Multiple sequence alignment - TraesCS7A01G280000

Loading Multiple Alignment...

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 TraesCS7A01G280000 chr7A 100.000 3112 0 0 1 3112 299381320 299378209 0.000000e+00 5747.0
1 TraesCS7A01G280000 chr7A 87.488 1079 108 13 2041 3112 11042698 11043756 0.000000e+00 1219.0
2 TraesCS7A01G280000 chr7A 86.875 320 22 10 3 306 634665339 634665024 1.070000e-89 340.0
3 TraesCS7A01G280000 chr7A 95.556 90 4 0 289 378 731525408 731525497 8.990000e-31 145.0
4 TraesCS7A01G280000 chr7A 93.750 96 5 1 284 378 634665138 634665043 3.240000e-30 143.0
5 TraesCS7A01G280000 chr1A 89.108 2837 236 48 284 3105 520853167 520855945 0.000000e+00 3459.0
6 TraesCS7A01G280000 chr1A 91.349 289 9 4 1 273 295971936 295971648 6.300000e-102 381.0
7 TraesCS7A01G280000 chr1A 95.833 96 3 1 284 378 295971730 295971635 1.490000e-33 154.0
8 TraesCS7A01G280000 chr1A 97.917 48 1 0 379 426 295971726 295971679 1.990000e-12 84.2
9 TraesCS7A01G280000 chr1A 97.917 48 1 0 379 426 520853171 520853218 1.990000e-12 84.2
10 TraesCS7A01G280000 chr6A 88.055 2838 262 51 284 3105 425737917 425740693 0.000000e+00 3291.0
11 TraesCS7A01G280000 chr6A 89.227 1281 119 13 1512 2783 270388761 270387491 0.000000e+00 1583.0
12 TraesCS7A01G280000 chr6A 86.961 974 87 20 288 1254 270434089 270433149 0.000000e+00 1059.0
13 TraesCS7A01G280000 chr6A 88.820 322 18 9 1 306 58443401 58443082 2.270000e-101 379.0
14 TraesCS7A01G280000 chr6A 89.860 286 14 4 1 273 270434296 270434013 1.370000e-93 353.0
15 TraesCS7A01G280000 chr6A 87.307 323 19 12 3 306 568068433 568068114 1.780000e-92 350.0
16 TraesCS7A01G280000 chr6A 98.000 50 1 0 379 428 425737921 425737970 1.540000e-13 87.9
17 TraesCS7A01G280000 chr2B 87.672 2839 265 40 284 3105 282448553 282451323 0.000000e+00 3225.0
18 TraesCS7A01G280000 chr2B 87.233 2851 271 49 284 3105 609288966 609286180 0.000000e+00 3162.0
19 TraesCS7A01G280000 chr2B 88.988 2016 174 28 284 2283 241245884 241247867 0.000000e+00 2449.0
20 TraesCS7A01G280000 chr2B 89.199 1324 94 19 818 2100 57159289 57157974 0.000000e+00 1607.0
21 TraesCS7A01G280000 chr2B 89.512 963 83 11 602 1546 787965359 787964397 0.000000e+00 1203.0
22 TraesCS7A01G280000 chr2B 89.789 284 14 4 1 270 282448350 282448632 1.780000e-92 350.0
23 TraesCS7A01G280000 chr2B 86.916 321 25 6 1 306 241245680 241245998 8.260000e-91 344.0
24 TraesCS7A01G280000 chr2B 85.106 329 23 6 2 306 609289178 609288852 2.330000e-81 313.0
25 TraesCS7A01G280000 chr6D 89.461 2021 160 30 284 2283 384291977 384289989 0.000000e+00 2503.0
26 TraesCS7A01G280000 chr6D 89.391 1838 172 16 1261 3087 210881629 210883454 0.000000e+00 2292.0
27 TraesCS7A01G280000 chr6D 90.657 289 11 5 1 273 384292183 384291895 1.360000e-98 370.0
28 TraesCS7A01G280000 chr6D 87.850 321 20 7 1 305 210873596 210873913 2.950000e-95 359.0
29 TraesCS7A01G280000 chr6D 87.538 329 16 6 1 306 291655078 291655404 1.060000e-94 357.0
30 TraesCS7A01G280000 chr6D 98.000 50 1 0 379 428 384291973 384291924 1.540000e-13 87.9
31 TraesCS7A01G280000 chr6D 96.000 50 2 0 379 428 291655294 291655343 7.150000e-12 82.4
32 TraesCS7A01G280000 chr4B 88.171 2012 182 39 284 2283 159346200 159348167 0.000000e+00 2346.0
33 TraesCS7A01G280000 chr4B 98.000 50 1 0 379 428 159346204 159346253 1.540000e-13 87.9
34 TraesCS7A01G280000 chr1B 89.857 1469 130 12 1646 3110 235375848 235374395 0.000000e+00 1869.0
35 TraesCS7A01G280000 chr2A 91.056 1297 94 12 818 2100 405467538 405468826 0.000000e+00 1733.0
36 TraesCS7A01G280000 chr3B 89.224 1327 91 20 818 2100 795066634 795067952 0.000000e+00 1611.0
37 TraesCS7A01G280000 chr3B 87.674 1079 107 12 2041 3112 818192589 818193648 0.000000e+00 1232.0
