Multiple sequence alignment - TraesCS5D01G281300

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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 TraesCS5D01G281300 chr5D 100.000 4563 0 0 1 4563 382492739 382497301 0.000000e+00 8427.0
1 TraesCS5D01G281300 chr5D 94.973 557 27 1 1781 2337 383084865 383085420 0.000000e+00 872.0
2 TraesCS5D01G281300 chr5D 83.819 686 75 18 2574 3244 382943172 382942508 1.800000e-173 619.0
3 TraesCS5D01G281300 chr5D 95.833 240 10 0 2650 2889 383085615 383085854 5.540000e-104 388.0
4 TraesCS5D01G281300 chr5D 83.571 420 50 12 1781 2194 382943772 382943366 4.310000e-100 375.0
5 TraesCS5D01G281300 chr5D 75.648 772 139 26 1031 1773 382946283 382945532 5.650000e-89 339.0
6 TraesCS5D01G281300 chr5D 87.730 163 19 1 4160 4322 18177817 18177656 6.030000e-44 189.0
7 TraesCS5D01G281300 chr5D 85.484 186 19 6 4143 4322 51845600 51845783 2.170000e-43 187.0
8 TraesCS5D01G281300 chr5D 98.148 54 1 0 2571 2624 383085563 383085616 1.350000e-15 95.3
9 TraesCS5D01G281300 chr5B 95.545 1751 57 7 840 2569 458903397 458905147 0.000000e+00 2782.0
10 TraesCS5D01G281300 chr5B 93.849 1512 52 11 2571 4047 458905189 458906694 0.000000e+00 2239.0
11 TraesCS5D01G281300 chr5B 88.215 857 83 11 1 848 458902468 458903315 0.000000e+00 1007.0
12 TraesCS5D01G281300 chr5B 90.987 233 18 2 4331 4561 458909296 458909527 1.230000e-80 311.0
13 TraesCS5D01G281300 chr5B 93.443 61 4 0 4102 4162 458906691 458906751 1.750000e-14 91.6
14 TraesCS5D01G281300 chr5A 96.356 1235 38 1 2571 3798 482920298 482921532 0.000000e+00 2025.0
15 TraesCS5D01G281300 chr5A 95.652 1104 41 4 840 1942 482907625 482908722 0.000000e+00 1766.0
16 TraesCS5D01G281300 chr5A 86.967 867 73 22 1 861 482906723 482907555 0.000000e+00 939.0
17 TraesCS5D01G281300 chr5A 97.455 393 10 0 1945 2337 482919765 482920157 0.000000e+00 671.0
18 TraesCS5D01G281300 chr5A 92.975 242 14 2 4321 4560 482921883 482922123 2.610000e-92 350.0
19 TraesCS5D01G281300 chr5A 90.222 225 15 2 3844 4065 482921545 482921765 2.080000e-73 287.0
20 TraesCS5D01G281300 chr5A 95.238 105 3 1 2465 2569 482920154 482920256 1.020000e-36 165.0
21 TraesCS5D01G281300 chr7D 95.588 136 6 0 2333 2468 577750711 577750846 7.690000e-53 219.0
22 TraesCS5D01G281300 chr3A 84.793 217 29 3 1 215 600066934 600066720 9.940000e-52 215.0
23 TraesCS5D01G281300 chr3A 93.431 137 8 1 2333 2468 724539867 724540003 7.740000e-48 202.0
24 TraesCS5D01G281300 chr3A 93.431 137 8 1 2333 2468 724540122 724540258 7.740000e-48 202.0
25 TraesCS5D01G281300 chr3A 93.233 133 9 0 2331 2463 654592105 654591973 3.600000e-46 196.0
26 TraesCS5D01G281300 chr2A 94.853 136 7 0 2333 2468 750366033 750366168 3.580000e-51 213.0
27 TraesCS5D01G281300 chr2A 94.030 134 7 1 2333 2466 514859204 514859072 7.740000e-48 202.0
28 TraesCS5D01G281300 chr7A 86.082 194 22 4 4373 4562 379929741 379929933 2.150000e-48 204.0
29 TraesCS5D01G281300 chr7A 86.705 173 20 3 4160 4331 8325500 8325330 6.030000e-44 189.0
30 TraesCS5D01G281300 chr7A 84.252 127 20 0 2340 2466 6627357 6627231 1.720000e-24 124.0
31 TraesCS5D01G281300 chr6B 88.024 167 19 1 4160 4326 36133665 36133500 3.600000e-46 196.0
32 TraesCS5D01G281300 chr6B 87.730 163 18 2 4160 4322 650598540 650598700 6.030000e-44 189.0
