Multiple sequence alignment - TraesCS5D01G354100

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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 TraesCS5D01G354100 chr5D 100.000 2619 0 0 1 2619 436348483 436351101 0.000000e+00 4837
1 TraesCS5D01G354100 chr5D 88.420 829 67 16 569 1373 436824600 436823777 0.000000e+00 972
2 TraesCS5D01G354100 chr5D 88.907 622 56 10 763 1373 436578191 436578810 0.000000e+00 754
3 TraesCS5D01G354100 chr5D 85.324 695 78 16 693 1373 440375812 440375128 0.000000e+00 697
4 TraesCS5D01G354100 chr5B 87.813 1559 109 43 587 2099 530334070 530335593 0.000000e+00 1751
5 TraesCS5D01G354100 chr5B 91.486 740 49 11 645 1373 530609045 530609781 0.000000e+00 1005
6 TraesCS5D01G354100 chr5B 87.846 831 73 15 569 1373 530974598 530973770 0.000000e+00 950
7 TraesCS5D01G354100 chr5B 85.366 820 76 25 570 1373 530613109 530613900 0.000000e+00 809
8 TraesCS5D01G354100 chr5B 88.889 558 27 17 1 553 530333546 530334073 0.000000e+00 654
9 TraesCS5D01G354100 chr5B 85.106 423 44 11 2109 2530 530339057 530339461 5.210000e-112 414
10 TraesCS5D01G354100 chr5A 86.548 1405 111 41 584 1939 550801586 550802961 0.000000e+00 1476
11 TraesCS5D01G354100 chr5A 87.204 719 50 25 685 1373 551041101 551041807 0.000000e+00 780
12 TraesCS5D01G354100 chr5A 86.003 693 68 21 693 1373 556534675 556534000 0.000000e+00 715
13 TraesCS5D01G354100 chr5A 81.560 564 60 18 1966 2528 550804090 550803570 2.410000e-115 425
14 TraesCS5D01G354100 chr5A 87.500 144 7 5 397 539 550798361 550798494 3.490000e-34 156
15 TraesCS5D01G354100 chr6A 87.290 535 53 12 847 1373 28666730 28666203 4.820000e-167 597


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 TraesCS5D01G354100 chr5D 436348483 436351101 2618 False 4837.000000 4837 100.000000 1 2619 1 chr5D.!!$F1 2618
1 TraesCS5D01G354100 chr5D 436823777 436824600 823 True 972.000000 972 88.420000 569 1373 1 chr5D.!!$R1 804
2 TraesCS5D01G354100 chr5D 436578191 436578810 619 False 754.000000 754 88.907000 763 1373 1 chr5D.!!$F2 610
3 TraesCS5D01G354100 chr5D 440375128 440375812 684 True 697.000000 697 85.324000 693 1373 1 chr5D.!!$R2 680
4 TraesCS5D01G354100 chr5B 530973770 530974598 828 True 950.000000 950 87.846000 569 1373 1 chr5B.!!$R1 804
5 TraesCS5D01G354100 chr5B 530333546 530339461 5915 False 939.666667 1751 87.269333 1 2530 3 chr5B.!!$F1 2529
6 TraesCS5D01G354100 chr5B 530609045 530613900 4855 False 907.000000 1005 88.426000 570 1373 2 chr5B.!!$F2 803
7 TraesCS5D01G354100 chr5A 550798361 550802961 4600 False 816.000000 1476 87.024000 397 1939 2 chr5A.!!$F2 1542
8 TraesCS5D01G354100 chr5A 551041101 551041807 706 False 780.000000 780 87.204000 685 1373 1 chr5A.!!$F1 688
9 TraesCS5D01G354100 chr5A 556534000 556534675 675 True 715.000000 715 86.003000 693 1373 1 chr5A.!!$R2 680
10 TraesCS5D01G354100 chr5A 550803570 550804090 520 True 425.000000 425 81.560000 1966 2528 1 chr5A.!!$R1 562
11 TraesCS5D01G354100 chr6A 28666203 28666730 527 True 597.000000 597 87.290000 847 1373 1 chr6A.!!$R1 526

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
