Multiple sequence alignment - TraesCS5D01G513000

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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 TraesCS5D01G513000 chr5D 100.000 3323 0 0 1 3323 537163607 537160285 0.000000e+00 6137.0
1 TraesCS5D01G513000 chr5D 94.488 2032 59 30 554 2550 537087879 537089892 0.000000e+00 3083.0
2 TraesCS5D01G513000 chr4A 92.546 2777 105 34 583 3323 632989561 632992271 0.000000e+00 3888.0
3 TraesCS5D01G513000 chr4A 94.477 2028 67 20 373 2378 633000217 632998213 0.000000e+00 3083.0
4 TraesCS5D01G513000 chr4A 84.571 1575 214 23 734 2293 685834814 685836374 0.000000e+00 1535.0
5 TraesCS5D01G513000 chr4A 84.951 206 24 2 46 244 632988538 632988743 5.620000e-48 202.0
6 TraesCS5D01G513000 chr4A 78.549 317 38 19 241 537 632989077 632989383 7.320000e-42 182.0
7 TraesCS5D01G513000 chr5B 94.298 2087 76 21 384 2449 677537104 677539168 0.000000e+00 3155.0
8 TraesCS5D01G513000 chr5B 95.669 1824 46 13 533 2334 677545254 677543442 0.000000e+00 2900.0
9 TraesCS5D01G513000 chr5B 82.971 1562 224 31 734 2263 643460757 643462308 0.000000e+00 1373.0
10 TraesCS5D01G513000 chr5B 85.573 506 40 18 2823 3316 677539466 677539950 1.780000e-137 499.0
11 TraesCS5D01G513000 chr5B 81.459 329 31 21 2487 2804 677539179 677539488 3.310000e-60 243.0
12 TraesCS5D01G513000 chr5B 83.010 206 28 4 46 244 677535172 677535377 2.630000e-41 180.0
13 TraesCS5D01G513000 chr5B 100.000 28 0 0 2790 2817 677539385 677539412 6.000000e-03 52.8
14 TraesCS5D01G513000 chr4D 84.929 1546 215 16 734 2268 479540668 479542206 0.000000e+00 1548.0
15 TraesCS5D01G513000 chr4B 84.298 1573 222 20 734 2293 606764722 606766282 0.000000e+00 1513.0
16 TraesCS5D01G513000 chr4B 81.392 1537 248 32 750 2256 624862933 624861405 0.000000e+00 1219.0
17 TraesCS5D01G513000 chr2A 82.656 1551 227 29 739 2263 18358280 18359814 0.000000e+00 1336.0


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 TraesCS5D01G513000 chr5D 537160285 537163607 3322 True 6137.00 6137 100.000000 1 3323 1 chr5D.!!$R1 3322
1 TraesCS5D01G513000 chr5D 537087879 537089892 2013 False 3083.00 3083 94.488000 554 2550 1 chr5D.!!$F1 1996
2 TraesCS5D01G513000 chr4A 632998213 633000217 2004 True 3083.00 3083 94.477000 373 2378 1 chr4A.!!$R1 2005
3 TraesCS5D01G513000 chr4A 685834814 685836374 1560 False 1535.00 1535 84.571000 734 2293 1 chr4A.!!$F1 1559
4 TraesCS5D01G513000 chr4A 632988538 632992271 3733 False 1424.00 3888 85.348667 46 3323 3 chr4A.!!$F2 3277
5 TraesCS5D01G513000 chr5B 677543442 677545254 1812 True 2900.00 2900 95.669000 533 2334 1 chr5B.!!$R1 1801
6 TraesCS5D01G513000 chr5B 643460757 643462308 1551 False 1373.00 1373 82.971000 734 2263 1 chr5B.!!$F1 1529
7 TraesCS5D01G513000 chr5B 677535172 677539950 4778 False 825.96 3155 88.868000 46 3316 5 chr5B.!!$F2 3270
8 TraesCS5D01G513000 chr4D 479540668 479542206 1538 False 1548.00 1548 84.929000 734 2268 1 chr4D.!!$F1 1534
9 TraesCS5D01G513000 chr4B 606764722 606766282 1560 False 1513.00 1513 84.298000 734 2293 1 chr4B.!!$F1 1559
10 TraesCS5D01G513000 chr4B 624861405 624862933 1528 True 1219.00 1219 81.392000 750 2256 1 chr4B.!!$R1 1506
11 TraesCS5D01G513000 chr2A 18358280 18359814 1534 False 1336.00 1336 82.656000 739 2263 1 chr2A.!!$F1 1524

