Multiple sequence alignment - TraesCS6A01G022100

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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 TraesCS6A01G022100 chr6A 100.000 3164 0 0 617 3780 11116828 11113665 0.000000e+00 5843.0
1 TraesCS6A01G022100 chr6A 100.000 516 0 0 1 516 11117444 11116929 0.000000e+00 953.0
2 TraesCS6A01G022100 chr6A 93.037 517 35 1 1 516 493890894 493890378 0.000000e+00 754.0
3 TraesCS6A01G022100 chr6A 81.352 858 143 7 1937 2785 11414820 11413971 0.000000e+00 682.0
4 TraesCS6A01G022100 chr6A 76.026 1097 214 28 1869 2921 11411167 11412258 1.200000e-144 523.0
5 TraesCS6A01G022100 chr6A 77.570 535 95 15 2266 2780 18563172 18563701 2.210000e-77 300.0
6 TraesCS6A01G022100 chrUn 98.214 2128 37 1 686 2813 172238434 172236308 0.000000e+00 3718.0
7 TraesCS6A01G022100 chrUn 100.000 516 0 0 1 516 297012999 297012484 0.000000e+00 953.0
8 TraesCS6A01G022100 chrUn 100.000 516 0 0 1 516 317955238 317954723 0.000000e+00 953.0
9 TraesCS6A01G022100 chrUn 83.150 908 144 3 1884 2782 71184521 71185428 0.000000e+00 821.0
10 TraesCS6A01G022100 chrUn 82.139 935 154 8 1863 2786 71238602 71237670 0.000000e+00 789.0
11 TraesCS6A01G022100 chrUn 80.020 981 161 21 1829 2786 324143930 324144898 0.000000e+00 693.0
12 TraesCS6A01G022100 chrUn 77.898 923 177 16 1876 2780 348465063 348464150 1.980000e-152 549.0
13 TraesCS6A01G022100 chrUn 81.425 463 67 11 1012 1464 71183887 71184340 9.980000e-96 361.0
14 TraesCS6A01G022100 chrUn 80.963 457 70 4 1081 1524 71239228 71238776 2.790000e-91 346.0
15 TraesCS6A01G022100 chrUn 81.436 404 69 4 1079 1479 71219482 71219882 3.640000e-85 326.0
16 TraesCS6A01G022100 chrUn 87.956 274 25 6 716 987 71183295 71183562 2.190000e-82 316.0
17 TraesCS6A01G022100 chrUn 81.378 392 64 7 1079 1465 71265412 71265025 1.020000e-80 311.0
18 TraesCS6A01G022100 chrUn 77.570 535 95 15 2266 2780 775486 774957 2.210000e-77 300.0
19 TraesCS6A01G022100 chrUn 78.505 428 67 15 2516 2919 71187504 71187078 1.350000e-64 257.0
20 TraesCS6A01G022100 chrUn 87.500 176 22 0 1884 2059 71199093 71198918 1.780000e-48 204.0
21 TraesCS6A01G022100 chrUn 98.990 99 1 0 2837 2935 357394204 357394106 1.080000e-40 178.0
22 TraesCS6A01G022100 chrUn 100.000 55 0 0 617 671 461637405 461637351 6.680000e-18 102.0
23 TraesCS6A01G022100 chr7D 91.001 689 33 17 2930 3590 566993191 566993878 0.000000e+00 902.0
24 TraesCS6A01G022100 chr7D 90.133 679 38 13 2939 3590 227753715 227753039 0.000000e+00 856.0
25 TraesCS6A01G022100 chr7D 92.353 510 24 6 2943 3439 528967439 528966932 0.000000e+00 712.0
26 TraesCS6A01G022100 chr7D 78.755 546 91 17 967 1503 6750220 6750749 3.620000e-90 342.0
27 TraesCS6A01G022100 chr7D 94.872 195 8 2 3587 3780 227752986 227752793 1.710000e-78 303.0
28 TraesCS6A01G022100 chr7D 93.814 194 12 0 3587 3780 566993931 566994124 3.690000e-75 292.0
29 TraesCS6A01G022100 chr5D 91.108 686 29 13 2937 3590 335873131 335872446 0.000000e+00 900.0
30 TraesCS6A01G022100 chr5D 90.694 677 30 10 2945 3590 62143450 62144124 0.000000e+00 870.0
31 TraesCS6A01G022100 chr5D 93.299 194 12 1 3587 3780 62144177 62144369 6.180000e-73 285.0
32 TraesCS6A01G022100 chr5D 92.784 194 11 1 3587 3780 335872393 335872203 1.030000e-70 278.0
33 TraesCS6A01G022100 chr7B 90.630 683 35 15 2936 3590 650042319 650043000 0.000000e+00 880.0
