Multiple sequence alignment - TraesCS3A01G490100

Loading Multiple Alignment...

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 TraesCS3A01G490100 chr3A 100.000 5638 0 0 1 5638 717855699 717850062 0.000000e+00 10412
1 TraesCS3A01G490100 chr3A 82.566 1216 184 22 3311 4510 717901208 717902411 0.000000e+00 1046
2 TraesCS3A01G490100 chr3A 86.104 806 102 9 4838 5638 16868972 16868172 0.000000e+00 859
3 TraesCS3A01G490100 chr3A 81.497 935 153 14 2224 3146 717898942 717899868 0.000000e+00 750
4 TraesCS3A01G490100 chr3A 81.465 874 143 10 1038 1898 717884908 717885775 0.000000e+00 699
5 TraesCS3A01G490100 chr3B 96.279 2956 86 7 1895 4843 785694685 785691747 0.000000e+00 4828
6 TraesCS3A01G490100 chr3B 92.464 1619 83 21 313 1901 785696354 785694745 0.000000e+00 2278
7 TraesCS3A01G490100 chr3B 82.544 2492 390 29 1895 4377 786137732 786140187 0.000000e+00 2150
8 TraesCS3A01G490100 chr3B 83.681 864 115 16 1037 1884 786136800 786137653 0.000000e+00 791
9 TraesCS3A01G490100 chr3B 87.097 341 24 8 1 321 785697106 785696766 8.920000e-98 368
10 TraesCS3A01G490100 chr3D 97.024 2016 44 4 1895 3910 587949460 587947461 0.000000e+00 3376
11 TraesCS3A01G490100 chr3D 91.554 1918 133 19 2 1901 587951426 587949520 0.000000e+00 2617
12 TraesCS3A01G490100 chr3D 93.248 548 33 1 3905 4448 587947382 587946835 0.000000e+00 804
13 TraesCS3A01G490100 chr3D 97.291 406 8 1 4440 4842 587946661 587946256 0.000000e+00 686
14 TraesCS3A01G490100 chr3D 78.306 484 69 23 3664 4142 591709940 591710392 4.300000e-71 279
15 TraesCS3A01G490100 chr4D 91.615 799 67 0 4840 5638 105379903 105380701 0.000000e+00 1105
16 TraesCS3A01G490100 chr5D 91.125 800 71 0 4839 5638 481937624 481936825 0.000000e+00 1085
17 TraesCS3A01G490100 chr5D 88.679 795 89 1 4839 5632 231798673 231799467 0.000000e+00 968
18 TraesCS3A01G490100 chr4B 86.967 798 98 6 4844 5638 620950069 620950863 0.000000e+00 893
19 TraesCS3A01G490100 chr4B 85.283 795 113 4 4846 5638 179265934 179266726 0.000000e+00 817
20 TraesCS3A01G490100 chr2A 85.466 805 108 8 4839 5638 682018604 682019404 0.000000e+00 830
21 TraesCS3A01G490100 chr6A 85.019 801 116 4 4839 5636 597865420 597864621 0.000000e+00 811
22 TraesCS3A01G490100 chr7B 84.491 806 118 7 4833 5635 741927574 741926773 0.000000e+00 789
23 TraesCS3A01G490100 chr5A 84.052 232 31 6 2884 3112 14289459 14289231 9.510000e-53 219


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 TraesCS3A01G490100 chr3A 717850062 717855699 5637 True 10412.000000 10412 100.000000 1 5638 1 chr3A.!!$R2 5637
1 TraesCS3A01G490100 chr3A 717898942 717902411 3469 False 898.000000 1046 82.031500 2224 4510 2 chr3A.!!$F2 2286
