Multiple sequence alignment - TraesCS4D01G086800

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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 TraesCS4D01G086800 chr4D 100.000 5830 0 0 1 5830 62103307 62097478 0.000000e+00 10767
1 TraesCS4D01G086800 chr4D 94.495 109 5 1 3163 3270 54412667 54412559 3.610000e-37 167
2 TraesCS4D01G086800 chr4B 97.583 3186 54 10 1 3174 90499711 90502885 0.000000e+00 5435
3 TraesCS4D01G086800 chr4B 95.333 2571 91 11 3268 5830 90502884 90505433 0.000000e+00 4056
4 TraesCS4D01G086800 chr4B 97.030 101 3 0 3169 3269 216814994 216815094 2.790000e-38 171
5 TraesCS4D01G086800 chr4A 97.450 3176 67 8 1 3174 535432630 535429467 0.000000e+00 5404
6 TraesCS4D01G086800 chr4A 95.585 2514 89 11 3268 5775 535429468 535426971 0.000000e+00 4008
7 TraesCS4D01G086800 chr3D 97.143 105 3 0 3166 3270 19269821 19269717 1.670000e-40 178
8 TraesCS4D01G086800 chr3D 94.393 107 6 0 3163 3269 495531617 495531511 1.300000e-36 165
9 TraesCS4D01G086800 chr7D 97.959 98 2 0 3172 3269 407716533 407716630 2.790000e-38 171
10 TraesCS4D01G086800 chr7D 96.117 103 4 0 3167 3269 407261199 407261301 1.000000e-37 169
11 TraesCS4D01G086800 chr2D 95.327 107 5 0 3163 3269 107204070 107204176 2.790000e-38 171
12 TraesCS4D01G086800 chr6A 94.444 108 5 1 3163 3269 600701741 600701848 1.300000e-36 165
13 TraesCS4D01G086800 chr5A 94.444 108 5 1 3163 3269 66095878 66095771 1.300000e-36 165


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 TraesCS4D01G086800 chr4D 62097478 62103307 5829 True 10767.0 10767 100.0000 1 5830 1 chr4D.!!$R2 5829
1 TraesCS4D01G086800 chr4B 90499711 90505433 5722 False 4745.5 5435 96.4580 1 5830 2 chr4B.!!$F2 5829
2 TraesCS4D01G086800 chr4A 535426971 535432630 5659 True 4706.0 5404 96.5175 1 5775 2 chr4A.!!$R1 5774

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
258 259 1.141657 TGTCCTTTGCTGTGAAGAGCT 59.858 47.619 0.86 0.00 39.90 4.09 F
665 677 1.931906 TGCTCTTGATGCTAGCTTCG 58.068 50.000 21.67 11.32 37.16 3.79 F
1889 1901 2.149578 CTGCAACTCCAGAACTCAAGG 58.850 52.381 0.00 0.00 34.77 3.61 F
2374 2386 3.134623 TGATCTGGTTGACTCACAGTTGT 59.865 43.478 0.00 0.00 34.02 3.32 F
4075 4089 1.271379 TCACGAAGTACCTGAACGCAT 59.729 47.619 0.00 0.00 41.61 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1590 2.311463 TGCAAAACGGGGAAATTGAGA 58.689 42.857 0.00 0.0 0.00 3.27 R
2660 2672 0.764369 TGACCAGGAACCAGCAGAGT 60.764 55.000 0.00 0.0 0.00 3.24 R
3094 3108 1.093972 TTCAGGCCGTATGCACAATG 58.906 50.000 0.00 0.0 43.89 2.82 R
4366 4383 0.799534 GCAGCATAAACAGCGCCAAG 60.800 55.000 2.29 0.0 37.01 3.61 R
