Multiple sequence alignment - TraesCS1B01G048300

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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 TraesCS1B01G048300 chr1B 100.000 4400 0 0 1 4400 28376862 28372463 0.000000e+00 8126.0
1 TraesCS1B01G048300 chr1B 91.724 2767 189 28 860 3606 28324906 28322160 0.000000e+00 3805.0
2 TraesCS1B01G048300 chr1B 91.828 2582 188 14 1045 3606 28308525 28305947 0.000000e+00 3578.0
3 TraesCS1B01G048300 chr1B 89.951 2468 203 22 1088 3534 28445634 28443191 0.000000e+00 3142.0
4 TraesCS1B01G048300 chr1B 85.213 2678 318 52 841 3483 28483484 28486118 0.000000e+00 2680.0
5 TraesCS1B01G048300 chr1B 90.813 283 25 1 3943 4224 28320859 28320577 1.160000e-100 377.0
6 TraesCS1B01G048300 chr1B 84.512 297 26 10 172 466 28325616 28325338 4.330000e-70 276.0
7 TraesCS1B01G048300 chr1B 87.562 201 21 1 3723 3923 28322006 28321810 3.420000e-56 230.0
8 TraesCS1B01G048300 chr1B 80.731 301 29 13 172 466 28309465 28309188 1.600000e-49 207.0
9 TraesCS1B01G048300 chr1B 84.906 212 20 7 3723 3934 28305730 28305531 2.070000e-48 204.0
10 TraesCS1B01G048300 chr1B 85.612 139 17 2 4262 4399 28320572 28320436 4.590000e-30 143.0
11 TraesCS1B01G048300 chr4A 92.056 2996 153 33 601 3537 675286158 675283189 0.000000e+00 4135.0
12 TraesCS1B01G048300 chr4A 89.773 176 12 4 160 331 675286649 675286476 2.060000e-53 220.0
13 TraesCS1B01G048300 chr4A 95.726 117 4 1 465 581 675286420 675286305 2.090000e-43 187.0
14 TraesCS1B01G048300 chr5B 91.681 2825 193 17 812 3608 641833079 641835889 0.000000e+00 3877.0
15 TraesCS1B01G048300 chr5B 88.066 2782 269 42 860 3606 641822021 641824774 0.000000e+00 3240.0
16 TraesCS1B01G048300 chr5B 83.466 1881 280 14 1620 3487 641814275 641812413 0.000000e+00 1722.0
17 TraesCS1B01G048300 chr5B 94.924 591 26 4 3637 4224 641835994 641836583 0.000000e+00 922.0
18 TraesCS1B01G048300 chr5B 90.339 383 25 6 29 405 641832332 641832708 3.950000e-135 492.0
19 TraesCS1B01G048300 chr5B 82.090 201 7 11 591 784 641832901 641833079 1.280000e-30 145.0
20 TraesCS1B01G048300 chr5B 94.595 37 2 0 3603 3639 641835935 641835971 1.710000e-04 58.4
21 TraesCS1B01G048300 chr1A 89.214 3078 219 49 583 3606 20927824 20924806 0.000000e+00 3740.0
22 TraesCS1B01G048300 chr1A 88.294 299 32 3 3928 4226 20923657 20923362 5.410000e-94 355.0
23 TraesCS1B01G048300 chr1A 90.400 125 12 0 3810 3934 20924737 20924613 9.790000e-37 165.0
24 TraesCS1B01G048300 chr1A 82.558 172 13 6 84 255 20928239 20928085 7.680000e-28 135.0
25 TraesCS1B01G048300 chr1D 90.896 2724 203 23 841 3537 19002702 18999997 0.000000e+00 3615.0
26 TraesCS1B01G048300 chr1D 89.933 2692 233 19 860 3534 19020999 19018329 0.000000e+00 3435.0
27 TraesCS1B01G048300 chr1D 92.203 2206 118 24 169 2360 19015414 19013249 0.000000e+00 3072.0
28 TraesCS1B01G048300 chr1D 92.804 1209 77 7 2402 3608 19013249 19012049 0.000000e+00 1742.0
29 TraesCS1B01G048300 chr1D 90.199 755 33 20 3637 4384 19011944 19011224 0.000000e+00 946.0
