Multiple sequence alignment - TraesCS1D01G337800

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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 TraesCS1D01G337800 chr1D 100.000 3412 0 0 1 3412 427320617 427317206 0.000000e+00 6301
1 TraesCS1D01G337800 chr1D 82.961 1479 200 33 1059 2505 427372368 427370910 0.000000e+00 1288
2 TraesCS1D01G337800 chr1D 83.148 1436 212 19 1082 2499 427332267 427330844 0.000000e+00 1284
3 TraesCS1D01G337800 chr1D 88.952 706 55 16 2715 3412 322390383 322389693 0.000000e+00 850
4 TraesCS1D01G337800 chr1D 86.932 704 70 15 2716 3412 9469382 9468694 0.000000e+00 771
5 TraesCS1D01G337800 chr1A 94.204 1777 75 18 965 2716 522511015 522509242 0.000000e+00 2686
6 TraesCS1D01G337800 chr1A 82.465 1517 212 37 1022 2505 522536007 522534512 0.000000e+00 1279
7 TraesCS1D01G337800 chr1A 82.870 1331 204 12 1130 2443 522516305 522514982 0.000000e+00 1173
8 TraesCS1D01G337800 chr1A 89.234 418 40 5 304 719 522511674 522511260 5.050000e-143 518
9 TraesCS1D01G337800 chr1B 94.247 1043 41 11 965 1989 577829424 577828383 0.000000e+00 1576
10 TraesCS1D01G337800 chr1B 83.618 1465 206 20 985 2420 578045555 578044096 0.000000e+00 1345
11 TraesCS1D01G337800 chr1B 81.569 1389 206 31 1139 2499 577913108 577911742 0.000000e+00 1101
12 TraesCS1D01G337800 chr1B 89.843 699 55 11 2716 3409 303227354 303228041 0.000000e+00 883
13 TraesCS1D01G337800 chr1B 91.034 580 44 6 147 719 577830334 577829756 0.000000e+00 776
14 TraesCS1D01G337800 chr1B 86.344 454 48 9 2066 2509 577828224 577827775 1.840000e-132 483
15 TraesCS1D01G337800 chr1B 92.946 241 12 5 732 970 577829691 577829454 2.520000e-91 346
16 TraesCS1D01G337800 chr1B 83.924 367 29 14 358 706 577920432 577920078 1.180000e-84 324
17 TraesCS1D01G337800 chr1B 81.461 178 20 7 2540 2714 577827777 577827610 2.140000e-27 134
18 TraesCS1D01G337800 chr5D 81.087 1729 271 41 973 2660 523314903 523313190 0.000000e+00 1330
19 TraesCS1D01G337800 chr5D 80.936 1731 270 42 973 2660 523187714 523186001 0.000000e+00 1314
20 TraesCS1D01G337800 chr3D 88.034 702 61 16 2716 3409 28333061 28333747 0.000000e+00 809
21 TraesCS1D01G337800 chr7D 88.000 700 61 16 2715 3406 459934501 459933817 0.000000e+00 806
22 TraesCS1D01G337800 chr7D 92.500 120 9 0 1 120 545252102 545251983 4.530000e-39 172
23 TraesCS1D01G337800 chr4D 87.746 710 54 21 2716 3409 55290940 55291632 0.000000e+00 798
24 TraesCS1D01G337800 chr4A 87.198 703 66 18 2716 3409 138449869 138450556 0.000000e+00 778
25 TraesCS1D01G337800 chr2D 87.129 707 66 18 2715 3412 582524187 582523497 0.000000e+00 778
26 TraesCS1D01G337800 chr2D 87.147 708 61 21 2713 3409 305767122 305767810 0.000000e+00 776
27 TraesCS1D01G337800 chr3A 94.783 115 6 0 1 115 364922411 364922297 2.710000e-41 180


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 TraesCS1D01G337800 chr1D 427317206 427320617 3411 True 6301 6301 100.000000 1 3412 1 chr1D.!!$R3 3411
1 TraesCS1D01G337800 chr1D 427370910 427372368 1458 True 1288 1288 82.961000 1059 2505 1 chr1D.!!$R5 1446
