Multiple sequence alignment - TraesCS3D01G129600

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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 TraesCS3D01G129600 chr3D 100.000 3095 0 0 1 3095 89640188 89637094 0.000000e+00 5716.0
1 TraesCS3D01G129600 chr3D 91.383 824 61 9 1333 2152 89628282 89627465 0.000000e+00 1120.0
2 TraesCS3D01G129600 chr3D 88.580 648 63 10 1326 1969 89547597 89546957 0.000000e+00 776.0
3 TraesCS3D01G129600 chr3D 93.243 444 25 5 2185 2625 89627390 89626949 0.000000e+00 649.0
4 TraesCS3D01G129600 chr3D 92.000 225 15 3 2606 2830 89626931 89626710 2.320000e-81 313.0
5 TraesCS3D01G129600 chr3D 95.205 146 7 0 1958 2103 89546410 89546265 6.670000e-57 231.0
6 TraesCS3D01G129600 chr3D 91.892 148 11 1 2916 3062 89626711 89626564 4.050000e-49 206.0
7 TraesCS3D01G129600 chr3D 82.353 136 20 2 975 1110 89553828 89553697 7.010000e-22 115.0
8 TraesCS3D01G129600 chr3D 87.059 85 11 0 2830 2914 477907359 477907443 2.540000e-16 97.1
9 TraesCS3D01G129600 chr3A 91.793 1986 95 32 746 2711 106398538 106396601 0.000000e+00 2702.0
10 TraesCS3D01G129600 chr3A 95.751 353 13 2 395 746 80095291 80095642 4.480000e-158 568.0
11 TraesCS3D01G129600 chr3A 96.491 171 6 0 1933 2103 106309127 106308957 1.820000e-72 283.0
12 TraesCS3D01G129600 chr3A 96.923 65 2 0 2769 2833 106396262 106396198 3.260000e-20 110.0
13 TraesCS3D01G129600 chr3B 93.599 1609 49 13 746 2354 139196770 139195216 0.000000e+00 2351.0
14 TraesCS3D01G129600 chr3B 86.953 1142 124 13 979 2103 139038909 139037776 0.000000e+00 1260.0
15 TraesCS3D01G129600 chr3B 91.429 525 42 2 2317 2838 139194976 139194452 0.000000e+00 717.0
16 TraesCS3D01G129600 chr3B 87.059 85 11 0 2830 2914 637089697 637089781 2.540000e-16 97.1
17 TraesCS3D01G129600 chr1D 94.324 740 41 1 1 740 104579893 104579155 0.000000e+00 1133.0
18 TraesCS3D01G129600 chr1D 87.059 85 11 0 2830 2914 101285232 101285148 2.540000e-16 97.1
19 TraesCS3D01G129600 chr5D 87.883 751 84 5 1 748 422768878 422769624 0.000000e+00 876.0
20 TraesCS3D01G129600 chr5D 87.668 746 86 3 1 743 205689666 205688924 0.000000e+00 863.0
21 TraesCS3D01G129600 chr5D 87.032 748 89 5 1 744 378210564 378209821 0.000000e+00 837.0
22 TraesCS3D01G129600 chr2A 87.703 740 88 2 3 741 276254442 276255179 0.000000e+00 859.0
23 TraesCS3D01G129600 chr2A 84.211 95 15 0 2821 2915 86440534 86440628 3.290000e-15 93.5
24 TraesCS3D01G129600 chr7B 87.166 748 92 2 1 746 279276050 279275305 0.000000e+00 846.0
25 TraesCS3D01G129600 chr7B 86.517 89 9 3 2830 2917 229199271 229199357 9.140000e-16 95.3
26 TraesCS3D01G129600 chr2B 85.279 754 104 4 1 751 549040210 549039461 0.000000e+00 771.0
27 TraesCS3D01G129600 chr1B 87.781 622 75 1 123 743 366270755 366270134 0.000000e+00 726.0
28 TraesCS3D01G129600 chr1B 72.960 429 98 16 1562 1980 334124068 334124488 1.940000e-27 134.0
29 TraesCS3D01G129600 chr1B 87.059 85 11 0 2830 2914 593785896 593785980 2.540000e-16 97.1
30 TraesCS3D01G129600 chr4A 77.458 661 137 10 1419 2073 696600891 696600237 4.840000e-103 385.0
31 TraesCS3D01G129600 chr4A 76.803 638 136 11 1442 2073 697573822 697574453 6.350000e-92 348.0
32 TraesCS3D01G129600 chr4A 78.834 326 64 4 1415 1736 697503357 697503681 6.720000e-52 215.0
