Multiple sequence alignment - TraesCS2B01G468000

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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 TraesCS2B01G468000 chr2B 100.000 3135 0 0 1 3135 663897758 663900892 0.000000e+00 5790.0
1 TraesCS2B01G468000 chr2B 82.122 1197 141 35 999 2187 663838018 663839149 0.000000e+00 957.0
2 TraesCS2B01G468000 chr2B 81.609 1218 149 28 999 2187 663828972 663830143 0.000000e+00 939.0
3 TraesCS2B01G468000 chr2B 83.915 802 82 34 999 1786 663886031 663886799 0.000000e+00 723.0
4 TraesCS2B01G468000 chr2B 75.610 820 151 33 1386 2187 663180828 663180040 8.270000e-96 361.0
5 TraesCS2B01G468000 chr2B 85.507 138 11 4 2238 2374 663180041 663179912 5.450000e-28 135.0
6 TraesCS2B01G468000 chr2B 90.244 82 8 0 1599 1680 53059466 53059385 1.190000e-19 108.0
7 TraesCS2B01G468000 chr2D 93.769 2006 96 9 363 2359 556641769 556643754 0.000000e+00 2985.0
8 TraesCS2B01G468000 chr2D 90.416 793 59 12 999 1786 556365491 556366271 0.000000e+00 1027.0
9 TraesCS2B01G468000 chr2D 80.862 1207 173 32 999 2188 556350547 556351712 0.000000e+00 896.0
10 TraesCS2B01G468000 chr2D 85.043 809 73 28 999 1784 556408039 556408822 0.000000e+00 780.0
11 TraesCS2B01G468000 chr2D 78.555 844 126 22 1370 2187 556339276 556340090 3.610000e-139 505.0
12 TraesCS2B01G468000 chr2D 89.347 291 27 2 2305 2595 556643800 556644086 2.300000e-96 363.0
13 TraesCS2B01G468000 chr2D 89.734 263 10 12 3 261 556641475 556641724 1.400000e-83 320.0
14 TraesCS2B01G468000 chr2D 86.283 226 17 7 2910 3135 556678125 556678336 1.880000e-57 233.0
15 TraesCS2B01G468000 chr2D 84.559 136 14 2 2242 2377 556351714 556351842 9.130000e-26 128.0
16 TraesCS2B01G468000 chr2D 79.856 139 14 7 2275 2412 556366629 556366754 4.310000e-14 89.8
17 TraesCS2B01G468000 chr2D 78.986 138 17 5 2275 2412 556334056 556334181 2.000000e-12 84.2
18 TraesCS2B01G468000 chr2D 82.243 107 10 3 2275 2381 556409182 556409279 2.000000e-12 84.2
19 TraesCS2B01G468000 chr2A 89.306 2291 187 28 363 2640 696314986 696317231 0.000000e+00 2820.0
20 TraesCS2B01G468000 chr2A 92.512 1843 105 20 943 2766 696825186 696827014 0.000000e+00 2608.0
21 TraesCS2B01G468000 chr2A 84.010 1207 152 16 999 2187 695999116 696000299 0.000000e+00 1122.0
22 TraesCS2B01G468000 chr2A 82.172 1206 146 36 999 2187 696040431 696041584 0.000000e+00 972.0
23 TraesCS2B01G468000 chr2A 85.820 811 70 32 999 1786 696219212 696220000 0.000000e+00 819.0
24 TraesCS2B01G468000 chr2A 88.848 269 14 11 2 261 696314626 696314887 1.810000e-82 316.0
25 TraesCS2B01G468000 chr2A 86.822 258 11 7 2900 3135 696827643 696827899 1.850000e-67 267.0
26 TraesCS2B01G468000 chr2A 86.875 160 16 3 2976 3135 696317788 696317942 1.160000e-39 174.0
27 TraesCS2B01G468000 chr2A 85.714 140 13 2 2238 2377 696000298 696000430 1.170000e-29 141.0
28 TraesCS2B01G468000 chr2A 85.315 143 14 2 2239 2381 696001276 696001411 1.170000e-29 141.0
29 TraesCS2B01G468000 chr2A 91.209 91 8 0 2899 2989 696317680 696317770 1.180000e-24 124.0
30 TraesCS2B01G468000 chr2A 78.537 205 20 11 555 739 696824630 696824830 2.560000e-21 113.0
31 TraesCS2B01G468000 chr2A 79.137 139 15 7 2275 2412 696220358 696220483 2.000000e-12 84.2


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 TraesCS2B01G468000 chr2B 663897758 663900892 3134 False 5790.000000 5790 100.0000 1 3135 1 chr2B.!!$F4 3134
1 TraesCS2B01G468000 chr2B 663838018 663839149 1131 False 957.000000 957 82.1220 999 2187 1 chr2B.!!$F2 1188