2 TraesCS1D01G337800 chr1D 427330844 427332267 1423 True 1284 1284 83.148000 1082 2499 1 chr1D.!!$R4 1417
3 TraesCS1D01G337800 chr1D 322389693 322390383 690 True 850 850 88.952000 2715 3412 1 chr1D.!!$R2 697
4 TraesCS1D01G337800 chr1D 9468694 9469382 688 True 771 771 86.932000 2716 3412 1 chr1D.!!$R1 696
5 TraesCS1D01G337800 chr1A 522509242 522516305 7063 True 1459 2686 88.769333 304 2716 3 chr1A.!!$R2 2412
6 TraesCS1D01G337800 chr1A 522534512 522536007 1495 True 1279 1279 82.465000 1022 2505 1 chr1A.!!$R1 1483
7 TraesCS1D01G337800 chr1B 578044096 578045555 1459 True 1345 1345 83.618000 985 2420 1 chr1B.!!$R3 1435
8 TraesCS1D01G337800 chr1B 577911742 577913108 1366 True 1101 1101 81.569000 1139 2499 1 chr1B.!!$R1 1360
9 TraesCS1D01G337800 chr1B 303227354 303228041 687 False 883 883 89.843000 2716 3409 1 chr1B.!!$F1 693
10 TraesCS1D01G337800 chr1B 577827610 577830334 2724 True 663 1576 89.206400 147 2714 5 chr1B.!!$R4 2567
11 TraesCS1D01G337800 chr5D 523313190 523314903 1713 True 1330 1330 81.087000 973 2660 1 chr5D.!!$R2 1687
12 TraesCS1D01G337800 chr5D 523186001 523187714 1713 True 1314 1314 80.936000 973 2660 1 chr5D.!!$R1 1687
13 TraesCS1D01G337800 chr3D 28333061 28333747 686 False 809 809 88.034000 2716 3409 1 chr3D.!!$F1 693
14 TraesCS1D01G337800 chr7D 459933817 459934501 684 True 806 806 88.000000 2715 3406 1 chr7D.!!$R1 691
15 TraesCS1D01G337800 chr4D 55290940 55291632 692 False 798 798 87.746000 2716 3409 1 chr4D.!!$F1 693
16 TraesCS1D01G337800 chr4A 138449869 138450556 687 False 778 778 87.198000 2716 3409 1 chr4A.!!$F1 693
17 TraesCS1D01G337800 chr2D 582523497 582524187 690 True 778 778 87.129000 2715 3412 1 chr2D.!!$R1 697
18 TraesCS1D01G337800 chr2D 305767122 305767810 688 False 776 776 87.147000 2713 3409 1 chr2D.!!$F1 696

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
241 242 0.034186 CTGCAAACCATAGGGAGGCA 60.034 55.0 0.00 5.84 38.05 4.75 F
361 4690 0.321034 CTGCTGTGTAGGCTGCTTCA 60.321 55.0 3.77 2.82 34.93 3.02 F
809 5198 0.801067 GCGCCTTGTATCGTTCGTCT 60.801 55.0 0.00 0.00 0.00 4.18 F
1009 5444 1.542492 ACCTTCAGAAATGCTGGCAG 58.458 50.0 10.94 10.94 44.98 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 5823 1.516386 CATGAGCCGTCGTAAGCGT 60.516 57.895 0.00 0.0 39.49 5.07 R
2192 6814 2.478292 ACGATTATCACCTTCCCACCT 58.522 47.619 0.00 0.0 0.00 4.00 R
2373 6995 1.898863 ACAGATCTAACCCCCAGCAT 58.101 50.000 0.00 0.0 0.00 3.79 R
2897 7524 0.178990 GGGAGCCGGGCAATAGATTT 60.179 55.000 23.09 0.0 0.00 2.17 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
17 18 4.164258 GCTTGTGACCTTGCACCT 57.836 55.556 0.00 0.00 37.99 4.00
18 19 1.656441 GCTTGTGACCTTGCACCTG 59.344 57.895 0.00 0.00 37.99 4.00
20 21 1.152777 TTGTGACCTTGCACCTGGG 60.153 57.895 0.00 0.00 37.99 4.45
21 22 1.932156 TTGTGACCTTGCACCTGGGT 61.932 55.000 0.00 0.00 37.99 4.51
30 31 3.749981 CACCTGGGTGCACTTCAC 58.250 61.111 17.98 5.66 44.90 3.18
38 39 3.484524 GTGCACTTCACAAGCCATG 57.515 52.632 10.32 0.00 44.98 3.66
