Multiple sequence alignment - TraesCS2A01G199100

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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 TraesCS2A01G199100 chr2A 100.000 5275 0 0 1 5275 171835264 171840538 0.000000e+00 9742.0
1 TraesCS2A01G199100 chr2B 99.509 5087 23 2 1 5087 93121153 93126237 0.000000e+00 9254.0
2 TraesCS2A01G199100 chr2B 95.556 45 1 1 5090 5134 364086127 364086084 2.640000e-08 71.3
3 TraesCS2A01G199100 chr2B 92.000 50 4 0 5088 5137 701213410 701213361 2.640000e-08 71.3
4 TraesCS2A01G199100 chr6A 99.145 4794 38 3 294 5087 46109085 46113875 0.000000e+00 8623.0
5 TraesCS2A01G199100 chr6A 99.141 931 7 1 4157 5087 46114727 46115656 0.000000e+00 1674.0
6 TraesCS2A01G199100 chr6A 98.997 299 2 1 1 298 46107400 46107698 7.780000e-148 534.0
7 TraesCS2A01G199100 chr6A 98.997 299 2 1 1 298 46138316 46138614 7.780000e-148 534.0
8 TraesCS2A01G199100 chr4B 99.145 4794 37 2 294 5087 445328200 445332989 0.000000e+00 8623.0
9 TraesCS2A01G199100 chr4B 99.082 4794 41 3 294 5087 622887439 622882649 0.000000e+00 8606.0
10 TraesCS2A01G199100 chr4B 99.329 298 2 0 1 298 622889123 622888826 1.670000e-149 540.0
11 TraesCS2A01G199100 chr4B 98.993 298 3 0 1 298 445326516 445326813 7.780000e-148 534.0
12 TraesCS2A01G199100 chr4B 96.026 151 6 0 5125 5275 34444805 34444655 4.080000e-61 246.0
13 TraesCS2A01G199100 chr3B 99.103 4794 40 2 294 5087 777040297 777035507 0.000000e+00 8612.0
14 TraesCS2A01G199100 chr3B 98.993 298 3 0 1 298 777041982 777041685 7.780000e-148 534.0
15 TraesCS2A01G199100 chrUn 98.273 4168 68 3 920 5087 269555825 269559988 0.000000e+00 7295.0
16 TraesCS2A01G199100 chr5A 99.197 3736 30 0 1352 5087 617311019 617307284 0.000000e+00 6734.0
17 TraesCS2A01G199100 chr6D 96.683 3045 85 12 1449 4487 360751640 360748606 0.000000e+00 5049.0
18 TraesCS2A01G199100 chr6D 97.465 1144 29 0 294 1437 360745736 360746879 0.000000e+00 1953.0
19 TraesCS2A01G199100 chr6D 97.378 1144 30 0 294 1437 360752859 360751716 0.000000e+00 1947.0
20 TraesCS2A01G199100 chr6D 97.987 298 6 0 1 298 360754543 360754246 7.830000e-143 518.0
21 TraesCS2A01G199100 chr6D 96.026 151 6 0 5125 5275 52496377 52496227 4.080000e-61 246.0
22 TraesCS2A01G199100 chr6D 93.617 47 1 2 5090 5136 232686641 232686597 9.480000e-08 69.4
23 TraesCS2A01G199100 chr1D 96.158 3045 102 6 1449 4487 485426288 485423253 0.000000e+00 4961.0
24 TraesCS2A01G199100 chr1D 97.220 1151 25 4 294 1444 42043820 42042677 0.000000e+00 1941.0
25 TraesCS2A01G199100 chr1D 96.066 610 23 1 4485 5093 485423217 485422608 0.000000e+00 992.0
26 TraesCS2A01G199100 chr1D 98.658 298 4 0 1 298 42045503 42045206 3.620000e-146 529.0
27 TraesCS2A01G199100 chr1D 98.658 298 4 0 1 298 485427898 485427601 3.620000e-146 529.0
28 TraesCS2A01G199100 chr1D 96.026 151 6 0 5125 5275 293701234 293701084 4.080000e-61 246.0
29 TraesCS2A01G199100 chr1D 96.026 151 6 0 5125 5275 313672428 313672578 4.080000e-61 246.0
30 TraesCS2A01G199100 chr7B 96.689 151 5 0 5125 5275 2436620 2436470 8.770000e-63 252.0
31 TraesCS2A01G199100 chr5B 96.689 151 5 0 5125 5275 662424380 662424530 8.770000e-63 252.0
32 TraesCS2A01G199100 chr4D 96.689 151 5 0 5125 5275 426767071 426767221 8.770000e-63 252.0
33 TraesCS2A01G199100 chr4D 93.617 47 3 0 5088 5134 47793961 47793915 2.640000e-08 71.3
34 TraesCS2A01G199100 chr4D 90.566 53 2 3 5074 5125 162064994 162065044 3.410000e-07 67.6