33 TraesCS3D01G129600 chr4A 75.983 229 47 7 1802 2026 2780342 2780118 9.070000e-21 111.0
34 TraesCS3D01G129600 chr5B 85.393 356 46 3 2 354 451442138 451442490 6.310000e-97 364.0
35 TraesCS3D01G129600 chr7A 90.110 91 9 0 2824 2914 509222365 509222455 5.420000e-23 119.0
36 TraesCS3D01G129600 chr7A 82.407 108 19 0 1569 1676 722332798 722332691 9.140000e-16 95.3
37 TraesCS3D01G129600 chr4B 88.764 89 8 2 2830 2918 163758239 163758325 1.170000e-19 108.0
38 TraesCS3D01G129600 chr2D 85.263 95 14 0 2821 2915 86080904 86080998 7.060000e-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 TraesCS3D01G129600 chr3D 89637094 89640188 3094 True 5716.0 5716 100.0000 1 3095 1 chr3D.!!$R2 3094
1 TraesCS3D01G129600 chr3D 89626564 89628282 1718 True 572.0 1120 92.1295 1333 3062 4 chr3D.!!$R4 1729
2 TraesCS3D01G129600 chr3D 89546265 89547597 1332 True 503.5 776 91.8925 1326 2103 2 chr3D.!!$R3 777
3 TraesCS3D01G129600 chr3A 106396198 106398538 2340 True 1406.0 2702 94.3580 746 2833 2 chr3A.!!$R2 2087
4 TraesCS3D01G129600 chr3B 139194452 139196770 2318 True 1534.0 2351 92.5140 746 2838 2 chr3B.!!$R2 2092
5 TraesCS3D01G129600 chr3B 139037776 139038909 1133 True 1260.0 1260 86.9530 979 2103 1 chr3B.!!$R1 1124
6 TraesCS3D01G129600 chr1D 104579155 104579893 738 True 1133.0 1133 94.3240 1 740 1 chr1D.!!$R2 739
7 TraesCS3D01G129600 chr5D 422768878 422769624 746 False 876.0 876 87.8830 1 748 1 chr5D.!!$F1 747
8 TraesCS3D01G129600 chr5D 205688924 205689666 742 True 863.0 863 87.6680 1 743 1 chr5D.!!$R1 742
9 TraesCS3D01G129600 chr5D 378209821 378210564 743 True 837.0 837 87.0320 1 744 1 chr5D.!!$R2 743
10 TraesCS3D01G129600 chr2A 276254442 276255179 737 False 859.0 859 87.7030 3 741 1 chr2A.!!$F2 738
11 TraesCS3D01G129600 chr7B 279275305 279276050 745 True 846.0 846 87.1660 1 746 1 chr7B.!!$R1 745
12 TraesCS3D01G129600 chr2B 549039461 549040210 749 True 771.0 771 85.2790 1 751 1 chr2B.!!$R1 750
13 TraesCS3D01G129600 chr1B 366270134 366270755 621 True 726.0 726 87.7810 123 743 1 chr1B.!!$R1 620
14 TraesCS3D01G129600 chr4A 696600237 696600891 654 True 385.0 385 77.4580 1419 2073 1 chr4A.!!$R2 654
15 TraesCS3D01G129600 chr4A 697573822 697574453 631 False 348.0 348 76.8030 1442 2073 1 chr4A.!!$F2 631

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
146 147 0.037326 ATTTGGAAGTCGCGAGCTCA 60.037 50.0 10.24 2.82 0.00 4.26 F
827 831 0.165079 TTCCTCGAACGAAATTGCGC 59.835 50.0 5.51 0.00 33.86 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 1294 0.247736 TCTTGAGAAAGGAGAGCGCC 59.752 55.0 2.29 0.0 0.00 6.53 R
2726 3953 0.379669 CAAGGCGACAATGCTGGATC 59.620 55.0 0.00 0.0 34.52 3.36 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
56 57 0.539438 TGGTTGTGGGGAACTGATGC 60.539 55.000 0.00 0.00 0.00 3.91
110 111 1.327690 TTCGCTGGCCGGATAGAAGT 61.328 55.000 18.31 0.00 37.59 3.01
117 118 1.440145 GCCGGATAGAAGTTGCTGGC 61.440 60.000 5.05 0.00 44.62 4.85
121 122 1.202533 GGATAGAAGTTGCTGGCGCTA 60.203 52.381 7.64 0.00 36.97 4.26
146 147 0.037326 ATTTGGAAGTCGCGAGCTCA 60.037 50.000 10.24 2.82 0.00 4.26
425 426 3.966665 GAGATGAGGATGAGGAAGGAAGT 59.033 47.826 0.00 0.00 0.00 3.01
714 716 6.072728 GCGCCTTCTATCTATGATCTCGATAT 60.073 42.308 0.00 0.00 0.00 1.63
