Multiple sequence alignment - TraesCS6B01G157500

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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 TraesCS6B01G157500 chr6B 100.000 3553 0 0 1 3553 159701616 159705168 0.000000e+00 6562.0
1 TraesCS6B01G157500 chr6B 83.351 1916 252 36 819 2684 95237723 95235825 0.000000e+00 1709.0
2 TraesCS6B01G157500 chr6B 82.292 1824 239 34 892 2684 665162313 665160543 0.000000e+00 1502.0
3 TraesCS6B01G157500 chr6B 81.419 1663 245 38 812 2438 711665163 711666797 0.000000e+00 1301.0
4 TraesCS6B01G157500 chr6B 82.562 1015 157 9 908 1904 665417554 665416542 0.000000e+00 876.0
5 TraesCS6B01G157500 chr6B 80.289 969 160 19 1503 2451 142099024 142098067 0.000000e+00 702.0
6 TraesCS6B01G157500 chr6B 86.111 108 12 2 578 684 95238092 95237987 2.900000e-21 113.0
7 TraesCS6B01G157500 chr6D 92.852 2798 135 25 784 3548 84084160 84086925 0.000000e+00 3999.0
8 TraesCS6B01G157500 chr6D 81.564 1573 228 36 901 2438 466544007 466545552 0.000000e+00 1242.0
9 TraesCS6B01G157500 chr6D 89.354 263 18 4 497 759 84083574 84083826 4.420000e-84 322.0
10 TraesCS6B01G157500 chr6D 93.333 75 5 0 400 474 84083504 84083578 1.040000e-20 111.0
11 TraesCS6B01G157500 chr6D 83.168 101 14 3 592 689 466552670 466552570 4.890000e-14 89.8
12 TraesCS6B01G157500 chr6A 92.523 2675 165 17 869 3523 101354085 101356744 0.000000e+00 3799.0
13 TraesCS6B01G157500 chr6A 91.948 2074 129 18 1052 3108 101315185 101317237 0.000000e+00 2870.0
14 TraesCS6B01G157500 chr6A 89.716 457 30 7 3107 3548 101317396 101317850 5.150000e-158 568.0
15 TraesCS6B01G157500 chr6A 88.514 148 15 1 911 1056 101306426 101306573 1.010000e-40 178.0
16 TraesCS6B01G157500 chr2D 83.797 1833 248 27 857 2667 493883369 493881564 0.000000e+00 1694.0
17 TraesCS6B01G157500 chr2A 85.051 1659 220 16 857 2496 639694687 639696336 0.000000e+00 1664.0
18 TraesCS6B01G157500 chr2A 81.631 1018 166 11 922 1925 581965117 581964107 0.000000e+00 824.0
19 TraesCS6B01G157500 chr2A 85.211 142 18 3 583 724 639694302 639694440 3.700000e-30 143.0
20 TraesCS6B01G157500 chr7A 81.025 1913 294 36 812 2682 219396810 219398695 0.000000e+00 1458.0
21 TraesCS6B01G157500 chr5B 83.983 718 88 14 1989 2684 330430315 330431027 0.000000e+00 664.0
22 TraesCS6B01G157500 chr4A 85.294 306 28 10 3099 3399 712810295 712810002 2.070000e-77 300.0
23 TraesCS6B01G157500 chr4A 85.294 306 26 12 3099 3399 712629864 712629573 7.460000e-77 298.0
24 TraesCS6B01G157500 chr4A 85.294 306 26 12 3099 3399 712646891 712646600 7.460000e-77 298.0
25 TraesCS6B01G157500 chr4A 83.279 305 28 17 3099 3398 614706977 614706691 3.520000e-65 259.0
26 TraesCS6B01G157500 chrUn 84.967 306 29 11 3099 3399 326632373 326632666 9.650000e-76 294.0


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 TraesCS6B01G157500 chr6B 159701616 159705168 3552 False 6562.000000 6562 100.000000 1 3553 1 chr6B.!!$F1 3552
1 TraesCS6B01G157500 chr6B 665160543 665162313 1770 True 1502.000000 1502 82.292000 892 2684 1 chr6B.!!$R2 1792
2 TraesCS6B01G157500 chr6B 711665163 711666797 1634 False 1301.000000 1301 81.419000 812 2438 1 chr6B.!!$F2 1626
3 TraesCS6B01G157500 chr6B 95235825 95238092 2267 True 911.000000 1709 84.731000 578 2684 2 chr6B.!!$R4 2106
4 TraesCS6B01G157500 chr6B 665416542 665417554 1012 True 876.000000 876 82.562000 908 1904 1 chr6B.!!$R3 996
