Multiple sequence alignment - TraesCS2A01G494800

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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 TraesCS2A01G494800 chr2A 100.000 6190 0 0 1 6190 726553994 726547805 0 11431
1 TraesCS2A01G494800 chr5A 98.357 2982 48 1 1 2981 535498370 535501351 0 5234
2 TraesCS2A01G494800 chr5A 98.240 1364 19 5 4713 6073 535501347 535502708 0 2381
3 TraesCS2A01G494800 chr4A 97.898 2997 47 3 1 2981 358819676 358822672 0 5171
4 TraesCS2A01G494800 chr4A 97.519 2983 72 2 1 2981 662771082 662768100 0 5097
5 TraesCS2A01G494800 chr4A 97.296 1738 42 4 2977 4712 28429771 28428037 0 2944
6 TraesCS2A01G494800 chr4A 97.343 1731 42 4 2982 4712 6247875 6249601 0 2939
7 TraesCS2A01G494800 chr4A 97.232 1734 45 3 2981 4712 338431069 338432801 0 2933
8 TraesCS2A01G494800 chr4A 98.016 1361 23 4 4713 6071 358822668 358824026 0 2361
9 TraesCS2A01G494800 chr4A 97.050 1356 35 5 4713 6066 662768104 662766752 0 2278
10 TraesCS2A01G494800 chr6A 97.554 2985 66 6 1 2981 585012168 585009187 0 5101
11 TraesCS2A01G494800 chr6A 97.578 1734 38 4 2981 4712 551661522 551659791 0 2966
12 TraesCS2A01G494800 chr6A 97.294 1737 41 6 2979 4712 551668410 551666677 0 2942
13 TraesCS2A01G494800 chr7B 97.184 2983 80 4 1 2981 558987214 558984234 0 5040
14 TraesCS2A01G494800 chr7B 97.509 1365 30 3 4713 6074 558984238 558982875 0 2329
15 TraesCS2A01G494800 chr5B 97.023 2990 72 7 1 2981 703515114 703512133 0 5012
16 TraesCS2A01G494800 chr5B 97.005 935 20 7 5136 6066 703511754 703510824 0 1565
17 TraesCS2A01G494800 chr1B 96.715 2983 83 9 1 2981 403618279 403621248 0 4951
18 TraesCS2A01G494800 chr1B 96.791 2431 65 7 554 2981 667558663 667561083 0 4045
19 TraesCS2A01G494800 chr1B 97.269 1355 31 5 4713 6063 667561079 667562431 0 2292
20 TraesCS2A01G494800 chr1B 96.581 936 26 6 5134 6067 403621633 403622564 0 1546
21 TraesCS2A01G494800 chr3D 97.195 1854 41 10 1134 2981 556686521 556688369 0 3125
22 TraesCS2A01G494800 chr3D 96.903 1356 34 7 4713 6066 556688365 556689714 0 2265
23 TraesCS2A01G494800 chr3A 97.458 1731 41 3 2982 4712 476372066 476373793 0 2950
24 TraesCS2A01G494800 chr7A 97.189 1743 47 2 2971 4713 710961598 710963338 0 2946
25 TraesCS2A01G494800 chr7A 97.290 1734 43 4 2981 4712 735877447 735879178 0 2939
26 TraesCS2A01G494800 chr1A 97.288 1733 43 4 2981 4712 578841873 578840144 0 2937
27 TraesCS2A01G494800 chr1A 87.677 779 86 7 4713 5489 105295561 105294791 0 898
28 TraesCS2A01G494800 chr5D 94.808 1695 82 5 1 1690 4421280 4419587 0 2638