2 TraesCS2B01G468000 chr2B 663828972 663830143 1171 False 939.000000 939 81.6090 999 2187 1 chr2B.!!$F1 1188
3 TraesCS2B01G468000 chr2B 663886031 663886799 768 False 723.000000 723 83.9150 999 1786 1 chr2B.!!$F3 787
4 TraesCS2B01G468000 chr2B 663179912 663180828 916 True 248.000000 361 80.5585 1386 2374 2 chr2B.!!$R2 988
5 TraesCS2B01G468000 chr2D 556641475 556644086 2611 False 1222.666667 2985 90.9500 3 2595 3 chr2D.!!$F7 2592
6 TraesCS2B01G468000 chr2D 556365491 556366754 1263 False 558.400000 1027 85.1360 999 2412 2 chr2D.!!$F5 1413
7 TraesCS2B01G468000 chr2D 556350547 556351842 1295 False 512.000000 896 82.7105 999 2377 2 chr2D.!!$F4 1378
8 TraesCS2B01G468000 chr2D 556339276 556340090 814 False 505.000000 505 78.5550 1370 2187 1 chr2D.!!$F2 817
9 TraesCS2B01G468000 chr2D 556408039 556409279 1240 False 432.100000 780 83.6430 999 2381 2 chr2D.!!$F6 1382
10 TraesCS2B01G468000 chr2A 696824630 696827899 3269 False 996.000000 2608 85.9570 555 3135 3 chr2A.!!$F5 2580
11 TraesCS2B01G468000 chr2A 696040431 696041584 1153 False 972.000000 972 82.1720 999 2187 1 chr2A.!!$F1 1188
12 TraesCS2B01G468000 chr2A 696314626 696317942 3316 False 858.500000 2820 89.0595 2 3135 4 chr2A.!!$F4 3133
13 TraesCS2B01G468000 chr2A 695999116 696001411 2295 False 468.000000 1122 85.0130 999 2381 3 chr2A.!!$F2 1382
14 TraesCS2B01G468000 chr2A 696219212 696220483 1271 False 451.600000 819 82.4785 999 2412 2 chr2A.!!$F3 1413

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
351 406 0.107410 AAACAGTGTTCTGCGGGTGA 60.107 50.0 9.4 0.0 44.77 4.02 F
1702 2076 0.031716 AGCAGCTCCTCCAGACCATA 60.032 55.0 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2467 0.758734 TAGTTCCATGGGCTCCATCG 59.241 55.0 13.02 0.0 43.15 3.84 R
2864 3664 0.539669 CCCCACCGCCTCTTTCTTTT 60.540 55.0 0.00 0.0 0.00 2.27 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
88 93 8.103948 AGTTTATGACCTTTGATTTGAGACAG 57.896 34.615 0.00 0.00 0.00 3.51
117 130 9.995003 AAAAACTAATATGCCATGTTTTCTGAA 57.005 25.926 4.64 0.00 39.10 3.02
118 131 8.986477 AAACTAATATGCCATGTTTTCTGAAC 57.014 30.769 0.00 0.00 0.00 3.18
129 142 5.818136 TGTTTTCTGAACTTGAAGGAGTG 57.182 39.130 0.00 0.00 0.00 3.51
139 152 5.036117 ACTTGAAGGAGTGCAGTTTTCTA 57.964 39.130 16.15 10.49 0.00 2.10
190 203 1.748493 TCGTAGGCCAAATCATTTGCC 59.252 47.619 5.01 9.59 39.31 4.52
209 222 1.791103 CGAAACCTCAAAGCCGCCAA 61.791 55.000 0.00 0.00 0.00 4.52
232 246 7.285858 CCAACAGGATTAGTTAGAGTAGCTAGT 59.714 40.741 0.00 0.00 0.00 2.57
233 247 9.339850 CAACAGGATTAGTTAGAGTAGCTAGTA 57.660 37.037 0.00 0.00 0.00 1.82
234 248 9.563748 AACAGGATTAGTTAGAGTAGCTAGTAG 57.436 37.037 0.00 0.00 0.00 2.57
235 249 7.662669 ACAGGATTAGTTAGAGTAGCTAGTAGC 59.337 40.741 14.62 14.62 42.84 3.58
264 278 3.386768 TCTCAAGAGACCAAAACGAGG 57.613 47.619 0.00 0.00 31.41 4.63
266 280 3.060602 CTCAAGAGACCAAAACGAGGAC 58.939 50.000 0.00 0.00 0.00 3.85
268 282 0.685660 AGAGACCAAAACGAGGACCC 59.314 55.000 0.00 0.00 0.00 4.46
269 283 0.395312 GAGACCAAAACGAGGACCCA 59.605 55.000 0.00 0.00 0.00 4.51
270 284 0.396811 AGACCAAAACGAGGACCCAG 59.603 55.000 0.00 0.00 0.00 4.45
271 285 0.108019 GACCAAAACGAGGACCCAGT 59.892 55.000 0.00 0.00 0.00 4.00
272 286 0.549469 ACCAAAACGAGGACCCAGTT 59.451 50.000 0.00 0.00 0.00 3.16
273 287 1.064240 ACCAAAACGAGGACCCAGTTT 60.064 47.619 8.60 8.60 39.45 2.66
274 288 1.336755 CCAAAACGAGGACCCAGTTTG 59.663 52.381 13.61 7.75 38.02 2.93
