Multiple sequence alignment - TraesCS3D01G012400

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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 TraesCS3D01G012400 chr3D 100.000 3452 0 0 1 3452 4344486 4347937 0.000000e+00 6375.0
1 TraesCS3D01G012400 chr3D 84.665 2765 310 70 32 2774 4316845 4319517 0.000000e+00 2652.0
2 TraesCS3D01G012400 chrUn 93.553 2823 136 18 635 3452 35644402 35647183 0.000000e+00 4163.0
3 TraesCS3D01G012400 chrUn 86.910 1971 223 21 571 2537 308557575 308559514 0.000000e+00 2178.0
4 TraesCS3D01G012400 chrUn 86.503 163 14 4 2719 2881 35631698 35631852 4.580000e-39 172.0
5 TraesCS3D01G012400 chr3A 93.807 2309 88 20 482 2788 9950402 9952657 0.000000e+00 3421.0
6 TraesCS3D01G012400 chr3A 86.576 2436 252 37 69 2486 9887452 9889830 0.000000e+00 2617.0
7 TraesCS3D01G012400 chr3A 89.339 666 41 10 2787 3444 9962208 9962851 0.000000e+00 809.0
8 TraesCS3D01G012400 chr3A 82.258 434 29 15 77 505 9948615 9949005 7.140000e-87 331.0
9 TraesCS3D01G012400 chr3A 78.610 187 26 8 3066 3243 9890447 9890628 1.010000e-20 111.0
10 TraesCS3D01G012400 chr3B 95.918 49 2 0 938 986 173904442 173904490 2.860000e-11 80.5
11 TraesCS3D01G012400 chr2B 95.918 49 2 0 938 986 391127540 391127588 2.860000e-11 80.5


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 TraesCS3D01G012400 chr3D 4344486 4347937 3451 False 6375 6375 100.0000 1 3452 1 chr3D.!!$F2 3451
1 TraesCS3D01G012400 chr3D 4316845 4319517 2672 False 2652 2652 84.6650 32 2774 1 chr3D.!!$F1 2742
2 TraesCS3D01G012400 chrUn 35644402 35647183 2781 False 4163 4163 93.5530 635 3452 1 chrUn.!!$F2 2817
3 TraesCS3D01G012400 chrUn 308557575 308559514 1939 False 2178 2178 86.9100 571 2537 1 chrUn.!!$F3 1966
4 TraesCS3D01G012400 chr3A 9948615 9952657 4042 False 1876 3421 88.0325 77 2788 2 chr3A.!!$F3 2711
5 TraesCS3D01G012400 chr3A 9887452 9890628 3176 False 1364 2617 82.5930 69 3243 2 chr3A.!!$F2 3174
6 TraesCS3D01G012400 chr3A 9962208 9962851 643 False 809 809 89.3390 2787 3444 1 chr3A.!!$F1 657

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
26 27 0.457443 TGCGAGGTCTGCTAGTGATG 59.543 55.0 0.0 0.0 0.0 3.07 F
28 29 0.743688 CGAGGTCTGCTAGTGATGCT 59.256 55.0 0.0 0.0 0.0 3.79 F
1568 3015 0.808125 TTGTTGCAACAGAACACGCT 59.192 45.0 29.5 0.0 40.5 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 3272 0.106819 ATGATCACCTTGCTGCCTCC 60.107 55.000 0.00 0.00 0.00 4.30 R
1959 3406 2.076863 CGTGGATGTTCTTCCAGGTTC 58.923 52.381 14.87 2.80 46.31 3.62 R