29 TraesCS2A01G494800 chr5D 94.808 1695 82 5 1 1690 4568308 4566615 0 2638
30 TraesCS2A01G494800 chr5D 94.749 1695 83 5 1 1690 4724791 4723098 0 2632
31 TraesCS2A01G494800 chr3B 97.511 1366 24 7 4713 6075 770748832 770747474 0 2326
32 TraesCS2A01G494800 chr4B 87.933 779 84 7 4713 5489 260076026 260075256 0 909


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 TraesCS2A01G494800 chr2A 726547805 726553994 6189 True 11431.0 11431 100.0000 1 6190 1 chr2A.!!$R1 6189
1 TraesCS2A01G494800 chr5A 535498370 535502708 4338 False 3807.5 5234 98.2985 1 6073 2 chr5A.!!$F1 6072
2 TraesCS2A01G494800 chr4A 358819676 358824026 4350 False 3766.0 5171 97.9570 1 6071 2 chr4A.!!$F3 6070
3 TraesCS2A01G494800 chr4A 662766752 662771082 4330 True 3687.5 5097 97.2845 1 6066 2 chr4A.!!$R2 6065
4 TraesCS2A01G494800 chr4A 28428037 28429771 1734 True 2944.0 2944 97.2960 2977 4712 1 chr4A.!!$R1 1735
5 TraesCS2A01G494800 chr4A 6247875 6249601 1726 False 2939.0 2939 97.3430 2982 4712 1 chr4A.!!$F1 1730
6 TraesCS2A01G494800 chr4A 338431069 338432801 1732 False 2933.0 2933 97.2320 2981 4712 1 chr4A.!!$F2 1731
7 TraesCS2A01G494800 chr6A 585009187 585012168 2981 True 5101.0 5101 97.5540 1 2981 1 chr6A.!!$R3 2980
8 TraesCS2A01G494800 chr6A 551659791 551661522 1731 True 2966.0 2966 97.5780 2981 4712 1 chr6A.!!$R1 1731
9 TraesCS2A01G494800 chr6A 551666677 551668410 1733 True 2942.0 2942 97.2940 2979 4712 1 chr6A.!!$R2 1733
10 TraesCS2A01G494800 chr7B 558982875 558987214 4339 True 3684.5 5040 97.3465 1 6074 2 chr7B.!!$R1 6073
11 TraesCS2A01G494800 chr5B 703510824 703515114 4290 True 3288.5 5012 97.0140 1 6066 2 chr5B.!!$R1 6065
12 TraesCS2A01G494800 chr1B 403618279 403622564 4285 False 3248.5 4951 96.6480 1 6067 2 chr1B.!!$F1 6066
13 TraesCS2A01G494800 chr1B 667558663 667562431 3768 False 3168.5 4045 97.0300 554 6063 2 chr1B.!!$F2 5509
14 TraesCS2A01G494800 chr3D 556686521 556689714 3193 False 2695.0 3125 97.0490 1134 6066 2 chr3D.!!$F1 4932
15 TraesCS2A01G494800 chr3A 476372066 476373793 1727 False 2950.0 2950 97.4580 2982 4712 1 chr3A.!!$F1 1730
16 TraesCS2A01G494800 chr7A 710961598 710963338 1740 False 2946.0 2946 97.1890 2971 4713 1 chr7A.!!$F1 1742
17 TraesCS2A01G494800 chr7A 735877447 735879178 1731 False 2939.0 2939 97.2900 2981 4712 1 chr7A.!!$F2 1731
18 TraesCS2A01G494800 chr1A 578840144 578841873 1729 True 2937.0 2937 97.2880 2981 4712 1 chr1A.!!$R2 1731
19 TraesCS2A01G494800 chr1A 105294791 105295561 770 True 898.0 898 87.6770 4713 5489 1 chr1A.!!$R1 776