38 TraesCS7A01G280000 chr3B 87.674 1079 107 12 2041 3112 818228337 818229396 0.000000e+00 1232.0
39 TraesCS7A01G280000 chr3B 87.385 325 19 7 1 306 145897318 145896997 1.370000e-93 353.0
40 TraesCS7A01G280000 chr6B 89.048 1324 96 19 818 2100 168771144 168772459 0.000000e+00 1596.0
41 TraesCS7A01G280000 chr3A 88.520 1324 103 18 818 2100 699162186 699163501 0.000000e+00 1557.0
42 TraesCS7A01G280000 chr3A 87.488 1079 109 14 2041 3112 550447982 550449041 0.000000e+00 1221.0
43 TraesCS7A01G280000 chr7B 90.493 1157 89 11 818 1960 49030858 49029709 0.000000e+00 1507.0
44 TraesCS7A01G280000 chr7D 88.601 1079 98 13 2041 3112 560903049 560904109 0.000000e+00 1288.0
45 TraesCS7A01G280000 chr2D 90.729 960 74 9 602 1546 650754425 650753466 0.000000e+00 1266.0
46 TraesCS7A01G280000 chr2D 98.000 50 1 0 379 428 617518816 617518865 1.540000e-13 87.9
47 TraesCS7A01G280000 chr5B 87.570 1070 106 14 2050 3112 487465726 487464677 0.000000e+00 1214.0
48 TraesCS7A01G280000 chr5B 87.462 327 18 6 1 306 239332740 239332416 3.820000e-94 355.0
49 TraesCS7A01G280000 chr5B 98.000 50 1 0 379 428 239332526 239332477 1.540000e-13 87.9
50 TraesCS7A01G280000 chr4D 89.869 306 11 5 1 287 465052126 465052430 2.930000e-100 375.0
51 TraesCS7A01G280000 chr4D 98.000 50 1 0 379 428 465052338 465052387 1.540000e-13 87.9
52 TraesCS7A01G280000 chr5A 87.654 324 20 6 1 306 543951031 543951352 2.950000e-95 359.0


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 TraesCS7A01G280000 chr7A 299378209 299381320 3111 True 5747.000000 5747 100.0000 1 3112 1 chr7A.!!$R1 3111
1 TraesCS7A01G280000 chr7A 11042698 11043756 1058 False 1219.000000 1219 87.4880 2041 3112 1 chr7A.!!$F1 1071
2 TraesCS7A01G280000 chr1A 520853167 520855945 2778 False 1771.600000 3459 93.5125 284 3105 2 chr1A.!!$F1 2821
3 TraesCS7A01G280000 chr6A 425737917 425740693 2776 False 1689.450000 3291 93.0275 284 3105 2 chr6A.!!$F1 2821
4 TraesCS7A01G280000 chr6A 270387491 270388761 1270 True 1583.000000 1583 89.2270 1512 2783 1 chr6A.!!$R2 1271
5 TraesCS7A01G280000 chr6A 270433149 270434296 1147 True 706.000000 1059 88.4105 1 1254 2 chr6A.!!$R4 1253
6 TraesCS7A01G280000 chr2B 282448350 282451323 2973 False 1787.500000 3225 88.7305 1 3105 2 chr2B.!!$F2 3104
7 TraesCS7A01G280000 chr2B 609286180 609289178 2998 True 1737.500000 3162 86.1695 2 3105 2 chr2B.!!$R3 3103
8 TraesCS7A01G280000 chr2B 57157974 57159289 1315 True 1607.000000 1607 89.1990 818 2100 1 chr2B.!!$R1 1282
9 TraesCS7A01G280000 chr2B 241245680 241247867 2187 False 1396.500000 2449 87.9520 1 2283 2 chr2B.!!$F1 2282
10 TraesCS7A01G280000 chr2B 787964397 787965359 962 True 1203.000000 1203 89.5120 602 1546 1 chr2B.!!$R2 944
11 TraesCS7A01G280000 chr6D 210881629 210883454 1825 False 2292.000000 2292 89.3910 1261 3087 1 chr6D.!!$F2 1826
12 TraesCS7A01G280000 chr6D 384289989 384292183 2194 True 986.966667 2503 92.7060 1 2283 3 chr6D.!!$R1 2282
13 TraesCS7A01G280000 chr4B 159346200 159348167 1967 False 1216.950000 2346 93.0855 284 2283 2 chr4B.!!$F1 1999
14 TraesCS7A01G280000 chr1B 235374395 235375848 1453 True 1869.000000 1869 89.8570 1646 3110 1 chr1B.!!$R1 1464
15 TraesCS7A01G280000 chr2A 405467538 405468826 1288 False 1733.000000 1733 91.0560 818 2100 1 chr2A.!!$F1 1282
16 TraesCS7A01G280000 chr3B 795066634 795067952 1318 False 1611.000000 1611 89.2240 818 2100 1 chr3B.!!$F1 1282
17 TraesCS7A01G280000 chr3B 818192589 818193648 1059 False 1232.000000 1232 87.6740 2041 3112 1 chr3B.!!$F2 1071
18 TraesCS7A01G280000 chr3B 818228337 818229396 1059 False 1232.000000 1232 87.6740 2041 3112 1 chr3B.!!$F3 1071
19 TraesCS7A01G280000 chr6B 168771144 168772459 1315 False 1596.000000 1596 89.0480 818 2100 1 chr6B.!!$F1 1282
