Multiple sequence alignment - TraesCS6B01G401100

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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 TraesCS6B01G401100 chr6B 100.000 2712 0 0 1 2712 677046643 677043932 0.000000e+00 5009.0
1 TraesCS6B01G401100 chr6B 95.896 1194 21 9 1301 2489 677336684 677335514 0.000000e+00 1908.0
2 TraesCS6B01G401100 chr6B 88.808 1242 87 24 899 2111 678356842 678358060 0.000000e+00 1476.0
3 TraesCS6B01G401100 chr6B 84.947 1136 97 43 943 2036 678174622 678175725 0.000000e+00 1083.0
4 TraesCS6B01G401100 chr6B 84.476 1050 82 42 899 1912 678092867 678091863 0.000000e+00 961.0
5 TraesCS6B01G401100 chr6B 84.304 1013 75 40 1012 1974 678542623 678543601 0.000000e+00 913.0
6 TraesCS6B01G401100 chr6B 80.135 1037 101 64 899 1887 676865971 676864992 0.000000e+00 676.0
7 TraesCS6B01G401100 chr6B 92.000 475 32 4 899 1371 677088449 677087979 0.000000e+00 662.0
8 TraesCS6B01G401100 chr6B 81.178 696 76 24 219 897 678173883 678174540 2.410000e-140 508.0
9 TraesCS6B01G401100 chr6B 82.042 529 66 22 1023 1537 676538326 676537813 8.980000e-115 424.0
10 TraesCS6B01G401100 chr6B 94.239 243 12 2 182 422 677090710 677090468 1.190000e-98 370.0
11 TraesCS6B01G401100 chr6B 94.064 219 11 2 170 386 677778164 677777946 5.600000e-87 331.0
12 TraesCS6B01G401100 chr6B 91.093 247 16 1 1368 1614 677087946 677087706 2.010000e-86 329.0
13 TraesCS6B01G401100 chr6B 88.261 230 12 5 375 593 678354094 678354319 7.450000e-66 261.0
14 TraesCS6B01G401100 chr6B 87.671 219 11 3 170 386 677910431 677910227 9.700000e-60 241.0
15 TraesCS6B01G401100 chr6B 79.104 402 42 25 1749 2110 677087691 677087292 3.490000e-59 239.0
16 TraesCS6B01G401100 chr6B 86.885 183 12 8 1862 2036 676865054 676864876 7.660000e-46 195.0
17 TraesCS6B01G401100 chr6B 87.075 147 9 5 1 138 676869101 676868956 1.010000e-34 158.0
18 TraesCS6B01G401100 chr6B 86.395 147 11 5 1 138 677337886 677337740 4.680000e-33 152.0
19 TraesCS6B01G401100 chr6B 97.674 86 2 0 2627 2712 677335067 677334982 6.050000e-32 148.0
20 TraesCS6B01G401100 chr6B 91.781 73 5 1 1 73 678354026 678354097 1.720000e-17 100.0
21 TraesCS6B01G401100 chr6B 78.882 161 21 8 2555 2712 677079294 677079144 2.220000e-16 97.1
22 TraesCS6B01G401100 chr6D 84.657 1473 136 52 336 1741 447279575 447278126 0.000000e+00 1386.0
23 TraesCS6B01G401100 chr6D 82.485 1022 107 40 1044 2032 447761100 447762082 0.000000e+00 830.0
24 TraesCS6B01G401100 chr6D 79.559 1179 116 59 898 2009 447737595 447738715 0.000000e+00 726.0
25 TraesCS6B01G401100 chr6D 78.320 1024 119 58 923 1899 447213904 447212937 1.410000e-157 566.0
26 TraesCS6B01G401100 chr6D 88.354 395 36 9 2110 2498 447277399 447277009 1.470000e-127 466.0
27 TraesCS6B01G401100 chr6D 82.745 510 36 23 1627 2108 447278122 447277637 9.040000e-110 407.0
28 TraesCS6B01G401100 chr6D 83.019 265 24 12 222 484 447737163 447737408 1.260000e-53 220.0
29 TraesCS6B01G401100 chr6D 79.805 307 49 9 510 811 447510999 447510701 7.610000e-51 211.0
30 TraesCS6B01G401100 chr6D 94.805 77 3 1 2035 2110 447738797 447738873 4.740000e-23 119.0
31 TraesCS6B01G401100 chr6D 96.296 54 1 1 256 308 447279631 447279578 1.340000e-13 87.9