20 TraesCS2A01G494800 chr5D 4419587 4421280 1693 True 2638.0 2638 94.8080 1 1690 1 chr5D.!!$R1 1689
21 TraesCS2A01G494800 chr5D 4566615 4568308 1693 True 2638.0 2638 94.8080 1 1690 1 chr5D.!!$R2 1689
22 TraesCS2A01G494800 chr5D 4723098 4724791 1693 True 2632.0 2632 94.7490 1 1690 1 chr5D.!!$R3 1689
23 TraesCS2A01G494800 chr3B 770747474 770748832 1358 True 2326.0 2326 97.5110 4713 6075 1 chr3B.!!$R1 1362
24 TraesCS2A01G494800 chr4B 260075256 260076026 770 True 909.0 909 87.9330 4713 5489 1 chr4B.!!$R1 776

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
289 293 0.605589 AGGGAGCGGGAAGTTTTTCG 60.606 55.000 0.00 0.0 33.98 3.46 F
1125 1138 1.002888 CAGCTCTGCAGGGAGAAGAAA 59.997 52.381 20.53 0.0 35.52 2.52 F
2976 3013 5.057149 GCCTTGTACGATTATCTGTGGATT 58.943 41.667 0.00 0.0 33.71 3.01 F
3170 3208 0.318699 CGATGATCCTAGCGCCGAAA 60.319 55.000 2.29 0.0 0.00 3.46 F
3713 3755 0.538118 CCCCGAAACTTGTCCCGATA 59.462 55.000 0.00 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 1244 4.019681 CGGGGGCTTACATATTCTAATGGA 60.020 45.833 0.00 0.0 0.00 3.41 R
2978 3015 0.970640 TGCTACGTTCCCTAACAGCA 59.029 50.000 0.00 0.0 40.42 4.41 R
4317 4361 1.260538 TGCTTTGGGTGTGCCAAACA 61.261 50.000 0.00 0.0 34.15 2.83 R
5139 5218 3.630168 GCCCCATTTGGCCATTTATTTT 58.370 40.909 6.09 0.0 46.11 1.82 R
5226 5306 0.897863 TGCCCGAAAATGGAACCCAG 60.898 55.000 0.00 0.0 36.75 4.45 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
221 225 3.858868 GACCGGAAGTGAGTGCGCA 62.859 63.158 9.46 5.66 0.00 6.09
289 293 0.605589 AGGGAGCGGGAAGTTTTTCG 60.606 55.000 0.00 0.00 33.98 3.46
402 406 4.265904 TGATCCTCAAACAAAGCGACTA 57.734 40.909 0.00 0.00 0.00 2.59
569 573 1.833630 TCACATCATCCAGACCAGGTC 59.166 52.381 12.25 12.25 0.00 3.85
769 773 7.833786 ACACGAAGGTAAACTAATATGTCTCA 58.166 34.615 0.00 0.00 0.00 3.27
786 790 3.315470 GTCTCATGCCACTCGTATAGTCA 59.685 47.826 0.00 0.00 35.76 3.41
1125 1138 1.002888 CAGCTCTGCAGGGAGAAGAAA 59.997 52.381 20.53 0.00 35.52 2.52
2076 2110 9.372369 AGATGTCTTTACTGTCAAGTTTATAGC 57.628 33.333 2.01 0.00 37.88 2.97
2503 2538 6.615726 ACATATGTAATGTGGGGTAGAAGACT 59.384 38.462 6.56 0.00 40.07 3.24
2976 3013 5.057149 GCCTTGTACGATTATCTGTGGATT 58.943 41.667 0.00 0.00 33.71 3.01
2977 3014 5.527582 GCCTTGTACGATTATCTGTGGATTT 59.472 40.000 0.00 0.00 33.71 2.17
2978 3015 6.038271 GCCTTGTACGATTATCTGTGGATTTT 59.962 38.462 0.00 0.00 33.71 1.82
2979 3016 7.409697 CCTTGTACGATTATCTGTGGATTTTG 58.590 38.462 0.00 0.00 33.71 2.44