33 TraesCS5D01G281300 chr6D 88.344 163 17 2 4160 4322 431160668 431160828 1.300000e-45 195.0
34 TraesCS5D01G281300 chr4D 86.705 173 21 2 4160 4331 479687260 479687431 1.680000e-44 191.0
35 TraesCS5D01G281300 chr1A 87.273 165 20 1 4159 4323 106220716 106220553 2.170000e-43 187.0
36 TraesCS5D01G281300 chr4B 86.127 173 22 2 4160 4331 606916763 606916934 7.800000e-43 185.0
37 TraesCS5D01G281300 chr2D 86.290 124 17 0 2343 2466 76635209 76635332 7.960000e-28 135.0


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 TraesCS5D01G281300 chr5D 382492739 382497301 4562 False 8427.000000 8427 100.000000 1 4563 1 chr5D.!!$F2 4562
1 TraesCS5D01G281300 chr5D 383084865 383085854 989 False 451.766667 872 96.318000 1781 2889 3 chr5D.!!$F3 1108
2 TraesCS5D01G281300 chr5D 382942508 382946283 3775 True 444.333333 619 81.012667 1031 3244 3 chr5D.!!$R2 2213
3 TraesCS5D01G281300 chr5B 458902468 458909527 7059 False 1286.120000 2782 92.407800 1 4561 5 chr5B.!!$F1 4560
4 TraesCS5D01G281300 chr5A 482906723 482908722 1999 False 1352.500000 1766 91.309500 1 1942 2 chr5A.!!$F1 1941
5 TraesCS5D01G281300 chr5A 482919765 482922123 2358 False 699.600000 2025 94.449200 1945 4560 5 chr5A.!!$F2 2615

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
183 184 2.880963 CCATCGTTGGGTGTTGTTTT 57.119 45.0 4.47 0.0 39.56 2.43 F
1314 1459 1.589414 CCCCTGTCCTTCTCCTGATT 58.411 55.0 0.00 0.0 0.00 2.57 F
1683 1834 0.032678 AGCTCAGTGTTGTGTCCTCG 59.967 55.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1343 1488 1.200519 CCCATTCCTCGTTCCTGGTA 58.799 55.0 0.00 0.0 0.00 3.25 R
2420 4333 0.107312 CCAGAATCTGTGGAGCAGGG 60.107 60.0 9.63 0.0 45.08 4.45 R
3586 5571 0.672342 GTCCCATTCTCATGCATGCC 59.328 55.0 22.25 0.0 0.00 4.40 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
116 117 6.966534 GGGAACACCAAATGATCATTAGAT 57.033 37.500 21.00 3.28 39.85 1.98
149 150 3.446161 ACAGATGAATGGCAATGGTTGAG 59.554 43.478 0.00 0.00 0.00 3.02
183 184 2.880963 CCATCGTTGGGTGTTGTTTT 57.119 45.000 4.47 0.00 39.56 2.43
217 218 4.799564 TGGTATCATTGCCCTTTGTTTC 57.200 40.909 0.00 0.00 0.00 2.78
418 426 8.874745 TTTGAAGATCGACGATTTTTACATTC 57.125 30.769 12.40 8.41 0.00 2.67
647 664 5.559770 TCAGTGATCAAGCAATTGAACCTA 58.440 37.500 10.34 0.00 34.24 3.08
648 665 6.003326 TCAGTGATCAAGCAATTGAACCTAA 58.997 36.000 10.34 0.00 34.24 2.69
655 672 9.206870 GATCAAGCAATTGAACCTAATTTTCAA 57.793 29.630 10.34 6.31 44.84 2.69
838 856 3.734735 AGTCGCTGAAGAAGTTTAACGAC 59.265 43.478 0.00 0.00 46.52 4.34
1314 1459 1.589414 CCCCTGTCCTTCTCCTGATT 58.411 55.000 0.00 0.00 0.00 2.57
1343 1488 1.269166 CGCGCGTCAGTAAGAAGAAT 58.731 50.000 24.19 0.00 0.00 2.40
1397 1542 2.433491 TTCGGACGCATGTTCCGG 60.433 61.111 27.46 15.14 46.03 5.14
1475 1620 2.434428 GATTATCAGCTGGGCATCCTG 58.566 52.381 15.13 0.00 35.38 3.86
1567 1718 8.011673 CCATCGCATTGTAGTGATTATGTTTAG 58.988 37.037 0.00 0.00 36.66 1.85
1683 1834 0.032678 AGCTCAGTGTTGTGTCCTCG 59.967 55.000 0.00 0.00 0.00 4.63
1942 3850 2.230750 AGTAGTCAGGTACGGCAGTTTC 59.769 50.000 0.00 0.00 0.00 2.78
2410 4323 2.159599 GCTGCTGTTCAAATCGAAGGAG 60.160 50.000 0.00 0.00 33.09 3.69
2420 4333 4.274950 TCAAATCGAAGGAGTTGTGGTTTC 59.725 41.667 4.50 0.00 45.74 2.78
