Multiple sequence alignment - TraesCS3D01G184600

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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 TraesCS3D01G184600 chr3D 100.000 3586 0 0 1 3586 170535973 170539558 0.000000e+00 6623.0
1 TraesCS3D01G184600 chr3D 90.323 155 9 5 1827 1978 441388667 441388818 7.850000e-47 198.0
2 TraesCS3D01G184600 chr3D 88.679 159 12 5 1825 1979 315480423 315480579 4.730000e-44 189.0
3 TraesCS3D01G184600 chr3B 92.451 2954 146 30 5 2928 245902987 245905893 0.000000e+00 4148.0
4 TraesCS3D01G184600 chr3B 89.259 540 24 11 2935 3459 245913134 245913654 0.000000e+00 645.0
5 TraesCS3D01G184600 chr3A 92.823 1463 70 14 5 1458 208031598 208033034 0.000000e+00 2087.0
6 TraesCS3D01G184600 chr3A 92.047 679 36 8 1801 2474 208033640 208034305 0.000000e+00 939.0
7 TraesCS3D01G184600 chr3A 84.838 897 64 32 2461 3336 208034324 208035169 0.000000e+00 837.0
8 TraesCS3D01G184600 chr3A 94.089 203 12 0 1541 1743 208033437 208033639 3.480000e-80 309.0
9 TraesCS3D01G184600 chr3A 89.677 155 10 5 1827 1978 582283215 582283366 3.650000e-45 193.0
10 TraesCS3D01G184600 chr3A 88.636 88 4 2 3341 3428 208065434 208065515 6.330000e-18 102.0
11 TraesCS3D01G184600 chr3A 79.730 148 3 9 3437 3584 208066279 208066399 8.250000e-12 82.4
12 TraesCS3D01G184600 chr4B 89.241 158 13 3 1823 1978 106227405 106227560 1.020000e-45 195.0
13 TraesCS3D01G184600 chr4B 88.961 154 13 3 1827 1978 438375181 438375332 1.700000e-43 187.0
14 TraesCS3D01G184600 chr2D 89.677 155 12 3 1826 1978 79056166 79056318 1.020000e-45 195.0
15 TraesCS3D01G184600 chr1A 87.500 168 16 4 1813 1978 395177614 395177450 4.730000e-44 189.0
16 TraesCS3D01G184600 chr7D 87.730 163 14 5 1819 1978 117755205 117755364 6.110000e-43 185.0


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 TraesCS3D01G184600 chr3D 170535973 170539558 3585 False 6623 6623 100.00000 1 3586 1 chr3D.!!$F1 3585
1 TraesCS3D01G184600 chr3B 245902987 245905893 2906 False 4148 4148 92.45100 5 2928 1 chr3B.!!$F1 2923
2 TraesCS3D01G184600 chr3B 245913134 245913654 520 False 645 645 89.25900 2935 3459 1 chr3B.!!$F2 524
3 TraesCS3D01G184600 chr3A 208031598 208035169 3571 False 1043 2087 90.94925 5 3336 4 chr3A.!!$F2 3331

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
404 414 0.320697 ACTGAACCCTAACGCAGTCC 59.679 55.0 0.00 0.0 45.0 3.85 F
405 415 0.736325 CTGAACCCTAACGCAGTCCG 60.736 60.0 0.00 0.0 45.0 4.79 F
1786 2129 0.538118 GTGCACCCCGGAACACTATA 59.462 55.0 5.22 0.0 0.0 1.31 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1480 0.178981 AGCATTGACCACTGCCAACT 60.179 50.0 8.43 0.0 37.67 3.16 R
2123 2471 0.333312 TGTTCGGGCCCATTACCATT 59.667 50.0 24.92 0.0 0.00 3.16 R
3548 3960 0.034059 GTGGAGTGGAGTGGTGAGTG 59.966 60.0 0.00 0.0 0.00 3.51 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
89 92 1.673033 CGTTCCGAATCCAGCAGAAGT 60.673 52.381 0.00 0.00 0.00 3.01
184 193 1.811679 GGGCTGCGCAGAAGTAGAC 60.812 63.158 40.21 20.12 0.00 2.59
232 241 1.636988 GGTACGAACATTCCCGACTG 58.363 55.000 0.00 0.00 0.00 3.51
348 357 3.255642 CGATTTGACTGGTCCAAAATGGT 59.744 43.478 4.98 0.00 39.03 3.55
360 369 6.325028 TGGTCCAAAATGGTAGATTGTTTTCA 59.675 34.615 0.00 0.00 39.03 2.69