790 792 2.936498 CGTAAGGCCCATTGAGTAACAG 59.064 50.000 0.00 0.00 0.00 3.16
827 831 0.165079 TTCCTCGAACGAAATTGCGC 59.835 50.000 5.51 0.00 33.86 6.09
907 911 2.756283 CTCGCGTTCCCCTCCTCT 60.756 66.667 5.77 0.00 0.00 3.69
908 912 3.068691 TCGCGTTCCCCTCCTCTG 61.069 66.667 5.77 0.00 0.00 3.35
909 913 4.148825 CGCGTTCCCCTCCTCTGG 62.149 72.222 0.00 0.00 0.00 3.86
910 914 4.475135 GCGTTCCCCTCCTCTGGC 62.475 72.222 0.00 0.00 0.00 4.85
911 915 3.787001 CGTTCCCCTCCTCTGGCC 61.787 72.222 0.00 0.00 0.00 5.36
912 916 2.285743 GTTCCCCTCCTCTGGCCT 60.286 66.667 3.32 0.00 0.00 5.19
913 917 2.041265 TTCCCCTCCTCTGGCCTC 59.959 66.667 3.32 0.00 0.00 4.70
914 918 3.642741 TTCCCCTCCTCTGGCCTCC 62.643 68.421 3.32 0.00 0.00 4.30
915 919 4.101077 CCCCTCCTCTGGCCTCCT 62.101 72.222 3.32 0.00 0.00 3.69
916 920 2.445654 CCCTCCTCTGGCCTCCTC 60.446 72.222 3.32 0.00 0.00 3.71
917 921 2.445654 CCTCCTCTGGCCTCCTCC 60.446 72.222 3.32 0.00 0.00 4.30
918 922 2.366167 CTCCTCTGGCCTCCTCCA 59.634 66.667 3.32 0.00 34.42 3.86
919 923 1.074623 CTCCTCTGGCCTCCTCCAT 60.075 63.158 3.32 0.00 35.22 3.41
920 924 1.074926 TCCTCTGGCCTCCTCCATC 60.075 63.158 3.32 0.00 35.22 3.51
921 925 2.146061 CCTCTGGCCTCCTCCATCC 61.146 68.421 3.32 0.00 35.22 3.51
922 926 1.074623 CTCTGGCCTCCTCCATCCT 60.075 63.158 3.32 0.00 35.22 3.24
923 927 1.074926 TCTGGCCTCCTCCATCCTC 60.075 63.158 3.32 0.00 35.22 3.71
924 928 1.074623 CTGGCCTCCTCCATCCTCT 60.075 63.158 3.32 0.00 35.22 3.69
925 929 1.074926 TGGCCTCCTCCATCCTCTC 60.075 63.158 3.32 0.00 0.00 3.20
926 930 1.841103 GGCCTCCTCCATCCTCTCC 60.841 68.421 0.00 0.00 0.00 3.71
927 931 1.074926 GCCTCCTCCATCCTCTCCA 60.075 63.158 0.00 0.00 0.00 3.86
928 932 1.120795 GCCTCCTCCATCCTCTCCAG 61.121 65.000 0.00 0.00 0.00 3.86
929 933 0.264359 CCTCCTCCATCCTCTCCAGT 59.736 60.000 0.00 0.00 0.00 4.00
930 934 1.703411 CTCCTCCATCCTCTCCAGTC 58.297 60.000 0.00 0.00 0.00 3.51
931 935 1.217689 CTCCTCCATCCTCTCCAGTCT 59.782 57.143 0.00 0.00 0.00 3.24
932 936 1.216678 TCCTCCATCCTCTCCAGTCTC 59.783 57.143 0.00 0.00 0.00 3.36
941 945 2.037367 TCCAGTCTCCACTCCCCG 59.963 66.667 0.00 0.00 0.00 5.73
1281 1294 3.611766 GCTTTAAGGCGGAAAAGAACCAG 60.612 47.826 11.69 0.00 35.19 4.00
1446 1462 1.815421 GTTCACCATCCGCTGCGAT 60.815 57.895 25.45 12.14 0.00 4.58
1764 1783 1.641577 GCTTCATGTACACGGACTCC 58.358 55.000 0.00 0.00 0.00 3.85
2066 2643 2.229792 TGTCAAGGAGTTGATTGCCAC 58.770 47.619 0.00 0.00 44.58 5.01
2104 2681 4.383444 CCTCAGCTCAGTGATGGTTGATTA 60.383 45.833 0.00 0.00 32.06 1.75
2129 2706 7.991084 TTGATTGATCCTAGGATGCTTATTG 57.009 36.000 29.32 0.00 34.60 1.90
2130 2707 7.320384 TGATTGATCCTAGGATGCTTATTGA 57.680 36.000 29.32 5.83 34.60 2.57
2131 2708 7.925622 TGATTGATCCTAGGATGCTTATTGAT 58.074 34.615 29.32 10.03 34.60 2.57
2132 2709 8.388589 TGATTGATCCTAGGATGCTTATTGATT 58.611 33.333 29.32 0.18 34.60 2.57
2133 2710 9.896645 GATTGATCCTAGGATGCTTATTGATTA 57.103 33.333 29.32 0.00 34.60 1.75
2162 2813 5.331876 CTTTGCAAGCTACTCCTACTACT 57.668 43.478 0.00 0.00 0.00 2.57
2163 2814 5.725362 CTTTGCAAGCTACTCCTACTACTT 58.275 41.667 0.00 0.00 0.00 2.24
2164 2815 6.845758 TTTGCAAGCTACTCCTACTACTTA 57.154 37.500 0.00 0.00 0.00 2.24