35 TraesCS2A01G199100 chr5D 96.026 151 6 0 5125 5275 500950814 500950964 4.080000e-61 246.0
36 TraesCS2A01G199100 chr1A 96.026 151 6 0 5125 5275 52489653 52489503 4.080000e-61 246.0
37 TraesCS2A01G199100 chr1A 97.727 44 1 0 5090 5133 327389699 327389742 5.660000e-10 76.8
38 TraesCS2A01G199100 chr3D 100.000 40 0 0 5088 5127 223088098 223088137 2.040000e-09 75.0
39 TraesCS2A01G199100 chr3A 92.157 51 4 0 5088 5138 204913537 204913487 7.330000e-09 73.1
40 TraesCS2A01G199100 chr3A 93.333 45 3 0 5088 5132 105388396 105388440 3.410000e-07 67.6


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 TraesCS2A01G199100 chr2A 171835264 171840538 5274 False 9742.000000 9742 100.000000 1 5275 1 chr2A.!!$F1 5274
1 TraesCS2A01G199100 chr2B 93121153 93126237 5084 False 9254.000000 9254 99.509000 1 5087 1 chr2B.!!$F1 5086
2 TraesCS2A01G199100 chr6A 46107400 46115656 8256 False 3610.333333 8623 99.094333 1 5087 3 chr6A.!!$F2 5086
3 TraesCS2A01G199100 chr4B 445326516 445332989 6473 False 4578.500000 8623 99.069000 1 5087 2 chr4B.!!$F1 5086
4 TraesCS2A01G199100 chr4B 622882649 622889123 6474 True 4573.000000 8606 99.205500 1 5087 2 chr4B.!!$R2 5086
5 TraesCS2A01G199100 chr3B 777035507 777041982 6475 True 4573.000000 8612 99.048000 1 5087 2 chr3B.!!$R1 5086
6 TraesCS2A01G199100 chrUn 269555825 269559988 4163 False 7295.000000 7295 98.273000 920 5087 1 chrUn.!!$F1 4167
7 TraesCS2A01G199100 chr5A 617307284 617311019 3735 True 6734.000000 6734 99.197000 1352 5087 1 chr5A.!!$R1 3735
8 TraesCS2A01G199100 chr6D 360748606 360754543 5937 True 2504.666667 5049 97.349333 1 4487 3 chr6D.!!$R3 4486
9 TraesCS2A01G199100 chr6D 360745736 360746879 1143 False 1953.000000 1953 97.465000 294 1437 1 chr6D.!!$F1 1143
10 TraesCS2A01G199100 chr1D 485422608 485427898 5290 True 2160.666667 4961 96.960667 1 5093 3 chr1D.!!$R3 5092
11 TraesCS2A01G199100 chr1D 42042677 42045503 2826 True 1235.000000 1941 97.939000 1 1444 2 chr1D.!!$R2 1443

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
919 2313 7.801104 TCATGCCTTTGGTAATCATCTACTAA 58.199 34.615 0.0 0.0 0.0 2.24 F
2550 4021 4.758674 GGCGAAGTTTAAGTCTAAAAGGGT 59.241 41.667 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3076 4547 2.408271 TCTGCTGCTACTTTCCATGG 57.592 50.000 4.97 4.97 0.0 3.66 R
4759 6277 2.872370 AGTAGTCGACGGTACATTTGC 58.128 47.619 10.46 0.00 0.0 3.68 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
919 2313 7.801104 TCATGCCTTTGGTAATCATCTACTAA 58.199 34.615 0.00 0.00 0.00 2.24
920 2314 8.439971 TCATGCCTTTGGTAATCATCTACTAAT 58.560 33.333 0.00 0.00 0.00 1.73
921 2315 9.071276 CATGCCTTTGGTAATCATCTACTAATT 57.929 33.333 0.00 0.00 0.00 1.40
1134 2533 5.068460 CGGTCTCAGACTAGAGGAAATTGAT 59.932 44.000 4.40 0.00 36.30 2.57
2550 4021 4.758674 GGCGAAGTTTAAGTCTAAAAGGGT 59.241 41.667 0.00 0.00 0.00 4.34
3076 4547 2.558359 AGTCAGGTGCAGTATTTTTGGC 59.442 45.455 0.00 0.00 0.00 4.52
3096 4567 2.715046 CCATGGAAAGTAGCAGCAGAA 58.285 47.619 5.56 0.00 0.00 3.02
4722 6240 1.414181 ACCATCTAATGAGCTGACGGG 59.586 52.381 0.00 0.00 0.00 5.28
4759 6277 3.139077 GTCATAAATAAGTCCAGCGGGG 58.861 50.000 2.05 0.00 38.37 5.73
5096 8394 9.502091 TGAAATATCTAGTAGTGCAAAAACTGT 57.498 29.630 7.02 0.00 0.00 3.55
5105 8403 1.418373 GCAAAAACTGTTGCGATCCC 58.582 50.000 0.00 0.00 44.05 3.85
5106 8404 1.934849 GCAAAAACTGTTGCGATCCCC 60.935 52.381 0.00 0.00 44.05 4.81
5107 8405 1.613437 CAAAAACTGTTGCGATCCCCT 59.387 47.619 0.00 0.00 0.00 4.79