362 371 7.433680 GTCCAAAATGGTAGATTGTTTTCACT 58.566 34.615 0.00 0.00 39.03 3.41
404 414 0.320697 ACTGAACCCTAACGCAGTCC 59.679 55.000 0.00 0.00 45.00 3.85
405 415 0.736325 CTGAACCCTAACGCAGTCCG 60.736 60.000 0.00 0.00 45.00 4.79
409 419 2.509336 CCTAACGCAGTCCGCCAG 60.509 66.667 0.00 0.00 45.00 4.85
442 452 1.153765 GGGCTGATTTCGCCTTTGC 60.154 57.895 11.35 0.00 46.73 3.68
510 520 1.281899 GGAAGTTTCCGCGATCTCTG 58.718 55.000 8.23 0.00 37.65 3.35
515 525 1.956629 TTTCCGCGATCTCTGACCCC 61.957 60.000 8.23 0.00 0.00 4.95
539 549 1.971357 AGTCTGTCGTTCCACTGGATT 59.029 47.619 0.00 0.00 0.00 3.01
573 583 2.354821 GCGGATTTCCTGGTATGAACAC 59.645 50.000 0.00 0.00 0.00 3.32
595 605 2.872245 TGTTCCTGTTCTTTCTTCAGCG 59.128 45.455 0.00 0.00 0.00 5.18
616 627 1.153289 CCAAGGCCGATCTCCTGTG 60.153 63.158 0.00 5.56 33.43 3.66
704 715 6.090763 CCAGTTTGAAACAAGTCTTTTTGTCC 59.909 38.462 11.02 0.00 40.24 4.02
785 796 3.538379 CCATCATGGCGCTGCTATA 57.462 52.632 7.64 0.00 0.00 1.31
794 805 1.464997 GGCGCTGCTATAACTTATGGC 59.535 52.381 7.64 9.61 42.29 4.40
819 830 7.809806 GCATAGCTGCCAATTTAGTTAATTAGG 59.190 37.037 0.00 0.00 42.88 2.69
824 836 8.846211 GCTGCCAATTTAGTTAATTAGGATGTA 58.154 33.333 7.05 0.00 34.69 2.29
826 838 8.846211 TGCCAATTTAGTTAATTAGGATGTAGC 58.154 33.333 7.05 0.00 34.69 3.58
835 847 8.893727 AGTTAATTAGGATGTAGCATTGTTGTC 58.106 33.333 0.00 0.00 0.00 3.18
846 858 5.814764 AGCATTGTTGTCTCTCATTCATC 57.185 39.130 0.00 0.00 0.00 2.92
865 877 3.761140 CACCAATGCATGCGGCCA 61.761 61.111 14.09 0.00 43.89 5.36
867 879 2.202824 CCAATGCATGCGGCCAAG 60.203 61.111 14.09 0.00 43.89 3.61
881 893 1.588082 CCAAGGCTTGGTCATGTGC 59.412 57.895 33.43 0.00 45.93 4.57
882 894 0.896940 CCAAGGCTTGGTCATGTGCT 60.897 55.000 33.43 0.00 45.93 4.40
933 946 4.251246 TGCGTGGGCAGTTCTTTT 57.749 50.000 0.00 0.00 46.21 2.27
1014 1027 2.020181 GCAGACATGGACATGGATGCA 61.020 52.381 25.72 0.00 45.54 3.96
1090 1103 5.702349 AAGAGTGCGTACAGTACTTAAGT 57.298 39.130 13.68 13.68 45.90 2.24
1235 1248 1.808945 CCAGTCCATCAGTGCTGAAAC 59.191 52.381 5.95 5.53 43.58 2.78
1271 1284 7.815840 TTGATGACAACTTTGGTGAGATTTA 57.184 32.000 0.00 0.00 0.00 1.40
1461 1480 6.650390 AGCAGCTGAACTTTTTCTTTTCAAAA 59.350 30.769 20.43 0.00 32.36 2.44
1474 1498 3.518634 TTTCAAAAGTTGGCAGTGGTC 57.481 42.857 0.00 0.00 0.00 4.02
1476 1500 2.451490 TCAAAAGTTGGCAGTGGTCAA 58.549 42.857 0.00 0.00 35.97 3.18
1596 1935 7.686438 TGTTATTGTAGAACATCAGCACAAT 57.314 32.000 0.00 0.00 41.40 2.71
1673 2012 9.825109 ATTCCTTAGTTCTCTTAAGACTATTGC 57.175 33.333 0.00 0.00 0.00 3.56
1786 2129 0.538118 GTGCACCCCGGAACACTATA 59.462 55.000 5.22 0.00 0.00 1.31
1861 2204 8.933955 CGTTCACAAATATAAGATGTTTTAGCG 58.066 33.333 0.00 0.00 0.00 4.26
1909 2252 4.468643 CACGTTTTAGTGTGTGTGTGTTT 58.531 39.130 0.00 0.00 37.35 2.83
1911 2254 6.252281 CACGTTTTAGTGTGTGTGTGTTTAT 58.748 36.000 0.00 0.00 37.35 1.40
1922 2265 7.487829 GTGTGTGTGTGTTTATTCATTTCAGTT 59.512 33.333 0.00 0.00 0.00 3.16
1943 2286 8.135529 TCAGTTCGTATGTAGTCCATATTGAAG 58.864 37.037 0.00 0.00 38.29 3.02
1971 2316 7.487829 CCAAAACATCTTATATTTGTGAACGGG 59.512 37.037 0.00 0.00 32.29 5.28
2007 2352 7.065803 TGCTTCAGTCCTTTATATGCTTGTAAC 59.934 37.037 0.00 0.00 0.00 2.50