275 289 2.294074 CAAAACGAGGACCCAGTTTGA 58.706 47.619 13.61 0.00 38.02 2.69
276 290 2.884639 CAAAACGAGGACCCAGTTTGAT 59.115 45.455 13.61 0.00 38.02 2.57
277 291 2.474410 AACGAGGACCCAGTTTGATC 57.526 50.000 0.00 0.00 0.00 2.92
278 292 1.348064 ACGAGGACCCAGTTTGATCA 58.652 50.000 0.00 0.00 0.00 2.92
279 293 1.697432 ACGAGGACCCAGTTTGATCAA 59.303 47.619 3.38 3.38 0.00 2.57
280 294 2.105821 ACGAGGACCCAGTTTGATCAAA 59.894 45.455 16.91 16.91 0.00 2.69
282 296 3.758554 CGAGGACCCAGTTTGATCAAAAT 59.241 43.478 22.07 18.55 31.33 1.82
284 298 5.163754 CGAGGACCCAGTTTGATCAAAATAC 60.164 44.000 22.07 11.25 31.33 1.89
285 299 5.016831 AGGACCCAGTTTGATCAAAATACC 58.983 41.667 22.07 19.12 31.33 2.73
288 302 6.239458 GGACCCAGTTTGATCAAAATACCAAA 60.239 38.462 22.07 0.00 31.33 3.28
289 303 6.758254 ACCCAGTTTGATCAAAATACCAAAG 58.242 36.000 22.07 8.22 31.33 2.77
290 304 6.165577 CCCAGTTTGATCAAAATACCAAAGG 58.834 40.000 22.07 15.91 31.33 3.11
291 305 5.639082 CCAGTTTGATCAAAATACCAAAGGC 59.361 40.000 22.07 6.26 31.33 4.35
292 306 6.222389 CAGTTTGATCAAAATACCAAAGGCA 58.778 36.000 22.07 0.00 31.33 4.75
294 308 6.875195 AGTTTGATCAAAATACCAAAGGCATG 59.125 34.615 22.07 0.00 31.33 4.06
295 309 5.341872 TGATCAAAATACCAAAGGCATGG 57.658 39.130 7.70 7.70 46.38 3.66
296 310 4.161942 TGATCAAAATACCAAAGGCATGGG 59.838 41.667 13.10 0.00 45.18 4.00
297 311 3.515562 TCAAAATACCAAAGGCATGGGT 58.484 40.909 13.10 4.12 45.18 4.51
298 312 4.678256 TCAAAATACCAAAGGCATGGGTA 58.322 39.130 13.10 6.38 45.18 3.69
301 356 5.414789 AAATACCAAAGGCATGGGTAAAC 57.585 39.130 13.10 0.00 45.18 2.01
316 371 2.949644 GGTAAACAGTGTTCTGCAGGTT 59.050 45.455 15.13 5.90 44.77 3.50
317 372 3.380320 GGTAAACAGTGTTCTGCAGGTTT 59.620 43.478 15.13 16.30 44.77 3.27
318 373 4.142249 GGTAAACAGTGTTCTGCAGGTTTT 60.142 41.667 15.13 5.74 44.77 2.43
319 374 4.535526 AAACAGTGTTCTGCAGGTTTTT 57.464 36.364 15.13 1.62 44.77 1.94
341 396 8.433421 TTTTTCTCTCTCGAATAAACAGTGTT 57.567 30.769 1.64 1.64 0.00 3.32
342 397 7.639162 TTTCTCTCTCGAATAAACAGTGTTC 57.361 36.000 9.40 0.00 0.00 3.18
343 398 6.576662 TCTCTCTCGAATAAACAGTGTTCT 57.423 37.500 9.40 2.67 0.00 3.01
344 399 6.382608 TCTCTCTCGAATAAACAGTGTTCTG 58.617 40.000 9.40 0.00 46.18 3.02
345 400 4.923871 TCTCTCGAATAAACAGTGTTCTGC 59.076 41.667 9.40 0.00 44.77 4.26
346 401 3.673338 TCTCGAATAAACAGTGTTCTGCG 59.327 43.478 9.40 10.41 44.77 5.18
347 402 2.734606 TCGAATAAACAGTGTTCTGCGG 59.265 45.455 9.40 0.00 44.77 5.69
348 403 2.159707 CGAATAAACAGTGTTCTGCGGG 60.160 50.000 9.40 0.00 44.77 6.13
349 404 2.561478 ATAAACAGTGTTCTGCGGGT 57.439 45.000 9.40 0.00 44.77 5.28
350 405 1.588674 TAAACAGTGTTCTGCGGGTG 58.411 50.000 9.40 0.00 44.77 4.61
351 406 0.107410 AAACAGTGTTCTGCGGGTGA 60.107 50.000 9.40 0.00 44.77 4.02
352 407 0.532862 AACAGTGTTCTGCGGGTGAG 60.533 55.000 1.64 0.00 44.77 3.51
353 408 1.367471 CAGTGTTCTGCGGGTGAGA 59.633 57.895 0.00 0.00 34.79 3.27
354 409 0.668706 CAGTGTTCTGCGGGTGAGAG 60.669 60.000 0.00 0.00 34.79 3.20
355 410 2.029844 GTGTTCTGCGGGTGAGAGC 61.030 63.158 0.00 0.00 0.00 4.09
356 411 2.435059 GTTCTGCGGGTGAGAGCC 60.435 66.667 0.00 0.00 0.00 4.70
357 412 3.706373 TTCTGCGGGTGAGAGCCC 61.706 66.667 0.00 0.00 45.21 5.19
370 425 3.453070 GAGCCCGGATCAGCACTCC 62.453 68.421 0.73 0.00 0.00 3.85
450 506 1.901833 CCCACCCCAAAATGAAGGAAG 59.098 52.381 0.00 0.00 0.00 3.46
519 576 3.928005 AGATGGTCCTCGTAGACAGTA 57.072 47.619 9.25 0.00 38.59 2.74
