Multiple sequence alignment - TraesCS5B01G364200

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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 TraesCS5B01G364200 chr5B 100.000 3644 0 0 1 3644 542954684 542951041 0.000000e+00 6730.0
1 TraesCS5B01G364200 chr5B 84.253 2375 271 59 511 2863 542983400 542981107 0.000000e+00 2218.0
2 TraesCS5B01G364200 chr5B 89.610 154 14 2 1 154 542983638 542983487 1.030000e-45 195.0
3 TraesCS5B01G364200 chr5D 96.260 2326 75 6 543 2862 445320397 445318078 0.000000e+00 3803.0
4 TraesCS5B01G364200 chr5D 89.316 1666 155 9 995 2643 445378706 445377047 0.000000e+00 2069.0
5 TraesCS5B01G364200 chr5D 85.064 944 83 24 23 947 445379611 445378707 0.000000e+00 909.0
6 TraesCS5B01G364200 chr5D 94.188 499 20 3 1 496 445320890 445320398 0.000000e+00 752.0
7 TraesCS5B01G364200 chr5D 83.034 613 60 24 3026 3603 445318076 445317473 1.940000e-142 516.0
8 TraesCS5B01G364200 chr5D 91.954 174 12 2 2861 3033 529218166 529218338 3.640000e-60 243.0
9 TraesCS5B01G364200 chr5D 76.568 303 45 21 3026 3317 445376858 445376571 3.790000e-30 143.0
10 TraesCS5B01G364200 chr5A 95.918 1960 59 10 1 1953 562894605 562892660 0.000000e+00 3157.0
11 TraesCS5B01G364200 chr5A 97.265 914 21 2 1951 2862 562892459 562891548 0.000000e+00 1546.0
12 TraesCS5B01G364200 chr5A 85.831 1101 128 11 995 2070 562992243 562991146 0.000000e+00 1144.0
13 TraesCS5B01G364200 chr5A 91.053 570 48 1 2074 2643 562977349 562976783 0.000000e+00 767.0
14 TraesCS5B01G364200 chr5A 82.764 615 63 23 3019 3603 562891550 562890949 3.250000e-140 508.0
15 TraesCS5B01G364200 chr5A 80.673 683 74 26 35 697 562993105 562992461 9.150000e-131 477.0
16 TraesCS5B01G364200 chr2D 76.503 1447 306 27 1212 2638 2512182 2510750 0.000000e+00 758.0
17 TraesCS5B01G364200 chr2D 76.259 695 155 8 1214 1903 2237463 2238152 9.620000e-96 361.0
18 TraesCS5B01G364200 chr2D 92.121 165 11 2 2858 3021 296364046 296364209 7.870000e-57 231.0
19 TraesCS5B01G364200 chr2D 100.000 30 0 0 3120 3149 636224129 636224100 5.080000e-04 56.5
20 TraesCS5B01G364200 chr4D 76.078 1275 279 20 1373 2629 4031487 4030221 3.070000e-180 641.0
21 TraesCS5B01G364200 chr4D 93.865 163 9 1 2861 3022 392415622 392415460 1.010000e-60 244.0
22 TraesCS5B01G364200 chr4D 92.727 165 11 1 2859 3022 34661525 34661689 1.690000e-58 237.0
23 TraesCS5B01G364200 chr4D 90.230 174 15 2 2853 3025 386984836 386984664 3.660000e-55 226.0
24 TraesCS5B01G364200 chr4D 88.770 187 12 7 2840 3022 435010350 435010531 1.700000e-53 220.0
25 TraesCS5B01G364200 chr1D 93.865 163 9 1 2861 3022 279722282 279722444 1.010000e-60 244.0
26 TraesCS5B01G364200 chr3D 91.379 174 14 1 2861 3033 87926161 87925988 1.690000e-58 237.0
27 TraesCS5B01G364200 chr7B 92.121 165 12 1 2861 3024 613181502 613181338 7.870000e-57 231.0
28 TraesCS5B01G364200 chr6D 90.278 144 12 2 244 386 12035372 12035514 1.730000e-43 187.0
29 TraesCS5B01G364200 chr6B 89.583 144 13 2 244 386 633503692 633503834 8.040000e-42 182.0


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 TraesCS5B01G364200 chr5B 542951041 542954684 3643 True 6730.000000 6730 100.000000 1 3644 1 chr5B.!!$R1 3643
1 TraesCS5B01G364200 chr5B 542981107 542983638 2531 True 1206.500000 2218 86.931500 1 2863 2 chr5B.!!$R2 2862
2 TraesCS5B01G364200 chr5D 445317473 445320890 3417 True 1690.333333 3803 91.160667 1 3603 3 chr5D.!!$R1 3602
