Multiple sequence alignment - TraesCS3D01G068100

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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 TraesCS3D01G068100 chr3D 100.000 5066 0 0 1 5066 30005701 30010766 0.000000e+00 9356
1 TraesCS3D01G068100 chr3A 90.438 3838 331 15 276 4099 41536495 41540310 0.000000e+00 5022
2 TraesCS3D01G068100 chr3A 88.600 3500 347 23 619 4104 41368441 41371902 0.000000e+00 4205
3 TraesCS3D01G068100 chr3A 87.560 3360 364 31 848 4181 41149803 41153134 0.000000e+00 3840
4 TraesCS3D01G068100 chr3A 88.469 3096 340 11 1001 4093 41048111 41051192 0.000000e+00 3723
5 TraesCS3D01G068100 chr3A 88.338 2641 299 3 983 3623 41616700 41619331 0.000000e+00 3162
6 TraesCS3D01G068100 chr3A 84.085 3192 474 23 873 4047 40936241 40939415 0.000000e+00 3049
7 TraesCS3D01G068100 chr3A 88.972 2394 236 20 2403 4781 41065874 41068254 0.000000e+00 2933
8 TraesCS3D01G068100 chr3A 87.404 2215 260 14 1982 4188 41238012 41240215 0.000000e+00 2527
9 TraesCS3D01G068100 chr3A 85.857 1506 194 13 882 2376 40947181 40948678 0.000000e+00 1583
10 TraesCS3D01G068100 chr3A 84.235 647 60 24 4422 5034 41375793 41376431 4.370000e-165 592
11 TraesCS3D01G068100 chr3A 89.961 259 25 1 378 636 41368127 41368384 2.920000e-87 333
12 TraesCS3D01G068100 chr3A 83.333 258 23 9 4765 5009 41068510 41068760 2.370000e-53 220
13 TraesCS3D01G068100 chr3A 94.776 134 6 1 9 141 41535916 41536049 1.850000e-49 207
14 TraesCS3D01G068100 chr3A 97.674 43 1 0 4348 4390 41375740 41375782 1.960000e-09 75
15 TraesCS3D01G068100 chr3B 85.809 4059 504 48 890 4913 51248982 51253003 0.000000e+00 4239
16 TraesCS3D01G068100 chr3B 92.172 2772 182 12 276 3027 51788741 51791497 0.000000e+00 3884
17 TraesCS3D01G068100 chr3B 86.617 3213 385 25 908 4109 51802549 51805727 0.000000e+00 3509
18 TraesCS3D01G068100 chr3B 85.397 3424 449 33 713 4111 51243035 51246432 0.000000e+00 3506
19 TraesCS3D01G068100 chr3B 86.391 3145 393 27 912 4042 52777842 52774719 0.000000e+00 3404


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 TraesCS3D01G068100 chr3D 30005701 30010766 5065 False 9356.00 9356 100.0000 1 5066 1 chr3D.!!$F1 5065
1 TraesCS3D01G068100 chr3A 41149803 41153134 3331 False 3840.00 3840 87.5600 848 4181 1 chr3A.!!$F4 3333
2 TraesCS3D01G068100 chr3A 41048111 41051192 3081 False 3723.00 3723 88.4690 1001 4093 1 chr3A.!!$F3 3092
3 TraesCS3D01G068100 chr3A 41616700 41619331 2631 False 3162.00 3162 88.3380 983 3623 1 chr3A.!!$F6 2640
4 TraesCS3D01G068100 chr3A 40936241 40939415 3174 False 3049.00 3049 84.0850 873 4047 1 chr3A.!!$F1 3174
5 TraesCS3D01G068100 chr3A 41535916 41540310 4394 False 2614.50 5022 92.6070 9 4099 2 chr3A.!!$F9 4090
6 TraesCS3D01G068100 chr3A 41238012 41240215 2203 False 2527.00 2527 87.4040 1982 4188 1 chr3A.!!$F5 2206
7 TraesCS3D01G068100 chr3A 40947181 40948678 1497 False 1583.00 1583 85.8570 882 2376 1 chr3A.!!$F2 1494
8 TraesCS3D01G068100 chr3A 41065874 41068760 2886 False 1576.50 2933 86.1525 2403 5009 2 chr3A.!!$F7 2606
9 TraesCS3D01G068100 chr3A 41368127 41376431 8304 False 1301.25 4205 90.1175 378 5034 4 chr3A.!!$F8 4656
10 TraesCS3D01G068100 chr3B 51788741 51791497 2756 False 3884.00 3884 92.1720 276 3027 1 chr3B.!!$F1 2751
11 TraesCS3D01G068100 chr3B 51243035 51253003 9968 False 3872.50 4239 85.6030 713 4913 2 chr3B.!!$F3 4200
12 TraesCS3D01G068100 chr3B 51802549 51805727 3178 False 3509.00 3509 86.6170 908 4109 1 chr3B.!!$F2 3201
13 TraesCS3D01G068100 chr3B 52774719 52777842 3123 True 3404.00 3404 86.3910 912 4042 1 chr3B.!!$R1 3130

