Multiple sequence alignment - TraesCS3A01G225200

Loading Multiple Alignment...

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 TraesCS3A01G225200 chr3A 100.000 6649 0 0 1 6649 422326929 422333577 0.000000e+00 12279.0
1 TraesCS3A01G225200 chr3B 94.787 6139 197 33 1 6077 411268265 411274342 0.000000e+00 9450.0
2 TraesCS3A01G225200 chr3D 93.900 5951 202 48 1 5894 310004542 309998696 0.000000e+00 8829.0
3 TraesCS3A01G225200 chr3D 89.431 246 4 7 5861 6106 309998665 309998442 2.350000e-74 291.0
4 TraesCS3A01G225200 chr3D 94.536 183 10 0 1 183 310117311 310117129 3.920000e-72 283.0
5 TraesCS3A01G225200 chr5B 99.038 520 5 0 6130 6649 483213254 483213773 0.000000e+00 933.0
6 TraesCS3A01G225200 chr5B 93.536 526 28 5 6125 6649 564796516 564795996 0.000000e+00 778.0
7 TraesCS3A01G225200 chr5B 100.000 59 0 0 4984 5042 63274798 63274740 7.050000e-20 110.0
8 TraesCS3A01G225200 chr7A 94.434 521 25 3 6130 6649 33376877 33376360 0.000000e+00 798.0
9 TraesCS3A01G225200 chr1B 88.850 287 29 2 6130 6415 535715039 535715323 3.820000e-92 350.0
10 TraesCS3A01G225200 chr1B 89.062 192 14 3 6459 6649 535724980 535725165 1.440000e-56 231.0
11 TraesCS3A01G225200 chr7D 90.909 187 13 4 6464 6646 529688145 529688331 1.430000e-61 248.0
12 TraesCS3A01G225200 chr7D 79.184 245 34 11 6127 6359 529685700 529685939 3.210000e-33 154.0
13 TraesCS3A01G225200 chr5A 83.333 192 16 8 6460 6649 535707797 535707974 5.340000e-36 163.0
14 TraesCS3A01G225200 chr5A 82.292 192 19 7 6460 6649 670537127 670536949 1.150000e-32 152.0
15 TraesCS3A01G225200 chr2A 81.308 107 11 9 6316 6419 622735681 622735581 1.990000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G225200 chr3A 422326929 422333577 6648 False 12279 12279 100.0000 1 6649 1 chr3A.!!$F1 6648
1 TraesCS3A01G225200 chr3B 411268265 411274342 6077 False 9450 9450 94.7870 1 6077 1 chr3B.!!$F1 6076
2 TraesCS3A01G225200 chr3D 309998442 310004542 6100 True 4560 8829 91.6655 1 6106 2 chr3D.!!$R2 6105
3 TraesCS3A01G225200 chr5B 483213254 483213773 519 False 933 933 99.0380 6130 6649 1 chr5B.!!$F1 519
4 TraesCS3A01G225200 chr5B 564795996 564796516 520 True 778 778 93.5360 6125 6649 1 chr5B.!!$R2 524
5 TraesCS3A01G225200 chr7A 33376360 33376877 517 True 798 798 94.4340 6130 6649 1 chr7A.!!$R1 519
6 TraesCS3A01G225200 chr7D 529685700 529688331 2631 False 201 248 85.0465 6127 6646 2 chr7D.!!$F1 519

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
742 749 0.179189 GCAAAGAAATCCAGCCGTCG 60.179 55.000 0.00 0.00 0.00 5.12 F
1780 1791 1.347378 AGGTTTGCGGATGCCATTTTT 59.653 42.857 0.64 0.00 41.78 1.94 F
2840 2862 1.798735 CTGCGTTTCTCCCTGCATG 59.201 57.895 0.00 0.00 36.64 4.06 F
3006 3028 0.324614 AATGTGCTCCGTCCATCACA 59.675 50.000 0.00 0.00 42.66 3.58 F
3007 3029 0.543277 ATGTGCTCCGTCCATCACAT 59.457 50.000 0.00 0.00 43.08 3.21 F
3008 3030 0.324614 TGTGCTCCGTCCATCACATT 59.675 50.000 0.00 0.00 34.87 2.71 F
3010 3032 0.612744 TGCTCCGTCCATCACATTCA 59.387 50.000 0.00 0.00 0.00 2.57 F
3011 3033 1.003003 TGCTCCGTCCATCACATTCAA 59.997 47.619 0.00 0.00 0.00 2.69 F
3644 3674 1.598130 GTGCTCTCCGCCAACAGTT 60.598 57.895 0.00 0.00 38.05 3.16 F