5603 5629 0.471591 ACGGGGCAACGGGGTATATA 60.472 55.000 5.83 0.0 38.39 0.86 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
64 65 2.356535 CCACCTTCCTCTCCTCCATTTG 60.357 54.545 0.00 0.00 0.00 2.32
258 259 1.141657 TGTCCTTTGCTGTGAAGAGCT 59.858 47.619 0.86 0.00 39.90 4.09
350 351 7.771183 TGCTGACTTCTTAACTTGTGATTTTT 58.229 30.769 0.00 0.00 0.00 1.94
413 414 7.755582 ATTTCGATTGTTTTAGCCTTAATGC 57.244 32.000 0.00 0.00 0.00 3.56
424 425 4.972514 AGCCTTAATGCTTTGCTCTTAC 57.027 40.909 0.00 0.00 38.85 2.34
428 429 6.071165 AGCCTTAATGCTTTGCTCTTACAATT 60.071 34.615 0.00 0.00 38.85 2.32
665 677 1.931906 TGCTCTTGATGCTAGCTTCG 58.068 50.000 21.67 11.32 37.16 3.79
716 728 8.899771 GGCTGCTTACAGTATAATTCCTTTTTA 58.100 33.333 0.00 0.00 46.30 1.52
758 770 8.133627 CCTTGGATAGAGTTAGAAATTGCAATG 58.866 37.037 13.82 0.00 0.00 2.82
836 848 8.926092 AGTTTCTCCTAGTTTTGCTTTCTTAT 57.074 30.769 0.00 0.00 0.00 1.73
892 904 9.710900 GAAGGAAATGTTTGGACATATCTTTTT 57.289 29.630 0.00 0.00 45.58 1.94
1218 1230 4.623932 TGACAGAAATACAGAAGTGCCT 57.376 40.909 0.00 0.00 0.00 4.75
1404 1416 4.156556 TCAGCTGAACATTTGAATACTGGC 59.843 41.667 15.67 0.00 0.00 4.85
1531 1543 8.078060 TGATGATACAAGTTACTTCATCAGGA 57.922 34.615 18.15 8.57 44.56 3.86
1889 1901 2.149578 CTGCAACTCCAGAACTCAAGG 58.850 52.381 0.00 0.00 34.77 3.61
1924 1936 9.987272 TCACAGGTGATTATGATACTATTCTTG 57.013 33.333 0.00 0.00 34.14 3.02
2374 2386 3.134623 TGATCTGGTTGACTCACAGTTGT 59.865 43.478 0.00 0.00 34.02 3.32
2566 2578 8.462016 CGAGAATTTCAAAGATTTACCTCCATT 58.538 33.333 0.00 0.00 0.00 3.16
2699 2711 7.598278 TGGTCATCGCATTTTAGTTTGTAAAT 58.402 30.769 0.00 0.00 0.00 1.40
3064 3077 5.188555 TGAAGCATTTGGACTAGATCTGAGT 59.811 40.000 5.18 5.07 0.00 3.41
3079 3092 6.601332 AGATCTGAGTTTGGTTAGTTTTCCA 58.399 36.000 0.00 0.00 0.00 3.53
3172 3186 5.546499 TCAGATTGGTCCAGTAGTACCTTTT 59.454 40.000 0.00 0.00 36.67 2.27
3173 3187 6.727231 TCAGATTGGTCCAGTAGTACCTTTTA 59.273 38.462 0.00 0.00 36.67 1.52
3174 3188 6.817140 CAGATTGGTCCAGTAGTACCTTTTAC 59.183 42.308 0.00 0.00 36.67 2.01
3175 3189 6.729569 AGATTGGTCCAGTAGTACCTTTTACT 59.270 38.462 0.00 0.00 36.67 2.24
3176 3190 5.990120 TGGTCCAGTAGTACCTTTTACTC 57.010 43.478 0.00 0.00 36.67 2.59
3177 3191 4.774200 TGGTCCAGTAGTACCTTTTACTCC 59.226 45.833 0.00 0.00 36.67 3.85
3178 3192 4.161189 GGTCCAGTAGTACCTTTTACTCCC 59.839 50.000 0.00 0.00 32.72 4.30
3179 3193 5.022122 GTCCAGTAGTACCTTTTACTCCCT 58.978 45.833 0.00 0.00 0.00 4.20
3180 3194 5.126869 GTCCAGTAGTACCTTTTACTCCCTC 59.873 48.000 0.00 0.00 0.00 4.30
3181 3195 4.405036 CCAGTAGTACCTTTTACTCCCTCC 59.595 50.000 0.00 0.00 0.00 4.30
3182 3196 4.097589 CAGTAGTACCTTTTACTCCCTCCG 59.902 50.000 0.00 0.00 0.00 4.63
