Multiple sequence alignment - TraesCS5B01G177900

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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 TraesCS5B01G177900 chr5B 100.000 4212 0 0 1 4212 325540454 325544665 0.000000e+00 7779.0
1 TraesCS5B01G177900 chr5D 91.246 3187 130 56 878 3955 286318219 286315073 0.000000e+00 4202.0
2 TraesCS5B01G177900 chr5D 90.243 3085 129 68 54 3047 286319043 286316040 0.000000e+00 3871.0
3 TraesCS5B01G177900 chr5D 96.407 167 5 1 4046 4212 286315068 286314903 1.490000e-69 274.0
4 TraesCS5B01G177900 chr5A 89.467 2478 98 66 1 2398 378551648 378554042 0.000000e+00 2979.0
5 TraesCS5B01G177900 chr5A 89.382 1441 74 34 2436 3836 378554142 378555543 0.000000e+00 1740.0
6 TraesCS5B01G177900 chr5A 93.870 261 16 0 3889 4149 378556629 378556889 1.100000e-105 394.0
7 TraesCS5B01G177900 chr5A 97.015 67 2 0 4146 4212 378557144 378557210 3.440000e-21 113.0
8 TraesCS5B01G177900 chr5A 91.667 84 2 1 3804 3887 378555545 378555623 1.240000e-20 111.0
9 TraesCS5B01G177900 chr2D 100.000 29 0 0 3540 3568 643893123 643893095 2.000000e-03 54.7


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 TraesCS5B01G177900 chr5B 325540454 325544665 4211 False 7779.000000 7779 100.0000 1 4212 1 chr5B.!!$F1 4211
1 TraesCS5B01G177900 chr5D 286314903 286319043 4140 True 2782.333333 4202 92.6320 54 4212 3 chr5D.!!$R1 4158
2 TraesCS5B01G177900 chr5A 378551648 378557210 5562 False 1067.400000 2979 92.2802 1 4212 5 chr5A.!!$F1 4211

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
590 648 0.107848 CGCTTATTCCGGTTGGACCT 60.108 55.000 0.0 0.0 46.45 3.85 F
852 932 0.249238 GTGCGCAATCAACCAACCAA 60.249 50.000 14.0 0.0 0.00 3.67 F
2081 2186 1.154263 CTTCACCGAGGACGACGTC 60.154 63.158 19.7 19.7 42.66 4.34 F
2867 3076 0.028902 GTGTTTCCACGACCAACTGC 59.971 55.000 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1939 0.173708 AGCCGACTCACCTTTCGATC 59.826 55.0 0.0 0.0 37.43 3.69 R
2837 3046 0.031857 TGGAAACACAAATGGCAGCG 59.968 50.0 0.0 0.0 33.40 5.18 R
3125 3371 0.516877 CTGCGATGAAAAACCGAGCA 59.483 50.0 0.0 0.0 0.00 4.26 R
3913 5212 1.774639 TGAAGCGAACGGTCAGTTAC 58.225 50.0 0.0 0.0 44.35 2.50 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
35 36 8.685838 TTAGGGCTAACACCATTGTTATAATC 57.314 34.615 0.00 0.00 45.25 1.75
39 40 6.910433 GGCTAACACCATTGTTATAATCAACG 59.090 38.462 0.00 0.00 45.25 4.10
42 43 5.879237 ACACCATTGTTATAATCAACGCTG 58.121 37.500 0.00 0.00 28.43 5.18
56 61 4.439057 TCAACGCTGGTAGTATCATTTCC 58.561 43.478 0.00 0.00 0.00 3.13
133 142 1.302832 GCTGGTGGTGCAAGCTAGT 60.303 57.895 0.00 0.00 41.00 2.57
162 171 1.971505 ATCATGGTCGCCCACGTCAT 61.972 55.000 0.00 0.00 45.65 3.06
207 218 4.767255 CCTGCTCGTCCCTGTGCC 62.767 72.222 0.00 0.00 0.00 5.01
211 222 4.436998 CTCGTCCCTGTGCCGTCC 62.437 72.222 0.00 0.00 0.00 4.79
212 223 4.988716 TCGTCCCTGTGCCGTCCT 62.989 66.667 0.00 0.00 0.00 3.85
214 225 4.436998 GTCCCTGTGCCGTCCTCG 62.437 72.222 0.00 0.00 0.00 4.63
215 226 4.671590 TCCCTGTGCCGTCCTCGA 62.672 66.667 0.00 0.00 39.71 4.04
232 243 1.068125 TCGATCAACCGCGAGAAGAAA 60.068 47.619 8.23 0.00 32.13 2.52
235 246 3.674423 GATCAACCGCGAGAAGAAATTG 58.326 45.455 8.23 0.00 0.00 2.32
258 269 1.141645 GTCCAACATCAACGCGTACA 58.858 50.000 14.46 1.28 0.00 2.90
259 270 1.136446 GTCCAACATCAACGCGTACAC 60.136 52.381 14.46 0.00 0.00 2.90
263 275 0.249531 ACATCAACGCGTACACCACA 60.250 50.000 14.46 0.00 0.00 4.17
264 276 1.075542 CATCAACGCGTACACCACAT 58.924 50.000 14.46 0.00 0.00 3.21
278 290 1.668793 CACATCACACGGCAGAGCA 60.669 57.895 0.00 0.00 0.00 4.26