712 3790 0.173255 ATCCAAAATTTCGCGGCAGG 59.827 50.0 6.13 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 8956 1.240256 CTCCGTTCCCCTCTCTATCG 58.76 60.0 0.0 0.0 0.0 2.92 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
27 28 7.753580 AGGTTTCTTTTTACTTCAACGACAAAG 59.246 33.333 0.00 0.00 0.00 2.77
44 45 0.178990 AAGGTCTCAACACTTGCCCC 60.179 55.000 0.00 0.00 0.00 5.80
69 70 0.687920 TGCCTTCCGTAACCACATGA 59.312 50.000 0.00 0.00 0.00 3.07
105 106 4.891168 TCAATGGCTTCAAGATGCATACAT 59.109 37.500 0.00 2.46 39.98 2.29
106 107 6.063404 TCAATGGCTTCAAGATGCATACATA 58.937 36.000 0.00 0.00 36.35 2.29
138 140 3.502211 CCAATAAGGCAATCGGTACCATC 59.498 47.826 13.54 0.00 0.00 3.51
146 148 3.605634 CAATCGGTACCATCAAAGGTGA 58.394 45.455 13.54 0.00 43.14 4.02
174 176 1.157585 GCGGAGACCTTGAAGTTTCC 58.842 55.000 0.00 0.00 37.61 3.13
176 178 2.810767 GCGGAGACCTTGAAGTTTCCTT 60.811 50.000 0.00 0.00 38.57 3.36
178 180 4.638304 CGGAGACCTTGAAGTTTCCTTTA 58.362 43.478 0.00 0.00 38.57 1.85
179 181 4.691216 CGGAGACCTTGAAGTTTCCTTTAG 59.309 45.833 0.00 0.00 38.57 1.85
180 182 5.622180 GGAGACCTTGAAGTTTCCTTTAGT 58.378 41.667 0.00 0.00 37.89 2.24
181 183 6.062749 GGAGACCTTGAAGTTTCCTTTAGTT 58.937 40.000 0.00 0.00 37.89 2.24
182 184 6.017026 GGAGACCTTGAAGTTTCCTTTAGTTG 60.017 42.308 0.00 0.00 37.89 3.16
183 185 6.659824 AGACCTTGAAGTTTCCTTTAGTTGA 58.340 36.000 0.00 0.00 0.00 3.18
184 186 7.290813 AGACCTTGAAGTTTCCTTTAGTTGAT 58.709 34.615 0.00 0.00 0.00 2.57
185 187 7.229506 AGACCTTGAAGTTTCCTTTAGTTGATG 59.770 37.037 0.00 0.00 0.00 3.07
186 188 6.265422 ACCTTGAAGTTTCCTTTAGTTGATGG 59.735 38.462 0.00 0.00 0.00 3.51
187 189 6.490040 CCTTGAAGTTTCCTTTAGTTGATGGA 59.510 38.462 0.00 0.00 0.00 3.41
188 190 7.177392 CCTTGAAGTTTCCTTTAGTTGATGGAT 59.823 37.037 0.00 0.00 0.00 3.41
189 191 9.231297 CTTGAAGTTTCCTTTAGTTGATGGATA 57.769 33.333 0.00 0.00 0.00 2.59
190 192 9.581289 TTGAAGTTTCCTTTAGTTGATGGATAA 57.419 29.630 0.00 0.00 0.00 1.75
191 193 9.581289 TGAAGTTTCCTTTAGTTGATGGATAAA 57.419 29.630 0.00 0.00 0.00 1.40
194 196 9.588096 AGTTTCCTTTAGTTGATGGATAAAACT 57.412 29.630 0.00 0.00 37.82 2.66
345 349 9.691362 TTTTAAAAATGTCTATTTCTCCACTGC 57.309 29.630 0.00 0.00 35.50 4.40
585 3647 2.504367 ACCTGAAAGAAACACCCGATG 58.496 47.619 0.00 0.00 34.07 3.84
712 3790 0.173255 ATCCAAAATTTCGCGGCAGG 59.827 50.000 6.13 0.00 0.00 4.85
779 3864 3.011517 CCTGCCAGCCACCTACCT 61.012 66.667 0.00 0.00 0.00 3.08
982 8199 1.071699 GGCTATAAATCCACCTCGCCA 59.928 52.381 0.00 0.00 36.37 5.69
1412 8666 1.931841 CTCGCACCACTTGATCAGATG 59.068 52.381 0.00 0.00 0.00 2.90
1450 8704 1.014352 AGGCGTTGTTCAGTGTTCAC 58.986 50.000 0.00 0.00 0.00 3.18
1482 8736 7.877612 TCGATGTAATTTATGATGTATGGTGCT 59.122 33.333 0.00 0.00 0.00 4.40
1500 8754 1.064654 GCTTGTTCGCTGGAATGGATC 59.935 52.381 0.00 0.00 34.05 3.36
1508 8762 1.677576 GCTGGAATGGATCAAATCGCA 59.322 47.619 0.00 0.00 0.00 5.10
1522 8776 6.827586 TCAAATCGCAGTTATTTACCCTTT 57.172 33.333 0.00 0.00 0.00 3.11
1543 8797 1.065854 ACTCGCCTTCAATCTCTTGGG 60.066 52.381 0.00 0.00 32.95 4.12
