Multiple sequence alignment - TraesCS6D01G235600

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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 TraesCS6D01G235600 chr6D 100.000 3080 0 0 1 3080 331530504 331533583 0.000000e+00 5688.0
1 TraesCS6D01G235600 chr6A 95.425 1989 72 12 856 2838 470411484 470413459 0.000000e+00 3151.0
2 TraesCS6D01G235600 chr6A 86.905 672 64 15 190 854 97318041 97317387 0.000000e+00 732.0
3 TraesCS6D01G235600 chr6A 92.079 101 7 1 2849 2949 52898212 52898311 1.150000e-29 141.0
4 TraesCS6D01G235600 chr6A 91.429 70 3 1 37 103 97318465 97318396 3.270000e-15 93.5
5 TraesCS6D01G235600 chr6B 95.279 1991 77 12 856 2838 489540840 489538859 0.000000e+00 3140.0
6 TraesCS6D01G235600 chr6B 88.854 323 29 3 199 517 172020715 172020396 1.040000e-104 390.0
7 TraesCS6D01G235600 chr6B 92.784 97 7 0 2854 2950 497258447 497258543 1.150000e-29 141.0
8 TraesCS6D01G235600 chr4D 97.203 858 21 2 1 855 47663720 47662863 0.000000e+00 1448.0
9 TraesCS6D01G235600 chr4D 96.266 857 29 2 1 855 364550380 364549525 0.000000e+00 1402.0
10 TraesCS6D01G235600 chr1D 96.620 858 26 2 1 855 355104811 355103954 0.000000e+00 1421.0
11 TraesCS6D01G235600 chr3D 96.498 828 29 0 1 828 340723232 340722405 0.000000e+00 1369.0
12 TraesCS6D01G235600 chr2A 86.122 735 65 14 137 855 773578954 773578241 0.000000e+00 758.0
13 TraesCS6D01G235600 chr2A 91.724 145 9 1 1 142 773579360 773579216 6.740000e-47 198.0
14 TraesCS6D01G235600 chr3B 87.994 658 51 8 190 844 416567189 416566557 0.000000e+00 752.0
15 TraesCS6D01G235600 chr3B 92.784 97 7 0 2854 2950 821088749 821088653 1.150000e-29 141.0
16 TraesCS6D01G235600 chr3B 92.708 96 7 0 2854 2949 70007074 70007169 4.140000e-29 139.0
17 TraesCS6D01G235600 chr5A 93.814 97 6 0 2854 2950 590580528 590580624 2.470000e-31 147.0
18 TraesCS6D01G235600 chr2D 93.814 97 6 0 2854 2950 14985266 14985362 2.470000e-31 147.0
19 TraesCS6D01G235600 chr7B 92.784 97 7 0 2854 2950 7333782 7333878 1.150000e-29 141.0
20 TraesCS6D01G235600 chr7A 91.262 103 8 1 2849 2951 701624532 701624431 4.140000e-29 139.0
21 TraesCS6D01G235600 chr3A 89.720 107 9 2 2849 2954 79450741 79450846 5.360000e-28 135.0


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 TraesCS6D01G235600 chr6D 331530504 331533583 3079 False 5688.00 5688 100.000 1 3080 1 chr6D.!!$F1 3079
1 TraesCS6D01G235600 chr6A 470411484 470413459 1975 False 3151.00 3151 95.425 856 2838 1 chr6A.!!$F2 1982
2 TraesCS6D01G235600 chr6A 97317387 97318465 1078 True 412.75 732 89.167 37 854 2 chr6A.!!$R1 817
3 TraesCS6D01G235600 chr6B 489538859 489540840 1981 True 3140.00 3140 95.279 856 2838 1 chr6B.!!$R2 1982
4 TraesCS6D01G235600 chr4D 47662863 47663720 857 True 1448.00 1448 97.203 1 855 1 chr4D.!!$R1 854
5 TraesCS6D01G235600 chr4D 364549525 364550380 855 True 1402.00 1402 96.266 1 855 1 chr4D.!!$R2 854
6 TraesCS6D01G235600 chr1D 355103954 355104811 857 True 1421.00 1421 96.620 1 855 1 chr1D.!!$R1 854
7 TraesCS6D01G235600 chr3D 340722405 340723232 827 True 1369.00 1369 96.498 1 828 1 chr3D.!!$R1 827
8 TraesCS6D01G235600 chr2A 773578241 773579360 1119 True 478.00 758 88.923 1 855 2 chr2A.!!$R1 854
9 TraesCS6D01G235600 chr3B 416566557 416567189 632 True 752.00 752 87.994 190 844 1 chr3B.!!$R1 654

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
724 1045 1.118838 CCAGGTTTGTGCTTTTCCCA 58.881 50.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2412 0.688087 ACCTCCGATTCCCCTGACTC 60.688 60.0 0.0 0.0 0.0 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
