Multiple sequence alignment - TraesCS2D01G021000

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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 TraesCS2D01G021000 chr2D 100.000 2155 0 0 1 2155 9786218 9788372 0.000000e+00 3980
1 TraesCS2D01G021000 chr2D 100.000 439 0 0 2624 3062 9788841 9789279 0.000000e+00 811
2 TraesCS2D01G021000 chr2D 97.070 273 3 1 2624 2896 638423889 638424156 3.600000e-124 455
3 TraesCS2D01G021000 chr2D 100.000 167 0 0 2896 3062 638424338 638424172 2.970000e-80 309
4 TraesCS2D01G021000 chr5D 98.565 2161 18 5 1 2155 503288385 503290538 0.000000e+00 3807
5 TraesCS2D01G021000 chr5D 97.449 2156 25 6 1 2155 6179862 6177736 0.000000e+00 3650
6 TraesCS2D01G021000 chr5D 94.824 2164 69 16 1 2155 513587303 513585174 0.000000e+00 3336
7 TraesCS2D01G021000 chr5D 97.464 276 5 1 2624 2899 503290739 503291012 1.290000e-128 470
8 TraesCS2D01G021000 chr5D 97.464 276 3 1 2624 2899 28034269 28034540 4.620000e-128 468
9 TraesCS2D01G021000 chr5D 100.000 166 0 0 2896 3061 512409510 512409345 1.070000e-79 307
10 TraesCS2D01G021000 chr5D 100.000 166 0 0 2896 3061 512416447 512416282 1.070000e-79 307
11 TraesCS2D01G021000 chr5D 99.401 167 1 0 2896 3062 6177083 6177249 1.380000e-78 303
12 TraesCS2D01G021000 chr1A 98.564 2159 20 5 1 2155 554459543 554461694 0.000000e+00 3805
13 TraesCS2D01G021000 chr1A 96.377 276 5 1 2624 2899 554462444 554462714 1.670000e-122 449
14 TraesCS2D01G021000 chr1A 100.000 167 0 0 2896 3062 554462897 554462731 2.970000e-80 309
15 TraesCS2D01G021000 chr6D 98.563 2157 20 8 1 2155 45510487 45508340 0.000000e+00 3801
16 TraesCS2D01G021000 chr6D 97.101 276 3 1 2624 2899 45508137 45507867 7.740000e-126 460
17 TraesCS2D01G021000 chr2B 98.144 2155 30 5 1 2155 474901412 474903556 0.000000e+00 3749
18 TraesCS2D01G021000 chr2B 97.078 308 7 2 95 402 25364566 25364261 4.530000e-143 518
19 TraesCS2D01G021000 chr2B 96.014 276 8 1 2624 2899 180567401 180567129 2.170000e-121 446
20 TraesCS2D01G021000 chr2B 95.636 275 9 1 2624 2898 474903758 474904029 3.620000e-119 438
21 TraesCS2D01G021000 chr2B 100.000 167 0 0 2896 3062 474904213 474904047 2.970000e-80 309
22 TraesCS2D01G021000 chr2B 96.178 157 5 1 1 157 637104100 637103945 3.920000e-64 255
23 TraesCS2D01G021000 chr4B 96.694 1936 48 8 1 1936 308682698 308680779 0.000000e+00 3206
24 TraesCS2D01G021000 chr5A 97.778 1665 27 10 2 1665 607199019 607197364 0.000000e+00 2861
25 TraesCS2D01G021000 chr5A 97.624 463 9 2 1694 2155 657431621 657432082 0.000000e+00 793
26 TraesCS2D01G021000 chr5A 96.552 116 3 1 2040 2155 267861179 267861065 1.120000e-44 191
27 TraesCS2D01G021000 chr1D 97.936 1502 24 5 1 1500 51876991 51875495 0.000000e+00 2595
28 TraesCS2D01G021000 chr1D 96.377 276 5 1 2624 2899 254434414 254434684 1.670000e-122 449
29 TraesCS2D01G021000 chr1D 95.652 276 10 1 2624 2899 51874545 51874272 2.800000e-120 442
30 TraesCS2D01G021000 chr1D 99.401 167 1 0 2896 3062 254434867 254434701 1.380000e-78 303