3 TraesCS5B01G364200 chr5D 445376571 445379611 3040 True 1040.333333 2069 83.649333 23 3317 3 chr5D.!!$R2 3294
4 TraesCS5B01G364200 chr5A 562890949 562894605 3656 True 1737.000000 3157 91.982333 1 3603 3 chr5A.!!$R2 3602
5 TraesCS5B01G364200 chr5A 562991146 562993105 1959 True 810.500000 1144 83.252000 35 2070 2 chr5A.!!$R3 2035
6 TraesCS5B01G364200 chr5A 562976783 562977349 566 True 767.000000 767 91.053000 2074 2643 1 chr5A.!!$R1 569
7 TraesCS5B01G364200 chr2D 2510750 2512182 1432 True 758.000000 758 76.503000 1212 2638 1 chr2D.!!$R1 1426
8 TraesCS5B01G364200 chr2D 2237463 2238152 689 False 361.000000 361 76.259000 1214 1903 1 chr2D.!!$F1 689
9 TraesCS5B01G364200 chr4D 4030221 4031487 1266 True 641.000000 641 76.078000 1373 2629 1 chr4D.!!$R1 1256

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
709 777 1.366679 CTGAACACGATGAGCATGCT 58.633 50.0 22.92 22.92 0.00 3.79 F
1730 1833 0.617413 CTGTCCTTGGACATGCCTCT 59.383 55.0 21.09 0.00 37.63 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1876 0.517316 GCATGGTGTGTCGGAGAAAC 59.483 55.0 0.0 0.0 46.98 2.78 R
3492 3915 0.320697 GCTAGTTCACCCAACGGACT 59.679 55.0 0.0 0.0 40.32 3.85 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
62 63 2.039480 ACAGAGTGTTCAGTGATGCCAT 59.961 45.455 0.00 0.00 0.00 4.40
397 402 2.949177 TTACTTTGCTTCCTCTGCCA 57.051 45.000 0.00 0.00 0.00 4.92
534 553 2.871096 TAGTGGAACCATCGGCTTTT 57.129 45.000 0.00 0.00 37.80 2.27
562 608 7.555195 TCATTCATTCAATCTGCTATTGTCTGT 59.445 33.333 10.77 0.00 0.00 3.41
709 777 1.366679 CTGAACACGATGAGCATGCT 58.633 50.000 22.92 22.92 0.00 3.79
1187 1290 5.069914 ACTTGTACATGTGGTCTTGTACTCA 59.930 40.000 13.19 9.37 46.29 3.41
1456 1559 1.282248 ATTCGCCGCCATATTCGACG 61.282 55.000 0.00 0.00 34.28 5.12
1533 1636 1.080093 GTTCGTGGGCGTGATCAGA 60.080 57.895 0.00 0.00 39.49 3.27
1693 1796 1.621317 TCACCGCCATGACAGTCTTTA 59.379 47.619 1.31 0.00 0.00 1.85
1730 1833 0.617413 CTGTCCTTGGACATGCCTCT 59.383 55.000 21.09 0.00 37.63 3.69
1773 1876 3.009115 ACGGTCATGGAGGTGGGG 61.009 66.667 0.00 0.00 0.00 4.96
2744 3112 5.231357 GTGTATGTGTGTGTGTCCATATACG 59.769 44.000 0.00 0.00 38.04 3.06
2752 3122 7.277098 GTGTGTGTGTCCATATACGTATTTTCT 59.723 37.037 14.33 0.00 0.00 2.52
2773 3143 4.511454 TCTCTTTCATGTCGGACAACTTTG 59.489 41.667 15.72 8.93 0.00 2.77
2863 3236 7.175467 TGCAAATGTTCTCAGAAATCATGTACT 59.825 33.333 0.00 0.00 0.00 2.73
2864 3237 7.695618 GCAAATGTTCTCAGAAATCATGTACTC 59.304 37.037 0.00 0.00 0.00 2.59
2865 3238 7.856145 AATGTTCTCAGAAATCATGTACTCC 57.144 36.000 0.00 0.00 0.00 3.85
2866 3239 5.734720 TGTTCTCAGAAATCATGTACTCCC 58.265 41.667 0.00 0.00 0.00 4.30
2867 3240 5.485353 TGTTCTCAGAAATCATGTACTCCCT 59.515 40.000 0.00 0.00 0.00 4.20
2868 3241 5.860941 TCTCAGAAATCATGTACTCCCTC 57.139 43.478 0.00 0.00 0.00 4.30
2869 3242 5.523588 TCTCAGAAATCATGTACTCCCTCT 58.476 41.667 0.00 0.00 0.00 3.69
2870 3243 5.362143 TCTCAGAAATCATGTACTCCCTCTG 59.638 44.000 0.00 0.00 0.00 3.35
2871 3244 5.026121 TCAGAAATCATGTACTCCCTCTGT 58.974 41.667 0.00 0.00 32.68 3.41
2872 3245 5.485353 TCAGAAATCATGTACTCCCTCTGTT 59.515 40.000 0.00 0.00 32.68 3.16
2873 3246 5.814705 CAGAAATCATGTACTCCCTCTGTTC 59.185 44.000 0.00 0.00 0.00 3.18
2874 3247 4.762289 AATCATGTACTCCCTCTGTTCC 57.238 45.455 0.00 0.00 0.00 3.62
2875 3248 3.474798 TCATGTACTCCCTCTGTTCCT 57.525 47.619 0.00 0.00 0.00 3.36
2876 3249 4.603094 TCATGTACTCCCTCTGTTCCTA 57.397 45.455 0.00 0.00 0.00 2.94