22 23 2.961062 GGCCCATCTGTCATATGCTTTT 59.039 45.455 0.00 0.00 0.00 2.27
176 455 1.992557 TGTTTCTCCCCACCATAAGCT 59.007 47.619 0.00 0.00 0.00 3.74
470 789 2.211353 GACTCTGGGTCTATTGTCGC 57.789 55.000 0.00 0.00 41.46 5.19
724 1045 1.118838 CCAGGTTTGTGCTTTTCCCA 58.881 50.000 0.00 0.00 0.00 4.37
743 1064 3.253677 CCCAGTGTGCCAAACGTATTTAA 59.746 43.478 0.00 0.00 0.00 1.52
775 1096 2.231716 TCGGGATCAGAAAGGTCAGA 57.768 50.000 0.00 0.00 0.00 3.27
813 1134 6.666113 GGAATTTGGAGGTGAGGGTTTATTTA 59.334 38.462 0.00 0.00 0.00 1.40
961 1285 2.203280 CAACCGAGCCCACACCAA 60.203 61.111 0.00 0.00 0.00 3.67
1237 1563 0.108804 CTACCGCAACATCCGTCTGT 60.109 55.000 0.00 0.00 0.00 3.41
1722 2048 3.386726 TCTTCCTTCTCGTCAAGTCCAAA 59.613 43.478 0.00 0.00 0.00 3.28
1790 2116 2.358737 GAACCACCGGAGCACCAG 60.359 66.667 9.46 0.00 35.59 4.00
1899 2228 3.625313 TCACGAATCTTGAAAGCAACACA 59.375 39.130 0.00 0.00 0.00 3.72
1998 2327 1.646189 GGACCTCTAAGAAGCTTGCG 58.354 55.000 2.10 0.00 0.00 4.85
2022 2351 2.605094 GCTGAACGAGCTTGACACA 58.395 52.632 8.31 3.87 45.21 3.72
2082 2411 2.146342 AGTGTGAATGAAGGCTGAACG 58.854 47.619 0.00 0.00 0.00 3.95
2083 2412 1.197721 GTGTGAATGAAGGCTGAACGG 59.802 52.381 0.00 0.00 0.00 4.44
2185 2514 0.890683 ACCTTTGCACTTGCCTATGC 59.109 50.000 0.00 0.00 42.40 3.14
2190 2519 0.325933 TGCACTTGCCTATGCTCTGT 59.674 50.000 0.00 0.00 42.55 3.41
2279 2611 4.612943 GTTTAGACGCTCCTAGATTCTGG 58.387 47.826 0.00 0.00 0.00 3.86
2353 2688 5.529060 ACTCTCAAGTTTCATTGTCCACTTC 59.471 40.000 0.00 0.00 28.74 3.01
2423 2758 9.277783 GTACTCCATATGCTATTTCTGTTTCAT 57.722 33.333 0.00 0.00 0.00 2.57
2445 2780 4.974645 TGTGGTTTCAGTAATGGACTCT 57.025 40.909 0.00 0.00 35.64 3.24
2446 2781 5.304686 TGTGGTTTCAGTAATGGACTCTT 57.695 39.130 0.00 0.00 35.64 2.85
2624 2959 2.419011 TACCAGTGCCCGGCAAATGT 62.419 55.000 15.39 13.36 41.47 2.71
2695 3030 4.464008 TGAACAGAATTTCTGGTGAAGCT 58.536 39.130 25.94 4.77 45.99 3.74
2768 3103 4.545610 TGTTTGAAAAGGATGCGACATTC 58.454 39.130 0.00 0.00 0.00 2.67
2795 3130 4.829064 TGACCCGATTGCTTTTATATGC 57.171 40.909 0.00 0.00 0.00 3.14
2838 3173 6.693466 TGATGTCATGATCATGTTTTTGCTT 58.307 32.000 30.01 14.62 39.72 3.91
2839 3174 6.809689 TGATGTCATGATCATGTTTTTGCTTC 59.190 34.615 30.01 20.06 39.72 3.86
2840 3175 6.335471 TGTCATGATCATGTTTTTGCTTCT 57.665 33.333 30.01 0.00 39.72 2.85
2841 3176 7.451501 TGTCATGATCATGTTTTTGCTTCTA 57.548 32.000 30.01 8.18 39.72 2.10
2842 3177 8.058667 TGTCATGATCATGTTTTTGCTTCTAT 57.941 30.769 30.01 0.00 39.72 1.98
2843 3178 9.176460 TGTCATGATCATGTTTTTGCTTCTATA 57.824 29.630 30.01 7.58 39.72 1.31
2850 3185 9.643693 ATCATGTTTTTGCTTCTATAAACTTGG 57.356 29.630 0.00 0.00 36.80 3.61
2851 3186 8.637986 TCATGTTTTTGCTTCTATAAACTTGGT 58.362 29.630 0.00 0.00 36.80 3.67
2852 3187 8.915654 CATGTTTTTGCTTCTATAAACTTGGTC 58.084 33.333 0.00 0.00 34.58 4.02
2853 3188 8.001881 TGTTTTTGCTTCTATAAACTTGGTCA 57.998 30.769 0.00 0.00 32.99 4.02
2854 3189 8.470805 TGTTTTTGCTTCTATAAACTTGGTCAA 58.529 29.630 0.00 0.00 32.99 3.18
2855 3190 9.308318 GTTTTTGCTTCTATAAACTTGGTCAAA 57.692 29.630 0.00 0.00 0.00 2.69
2857 3192 9.474920 TTTTGCTTCTATAAACTTGGTCAAATG 57.525 29.630 0.00 0.00 0.00 2.32
2858 3193 7.759489 TGCTTCTATAAACTTGGTCAAATGT 57.241 32.000 0.00 0.00 0.00 2.71
2859 3194 8.177119 TGCTTCTATAAACTTGGTCAAATGTT 57.823 30.769 0.00 0.00 0.00 2.71
2860 3195 8.637986 TGCTTCTATAAACTTGGTCAAATGTTT 58.362 29.630 0.00 0.00 36.69 2.83
2888 3223 8.601845 ATTGTCTTTTATTAACTTGGCCAAAC 57.398 30.769 20.91 10.44 0.00 2.93
