Multiple sequence alignment - TraesCS3A01G078400

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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 TraesCS3A01G078400 chr3A 100.000 3510 0 0 1 3510 50729028 50725519 0.000000e+00 6482
1 TraesCS3A01G078400 chr3D 89.875 3526 171 85 38 3510 39326848 39323456 0.000000e+00 4362
2 TraesCS3A01G078400 chr3B 87.003 1862 126 70 1680 3510 62314175 62312399 0.000000e+00 1991
3 TraesCS3A01G078400 chr3B 90.300 1567 80 30 1 1548 62316331 62314818 0.000000e+00 1986
4 TraesCS3A01G078400 chr3B 87.983 724 49 16 2797 3510 62300770 62300075 0.000000e+00 821
5 TraesCS3A01G078400 chr2D 86.111 252 27 6 1243 1493 54487722 54487478 7.470000e-67 265
6 TraesCS3A01G078400 chr2D 85.837 233 30 3 1244 1476 175331641 175331870 9.730000e-61 244
7 TraesCS3A01G078400 chr2B 85.714 252 28 6 1243 1493 85177655 85177411 3.480000e-65 259
8 TraesCS3A01G078400 chr2B 85.317 252 29 6 1243 1493 85074277 85074521 1.620000e-63 254
9 TraesCS3A01G078400 chr2A 85.259 251 31 4 1243 1493 54882637 54882881 1.620000e-63 254
10 TraesCS3A01G078400 chr5A 77.986 427 66 22 1073 1494 645726285 645726688 3.500000e-60 243
11 TraesCS3A01G078400 chr4B 84.519 239 31 5 1244 1482 380653800 380654032 7.580000e-57 231
12 TraesCS3A01G078400 chr4B 75.799 438 70 28 1073 1497 103056375 103055961 4.630000e-44 189
13 TraesCS3A01G078400 chr4A 76.256 438 68 27 1073 1497 521919877 521919463 2.140000e-47 200
14 TraesCS3A01G078400 chr4D 75.626 439 69 29 1073 1497 69680129 69679715 2.150000e-42 183


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 TraesCS3A01G078400 chr3A 50725519 50729028 3509 True 6482.0 6482 100.0000 1 3510 1 chr3A.!!$R1 3509
1 TraesCS3A01G078400 chr3D 39323456 39326848 3392 True 4362.0 4362 89.8750 38 3510 1 chr3D.!!$R1 3472
2 TraesCS3A01G078400 chr3B 62312399 62316331 3932 True 1988.5 1991 88.6515 1 3510 2 chr3B.!!$R2 3509
3 TraesCS3A01G078400 chr3B 62300075 62300770 695 True 821.0 821 87.9830 2797 3510 1 chr3B.!!$R1 713

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
415 433 0.523968 CCGATGTTTGCATTCCAGCG 60.524 55.0 10.33 10.33 37.7 5.18 F
1813 2392 0.106519 AACTTGGCAGCAACTCACCT 60.107 50.0 0.00 0.00 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2906 0.250295 CAGTGGTGCCGAGGAAGAAA 60.250 55.0 0.0 0.0 0.0 2.52 R
3062 3683 0.036010 CCTTGGGTGCGATGACTTCT 60.036 55.0 0.0 0.0 0.0 2.85 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
79 80 9.251792 GTTGTGTCGGTTGTTATACATATATGA 57.748 33.333 19.63 3.73 0.00 2.15
116 117 8.185003 AGTTGTCAAACTTGCATTTTAAAGAC 57.815 30.769 0.00 0.00 44.47 3.01
145 146 4.329462 AGTCCAAAAATGCGCCTTTTTA 57.671 36.364 27.92 15.86 36.45 1.52
147 148 5.304778 AGTCCAAAAATGCGCCTTTTTATT 58.695 33.333 27.92 13.28 36.45 1.40
152 153 7.442666 TCCAAAAATGCGCCTTTTTATTAAGTT 59.557 29.630 27.92 8.30 36.45 2.66
166 167 9.444600 TTTTTATTAAGTTGTGGGAGTAGCTAG 57.555 33.333 0.00 0.00 0.00 3.42
187 188 4.464008 AGCTGAAATTTCTGTGGACTCAA 58.536 39.130 21.66 0.00 0.00 3.02
216 217 7.867403 ACTAAAAATTGCACACTACCAATTCTG 59.133 33.333 0.00 0.00 39.88 3.02
222 223 4.887071 TGCACACTACCAATTCTGAAGTTT 59.113 37.500 0.00 0.00 0.00 2.66
255 256 7.446931 TGAAATGTGCAAGTAGAACCTTATTGA 59.553 33.333 0.00 0.00 0.00 2.57
273 274 3.374220 TGAACTTTTGAGCTTGCATGG 57.626 42.857 1.34 0.00 0.00 3.66
357 375 8.644318 AAGCAATTCTCAATCAATCAATTAGC 57.356 30.769 0.00 0.00 0.00 3.09
