Multiple sequence alignment - TraesCS7D01G508800

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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 TraesCS7D01G508800 chr7D 100.000 4082 0 0 844 4925 612436494 612440575 0.000000e+00 7539.0
1 TraesCS7D01G508800 chr7D 91.020 3274 228 32 900 4132 611235322 611232074 0.000000e+00 4357.0
2 TraesCS7D01G508800 chr7D 100.000 186 0 0 1 186 612435651 612435836 1.310000e-90 344.0
3 TraesCS7D01G508800 chr7D 89.474 114 12 0 4269 4382 183211782 183211669 1.430000e-30 145.0
4 TraesCS7D01G508800 chr7D 96.053 76 3 0 4628 4703 612440207 612440282 1.860000e-24 124.0
5 TraesCS7D01G508800 chr7D 96.053 76 3 0 4557 4632 612440278 612440353 1.860000e-24 124.0
6 TraesCS7D01G508800 chr7A 97.116 3433 84 7 844 4270 702978695 702975272 0.000000e+00 5777.0
7 TraesCS7D01G508800 chr7A 90.710 3294 241 33 876 4130 701274695 701271428 0.000000e+00 4327.0
8 TraesCS7D01G508800 chr7A 96.104 154 6 0 4772 4925 702975046 702974893 8.180000e-63 252.0
9 TraesCS7D01G508800 chr7A 96.000 125 2 2 4424 4546 702975163 702975040 3.010000e-47 200.0
10 TraesCS7D01G508800 chr7A 86.139 101 13 1 4533 4632 701270956 701270856 1.870000e-19 108.0
11 TraesCS7D01G508800 chr7A 82.114 123 17 4 4645 4762 701265420 701265298 3.140000e-17 100.0
12 TraesCS7D01G508800 chr7A 100.000 48 0 0 13 60 702979792 702979745 6.790000e-14 89.8
13 TraesCS7D01G508800 chr7A 94.643 56 3 0 4376 4431 702975251 702975196 2.440000e-13 87.9
14 TraesCS7D01G508800 chr7A 85.393 89 3 4 3954 4032 703527434 703527522 3.160000e-12 84.2
15 TraesCS7D01G508800 chr7B 96.597 3438 102 6 845 4270 701869070 701872504 0.000000e+00 5686.0
16 TraesCS7D01G508800 chr7B 91.124 3301 238 28 876 4132 700396031 700392742 0.000000e+00 4421.0
17 TraesCS7D01G508800 chr7B 93.939 297 15 3 4632 4925 701872829 701873125 3.500000e-121 446.0
18 TraesCS7D01G508800 chr7B 93.434 198 10 2 4438 4632 701872703 701872900 1.730000e-74 291.0
19 TraesCS7D01G508800 chr7B 93.506 154 3 2 13 163 701868314 701868463 6.420000e-54 222.0
20 TraesCS7D01G508800 chr7B 82.063 223 19 11 4703 4916 700392127 700391917 2.360000e-38 171.0
21 TraesCS7D01G508800 chr7B 80.645 217 24 8 4646 4856 700382355 700382151 8.540000e-33 152.0
22 TraesCS7D01G508800 chr7B 83.740 123 15 4 4645 4762 700384822 700384700 1.450000e-20 111.0
23 TraesCS7D01G508800 chr7B 94.643 56 3 0 4376 4431 701872525 701872580 2.440000e-13 87.9
24 TraesCS7D01G508800 chr3A 88.601 193 16 5 1003 1195 152001010 152000824 3.830000e-56 230.0
25 TraesCS7D01G508800 chr5B 91.743 109 9 0 4269 4377 558559073 558558965 8.540000e-33 152.0
26 TraesCS7D01G508800 chr1B 91.743 109 9 0 4267 4375 492303981 492303873 8.540000e-33 152.0
27 TraesCS7D01G508800 chr5D 90.435 115 10 1 4262 4375 18085129 18085015 3.070000e-32 150.0
28 TraesCS7D01G508800 chr5D 91.589 107 9 0 4269 4375 268274817 268274711 1.100000e-31 148.0
29 TraesCS7D01G508800 chr1D 90.991 111 10 0 4265 4375 403331793 403331683 3.070000e-32 150.0
30 TraesCS7D01G508800 chr4B 90.909 110 10 0 4269 4378 372823053 372822944 1.100000e-31 148.0
31 TraesCS7D01G508800 chr3D 90.000 110 11 0 4270 4379 597483193 597483302 5.140000e-30 143.0