2985 3022 6.597672 ACGATTATCTGTGGATTTTGCTGTTA 59.402 34.615 0.00 0.00 33.71 2.41
3170 3208 0.318699 CGATGATCCTAGCGCCGAAA 60.319 55.000 2.29 0.00 0.00 3.46
3713 3755 0.538118 CCCCGAAACTTGTCCCGATA 59.462 55.000 0.00 0.00 0.00 2.92
4117 4161 2.140717 CGTTACCGGCAAGTCTCTTTT 58.859 47.619 0.00 0.00 0.00 2.27
4142 4186 2.675603 CGTTCCGTAACACATCATCCCA 60.676 50.000 0.00 0.00 35.16 4.37
4180 4224 4.674475 TCACATTGTGCACATTATGATGC 58.326 39.130 29.44 6.05 42.40 3.91
4284 4328 5.014858 AGACACTTTCGGAGATACCTGTAA 58.985 41.667 0.00 0.00 35.04 2.41
4317 4361 2.027192 AGCCATCCAGTTACGTTGTGAT 60.027 45.455 0.00 0.00 0.00 3.06
4830 4876 4.776837 TGGATGCATTGGTTTATGTTTCCT 59.223 37.500 0.00 0.00 33.51 3.36
5076 5123 6.579666 AATGTAAGATGCAGTGAAACATGT 57.420 33.333 0.00 0.00 41.43 3.21
6067 6156 2.199236 GCACGGGCATTGTACTAGTAC 58.801 52.381 23.58 23.58 40.72 2.73
6074 6163 6.261826 ACGGGCATTGTACTAGTACTAGTAAG 59.738 42.308 33.96 25.51 46.55 2.34
6075 6164 6.484643 CGGGCATTGTACTAGTACTAGTAAGA 59.515 42.308 33.96 26.61 46.55 2.10
6076 6165 7.307870 CGGGCATTGTACTAGTACTAGTAAGAG 60.308 44.444 33.96 25.50 46.55 2.85
6077 6166 7.501892 GGGCATTGTACTAGTACTAGTAAGAGT 59.498 40.741 33.96 21.40 46.55 3.24
6078 6167 8.901793 GGCATTGTACTAGTACTAGTAAGAGTT 58.098 37.037 33.96 19.27 46.55 3.01
6079 6168 9.719279 GCATTGTACTAGTACTAGTAAGAGTTG 57.281 37.037 33.96 26.51 46.55 3.16
6086 6175 9.902684 ACTAGTACTAGTAAGAGTTGATTAGCA 57.097 33.333 29.96 0.00 43.98 3.49
6088 6177 8.577048 AGTACTAGTAAGAGTTGATTAGCACA 57.423 34.615 3.61 0.00 0.00 4.57
6089 6178 9.021807 AGTACTAGTAAGAGTTGATTAGCACAA 57.978 33.333 3.61 0.00 0.00 3.33
6090 6179 9.074443 GTACTAGTAAGAGTTGATTAGCACAAC 57.926 37.037 3.61 0.00 45.15 3.32
6101 6190 8.606727 GTTGATTAGCACAACTGTTGATAATC 57.393 34.615 27.42 27.42 42.63 1.75
6102 6191 8.454106 GTTGATTAGCACAACTGTTGATAATCT 58.546 33.333 30.01 20.98 42.63 2.40
6103 6192 7.977904 TGATTAGCACAACTGTTGATAATCTG 58.022 34.615 30.01 20.38 36.40 2.90
6104 6193 4.691860 AGCACAACTGTTGATAATCTGC 57.308 40.909 26.00 21.60 0.00 4.26
6105 6194 4.074259 AGCACAACTGTTGATAATCTGCA 58.926 39.130 26.00 0.00 30.39 4.41
6106 6195 4.083110 AGCACAACTGTTGATAATCTGCAC 60.083 41.667 26.00 2.59 30.39 4.57
6107 6196 4.320421 GCACAACTGTTGATAATCTGCACA 60.320 41.667 26.00 0.00 0.00 4.57
6108 6197 5.620654 GCACAACTGTTGATAATCTGCACAT 60.621 40.000 26.00 0.00 0.00 3.21
6109 6198 6.025896 CACAACTGTTGATAATCTGCACATC 58.974 40.000 26.00 0.00 0.00 3.06
