Multiple sequence alignment - TraesCS1B01G238500

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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 TraesCS1B01G238500 chr1B 100.000 2216 0 0 1 2216 426496810 426499025 0.000000e+00 4093.0
1 TraesCS1B01G238500 chr1B 90.110 1638 111 21 595 2216 133111823 133113425 0.000000e+00 2080.0
2 TraesCS1B01G238500 chr1B 81.633 245 12 9 357 579 133111621 133111854 2.930000e-39 172.0
3 TraesCS1B01G238500 chr7A 91.714 1581 113 11 643 2216 627045705 627047274 0.000000e+00 2178.0
4 TraesCS1B01G238500 chr7A 92.385 998 68 5 1004 1999 580505038 580506029 0.000000e+00 1415.0
5 TraesCS1B01G238500 chr7A 89.744 780 68 7 643 1418 627119893 627120664 0.000000e+00 987.0
6 TraesCS1B01G238500 chr7A 82.560 797 107 20 1442 2216 627235199 627235985 0.000000e+00 673.0
7 TraesCS1B01G238500 chr7A 93.976 166 10 0 2051 2216 627009340 627009505 3.650000e-63 252.0
8 TraesCS1B01G238500 chr7A 78.731 268 19 18 360 609 627008770 627009017 6.380000e-31 145.0
9 TraesCS1B01G238500 chr7A 84.416 154 13 7 433 579 627045525 627045674 8.250000e-30 141.0
10 TraesCS1B01G238500 chr7A 84.416 154 13 7 433 579 627119713 627119862 8.250000e-30 141.0
11 TraesCS1B01G238500 chr7A 81.646 158 8 6 433 575 626992805 626992956 6.470000e-21 111.0
12 TraesCS1B01G238500 chr7A 86.087 115 3 7 614 725 627008988 627009092 6.470000e-21 111.0
13 TraesCS1B01G238500 chr7A 90.361 83 5 2 595 674 626992929 626993011 3.010000e-19 106.0
14 TraesCS1B01G238500 chr7A 94.643 56 3 0 28 83 628389893 628389948 1.090000e-13 87.9
15 TraesCS1B01G238500 chr5D 92.837 1396 84 8 824 2216 289421519 289422901 0.000000e+00 2010.0
16 TraesCS1B01G238500 chr5D 94.433 952 47 6 937 1884 289727724 289728673 0.000000e+00 1459.0
17 TraesCS1B01G238500 chr5D 86.306 942 75 14 1102 2004 23823507 23824433 0.000000e+00 976.0
18 TraesCS1B01G238500 chr5D 92.857 112 7 1 615 725 289727465 289727576 6.330000e-36 161.0
19 TraesCS1B01G238500 chr5D 78.229 271 27 20 1 263 289726995 289727241 6.380000e-31 145.0
20 TraesCS1B01G238500 chr5D 82.199 191 11 8 433 609 289421261 289421442 2.290000e-30 143.0
21 TraesCS1B01G238500 chr5D 81.152 191 12 7 433 609 289727311 289727491 4.960000e-27 132.0
22 TraesCS1B01G238500 chr5D 86.726 113 4 5 614 725 289421415 289421517 5.000000e-22 115.0
23 TraesCS1B01G238500 chr7B 86.382 1476 143 47 771 2216 588878990 588880437 0.000000e+00 1559.0
24 TraesCS1B01G238500 chr7B 87.901 405 33 6 642 1038 589734924 589734528 1.550000e-126 462.0
25 TraesCS1B01G238500 chr7B 85.632 348 27 8 634 980 588823792 588824117 5.860000e-91 344.0
26 TraesCS1B01G238500 chr6A 89.991 1089 92 10 771 1859 107263816 107262745 0.000000e+00 1391.0
27 TraesCS1B01G238500 chr6A 91.045 134 12 0 648 781 107263971 107263838 4.860000e-42 182.0
28 TraesCS1B01G238500 chr2B 88.676 1095 84 18 625 1719 182134122 182135176 0.000000e+00 1299.0
29 TraesCS1B01G238500 chr2B 93.151 438 19 2 1750 2185 182135174 182135602 1.120000e-177 632.0
30 TraesCS1B01G238500 chr2B 80.229 349 38 21 1 335 182133637 182133968 1.320000e-57 233.0
31 TraesCS1B01G238500 chr2B 77.027 222 19 19 41 258 135512740 135512547 5.040000e-17 99.0