2889 3224 7.354751 TGTCTTTTATTAACTTGGCCAAACT 57.645 32.000 20.91 11.81 0.00 2.66
2890 3225 7.787028 TGTCTTTTATTAACTTGGCCAAACTT 58.213 30.769 20.91 15.55 0.00 2.66
2891 3226 8.261522 TGTCTTTTATTAACTTGGCCAAACTTT 58.738 29.630 20.91 14.80 0.00 2.66
2892 3227 9.752961 GTCTTTTATTAACTTGGCCAAACTTTA 57.247 29.630 20.91 13.80 0.00 1.85
2897 3232 9.921637 TTATTAACTTGGCCAAACTTTATGAAG 57.078 29.630 20.91 5.88 38.87 3.02
2923 3258 5.523013 GACTTCAGTCAACTCTAATGTGC 57.477 43.478 1.86 0.00 44.18 4.57
2924 3259 4.960938 ACTTCAGTCAACTCTAATGTGCA 58.039 39.130 0.00 0.00 0.00 4.57
2925 3260 4.993584 ACTTCAGTCAACTCTAATGTGCAG 59.006 41.667 0.00 0.00 0.00 4.41
2926 3261 4.871933 TCAGTCAACTCTAATGTGCAGA 57.128 40.909 0.00 0.00 0.00 4.26
2927 3262 4.814147 TCAGTCAACTCTAATGTGCAGAG 58.186 43.478 0.00 0.00 44.28 3.35
2943 3278 9.643693 AATGTGCAGAGTAAATAAAAATGAAGG 57.356 29.630 0.00 0.00 0.00 3.46
2944 3279 7.601856 TGTGCAGAGTAAATAAAAATGAAGGG 58.398 34.615 0.00 0.00 0.00 3.95
2945 3280 7.450014 TGTGCAGAGTAAATAAAAATGAAGGGA 59.550 33.333 0.00 0.00 0.00 4.20
2946 3281 7.970614 GTGCAGAGTAAATAAAAATGAAGGGAG 59.029 37.037 0.00 0.00 0.00 4.30
2947 3282 7.669722 TGCAGAGTAAATAAAAATGAAGGGAGT 59.330 33.333 0.00 0.00 0.00 3.85
2948 3283 9.174166 GCAGAGTAAATAAAAATGAAGGGAGTA 57.826 33.333 0.00 0.00 0.00 2.59
2952 3287 9.239551 AGTAAATAAAAATGAAGGGAGTACACC 57.760 33.333 0.00 0.00 0.00 4.16
2960 3295 2.612760 GGGAGTACACCCCTAACCC 58.387 63.158 17.09 2.05 43.81 4.11
2961 3296 0.252835 GGGAGTACACCCCTAACCCA 60.253 60.000 17.09 0.00 43.81 4.51
2962 3297 1.627195 GGGAGTACACCCCTAACCCAT 60.627 57.143 17.09 0.00 43.81 4.00
2963 3298 2.202707 GGAGTACACCCCTAACCCATT 58.797 52.381 0.00 0.00 0.00 3.16
2964 3299 3.387012 GGAGTACACCCCTAACCCATTA 58.613 50.000 0.00 0.00 0.00 1.90
2965 3300 3.781965 GGAGTACACCCCTAACCCATTAA 59.218 47.826 0.00 0.00 0.00 1.40
2966 3301 4.141551 GGAGTACACCCCTAACCCATTAAG 60.142 50.000 0.00 0.00 0.00 1.85
2967 3302 2.820728 ACACCCCTAACCCATTAAGC 57.179 50.000 0.00 0.00 0.00 3.09
2968 3303 1.997040 ACACCCCTAACCCATTAAGCA 59.003 47.619 0.00 0.00 0.00 3.91
2969 3304 2.585432 ACACCCCTAACCCATTAAGCAT 59.415 45.455 0.00 0.00 0.00 3.79
2970 3305 2.958355 CACCCCTAACCCATTAAGCATG 59.042 50.000 0.00 0.00 0.00 4.06
2971 3306 2.856231 ACCCCTAACCCATTAAGCATGA 59.144 45.455 0.00 0.00 34.31 3.07
2972 3307 3.270960 ACCCCTAACCCATTAAGCATGAA 59.729 43.478 0.00 0.00 34.31 2.57
2973 3308 3.636764 CCCCTAACCCATTAAGCATGAAC 59.363 47.826 0.00 0.00 34.31 3.18
2974 3309 3.636764 CCCTAACCCATTAAGCATGAACC 59.363 47.826 0.00 0.00 34.31 3.62
2975 3310 4.277476 CCTAACCCATTAAGCATGAACCA 58.723 43.478 0.00 0.00 34.31 3.67
2976 3311 4.709397 CCTAACCCATTAAGCATGAACCAA 59.291 41.667 0.00 0.00 34.31 3.67
2977 3312 5.186797 CCTAACCCATTAAGCATGAACCAAA 59.813 40.000 0.00 0.00 34.31 3.28
2978 3313 5.559148 AACCCATTAAGCATGAACCAAAA 57.441 34.783 0.00 0.00 34.31 2.44
2979 3314 5.151297 ACCCATTAAGCATGAACCAAAAG 57.849 39.130 0.00 0.00 34.31 2.27
2980 3315 3.934579 CCCATTAAGCATGAACCAAAAGC 59.065 43.478 0.00 0.00 34.31 3.51
2981 3316 4.322953 CCCATTAAGCATGAACCAAAAGCT 60.323 41.667 0.00 0.00 34.31 3.74
2982 3317 5.105392 CCCATTAAGCATGAACCAAAAGCTA 60.105 40.000 0.00 0.00 34.31 3.32
2983 3318 5.807011 CCATTAAGCATGAACCAAAAGCTAC 59.193 40.000 0.00 0.00 34.31 3.58
2984 3319 3.942130 AAGCATGAACCAAAAGCTACC 57.058 42.857 0.00 0.00 34.66 3.18
2985 3320 3.160679 AGCATGAACCAAAAGCTACCT 57.839 42.857 0.00 0.00 33.06 3.08
2986 3321 3.084786 AGCATGAACCAAAAGCTACCTC 58.915 45.455 0.00 0.00 33.06 3.85
