Multiple sequence alignment - TraesCS1D01G166800

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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 TraesCS1D01G166800 chr1D 100.000 4331 0 0 1 4331 238065008 238069338 0.000000e+00 7998.0
1 TraesCS1D01G166800 chr1D 93.617 47 2 1 3734 3780 451859094 451859049 7.770000e-08 69.4
2 TraesCS1D01G166800 chr1D 100.000 36 0 0 3738 3773 162713720 162713755 2.800000e-07 67.6
3 TraesCS1D01G166800 chr1B 94.997 1939 91 4 1540 3477 336275424 336273491 0.000000e+00 3038.0
4 TraesCS1D01G166800 chr1B 94.969 636 24 6 911 1542 336276286 336275655 0.000000e+00 990.0
5 TraesCS1D01G166800 chr1B 87.027 555 38 12 3805 4331 336210813 336210265 2.880000e-166 595.0
6 TraesCS1D01G166800 chr1B 89.617 183 18 1 3212 3394 634149654 634149835 9.370000e-57 231.0
7 TraesCS1D01G166800 chr1B 97.500 40 1 0 3734 3773 621487513 621487474 7.770000e-08 69.4
8 TraesCS1D01G166800 chr1B 97.368 38 1 0 3870 3907 634149896 634149933 1.010000e-06 65.8
9 TraesCS1D01G166800 chr1A 94.325 1727 67 18 2036 3738 301774253 301775972 0.000000e+00 2617.0
10 TraesCS1D01G166800 chr1A 92.985 1568 68 18 493 2038 301772545 301774092 0.000000e+00 2248.0
11 TraesCS1D01G166800 chr1A 92.477 545 18 5 3805 4328 301775973 301776515 0.000000e+00 758.0
12 TraesCS1D01G166800 chr1A 86.822 516 50 6 1 500 301771996 301772509 1.050000e-155 560.0
13 TraesCS1D01G166800 chr1A 89.617 183 18 1 3212 3394 140371757 140371576 9.370000e-57 231.0
14 TraesCS1D01G166800 chr1A 97.368 38 1 0 3870 3907 140371515 140371478 1.010000e-06 65.8
15 TraesCS1D01G166800 chr2B 89.617 183 18 1 3212 3394 743321815 743321996 9.370000e-57 231.0
16 TraesCS1D01G166800 chr2B 97.368 38 1 0 3870 3907 743322057 743322094 1.010000e-06 65.8
17 TraesCS1D01G166800 chr3B 100.000 38 0 0 3740 3777 752295104 752295141 2.160000e-08 71.3
18 TraesCS1D01G166800 chr5B 92.157 51 1 2 3740 3790 582898566 582898519 7.770000e-08 69.4
19 TraesCS1D01G166800 chr2D 97.500 40 1 0 3739 3778 383338144 383338105 7.770000e-08 69.4
20 TraesCS1D01G166800 chr6D 95.238 42 2 0 3737 3778 137543099 137543140 2.800000e-07 67.6
21 TraesCS1D01G166800 chr4B 97.436 39 1 0 3740 3778 643020036 643020074 2.800000e-07 67.6
22 TraesCS1D01G166800 chr7B 86.667 60 6 2 3733 3790 92964102 92964043 1.010000e-06 65.8


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 TraesCS1D01G166800 chr1D 238065008 238069338 4330 False 7998.00 7998 100.00000 1 4331 1 chr1D.!!$F2 4330
1 TraesCS1D01G166800 chr1B 336273491 336276286 2795 True 2014.00 3038 94.98300 911 3477 2 chr1B.!!$R3 2566
2 TraesCS1D01G166800 chr1B 336210265 336210813 548 True 595.00 595 87.02700 3805 4331 1 chr1B.!!$R1 526
3 TraesCS1D01G166800 chr1A 301771996 301776515 4519 False 1545.75 2617 91.65225 1 4328 4 chr1A.!!$F1 4327

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
683 742 0.591170 CACATCAAACCGAAAGCCGT 59.409 50.0 0.0 0.0 36.31 5.68 F
1470 1543 0.745486 TGCCATTGACAGATGCGAGG 60.745 55.0 0.0 0.0 0.00 4.63 F
