Multiple sequence alignment - TraesCS4B01G075200

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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 TraesCS4B01G075200 chr4B 100.000 2965 0 0 1 2965 71247203 71244239 0.000000e+00 5476.0
1 TraesCS4B01G075200 chr4B 88.022 718 59 13 1178 1892 71223680 71222987 0.000000e+00 824.0
2 TraesCS4B01G075200 chr4B 87.416 596 37 13 1177 1757 71233126 71232554 0.000000e+00 651.0
3 TraesCS4B01G075200 chr4B 87.805 410 36 7 771 1178 71233736 71233339 4.470000e-128 468.0
4 TraesCS4B01G075200 chr4B 95.376 173 5 1 1932 2101 71222984 71222812 3.770000e-69 272.0
5 TraesCS4B01G075200 chr4B 94.253 174 10 0 1932 2105 71226255 71226082 1.750000e-67 267.0
6 TraesCS4B01G075200 chr4B 90.972 144 13 0 1752 1895 71226399 71226256 8.390000e-46 195.0
7 TraesCS4B01G075200 chr7A 99.281 834 6 0 2132 2965 247267667 247266834 0.000000e+00 1507.0
8 TraesCS4B01G075200 chr3B 98.818 846 7 2 2123 2965 273234127 273234972 0.000000e+00 1504.0
9 TraesCS4B01G075200 chr6A 99.042 835 7 1 2132 2965 60392257 60391423 0.000000e+00 1496.0
10 TraesCS4B01G075200 chr6A 98.580 845 10 1 2123 2965 556560498 556559654 0.000000e+00 1493.0
11 TraesCS4B01G075200 chr6A 98.339 843 13 1 2123 2965 564977027 564977868 0.000000e+00 1478.0
12 TraesCS4B01G075200 chr6A 90.643 855 62 8 2128 2965 490314625 490315478 0.000000e+00 1120.0
13 TraesCS4B01G075200 chr7B 98.467 848 10 2 2120 2965 579513061 579512215 0.000000e+00 1491.0
14 TraesCS4B01G075200 chr6B 98.563 835 11 1 2132 2965 707616998 707616164 0.000000e+00 1474.0
15 TraesCS4B01G075200 chr4D 93.505 893 51 5 1177 2067 48537164 48536277 0.000000e+00 1321.0
16 TraesCS4B01G075200 chr4D 91.906 939 59 11 1177 2113 48535658 48534735 0.000000e+00 1297.0
17 TraesCS4B01G075200 chr4D 91.504 718 46 9 1177 1893 48533619 48532916 0.000000e+00 974.0
18 TraesCS4B01G075200 chr4D 90.538 539 33 6 645 1178 48537902 48537377 0.000000e+00 697.0
19 TraesCS4B01G075200 chr4D 89.593 442 37 5 738 1178 48534265 48533832 1.200000e-153 553.0
20 TraesCS4B01G075200 chr4D 92.803 264 10 2 1 256 48538526 48538264 1.000000e-99 374.0
21 TraesCS4B01G075200 chr4D 86.667 345 19 11 305 648 48538259 48537941 1.010000e-94 357.0
22 TraesCS4B01G075200 chr4D 87.027 185 20 3 754 938 48535976 48535796 3.870000e-49 206.0
23 TraesCS4B01G075200 chr4A 92.865 897 50 8 1177 2067 548821107 548821995 0.000000e+00 1290.0
24 TraesCS4B01G075200 chr4A 90.461 933 62 13 1177 2105 548822902 548823811 0.000000e+00 1205.0
25 TraesCS4B01G075200 chr4A 92.608 487 25 6 645 1131 548820375 548820850 0.000000e+00 689.0
26 TraesCS4B01G075200 chr4A 93.410 349 17 3 305 648 548819989 548820336 2.040000e-141 512.0
27 TraesCS4B01G075200 chr4A 87.330 442 45 7 738 1178 548822258 548822689 2.050000e-136 496.0
28 TraesCS4B01G075200 chr4A 90.441 272 8 6 1 256 548819715 548819984 2.830000e-90 342.0
