Multiple sequence alignment - TraesCS1A01G054600

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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 TraesCS1A01G054600 chr1A 100.000 3220 0 0 1 3220 36171789 36175008 0.000000e+00 5947.0
1 TraesCS1A01G054600 chr1A 95.576 2690 96 7 209 2893 36185505 36188176 0.000000e+00 4287.0
2 TraesCS1A01G054600 chr1A 87.415 2344 273 16 524 2860 36615691 36613363 0.000000e+00 2675.0
3 TraesCS1A01G054600 chr1A 98.958 96 1 0 2918 3013 36188377 36188282 4.270000e-39 172.0
4 TraesCS1A01G054600 chr1A 88.421 95 11 0 2918 3012 36613130 36613224 7.300000e-22 115.0
5 TraesCS1A01G054600 chr1A 85.000 80 9 3 2924 3001 36756242 36756320 9.580000e-11 78.7
6 TraesCS1A01G054600 chr1A 97.368 38 1 0 2970 3007 37505324 37505287 7.460000e-07 65.8
7 TraesCS1A01G054600 chr1D 93.985 2893 162 6 3 2893 36615168 36618050 0.000000e+00 4368.0
8 TraesCS1A01G054600 chr1D 92.896 2013 143 0 767 2779 37432446 37430434 0.000000e+00 2926.0
9 TraesCS1A01G054600 chr1D 87.544 2529 305 9 334 2860 36621910 36624430 0.000000e+00 2916.0
10 TraesCS1A01G054600 chr1D 85.926 2501 318 19 366 2859 38581360 38583833 0.000000e+00 2638.0
11 TraesCS1A01G054600 chr1D 91.579 95 8 0 2919 3013 36618250 36618156 7.250000e-27 132.0
12 TraesCS1A01G054600 chr1D 100.000 34 0 0 2974 3007 38368018 38367985 2.680000e-06 63.9
13 TraesCS1A01G054600 chr1D 81.707 82 9 1 2926 3007 38584047 38583972 2.680000e-06 63.9
14 TraesCS1A01G054600 chr1B 91.465 2894 233 8 1 2893 56490589 56493469 0.000000e+00 3964.0
15 TraesCS1A01G054600 chr1B 89.237 2871 260 16 3 2860 56617512 56620346 0.000000e+00 3544.0
16 TraesCS1A01G054600 chr1B 88.981 2541 244 18 329 2860 56499108 56501621 0.000000e+00 3109.0
17 TraesCS1A01G054600 chr1B 87.368 95 12 0 2918 3012 57015847 57015941 3.400000e-20 110.0
18 TraesCS1A01G054600 chr1B 92.727 55 2 2 172 226 57018431 57018379 9.580000e-11 78.7
19 TraesCS1A01G054600 chr1B 84.810 79 11 1 2924 3001 57373866 57373944 9.580000e-11 78.7
20 TraesCS1A01G054600 chr6B 96.667 210 6 1 3011 3220 139467736 139467944 6.610000e-92 348.0
21 TraesCS1A01G054600 chr6A 96.117 206 8 0 3015 3220 136542923 136543128 1.430000e-88 337.0
22 TraesCS1A01G054600 chr6A 93.689 206 13 0 3015 3220 604896696 604896901 3.120000e-80 309.0
23 TraesCS1A01G054600 chr2B 95.146 206 10 0 3015 3220 733460652 733460857 3.100000e-85 326.0
24 TraesCS1A01G054600 chr3A 93.365 211 13 1 3010 3220 495078629 495078420 8.670000e-81 311.0
25 TraesCS1A01G054600 chrUn 93.720 207 12 1 3015 3220 11858495 11858701 3.120000e-80 309.0
26 TraesCS1A01G054600 chr5B 93.689 206 13 0 3015 3220 581716548 581716753 3.120000e-80 309.0
27 TraesCS1A01G054600 chr5A 93.689 206 13 0 3015 3220 687142397 687142602 3.120000e-80 309.0
28 TraesCS1A01G054600 chr4A 93.689 206 13 0 3015 3220 741780963 741781168 3.120000e-80 309.0


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 TraesCS1A01G054600 chr1A 36171789 36175008 3219 False 5947 5947 100.0000 1 3220 1 chr1A.!!$F1 3219
1 TraesCS1A01G054600 chr1A 36185505 36188176 2671 False 4287 4287 95.5760 209 2893 1 chr1A.!!$F2 2684
2 TraesCS1A01G054600 chr1A 36613363 36615691 2328 True 2675 2675 87.4150 524 2860 1 chr1A.!!$R2 2336
3 TraesCS1A01G054600 chr1D 36615168 36624430 9262 False 3642 4368 90.7645 3 2893 2 chr1D.!!$F2 2890