1571 1887 0.774908 TGGGGAAACGGAATGAGGTT 59.225 50.0 0.0 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2701 0.813210 CTTCTGCTGCTCCGATTCCC 60.813 60.000 0.00 0.0 0.00 3.97 R
2916 3403 1.429463 GGTAACCAGTGAGCAAGACG 58.571 55.000 0.00 0.0 0.00 4.18 R
3542 4045 1.994779 GTGGCGAAATTTTGCAGGATG 59.005 47.619 27.54 0.0 39.39 3.51 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
20 21 3.922171 GTGAGGAGAAATGGATGAGGT 57.078 47.619 0.00 0.00 0.00 3.85
21 22 3.539604 GTGAGGAGAAATGGATGAGGTG 58.460 50.000 0.00 0.00 0.00 4.00
23 24 2.774234 GAGGAGAAATGGATGAGGTGGA 59.226 50.000 0.00 0.00 0.00 4.02
36 37 2.391972 GGTGGAATGGGGGTAGGGG 61.392 68.421 0.00 0.00 0.00 4.79
58 59 1.605451 TTCGGGAGACTTCGCCTCA 60.605 57.895 0.00 0.00 39.59 3.86
61 62 1.671742 GGGAGACTTCGCCTCAACA 59.328 57.895 0.00 0.00 36.01 3.33
67 68 1.213094 ACTTCGCCTCAACACGAACG 61.213 55.000 0.00 0.00 42.85 3.95
83 84 0.729478 AACGAGTCGCTGTGATGACG 60.729 55.000 13.59 3.95 40.05 4.35
88 89 2.738139 CGCTGTGATGACGTGGCA 60.738 61.111 0.00 0.00 0.00 4.92
93 94 1.603802 CTGTGATGACGTGGCAAGTTT 59.396 47.619 7.66 0.00 0.00 2.66
119 120 1.227527 CCAAGATATGTGCGGGCGA 60.228 57.895 0.00 0.00 0.00 5.54
121 122 1.337728 CCAAGATATGTGCGGGCGATA 60.338 52.381 0.00 0.00 0.00 2.92
130 131 1.881252 GCGGGCGATACAACGACAT 60.881 57.895 0.00 0.00 43.73 3.06
141 142 2.650322 ACAACGACATCAAGGGTGTTT 58.350 42.857 0.00 0.00 0.00 2.83
142 143 2.357637 ACAACGACATCAAGGGTGTTTG 59.642 45.455 0.00 0.00 0.00 2.93
155 156 1.234821 GTGTTTGGGACGAGATTGCA 58.765 50.000 0.00 0.00 0.00 4.08
157 158 2.034053 GTGTTTGGGACGAGATTGCAAA 59.966 45.455 1.71 0.00 0.00 3.68
166 167 5.444122 GGACGAGATTGCAAAATATAGCAC 58.556 41.667 1.71 0.00 41.05 4.40
167 168 5.083136 ACGAGATTGCAAAATATAGCACG 57.917 39.130 1.71 0.00 41.05 5.34
187 189 3.004106 ACGTTCGGGAGTTATAGATTCCG 59.996 47.826 0.00 0.00 35.06 4.30
188 190 3.611057 CGTTCGGGAGTTATAGATTCCGG 60.611 52.174 0.00 0.00 35.06 5.14
249 251 3.840890 AACAAAAGCGAACTCACACAA 57.159 38.095 0.00 0.00 0.00 3.33
253 255 1.498865 AAGCGAACTCACACAAGCCG 61.499 55.000 0.00 0.00 0.00 5.52
266 268 2.618241 CACAAGCCGCACATATAACCAT 59.382 45.455 0.00 0.00 0.00 3.55
267 269 3.066621 CACAAGCCGCACATATAACCATT 59.933 43.478 0.00 0.00 0.00 3.16
270 272 3.550820 AGCCGCACATATAACCATTCAA 58.449 40.909 0.00 0.00 0.00 2.69
277 279 5.501715 CACATATAACCATTCAAGCACGTC 58.498 41.667 0.00 0.00 0.00 4.34
295 309 2.293677 CGTCTCCTAGTCACACACACTT 59.706 50.000 0.00 0.00 0.00 3.16
305 319 7.550551 CCTAGTCACACACACTTTAATGATGAT 59.449 37.037 0.00 0.00 0.00 2.45
356 370 5.917541 AAGTTTTACTACACACACCATCG 57.082 39.130 0.00 0.00 0.00 3.84
363 377 5.752892 ACTACACACACCATCGTATAGAG 57.247 43.478 0.00 0.00 0.00 2.43
367 381 5.592054 ACACACACCATCGTATAGAGATTG 58.408 41.667 0.00 0.00 0.00 2.67
462 476 3.183793 TGCACTGTAGTATCATGGCTG 57.816 47.619 0.00 0.00 0.00 4.85
468 482 3.879295 CTGTAGTATCATGGCTGGTTTGG 59.121 47.826 0.00 0.00 0.00 3.28
474 490 5.829924 AGTATCATGGCTGGTTTGGAAATAG 59.170 40.000 0.00 0.00 0.00 1.73
488 504 8.850156 GGTTTGGAAATAGTATCATATGTGCTT 58.150 33.333 1.90 0.00 0.00 3.91
493 509 9.593134 GGAAATAGTATCATATGTGCTTAGAGG 57.407 37.037 1.90 0.00 0.00 3.69