5 TraesCS6B01G157500 chr6B 142098067 142099024 957 True 702.000000 702 80.289000 1503 2451 1 chr6B.!!$R1 948
6 TraesCS6B01G157500 chr6D 84083504 84086925 3421 False 1477.333333 3999 91.846333 400 3548 3 chr6D.!!$F2 3148
7 TraesCS6B01G157500 chr6D 466544007 466545552 1545 False 1242.000000 1242 81.564000 901 2438 1 chr6D.!!$F1 1537
8 TraesCS6B01G157500 chr6A 101354085 101356744 2659 False 3799.000000 3799 92.523000 869 3523 1 chr6A.!!$F2 2654
9 TraesCS6B01G157500 chr6A 101315185 101317850 2665 False 1719.000000 2870 90.832000 1052 3548 2 chr6A.!!$F3 2496
10 TraesCS6B01G157500 chr2D 493881564 493883369 1805 True 1694.000000 1694 83.797000 857 2667 1 chr2D.!!$R1 1810
11 TraesCS6B01G157500 chr2A 639694302 639696336 2034 False 903.500000 1664 85.131000 583 2496 2 chr2A.!!$F1 1913
12 TraesCS6B01G157500 chr2A 581964107 581965117 1010 True 824.000000 824 81.631000 922 1925 1 chr2A.!!$R1 1003
13 TraesCS6B01G157500 chr7A 219396810 219398695 1885 False 1458.000000 1458 81.025000 812 2682 1 chr7A.!!$F1 1870
14 TraesCS6B01G157500 chr5B 330430315 330431027 712 False 664.000000 664 83.983000 1989 2684 1 chr5B.!!$F1 695

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
321 322 0.179124 CTGTAGGCGAGACAGGCTTC 60.179 60.0 8.75 0.0 45.21 3.86 F
323 324 0.179124 GTAGGCGAGACAGGCTTCTG 60.179 60.0 0.00 0.0 45.21 3.02 F
1383 1856 0.250513 AGATCACAACGGAGAAGGCC 59.749 55.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1343 1816 0.463654 AAACTCAGCTGCGTCAACCA 60.464 50.000 10.27 0.0 0.0 3.67 R
1445 1918 1.860950 CGAATACATCCGGACAAGCAG 59.139 52.381 6.12 0.0 0.0 4.24 R
2982 3561 1.106285 GAACCACCAATCTGCATCCC 58.894 55.000 0.00 0.0 0.0 3.85 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
41 42 9.072294 ACGCTATATATGTTTCAAAAACTTTGC 57.928 29.630 0.00 0.00 0.00 3.68
42 43 9.071221 CGCTATATATGTTTCAAAAACTTTGCA 57.929 29.630 0.00 0.00 0.00 4.08
72 73 7.693969 TTTTTGAAATGTGGGAACATTTTGT 57.306 28.000 15.73 0.00 46.56 2.83
73 74 6.917217 TTTGAAATGTGGGAACATTTTGTC 57.083 33.333 15.73 6.56 46.56 3.18
74 75 5.604758 TGAAATGTGGGAACATTTTGTCA 57.395 34.783 15.73 8.65 46.56 3.58
75 76 6.172136 TGAAATGTGGGAACATTTTGTCAT 57.828 33.333 15.73 0.00 46.56 3.06
76 77 6.590068 TGAAATGTGGGAACATTTTGTCATT 58.410 32.000 15.73 0.00 46.56 2.57
77 78 6.482641 TGAAATGTGGGAACATTTTGTCATTG 59.517 34.615 15.73 0.00 46.56 2.82
78 79 5.549742 ATGTGGGAACATTTTGTCATTGT 57.450 34.783 0.00 0.00 46.14 2.71
79 80 5.350504 TGTGGGAACATTTTGTCATTGTT 57.649 34.783 0.00 0.00 46.14 2.83
80 81 6.471233 TGTGGGAACATTTTGTCATTGTTA 57.529 33.333 0.00 0.00 46.14 2.41
81 82 6.276847 TGTGGGAACATTTTGTCATTGTTAC 58.723 36.000 0.00 0.00 46.14 2.50
82 83 6.127338 TGTGGGAACATTTTGTCATTGTTACA 60.127 34.615 7.81 0.00 46.14 2.41
83 84 6.758886 GTGGGAACATTTTGTCATTGTTACAA 59.241 34.615 0.00 0.00 46.14 2.41
84 85 7.278868 GTGGGAACATTTTGTCATTGTTACAAA 59.721 33.333 0.66 0.00 46.14 2.83
258 259 5.117355 AGAACGAAATTCTAGTGACGTCA 57.883 39.130 15.76 15.76 46.38 4.35
259 260 5.154932 AGAACGAAATTCTAGTGACGTCAG 58.845 41.667 20.73 7.81 46.38 3.51
260 261 3.243336 ACGAAATTCTAGTGACGTCAGC 58.757 45.455 20.73 13.85 0.00 4.26
261 262 3.242518 CGAAATTCTAGTGACGTCAGCA 58.757 45.455 20.73 8.73 0.00 4.41
262 263 3.859961 CGAAATTCTAGTGACGTCAGCAT 59.140 43.478 20.73 10.74 0.00 3.79