32 TraesCS7D01G508800 chr6B 88.235 119 11 2 4266 4384 287149140 287149025 6.650000e-29 139.0


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 TraesCS7D01G508800 chr7D 612435651 612440575 4924 False 2032.75 7539 98.0265 1 4925 4 chr7D.!!$F1 4924
1 TraesCS7D01G508800 chr7D 611232074 611235322 3248 True 4357.00 4357 91.0200 900 4132 1 chr7D.!!$R2 3232
2 TraesCS7D01G508800 chr7A 701270856 701274695 3839 True 2217.50 4327 88.4245 876 4632 2 chr7A.!!$R2 3756
3 TraesCS7D01G508800 chr7A 702974893 702979792 4899 True 1281.34 5777 96.7726 13 4925 5 chr7A.!!$R3 4912
4 TraesCS7D01G508800 chr7B 700391917 700396031 4114 True 2296.00 4421 86.5935 876 4916 2 chr7B.!!$R2 4040
5 TraesCS7D01G508800 chr7B 701868314 701873125 4811 False 1346.58 5686 94.4238 13 4925 5 chr7B.!!$F1 4912

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
70 71 4.436998 GACCGACGACCCAGCCAG 62.437 72.222 0.00 0.0 0.00 4.85 F
1872 2606 1.599542 GTATGCGACAAGAGATTGCCC 59.400 52.381 0.00 0.0 0.00 5.36 F
1902 2636 0.685097 ATAGGTGCAAGGTCACGTGT 59.315 50.000 16.51 0.0 37.83 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2636 0.959553 GTGGACACTCTCCTTCGTGA 59.040 55.0 0.0 0.0 40.26 4.35 R
3555 4289 0.385029 CTCCATCTCTCTGTGCTCCG 59.615 60.0 0.0 0.0 0.00 4.63 R
4020 4797 2.808543 CAACAGCCAGGAACTACTTGAC 59.191 50.0 0.0 0.0 36.02 3.18 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
70 71 4.436998 GACCGACGACCCAGCCAG 62.437 72.222 0.00 0.00 0.00 4.85
1872 2606 1.599542 GTATGCGACAAGAGATTGCCC 59.400 52.381 0.00 0.00 0.00 5.36
1902 2636 0.685097 ATAGGTGCAAGGTCACGTGT 59.315 50.000 16.51 0.00 37.83 4.49
1992 2726 2.018355 TGGTGGAGTGCTACAAGGTA 57.982 50.000 0.00 0.00 0.00 3.08
2145 2879 1.878211 TCTGCCAGATACCATGTGGA 58.122 50.000 5.96 0.00 46.04 4.02
2214 2948 3.357079 CACTGTGACCCTTGCCGC 61.357 66.667 0.32 0.00 0.00 6.53
2484 3218 2.626780 GCCCTGTGGAAAGAACCGC 61.627 63.158 0.00 0.00 40.43 5.68
2946 3680 1.442526 CGCCCAATCTGGATGCACTC 61.443 60.000 0.00 0.00 40.96 3.51
3342 4076 3.455469 GCAATGCTGGACCTGCCC 61.455 66.667 19.56 3.31 34.97 5.36
3555 4289 1.001378 GTGTCAAGCAATGTGTGGGTC 60.001 52.381 0.00 0.00 0.00 4.46
3956 4727 4.593206 AGGTAGTTTGGTCAAGATGACTCA 59.407 41.667 10.06 4.47 46.19 3.41
4020 4797 1.792949 GAAGCTGTTACTGTGTCACCG 59.207 52.381 0.00 0.00 0.00 4.94
4173 5016 2.418368 TCCAGTTGTGAGTGTTTGCT 57.582 45.000 0.00 0.00 0.00 3.91
4192 5035 0.756442 TGCTTTGGCACTGCTTTCCT 60.756 50.000 11.36 0.00 44.28 3.36
4275 5123 8.528044 TTACAATGTTTTTCAAACTACTCCCT 57.472 30.769 0.00 0.00 0.00 4.20
4276 5124 7.039313 ACAATGTTTTTCAAACTACTCCCTC 57.961 36.000 1.33 0.00 0.00 4.30
4278 5126 4.131596 TGTTTTTCAAACTACTCCCTCCG 58.868 43.478 1.33 0.00 0.00 4.63
4279 5127 4.132336 GTTTTTCAAACTACTCCCTCCGT 58.868 43.478 0.00 0.00 0.00 4.69
4280 5128 3.672767 TTTCAAACTACTCCCTCCGTC 57.327 47.619 0.00 0.00 0.00 4.79
4282 5130 0.172803 CAAACTACTCCCTCCGTCCG 59.827 60.000 0.00 0.00 0.00 4.79
4283 5131 0.969409 AAACTACTCCCTCCGTCCGG 60.969 60.000 0.00 0.00 0.00 5.14
4284 5132 1.856539 AACTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