2 TraesCS3A01G490100 chr3A 16868172 16868972 800 True 859.000000 859 86.104000 4838 5638 1 chr3A.!!$R1 800
3 TraesCS3A01G490100 chr3A 717884908 717885775 867 False 699.000000 699 81.465000 1038 1898 1 chr3A.!!$F1 860
4 TraesCS3A01G490100 chr3B 785691747 785697106 5359 True 2491.333333 4828 91.946667 1 4843 3 chr3B.!!$R1 4842
5 TraesCS3A01G490100 chr3B 786136800 786140187 3387 False 1470.500000 2150 83.112500 1037 4377 2 chr3B.!!$F1 3340
6 TraesCS3A01G490100 chr3D 587946256 587951426 5170 True 1870.750000 3376 94.779250 2 4842 4 chr3D.!!$R1 4840
7 TraesCS3A01G490100 chr4D 105379903 105380701 798 False 1105.000000 1105 91.615000 4840 5638 1 chr4D.!!$F1 798
8 TraesCS3A01G490100 chr5D 481936825 481937624 799 True 1085.000000 1085 91.125000 4839 5638 1 chr5D.!!$R1 799
9 TraesCS3A01G490100 chr5D 231798673 231799467 794 False 968.000000 968 88.679000 4839 5632 1 chr5D.!!$F1 793
10 TraesCS3A01G490100 chr4B 620950069 620950863 794 False 893.000000 893 86.967000 4844 5638 1 chr4B.!!$F2 794
11 TraesCS3A01G490100 chr4B 179265934 179266726 792 False 817.000000 817 85.283000 4846 5638 1 chr4B.!!$F1 792
12 TraesCS3A01G490100 chr2A 682018604 682019404 800 False 830.000000 830 85.466000 4839 5638 1 chr2A.!!$F1 799
13 TraesCS3A01G490100 chr6A 597864621 597865420 799 True 811.000000 811 85.019000 4839 5636 1 chr6A.!!$R1 797
14 TraesCS3A01G490100 chr7B 741926773 741927574 801 True 789.000000 789 84.491000 4833 5635 1 chr7B.!!$R1 802

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
450 896 0.527385 GCTGGCGAGCAGTCTAAGAG 60.527 60.000 16.60 0.0 45.46 2.85 F
1625 2128 0.107459 GCCTGGATGTCCTTGACCTC 60.107 60.000 0.00 0.0 36.82 3.85 F
3068 3646 0.039618 GATCCCTTGCCACTTTCCCA 59.960 55.000 0.00 0.0 0.00 4.37 F
3510 5281 2.726821 CCATTAGAAGCTTTGAGGCCA 58.273 47.619 5.01 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2623 0.179124 CACCTCGAGCTTGGACTAGC 60.179 60.0 6.99 0.0 41.53 3.42 R
3534 5305 0.809636 CGTATCAGGTTGCGATGCCA 60.810 55.0 0.00 0.0 0.00 4.92 R
4087 5949 0.178068 TAGCATCCGTTGGCCTCTTC 59.822 55.0 3.32 0.0 0.00 2.87 R
5200 7252 0.687757 AGGGCTAGATGCGACCTTGA 60.688 55.0 0.00 0.0 44.05 3.02 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
28 29 2.755650 CAGGTGTTCTACTTTGAGCGT 58.244 47.619 0.00 0.00 0.00 5.07
34 35 0.666274 TCTACTTTGAGCGTGCCACG 60.666 55.000 13.95 13.95 45.88 4.94
84 98 1.582968 GAGTGGTGGTCGTCGCTAA 59.417 57.895 0.00 0.00 0.00 3.09
140 154 0.967380 AGGCAATGGCGCTAAAGCTT 60.967 50.000 17.59 9.63 42.47 3.74
245 262 1.245376 TGGTGTCAGCATACGGACGA 61.245 55.000 0.00 0.00 43.13 4.20
274 291 2.284190 GGCAGGAAGAGAATGCTACAC 58.716 52.381 0.00 0.00 39.88 2.90
