Multiple sequence alignment - TraesCS5D01G334600

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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 TraesCS5D01G334600 chr5D 100.000 3533 0 0 1 3533 424126805 424123273 0.000000e+00 6525.0
1 TraesCS5D01G334600 chr5D 82.595 1534 259 5 994 2520 424166933 424165401 0.000000e+00 1347.0
2 TraesCS5D01G334600 chr5D 79.765 341 42 19 229 547 8182002 8181667 4.590000e-54 222.0
3 TraesCS5D01G334600 chr5D 81.481 189 24 9 226 406 8363316 8363501 1.020000e-30 145.0
4 TraesCS5D01G334600 chr5A 94.570 3131 133 14 38 3153 537770181 537767073 0.000000e+00 4806.0
5 TraesCS5D01G334600 chr5A 82.345 1535 261 6 994 2520 537788145 537786613 0.000000e+00 1325.0
6 TraesCS5D01G334600 chr5A 92.982 285 13 3 3254 3533 537767077 537766795 3.280000e-110 409.0
7 TraesCS5D01G334600 chr5A 95.238 126 3 3 3134 3257 16499937 16500061 2.780000e-46 196.0
8 TraesCS5D01G334600 chr5A 80.228 263 49 3 287 547 66194847 66195108 1.000000e-45 195.0
9 TraesCS5D01G334600 chr5A 93.077 130 7 2 3136 3265 119066885 119067012 4.660000e-44 189.0
10 TraesCS5D01G334600 chr5B 91.821 2922 182 29 3 2884 512842651 512839747 0.000000e+00 4019.0
11 TraesCS5D01G334600 chr5B 82.203 1534 265 5 994 2520 512943131 512941599 0.000000e+00 1314.0
12 TraesCS5D01G334600 chr2A 90.250 1518 123 9 1111 2621 2188244 2186745 0.000000e+00 1960.0
13 TraesCS5D01G334600 chr2A 86.170 188 21 3 914 1098 2189132 2188947 7.740000e-47 198.0
14 TraesCS5D01G334600 chr2A 82.558 86 9 6 3093 3177 767942928 767943008 1.760000e-08 71.3
15 TraesCS5D01G334600 chr2B 71.841 1282 305 42 1289 2533 778003962 778002700 2.050000e-82 316.0
16 TraesCS5D01G334600 chr2B 86.034 179 23 2 371 548 25632142 25631965 1.290000e-44 191.0
17 TraesCS5D01G334600 chr2B 97.222 36 1 0 3485 3520 413448907 413448872 1.060000e-05 62.1
18 TraesCS5D01G334600 chrUn 71.529 1282 309 43 1289 2533 242563711 242564973 9.590000e-76 294.0
19 TraesCS5D01G334600 chrUn 71.529 1282 309 42 1289 2533 316214329 316213067 9.590000e-76 294.0
20 TraesCS5D01G334600 chr7D 83.142 261 33 9 296 551 170344070 170343816 9.870000e-56 228.0
21 TraesCS5D01G334600 chr7D 99.099 111 0 1 3151 3261 248393512 248393403 7.740000e-47 198.0
22 TraesCS5D01G334600 chr2D 84.444 225 32 3 327 548 446202433 446202657 5.940000e-53 219.0
23 TraesCS5D01G334600 chr4A 87.363 182 22 1 371 551 7158339 7158158 1.290000e-49 207.0
24 TraesCS5D01G334600 chr4A 96.748 123 2 2 3138 3258 557549914 557549792 1.660000e-48 204.0
25 TraesCS5D01G334600 chr4A 94.697 132 5 2 3147 3276 593739134 593739003 1.660000e-48 204.0
26 TraesCS5D01G334600 chr4A 99.107 112 1 0 3147 3258 576122159 576122270 5.980000e-48 202.0
27 TraesCS5D01G334600 chr3A 100.000 109 0 0 3150 3258 46169100 46169208 5.980000e-48 202.0
28 TraesCS5D01G334600 chr6A 97.436 117 2 1 3149 3265 183352233 183352118 7.740000e-47 198.0
29 TraesCS5D01G334600 chr3D 86.932 176 22 1 373 547 131348886 131349061 2.780000e-46 196.0
30 TraesCS5D01G334600 chr3D 95.902 122 3 2 3147 3267 134497419 134497299 2.780000e-46 196.0
31 TraesCS5D01G334600 chr1B 86.517 178 23 1 371 547 223751208 223751385 1.000000e-45 195.0