34 TraesCS6A01G022100 chr7B 92.784 194 13 1 3587 3780 650043053 650043245 2.880000e-71 279.0
35 TraesCS6A01G022100 chr4A 89.781 685 33 13 2937 3590 42690539 42691217 0.000000e+00 843.0
36 TraesCS6A01G022100 chr4A 89.589 682 38 10 2937 3590 49499809 49500485 0.000000e+00 835.0
37 TraesCS6A01G022100 chr4A 93.750 512 30 2 1 510 582667831 582668342 0.000000e+00 767.0
38 TraesCS6A01G022100 chr4A 77.163 578 101 20 967 1531 733560357 733559798 1.320000e-79 307.0
39 TraesCS6A01G022100 chr1D 89.520 687 42 15 2931 3590 451871960 451871277 0.000000e+00 843.0
40 TraesCS6A01G022100 chr1D 93.385 514 32 2 1 513 108933893 108934405 0.000000e+00 760.0
41 TraesCS6A01G022100 chr1D 92.857 196 12 1 3587 3780 451871223 451871028 2.220000e-72 283.0
42 TraesCS6A01G022100 chr1D 100.000 28 0 0 1586 1613 28391473 28391446 7.000000e-03 52.8
43 TraesCS6A01G022100 chr7A 94.600 500 26 1 1 499 643684099 643684598 0.000000e+00 773.0
44 TraesCS6A01G022100 chr7A 78.286 525 85 18 964 1477 7702275 7702781 1.020000e-80 311.0
45 TraesCS6A01G022100 chr7A 100.000 28 0 0 2930 2957 588746035 588746062 7.000000e-03 52.8
46 TraesCS6A01G022100 chr2D 93.786 515 30 2 1 513 473187667 473188181 0.000000e+00 773.0
47 TraesCS6A01G022100 chr2D 93.050 518 33 3 1 516 406047233 406046717 0.000000e+00 754.0
48 TraesCS6A01G022100 chr1A 93.605 516 29 4 2 513 175275885 175276400 0.000000e+00 767.0
49 TraesCS6A01G022100 chr5A 89.280 625 30 18 2996 3590 531691465 531690848 0.000000e+00 749.0
50 TraesCS6A01G022100 chr5A 91.710 193 12 4 3588 3780 531690794 531690606 8.050000e-67 265.0
51 TraesCS6A01G022100 chr6D 79.737 913 168 9 1886 2785 9907474 9906566 0.000000e+00 645.0
52 TraesCS6A01G022100 chr6D 81.818 440 73 5 1081 1517 9908012 9907577 2.780000e-96 363.0
53 TraesCS6A01G022100 chr6D 82.532 395 40 18 854 1241 9909195 9908823 1.690000e-83 320.0
54 TraesCS6A01G022100 chr6B 87.045 494 35 18 3125 3590 1405734 1405242 7.190000e-147 531.0
55 TraesCS6A01G022100 chr6B 79.892 557 101 10 1829 2381 18043101 18042552 7.610000e-107 398.0
56 TraesCS6A01G022100 chr6B 81.004 458 74 11 1070 1519 18299920 18299468 6.010000e-93 351.0
57 TraesCS6A01G022100 chr6B 91.795 195 15 1 3587 3780 1405187 1404993 1.730000e-68 270.0
58 TraesCS6A01G022100 chr6B 78.870 407 68 10 1021 1416 18324657 18324258 3.750000e-65 259.0
59 TraesCS6A01G022100 chr6B 78.415 366 62 10 2371 2722 18163056 18163418 4.910000e-54 222.0
60 TraesCS6A01G022100 chr3D 91.398 186 14 2 3596 3780 568834827 568835011 1.740000e-63 254.0
61 TraesCS6A01G022100 chr2B 82.456 114 18 2 1277 1389 534707892 534708004 8.640000e-17 99.0
62 TraesCS6A01G022100 chr2A 84.848 99 13 2 1292 1389 595345319 595345222 8.640000e-17 99.0


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 TraesCS6A01G022100 chr6A 11113665 11117444 3779 True 3398.000000 5843 100.000000 1 3780 2 chr6A.!!$R3 3779
1 TraesCS6A01G022100 chr6A 493890378 493890894 516 True 754.000000 754 93.037000 1 516 1 chr6A.!!$R2 515
2 TraesCS6A01G022100 chr6A 11413971 11414820 849 True 682.000000 682 81.352000 1937 2785 1 chr6A.!!$R1 848
3 TraesCS6A01G022100 chr6A 11411167 11412258 1091 False 523.000000 523 76.026000 1869 2921 1 chr6A.!!$F1 1052
4 TraesCS6A01G022100 chr6A 18563172 18563701 529 False 300.000000 300 77.570000 2266 2780 1 chr6A.!!$F2 514