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
41 42 0.034896 CGTTGCTTGGGTGAGTACCT 59.965 55.0 0.00 0.0 46.66 3.08 F
321 666 0.541764 GGGGCCCACACTGAAATTCA 60.542 55.0 26.86 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 3928 3.371097 GAAGATCTCGGCGGGCACA 62.371 63.158 7.21 0.0 0.00 4.57 R
2385 4338 7.414098 CCCAACAAATTACGGATCTTTGACTAG 60.414 40.741 10.39 0.0 34.69 2.57 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
26 27 2.639286 GGCACTGCCTCAACGTTG 59.361 61.111 22.35 22.35 46.69 4.10
27 28 2.050985 GCACTGCCTCAACGTTGC 60.051 61.111 23.47 12.65 0.00 4.17
28 29 2.546494 GCACTGCCTCAACGTTGCT 61.546 57.895 23.47 0.00 0.00 3.91
29 30 2.024918 CACTGCCTCAACGTTGCTT 58.975 52.632 23.47 1.04 0.00 3.91
30 31 0.317269 CACTGCCTCAACGTTGCTTG 60.317 55.000 23.47 14.15 0.00 4.01
31 32 1.283793 CTGCCTCAACGTTGCTTGG 59.716 57.895 23.47 22.54 0.00 3.61
32 33 2.133742 CTGCCTCAACGTTGCTTGGG 62.134 60.000 23.47 20.25 0.00 4.12
33 34 2.193536 GCCTCAACGTTGCTTGGGT 61.194 57.895 23.47 0.00 0.00 4.51
34 35 1.654220 CCTCAACGTTGCTTGGGTG 59.346 57.895 23.47 0.00 0.00 4.61
35 36 0.817634 CCTCAACGTTGCTTGGGTGA 60.818 55.000 23.47 2.63 0.00 4.02
36 37 0.588252 CTCAACGTTGCTTGGGTGAG 59.412 55.000 23.47 9.24 0.00 3.51
37 38 0.107410 TCAACGTTGCTTGGGTGAGT 60.107 50.000 23.47 0.00 0.00 3.41
38 39 1.139256 TCAACGTTGCTTGGGTGAGTA 59.861 47.619 23.47 0.00 0.00 2.59
39 40 1.263217 CAACGTTGCTTGGGTGAGTAC 59.737 52.381 16.51 0.00 0.00 2.73
40 41 0.250166 ACGTTGCTTGGGTGAGTACC 60.250 55.000 0.00 0.00 46.76 3.34
41 42 0.034896 CGTTGCTTGGGTGAGTACCT 59.965 55.000 0.00 0.00 46.66 3.08
42 43 1.542547 CGTTGCTTGGGTGAGTACCTT 60.543 52.381 0.00 0.00 46.66 3.50
43 44 2.289195 CGTTGCTTGGGTGAGTACCTTA 60.289 50.000 0.00 0.00 46.66 2.69
44 45 3.618997 CGTTGCTTGGGTGAGTACCTTAT 60.619 47.826 0.00 0.00 46.66 1.73
45 46 3.627395 TGCTTGGGTGAGTACCTTATG 57.373 47.619 0.00 0.00 46.66 1.90
46 47 2.289565 GCTTGGGTGAGTACCTTATGC 58.710 52.381 0.00 0.00 46.66 3.14
47 48 2.919228 CTTGGGTGAGTACCTTATGCC 58.081 52.381 0.00 0.00 46.66 4.40
48 49 1.959710 TGGGTGAGTACCTTATGCCA 58.040 50.000 0.00 0.00 46.66 4.92
49 50 1.557832 TGGGTGAGTACCTTATGCCAC 59.442 52.381 0.00 0.00 46.66 5.01
50 51 1.134189 GGGTGAGTACCTTATGCCACC 60.134 57.143 0.00 0.00 46.66 4.61
51 52 1.557832 GGTGAGTACCTTATGCCACCA 59.442 52.381 0.00 0.00 43.97 4.17
76 77 2.686106 GAGGGGGCGAGGGTGTTA 60.686 66.667 0.00 0.00 0.00 2.41
77 78 2.687566 AGGGGGCGAGGGTGTTAG 60.688 66.667 0.00 0.00 0.00 2.34
83 84 2.399356 GCGAGGGTGTTAGCTTGGC 61.399 63.158 0.00 0.00 0.00 4.52
91 92 2.914379 GTTAGCTTGGCTGACACGT 58.086 52.632 9.09 0.00 43.26 4.49
92 93 1.226746 GTTAGCTTGGCTGACACGTT 58.773 50.000 9.09 0.00 43.26 3.99
101 102 1.287730 GCTGACACGTTCCAGAGCAG 61.288 60.000 15.79 6.16 32.37 4.24
127 128 1.374125 CATGTCGGAACAGCGACCA 60.374 57.895 0.00 0.00 39.20 4.02
163 164 2.109181 GACCATGTAGGGCCTCGC 59.891 66.667 10.74 4.99 40.85 5.03
247 592 1.407979 CAACTACGGAGGGCTTATCGT 59.592 52.381 0.00 3.36 39.30 3.73
258 603 5.019785 AGGGCTTATCGTAGTTTTACAGG 57.980 43.478 0.00 0.00 0.00 4.00
273 618 3.005539 AGGCTCGGCTGATGTGGT 61.006 61.111 0.00 0.00 0.00 4.16
280 625 3.126831 CTCGGCTGATGTGGTCTATTTC 58.873 50.000 0.00 0.00 0.00 2.17