32 TraesCS6B01G401100 chr6A 83.903 1112 102 38 955 2036 594254310 594253246 0.000000e+00 990.0
33 TraesCS6B01G401100 chr6A 83.348 1117 110 43 956 2036 593992465 593991389 0.000000e+00 963.0
34 TraesCS6B01G401100 chr6A 84.598 909 83 37 923 1794 594365580 594366468 0.000000e+00 850.0
35 TraesCS6B01G401100 chr6A 81.222 1129 130 54 936 2022 593930035 593928947 0.000000e+00 835.0
36 TraesCS6B01G401100 chr6A 77.881 1293 143 72 910 2110 594319131 594320372 0.000000e+00 671.0
37 TraesCS6B01G401100 chr6A 83.333 618 55 17 1 594 594255521 594254928 6.650000e-146 527.0
38 TraesCS6B01G401100 chr6A 86.512 215 26 2 517 728 594318484 594318698 1.620000e-57 233.0
39 TraesCS6B01G401100 chr6A 84.874 238 25 8 2110 2342 594320616 594320847 2.100000e-56 230.0
40 TraesCS6B01G401100 chr6A 77.122 271 32 20 225 484 593776417 593776668 2.190000e-26 130.0
41 TraesCS6B01G401100 chr6A 81.935 155 10 4 761 897 594318903 594319057 6.140000e-22 115.0


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 TraesCS6B01G401100 chr6B 677043932 677046643 2711 True 5009.000000 5009 100.000000 1 2712 1 chr6B.!!$R2 2711
1 TraesCS6B01G401100 chr6B 678091863 678092867 1004 True 961.000000 961 84.476000 899 1912 1 chr6B.!!$R6 1013
2 TraesCS6B01G401100 chr6B 678542623 678543601 978 False 913.000000 913 84.304000 1012 1974 1 chr6B.!!$F1 962
3 TraesCS6B01G401100 chr6B 678173883 678175725 1842 False 795.500000 1083 83.062500 219 2036 2 chr6B.!!$F2 1817
4 TraesCS6B01G401100 chr6B 677334982 677337886 2904 True 736.000000 1908 93.321667 1 2712 3 chr6B.!!$R9 2711
5 TraesCS6B01G401100 chr6B 678354026 678358060 4034 False 612.333333 1476 89.616667 1 2111 3 chr6B.!!$F3 2110
6 TraesCS6B01G401100 chr6B 676537813 676538326 513 True 424.000000 424 82.042000 1023 1537 1 chr6B.!!$R1 514
7 TraesCS6B01G401100 chr6B 677087292 677090710 3418 True 400.000000 662 89.109000 182 2110 4 chr6B.!!$R8 1928
8 TraesCS6B01G401100 chr6B 676864876 676869101 4225 True 343.000000 676 84.698333 1 2036 3 chr6B.!!$R7 2035
9 TraesCS6B01G401100 chr6D 447761100 447762082 982 False 830.000000 830 82.485000 1044 2032 1 chr6D.!!$F1 988
10 TraesCS6B01G401100 chr6D 447277009 447279631 2622 True 586.725000 1386 88.013000 256 2498 4 chr6D.!!$R3 2242
11 TraesCS6B01G401100 chr6D 447212937 447213904 967 True 566.000000 566 78.320000 923 1899 1 chr6D.!!$R1 976
12 TraesCS6B01G401100 chr6D 447737163 447738873 1710 False 355.000000 726 85.794333 222 2110 3 chr6D.!!$F2 1888
13 TraesCS6B01G401100 chr6A 593991389 593992465 1076 True 963.000000 963 83.348000 956 2036 1 chr6A.!!$R2 1080
14 TraesCS6B01G401100 chr6A 594365580 594366468 888 False 850.000000 850 84.598000 923 1794 1 chr6A.!!$F2 871
15 TraesCS6B01G401100 chr6A 593928947 593930035 1088 True 835.000000 835 81.222000 936 2022 1 chr6A.!!$R1 1086
16 TraesCS6B01G401100 chr6A 594253246 594255521 2275 True 758.500000 990 83.618000 1 2036 2 chr6A.!!$R3 2035
17 TraesCS6B01G401100 chr6A 594318484 594320847 2363 False 312.250000 671 82.800500 517 2342 4 chr6A.!!$F3 1825

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