5 TraesCS6A01G022100 chrUn 172236308 172238434 2126 True 3718.000000 3718 98.214000 686 2813 1 chrUn.!!$R5 2127
6 TraesCS6A01G022100 chrUn 297012484 297012999 515 True 953.000000 953 100.000000 1 516 1 chrUn.!!$R6 515
7 TraesCS6A01G022100 chrUn 317954723 317955238 515 True 953.000000 953 100.000000 1 516 1 chrUn.!!$R7 515
8 TraesCS6A01G022100 chrUn 324143930 324144898 968 False 693.000000 693 80.020000 1829 2786 1 chrUn.!!$F2 957
9 TraesCS6A01G022100 chrUn 71237670 71239228 1558 True 567.500000 789 81.551000 1081 2786 2 chrUn.!!$R11 1705
10 TraesCS6A01G022100 chrUn 348464150 348465063 913 True 549.000000 549 77.898000 1876 2780 1 chrUn.!!$R8 904
11 TraesCS6A01G022100 chrUn 71183295 71185428 2133 False 499.333333 821 84.177000 716 2782 3 chrUn.!!$F3 2066
12 TraesCS6A01G022100 chrUn 774957 775486 529 True 300.000000 300 77.570000 2266 2780 1 chrUn.!!$R1 514
13 TraesCS6A01G022100 chr7D 528966932 528967439 507 True 712.000000 712 92.353000 2943 3439 1 chr7D.!!$R1 496
14 TraesCS6A01G022100 chr7D 566993191 566994124 933 False 597.000000 902 92.407500 2930 3780 2 chr7D.!!$F2 850
15 TraesCS6A01G022100 chr7D 227752793 227753715 922 True 579.500000 856 92.502500 2939 3780 2 chr7D.!!$R2 841
16 TraesCS6A01G022100 chr7D 6750220 6750749 529 False 342.000000 342 78.755000 967 1503 1 chr7D.!!$F1 536
17 TraesCS6A01G022100 chr5D 335872203 335873131 928 True 589.000000 900 91.946000 2937 3780 2 chr5D.!!$R1 843
18 TraesCS6A01G022100 chr5D 62143450 62144369 919 False 577.500000 870 91.996500 2945 3780 2 chr5D.!!$F1 835
19 TraesCS6A01G022100 chr7B 650042319 650043245 926 False 579.500000 880 91.707000 2936 3780 2 chr7B.!!$F1 844
20 TraesCS6A01G022100 chr4A 42690539 42691217 678 False 843.000000 843 89.781000 2937 3590 1 chr4A.!!$F1 653
21 TraesCS6A01G022100 chr4A 49499809 49500485 676 False 835.000000 835 89.589000 2937 3590 1 chr4A.!!$F2 653
22 TraesCS6A01G022100 chr4A 582667831 582668342 511 False 767.000000 767 93.750000 1 510 1 chr4A.!!$F3 509
23 TraesCS6A01G022100 chr4A 733559798 733560357 559 True 307.000000 307 77.163000 967 1531 1 chr4A.!!$R1 564
24 TraesCS6A01G022100 chr1D 108933893 108934405 512 False 760.000000 760 93.385000 1 513 1 chr1D.!!$F1 512
25 TraesCS6A01G022100 chr1D 451871028 451871960 932 True 563.000000 843 91.188500 2931 3780 2 chr1D.!!$R2 849
26 TraesCS6A01G022100 chr7A 7702275 7702781 506 False 311.000000 311 78.286000 964 1477 1 chr7A.!!$F1 513
27 TraesCS6A01G022100 chr2D 473187667 473188181 514 False 773.000000 773 93.786000 1 513 1 chr2D.!!$F1 512
28 TraesCS6A01G022100 chr2D 406046717 406047233 516 True 754.000000 754 93.050000 1 516 1 chr2D.!!$R1 515
29 TraesCS6A01G022100 chr1A 175275885 175276400 515 False 767.000000 767 93.605000 2 513 1 chr1A.!!$F1 511
30 TraesCS6A01G022100 chr5A 531690606 531691465 859 True 507.000000 749 90.495000 2996 3780 2 chr5A.!!$R1 784
31 TraesCS6A01G022100 chr6D 9906566 9909195 2629 True 442.666667 645 81.362333 854 2785 3 chr6D.!!$R1 1931
32 TraesCS6A01G022100 chr6B 1404993 1405734 741 True 400.500000 531 89.420000 3125 3780 2 chr6B.!!$R4 655
33 TraesCS6A01G022100 chr6B 18042552 18043101 549 True 398.000000 398 79.892000 1829 2381 1 chr6B.!!$R1 552

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
654 662 0.328258 ACACCCCATTGTGGCTACTC 59.672 55.0 0.64 0.0 40.62 2.59 F