537 594 7.169591 AGACAGTACATCTTCTATATACCGCT 58.830 38.462 0.00 0.00 0.00 5.52
542 599 5.262009 ACATCTTCTATATACCGCTGCCTA 58.738 41.667 0.00 0.00 0.00 3.93
603 663 0.109272 CCTCGTGACATGCGTACACT 60.109 55.000 11.71 0.00 33.13 3.55
694 768 3.136626 AGCAACTACCCTCTTTGACTTGT 59.863 43.478 0.00 0.00 0.00 3.16
725 805 4.724036 GCACGCCTTTTGTTTAGAGTATCG 60.724 45.833 0.00 0.00 42.67 2.92
758 1025 4.796110 ACTGTTGGATAGTAATGGCCAT 57.204 40.909 14.09 14.09 0.00 4.40
840 1109 4.293648 CCGTCTGCACCACGACCA 62.294 66.667 13.80 0.00 39.75 4.02
872 1143 2.739996 CCAGCAGCCCGAGGAAGAT 61.740 63.158 0.00 0.00 0.00 2.40
916 1190 0.955428 TTGCTTCTGACCACCGCATC 60.955 55.000 0.00 0.00 0.00 3.91
917 1191 1.078848 GCTTCTGACCACCGCATCT 60.079 57.895 0.00 0.00 0.00 2.90
918 1192 0.175760 GCTTCTGACCACCGCATCTA 59.824 55.000 0.00 0.00 0.00 1.98
919 1193 1.202580 GCTTCTGACCACCGCATCTAT 60.203 52.381 0.00 0.00 0.00 1.98
920 1194 2.748605 CTTCTGACCACCGCATCTATC 58.251 52.381 0.00 0.00 0.00 2.08
921 1195 1.775385 TCTGACCACCGCATCTATCA 58.225 50.000 0.00 0.00 0.00 2.15
922 1196 1.683385 TCTGACCACCGCATCTATCAG 59.317 52.381 0.00 0.00 35.87 2.90
923 1197 1.683385 CTGACCACCGCATCTATCAGA 59.317 52.381 0.00 0.00 36.50 3.27
981 1255 3.062466 CAGAGGAGGTCGCCGTCA 61.062 66.667 0.00 0.00 0.00 4.35
1275 1550 2.349755 GGCCTCGGCAACAGGTAA 59.650 61.111 10.51 0.00 44.11 2.85
1312 1615 4.394729 GTCCAAATCCAACTACTCCACAA 58.605 43.478 0.00 0.00 0.00 3.33
1531 1884 4.809496 AAGCTCCTGCGCATGGGG 62.809 66.667 12.24 16.08 45.42 4.96
1702 2076 0.031716 AGCAGCTCCTCCAGACCATA 60.032 55.000 0.00 0.00 0.00 2.74
1766 2143 0.383491 CGCAAACTCAGTGCTGAACG 60.383 55.000 3.36 0.00 39.95 3.95
2116 2543 4.780021 TCTTTCTGGAAGGAGCTACTTGAT 59.220 41.667 18.22 0.00 35.98 2.57
2151 2578 6.853872 CGTCTATAGTTTCTTTCTCCAGATCG 59.146 42.308 0.00 0.00 0.00 3.69
2152 2579 7.254829 CGTCTATAGTTTCTTTCTCCAGATCGA 60.255 40.741 0.00 0.00 0.00 3.59
2155 2582 9.757227 CTATAGTTTCTTTCTCCAGATCGAAAT 57.243 33.333 0.00 0.00 30.75 2.17
2157 2584 9.757227 ATAGTTTCTTTCTCCAGATCGAAATAG 57.243 33.333 0.00 0.00 30.75 1.73
2159 2586 8.482128 AGTTTCTTTCTCCAGATCGAAATAGAT 58.518 33.333 0.00 0.00 30.75 1.98
2261 2691 6.463614 GCAGTGTTAGATCCATCATAGAGGTT 60.464 42.308 0.00 0.00 0.00 3.50
2301 2733 6.680874 ACATGCATTGATTTGTTTGTGTTT 57.319 29.167 0.00 0.00 0.00 2.83
2302 2734 7.086230 ACATGCATTGATTTGTTTGTGTTTT 57.914 28.000 0.00 0.00 0.00 2.43
2343 2868 9.743057 CAATAGATTTGGTTTTTGTCAGTGTAA 57.257 29.630 0.00 0.00 0.00 2.41
2377 2902 5.571741 GTCAATTGCTGATTTGATGTGACTG 59.428 40.000 0.00 0.00 36.14 3.51
2381 2906 3.076621 GCTGATTTGATGTGACTGGTGA 58.923 45.455 0.00 0.00 0.00 4.02
2382 2907 3.693085 GCTGATTTGATGTGACTGGTGAT 59.307 43.478 0.00 0.00 0.00 3.06
2440 2967 5.740290 TCAAAAAGGAGGATTACTCTCGT 57.260 39.130 0.00 0.00 45.83 4.18
2453 2980 1.203523 ACTCTCGTCCTCTGCATCAAC 59.796 52.381 0.00 0.00 0.00 3.18
2470 2997 1.068610 CAACCGGTGCACATAACCAAG 60.069 52.381 20.43 0.00 37.57 3.61
2517 3044 4.564041 ACTACAGTGAGATTGCAGACAAG 58.436 43.478 0.00 0.00 39.69 3.16
2562 3089 4.228899 ACAACGGTGTGGACAACC 57.771 55.556 4.62 0.00 36.31 3.77
2626 3153 1.963172 CGGTTAGTGGGGCCTTAATC 58.037 55.000 0.84 0.00 0.00 1.75
2754 3294 3.627395 ACACCAGCTCGATTTGGATTA 57.373 42.857 18.99 0.00 37.89 1.75
2761 3301 4.813161 CAGCTCGATTTGGATTACTCATGT 59.187 41.667 0.00 0.00 0.00 3.21
2861 3661 8.856153 ATGTTGACTATTTAATGTACACCACA 57.144 30.769 0.00 0.00 42.69 4.17