2090 2437 2.104111 TGGGAGTTCTTCGTCAATGTGT 59.896 45.455 0.00 0.00 0.00 3.72
2136 2484 5.351948 AATTTACACAATGGTAATGGGCC 57.648 39.130 0.00 0.00 33.56 5.80
2363 2713 6.784473 AGTCTTCATTTTGGGGAATCTTTCTT 59.216 34.615 0.00 0.00 0.00 2.52
2408 2758 3.255642 TCTTTGTTATGTTCTTGCAGGCC 59.744 43.478 0.00 0.00 0.00 5.19
2426 2776 5.770162 GCAGGCCAAACAGGAGTAATTATAT 59.230 40.000 5.01 0.00 41.22 0.86
2474 2824 2.639286 GCCAACACTGTTGCTCCG 59.361 61.111 15.42 4.33 0.00 4.63
2570 2952 0.394488 TGGTGAACGGCAAGGTGAAA 60.394 50.000 0.00 0.00 0.00 2.69
2577 2959 1.947456 ACGGCAAGGTGAAAGAAGTTC 59.053 47.619 0.00 0.00 36.70 3.01
2629 3011 6.147821 TCAAGCTTACTATGAAGACAGTTTGC 59.852 38.462 0.00 0.00 32.17 3.68
2669 3051 4.261825 GGAGTCGATGAGCTTATTACTGCT 60.262 45.833 14.65 0.00 42.82 4.24
2671 3053 5.285651 AGTCGATGAGCTTATTACTGCTTC 58.714 41.667 6.63 0.00 39.91 3.86
2705 3087 5.160607 ACCACTACTAGTTAGCAATGCAA 57.839 39.130 8.35 0.00 0.00 4.08
2773 3155 1.070601 ACTGGAAGGTTGCATTTTGCC 59.929 47.619 0.00 0.00 40.23 4.52
2847 3229 2.334946 TGCTGGGCATTGCGAAGTC 61.335 57.895 1.91 0.79 31.71 3.01
2848 3230 2.787249 CTGGGCATTGCGAAGTCG 59.213 61.111 1.91 0.00 43.27 4.18
2875 3257 6.222389 CAAAGTCCAAACTGATGGCAAATTA 58.778 36.000 0.00 0.00 40.46 1.40
2938 3325 0.669619 TTGCACACTCAGCATGTTGG 59.330 50.000 9.87 3.34 42.33 3.77
2939 3326 0.179023 TGCACACTCAGCATGTTGGA 60.179 50.000 9.87 0.00 37.02 3.53
2972 3359 0.320334 TGACCGATCTTGCTTGCGAA 60.320 50.000 0.00 0.00 0.00 4.70
2997 3384 6.879458 ACTAACCAAGTAGTTCATCCATCAAC 59.121 38.462 0.00 0.00 36.36 3.18
3012 3399 4.517075 TCCATCAACGTTACTGCAAATTCA 59.483 37.500 0.00 0.00 0.00 2.57
3034 3421 4.630940 CACATTGGCATGTTTGGGTTTATC 59.369 41.667 0.00 0.00 41.16 1.75
3036 3423 5.012975 ACATTGGCATGTTTGGGTTTATCTT 59.987 36.000 0.00 0.00 41.16 2.40
3059 3458 4.817063 CATCTTTGCGCGCCCACG 62.817 66.667 30.77 13.18 44.07 4.94
3083 3482 6.140737 CGCGAATGAAGTGCCTTAAATTAATC 59.859 38.462 0.00 0.00 0.00 1.75
3202 3611 8.581578 TCATCATTATCATTGGATCACAAATGG 58.418 33.333 12.44 2.97 43.46 3.16
3218 3627 7.106890 TCACAAATGGTCCTATTATTTCACGA 58.893 34.615 0.00 0.00 0.00 4.35
3219 3628 7.608376 TCACAAATGGTCCTATTATTTCACGAA 59.392 33.333 0.00 0.00 0.00 3.85
3220 3629 8.240682 CACAAATGGTCCTATTATTTCACGAAA 58.759 33.333 0.00 0.00 34.46 3.46
3221 3630 8.798402 ACAAATGGTCCTATTATTTCACGAAAA 58.202 29.630 0.00 0.00 33.56 2.29
3222 3631 9.072294 CAAATGGTCCTATTATTTCACGAAAAC 57.928 33.333 0.00 0.00 33.56 2.43
3223 3632 8.575649 AATGGTCCTATTATTTCACGAAAACT 57.424 30.769 0.00 0.00 33.56 2.66
3224 3633 7.989416 TGGTCCTATTATTTCACGAAAACTT 57.011 32.000 0.00 0.00 33.56 2.66
3225 3634 9.675464 ATGGTCCTATTATTTCACGAAAACTTA 57.325 29.630 0.00 0.00 33.56 2.24
3226 3635 8.938906 TGGTCCTATTATTTCACGAAAACTTAC 58.061 33.333 0.00 0.00 33.56 2.34
3227 3636 8.112449 GGTCCTATTATTTCACGAAAACTTACG 58.888 37.037 0.00 0.00 33.56 3.18
3228 3637 8.650714 GTCCTATTATTTCACGAAAACTTACGT 58.349 33.333 0.00 0.00 43.50 3.57
3229 3638 9.206870 TCCTATTATTTCACGAAAACTTACGTT 57.793 29.630 0.00 0.00 40.76 3.99
3230 3639 9.815936 CCTATTATTTCACGAAAACTTACGTTT 57.184 29.630 0.00 0.00 44.87 3.60
3265 3674 6.978659 TGCAAATACGTTTGTGGAAATTGTAA 59.021 30.769 0.00 0.00 45.14 2.41