263 264 4.259570 CGAAATTCTAGTGACGTCAGCATG 60.260 45.833 20.73 9.78 37.54 4.06
282 283 4.883026 CGTGAACGTCCTACTGGG 57.117 61.111 0.00 0.00 34.11 4.45
283 284 1.445582 CGTGAACGTCCTACTGGGC 60.446 63.158 0.00 0.00 34.39 5.36
307 308 3.760035 ACCGGCGGTGCTCTGTAG 61.760 66.667 33.71 0.00 32.98 2.74
308 309 4.514577 CCGGCGGTGCTCTGTAGG 62.515 72.222 19.97 0.00 0.00 3.18
311 312 4.129737 GCGGTGCTCTGTAGGCGA 62.130 66.667 0.00 0.00 0.00 5.54
312 313 2.103143 CGGTGCTCTGTAGGCGAG 59.897 66.667 0.00 0.00 0.00 5.03
313 314 2.407428 CGGTGCTCTGTAGGCGAGA 61.407 63.158 0.00 0.00 0.00 4.04
314 315 1.139947 GGTGCTCTGTAGGCGAGAC 59.860 63.158 0.00 0.00 0.00 3.36
315 316 1.595993 GGTGCTCTGTAGGCGAGACA 61.596 60.000 0.00 0.00 0.00 3.41
316 317 0.179150 GTGCTCTGTAGGCGAGACAG 60.179 60.000 9.98 9.98 44.75 3.51
317 318 1.315981 TGCTCTGTAGGCGAGACAGG 61.316 60.000 14.49 8.49 43.76 4.00
318 319 1.435515 CTCTGTAGGCGAGACAGGC 59.564 63.158 14.49 0.00 43.76 4.85
320 321 0.612174 TCTGTAGGCGAGACAGGCTT 60.612 55.000 14.49 0.00 45.21 4.35
321 322 0.179124 CTGTAGGCGAGACAGGCTTC 60.179 60.000 8.75 0.00 45.21 3.86
322 323 0.612174 TGTAGGCGAGACAGGCTTCT 60.612 55.000 0.00 0.00 45.21 2.85
323 324 0.179124 GTAGGCGAGACAGGCTTCTG 60.179 60.000 0.00 0.00 45.21 3.02
324 325 1.949847 TAGGCGAGACAGGCTTCTGC 61.950 60.000 0.00 7.72 45.21 4.26
325 326 2.264166 GCGAGACAGGCTTCTGCT 59.736 61.111 4.31 0.00 42.06 4.24
326 327 1.809209 GCGAGACAGGCTTCTGCTC 60.809 63.158 4.31 0.00 42.06 4.26
327 328 1.515952 CGAGACAGGCTTCTGCTCG 60.516 63.158 17.94 17.94 46.81 5.03
328 329 1.153667 GAGACAGGCTTCTGCTCGG 60.154 63.158 4.31 0.00 42.06 4.63
329 330 2.817396 GACAGGCTTCTGCTCGGC 60.817 66.667 0.00 0.00 42.06 5.54
330 331 4.400961 ACAGGCTTCTGCTCGGCC 62.401 66.667 0.00 0.00 45.57 6.13
333 334 4.537433 GGCTTCTGCTCGGCCGAT 62.537 66.667 31.19 0.00 39.59 4.18
334 335 2.964389 GCTTCTGCTCGGCCGATC 60.964 66.667 31.19 26.15 36.03 3.69
335 336 2.279784 CTTCTGCTCGGCCGATCC 60.280 66.667 31.19 22.60 0.00 3.36
336 337 2.759973 TTCTGCTCGGCCGATCCT 60.760 61.111 31.19 0.00 0.00 3.24
337 338 2.967929 CTTCTGCTCGGCCGATCCTG 62.968 65.000 31.19 24.08 0.00 3.86
348 349 2.832931 CGATCCTGCGGATTCATCC 58.167 57.895 10.72 0.00 43.27 3.51
349 350 0.319728 CGATCCTGCGGATTCATCCT 59.680 55.000 10.72 0.00 43.27 3.24
350 351 1.671261 CGATCCTGCGGATTCATCCTC 60.671 57.143 10.72 0.00 43.27 3.71
351 352 0.689623 ATCCTGCGGATTCATCCTCC 59.310 55.000 4.30 0.00 39.79 4.30
352 353 0.690744 TCCTGCGGATTCATCCTCCA 60.691 55.000 4.30 1.00 44.93 3.86
353 354 0.533755 CCTGCGGATTCATCCTCCAC 60.534 60.000 4.30 0.00 44.93 4.02
354 355 0.877649 CTGCGGATTCATCCTCCACG 60.878 60.000 4.30 0.00 44.93 4.94
355 356 2.247437 GCGGATTCATCCTCCACGC 61.247 63.158 4.30 0.00 44.93 5.34
356 357 1.595382 CGGATTCATCCTCCACGCC 60.595 63.158 4.30 0.00 44.93 5.68
357 358 1.595382 GGATTCATCCTCCACGCCG 60.595 63.158 0.00 0.00 43.73 6.46
358 359 2.203070 ATTCATCCTCCACGCCGC 60.203 61.111 0.00 0.00 0.00 6.53
359 360 3.757248 ATTCATCCTCCACGCCGCC 62.757 63.158 0.00 0.00 0.00 6.13
361 362 4.552365 CATCCTCCACGCCGCCAT 62.552 66.667 0.00 0.00 0.00 4.40
362 363 4.241555 ATCCTCCACGCCGCCATC 62.242 66.667 0.00 0.00 0.00 3.51
434 435 3.016971 CCATCTCCTGCCACCCCA 61.017 66.667 0.00 0.00 0.00 4.96
467 468 1.722636 CGCCGGTCACTACCTCTACC 61.723 65.000 1.90 0.00 44.35 3.18
468 469 0.395448 GCCGGTCACTACCTCTACCT 60.395 60.000 1.90 0.00 44.35 3.08