31 TraesCS2D01G021000 chr4D 95.641 1606 63 2 550 2155 207070648 207069050 0.000000e+00 2571
32 TraesCS2D01G021000 chr2A 97.785 632 9 3 292 920 588081858 588082487 0.000000e+00 1085
33 TraesCS2D01G021000 chr2A 98.864 264 1 2 1 264 334594982 334594721 1.290000e-128 470
34 TraesCS2D01G021000 chr7A 97.281 331 4 5 380 710 591434728 591435053 9.590000e-155 556
35 TraesCS2D01G021000 chr3A 98.969 194 2 0 1905 2098 187128465 187128272 6.280000e-92 348
36 TraesCS2D01G021000 chr3A 98.148 108 2 0 1698 1805 313341928 313342035 4.030000e-44 189
37 TraesCS2D01G021000 chr5B 100.000 167 0 0 2896 3062 647664601 647664435 2.970000e-80 309
38 TraesCS2D01G021000 chrUn 100.000 166 0 0 2897 3062 39512823 39512658 1.070000e-79 307
39 TraesCS2D01G021000 chr3B 98.039 153 3 0 2003 2155 147679434 147679282 1.810000e-67 267
40 TraesCS2D01G021000 chr6B 96.460 113 4 0 2043 2155 160195394 160195506 1.450000e-43 187


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 TraesCS2D01G021000 chr2D 9786218 9789279 3061 False 2395.5 3980 100.0000 1 3062 2 chr2D.!!$F2 3061
1 TraesCS2D01G021000 chr5D 6177736 6179862 2126 True 3650.0 3650 97.4490 1 2155 1 chr5D.!!$R1 2154
2 TraesCS2D01G021000 chr5D 513585174 513587303 2129 True 3336.0 3336 94.8240 1 2155 1 chr5D.!!$R4 2154
3 TraesCS2D01G021000 chr5D 503288385 503291012 2627 False 2138.5 3807 98.0145 1 2899 2 chr5D.!!$F3 2898
4 TraesCS2D01G021000 chr1A 554459543 554462714 3171 False 2127.0 3805 97.4705 1 2899 2 chr1A.!!$F1 2898
5 TraesCS2D01G021000 chr6D 45507867 45510487 2620 True 2130.5 3801 97.8320 1 2899 2 chr6D.!!$R1 2898
6 TraesCS2D01G021000 chr2B 474901412 474904029 2617 False 2093.5 3749 96.8900 1 2898 2 chr2B.!!$F1 2897
7 TraesCS2D01G021000 chr4B 308680779 308682698 1919 True 3206.0 3206 96.6940 1 1936 1 chr4B.!!$R1 1935
8 TraesCS2D01G021000 chr5A 607197364 607199019 1655 True 2861.0 2861 97.7780 2 1665 1 chr5A.!!$R2 1663
9 TraesCS2D01G021000 chr1D 51874272 51876991 2719 True 1518.5 2595 96.7940 1 2899 2 chr1D.!!$R2 2898
10 TraesCS2D01G021000 chr4D 207069050 207070648 1598 True 2571.0 2571 95.6410 550 2155 1 chr4D.!!$R1 1605
11 TraesCS2D01G021000 chr2A 588081858 588082487 629 False 1085.0 1085 97.7850 292 920 1 chr2A.!!$F1 628

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
903 946 4.599047 TTGAAAAAGGGCATTGAACGAT 57.401 36.364 0.0 0.0 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2900 3588 0.027979 CTCGCCGTGCATTTGTATGG 59.972 55.0 2.82 2.82 39.44 2.74 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
903 946 4.599047 TTGAAAAAGGGCATTGAACGAT 57.401 36.364 0.00 0.00 0.00 3.73
1300 1344 2.044946 GGCCCGAAGCACAAGGAT 60.045 61.111 0.00 0.00 46.50 3.24
1357 1401 1.002087 CTTTTGTAGCTCTCCACGGGT 59.998 52.381 0.00 0.00 0.00 5.28
1886 2571 2.069273 CTTGGCTCTGAACTTACGTGG 58.931 52.381 0.00 0.00 0.00 4.94
2667 3352 2.032680 TAGGCTTCGGTGGCATTTAC 57.967 50.000 0.00 0.00 34.73 2.01