533 592 5.187381 TCACAATCCATGTAATGCCAAACAT 59.813 36.000 0.00 0.00 44.97 2.71
679 738 7.076842 AGTAATCATCACATCAAACCGAAAG 57.923 36.000 0.00 0.00 0.00 2.62
682 741 0.871722 TCACATCAAACCGAAAGCCG 59.128 50.000 0.00 0.00 38.18 5.52
683 742 0.591170 CACATCAAACCGAAAGCCGT 59.409 50.000 0.00 0.00 36.31 5.68
728 789 9.890629 TTTTACAGTGCTTCTTATCATGATACT 57.109 29.630 15.10 7.04 0.00 2.12
757 818 9.541884 AAATGTAACCATTTTCAGGGTATAACT 57.458 29.630 0.00 0.00 46.61 2.24
762 823 7.939784 ACCATTTTCAGGGTATAACTCTTTC 57.060 36.000 0.00 0.00 35.09 2.62
771 832 7.048512 CAGGGTATAACTCTTTCTAGGGTTTG 58.951 42.308 0.00 0.00 42.52 2.93
773 834 7.902941 AGGGTATAACTCTTTCTAGGGTTTGTA 59.097 37.037 0.00 0.00 42.52 2.41
774 835 8.712103 GGGTATAACTCTTTCTAGGGTTTGTAT 58.288 37.037 0.00 0.00 42.52 2.29
832 902 9.438291 CAGGCTTTAATATTTTCTCAATACACG 57.562 33.333 0.00 0.00 0.00 4.49
900 970 9.996554 TCAAGTTGACATCTAAAAGAAGATACA 57.003 29.630 0.08 0.00 34.40 2.29
906 976 9.731819 TGACATCTAAAAGAAGATACACGATAC 57.268 33.333 0.00 0.00 34.40 2.24
932 1002 5.982465 TGTAGTAAAACGTAAAACCGCTT 57.018 34.783 0.00 0.00 0.00 4.68
1337 1410 3.155167 CCAGGCCCTCGAGGTACC 61.155 72.222 29.25 27.52 38.26 3.34
1358 1431 4.052518 CTCCCCCTTGCCCCACTG 62.053 72.222 0.00 0.00 0.00 3.66
1363 1436 2.833913 CCCTTGCCCCACTGACTGT 61.834 63.158 0.00 0.00 0.00 3.55
1373 1446 2.126307 CTGACTGTCCGTCGGCTG 60.126 66.667 6.34 8.55 45.87 4.85
1376 1449 1.300697 GACTGTCCGTCGGCTGTTT 60.301 57.895 6.34 0.00 32.04 2.83
1412 1485 2.683211 AGCTTCCCATGGTTCTGTTT 57.317 45.000 11.73 0.00 0.00 2.83
1470 1543 0.745486 TGCCATTGACAGATGCGAGG 60.745 55.000 0.00 0.00 0.00 4.63
1565 1881 3.245264 ACTTCTCAATGGGGAAACGGAAT 60.245 43.478 0.00 0.00 0.00 3.01
1566 1882 2.722094 TCTCAATGGGGAAACGGAATG 58.278 47.619 0.00 0.00 0.00 2.67
1567 1883 2.307392 TCTCAATGGGGAAACGGAATGA 59.693 45.455 0.00 0.00 0.00 2.57
1568 1884 2.684881 CTCAATGGGGAAACGGAATGAG 59.315 50.000 0.00 0.00 0.00 2.90
1569 1885 1.750778 CAATGGGGAAACGGAATGAGG 59.249 52.381 0.00 0.00 0.00 3.86
1570 1886 0.999712 ATGGGGAAACGGAATGAGGT 59.000 50.000 0.00 0.00 0.00 3.85
1571 1887 0.774908 TGGGGAAACGGAATGAGGTT 59.225 50.000 0.00 0.00 0.00 3.50
1572 1888 1.271707 TGGGGAAACGGAATGAGGTTC 60.272 52.381 0.00 0.00 36.04 3.62
1573 1889 1.271707 GGGGAAACGGAATGAGGTTCA 60.272 52.381 0.00 0.00 38.64 3.18
1574 1890 2.510613 GGGAAACGGAATGAGGTTCAA 58.489 47.619 0.00 0.00 38.64 2.69
1804 2127 4.922206 TGGTGCATAAAGAAGAGGATGTT 58.078 39.130 0.00 0.00 0.00 2.71
1814 2137 6.566197 AAGAAGAGGATGTTGTGTTCAATC 57.434 37.500 0.00 0.00 35.92 2.67
1852 2175 7.041372 GCCTTATGTCACAGACTTGAAGTTTAA 60.041 37.037 0.00 0.00 33.15 1.52
1880 2204 4.101114 TGAGGAGTTTAATCTGGCCTGTA 58.899 43.478 3.32 0.00 0.00 2.74
2214 2701 4.002982 TGGATTTGATCGGTCAAGTTCAG 58.997 43.478 10.65 0.00 44.62 3.02
2257 2744 5.735354 GCCTATTTCAATCAACTGCCTGATG 60.735 44.000 0.00 0.00 36.16 3.07
2259 2746 6.264744 CCTATTTCAATCAACTGCCTGATGAT 59.735 38.462 0.00 0.00 39.43 2.45
2424 2911 6.570764 GCCTCTATACTAACATAGGACAGCAC 60.571 46.154 0.00 0.00 0.00 4.40