2165 2816 5.831702 TGCAAGCTACTCCTACTACTTAC 57.168 43.478 0.00 0.00 0.00 2.34
2166 2817 5.507637 TGCAAGCTACTCCTACTACTTACT 58.492 41.667 0.00 0.00 0.00 2.24
2167 2818 6.656902 TGCAAGCTACTCCTACTACTTACTA 58.343 40.000 0.00 0.00 0.00 1.82
2213 2864 0.108186 TCAGCAATGGTACTCTGGCG 60.108 55.000 0.00 0.00 0.00 5.69
2248 2899 8.450578 TCTTGTCATGTTCAAAAAGACTACAT 57.549 30.769 0.00 0.00 29.78 2.29
2354 3286 5.048504 GCAGTTGAATCTCCATTTGTTCTGA 60.049 40.000 0.00 0.00 0.00 3.27
2397 3329 8.677148 AACGTCTATTCTGCAAATTATATGGT 57.323 30.769 0.00 0.00 0.00 3.55
2448 3395 5.236478 AGAGTTTCGGATAAATAACGCATGG 59.764 40.000 0.00 0.00 0.00 3.66
2486 3434 5.243060 GGTTTTACTAATCCAAGTTGCCTGT 59.757 40.000 0.00 0.00 0.00 4.00
2490 3438 5.435686 ACTAATCCAAGTTGCCTGTGATA 57.564 39.130 0.00 0.00 0.00 2.15
2493 3441 6.891908 ACTAATCCAAGTTGCCTGTGATATTT 59.108 34.615 0.00 0.00 0.00 1.40
2569 3519 0.387202 CATTTTCACCCGGTTGCACA 59.613 50.000 0.00 0.00 0.00 4.57
2574 3524 1.529226 TCACCCGGTTGCACATTTAG 58.471 50.000 0.00 0.00 0.00 1.85
2629 3579 5.149273 CGTCAATCCTTGAGTTCAACATTG 58.851 41.667 11.91 11.91 41.01 2.82
2652 3636 6.000840 TGTGTATGATTTCCAGTTTGCACTA 58.999 36.000 0.00 0.00 0.00 2.74
2659 3643 9.643693 ATGATTTCCAGTTTGCACTAATTTTAG 57.356 29.630 0.00 0.00 36.82 1.85
2661 3645 9.476202 GATTTCCAGTTTGCACTAATTTTAGTT 57.524 29.630 0.21 0.00 41.82 2.24
2680 3664 9.973661 TTTTAGTTCTCAATGGAGGAATTGATA 57.026 29.630 0.00 0.00 43.70 2.15
2697 3682 8.514594 GGAATTGATAATCTCGCAAATCCATTA 58.485 33.333 0.00 0.00 39.96 1.90
2700 3685 8.853077 TTGATAATCTCGCAAATCCATTATCT 57.147 30.769 10.00 0.00 37.35 1.98
2807 4075 7.602753 AGTTAGAAACCAGTAAATTTGGATGC 58.397 34.615 0.00 0.00 39.08 3.91
2869 4137 9.249053 TGAAATATAAGACATTTTTGTAGGCCA 57.751 29.630 5.01 0.00 0.00 5.36
2870 4138 9.736023 GAAATATAAGACATTTTTGTAGGCCAG 57.264 33.333 5.01 0.00 0.00 4.85
2871 4139 8.823220 AATATAAGACATTTTTGTAGGCCAGT 57.177 30.769 5.01 0.00 0.00 4.00
2872 4140 8.823220 ATATAAGACATTTTTGTAGGCCAGTT 57.177 30.769 5.01 0.00 0.00 3.16
2873 4141 5.869649 AAGACATTTTTGTAGGCCAGTTT 57.130 34.783 5.01 0.00 0.00 2.66
2874 4142 6.969993 AAGACATTTTTGTAGGCCAGTTTA 57.030 33.333 5.01 0.00 0.00 2.01
2875 4143 6.575162 AGACATTTTTGTAGGCCAGTTTAG 57.425 37.500 5.01 0.00 0.00 1.85
2876 4144 5.048013 AGACATTTTTGTAGGCCAGTTTAGC 60.048 40.000 5.01 0.00 0.00 3.09
2886 4154 3.570926 GCCAGTTTAGCCTACAAAACC 57.429 47.619 0.00 0.00 36.46 3.27
2887 4155 2.095415 GCCAGTTTAGCCTACAAAACCG 60.095 50.000 0.00 0.00 36.46 4.44
2888 4156 3.143728 CCAGTTTAGCCTACAAAACCGT 58.856 45.455 0.00 0.00 36.46 4.83
2889 4157 3.187842 CCAGTTTAGCCTACAAAACCGTC 59.812 47.826 0.00 0.00 36.46 4.79
2890 4158 4.062991 CAGTTTAGCCTACAAAACCGTCT 58.937 43.478 0.00 0.00 36.46 4.18
2891 4159 4.514066 CAGTTTAGCCTACAAAACCGTCTT 59.486 41.667 0.00 0.00 36.46 3.01
2892 4160 5.697633 CAGTTTAGCCTACAAAACCGTCTTA 59.302 40.000 0.00 0.00 36.46 2.10
2893 4161 6.370718 CAGTTTAGCCTACAAAACCGTCTTAT 59.629 38.462 0.00 0.00 36.46 1.73
2894 4162 7.546667 CAGTTTAGCCTACAAAACCGTCTTATA 59.453 37.037 0.00 0.00 36.46 0.98
2895 4163 8.262933 AGTTTAGCCTACAAAACCGTCTTATAT 58.737 33.333 0.00 0.00 36.46 0.86
2896 4164 8.886719 GTTTAGCCTACAAAACCGTCTTATATT 58.113 33.333 0.00 0.00 30.93 1.28