2899 3587 1.681229 ATTTGACCCTTAGCCCCAGA 58.319 50.000 0.00 0.00 0.00 3.86
2900 3588 0.696501 TTTGACCCTTAGCCCCAGAC 59.303 55.000 0.00 0.00 0.00 3.51
2901 3589 1.205460 TTGACCCTTAGCCCCAGACC 61.205 60.000 0.00 0.00 0.00 3.85
2902 3590 1.615424 GACCCTTAGCCCCAGACCA 60.615 63.158 0.00 0.00 0.00 4.02
2903 3591 0.988678 GACCCTTAGCCCCAGACCAT 60.989 60.000 0.00 0.00 0.00 3.55
2904 3592 0.345502 ACCCTTAGCCCCAGACCATA 59.654 55.000 0.00 0.00 0.00 2.74
2905 3593 0.765510 CCCTTAGCCCCAGACCATAC 59.234 60.000 0.00 0.00 0.00 2.39
2906 3594 1.507140 CCTTAGCCCCAGACCATACA 58.493 55.000 0.00 0.00 0.00 2.29
2907 3595 1.843851 CCTTAGCCCCAGACCATACAA 59.156 52.381 0.00 0.00 0.00 2.41
2908 3596 2.241176 CCTTAGCCCCAGACCATACAAA 59.759 50.000 0.00 0.00 0.00 2.83
2909 3597 3.117512 CCTTAGCCCCAGACCATACAAAT 60.118 47.826 0.00 0.00 0.00 2.32
2910 3598 2.442236 AGCCCCAGACCATACAAATG 57.558 50.000 0.00 0.00 0.00 2.32
2911 3599 0.746659 GCCCCAGACCATACAAATGC 59.253 55.000 0.00 0.00 0.00 3.56
2912 3600 1.959508 GCCCCAGACCATACAAATGCA 60.960 52.381 0.00 0.00 0.00 3.96
2913 3601 1.750778 CCCCAGACCATACAAATGCAC 59.249 52.381 0.00 0.00 0.00 4.57
2914 3602 1.401552 CCCAGACCATACAAATGCACG 59.598 52.381 0.00 0.00 0.00 5.34
2915 3603 1.401552 CCAGACCATACAAATGCACGG 59.598 52.381 0.00 0.00 0.00 4.94
2916 3604 1.094785 AGACCATACAAATGCACGGC 58.905 50.000 0.00 0.00 0.00 5.68
2917 3605 0.248054 GACCATACAAATGCACGGCG 60.248 55.000 4.80 4.80 0.00 6.46
2918 3606 0.675208 ACCATACAAATGCACGGCGA 60.675 50.000 16.62 0.00 0.00 5.54
2919 3607 0.027979 CCATACAAATGCACGGCGAG 59.972 55.000 16.62 7.03 0.00 5.03
2920 3608 0.589729 CATACAAATGCACGGCGAGC 60.590 55.000 22.31 22.31 0.00 5.03
2921 3609 1.714899 ATACAAATGCACGGCGAGCC 61.715 55.000 25.59 3.59 0.00 4.70
2922 3610 4.481112 CAAATGCACGGCGAGCCC 62.481 66.667 25.59 5.47 0.00 5.19
2924 3612 4.802051 AATGCACGGCGAGCCCAT 62.802 61.111 25.59 11.35 0.00 4.00
2937 3625 3.287445 CCCATGCGAAGGGTTTGG 58.713 61.111 0.00 0.00 41.61 3.28
2938 3626 1.606313 CCCATGCGAAGGGTTTGGT 60.606 57.895 0.00 0.00 41.61 3.67
2939 3627 1.184970 CCCATGCGAAGGGTTTGGTT 61.185 55.000 0.00 0.00 41.61 3.67
2940 3628 1.540267 CCATGCGAAGGGTTTGGTTA 58.460 50.000 0.00 0.00 0.00 2.85
2941 3629 1.889829 CCATGCGAAGGGTTTGGTTAA 59.110 47.619 0.00 0.00 0.00 2.01
2942 3630 2.297597 CCATGCGAAGGGTTTGGTTAAA 59.702 45.455 0.00 0.00 0.00 1.52
2943 3631 3.243907 CCATGCGAAGGGTTTGGTTAAAA 60.244 43.478 0.00 0.00 0.00 1.52
2944 3632 4.562552 CCATGCGAAGGGTTTGGTTAAAAT 60.563 41.667 0.00 0.00 0.00 1.82
2945 3633 5.336849 CCATGCGAAGGGTTTGGTTAAAATA 60.337 40.000 0.00 0.00 0.00 1.40
2946 3634 5.986501 TGCGAAGGGTTTGGTTAAAATAT 57.013 34.783 0.00 0.00 0.00 1.28
2947 3635 5.715070 TGCGAAGGGTTTGGTTAAAATATG 58.285 37.500 0.00 0.00 0.00 1.78
2948 3636 4.565166 GCGAAGGGTTTGGTTAAAATATGC 59.435 41.667 0.00 0.00 0.00 3.14
2949 3637 5.106442 CGAAGGGTTTGGTTAAAATATGCC 58.894 41.667 0.00 0.00 0.00 4.40