5336 5383 0.254178 AAAGGCGAGGATGTCATGCT 59.746 50.000 6.55 6.55 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2260 1.068055 CAACAAATCCTCCTGTGCTGC 60.068 52.381 0.00 0.0 0.00 5.25 R
2991 3013 0.612744 TGAATGTGATGGACGGAGCA 59.387 50.000 0.00 0.0 0.00 4.26 R
4133 4172 2.073816 GGTACAACAGTTGGTCGGATG 58.926 52.381 17.76 0.0 34.12 3.51 R
4909 4948 3.871594 CCGTTCCTACTTCACCAATGATC 59.128 47.826 0.00 0.0 33.85 2.92 R
4963 5002 4.134563 GGGAAAGAAGACAACAGCAGTTA 58.865 43.478 0.00 0.0 35.85 2.24 R
5115 5154 4.916983 TTGGGAGACACACATGAAAAAG 57.083 40.909 0.00 0.0 0.00 2.27 R
5116 5155 5.362143 TCAATTGGGAGACACACATGAAAAA 59.638 36.000 5.42 0.0 0.00 1.94 R
5123 5162 2.229792 GCTTCAATTGGGAGACACACA 58.770 47.619 5.42 0.0 0.00 3.72 R
5376 5423 0.750249 TGACAGTCTCTTCGGTTGCA 59.250 50.000 1.31 0.0 0.00 4.08 R
6211 6358 2.108250 ACAGTATCAGTGGTTTTGGGCT 59.892 45.455 0.00 0.0 0.00 5.19 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
54 55 7.792048 GTGTTTTCCGTTTCAATATCTTTTTGC 59.208 33.333 0.00 0.00 0.00 3.68
77 78 6.070653 TGCGGGGAAGAGTTATAGTAAGAAAA 60.071 38.462 0.00 0.00 0.00 2.29
100 101 8.515473 AAAAACGACAATAAAAAGATAGTGGC 57.485 30.769 0.00 0.00 0.00 5.01
116 117 2.238898 AGTGGCCCCTTGTTGTATAGTC 59.761 50.000 0.00 0.00 0.00 2.59
147 148 1.025041 CACTCATCCTCGTCCATCGA 58.975 55.000 0.00 0.00 46.83 3.59
152 153 0.183971 ATCCTCGTCCATCGACTCCT 59.816 55.000 0.00 0.00 44.01 3.69
172 173 3.314635 CCTACTCCACGTGTATGTACTCC 59.685 52.174 15.65 0.00 0.00 3.85
178 179 1.097232 CGTGTATGTACTCCCGTGGA 58.903 55.000 0.00 0.00 0.00 4.02
214 215 3.493129 TGTAGTTGCTCTTGTTAACTGCG 59.507 43.478 7.22 0.00 39.07 5.18
229 230 0.379669 CTGCGCACATCCAATCTTCC 59.620 55.000 5.66 0.00 0.00 3.46
232 233 1.599542 GCGCACATCCAATCTTCCTAC 59.400 52.381 0.30 0.00 0.00 3.18
237 238 5.279206 CGCACATCCAATCTTCCTACTATCT 60.279 44.000 0.00 0.00 0.00 1.98
243 244 9.061435 CATCCAATCTTCCTACTATCTTTTTCC 57.939 37.037 0.00 0.00 0.00 3.13
245 246 8.781951 TCCAATCTTCCTACTATCTTTTTCCAT 58.218 33.333 0.00 0.00 0.00 3.41
260 261 8.706492 TCTTTTTCCATAATATACGACGTGTT 57.294 30.769 11.56 5.61 0.00 3.32
261 262 9.800433 TCTTTTTCCATAATATACGACGTGTTA 57.200 29.630 11.56 7.66 0.00 2.41
331 334 7.520798 TCTTATTCAATTGGGATCTATGCACT 58.479 34.615 5.42 0.00 0.00 4.40
341 344 9.812347 ATTGGGATCTATGCACTAATTTTATGA 57.188 29.630 0.00 0.00 0.00 2.15
365 368 7.816995 TGAACAAAAATGTGTAATAATCCAGGC 59.183 33.333 0.00 0.00 0.00 4.85
367 370 5.869649 AAAATGTGTAATAATCCAGGCCC 57.130 39.130 0.00 0.00 0.00 5.80
376 379 0.765510 AATCCAGGCCCGATAGTTCC 59.234 55.000 0.00 0.00 0.00 3.62
394 397 9.736023 GATAGTTCCGATTATCAAGCAAATTTT 57.264 29.630 0.00 0.00 0.00 1.82
412 415 7.501515 CAAATTTTGCGGAACTCTAAACATTC 58.498 34.615 0.00 0.00 0.00 2.67
416 419 2.617021 GCGGAACTCTAAACATTCCCCA 60.617 50.000 0.00 0.00 39.01 4.96
417 420 3.886123 CGGAACTCTAAACATTCCCCAT 58.114 45.455 0.00 0.00 39.01 4.00
418 421 3.627577 CGGAACTCTAAACATTCCCCATG 59.372 47.826 0.00 0.00 39.01 3.66
420 423 4.640647 GGAACTCTAAACATTCCCCATGTC 59.359 45.833 0.00 0.00 46.23 3.06
421 424 5.501156 GAACTCTAAACATTCCCCATGTCT 58.499 41.667 0.00 0.00 46.23 3.41
