Multiple sequence alignment - TraesCS7D01G206000

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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 TraesCS7D01G206000 chr7D 100.000 4613 0 0 1 4613 163259728 163255116 0.000000e+00 8519.0
1 TraesCS7D01G206000 chr7D 91.347 809 41 13 1 785 511148507 511149310 0.000000e+00 1079.0
2 TraesCS7D01G206000 chr7D 91.310 794 44 11 1 784 214775886 214775108 0.000000e+00 1061.0
3 TraesCS7D01G206000 chr7D 100.000 42 0 0 2512 2553 163257177 163257136 1.380000e-10 78.7
4 TraesCS7D01G206000 chr7D 100.000 42 0 0 2552 2593 163257217 163257176 1.380000e-10 78.7
5 TraesCS7D01G206000 chr7B 93.690 1759 72 13 803 2553 125506664 125504937 0.000000e+00 2597.0
6 TraesCS7D01G206000 chr7B 92.690 1669 73 24 2962 4613 125504589 125502953 0.000000e+00 2361.0
7 TraesCS7D01G206000 chr7B 91.599 369 16 5 2561 2915 125504969 125504602 3.210000e-136 496.0
8 TraesCS7D01G206000 chr7A 93.444 1754 76 17 2876 4613 164399928 164398198 0.000000e+00 2566.0
9 TraesCS7D01G206000 chr7A 95.526 1140 39 6 815 1950 164402461 164401330 0.000000e+00 1812.0
10 TraesCS7D01G206000 chr7A 91.832 404 23 4 1996 2394 164401331 164400933 5.210000e-154 555.0
11 TraesCS7D01G206000 chr6D 92.569 794 45 10 1 785 396978407 396977619 0.000000e+00 1127.0
12 TraesCS7D01G206000 chr6D 81.889 646 91 16 1066 1701 385955841 385956470 5.290000e-144 521.0
13 TraesCS7D01G206000 chr5B 89.698 796 68 11 1 787 214439512 214440302 0.000000e+00 1003.0
14 TraesCS7D01G206000 chr5B 86.003 793 98 8 1 783 416016121 416015332 0.000000e+00 837.0
15 TraesCS7D01G206000 chr3B 88.889 801 67 17 1 787 814637788 814638580 0.000000e+00 966.0
16 TraesCS7D01G206000 chr3B 80.075 803 139 14 1 786 469814596 469813798 1.110000e-160 577.0
17 TraesCS7D01G206000 chr2B 88.185 584 33 10 222 787 109196157 109195592 0.000000e+00 664.0
18 TraesCS7D01G206000 chr2B 86.396 566 63 9 228 782 782729897 782729335 1.420000e-169 606.0
19 TraesCS7D01G206000 chr4D 81.887 795 131 8 1 785 471227107 471227898 0.000000e+00 658.0
20 TraesCS7D01G206000 chr6B 81.406 640 104 11 1066 1701 576362041 576362669 4.120000e-140 508.0
21 TraesCS7D01G206000 chr6A 81.123 641 105 12 1066 1701 530279211 530279840 2.480000e-137 499.0


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 TraesCS7D01G206000 chr7D 163255116 163259728 4612 True 2892.133333 8519 100.000000 1 4613 3 chr7D.!!$R2 4612
1 TraesCS7D01G206000 chr7D 511148507 511149310 803 False 1079.000000 1079 91.347000 1 785 1 chr7D.!!$F1 784
2 TraesCS7D01G206000 chr7D 214775108 214775886 778 True 1061.000000 1061 91.310000 1 784 1 chr7D.!!$R1 783
3 TraesCS7D01G206000 chr7B 125502953 125506664 3711 True 1818.000000 2597 92.659667 803 4613 3 chr7B.!!$R1 3810
4 TraesCS7D01G206000 chr7A 164398198 164402461 4263 True 1644.333333 2566 93.600667 815 4613 3 chr7A.!!$R1 3798
5 TraesCS7D01G206000 chr6D 396977619 396978407 788 True 1127.000000 1127 92.569000 1 785 1 chr6D.!!$R1 784
6 TraesCS7D01G206000 chr6D 385955841 385956470 629 False 521.000000 521 81.889000 1066 1701 1 chr6D.!!$F1 635
7 TraesCS7D01G206000 chr5B 214439512 214440302 790 False 1003.000000 1003 89.698000 1 787 1 chr5B.!!$F1 786
8 TraesCS7D01G206000 chr5B 416015332 416016121 789 True 837.000000 837 86.003000 1 783 1 chr5B.!!$R1 782
9 TraesCS7D01G206000 chr3B 814637788 814638580 792 False 966.000000 966 88.889000 1 787 1 chr3B.!!$F1 786
10 TraesCS7D01G206000 chr3B 469813798 469814596 798 True 577.000000 577 80.075000 1 786 1 chr3B.!!$R1 785