328 344 2.104331 CTACCACGCGCCACTAGG 59.896 66.667 5.73 0.90 38.23 3.02
347 363 1.048160 GGGAGAGAGCAGAAGGGGAG 61.048 65.000 0.00 0.00 0.00 4.30
388 404 1.136252 TCGTCGTCGAACTCTAAACCG 60.136 52.381 1.37 0.00 43.34 4.44
389 405 0.980525 GTCGTCGAACTCTAAACCGC 59.019 55.000 0.00 0.00 0.00 5.68
390 406 0.453282 TCGTCGAACTCTAAACCGCG 60.453 55.000 0.00 0.00 0.00 6.46
391 407 1.700595 GTCGAACTCTAAACCGCGC 59.299 57.895 0.00 0.00 0.00 6.86
392 408 1.798725 TCGAACTCTAAACCGCGCG 60.799 57.895 25.67 25.67 0.00 6.86
426 442 4.168291 CCAGGAGCGAGAAGGGGC 62.168 72.222 0.00 0.00 0.00 5.80
429 445 3.145551 GGAGCGAGAAGGGGCGTA 61.146 66.667 0.00 0.00 0.00 4.42
453 485 3.238497 GTTTGGGTTGGGTGGGGC 61.238 66.667 0.00 0.00 0.00 5.80
509 558 2.904866 GTGGTTGCGTTGCCCTCA 60.905 61.111 0.00 0.00 0.00 3.86
510 559 2.115052 TGGTTGCGTTGCCCTCAT 59.885 55.556 0.00 0.00 0.00 2.90
511 560 2.267351 TGGTTGCGTTGCCCTCATG 61.267 57.895 0.00 0.00 0.00 3.07
544 602 0.742990 TCACACGGCCGGAATGAATC 60.743 55.000 31.76 0.00 0.00 2.52
545 603 1.451387 ACACGGCCGGAATGAATCC 60.451 57.895 31.76 0.00 45.57 3.01
573 631 2.604174 CGTGGATTTATCGGGCCGC 61.604 63.158 23.83 5.62 0.00 6.53
590 648 0.107848 CGCTTATTCCGGTTGGACCT 60.108 55.000 0.00 0.00 46.45 3.85
733 795 1.931263 GCCGCGGCTATAAACTCTCTC 60.931 57.143 41.71 8.51 38.26 3.20
845 925 4.776647 GGCCGGTGCGCAATCAAC 62.777 66.667 14.00 0.00 38.85 3.18
847 927 3.361158 CCGGTGCGCAATCAACCA 61.361 61.111 14.00 0.00 0.00 3.67
849 929 1.729131 CGGTGCGCAATCAACCAAC 60.729 57.895 14.00 0.00 0.00 3.77
851 931 1.361993 GTGCGCAATCAACCAACCA 59.638 52.632 14.00 0.00 0.00 3.67
852 932 0.249238 GTGCGCAATCAACCAACCAA 60.249 50.000 14.00 0.00 0.00 3.67
914 1008 1.827344 TCAGCCATTGTCGAGTGATCT 59.173 47.619 0.00 0.00 0.00 2.75
1036 1130 3.070734 GCTAGCCAAGATCATCTTCTCCA 59.929 47.826 2.29 0.00 33.78 3.86
1348 1442 2.408022 CGGCGGAGAAGGAGTACG 59.592 66.667 0.00 0.00 0.00 3.67
1350 1444 2.104530 GCGGAGAAGGAGTACGCC 59.895 66.667 7.70 7.70 44.01 5.68
1842 1939 1.457346 GCCTCAACAAGATCAGGGTG 58.543 55.000 0.00 0.00 0.00 4.61
1857 1954 1.550976 AGGGTGATCGAAAGGTGAGTC 59.449 52.381 0.00 0.00 0.00 3.36
2081 2186 1.154263 CTTCACCGAGGACGACGTC 60.154 63.158 19.70 19.70 42.66 4.34
2102 2207 4.273969 GTCGCCAATTATTTCGGGTAATCA 59.726 41.667 0.00 0.00 0.00 2.57
2111 2216 9.965824 AATTATTTCGGGTAATCATTCATTCAC 57.034 29.630 0.00 0.00 0.00 3.18
2112 2217 5.828299 TTTCGGGTAATCATTCATTCACC 57.172 39.130 0.00 0.00 0.00 4.02
2114 2219 2.884639 CGGGTAATCATTCATTCACCCC 59.115 50.000 0.35 0.00 42.23 4.95
2115 2220 3.435026 CGGGTAATCATTCATTCACCCCT 60.435 47.826 0.35 0.00 42.23 4.79
2116 2221 4.546674 GGGTAATCATTCATTCACCCCTT 58.453 43.478 0.00 0.00 39.83 3.95
2117 2222 4.584743 GGGTAATCATTCATTCACCCCTTC 59.415 45.833 0.00 0.00 39.83 3.46
2118 2223 4.275936 GGTAATCATTCATTCACCCCTTCG 59.724 45.833 0.00 0.00 0.00 3.79
2120 2225 3.433306 TCATTCATTCACCCCTTCGTT 57.567 42.857 0.00 0.00 0.00 3.85
2121 2226 3.343617 TCATTCATTCACCCCTTCGTTC 58.656 45.455 0.00 0.00 0.00 3.95
2123 2228 3.433306 TTCATTCACCCCTTCGTTCAT 57.567 42.857 0.00 0.00 0.00 2.57
2124 2229 3.433306 TCATTCACCCCTTCGTTCATT 57.567 42.857 0.00 0.00 0.00 2.57
2125 2230 3.343617 TCATTCACCCCTTCGTTCATTC 58.656 45.455 0.00 0.00 0.00 2.67
2126 2231 2.940994 TTCACCCCTTCGTTCATTCA 57.059 45.000 0.00 0.00 0.00 2.57
2127 2232 3.433306 TTCACCCCTTCGTTCATTCAT 57.567 42.857 0.00 0.00 0.00 2.57
2128 2233 3.433306 TCACCCCTTCGTTCATTCATT 57.567 42.857 0.00 0.00 0.00 2.57
2129 2234 3.343617 TCACCCCTTCGTTCATTCATTC 58.656 45.455 0.00 0.00 0.00 2.67