4285 5133 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
4287 5135 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4289 5137 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4291 5139 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4292 5140 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4293 5141 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4294 5142 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4295 5143 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
4296 5144 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
4297 5145 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
4298 5146 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
4299 5147 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
4300 5148 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
4301 5149 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
4302 5150 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
4303 5151 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
4304 5152 4.034048 CGGAAATACTTGTCGGAGAAATGG 59.966 45.833 0.00 0.00 39.69 3.16
4305 5153 5.183228 GGAAATACTTGTCGGAGAAATGGA 58.817 41.667 0.00 0.00 39.69 3.41
4306 5154 5.823045 GGAAATACTTGTCGGAGAAATGGAT 59.177 40.000 0.00 0.00 39.69 3.41
4307 5155 6.238484 GGAAATACTTGTCGGAGAAATGGATG 60.238 42.308 0.00 0.00 39.69 3.51
4308 5156 2.359900 ACTTGTCGGAGAAATGGATGC 58.640 47.619 0.00 0.00 39.69 3.91
4309 5157 2.290260 ACTTGTCGGAGAAATGGATGCA 60.290 45.455 0.00 0.00 39.69 3.96
4310 5158 2.715749 TGTCGGAGAAATGGATGCAT 57.284 45.000 0.00 0.00 39.69 3.96
4311 5159 2.564771 TGTCGGAGAAATGGATGCATC 58.435 47.619 18.81 18.81 39.69 3.91
4312 5160 2.171237 TGTCGGAGAAATGGATGCATCT 59.829 45.455 25.28 5.75 39.69 2.90
4313 5161 2.547211 GTCGGAGAAATGGATGCATCTG 59.453 50.000 25.28 4.42 39.69 2.90
4314 5162 1.878088 CGGAGAAATGGATGCATCTGG 59.122 52.381 25.28 2.16 0.00 3.86
4315 5163 2.486013 CGGAGAAATGGATGCATCTGGA 60.486 50.000 25.28 10.86 0.00 3.86
4316 5164 2.883386 GGAGAAATGGATGCATCTGGAC 59.117 50.000 25.28 9.96 0.00 4.02
4317 5165 2.547211 GAGAAATGGATGCATCTGGACG 59.453 50.000 25.28 0.00 0.00 4.79
4318 5166 1.605710 GAAATGGATGCATCTGGACGG 59.394 52.381 25.28 0.00 0.00 4.79
4319 5167 0.839277 AATGGATGCATCTGGACGGA 59.161 50.000 25.28 2.76 0.00 4.69
4320 5168 1.062364 ATGGATGCATCTGGACGGAT 58.938 50.000 25.28 4.82 0.00 4.18
4321 5169 0.839277 TGGATGCATCTGGACGGATT 59.161 50.000 25.28 0.00 0.00 3.01
4322 5170 1.212688 TGGATGCATCTGGACGGATTT 59.787 47.619 25.28 0.00 0.00 2.17
4323 5171 2.301346 GGATGCATCTGGACGGATTTT 58.699 47.619 25.28 0.00 0.00 1.82
4324 5172 3.118075 TGGATGCATCTGGACGGATTTTA 60.118 43.478 25.28 0.00 0.00 1.52
4325 5173 3.499918 GGATGCATCTGGACGGATTTTAG 59.500 47.826 25.28 0.00 0.00 1.85
4326 5174 3.627395 TGCATCTGGACGGATTTTAGT 57.373 42.857 0.00 0.00 0.00 2.24
4327 5175 3.950397 TGCATCTGGACGGATTTTAGTT 58.050 40.909 0.00 0.00 0.00 2.24
4328 5176 3.938963 TGCATCTGGACGGATTTTAGTTC 59.061 43.478 0.00 0.00 0.00 3.01
4329 5177 4.192317 GCATCTGGACGGATTTTAGTTCT 58.808 43.478 0.00 0.00 0.00 3.01