11 TraesCS7D01G206000 chr2B 109195592 109196157 565 True 664.000000 664 88.185000 222 787 1 chr2B.!!$R1 565
12 TraesCS7D01G206000 chr2B 782729335 782729897 562 True 606.000000 606 86.396000 228 782 1 chr2B.!!$R2 554
13 TraesCS7D01G206000 chr4D 471227107 471227898 791 False 658.000000 658 81.887000 1 785 1 chr4D.!!$F1 784
14 TraesCS7D01G206000 chr6B 576362041 576362669 628 False 508.000000 508 81.406000 1066 1701 1 chr6B.!!$F1 635
15 TraesCS7D01G206000 chr6A 530279211 530279840 629 False 499.000000 499 81.123000 1066 1701 1 chr6A.!!$F1 635

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
413 433 0.631212 AATCAACATCCCTCCCCACC 59.369 55.000 0.00 0.0 0.00 4.61 F
980 1031 1.201812 GCATCAAACACTAGCACGTCG 60.202 52.381 0.00 0.0 0.00 5.12 F
1918 1969 0.107081 CGTCCAAGGTAACCACACCA 59.893 55.000 0.00 0.0 41.40 4.17 F
2375 2432 0.384309 CATGTCTGCACCATGATGGC 59.616 55.000 12.25 0.0 42.67 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1362 0.116143 AGTTGCAGAGGGAGGAGAGT 59.884 55.0 0.00 0.0 0.00 3.24 R
2131 2182 0.451783 CAAGTAACCGGATTGGCAGC 59.548 55.0 9.46 0.0 43.94 5.25 R
3198 3831 0.549950 AGCTACGGAGTACCCTAGCA 59.450 55.0 20.46 0.0 46.08 3.49 R
3615 4250 0.704076 ATCCCTGCTGCAACCCTTAA 59.296 50.0 3.02 0.0 0.00 1.85 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
18 19 1.287815 TCGACGTTCAACCGCAGAT 59.712 52.632 0.00 0.00 0.00 2.90
27 28 3.793797 TCAACCGCAGATATCTTTCGA 57.206 42.857 19.99 3.72 0.00 3.71
220 221 3.484547 CGTAGTTGGGCGCCGTTC 61.485 66.667 22.54 12.76 0.00 3.95
411 431 1.619432 GCAAATCAACATCCCTCCCCA 60.619 52.381 0.00 0.00 0.00 4.96
412 432 2.102578 CAAATCAACATCCCTCCCCAC 58.897 52.381 0.00 0.00 0.00 4.61
413 433 0.631212 AATCAACATCCCTCCCCACC 59.369 55.000 0.00 0.00 0.00 4.61
414 434 1.289244 ATCAACATCCCTCCCCACCC 61.289 60.000 0.00 0.00 0.00 4.61
415 435 2.617215 AACATCCCTCCCCACCCC 60.617 66.667 0.00 0.00 0.00 4.95
416 436 4.779486 ACATCCCTCCCCACCCCC 62.779 72.222 0.00 0.00 0.00 5.40
435 455 3.256960 ACCCCCAACAGCACGGAT 61.257 61.111 0.00 0.00 0.00 4.18
622 660 2.487762 GCCATCCTTGACGAAATTCACA 59.512 45.455 0.00 0.00 0.00 3.58
625 663 4.475944 CATCCTTGACGAAATTCACAACC 58.524 43.478 0.00 0.00 0.00 3.77
741 785 1.296867 GTTCGCATTGATCGCACGG 60.297 57.895 0.00 0.00 0.00 4.94
787 834 8.189460 CCCTTCTATAAAGATATGGTACGCTAC 58.811 40.741 0.00 0.00 0.00 3.58
788 835 8.958506 CCTTCTATAAAGATATGGTACGCTACT 58.041 37.037 0.00 0.00 0.00 2.57
789 836 9.991388 CTTCTATAAAGATATGGTACGCTACTC 57.009 37.037 0.00 0.00 0.00 2.59
790 837 9.736414 TTCTATAAAGATATGGTACGCTACTCT 57.264 33.333 0.00 0.00 0.00 3.24
791 838 9.381033 TCTATAAAGATATGGTACGCTACTCTC 57.619 37.037 0.00 0.00 0.00 3.20
792 839 5.359716 AAAGATATGGTACGCTACTCTCG 57.640 43.478 0.00 0.00 0.00 4.04
793 840 3.336468 AGATATGGTACGCTACTCTCGG 58.664 50.000 0.00 0.00 0.00 4.63
794 841 2.916702 TATGGTACGCTACTCTCGGA 57.083 50.000 0.00 0.00 0.00 4.55
795 842 2.048444 ATGGTACGCTACTCTCGGAA 57.952 50.000 0.00 0.00 0.00 4.30
796 843 1.825090 TGGTACGCTACTCTCGGAAA 58.175 50.000 0.00 0.00 0.00 3.13
797 844 2.161855 TGGTACGCTACTCTCGGAAAA 58.838 47.619 0.00 0.00 0.00 2.29
798 845 2.557924 TGGTACGCTACTCTCGGAAAAA 59.442 45.455 0.00 0.00 0.00 1.94
887 938 1.561643 TCAAGCCTACTCCACTCCAG 58.438 55.000 0.00 0.00 0.00 3.86
947 998 2.102252 CGCTTATCTTCCTCAGCTTCCT 59.898 50.000 0.00 0.00 0.00 3.36
949 1000 4.627058 GCTTATCTTCCTCAGCTTCCTAC 58.373 47.826 0.00 0.00 0.00 3.18