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
198 293 1.202313 GCACTCTCATCGGTCTGTACC 60.202 57.143 0.00 0.00 42.95 3.34 F
1272 1700 0.322906 AAGGAAGCAAGCTACTGCCC 60.323 55.000 9.65 4.22 43.73 5.36 F
2983 3436 1.643310 TCCAAAAGGCATGGGGAAAG 58.357 50.000 0.00 0.00 38.54 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2445 0.691078 GCTCCCATCCCACCTCTACA 60.691 60.0 0.00 0.0 0.0 2.74 R
3180 3633 0.171455 CACGTCCAGTCCACTCTAGC 59.829 60.0 0.00 0.0 0.0 3.42 R
4314 10670 0.320946 CTGCCACAATTTTGCCCAGG 60.321 55.0 3.77 0.0 0.0 4.45 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
45 46 2.555325 TGCACTGCATTTTTCAGAGGAG 59.445 45.455 0.00 0.00 35.61 3.69
146 241 7.708752 TCTTCTTCTTCTTCTTCTTCTGTTCAC 59.291 37.037 0.00 0.00 0.00 3.18
161 256 2.473609 TGTTCACGCTAAGTTGCTAACG 59.526 45.455 0.00 0.00 36.23 3.18
198 293 1.202313 GCACTCTCATCGGTCTGTACC 60.202 57.143 0.00 0.00 42.95 3.34
223 318 6.980397 CCAGGTATATTTGTTGATTTTGCTCC 59.020 38.462 0.00 0.00 0.00 4.70
224 319 7.363705 CCAGGTATATTTGTTGATTTTGCTCCA 60.364 37.037 0.00 0.00 0.00 3.86
226 321 8.199449 AGGTATATTTGTTGATTTTGCTCCATG 58.801 33.333 0.00 0.00 0.00 3.66
227 322 8.196771 GGTATATTTGTTGATTTTGCTCCATGA 58.803 33.333 0.00 0.00 0.00 3.07
228 323 9.754382 GTATATTTGTTGATTTTGCTCCATGAT 57.246 29.630 0.00 0.00 0.00 2.45
230 325 6.788684 TTTGTTGATTTTGCTCCATGATTG 57.211 33.333 0.00 0.00 0.00 2.67
231 326 5.725325 TGTTGATTTTGCTCCATGATTGA 57.275 34.783 0.00 0.00 0.00 2.57
232 327 6.099159 TGTTGATTTTGCTCCATGATTGAA 57.901 33.333 0.00 0.00 0.00 2.69
233 328 6.160684 TGTTGATTTTGCTCCATGATTGAAG 58.839 36.000 0.00 0.00 0.00 3.02
234 329 5.988310 TGATTTTGCTCCATGATTGAAGT 57.012 34.783 0.00 0.00 0.00 3.01
235 330 5.716094 TGATTTTGCTCCATGATTGAAGTG 58.284 37.500 0.00 0.00 0.00 3.16
236 331 5.477637 TGATTTTGCTCCATGATTGAAGTGA 59.522 36.000 0.00 0.00 0.00 3.41
237 332 5.988310 TTTTGCTCCATGATTGAAGTGAT 57.012 34.783 0.00 0.00 0.00 3.06
238 333 5.571784 TTTGCTCCATGATTGAAGTGATC 57.428 39.130 0.00 0.00 0.00 2.92
241 336 3.564644 GCTCCATGATTGAAGTGATCCTG 59.435 47.826 0.00 0.00 0.00 3.86
242 337 4.778579 CTCCATGATTGAAGTGATCCTGT 58.221 43.478 0.00 0.00 0.00 4.00
244 339 5.188434 TCCATGATTGAAGTGATCCTGTTC 58.812 41.667 0.00 0.00 0.00 3.18
253 396 6.226787 TGAAGTGATCCTGTTCTTCTTCTTC 58.773 40.000 0.00 0.00 37.67 2.87
254 397 6.042552 TGAAGTGATCCTGTTCTTCTTCTTCT 59.957 38.462 0.00 0.00 37.67 2.85
257 400 6.042552 AGTGATCCTGTTCTTCTTCTTCTTCA 59.957 38.462 0.00 0.00 0.00 3.02
260 403 5.605534 TCCTGTTCTTCTTCTTCTTCACTG 58.394 41.667 0.00 0.00 0.00 3.66
261 404 5.363868 TCCTGTTCTTCTTCTTCTTCACTGA 59.636 40.000 0.00 0.00 0.00 3.41
264 407 6.820335 TGTTCTTCTTCTTCTTCACTGATGA 58.180 36.000 0.00 0.00 0.00 2.92
268 411 7.674120 TCTTCTTCTTCTTCACTGATGATTGA 58.326 34.615 0.00 0.00 33.85 2.57
269 412 8.152898 TCTTCTTCTTCTTCACTGATGATTGAA 58.847 33.333 0.00 4.09 33.85 2.69
270 413 8.681486 TTCTTCTTCTTCACTGATGATTGAAA 57.319 30.769 0.00 0.00 33.85 2.69
271 414 8.320396 TCTTCTTCTTCACTGATGATTGAAAG 57.680 34.615 0.00 0.16 33.85 2.62
272 415 8.152898 TCTTCTTCTTCACTGATGATTGAAAGA 58.847 33.333 0.00 2.00 33.85 2.52
273 416 7.902387 TCTTCTTCACTGATGATTGAAAGAG 57.098 36.000 0.00 0.00 33.85 2.85
274 417 7.674120 TCTTCTTCACTGATGATTGAAAGAGA 58.326 34.615 0.00 0.00 33.85 3.10
339 652 9.109393 GTATTTTCTTCATATTGCAGGTGTAGA 57.891 33.333 0.00 0.00 0.00 2.59
414 727 6.618287 TTAAGAATAGCAATTGGATGACCG 57.382 37.500 7.72 0.00 39.42 4.79
503 817 6.424883 TGGAAGAGTGGTTTGTAAGGTAAAA 58.575 36.000 0.00 0.00 0.00 1.52
628 1016 7.607991 ACAAATATATGGCTTCTATGCACTACC 59.392 37.037 0.00 0.00 34.04 3.18