3164 4761 0.179192 TTCGCAAGCAGCAATAAGCG 60.179 50.000 9.68 9.68 46.13 4.68 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
18 19 1.803289 GGGATTTTGCGAGGTCTGC 59.197 57.895 0.00 0.00 0.00 4.26
19 20 0.678048 GGGATTTTGCGAGGTCTGCT 60.678 55.000 0.00 0.00 0.00 4.24
20 21 1.406887 GGGATTTTGCGAGGTCTGCTA 60.407 52.381 0.00 0.00 0.00 3.49
21 22 1.936547 GGATTTTGCGAGGTCTGCTAG 59.063 52.381 0.00 0.00 0.00 3.42
22 23 2.622436 GATTTTGCGAGGTCTGCTAGT 58.378 47.619 0.00 0.00 0.00 2.57
23 24 1.795768 TTTTGCGAGGTCTGCTAGTG 58.204 50.000 0.00 0.00 0.00 2.74
24 25 0.966179 TTTGCGAGGTCTGCTAGTGA 59.034 50.000 0.00 0.00 0.00 3.41
25 26 1.186200 TTGCGAGGTCTGCTAGTGAT 58.814 50.000 0.00 0.00 0.00 3.06
26 27 0.457443 TGCGAGGTCTGCTAGTGATG 59.543 55.000 0.00 0.00 0.00 3.07
27 28 0.873743 GCGAGGTCTGCTAGTGATGC 60.874 60.000 0.00 0.00 0.00 3.91
28 29 0.743688 CGAGGTCTGCTAGTGATGCT 59.256 55.000 0.00 0.00 0.00 3.79
29 30 1.268999 CGAGGTCTGCTAGTGATGCTC 60.269 57.143 0.00 0.00 0.00 4.26
30 31 2.031120 GAGGTCTGCTAGTGATGCTCT 58.969 52.381 0.00 0.00 0.00 4.09
36 37 3.703556 TCTGCTAGTGATGCTCTAAGCTT 59.296 43.478 3.48 3.48 42.97 3.74
40 41 4.272261 GCTAGTGATGCTCTAAGCTTTTCC 59.728 45.833 3.20 0.00 42.97 3.13
48 49 3.807209 GCTCTAAGCTTTTCCTGGACACA 60.807 47.826 3.20 0.00 38.45 3.72
50 51 4.985538 TCTAAGCTTTTCCTGGACACATT 58.014 39.130 3.20 0.00 0.00 2.71
54 55 4.729868 AGCTTTTCCTGGACACATTACTT 58.270 39.130 0.00 0.00 0.00 2.24
56 57 5.705905 AGCTTTTCCTGGACACATTACTTAC 59.294 40.000 0.00 0.00 0.00 2.34
61 62 4.525487 TCCTGGACACATTACTTACGAGTT 59.475 41.667 0.00 0.00 37.33 3.01
85 86 1.781555 GATTGGTATCGATGCGGCG 59.218 57.895 8.54 0.51 0.00 6.46
112 113 4.131088 GAGGACACCGACCGAGCC 62.131 72.222 0.00 0.00 0.00 4.70
146 147 2.511600 GTAGCGATGGCGGCTGTT 60.512 61.111 11.43 0.58 46.35 3.16
219 224 4.946157 AGCATAGCATGTTTAACAAGAGCT 59.054 37.500 20.47 20.47 38.04 4.09
220 225 6.115446 AGCATAGCATGTTTAACAAGAGCTA 58.885 36.000 22.49 22.49 39.51 3.32
221 226 6.259608 AGCATAGCATGTTTAACAAGAGCTAG 59.740 38.462 23.58 18.66 39.00 3.42
222 227 6.037610 GCATAGCATGTTTAACAAGAGCTAGT 59.962 38.462 23.58 14.85 39.00 2.57
223 228 7.414540 GCATAGCATGTTTAACAAGAGCTAGTT 60.415 37.037 23.58 12.98 39.00 2.24
224 229 6.884280 AGCATGTTTAACAAGAGCTAGTTT 57.116 33.333 17.07 0.00 34.56 2.66
225 230 7.979444 AGCATGTTTAACAAGAGCTAGTTTA 57.021 32.000 17.07 0.00 34.56 2.01
226 231 8.567285 AGCATGTTTAACAAGAGCTAGTTTAT 57.433 30.769 17.07 0.00 34.56 1.40