655 663 0.620556 CACCCCATTGTGGCTACTCT 59.379 55.0 0.64 0.0 35.79 3.24 F
2257 3760 0.102663 TGTGGCAGTGCATGTGTTTG 59.897 50.0 18.61 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 3617 2.223409 GGTGAAAACCTCGTTGACAACC 60.223 50.0 12.66 0.0 0.00 3.77 R
2667 4189 2.718487 TATGCTGCCATCCCCATGCC 62.718 60.0 0.00 0.0 32.85 4.40 R
3156 4683 0.464036 TAACTATCTGCCGCACTGGG 59.536 55.0 0.00 0.0 38.63 4.45 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
641 649 8.260270 CATGTTACTAGTTTAAGTTACACCCC 57.740 38.462 0.00 0.00 40.59 4.95
642 650 7.372260 TGTTACTAGTTTAAGTTACACCCCA 57.628 36.000 0.00 0.00 34.92 4.96
643 651 7.976712 TGTTACTAGTTTAAGTTACACCCCAT 58.023 34.615 0.00 0.00 34.92 4.00
644 652 8.439172 TGTTACTAGTTTAAGTTACACCCCATT 58.561 33.333 0.00 0.00 34.92 3.16
645 653 8.724229 GTTACTAGTTTAAGTTACACCCCATTG 58.276 37.037 0.00 0.00 31.09 2.82
646 654 6.844829 ACTAGTTTAAGTTACACCCCATTGT 58.155 36.000 0.00 0.00 0.00 2.71
647 655 6.713450 ACTAGTTTAAGTTACACCCCATTGTG 59.287 38.462 0.00 0.00 42.05 3.33
648 656 4.830600 AGTTTAAGTTACACCCCATTGTGG 59.169 41.667 0.00 0.00 40.62 4.17
649 657 1.627864 AAGTTACACCCCATTGTGGC 58.372 50.000 0.00 0.00 40.62 5.01
650 658 0.777446 AGTTACACCCCATTGTGGCT 59.223 50.000 0.00 0.00 40.62 4.75
651 659 1.989586 AGTTACACCCCATTGTGGCTA 59.010 47.619 0.00 0.00 40.62 3.93
652 660 2.089201 GTTACACCCCATTGTGGCTAC 58.911 52.381 0.00 0.00 40.62 3.58
653 661 1.663911 TACACCCCATTGTGGCTACT 58.336 50.000 0.64 0.00 40.62 2.57
654 662 0.328258 ACACCCCATTGTGGCTACTC 59.672 55.000 0.64 0.00 40.62 2.59
655 663 0.620556 CACCCCATTGTGGCTACTCT 59.379 55.000 0.64 0.00 35.79 3.24
656 664 1.837439 CACCCCATTGTGGCTACTCTA 59.163 52.381 0.64 0.00 35.79 2.43
657 665 2.238646 CACCCCATTGTGGCTACTCTAA 59.761 50.000 0.64 0.00 35.79 2.10
658 666 2.916934 ACCCCATTGTGGCTACTCTAAA 59.083 45.455 0.64 0.00 35.79 1.85
659 667 3.332485 ACCCCATTGTGGCTACTCTAAAA 59.668 43.478 0.64 0.00 35.79 1.52
660 668 4.202631 ACCCCATTGTGGCTACTCTAAAAA 60.203 41.667 0.64 0.00 35.79 1.94
786 794 6.588756 CACCAATGTCTTTTGATTTCCATCAG 59.411 38.462 0.00 0.00 40.66 2.90
823 832 1.468736 GGTACCGTACTACAGCTGTGC 60.469 57.143 29.57 14.72 0.00 4.57
861 870 5.014858 AGGATTCCATATCACCATGAATGC 58.985 41.667 5.29 0.00 0.00 3.56
902 911 5.175388 ACTACCTTTAATTGTCTGGTCCC 57.825 43.478 0.00 0.00 32.74 4.46
1075 1388 2.027653 GCAGGAAGGAGAAACAGCTACT 60.028 50.000 0.00 0.00 0.00 2.57
1579 2877 6.844097 TTTGGTTTTGTCCTAAGTCAGTTT 57.156 33.333 0.00 0.00 0.00 2.66
2046 3525 4.143333 CCCCTACCACGACCGCAG 62.143 72.222 0.00 0.00 0.00 5.18
2257 3760 0.102663 TGTGGCAGTGCATGTGTTTG 59.897 50.000 18.61 0.00 0.00 2.93
2667 4189 1.672030 TGCACCTGATTGACAGCGG 60.672 57.895 0.00 0.00 44.52 5.52
2831 4358 3.914426 TTCTTTGAGCACCTCCTATCC 57.086 47.619 0.00 0.00 0.00 2.59
2832 4359 3.121929 TCTTTGAGCACCTCCTATCCT 57.878 47.619 0.00 0.00 0.00 3.24
2833 4360 4.265856 TCTTTGAGCACCTCCTATCCTA 57.734 45.455 0.00 0.00 0.00 2.94
2834 4361 4.820775 TCTTTGAGCACCTCCTATCCTAT 58.179 43.478 0.00 0.00 0.00 2.57
2835 4362 4.590647 TCTTTGAGCACCTCCTATCCTATG 59.409 45.833 0.00 0.00 0.00 2.23
2836 4363 3.619900 TGAGCACCTCCTATCCTATGT 57.380 47.619 0.00 0.00 0.00 2.29
2837 4364 3.501349 TGAGCACCTCCTATCCTATGTC 58.499 50.000 0.00 0.00 0.00 3.06
2838 4365 3.141083 TGAGCACCTCCTATCCTATGTCT 59.859 47.826 0.00 0.00 0.00 3.41