422 425 4.848357 ACTCTAAACATTCCCCATGTCTG 58.152 43.478 0.00 0.00 46.23 3.51
423 426 4.289672 ACTCTAAACATTCCCCATGTCTGT 59.710 41.667 0.00 0.00 46.23 3.41
424 427 4.588899 TCTAAACATTCCCCATGTCTGTG 58.411 43.478 0.00 0.00 46.23 3.66
425 428 1.549203 AACATTCCCCATGTCTGTGC 58.451 50.000 0.00 0.00 46.23 4.57
426 429 0.700564 ACATTCCCCATGTCTGTGCT 59.299 50.000 0.00 0.00 43.17 4.40
427 430 1.915489 ACATTCCCCATGTCTGTGCTA 59.085 47.619 0.00 0.00 43.17 3.49
428 431 2.308570 ACATTCCCCATGTCTGTGCTAA 59.691 45.455 0.00 0.00 43.17 3.09
429 432 3.053395 ACATTCCCCATGTCTGTGCTAAT 60.053 43.478 0.00 0.00 43.17 1.73
430 433 3.737559 TTCCCCATGTCTGTGCTAATT 57.262 42.857 0.00 0.00 0.00 1.40
431 434 3.737559 TCCCCATGTCTGTGCTAATTT 57.262 42.857 0.00 0.00 0.00 1.82
432 435 4.046286 TCCCCATGTCTGTGCTAATTTT 57.954 40.909 0.00 0.00 0.00 1.82
433 436 4.415596 TCCCCATGTCTGTGCTAATTTTT 58.584 39.130 0.00 0.00 0.00 1.94
434 437 4.220382 TCCCCATGTCTGTGCTAATTTTTG 59.780 41.667 0.00 0.00 0.00 2.44
435 438 4.021192 CCCCATGTCTGTGCTAATTTTTGT 60.021 41.667 0.00 0.00 0.00 2.83
491 495 0.598065 GGAATGTGGTCCTTGTGCAC 59.402 55.000 10.75 10.75 34.56 4.57
510 514 0.902531 CTCACCCGAGTACACCCATT 59.097 55.000 0.00 0.00 34.29 3.16
520 524 0.330941 TACACCCATTGATGCCTGCA 59.669 50.000 0.00 0.00 0.00 4.41
529 535 2.358125 ATGCCTGCAACGCGTGTA 60.358 55.556 14.98 5.87 0.00 2.90
538 544 1.790123 GCAACGCGTGTATGGATTGTG 60.790 52.381 14.98 3.84 0.00 3.33
566 572 7.305019 GGTGCGCTTTTAATAATAAAGTAACGC 60.305 37.037 9.73 0.00 38.57 4.84
611 618 2.347731 GGGGCGAGAAAACAGAGTAAG 58.652 52.381 0.00 0.00 0.00 2.34
662 669 4.884668 AACCTTCCGTCAGTAGATGAAA 57.115 40.909 0.00 0.00 40.43 2.69
663 670 4.884668 ACCTTCCGTCAGTAGATGAAAA 57.115 40.909 0.00 0.00 40.43 2.29
670 677 3.367932 CGTCAGTAGATGAAAACGTGCAT 59.632 43.478 0.00 0.00 40.43 3.96
742 749 0.179189 GCAAAGAAATCCAGCCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
789 796 3.433598 CCTCTGGCAATTCCGAATCCTTA 60.434 47.826 0.00 0.00 37.80 2.69
790 797 4.199310 CTCTGGCAATTCCGAATCCTTAA 58.801 43.478 0.00 0.00 37.80 1.85
865 872 5.564259 CGTCCCCGTCTTCTATATAAACAGG 60.564 48.000 0.00 0.00 0.00 4.00
1362 1373 2.094854 ACTAACTTCTAGGCCGTCAACG 60.095 50.000 0.00 0.00 39.44 4.10
1408 1419 1.807755 GCAGCTAACCATCGAGCATGA 60.808 52.381 0.00 0.00 41.36 3.07
1526 1537 1.381872 CCACATCCGGGTCCTCTCT 60.382 63.158 0.00 0.00 0.00 3.10
1578 1589 1.949847 ATCAGGTTCGCCTCCTCGTG 61.950 60.000 0.00 0.00 46.86 4.35
1780 1791 1.347378 AGGTTTGCGGATGCCATTTTT 59.653 42.857 0.64 0.00 41.78 1.94
1941 1960 6.211184 ACATTTGATTGCTATTTTGAGGGACA 59.789 34.615 0.00 0.00 0.00 4.02
2259 2281 2.233271 CAGCACAGGAGGATTTGTTGT 58.767 47.619 0.00 0.00 0.00 3.32
2510 2532 1.803289 GGAAGCTCCGACATTTGCC 59.197 57.895 0.00 0.00 0.00 4.52
2623 2645 6.262944 ACAATTTCTGTGCTGTTCTGATTGTA 59.737 34.615 0.00 0.00 36.69 2.41
2834 2856 3.435186 GCCTGCTGCGTTTCTCCC 61.435 66.667 0.00 0.00 0.00 4.30
2840 2862 1.798735 CTGCGTTTCTCCCTGCATG 59.201 57.895 0.00 0.00 36.64 4.06
2903 2925 5.907197 ATATTTTCTCGTCACTTATGCCG 57.093 39.130 0.00 0.00 0.00 5.69
2991 3013 9.603921 GATTTATGGTCCATCAAATTCAAATGT 57.396 29.630 7.92 0.00 0.00 2.71