4 TraesCS1A01G054600 chr1D 37430434 37432446 2012 True 2926 2926 92.8960 767 2779 1 chr1D.!!$R2 2012
5 TraesCS1A01G054600 chr1D 38581360 38583833 2473 False 2638 2638 85.9260 366 2859 1 chr1D.!!$F1 2493
6 TraesCS1A01G054600 chr1B 56490589 56493469 2880 False 3964 3964 91.4650 1 2893 1 chr1B.!!$F1 2892
7 TraesCS1A01G054600 chr1B 56617512 56620346 2834 False 3544 3544 89.2370 3 2860 1 chr1B.!!$F3 2857
8 TraesCS1A01G054600 chr1B 56499108 56501621 2513 False 3109 3109 88.9810 329 2860 1 chr1B.!!$F2 2531

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
834 861 1.512926 GAACGATGCCACTGTTGTCT 58.487 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2773 2803 0.333312 AGAGATGGTCCTGTCCTCGT 59.667 55.0 0.0 0.0 0.0 4.18 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
95 96 9.388506 CTCAACATAGAATCAGTAACCTCAAAT 57.611 33.333 0.00 0.00 0.00 2.32
106 107 6.040955 TCAGTAACCTCAAATATCTGCGAGAT 59.959 38.462 0.00 4.45 38.70 2.75
147 148 7.884257 TGCATTCATATGAAGAAAAGTGAACA 58.116 30.769 21.97 7.29 37.48 3.18
273 275 9.421806 CTGTGCAAAAATCCATAAGATAAAACA 57.578 29.630 0.00 0.00 33.66 2.83
596 621 7.674120 AGTCTCATATGCAGCATATCAACTAA 58.326 34.615 22.94 0.00 35.18 2.24
606 631 6.473455 GCAGCATATCAACTAATCAACCAAAC 59.527 38.462 0.00 0.00 0.00 2.93
695 722 3.871485 AGAGAGACAACATCAATGAGGC 58.129 45.455 0.00 0.00 0.00 4.70
834 861 1.512926 GAACGATGCCACTGTTGTCT 58.487 50.000 0.00 0.00 0.00 3.41
835 862 1.873591 GAACGATGCCACTGTTGTCTT 59.126 47.619 0.00 0.00 0.00 3.01
864 891 7.692460 TGAAAACATATTGTCAGCATCTTCT 57.308 32.000 0.00 0.00 28.21 2.85
896 923 7.280205 TCCGCCTTTTAGAAGATTTCTTATCAC 59.720 37.037 0.00 0.00 41.14 3.06
1105 1132 9.588096 AATTATTTCTACAAAGACCTCCAAGTT 57.412 29.630 0.00 0.00 0.00 2.66
1711 1738 2.034878 TCTCAATAGCATCGGTCAGCT 58.965 47.619 0.00 0.00 44.55 4.24
1713 1740 2.543012 CTCAATAGCATCGGTCAGCTTG 59.457 50.000 0.00 0.00 42.05 4.01
1731 1758 0.112995 TGCCCATTCTGGAAAGTGCT 59.887 50.000 0.00 0.00 40.96 4.40
2077 2107 4.095932 ACGAGTTGCGAGTGACAATATCTA 59.904 41.667 0.00 0.00 44.57 1.98
2164 2194 4.768448 TGGAATATCCATGGATCATGCAAC 59.232 41.667 30.61 15.21 42.67 4.17
2440 2470 0.320247 CATATGGAGCAGGTCGAGCC 60.320 60.000 11.73 3.31 37.58 4.70
2482 2512 3.305629 GTCGCATAAGCTCTTCAGAACAG 59.694 47.826 0.00 0.00 39.10 3.16
2492 2522 4.180057 CTCTTCAGAACAGTGGAGTATGC 58.820 47.826 0.00 0.00 0.00 3.14
2499 2529 1.141881 AGTGGAGTATGCGAAGGCG 59.858 57.895 0.00 0.00 44.10 5.52
2593 2623 0.322008 GAGGCACTTGAGGAAGGTGG 60.322 60.000 0.00 0.00 41.55 4.61
2672 2702 4.415150 TAGGTCCGGGCGAGACGT 62.415 66.667 0.00 0.00 34.97 4.34
2753 2783 2.250939 CGGCTTGTTCTCGGCACAA 61.251 57.895 0.00 0.00 33.09 3.33
2773 2803 2.654877 GGTTGAAGAGGGCGACGA 59.345 61.111 0.00 0.00 0.00 4.20
2779 2809 3.914579 AAGAGGGCGACGACGAGGA 62.915 63.158 12.29 0.00 42.66 3.71
2799 2829 1.485480 ACAGGACCATCTCTGATGCAG 59.515 52.381 0.00 0.00 35.20 4.41
2800 2830 1.129917 AGGACCATCTCTGATGCAGG 58.870 55.000 0.00 0.00 31.51 4.85
2804 2834 1.597302 CATCTCTGATGCAGGCGGG 60.597 63.158 0.00 0.00 31.51 6.13
2875 2905 2.709883 CGCCCCGGCATCATTGTTT 61.710 57.895 6.52 0.00 42.06 2.83
2876 2906 1.141665 GCCCCGGCATCATTGTTTC 59.858 57.895 0.00 0.00 41.49 2.78
2878 2908 0.969917 CCCCGGCATCATTGTTTCCA 60.970 55.000 0.00 0.00 0.00 3.53