2839 4366 3.505386 AGCACCTCCTATCCTATGTCTG 58.495 50.000 0.00 0.00 0.00 3.51
2840 4367 3.116939 AGCACCTCCTATCCTATGTCTGT 60.117 47.826 0.00 0.00 0.00 3.41
2841 4368 3.643792 GCACCTCCTATCCTATGTCTGTT 59.356 47.826 0.00 0.00 0.00 3.16
2842 4369 4.502259 GCACCTCCTATCCTATGTCTGTTG 60.502 50.000 0.00 0.00 0.00 3.33
2843 4370 4.895889 CACCTCCTATCCTATGTCTGTTGA 59.104 45.833 0.00 0.00 0.00 3.18
2844 4371 5.363868 CACCTCCTATCCTATGTCTGTTGAA 59.636 44.000 0.00 0.00 0.00 2.69
2845 4372 6.042552 CACCTCCTATCCTATGTCTGTTGAAT 59.957 42.308 0.00 0.00 0.00 2.57
2846 4373 7.233553 CACCTCCTATCCTATGTCTGTTGAATA 59.766 40.741 0.00 0.00 0.00 1.75
2847 4374 7.958583 ACCTCCTATCCTATGTCTGTTGAATAT 59.041 37.037 0.00 0.00 0.00 1.28
2848 4375 8.820831 CCTCCTATCCTATGTCTGTTGAATATT 58.179 37.037 0.00 0.00 0.00 1.28
2873 4400 9.947433 TTTTAGTTTCAGTTAATCCGGATCTAA 57.053 29.630 19.43 13.97 0.00 2.10
2888 4415 9.877178 ATCCGGATCTAATAATTTGTATGTCTC 57.123 33.333 12.38 0.00 0.00 3.36
2889 4416 8.027189 TCCGGATCTAATAATTTGTATGTCTCG 58.973 37.037 0.00 0.00 0.00 4.04
2890 4417 7.275779 CCGGATCTAATAATTTGTATGTCTCGG 59.724 40.741 0.00 0.00 0.00 4.63
2891 4418 8.027189 CGGATCTAATAATTTGTATGTCTCGGA 58.973 37.037 0.00 0.00 0.00 4.55
2892 4419 9.360093 GGATCTAATAATTTGTATGTCTCGGAG 57.640 37.037 0.00 0.00 0.00 4.63
2893 4420 9.915629 GATCTAATAATTTGTATGTCTCGGAGT 57.084 33.333 4.69 0.00 0.00 3.85
2894 4421 9.698309 ATCTAATAATTTGTATGTCTCGGAGTG 57.302 33.333 4.69 0.00 0.00 3.51
2895 4422 8.692710 TCTAATAATTTGTATGTCTCGGAGTGT 58.307 33.333 4.69 0.00 0.00 3.55
2896 4423 9.961265 CTAATAATTTGTATGTCTCGGAGTGTA 57.039 33.333 4.69 0.00 0.00 2.90
2898 4425 9.832445 AATAATTTGTATGTCTCGGAGTGTATT 57.168 29.630 4.69 0.00 0.00 1.89
2899 4426 7.539712 AATTTGTATGTCTCGGAGTGTATTG 57.460 36.000 4.69 0.00 0.00 1.90
2900 4427 4.649088 TGTATGTCTCGGAGTGTATTGG 57.351 45.455 4.69 0.00 0.00 3.16
2901 4428 4.274978 TGTATGTCTCGGAGTGTATTGGA 58.725 43.478 4.69 0.00 0.00 3.53
2902 4429 4.338400 TGTATGTCTCGGAGTGTATTGGAG 59.662 45.833 4.69 0.00 0.00 3.86
2903 4430 3.081710 TGTCTCGGAGTGTATTGGAGA 57.918 47.619 4.69 0.00 0.00 3.71
2904 4431 3.423996 GTCTCGGAGTGTATTGGAGAC 57.576 52.381 4.69 4.02 44.51 3.36
2905 4432 2.014857 TCTCGGAGTGTATTGGAGACG 58.985 52.381 4.69 0.00 0.00 4.18
2906 4433 1.743958 CTCGGAGTGTATTGGAGACGT 59.256 52.381 0.00 0.00 0.00 4.34
2907 4434 1.471287 TCGGAGTGTATTGGAGACGTG 59.529 52.381 0.00 0.00 0.00 4.49
2908 4435 1.641577 GGAGTGTATTGGAGACGTGC 58.358 55.000 0.00 0.00 0.00 5.34
2909 4436 1.067142 GGAGTGTATTGGAGACGTGCA 60.067 52.381 0.00 0.00 0.00 4.57
2910 4437 2.418746 GGAGTGTATTGGAGACGTGCAT 60.419 50.000 0.00 0.00 0.00 3.96
2911 4438 2.604914 GAGTGTATTGGAGACGTGCATG 59.395 50.000 3.82 3.82 0.00 4.06
2912 4439 1.665679 GTGTATTGGAGACGTGCATGG 59.334 52.381 11.36 0.00 0.00 3.66
2913 4440 1.552792 TGTATTGGAGACGTGCATGGA 59.447 47.619 11.36 0.00 0.00 3.41
2914 4441 1.933853 GTATTGGAGACGTGCATGGAC 59.066 52.381 11.36 7.39 0.00 4.02
2915 4442 0.324614 ATTGGAGACGTGCATGGACA 59.675 50.000 18.05 0.52 0.00 4.02
2916 4443 0.107643 TTGGAGACGTGCATGGACAA 59.892 50.000 18.05 6.79 0.00 3.18
2917 4444 0.324614 TGGAGACGTGCATGGACAAT 59.675 50.000 18.05 4.40 0.00 2.71
2918 4445 1.271325 TGGAGACGTGCATGGACAATT 60.271 47.619 18.05 0.23 0.00 2.32
2919 4446 1.131126 GGAGACGTGCATGGACAATTG 59.869 52.381 18.05 3.24 0.00 2.32
