Multiple sequence alignment - TraesCS3A01G245000

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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 TraesCS3A01G245000 chr3A 100.000 5372 0 0 1 5372 458683490 458678119 0.000000e+00 9921.0
1 TraesCS3A01G245000 chr3D 94.299 5385 131 69 96 5370 344337587 344342905 0.000000e+00 8082.0
2 TraesCS3A01G245000 chr3B 94.164 5072 122 69 388 5372 443803307 443808291 0.000000e+00 7566.0
3 TraesCS3A01G245000 chr3B 84.878 205 9 10 39 236 443802639 443802828 2.550000e-43 187.0
4 TraesCS3A01G245000 chr1B 82.751 858 96 32 965 1807 534298215 534299035 0.000000e+00 717.0
5 TraesCS3A01G245000 chr7A 85.283 530 66 6 996 1525 33657522 33658039 2.200000e-148 536.0
6 TraesCS3A01G245000 chr7A 90.129 233 22 1 1572 1803 33658041 33658273 8.740000e-78 302.0
7 TraesCS3A01G245000 chr7B 84.944 538 63 10 989 1525 622301295 622300775 3.680000e-146 529.0
8 TraesCS3A01G245000 chr7B 92.574 202 14 1 1572 1772 622300773 622300572 6.810000e-74 289.0
9 TraesCS3A01G245000 chr4A 81.550 542 63 14 989 1525 716835122 716834613 3.870000e-111 412.0
10 TraesCS3A01G245000 chr4A 88.618 246 19 3 1572 1808 716834611 716834366 1.890000e-74 291.0
11 TraesCS3A01G245000 chr6B 81.365 542 63 15 989 1525 244561784 244562292 1.800000e-109 407.0
12 TraesCS3A01G245000 chr6B 91.597 238 19 1 1572 1808 244562294 244562531 1.440000e-85 327.0
13 TraesCS3A01G245000 chr6B 88.679 106 11 1 1572 1676 693888104 693887999 1.570000e-25 128.0
14 TraesCS3A01G245000 chr6B 86.076 79 9 1 1729 1807 693888012 693887936 3.450000e-12 84.2
15 TraesCS3A01G245000 chr5B 77.391 690 149 6 3350 4034 320153339 320152652 2.330000e-108 403.0
16 TraesCS3A01G245000 chr4B 90.833 240 20 2 1572 1809 613388609 613388848 2.410000e-83 320.0


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 TraesCS3A01G245000 chr3A 458678119 458683490 5371 True 9921.0 9921 100.000 1 5372 1 chr3A.!!$R1 5371
1 TraesCS3A01G245000 chr3D 344337587 344342905 5318 False 8082.0 8082 94.299 96 5370 1 chr3D.!!$F1 5274
2 TraesCS3A01G245000 chr3B 443802639 443808291 5652 False 3876.5 7566 89.521 39 5372 2 chr3B.!!$F1 5333
3 TraesCS3A01G245000 chr1B 534298215 534299035 820 False 717.0 717 82.751 965 1807 1 chr1B.!!$F1 842
4 TraesCS3A01G245000 chr7A 33657522 33658273 751 False 419.0 536 87.706 996 1803 2 chr7A.!!$F1 807
5 TraesCS3A01G245000 chr7B 622300572 622301295 723 True 409.0 529 88.759 989 1772 2 chr7B.!!$R1 783
6 TraesCS3A01G245000 chr4A 716834366 716835122 756 True 351.5 412 85.084 989 1808 2 chr4A.!!$R1 819
7 TraesCS3A01G245000 chr6B 244561784 244562531 747 False 367.0 407 86.481 989 1808 2 chr6B.!!$F1 819
8 TraesCS3A01G245000 chr5B 320152652 320153339 687 True 403.0 403 77.391 3350 4034 1 chr5B.!!$R1 684

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
98 99 0.096976 GAACCAGCGCGTACTACGTA 59.903 55.000 8.43 0.0 44.73 3.57 F
99 100 0.179189 AACCAGCGCGTACTACGTAC 60.179 55.000 8.43 0.0 44.73 3.67 F
700 1057 0.187361 TGCTTAGCTTTGGGTTGGGT 59.813 50.000 5.60 0.0 0.00 4.51 F
853 1228 0.744281 CCTCTCTCGCTTCTTCTCCC 59.256 60.000 0.00 0.0 0.00 4.30 F
936 1333 1.006519 CCACTCTCTCTCCCTTCTCCA 59.993 57.143 0.00 0.0 0.00 3.86 F
2115 2552 1.071471 CTCCAACTGCACCGACCTT 59.929 57.895 0.00 0.0 0.00 3.50 F
3120 3557 1.211457 CATACTGGGCAAGGCTCTTCT 59.789 52.381 0.00 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1952 0.827925 TTGCTGGACAGGTCGAGAGT 60.828 55.000 14.53 0.0 37.59 3.24 R
2013 2450 1.274703 TGGGATCTTGGCAGAGGGTC 61.275 60.000 0.00 0.0 30.36 4.46 R