29 TraesCS4B01G075200 chr5B 92.317 846 50 12 2125 2965 531353401 531352566 0.000000e+00 1188.0
30 TraesCS4B01G075200 chr2B 76.722 842 165 27 2132 2965 550658195 550657377 9.760000e-120 440.0
31 TraesCS4B01G075200 chr2B 98.148 162 1 2 2123 2283 629816674 629816834 6.260000e-72 281.0
32 TraesCS4B01G075200 chrUn 94.853 136 5 2 2117 2252 31696442 31696309 8.330000e-51 211.0
33 TraesCS4B01G075200 chr1B 91.111 45 4 0 649 693 95662234 95662278 8.870000e-06 62.1


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 TraesCS4B01G075200 chr4B 71244239 71247203 2964 True 5476.000000 5476 100.000000 1 2965 1 chr4B.!!$R1 2964
1 TraesCS4B01G075200 chr4B 71232554 71233736 1182 True 559.500000 651 87.610500 771 1757 2 chr4B.!!$R3 986
2 TraesCS4B01G075200 chr4B 71222812 71226399 3587 True 389.500000 824 92.155750 1178 2105 4 chr4B.!!$R2 927
3 TraesCS4B01G075200 chr7A 247266834 247267667 833 True 1507.000000 1507 99.281000 2132 2965 1 chr7A.!!$R1 833
4 TraesCS4B01G075200 chr3B 273234127 273234972 845 False 1504.000000 1504 98.818000 2123 2965 1 chr3B.!!$F1 842
5 TraesCS4B01G075200 chr6A 60391423 60392257 834 True 1496.000000 1496 99.042000 2132 2965 1 chr6A.!!$R1 833
6 TraesCS4B01G075200 chr6A 556559654 556560498 844 True 1493.000000 1493 98.580000 2123 2965 1 chr6A.!!$R2 842
7 TraesCS4B01G075200 chr6A 564977027 564977868 841 False 1478.000000 1478 98.339000 2123 2965 1 chr6A.!!$F2 842
8 TraesCS4B01G075200 chr6A 490314625 490315478 853 False 1120.000000 1120 90.643000 2128 2965 1 chr6A.!!$F1 837
9 TraesCS4B01G075200 chr7B 579512215 579513061 846 True 1491.000000 1491 98.467000 2120 2965 1 chr7B.!!$R1 845
10 TraesCS4B01G075200 chr6B 707616164 707616998 834 True 1474.000000 1474 98.563000 2132 2965 1 chr6B.!!$R1 833
11 TraesCS4B01G075200 chr4D 48532916 48538526 5610 True 722.375000 1321 90.442875 1 2113 8 chr4D.!!$R1 2112
12 TraesCS4B01G075200 chr4A 548819715 548823811 4096 False 755.666667 1290 91.185833 1 2105 6 chr4A.!!$F1 2104
13 TraesCS4B01G075200 chr5B 531352566 531353401 835 True 1188.000000 1188 92.317000 2125 2965 1 chr5B.!!$R1 840
14 TraesCS4B01G075200 chr2B 550657377 550658195 818 True 440.000000 440 76.722000 2132 2965 1 chr2B.!!$R1 833

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
226 243 0.539518 GAGGAGAGCTTCTTGGGGAC 59.460 60.0 0.0 0.0 0.0 4.46 F
1597 1892 0.531532 CAGATAGCTGGGCTGAACCG 60.532 60.0 0.0 0.0 40.1 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 2011 0.036022 GCCAGAGTGAGCTCAAGGTT 59.964 55.000 20.19 4.38 44.00 3.50 R
2616 7599 2.086094 CGGTTACCGCTTTATTTGGGT 58.914 47.619 11.93 0.00 41.17 4.51 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
34 35 0.861837 GATTCGTTCGGCATGCCTAG 59.138 55.000 33.07 19.53 0.00 3.02
121 122 1.760086 CATCACCTCCCTCTCGCCT 60.760 63.158 0.00 0.00 0.00 5.52