2950 3638 5.336849 CGAAGGGTTTGGTTAAAATATGCCA 60.337 40.000 0.00 0.00 0.00 4.92
2951 3639 6.441088 AAGGGTTTGGTTAAAATATGCCAA 57.559 33.333 0.00 0.00 39.00 4.52
2952 3640 6.441088 AGGGTTTGGTTAAAATATGCCAAA 57.559 33.333 3.78 3.78 45.36 3.28
2957 3645 7.602517 TTTGGTTAAAATATGCCAAATTCCG 57.397 32.000 3.78 0.00 43.49 4.30
2958 3646 5.112686 TGGTTAAAATATGCCAAATTCCGC 58.887 37.500 0.00 0.00 0.00 5.54
2959 3647 4.509970 GGTTAAAATATGCCAAATTCCGCC 59.490 41.667 0.00 0.00 0.00 6.13
2960 3648 3.902881 AAAATATGCCAAATTCCGCCA 57.097 38.095 0.00 0.00 0.00 5.69
2961 3649 3.902881 AAATATGCCAAATTCCGCCAA 57.097 38.095 0.00 0.00 0.00 4.52
2962 3650 3.902881 AATATGCCAAATTCCGCCAAA 57.097 38.095 0.00 0.00 0.00 3.28
2963 3651 4.420522 AATATGCCAAATTCCGCCAAAT 57.579 36.364 0.00 0.00 0.00 2.32
2964 3652 5.543507 AATATGCCAAATTCCGCCAAATA 57.456 34.783 0.00 0.00 0.00 1.40
2965 3653 2.663826 TGCCAAATTCCGCCAAATAC 57.336 45.000 0.00 0.00 0.00 1.89
2966 3654 1.895798 TGCCAAATTCCGCCAAATACA 59.104 42.857 0.00 0.00 0.00 2.29
2967 3655 2.267426 GCCAAATTCCGCCAAATACAC 58.733 47.619 0.00 0.00 0.00 2.90
2968 3656 2.353208 GCCAAATTCCGCCAAATACACA 60.353 45.455 0.00 0.00 0.00 3.72
2969 3657 3.862642 GCCAAATTCCGCCAAATACACAA 60.863 43.478 0.00 0.00 0.00 3.33
2970 3658 4.310769 CCAAATTCCGCCAAATACACAAA 58.689 39.130 0.00 0.00 0.00 2.83
2971 3659 4.934602 CCAAATTCCGCCAAATACACAAAT 59.065 37.500 0.00 0.00 0.00 2.32
2972 3660 6.102663 CCAAATTCCGCCAAATACACAAATA 58.897 36.000 0.00 0.00 0.00 1.40
2973 3661 6.591834 CCAAATTCCGCCAAATACACAAATAA 59.408 34.615 0.00 0.00 0.00 1.40
2974 3662 7.118390 CCAAATTCCGCCAAATACACAAATAAA 59.882 33.333 0.00 0.00 0.00 1.40
2975 3663 8.499162 CAAATTCCGCCAAATACACAAATAAAA 58.501 29.630 0.00 0.00 0.00 1.52
2976 3664 7.589574 ATTCCGCCAAATACACAAATAAAAC 57.410 32.000 0.00 0.00 0.00 2.43
2977 3665 5.471257 TCCGCCAAATACACAAATAAAACC 58.529 37.500 0.00 0.00 0.00 3.27
2978 3666 4.627900 CCGCCAAATACACAAATAAAACCC 59.372 41.667 0.00 0.00 0.00 4.11
2979 3667 5.230942 CGCCAAATACACAAATAAAACCCA 58.769 37.500 0.00 0.00 0.00 4.51
2980 3668 5.696724 CGCCAAATACACAAATAAAACCCAA 59.303 36.000 0.00 0.00 0.00 4.12
2981 3669 6.346999 CGCCAAATACACAAATAAAACCCAAC 60.347 38.462 0.00 0.00 0.00 3.77
2982 3670 6.072948 GCCAAATACACAAATAAAACCCAACC 60.073 38.462 0.00 0.00 0.00 3.77
2983 3671 6.992715 CCAAATACACAAATAAAACCCAACCA 59.007 34.615 0.00 0.00 0.00 3.67
2984 3672 7.663493 CCAAATACACAAATAAAACCCAACCAT 59.337 33.333 0.00 0.00 0.00 3.55
2985 3673 9.712305 CAAATACACAAATAAAACCCAACCATA 57.288 29.630 0.00 0.00 0.00 2.74
2986 3674 9.713713 AAATACACAAATAAAACCCAACCATAC 57.286 29.630 0.00 0.00 0.00 2.39
2987 3675 6.732896 ACACAAATAAAACCCAACCATACA 57.267 33.333 0.00 0.00 0.00 2.29
2988 3676 7.309770 ACACAAATAAAACCCAACCATACAT 57.690 32.000 0.00 0.00 0.00 2.29
2989 3677 7.158021 ACACAAATAAAACCCAACCATACATG 58.842 34.615 0.00 0.00 0.00 3.21
2990 3678 6.091986 CACAAATAAAACCCAACCATACATGC 59.908 38.462 0.00 0.00 0.00 4.06