2992 3014 8.774890 TTTATGGTCCATCAAATTCAAATGTG 57.225 30.769 7.92 0.00 0.00 3.21
2993 3015 4.567971 TGGTCCATCAAATTCAAATGTGC 58.432 39.130 0.00 0.00 0.00 4.57
2994 3016 4.283978 TGGTCCATCAAATTCAAATGTGCT 59.716 37.500 0.00 0.00 0.00 4.40
2995 3017 4.866486 GGTCCATCAAATTCAAATGTGCTC 59.134 41.667 0.00 0.00 0.00 4.26
2996 3018 4.866486 GTCCATCAAATTCAAATGTGCTCC 59.134 41.667 0.00 0.00 0.00 4.70
2997 3019 3.861113 CCATCAAATTCAAATGTGCTCCG 59.139 43.478 0.00 0.00 0.00 4.63
2998 3020 4.487948 CATCAAATTCAAATGTGCTCCGT 58.512 39.130 0.00 0.00 0.00 4.69
2999 3021 4.159377 TCAAATTCAAATGTGCTCCGTC 57.841 40.909 0.00 0.00 0.00 4.79
3000 3022 3.057596 TCAAATTCAAATGTGCTCCGTCC 60.058 43.478 0.00 0.00 0.00 4.79
3001 3023 2.198827 ATTCAAATGTGCTCCGTCCA 57.801 45.000 0.00 0.00 0.00 4.02
3002 3024 2.198827 TTCAAATGTGCTCCGTCCAT 57.801 45.000 0.00 0.00 0.00 3.41
3003 3025 1.737838 TCAAATGTGCTCCGTCCATC 58.262 50.000 0.00 0.00 0.00 3.51
3004 3026 1.003003 TCAAATGTGCTCCGTCCATCA 59.997 47.619 0.00 0.00 0.00 3.07
3005 3027 1.131126 CAAATGTGCTCCGTCCATCAC 59.869 52.381 0.00 0.00 0.00 3.06
3006 3028 0.324614 AATGTGCTCCGTCCATCACA 59.675 50.000 0.00 0.00 42.66 3.58
3007 3029 0.543277 ATGTGCTCCGTCCATCACAT 59.457 50.000 0.00 0.00 43.08 3.21
3008 3030 0.324614 TGTGCTCCGTCCATCACATT 59.675 50.000 0.00 0.00 34.87 2.71
3009 3031 1.009829 GTGCTCCGTCCATCACATTC 58.990 55.000 0.00 0.00 0.00 2.67
3010 3032 0.612744 TGCTCCGTCCATCACATTCA 59.387 50.000 0.00 0.00 0.00 2.57
3011 3033 1.003003 TGCTCCGTCCATCACATTCAA 59.997 47.619 0.00 0.00 0.00 2.69
3012 3034 2.083774 GCTCCGTCCATCACATTCAAA 58.916 47.619 0.00 0.00 0.00 2.69
3013 3035 2.684881 GCTCCGTCCATCACATTCAAAT 59.315 45.455 0.00 0.00 0.00 2.32
3014 3036 3.488047 GCTCCGTCCATCACATTCAAATG 60.488 47.826 1.20 1.20 42.10 2.32
3272 3302 7.549839 ACATTGCATTGCTTATGTTATGACTT 58.450 30.769 18.18 1.38 33.40 3.01
3313 3343 9.985730 ATTTTCTTTTTGCAGATGATAACTTCA 57.014 25.926 0.00 0.00 39.12 3.02
3644 3674 1.598130 GTGCTCTCCGCCAACAGTT 60.598 57.895 0.00 0.00 38.05 3.16
3778 3808 2.235402 GGTCCCTGAATACAGAAACGGA 59.765 50.000 0.00 0.00 46.03 4.69
4106 4145 4.219033 CAATTTTGCGTAAGTCACAGGTC 58.781 43.478 0.00 0.00 41.68 3.85
4133 4172 4.144555 CAGACAACGAATTCGAAAAGCTC 58.855 43.478 33.05 16.72 43.02 4.09
4196 4235 5.007921 CACATTTGATGACATCGGAGCATTA 59.992 40.000 10.79 0.00 0.00 1.90
4744 4783 3.193479 AGATGAGTTGCTGACGTGTCATA 59.807 43.478 2.72 0.00 39.13 2.15
4909 4948 5.128499 AGTGATCTGAAGGTAACATCTCTGG 59.872 44.000 0.00 0.00 41.41 3.86
4930 4969 3.871594 GGATCATTGGTGAAGTAGGAACG 59.128 47.826 0.00 0.00 38.01 3.95
4941 4980 7.147620 TGGTGAAGTAGGAACGGTATATTCAAT 60.148 37.037 0.00 0.00 0.00 2.57
5116 5155 9.507329 TTTTATGAGCAGTAGATTTGTCTTTCT 57.493 29.630 0.00 0.00 0.00 2.52
5121 5160 8.345565 TGAGCAGTAGATTTGTCTTTCTTTTTC 58.654 33.333 0.00 0.00 0.00 2.29
5122 5161 8.225603 AGCAGTAGATTTGTCTTTCTTTTTCA 57.774 30.769 0.00 0.00 0.00 2.69
5123 5162 8.854117 AGCAGTAGATTTGTCTTTCTTTTTCAT 58.146 29.630 0.00 0.00 0.00 2.57
5182 5229 3.305110 GGTTTGGTTTAGATGTGTTGCG 58.695 45.455 0.00 0.00 0.00 4.85