4330 5178 4.034510 GCATCTGGACGGATTTTAGTTCTG 59.965 45.833 0.00 0.00 0.00 3.02
4331 5179 3.596214 TCTGGACGGATTTTAGTTCTGC 58.404 45.455 0.00 0.00 0.00 4.26
4332 5180 3.007506 TCTGGACGGATTTTAGTTCTGCA 59.992 43.478 0.00 0.00 0.00 4.41
4333 5181 3.941483 CTGGACGGATTTTAGTTCTGCAT 59.059 43.478 0.00 0.00 0.00 3.96
4334 5182 5.092554 TGGACGGATTTTAGTTCTGCATA 57.907 39.130 0.00 0.00 0.00 3.14
4335 5183 4.873827 TGGACGGATTTTAGTTCTGCATAC 59.126 41.667 0.00 0.00 0.00 2.39
4336 5184 4.873827 GGACGGATTTTAGTTCTGCATACA 59.126 41.667 0.00 0.00 0.00 2.29
4337 5185 5.527582 GGACGGATTTTAGTTCTGCATACAT 59.472 40.000 0.00 0.00 0.00 2.29
4338 5186 6.292919 GGACGGATTTTAGTTCTGCATACATC 60.293 42.308 0.00 0.00 0.00 3.06
4339 5187 5.527582 ACGGATTTTAGTTCTGCATACATCC 59.472 40.000 0.00 0.00 0.00 3.51
4340 5188 5.527214 CGGATTTTAGTTCTGCATACATCCA 59.473 40.000 12.62 0.00 0.00 3.41
4341 5189 6.205464 CGGATTTTAGTTCTGCATACATCCAT 59.795 38.462 12.62 0.00 0.00 3.41
4342 5190 7.255242 CGGATTTTAGTTCTGCATACATCCATT 60.255 37.037 12.62 0.00 0.00 3.16
4343 5191 8.416329 GGATTTTAGTTCTGCATACATCCATTT 58.584 33.333 0.00 0.00 0.00 2.32
4344 5192 9.455847 GATTTTAGTTCTGCATACATCCATTTC 57.544 33.333 0.00 0.00 0.00 2.17
4345 5193 7.936496 TTTAGTTCTGCATACATCCATTTCA 57.064 32.000 0.00 0.00 0.00 2.69
4346 5194 7.936496 TTAGTTCTGCATACATCCATTTCAA 57.064 32.000 0.00 0.00 0.00 2.69
4347 5195 6.199937 AGTTCTGCATACATCCATTTCAAC 57.800 37.500 0.00 0.00 0.00 3.18
4348 5196 4.880886 TCTGCATACATCCATTTCAACG 57.119 40.909 0.00 0.00 0.00 4.10
4349 5197 4.512484 TCTGCATACATCCATTTCAACGA 58.488 39.130 0.00 0.00 0.00 3.85
4350 5198 4.332543 TCTGCATACATCCATTTCAACGAC 59.667 41.667 0.00 0.00 0.00 4.34
4351 5199 4.006319 TGCATACATCCATTTCAACGACA 58.994 39.130 0.00 0.00 0.00 4.35
4352 5200 4.457257 TGCATACATCCATTTCAACGACAA 59.543 37.500 0.00 0.00 0.00 3.18
4353 5201 5.030295 GCATACATCCATTTCAACGACAAG 58.970 41.667 0.00 0.00 0.00 3.16
4354 5202 5.391950 GCATACATCCATTTCAACGACAAGT 60.392 40.000 0.00 0.00 0.00 3.16
4355 5203 6.183360 GCATACATCCATTTCAACGACAAGTA 60.183 38.462 0.00 0.00 0.00 2.24
4356 5204 7.625395 GCATACATCCATTTCAACGACAAGTAA 60.625 37.037 0.00 0.00 0.00 2.24
4357 5205 6.817765 ACATCCATTTCAACGACAAGTAAT 57.182 33.333 0.00 0.00 0.00 1.89
4358 5206 7.214467 ACATCCATTTCAACGACAAGTAATT 57.786 32.000 0.00 0.00 0.00 1.40
4359 5207 7.305474 ACATCCATTTCAACGACAAGTAATTC 58.695 34.615 0.00 0.00 0.00 2.17
4360 5208 6.249035 TCCATTTCAACGACAAGTAATTCC 57.751 37.500 0.00 0.00 0.00 3.01
4361 5209 5.086058 CCATTTCAACGACAAGTAATTCCG 58.914 41.667 0.00 0.00 0.00 4.30
4362 5210 4.735662 TTTCAACGACAAGTAATTCCGG 57.264 40.909 0.00 0.00 0.00 5.14
4363 5211 3.663995 TCAACGACAAGTAATTCCGGA 57.336 42.857 0.00 0.00 0.00 5.14
4364 5212 3.319755 TCAACGACAAGTAATTCCGGAC 58.680 45.455 1.83 0.00 0.00 4.79
4365 5213 1.986698 ACGACAAGTAATTCCGGACG 58.013 50.000 1.83 3.25 0.00 4.79
4366 5214 1.274596 CGACAAGTAATTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
4367 5215 1.135315 CGACAAGTAATTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
4368 5216 2.537401 GACAAGTAATTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