2991 3679 5.351948 AATAAAACCCAACCATACATGCC 57.648 39.130 0.00 0.00 0.00 4.40
2992 3680 1.567357 AAACCCAACCATACATGCCC 58.433 50.000 0.00 0.00 0.00 5.36
2993 3681 0.411452 AACCCAACCATACATGCCCA 59.589 50.000 0.00 0.00 0.00 5.36
2994 3682 0.324275 ACCCAACCATACATGCCCAC 60.324 55.000 0.00 0.00 0.00 4.61
2995 3683 1.042559 CCCAACCATACATGCCCACC 61.043 60.000 0.00 0.00 0.00 4.61
2996 3684 0.324183 CCAACCATACATGCCCACCA 60.324 55.000 0.00 0.00 0.00 4.17
2997 3685 1.554836 CAACCATACATGCCCACCAA 58.445 50.000 0.00 0.00 0.00 3.67
2998 3686 2.109774 CAACCATACATGCCCACCAAT 58.890 47.619 0.00 0.00 0.00 3.16
2999 3687 2.500910 CAACCATACATGCCCACCAATT 59.499 45.455 0.00 0.00 0.00 2.32
3000 3688 3.678965 ACCATACATGCCCACCAATTA 57.321 42.857 0.00 0.00 0.00 1.40
3001 3689 4.197559 ACCATACATGCCCACCAATTAT 57.802 40.909 0.00 0.00 0.00 1.28
3002 3690 5.332106 ACCATACATGCCCACCAATTATA 57.668 39.130 0.00 0.00 0.00 0.98
3003 3691 5.902760 ACCATACATGCCCACCAATTATAT 58.097 37.500 0.00 0.00 0.00 0.86
3004 3692 5.951747 ACCATACATGCCCACCAATTATATC 59.048 40.000 0.00 0.00 0.00 1.63
3005 3693 6.189859 CCATACATGCCCACCAATTATATCT 58.810 40.000 0.00 0.00 0.00 1.98
3006 3694 6.664816 CCATACATGCCCACCAATTATATCTT 59.335 38.462 0.00 0.00 0.00 2.40
3007 3695 7.148018 CCATACATGCCCACCAATTATATCTTC 60.148 40.741 0.00 0.00 0.00 2.87
3008 3696 5.957132 ACATGCCCACCAATTATATCTTCT 58.043 37.500 0.00 0.00 0.00 2.85
3009 3697 7.090319 ACATGCCCACCAATTATATCTTCTA 57.910 36.000 0.00 0.00 0.00 2.10
3010 3698 7.526041 ACATGCCCACCAATTATATCTTCTAA 58.474 34.615 0.00 0.00 0.00 2.10
3011 3699 8.004215 ACATGCCCACCAATTATATCTTCTAAA 58.996 33.333 0.00 0.00 0.00 1.85
3012 3700 9.028284 CATGCCCACCAATTATATCTTCTAAAT 57.972 33.333 0.00 0.00 0.00 1.40
3013 3701 8.635765 TGCCCACCAATTATATCTTCTAAATC 57.364 34.615 0.00 0.00 0.00 2.17
3014 3702 8.224025 TGCCCACCAATTATATCTTCTAAATCA 58.776 33.333 0.00 0.00 0.00 2.57
3015 3703 9.247861 GCCCACCAATTATATCTTCTAAATCAT 57.752 33.333 0.00 0.00 0.00 2.45
3032 3720 9.817809 TCTAAATCATCTACACTAACAATCCAC 57.182 33.333 0.00 0.00 0.00 4.02
3033 3721 7.865706 AAATCATCTACACTAACAATCCACC 57.134 36.000 0.00 0.00 0.00 4.61
3034 3722 5.353394 TCATCTACACTAACAATCCACCC 57.647 43.478 0.00 0.00 0.00 4.61
3035 3723 5.030147 TCATCTACACTAACAATCCACCCT 58.970 41.667 0.00 0.00 0.00 4.34
3036 3724 5.487488 TCATCTACACTAACAATCCACCCTT 59.513 40.000 0.00 0.00 0.00 3.95
3037 3725 5.416271 TCTACACTAACAATCCACCCTTC 57.584 43.478 0.00 0.00 0.00 3.46
3038 3726 5.091552 TCTACACTAACAATCCACCCTTCT 58.908 41.667 0.00 0.00 0.00 2.85
3039 3727 4.287766 ACACTAACAATCCACCCTTCTC 57.712 45.455 0.00 0.00 0.00 2.87
3040 3728 3.009143 ACACTAACAATCCACCCTTCTCC 59.991 47.826 0.00 0.00 0.00 3.71
3041 3729 3.009033 CACTAACAATCCACCCTTCTCCA 59.991 47.826 0.00 0.00 0.00 3.86
3042 3730 2.586648 AACAATCCACCCTTCTCCAC 57.413 50.000 0.00 0.00 0.00 4.02
3043 3731 0.698818 ACAATCCACCCTTCTCCACC 59.301 55.000 0.00 0.00 0.00 4.61