2516 3003 4.678509 TTTGCATAAACTCTTACGGCAG 57.321 40.909 0.00 0.00 34.18 4.85
2592 3079 4.917415 CCTCAAATTGTTGTCGATTGGAAC 59.083 41.667 0.00 0.00 36.07 3.62
2628 3115 2.419574 GGCGAGCAACTACATTAAGGGA 60.420 50.000 0.00 0.00 0.00 4.20
2715 3202 6.222038 TCAGATAACTACAACCACCTGATC 57.778 41.667 0.00 0.00 0.00 2.92
2916 3403 2.178912 TCGACTTCCATGTCCCAAAC 57.821 50.000 0.00 0.00 33.70 2.93
3059 3546 0.674895 GCGGAGAAAGGTGATGCTGT 60.675 55.000 0.00 0.00 0.00 4.40
3111 3598 0.243095 GTGTTTACGCTCCGAGGAGT 59.757 55.000 19.22 5.27 43.70 3.85
3586 4089 6.180472 CAAAAAGGTATCCATAGTGGTCTGT 58.820 40.000 0.00 0.00 39.03 3.41
3590 4093 0.839946 ATCCATAGTGGTCTGTGCCC 59.160 55.000 0.00 0.00 39.03 5.36
3591 4094 0.546507 TCCATAGTGGTCTGTGCCCA 60.547 55.000 0.00 0.00 39.03 5.36
3592 4095 0.327924 CCATAGTGGTCTGTGCCCAA 59.672 55.000 0.00 0.00 32.72 4.12
3593 4096 1.271871 CCATAGTGGTCTGTGCCCAAA 60.272 52.381 0.00 0.00 32.72 3.28
3672 4186 3.686726 GCCTCCACAGATGTCTTTTGTAG 59.313 47.826 0.00 0.00 0.00 2.74
3687 4201 8.410141 TGTCTTTTGTAGGTGAAATTTTACAGG 58.590 33.333 14.30 4.23 0.00 4.00
3688 4202 8.626526 GTCTTTTGTAGGTGAAATTTTACAGGA 58.373 33.333 14.30 6.00 0.00 3.86
3689 4203 9.362151 TCTTTTGTAGGTGAAATTTTACAGGAT 57.638 29.630 14.30 1.21 0.00 3.24
3750 4264 5.997384 AAATTGTCTACTACTCCCTTCGT 57.003 39.130 0.00 0.00 0.00 3.85
3751 4265 5.579564 AATTGTCTACTACTCCCTTCGTC 57.420 43.478 0.00 0.00 0.00 4.20
3752 4266 3.996921 TGTCTACTACTCCCTTCGTCT 57.003 47.619 0.00 0.00 0.00 4.18
3753 4267 3.871485 TGTCTACTACTCCCTTCGTCTC 58.129 50.000 0.00 0.00 0.00 3.36
3754 4268 3.262660 TGTCTACTACTCCCTTCGTCTCA 59.737 47.826 0.00 0.00 0.00 3.27
3755 4269 4.080469 TGTCTACTACTCCCTTCGTCTCAT 60.080 45.833 0.00 0.00 0.00 2.90
3756 4270 5.129980 TGTCTACTACTCCCTTCGTCTCATA 59.870 44.000 0.00 0.00 0.00 2.15
3757 4271 6.054295 GTCTACTACTCCCTTCGTCTCATAA 58.946 44.000 0.00 0.00 0.00 1.90
3758 4272 6.711645 GTCTACTACTCCCTTCGTCTCATAAT 59.288 42.308 0.00 0.00 0.00 1.28
3759 4273 7.877097 GTCTACTACTCCCTTCGTCTCATAATA 59.123 40.741 0.00 0.00 0.00 0.98
3760 4274 8.604184 TCTACTACTCCCTTCGTCTCATAATAT 58.396 37.037 0.00 0.00 0.00 1.28
3761 4275 9.887629 CTACTACTCCCTTCGTCTCATAATATA 57.112 37.037 0.00 0.00 0.00 0.86
3763 4277 9.233649 ACTACTCCCTTCGTCTCATAATATAAG 57.766 37.037 0.00 0.00 0.00 1.73
3764 4278 9.451002 CTACTCCCTTCGTCTCATAATATAAGA 57.549 37.037 0.00 0.00 0.00 2.10
3765 4279 8.343168 ACTCCCTTCGTCTCATAATATAAGAG 57.657 38.462 0.00 0.00 0.00 2.85
3766 4280 7.094118 ACTCCCTTCGTCTCATAATATAAGAGC 60.094 40.741 0.00 0.00 0.00 4.09
3767 4281 6.030849 CCCTTCGTCTCATAATATAAGAGCG 58.969 44.000 0.00 0.00 33.46 5.03
3768 4282 6.349445 CCCTTCGTCTCATAATATAAGAGCGT 60.349 42.308 0.00 0.00 33.70 5.07
3769 4283 7.085116 CCTTCGTCTCATAATATAAGAGCGTT 58.915 38.462 0.00 0.00 33.70 4.84
3770 4284 7.595502 CCTTCGTCTCATAATATAAGAGCGTTT 59.404 37.037 0.00 0.00 33.70 3.60
3771 4285 8.867112 TTCGTCTCATAATATAAGAGCGTTTT 57.133 30.769 0.00 0.00 33.70 2.43
3772 4286 8.867112 TCGTCTCATAATATAAGAGCGTTTTT 57.133 30.769 0.00 0.00 33.70 1.94