358 376 7.778083 AGCAATTCTCAATCAATCAATTAGCA 58.222 30.769 0.00 0.00 0.00 3.49
363 381 8.442632 TTCTCAATCAATCAATTAGCAGTAGG 57.557 34.615 0.00 0.00 0.00 3.18
364 382 6.994496 TCTCAATCAATCAATTAGCAGTAGGG 59.006 38.462 0.00 0.00 0.00 3.53
365 383 6.064060 TCAATCAATCAATTAGCAGTAGGGG 58.936 40.000 0.00 0.00 0.00 4.79
366 384 4.437682 TCAATCAATTAGCAGTAGGGGG 57.562 45.455 0.00 0.00 0.00 5.40
383 401 3.607490 GGGGGTAGGAGTGTAGACATA 57.393 52.381 0.00 0.00 0.00 2.29
384 402 3.498334 GGGGGTAGGAGTGTAGACATAG 58.502 54.545 0.00 0.00 0.00 2.23
387 405 2.892215 GGTAGGAGTGTAGACATAGCCC 59.108 54.545 0.00 0.00 0.00 5.19
400 418 4.074970 GACATAGCCCATGATTTTCCGAT 58.925 43.478 0.00 0.00 38.10 4.18
415 433 0.523968 CCGATGTTTGCATTCCAGCG 60.524 55.000 10.33 10.33 37.70 5.18
427 445 6.185852 TGCATTCCAGCGATGAATATAATG 57.814 37.500 0.06 5.39 37.31 1.90
432 450 7.658179 TTCCAGCGATGAATATAATGTTCTC 57.342 36.000 0.06 0.00 0.00 2.87
447 465 6.482898 AATGTTCTCAGATATGTCTCAGCT 57.517 37.500 0.00 0.00 30.42 4.24
448 466 7.594351 AATGTTCTCAGATATGTCTCAGCTA 57.406 36.000 0.00 0.00 30.42 3.32
449 467 6.631971 TGTTCTCAGATATGTCTCAGCTAG 57.368 41.667 0.00 0.00 30.42 3.42
450 468 5.009510 TGTTCTCAGATATGTCTCAGCTAGC 59.990 44.000 6.62 6.62 30.42 3.42
451 469 4.723309 TCTCAGATATGTCTCAGCTAGCA 58.277 43.478 18.83 0.00 30.42 3.49
452 470 4.761227 TCTCAGATATGTCTCAGCTAGCAG 59.239 45.833 18.83 9.54 30.42 4.24
453 471 3.255395 TCAGATATGTCTCAGCTAGCAGC 59.745 47.826 18.83 3.81 35.14 5.25
454 472 3.005578 CAGATATGTCTCAGCTAGCAGCA 59.994 47.826 18.83 9.19 36.67 4.41
455 473 3.256383 AGATATGTCTCAGCTAGCAGCAG 59.744 47.826 18.83 9.30 45.56 4.24
456 474 1.482954 ATGTCTCAGCTAGCAGCAGA 58.517 50.000 18.83 11.59 45.56 4.26
457 475 1.482954 TGTCTCAGCTAGCAGCAGAT 58.517 50.000 18.83 0.00 45.56 2.90
458 476 1.136500 TGTCTCAGCTAGCAGCAGATG 59.864 52.381 18.83 5.20 45.56 2.90
459 477 1.408340 GTCTCAGCTAGCAGCAGATGA 59.592 52.381 18.83 9.64 45.56 2.92
460 478 1.408340 TCTCAGCTAGCAGCAGATGAC 59.592 52.381 18.83 0.00 45.56 3.06
461 479 1.409790 CTCAGCTAGCAGCAGATGACT 59.590 52.381 18.83 0.00 45.56 3.41
462 480 2.622470 CTCAGCTAGCAGCAGATGACTA 59.378 50.000 18.83 0.00 45.56 2.59
463 481 3.229293 TCAGCTAGCAGCAGATGACTAT 58.771 45.455 18.83 0.00 45.56 2.12
464 482 3.005578 TCAGCTAGCAGCAGATGACTATG 59.994 47.826 18.83 1.24 45.56 2.23
465 483 2.067766 GCTAGCAGCAGATGACTATGC 58.932 52.381 10.63 0.00 41.89 3.14
471 489 3.463944 CAGCAGATGACTATGCATGTGA 58.536 45.455 10.16 0.00 45.01 3.58
530 548 9.174166 AGAACATACATAAAAACACCTGGTATC 57.826 33.333 0.00 0.00 0.00 2.24
626 644 8.897872 AATATCCATCTTTTCCAATCATTTGC 57.102 30.769 0.00 0.00 0.00 3.68
745 765 8.956426 TCCAACAAATTAAAGATACTAGCCAAG 58.044 33.333 0.00 0.00 0.00 3.61
746 766 8.739972 CCAACAAATTAAAGATACTAGCCAAGT 58.260 33.333 0.00 0.00 42.62 3.16
841 862 1.714899 CGGCGGCCAAGAATTACAGG 61.715 60.000 20.71 0.00 0.00 4.00
868 889 4.007644 TGCACCGGAGCACCTCAG 62.008 66.667 23.37 0.00 40.11 3.35
902 923 3.866582 CCCATCGGCTCCACCTCC 61.867 72.222 0.00 0.00 35.61 4.30
994 1015 3.723348 GAGCGTTCGGGTTGCCAC 61.723 66.667 0.00 0.00 0.00 5.01
995 1016 4.250305 AGCGTTCGGGTTGCCACT 62.250 61.111 0.00 0.00 0.00 4.00
996 1017 3.284449 GCGTTCGGGTTGCCACTT 61.284 61.111 0.00 0.00 0.00 3.16
997 1018 2.637025 CGTTCGGGTTGCCACTTG 59.363 61.111 0.00 0.00 0.00 3.16