2882 2912 1.135053 CGGCATCATTGTTTCCATGCA 60.135 47.619 8.86 0.00 42.94 3.96
2897 2927 2.486966 GCAGCAGCAATTCCGGTC 59.513 61.111 0.00 0.00 41.58 4.79
2898 2928 3.056313 GCAGCAGCAATTCCGGTCC 62.056 63.158 0.00 0.00 41.58 4.46
2900 2930 3.140814 GCAGCAATTCCGGTCCCC 61.141 66.667 0.00 0.00 0.00 4.81
2911 2941 1.370064 CGGTCCCCGGTATCATTCC 59.630 63.158 0.00 0.00 44.15 3.01
2913 2943 0.685660 GGTCCCCGGTATCATTCCTC 59.314 60.000 0.00 0.00 0.00 3.71
2915 2945 1.004918 CCCCGGTATCATTCCTCGC 60.005 63.158 0.00 0.00 0.00 5.03
2917 2947 1.004918 CCGGTATCATTCCTCGCCC 60.005 63.158 0.00 0.00 0.00 6.13
2918 2948 1.004918 CGGTATCATTCCTCGCCCC 60.005 63.158 0.00 0.00 0.00 5.80
2920 2950 1.746517 GTATCATTCCTCGCCCCGT 59.253 57.895 0.00 0.00 0.00 5.28
2922 2952 0.105964 TATCATTCCTCGCCCCGTTG 59.894 55.000 0.00 0.00 0.00 4.10
2923 2953 1.910580 ATCATTCCTCGCCCCGTTGT 61.911 55.000 0.00 0.00 0.00 3.32
2924 2954 1.674322 CATTCCTCGCCCCGTTGTT 60.674 57.895 0.00 0.00 0.00 2.83
2925 2955 1.376812 ATTCCTCGCCCCGTTGTTC 60.377 57.895 0.00 0.00 0.00 3.18
2936 2966 4.699522 GTTGTTCCGCCTCCGCCT 62.700 66.667 0.00 0.00 0.00 5.52
2937 2967 4.388499 TTGTTCCGCCTCCGCCTC 62.388 66.667 0.00 0.00 0.00 4.70
2949 2979 4.951963 CGCCTCCGCCGATCCTTC 62.952 72.222 0.00 0.00 0.00 3.46
2950 2980 3.849951 GCCTCCGCCGATCCTTCA 61.850 66.667 0.00 0.00 0.00 3.02
2951 2981 2.107141 CCTCCGCCGATCCTTCAC 59.893 66.667 0.00 0.00 0.00 3.18
2952 2982 2.278857 CTCCGCCGATCCTTCACG 60.279 66.667 0.00 0.00 0.00 4.35
2953 2983 2.752640 TCCGCCGATCCTTCACGA 60.753 61.111 0.00 0.00 0.00 4.35
2954 2984 2.582498 CCGCCGATCCTTCACGAC 60.582 66.667 0.00 0.00 0.00 4.34
2955 2985 2.949678 CGCCGATCCTTCACGACG 60.950 66.667 0.00 0.00 0.00 5.12
2956 2986 3.255379 GCCGATCCTTCACGACGC 61.255 66.667 0.00 0.00 0.00 5.19
2957 2987 2.582498 CCGATCCTTCACGACGCC 60.582 66.667 0.00 0.00 0.00 5.68
2958 2988 2.949678 CGATCCTTCACGACGCCG 60.950 66.667 0.00 0.00 42.50 6.46
2960 2990 1.065928 GATCCTTCACGACGCCGAT 59.934 57.895 0.00 0.00 39.50 4.18
2961 2991 1.209275 GATCCTTCACGACGCCGATG 61.209 60.000 0.00 0.00 39.50 3.84
2962 2992 1.945354 ATCCTTCACGACGCCGATGT 61.945 55.000 0.00 0.00 39.50 3.06
2963 2993 2.158959 CCTTCACGACGCCGATGTC 61.159 63.158 0.00 0.00 39.50 3.06
2965 2995 2.812542 CTTCACGACGCCGATGTCCA 62.813 60.000 0.00 0.00 39.50 4.02
2966 2996 2.423290 TTCACGACGCCGATGTCCAA 62.423 55.000 0.00 0.00 39.50 3.53
2968 2998 2.431771 CGACGCCGATGTCCAACA 60.432 61.111 0.00 0.00 38.22 3.33
2975 3005 4.963878 GATGTCCAACATCCGCCT 57.036 55.556 8.56 0.00 46.99 5.52
2976 3006 2.695314 GATGTCCAACATCCGCCTC 58.305 57.895 8.56 0.00 46.99 4.70
2978 3008 1.274703 ATGTCCAACATCCGCCTCCT 61.275 55.000 0.00 0.00 32.38 3.69
2979 3009 1.153349 GTCCAACATCCGCCTCCTC 60.153 63.158 0.00 0.00 0.00 3.71
2980 3010 2.190578 CCAACATCCGCCTCCTCC 59.809 66.667 0.00 0.00 0.00 4.30
2982 3012 4.162690 AACATCCGCCTCCTCCGC 62.163 66.667 0.00 0.00 0.00 5.54
2999 3029 4.154347 CCGCAGCTCCTCCTCCAC 62.154 72.222 0.00 0.00 0.00 4.02
3000 3030 4.154347 CGCAGCTCCTCCTCCACC 62.154 72.222 0.00 0.00 0.00 4.61
3001 3031 2.686835 GCAGCTCCTCCTCCACCT 60.687 66.667 0.00 0.00 0.00 4.00
3002 3032 2.730524 GCAGCTCCTCCTCCACCTC 61.731 68.421 0.00 0.00 0.00 3.85
3003 3033 2.063378 CAGCTCCTCCTCCACCTCC 61.063 68.421 0.00 0.00 0.00 4.30
3004 3034 2.039624 GCTCCTCCTCCACCTCCA 59.960 66.667 0.00 0.00 0.00 3.86