6110 6199 5.942236 ACAACTGTTGATAATCTGCACATCT 59.058 36.000 26.00 0.00 0.00 2.90
6111 6200 6.432162 ACAACTGTTGATAATCTGCACATCTT 59.568 34.615 26.00 0.00 0.00 2.40
6112 6201 6.432607 ACTGTTGATAATCTGCACATCTTG 57.567 37.500 0.00 0.00 0.00 3.02
6148 6237 3.414700 GGCGTTGAGGCGTGACTG 61.415 66.667 0.00 0.00 35.04 3.51
6149 6238 2.355837 GCGTTGAGGCGTGACTGA 60.356 61.111 0.00 0.00 0.00 3.41
6150 6239 1.954146 GCGTTGAGGCGTGACTGAA 60.954 57.895 0.00 0.00 0.00 3.02
6151 6240 1.891060 GCGTTGAGGCGTGACTGAAG 61.891 60.000 0.00 0.00 0.00 3.02
6152 6241 0.318699 CGTTGAGGCGTGACTGAAGA 60.319 55.000 0.00 0.00 0.00 2.87
6153 6242 1.865865 GTTGAGGCGTGACTGAAGAA 58.134 50.000 0.00 0.00 0.00 2.52
6154 6243 2.417719 GTTGAGGCGTGACTGAAGAAT 58.582 47.619 0.00 0.00 0.00 2.40
6155 6244 2.370281 TGAGGCGTGACTGAAGAATC 57.630 50.000 0.00 0.00 0.00 2.52
6156 6245 1.895798 TGAGGCGTGACTGAAGAATCT 59.104 47.619 0.00 0.00 0.00 2.40
6157 6246 2.266554 GAGGCGTGACTGAAGAATCTG 58.733 52.381 0.00 0.00 0.00 2.90
6158 6247 1.620819 AGGCGTGACTGAAGAATCTGT 59.379 47.619 0.00 0.00 40.06 3.41
6159 6248 2.037772 AGGCGTGACTGAAGAATCTGTT 59.962 45.455 0.00 0.00 37.80 3.16
6160 6249 2.413453 GGCGTGACTGAAGAATCTGTTC 59.587 50.000 0.00 0.00 37.80 3.18
6161 6250 2.413453 GCGTGACTGAAGAATCTGTTCC 59.587 50.000 0.00 0.00 37.80 3.62
6162 6251 2.996621 CGTGACTGAAGAATCTGTTCCC 59.003 50.000 0.00 0.00 37.80 3.97
6163 6252 3.339141 GTGACTGAAGAATCTGTTCCCC 58.661 50.000 0.00 0.00 37.80 4.81
6164 6253 3.008485 GTGACTGAAGAATCTGTTCCCCT 59.992 47.826 0.00 0.00 37.80 4.79
6165 6254 4.223032 GTGACTGAAGAATCTGTTCCCCTA 59.777 45.833 0.00 0.00 37.80 3.53
6166 6255 5.032846 TGACTGAAGAATCTGTTCCCCTAT 58.967 41.667 0.00 0.00 37.80 2.57
6167 6256 5.488919 TGACTGAAGAATCTGTTCCCCTATT 59.511 40.000 0.00 0.00 37.80 1.73
6168 6257 5.995446 ACTGAAGAATCTGTTCCCCTATTC 58.005 41.667 0.00 0.00 34.44 1.75
6169 6258 5.488919 ACTGAAGAATCTGTTCCCCTATTCA 59.511 40.000 0.00 0.00 34.44 2.57
6170 6259 6.159398 ACTGAAGAATCTGTTCCCCTATTCAT 59.841 38.462 0.00 0.00 34.44 2.57
6171 6260 6.359804 TGAAGAATCTGTTCCCCTATTCATG 58.640 40.000 0.00 0.00 34.81 3.07
6172 6261 4.723309 AGAATCTGTTCCCCTATTCATGC 58.277 43.478 0.00 0.00 34.81 4.06
6173 6262 3.515602 ATCTGTTCCCCTATTCATGCC 57.484 47.619 0.00 0.00 0.00 4.40
6174 6263 2.204463 TCTGTTCCCCTATTCATGCCA 58.796 47.619 0.00 0.00 0.00 4.92
6175 6264 2.785269 TCTGTTCCCCTATTCATGCCAT 59.215 45.455 0.00 0.00 0.00 4.40
6176 6265 2.889045 CTGTTCCCCTATTCATGCCATG 59.111 50.000 0.00 0.00 0.00 3.66