20 TraesCS7A01G280000 chr3A 699162186 699163501 1315 False 1557.000000 1557 88.5200 818 2100 1 chr3A.!!$F2 1282
21 TraesCS7A01G280000 chr3A 550447982 550449041 1059 False 1221.000000 1221 87.4880 2041 3112 1 chr3A.!!$F1 1071
22 TraesCS7A01G280000 chr7B 49029709 49030858 1149 True 1507.000000 1507 90.4930 818 1960 1 chr7B.!!$R1 1142
23 TraesCS7A01G280000 chr7D 560903049 560904109 1060 False 1288.000000 1288 88.6010 2041 3112 1 chr7D.!!$F1 1071
24 TraesCS7A01G280000 chr2D 650753466 650754425 959 True 1266.000000 1266 90.7290 602 1546 1 chr2D.!!$R1 944
25 TraesCS7A01G280000 chr5B 487464677 487465726 1049 True 1214.000000 1214 87.5700 2050 3112 1 chr5B.!!$R1 1062

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
719 796 1.002544 GCTGTTACTGCCTCCAGAAGT 59.997 52.381 2.72 0.0 41.77 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2645 2858 0.251341 AGGGGCAGGTTTTACAGCAG 60.251 55.0 0.0 0.0 0.0 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
63 65 2.516227 TCCACTCGAGAGGTCTGAAT 57.484 50.000 25.49 0.00 0.00 2.57
228 256 5.135508 ACTGTAACAGTTGTACTAGCAGG 57.864 43.478 0.00 0.00 42.59 4.85
229 257 4.831155 ACTGTAACAGTTGTACTAGCAGGA 59.169 41.667 0.00 0.00 42.59 3.86
230 258 5.480772 ACTGTAACAGTTGTACTAGCAGGAT 59.519 40.000 0.00 0.00 42.59 3.24
231 259 6.014499 ACTGTAACAGTTGTACTAGCAGGATT 60.014 38.462 0.00 0.00 42.59 3.01
232 260 7.177921 ACTGTAACAGTTGTACTAGCAGGATTA 59.822 37.037 0.00 0.00 42.59 1.75
233 261 8.074613 TGTAACAGTTGTACTAGCAGGATTAT 57.925 34.615 0.00 0.00 0.00 1.28
234 262 8.195436 TGTAACAGTTGTACTAGCAGGATTATC 58.805 37.037 0.00 0.00 0.00 1.75
235 263 6.163135 ACAGTTGTACTAGCAGGATTATCC 57.837 41.667 2.40 2.40 36.58 2.59
248 276 3.669536 GGATTATCCTAGAAGCTGTGCC 58.330 50.000 3.59 0.00 32.53 5.01
249 277 3.071602 GGATTATCCTAGAAGCTGTGCCA 59.928 47.826 3.59 0.00 32.53 4.92
250 278 4.444876 GGATTATCCTAGAAGCTGTGCCAA 60.445 45.833 3.59 0.00 32.53 4.52
251 279 4.778213 TTATCCTAGAAGCTGTGCCAAT 57.222 40.909 0.00 0.00 0.00 3.16
252 280 3.659183 ATCCTAGAAGCTGTGCCAATT 57.341 42.857 0.00 0.00 0.00 2.32
253 281 3.439857 TCCTAGAAGCTGTGCCAATTT 57.560 42.857 0.00 0.00 0.00 1.82
254 282 3.766545 TCCTAGAAGCTGTGCCAATTTT 58.233 40.909 0.00 0.00 0.00 1.82
255 283 4.151883 TCCTAGAAGCTGTGCCAATTTTT 58.848 39.130 0.00 0.00 0.00 1.94
256 284 4.218417 TCCTAGAAGCTGTGCCAATTTTTC 59.782 41.667 0.00 0.00 0.00 2.29
257 285 4.022068 CCTAGAAGCTGTGCCAATTTTTCA 60.022 41.667 0.00 0.00 0.00 2.69
258 286 4.612264 AGAAGCTGTGCCAATTTTTCAT 57.388 36.364 0.00 0.00 0.00 2.57
259 287 4.563061 AGAAGCTGTGCCAATTTTTCATC 58.437 39.130 0.00 0.00 0.00 2.92
260 288 4.039488 AGAAGCTGTGCCAATTTTTCATCA 59.961 37.500 0.00 0.00 0.00 3.07
261 289 4.339872 AGCTGTGCCAATTTTTCATCAA 57.660 36.364 0.00 0.00 0.00 2.57
262 290 4.901868 AGCTGTGCCAATTTTTCATCAAT 58.098 34.783 0.00 0.00 0.00 2.57
263 291 5.310451 AGCTGTGCCAATTTTTCATCAATT 58.690 33.333 0.00 0.00 0.00 2.32
264 292 5.180492 AGCTGTGCCAATTTTTCATCAATTG 59.820 36.000 0.00 0.00 40.11 2.32
265 293 5.179742 GCTGTGCCAATTTTTCATCAATTGA 59.820 36.000 11.26 11.26 42.10 2.57
266 294 6.128117 GCTGTGCCAATTTTTCATCAATTGAT 60.128 34.615 15.36 15.36 42.10 2.57
267 295 7.064847 GCTGTGCCAATTTTTCATCAATTGATA 59.935 33.333 20.32 5.48 42.10 2.15
268 296 8.843885 TGTGCCAATTTTTCATCAATTGATAA 57.156 26.923 20.32 11.65 42.10 1.75
269 297 8.719648 TGTGCCAATTTTTCATCAATTGATAAC 58.280 29.630 20.32 1.17 42.10 1.89
270 298 7.899330 GTGCCAATTTTTCATCAATTGATAACG 59.101 33.333 20.32 9.05 42.10 3.18
271 299 6.901357 GCCAATTTTTCATCAATTGATAACGC 59.099 34.615 20.32 9.98 42.10 4.84
272 300 7.412781 GCCAATTTTTCATCAATTGATAACGCA 60.413 33.333 20.32 6.02 42.10 5.24