1545 8799 2.168521 CTCGCCTTCAATCTCTTGGGTA 59.831 50.000 0.00 0.00 32.95 3.69
1549 8803 4.684485 CGCCTTCAATCTCTTGGGTAATCT 60.684 45.833 0.00 0.00 32.95 2.40
1552 8806 6.632672 GCCTTCAATCTCTTGGGTAATCTACA 60.633 42.308 0.00 0.00 32.95 2.74
1553 8807 7.512992 CCTTCAATCTCTTGGGTAATCTACAT 58.487 38.462 0.00 0.00 32.95 2.29
1554 8808 7.995488 CCTTCAATCTCTTGGGTAATCTACATT 59.005 37.037 0.00 0.00 32.95 2.71
1555 8809 8.964476 TTCAATCTCTTGGGTAATCTACATTC 57.036 34.615 0.00 0.00 32.95 2.67
1566 8820 6.370718 GGGTAATCTACATTCGTGTGTTCTTT 59.629 38.462 1.17 0.00 33.62 2.52
1567 8821 7.546667 GGGTAATCTACATTCGTGTGTTCTTTA 59.453 37.037 1.17 0.00 33.62 1.85
1579 8833 5.236478 CGTGTGTTCTTTAGTCTGTTTCCAT 59.764 40.000 0.00 0.00 0.00 3.41
1580 8834 6.238374 CGTGTGTTCTTTAGTCTGTTTCCATT 60.238 38.462 0.00 0.00 0.00 3.16
1583 8837 8.188139 TGTGTTCTTTAGTCTGTTTCCATTTTC 58.812 33.333 0.00 0.00 0.00 2.29
1584 8838 8.406297 GTGTTCTTTAGTCTGTTTCCATTTTCT 58.594 33.333 0.00 0.00 0.00 2.52
1585 8839 8.966868 TGTTCTTTAGTCTGTTTCCATTTTCTT 58.033 29.630 0.00 0.00 0.00 2.52
1593 8847 8.571336 AGTCTGTTTCCATTTTCTTATTCTGTG 58.429 33.333 0.00 0.00 0.00 3.66
1612 8867 5.121611 TCTGTGTATAACTGTTGCCAAATCG 59.878 40.000 2.69 0.00 0.00 3.34
1614 8869 5.239744 TGTGTATAACTGTTGCCAAATCGTT 59.760 36.000 2.69 0.00 0.00 3.85
1616 8871 5.470437 TGTATAACTGTTGCCAAATCGTTCA 59.530 36.000 2.69 0.00 0.00 3.18
1618 8873 3.559238 ACTGTTGCCAAATCGTTCATC 57.441 42.857 0.00 0.00 0.00 2.92
1621 8876 2.228582 TGTTGCCAAATCGTTCATCTGG 59.771 45.455 0.00 0.00 0.00 3.86
1622 8877 2.487762 GTTGCCAAATCGTTCATCTGGA 59.512 45.455 0.00 0.00 0.00 3.86
1624 8879 2.083774 GCCAAATCGTTCATCTGGACA 58.916 47.619 0.00 0.00 0.00 4.02
1626 8881 3.876914 GCCAAATCGTTCATCTGGACATA 59.123 43.478 0.00 0.00 0.00 2.29
1629 8884 5.008019 CCAAATCGTTCATCTGGACATAAGG 59.992 44.000 0.00 0.00 0.00 2.69
1635 8890 4.689612 TCATCTGGACATAAGGTTAGGC 57.310 45.455 0.00 0.00 0.00 3.93
1644 8899 5.775701 GGACATAAGGTTAGGCTATCTCTGA 59.224 44.000 0.00 0.00 0.00 3.27
1677 8932 7.305474 ACGATATCGAAAGCAAAATTCAGTTT 58.695 30.769 30.75 0.00 43.02 2.66
1701 8956 1.688735 AGGCCTGAAGGTTTTGCTTTC 59.311 47.619 3.11 0.00 37.57 2.62
1743 8998 1.594862 GCTCATCGACCGAAGAATTGG 59.405 52.381 0.00 0.00 0.00 3.16
1774 9029 1.872952 TGTTTGGTCGAGAACTGCATG 59.127 47.619 0.00 0.00 0.00 4.06
1801 9060 5.369833 GCCTCTTCTATTTTACCTTCCTCC 58.630 45.833 0.00 0.00 0.00 4.30
1830 9109 5.363562 TCAGCTATCAGTTGAACATGGAT 57.636 39.130 0.00 0.48 32.42 3.41
1835 9114 3.071874 TCAGTTGAACATGGATGACCC 57.928 47.619 0.00 0.00 34.81 4.46
2104 9396 9.950680 AGCTAATATGTGGATTGAATAAAAACG 57.049 29.630 0.00 0.00 0.00 3.60
2115 12861 8.122952 GGATTGAATAAAAACGGACAGAGTATG 58.877 37.037 0.00 0.00 0.00 2.39
2134 12880 7.947332 AGAGTATGTATGTCACTATGTGAGGAT 59.053 37.037 0.20 0.10 43.57 3.24
2169 12915 3.857157 TTTCTAACTTCTGCAGGTGGT 57.143 42.857 15.13 8.26 0.00 4.16
2217 12963 7.842887 AGTTCTGATAATAGTACTCCCTTCC 57.157 40.000 0.00 0.00 0.00 3.46
2253 12999 9.515226 ACTTCACATATAACCACATGTAAGTTT 57.485 29.630 16.14 8.78 33.66 2.66