32 TraesCS5D01G334600 chr1B 97.297 37 1 0 3485 3521 1733395 1733431 2.940000e-06 63.9
33 TraesCS5D01G334600 chr4D 77.885 312 50 13 251 544 470204029 470204339 3.620000e-40 176.0
34 TraesCS5D01G334600 chr1D 80.952 105 13 5 46 144 492900643 492900746 3.780000e-10 76.8
35 TraesCS5D01G334600 chr6B 100.000 34 0 0 3488 3521 157110869 157110902 2.940000e-06 63.9
36 TraesCS5D01G334600 chr7A 94.444 36 2 0 3485 3520 122178233 122178268 4.930000e-04 56.5
37 TraesCS5D01G334600 chr4B 100.000 30 0 0 3485 3514 146471682 146471711 4.930000e-04 56.5
38 TraesCS5D01G334600 chr1A 100.000 29 0 0 3485 3513 472082287 472082315 2.000000e-03 54.7


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 TraesCS5D01G334600 chr5D 424123273 424126805 3532 True 6525.0 6525 100.000 1 3533 1 chr5D.!!$R2 3532
1 TraesCS5D01G334600 chr5D 424165401 424166933 1532 True 1347.0 1347 82.595 994 2520 1 chr5D.!!$R3 1526
2 TraesCS5D01G334600 chr5A 537766795 537770181 3386 True 2607.5 4806 93.776 38 3533 2 chr5A.!!$R2 3495
3 TraesCS5D01G334600 chr5A 537786613 537788145 1532 True 1325.0 1325 82.345 994 2520 1 chr5A.!!$R1 1526
4 TraesCS5D01G334600 chr5B 512839747 512842651 2904 True 4019.0 4019 91.821 3 2884 1 chr5B.!!$R1 2881
5 TraesCS5D01G334600 chr5B 512941599 512943131 1532 True 1314.0 1314 82.203 994 2520 1 chr5B.!!$R2 1526
6 TraesCS5D01G334600 chr2A 2186745 2189132 2387 True 1079.0 1960 88.210 914 2621 2 chr2A.!!$R1 1707
7 TraesCS5D01G334600 chr2B 778002700 778003962 1262 True 316.0 316 71.841 1289 2533 1 chr2B.!!$R3 1244
8 TraesCS5D01G334600 chrUn 242563711 242564973 1262 False 294.0 294 71.529 1289 2533 1 chrUn.!!$F1 1244
9 TraesCS5D01G334600 chrUn 316213067 316214329 1262 True 294.0 294 71.529 1289 2533 1 chrUn.!!$R1 1244

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
529 538 0.039437 GTCCAACTCGCTCGAACTCA 60.039 55.000 0.00 0.00 0.00 3.41 F
599 608 0.607489 ACATGCCTCACTTCAGCACC 60.607 55.000 0.00 0.00 39.77 5.01 F
1214 1921 0.615850 GCCTTTGACCTCCTAGCACT 59.384 55.000 0.00 0.00 0.00 4.40 F
1381 2088 1.001268 GCTCACTCTTCACTGTCGACA 60.001 52.381 18.88 18.88 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 2152 0.108585 AACACGTGTTCATCAGCCCT 59.891 50.0 27.7 1.89 31.64 5.19 R
1798 2507 0.179468 ATAACATGGTCGTTCCCCCG 59.821 55.0 0.0 0.00 34.77 5.73 R
2164 2894 0.381801 CCACTTGGCATTACATCGGC 59.618 55.0 0.0 0.00 0.00 5.54 R
3241 4002 0.327924 TACGTACTCCCTCCGTTCCA 59.672 55.0 0.0 0.00 36.12 3.53 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
68 70 5.763444 TCGAAAAGAAACGAGCTGAATAG 57.237 39.130 0.00 0.00 34.49 1.73
96 102 8.809468 ACTATATGTAGCTCGATCCAGAAATA 57.191 34.615 0.00 0.00 0.00 1.40
151 157 6.505044 TTAGCTCGATAACTCGGCATAATA 57.495 37.500 0.00 0.00 45.10 0.98
355 363 2.224670 TGTTGTGCCTTACCTAGTTGGG 60.225 50.000 0.00 0.00 41.11 4.12
424 432 1.201343 GCTCGAGATCGTTACAAGCC 58.799 55.000 18.75 0.00 40.80 4.35
438 446 5.448225 CGTTACAAGCCGAGTAAGAGTCATA 60.448 44.000 0.00 0.00 32.56 2.15
444 452 7.231722 ACAAGCCGAGTAAGAGTCATATTCTAT 59.768 37.037 0.00 0.00 0.00 1.98
482 490 2.793946 CCAATTTGGGCTCGCTCG 59.206 61.111 7.60 0.00 32.67 5.03