2877 3250 4.942944 TCATGTACTCCCTCTGTTCCTAA 58.057 43.478 0.00 0.00 0.00 2.69
2878 3251 5.338632 TCATGTACTCCCTCTGTTCCTAAA 58.661 41.667 0.00 0.00 0.00 1.85
2879 3252 5.964477 TCATGTACTCCCTCTGTTCCTAAAT 59.036 40.000 0.00 0.00 0.00 1.40
2880 3253 7.130099 TCATGTACTCCCTCTGTTCCTAAATA 58.870 38.462 0.00 0.00 0.00 1.40
2881 3254 7.789831 TCATGTACTCCCTCTGTTCCTAAATAT 59.210 37.037 0.00 0.00 0.00 1.28
2882 3255 9.090103 CATGTACTCCCTCTGTTCCTAAATATA 57.910 37.037 0.00 0.00 0.00 0.86
2883 3256 9.670442 ATGTACTCCCTCTGTTCCTAAATATAA 57.330 33.333 0.00 0.00 0.00 0.98
2884 3257 9.144298 TGTACTCCCTCTGTTCCTAAATATAAG 57.856 37.037 0.00 0.00 0.00 1.73
2885 3258 9.145442 GTACTCCCTCTGTTCCTAAATATAAGT 57.855 37.037 0.00 0.00 0.00 2.24
2886 3259 8.252624 ACTCCCTCTGTTCCTAAATATAAGTC 57.747 38.462 0.00 0.00 0.00 3.01
2887 3260 8.068733 ACTCCCTCTGTTCCTAAATATAAGTCT 58.931 37.037 0.00 0.00 0.00 3.24
2888 3261 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
2889 3262 9.280456 TCCCTCTGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
2890 3263 9.907229 CCCTCTGTTCCTAAATATAAGTCTTTT 57.093 33.333 0.00 0.00 0.00 2.27
2930 3303 9.393512 AGGAACTACATACGGATGTATATAGAC 57.606 37.037 20.64 9.46 45.42 2.59
2931 3304 9.170734 GGAACTACATACGGATGTATATAGACA 57.829 37.037 20.64 2.07 45.42 3.41
2963 3336 8.976986 AGAGTGTTTATTCATTCATTTTGCTC 57.023 30.769 0.00 0.00 0.00 4.26
2964 3337 7.752239 AGAGTGTTTATTCATTCATTTTGCTCG 59.248 33.333 0.00 0.00 0.00 5.03
2965 3338 7.370383 AGTGTTTATTCATTCATTTTGCTCGT 58.630 30.769 0.00 0.00 0.00 4.18
2966 3339 8.511321 AGTGTTTATTCATTCATTTTGCTCGTA 58.489 29.630 0.00 0.00 0.00 3.43
2967 3340 9.289303 GTGTTTATTCATTCATTTTGCTCGTAT 57.711 29.630 0.00 0.00 0.00 3.06
2968 3341 9.288124 TGTTTATTCATTCATTTTGCTCGTATG 57.712 29.630 0.00 0.00 0.00 2.39
2969 3342 9.289303 GTTTATTCATTCATTTTGCTCGTATGT 57.711 29.630 0.00 0.00 0.00 2.29
2972 3345 7.609760 TTCATTCATTTTGCTCGTATGTAGT 57.390 32.000 0.00 0.00 0.00 2.73
2973 3346 7.234187 TCATTCATTTTGCTCGTATGTAGTC 57.766 36.000 0.00 0.00 0.00 2.59
2974 3347 7.041721 TCATTCATTTTGCTCGTATGTAGTCT 58.958 34.615 0.00 0.00 0.00 3.24
2975 3348 6.647212 TTCATTTTGCTCGTATGTAGTCTG 57.353 37.500 0.00 0.00 0.00 3.51
2976 3349 4.566759 TCATTTTGCTCGTATGTAGTCTGC 59.433 41.667 0.00 0.00 0.00 4.26
2977 3350 3.586100 TTTGCTCGTATGTAGTCTGCA 57.414 42.857 0.00 0.00 0.00 4.41
2978 3351 3.801114 TTGCTCGTATGTAGTCTGCAT 57.199 42.857 8.57 8.57 0.00 3.96
2979 3352 3.801114 TGCTCGTATGTAGTCTGCATT 57.199 42.857 8.84 0.00 0.00 3.56
2980 3353 3.447742 TGCTCGTATGTAGTCTGCATTG 58.552 45.455 8.84 3.06 0.00 2.82
2981 3354 3.130340 TGCTCGTATGTAGTCTGCATTGA 59.870 43.478 8.84 6.99 0.00 2.57
2982 3355 4.112634 GCTCGTATGTAGTCTGCATTGAA 58.887 43.478 8.84 0.00 0.00 2.69
2983 3356 4.566759 GCTCGTATGTAGTCTGCATTGAAA 59.433 41.667 8.84 0.00 0.00 2.69
2984 3357 5.235186 GCTCGTATGTAGTCTGCATTGAAAT 59.765 40.000 8.84 0.00 0.00 2.17
2985 3358 6.563010 GCTCGTATGTAGTCTGCATTGAAATC 60.563 42.308 8.84 0.00 0.00 2.17
2986 3359 6.573434 TCGTATGTAGTCTGCATTGAAATCT 58.427 36.000 8.84 0.00 0.00 2.40
2987 3360 6.697455 TCGTATGTAGTCTGCATTGAAATCTC 59.303 38.462 8.84 0.00 0.00 2.75
2988 3361 6.699204 CGTATGTAGTCTGCATTGAAATCTCT 59.301 38.462 8.84 0.00 0.00 3.10
2989 3362 7.223582 CGTATGTAGTCTGCATTGAAATCTCTT 59.776 37.037 8.84 0.00 0.00 2.85
2990 3363 9.534565 GTATGTAGTCTGCATTGAAATCTCTTA 57.465 33.333 8.84 0.00 0.00 2.10