39 40 0.670162 GTGCACTTCACAAGCCATGT 59.330 50.000 10.32 0.00 44.98 3.21
40 41 1.879380 GTGCACTTCACAAGCCATGTA 59.121 47.619 10.32 0.00 44.98 2.29
42 43 2.293122 TGCACTTCACAAGCCATGTAAC 59.707 45.455 0.00 0.00 41.46 2.50
43 44 2.554032 GCACTTCACAAGCCATGTAACT 59.446 45.455 0.00 0.00 41.46 2.24
44 45 3.610114 GCACTTCACAAGCCATGTAACTG 60.610 47.826 0.00 0.00 41.46 3.16
45 46 3.565482 CACTTCACAAGCCATGTAACTGT 59.435 43.478 0.00 0.00 41.46 3.55
46 47 4.754618 CACTTCACAAGCCATGTAACTGTA 59.245 41.667 0.00 0.00 41.46 2.74
48 49 4.617253 TCACAAGCCATGTAACTGTACT 57.383 40.909 0.00 0.00 41.46 2.73
49 50 4.968259 TCACAAGCCATGTAACTGTACTT 58.032 39.130 0.00 0.00 41.46 2.24
50 51 4.994852 TCACAAGCCATGTAACTGTACTTC 59.005 41.667 0.00 0.00 41.46 3.01
51 52 4.754618 CACAAGCCATGTAACTGTACTTCA 59.245 41.667 0.00 0.00 41.46 3.02
52 53 5.412594 CACAAGCCATGTAACTGTACTTCAT 59.587 40.000 0.00 0.00 41.46 2.57
56 57 4.572389 GCCATGTAACTGTACTTCATCTGG 59.428 45.833 0.00 0.00 0.00 3.86
57 58 4.572389 CCATGTAACTGTACTTCATCTGGC 59.428 45.833 0.00 0.00 0.00 4.85
58 59 5.423015 CATGTAACTGTACTTCATCTGGCT 58.577 41.667 0.00 0.00 0.00 4.75
59 60 5.483685 TGTAACTGTACTTCATCTGGCTT 57.516 39.130 0.00 0.00 0.00 4.35
61 62 7.182817 TGTAACTGTACTTCATCTGGCTTAT 57.817 36.000 0.00 0.00 0.00 1.73
85 86 7.496529 TGCCTCTTTTGAAATATAAGATCGG 57.503 36.000 0.00 0.00 0.00 4.18
86 87 6.017109 TGCCTCTTTTGAAATATAAGATCGGC 60.017 38.462 0.00 0.00 38.62 5.54
89 90 7.259290 TCTTTTGAAATATAAGATCGGCCAC 57.741 36.000 2.24 0.00 0.00 5.01
90 91 5.666969 TTTGAAATATAAGATCGGCCACG 57.333 39.130 2.24 0.00 42.74 4.94
102 103 2.032681 GCCACGAGCCACCTTCTT 59.967 61.111 0.00 0.00 34.35 2.52
103 104 1.295423 GCCACGAGCCACCTTCTTA 59.705 57.895 0.00 0.00 34.35 2.10
105 106 1.679032 GCCACGAGCCACCTTCTTATT 60.679 52.381 0.00 0.00 34.35 1.40
106 107 2.711542 CCACGAGCCACCTTCTTATTT 58.288 47.619 0.00 0.00 0.00 1.40
107 108 3.081804 CCACGAGCCACCTTCTTATTTT 58.918 45.455 0.00 0.00 0.00 1.82
108 109 3.127030 CCACGAGCCACCTTCTTATTTTC 59.873 47.826 0.00 0.00 0.00 2.29
109 110 3.751175 CACGAGCCACCTTCTTATTTTCA 59.249 43.478 0.00 0.00 0.00 2.69
110 111 4.215399 CACGAGCCACCTTCTTATTTTCAA 59.785 41.667 0.00 0.00 0.00 2.69
111 112 4.825085 ACGAGCCACCTTCTTATTTTCAAA 59.175 37.500 0.00 0.00 0.00 2.69
113 114 6.183360 ACGAGCCACCTTCTTATTTTCAAAAA 60.183 34.615 0.00 0.00 0.00 1.94
135 136 5.757850 AAGAAATCGTTTGTTCTCAAGCT 57.242 34.783 0.00 0.00 32.90 3.74
136 137 5.349824 AGAAATCGTTTGTTCTCAAGCTC 57.650 39.130 0.00 0.00 34.88 4.09
139 140 5.695851 AATCGTTTGTTCTCAAGCTCATT 57.304 34.783 0.00 0.00 34.88 2.57
142 143 3.250762 CGTTTGTTCTCAAGCTCATTCCA 59.749 43.478 0.00 0.00 34.88 3.53
143 144 4.083110 CGTTTGTTCTCAAGCTCATTCCAT 60.083 41.667 0.00 0.00 34.88 3.41
144 145 5.159209 GTTTGTTCTCAAGCTCATTCCATG 58.841 41.667 0.00 0.00 34.88 3.66
145 146 3.349927 TGTTCTCAAGCTCATTCCATGG 58.650 45.455 4.97 4.97 0.00 3.66
147 148 3.272574 TCTCAAGCTCATTCCATGGAC 57.727 47.619 15.91 1.97 0.00 4.02
148 149 2.573009 TCTCAAGCTCATTCCATGGACA 59.427 45.455 15.91 6.51 0.00 4.02