32 TraesCS1B01G238500 chr2B 100.000 45 0 0 2172 2216 182140525 182140569 1.410000e-12 84.2
33 TraesCS1B01G238500 chr3A 88.372 903 83 5 1102 2004 723440603 723439723 0.000000e+00 1066.0
34 TraesCS1B01G238500 chr3A 81.452 124 10 9 44 165 55501325 55501437 3.030000e-14 89.8
35 TraesCS1B01G238500 chr7D 95.349 172 8 0 2045 2216 545268176 545268347 7.800000e-70 274.0
36 TraesCS1B01G238500 chr7D 86.567 201 13 7 185 375 545267007 545267203 2.230000e-50 209.0
37 TraesCS1B01G238500 chr7D 84.328 134 6 6 28 161 545622510 545622628 1.390000e-22 117.0
38 TraesCS1B01G238500 chr7D 93.056 72 3 2 1 72 545619761 545619830 1.080000e-18 104.0
39 TraesCS1B01G238500 chr7D 100.000 37 0 0 516 552 545267394 545267430 3.950000e-08 69.4
40 TraesCS1B01G238500 chr3B 80.435 92 8 7 61 152 68346889 68346970 6.610000e-06 62.1
41 TraesCS1B01G238500 chr6B 100.000 31 0 0 379 409 50336538 50336568 8.550000e-05 58.4


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 TraesCS1B01G238500 chr1B 426496810 426499025 2215 False 4093.000000 4093 100.00000 1 2216 1 chr1B.!!$F1 2215
1 TraesCS1B01G238500 chr1B 133111621 133113425 1804 False 1126.000000 2080 85.87150 357 2216 2 chr1B.!!$F2 1859
2 TraesCS1B01G238500 chr7A 580505038 580506029 991 False 1415.000000 1415 92.38500 1004 1999 1 chr7A.!!$F1 995
3 TraesCS1B01G238500 chr7A 627045525 627047274 1749 False 1159.500000 2178 88.06500 433 2216 2 chr7A.!!$F6 1783
4 TraesCS1B01G238500 chr7A 627235199 627235985 786 False 673.000000 673 82.56000 1442 2216 1 chr7A.!!$F2 774
5 TraesCS1B01G238500 chr7A 627119713 627120664 951 False 564.000000 987 87.08000 433 1418 2 chr7A.!!$F7 985
6 TraesCS1B01G238500 chr5D 23823507 23824433 926 False 976.000000 976 86.30600 1102 2004 1 chr5D.!!$F1 902
7 TraesCS1B01G238500 chr5D 289421261 289422901 1640 False 756.000000 2010 87.25400 433 2216 3 chr5D.!!$F2 1783
8 TraesCS1B01G238500 chr5D 289726995 289728673 1678 False 474.250000 1459 86.66775 1 1884 4 chr5D.!!$F3 1883
9 TraesCS1B01G238500 chr7B 588878990 588880437 1447 False 1559.000000 1559 86.38200 771 2216 1 chr7B.!!$F2 1445
10 TraesCS1B01G238500 chr6A 107262745 107263971 1226 True 786.500000 1391 90.51800 648 1859 2 chr6A.!!$R1 1211
11 TraesCS1B01G238500 chr2B 182133637 182135602 1965 False 721.333333 1299 87.35200 1 2185 3 chr2B.!!$F2 2184
12 TraesCS1B01G238500 chr3A 723439723 723440603 880 True 1066.000000 1066 88.37200 1102 2004 1 chr3A.!!$R1 902

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
116 125 0.036952 CAGATCGATCGGGATTGGGG 60.037 60.0 19.33 0.0 0.0 4.96 F
117 126 0.178932 AGATCGATCGGGATTGGGGA 60.179 55.0 19.33 0.0 0.0 4.81 F
171 196 0.532862 CGACAGGGCGGCAATATCTT 60.533 55.0 12.47 0.0 0.0 2.40 F
284 315 1.157870 AACGCGCCCTAATGAATCCG 61.158 55.0 5.73 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 1264 0.036952 CAGCTCCAATGTCGACCAGT 60.037 55.000 14.12 0.0 0.0 4.00 R
1050 1303 1.134907 GGCCAATCAAGCAGGACAATG 60.135 52.381 0.00 0.0 0.0 2.82 R
1100 1353 1.146041 GCGCTGATCCATGGGTGTA 59.854 57.895 13.02 0.0 0.0 2.90 R
1275 1528 1.197721 GAGCTTGTGGATCCGTTGTTG 59.802 52.381 7.39 0.0 0.0 3.33 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