2115 2552 0.322636 GACTGAGGTCGAGGGAGACA 60.323 60.000 0.00 0.0 42.62 3.41 R
2787 3224 0.676736 GCTCCTTGGGTATCTCGGAG 59.323 60.000 0.00 0.0 43.18 4.63 R
3063 3500 1.227823 TGGAAAGCCACACAGACCG 60.228 57.895 0.00 0.0 39.92 4.79 R
3762 4202 0.465460 TGCAGTTGTGGTGGAGGAAC 60.465 55.000 0.00 0.0 0.00 3.62 R
5034 5535 0.167908 CACCACACACACACACACAC 59.832 55.000 0.00 0.0 0.00 3.82 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
18 19 3.972107 ACGGTCTGCAAGTTTACGA 57.028 47.368 0.00 0.00 33.76 3.43
19 20 1.494824 ACGGTCTGCAAGTTTACGAC 58.505 50.000 0.00 0.00 33.76 4.34
20 21 1.068127 ACGGTCTGCAAGTTTACGACT 59.932 47.619 0.00 0.00 41.47 4.18
21 22 2.294233 ACGGTCTGCAAGTTTACGACTA 59.706 45.455 0.00 0.00 37.72 2.59
22 23 2.915463 CGGTCTGCAAGTTTACGACTAG 59.085 50.000 0.00 0.00 37.72 2.57
23 24 3.611057 CGGTCTGCAAGTTTACGACTAGT 60.611 47.826 0.00 0.00 37.72 2.57
24 25 4.378770 CGGTCTGCAAGTTTACGACTAGTA 60.379 45.833 0.00 0.00 37.72 1.82
25 26 5.464168 GGTCTGCAAGTTTACGACTAGTAA 58.536 41.667 0.00 0.00 43.05 2.24
26 27 5.572126 GGTCTGCAAGTTTACGACTAGTAAG 59.428 44.000 0.00 0.00 45.10 2.34
27 28 6.376978 GTCTGCAAGTTTACGACTAGTAAGA 58.623 40.000 0.00 0.00 45.10 2.10
28 29 6.305160 GTCTGCAAGTTTACGACTAGTAAGAC 59.695 42.308 0.00 0.00 45.10 3.01
29 30 5.149273 TGCAAGTTTACGACTAGTAAGACG 58.851 41.667 0.00 0.00 45.10 4.18
30 31 5.049474 TGCAAGTTTACGACTAGTAAGACGA 60.049 40.000 8.52 0.00 45.10 4.20
31 32 6.026513 GCAAGTTTACGACTAGTAAGACGAT 58.973 40.000 8.52 0.00 45.10 3.73
32 33 6.525976 GCAAGTTTACGACTAGTAAGACGATT 59.474 38.462 8.52 0.00 45.10 3.34
33 34 7.461156 GCAAGTTTACGACTAGTAAGACGATTG 60.461 40.741 8.52 5.36 45.10 2.67
34 35 7.138692 AGTTTACGACTAGTAAGACGATTGT 57.861 36.000 8.52 0.00 45.10 2.71
35 36 7.239972 AGTTTACGACTAGTAAGACGATTGTC 58.760 38.462 4.78 4.78 45.10 3.18
36 37 7.881859 AGTTTACGACTAGTAAGACGATTGTCG 60.882 40.741 7.46 10.39 45.10 4.35
51 52 3.278668 TTGTCGACTTGGGTTTTGGTA 57.721 42.857 17.92 0.00 0.00 3.25
63 64 3.494573 GGGTTTTGGTATTTTGCGGGAAA 60.495 43.478 0.00 0.00 0.00 3.13
64 65 3.495377 GGTTTTGGTATTTTGCGGGAAAC 59.505 43.478 0.00 0.00 0.00 2.78
94 95 2.486504 CCGAACCAGCGCGTACTA 59.513 61.111 8.43 0.00 0.00 1.82
95 96 1.870901 CCGAACCAGCGCGTACTAC 60.871 63.158 8.43 0.00 0.00 2.73
96 97 2.212983 CGAACCAGCGCGTACTACG 61.213 63.158 8.43 4.12 45.88 3.51
97 98 1.154150 GAACCAGCGCGTACTACGT 60.154 57.895 8.43 0.00 44.73 3.57
98 99 0.096976 GAACCAGCGCGTACTACGTA 59.903 55.000 8.43 0.00 44.73 3.57
99 100 0.179189 AACCAGCGCGTACTACGTAC 60.179 55.000 8.43 0.00 44.73 3.67
118 119 0.803380 CGGTTACGGTTAGCGAAGGG 60.803 60.000 11.70 0.00 38.68 3.95
120 121 1.633561 GTTACGGTTAGCGAAGGGTC 58.366 55.000 11.70 0.00 0.00 4.46
140 141 1.334329 CGAACAAACTAAACCACGGCC 60.334 52.381 0.00 0.00 0.00 6.13
288 296 3.396951 GGGGACGAGAGAGAGAGAG 57.603 63.158 0.00 0.00 0.00 3.20
289 297 0.834612 GGGGACGAGAGAGAGAGAGA 59.165 60.000 0.00 0.00 0.00 3.10
290 298 1.202651 GGGGACGAGAGAGAGAGAGAG 60.203 61.905 0.00 0.00 0.00 3.20
291 299 1.760613 GGGACGAGAGAGAGAGAGAGA 59.239 57.143 0.00 0.00 0.00 3.10
292 300 2.224066 GGGACGAGAGAGAGAGAGAGAG 60.224 59.091 0.00 0.00 0.00 3.20
293 301 2.693591 GGACGAGAGAGAGAGAGAGAGA 59.306 54.545 0.00 0.00 0.00 3.10
294 302 3.243569 GGACGAGAGAGAGAGAGAGAGAG 60.244 56.522 0.00 0.00 0.00 3.20
295 303 3.632333 ACGAGAGAGAGAGAGAGAGAGA 58.368 50.000 0.00 0.00 0.00 3.10
299 307 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
402 737 4.270008 CCCACCTCGGAATTAAAGACAAT 58.730 43.478 0.00 0.00 36.56 2.71