273 301 8.111836 CCAATTTTTCATCAATTGATAACGCAG 58.888 33.333 20.32 7.64 42.10 5.18
274 302 7.760131 ATTTTTCATCAATTGATAACGCAGG 57.240 32.000 20.32 6.95 33.34 4.85
275 303 6.507958 TTTTCATCAATTGATAACGCAGGA 57.492 33.333 20.32 9.15 33.34 3.86
276 304 6.507958 TTTCATCAATTGATAACGCAGGAA 57.492 33.333 20.32 14.19 33.34 3.36
277 305 5.484173 TCATCAATTGATAACGCAGGAAC 57.516 39.130 20.32 0.00 32.63 3.62
278 306 4.940654 TCATCAATTGATAACGCAGGAACA 59.059 37.500 20.32 0.00 32.63 3.18
279 307 5.589855 TCATCAATTGATAACGCAGGAACAT 59.410 36.000 20.32 0.00 32.63 2.71
280 308 6.765512 TCATCAATTGATAACGCAGGAACATA 59.234 34.615 20.32 0.00 32.63 2.29
281 309 6.603237 TCAATTGATAACGCAGGAACATAG 57.397 37.500 3.38 0.00 0.00 2.23
282 310 6.112734 TCAATTGATAACGCAGGAACATAGT 58.887 36.000 3.38 0.00 0.00 2.12
283 311 6.257849 TCAATTGATAACGCAGGAACATAGTC 59.742 38.462 3.38 0.00 0.00 2.59
284 312 4.729227 TGATAACGCAGGAACATAGTCA 57.271 40.909 0.00 0.00 0.00 3.41
285 313 5.079689 TGATAACGCAGGAACATAGTCAA 57.920 39.130 0.00 0.00 0.00 3.18
286 314 5.483811 TGATAACGCAGGAACATAGTCAAA 58.516 37.500 0.00 0.00 0.00 2.69
287 315 6.112734 TGATAACGCAGGAACATAGTCAAAT 58.887 36.000 0.00 0.00 0.00 2.32
346 375 5.904362 ATCCTAGAAGTTGTGCCAATTTC 57.096 39.130 12.24 12.24 0.00 2.17
412 441 5.135508 ACTGTTACAGTTGTACTAGCAGG 57.864 43.478 12.76 0.00 42.59 4.85
413 442 4.831155 ACTGTTACAGTTGTACTAGCAGGA 59.169 41.667 12.76 0.00 42.59 3.86
414 443 5.480772 ACTGTTACAGTTGTACTAGCAGGAT 59.519 40.000 12.76 0.00 42.59 3.24
415 444 6.014499 ACTGTTACAGTTGTACTAGCAGGATT 60.014 38.462 12.76 0.00 42.59 3.01
416 445 7.177921 ACTGTTACAGTTGTACTAGCAGGATTA 59.822 37.037 12.76 0.00 42.59 1.75
417 446 8.074613 TGTTACAGTTGTACTAGCAGGATTAT 57.925 34.615 0.00 0.00 0.00 1.28
418 447 8.195436 TGTTACAGTTGTACTAGCAGGATTATC 58.805 37.037 0.00 0.00 0.00 1.75
419 448 6.163135 ACAGTTGTACTAGCAGGATTATCC 57.837 41.667 2.40 2.40 36.58 2.59
435 464 7.768807 GGATTATCCTAGAAGCTCAGTAAGA 57.231 40.000 3.59 0.00 32.53 2.10
436 465 8.361169 GGATTATCCTAGAAGCTCAGTAAGAT 57.639 38.462 3.59 0.00 32.53 2.40
437 466 9.469097 GGATTATCCTAGAAGCTCAGTAAGATA 57.531 37.037 3.59 0.00 32.53 1.98
440 469 7.759489 ATCCTAGAAGCTCAGTAAGATAGTG 57.241 40.000 0.00 0.00 0.00 2.74
441 470 6.901300 TCCTAGAAGCTCAGTAAGATAGTGA 58.099 40.000 0.00 0.00 36.71 3.41
442 471 7.347252 TCCTAGAAGCTCAGTAAGATAGTGAA 58.653 38.462 0.00 0.00 37.65 3.18
489 566 9.844257 ATAATTCTCACTTTCTATGCTAAGCTT 57.156 29.630 3.48 3.48 0.00 3.74
561 638 4.411256 ACGAACCTCCAGTTTCTACAAA 57.589 40.909 0.00 0.00 39.40 2.83
579 656 7.103641 TCTACAAACAGAAGAAAAGTGAGTGT 58.896 34.615 0.00 0.00 0.00 3.55
625 702 5.936686 TCTCAGCATAAGCATGATAAAGC 57.063 39.130 0.00 0.00 45.49 3.51
660 737 6.825610 ACTTGGCTTATTGTTTTGGAAATCA 58.174 32.000 0.00 0.00 0.00 2.57
697 774 4.440525 CCTGCTTGTTTTTGTGATCACTGT 60.441 41.667 25.55 0.00 0.00 3.55
719 796 1.002544 GCTGTTACTGCCTCCAGAAGT 59.997 52.381 2.72 0.00 41.77 3.01
738 815 5.182760 AGAAGTTGCAATCTAAAGCCTTCTG 59.817 40.000 18.48 0.00 37.71 3.02
763 840 9.734984 TGTAAGGATATCATCACGAAGTAGATA 57.265 33.333 4.83 0.00 41.61 1.98
804 881 6.212589 TGAGATAACAGTACTGATTGGTTGGA 59.787 38.462 29.30 0.76 0.00 3.53
881 963 3.686241 TGTTCATGCTTTCCTCAGATTCG 59.314 43.478 0.00 0.00 0.00 3.34
1113 1200 6.037720 TGTCTAAAATTGCGACTCAGAAACAA 59.962 34.615 0.00 0.00 0.00 2.83
1123 1217 5.677178 GCGACTCAGAAACAACTTTTAACTG 59.323 40.000 0.00 0.00 0.00 3.16
1163 1258 5.920193 AATGGGATGAACATTGTAGGTTG 57.080 39.130 0.00 0.00 37.18 3.77
1280 1378 2.620367 GCATCAAATGGGACCCTGTACA 60.620 50.000 13.00 0.00 0.00 2.90
1389 1495 7.728083 TCATTTGTTTTCTTCCTTTAGATGGGA 59.272 33.333 0.00 0.00 0.00 4.37