3044 3732 0.698238 CAATCCACCCTTCTCCACCA 59.302 55.000 0.00 0.00 0.00 4.17
3045 3733 1.075374 CAATCCACCCTTCTCCACCAA 59.925 52.381 0.00 0.00 0.00 3.67
3046 3734 1.455822 ATCCACCCTTCTCCACCAAA 58.544 50.000 0.00 0.00 0.00 3.28
3047 3735 1.227249 TCCACCCTTCTCCACCAAAA 58.773 50.000 0.00 0.00 0.00 2.44
3048 3736 1.144913 TCCACCCTTCTCCACCAAAAG 59.855 52.381 0.00 0.00 0.00 2.27
3049 3737 1.620822 CACCCTTCTCCACCAAAAGG 58.379 55.000 0.00 0.00 39.44 3.11
3050 3738 1.144913 CACCCTTCTCCACCAAAAGGA 59.855 52.381 1.99 0.00 41.78 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1300 1344 7.148373 GCCTAATTGACACCAACGAGTAAAATA 60.148 37.037 0.00 0.00 34.72 1.40
1357 1401 7.759489 ACATGAAACCTATTAGTGCAAAAGA 57.241 32.000 0.00 0.00 0.00 2.52
1886 2571 3.686016 TCCTGGGAAACAAAGTCATAGC 58.314 45.455 0.00 0.00 0.00 2.97
2899 3587 0.675208 TCGCCGTGCATTTGTATGGT 60.675 50.000 8.43 0.00 38.79 3.55
2900 3588 0.027979 CTCGCCGTGCATTTGTATGG 59.972 55.000 2.82 2.82 39.44 2.74
2901 3589 0.589729 GCTCGCCGTGCATTTGTATG 60.590 55.000 6.24 0.00 34.76 2.39
2902 3590 1.714899 GGCTCGCCGTGCATTTGTAT 61.715 55.000 13.51 0.00 0.00 2.29
2903 3591 2.395360 GGCTCGCCGTGCATTTGTA 61.395 57.895 13.51 0.00 0.00 2.41
2904 3592 3.737172 GGCTCGCCGTGCATTTGT 61.737 61.111 13.51 0.00 0.00 2.83
2905 3593 4.481112 GGGCTCGCCGTGCATTTG 62.481 66.667 13.51 0.00 36.85 2.32
2907 3595 4.802051 ATGGGCTCGCCGTGCATT 62.802 61.111 13.51 0.00 36.85 3.56
2921 3609 1.540267 TAACCAAACCCTTCGCATGG 58.460 50.000 0.00 0.00 37.19 3.66
2922 3610 3.651803 TTTAACCAAACCCTTCGCATG 57.348 42.857 0.00 0.00 0.00 4.06
2923 3611 4.882842 ATTTTAACCAAACCCTTCGCAT 57.117 36.364 0.00 0.00 0.00 4.73
2924 3612 5.715070 CATATTTTAACCAAACCCTTCGCA 58.285 37.500 0.00 0.00 0.00 5.10
2925 3613 4.565166 GCATATTTTAACCAAACCCTTCGC 59.435 41.667 0.00 0.00 0.00 4.70
2926 3614 5.106442 GGCATATTTTAACCAAACCCTTCG 58.894 41.667 0.00 0.00 0.00 3.79
2927 3615 6.043854 TGGCATATTTTAACCAAACCCTTC 57.956 37.500 0.00 0.00 0.00 3.46
2928 3616 6.441088 TTGGCATATTTTAACCAAACCCTT 57.559 33.333 0.00 0.00 39.17 3.95
2929 3617 6.441088 TTTGGCATATTTTAACCAAACCCT 57.559 33.333 2.06 0.00 44.92 4.34
2934 3622 5.582665 GCGGAATTTGGCATATTTTAACCAA 59.417 36.000 4.66 0.00 40.34 3.67
2935 3623 5.112686 GCGGAATTTGGCATATTTTAACCA 58.887 37.500 4.66 0.00 0.00 3.67
2936 3624 4.509970 GGCGGAATTTGGCATATTTTAACC 59.490 41.667 4.66 1.21 0.00 2.85
2937 3625 5.112686 TGGCGGAATTTGGCATATTTTAAC 58.887 37.500 4.66 0.00 36.93 2.01
2938 3626 5.344743 TGGCGGAATTTGGCATATTTTAA 57.655 34.783 4.66 0.00 36.93 1.52
2939 3627 5.344743 TTGGCGGAATTTGGCATATTTTA 57.655 34.783 4.66 0.00 41.88 1.52
2940 3628 3.902881 TGGCGGAATTTGGCATATTTT 57.097 38.095 4.66 0.00 36.93 1.82
2941 3629 3.902881 TTGGCGGAATTTGGCATATTT 57.097 38.095 4.66 0.00 41.88 1.40
2942 3630 3.902881 TTTGGCGGAATTTGGCATATT 57.097 38.095 2.68 2.68 41.88 1.28
2943 3631 4.343526 TGTATTTGGCGGAATTTGGCATAT 59.656 37.500 8.38 10.88 41.88 1.78