410 745 7.385778 TCGGAATTAAAGACAATAACCCTTG 57.614 36.000 0.00 0.00 0.00 3.61
430 765 4.043200 GAAGCAACGCAGCCCACC 62.043 66.667 0.00 0.00 34.23 4.61
498 846 3.343788 CTCGCTCCTCCACCACGAC 62.344 68.421 0.00 0.00 0.00 4.34
511 859 1.067669 ACCACGACGATGATGATGAGG 59.932 52.381 0.00 0.00 0.00 3.86
533 881 1.821136 CCAAAGCAGTCATTTCCTCCC 59.179 52.381 0.00 0.00 0.00 4.30
534 882 1.470098 CAAAGCAGTCATTTCCTCCCG 59.530 52.381 0.00 0.00 0.00 5.14
535 883 0.678048 AAGCAGTCATTTCCTCCCGC 60.678 55.000 0.00 0.00 0.00 6.13
652 1009 0.887387 TTGGCTGGTTGGTTAGCGTC 60.887 55.000 0.00 0.00 40.78 5.19
653 1010 2.388232 GGCTGGTTGGTTAGCGTCG 61.388 63.158 0.00 0.00 40.78 5.12
654 1011 3.023591 GCTGGTTGGTTAGCGTCGC 62.024 63.158 9.80 9.80 0.00 5.19
655 1012 2.357760 TGGTTGGTTAGCGTCGCC 60.358 61.111 14.86 0.00 0.00 5.54
697 1054 0.240945 CCGTGCTTAGCTTTGGGTTG 59.759 55.000 5.60 0.00 0.00 3.77
698 1055 0.240945 CGTGCTTAGCTTTGGGTTGG 59.759 55.000 5.60 0.00 0.00 3.77
699 1056 0.603065 GTGCTTAGCTTTGGGTTGGG 59.397 55.000 5.60 0.00 0.00 4.12
700 1057 0.187361 TGCTTAGCTTTGGGTTGGGT 59.813 50.000 5.60 0.00 0.00 4.51
701 1058 1.338107 GCTTAGCTTTGGGTTGGGTT 58.662 50.000 0.00 0.00 0.00 4.11
702 1059 2.158445 TGCTTAGCTTTGGGTTGGGTTA 60.158 45.455 5.60 0.00 0.00 2.85
703 1060 2.492088 GCTTAGCTTTGGGTTGGGTTAG 59.508 50.000 0.00 0.00 0.00 2.34
851 1226 1.676006 CCTCCTCTCTCGCTTCTTCTC 59.324 57.143 0.00 0.00 0.00 2.87
852 1227 1.676006 CTCCTCTCTCGCTTCTTCTCC 59.324 57.143 0.00 0.00 0.00 3.71
853 1228 0.744281 CCTCTCTCGCTTCTTCTCCC 59.256 60.000 0.00 0.00 0.00 4.30
854 1229 1.684869 CCTCTCTCGCTTCTTCTCCCT 60.685 57.143 0.00 0.00 0.00 4.20
855 1230 2.099405 CTCTCTCGCTTCTTCTCCCTT 58.901 52.381 0.00 0.00 0.00 3.95
856 1231 2.096248 TCTCTCGCTTCTTCTCCCTTC 58.904 52.381 0.00 0.00 0.00 3.46
857 1232 2.099405 CTCTCGCTTCTTCTCCCTTCT 58.901 52.381 0.00 0.00 0.00 2.85
858 1233 2.096248 TCTCGCTTCTTCTCCCTTCTC 58.904 52.381 0.00 0.00 0.00 2.87
859 1234 2.099405 CTCGCTTCTTCTCCCTTCTCT 58.901 52.381 0.00 0.00 0.00 3.10
860 1235 2.096248 TCGCTTCTTCTCCCTTCTCTC 58.904 52.381 0.00 0.00 0.00 3.20
861 1236 2.099405 CGCTTCTTCTCCCTTCTCTCT 58.901 52.381 0.00 0.00 0.00 3.10
862 1237 2.099098 CGCTTCTTCTCCCTTCTCTCTC 59.901 54.545 0.00 0.00 0.00 3.20
863 1238 2.430694 GCTTCTTCTCCCTTCTCTCTCC 59.569 54.545 0.00 0.00 0.00 3.71
864 1239 2.428544 TCTTCTCCCTTCTCTCTCCG 57.571 55.000 0.00 0.00 0.00 4.63
865 1240 1.636519 TCTTCTCCCTTCTCTCTCCGT 59.363 52.381 0.00 0.00 0.00 4.69
866 1241 2.021457 CTTCTCCCTTCTCTCTCCGTC 58.979 57.143 0.00 0.00 0.00 4.79
926 1323 1.272985 CCCTCACTTCCCACTCTCTCT 60.273 57.143 0.00 0.00 0.00 3.10
928 1325 2.099405 CTCACTTCCCACTCTCTCTCC 58.901 57.143 0.00 0.00 0.00 3.71
930 1327 1.089123 ACTTCCCACTCTCTCTCCCT 58.911 55.000 0.00 0.00 0.00 4.20
935 1332 1.687996 CCCACTCTCTCTCCCTTCTCC 60.688 61.905 0.00 0.00 0.00 3.71
936 1333 1.006519 CCACTCTCTCTCCCTTCTCCA 59.993 57.143 0.00 0.00 0.00 3.86
970 1377 1.075425 CTTCTGCAGACCGCTTCTCG 61.075 60.000 18.03 0.00 43.06 4.04
997 1404 1.153549 CAAGGTAGAGCGTGCTCCC 60.154 63.158 17.76 12.77 43.70 4.30
1460 1886 1.811266 CGCTGAATCTGTCCGGTGG 60.811 63.158 0.00 0.00 0.00 4.61
2115 2552 1.071471 CTCCAACTGCACCGACCTT 59.929 57.895 0.00 0.00 0.00 3.50
2424 2861 2.593257 GCAATCTTGAAGCTGAGCAAC 58.407 47.619 7.39 0.00 0.00 4.17
2658 3095 2.102252 GGAGTTCTCAAGCATCCGATCT 59.898 50.000 2.24 0.00 0.00 2.75
2772 3209 6.263842 GCTCCATGATATTTCTGGATTTGTCA 59.736 38.462 0.00 0.00 38.36 3.58
2787 3224 6.183360 TGGATTTGTCATTTAATCAGCTCGAC 60.183 38.462 0.00 0.00 33.43 4.20