281 626 2.766263 TCGGCTGATGTGGTCTATTTCT 59.234 45.455 0.00 0.00 0.00 2.52
282 627 3.958147 TCGGCTGATGTGGTCTATTTCTA 59.042 43.478 0.00 0.00 0.00 2.10
295 640 8.135529 GTGGTCTATTTCTATTGGTAATTTGGC 58.864 37.037 0.00 0.00 0.00 4.52
317 662 4.966787 GCGGGGCCCACACTGAAA 62.967 66.667 26.86 0.00 0.00 2.69
318 663 2.035626 CGGGGCCCACACTGAAAT 59.964 61.111 26.86 0.00 0.00 2.17
319 664 1.606313 CGGGGCCCACACTGAAATT 60.606 57.895 26.86 0.00 0.00 1.82
320 665 1.595093 CGGGGCCCACACTGAAATTC 61.595 60.000 26.86 0.00 0.00 2.17
321 666 0.541764 GGGGCCCACACTGAAATTCA 60.542 55.000 26.86 0.00 0.00 2.57
322 667 1.337118 GGGCCCACACTGAAATTCAA 58.663 50.000 19.95 0.00 0.00 2.69
323 668 1.273327 GGGCCCACACTGAAATTCAAG 59.727 52.381 19.95 0.00 0.00 3.02
324 669 1.273327 GGCCCACACTGAAATTCAAGG 59.727 52.381 0.00 0.00 0.00 3.61
325 670 1.273327 GCCCACACTGAAATTCAAGGG 59.727 52.381 14.36 14.36 38.10 3.95
326 671 2.875296 CCCACACTGAAATTCAAGGGA 58.125 47.619 13.78 0.00 37.22 4.20
327 672 2.821969 CCCACACTGAAATTCAAGGGAG 59.178 50.000 13.78 2.32 37.22 4.30
328 673 3.498481 CCCACACTGAAATTCAAGGGAGA 60.498 47.826 13.78 0.00 37.22 3.71
329 674 3.755378 CCACACTGAAATTCAAGGGAGAG 59.245 47.826 0.00 0.00 0.00 3.20
330 675 4.505566 CCACACTGAAATTCAAGGGAGAGA 60.506 45.833 0.00 0.00 0.00 3.10
336 681 7.495279 CACTGAAATTCAAGGGAGAGAGATTAG 59.505 40.741 0.00 0.00 0.00 1.73
339 684 7.180946 TGAAATTCAAGGGAGAGAGATTAGTGA 59.819 37.037 0.00 0.00 0.00 3.41
342 687 3.611025 AGGGAGAGAGATTAGTGAGGG 57.389 52.381 0.00 0.00 0.00 4.30
343 688 3.135279 AGGGAGAGAGATTAGTGAGGGA 58.865 50.000 0.00 0.00 0.00 4.20
349 694 5.837829 AGAGAGATTAGTGAGGGAAGAAGT 58.162 41.667 0.00 0.00 0.00 3.01
352 697 7.724061 AGAGAGATTAGTGAGGGAAGAAGTATC 59.276 40.741 0.00 0.00 0.00 2.24
357 702 4.941713 AGTGAGGGAAGAAGTATCAGTCT 58.058 43.478 0.00 0.00 0.00 3.24
359 704 3.449018 TGAGGGAAGAAGTATCAGTCTGC 59.551 47.826 0.00 0.00 0.00 4.26
363 708 5.362430 AGGGAAGAAGTATCAGTCTGCTAAG 59.638 44.000 0.00 0.00 0.00 2.18
367 712 7.283580 GGAAGAAGTATCAGTCTGCTAAGTCTA 59.716 40.741 0.00 0.00 0.00 2.59
450 2148 4.692625 CCCATGATATCCTTGTCAACGATC 59.307 45.833 0.00 0.00 0.00 3.69
466 2164 2.158900 ACGATCGAGCATGGAAATTCCT 60.159 45.455 24.34 0.00 37.46 3.36
468 2166 1.939974 TCGAGCATGGAAATTCCTCG 58.060 50.000 13.78 13.45 44.76 4.63
516 2214 0.978146 ACTTCATGCTACCGGGAGCT 60.978 55.000 37.67 21.37 43.27 4.09
526 2224 1.640917 ACCGGGAGCTTAGACAAGAA 58.359 50.000 6.32 0.00 33.20 2.52
528 2226 2.028020 ACCGGGAGCTTAGACAAGAAAG 60.028 50.000 6.32 0.00 33.20 2.62
799 2670 1.736645 CTTCACCGCCATCGTCGTT 60.737 57.895 0.00 0.00 0.00 3.85
1278 3150 2.143876 TCGTCACCCTCATCATCTCA 57.856 50.000 0.00 0.00 0.00 3.27
1998 3928 2.184167 CAACGCCACCACCTTCGTT 61.184 57.895 0.00 0.00 44.62 3.85
2391 4344 0.036952 GCAGGCTGTTGAGCTAGTCA 60.037 55.000 17.16 0.00 45.44 3.41
2438 4391 3.121544 TGTTTTGTGATACGTACACGCA 58.878 40.909 17.49 14.92 44.43 5.24
2448 4401 8.127954 TGTGATACGTACACGCATAAAATACTA 58.872 33.333 17.49 0.75 44.43 1.82
2449 4402 9.121517 GTGATACGTACACGCATAAAATACTAT 57.878 33.333 0.00 0.00 44.43 2.12
2450 4403 9.681692 TGATACGTACACGCATAAAATACTATT 57.318 29.630 0.00 0.00 44.43 1.73
2453 4406 8.854979 ACGTACACGCATAAAATACTATTACA 57.145 30.769 0.85 0.00 44.43 2.41
