Multiple sequence alignment - TraesCS1B01G132500

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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 TraesCS1B01G132500 chr1B 100.000 3950 0 0 1 3950 166660177 166656228 0.000000e+00 7295
1 TraesCS1B01G132500 chr1D 95.539 3407 124 19 1 3400 110011574 110008189 0.000000e+00 5424
2 TraesCS1B01G132500 chr1D 91.513 542 32 8 3422 3950 110008134 110007594 0.000000e+00 734
3 TraesCS1B01G132500 chr1D 87.293 181 23 0 1 181 446661552 446661372 1.440000e-49 207
4 TraesCS1B01G132500 chr1A 94.992 3315 135 17 1 3305 113880979 113877686 0.000000e+00 5173
5 TraesCS1B01G132500 chr1A 88.395 698 43 15 3291 3950 113875289 113874592 0.000000e+00 806
6 TraesCS1B01G132500 chr2B 91.981 212 15 2 1 211 416251220 416251010 2.980000e-76 296
7 TraesCS1B01G132500 chr3A 90.521 211 20 0 1 211 77346747 77346537 3.010000e-71 279
8 TraesCS1B01G132500 chr7D 88.462 182 19 2 1 181 490745632 490745452 6.650000e-53 219
9 TraesCS1B01G132500 chr7D 87.568 185 21 2 1 184 490779023 490778840 3.090000e-51 213
10 TraesCS1B01G132500 chr5B 87.845 181 22 0 1 181 299946370 299946190 3.090000e-51 213
11 TraesCS1B01G132500 chr3B 87.912 182 20 2 1 181 785576242 785576422 3.090000e-51 213


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 TraesCS1B01G132500 chr1B 166656228 166660177 3949 True 7295.0 7295 100.0000 1 3950 1 chr1B.!!$R1 3949
1 TraesCS1B01G132500 chr1D 110007594 110011574 3980 True 3079.0 5424 93.5260 1 3950 2 chr1D.!!$R2 3949
2 TraesCS1B01G132500 chr1A 113874592 113880979 6387 True 2989.5 5173 91.6935 1 3950 2 chr1A.!!$R1 3949

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
125 127 0.109532 TGAATCAAGTTGCCGGACCA 59.890 50.000 5.05 0.0 0.00 4.02 F
1625 1629 1.003118 GTGTCCATTGGCTCTGGTGTA 59.997 52.381 0.00 0.0 35.19 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1843 1.095600 GATCCTCCCGCAGTTTTTCC 58.904 55.0 0.0 0.0 0.00 3.13 R
3366 5792 0.106335 CTTCAGCATCTGCCTCCGAT 59.894 55.0 0.0 0.0 43.38 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
84 85 5.164620 TGCTGTCCATTCTTATTGTCTGA 57.835 39.130 0.00 0.00 0.00 3.27
86 87 4.333926 GCTGTCCATTCTTATTGTCTGACC 59.666 45.833 5.17 0.00 0.00 4.02
92 93 6.051717 CCATTCTTATTGTCTGACCGAGATT 58.948 40.000 5.17 0.00 31.63 2.40