3289 3699 2.885894 GAGCGGCTTCTATGTACTACCT 59.114 50.000 2.97 0.00 0.00 3.08
3359 3771 5.321516 ACAATCTAAAATGCTTAACGTCGC 58.678 37.500 0.00 0.00 0.00 5.19
3383 3795 2.146073 AACGCCATCTGTTTGCTGCC 62.146 55.000 0.00 0.00 0.00 4.85
3429 3841 2.811317 GGCTGAGCGGTCGTCTTG 60.811 66.667 10.46 0.00 0.00 3.02
3439 3851 2.186076 CGGTCGTCTTGAGCATAGTTC 58.814 52.381 0.00 0.00 45.52 3.01
3459 3871 4.942761 TCTTTCAGCCAGATTTTGCTTT 57.057 36.364 0.00 0.00 35.12 3.51
3460 3872 5.280654 TCTTTCAGCCAGATTTTGCTTTT 57.719 34.783 0.00 0.00 35.12 2.27
3461 3873 5.291971 TCTTTCAGCCAGATTTTGCTTTTC 58.708 37.500 0.00 0.00 35.12 2.29
3462 3874 4.942761 TTCAGCCAGATTTTGCTTTTCT 57.057 36.364 0.00 0.00 35.12 2.52
3463 3875 4.510038 TCAGCCAGATTTTGCTTTTCTC 57.490 40.909 0.00 0.00 35.12 2.87
3464 3876 3.256631 TCAGCCAGATTTTGCTTTTCTCC 59.743 43.478 0.00 0.00 35.12 3.71
3465 3877 3.006110 CAGCCAGATTTTGCTTTTCTCCA 59.994 43.478 0.00 0.00 35.12 3.86
3466 3878 3.257624 AGCCAGATTTTGCTTTTCTCCAG 59.742 43.478 0.00 0.00 32.94 3.86
3467 3879 3.582780 CCAGATTTTGCTTTTCTCCAGC 58.417 45.455 0.00 0.00 37.82 4.85
3468 3880 3.257624 CCAGATTTTGCTTTTCTCCAGCT 59.742 43.478 0.00 0.00 38.19 4.24
3469 3881 4.460382 CCAGATTTTGCTTTTCTCCAGCTA 59.540 41.667 0.00 0.00 38.19 3.32
3470 3882 5.397326 CAGATTTTGCTTTTCTCCAGCTAC 58.603 41.667 0.00 0.00 38.19 3.58
3471 3883 3.896648 TTTTGCTTTTCTCCAGCTACG 57.103 42.857 0.00 0.00 38.19 3.51
3472 3884 1.808411 TTGCTTTTCTCCAGCTACGG 58.192 50.000 0.00 0.00 38.19 4.02
3473 3885 0.036388 TGCTTTTCTCCAGCTACGGG 60.036 55.000 0.00 0.00 38.19 5.28
3474 3886 1.369839 GCTTTTCTCCAGCTACGGGC 61.370 60.000 0.00 0.00 42.19 6.13
3483 3895 4.014065 GCTACGGGCGTGATTCTC 57.986 61.111 0.00 0.00 0.00 2.87
3484 3896 1.141019 GCTACGGGCGTGATTCTCA 59.859 57.895 0.00 0.00 0.00 3.27
3485 3897 0.459585 GCTACGGGCGTGATTCTCAA 60.460 55.000 0.00 0.00 0.00 3.02
3486 3898 2.004583 CTACGGGCGTGATTCTCAAA 57.995 50.000 0.00 0.00 0.00 2.69
3487 3899 2.343101 CTACGGGCGTGATTCTCAAAA 58.657 47.619 0.00 0.00 0.00 2.44
3488 3900 1.600023 ACGGGCGTGATTCTCAAAAA 58.400 45.000 0.00 0.00 0.00 1.94
3529 3941 5.697473 AAAAAGAAGAAGAAGCTACTGGC 57.303 39.130 0.00 0.00 42.19 4.85
3538 3950 0.599558 AAGCTACTGGCGTTACACGA 59.400 50.000 0.00 0.00 46.05 4.35
3539 3951 0.815734 AGCTACTGGCGTTACACGAT 59.184 50.000 0.00 0.00 46.05 3.73
3540 3952 1.203994 AGCTACTGGCGTTACACGATT 59.796 47.619 0.00 0.00 46.05 3.34
3541 3953 1.323534 GCTACTGGCGTTACACGATTG 59.676 52.381 0.00 0.00 46.05 2.67
3542 3954 1.924524 CTACTGGCGTTACACGATTGG 59.075 52.381 0.00 0.00 46.05 3.16
3543 3955 0.319083 ACTGGCGTTACACGATTGGA 59.681 50.000 0.00 0.00 46.05 3.53
3544 3956 1.066430 ACTGGCGTTACACGATTGGAT 60.066 47.619 0.00 0.00 46.05 3.41
3545 3957 2.006888 CTGGCGTTACACGATTGGATT 58.993 47.619 0.00 0.00 46.05 3.01
3546 3958 2.418628 CTGGCGTTACACGATTGGATTT 59.581 45.455 0.00 0.00 46.05 2.17
3547 3959 3.597255 TGGCGTTACACGATTGGATTTA 58.403 40.909 0.00 0.00 46.05 1.40
3548 3960 3.371591 TGGCGTTACACGATTGGATTTAC 59.628 43.478 0.00 0.00 46.05 2.01
3549 3961 3.371591 GGCGTTACACGATTGGATTTACA 59.628 43.478 0.00 0.00 46.05 2.41
3550 3962 4.328667 GCGTTACACGATTGGATTTACAC 58.671 43.478 0.00 0.00 46.05 2.90
3551 3963 4.092383 GCGTTACACGATTGGATTTACACT 59.908 41.667 0.00 0.00 46.05 3.55