489 497 1.581934 TTGGGCTCGCTCGAATATTG 58.418 50.000 0.00 0.00 0.00 1.90
502 511 5.559799 GCTCGAATATTGAATGAGTTGAGCC 60.560 44.000 12.29 1.23 39.24 4.70
506 515 2.839486 TTGAATGAGTTGAGCCGAGT 57.161 45.000 0.00 0.00 0.00 4.18
529 538 0.039437 GTCCAACTCGCTCGAACTCA 60.039 55.000 0.00 0.00 0.00 3.41
599 608 0.607489 ACATGCCTCACTTCAGCACC 60.607 55.000 0.00 0.00 39.77 5.01
617 626 1.517257 CAGAGGCCACATCGACGTC 60.517 63.158 5.01 5.18 0.00 4.34
621 630 3.179265 GCCACATCGACGTCACGG 61.179 66.667 17.16 8.69 0.00 4.94
638 647 1.813192 GGAGACGAGGCAGGAGAAG 59.187 63.158 0.00 0.00 0.00 2.85
989 1003 4.019411 TGCATCTCCGAGATCTCTCTCTAT 60.019 45.833 20.26 5.13 44.92 1.98
1046 1060 1.287425 GCATTCTCGTTCTTACCGGG 58.713 55.000 6.32 0.00 0.00 5.73
1051 1065 0.886563 CTCGTTCTTACCGGGACTGT 59.113 55.000 6.32 0.00 0.00 3.55
1214 1921 0.615850 GCCTTTGACCTCCTAGCACT 59.384 55.000 0.00 0.00 0.00 4.40
1248 1955 4.080299 AGCCTAAAGTTTGCCATAGCTAGT 60.080 41.667 0.00 0.00 40.80 2.57
1269 1976 7.338957 GCTAGTATACGGATATTCCTAACCTGT 59.661 40.741 0.00 0.00 33.30 4.00
1305 2012 5.667539 TCCAACACATTTTCACCTTGAAA 57.332 34.783 0.00 0.00 43.84 2.69
1381 2088 1.001268 GCTCACTCTTCACTGTCGACA 60.001 52.381 18.88 18.88 0.00 4.35
1382 2089 2.543861 GCTCACTCTTCACTGTCGACAA 60.544 50.000 20.49 1.33 0.00 3.18
1419 2128 3.098555 CGCACGAATTACCAGGGC 58.901 61.111 0.00 0.00 0.00 5.19
1443 2152 3.246112 AGCAGCCCACGGTTGGTA 61.246 61.111 0.00 0.00 42.42 3.25
1575 2284 2.307929 CTCGTGTTCGACCTATATGCG 58.692 52.381 0.00 0.00 41.35 4.73
1798 2507 3.204306 TGGACATGATCATGAAGAGGC 57.796 47.619 36.37 14.34 41.20 4.70
2080 2810 7.225341 CGATGTTGGATCTAGATGATGTCAAAA 59.775 37.037 10.74 2.91 35.14 2.44
2164 2894 1.564622 CGCAAGTCTGTTGTCACCG 59.435 57.895 0.00 0.00 0.00 4.94
2675 3414 2.074579 TCCCCCACCAAATTACTTCCA 58.925 47.619 0.00 0.00 0.00 3.53
2966 3726 3.666345 ACGGAGGGAGTTGTATCTACT 57.334 47.619 0.00 0.00 0.00 2.57
2970 3730 4.024218 CGGAGGGAGTTGTATCTACTTACG 60.024 50.000 0.00 0.00 0.00 3.18
3047 3807 8.570068 TTAGATGGTGTTTTTCATACCCTTAC 57.430 34.615 0.00 0.00 33.51 2.34
3060 3820 7.154435 TCATACCCTTACGATAATCTAGCAC 57.846 40.000 0.00 0.00 0.00 4.40
3065 3825 6.548622 ACCCTTACGATAATCTAGCACAACTA 59.451 38.462 0.00 0.00 0.00 2.24
3077 3837 1.530441 GCACAACTATCACATGCAGCG 60.530 52.381 0.00 0.00 36.30 5.18
3082 3842 4.635765 ACAACTATCACATGCAGCGTTTAT 59.364 37.500 0.00 0.00 0.00 1.40
3092 3852 6.367149 CACATGCAGCGTTTATAGTCATCTAT 59.633 38.462 0.00 0.00 39.77 1.98
3098 3858 7.169982 GCAGCGTTTATAGTCATCTATTCACTT 59.830 37.037 0.00 0.00 37.89 3.16
3143 3904 9.825972 CGTTAATTGAACTATGTCAATGTTTCT 57.174 29.630 1.41 0.00 45.42 2.52
3148 3909 9.725019 ATTGAACTATGTCAATGTTTCTCAGTA 57.275 29.630 0.00 0.00 44.65 2.74
3149 3910 8.763049 TGAACTATGTCAATGTTTCTCAGTAG 57.237 34.615 0.00 0.00 0.00 2.57
3150 3911 8.367911 TGAACTATGTCAATGTTTCTCAGTAGT 58.632 33.333 0.00 0.00 0.00 2.73
3151 3912 9.856488 GAACTATGTCAATGTTTCTCAGTAGTA 57.144 33.333 0.00 0.00 0.00 1.82
3152 3913 9.640963 AACTATGTCAATGTTTCTCAGTAGTAC 57.359 33.333 0.00 0.00 0.00 2.73
3153 3914 9.026121 ACTATGTCAATGTTTCTCAGTAGTACT 57.974 33.333 0.00 0.00 0.00 2.73