2130 2235 3.081061 CACCCCTTCGTTCATTCATTCA 58.919 45.455 0.00 0.00 0.00 2.57
2131 2236 3.696051 CACCCCTTCGTTCATTCATTCAT 59.304 43.478 0.00 0.00 0.00 2.57
2132 2237 3.947834 ACCCCTTCGTTCATTCATTCATC 59.052 43.478 0.00 0.00 0.00 2.92
2133 2238 3.947196 CCCCTTCGTTCATTCATTCATCA 59.053 43.478 0.00 0.00 0.00 3.07
2134 2239 4.398988 CCCCTTCGTTCATTCATTCATCAA 59.601 41.667 0.00 0.00 0.00 2.57
2135 2240 5.105797 CCCCTTCGTTCATTCATTCATCAAA 60.106 40.000 0.00 0.00 0.00 2.69
2136 2241 6.406177 CCCCTTCGTTCATTCATTCATCAAAT 60.406 38.462 0.00 0.00 0.00 2.32
2137 2242 7.037438 CCCTTCGTTCATTCATTCATCAAATT 58.963 34.615 0.00 0.00 0.00 1.82
2138 2243 7.221452 CCCTTCGTTCATTCATTCATCAAATTC 59.779 37.037 0.00 0.00 0.00 2.17
2141 2246 8.042944 TCGTTCATTCATTCATCAAATTCTCA 57.957 30.769 0.00 0.00 0.00 3.27
2154 2262 9.281371 TCATCAAATTCTCAATATGCTAGGAAG 57.719 33.333 0.00 0.00 0.00 3.46
2162 2270 6.270927 TCTCAATATGCTAGGAAGGCTTATGT 59.729 38.462 0.00 0.00 32.77 2.29
2166 2274 4.301072 TGCTAGGAAGGCTTATGTGTTT 57.699 40.909 0.00 0.00 0.00 2.83
2167 2275 4.009675 TGCTAGGAAGGCTTATGTGTTTG 58.990 43.478 0.00 0.00 0.00 2.93
2168 2276 4.010349 GCTAGGAAGGCTTATGTGTTTGT 58.990 43.478 0.00 0.00 0.00 2.83
2174 2282 6.322712 AGGAAGGCTTATGTGTTTGTTTGTTA 59.677 34.615 0.00 0.00 0.00 2.41
2175 2283 6.981559 GGAAGGCTTATGTGTTTGTTTGTTAA 59.018 34.615 0.00 0.00 0.00 2.01
2176 2284 7.042992 GGAAGGCTTATGTGTTTGTTTGTTAAC 60.043 37.037 0.00 0.00 34.75 2.01
2177 2285 6.868622 AGGCTTATGTGTTTGTTTGTTAACA 58.131 32.000 3.59 3.59 42.34 2.41
2191 2301 1.790043 GTTAACAATTTGTGTGGCGGC 59.210 47.619 0.00 0.00 40.60 6.53
2386 2496 7.741027 AATGCATCAATGAGAGGTAACATAG 57.259 36.000 0.00 0.00 41.41 2.23
2551 2755 6.711645 CCAGAGTTCTATCCAGGTACTACTAC 59.288 46.154 0.00 0.00 36.02 2.73
2584 2789 7.121463 ACAAACAGTAATGTAGTTTCAACACCA 59.879 33.333 0.00 0.00 33.54 4.17
2588 2797 7.719633 ACAGTAATGTAGTTTCAACACCAGATT 59.280 33.333 0.00 0.00 0.00 2.40
2598 2807 9.097257 AGTTTCAACACCAGATTAAAATTTGTG 57.903 29.630 0.00 0.00 0.00 3.33
2599 2808 9.092876 GTTTCAACACCAGATTAAAATTTGTGA 57.907 29.630 8.93 0.00 0.00 3.58
2600 2809 8.641499 TTCAACACCAGATTAAAATTTGTGAC 57.359 30.769 8.93 0.00 0.00 3.67
2763 2972 2.742372 CAGTGCGCCGCCTACTTT 60.742 61.111 6.63 0.00 0.00 2.66
2845 3054 3.683937 GTTGGTTGCCGCTGCCAT 61.684 61.111 0.00 0.00 36.33 4.40
2846 3055 2.916703 TTGGTTGCCGCTGCCATT 60.917 55.556 0.00 0.00 36.33 3.16
2848 3057 2.432972 GGTTGCCGCTGCCATTTG 60.433 61.111 0.00 0.00 36.33 2.32
2849 3058 2.339712 GTTGCCGCTGCCATTTGT 59.660 55.556 0.00 0.00 36.33 2.83
2850 3059 2.023223 GTTGCCGCTGCCATTTGTG 61.023 57.895 0.00 0.00 36.33 3.33
2851 3060 2.497173 TTGCCGCTGCCATTTGTGT 61.497 52.632 0.00 0.00 36.33 3.72
2852 3061 2.025767 TTGCCGCTGCCATTTGTGTT 62.026 50.000 0.00 0.00 36.33 3.32
2853 3062 1.300853 GCCGCTGCCATTTGTGTTT 60.301 52.632 0.00 0.00 0.00 2.83
2854 3063 1.284297 GCCGCTGCCATTTGTGTTTC 61.284 55.000 0.00 0.00 0.00 2.78
2855 3064 0.667184 CCGCTGCCATTTGTGTTTCC 60.667 55.000 0.00 0.00 0.00 3.13
2856 3065 0.031857 CGCTGCCATTTGTGTTTCCA 59.968 50.000 0.00 0.00 0.00 3.53
2857 3066 1.501169 GCTGCCATTTGTGTTTCCAC 58.499 50.000 0.00 0.00 42.19 4.02
2858 3067 1.769733 CTGCCATTTGTGTTTCCACG 58.230 50.000 0.00 0.00 44.92 4.94
2859 3068 1.336440 CTGCCATTTGTGTTTCCACGA 59.664 47.619 0.00 0.00 44.92 4.35
2860 3069 1.066303 TGCCATTTGTGTTTCCACGAC 59.934 47.619 0.00 0.00 44.92 4.34
2861 3070 1.601914 GCCATTTGTGTTTCCACGACC 60.602 52.381 0.00 0.00 44.92 4.79
2862 3071 1.678627 CCATTTGTGTTTCCACGACCA 59.321 47.619 0.00 0.00 44.92 4.02