311 756 5.707764 GGAAAGAATGCTAGAAAGAGTGGTT 59.292 40.000 0.00 0.00 0.00 3.67
378 824 1.721804 GCGAGCAACTTAGCGTTCAAC 60.722 52.381 0.00 0.00 40.15 3.18
381 827 1.202770 AGCAACTTAGCGTTCAACCCT 60.203 47.619 0.00 0.00 40.15 4.34
382 828 2.038033 AGCAACTTAGCGTTCAACCCTA 59.962 45.455 0.00 0.00 40.15 3.53
384 830 3.251487 GCAACTTAGCGTTCAACCCTAAA 59.749 43.478 0.00 0.00 32.27 1.85
386 832 3.405831 ACTTAGCGTTCAACCCTAAACC 58.594 45.455 0.00 0.00 0.00 3.27
387 833 2.477845 TAGCGTTCAACCCTAAACCC 57.522 50.000 0.00 0.00 0.00 4.11
388 834 0.769247 AGCGTTCAACCCTAAACCCT 59.231 50.000 0.00 0.00 0.00 4.34
389 835 1.980036 AGCGTTCAACCCTAAACCCTA 59.020 47.619 0.00 0.00 0.00 3.53
390 836 2.372837 AGCGTTCAACCCTAAACCCTAA 59.627 45.455 0.00 0.00 0.00 2.69
391 837 3.148412 GCGTTCAACCCTAAACCCTAAA 58.852 45.455 0.00 0.00 0.00 1.85
392 838 3.058016 GCGTTCAACCCTAAACCCTAAAC 60.058 47.826 0.00 0.00 0.00 2.01
393 839 3.503363 CGTTCAACCCTAAACCCTAAACC 59.497 47.826 0.00 0.00 0.00 3.27
395 841 5.512921 CGTTCAACCCTAAACCCTAAACCTA 60.513 44.000 0.00 0.00 0.00 3.08
397 843 7.581270 CGTTCAACCCTAAACCCTAAACCTATA 60.581 40.741 0.00 0.00 0.00 1.31
398 844 7.827603 TCAACCCTAAACCCTAAACCTATAA 57.172 36.000 0.00 0.00 0.00 0.98
399 845 7.864770 TCAACCCTAAACCCTAAACCTATAAG 58.135 38.462 0.00 0.00 0.00 1.73
405 851 9.970553 CCTAAACCCTAAACCTATAAGTCTTTT 57.029 33.333 0.00 0.00 0.00 2.27
435 881 6.662414 TTATTCGACTCAAATTACTGCTGG 57.338 37.500 0.00 0.00 0.00 4.85
450 896 0.527385 GCTGGCGAGCAGTCTAAGAG 60.527 60.000 16.60 0.00 45.46 2.85
459 905 1.484240 GCAGTCTAAGAGCCATGGAGT 59.516 52.381 18.40 0.01 0.00 3.85
470 916 2.093235 AGCCATGGAGTGTTTAGAGAGC 60.093 50.000 18.40 0.00 0.00 4.09
533 982 3.728845 TCTGCTGTAGTGACAAGGTTTC 58.271 45.455 0.00 0.00 34.35 2.78
537 986 3.625764 GCTGTAGTGACAAGGTTTCACAA 59.374 43.478 5.36 0.00 45.00 3.33
538 987 4.495844 GCTGTAGTGACAAGGTTTCACAAC 60.496 45.833 5.36 0.00 45.00 3.32
673 1123 5.047847 CCAATCTCCAACACGTCGTATATT 58.952 41.667 0.00 0.00 0.00 1.28
699 1150 7.014808 TGGATCCACACACGTATAGATAATCAA 59.985 37.037 11.44 0.00 0.00 2.57
860 1324 2.009774 CGTACATCAGGCAGGAAAAGG 58.990 52.381 0.00 0.00 0.00 3.11
870 1334 4.010349 AGGCAGGAAAAGGTCGATTTTAG 58.990 43.478 0.00 0.00 32.62 1.85
894 1358 6.207614 AGAGATCATGGCGCATATATACGTAT 59.792 38.462 13.54 13.54 0.00 3.06
927 1392 1.174078 TAGAACACGACGAGCCACCA 61.174 55.000 0.00 0.00 0.00 4.17
943 1408 2.666862 CAACCGGCGGCACTAACA 60.667 61.111 28.71 0.00 0.00 2.41
1034 1506 7.444183 CCAAAAGGACTACTGTAAACATTCTCA 59.556 37.037 0.00 0.00 0.00 3.27
1035 1507 9.003658 CAAAAGGACTACTGTAAACATTCTCAT 57.996 33.333 0.00 0.00 0.00 2.90
1316 1804 2.175322 GTCCCACTCGACGTCGAC 59.825 66.667 34.97 21.42 44.22 4.20