5108 8406 2.817258 CAAAAACTGTTGCGATCCCCTA 59.183 45.455 0.00 0.00 0.00 3.53
5109 8407 3.366052 AAAACTGTTGCGATCCCCTAT 57.634 42.857 0.00 0.00 0.00 2.57
5110 8408 4.497291 AAAACTGTTGCGATCCCCTATA 57.503 40.909 0.00 0.00 0.00 1.31
5111 8409 3.470645 AACTGTTGCGATCCCCTATAC 57.529 47.619 0.00 0.00 0.00 1.47
5112 8410 2.679082 ACTGTTGCGATCCCCTATACT 58.321 47.619 0.00 0.00 0.00 2.12
5113 8411 3.039011 ACTGTTGCGATCCCCTATACTT 58.961 45.455 0.00 0.00 0.00 2.24
5114 8412 4.220724 ACTGTTGCGATCCCCTATACTTA 58.779 43.478 0.00 0.00 0.00 2.24
5115 8413 4.838986 ACTGTTGCGATCCCCTATACTTAT 59.161 41.667 0.00 0.00 0.00 1.73
5116 8414 5.147330 TGTTGCGATCCCCTATACTTATG 57.853 43.478 0.00 0.00 0.00 1.90
5117 8415 4.020573 TGTTGCGATCCCCTATACTTATGG 60.021 45.833 0.00 0.00 0.00 2.74
5118 8416 3.104512 TGCGATCCCCTATACTTATGGG 58.895 50.000 0.00 0.00 40.59 4.00
5119 8417 3.105283 GCGATCCCCTATACTTATGGGT 58.895 50.000 0.00 0.00 39.31 4.51
5120 8418 3.518303 GCGATCCCCTATACTTATGGGTT 59.482 47.826 0.00 0.00 39.31 4.11
5121 8419 4.713321 GCGATCCCCTATACTTATGGGTTA 59.287 45.833 0.00 0.00 39.31 2.85
5122 8420 5.365895 GCGATCCCCTATACTTATGGGTTAT 59.634 44.000 0.00 0.00 39.31 1.89
5123 8421 6.462628 GCGATCCCCTATACTTATGGGTTATC 60.463 46.154 0.00 0.00 39.31 1.75
5124 8422 6.610020 CGATCCCCTATACTTATGGGTTATCA 59.390 42.308 0.00 0.00 39.31 2.15
5125 8423 7.125204 CGATCCCCTATACTTATGGGTTATCAA 59.875 40.741 0.00 0.00 39.31 2.57
5126 8424 8.766492 ATCCCCTATACTTATGGGTTATCAAA 57.234 34.615 0.00 0.00 39.31 2.69
5127 8425 7.981142 TCCCCTATACTTATGGGTTATCAAAC 58.019 38.462 0.00 0.00 39.31 2.93
5128 8426 7.797617 TCCCCTATACTTATGGGTTATCAAACT 59.202 37.037 0.00 0.00 39.31 2.66
5129 8427 8.445588 CCCCTATACTTATGGGTTATCAAACTT 58.554 37.037 0.00 0.00 39.31 2.66
5130 8428 9.503399 CCCTATACTTATGGGTTATCAAACTTC 57.497 37.037 0.00 0.00 36.32 3.01
5136 8434 9.396022 ACTTATGGGTTATCAAACTTCTACATG 57.604 33.333 0.00 0.00 35.81 3.21
5137 8435 6.699575 ATGGGTTATCAAACTTCTACATGC 57.300 37.500 0.00 0.00 35.81 4.06
5138 8436 4.947388 TGGGTTATCAAACTTCTACATGCC 59.053 41.667 0.00 0.00 35.81 4.40
5139 8437 4.947388 GGGTTATCAAACTTCTACATGCCA 59.053 41.667 0.00 0.00 35.81 4.92
5140 8438 5.417580 GGGTTATCAAACTTCTACATGCCAA 59.582 40.000 0.00 0.00 35.81 4.52
5141 8439 6.071616 GGGTTATCAAACTTCTACATGCCAAA 60.072 38.462 0.00 0.00 35.81 3.28
5142 8440 6.806739 GGTTATCAAACTTCTACATGCCAAAC 59.193 38.462 0.00 0.00 35.81 2.93
5143 8441 7.309194 GGTTATCAAACTTCTACATGCCAAACT 60.309 37.037 0.00 0.00 35.81 2.66
5144 8442 5.437289 TCAAACTTCTACATGCCAAACTG 57.563 39.130 0.00 0.00 0.00 3.16
5145 8443 5.129634 TCAAACTTCTACATGCCAAACTGA 58.870 37.500 0.00 0.00 0.00 3.41
5146 8444 5.008613 TCAAACTTCTACATGCCAAACTGAC 59.991 40.000 0.00 0.00 0.00 3.51
5147 8445 4.085357 ACTTCTACATGCCAAACTGACA 57.915 40.909 0.00 0.00 0.00 3.58
5148 8446 4.460263 ACTTCTACATGCCAAACTGACAA 58.540 39.130 0.00 0.00 0.00 3.18
5149 8447 5.072741 ACTTCTACATGCCAAACTGACAAT 58.927 37.500 0.00 0.00 0.00 2.71
5150 8448 5.536161 ACTTCTACATGCCAAACTGACAATT 59.464 36.000 0.00 0.00 0.00 2.32
5151 8449 6.040842 ACTTCTACATGCCAAACTGACAATTT 59.959 34.615 0.00 0.00 0.00 1.82
5152 8450 7.230510 ACTTCTACATGCCAAACTGACAATTTA 59.769 33.333 0.00 0.00 0.00 1.40
5153 8451 7.517614 TCTACATGCCAAACTGACAATTTAA 57.482 32.000 0.00 0.00 0.00 1.52
5154 8452 7.592938 TCTACATGCCAAACTGACAATTTAAG 58.407 34.615 0.00 0.00 0.00 1.85