2863 3072 2.099921 CCATTTGTGTTTCCACGACCAA 59.900 45.455 0.00 0.00 44.92 3.67
2864 3073 2.923605 TTTGTGTTTCCACGACCAAC 57.076 45.000 0.00 0.00 44.92 3.77
2865 3074 2.116827 TTGTGTTTCCACGACCAACT 57.883 45.000 0.00 0.00 44.92 3.16
2866 3075 1.374560 TGTGTTTCCACGACCAACTG 58.625 50.000 0.00 0.00 44.92 3.16
2867 3076 0.028902 GTGTTTCCACGACCAACTGC 59.971 55.000 0.00 0.00 0.00 4.40
2900 3109 9.868277 TTCTCTCTGTTTCTTATCTTTCTGATC 57.132 33.333 0.00 0.00 36.65 2.92
3031 3243 2.353579 ACAGGCAAACAACAACTACGAC 59.646 45.455 0.00 0.00 0.00 4.34
3048 3264 1.130749 CGACGACCAAGAGAGGTACTG 59.869 57.143 0.00 0.00 43.38 2.74
3051 3267 1.546476 CGACCAAGAGAGGTACTGCTT 59.454 52.381 0.00 0.00 43.38 3.91
3061 3277 3.006323 AGAGGTACTGCTTCTCAAGTGTG 59.994 47.826 0.00 0.00 41.55 3.82
3062 3278 1.801178 GGTACTGCTTCTCAAGTGTGC 59.199 52.381 0.00 0.00 0.00 4.57
3063 3279 2.483876 GTACTGCTTCTCAAGTGTGCA 58.516 47.619 0.00 0.00 0.00 4.57
3065 3281 1.878088 ACTGCTTCTCAAGTGTGCATG 59.122 47.619 0.00 0.00 33.02 4.06
3066 3282 1.878088 CTGCTTCTCAAGTGTGCATGT 59.122 47.619 0.00 0.00 33.02 3.21
3068 3284 3.678289 TGCTTCTCAAGTGTGCATGTAT 58.322 40.909 0.00 0.00 0.00 2.29
3069 3285 4.831107 TGCTTCTCAAGTGTGCATGTATA 58.169 39.130 0.00 0.00 0.00 1.47
3070 3286 5.430886 TGCTTCTCAAGTGTGCATGTATAT 58.569 37.500 0.00 0.00 0.00 0.86
3071 3287 5.295045 TGCTTCTCAAGTGTGCATGTATATG 59.705 40.000 0.00 0.00 37.36 1.78
3080 3324 6.005823 AGTGTGCATGTATATGTGCCATTAT 58.994 36.000 1.14 0.00 40.56 1.28
3084 3328 6.372381 GTGCATGTATATGTGCCATTATCTGA 59.628 38.462 1.14 0.00 40.56 3.27
3089 3335 8.326680 TGTATATGTGCCATTATCTGATGTTG 57.673 34.615 0.00 0.00 0.00 3.33
3090 3336 8.156165 TGTATATGTGCCATTATCTGATGTTGA 58.844 33.333 0.00 0.00 0.00 3.18
3091 3337 9.170734 GTATATGTGCCATTATCTGATGTTGAT 57.829 33.333 0.00 0.00 0.00 2.57
3092 3338 6.570672 ATGTGCCATTATCTGATGTTGATC 57.429 37.500 0.00 0.00 0.00 2.92
3093 3339 4.512571 TGTGCCATTATCTGATGTTGATCG 59.487 41.667 0.00 0.00 0.00 3.69
3094 3340 4.751600 GTGCCATTATCTGATGTTGATCGA 59.248 41.667 0.00 0.00 0.00 3.59
3101 3347 4.639135 TCTGATGTTGATCGAATCGAGT 57.361 40.909 12.00 0.00 39.91 4.18
3102 3348 4.998788 TCTGATGTTGATCGAATCGAGTT 58.001 39.130 12.00 0.00 39.91 3.01
3103 3349 5.410924 TCTGATGTTGATCGAATCGAGTTT 58.589 37.500 12.00 0.00 39.91 2.66
3108 3354 4.747605 TGTTGATCGAATCGAGTTTGTTCA 59.252 37.500 12.00 5.89 39.91 3.18
3120 3366 5.049474 TCGAGTTTGTTCATCCTTGTTCATG 60.049 40.000 0.00 0.00 0.00 3.07
3122 3368 3.940209 TTGTTCATCCTTGTTCATGCC 57.060 42.857 0.00 0.00 0.00 4.40
3125 3371 3.833650 TGTTCATCCTTGTTCATGCCATT 59.166 39.130 0.00 0.00 0.00 3.16
3126 3372 4.178540 GTTCATCCTTGTTCATGCCATTG 58.821 43.478 0.00 0.00 0.00 2.82
3137 3383 1.994779 CATGCCATTGCTCGGTTTTTC 59.005 47.619 0.00 0.00 38.71 2.29
3154 3401 1.825090 TTCATCGCAGCAACCAGATT 58.175 45.000 0.00 0.00 0.00 2.40
3187 3434 3.982372 GAGCCCGTTCGCATCGTCA 62.982 63.158 0.00 0.00 0.00 4.35
3220 3467 1.097547 ACGGCATATGAACAGGCAGC 61.098 55.000 6.97 0.00 0.00 5.25
3339 3587 0.881118 GGAATCAGCAAAGCAACCGA 59.119 50.000 0.00 0.00 0.00 4.69
3385 3633 4.444022 GGACATAATGCAGAGGAGACACAT 60.444 45.833 0.00 0.00 0.00 3.21
3398 3646 2.476619 GAGACACATGACACAGTTTCGG 59.523 50.000 0.00 0.00 0.00 4.30
3433 3683 3.051081 AGAGGTGACACATGAAAGAGC 57.949 47.619 8.08 0.00 0.00 4.09
3449 3699 6.634805 TGAAAGAGCGAGATCTTTTCATACT 58.365 36.000 16.06 0.00 46.84 2.12
3841 4136 7.112452 ACATATGACTGCAGTCTGTGTATAA 57.888 36.000 38.81 21.91 44.99 0.98