2875 3675 7.504924 TGTACACCACATAAAAAGAAAGAGG 57.495 36.000 0.00 0.00 30.04 3.69
2876 3676 5.453567 ACACCACATAAAAAGAAAGAGGC 57.546 39.130 0.00 0.00 0.00 4.70
2877 3677 4.023193 ACACCACATAAAAAGAAAGAGGCG 60.023 41.667 0.00 0.00 0.00 5.52
2878 3678 3.506067 ACCACATAAAAAGAAAGAGGCGG 59.494 43.478 0.00 0.00 0.00 6.13
2879 3679 3.506067 CCACATAAAAAGAAAGAGGCGGT 59.494 43.478 0.00 0.00 0.00 5.68
2880 3680 4.475944 CACATAAAAAGAAAGAGGCGGTG 58.524 43.478 0.00 0.00 0.00 4.94
2881 3681 3.506067 ACATAAAAAGAAAGAGGCGGTGG 59.494 43.478 0.00 0.00 0.00 4.61
2882 3682 1.328279 AAAAAGAAAGAGGCGGTGGG 58.672 50.000 0.00 0.00 0.00 4.61
2883 3683 0.539669 AAAAGAAAGAGGCGGTGGGG 60.540 55.000 0.00 0.00 0.00 4.96
2884 3684 2.426305 AAAGAAAGAGGCGGTGGGGG 62.426 60.000 0.00 0.00 0.00 5.40
2911 3946 6.118170 GGGGGTTACTTGTTTTATAGAGACC 58.882 44.000 0.00 0.00 0.00 3.85
2913 3948 6.822170 GGGGTTACTTGTTTTATAGAGACCAG 59.178 42.308 0.00 0.00 0.00 4.00
3106 4614 4.467082 TGTAGATCGGGTAAAGCCTAAACA 59.533 41.667 0.00 0.00 37.43 2.83
3110 4618 3.404899 TCGGGTAAAGCCTAAACACTTG 58.595 45.455 0.00 0.00 37.43 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 8.099364 TCTGTCTCAAATCAAAGGTCATAAAC 57.901 34.615 0.00 0.00 0.00 2.01
96 109 8.461222 TCAAGTTCAGAAAACATGGCATATTAG 58.539 33.333 0.00 0.00 0.00 1.73
97 110 8.347004 TCAAGTTCAGAAAACATGGCATATTA 57.653 30.769 0.00 0.00 0.00 0.98
98 111 7.230849 TCAAGTTCAGAAAACATGGCATATT 57.769 32.000 0.00 0.00 0.00 1.28
100 113 6.294675 CCTTCAAGTTCAGAAAACATGGCATA 60.295 38.462 0.00 0.00 0.00 3.14
101 114 5.510179 CCTTCAAGTTCAGAAAACATGGCAT 60.510 40.000 0.00 0.00 0.00 4.40
102 115 4.202141 CCTTCAAGTTCAGAAAACATGGCA 60.202 41.667 0.00 0.00 0.00 4.92
103 116 4.037923 TCCTTCAAGTTCAGAAAACATGGC 59.962 41.667 0.00 0.00 0.00 4.40
104 117 5.300286 ACTCCTTCAAGTTCAGAAAACATGG 59.700 40.000 0.00 0.00 0.00 3.66
105 118 6.204359 CACTCCTTCAAGTTCAGAAAACATG 58.796 40.000 0.00 0.00 0.00 3.21
106 119 5.221126 GCACTCCTTCAAGTTCAGAAAACAT 60.221 40.000 0.00 0.00 0.00 2.71
108 121 4.096382 TGCACTCCTTCAAGTTCAGAAAAC 59.904 41.667 0.00 0.00 0.00 2.43
109 122 4.269183 TGCACTCCTTCAAGTTCAGAAAA 58.731 39.130 0.00 0.00 0.00 2.29
110 123 3.879295 CTGCACTCCTTCAAGTTCAGAAA 59.121 43.478 0.00 0.00 41.32 2.52
111 124 3.118261 ACTGCACTCCTTCAAGTTCAGAA 60.118 43.478 10.00 0.00 41.32 3.02
112 125 2.435805 ACTGCACTCCTTCAAGTTCAGA 59.564 45.455 10.00 0.00 41.32 3.27
113 126 2.843701 ACTGCACTCCTTCAAGTTCAG 58.156 47.619 2.79 2.79 43.46 3.02
114 127 3.281727 AACTGCACTCCTTCAAGTTCA 57.718 42.857 0.00 0.00 0.00 3.18
115 128 4.336713 AGAAAACTGCACTCCTTCAAGTTC 59.663 41.667 0.00 0.00 0.00 3.01
116 129 4.273318 AGAAAACTGCACTCCTTCAAGTT 58.727 39.130 0.00 0.00 0.00 2.66
117 130 3.891049 AGAAAACTGCACTCCTTCAAGT 58.109 40.909 0.00 0.00 0.00 3.16
118 131 5.702670 TGATAGAAAACTGCACTCCTTCAAG 59.297 40.000 0.00 0.00 0.00 3.02
190 203 1.791103 TTGGCGGCTTTGAGGTTTCG 61.791 55.000 11.43 0.00 0.00 3.46
209 222 7.662669 GCTACTAGCTACTCTAACTAATCCTGT 59.337 40.741 0.35 0.00 38.45 4.00
232 246 5.045797 TGGTCTCTTGAGACACTACTAGCTA 60.046 44.000 25.94 0.00 40.38 3.32
233 247 4.263550 TGGTCTCTTGAGACACTACTAGCT 60.264 45.833 25.94 0.00 40.38 3.32
234 248 4.011023 TGGTCTCTTGAGACACTACTAGC 58.989 47.826 25.94 11.12 40.38 3.42
235 249 6.576662 TTTGGTCTCTTGAGACACTACTAG 57.423 41.667 25.94 0.00 40.38 2.57
261 275 5.125578 GGTATTTTGATCAAACTGGGTCCTC 59.874 44.000 20.35 4.40 0.00 3.71
