Multiple sequence alignment - TraesCS5A01G092600

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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 TraesCS5A01G092600 chr5A 100.000 5119 0 0 1 5119 128425850 128430968 0.000000e+00 9454.0
1 TraesCS5A01G092600 chr5A 80.236 678 68 31 4467 5119 37974632 37975268 2.810000e-122 449.0
2 TraesCS5A01G092600 chr5A 84.559 136 19 2 2799 2932 94920763 94920628 3.220000e-27 134.0
3 TraesCS5A01G092600 chr5A 84.559 136 19 2 2799 2932 99084597 99084732 3.220000e-27 134.0
4 TraesCS5A01G092600 chr5D 94.390 5027 149 49 161 5119 118834308 118839269 0.000000e+00 7598.0
5 TraesCS5A01G092600 chr5D 80.639 563 57 22 4575 5119 47857639 47858167 6.220000e-104 388.0
6 TraesCS5A01G092600 chr5B 94.543 4068 113 36 273 4291 130910560 130914567 0.000000e+00 6181.0
7 TraesCS5A01G092600 chr5B 90.293 649 42 9 4477 5119 130914725 130915358 0.000000e+00 830.0
8 TraesCS5A01G092600 chr5B 88.095 210 22 3 4911 5119 50510811 50511018 3.960000e-61 246.0
9 TraesCS5A01G092600 chr5B 92.593 108 5 3 4572 4679 50510480 50510584 8.880000e-33 152.0
10 TraesCS5A01G092600 chr5B 84.672 137 18 3 2799 2932 606705542 606705678 3.220000e-27 134.0
11 TraesCS5A01G092600 chr1D 87.500 144 18 0 2789 2932 287831115 287830972 3.170000e-37 167.0
12 TraesCS5A01G092600 chr1B 85.034 147 22 0 3061 3207 389535051 389534905 3.190000e-32 150.0
13 TraesCS5A01G092600 chr1A 86.029 136 17 2 2799 2932 592524491 592524626 1.490000e-30 145.0
14 TraesCS5A01G092600 chr1A 100.000 28 0 0 96 123 319887170 319887143 9.000000e-03 52.8
15 TraesCS5A01G092600 chr7B 84.559 136 19 2 2799 2932 33979693 33979558 3.220000e-27 134.0
16 TraesCS5A01G092600 chr6B 84.559 136 19 2 2799 2932 63717473 63717608 3.220000e-27 134.0
17 TraesCS5A01G092600 chr3B 92.771 83 6 0 3272 3354 400527820 400527738 2.500000e-23 121.0
18 TraesCS5A01G092600 chr3B 89.157 83 9 0 3093 3175 660066368 660066450 2.520000e-18 104.0
19 TraesCS5A01G092600 chr7A 88.421 95 7 2 2142 2235 503779648 503779557 1.510000e-20 111.0
20 TraesCS5A01G092600 chr2B 85.149 101 10 2 5020 5119 11286937 11287033 1.170000e-16 99.0
21 TraesCS5A01G092600 chr4A 93.750 64 4 0 3278 3341 549001657 549001594 4.220000e-16 97.1
22 TraesCS5A01G092600 chr3A 91.304 46 1 2 2327 2372 477682152 477682110 5.540000e-05 60.2


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 TraesCS5A01G092600 chr5A 128425850 128430968 5118 False 9454.0 9454 100.000 1 5119 1 chr5A.!!$F3 5118
1 TraesCS5A01G092600 chr5A 37974632 37975268 636 False 449.0 449 80.236 4467 5119 1 chr5A.!!$F1 652
2 TraesCS5A01G092600 chr5D 118834308 118839269 4961 False 7598.0 7598 94.390 161 5119 1 chr5D.!!$F2 4958
3 TraesCS5A01G092600 chr5D 47857639 47858167 528 False 388.0 388 80.639 4575 5119 1 chr5D.!!$F1 544
4 TraesCS5A01G092600 chr5B 130910560 130915358 4798 False 3505.5 6181 92.418 273 5119 2 chr5B.!!$F3 4846

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
242 246 0.331616 CCTCCCCCGAATTGTTTCCT 59.668 55.000 0.0 0.0 0.00 3.36 F
509 514 0.535780 CCTGCACAGCAAGTCCAAGA 60.536 55.000 0.0 0.0 38.41 3.02 F
510 515 0.873054 CTGCACAGCAAGTCCAAGAG 59.127 55.000 0.0 0.0 38.41 2.85 F
577 582 0.890683 CTGTCGGGGTTAGGTACGTT 59.109 55.000 0.0 0.0 0.00 3.99 F
687 695 1.550179 GCCAAAAGAAAGCCCCCTACT 60.550 52.381 0.0 0.0 0.00 2.57 F
1142 1166 1.656441 CAGCAGGTCACTTGGTTGC 59.344 57.895 0.0 0.0 35.09 4.17 F