2267 13013 9.515020 CACATGTAAGTTTTGTGTCAAGTTAAT 57.485 29.630 0.00 0.00 36.77 1.40
2287 13034 8.955388 AGTTAATTTTTGCAAAGTTTGACCAAT 58.045 25.926 19.82 8.06 0.00 3.16
2289 13036 9.565213 TTAATTTTTGCAAAGTTTGACCAATTG 57.435 25.926 19.82 0.00 0.00 2.32
2467 13214 7.872483 ACTTATTTGCCAACTAAAAATGACTGG 59.128 33.333 0.00 0.00 0.00 4.00
2471 13218 4.278170 TGCCAACTAAAAATGACTGGAGTG 59.722 41.667 0.00 0.00 0.00 3.51
2477 13224 9.003658 CAACTAAAAATGACTGGAGTGAGTAAT 57.996 33.333 0.00 0.00 0.00 1.89
2530 13277 3.305676 GCACTGACACACTAGACATGACT 60.306 47.826 0.00 0.00 0.00 3.41
2531 13278 4.480541 CACTGACACACTAGACATGACTC 58.519 47.826 0.00 0.00 0.00 3.36
2532 13279 4.217334 CACTGACACACTAGACATGACTCT 59.783 45.833 0.00 0.00 0.00 3.24
2533 13280 4.457603 ACTGACACACTAGACATGACTCTC 59.542 45.833 0.00 0.00 0.00 3.20
2534 13281 4.398319 TGACACACTAGACATGACTCTCA 58.602 43.478 0.00 0.00 0.00 3.27
2535 13282 4.827284 TGACACACTAGACATGACTCTCAA 59.173 41.667 0.00 0.00 0.00 3.02
2536 13283 5.301805 TGACACACTAGACATGACTCTCAAA 59.698 40.000 0.00 0.00 0.00 2.69
2537 13284 6.161855 ACACACTAGACATGACTCTCAAAA 57.838 37.500 0.00 0.00 0.00 2.44
2538 13285 6.582636 ACACACTAGACATGACTCTCAAAAA 58.417 36.000 0.00 0.00 0.00 1.94
2566 13313 6.851222 AAAAAGACACACTAGACATGACAG 57.149 37.500 0.00 0.00 0.00 3.51
2567 13314 3.584406 AGACACACTAGACATGACAGC 57.416 47.619 0.00 0.00 0.00 4.40
2568 13315 2.893489 AGACACACTAGACATGACAGCA 59.107 45.455 0.00 0.00 0.00 4.41
2569 13316 2.989840 GACACACTAGACATGACAGCAC 59.010 50.000 0.00 0.00 0.00 4.40
2570 13317 1.988467 CACACTAGACATGACAGCACG 59.012 52.381 0.00 0.00 0.00 5.34
2571 13318 1.613925 ACACTAGACATGACAGCACGT 59.386 47.619 0.00 0.00 0.00 4.49
2572 13319 2.254459 CACTAGACATGACAGCACGTC 58.746 52.381 0.00 0.00 45.61 4.34
2573 13320 1.202582 ACTAGACATGACAGCACGTCC 59.797 52.381 0.00 0.00 44.71 4.79
2574 13321 1.202348 CTAGACATGACAGCACGTCCA 59.798 52.381 0.00 0.00 44.71 4.02
2575 13322 0.610174 AGACATGACAGCACGTCCAT 59.390 50.000 0.00 0.00 44.71 3.41
2576 13323 1.002366 GACATGACAGCACGTCCATC 58.998 55.000 0.00 0.00 44.71 3.51
2577 13324 0.321346 ACATGACAGCACGTCCATCA 59.679 50.000 0.00 0.00 44.71 3.07
2578 13325 1.270785 ACATGACAGCACGTCCATCAA 60.271 47.619 0.00 0.00 44.71 2.57
2579 13326 1.805943 CATGACAGCACGTCCATCAAA 59.194 47.619 4.07 0.00 44.71 2.69
2580 13327 2.183478 TGACAGCACGTCCATCAAAT 57.817 45.000 4.07 0.00 44.71 2.32
2581 13328 2.503331 TGACAGCACGTCCATCAAATT 58.497 42.857 4.07 0.00 44.71 1.82
2582 13329 2.884012 TGACAGCACGTCCATCAAATTT 59.116 40.909 4.07 0.00 44.71 1.82
2583 13330 3.236816 GACAGCACGTCCATCAAATTTG 58.763 45.455 12.15 12.15 38.85 2.32
2584 13331 2.622942 ACAGCACGTCCATCAAATTTGT 59.377 40.909 17.47 3.04 0.00 2.83
2585 13332 2.981805 CAGCACGTCCATCAAATTTGTG 59.018 45.455 17.47 14.01 0.00 3.33
2586 13333 2.622942 AGCACGTCCATCAAATTTGTGT 59.377 40.909 17.47 5.65 0.00 3.72
2587 13334 3.068024 AGCACGTCCATCAAATTTGTGTT 59.932 39.130 17.47 2.55 0.00 3.32
2588 13335 3.425193 GCACGTCCATCAAATTTGTGTTC 59.575 43.478 17.47 9.13 0.00 3.18