66 73 3.157949 GCGGGAGGGAGGAAGAGG 61.158 72.222 0.00 0.00 0.00 3.69
67 74 2.690452 CGGGAGGGAGGAAGAGGA 59.310 66.667 0.00 0.00 0.00 3.71
68 75 1.234529 CGGGAGGGAGGAAGAGGAT 59.765 63.158 0.00 0.00 0.00 3.24
70 77 1.414866 GGGAGGGAGGAAGAGGATGC 61.415 65.000 0.00 0.00 0.00 3.91
71 78 1.745264 GAGGGAGGAAGAGGATGCG 59.255 63.158 0.00 0.00 0.00 4.73
73 80 2.439104 GGGAGGAAGAGGATGCGCT 61.439 63.158 9.73 0.00 0.00 5.92
80 89 4.925861 GAGGATGCGCTGGAGGCC 62.926 72.222 9.73 0.00 37.74 5.19
102 111 1.198713 TCAGAGGGCAAGGTCAGATC 58.801 55.000 0.00 0.00 0.00 2.75
113 122 1.615883 AGGTCAGATCGATCGGGATTG 59.384 52.381 22.72 14.08 0.00 2.67
116 125 0.036952 CAGATCGATCGGGATTGGGG 60.037 60.000 19.33 0.00 0.00 4.96
117 126 0.178932 AGATCGATCGGGATTGGGGA 60.179 55.000 19.33 0.00 0.00 4.81
121 131 1.821061 CGATCGGGATTGGGGAGGAG 61.821 65.000 7.38 0.00 0.00 3.69
138 148 3.119096 GACGGGGCGAGCAAGAAC 61.119 66.667 0.00 0.00 0.00 3.01
140 150 4.735132 CGGGGCGAGCAAGAACGA 62.735 66.667 0.00 0.00 0.00 3.85
141 151 2.815647 GGGGCGAGCAAGAACGAG 60.816 66.667 0.00 0.00 0.00 4.18
143 153 2.261671 GGCGAGCAAGAACGAGGA 59.738 61.111 0.00 0.00 0.00 3.71
168 193 2.591715 GCGACAGGGCGGCAATAT 60.592 61.111 12.47 0.00 0.00 1.28
169 194 2.607892 GCGACAGGGCGGCAATATC 61.608 63.158 12.47 1.28 0.00 1.63
170 195 1.069765 CGACAGGGCGGCAATATCT 59.930 57.895 12.47 0.00 0.00 1.98
171 196 0.532862 CGACAGGGCGGCAATATCTT 60.533 55.000 12.47 0.00 0.00 2.40
172 197 1.270094 CGACAGGGCGGCAATATCTTA 60.270 52.381 12.47 0.00 0.00 2.10
173 198 2.612972 CGACAGGGCGGCAATATCTTAT 60.613 50.000 12.47 0.00 0.00 1.73
174 199 3.003480 GACAGGGCGGCAATATCTTATC 58.997 50.000 12.47 0.00 0.00 1.75
175 200 2.639839 ACAGGGCGGCAATATCTTATCT 59.360 45.455 12.47 0.00 0.00 1.98
176 201 3.005554 CAGGGCGGCAATATCTTATCTG 58.994 50.000 12.47 0.34 0.00 2.90
177 202 2.639839 AGGGCGGCAATATCTTATCTGT 59.360 45.455 12.47 0.00 0.00 3.41
178 203 3.003480 GGGCGGCAATATCTTATCTGTC 58.997 50.000 12.47 0.00 0.00 3.51
179 204 2.668457 GGCGGCAATATCTTATCTGTCG 59.332 50.000 3.07 0.00 39.78 4.35
180 205 3.575630 GCGGCAATATCTTATCTGTCGA 58.424 45.455 1.23 0.00 39.16 4.20
181 206 4.177026 GCGGCAATATCTTATCTGTCGAT 58.823 43.478 1.23 0.00 39.16 3.59
182 207 4.032217 GCGGCAATATCTTATCTGTCGATG 59.968 45.833 1.23 0.00 39.16 3.84
183 208 4.564372 CGGCAATATCTTATCTGTCGATGG 59.436 45.833 0.00 0.00 39.16 3.51
209 240 4.899239 CGAGTCGGCCCAGGCATC 62.899 72.222 11.50 1.98 44.11 3.91
227 258 3.349472 GCTAAAACGCGCGCTTTC 58.651 55.556 31.58 16.67 0.00 2.62
284 315 1.157870 AACGCGCCCTAATGAATCCG 61.158 55.000 5.73 0.00 0.00 4.18
286 317 1.284982 CGCGCCCTAATGAATCCGAG 61.285 60.000 0.00 0.00 0.00 4.63
335 367 5.451937 CCAACTAGCACTAATGAATCCGAGA 60.452 44.000 0.00 0.00 0.00 4.04
336 368 6.219473 CAACTAGCACTAATGAATCCGAGAT 58.781 40.000 0.00 0.00 0.00 2.75
337 369 6.412362 ACTAGCACTAATGAATCCGAGATT 57.588 37.500 0.00 0.00 0.00 2.40
338 370 6.451393 ACTAGCACTAATGAATCCGAGATTC 58.549 40.000 15.59 15.59 0.00 2.52
339 371 4.636249 AGCACTAATGAATCCGAGATTCC 58.364 43.478 18.17 6.49 0.00 3.01
340 372 3.430218 GCACTAATGAATCCGAGATTCCG 59.570 47.826 18.17 10.16 0.00 4.30