469 470 1.677942 CCGGTCACTACCTCTACCTC 58.322 60.000 0.00 0.00 44.35 3.85
470 471 1.677942 CGGTCACTACCTCTACCTCC 58.322 60.000 0.00 0.00 44.35 4.30
471 472 1.212441 CGGTCACTACCTCTACCTCCT 59.788 57.143 0.00 0.00 44.35 3.69
472 473 2.657143 GGTCACTACCTCTACCTCCTG 58.343 57.143 0.00 0.00 43.08 3.86
473 474 2.657143 GTCACTACCTCTACCTCCTGG 58.343 57.143 0.00 0.00 39.83 4.45
474 475 5.230333 GGTCACTACCTCTACCTCCTGGT 62.230 56.522 0.00 0.00 45.24 4.00
475 476 2.653366 TCACTACCTCTACCTCCTGGTT 59.347 50.000 0.00 0.00 46.05 3.67
476 477 3.077088 TCACTACCTCTACCTCCTGGTTT 59.923 47.826 0.00 0.00 46.05 3.27
477 478 3.838903 CACTACCTCTACCTCCTGGTTTT 59.161 47.826 0.00 0.00 46.05 2.43
478 479 4.286291 CACTACCTCTACCTCCTGGTTTTT 59.714 45.833 0.00 0.00 46.05 1.94
513 514 3.146104 CCTCCTGGGTTATTATGCCTG 57.854 52.381 0.00 0.00 0.00 4.85
514 515 2.224867 CCTCCTGGGTTATTATGCCTGG 60.225 54.545 0.00 0.00 0.00 4.45
515 516 1.144913 TCCTGGGTTATTATGCCTGGC 59.855 52.381 12.87 12.87 0.00 4.85
516 517 1.145738 CCTGGGTTATTATGCCTGGCT 59.854 52.381 21.03 8.02 0.00 4.75
541 542 3.183574 GGCTGCGTTTTTGGTGAAATAAC 59.816 43.478 0.00 0.00 0.00 1.89
547 548 0.882474 TTTGGTGAAATAACCCCGCG 59.118 50.000 0.00 0.00 39.70 6.46
597 598 4.427096 TCAGATAGGAGATCGATTTCGC 57.573 45.455 9.60 3.62 39.60 4.70
630 632 1.197036 GCGCAGTCCAAAAGGAGTAAC 59.803 52.381 0.30 0.00 0.00 2.50
636 638 6.436261 GCAGTCCAAAAGGAGTAACTTTTAC 58.564 40.000 3.89 1.18 45.96 2.01
644 646 9.683069 CAAAAGGAGTAACTTTTACTCGTAGTA 57.317 33.333 17.26 0.00 45.96 1.82
750 807 1.924524 CGTCCATCGAATAAGTTGCGT 59.075 47.619 0.00 0.00 42.86 5.24
752 809 3.187700 GTCCATCGAATAAGTTGCGTCT 58.812 45.455 0.00 0.00 0.00 4.18
777 834 1.669604 TAGTCTGTTTTGTTGCGCCA 58.330 45.000 4.18 0.00 0.00 5.69
861 1290 2.883730 TCGCCGTAGACGCAATGC 60.884 61.111 0.00 0.00 38.18 3.56
866 1295 0.796312 CCGTAGACGCAATGCAAGTT 59.204 50.000 5.91 0.00 38.18 2.66
867 1296 1.996898 CCGTAGACGCAATGCAAGTTA 59.003 47.619 5.91 0.00 38.18 2.24
974 1423 2.174349 GCGGAAAGCAACTCGCAG 59.826 61.111 9.07 0.00 46.33 5.18
1128 1586 1.091771 CCATGCTCACGCGGATCTTT 61.092 55.000 12.47 0.00 39.65 2.52
1235 1708 5.733676 TGTAACAGATAGCATCTTGAGCAA 58.266 37.500 0.00 0.00 37.58 3.91
1383 1856 0.250513 AGATCACAACGGAGAAGGCC 59.749 55.000 0.00 0.00 0.00 5.19
1445 1918 5.456822 GGAAGCAGTTCAATGATTTTATCGC 59.543 40.000 0.00 0.00 33.93 4.58
1543 2016 0.809385 CATCCTCAGCACTTGCAAGG 59.191 55.000 29.18 18.79 45.16 3.61
1586 2059 1.967066 CTATTGCGACTCAGGGATCCT 59.033 52.381 12.58 0.00 0.00 3.24
2010 2517 6.544197 TGGAACTTGCACTGAGTTTGTATTTA 59.456 34.615 3.86 0.00 37.46 1.40
2381 2891 3.689347 TGTGGAAGCTGCAGTGAATATT 58.311 40.909 16.64 1.04 0.00 1.28
2427 2937 0.884704 GATGTGTGGACGCTGTGGTT 60.885 55.000 0.00 0.00 0.00 3.67
2547 3064 1.396301 CAGCTCTGATTCACTTTCGGC 59.604 52.381 0.00 0.00 0.00 5.54
2565 3082 5.105567 TCGGCCCTAACTGAAAAATGATA 57.894 39.130 0.00 0.00 0.00 2.15
2566 3083 4.879545 TCGGCCCTAACTGAAAAATGATAC 59.120 41.667 0.00 0.00 0.00 2.24
2567 3084 4.638421 CGGCCCTAACTGAAAAATGATACA 59.362 41.667 0.00 0.00 0.00 2.29
2570 3087 6.071616 GGCCCTAACTGAAAAATGATACACAA 60.072 38.462 0.00 0.00 0.00 3.33
2674 3230 2.587522 ACTCTTGCTTTCCCTTCAACC 58.412 47.619 0.00 0.00 0.00 3.77
2704 3274 2.104792 TGAGCCTCCATAATGTAGCACC 59.895 50.000 0.00 0.00 0.00 5.01