2421 4334 2.249844 TCGAAGGAGTTGTGGTTTCC 57.750 50.000 0.00 0.00 0.00 3.13
2491 4404 5.688814 TGAGTGATGGATGAGAAAGATGT 57.311 39.130 0.00 0.00 0.00 3.06
2569 4491 6.183360 CCCAGTTAAACTTTGCTTCTTGAGAA 60.183 38.462 0.00 0.00 0.00 2.87
2702 4664 2.945668 GCCACATGAACCCTGATAACTC 59.054 50.000 0.00 0.00 0.00 3.01
2815 4777 5.418524 AGGCATGATGTATTGTTAAACTGCA 59.581 36.000 0.00 0.00 0.00 4.41
2963 4935 1.675714 CGTATGTGCCTCTGCTGGAAA 60.676 52.381 0.00 0.00 38.71 3.13
3006 4985 5.828328 GTGGCCTAATATTGGAGCTTTAACT 59.172 40.000 3.32 0.00 0.00 2.24
3554 5539 5.306114 TGTCTCTCCCTATGACGATTCTA 57.694 43.478 0.00 0.00 33.81 2.10
3555 5540 5.691896 TGTCTCTCCCTATGACGATTCTAA 58.308 41.667 0.00 0.00 33.81 2.10
3586 5571 1.280133 TGAGGCTCAGGTTCTTGATGG 59.720 52.381 14.43 0.00 0.00 3.51
3602 5587 1.272490 GATGGGCATGCATGAGAATGG 59.728 52.381 30.64 1.83 30.83 3.16
3645 5630 0.321919 CTGGATGGGCATGTATCGGG 60.322 60.000 0.00 0.00 0.00 5.14
3660 5645 1.848652 TCGGGTCAAACTCCTAGAGG 58.151 55.000 0.00 0.00 33.35 3.69
3684 5669 7.279981 AGGTTTGCAAGGAATTTTGTTTAGTTC 59.720 33.333 0.00 0.00 0.00 3.01
3690 5675 6.419484 AGGAATTTTGTTTAGTTCAAGGGG 57.581 37.500 0.00 0.00 0.00 4.79
3694 5679 6.800072 ATTTTGTTTAGTTCAAGGGGTTCA 57.200 33.333 0.00 0.00 0.00 3.18
3714 5699 0.317938 GTGTAGTAGCGCCTCATCCG 60.318 60.000 2.29 0.00 0.00 4.18
3804 5817 4.160439 TCATCTGTACAAGCCACCTCTTAG 59.840 45.833 0.00 0.00 0.00 2.18
4023 6039 5.336770 CCGTGCATGTACAGTATCTGGATAT 60.337 44.000 14.55 0.00 35.51 1.63
4024 6040 6.127730 CCGTGCATGTACAGTATCTGGATATA 60.128 42.308 14.55 0.00 35.51 0.86
4025 6041 7.312899 CGTGCATGTACAGTATCTGGATATAA 58.687 38.462 14.55 0.00 35.51 0.98
4026 6042 7.486232 CGTGCATGTACAGTATCTGGATATAAG 59.514 40.741 14.55 0.00 35.51 1.73
4058 6074 3.134127 GGATCGCAGCACCCCAAC 61.134 66.667 0.00 0.00 0.00 3.77
4065 6081 2.034879 CAGCACCCCAACGCTACAG 61.035 63.158 0.00 0.00 36.50 2.74
4067 6083 1.189524 AGCACCCCAACGCTACAGTA 61.190 55.000 0.00 0.00 36.50 2.74
4069 6085 0.390735 CACCCCAACGCTACAGTACC 60.391 60.000 0.00 0.00 0.00 3.34
4071 6087 0.108329 CCCCAACGCTACAGTACCTG 60.108 60.000 0.00 0.00 37.52 4.00
4072 6088 0.892755 CCCAACGCTACAGTACCTGA 59.107 55.000 0.00 0.00 35.18 3.86
4074 6090 1.816835 CCAACGCTACAGTACCTGAGA 59.183 52.381 0.00 0.00 35.18 3.27
4075 6091 2.427453 CCAACGCTACAGTACCTGAGAT 59.573 50.000 0.00 0.00 35.18 2.75
4076 6092 3.489398 CCAACGCTACAGTACCTGAGATC 60.489 52.174 0.00 0.00 35.18 2.75
4077 6093 1.941294 ACGCTACAGTACCTGAGATCG 59.059 52.381 0.00 0.00 35.18 3.69
4078 6094 2.210961 CGCTACAGTACCTGAGATCGA 58.789 52.381 0.00 0.00 35.18 3.59
4080 6096 3.364465 CGCTACAGTACCTGAGATCGATG 60.364 52.174 0.54 0.00 35.18 3.84
4081 6097 3.566322 GCTACAGTACCTGAGATCGATGT 59.434 47.826 0.54 0.00 35.18 3.06
4083 6099 4.377839 ACAGTACCTGAGATCGATGTTG 57.622 45.455 0.54 0.00 35.18 3.33
4084 6100 4.017126 ACAGTACCTGAGATCGATGTTGA 58.983 43.478 0.54 0.00 35.18 3.18
4085 6101 4.646945 ACAGTACCTGAGATCGATGTTGAT 59.353 41.667 0.54 0.00 35.18 2.57
4089 6128 4.836825 ACCTGAGATCGATGTTGATTTGT 58.163 39.130 0.54 0.00 0.00 2.83
4093 6132 7.086376 CCTGAGATCGATGTTGATTTGTTTTT 58.914 34.615 0.54 0.00 0.00 1.94
4094 6133 8.236586 CCTGAGATCGATGTTGATTTGTTTTTA 58.763 33.333 0.54 0.00 0.00 1.52