4369 5217 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4370 5218 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4371 5219 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
4372 5220 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4373 5221 0.032813 TAATTCCGGACGGAGGGAGT 60.033 55.000 13.64 1.45 46.06 3.85
4374 5222 0.032813 AATTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4410 5261 3.497103 TGCCATCTCCCTGTTATCATG 57.503 47.619 0.00 0.00 0.00 3.07
4413 5264 4.210331 GCCATCTCCCTGTTATCATGTTT 58.790 43.478 0.00 0.00 0.00 2.83
4543 5531 6.064846 TGACTCTGAGAAATGTGAAAAAGC 57.935 37.500 12.44 0.00 0.00 3.51
4579 5567 8.752005 ACAGAAAATGCCATACATATGTTAGT 57.248 30.769 14.77 0.00 38.34 2.24
4636 5624 9.744468 ATTTATCAACGGTATTTAGAAAATGCC 57.256 29.630 8.85 8.85 0.00 4.40
4637 5625 6.767524 ATCAACGGTATTTAGAAAATGCCA 57.232 33.333 16.40 1.53 32.78 4.92
4638 5626 6.767524 TCAACGGTATTTAGAAAATGCCAT 57.232 33.333 16.40 2.07 32.78 4.40
4639 5627 7.867305 TCAACGGTATTTAGAAAATGCCATA 57.133 32.000 16.40 0.44 32.78 2.74
4640 5628 7.699566 TCAACGGTATTTAGAAAATGCCATAC 58.300 34.615 16.40 0.00 32.78 2.39
4641 5629 7.337184 TCAACGGTATTTAGAAAATGCCATACA 59.663 33.333 16.40 0.00 32.78 2.29
4642 5630 7.817418 ACGGTATTTAGAAAATGCCATACAT 57.183 32.000 16.40 0.00 42.30 2.29
4643 5631 8.911918 ACGGTATTTAGAAAATGCCATACATA 57.088 30.769 16.40 0.00 38.34 2.29
4645 5633 9.773328 CGGTATTTAGAAAATGCCATACATATG 57.227 33.333 16.40 0.00 38.34 1.78
4656 5644 6.618287 TGCCATACATATGTTAGAAACTGC 57.382 37.500 14.77 6.73 31.82 4.40
4657 5645 6.118852 TGCCATACATATGTTAGAAACTGCA 58.881 36.000 14.77 9.05 31.82 4.41
4659 5647 7.285172 TGCCATACATATGTTAGAAACTGCAAT 59.715 33.333 14.77 0.00 31.82 3.56
4660 5648 7.592533 GCCATACATATGTTAGAAACTGCAATG 59.407 37.037 14.77 6.75 31.82 2.82
4661 5649 8.839343 CCATACATATGTTAGAAACTGCAATGA 58.161 33.333 14.77 0.00 31.82 2.57
4664 5652 8.510243 ACATATGTTAGAAACTGCAATGATCA 57.490 30.769 1.41 0.00 0.00 2.92
4665 5653 8.400947 ACATATGTTAGAAACTGCAATGATCAC 58.599 33.333 1.41 0.00 0.00 3.06
4667 5655 6.245115 TGTTAGAAACTGCAATGATCACTG 57.755 37.500 0.00 0.00 0.00 3.66
4670 5658 5.814764 AGAAACTGCAATGATCACTGATC 57.185 39.130 8.65 11.59 39.31 2.92
4774 5777 6.114221 GCAAAATGCTCATATGTTGCAAAT 57.886 33.333 22.40 14.96 40.96 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.611674 GTTGGGGTTGGGTTGCGG 61.612 66.667 0.00 0.00 0.00 5.69
72 73 3.611674 GGTTGGGGTTGGGTTGCG 61.612 66.667 0.00 0.00 0.00 4.85
1459 2193 1.900016 ACGTGACAGGCGTACTCCA 60.900 57.895 4.38 0.00 41.06 3.86
1902 2636 0.959553 GTGGACACTCTCCTTCGTGA 59.040 55.000 0.00 0.00 40.26 4.35
2484 3218 0.892755 AAGCATGCAGTCCACATTGG 59.107 50.000 21.98 0.00 39.43 3.16
2652 3386 1.021390 CATCTGGGCAAGGTGACGAC 61.021 60.000 0.00 0.00 39.66 4.34
2946 3680 4.687483 GCATTTGAGTTCTCACCAAAATGG 59.313 41.667 18.35 0.00 45.02 3.16
3015 3749 0.937441 ACCTCTCCTCTATGGCCAGA 59.063 55.000 13.05 5.45 35.26 3.86
3342 4076 2.104451 AGAGCTAACATCAGCATCCCTG 59.896 50.000 0.00 0.00 44.35 4.45
3555 4289 0.385029 CTCCATCTCTCTGTGCTCCG 59.615 60.000 0.00 0.00 0.00 4.63