1395 1504 6.448369 TTCTTCCTTTAGATGGGAAAGTGA 57.552 37.500 0.00 0.00 40.53 3.41
1412 1521 2.108952 AGTGACCCAATTCTCTTGGCTT 59.891 45.455 0.00 0.00 38.23 4.35
1415 1524 3.282885 GACCCAATTCTCTTGGCTTAGG 58.717 50.000 0.00 0.00 38.23 2.69
1498 1607 3.367910 CCTCCTTTCGCTATATCAGAGCC 60.368 52.174 0.00 0.00 36.53 4.70
1614 1730 9.399797 AGACAATTGCTCATGAGTTAATCATTA 57.600 29.630 23.38 0.00 46.97 1.90
1655 1771 1.258445 CGTCTACTGAAGCCCCACCT 61.258 60.000 0.00 0.00 0.00 4.00
1694 1810 0.251121 CCAACCTGTGCATGGGTGTA 60.251 55.000 20.52 0.00 40.51 2.90
1793 1909 1.279271 AGGTAAGCAAAGCGATCCACT 59.721 47.619 0.00 0.00 0.00 4.00
1809 1925 5.645497 CGATCCACTTTTCCTCTTTCTCATT 59.355 40.000 0.00 0.00 0.00 2.57
1816 1932 8.046107 CACTTTTCCTCTTTCTCATTAGATCCT 58.954 37.037 0.00 0.00 0.00 3.24
2018 2216 3.382546 ACCTTCAATATCATGCTTGCACC 59.617 43.478 0.00 0.00 0.00 5.01
2031 2229 1.408340 CTTGCACCCACATGTTGTTCA 59.592 47.619 0.00 0.00 0.00 3.18
2056 2254 0.533491 CACCATGAATGTTGCCCAGG 59.467 55.000 0.00 0.00 0.00 4.45
2072 2270 0.458669 CAGGATTGCCATGCCTTCAC 59.541 55.000 0.00 0.00 36.29 3.18
2092 2290 5.899299 TCACCTTTCGCTATAAGTTCCTAC 58.101 41.667 0.00 0.00 0.00 3.18
2100 2298 3.004944 GCTATAAGTTCCTACGCTGCTCT 59.995 47.826 0.00 0.00 0.00 4.09
2110 2308 2.543777 ACGCTGCTCTTTTTCAGGTA 57.456 45.000 0.00 0.00 0.00 3.08
2174 2372 3.872696 TGAGATCAAAGCAGCGGATTTA 58.127 40.909 0.00 0.00 30.11 1.40
2182 2381 8.621532 ATCAAAGCAGCGGATTTATAGATTTA 57.378 30.769 0.00 0.00 30.11 1.40
2200 2400 7.626999 AGATTTATGGGTATTGGTGCTACTA 57.373 36.000 0.00 0.00 0.00 1.82
2231 2431 2.643551 CGGCTTATGGTCTTTGGTCAT 58.356 47.619 0.00 0.00 0.00 3.06
2288 2489 7.408756 TGTTAAATCTCATTTAGCTTGGCAT 57.591 32.000 0.00 0.00 37.02 4.40
2304 2505 5.627503 GCTTGGCATCTCCATTTATTGGTTT 60.628 40.000 0.00 0.00 46.04 3.27
2309 2510 4.059773 TCTCCATTTATTGGTTTGGGCT 57.940 40.909 0.00 0.00 46.52 5.19
2340 2541 1.202348 CCTGTCGAGCAGTATCACTGG 60.202 57.143 8.31 0.00 46.01 4.00
2353 2554 6.462500 CAGTATCACTGGCTAGAAGCATAAT 58.538 40.000 3.17 0.00 44.75 1.28
2421 2628 2.032178 GCTAGCGAAATTTGGCTGGTAG 59.968 50.000 30.79 22.68 42.36 3.18
2532 2742 1.218844 TAGTAAAGATGGGGTGGGGC 58.781 55.000 0.00 0.00 0.00 5.80
2645 2858 3.222603 AGATGTTCCTGTTGGTTTGTCC 58.777 45.455 0.00 0.00 34.23 4.02
2653 2866 2.948979 CTGTTGGTTTGTCCTGCTGTAA 59.051 45.455 0.00 0.00 37.07 2.41
2728 2941 4.690748 AGTAATGGACGTTCACAGTTCATG 59.309 41.667 0.00 0.00 37.83 3.07
2734 2947 2.102420 ACGTTCACAGTTCATGGTCTCA 59.898 45.455 0.00 0.00 0.00 3.27
2762 2975 0.035152 ATTTGATGACAGGAGCCGCA 60.035 50.000 0.00 0.00 0.00 5.69
2763 2976 0.250684 TTTGATGACAGGAGCCGCAA 60.251 50.000 0.00 0.00 0.00 4.85
2841 3055 8.681486 AGTGCATCTTATCATTTAGCAATACA 57.319 30.769 0.00 0.00 31.78 2.29
2851 3065 5.418524 TCATTTAGCAATACATTGGCTGTGT 59.581 36.000 4.23 1.34 38.92 3.72
2887 3101 8.539117 TCAATGGAGATCTTCTGTAGATGTAA 57.461 34.615 1.86 0.00 43.75 2.41
2919 3137 8.641499 TTTTTCATGCGTTAAACTTCTCAATT 57.359 26.923 0.00 0.00 0.00 2.32
2941 3159 3.005684 TGTTGACCATGGAAAATCTGTGC 59.994 43.478 21.47 0.01 0.00 4.57
2953 3171 5.368256 AAAATCTGTGCAGTTCTCATGTC 57.632 39.130 0.00 0.00 0.00 3.06
3055 3273 8.248253 TCTCTTGCGTATTTACATCAAAGACTA 58.752 33.333 0.00 0.00 36.41 2.59
3082 3300 6.828502 TTCGAATGCTTATCATGTACAGTC 57.171 37.500 0.33 0.00 35.13 3.51
3087 3305 7.115520 CGAATGCTTATCATGTACAGTCCTAAG 59.884 40.741 0.33 7.20 35.13 2.18
3095 3313 2.042569 TGTACAGTCCTAAGCTCCCTGA 59.957 50.000 0.00 0.00 0.00 3.86
3105 3323 1.925972 GCTCCCTGACCCCTCCTTT 60.926 63.158 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 6.452494 TCCTTAAGTTATTCAGACCTCTCG 57.548 41.667 0.97 0.00 0.00 4.04
88 105 3.615155 TGCGTGGACCATGATTTTGATA 58.385 40.909 18.32 0.00 0.00 2.15