3552 3964 5.723135 GCGTTACACGATTGGATTTACACTC 60.723 44.000 0.00 0.00 46.05 3.51
3553 3965 5.346551 CGTTACACGATTGGATTTACACTCA 59.653 40.000 0.00 0.00 46.05 3.41
3554 3966 6.531439 GTTACACGATTGGATTTACACTCAC 58.469 40.000 0.00 0.00 0.00 3.51
3555 3967 4.000988 ACACGATTGGATTTACACTCACC 58.999 43.478 0.00 0.00 0.00 4.02
3556 3968 4.000325 CACGATTGGATTTACACTCACCA 59.000 43.478 0.00 0.00 0.00 4.17
3557 3969 4.000988 ACGATTGGATTTACACTCACCAC 58.999 43.478 0.00 0.00 0.00 4.16
3558 3970 4.253685 CGATTGGATTTACACTCACCACT 58.746 43.478 0.00 0.00 0.00 4.00
3559 3971 4.330074 CGATTGGATTTACACTCACCACTC 59.670 45.833 0.00 0.00 0.00 3.51
3560 3972 3.695830 TGGATTTACACTCACCACTCC 57.304 47.619 0.00 0.00 0.00 3.85
3561 3973 2.976185 TGGATTTACACTCACCACTCCA 59.024 45.455 0.00 0.00 0.00 3.86
3562 3974 3.244422 TGGATTTACACTCACCACTCCAC 60.244 47.826 0.00 0.00 0.00 4.02
3563 3975 3.008049 GGATTTACACTCACCACTCCACT 59.992 47.826 0.00 0.00 0.00 4.00
3564 3976 3.746045 TTTACACTCACCACTCCACTC 57.254 47.619 0.00 0.00 0.00 3.51
3565 3977 1.629043 TACACTCACCACTCCACTCC 58.371 55.000 0.00 0.00 0.00 3.85
3566 3978 0.398522 ACACTCACCACTCCACTCCA 60.399 55.000 0.00 0.00 0.00 3.86
3567 3979 0.034059 CACTCACCACTCCACTCCAC 59.966 60.000 0.00 0.00 0.00 4.02
3568 3980 1.290324 CTCACCACTCCACTCCACG 59.710 63.158 0.00 0.00 0.00 4.94
3569 3981 2.357517 CACCACTCCACTCCACGC 60.358 66.667 0.00 0.00 0.00 5.34
3570 3982 2.524394 ACCACTCCACTCCACGCT 60.524 61.111 0.00 0.00 0.00 5.07
3571 3983 2.262915 CCACTCCACTCCACGCTC 59.737 66.667 0.00 0.00 0.00 5.03
3572 3984 2.262915 CACTCCACTCCACGCTCC 59.737 66.667 0.00 0.00 0.00 4.70
3573 3985 2.118513 ACTCCACTCCACGCTCCT 59.881 61.111 0.00 0.00 0.00 3.69
3574 3986 1.979693 ACTCCACTCCACGCTCCTC 60.980 63.158 0.00 0.00 0.00 3.71
3575 3987 3.057547 CTCCACTCCACGCTCCTCG 62.058 68.421 0.00 0.00 45.38 4.63
3576 3988 4.135153 CCACTCCACGCTCCTCGG 62.135 72.222 0.00 0.00 43.86 4.63
3577 3989 3.374402 CACTCCACGCTCCTCGGT 61.374 66.667 0.00 0.00 43.86 4.69
3578 3990 2.600769 ACTCCACGCTCCTCGGTT 60.601 61.111 0.00 0.00 43.86 4.44
3579 3991 2.182030 CTCCACGCTCCTCGGTTC 59.818 66.667 0.00 0.00 43.86 3.62
3580 3992 3.358076 CTCCACGCTCCTCGGTTCC 62.358 68.421 0.00 0.00 43.86 3.62
3581 3993 4.452733 CCACGCTCCTCGGTTCCC 62.453 72.222 0.00 0.00 43.86 3.97
3582 3994 4.452733 CACGCTCCTCGGTTCCCC 62.453 72.222 0.00 0.00 43.86 4.81
3585 3997 3.471806 GCTCCTCGGTTCCCCCTC 61.472 72.222 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.273886 GAAGGGAAGGGATAGCTAGCG 59.726 57.143 9.55 0.00 0.00 4.26
3 4 2.977808 CCAGAAGGGAAGGGATAGCTA 58.022 52.381 0.00 0.00 40.01 3.32
169 178 2.575694 ATCTGTCTACTTCTGCGCAG 57.424 50.000 31.53 31.53 0.00 5.18
177 186 3.957497 AGCCTCGATCAATCTGTCTACTT 59.043 43.478 0.00 0.00 0.00 2.24
184 193 3.577667 GAGATGAGCCTCGATCAATCTG 58.422 50.000 0.00 0.00 29.85 2.90
221 230 1.519455 GCGAGGTCAGTCGGGAATG 60.519 63.158 0.00 0.00 40.44 2.67
232 241 5.720261 AAATATTCGAAGAAAGCGAGGTC 57.280 39.130 3.35 0.00 45.90 3.85
348 357 7.441017 CCCCAAAATTCAGTGAAAACAATCTA 58.559 34.615 10.14 0.00 0.00 1.98
360 369 4.207698 ACCTAAACCCCCAAAATTCAGT 57.792 40.909 0.00 0.00 0.00 3.41