4020 4797 2.808543 CAACAGCCAGGAACTACTTGAC 59.191 50.000 0.00 0.00 36.02 3.18
4152 4995 3.067180 CAGCAAACACTCACAACTGGATT 59.933 43.478 0.00 0.00 0.00 3.01
4260 5108 2.301009 GGACGGAGGGAGTAGTTTGAAA 59.699 50.000 0.00 0.00 0.00 2.69
4270 5118 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4272 5120 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4273 5121 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4275 5123 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
4276 5124 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
4278 5126 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
4279 5127 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
4280 5128 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
4282 5130 5.183228 TCCATTTCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
4283 5131 6.719365 CATCCATTTCTCCGACAAGTATTTC 58.281 40.000 0.00 0.00 0.00 2.17
4284 5132 5.066505 GCATCCATTTCTCCGACAAGTATTT 59.933 40.000 0.00 0.00 0.00 1.40
4285 5133 4.576463 GCATCCATTTCTCCGACAAGTATT 59.424 41.667 0.00 0.00 0.00 1.89
4287 5135 3.055458 TGCATCCATTTCTCCGACAAGTA 60.055 43.478 0.00 0.00 0.00 2.24
4289 5137 2.358957 TGCATCCATTTCTCCGACAAG 58.641 47.619 0.00 0.00 0.00 3.16
4291 5139 2.171237 AGATGCATCCATTTCTCCGACA 59.829 45.455 23.06 0.00 0.00 4.35
4292 5140 2.547211 CAGATGCATCCATTTCTCCGAC 59.453 50.000 23.06 0.00 0.00 4.79
4293 5141 2.486013 CCAGATGCATCCATTTCTCCGA 60.486 50.000 23.06 0.00 0.00 4.55
4294 5142 1.878088 CCAGATGCATCCATTTCTCCG 59.122 52.381 23.06 1.12 0.00 4.63
4295 5143 2.883386 GTCCAGATGCATCCATTTCTCC 59.117 50.000 23.06 0.00 0.00 3.71
4296 5144 2.547211 CGTCCAGATGCATCCATTTCTC 59.453 50.000 23.06 6.86 0.00 2.87
4297 5145 2.569059 CGTCCAGATGCATCCATTTCT 58.431 47.619 23.06 0.61 0.00 2.52
4298 5146 1.605710 CCGTCCAGATGCATCCATTTC 59.394 52.381 23.06 9.30 0.00 2.17
4299 5147 1.212688 TCCGTCCAGATGCATCCATTT 59.787 47.619 23.06 1.26 0.00 2.32
4300 5148 0.839277 TCCGTCCAGATGCATCCATT 59.161 50.000 23.06 1.67 0.00 3.16
4301 5149 1.062364 ATCCGTCCAGATGCATCCAT 58.938 50.000 23.06 2.49 0.00 3.41
4302 5150 0.839277 AATCCGTCCAGATGCATCCA 59.161 50.000 23.06 4.77 0.00 3.41
4303 5151 1.972872 AAATCCGTCCAGATGCATCC 58.027 50.000 23.06 6.84 0.00 3.51
4304 5152 4.130118 ACTAAAATCCGTCCAGATGCATC 58.870 43.478 19.37 19.37 0.00 3.91
4305 5153 4.156455 ACTAAAATCCGTCCAGATGCAT 57.844 40.909 0.00 0.00 0.00 3.96
4306 5154 3.627395 ACTAAAATCCGTCCAGATGCA 57.373 42.857 0.00 0.00 0.00 3.96
4307 5155 4.034510 CAGAACTAAAATCCGTCCAGATGC 59.965 45.833 0.00 0.00 0.00 3.91
4308 5156 4.034510 GCAGAACTAAAATCCGTCCAGATG 59.965 45.833 0.00 0.00 0.00 2.90
4309 5157 4.192317 GCAGAACTAAAATCCGTCCAGAT 58.808 43.478 0.00 0.00 0.00 2.90
4310 5158 3.007506 TGCAGAACTAAAATCCGTCCAGA 59.992 43.478 0.00 0.00 0.00 3.86
4311 5159 3.334691 TGCAGAACTAAAATCCGTCCAG 58.665 45.455 0.00 0.00 0.00 3.86
4312 5160 3.410631 TGCAGAACTAAAATCCGTCCA 57.589 42.857 0.00 0.00 0.00 4.02
4313 5161 4.873827 TGTATGCAGAACTAAAATCCGTCC 59.126 41.667 0.00 0.00 0.00 4.79
4314 5162 6.292919 GGATGTATGCAGAACTAAAATCCGTC 60.293 42.308 0.00 0.00 0.00 4.79
4315 5163 5.527582 GGATGTATGCAGAACTAAAATCCGT 59.472 40.000 0.00 0.00 0.00 4.69