30 TraesCS1B01G048300 chr1D 86.093 302 20 7 3925 4219 18999609 18999323 5.530000e-79 305.0
31 TraesCS1B01G048300 chr1D 91.724 145 8 3 169 312 19004471 19004330 9.650000e-47 198.0
32 TraesCS1B01G048300 chr1D 90.476 105 7 2 169 273 19005416 19005315 7.680000e-28 135.0
33 TraesCS1B01G048300 chr1D 84.672 137 14 5 591 726 19003025 19002895 3.570000e-26 130.0
34 TraesCS1B01G048300 chr1D 88.235 51 5 1 3447 3497 19046142 19046191 4.750000e-05 60.2
35 TraesCS1B01G048300 chr1D 94.595 37 2 0 3603 3639 19012003 19011967 1.710000e-04 58.4


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 TraesCS1B01G048300 chr1B 28372463 28376862 4399 True 8126.000000 8126 100.000000 1 4400 1 chr1B.!!$R1 4399
1 TraesCS1B01G048300 chr1B 28443191 28445634 2443 True 3142.000000 3142 89.951000 1088 3534 1 chr1B.!!$R2 2446
2 TraesCS1B01G048300 chr1B 28483484 28486118 2634 False 2680.000000 2680 85.213000 841 3483 1 chr1B.!!$F1 2642
3 TraesCS1B01G048300 chr1B 28305531 28309465 3934 True 1329.666667 3578 85.821667 172 3934 3 chr1B.!!$R3 3762
4 TraesCS1B01G048300 chr1B 28320436 28325616 5180 True 966.200000 3805 88.044600 172 4399 5 chr1B.!!$R4 4227
5 TraesCS1B01G048300 chr4A 675283189 675286649 3460 True 1514.000000 4135 92.518333 160 3537 3 chr4A.!!$R1 3377
6 TraesCS1B01G048300 chr5B 641822021 641824774 2753 False 3240.000000 3240 88.066000 860 3606 1 chr5B.!!$F1 2746
7 TraesCS1B01G048300 chr5B 641812413 641814275 1862 True 1722.000000 1722 83.466000 1620 3487 1 chr5B.!!$R1 1867
8 TraesCS1B01G048300 chr5B 641832332 641836583 4251 False 1098.880000 3877 90.725800 29 4224 5 chr5B.!!$F2 4195
9 TraesCS1B01G048300 chr1A 20923362 20928239 4877 True 1098.750000 3740 87.616500 84 4226 4 chr1A.!!$R1 4142
10 TraesCS1B01G048300 chr1D 19011224 19020999 9775 True 1850.680000 3435 91.946800 169 4384 5 chr1D.!!$R2 4215
11 TraesCS1B01G048300 chr1D 18999323 19005416 6093 True 876.600000 3615 88.772200 169 4219 5 chr1D.!!$R1 4050

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
759 8403 0.035056 AGTGGCATGGACCAAGTAGC 60.035 55.0 0.00 0.3 42.70 3.58 F
1594 9473 0.623723 TCCTTAATGCCGGAGCCTTT 59.376 50.0 5.05 0.0 38.69 3.11 F
2878 10760 0.684479 AGGACCTGCTGCTCACGATA 60.684 55.0 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
2704 10583 0.548031 AGGCGACCATGAATGTGGAT 59.452 50.000 0.0 0.0 42.02 3.41 R
3111 10993 0.604073 TTCGGTGATACGGTTCTGCA 59.396 50.000 0.0 0.0 0.00 4.41 R
4002 13041 1.204704 GGCCACCCTGTAAATTTCAGC 59.795 52.381 0.0 0.0 0.00 4.26 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 2.142220 TCCCTGTCCCTTGACACAC 58.858 57.895 0.00 0.00 46.40 3.82
19 20 0.692756 TCCCTGTCCCTTGACACACA 60.693 55.000 0.00 0.00 46.40 3.72
20 21 0.250467 CCCTGTCCCTTGACACACAG 60.250 60.000 0.00 0.00 46.40 3.66
21 22 0.758734 CCTGTCCCTTGACACACAGA 59.241 55.000 0.00 0.00 46.40 3.41
22 23 1.270518 CCTGTCCCTTGACACACAGAG 60.271 57.143 0.00 0.00 46.40 3.35
23 24 1.688735 CTGTCCCTTGACACACAGAGA 59.311 52.381 0.00 0.00 46.40 3.10
24 25 2.301296 CTGTCCCTTGACACACAGAGAT 59.699 50.000 0.00 0.00 46.40 2.75