2944 3632 3.701542 TGTATTTGGCGGAATTTGGCATA 59.298 39.130 8.38 5.12 41.88 3.14
2945 3633 2.499289 TGTATTTGGCGGAATTTGGCAT 59.501 40.909 8.38 0.00 41.88 4.40
2946 3634 1.895798 TGTATTTGGCGGAATTTGGCA 59.104 42.857 4.12 4.12 40.47 4.92
2947 3635 2.267426 GTGTATTTGGCGGAATTTGGC 58.733 47.619 0.00 0.00 0.00 4.52
2948 3636 3.584406 TGTGTATTTGGCGGAATTTGG 57.416 42.857 0.00 0.00 0.00 3.28
2949 3637 7.588143 TTATTTGTGTATTTGGCGGAATTTG 57.412 32.000 0.00 0.00 0.00 2.32
2950 3638 8.499967 GTTTTATTTGTGTATTTGGCGGAATTT 58.500 29.630 0.00 0.00 0.00 1.82
2951 3639 7.118535 GGTTTTATTTGTGTATTTGGCGGAATT 59.881 33.333 0.00 0.00 0.00 2.17
2952 3640 6.592220 GGTTTTATTTGTGTATTTGGCGGAAT 59.408 34.615 0.00 0.00 0.00 3.01
2953 3641 5.927115 GGTTTTATTTGTGTATTTGGCGGAA 59.073 36.000 0.00 0.00 0.00 4.30
2954 3642 5.471257 GGTTTTATTTGTGTATTTGGCGGA 58.529 37.500 0.00 0.00 0.00 5.54
2955 3643 4.627900 GGGTTTTATTTGTGTATTTGGCGG 59.372 41.667 0.00 0.00 0.00 6.13
2956 3644 5.230942 TGGGTTTTATTTGTGTATTTGGCG 58.769 37.500 0.00 0.00 0.00 5.69
2957 3645 6.072948 GGTTGGGTTTTATTTGTGTATTTGGC 60.073 38.462 0.00 0.00 0.00 4.52
2958 3646 6.992715 TGGTTGGGTTTTATTTGTGTATTTGG 59.007 34.615 0.00 0.00 0.00 3.28
2959 3647 8.614469 ATGGTTGGGTTTTATTTGTGTATTTG 57.386 30.769 0.00 0.00 0.00 2.32
2960 3648 9.713713 GTATGGTTGGGTTTTATTTGTGTATTT 57.286 29.630 0.00 0.00 0.00 1.40
2961 3649 8.871125 TGTATGGTTGGGTTTTATTTGTGTATT 58.129 29.630 0.00 0.00 0.00 1.89
2962 3650 8.423906 TGTATGGTTGGGTTTTATTTGTGTAT 57.576 30.769 0.00 0.00 0.00 2.29
2963 3651 7.834881 TGTATGGTTGGGTTTTATTTGTGTA 57.165 32.000 0.00 0.00 0.00 2.90
2964 3652 6.732896 TGTATGGTTGGGTTTTATTTGTGT 57.267 33.333 0.00 0.00 0.00 3.72
2965 3653 6.091986 GCATGTATGGTTGGGTTTTATTTGTG 59.908 38.462 0.00 0.00 0.00 3.33
2966 3654 6.169800 GCATGTATGGTTGGGTTTTATTTGT 58.830 36.000 0.00 0.00 0.00 2.83
2967 3655 5.584251 GGCATGTATGGTTGGGTTTTATTTG 59.416 40.000 0.00 0.00 0.00 2.32
2968 3656 5.338789 GGGCATGTATGGTTGGGTTTTATTT 60.339 40.000 0.00 0.00 0.00 1.40
2969 3657 4.163268 GGGCATGTATGGTTGGGTTTTATT 59.837 41.667 0.00 0.00 0.00 1.40
2970 3658 3.709141 GGGCATGTATGGTTGGGTTTTAT 59.291 43.478 0.00 0.00 0.00 1.40
2971 3659 3.100671 GGGCATGTATGGTTGGGTTTTA 58.899 45.455 0.00 0.00 0.00 1.52
2972 3660 1.905894 GGGCATGTATGGTTGGGTTTT 59.094 47.619 0.00 0.00 0.00 2.43
2973 3661 1.203237 TGGGCATGTATGGTTGGGTTT 60.203 47.619 0.00 0.00 0.00 3.27
2974 3662 0.411452 TGGGCATGTATGGTTGGGTT 59.589 50.000 0.00 0.00 0.00 4.11
2975 3663 0.324275 GTGGGCATGTATGGTTGGGT 60.324 55.000 0.00 0.00 0.00 4.51
2976 3664 1.042559 GGTGGGCATGTATGGTTGGG 61.043 60.000 0.00 0.00 0.00 4.12
2977 3665 0.324183 TGGTGGGCATGTATGGTTGG 60.324 55.000 0.00 0.00 0.00 3.77
2978 3666 1.554836 TTGGTGGGCATGTATGGTTG 58.445 50.000 0.00 0.00 0.00 3.77
2979 3667 2.548464 ATTGGTGGGCATGTATGGTT 57.452 45.000 0.00 0.00 0.00 3.67
2980 3668 2.548464 AATTGGTGGGCATGTATGGT 57.452 45.000 0.00 0.00 0.00 3.55