4316 5164 5.527214 TGGATGTATGCAGAACTAAAATCCG 59.473 40.000 11.39 0.00 34.97 4.18
4317 5165 6.942532 TGGATGTATGCAGAACTAAAATCC 57.057 37.500 10.10 10.10 33.23 3.01
4318 5166 9.455847 GAAATGGATGTATGCAGAACTAAAATC 57.544 33.333 0.00 0.00 0.00 2.17
4319 5167 8.970020 TGAAATGGATGTATGCAGAACTAAAAT 58.030 29.630 0.00 0.00 0.00 1.82
4320 5168 8.347004 TGAAATGGATGTATGCAGAACTAAAA 57.653 30.769 0.00 0.00 0.00 1.52
4321 5169 7.936496 TGAAATGGATGTATGCAGAACTAAA 57.064 32.000 0.00 0.00 0.00 1.85
4322 5170 7.413988 CGTTGAAATGGATGTATGCAGAACTAA 60.414 37.037 0.00 0.00 0.00 2.24
4323 5171 6.037062 CGTTGAAATGGATGTATGCAGAACTA 59.963 38.462 0.00 0.00 0.00 2.24
4324 5172 5.163723 CGTTGAAATGGATGTATGCAGAACT 60.164 40.000 0.00 0.00 0.00 3.01
4325 5173 5.030295 CGTTGAAATGGATGTATGCAGAAC 58.970 41.667 0.00 0.00 0.00 3.01
4326 5174 4.940654 TCGTTGAAATGGATGTATGCAGAA 59.059 37.500 0.00 0.00 0.00 3.02
4327 5175 4.332543 GTCGTTGAAATGGATGTATGCAGA 59.667 41.667 0.00 0.00 0.00 4.26
4328 5176 4.094739 TGTCGTTGAAATGGATGTATGCAG 59.905 41.667 0.00 0.00 0.00 4.41
4329 5177 4.006319 TGTCGTTGAAATGGATGTATGCA 58.994 39.130 0.00 0.00 0.00 3.96
4330 5178 4.614555 TGTCGTTGAAATGGATGTATGC 57.385 40.909 0.00 0.00 0.00 3.14
4331 5179 6.182039 ACTTGTCGTTGAAATGGATGTATG 57.818 37.500 0.00 0.00 0.00 2.39
4332 5180 7.915293 TTACTTGTCGTTGAAATGGATGTAT 57.085 32.000 0.00 0.00 0.00 2.29
4333 5181 7.915293 ATTACTTGTCGTTGAAATGGATGTA 57.085 32.000 0.00 0.00 0.00 2.29
4334 5182 6.817765 ATTACTTGTCGTTGAAATGGATGT 57.182 33.333 0.00 0.00 0.00 3.06
4335 5183 6.747280 GGAATTACTTGTCGTTGAAATGGATG 59.253 38.462 0.00 0.00 0.00 3.51
4336 5184 6.403200 CGGAATTACTTGTCGTTGAAATGGAT 60.403 38.462 0.00 0.00 0.00 3.41
4337 5185 5.106869 CGGAATTACTTGTCGTTGAAATGGA 60.107 40.000 0.00 0.00 0.00 3.41
4338 5186 5.086058 CGGAATTACTTGTCGTTGAAATGG 58.914 41.667 0.00 0.00 0.00 3.16
4339 5187 5.086058 CCGGAATTACTTGTCGTTGAAATG 58.914 41.667 0.00 0.00 0.00 2.32
4340 5188 4.998672 TCCGGAATTACTTGTCGTTGAAAT 59.001 37.500 0.00 0.00 0.00 2.17
4341 5189 4.211794 GTCCGGAATTACTTGTCGTTGAAA 59.788 41.667 5.23 0.00 0.00 2.69
4342 5190 3.742369 GTCCGGAATTACTTGTCGTTGAA 59.258 43.478 5.23 0.00 0.00 2.69
4343 5191 3.319755 GTCCGGAATTACTTGTCGTTGA 58.680 45.455 5.23 0.00 0.00 3.18
4344 5192 2.091588 CGTCCGGAATTACTTGTCGTTG 59.908 50.000 5.23 0.00 0.00 4.10
4345 5193 2.331194 CGTCCGGAATTACTTGTCGTT 58.669 47.619 5.23 0.00 0.00 3.85
4346 5194 1.403249 CCGTCCGGAATTACTTGTCGT 60.403 52.381 5.23 0.00 37.50 4.34
4347 5195 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
4348 5196 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4349 5197 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4350 5198 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4351 5199 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
4352 5200 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
4353 5201 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
4354 5202 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
4355 5203 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