980 1031 1.201812 GCATCAAACACTAGCACGTCG 60.202 52.381 0.00 0.00 0.00 5.12
1260 1311 2.716017 GCTCTACCAGTGCCGCTCT 61.716 63.158 0.00 0.00 0.00 4.09
1911 1962 3.866356 GGCGACGTCCAAGGTAAC 58.134 61.111 10.58 0.00 0.00 2.50
1916 1967 1.505425 GACGTCCAAGGTAACCACAC 58.495 55.000 3.51 0.00 37.17 3.82
1918 1969 0.107081 CGTCCAAGGTAACCACACCA 59.893 55.000 0.00 0.00 41.40 4.17
1919 1970 1.601166 GTCCAAGGTAACCACACCAC 58.399 55.000 0.00 0.00 41.40 4.16
1920 1971 1.134037 GTCCAAGGTAACCACACCACA 60.134 52.381 0.00 0.00 41.40 4.17
1922 1973 1.314730 CAAGGTAACCACACCACACC 58.685 55.000 0.00 0.00 41.40 4.16
1923 1974 0.920438 AAGGTAACCACACCACACCA 59.080 50.000 0.00 0.00 41.40 4.17
1962 2013 1.140652 CTTGCCCTCCTCAGATCCTTC 59.859 57.143 0.00 0.00 0.00 3.46
1973 2024 2.026822 TCAGATCCTTCCTTCCACTTGC 60.027 50.000 0.00 0.00 0.00 4.01
1977 2028 1.667830 CTTCCTTCCACTTGCGCGA 60.668 57.895 12.10 0.00 0.00 5.87
1978 2029 1.901650 CTTCCTTCCACTTGCGCGAC 61.902 60.000 12.10 0.88 0.00 5.19
1979 2030 3.777925 CCTTCCACTTGCGCGACG 61.778 66.667 12.10 0.00 0.00 5.12
1992 2043 1.847027 GCGCGACGTAGAATTTTCAGC 60.847 52.381 12.10 0.00 0.00 4.26
2012 2063 2.286242 GCTGCTGATTGATGATCACACG 60.286 50.000 0.00 0.00 39.83 4.49
2037 2088 4.327087 CGTGTACGTACCACCTTAATTTCC 59.673 45.833 22.43 0.00 34.11 3.13
2088 2139 1.080907 CTCGCATCGATGATCGGCT 60.081 57.895 29.20 0.00 40.88 5.52
2220 2276 1.467875 CTAGCTTGCACTACGCGTAG 58.532 55.000 37.61 37.61 46.97 3.51
2261 2317 1.265095 TGAGACGGGCGTACGATTATC 59.735 52.381 21.65 10.50 37.61 1.75
2275 2331 9.354544 GCGTACGATTATCTTTGTTAAGAATTC 57.645 33.333 21.65 0.00 43.32 2.17
2276 2332 9.551200 CGTACGATTATCTTTGTTAAGAATTCG 57.449 33.333 10.44 0.00 43.32 3.34
2277 2333 9.354544 GTACGATTATCTTTGTTAAGAATTCGC 57.645 33.333 0.00 0.00 43.32 4.70
2280 2336 9.784824 CGATTATCTTTGTTAAGAATTCGCTAG 57.215 33.333 0.00 0.00 43.32 3.42
2288 2345 3.477210 AAGAATTCGCTAGGATCACCC 57.523 47.619 0.00 0.00 36.73 4.61
2375 2432 0.384309 CATGTCTGCACCATGATGGC 59.616 55.000 12.25 0.00 42.67 4.40
2376 2433 0.754217 ATGTCTGCACCATGATGGCC 60.754 55.000 12.25 3.44 42.67 5.36
2381 2438 3.879682 CACCATGATGGCCGCACG 61.880 66.667 12.25 0.00 42.67 5.34
2412 2470 3.625853 AGGGGAAGCTTTCTAGATTTGC 58.374 45.455 4.35 0.00 28.22 3.68
2446 2516 8.110860 ACTACAGTTGCTATTTACAAAATGCT 57.889 30.769 0.00 0.00 0.00 3.79
2447 2517 9.226606 ACTACAGTTGCTATTTACAAAATGCTA 57.773 29.630 0.00 0.00 0.00 3.49
2471 2541 7.124573 AGTTGCCTTTTCTTCAGGTTTAATT 57.875 32.000 0.00 0.00 33.40 1.40
2509 2579 4.380867 GCACTACAATGCAAGGCAAATACT 60.381 41.667 0.00 0.00 43.62 2.12
2510 2580 5.335127 CACTACAATGCAAGGCAAATACTC 58.665 41.667 0.00 0.00 43.62 2.59
2512 2582 3.164268 ACAATGCAAGGCAAATACTCCA 58.836 40.909 0.00 0.00 43.62 3.86
2513 2583 3.770933 ACAATGCAAGGCAAATACTCCAT 59.229 39.130 0.00 0.00 43.62 3.41
2514 2584 4.955450 ACAATGCAAGGCAAATACTCCATA 59.045 37.500 0.00 0.00 43.62 2.74
2515 2585 5.068198 ACAATGCAAGGCAAATACTCCATAG 59.932 40.000 0.00 0.00 43.62 2.23
2516 2586 4.502105 TGCAAGGCAAATACTCCATAGA 57.498 40.909 0.00 0.00 34.76 1.98
2519 2589 4.276926 GCAAGGCAAATACTCCATAGAAGG 59.723 45.833 0.00 0.00 0.00 3.46
2520 2590 5.684704 CAAGGCAAATACTCCATAGAAGGA 58.315 41.667 0.00 0.00 36.00 3.36
2535 2605 7.844779 TCCATAGAAGGAGTATTTGGTTAGAGT 59.155 37.037 0.00 0.00 32.77 3.24
2536 2606 8.487028 CCATAGAAGGAGTATTTGGTTAGAGTT 58.513 37.037 0.00 0.00 0.00 3.01
2537 2607 9.892130 CATAGAAGGAGTATTTGGTTAGAGTTT 57.108 33.333 0.00 0.00 0.00 2.66