5155 8453 5.540911 ACATGCCAAACTGACAATTTAAGG 58.459 37.500 0.00 0.00 0.00 2.69
5156 8454 3.988819 TGCCAAACTGACAATTTAAGGC 58.011 40.909 4.29 4.29 39.95 4.35
5157 8455 3.386078 TGCCAAACTGACAATTTAAGGCA 59.614 39.130 8.79 8.79 46.31 4.75
5158 8456 4.040217 TGCCAAACTGACAATTTAAGGCAT 59.960 37.500 8.79 0.00 43.93 4.40
5159 8457 5.244851 TGCCAAACTGACAATTTAAGGCATA 59.755 36.000 8.79 0.00 43.93 3.14
5160 8458 5.807011 GCCAAACTGACAATTTAAGGCATAG 59.193 40.000 6.00 0.00 39.35 2.23
5161 8459 6.572314 GCCAAACTGACAATTTAAGGCATAGT 60.572 38.462 6.00 0.00 39.35 2.12
5162 8460 7.029563 CCAAACTGACAATTTAAGGCATAGTC 58.970 38.462 0.00 0.00 0.00 2.59
5163 8461 6.759497 AACTGACAATTTAAGGCATAGTCC 57.241 37.500 0.00 0.00 0.00 3.85
5164 8462 5.815581 ACTGACAATTTAAGGCATAGTCCA 58.184 37.500 0.00 0.00 0.00 4.02
5165 8463 6.426587 ACTGACAATTTAAGGCATAGTCCAT 58.573 36.000 0.00 0.00 0.00 3.41
5166 8464 6.891908 ACTGACAATTTAAGGCATAGTCCATT 59.108 34.615 0.00 0.00 0.00 3.16
5167 8465 7.099266 TGACAATTTAAGGCATAGTCCATTG 57.901 36.000 0.00 0.00 0.00 2.82
5168 8466 6.663093 TGACAATTTAAGGCATAGTCCATTGT 59.337 34.615 0.00 0.00 0.00 2.71
5169 8467 7.178274 TGACAATTTAAGGCATAGTCCATTGTT 59.822 33.333 0.00 0.00 0.00 2.83
5170 8468 7.547227 ACAATTTAAGGCATAGTCCATTGTTC 58.453 34.615 0.00 0.00 0.00 3.18
5171 8469 7.178274 ACAATTTAAGGCATAGTCCATTGTTCA 59.822 33.333 0.00 0.00 0.00 3.18
5172 8470 6.509418 TTTAAGGCATAGTCCATTGTTCAC 57.491 37.500 0.00 0.00 0.00 3.18
5173 8471 4.307032 AAGGCATAGTCCATTGTTCACT 57.693 40.909 0.00 0.00 0.00 3.41
5174 8472 4.307032 AGGCATAGTCCATTGTTCACTT 57.693 40.909 0.00 0.00 0.00 3.16
5175 8473 4.012374 AGGCATAGTCCATTGTTCACTTG 58.988 43.478 0.00 0.00 0.00 3.16
5176 8474 3.758554 GGCATAGTCCATTGTTCACTTGT 59.241 43.478 0.00 0.00 0.00 3.16
5177 8475 4.379813 GGCATAGTCCATTGTTCACTTGTG 60.380 45.833 0.00 0.00 0.00 3.33
5178 8476 4.455533 GCATAGTCCATTGTTCACTTGTGA 59.544 41.667 0.00 0.00 0.00 3.58
5179 8477 5.048782 GCATAGTCCATTGTTCACTTGTGAA 60.049 40.000 11.62 11.62 0.00 3.18
5180 8478 6.605849 CATAGTCCATTGTTCACTTGTGAAG 58.394 40.000 15.44 5.18 0.00 3.02
5181 8479 4.780815 AGTCCATTGTTCACTTGTGAAGA 58.219 39.130 15.44 12.12 0.00 2.87
5182 8480 5.192927 AGTCCATTGTTCACTTGTGAAGAA 58.807 37.500 22.17 22.17 35.91 2.52
5183 8481 5.652014 AGTCCATTGTTCACTTGTGAAGAAA 59.348 36.000 23.22 17.14 35.27 2.52
5184 8482 6.322201 AGTCCATTGTTCACTTGTGAAGAAAT 59.678 34.615 23.22 18.23 35.27 2.17
5185 8483 6.638468 GTCCATTGTTCACTTGTGAAGAAATC 59.362 38.462 23.22 10.66 35.27 2.17
5186 8484 6.547141 TCCATTGTTCACTTGTGAAGAAATCT 59.453 34.615 23.22 9.93 35.27 2.40
5187 8485 7.719193 TCCATTGTTCACTTGTGAAGAAATCTA 59.281 33.333 23.22 11.22 35.27 1.98
5188 8486 8.352201 CCATTGTTCACTTGTGAAGAAATCTAA 58.648 33.333 23.22 6.56 35.27 2.10
5189 8487 9.903682 CATTGTTCACTTGTGAAGAAATCTAAT 57.096 29.630 23.22 8.81 35.27 1.73
5191 8489 8.099364 TGTTCACTTGTGAAGAAATCTAATCC 57.901 34.615 15.44 1.96 0.00 3.01
5192 8490 7.939039 TGTTCACTTGTGAAGAAATCTAATCCT 59.061 33.333 15.44 0.00 0.00 3.24
5193 8491 7.912056 TCACTTGTGAAGAAATCTAATCCTG 57.088 36.000 0.44 0.00 0.00 3.86
5194 8492 7.453393 TCACTTGTGAAGAAATCTAATCCTGT 58.547 34.615 0.44 0.00 0.00 4.00
5195 8493 7.939039 TCACTTGTGAAGAAATCTAATCCTGTT 59.061 33.333 0.44 0.00 0.00 3.16
5196 8494 8.019669 CACTTGTGAAGAAATCTAATCCTGTTG 58.980 37.037 0.00 0.00 0.00 3.33
5197 8495 6.500684 TGTGAAGAAATCTAATCCTGTTGC 57.499 37.500 0.00 0.00 0.00 4.17