97 98 3.744238 TTGTCTGACCGAGATTGTTCA 57.256 42.857 5.17 0.00 31.63 3.18
99 101 2.288825 TGTCTGACCGAGATTGTTCACC 60.289 50.000 5.17 0.00 31.63 4.02
120 122 2.662791 CGTTCACTGAATCAAGTTGCCG 60.663 50.000 0.00 0.00 0.00 5.69
125 127 0.109532 TGAATCAAGTTGCCGGACCA 59.890 50.000 5.05 0.00 0.00 4.02
149 151 1.206878 ATCAGGCAGGCACACATAGA 58.793 50.000 0.00 0.00 0.00 1.98
159 161 2.484417 GGCACACATAGATGTAGCTGCT 60.484 50.000 7.57 7.57 39.39 4.24
160 162 2.799412 GCACACATAGATGTAGCTGCTC 59.201 50.000 4.91 0.00 39.39 4.26
216 218 4.158394 TGCCAGCCATTTTATTCTCTCAAC 59.842 41.667 0.00 0.00 0.00 3.18
222 224 5.185828 GCCATTTTATTCTCTCAACAGGGTT 59.814 40.000 0.00 0.00 0.00 4.11
223 225 6.625960 GCCATTTTATTCTCTCAACAGGGTTC 60.626 42.308 0.00 0.00 0.00 3.62
267 269 4.158579 AGCTACAAGATCTGATCAACGTCA 59.841 41.667 19.12 0.00 0.00 4.35
276 278 3.818773 TCTGATCAACGTCACTGTCTGTA 59.181 43.478 0.00 0.00 0.00 2.74
278 280 4.733850 TGATCAACGTCACTGTCTGTATC 58.266 43.478 0.00 0.00 0.00 2.24
281 283 4.795268 TCAACGTCACTGTCTGTATCTTC 58.205 43.478 0.00 0.00 0.00 2.87
282 284 4.519350 TCAACGTCACTGTCTGTATCTTCT 59.481 41.667 0.00 0.00 0.00 2.85
287 289 7.603651 ACGTCACTGTCTGTATCTTCTTTAAT 58.396 34.615 0.00 0.00 0.00 1.40
660 663 2.471743 GTGTGTGAAAGACGTACTCTGC 59.528 50.000 0.00 0.00 29.10 4.26
724 727 1.450312 GGCAGGTCACTCAATCGGG 60.450 63.158 0.00 0.00 0.00 5.14
743 746 3.307480 CGGGGTTGAAGTAAAGTCCTGAT 60.307 47.826 0.00 0.00 0.00 2.90
812 815 4.766891 CCCTTTGATCCTGTGTTACATTGT 59.233 41.667 0.00 0.00 0.00 2.71
918 921 4.511454 TCACTTCTGTTGTGTGTATCTTGC 59.489 41.667 0.00 0.00 36.83 4.01
924 927 3.324846 TGTTGTGTGTATCTTGCTCTCCT 59.675 43.478 0.00 0.00 0.00 3.69
925 928 4.202357 TGTTGTGTGTATCTTGCTCTCCTT 60.202 41.667 0.00 0.00 0.00 3.36
970 973 7.974482 TGAATCATTATCAGGTCTGCATAAG 57.026 36.000 0.00 0.00 0.00 1.73
1218 1221 4.442052 GCTAGACAATAGTGATGTGCAGGA 60.442 45.833 0.00 0.00 0.00 3.86
1267 1270 4.569761 TCTAGTCTAACAAGCTATGCGG 57.430 45.455 0.00 0.00 0.00 5.69
1270 1273 1.327764 GTCTAACAAGCTATGCGGTGC 59.672 52.381 0.00 0.00 0.00 5.01
1547 1551 2.577563 TGCCCCTGAATCAGATTCTGAA 59.422 45.455 24.61 3.60 44.04 3.02
1625 1629 1.003118 GTGTCCATTGGCTCTGGTGTA 59.997 52.381 0.00 0.00 35.19 2.90
1904 1908 1.136147 CATTGGAAGCTGCGCTGTC 59.864 57.895 16.05 6.27 39.62 3.51