2992 3365 8.846943 TGTAGTCTGCATTGAAATCTCTTAAA 57.153 30.769 0.00 0.00 0.00 1.52
2993 3366 9.283768 TGTAGTCTGCATTGAAATCTCTTAAAA 57.716 29.630 0.00 0.00 0.00 1.52
2994 3367 9.766277 GTAGTCTGCATTGAAATCTCTTAAAAG 57.234 33.333 0.00 0.00 0.00 2.27
2995 3368 8.627208 AGTCTGCATTGAAATCTCTTAAAAGA 57.373 30.769 0.00 0.00 0.00 2.52
2996 3369 8.510505 AGTCTGCATTGAAATCTCTTAAAAGAC 58.489 33.333 0.00 0.00 0.00 3.01
2997 3370 8.510505 GTCTGCATTGAAATCTCTTAAAAGACT 58.489 33.333 0.00 0.00 0.00 3.24
2998 3371 9.071276 TCTGCATTGAAATCTCTTAAAAGACTT 57.929 29.630 0.00 0.00 0.00 3.01
3012 3385 9.211485 TCTTAAAAGACTTACATTTAGGAACGG 57.789 33.333 0.00 0.00 29.57 4.44
3013 3386 9.211485 CTTAAAAGACTTACATTTAGGAACGGA 57.789 33.333 0.00 0.00 0.00 4.69
3014 3387 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
3015 3388 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3016 3389 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3017 3390 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
3018 3391 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
3019 3392 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
3020 3393 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
3021 3394 3.705072 ACATTTAGGAACGGAGGGAGTAG 59.295 47.826 0.00 0.00 0.00 2.57
3022 3395 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
3134 3514 1.202915 AGTGAATGGGTGTGTGCATCA 60.203 47.619 0.00 0.00 0.00 3.07
3158 3538 0.823769 ATGCAGAGGCCGAGACGATA 60.824 55.000 0.00 0.00 40.13 2.92
3167 3547 1.269154 GCCGAGACGATACCTCCTTTC 60.269 57.143 0.00 0.00 0.00 2.62
3178 3558 8.857694 ACGATACCTCCTTTCTGAAAAATAAA 57.142 30.769 4.18 0.00 0.00 1.40
3179 3559 8.727910 ACGATACCTCCTTTCTGAAAAATAAAC 58.272 33.333 4.18 0.00 0.00 2.01
3242 3631 4.640201 AGCACACAGGCGTATATTTTTCAT 59.360 37.500 0.00 0.00 39.27 2.57
3362 3754 4.208460 GCATCAATCCATTTGCAAATCTCG 59.792 41.667 21.70 10.95 35.16 4.04
3373 3765 2.095110 TGCAAATCTCGAGCACCAAATG 60.095 45.455 7.81 1.05 32.55 2.32
3390 3782 2.502213 ATGCGGATGACAATTGCATG 57.498 45.000 16.66 7.56 44.02 4.06
3395 3787 2.289820 CGGATGACAATTGCATGAGGAG 59.710 50.000 16.66 3.98 0.00 3.69
3396 3788 3.285484 GGATGACAATTGCATGAGGAGT 58.715 45.455 16.66 0.00 0.00 3.85
3433 3845 9.686683 ATCTTTTGATGTACTAGTTAATTGCCT 57.313 29.630 0.00 0.00 37.85 4.75
3437 3849 4.196626 TGTACTAGTTAATTGCCTGCGT 57.803 40.909 0.00 0.00 0.00 5.24
3448 3861 1.890876 TGCCTGCGTGTTGTCTTTAT 58.109 45.000 0.00 0.00 0.00 1.40
3450 3863 2.621055 TGCCTGCGTGTTGTCTTTATTT 59.379 40.909 0.00 0.00 0.00 1.40
3452 3865 4.048504 GCCTGCGTGTTGTCTTTATTTTT 58.951 39.130 0.00 0.00 0.00 1.94
3479 3902 4.169452 TGGCCATACCAGCTTCCT 57.831 55.556 0.00 0.00 46.36 3.36
3481 3904 0.034186 TGGCCATACCAGCTTCCTTG 60.034 55.000 0.00 0.00 46.36 3.61
3487 3910 0.704076 TACCAGCTTCCTTGGCCAAT 59.296 50.000 20.85 2.78 39.39 3.16
3489 3912 0.533951 CCAGCTTCCTTGGCCAATTC 59.466 55.000 20.85 6.55 0.00 2.17
3491 3914 0.411058 AGCTTCCTTGGCCAATTCCT 59.589 50.000 20.85 8.44 0.00 3.36
3492 3915 1.640670 AGCTTCCTTGGCCAATTCCTA 59.359 47.619 20.85 2.25 0.00 2.94
3496 3919 1.564348 TCCTTGGCCAATTCCTAGTCC 59.436 52.381 20.85 0.00 0.00 3.85
3505 3928 1.946984 ATTCCTAGTCCGTTGGGTGA 58.053 50.000 0.00 0.00 33.83 4.02
3506 3929 1.719529 TTCCTAGTCCGTTGGGTGAA 58.280 50.000 0.00 0.00 33.83 3.18
3549 3972 4.809496 CCATGCCGGAAGCCTGCT 62.809 66.667 5.05 0.00 42.71 4.24
3550 3973 3.515286 CATGCCGGAAGCCTGCTG 61.515 66.667 5.05 0.00 42.71 4.41