3063 3500 5.799827 AGAGCCAGTATGAGAATAACTCC 57.200 43.478 0.00 0.00 44.34 3.85
3069 3506 5.508153 CCAGTATGAGAATAACTCCGGTCTG 60.508 48.000 0.00 0.00 44.34 3.51
3094 3531 2.221906 CTTTCCACTGCCAGCATGCC 62.222 60.000 15.66 0.00 31.97 4.40
3097 3534 2.675423 CACTGCCAGCATGCCAGT 60.675 61.111 18.78 18.78 31.97 4.00
3120 3557 1.211457 CATACTGGGCAAGGCTCTTCT 59.789 52.381 0.00 0.00 0.00 2.85
3198 3635 1.991965 CTCTTGTTCTCGCTCTTCTGC 59.008 52.381 0.00 0.00 0.00 4.26
3219 3656 4.341806 TGCATATTTGGGTTGGTCATCATC 59.658 41.667 0.00 0.00 0.00 2.92
3471 3908 3.433598 CCGGTGGATTTGGTGATGTCTAT 60.434 47.826 0.00 0.00 0.00 1.98
3762 4202 2.768492 GGCAGCAAGAGGATTGGCG 61.768 63.158 0.00 0.00 0.00 5.69
3789 4229 1.614903 CACCACAACTGCATTCCACAT 59.385 47.619 0.00 0.00 0.00 3.21
3846 4286 2.419159 CGTTGATGAGAATCTGGAGGCA 60.419 50.000 0.00 0.00 34.92 4.75
3861 4301 3.078891 GAGGCAAGGGTCTCAGATTTT 57.921 47.619 0.00 0.00 45.28 1.82
3987 4427 0.107214 CCACCAAGGGCGATGTGTAT 60.107 55.000 0.00 0.00 0.00 2.29
4105 4545 3.607422 TGCACACAAAGTTGAAGATCG 57.393 42.857 0.00 0.00 0.00 3.69
4143 4583 1.522580 GCTGCTGAAGGACGATCCC 60.523 63.158 0.00 0.00 37.19 3.85
4210 4650 3.391665 CTGGATGACAGGCCGTCCC 62.392 68.421 20.21 16.18 44.71 4.46
4434 4874 3.908081 AGCAACACGTCCGTCCGT 61.908 61.111 0.00 0.00 42.87 4.69
4435 4875 3.400590 GCAACACGTCCGTCCGTC 61.401 66.667 0.00 0.00 39.45 4.79
4436 4876 2.732094 CAACACGTCCGTCCGTCC 60.732 66.667 0.00 0.00 39.45 4.79
4437 4877 3.218470 AACACGTCCGTCCGTCCA 61.218 61.111 0.00 0.00 39.45 4.02
4438 4878 2.567497 AACACGTCCGTCCGTCCAT 61.567 57.895 0.00 0.00 39.45 3.41
4444 4884 1.608336 TCCGTCCGTCCATCCAGTT 60.608 57.895 0.00 0.00 0.00 3.16
4505 4947 3.327172 AGATGCTGATACCATCCTGAAGG 59.673 47.826 0.00 0.00 39.87 3.46
4581 5027 1.286248 TTTCCCTCCCTTGTAGCTCC 58.714 55.000 0.00 0.00 0.00 4.70
4596 5042 1.221021 CTCCCGTAAGTCCCAAGCC 59.779 63.158 0.00 0.00 0.00 4.35
4683 5129 3.678072 TCAGCTCCTCGTTTATTTTGTCG 59.322 43.478 0.00 0.00 0.00 4.35
4696 5142 0.883153 TTTGTCGTAGCGCTCCAGTA 59.117 50.000 16.34 0.00 0.00 2.74
4761 5234 1.203287 GCAAATTCCCTCCACTGCTTC 59.797 52.381 0.00 0.00 0.00 3.86
4764 5237 3.922171 AATTCCCTCCACTGCTTCTAG 57.078 47.619 0.00 0.00 0.00 2.43
4765 5238 2.327325 TTCCCTCCACTGCTTCTAGT 57.673 50.000 0.00 0.00 0.00 2.57
4777 5250 2.878406 TGCTTCTAGTGTTCTTGTTGCC 59.122 45.455 0.00 0.00 0.00 4.52
4809 5283 3.552684 GCTGGCATTTGTACAATGTGTGT 60.553 43.478 9.56 0.00 44.82 3.72
4810 5284 4.619973 CTGGCATTTGTACAATGTGTGTT 58.380 39.130 9.56 0.00 41.98 3.32
4815 5289 5.059587 GCATTTGTACAATGTGTGTTCATCG 59.940 40.000 9.56 0.00 41.98 3.84
4823 5297 3.401033 TGTGTGTTCATCGGTTGATCT 57.599 42.857 0.00 0.00 33.34 2.75
4837 5311 5.104693 TCGGTTGATCTAAACATGGTACCAT 60.105 40.000 22.23 22.23 37.08 3.55
4863 5337 2.431057 AGATGCACGGTAGAAACCCTAG 59.569 50.000 0.00 0.00 43.54 3.02
4906 5402 1.971695 GGGTTGGGCAGTGCAGTAC 60.972 63.158 18.61 10.53 0.00 2.73
4907 5403 1.073199 GGTTGGGCAGTGCAGTACT 59.927 57.895 18.61 0.00 41.36 2.73
4954 5455 2.281761 AGGCCAAGGTGAACAGCG 60.282 61.111 5.01 0.00 0.00 5.18
5041 5542 4.626081 GGCCTCGCCTGTGTGTGT 62.626 66.667 0.00 0.00 46.69 3.72
5042 5543 3.349006 GCCTCGCCTGTGTGTGTG 61.349 66.667 0.00 0.00 0.00 3.82
5043 5544 2.108976 CCTCGCCTGTGTGTGTGT 59.891 61.111 0.00 0.00 0.00 3.72
5044 5545 2.246739 CCTCGCCTGTGTGTGTGTG 61.247 63.158 0.00 0.00 0.00 3.82
5045 5546 1.521457 CTCGCCTGTGTGTGTGTGT 60.521 57.895 0.00 0.00 0.00 3.72
5046 5547 1.765161 CTCGCCTGTGTGTGTGTGTG 61.765 60.000 0.00 0.00 0.00 3.82