3154 3915 9.509855 CTATGTCAATGTTTCTCAGTAGTACTC 57.490 37.037 0.00 0.00 0.00 2.59
3155 3916 6.688578 TGTCAATGTTTCTCAGTAGTACTCC 58.311 40.000 0.00 0.00 0.00 3.85
3156 3917 6.100668 GTCAATGTTTCTCAGTAGTACTCCC 58.899 44.000 0.00 0.00 0.00 4.30
3157 3918 6.017192 TCAATGTTTCTCAGTAGTACTCCCT 58.983 40.000 0.00 0.00 0.00 4.20
3158 3919 6.153000 TCAATGTTTCTCAGTAGTACTCCCTC 59.847 42.308 0.00 0.00 0.00 4.30
3159 3920 4.342359 TGTTTCTCAGTAGTACTCCCTCC 58.658 47.826 0.00 0.00 0.00 4.30
3160 3921 3.278668 TTCTCAGTAGTACTCCCTCCG 57.721 52.381 0.00 0.00 0.00 4.63
3161 3922 2.194859 TCTCAGTAGTACTCCCTCCGT 58.805 52.381 0.00 0.00 0.00 4.69
3162 3923 2.575279 TCTCAGTAGTACTCCCTCCGTT 59.425 50.000 0.00 0.00 0.00 4.44
3163 3924 2.944349 CTCAGTAGTACTCCCTCCGTTC 59.056 54.545 0.00 0.00 0.00 3.95
3164 3925 2.022934 CAGTAGTACTCCCTCCGTTCC 58.977 57.143 0.00 0.00 0.00 3.62
3165 3926 1.020437 GTAGTACTCCCTCCGTTCCG 58.980 60.000 0.00 0.00 0.00 4.30
3166 3927 0.911769 TAGTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
3167 3928 0.038744 AGTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
3168 3929 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
3169 3930 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
3170 3931 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3171 3932 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3172 3933 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3173 3934 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3174 3935 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3175 3936 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3176 3937 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3177 3938 3.581755 CTCCGTTCCGAATTACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3178 3939 3.319755 TCCGTTCCGAATTACTTGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
3179 3940 3.061322 CCGTTCCGAATTACTTGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
3180 3941 3.122948 CCGTTCCGAATTACTTGTCACAG 59.877 47.826 0.00 0.00 0.00 3.66
3181 3942 3.122948 CGTTCCGAATTACTTGTCACAGG 59.877 47.826 0.00 0.00 0.00 4.00
3182 3943 4.062991 GTTCCGAATTACTTGTCACAGGT 58.937 43.478 0.00 0.00 0.00 4.00
3183 3944 5.232463 GTTCCGAATTACTTGTCACAGGTA 58.768 41.667 0.00 0.00 0.00 3.08
3184 3945 5.670792 TCCGAATTACTTGTCACAGGTAT 57.329 39.130 0.00 0.00 0.00 2.73
3185 3946 5.416083 TCCGAATTACTTGTCACAGGTATG 58.584 41.667 0.00 0.00 0.00 2.39
3186 3947 4.570772 CCGAATTACTTGTCACAGGTATGG 59.429 45.833 0.00 0.00 0.00 2.74
3187 3948 5.416083 CGAATTACTTGTCACAGGTATGGA 58.584 41.667 0.00 0.00 0.00 3.41
3188 3949 6.049149 CGAATTACTTGTCACAGGTATGGAT 58.951 40.000 0.00 0.00 0.00 3.41
3189 3950 6.018751 CGAATTACTTGTCACAGGTATGGATG 60.019 42.308 0.00 0.00 0.00 3.51
3190 3951 5.755409 TTACTTGTCACAGGTATGGATGT 57.245 39.130 0.00 0.00 0.00 3.06
3191 3952 6.860790 TTACTTGTCACAGGTATGGATGTA 57.139 37.500 0.00 0.00 0.00 2.29
3192 3953 5.957771 ACTTGTCACAGGTATGGATGTAT 57.042 39.130 0.00 0.00 0.00 2.29
3193 3954 5.918608 ACTTGTCACAGGTATGGATGTATC 58.081 41.667 0.00 0.00 0.00 2.24
3194 3955 5.663106 ACTTGTCACAGGTATGGATGTATCT 59.337 40.000 0.00 0.00 0.00 1.98