3559 3982 2.182732 GAAGCCTGCTGCCTGAGAGT 62.183 60.000 0.00 0.00 42.71 3.24
3576 3999 5.815581 TGAGAGTGTATTTGGCCTGTTTAT 58.184 37.500 3.32 0.00 0.00 1.40
3580 4003 5.815581 AGTGTATTTGGCCTGTTTATCTGA 58.184 37.500 3.32 0.00 0.00 3.27
3603 4026 1.264288 GGATTCTTTGCCCGCGATAAG 59.736 52.381 8.23 5.40 0.00 1.73
3604 4027 1.264288 GATTCTTTGCCCGCGATAAGG 59.736 52.381 8.23 0.00 0.00 2.69
3605 4028 0.250793 TTCTTTGCCCGCGATAAGGA 59.749 50.000 8.23 2.48 0.00 3.36
3606 4029 0.250793 TCTTTGCCCGCGATAAGGAA 59.749 50.000 8.23 0.00 0.00 3.36
3607 4030 0.657840 CTTTGCCCGCGATAAGGAAG 59.342 55.000 8.23 0.00 0.00 3.46
3608 4031 1.373590 TTTGCCCGCGATAAGGAAGC 61.374 55.000 8.23 0.00 0.00 3.86
3609 4032 2.109181 GCCCGCGATAAGGAAGCT 59.891 61.111 8.23 0.00 0.00 3.74
3610 4033 2.247437 GCCCGCGATAAGGAAGCTG 61.247 63.158 8.23 0.00 0.00 4.24
3611 4034 1.144057 CCCGCGATAAGGAAGCTGT 59.856 57.895 8.23 0.00 0.00 4.40
3612 4035 1.154205 CCCGCGATAAGGAAGCTGTG 61.154 60.000 8.23 0.00 0.00 3.66
3613 4036 1.638467 CGCGATAAGGAAGCTGTGC 59.362 57.895 0.00 0.00 0.00 4.57
3614 4037 1.083806 CGCGATAAGGAAGCTGTGCA 61.084 55.000 0.00 0.00 0.00 4.57
3615 4038 1.303309 GCGATAAGGAAGCTGTGCAT 58.697 50.000 0.00 0.00 0.00 3.96
3616 4039 1.262683 GCGATAAGGAAGCTGTGCATC 59.737 52.381 0.00 0.00 0.00 3.91
3617 4040 2.831333 CGATAAGGAAGCTGTGCATCT 58.169 47.619 0.00 0.00 0.00 2.90
3618 4041 3.201290 CGATAAGGAAGCTGTGCATCTT 58.799 45.455 0.00 0.00 0.00 2.40
3619 4042 3.002042 CGATAAGGAAGCTGTGCATCTTG 59.998 47.826 0.00 0.00 0.00 3.02
3620 4043 2.574006 AAGGAAGCTGTGCATCTTGA 57.426 45.000 0.00 0.00 0.00 3.02
3621 4044 2.803030 AGGAAGCTGTGCATCTTGAT 57.197 45.000 0.00 0.00 0.00 2.57
3622 4045 3.083122 AGGAAGCTGTGCATCTTGATT 57.917 42.857 0.00 0.00 0.00 2.57
3623 4046 3.428532 AGGAAGCTGTGCATCTTGATTT 58.571 40.909 0.00 0.00 0.00 2.17
3624 4047 3.830755 AGGAAGCTGTGCATCTTGATTTT 59.169 39.130 0.00 0.00 0.00 1.82
3625 4048 4.082354 AGGAAGCTGTGCATCTTGATTTTC 60.082 41.667 0.00 0.00 0.00 2.29
3626 4049 4.082354 GGAAGCTGTGCATCTTGATTTTCT 60.082 41.667 0.00 0.00 0.00 2.52
3627 4050 5.464030 AAGCTGTGCATCTTGATTTTCTT 57.536 34.783 0.00 0.00 0.00 2.52
3628 4051 5.056894 AGCTGTGCATCTTGATTTTCTTC 57.943 39.130 0.00 0.00 0.00 2.87
3629 4052 4.521639 AGCTGTGCATCTTGATTTTCTTCA 59.478 37.500 0.00 0.00 0.00 3.02
3630 4053 5.010314 AGCTGTGCATCTTGATTTTCTTCAA 59.990 36.000 0.00 0.00 34.55 2.69
3631 4054 5.867716 GCTGTGCATCTTGATTTTCTTCAAT 59.132 36.000 0.00 0.00 35.20 2.57
3632 4055 6.367969 GCTGTGCATCTTGATTTTCTTCAATT 59.632 34.615 0.00 0.00 35.20 2.32
3633 4056 7.621426 GCTGTGCATCTTGATTTTCTTCAATTG 60.621 37.037 0.00 0.00 35.20 2.32
3634 4057 6.146510 TGTGCATCTTGATTTTCTTCAATTGC 59.853 34.615 0.00 11.95 40.93 3.56
3635 4058 6.146510 GTGCATCTTGATTTTCTTCAATTGCA 59.853 34.615 15.23 15.23 44.10 4.08
3636 4059 6.876789 TGCATCTTGATTTTCTTCAATTGCAT 59.123 30.769 15.23 0.00 42.92 3.96
3637 4060 7.389330 TGCATCTTGATTTTCTTCAATTGCATT 59.611 29.630 15.23 0.00 42.92 3.56
3638 4061 7.692291 GCATCTTGATTTTCTTCAATTGCATTG 59.308 33.333 0.00 0.00 40.61 2.82
3639 4062 7.661127 TCTTGATTTTCTTCAATTGCATTGG 57.339 32.000 0.00 0.00 40.61 3.16
3640 4063 7.218614 TCTTGATTTTCTTCAATTGCATTGGT 58.781 30.769 0.00 0.00 40.61 3.67
3641 4064 7.385752 TCTTGATTTTCTTCAATTGCATTGGTC 59.614 33.333 0.00 0.00 40.61 4.02
3642 4065 6.522946 TGATTTTCTTCAATTGCATTGGTCA 58.477 32.000 0.00 0.00 40.61 4.02