5184 5231 1.890876 TGGTTTAGATGTGTTGCGCT 58.109 45.000 9.73 0.00 0.00 5.92
5203 5250 6.579865 TGCGCTAATCATATCATCATCTCAT 58.420 36.000 9.73 0.00 0.00 2.90
5206 5253 6.702282 CGCTAATCATATCATCATCTCATGCT 59.298 38.462 0.00 0.00 0.00 3.79
5212 5259 1.766496 TCATCATCTCATGCTGGCTCA 59.234 47.619 0.00 0.00 0.00 4.26
5227 5274 4.384056 CTGGCTCAATAATTCGATGTCCT 58.616 43.478 0.00 0.00 0.00 3.85
5262 5309 3.923017 AATGCAGTGCAAGTTAAGGAC 57.077 42.857 23.90 0.00 43.62 3.85
5287 5334 0.465460 AGCGCAACCCAAAAGTCAGA 60.465 50.000 11.47 0.00 0.00 3.27
5308 5355 4.748679 GCGCGGCACAAAGCTCAG 62.749 66.667 8.83 0.00 44.79 3.35
5326 5373 1.198637 CAGAAAGCAAGAAAGGCGAGG 59.801 52.381 0.00 0.00 36.08 4.63
5336 5383 0.254178 AAAGGCGAGGATGTCATGCT 59.746 50.000 6.55 6.55 0.00 3.79
5354 5401 1.547901 GCTAGAAACCAAGCAAGGGGT 60.548 52.381 0.00 0.00 38.63 4.95
5376 5423 1.141053 ACAGAGAAAGGCGTCAAAGGT 59.859 47.619 0.00 0.00 0.00 3.50
5454 5501 3.372206 CGAAGGATCAAGTAAGTTGCTGG 59.628 47.826 0.00 0.00 35.94 4.85
5459 5506 4.702131 GGATCAAGTAAGTTGCTGGTGAAT 59.298 41.667 0.00 0.00 35.94 2.57
5494 5541 4.529716 AGTCTAAACCTTTTCACCCCAA 57.470 40.909 0.00 0.00 0.00 4.12
5540 5587 0.955428 TTGACGCTACGTAGGTCGGT 60.955 55.000 25.66 14.13 41.37 4.69
5543 5590 2.103736 GCTACGTAGGTCGGTGCC 59.896 66.667 23.47 0.90 44.69 5.01
5654 5701 5.639506 GCTCTCATACTTCTTGTAGTGCAAA 59.360 40.000 0.00 0.00 36.53 3.68
5674 5721 6.948886 TGCAAAGGTTGGGAGTTTGTATATAA 59.051 34.615 0.00 0.00 34.32 0.98
5785 5838 4.749598 CCATTGGAGGCTGTTTGTTTAAAC 59.250 41.667 11.54 11.54 45.04 2.01
5800 5877 9.149556 GTTTGTTTAAACAGTTGTTGTGAAAAC 57.850 29.630 19.72 12.97 44.38 2.43
5855 5932 6.925610 TCTGGGAATGAATCGATTAACTTG 57.074 37.500 11.38 0.00 0.00 3.16
5874 5951 7.898014 AACTTGGAACTTGTTAGAATTCCTT 57.102 32.000 0.65 0.00 41.11 3.36
5878 5955 6.601332 TGGAACTTGTTAGAATTCCTTGAGT 58.399 36.000 0.65 0.00 41.11 3.41
5879 5956 7.741785 TGGAACTTGTTAGAATTCCTTGAGTA 58.258 34.615 0.65 0.00 41.11 2.59
5880 5957 7.660208 TGGAACTTGTTAGAATTCCTTGAGTAC 59.340 37.037 0.65 0.00 41.11 2.73
5881 5958 7.878644 GGAACTTGTTAGAATTCCTTGAGTACT 59.121 37.037 0.65 0.00 38.08 2.73
5882 5959 9.274206 GAACTTGTTAGAATTCCTTGAGTACTT 57.726 33.333 0.65 0.00 0.00 2.24
6108 6255 4.200838 CCATATTTGGGGTTTGTGTTCC 57.799 45.455 0.00 0.00 39.56 3.62
6109 6256 3.367910 CCATATTTGGGGTTTGTGTTCCG 60.368 47.826 0.00 0.00 39.56 4.30
6110 6257 0.391228 ATTTGGGGTTTGTGTTCCGC 59.609 50.000 0.00 0.00 37.22 5.54
6111 6258 0.970937 TTTGGGGTTTGTGTTCCGCA 60.971 50.000 0.00 0.00 43.17 5.69
6112 6259 1.379977 TGGGGTTTGTGTTCCGCAA 60.380 52.632 0.00 0.00 42.22 4.85
6113 6260 1.362355 GGGGTTTGTGTTCCGCAAG 59.638 57.895 0.00 0.00 35.27 4.01
6114 6261 1.104577 GGGGTTTGTGTTCCGCAAGA 61.105 55.000 0.00 0.00 43.02 3.02
6115 6262 0.030235 GGGTTTGTGTTCCGCAAGAC 59.970 55.000 0.00 0.00 43.02 3.01
6116 6263 0.316689 GGTTTGTGTTCCGCAAGACG 60.317 55.000 0.00 0.00 43.15 4.18
6125 6272 4.963815 CGCAAGACGGCCATTTTT 57.036 50.000 2.24 0.00 43.02 1.94
6128 6275 2.874849 CGCAAGACGGCCATTTTTATT 58.125 42.857 2.24 0.00 43.02 1.40