2758 3329 4.746729 TGCATTGGAATAAGTTGATGTGC 58.253 39.130 0.00 0.00 0.00 4.57
2778 3349 2.898705 CTCACTGCTTCCATAGTCCAC 58.101 52.381 0.00 0.00 0.00 4.02
2821 3396 4.798387 CAGGAACAACAAACAGTAAGCAAC 59.202 41.667 0.00 0.00 0.00 4.17
2863 3438 4.024048 CGGTTTCTATTTGTGCAGACAGTT 60.024 41.667 0.00 0.00 32.26 3.16
2868 3443 8.342634 GTTTCTATTTGTGCAGACAGTTTAGAA 58.657 33.333 0.00 0.00 32.48 2.10
2871 3446 5.888691 TTTGTGCAGACAGTTTAGAAACA 57.111 34.783 7.82 0.00 41.30 2.83
2872 3447 6.449635 TTTGTGCAGACAGTTTAGAAACAT 57.550 33.333 7.82 0.00 41.30 2.71
2873 3448 6.449635 TTGTGCAGACAGTTTAGAAACATT 57.550 33.333 7.82 0.00 41.30 2.71
2874 3449 7.561021 TTGTGCAGACAGTTTAGAAACATTA 57.439 32.000 7.82 0.00 41.30 1.90
2875 3450 7.744087 TGTGCAGACAGTTTAGAAACATTAT 57.256 32.000 7.82 0.00 41.30 1.28
2876 3451 8.165239 TGTGCAGACAGTTTAGAAACATTATT 57.835 30.769 7.82 0.00 41.30 1.40
2877 3452 8.629158 TGTGCAGACAGTTTAGAAACATTATTT 58.371 29.630 7.82 0.00 41.30 1.40
2910 3485 6.657966 TCTTATCTAGAAAACTGACTCCGTGA 59.342 38.462 0.00 0.00 0.00 4.35
2920 3495 5.860941 ACTGACTCCGTGATGATTAGAAT 57.139 39.130 0.00 0.00 0.00 2.40
2925 3500 9.347934 CTGACTCCGTGATGATTAGAATATTAC 57.652 37.037 0.00 0.00 0.00 1.89
2927 3502 9.862371 GACTCCGTGATGATTAGAATATTACAT 57.138 33.333 0.00 0.00 0.00 2.29
2951 3530 8.815189 CATTTTATCTATGGATATGCACTCTCG 58.185 37.037 0.00 0.00 34.78 4.04
2993 3572 4.851639 AGAAGTACTTGGGATGCAGATT 57.148 40.909 14.14 0.00 0.00 2.40
3005 3584 2.655090 TGCAGATTGGTGGTTCAAGA 57.345 45.000 0.00 0.00 0.00 3.02
3006 3585 2.942804 TGCAGATTGGTGGTTCAAGAA 58.057 42.857 0.00 0.00 0.00 2.52
3037 3616 6.272822 AGACCATCCAACTTATTTTTGCTC 57.727 37.500 0.00 0.00 0.00 4.26
3046 3625 4.578871 ACTTATTTTTGCTCCAATTGGCC 58.421 39.130 20.33 13.15 34.44 5.36
3048 3627 2.252976 TTTTTGCTCCAATTGGCCAC 57.747 45.000 20.33 11.47 34.44 5.01
3250 4000 9.109246 TCTCTTGGATTCATATGACATATCCTT 57.891 33.333 25.22 0.17 36.55 3.36
3251 4001 9.736414 CTCTTGGATTCATATGACATATCCTTT 57.264 33.333 25.22 0.00 36.55 3.11
3307 4057 8.621532 TCACAGAATAATAATCCCATAAGCAC 57.378 34.615 0.00 0.00 0.00 4.40
3321 4071 5.685511 CCCATAAGCACGTGTAAATTAATGC 59.314 40.000 18.38 0.00 0.00 3.56
3342 4092 5.231702 TGCATGGAAATTTGTTCACTCATG 58.768 37.500 0.00 0.00 35.30 3.07
3380 4134 5.296780 TGTGATTGGTCTTGAAAGTCTGTTC 59.703 40.000 0.00 0.00 0.00 3.18
3385 4139 6.419484 TGGTCTTGAAAGTCTGTTCAGATA 57.581 37.500 5.80 0.00 38.69 1.98
3423 4178 3.945346 TGCCTTTTATCGCTGGAAACTA 58.055 40.909 0.00 0.00 0.00 2.24
3436 4191 4.201990 GCTGGAAACTAAGAGATGCATTGG 60.202 45.833 0.00 0.00 0.00 3.16
3481 4236 9.558396 TTGAAAATTTTCCAACTTGCATATCTT 57.442 25.926 24.51 0.00 36.36 2.40
3488 4243 8.537728 TTTCCAACTTGCATATCTTGGATTAT 57.462 30.769 12.95 0.00 41.40 1.28
3536 4294 3.957497 TCTAAATGTGTTTGGTTGCAGGT 59.043 39.130 0.00 0.00 0.00 4.00
3548 4306 2.423577 GTTGCAGGTCGAATGGTAAGT 58.576 47.619 0.00 0.00 0.00 2.24
3549 4307 3.592059 GTTGCAGGTCGAATGGTAAGTA 58.408 45.455 0.00 0.00 0.00 2.24
3550 4308 4.189231 GTTGCAGGTCGAATGGTAAGTAT 58.811 43.478 0.00 0.00 0.00 2.12
3551 4309 4.054780 TGCAGGTCGAATGGTAAGTATC 57.945 45.455 0.00 0.00 0.00 2.24
3552 4310 3.050619 GCAGGTCGAATGGTAAGTATCG 58.949 50.000 0.00 0.00 36.67 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.072294 GCAAAGTTTTTGAAACATATATAGCGT 57.928 29.630 5.77 0.00 0.00 5.07