2897 4165 9.452287 TTTAGCCTACAAAACCGTCTTATATTT 57.548 29.630 0.00 0.00 0.00 1.40
2898 4166 7.933215 AGCCTACAAAACCGTCTTATATTTT 57.067 32.000 0.00 0.00 0.00 1.82
2899 4167 7.758495 AGCCTACAAAACCGTCTTATATTTTG 58.242 34.615 6.72 6.72 44.11 2.44
2900 4168 7.608761 AGCCTACAAAACCGTCTTATATTTTGA 59.391 33.333 13.56 0.01 42.15 2.69
2901 4169 8.403236 GCCTACAAAACCGTCTTATATTTTGAT 58.597 33.333 13.56 3.21 42.15 2.57
2909 4177 6.946229 CGTCTTATATTTTGATACGGAGGG 57.054 41.667 0.00 0.00 0.00 4.30
2910 4178 6.684686 CGTCTTATATTTTGATACGGAGGGA 58.315 40.000 0.00 0.00 0.00 4.20
2911 4179 6.807230 CGTCTTATATTTTGATACGGAGGGAG 59.193 42.308 0.00 0.00 0.00 4.30
2912 4180 7.523380 CGTCTTATATTTTGATACGGAGGGAGT 60.523 40.741 0.00 0.00 0.00 3.85
2913 4181 8.800332 GTCTTATATTTTGATACGGAGGGAGTA 58.200 37.037 0.00 0.00 0.00 2.59
2914 4182 8.800332 TCTTATATTTTGATACGGAGGGAGTAC 58.200 37.037 0.00 0.00 0.00 2.73
2915 4183 8.716674 TTATATTTTGATACGGAGGGAGTACT 57.283 34.615 0.00 0.00 0.00 2.73
2916 4184 5.952347 ATTTTGATACGGAGGGAGTACTT 57.048 39.130 0.00 0.00 0.00 2.24
2919 4187 4.730949 TGATACGGAGGGAGTACTTTTG 57.269 45.455 0.00 0.00 0.00 2.44
2924 4192 2.302157 CGGAGGGAGTACTTTTGAAGGT 59.698 50.000 0.00 0.00 0.00 3.50
2929 4197 5.762279 AGGGAGTACTTTTGAAGGTTTTCA 58.238 37.500 0.00 0.00 41.44 2.69
2942 4210 2.095263 AGGTTTTCAATGAATCACGGCG 60.095 45.455 4.80 4.80 0.00 6.46
3008 4277 5.739752 TCATCGGAAGCTATGATTTTGTG 57.260 39.130 0.00 0.00 0.00 3.33
3033 4302 8.649841 TGTTCCGTTATTATCTAGAAAAACACG 58.350 33.333 0.00 7.06 0.00 4.49
3037 4306 7.276218 CCGTTATTATCTAGAAAAACACGACCA 59.724 37.037 17.70 0.00 0.00 4.02
3041 4310 4.659111 TCTAGAAAAACACGACCACTGA 57.341 40.909 0.00 0.00 0.00 3.41
3091 4360 4.936974 CATTTGAATGCGTTGTTGATGTG 58.063 39.130 0.00 0.00 0.00 3.21
3092 4361 3.978718 TTGAATGCGTTGTTGATGTGA 57.021 38.095 0.00 0.00 0.00 3.58
3093 4362 4.502171 TTGAATGCGTTGTTGATGTGAT 57.498 36.364 0.00 0.00 0.00 3.06
3094 4363 3.824151 TGAATGCGTTGTTGATGTGATG 58.176 40.909 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.453155 CCACAACCAGGTGATACTGC 58.547 55.000 0.00 0.00 41.32 4.40
56 57 1.528586 CAGAACGTGCAGAGAACCTTG 59.471 52.381 0.00 0.00 0.00 3.61
83 84 3.058160 GGCCAGCGAAGTGTGCAT 61.058 61.111 0.00 0.00 33.85 3.96
117 118 4.271687 GCGACTTCCAAATTTGTATAGCG 58.728 43.478 16.73 14.31 0.00 4.26
121 122 3.181510 GCTCGCGACTTCCAAATTTGTAT 60.182 43.478 16.73 0.00 0.00 2.29
146 147 3.931468 CGAGAAGATCTTGCATGTGTTCT 59.069 43.478 14.00 0.00 0.00 3.01
234 235 0.107703 CACATAGTGGACATGCCGGT 60.108 55.000 1.90 0.00 40.66 5.28
425 426 2.226330 CCAAAGTGATCACCGTCCAAA 58.774 47.619 22.21 0.00 0.00 3.28
590 591 7.355890 GCTACTATCCAACCTATCTACCCTAT 58.644 42.308 0.00 0.00 0.00 2.57
756 758 2.745821 GGCCTTACGTTTTCCTCGAAAT 59.254 45.455 0.00 0.00 31.34 2.17
760 762 0.320946 TGGGCCTTACGTTTTCCTCG 60.321 55.000 4.53 0.00 0.00 4.63
764 766 2.817844 ACTCAATGGGCCTTACGTTTTC 59.182 45.455 4.53 0.00 0.00 2.29
790 792 1.204704 GAAATGGGCTTTGGCACCTAC 59.795 52.381 0.00 0.00 42.08 3.18
827 831 0.320374 TCTTCTACAACACGGGCCTG 59.680 55.000 11.02 11.02 0.00 4.85
838 842 2.241430 TCTGGATCGGGACTCTTCTACA 59.759 50.000 0.00 0.00 0.00 2.74
881 885 2.868787 GAACGCGAGGACGACGAC 60.869 66.667 15.93 0.00 42.66 4.34