998 1019 2.335011 GTTCGGGTTGCCACTTGC 59.665 61.111 0.00 0.00 41.77 4.01
999 1020 2.909965 TTCGGGTTGCCACTTGCC 60.910 61.111 0.00 0.00 40.16 4.52
1290 1311 1.598685 CAAGTACCCCAACGGCGTT 60.599 57.895 21.19 21.19 33.26 4.84
1550 1571 1.144057 CCTCCATGAGGGTACGTGC 59.856 63.158 0.00 0.00 45.43 5.34
1551 1572 1.330655 CCTCCATGAGGGTACGTGCT 61.331 60.000 3.01 0.00 45.43 4.40
1552 1573 1.399714 CTCCATGAGGGTACGTGCTA 58.600 55.000 3.01 0.00 38.11 3.49
1553 1574 1.754803 CTCCATGAGGGTACGTGCTAA 59.245 52.381 3.01 0.00 38.11 3.09
1574 1595 1.851053 CGTTCATGCATGTCTCTCTCG 59.149 52.381 25.43 15.46 0.00 4.04
1575 1596 2.200067 GTTCATGCATGTCTCTCTCGG 58.800 52.381 25.43 0.00 0.00 4.63
1577 1598 1.827344 TCATGCATGTCTCTCTCGGTT 59.173 47.619 25.43 0.00 0.00 4.44
1587 2139 2.239907 TCTCTCTCGGTTCTCTCCATCA 59.760 50.000 0.00 0.00 0.00 3.07
1723 2293 9.692325 ATCTTTTGCTCTCTTCTTATTATTGGT 57.308 29.630 0.00 0.00 0.00 3.67
1724 2294 9.520515 TCTTTTGCTCTCTTCTTATTATTGGTT 57.479 29.630 0.00 0.00 0.00 3.67
1725 2295 9.565213 CTTTTGCTCTCTTCTTATTATTGGTTG 57.435 33.333 0.00 0.00 0.00 3.77
1726 2296 6.683974 TGCTCTCTTCTTATTATTGGTTGC 57.316 37.500 0.00 0.00 0.00 4.17
1745 2315 1.494766 CGTTGCGTGTGTGTGGATGA 61.495 55.000 0.00 0.00 0.00 2.92
1766 2336 2.608261 ACAGTGAGTTAAGCTCGACTGC 60.608 50.000 20.83 0.00 45.91 4.40
1767 2337 4.864969 ACAGTGAGTTAAGCTCGACTGCT 61.865 47.826 20.83 0.00 45.91 4.24
1768 2338 6.623443 ACAGTGAGTTAAGCTCGACTGCTC 62.623 50.000 20.83 4.37 45.91 4.26
1769 2339 1.540407 GAGTTAAGCTCGACTGCTCG 58.460 55.000 6.67 0.00 43.24 5.03
1770 2340 1.130749 GAGTTAAGCTCGACTGCTCGA 59.869 52.381 6.67 0.00 46.85 4.04
1783 2353 2.464682 GCTCGAGCAAGCAACTCAT 58.535 52.632 31.91 0.00 42.05 2.90
1797 2376 3.755378 GCAACTCATCTGGTCAATGAACT 59.245 43.478 0.00 0.00 32.96 3.01
1798 2377 4.217118 GCAACTCATCTGGTCAATGAACTT 59.783 41.667 0.00 0.00 32.96 2.66
1805 2384 0.961019 GGTCAATGAACTTGGCAGCA 59.039 50.000 0.00 0.00 41.44 4.41
1810 2389 1.985473 ATGAACTTGGCAGCAACTCA 58.015 45.000 0.00 0.00 0.00 3.41
1813 2392 0.106519 AACTTGGCAGCAACTCACCT 60.107 50.000 0.00 0.00 0.00 4.00
1816 2395 1.165907 TTGGCAGCAACTCACCTTCG 61.166 55.000 0.00 0.00 0.00 3.79
1818 2397 1.571460 GCAGCAACTCACCTTCGTG 59.429 57.895 0.00 0.00 41.72 4.35
1845 2433 6.901615 TCTTTTACCCATGGGATCTTCTTA 57.098 37.500 38.07 14.43 38.96 2.10
1846 2434 6.659824 TCTTTTACCCATGGGATCTTCTTAC 58.340 40.000 38.07 0.00 38.96 2.34
1852 2440 1.893315 TGGGATCTTCTTACCCCCAG 58.107 55.000 0.00 0.00 41.78 4.45
1871 2459 4.952335 CCCAGGAAAGAGACTTGCATTATT 59.048 41.667 0.00 0.00 0.00 1.40
1877 2465 7.127339 AGGAAAGAGACTTGCATTATTACCCTA 59.873 37.037 0.00 0.00 0.00 3.53
1878 2466 7.442666 GGAAAGAGACTTGCATTATTACCCTAG 59.557 40.741 0.00 0.00 0.00 3.02
1879 2467 5.859495 AGAGACTTGCATTATTACCCTAGC 58.141 41.667 0.00 0.00 0.00 3.42
1880 2468 5.604650 AGAGACTTGCATTATTACCCTAGCT 59.395 40.000 0.00 0.00 0.00 3.32
1881 2469 6.782988 AGAGACTTGCATTATTACCCTAGCTA 59.217 38.462 0.00 0.00 0.00 3.32
1904 2492 6.642707 ACAAGCTACATCCTACTAGCTAAG 57.357 41.667 0.00 0.00 44.05 2.18
1953 2545 1.017387 TGTTGCAACATACACGCACA 58.983 45.000 27.96 1.91 34.87 4.57
1954 2546 1.268285 TGTTGCAACATACACGCACAC 60.268 47.619 27.96 0.00 34.87 3.82
1955 2547 1.017387 TTGCAACATACACGCACACA 58.983 45.000 0.00 0.00 34.87 3.72
1956 2548 0.306228 TGCAACATACACGCACACAC 59.694 50.000 0.00 0.00 0.00 3.82