3005 3035 2.363172 GCTCCTCCTCCACCTCCAC 61.363 68.421 0.00 0.00 0.00 4.02
3006 3036 1.687493 CTCCTCCTCCACCTCCACC 60.687 68.421 0.00 0.00 0.00 4.61
3007 3037 2.689034 CCTCCTCCACCTCCACCC 60.689 72.222 0.00 0.00 0.00 4.61
3008 3038 2.689034 CTCCTCCACCTCCACCCC 60.689 72.222 0.00 0.00 0.00 4.95
3009 3039 4.348495 TCCTCCACCTCCACCCCC 62.348 72.222 0.00 0.00 0.00 5.40
3010 3040 4.675303 CCTCCACCTCCACCCCCA 62.675 72.222 0.00 0.00 0.00 4.96
3011 3041 3.330720 CTCCACCTCCACCCCCAC 61.331 72.222 0.00 0.00 0.00 4.61
3012 3042 4.995058 TCCACCTCCACCCCCACC 62.995 72.222 0.00 0.00 0.00 4.61
3019 3049 4.198224 CCACCCCCACCGTGTGTT 62.198 66.667 0.00 0.00 0.00 3.32
3020 3050 2.124067 CACCCCCACCGTGTGTTT 60.124 61.111 0.00 0.00 0.00 2.83
3021 3051 1.755008 CACCCCCACCGTGTGTTTT 60.755 57.895 0.00 0.00 0.00 2.43
3023 3053 1.454111 CCCCCACCGTGTGTTTTGA 60.454 57.895 0.00 0.00 0.00 2.69
3025 3055 1.036707 CCCCACCGTGTGTTTTGATT 58.963 50.000 0.00 0.00 0.00 2.57
3026 3056 1.410882 CCCCACCGTGTGTTTTGATTT 59.589 47.619 0.00 0.00 0.00 2.17
3027 3057 2.159028 CCCCACCGTGTGTTTTGATTTT 60.159 45.455 0.00 0.00 0.00 1.82
3028 3058 3.120041 CCCACCGTGTGTTTTGATTTTC 58.880 45.455 0.00 0.00 0.00 2.29
3029 3059 2.786578 CCACCGTGTGTTTTGATTTTCG 59.213 45.455 0.00 0.00 0.00 3.46
3031 3061 1.784283 CCGTGTGTTTTGATTTTCGGC 59.216 47.619 0.00 0.00 0.00 5.54
3032 3062 1.784283 CGTGTGTTTTGATTTTCGGCC 59.216 47.619 0.00 0.00 0.00 6.13
3033 3063 1.784283 GTGTGTTTTGATTTTCGGCCG 59.216 47.619 22.12 22.12 0.00 6.13
3034 3064 0.781787 GTGTTTTGATTTTCGGCCGC 59.218 50.000 23.51 6.50 0.00 6.53
3036 3066 1.202417 TGTTTTGATTTTCGGCCGCAA 60.202 42.857 23.51 14.89 0.00 4.85
3037 3067 1.861575 GTTTTGATTTTCGGCCGCAAA 59.138 42.857 24.67 24.67 0.00 3.68
3038 3068 2.225068 TTTGATTTTCGGCCGCAAAA 57.775 40.000 26.06 26.26 0.00 2.44
3039 3069 2.447244 TTGATTTTCGGCCGCAAAAT 57.553 40.000 30.79 30.79 36.38 1.82
3041 3071 1.000283 TGATTTTCGGCCGCAAAATGT 60.000 42.857 33.25 19.31 34.30 2.71
3051 3081 0.991344 CGCAAAATGTGGATTTCGGC 59.009 50.000 0.00 0.00 30.02 5.54
3054 3084 1.201181 CAAAATGTGGATTTCGGCCGA 59.799 47.619 27.28 27.28 30.02 5.54
3056 3086 1.762708 AATGTGGATTTCGGCCGAAT 58.237 45.000 38.89 27.72 33.79 3.34
3058 3088 1.540267 TGTGGATTTCGGCCGAATTT 58.460 45.000 38.89 28.86 33.79 1.82
3059 3089 1.470890 TGTGGATTTCGGCCGAATTTC 59.529 47.619 38.89 33.33 33.79 2.17
3060 3090 0.730265 TGGATTTCGGCCGAATTTCG 59.270 50.000 38.89 11.81 40.07 3.46
3080 4748 1.078214 CCATCTCGGCTTGAGGCAA 60.078 57.895 5.38 0.00 45.32 4.52
3081 4749 0.677731 CCATCTCGGCTTGAGGCAAA 60.678 55.000 5.38 0.00 45.32 3.68
3082 4750 1.167851 CATCTCGGCTTGAGGCAAAA 58.832 50.000 5.38 0.00 45.32 2.44
3083 4751 1.541147 CATCTCGGCTTGAGGCAAAAA 59.459 47.619 5.38 0.00 45.32 1.94
3086 4754 0.667993 TCGGCTTGAGGCAAAAAGTG 59.332 50.000 5.38 0.00 44.01 3.16
3094 4762 5.619981 GCTTGAGGCAAAAAGTGTATGTAGG 60.620 44.000 0.00 0.00 41.35 3.18
3095 4763 3.756434 TGAGGCAAAAAGTGTATGTAGGC 59.244 43.478 0.00 0.00 0.00 3.93
3096 4764 3.089284 AGGCAAAAAGTGTATGTAGGCC 58.911 45.455 0.00 0.00 39.14 5.19
3097 4765 2.159435 GGCAAAAAGTGTATGTAGGCCG 60.159 50.000 0.00 0.00 0.00 6.13
3098 4766 2.745281 GCAAAAAGTGTATGTAGGCCGA 59.255 45.455 0.00 0.00 0.00 5.54
3101 4769 5.621329 GCAAAAAGTGTATGTAGGCCGAAAT 60.621 40.000 0.00 0.00 0.00 2.17