1397 1885 3.512516 GCCAACATGAGCGGCTCC 61.513 66.667 26.00 9.70 42.78 4.70
1475 1972 4.641645 CTGTCCGGCAACAGGGCA 62.642 66.667 14.14 0.00 42.42 5.36
1490 1987 1.217183 AGGGCACTAAGAGGATCCGTA 59.783 52.381 5.98 0.00 33.66 4.02
1625 2128 0.107459 GCCTGGATGTCCTTGACCTC 60.107 60.000 0.00 0.00 36.82 3.85
1856 2359 1.729586 ACCTCTCCAGCAACCACTTA 58.270 50.000 0.00 0.00 0.00 2.24
1888 2392 2.974698 GCCAGACACACGCTGCTT 60.975 61.111 0.00 0.00 32.06 3.91
1986 2555 1.684248 GGCTTGCCAATCTGAGGATGT 60.684 52.381 6.79 0.00 31.75 3.06
2055 2624 3.423154 CGAACACCGGCTCCAAGC 61.423 66.667 0.00 0.00 41.46 4.01
2056 2625 2.032681 GAACACCGGCTCCAAGCT 59.967 61.111 0.00 0.00 41.99 3.74
2247 2816 1.186200 GGGAGAACAAATTGGAGGGC 58.814 55.000 0.00 0.00 0.00 5.19
2256 2825 0.179045 AATTGGAGGGCGAGATTCCG 60.179 55.000 0.00 0.00 33.60 4.30
2370 2939 4.063689 AGAATCTGAAATGGATAGCGCTG 58.936 43.478 22.90 0.00 0.00 5.18
2606 3183 0.250234 ATGATAGCGCGGCCACATAT 59.750 50.000 8.83 0.00 0.00 1.78
2607 3184 0.892063 TGATAGCGCGGCCACATATA 59.108 50.000 8.83 0.00 0.00 0.86
2776 3353 2.867975 AGCACACTTTGAAAAGCAATGC 59.132 40.909 14.17 14.17 39.64 3.56
2858 3436 7.182817 ACTTGGTAAGATGAACTATGTAGCA 57.817 36.000 0.00 0.00 0.00 3.49
2993 3571 4.255999 CGAGTTCATTTTCGTTGCTATCG 58.744 43.478 0.00 0.00 32.44 2.92
3068 3646 0.039618 GATCCCTTGCCACTTTCCCA 59.960 55.000 0.00 0.00 0.00 4.37
3118 3696 4.521062 CGGCTTCCCTCTGCCTCG 62.521 72.222 0.00 0.00 46.42 4.63
3189 3767 6.470278 ACCACTTCCAGTAATAAGTACAACC 58.530 40.000 0.00 0.00 34.88 3.77
3190 3768 6.271624 ACCACTTCCAGTAATAAGTACAACCT 59.728 38.462 0.00 0.00 34.88 3.50
3191 3769 6.817140 CCACTTCCAGTAATAAGTACAACCTC 59.183 42.308 0.00 0.00 34.88 3.85
3192 3770 6.817140 CACTTCCAGTAATAAGTACAACCTCC 59.183 42.308 0.00 0.00 34.88 4.30
3193 3771 6.729569 ACTTCCAGTAATAAGTACAACCTCCT 59.270 38.462 0.00 0.00 34.88 3.69
3194 3772 7.897565 ACTTCCAGTAATAAGTACAACCTCCTA 59.102 37.037 0.00 0.00 34.88 2.94
3195 3773 8.669055 TTCCAGTAATAAGTACAACCTCCTAA 57.331 34.615 0.00 0.00 34.88 2.69
3196 3774 8.071177 TCCAGTAATAAGTACAACCTCCTAAC 57.929 38.462 0.00 0.00 34.88 2.34
3197 3775 7.675195 TCCAGTAATAAGTACAACCTCCTAACA 59.325 37.037 0.00 0.00 34.88 2.41
3243 3821 3.563808 TGTCACGCTAGCTTTTGTCATTT 59.436 39.130 13.93 0.00 0.00 2.32
3468 5239 5.762711 GGTTTGATGGTTGCAATAAAGGTTT 59.237 36.000 0.59 0.00 0.00 3.27
3510 5281 2.726821 CCATTAGAAGCTTTGAGGCCA 58.273 47.619 5.01 0.00 0.00 5.36
3844 5615 3.868077 GCAAGACTACTACAAGCTGATGG 59.132 47.826 0.00 0.00 0.00 3.51
3874 5645 3.065233 GCGTTCTCCATTAACATGCATGA 59.935 43.478 32.75 11.53 0.00 3.07