16 17 9.071221 TGCAAAGTTTTTGAAACATATATAGCG 57.929 29.630 5.77 0.00 0.00 4.26
56 57 5.549742 ACAATGACAAAATGTTCCCACAT 57.450 34.783 0.00 0.00 46.34 3.21
57 58 5.350504 AACAATGACAAAATGTTCCCACA 57.649 34.783 0.00 0.00 32.02 4.17
58 59 6.276847 TGTAACAATGACAAAATGTTCCCAC 58.723 36.000 7.62 3.57 38.22 4.61
59 60 6.471233 TGTAACAATGACAAAATGTTCCCA 57.529 33.333 7.62 4.91 38.22 4.37
60 61 7.778470 TTTGTAACAATGACAAAATGTTCCC 57.222 32.000 7.62 3.00 42.33 3.97
229 230 9.807386 CGTCACTAGAATTTCGTTCTAATTTTT 57.193 29.630 0.00 0.00 46.09 1.94
230 231 8.985805 ACGTCACTAGAATTTCGTTCTAATTTT 58.014 29.630 0.00 0.00 46.09 1.82
231 232 8.530269 ACGTCACTAGAATTTCGTTCTAATTT 57.470 30.769 0.00 0.00 46.09 1.82
232 233 7.811236 TGACGTCACTAGAATTTCGTTCTAATT 59.189 33.333 15.76 0.00 46.09 1.40
233 234 7.310664 TGACGTCACTAGAATTTCGTTCTAAT 58.689 34.615 15.76 0.00 46.09 1.73
234 235 6.671190 TGACGTCACTAGAATTTCGTTCTAA 58.329 36.000 15.76 0.00 46.09 2.10
235 236 6.245115 TGACGTCACTAGAATTTCGTTCTA 57.755 37.500 15.76 0.00 45.28 2.10
237 238 4.201504 GCTGACGTCACTAGAATTTCGTTC 60.202 45.833 15.76 0.00 37.08 3.95
238 239 3.673809 GCTGACGTCACTAGAATTTCGTT 59.326 43.478 15.76 0.00 0.00 3.85
239 240 3.243336 GCTGACGTCACTAGAATTTCGT 58.757 45.455 15.76 0.00 0.00 3.85
240 241 3.242518 TGCTGACGTCACTAGAATTTCG 58.757 45.455 15.76 1.68 0.00 3.46
241 242 4.864806 TCATGCTGACGTCACTAGAATTTC 59.135 41.667 15.76 0.00 0.00 2.17
242 243 4.627467 GTCATGCTGACGTCACTAGAATTT 59.373 41.667 15.76 0.00 37.67 1.82
243 244 4.177026 GTCATGCTGACGTCACTAGAATT 58.823 43.478 15.76 0.00 37.67 2.17
244 245 3.775202 GTCATGCTGACGTCACTAGAAT 58.225 45.455 15.76 2.12 37.67 2.40
245 246 3.217599 GTCATGCTGACGTCACTAGAA 57.782 47.619 15.76 0.00 37.67 2.10
246 247 2.921634 GTCATGCTGACGTCACTAGA 57.078 50.000 15.76 7.61 37.67 2.43
265 266 1.445582 GCCCAGTAGGACGTTCACG 60.446 63.158 0.00 0.00 40.08 4.35
266 267 1.445582 CGCCCAGTAGGACGTTCAC 60.446 63.158 0.00 0.00 38.24 3.18
267 268 1.592400 CTCGCCCAGTAGGACGTTCA 61.592 60.000 0.00 0.00 38.24 3.18
268 269 1.139095 CTCGCCCAGTAGGACGTTC 59.861 63.158 0.00 0.00 38.24 3.95
269 270 3.003113 GCTCGCCCAGTAGGACGTT 62.003 63.158 0.00 0.00 38.24 3.99
270 271 3.450115 GCTCGCCCAGTAGGACGT 61.450 66.667 0.00 0.00 38.24 4.34
271 272 4.208686 GGCTCGCCCAGTAGGACG 62.209 72.222 0.00 0.00 38.24 4.79
290 291 3.760035 CTACAGAGCACCGCCGGT 61.760 66.667 1.02 1.02 35.62 5.28
291 292 4.514577 CCTACAGAGCACCGCCGG 62.515 72.222 0.00 0.00 0.00 6.13
294 295 4.129737 TCGCCTACAGAGCACCGC 62.130 66.667 0.00 0.00 0.00 5.68
295 296 2.103143 CTCGCCTACAGAGCACCG 59.897 66.667 0.00 0.00 0.00 4.94
296 297 1.139947 GTCTCGCCTACAGAGCACC 59.860 63.158 0.00 0.00 35.79 5.01
297 298 0.179150 CTGTCTCGCCTACAGAGCAC 60.179 60.000 5.92 0.00 45.89 4.40
298 299 1.315981 CCTGTCTCGCCTACAGAGCA 61.316 60.000 11.67 0.00 45.89 4.26
299 300 1.435515 CCTGTCTCGCCTACAGAGC 59.564 63.158 11.67 0.00 45.89 4.09
300 301 1.034838 AGCCTGTCTCGCCTACAGAG 61.035 60.000 11.67 0.00 45.89 3.35
301 302 0.612174 AAGCCTGTCTCGCCTACAGA 60.612 55.000 11.67 0.00 45.89 3.41
302 303 0.179124 GAAGCCTGTCTCGCCTACAG 60.179 60.000 0.00 0.00 43.26 2.74
303 304 0.612174 AGAAGCCTGTCTCGCCTACA 60.612 55.000 0.00 0.00 0.00 2.74
304 305 0.179124 CAGAAGCCTGTCTCGCCTAC 60.179 60.000 0.00 0.00 35.70 3.18
305 306 1.949847 GCAGAAGCCTGTCTCGCCTA 61.950 60.000 0.00 0.00 42.35 3.93