6177 6266 2.242043 GTTCCCCTATTCATGCCATGG 58.758 52.381 7.63 7.63 0.00 3.66
6178 6267 1.533187 TCCCCTATTCATGCCATGGT 58.467 50.000 14.67 0.00 0.00 3.55
6179 6268 2.712384 TCCCCTATTCATGCCATGGTA 58.288 47.619 14.67 9.89 0.00 3.25
6180 6269 3.268146 TCCCCTATTCATGCCATGGTAT 58.732 45.455 14.67 12.26 0.00 2.73
6181 6270 3.266772 TCCCCTATTCATGCCATGGTATC 59.733 47.826 13.03 0.00 0.00 2.24
6182 6271 3.273434 CCCTATTCATGCCATGGTATCG 58.727 50.000 13.03 8.87 0.00 2.92
6183 6272 3.273434 CCTATTCATGCCATGGTATCGG 58.727 50.000 13.03 3.00 0.00 4.18
6184 6273 2.957402 ATTCATGCCATGGTATCGGT 57.043 45.000 13.03 0.00 0.00 4.69
6185 6274 2.727123 TTCATGCCATGGTATCGGTT 57.273 45.000 13.03 0.00 0.00 4.44
6186 6275 3.847671 TTCATGCCATGGTATCGGTTA 57.152 42.857 13.03 0.00 0.00 2.85
6187 6276 3.847671 TCATGCCATGGTATCGGTTAA 57.152 42.857 13.03 0.00 0.00 2.01
6188 6277 3.472652 TCATGCCATGGTATCGGTTAAC 58.527 45.455 13.03 0.00 0.00 2.01
6189 6278 3.135712 TCATGCCATGGTATCGGTTAACT 59.864 43.478 13.03 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
241 245 3.005554 CGTCTTGCATTGATGAAGACCT 58.994 45.455 19.16 0.00 39.27 3.85
289 293 1.434696 CTTCCACATTCATGCGGCC 59.565 57.895 0.00 0.00 30.18 6.13
402 406 4.486090 CATAGTACAGAAACACGCTGACT 58.514 43.478 0.00 0.00 36.86 3.41
769 773 2.965831 ACCATGACTATACGAGTGGCAT 59.034 45.455 0.00 0.00 39.06 4.40
786 790 6.668283 AGTACACTATAGTCAAGGACAACCAT 59.332 38.462 1.26 0.00 38.94 3.55
879 885 2.564771 CATGGTCATTATCACCGCTGT 58.435 47.619 0.00 0.00 36.61 4.40
1215 1244 4.019681 CGGGGGCTTACATATTCTAATGGA 60.020 45.833 0.00 0.00 0.00 3.41
2076 2110 7.085023 TCAGGTAATGAAGGACCATTTGATGG 61.085 42.308 5.43 5.43 45.32 3.51
2503 2538 5.127845 CAGAAATCCCTAGCAAGAGACACTA 59.872 44.000 0.00 0.00 0.00 2.74
2947 2984 5.755375 ACAGATAATCGTACAAGGCATTCTG 59.245 40.000 0.00 0.00 34.51 3.02
2960 2997 4.943705 ACAGCAAAATCCACAGATAATCGT 59.056 37.500 0.00 0.00 30.42 3.73
2976 3013 2.224329 TGCTACGTTCCCTAACAGCAAA 60.224 45.455 3.02 0.00 40.01 3.68
2977 3014 1.345089 TGCTACGTTCCCTAACAGCAA 59.655 47.619 3.02 0.00 40.01 3.91
2978 3015 0.970640 TGCTACGTTCCCTAACAGCA 59.029 50.000 0.00 0.00 40.42 4.41
2979 3016 1.337447 TGTGCTACGTTCCCTAACAGC 60.337 52.381 0.00 0.00 35.96 4.40
2985 3022 3.134574 TGAATTTGTGCTACGTTCCCT 57.865 42.857 0.00 0.00 0.00 4.20
3713 3755 5.746990 ATATAGGAAGTGCTATTTCGGCT 57.253 39.130 0.00 0.00 0.00 5.52
3750 3794 0.036671 GGAGTTCCGAAATGGTCCGT 60.037 55.000 0.00 0.00 39.52 4.69
4008 4052 4.218417 GGGGATTGAATACGGGATTGATTG 59.782 45.833 0.00 0.00 0.00 2.67