227 232 8.454106 AGCATGTTTAACAAGAGCTAGTTTATG 58.546 33.333 17.07 2.69 34.56 1.90
228 233 7.218963 GCATGTTTAACAAGAGCTAGTTTATGC 59.781 37.037 0.66 0.00 0.00 3.14
229 234 7.737972 TGTTTAACAAGAGCTAGTTTATGCA 57.262 32.000 0.00 0.00 0.00 3.96
230 235 7.581476 TGTTTAACAAGAGCTAGTTTATGCAC 58.419 34.615 0.00 0.00 0.00 4.57
231 236 4.928661 AACAAGAGCTAGTTTATGCACG 57.071 40.909 0.00 0.00 0.00 5.34
232 237 3.926616 ACAAGAGCTAGTTTATGCACGT 58.073 40.909 0.00 0.00 0.00 4.49
233 238 3.927142 ACAAGAGCTAGTTTATGCACGTC 59.073 43.478 0.00 0.00 0.00 4.34
234 239 3.868757 AGAGCTAGTTTATGCACGTCA 57.131 42.857 0.00 0.00 0.00 4.35
235 240 4.188247 AGAGCTAGTTTATGCACGTCAA 57.812 40.909 0.00 0.00 0.00 3.18
236 241 4.759782 AGAGCTAGTTTATGCACGTCAAT 58.240 39.130 0.00 0.00 0.00 2.57
237 242 4.568359 AGAGCTAGTTTATGCACGTCAATG 59.432 41.667 0.00 0.00 0.00 2.82
238 243 4.503910 AGCTAGTTTATGCACGTCAATGA 58.496 39.130 0.00 0.00 0.00 2.57
239 244 4.568359 AGCTAGTTTATGCACGTCAATGAG 59.432 41.667 0.00 0.00 0.00 2.90
240 245 3.747099 AGTTTATGCACGTCAATGAGC 57.253 42.857 0.00 0.00 0.00 4.26
241 246 3.338249 AGTTTATGCACGTCAATGAGCT 58.662 40.909 0.00 0.00 0.00 4.09
259 264 4.329801 TGAGCTAGTTTATGCACGTCAATG 59.670 41.667 0.00 0.00 0.00 2.82
304 309 2.099098 GTGCACCAGATAATTTTCCCCG 59.901 50.000 5.22 0.00 0.00 5.73
306 311 2.099098 GCACCAGATAATTTTCCCCGTG 59.901 50.000 0.00 0.00 0.00 4.94
329 334 7.148755 CGTGTGTACCCAACTAATTTAGTGTAC 60.149 40.741 19.21 19.21 39.39 2.90
614 2050 7.604164 CCTTCTCTGAAACACAAGATAAGCTTA 59.396 37.037 8.99 8.99 34.31 3.09
731 2173 7.660208 GTCAAATACTCCTTCAGGAAACTACAA 59.340 37.037 0.00 0.00 44.91 2.41
732 2174 7.660208 TCAAATACTCCTTCAGGAAACTACAAC 59.340 37.037 0.00 0.00 44.91 3.32
926 2373 6.000891 TGTCAAATTCCATCTCAAAACTCG 57.999 37.500 0.00 0.00 0.00 4.18
935 2382 6.522054 TCCATCTCAAAACTCGTAGACTTTT 58.478 36.000 0.00 0.00 33.93 2.27
936 2383 6.423905 TCCATCTCAAAACTCGTAGACTTTTG 59.576 38.462 7.89 7.89 45.21 2.44
1050 2497 3.758300 CGAATTTGTTAGCCGCTTCATT 58.242 40.909 0.00 0.00 0.00 2.57
1144 2591 4.840271 TCTCCTAATGAGAGTACACACGA 58.160 43.478 0.00 0.00 45.29 4.35
1202 2649 1.890979 GGATGGTGATGCAGCTCCG 60.891 63.158 17.44 0.00 32.61 4.63
1240 2687 3.343941 TGTACCAAGGCTACCATGTTC 57.656 47.619 0.00 0.00 0.00 3.18
1268 2715 2.029918 CCTTCAGGTACCAAAGCTTTGC 60.030 50.000 29.93 17.96 36.86 3.68
1461 2908 2.684192 TTTTGGGTGGATGCGACCGT 62.684 55.000 0.00 0.00 32.93 4.83
1568 3015 0.808125 TTGTTGCAACAGAACACGCT 59.192 45.000 29.50 0.00 40.50 5.07