1957 2549 0.721155 GCAACATACACGCACACACG 60.721 55.000 0.00 0.00 39.50 4.49
2134 2738 0.690762 ACCACCACCATCAGTACCAC 59.309 55.000 0.00 0.00 0.00 4.16
2137 2741 0.690762 ACCACCATCAGTACCACCAC 59.309 55.000 0.00 0.00 0.00 4.16
2140 2744 0.690762 ACCATCAGTACCACCACCAC 59.309 55.000 0.00 0.00 0.00 4.16
2149 2753 2.981909 CACCACCACCAGCAGCAG 60.982 66.667 0.00 0.00 0.00 4.24
2292 2899 1.291588 CGGAGACTGCAAGCTCTGT 59.708 57.895 13.55 0.00 38.12 3.41
2299 2906 2.437359 GCAAGCTCTGTCGGCCAT 60.437 61.111 2.24 0.00 0.00 4.40
2513 3126 4.581722 CCAGCAGGACAGGATATGATCCA 61.582 52.174 8.19 0.00 44.82 3.41
2545 3158 6.688073 TGATAATTAGGGCTAGGAGAAAGG 57.312 41.667 0.00 0.00 0.00 3.11
2546 3159 6.151049 TGATAATTAGGGCTAGGAGAAAGGT 58.849 40.000 0.00 0.00 0.00 3.50
2556 3169 2.952116 AGGAGAAAGGTAGCTAGCGAT 58.048 47.619 16.82 9.96 0.00 4.58
2559 3172 3.804873 GGAGAAAGGTAGCTAGCGATTTG 59.195 47.826 16.82 0.00 0.00 2.32
2565 3178 5.793030 AGGTAGCTAGCGATTTGACTATT 57.207 39.130 16.82 0.00 0.00 1.73
2573 3186 2.420022 GCGATTTGACTATTGCCACACT 59.580 45.455 0.00 0.00 0.00 3.55
2574 3187 3.621268 GCGATTTGACTATTGCCACACTA 59.379 43.478 0.00 0.00 0.00 2.74
2594 3207 9.750125 CACACTATAGCTAGTTGATTATTCACA 57.250 33.333 0.00 0.00 35.99 3.58
2627 3246 2.631384 TCAATGGATCGTGGGGGATAT 58.369 47.619 0.00 0.00 0.00 1.63
2672 3291 8.534954 TGTAGATCAGGCTAAATTAGTACAGT 57.465 34.615 1.68 0.00 0.00 3.55
2673 3292 9.636789 TGTAGATCAGGCTAAATTAGTACAGTA 57.363 33.333 1.68 0.00 0.00 2.74
2720 3339 8.906867 TGTAACATACTATTATATAGGCCGGAC 58.093 37.037 5.05 0.00 0.00 4.79
2745 3364 9.810545 ACTAGCTAGAAGAAGAACACAATTATC 57.189 33.333 27.45 0.00 0.00 1.75
2748 3367 9.377312 AGCTAGAAGAAGAACACAATTATCTTC 57.623 33.333 6.64 6.64 45.97 2.87
2824 3445 4.284234 TGTAGGGTGAACTAGGGTGTAAAC 59.716 45.833 0.00 0.00 0.00 2.01
2828 3449 4.284234 GGGTGAACTAGGGTGTAAACTGTA 59.716 45.833 0.00 0.00 0.00 2.74
2922 3543 5.183713 ACTTTTGGATGAATCAATTCGAGCA 59.816 36.000 0.00 0.00 39.62 4.26
2941 3562 5.403766 CGAGCATGGAATACTAGCAACTTAG 59.596 44.000 0.00 0.00 0.00 2.18
2942 3563 5.059833 AGCATGGAATACTAGCAACTTAGC 58.940 41.667 0.00 0.00 0.00 3.09
3010 3631 9.515226 AGTGCATGTACTTTAAAATAAAGAGGA 57.485 29.630 11.03 1.17 0.00 3.71
3040 3661 5.948992 ATGGCTTGTCTTTTGTTCTACTC 57.051 39.130 0.00 0.00 0.00 2.59
3062 3683 3.500289 CCCAGAAAGGTTGGATTCCTTGA 60.500 47.826 3.95 0.00 43.50 3.02
3116 3737 3.427573 TCGAGAGAGACACCCATGTAAA 58.572 45.455 0.00 0.00 35.01 2.01
3131 3752 7.279090 CACCCATGTAAATATGTAGACGAACAA 59.721 37.037 0.00 0.00 32.02 2.83
3153 3774 4.820284 GCAATAAGCTAAGCTAGTTGGG 57.180 45.455 0.00 0.00 38.25 4.12
3162 3783 5.707764 AGCTAAGCTAGTTGGGAAAAAGAAG 59.292 40.000 0.00 0.00 36.99 2.85
3225 3851 0.037447 TGCATGGACACCGATGGAAA 59.963 50.000 0.00 0.00 0.00 3.13
3227 3853 1.950484 GCATGGACACCGATGGAAACT 60.950 52.381 0.00 0.00 0.00 2.66
3246 3872 2.897969 ACTAGTGTGTGTCCCACCTAAG 59.102 50.000 0.00 0.00 43.85 2.18
3249 3875 1.692519 GTGTGTGTCCCACCTAAGAGT 59.307 52.381 0.00 0.00 43.85 3.24
3254 3882 0.108281 GTCCCACCTAAGAGTTCGGC 60.108 60.000 0.00 0.00 0.00 5.54
3268 3896 3.482436 AGTTCGGCACCACAAAATTCTA 58.518 40.909 0.00 0.00 0.00 2.10
3269 3897 4.079253 AGTTCGGCACCACAAAATTCTAT 58.921 39.130 0.00 0.00 0.00 1.98
3270 3898 4.082787 AGTTCGGCACCACAAAATTCTATG 60.083 41.667 0.00 0.00 0.00 2.23