5198 8496 6.240894 TGTGAAGAAATCTAATCCTGTTGCT 58.759 36.000 0.00 0.00 0.00 3.91
5199 8497 6.372659 TGTGAAGAAATCTAATCCTGTTGCTC 59.627 38.462 0.00 0.00 0.00 4.26
5200 8498 6.597280 GTGAAGAAATCTAATCCTGTTGCTCT 59.403 38.462 0.00 0.00 0.00 4.09
5201 8499 7.766278 GTGAAGAAATCTAATCCTGTTGCTCTA 59.234 37.037 0.00 0.00 0.00 2.43
5202 8500 7.984050 TGAAGAAATCTAATCCTGTTGCTCTAG 59.016 37.037 0.00 0.00 0.00 2.43
5203 8501 6.825610 AGAAATCTAATCCTGTTGCTCTAGG 58.174 40.000 0.00 0.00 35.34 3.02
5204 8502 6.385467 AGAAATCTAATCCTGTTGCTCTAGGT 59.615 38.462 0.00 0.00 35.54 3.08
5205 8503 5.543507 ATCTAATCCTGTTGCTCTAGGTG 57.456 43.478 0.00 0.00 35.54 4.00
5206 8504 3.706594 TCTAATCCTGTTGCTCTAGGTGG 59.293 47.826 0.00 0.00 35.54 4.61
5207 8505 2.254152 ATCCTGTTGCTCTAGGTGGA 57.746 50.000 0.00 0.00 35.54 4.02
5208 8506 2.024176 TCCTGTTGCTCTAGGTGGAA 57.976 50.000 0.00 0.00 35.54 3.53
5209 8507 1.902508 TCCTGTTGCTCTAGGTGGAAG 59.097 52.381 0.00 0.00 35.54 3.46
5210 8508 1.625818 CCTGTTGCTCTAGGTGGAAGT 59.374 52.381 0.00 0.00 0.00 3.01
5211 8509 2.039084 CCTGTTGCTCTAGGTGGAAGTT 59.961 50.000 0.00 0.00 0.00 2.66
5212 8510 3.330267 CTGTTGCTCTAGGTGGAAGTTC 58.670 50.000 0.00 0.00 0.00 3.01
5213 8511 2.703536 TGTTGCTCTAGGTGGAAGTTCA 59.296 45.455 5.01 0.00 0.00 3.18
5214 8512 3.135712 TGTTGCTCTAGGTGGAAGTTCAA 59.864 43.478 5.01 0.00 0.00 2.69
5215 8513 3.402628 TGCTCTAGGTGGAAGTTCAAC 57.597 47.619 5.01 3.14 0.00 3.18
5216 8514 2.972713 TGCTCTAGGTGGAAGTTCAACT 59.027 45.455 10.26 4.52 38.40 3.16
5217 8515 3.391296 TGCTCTAGGTGGAAGTTCAACTT 59.609 43.478 1.21 1.21 41.95 2.66
5218 8516 4.591498 TGCTCTAGGTGGAAGTTCAACTTA 59.409 41.667 10.26 6.23 38.80 2.24
5219 8517 5.071250 TGCTCTAGGTGGAAGTTCAACTTAA 59.929 40.000 10.26 0.00 38.80 1.85
5220 8518 5.408909 GCTCTAGGTGGAAGTTCAACTTAAC 59.591 44.000 10.26 4.97 38.80 2.01
5221 8519 6.488769 TCTAGGTGGAAGTTCAACTTAACA 57.511 37.500 10.26 2.86 38.80 2.41
5222 8520 6.522054 TCTAGGTGGAAGTTCAACTTAACAG 58.478 40.000 10.26 0.55 38.80 3.16
5223 8521 5.112129 AGGTGGAAGTTCAACTTAACAGT 57.888 39.130 10.26 0.00 38.80 3.55
5224 8522 5.123936 AGGTGGAAGTTCAACTTAACAGTC 58.876 41.667 10.26 2.04 38.80 3.51
5225 8523 5.104485 AGGTGGAAGTTCAACTTAACAGTCT 60.104 40.000 10.26 4.11 38.80 3.24
5226 8524 5.236695 GGTGGAAGTTCAACTTAACAGTCTC 59.763 44.000 10.26 0.00 38.80 3.36
5227 8525 5.236695 GTGGAAGTTCAACTTAACAGTCTCC 59.763 44.000 1.74 0.00 38.80 3.71
5228 8526 5.104693 TGGAAGTTCAACTTAACAGTCTCCA 60.105 40.000 1.74 0.73 38.80 3.86
5229 8527 5.236695 GGAAGTTCAACTTAACAGTCTCCAC 59.763 44.000 1.74 0.00 38.80 4.02
5230 8528 5.615925 AGTTCAACTTAACAGTCTCCACT 57.384 39.130 0.00 0.00 30.45 4.00
5231 8529 5.817816 AAGTTCAACTTAACAGTCTCCACTG 59.182 40.000 0.00 0.45 45.20 3.66
5232 8530 6.351881 AAGTTCAACTTAACAGTCTCCACTGA 60.352 38.462 0.00 0.00 43.82 3.41
5233 8531 7.796916 AAGTTCAACTTAACAGTCTCCACTGAA 60.797 37.037 0.00 0.00 43.82 3.02
5247 8545 9.995003 AGTCTCCACTGAAATTTCTGATATATC 57.005 33.333 26.21 5.73 0.00 1.63
5248 8546 9.770097 GTCTCCACTGAAATTTCTGATATATCA 57.230 33.333 26.21 14.64 35.16 2.15
5268 8566 6.907206 ATCAAACATTGTTTGGAACAGTTG 57.093 33.333 31.52 12.38 43.27 3.16
5269 8567 6.030548 TCAAACATTGTTTGGAACAGTTGA 57.969 33.333 31.52 14.17 43.27 3.18
5270 8568 5.866633 TCAAACATTGTTTGGAACAGTTGAC 59.133 36.000 31.52 0.00 43.27 3.18
5271 8569 5.398603 AACATTGTTTGGAACAGTTGACA 57.601 34.783 0.00 0.00 43.27 3.58
5272 8570 5.398603 ACATTGTTTGGAACAGTTGACAA 57.601 34.783 0.00 0.00 43.27 3.18