3842 4137 7.730084 ACATATGACTGCAGTCTGTGTATAAT 58.270 34.615 38.81 26.08 44.99 1.28
3843 4138 7.654923 ACATATGACTGCAGTCTGTGTATAATG 59.345 37.037 38.81 28.69 44.99 1.90
3844 4139 5.405935 TGACTGCAGTCTGTGTATAATGT 57.594 39.130 38.81 6.79 44.99 2.71
3845 4140 5.793817 TGACTGCAGTCTGTGTATAATGTT 58.206 37.500 38.81 5.22 44.99 2.71
3913 5212 7.867445 AAAATAGCAAACATAGAACAAACCG 57.133 32.000 0.00 0.00 0.00 4.44
3914 5213 6.569179 AATAGCAAACATAGAACAAACCGT 57.431 33.333 0.00 0.00 0.00 4.83
3919 5218 5.623673 GCAAACATAGAACAAACCGTAACTG 59.376 40.000 0.00 0.00 0.00 3.16
3920 5219 6.512091 GCAAACATAGAACAAACCGTAACTGA 60.512 38.462 0.00 0.00 0.00 3.41
3923 5222 2.476821 AGAACAAACCGTAACTGACCG 58.523 47.619 0.00 0.00 0.00 4.79
3949 5248 3.000724 GCTTCAATCATCTCGTGCAGTAC 59.999 47.826 0.00 0.00 0.00 2.73
3955 5254 2.820197 TCATCTCGTGCAGTACTCAACT 59.180 45.455 0.00 0.00 39.81 3.16
4011 5310 3.316308 CCAAGTCAACCAAGAAGTTCCAG 59.684 47.826 0.00 0.00 0.00 3.86
4064 5363 2.557317 GACTGAACAAACCAACCGAGA 58.443 47.619 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.560068 GGGAAATGATACTACCAGCGTTG 59.440 47.826 0.00 0.00 0.00 4.10
39 40 3.857157 TGGGGAAATGATACTACCAGC 57.143 47.619 0.00 0.00 0.00 4.85
42 43 5.310857 AGGATCTTGGGGAAATGATACTACC 59.689 44.000 0.00 0.00 29.15 3.18
56 61 3.878667 GCCGGGGAGGATCTTGGG 61.879 72.222 2.18 0.00 45.00 4.12
133 142 0.459899 CGACCATGATCGACCTTCCA 59.540 55.000 2.28 0.00 45.13 3.53
207 218 2.949678 CGCGGTTGATCGAGGACG 60.950 66.667 0.00 0.00 41.26 4.79
208 219 1.586564 CTCGCGGTTGATCGAGGAC 60.587 63.158 6.13 0.00 45.89 3.85
209 220 2.798689 CTCGCGGTTGATCGAGGA 59.201 61.111 6.13 0.00 45.89 3.71
212 223 0.524414 TTCTTCTCGCGGTTGATCGA 59.476 50.000 6.13 0.00 0.00 3.59
214 225 3.674423 CAATTTCTTCTCGCGGTTGATC 58.326 45.455 6.13 0.00 0.00 2.92
215 226 2.159517 GCAATTTCTTCTCGCGGTTGAT 60.160 45.455 6.13 0.00 0.00 2.57
232 243 2.671914 GCGTTGATGTTGGACATGCAAT 60.672 45.455 0.00 0.00 39.27 3.56
235 246 0.794229 CGCGTTGATGTTGGACATGC 60.794 55.000 0.00 0.00 39.27 4.06
258 269 1.004560 CTCTGCCGTGTGATGTGGT 60.005 57.895 0.00 0.00 0.00 4.16
259 270 2.393768 GCTCTGCCGTGTGATGTGG 61.394 63.158 0.00 0.00 0.00 4.17
263 275 1.153289 GGATGCTCTGCCGTGTGAT 60.153 57.895 0.00 0.00 0.00 3.06
264 276 2.265739 GGATGCTCTGCCGTGTGA 59.734 61.111 0.00 0.00 0.00 3.58
316 328 4.753662 TCTCCCCTAGTGGCGCGT 62.754 66.667 8.43 0.00 0.00 6.01
318 330 2.442272 TCTCTCCCCTAGTGGCGC 60.442 66.667 0.00 0.00 0.00 6.53
325 341 0.263172 CCCTTCTGCTCTCTCCCCTA 59.737 60.000 0.00 0.00 0.00 3.53
328 344 1.002274 TCCCCTTCTGCTCTCTCCC 59.998 63.158 0.00 0.00 0.00 4.30
347 363 3.650070 TGATCATATGGAGACTGCGTC 57.350 47.619 2.13 1.15 0.00 5.19
426 442 1.268133 CCAACCCAAACACAACGTACG 60.268 52.381 15.01 15.01 0.00 3.67
429 445 0.612453 ACCCAACCCAAACACAACGT 60.612 50.000 0.00 0.00 0.00 3.99
511 560 2.287188 CCGTGTGAAATATGCTGGATGC 60.287 50.000 0.00 0.00 43.25 3.91
544 602 5.927030 CGATAAATCCACGGACAAATATGG 58.073 41.667 0.00 0.00 0.00 2.74
554 612 1.959226 CGGCCCGATAAATCCACGG 60.959 63.158 0.00 0.00 45.24 4.94
573 631 2.017113 GCCAGGTCCAACCGGAATAAG 61.017 57.143 9.46 0.00 45.20 1.73
590 648 2.488891 GCTATATCAACCATGGGTGCCA 60.489 50.000 25.89 15.01 35.34 4.92
806 885 2.815298 CGACGGGAGAGAGAGACGC 61.815 68.421 0.00 0.00 0.00 5.19
834 914 0.678395 ATTGGTTGGTTGATTGCGCA 59.322 45.000 5.66 5.66 0.00 6.09
835 915 1.336702 TGATTGGTTGGTTGATTGCGC 60.337 47.619 0.00 0.00 0.00 6.09
836 916 2.721274 TGATTGGTTGGTTGATTGCG 57.279 45.000 0.00 0.00 0.00 4.85
837 917 4.567971 TGATTGATTGGTTGGTTGATTGC 58.432 39.130 0.00 0.00 0.00 3.56