952 7587 0.03716 TACCAAACCGCCCCTCTTTC 59.963 55.0 0.0 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 9882 0.033405 TACCCGAAGCTCTAGTGGCT 60.033 55.0 7.05 7.05 42.31 4.75 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
103 113 1.471676 CGACCAGAATCGGAGGAAAGG 60.472 57.143 0.00 0.00 38.47 3.11
116 126 3.386867 GAAAGGCAGATGCACCGCG 62.387 63.158 7.19 0.00 44.36 6.46
138 148 2.616634 AGCAACAGCGATCAGATCAT 57.383 45.000 11.12 0.00 0.00 2.45
142 157 0.599466 ACAGCGATCAGATCATGGCG 60.599 55.000 11.12 5.48 33.02 5.69
147 162 2.057316 CGATCAGATCATGGCGTCTTC 58.943 52.381 11.12 0.00 0.00 2.87
155 170 3.989698 ATGGCGTCTTCTCGTGGCG 62.990 63.158 0.00 0.00 0.00 5.69
156 171 4.719369 GGCGTCTTCTCGTGGCGT 62.719 66.667 0.00 0.00 0.00 5.68
158 173 2.805353 CGTCTTCTCGTGGCGTGG 60.805 66.667 0.00 0.00 0.00 4.94
258 329 3.613432 CGACTGATGCTGATGCTATGCTA 60.613 47.826 0.00 0.00 40.48 3.49
423 521 3.418675 TCTGAACGTTCGGAGATGC 57.581 52.632 31.15 4.12 37.65 3.91
458 1903 1.557443 GACCGTCCTTTCAGTGTGCG 61.557 60.000 0.00 0.00 0.00 5.34
506 4456 4.081406 CTCAAAAATGTGATGGGTCCTGA 58.919 43.478 0.00 0.00 0.00 3.86
607 6094 4.096833 GTGTGCTCCTGAAAATATCATGCA 59.903 41.667 0.00 0.00 37.44 3.96
635 6122 2.331805 CGCTCCTCCCGTATGACG 59.668 66.667 0.00 0.00 42.11 4.35
648 6135 3.181520 CCGTATGACGCTTTTTCTGAAGG 60.182 47.826 0.00 0.00 40.91 3.46
669 6159 7.019693 AAGGGAAACTTACGAATCAGTCGGA 62.020 44.000 0.00 0.00 42.47 4.55
686 6176 2.542178 TCGGATTCACACAGAAACAACG 59.458 45.455 0.00 0.00 40.22 4.10
712 6202 0.037326 TCCGACTCATTGGTGCAGAC 60.037 55.000 0.00 0.00 0.00 3.51
728 6218 5.821204 GTGCAGACACCATTGGATTAATAC 58.179 41.667 10.37 0.00 41.21 1.89
730 6220 5.589855 TGCAGACACCATTGGATTAATACAG 59.410 40.000 10.37 0.00 0.00 2.74
732 6222 6.765989 GCAGACACCATTGGATTAATACAGTA 59.234 38.462 10.37 0.00 0.00 2.74
733 6223 7.445402 GCAGACACCATTGGATTAATACAGTAT 59.555 37.037 10.37 0.00 0.00 2.12
734 6224 9.996554 CAGACACCATTGGATTAATACAGTATA 57.003 33.333 10.37 0.00 0.00 1.47
752 7120 6.072119 ACAGTATATGAATGAATCGCGAGGTA 60.072 38.462 16.66 2.84 0.00 3.08
789 7168 5.118510 GGTTTGTAATGCAAGAAATTGACCG 59.881 40.000 0.00 0.00 38.47 4.79
793 7172 4.599047 AATGCAAGAAATTGACCGGAAA 57.401 36.364 9.46 1.81 0.00 3.13
844 7232 3.275338 GCATGCGCCCTACAGCTC 61.275 66.667 4.18 0.00 0.00 4.09
852 7411 0.744414 GCCCTACAGCTCAATCGCAA 60.744 55.000 0.00 0.00 0.00 4.85
853 7412 1.293924 CCCTACAGCTCAATCGCAAG 58.706 55.000 0.00 0.00 0.00 4.01
897 7465 2.236223 CTCAGACGCCCACTGCATCT 62.236 60.000 0.00 0.00 44.91 2.90
924 7558 0.739813 CTCCAGGTTCTTAACGCCCG 60.740 60.000 0.00 0.00 0.00 6.13
925 7559 2.396157 CCAGGTTCTTAACGCCCGC 61.396 63.158 0.00 0.00 0.00 6.13
926 7560 2.046604 AGGTTCTTAACGCCCGCC 60.047 61.111 0.00 0.00 0.00 6.13
941 7576 1.203758 CCCGCCAGAATTTACCAAACC 59.796 52.381 0.00 0.00 0.00 3.27
949 7584 0.702316 ATTTACCAAACCGCCCCTCT 59.298 50.000 0.00 0.00 0.00 3.69
952 7587 0.037160 TACCAAACCGCCCCTCTTTC 59.963 55.000 0.00 0.00 0.00 2.62
953 7588 1.074951 CCAAACCGCCCCTCTTTCT 59.925 57.895 0.00 0.00 0.00 2.52
954 7589 0.960861 CCAAACCGCCCCTCTTTCTC 60.961 60.000 0.00 0.00 0.00 2.87