1804 3251 4.158384 CAACGATTGGAGAAAATTCCACG 58.842 43.478 0.00 0.00 46.61 4.94
1825 3272 3.184178 CGCATTTGTTAAAAGGTTGGCTG 59.816 43.478 0.00 0.00 29.78 4.85
1830 3277 1.272490 GTTAAAAGGTTGGCTGGAGGC 59.728 52.381 0.00 0.00 41.50 4.70
1942 3389 8.949421 AGGAATTATGGTACCTATTCAAGACAT 58.051 33.333 23.88 7.82 0.00 3.06
1958 3405 3.233507 AGACATTGGCATTTGGAAGTGT 58.766 40.909 0.00 0.00 0.00 3.55
1959 3406 3.006110 AGACATTGGCATTTGGAAGTGTG 59.994 43.478 0.00 0.00 0.00 3.82
1964 3411 1.963515 GGCATTTGGAAGTGTGAACCT 59.036 47.619 0.00 0.00 0.00 3.50
1993 3440 6.379133 AGAACATCCACGACTAGTACCAATAA 59.621 38.462 0.00 0.00 0.00 1.40
2056 3503 8.246180 CACTTCTTGTTATAAATCCAGTTGCAT 58.754 33.333 0.00 0.00 0.00 3.96
2383 3830 4.265904 TCAGCATCTTACTTTGTTCCGA 57.734 40.909 0.00 0.00 0.00 4.55
2540 3992 5.418676 TCTTTTTGCAAAGACCCAAAGAAG 58.581 37.500 15.81 11.83 42.99 2.85
2547 3999 4.039124 GCAAAGACCCAAAGAAGGATTTGA 59.961 41.667 12.91 0.00 41.71 2.69
2578 4032 0.464452 ATACTAAGGCCACTCCGTGC 59.536 55.000 5.01 0.00 40.77 5.34
2623 4078 5.394773 GGTCCTTTTTCTCTCGCTCTATTCT 60.395 44.000 0.00 0.00 0.00 2.40
2624 4079 6.103330 GTCCTTTTTCTCTCGCTCTATTCTT 58.897 40.000 0.00 0.00 0.00 2.52
2625 4080 6.254804 GTCCTTTTTCTCTCGCTCTATTCTTC 59.745 42.308 0.00 0.00 0.00 2.87
2626 4081 5.522097 CCTTTTTCTCTCGCTCTATTCTTCC 59.478 44.000 0.00 0.00 0.00 3.46
2627 4082 5.923733 TTTTCTCTCGCTCTATTCTTCCT 57.076 39.130 0.00 0.00 0.00 3.36
2628 4083 5.923733 TTTCTCTCGCTCTATTCTTCCTT 57.076 39.130 0.00 0.00 0.00 3.36
2629 4084 5.923733 TTCTCTCGCTCTATTCTTCCTTT 57.076 39.130 0.00 0.00 0.00 3.11
2630 4085 5.923733 TCTCTCGCTCTATTCTTCCTTTT 57.076 39.130 0.00 0.00 0.00 2.27
2631 4086 7.406031 TTCTCTCGCTCTATTCTTCCTTTTA 57.594 36.000 0.00 0.00 0.00 1.52
2632 4087 7.589958 TCTCTCGCTCTATTCTTCCTTTTAT 57.410 36.000 0.00 0.00 0.00 1.40
2633 4088 8.693120 TCTCTCGCTCTATTCTTCCTTTTATA 57.307 34.615 0.00 0.00 0.00 0.98
2634 4089 8.569641 TCTCTCGCTCTATTCTTCCTTTTATAC 58.430 37.037 0.00 0.00 0.00 1.47
2635 4090 8.234136 TCTCGCTCTATTCTTCCTTTTATACA 57.766 34.615 0.00 0.00 0.00 2.29
2636 4091 8.861086 TCTCGCTCTATTCTTCCTTTTATACAT 58.139 33.333 0.00 0.00 0.00 2.29
2637 4092 9.482627 CTCGCTCTATTCTTCCTTTTATACATT 57.517 33.333 0.00 0.00 0.00 2.71
2638 4093 9.832445 TCGCTCTATTCTTCCTTTTATACATTT 57.168 29.630 0.00 0.00 0.00 2.32
2767 4225 2.971660 TGTCAGGACTTCGACACAAA 57.028 45.000 0.65 0.00 37.23 2.83