149 150 2.943690 CTCAAGCTCATTCCATGGACAG 59.056 50.000 15.91 11.88 0.00 3.51
150 151 1.404391 CAAGCTCATTCCATGGACAGC 59.596 52.381 23.61 23.61 0.00 4.40
151 152 0.463295 AGCTCATTCCATGGACAGCG 60.463 55.000 24.23 13.56 30.89 5.18
188 189 4.335315 CCGGTGCATAACATCTACAAATGT 59.665 41.667 0.00 0.00 41.60 2.71
198 199 5.931532 ACATCTACAAATGTTCGCTCTTTG 58.068 37.500 0.00 0.00 36.47 2.77
199 200 5.106555 ACATCTACAAATGTTCGCTCTTTGG 60.107 40.000 0.00 0.00 36.47 3.28
241 242 0.034186 CTGCAAACCATAGGGAGGCA 60.034 55.000 0.00 5.84 38.05 4.75
242 243 0.407528 TGCAAACCATAGGGAGGCAA 59.592 50.000 0.00 0.00 35.96 4.52
278 279 4.559502 CGGAGATGATTCAGAATAAGGCGA 60.560 45.833 0.00 0.00 0.00 5.54
285 286 2.660572 TCAGAATAAGGCGAGAGAGCT 58.339 47.619 0.00 0.00 37.29 4.09
330 4659 2.193536 GTGGTTGTCAGTGGGGTGC 61.194 63.158 0.00 0.00 0.00 5.01
340 4669 1.614226 GTGGGGTGCCTGGGTAGTA 60.614 63.158 0.00 0.00 0.00 1.82
361 4690 0.321034 CTGCTGTGTAGGCTGCTTCA 60.321 55.000 3.77 2.82 34.93 3.02
420 4755 1.134226 CTTGTACCGTGACGTTGGTC 58.866 55.000 10.82 5.19 43.71 4.02
515 4850 6.313905 CGTGATGTCCTAGCTAGAAAATGTTT 59.686 38.462 22.70 0.00 0.00 2.83
557 4892 3.054166 CGTGTCTTGACCGTGTGATAAA 58.946 45.455 0.00 0.00 0.00 1.40
613 4948 6.393171 GCTTGTGGAATTGCTCTATTTTCTT 58.607 36.000 0.00 0.00 0.00 2.52
619 4954 7.336931 GTGGAATTGCTCTATTTTCTTGAGGTA 59.663 37.037 0.00 0.00 0.00 3.08
635 4970 7.630082 TCTTGAGGTATGTAATTTGGTAGCTT 58.370 34.615 0.00 0.00 0.00 3.74
720 5056 7.899178 TTTTTCGAAGCAGAATATGTACAGA 57.101 32.000 0.33 0.00 0.00 3.41
721 5057 7.525688 TTTTCGAAGCAGAATATGTACAGAG 57.474 36.000 0.33 0.00 0.00 3.35
722 5058 5.188327 TCGAAGCAGAATATGTACAGAGG 57.812 43.478 0.33 0.00 0.00 3.69
727 5115 7.867909 CGAAGCAGAATATGTACAGAGGAAATA 59.132 37.037 0.33 0.00 0.00 1.40
728 5116 9.717942 GAAGCAGAATATGTACAGAGGAAATAT 57.282 33.333 0.33 0.00 0.00 1.28
730 5118 8.654997 AGCAGAATATGTACAGAGGAAATATGT 58.345 33.333 0.33 0.00 37.13 2.29
780 5169 8.818622 AAAAGAAGGTAAGGTTTTGTAAGAGT 57.181 30.769 0.00 0.00 0.00 3.24
783 5172 5.043737 AGGTAAGGTTTTGTAAGAGTGCA 57.956 39.130 0.00 0.00 0.00 4.57
790 5179 4.261197 GGTTTTGTAAGAGTGCAACCTCAG 60.261 45.833 7.05 0.00 37.80 3.35
807 5196 1.076533 CAGCGCCTTGTATCGTTCGT 61.077 55.000 2.29 0.00 0.00 3.85
809 5198 0.801067 GCGCCTTGTATCGTTCGTCT 60.801 55.000 0.00 0.00 0.00 4.18
831 5220 5.241949 TCTGTGTACTTTGTTTGGTTGTTGT 59.758 36.000 0.00 0.00 0.00 3.32
849 5238 6.821031 TGTTGTTTTATATACAAAGCGGGT 57.179 33.333 3.33 0.00 37.26 5.28
870 5259 2.618053 CGAAAGCCTGTTTCGGTAGAT 58.382 47.619 11.18 0.00 45.17 1.98
875 5264 6.477688 CGAAAGCCTGTTTCGGTAGATAAATA 59.522 38.462 11.18 0.00 45.17 1.40
968 5400 4.201657 CTGATAGCCACCATTCACATTGA 58.798 43.478 0.00 0.00 0.00 2.57
982 5414 8.028354 CCATTCACATTGATGCTGTAAGTTTAA 58.972 33.333 0.00 0.00 35.30 1.52
1009 5444 1.542492 ACCTTCAGAAATGCTGGCAG 58.458 50.000 10.94 10.94 44.98 4.85
1051 5487 8.385898 TCTTAAATAACTTATTACCCATGGCG 57.614 34.615 6.09 2.02 0.00 5.69