957 7592 2.689034 CCGCCCCTCTTTCTCCCT 60.689 66.667 0.00 0.00 0.00 4.20
1054 7745 1.059584 TGAGACACCAAAGCCCCTCA 61.060 55.000 0.00 0.00 0.00 3.86
1192 7901 1.153939 CTCCCGTGTCAAGCTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
1305 8038 4.324991 GACGAACCACCCCGGCTT 62.325 66.667 0.00 0.00 39.03 4.35
1723 8662 6.938596 TCCGTTCGATGTATAGAAGGAAGATA 59.061 38.462 8.37 0.00 35.11 1.98
1779 8740 6.007703 AGTTTTAAGACCCAATTCGATTCCA 58.992 36.000 0.00 0.00 0.00 3.53
2118 9456 0.106519 CCTCCGCAAGAATCCCCAAT 60.107 55.000 0.00 0.00 43.02 3.16
2189 9527 5.725362 ACTGAGGATTTTTCTTCGTCCTAG 58.275 41.667 0.00 0.00 41.03 3.02
2248 9590 4.846137 CGTGGTATTTTTCTTTTCAGAGCG 59.154 41.667 0.00 0.00 0.00 5.03
2252 9594 2.774439 TTTTCTTTTCAGAGCGGTGC 57.226 45.000 0.00 0.00 0.00 5.01
2556 9899 3.622514 AGCCACTAGAGCTTCGGG 58.377 61.111 0.00 0.00 37.24 5.14
2557 9900 1.305381 AGCCACTAGAGCTTCGGGT 60.305 57.895 0.00 0.00 37.24 5.28
2558 9901 0.033405 AGCCACTAGAGCTTCGGGTA 60.033 55.000 0.00 0.00 37.24 3.69
2559 9902 0.386113 GCCACTAGAGCTTCGGGTAG 59.614 60.000 0.00 0.00 0.00 3.18
2560 9903 1.033574 CCACTAGAGCTTCGGGTAGG 58.966 60.000 0.00 0.00 0.00 3.18
2561 9904 1.033574 CACTAGAGCTTCGGGTAGGG 58.966 60.000 0.00 0.00 0.00 3.53
2562 9905 0.924823 ACTAGAGCTTCGGGTAGGGA 59.075 55.000 0.00 0.00 0.00 4.20
2563 9906 1.320507 CTAGAGCTTCGGGTAGGGAC 58.679 60.000 0.00 0.00 0.00 4.46
2564 9907 0.627451 TAGAGCTTCGGGTAGGGACA 59.373 55.000 0.00 0.00 0.00 4.02
2565 9908 0.684805 AGAGCTTCGGGTAGGGACAG 60.685 60.000 0.00 0.00 0.00 3.51
2566 9909 1.677637 GAGCTTCGGGTAGGGACAGG 61.678 65.000 0.00 0.00 0.00 4.00
2567 9910 1.684734 GCTTCGGGTAGGGACAGGA 60.685 63.158 0.00 0.00 0.00 3.86
2568 9911 1.957765 GCTTCGGGTAGGGACAGGAC 61.958 65.000 0.00 0.00 0.00 3.85
2569 9912 0.613853 CTTCGGGTAGGGACAGGACA 60.614 60.000 0.00 0.00 0.00 4.02
2570 9913 0.178926 TTCGGGTAGGGACAGGACAA 60.179 55.000 0.00 0.00 0.00 3.18
2571 9914 0.178926 TCGGGTAGGGACAGGACAAA 60.179 55.000 0.00 0.00 0.00 2.83
2572 9915 0.909623 CGGGTAGGGACAGGACAAAT 59.090 55.000 0.00 0.00 0.00 2.32
2573 9916 1.406887 CGGGTAGGGACAGGACAAATG 60.407 57.143 0.00 0.00 0.00 2.32
2574 9917 1.682087 GGGTAGGGACAGGACAAATGC 60.682 57.143 0.00 0.00 0.00 3.56
2575 9918 1.004277 GGTAGGGACAGGACAAATGCA 59.996 52.381 0.00 0.00 0.00 3.96
2576 9919 2.359900 GTAGGGACAGGACAAATGCAG 58.640 52.381 0.00 0.00 0.00 4.41
2577 9920 0.610232 AGGGACAGGACAAATGCAGC 60.610 55.000 0.00 0.00 0.00 5.25
2578 9921 0.895100 GGGACAGGACAAATGCAGCA 60.895 55.000 0.00 0.00 0.00 4.41
2579 9922 1.180029 GGACAGGACAAATGCAGCAT 58.820 50.000 0.52 0.52 0.00 3.79
2580 9923 1.135199 GGACAGGACAAATGCAGCATG 60.135 52.381 9.18 0.77 40.87 4.06
2581 9924 1.814394 GACAGGACAAATGCAGCATGA 59.186 47.619 9.18 0.00 39.69 3.07
2582 9925 2.229543 GACAGGACAAATGCAGCATGAA 59.770 45.455 9.18 0.00 39.69 2.57
2583 9926 2.230508 ACAGGACAAATGCAGCATGAAG 59.769 45.455 9.18 4.55 39.69 3.02
2584 9927 1.822990 AGGACAAATGCAGCATGAAGG 59.177 47.619 9.18 1.52 39.69 3.46
2585 9928 1.134907 GGACAAATGCAGCATGAAGGG 60.135 52.381 9.18 0.00 39.69 3.95
2586 9929 1.820519 GACAAATGCAGCATGAAGGGA 59.179 47.619 9.18 0.00 39.69 4.20