839 919 7.179694 AGAGATTGATTGATTGGTTGGTTGATT 59.820 33.333 0.00 0.00 0.00 2.57
840 920 6.666546 AGAGATTGATTGATTGGTTGGTTGAT 59.333 34.615 0.00 0.00 0.00 2.57
841 921 6.012113 AGAGATTGATTGATTGGTTGGTTGA 58.988 36.000 0.00 0.00 0.00 3.18
842 922 6.276832 AGAGATTGATTGATTGGTTGGTTG 57.723 37.500 0.00 0.00 0.00 3.77
844 924 5.337009 GCAAGAGATTGATTGATTGGTTGGT 60.337 40.000 0.00 0.00 0.00 3.67
845 925 5.107133 GCAAGAGATTGATTGATTGGTTGG 58.893 41.667 0.00 0.00 0.00 3.77
847 927 5.620654 CGTGCAAGAGATTGATTGATTGGTT 60.621 40.000 0.00 0.00 0.00 3.67
849 929 4.142534 ACGTGCAAGAGATTGATTGATTGG 60.143 41.667 6.65 0.00 0.00 3.16
851 931 5.633830 AACGTGCAAGAGATTGATTGATT 57.366 34.783 6.65 0.00 0.00 2.57
852 932 5.633830 AAACGTGCAAGAGATTGATTGAT 57.366 34.783 6.65 0.00 0.00 2.57
892 985 2.768253 TCACTCGACAATGGCTGAAT 57.232 45.000 0.00 0.00 0.00 2.57
914 1008 5.923733 AAAACCAACAAGTAATCACCACA 57.076 34.783 0.00 0.00 0.00 4.17
1036 1130 2.608988 CTCCACCTCCTGCACCCT 60.609 66.667 0.00 0.00 0.00 4.34
1443 1540 3.909285 GCGGCGGAGTAGTACCCC 61.909 72.222 9.78 0.00 0.00 4.95
1491 1588 0.962356 GTCTCGAGGACACCCCGTTA 60.962 60.000 13.56 0.00 43.94 3.18
1638 1735 1.073125 TCTATCTCCAGGCTCTCGAGG 59.927 57.143 13.56 4.50 0.00 4.63
1641 1738 2.559698 TCTCTATCTCCAGGCTCTCG 57.440 55.000 0.00 0.00 0.00 4.04
1842 1939 0.173708 AGCCGACTCACCTTTCGATC 59.826 55.000 0.00 0.00 37.43 3.69
1857 1954 2.403987 CGTCTACGTCCAGAGCCG 59.596 66.667 0.00 0.00 34.11 5.52
2081 2186 4.822036 TGATTACCCGAAATAATTGGCG 57.178 40.909 0.00 0.00 0.00 5.69
2102 2207 3.433306 TGAACGAAGGGGTGAATGAAT 57.567 42.857 0.00 0.00 0.00 2.57
2111 2216 3.947196 TGATGAATGAATGAACGAAGGGG 59.053 43.478 0.00 0.00 0.00 4.79
2112 2217 5.565592 TTGATGAATGAATGAACGAAGGG 57.434 39.130 0.00 0.00 0.00 3.95
2114 2219 8.906636 AGAATTTGATGAATGAATGAACGAAG 57.093 30.769 0.00 0.00 0.00 3.79
2115 2220 8.513774 TGAGAATTTGATGAATGAATGAACGAA 58.486 29.630 0.00 0.00 0.00 3.85
2116 2221 8.042944 TGAGAATTTGATGAATGAATGAACGA 57.957 30.769 0.00 0.00 0.00 3.85
2117 2222 8.677871 TTGAGAATTTGATGAATGAATGAACG 57.322 30.769 0.00 0.00 0.00 3.95
2125 2230 9.841880 CCTAGCATATTGAGAATTTGATGAATG 57.158 33.333 0.00 0.00 0.00 2.67
2126 2231 9.803507 TCCTAGCATATTGAGAATTTGATGAAT 57.196 29.630 0.00 0.00 0.00 2.57
2127 2232 9.631257 TTCCTAGCATATTGAGAATTTGATGAA 57.369 29.630 0.00 0.00 0.00 2.57
2128 2233 9.281371 CTTCCTAGCATATTGAGAATTTGATGA 57.719 33.333 0.00 0.00 0.00 2.92
2129 2234 8.512956 CCTTCCTAGCATATTGAGAATTTGATG 58.487 37.037 0.00 0.00 0.00 3.07
2130 2235 7.176340 GCCTTCCTAGCATATTGAGAATTTGAT 59.824 37.037 0.00 0.00 0.00 2.57
2131 2236 6.488006 GCCTTCCTAGCATATTGAGAATTTGA 59.512 38.462 0.00 0.00 0.00 2.69
2132 2237 6.489361 AGCCTTCCTAGCATATTGAGAATTTG 59.511 38.462 0.00 0.00 0.00 2.32
2133 2238 6.608922 AGCCTTCCTAGCATATTGAGAATTT 58.391 36.000 0.00 0.00 0.00 1.82
2134 2239 6.198237 AGCCTTCCTAGCATATTGAGAATT 57.802 37.500 0.00 0.00 0.00 2.17
2135 2240 5.839517 AGCCTTCCTAGCATATTGAGAAT 57.160 39.130 0.00 0.00 0.00 2.40
2136 2241 5.636903 AAGCCTTCCTAGCATATTGAGAA 57.363 39.130 0.00 0.00 0.00 2.87
2137 2242 6.270927 ACATAAGCCTTCCTAGCATATTGAGA 59.729 38.462 0.00 0.00 0.00 3.27
2138 2243 6.370994 CACATAAGCCTTCCTAGCATATTGAG 59.629 42.308 0.00 0.00 0.00 3.02
2141 2246 6.192970 ACACATAAGCCTTCCTAGCATATT 57.807 37.500 0.00 0.00 0.00 1.28
2154 2262 7.527084 TTGTTAACAAACAAACACATAAGCC 57.473 32.000 18.54 0.00 39.46 4.35
2162 2270 7.576236 CCACACAAATTGTTAACAAACAAACA 58.424 30.769 23.97 0.49 44.70 2.83