2539 2609 8.622948 AGAAGGAGTATTTGGTTAGAGTTTTG 57.377 34.615 0.00 0.00 0.00 2.44
2540 2610 8.218488 AGAAGGAGTATTTGGTTAGAGTTTTGT 58.782 33.333 0.00 0.00 0.00 2.83
2542 2612 8.762481 AGGAGTATTTGGTTAGAGTTTTGTTT 57.238 30.769 0.00 0.00 0.00 2.83
2544 2614 8.626526 GGAGTATTTGGTTAGAGTTTTGTTTCA 58.373 33.333 0.00 0.00 0.00 2.69
2545 2615 9.665264 GAGTATTTGGTTAGAGTTTTGTTTCAG 57.335 33.333 0.00 0.00 0.00 3.02
2546 2616 9.403583 AGTATTTGGTTAGAGTTTTGTTTCAGA 57.596 29.630 0.00 0.00 0.00 3.27
2548 2618 8.926715 ATTTGGTTAGAGTTTTGTTTCAGAAC 57.073 30.769 0.00 0.00 36.29 3.01
2549 2619 6.445357 TGGTTAGAGTTTTGTTTCAGAACC 57.555 37.500 0.00 0.00 34.80 3.62
2550 2620 5.946972 TGGTTAGAGTTTTGTTTCAGAACCA 59.053 36.000 0.00 0.00 38.33 3.67
2551 2621 6.127842 TGGTTAGAGTTTTGTTTCAGAACCAC 60.128 38.462 0.00 0.00 37.00 4.16
2552 2622 6.127842 GGTTAGAGTTTTGTTTCAGAACCACA 60.128 38.462 0.00 0.00 34.36 4.17
2553 2623 7.416326 GGTTAGAGTTTTGTTTCAGAACCACAT 60.416 37.037 0.00 0.00 34.36 3.21
2555 2625 7.264373 AGAGTTTTGTTTCAGAACCACATAG 57.736 36.000 0.70 0.00 34.80 2.23
2556 2626 7.054124 AGAGTTTTGTTTCAGAACCACATAGA 58.946 34.615 0.70 0.00 34.80 1.98
2557 2627 7.556275 AGAGTTTTGTTTCAGAACCACATAGAA 59.444 33.333 0.70 0.00 34.80 2.10
2558 2628 7.707104 AGTTTTGTTTCAGAACCACATAGAAG 58.293 34.615 0.70 0.00 34.80 2.85
2559 2629 6.633500 TTTGTTTCAGAACCACATAGAAGG 57.367 37.500 0.00 0.00 34.80 3.46
2603 2673 3.194861 TCAGAACCACACTTCGACAAAG 58.805 45.455 0.00 0.00 41.08 2.77
2615 2685 7.112148 CACACTTCGACAAAGCTAAAGAAAATC 59.888 37.037 0.00 0.00 38.67 2.17
2628 2871 8.220559 AGCTAAAGAAAATCTTATCAGGCCATA 58.779 33.333 5.01 0.00 35.27 2.74
2704 2949 9.653287 TTCTTAGACTGACAATATAAACAGTGG 57.347 33.333 11.47 3.08 42.45 4.00
2715 2960 1.172180 AAACAGTGGGCGACATGGTG 61.172 55.000 1.61 0.00 0.00 4.17
2753 2998 7.046033 GTCAAAATCTACTCCGGAAATTAGGA 58.954 38.462 5.23 0.00 34.93 2.94
2817 3062 5.987347 CAGGTAGAACGTTCCTTCAGTTTTA 59.013 40.000 24.22 4.44 0.00 1.52
2818 3063 6.649557 CAGGTAGAACGTTCCTTCAGTTTTAT 59.350 38.462 24.22 4.19 0.00 1.40
2823 3068 8.851960 AGAACGTTCCTTCAGTTTTATTTTTC 57.148 30.769 24.22 0.00 0.00 2.29
2915 3547 1.071471 AGTTCGACCCTGCTTGTGG 59.929 57.895 0.00 0.00 0.00 4.17
2916 3548 2.281484 TTCGACCCTGCTTGTGGC 60.281 61.111 0.00 0.00 42.22 5.01
2939 3571 2.410785 CATTCCCTAATGCATGCACG 57.589 50.000 25.37 14.23 36.35 5.34
2970 3603 2.683768 AGATGGCCCTCCTAGTTACTG 58.316 52.381 0.00 0.00 0.00 2.74
3105 3738 4.437682 TGTGGATTCACTTTCCTGTTCT 57.562 40.909 5.55 0.00 43.94 3.01
3106 3739 4.792068 TGTGGATTCACTTTCCTGTTCTT 58.208 39.130 5.55 0.00 43.94 2.52
3107 3740 4.821805 TGTGGATTCACTTTCCTGTTCTTC 59.178 41.667 5.55 0.00 43.94 2.87
3198 3831 2.847234 TCTCTGGCACCCACCGTT 60.847 61.111 0.00 0.00 0.00 4.44
3212 3845 1.318158 ACCGTTGCTAGGGTACTCCG 61.318 60.000 10.88 0.00 40.64 4.63
3411 4045 0.460284 CAGATGGTTCCGGGAAGACG 60.460 60.000 10.35 0.00 0.00 4.18
3509 4143 1.092348 GCCAATGGTAAGACCCGAAC 58.908 55.000 0.00 0.00 37.50 3.95
3534 4168 1.716581 GCCGAGAATCATCGTCGAATC 59.283 52.381 0.00 0.00 41.12 2.52
3615 4250 1.553706 ATGCAGGCAAAAGCTAAGCT 58.446 45.000 0.00 0.00 42.56 3.74
3744 4380 6.461110 TTATAGGGTCTCTCTTTTACCGTG 57.539 41.667 0.00 0.00 33.66 4.94
3745 4381 2.606378 AGGGTCTCTCTTTTACCGTGT 58.394 47.619 0.00 0.00 33.89 4.49
3746 4382 2.561858 AGGGTCTCTCTTTTACCGTGTC 59.438 50.000 0.00 0.00 33.89 3.67
3747 4383 2.298163 GGGTCTCTCTTTTACCGTGTCA 59.702 50.000 0.00 0.00 33.89 3.58