1056 5492 2.436542 ACTTATTACCCATGGCGCTACA 59.563 45.455 6.09 0.00 0.00 2.74
1162 5633 4.385358 ACAAAATGTCACCCACTCAAAC 57.615 40.909 0.00 0.00 0.00 2.93
1352 5823 2.105477 GCTCCATCCATCTAAGCTTCCA 59.895 50.000 0.00 0.00 0.00 3.53
1431 5905 2.140792 ACCACGGCAGACAAGGAGT 61.141 57.895 0.00 0.00 0.00 3.85
1533 6007 4.828939 TGATGCTTGATTCAACTGTCCTTT 59.171 37.500 0.00 0.00 0.00 3.11
1933 6407 3.496160 GCTCTTTTCCTGAAGGTACACCA 60.496 47.826 0.38 0.00 38.89 4.17
2017 6607 8.481974 TTTGTATTTAGCTTCTTATGCGTACA 57.518 30.769 0.00 0.00 35.28 2.90
2231 6853 4.219919 TCGTAGATATGGTGGTTGGATCA 58.780 43.478 0.00 0.00 0.00 2.92
2373 6995 8.609176 GGTTCAGCGAGTACAAAATTATATCAA 58.391 33.333 0.00 0.00 0.00 2.57
2410 7032 5.138758 TCTGTTATTGAGCTCTACCCCTA 57.861 43.478 16.19 0.00 0.00 3.53
2413 7035 6.442564 TCTGTTATTGAGCTCTACCCCTAAAA 59.557 38.462 16.19 0.00 0.00 1.52
2421 7043 2.838202 CTCTACCCCTAAAAGCTCCACA 59.162 50.000 0.00 0.00 0.00 4.17
2428 7050 4.321974 CCCCTAAAAGCTCCACACAAAATC 60.322 45.833 0.00 0.00 0.00 2.17
2513 7137 1.335496 GTATGCGTGTGGTTTGGTGTT 59.665 47.619 0.00 0.00 0.00 3.32
2516 7140 1.508545 CGTGTGGTTTGGTGTTGCA 59.491 52.632 0.00 0.00 0.00 4.08
2517 7141 0.525242 CGTGTGGTTTGGTGTTGCAG 60.525 55.000 0.00 0.00 0.00 4.41
2529 7153 4.917385 TGGTGTTGCAGGATATGTTTACT 58.083 39.130 0.00 0.00 0.00 2.24
2558 7182 3.846754 GCATTTTGCGAGGTGTGC 58.153 55.556 0.00 0.00 31.71 4.57
2673 7299 2.859165 ACCATCTACAGTTGGGTGTG 57.141 50.000 10.37 0.00 38.81 3.82
2676 7302 3.007614 ACCATCTACAGTTGGGTGTGTAC 59.992 47.826 10.37 0.00 38.81 2.90
2682 7308 3.805207 ACAGTTGGGTGTGTACTTTCTC 58.195 45.455 0.00 0.00 0.00 2.87
2883 7510 7.081526 AGATGTGTCAATCTAATCAAGCAAC 57.918 36.000 0.00 0.00 35.09 4.17
2914 7541 4.327680 AGAATAAATCTATTGCCCGGCTC 58.672 43.478 11.61 0.00 36.32 4.70
2917 7544 1.352622 AATCTATTGCCCGGCTCCCA 61.353 55.000 11.61 0.00 0.00 4.37
2920 7547 2.388890 CTATTGCCCGGCTCCCAGAG 62.389 65.000 11.61 0.00 0.00 3.35
2948 7580 2.508751 CCTAACCCTAGCCGCCTCC 61.509 68.421 0.00 0.00 0.00 4.30
2949 7581 1.760875 CTAACCCTAGCCGCCTCCA 60.761 63.158 0.00 0.00 0.00 3.86
2950 7582 1.749334 CTAACCCTAGCCGCCTCCAG 61.749 65.000 0.00 0.00 0.00 3.86
2953 7585 3.922640 CCTAGCCGCCTCCAGCTC 61.923 72.222 0.00 0.00 40.56 4.09
2954 7586 3.922640 CTAGCCGCCTCCAGCTCC 61.923 72.222 0.00 0.00 40.56 4.70
3174 7831 3.859414 GCCGCTGCCTCTCTCCAT 61.859 66.667 0.00 0.00 0.00 3.41
3177 7834 2.780094 CGCTGCCTCTCTCCATCGT 61.780 63.158 0.00 0.00 0.00 3.73
3190 7847 4.087892 ATCGTGCCGCTGCCTCTT 62.088 61.111 0.00 0.00 36.33 2.85
3239 7911 3.461773 CCTCCATCGGCCAGACGT 61.462 66.667 2.24 0.00 34.94 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.656441 CAGGTGCAAGGTCACAAGC 59.344 57.895 0.00 0.00 38.66 4.01
3 4 2.382770 ACCCAGGTGCAAGGTCACA 61.383 57.895 0.00 0.00 38.66 3.58
4 5 1.898574 CACCCAGGTGCAAGGTCAC 60.899 63.158 3.41 0.00 39.39 3.67
5 6 2.515398 CACCCAGGTGCAAGGTCA 59.485 61.111 3.41 0.00 39.39 4.02
21 22 2.268762 TACATGGCTTGTGAAGTGCA 57.731 45.000 15.57 0.00 39.48 4.57