2981 3669 6.189859 AGATATAATTGGTGGGCATGTATGG 58.810 40.000 0.00 0.00 0.00 2.74
2982 3670 7.613022 AGAAGATATAATTGGTGGGCATGTATG 59.387 37.037 0.00 0.00 0.00 2.39
2983 3671 7.702785 AGAAGATATAATTGGTGGGCATGTAT 58.297 34.615 0.00 0.00 0.00 2.29
2984 3672 7.090319 AGAAGATATAATTGGTGGGCATGTA 57.910 36.000 0.00 0.00 0.00 2.29
2985 3673 5.957132 AGAAGATATAATTGGTGGGCATGT 58.043 37.500 0.00 0.00 0.00 3.21
2986 3674 8.408043 TTTAGAAGATATAATTGGTGGGCATG 57.592 34.615 0.00 0.00 0.00 4.06
2987 3675 9.247861 GATTTAGAAGATATAATTGGTGGGCAT 57.752 33.333 0.00 0.00 0.00 4.40
2988 3676 8.224025 TGATTTAGAAGATATAATTGGTGGGCA 58.776 33.333 0.00 0.00 0.00 5.36
2989 3677 8.635765 TGATTTAGAAGATATAATTGGTGGGC 57.364 34.615 0.00 0.00 0.00 5.36
3006 3694 9.817809 GTGGATTGTTAGTGTAGATGATTTAGA 57.182 33.333 0.00 0.00 0.00 2.10
3007 3695 9.046296 GGTGGATTGTTAGTGTAGATGATTTAG 57.954 37.037 0.00 0.00 0.00 1.85
3008 3696 7.990886 GGGTGGATTGTTAGTGTAGATGATTTA 59.009 37.037 0.00 0.00 0.00 1.40
3009 3697 6.828785 GGGTGGATTGTTAGTGTAGATGATTT 59.171 38.462 0.00 0.00 0.00 2.17
3010 3698 6.158695 AGGGTGGATTGTTAGTGTAGATGATT 59.841 38.462 0.00 0.00 0.00 2.57
3011 3699 5.667626 AGGGTGGATTGTTAGTGTAGATGAT 59.332 40.000 0.00 0.00 0.00 2.45
3012 3700 5.030147 AGGGTGGATTGTTAGTGTAGATGA 58.970 41.667 0.00 0.00 0.00 2.92
3013 3701 5.359194 AGGGTGGATTGTTAGTGTAGATG 57.641 43.478 0.00 0.00 0.00 2.90
3014 3702 5.726793 AGAAGGGTGGATTGTTAGTGTAGAT 59.273 40.000 0.00 0.00 0.00 1.98
3015 3703 5.091552 AGAAGGGTGGATTGTTAGTGTAGA 58.908 41.667 0.00 0.00 0.00 2.59
3016 3704 5.420409 GAGAAGGGTGGATTGTTAGTGTAG 58.580 45.833 0.00 0.00 0.00 2.74
3017 3705 4.224370 GGAGAAGGGTGGATTGTTAGTGTA 59.776 45.833 0.00 0.00 0.00 2.90
3018 3706 3.009143 GGAGAAGGGTGGATTGTTAGTGT 59.991 47.826 0.00 0.00 0.00 3.55
3019 3707 3.009033 TGGAGAAGGGTGGATTGTTAGTG 59.991 47.826 0.00 0.00 0.00 2.74
3020 3708 3.009143 GTGGAGAAGGGTGGATTGTTAGT 59.991 47.826 0.00 0.00 0.00 2.24
3021 3709 3.610911 GTGGAGAAGGGTGGATTGTTAG 58.389 50.000 0.00 0.00 0.00 2.34
3022 3710 2.307686 GGTGGAGAAGGGTGGATTGTTA 59.692 50.000 0.00 0.00 0.00 2.41
3023 3711 1.075536 GGTGGAGAAGGGTGGATTGTT 59.924 52.381 0.00 0.00 0.00 2.83
3024 3712 0.698818 GGTGGAGAAGGGTGGATTGT 59.301 55.000 0.00 0.00 0.00 2.71
3025 3713 0.698238 TGGTGGAGAAGGGTGGATTG 59.302 55.000 0.00 0.00 0.00 2.67
3026 3714 1.455822 TTGGTGGAGAAGGGTGGATT 58.544 50.000 0.00 0.00 0.00 3.01
3027 3715 1.455822 TTTGGTGGAGAAGGGTGGAT 58.544 50.000 0.00 0.00 0.00 3.41
3028 3716 1.144913 CTTTTGGTGGAGAAGGGTGGA 59.855 52.381 0.00 0.00 0.00 4.02
3029 3717 1.620822 CTTTTGGTGGAGAAGGGTGG 58.379 55.000 0.00 0.00 0.00 4.61
3030 3718 1.144913 TCCTTTTGGTGGAGAAGGGTG 59.855 52.381 0.00 0.00 40.25 4.61
3031 3719 1.529744 TCCTTTTGGTGGAGAAGGGT 58.470 50.000 0.00 0.00 40.25 4.34
3037 3725 7.996098 TTACTAAAATCTCCTTTTGGTGGAG 57.004 36.000 8.97 3.57 45.04 3.86


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

AutoCloner maintained by Alex Coulton.