3271 3899 3.417101 TCGGCACCACAAAATTCTATGT 58.583 40.909 0.00 0.00 0.00 2.29
3272 3900 4.580868 TCGGCACCACAAAATTCTATGTA 58.419 39.130 0.00 0.00 0.00 2.29
3273 3901 4.634004 TCGGCACCACAAAATTCTATGTAG 59.366 41.667 0.00 0.00 0.00 2.74
3274 3902 4.634004 CGGCACCACAAAATTCTATGTAGA 59.366 41.667 0.00 0.00 0.00 2.59
3275 3903 5.220662 CGGCACCACAAAATTCTATGTAGAG 60.221 44.000 0.00 0.00 33.21 2.43
3276 3904 5.449177 GGCACCACAAAATTCTATGTAGAGC 60.449 44.000 0.00 0.00 33.21 4.09
3277 3905 5.123820 GCACCACAAAATTCTATGTAGAGCA 59.876 40.000 0.00 0.00 33.21 4.26
3278 3906 6.183360 GCACCACAAAATTCTATGTAGAGCAT 60.183 38.462 0.00 0.00 41.42 3.79
3279 3907 7.191551 CACCACAAAATTCTATGTAGAGCATG 58.808 38.462 0.00 0.00 38.47 4.06
3280 3908 7.066163 CACCACAAAATTCTATGTAGAGCATGA 59.934 37.037 0.00 0.00 38.47 3.07
3281 3909 7.611467 ACCACAAAATTCTATGTAGAGCATGAA 59.389 33.333 0.00 0.00 38.47 2.57
3282 3910 8.461222 CCACAAAATTCTATGTAGAGCATGAAA 58.539 33.333 0.00 0.00 38.47 2.69
3283 3911 9.844790 CACAAAATTCTATGTAGAGCATGAAAA 57.155 29.630 0.00 0.00 38.47 2.29
3284 3912 9.846248 ACAAAATTCTATGTAGAGCATGAAAAC 57.154 29.630 0.00 0.00 38.47 2.43
3285 3913 9.844790 CAAAATTCTATGTAGAGCATGAAAACA 57.155 29.630 0.00 0.00 38.47 2.83
3294 3922 7.592938 TGTAGAGCATGAAAACATTTTACTGG 58.407 34.615 0.00 0.00 0.00 4.00
3348 3976 9.183368 ACCAAAAATCAAATTACAAACACCATT 57.817 25.926 0.00 0.00 0.00 3.16
3402 4034 3.949754 TCTCCATACGTAGGTTGAATCGT 59.050 43.478 6.48 0.00 39.74 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 8.129211 GCAAGTTTGACAACTAGTTTCTATTGT 58.871 33.333 5.07 0.00 42.89 2.71
116 117 2.977169 CGCATTTTTGGACTTAACACGG 59.023 45.455 0.00 0.00 0.00 4.94
145 146 4.717280 AGCTAGCTACTCCCACAACTTAAT 59.283 41.667 17.69 0.00 0.00 1.40
147 148 3.447586 CAGCTAGCTACTCCCACAACTTA 59.552 47.826 18.86 0.00 0.00 2.24
152 153 2.231716 TTCAGCTAGCTACTCCCACA 57.768 50.000 18.86 0.00 0.00 4.17
166 167 4.836125 TTGAGTCCACAGAAATTTCAGC 57.164 40.909 19.99 0.00 0.00 4.26
222 223 5.610398 TCTACTTGCACATTTCAAGAGTGA 58.390 37.500 9.40 2.66 42.52 3.41
233 234 6.942576 AGTTCAATAAGGTTCTACTTGCACAT 59.057 34.615 0.00 0.00 32.02 3.21
241 242 8.100508 AGCTCAAAAGTTCAATAAGGTTCTAC 57.899 34.615 0.00 0.00 0.00 2.59
255 256 1.413445 TGCCATGCAAGCTCAAAAGTT 59.587 42.857 12.69 0.00 34.76 2.66
363 381 2.473576 ATGTCTACACTCCTACCCCC 57.526 55.000 0.00 0.00 0.00 5.40
364 382 2.892215 GCTATGTCTACACTCCTACCCC 59.108 54.545 0.00 0.00 0.00 4.95
365 383 2.892215 GGCTATGTCTACACTCCTACCC 59.108 54.545 0.00 0.00 0.00 3.69
366 384 2.892215 GGGCTATGTCTACACTCCTACC 59.108 54.545 0.00 0.00 0.00 3.18
367 385 3.563223 TGGGCTATGTCTACACTCCTAC 58.437 50.000 0.00 0.00 0.00 3.18
368 386 3.965470 TGGGCTATGTCTACACTCCTA 57.035 47.619 0.00 0.00 0.00 2.94
369 387 2.848678 TGGGCTATGTCTACACTCCT 57.151 50.000 0.00 0.00 0.00 3.69
370 388 2.965831 TCATGGGCTATGTCTACACTCC 59.034 50.000 10.81 0.00 38.01 3.85
371 389 4.881019 ATCATGGGCTATGTCTACACTC 57.119 45.455 10.81 0.00 38.01 3.51
375 393 4.452455 CGGAAAATCATGGGCTATGTCTAC 59.548 45.833 10.81 1.03 38.01 2.59
383 401 2.442236 ACATCGGAAAATCATGGGCT 57.558 45.000 0.00 0.00 0.00 5.19
384 402 3.189285 CAAACATCGGAAAATCATGGGC 58.811 45.455 0.00 0.00 0.00 5.36
387 405 5.005971 GGAATGCAAACATCGGAAAATCATG 59.994 40.000 0.00 0.00 34.62 3.07
400 418 1.532523 TCATCGCTGGAATGCAAACA 58.467 45.000 0.00 0.00 0.00 2.83