2589 13336 3.980775 CACGTCCATCAAATTTGTGTTCC 59.019 43.478 17.47 4.39 0.00 3.62
2590 13337 3.233578 CGTCCATCAAATTTGTGTTCCG 58.766 45.455 17.47 11.66 0.00 4.30
2591 13338 3.058570 CGTCCATCAAATTTGTGTTCCGA 60.059 43.478 17.47 5.93 0.00 4.55
2592 13339 4.379394 CGTCCATCAAATTTGTGTTCCGAT 60.379 41.667 17.47 0.00 0.00 4.18
2593 13340 5.163804 CGTCCATCAAATTTGTGTTCCGATA 60.164 40.000 17.47 0.00 0.00 2.92
2594 13341 6.616947 GTCCATCAAATTTGTGTTCCGATAA 58.383 36.000 17.47 0.00 0.00 1.75
2595 13342 6.526674 GTCCATCAAATTTGTGTTCCGATAAC 59.473 38.462 17.47 1.72 0.00 1.89
2596 13343 6.207614 TCCATCAAATTTGTGTTCCGATAACA 59.792 34.615 17.47 0.00 0.00 2.41
2597 13344 6.865726 CCATCAAATTTGTGTTCCGATAACAA 59.134 34.615 17.47 0.00 32.19 2.83
2598 13345 7.545265 CCATCAAATTTGTGTTCCGATAACAAT 59.455 33.333 17.47 0.00 34.04 2.71
2599 13346 9.566530 CATCAAATTTGTGTTCCGATAACAATA 57.433 29.630 17.47 0.00 34.04 1.90
2600 13347 8.958175 TCAAATTTGTGTTCCGATAACAATAC 57.042 30.769 17.47 0.00 34.04 1.89
2601 13348 8.024285 TCAAATTTGTGTTCCGATAACAATACC 58.976 33.333 17.47 0.00 34.04 2.73
2602 13349 5.533533 TTTGTGTTCCGATAACAATACCG 57.466 39.130 5.08 0.00 34.04 4.02
2603 13350 2.931325 TGTGTTCCGATAACAATACCGC 59.069 45.455 5.08 0.00 31.20 5.68
2604 13351 2.931325 GTGTTCCGATAACAATACCGCA 59.069 45.455 5.08 0.00 31.20 5.69
2605 13352 3.371591 GTGTTCCGATAACAATACCGCAA 59.628 43.478 5.08 0.00 31.20 4.85
2606 13353 4.001652 TGTTCCGATAACAATACCGCAAA 58.998 39.130 1.38 0.00 0.00 3.68
2607 13354 4.636648 TGTTCCGATAACAATACCGCAAAT 59.363 37.500 1.38 0.00 0.00 2.32
2608 13355 4.804608 TCCGATAACAATACCGCAAATG 57.195 40.909 0.00 0.00 0.00 2.32
2609 13356 4.443621 TCCGATAACAATACCGCAAATGA 58.556 39.130 0.00 0.00 0.00 2.57
2610 13357 5.060506 TCCGATAACAATACCGCAAATGAT 58.939 37.500 0.00 0.00 0.00 2.45
2611 13358 5.178623 TCCGATAACAATACCGCAAATGATC 59.821 40.000 0.00 0.00 0.00 2.92
2612 13359 5.382303 CGATAACAATACCGCAAATGATCC 58.618 41.667 0.00 0.00 0.00 3.36
2613 13360 5.179368 CGATAACAATACCGCAAATGATCCT 59.821 40.000 0.00 0.00 0.00 3.24
2614 13361 6.293407 CGATAACAATACCGCAAATGATCCTT 60.293 38.462 0.00 0.00 0.00 3.36
2615 13362 5.659440 AACAATACCGCAAATGATCCTTT 57.341 34.783 0.00 0.00 0.00 3.11
2616 13363 5.248870 ACAATACCGCAAATGATCCTTTC 57.751 39.130 0.00 0.00 0.00 2.62
2617 13364 4.949856 ACAATACCGCAAATGATCCTTTCT 59.050 37.500 0.00 0.00 0.00 2.52
2618 13365 5.418840 ACAATACCGCAAATGATCCTTTCTT 59.581 36.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.596497 AGACCTTTGTCGTTGAAGTAAAAAGA 59.404 34.615 0.00 0.00 46.51 2.52
20 21 2.286418 GCAAGTGTTGAGACCTTTGTCG 60.286 50.000 0.00 0.00 46.51 4.35
27 28 0.890996 CTGGGGCAAGTGTTGAGACC 60.891 60.000 0.00 0.00 0.00 3.85
115 117 2.227194 GGTACCGATTGCCTTATTGGG 58.773 52.381 0.00 0.00 33.92 4.12
125 127 3.605634 TCACCTTTGATGGTACCGATTG 58.394 45.455 7.57 0.00 38.45 2.67
138 140 0.588252 CGCCAAGTGTCTCACCTTTG 59.412 55.000 0.00 0.00 34.49 2.77
146 148 1.122019 AAGGTCTCCGCCAAGTGTCT 61.122 55.000 0.00 0.00 0.00 3.41
197 199 8.303876 GTTTTATCTATCAACTCCCTGCAAAAA 58.696 33.333 0.00 0.00 0.00 1.94