5273 8571 5.788450 ACATTGTTTGGAACAGTTGACAAA 58.212 33.333 8.12 8.12 43.27 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
656 2050 9.546428 TGTTCAGTAATCATCATCGTCATATTT 57.454 29.630 0.00 0.00 0.00 1.40
874 2268 7.437862 GGCATGATAGTAGAAGAAGAGAACAAG 59.562 40.741 0.00 0.00 0.00 3.16
1134 2533 1.766494 TGGGAACTATAAGCGGTCGA 58.234 50.000 0.00 0.00 0.00 4.20
3076 4547 2.408271 TCTGCTGCTACTTTCCATGG 57.592 50.000 4.97 4.97 0.00 3.66
4759 6277 2.872370 AGTAGTCGACGGTACATTTGC 58.128 47.619 10.46 0.00 0.00 3.68
5087 8385 1.613437 AGGGGATCGCAACAGTTTTTG 59.387 47.619 12.32 0.00 0.00 2.44
5088 8386 1.995376 AGGGGATCGCAACAGTTTTT 58.005 45.000 12.32 0.00 0.00 1.94
5091 8389 3.039011 AGTATAGGGGATCGCAACAGTT 58.961 45.455 12.32 0.00 0.00 3.16
5093 8391 3.753294 AAGTATAGGGGATCGCAACAG 57.247 47.619 12.32 0.00 0.00 3.16
5094 8392 4.020573 CCATAAGTATAGGGGATCGCAACA 60.021 45.833 12.32 0.00 29.12 3.33
5095 8393 4.504858 CCATAAGTATAGGGGATCGCAAC 58.495 47.826 12.32 4.19 29.12 4.17
5096 8394 4.819105 CCATAAGTATAGGGGATCGCAA 57.181 45.455 12.32 0.00 29.12 4.85
5110 8408 9.396022 CATGTAGAAGTTTGATAACCCATAAGT 57.604 33.333 0.00 0.00 34.71 2.24
5111 8409 8.345565 GCATGTAGAAGTTTGATAACCCATAAG 58.654 37.037 0.00 0.00 34.71 1.73
5112 8410 7.284489 GGCATGTAGAAGTTTGATAACCCATAA 59.716 37.037 0.00 0.00 34.71 1.90
5113 8411 6.770785 GGCATGTAGAAGTTTGATAACCCATA 59.229 38.462 0.00 0.00 34.71 2.74
5114 8412 5.594317 GGCATGTAGAAGTTTGATAACCCAT 59.406 40.000 0.00 0.00 34.71 4.00
5115 8413 4.947388 GGCATGTAGAAGTTTGATAACCCA 59.053 41.667 0.00 0.00 34.71 4.51
5116 8414 4.947388 TGGCATGTAGAAGTTTGATAACCC 59.053 41.667 0.00 0.00 34.71 4.11
5117 8415 6.509418 TTGGCATGTAGAAGTTTGATAACC 57.491 37.500 0.00 0.00 34.71 2.85
5118 8416 7.538678 CAGTTTGGCATGTAGAAGTTTGATAAC 59.461 37.037 0.00 0.00 34.36 1.89
5119 8417 7.446931 TCAGTTTGGCATGTAGAAGTTTGATAA 59.553 33.333 0.00 0.00 0.00 1.75
5120 8418 6.939730 TCAGTTTGGCATGTAGAAGTTTGATA 59.060 34.615 0.00 0.00 0.00 2.15
5121 8419 5.769662 TCAGTTTGGCATGTAGAAGTTTGAT 59.230 36.000 0.00 0.00 0.00 2.57
5122 8420 5.008613 GTCAGTTTGGCATGTAGAAGTTTGA 59.991 40.000 0.00 0.00 0.00 2.69
5123 8421 5.215160 GTCAGTTTGGCATGTAGAAGTTTG 58.785 41.667 0.00 0.00 0.00 2.93
5124 8422 4.887071 TGTCAGTTTGGCATGTAGAAGTTT 59.113 37.500 0.00 0.00 0.00 2.66
5125 8423 4.460263 TGTCAGTTTGGCATGTAGAAGTT 58.540 39.130 0.00 0.00 0.00 2.66
5126 8424 4.085357 TGTCAGTTTGGCATGTAGAAGT 57.915 40.909 0.00 0.00 0.00 3.01
5127 8425 5.633830 ATTGTCAGTTTGGCATGTAGAAG 57.366 39.130 0.00 0.00 29.04 2.85
5128 8426 6.403866 AAATTGTCAGTTTGGCATGTAGAA 57.596 33.333 0.00 0.00 29.04 2.10
5129 8427 7.309133 CCTTAAATTGTCAGTTTGGCATGTAGA 60.309 37.037 3.71 0.00 29.04 2.59
5130 8428 6.808212 CCTTAAATTGTCAGTTTGGCATGTAG 59.192 38.462 3.71 0.00 29.04 2.74
5131 8429 6.686630 CCTTAAATTGTCAGTTTGGCATGTA 58.313 36.000 3.71 0.00 29.04 2.29
5132 8430 5.540911 CCTTAAATTGTCAGTTTGGCATGT 58.459 37.500 3.71 0.00 29.04 3.21
5133 8431 4.389687 GCCTTAAATTGTCAGTTTGGCATG 59.610 41.667 13.94 0.00 37.91 4.06
5134 8432 4.040217 TGCCTTAAATTGTCAGTTTGGCAT 59.960 37.500 16.32 0.00 42.20 4.40
5135 8433 3.386078 TGCCTTAAATTGTCAGTTTGGCA 59.614 39.130 16.32 16.32 44.41 4.92
5136 8434 3.988819 TGCCTTAAATTGTCAGTTTGGC 58.011 40.909 12.61 12.61 38.42 4.52
5137 8435 6.924111 ACTATGCCTTAAATTGTCAGTTTGG 58.076 36.000 3.71 0.00 0.00 3.28