427 445 5.009510 TGCTAGCTGAGACATATCTGAGAAC 59.990 44.000 17.23 0.00 38.39 3.01
432 450 3.005578 TGCTGCTAGCTGAGACATATCTG 59.994 47.826 24.19 0.00 42.97 2.90
443 461 3.318886 CATAGTCATCTGCTGCTAGCTG 58.681 50.000 17.23 16.92 42.97 4.24
444 462 2.288948 GCATAGTCATCTGCTGCTAGCT 60.289 50.000 17.23 0.00 42.97 3.32
445 463 2.067766 GCATAGTCATCTGCTGCTAGC 58.932 52.381 8.10 8.10 42.82 3.42
446 464 3.382048 TGCATAGTCATCTGCTGCTAG 57.618 47.619 0.00 0.00 39.16 3.42
447 465 3.070590 ACATGCATAGTCATCTGCTGCTA 59.929 43.478 0.00 0.00 39.16 3.49
448 466 2.158798 ACATGCATAGTCATCTGCTGCT 60.159 45.455 0.00 0.00 39.16 4.24
449 467 2.031944 CACATGCATAGTCATCTGCTGC 60.032 50.000 0.00 0.00 39.16 5.25
450 468 3.463944 TCACATGCATAGTCATCTGCTG 58.536 45.455 0.00 0.00 39.16 4.41
451 469 3.832615 TCACATGCATAGTCATCTGCT 57.167 42.857 0.00 0.00 39.16 4.24
452 470 4.784329 CATTCACATGCATAGTCATCTGC 58.216 43.478 0.00 0.00 38.87 4.26
483 501 8.152898 TGTTCTCATTGACTCCATATTCCTATG 58.847 37.037 0.00 0.00 35.47 2.23
626 644 6.380995 TGAATGGACGAAGAAATCAATTGTG 58.619 36.000 5.13 0.00 0.00 3.33
736 756 3.614399 GTGCTCACACTTGGCTAGT 57.386 52.632 0.00 0.00 43.85 2.57
746 766 0.673437 TCACGTCATCAGTGCTCACA 59.327 50.000 2.63 0.00 39.31 3.58
802 822 1.967066 GGTGACGAGAGGGATGATGAT 59.033 52.381 0.00 0.00 0.00 2.45
867 888 1.202568 GGGTACGGTTATAAAGGCGCT 60.203 52.381 7.64 0.00 0.00 5.92
868 889 1.220529 GGGTACGGTTATAAAGGCGC 58.779 55.000 0.00 0.00 0.00 6.53
905 926 4.177783 GAGACGGAGGAGAACTGAAATTC 58.822 47.826 0.00 0.00 0.00 2.17
991 1012 0.460109 TCGATCGTCATGGCAAGTGG 60.460 55.000 15.94 0.00 0.00 4.00
992 1013 0.926155 CTCGATCGTCATGGCAAGTG 59.074 55.000 15.94 0.00 0.00 3.16
993 1014 0.807667 GCTCGATCGTCATGGCAAGT 60.808 55.000 15.94 0.00 0.00 3.16
994 1015 0.529337 AGCTCGATCGTCATGGCAAG 60.529 55.000 15.94 3.34 0.00 4.01
995 1016 0.807275 CAGCTCGATCGTCATGGCAA 60.807 55.000 15.94 0.00 0.00 4.52
996 1017 1.227060 CAGCTCGATCGTCATGGCA 60.227 57.895 15.94 0.00 0.00 4.92
997 1018 2.593134 GCAGCTCGATCGTCATGGC 61.593 63.158 15.94 12.24 0.00 4.40
998 1019 1.213733 CTGCAGCTCGATCGTCATGG 61.214 60.000 15.94 3.77 0.00 3.66
999 1020 0.248784 TCTGCAGCTCGATCGTCATG 60.249 55.000 15.94 12.62 0.00 3.07
1431 1452 3.276857 CATGATCCAGTTGGTCTTGAGG 58.723 50.000 0.00 0.00 36.34 3.86
1549 1570 2.932614 AGAGACATGCATGAACGTTAGC 59.067 45.455 32.75 6.85 0.00 3.09
1550 1571 4.428209 AGAGAGACATGCATGAACGTTAG 58.572 43.478 32.75 4.14 0.00 2.34
1551 1572 4.424626 GAGAGAGACATGCATGAACGTTA 58.575 43.478 32.75 0.00 0.00 3.18
1552 1573 3.257393 GAGAGAGACATGCATGAACGTT 58.743 45.455 32.75 17.26 0.00 3.99
1553 1574 2.733542 CGAGAGAGACATGCATGAACGT 60.734 50.000 32.75 10.70 0.00 3.99
1574 1595 7.554118 TGAAGATACAAAATGATGGAGAGAACC 59.446 37.037 0.00 0.00 0.00 3.62
1575 1596 8.498054 TGAAGATACAAAATGATGGAGAGAAC 57.502 34.615 0.00 0.00 0.00 3.01
1577 1598 9.690913 AAATGAAGATACAAAATGATGGAGAGA 57.309 29.630 0.00 0.00 0.00 3.10
1721 2291 2.650602 CACACACGCAACGCAACC 60.651 61.111 0.00 0.00 0.00 3.77
1722 2292 2.099446 ACACACACGCAACGCAAC 59.901 55.556 0.00 0.00 0.00 4.17
1723 2293 2.099254 CACACACACGCAACGCAA 59.901 55.556 0.00 0.00 0.00 4.85
1724 2294 3.870422 CCACACACACGCAACGCA 61.870 61.111 0.00 0.00 0.00 5.24
1725 2295 2.892334 ATCCACACACACGCAACGC 61.892 57.895 0.00 0.00 0.00 4.84
1726 2296 1.082821 CATCCACACACACGCAACG 60.083 57.895 0.00 0.00 0.00 4.10