2037 2041 2.485814 GCTTGGAGAACTTTCAGCGAAT 59.514 45.455 0.00 0.00 0.00 3.34
2113 2117 8.237811 AGTTATCACAAATTTTGAAGGTGAGT 57.762 30.769 15.81 2.02 41.27 3.41
2146 2150 0.761187 ACAGGAGAAGTTGCAGCTCA 59.239 50.000 2.60 0.00 0.00 4.26
2223 2227 0.183492 AGGTGGTGAAGCTGCAAGAA 59.817 50.000 0.00 0.00 34.56 2.52
2310 2314 4.090090 ACCTAGAAGCACAGCTAGAAAGA 58.910 43.478 0.00 0.00 38.25 2.52
2316 2320 1.919918 CACAGCTAGAAAGAGCCTCG 58.080 55.000 0.00 0.00 43.97 4.63
2405 2409 5.972107 AAACATTCACTGGAGAAATCTGG 57.028 39.130 0.00 0.00 0.00 3.86
2521 2525 3.209410 GACAGGGCAGAAGAATACATGG 58.791 50.000 0.00 0.00 0.00 3.66
2576 2580 2.821969 ACCTTGCCAATCTTACAAGCAG 59.178 45.455 0.00 0.00 39.55 4.24
2700 2704 3.330267 CCACCTTAGTCAGCTTCAACTC 58.670 50.000 0.00 0.00 0.00 3.01
2709 2713 0.036577 AGCTTCAACTCGAGCATGCT 60.037 50.000 22.92 22.92 0.00 3.79
2718 2722 4.090138 ACTCGAGCATGCTAAGATATCG 57.910 45.455 27.68 21.69 0.00 2.92
2727 2731 3.491342 TGCTAAGATATCGGCAGAGTCT 58.509 45.455 13.98 0.00 0.00 3.24
2751 2755 0.764271 TTGTGCATGAGTCCCTGTCA 59.236 50.000 0.00 0.00 0.00 3.58
2754 2758 1.002430 GTGCATGAGTCCCTGTCAGAA 59.998 52.381 0.00 0.00 0.00 3.02
2957 2961 3.368571 GGCAGCCTGACCAAGTGC 61.369 66.667 3.29 0.00 0.00 4.40
2958 2962 2.595463 GCAGCCTGACCAAGTGCA 60.595 61.111 0.00 0.00 34.18 4.57
2961 2965 1.001641 AGCCTGACCAAGTGCATCC 60.002 57.895 0.00 0.00 0.00 3.51
2962 2966 1.001641 GCCTGACCAAGTGCATCCT 60.002 57.895 0.00 0.00 0.00 3.24
2963 2967 0.610232 GCCTGACCAAGTGCATCCTT 60.610 55.000 0.00 0.00 0.00 3.36
2975 2982 1.339055 TGCATCCTTCTTGTTCCCGAG 60.339 52.381 0.00 0.00 0.00 4.63
2996 3003 5.551760 AGATCCTTTTGTGCTTACGAATG 57.448 39.130 0.00 0.00 0.00 2.67
2999 3006 2.556622 CCTTTTGTGCTTACGAATGGGT 59.443 45.455 0.00 0.00 0.00 4.51
3001 3008 4.216687 CCTTTTGTGCTTACGAATGGGTTA 59.783 41.667 0.00 0.00 0.00 2.85
3016 3024 6.747280 CGAATGGGTTATGTAGCTTTTTCAAG 59.253 38.462 0.00 0.00 0.00 3.02
3049 3057 3.809279 TCTGTTATGTCTGTGTGCAACTG 59.191 43.478 0.00 0.00 38.04 3.16
3064 3072 4.424061 GCAACTGCAATGTAATGTGAGA 57.576 40.909 0.00 0.00 41.59 3.27
3066 3074 4.618489 GCAACTGCAATGTAATGTGAGAAC 59.382 41.667 0.00 0.00 41.59 3.01
3086 3094 2.398252 CATGTCAGTCATGTCTGGCT 57.602 50.000 22.09 8.04 46.18 4.75