5138 8436 7.029563 GGACTATGCCTTAAATTGTCAGTTTG 58.970 38.462 3.71 0.00 33.25 2.93
5139 8437 6.719370 TGGACTATGCCTTAAATTGTCAGTTT 59.281 34.615 0.00 0.00 33.25 2.66
5140 8438 6.245408 TGGACTATGCCTTAAATTGTCAGTT 58.755 36.000 0.00 0.00 33.25 3.16
5141 8439 5.815581 TGGACTATGCCTTAAATTGTCAGT 58.184 37.500 0.00 0.00 33.25 3.41
5142 8440 6.949352 ATGGACTATGCCTTAAATTGTCAG 57.051 37.500 0.00 0.00 33.25 3.51
5143 8441 6.663093 ACAATGGACTATGCCTTAAATTGTCA 59.337 34.615 0.00 0.00 33.01 3.58
5144 8442 7.100458 ACAATGGACTATGCCTTAAATTGTC 57.900 36.000 0.00 0.00 33.01 3.18
5145 8443 7.178274 TGAACAATGGACTATGCCTTAAATTGT 59.822 33.333 0.00 0.00 38.33 2.71
5146 8444 7.489113 GTGAACAATGGACTATGCCTTAAATTG 59.511 37.037 0.00 0.00 0.00 2.32
5147 8445 7.397192 AGTGAACAATGGACTATGCCTTAAATT 59.603 33.333 0.00 0.00 0.00 1.82
5148 8446 6.891908 AGTGAACAATGGACTATGCCTTAAAT 59.108 34.615 0.00 0.00 0.00 1.40
5149 8447 6.245408 AGTGAACAATGGACTATGCCTTAAA 58.755 36.000 0.00 0.00 0.00 1.52
5150 8448 5.815581 AGTGAACAATGGACTATGCCTTAA 58.184 37.500 0.00 0.00 0.00 1.85
5151 8449 5.435686 AGTGAACAATGGACTATGCCTTA 57.564 39.130 0.00 0.00 0.00 2.69
5152 8450 4.307032 AGTGAACAATGGACTATGCCTT 57.693 40.909 0.00 0.00 0.00 4.35
5153 8451 4.012374 CAAGTGAACAATGGACTATGCCT 58.988 43.478 0.00 0.00 0.00 4.75
5154 8452 3.758554 ACAAGTGAACAATGGACTATGCC 59.241 43.478 0.00 0.00 0.00 4.40
5155 8453 4.455533 TCACAAGTGAACAATGGACTATGC 59.544 41.667 0.00 0.00 36.53 3.14
5156 8454 6.427853 TCTTCACAAGTGAACAATGGACTATG 59.572 38.462 11.34 0.00 43.90 2.23
5157 8455 6.533730 TCTTCACAAGTGAACAATGGACTAT 58.466 36.000 11.34 0.00 43.90 2.12
5158 8456 5.924356 TCTTCACAAGTGAACAATGGACTA 58.076 37.500 11.34 0.00 43.90 2.59
5159 8457 4.780815 TCTTCACAAGTGAACAATGGACT 58.219 39.130 11.34 0.00 43.90 3.85
5160 8458 5.499139 TTCTTCACAAGTGAACAATGGAC 57.501 39.130 11.34 0.00 43.90 4.02
5161 8459 6.547141 AGATTTCTTCACAAGTGAACAATGGA 59.453 34.615 11.34 4.91 43.90 3.41
5162 8460 6.742109 AGATTTCTTCACAAGTGAACAATGG 58.258 36.000 11.34 2.70 43.90 3.16
5163 8461 9.903682 ATTAGATTTCTTCACAAGTGAACAATG 57.096 29.630 11.34 3.04 43.90 2.82
5165 8463 8.567948 GGATTAGATTTCTTCACAAGTGAACAA 58.432 33.333 11.34 5.63 43.90 2.83
5166 8464 7.939039 AGGATTAGATTTCTTCACAAGTGAACA 59.061 33.333 11.34 0.00 43.90 3.18
5167 8465 8.233190 CAGGATTAGATTTCTTCACAAGTGAAC 58.767 37.037 11.34 2.51 43.90 3.18
5168 8466 7.939039 ACAGGATTAGATTTCTTCACAAGTGAA 59.061 33.333 14.29 14.29 46.27 3.18
5169 8467 7.453393 ACAGGATTAGATTTCTTCACAAGTGA 58.547 34.615 0.00 0.00 37.91 3.41
5170 8468 7.678947 ACAGGATTAGATTTCTTCACAAGTG 57.321 36.000 0.00 0.00 0.00 3.16
5171 8469 7.308830 GCAACAGGATTAGATTTCTTCACAAGT 60.309 37.037 0.00 0.00 0.00 3.16
5172 8470 7.025963 GCAACAGGATTAGATTTCTTCACAAG 58.974 38.462 0.00 0.00 0.00 3.16
5173 8471 6.716628 AGCAACAGGATTAGATTTCTTCACAA 59.283 34.615 0.00 0.00 0.00 3.33
5174 8472 6.240894 AGCAACAGGATTAGATTTCTTCACA 58.759 36.000 0.00 0.00 0.00 3.58
5175 8473 6.597280 AGAGCAACAGGATTAGATTTCTTCAC 59.403 38.462 0.00 0.00 0.00 3.18
5176 8474 6.715280 AGAGCAACAGGATTAGATTTCTTCA 58.285 36.000 0.00 0.00 0.00 3.02
5177 8475 7.440856 CCTAGAGCAACAGGATTAGATTTCTTC 59.559 40.741 0.00 0.00 33.42 2.87
5178 8476 7.092668 ACCTAGAGCAACAGGATTAGATTTCTT 60.093 37.037 4.67 0.00 35.76 2.52
5179 8477 6.385467 ACCTAGAGCAACAGGATTAGATTTCT 59.615 38.462 4.67 0.00 35.76 2.52
5180 8478 6.481644 CACCTAGAGCAACAGGATTAGATTTC 59.518 42.308 4.67 0.00 35.76 2.17