125 126 4.168291 CCTCCCTCTCGCCTTGGC 62.168 72.222 0.75 0.75 0.00 4.52
202 219 1.000274 CTGGCCTGGTAAACAAACTGC 60.000 52.381 3.32 0.00 0.00 4.40
226 243 0.539518 GAGGAGAGCTTCTTGGGGAC 59.460 60.000 0.00 0.00 0.00 4.46
256 273 2.026169 GGAGTACCTTTCTTTGGGAGGG 60.026 54.545 0.00 0.00 34.81 4.30
258 275 1.990327 GTACCTTTCTTTGGGAGGGGA 59.010 52.381 0.00 0.00 34.81 4.81
259 276 1.541275 ACCTTTCTTTGGGAGGGGAA 58.459 50.000 0.00 0.00 34.81 3.97
261 278 2.454772 ACCTTTCTTTGGGAGGGGAATT 59.545 45.455 0.00 0.00 34.81 2.17
262 279 3.116356 ACCTTTCTTTGGGAGGGGAATTT 60.116 43.478 0.00 0.00 34.81 1.82
263 280 3.909995 CCTTTCTTTGGGAGGGGAATTTT 59.090 43.478 0.00 0.00 0.00 1.82
264 281 4.350816 CCTTTCTTTGGGAGGGGAATTTTT 59.649 41.667 0.00 0.00 0.00 1.94
265 282 5.513094 CCTTTCTTTGGGAGGGGAATTTTTC 60.513 44.000 0.00 0.00 0.00 2.29
278 295 5.673337 GGAATTTTTCCTTGCCTTGTTTC 57.327 39.130 0.00 0.00 46.57 2.78
279 296 5.368145 GGAATTTTTCCTTGCCTTGTTTCT 58.632 37.500 0.00 0.00 46.57 2.52
280 297 5.822519 GGAATTTTTCCTTGCCTTGTTTCTT 59.177 36.000 0.00 0.00 46.57 2.52
281 298 6.017934 GGAATTTTTCCTTGCCTTGTTTCTTC 60.018 38.462 0.00 0.00 46.57 2.87
282 299 5.675684 TTTTTCCTTGCCTTGTTTCTTCT 57.324 34.783 0.00 0.00 0.00 2.85
283 300 5.675684 TTTTCCTTGCCTTGTTTCTTCTT 57.324 34.783 0.00 0.00 0.00 2.52
284 301 4.918810 TTCCTTGCCTTGTTTCTTCTTC 57.081 40.909 0.00 0.00 0.00 2.87
285 302 4.170468 TCCTTGCCTTGTTTCTTCTTCT 57.830 40.909 0.00 0.00 0.00 2.85
286 303 4.536765 TCCTTGCCTTGTTTCTTCTTCTT 58.463 39.130 0.00 0.00 0.00 2.52
287 304 4.580580 TCCTTGCCTTGTTTCTTCTTCTTC 59.419 41.667 0.00 0.00 0.00 2.87
288 305 4.582240 CCTTGCCTTGTTTCTTCTTCTTCT 59.418 41.667 0.00 0.00 0.00 2.85
289 306 5.068329 CCTTGCCTTGTTTCTTCTTCTTCTT 59.932 40.000 0.00 0.00 0.00 2.52
290 307 5.757850 TGCCTTGTTTCTTCTTCTTCTTC 57.242 39.130 0.00 0.00 0.00 2.87
291 308 5.440610 TGCCTTGTTTCTTCTTCTTCTTCT 58.559 37.500 0.00 0.00 0.00 2.85
292 309 5.888161 TGCCTTGTTTCTTCTTCTTCTTCTT 59.112 36.000 0.00 0.00 0.00 2.52
293 310 6.038714 TGCCTTGTTTCTTCTTCTTCTTCTTC 59.961 38.462 0.00 0.00 0.00 2.87
294 311 6.262049 GCCTTGTTTCTTCTTCTTCTTCTTCT 59.738 38.462 0.00 0.00 0.00 2.85
295 312 7.638134 CCTTGTTTCTTCTTCTTCTTCTTCTG 58.362 38.462 0.00 0.00 0.00 3.02
296 313 7.497249 CCTTGTTTCTTCTTCTTCTTCTTCTGA 59.503 37.037 0.00 0.00 0.00 3.27
297 314 8.970859 TTGTTTCTTCTTCTTCTTCTTCTGAT 57.029 30.769 0.00 0.00 0.00 2.90
298 315 8.600449 TGTTTCTTCTTCTTCTTCTTCTGATC 57.400 34.615 0.00 0.00 0.00 2.92
299 316 7.659390 TGTTTCTTCTTCTTCTTCTTCTGATCC 59.341 37.037 0.00 0.00 0.00 3.36
300 317 5.960113 TCTTCTTCTTCTTCTTCTGATCCG 58.040 41.667 0.00 0.00 0.00 4.18
301 318 5.712446 TCTTCTTCTTCTTCTTCTGATCCGA 59.288 40.000 0.00 0.00 0.00 4.55
302 319 5.574891 TCTTCTTCTTCTTCTGATCCGAG 57.425 43.478 0.00 0.00 0.00 4.63
303 320 4.400884 TCTTCTTCTTCTTCTGATCCGAGG 59.599 45.833 0.00 0.00 0.00 4.63