198 200 7.669722 AGTTTTATCTATCAACTCCCTGCAAAA 59.330 33.333 0.00 0.00 0.00 2.44
199 201 7.175104 AGTTTTATCTATCAACTCCCTGCAAA 58.825 34.615 0.00 0.00 0.00 3.68
200 202 6.721318 AGTTTTATCTATCAACTCCCTGCAA 58.279 36.000 0.00 0.00 0.00 4.08
201 203 6.313519 AGTTTTATCTATCAACTCCCTGCA 57.686 37.500 0.00 0.00 0.00 4.41
202 204 6.852858 GAGTTTTATCTATCAACTCCCTGC 57.147 41.667 0.00 0.00 40.33 4.85
207 209 8.948631 TCACATGGAGTTTTATCTATCAACTC 57.051 34.615 0.00 3.17 43.87 3.01
454 461 4.504097 GGTTTCAAGAATGCAAACTGTCAC 59.496 41.667 0.00 0.00 32.22 3.67
561 574 4.320870 TCGGGTGTTTCTTTCAGGTATTC 58.679 43.478 0.00 0.00 0.00 1.75
567 580 3.138304 TGACATCGGGTGTTTCTTTCAG 58.862 45.455 0.00 0.00 42.36 3.02
605 3667 5.709966 ACAATTTGGAAAGCGTATTTCTCC 58.290 37.500 12.82 2.12 0.00 3.71
794 3886 4.864334 GGGTGCAGGGATGCGAGG 62.864 72.222 0.00 0.00 37.69 4.63
795 3887 4.864334 GGGGTGCAGGGATGCGAG 62.864 72.222 0.00 0.00 37.69 5.03
982 8199 3.353836 GATGGTTGTGCCGTGCGT 61.354 61.111 0.00 0.00 41.21 5.24
1389 8643 0.390340 TGATCAAGTGGTGCGAGCTC 60.390 55.000 2.73 2.73 0.00 4.09
1450 8704 7.351414 ACATCATAAATTACATCGATCACCG 57.649 36.000 0.00 0.00 40.25 4.94
1482 8736 2.488204 TGATCCATTCCAGCGAACAA 57.512 45.000 0.00 0.00 0.00 2.83
1500 8754 7.758495 AGTAAAGGGTAAATAACTGCGATTTG 58.242 34.615 0.00 0.00 0.00 2.32
1508 8762 5.688814 AGGCGAGTAAAGGGTAAATAACT 57.311 39.130 0.00 0.00 0.00 2.24
1522 8776 2.168521 CCCAAGAGATTGAAGGCGAGTA 59.831 50.000 0.00 0.00 0.00 2.59
1543 8797 9.136952 ACTAAAGAACACACGAATGTAGATTAC 57.863 33.333 0.00 0.00 36.72 1.89
1545 8799 8.088981 AGACTAAAGAACACACGAATGTAGATT 58.911 33.333 0.00 0.00 36.72 2.40
1549 8803 6.509656 ACAGACTAAAGAACACACGAATGTA 58.490 36.000 0.00 0.00 36.72 2.29
1552 8806 6.018180 GGAAACAGACTAAAGAACACACGAAT 60.018 38.462 0.00 0.00 0.00 3.34
1553 8807 5.292589 GGAAACAGACTAAAGAACACACGAA 59.707 40.000 0.00 0.00 0.00 3.85
1554 8808 4.807304 GGAAACAGACTAAAGAACACACGA 59.193 41.667 0.00 0.00 0.00 4.35
1555 8809 4.569162 TGGAAACAGACTAAAGAACACACG 59.431 41.667 0.00 0.00 35.01 4.49
1580 8834 8.726988 GGCAACAGTTATACACAGAATAAGAAA 58.273 33.333 0.00 0.00 0.00 2.52
1583 8837 7.609760 TGGCAACAGTTATACACAGAATAAG 57.390 36.000 0.00 0.00 46.17 1.73
1603 8858 2.083774 GTCCAGATGAACGATTTGGCA 58.916 47.619 0.00 0.00 36.44 4.92
1612 8867 4.816925 GCCTAACCTTATGTCCAGATGAAC 59.183 45.833 0.00 0.00 0.00 3.18
1614 8869 4.298626 AGCCTAACCTTATGTCCAGATGA 58.701 43.478 0.00 0.00 0.00 2.92
1616 8871 6.326970 AGATAGCCTAACCTTATGTCCAGAT 58.673 40.000 0.00 0.00 0.00 2.90
1618 8873 5.777732 AGAGATAGCCTAACCTTATGTCCAG 59.222 44.000 0.00 0.00 0.00 3.86
1621 8876 6.902771 TCAGAGATAGCCTAACCTTATGTC 57.097 41.667 0.00 0.00 0.00 3.06
1622 8877 7.863901 ATTCAGAGATAGCCTAACCTTATGT 57.136 36.000 0.00 0.00 0.00 2.29
1624 8879 8.497910 TGAATTCAGAGATAGCCTAACCTTAT 57.502 34.615 3.38 0.00 0.00 1.73
1626 8881 6.183361 CCTGAATTCAGAGATAGCCTAACCTT 60.183 42.308 32.49 0.00 46.59 3.50
1629 8884 6.220201 GTCCTGAATTCAGAGATAGCCTAAC 58.780 44.000 32.49 12.51 46.59 2.34
1635 8890 7.065204 TCGATATCGTCCTGAATTCAGAGATAG 59.935 40.741 32.49 22.66 42.32 2.08