3087 3095 2.277969 CATGTCAGTCATGTCTGGCTC 58.722 52.381 22.09 12.55 46.18 4.70
3088 3096 0.244721 TGTCAGTCATGTCTGGCTCG 59.755 55.000 22.09 0.00 40.28 5.03
3089 3097 0.459237 GTCAGTCATGTCTGGCTCGG 60.459 60.000 15.97 0.00 34.25 4.63
3090 3098 0.611896 TCAGTCATGTCTGGCTCGGA 60.612 55.000 18.04 0.00 34.25 4.55
3091 3099 0.247460 CAGTCATGTCTGGCTCGGAA 59.753 55.000 11.62 0.00 34.25 4.30
3092 3100 0.976641 AGTCATGTCTGGCTCGGAAA 59.023 50.000 0.00 0.00 28.85 3.13
3128 3136 0.592637 TCCGTCGTCGTTTGCTCTTA 59.407 50.000 0.71 0.00 35.01 2.10
3143 3151 7.950496 CGTTTGCTCTTATTACTTCTGTTACAC 59.050 37.037 0.00 0.00 0.00 2.90
3195 3209 4.729227 ATGTTTTGGTCTTTGAAACGGT 57.271 36.364 0.00 0.00 36.36 4.83
3208 3222 3.061322 TGAAACGGTGATGTTAGTTCGG 58.939 45.455 0.00 0.00 0.00 4.30
3210 3224 0.319083 ACGGTGATGTTAGTTCGGCA 59.681 50.000 0.00 0.00 0.00 5.69
3212 3226 2.006888 CGGTGATGTTAGTTCGGCAAT 58.993 47.619 0.00 0.00 0.00 3.56
3215 3229 3.063997 GGTGATGTTAGTTCGGCAATCTG 59.936 47.826 0.00 0.00 0.00 2.90
3225 3239 3.612251 GCAATCTGTGGCATGCCT 58.388 55.556 35.53 14.23 36.94 4.75
3244 3258 4.081972 TGCCTGAGTCAGTCTTGTATCTTC 60.082 45.833 18.74 0.00 0.00 2.87
3250 3264 6.151144 TGAGTCAGTCTTGTATCTTCGAATCA 59.849 38.462 0.00 0.00 0.00 2.57
3270 3284 7.484641 CGAATCAAAAGTTGAGTTTGTCAAGAA 59.515 33.333 0.00 0.00 46.18 2.52
3272 3286 9.487790 AATCAAAAGTTGAGTTTGTCAAGAAAA 57.512 25.926 0.00 0.00 46.18 2.29
3274 3288 8.356657 TCAAAAGTTGAGTTTGTCAAGAAAAGA 58.643 29.630 0.00 0.00 46.18 2.52
3275 3289 8.642020 CAAAAGTTGAGTTTGTCAAGAAAAGAG 58.358 33.333 0.00 0.00 46.18 2.85
3276 3290 7.687941 AAGTTGAGTTTGTCAAGAAAAGAGA 57.312 32.000 0.00 0.00 46.18 3.10
3289 3303 6.547141 TCAAGAAAAGAGAGAATTTTCCTGCA 59.453 34.615 7.37 0.00 44.21 4.41
3312 5738 9.866798 TGCATATGTCTCAAGAGTATTATGATC 57.133 33.333 4.29 0.00 0.00 2.92
3321 5747 7.674120 TCAAGAGTATTATGATCCAGATGTGG 58.326 38.462 1.45 1.45 46.63 4.17
3353 5779 5.393787 GCTGCAGGAAGAAATTCATCATTCA 60.394 40.000 17.12 0.00 0.00 2.57
3387 5813 1.224039 GGAGGCAGATGCTGAAGCT 59.776 57.895 4.59 0.00 42.66 3.74
3393 5820 0.179702 CAGATGCTGAAGCTAGCCCA 59.820 55.000 12.13 9.17 43.02 5.36
3396 5823 0.107312 ATGCTGAAGCTAGCCCAGTG 60.107 55.000 26.00 11.20 43.02 3.66
3402 5835 3.136791 GCTAGCCCAGTGCAAGCC 61.137 66.667 2.29 0.00 44.83 4.35