362 371 6.616137 AGTTAAACCTAAACCCCCAAAATTCA 59.384 34.615 0.00 0.00 0.00 2.57
510 520 1.744522 GAACGACAGACTAGAGGGGTC 59.255 57.143 0.00 0.00 0.00 4.46
515 525 2.162608 CCAGTGGAACGACAGACTAGAG 59.837 54.545 1.68 0.00 45.86 2.43
573 583 3.059325 CGCTGAAGAAAGAACAGGAACAG 60.059 47.826 0.00 0.00 33.00 3.16
616 627 2.690778 GCGCATTGGTCACTGTCCC 61.691 63.158 0.30 0.00 0.00 4.46
663 674 5.180492 TCAAACTGGATCAATTACACGGTTC 59.820 40.000 0.00 0.00 30.87 3.62
704 715 3.428870 GCTGTCATAATCCGTCCGTAATG 59.571 47.826 0.00 0.00 0.00 1.90
776 787 4.033358 GCTATGCCATAAGTTATAGCAGCG 59.967 45.833 18.65 13.39 44.50 5.18
794 805 9.066892 TCCTAATTAACTAAATTGGCAGCTATG 57.933 33.333 0.00 0.00 38.29 2.23
795 806 9.813826 ATCCTAATTAACTAAATTGGCAGCTAT 57.186 29.630 0.00 0.00 38.29 2.97
819 830 6.314648 TGAATGAGAGACAACAATGCTACATC 59.685 38.462 0.00 0.00 0.00 3.06
824 836 4.331992 CGATGAATGAGAGACAACAATGCT 59.668 41.667 0.00 0.00 0.00 3.79
825 837 4.585364 CGATGAATGAGAGACAACAATGC 58.415 43.478 0.00 0.00 0.00 3.56
826 838 4.093850 TGCGATGAATGAGAGACAACAATG 59.906 41.667 0.00 0.00 0.00 2.82
835 847 2.286831 GCATTGGTGCGATGAATGAGAG 60.287 50.000 0.00 0.00 42.28 3.20
865 877 0.963962 CAAGCACATGACCAAGCCTT 59.036 50.000 0.00 0.00 0.00 4.35
867 879 1.080298 GCAAGCACATGACCAAGCC 60.080 57.895 0.00 0.00 0.00 4.35
875 887 0.032952 ACCAAGCAAGCAAGCACATG 59.967 50.000 3.19 0.00 36.85 3.21
876 888 1.619654 TACCAAGCAAGCAAGCACAT 58.380 45.000 3.19 0.00 36.85 3.21
877 889 1.270274 CATACCAAGCAAGCAAGCACA 59.730 47.619 3.19 0.00 36.85 4.57
878 890 1.541147 TCATACCAAGCAAGCAAGCAC 59.459 47.619 3.19 0.00 36.85 4.40
879 891 1.908344 TCATACCAAGCAAGCAAGCA 58.092 45.000 3.19 0.00 36.85 3.91
880 892 2.424601 TCATCATACCAAGCAAGCAAGC 59.575 45.455 0.00 0.00 0.00 4.01
881 893 4.913335 ATCATCATACCAAGCAAGCAAG 57.087 40.909 0.00 0.00 0.00 4.01
882 894 5.297527 CACTATCATCATACCAAGCAAGCAA 59.702 40.000 0.00 0.00 0.00 3.91
933 946 9.739276 ACAATATCAACCAATAAGAAGAGAACA 57.261 29.630 0.00 0.00 0.00 3.18
1014 1027 3.684305 TGACGATTGCTGAACGAAATGAT 59.316 39.130 0.00 0.00 0.00 2.45
1090 1103 1.562008 TCCACCTTGAGTGTGTTGGAA 59.438 47.619 0.00 0.00 45.74 3.53
1235 1248 7.473027 AAGTTGTCATCAAAATCTTTGCAAG 57.527 32.000 0.00 0.00 35.20 4.01
1271 1284 7.714813 GGCAAATAAAACCAATATAGGTGCATT 59.285 33.333 0.00 0.00 42.25 3.56
1461 1480 0.178981 AGCATTGACCACTGCCAACT 60.179 50.000 8.43 0.00 37.67 3.16
1572 1911 7.686438 ATTGTGCTGATGTTCTACAATAACA 57.314 32.000 0.00 0.00 39.43 2.41
1596 1935 2.884012 CCAACACAAGCAATCACCTGTA 59.116 45.455 0.00 0.00 0.00 2.74
1654 1993 4.710375 TCGGGCAATAGTCTTAAGAGAACT 59.290 41.667 5.12 2.93 32.66 3.01
1673 2012 6.522054 TGGCTTTAGATTCTTAAGTATCGGG 58.478 40.000 14.28 8.48 0.00 5.14
1815 2158 5.340439 ACGGAGGGAGTACTTGAATAAAG 57.660 43.478 0.00 0.00 42.07 1.85
1866 2209 7.821652 ACGTGTCTATATACATCTGATTCAGG 58.178 38.462 13.59 1.40 31.51 3.86
1909 2252 8.471609 TGGACTACATACGAACTGAAATGAATA 58.528 33.333 0.00 0.00 0.00 1.75
1911 2254 6.693466 TGGACTACATACGAACTGAAATGAA 58.307 36.000 0.00 0.00 0.00 2.57
1922 2265 6.548251 TGGACTTCAATATGGACTACATACGA 59.452 38.462 0.00 0.00 44.41 3.43
1943 2286 9.061610 CGTTCACAAATATAAGATGTTTTGGAC 57.938 33.333 0.00 0.00 34.23 4.02
2066 2413 2.543777 TTGACGAAGAACTCCCAAGG 57.456 50.000 0.00 0.00 0.00 3.61