2587 9930 1.547372 ACAAATGCAGCATGAAGGGAC 59.453 47.619 9.18 0.00 39.69 4.46
2588 9931 1.546923 CAAATGCAGCATGAAGGGACA 59.453 47.619 9.18 0.00 39.69 4.02
2589 9932 1.927487 AATGCAGCATGAAGGGACAA 58.073 45.000 9.18 0.00 39.69 3.18
2590 9933 1.927487 ATGCAGCATGAAGGGACAAA 58.073 45.000 7.23 0.00 39.69 2.83
2591 9934 1.250328 TGCAGCATGAAGGGACAAAG 58.750 50.000 0.00 0.00 39.69 2.77
2592 9935 0.108945 GCAGCATGAAGGGACAAAGC 60.109 55.000 0.00 0.00 39.69 3.51
2593 9936 0.529378 CAGCATGAAGGGACAAAGCC 59.471 55.000 0.00 0.00 39.69 4.35
2594 9937 0.112995 AGCATGAAGGGACAAAGCCA 59.887 50.000 0.00 0.00 0.00 4.75
2595 9938 0.529378 GCATGAAGGGACAAAGCCAG 59.471 55.000 0.00 0.00 0.00 4.85
2596 9939 1.887956 GCATGAAGGGACAAAGCCAGA 60.888 52.381 0.00 0.00 0.00 3.86
2597 9940 2.089980 CATGAAGGGACAAAGCCAGAG 58.910 52.381 0.00 0.00 0.00 3.35
2598 9941 0.401738 TGAAGGGACAAAGCCAGAGG 59.598 55.000 0.00 0.00 0.00 3.69
2609 9952 2.997315 CCAGAGGCAGACACCGGA 60.997 66.667 9.46 0.00 33.69 5.14
2610 9953 2.575993 CAGAGGCAGACACCGGAG 59.424 66.667 9.46 1.26 33.69 4.63
2611 9954 3.386237 AGAGGCAGACACCGGAGC 61.386 66.667 9.46 3.54 33.69 4.70
2612 9955 3.695606 GAGGCAGACACCGGAGCA 61.696 66.667 9.46 0.00 33.69 4.26
2613 9956 3.941657 GAGGCAGACACCGGAGCAC 62.942 68.421 9.46 0.00 33.69 4.40
2615 9958 4.008933 GCAGACACCGGAGCACCT 62.009 66.667 9.46 0.00 0.00 4.00
2616 9959 2.646175 GCAGACACCGGAGCACCTA 61.646 63.158 9.46 0.00 0.00 3.08
2617 9960 1.513158 CAGACACCGGAGCACCTAG 59.487 63.158 9.46 0.00 0.00 3.02
2618 9961 1.682684 AGACACCGGAGCACCTAGG 60.683 63.158 9.46 7.41 0.00 3.02
2619 9962 1.982938 GACACCGGAGCACCTAGGT 60.983 63.158 9.21 9.21 37.49 3.08
2620 9963 1.946475 GACACCGGAGCACCTAGGTC 61.946 65.000 12.84 7.35 43.99 3.85
2626 9969 3.160872 GAGCACCTAGGTCCAAAGC 57.839 57.895 12.84 12.45 38.82 3.51
2627 9970 0.324943 GAGCACCTAGGTCCAAAGCA 59.675 55.000 19.97 0.00 38.82 3.91
2628 9971 0.036875 AGCACCTAGGTCCAAAGCAC 59.963 55.000 19.97 1.49 0.00 4.40
2629 9972 0.036875 GCACCTAGGTCCAAAGCACT 59.963 55.000 12.84 0.00 0.00 4.40
2630 9973 1.545651 GCACCTAGGTCCAAAGCACTT 60.546 52.381 12.84 0.00 0.00 3.16
2631 9974 2.290071 GCACCTAGGTCCAAAGCACTTA 60.290 50.000 12.84 0.00 0.00 2.24
2632 9975 3.600388 CACCTAGGTCCAAAGCACTTAG 58.400 50.000 12.84 0.00 0.00 2.18
2633 9976 2.572104 ACCTAGGTCCAAAGCACTTAGG 59.428 50.000 9.21 7.52 45.13 2.69
2634 9977 2.633488 CTAGGTCCAAAGCACTTAGGC 58.367 52.381 0.00 0.00 0.00 3.93
2685 10337 6.264744 TGAAGAGAAACCGTCCTATATCGAAT 59.735 38.462 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 113 3.264897 CTACCGCGGTGCATCTGC 61.265 66.667 40.02 9.30 44.34 4.26
116 126 2.131183 GATCTGATCGCTGTTGCTACC 58.869 52.381 1.26 0.00 36.97 3.18
138 148 4.717629 CGCCACGAGAAGACGCCA 62.718 66.667 0.00 0.00 36.70 5.69
142 157 3.112709 GCCACGCCACGAGAAGAC 61.113 66.667 0.00 0.00 0.00 3.01
258 329 1.202582 CCGACCTCTGAAGTTCGACAT 59.797 52.381 0.00 0.00 0.00 3.06
351 441 2.254703 GACCTGATCGACGTGACGCT 62.255 60.000 4.25 0.00 0.00 5.07
458 1903 1.335597 GCTTTCAGTAAACCGGTTGCC 60.336 52.381 23.08 14.44 0.00 4.52
538 4488 3.279875 GGCAATGCCGACCCGATC 61.280 66.667 9.14 0.00 39.62 3.69