25 26 2.037641 TGTCCCTTGACACACAGAGATG 59.962 50.000 0.00 0.00 46.40 2.90
27 28 1.446907 CCTTGACACACAGAGATGCC 58.553 55.000 0.00 0.00 0.00 4.40
29 30 2.497138 CTTGACACACAGAGATGCCAA 58.503 47.619 0.00 0.00 0.00 4.52
30 31 2.636647 TGACACACAGAGATGCCAAA 57.363 45.000 0.00 0.00 0.00 3.28
31 32 2.221169 TGACACACAGAGATGCCAAAC 58.779 47.619 0.00 0.00 0.00 2.93
38 39 4.037208 ACACAGAGATGCCAAACAGAAAAG 59.963 41.667 0.00 0.00 0.00 2.27
75 76 2.340809 CTGGACACGGGCGTTACA 59.659 61.111 0.00 0.00 0.00 2.41
76 77 1.079405 CTGGACACGGGCGTTACAT 60.079 57.895 0.00 0.00 0.00 2.29
113 114 2.444624 GCACTTCTCGCGCGAATCA 61.445 57.895 33.99 17.57 0.00 2.57
164 165 2.408704 CGTCGACTGAAACTTGGCTAAG 59.591 50.000 14.70 8.47 39.86 2.18
180 181 4.275689 TGGCTAAGTCGGCAATGAAATATG 59.724 41.667 0.00 0.00 36.45 1.78
182 183 4.515191 GCTAAGTCGGCAATGAAATATGGA 59.485 41.667 0.00 0.00 0.00 3.41
183 184 4.900635 AAGTCGGCAATGAAATATGGAC 57.099 40.909 0.00 0.00 0.00 4.02
187 5600 3.627123 TCGGCAATGAAATATGGACACAG 59.373 43.478 0.00 0.00 0.00 3.66
252 6613 3.826157 CTGGTCCTAATTTTCTGTGGCAA 59.174 43.478 0.00 0.00 0.00 4.52
301 6666 1.269517 GGATGACTGACGAGAGGATGC 60.270 57.143 0.00 0.00 0.00 3.91
303 6668 1.064946 GACTGACGAGAGGATGCCG 59.935 63.158 0.00 0.00 0.00 5.69
304 6669 1.658686 GACTGACGAGAGGATGCCGT 61.659 60.000 0.00 0.00 39.41 5.68
306 6671 0.803768 CTGACGAGAGGATGCCGTTG 60.804 60.000 0.00 0.00 36.60 4.10
311 7713 1.535462 CGAGAGGATGCCGTTGTTTTT 59.465 47.619 0.00 0.00 0.00 1.94
312 7714 2.412847 CGAGAGGATGCCGTTGTTTTTC 60.413 50.000 0.00 0.00 0.00 2.29
341 7748 0.661020 CGTTTCCACCGAGCAAACTT 59.339 50.000 0.00 0.00 0.00 2.66
343 7750 2.288458 CGTTTCCACCGAGCAAACTTAA 59.712 45.455 0.00 0.00 0.00 1.85
393 7802 0.472044 TGGCAAGTCAAGTGGCACTA 59.528 50.000 22.37 2.68 45.61 2.74
394 7803 0.875059 GGCAAGTCAAGTGGCACTAC 59.125 55.000 22.37 16.39 41.05 2.73
407 7816 2.224185 TGGCACTACATCTTTCACACGT 60.224 45.455 0.00 0.00 0.00 4.49
408 7817 3.006003 TGGCACTACATCTTTCACACGTA 59.994 43.478 0.00 0.00 0.00 3.57
409 7818 3.367025 GGCACTACATCTTTCACACGTAC 59.633 47.826 0.00 0.00 0.00 3.67
411 7820 3.606777 CACTACATCTTTCACACGTACGG 59.393 47.826 21.06 11.05 0.00 4.02
412 7821 2.806608 ACATCTTTCACACGTACGGT 57.193 45.000 21.06 11.73 0.00 4.83
434 7843 3.055891 TGGTATACATATCATGCAGCGCT 60.056 43.478 2.64 2.64 0.00 5.92
465 7918 1.226746 GCAAACCGGAATATCCCTCG 58.773 55.000 9.46 0.00 31.13 4.63
477 7946 3.691342 CCCTCGCTGGTGACCGAA 61.691 66.667 0.00 0.00 32.56 4.30
553 8030 9.555727 ACAAAATACTAGTGAAAGTGAAAGCTA 57.444 29.630 5.39 0.00 0.00 3.32
568 8046 6.769822 AGTGAAAGCTATTGTGGATCATTAGG 59.230 38.462 0.00 0.00 33.28 2.69
581 8059 6.017605 GTGGATCATTAGGCAGATAACAACTG 60.018 42.308 0.00 0.00 38.27 3.16
632 8237 1.369625 CAAAGACCATACCTCCGTGC 58.630 55.000 0.00 0.00 0.00 5.34
633 8238 0.108329 AAAGACCATACCTCCGTGCG 60.108 55.000 0.00 0.00 0.00 5.34
634 8239 1.255667 AAGACCATACCTCCGTGCGT 61.256 55.000 0.00 0.00 0.00 5.24