22 23 2.554032 AGTTACATGGCTTGTGAAGTGC 59.446 45.455 15.57 0.00 39.48 4.40
24 25 3.820557 ACAGTTACATGGCTTGTGAAGT 58.179 40.909 15.57 7.38 39.48 3.01
26 27 4.968259 AGTACAGTTACATGGCTTGTGAA 58.032 39.130 15.57 4.32 39.48 3.18
27 28 4.617253 AGTACAGTTACATGGCTTGTGA 57.383 40.909 15.57 5.11 39.48 3.58
29 30 4.968259 TGAAGTACAGTTACATGGCTTGT 58.032 39.130 11.04 11.04 42.62 3.16
30 31 5.877012 AGATGAAGTACAGTTACATGGCTTG 59.123 40.000 0.00 0.00 0.00 4.01
31 32 5.877012 CAGATGAAGTACAGTTACATGGCTT 59.123 40.000 0.00 0.00 0.00 4.35
32 33 5.423015 CAGATGAAGTACAGTTACATGGCT 58.577 41.667 0.00 0.00 0.00 4.75
33 34 4.572389 CCAGATGAAGTACAGTTACATGGC 59.428 45.833 0.00 0.00 0.00 4.40
35 36 5.423015 AGCCAGATGAAGTACAGTTACATG 58.577 41.667 0.00 0.00 0.00 3.21
37 38 5.483685 AAGCCAGATGAAGTACAGTTACA 57.516 39.130 0.00 0.00 0.00 2.41
38 39 6.018669 GCATAAGCCAGATGAAGTACAGTTAC 60.019 42.308 0.00 0.00 33.58 2.50
39 40 6.049149 GCATAAGCCAGATGAAGTACAGTTA 58.951 40.000 0.00 0.00 33.58 2.24
40 41 4.878397 GCATAAGCCAGATGAAGTACAGTT 59.122 41.667 0.00 0.00 33.58 3.16
59 60 9.219603 CCGATCTTATATTTCAAAAGAGGCATA 57.780 33.333 0.00 0.00 33.05 3.14
61 62 6.017109 GCCGATCTTATATTTCAAAAGAGGCA 60.017 38.462 9.16 0.00 39.02 4.75
64 65 7.355778 GTGGCCGATCTTATATTTCAAAAGAG 58.644 38.462 0.00 0.00 33.05 2.85
65 66 6.018262 CGTGGCCGATCTTATATTTCAAAAGA 60.018 38.462 0.00 0.00 35.63 2.52
66 67 6.018262 TCGTGGCCGATCTTATATTTCAAAAG 60.018 38.462 0.00 0.00 38.40 2.27
67 68 5.818336 TCGTGGCCGATCTTATATTTCAAAA 59.182 36.000 0.00 0.00 38.40 2.44
68 69 5.361427 TCGTGGCCGATCTTATATTTCAAA 58.639 37.500 0.00 0.00 38.40 2.69
73 74 2.960819 GCTCGTGGCCGATCTTATATT 58.039 47.619 0.00 0.00 43.27 1.28
74 75 2.656560 GCTCGTGGCCGATCTTATAT 57.343 50.000 0.00 0.00 43.27 0.86
85 86 0.107654 ATAAGAAGGTGGCTCGTGGC 60.108 55.000 3.80 3.80 40.90 5.01
86 87 2.403252 AATAAGAAGGTGGCTCGTGG 57.597 50.000 0.00 0.00 0.00 4.94
89 90 5.371115 TTTGAAAATAAGAAGGTGGCTCG 57.629 39.130 0.00 0.00 0.00 5.03
110 111 7.035612 AGCTTGAGAACAAACGATTTCTTTTT 58.964 30.769 0.00 0.00 35.49 1.94
111 112 6.564328 AGCTTGAGAACAAACGATTTCTTTT 58.436 32.000 0.00 0.00 35.49 2.27
113 114 5.296780 TGAGCTTGAGAACAAACGATTTCTT 59.703 36.000 0.00 0.00 35.49 2.52
114 115 4.816385 TGAGCTTGAGAACAAACGATTTCT 59.184 37.500 0.00 0.00 35.49 2.52
115 116 5.095691 TGAGCTTGAGAACAAACGATTTC 57.904 39.130 0.00 0.00 35.49 2.17
117 118 5.335191 GGAATGAGCTTGAGAACAAACGATT 60.335 40.000 0.00 0.00 35.49 3.34
120 121 3.250762 TGGAATGAGCTTGAGAACAAACG 59.749 43.478 0.00 0.00 35.49 3.60
121 122 4.836125 TGGAATGAGCTTGAGAACAAAC 57.164 40.909 0.00 0.00 35.49 2.93
136 137 1.131126 GAACACGCTGTCCATGGAATG 59.869 52.381 18.20 13.29 46.21 2.67
139 140 1.003839 GGAACACGCTGTCCATGGA 60.004 57.895 11.44 11.44 0.00 3.41
142 143 1.204146 ATAGGGAACACGCTGTCCAT 58.796 50.000 0.00 0.00 0.00 3.41
143 144 0.981183 AATAGGGAACACGCTGTCCA 59.019 50.000 0.00 0.00 0.00 4.02
144 145 1.207329 AGAATAGGGAACACGCTGTCC 59.793 52.381 0.00 0.00 0.00 4.02