304 321 3.702792 TCTTCTTCTTCTGATCCGAGGT 58.297 45.455 0.00 0.00 0.00 3.85
305 322 3.445450 TCTTCTTCTTCTGATCCGAGGTG 59.555 47.826 0.00 0.00 0.00 4.00
306 323 2.103373 TCTTCTTCTGATCCGAGGTGG 58.897 52.381 0.00 0.00 40.09 4.61
331 348 1.110442 CAAAACAGAGGTGGGCACAA 58.890 50.000 0.00 0.00 0.00 3.33
339 356 1.073284 GAGGTGGGCACAACCTTCTTA 59.927 52.381 0.00 0.00 39.10 2.10
347 364 3.879892 GGCACAACCTTCTTATGATCTCC 59.120 47.826 0.00 0.00 34.51 3.71
378 395 6.432472 GTCTTGTTTCTTCTTCTTCCATGGAT 59.568 38.462 17.06 0.00 0.00 3.41
383 400 4.458397 TCTTCTTCTTCCATGGATCATGC 58.542 43.478 17.06 0.00 40.20 4.06
400 418 4.147449 CGTGGCATGCCTCCGAGA 62.147 66.667 35.53 13.42 36.94 4.04
457 475 2.935201 CTCTAGCCTTGTGATGTTCTGC 59.065 50.000 0.00 0.00 0.00 4.26
493 511 2.758770 TTTCGGAAGGTCGAGTGGCG 62.759 60.000 0.00 0.00 40.42 5.69
522 540 3.157087 GTCTGAAAGGGAATTTGCCAGA 58.843 45.455 9.80 0.40 32.29 3.86
545 563 1.133407 CTTCTTTCTCCGTCTCCCTCG 59.867 57.143 0.00 0.00 0.00 4.63
594 616 6.073440 TGTCATAGAAAGAACAGTTTTACGGC 60.073 38.462 0.00 0.00 0.00 5.68
620 642 2.076100 CCAGAAGCGTAACAGAATGCA 58.924 47.619 0.00 0.00 42.53 3.96
656 720 8.533153 GTTAGAGAAATACAGTACGAAATCAGC 58.467 37.037 0.00 0.00 0.00 4.26
660 724 1.614385 ACAGTACGAAATCAGCGACG 58.386 50.000 0.00 0.00 0.00 5.12
670 734 5.918576 ACGAAATCAGCGACGATTAATATGA 59.081 36.000 0.00 0.00 34.49 2.15
717 781 4.955450 TCGGTTGTATTAGGGTGTAAGCTA 59.045 41.667 0.00 0.00 0.00 3.32
718 782 5.599656 TCGGTTGTATTAGGGTGTAAGCTAT 59.400 40.000 0.00 0.00 0.00 2.97
719 783 6.777091 TCGGTTGTATTAGGGTGTAAGCTATA 59.223 38.462 0.00 0.00 0.00 1.31
720 784 7.287466 TCGGTTGTATTAGGGTGTAAGCTATAA 59.713 37.037 0.00 0.00 0.00 0.98
721 785 7.383300 CGGTTGTATTAGGGTGTAAGCTATAAC 59.617 40.741 0.00 0.00 0.00 1.89
722 786 8.427276 GGTTGTATTAGGGTGTAAGCTATAACT 58.573 37.037 0.00 0.00 0.00 2.24
751 815 8.614469 AAGTTCAACCTGAAAAACAAATGAAA 57.386 26.923 0.00 0.00 38.22 2.69
752 816 8.791327 AGTTCAACCTGAAAAACAAATGAAAT 57.209 26.923 0.00 0.00 38.22 2.17
887 955 9.605955 CAACAAATATTTCGACACTGAACATAA 57.394 29.630 0.00 0.00 0.00 1.90
1099 1167 6.376299 TCGTGTGAACACTATTCTACCTATGT 59.624 38.462 11.55 0.00 44.34 2.29
1108 1176 7.287927 ACACTATTCTACCTATGTGTATGTGCT 59.712 37.037 0.00 0.00 36.96 4.40
1122 1190 5.932303 GTGTATGTGCTTCTTCCAGTAGAAA 59.068 40.000 0.00 0.00 33.96 2.52
1125 1193 8.318412 TGTATGTGCTTCTTCCAGTAGAAAATA 58.682 33.333 0.00 0.00 33.96 1.40
1152 1226 1.410004 CTTCCAGTATACAGCCGGGA 58.590 55.000 2.18 1.32 0.00 5.14
1180 1469 2.097466 CAGCGTCACAAACTTTTCCTGT 59.903 45.455 0.00 0.00 0.00 4.00
1220 1510 6.838090 TGATGCCACTCATTCCCAAAATATAA 59.162 34.615 0.00 0.00 35.05 0.98
1255 1545 3.389983 TCTGTAGCCTGTAGTTTGGTGTT 59.610 43.478 0.00 0.00 0.00 3.32
1287 1577 3.678529 GCAAACAAGGGAAACTCTTTGCA 60.679 43.478 13.34 0.00 44.44 4.08
1289 1579 1.676006 ACAAGGGAAACTCTTTGCACG 59.324 47.619 0.00 0.00 32.01 5.34