3773 4287 8.752254 TCGTCTCATAATATAAGAGCGTTTTTG 58.248 33.333 0.00 0.00 33.70 2.44
3774 4288 8.752254 CGTCTCATAATATAAGAGCGTTTTTGA 58.248 33.333 0.00 0.00 0.00 2.69
3781 4295 8.732746 AATATAAGAGCGTTTTTGATACACCT 57.267 30.769 0.00 0.00 0.00 4.00
3782 4296 4.749245 AAGAGCGTTTTTGATACACCTG 57.251 40.909 0.00 0.00 0.00 4.00
3783 4297 3.740115 AGAGCGTTTTTGATACACCTGT 58.260 40.909 0.00 0.00 0.00 4.00
3784 4298 3.746492 AGAGCGTTTTTGATACACCTGTC 59.254 43.478 0.00 0.00 0.00 3.51
3785 4299 3.472652 AGCGTTTTTGATACACCTGTCA 58.527 40.909 0.00 0.00 0.00 3.58
3786 4300 3.880490 AGCGTTTTTGATACACCTGTCAA 59.120 39.130 0.00 0.00 32.86 3.18
3787 4301 4.336993 AGCGTTTTTGATACACCTGTCAAA 59.663 37.500 0.00 0.00 41.21 2.69
3788 4302 5.038033 GCGTTTTTGATACACCTGTCAAAA 58.962 37.500 8.66 8.66 46.64 2.44
3793 4307 6.633500 TTTGATACACCTGTCAAAAAGAGG 57.367 37.500 0.00 0.00 44.21 3.69
3794 4308 4.651778 TGATACACCTGTCAAAAAGAGGG 58.348 43.478 0.00 0.00 42.90 4.30
3795 4309 4.349636 TGATACACCTGTCAAAAAGAGGGA 59.650 41.667 0.00 0.00 42.90 4.20
3796 4310 3.214696 ACACCTGTCAAAAAGAGGGAG 57.785 47.619 0.00 0.00 42.90 4.30
3797 4311 2.509964 ACACCTGTCAAAAAGAGGGAGT 59.490 45.455 0.00 0.00 42.90 3.85
3798 4312 3.714798 ACACCTGTCAAAAAGAGGGAGTA 59.285 43.478 0.00 0.00 42.90 2.59
3799 4313 4.065789 CACCTGTCAAAAAGAGGGAGTAC 58.934 47.826 0.00 0.00 42.90 2.73
3800 4314 3.974642 ACCTGTCAAAAAGAGGGAGTACT 59.025 43.478 0.00 0.00 42.90 2.73
3801 4315 5.011738 CACCTGTCAAAAAGAGGGAGTACTA 59.988 44.000 0.00 0.00 42.90 1.82
3802 4316 5.785940 ACCTGTCAAAAAGAGGGAGTACTAT 59.214 40.000 0.00 0.00 42.90 2.12
3803 4317 6.272558 ACCTGTCAAAAAGAGGGAGTACTATT 59.727 38.462 0.00 0.00 42.90 1.73
3844 4358 3.192466 GTTCATGCAGGAAAATCCATGC 58.808 45.455 16.43 11.48 39.61 4.06
3849 4363 0.179129 CAGGAAAATCCATGCCGCAC 60.179 55.000 0.00 0.00 39.61 5.34
4020 4578 9.996554 CTGGAGTACAACCATGACATTATATTA 57.003 33.333 11.26 0.00 36.79 0.98
4126 4687 0.038744 CATCCAGCCTGAACCAAGGT 59.961 55.000 0.00 0.00 39.75 3.50
4151 4712 9.685828 GTAGCAAAAATGAAGTGGTAATACAAA 57.314 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.774234 TCCACCTCATCCATTTCTCCTC 59.226 50.000 0.00 0.00 0.00 3.71
20 21 2.045474 CCCCCTACCCCCATTCCA 59.955 66.667 0.00 0.00 0.00 3.53
21 22 3.508685 GCCCCCTACCCCCATTCC 61.509 72.222 0.00 0.00 0.00 3.01
23 24 4.771745 ACGCCCCCTACCCCCATT 62.772 66.667 0.00 0.00 0.00 3.16
36 37 2.506438 CGAAGTCTCCCGAACGCC 60.506 66.667 0.00 0.00 0.00 5.68
67 68 1.073216 CCACGTCATCACAGCGACTC 61.073 60.000 0.00 0.00 0.00 3.36
88 89 1.795170 ATCTTGGCGCACGCAAACTT 61.795 50.000 17.69 0.00 44.11 2.66
93 94 1.449423 ACATATCTTGGCGCACGCA 60.449 52.632 17.69 0.00 44.11 5.24
119 120 3.695830 ACACCCTTGATGTCGTTGTAT 57.304 42.857 0.00 0.00 0.00 2.29
121 122 2.341846 AACACCCTTGATGTCGTTGT 57.658 45.000 0.00 0.00 0.00 3.32
130 131 0.107831 CTCGTCCCAAACACCCTTGA 59.892 55.000 0.00 0.00 0.00 3.02
141 142 4.515191 GCTATATTTTGCAATCTCGTCCCA 59.485 41.667 0.00 0.00 0.00 4.37
142 143 4.515191 TGCTATATTTTGCAATCTCGTCCC 59.485 41.667 0.00 0.00 36.15 4.46