1745 2315 2.608261 GCAGTCGAGCTTAACTCACTGT 60.608 50.000 21.17 0.00 45.91 3.55
1765 2335 0.373024 GATGAGTTGCTTGCTCGAGC 59.627 55.000 30.42 30.42 43.00 5.03
1766 2336 1.659601 CAGATGAGTTGCTTGCTCGAG 59.340 52.381 8.45 8.45 35.85 4.04
1767 2337 1.673923 CCAGATGAGTTGCTTGCTCGA 60.674 52.381 0.00 0.00 35.85 4.04
1768 2338 0.725686 CCAGATGAGTTGCTTGCTCG 59.274 55.000 0.00 0.00 35.85 5.03
1769 2339 1.736681 GACCAGATGAGTTGCTTGCTC 59.263 52.381 0.00 0.00 0.00 4.26
1770 2340 1.072806 TGACCAGATGAGTTGCTTGCT 59.927 47.619 0.00 0.00 0.00 3.91
1783 2353 2.507484 CTGCCAAGTTCATTGACCAGA 58.493 47.619 0.00 0.00 41.83 3.86
1797 2376 1.165907 CGAAGGTGAGTTGCTGCCAA 61.166 55.000 0.00 0.00 0.00 4.52
1798 2377 1.597854 CGAAGGTGAGTTGCTGCCA 60.598 57.895 0.00 0.00 0.00 4.92
1813 2392 3.570550 CCATGGGTAAAAGAAACCACGAA 59.429 43.478 2.85 0.00 38.87 3.85
1816 2395 3.502356 TCCCATGGGTAAAAGAAACCAC 58.498 45.455 30.28 0.00 38.87 4.16
1818 2397 4.610333 AGATCCCATGGGTAAAAGAAACC 58.390 43.478 30.28 0.00 36.47 3.27
1845 2433 1.068121 CAAGTCTCTTTCCTGGGGGT 58.932 55.000 0.00 0.00 0.00 4.95
1846 2434 0.322906 GCAAGTCTCTTTCCTGGGGG 60.323 60.000 0.00 0.00 0.00 5.40
1852 2440 6.122964 AGGGTAATAATGCAAGTCTCTTTCC 58.877 40.000 0.00 0.00 0.00 3.13
1878 2466 4.800784 GCTAGTAGGATGTAGCTTGTAGC 58.199 47.826 0.00 0.00 42.84 3.58
1891 2479 4.165565 TGACAGGTAGCTTAGCTAGTAGGA 59.834 45.833 14.87 0.00 42.11 2.94
1904 2492 2.386661 TGCTAAGCTTGACAGGTAGC 57.613 50.000 9.86 8.74 37.66 3.58
1918 2510 2.540769 GCAACAAACAGTCGCTTGCTAA 60.541 45.455 0.00 0.00 35.41 3.09
1953 2545 2.029290 GGAGAATCAGTACCACACGTGT 60.029 50.000 17.22 17.22 36.25 4.49
1954 2546 2.231478 AGGAGAATCAGTACCACACGTG 59.769 50.000 15.48 15.48 36.25 4.49
1955 2547 2.526432 AGGAGAATCAGTACCACACGT 58.474 47.619 0.00 0.00 36.25 4.49
1956 2548 3.254060 CAAGGAGAATCAGTACCACACG 58.746 50.000 0.00 0.00 36.25 4.49
1957 2549 3.997021 CACAAGGAGAATCAGTACCACAC 59.003 47.826 0.00 0.00 36.25 3.82
1964 2556 2.089980 GCATGCACAAGGAGAATCAGT 58.910 47.619 14.21 0.00 36.25 3.41
1993 2594 2.109126 GCAGAGCACCCAATCGTCC 61.109 63.158 0.00 0.00 0.00 4.79
2074 2675 4.124351 TCCATGGACGACCGCGAC 62.124 66.667 11.44 0.00 41.64 5.19
2075 2676 4.124351 GTCCATGGACGACCGCGA 62.124 66.667 28.52 0.00 41.64 5.87
2134 2738 4.960866 TGCTGCTGCTGGTGGTGG 62.961 66.667 17.00 0.00 40.48 4.61
2149 2753 2.331132 GGTGTCCTCTTGCTGCTGC 61.331 63.158 8.89 8.89 40.20 5.25
2292 2899 1.220749 CCGAGGAAGAAATGGCCGA 59.779 57.895 0.00 0.00 0.00 5.54
2299 2906 0.250295 CAGTGGTGCCGAGGAAGAAA 60.250 55.000 0.00 0.00 0.00 2.52
2513 3126 5.850046 AGCCCTAATTATCAAGGTAGCAT 57.150 39.130 0.00 0.00 0.00 3.79
2521 3134 6.619852 ACCTTTCTCCTAGCCCTAATTATCAA 59.380 38.462 0.00 0.00 0.00 2.57
2524 3137 6.213802 GCTACCTTTCTCCTAGCCCTAATTAT 59.786 42.308 0.00 0.00 0.00 1.28
2545 3158 4.150804 GGCAATAGTCAAATCGCTAGCTAC 59.849 45.833 13.93 1.52 0.00 3.58
2546 3159 4.202212 TGGCAATAGTCAAATCGCTAGCTA 60.202 41.667 13.93 1.26 0.00 3.32
2556 3169 5.989477 AGCTATAGTGTGGCAATAGTCAAA 58.011 37.500 0.84 0.00 36.65 2.69
2559 3172 6.334102 ACTAGCTATAGTGTGGCAATAGTC 57.666 41.667 0.84 0.27 40.84 2.59
2565 3178 5.614324 AATCAACTAGCTATAGTGTGGCA 57.386 39.130 0.84 0.00 41.54 4.92
2573 3186 9.645059 GCATCTGTGAATAATCAACTAGCTATA 57.355 33.333 0.00 0.00 37.30 1.31
2574 3187 7.605691 GGCATCTGTGAATAATCAACTAGCTAT 59.394 37.037 0.00 0.00 37.30 2.97