4095 6134 9.611284 CTGAGATCGATGTTGATTTGTTTTTAA 57.389 29.630 0.54 0.00 0.00 1.52
4096 6135 9.958234 TGAGATCGATGTTGATTTGTTTTTAAA 57.042 25.926 0.54 0.00 0.00 1.52
4144 6183 2.375174 TCACTGGCAAACCCTGAAGTAT 59.625 45.455 0.00 0.00 36.47 2.12
4159 6198 6.769822 CCCTGAAGTATAGAAAGATGCATGTT 59.230 38.462 2.46 2.58 0.00 2.71
4160 6199 7.933577 CCCTGAAGTATAGAAAGATGCATGTTA 59.066 37.037 9.82 0.00 0.00 2.41
4161 6200 8.768955 CCTGAAGTATAGAAAGATGCATGTTAC 58.231 37.037 9.82 4.01 0.00 2.50
4162 6201 9.539825 CTGAAGTATAGAAAGATGCATGTTACT 57.460 33.333 9.82 6.33 0.00 2.24
4163 6202 9.534565 TGAAGTATAGAAAGATGCATGTTACTC 57.465 33.333 9.82 4.89 0.00 2.59
4164 6203 8.894768 AAGTATAGAAAGATGCATGTTACTCC 57.105 34.615 9.82 0.44 0.00 3.85
4165 6204 7.445945 AGTATAGAAAGATGCATGTTACTCCC 58.554 38.462 9.82 0.00 0.00 4.30
4166 6205 4.851639 AGAAAGATGCATGTTACTCCCT 57.148 40.909 9.82 0.00 0.00 4.20
4167 6206 4.775236 AGAAAGATGCATGTTACTCCCTC 58.225 43.478 9.82 2.70 0.00 4.30
4168 6207 4.472833 AGAAAGATGCATGTTACTCCCTCT 59.527 41.667 9.82 5.04 0.00 3.69
4169 6208 3.834489 AGATGCATGTTACTCCCTCTG 57.166 47.619 2.46 0.00 0.00 3.35
4170 6209 3.110705 AGATGCATGTTACTCCCTCTGT 58.889 45.455 2.46 0.00 0.00 3.41
4171 6210 3.521126 AGATGCATGTTACTCCCTCTGTT 59.479 43.478 2.46 0.00 0.00 3.16
4172 6211 3.334583 TGCATGTTACTCCCTCTGTTC 57.665 47.619 0.00 0.00 0.00 3.18
4173 6212 2.027192 TGCATGTTACTCCCTCTGTTCC 60.027 50.000 0.00 0.00 0.00 3.62
4174 6213 2.237392 GCATGTTACTCCCTCTGTTCCT 59.763 50.000 0.00 0.00 0.00 3.36
4175 6214 3.866651 CATGTTACTCCCTCTGTTCCTG 58.133 50.000 0.00 0.00 0.00 3.86
4176 6215 3.254093 TGTTACTCCCTCTGTTCCTGA 57.746 47.619 0.00 0.00 0.00 3.86
4177 6216 3.583228 TGTTACTCCCTCTGTTCCTGAA 58.417 45.455 0.00 0.00 0.00 3.02
4178 6217 4.168101 TGTTACTCCCTCTGTTCCTGAAT 58.832 43.478 0.00 0.00 0.00 2.57
4179 6218 5.338632 TGTTACTCCCTCTGTTCCTGAATA 58.661 41.667 0.00 0.00 0.00 1.75
4180 6219 5.964477 TGTTACTCCCTCTGTTCCTGAATAT 59.036 40.000 0.00 0.00 0.00 1.28
4181 6220 7.130099 TGTTACTCCCTCTGTTCCTGAATATA 58.870 38.462 0.00 0.00 0.00 0.86
4182 6221 7.622081 TGTTACTCCCTCTGTTCCTGAATATAA 59.378 37.037 0.00 0.00 0.00 0.98
4183 6222 6.739331 ACTCCCTCTGTTCCTGAATATAAG 57.261 41.667 0.00 0.00 0.00 1.73
4184 6223 6.206042 ACTCCCTCTGTTCCTGAATATAAGT 58.794 40.000 0.00 0.00 0.00 2.24
4185 6224 6.325286 ACTCCCTCTGTTCCTGAATATAAGTC 59.675 42.308 0.00 0.00 0.00 3.01
4186 6225 5.602978 TCCCTCTGTTCCTGAATATAAGTCC 59.397 44.000 0.00 0.00 0.00 3.85
4187 6226 5.604650 CCCTCTGTTCCTGAATATAAGTCCT 59.395 44.000 0.00 0.00 0.00 3.85
4188 6227 6.100424 CCCTCTGTTCCTGAATATAAGTCCTT 59.900 42.308 0.00 0.00 0.00 3.36
4189 6228 7.366011 CCCTCTGTTCCTGAATATAAGTCCTTT 60.366 40.741 0.00 0.00 0.00 3.11
4190 6229 8.049721 CCTCTGTTCCTGAATATAAGTCCTTTT 58.950 37.037 0.00 0.00 0.00 2.27
4208 6247 9.620259 AGTCCTTTTAGAGATTTCAATATGGAC 57.380 33.333 0.00 0.00 38.27 4.02
4209 6248 9.620259 GTCCTTTTAGAGATTTCAATATGGACT 57.380 33.333 0.00 0.00 35.99 3.85
4217 6256 9.152327 AGAGATTTCAATATGGACTACAGATGA 57.848 33.333 0.00 0.00 29.94 2.92
4218 6257 9.770097 GAGATTTCAATATGGACTACAGATGAA 57.230 33.333 0.00 0.00 29.94 2.57
4219 6258 9.775854 AGATTTCAATATGGACTACAGATGAAG 57.224 33.333 0.00 0.00 33.37 3.02