3183 3197 3.181393 AGTACCTTTTACTCCCTCCGT 57.819 47.619 0.00 0.00 0.00 4.69
3184 3198 3.514539 AGTACCTTTTACTCCCTCCGTT 58.485 45.455 0.00 0.00 0.00 4.44
3185 3199 3.513119 AGTACCTTTTACTCCCTCCGTTC 59.487 47.826 0.00 0.00 0.00 3.95
3186 3200 1.627329 ACCTTTTACTCCCTCCGTTCC 59.373 52.381 0.00 0.00 0.00 3.62
3187 3201 1.626825 CCTTTTACTCCCTCCGTTCCA 59.373 52.381 0.00 0.00 0.00 3.53
3188 3202 2.039348 CCTTTTACTCCCTCCGTTCCAA 59.961 50.000 0.00 0.00 0.00 3.53
3189 3203 3.497227 CCTTTTACTCCCTCCGTTCCAAA 60.497 47.826 0.00 0.00 0.00 3.28
3190 3204 3.860968 TTTACTCCCTCCGTTCCAAAA 57.139 42.857 0.00 0.00 0.00 2.44
3191 3205 4.376225 TTTACTCCCTCCGTTCCAAAAT 57.624 40.909 0.00 0.00 0.00 1.82
3192 3206 5.502089 TTTACTCCCTCCGTTCCAAAATA 57.498 39.130 0.00 0.00 0.00 1.40
3193 3207 5.502089 TTACTCCCTCCGTTCCAAAATAA 57.498 39.130 0.00 0.00 0.00 1.40
3194 3208 4.376225 ACTCCCTCCGTTCCAAAATAAA 57.624 40.909 0.00 0.00 0.00 1.40
3195 3209 4.930696 ACTCCCTCCGTTCCAAAATAAAT 58.069 39.130 0.00 0.00 0.00 1.40
3196 3210 4.705023 ACTCCCTCCGTTCCAAAATAAATG 59.295 41.667 0.00 0.00 0.00 2.32
3197 3211 4.924625 TCCCTCCGTTCCAAAATAAATGA 58.075 39.130 0.00 0.00 0.00 2.57
3198 3212 4.703093 TCCCTCCGTTCCAAAATAAATGAC 59.297 41.667 0.00 0.00 0.00 3.06
3199 3213 4.705023 CCCTCCGTTCCAAAATAAATGACT 59.295 41.667 0.00 0.00 0.00 3.41
3200 3214 5.163652 CCCTCCGTTCCAAAATAAATGACTC 60.164 44.000 0.00 0.00 0.00 3.36
3201 3215 5.414454 CCTCCGTTCCAAAATAAATGACTCA 59.586 40.000 0.00 0.00 0.00 3.41
3202 3216 6.072175 CCTCCGTTCCAAAATAAATGACTCAA 60.072 38.462 0.00 0.00 0.00 3.02
3203 3217 6.674066 TCCGTTCCAAAATAAATGACTCAAC 58.326 36.000 0.00 0.00 0.00 3.18
3204 3218 6.488683 TCCGTTCCAAAATAAATGACTCAACT 59.511 34.615 0.00 0.00 0.00 3.16
3205 3219 7.013846 TCCGTTCCAAAATAAATGACTCAACTT 59.986 33.333 0.00 0.00 0.00 2.66
3206 3220 7.651704 CCGTTCCAAAATAAATGACTCAACTTT 59.348 33.333 0.00 0.00 0.00 2.66
3207 3221 8.479280 CGTTCCAAAATAAATGACTCAACTTTG 58.521 33.333 0.00 0.00 0.00 2.77
3208 3222 9.313118 GTTCCAAAATAAATGACTCAACTTTGT 57.687 29.630 0.00 0.00 0.00 2.83
3210 3224 9.959749 TCCAAAATAAATGACTCAACTTTGTAC 57.040 29.630 0.00 0.00 0.00 2.90
3211 3225 9.965824 CCAAAATAAATGACTCAACTTTGTACT 57.034 29.630 0.00 0.00 0.00 2.73
3242 3256 7.797038 AGTACAAAGTTAGTACAAAGTTGGG 57.203 36.000 6.30 0.00 43.24 4.12
3243 3257 7.341030 AGTACAAAGTTAGTACAAAGTTGGGT 58.659 34.615 6.30 0.00 43.24 4.51
3244 3258 8.485392 AGTACAAAGTTAGTACAAAGTTGGGTA 58.515 33.333 6.30 0.00 43.24 3.69
3245 3259 9.108284 GTACAAAGTTAGTACAAAGTTGGGTAA 57.892 33.333 0.00 0.00 41.08 2.85