3411 5844 0.322975 CAGTGCAAGCCAGGTCTAGT 59.677 55.000 0.00 0.00 0.00 2.57
3420 5853 2.307098 AGCCAGGTCTAGTGCATCTTTT 59.693 45.455 0.00 0.00 0.00 2.27
3421 5854 3.084786 GCCAGGTCTAGTGCATCTTTTT 58.915 45.455 0.00 0.00 0.00 1.94
3422 5855 3.119708 GCCAGGTCTAGTGCATCTTTTTG 60.120 47.826 0.00 0.00 0.00 2.44
3424 5857 4.520492 CCAGGTCTAGTGCATCTTTTTGTT 59.480 41.667 0.00 0.00 0.00 2.83
3425 5858 5.010012 CCAGGTCTAGTGCATCTTTTTGTTT 59.990 40.000 0.00 0.00 0.00 2.83
3426 5859 6.145535 CAGGTCTAGTGCATCTTTTTGTTTC 58.854 40.000 0.00 0.00 0.00 2.78
3427 5860 6.016777 CAGGTCTAGTGCATCTTTTTGTTTCT 60.017 38.462 0.00 0.00 0.00 2.52
3428 5861 7.173218 CAGGTCTAGTGCATCTTTTTGTTTCTA 59.827 37.037 0.00 0.00 0.00 2.10
3429 5862 7.885399 AGGTCTAGTGCATCTTTTTGTTTCTAT 59.115 33.333 0.00 0.00 0.00 1.98
3461 5922 4.334443 CAAATTCCTATGAAGTTCACGCG 58.666 43.478 7.96 3.53 36.70 6.01
3465 5926 3.250744 TCCTATGAAGTTCACGCGAAAG 58.749 45.455 15.93 1.66 31.43 2.62
3476 5937 0.392998 ACGCGAAAGAGGCCATTGAT 60.393 50.000 15.93 0.00 34.13 2.57
3483 5944 6.503524 GCGAAAGAGGCCATTGATTAATTTA 58.496 36.000 5.01 0.00 0.00 1.40
3535 5996 7.369803 TCAAGTCTGAAGTTATTGATTCTGC 57.630 36.000 0.00 0.00 0.00 4.26
3542 6003 8.768019 TCTGAAGTTATTGATTCTGCGAATATG 58.232 33.333 4.19 0.00 0.00 1.78
3596 6062 4.970662 TCTATTTTTGCTCATGCCTCAC 57.029 40.909 0.00 0.00 38.71 3.51
3598 6064 0.597568 TTTTTGCTCATGCCTCACCG 59.402 50.000 0.00 0.00 38.71 4.94
3634 6100 2.341846 TTCCCGATCAATTGCCTACC 57.658 50.000 0.00 0.00 0.00 3.18
3829 6298 9.865321 ATCCATCACATTGTTCTTTTGATTTAG 57.135 29.630 0.00 0.00 0.00 1.85
3876 6349 2.029380 GCCTGGAAAATACGCCAAAGTT 60.029 45.455 0.00 0.00 32.95 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.250513 GGATTCAGGCAAGAGGTCGT 59.749 55.000 0.00 0.00 0.00 4.34
84 85 1.069513 TGAACGGTGAACAATCTCGGT 59.930 47.619 0.00 0.00 35.09 4.69
86 87 2.155732 CAGTGAACGGTGAACAATCTCG 59.844 50.000 0.00 0.00 0.00 4.04
92 93 3.186702 TGATTCAGTGAACGGTGAACA 57.813 42.857 7.96 0.00 35.55 3.18
97 98 2.290641 GCAACTTGATTCAGTGAACGGT 59.709 45.455 7.96 2.17 0.00 4.83
99 101 2.662791 CGGCAACTTGATTCAGTGAACG 60.663 50.000 7.96 0.00 0.00 3.95
120 122 0.181350 CCTGCCTGATAGGTTGGTCC 59.819 60.000 0.00 0.00 37.80 4.46
125 127 0.035056 GTGTGCCTGCCTGATAGGTT 60.035 55.000 0.00 0.00 37.80 3.50