3748 4384 3.056035 GGGTCTCTCTTTTACCGTGTCAT 60.056 47.826 0.00 0.00 33.89 3.06
3749 4385 4.174762 GGTCTCTCTTTTACCGTGTCATC 58.825 47.826 0.00 0.00 0.00 2.92
3750 4386 4.321750 GGTCTCTCTTTTACCGTGTCATCA 60.322 45.833 0.00 0.00 0.00 3.07
3751 4387 5.411781 GTCTCTCTTTTACCGTGTCATCAT 58.588 41.667 0.00 0.00 0.00 2.45
3752 4388 6.405508 GGTCTCTCTTTTACCGTGTCATCATA 60.406 42.308 0.00 0.00 0.00 2.15
3753 4389 6.693545 GTCTCTCTTTTACCGTGTCATCATAG 59.306 42.308 0.00 0.00 0.00 2.23
3754 4390 5.902681 TCTCTTTTACCGTGTCATCATAGG 58.097 41.667 0.00 0.00 0.00 2.57
3774 4410 2.316108 GGCCAGAAAAACAAAGGGAGA 58.684 47.619 0.00 0.00 0.00 3.71
3850 4486 9.408069 CTACTAGCCACTAAGGAAAATATTACG 57.592 37.037 0.00 0.00 41.22 3.18
3851 4487 6.704937 ACTAGCCACTAAGGAAAATATTACGC 59.295 38.462 0.00 0.00 41.22 4.42
3852 4488 5.433526 AGCCACTAAGGAAAATATTACGCA 58.566 37.500 0.00 0.00 41.22 5.24
3853 4489 5.883673 AGCCACTAAGGAAAATATTACGCAA 59.116 36.000 0.00 0.00 41.22 4.85
3936 4575 2.799978 TGTTGTACTGCTGTTCATGTCG 59.200 45.455 0.09 0.00 0.00 4.35
3941 4582 1.526887 ACTGCTGTTCATGTCGTTTCG 59.473 47.619 0.00 0.00 0.00 3.46
3948 4589 3.242478 TGTTCATGTCGTTTCGTTGGTTC 60.242 43.478 0.00 0.00 0.00 3.62
4018 4665 4.634012 TTAGTACAATCTTGTGGGCTGT 57.366 40.909 5.84 0.00 42.31 4.40
4019 4666 3.508845 AGTACAATCTTGTGGGCTGTT 57.491 42.857 5.84 0.00 42.31 3.16
4035 4682 6.546034 GTGGGCTGTTGTTGGAGTAAATATAT 59.454 38.462 0.00 0.00 0.00 0.86
4037 4684 8.275758 TGGGCTGTTGTTGGAGTAAATATATAA 58.724 33.333 0.00 0.00 0.00 0.98
4039 4686 9.946165 GGCTGTTGTTGGAGTAAATATATAAAC 57.054 33.333 0.00 0.00 0.00 2.01
4063 4710 9.846248 AACTTTCTCAAAATATATGTTGCTGAC 57.154 29.630 10.38 0.00 0.00 3.51
4080 4727 1.074084 TGACTAATGCGGTTGGGGAAA 59.926 47.619 0.00 0.00 0.00 3.13
4081 4728 1.743394 GACTAATGCGGTTGGGGAAAG 59.257 52.381 0.00 0.00 0.00 2.62
4092 4739 4.464597 CGGTTGGGGAAAGGAATAATTTCA 59.535 41.667 1.37 0.00 38.21 2.69
4176 4826 9.910511 CAAAATGCATCTTTATGTAATCTTTGC 57.089 29.630 0.00 0.00 35.38 3.68
4262 4912 6.766944 ACCAATTGTGAATTCAAAAGCATGAA 59.233 30.769 16.02 2.66 43.03 2.57
4271 4921 8.015087 TGAATTCAAAAGCATGAAGTACGTTAG 58.985 33.333 5.45 0.00 42.21 2.34
4287 4937 7.153985 AGTACGTTAGTTATGCAAACAAGGTA 58.846 34.615 0.00 14.00 0.00 3.08
4311 4962 4.520179 TGCAACTCATCATGTGCTAATCT 58.480 39.130 5.47 0.00 0.00 2.40
4345 4996 3.381590 GTGGCCTTTCTGTCAATAATCCC 59.618 47.826 3.32 0.00 0.00 3.85
4525 5185 3.685272 GGAGGTTCAGCTTAAGCAGTAAC 59.315 47.826 28.39 24.45 45.16 2.50
4569 5229 3.349927 ACAAAGTATTAGAAACCGGGGC 58.650 45.455 6.32 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.450082 TGTAGCAGTGCTTCGAAAGATA 57.550 40.909 25.23 0.00 40.44 1.98
27 28 3.065371 GTGAACTGTTTGTAGCAGTGCTT 59.935 43.478 25.23 7.65 45.36 3.91
220 221 3.611057 GCCAGACAAAGATCTTGCACTTG 60.611 47.826 9.17 5.63 37.33 3.16
414 434 4.994756 GTGCTGTTGGGGGTGGGG 62.995 72.222 0.00 0.00 0.00 4.96
417 437 2.191786 TATCCGTGCTGTTGGGGGTG 62.192 60.000 0.00 0.00 0.00 4.61
418 438 1.921346 TATCCGTGCTGTTGGGGGT 60.921 57.895 0.00 0.00 0.00 4.95
419 439 1.451387 GTATCCGTGCTGTTGGGGG 60.451 63.158 0.00 0.00 0.00 5.40
420 440 0.107214 ATGTATCCGTGCTGTTGGGG 60.107 55.000 0.00 0.00 0.00 4.96
625 663 2.029288 CTACACCTGCACTGTGCCG 61.029 63.158 28.17 22.06 44.23 5.69
741 785 8.797438 AGAAGGGAGAAAACAATTTACAAGATC 58.203 33.333 0.00 0.00 0.00 2.75
798 845 6.490040 ACTGTCACCAGCATAGTATTGTTTTT 59.510 34.615 0.00 0.00 42.81 1.94
799 846 6.003950 ACTGTCACCAGCATAGTATTGTTTT 58.996 36.000 0.00 0.00 42.81 2.43