155 156 4.133013 ACTCCCGAACGTGCTATATTTT 57.867 40.909 0.00 0.00 0.00 1.82
157 158 3.814005 AACTCCCGAACGTGCTATATT 57.186 42.857 0.00 0.00 0.00 1.28
166 167 3.562505 CGGAATCTATAACTCCCGAACG 58.437 50.000 0.00 0.00 39.31 3.95
167 168 3.571401 TCCGGAATCTATAACTCCCGAAC 59.429 47.826 0.00 0.00 39.31 3.95
231 233 2.111756 GCTTGTGTGAGTTCGCTTTTG 58.888 47.619 0.00 0.00 0.00 2.44
235 237 1.956170 CGGCTTGTGTGAGTTCGCT 60.956 57.895 0.00 0.00 0.00 4.93
236 238 2.551270 CGGCTTGTGTGAGTTCGC 59.449 61.111 0.00 0.00 0.00 4.70
237 239 2.243957 TGCGGCTTGTGTGAGTTCG 61.244 57.895 0.00 0.00 0.00 3.95
238 240 1.279840 GTGCGGCTTGTGTGAGTTC 59.720 57.895 0.00 0.00 0.00 3.01
239 241 0.819259 ATGTGCGGCTTGTGTGAGTT 60.819 50.000 0.00 0.00 0.00 3.01
240 242 0.034756 TATGTGCGGCTTGTGTGAGT 59.965 50.000 0.00 0.00 0.00 3.41
249 251 3.207265 TGAATGGTTATATGTGCGGCT 57.793 42.857 0.00 0.00 0.00 5.52
253 255 4.201910 ACGTGCTTGAATGGTTATATGTGC 60.202 41.667 0.00 0.00 0.00 4.57
266 268 2.030185 GTGACTAGGAGACGTGCTTGAA 60.030 50.000 0.00 0.00 0.00 2.69
267 269 1.540267 GTGACTAGGAGACGTGCTTGA 59.460 52.381 0.00 0.00 0.00 3.02
270 272 0.882474 GTGTGACTAGGAGACGTGCT 59.118 55.000 0.00 0.00 0.00 4.40
277 279 6.455647 TCATTAAAGTGTGTGTGACTAGGAG 58.544 40.000 0.00 0.00 0.00 3.69
336 350 6.956299 ATACGATGGTGTGTGTAGTAAAAC 57.044 37.500 0.00 0.00 0.00 2.43
354 368 4.642445 TTTCCGCACAATCTCTATACGA 57.358 40.909 0.00 0.00 0.00 3.43
356 370 5.116882 AGGTTTTCCGCACAATCTCTATAC 58.883 41.667 0.00 0.00 46.35 1.47
402 416 9.846248 CATTATTATTAAATACCAGCCTCTTGC 57.154 33.333 0.00 0.00 41.71 4.01
448 462 4.150897 TCCAAACCAGCCATGATACTAC 57.849 45.455 0.00 0.00 0.00 2.73
462 476 8.396272 AGCACATATGATACTATTTCCAAACC 57.604 34.615 10.38 0.00 0.00 3.27
748 809 6.955364 ACAAACCCTAGAAAGAGTTATACCC 58.045 40.000 0.00 0.00 0.00 3.69
897 967 8.795786 ACGTTTTACTACAAAAGTATCGTGTA 57.204 30.769 0.00 0.00 40.41 2.90
906 976 6.906678 AGCGGTTTTACGTTTTACTACAAAAG 59.093 34.615 0.00 0.00 35.98 2.27
911 981 6.215477 AGAAGCGGTTTTACGTTTTACTAC 57.785 37.500 0.00 0.00 37.41 2.73
1125 1198 1.599576 GCTGTTGGAGGGAGGAGAC 59.400 63.158 0.00 0.00 0.00 3.36
1348 1421 2.836154 GGACAGTCAGTGGGGCAA 59.164 61.111 2.17 0.00 0.00 4.52
1358 1431 1.300697 AAACAGCCGACGGACAGTC 60.301 57.895 20.50 0.00 46.16 3.51
1363 1436 0.034198 TTCATCAAACAGCCGACGGA 59.966 50.000 20.50 0.00 0.00 4.69
1373 1446 2.352503 ACTGCCGCATTTCATCAAAC 57.647 45.000 0.00 0.00 0.00 2.93
1376 1449 1.016627 GCTACTGCCGCATTTCATCA 58.983 50.000 0.00 0.00 0.00 3.07
1412 1485 0.107214 CCGCAAGAGATAAAGGGGCA 60.107 55.000 0.00 0.00 43.02 5.36
1470 1543 4.187694 GTCACCATCTCAGAAATGTCCTC 58.812 47.826 0.00 0.00 0.00 3.71
1565 1881 3.390967 TCTCCACATGAACTTGAACCTCA 59.609 43.478 0.00 0.00 0.00 3.86
1566 1882 4.008074 TCTCCACATGAACTTGAACCTC 57.992 45.455 0.00 0.00 0.00 3.85
1567 1883 4.647564 ATCTCCACATGAACTTGAACCT 57.352 40.909 0.00 0.00 0.00 3.50
1568 1884 4.761739 TGAATCTCCACATGAACTTGAACC 59.238 41.667 0.00 0.00 0.00 3.62
1569 1885 5.947228 TGAATCTCCACATGAACTTGAAC 57.053 39.130 0.00 0.00 0.00 3.18
1570 1886 7.283807 CCATATGAATCTCCACATGAACTTGAA 59.716 37.037 3.65 0.00 0.00 2.69