306 307 2.977178 CAGAAGCCTGTCTCGCCT 59.023 61.111 0.00 0.00 35.70 5.52
307 308 2.817396 GCAGAAGCCTGTCTCGCC 60.817 66.667 0.00 0.00 42.35 5.54
308 309 1.809209 GAGCAGAAGCCTGTCTCGC 60.809 63.158 0.00 0.00 43.56 5.03
309 310 4.492955 GAGCAGAAGCCTGTCTCG 57.507 61.111 0.00 0.00 43.56 4.04
310 311 1.153667 CCGAGCAGAAGCCTGTCTC 60.154 63.158 0.00 0.00 43.56 3.36
311 312 2.977178 CCGAGCAGAAGCCTGTCT 59.023 61.111 0.00 0.00 43.56 3.41
312 313 2.817396 GCCGAGCAGAAGCCTGTC 60.817 66.667 0.00 0.00 43.56 3.51
313 314 4.400961 GGCCGAGCAGAAGCCTGT 62.401 66.667 0.00 0.00 43.62 4.00
316 317 4.537433 ATCGGCCGAGCAGAAGCC 62.537 66.667 33.87 0.00 43.56 4.35
317 318 2.964389 GATCGGCCGAGCAGAAGC 60.964 66.667 36.69 10.47 36.25 3.86
318 319 2.279784 GGATCGGCCGAGCAGAAG 60.280 66.667 40.53 4.51 36.25 2.85
319 320 2.759973 AGGATCGGCCGAGCAGAA 60.760 61.111 40.53 15.54 43.43 3.02
320 321 3.531207 CAGGATCGGCCGAGCAGA 61.531 66.667 40.53 16.37 43.43 4.26
340 341 2.247437 GCGGCGTGGAGGATGAATC 61.247 63.158 9.37 0.00 0.00 2.52
341 342 2.203070 GCGGCGTGGAGGATGAAT 60.203 61.111 9.37 0.00 0.00 2.57
342 343 4.467084 GGCGGCGTGGAGGATGAA 62.467 66.667 9.37 0.00 0.00 2.57
344 345 4.552365 ATGGCGGCGTGGAGGATG 62.552 66.667 9.37 0.00 0.00 3.51
345 346 4.241555 GATGGCGGCGTGGAGGAT 62.242 66.667 9.10 0.00 0.00 3.24
391 392 3.390521 TAGAGTGGTGCTGGCCGG 61.391 66.667 7.41 7.41 0.00 6.13
392 393 2.125512 GTAGAGTGGTGCTGGCCG 60.126 66.667 0.00 0.00 0.00 6.13
393 394 2.269241 GGTAGAGTGGTGCTGGCC 59.731 66.667 0.00 0.00 0.00 5.36
394 395 1.376037 GTGGTAGAGTGGTGCTGGC 60.376 63.158 0.00 0.00 0.00 4.85
395 396 1.079819 CGTGGTAGAGTGGTGCTGG 60.080 63.158 0.00 0.00 0.00 4.85
396 397 1.738099 GCGTGGTAGAGTGGTGCTG 60.738 63.158 0.00 0.00 0.00 4.41
397 398 2.657237 GCGTGGTAGAGTGGTGCT 59.343 61.111 0.00 0.00 0.00 4.40
398 399 2.434359 GGCGTGGTAGAGTGGTGC 60.434 66.667 0.00 0.00 0.00 5.01
479 480 5.179452 CCCAGGAGGTATTCTCTCAAAAA 57.821 43.478 0.00 0.00 42.10 1.94
480 481 4.844349 CCCAGGAGGTATTCTCTCAAAA 57.156 45.455 0.00 0.00 42.10 2.44
493 494 2.224867 CCAGGCATAATAACCCAGGAGG 60.225 54.545 0.00 0.00 43.78 4.30
494 495 2.815589 GCCAGGCATAATAACCCAGGAG 60.816 54.545 6.55 0.00 0.00 3.69
495 496 1.144913 GCCAGGCATAATAACCCAGGA 59.855 52.381 6.55 0.00 0.00 3.86
511 512 0.530431 AAAAACGCAGCCAAAGCCAG 60.530 50.000 0.00 0.00 41.25 4.85
512 513 0.809241 CAAAAACGCAGCCAAAGCCA 60.809 50.000 0.00 0.00 41.25 4.75
513 514 1.498043 CCAAAAACGCAGCCAAAGCC 61.498 55.000 0.00 0.00 41.25 4.35
514 515 0.809636 ACCAAAAACGCAGCCAAAGC 60.810 50.000 0.00 0.00 40.32 3.51
515 516 0.929615 CACCAAAAACGCAGCCAAAG 59.070 50.000 0.00 0.00 0.00 2.77
516 517 0.532573 TCACCAAAAACGCAGCCAAA 59.467 45.000 0.00 0.00 0.00 3.28
547 548 1.338136 TTCTTCCGCCTCTGGATCCC 61.338 60.000 9.90 0.00 38.00 3.85
554 555 0.322636 TCGACTCTTCTTCCGCCTCT 60.323 55.000 0.00 0.00 0.00 3.69
630 632 9.999009 TCAACAGACATATACTACGAGTAAAAG 57.001 33.333 0.00 0.00 33.89 2.27
636 638 7.921787 ACTTCTCAACAGACATATACTACGAG 58.078 38.462 0.00 0.00 0.00 4.18
644 646 9.376075 CTGATTACAACTTCTCAACAGACATAT 57.624 33.333 0.00 0.00 0.00 1.78
645 647 8.585018 TCTGATTACAACTTCTCAACAGACATA 58.415 33.333 0.00 0.00 0.00 2.29
731 766 3.187700 AGACGCAACTTATTCGATGGAC 58.812 45.455 0.00 0.00 0.00 4.02
734 769 3.843426 GGAGACGCAACTTATTCGATG 57.157 47.619 0.00 0.00 0.00 3.84