3295 3340 1.005805 CCATTCACCCTTGATGGACCA 59.994 52.381 0.0 0.0 38.35 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 1547 2.025981 TGGGGAGTTTGATCCATGTCTG 60.026 50.000 0.00 0.00 41.52 3.51 R
2371 2409 2.029290 GCCACGAGACACTCCTAAGAAA 60.029 50.000 0.00 0.00 0.00 2.52 R
2404 2442 2.070262 TGCTGTCGACAATGTCTGAG 57.930 50.000 20.49 6.26 0.00 3.35 R
2494 2532 4.828939 TGGATTGCAGAAATCAAGTCAGTT 59.171 37.500 3.34 0.00 45.69 3.16 R
3112 3157 4.320421 GCATGCATTGTGATAAATCCGCTA 60.320 41.667 14.21 0.00 0.00 4.26 R
3458 3514 0.469917 CACACGAGCCCATCCCTAAT 59.530 55.000 0.00 0.00 0.00 1.73 R
4950 5064 2.281484 ACGGTGCCAGAACGCATT 60.281 55.556 0.00 0.00 41.70 3.56 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
25 26 5.365021 AGGGACTCTTGGATCTTACAATG 57.635 43.478 0.00 0.00 0.00 2.82
26 27 5.032846 AGGGACTCTTGGATCTTACAATGA 58.967 41.667 0.00 0.00 0.00 2.57
27 28 5.130145 AGGGACTCTTGGATCTTACAATGAG 59.870 44.000 0.00 1.51 33.40 2.90
28 29 5.129485 GGGACTCTTGGATCTTACAATGAGA 59.871 44.000 12.22 0.00 32.48 3.27
29 30 6.352222 GGGACTCTTGGATCTTACAATGAGAA 60.352 42.308 12.22 0.00 32.48 2.87
30 31 7.106239 GGACTCTTGGATCTTACAATGAGAAA 58.894 38.462 12.22 0.00 32.48 2.52
31 32 7.279758 GGACTCTTGGATCTTACAATGAGAAAG 59.720 40.741 12.22 0.00 32.48 2.62
32 33 7.684529 ACTCTTGGATCTTACAATGAGAAAGT 58.315 34.615 12.22 0.00 32.48 2.66
33 34 8.160106 ACTCTTGGATCTTACAATGAGAAAGTT 58.840 33.333 12.22 0.00 32.48 2.66
34 35 8.327941 TCTTGGATCTTACAATGAGAAAGTTG 57.672 34.615 0.00 0.00 0.00 3.16
35 36 7.391554 TCTTGGATCTTACAATGAGAAAGTTGG 59.608 37.037 0.00 0.00 0.00 3.77
36 37 6.542821 TGGATCTTACAATGAGAAAGTTGGT 58.457 36.000 0.00 0.00 0.00 3.67
37 38 6.655003 TGGATCTTACAATGAGAAAGTTGGTC 59.345 38.462 0.00 0.00 0.00 4.02
38 39 6.655003 GGATCTTACAATGAGAAAGTTGGTCA 59.345 38.462 0.00 0.00 0.00 4.02
39 40 7.148340 GGATCTTACAATGAGAAAGTTGGTCAG 60.148 40.741 0.00 0.00 0.00 3.51
40 41 5.470098 TCTTACAATGAGAAAGTTGGTCAGC 59.530 40.000 0.00 0.00 0.00 4.26
41 42 3.554934 ACAATGAGAAAGTTGGTCAGCA 58.445 40.909 0.00 0.00 0.00 4.41
42 43 3.567164 ACAATGAGAAAGTTGGTCAGCAG 59.433 43.478 0.00 0.00 0.00 4.24
43 44 2.260844 TGAGAAAGTTGGTCAGCAGG 57.739 50.000 0.00 0.00 0.00 4.85
44 45 1.490490 TGAGAAAGTTGGTCAGCAGGT 59.510 47.619 0.00 0.00 0.00 4.00
45 46 2.703536 TGAGAAAGTTGGTCAGCAGGTA 59.296 45.455 0.00 0.00 0.00 3.08
46 47 3.327757 TGAGAAAGTTGGTCAGCAGGTAT 59.672 43.478 0.00 0.00 0.00 2.73
47 48 4.530553 TGAGAAAGTTGGTCAGCAGGTATA 59.469 41.667 0.00 0.00 0.00 1.47
48 49 5.091261 AGAAAGTTGGTCAGCAGGTATAG 57.909 43.478 0.00 0.00 0.00 1.31
49 50 4.777896 AGAAAGTTGGTCAGCAGGTATAGA 59.222 41.667 0.00 0.00 0.00 1.98
50 51 5.426833 AGAAAGTTGGTCAGCAGGTATAGAT 59.573 40.000 0.00 0.00 0.00 1.98
51 52 6.611642 AGAAAGTTGGTCAGCAGGTATAGATA 59.388 38.462 0.00 0.00 0.00 1.98
52 53 7.291182 AGAAAGTTGGTCAGCAGGTATAGATAT 59.709 37.037 0.00 0.00 0.00 1.63
53 54 8.492415 AAAGTTGGTCAGCAGGTATAGATATA 57.508 34.615 0.00 0.00 0.00 0.86
54 55 7.710676 AGTTGGTCAGCAGGTATAGATATAG 57.289 40.000 0.00 0.00 0.00 1.31
55 56 7.471041 AGTTGGTCAGCAGGTATAGATATAGA 58.529 38.462 0.00 0.00 0.00 1.98
56 57 8.119246 AGTTGGTCAGCAGGTATAGATATAGAT 58.881 37.037 0.00 0.00 0.00 1.98
57 58 9.409918 GTTGGTCAGCAGGTATAGATATAGATA 57.590 37.037 0.00 0.00 0.00 1.98
127 128 9.981460 AAGTTGGATCATCTATTTTAAAGGAGT 57.019 29.630 0.00 0.00 0.00 3.85
146 147 7.745620 AGGAGTAAATTGTTTCTCGAATTGT 57.254 32.000 0.00 0.00 0.00 2.71