133 160 0.109342 AGGCCCCTATGAAATCAGCG 59.891 55.000 0.00 0.00 0.00 5.18
207 235 5.386958 TCCTGCTAGTACAACTGTTACAG 57.613 43.478 11.21 11.21 37.52 2.74
208 236 5.995565 ATCCTGCTAGTACAACTGTTACA 57.004 39.130 0.00 0.00 0.00 2.41
209 237 7.652507 GGATAATCCTGCTAGTACAACTGTTAC 59.347 40.741 0.00 0.00 32.53 2.50
210 238 7.723324 GGATAATCCTGCTAGTACAACTGTTA 58.277 38.462 0.00 0.00 32.53 2.41
211 239 6.583562 GGATAATCCTGCTAGTACAACTGTT 58.416 40.000 0.00 0.00 32.53 3.16
212 240 6.163135 GGATAATCCTGCTAGTACAACTGT 57.837 41.667 0.00 0.00 32.53 3.55
225 253 8.593134 TTGGCACAGCTTCTAGGATAATCCTG 62.593 46.154 0.00 0.00 44.49 3.86
226 254 6.639227 TTGGCACAGCTTCTAGGATAATCCT 61.639 44.000 0.00 0.00 46.12 3.24
227 255 3.071602 TGGCACAGCTTCTAGGATAATCC 59.928 47.826 0.00 0.00 36.58 3.01
228 256 4.342862 TGGCACAGCTTCTAGGATAATC 57.657 45.455 0.00 0.00 0.00 1.75
229 257 4.778213 TTGGCACAGCTTCTAGGATAAT 57.222 40.909 0.00 0.00 42.39 1.28
230 258 4.778213 ATTGGCACAGCTTCTAGGATAA 57.222 40.909 0.00 0.00 42.39 1.75
231 259 4.778213 AATTGGCACAGCTTCTAGGATA 57.222 40.909 0.00 0.00 42.39 2.59
232 260 3.659183 AATTGGCACAGCTTCTAGGAT 57.341 42.857 0.00 0.00 42.39 3.24
233 261 3.439857 AAATTGGCACAGCTTCTAGGA 57.560 42.857 0.00 0.00 42.39 2.94
234 262 4.022068 TGAAAAATTGGCACAGCTTCTAGG 60.022 41.667 0.00 0.00 42.39 3.02
235 263 5.125100 TGAAAAATTGGCACAGCTTCTAG 57.875 39.130 0.00 0.00 42.39 2.43
236 264 5.243507 TGATGAAAAATTGGCACAGCTTCTA 59.756 36.000 0.00 0.00 42.39 2.10
237 265 4.039488 TGATGAAAAATTGGCACAGCTTCT 59.961 37.500 0.00 0.00 42.39 2.85
238 266 4.309099 TGATGAAAAATTGGCACAGCTTC 58.691 39.130 0.00 0.00 42.39 3.86
239 267 4.339872 TGATGAAAAATTGGCACAGCTT 57.660 36.364 0.00 0.00 42.39 3.74
240 268 4.339872 TTGATGAAAAATTGGCACAGCT 57.660 36.364 0.00 0.00 42.39 4.24
241 269 5.179742 TCAATTGATGAAAAATTGGCACAGC 59.820 36.000 3.38 0.00 42.63 4.40
242 270 6.788684 TCAATTGATGAAAAATTGGCACAG 57.211 33.333 3.38 0.00 42.63 3.66
243 271 8.719648 GTTATCAATTGATGAAAAATTGGCACA 58.280 29.630 27.59 2.74 42.63 4.57
244 272 7.899330 CGTTATCAATTGATGAAAAATTGGCAC 59.101 33.333 27.59 5.80 42.63 5.01
245 273 7.412781 GCGTTATCAATTGATGAAAAATTGGCA 60.413 33.333 27.59 3.36 42.63 4.92
246 274 6.901357 GCGTTATCAATTGATGAAAAATTGGC 59.099 34.615 27.59 15.17 42.63 4.52
247 275 7.961855 TGCGTTATCAATTGATGAAAAATTGG 58.038 30.769 27.59 10.56 42.63 3.16
248 276 8.111836 CCTGCGTTATCAATTGATGAAAAATTG 58.888 33.333 27.59 12.97 42.54 2.32
249 277 8.034215 TCCTGCGTTATCAATTGATGAAAAATT 58.966 29.630 27.59 5.27 42.54 1.82
250 278 7.546358 TCCTGCGTTATCAATTGATGAAAAAT 58.454 30.769 27.59 5.99 42.54 1.82
251 279 6.918626 TCCTGCGTTATCAATTGATGAAAAA 58.081 32.000 27.59 13.20 42.54 1.94
252 280 6.507958 TCCTGCGTTATCAATTGATGAAAA 57.492 33.333 27.59 13.53 42.54 2.29
253 281 6.072230 TGTTCCTGCGTTATCAATTGATGAAA 60.072 34.615 27.59 14.21 42.54 2.69
254 282 5.414144 TGTTCCTGCGTTATCAATTGATGAA 59.586 36.000 27.59 17.85 42.54 2.57
255 283 4.940654 TGTTCCTGCGTTATCAATTGATGA 59.059 37.500 27.59 18.74 43.67 2.92
256 284 5.233957 TGTTCCTGCGTTATCAATTGATG 57.766 39.130 27.59 14.20 36.05 3.07
257 285 6.767902 ACTATGTTCCTGCGTTATCAATTGAT 59.232 34.615 23.75 23.75 38.51 2.57
258 286 6.112734 ACTATGTTCCTGCGTTATCAATTGA 58.887 36.000 11.26 11.26 0.00 2.57
259 287 6.037062 TGACTATGTTCCTGCGTTATCAATTG 59.963 38.462 0.00 0.00 0.00 2.32
260 288 6.112734 TGACTATGTTCCTGCGTTATCAATT 58.887 36.000 0.00 0.00 0.00 2.32
261 289 5.670485 TGACTATGTTCCTGCGTTATCAAT 58.330 37.500 0.00 0.00 0.00 2.57
262 290 5.079689 TGACTATGTTCCTGCGTTATCAA 57.920 39.130 0.00 0.00 0.00 2.57
263 291 4.729227 TGACTATGTTCCTGCGTTATCA 57.271 40.909 0.00 0.00 0.00 2.15