341 373 4.796290 GCACTAATGAATCCGAGATTCCGA 60.796 45.833 18.17 6.63 0.00 4.55
342 374 4.920340 CACTAATGAATCCGAGATTCCGAG 59.080 45.833 18.17 15.08 0.00 4.63
343 375 4.585162 ACTAATGAATCCGAGATTCCGAGT 59.415 41.667 18.17 15.50 0.00 4.18
344 376 5.768662 ACTAATGAATCCGAGATTCCGAGTA 59.231 40.000 18.17 8.16 0.00 2.59
345 377 3.984508 TGAATCCGAGATTCCGAGTAC 57.015 47.619 18.17 0.00 0.00 2.73
348 380 5.314529 TGAATCCGAGATTCCGAGTACTAT 58.685 41.667 18.17 0.00 0.00 2.12
399 444 3.574614 GTCTCTCTGCTTCAGTTCAGAC 58.425 50.000 0.00 1.66 35.66 3.51
410 455 3.383620 CAGTTCAGACTGCAGAGTTCT 57.616 47.619 23.35 10.38 46.08 3.01
412 457 3.740321 CAGTTCAGACTGCAGAGTTCTTC 59.260 47.826 23.35 6.14 46.08 2.87
501 561 7.539712 TTATTTCGAGATCCTGATGTGTTTC 57.460 36.000 0.00 0.00 0.00 2.78
511 571 6.025749 TCCTGATGTGTTTCTAGTGTGTAG 57.974 41.667 0.00 0.00 0.00 2.74
512 572 5.538813 TCCTGATGTGTTTCTAGTGTGTAGT 59.461 40.000 0.00 0.00 0.00 2.73
513 573 6.041637 TCCTGATGTGTTTCTAGTGTGTAGTT 59.958 38.462 0.00 0.00 0.00 2.24
514 574 6.146184 CCTGATGTGTTTCTAGTGTGTAGTTG 59.854 42.308 0.00 0.00 0.00 3.16
519 593 5.047847 TGTTTCTAGTGTGTAGTTGCTGAC 58.952 41.667 0.00 0.00 0.00 3.51
552 631 3.809832 GCTGCTTGTCAAGTTGAAGTCTA 59.190 43.478 14.03 0.00 0.00 2.59
553 632 4.084118 GCTGCTTGTCAAGTTGAAGTCTAG 60.084 45.833 14.03 5.38 0.00 2.43
554 633 5.023533 TGCTTGTCAAGTTGAAGTCTAGT 57.976 39.130 14.03 0.00 0.00 2.57
555 634 5.050490 TGCTTGTCAAGTTGAAGTCTAGTC 58.950 41.667 14.03 0.00 0.00 2.59
556 635 5.163405 TGCTTGTCAAGTTGAAGTCTAGTCT 60.163 40.000 14.03 0.00 0.00 3.24
557 636 5.176590 GCTTGTCAAGTTGAAGTCTAGTCTG 59.823 44.000 14.03 0.00 0.00 3.51
558 637 6.465439 TTGTCAAGTTGAAGTCTAGTCTGA 57.535 37.500 7.25 0.00 0.00 3.27
559 638 6.656632 TGTCAAGTTGAAGTCTAGTCTGAT 57.343 37.500 7.25 0.00 0.00 2.90
560 639 7.055667 TGTCAAGTTGAAGTCTAGTCTGATT 57.944 36.000 7.25 0.00 0.00 2.57
561 640 8.178313 TGTCAAGTTGAAGTCTAGTCTGATTA 57.822 34.615 7.25 0.00 0.00 1.75
562 641 8.807118 TGTCAAGTTGAAGTCTAGTCTGATTAT 58.193 33.333 7.25 0.00 0.00 1.28
563 642 9.081997 GTCAAGTTGAAGTCTAGTCTGATTATG 57.918 37.037 7.25 0.00 0.00 1.90
564 643 7.761704 TCAAGTTGAAGTCTAGTCTGATTATGC 59.238 37.037 2.20 0.00 0.00 3.14
565 644 6.269315 AGTTGAAGTCTAGTCTGATTATGCG 58.731 40.000 0.00 0.00 0.00 4.73
566 645 4.611943 TGAAGTCTAGTCTGATTATGCGC 58.388 43.478 0.00 0.00 0.00 6.09
567 646 4.097892 TGAAGTCTAGTCTGATTATGCGCA 59.902 41.667 14.96 14.96 0.00 6.09
568 647 4.655762 AGTCTAGTCTGATTATGCGCAA 57.344 40.909 17.11 0.00 0.00 4.85
569 648 5.011090 AGTCTAGTCTGATTATGCGCAAA 57.989 39.130 17.11 10.98 0.00 3.68
570 649 5.419542 AGTCTAGTCTGATTATGCGCAAAA 58.580 37.500 17.11 2.00 0.00 2.44
571 650 5.874810 AGTCTAGTCTGATTATGCGCAAAAA 59.125 36.000 17.11 13.09 0.00 1.94
612 691 4.188948 GACTTGAAGTCTGATTATGCGC 57.811 45.455 17.61 0.00 41.88 6.09
613 692 3.599343 ACTTGAAGTCTGATTATGCGCA 58.401 40.909 14.96 14.96 0.00 6.09
614 693 4.002982 ACTTGAAGTCTGATTATGCGCAA 58.997 39.130 17.11 0.00 0.00 4.85
615 694 4.455533 ACTTGAAGTCTGATTATGCGCAAA 59.544 37.500 17.11 10.98 0.00 3.68
616 695 5.048782 ACTTGAAGTCTGATTATGCGCAAAA 60.049 36.000 17.11 2.00 0.00 2.44