2576 4544 6.734104 ATTGCACTCAAAGTTTAGAGCTAG 57.266 37.500 12.27 0.00 35.56 3.42
2624 4634 2.497675 GAGTTGGTCAGTGATGAGCCTA 59.502 50.000 0.00 0.00 35.63 3.93
2625 4635 2.906389 AGTTGGTCAGTGATGAGCCTAA 59.094 45.455 0.00 0.00 35.63 2.69
2626 4636 3.055530 AGTTGGTCAGTGATGAGCCTAAG 60.056 47.826 0.00 0.00 35.63 2.18
2627 4637 1.833630 TGGTCAGTGATGAGCCTAAGG 59.166 52.381 0.00 0.00 35.63 2.69
2628 4638 2.111384 GGTCAGTGATGAGCCTAAGGA 58.889 52.381 0.00 0.00 0.00 3.36
2629 4639 2.159028 GGTCAGTGATGAGCCTAAGGAC 60.159 54.545 0.00 0.00 0.00 3.85
2630 4640 2.111384 TCAGTGATGAGCCTAAGGACC 58.889 52.381 0.00 0.00 0.00 4.46
2631 4641 2.114616 CAGTGATGAGCCTAAGGACCT 58.885 52.381 0.00 0.00 0.00 3.85
2724 4734 4.612264 TTAGTTCCTGTCACTGGTTACC 57.388 45.455 0.00 0.00 0.00 2.85
2778 4796 4.594675 AGGCTAGTCAAGAGTCTCCTTA 57.405 45.455 0.00 0.00 0.00 2.69
2783 4801 7.037945 AGGCTAGTCAAGAGTCTCCTTAATTTT 60.038 37.037 0.00 0.00 0.00 1.82
2784 4802 7.065204 GGCTAGTCAAGAGTCTCCTTAATTTTG 59.935 40.741 0.00 0.00 0.00 2.44
2785 4803 7.604545 GCTAGTCAAGAGTCTCCTTAATTTTGT 59.395 37.037 0.00 0.00 0.00 2.83
2786 4804 7.736447 AGTCAAGAGTCTCCTTAATTTTGTG 57.264 36.000 0.00 0.00 0.00 3.33
2787 4805 7.509546 AGTCAAGAGTCTCCTTAATTTTGTGA 58.490 34.615 0.00 0.00 0.00 3.58
2788 4806 7.659390 AGTCAAGAGTCTCCTTAATTTTGTGAG 59.341 37.037 0.00 0.00 0.00 3.51
2789 4807 7.442666 GTCAAGAGTCTCCTTAATTTTGTGAGT 59.557 37.037 0.00 0.00 0.00 3.41
2790 4808 8.647796 TCAAGAGTCTCCTTAATTTTGTGAGTA 58.352 33.333 0.00 0.00 0.00 2.59
2791 4809 8.930760 CAAGAGTCTCCTTAATTTTGTGAGTAG 58.069 37.037 0.00 0.00 0.00 2.57
2792 4810 8.196378 AGAGTCTCCTTAATTTTGTGAGTAGT 57.804 34.615 0.00 0.00 0.00 2.73
2793 4811 8.652290 AGAGTCTCCTTAATTTTGTGAGTAGTT 58.348 33.333 0.00 0.00 0.00 2.24
2794 4812 8.834749 AGTCTCCTTAATTTTGTGAGTAGTTC 57.165 34.615 0.00 0.00 0.00 3.01
2795 4813 7.878644 AGTCTCCTTAATTTTGTGAGTAGTTCC 59.121 37.037 0.00 0.00 0.00 3.62
2796 4814 7.878644 GTCTCCTTAATTTTGTGAGTAGTTCCT 59.121 37.037 0.00 0.00 0.00 3.36
2797 4815 7.878127 TCTCCTTAATTTTGTGAGTAGTTCCTG 59.122 37.037 0.00 0.00 0.00 3.86
2798 4816 7.514721 TCCTTAATTTTGTGAGTAGTTCCTGT 58.485 34.615 0.00 0.00 0.00 4.00
2799 4817 7.660208 TCCTTAATTTTGTGAGTAGTTCCTGTC 59.340 37.037 0.00 0.00 0.00 3.51
2800 4818 7.444183 CCTTAATTTTGTGAGTAGTTCCTGTCA 59.556 37.037 0.00 0.00 0.00 3.58
2801 4819 6.619801 AATTTTGTGAGTAGTTCCTGTCAC 57.380 37.500 0.00 0.00 39.85 3.67
2802 4820 5.353394 TTTTGTGAGTAGTTCCTGTCACT 57.647 39.130 3.25 0.00 40.06 3.41
2803 4821 4.322080 TTGTGAGTAGTTCCTGTCACTG 57.678 45.455 3.25 0.00 40.06 3.66
2804 4822 2.628178 TGTGAGTAGTTCCTGTCACTGG 59.372 50.000 0.00 0.00 40.06 4.00
2805 4823 2.628657 GTGAGTAGTTCCTGTCACTGGT 59.371 50.000 0.00 0.00 37.04 4.00
2806 4824 3.069729 GTGAGTAGTTCCTGTCACTGGTT 59.930 47.826 0.00 0.00 37.04 3.67
2807 4825 4.280174 GTGAGTAGTTCCTGTCACTGGTTA 59.720 45.833 0.00 0.00 37.04 2.85
2808 4826 4.280174 TGAGTAGTTCCTGTCACTGGTTAC 59.720 45.833 0.00 1.18 0.00 2.50
2809 4827 4.481072 AGTAGTTCCTGTCACTGGTTACT 58.519 43.478 13.06 13.06 0.00 2.24
2810 4828 4.900054 AGTAGTTCCTGTCACTGGTTACTT 59.100 41.667 13.51 0.00 0.00 2.24
2811 4829 6.073314 AGTAGTTCCTGTCACTGGTTACTTA 58.927 40.000 13.51 2.47 0.00 2.24