907 911 1.074926 GAGAGGATGGAGGAGGCCA 60.075 63.158 5.01 0.00 43.23 5.36
908 912 1.841103 GGAGAGGATGGAGGAGGCC 60.841 68.421 0.00 0.00 0.00 5.19
909 913 1.074926 TGGAGAGGATGGAGGAGGC 60.075 63.158 0.00 0.00 0.00 4.70
910 914 0.264359 ACTGGAGAGGATGGAGGAGG 59.736 60.000 0.00 0.00 0.00 4.30
911 915 1.217689 AGACTGGAGAGGATGGAGGAG 59.782 57.143 0.00 0.00 0.00 3.69
912 916 1.216678 GAGACTGGAGAGGATGGAGGA 59.783 57.143 0.00 0.00 0.00 3.71
913 917 1.703411 GAGACTGGAGAGGATGGAGG 58.297 60.000 0.00 0.00 0.00 4.30
914 918 1.063341 TGGAGACTGGAGAGGATGGAG 60.063 57.143 0.00 0.00 0.00 3.86
915 919 1.010795 TGGAGACTGGAGAGGATGGA 58.989 55.000 0.00 0.00 0.00 3.41
916 920 1.118838 GTGGAGACTGGAGAGGATGG 58.881 60.000 0.00 0.00 0.00 3.51
917 921 2.031120 GAGTGGAGACTGGAGAGGATG 58.969 57.143 0.00 0.00 30.16 3.51
918 922 1.063266 GGAGTGGAGACTGGAGAGGAT 60.063 57.143 0.00 0.00 30.16 3.24
919 923 0.333312 GGAGTGGAGACTGGAGAGGA 59.667 60.000 0.00 0.00 30.16 3.71
920 924 0.686112 GGGAGTGGAGACTGGAGAGG 60.686 65.000 0.00 0.00 30.16 3.69
921 925 0.686112 GGGGAGTGGAGACTGGAGAG 60.686 65.000 0.00 0.00 30.16 3.20
922 926 1.388531 GGGGAGTGGAGACTGGAGA 59.611 63.158 0.00 0.00 30.16 3.71
923 927 2.055042 CGGGGAGTGGAGACTGGAG 61.055 68.421 0.00 0.00 30.16 3.86
924 928 2.037367 CGGGGAGTGGAGACTGGA 59.963 66.667 0.00 0.00 30.16 3.86
925 929 3.775654 GCGGGGAGTGGAGACTGG 61.776 72.222 0.00 0.00 30.16 4.00
926 930 2.681778 AGCGGGGAGTGGAGACTG 60.682 66.667 0.00 0.00 30.16 3.51
927 931 2.363147 GAGCGGGGAGTGGAGACT 60.363 66.667 0.00 0.00 33.98 3.24
928 932 3.462678 GGAGCGGGGAGTGGAGAC 61.463 72.222 0.00 0.00 0.00 3.36
929 933 3.317436 ATGGAGCGGGGAGTGGAGA 62.317 63.158 0.00 0.00 0.00 3.71
930 934 2.765807 ATGGAGCGGGGAGTGGAG 60.766 66.667 0.00 0.00 0.00 3.86
931 935 2.764128 GATGGAGCGGGGAGTGGA 60.764 66.667 0.00 0.00 0.00 4.02
932 936 3.866582 GGATGGAGCGGGGAGTGG 61.867 72.222 0.00 0.00 0.00 4.00
941 945 1.599240 GATTCGGCAGGGATGGAGC 60.599 63.158 0.00 0.00 0.00 4.70
1278 1291 1.153469 GAGAAAGGAGAGCGCCTGG 60.153 63.158 2.29 0.00 38.58 4.45
1281 1294 0.247736 TCTTGAGAAAGGAGAGCGCC 59.752 55.000 2.29 0.00 0.00 6.53
2066 2643 2.013483 GAGGCATCGATCGAGCACG 61.013 63.158 28.28 17.36 41.26 5.34
2104 2681 8.388589 TCAATAAGCATCCTAGGATCAATCAAT 58.611 33.333 22.02 7.96 31.62 2.57
2154 2805 8.563123 TGCATATGTAGCTAGTAAGTAGTAGG 57.437 38.462 4.29 0.00 31.39 3.18
2158 2809 7.542890 AGCATGCATATGTAGCTAGTAAGTAG 58.457 38.462 21.98 0.00 36.65 2.57
2159 2810 7.394641 AGAGCATGCATATGTAGCTAGTAAGTA 59.605 37.037 21.98 0.00 36.65 2.24
2160 2811 6.210385 AGAGCATGCATATGTAGCTAGTAAGT 59.790 38.462 21.98 0.00 36.65 2.24
2161 2812 6.629128 AGAGCATGCATATGTAGCTAGTAAG 58.371 40.000 21.98 0.00 36.65 2.34
2162 2813 6.435591 AGAGAGCATGCATATGTAGCTAGTAA 59.564 38.462 21.98 0.00 36.65 2.24
2163 2814 5.948758 AGAGAGCATGCATATGTAGCTAGTA 59.051 40.000 21.98 0.00 36.65 1.82
2164 2815 4.771577 AGAGAGCATGCATATGTAGCTAGT 59.228 41.667 21.98 8.58 36.65 2.57
2165 2816 5.125900 AGAGAGAGCATGCATATGTAGCTAG 59.874 44.000 21.98 0.00 36.65 3.42
2166 2817 5.015515 AGAGAGAGCATGCATATGTAGCTA 58.984 41.667 21.98 0.00 36.65 3.32
2167 2818 3.833650 AGAGAGAGCATGCATATGTAGCT 59.166 43.478 21.98 15.35 36.65 3.32