147 148 7.584987 AGGAGTAAATTGTTTCTCGAATTGTG 58.415 34.615 0.00 0.00 0.00 3.33
148 149 6.801862 GGAGTAAATTGTTTCTCGAATTGTGG 59.198 38.462 0.00 0.00 0.00 4.17
149 150 7.272037 AGTAAATTGTTTCTCGAATTGTGGT 57.728 32.000 0.00 0.00 0.00 4.16
150 151 7.138736 AGTAAATTGTTTCTCGAATTGTGGTG 58.861 34.615 0.00 0.00 0.00 4.17
151 152 5.514274 AATTGTTTCTCGAATTGTGGTGT 57.486 34.783 0.00 0.00 0.00 4.16
152 153 6.627395 AATTGTTTCTCGAATTGTGGTGTA 57.373 33.333 0.00 0.00 0.00 2.90
153 154 5.412526 TTGTTTCTCGAATTGTGGTGTAC 57.587 39.130 0.00 0.00 0.00 2.90
154 155 3.810941 TGTTTCTCGAATTGTGGTGTACC 59.189 43.478 0.00 0.00 0.00 3.34
155 156 4.062991 GTTTCTCGAATTGTGGTGTACCT 58.937 43.478 2.32 0.00 36.82 3.08
156 157 5.221481 TGTTTCTCGAATTGTGGTGTACCTA 60.221 40.000 2.32 0.00 36.82 3.08
157 158 4.713824 TCTCGAATTGTGGTGTACCTAG 57.286 45.455 2.32 0.00 36.82 3.02
158 159 4.084287 TCTCGAATTGTGGTGTACCTAGT 58.916 43.478 2.32 0.00 36.82 2.57
159 160 4.157289 TCTCGAATTGTGGTGTACCTAGTC 59.843 45.833 2.32 0.00 36.82 2.59
171 172 6.495872 TGGTGTACCTAGTCAGTTCAGTAATT 59.504 38.462 2.32 0.00 36.82 1.40
186 187 3.621715 CAGTAATTTTCTCCACGGTAGCC 59.378 47.826 0.00 0.00 0.00 3.93
187 188 2.871096 AATTTTCTCCACGGTAGCCA 57.129 45.000 0.00 0.00 0.00 4.75
188 189 3.366052 AATTTTCTCCACGGTAGCCAT 57.634 42.857 0.00 0.00 0.00 4.40
191 192 0.535335 TTCTCCACGGTAGCCATCAC 59.465 55.000 0.00 0.00 0.00 3.06
192 193 1.226974 CTCCACGGTAGCCATCACG 60.227 63.158 0.00 0.00 0.00 4.35
193 194 2.202878 CCACGGTAGCCATCACGG 60.203 66.667 0.00 0.00 38.11 4.94
242 246 0.331616 CCTCCCCCGAATTGTTTCCT 59.668 55.000 0.00 0.00 0.00 3.36
250 254 1.885887 CGAATTGTTTCCTCTTGGGCA 59.114 47.619 0.00 0.00 34.39 5.36
251 255 2.295909 CGAATTGTTTCCTCTTGGGCAA 59.704 45.455 0.00 0.00 34.39 4.52
252 256 3.056607 CGAATTGTTTCCTCTTGGGCAAT 60.057 43.478 0.00 0.00 34.64 3.56
253 257 4.498241 GAATTGTTTCCTCTTGGGCAATC 58.502 43.478 0.00 0.00 33.30 2.67
254 258 1.923356 TGTTTCCTCTTGGGCAATCC 58.077 50.000 0.00 0.00 34.39 3.01
259 263 0.627986 CCTCTTGGGCAATCCTCCTT 59.372 55.000 0.00 0.00 36.20 3.36
260 264 1.684248 CCTCTTGGGCAATCCTCCTTG 60.684 57.143 0.00 0.00 36.20 3.61
372 377 3.864686 CGCCCGCATCAAAGACGG 61.865 66.667 0.00 0.00 46.50 4.79
452 457 0.977395 ACTTTCCCAACTCTCCTCGG 59.023 55.000 0.00 0.00 0.00 4.63
483 488 3.059982 CGTGTGCCTTCCTCTCCA 58.940 61.111 0.00 0.00 0.00 3.86
507 512 2.195567 GCCTGCACAGCAAGTCCAA 61.196 57.895 0.00 0.00 38.41 3.53
508 513 1.954528 CCTGCACAGCAAGTCCAAG 59.045 57.895 0.00 0.00 38.41 3.61
509 514 0.535780 CCTGCACAGCAAGTCCAAGA 60.536 55.000 0.00 0.00 38.41 3.02
510 515 0.873054 CTGCACAGCAAGTCCAAGAG 59.127 55.000 0.00 0.00 38.41 2.85
577 582 0.890683 CTGTCGGGGTTAGGTACGTT 59.109 55.000 0.00 0.00 0.00 3.99
590 595 8.783093 GGGTTAGGTACGTTTGTATTTTACTTT 58.217 33.333 0.00 0.00 32.11 2.66
687 695 1.550179 GCCAAAAGAAAGCCCCCTACT 60.550 52.381 0.00 0.00 0.00 2.57
747 755 3.988379 TCACATGTTCTGTTGCTTTCC 57.012 42.857 0.00 0.00 35.29 3.13
848 872 4.562963 GGTTACTTTGTCCCCTGTAGTGAG 60.563 50.000 0.00 0.00 0.00 3.51
870 894 1.827344 GGGGATTCTTGCCTTTTCCTG 59.173 52.381 0.00 0.00 32.95 3.86
910 934 2.270352 TGGAAAATCTGTGAACGCCT 57.730 45.000 0.00 0.00 0.00 5.52
977 1001 2.189594 CTGTCTCACAGGGATTTGCA 57.810 50.000 0.00 0.00 42.35 4.08
978 1002 2.719739 CTGTCTCACAGGGATTTGCAT 58.280 47.619 0.00 0.00 42.35 3.96
979 1003 3.877559 CTGTCTCACAGGGATTTGCATA 58.122 45.455 0.00 0.00 42.35 3.14