2812 4830 6.724905 AGTAGTTCCTGTCACTGGTTACTTAT 59.275 38.462 13.51 4.27 0.00 1.73
2813 4831 6.435292 AGTTCCTGTCACTGGTTACTTATT 57.565 37.500 0.00 0.00 0.00 1.40
2814 4832 6.231211 AGTTCCTGTCACTGGTTACTTATTG 58.769 40.000 0.00 0.00 0.00 1.90
2815 4833 5.160607 TCCTGTCACTGGTTACTTATTGG 57.839 43.478 0.00 0.00 0.00 3.16
2816 4834 4.841813 TCCTGTCACTGGTTACTTATTGGA 59.158 41.667 0.00 0.00 0.00 3.53
2970 4994 5.756195 TTGCATACATAAACCAGATCAGC 57.244 39.130 0.00 0.00 0.00 4.26
3070 5095 4.081531 CCCAATGCACATCTGTTGGTTTAT 60.082 41.667 12.33 0.00 39.52 1.40
3108 5135 8.585018 CACCTTATTTACAGGGAAAGAAATGTT 58.415 33.333 0.00 0.00 35.46 2.71
3110 5137 7.968405 CCTTATTTACAGGGAAAGAAATGTTCG 59.032 37.037 0.00 0.00 34.02 3.95
3114 5141 3.146066 CAGGGAAAGAAATGTTCGGACA 58.854 45.455 0.00 0.00 40.71 4.02
3118 5145 3.004315 GGAAAGAAATGTTCGGACAAGCA 59.996 43.478 0.00 0.00 39.66 3.91
3119 5146 4.499019 GGAAAGAAATGTTCGGACAAGCAA 60.499 41.667 0.00 0.00 39.66 3.91
3127 5154 3.069016 TGTTCGGACAAGCAAGAGTAAGA 59.931 43.478 0.00 0.00 31.49 2.10
3149 5187 0.397675 TTGCAACCCACCAATCCACA 60.398 50.000 0.00 0.00 0.00 4.17
3166 5204 7.179160 CCAATCCACATGACAGAGATATAGGTA 59.821 40.741 0.00 0.00 0.00 3.08
3188 5226 3.129287 AGATACTGCCTTGCAATTTTCCG 59.871 43.478 0.00 0.00 38.41 4.30
3219 5257 3.242969 CGGTGAAGAAGATCATTGGCATG 60.243 47.826 0.00 0.00 0.00 4.06
3225 5266 7.227314 GTGAAGAAGATCATTGGCATGTATACA 59.773 37.037 8.27 8.27 0.00 2.29
3278 5319 6.944862 AGTCAACTCAAATCAGCCTTAAATCT 59.055 34.615 0.00 0.00 0.00 2.40
3290 5331 9.692325 ATCAGCCTTAAATCTAAGAAATTGACT 57.308 29.630 0.00 0.00 37.32 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.050985 GCAACGTTGAGGCAGTGC 60.051 61.111 31.62 10.80 0.00 4.40
11 12 0.317269 CAAGCAACGTTGAGGCAGTG 60.317 55.000 31.62 14.00 0.00 3.66
12 13 1.447317 CCAAGCAACGTTGAGGCAGT 61.447 55.000 31.62 6.02 0.00 4.40
13 14 1.283793 CCAAGCAACGTTGAGGCAG 59.716 57.895 31.62 14.62 0.00 4.85
14 15 2.192861 CCCAAGCAACGTTGAGGCA 61.193 57.895 31.62 0.00 0.00 4.75
15 16 2.193536 ACCCAAGCAACGTTGAGGC 61.194 57.895 31.62 16.49 0.00 4.70
16 17 0.817634 TCACCCAAGCAACGTTGAGG 60.818 55.000 31.62 25.44 0.00 3.86
17 18 0.588252 CTCACCCAAGCAACGTTGAG 59.412 55.000 31.62 18.68 0.00 3.02
18 19 0.107410 ACTCACCCAAGCAACGTTGA 60.107 50.000 31.62 7.32 0.00 3.18
19 20 1.263217 GTACTCACCCAAGCAACGTTG 59.737 52.381 23.90 23.90 0.00 4.10
20 21 1.589803 GTACTCACCCAAGCAACGTT 58.410 50.000 0.00 0.00 0.00 3.99
21 22 0.250166 GGTACTCACCCAAGCAACGT 60.250 55.000 0.00 0.00 39.11 3.99
22 23 2.540145 GGTACTCACCCAAGCAACG 58.460 57.895 0.00 0.00 39.11 4.10
31 32 1.557832 TGGTGGCATAAGGTACTCACC 59.442 52.381 0.00 0.00 46.19 4.02
32 33 2.420129 CCTGGTGGCATAAGGTACTCAC 60.420 54.545 9.62 0.00 38.49 3.51
33 34 1.837439 CCTGGTGGCATAAGGTACTCA 59.163 52.381 9.62 0.00 38.49 3.41
34 35 2.116238 TCCTGGTGGCATAAGGTACTC 58.884 52.381 15.57 0.00 38.49 2.59
36 37 1.472728 CGTCCTGGTGGCATAAGGTAC 60.473 57.143 15.57 11.94 32.59 3.34
37 38 0.828022 CGTCCTGGTGGCATAAGGTA 59.172 55.000 15.57 3.43 32.59 3.08
38 39 0.907704 TCGTCCTGGTGGCATAAGGT 60.908 55.000 15.57 0.00 32.59 3.50
39 40 0.462047 GTCGTCCTGGTGGCATAAGG 60.462 60.000 11.19 11.19 0.00 2.69