4023 4067 2.691409 CGCTAGACAAAGGGGATTGA 57.309 50.000 0.00 0.00 34.38 2.57
4180 4224 2.722201 GGCCCACTCGGTAGGACAG 61.722 68.421 0.00 0.00 0.00 3.51
4284 4328 6.515512 AACTGGATGGCTATAAAGGTACAT 57.484 37.500 0.00 0.00 0.00 2.29
4317 4361 1.260538 TGCTTTGGGTGTGCCAAACA 61.261 50.000 0.00 0.00 34.15 2.83
4772 4818 5.181748 AGCTCTACTTGATGACAACCAATC 58.818 41.667 0.00 0.00 32.27 2.67
5139 5218 3.630168 GCCCCATTTGGCCATTTATTTT 58.370 40.909 6.09 0.00 46.11 1.82
5226 5306 0.897863 TGCCCGAAAATGGAACCCAG 60.898 55.000 0.00 0.00 36.75 4.45
5315 5395 8.642020 CAAGTGCAAAAGTTAATGAATCTAAGC 58.358 33.333 0.00 0.00 0.00 3.09
5483 5567 1.078001 CCTTATCCCCACCGCGTTT 60.078 57.895 4.92 0.00 0.00 3.60
6076 6165 8.454106 AGATTATCAACAGTTGTGCTAATCAAC 58.546 33.333 26.38 14.34 43.51 3.18
6077 6166 8.453320 CAGATTATCAACAGTTGTGCTAATCAA 58.547 33.333 26.38 7.80 34.27 2.57
6078 6167 7.414429 GCAGATTATCAACAGTTGTGCTAATCA 60.414 37.037 26.38 8.30 34.27 2.57
6079 6168 6.909357 GCAGATTATCAACAGTTGTGCTAATC 59.091 38.462 22.31 22.31 33.31 1.75
6080 6169 6.375174 TGCAGATTATCAACAGTTGTGCTAAT 59.625 34.615 19.44 16.35 0.00 1.73
6081 6170 5.704978 TGCAGATTATCAACAGTTGTGCTAA 59.295 36.000 19.44 13.46 0.00 3.09
6082 6171 5.122239 GTGCAGATTATCAACAGTTGTGCTA 59.878 40.000 19.44 8.27 0.00 3.49
6083 6172 4.074259 TGCAGATTATCAACAGTTGTGCT 58.926 39.130 19.44 7.93 0.00 4.40
6084 6173 4.161333 GTGCAGATTATCAACAGTTGTGC 58.839 43.478 13.14 13.89 0.00 4.57
6085 6174 5.361135 TGTGCAGATTATCAACAGTTGTG 57.639 39.130 13.14 4.27 0.00 3.33
6086 6175 5.942236 AGATGTGCAGATTATCAACAGTTGT 59.058 36.000 13.14 3.72 0.00 3.32
6087 6176 6.432607 AGATGTGCAGATTATCAACAGTTG 57.567 37.500 6.99 6.99 0.00 3.16
6088 6177 6.849502 CAAGATGTGCAGATTATCAACAGTT 58.150 36.000 0.00 0.00 0.00 3.16
6089 6178 6.432607 CAAGATGTGCAGATTATCAACAGT 57.567 37.500 0.00 0.00 0.00 3.55
6131 6220 3.414700 CAGTCACGCCTCAACGCC 61.415 66.667 0.00 0.00 36.19 5.68
6132 6221 1.891060 CTTCAGTCACGCCTCAACGC 61.891 60.000 0.00 0.00 36.19 4.84
6133 6222 0.318699 TCTTCAGTCACGCCTCAACG 60.319 55.000 0.00 0.00 39.50 4.10
6134 6223 1.865865 TTCTTCAGTCACGCCTCAAC 58.134 50.000 0.00 0.00 0.00 3.18
6135 6224 2.300152 AGATTCTTCAGTCACGCCTCAA 59.700 45.455 0.00 0.00 0.00 3.02
6136 6225 1.895798 AGATTCTTCAGTCACGCCTCA 59.104 47.619 0.00 0.00 0.00 3.86
6137 6226 2.266554 CAGATTCTTCAGTCACGCCTC 58.733 52.381 0.00 0.00 0.00 4.70
6138 6227 1.620819 ACAGATTCTTCAGTCACGCCT 59.379 47.619 0.00 0.00 0.00 5.52