3195 3956 6.839134 ACTTGTCACAGGTATGGATGTATCTA 59.161 38.462 0.00 0.00 0.00 1.98
3196 3957 6.901081 TGTCACAGGTATGGATGTATCTAG 57.099 41.667 0.00 0.00 0.00 2.43
3197 3958 6.610830 TGTCACAGGTATGGATGTATCTAGA 58.389 40.000 0.00 0.00 0.00 2.43
3198 3959 7.241628 TGTCACAGGTATGGATGTATCTAGAT 58.758 38.462 10.73 10.73 0.00 1.98
3199 3960 7.177392 TGTCACAGGTATGGATGTATCTAGATG 59.823 40.741 15.79 0.00 0.00 2.90
3200 3961 7.177568 GTCACAGGTATGGATGTATCTAGATGT 59.822 40.741 15.79 1.25 0.00 3.06
3201 3962 8.390921 TCACAGGTATGGATGTATCTAGATGTA 58.609 37.037 15.79 4.44 0.00 2.29
3202 3963 9.194972 CACAGGTATGGATGTATCTAGATGTAT 57.805 37.037 15.79 9.11 0.00 2.29
3203 3964 9.775539 ACAGGTATGGATGTATCTAGATGTATT 57.224 33.333 15.79 0.00 0.00 1.89
3229 3990 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
3230 3991 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
3231 3992 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
3232 3993 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3233 3994 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
3234 3995 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
3235 3996 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
3236 3997 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
3237 3998 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
3238 3999 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
3239 4000 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
3240 4001 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
3241 4002 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
3242 4003 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
3243 4004 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
3244 4005 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
3245 4006 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
3246 4007 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
3247 4008 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3248 4009 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
3249 4010 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
3250 4011 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
3251 4012 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3252 4013 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3286 4047 8.580720 ACTAATGGCTACTATTGTACTGATCTG 58.419 37.037 0.00 0.00 0.00 2.90
3287 4048 7.603180 AATGGCTACTATTGTACTGATCTGA 57.397 36.000 6.60 0.00 0.00 3.27
3309 4075 7.950684 TCTGAGGAGTACAATAGTAGCCATTAT 59.049 37.037 0.00 0.00 31.50 1.28
3310 4076 9.244292 CTGAGGAGTACAATAGTAGCCATTATA 57.756 37.037 0.00 0.00 31.50 0.98
3311 4077 9.596308 TGAGGAGTACAATAGTAGCCATTATAA 57.404 33.333 0.00 0.00 31.50 0.98
3350 4116 3.518590 GGTGACATAGTTCGGTTACTGG 58.481 50.000 0.00 0.00 0.00 4.00
3355 4121 2.352503 TAGTTCGGTTACTGGCGTTC 57.647 50.000 0.00 0.00 0.00 3.95
3374 4140 7.061210 TGGCGTTCAATAAAATCATTTACAACG 59.939 33.333 12.78 12.78 40.50 4.10
3379 4145 8.568676 TCAATAAAATCATTTACAACGAGGGA 57.431 30.769 0.00 0.00 33.98 4.20
3384 4150 4.735662 TCATTTACAACGAGGGAAAACG 57.264 40.909 0.00 0.00 0.00 3.60