1294 1584 1.543871 GGAAACTCTTTGCACGGGGTA 60.544 52.381 0.00 0.00 0.00 3.69
1317 1607 7.707035 GGTATGAGTGTGACTTCCTAAGTAATG 59.293 40.741 0.00 0.00 43.03 1.90
1318 1608 6.037786 TGAGTGTGACTTCCTAAGTAATGG 57.962 41.667 0.00 0.00 43.03 3.16
1324 1614 7.123247 GTGTGACTTCCTAAGTAATGGTAGGTA 59.877 40.741 0.00 0.00 43.03 3.08
1325 1615 7.341256 TGTGACTTCCTAAGTAATGGTAGGTAG 59.659 40.741 0.00 0.00 43.03 3.18
1326 1616 6.837568 TGACTTCCTAAGTAATGGTAGGTAGG 59.162 42.308 7.87 0.00 43.03 3.18
1327 1617 6.141790 ACTTCCTAAGTAATGGTAGGTAGGG 58.858 44.000 7.87 0.00 40.69 3.53
1328 1618 5.756314 TCCTAAGTAATGGTAGGTAGGGT 57.244 43.478 0.00 0.00 30.97 4.34
1333 1623 2.801077 AATGGTAGGTAGGGTTGCAC 57.199 50.000 0.00 0.00 0.00 4.57
1335 1625 1.219935 GGTAGGTAGGGTTGCACCG 59.780 63.158 0.00 0.00 39.83 4.94
1339 1629 3.053896 GTAGGGTTGCACCGTGCC 61.054 66.667 20.67 6.15 44.23 5.01
1365 1655 8.805175 CCTCTCTGCATCCTATTATATATCCAG 58.195 40.741 0.00 0.00 0.00 3.86
1390 1680 6.819397 TGATGGAGGTACGAATAGTCATAG 57.181 41.667 0.00 0.00 0.00 2.23
1393 1683 4.825634 TGGAGGTACGAATAGTCATAGGTG 59.174 45.833 0.00 0.00 0.00 4.00
1397 1687 5.998981 AGGTACGAATAGTCATAGGTGAGAG 59.001 44.000 0.00 0.00 34.36 3.20
1409 1699 7.942341 AGTCATAGGTGAGAGGAAATAGAGTAG 59.058 40.741 0.00 0.00 34.36 2.57
1425 1715 5.652994 AGAGTAGAAGCAAGTAGTTGAGG 57.347 43.478 14.64 0.00 35.46 3.86
1431 1721 4.938226 AGAAGCAAGTAGTTGAGGCATTAC 59.062 41.667 14.64 0.00 35.46 1.89
1432 1722 4.286297 AGCAAGTAGTTGAGGCATTACA 57.714 40.909 14.64 0.00 35.46 2.41
1445 1738 6.889198 TGAGGCATTACAGCTAGTTTCTAAT 58.111 36.000 0.00 0.00 34.17 1.73
1477 1772 2.606308 GCATCAGTTGTGCACTTCAAGG 60.606 50.000 19.41 2.96 42.08 3.61
1482 1777 2.172717 AGTTGTGCACTTCAAGGTAGGT 59.827 45.455 19.41 0.00 27.32 3.08
1495 1790 4.821805 TCAAGGTAGGTGAAAAAGCTTCTG 59.178 41.667 0.00 0.00 37.85 3.02
1499 1794 3.297134 AGGTGAAAAAGCTTCTGACCA 57.703 42.857 16.15 2.48 30.45 4.02
1502 1797 4.279420 AGGTGAAAAAGCTTCTGACCAATC 59.721 41.667 16.15 1.94 30.45 2.67
1581 1876 2.169978 CAACTGATGAGGGAGATGCAGA 59.830 50.000 0.00 0.00 0.00 4.26
1597 1892 0.531532 CAGATAGCTGGGCTGAACCG 60.532 60.000 0.00 0.00 40.10 4.44
1604 1899 4.115199 GGGCTGAACCGGGCTCAT 62.115 66.667 6.32 0.00 40.62 2.90
1625 1920 5.348724 TCATGCTGAGACGAAACATAAACTC 59.651 40.000 0.00 0.00 0.00 3.01
1690 1985 1.906990 AGCTTCTCAAACAGCTGCAT 58.093 45.000 15.27 0.00 44.98 3.96
1863 2158 2.297701 TCAAGGAGTTTGACACAAGGC 58.702 47.619 0.00 0.00 40.82 4.35
1918 2213 2.204237 CATTGCCGATGAGACGAATCA 58.796 47.619 0.00 0.00 38.03 2.57
2023 3853 6.928492 AGAGAAAGAAGAAGAGATGTTGTCAC 59.072 38.462 0.00 0.00 0.00 3.67
2024 3854 6.825610 AGAAAGAAGAAGAGATGTTGTCACT 58.174 36.000 0.00 0.00 0.00 3.41
2039 3869 5.237127 TGTTGTCACTTCACAGAGCTAATTG 59.763 40.000 0.00 0.00 0.00 2.32