2594 3207 1.620323 TCCATTGATCGATCGGCATCT 59.380 47.619 20.03 2.50 0.00 2.90
2618 3237 7.952847 ATGCATGAGTAATATATATCCCCCA 57.047 36.000 0.00 0.00 0.00 4.96
2703 3322 7.451732 TCTAGCTAGTCCGGCCTATATAATAG 58.548 42.308 20.10 0.00 0.00 1.73
2707 3326 5.427806 TCTTCTAGCTAGTCCGGCCTATATA 59.572 44.000 20.10 0.00 0.00 0.86
2708 3327 4.227754 TCTTCTAGCTAGTCCGGCCTATAT 59.772 45.833 20.10 0.00 0.00 0.86
2709 3328 3.586174 TCTTCTAGCTAGTCCGGCCTATA 59.414 47.826 20.10 0.00 0.00 1.31
2745 3364 8.177119 ACAATCAGTTCTAGCTATCTAGGAAG 57.823 38.462 0.00 0.00 42.01 3.46
2747 3366 8.661345 TCTACAATCAGTTCTAGCTATCTAGGA 58.339 37.037 0.00 0.00 42.01 2.94
2748 3367 8.856153 TCTACAATCAGTTCTAGCTATCTAGG 57.144 38.462 0.00 0.00 42.01 3.02
2922 3543 5.471456 GCATGCTAAGTTGCTAGTATTCCAT 59.529 40.000 11.37 0.00 35.95 3.41
2942 3563 3.890756 TCCCCTAACATAAAGCATGCATG 59.109 43.478 22.70 22.70 38.29 4.06
3040 3661 2.827921 CAAGGAATCCAACCTTTCTGGG 59.172 50.000 0.61 0.00 44.13 4.45
3062 3683 0.036010 CCTTGGGTGCGATGACTTCT 60.036 55.000 0.00 0.00 0.00 2.85
3116 3737 7.178712 GCTTATTGCTTGTTCGTCTACATAT 57.821 36.000 0.00 0.00 38.95 1.78
3191 3817 3.096852 CCATGCATGGGAATATCAGCAT 58.903 45.455 34.31 0.00 44.31 3.79
3246 3872 2.293399 AGAATTTTGTGGTGCCGAACTC 59.707 45.455 0.00 0.00 0.00 3.01
3249 3875 3.823873 ACATAGAATTTTGTGGTGCCGAA 59.176 39.130 0.00 0.00 0.00 4.30
3254 3882 6.741992 TGCTCTACATAGAATTTTGTGGTG 57.258 37.500 0.00 0.00 0.00 4.17
3268 3896 8.246180 CCAGTAAAATGTTTTCATGCTCTACAT 58.754 33.333 0.00 0.00 40.79 2.29
3269 3897 7.446931 TCCAGTAAAATGTTTTCATGCTCTACA 59.553 33.333 0.00 0.00 40.79 2.74
3270 3898 7.816640 TCCAGTAAAATGTTTTCATGCTCTAC 58.183 34.615 0.00 0.00 40.79 2.59
3271 3899 7.994425 TCCAGTAAAATGTTTTCATGCTCTA 57.006 32.000 0.00 0.00 40.79 2.43
3272 3900 6.899393 TCCAGTAAAATGTTTTCATGCTCT 57.101 33.333 0.00 0.00 40.79 4.09
3273 3901 7.945033 TTTCCAGTAAAATGTTTTCATGCTC 57.055 32.000 0.00 0.00 40.79 4.26
3274 3902 8.729805 TTTTTCCAGTAAAATGTTTTCATGCT 57.270 26.923 0.00 0.00 40.79 3.79
3275 3903 8.825745 TCTTTTTCCAGTAAAATGTTTTCATGC 58.174 29.630 0.00 0.00 40.79 4.06
3277 3905 9.883142 TGTCTTTTTCCAGTAAAATGTTTTCAT 57.117 25.926 0.00 0.00 43.05 2.57
3278 3906 9.712305 TTGTCTTTTTCCAGTAAAATGTTTTCA 57.288 25.926 0.00 0.00 36.94 2.69
3282 3910 9.325198 GGATTTGTCTTTTTCCAGTAAAATGTT 57.675 29.630 0.00 0.00 36.94 2.71
3283 3911 8.482128 TGGATTTGTCTTTTTCCAGTAAAATGT 58.518 29.630 0.00 0.00 36.94 2.71
3284 3912 8.885494 TGGATTTGTCTTTTTCCAGTAAAATG 57.115 30.769 0.00 0.00 36.94 2.32
3285 3913 9.325198 GTTGGATTTGTCTTTTTCCAGTAAAAT 57.675 29.630 0.00 0.00 39.33 1.82
3286 3914 8.536175 AGTTGGATTTGTCTTTTTCCAGTAAAA 58.464 29.630 0.00 0.00 39.33 1.52
3287 3915 8.073467 AGTTGGATTTGTCTTTTTCCAGTAAA 57.927 30.769 0.00 0.00 39.33 2.01
3288 3916 7.654022 AGTTGGATTTGTCTTTTTCCAGTAA 57.346 32.000 0.00 0.00 39.33 2.24
3289 3917 8.792633 CATAGTTGGATTTGTCTTTTTCCAGTA 58.207 33.333 0.00 0.00 39.33 2.74
3290 3918 7.505585 TCATAGTTGGATTTGTCTTTTTCCAGT 59.494 33.333 0.00 0.00 39.33 4.00
3291 3919 7.885297 TCATAGTTGGATTTGTCTTTTTCCAG 58.115 34.615 0.00 0.00 39.33 3.86
3292 3920 7.831691 TCATAGTTGGATTTGTCTTTTTCCA 57.168 32.000 0.00 0.00 36.49 3.53
3475 4108 3.631686 GCCAATGCACAATATCACCACTA 59.368 43.478 0.00 0.00 37.47 2.74


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

AutoCloner maintained by Alex Coulton.