980 1004 3.609853 TGTCTCACAGGGATTTGCATAC 58.390 45.455 0.00 0.00 0.00 2.39
981 1005 3.264193 TGTCTCACAGGGATTTGCATACT 59.736 43.478 0.00 0.00 0.00 2.12
982 1006 3.873952 GTCTCACAGGGATTTGCATACTC 59.126 47.826 0.00 0.00 0.00 2.59
983 1007 3.519107 TCTCACAGGGATTTGCATACTCA 59.481 43.478 0.00 0.00 0.00 3.41
984 1008 3.609853 TCACAGGGATTTGCATACTCAC 58.390 45.455 0.00 0.00 0.00 3.51
985 1009 2.684881 CACAGGGATTTGCATACTCACC 59.315 50.000 0.00 0.00 0.00 4.02
986 1010 2.308570 ACAGGGATTTGCATACTCACCA 59.691 45.455 0.00 0.00 0.00 4.17
987 1011 2.684881 CAGGGATTTGCATACTCACCAC 59.315 50.000 0.00 0.00 0.00 4.16
988 1012 2.578021 AGGGATTTGCATACTCACCACT 59.422 45.455 0.00 0.00 0.00 4.00
989 1013 3.780294 AGGGATTTGCATACTCACCACTA 59.220 43.478 0.00 0.00 0.00 2.74
990 1014 4.413520 AGGGATTTGCATACTCACCACTAT 59.586 41.667 0.00 0.00 0.00 2.12
997 1021 8.492673 TTTGCATACTCACCACTATAAAGAAG 57.507 34.615 0.00 0.00 0.00 2.85
1081 1105 4.415150 CTGTGATGCCCCGGTGCT 62.415 66.667 11.12 0.00 0.00 4.40
1142 1166 1.656441 CAGCAGGTCACTTGGTTGC 59.344 57.895 0.00 0.00 35.09 4.17
1345 1382 4.910195 TGTCTTGATCTATGCTGTTGGTT 58.090 39.130 0.00 0.00 0.00 3.67
1355 1392 9.277783 GATCTATGCTGTTGGTTATCAAACTAT 57.722 33.333 0.00 0.00 37.08 2.12
1459 1496 4.209307 TGGAACGGCTATGTTAATGACA 57.791 40.909 0.00 0.00 43.71 3.58
1510 1547 7.646922 GCTTCATCATTGAGTGATCAAAATACC 59.353 37.037 0.00 0.00 45.76 2.73
2046 2084 6.092259 ACTGTCTGCACCGATAAATAAAAGAC 59.908 38.462 0.00 0.00 33.72 3.01
2102 2140 9.874205 AAATTCTCTTGAAGAAAACACAATTCA 57.126 25.926 0.00 0.00 46.85 2.57
2114 2152 8.997323 AGAAAACACAATTCACAATTTTGAACA 58.003 25.926 9.13 0.00 38.31 3.18
2156 2194 6.096673 TGAGTCTTGTAGATTGTGCTTACA 57.903 37.500 0.00 0.00 0.00 2.41
2404 2442 2.895372 CGTGGCGGGGCAAGTATC 60.895 66.667 0.00 0.00 0.00 2.24
2494 2532 5.818678 ACAAGGTGGTATGTTGAAGACTA 57.181 39.130 0.00 0.00 0.00 2.59
3000 3045 4.119862 TCTGCAAGCGGACAATAGAATAC 58.880 43.478 0.00 0.00 0.00 1.89
3112 3157 2.290577 GGTGAAGCTGATGGGAAGAAGT 60.291 50.000 0.00 0.00 0.00 3.01
3207 3252 5.485662 AACTCTTTAACTTGTGCTGTGTC 57.514 39.130 0.00 0.00 0.00 3.67
3295 3340 1.005805 CCATTCACCCTTGATGGACCA 59.994 52.381 0.00 0.00 38.35 4.02
3298 3343 2.286365 TCACCCTTGATGGACCAAAC 57.714 50.000 0.00 0.00 38.35 2.93
3358 3403 1.956477 GGGTTTGCTCTCATGTGTGTT 59.044 47.619 0.00 0.00 0.00 3.32
3407 3460 9.941664 GATTACCTTCACATACAAGATCAATTG 57.058 33.333 0.00 0.00 36.22 2.32
3471 3527 3.397527 TCTCTTGAATTAGGGATGGGCT 58.602 45.455 0.00 0.00 0.00 5.19
3492 3548 3.137533 TCGTGTGTGCATCAATTGAGAA 58.862 40.909 14.54 0.00 0.00 2.87
3495 3551 3.665409 GTGTGTGCATCAATTGAGAAACG 59.335 43.478 14.54 1.29 0.00 3.60
3497 3553 4.202000 TGTGTGCATCAATTGAGAAACGTT 60.202 37.500 14.54 0.00 0.00 3.99
3498 3554 4.146961 GTGTGCATCAATTGAGAAACGTTG 59.853 41.667 14.54 6.45 0.00 4.10
3499 3555 3.120121 GTGCATCAATTGAGAAACGTTGC 59.880 43.478 14.54 16.04 0.00 4.17
3500 3556 3.243334 TGCATCAATTGAGAAACGTTGCA 60.243 39.130 20.93 20.93 35.42 4.08
3501 3557 3.362831 GCATCAATTGAGAAACGTTGCAG 59.637 43.478 18.43 0.00 0.00 4.41
3502 3558 4.539870 CATCAATTGAGAAACGTTGCAGT 58.460 39.130 14.54 0.00 0.00 4.40
3505 3561 6.312399 TCAATTGAGAAACGTTGCAGTATT 57.688 33.333 9.44 1.74 0.00 1.89
3546 3602 8.743085 AGAATTGTTATGTGAGATATTGCACT 57.257 30.769 9.42 0.00 36.05 4.40
3574 3632 5.178096 TCCAGGAATATTTGCAGAAGTCA 57.822 39.130 0.00 0.00 0.00 3.41