145 146 2.541556 GAGAATAGGGAACACGCTGTC 58.458 52.381 0.00 0.00 0.00 3.51
147 148 1.802880 CGGAGAATAGGGAACACGCTG 60.803 57.143 0.00 0.00 0.00 5.18
148 149 0.460311 CGGAGAATAGGGAACACGCT 59.540 55.000 0.00 0.00 0.00 5.07
149 150 0.529992 CCGGAGAATAGGGAACACGC 60.530 60.000 0.00 0.00 0.00 5.34
150 151 0.822164 ACCGGAGAATAGGGAACACG 59.178 55.000 9.46 0.00 0.00 4.49
151 152 1.742750 GCACCGGAGAATAGGGAACAC 60.743 57.143 9.46 0.00 0.00 3.32
188 189 1.069090 ACTGCGACCAAAGAGCGAA 59.931 52.632 0.00 0.00 0.00 4.70
215 216 2.290896 CCCTATGGTTTGCAGGACAGAA 60.291 50.000 4.91 0.00 0.00 3.02
248 249 1.329906 CTGAATCATCTCCGTTGCAGC 59.670 52.381 0.00 0.00 0.00 5.25
249 250 2.897436 TCTGAATCATCTCCGTTGCAG 58.103 47.619 0.00 0.00 0.00 4.41
255 256 3.677121 CGCCTTATTCTGAATCATCTCCG 59.323 47.826 6.10 0.75 0.00 4.63
285 286 5.714333 TGATGGCAACCTAAAATAAGCTGAA 59.286 36.000 0.00 0.00 0.00 3.02
293 294 3.099141 CACCCTGATGGCAACCTAAAAT 58.901 45.455 0.00 0.00 37.83 1.82
298 299 1.729267 AACCACCCTGATGGCAACCT 61.729 55.000 0.00 0.00 44.33 3.50
330 4659 0.537188 CACAGCAGGTACTACCCAGG 59.463 60.000 1.19 0.00 39.75 4.45
340 4669 1.772819 AAGCAGCCTACACAGCAGGT 61.773 55.000 0.00 0.00 35.45 4.00
420 4755 1.072965 AGCAGGAGTTTCAGTGGGAAG 59.927 52.381 0.00 0.00 36.72 3.46
515 4850 4.196193 CGCTTCTCACACCCCAAATATAA 58.804 43.478 0.00 0.00 0.00 0.98
613 4948 6.717289 ACAAGCTACCAAATTACATACCTCA 58.283 36.000 0.00 0.00 0.00 3.86
619 4954 5.301805 GGGCATACAAGCTACCAAATTACAT 59.698 40.000 0.00 0.00 34.17 2.29
635 4970 6.882768 AAATTTTATTCCTTGGGGCATACA 57.117 33.333 0.00 0.00 0.00 2.29
700 5035 4.887655 TCCTCTGTACATATTCTGCTTCGA 59.112 41.667 0.00 0.00 0.00 3.71
719 5055 5.303078 TCAGGCTCTACTCACATATTTCCTC 59.697 44.000 0.00 0.00 0.00 3.71
720 5056 5.211973 TCAGGCTCTACTCACATATTTCCT 58.788 41.667 0.00 0.00 0.00 3.36
721 5057 5.537300 TCAGGCTCTACTCACATATTTCC 57.463 43.478 0.00 0.00 0.00 3.13
722 5058 9.717942 AAATATCAGGCTCTACTCACATATTTC 57.282 33.333 0.00 0.00 0.00 2.17
727 5115 7.129457 TGAAAATATCAGGCTCTACTCACAT 57.871 36.000 0.00 0.00 33.04 3.21
728 5116 6.544928 TGAAAATATCAGGCTCTACTCACA 57.455 37.500 0.00 0.00 33.04 3.58
777 5166 3.426568 GGCGCTGAGGTTGCACTC 61.427 66.667 7.64 0.00 37.99 3.51
780 5169 2.390306 TACAAGGCGCTGAGGTTGCA 62.390 55.000 7.64 0.00 0.00 4.08
783 5172 0.460284 CGATACAAGGCGCTGAGGTT 60.460 55.000 7.64 0.00 0.00 3.50
790 5179 0.801067 AGACGAACGATACAAGGCGC 60.801 55.000 0.00 0.00 0.00 6.53
807 5196 5.241949 ACAACAACCAAACAAAGTACACAGA 59.758 36.000 0.00 0.00 0.00 3.41
809 5198 5.455056 ACAACAACCAAACAAAGTACACA 57.545 34.783 0.00 0.00 0.00 3.72
831 5220 6.457257 GCTTTCGACCCGCTTTGTATATAAAA 60.457 38.462 0.00 0.00 0.00 1.52
840 5229 1.966451 AGGCTTTCGACCCGCTTTG 60.966 57.895 0.00 0.00 0.00 2.77
968 5400 8.863872 AGGTATTTGAGTTAAACTTACAGCAT 57.136 30.769 0.00 0.00 0.00 3.79
982 5414 5.416952 CCAGCATTTCTGAAGGTATTTGAGT 59.583 40.000 0.00 0.00 45.72 3.41
1051 5487 5.179368 TCAACTTGCTAAGACACAATGTAGC 59.821 40.000 0.00 0.00 31.87 3.58
1056 5492 6.095440 ACAAACTCAACTTGCTAAGACACAAT 59.905 34.615 3.37 0.00 0.00 2.71