2987 3322 2.164422 GCATGAACCAAAAGCTACCTCC 59.836 50.000 0.00 0.00 0.00 4.30
2988 3323 3.690460 CATGAACCAAAAGCTACCTCCT 58.310 45.455 0.00 0.00 0.00 3.69
2989 3324 3.876309 TGAACCAAAAGCTACCTCCTT 57.124 42.857 0.00 0.00 0.00 3.36
2990 3325 4.986054 TGAACCAAAAGCTACCTCCTTA 57.014 40.909 0.00 0.00 0.00 2.69
2991 3326 4.906618 TGAACCAAAAGCTACCTCCTTAG 58.093 43.478 0.00 0.00 0.00 2.18
2992 3327 4.349930 TGAACCAAAAGCTACCTCCTTAGT 59.650 41.667 0.00 0.00 0.00 2.24
2993 3328 4.995624 ACCAAAAGCTACCTCCTTAGTT 57.004 40.909 0.00 0.00 0.00 2.24
2994 3329 4.907809 ACCAAAAGCTACCTCCTTAGTTC 58.092 43.478 0.00 0.00 0.00 3.01
2995 3330 4.262617 CCAAAAGCTACCTCCTTAGTTCC 58.737 47.826 0.00 0.00 0.00 3.62
2996 3331 4.019231 CCAAAAGCTACCTCCTTAGTTCCT 60.019 45.833 0.00 0.00 0.00 3.36
2997 3332 5.515008 CCAAAAGCTACCTCCTTAGTTCCTT 60.515 44.000 0.00 0.00 0.00 3.36
2998 3333 5.844773 AAAGCTACCTCCTTAGTTCCTTT 57.155 39.130 0.00 0.00 0.00 3.11
2999 3334 6.947376 AAAGCTACCTCCTTAGTTCCTTTA 57.053 37.500 0.00 0.00 0.00 1.85
3000 3335 7.512117 AAAGCTACCTCCTTAGTTCCTTTAT 57.488 36.000 0.00 0.00 0.00 1.40
3001 3336 7.512117 AAGCTACCTCCTTAGTTCCTTTATT 57.488 36.000 0.00 0.00 0.00 1.40
3002 3337 7.512117 AGCTACCTCCTTAGTTCCTTTATTT 57.488 36.000 0.00 0.00 0.00 1.40
3003 3338 7.566569 AGCTACCTCCTTAGTTCCTTTATTTC 58.433 38.462 0.00 0.00 0.00 2.17
3004 3339 7.182206 AGCTACCTCCTTAGTTCCTTTATTTCA 59.818 37.037 0.00 0.00 0.00 2.69
3005 3340 7.827729 GCTACCTCCTTAGTTCCTTTATTTCAA 59.172 37.037 0.00 0.00 0.00 2.69
3006 3341 7.997773 ACCTCCTTAGTTCCTTTATTTCAAC 57.002 36.000 0.00 0.00 0.00 3.18
3007 3342 7.523415 ACCTCCTTAGTTCCTTTATTTCAACA 58.477 34.615 0.00 0.00 0.00 3.33
3008 3343 7.447545 ACCTCCTTAGTTCCTTTATTTCAACAC 59.552 37.037 0.00 0.00 0.00 3.32
3009 3344 7.360946 CCTCCTTAGTTCCTTTATTTCAACACG 60.361 40.741 0.00 0.00 0.00 4.49
3010 3345 6.993902 TCCTTAGTTCCTTTATTTCAACACGT 59.006 34.615 0.00 0.00 0.00 4.49
3011 3346 7.172019 TCCTTAGTTCCTTTATTTCAACACGTC 59.828 37.037 0.00 0.00 0.00 4.34
3012 3347 7.041644 CCTTAGTTCCTTTATTTCAACACGTCA 60.042 37.037 0.00 0.00 0.00 4.35
3013 3348 6.877611 AGTTCCTTTATTTCAACACGTCAT 57.122 33.333 0.00 0.00 0.00 3.06
3014 3349 6.899114 AGTTCCTTTATTTCAACACGTCATC 58.101 36.000 0.00 0.00 0.00 2.92
3015 3350 5.873179 TCCTTTATTTCAACACGTCATCC 57.127 39.130 0.00 0.00 0.00 3.51
3016 3351 4.390603 TCCTTTATTTCAACACGTCATCCG 59.609 41.667 0.00 0.00 44.03 4.18
3025 3360 3.238241 CGTCATCCGTGTCGTCGC 61.238 66.667 0.00 0.00 33.26 5.19
3026 3361 2.178521 GTCATCCGTGTCGTCGCT 59.821 61.111 0.00 0.00 0.00 4.93
3027 3362 1.443872 GTCATCCGTGTCGTCGCTT 60.444 57.895 0.00 0.00 0.00 4.68
3028 3363 0.179181 GTCATCCGTGTCGTCGCTTA 60.179 55.000 0.00 0.00 0.00 3.09
3029 3364 0.736636 TCATCCGTGTCGTCGCTTAT 59.263 50.000 0.00 0.00 0.00 1.73
3030 3365 0.846401 CATCCGTGTCGTCGCTTATG 59.154 55.000 0.00 0.00 0.00 1.90
3031 3366 0.870307 ATCCGTGTCGTCGCTTATGC 60.870 55.000 0.00 0.00 0.00 3.14
3032 3367 1.516386 CCGTGTCGTCGCTTATGCT 60.516 57.895 0.00 0.00 36.97 3.79
3033 3368 1.472276 CCGTGTCGTCGCTTATGCTC 61.472 60.000 0.00 0.00 36.97 4.26
3034 3369 0.523546 CGTGTCGTCGCTTATGCTCT 60.524 55.000 0.00 0.00 36.97 4.09
3035 3370 1.630148 GTGTCGTCGCTTATGCTCTT 58.370 50.000 0.00 0.00 36.97 2.85
3036 3371 1.993370 GTGTCGTCGCTTATGCTCTTT 59.007 47.619 0.00 0.00 36.97 2.52
3037 3372 2.028165 GTGTCGTCGCTTATGCTCTTTC 59.972 50.000 0.00 0.00 36.97 2.62
3038 3373 1.588861 GTCGTCGCTTATGCTCTTTCC 59.411 52.381 0.00 0.00 36.97 3.13
3039 3374 1.203758 TCGTCGCTTATGCTCTTTCCA 59.796 47.619 0.00 0.00 36.97 3.53