40 41 0.806102 CGTCGTCCTGGTGGCATAAG 60.806 60.000 0.00 0.00 0.00 1.73
41 42 1.216977 CGTCGTCCTGGTGGCATAA 59.783 57.895 0.00 0.00 0.00 1.90
42 43 1.663379 CTCGTCGTCCTGGTGGCATA 61.663 60.000 0.00 0.00 0.00 3.14
43 44 2.994995 TCGTCGTCCTGGTGGCAT 60.995 61.111 0.00 0.00 0.00 4.40
44 45 3.680786 CTCGTCGTCCTGGTGGCA 61.681 66.667 0.00 0.00 0.00 4.92
45 46 4.436998 CCTCGTCGTCCTGGTGGC 62.437 72.222 0.00 0.00 0.00 5.01
46 47 3.760035 CCCTCGTCGTCCTGGTGG 61.760 72.222 0.00 0.00 0.00 4.61
47 48 3.760035 CCCCTCGTCGTCCTGGTG 61.760 72.222 0.00 0.00 0.00 4.17
76 77 1.598130 GGAACGTGTCAGCCAAGCT 60.598 57.895 0.00 0.00 40.77 3.74
77 78 1.845809 CTGGAACGTGTCAGCCAAGC 61.846 60.000 5.63 0.00 0.00 4.01
83 84 0.668706 CCTGCTCTGGAACGTGTCAG 60.669 60.000 10.97 10.97 0.00 3.51
88 89 4.379243 CCGCCTGCTCTGGAACGT 62.379 66.667 0.00 0.00 0.00 3.99
91 92 4.020617 CCACCGCCTGCTCTGGAA 62.021 66.667 0.00 0.00 0.00 3.53
116 117 3.123621 CACACTTTCTATGGTCGCTGTTC 59.876 47.826 0.00 0.00 0.00 3.18
127 128 2.094854 GTCCGTCGACCACACTTTCTAT 60.095 50.000 10.58 0.00 32.40 1.98
158 159 2.477972 TTCACTGAGCTCACGCGAGG 62.478 60.000 15.93 4.41 42.32 4.63
163 164 0.108898 CCCTCTTCACTGAGCTCACG 60.109 60.000 13.74 11.72 33.02 4.35
189 190 3.119291 CGAGTGCAGAGAATACCATGTC 58.881 50.000 0.00 0.00 0.00 3.06
247 592 1.897133 TCAGCCGAGCCTGTAAAACTA 59.103 47.619 0.00 0.00 34.47 2.24
258 603 0.390860 ATAGACCACATCAGCCGAGC 59.609 55.000 0.00 0.00 0.00 5.03
273 618 7.284074 TCCGCCAAATTACCAATAGAAATAGA 58.716 34.615 0.00 0.00 0.00 1.98
280 625 3.548014 CGCTTCCGCCAAATTACCAATAG 60.548 47.826 0.00 0.00 0.00 1.73
281 626 2.356382 CGCTTCCGCCAAATTACCAATA 59.644 45.455 0.00 0.00 0.00 1.90
282 627 1.134175 CGCTTCCGCCAAATTACCAAT 59.866 47.619 0.00 0.00 0.00 3.16
311 656 6.385766 AATCTCTCTCCCTTGAATTTCAGT 57.614 37.500 0.00 0.00 0.00 3.41
314 659 7.560368 TCACTAATCTCTCTCCCTTGAATTTC 58.440 38.462 0.00 0.00 0.00 2.17
317 662 5.602145 CCTCACTAATCTCTCTCCCTTGAAT 59.398 44.000 0.00 0.00 0.00 2.57
318 663 4.959210 CCTCACTAATCTCTCTCCCTTGAA 59.041 45.833 0.00 0.00 0.00 2.69
319 664 4.541705 CCTCACTAATCTCTCTCCCTTGA 58.458 47.826 0.00 0.00 0.00 3.02
320 665 3.640967 CCCTCACTAATCTCTCTCCCTTG 59.359 52.174 0.00 0.00 0.00 3.61
321 666 3.533907 TCCCTCACTAATCTCTCTCCCTT 59.466 47.826 0.00 0.00 0.00 3.95
322 667 3.135279 TCCCTCACTAATCTCTCTCCCT 58.865 50.000 0.00 0.00 0.00 4.20
323 668 3.603965 TCCCTCACTAATCTCTCTCCC 57.396 52.381 0.00 0.00 0.00 4.30
324 669 4.798882 TCTTCCCTCACTAATCTCTCTCC 58.201 47.826 0.00 0.00 0.00 3.71
325 670 5.891551 ACTTCTTCCCTCACTAATCTCTCTC 59.108 44.000 0.00 0.00 0.00 3.20
326 671 5.837829 ACTTCTTCCCTCACTAATCTCTCT 58.162 41.667 0.00 0.00 0.00 3.10
327 672 7.504238 TGATACTTCTTCCCTCACTAATCTCTC 59.496 40.741 0.00 0.00 0.00 3.20
328 673 7.358263 TGATACTTCTTCCCTCACTAATCTCT 58.642 38.462 0.00 0.00 0.00 3.10
329 674 7.286775 ACTGATACTTCTTCCCTCACTAATCTC 59.713 40.741 0.00 0.00 0.00 2.75
330 675 7.129425 ACTGATACTTCTTCCCTCACTAATCT 58.871 38.462 0.00 0.00 0.00 2.40
336 681 4.679372 GCAGACTGATACTTCTTCCCTCAC 60.679 50.000 6.65 0.00 0.00 3.51
339 684 3.718723 AGCAGACTGATACTTCTTCCCT 58.281 45.455 6.65 0.00 0.00 4.20
342 687 7.095695 AGACTTAGCAGACTGATACTTCTTC 57.904 40.000 6.65 0.00 0.00 2.87