627 6114 3.181520 CCCTTCAGAAAAAGCGTCATACG 60.182 47.826 0.00 0.00 45.88 3.06
635 6122 5.008316 TCGTAAGTTTCCCTTCAGAAAAAGC 59.992 40.000 0.00 0.00 37.49 3.51
669 6159 6.801539 ACATATCGTTGTTTCTGTGTGAAT 57.198 33.333 0.00 0.00 34.24 2.57
677 6167 4.817517 AGTCGGAACATATCGTTGTTTCT 58.182 39.130 3.43 0.05 39.85 2.52
686 6176 3.248602 GCACCAATGAGTCGGAACATATC 59.751 47.826 0.00 0.00 0.00 1.63
728 6218 5.164233 ACCTCGCGATTCATTCATATACTG 58.836 41.667 10.36 0.00 0.00 2.74
730 6220 6.251589 CAGTACCTCGCGATTCATTCATATAC 59.748 42.308 10.36 0.79 0.00 1.47
732 6222 5.164233 CAGTACCTCGCGATTCATTCATAT 58.836 41.667 10.36 0.00 0.00 1.78
733 6223 4.546570 CAGTACCTCGCGATTCATTCATA 58.453 43.478 10.36 0.00 0.00 2.15
734 6224 3.384668 CAGTACCTCGCGATTCATTCAT 58.615 45.455 10.36 0.00 0.00 2.57
736 6226 2.128035 CCAGTACCTCGCGATTCATTC 58.872 52.381 10.36 0.00 0.00 2.67
737 6227 1.480954 ACCAGTACCTCGCGATTCATT 59.519 47.619 10.36 0.00 0.00 2.57
739 6229 0.454600 GACCAGTACCTCGCGATTCA 59.545 55.000 10.36 0.00 0.00 2.57
744 7112 2.202623 GCTGACCAGTACCTCGCG 60.203 66.667 0.00 0.00 0.00 5.87
752 7120 0.255890 ACAAACCAGTGCTGACCAGT 59.744 50.000 0.02 0.00 0.00 4.00
840 7219 0.745845 AATCGGCTTGCGATTGAGCT 60.746 50.000 8.07 0.00 38.89 4.09
897 7465 0.768221 AAGAACCTGGAGTCTGGCCA 60.768 55.000 4.71 4.71 35.65 5.36
924 7558 1.403647 GGCGGTTTGGTAAATTCTGGC 60.404 52.381 0.00 0.00 0.00 4.85
925 7559 1.203758 GGGCGGTTTGGTAAATTCTGG 59.796 52.381 0.00 0.00 0.00 3.86
926 7560 1.203758 GGGGCGGTTTGGTAAATTCTG 59.796 52.381 0.00 0.00 0.00 3.02
941 7576 1.222113 GAAGGGAGAAAGAGGGGCG 59.778 63.158 0.00 0.00 0.00 6.13
949 7584 2.480255 TAGGCCGGGGAAGGGAGAAA 62.480 60.000 2.18 0.00 0.00 2.52
952 7587 0.473117 TTATAGGCCGGGGAAGGGAG 60.473 60.000 2.18 0.00 0.00 4.30
953 7588 0.029887 TTTATAGGCCGGGGAAGGGA 60.030 55.000 2.18 0.00 0.00 4.20
954 7589 0.848053 TTTTATAGGCCGGGGAAGGG 59.152 55.000 2.18 0.00 0.00 3.95
957 7592 1.816183 CGCATTTTATAGGCCGGGGAA 60.816 52.381 2.18 0.00 0.00 3.97
1054 7745 4.032310 AGCAGTTCAGAATCAGAGGAGAT 58.968 43.478 0.00 0.00 0.00 2.75
1252 7985 3.470888 CGACGGATCTTGGGGGCT 61.471 66.667 0.00 0.00 0.00 5.19
1305 8038 4.704833 GGAGGCTGCAGCGGAACA 62.705 66.667 31.19 0.00 43.26 3.18
1723 8662 2.772622 CGGCCTAATCCCCCACCT 60.773 66.667 0.00 0.00 0.00 4.00
1779 8740 2.122768 AGCTAGCTAATTGACCAGCCT 58.877 47.619 17.69 0.00 38.61 4.58
2118 9456 6.055588 ACTCTGACCGAAATTTCTTCAGAAA 58.944 36.000 30.09 19.29 46.60 2.52
2236 9574 1.618837 AGTAGCACCGCTCTGAAAAGA 59.381 47.619 0.00 0.00 40.44 2.52
2248 9590 6.451064 AGCCAACAATAAAATAGTAGCACC 57.549 37.500 0.00 0.00 0.00 5.01
2252 9594 7.556275 TCCCTCAAGCCAACAATAAAATAGTAG 59.444 37.037 0.00 0.00 0.00 2.57
2539 9882 0.033405 TACCCGAAGCTCTAGTGGCT 60.033 55.000 7.05 7.05 42.31 4.75
2540 9883 0.386113 CTACCCGAAGCTCTAGTGGC 59.614 60.000 0.00 3.03 0.00 5.01
2541 9884 1.033574 CCTACCCGAAGCTCTAGTGG 58.966 60.000 0.00 0.00 0.00 4.00
2542 9885 1.033574 CCCTACCCGAAGCTCTAGTG 58.966 60.000 0.00 0.00 0.00 2.74
2543 9886 0.924823 TCCCTACCCGAAGCTCTAGT 59.075 55.000 0.00 0.00 0.00 2.57