3717 3775 7.936301 ACAACATTTAACTTAACCAATGCCATT 59.064 29.630 0.00 0.00 30.96 3.16
3718 3776 8.782144 CAACATTTAACTTAACCAATGCCATTT 58.218 29.630 0.00 0.00 30.96 2.32
4004 4062 2.227626 CACAACCGGAATATGCAACACA 59.772 45.455 9.46 0.00 0.00 3.72
4132 4190 7.094420 TGACTTTTGTTGATCAGTTCTTGACAA 60.094 33.333 3.35 3.35 38.99 3.18
4135 4193 4.522114 TGTTGATCAGTTCTTGACAACCA 58.478 39.130 0.00 0.00 41.68 3.67
4397 4476 8.692710 ACATCTTATATTCGTGAACAGGAGTAA 58.307 33.333 4.46 3.15 0.00 2.24
4569 4662 2.224499 TGTCTGCCATTTGAGTACAGCA 60.224 45.455 0.00 0.00 0.00 4.41
4813 4919 4.091509 CGTCATGGTTTAAGACACTAGTGC 59.908 45.833 22.90 14.96 32.68 4.40
4815 4921 2.409975 TGGTTTAAGACACTAGTGCGC 58.590 47.619 22.90 14.77 0.00 6.09
4869 4975 6.127675 ACCGACTCAAAATAGTAGAGAAGGTC 60.128 42.308 0.00 0.00 37.79 3.85
4881 4987 3.851098 AGAGAAGGTCAAACGATGCTAC 58.149 45.455 0.00 0.00 0.00 3.58
4887 4993 2.602878 GTCAAACGATGCTACGGAGAA 58.397 47.619 0.00 0.00 37.61 2.87
4941 5055 5.065704 TCAAACTGCAACTGTAAGCAAAA 57.934 34.783 8.81 0.00 40.73 2.44
4950 5064 6.317642 TGCAACTGTAAGCAAAAGAACTCTAA 59.682 34.615 5.51 0.00 37.90 2.10
5061 5187 6.231951 AGCTATCTATCTACTTGTGTAGCGA 58.768 40.000 0.00 0.00 44.26 4.93
5062 5188 6.370442 AGCTATCTATCTACTTGTGTAGCGAG 59.630 42.308 0.00 0.00 44.26 5.03
5064 5190 4.778579 TCTATCTACTTGTGTAGCGAGGT 58.221 43.478 0.00 0.00 44.26 3.85
5065 5191 5.191426 TCTATCTACTTGTGTAGCGAGGTT 58.809 41.667 0.00 0.00 44.26 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.282496 TGTAAGATCCAAGAGTCCCTCTC 58.718 47.826 0.00 0.00 40.28 3.20
1 2 4.338795 TGTAAGATCCAAGAGTCCCTCT 57.661 45.455 0.00 0.00 43.37 3.69
2 3 5.129485 TCATTGTAAGATCCAAGAGTCCCTC 59.871 44.000 0.00 0.00 0.00 4.30
3 4 5.032846 TCATTGTAAGATCCAAGAGTCCCT 58.967 41.667 0.00 0.00 0.00 4.20
4 5 5.129485 TCTCATTGTAAGATCCAAGAGTCCC 59.871 44.000 0.00 0.00 0.00 4.46
5 6 6.227298 TCTCATTGTAAGATCCAAGAGTCC 57.773 41.667 0.00 0.00 0.00 3.85
6 7 7.821846 ACTTTCTCATTGTAAGATCCAAGAGTC 59.178 37.037 0.00 0.00 0.00 3.36
7 8 7.684529 ACTTTCTCATTGTAAGATCCAAGAGT 58.315 34.615 0.00 0.00 0.00 3.24
8 9 8.449397 CAACTTTCTCATTGTAAGATCCAAGAG 58.551 37.037 0.00 0.00 0.00 2.85
9 10 7.391554 CCAACTTTCTCATTGTAAGATCCAAGA 59.608 37.037 0.00 0.00 0.00 3.02
10 11 7.175641 ACCAACTTTCTCATTGTAAGATCCAAG 59.824 37.037 0.00 0.00 0.00 3.61
11 12 7.004086 ACCAACTTTCTCATTGTAAGATCCAA 58.996 34.615 0.00 0.00 0.00 3.53
12 13 6.542821 ACCAACTTTCTCATTGTAAGATCCA 58.457 36.000 0.00 0.00 0.00 3.41
13 14 6.655003 TGACCAACTTTCTCATTGTAAGATCC 59.345 38.462 0.00 0.00 0.00 3.36
14 15 7.625185 GCTGACCAACTTTCTCATTGTAAGATC 60.625 40.741 0.00 0.00 0.00 2.75
15 16 6.150140 GCTGACCAACTTTCTCATTGTAAGAT 59.850 38.462 0.00 0.00 0.00 2.40
16 17 5.470098 GCTGACCAACTTTCTCATTGTAAGA 59.530 40.000 0.00 0.00 0.00 2.10
17 18 5.239306 TGCTGACCAACTTTCTCATTGTAAG 59.761 40.000 0.00 0.00 0.00 2.34
18 19 5.129634 TGCTGACCAACTTTCTCATTGTAA 58.870 37.500 0.00 0.00 0.00 2.41
19 20 4.713553 TGCTGACCAACTTTCTCATTGTA 58.286 39.130 0.00 0.00 0.00 2.41
20 21 3.554934 TGCTGACCAACTTTCTCATTGT 58.445 40.909 0.00 0.00 0.00 2.71
21 22 3.057736 CCTGCTGACCAACTTTCTCATTG 60.058 47.826 0.00 0.00 0.00 2.82
22 23 3.152341 CCTGCTGACCAACTTTCTCATT 58.848 45.455 0.00 0.00 0.00 2.57
23 24 2.107204 ACCTGCTGACCAACTTTCTCAT 59.893 45.455 0.00 0.00 0.00 2.90
24 25 1.490490 ACCTGCTGACCAACTTTCTCA 59.510 47.619 0.00 0.00 0.00 3.27