343 688 8.760980 ATAGACTTAGCAGACTGATACTTCTT 57.239 34.615 6.65 0.00 0.00 2.52
374 719 7.615365 TCAATATCCCAGCAAAATTGTTAGACT 59.385 33.333 0.00 0.00 0.00 3.24
375 720 7.771183 TCAATATCCCAGCAAAATTGTTAGAC 58.229 34.615 0.00 0.00 0.00 2.59
376 721 7.953005 TCAATATCCCAGCAAAATTGTTAGA 57.047 32.000 0.00 0.00 0.00 2.10
379 724 8.707449 ACATATCAATATCCCAGCAAAATTGTT 58.293 29.630 0.00 0.00 0.00 2.83
380 725 8.253867 ACATATCAATATCCCAGCAAAATTGT 57.746 30.769 0.00 0.00 0.00 2.71
381 726 8.984764 CAACATATCAATATCCCAGCAAAATTG 58.015 33.333 0.00 0.00 0.00 2.32
382 727 7.658575 GCAACATATCAATATCCCAGCAAAATT 59.341 33.333 0.00 0.00 0.00 1.82
384 729 6.097981 TGCAACATATCAATATCCCAGCAAAA 59.902 34.615 0.00 0.00 0.00 2.44
385 730 5.597594 TGCAACATATCAATATCCCAGCAAA 59.402 36.000 0.00 0.00 0.00 3.68
387 732 4.727677 TGCAACATATCAATATCCCAGCA 58.272 39.130 0.00 0.00 0.00 4.41
391 2082 7.692460 TCTGAATGCAACATATCAATATCCC 57.308 36.000 0.00 0.00 0.00 3.85
403 2094 8.579006 GGGAAATTATATGATCTGAATGCAACA 58.421 33.333 0.00 0.00 0.00 3.33
422 2113 6.039717 CGTTGACAAGGATATCATGGGAAATT 59.960 38.462 4.83 0.00 0.00 1.82
466 2164 2.568062 TGTAAAGCTGTTACCATCCCGA 59.432 45.455 12.99 0.00 0.00 5.14
468 2166 3.066760 GCATGTAAAGCTGTTACCATCCC 59.933 47.826 12.99 0.13 0.00 3.85
507 2205 1.640917 TTCTTGTCTAAGCTCCCGGT 58.359 50.000 0.00 0.00 33.82 5.28
508 2206 2.622436 CTTTCTTGTCTAAGCTCCCGG 58.378 52.381 0.00 0.00 33.82 5.73
1998 3928 3.371097 GAAGATCTCGGCGGGCACA 62.371 63.158 7.21 0.00 0.00 4.57
2385 4338 7.414098 CCCAACAAATTACGGATCTTTGACTAG 60.414 40.741 10.39 0.00 34.69 2.57
2391 4344 7.712204 ATTACCCAACAAATTACGGATCTTT 57.288 32.000 0.00 0.00 0.00 2.52
2394 4347 7.317390 ACAAATTACCCAACAAATTACGGATC 58.683 34.615 0.00 0.00 0.00 3.36
2395 4348 7.234661 ACAAATTACCCAACAAATTACGGAT 57.765 32.000 0.00 0.00 0.00 4.18
2396 4349 6.651975 ACAAATTACCCAACAAATTACGGA 57.348 33.333 0.00 0.00 0.00 4.69
2397 4350 7.716768 AAACAAATTACCCAACAAATTACGG 57.283 32.000 0.00 0.00 0.00 4.02
2398 4351 8.604890 ACAAAACAAATTACCCAACAAATTACG 58.395 29.630 0.00 0.00 0.00 3.18
2399 4352 9.709600 CACAAAACAAATTACCCAACAAATTAC 57.290 29.630 0.00 0.00 0.00 1.89
2448 4401 3.881089 GCCCGCAAACCTATAGTTGTAAT 59.119 43.478 0.00 0.00 39.19 1.89
2449 4402 3.272581 GCCCGCAAACCTATAGTTGTAA 58.727 45.455 0.00 0.00 39.19 2.41
2450 4403 2.420408 GGCCCGCAAACCTATAGTTGTA 60.420 50.000 0.00 0.00 39.19 2.41
2452 4405 1.021968 GGCCCGCAAACCTATAGTTG 58.978 55.000 0.00 0.00 39.19 3.16
2453 4406 0.621609 TGGCCCGCAAACCTATAGTT 59.378 50.000 0.00 0.00 41.81 2.24
2576 4544 3.957474 GCGTTAGCTTTGCTCACTC 57.043 52.632 0.00 0.00 40.44 3.51
2624 4634 3.831911 CTGAAGAGAGTCTTGAGGTCCTT 59.168 47.826 0.00 0.00 36.73 3.36
2625 4635 3.181423 ACTGAAGAGAGTCTTGAGGTCCT 60.181 47.826 7.85 0.00 41.17 3.85
2626 4636 3.161866 ACTGAAGAGAGTCTTGAGGTCC 58.838 50.000 7.85 0.00 41.17 4.46
2627 4637 3.823873 TGACTGAAGAGAGTCTTGAGGTC 59.176 47.826 7.85 7.03 41.17 3.85
2628 4638 3.838565 TGACTGAAGAGAGTCTTGAGGT 58.161 45.455 7.85 0.00 41.17 3.85
2629 4639 4.555262 GTTGACTGAAGAGAGTCTTGAGG 58.445 47.826 7.85 0.00 41.17 3.86
2630 4640 4.023622 TCGTTGACTGAAGAGAGTCTTGAG 60.024 45.833 0.00 2.06 42.31 3.02
2631 4641 3.883489 TCGTTGACTGAAGAGAGTCTTGA 59.117 43.478 0.00 0.00 42.58 3.02