2768 4226 2.546778 TGTCAGGACTTCGACACAAAC 58.453 47.619 0.65 0.00 37.23 2.93
2921 4464 0.529992 CTCCTACGCCATCGGTTTCC 60.530 60.000 0.00 0.00 40.69 3.13
2926 4478 0.899720 ACGCCATCGGTTTCCTCTTA 59.100 50.000 0.00 0.00 40.69 2.10
2977 4543 5.147330 AGATTACCATGACGTTTGAGACA 57.853 39.130 0.00 0.00 0.00 3.41
3160 4757 1.600413 GCTTGAACCGCCAAAAGTCTG 60.600 52.381 0.00 0.00 0.00 3.51
3164 4761 0.102300 AACCGCCAAAAGTCTGTTGC 59.898 50.000 0.00 0.00 0.00 4.17
3182 4779 1.425031 CGCTTATTGCTGCTTGCGA 59.575 52.632 15.47 0.00 46.63 5.10
3198 4796 4.320202 GCTTGCGAAATAGAAAGGTCAACA 60.320 41.667 0.00 0.00 0.00 3.33
3227 4827 1.950973 TAGCATGTGTCGGCCGCTTA 61.951 55.000 23.51 5.91 34.18 3.09
3247 4847 9.099454 CCGCTTAATTGGATTATCTTAGATACC 57.901 37.037 0.81 2.02 0.00 2.73
3334 4934 7.173907 AGACAGAAGGTGTACAAGAAATTGATG 59.826 37.037 0.00 0.00 40.56 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.678048 AGCAGACCTCGCAAAATCCC 60.678 55.000 0.00 0.00 0.00 3.85
1 2 1.936547 CTAGCAGACCTCGCAAAATCC 59.063 52.381 0.00 0.00 0.00 3.01
2 3 2.349886 CACTAGCAGACCTCGCAAAATC 59.650 50.000 0.00 0.00 0.00 2.17
3 4 2.028112 TCACTAGCAGACCTCGCAAAAT 60.028 45.455 0.00 0.00 0.00 1.82
4 5 1.343142 TCACTAGCAGACCTCGCAAAA 59.657 47.619 0.00 0.00 0.00 2.44
5 6 0.966179 TCACTAGCAGACCTCGCAAA 59.034 50.000 0.00 0.00 0.00 3.68
6 7 1.134995 CATCACTAGCAGACCTCGCAA 60.135 52.381 0.00 0.00 0.00 4.85
7 8 0.457443 CATCACTAGCAGACCTCGCA 59.543 55.000 0.00 0.00 0.00 5.10
8 9 0.873743 GCATCACTAGCAGACCTCGC 60.874 60.000 0.00 0.00 0.00 5.03
9 10 0.743688 AGCATCACTAGCAGACCTCG 59.256 55.000 0.00 0.00 0.00 4.63
10 11 2.031120 AGAGCATCACTAGCAGACCTC 58.969 52.381 0.00 0.00 37.82 3.85
11 12 2.157640 AGAGCATCACTAGCAGACCT 57.842 50.000 0.00 0.00 37.82 3.85
12 13 3.798548 GCTTAGAGCATCACTAGCAGACC 60.799 52.174 0.00 0.00 41.89 3.85
13 14 3.068024 AGCTTAGAGCATCACTAGCAGAC 59.932 47.826 2.47 0.00 45.56 3.51
14 15 3.295093 AGCTTAGAGCATCACTAGCAGA 58.705 45.455 2.47 0.00 45.56 4.26
15 16 3.731652 AGCTTAGAGCATCACTAGCAG 57.268 47.619 2.47 0.00 45.56 4.24
16 17 4.478206 AAAGCTTAGAGCATCACTAGCA 57.522 40.909 0.00 0.00 45.56 3.49
17 18 4.272261 GGAAAAGCTTAGAGCATCACTAGC 59.728 45.833 0.00 0.00 45.56 3.42
18 19 5.523188 CAGGAAAAGCTTAGAGCATCACTAG 59.477 44.000 0.00 0.00 45.56 2.57
19 20 5.423015 CAGGAAAAGCTTAGAGCATCACTA 58.577 41.667 0.00 0.00 45.56 2.74
20 21 4.260170 CAGGAAAAGCTTAGAGCATCACT 58.740 43.478 0.00 0.00 45.56 3.41
21 22 3.376546 CCAGGAAAAGCTTAGAGCATCAC 59.623 47.826 0.00 0.00 45.56 3.06