2080 3910 1.271379 ACAAGAGATGACCGCGTAACA 59.729 47.619 4.92 2.11 0.00 2.41
2094 3924 2.599082 GCGTAACAGTCTCCATCTTTCG 59.401 50.000 0.00 0.00 0.00 3.46
2108 3938 5.013079 TCCATCTTTCGGAGGCATATGTAAT 59.987 40.000 4.29 0.00 0.00 1.89
2113 3943 7.907389 TCTTTCGGAGGCATATGTAATATCTT 58.093 34.615 4.29 0.00 37.44 2.40
2114 3944 8.375506 TCTTTCGGAGGCATATGTAATATCTTT 58.624 33.333 4.29 0.00 37.44 2.52
2207 7149 4.646492 CCCTCTTATTAACCAAAGCAGCAT 59.354 41.667 0.00 0.00 0.00 3.79
2616 7599 5.595542 CAGAATCAATCCCATTAAGCCAAGA 59.404 40.000 0.00 0.00 0.00 3.02
2782 7765 6.038271 GTCCTGTCCAATTACGCTTTATCAAT 59.962 38.462 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 3.213206 AGATATGATTTGAGGCGCCAA 57.787 42.857 31.54 15.47 0.00 4.52
125 126 8.855110 AGGTAGATATAGATATGATTTGAGGCG 58.145 37.037 0.00 0.00 0.00 5.52
202 219 2.093553 CCCAAGAAGCTCTCCTCTCTTG 60.094 54.545 14.14 14.14 35.64 3.02
226 243 1.208293 GAAAGGTACTCCCTCTGCCTG 59.792 57.143 0.00 0.00 45.47 4.85
243 260 4.349636 GGAAAAATTCCCCTCCCAAAGAAA 59.650 41.667 0.00 0.00 44.30 2.52
258 275 6.653020 AGAAGAAACAAGGCAAGGAAAAATT 58.347 32.000 0.00 0.00 0.00 1.82
259 276 6.239217 AGAAGAAACAAGGCAAGGAAAAAT 57.761 33.333 0.00 0.00 0.00 1.82
261 278 5.422012 AGAAGAAGAAACAAGGCAAGGAAAA 59.578 36.000 0.00 0.00 0.00 2.29
262 279 4.956075 AGAAGAAGAAACAAGGCAAGGAAA 59.044 37.500 0.00 0.00 0.00 3.13
263 280 4.536765 AGAAGAAGAAACAAGGCAAGGAA 58.463 39.130 0.00 0.00 0.00 3.36
264 281 4.170468 AGAAGAAGAAACAAGGCAAGGA 57.830 40.909 0.00 0.00 0.00 3.36
265 282 4.582240 AGAAGAAGAAGAAACAAGGCAAGG 59.418 41.667 0.00 0.00 0.00 3.61
266 283 5.764487 AGAAGAAGAAGAAACAAGGCAAG 57.236 39.130 0.00 0.00 0.00 4.01
267 284 5.888161 AGAAGAAGAAGAAGAAACAAGGCAA 59.112 36.000 0.00 0.00 0.00 4.52
268 285 5.440610 AGAAGAAGAAGAAGAAACAAGGCA 58.559 37.500 0.00 0.00 0.00 4.75
269 286 6.262049 AGAAGAAGAAGAAGAAGAAACAAGGC 59.738 38.462 0.00 0.00 0.00 4.35
270 287 7.497249 TCAGAAGAAGAAGAAGAAGAAACAAGG 59.503 37.037 0.00 0.00 0.00 3.61
271 288 8.430801 TCAGAAGAAGAAGAAGAAGAAACAAG 57.569 34.615 0.00 0.00 0.00 3.16
272 289 8.970859 ATCAGAAGAAGAAGAAGAAGAAACAA 57.029 30.769 0.00 0.00 0.00 2.83
273 290 7.659390 GGATCAGAAGAAGAAGAAGAAGAAACA 59.341 37.037 0.00 0.00 0.00 2.83
274 291 7.148656 CGGATCAGAAGAAGAAGAAGAAGAAAC 60.149 40.741 0.00 0.00 0.00 2.78
275 292 6.870965 CGGATCAGAAGAAGAAGAAGAAGAAA 59.129 38.462 0.00 0.00 0.00 2.52
276 293 6.209589 TCGGATCAGAAGAAGAAGAAGAAGAA 59.790 38.462 0.00 0.00 0.00 2.52
277 294 5.712446 TCGGATCAGAAGAAGAAGAAGAAGA 59.288 40.000 0.00 0.00 0.00 2.87
278 295 5.960113 TCGGATCAGAAGAAGAAGAAGAAG 58.040 41.667 0.00 0.00 0.00 2.85
279 296 5.105554 CCTCGGATCAGAAGAAGAAGAAGAA 60.106 44.000 0.00 0.00 0.00 2.52
280 297 4.400884 CCTCGGATCAGAAGAAGAAGAAGA 59.599 45.833 0.00 0.00 0.00 2.87
281 298 4.159506 ACCTCGGATCAGAAGAAGAAGAAG 59.840 45.833 0.00 0.00 0.00 2.85