3040 3375 1.590238 CGTCGCTTATGCTCTTTCCAG 59.410 52.381 0.00 0.00 36.97 3.86
3041 3376 1.328986 GTCGCTTATGCTCTTTCCAGC 59.671 52.381 0.00 0.00 40.13 4.85
3047 3382 3.806941 TGCTCTTTCCAGCACTTGT 57.193 47.368 0.00 0.00 44.73 3.16
3048 3383 2.057137 TGCTCTTTCCAGCACTTGTT 57.943 45.000 0.00 0.00 44.73 2.83
3049 3384 1.677576 TGCTCTTTCCAGCACTTGTTG 59.322 47.619 0.00 0.00 44.73 3.33
3050 3385 1.949525 GCTCTTTCCAGCACTTGTTGA 59.050 47.619 0.00 0.00 39.43 3.18
3051 3386 2.555757 GCTCTTTCCAGCACTTGTTGAT 59.444 45.455 0.00 0.00 39.43 2.57
3052 3387 3.611057 GCTCTTTCCAGCACTTGTTGATG 60.611 47.826 0.00 0.00 41.64 3.07
3057 3392 0.038892 CAGCACTTGTTGATGGTGGC 60.039 55.000 0.00 0.00 38.02 5.01
3058 3393 1.181098 AGCACTTGTTGATGGTGGCC 61.181 55.000 0.00 0.00 0.00 5.36
3059 3394 1.462731 GCACTTGTTGATGGTGGCCA 61.463 55.000 0.00 0.00 38.19 5.36
3060 3395 0.314935 CACTTGTTGATGGTGGCCAC 59.685 55.000 28.57 28.57 35.80 5.01
3061 3396 0.106268 ACTTGTTGATGGTGGCCACA 60.106 50.000 35.78 22.39 35.80 4.17
3062 3397 1.259609 CTTGTTGATGGTGGCCACAT 58.740 50.000 35.78 25.77 35.80 3.21
3063 3398 1.619827 CTTGTTGATGGTGGCCACATT 59.380 47.619 35.78 22.81 35.80 2.71
3064 3399 1.714541 TGTTGATGGTGGCCACATTT 58.285 45.000 35.78 20.17 35.80 2.32
3065 3400 2.045524 TGTTGATGGTGGCCACATTTT 58.954 42.857 35.78 17.59 35.80 1.82
3066 3401 2.224233 TGTTGATGGTGGCCACATTTTG 60.224 45.455 35.78 0.00 35.80 2.44
3067 3402 2.006805 TGATGGTGGCCACATTTTGA 57.993 45.000 35.78 12.44 35.80 2.69
3068 3403 2.323599 TGATGGTGGCCACATTTTGAA 58.676 42.857 35.78 12.45 35.80 2.69
3069 3404 2.036992 TGATGGTGGCCACATTTTGAAC 59.963 45.455 35.78 17.03 35.80 3.18
3070 3405 1.489481 TGGTGGCCACATTTTGAACA 58.511 45.000 35.78 19.46 0.00 3.18
3071 3406 2.045524 TGGTGGCCACATTTTGAACAT 58.954 42.857 35.78 0.00 0.00 2.71
3072 3407 2.036992 TGGTGGCCACATTTTGAACATC 59.963 45.455 35.78 15.06 0.00 3.06
3073 3408 2.327568 GTGGCCACATTTTGAACATCG 58.672 47.619 31.23 0.00 0.00 3.84
3074 3409 1.271934 TGGCCACATTTTGAACATCGG 59.728 47.619 0.00 0.00 0.00 4.18
3075 3410 1.272212 GGCCACATTTTGAACATCGGT 59.728 47.619 0.00 0.00 0.00 4.69
3076 3411 2.490115 GGCCACATTTTGAACATCGGTA 59.510 45.455 0.00 0.00 0.00 4.02
3077 3412 3.130340 GGCCACATTTTGAACATCGGTAT 59.870 43.478 0.00 0.00 0.00 2.73
3078 3413 4.381505 GGCCACATTTTGAACATCGGTATT 60.382 41.667 0.00 0.00 0.00 1.89
3079 3414 5.167845 GCCACATTTTGAACATCGGTATTT 58.832 37.500 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.026822 GGCACTGAAGAAGAGATTGGGA 60.027 50.000 0.00 0.00 0.00 4.37
411 725 2.872858 GACGTTCTTCTTGTTTGAGGCT 59.127 45.455 0.00 0.00 0.00 4.58
470 789 2.435938 ATGGCAGCCAACGTACGG 60.436 61.111 20.84 2.64 36.95 4.02
530 849 3.736224 ACCCCAGCAGAGGCCATG 61.736 66.667 5.01 4.20 42.56 3.66
622 941 3.740397 TACCTACGCGCGCACTGT 61.740 61.111 32.58 22.80 0.00 3.55
724 1045 4.139038 ACCTTAAATACGTTTGGCACACT 58.861 39.130 0.00 0.00 39.29 3.55
743 1064 2.225041 TGATCCCGATCTATCCGAACCT 60.225 50.000 6.28 0.00 38.60 3.50
775 1096 5.280215 CCTCCAAATTCCTGAAGTCTGTACT 60.280 44.000 0.00 0.00 37.65 2.73
813 1134 1.333177 GAGATGGTAGAGCCGGACAT 58.667 55.000 5.05 0.00 41.21 3.06
961 1285 0.899720 TGGAATCGGGCGTTTCTAGT 59.100 50.000 0.00 0.00 0.00 2.57
1572 1898 2.504244 CACGCGTCCTCCTCGAAC 60.504 66.667 9.86 0.00 0.00 3.95
1899 2228 2.958513 GGTGGTCACCGAGTAGACT 58.041 57.895 4.22 0.00 42.29 3.24
2082 2411 1.403687 CCTCCGATTCCCCTGACTCC 61.404 65.000 0.00 0.00 0.00 3.85
2083 2412 0.688087 ACCTCCGATTCCCCTGACTC 60.688 60.000 0.00 0.00 0.00 3.36