3393 4159 4.050852 ACGAGGGAAAACGGATATACAC 57.949 45.455 0.00 0.00 0.00 2.90
3474 4240 7.772332 ACAGACGGAAATGTCAGTAATATTC 57.228 36.000 0.00 0.00 41.41 1.75
3480 4246 6.202954 CGGAAATGTCAGTAATATTCCAGTCC 59.797 42.308 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 5.709966 TCGTTTCTTTTCGAGATGATCTCA 58.290 37.500 21.22 6.84 43.55 3.27
68 70 7.147143 TCTGGATCGAGCTACATATAGTTTC 57.853 40.000 0.00 0.00 0.00 2.78
424 432 8.325282 CGAGCTATAGAATATGACTCTTACTCG 58.675 40.741 3.21 3.37 34.63 4.18
482 490 5.525378 ACTCGGCTCAACTCATTCAATATTC 59.475 40.000 0.00 0.00 0.00 1.75
489 497 2.370281 TGACTCGGCTCAACTCATTC 57.630 50.000 0.00 0.00 0.00 2.67
506 515 0.671796 TTCGAGCGAGTTGGACTTGA 59.328 50.000 0.00 0.00 31.05 3.02
529 538 1.293498 CTAGGGCTGCACACGAGTT 59.707 57.895 4.01 0.00 0.00 3.01
599 608 1.517257 GACGTCGATGTGGCCTCTG 60.517 63.158 16.54 0.00 0.00 3.35
617 626 3.057547 CTCCTGCCTCGTCTCCGTG 62.058 68.421 0.00 0.00 35.01 4.94
621 630 1.140804 GCTTCTCCTGCCTCGTCTC 59.859 63.158 0.00 0.00 0.00 3.36
638 647 1.068434 TGGCTACCTTTTGCAGTTTGC 59.932 47.619 0.00 0.00 45.29 3.68
989 1003 4.565360 GCTGCATGCATGGACCTA 57.435 55.556 27.34 0.00 42.31 3.08
1041 1055 1.192428 GTATGGAGAACAGTCCCGGT 58.808 55.000 0.00 0.00 35.49 5.28
1046 1060 3.931578 AGCACAAGTATGGAGAACAGTC 58.068 45.455 0.00 0.00 0.00 3.51
1051 1065 5.483685 ACAAGTAGCACAAGTATGGAGAA 57.516 39.130 0.00 0.00 0.00 2.87
1248 1955 6.435277 GGTCACAGGTTAGGAATATCCGTATA 59.565 42.308 0.00 0.00 42.75 1.47
1269 1976 3.329225 TGTGTTGGATATTCACTGGGTCA 59.671 43.478 0.00 0.00 33.82 4.02
1305 2012 2.445525 ACCCTTGGGATAGTTTGTGTGT 59.554 45.455 13.39 0.00 0.00 3.72
1381 2088 1.733041 CACGACGACATGGCTCGTT 60.733 57.895 19.26 6.53 46.80 3.85
1443 2152 0.108585 AACACGTGTTCATCAGCCCT 59.891 50.000 27.70 1.89 31.64 5.19
1465 2174 0.830648 CCCTTCTCCACCTTATCGCA 59.169 55.000 0.00 0.00 0.00 5.10
1575 2284 1.202687 TCCATGCCGAAGATGGTCATC 60.203 52.381 2.92 2.92 41.19 2.92
1706 2415 1.091771 AATGTCCAAGCGCCTCATCG 61.092 55.000 2.29 0.00 0.00 3.84
1765 2474 1.542472 CATGTCCATTGTGAAGCAGCA 59.458 47.619 0.00 0.00 0.00 4.41
1798 2507 0.179468 ATAACATGGTCGTTCCCCCG 59.821 55.000 0.00 0.00 34.77 5.73
1850 2565 7.624360 TTGTATCTTGGGTCATTGACATAAC 57.376 36.000 18.09 6.19 33.68 1.89
2080 2810 3.509967 GTGGCTTGCAAATAAACTAGGGT 59.490 43.478 0.00 0.00 0.00 4.34
2164 2894 0.381801 CCACTTGGCATTACATCGGC 59.618 55.000 0.00 0.00 0.00 5.54
2675 3414 8.706322 AACTTTGGTATTTATGTTTCAGTCCT 57.294 30.769 0.00 0.00 0.00 3.85
2936 3696 2.173519 ACTCCCTCCGTATCGAAACAA 58.826 47.619 0.00 0.00 0.00 2.83
3019 3779 7.643123 AGGGTATGAAAAACACCATCTAATCT 58.357 34.615 0.00 0.00 33.78 2.40
3047 3807 7.411264 GCATGTGATAGTTGTGCTAGATTATCG 60.411 40.741 0.00 0.00 32.45 2.92
3057 3817 1.530441 CGCTGCATGTGATAGTTGTGC 60.530 52.381 0.00 0.00 36.39 4.57
3060 3820 3.476295 AAACGCTGCATGTGATAGTTG 57.524 42.857 0.00 0.00 0.00 3.16
3065 3825 4.441792 TGACTATAAACGCTGCATGTGAT 58.558 39.130 0.00 0.00 0.00 3.06
3098 3858 5.524971 AACGATCTTATATTGTGGGACGA 57.475 39.130 0.00 0.00 0.00 4.20
3136 3897 4.957327 GGAGGGAGTACTACTGAGAAACAT 59.043 45.833 4.77 0.00 0.00 2.71