4087 5949 3.244561 TGCTCCTTGAAGTCTTTACTGGG 60.245 47.826 0.00 0.00 35.62 4.45
4122 5984 4.142381 GGATGCTATGTTTGTTGGAGAACC 60.142 45.833 0.00 0.00 0.00 3.62
4142 6004 1.679680 CGAGCCTTAGACGATGGGTTA 59.320 52.381 0.00 0.00 33.40 2.85
4161 6023 5.170748 GGTTAATCAATTGTTTCAGGCAGG 58.829 41.667 5.13 0.00 0.00 4.85
4206 6068 0.179156 CGGCTACTGCAATGCTTTGG 60.179 55.000 13.62 0.00 41.91 3.28
4300 6162 5.386924 AGGATAACTATGAGCGAGGTAGTT 58.613 41.667 10.25 10.25 40.60 2.24
4305 6167 9.525409 GATAACTATGAGCGAGGTAGTTTTAAA 57.475 33.333 10.53 0.00 38.95 1.52
4420 6282 5.444122 CATGAAGAACTGTTTCGGAGAAAC 58.556 41.667 16.17 16.17 45.90 2.78
4432 6294 3.881220 TCGGAGAAACAAAAAGGACAGT 58.119 40.909 0.00 0.00 0.00 3.55
4633 6677 9.344772 TGTTTTGTGGACATAAAGTAGTAATGT 57.655 29.630 0.00 0.00 36.57 2.71
4653 6698 5.659440 TGTCTTCTTTGCTGGTTCTTTTT 57.341 34.783 0.00 0.00 0.00 1.94
4661 6706 8.181904 TCTTTGCTGGTTCTTTTTCTATCATT 57.818 30.769 0.00 0.00 0.00 2.57
4862 6913 1.614996 TTCAAGGATGCGCCAAAGAA 58.385 45.000 4.18 0.00 40.02 2.52
4923 6974 4.081697 GGCAAAGGTAATGTTACAAGCCAT 60.082 41.667 15.69 0.00 37.46 4.40
4934 6986 4.830046 TGTTACAAGCCATGGTTACACAAT 59.170 37.500 14.67 0.00 0.00 2.71
4987 7039 6.289064 CACTATCCAACCTATCTACCAAACC 58.711 44.000 0.00 0.00 0.00 3.27
5055 7107 0.539051 ACCCTCAAGCTCAATCCTCG 59.461 55.000 0.00 0.00 0.00 4.63
5072 7124 3.838795 GTAAGCACGGCGTCTGCG 61.839 66.667 10.85 0.00 44.10 5.18
5107 7159 3.181497 CCATTCAACACGATGTCATTCCC 60.181 47.826 0.00 0.00 0.00 3.97
5185 7237 0.923358 TGTTTCTGTGGGTTGAGGGT 59.077 50.000 0.00 0.00 0.00 4.34
5215 7267 3.459232 TTCCATCAAGGTCGCATCTAG 57.541 47.619 0.00 0.00 39.02 2.43
5217 7269 1.506493 CATCAAGGTCGCATCTAGCC 58.494 55.000 0.00 0.00 41.38 3.93
5273 7325 2.111043 CTGGTCCACACTTGCCGT 59.889 61.111 0.00 0.00 0.00 5.68
5303 7355 1.610038 CAGCCAAGCAACAAGTGATCA 59.390 47.619 0.00 0.00 0.00 2.92
5339 7391 1.355381 TGATCACAGAAGGGGCATGTT 59.645 47.619 0.00 0.00 0.00 2.71
5355 7407 2.610859 TTGAGGGGTGAGGGAGCC 60.611 66.667 0.00 0.00 42.09 4.70
5356 7408 3.194025 TTGAGGGGTGAGGGAGCCT 62.194 63.158 0.00 0.00 42.49 4.58
5357 7409 3.086600 GAGGGGTGAGGGAGCCTG 61.087 72.222 0.00 0.00 42.49 4.85
5361 7413 1.995626 GGGTGAGGGAGCCTGCTTA 60.996 63.158 0.00 0.00 39.39 3.09
5389 7441 2.918230 CTATCCGCCGTCCAACACCC 62.918 65.000 0.00 0.00 0.00 4.61
5408 7460 3.704231 ATTCCTTGCCGCGAGCCAT 62.704 57.895 8.23 0.00 42.71 4.40
5450 7502 3.955471 TGGAGCTCTCGATTTCCAAATT 58.045 40.909 14.64 0.00 36.81 1.82
5465 7517 0.757188 AAATTTGGGTGGCACCGTCA 60.757 50.000 29.18 19.93 39.83 4.35
5512 7564 2.295253 CTGTAAGCCGACCTAACAGG 57.705 55.000 0.00 0.00 42.49 4.00
5557 7609 2.036992 CCCAGTAGATCCTGTCATCTGC 59.963 54.545 0.00 0.00 36.14 4.26