3643 4066 6.990939 TGATTTTCTTCAATTGCATTGGTCAA 59.009 30.769 0.00 0.00 40.61 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 2.041485 TGATGCAGAGAATCCCCAAACA 59.959 45.455 0.00 0.00 33.66 2.83
252 254 3.507233 TCTTTTAAGCCCAACAGATGCAG 59.493 43.478 0.00 0.00 0.00 4.41
265 267 5.880054 TGTGTTCAGGCTATCTTTTAAGC 57.120 39.130 0.00 0.00 38.03 3.09
397 402 0.111253 CAACTTCAACCCCAGGCTCT 59.889 55.000 0.00 0.00 0.00 4.09
534 553 8.963725 AGACAATAGCAGATTGAATGAATGAAA 58.036 29.630 15.91 0.00 33.51 2.69
547 593 8.565896 TTGTATTTCAACAGACAATAGCAGAT 57.434 30.769 0.00 0.00 0.00 2.90
626 681 1.908619 GAAAAACCATGGCCATCCCTT 59.091 47.619 17.61 6.05 0.00 3.95
709 777 0.387929 GGAACAGACGACAGACCACA 59.612 55.000 0.00 0.00 0.00 4.17
815 891 7.149307 TCGATGCGATATGAACAAGGTATTTA 58.851 34.615 0.00 0.00 0.00 1.40
818 894 5.134202 TCGATGCGATATGAACAAGGTAT 57.866 39.130 0.00 0.00 0.00 2.73
967 1051 4.605064 AGTGGCCACTGCACAATT 57.395 50.000 37.39 11.23 40.75 2.32
993 1077 2.187958 CCCTCTGAGTCCATTGGTACA 58.812 52.381 1.86 1.43 0.00 2.90
1187 1290 5.744300 GCTGCTGGGTCATTTGATCTACTAT 60.744 44.000 0.00 0.00 0.00 2.12
1456 1559 0.610232 AAGAAGCCACCAGCCATGAC 60.610 55.000 0.00 0.00 45.47 3.06
1533 1636 2.193536 GTCAGCAAACCGTGGGCTT 61.194 57.895 0.00 0.00 35.27 4.35
1693 1796 2.032681 GAAGCCAGGGTCAACGCT 59.967 61.111 0.00 0.00 39.95 5.07
1730 1833 1.377202 GCAAGGGAGGCGTCAATCA 60.377 57.895 8.91 0.00 0.00 2.57
1773 1876 0.517316 GCATGGTGTGTCGGAGAAAC 59.483 55.000 0.00 0.00 46.98 2.78
2744 3112 6.721571 TGTCCGACATGAAAGAGAAAATAC 57.278 37.500 0.00 0.00 0.00 1.89
2752 3122 4.196193 ACAAAGTTGTCCGACATGAAAGA 58.804 39.130 1.09 0.00 36.50 2.52
2773 3143 3.656045 CCACCCGTTGCCGTGAAC 61.656 66.667 0.00 0.00 31.36 3.18
2863 3236 8.855804 AAGACTTATATTTAGGAACAGAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
2864 3237 9.907229 AAAAGACTTATATTTAGGAACAGAGGG 57.093 33.333 0.00 0.00 0.00 4.30
2892 3265 8.361139 CCGTATGTAGTTCCTATTGAAATCTCT 58.639 37.037 0.00 0.00 33.94 3.10
2893 3266 8.358148 TCCGTATGTAGTTCCTATTGAAATCTC 58.642 37.037 0.00 0.00 33.94 2.75
2894 3267 8.246430 TCCGTATGTAGTTCCTATTGAAATCT 57.754 34.615 0.00 0.00 33.94 2.40
2895 3268 8.926710 CATCCGTATGTAGTTCCTATTGAAATC 58.073 37.037 0.00 0.00 33.94 2.17
2896 3269 8.429641 ACATCCGTATGTAGTTCCTATTGAAAT 58.570 33.333 0.00 0.00 44.66 2.17
2897 3270 7.788026 ACATCCGTATGTAGTTCCTATTGAAA 58.212 34.615 0.00 0.00 44.66 2.69
2898 3271 7.356089 ACATCCGTATGTAGTTCCTATTGAA 57.644 36.000 0.00 0.00 44.66 2.69
2899 3272 6.971726 ACATCCGTATGTAGTTCCTATTGA 57.028 37.500 0.00 0.00 44.66 2.57
2938 3311 7.752239 CGAGCAAAATGAATGAATAAACACTCT 59.248 33.333 0.00 0.00 0.00 3.24
2939 3312 7.538678 ACGAGCAAAATGAATGAATAAACACTC 59.461 33.333 0.00 0.00 0.00 3.51
2940 3313 7.370383 ACGAGCAAAATGAATGAATAAACACT 58.630 30.769 0.00 0.00 0.00 3.55
2941 3314 7.566858 ACGAGCAAAATGAATGAATAAACAC 57.433 32.000 0.00 0.00 0.00 3.32
2942 3315 9.288124 CATACGAGCAAAATGAATGAATAAACA 57.712 29.630 0.00 0.00 0.00 2.83
2943 3316 9.289303 ACATACGAGCAAAATGAATGAATAAAC 57.711 29.630 0.00 0.00 0.00 2.01
2946 3319 9.325198 ACTACATACGAGCAAAATGAATGAATA 57.675 29.630 0.00 0.00 0.00 1.75
2947 3320 8.213518 ACTACATACGAGCAAAATGAATGAAT 57.786 30.769 0.00 0.00 0.00 2.57
2948 3321 7.549134 AGACTACATACGAGCAAAATGAATGAA 59.451 33.333 0.00 0.00 0.00 2.57
2949 3322 7.010460 CAGACTACATACGAGCAAAATGAATGA 59.990 37.037 0.00 0.00 0.00 2.57