264 278 5.975693 TGGTATTTTGATCAAACTGGGTC 57.024 39.130 20.35 8.89 0.00 4.46
266 280 6.165577 CCTTTGGTATTTTGATCAAACTGGG 58.834 40.000 20.35 10.05 0.00 4.45
268 282 6.222389 TGCCTTTGGTATTTTGATCAAACTG 58.778 36.000 20.35 3.34 0.00 3.16
269 283 6.418057 TGCCTTTGGTATTTTGATCAAACT 57.582 33.333 20.35 17.19 0.00 2.66
270 284 6.092533 CCATGCCTTTGGTATTTTGATCAAAC 59.907 38.462 20.35 10.09 31.74 2.93
271 285 6.171921 CCATGCCTTTGGTATTTTGATCAAA 58.828 36.000 16.91 16.91 31.74 2.69
272 286 5.338219 CCCATGCCTTTGGTATTTTGATCAA 60.338 40.000 3.38 3.38 34.77 2.57
273 287 4.161942 CCCATGCCTTTGGTATTTTGATCA 59.838 41.667 0.00 0.00 34.77 2.92
274 288 4.162131 ACCCATGCCTTTGGTATTTTGATC 59.838 41.667 0.00 0.00 34.77 2.92
275 289 4.103342 ACCCATGCCTTTGGTATTTTGAT 58.897 39.130 0.00 0.00 34.77 2.57
276 290 3.515562 ACCCATGCCTTTGGTATTTTGA 58.484 40.909 0.00 0.00 34.77 2.69
277 291 3.979101 ACCCATGCCTTTGGTATTTTG 57.021 42.857 0.00 0.00 34.77 2.44
278 292 5.308237 TGTTTACCCATGCCTTTGGTATTTT 59.692 36.000 0.00 0.00 34.73 1.82
279 293 4.841246 TGTTTACCCATGCCTTTGGTATTT 59.159 37.500 0.00 0.00 34.73 1.40
280 294 4.421131 TGTTTACCCATGCCTTTGGTATT 58.579 39.130 0.00 0.00 34.73 1.89
282 296 3.181427 ACTGTTTACCCATGCCTTTGGTA 60.181 43.478 0.00 0.00 34.77 3.25
284 298 2.029110 CACTGTTTACCCATGCCTTTGG 60.029 50.000 0.00 0.00 36.46 3.28
285 299 2.627699 ACACTGTTTACCCATGCCTTTG 59.372 45.455 0.00 0.00 0.00 2.77
288 302 2.108250 AGAACACTGTTTACCCATGCCT 59.892 45.455 0.00 0.00 0.00 4.75
289 303 2.228822 CAGAACACTGTTTACCCATGCC 59.771 50.000 0.00 0.00 0.00 4.40
290 304 2.351738 GCAGAACACTGTTTACCCATGC 60.352 50.000 0.00 0.00 34.51 4.06
291 305 2.884012 TGCAGAACACTGTTTACCCATG 59.116 45.455 0.00 0.00 34.51 3.66
292 306 3.149196 CTGCAGAACACTGTTTACCCAT 58.851 45.455 8.42 0.00 34.51 4.00
294 308 1.880027 CCTGCAGAACACTGTTTACCC 59.120 52.381 17.39 0.00 34.51 3.69
295 309 2.572290 ACCTGCAGAACACTGTTTACC 58.428 47.619 17.39 0.00 34.51 2.85
296 310 4.632538 AAACCTGCAGAACACTGTTTAC 57.367 40.909 17.39 0.00 34.51 2.01
297 311 5.652994 AAAAACCTGCAGAACACTGTTTA 57.347 34.783 17.39 0.00 31.29 2.01
298 312 4.535526 AAAAACCTGCAGAACACTGTTT 57.464 36.364 17.39 12.70 32.30 2.83
316 371 8.433421 AACACTGTTTATTCGAGAGAGAAAAA 57.567 30.769 0.00 0.00 43.69 1.94
317 372 7.926555 AGAACACTGTTTATTCGAGAGAGAAAA 59.073 33.333 0.00 0.00 43.69 2.29
318 373 7.382488 CAGAACACTGTTTATTCGAGAGAGAAA 59.618 37.037 0.00 0.00 43.69 2.52
319 374 6.863645 CAGAACACTGTTTATTCGAGAGAGAA 59.136 38.462 0.00 0.00 43.69 2.87
320 375 6.382608 CAGAACACTGTTTATTCGAGAGAGA 58.617 40.000 0.00 0.00 43.69 3.10
321 376 5.061560 GCAGAACACTGTTTATTCGAGAGAG 59.938 44.000 0.00 0.00 36.33 3.20
322 377 4.923871 GCAGAACACTGTTTATTCGAGAGA 59.076 41.667 0.00 0.00 34.47 3.10
323 378 4.201532 CGCAGAACACTGTTTATTCGAGAG 60.202 45.833 0.00 0.00 34.51 3.20
324 379 3.673338 CGCAGAACACTGTTTATTCGAGA 59.327 43.478 0.00 0.00 34.51 4.04
325 380 3.181530 CCGCAGAACACTGTTTATTCGAG 60.182 47.826 0.00 0.00 34.51 4.04
326 381 2.734606 CCGCAGAACACTGTTTATTCGA 59.265 45.455 0.00 0.00 34.51 3.71
327 382 2.159707 CCCGCAGAACACTGTTTATTCG 60.160 50.000 0.00 0.00 34.51 3.34
328 383 2.812011 ACCCGCAGAACACTGTTTATTC 59.188 45.455 0.00 0.00 34.51 1.75
329 384 2.552315 CACCCGCAGAACACTGTTTATT 59.448 45.455 0.00 0.00 34.51 1.40
330 385 2.151202 CACCCGCAGAACACTGTTTAT 58.849 47.619 0.00 0.00 34.51 1.40
331 386 1.139256 TCACCCGCAGAACACTGTTTA 59.861 47.619 0.00 0.00 34.51 2.01