3110 4819 3.088532 TGTAGGCCGAAATTGCTCAAAT 58.911 40.909 0.00 0.00 0.00 2.32
3121 4830 8.288913 CCGAAATTGCTCAAATTTGGTAAATTT 58.711 29.630 23.51 23.51 46.29 1.82
3122 4831 9.662545 CGAAATTGCTCAAATTTGGTAAATTTT 57.337 25.926 23.80 16.21 46.01 1.82
3124 4833 9.747293 AAATTGCTCAAATTTGGTAAATTTTGG 57.253 25.926 17.90 6.84 46.01 3.28
3125 4834 7.872113 TTGCTCAAATTTGGTAAATTTTGGT 57.128 28.000 17.90 0.00 46.01 3.67
3145 4854 8.873215 TTTGGTTAAATTTAAGTCAAATCGCA 57.127 26.923 22.41 10.49 35.74 5.10
3146 4855 8.514136 TTGGTTAAATTTAAGTCAAATCGCAG 57.486 30.769 10.92 0.00 35.74 5.18
3157 6349 4.984161 AGTCAAATCGCAGTCAAAATTTGG 59.016 37.500 5.83 0.00 38.83 3.28
3158 6350 4.744631 GTCAAATCGCAGTCAAAATTTGGT 59.255 37.500 5.83 0.00 38.83 3.67
3163 6355 4.942852 TCGCAGTCAAAATTTGGTCAAAT 58.057 34.783 5.83 3.34 42.35 2.32
3177 6369 7.401955 TTTGGTCAAATTTCAGCCAAAAATT 57.598 28.000 19.63 0.00 43.55 1.82
3180 6372 7.256286 TGGTCAAATTTCAGCCAAAAATTTTG 58.744 30.769 11.24 11.24 41.82 2.44
3182 6374 7.972832 GGTCAAATTTCAGCCAAAAATTTTGAA 59.027 29.630 18.98 6.08 41.82 2.69
3187 6379 8.874744 ATTTCAGCCAAAAATTTTGAAAATGG 57.125 26.923 18.98 13.92 40.07 3.16
3190 6382 3.980134 GCCAAAAATTTTGAAAATGGCCG 59.020 39.130 24.04 1.32 44.64 6.13
3194 6386 6.922407 CCAAAAATTTTGAAAATGGCCGAAAT 59.078 30.769 18.98 0.00 0.00 2.17
3195 6387 7.437565 CCAAAAATTTTGAAAATGGCCGAAATT 59.562 29.630 18.98 0.00 37.74 1.82
3196 6388 8.478494 CAAAAATTTTGAAAATGGCCGAAATTC 58.522 29.630 12.75 0.56 36.10 2.17
3197 6389 4.981389 TTTTGAAAATGGCCGAAATTCG 57.019 36.364 8.62 8.62 40.07 3.34
3207 6399 1.934463 CGAAATTCGGCCATCTCGG 59.066 57.895 7.61 0.00 36.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.202609 ACCTGGAAGAATGGATGTTTGAGT 60.203 41.667 0.00 0.00 34.07 3.41
79 80 6.582636 TCGCAGATATTTGAGGTTACTGATT 58.417 36.000 0.00 0.00 0.00 2.57
99 100 8.454894 TGCATTTTTAGTAATGTAAATCTCGCA 58.545 29.630 0.00 0.00 37.72 5.10
322 327 2.297597 CGATCGGGAAAAGATAGGAGCT 59.702 50.000 7.38 0.00 0.00 4.09
695 722 5.931146 AGTATCTCACTTGAAGCTTCAACTG 59.069 40.000 32.86 30.52 41.88 3.16
834 861 9.142515 GATGCTGACAATATGTTTTCATCAAAA 57.857 29.630 0.06 0.00 41.25 2.44
835 862 8.525316 AGATGCTGACAATATGTTTTCATCAAA 58.475 29.630 15.39 0.00 41.25 2.69
1121 1148 3.214328 AGTGGAACAACAGTGGACATTC 58.786 45.455 0.00 0.00 44.16 2.67
1731 1758 7.136822 AGTCACCTATTCCATTGTAATAGCA 57.863 36.000 4.01 0.00 36.17 3.49
1767 1794 0.988832 AAATGCGGGGACAAGGAGTA 59.011 50.000 0.00 0.00 0.00 2.59
2077 2107 0.924090 AAAAGCCGGGGCCTTATACT 59.076 50.000 2.18 0.00 43.17 2.12
2164 2194 9.119418 TGTTCAACCCAATAATGTGACATATAG 57.881 33.333 0.00 0.00 0.00 1.31
2440 2470 2.219458 CAATAGCATGAGTCAGCAGGG 58.781 52.381 14.37 0.00 0.00 4.45
2482 2512 1.146358 GACGCCTTCGCATACTCCAC 61.146 60.000 0.00 0.00 39.84 4.02
2492 2522 3.414700 GTGTGCCTGACGCCTTCG 61.415 66.667 0.00 0.00 42.43 3.79
2593 2623 0.949105 ACAAACGAGATCACCGCCAC 60.949 55.000 7.33 0.00 0.00 5.01
2734 2764 2.665185 GTGCCGAGAACAAGCCGT 60.665 61.111 0.00 0.00 0.00 5.68
2753 2783 3.311110 TCGCCCTCTTCAACCGCT 61.311 61.111 0.00 0.00 0.00 5.52
2773 2803 0.333312 AGAGATGGTCCTGTCCTCGT 59.667 55.000 0.00 0.00 0.00 4.18
2779 2809 1.485480 CTGCATCAGAGATGGTCCTGT 59.515 52.381 8.87 0.00 32.44 4.00
2781 2811 1.129917 CCTGCATCAGAGATGGTCCT 58.870 55.000 8.87 0.00 32.44 3.85