617 696 5.369685 TGAAGTCTGATTATGCGCAAAAA 57.630 34.783 17.11 13.09 0.00 1.94
653 787 7.588143 AGTCTGATTATTCTGAAGTTGAACG 57.412 36.000 0.00 0.00 32.39 3.95
781 955 6.469782 AGGAACAACAAGACATGAAACATT 57.530 33.333 0.00 0.00 0.00 2.71
785 959 5.603596 ACAACAAGACATGAAACATTGCAT 58.396 33.333 0.00 0.00 0.00 3.96
804 1003 9.108449 CATTGCATGTTTGAATTACAATGTTTG 57.892 29.630 0.00 0.00 38.56 2.93
805 1004 8.429493 TTGCATGTTTGAATTACAATGTTTGA 57.571 26.923 0.00 0.00 38.36 2.69
806 1005 8.429493 TGCATGTTTGAATTACAATGTTTGAA 57.571 26.923 0.00 0.00 38.36 2.69
807 1006 8.886719 TGCATGTTTGAATTACAATGTTTGAAA 58.113 25.926 0.00 0.00 38.36 2.69
808 1007 9.713740 GCATGTTTGAATTACAATGTTTGAAAA 57.286 25.926 0.00 0.00 38.36 2.29
824 1023 9.918630 ATGTTTGAAAATAGGAAAATCAGTCTG 57.081 29.630 0.00 0.00 0.00 3.51
825 1024 8.359642 TGTTTGAAAATAGGAAAATCAGTCTGG 58.640 33.333 0.00 0.00 0.00 3.86
826 1025 8.360390 GTTTGAAAATAGGAAAATCAGTCTGGT 58.640 33.333 0.00 0.00 0.00 4.00
827 1026 9.581289 TTTGAAAATAGGAAAATCAGTCTGGTA 57.419 29.630 0.00 0.00 0.00 3.25
828 1027 8.792830 TGAAAATAGGAAAATCAGTCTGGTAG 57.207 34.615 0.00 0.00 0.00 3.18
829 1028 8.383175 TGAAAATAGGAAAATCAGTCTGGTAGT 58.617 33.333 0.00 0.00 0.00 2.73
830 1029 9.232473 GAAAATAGGAAAATCAGTCTGGTAGTT 57.768 33.333 0.00 0.00 0.00 2.24
847 1050 4.024641 GGTAGTTTTGGTACCACAGAAACG 60.025 45.833 24.75 0.00 39.94 3.60
923 1130 1.950909 CCTGTGTCGTAAAAAGCCCAA 59.049 47.619 0.00 0.00 0.00 4.12
942 1149 5.122239 GCCCAAAATCCTTGCTTACATTTTC 59.878 40.000 0.00 0.00 0.00 2.29
994 1247 3.081804 CCATTATATCAAACCTCCGGGC 58.918 50.000 0.00 0.00 35.63 6.13
1011 1264 2.483013 CGGGCCTAGAATGATTCGAACA 60.483 50.000 0.84 1.02 34.02 3.18
1050 1303 4.270325 GCTGAACTCGTTATGGTTATGTCC 59.730 45.833 0.00 0.00 0.00 4.02
1100 1353 1.735018 CGATGTCGTGTCTCTCTCAGT 59.265 52.381 0.00 0.00 34.11 3.41
1173 1426 1.822990 CATTCAGGGTTCAGCATTGCT 59.177 47.619 5.03 5.03 40.77 3.91
1270 1523 2.572290 TCTCAGCGACTTCATATCCGA 58.428 47.619 0.00 0.00 0.00 4.55
1275 1528 0.317479 CGACTTCATATCCGACCCCC 59.683 60.000 0.00 0.00 0.00 5.40
1390 1643 4.143326 GCAGCGCAAAAGAAGGAAAATAAC 60.143 41.667 11.47 0.00 0.00 1.89
1398 1651 6.686484 AAAGAAGGAAAATAACCTGGCAAT 57.314 33.333 0.00 0.00 37.85 3.56
1525 1779 4.441415 CGCTTGTCGAGTATGGTATTCTTC 59.559 45.833 0.00 0.00 41.67 2.87
1743 2024 0.464452 CTCGTTCCCATGACCCTACC 59.536 60.000 0.00 0.00 0.00 3.18
2063 2422 7.410174 TCAATTATGATGTGGAACTAGGGTTT 58.590 34.615 0.00 0.00 38.04 3.27
2064 2423 7.556275 TCAATTATGATGTGGAACTAGGGTTTC 59.444 37.037 0.00 0.00 38.04 2.78
2113 2475 4.534794 TTGCATTCGTGCACATACATAG 57.465 40.909 18.64 0.00 45.32 2.23
2137 2499 1.325338 GAATTAAACGAGGCGCGCTTA 59.675 47.619 32.29 18.10 46.04 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.933064 CCGGATCCGTGCTCTCGC 62.933 72.222 31.22 0.00 37.81 5.03
30 31 4.933064 GCCGGATCCGTGCTCTCG 62.933 72.222 31.22 15.83 37.81 4.04
31 32 4.933064 CGCCGGATCCGTGCTCTC 62.933 72.222 31.34 15.70 37.81 3.20
49 56 2.956077 ATCCTCTTCCTCCCTCCCGC 62.956 65.000 0.00 0.00 0.00 6.13
50 57 1.118356 CATCCTCTTCCTCCCTCCCG 61.118 65.000 0.00 0.00 0.00 5.14
60 67 1.227497 CCTCCAGCGCATCCTCTTC 60.227 63.158 11.47 0.00 0.00 2.87