4220 6259 7.792374 TTTCAATATGGACTACAGATGAAGC 57.208 36.000 0.00 0.00 33.37 3.86
4221 6260 6.484364 TCAATATGGACTACAGATGAAGCA 57.516 37.500 0.00 0.00 29.94 3.91
4222 6261 6.888105 TCAATATGGACTACAGATGAAGCAA 58.112 36.000 0.00 0.00 29.94 3.91
4223 6262 7.337938 TCAATATGGACTACAGATGAAGCAAA 58.662 34.615 0.00 0.00 29.94 3.68
4224 6263 7.828717 TCAATATGGACTACAGATGAAGCAAAA 59.171 33.333 0.00 0.00 29.94 2.44
4225 6264 8.627403 CAATATGGACTACAGATGAAGCAAAAT 58.373 33.333 0.00 0.00 29.94 1.82
4226 6265 5.885230 TGGACTACAGATGAAGCAAAATG 57.115 39.130 0.00 0.00 0.00 2.32
4227 6266 5.559770 TGGACTACAGATGAAGCAAAATGA 58.440 37.500 0.00 0.00 0.00 2.57
4228 6267 5.645067 TGGACTACAGATGAAGCAAAATGAG 59.355 40.000 0.00 0.00 0.00 2.90
4229 6268 5.645497 GGACTACAGATGAAGCAAAATGAGT 59.355 40.000 0.00 0.00 0.00 3.41
4230 6269 6.818644 GGACTACAGATGAAGCAAAATGAGTA 59.181 38.462 0.00 0.00 0.00 2.59
4231 6270 7.334421 GGACTACAGATGAAGCAAAATGAGTAA 59.666 37.037 0.00 0.00 0.00 2.24
4232 6271 8.621532 ACTACAGATGAAGCAAAATGAGTAAA 57.378 30.769 0.00 0.00 0.00 2.01
4233 6272 9.236006 ACTACAGATGAAGCAAAATGAGTAAAT 57.764 29.630 0.00 0.00 0.00 1.40
4234 6273 9.713740 CTACAGATGAAGCAAAATGAGTAAATC 57.286 33.333 0.00 0.00 0.00 2.17
4235 6274 8.345724 ACAGATGAAGCAAAATGAGTAAATCT 57.654 30.769 0.00 0.00 0.00 2.40
4236 6275 9.453572 ACAGATGAAGCAAAATGAGTAAATCTA 57.546 29.630 0.00 0.00 0.00 1.98
4270 6309 9.999009 AAATATGTCTATATACATCCGTACGTG 57.001 33.333 15.21 9.44 40.52 4.49
4271 6310 5.868043 TGTCTATATACATCCGTACGTGG 57.132 43.478 15.21 5.54 0.00 4.94
4272 6311 5.308014 TGTCTATATACATCCGTACGTGGT 58.692 41.667 15.21 11.27 0.00 4.16
4273 6312 5.764686 TGTCTATATACATCCGTACGTGGTT 59.235 40.000 15.21 1.80 0.00 3.67
4274 6313 6.073058 TGTCTATATACATCCGTACGTGGTTC 60.073 42.308 15.21 0.00 0.00 3.62
4275 6314 5.997129 TCTATATACATCCGTACGTGGTTCA 59.003 40.000 15.21 1.52 0.00 3.18
4276 6315 5.717078 ATATACATCCGTACGTGGTTCAT 57.283 39.130 15.21 2.95 0.00 2.57
4277 6316 6.822667 ATATACATCCGTACGTGGTTCATA 57.177 37.500 15.21 5.05 0.00 2.15
4278 6317 3.431922 ACATCCGTACGTGGTTCATAG 57.568 47.619 15.21 0.00 0.00 2.23
4279 6318 2.756760 ACATCCGTACGTGGTTCATAGT 59.243 45.455 15.21 0.00 0.00 2.12
4280 6319 2.925578 TCCGTACGTGGTTCATAGTG 57.074 50.000 15.21 0.00 0.00 2.74
4281 6320 2.435422 TCCGTACGTGGTTCATAGTGA 58.565 47.619 15.21 0.00 0.00 3.41
4282 6321 2.819019 TCCGTACGTGGTTCATAGTGAA 59.181 45.455 15.21 0.00 33.32 3.18
4283 6322 3.255395 TCCGTACGTGGTTCATAGTGAAA 59.745 43.478 15.21 0.00 38.22 2.69
4284 6323 4.082081 TCCGTACGTGGTTCATAGTGAAAT 60.082 41.667 15.21 0.00 38.22 2.17
4285 6324 4.266976 CCGTACGTGGTTCATAGTGAAATC 59.733 45.833 15.21 0.00 38.22 2.17
4286 6325 5.100259 CGTACGTGGTTCATAGTGAAATCT 58.900 41.667 7.22 0.00 38.22 2.40
4287 6326 5.229469 CGTACGTGGTTCATAGTGAAATCTC 59.771 44.000 7.22 0.00 38.22 2.75
4288 6327 5.407407 ACGTGGTTCATAGTGAAATCTCT 57.593 39.130 0.00 0.00 38.22 3.10
4289 6328 6.525578 ACGTGGTTCATAGTGAAATCTCTA 57.474 37.500 0.00 0.00 38.22 2.43
4290 6329 6.931838 ACGTGGTTCATAGTGAAATCTCTAA 58.068 36.000 0.00 0.00 38.22 2.10
4291 6330 7.383687 ACGTGGTTCATAGTGAAATCTCTAAA 58.616 34.615 0.00 0.00 38.22 1.85