1571 1887 6.769341 CCATATGAATCTCCACATGAACTTGA 59.231 38.462 3.65 0.00 0.00 3.02
1572 1888 6.769341 TCCATATGAATCTCCACATGAACTTG 59.231 38.462 3.65 0.00 0.00 3.16
1573 1889 6.903516 TCCATATGAATCTCCACATGAACTT 58.096 36.000 3.65 0.00 0.00 2.66
1574 1890 6.505048 TCCATATGAATCTCCACATGAACT 57.495 37.500 3.65 0.00 0.00 3.01
1804 2127 8.579850 AGGCAGATAAAAATAGATTGAACACA 57.420 30.769 0.00 0.00 0.00 3.72
1814 2137 9.330063 TCTGTGACATAAGGCAGATAAAAATAG 57.670 33.333 0.00 0.00 33.62 1.73
1852 2175 5.136105 GCCAGATTAAACTCCTCATTCCAT 58.864 41.667 0.00 0.00 0.00 3.41
2039 2363 9.909644 CATAATTAGTAGCGACAAACTATAGGT 57.090 33.333 4.43 0.00 0.00 3.08
2057 2544 6.905578 GGTACGCAAAATACCCCATAATTAG 58.094 40.000 0.00 0.00 36.80 1.73
2214 2701 0.813210 CTTCTGCTGCTCCGATTCCC 60.813 60.000 0.00 0.00 0.00 3.97
2257 2744 4.674281 AGGGTTTCTCCGTCTTATCATC 57.326 45.455 0.00 0.00 37.00 2.92
2259 2746 3.379372 CGTAGGGTTTCTCCGTCTTATCA 59.621 47.826 0.00 0.00 37.00 2.15
2357 2844 2.024414 GACTGCAGAACACAAAACCCT 58.976 47.619 23.35 0.00 0.00 4.34
2628 3115 3.593780 AGATTGCCTTCTCCCTTAGGTTT 59.406 43.478 0.00 0.00 33.91 3.27
2699 3186 2.188817 GGGAGATCAGGTGGTTGTAGT 58.811 52.381 0.00 0.00 0.00 2.73
2715 3202 2.443016 AGCTGGCCGTAGAGGGAG 60.443 66.667 0.00 0.00 41.48 4.30
2916 3403 1.429463 GGTAACCAGTGAGCAAGACG 58.571 55.000 0.00 0.00 0.00 4.18
3059 3546 6.707440 TTTTTGTCAACTCATAGGCTTTCA 57.293 33.333 0.00 0.00 0.00 2.69
3219 3706 5.473846 GTCGGTCATATCTGAGTTCATAGGA 59.526 44.000 0.00 0.00 30.18 2.94
3387 3874 7.803189 CGAGTAAAATATCAAATGAATTCCGGG 59.197 37.037 0.00 0.00 0.00 5.73
3542 4045 1.994779 GTGGCGAAATTTTGCAGGATG 59.005 47.619 27.54 0.00 39.39 3.51
3636 4147 1.215673 TGGAGGCCTGTACACCAAAAA 59.784 47.619 12.00 0.00 0.00 1.94
3641 4152 1.192146 TCTGTGGAGGCCTGTACACC 61.192 60.000 12.00 4.89 33.07 4.16
3645 4156 1.195115 GACATCTGTGGAGGCCTGTA 58.805 55.000 12.00 0.00 0.00 2.74
3646 4157 0.546267 AGACATCTGTGGAGGCCTGT 60.546 55.000 12.00 0.00 0.00 4.00
3647 4158 0.617413 AAGACATCTGTGGAGGCCTG 59.383 55.000 12.00 0.00 0.00 4.85
3648 4159 1.366319 AAAGACATCTGTGGAGGCCT 58.634 50.000 3.86 3.86 0.00 5.19
3652 4166 4.692625 CACCTACAAAAGACATCTGTGGAG 59.307 45.833 0.00 0.00 0.00 3.86
3654 4168 4.641396 TCACCTACAAAAGACATCTGTGG 58.359 43.478 0.00 0.00 0.00 4.17
3728 4242 5.715753 AGACGAAGGGAGTAGTAGACAATTT 59.284 40.000 0.00 0.00 0.00 1.82
3729 4243 5.262804 AGACGAAGGGAGTAGTAGACAATT 58.737 41.667 0.00 0.00 0.00 2.32
3730 4244 4.857679 AGACGAAGGGAGTAGTAGACAAT 58.142 43.478 0.00 0.00 0.00 2.71
3738 4252 9.451002 TCTTATATTATGAGACGAAGGGAGTAG 57.549 37.037 0.00 0.00 0.00 2.57
3739 4253 9.451002 CTCTTATATTATGAGACGAAGGGAGTA 57.549 37.037 0.00 0.00 33.20 2.59
3740 4254 7.094118 GCTCTTATATTATGAGACGAAGGGAGT 60.094 40.741 0.00 0.00 33.20 3.85
3741 4255 7.254852 GCTCTTATATTATGAGACGAAGGGAG 58.745 42.308 0.00 0.00 33.20 4.30
3742 4256 6.127980 CGCTCTTATATTATGAGACGAAGGGA 60.128 42.308 11.45 0.00 34.62 4.20
3743 4257 6.030849 CGCTCTTATATTATGAGACGAAGGG 58.969 44.000 11.45 2.16 34.62 3.95