2804 2834 4.208686 CTACGTCCTCTGCCGCCC 62.209 72.222 0.00 0.00 0.00 6.13
2865 2895 6.932887 TGCTGCTGCATGGAAACAATGATG 62.933 45.833 14.93 0.00 45.31 3.07
2867 2897 3.661811 TGCTGCTGCATGGAAACAATGA 61.662 45.455 14.93 0.00 45.31 2.57
2869 2899 0.970640 TGCTGCTGCATGGAAACAAT 59.029 45.000 14.93 0.00 45.31 2.71
2870 2900 2.427742 TGCTGCTGCATGGAAACAA 58.572 47.368 14.93 0.00 45.31 2.83
2871 2901 4.177673 TGCTGCTGCATGGAAACA 57.822 50.000 14.93 0.00 45.31 2.83
2882 2912 2.044946 GGGACCGGAATTGCTGCT 60.045 61.111 9.46 0.00 0.00 4.24
2895 2925 0.317479 CGAGGAATGATACCGGGGAC 59.683 60.000 6.32 0.00 0.00 4.46
2896 2926 1.469335 GCGAGGAATGATACCGGGGA 61.469 60.000 6.32 0.00 0.00 4.81
2897 2927 1.004918 GCGAGGAATGATACCGGGG 60.005 63.158 6.32 0.00 0.00 5.73
2898 2928 1.004918 GGCGAGGAATGATACCGGG 60.005 63.158 6.32 0.00 0.00 5.73
2900 2930 1.004918 GGGGCGAGGAATGATACCG 60.005 63.158 0.00 0.00 0.00 4.02
2904 2934 1.153168 CAACGGGGCGAGGAATGAT 60.153 57.895 0.00 0.00 0.00 2.45
2905 2935 2.119484 AACAACGGGGCGAGGAATGA 62.119 55.000 0.00 0.00 0.00 2.57
2906 2936 1.644786 GAACAACGGGGCGAGGAATG 61.645 60.000 0.00 0.00 0.00 2.67
2907 2937 1.376812 GAACAACGGGGCGAGGAAT 60.377 57.895 0.00 0.00 0.00 3.01
2909 2939 4.011517 GGAACAACGGGGCGAGGA 62.012 66.667 0.00 0.00 0.00 3.71
2935 2965 2.278857 CGTGAAGGATCGGCGGAG 60.279 66.667 7.21 0.00 0.00 4.63
2936 2966 2.752640 TCGTGAAGGATCGGCGGA 60.753 61.111 7.21 0.00 0.00 5.54
2937 2967 2.582498 GTCGTGAAGGATCGGCGG 60.582 66.667 7.21 0.00 0.00 6.13
2939 2969 3.255379 GCGTCGTGAAGGATCGGC 61.255 66.667 0.00 0.00 0.00 5.54
2941 2971 2.663630 ATCGGCGTCGTGAAGGATCG 62.664 60.000 10.18 0.00 37.69 3.69
2942 2972 1.065928 ATCGGCGTCGTGAAGGATC 59.934 57.895 10.18 0.00 37.69 3.36
2943 2973 1.226974 CATCGGCGTCGTGAAGGAT 60.227 57.895 10.18 0.00 37.69 3.24
2944 2974 2.180769 CATCGGCGTCGTGAAGGA 59.819 61.111 10.18 0.00 37.69 3.36
2945 2975 2.126071 ACATCGGCGTCGTGAAGG 60.126 61.111 10.18 0.00 37.69 3.46
2948 2978 2.921797 TTGGACATCGGCGTCGTGA 61.922 57.895 10.18 0.00 36.73 4.35
2949 2979 2.431771 TTGGACATCGGCGTCGTG 60.432 61.111 10.18 9.95 36.73 4.35
2950 2980 2.431942 GTTGGACATCGGCGTCGT 60.432 61.111 10.18 5.06 36.73 4.34
2951 2981 1.752501 GATGTTGGACATCGGCGTCG 61.753 60.000 1.15 1.15 44.55 5.12
2952 2982 2.006772 GATGTTGGACATCGGCGTC 58.993 57.895 6.85 0.00 44.55 5.19
2953 2983 4.201951 GATGTTGGACATCGGCGT 57.798 55.556 6.85 0.00 44.55 5.68
2960 2990 1.899437 GAGGAGGCGGATGTTGGACA 61.899 60.000 0.00 0.00 0.00 4.02
2961 2991 1.153349 GAGGAGGCGGATGTTGGAC 60.153 63.158 0.00 0.00 0.00 4.02
2962 2992 2.367202 GGAGGAGGCGGATGTTGGA 61.367 63.158 0.00 0.00 0.00 3.53
2963 2993 2.190578 GGAGGAGGCGGATGTTGG 59.809 66.667 0.00 0.00 0.00 3.77
2965 2995 4.162690 GCGGAGGAGGCGGATGTT 62.163 66.667 0.00 0.00 0.00 2.71
2982 3012 4.154347 GTGGAGGAGGAGCTGCGG 62.154 72.222 0.00 0.00 0.00 5.69
2983 3013 4.154347 GGTGGAGGAGGAGCTGCG 62.154 72.222 0.00 0.00 0.00 5.18
2984 3014 2.686835 AGGTGGAGGAGGAGCTGC 60.687 66.667 0.00 0.00 0.00 5.25
2985 3015 2.063378 GGAGGTGGAGGAGGAGCTG 61.063 68.421 0.00 0.00 0.00 4.24
2986 3016 2.366570 GGAGGTGGAGGAGGAGCT 59.633 66.667 0.00 0.00 0.00 4.09
2988 3018 1.687493 GGTGGAGGTGGAGGAGGAG 60.687 68.421 0.00 0.00 0.00 3.69
2989 3019 2.450243 GGTGGAGGTGGAGGAGGA 59.550 66.667 0.00 0.00 0.00 3.71