332 387 0.107410 TCACCCGCAGAACACTGTTT 60.107 50.000 0.00 0.00 34.51 2.83
333 388 0.532862 CTCACCCGCAGAACACTGTT 60.533 55.000 0.00 0.00 34.51 3.16
334 389 1.069765 CTCACCCGCAGAACACTGT 59.930 57.895 0.00 0.00 34.51 3.55
335 390 0.668706 CTCTCACCCGCAGAACACTG 60.669 60.000 0.00 0.00 35.06 3.66
336 391 1.668294 CTCTCACCCGCAGAACACT 59.332 57.895 0.00 0.00 0.00 3.55
337 392 2.029844 GCTCTCACCCGCAGAACAC 61.030 63.158 0.00 0.00 0.00 3.32
338 393 2.343758 GCTCTCACCCGCAGAACA 59.656 61.111 0.00 0.00 0.00 3.18
339 394 2.435059 GGCTCTCACCCGCAGAAC 60.435 66.667 0.00 0.00 0.00 3.01
340 395 3.706373 GGGCTCTCACCCGCAGAA 61.706 66.667 0.00 0.00 40.98 3.02
347 402 2.818132 CTGATCCGGGCTCTCACC 59.182 66.667 0.00 0.00 0.00 4.02
348 403 2.107953 GCTGATCCGGGCTCTCAC 59.892 66.667 0.00 0.00 0.00 3.51
349 404 2.364186 TGCTGATCCGGGCTCTCA 60.364 61.111 0.00 0.00 0.00 3.27
350 405 2.107953 GTGCTGATCCGGGCTCTC 59.892 66.667 0.00 0.00 0.00 3.20
351 406 2.364842 AGTGCTGATCCGGGCTCT 60.365 61.111 0.00 0.00 0.00 4.09
352 407 2.107953 GAGTGCTGATCCGGGCTC 59.892 66.667 0.00 0.00 0.00 4.70
353 408 3.474570 GGAGTGCTGATCCGGGCT 61.475 66.667 0.00 0.00 0.00 5.19
358 413 0.460987 CACCTTCGGAGTGCTGATCC 60.461 60.000 0.00 0.00 0.00 3.36
359 414 3.056628 CACCTTCGGAGTGCTGATC 57.943 57.895 0.00 0.00 0.00 2.92
377 432 1.539280 GGAGCTATCGTCAAAGGAGGC 60.539 57.143 0.00 0.00 0.00 4.70
450 506 6.039159 AGGATCTGGTTAGTTAAGTACGCTAC 59.961 42.308 0.00 0.00 0.00 3.58
482 538 4.585162 ACCATCTATGTAGTGTAGCACCTC 59.415 45.833 0.00 0.00 34.49 3.85
519 576 4.090090 AGGCAGCGGTATATAGAAGATGT 58.910 43.478 0.00 0.00 0.00 3.06
603 663 0.537653 TTCACACACGGTCCACTTGA 59.462 50.000 0.00 0.00 0.00 3.02
634 706 6.183360 CCACGTAAGACCAGATATATACTCCG 60.183 46.154 0.00 0.00 43.62 4.63
639 711 5.326900 TGGCCACGTAAGACCAGATATATA 58.673 41.667 0.00 0.00 43.62 0.86
725 805 5.938125 ACTATCCAACAGTTTGTGTATGTCC 59.062 40.000 0.00 0.00 39.03 4.02
758 1025 3.507162 TTTCCTTCCATTCTGCTGTCA 57.493 42.857 0.00 0.00 0.00 3.58
840 1109 4.585162 GGGCTGCTGGTATATATAGATCGT 59.415 45.833 0.00 0.00 0.00 3.73
872 1143 8.915057 AGCTAGGTATACGACTATGTTTCTTA 57.085 34.615 0.00 0.00 0.00 2.10
916 1190 2.352225 GGGCGCTGTGATAGTCTGATAG 60.352 54.545 7.64 0.00 0.00 2.08
917 1191 1.613925 GGGCGCTGTGATAGTCTGATA 59.386 52.381 7.64 0.00 0.00 2.15
918 1192 0.390860 GGGCGCTGTGATAGTCTGAT 59.609 55.000 7.64 0.00 0.00 2.90
919 1193 1.816537 GGGCGCTGTGATAGTCTGA 59.183 57.895 7.64 0.00 0.00 3.27
920 1194 1.589993 CGGGCGCTGTGATAGTCTG 60.590 63.158 7.64 0.00 0.00 3.51
921 1195 1.729470 CTCGGGCGCTGTGATAGTCT 61.729 60.000 7.64 0.00 0.00 3.24
922 1196 1.299468 CTCGGGCGCTGTGATAGTC 60.299 63.158 7.64 0.00 0.00 2.59
923 1197 2.808315 CTCGGGCGCTGTGATAGT 59.192 61.111 7.64 0.00 0.00 2.12
992 1267 1.955208 GCGACCTCCCCATCACAATTT 60.955 52.381 0.00 0.00 0.00 1.82
994 1269 1.224592 GCGACCTCCCCATCACAAT 59.775 57.895 0.00 0.00 0.00 2.71
1312 1615 1.078072 TGTTGTGCGAGTGGTGGTT 60.078 52.632 0.00 0.00 0.00 3.67
1637 2008 1.828660 CGGTGTCTAGGCCTCCGAT 60.829 63.158 22.10 0.00 43.22 4.18
1702 2076 2.665185 GCGTCGTTGTTGGAGCCT 60.665 61.111 0.00 0.00 0.00 4.58
1766 2143 1.513586 GAACGATGCTGCTGCTTGC 60.514 57.895 17.00 6.23 40.48 4.01
1845 2240 1.347707 TGGAGGTGTTGCAGAGGTAAG 59.652 52.381 0.00 0.00 0.00 2.34
2040 2467 0.758734 TAGTTCCATGGGCTCCATCG 59.241 55.000 13.02 0.00 43.15 3.84
2157 2584 9.534565 ACAGAACTATCATACACAACACATATC 57.465 33.333 0.00 0.00 0.00 1.63