3137 3898 4.342359 GGAGGGAGTACTACTGAGAAACA 58.658 47.826 4.77 0.00 0.00 2.83
3143 3904 2.356535 GGAACGGAGGGAGTACTACTGA 60.357 54.545 4.77 0.00 0.00 3.41
3160 3921 4.062991 ACCTGTGACAAGTAATTCGGAAC 58.937 43.478 0.00 0.00 0.00 3.62
3161 3922 4.345859 ACCTGTGACAAGTAATTCGGAA 57.654 40.909 0.00 0.00 0.00 4.30
3162 3923 5.416083 CATACCTGTGACAAGTAATTCGGA 58.584 41.667 0.00 0.00 0.00 4.55
3163 3924 4.570772 CCATACCTGTGACAAGTAATTCGG 59.429 45.833 0.00 0.00 0.00 4.30
3164 3925 5.416083 TCCATACCTGTGACAAGTAATTCG 58.584 41.667 0.00 0.00 0.00 3.34
3165 3926 6.823689 ACATCCATACCTGTGACAAGTAATTC 59.176 38.462 0.00 0.00 0.00 2.17
3166 3927 6.721318 ACATCCATACCTGTGACAAGTAATT 58.279 36.000 0.00 0.00 0.00 1.40
3167 3928 6.313519 ACATCCATACCTGTGACAAGTAAT 57.686 37.500 0.00 0.00 0.00 1.89
3168 3929 5.755409 ACATCCATACCTGTGACAAGTAA 57.245 39.130 0.00 0.00 0.00 2.24
3169 3930 6.839134 AGATACATCCATACCTGTGACAAGTA 59.161 38.462 0.00 0.00 0.00 2.24
3170 3931 5.663106 AGATACATCCATACCTGTGACAAGT 59.337 40.000 0.00 0.00 0.00 3.16
3171 3932 6.166984 AGATACATCCATACCTGTGACAAG 57.833 41.667 0.00 0.00 0.00 3.16
3172 3933 7.066781 TCTAGATACATCCATACCTGTGACAA 58.933 38.462 0.00 0.00 0.00 3.18
3173 3934 6.610830 TCTAGATACATCCATACCTGTGACA 58.389 40.000 0.00 0.00 0.00 3.58
3174 3935 7.177568 ACATCTAGATACATCCATACCTGTGAC 59.822 40.741 4.54 0.00 0.00 3.67
3175 3936 7.241628 ACATCTAGATACATCCATACCTGTGA 58.758 38.462 4.54 0.00 0.00 3.58
3176 3937 7.473735 ACATCTAGATACATCCATACCTGTG 57.526 40.000 4.54 0.00 0.00 3.66
3177 3938 9.775539 AATACATCTAGATACATCCATACCTGT 57.224 33.333 4.54 0.00 0.00 4.00
3203 3964 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
3204 3965 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
3205 3966 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3206 3967 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3207 3968 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
3208 3969 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
3209 3970 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
3210 3971 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
3211 3972 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
3212 3973 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
3213 3974 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
3214 3975 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
3215 3976 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
3216 3977 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
3217 3978 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
3218 3979 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
3219 3980 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
3220 3981 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
3221 3982 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
3222 3983 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3223 3984 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
3224 3985 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
3225 3986 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