644 1032 7.197071 TGCACTACCTGTTGTTATTAACTTG 57.803 36.000 7.99 0.00 0.00 3.16
755 1154 4.947645 ACACATGTAAATTTGCAAGCACT 58.052 34.783 13.11 0.00 0.00 4.40
801 1201 3.806380 CTCAGGGATTCAGACCTCAATG 58.194 50.000 0.00 0.00 34.05 2.82
1016 1444 2.195567 CCATGGCGGCCATACTTGG 61.196 63.158 32.52 26.53 43.15 3.61
1118 1546 0.607112 CTCAGAGAAGTCCTGCAGCA 59.393 55.000 8.66 0.00 0.00 4.41
1167 1595 2.026822 TGATGCTGAGAAAAGGAGGACC 60.027 50.000 0.00 0.00 0.00 4.46
1272 1700 0.322906 AAGGAAGCAAGCTACTGCCC 60.323 55.000 9.65 4.22 43.73 5.36
1745 2195 4.220163 TCTTCTTAAAGAGGTTCTCCGGAC 59.780 45.833 0.00 0.00 36.59 4.79
1891 2341 4.828939 TGGATCTATTAAGGCCTGCATTTG 59.171 41.667 5.69 0.00 0.00 2.32
1892 2342 4.321527 GGATCTATTAAGGCCTGCATTTGC 60.322 45.833 5.69 0.00 42.50 3.68
1924 2374 6.882140 TGAAACAACATCCGGAGTAATATTGT 59.118 34.615 11.34 10.67 0.00 2.71
1956 2406 6.018425 CACGAGATGATCAAATTACAAGGAGG 60.018 42.308 0.00 0.00 0.00 4.30
1995 2445 3.069300 CCCATCGAGTTGATCTCATGTCT 59.931 47.826 0.00 0.00 42.88 3.41
2076 2526 4.023536 GTGCAGAATTTAAGAAACACGGGA 60.024 41.667 0.00 0.00 0.00 5.14
2325 2775 6.340522 TGAAGATTCTATCATTGAGCGTGAA 58.659 36.000 0.00 0.00 0.00 3.18
2451 2901 5.753721 ATCTCCTCCAGCCAGATATTAAC 57.246 43.478 0.00 0.00 0.00 2.01
2493 2943 3.675228 GCAAAATGCATGACCTCTTGAGG 60.675 47.826 14.58 14.58 44.26 3.86
2553 3003 8.677300 TCTGTTGGAGATGTTGAATTATTAAGC 58.323 33.333 0.00 0.00 0.00 3.09
2656 3109 4.349636 TGGATGTTAAGGTGAGGACTTTCA 59.650 41.667 0.00 0.00 0.00 2.69
2724 3177 4.530946 AGATTCCTCCTCCTTCGTGTTTTA 59.469 41.667 0.00 0.00 0.00 1.52
2759 3212 3.569701 ACACTTGTACAAAGCATTCCAGG 59.430 43.478 10.03 0.00 0.00 4.45
2829 3282 2.158957 TGGCATATCTTGTCTTCCGGAC 60.159 50.000 1.83 0.00 44.70 4.79
2866 3319 3.686916 AGAACCTTCAAGTACTGAGCC 57.313 47.619 0.00 0.00 34.81 4.70
2870 3323 2.972713 ACCTTCAAGTACTGAGCCTGAA 59.027 45.455 0.00 1.20 34.81 3.02
2931 3384 3.568538 CCTGTTGTGCAGTTTAAGATGC 58.431 45.455 6.95 6.95 43.55 3.91
2976 3429 3.967332 AATCAGGTTCCAAAAGGCATG 57.033 42.857 0.00 0.00 0.00 4.06
2983 3436 1.643310 TCCAAAAGGCATGGGGAAAG 58.357 50.000 0.00 0.00 38.54 2.62
3060 3513 5.822519 TGCTGTTATACAAGATGGATGGAAC 59.177 40.000 0.00 0.00 0.00 3.62
3194 3647 4.404073 AGAACTAATGCTAGAGTGGACTGG 59.596 45.833 0.00 0.00 0.00 4.00
3223 3676 5.454045 GGAGAGGGACCATATTCAGAAGAAC 60.454 48.000 0.00 0.00 36.39 3.01
3270 3723 0.753262 AGCAGCTAATACCTCCACCG 59.247 55.000 0.00 0.00 0.00 4.94
3314 3767 0.958876 GGATTCTTTGGTCGGCGGTT 60.959 55.000 7.21 0.00 0.00 4.44
3412 3865 1.147824 CCACCCATCTGGCAGCTAG 59.852 63.158 10.34 0.00 37.83 3.42
3438 3891 7.914346 GCCAACTTGAAATATCTGAGAATTGAG 59.086 37.037 0.00 0.00 0.00 3.02
3453 3906 0.983467 TTGAGGGAGCACATGCAGTA 59.017 50.000 6.64 0.00 45.16 2.74
3547 9757 5.928264 CCAAAACTTGAATGGTTGATCTTCC 59.072 40.000 0.00 0.00 0.00 3.46
3764 9974 0.818040 GACACCGCCTGTTTGAAGGT 60.818 55.000 0.00 0.00 39.75 3.50
3775 9985 5.562890 GCCTGTTTGAAGGTGCTTAGTTTAG 60.563 44.000 0.00 0.00 39.75 1.85
3842 10052 2.094417 GTGAGCTCCTTGTTATTGACGC 59.906 50.000 12.15 0.00 0.00 5.19
3955 10165 1.303317 AGTTTGCGGCAACTAGGGG 60.303 57.895 16.15 0.00 0.00 4.79
3973 10186 2.622977 GGGGTGGACAAGGATATGCAAA 60.623 50.000 0.00 0.00 0.00 3.68
3991 10204 3.442977 GCAAAAGATCTCTTCATGCTGGT 59.557 43.478 17.00 0.00 41.50 4.00
4047 10260 5.896106 TCATGGCGAAGATCTGGATATCTAT 59.104 40.000 0.00 0.00 35.10 1.98
4060 10282 9.707957 ATCTGGATATCTATACTCTGTTTAGGG 57.292 37.037 2.05 0.00 0.00 3.53
4066 10289 9.689501 ATATCTATACTCTGTTTAGGGAGTAGC 57.310 37.037 8.44 0.00 44.71 3.58