2920 4447 1.806542 GAGACGTGCATGGACAATTGT 59.193 47.619 18.05 11.78 0.00 2.71
2921 4448 3.000041 GAGACGTGCATGGACAATTGTA 59.000 45.455 18.05 0.00 0.00 2.41
2922 4449 3.609853 AGACGTGCATGGACAATTGTAT 58.390 40.909 18.05 0.00 0.00 2.29
2923 4450 3.374988 AGACGTGCATGGACAATTGTATG 59.625 43.478 18.05 13.50 0.00 2.39
2924 4451 2.159393 ACGTGCATGGACAATTGTATGC 60.159 45.455 28.06 28.06 44.56 3.14
2925 4452 2.097954 CGTGCATGGACAATTGTATGCT 59.902 45.455 31.55 10.81 44.59 3.79
2926 4453 3.427909 CGTGCATGGACAATTGTATGCTT 60.428 43.478 31.55 8.44 44.59 3.91
2927 4454 3.861113 GTGCATGGACAATTGTATGCTTG 59.139 43.478 31.55 17.87 44.59 4.01
2928 4455 2.861935 GCATGGACAATTGTATGCTTGC 59.138 45.455 27.72 19.57 41.89 4.01
2998 4525 3.595709 TCATTCGTTCACCGTTGAAAC 57.404 42.857 0.00 0.00 43.52 2.78
3036 4563 5.815740 CGAGGTGGTACTAAATATTTGTGCT 59.184 40.000 11.05 0.00 0.00 4.40
3085 4612 3.127895 CAGATTTTTCGTATTTGGGCCGA 59.872 43.478 0.00 0.00 0.00 5.54
3089 4616 2.116827 TTCGTATTTGGGCCGAACAT 57.883 45.000 8.77 0.00 35.85 2.71
3101 4628 2.964978 GAACATGCTGTGGCCCAC 59.035 61.111 7.01 7.01 37.74 4.61
3156 4683 1.732259 CTGCGGACACACTATTTGACC 59.268 52.381 0.00 0.00 0.00 4.02
3485 5046 9.302345 TGTTAATGTCTGCGTTTAAAAATGAAA 57.698 25.926 0.00 0.00 0.00 2.69
3599 5222 7.999679 TCATGTCTTCAGAAAAACATTGTTCT 58.000 30.769 1.83 0.00 34.37 3.01
3726 5351 1.539827 GTTGGCCATTCGTTAGCTGTT 59.460 47.619 6.09 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
616 624 7.879160 TGGGGTGTAACTTAAACTAGTAACATG 59.121 37.037 0.00 0.00 36.74 3.21
617 625 7.976712 TGGGGTGTAACTTAAACTAGTAACAT 58.023 34.615 0.00 0.00 36.74 2.71
618 626 7.372260 TGGGGTGTAACTTAAACTAGTAACA 57.628 36.000 0.00 0.00 36.74 2.41
619 627 8.724229 CAATGGGGTGTAACTTAAACTAGTAAC 58.276 37.037 0.00 0.00 36.74 2.50
620 628 8.439172 ACAATGGGGTGTAACTTAAACTAGTAA 58.561 33.333 0.00 0.00 36.74 2.24
621 629 7.879160 CACAATGGGGTGTAACTTAAACTAGTA 59.121 37.037 0.00 0.00 36.74 1.82
622 630 6.713450 CACAATGGGGTGTAACTTAAACTAGT 59.287 38.462 0.00 0.00 36.74 2.57
623 631 6.150474 CCACAATGGGGTGTAACTTAAACTAG 59.850 42.308 0.00 0.00 37.06 2.57
624 632 6.005198 CCACAATGGGGTGTAACTTAAACTA 58.995 40.000 0.00 0.00 37.06 2.24
625 633 4.830600 CCACAATGGGGTGTAACTTAAACT 59.169 41.667 0.00 0.00 37.06 2.66
626 634 4.559906 GCCACAATGGGGTGTAACTTAAAC 60.560 45.833 2.41 0.00 38.19 2.01
627 635 3.574826 GCCACAATGGGGTGTAACTTAAA 59.425 43.478 2.41 0.00 38.19 1.52
628 636 3.158676 GCCACAATGGGGTGTAACTTAA 58.841 45.455 2.41 0.00 38.19 1.85
629 637 2.377193 AGCCACAATGGGGTGTAACTTA 59.623 45.455 2.41 0.00 38.19 2.24
630 638 1.146982 AGCCACAATGGGGTGTAACTT 59.853 47.619 2.41 0.00 38.19 2.66
631 639 0.777446 AGCCACAATGGGGTGTAACT 59.223 50.000 2.41 0.00 38.19 2.24
632 640 2.089201 GTAGCCACAATGGGGTGTAAC 58.911 52.381 2.41 0.00 39.43 2.50
633 641 1.989586 AGTAGCCACAATGGGGTGTAA 59.010 47.619 2.41 0.00 39.43 2.41
634 642 1.557832 GAGTAGCCACAATGGGGTGTA 59.442 52.381 2.41 0.00 39.43 2.90
635 643 0.328258 GAGTAGCCACAATGGGGTGT 59.672 55.000 2.41 0.00 39.43 4.16
636 644 0.620556 AGAGTAGCCACAATGGGGTG 59.379 55.000 2.41 0.00 39.43 4.61
637 645 2.263895 TAGAGTAGCCACAATGGGGT 57.736 50.000 2.41 0.29 38.19 4.95
638 646 3.644966 TTTAGAGTAGCCACAATGGGG 57.355 47.619 0.00 0.00 38.19 4.96
710 718 2.485426 TCAGTGTCTCGGTTAACCTACG 59.515 50.000 22.12 9.54 0.00 3.51