2544 9887 1.320507 GTCCCTACCCGAAGCTCTAG 58.679 60.000 0.00 0.00 0.00 2.43
2545 9888 0.627451 TGTCCCTACCCGAAGCTCTA 59.373 55.000 0.00 0.00 0.00 2.43
2546 9889 0.684805 CTGTCCCTACCCGAAGCTCT 60.685 60.000 0.00 0.00 0.00 4.09
2547 9890 1.677637 CCTGTCCCTACCCGAAGCTC 61.678 65.000 0.00 0.00 0.00 4.09
2548 9891 1.686110 CCTGTCCCTACCCGAAGCT 60.686 63.158 0.00 0.00 0.00 3.74
2549 9892 1.684734 TCCTGTCCCTACCCGAAGC 60.685 63.158 0.00 0.00 0.00 3.86
2550 9893 0.613853 TGTCCTGTCCCTACCCGAAG 60.614 60.000 0.00 0.00 0.00 3.79
2551 9894 0.178926 TTGTCCTGTCCCTACCCGAA 60.179 55.000 0.00 0.00 0.00 4.30
2552 9895 0.178926 TTTGTCCTGTCCCTACCCGA 60.179 55.000 0.00 0.00 0.00 5.14
2553 9896 0.909623 ATTTGTCCTGTCCCTACCCG 59.090 55.000 0.00 0.00 0.00 5.28
2554 9897 1.682087 GCATTTGTCCTGTCCCTACCC 60.682 57.143 0.00 0.00 0.00 3.69
2555 9898 1.004277 TGCATTTGTCCTGTCCCTACC 59.996 52.381 0.00 0.00 0.00 3.18
2556 9899 2.359900 CTGCATTTGTCCTGTCCCTAC 58.640 52.381 0.00 0.00 0.00 3.18
2557 9900 1.340017 GCTGCATTTGTCCTGTCCCTA 60.340 52.381 0.00 0.00 0.00 3.53
2558 9901 0.610232 GCTGCATTTGTCCTGTCCCT 60.610 55.000 0.00 0.00 0.00 4.20
2559 9902 0.895100 TGCTGCATTTGTCCTGTCCC 60.895 55.000 0.00 0.00 0.00 4.46
2560 9903 1.135199 CATGCTGCATTTGTCCTGTCC 60.135 52.381 13.38 0.00 0.00 4.02
2561 9904 1.814394 TCATGCTGCATTTGTCCTGTC 59.186 47.619 13.38 0.00 0.00 3.51
2562 9905 1.913778 TCATGCTGCATTTGTCCTGT 58.086 45.000 13.38 0.00 0.00 4.00
2563 9906 2.416836 CCTTCATGCTGCATTTGTCCTG 60.417 50.000 13.38 1.23 0.00 3.86
2564 9907 1.822990 CCTTCATGCTGCATTTGTCCT 59.177 47.619 13.38 0.00 0.00 3.85
2565 9908 1.134907 CCCTTCATGCTGCATTTGTCC 60.135 52.381 13.38 0.00 0.00 4.02
2566 9909 1.820519 TCCCTTCATGCTGCATTTGTC 59.179 47.619 13.38 0.00 0.00 3.18
2567 9910 1.547372 GTCCCTTCATGCTGCATTTGT 59.453 47.619 13.38 0.00 0.00 2.83
2568 9911 1.546923 TGTCCCTTCATGCTGCATTTG 59.453 47.619 13.38 4.48 0.00 2.32
2569 9912 1.927487 TGTCCCTTCATGCTGCATTT 58.073 45.000 13.38 0.00 0.00 2.32
2570 9913 1.927487 TTGTCCCTTCATGCTGCATT 58.073 45.000 13.38 0.00 0.00 3.56
2571 9914 1.822990 CTTTGTCCCTTCATGCTGCAT 59.177 47.619 9.81 9.81 0.00 3.96
2572 9915 1.250328 CTTTGTCCCTTCATGCTGCA 58.750 50.000 4.13 4.13 0.00 4.41
2573 9916 0.108945 GCTTTGTCCCTTCATGCTGC 60.109 55.000 0.00 0.00 0.00 5.25
2574 9917 0.529378 GGCTTTGTCCCTTCATGCTG 59.471 55.000 0.00 0.00 0.00 4.41
2575 9918 0.112995 TGGCTTTGTCCCTTCATGCT 59.887 50.000 0.00 0.00 0.00 3.79
2576 9919 0.529378 CTGGCTTTGTCCCTTCATGC 59.471 55.000 0.00 0.00 0.00 4.06
2577 9920 2.089980 CTCTGGCTTTGTCCCTTCATG 58.910 52.381 0.00 0.00 0.00 3.07
2578 9921 1.005215 CCTCTGGCTTTGTCCCTTCAT 59.995 52.381 0.00 0.00 0.00 2.57
2579 9922 0.401738 CCTCTGGCTTTGTCCCTTCA 59.598 55.000 0.00 0.00 0.00 3.02
2580 9923 0.962855 GCCTCTGGCTTTGTCCCTTC 60.963 60.000 0.73 0.00 46.69 3.46
2581 9924 1.075659 GCCTCTGGCTTTGTCCCTT 59.924 57.895 0.73 0.00 46.69 3.95
2582 9925 2.759795 GCCTCTGGCTTTGTCCCT 59.240 61.111 0.73 0.00 46.69 4.20
2592 9935 2.997315 TCCGGTGTCTGCCTCTGG 60.997 66.667 0.00 0.00 0.00 3.86
2593 9936 2.575993 CTCCGGTGTCTGCCTCTG 59.424 66.667 0.00 0.00 0.00 3.35
2594 9937 3.386237 GCTCCGGTGTCTGCCTCT 61.386 66.667 0.00 0.00 0.00 3.69