3246 3260 8.756486 ACAAAGTTAGTACAAAGTTGGGTAAT 57.244 30.769 0.00 0.00 0.00 1.89
3247 3261 8.843262 ACAAAGTTAGTACAAAGTTGGGTAATC 58.157 33.333 0.00 0.00 0.00 1.75
3248 3262 9.063615 CAAAGTTAGTACAAAGTTGGGTAATCT 57.936 33.333 0.00 0.00 0.00 2.40
3255 3269 9.020731 AGTACAAAGTTGGGTAATCTATTTTGG 57.979 33.333 0.00 0.00 0.00 3.28
3256 3270 9.016438 GTACAAAGTTGGGTAATCTATTTTGGA 57.984 33.333 0.00 0.00 0.00 3.53
3257 3271 8.485578 ACAAAGTTGGGTAATCTATTTTGGAA 57.514 30.769 0.00 0.00 0.00 3.53
3258 3272 8.364894 ACAAAGTTGGGTAATCTATTTTGGAAC 58.635 33.333 0.00 0.00 0.00 3.62
3259 3273 6.753107 AGTTGGGTAATCTATTTTGGAACG 57.247 37.500 0.00 0.00 0.00 3.95
3260 3274 5.650703 AGTTGGGTAATCTATTTTGGAACGG 59.349 40.000 0.00 0.00 0.00 4.44
3261 3275 5.438698 TGGGTAATCTATTTTGGAACGGA 57.561 39.130 0.00 0.00 0.00 4.69
3262 3276 5.433526 TGGGTAATCTATTTTGGAACGGAG 58.566 41.667 0.00 0.00 0.00 4.63
3263 3277 4.820173 GGGTAATCTATTTTGGAACGGAGG 59.180 45.833 0.00 0.00 0.00 4.30
3264 3278 4.820173 GGTAATCTATTTTGGAACGGAGGG 59.180 45.833 0.00 0.00 0.00 4.30
3265 3279 4.855298 AATCTATTTTGGAACGGAGGGA 57.145 40.909 0.00 0.00 0.00 4.20
3266 3280 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
3292 3306 3.019564 ACCTAGCATCATGCCAAAACTC 58.980 45.455 5.84 0.00 46.52 3.01
3476 3490 1.580845 CTTGCAGCCCTTCGGACTTG 61.581 60.000 0.00 0.00 0.00 3.16
3617 3631 7.559897 TGTTAGTTGACCCAGAAATTCTTCTTT 59.440 33.333 0.00 0.00 40.05 2.52
3683 3697 7.183657 AGGAATTGAGAATCCTAGAGAAAACCT 59.816 37.037 0.00 0.00 44.24 3.50
3728 3742 1.739035 GCAGGTGCGTACAATAGCTCA 60.739 52.381 5.86 0.00 0.00 4.26
3831 3845 4.142609 ACGTGAATTGATGCACTCCTAT 57.857 40.909 0.00 0.00 32.98 2.57
3863 3877 3.820467 CCTAAAGTGGTCACATTCTGCAA 59.180 43.478 3.82 0.00 0.00 4.08
3950 3964 5.576774 GCATACCAAAACAAGGTTCAATAGC 59.423 40.000 0.00 0.00 40.54 2.97
4075 4089 1.271379 TCACGAAGTACCTGAACGCAT 59.729 47.619 0.00 0.00 41.61 4.73
4077 4091 2.597305 CACGAAGTACCTGAACGCATAC 59.403 50.000 0.00 0.00 41.61 2.39
4288 4304 4.708726 ATCAACCAAAGCATAAGTCTGC 57.291 40.909 0.00 0.00 42.62 4.26
4331 4348 2.891580 TGTCAGTTAAGCTTCGAGGACT 59.108 45.455 0.00 0.00 0.00 3.85
4366 4383 1.359848 CCAGTGATACTGTTGGCGTC 58.640 55.000 8.04 0.00 44.50 5.19
4704 4722 4.020128 AGGACTACAAGGGTAAGAGCAAAG 60.020 45.833 0.00 0.00 0.00 2.77
4749 4767 8.314361 AGTGGCTACTCAAGATGGGAACATAC 62.314 46.154 0.00 0.00 42.18 2.39
4855 4873 3.708631 AGATGATTGGGATCGAACTGTCT 59.291 43.478 0.00 0.00 34.91 3.41
4993 5011 3.828451 ACTGCCATTTTTGTACAGCTGAT 59.172 39.130 23.35 7.41 31.46 2.90
5013 5031 6.065976 TGATGATCATTACAAGAGTTGGGT 57.934 37.500 10.14 0.00 34.12 4.51
5024 5042 4.099573 ACAAGAGTTGGGTGATACCGATAG 59.900 45.833 0.00 0.00 39.83 2.08