4094 10321 6.349280 GCTCAAGGTATATTTGAACACTGCAA 60.349 38.462 0.00 0.00 34.41 4.08
4100 10327 2.292103 TTTGAACACTGCAAACTGGC 57.708 45.000 0.00 0.00 30.87 4.85
4111 10339 4.399303 ACTGCAAACTGGCTGGATATTTAC 59.601 41.667 0.00 0.00 37.08 2.01
4112 10340 4.599041 TGCAAACTGGCTGGATATTTACT 58.401 39.130 0.00 0.00 34.04 2.24
4113 10341 5.016173 TGCAAACTGGCTGGATATTTACTT 58.984 37.500 0.00 0.00 34.04 2.24
4114 10342 6.184068 TGCAAACTGGCTGGATATTTACTTA 58.816 36.000 0.00 0.00 34.04 2.24
4115 10343 6.833416 TGCAAACTGGCTGGATATTTACTTAT 59.167 34.615 0.00 0.00 34.04 1.73
4168 10409 9.897744 GTTCATATTCTCACAAGACAATTTTCA 57.102 29.630 0.00 0.00 0.00 2.69
4201 10553 1.404748 CATGCATTGGAACGCCATACA 59.595 47.619 0.00 0.00 45.46 2.29
4202 10554 1.539157 TGCATTGGAACGCCATACAA 58.461 45.000 0.00 0.00 45.46 2.41
4205 10557 3.115554 GCATTGGAACGCCATACAATTC 58.884 45.455 0.00 0.00 45.46 2.17
4268 10622 4.327680 GCATCCAAACCTAACTTCTCAGT 58.672 43.478 0.00 0.00 33.11 3.41
4271 10625 6.599638 GCATCCAAACCTAACTTCTCAGTATT 59.400 38.462 0.00 0.00 30.68 1.89
4280 10636 6.655003 CCTAACTTCTCAGTATTTGCTTCCAA 59.345 38.462 0.00 0.00 30.68 3.53
4284 10640 7.955918 ACTTCTCAGTATTTGCTTCCAAAAAT 58.044 30.769 0.00 0.00 43.58 1.82
4297 10653 7.249147 TGCTTCCAAAAATCAAATTGTGTTTG 58.751 30.769 9.88 9.88 0.00 2.93
4391 14224 1.645034 CACGAGTCATACCAAGCTGG 58.355 55.000 0.00 0.00 45.02 4.85
4409 14242 1.635817 GGGGAAGCCTGTCCATGCTA 61.636 60.000 0.00 0.00 39.70 3.49
4413 14246 1.403323 GAAGCCTGTCCATGCTAAAGC 59.597 52.381 0.00 0.00 36.66 3.51
4418 14251 2.430465 CTGTCCATGCTAAAGCTGTGT 58.570 47.619 3.26 0.00 42.66 3.72
4444 14279 1.138337 CATGATCTGTAGCGAGCTGC 58.862 55.000 7.99 7.07 46.98 5.25
4496 14331 5.922960 AGGTGCCCTGGAATTATTGTATA 57.077 39.130 0.00 0.00 29.57 1.47
4499 14334 6.102615 AGGTGCCCTGGAATTATTGTATAGAA 59.897 38.462 0.00 0.00 29.57 2.10
4529 14368 8.840867 CGTCTTATTTCTTTCTGAATTTTTCCG 58.159 33.333 0.00 0.00 34.24 4.30
4567 14406 2.166870 TGAATCTGCATGGCATGGTTTC 59.833 45.455 27.48 20.07 38.13 2.78
4577 14416 1.418373 GCATGGTTTCGTTCTTTGGC 58.582 50.000 0.00 0.00 0.00 4.52
4603 14445 6.809196 TGTAACCCACGCATTTCATTTTATTC 59.191 34.615 0.00 0.00 0.00 1.75
4649 14491 2.221169 CTTTGCTGTAGTGAACCTGCA 58.779 47.619 0.00 0.00 35.61 4.41
4716 14564 7.441890 TTGGCACGATTTTATTCTTTGAGTA 57.558 32.000 0.00 0.00 0.00 2.59
4717 14565 7.624360 TGGCACGATTTTATTCTTTGAGTAT 57.376 32.000 0.00 0.00 0.00 2.12
4750 14598 6.713762 ATTTGGTTGTGTTTCATTCTGAGA 57.286 33.333 0.00 0.00 0.00 3.27
4756 14605 4.728772 TGTGTTTCATTCTGAGATTGGGT 58.271 39.130 4.70 0.00 0.00 4.51
4783 14632 2.801063 CTTTGCCACACTGAAACTGTG 58.199 47.619 0.00 0.00 39.05 3.66
4787 14636 1.873591 GCCACACTGAAACTGTGTAGG 59.126 52.381 12.44 15.07 42.87 3.18
4795 14913 4.283467 ACTGAAACTGTGTAGGCTGTATCA 59.717 41.667 0.00 0.00 0.00 2.15
4802 14920 5.656859 ACTGTGTAGGCTGTATCACTATTGA 59.343 40.000 0.00 0.00 35.73 2.57
4846 14969 2.191400 TCTCTGAATGGAAGTGGGGAG 58.809 52.381 0.00 0.00 0.00 4.30
4850 14973 2.821969 CTGAATGGAAGTGGGGAGTTTG 59.178 50.000 0.00 0.00 0.00 2.93
4863 14986 4.081365 TGGGGAGTTTGGTTTTGTTTCTTC 60.081 41.667 0.00 0.00 0.00 2.87
4869 14992 5.810074 AGTTTGGTTTTGTTTCTTCGAATGG 59.190 36.000 0.00 0.00 0.00 3.16
4884 15007 7.843490 CTTCGAATGGAAGTGAAAACCTATA 57.157 36.000 0.00 0.00 45.82 1.31
4902 15038 4.825634 CCTATAGGTGTTCCACTGTATCGA 59.174 45.833 10.96 0.00 34.40 3.59
5012 15148 1.817099 GGCGATCCAGGAGCACAAG 60.817 63.158 5.34 0.00 0.00 3.16
5020 15156 4.021925 GGAGCACAAGCCCGGAGT 62.022 66.667 0.73 0.00 43.56 3.85
5034 15170 1.891616 GGAGTGAGGGACGAAGGTC 59.108 63.158 0.00 0.00 42.66 3.85