264 292 6.604735 ATTTGACTATGTTCCTGCGTTATC 57.395 37.500 0.00 0.00 0.00 1.75
265 293 8.677148 ATAATTTGACTATGTTCCTGCGTTAT 57.323 30.769 0.00 0.00 0.00 1.89
266 294 8.500753 AATAATTTGACTATGTTCCTGCGTTA 57.499 30.769 0.00 0.00 0.00 3.18
267 295 7.391148 AATAATTTGACTATGTTCCTGCGTT 57.609 32.000 0.00 0.00 0.00 4.84
268 296 8.677148 ATAATAATTTGACTATGTTCCTGCGT 57.323 30.769 0.00 0.00 0.00 5.24
269 297 9.385902 CAATAATAATTTGACTATGTTCCTGCG 57.614 33.333 0.00 0.00 0.00 5.18
391 420 5.386958 TCCTGCTAGTACAACTGTAACAG 57.613 43.478 0.00 0.00 37.52 3.16
392 421 5.995565 ATCCTGCTAGTACAACTGTAACA 57.004 39.130 0.00 0.00 31.52 2.41
393 422 7.652507 GGATAATCCTGCTAGTACAACTGTAAC 59.347 40.741 0.00 0.00 32.53 2.50
394 423 7.723324 GGATAATCCTGCTAGTACAACTGTAA 58.277 38.462 0.00 0.00 32.53 2.41
395 424 7.286215 GGATAATCCTGCTAGTACAACTGTA 57.714 40.000 0.00 0.00 32.53 2.74
396 425 6.163135 GGATAATCCTGCTAGTACAACTGT 57.837 41.667 0.00 0.00 32.53 3.55
411 440 7.768807 TCTTACTGAGCTTCTAGGATAATCC 57.231 40.000 0.00 0.00 36.58 3.01
414 443 9.290988 CACTATCTTACTGAGCTTCTAGGATAA 57.709 37.037 0.00 0.00 0.00 1.75
415 444 8.661345 TCACTATCTTACTGAGCTTCTAGGATA 58.339 37.037 0.00 0.00 0.00 2.59
416 445 7.522542 TCACTATCTTACTGAGCTTCTAGGAT 58.477 38.462 0.00 0.00 0.00 3.24
417 446 6.901300 TCACTATCTTACTGAGCTTCTAGGA 58.099 40.000 0.00 0.00 0.00 2.94
418 447 7.575414 TTCACTATCTTACTGAGCTTCTAGG 57.425 40.000 0.00 0.00 0.00 3.02
419 448 8.845227 TGATTCACTATCTTACTGAGCTTCTAG 58.155 37.037 0.00 0.00 34.17 2.43
420 449 8.753497 TGATTCACTATCTTACTGAGCTTCTA 57.247 34.615 0.00 0.00 34.17 2.10
421 450 7.652524 TGATTCACTATCTTACTGAGCTTCT 57.347 36.000 0.00 0.00 34.17 2.85
422 451 8.359642 AGATGATTCACTATCTTACTGAGCTTC 58.640 37.037 0.00 0.00 34.17 3.86
423 452 8.248904 AGATGATTCACTATCTTACTGAGCTT 57.751 34.615 0.00 0.00 34.17 3.74
424 453 7.838079 AGATGATTCACTATCTTACTGAGCT 57.162 36.000 0.00 0.00 34.17 4.09
425 454 8.763356 CAAAGATGATTCACTATCTTACTGAGC 58.237 37.037 0.00 0.00 41.45 4.26
426 455 9.814899 ACAAAGATGATTCACTATCTTACTGAG 57.185 33.333 0.00 0.00 41.45 3.35
464 541 9.102757 CAAGCTTAGCATAGAAAGTGAGAATTA 57.897 33.333 7.07 0.00 0.00 1.40
489 566 7.502226 ACACCTCAACTTGTATCTTCAAATTCA 59.498 33.333 0.00 0.00 0.00 2.57
548 625 7.698130 CACTTTTCTTCTGTTTGTAGAAACTGG 59.302 37.037 18.23 10.94 40.24 4.00
557 634 6.575162 AACACTCACTTTTCTTCTGTTTGT 57.425 33.333 0.00 0.00 0.00 2.83
606 683 3.231965 GCGCTTTATCATGCTTATGCTG 58.768 45.455 0.00 0.00 40.48 4.41
625 702 4.389576 GCCAAGTCGGTTGCTGCG 62.390 66.667 0.00 0.00 36.97 5.18
660 737 2.193536 GCAGGAAAGCACCGGTTGT 61.194 57.895 2.97 0.00 34.73 3.32
672 749 4.402155 AGTGATCACAAAAACAAGCAGGAA 59.598 37.500 27.02 0.00 0.00 3.36
697 774 1.055849 TCTGGAGGCAGTAACAGCAA 58.944 50.000 0.00 0.00 0.00 3.91
719 796 5.415701 CCTTACAGAAGGCTTTAGATTGCAA 59.584 40.000 0.00 0.00 45.91 4.08
770 847 1.478510 ACTGTTATCTCACCGCTCCAG 59.521 52.381 0.00 0.00 0.00 3.86
849 927 5.186409 AGGAAAGCATGAACACAATAGCAAT 59.814 36.000 0.00 0.00 0.00 3.56
856 934 3.819368 TCTGAGGAAAGCATGAACACAA 58.181 40.909 0.00 0.00 0.00 3.33
881 963 4.454728 TGGCAAACTTTTCAGCATATCC 57.545 40.909 0.00 0.00 0.00 2.59
983 1065 6.270927 CAGGTCCATCCTTCATTATTCCTCTA 59.729 42.308 0.00 0.00 45.67 2.43
985 1067 5.072329 TCAGGTCCATCCTTCATTATTCCTC 59.928 44.000 0.00 0.00 45.67 3.71
991 1073 3.736094 ACCTCAGGTCCATCCTTCATTA 58.264 45.455 0.00 0.00 45.67 1.90
1138 1233 6.530019 ACCTACAATGTTCATCCCATTTTC 57.470 37.500 0.00 0.00 30.28 2.29
1163 1258 3.507233 TGATTCAACCTTGCCAGATCAAC 59.493 43.478 0.00 0.00 0.00 3.18
1280 1378 5.952947 AGATAGACTTACAGTGTAGGTGCTT 59.047 40.000 21.49 10.03 26.94 3.91
1331 1435 6.033341 TCTACAACACACAGAAAATGCAAAC 58.967 36.000 0.00 0.00 0.00 2.93