61 68 2.906458 CCTCCAGCGCATCCTCTT 59.094 61.111 11.47 0.00 0.00 2.85
62 69 3.859414 GCCTCCAGCGCATCCTCT 61.859 66.667 11.47 0.00 0.00 3.69
63 70 4.925861 GGCCTCCAGCGCATCCTC 62.926 72.222 11.47 0.00 45.17 3.71
66 73 4.615815 ATCGGCCTCCAGCGCATC 62.616 66.667 11.47 0.00 45.17 3.91
67 74 4.615815 GATCGGCCTCCAGCGCAT 62.616 66.667 11.47 0.00 45.17 4.73
70 77 3.496875 CTCTGATCGGCCTCCAGCG 62.497 68.421 0.00 0.00 45.17 5.18
71 78 2.420890 CTCTGATCGGCCTCCAGC 59.579 66.667 0.00 0.00 42.60 4.85
73 80 2.444706 CCCTCTGATCGGCCTCCA 60.445 66.667 0.00 0.00 0.00 3.86
80 89 0.179089 CTGACCTTGCCCTCTGATCG 60.179 60.000 0.00 0.00 0.00 3.69
85 94 0.324738 TCGATCTGACCTTGCCCTCT 60.325 55.000 0.00 0.00 0.00 3.69
92 101 2.002505 ATCCCGATCGATCTGACCTT 57.997 50.000 22.43 2.81 0.00 3.50
102 111 1.821061 CTCCTCCCCAATCCCGATCG 61.821 65.000 8.51 8.51 0.00 3.69
121 131 3.119096 GTTCTTGCTCGCCCCGTC 61.119 66.667 0.00 0.00 0.00 4.79
159 184 3.575630 TCGACAGATAAGATATTGCCGC 58.424 45.455 0.00 0.00 0.00 6.53
160 185 4.564372 CCATCGACAGATAAGATATTGCCG 59.436 45.833 0.00 0.00 34.85 5.69
161 186 5.482908 ACCATCGACAGATAAGATATTGCC 58.517 41.667 0.00 0.00 34.85 4.52
162 187 7.171508 TCAAACCATCGACAGATAAGATATTGC 59.828 37.037 0.00 0.00 34.85 3.56
163 188 8.593492 TCAAACCATCGACAGATAAGATATTG 57.407 34.615 0.00 0.00 34.85 1.90
164 189 9.784531 ATTCAAACCATCGACAGATAAGATATT 57.215 29.630 0.00 0.00 34.85 1.28
165 190 9.429359 GATTCAAACCATCGACAGATAAGATAT 57.571 33.333 0.00 0.00 34.85 1.63
166 191 7.872993 GGATTCAAACCATCGACAGATAAGATA 59.127 37.037 0.00 0.00 34.85 1.98
167 192 6.708054 GGATTCAAACCATCGACAGATAAGAT 59.292 38.462 0.00 0.00 34.85 2.40
168 193 6.049149 GGATTCAAACCATCGACAGATAAGA 58.951 40.000 0.00 0.00 34.85 2.10
169 194 5.050769 CGGATTCAAACCATCGACAGATAAG 60.051 44.000 0.00 0.00 34.85 1.73
170 195 4.808895 CGGATTCAAACCATCGACAGATAA 59.191 41.667 0.00 0.00 34.85 1.75
171 196 4.098807 TCGGATTCAAACCATCGACAGATA 59.901 41.667 0.00 0.00 34.85 1.98
172 197 3.118775 TCGGATTCAAACCATCGACAGAT 60.119 43.478 0.00 0.00 37.65 2.90
173 198 2.232696 TCGGATTCAAACCATCGACAGA 59.767 45.455 0.00 0.00 0.00 3.41
174 199 2.604914 CTCGGATTCAAACCATCGACAG 59.395 50.000 0.00 0.00 0.00 3.51
175 200 2.028476 ACTCGGATTCAAACCATCGACA 60.028 45.455 0.00 0.00 0.00 4.35
176 201 2.603560 GACTCGGATTCAAACCATCGAC 59.396 50.000 0.00 0.00 0.00 4.20
177 202 2.734175 CGACTCGGATTCAAACCATCGA 60.734 50.000 0.00 0.00 32.47 3.59
178 203 1.588404 CGACTCGGATTCAAACCATCG 59.412 52.381 0.00 0.00 0.00 3.84
225 256 4.084745 CGACTCGGATTCAAAAACGAAGAA 60.085 41.667 0.00 0.00 34.70 2.52
226 257 3.427528 CGACTCGGATTCAAAAACGAAGA 59.572 43.478 0.00 0.00 34.70 2.87
227 258 3.722123 CGACTCGGATTCAAAAACGAAG 58.278 45.455 0.00 0.00 34.70 3.79
299 331 5.574188 AGTGCTAGTTGGAAAGATGGAAAT 58.426 37.500 0.00 0.00 0.00 2.17
399 444 7.981789 TGTACAATATAAGGAAGAACTCTGCAG 59.018 37.037 7.63 7.63 0.00 4.41
401 446 7.982354 AGTGTACAATATAAGGAAGAACTCTGC 59.018 37.037 0.00 0.00 0.00 4.26
409 454 9.915629 GATCAGGTAGTGTACAATATAAGGAAG 57.084 37.037 6.28 0.00 0.00 3.46
410 455 9.656323 AGATCAGGTAGTGTACAATATAAGGAA 57.344 33.333 6.28 0.00 0.00 3.36