5035 15171 0.612453 GGAGTGAGGGACGAAGGTCT 60.612 60.000 0.00 0.00 42.97 3.85
5036 15172 0.528470 GAGTGAGGGACGAAGGTCTG 59.472 60.000 0.00 0.00 42.97 3.51
5037 15173 0.900647 AGTGAGGGACGAAGGTCTGG 60.901 60.000 0.00 0.00 42.97 3.86
5038 15174 0.898789 GTGAGGGACGAAGGTCTGGA 60.899 60.000 0.00 0.00 42.97 3.86
5039 15175 0.178944 TGAGGGACGAAGGTCTGGAA 60.179 55.000 0.00 0.00 42.97 3.53
5040 15176 1.196012 GAGGGACGAAGGTCTGGAAT 58.804 55.000 0.00 0.00 42.97 3.01
5041 15177 1.555533 GAGGGACGAAGGTCTGGAATT 59.444 52.381 0.00 0.00 42.97 2.17
5042 15178 1.985895 AGGGACGAAGGTCTGGAATTT 59.014 47.619 0.00 0.00 42.97 1.82
5043 15179 2.084546 GGGACGAAGGTCTGGAATTTG 58.915 52.381 0.00 0.00 42.97 2.32
5044 15180 2.084546 GGACGAAGGTCTGGAATTTGG 58.915 52.381 0.00 0.00 42.97 3.28
5045 15181 2.084546 GACGAAGGTCTGGAATTTGGG 58.915 52.381 0.00 0.00 40.15 4.12
5046 15182 0.811281 CGAAGGTCTGGAATTTGGGC 59.189 55.000 0.00 0.00 0.00 5.36
5047 15183 0.811281 GAAGGTCTGGAATTTGGGCG 59.189 55.000 0.00 0.00 0.00 6.13
5048 15184 0.404040 AAGGTCTGGAATTTGGGCGA 59.596 50.000 0.00 0.00 0.00 5.54
5049 15185 0.404040 AGGTCTGGAATTTGGGCGAA 59.596 50.000 0.00 0.00 0.00 4.70
5050 15186 1.005924 AGGTCTGGAATTTGGGCGAAT 59.994 47.619 0.00 0.00 0.00 3.34
5051 15187 1.134946 GGTCTGGAATTTGGGCGAATG 59.865 52.381 0.00 0.00 0.00 2.67
5052 15188 1.134946 GTCTGGAATTTGGGCGAATGG 59.865 52.381 0.00 0.00 0.00 3.16
5053 15189 0.179103 CTGGAATTTGGGCGAATGGC 60.179 55.000 0.00 0.00 42.51 4.40
5054 15190 1.226945 GGAATTTGGGCGAATGGCG 60.227 57.895 0.00 0.00 44.92 5.69
5055 15191 1.662438 GGAATTTGGGCGAATGGCGA 61.662 55.000 0.00 0.00 44.92 5.54
5056 15192 0.172352 GAATTTGGGCGAATGGCGAA 59.828 50.000 0.00 0.00 44.92 4.70
5057 15193 3.765051 TTTGGGCGAATGGCGAAA 58.235 50.000 0.00 0.00 44.09 3.46
5058 15194 1.583986 TTTGGGCGAATGGCGAAAG 59.416 52.632 0.00 0.00 42.05 2.62
5059 15195 0.891449 TTTGGGCGAATGGCGAAAGA 60.891 50.000 0.00 0.00 42.05 2.52
5060 15196 0.679640 TTGGGCGAATGGCGAAAGAT 60.680 50.000 0.00 0.00 44.92 2.40
5061 15197 1.356624 GGGCGAATGGCGAAAGATG 59.643 57.895 0.00 0.00 44.92 2.90
5062 15198 1.095228 GGGCGAATGGCGAAAGATGA 61.095 55.000 0.00 0.00 44.92 2.92
5063 15199 0.028110 GGCGAATGGCGAAAGATGAC 59.972 55.000 0.00 0.00 44.92 3.06
5064 15200 0.315382 GCGAATGGCGAAAGATGACG 60.315 55.000 0.00 0.00 44.57 4.35
5065 15201 1.277326 CGAATGGCGAAAGATGACGA 58.723 50.000 0.00 0.00 44.57 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.616076 GCTGTGGCTATGGCTCTGTATAG 60.616 52.174 0.00 0.00 38.73 1.31
1 2 2.300152 GCTGTGGCTATGGCTCTGTATA 59.700 50.000 0.00 0.00 38.73 1.47
2 3 1.071385 GCTGTGGCTATGGCTCTGTAT 59.929 52.381 0.00 0.00 38.73 2.29
3 4 0.465705 GCTGTGGCTATGGCTCTGTA 59.534 55.000 0.00 0.00 38.73 2.74
4 5 1.222936 GCTGTGGCTATGGCTCTGT 59.777 57.895 0.00 0.00 38.73 3.41
5 6 4.137879 GCTGTGGCTATGGCTCTG 57.862 61.111 0.00 0.71 38.73 3.35
23 24 2.957680 TCCTCTGAAAAATGCAGTGCAA 59.042 40.909 23.90 5.75 43.62 4.08
26 27 2.490903 CCCTCCTCTGAAAAATGCAGTG 59.509 50.000 0.00 0.00 34.98 3.66
28 29 2.097825 CCCCTCCTCTGAAAAATGCAG 58.902 52.381 0.00 0.00 34.71 4.41
52 53 1.476007 ATCGGAGCATACTGGAGCCC 61.476 60.000 0.00 0.00 0.00 5.19
161 256 1.823041 GCTGCAAGGGGAGATCTGC 60.823 63.158 5.52 5.52 33.71 4.26
171 266 1.088340 CCGATGAGAGTGCTGCAAGG 61.088 60.000 2.77 0.00 0.00 3.61
198 293 6.980397 GGAGCAAAATCAACAAATATACCTGG 59.020 38.462 0.00 0.00 0.00 4.45
223 318 6.598457 AGAAGAACAGGATCACTTCAATCATG 59.402 38.462 0.00 0.00 40.47 3.07
224 319 6.719301 AGAAGAACAGGATCACTTCAATCAT 58.281 36.000 0.00 0.00 40.47 2.45