4292 6331 7.876068 ACGTGGTTCATAGTGAAATCTCTAAAA 59.124 33.333 0.00 0.00 38.22 1.52
4293 6332 8.383619 CGTGGTTCATAGTGAAATCTCTAAAAG 58.616 37.037 0.00 0.00 38.22 2.27
4294 6333 8.669243 GTGGTTCATAGTGAAATCTCTAAAAGG 58.331 37.037 0.00 0.00 38.22 3.11
4295 6334 8.602424 TGGTTCATAGTGAAATCTCTAAAAGGA 58.398 33.333 0.00 0.00 38.22 3.36
4296 6335 8.884726 GGTTCATAGTGAAATCTCTAAAAGGAC 58.115 37.037 0.00 0.00 38.22 3.85
4297 6336 9.660180 GTTCATAGTGAAATCTCTAAAAGGACT 57.340 33.333 0.00 0.00 38.22 3.85
4478 9054 1.408474 CTTACGCGTTACTCACCCGC 61.408 60.000 20.78 0.00 43.74 6.13
4561 9139 1.556911 TGAGCCAGGATCAAACTCTCC 59.443 52.381 4.42 0.00 0.00 3.71
4562 9140 1.836802 GAGCCAGGATCAAACTCTCCT 59.163 52.381 0.00 0.00 42.75 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.006386 AGACCCAAAAGATGATTGTCACTC 58.994 41.667 0.00 0.00 0.00 3.51
149 150 1.202463 CGATGGGGAGACATGAGACAC 60.202 57.143 0.00 0.00 0.00 3.67
182 183 6.285224 CAATGATACCATGTACCGGAGTTAA 58.715 40.000 9.46 0.00 32.36 2.01
183 184 5.740803 GCAATGATACCATGTACCGGAGTTA 60.741 44.000 9.46 0.00 32.36 2.24
395 403 6.528774 TCGAATGTAAAAATCGTCGATCTTCA 59.471 34.615 8.45 4.87 37.79 3.02
399 407 5.052829 TCGTCGAATGTAAAAATCGTCGATC 60.053 40.000 8.45 0.00 46.22 3.69
402 410 4.473441 TCGTCGAATGTAAAAATCGTCG 57.527 40.909 7.50 7.50 44.90 5.12
403 411 6.682241 CATTCGTCGAATGTAAAAATCGTC 57.318 37.500 30.97 0.00 42.89 4.20
418 426 6.917059 TCAACAAATTTGAAAACATTCGTCG 58.083 32.000 24.64 0.00 0.00 5.12
621 638 5.106038 GGTTCAATTGCTTGATCACTGATGA 60.106 40.000 0.00 0.00 40.95 2.92
622 639 5.100259 GGTTCAATTGCTTGATCACTGATG 58.900 41.667 0.00 0.00 40.95 3.07
623 640 5.014858 AGGTTCAATTGCTTGATCACTGAT 58.985 37.500 0.00 0.00 40.95 2.90
797 815 4.025229 CGACTGGACTGTTTCGATGAAAAA 60.025 41.667 0.00 0.00 33.14 1.94
838 856 0.232303 GCCGAACTGTCTGTTTCGTG 59.768 55.000 3.35 0.00 39.30 4.35
1343 1488 1.200519 CCCATTCCTCGTTCCTGGTA 58.799 55.000 0.00 0.00 0.00 3.25
1475 1620 5.901336 GCAATTGAAATCAAACGAACCAAAC 59.099 36.000 10.34 0.00 39.55 2.93
1683 1834 3.118592 ACTTGTGGCTTCTATGTAGCTCC 60.119 47.826 0.00 0.00 38.67 4.70
1942 3850 1.811965 TGCAAGTGATGATTTGGGACG 59.188 47.619 0.00 0.00 0.00 4.79
2420 4333 0.107312 CCAGAATCTGTGGAGCAGGG 60.107 60.000 9.63 0.00 45.08 4.45
2421 4334 0.107312 CCCAGAATCTGTGGAGCAGG 60.107 60.000 9.63 0.00 45.08 4.85
2569 4491 2.619074 GCAGTCTGAATACCTTTGCCCT 60.619 50.000 3.32 0.00 0.00 5.19
2702 4664 3.865446 TGACATACTGGACATGAAGCTG 58.135 45.455 0.00 0.00 0.00 4.24
2815 4777 2.502142 TGCAGTGCAATGAGAGGAAT 57.498 45.000 20.00 0.00 34.76 3.01
2963 4935 4.379652 CCACAAAGTAAGCTTGGCAAAAT 58.620 39.130 9.86 0.00 34.71 1.82
3554 5539 5.026790 ACCTGAGCCTCATAACTAGTTCTT 58.973 41.667 12.39 0.00 0.00 2.52
3555 5540 4.615513 ACCTGAGCCTCATAACTAGTTCT 58.384 43.478 12.39 1.28 0.00 3.01
3586 5571 0.672342 GTCCCATTCTCATGCATGCC 59.328 55.000 22.25 0.00 0.00 4.40
3645 5630 3.740115 TGCAAACCTCTAGGAGTTTGAC 58.260 45.455 28.15 21.86 35.17 3.18
3660 5645 7.969314 TGAACTAAACAAAATTCCTTGCAAAC 58.031 30.769 0.00 0.00 0.00 2.93
3684 5669 2.674177 CGCTACTACACTGAACCCCTTG 60.674 54.545 0.00 0.00 0.00 3.61
3690 5675 1.201647 TGAGGCGCTACTACACTGAAC 59.798 52.381 7.64 0.00 0.00 3.18
3694 5679 1.033574 GGATGAGGCGCTACTACACT 58.966 55.000 7.64 0.00 0.00 3.55