25 26 2.262423 ACCTGCTGACCAACTTTCTC 57.738 50.000 0.00 0.00 0.00 2.87
26 27 4.777896 TCTATACCTGCTGACCAACTTTCT 59.222 41.667 0.00 0.00 0.00 2.52
27 28 5.086104 TCTATACCTGCTGACCAACTTTC 57.914 43.478 0.00 0.00 0.00 2.62
28 29 5.700402 ATCTATACCTGCTGACCAACTTT 57.300 39.130 0.00 0.00 0.00 2.66
29 30 7.950684 TCTATATCTATACCTGCTGACCAACTT 59.049 37.037 0.00 0.00 0.00 2.66
30 31 7.471041 TCTATATCTATACCTGCTGACCAACT 58.529 38.462 0.00 0.00 0.00 3.16
31 32 7.704578 TCTATATCTATACCTGCTGACCAAC 57.295 40.000 0.00 0.00 0.00 3.77
101 102 9.981460 ACTCCTTTAAAATAGATGATCCAACTT 57.019 29.630 4.01 0.00 0.00 2.66
120 121 8.630037 ACAATTCGAGAAACAATTTACTCCTTT 58.370 29.630 0.00 0.00 0.00 3.11
121 122 8.076178 CACAATTCGAGAAACAATTTACTCCTT 58.924 33.333 0.00 0.00 0.00 3.36
122 123 7.308589 CCACAATTCGAGAAACAATTTACTCCT 60.309 37.037 0.00 0.00 0.00 3.69
123 124 6.801862 CCACAATTCGAGAAACAATTTACTCC 59.198 38.462 0.00 0.00 0.00 3.85
124 125 7.323656 CACCACAATTCGAGAAACAATTTACTC 59.676 37.037 0.00 0.00 0.00 2.59
125 126 7.138736 CACCACAATTCGAGAAACAATTTACT 58.861 34.615 0.00 0.00 0.00 2.24
126 127 6.915843 ACACCACAATTCGAGAAACAATTTAC 59.084 34.615 0.00 0.00 0.00 2.01
127 128 7.033530 ACACCACAATTCGAGAAACAATTTA 57.966 32.000 0.00 0.00 0.00 1.40
128 129 5.901552 ACACCACAATTCGAGAAACAATTT 58.098 33.333 0.00 0.00 0.00 1.82
129 130 5.514274 ACACCACAATTCGAGAAACAATT 57.486 34.783 0.00 0.00 0.00 2.32
130 131 5.048991 GGTACACCACAATTCGAGAAACAAT 60.049 40.000 0.00 0.00 35.64 2.71
131 132 4.273969 GGTACACCACAATTCGAGAAACAA 59.726 41.667 0.00 0.00 35.64 2.83
132 133 3.810941 GGTACACCACAATTCGAGAAACA 59.189 43.478 0.00 0.00 35.64 2.83
133 134 4.062991 AGGTACACCACAATTCGAGAAAC 58.937 43.478 0.38 0.00 38.89 2.78
134 135 4.345859 AGGTACACCACAATTCGAGAAA 57.654 40.909 0.38 0.00 38.89 2.52
135 136 4.525487 ACTAGGTACACCACAATTCGAGAA 59.475 41.667 0.38 0.00 38.89 2.87
136 137 4.084287 ACTAGGTACACCACAATTCGAGA 58.916 43.478 0.38 0.00 38.89 4.04
137 138 4.082408 TGACTAGGTACACCACAATTCGAG 60.082 45.833 0.38 0.00 38.89 4.04
138 139 3.827876 TGACTAGGTACACCACAATTCGA 59.172 43.478 0.38 0.00 38.89 3.71
139 140 4.174009 CTGACTAGGTACACCACAATTCG 58.826 47.826 0.38 0.00 38.89 3.34
140 141 5.148651 ACTGACTAGGTACACCACAATTC 57.851 43.478 0.38 0.00 38.89 2.17
141 142 5.071250 TGAACTGACTAGGTACACCACAATT 59.929 40.000 0.38 0.00 38.89 2.32
142 143 4.591498 TGAACTGACTAGGTACACCACAAT 59.409 41.667 0.38 0.00 38.89 2.71
143 144 3.962063 TGAACTGACTAGGTACACCACAA 59.038 43.478 0.38 0.00 38.89 3.33
144 145 3.568443 TGAACTGACTAGGTACACCACA 58.432 45.455 0.38 0.00 38.89 4.17
145 146 3.573110 ACTGAACTGACTAGGTACACCAC 59.427 47.826 0.38 0.00 38.89 4.16
146 147 3.840991 ACTGAACTGACTAGGTACACCA 58.159 45.455 0.38 0.00 38.89 4.17
147 148 5.972107 TTACTGAACTGACTAGGTACACC 57.028 43.478 0.00 0.00 0.00 4.16
148 149 8.828688 AAAATTACTGAACTGACTAGGTACAC 57.171 34.615 0.00 0.00 0.00 2.90
149 150 8.867097 AGAAAATTACTGAACTGACTAGGTACA 58.133 33.333 0.00 0.00 0.00 2.90
150 151 9.356433 GAGAAAATTACTGAACTGACTAGGTAC 57.644 37.037 0.00 0.00 0.00 3.34
151 152 8.529476 GGAGAAAATTACTGAACTGACTAGGTA 58.471 37.037 0.00 0.00 0.00 3.08
152 153 7.016268 TGGAGAAAATTACTGAACTGACTAGGT 59.984 37.037 0.00 0.00 0.00 3.08
153 154 7.332182 GTGGAGAAAATTACTGAACTGACTAGG 59.668 40.741 0.00 0.00 0.00 3.02
154 155 7.062371 CGTGGAGAAAATTACTGAACTGACTAG 59.938 40.741 0.00 0.00 0.00 2.57