226 321 6.878389 AGAAGAAGAACAGGATCACTTCAATC 59.122 38.462 0.00 0.00 40.47 2.67
227 322 6.777782 AGAAGAAGAACAGGATCACTTCAAT 58.222 36.000 0.00 0.00 40.47 2.57
228 323 6.179906 AGAAGAAGAACAGGATCACTTCAA 57.820 37.500 0.00 0.00 40.47 2.69
230 325 6.463360 AGAAGAAGAAGAACAGGATCACTTC 58.537 40.000 0.00 0.00 38.96 3.01
231 326 6.432403 AGAAGAAGAAGAACAGGATCACTT 57.568 37.500 0.00 0.00 0.00 3.16
232 327 6.042552 TGAAGAAGAAGAAGAACAGGATCACT 59.957 38.462 0.00 0.00 0.00 3.41
233 328 6.147000 GTGAAGAAGAAGAAGAACAGGATCAC 59.853 42.308 0.00 0.00 0.00 3.06
234 329 6.042552 AGTGAAGAAGAAGAAGAACAGGATCA 59.957 38.462 0.00 0.00 0.00 2.92
235 330 6.368516 CAGTGAAGAAGAAGAAGAACAGGATC 59.631 42.308 0.00 0.00 0.00 3.36
236 331 6.042552 TCAGTGAAGAAGAAGAAGAACAGGAT 59.957 38.462 0.00 0.00 0.00 3.24
237 332 5.363868 TCAGTGAAGAAGAAGAAGAACAGGA 59.636 40.000 0.00 0.00 0.00 3.86
238 333 5.605534 TCAGTGAAGAAGAAGAAGAACAGG 58.394 41.667 0.00 0.00 0.00 4.00
241 336 7.903995 ATCATCAGTGAAGAAGAAGAAGAAC 57.096 36.000 1.59 0.00 38.01 3.01
242 337 8.152898 TCAATCATCAGTGAAGAAGAAGAAGAA 58.847 33.333 1.59 0.00 38.01 2.52
244 339 7.902387 TCAATCATCAGTGAAGAAGAAGAAG 57.098 36.000 1.59 0.00 38.01 2.85
253 396 8.041829 ACATTCTCTTTCAATCATCAGTGAAG 57.958 34.615 0.00 0.00 37.86 3.02
254 397 7.991084 ACATTCTCTTTCAATCATCAGTGAA 57.009 32.000 0.00 0.00 38.01 3.18
257 400 9.160496 GAGTTACATTCTCTTTCAATCATCAGT 57.840 33.333 0.00 0.00 0.00 3.41
260 403 8.498054 TGGAGTTACATTCTCTTTCAATCATC 57.502 34.615 0.00 0.00 33.06 2.92
261 404 9.471702 AATGGAGTTACATTCTCTTTCAATCAT 57.528 29.630 0.00 0.00 36.36 2.45
264 407 9.082313 ACAAATGGAGTTACATTCTCTTTCAAT 57.918 29.630 0.00 0.00 40.01 2.57
268 411 8.352942 GTGAACAAATGGAGTTACATTCTCTTT 58.647 33.333 0.00 0.00 40.01 2.52
269 412 7.721399 AGTGAACAAATGGAGTTACATTCTCTT 59.279 33.333 0.00 0.00 40.01 2.85
270 413 7.227156 AGTGAACAAATGGAGTTACATTCTCT 58.773 34.615 0.00 0.00 40.01 3.10
271 414 7.440523 AGTGAACAAATGGAGTTACATTCTC 57.559 36.000 0.00 0.00 40.01 2.87
272 415 8.157476 ACTAGTGAACAAATGGAGTTACATTCT 58.843 33.333 0.00 0.00 40.01 2.40
273 416 8.324163 ACTAGTGAACAAATGGAGTTACATTC 57.676 34.615 0.00 0.00 40.01 2.67
274 417 8.567948 CAACTAGTGAACAAATGGAGTTACATT 58.432 33.333 0.00 0.00 42.56 2.71
339 652 4.082354 GGAAAGAGAATGTGATTGCTGCTT 60.082 41.667 0.00 0.00 0.00 3.91
414 727 3.916761 TGAAGATGCAATTTGCTCCAAC 58.083 40.909 21.19 10.95 45.31 3.77
442 755 7.364762 CCCACTGATAGTAAGAACCAATAGTGT 60.365 40.741 0.00 0.00 32.23 3.55
503 817 7.828712 AGTTACGAAACTAAGATAGCAAGTCT 58.171 34.615 0.00 0.00 44.26 3.24
628 1016 8.746922 ATGTTGCATCAAGTTAATAACAACAG 57.253 30.769 5.89 0.00 46.29 3.16
644 1032 2.723124 ACCACGGAAAATGTTGCATC 57.277 45.000 0.00 0.00 0.00 3.91
755 1154 3.496884 GGCACTCTGTCATTTCGTTGTTA 59.503 43.478 0.00 0.00 0.00 2.41
1016 1444 3.490419 GGCACATGATCCAAGCAAAGATC 60.490 47.826 0.00 3.62 39.50 2.75
1167 1595 6.088824 CCAATTGTTTACTGCTAGCTCTTTG 58.911 40.000 17.23 6.73 0.00 2.77
1272 1700 3.905784 TGATGATGATGAAGGATCGTCG 58.094 45.455 0.00 0.00 46.51 5.12
1400 1832 9.287373 AGAATACCGTGTCCTTTAAAATGTTTA 57.713 29.630 0.00 0.00 0.00 2.01
1745 2195 2.946990 TGCTCATGATGCACACCAATAG 59.053 45.455 13.62 0.00 35.31 1.73
1891 2341 4.104776 CCGGATGTTGTTTCATGTAATGC 58.895 43.478 0.00 0.00 46.21 3.56
1893 2343 5.253330 ACTCCGGATGTTGTTTCATGTAAT 58.747 37.500 3.57 0.00 0.00 1.89
1894 2344 4.647611 ACTCCGGATGTTGTTTCATGTAA 58.352 39.130 3.57 0.00 0.00 2.41
1895 2345 4.280436 ACTCCGGATGTTGTTTCATGTA 57.720 40.909 3.57 0.00 0.00 2.29
1896 2346 3.140325 ACTCCGGATGTTGTTTCATGT 57.860 42.857 3.57 0.00 0.00 3.21