5047 5548 2.106074 CGCCTGTGTGTGTGTGTGT 61.106 57.895 0.00 0.00 0.00 3.72
5048 5549 1.429021 GCCTGTGTGTGTGTGTGTG 59.571 57.895 0.00 0.00 0.00 3.82
5049 5550 1.305219 GCCTGTGTGTGTGTGTGTGT 61.305 55.000 0.00 0.00 0.00 3.72
5050 5551 0.447406 CCTGTGTGTGTGTGTGTGTG 59.553 55.000 0.00 0.00 0.00 3.82
5134 5639 4.234574 CACGGCCACCTTTCTTTAATTTC 58.765 43.478 2.24 0.00 0.00 2.17
5251 5756 3.814842 TGCTTATCTTAATCGCATGGGTG 59.185 43.478 9.86 0.00 0.00 4.61
5252 5757 3.189287 GCTTATCTTAATCGCATGGGTGG 59.811 47.826 9.86 0.00 0.00 4.61
5253 5758 1.609208 ATCTTAATCGCATGGGTGGC 58.391 50.000 9.86 0.00 0.00 5.01
5284 5789 1.207329 CTCGCCCTATTATACTGCCCC 59.793 57.143 0.00 0.00 0.00 5.80
5345 5850 4.276183 GCTTAGGCCTTGCTAAACTAATCC 59.724 45.833 12.58 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.068127 AGTCGTAAACTTGCAGACCGT 59.932 47.619 0.00 0.00 33.03 4.83
1 2 1.779569 AGTCGTAAACTTGCAGACCG 58.220 50.000 0.00 0.00 33.03 4.79
4 5 6.376978 GTCTTACTAGTCGTAAACTTGCAGA 58.623 40.000 0.00 0.00 39.55 4.26
5 6 5.283247 CGTCTTACTAGTCGTAAACTTGCAG 59.717 44.000 0.00 0.00 39.55 4.41
6 7 5.049474 TCGTCTTACTAGTCGTAAACTTGCA 60.049 40.000 0.00 0.00 39.55 4.08
7 8 5.385617 TCGTCTTACTAGTCGTAAACTTGC 58.614 41.667 0.00 0.00 39.55 4.01
8 9 7.536622 ACAATCGTCTTACTAGTCGTAAACTTG 59.463 37.037 0.00 0.58 39.55 3.16
9 10 7.588512 ACAATCGTCTTACTAGTCGTAAACTT 58.411 34.615 0.00 0.00 39.55 2.66
10 11 7.138692 ACAATCGTCTTACTAGTCGTAAACT 57.861 36.000 0.00 0.00 42.33 2.66
11 12 6.191775 CGACAATCGTCTTACTAGTCGTAAAC 59.808 42.308 0.00 0.00 41.49 2.01
12 13 6.090763 TCGACAATCGTCTTACTAGTCGTAAA 59.909 38.462 0.00 0.00 45.19 2.01
13 14 5.576774 TCGACAATCGTCTTACTAGTCGTAA 59.423 40.000 0.00 0.00 45.19 3.18
14 15 5.004821 GTCGACAATCGTCTTACTAGTCGTA 59.995 44.000 11.55 0.00 45.19 3.43
15 16 3.928992 TCGACAATCGTCTTACTAGTCGT 59.071 43.478 0.00 0.00 45.19 4.34
16 17 4.032672 AGTCGACAATCGTCTTACTAGTCG 59.967 45.833 19.50 0.00 46.00 4.18
17 18 5.467902 AGTCGACAATCGTCTTACTAGTC 57.532 43.478 19.50 0.00 41.35 2.59
18 19 5.391736 CCAAGTCGACAATCGTCTTACTAGT 60.392 44.000 19.50 0.00 43.94 2.57
19 20 5.029014 CCAAGTCGACAATCGTCTTACTAG 58.971 45.833 19.50 0.00 43.94 2.57
20 21 4.142534 CCCAAGTCGACAATCGTCTTACTA 60.143 45.833 19.50 0.00 43.94 1.82
21 22 3.367087 CCCAAGTCGACAATCGTCTTACT 60.367 47.826 19.50 0.00 43.94 2.24
22 23 2.921754 CCCAAGTCGACAATCGTCTTAC 59.078 50.000 19.50 0.00 43.94 2.34
23 24 2.559668 ACCCAAGTCGACAATCGTCTTA 59.440 45.455 19.50 0.00 43.94 2.10
24 25 1.343465 ACCCAAGTCGACAATCGTCTT 59.657 47.619 19.50 5.15 45.93 3.01
25 26 0.966920 ACCCAAGTCGACAATCGTCT 59.033 50.000 19.50 0.00 39.73 4.18
26 27 1.792006 AACCCAAGTCGACAATCGTC 58.208 50.000 19.50 0.00 41.35 4.20
27 28 2.249844 AAACCCAAGTCGACAATCGT 57.750 45.000 19.50 5.44 41.35 3.73
28 29 2.350388 CCAAAACCCAAGTCGACAATCG 60.350 50.000 19.50 4.76 42.10 3.34
29 30 2.621526 ACCAAAACCCAAGTCGACAATC 59.378 45.455 19.50 0.00 0.00 2.67
30 31 2.661718 ACCAAAACCCAAGTCGACAAT 58.338 42.857 19.50 2.80 0.00 2.71
31 32 2.131776 ACCAAAACCCAAGTCGACAA 57.868 45.000 19.50 0.00 0.00 3.18
32 33 3.495434 ATACCAAAACCCAAGTCGACA 57.505 42.857 19.50 0.00 0.00 4.35
33 34 4.841443 AAATACCAAAACCCAAGTCGAC 57.159 40.909 7.70 7.70 0.00 4.20
34 35 4.500035 GCAAAATACCAAAACCCAAGTCGA 60.500 41.667 0.00 0.00 0.00 4.20
35 36 3.738791 GCAAAATACCAAAACCCAAGTCG 59.261 43.478 0.00 0.00 0.00 4.18
36 37 3.738791 CGCAAAATACCAAAACCCAAGTC 59.261 43.478 0.00 0.00 0.00 3.01