635 8240 1.518572 GACCATACCTCCGTGCGTG 60.519 63.158 0.00 0.00 0.00 5.34
729 8354 6.259638 TGTTTGAAACGTTCACCATTAGAAC 58.740 36.000 0.00 3.06 39.87 3.01
757 8401 0.249120 CGAGTGGCATGGACCAAGTA 59.751 55.000 0.00 0.00 42.70 2.24
758 8402 1.740380 CGAGTGGCATGGACCAAGTAG 60.740 57.143 0.00 0.00 42.70 2.57
759 8403 0.035056 AGTGGCATGGACCAAGTAGC 60.035 55.000 0.00 0.30 42.70 3.58
788 8432 5.983540 AGATTCGTTTCTCCTAAGAGCAAT 58.016 37.500 0.00 0.00 40.22 3.56
871 8640 1.694525 TCAAGTCCACACCCACCCA 60.695 57.895 0.00 0.00 0.00 4.51
872 8641 1.528309 CAAGTCCACACCCACCCAC 60.528 63.158 0.00 0.00 0.00 4.61
948 8752 0.972983 TCCCTCGCTTTCCTCTCCAG 60.973 60.000 0.00 0.00 0.00 3.86
1075 8924 1.945354 GATGGAGTGCGAGAACGGGA 61.945 60.000 0.00 0.00 40.15 5.14
1197 9046 2.746277 GCGGTGAAGCGGATGGTT 60.746 61.111 3.89 0.00 38.83 3.67
1233 9082 2.677228 GTGGTGACCATGGAGGGG 59.323 66.667 21.47 0.00 43.89 4.79
1523 9394 4.817517 TGATCGTCCTGTACTCCTTTTTC 58.182 43.478 0.00 0.00 0.00 2.29
1594 9473 0.623723 TCCTTAATGCCGGAGCCTTT 59.376 50.000 5.05 0.00 38.69 3.11
2005 9884 3.010420 GCTTTTCGAGGCTAACATCCTT 58.990 45.455 0.00 0.00 33.24 3.36
2116 9995 3.781307 CACCCCGGGCAGATCGAA 61.781 66.667 17.73 0.00 0.00 3.71
2584 10463 0.739112 GCTCCGAGCTCCAGTTCTTG 60.739 60.000 13.42 0.00 38.45 3.02
2636 10515 2.677836 GCCGAGCAACACAATCAAGATA 59.322 45.455 0.00 0.00 0.00 1.98
2728 10607 1.167851 CATTCATGGTCGCCTTGTGT 58.832 50.000 10.16 1.28 31.64 3.72
2781 10660 1.071542 TGTCAAGGATGCCGTCAAGAA 59.928 47.619 0.00 0.00 0.00 2.52
2878 10760 0.684479 AGGACCTGCTGCTCACGATA 60.684 55.000 0.00 0.00 0.00 2.92
3005 10887 3.432588 CCGAGCTCGACGTGGAGT 61.433 66.667 36.59 14.25 43.02 3.85
3054 10936 4.074526 GCAGGAGCTCCGTGCAGA 62.075 66.667 33.85 0.00 45.94 4.26
3084 10966 4.115199 GGTTGAGGCTGCCCGGAT 62.115 66.667 16.57 0.00 35.76 4.18
3185 11067 0.537653 GGAGCTTGGGACTGAGTACC 59.462 60.000 6.98 6.98 36.98 3.34
3268 11150 3.422303 GGCAAGCACATCGACGCA 61.422 61.111 6.14 0.00 0.00 5.24
3316 11198 0.543749 GTGAGCCCTTGCCTATCTGT 59.456 55.000 0.00 0.00 38.69 3.41
3321 11203 2.243221 AGCCCTTGCCTATCTGTTGAAT 59.757 45.455 0.00 0.00 38.69 2.57
3539 11469 8.313944 AGGGTACAGTGTATGACAAATATACA 57.686 34.615 6.21 0.00 38.36 2.29
3606 11612 3.317993 ACCAACAGTGCAAAACATCTACC 59.682 43.478 0.00 0.00 0.00 3.18
3684 11715 7.869937 TGTTTCAGTTTTCTGTTGACAAATTCA 59.130 29.630 0.00 0.00 46.98 2.57
3685 11716 8.375465 GTTTCAGTTTTCTGTTGACAAATTCAG 58.625 33.333 0.00 0.00 46.98 3.02
3686 11717 7.389803 TCAGTTTTCTGTTGACAAATTCAGA 57.610 32.000 3.52 3.52 46.98 3.27
3717 11769 8.147642 CATGTAATGGAAGAAGGATTGTACTC 57.852 38.462 0.00 0.00 41.79 2.59
3718 11770 7.496346 TGTAATGGAAGAAGGATTGTACTCT 57.504 36.000 0.00 0.00 0.00 3.24
3719 11771 7.331026 TGTAATGGAAGAAGGATTGTACTCTG 58.669 38.462 0.00 0.00 0.00 3.35
3720 11772 6.380079 AATGGAAGAAGGATTGTACTCTGT 57.620 37.500 0.00 0.00 0.00 3.41
3767 11820 7.861629 TCTGTTCCTGAATGGTCATAAGTAAT 58.138 34.615 0.00 0.00 37.07 1.89
4002 13041 0.391263 GGTTGGCCTCCGTCAGTTAG 60.391 60.000 3.32 0.00 0.00 2.34