2990 3020 2.689034 GGGTGGAGGTGGAGGAGG 60.689 72.222 0.00 0.00 0.00 4.30
2991 3021 2.689034 GGGGTGGAGGTGGAGGAG 60.689 72.222 0.00 0.00 0.00 3.69
2992 3022 4.348495 GGGGGTGGAGGTGGAGGA 62.348 72.222 0.00 0.00 0.00 3.71
2994 3024 3.330720 GTGGGGGTGGAGGTGGAG 61.331 72.222 0.00 0.00 0.00 3.86
2995 3025 4.995058 GGTGGGGGTGGAGGTGGA 62.995 72.222 0.00 0.00 0.00 4.02
3000 3030 4.329545 CACACGGTGGGGGTGGAG 62.330 72.222 13.48 0.00 39.69 3.86
3002 3032 3.724826 AAACACACGGTGGGGGTGG 62.725 63.158 15.88 0.00 39.69 4.61
3003 3033 1.755008 AAAACACACGGTGGGGGTG 60.755 57.895 15.88 5.14 37.94 4.61
3004 3034 1.755008 CAAAACACACGGTGGGGGT 60.755 57.895 15.88 5.96 37.94 4.95
3005 3035 0.825840 ATCAAAACACACGGTGGGGG 60.826 55.000 15.88 5.31 37.94 5.40
3006 3036 1.036707 AATCAAAACACACGGTGGGG 58.963 50.000 15.88 7.88 37.94 4.96
3007 3037 2.880963 AAATCAAAACACACGGTGGG 57.119 45.000 9.24 9.24 37.94 4.61
3008 3038 2.786578 CGAAAATCAAAACACACGGTGG 59.213 45.455 13.48 4.17 37.94 4.61
3009 3039 2.786578 CCGAAAATCAAAACACACGGTG 59.213 45.455 6.58 6.58 39.75 4.94
3010 3040 2.796735 GCCGAAAATCAAAACACACGGT 60.797 45.455 0.00 0.00 40.95 4.83
3011 3041 1.784283 GCCGAAAATCAAAACACACGG 59.216 47.619 0.00 0.00 41.63 4.94
3012 3042 1.784283 GGCCGAAAATCAAAACACACG 59.216 47.619 0.00 0.00 0.00 4.49
3014 3044 1.866063 GCGGCCGAAAATCAAAACACA 60.866 47.619 33.48 0.00 0.00 3.72
3015 3045 0.781787 GCGGCCGAAAATCAAAACAC 59.218 50.000 33.48 1.16 0.00 3.32
3016 3046 0.385751 TGCGGCCGAAAATCAAAACA 59.614 45.000 33.48 10.37 0.00 2.83
3018 3048 2.225068 TTTGCGGCCGAAAATCAAAA 57.775 40.000 33.48 5.17 0.00 2.44
3019 3049 2.225068 TTTTGCGGCCGAAAATCAAA 57.775 40.000 31.40 24.80 0.00 2.69
3020 3050 2.064762 CATTTTGCGGCCGAAAATCAA 58.935 42.857 31.40 20.52 31.96 2.57
3021 3051 1.000283 ACATTTTGCGGCCGAAAATCA 60.000 42.857 31.40 18.57 31.96 2.57
3023 3053 1.427435 CACATTTTGCGGCCGAAAAT 58.573 45.000 31.40 29.11 34.10 1.82
3025 3055 1.006805 CCACATTTTGCGGCCGAAA 60.007 52.632 33.48 25.41 0.00 3.46
3026 3056 1.247419 ATCCACATTTTGCGGCCGAA 61.247 50.000 33.48 19.06 0.00 4.30
3027 3057 1.247419 AATCCACATTTTGCGGCCGA 61.247 50.000 33.48 11.82 0.00 5.54
3028 3058 0.389687 AAATCCACATTTTGCGGCCG 60.390 50.000 24.05 24.05 0.00 6.13
3029 3059 1.358877 GAAATCCACATTTTGCGGCC 58.641 50.000 0.00 0.00 31.94 6.13
3031 3061 1.627879 CCGAAATCCACATTTTGCGG 58.372 50.000 0.00 0.00 34.70 5.69
3032 3062 0.991344 GCCGAAATCCACATTTTGCG 59.009 50.000 0.00 0.00 33.42 4.85
3033 3063 1.358877 GGCCGAAATCCACATTTTGC 58.641 50.000 0.00 0.00 33.42 3.68
3034 3064 1.201181 TCGGCCGAAATCCACATTTTG 59.799 47.619 28.99 0.00 31.94 2.44
3036 3066 1.540267 TTCGGCCGAAATCCACATTT 58.460 45.000 37.13 0.00 34.70 2.32
3037 3067 1.762708 ATTCGGCCGAAATCCACATT 58.237 45.000 41.31 21.74 37.69 2.71
3038 3068 1.762708 AATTCGGCCGAAATCCACAT 58.237 45.000 41.31 22.51 37.69 3.21
3039 3069 1.470890 GAAATTCGGCCGAAATCCACA 59.529 47.619 41.31 20.42 37.69 4.17
3041 3071 0.730265 CGAAATTCGGCCGAAATCCA 59.270 50.000 41.31 22.04 37.69 3.41
3062 3092 0.677731 TTTGCCTCAAGCCGAGATGG 60.678 55.000 2.33 0.00 45.45 3.51
3063 3093 1.167851 TTTTGCCTCAAGCCGAGATG 58.832 50.000 2.33 0.00 45.45 2.90
3064 3094 1.815003 CTTTTTGCCTCAAGCCGAGAT 59.185 47.619 2.33 0.00 45.45 2.75
3065 3095 1.238439 CTTTTTGCCTCAAGCCGAGA 58.762 50.000 2.33 0.00 45.45 4.04