37 38 3.493524 CCGCAAAATACCAAAACCCAAGT 60.494 43.478 0.00 0.00 0.00 3.16
38 39 3.063485 CCGCAAAATACCAAAACCCAAG 58.937 45.455 0.00 0.00 0.00 3.61
39 40 2.224305 CCCGCAAAATACCAAAACCCAA 60.224 45.455 0.00 0.00 0.00 4.12
40 41 1.344763 CCCGCAAAATACCAAAACCCA 59.655 47.619 0.00 0.00 0.00 4.51
41 42 1.619332 TCCCGCAAAATACCAAAACCC 59.381 47.619 0.00 0.00 0.00 4.11
42 43 3.388345 TTCCCGCAAAATACCAAAACC 57.612 42.857 0.00 0.00 0.00 3.27
43 44 4.210328 CAGTTTCCCGCAAAATACCAAAAC 59.790 41.667 0.00 0.00 0.00 2.43
51 52 1.940752 GCATGCAGTTTCCCGCAAAAT 60.941 47.619 14.21 0.00 42.37 1.82
96 97 2.177173 CTTCGCTAACCGTAACCGTAC 58.823 52.381 0.00 0.00 38.35 3.67
97 98 1.132262 CCTTCGCTAACCGTAACCGTA 59.868 52.381 0.00 0.00 38.35 4.02
98 99 0.109132 CCTTCGCTAACCGTAACCGT 60.109 55.000 0.00 0.00 38.35 4.83
99 100 0.803380 CCCTTCGCTAACCGTAACCG 60.803 60.000 0.00 0.00 38.35 4.44
100 101 0.247460 ACCCTTCGCTAACCGTAACC 59.753 55.000 0.00 0.00 38.35 2.85
101 102 1.633561 GACCCTTCGCTAACCGTAAC 58.366 55.000 0.00 0.00 38.35 2.50
102 103 0.171007 CGACCCTTCGCTAACCGTAA 59.829 55.000 0.00 0.00 38.71 3.18
118 119 2.600556 GCCGTGGTTTAGTTTGTTCGAC 60.601 50.000 0.00 0.00 0.00 4.20
120 121 1.334329 GGCCGTGGTTTAGTTTGTTCG 60.334 52.381 0.00 0.00 0.00 3.95
283 291 0.469917 CCCGCTCTCTCTCTCTCTCT 59.530 60.000 0.00 0.00 0.00 3.10
287 295 2.600731 CCCCCGCTCTCTCTCTCT 59.399 66.667 0.00 0.00 0.00 3.10
288 296 3.223589 GCCCCCGCTCTCTCTCTC 61.224 72.222 0.00 0.00 0.00 3.20
289 297 2.887738 AATGCCCCCGCTCTCTCTCT 62.888 60.000 0.00 0.00 35.36 3.10
290 298 2.439104 AATGCCCCCGCTCTCTCTC 61.439 63.158 0.00 0.00 35.36 3.20
291 299 2.366167 AATGCCCCCGCTCTCTCT 60.366 61.111 0.00 0.00 35.36 3.10
292 300 2.203126 CAATGCCCCCGCTCTCTC 60.203 66.667 0.00 0.00 35.36 3.20
293 301 3.011517 ACAATGCCCCCGCTCTCT 61.012 61.111 0.00 0.00 35.36 3.10
294 302 2.825836 CACAATGCCCCCGCTCTC 60.826 66.667 0.00 0.00 35.36 3.20
295 303 4.431131 CCACAATGCCCCCGCTCT 62.431 66.667 0.00 0.00 35.36 4.09
299 307 4.820744 CTCCCCACAATGCCCCCG 62.821 72.222 0.00 0.00 0.00 5.73
402 737 1.231958 CGTTGCTTCGCCAAGGGTTA 61.232 55.000 0.00 0.00 0.00 2.85
498 846 1.878088 CTTTGGGCCTCATCATCATCG 59.122 52.381 4.53 0.00 0.00 3.84
511 859 1.203287 GAGGAAATGACTGCTTTGGGC 59.797 52.381 0.00 0.00 42.22 5.36
631 988 1.586154 CGCTAACCAACCAGCCAAGG 61.586 60.000 0.00 0.00 34.15 3.61
633 990 0.887387 GACGCTAACCAACCAGCCAA 60.887 55.000 0.00 0.00 34.15 4.52
634 991 1.302192 GACGCTAACCAACCAGCCA 60.302 57.895 0.00 0.00 34.15 4.75
635 992 2.388232 CGACGCTAACCAACCAGCC 61.388 63.158 0.00 0.00 34.15 4.85
636 993 3.023591 GCGACGCTAACCAACCAGC 62.024 63.158 13.73 0.00 0.00 4.85
697 1054 6.238566 GCGATTTGATTAACCTAACCTAACCC 60.239 42.308 0.00 0.00 0.00 4.11
698 1055 6.316890 TGCGATTTGATTAACCTAACCTAACC 59.683 38.462 0.00 0.00 0.00 2.85
699 1056 7.184779 GTGCGATTTGATTAACCTAACCTAAC 58.815 38.462 0.00 0.00 0.00 2.34
700 1057 6.316890 GGTGCGATTTGATTAACCTAACCTAA 59.683 38.462 0.00 0.00 0.00 2.69
701 1058 5.818857 GGTGCGATTTGATTAACCTAACCTA 59.181 40.000 0.00 0.00 0.00 3.08
702 1059 4.638865 GGTGCGATTTGATTAACCTAACCT 59.361 41.667 0.00 0.00 0.00 3.50
703 1060 4.495184 CGGTGCGATTTGATTAACCTAACC 60.495 45.833 0.00 0.00 0.00 2.85
830 1193 0.102300 GAAGAAGCGAGAGAGGAGGC 59.898 60.000 0.00 0.00 0.00 4.70
831 1194 1.676006 GAGAAGAAGCGAGAGAGGAGG 59.324 57.143 0.00 0.00 0.00 4.30
851 1226 1.758906 GGGGACGGAGAGAGAAGGG 60.759 68.421 0.00 0.00 0.00 3.95
852 1227 1.758906 GGGGGACGGAGAGAGAAGG 60.759 68.421 0.00 0.00 0.00 3.46
853 1228 0.753848 GAGGGGGACGGAGAGAGAAG 60.754 65.000 0.00 0.00 0.00 2.85