4061 13106 1.334243 CTACACAGCGGAGTAGTAGGC 59.666 57.143 12.08 0.00 34.63 3.93
4092 13137 5.659440 AGAATTCAGAGAAGAGACTGACC 57.341 43.478 8.44 0.00 41.82 4.02
4230 13294 7.902387 CTCTTGTAGCTGATGTGCAATATAT 57.098 36.000 0.00 0.00 34.99 0.86
4231 13295 8.992835 CTCTTGTAGCTGATGTGCAATATATA 57.007 34.615 0.00 0.00 34.99 0.86
4232 13296 9.428097 CTCTTGTAGCTGATGTGCAATATATAA 57.572 33.333 0.00 0.00 34.99 0.98
4233 13297 9.428097 TCTTGTAGCTGATGTGCAATATATAAG 57.572 33.333 0.00 0.00 34.99 1.73
4234 13298 7.601073 TGTAGCTGATGTGCAATATATAAGC 57.399 36.000 0.00 0.00 35.22 3.09
4235 13299 7.389232 TGTAGCTGATGTGCAATATATAAGCT 58.611 34.615 14.33 14.33 44.43 3.74
4236 13300 6.981762 AGCTGATGTGCAATATATAAGCTC 57.018 37.500 10.38 7.92 39.78 4.09
4237 13301 6.709281 AGCTGATGTGCAATATATAAGCTCT 58.291 36.000 10.38 0.00 39.78 4.09
4238 13302 6.817641 AGCTGATGTGCAATATATAAGCTCTC 59.182 38.462 10.38 7.56 39.78 3.20
4239 13303 6.817641 GCTGATGTGCAATATATAAGCTCTCT 59.182 38.462 10.38 1.73 32.91 3.10
4240 13304 7.333921 GCTGATGTGCAATATATAAGCTCTCTT 59.666 37.037 10.38 0.00 32.91 2.85
4241 13305 9.217278 CTGATGTGCAATATATAAGCTCTCTTT 57.783 33.333 10.38 0.00 33.85 2.52
4242 13306 9.212641 TGATGTGCAATATATAAGCTCTCTTTC 57.787 33.333 10.38 5.52 33.85 2.62
4243 13307 9.212641 GATGTGCAATATATAAGCTCTCTTTCA 57.787 33.333 10.38 0.00 33.85 2.69
4244 13308 8.370493 TGTGCAATATATAAGCTCTCTTTCAC 57.630 34.615 10.38 0.79 33.85 3.18
4245 13309 8.206867 TGTGCAATATATAAGCTCTCTTTCACT 58.793 33.333 10.38 0.00 33.85 3.41
4246 13310 9.698309 GTGCAATATATAAGCTCTCTTTCACTA 57.302 33.333 10.38 0.00 33.85 2.74
4305 13369 3.681593 TGTGTAAGGATTGTAACAGCCC 58.318 45.455 0.00 0.00 0.00 5.19
4308 13372 4.156008 GTGTAAGGATTGTAACAGCCCTTG 59.844 45.833 11.88 0.00 37.73 3.61
4309 13373 3.806949 AAGGATTGTAACAGCCCTTGA 57.193 42.857 0.00 0.00 36.03 3.02
4314 13378 6.534634 AGGATTGTAACAGCCCTTGATATAC 58.465 40.000 0.00 0.00 0.00 1.47
4316 13380 6.770785 GGATTGTAACAGCCCTTGATATACAA 59.229 38.462 0.00 0.00 37.77 2.41
4317 13381 7.448469 GGATTGTAACAGCCCTTGATATACAAT 59.552 37.037 7.70 7.70 41.47 2.71
4381 13445 9.743057 CAATGTGTTAAACTTGAATTAGAACCA 57.257 29.630 0.00 0.00 0.00 3.67
4396 13460 4.052159 AGAACCAGCTACATCAGAATCG 57.948 45.455 0.00 0.00 0.00 3.34
4399 13463 1.506493 CAGCTACATCAGAATCGCCC 58.494 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.693069 CATCTCTGTGTGTCAAGGGAC 58.307 52.381 0.00 0.00 44.57 4.46
6 7 1.002430 GCATCTCTGTGTGTCAAGGGA 59.998 52.381 0.00 0.00 0.00 4.20
8 9 1.271001 TGGCATCTCTGTGTGTCAAGG 60.271 52.381 0.00 0.00 0.00 3.61
10 11 2.618241 GTTTGGCATCTCTGTGTGTCAA 59.382 45.455 0.00 0.00 38.09 3.18
11 12 2.221169 GTTTGGCATCTCTGTGTGTCA 58.779 47.619 0.00 0.00 0.00 3.58
12 13 2.221169 TGTTTGGCATCTCTGTGTGTC 58.779 47.619 0.00 0.00 0.00 3.67
15 16 2.936919 TCTGTTTGGCATCTCTGTGT 57.063 45.000 0.00 0.00 0.00 3.72
18 19 4.758674 TCTCTTTTCTGTTTGGCATCTCTG 59.241 41.667 0.00 0.00 0.00 3.35
19 20 4.978099 TCTCTTTTCTGTTTGGCATCTCT 58.022 39.130 0.00 0.00 0.00 3.10