2185 2514 7.548196 TGTTGGTTTTAACTTCACTACAGAG 57.452 36.000 0.00 0.00 0.00 3.35
2190 2519 5.889289 AGGCTTGTTGGTTTTAACTTCACTA 59.111 36.000 0.00 0.00 0.00 2.74
2279 2611 3.967203 GCTTCAGGCTGATCAGAAATC 57.033 47.619 27.04 11.58 38.06 2.17
2423 2758 5.304686 AGAGTCCATTACTGAAACCACAA 57.695 39.130 0.00 0.00 39.07 3.33
2461 2796 8.143835 TGAGACTCTGATTCAATTATTCGCATA 58.856 33.333 3.68 0.00 0.00 3.14
2468 2803 7.711772 CAGCTTCTGAGACTCTGATTCAATTAT 59.288 37.037 12.29 0.00 32.44 1.28
2479 2814 2.300956 TGTCCAGCTTCTGAGACTCT 57.699 50.000 3.68 0.00 34.85 3.24
2610 2945 1.139520 GATCACATTTGCCGGGCAC 59.860 57.895 23.78 3.40 38.71 5.01
2624 2959 6.885918 TCAATCAACTAGAGGCAAATTGATCA 59.114 34.615 0.00 0.00 38.69 2.92
2695 3030 3.304911 TCAGGTGTTCCCATCACAAAA 57.695 42.857 0.00 0.00 37.52 2.44
2768 3103 4.382728 GCAATCGGGTCATTTGCG 57.617 55.556 0.00 0.00 36.72 4.85
2771 3106 6.215845 GCATATAAAAGCAATCGGGTCATTT 58.784 36.000 0.00 0.00 0.00 2.32
2862 3197 9.699703 GTTTGGCCAAGTTAATAAAAGACAATA 57.300 29.630 19.48 0.00 0.00 1.90
2863 3198 8.428852 AGTTTGGCCAAGTTAATAAAAGACAAT 58.571 29.630 19.48 0.00 0.00 2.71
2864 3199 7.787028 AGTTTGGCCAAGTTAATAAAAGACAA 58.213 30.769 19.48 0.00 0.00 3.18
2865 3200 7.354751 AGTTTGGCCAAGTTAATAAAAGACA 57.645 32.000 19.48 0.00 0.00 3.41
2866 3201 8.657074 AAAGTTTGGCCAAGTTAATAAAAGAC 57.343 30.769 19.48 9.28 0.00 3.01
2871 3206 9.921637 CTTCATAAAGTTTGGCCAAGTTAATAA 57.078 29.630 19.48 13.99 0.00 1.40
2872 3207 9.084533 ACTTCATAAAGTTTGGCCAAGTTAATA 57.915 29.630 19.48 10.01 43.28 0.98
2873 3208 7.962441 ACTTCATAAAGTTTGGCCAAGTTAAT 58.038 30.769 19.48 7.37 43.28 1.40
2874 3209 7.354751 ACTTCATAAAGTTTGGCCAAGTTAA 57.645 32.000 19.48 0.00 43.28 2.01
2875 3210 6.969993 ACTTCATAAAGTTTGGCCAAGTTA 57.030 33.333 19.48 17.51 43.28 2.24
2876 3211 5.869649 ACTTCATAAAGTTTGGCCAAGTT 57.130 34.783 19.48 15.96 43.28 2.66
2901 3236 4.991056 TGCACATTAGAGTTGACTGAAGTC 59.009 41.667 3.41 3.41 44.97 3.01
2902 3237 4.960938 TGCACATTAGAGTTGACTGAAGT 58.039 39.130 0.00 0.00 0.00 3.01
2903 3238 5.233225 TCTGCACATTAGAGTTGACTGAAG 58.767 41.667 0.00 0.00 0.00 3.02
2904 3239 5.213891 TCTGCACATTAGAGTTGACTGAA 57.786 39.130 0.00 0.00 0.00 3.02
2905 3240 4.814147 CTCTGCACATTAGAGTTGACTGA 58.186 43.478 0.00 0.00 37.48 3.41
2917 3252 9.643693 CCTTCATTTTTATTTACTCTGCACATT 57.356 29.630 0.00 0.00 0.00 2.71
2918 3253 8.253113 CCCTTCATTTTTATTTACTCTGCACAT 58.747 33.333 0.00 0.00 0.00 3.21
2919 3254 7.450014 TCCCTTCATTTTTATTTACTCTGCACA 59.550 33.333 0.00 0.00 0.00 4.57
2920 3255 7.826690 TCCCTTCATTTTTATTTACTCTGCAC 58.173 34.615 0.00 0.00 0.00 4.57
2921 3256 7.669722 ACTCCCTTCATTTTTATTTACTCTGCA 59.330 33.333 0.00 0.00 0.00 4.41
2922 3257 8.056407 ACTCCCTTCATTTTTATTTACTCTGC 57.944 34.615 0.00 0.00 0.00 4.26
2926 3261 9.239551 GGTGTACTCCCTTCATTTTTATTTACT 57.760 33.333 2.33 0.00 0.00 2.24
2927 3262 8.464404 GGGTGTACTCCCTTCATTTTTATTTAC 58.536 37.037 23.22 0.00 43.85 2.01
2928 3263 7.616542 GGGGTGTACTCCCTTCATTTTTATTTA 59.383 37.037 27.78 0.00 46.27 1.40
2929 3264 6.439375 GGGGTGTACTCCCTTCATTTTTATTT 59.561 38.462 27.78 0.00 46.27 1.40
2930 3265 5.955959 GGGGTGTACTCCCTTCATTTTTATT 59.044 40.000 27.78 0.00 46.27 1.40
2931 3266 5.516044 GGGGTGTACTCCCTTCATTTTTAT 58.484 41.667 27.78 0.00 46.27 1.40
2932 3267 4.925836 GGGGTGTACTCCCTTCATTTTTA 58.074 43.478 27.78 0.00 46.27 1.52
2933 3268 3.774734 GGGGTGTACTCCCTTCATTTTT 58.225 45.455 27.78 0.00 46.27 1.94
2934 3269 3.451402 GGGGTGTACTCCCTTCATTTT 57.549 47.619 27.78 0.00 46.27 1.82