282 299 4.081972 CACCTCGGATCAGAAGAAGAAGAA 60.082 45.833 0.00 0.00 0.00 2.52
283 300 3.445450 CACCTCGGATCAGAAGAAGAAGA 59.555 47.826 0.00 0.00 0.00 2.87
284 301 3.430098 CCACCTCGGATCAGAAGAAGAAG 60.430 52.174 0.00 0.00 36.56 2.85
285 302 2.497675 CCACCTCGGATCAGAAGAAGAA 59.502 50.000 0.00 0.00 36.56 2.52
286 303 2.103373 CCACCTCGGATCAGAAGAAGA 58.897 52.381 0.00 0.00 36.56 2.87
287 304 2.103373 TCCACCTCGGATCAGAAGAAG 58.897 52.381 0.00 0.00 39.64 2.85
288 305 2.231716 TCCACCTCGGATCAGAAGAA 57.768 50.000 0.00 0.00 39.64 2.52
289 306 2.231716 TTCCACCTCGGATCAGAAGA 57.768 50.000 0.00 0.00 45.80 2.87
290 307 3.003480 GTTTTCCACCTCGGATCAGAAG 58.997 50.000 0.00 0.00 45.80 2.85
291 308 2.290071 GGTTTTCCACCTCGGATCAGAA 60.290 50.000 0.00 0.00 45.80 3.02
292 309 1.278127 GGTTTTCCACCTCGGATCAGA 59.722 52.381 0.00 0.00 45.80 3.27
293 310 1.739067 GGTTTTCCACCTCGGATCAG 58.261 55.000 0.00 0.00 45.80 2.90
294 311 3.948735 GGTTTTCCACCTCGGATCA 57.051 52.632 0.00 0.00 45.80 2.92
305 322 2.102420 CCCACCTCTGTTTTGGTTTTCC 59.898 50.000 0.00 0.00 41.14 3.13
306 323 2.483013 GCCCACCTCTGTTTTGGTTTTC 60.483 50.000 0.00 0.00 33.75 2.29
307 324 1.484653 GCCCACCTCTGTTTTGGTTTT 59.515 47.619 0.00 0.00 33.75 2.43
331 348 5.284582 ACAAGGAGGAGATCATAAGAAGGT 58.715 41.667 0.00 0.00 0.00 3.50
339 356 5.250313 AGAAACAAGACAAGGAGGAGATCAT 59.750 40.000 0.00 0.00 0.00 2.45
347 364 6.017523 GGAAGAAGAAGAAACAAGACAAGGAG 60.018 42.308 0.00 0.00 0.00 3.69
383 400 3.451556 ATCTCGGAGGCATGCCACG 62.452 63.158 37.18 35.61 39.13 4.94
396 414 2.487762 GGATCTGCCTACTCTGATCTCG 59.512 54.545 0.00 0.00 39.71 4.04
484 502 4.476410 CTAGCGCACGCCACTCGA 62.476 66.667 11.47 0.00 43.17 4.04
493 511 0.246635 TCCCTTTCAGACTAGCGCAC 59.753 55.000 11.47 0.00 0.00 5.34
522 540 1.208293 GGGAGACGGAGAAAGAAGCAT 59.792 52.381 0.00 0.00 0.00 3.79
648 670 8.798640 GATTCATATTAATCGTCGCTGATTTC 57.201 34.615 7.17 0.00 39.27 2.17
660 724 8.068892 AGTACTCCCTCCGATTCATATTAATC 57.931 38.462 0.00 0.25 33.37 1.75
670 734 5.455872 TCAAATCTAGTACTCCCTCCGATT 58.544 41.667 0.00 0.00 0.00 3.34
723 787 9.883142 TCATTTGTTTTTCAGGTTGAACTTATT 57.117 25.926 0.00 0.00 35.89 1.40
734 798 9.288124 GAAACCAAATTTCATTTGTTTTTCAGG 57.712 29.630 18.11 0.00 42.42 3.86
887 955 9.812347 TCTGACATAAATGGCAATAATAGGATT 57.188 29.630 0.00 0.00 46.90 3.01
1035 1103 6.266168 TGTTGTCTGAATGTTTGTTCTTGT 57.734 33.333 0.00 0.00 0.00 3.16
1080 1148 9.464714 CACATACACATAGGTAGAATAGTGTTC 57.535 37.037 0.00 0.00 40.33 3.18
1099 1167 5.738619 TTCTACTGGAAGAAGCACATACA 57.261 39.130 0.00 0.00 37.43 2.29
1108 1176 6.395629 CGTGTCCTATTTTCTACTGGAAGAA 58.604 40.000 0.00 0.00 37.43 2.52
1122 1190 4.647853 TGTATACTGGAAGCGTGTCCTATT 59.352 41.667 4.17 0.00 38.62 1.73
1125 1193 2.427453 CTGTATACTGGAAGCGTGTCCT 59.573 50.000 4.17 0.00 38.62 3.85
1152 1226 1.823470 TTTGTGACGCTGCCTGCTT 60.823 52.632 0.00 0.00 40.11 3.91