5565 7617 2.747460 TGTCATCTGCGCCTTGCC 60.747 61.111 4.18 0.00 45.60 4.52
5578 7630 0.911769 CCTTGCCTGAGGACCACATA 59.088 55.000 0.65 0.00 39.25 2.29
5591 7643 3.262420 GACCACATATTGCGTCTTGTCT 58.738 45.455 0.00 0.00 0.00 3.41
5609 7661 3.070878 TGTCTACAAGCACCATGAACTCA 59.929 43.478 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.690633 TCAGCATCACCCCTCTCCC 60.691 63.158 0.00 0.00 0.00 4.30
84 98 5.882557 CCTATGAAGGCAACAACACTTCTAT 59.117 40.000 0.00 0.00 40.83 1.98
140 154 2.359354 CGCCCGTTCCCACATTCA 60.359 61.111 0.00 0.00 0.00 2.57
245 262 0.886490 CTCTTCCTGCCAAACGCTGT 60.886 55.000 0.00 0.00 38.78 4.40
378 824 7.687383 AGACTTATAGGTTTAGGGTTTAGGG 57.313 40.000 0.00 0.00 0.00 3.53
405 851 8.673711 CAGTAATTTGAGTCGAATAATGGGAAA 58.326 33.333 6.02 0.00 0.00 3.13
406 852 7.201696 GCAGTAATTTGAGTCGAATAATGGGAA 60.202 37.037 6.02 0.00 0.00 3.97
407 853 6.260050 GCAGTAATTTGAGTCGAATAATGGGA 59.740 38.462 6.02 0.00 0.00 4.37
408 854 6.260936 AGCAGTAATTTGAGTCGAATAATGGG 59.739 38.462 6.02 0.00 0.00 4.00
409 855 7.128331 CAGCAGTAATTTGAGTCGAATAATGG 58.872 38.462 6.02 0.00 0.00 3.16
421 867 1.086696 GCTCGCCAGCAGTAATTTGA 58.913 50.000 0.00 0.00 46.06 2.69
435 881 0.103937 ATGGCTCTTAGACTGCTCGC 59.896 55.000 0.00 0.00 0.00 5.03
450 896 2.093235 AGCTCTCTAAACACTCCATGGC 60.093 50.000 6.96 0.00 0.00 4.40
459 905 3.083122 AGTACGGGAGCTCTCTAAACA 57.917 47.619 12.81 0.00 0.00 2.83
470 916 4.243270 CCAAAAGTCACTTAGTACGGGAG 58.757 47.826 0.00 0.00 0.00 4.30
533 982 7.061905 ACGATCTTCTTCTATTGTTACGTTGTG 59.938 37.037 0.00 0.00 0.00 3.33
537 986 7.192232 GGTACGATCTTCTTCTATTGTTACGT 58.808 38.462 0.00 0.00 0.00 3.57
538 987 6.636044 GGGTACGATCTTCTTCTATTGTTACG 59.364 42.308 0.00 0.00 0.00 3.18
619 1068 6.197655 CCATTTTTCATGATATGCACGTGAAG 59.802 38.462 22.23 0.00 41.89 3.02
673 1123 6.492087 TGATTATCTATACGTGTGTGGATCCA 59.508 38.462 11.44 11.44 0.00 3.41
860 1324 3.120854 GCGCCATGATCTCTAAAATCGAC 60.121 47.826 0.00 0.00 0.00 4.20
870 1334 4.611943 ACGTATATATGCGCCATGATCTC 58.388 43.478 21.13 0.00 39.55 2.75
894 1358 5.298777 GTCGTGTTCTAGCTAGGGAGAATTA 59.701 44.000 20.58 1.04 34.34 1.40
927 1392 1.302993 ATTGTTAGTGCCGCCGGTT 60.303 52.632 4.45 0.00 0.00 4.44
943 1408 5.605534 CAAGCAGTGCTAGTAGGTATGATT 58.394 41.667 20.09 0.00 38.25 2.57
978 1450 1.406069 CCGGATGAGCTGCACTAAGTT 60.406 52.381 0.00 0.00 0.00 2.66
982 1454 1.676678 GGACCGGATGAGCTGCACTA 61.677 60.000 9.46 0.00 0.00 2.74
1034 1506 0.319728 CGCCCAGTGCTCAGCTATAT 59.680 55.000 0.00 0.00 38.05 0.86
1035 1507 1.043116 ACGCCCAGTGCTCAGCTATA 61.043 55.000 0.00 0.00 38.05 1.31
1157 1645 3.890936 GAACCGCTCCAGCAGCTGT 62.891 63.158 21.26 0.00 46.80 4.40