155 156 6.866770 CGTGGAGAAAATTACTGAACTGACTA 59.133 38.462 0.00 0.00 0.00 2.59
156 157 5.696724 CGTGGAGAAAATTACTGAACTGACT 59.303 40.000 0.00 0.00 0.00 3.41
157 158 5.107065 CCGTGGAGAAAATTACTGAACTGAC 60.107 44.000 0.00 0.00 0.00 3.51
158 159 4.994852 CCGTGGAGAAAATTACTGAACTGA 59.005 41.667 0.00 0.00 0.00 3.41
159 160 4.755123 ACCGTGGAGAAAATTACTGAACTG 59.245 41.667 0.00 0.00 0.00 3.16
171 172 1.066430 GTGATGGCTACCGTGGAGAAA 60.066 52.381 0.00 0.00 0.00 2.52
186 187 2.446848 ATGGAGGAGGCCCGTGATG 61.447 63.158 0.00 0.00 37.58 3.07
187 188 2.040464 ATGGAGGAGGCCCGTGAT 60.040 61.111 0.00 0.00 37.58 3.06
188 189 3.083349 CATGGAGGAGGCCCGTGA 61.083 66.667 0.00 0.00 41.97 4.35
242 246 1.075601 ACAAGGAGGATTGCCCAAGA 58.924 50.000 0.00 0.00 37.41 3.02
250 254 2.373169 TGAGCTGACAACAAGGAGGATT 59.627 45.455 0.00 0.00 0.00 3.01
251 255 1.980765 TGAGCTGACAACAAGGAGGAT 59.019 47.619 0.00 0.00 0.00 3.24
252 256 1.423584 TGAGCTGACAACAAGGAGGA 58.576 50.000 0.00 0.00 0.00 3.71
253 257 2.260844 TTGAGCTGACAACAAGGAGG 57.739 50.000 0.00 0.00 0.00 4.30
254 258 4.637483 TTTTTGAGCTGACAACAAGGAG 57.363 40.909 0.00 0.00 0.00 3.69
507 512 0.892063 GGAAACGCACCTCTCTCTCT 59.108 55.000 0.00 0.00 0.00 3.10
508 513 0.892063 AGGAAACGCACCTCTCTCTC 59.108 55.000 0.00 0.00 31.43 3.20
509 514 0.605589 CAGGAAACGCACCTCTCTCT 59.394 55.000 0.00 0.00 35.35 3.10
510 515 1.016653 GCAGGAAACGCACCTCTCTC 61.017 60.000 0.00 0.00 35.35 3.20
590 595 4.992319 CCAACCATCGCGATTTTATACCTA 59.008 41.667 21.14 0.00 0.00 3.08
687 695 4.080919 CAGGACAAATCATGTGAGTAGGGA 60.081 45.833 0.00 0.00 44.12 4.20
816 835 3.826729 GGGACAAAGTAACCAGCTGAATT 59.173 43.478 17.39 11.79 0.00 2.17
817 836 3.421844 GGGACAAAGTAACCAGCTGAAT 58.578 45.455 17.39 5.82 0.00 2.57
870 894 4.260784 CCAACAGCAACTCAACTGTAGAAC 60.261 45.833 0.00 0.00 46.17 3.01
970 994 8.662781 TCTTTATAGTGGTGAGTATGCAAATC 57.337 34.615 0.00 0.00 0.00 2.17
971 995 9.113838 CTTCTTTATAGTGGTGAGTATGCAAAT 57.886 33.333 0.00 0.00 0.00 2.32
972 996 7.065803 GCTTCTTTATAGTGGTGAGTATGCAAA 59.934 37.037 0.00 0.00 0.00 3.68
973 997 6.538742 GCTTCTTTATAGTGGTGAGTATGCAA 59.461 38.462 0.00 0.00 0.00 4.08
974 998 6.049149 GCTTCTTTATAGTGGTGAGTATGCA 58.951 40.000 0.00 0.00 0.00 3.96
975 999 5.467063 GGCTTCTTTATAGTGGTGAGTATGC 59.533 44.000 0.00 0.00 0.00 3.14
976 1000 6.582636 TGGCTTCTTTATAGTGGTGAGTATG 58.417 40.000 0.00 0.00 0.00 2.39
977 1001 6.808321 TGGCTTCTTTATAGTGGTGAGTAT 57.192 37.500 0.00 0.00 0.00 2.12
978 1002 6.408092 CCATGGCTTCTTTATAGTGGTGAGTA 60.408 42.308 0.00 0.00 0.00 2.59
979 1003 5.431765 CATGGCTTCTTTATAGTGGTGAGT 58.568 41.667 0.00 0.00 0.00 3.41
980 1004 4.818546 CCATGGCTTCTTTATAGTGGTGAG 59.181 45.833 0.00 0.00 0.00 3.51
981 1005 4.780815 CCATGGCTTCTTTATAGTGGTGA 58.219 43.478 0.00 0.00 0.00 4.02
982 1006 3.316308 GCCATGGCTTCTTTATAGTGGTG 59.684 47.826 29.98 0.00 38.26 4.17
983 1007 3.555966 GCCATGGCTTCTTTATAGTGGT 58.444 45.455 29.98 0.00 38.26 4.16
997 1021 2.323580 GCGATGCTAGAGCCATGGC 61.324 63.158 30.12 30.12 41.18 4.40
1081 1105 4.039852 TCCAATAGTACATCGCAAGCCATA 59.960 41.667 0.00 0.00 37.18 2.74
1459 1496 2.614057 CCTTCAAAAGTGCTCTGTCGTT 59.386 45.455 0.00 0.00 0.00 3.85
1510 1547 2.025981 TGGGGAGTTTGATCCATGTCTG 60.026 50.000 0.00 0.00 41.52 3.51
2102 2140 2.808244 CACGGCACTGTTCAAAATTGT 58.192 42.857 0.00 0.00 0.00 2.71
2156 2194 7.540299 TGTTTTTCACTCCGTATTTTTCAAGT 58.460 30.769 0.00 0.00 0.00 3.16