1161 1235 2.844122 ACAGGAAAAGTTTGTGACGC 57.156 45.000 0.00 0.00 0.00 5.19
1180 1469 4.467795 GTGGCATCAGGATATAGCCTCTTA 59.532 45.833 6.56 0.00 45.42 2.10
1220 1510 2.237392 GGCTACAGAGTCTGGTTTGGAT 59.763 50.000 23.79 3.85 35.51 3.41
1255 1545 1.600023 CCTTGTTTGCACGGTAGGAA 58.400 50.000 0.00 0.00 30.22 3.36
1287 1577 1.549170 GAAGTCACACTCATACCCCGT 59.451 52.381 0.00 0.00 0.00 5.28
1289 1579 2.188817 AGGAAGTCACACTCATACCCC 58.811 52.381 0.00 0.00 0.00 4.95
1294 1584 6.213600 ACCATTACTTAGGAAGTCACACTCAT 59.786 38.462 0.00 0.00 41.77 2.90
1333 1623 2.202987 GATGCAGAGAGGGCACGG 60.203 66.667 0.00 0.00 45.23 4.94
1335 1625 1.055040 ATAGGATGCAGAGAGGGCAC 58.945 55.000 0.00 0.00 45.23 5.01
1339 1629 8.718158 TGGATATATAATAGGATGCAGAGAGG 57.282 38.462 0.00 0.00 0.00 3.69
1365 1655 5.258456 TGACTATTCGTACCTCCATCAAC 57.742 43.478 0.00 0.00 0.00 3.18
1390 1680 5.361285 TGCTTCTACTCTATTTCCTCTCACC 59.639 44.000 0.00 0.00 0.00 4.02
1393 1683 7.107639 ACTTGCTTCTACTCTATTTCCTCTC 57.892 40.000 0.00 0.00 0.00 3.20
1397 1687 8.251721 TCAACTACTTGCTTCTACTCTATTTCC 58.748 37.037 0.00 0.00 0.00 3.13
1409 1699 4.695455 TGTAATGCCTCAACTACTTGCTTC 59.305 41.667 0.00 0.00 0.00 3.86
1425 1715 8.142994 TGCTTATTAGAAACTAGCTGTAATGC 57.857 34.615 0.00 0.00 33.15 3.56
1431 1721 8.346476 CAGTACTGCTTATTAGAAACTAGCTG 57.654 38.462 10.54 0.00 37.00 4.24
1460 1753 2.549754 CCTACCTTGAAGTGCACAACTG 59.450 50.000 21.04 4.63 39.81 3.16
1461 1754 2.172717 ACCTACCTTGAAGTGCACAACT 59.827 45.455 21.04 2.23 42.60 3.16
1463 1756 2.171659 TCACCTACCTTGAAGTGCACAA 59.828 45.455 21.04 3.62 0.00 3.33
1477 1772 4.134563 TGGTCAGAAGCTTTTTCACCTAC 58.865 43.478 13.43 0.81 0.00 3.18
1482 1777 4.261741 GCAGATTGGTCAGAAGCTTTTTCA 60.262 41.667 0.00 0.00 0.00 2.69
1495 1790 2.872370 GCAAAGATGTGCAGATTGGTC 58.128 47.619 0.00 0.00 44.29 4.02
1581 1876 2.746375 CCCGGTTCAGCCCAGCTAT 61.746 63.158 0.00 0.00 36.40 2.97
1604 1899 3.673338 CGAGTTTATGTTTCGTCTCAGCA 59.327 43.478 0.00 0.00 0.00 4.41
1716 2011 0.036022 GCCAGAGTGAGCTCAAGGTT 59.964 55.000 20.19 4.38 44.00 3.50
1721 2016 1.372683 GGTTGCCAGAGTGAGCTCA 59.627 57.895 13.74 13.74 44.00 4.26
1863 2158 2.235650 TCTCAATCTGAAGCCTCACCAG 59.764 50.000 0.00 0.00 0.00 4.00
2023 3853 4.005650 TGAAGCCAATTAGCTCTGTGAAG 58.994 43.478 0.00 0.00 44.11 3.02
2024 3854 4.019792 TGAAGCCAATTAGCTCTGTGAA 57.980 40.909 0.00 0.00 44.11 3.18
2028 3858 4.771590 TTGTTGAAGCCAATTAGCTCTG 57.228 40.909 0.00 0.00 44.11 3.35
2039 3869 5.229423 TGTCTATTGCAAATTGTTGAAGCC 58.771 37.500 1.71 0.00 36.83 4.35
2207 7149 4.568072 ATGGAACCTTGTATGCACACTA 57.432 40.909 0.00 0.00 33.30 2.74
2616 7599 2.086094 CGGTTACCGCTTTATTTGGGT 58.914 47.619 11.93 0.00 41.17 4.51
2782 7765 5.652014 ACAAGTCATTCTCACAAAGGACAAA 59.348 36.000 4.53 0.00 41.22 2.83


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

AutoCloner maintained by Alex Coulton.