1644 8899 4.693283 TGCTTTCGATATCGTCCTGAATT 58.307 39.130 23.61 0.00 40.80 2.17
1677 8932 1.412343 GCAAAACCTTCAGGCCTTTCA 59.588 47.619 0.00 0.00 39.32 2.69
1701 8956 1.240256 CTCCGTTCCCCTCTCTATCG 58.760 60.000 0.00 0.00 0.00 2.92
1716 8971 2.725008 GGTCGATGAGCTCCTCCG 59.275 66.667 12.15 11.85 0.00 4.63
1743 8998 1.617740 GACCAAACAAATAGCTGCGC 58.382 50.000 0.00 0.00 0.00 6.09
1774 9029 4.403585 AGGTAAAATAGAAGAGGCGACC 57.596 45.455 0.00 0.00 0.00 4.79
1801 9060 5.177511 TGTTCAACTGATAGCTGAAAAGACG 59.822 40.000 0.00 0.00 32.77 4.18
1830 9109 6.442541 TGGTTTAGAAGAGTAATTGGGTCA 57.557 37.500 0.00 0.00 0.00 4.02
1835 9114 8.237267 GGTGTGATTGGTTTAGAAGAGTAATTG 58.763 37.037 0.00 0.00 0.00 2.32
2065 9351 7.828717 TCCACATATTAGCTTTGATTCAAGTCA 59.171 33.333 0.00 0.00 0.00 3.41
2066 9352 8.213518 TCCACATATTAGCTTTGATTCAAGTC 57.786 34.615 0.00 0.00 0.00 3.01
2067 9353 8.757982 ATCCACATATTAGCTTTGATTCAAGT 57.242 30.769 0.00 0.00 0.00 3.16
2068 9354 9.459640 CAATCCACATATTAGCTTTGATTCAAG 57.540 33.333 0.00 0.00 0.00 3.02
2104 9396 7.013369 TCACATAGTGACATACATACTCTGTCC 59.987 40.741 0.00 0.00 37.67 4.02
2107 9399 7.229506 TCCTCACATAGTGACATACATACTCTG 59.770 40.741 0.00 0.00 37.67 3.35
2169 12915 2.054799 ACAGTTCTCCCCAACAGCTTA 58.945 47.619 0.00 0.00 0.00 3.09
2233 12979 9.554724 GACACAAAACTTACATGTGGTTATATG 57.445 33.333 9.11 14.06 46.67 1.78
2235 12981 8.678593 TGACACAAAACTTACATGTGGTTATA 57.321 30.769 9.11 0.00 46.67 0.98
2238 12984 5.906113 TGACACAAAACTTACATGTGGTT 57.094 34.783 9.11 10.63 46.67 3.67
2240 12986 5.890334 ACTTGACACAAAACTTACATGTGG 58.110 37.500 9.11 3.79 46.67 4.17
2248 12994 8.778358 TGCAAAAATTAACTTGACACAAAACTT 58.222 25.926 0.00 0.00 0.00 2.66
2249 12995 8.316640 TGCAAAAATTAACTTGACACAAAACT 57.683 26.923 0.00 0.00 0.00 2.66
2250 12996 8.941127 TTGCAAAAATTAACTTGACACAAAAC 57.059 26.923 0.00 0.00 0.00 2.43
2251 12997 9.604626 CTTTGCAAAAATTAACTTGACACAAAA 57.395 25.926 13.84 0.00 0.00 2.44
2252 12998 8.778358 ACTTTGCAAAAATTAACTTGACACAAA 58.222 25.926 13.84 0.00 0.00 2.83
2253 12999 8.316640 ACTTTGCAAAAATTAACTTGACACAA 57.683 26.923 13.84 0.00 0.00 3.33
2254 13000 7.897575 ACTTTGCAAAAATTAACTTGACACA 57.102 28.000 13.84 0.00 0.00 3.72
2267 13013 6.566197 ACAATTGGTCAAACTTTGCAAAAA 57.434 29.167 13.84 2.22 0.00 1.94
2424 13171 8.868916 GCAAATAAGTTTTGTCTCAAGTCAAAA 58.131 29.630 9.93 9.93 39.44 2.44
2467 13214 5.363101 TGCAAGGATCATCATTACTCACTC 58.637 41.667 0.00 0.00 0.00 3.51
2471 13218 5.919141 GCAATTGCAAGGATCATCATTACTC 59.081 40.000 25.36 0.00 41.59 2.59
2499 13246 3.619767 TGTCAGTGCTGAGCCGCT 61.620 61.111 0.23 0.00 40.75 5.52
2543 13290 5.237344 GCTGTCATGTCTAGTGTGTCTTTTT 59.763 40.000 0.00 0.00 0.00 1.94
2544 13291 4.752101 GCTGTCATGTCTAGTGTGTCTTTT 59.248 41.667 0.00 0.00 0.00 2.27
2545 13292 4.202253 TGCTGTCATGTCTAGTGTGTCTTT 60.202 41.667 0.00 0.00 0.00 2.52
2546 13293 3.321968 TGCTGTCATGTCTAGTGTGTCTT 59.678 43.478 0.00 0.00 0.00 3.01
2547 13294 2.893489 TGCTGTCATGTCTAGTGTGTCT 59.107 45.455 0.00 0.00 0.00 3.41
2548 13295 2.989840 GTGCTGTCATGTCTAGTGTGTC 59.010 50.000 0.00 0.00 0.00 3.67