2166 2274 4.327357 CGCCACACAAATTGTTAACAAACA 59.673 37.500 23.97 2.84 39.55 2.83
2167 2275 4.260011 CCGCCACACAAATTGTTAACAAAC 60.260 41.667 23.97 5.64 39.55 2.93
2168 2276 3.865745 CCGCCACACAAATTGTTAACAAA 59.134 39.130 23.97 8.78 39.55 2.83
2174 2282 1.068921 GGCCGCCACACAAATTGTT 59.931 52.632 3.91 0.00 35.67 2.83
2175 2283 2.086251 CTGGCCGCCACACAAATTGT 62.086 55.000 8.43 0.00 39.97 2.71
2176 2284 1.373246 CTGGCCGCCACACAAATTG 60.373 57.895 8.43 0.00 0.00 2.32
2177 2285 2.573083 CCTGGCCGCCACACAAATT 61.573 57.895 8.43 0.00 0.00 1.82
2228 2338 1.237285 ACATTCGCTGGTCTTGGCAC 61.237 55.000 0.00 0.00 0.00 5.01
2386 2496 6.603940 AAGATAGCCAGGATGAAGAGTATC 57.396 41.667 0.00 0.00 39.69 2.24
2420 2544 8.850156 ACTAAGTTGTATGAATGCTTCTTTTGT 58.150 29.630 0.00 0.00 0.00 2.83
2425 2549 8.616076 GCATTACTAAGTTGTATGAATGCTTCT 58.384 33.333 8.93 0.00 34.20 2.85
2429 2553 8.131100 ACATGCATTACTAAGTTGTATGAATGC 58.869 33.333 0.00 9.20 37.06 3.56
2460 2664 0.621082 TTGTTGGTCCTGTCCACACA 59.379 50.000 0.00 0.00 37.20 3.72
2556 2761 9.429600 GTGTTGAAACTACATTACTGTTTGTAC 57.570 33.333 0.00 0.00 36.79 2.90
2588 2797 9.211485 GGTAGTGTTAGCTAGTCACAAATTTTA 57.789 33.333 23.41 10.41 34.94 1.52
2598 2807 6.095720 AGTTCATCTGGTAGTGTTAGCTAGTC 59.904 42.308 0.00 0.00 0.00 2.59
2599 2808 5.952947 AGTTCATCTGGTAGTGTTAGCTAGT 59.047 40.000 0.00 0.00 0.00 2.57
2600 2809 6.458232 AGTTCATCTGGTAGTGTTAGCTAG 57.542 41.667 0.00 0.00 0.00 3.42
2763 2972 1.451927 GTCCCCGATGCTGCAATCA 60.452 57.895 6.36 0.00 0.00 2.57
2787 2996 0.840722 GGGAGTGGGAGTTGAAGGGA 60.841 60.000 0.00 0.00 0.00 4.20
2830 3039 2.916703 AAATGGCAGCGGCAACCA 60.917 55.556 11.88 15.13 42.43 3.67
2837 3046 0.031857 TGGAAACACAAATGGCAGCG 59.968 50.000 0.00 0.00 33.40 5.18
2849 3058 0.393132 TGCAGTTGGTCGTGGAAACA 60.393 50.000 0.00 0.00 38.70 2.83
2850 3059 0.307760 CTGCAGTTGGTCGTGGAAAC 59.692 55.000 5.25 0.00 0.00 2.78
2851 3060 0.107410 ACTGCAGTTGGTCGTGGAAA 60.107 50.000 15.25 0.00 0.00 3.13
2852 3061 0.531974 GACTGCAGTTGGTCGTGGAA 60.532 55.000 22.65 0.00 0.00 3.53
2853 3062 1.069090 GACTGCAGTTGGTCGTGGA 59.931 57.895 22.65 0.00 0.00 4.02
2854 3063 0.532862 AAGACTGCAGTTGGTCGTGG 60.533 55.000 22.65 0.00 37.52 4.94
2855 3064 1.299541 AAAGACTGCAGTTGGTCGTG 58.700 50.000 22.65 0.00 37.52 4.35
2856 3065 1.940613 GAAAAGACTGCAGTTGGTCGT 59.059 47.619 22.65 3.41 37.52 4.34
2857 3066 2.213499 AGAAAAGACTGCAGTTGGTCG 58.787 47.619 22.65 0.00 37.52 4.79
2858 3067 3.471680 AGAGAAAAGACTGCAGTTGGTC 58.528 45.455 22.65 15.48 0.00 4.02
2859 3068 3.135530 AGAGAGAAAAGACTGCAGTTGGT 59.864 43.478 22.65 6.13 0.00 3.67
2860 3069 3.497640 CAGAGAGAAAAGACTGCAGTTGG 59.502 47.826 22.65 0.00 0.00 3.77
2861 3070 4.125703 ACAGAGAGAAAAGACTGCAGTTG 58.874 43.478 22.65 13.24 34.25 3.16
2862 3071 4.414337 ACAGAGAGAAAAGACTGCAGTT 57.586 40.909 22.65 4.27 34.25 3.16
2863 3072 4.414337 AACAGAGAGAAAAGACTGCAGT 57.586 40.909 21.88 21.88 34.25 4.40
2864 3073 5.055812 AGAAACAGAGAGAAAAGACTGCAG 58.944 41.667 13.48 13.48 34.25 4.41
2865 3074 5.028549 AGAAACAGAGAGAAAAGACTGCA 57.971 39.130 0.00 0.00 34.25 4.41
2866 3075 7.602265 AGATAAGAAACAGAGAGAAAAGACTGC 59.398 37.037 0.00 0.00 34.25 4.40
2867 3076 9.487790 AAGATAAGAAACAGAGAGAAAAGACTG 57.512 33.333 0.00 0.00 36.58 3.51
2900 3109 4.655762 TGGAACCTGAAGACGAGATATG 57.344 45.455 0.00 0.00 0.00 1.78
2903 3112 2.234908 CCTTGGAACCTGAAGACGAGAT 59.765 50.000 0.00 0.00 0.00 2.75
2904 3113 1.618837 CCTTGGAACCTGAAGACGAGA 59.381 52.381 0.00 0.00 0.00 4.04
2905 3114 1.618837 TCCTTGGAACCTGAAGACGAG 59.381 52.381 0.00 0.00 0.00 4.18