20 21 5.695851 TTCTCTTTTCTGTTTGGCATCTC 57.304 39.130 0.00 0.00 0.00 2.75
21 22 6.469782 TTTTCTCTTTTCTGTTTGGCATCT 57.530 33.333 0.00 0.00 0.00 2.90
22 23 6.018751 GGTTTTTCTCTTTTCTGTTTGGCATC 60.019 38.462 0.00 0.00 0.00 3.91
23 24 5.817296 GGTTTTTCTCTTTTCTGTTTGGCAT 59.183 36.000 0.00 0.00 0.00 4.40
24 25 5.175127 GGTTTTTCTCTTTTCTGTTTGGCA 58.825 37.500 0.00 0.00 0.00 4.92
25 26 5.175127 TGGTTTTTCTCTTTTCTGTTTGGC 58.825 37.500 0.00 0.00 0.00 4.52
27 28 5.868801 TGCTGGTTTTTCTCTTTTCTGTTTG 59.131 36.000 0.00 0.00 0.00 2.93
29 30 5.659440 TGCTGGTTTTTCTCTTTTCTGTT 57.341 34.783 0.00 0.00 0.00 3.16
30 31 5.659440 TTGCTGGTTTTTCTCTTTTCTGT 57.341 34.783 0.00 0.00 0.00 3.41
31 32 5.868801 TGTTTGCTGGTTTTTCTCTTTTCTG 59.131 36.000 0.00 0.00 0.00 3.02
38 39 2.101415 AGCCTGTTTGCTGGTTTTTCTC 59.899 45.455 0.00 0.00 40.90 2.87
75 76 2.562738 GCTTTGTCTTGTTTGGGCCTAT 59.437 45.455 4.53 0.00 0.00 2.57
76 77 1.960689 GCTTTGTCTTGTTTGGGCCTA 59.039 47.619 4.53 0.00 0.00 3.93
82 83 4.031028 CGAGAAGTGCTTTGTCTTGTTTG 58.969 43.478 0.00 0.00 0.00 2.93
113 114 3.372206 CGTCGGATCTTTCTTTGCTTCAT 59.628 43.478 0.00 0.00 0.00 2.57
164 165 3.376859 TGTGTCCATATTTCATTGCCGAC 59.623 43.478 0.00 0.00 0.00 4.79
180 181 0.104304 ACCAAGTCGTGTCTGTGTCC 59.896 55.000 0.00 0.00 0.00 4.02
182 183 0.535335 ACACCAAGTCGTGTCTGTGT 59.465 50.000 0.00 0.00 43.50 3.72
183 184 0.930310 CACACCAAGTCGTGTCTGTG 59.070 55.000 0.00 0.00 45.14 3.66
187 5600 2.601562 GGTCACACCAAGTCGTGTC 58.398 57.895 0.00 0.00 45.14 3.67
252 6613 4.798433 TGAACGCCATCACAAGCT 57.202 50.000 0.00 0.00 0.00 3.74
301 6666 5.754778 ACGATTTCTTAGGAAAAACAACGG 58.245 37.500 3.93 0.00 43.51 4.44
303 6668 7.703197 TGGAAACGATTTCTTAGGAAAAACAAC 59.297 33.333 3.93 0.00 43.51 3.32
304 6669 7.703197 GTGGAAACGATTTCTTAGGAAAAACAA 59.297 33.333 3.93 0.00 43.51 2.83
306 6671 6.639686 GGTGGAAACGATTTCTTAGGAAAAAC 59.360 38.462 3.93 1.72 43.51 2.43
311 7713 3.258872 TCGGTGGAAACGATTTCTTAGGA 59.741 43.478 0.00 0.00 39.59 2.94
312 7714 3.592059 TCGGTGGAAACGATTTCTTAGG 58.408 45.455 0.00 0.00 39.59 2.69
341 7748 2.810400 GCCACTTGACTTGCCAGACTTA 60.810 50.000 0.00 0.00 0.00 2.24
343 7750 0.536006 GCCACTTGACTTGCCAGACT 60.536 55.000 0.00 0.00 0.00 3.24
393 7802 2.400399 CACCGTACGTGTGAAAGATGT 58.600 47.619 23.91 5.97 37.73 3.06
394 7803 1.724623 CCACCGTACGTGTGAAAGATG 59.275 52.381 27.58 13.08 41.26 2.90
407 7816 5.623596 GCTGCATGATATGTATACCACCGTA 60.624 44.000 0.00 0.00 0.00 4.02
408 7817 4.820897 CTGCATGATATGTATACCACCGT 58.179 43.478 0.00 0.00 0.00 4.83
409 7818 3.618594 GCTGCATGATATGTATACCACCG 59.381 47.826 0.00 0.00 0.00 4.94
411 7820 3.062639 GCGCTGCATGATATGTATACCAC 59.937 47.826 0.00 0.00 0.00 4.16
412 7821 3.055891 AGCGCTGCATGATATGTATACCA 60.056 43.478 10.39 0.00 0.00 3.25
413 7822 3.525537 AGCGCTGCATGATATGTATACC 58.474 45.455 10.39 0.00 0.00 2.73
414 7823 4.428209 AGAGCGCTGCATGATATGTATAC 58.572 43.478 18.48 0.00 0.00 1.47
415 7824 4.725790 AGAGCGCTGCATGATATGTATA 57.274 40.909 18.48 0.00 0.00 1.47