4356 5204 0.467659 CTACTCCCTCCGTCCGGAAT 60.468 60.000 5.23 0.00 44.66 3.01
4357 5205 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
4358 5206 1.856539 AACTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
4359 5207 1.379576 AACTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
4360 5208 0.394080 AGAACTACTCCCTCCGTCCG 60.394 60.000 0.00 0.00 0.00 4.79
4361 5209 1.849977 AAGAACTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
4362 5210 5.047448 AGTTTAAAGAACTACTCCCTCCGTC 60.047 44.000 0.00 0.00 0.00 4.79
4363 5211 4.837298 AGTTTAAAGAACTACTCCCTCCGT 59.163 41.667 0.00 0.00 0.00 4.69
4364 5212 5.169295 CAGTTTAAAGAACTACTCCCTCCG 58.831 45.833 0.00 0.00 0.00 4.63
4365 5213 4.936411 GCAGTTTAAAGAACTACTCCCTCC 59.064 45.833 0.00 0.00 0.00 4.30
4366 5214 5.795972 AGCAGTTTAAAGAACTACTCCCTC 58.204 41.667 0.00 0.00 0.00 4.30
4367 5215 5.827326 AGCAGTTTAAAGAACTACTCCCT 57.173 39.130 0.00 0.00 0.00 4.20
4368 5216 5.334957 GCAAGCAGTTTAAAGAACTACTCCC 60.335 44.000 0.00 0.00 0.00 4.30
4369 5217 5.334957 GGCAAGCAGTTTAAAGAACTACTCC 60.335 44.000 0.00 0.00 0.00 3.85
4370 5218 5.238650 TGGCAAGCAGTTTAAAGAACTACTC 59.761 40.000 0.00 0.00 0.00 2.59
4371 5219 5.130350 TGGCAAGCAGTTTAAAGAACTACT 58.870 37.500 0.00 0.00 0.00 2.57
4372 5220 5.432885 TGGCAAGCAGTTTAAAGAACTAC 57.567 39.130 0.00 0.00 0.00 2.73
4373 5221 6.003950 AGATGGCAAGCAGTTTAAAGAACTA 58.996 36.000 0.00 0.00 0.00 2.24
4374 5222 4.829492 AGATGGCAAGCAGTTTAAAGAACT 59.171 37.500 0.00 0.00 0.00 3.01
4410 5261 7.486551 TGCACAAACTAGTTTCACATAACAAAC 59.513 33.333 18.00 0.00 33.42 2.93
4413 5264 6.685527 TGCACAAACTAGTTTCACATAACA 57.314 33.333 18.00 7.14 0.00 2.41
4543 5531 3.730715 GGCATTTTCTGTTTCAGTCGTTG 59.269 43.478 0.00 0.00 32.61 4.10
4632 5620 6.772233 TGCAGTTTCTAACATATGTATGGCAT 59.228 34.615 9.21 4.88 41.42 4.40
4634 5622 6.618287 TGCAGTTTCTAACATATGTATGGC 57.382 37.500 9.21 5.65 38.00 4.40
4638 5626 9.612066 TGATCATTGCAGTTTCTAACATATGTA 57.388 29.630 9.21 0.00 0.00 2.29
4639 5627 8.400947 GTGATCATTGCAGTTTCTAACATATGT 58.599 33.333 1.41 1.41 0.00 2.29
4640 5628 8.618677 AGTGATCATTGCAGTTTCTAACATATG 58.381 33.333 0.00 0.00 0.00 1.78
4641 5629 8.618677 CAGTGATCATTGCAGTTTCTAACATAT 58.381 33.333 5.17 0.00 0.00 1.78
4642 5630 7.823799 TCAGTGATCATTGCAGTTTCTAACATA 59.176 33.333 13.08 0.00 0.00 2.29
4643 5631 6.656270 TCAGTGATCATTGCAGTTTCTAACAT 59.344 34.615 13.08 0.00 0.00 2.71
4645 5633 6.486253 TCAGTGATCATTGCAGTTTCTAAC 57.514 37.500 13.08 0.00 0.00 2.34
4646 5634 6.880529 TGATCAGTGATCATTGCAGTTTCTAA 59.119 34.615 28.18 4.08 43.11 2.10
4647 5635 6.408869 TGATCAGTGATCATTGCAGTTTCTA 58.591 36.000 28.18 4.49 43.11 2.10
4649 5637 5.123502 ACTGATCAGTGATCATTGCAGTTTC 59.876 40.000 30.97 5.73 46.16 2.78
4652 5640 4.217836 ACTGATCAGTGATCATTGCAGT 57.782 40.909 30.97 22.74 46.16 4.40
4719 5720 3.009584 AGCAAAGAGAACTTCCCCTAAGG 59.990 47.826 0.00 0.00 39.73 2.69
4723 5724 4.104897 AGTTAAGCAAAGAGAACTTCCCCT 59.895 41.667 0.00 0.00 35.05 4.79
4801 5805 6.155827 TGATAGCACAAGCATTTAAACAACC 58.844 36.000 0.00 0.00 45.49 3.77


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

AutoCloner maintained by Alex Coulton.