1362 1467 8.534496 CCCATCTAAAGGAAGAAAACAAATGAT 58.466 33.333 0.00 0.00 0.00 2.45
1389 1495 2.893489 GCCAAGAGAATTGGGTCACTTT 59.107 45.455 8.62 0.00 39.90 2.66
1412 1521 4.278170 CCAATGGCTATTTTCATTCGCCTA 59.722 41.667 0.00 0.00 41.25 3.93
1415 1524 2.796593 GCCAATGGCTATTTTCATTCGC 59.203 45.455 18.47 0.00 46.69 4.70
1498 1607 9.516314 TCTGTAACATATACTGAATTGAGTTCG 57.484 33.333 1.98 0.00 39.80 3.95
1516 1626 5.586155 TGGGGGTAAAATCTTCTGTAACA 57.414 39.130 0.00 0.00 0.00 2.41
1548 1658 6.770785 AGTTCAGTTTGTACAGAAAAGCCATA 59.229 34.615 0.00 0.00 32.47 2.74
1614 1730 1.482182 TGTCGTCAGCCTGCTCATAAT 59.518 47.619 0.00 0.00 0.00 1.28
1655 1771 4.193334 CTCTCCCATCGCGTCGCA 62.193 66.667 18.75 4.89 0.00 5.10
1684 1800 1.369091 CTGCGTTCCTACACCCATGC 61.369 60.000 0.00 0.00 0.00 4.06
1750 1866 1.304134 AAGACGGGCAATGAACCCC 60.304 57.895 0.00 0.00 45.37 4.95
1793 1909 9.813826 AAAAGGATCTAATGAGAAAGAGGAAAA 57.186 29.630 0.00 0.00 34.61 2.29
1809 1925 8.347004 TGCAACATCACAATAAAAAGGATCTA 57.653 30.769 0.00 0.00 0.00 1.98
2018 2216 2.859538 GTGCTGTTTGAACAACATGTGG 59.140 45.455 0.00 0.00 37.34 4.17
2056 2254 1.188863 AAGGTGAAGGCATGGCAATC 58.811 50.000 22.64 18.49 0.00 2.67
2072 2270 3.734735 GCGTAGGAACTTATAGCGAAAGG 59.265 47.826 0.00 0.00 41.75 3.11
2092 2290 2.808543 AGTTACCTGAAAAAGAGCAGCG 59.191 45.455 0.00 0.00 0.00 5.18
2100 2298 6.137794 TCGCATGAAAAGTTACCTGAAAAA 57.862 33.333 0.00 0.00 0.00 1.94
2110 2308 7.440523 AGAAGTAGAAATCGCATGAAAAGTT 57.559 32.000 0.00 0.00 0.00 2.66
2140 2338 9.118300 CTGCTTTGATCTCAAGGTATTTTCTAT 57.882 33.333 4.29 0.00 37.15 1.98
2154 2352 5.928839 TCTATAAATCCGCTGCTTTGATCTC 59.071 40.000 0.00 0.00 0.00 2.75
2174 2372 8.219660 AGTAGCACCAATACCCATAAATCTAT 57.780 34.615 0.00 0.00 0.00 1.98
2182 2381 4.907875 AGATGTAGTAGCACCAATACCCAT 59.092 41.667 0.00 0.00 0.00 4.00
2200 2400 1.349026 CCATAAGCCGGATGGAGATGT 59.651 52.381 14.17 0.00 45.89 3.06
2231 2431 3.005050 ACAACGTCGTACCTCAGAATCAA 59.995 43.478 0.00 0.00 0.00 2.57
2273 2474 3.650281 TGGAGATGCCAAGCTAAATGA 57.350 42.857 0.00 0.00 45.87 2.57
2304 2505 2.156098 AGGGTCTTTGCTCAGCCCA 61.156 57.895 0.00 0.00 41.67 5.36
2309 2510 0.318441 CTCGACAGGGTCTTTGCTCA 59.682 55.000 0.00 0.00 0.00 4.26
2340 2541 9.578439 ACTGATTTGAAAAATTATGCTTCTAGC 57.422 29.630 0.00 0.00 42.82 3.42
2411 2618 1.816183 CGGACCAAAACTACCAGCCAA 60.816 52.381 0.00 0.00 0.00 4.52
2421 2628 3.867493 GCTACCTACATACGGACCAAAAC 59.133 47.826 0.00 0.00 0.00 2.43
2645 2858 0.251341 AGGGGCAGGTTTTACAGCAG 60.251 55.000 0.00 0.00 0.00 4.24
2653 2866 2.582636 ACAGATGAATAGGGGCAGGTTT 59.417 45.455 0.00 0.00 0.00 3.27
2741 2954 1.742761 CGGCTCCTGTCATCAAATGT 58.257 50.000 0.00 0.00 0.00 2.71
2751 2964 0.107831 TGTAAAGTTGCGGCTCCTGT 59.892 50.000 0.00 0.00 0.00 4.00
2762 2975 7.040409 GGTTTCACATCCATCTTCTGTAAAGTT 60.040 37.037 0.00 0.00 0.00 2.66
2763 2976 6.431234 GGTTTCACATCCATCTTCTGTAAAGT 59.569 38.462 0.00 0.00 0.00 2.66
2823 3037 8.355169 ACAGCCAATGTATTGCTAAATGATAAG 58.645 33.333 0.00 0.00 41.60 1.73
2841 3055 3.920817 TGGGGAGACACAGCCAAT 58.079 55.556 0.00 0.00 40.38 3.16
2919 3137 3.005684 GCACAGATTTTCCATGGTCAACA 59.994 43.478 12.58 0.00 0.00 3.33
2941 3159 7.984050 AGAAACATATGTAGGACATGAGAACTG 59.016 37.037 9.21 0.00 39.53 3.16
2953 3171 6.884295 TCCTTGAAACCAGAAACATATGTAGG 59.116 38.462 9.21 11.24 0.00 3.18
3026 3244 9.594478 TCTTTGATGTAAATACGCAAGAGATTA 57.406 29.630 0.00 0.00 43.62 1.75
3055 3273 8.677300 ACTGTACATGATAAGCATTCGAAAAAT 58.323 29.630 0.00 0.00 34.15 1.82
3082 3300 1.003573 AGGGGTCAGGGAGCTTAGG 59.996 63.158 0.00 0.00 0.00 2.69
3087 3305 1.501654 AAAAGGAGGGGTCAGGGAGC 61.502 60.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.