22 23 3.264193 TCCAGGAAAAGCTTAGAGCATCA 59.736 43.478 0.00 0.00 45.56 3.07
23 24 3.625313 GTCCAGGAAAAGCTTAGAGCATC 59.375 47.826 0.00 0.00 45.56 3.91
24 25 3.009473 TGTCCAGGAAAAGCTTAGAGCAT 59.991 43.478 0.00 0.00 45.56 3.79
25 26 2.371841 TGTCCAGGAAAAGCTTAGAGCA 59.628 45.455 0.00 0.00 45.56 4.26
26 27 2.744741 GTGTCCAGGAAAAGCTTAGAGC 59.255 50.000 0.00 0.00 42.84 4.09
27 28 4.008074 TGTGTCCAGGAAAAGCTTAGAG 57.992 45.455 0.00 0.00 0.00 2.43
28 29 4.640771 ATGTGTCCAGGAAAAGCTTAGA 57.359 40.909 0.00 0.00 0.00 2.10
29 30 5.940470 AGTAATGTGTCCAGGAAAAGCTTAG 59.060 40.000 0.00 0.00 0.00 2.18
30 31 5.876357 AGTAATGTGTCCAGGAAAAGCTTA 58.124 37.500 0.00 0.00 0.00 3.09
36 37 5.011329 ACTCGTAAGTAATGTGTCCAGGAAA 59.989 40.000 0.00 0.00 32.59 3.13
40 41 5.466819 TGAACTCGTAAGTAATGTGTCCAG 58.533 41.667 0.00 0.00 33.48 3.86
48 49 6.034591 CCAATCGACTGAACTCGTAAGTAAT 58.965 40.000 0.00 0.00 33.48 1.89
50 51 4.456911 ACCAATCGACTGAACTCGTAAGTA 59.543 41.667 0.00 0.00 33.48 2.24
54 55 5.165911 GATACCAATCGACTGAACTCGTA 57.834 43.478 0.00 0.00 35.10 3.43
85 86 4.699522 GTGTCCTCCGCCACCACC 62.700 72.222 0.00 0.00 0.00 4.61
113 114 2.564553 CTACCGCTGCTGTCTCCACC 62.565 65.000 0.00 0.00 0.00 4.61
122 123 4.899239 GCCATCGCTACCGCTGCT 62.899 66.667 0.00 0.00 29.75 4.24
188 189 6.095300 TGTTAAACATGCTATGCTTGTGCTAT 59.905 34.615 10.93 3.14 44.18 2.97
219 224 4.503910 AGCTCATTGACGTGCATAAACTA 58.496 39.130 0.00 0.00 0.00 2.24
220 225 3.338249 AGCTCATTGACGTGCATAAACT 58.662 40.909 0.00 0.00 0.00 2.66
221 226 3.747099 AGCTCATTGACGTGCATAAAC 57.253 42.857 0.00 0.00 0.00 2.01
222 227 4.503910 ACTAGCTCATTGACGTGCATAAA 58.496 39.130 0.00 0.00 0.00 1.40
223 228 4.123497 ACTAGCTCATTGACGTGCATAA 57.877 40.909 0.00 0.00 0.00 1.90
224 229 3.801114 ACTAGCTCATTGACGTGCATA 57.199 42.857 0.00 0.00 0.00 3.14
225 230 2.680312 ACTAGCTCATTGACGTGCAT 57.320 45.000 0.00 0.00 0.00 3.96
226 231 2.455674 AACTAGCTCATTGACGTGCA 57.544 45.000 0.00 0.00 0.00 4.57
227 232 4.783450 GCATAAACTAGCTCATTGACGTGC 60.783 45.833 0.00 0.00 0.00 5.34
228 233 4.329801 TGCATAAACTAGCTCATTGACGTG 59.670 41.667 0.00 0.00 0.00 4.49
229 234 4.330074 GTGCATAAACTAGCTCATTGACGT 59.670 41.667 0.00 0.00 0.00 4.34
230 235 4.548916 CGTGCATAAACTAGCTCATTGACG 60.549 45.833 0.00 0.00 0.00 4.35
231 236 4.330074 ACGTGCATAAACTAGCTCATTGAC 59.670 41.667 0.00 0.00 0.00 3.18
232 237 4.503910 ACGTGCATAAACTAGCTCATTGA 58.496 39.130 0.00 0.00 0.00 2.57
233 238 4.329801 TGACGTGCATAAACTAGCTCATTG 59.670 41.667 0.00 0.00 0.00 2.82