149 151 2.938756 GCAAAGGACAGAGCAGCTACAT 60.939 50.000 0.00 0.00 0.00 2.29
216 218 1.840737 TCCGAGAAGAGAGAACCCTG 58.159 55.000 0.00 0.00 0.00 4.45
222 224 5.241949 GCTACCAATTATCCGAGAAGAGAGA 59.758 44.000 0.00 0.00 0.00 3.10
223 225 5.242838 AGCTACCAATTATCCGAGAAGAGAG 59.757 44.000 0.00 0.00 0.00 3.20
278 280 9.921637 TGTAAACTGGGCAAATAATTAAAGAAG 57.078 29.630 0.00 0.00 0.00 2.85
281 283 8.603181 GCATGTAAACTGGGCAAATAATTAAAG 58.397 33.333 0.00 0.00 0.00 1.85
282 284 8.317679 AGCATGTAAACTGGGCAAATAATTAAA 58.682 29.630 0.00 0.00 0.00 1.52
287 289 7.777910 AGTATAGCATGTAAACTGGGCAAATAA 59.222 33.333 0.00 0.00 0.00 1.40
660 663 2.753452 GGATATGCAATGATCTGGCCAG 59.247 50.000 27.87 27.87 0.00 4.85
710 713 0.323629 TCAACCCCGATTGAGTGACC 59.676 55.000 0.00 0.00 33.62 4.02
724 727 5.998363 ACAAGATCAGGACTTTACTTCAACC 59.002 40.000 0.00 0.00 0.00 3.77
743 746 1.484038 AAGTTGCTGGCCAAACAAGA 58.516 45.000 19.92 0.04 34.68 3.02
837 840 8.191534 AGACAGTTTACTACTACAGAAACCAT 57.808 34.615 0.00 0.00 34.56 3.55
918 921 7.786030 TGGATATACAAGTGAGAAAAGGAGAG 58.214 38.462 0.00 0.00 0.00 3.20
1184 1187 8.840833 TCACTATTGTCTAGCAAACAACAATA 57.159 30.769 10.38 10.38 41.31 1.90
1218 1221 7.571919 AGACTGGAATCATACATGAATGAAGT 58.428 34.615 0.00 0.00 40.69 3.01
1267 1270 8.515414 AGAAAGGTTATATTCAGAAAACAGCAC 58.485 33.333 0.00 0.00 0.00 4.40
1431 1435 2.024918 CAAGGGTGCGATACATGCC 58.975 57.895 0.00 0.00 0.00 4.40
1547 1551 3.766591 CTGTAGATGGAGGAGACTGTGTT 59.233 47.826 0.00 0.00 44.43 3.32
1625 1629 3.118956 CCTTCTTGGATACGTCAGAGCTT 60.119 47.826 0.00 0.00 42.51 3.74
1839 1843 1.095600 GATCCTCCCGCAGTTTTTCC 58.904 55.000 0.00 0.00 0.00 3.13
1904 1908 2.223144 TCAGTCTCATTTTTGTTCGCCG 59.777 45.455 0.00 0.00 0.00 6.46
2037 2041 7.935210 TCAAGAGCAGATTTATCATGCAGATAA 59.065 33.333 11.99 11.99 45.18 1.75
2113 2117 4.415881 TCTCCTGTGACAGTTTTGCTAA 57.584 40.909 12.15 0.00 0.00 3.09
2146 2150 1.859302 AGCTCTTCAATCCGAGACCT 58.141 50.000 0.00 0.00 0.00 3.85
2223 2227 6.579666 TCTGCTTTTGTATTCTTCATTGCT 57.420 33.333 0.00 0.00 0.00 3.91
2310 2314 2.479566 TTGATTTCTCTTGCGAGGCT 57.520 45.000 0.00 0.00 37.86 4.58
2316 2320 5.295540 GTCCTGGAGTATTGATTTCTCTTGC 59.704 44.000 0.00 0.00 0.00 4.01
2405 2409 3.247648 TGTTGAAAGTTCAGCGCTAAGAC 59.752 43.478 10.99 9.36 40.72 3.01