2123 2471 0.333312 TGTTCGGGCCCATTACCATT 59.667 50.000 24.92 0.00 0.00 3.16
2136 2484 8.475331 AAGATACACAAGTAGTAAATGTTCGG 57.525 34.615 0.00 0.00 32.86 4.30
2363 2713 9.461312 AAGATATACATAAAACTTGAAGCCACA 57.539 29.630 0.00 0.00 0.00 4.17
2474 2824 5.221362 ACAGGGTTTAATGTTGTTACAAGGC 60.221 40.000 0.00 0.00 37.91 4.35
2590 2972 1.669779 AGCTTGATCTCGCAAATGAGC 59.330 47.619 9.01 0.00 35.90 4.26
2591 2973 4.569966 AGTAAGCTTGATCTCGCAAATGAG 59.430 41.667 9.86 0.00 37.33 2.90
2629 3011 1.954146 CCGGGAGACACACACAACG 60.954 63.158 0.00 0.00 0.00 4.10
2695 3077 3.749665 AAGGTTTGCTTTGCATTGCTA 57.250 38.095 10.49 0.00 38.76 3.49
2773 3155 2.553086 GAGAAAGAGCTCAGGCATCAG 58.447 52.381 17.77 0.00 41.70 2.90
2847 3229 2.226437 CCATCAGTTTGGACTTTGGACG 59.774 50.000 0.00 0.00 38.21 4.79
2848 3230 2.029918 GCCATCAGTTTGGACTTTGGAC 60.030 50.000 8.66 0.00 38.21 4.02
2972 3359 6.620877 TGATGGATGAACTACTTGGTTAGT 57.379 37.500 0.00 0.00 41.04 2.24
2997 3384 3.364621 GCCAATGTGAATTTGCAGTAACG 59.635 43.478 0.00 0.00 0.00 3.18
3055 3452 2.034879 AGGCACTTCATTCGCGTGG 61.035 57.895 5.77 0.00 27.25 4.94
3083 3482 4.701651 TGATTGTAAGCATCCTGTTCCTTG 59.298 41.667 0.00 0.00 0.00 3.61
3188 3597 8.837099 AAATAATAGGACCATTTGTGATCCAA 57.163 30.769 0.00 0.00 33.33 3.53
3227 3636 8.563133 CAAACGTATTTGCAAGTTTTTGAAAAC 58.437 29.630 10.78 10.55 43.02 2.43
3228 3637 8.647035 CAAACGTATTTGCAAGTTTTTGAAAA 57.353 26.923 10.78 0.00 44.05 2.29
3265 3674 2.938838 AGTACATAGAAGCCGCTCTCT 58.061 47.619 0.00 1.99 0.00 3.10
3307 3717 5.010922 TGAATTTTGCACAAGTAGAGCCAAT 59.989 36.000 0.00 0.00 32.33 3.16
3337 3747 5.320723 TGCGACGTTAAGCATTTTAGATTG 58.679 37.500 9.66 0.00 38.59 2.67
3359 3771 1.987770 GCAAACAGATGGCGTTGAATG 59.012 47.619 0.00 0.00 0.00 2.67
3383 3795 2.343475 AATAGCATGGGCCGGACTGG 62.343 60.000 7.57 0.00 42.56 4.00
3415 3827 1.877576 ATGCTCAAGACGACCGCTCA 61.878 55.000 0.00 0.00 0.00 4.26
3420 3832 3.512033 AGAACTATGCTCAAGACGACC 57.488 47.619 0.00 0.00 0.00 4.79
3429 3841 3.866651 TCTGGCTGAAAGAACTATGCTC 58.133 45.455 0.00 0.00 34.07 4.26
3439 3851 5.295152 AGAAAAGCAAAATCTGGCTGAAAG 58.705 37.500 0.00 0.00 40.93 2.62
3459 3871 2.678934 ACGCCCGTAGCTGGAGAA 60.679 61.111 0.00 0.00 40.39 2.87
3460 3872 3.449227 CACGCCCGTAGCTGGAGA 61.449 66.667 0.00 0.00 40.39 3.71
3461 3873 2.298158 AATCACGCCCGTAGCTGGAG 62.298 60.000 0.00 0.00 40.39 3.86
3462 3874 2.292794 GAATCACGCCCGTAGCTGGA 62.293 60.000 0.00 0.00 40.39 3.86
3463 3875 1.883084 GAATCACGCCCGTAGCTGG 60.883 63.158 0.00 0.00 40.39 4.85
3464 3876 0.872021 GAGAATCACGCCCGTAGCTG 60.872 60.000 0.00 0.00 34.97 4.24
3465 3877 1.320344 TGAGAATCACGCCCGTAGCT 61.320 55.000 0.00 0.00 42.56 3.32
3466 3878 1.141019 TGAGAATCACGCCCGTAGC 59.859 57.895 0.00 0.00 42.56 3.58
3507 3919 4.214332 CGCCAGTAGCTTCTTCTTCTTTTT 59.786 41.667 0.00 0.00 40.39 1.94
3508 3920 3.748568 CGCCAGTAGCTTCTTCTTCTTTT 59.251 43.478 0.00 0.00 40.39 2.27
3509 3921 3.244249 ACGCCAGTAGCTTCTTCTTCTTT 60.244 43.478 0.00 0.00 40.39 2.52
3510 3922 2.300437 ACGCCAGTAGCTTCTTCTTCTT 59.700 45.455 0.00 0.00 40.39 2.52
3511 3923 1.896465 ACGCCAGTAGCTTCTTCTTCT 59.104 47.619 0.00 0.00 40.39 2.85