6139 6228 2.086054 ACAGATTCTTCAGTCACGCC 57.914 50.000 0.00 0.00 0.00 5.68
6140 6229 2.413453 GGAACAGATTCTTCAGTCACGC 59.587 50.000 0.00 0.00 34.98 5.34
6141 6230 2.996621 GGGAACAGATTCTTCAGTCACG 59.003 50.000 0.00 0.00 34.98 4.35
6142 6231 3.008485 AGGGGAACAGATTCTTCAGTCAC 59.992 47.826 0.00 0.00 34.98 3.67
6143 6232 3.251484 AGGGGAACAGATTCTTCAGTCA 58.749 45.455 0.00 0.00 34.98 3.41
6144 6233 3.990959 AGGGGAACAGATTCTTCAGTC 57.009 47.619 0.00 0.00 34.98 3.51
6145 6234 5.488919 TGAATAGGGGAACAGATTCTTCAGT 59.511 40.000 0.00 0.00 35.25 3.41
6146 6235 5.994250 TGAATAGGGGAACAGATTCTTCAG 58.006 41.667 0.00 0.00 35.25 3.02
6147 6236 6.359804 CATGAATAGGGGAACAGATTCTTCA 58.640 40.000 0.00 0.00 35.25 3.02
6148 6237 5.240403 GCATGAATAGGGGAACAGATTCTTC 59.760 44.000 0.00 0.00 35.25 2.87
6149 6238 5.136105 GCATGAATAGGGGAACAGATTCTT 58.864 41.667 0.00 0.00 35.25 2.52
6150 6239 4.446889 GGCATGAATAGGGGAACAGATTCT 60.447 45.833 0.00 0.00 35.25 2.40
6151 6240 3.823304 GGCATGAATAGGGGAACAGATTC 59.177 47.826 0.00 0.00 34.95 2.52
6152 6241 3.205056 TGGCATGAATAGGGGAACAGATT 59.795 43.478 0.00 0.00 0.00 2.40
6153 6242 2.785269 TGGCATGAATAGGGGAACAGAT 59.215 45.455 0.00 0.00 0.00 2.90
6154 6243 2.204463 TGGCATGAATAGGGGAACAGA 58.796 47.619 0.00 0.00 0.00 3.41
6155 6244 2.734755 TGGCATGAATAGGGGAACAG 57.265 50.000 0.00 0.00 0.00 3.16
6156 6245 2.424667 CCATGGCATGAATAGGGGAACA 60.425 50.000 28.43 0.00 0.00 3.18
6157 6246 2.242043 CCATGGCATGAATAGGGGAAC 58.758 52.381 28.43 0.00 0.00 3.62
6158 6247 1.858910 ACCATGGCATGAATAGGGGAA 59.141 47.619 28.43 0.00 0.00 3.97
6159 6248 1.533187 ACCATGGCATGAATAGGGGA 58.467 50.000 28.43 0.00 0.00 4.81
6160 6249 3.624777 GATACCATGGCATGAATAGGGG 58.375 50.000 28.43 12.38 0.00 4.79
6161 6250 3.273434 CGATACCATGGCATGAATAGGG 58.727 50.000 28.43 13.13 0.00 3.53
6162 6251 3.273434 CCGATACCATGGCATGAATAGG 58.727 50.000 28.43 22.96 0.00 2.57
6163 6252 3.942829 ACCGATACCATGGCATGAATAG 58.057 45.455 28.43 18.89 0.00 1.73
6164 6253 4.365514 AACCGATACCATGGCATGAATA 57.634 40.909 28.43 19.20 0.00 1.75
6165 6254 2.957402 ACCGATACCATGGCATGAAT 57.043 45.000 28.43 19.88 0.00 2.57
6166 6255 2.727123 AACCGATACCATGGCATGAA 57.273 45.000 28.43 16.08 0.00 2.57
6167 6256 3.135712 AGTTAACCGATACCATGGCATGA 59.864 43.478 28.43 10.28 0.00 3.07
6168 6257 3.476552 AGTTAACCGATACCATGGCATG 58.523 45.455 20.56 20.56 0.00 4.06
6169 6258 3.857157 AGTTAACCGATACCATGGCAT 57.143 42.857 13.04 3.73 0.00 4.40


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

AutoCloner maintained by Alex Coulton.