3226 3987 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
3227 3988 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
3228 3989 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
3229 3990 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
3230 3991 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
3231 3992 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3232 3993 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3233 3994 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3234 3995 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3235 3996 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3236 3997 3.119029 CGTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
3237 3998 2.354403 CGTACTCCCTCCGTTCCAAATT 60.354 50.000 0.00 0.00 0.00 1.82
3238 3999 1.206371 CGTACTCCCTCCGTTCCAAAT 59.794 52.381 0.00 0.00 0.00 2.32
3239 4000 0.604578 CGTACTCCCTCCGTTCCAAA 59.395 55.000 0.00 0.00 0.00 3.28
3240 4001 0.540365 ACGTACTCCCTCCGTTCCAA 60.540 55.000 0.00 0.00 0.00 3.53
3241 4002 0.327924 TACGTACTCCCTCCGTTCCA 59.672 55.000 0.00 0.00 36.12 3.53
3242 4003 0.735471 GTACGTACTCCCTCCGTTCC 59.265 60.000 18.47 0.00 36.12 3.62
3243 4004 1.743996 AGTACGTACTCCCTCCGTTC 58.256 55.000 22.45 0.00 36.12 3.95
3244 4005 3.350219 TTAGTACGTACTCCCTCCGTT 57.650 47.619 30.53 7.49 37.73 4.44
3245 4006 3.209410 CATTAGTACGTACTCCCTCCGT 58.791 50.000 30.53 8.23 37.73 4.69
3246 4007 2.551459 CCATTAGTACGTACTCCCTCCG 59.449 54.545 30.53 14.22 37.73 4.63
3247 4008 2.295629 GCCATTAGTACGTACTCCCTCC 59.704 54.545 30.53 14.23 37.73 4.30
3248 4009 3.220940 AGCCATTAGTACGTACTCCCTC 58.779 50.000 30.53 16.66 37.73 4.30
3249 4010 3.309600 AGCCATTAGTACGTACTCCCT 57.690 47.619 30.53 16.92 37.73 4.20
3250 4011 4.140536 AGTAGCCATTAGTACGTACTCCC 58.859 47.826 30.53 15.15 37.73 4.30
3251 4012 7.040823 ACAATAGTAGCCATTAGTACGTACTCC 60.041 40.741 30.53 14.84 37.73 3.85
3252 4013 7.869800 ACAATAGTAGCCATTAGTACGTACTC 58.130 38.462 30.53 16.32 37.73 2.59
3309 4075 9.833917 TGTCACCGTTTCCAATATTATGTATTA 57.166 29.630 0.00 0.00 0.00 0.98
3310 4076 8.740123 TGTCACCGTTTCCAATATTATGTATT 57.260 30.769 0.00 0.00 0.00 1.89
3311 4077 8.918202 ATGTCACCGTTTCCAATATTATGTAT 57.082 30.769 0.00 0.00 0.00 2.29
3321 4087 3.061322 CGAACTATGTCACCGTTTCCAA 58.939 45.455 0.00 0.00 0.00 3.53
3329 4095 3.518590 CCAGTAACCGAACTATGTCACC 58.481 50.000 0.00 0.00 0.00 4.02
3350 4116 8.152582 TCGTTGTAAATGATTTTATTGAACGC 57.847 30.769 0.00 0.00 36.82 4.84
3355 4121 9.632807 TTTCCCTCGTTGTAAATGATTTTATTG 57.367 29.630 0.00 0.00 41.77 1.90
3374 4140 5.607477 TGATGTGTATATCCGTTTTCCCTC 58.393 41.667 0.00 0.00 0.00 4.30
3379 4145 5.588648 CAGGGTTGATGTGTATATCCGTTTT 59.411 40.000 0.00 0.00 0.00 2.43
3384 4150 4.102524 TGACCAGGGTTGATGTGTATATCC 59.897 45.833 0.00 0.00 0.00 2.59
3393 4159 3.081061 TCGAAAATGACCAGGGTTGATG 58.919 45.455 0.00 0.00 0.00 3.07
3474 4240 1.890876 TGTTTTGGATGACGGACTGG 58.109 50.000 0.00 0.00 0.00 4.00
3480 4246 9.225201 CACAAATATAAGATGTTTTGGATGACG 57.775 33.333 0.00 0.00 34.23 4.35


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

AutoCloner maintained by Alex Coulton.