2159 2586 9.797556 GTACAGAACTATCATACACAACACATA 57.202 33.333 0.00 0.00 0.00 2.29
2343 2868 5.733620 ATCAGCAATTGACAACCTTCAAT 57.266 34.783 10.34 0.00 46.18 2.57
2440 2967 1.296392 CACCGGTTGATGCAGAGGA 59.704 57.895 2.97 0.00 0.00 3.71
2453 2980 1.240641 TGCTTGGTTATGTGCACCGG 61.241 55.000 15.69 0.00 37.07 5.28
2499 3026 3.396560 TGACTTGTCTGCAATCTCACTG 58.603 45.455 2.35 0.00 33.65 3.66
2517 3044 2.280628 AGCTAGCCTATGCGTTTTGAC 58.719 47.619 12.13 0.00 44.33 3.18
2562 3089 6.021596 GTGGTAATTGTGATGAAGCGTTTAG 58.978 40.000 0.00 0.00 0.00 1.85
2836 3636 8.856153 TGTGGTGTACATTAAATAGTCAACAT 57.144 30.769 0.00 0.00 33.42 2.71
2851 3651 6.016610 GCCTCTTTCTTTTTATGTGGTGTACA 60.017 38.462 0.00 0.00 44.87 2.90
2852 3652 6.379386 GCCTCTTTCTTTTTATGTGGTGTAC 58.621 40.000 0.00 0.00 0.00 2.90
2853 3653 5.180492 CGCCTCTTTCTTTTTATGTGGTGTA 59.820 40.000 0.00 0.00 0.00 2.90
2854 3654 4.023193 CGCCTCTTTCTTTTTATGTGGTGT 60.023 41.667 0.00 0.00 0.00 4.16
2855 3655 4.475944 CGCCTCTTTCTTTTTATGTGGTG 58.524 43.478 0.00 0.00 0.00 4.17
2856 3656 3.506067 CCGCCTCTTTCTTTTTATGTGGT 59.494 43.478 0.00 0.00 0.00 4.16
2857 3657 3.506067 ACCGCCTCTTTCTTTTTATGTGG 59.494 43.478 0.00 0.00 0.00 4.17
2858 3658 4.475944 CACCGCCTCTTTCTTTTTATGTG 58.524 43.478 0.00 0.00 0.00 3.21
2859 3659 3.506067 CCACCGCCTCTTTCTTTTTATGT 59.494 43.478 0.00 0.00 0.00 2.29
2860 3660 3.119495 CCCACCGCCTCTTTCTTTTTATG 60.119 47.826 0.00 0.00 0.00 1.90
2861 3661 3.089284 CCCACCGCCTCTTTCTTTTTAT 58.911 45.455 0.00 0.00 0.00 1.40
2862 3662 2.510613 CCCACCGCCTCTTTCTTTTTA 58.489 47.619 0.00 0.00 0.00 1.52
2863 3663 1.328279 CCCACCGCCTCTTTCTTTTT 58.672 50.000 0.00 0.00 0.00 1.94
2864 3664 0.539669 CCCCACCGCCTCTTTCTTTT 60.540 55.000 0.00 0.00 0.00 2.27
2865 3665 1.074951 CCCCACCGCCTCTTTCTTT 59.925 57.895 0.00 0.00 0.00 2.52
2866 3666 2.757077 CCCCACCGCCTCTTTCTT 59.243 61.111 0.00 0.00 0.00 2.52
2867 3667 3.330720 CCCCCACCGCCTCTTTCT 61.331 66.667 0.00 0.00 0.00 2.52
2887 3687 6.118170 GGTCTCTATAAAACAAGTAACCCCC 58.882 44.000 0.00 0.00 0.00 5.40
2888 3688 6.714278 TGGTCTCTATAAAACAAGTAACCCC 58.286 40.000 0.00 0.00 0.00 4.95
2889 3689 6.822170 CCTGGTCTCTATAAAACAAGTAACCC 59.178 42.308 0.00 0.00 0.00 4.11
2890 3690 7.333672 CACCTGGTCTCTATAAAACAAGTAACC 59.666 40.741 0.00 0.00 0.00 2.85
2891 3691 8.092687 TCACCTGGTCTCTATAAAACAAGTAAC 58.907 37.037 0.00 0.00 0.00 2.50
2892 3692 8.197592 TCACCTGGTCTCTATAAAACAAGTAA 57.802 34.615 0.00 0.00 0.00 2.24
2893 3693 7.453752 ACTCACCTGGTCTCTATAAAACAAGTA 59.546 37.037 0.00 0.00 0.00 2.24
2894 3694 6.270231 ACTCACCTGGTCTCTATAAAACAAGT 59.730 38.462 0.00 0.00 0.00 3.16
2895 3695 6.591834 CACTCACCTGGTCTCTATAAAACAAG 59.408 42.308 0.00 0.00 0.00 3.16
2896 3696 6.042781 ACACTCACCTGGTCTCTATAAAACAA 59.957 38.462 0.00 0.00 0.00 2.83
2897 3697 5.542635 ACACTCACCTGGTCTCTATAAAACA 59.457 40.000 0.00 0.00 0.00 2.83
2911 3946 2.768253 TGGATAGCAACACTCACCTG 57.232 50.000 0.00 0.00 0.00 4.00
2913 3948 3.265791 CTCTTGGATAGCAACACTCACC 58.734 50.000 0.00 0.00 0.00 4.02
2981 4016 9.705290 GTGATTAGAAATGGTTTTGTTTGGTAT 57.295 29.630 0.00 0.00 0.00 2.73
3071 4579 3.128242 CCCGATCTACACTTAACACGTCT 59.872 47.826 0.00 0.00 0.00 4.18
3106 4614 6.368779 TGTAACTAACTAGAATGGGCAAGT 57.631 37.500 0.00 0.00 0.00 3.16
3110 4618 6.171213 ACACTTGTAACTAACTAGAATGGGC 58.829 40.000 0.00 0.00 35.26 5.36


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

AutoCloner maintained by Alex Coulton.