3744 4258 6.613233 ACGCTCTTATATTATGAGACGAAGG 58.387 40.000 18.20 3.81 35.57 3.46
3745 4259 8.508800 AAACGCTCTTATATTATGAGACGAAG 57.491 34.615 18.20 4.07 35.57 3.79
3746 4260 8.867112 AAAACGCTCTTATATTATGAGACGAA 57.133 30.769 18.20 0.00 35.57 3.85
3747 4261 8.752254 CAAAAACGCTCTTATATTATGAGACGA 58.248 33.333 18.20 0.00 35.57 4.20
3748 4262 8.752254 TCAAAAACGCTCTTATATTATGAGACG 58.248 33.333 13.57 13.57 36.53 4.18
3755 4269 9.826574 AGGTGTATCAAAAACGCTCTTATATTA 57.173 29.630 0.00 0.00 0.00 0.98
3756 4270 8.612619 CAGGTGTATCAAAAACGCTCTTATATT 58.387 33.333 0.00 0.00 0.00 1.28
3757 4271 7.769044 ACAGGTGTATCAAAAACGCTCTTATAT 59.231 33.333 0.00 0.00 0.00 0.86
3758 4272 7.101054 ACAGGTGTATCAAAAACGCTCTTATA 58.899 34.615 0.00 0.00 0.00 0.98
3759 4273 5.938125 ACAGGTGTATCAAAAACGCTCTTAT 59.062 36.000 0.00 0.00 0.00 1.73
3760 4274 5.302360 ACAGGTGTATCAAAAACGCTCTTA 58.698 37.500 0.00 0.00 0.00 2.10
3761 4275 4.134563 ACAGGTGTATCAAAAACGCTCTT 58.865 39.130 0.00 0.00 0.00 2.85
3762 4276 3.740115 ACAGGTGTATCAAAAACGCTCT 58.260 40.909 0.00 0.00 0.00 4.09
3763 4277 3.496884 TGACAGGTGTATCAAAAACGCTC 59.503 43.478 0.00 0.00 0.00 5.03
3764 4278 3.472652 TGACAGGTGTATCAAAAACGCT 58.527 40.909 0.00 0.00 0.00 5.07
3765 4279 3.889196 TGACAGGTGTATCAAAAACGC 57.111 42.857 0.00 0.00 0.00 4.84
3770 4284 5.534654 CCCTCTTTTTGACAGGTGTATCAAA 59.465 40.000 0.00 0.00 41.80 2.69
3771 4285 5.070001 CCCTCTTTTTGACAGGTGTATCAA 58.930 41.667 0.00 0.00 33.03 2.57
3772 4286 4.349636 TCCCTCTTTTTGACAGGTGTATCA 59.650 41.667 0.00 0.00 0.00 2.15
3773 4287 4.906618 TCCCTCTTTTTGACAGGTGTATC 58.093 43.478 0.00 0.00 0.00 2.24
3774 4288 4.351111 ACTCCCTCTTTTTGACAGGTGTAT 59.649 41.667 0.00 0.00 0.00 2.29
3775 4289 3.714798 ACTCCCTCTTTTTGACAGGTGTA 59.285 43.478 0.00 0.00 0.00 2.90
3776 4290 2.509964 ACTCCCTCTTTTTGACAGGTGT 59.490 45.455 0.00 0.00 0.00 4.16
3777 4291 3.214696 ACTCCCTCTTTTTGACAGGTG 57.785 47.619 0.00 0.00 0.00 4.00
3778 4292 3.974642 AGTACTCCCTCTTTTTGACAGGT 59.025 43.478 0.00 0.00 0.00 4.00
3779 4293 4.625607 AGTACTCCCTCTTTTTGACAGG 57.374 45.455 0.00 0.00 0.00 4.00
3780 4294 8.622948 AAAATAGTACTCCCTCTTTTTGACAG 57.377 34.615 0.00 0.00 0.00 3.51
3787 4301 9.392259 CCGAAAATAAAATAGTACTCCCTCTTT 57.608 33.333 0.00 0.00 0.00 2.52
3788 4302 8.765517 TCCGAAAATAAAATAGTACTCCCTCTT 58.234 33.333 0.00 0.00 0.00 2.85
3789 4303 8.315220 TCCGAAAATAAAATAGTACTCCCTCT 57.685 34.615 0.00 0.00 0.00 3.69
3790 4304 9.557061 AATCCGAAAATAAAATAGTACTCCCTC 57.443 33.333 0.00 0.00 0.00 4.30
3791 4305 9.916360 AAATCCGAAAATAAAATAGTACTCCCT 57.084 29.630 0.00 0.00 0.00 4.20
3849 4363 5.668376 GCACAATTACATTTTCACGCCAATG 60.668 40.000 0.00 0.00 36.59 2.82
3856 4370 8.759641 TGTATTGTTGCACAATTACATTTTCAC 58.240 29.630 16.19 8.39 45.80 3.18
4000 4541 7.882791 CCCTGCTAATATAATGTCATGGTTGTA 59.117 37.037 0.00 0.00 0.00 2.41
4020 4578 1.078426 GTTCGTGTATGCCCCTGCT 60.078 57.895 0.00 0.00 38.71 4.24
4151 4712 3.651423 ACCTCTTAAGTGGCCTGTTAGTT 59.349 43.478 20.93 0.00 32.19 2.24


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

AutoCloner maintained by Alex Coulton.