5215 5240 9.599866 TTGTCTTCGTGATGATATTTGAAGTAT 57.400 29.630 0.00 0.00 35.51 2.12
5241 5266 5.884792 AGAAGATTTGCAAGGAAGGATGTAG 59.115 40.000 0.00 0.00 0.00 2.74
5242 5267 5.184892 AGATTTGCAAGGAAGGATGTAGT 57.815 39.130 0.00 0.00 0.00 2.73
5243 5268 6.313519 AGATTTGCAAGGAAGGATGTAGTA 57.686 37.500 0.00 0.00 0.00 1.82
5246 5271 4.202245 TGCAAGGAAGGATGTAGTACAC 57.798 45.455 4.80 0.00 0.00 2.90
5267 5292 5.643777 ACACTACAAATACCACAGATTGCTC 59.356 40.000 0.00 0.00 0.00 4.26
5279 5304 8.894768 ACCACAGATTGCTCTAGTAAATTATC 57.105 34.615 0.00 0.00 0.00 1.75
5317 5342 7.807977 ACATAGTTCTGAACAAACATTGAGT 57.192 32.000 21.50 5.10 0.00 3.41
5318 5343 8.225603 ACATAGTTCTGAACAAACATTGAGTT 57.774 30.769 21.50 0.17 43.89 3.01
5324 5349 7.019774 TCTGAACAAACATTGAGTTGAGAAG 57.980 36.000 10.43 5.89 41.19 2.85
5371 5396 2.747177 TGTAGTCCAGTATCCCACCAG 58.253 52.381 0.00 0.00 0.00 4.00
5385 5410 0.695924 CACCAGGACAACCCATGGTA 59.304 55.000 11.73 0.00 41.46 3.25
5386 5411 1.284785 CACCAGGACAACCCATGGTAT 59.715 52.381 11.73 0.00 41.46 2.73
5446 5471 2.207501 CTTGGGCCTGCCTCAGTCAT 62.208 60.000 4.53 0.00 36.10 3.06
5456 5481 5.048434 GCCTGCCTCAGTCATATAATTTTCC 60.048 44.000 0.00 0.00 0.00 3.13
5457 5482 6.064060 CCTGCCTCAGTCATATAATTTTCCA 58.936 40.000 0.00 0.00 0.00 3.53
5508 5534 0.591659 CATGATGCTGCTGGGAATCG 59.408 55.000 0.00 0.00 0.00 3.34
5643 5669 4.679654 CGTATCTTGAAAACAAAAGGTGGC 59.320 41.667 0.00 0.00 0.00 5.01
5775 5801 0.905337 GTGACTCCCTACCTGGCTGT 60.905 60.000 0.00 0.00 0.00 4.40
5810 5836 3.605749 CTGGGTGGGTGGCACTACG 62.606 68.421 18.45 1.73 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.326297 CCCCTCACTCCATTCTAATCCTC 59.674 52.174 0.00 0.00 0.00 3.71
428 429 9.912634 GTCATTCTTCTGGTTAAAATTGATTCA 57.087 29.630 0.00 0.00 0.00 2.57
892 904 9.177608 CCAAATTCCAGACTGTAATATGAAGAA 57.822 33.333 0.93 0.00 0.00 2.52
893 905 8.548025 TCCAAATTCCAGACTGTAATATGAAGA 58.452 33.333 0.93 0.00 0.00 2.87
1061 1073 9.301153 CTTGTTTAGTGCATTTAGAACAAAAGT 57.699 29.630 14.44 0.00 36.79 2.66
1218 1230 5.003804 GGCTTCTCTTTCAACTGGACATTA 58.996 41.667 0.00 0.00 0.00 1.90
1575 1587 3.005367 GCAAAACGGGGAAATTGAGAAGA 59.995 43.478 0.00 0.00 0.00 2.87
1576 1588 3.243704 TGCAAAACGGGGAAATTGAGAAG 60.244 43.478 0.00 0.00 0.00 2.85
1577 1589 2.695666 TGCAAAACGGGGAAATTGAGAA 59.304 40.909 0.00 0.00 0.00 2.87
1578 1590 2.311463 TGCAAAACGGGGAAATTGAGA 58.689 42.857 0.00 0.00 0.00 3.27
1579 1591 2.810439 TGCAAAACGGGGAAATTGAG 57.190 45.000 0.00 0.00 0.00 3.02
1580 1592 3.760580 AATGCAAAACGGGGAAATTGA 57.239 38.095 0.00 0.00 0.00 2.57