5181 8479 6.352516 CACCTAGAGCAACAGGATTAGATTT 58.647 40.000 4.67 0.00 35.76 2.17
5182 8480 5.163258 CCACCTAGAGCAACAGGATTAGATT 60.163 44.000 4.67 0.00 35.76 2.40
5183 8481 4.346418 CCACCTAGAGCAACAGGATTAGAT 59.654 45.833 4.67 0.00 35.76 1.98
5184 8482 3.706594 CCACCTAGAGCAACAGGATTAGA 59.293 47.826 4.67 0.00 35.76 2.10
5185 8483 3.706594 TCCACCTAGAGCAACAGGATTAG 59.293 47.826 4.67 0.00 35.76 1.73
5186 8484 3.719871 TCCACCTAGAGCAACAGGATTA 58.280 45.455 4.67 0.00 35.76 1.75
5187 8485 2.551270 TCCACCTAGAGCAACAGGATT 58.449 47.619 4.67 0.00 35.76 3.01
5188 8486 2.254152 TCCACCTAGAGCAACAGGAT 57.746 50.000 4.67 0.00 35.76 3.24
5189 8487 1.902508 CTTCCACCTAGAGCAACAGGA 59.097 52.381 4.67 0.00 35.76 3.86
5190 8488 1.625818 ACTTCCACCTAGAGCAACAGG 59.374 52.381 0.00 0.00 37.97 4.00
5191 8489 3.244215 TGAACTTCCACCTAGAGCAACAG 60.244 47.826 0.00 0.00 0.00 3.16
5192 8490 2.703536 TGAACTTCCACCTAGAGCAACA 59.296 45.455 0.00 0.00 0.00 3.33
5193 8491 3.402628 TGAACTTCCACCTAGAGCAAC 57.597 47.619 0.00 0.00 0.00 4.17
5194 8492 3.391296 AGTTGAACTTCCACCTAGAGCAA 59.609 43.478 0.00 0.00 0.00 3.91
5195 8493 2.972713 AGTTGAACTTCCACCTAGAGCA 59.027 45.455 0.00 0.00 0.00 4.26
5196 8494 3.686916 AGTTGAACTTCCACCTAGAGC 57.313 47.619 0.00 0.00 0.00 4.09
5197 8495 6.522054 TGTTAAGTTGAACTTCCACCTAGAG 58.478 40.000 14.64 0.00 39.51 2.43
5198 8496 6.099269 ACTGTTAAGTTGAACTTCCACCTAGA 59.901 38.462 14.64 0.00 39.51 2.43
5199 8497 6.289064 ACTGTTAAGTTGAACTTCCACCTAG 58.711 40.000 14.64 9.27 39.51 3.02
5200 8498 6.099269 AGACTGTTAAGTTGAACTTCCACCTA 59.901 38.462 14.64 0.00 39.51 3.08
5201 8499 5.104485 AGACTGTTAAGTTGAACTTCCACCT 60.104 40.000 14.64 7.63 39.51 4.00
5202 8500 5.123936 AGACTGTTAAGTTGAACTTCCACC 58.876 41.667 14.64 5.75 39.51 4.61
5203 8501 5.236695 GGAGACTGTTAAGTTGAACTTCCAC 59.763 44.000 14.64 12.71 39.51 4.02
5204 8502 5.104693 TGGAGACTGTTAAGTTGAACTTCCA 60.105 40.000 14.64 10.21 39.51 3.53
5205 8503 5.236695 GTGGAGACTGTTAAGTTGAACTTCC 59.763 44.000 14.64 7.61 39.51 3.46
5206 8504 6.018669 CAGTGGAGACTGTTAAGTTGAACTTC 60.019 42.308 14.64 1.74 44.15 3.01
5207 8505 5.817816 CAGTGGAGACTGTTAAGTTGAACTT 59.182 40.000 15.57 15.57 44.15 2.66
5208 8506 5.360591 CAGTGGAGACTGTTAAGTTGAACT 58.639 41.667 0.00 0.00 44.15 3.01
5209 8507 5.659048 CAGTGGAGACTGTTAAGTTGAAC 57.341 43.478 0.00 0.00 44.15 3.18
5221 8519 9.995003 GATATATCAGAAATTTCAGTGGAGACT 57.005 33.333 19.99 2.03 0.00 3.24
5222 8520 9.770097 TGATATATCAGAAATTTCAGTGGAGAC 57.230 33.333 19.99 6.66 32.11 3.36
5242 8540 9.689976 CAACTGTTCCAAACAATGTTTGATATA 57.310 29.630 32.93 19.39 41.61 0.86
5243 8541 8.420222 TCAACTGTTCCAAACAATGTTTGATAT 58.580 29.630 32.93 13.83 41.61 1.63
5244 8542 7.704472 GTCAACTGTTCCAAACAATGTTTGATA 59.296 33.333 32.93 20.60 41.61 2.15
5245 8543 6.534793 GTCAACTGTTCCAAACAATGTTTGAT 59.465 34.615 32.93 12.95 41.61 2.57
5246 8544 5.866633 GTCAACTGTTCCAAACAATGTTTGA 59.133 36.000 32.93 19.36 41.61 2.69
5247 8545 5.636965 TGTCAACTGTTCCAAACAATGTTTG 59.363 36.000 26.80 26.80 41.61 2.93
5248 8546 5.788450 TGTCAACTGTTCCAAACAATGTTT 58.212 33.333 5.41 5.41 41.61 2.83
5249 8547 5.398603 TGTCAACTGTTCCAAACAATGTT 57.601 34.783 0.00 0.00 41.61 2.71
5250 8548 5.398603 TTGTCAACTGTTCCAAACAATGT 57.601 34.783 0.00 0.00 41.61 2.71
5251 8549 6.093532 GTTTGTCAACTGTTCCAAACAATG 57.906 37.500 25.39 3.24 43.70 2.82


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

AutoCloner maintained by Alex Coulton.