1924 2374 7.604545 TGTAATTTGATCATCTCGTGTGGTTAA 59.395 33.333 0.00 0.00 0.00 2.01
1956 2406 4.142359 CGATGGGTATGCTCTACACCTATC 60.142 50.000 6.33 6.33 43.30 2.08
1995 2445 0.691078 GCTCCCATCCCACCTCTACA 60.691 60.000 0.00 0.00 0.00 2.74
2076 2526 7.040755 TGACCACATTTACGAACAATCTCAATT 60.041 33.333 0.00 0.00 0.00 2.32
2257 2707 1.069204 ACACTGCTTCAGACGATGTGT 59.931 47.619 0.29 0.00 35.18 3.72
2325 2775 5.044846 AGCAATCCATAACCTGGTAACTTCT 60.045 40.000 0.00 0.00 46.08 2.85
2451 2901 2.608752 GCATTCAGCCTGGTCAAAACTG 60.609 50.000 0.00 0.00 37.23 3.16
2493 2943 8.562892 TCTCTTGATATATTTAAAGCAAGCTGC 58.437 33.333 0.00 0.00 45.46 5.25
2528 2978 7.641411 CGCTTAATAATTCAACATCTCCAACAG 59.359 37.037 0.00 0.00 0.00 3.16
2553 3003 4.320690 CGCAGTTTTGACATATTTTCACCG 59.679 41.667 0.00 0.00 0.00 4.94
2656 3109 6.229936 TCTCGTTGCACCCTTAATAGTTAT 57.770 37.500 0.00 0.00 0.00 1.89
2724 3177 8.951787 TTTGTACAAGTGTGTAATTCAGTACT 57.048 30.769 8.56 0.00 41.89 2.73
2829 3282 3.282885 GTTCTTTAGGGAGCCAATGGAG 58.717 50.000 2.05 0.00 0.00 3.86
2866 3319 3.692593 TGCAGATCATGACACCATTTCAG 59.307 43.478 0.00 0.00 0.00 3.02
2870 3323 2.011947 CGTGCAGATCATGACACCATT 58.988 47.619 0.00 0.00 34.44 3.16
2931 3384 4.589216 TTCTGTGCCAAAAAGATCAAGG 57.411 40.909 0.00 0.00 0.00 3.61
2976 3429 0.693049 TGAGGAGCTTCACTTTCCCC 59.307 55.000 0.00 0.00 0.00 4.81
2983 3436 5.978814 TCCTAAATAAGTGAGGAGCTTCAC 58.021 41.667 10.07 10.07 46.14 3.18
3079 3532 3.724508 AAGATACCTCATCTGCGTCAG 57.275 47.619 1.02 1.02 43.56 3.51
3082 3535 3.957497 AGAGAAAGATACCTCATCTGCGT 59.043 43.478 0.00 0.00 43.56 5.24
3180 3633 0.171455 CACGTCCAGTCCACTCTAGC 59.829 60.000 0.00 0.00 0.00 3.42
3194 3647 1.705873 ATATGGTCCCTCTCCACGTC 58.294 55.000 0.00 0.00 37.81 4.34
3270 3723 7.148069 CCAAAAATACATAGGTCTTCCAGGTTC 60.148 40.741 0.00 0.00 35.89 3.62
3314 3767 3.119225 GTACCAAACCAGGTGGCAA 57.881 52.632 0.00 0.00 43.14 4.52
3412 3865 7.765307 TCAATTCTCAGATATTTCAAGTTGGC 58.235 34.615 2.34 0.00 0.00 4.52
3438 3891 0.322456 TGGTTACTGCATGTGCTCCC 60.322 55.000 6.55 0.35 42.66 4.30
3775 9985 4.454847 GGCCTTCAAGTTGTTTAGTCCTAC 59.545 45.833 2.11 0.00 0.00 3.18
3818 10028 3.686726 GTCAATAACAAGGAGCTCACAGG 59.313 47.826 17.19 4.21 0.00 4.00
3842 10052 1.612726 CCTTCTCCAGGCCTTCACAAG 60.613 57.143 0.00 3.20 35.13 3.16
3944 10154 0.322546 CTTGTCCACCCCTAGTTGCC 60.323 60.000 0.00 0.00 0.00 4.52
3955 10165 5.591877 AGATCTTTTGCATATCCTTGTCCAC 59.408 40.000 0.00 0.00 0.00 4.02
3973 10186 3.015327 GCAACCAGCATGAAGAGATCTT 58.985 45.455 0.00 0.00 44.79 2.40
3991 10204 2.269978 GCTCTTGAAGCCCATGCAA 58.730 52.632 0.00 0.00 45.92 4.08
4047 10260 4.279145 CCAGCTACTCCCTAAACAGAGTA 58.721 47.826 0.00 0.00 0.00 2.59
4060 10282 5.476091 AATATACCTTGAGCCAGCTACTC 57.524 43.478 8.63 8.63 34.62 2.59
4066 10289 5.882557 AGTGTTCAAATATACCTTGAGCCAG 59.117 40.000 9.41 0.00 34.25 4.85
4113 10341 9.679661 TGGCTGAAATCAAAGACATACTAAATA 57.320 29.630 0.00 0.00 0.00 1.40
4114 10342 8.579850 TGGCTGAAATCAAAGACATACTAAAT 57.420 30.769 0.00 0.00 0.00 1.40
4115 10343 7.994425 TGGCTGAAATCAAAGACATACTAAA 57.006 32.000 0.00 0.00 0.00 1.85
4119 10353 5.126061 ACCATGGCTGAAATCAAAGACATAC 59.874 40.000 13.04 0.00 40.27 2.39
4121 10355 4.091549 ACCATGGCTGAAATCAAAGACAT 58.908 39.130 13.04 0.00 43.11 3.06
4168 10409 4.641541 TCCAATGCATGAATCGAATGAGTT 59.358 37.500 0.00 0.00 0.00 3.01
4251 10605 7.440523 AGCAAATACTGAGAAGTTAGGTTTG 57.559 36.000 0.00 0.00 32.06 2.93
4260 10614 8.084073 TGATTTTTGGAAGCAAATACTGAGAAG 58.916 33.333 0.00 0.00 0.00 2.85
4268 10622 9.118300 ACACAATTTGATTTTTGGAAGCAAATA 57.882 25.926 13.29 0.00 37.97 1.40