2603 2607 2.813754 GCCAGCTTGTTATCAACTGTGA 59.186 45.455 11.66 0.00 38.41 3.58
2700 2704 1.923204 GCCGATATCTTAGCATGCTCG 59.077 52.381 26.57 19.20 0.00 5.03
2727 2731 2.681682 CAGGGACTCATGCACAATAGCA 60.682 50.000 0.00 0.00 44.24 3.49
2751 2755 2.660258 AAACCCGAGCACGCAGTTCT 62.660 55.000 9.78 0.88 41.61 3.01
2778 2782 1.768275 TGCTTCTCCACAAGTTCCTCA 59.232 47.619 0.00 0.00 0.00 3.86
2841 2845 1.815003 GTGAAGCACAGCTGCCTAATT 59.185 47.619 15.27 1.50 45.53 1.40
2957 2961 3.462021 GATCTCGGGAACAAGAAGGATG 58.538 50.000 0.00 0.00 0.00 3.51
2958 2962 2.436173 GGATCTCGGGAACAAGAAGGAT 59.564 50.000 0.00 0.00 0.00 3.24
2961 2965 3.618690 AAGGATCTCGGGAACAAGAAG 57.381 47.619 0.00 0.00 0.00 2.85
2962 2966 4.072131 CAAAAGGATCTCGGGAACAAGAA 58.928 43.478 0.00 0.00 0.00 2.52
2963 2967 3.072476 ACAAAAGGATCTCGGGAACAAGA 59.928 43.478 0.00 0.00 0.00 3.02
2975 2982 4.438744 CCCATTCGTAAGCACAAAAGGATC 60.439 45.833 0.00 0.00 37.18 3.36
2996 3003 6.430000 TCTCACTTGAAAAAGCTACATAACCC 59.570 38.462 0.00 0.00 0.00 4.11
2999 3006 8.902540 TCTTCTCACTTGAAAAAGCTACATAA 57.097 30.769 0.00 0.00 0.00 1.90
3001 3008 7.500559 AGTTCTTCTCACTTGAAAAAGCTACAT 59.499 33.333 0.00 0.00 0.00 2.29
3016 3024 6.364706 CACAGACATAACAGAGTTCTTCTCAC 59.635 42.308 0.00 0.00 44.98 3.51
3049 3057 5.106197 TGACATGGTTCTCACATTACATTGC 60.106 40.000 0.00 0.00 0.00 3.56
3174 3182 4.158764 TCACCGTTTCAAAGACCAAAACAT 59.841 37.500 0.00 0.00 33.51 2.71
3195 3209 3.684305 CACAGATTGCCGAACTAACATCA 59.316 43.478 0.00 0.00 0.00 3.07
3208 3222 1.141019 CAGGCATGCCACAGATTGC 59.859 57.895 37.18 8.13 38.92 3.56
3210 3224 0.330604 ACTCAGGCATGCCACAGATT 59.669 50.000 37.18 21.96 38.92 2.40
3212 3226 1.297689 GACTCAGGCATGCCACAGA 59.702 57.895 37.18 27.89 38.92 3.41
3215 3229 1.002868 ACTGACTCAGGCATGCCAC 60.003 57.895 37.18 21.59 38.92 5.01
3223 3237 4.396478 TCGAAGATACAAGACTGACTCAGG 59.604 45.833 10.86 0.00 35.51 3.86
3225 3239 5.959618 TTCGAAGATACAAGACTGACTCA 57.040 39.130 0.00 0.00 35.04 3.41
3244 3258 6.966632 TCTTGACAAACTCAACTTTTGATTCG 59.033 34.615 1.97 0.00 39.30 3.34
3250 3264 8.576442 TCTCTTTTCTTGACAAACTCAACTTTT 58.424 29.630 0.00 0.00 33.65 2.27
3270 3284 7.833183 AGACATATGCAGGAAAATTCTCTCTTT 59.167 33.333 1.58 0.00 0.00 2.52
3272 3286 6.897986 AGACATATGCAGGAAAATTCTCTCT 58.102 36.000 1.58 0.00 0.00 3.10