234 239 4.503910 TGACGTGCATAAACTAGCTCATT 58.496 39.130 0.00 0.00 0.00 2.57
235 240 4.123497 TGACGTGCATAAACTAGCTCAT 57.877 40.909 0.00 0.00 0.00 2.90
236 241 3.586100 TGACGTGCATAAACTAGCTCA 57.414 42.857 0.00 0.00 0.00 4.26
237 242 4.330074 ACATTGACGTGCATAAACTAGCTC 59.670 41.667 0.00 0.00 0.00 4.09
238 243 4.253685 ACATTGACGTGCATAAACTAGCT 58.746 39.130 0.00 0.00 0.00 3.32
239 244 4.600012 ACATTGACGTGCATAAACTAGC 57.400 40.909 0.00 0.00 0.00 3.42
240 245 6.164408 TCAACATTGACGTGCATAAACTAG 57.836 37.500 0.00 0.00 31.01 2.57
241 246 6.348132 CCTTCAACATTGACGTGCATAAACTA 60.348 38.462 0.00 0.00 36.83 2.24
259 264 0.661483 GCTTGCACTTCGCCTTCAAC 60.661 55.000 0.00 0.00 41.33 3.18
301 306 2.773993 ATTAGTTGGGTACACACGGG 57.226 50.000 0.00 0.00 0.00 5.28
304 309 7.874528 AGTACACTAAATTAGTTGGGTACACAC 59.125 37.037 22.78 8.65 37.78 3.82
306 311 9.927668 TTAGTACACTAAATTAGTTGGGTACAC 57.072 33.333 22.78 9.38 37.78 2.90
569 2004 7.340487 AGAGAAGGAACCAAAATCATATGAACC 59.660 37.037 9.99 4.01 0.00 3.62
575 2010 7.723616 TGTTTCAGAGAAGGAACCAAAATCATA 59.276 33.333 0.00 0.00 0.00 2.15
585 2020 7.572168 GCTTATCTTGTGTTTCAGAGAAGGAAC 60.572 40.741 5.87 0.00 0.00 3.62
672 2114 2.086869 CAAGGACATGCCAACTACCAG 58.913 52.381 8.58 0.00 40.02 4.00
731 2173 3.788227 TCAATGCTCCTAGTGTTTGGT 57.212 42.857 0.00 0.00 0.00 3.67
732 2174 4.460382 ACATTCAATGCTCCTAGTGTTTGG 59.540 41.667 0.00 0.00 0.00 3.28
859 2302 0.591170 TTAGTGCTGCGTTGAAAGCC 59.409 50.000 0.00 0.00 38.71 4.35
935 2382 2.101750 TGAGTGTCTACTTTGGCGAACA 59.898 45.455 0.00 0.00 37.25 3.18
936 2383 2.750948 TGAGTGTCTACTTTGGCGAAC 58.249 47.619 0.00 0.00 37.25 3.95
1050 2497 6.500751 AGGAGTACTTGTTTATCAGGAAGGAA 59.499 38.462 0.00 0.00 0.00 3.36
1144 2591 4.015084 CTCCCATCTGCTTCTTCAACAAT 58.985 43.478 0.00 0.00 0.00 2.71
1202 2649 0.458669 CATGGCCTCTGAATGCAACC 59.541 55.000 3.32 0.00 0.00 3.77
1208 2655 2.092212 CCTTGGTACATGGCCTCTGAAT 60.092 50.000 3.32 0.00 46.55 2.57
1268 2715 0.933097 CTCGATGATGCCTTTGTCCG 59.067 55.000 0.00 0.00 0.00 4.79
1804 3251 3.498018 CCAGCCAACCTTTTAACAAATGC 59.502 43.478 0.00 0.00 0.00 3.56
1825 3272 0.106819 ATGATCACCTTGCTGCCTCC 60.107 55.000 0.00 0.00 0.00 4.30
1830 3277 7.281774 AGTTTACTTATGATGATCACCTTGCTG 59.718 37.037 0.00 0.00 0.00 4.41
1883 3330 8.711457 ACAAATTATTGAGAAAAATTGGCTTCG 58.289 29.630 0.00 0.00 38.94 3.79
1942 3389 2.102252 GGTTCACACTTCCAAATGCCAA 59.898 45.455 0.00 0.00 0.00 4.52