2379 3311 8.546083 TGGGTTAACCATATAATTTGCAGAAT 57.454 30.769 25.71 0.00 46.80 2.40
2397 3329 4.993705 AGAGGAGAACACAATGGGTTAA 57.006 40.909 0.00 0.00 0.00 2.01
2493 3441 9.357652 CTTTTCAGAAATCAACTCAGACAAAAA 57.642 29.630 0.00 0.00 0.00 1.94
2502 3450 5.532779 AGTCACCCTTTTCAGAAATCAACTC 59.467 40.000 0.00 0.00 0.00 3.01
2506 3454 5.445069 TGAAGTCACCCTTTTCAGAAATCA 58.555 37.500 0.00 0.00 32.03 2.57
2545 3495 3.249917 GCAACCGGGTGAAAATGTAATG 58.750 45.455 27.49 0.00 0.00 1.90
2569 3519 7.466804 TCCCAAGTAATGTTCTTCCACTAAAT 58.533 34.615 0.00 0.00 0.00 1.40
2574 3524 4.906618 TCTCCCAAGTAATGTTCTTCCAC 58.093 43.478 0.00 0.00 0.00 4.02
2629 3579 5.376854 AGTGCAAACTGGAAATCATACAC 57.623 39.130 0.00 0.00 0.00 2.90
2652 3636 9.312904 TCAATTCCTCCATTGAGAACTAAAATT 57.687 29.630 0.00 0.00 41.42 1.82
2659 3643 8.688747 AGATTATCAATTCCTCCATTGAGAAC 57.311 34.615 5.80 2.26 43.60 3.01
2661 3645 7.157347 CGAGATTATCAATTCCTCCATTGAGA 58.843 38.462 0.00 0.00 44.52 3.27
2680 3664 5.178252 CGACAGATAATGGATTTGCGAGATT 59.822 40.000 0.00 0.00 0.00 2.40
2697 3682 4.853924 AATTTCTTTTGCACCGACAGAT 57.146 36.364 0.00 0.00 0.00 2.90
2726 3953 0.379669 CAAGGCGACAATGCTGGATC 59.620 55.000 0.00 0.00 34.52 3.36
2801 4067 6.267471 AGTTTACTGAAGAAAAATGGCATCCA 59.733 34.615 0.00 0.00 38.19 3.41
2843 4111 9.249053 TGGCCTACAAAAATGTCTTATATTTCA 57.751 29.630 3.32 0.00 0.00 2.69
2844 4112 9.736023 CTGGCCTACAAAAATGTCTTATATTTC 57.264 33.333 3.32 0.00 0.00 2.17
2845 4113 9.255029 ACTGGCCTACAAAAATGTCTTATATTT 57.745 29.630 3.32 0.00 0.00 1.40
2846 4114 8.823220 ACTGGCCTACAAAAATGTCTTATATT 57.177 30.769 3.32 0.00 0.00 1.28
2847 4115 8.823220 AACTGGCCTACAAAAATGTCTTATAT 57.177 30.769 3.32 0.00 0.00 0.86
2848 4116 8.644374 AAACTGGCCTACAAAAATGTCTTATA 57.356 30.769 3.32 0.00 0.00 0.98
2849 4117 7.539034 AAACTGGCCTACAAAAATGTCTTAT 57.461 32.000 3.32 0.00 0.00 1.73
2850 4118 6.969993 AAACTGGCCTACAAAAATGTCTTA 57.030 33.333 3.32 0.00 0.00 2.10
2851 4119 5.869649 AAACTGGCCTACAAAAATGTCTT 57.130 34.783 3.32 0.00 0.00 3.01
2852 4120 5.048013 GCTAAACTGGCCTACAAAAATGTCT 60.048 40.000 3.32 0.00 0.00 3.41
2853 4121 5.161358 GCTAAACTGGCCTACAAAAATGTC 58.839 41.667 3.32 0.00 0.00 3.06
2854 4122 4.021456 GGCTAAACTGGCCTACAAAAATGT 60.021 41.667 3.32 0.00 45.57 2.71
2855 4123 4.494484 GGCTAAACTGGCCTACAAAAATG 58.506 43.478 3.32 0.00 45.57 2.32
2856 4124 4.801330 GGCTAAACTGGCCTACAAAAAT 57.199 40.909 3.32 0.00 45.57 1.82
2866 4134 2.095415 CGGTTTTGTAGGCTAAACTGGC 60.095 50.000 10.92 0.00 40.49 4.85
2867 4135 3.143728 ACGGTTTTGTAGGCTAAACTGG 58.856 45.455 19.25 11.06 44.86 4.00
2868 4136 4.062991 AGACGGTTTTGTAGGCTAAACTG 58.937 43.478 15.39 15.39 45.51 3.16
2869 4137 4.347360 AGACGGTTTTGTAGGCTAAACT 57.653 40.909 10.32 0.00 39.25 2.66
2870 4138 6.732531 ATAAGACGGTTTTGTAGGCTAAAC 57.267 37.500 0.00 0.00 38.80 2.01
2871 4139 9.452287 AAATATAAGACGGTTTTGTAGGCTAAA 57.548 29.630 0.00 0.00 0.00 1.85
2872 4140 9.452287 AAAATATAAGACGGTTTTGTAGGCTAA 57.548 29.630 0.00 0.00 0.00 3.09
2873 4141 8.885722 CAAAATATAAGACGGTTTTGTAGGCTA 58.114 33.333 0.00 0.00 37.00 3.93
2874 4142 7.608761 TCAAAATATAAGACGGTTTTGTAGGCT 59.391 33.333 8.65 0.00 40.55 4.58
2875 4143 7.754625 TCAAAATATAAGACGGTTTTGTAGGC 58.245 34.615 8.65 0.00 40.55 3.93