3274 3288 6.656902 TGAGACATATGCAGGAAAATTCTCT 58.343 36.000 1.58 0.00 0.00 3.10
3275 3289 6.932356 TGAGACATATGCAGGAAAATTCTC 57.068 37.500 1.58 5.08 0.00 2.87
3276 3290 7.114754 TCTTGAGACATATGCAGGAAAATTCT 58.885 34.615 1.58 0.00 0.00 2.40
3312 5738 0.617413 AGCTTCCTCACCACATCTGG 59.383 55.000 0.00 0.00 44.26 3.86
3321 5747 0.322975 TCTTCCTGCAGCTTCCTCAC 59.677 55.000 8.66 0.00 0.00 3.51
3353 5779 3.643320 TGCCTCCGATTCAGTGAGATTAT 59.357 43.478 0.00 0.00 0.00 1.28
3366 5792 0.106335 CTTCAGCATCTGCCTCCGAT 59.894 55.000 0.00 0.00 43.38 4.18
3387 5813 2.352422 CTGGCTTGCACTGGGCTA 59.648 61.111 2.50 0.00 45.15 3.93
3393 5820 0.322975 CACTAGACCTGGCTTGCACT 59.677 55.000 0.00 0.00 0.00 4.40
3396 5823 0.393537 ATGCACTAGACCTGGCTTGC 60.394 55.000 0.00 1.07 0.00 4.01
3402 5835 5.695851 AACAAAAAGATGCACTAGACCTG 57.304 39.130 0.00 0.00 0.00 4.00
3420 5853 9.134734 GGAATTTGCGACAATTTATAGAAACAA 57.865 29.630 0.00 0.00 0.00 2.83
3421 5854 8.519526 AGGAATTTGCGACAATTTATAGAAACA 58.480 29.630 0.00 0.00 0.00 2.83
3422 5855 8.911247 AGGAATTTGCGACAATTTATAGAAAC 57.089 30.769 0.00 0.00 0.00 2.78
3425 5858 9.554395 TCATAGGAATTTGCGACAATTTATAGA 57.446 29.630 0.00 0.00 0.00 1.98
3428 5861 8.686334 ACTTCATAGGAATTTGCGACAATTTAT 58.314 29.630 0.00 0.00 31.34 1.40
3429 5862 8.050778 ACTTCATAGGAATTTGCGACAATTTA 57.949 30.769 0.00 0.00 31.34 1.40
3436 5897 4.092821 CGTGAACTTCATAGGAATTTGCGA 59.907 41.667 0.00 0.00 30.03 5.10
3437 5898 4.334443 CGTGAACTTCATAGGAATTTGCG 58.666 43.478 0.00 0.00 31.34 4.85
3523 5984 7.227314 ACTTCAGCATATTCGCAGAATCAATAA 59.773 33.333 6.99 0.00 45.90 1.40
3524 5985 6.707608 ACTTCAGCATATTCGCAGAATCAATA 59.292 34.615 6.99 0.00 45.90 1.90
3535 5996 6.653273 TCAGAAAAGACTTCAGCATATTCG 57.347 37.500 0.00 0.00 0.00 3.34
3578 6044 1.203052 CGGTGAGGCATGAGCAAAAAT 59.797 47.619 0.00 0.00 44.61 1.82
3585 6051 0.804989 GGAAAACGGTGAGGCATGAG 59.195 55.000 0.00 0.00 0.00 2.90
3596 6062 5.407502 GGGAAAATATGACAAGGAAAACGG 58.592 41.667 0.00 0.00 0.00 4.44
3598 6064 6.262193 TCGGGAAAATATGACAAGGAAAAC 57.738 37.500 0.00 0.00 0.00 2.43
3647 6113 2.193248 GAAGCCCAGGATTCCGGG 59.807 66.667 21.51 21.51 39.28 5.73
3876 6349 2.825532 GCCAGTTATGAAAGGGAAAGCA 59.174 45.455 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.