2595 9938 3.695606 TGCTCCGGTGTCTGCCTC 61.696 66.667 0.00 0.00 0.00 4.70
2596 9939 4.008933 GTGCTCCGGTGTCTGCCT 62.009 66.667 0.00 0.00 0.00 4.75
2598 9941 2.564553 CTAGGTGCTCCGGTGTCTGC 62.565 65.000 0.00 0.12 39.05 4.26
2599 9942 1.513158 CTAGGTGCTCCGGTGTCTG 59.487 63.158 0.00 0.00 39.05 3.51
2600 9943 1.682684 CCTAGGTGCTCCGGTGTCT 60.683 63.158 0.00 1.48 39.05 3.41
2601 9944 1.946475 GACCTAGGTGCTCCGGTGTC 61.946 65.000 22.10 8.13 39.05 3.67
2602 9945 1.982938 GACCTAGGTGCTCCGGTGT 60.983 63.158 22.10 2.95 39.05 4.16
2603 9946 2.722201 GGACCTAGGTGCTCCGGTG 61.722 68.421 25.07 0.00 39.05 4.94
2604 9947 2.363925 GGACCTAGGTGCTCCGGT 60.364 66.667 25.07 4.27 39.05 5.28
2605 9948 1.550130 TTTGGACCTAGGTGCTCCGG 61.550 60.000 30.72 0.00 37.36 5.14
2606 9949 0.108138 CTTTGGACCTAGGTGCTCCG 60.108 60.000 30.72 16.24 37.36 4.63
2607 9950 0.393132 GCTTTGGACCTAGGTGCTCC 60.393 60.000 30.72 20.79 37.36 4.70
2608 9951 0.324943 TGCTTTGGACCTAGGTGCTC 59.675 55.000 30.72 18.18 37.36 4.26
2609 9952 0.036875 GTGCTTTGGACCTAGGTGCT 59.963 55.000 30.72 2.06 37.36 4.40
2610 9953 0.036875 AGTGCTTTGGACCTAGGTGC 59.963 55.000 25.53 25.53 36.97 5.01
2611 9954 2.568623 AAGTGCTTTGGACCTAGGTG 57.431 50.000 22.10 5.35 0.00 4.00
2612 9955 2.572104 CCTAAGTGCTTTGGACCTAGGT 59.428 50.000 16.26 16.26 37.61 3.08
2613 9956 2.681097 GCCTAAGTGCTTTGGACCTAGG 60.681 54.545 7.41 7.41 37.61 3.02
2614 9957 2.633488 GCCTAAGTGCTTTGGACCTAG 58.367 52.381 14.79 0.00 37.61 3.02
2615 9958 1.066430 CGCCTAAGTGCTTTGGACCTA 60.066 52.381 14.79 0.00 37.61 3.08
2616 9959 0.321653 CGCCTAAGTGCTTTGGACCT 60.322 55.000 14.79 0.00 37.61 3.85
2617 9960 0.605589 ACGCCTAAGTGCTTTGGACC 60.606 55.000 14.79 0.00 37.61 4.46
2618 9961 0.517316 CACGCCTAAGTGCTTTGGAC 59.483 55.000 14.79 6.67 37.61 4.02
2619 9962 0.605319 CCACGCCTAAGTGCTTTGGA 60.605 55.000 14.79 0.00 40.59 3.53
2620 9963 1.875963 CCACGCCTAAGTGCTTTGG 59.124 57.895 7.82 7.82 40.59 3.28
2621 9964 1.210155 GCCACGCCTAAGTGCTTTG 59.790 57.895 0.00 0.00 40.59 2.77
2622 9965 0.955919 GAGCCACGCCTAAGTGCTTT 60.956 55.000 0.00 0.00 40.59 3.51
2623 9966 1.376037 GAGCCACGCCTAAGTGCTT 60.376 57.895 0.00 0.00 40.59 3.91
2624 9967 2.111999 TTGAGCCACGCCTAAGTGCT 62.112 55.000 0.00 0.00 40.59 4.40
2625 9968 1.234615 TTTGAGCCACGCCTAAGTGC 61.235 55.000 0.00 0.00 40.59 4.40
2626 9969 0.517316 GTTTGAGCCACGCCTAAGTG 59.483 55.000 0.00 0.00 41.53 3.16
2627 9970 0.396811 AGTTTGAGCCACGCCTAAGT 59.603 50.000 0.00 0.00 0.00 2.24
2628 9971 1.523758 AAGTTTGAGCCACGCCTAAG 58.476 50.000 0.00 0.00 0.00 2.18
2629 9972 2.843401 TAAGTTTGAGCCACGCCTAA 57.157 45.000 0.00 0.00 0.00 2.69
2630 9973 2.235155 TGATAAGTTTGAGCCACGCCTA 59.765 45.455 0.00 0.00 0.00 3.93
2631 9974 1.003118 TGATAAGTTTGAGCCACGCCT 59.997 47.619 0.00 0.00 0.00 5.52
2632 9975 1.130561 GTGATAAGTTTGAGCCACGCC 59.869 52.381 0.00 0.00 0.00 5.68
2633 9976 1.130561 GGTGATAAGTTTGAGCCACGC 59.869 52.381 0.00 0.00 0.00 5.34
2634 9977 2.416547 CTGGTGATAAGTTTGAGCCACG 59.583 50.000 0.00 0.00 0.00 4.94
2685 10337 3.234353 TGAGGCTGAGAAAGAAGAGTCA 58.766 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.