854 1229 1.215679 AGAGGGGGACGGAGAGAGAA 61.216 60.000 0.00 0.00 0.00 2.87
855 1230 1.215679 AAGAGGGGGACGGAGAGAGA 61.216 60.000 0.00 0.00 0.00 3.10
856 1231 0.324830 AAAGAGGGGGACGGAGAGAG 60.325 60.000 0.00 0.00 0.00 3.20
857 1232 0.324460 GAAAGAGGGGGACGGAGAGA 60.324 60.000 0.00 0.00 0.00 3.10
858 1233 0.324830 AGAAAGAGGGGGACGGAGAG 60.325 60.000 0.00 0.00 0.00 3.20
859 1234 0.116541 AAGAAAGAGGGGGACGGAGA 59.883 55.000 0.00 0.00 0.00 3.71
860 1235 0.984995 AAAGAAAGAGGGGGACGGAG 59.015 55.000 0.00 0.00 0.00 4.63
861 1236 0.981943 GAAAGAAAGAGGGGGACGGA 59.018 55.000 0.00 0.00 0.00 4.69
862 1237 0.984995 AGAAAGAAAGAGGGGGACGG 59.015 55.000 0.00 0.00 0.00 4.79
863 1238 2.861147 AAGAAAGAAAGAGGGGGACG 57.139 50.000 0.00 0.00 0.00 4.79
864 1239 4.042311 AGAGAAAGAAAGAAAGAGGGGGAC 59.958 45.833 0.00 0.00 0.00 4.46
865 1240 4.243643 AGAGAAAGAAAGAAAGAGGGGGA 58.756 43.478 0.00 0.00 0.00 4.81
866 1241 4.566697 GGAGAGAAAGAAAGAAAGAGGGGG 60.567 50.000 0.00 0.00 0.00 5.40
901 1283 1.229529 GTGGGAAGTGAGGGGGAGA 60.230 63.158 0.00 0.00 0.00 3.71
926 1323 1.290431 AGCAGAGAGATGGAGAAGGGA 59.710 52.381 0.00 0.00 0.00 4.20
928 1325 1.688197 GGAGCAGAGAGATGGAGAAGG 59.312 57.143 0.00 0.00 0.00 3.46
930 1327 1.007600 TGGGAGCAGAGAGATGGAGAA 59.992 52.381 0.00 0.00 0.00 2.87
935 1332 2.109774 AGAAGTGGGAGCAGAGAGATG 58.890 52.381 0.00 0.00 0.00 2.90
936 1333 2.109774 CAGAAGTGGGAGCAGAGAGAT 58.890 52.381 0.00 0.00 0.00 2.75
970 1377 2.688958 ACGCTCTACCTTGAGACCATAC 59.311 50.000 0.00 0.00 36.23 2.39
1250 1676 3.548306 CTGAGCTGCAGCAGGGTGT 62.548 63.158 38.24 18.66 45.16 4.16
1439 1865 1.519455 CCGGACAGATTCAGCGTCC 60.519 63.158 0.00 8.95 44.79 4.79
1444 1870 1.021390 GCACCACCGGACAGATTCAG 61.021 60.000 9.46 0.00 0.00 3.02
1525 1952 0.827925 TTGCTGGACAGGTCGAGAGT 60.828 55.000 14.53 0.00 37.59 3.24
2013 2450 1.274703 TGGGATCTTGGCAGAGGGTC 61.275 60.000 0.00 0.00 30.36 4.46
2115 2552 0.322636 GACTGAGGTCGAGGGAGACA 60.323 60.000 0.00 0.00 42.62 3.41
2424 2861 2.472695 TCTGTCCGGTGAAGGAATTG 57.527 50.000 0.00 0.00 42.77 2.32
2658 3095 1.899437 GCATCCGACCAAGGTCCTCA 61.899 60.000 13.35 0.00 41.76 3.86
2787 3224 0.676736 GCTCCTTGGGTATCTCGGAG 59.323 60.000 0.00 0.00 43.18 4.63
3063 3500 1.227823 TGGAAAGCCACACAGACCG 60.228 57.895 0.00 0.00 39.92 4.79
3097 3534 2.124736 GCCTTGCCCAGTATGCGA 60.125 61.111 0.00 0.00 31.97 5.10
3120 3557 1.377987 GCTGGATTGGCCACCGTTA 60.378 57.895 3.88 0.00 43.33 3.18
3198 3635 4.557296 GCGATGATGACCAACCCAAATATG 60.557 45.833 0.00 0.00 0.00 1.78
3219 3656 1.760268 GCTTCTTGCTCTCGATGGCG 61.760 60.000 5.51 0.00 38.95 5.69
3471 3908 1.678728 CCATCCTTGAGCGTTGCCTTA 60.679 52.381 0.00 0.00 0.00 2.69
3741 4181 1.000521 CAATCCTCTTGCTGCCCCA 60.001 57.895 0.00 0.00 0.00 4.96
3762 4202 0.465460 TGCAGTTGTGGTGGAGGAAC 60.465 55.000 0.00 0.00 0.00 3.62
3789 4229 3.960755 ACTTCATGTCTCGGTGGATGATA 59.039 43.478 0.00 0.00 0.00 2.15
3846 4286 2.978156 TGCCAAAATCTGAGACCCTT 57.022 45.000 0.00 0.00 0.00 3.95
3861 4301 1.228033 CATCATCCTCGCCATGCCA 60.228 57.895 0.00 0.00 0.00 4.92
3927 4367 0.547712 ACTCTGGTGGCACATACCCT 60.548 55.000 20.82 0.00 44.52 4.34
3987 4427 1.135527 AGCAATACAACGCCGTAGCTA 59.864 47.619 0.00 0.00 36.60 3.32
4105 4545 2.686816 CCGGGTCAAACACATCGGC 61.687 63.158 0.00 0.00 36.82 5.54
4171 4611 1.253116 CATGCACACGCGATTTTCAG 58.747 50.000 15.93 0.00 42.97 3.02
4434 4874 2.770130 GGCCCCAAACTGGATGGA 59.230 61.111 0.00 0.00 40.96 3.41
4435 4875 2.755469 CGGCCCCAAACTGGATGG 60.755 66.667 0.00 0.00 40.96 3.51