1475 1972 3.215975 GTCAGCTACGGATCCTCTTAGT 58.784 50.000 10.75 2.10 0.00 2.24
1625 2128 0.790207 CGGTGATGTTGTTGTCCGAG 59.210 55.000 0.00 0.00 40.29 4.63
1856 2359 3.680786 GGCGGAAAAGCGCCCTTT 61.681 61.111 2.29 3.86 44.75 3.11
1986 2555 0.671796 TCGTTCGAGCTGAAGTCCAA 59.328 50.000 0.00 0.00 37.23 3.53
2054 2623 0.179124 CACCTCGAGCTTGGACTAGC 60.179 60.000 6.99 0.00 41.53 3.42
2055 2624 0.179124 GCACCTCGAGCTTGGACTAG 60.179 60.000 6.99 0.00 0.00 2.57
2056 2625 0.612174 AGCACCTCGAGCTTGGACTA 60.612 55.000 6.99 0.00 39.87 2.59
2117 2686 2.641815 AGGCTTTCACAGTTGGAGATCT 59.358 45.455 0.00 0.00 0.00 2.75
2247 2816 1.586564 GAGCGACACCGGAATCTCG 60.587 63.158 9.46 9.46 36.06 4.04
2474 3048 1.189752 CTTGCAGTCTCCTAGCTCCA 58.810 55.000 0.00 0.00 0.00 3.86
2594 3171 3.245284 GCAAGTATATATATGTGGCCGCG 59.755 47.826 12.58 0.00 0.00 6.46
2606 3183 3.294102 CTCGTCGTTGCGCAAGTATATA 58.706 45.455 25.78 6.95 41.68 0.86
2607 3184 2.117137 CTCGTCGTTGCGCAAGTATAT 58.883 47.619 25.78 0.00 41.68 0.86
2776 3353 4.103785 ACAGGTCCAAGAATATCATGGAGG 59.896 45.833 4.67 1.70 43.92 4.30
2853 3431 3.561310 TGCCGAAGATTCATGATTGCTAC 59.439 43.478 0.00 0.00 0.00 3.58
2858 3436 5.066375 TCGATTTTGCCGAAGATTCATGATT 59.934 36.000 0.00 0.00 32.64 2.57
2972 3550 5.204673 ACGATAGCAACGAAAATGAACTC 57.795 39.130 0.00 0.00 42.67 3.01
2993 3571 7.371159 TGTATGATAGATCAATCTCCGACAAC 58.629 38.462 0.00 0.00 40.69 3.32
3068 3646 4.338879 AGTTGTTTGCATATTGGCTCTCT 58.661 39.130 0.00 0.00 34.04 3.10
3118 3696 3.501828 GGGTTTCAAAAATGGTTGGCATC 59.498 43.478 0.00 0.00 0.00 3.91
3194 3772 8.417884 GCTGAGAGTAGGATTATTAGAAGTGTT 58.582 37.037 0.00 0.00 0.00 3.32
3195 3773 7.782644 AGCTGAGAGTAGGATTATTAGAAGTGT 59.217 37.037 0.00 0.00 0.00 3.55
3196 3774 8.081633 CAGCTGAGAGTAGGATTATTAGAAGTG 58.918 40.741 8.42 0.00 0.00 3.16
3197 3775 7.782644 ACAGCTGAGAGTAGGATTATTAGAAGT 59.217 37.037 23.35 0.00 0.00 3.01
3262 5033 6.916387 GTCGACTTTATTTCTCCACGATATGA 59.084 38.462 8.70 0.00 0.00 2.15
3468 5239 1.227704 ACGTGGACCGCATGTCAAA 60.228 52.632 5.75 0.00 46.38 2.69
3534 5305 0.809636 CGTATCAGGTTGCGATGCCA 60.810 55.000 0.00 0.00 0.00 4.92
3844 5615 4.927425 TGTTAATGGAGAACGCAGAGTTAC 59.073 41.667 0.00 0.00 44.35 2.50
3874 5645 3.585289 TGGTGACATGTACCCAATAGTGT 59.415 43.478 12.38 0.00 37.40 3.55
3933 5791 7.539034 AGTTAATTGGTGGCTTAACAAGAAT 57.461 32.000 8.46 0.00 39.29 2.40
3969 5827 5.807011 GGATAAATGCACATTCCAACTGAAC 59.193 40.000 0.00 0.00 35.31 3.18
4087 5949 0.178068 TAGCATCCGTTGGCCTCTTC 59.822 55.000 3.32 0.00 0.00 2.87
4122 5984 0.460311 AACCCATCGTCTAAGGCTCG 59.540 55.000 0.00 0.00 0.00 5.03