3512 3924 2.371910 ACGCCAGTAGCTTCTTCTTC 57.628 50.000 0.00 0.00 40.39 2.87
3513 3925 2.841442 AACGCCAGTAGCTTCTTCTT 57.159 45.000 0.00 0.00 40.39 2.52
3514 3926 2.561419 TGTAACGCCAGTAGCTTCTTCT 59.439 45.455 0.00 0.00 40.39 2.85
3515 3927 2.666994 GTGTAACGCCAGTAGCTTCTTC 59.333 50.000 0.00 0.00 40.39 2.87
3516 3928 2.685100 GTGTAACGCCAGTAGCTTCTT 58.315 47.619 0.00 0.00 40.39 2.52
3517 3929 2.365408 GTGTAACGCCAGTAGCTTCT 57.635 50.000 0.00 0.00 40.39 2.85
3530 3942 6.401796 GGTGAGTGTAAATCCAATCGTGTAAC 60.402 42.308 0.00 0.00 32.32 2.50
3531 3943 5.640357 GGTGAGTGTAAATCCAATCGTGTAA 59.360 40.000 0.00 0.00 32.32 2.41
3532 3944 5.172934 GGTGAGTGTAAATCCAATCGTGTA 58.827 41.667 0.00 0.00 32.32 2.90
3533 3945 4.000988 GGTGAGTGTAAATCCAATCGTGT 58.999 43.478 0.00 0.00 32.32 4.49
3534 3946 4.000325 TGGTGAGTGTAAATCCAATCGTG 59.000 43.478 0.00 0.00 32.32 4.35
3535 3947 4.000988 GTGGTGAGTGTAAATCCAATCGT 58.999 43.478 0.00 0.00 32.32 3.73
3536 3948 4.253685 AGTGGTGAGTGTAAATCCAATCG 58.746 43.478 0.00 0.00 32.32 3.34
3537 3949 4.636206 GGAGTGGTGAGTGTAAATCCAATC 59.364 45.833 0.00 0.00 40.86 2.67
3538 3950 4.042809 TGGAGTGGTGAGTGTAAATCCAAT 59.957 41.667 0.00 0.00 32.84 3.16
3539 3951 3.392947 TGGAGTGGTGAGTGTAAATCCAA 59.607 43.478 0.00 0.00 32.84 3.53
3540 3952 2.976185 TGGAGTGGTGAGTGTAAATCCA 59.024 45.455 0.00 0.00 33.33 3.41
3541 3953 3.008049 AGTGGAGTGGTGAGTGTAAATCC 59.992 47.826 0.00 0.00 0.00 3.01
3542 3954 4.246458 GAGTGGAGTGGTGAGTGTAAATC 58.754 47.826 0.00 0.00 0.00 2.17
3543 3955 3.008049 GGAGTGGAGTGGTGAGTGTAAAT 59.992 47.826 0.00 0.00 0.00 1.40
3544 3956 2.367567 GGAGTGGAGTGGTGAGTGTAAA 59.632 50.000 0.00 0.00 0.00 2.01
3545 3957 1.968493 GGAGTGGAGTGGTGAGTGTAA 59.032 52.381 0.00 0.00 0.00 2.41
3546 3958 1.133294 TGGAGTGGAGTGGTGAGTGTA 60.133 52.381 0.00 0.00 0.00 2.90
3547 3959 0.398522 TGGAGTGGAGTGGTGAGTGT 60.399 55.000 0.00 0.00 0.00 3.55
3548 3960 0.034059 GTGGAGTGGAGTGGTGAGTG 59.966 60.000 0.00 0.00 0.00 3.51
3549 3961 1.464376 CGTGGAGTGGAGTGGTGAGT 61.464 60.000 0.00 0.00 0.00 3.41
3550 3962 1.290324 CGTGGAGTGGAGTGGTGAG 59.710 63.158 0.00 0.00 0.00 3.51
3551 3963 2.867855 GCGTGGAGTGGAGTGGTGA 61.868 63.158 0.00 0.00 0.00 4.02
3552 3964 2.357517 GCGTGGAGTGGAGTGGTG 60.358 66.667 0.00 0.00 0.00 4.17
3553 3965 2.524394 AGCGTGGAGTGGAGTGGT 60.524 61.111 0.00 0.00 0.00 4.16
3554 3966 2.262915 GAGCGTGGAGTGGAGTGG 59.737 66.667 0.00 0.00 0.00 4.00
3555 3967 2.219325 GAGGAGCGTGGAGTGGAGTG 62.219 65.000 0.00 0.00 0.00 3.51
3556 3968 1.979693 GAGGAGCGTGGAGTGGAGT 60.980 63.158 0.00 0.00 0.00 3.85
3557 3969 2.888863 GAGGAGCGTGGAGTGGAG 59.111 66.667 0.00 0.00 0.00 3.86
3558 3970 3.062466 CGAGGAGCGTGGAGTGGA 61.062 66.667 0.00 0.00 34.64 4.02
3559 3971 4.135153 CCGAGGAGCGTGGAGTGG 62.135 72.222 0.00 0.00 38.67 4.00
3560 3972 2.820767 GAACCGAGGAGCGTGGAGTG 62.821 65.000 0.00 0.00 38.67 3.51
3561 3973 2.600769 AACCGAGGAGCGTGGAGT 60.601 61.111 0.00 0.00 38.67 3.85
3562 3974 2.182030 GAACCGAGGAGCGTGGAG 59.818 66.667 0.00 0.00 38.67 3.86
3563 3975 3.379445 GGAACCGAGGAGCGTGGA 61.379 66.667 0.00 0.00 38.67 4.02
3564 3976 4.452733 GGGAACCGAGGAGCGTGG 62.453 72.222 0.00 0.00 40.86 4.94


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

AutoCloner maintained by Alex Coulton.