2950 3323 7.121911 CAGACTACATACGAGCAAAATGAATG 58.878 38.462 0.00 0.00 0.00 2.67
2951 3324 6.238211 GCAGACTACATACGAGCAAAATGAAT 60.238 38.462 0.00 0.00 0.00 2.57
2952 3325 5.063438 GCAGACTACATACGAGCAAAATGAA 59.937 40.000 0.00 0.00 0.00 2.57
2953 3326 4.566759 GCAGACTACATACGAGCAAAATGA 59.433 41.667 0.00 0.00 0.00 2.57
2954 3327 4.329801 TGCAGACTACATACGAGCAAAATG 59.670 41.667 0.00 0.00 0.00 2.32
2955 3328 4.503910 TGCAGACTACATACGAGCAAAAT 58.496 39.130 0.00 0.00 0.00 1.82
2956 3329 3.920446 TGCAGACTACATACGAGCAAAA 58.080 40.909 0.00 0.00 0.00 2.44
2957 3330 3.586100 TGCAGACTACATACGAGCAAA 57.414 42.857 0.00 0.00 0.00 3.68
2958 3331 3.801114 ATGCAGACTACATACGAGCAA 57.199 42.857 0.00 0.00 33.91 3.91
2959 3332 3.130340 TCAATGCAGACTACATACGAGCA 59.870 43.478 0.00 0.00 34.78 4.26
2960 3333 3.706698 TCAATGCAGACTACATACGAGC 58.293 45.455 0.00 0.00 0.00 5.03
2961 3334 6.699204 AGATTTCAATGCAGACTACATACGAG 59.301 38.462 0.00 0.00 0.00 4.18
2962 3335 6.573434 AGATTTCAATGCAGACTACATACGA 58.427 36.000 0.00 0.00 0.00 3.43
2963 3336 6.699204 AGAGATTTCAATGCAGACTACATACG 59.301 38.462 0.00 0.00 0.00 3.06
2964 3337 8.430801 AAGAGATTTCAATGCAGACTACATAC 57.569 34.615 0.00 0.00 0.00 2.39
2966 3339 9.453572 TTTAAGAGATTTCAATGCAGACTACAT 57.546 29.630 0.00 0.00 0.00 2.29
2967 3340 8.846943 TTTAAGAGATTTCAATGCAGACTACA 57.153 30.769 0.00 0.00 0.00 2.74
2968 3341 9.766277 CTTTTAAGAGATTTCAATGCAGACTAC 57.234 33.333 0.00 0.00 0.00 2.73
2969 3342 9.725019 TCTTTTAAGAGATTTCAATGCAGACTA 57.275 29.630 0.00 0.00 0.00 2.59
2970 3343 8.510505 GTCTTTTAAGAGATTTCAATGCAGACT 58.489 33.333 0.00 0.00 35.32 3.24
2971 3344 8.510505 AGTCTTTTAAGAGATTTCAATGCAGAC 58.489 33.333 0.00 0.00 35.32 3.51
2972 3345 8.627208 AGTCTTTTAAGAGATTTCAATGCAGA 57.373 30.769 0.00 0.00 35.32 4.26
2986 3359 9.211485 CCGTTCCTAAATGTAAGTCTTTTAAGA 57.789 33.333 0.00 0.00 0.00 2.10
2987 3360 9.211485 TCCGTTCCTAAATGTAAGTCTTTTAAG 57.789 33.333 0.00 0.00 0.00 1.85
2988 3361 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTAA 57.789 33.333 0.00 0.00 0.00 1.52
2989 3362 7.820872 CCTCCGTTCCTAAATGTAAGTCTTTTA 59.179 37.037 0.00 0.00 0.00 1.52
2990 3363 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
2991 3364 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2992 3365 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2993 3366 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2994 3367 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2995 3368 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2996 3369 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
2997 3370 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2998 3371 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2999 3372 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
3000 3373 3.958798 TCTACTCCCTCCGTTCCTAAATG 59.041 47.826 0.00 0.00 0.00 2.32
3001 3374 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3002 3375 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
3003 3376 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
3004 3377 3.744940 TTTCTACTCCCTCCGTTCCTA 57.255 47.619 0.00 0.00 0.00 2.94
3005 3378 2.617840 TTTCTACTCCCTCCGTTCCT 57.382 50.000 0.00 0.00 0.00 3.36
3006 3379 3.690475 TTTTTCTACTCCCTCCGTTCC 57.310 47.619 0.00 0.00 0.00 3.62
3096 3469 9.100554 CCATTCACTACCAAAAATATACGTACA 57.899 33.333 0.00 0.00 0.00 2.90
3101 3474 8.188139 CACACCCATTCACTACCAAAAATATAC 58.812 37.037 0.00 0.00 0.00 1.47