6211 6358 6.269077 ACCAATATCCGGTTGACATCTGTATA 59.731 38.462 0.00 0.00 30.53 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 6.349860 GGGCCACTATCTTTTTATTGTCGTTT 60.350 38.462 4.39 0.00 0.00 3.60
100 101 3.689649 GCAACAGACTATACAACAAGGGG 59.310 47.826 0.00 0.00 0.00 4.79
147 148 3.083122 ACATACACGTGGAGTAGGAGT 57.917 47.619 21.57 1.82 0.00 3.85
152 153 3.282021 GGGAGTACATACACGTGGAGTA 58.718 50.000 21.57 15.58 0.00 2.59
178 179 2.622942 CAACTACACTTGGTTGGTGCAT 59.377 45.455 0.00 0.00 39.08 3.96
214 215 6.107901 AGATAGTAGGAAGATTGGATGTGC 57.892 41.667 0.00 0.00 0.00 4.57
296 297 8.208718 TCCCAATTGAATAAGAGTTTATCGTG 57.791 34.615 7.12 0.00 0.00 4.35
302 303 8.854117 GCATAGATCCCAATTGAATAAGAGTTT 58.146 33.333 7.12 0.00 0.00 2.66
303 304 8.000709 TGCATAGATCCCAATTGAATAAGAGTT 58.999 33.333 7.12 0.00 0.00 3.01
341 344 7.102993 GGCCTGGATTATTACACATTTTTGTT 58.897 34.615 0.00 0.00 0.00 2.83
365 368 3.927142 GCTTGATAATCGGAACTATCGGG 59.073 47.826 6.18 3.75 0.00 5.14
367 370 6.525121 TTTGCTTGATAATCGGAACTATCG 57.475 37.500 6.18 0.00 0.00 2.92
394 397 2.706890 GGGAATGTTTAGAGTTCCGCA 58.293 47.619 0.00 0.00 41.80 5.69
408 411 2.715749 TAGCACAGACATGGGGAATG 57.284 50.000 0.00 0.00 42.48 2.67
412 415 4.021192 ACAAAAATTAGCACAGACATGGGG 60.021 41.667 0.00 0.00 0.00 4.96
416 419 7.275888 TCTCAACAAAAATTAGCACAGACAT 57.724 32.000 0.00 0.00 0.00 3.06
417 420 6.691754 TCTCAACAAAAATTAGCACAGACA 57.308 33.333 0.00 0.00 0.00 3.41
418 421 7.702348 AGTTTCTCAACAAAAATTAGCACAGAC 59.298 33.333 0.00 0.00 35.05 3.51
419 422 7.771183 AGTTTCTCAACAAAAATTAGCACAGA 58.229 30.769 0.00 0.00 35.05 3.41
420 423 7.992180 AGTTTCTCAACAAAAATTAGCACAG 57.008 32.000 0.00 0.00 35.05 3.66
423 426 8.977505 GCAATAGTTTCTCAACAAAAATTAGCA 58.022 29.630 0.00 0.00 35.05 3.49
424 427 8.977505 TGCAATAGTTTCTCAACAAAAATTAGC 58.022 29.630 0.00 0.00 35.05 3.09
427 430 8.947055 AGTGCAATAGTTTCTCAACAAAAATT 57.053 26.923 0.00 0.00 35.05 1.82
428 431 9.683069 CTAGTGCAATAGTTTCTCAACAAAAAT 57.317 29.630 12.98 0.00 35.05 1.82
429 432 8.898761 TCTAGTGCAATAGTTTCTCAACAAAAA 58.101 29.630 19.77 0.00 35.05 1.94
430 433 8.445275 TCTAGTGCAATAGTTTCTCAACAAAA 57.555 30.769 19.77 0.00 35.05 2.44
431 434 8.445275 TTCTAGTGCAATAGTTTCTCAACAAA 57.555 30.769 19.77 1.32 35.05 2.83
432 435 8.445275 TTTCTAGTGCAATAGTTTCTCAACAA 57.555 30.769 19.77 2.01 35.05 2.83
433 436 7.931407 TCTTTCTAGTGCAATAGTTTCTCAACA 59.069 33.333 19.77 0.00 35.05 3.33
434 437 8.311650 TCTTTCTAGTGCAATAGTTTCTCAAC 57.688 34.615 19.77 0.00 0.00 3.18
435 438 8.774586 GTTCTTTCTAGTGCAATAGTTTCTCAA 58.225 33.333 19.77 4.08 0.00 3.02
510 514 3.725459 CACGCGTTGCAGGCATCA 61.725 61.111 10.22 0.00 0.00 3.07
520 524 1.999735 CTCACAATCCATACACGCGTT 59.000 47.619 10.22 3.81 0.00 4.84
529 535 0.322816 AAGCGCACCTCACAATCCAT 60.323 50.000 11.47 0.00 0.00 3.41
538 544 9.218359 GTTACTTTATTATTAAAAGCGCACCTC 57.782 33.333 11.47 0.00 37.44 3.85
579 585 5.664294 TTTCTCGCCCCGCTTTATATATA 57.336 39.130 0.00 0.00 0.00 0.86
580 586 4.546829 TTTCTCGCCCCGCTTTATATAT 57.453 40.909 0.00 0.00 0.00 0.86
590 596 0.245539 TACTCTGTTTTCTCGCCCCG 59.754 55.000 0.00 0.00 0.00 5.73
611 618 4.259356 AGTTAACAGCCGGATAGAAAACC 58.741 43.478 5.05 0.00 0.00 3.27