714 722 3.382048 ACTTCAGTGTCTCGGTTAACC 57.618 47.619 15.13 15.13 0.00 2.85
786 794 0.254178 ACCATGATGCTGTCTCCCAC 59.746 55.000 0.00 0.00 0.00 4.61
823 832 6.897259 TGGAATCCTATCGTTTTCTTTACG 57.103 37.500 0.00 0.00 40.23 3.18
902 911 6.849588 TTGACATATGATCAGAATCAACCG 57.150 37.500 10.38 0.00 44.85 4.44
1620 2918 6.071221 TGCTTCAAGCTATCACCAAATTTGAT 60.071 34.615 19.86 7.98 42.97 2.57
2046 3525 3.822403 TTGCGCGCAAACAAGAGGC 62.822 57.895 41.45 4.24 32.44 4.70
2137 3617 2.223409 GGTGAAAACCTCGTTGACAACC 60.223 50.000 12.66 0.00 0.00 3.77
2667 4189 2.718487 TATGCTGCCATCCCCATGCC 62.718 60.000 0.00 0.00 32.85 4.40
2813 4340 4.346418 ACATAGGATAGGAGGTGCTCAAAG 59.654 45.833 0.00 0.00 31.08 2.77
2814 4341 4.298626 ACATAGGATAGGAGGTGCTCAAA 58.701 43.478 0.00 0.00 31.08 2.69
2815 4342 3.898123 GACATAGGATAGGAGGTGCTCAA 59.102 47.826 0.00 0.00 31.08 3.02
2816 4343 3.141083 AGACATAGGATAGGAGGTGCTCA 59.859 47.826 0.00 0.00 31.08 4.26
2817 4344 3.509575 CAGACATAGGATAGGAGGTGCTC 59.490 52.174 0.00 0.00 0.00 4.26
2818 4345 3.116939 ACAGACATAGGATAGGAGGTGCT 60.117 47.826 0.00 0.00 0.00 4.40
2819 4346 3.235200 ACAGACATAGGATAGGAGGTGC 58.765 50.000 0.00 0.00 0.00 5.01
2820 4347 4.895889 TCAACAGACATAGGATAGGAGGTG 59.104 45.833 0.00 0.00 0.00 4.00
2821 4348 5.144159 TCAACAGACATAGGATAGGAGGT 57.856 43.478 0.00 0.00 0.00 3.85
2822 4349 6.678568 ATTCAACAGACATAGGATAGGAGG 57.321 41.667 0.00 0.00 0.00 4.30
2847 4374 9.947433 TTAGATCCGGATTAACTGAAACTAAAA 57.053 29.630 20.22 0.00 0.00 1.52
2862 4389 9.877178 GAGACATACAAATTATTAGATCCGGAT 57.123 33.333 19.21 19.21 0.00 4.18
2863 4390 8.027189 CGAGACATACAAATTATTAGATCCGGA 58.973 37.037 6.61 6.61 0.00 5.14
2864 4391 7.275779 CCGAGACATACAAATTATTAGATCCGG 59.724 40.741 0.00 0.00 0.00 5.14
2865 4392 8.027189 TCCGAGACATACAAATTATTAGATCCG 58.973 37.037 0.00 0.00 0.00 4.18
2866 4393 9.360093 CTCCGAGACATACAAATTATTAGATCC 57.640 37.037 0.00 0.00 0.00 3.36
2867 4394 9.915629 ACTCCGAGACATACAAATTATTAGATC 57.084 33.333 1.33 0.00 0.00 2.75
2868 4395 9.698309 CACTCCGAGACATACAAATTATTAGAT 57.302 33.333 1.33 0.00 0.00 1.98
2869 4396 8.692710 ACACTCCGAGACATACAAATTATTAGA 58.307 33.333 1.33 0.00 0.00 2.10
2870 4397 8.873215 ACACTCCGAGACATACAAATTATTAG 57.127 34.615 1.33 0.00 0.00 1.73
2872 4399 9.832445 AATACACTCCGAGACATACAAATTATT 57.168 29.630 1.33 0.00 0.00 1.40
2873 4400 9.261180 CAATACACTCCGAGACATACAAATTAT 57.739 33.333 1.33 0.00 0.00 1.28
2874 4401 7.709182 CCAATACACTCCGAGACATACAAATTA 59.291 37.037 1.33 0.00 0.00 1.40
2875 4402 6.538742 CCAATACACTCCGAGACATACAAATT 59.461 38.462 1.33 0.00 0.00 1.82
2876 4403 6.049149 CCAATACACTCCGAGACATACAAAT 58.951 40.000 1.33 0.00 0.00 2.32
2877 4404 5.186215 TCCAATACACTCCGAGACATACAAA 59.814 40.000 1.33 0.00 0.00 2.83
2878 4405 4.707934 TCCAATACACTCCGAGACATACAA 59.292 41.667 1.33 0.00 0.00 2.41
2879 4406 4.274978 TCCAATACACTCCGAGACATACA 58.725 43.478 1.33 0.00 0.00 2.29
2880 4407 4.579340 TCTCCAATACACTCCGAGACATAC 59.421 45.833 1.33 0.00 0.00 2.39
2881 4408 4.579340 GTCTCCAATACACTCCGAGACATA 59.421 45.833 1.33 0.00 45.65 2.29
2882 4409 3.381908 GTCTCCAATACACTCCGAGACAT 59.618 47.826 1.33 0.00 45.65 3.06
2883 4410 2.753452 GTCTCCAATACACTCCGAGACA 59.247 50.000 1.33 0.00 45.65 3.41
2884 4411 2.223294 CGTCTCCAATACACTCCGAGAC 60.223 54.545 1.33 5.62 43.84 3.36
2885 4412 2.014857 CGTCTCCAATACACTCCGAGA 58.985 52.381 1.33 0.00 0.00 4.04