800 847 5.412594 CACTGTCACCAGCATAGTATTGTTT 59.587 40.000 0.00 0.00 42.81 2.83
801 848 4.937620 CACTGTCACCAGCATAGTATTGTT 59.062 41.667 0.00 0.00 42.81 2.83
887 938 3.428316 GGCAGTAGCTAGTGTTCTGAGTC 60.428 52.174 25.71 9.54 41.70 3.36
980 1031 0.799393 GCTTGGAACTTCTCGGCTTC 59.201 55.000 0.00 0.00 0.00 3.86
1153 1204 4.500116 GAGGGTCGAGAGCACGGC 62.500 72.222 4.64 0.00 37.15 5.68
1311 1362 0.116143 AGTTGCAGAGGGAGGAGAGT 59.884 55.000 0.00 0.00 0.00 3.24
1854 1905 1.080025 GTATCCGTATCCGCTGCCC 60.080 63.158 0.00 0.00 0.00 5.36
1911 1962 2.203466 TGGCATGGTGTGGTGTGG 60.203 61.111 0.00 0.00 0.00 4.17
1916 1967 1.592743 CAATGGTGGCATGGTGTGG 59.407 57.895 0.00 0.00 0.00 4.17
1918 1969 4.116926 CCAATGGTGGCATGGTGT 57.883 55.556 0.00 0.00 38.35 4.16
1950 2001 2.476199 AGTGGAAGGAAGGATCTGAGG 58.524 52.381 0.00 0.00 0.00 3.86
1973 2024 1.654105 AGCTGAAAATTCTACGTCGCG 59.346 47.619 0.00 0.00 0.00 5.87
1977 2028 3.664107 TCAGCAGCTGAAAATTCTACGT 58.336 40.909 23.41 0.00 37.57 3.57
1978 2029 4.871993 ATCAGCAGCTGAAAATTCTACG 57.128 40.909 28.78 0.00 44.04 3.51
1979 2030 6.187125 TCAATCAGCAGCTGAAAATTCTAC 57.813 37.500 28.78 0.00 44.04 2.59
1992 2043 2.287103 CCGTGTGATCATCAATCAGCAG 59.713 50.000 0.00 0.00 45.06 4.24
2012 2063 0.525761 TAAGGTGGTACGTACACGCC 59.474 55.000 26.36 26.36 44.43 5.68
2037 2088 5.776744 ACTAGATAACGGTAATTAAGCCCG 58.223 41.667 10.54 10.54 46.93 6.13
2088 2139 1.001520 TCCATTTTCTTCAGCGTCCGA 59.998 47.619 0.00 0.00 0.00 4.55
2131 2182 0.451783 CAAGTAACCGGATTGGCAGC 59.548 55.000 9.46 0.00 43.94 5.25
2220 2276 8.131731 GTCTCAAAAGAAGGCATAATTGTATCC 58.868 37.037 0.00 0.00 31.93 2.59
2261 2317 7.402640 GTGATCCTAGCGAATTCTTAACAAAG 58.597 38.462 3.52 0.00 0.00 2.77
2275 2331 1.338200 GCCTAATGGGTGATCCTAGCG 60.338 57.143 0.00 0.00 37.43 4.26
2276 2332 1.003696 GGCCTAATGGGTGATCCTAGC 59.996 57.143 0.00 0.00 37.43 3.42
2277 2333 2.039084 GTGGCCTAATGGGTGATCCTAG 59.961 54.545 3.32 0.00 37.43 3.02
2280 2336 0.846693 AGTGGCCTAATGGGTGATCC 59.153 55.000 3.32 0.00 37.43 3.36
2288 2345 5.116180 TCTGTTTTCGATAGTGGCCTAATG 58.884 41.667 3.32 0.00 37.40 1.90
2375 2432 3.731089 TCCCCTAAATTTATACGTGCGG 58.269 45.455 0.00 0.00 0.00 5.69
2376 2433 4.319261 GCTTCCCCTAAATTTATACGTGCG 60.319 45.833 0.00 0.00 0.00 5.34
2412 2470 3.193157 AGCAACTGTAGTACGTACGTG 57.807 47.619 30.25 14.88 33.87 4.49
2471 2541 5.149973 TGTAGTGCCGATTAACAGGTAAA 57.850 39.130 0.00 0.00 0.00 2.01
2509 2579 7.844779 ACTCTAACCAAATACTCCTTCTATGGA 59.155 37.037 0.00 0.00 34.52 3.41
2510 2580 8.024145 ACTCTAACCAAATACTCCTTCTATGG 57.976 38.462 0.00 0.00 0.00 2.74
2513 2583 9.720769 CAAAACTCTAACCAAATACTCCTTCTA 57.279 33.333 0.00 0.00 0.00 2.10
2514 2584 8.218488 ACAAAACTCTAACCAAATACTCCTTCT 58.782 33.333 0.00 0.00 0.00 2.85
2515 2585 8.392372 ACAAAACTCTAACCAAATACTCCTTC 57.608 34.615 0.00 0.00 0.00 3.46
2516 2586 8.762481 AACAAAACTCTAACCAAATACTCCTT 57.238 30.769 0.00 0.00 0.00 3.36
2519 2589 9.665264 CTGAAACAAAACTCTAACCAAATACTC 57.335 33.333 0.00 0.00 0.00 2.59
2520 2590 9.403583 TCTGAAACAAAACTCTAACCAAATACT 57.596 29.630 0.00 0.00 0.00 2.12
2523 2593 7.979537 GGTTCTGAAACAAAACTCTAACCAAAT 59.020 33.333 0.00 0.00 37.10 2.32
2525 2595 6.434652 TGGTTCTGAAACAAAACTCTAACCAA 59.565 34.615 5.50 0.00 40.48 3.67
2526 2596 5.946972 TGGTTCTGAAACAAAACTCTAACCA 59.053 36.000 5.50 0.00 40.99 3.67
2527 2597 6.127842 TGTGGTTCTGAAACAAAACTCTAACC 60.128 38.462 10.14 0.00 37.10 2.85
2528 2598 6.848451 TGTGGTTCTGAAACAAAACTCTAAC 58.152 36.000 10.14 0.00 37.10 2.34