412 457 9.915629 GAAGATCAGGTAGTGTACAATATAAGG 57.084 37.037 6.28 0.00 0.00 2.69
465 517 2.923655 CTCGAAATAAGCGCTGTTCTGA 59.076 45.455 12.58 14.65 0.00 3.27
501 561 3.508012 AGAGGTCAGCAACTACACACTAG 59.492 47.826 0.00 0.00 0.00 2.57
511 571 1.801178 GCAACTACAGAGGTCAGCAAC 59.199 52.381 0.00 0.00 0.00 4.17
512 572 1.694150 AGCAACTACAGAGGTCAGCAA 59.306 47.619 0.00 0.00 0.00 3.91
513 573 1.001293 CAGCAACTACAGAGGTCAGCA 59.999 52.381 0.00 0.00 0.00 4.41
514 574 1.719600 CAGCAACTACAGAGGTCAGC 58.280 55.000 0.00 0.00 0.00 4.26
519 593 2.072298 GACAAGCAGCAACTACAGAGG 58.928 52.381 0.00 0.00 0.00 3.69
591 670 3.618594 TGCGCATAATCAGACTTCAAGTC 59.381 43.478 5.66 9.78 45.38 3.01
592 671 3.599343 TGCGCATAATCAGACTTCAAGT 58.401 40.909 5.66 0.00 0.00 3.16
593 672 4.604843 TTGCGCATAATCAGACTTCAAG 57.395 40.909 12.75 0.00 0.00 3.02
594 673 5.369685 TTTTGCGCATAATCAGACTTCAA 57.630 34.783 12.75 0.00 0.00 2.69
595 674 5.369685 TTTTTGCGCATAATCAGACTTCA 57.630 34.783 12.75 0.00 0.00 3.02
618 697 9.354673 TCAGAATAATCAGACTTCAACCTTTTT 57.645 29.630 0.00 0.00 0.00 1.94
619 698 8.924511 TCAGAATAATCAGACTTCAACCTTTT 57.075 30.769 0.00 0.00 0.00 2.27
620 699 8.924511 TTCAGAATAATCAGACTTCAACCTTT 57.075 30.769 0.00 0.00 0.00 3.11
621 700 8.160106 ACTTCAGAATAATCAGACTTCAACCTT 58.840 33.333 0.00 0.00 0.00 3.50
622 701 7.684529 ACTTCAGAATAATCAGACTTCAACCT 58.315 34.615 0.00 0.00 0.00 3.50
623 702 7.913674 ACTTCAGAATAATCAGACTTCAACC 57.086 36.000 0.00 0.00 0.00 3.77
624 703 8.993121 TCAACTTCAGAATAATCAGACTTCAAC 58.007 33.333 0.00 0.00 0.00 3.18
625 704 9.559732 TTCAACTTCAGAATAATCAGACTTCAA 57.440 29.630 0.00 0.00 0.00 2.69
626 705 8.993121 GTTCAACTTCAGAATAATCAGACTTCA 58.007 33.333 0.00 0.00 0.00 3.02
627 706 8.165428 CGTTCAACTTCAGAATAATCAGACTTC 58.835 37.037 0.00 0.00 0.00 3.01
628 707 7.657761 ACGTTCAACTTCAGAATAATCAGACTT 59.342 33.333 0.00 0.00 0.00 3.01
629 708 7.116948 CACGTTCAACTTCAGAATAATCAGACT 59.883 37.037 0.00 0.00 0.00 3.24
630 709 7.230222 CACGTTCAACTTCAGAATAATCAGAC 58.770 38.462 0.00 0.00 0.00 3.51
631 710 6.128553 GCACGTTCAACTTCAGAATAATCAGA 60.129 38.462 0.00 0.00 0.00 3.27
632 711 6.017933 GCACGTTCAACTTCAGAATAATCAG 58.982 40.000 0.00 0.00 0.00 2.90
633 712 5.106712 GGCACGTTCAACTTCAGAATAATCA 60.107 40.000 0.00 0.00 0.00 2.57
653 787 0.602905 AACTGACACTTAGCCGGCAC 60.603 55.000 31.54 10.75 0.00 5.01
781 955 8.429493 TTCAAACATTGTAATTCAAACATGCA 57.571 26.923 0.00 0.00 39.62 3.96
802 1001 9.231297 CTACCAGACTGATTTTCCTATTTTCAA 57.769 33.333 3.32 0.00 0.00 2.69
803 1002 8.383175 ACTACCAGACTGATTTTCCTATTTTCA 58.617 33.333 3.32 0.00 0.00 2.69
804 1003 8.794335 ACTACCAGACTGATTTTCCTATTTTC 57.206 34.615 3.32 0.00 0.00 2.29
805 1004 9.588096 AAACTACCAGACTGATTTTCCTATTTT 57.412 29.630 3.32 0.00 0.00 1.82
806 1005 9.588096 AAAACTACCAGACTGATTTTCCTATTT 57.412 29.630 3.32 0.00 0.00 1.40
807 1006 9.014297 CAAAACTACCAGACTGATTTTCCTATT 57.986 33.333 3.32 0.00 0.00 1.73
808 1007 7.611855 CCAAAACTACCAGACTGATTTTCCTAT 59.388 37.037 3.32 0.00 0.00 2.57
809 1008 6.940298 CCAAAACTACCAGACTGATTTTCCTA 59.060 38.462 3.32 0.00 0.00 2.94
810 1009 5.770162 CCAAAACTACCAGACTGATTTTCCT 59.230 40.000 3.32 0.00 0.00 3.36