2549 13296 2.608016 CGTGCTGTCATGTCTAGTGTGT 60.608 50.000 0.00 0.00 0.00 3.72
2550 13297 1.988467 CGTGCTGTCATGTCTAGTGTG 59.012 52.381 0.00 0.00 0.00 3.82
2551 13298 1.613925 ACGTGCTGTCATGTCTAGTGT 59.386 47.619 0.00 0.00 37.94 3.55
2552 13299 2.354109 ACGTGCTGTCATGTCTAGTG 57.646 50.000 0.00 0.00 37.94 2.74
2563 13310 2.622942 ACAAATTTGATGGACGTGCTGT 59.377 40.909 24.64 0.00 0.00 4.40
2564 13311 2.981805 CACAAATTTGATGGACGTGCTG 59.018 45.455 24.64 4.59 0.00 4.41
2565 13312 2.622942 ACACAAATTTGATGGACGTGCT 59.377 40.909 24.64 0.00 0.00 4.40
2566 13313 3.011949 ACACAAATTTGATGGACGTGC 57.988 42.857 24.64 0.00 0.00 5.34
2567 13314 3.980775 GGAACACAAATTTGATGGACGTG 59.019 43.478 24.64 12.38 0.00 4.49
2568 13315 3.304391 CGGAACACAAATTTGATGGACGT 60.304 43.478 24.64 8.36 0.00 4.34
2569 13316 3.058570 TCGGAACACAAATTTGATGGACG 60.059 43.478 24.64 19.87 0.00 4.79
2570 13317 4.497473 TCGGAACACAAATTTGATGGAC 57.503 40.909 24.64 14.58 0.00 4.02
2571 13318 6.207614 TGTTATCGGAACACAAATTTGATGGA 59.792 34.615 24.64 11.99 0.00 3.41
2572 13319 6.385843 TGTTATCGGAACACAAATTTGATGG 58.614 36.000 24.64 14.74 0.00 3.51
2573 13320 7.865875 TTGTTATCGGAACACAAATTTGATG 57.134 32.000 24.64 18.94 0.00 3.07
2574 13321 9.567848 GTATTGTTATCGGAACACAAATTTGAT 57.432 29.630 24.64 9.34 34.19 2.57
2575 13322 8.024285 GGTATTGTTATCGGAACACAAATTTGA 58.976 33.333 24.64 0.36 34.19 2.69
2576 13323 7.007905 CGGTATTGTTATCGGAACACAAATTTG 59.992 37.037 16.67 16.67 34.19 2.32
2577 13324 7.024768 CGGTATTGTTATCGGAACACAAATTT 58.975 34.615 8.81 0.00 34.19 1.82
2578 13325 6.548171 CGGTATTGTTATCGGAACACAAATT 58.452 36.000 8.81 0.00 34.19 1.82
2579 13326 5.448089 GCGGTATTGTTATCGGAACACAAAT 60.448 40.000 8.81 0.00 34.19 2.32
2580 13327 4.142859 GCGGTATTGTTATCGGAACACAAA 60.143 41.667 8.81 0.00 34.19 2.83
2581 13328 3.371591 GCGGTATTGTTATCGGAACACAA 59.628 43.478 7.55 7.55 32.42 3.33
2582 13329 2.931325 GCGGTATTGTTATCGGAACACA 59.069 45.455 3.65 0.00 32.42 3.72
2583 13330 2.931325 TGCGGTATTGTTATCGGAACAC 59.069 45.455 3.65 0.00 32.42 3.32
2584 13331 3.248495 TGCGGTATTGTTATCGGAACA 57.752 42.857 0.34 0.34 32.42 3.18
2585 13332 4.603231 TTTGCGGTATTGTTATCGGAAC 57.397 40.909 0.00 0.00 41.20 3.62
2586 13333 4.876679 TCATTTGCGGTATTGTTATCGGAA 59.123 37.500 0.00 0.00 40.00 4.30
2587 13334 4.443621 TCATTTGCGGTATTGTTATCGGA 58.556 39.130 0.00 0.00 32.42 4.55
2588 13335 4.804608 TCATTTGCGGTATTGTTATCGG 57.195 40.909 0.00 0.00 32.42 4.18
2589 13336 5.179368 AGGATCATTTGCGGTATTGTTATCG 59.821 40.000 0.00 0.00 34.98 2.92
2590 13337 6.560253 AGGATCATTTGCGGTATTGTTATC 57.440 37.500 0.00 0.00 0.00 1.75
2591 13338 6.959639 AAGGATCATTTGCGGTATTGTTAT 57.040 33.333 0.00 0.00 0.00 1.89
2592 13339 6.601613 AGAAAGGATCATTTGCGGTATTGTTA 59.398 34.615 10.56 0.00 0.00 2.41
2593 13340 5.418840 AGAAAGGATCATTTGCGGTATTGTT 59.581 36.000 10.56 0.00 0.00 2.83
2594 13341 4.949856 AGAAAGGATCATTTGCGGTATTGT 59.050 37.500 10.56 0.00 0.00 2.71
2595 13342 5.505173 AGAAAGGATCATTTGCGGTATTG 57.495 39.130 10.56 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.