2529 2599 7.639113 ATGTGGTTCTGAAACAAAACTCTAA 57.361 32.000 10.14 0.00 37.10 2.10
2531 2601 7.054124 TCTATGTGGTTCTGAAACAAAACTCT 58.946 34.615 10.14 0.00 37.10 3.24
2532 2602 7.259290 TCTATGTGGTTCTGAAACAAAACTC 57.741 36.000 10.14 0.00 37.10 3.01
2533 2603 7.201821 CCTTCTATGTGGTTCTGAAACAAAACT 60.202 37.037 10.14 0.00 37.10 2.66
2535 2605 6.831353 TCCTTCTATGTGGTTCTGAAACAAAA 59.169 34.615 10.14 2.05 37.10 2.44
2536 2606 6.361433 TCCTTCTATGTGGTTCTGAAACAAA 58.639 36.000 10.14 5.03 37.10 2.83
2537 2607 5.935945 TCCTTCTATGTGGTTCTGAAACAA 58.064 37.500 10.14 1.45 37.10 2.83
2538 2608 5.071788 ACTCCTTCTATGTGGTTCTGAAACA 59.928 40.000 3.54 3.54 37.10 2.83
2539 2609 5.552178 ACTCCTTCTATGTGGTTCTGAAAC 58.448 41.667 0.00 0.00 34.46 2.78
2540 2610 5.825593 ACTCCTTCTATGTGGTTCTGAAA 57.174 39.130 0.00 0.00 0.00 2.69
2542 2612 7.331026 CAAATACTCCTTCTATGTGGTTCTGA 58.669 38.462 0.00 0.00 0.00 3.27
2544 2614 6.215636 ACCAAATACTCCTTCTATGTGGTTCT 59.784 38.462 0.00 0.00 38.57 3.01
2545 2615 6.415573 ACCAAATACTCCTTCTATGTGGTTC 58.584 40.000 0.00 0.00 38.57 3.62
2546 2616 6.388619 ACCAAATACTCCTTCTATGTGGTT 57.611 37.500 0.00 0.00 38.57 3.67
2548 2618 7.792032 TCTAACCAAATACTCCTTCTATGTGG 58.208 38.462 0.00 0.00 35.69 4.17
2549 2619 8.478877 ACTCTAACCAAATACTCCTTCTATGTG 58.521 37.037 0.00 0.00 0.00 3.21
2550 2620 8.611051 ACTCTAACCAAATACTCCTTCTATGT 57.389 34.615 0.00 0.00 0.00 2.29
2551 2621 9.892130 AAACTCTAACCAAATACTCCTTCTATG 57.108 33.333 0.00 0.00 0.00 2.23
2553 2623 9.720769 CAAAACTCTAACCAAATACTCCTTCTA 57.279 33.333 0.00 0.00 0.00 2.10
2555 2625 8.392372 ACAAAACTCTAACCAAATACTCCTTC 57.608 34.615 0.00 0.00 0.00 3.46
2556 2626 8.762481 AACAAAACTCTAACCAAATACTCCTT 57.238 30.769 0.00 0.00 0.00 3.36
2557 2627 8.762481 AAACAAAACTCTAACCAAATACTCCT 57.238 30.769 0.00 0.00 0.00 3.69
2558 2628 8.626526 TGAAACAAAACTCTAACCAAATACTCC 58.373 33.333 0.00 0.00 0.00 3.85
2559 2629 9.665264 CTGAAACAAAACTCTAACCAAATACTC 57.335 33.333 0.00 0.00 0.00 2.59
2587 2657 2.902705 TAGCTTTGTCGAAGTGTGGT 57.097 45.000 0.00 0.00 37.69 4.16
2603 2673 6.699575 TGGCCTGATAAGATTTTCTTTAGC 57.300 37.500 3.32 0.00 37.89 3.09
2628 2871 3.206150 CACACTTCAGTTGTAGCCAAGT 58.794 45.455 0.00 0.00 34.50 3.16
2704 2949 1.153429 GTACCCTCACCATGTCGCC 60.153 63.158 0.00 0.00 0.00 5.54
2724 2969 2.426024 TCCGGAGTAGATTTTGACGGAG 59.574 50.000 0.00 0.00 43.22 4.63
2753 2998 4.816126 TGATACCCTAGGCAGTAGTCATT 58.184 43.478 2.05 0.00 0.00 2.57
2817 3062 7.168219 TCTACTTGCATAGTGTGAGGAAAAAT 58.832 34.615 10.59 0.00 37.73 1.82
2818 3063 6.530120 TCTACTTGCATAGTGTGAGGAAAAA 58.470 36.000 10.59 0.00 37.73 1.94
2823 3068 5.528043 AGATCTACTTGCATAGTGTGAGG 57.472 43.478 10.59 0.00 37.73 3.86
2939 3571 1.421646 AGGGCCATCTACTATGCCAAC 59.578 52.381 6.18 0.00 45.83 3.77
2970 3603 4.142315 ACACACCATCATTTGCTGCTAATC 60.142 41.667 6.35 0.00 0.00 1.75
3105 3738 3.489355 TGCTTGGCTCAATGAAGAAGAA 58.511 40.909 0.00 0.00 0.00 2.52
3106 3739 3.144657 TGCTTGGCTCAATGAAGAAGA 57.855 42.857 0.00 0.00 0.00 2.87
3107 3740 5.298527 TGATATGCTTGGCTCAATGAAGAAG 59.701 40.000 0.00 0.00 0.00 2.85
3198 3831 0.549950 AGCTACGGAGTACCCTAGCA 59.450 55.000 20.46 0.00 46.08 3.49
3300 3934 9.162764 GCTCTGTTTGATAATCCTTTACAACTA 57.837 33.333 0.00 0.00 0.00 2.24
3303 3937 7.446931 TGTGCTCTGTTTGATAATCCTTTACAA 59.553 33.333 0.00 0.00 0.00 2.41
3314 3948 3.379057 CCATGCATGTGCTCTGTTTGATA 59.621 43.478 24.58 0.00 42.66 2.15
3411 4045 2.675056 GCCGATGATGATGGCGAGC 61.675 63.158 0.00 0.00 39.30 5.03