4142 6004 3.896888 TGACCTGCCTGAAACAATTGATT 59.103 39.130 13.59 6.54 0.00 2.57
4161 6023 5.633830 ATCCATGACATGAACAAGTTGAC 57.366 39.130 17.24 3.98 0.00 3.18
4206 6068 4.418392 CACAAGAAAGCTAATGTCCATGC 58.582 43.478 0.00 0.00 0.00 4.06
4300 6162 8.670135 TCTGTTTTGACGTTCTTCATCTTTAAA 58.330 29.630 0.00 0.00 0.00 1.52
4305 6167 5.360591 ACTCTGTTTTGACGTTCTTCATCT 58.639 37.500 0.00 0.00 0.00 2.90
4359 6221 5.305128 AGGTTGACCAATCATTGTGAAACAT 59.695 36.000 2.56 0.00 43.10 2.71
4363 6225 4.501229 GCAAGGTTGACCAATCATTGTGAA 60.501 41.667 2.56 0.00 38.89 3.18
4450 6494 5.124936 ACAAAGAAAACGCCAACTAGTTCTT 59.875 36.000 4.77 0.62 37.01 2.52
4633 6677 7.502226 TGATAGAAAAAGAACCAGCAAAGAAGA 59.498 33.333 0.00 0.00 0.00 2.87
4814 6862 6.240894 AGAGTCAGCCACTATTTCATTTGAA 58.759 36.000 0.00 0.00 34.41 2.69
4862 6913 3.740631 TCTATGCTTCTGATGCGTCAT 57.259 42.857 9.53 0.00 32.98 3.06
4923 6974 4.950475 TGGACACTTTTGATTGTGTAACCA 59.050 37.500 0.00 0.00 45.94 3.67
4934 6986 0.950836 CCGCATGTGGACACTTTTGA 59.049 50.000 21.19 0.00 0.00 2.69
5001 7053 2.746362 CTGCTGGTTTGCTTAAGGAGAG 59.254 50.000 4.29 0.00 30.34 3.20
5055 7107 3.838795 CGCAGACGCCGTGCTTAC 61.839 66.667 0.00 0.00 38.88 2.34
5090 7142 1.128507 CACGGGAATGACATCGTGTTG 59.871 52.381 16.08 0.00 45.15 3.33
5136 7188 1.485066 GGAGACATGGACGGTGGTAAT 59.515 52.381 0.00 0.00 0.00 1.89
5185 7237 1.005805 CCTTGATGGAATGGTGGACCA 59.994 52.381 0.00 0.00 44.55 4.02
5200 7252 0.687757 AGGGCTAGATGCGACCTTGA 60.688 55.000 0.00 0.00 44.05 3.02
5273 7325 2.616330 GCTTGGCTGCGTGTTAGCA 61.616 57.895 0.00 0.00 45.96 3.49
5303 7355 2.702478 TGATCAGGAGCAGGAATCGATT 59.298 45.455 11.20 11.20 0.00 3.34
5339 7391 3.615811 AGGCTCCCTCACCCCTCA 61.616 66.667 0.00 0.00 0.00 3.86
5355 7407 4.154918 GGCGGATAGATTGGAAATAAGCAG 59.845 45.833 0.00 0.00 0.00 4.24
5356 7408 4.072131 GGCGGATAGATTGGAAATAAGCA 58.928 43.478 0.00 0.00 0.00 3.91
5357 7409 3.125316 CGGCGGATAGATTGGAAATAAGC 59.875 47.826 0.00 0.00 0.00 3.09
5361 7413 2.550208 GGACGGCGGATAGATTGGAAAT 60.550 50.000 13.24 0.00 0.00 2.17
5389 7441 3.880846 GGCTCGCGGCAAGGAATG 61.881 66.667 18.87 0.00 44.01 2.67
5408 7460 5.529430 TCCAAATTCTTGCAAGTTCTTCGTA 59.471 36.000 25.19 1.00 0.00 3.43
5450 7502 4.947147 GCTGACGGTGCCACCCAA 62.947 66.667 8.62 0.00 33.75 4.12
5465 7517 2.110627 GCTGGCATGATCGAGGCT 59.889 61.111 0.00 0.00 0.00 4.58
5512 7564 3.378399 GAGAGCTCGGGGCAGTTCC 62.378 68.421 8.37 0.00 44.79 3.62
5557 7609 4.020617 TGGTCCTCAGGCAAGGCG 62.021 66.667 1.27 0.00 36.29 5.52
5565 7617 2.159043 AGACGCAATATGTGGTCCTCAG 60.159 50.000 0.00 0.00 31.39 3.35
5591 7643 2.412870 CGTGAGTTCATGGTGCTTGTA 58.587 47.619 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.