3031 3243 1.178276 AGCAGTACCTCTCTTGGTCG 58.822 55.000 0.00 0.00 41.22 4.79
3048 3264 5.295292 ACATATACATGCACACTTGAGAAGC 59.705 40.000 0.00 0.00 35.39 3.86
3051 3267 4.571984 GCACATATACATGCACACTTGAGA 59.428 41.667 5.38 0.00 41.65 3.27
3056 3272 3.280197 TGGCACATATACATGCACACT 57.720 42.857 11.17 0.00 43.93 3.55
3071 3287 4.751600 TCGATCAACATCAGATAATGGCAC 59.248 41.667 0.00 0.00 0.00 5.01
3080 3324 4.639135 ACTCGATTCGATCAACATCAGA 57.361 40.909 9.54 0.00 34.61 3.27
3084 3328 5.408299 TGAACAAACTCGATTCGATCAACAT 59.592 36.000 9.54 0.00 34.61 2.71
3089 3335 4.806247 AGGATGAACAAACTCGATTCGATC 59.194 41.667 9.54 3.80 34.61 3.69
3090 3336 4.759782 AGGATGAACAAACTCGATTCGAT 58.240 39.130 9.54 0.00 34.61 3.59
3091 3337 4.188247 AGGATGAACAAACTCGATTCGA 57.812 40.909 8.70 8.70 0.00 3.71
3092 3338 4.152402 ACAAGGATGAACAAACTCGATTCG 59.848 41.667 0.00 0.00 0.00 3.34
3093 3339 5.613358 ACAAGGATGAACAAACTCGATTC 57.387 39.130 0.00 0.00 0.00 2.52
3094 3340 5.530915 TGAACAAGGATGAACAAACTCGATT 59.469 36.000 0.00 0.00 0.00 3.34
3101 3347 3.640498 TGGCATGAACAAGGATGAACAAA 59.360 39.130 0.00 0.00 0.00 2.83
3102 3348 3.229293 TGGCATGAACAAGGATGAACAA 58.771 40.909 0.00 0.00 0.00 2.83
3103 3349 2.874014 TGGCATGAACAAGGATGAACA 58.126 42.857 0.00 0.00 0.00 3.18
3108 3354 2.429610 GAGCAATGGCATGAACAAGGAT 59.570 45.455 0.00 0.00 44.61 3.24
3120 3366 2.262211 GATGAAAAACCGAGCAATGGC 58.738 47.619 0.00 0.00 41.61 4.40
3122 3368 1.913403 GCGATGAAAAACCGAGCAATG 59.087 47.619 0.00 0.00 0.00 2.82
3125 3371 0.516877 CTGCGATGAAAAACCGAGCA 59.483 50.000 0.00 0.00 0.00 4.26
3126 3372 0.794605 GCTGCGATGAAAAACCGAGC 60.795 55.000 0.00 0.00 0.00 5.03
3137 3383 1.089112 TCAATCTGGTTGCTGCGATG 58.911 50.000 0.00 0.00 37.74 3.84
3220 3467 5.065474 TGGTAGTTCGTGTTTCTTTCTTTGG 59.935 40.000 0.00 0.00 0.00 3.28
3339 3587 5.817816 CCGCCTCTATCTACAGAAAAACAAT 59.182 40.000 0.00 0.00 0.00 2.71
3385 3633 2.159212 TCGTTCTTCCGAAACTGTGTCA 60.159 45.455 0.00 0.00 33.15 3.58
3414 3662 1.728971 CGCTCTTTCATGTGTCACCTC 59.271 52.381 0.00 0.00 0.00 3.85
3424 3674 7.271511 AGTATGAAAAGATCTCGCTCTTTCAT 58.728 34.615 24.90 24.90 43.05 2.57
3433 3683 9.302345 TGCTAGTAAAAGTATGAAAAGATCTCG 57.698 33.333 0.00 0.00 0.00 4.04
3449 3699 7.946207 TCACCATTTTGAATGTGCTAGTAAAA 58.054 30.769 0.00 0.00 0.00 1.52
3596 3846 2.289569 TGCCCTTTCAAAATGATGGCAC 60.290 45.455 12.10 0.00 39.42 5.01
3805 4095 7.718314 ACTGCAGTCATATGTCATTTGTGATAT 59.282 33.333 15.25 0.00 0.00 1.63
3841 4136 4.096984 GCACATTTCTAGCTGCCTAAACAT 59.903 41.667 0.00 0.00 0.00 2.71
3842 4137 3.440173 GCACATTTCTAGCTGCCTAAACA 59.560 43.478 0.00 0.00 0.00 2.83
3843 4138 3.440173 TGCACATTTCTAGCTGCCTAAAC 59.560 43.478 0.00 0.00 0.00 2.01
3844 4139 3.684908 TGCACATTTCTAGCTGCCTAAA 58.315 40.909 0.00 0.00 0.00 1.85
3845 4140 3.348647 TGCACATTTCTAGCTGCCTAA 57.651 42.857 0.00 0.00 0.00 2.69
3887 5186 8.846607 CGGTTTGTTCTATGTTTGCTATTTTAC 58.153 33.333 0.00 0.00 0.00 2.01
3913 5212 1.774639 TGAAGCGAACGGTCAGTTAC 58.225 50.000 0.00 0.00 44.35 2.50
3914 5213 2.512485 TTGAAGCGAACGGTCAGTTA 57.488 45.000 0.00 0.00 44.35 2.24
3919 5218 2.271800 AGATGATTGAAGCGAACGGTC 58.728 47.619 0.00 0.00 0.00 4.79
3920 5219 2.271800 GAGATGATTGAAGCGAACGGT 58.728 47.619 0.00 0.00 0.00 4.83
3923 5222 2.535732 GCACGAGATGATTGAAGCGAAC 60.536 50.000 0.00 0.00 0.00 3.95
3992 5291 3.199946 TGTCTGGAACTTCTTGGTTGACT 59.800 43.478 0.00 0.00 0.00 3.41
4064 5363 3.450457 GTCAGAGGAGATCCAATGACTGT 59.550 47.826 20.69 0.00 44.03 3.55


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

AutoCloner maintained by Alex Coulton.