2886 4413 1.743958 ACGTCTCCAATACACTCCGAG 59.256 52.381 0.00 0.00 0.00 4.63
2887 4414 1.471287 CACGTCTCCAATACACTCCGA 59.529 52.381 0.00 0.00 0.00 4.55
2888 4415 1.909376 CACGTCTCCAATACACTCCG 58.091 55.000 0.00 0.00 0.00 4.63
2889 4416 1.067142 TGCACGTCTCCAATACACTCC 60.067 52.381 0.00 0.00 0.00 3.85
2890 4417 2.363788 TGCACGTCTCCAATACACTC 57.636 50.000 0.00 0.00 0.00 3.51
2891 4418 2.621338 CATGCACGTCTCCAATACACT 58.379 47.619 0.00 0.00 0.00 3.55
2892 4419 1.665679 CCATGCACGTCTCCAATACAC 59.334 52.381 0.00 0.00 0.00 2.90
2893 4420 1.552792 TCCATGCACGTCTCCAATACA 59.447 47.619 0.00 0.00 0.00 2.29
2894 4421 1.933853 GTCCATGCACGTCTCCAATAC 59.066 52.381 0.00 0.00 0.00 1.89
2895 4422 1.552792 TGTCCATGCACGTCTCCAATA 59.447 47.619 0.00 0.00 0.00 1.90
2896 4423 0.324614 TGTCCATGCACGTCTCCAAT 59.675 50.000 0.00 0.00 0.00 3.16
2897 4424 0.107643 TTGTCCATGCACGTCTCCAA 59.892 50.000 0.00 0.00 0.00 3.53
2898 4425 0.324614 ATTGTCCATGCACGTCTCCA 59.675 50.000 0.00 0.00 0.00 3.86
2899 4426 1.131126 CAATTGTCCATGCACGTCTCC 59.869 52.381 0.00 0.00 0.00 3.71
2900 4427 1.806542 ACAATTGTCCATGCACGTCTC 59.193 47.619 4.92 0.00 0.00 3.36
2901 4428 1.896220 ACAATTGTCCATGCACGTCT 58.104 45.000 4.92 0.00 0.00 4.18
2902 4429 3.683989 CATACAATTGTCCATGCACGTC 58.316 45.455 15.85 0.00 0.00 4.34
2903 4430 2.159393 GCATACAATTGTCCATGCACGT 60.159 45.455 29.08 2.97 38.93 4.49
2904 4431 2.097954 AGCATACAATTGTCCATGCACG 59.902 45.455 32.59 7.17 40.59 5.34
2905 4432 3.788333 AGCATACAATTGTCCATGCAC 57.212 42.857 32.59 15.51 40.59 4.57
2906 4433 3.676598 GCAAGCATACAATTGTCCATGCA 60.677 43.478 32.59 12.58 40.59 3.96
2907 4434 2.861935 GCAAGCATACAATTGTCCATGC 59.138 45.455 27.75 27.75 39.22 4.06
2908 4435 4.112716 TGCAAGCATACAATTGTCCATG 57.887 40.909 15.85 15.01 0.00 3.66
2909 4436 4.647853 AGATGCAAGCATACAATTGTCCAT 59.352 37.500 15.85 0.53 36.70 3.41
2910 4437 4.018490 AGATGCAAGCATACAATTGTCCA 58.982 39.130 15.85 0.00 36.70 4.02
2911 4438 4.644103 AGATGCAAGCATACAATTGTCC 57.356 40.909 15.85 5.06 36.70 4.02
2912 4439 8.944029 AGATATAGATGCAAGCATACAATTGTC 58.056 33.333 15.85 0.42 36.70 3.18
2913 4440 8.859236 AGATATAGATGCAAGCATACAATTGT 57.141 30.769 16.68 16.68 36.70 2.71
2918 4445 9.426534 AGGTATAGATATAGATGCAAGCATACA 57.573 33.333 7.64 0.00 36.70 2.29
2921 4448 9.653516 AGTAGGTATAGATATAGATGCAAGCAT 57.346 33.333 7.35 7.35 39.69 3.79
2982 4509 5.064962 AACAATAAGTTTCAACGGTGAACGA 59.935 36.000 17.13 0.00 43.52 3.85
2998 4525 5.277857 ACCACCTCGGATAGAACAATAAG 57.722 43.478 0.00 0.00 38.63 1.73
3101 4628 2.624838 CAAATAAGTGGGCTGGCTATGG 59.375 50.000 0.00 0.00 0.00 2.74
3141 4668 3.074412 CACTGGGGTCAAATAGTGTGTC 58.926 50.000 0.00 0.00 36.63 3.67
3143 4670 1.812571 GCACTGGGGTCAAATAGTGTG 59.187 52.381 0.00 0.00 41.84 3.82
3156 4683 0.464036 TAACTATCTGCCGCACTGGG 59.536 55.000 0.00 0.00 38.63 4.45
3319 4848 6.864342 TGTTCCAAACATTTTAAGAAACGGA 58.136 32.000 0.00 0.00 36.25 4.69
3613 5236 6.421801 GCCGAATATTCTTGGAAAATTGGATG 59.578 38.462 13.45 0.00 0.00 3.51
3614 5237 6.098124 TGCCGAATATTCTTGGAAAATTGGAT 59.902 34.615 13.45 0.00 0.00 3.41
3703 5328 0.878416 GCTAACGAATGGCCAACACA 59.122 50.000 10.96 0.00 0.00 3.72
3705 5330 1.164411 CAGCTAACGAATGGCCAACA 58.836 50.000 10.96 0.00 35.85 3.33


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

AutoCloner maintained by Alex Coulton.