3066 3096 0.954452 ACTTTTTGCCTCAAGCCGAG 59.046 50.000 0.00 0.00 42.71 4.63
3067 3097 0.667993 CACTTTTTGCCTCAAGCCGA 59.332 50.000 0.00 0.00 42.71 5.54
3075 4743 3.089284 GGCCTACATACACTTTTTGCCT 58.911 45.455 0.00 0.00 33.64 4.75
3077 4745 2.745281 TCGGCCTACATACACTTTTTGC 59.255 45.455 0.00 0.00 0.00 3.68
3080 4748 5.621329 GCAATTTCGGCCTACATACACTTTT 60.621 40.000 0.00 0.00 0.00 2.27
3081 4749 4.142469 GCAATTTCGGCCTACATACACTTT 60.142 41.667 0.00 0.00 0.00 2.66
3082 4750 3.377172 GCAATTTCGGCCTACATACACTT 59.623 43.478 0.00 0.00 0.00 3.16
3083 4751 2.943033 GCAATTTCGGCCTACATACACT 59.057 45.455 0.00 0.00 0.00 3.55
3086 4754 3.202906 TGAGCAATTTCGGCCTACATAC 58.797 45.455 0.00 0.00 0.00 2.39
3094 4762 3.066380 ACCAAATTTGAGCAATTTCGGC 58.934 40.909 19.86 0.00 42.28 5.54
3095 4763 6.777526 TTTACCAAATTTGAGCAATTTCGG 57.222 33.333 19.86 1.12 42.28 4.30
3121 4830 8.138712 ACTGCGATTTGACTTAAATTTAACCAA 58.861 29.630 6.54 10.60 39.06 3.67
3122 4831 7.653647 ACTGCGATTTGACTTAAATTTAACCA 58.346 30.769 6.54 5.56 39.06 3.67
3123 4832 7.806014 TGACTGCGATTTGACTTAAATTTAACC 59.194 33.333 6.54 3.19 39.06 2.85
3124 4833 8.722342 TGACTGCGATTTGACTTAAATTTAAC 57.278 30.769 6.54 0.00 39.06 2.01
3125 4834 9.737427 TTTGACTGCGATTTGACTTAAATTTAA 57.263 25.926 10.16 10.16 39.06 1.52
3129 4838 8.816640 AATTTTGACTGCGATTTGACTTAAAT 57.183 26.923 0.00 0.00 41.59 1.40
3132 4841 6.640499 CCAAATTTTGACTGCGATTTGACTTA 59.360 34.615 10.72 0.00 40.26 2.24
3133 4842 5.463061 CCAAATTTTGACTGCGATTTGACTT 59.537 36.000 10.72 0.00 40.26 3.01
3134 4843 4.984161 CCAAATTTTGACTGCGATTTGACT 59.016 37.500 10.72 0.00 40.26 3.41
3135 4844 4.744631 ACCAAATTTTGACTGCGATTTGAC 59.255 37.500 10.72 0.00 40.26 3.18
3137 4846 4.744137 TGACCAAATTTTGACTGCGATTTG 59.256 37.500 10.72 0.00 38.54 2.32
3138 4847 4.942852 TGACCAAATTTTGACTGCGATTT 58.057 34.783 10.72 0.00 0.00 2.17
3139 4848 4.582701 TGACCAAATTTTGACTGCGATT 57.417 36.364 10.72 0.00 0.00 3.34
3140 4849 4.582701 TTGACCAAATTTTGACTGCGAT 57.417 36.364 10.72 0.00 0.00 4.58
3142 4851 5.655893 AATTTGACCAAATTTTGACTGCG 57.344 34.783 13.26 0.00 45.67 5.18
3157 6349 8.908172 TTCAAAATTTTTGGCTGAAATTTGAC 57.092 26.923 19.06 0.00 42.64 3.18
3158 6350 9.918630 TTTTCAAAATTTTTGGCTGAAATTTGA 57.081 22.222 19.06 13.64 42.64 2.69
3163 6355 6.755607 GCCATTTTCAAAATTTTTGGCTGAAA 59.244 30.769 25.92 18.36 43.68 2.69
3164 6356 6.271566 GCCATTTTCAAAATTTTTGGCTGAA 58.728 32.000 25.92 14.48 43.68 3.02
3166 6358 4.983538 GGCCATTTTCAAAATTTTTGGCTG 59.016 37.500 29.24 10.83 45.74 4.85
3167 6359 4.261530 CGGCCATTTTCAAAATTTTTGGCT 60.262 37.500 29.24 0.00 45.74 4.75
3169 6361 5.429957 TCGGCCATTTTCAAAATTTTTGG 57.570 34.783 19.06 12.38 0.00 3.28
3170 6362 7.927305 ATTTCGGCCATTTTCAAAATTTTTG 57.073 28.000 14.41 14.41 0.00 2.44
3171 6363 7.378194 CGAATTTCGGCCATTTTCAAAATTTTT 59.622 29.630 10.95 0.00 36.00 1.94
3172 6364 6.855403 CGAATTTCGGCCATTTTCAAAATTTT 59.145 30.769 10.95 0.00 36.00 1.82
3173 6365 6.369799 CGAATTTCGGCCATTTTCAAAATTT 58.630 32.000 10.95 0.00 36.00 1.82
3174 6366 5.925907 CGAATTTCGGCCATTTTCAAAATT 58.074 33.333 10.95 3.00 36.00 1.82
3175 6367 5.529014 CGAATTTCGGCCATTTTCAAAAT 57.471 34.783 10.95 0.00 36.00 1.82
3176 6368 4.981389 CGAATTTCGGCCATTTTCAAAA 57.019 36.364 10.95 0.00 36.00 2.44


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

AutoCloner maintained by Alex Coulton.