3730 5715 0.036294 GCTCCCATATTCTACGCCCC 60.036 60.000 0.00 0.00 0.00 5.80
3958 5971 0.258774 ACTCCAAACAAGCACACCCT 59.741 50.000 0.00 0.00 0.00 4.34
3959 5972 1.607148 GTACTCCAAACAAGCACACCC 59.393 52.381 0.00 0.00 0.00 4.61
4023 6039 4.553351 CGATCCGTCGCATGTACTTACTTA 60.553 45.833 0.00 0.00 41.49 2.24
4024 6040 3.703420 GATCCGTCGCATGTACTTACTT 58.297 45.455 0.00 0.00 0.00 2.24
4025 6041 2.286831 CGATCCGTCGCATGTACTTACT 60.287 50.000 0.00 0.00 41.49 2.24
4026 6042 2.041966 CGATCCGTCGCATGTACTTAC 58.958 52.381 0.00 0.00 41.49 2.34
4065 6081 5.812642 ACAAATCAACATCGATCTCAGGTAC 59.187 40.000 0.00 0.00 0.00 3.34
4067 6083 4.836825 ACAAATCAACATCGATCTCAGGT 58.163 39.130 0.00 0.00 0.00 4.00
4069 6085 9.611284 TTAAAAACAAATCAACATCGATCTCAG 57.389 29.630 0.00 0.00 0.00 3.35
4107 6146 1.906574 AGTGAACGATTGGGCCTTCTA 59.093 47.619 4.53 0.00 0.00 2.10
4144 6183 5.663106 AGAGGGAGTAACATGCATCTTTCTA 59.337 40.000 0.00 0.00 26.14 2.10
4159 6198 7.363031 ACTTATATTCAGGAACAGAGGGAGTA 58.637 38.462 0.00 0.00 0.00 2.59
4160 6199 6.206042 ACTTATATTCAGGAACAGAGGGAGT 58.794 40.000 0.00 0.00 0.00 3.85
4161 6200 6.239458 GGACTTATATTCAGGAACAGAGGGAG 60.239 46.154 0.00 0.00 0.00 4.30
4162 6201 5.602978 GGACTTATATTCAGGAACAGAGGGA 59.397 44.000 0.00 0.00 0.00 4.20
4163 6202 5.604650 AGGACTTATATTCAGGAACAGAGGG 59.395 44.000 0.00 0.00 0.00 4.30
4164 6203 6.739331 AGGACTTATATTCAGGAACAGAGG 57.261 41.667 0.00 0.00 0.00 3.69
4182 6221 9.620259 GTCCATATTGAAATCTCTAAAAGGACT 57.380 33.333 0.00 0.00 37.06 3.85
4183 6222 9.620259 AGTCCATATTGAAATCTCTAAAAGGAC 57.380 33.333 0.00 0.00 39.53 3.85
4191 6230 9.152327 TCATCTGTAGTCCATATTGAAATCTCT 57.848 33.333 0.00 0.00 0.00 3.10
4192 6231 9.770097 TTCATCTGTAGTCCATATTGAAATCTC 57.230 33.333 0.00 0.00 0.00 2.75
4193 6232 9.775854 CTTCATCTGTAGTCCATATTGAAATCT 57.224 33.333 0.00 0.00 0.00 2.40
4194 6233 8.502387 GCTTCATCTGTAGTCCATATTGAAATC 58.498 37.037 0.00 0.00 0.00 2.17
4195 6234 7.994911 TGCTTCATCTGTAGTCCATATTGAAAT 59.005 33.333 0.00 0.00 0.00 2.17
4196 6235 7.337938 TGCTTCATCTGTAGTCCATATTGAAA 58.662 34.615 0.00 0.00 0.00 2.69
4197 6236 6.888105 TGCTTCATCTGTAGTCCATATTGAA 58.112 36.000 0.00 0.00 0.00 2.69
4198 6237 6.484364 TGCTTCATCTGTAGTCCATATTGA 57.516 37.500 0.00 0.00 0.00 2.57
4199 6238 7.558161 TTTGCTTCATCTGTAGTCCATATTG 57.442 36.000 0.00 0.00 0.00 1.90
4200 6239 8.627403 CATTTTGCTTCATCTGTAGTCCATATT 58.373 33.333 0.00 0.00 0.00 1.28
4201 6240 7.994911 TCATTTTGCTTCATCTGTAGTCCATAT 59.005 33.333 0.00 0.00 0.00 1.78
4202 6241 7.337938 TCATTTTGCTTCATCTGTAGTCCATA 58.662 34.615 0.00 0.00 0.00 2.74
4203 6242 6.182627 TCATTTTGCTTCATCTGTAGTCCAT 58.817 36.000 0.00 0.00 0.00 3.41
4204 6243 5.559770 TCATTTTGCTTCATCTGTAGTCCA 58.440 37.500 0.00 0.00 0.00 4.02
4205 6244 5.645497 ACTCATTTTGCTTCATCTGTAGTCC 59.355 40.000 0.00 0.00 0.00 3.85
4206 6245 6.734104 ACTCATTTTGCTTCATCTGTAGTC 57.266 37.500 0.00 0.00 0.00 2.59
4207 6246 8.621532 TTTACTCATTTTGCTTCATCTGTAGT 57.378 30.769 0.00 0.00 0.00 2.73
4208 6247 9.713740 GATTTACTCATTTTGCTTCATCTGTAG 57.286 33.333 0.00 0.00 0.00 2.74
4209 6248 9.453572 AGATTTACTCATTTTGCTTCATCTGTA 57.546 29.630 0.00 0.00 0.00 2.74
4210 6249 8.345724 AGATTTACTCATTTTGCTTCATCTGT 57.654 30.769 0.00 0.00 0.00 3.41