662 669 2.710377 TGCAGAGGAATAATGCACGTT 58.290 42.857 0.00 0.00 44.56 3.99
663 670 2.401583 TGCAGAGGAATAATGCACGT 57.598 45.000 0.00 0.00 44.56 4.49
670 677 5.250200 ACCGTTGTTTATGCAGAGGAATAA 58.750 37.500 0.00 0.00 0.00 1.40
1289 1300 2.907392 GCGAAGTCGTATACTAATCGGC 59.093 50.000 14.64 3.19 38.39 5.54
1362 1373 2.606108 GCCAAACACATTCGAATTCCC 58.394 47.619 8.21 0.00 0.00 3.97
1396 1407 3.873361 ACAATGTAACTCATGCTCGATGG 59.127 43.478 0.00 0.00 36.81 3.51
1578 1589 5.146010 TCAAGCCAACCCACATTTTAATC 57.854 39.130 0.00 0.00 0.00 1.75
1861 1873 5.231702 ACGGGATTAACAAACTAACCAGA 57.768 39.130 0.00 0.00 0.00 3.86
1941 1960 6.128336 CGCACTGAAAATTCTGAATTCTCTCT 60.128 38.462 15.43 0.00 0.00 3.10
2238 2260 1.068055 CAACAAATCCTCCTGTGCTGC 60.068 52.381 0.00 0.00 0.00 5.25
2259 2281 6.764085 TGCAAGTTTTTACAAGCTAGTAGACA 59.236 34.615 0.00 0.00 0.00 3.41
2510 2532 6.582437 AACCGTGCAAGAACAAAAATAAAG 57.418 33.333 0.00 0.00 0.00 1.85
2623 2645 9.362539 GAGTCTGCATTAATGTTTCATGAAAAT 57.637 29.630 22.07 14.34 31.33 1.82
2903 2925 2.987413 TCAATCAACACATGAACCGC 57.013 45.000 0.00 0.00 42.54 5.68
2991 3013 0.612744 TGAATGTGATGGACGGAGCA 59.387 50.000 0.00 0.00 0.00 4.26
2992 3014 1.737838 TTGAATGTGATGGACGGAGC 58.262 50.000 0.00 0.00 0.00 4.70
2993 3015 4.282950 CATTTGAATGTGATGGACGGAG 57.717 45.455 0.00 0.00 0.00 4.63
3004 3026 5.422970 ACCAATATGGAGCACATTTGAATGT 59.577 36.000 2.85 3.60 44.82 2.71
3005 3027 5.909477 ACCAATATGGAGCACATTTGAATG 58.091 37.500 2.85 2.29 40.96 2.67
3006 3028 6.154877 TGAACCAATATGGAGCACATTTGAAT 59.845 34.615 2.85 0.00 40.96 2.57
3007 3029 5.479724 TGAACCAATATGGAGCACATTTGAA 59.520 36.000 2.85 0.00 40.96 2.69
3008 3030 5.015515 TGAACCAATATGGAGCACATTTGA 58.984 37.500 2.85 0.00 40.96 2.69
3009 3031 5.327616 TGAACCAATATGGAGCACATTTG 57.672 39.130 2.85 4.90 40.96 2.32
3010 3032 5.069516 GGATGAACCAATATGGAGCACATTT 59.930 40.000 2.85 0.00 40.96 2.32
3011 3033 4.586001 GGATGAACCAATATGGAGCACATT 59.414 41.667 2.85 0.00 40.96 2.71
3012 3034 4.147321 GGATGAACCAATATGGAGCACAT 58.853 43.478 2.85 3.37 40.96 3.21
3013 3035 3.053768 TGGATGAACCAATATGGAGCACA 60.054 43.478 2.85 0.00 46.75 4.57
3014 3036 3.554934 TGGATGAACCAATATGGAGCAC 58.445 45.455 2.85 0.00 46.75 4.40
3313 3343 6.183360 CGATAACTGGATTGCATTCAGAAACT 60.183 38.462 15.36 3.48 33.19 2.66
3388 3418 6.698329 TGCTCAACATTTTCTTGAACATTGAG 59.302 34.615 6.34 6.34 42.93 3.02
3644 3674 5.807909 TGAGTCCAAATCATCACAGATCAA 58.192 37.500 0.00 0.00 0.00 2.57
3778 3808 5.108187 TCTCTGCAGGAATAATGAGCTTT 57.892 39.130 15.13 0.00 0.00 3.51
4106 4145 2.672714 TCGAATTCGTTGTCTGGAGTG 58.327 47.619 25.93 0.00 40.80 3.51
4133 4172 2.073816 GGTACAACAGTTGGTCGGATG 58.926 52.381 17.76 0.00 34.12 3.51
4196 4235 8.816894 TCCTGAAGTGACTCTTTTATATCAGTT 58.183 33.333 6.08 0.00 37.42 3.16
4701 4740 5.227908 TCTAGAGGTCATCAAAACACGTTC 58.772 41.667 0.00 0.00 0.00 3.95
4909 4948 3.871594 CCGTTCCTACTTCACCAATGATC 59.128 47.826 0.00 0.00 33.85 2.92
4958 4997 7.173390 GGAAAGAAGACAACAGCAGTTATAGTT 59.827 37.037 0.00 0.00 35.85 2.24
4963 5002 4.134563 GGGAAAGAAGACAACAGCAGTTA 58.865 43.478 0.00 0.00 35.85 2.24
5115 5154 4.916983 TTGGGAGACACACATGAAAAAG 57.083 40.909 0.00 0.00 0.00 2.27