1924 1936 9.188588 CATGCATTCCAATCAAAATATCAGTAC 57.811 33.333 0.00 0.00 0.00 2.73
2660 2672 0.764369 TGACCAGGAACCAGCAGAGT 60.764 55.000 0.00 0.00 0.00 3.24
3064 3077 7.113658 TGCAATAAGTGGAAAACTAACCAAA 57.886 32.000 0.00 0.00 38.56 3.28
3079 3092 4.021280 TGCACAATGTTCCATGCAATAAGT 60.021 37.500 0.00 0.00 44.72 2.24
3094 3108 1.093972 TTCAGGCCGTATGCACAATG 58.906 50.000 0.00 0.00 43.89 2.82
3172 3186 5.502089 TTTATTTTGGAACGGAGGGAGTA 57.498 39.130 0.00 0.00 0.00 2.59
3173 3187 4.376225 TTTATTTTGGAACGGAGGGAGT 57.624 40.909 0.00 0.00 0.00 3.85
3174 3188 4.947388 TCATTTATTTTGGAACGGAGGGAG 59.053 41.667 0.00 0.00 0.00 4.30
3175 3189 4.703093 GTCATTTATTTTGGAACGGAGGGA 59.297 41.667 0.00 0.00 0.00 4.20
3176 3190 4.705023 AGTCATTTATTTTGGAACGGAGGG 59.295 41.667 0.00 0.00 0.00 4.30
3177 3191 5.414454 TGAGTCATTTATTTTGGAACGGAGG 59.586 40.000 0.00 0.00 0.00 4.30
3178 3192 6.494893 TGAGTCATTTATTTTGGAACGGAG 57.505 37.500 0.00 0.00 0.00 4.63
3179 3193 6.488683 AGTTGAGTCATTTATTTTGGAACGGA 59.511 34.615 0.00 0.00 0.00 4.69
3180 3194 6.677913 AGTTGAGTCATTTATTTTGGAACGG 58.322 36.000 0.00 0.00 0.00 4.44
3181 3195 8.479280 CAAAGTTGAGTCATTTATTTTGGAACG 58.521 33.333 0.00 0.00 0.00 3.95
3182 3196 9.313118 ACAAAGTTGAGTCATTTATTTTGGAAC 57.687 29.630 12.94 0.00 0.00 3.62
3184 3198 9.959749 GTACAAAGTTGAGTCATTTATTTTGGA 57.040 29.630 12.94 4.81 0.00 3.53
3185 3199 9.965824 AGTACAAAGTTGAGTCATTTATTTTGG 57.034 29.630 12.94 0.78 0.00 3.28
3216 3230 9.328845 CCCAACTTTGTACTAACTTTGTACTAA 57.671 33.333 12.73 10.75 40.44 2.24
3217 3231 8.485392 ACCCAACTTTGTACTAACTTTGTACTA 58.515 33.333 12.73 4.86 40.44 1.82
3218 3232 7.341030 ACCCAACTTTGTACTAACTTTGTACT 58.659 34.615 12.73 0.00 40.44 2.73
3219 3233 7.558161 ACCCAACTTTGTACTAACTTTGTAC 57.442 36.000 6.58 6.58 40.27 2.90
3220 3234 9.850198 ATTACCCAACTTTGTACTAACTTTGTA 57.150 29.630 0.00 0.00 0.00 2.41
3221 3235 8.756486 ATTACCCAACTTTGTACTAACTTTGT 57.244 30.769 0.00 0.00 0.00 2.83
3222 3236 9.063615 AGATTACCCAACTTTGTACTAACTTTG 57.936 33.333 0.00 0.00 0.00 2.77
3229 3243 9.020731 CCAAAATAGATTACCCAACTTTGTACT 57.979 33.333 0.00 0.00 0.00 2.73
3230 3244 9.016438 TCCAAAATAGATTACCCAACTTTGTAC 57.984 33.333 0.00 0.00 0.00 2.90
3231 3245 9.589461 TTCCAAAATAGATTACCCAACTTTGTA 57.411 29.630 0.00 0.00 0.00 2.41
3232 3246 8.364894 GTTCCAAAATAGATTACCCAACTTTGT 58.635 33.333 0.00 0.00 0.00 2.83
3233 3247 7.540745 CGTTCCAAAATAGATTACCCAACTTTG 59.459 37.037 0.00 0.00 0.00 2.77
3234 3248 7.309560 CCGTTCCAAAATAGATTACCCAACTTT 60.310 37.037 0.00 0.00 0.00 2.66
3235 3249 6.152154 CCGTTCCAAAATAGATTACCCAACTT 59.848 38.462 0.00 0.00 0.00 2.66
3236 3250 5.650703 CCGTTCCAAAATAGATTACCCAACT 59.349 40.000 0.00 0.00 0.00 3.16