1958 3405 2.549992 CGTGGATGTTCTTCCAGGTTCA 60.550 50.000 14.87 0.00 46.31 3.18
1959 3406 2.076863 CGTGGATGTTCTTCCAGGTTC 58.923 52.381 14.87 2.80 46.31 3.62
1964 3411 3.162666 ACTAGTCGTGGATGTTCTTCCA 58.837 45.455 3.75 3.75 43.56 3.53
1993 3440 5.622914 GCAACATCTTGGCATATTCTTGTGT 60.623 40.000 0.00 0.00 0.00 3.72
2056 3503 7.913789 ACATTCAGGTTGTTCCTTAGTACATA 58.086 34.615 0.00 0.00 45.67 2.29
2064 3511 3.593442 TGGACATTCAGGTTGTTCCTT 57.407 42.857 0.00 0.00 45.67 3.36
2383 3830 2.208872 AGGCATATCCTGAACCCAGTT 58.791 47.619 0.00 0.00 45.54 3.16
2503 3955 9.474920 CTTTGCAAAAAGACCACTAATTTCATA 57.525 29.630 13.84 0.00 31.58 2.15
2540 3992 5.615289 AGTATGCCTAGTGACATCAAATCC 58.385 41.667 0.00 0.00 0.00 3.01
2547 3999 3.325135 GGCCTTAGTATGCCTAGTGACAT 59.675 47.826 0.00 0.00 44.46 3.06
2578 4032 6.372659 GGACCATATACATGCAGAATTACAGG 59.627 42.308 0.00 0.00 0.00 4.00
2638 4093 9.240159 GAAGTATAAAAGGAAGTTTCGCAAAAA 57.760 29.630 0.00 0.00 0.00 1.94
2639 4094 8.407064 TGAAGTATAAAAGGAAGTTTCGCAAAA 58.593 29.630 0.00 0.00 0.00 2.44
2640 4095 7.932335 TGAAGTATAAAAGGAAGTTTCGCAAA 58.068 30.769 0.00 0.00 0.00 3.68
2641 4096 7.499321 TGAAGTATAAAAGGAAGTTTCGCAA 57.501 32.000 0.00 0.00 0.00 4.85
2642 4097 7.681939 ATGAAGTATAAAAGGAAGTTTCGCA 57.318 32.000 0.00 0.00 0.00 5.10
2643 4098 7.696872 GGAATGAAGTATAAAAGGAAGTTTCGC 59.303 37.037 0.00 0.00 0.00 4.70
2644 4099 8.947115 AGGAATGAAGTATAAAAGGAAGTTTCG 58.053 33.333 0.00 0.00 0.00 3.46
2790 4250 2.115910 CTCCACCCAGCCAAAGCA 59.884 61.111 0.00 0.00 43.56 3.91
2855 4356 5.789643 ACATTTTGGTTCTGCTACAATGT 57.210 34.783 0.00 0.00 0.00 2.71
2921 4464 8.628630 ATTTTTCTCTCCTCAGGTTTTAAGAG 57.371 34.615 0.57 0.57 33.22 2.85
2977 4543 4.972751 AATTTTGTAACCAACAGGCCAT 57.027 36.364 5.01 0.00 39.87 4.40
3042 4635 7.770897 GTCACCATCAGATTGACTTATAACCTT 59.229 37.037 7.69 0.00 37.31 3.50
3043 4636 7.275920 GTCACCATCAGATTGACTTATAACCT 58.724 38.462 7.69 0.00 37.31 3.50
3049 4642 4.080919 CCAGGTCACCATCAGATTGACTTA 60.081 45.833 12.91 0.00 39.72 2.24
3164 4761 0.179192 TTCGCAAGCAGCAATAAGCG 60.179 50.000 9.68 9.68 46.13 4.68
3182 4779 5.567423 GCAGCCATTGTTGACCTTTCTATTT 60.567 40.000 0.00 0.00 0.00 1.40
3213 4811 1.302383 CCAATTAAGCGGCCGACACA 61.302 55.000 33.48 10.02 0.00 3.72
3219 4819 5.938125 TCTAAGATAATCCAATTAAGCGGCC 59.062 40.000 0.00 0.00 0.00 6.13
3334 4934 5.006746 GCAGTACTACATGTCCATTGTAAGC 59.993 44.000 0.00 4.28 0.00 3.09


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

AutoCloner maintained by Alex Coulton.