2778 4796 6.260936 CAGTGACAGGAACTACTCACAAAATT 59.739 38.462 0.00 0.00 43.72 1.82
2783 4801 2.628178 CCAGTGACAGGAACTACTCACA 59.372 50.000 0.00 0.00 43.72 3.58
2784 4802 2.628657 ACCAGTGACAGGAACTACTCAC 59.371 50.000 0.00 0.00 42.43 3.51
2785 4803 2.958818 ACCAGTGACAGGAACTACTCA 58.041 47.619 0.00 0.00 36.02 3.41
2786 4804 4.523558 AGTAACCAGTGACAGGAACTACTC 59.476 45.833 0.00 0.00 36.02 2.59
2787 4805 4.481072 AGTAACCAGTGACAGGAACTACT 58.519 43.478 0.00 2.19 36.02 2.57
2788 4806 4.868314 AGTAACCAGTGACAGGAACTAC 57.132 45.455 0.00 0.00 36.02 2.73
2789 4807 7.383687 CAATAAGTAACCAGTGACAGGAACTA 58.616 38.462 0.00 0.00 36.02 2.24
2790 4808 6.231211 CAATAAGTAACCAGTGACAGGAACT 58.769 40.000 0.00 1.10 43.88 3.01
2791 4809 5.411669 CCAATAAGTAACCAGTGACAGGAAC 59.588 44.000 0.00 0.00 0.00 3.62
2792 4810 5.308497 TCCAATAAGTAACCAGTGACAGGAA 59.692 40.000 0.00 0.00 0.00 3.36
2793 4811 4.841813 TCCAATAAGTAACCAGTGACAGGA 59.158 41.667 0.00 0.00 0.00 3.86
2794 4812 5.160607 TCCAATAAGTAACCAGTGACAGG 57.839 43.478 0.00 0.00 0.00 4.00
2795 4813 5.794894 ACTCCAATAAGTAACCAGTGACAG 58.205 41.667 0.00 0.00 0.00 3.51
2796 4814 5.818678 ACTCCAATAAGTAACCAGTGACA 57.181 39.130 0.00 0.00 0.00 3.58
2797 4815 6.932947 ACTACTCCAATAAGTAACCAGTGAC 58.067 40.000 0.00 0.00 31.56 3.67
2798 4816 7.549147 AACTACTCCAATAAGTAACCAGTGA 57.451 36.000 0.00 0.00 31.56 3.41
2799 4817 8.617290 AAAACTACTCCAATAAGTAACCAGTG 57.383 34.615 0.00 0.00 31.56 3.66
2800 4818 8.657712 AGAAAACTACTCCAATAAGTAACCAGT 58.342 33.333 0.00 0.00 31.56 4.00
2813 4831 9.804977 ACTAAGAAGTACTAGAAAACTACTCCA 57.195 33.333 0.00 0.00 32.84 3.86
2889 4907 2.093658 TCGGTCTGGTGCCTTAATCTTC 60.094 50.000 0.00 0.00 0.00 2.87
2963 4987 5.480642 TTGTTCTCTTTCAGAGCTGATCT 57.519 39.130 0.37 0.00 42.04 2.75
2965 4989 5.472820 CCTTTTGTTCTCTTTCAGAGCTGAT 59.527 40.000 0.37 0.00 42.04 2.90
2970 4994 5.586243 TGACACCTTTTGTTCTCTTTCAGAG 59.414 40.000 0.00 0.00 40.30 3.35
2974 4998 5.909610 CGATTGACACCTTTTGTTCTCTTTC 59.090 40.000 0.00 0.00 39.17 2.62
3035 5060 2.288961 GCATTGGGTTTGATGCAGAG 57.711 50.000 3.65 0.00 46.03 3.35
3070 5095 9.778741 CCTGTAAATAAGGTGCTAATATCAAGA 57.221 33.333 0.00 0.00 0.00 3.02
3108 5135 5.854010 ATATCTTACTCTTGCTTGTCCGA 57.146 39.130 0.00 0.00 0.00 4.55
3110 5137 5.586243 TGCAATATCTTACTCTTGCTTGTCC 59.414 40.000 7.52 0.00 43.33 4.02
3114 5141 5.358160 GGGTTGCAATATCTTACTCTTGCTT 59.642 40.000 0.59 0.00 43.33 3.91
3118 5145 5.193679 GGTGGGTTGCAATATCTTACTCTT 58.806 41.667 0.59 0.00 0.00 2.85
3119 5146 4.227300 TGGTGGGTTGCAATATCTTACTCT 59.773 41.667 0.59 0.00 0.00 3.24
3127 5154 2.765699 GTGGATTGGTGGGTTGCAATAT 59.234 45.455 0.59 0.00 0.00 1.28
3149 5187 7.777910 GGCAGTATCTACCTATATCTCTGTCAT 59.222 40.741 0.00 0.00 0.00 3.06
3166 5204 3.129287 CGGAAAATTGCAAGGCAGTATCT 59.871 43.478 4.94 0.00 40.61 1.98
3188 5226 0.861837 CTTCTTCACCGTGCTCACAC 59.138 55.000 0.69 0.00 43.76 3.82
3219 5257 4.585879 ACCTTGACCCAACACATGTATAC 58.414 43.478 0.00 0.00 0.00 1.47
3225 5266 2.978156 ATGACCTTGACCCAACACAT 57.022 45.000 0.00 0.00 0.00 3.21
3287 5328 9.552114 CTATCAATGATTTTGTTTGACTCAGTC 57.448 33.333 0.00 0.00 32.61 3.51


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

AutoCloner maintained by Alex Coulton.