416 7825 3.606595 AGAGCGCTGCATGATATGTAT 57.393 42.857 18.48 0.00 0.00 2.29
417 7826 3.119352 CCTAGAGCGCTGCATGATATGTA 60.119 47.826 18.48 0.00 0.00 2.29
418 7827 2.353505 CCTAGAGCGCTGCATGATATGT 60.354 50.000 18.48 0.00 0.00 2.29
419 7828 2.094338 TCCTAGAGCGCTGCATGATATG 60.094 50.000 18.48 0.00 0.00 1.78
420 7829 2.094286 GTCCTAGAGCGCTGCATGATAT 60.094 50.000 18.48 0.00 0.00 1.63
421 7830 1.270826 GTCCTAGAGCGCTGCATGATA 59.729 52.381 18.48 0.00 0.00 2.15
422 7831 0.033228 GTCCTAGAGCGCTGCATGAT 59.967 55.000 18.48 0.00 0.00 2.45
423 7832 1.439228 GTCCTAGAGCGCTGCATGA 59.561 57.895 18.48 2.93 0.00 3.07
434 7843 0.320374 CGGTTTGCACTGGTCCTAGA 59.680 55.000 0.00 0.00 0.00 2.43
465 7918 2.279918 ACGTGTTCGGTCACCAGC 60.280 61.111 0.00 0.00 41.85 4.85
477 7946 5.682943 TTTAATCTTAAGCTTGCACGTGT 57.317 34.783 18.38 0.00 0.00 4.49
553 8030 6.604171 TGTTATCTGCCTAATGATCCACAAT 58.396 36.000 0.00 0.00 0.00 2.71
581 8059 2.086054 ATCTGTGACTCGTCCAAAGC 57.914 50.000 0.00 0.00 0.00 3.51
659 8270 6.142480 GCACGATGCATAAACTACTACTGTAG 59.858 42.308 13.13 13.13 45.68 2.74
729 8354 0.994995 CATGCCACTCGTCTTCTTCG 59.005 55.000 0.00 0.00 0.00 3.79
757 8401 4.211920 AGGAGAAACGAATCTAGCTAGCT 58.788 43.478 23.12 23.12 0.00 3.32
758 8402 4.577834 AGGAGAAACGAATCTAGCTAGC 57.422 45.455 16.35 6.62 0.00 3.42
759 8403 7.499321 TCTTAGGAGAAACGAATCTAGCTAG 57.501 40.000 15.01 15.01 0.00 3.42
788 8432 1.002257 ATGCATGCAACGACCCAGA 60.002 52.632 26.68 0.00 0.00 3.86
871 8640 2.371391 AAATAGGTAGGGTGGTGGGT 57.629 50.000 0.00 0.00 0.00 4.51
872 8641 3.117776 GGTTAAATAGGTAGGGTGGTGGG 60.118 52.174 0.00 0.00 0.00 4.61
948 8752 0.514691 CGCTGAAGTGGAGCTCAAAC 59.485 55.000 17.19 13.15 34.03 2.93
1131 8980 2.895424 CGCCTTCCCCCAGTTCAGT 61.895 63.158 0.00 0.00 0.00 3.41
1166 9015 2.745884 CCGCGTCCAAATGGCTCA 60.746 61.111 4.92 0.00 34.44 4.26
1197 9046 1.452651 CGGCCTACGGTACTCCTCA 60.453 63.158 0.00 0.00 39.42 3.86
1498 9360 3.088789 AGGAGTACAGGACGATCAACT 57.911 47.619 0.00 0.00 0.00 3.16
1523 9394 6.521151 AATAAGGCTTCCAGATCACAAAAG 57.479 37.500 1.30 0.00 0.00 2.27
1564 9436 4.201950 CCGGCATTAAGGAATCTGAACAAG 60.202 45.833 0.00 0.00 0.00 3.16
2116 9995 3.769369 CTCCATGATGGCGGCAGCT 62.769 63.158 27.84 6.81 44.37 4.24
2584 10463 4.589675 TTGGTCACCGGGTTGCCC 62.590 66.667 6.32 0.00 41.09 5.36
2636 10515 4.405358 GGAGATGAGACCAAGAGAGTTGAT 59.595 45.833 0.00 0.00 0.00 2.57
2704 10583 0.548031 AGGCGACCATGAATGTGGAT 59.452 50.000 0.00 0.00 42.02 3.41
2728 10607 3.147595 CGGAGGTCGATGGCCTGA 61.148 66.667 3.32 0.00 42.43 3.86
3005 10887 2.555325 CAAGCTTGGCAAAGACAGATGA 59.445 45.455 19.14 0.00 35.19 2.92
3054 10936 1.630878 CCTCAACCTCCTTTGGTAGCT 59.369 52.381 0.00 0.00 39.83 3.32
3111 10993 0.604073 TTCGGTGATACGGTTCTGCA 59.396 50.000 0.00 0.00 0.00 4.41
3185 11067 1.216710 GCGTCTTCTCCCCAGTCAG 59.783 63.158 0.00 0.00 0.00 3.51
3316 11198 8.597167 TCTTCAGTTTCTTGATCCTCTATTCAA 58.403 33.333 0.00 0.00 0.00 2.69
3321 11203 7.671819 TCTTCTCTTCAGTTTCTTGATCCTCTA 59.328 37.037 0.00 0.00 0.00 2.43