750 807 4.451096 GCAACAAAACAGACTAATCGGAGA 59.549 41.667 0.00 0.00 45.75 3.71
752 809 3.185594 CGCAACAAAACAGACTAATCGGA 59.814 43.478 0.00 0.00 0.00 4.55
797 1140 4.887071 TCGGATCAACCTTATTGGATTTGG 59.113 41.667 0.00 0.00 39.71 3.28
867 1296 9.458727 ACATCATCAGACACAAAAGAAGAATAT 57.541 29.630 0.00 0.00 0.00 1.28
936 1383 2.030363 CGTTGCATTTAGCTGGAACCAA 60.030 45.455 0.00 0.00 42.48 3.67
938 1385 1.732405 GCGTTGCATTTAGCTGGAACC 60.732 52.381 0.00 0.00 42.48 3.62
1128 1586 5.546499 ACCTGGAATGGAACTAACACTTAGA 59.454 40.000 0.00 0.00 36.73 2.10
1235 1708 1.627297 GGTGATCTCCGGGCTCCTTT 61.627 60.000 0.00 0.00 0.00 3.11
1343 1816 0.463654 AAACTCAGCTGCGTCAACCA 60.464 50.000 10.27 0.00 0.00 3.67
1445 1918 1.860950 CGAATACATCCGGACAAGCAG 59.139 52.381 6.12 0.00 0.00 4.24
1543 2016 4.524749 GTTAAACGCAAAGACTCCAAGAC 58.475 43.478 0.00 0.00 0.00 3.01
1586 2059 5.932303 GCATGTTCTACTTGGAGTACAGAAA 59.068 40.000 0.00 0.00 31.30 2.52
2427 2937 3.388024 CCTTTGATCTCGGGATCCAAGTA 59.612 47.826 28.07 8.04 43.96 2.24
2734 3305 6.321945 AGCACATCAACTTATTCCAATGCATA 59.678 34.615 0.00 0.00 0.00 3.14
2758 3329 2.234661 TGTGGACTATGGAAGCAGTGAG 59.765 50.000 0.00 0.00 0.00 3.51
2778 3349 6.524734 TCCTGCACTAATCCTTATGTATGTG 58.475 40.000 0.00 0.00 0.00 3.21
2821 3396 2.187946 GGAGGGCGACATGAGTGG 59.812 66.667 0.00 0.00 0.00 4.00
2890 3465 4.765339 TCATCACGGAGTCAGTTTTCTAGA 59.235 41.667 0.00 0.00 41.61 2.43
2895 3470 6.037786 TCTAATCATCACGGAGTCAGTTTT 57.962 37.500 0.00 0.00 41.61 2.43
2925 3500 8.815189 CGAGAGTGCATATCCATAGATAAAATG 58.185 37.037 0.00 0.00 38.47 2.32
2927 3502 7.896811 ACGAGAGTGCATATCCATAGATAAAA 58.103 34.615 0.00 0.00 46.97 1.52
2982 3561 1.106285 GAACCACCAATCTGCATCCC 58.894 55.000 0.00 0.00 0.00 3.85
3018 3597 7.148373 CCAATTGGAGCAAAAATAAGTTGGATG 60.148 37.037 20.50 0.00 35.57 3.51
3032 3611 1.804396 CGTGTGGCCAATTGGAGCAA 61.804 55.000 29.02 3.96 37.39 3.91
3037 3616 2.029470 ACATTTACGTGTGGCCAATTGG 60.029 45.455 20.81 20.81 38.53 3.16
3046 3625 6.533819 TTTGTTCTAGGACATTTACGTGTG 57.466 37.500 4.23 0.00 31.16 3.82
3048 3627 9.702726 CATATTTTGTTCTAGGACATTTACGTG 57.297 33.333 4.23 0.00 0.00 4.49
3190 3934 2.275318 GGCAACTTGATTCTCTCTCGG 58.725 52.381 0.00 0.00 0.00 4.63
3250 4000 8.806429 TTTAATGAGGTCTTCATCTAATGCAA 57.194 30.769 0.00 0.00 45.82 4.08
3251 4001 8.677300 GTTTTAATGAGGTCTTCATCTAATGCA 58.323 33.333 0.00 0.00 45.82 3.96
3287 4037 7.435068 ACACGTGCTTATGGGATTATTATTC 57.565 36.000 17.22 0.00 0.00 1.75
3307 4057 8.655092 ACAAATTTCCATGCATTAATTTACACG 58.345 29.630 17.12 11.08 31.14 4.49
3321 4071 5.786311 ACCATGAGTGAACAAATTTCCATG 58.214 37.500 0.00 0.00 0.00 3.66
3342 4092 3.296628 CAATCACAGCACACGTTTTACC 58.703 45.455 0.00 0.00 0.00 2.85
3404 4159 6.106673 TCTCTTAGTTTCCAGCGATAAAAGG 58.893 40.000 0.00 0.00 0.00 3.11
3410 4165 3.118629 TGCATCTCTTAGTTTCCAGCGAT 60.119 43.478 0.00 0.00 0.00 4.58
3423 4178 3.370840 TTGTAGGCCAATGCATCTCTT 57.629 42.857 5.01 0.00 40.13 2.85
3436 4191 5.596836 TCAATTCCATTGGATTTGTAGGC 57.403 39.130 27.33 0.00 41.24 3.93
3461 4216 6.855763 TCCAAGATATGCAAGTTGGAAAAT 57.144 33.333 16.03 0.00 44.33 1.82
3488 4243 8.999895 AGGCCCAAACTTCTATTACTAATCTAA 58.000 33.333 0.00 0.00 0.00 2.10
3499 4257 5.888161 CACATTTAGAGGCCCAAACTTCTAT 59.112 40.000 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.