2942 3277 0.252835 TGGGTTAGGGGTGTACTCCC 60.253 60.000 22.58 22.58 46.31 4.30
2943 3278 1.889174 ATGGGTTAGGGGTGTACTCC 58.111 55.000 5.35 5.35 0.00 3.85
2944 3279 4.685302 GCTTAATGGGTTAGGGGTGTACTC 60.685 50.000 0.00 0.00 0.00 2.59
2945 3280 3.201487 GCTTAATGGGTTAGGGGTGTACT 59.799 47.826 0.00 0.00 0.00 2.73
2946 3281 3.054213 TGCTTAATGGGTTAGGGGTGTAC 60.054 47.826 0.00 0.00 0.00 2.90
2947 3282 3.191273 TGCTTAATGGGTTAGGGGTGTA 58.809 45.455 0.00 0.00 0.00 2.90
2948 3283 1.997040 TGCTTAATGGGTTAGGGGTGT 59.003 47.619 0.00 0.00 0.00 4.16
2949 3284 2.818751 TGCTTAATGGGTTAGGGGTG 57.181 50.000 0.00 0.00 0.00 4.61
2950 3285 2.856231 TCATGCTTAATGGGTTAGGGGT 59.144 45.455 0.00 0.00 36.86 4.95
2951 3286 3.593442 TCATGCTTAATGGGTTAGGGG 57.407 47.619 0.00 0.00 36.86 4.79
2952 3287 3.636764 GGTTCATGCTTAATGGGTTAGGG 59.363 47.826 0.00 0.00 36.86 3.53
2953 3288 4.277476 TGGTTCATGCTTAATGGGTTAGG 58.723 43.478 0.00 0.00 36.86 2.69
2954 3289 5.913137 TTGGTTCATGCTTAATGGGTTAG 57.087 39.130 0.00 0.00 36.86 2.34
2955 3290 6.672266 TTTTGGTTCATGCTTAATGGGTTA 57.328 33.333 0.00 0.00 36.86 2.85
2956 3291 5.550290 CTTTTGGTTCATGCTTAATGGGTT 58.450 37.500 0.00 0.00 36.86 4.11
2957 3292 4.563374 GCTTTTGGTTCATGCTTAATGGGT 60.563 41.667 0.00 0.00 36.86 4.51
2958 3293 3.934579 GCTTTTGGTTCATGCTTAATGGG 59.065 43.478 0.00 0.00 36.86 4.00
2959 3294 4.824289 AGCTTTTGGTTCATGCTTAATGG 58.176 39.130 0.00 0.00 36.86 3.16
2960 3295 5.807011 GGTAGCTTTTGGTTCATGCTTAATG 59.193 40.000 0.00 0.00 37.66 1.90
2961 3296 5.716703 AGGTAGCTTTTGGTTCATGCTTAAT 59.283 36.000 0.00 0.00 35.47 1.40
2962 3297 5.076873 AGGTAGCTTTTGGTTCATGCTTAA 58.923 37.500 0.00 0.00 35.47 1.85
2963 3298 4.662278 AGGTAGCTTTTGGTTCATGCTTA 58.338 39.130 0.00 0.00 35.47 3.09
2964 3299 3.500343 AGGTAGCTTTTGGTTCATGCTT 58.500 40.909 0.00 0.00 35.47 3.91
2965 3300 3.084786 GAGGTAGCTTTTGGTTCATGCT 58.915 45.455 0.00 0.00 37.72 3.79
2966 3301 2.164422 GGAGGTAGCTTTTGGTTCATGC 59.836 50.000 0.00 0.00 0.00 4.06
2967 3302 3.690460 AGGAGGTAGCTTTTGGTTCATG 58.310 45.455 0.00 0.00 0.00 3.07
2968 3303 4.388577 AAGGAGGTAGCTTTTGGTTCAT 57.611 40.909 0.00 0.00 0.00 2.57
2969 3304 3.876309 AAGGAGGTAGCTTTTGGTTCA 57.124 42.857 0.00 0.00 0.00 3.18
2970 3305 4.907809 ACTAAGGAGGTAGCTTTTGGTTC 58.092 43.478 0.00 0.00 0.00 3.62
2971 3306 4.995624 ACTAAGGAGGTAGCTTTTGGTT 57.004 40.909 0.00 0.00 0.00 3.67
2972 3307 4.263374 GGAACTAAGGAGGTAGCTTTTGGT 60.263 45.833 0.00 0.00 0.00 3.67
2973 3308 4.019231 AGGAACTAAGGAGGTAGCTTTTGG 60.019 45.833 0.00 0.00 36.02 3.28
2974 3309 5.167303 AGGAACTAAGGAGGTAGCTTTTG 57.833 43.478 0.00 0.00 36.02 2.44
2975 3310 5.844773 AAGGAACTAAGGAGGTAGCTTTT 57.155 39.130 0.00 0.00 38.49 2.27
2976 3311 5.844773 AAAGGAACTAAGGAGGTAGCTTT 57.155 39.130 0.00 0.00 38.49 3.51
2977 3312 7.512117 AATAAAGGAACTAAGGAGGTAGCTT 57.488 36.000 0.00 0.00 38.49 3.74
2978 3313 7.182206 TGAAATAAAGGAACTAAGGAGGTAGCT 59.818 37.037 0.00 0.00 38.49 3.32
2979 3314 7.336396 TGAAATAAAGGAACTAAGGAGGTAGC 58.664 38.462 0.00 0.00 38.49 3.58
2980 3315 9.163899 GTTGAAATAAAGGAACTAAGGAGGTAG 57.836 37.037 0.00 0.00 38.49 3.18
2981 3316 8.662255 TGTTGAAATAAAGGAACTAAGGAGGTA 58.338 33.333 0.00 0.00 38.49 3.08
2982 3317 7.447545 GTGTTGAAATAAAGGAACTAAGGAGGT 59.552 37.037 0.00 0.00 38.49 3.85
2983 3318 7.360946 CGTGTTGAAATAAAGGAACTAAGGAGG 60.361 40.741 0.00 0.00 38.49 4.30
2984 3319 7.172703 ACGTGTTGAAATAAAGGAACTAAGGAG 59.827 37.037 0.00 0.00 38.49 3.69
2985 3320 6.993902 ACGTGTTGAAATAAAGGAACTAAGGA 59.006 34.615 0.00 0.00 38.49 3.36