3237 3251 5.648960 TCCGTTCCAAAATAGATTACCCAAC 59.351 40.000 0.00 0.00 0.00 3.77
3238 3252 5.817784 TCCGTTCCAAAATAGATTACCCAA 58.182 37.500 0.00 0.00 0.00 4.12
3239 3253 5.433526 CTCCGTTCCAAAATAGATTACCCA 58.566 41.667 0.00 0.00 0.00 4.51
3240 3254 4.820173 CCTCCGTTCCAAAATAGATTACCC 59.180 45.833 0.00 0.00 0.00 3.69
3241 3255 4.820173 CCCTCCGTTCCAAAATAGATTACC 59.180 45.833 0.00 0.00 0.00 2.85
3242 3256 5.677567 TCCCTCCGTTCCAAAATAGATTAC 58.322 41.667 0.00 0.00 0.00 1.89
3243 3257 5.427481 ACTCCCTCCGTTCCAAAATAGATTA 59.573 40.000 0.00 0.00 0.00 1.75
3244 3258 4.227527 ACTCCCTCCGTTCCAAAATAGATT 59.772 41.667 0.00 0.00 0.00 2.40
3245 3259 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3246 3260 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3247 3261 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3248 3262 5.502089 TTTACTCCCTCCGTTCCAAAATA 57.498 39.130 0.00 0.00 0.00 1.40
3249 3263 4.376225 TTTACTCCCTCCGTTCCAAAAT 57.624 40.909 0.00 0.00 0.00 1.82
3250 3264 3.860968 TTTACTCCCTCCGTTCCAAAA 57.139 42.857 0.00 0.00 0.00 2.44
3251 3265 3.479489 GTTTTACTCCCTCCGTTCCAAA 58.521 45.455 0.00 0.00 0.00 3.28
3252 3266 2.224597 GGTTTTACTCCCTCCGTTCCAA 60.225 50.000 0.00 0.00 0.00 3.53
3253 3267 1.348696 GGTTTTACTCCCTCCGTTCCA 59.651 52.381 0.00 0.00 0.00 3.53
3254 3268 1.627329 AGGTTTTACTCCCTCCGTTCC 59.373 52.381 0.00 0.00 0.00 3.62
3255 3269 3.678252 GCTAGGTTTTACTCCCTCCGTTC 60.678 52.174 0.00 0.00 32.08 3.95
3256 3270 2.235650 GCTAGGTTTTACTCCCTCCGTT 59.764 50.000 0.00 0.00 32.08 4.44
3257 3271 1.829849 GCTAGGTTTTACTCCCTCCGT 59.170 52.381 0.00 0.00 32.08 4.69
3258 3272 1.829222 TGCTAGGTTTTACTCCCTCCG 59.171 52.381 0.00 0.00 32.08 4.63
3259 3273 3.454812 TGATGCTAGGTTTTACTCCCTCC 59.545 47.826 0.00 0.00 32.08 4.30
3260 3274 4.755266 TGATGCTAGGTTTTACTCCCTC 57.245 45.455 0.00 0.00 32.08 4.30
3261 3275 4.687219 GCATGATGCTAGGTTTTACTCCCT 60.687 45.833 10.72 0.00 40.96 4.20
3262 3276 3.565902 GCATGATGCTAGGTTTTACTCCC 59.434 47.826 10.72 0.00 40.96 4.30
3263 3277 3.565902 GGCATGATGCTAGGTTTTACTCC 59.434 47.826 17.84 0.00 44.28 3.85
3264 3278 4.199310 TGGCATGATGCTAGGTTTTACTC 58.801 43.478 17.84 0.00 44.28 2.59
3265 3279 4.235079 TGGCATGATGCTAGGTTTTACT 57.765 40.909 17.84 0.00 44.28 2.24
3266 3280 4.981806 TTGGCATGATGCTAGGTTTTAC 57.018 40.909 17.84 0.00 44.28 2.01
3292 3306 5.922053 TGATGATCTTCACCAGGTTAGATG 58.078 41.667 15.82 3.32 0.00 2.90
3423 3437 8.279970 TCTGTTCTGAAAAACTGAAGAATTGA 57.720 30.769 0.00 0.00 37.18 2.57
3476 3490 2.617274 GCTCGGTGGACACTTTGGC 61.617 63.158 2.13 0.00 0.00 4.52
3683 3697 7.038154 GGTTTAATAGAACCATATGCAGCAA 57.962 36.000 0.00 0.00 46.66 3.91