3488 11399 7.383687 TCTAACTTACATCAGGTTGTACAAGG 58.616 38.462 8.98 1.99 31.98 3.61
3539 11469 9.436957 CTGTTCTAATGGTAGATGTTTTACAGT 57.563 33.333 0.00 0.00 35.17 3.55
3540 11470 9.436957 ACTGTTCTAATGGTAGATGTTTTACAG 57.563 33.333 0.00 0.00 40.46 2.74
3541 11471 9.214957 CACTGTTCTAATGGTAGATGTTTTACA 57.785 33.333 0.00 0.00 36.23 2.41
3542 11472 8.665685 CCACTGTTCTAATGGTAGATGTTTTAC 58.334 37.037 0.00 0.00 36.23 2.01
3547 11477 5.721960 AGACCACTGTTCTAATGGTAGATGT 59.278 40.000 0.00 0.00 46.86 3.06
3548 11478 6.045318 CAGACCACTGTTCTAATGGTAGATG 58.955 44.000 0.00 0.00 46.86 2.90
3549 11479 5.129485 CCAGACCACTGTTCTAATGGTAGAT 59.871 44.000 0.00 0.00 46.86 1.98
3550 11480 4.466370 CCAGACCACTGTTCTAATGGTAGA 59.534 45.833 0.00 0.00 46.86 2.59
3551 11481 4.223032 ACCAGACCACTGTTCTAATGGTAG 59.777 45.833 0.00 0.00 46.86 3.18
3554 11484 3.338249 CACCAGACCACTGTTCTAATGG 58.662 50.000 0.00 0.00 42.05 3.16
3555 11485 3.007940 TCCACCAGACCACTGTTCTAATG 59.992 47.826 0.00 0.00 42.05 1.90
3556 11486 3.248024 TCCACCAGACCACTGTTCTAAT 58.752 45.455 0.00 0.00 42.05 1.73
3684 11715 6.385176 TCCTTCTTCCATTACATGTCAGATCT 59.615 38.462 0.00 0.00 0.00 2.75
3685 11716 6.586344 TCCTTCTTCCATTACATGTCAGATC 58.414 40.000 0.00 0.00 0.00 2.75
3686 11717 6.566079 TCCTTCTTCCATTACATGTCAGAT 57.434 37.500 0.00 0.00 0.00 2.90
3718 11770 6.233434 AGAGAAACAAGTCATCTGCATAACA 58.767 36.000 0.00 0.00 0.00 2.41
3719 11771 6.593382 AGAGAGAAACAAGTCATCTGCATAAC 59.407 38.462 0.00 0.00 0.00 1.89
3720 11772 6.592994 CAGAGAGAAACAAGTCATCTGCATAA 59.407 38.462 0.00 0.00 31.18 1.90
3767 11820 5.621193 GCCCAAGGCTATATCAGTTTAGAA 58.379 41.667 0.00 0.00 46.69 2.10
4002 13041 1.204704 GGCCACCCTGTAAATTTCAGC 59.795 52.381 0.00 0.00 0.00 4.26
4061 13106 6.422100 TCTCTTCTCTGAATTCTTTGACAACG 59.578 38.462 7.05 0.00 0.00 4.10
4092 13137 3.550437 AAAATCTCCATCACTCCCTCG 57.450 47.619 0.00 0.00 0.00 4.63
4250 13314 9.239551 GGGAAACAAAACTACTACTCCATAATT 57.760 33.333 0.00 0.00 0.00 1.40
4251 13315 7.832685 GGGGAAACAAAACTACTACTCCATAAT 59.167 37.037 0.00 0.00 0.00 1.28
4252 13316 7.017850 AGGGGAAACAAAACTACTACTCCATAA 59.982 37.037 0.00 0.00 0.00 1.90
4253 13317 6.502863 AGGGGAAACAAAACTACTACTCCATA 59.497 38.462 0.00 0.00 0.00 2.74
4254 13318 5.312443 AGGGGAAACAAAACTACTACTCCAT 59.688 40.000 0.00 0.00 0.00 3.41
4255 13319 4.661709 AGGGGAAACAAAACTACTACTCCA 59.338 41.667 0.00 0.00 0.00 3.86
4256 13320 5.238624 AGGGGAAACAAAACTACTACTCC 57.761 43.478 0.00 0.00 0.00 3.85
4257 13321 6.769341 TCAAAGGGGAAACAAAACTACTACTC 59.231 38.462 0.00 0.00 0.00 2.59
4258 13322 6.665695 TCAAAGGGGAAACAAAACTACTACT 58.334 36.000 0.00 0.00 0.00 2.57
4259 13323 6.947644 TCAAAGGGGAAACAAAACTACTAC 57.052 37.500 0.00 0.00 0.00 2.73
4260 13324 7.562088 ACAATCAAAGGGGAAACAAAACTACTA 59.438 33.333 0.00 0.00 0.00 1.82
4370 13434 7.095857 CGATTCTGATGTAGCTGGTTCTAATTC 60.096 40.741 0.00 0.00 0.00 2.17
4381 13445 3.997672 GGGCGATTCTGATGTAGCT 57.002 52.632 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.