811 1010 5.535030 ACCAAAACTACCAGACTGATTTTCC 59.465 40.000 3.32 0.00 0.00 3.13
812 1011 6.635030 ACCAAAACTACCAGACTGATTTTC 57.365 37.500 3.32 0.00 0.00 2.29
813 1012 6.489022 GGTACCAAAACTACCAGACTGATTTT 59.511 38.462 7.15 2.90 34.74 1.82
814 1013 6.002082 GGTACCAAAACTACCAGACTGATTT 58.998 40.000 7.15 0.00 34.74 2.17
815 1014 5.072600 TGGTACCAAAACTACCAGACTGATT 59.927 40.000 13.60 0.00 39.02 2.57
816 1015 4.595781 TGGTACCAAAACTACCAGACTGAT 59.404 41.667 13.60 0.00 39.02 2.90
817 1016 3.968649 TGGTACCAAAACTACCAGACTGA 59.031 43.478 13.60 0.00 39.02 3.41
818 1017 4.062991 GTGGTACCAAAACTACCAGACTG 58.937 47.826 18.31 0.00 43.54 3.51
819 1018 3.712733 TGTGGTACCAAAACTACCAGACT 59.287 43.478 18.31 0.00 43.54 3.24
820 1019 4.062991 CTGTGGTACCAAAACTACCAGAC 58.937 47.826 18.31 0.00 43.54 3.51
821 1020 3.968649 TCTGTGGTACCAAAACTACCAGA 59.031 43.478 18.31 19.21 43.54 3.86
822 1021 4.345859 TCTGTGGTACCAAAACTACCAG 57.654 45.455 18.31 17.19 43.54 4.00
823 1022 4.774660 TTCTGTGGTACCAAAACTACCA 57.225 40.909 18.31 7.58 41.19 3.25
824 1023 4.024641 CGTTTCTGTGGTACCAAAACTACC 60.025 45.833 26.65 12.46 35.13 3.18
825 1024 4.571984 ACGTTTCTGTGGTACCAAAACTAC 59.428 41.667 26.65 17.76 0.00 2.73
826 1025 4.571580 CACGTTTCTGTGGTACCAAAACTA 59.428 41.667 26.65 10.03 36.20 2.24
827 1026 3.375922 CACGTTTCTGTGGTACCAAAACT 59.624 43.478 26.65 16.67 36.20 2.66
828 1027 3.127376 ACACGTTTCTGTGGTACCAAAAC 59.873 43.478 22.66 22.66 44.21 2.43
829 1028 3.345414 ACACGTTTCTGTGGTACCAAAA 58.655 40.909 18.31 11.25 44.21 2.44
830 1029 2.988570 ACACGTTTCTGTGGTACCAAA 58.011 42.857 18.31 11.13 44.21 3.28
877 1084 4.031089 GTGCAGCACATATTCGAGATATCG 59.969 45.833 21.22 2.64 34.08 2.92
923 1130 9.423061 GTACAATGAAAATGTAAGCAAGGATTT 57.577 29.630 0.00 0.00 35.21 2.17
953 1206 5.738619 TGGAGAACATTCAGTAGTAGCAA 57.261 39.130 0.00 0.00 0.00 3.91
994 1247 4.759782 ACCAGTGTTCGAATCATTCTAGG 58.240 43.478 0.00 0.00 0.00 3.02
1011 1264 0.036952 CAGCTCCAATGTCGACCAGT 60.037 55.000 14.12 0.00 0.00 4.00
1050 1303 1.134907 GGCCAATCAAGCAGGACAATG 60.135 52.381 0.00 0.00 0.00 2.82
1100 1353 1.146041 GCGCTGATCCATGGGTGTA 59.854 57.895 13.02 0.00 0.00 2.90
1173 1426 1.536940 CCACCATGACAGATGTTGCA 58.463 50.000 0.00 0.00 0.00 4.08
1270 1523 2.157452 TGGATCCGTTGTTGGGGGT 61.157 57.895 7.39 0.00 0.00 4.95
1275 1528 1.197721 GAGCTTGTGGATCCGTTGTTG 59.802 52.381 7.39 0.00 0.00 3.33
1390 1643 5.186797 TGGGATGTTTACTTTTATTGCCAGG 59.813 40.000 0.00 0.00 0.00 4.45
1398 1651 8.642935 TCACATTCATGGGATGTTTACTTTTA 57.357 30.769 11.42 0.00 34.77 1.52
1447 1700 9.371136 GATGTGAGTGAACTGAACATCTATTTA 57.629 33.333 19.38 0.00 40.26 1.40
1525 1779 2.104111 TCTGGTGATTATTAGTGGCCGG 59.896 50.000 0.00 0.00 0.00 6.13
1743 2024 2.161486 GTAGCAGAAGAGCGCACGG 61.161 63.158 11.47 0.00 40.15 4.94
1890 2204 4.741928 ACAGGGTTAACAGAGGGAATTT 57.258 40.909 8.10 0.00 0.00 1.82
2063 2422 7.491372 CGTCTACAATTAAATCAAGGCTACAGA 59.509 37.037 0.00 0.00 0.00 3.41
2064 2423 7.254455 CCGTCTACAATTAAATCAAGGCTACAG 60.254 40.741 0.00 0.00 0.00 2.74
2113 2475 1.789054 CGCGCCTCGTTTAATTCCAAC 60.789 52.381 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.