2371 2409 2.029290 GCCACGAGACACTCCTAAGAAA 60.029 50.000 0.00 0.00 0.00 2.52
2404 2442 2.070262 TGCTGTCGACAATGTCTGAG 57.930 50.000 20.49 6.26 0.00 3.35
2446 2484 7.835822 AGTAAACATATTTTTGCAGCATACCA 58.164 30.769 0.00 0.00 0.00 3.25
2483 2521 7.987458 AGAAATCAAGTCAGTTAGTCTTCAACA 59.013 33.333 0.00 0.00 0.00 3.33
2494 2532 4.828939 TGGATTGCAGAAATCAAGTCAGTT 59.171 37.500 3.34 0.00 45.69 3.16
3112 3157 4.320421 GCATGCATTGTGATAAATCCGCTA 60.320 41.667 14.21 0.00 0.00 4.26
3207 3252 4.503991 GGATATAGTGAGTTGGAAGGGCAG 60.504 50.000 0.00 0.00 0.00 4.85
3295 3340 0.883370 GGTGCCGAAGAACTCCGTTT 60.883 55.000 0.00 0.00 0.00 3.60
3298 3343 1.004918 AAGGTGCCGAAGAACTCCG 60.005 57.895 0.00 0.00 0.00 4.63
3407 3460 3.219281 TGGCAGTTAAGTTTCCCAAGAC 58.781 45.455 0.00 0.00 0.00 3.01
3458 3514 0.469917 CACACGAGCCCATCCCTAAT 59.530 55.000 0.00 0.00 0.00 1.73
3471 3527 2.765122 TCTCAATTGATGCACACACGA 58.235 42.857 8.96 0.00 0.00 4.35
3492 3548 5.065988 ACAGAACAGAAAATACTGCAACGTT 59.934 36.000 0.00 0.00 41.06 3.99
3495 3551 7.414436 TGTAACAGAACAGAAAATACTGCAAC 58.586 34.615 0.00 0.00 41.06 4.17
3497 3553 7.497579 TCTTGTAACAGAACAGAAAATACTGCA 59.502 33.333 0.00 0.00 41.06 4.41
3498 3554 7.861630 TCTTGTAACAGAACAGAAAATACTGC 58.138 34.615 0.00 0.00 41.06 4.40
3527 3583 9.869844 GAAACATAGTGCAATATCTCACATAAC 57.130 33.333 3.16 0.00 35.76 1.89
3538 3594 8.995027 AATATTCCTGGAAACATAGTGCAATA 57.005 30.769 14.03 0.00 41.51 1.90
3541 3597 6.405731 GCAAATATTCCTGGAAACATAGTGCA 60.406 38.462 14.03 0.00 41.51 4.57
3543 3599 7.067372 TCTGCAAATATTCCTGGAAACATAGTG 59.933 37.037 14.03 11.71 41.51 2.74
3546 3602 7.615365 ACTTCTGCAAATATTCCTGGAAACATA 59.385 33.333 14.03 1.80 41.51 2.29
3684 3742 9.877178 TTGGTTAAGTTAAATGTTGTGTCATTT 57.123 25.926 0.00 9.12 45.83 2.32
3717 3775 6.762333 TCTGAAATGAGACTTGATCTGTGAA 58.238 36.000 0.00 0.00 38.00 3.18
3718 3776 6.210185 TCTCTGAAATGAGACTTGATCTGTGA 59.790 38.462 0.00 0.00 38.00 3.58
4004 4062 2.843401 TTGGCAGGTACACGTTATGT 57.157 45.000 0.00 0.00 46.06 2.29
4317 4379 9.495572 TGGACTGAAATTTGTTTACAAGTTTTT 57.504 25.926 14.58 8.11 42.96 1.94
4318 4380 8.931775 GTGGACTGAAATTTGTTTACAAGTTTT 58.068 29.630 14.58 10.01 42.96 2.43
4319 4381 8.091449 TGTGGACTGAAATTTGTTTACAAGTTT 58.909 29.630 13.66 13.66 44.70 2.66
4324 4386 6.977502 CACATGTGGACTGAAATTTGTTTACA 59.022 34.615 18.51 0.00 0.00 2.41
4325 4387 7.393551 CACATGTGGACTGAAATTTGTTTAC 57.606 36.000 18.51 0.00 0.00 2.01
4569 4662 8.814038 AGAAATTAGAGGCAATGTATGTCTTT 57.186 30.769 0.00 0.00 46.26 2.52
4857 4963 3.511934 AGCATCGTTTGACCTTCTCTACT 59.488 43.478 0.00 0.00 0.00 2.57
4869 4975 4.317139 CGTAATTCTCCGTAGCATCGTTTG 60.317 45.833 0.00 0.00 0.00 2.93
4881 4987 4.496010 CGAGCCTATATCCGTAATTCTCCG 60.496 50.000 0.00 0.00 0.00 4.63
4887 4993 6.541641 CCTTAGTACGAGCCTATATCCGTAAT 59.458 42.308 0.00 0.00 38.89 1.89
4950 5064 2.281484 ACGGTGCCAGAACGCATT 60.281 55.556 0.00 0.00 41.70 3.56
4966 5080 8.050930 TCCATTTTACAAAGGGTATAGAAGGAC 58.949 37.037 0.20 0.00 0.00 3.85
5061 5187 5.564550 ACTGCAGATTGATCAAGTTAACCT 58.435 37.500 23.35 0.00 0.00 3.50
5062 5188 5.886960 ACTGCAGATTGATCAAGTTAACC 57.113 39.130 23.35 1.12 0.00 2.85
5064 5190 6.348458 CCGAAACTGCAGATTGATCAAGTTAA 60.348 38.462 23.35 0.00 31.44 2.01
5065 5191 5.122239 CCGAAACTGCAGATTGATCAAGTTA 59.878 40.000 23.35 0.00 31.44 2.24


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

AutoCloner maintained by Alex Coulton.