4436 4876 2.755469 CCGGCCCCAAACTGGATG 60.755 66.667 0.00 0.00 40.96 3.51
4437 4877 4.060667 CCCGGCCCCAAACTGGAT 62.061 66.667 0.00 0.00 40.96 3.41
4505 4947 2.051345 CTTGCGTTGCGTGGGAAC 60.051 61.111 0.00 0.00 0.00 3.62
4553 4996 4.160329 ACAAGGGAGGGAAAATTTCTTCC 58.840 43.478 16.12 16.12 43.69 3.46
4554 4997 5.105716 GCTACAAGGGAGGGAAAATTTCTTC 60.106 44.000 5.65 4.33 0.00 2.87
4555 4998 4.772624 GCTACAAGGGAGGGAAAATTTCTT 59.227 41.667 5.65 0.00 0.00 2.52
4581 5027 1.447314 GACGGCTTGGGACTTACGG 60.447 63.158 0.00 0.00 0.00 4.02
4596 5042 5.473846 ACTCCTATAGGTACATGACATGACG 59.526 44.000 22.19 0.00 36.34 4.35
4636 5082 3.864789 AGCTGGGAAAGAAAGACAAGA 57.135 42.857 0.00 0.00 0.00 3.02
4640 5086 4.580580 TGAAGAAAGCTGGGAAAGAAAGAC 59.419 41.667 0.00 0.00 0.00 3.01
4683 5129 1.562017 GCTCTTTACTGGAGCGCTAC 58.438 55.000 14.39 14.39 45.01 3.58
4732 5178 0.404040 AGGGAATTTGCACCGGAGAA 59.596 50.000 9.46 0.00 0.00 2.87
4736 5182 1.304052 TGGAGGGAATTTGCACCGG 60.304 57.895 0.00 0.00 0.00 5.28
4745 5191 2.503356 CACTAGAAGCAGTGGAGGGAAT 59.497 50.000 0.00 0.00 41.88 3.01
4761 5234 3.664107 TGCTAGGCAACAAGAACACTAG 58.336 45.455 0.00 0.00 34.76 2.57
4764 5237 2.222027 ACTGCTAGGCAACAAGAACAC 58.778 47.619 0.00 0.00 38.41 3.32
4765 5238 2.618241 CAACTGCTAGGCAACAAGAACA 59.382 45.455 0.00 0.00 38.41 3.18
4809 5283 5.496556 ACCATGTTTAGATCAACCGATGAA 58.503 37.500 0.00 0.00 42.54 2.57
4810 5284 5.097742 ACCATGTTTAGATCAACCGATGA 57.902 39.130 0.00 0.00 43.67 2.92
4815 5289 7.257722 CAAATGGTACCATGTTTAGATCAACC 58.742 38.462 28.00 0.00 36.68 3.77
4823 5297 5.394005 GCATCTGCAAATGGTACCATGTTTA 60.394 40.000 28.00 12.31 41.59 2.01
4837 5311 4.909241 GGTTTCTACCGTGCATCTGCAAA 61.909 47.826 6.41 0.00 43.28 3.68
4863 5337 3.456280 CTCTCAGATTTACTGCTCAGGC 58.544 50.000 1.66 0.00 45.38 4.85
5029 5530 2.106074 ACACACACACACACAGGCG 61.106 57.895 0.00 0.00 0.00 5.52
5030 5531 1.305219 ACACACACACACACACAGGC 61.305 55.000 0.00 0.00 0.00 4.85
5031 5532 0.447406 CACACACACACACACACAGG 59.553 55.000 0.00 0.00 0.00 4.00
5032 5533 0.447406 CCACACACACACACACACAG 59.553 55.000 0.00 0.00 0.00 3.66
5033 5534 0.250510 ACCACACACACACACACACA 60.251 50.000 0.00 0.00 0.00 3.72
5034 5535 0.167908 CACCACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
5035 5536 0.957888 CCACCACACACACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
5037 5538 1.377856 CCCACCACACACACACACA 60.378 57.895 0.00 0.00 0.00 3.72
5038 5539 2.118404 CCCCACCACACACACACAC 61.118 63.158 0.00 0.00 0.00 3.82
5039 5540 2.273776 CCCCACCACACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
5040 5541 3.216292 GCCCCACCACACACACAC 61.216 66.667 0.00 0.00 0.00 3.82
5041 5542 4.514585 GGCCCCACCACACACACA 62.515 66.667 0.00 0.00 38.86 3.72
5042 5543 4.514585 TGGCCCCACCACACACAC 62.515 66.667 0.00 0.00 46.36 3.82
5043 5544 4.202574 CTGGCCCCACCACACACA 62.203 66.667 0.00 0.00 46.36 3.72
5044 5545 4.974721 CCTGGCCCCACCACACAC 62.975 72.222 0.00 0.00 46.36 3.82
5086 5591 0.375106 GAGTGCGCCTTCTTGTATGC 59.625 55.000 4.18 0.00 0.00 3.14
5087 5592 1.394917 GTGAGTGCGCCTTCTTGTATG 59.605 52.381 4.18 0.00 0.00 2.39
5088 5593 1.726853 GTGAGTGCGCCTTCTTGTAT 58.273 50.000 4.18 0.00 0.00 2.29
5134 5639 3.373565 GACAAAGCAAGCCCCGGG 61.374 66.667 15.80 15.80 0.00 5.73
5251 5756 3.512516 GCGAGGAGCCATGTTGCC 61.513 66.667 0.00 0.00 40.81 4.52
5284 5789 9.315525 CACCATGCATCTATAATAGAGAAGATG 57.684 37.037 0.00 6.78 45.26 2.90
5345 5850 0.809385 CTTGCTTGCTGGACATGGAG 59.191 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.