4244 6283 9.999009 CACGTACGGATGTATATAGACATATTT 57.001 33.333 21.06 3.30 40.18 1.40
4245 6284 8.618677 CCACGTACGGATGTATATAGACATATT 58.381 37.037 21.06 3.62 40.18 1.28
4246 6285 7.772292 ACCACGTACGGATGTATATAGACATAT 59.228 37.037 21.06 5.08 40.18 1.78
4247 6286 7.105588 ACCACGTACGGATGTATATAGACATA 58.894 38.462 21.06 0.00 40.18 2.29
4248 6287 5.942236 ACCACGTACGGATGTATATAGACAT 59.058 40.000 21.06 12.70 42.82 3.06
4249 6288 5.308014 ACCACGTACGGATGTATATAGACA 58.692 41.667 21.06 2.07 32.11 3.41
4250 6289 5.869753 ACCACGTACGGATGTATATAGAC 57.130 43.478 21.06 0.00 32.11 2.59
4251 6290 5.997129 TGAACCACGTACGGATGTATATAGA 59.003 40.000 21.06 0.00 32.11 1.98
4252 6291 6.245115 TGAACCACGTACGGATGTATATAG 57.755 41.667 21.06 0.00 32.11 1.31
4253 6292 6.822667 ATGAACCACGTACGGATGTATATA 57.177 37.500 21.06 0.00 32.11 0.86
4254 6293 5.717078 ATGAACCACGTACGGATGTATAT 57.283 39.130 21.06 8.28 32.11 0.86
4255 6294 5.764686 ACTATGAACCACGTACGGATGTATA 59.235 40.000 21.06 9.62 32.11 1.47
4256 6295 4.581824 ACTATGAACCACGTACGGATGTAT 59.418 41.667 21.06 8.99 32.11 2.29
4257 6296 3.947196 ACTATGAACCACGTACGGATGTA 59.053 43.478 21.06 1.50 0.00 2.29
4258 6297 2.756760 ACTATGAACCACGTACGGATGT 59.243 45.455 21.06 10.36 0.00 3.06
4259 6298 3.113322 CACTATGAACCACGTACGGATG 58.887 50.000 21.06 9.60 0.00 3.51
4260 6299 3.018856 TCACTATGAACCACGTACGGAT 58.981 45.455 21.06 0.82 0.00 4.18
4261 6300 2.435422 TCACTATGAACCACGTACGGA 58.565 47.619 21.06 0.00 0.00 4.69
4262 6301 2.925578 TCACTATGAACCACGTACGG 57.074 50.000 21.06 8.46 0.00 4.02
4263 6302 5.100259 AGATTTCACTATGAACCACGTACG 58.900 41.667 15.01 15.01 35.89 3.67
4264 6303 6.331061 AGAGATTTCACTATGAACCACGTAC 58.669 40.000 0.00 0.00 35.89 3.67
4265 6304 6.525578 AGAGATTTCACTATGAACCACGTA 57.474 37.500 0.00 0.00 35.89 3.57
4266 6305 5.407407 AGAGATTTCACTATGAACCACGT 57.593 39.130 0.00 0.00 35.89 4.49
4267 6306 7.827819 TTTAGAGATTTCACTATGAACCACG 57.172 36.000 0.00 0.00 35.89 4.94
4268 6307 8.669243 CCTTTTAGAGATTTCACTATGAACCAC 58.331 37.037 0.00 0.00 35.89 4.16
4269 6308 8.602424 TCCTTTTAGAGATTTCACTATGAACCA 58.398 33.333 0.00 0.00 35.89 3.67
4270 6309 8.884726 GTCCTTTTAGAGATTTCACTATGAACC 58.115 37.037 0.00 0.00 35.89 3.62
4271 6310 9.660180 AGTCCTTTTAGAGATTTCACTATGAAC 57.340 33.333 0.00 0.00 35.89 3.18
4305 6344 9.442047 CATTCATAACTACTCTCCTTTGTTTCT 57.558 33.333 0.00 0.00 0.00 2.52
4306 6345 9.436957 TCATTCATAACTACTCTCCTTTGTTTC 57.563 33.333 0.00 0.00 0.00 2.78
4307 6346 9.793259 TTCATTCATAACTACTCTCCTTTGTTT 57.207 29.630 0.00 0.00 0.00 2.83
4308 6347 9.793259 TTTCATTCATAACTACTCTCCTTTGTT 57.207 29.630 0.00 0.00 0.00 2.83
4309 6348 9.793259 TTTTCATTCATAACTACTCTCCTTTGT 57.207 29.630 0.00 0.00 0.00 2.83
4375 8951 3.234386 CAAAAGAAGAAATCCGCCGAAC 58.766 45.455 0.00 0.00 0.00 3.95
4410 8986 8.413229 ACAACTGAAAACAATTGCTAATACACT 58.587 29.630 5.05 0.00 0.00 3.55
4412 8988 9.593134 AAACAACTGAAAACAATTGCTAATACA 57.407 25.926 5.05 0.00 0.00 2.29
4478 9054 1.157870 AAGTGGTGTTTCTCGTGCCG 61.158 55.000 0.00 0.00 0.00 5.69
4479 9055 0.586802 GAAGTGGTGTTTCTCGTGCC 59.413 55.000 0.00 0.00 0.00 5.01
4480 9056 0.586802 GGAAGTGGTGTTTCTCGTGC 59.413 55.000 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.