3444 4078 3.001414 GAGGAAGATGATGATGATGGCG 58.999 50.000 0.00 0.00 0.00 5.69
3526 4160 4.800471 TGAACATTCTGAGATGATTCGACG 59.200 41.667 0.00 0.00 0.00 5.12
3534 4168 6.819397 ATATGCCATGAACATTCTGAGATG 57.181 37.500 6.52 0.00 0.00 2.90
3615 4250 0.704076 ATCCCTGCTGCAACCCTTAA 59.296 50.000 3.02 0.00 0.00 1.85
3651 4286 3.993081 GACCGATCCAATCTGAGCTAATG 59.007 47.826 0.00 0.00 0.00 1.90
3725 4361 2.561858 GACACGGTAAAAGAGAGACCCT 59.438 50.000 0.00 0.00 0.00 4.34
3727 4363 3.655276 TGACACGGTAAAAGAGAGACC 57.345 47.619 0.00 0.00 0.00 3.85
3728 4364 4.806330 TGATGACACGGTAAAAGAGAGAC 58.194 43.478 0.00 0.00 0.00 3.36
3729 4365 5.661056 ATGATGACACGGTAAAAGAGAGA 57.339 39.130 0.00 0.00 0.00 3.10
3730 4366 5.980116 CCTATGATGACACGGTAAAAGAGAG 59.020 44.000 0.00 0.00 0.00 3.20
3739 4375 0.980754 TGGCCCTATGATGACACGGT 60.981 55.000 0.00 0.00 0.00 4.83
3744 4380 4.016444 TGTTTTTCTGGCCCTATGATGAC 58.984 43.478 0.00 0.00 0.00 3.06
3745 4381 4.314522 TGTTTTTCTGGCCCTATGATGA 57.685 40.909 0.00 0.00 0.00 2.92
3746 4382 5.404466 TTTGTTTTTCTGGCCCTATGATG 57.596 39.130 0.00 0.00 0.00 3.07
3747 4383 4.467438 CCTTTGTTTTTCTGGCCCTATGAT 59.533 41.667 0.00 0.00 0.00 2.45
3748 4384 3.831911 CCTTTGTTTTTCTGGCCCTATGA 59.168 43.478 0.00 0.00 0.00 2.15
3749 4385 3.055891 CCCTTTGTTTTTCTGGCCCTATG 60.056 47.826 0.00 0.00 0.00 2.23
3750 4386 3.173151 CCCTTTGTTTTTCTGGCCCTAT 58.827 45.455 0.00 0.00 0.00 2.57
3751 4387 2.178106 TCCCTTTGTTTTTCTGGCCCTA 59.822 45.455 0.00 0.00 0.00 3.53
3752 4388 1.062505 TCCCTTTGTTTTTCTGGCCCT 60.063 47.619 0.00 0.00 0.00 5.19
3753 4389 1.344438 CTCCCTTTGTTTTTCTGGCCC 59.656 52.381 0.00 0.00 0.00 5.80
3754 4390 2.035961 GTCTCCCTTTGTTTTTCTGGCC 59.964 50.000 0.00 0.00 0.00 5.36
3792 4428 4.844085 TGGAATCTTCAGTTCCCTACTTCA 59.156 41.667 2.73 0.00 43.60 3.02
3862 4501 9.561069 AGTGGTCACTTCAACAAATATATATCC 57.439 33.333 0.00 0.00 38.83 2.59
3936 4575 2.601266 CCATCACACGAACCAACGAAAC 60.601 50.000 0.00 0.00 37.03 2.78
3941 4582 0.889186 AGCCCATCACACGAACCAAC 60.889 55.000 0.00 0.00 0.00 3.77
3948 4589 2.022764 TTACATGAGCCCATCACACG 57.977 50.000 0.00 0.00 41.91 4.49
4037 4684 9.846248 GTCAGCAACATATATTTTGAGAAAGTT 57.154 29.630 14.44 0.00 0.00 2.66
4063 4710 1.102978 CCTTTCCCCAACCGCATTAG 58.897 55.000 0.00 0.00 0.00 1.73
4080 4727 8.469200 TCGCAAAAGATGATTGAAATTATTCCT 58.531 29.630 0.00 0.00 34.49 3.36
4081 4728 8.633075 TCGCAAAAGATGATTGAAATTATTCC 57.367 30.769 0.00 0.00 34.49 3.01
4092 4739 2.421424 GTGGCTCTCGCAAAAGATGATT 59.579 45.455 0.00 0.00 38.10 2.57
4111 4758 3.567164 GCCTCATGATGATAACCCTTGTG 59.433 47.826 1.72 0.00 0.00 3.33
4112 4759 3.202818 TGCCTCATGATGATAACCCTTGT 59.797 43.478 1.72 0.00 0.00 3.16
4114 4761 4.736611 ATGCCTCATGATGATAACCCTT 57.263 40.909 1.72 0.00 0.00 3.95
4168 4818 7.033791 CAGCAATGATCTTAACAGCAAAGATT 58.966 34.615 0.00 0.00 42.38 2.40
4176 4826 4.940046 ACTCACCAGCAATGATCTTAACAG 59.060 41.667 0.00 0.00 0.00 3.16
4262 4912 5.993441 ACCTTGTTTGCATAACTAACGTACT 59.007 36.000 11.34 0.00 36.88 2.73
4271 4921 5.925969 AGTTGCATTACCTTGTTTGCATAAC 59.074 36.000 0.00 0.00 43.91 1.89
4287 4937 5.593095 AGATTAGCACATGATGAGTTGCATT 59.407 36.000 0.00 0.00 37.34 3.56
4525 5185 5.964958 AAGAGATGTTTATGGTGGTTGTG 57.035 39.130 0.00 0.00 0.00 3.33
4569 5229 6.696411 TCAACCTTTGCCTTATATTTTGGTG 58.304 36.000 0.00 0.00 0.00 4.17
4582 5242 1.886542 ACTCGGAATTCAACCTTTGCC 59.113 47.619 7.93 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.