3134 3514 1.274728 GTCTCGGCCTCTGCATCATAT 59.725 52.381 0.00 0.00 40.13 1.78
3158 3538 9.546428 CAAATGTTTATTTTTCAGAAAGGAGGT 57.454 29.630 0.00 0.00 34.34 3.85
3178 3558 4.339247 AGTTCAGCTTGCTACAACAAATGT 59.661 37.500 14.89 0.00 46.36 2.71
3179 3559 4.678287 CAGTTCAGCTTGCTACAACAAATG 59.322 41.667 14.89 5.36 0.00 2.32
3230 3619 8.388484 AGAGAGGCATGTGATGAAAAATATAC 57.612 34.615 0.00 0.00 0.00 1.47
3242 3631 1.576577 ACATGGAGAGAGGCATGTGA 58.423 50.000 0.00 0.00 36.96 3.58
3330 3722 8.866970 TGCAAATGGATTGATGCTATAGATAA 57.133 30.769 3.21 0.00 41.85 1.75
3339 3731 4.208460 CGAGATTTGCAAATGGATTGATGC 59.792 41.667 28.67 11.01 41.85 3.91
3373 3765 1.268896 CCTCATGCAATTGTCATCCGC 60.269 52.381 7.40 0.00 0.00 5.54
3375 3767 3.285484 ACTCCTCATGCAATTGTCATCC 58.715 45.455 7.40 0.00 0.00 3.51
3376 3768 4.978083 AACTCCTCATGCAATTGTCATC 57.022 40.909 7.40 0.00 0.00 2.92
3377 3769 5.733620 AAAACTCCTCATGCAATTGTCAT 57.266 34.783 7.40 8.27 0.00 3.06
3409 3821 7.698130 GCAGGCAATTAACTAGTACATCAAAAG 59.302 37.037 0.00 0.00 0.00 2.27
3415 3827 4.570772 CACGCAGGCAATTAACTAGTACAT 59.429 41.667 0.00 0.00 0.00 2.29
3417 3829 3.930848 ACACGCAGGCAATTAACTAGTAC 59.069 43.478 0.00 0.00 0.00 2.73
3420 3832 3.188460 ACAACACGCAGGCAATTAACTAG 59.812 43.478 0.00 0.00 0.00 2.57
3421 3833 3.142951 ACAACACGCAGGCAATTAACTA 58.857 40.909 0.00 0.00 0.00 2.24
3479 3902 0.988832 ACGGACTAGGAATTGGCCAA 59.011 50.000 23.00 23.00 0.00 4.52
3481 3904 1.379527 CAACGGACTAGGAATTGGCC 58.620 55.000 0.00 0.00 0.00 5.36
3487 3910 1.345415 GTTCACCCAACGGACTAGGAA 59.655 52.381 0.00 0.00 0.00 3.36
3489 3912 0.974383 AGTTCACCCAACGGACTAGG 59.026 55.000 0.00 0.00 40.32 3.02
3491 3914 1.547372 GCTAGTTCACCCAACGGACTA 59.453 52.381 0.00 0.00 40.32 2.59
3492 3915 0.320697 GCTAGTTCACCCAACGGACT 59.679 55.000 0.00 0.00 40.32 3.85
3496 3919 2.069273 CAGAAGCTAGTTCACCCAACG 58.931 52.381 0.00 0.00 40.32 4.10
3547 3970 2.012673 CCAAATACACTCTCAGGCAGC 58.987 52.381 0.00 0.00 0.00 5.25
3548 3971 2.012673 GCCAAATACACTCTCAGGCAG 58.987 52.381 0.00 0.00 40.29 4.85
3549 3972 1.340017 GGCCAAATACACTCTCAGGCA 60.340 52.381 0.00 0.00 42.26 4.75
3550 3973 1.065126 AGGCCAAATACACTCTCAGGC 60.065 52.381 5.01 0.00 39.86 4.85
3551 3974 2.026822 ACAGGCCAAATACACTCTCAGG 60.027 50.000 5.01 0.00 0.00 3.86
3559 3982 5.593909 CCATCAGATAAACAGGCCAAATACA 59.406 40.000 5.01 0.00 0.00 2.29
3576 3999 1.408683 CGGGCAAAGAATCCCATCAGA 60.409 52.381 0.00 0.00 42.75 3.27
3580 4003 2.120909 CGCGGGCAAAGAATCCCAT 61.121 57.895 0.00 0.00 42.75 4.00
3603 4026 3.863142 AAATCAAGATGCACAGCTTCC 57.137 42.857 0.00 0.00 34.42 3.46
3604 4027 5.056894 AGAAAATCAAGATGCACAGCTTC 57.943 39.130 0.00 0.00 34.42 3.86
3605 4028 5.010314 TGAAGAAAATCAAGATGCACAGCTT 59.990 36.000 0.00 0.00 37.57 3.74
3606 4029 4.521639 TGAAGAAAATCAAGATGCACAGCT 59.478 37.500 0.00 0.00 0.00 4.24
3607 4030 4.801891 TGAAGAAAATCAAGATGCACAGC 58.198 39.130 0.00 0.00 0.00 4.40
3608 4031 7.621426 GCAATTGAAGAAAATCAAGATGCACAG 60.621 37.037 10.34 0.00 45.65 3.66
3609 4032 6.146510 GCAATTGAAGAAAATCAAGATGCACA 59.853 34.615 10.34 0.00 45.65 4.57
3610 4033 6.531439 GCAATTGAAGAAAATCAAGATGCAC 58.469 36.000 10.34 0.00 45.65 4.57
3611 4034 6.715344 GCAATTGAAGAAAATCAAGATGCA 57.285 33.333 10.34 0.00 45.65 3.96
3612 4035 6.715344 TGCAATTGAAGAAAATCAAGATGC 57.285 33.333 10.34 16.95 46.07 3.91


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

AutoCloner maintained by Alex Coulton.