCTAACTACTATAG 57.305 41.667 0.00 0.00 33.79 1.31
1335 4763 3.832490 TCATGGACACAGTGCTAACTACT 59.168 43.478 0.00 0.00 33.79 2.57
1341 4769 4.941263 GGTTTATTCATGGACACAGTGCTA 59.059 41.667 0.00 0.00 0.00 3.49
1342 4770 3.758554 GGTTTATTCATGGACACAGTGCT 59.241 43.478 0.00 0.00 0.00 4.40
1343 4771 3.758554 AGGTTTATTCATGGACACAGTGC 59.241 43.478 0.00 0.00 0.00 4.40
1344 4772 4.093408 CGAGGTTTATTCATGGACACAGTG 59.907 45.833 0.00 0.00 0.00 3.66
1391 4823 2.949644 GCCTGCGTTTCTTATACCCATT 59.050 45.455 0.00 0.00 0.00 3.16
1702 5134 9.929722 TCGATTTACATGAAATTAATTTCCTCG 57.070 29.630 29.31 23.45 44.16 4.63
1732 5164 1.676014 GCGTATTCTTGGAGCTGTGGT 60.676 52.381 0.00 0.00 0.00 4.16
1802 5234 2.032071 GTGCACTTGGTAGCGGGT 59.968 61.111 10.32 0.00 0.00 5.28
1809 5241 0.591170 GCATTGTACGTGCACTTGGT 59.409 50.000 16.19 8.21 42.08 3.67
1822 5254 3.988379 ATTTGTGAAGACGTGCATTGT 57.012 38.095 0.00 0.00 0.00 2.71
2065 5498 5.518848 TGCCTGCATAGTTAATGGATTTG 57.481 39.130 0.00 0.00 35.12 2.32


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

AutoCloner maintained by Alex Coulton.