2879 4147 8.392612 CCGTATCAAAATATAAGACGGTTTTGT 58.607 33.333 2.49 0.00 42.55 2.83
2880 4148 8.605746 TCCGTATCAAAATATAAGACGGTTTTG 58.394 33.333 10.05 4.61 46.44 2.44
2881 4149 8.721019 TCCGTATCAAAATATAAGACGGTTTT 57.279 30.769 10.05 0.00 46.44 2.43
2882 4150 7.440255 CCTCCGTATCAAAATATAAGACGGTTT 59.560 37.037 10.05 0.00 46.44 3.27
2883 4151 6.927381 CCTCCGTATCAAAATATAAGACGGTT 59.073 38.462 10.05 0.00 46.44 4.44
2884 4152 6.453092 CCTCCGTATCAAAATATAAGACGGT 58.547 40.000 10.05 0.00 46.44 4.83
2886 4154 6.684686 TCCCTCCGTATCAAAATATAAGACG 58.315 40.000 0.00 0.00 0.00 4.18
2887 4155 7.668492 ACTCCCTCCGTATCAAAATATAAGAC 58.332 38.462 0.00 0.00 0.00 3.01
2888 4156 7.850935 ACTCCCTCCGTATCAAAATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
2889 4157 8.804204 AGTACTCCCTCCGTATCAAAATATAAG 58.196 37.037 0.00 0.00 0.00 1.73
2890 4158 8.716674 AGTACTCCCTCCGTATCAAAATATAA 57.283 34.615 0.00 0.00 0.00 0.98
2891 4159 8.716674 AAGTACTCCCTCCGTATCAAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
2892 4160 7.613551 AAGTACTCCCTCCGTATCAAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
2893 4161 7.427989 AAAGTACTCCCTCCGTATCAAAATA 57.572 36.000 0.00 0.00 0.00 1.40
2894 4162 5.952347 AAGTACTCCCTCCGTATCAAAAT 57.048 39.130 0.00 0.00 0.00 1.82
2895 4163 5.750352 AAAGTACTCCCTCCGTATCAAAA 57.250 39.130 0.00 0.00 0.00 2.44
2896 4164 5.246656 TCAAAAGTACTCCCTCCGTATCAAA 59.753 40.000 0.00 0.00 0.00 2.69
2897 4165 4.773674 TCAAAAGTACTCCCTCCGTATCAA 59.226 41.667 0.00 0.00 0.00 2.57
2898 4166 4.346730 TCAAAAGTACTCCCTCCGTATCA 58.653 43.478 0.00 0.00 0.00 2.15
2899 4167 4.996788 TCAAAAGTACTCCCTCCGTATC 57.003 45.455 0.00 0.00 0.00 2.24
2900 4168 4.161754 CCTTCAAAAGTACTCCCTCCGTAT 59.838 45.833 0.00 0.00 0.00 3.06
2901 4169 3.512724 CCTTCAAAAGTACTCCCTCCGTA 59.487 47.826 0.00 0.00 0.00 4.02
2902 4170 2.302157 CCTTCAAAAGTACTCCCTCCGT 59.698 50.000 0.00 0.00 0.00 4.69
2903 4171 2.302157 ACCTTCAAAAGTACTCCCTCCG 59.698 50.000 0.00 0.00 0.00 4.63
2904 4172 4.368565 AACCTTCAAAAGTACTCCCTCC 57.631 45.455 0.00 0.00 0.00 4.30
2905 4173 5.826208 TGAAAACCTTCAAAAGTACTCCCTC 59.174 40.000 0.00 0.00 38.65 4.30
2906 4174 5.762279 TGAAAACCTTCAAAAGTACTCCCT 58.238 37.500 0.00 0.00 38.65 4.20
2907 4175 6.459670 TTGAAAACCTTCAAAAGTACTCCC 57.540 37.500 0.00 0.00 46.24 4.30
2919 4187 3.920412 GCCGTGATTCATTGAAAACCTTC 59.080 43.478 2.68 0.00 0.00 3.46
2924 4192 2.550180 TGTCGCCGTGATTCATTGAAAA 59.450 40.909 2.68 0.00 0.00 2.29
2929 4197 0.249120 TCCTGTCGCCGTGATTCATT 59.751 50.000 0.00 0.00 0.00 2.57
2931 4199 1.080093 GTCCTGTCGCCGTGATTCA 60.080 57.895 0.00 0.00 0.00 2.57
2942 4210 3.067106 CACATGTTGTAGTGGTCCTGTC 58.933 50.000 0.00 0.00 32.24 3.51
3008 4277 8.863049 TCGTGTTTTTCTAGATAATAACGGAAC 58.137 33.333 20.36 7.45 0.00 3.62
3069 4338 4.680567 TCACATCAACAACGCATTCAAATG 59.319 37.500 0.00 0.00 39.40 2.32
3070 4339 4.869215 TCACATCAACAACGCATTCAAAT 58.131 34.783 0.00 0.00 0.00 2.32
3071 4340 4.298744 TCACATCAACAACGCATTCAAA 57.701 36.364 0.00 0.00 0.00 2.69
3072 4341 3.978718 TCACATCAACAACGCATTCAA 57.021 38.095 0.00 0.00 0.00 2.69
3073 4342 3.824151 CATCACATCAACAACGCATTCA 58.176 40.909 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.