5116 5155 5.362143 TCAATTGGGAGACACACATGAAAAA 59.638 36.000 5.42 0.00 0.00 1.94
5121 5160 3.366679 GCTTCAATTGGGAGACACACATG 60.367 47.826 5.42 0.00 0.00 3.21
5122 5161 2.821969 GCTTCAATTGGGAGACACACAT 59.178 45.455 5.42 0.00 0.00 3.21
5123 5162 2.229792 GCTTCAATTGGGAGACACACA 58.770 47.619 5.42 0.00 0.00 3.72
5203 5250 3.544684 ACATCGAATTATTGAGCCAGCA 58.455 40.909 0.00 0.00 0.00 4.41
5206 5253 4.422073 AGGACATCGAATTATTGAGCCA 57.578 40.909 0.00 0.00 0.00 4.75
5227 5274 5.590259 GCACTGCATTTTCCTTCTTATCCTA 59.410 40.000 0.00 0.00 0.00 2.94
5262 5309 1.743321 TTTTGGGTTGCGCTTCTGGG 61.743 55.000 9.73 0.00 0.00 4.45
5308 5355 1.523758 TCCTCGCCTTTCTTGCTTTC 58.476 50.000 0.00 0.00 0.00 2.62
5326 5373 3.691118 TGCTTGGTTTCTAGCATGACATC 59.309 43.478 0.00 0.00 44.36 3.06
5336 5383 1.777878 TCACCCCTTGCTTGGTTTCTA 59.222 47.619 0.00 0.00 30.70 2.10
5354 5401 2.483876 CTTTGACGCCTTTCTCTGTCA 58.516 47.619 0.00 0.00 39.42 3.58
5376 5423 0.750249 TGACAGTCTCTTCGGTTGCA 59.250 50.000 1.31 0.00 0.00 4.08
5387 5434 1.915769 GGCCTGAGGGTGACAGTCT 60.916 63.158 0.00 0.00 34.04 3.24
5471 5518 5.649970 TGGGGTGAAAAGGTTTAGACTAA 57.350 39.130 0.00 0.00 0.00 2.24
5494 5541 5.560183 GCGTAATTGTTTAGCAGTGTGTTCT 60.560 40.000 0.00 0.00 0.00 3.01
5543 5590 1.222936 CCCCTCACTAGCCAAGCTG 59.777 63.158 0.00 0.00 40.10 4.24
5674 5721 5.356751 ACATTCAACCGCACATACACATATT 59.643 36.000 0.00 0.00 0.00 1.28
5785 5838 2.107366 AGGGGGTTTTCACAACAACTG 58.893 47.619 0.00 0.00 0.00 3.16
5855 5932 7.878644 AGTACTCAAGGAATTCTAACAAGTTCC 59.121 37.037 5.23 0.00 40.28 3.62
5874 5951 6.150976 CACCAAAAAGATGCCATAAGTACTCA 59.849 38.462 0.00 0.00 0.00 3.41
5878 5955 6.480763 TCTCACCAAAAAGATGCCATAAGTA 58.519 36.000 0.00 0.00 0.00 2.24
5879 5956 5.324409 TCTCACCAAAAAGATGCCATAAGT 58.676 37.500 0.00 0.00 0.00 2.24
5880 5957 5.902613 TCTCACCAAAAAGATGCCATAAG 57.097 39.130 0.00 0.00 0.00 1.73
5881 5958 5.185635 CCTTCTCACCAAAAAGATGCCATAA 59.814 40.000 0.00 0.00 0.00 1.90
5882 5959 4.706476 CCTTCTCACCAAAAAGATGCCATA 59.294 41.667 0.00 0.00 0.00 2.74
5883 5960 3.512724 CCTTCTCACCAAAAAGATGCCAT 59.487 43.478 0.00 0.00 0.00 4.40
6108 6255 2.559998 ATAAAAATGGCCGTCTTGCG 57.440 45.000 0.00 0.00 40.95 4.85
6109 6256 2.929398 CCAATAAAAATGGCCGTCTTGC 59.071 45.455 0.00 0.00 0.00 4.01
6110 6257 3.194542 TCCCAATAAAAATGGCCGTCTTG 59.805 43.478 0.00 0.00 36.58 3.02
6111 6258 3.436243 TCCCAATAAAAATGGCCGTCTT 58.564 40.909 0.00 0.00 36.58 3.01
6112 6259 3.094484 TCCCAATAAAAATGGCCGTCT 57.906 42.857 0.00 0.00 36.58 4.18
6113 6260 4.119136 CAATCCCAATAAAAATGGCCGTC 58.881 43.478 0.00 0.00 36.58 4.79
6114 6261 3.517500 ACAATCCCAATAAAAATGGCCGT 59.482 39.130 0.00 0.00 36.58 5.68
6115 6262 4.119136 GACAATCCCAATAAAAATGGCCG 58.881 43.478 0.00 0.00 36.58 6.13
6116 6263 5.357742 AGACAATCCCAATAAAAATGGCC 57.642 39.130 0.00 0.00 36.58 5.36
6117 6264 8.829612 CAAATAGACAATCCCAATAAAAATGGC 58.170 33.333 0.00 0.00 36.58 4.40
6192 6339 3.006967 GGCTATACAGATGTCAACCGGAT 59.993 47.826 9.46 0.00 0.00 4.18
6211 6358 2.108250 ACAGTATCAGTGGTTTTGGGCT 59.892 45.455 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.