4271 10625 6.998968 ACACAATTTGATTTTTGGAAGCAA 57.001 29.167 2.79 0.00 0.00 3.91
4297 10653 8.752005 TTGCCCAGGATATAATATGAATTAGC 57.248 34.615 0.00 0.00 31.18 3.09
4314 10670 0.320946 CTGCCACAATTTTGCCCAGG 60.321 55.000 3.77 0.00 0.00 4.45
4317 10673 1.672030 GGCTGCCACAATTTTGCCC 60.672 57.895 15.17 0.00 34.81 5.36
4409 14242 2.862541 TCATGGCACTTACACAGCTTT 58.137 42.857 0.00 0.00 0.00 3.51
4413 14246 3.603532 ACAGATCATGGCACTTACACAG 58.396 45.455 0.00 0.00 0.00 3.66
4418 14251 2.693074 TCGCTACAGATCATGGCACTTA 59.307 45.455 0.00 0.00 0.00 2.24
4444 14279 6.442513 AGAAAAACAGGACACTTCTTTCAG 57.557 37.500 0.00 0.00 0.00 3.02
4522 14360 2.215196 CAACGAAGGTCTCCGGAAAAA 58.785 47.619 5.23 0.00 0.00 1.94
4525 14363 1.270550 GTACAACGAAGGTCTCCGGAA 59.729 52.381 5.23 0.00 0.00 4.30
4529 14368 3.655276 TTCAGTACAACGAAGGTCTCC 57.345 47.619 0.00 0.00 0.00 3.71
4567 14406 1.600023 TGGGTTACAGCCAAAGAACG 58.400 50.000 0.00 0.00 43.74 3.95
4577 14416 3.848272 AATGAAATGCGTGGGTTACAG 57.152 42.857 0.00 0.00 0.00 2.74
4603 14445 1.315257 CGGCCCCAAGTTCAGAATGG 61.315 60.000 0.00 0.00 36.16 3.16
4649 14491 0.741915 AAACAACGAAACCGTGCCAT 59.258 45.000 0.00 0.00 40.55 4.40
4669 14513 8.859156 CCAAAACGAAATTCATCGATTACATTT 58.141 29.630 6.54 0.39 45.48 2.32
4678 14526 2.338228 CGTGCCAAAACGAAATTCATCG 59.662 45.455 0.00 0.00 46.49 3.84
4716 14564 6.385649 AACACAACCAAATTCGTCACTTAT 57.614 33.333 0.00 0.00 0.00 1.73
4717 14565 5.821516 AACACAACCAAATTCGTCACTTA 57.178 34.783 0.00 0.00 0.00 2.24
4750 14598 0.613012 GGCAAAGCCTCAGACCCAAT 60.613 55.000 0.00 0.00 46.69 3.16
4783 14632 7.549488 ACAAAACTCAATAGTGATACAGCCTAC 59.451 37.037 0.00 0.00 35.62 3.18
4787 14636 8.507249 AGAAACAAAACTCAATAGTGATACAGC 58.493 33.333 0.00 0.00 35.62 4.40
4819 14942 5.105997 CCCACTTCCATTCAGAGAATCAAAC 60.106 44.000 0.00 0.00 37.82 2.93
4829 14952 2.821969 CAAACTCCCCACTTCCATTCAG 59.178 50.000 0.00 0.00 0.00 3.02
4846 14969 5.808030 TCCATTCGAAGAAACAAAACCAAAC 59.192 36.000 3.35 0.00 45.90 2.93
4863 14986 6.604735 CCTATAGGTTTTCACTTCCATTCG 57.395 41.667 10.96 0.00 0.00 3.34
4902 15038 5.904941 TGTCTTTTGAATGATGCAGTTTGT 58.095 33.333 0.00 0.00 0.00 2.83
4998 15134 2.679716 GGGCTTGTGCTCCTGGAT 59.320 61.111 0.00 0.00 39.59 3.41
5020 15156 0.178944 TTCCAGACCTTCGTCCCTCA 60.179 55.000 0.00 0.00 40.12 3.86
5027 15163 0.811281 GCCCAAATTCCAGACCTTCG 59.189 55.000 0.00 0.00 0.00 3.79
5029 15165 0.404040 TCGCCCAAATTCCAGACCTT 59.596 50.000 0.00 0.00 0.00 3.50
5034 15170 0.179103 GCCATTCGCCCAAATTCCAG 60.179 55.000 0.00 0.00 0.00 3.86
5035 15171 1.896694 GCCATTCGCCCAAATTCCA 59.103 52.632 0.00 0.00 0.00 3.53
5036 15172 1.226945 CGCCATTCGCCCAAATTCC 60.227 57.895 0.00 0.00 0.00 3.01
5037 15173 0.172352 TTCGCCATTCGCCCAAATTC 59.828 50.000 0.00 0.00 38.27 2.17
5038 15174 0.605589 TTTCGCCATTCGCCCAAATT 59.394 45.000 0.00 0.00 38.27 1.82
5039 15175 0.173255 CTTTCGCCATTCGCCCAAAT 59.827 50.000 0.00 0.00 38.27 2.32
5040 15176 0.891449 TCTTTCGCCATTCGCCCAAA 60.891 50.000 0.00 0.00 38.27 3.28
5041 15177 0.679640 ATCTTTCGCCATTCGCCCAA 60.680 50.000 0.00 0.00 38.27 4.12
5042 15178 1.077787 ATCTTTCGCCATTCGCCCA 60.078 52.632 0.00 0.00 38.27 5.36
5043 15179 1.095228 TCATCTTTCGCCATTCGCCC 61.095 55.000 0.00 0.00 38.27 6.13
5044 15180 0.028110 GTCATCTTTCGCCATTCGCC 59.972 55.000 0.00 0.00 38.27 5.54
5045 15181 0.315382 CGTCATCTTTCGCCATTCGC 60.315 55.000 0.00 0.00 38.27 4.70
5046 15182 1.277326 TCGTCATCTTTCGCCATTCG 58.723 50.000 0.00 0.00 40.15 3.34


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

AutoCloner maintained by Alex Coulton.