2986 3321 7.041644 TGACGTGTTGAAATAAAGGAACTAAGG 60.042 37.037 0.00 0.00 38.49 2.69
2987 3322 7.857569 TGACGTGTTGAAATAAAGGAACTAAG 58.142 34.615 0.00 0.00 38.49 2.18
2988 3323 7.789273 TGACGTGTTGAAATAAAGGAACTAA 57.211 32.000 0.00 0.00 38.49 2.24
2989 3324 7.118680 GGATGACGTGTTGAAATAAAGGAACTA 59.881 37.037 0.00 0.00 38.49 2.24
2990 3325 9.158682 CGGATGACGTGTTGAAATAAAGGAACT 62.159 40.741 0.00 0.00 38.08 3.01
2991 3326 6.084277 GGATGACGTGTTGAAATAAAGGAAC 58.916 40.000 0.00 0.00 0.00 3.62
2992 3327 5.106869 CGGATGACGTGTTGAAATAAAGGAA 60.107 40.000 0.00 0.00 37.93 3.36
2993 3328 4.390603 CGGATGACGTGTTGAAATAAAGGA 59.609 41.667 0.00 0.00 37.93 3.36
2994 3329 4.647964 CGGATGACGTGTTGAAATAAAGG 58.352 43.478 0.00 0.00 37.93 3.11
3009 3344 0.179181 TAAGCGACGACACGGATGAC 60.179 55.000 0.00 0.00 0.00 3.06
3010 3345 0.736636 ATAAGCGACGACACGGATGA 59.263 50.000 0.00 0.00 0.00 2.92
3011 3346 0.846401 CATAAGCGACGACACGGATG 59.154 55.000 0.00 0.00 0.00 3.51
3012 3347 0.870307 GCATAAGCGACGACACGGAT 60.870 55.000 0.00 0.00 0.00 4.18
3013 3348 1.515519 GCATAAGCGACGACACGGA 60.516 57.895 0.00 0.00 0.00 4.69
3014 3349 2.995482 GCATAAGCGACGACACGG 59.005 61.111 0.00 0.00 0.00 4.94
3021 3356 3.252160 TGCTGGAAAGAGCATAAGCGAC 61.252 50.000 0.00 0.00 44.16 5.19
3022 3357 1.066215 TGCTGGAAAGAGCATAAGCGA 60.066 47.619 0.00 0.00 44.16 4.93
3023 3358 1.372582 TGCTGGAAAGAGCATAAGCG 58.627 50.000 0.00 0.00 44.16 4.68
3029 3364 1.677576 CAACAAGTGCTGGAAAGAGCA 59.322 47.619 0.00 0.00 46.87 4.26
3030 3365 1.949525 TCAACAAGTGCTGGAAAGAGC 59.050 47.619 0.00 0.00 39.62 4.09
3031 3366 3.057736 CCATCAACAAGTGCTGGAAAGAG 60.058 47.826 0.00 0.00 44.97 2.85
3032 3367 2.886523 CCATCAACAAGTGCTGGAAAGA 59.113 45.455 0.00 0.00 44.97 2.52
3033 3368 2.624838 ACCATCAACAAGTGCTGGAAAG 59.375 45.455 3.36 0.00 44.97 2.62
3034 3369 2.361757 CACCATCAACAAGTGCTGGAAA 59.638 45.455 3.36 0.00 44.97 3.13
3035 3370 1.955778 CACCATCAACAAGTGCTGGAA 59.044 47.619 3.36 0.00 44.97 3.53
3036 3371 1.608055 CACCATCAACAAGTGCTGGA 58.392 50.000 3.36 0.00 44.97 3.86
3038 3373 0.038892 GCCACCATCAACAAGTGCTG 60.039 55.000 0.00 0.00 0.00 4.41
3039 3374 1.181098 GGCCACCATCAACAAGTGCT 61.181 55.000 0.00 0.00 0.00 4.40
3040 3375 1.290009 GGCCACCATCAACAAGTGC 59.710 57.895 0.00 0.00 0.00 4.40
3041 3376 0.314935 GTGGCCACCATCAACAAGTG 59.685 55.000 26.31 0.00 35.28 3.16
3042 3377 0.106268 TGTGGCCACCATCAACAAGT 60.106 50.000 32.62 0.00 35.28 3.16
3043 3378 1.259609 ATGTGGCCACCATCAACAAG 58.740 50.000 32.62 0.00 35.28 3.16
3044 3379 1.714541 AATGTGGCCACCATCAACAA 58.285 45.000 32.62 12.24 35.28 2.83
3045 3380 1.714541 AAATGTGGCCACCATCAACA 58.285 45.000 32.62 13.12 35.28 3.33
3046 3381 2.036992 TCAAAATGTGGCCACCATCAAC 59.963 45.455 32.62 6.89 35.28 3.18
3047 3382 2.323599 TCAAAATGTGGCCACCATCAA 58.676 42.857 32.62 14.67 35.28 2.57
3048 3383 2.006805 TCAAAATGTGGCCACCATCA 57.993 45.000 32.62 15.15 35.28 3.07
3049 3384 2.036992 TGTTCAAAATGTGGCCACCATC 59.963 45.455 32.62 8.97 35.28 3.51
3050 3385 2.045524 TGTTCAAAATGTGGCCACCAT 58.954 42.857 32.62 21.85 35.28 3.55
3051 3386 1.489481 TGTTCAAAATGTGGCCACCA 58.511 45.000 32.62 20.58 0.00 4.17
3052 3387 2.687370 GATGTTCAAAATGTGGCCACC 58.313 47.619 32.62 15.02 0.00 4.61
3053 3388 2.327568 CGATGTTCAAAATGTGGCCAC 58.672 47.619 29.67 29.67 0.00 5.01
3054 3389 1.271934 CCGATGTTCAAAATGTGGCCA 59.728 47.619 0.00 0.00 0.00 5.36
3055 3390 1.272212 ACCGATGTTCAAAATGTGGCC 59.728 47.619 0.00 0.00 0.00 5.36
3056 3391 2.723124 ACCGATGTTCAAAATGTGGC 57.277 45.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.