1162 5633 4.800249 GCAGATCCTGAGAGCTATTCTTGG 60.800 50.000 0.00 0.00 36.33 3.61
1352 5823 1.516386 CATGAGCCGTCGTAAGCGT 60.516 57.895 0.00 0.00 39.49 5.07
1431 5905 4.076394 GTTGGGGTAAGCACATAAACAGA 58.924 43.478 0.00 0.00 0.00 3.41
1642 6116 3.304592 CGCATTGTTGATTGACTGGTTGA 60.305 43.478 0.00 0.00 0.00 3.18
1933 6407 8.090831 GTGCAAAGGGAAGAGAAAAATCTAAAT 58.909 33.333 0.00 0.00 0.00 1.40
2017 6607 5.257082 AGCTTACGTTTGTGGTTCAATTT 57.743 34.783 0.00 0.00 35.84 1.82
2192 6814 2.478292 ACGATTATCACCTTCCCACCT 58.522 47.619 0.00 0.00 0.00 4.00
2231 6853 4.046286 TGTAACAATCTCATTTGGCCCT 57.954 40.909 0.00 0.00 0.00 5.19
2373 6995 1.898863 ACAGATCTAACCCCCAGCAT 58.101 50.000 0.00 0.00 0.00 3.79
2410 7032 5.051816 CACATGATTTTGTGTGGAGCTTTT 58.948 37.500 0.00 0.00 41.65 2.27
2413 7035 3.928727 CACATGATTTTGTGTGGAGCT 57.071 42.857 0.00 0.00 41.65 4.09
2421 7043 8.506168 AATACGATTACTCCACATGATTTTGT 57.494 30.769 0.00 0.00 0.00 2.83
2455 7078 5.970317 ATGCTCTTCATGACATTTTGTGA 57.030 34.783 0.00 0.00 33.26 3.58
2516 7140 4.510167 AAGCTGGCAGTAAACATATCCT 57.490 40.909 17.16 0.00 0.00 3.24
2517 7141 6.672147 CAATAAGCTGGCAGTAAACATATCC 58.328 40.000 17.16 0.00 0.00 2.59
2529 7153 2.348660 GCAAAATGCAATAAGCTGGCA 58.651 42.857 0.00 5.28 44.26 4.92
2558 7182 3.924686 GGTAATCACTGGTCACAACTACG 59.075 47.826 0.00 0.00 0.00 3.51
2673 7299 9.823647 TCATTCATTATCTCCTTGAGAAAGTAC 57.176 33.333 0.00 0.00 42.27 2.73
2883 7510 9.415544 GGGCAATAGATTTATTCTTATTGCTTG 57.584 33.333 20.67 0.00 42.86 4.01
2891 7518 4.729868 AGCCGGGCAATAGATTTATTCTT 58.270 39.130 23.09 0.00 35.79 2.52
2893 7520 3.440522 GGAGCCGGGCAATAGATTTATTC 59.559 47.826 23.09 4.84 0.00 1.75
2894 7521 3.421844 GGAGCCGGGCAATAGATTTATT 58.578 45.455 23.09 0.00 0.00 1.40
2897 7524 0.178990 GGGAGCCGGGCAATAGATTT 60.179 55.000 23.09 0.00 0.00 2.17
2898 7525 1.352622 TGGGAGCCGGGCAATAGATT 61.353 55.000 23.09 0.00 0.00 2.40
2899 7526 1.770110 TGGGAGCCGGGCAATAGAT 60.770 57.895 23.09 0.00 0.00 1.98
2900 7527 2.366301 TGGGAGCCGGGCAATAGA 60.366 61.111 23.09 0.00 0.00 1.98
2901 7528 2.111878 CTGGGAGCCGGGCAATAG 59.888 66.667 23.09 9.80 0.00 1.73
2902 7529 2.366301 TCTGGGAGCCGGGCAATA 60.366 61.111 23.09 3.43 0.00 1.90
2903 7530 3.801997 CTCTGGGAGCCGGGCAAT 61.802 66.667 23.09 0.00 0.00 3.56
2917 7544 1.381463 GTTAGGGTCCGGCTCCTCT 60.381 63.158 16.98 12.79 34.75 3.69
2920 7547 2.594365 TAGGGTTAGGGTCCGGCTCC 62.594 65.000 0.00 0.97 0.00 4.70
2924 7551 2.138831 GGCTAGGGTTAGGGTCCGG 61.139 68.421 0.00 0.00 0.00 5.14
2925 7552 2.496291 CGGCTAGGGTTAGGGTCCG 61.496 68.421 0.00 0.00 0.00 4.79
2926 7553 2.804912 GCGGCTAGGGTTAGGGTCC 61.805 68.421 0.00 0.00 0.00 4.46
2927 7554 2.804912 GGCGGCTAGGGTTAGGGTC 61.805 68.421 0.00 0.00 0.00 4.46
2928 7555 2.767073 GGCGGCTAGGGTTAGGGT 60.767 66.667 0.00 0.00 0.00 4.34
2929 7556 2.446036 AGGCGGCTAGGGTTAGGG 60.446 66.667 11.03 0.00 0.00 3.53
3221 7893 3.461773 CGTCTGGCCGATGGAGGT 61.462 66.667 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.