3950 3964 2.358957 TCCTTTGGATTGAGATGTGCG 58.641 47.619 0.00 0.00 0.00 5.34
4254 4270 5.050837 GCTTTGGTTGATTAAACAGCAGTTG 60.051 40.000 0.00 0.00 40.86 3.16
4288 4304 8.400186 TGACATATTATGTGATTTTCTGCTGTG 58.600 33.333 13.93 0.00 45.03 3.66
4366 4383 0.799534 GCAGCATAAACAGCGCCAAG 60.800 55.000 2.29 0.00 37.01 3.61
4673 4690 4.000928 ACCCTTGTAGTCCTGATCAGAT 57.999 45.455 24.62 11.72 0.00 2.90
4704 4722 4.932200 CACTGGACCAGAGAAATTGACTAC 59.068 45.833 28.56 0.00 35.18 2.73
4749 4767 5.638657 GCTCATGTTCTCTAAGCATATCCTG 59.361 44.000 0.00 0.00 33.21 3.86
4760 4778 4.471904 AACATTCCGCTCATGTTCTCTA 57.528 40.909 0.00 0.00 40.17 2.43
4839 4857 5.395324 GGAATCTTAGACAGTTCGATCCCAA 60.395 44.000 0.00 0.00 0.00 4.12
4855 4873 7.523293 TGAACTTTGAAATGCTGGAATCTTA 57.477 32.000 0.00 0.00 0.00 2.10
4904 4922 7.010091 GCTCTTCTAGAGATGCTTTGTAGAAAC 59.990 40.741 7.85 0.00 45.07 2.78
4993 5011 5.497464 TCACCCAACTCTTGTAATGATCA 57.503 39.130 0.00 0.00 0.00 2.92
5013 5031 8.440059 CGCTTAAAAATAATGCTATCGGTATCA 58.560 33.333 0.00 0.00 0.00 2.15
5024 5042 4.920376 TCTGCCTCGCTTAAAAATAATGC 58.080 39.130 0.00 0.00 0.00 3.56
5215 5240 6.248433 ACATCCTTCCTTGCAAATCTTCTTA 58.752 36.000 0.00 0.00 0.00 2.10
5241 5266 6.594159 AGCAATCTGTGGTATTTGTAGTGTAC 59.406 38.462 0.00 0.00 35.75 2.90
5242 5267 6.707290 AGCAATCTGTGGTATTTGTAGTGTA 58.293 36.000 0.00 0.00 35.75 2.90
5243 5268 5.560724 AGCAATCTGTGGTATTTGTAGTGT 58.439 37.500 0.00 0.00 35.75 3.55
5246 5271 7.268586 ACTAGAGCAATCTGTGGTATTTGTAG 58.731 38.462 0.00 0.00 38.34 2.74
5279 5304 8.777865 TCAGAACTATGTTCTTTATGTTCAGG 57.222 34.615 9.89 0.00 37.03 3.86
5324 5349 6.982141 TGCTTTATCATGAGAAATTTGCCATC 59.018 34.615 15.44 0.57 0.00 3.51
5371 5396 3.222173 TGCATATACCATGGGTTGTCC 57.778 47.619 18.09 0.61 37.09 4.02
5374 5399 5.653507 GCATAATGCATATACCATGGGTTG 58.346 41.667 18.09 8.77 44.26 3.77
5508 5534 2.017049 ACCAATTGCAGCTATCGTTCC 58.983 47.619 0.00 0.00 0.00 3.62
5601 5627 2.109774 CGGGGCAACGGGGTATATATA 58.890 52.381 0.00 0.00 37.60 0.86
5602 5628 0.906775 CGGGGCAACGGGGTATATAT 59.093 55.000 0.00 0.00 37.60 0.86
5603 5629 0.471591 ACGGGGCAACGGGGTATATA 60.472 55.000 5.83 0.00 38.39 0.86
5604 5630 0.471591 TACGGGGCAACGGGGTATAT 60.472 55.000 5.83 0.00 38.39 0.86
5605 5631 0.471591 ATACGGGGCAACGGGGTATA 60.472 55.000 5.83 0.00 38.39 1.47
5606 5632 1.761500 GATACGGGGCAACGGGGTAT 61.761 60.000 5.83 0.00 38.39 2.73
5613 5639 2.554893 TGTTTTCAAGATACGGGGCAAC 59.445 45.455 0.00 0.00 0.00 4.17
5643 5669 5.781210 TGTTAGCAGGATCAGATCTACAG 57.219 43.478 10.36 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.