Multiple sequence alignment - TraesCS5D01G294800

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 TraesCS5D01G294800 chr5D 100.000 6248 0 0 1 6248 391981908 391975661 0.000000e+00 11538.0
1 TraesCS5D01G294800 chr5D 96.250 240 8 1 6009 6248 391909752 391909514 5.870000e-105 392.0
2 TraesCS5D01G294800 chr5D 95.000 240 12 0 6009 6248 396784232 396783993 1.640000e-100 377.0
3 TraesCS5D01G294800 chr5D 73.464 358 74 18 3454 3802 437808996 437808651 1.420000e-21 115.0
4 TraesCS5D01G294800 chr5D 72.951 366 70 22 3454 3802 437696065 437696418 3.990000e-17 100.0
5 TraesCS5D01G294800 chr5D 100.000 51 0 0 5646 5696 391976214 391976164 1.850000e-15 95.3
6 TraesCS5D01G294800 chr5D 74.153 236 36 21 3641 3858 370108027 370108255 2.420000e-09 75.0
7 TraesCS5D01G294800 chr5D 100.000 39 0 0 2890 2928 391978981 391978943 8.690000e-09 73.1
8 TraesCS5D01G294800 chr5D 100.000 39 0 0 2928 2966 391979019 391978981 8.690000e-09 73.1
9 TraesCS5D01G294800 chr5D 81.481 81 13 2 3641 3720 437617363 437617284 1.450000e-06 65.8
10 TraesCS5D01G294800 chr5D 100.000 28 0 0 5645 5672 234845616 234845589 1.100000e-02 52.8
11 TraesCS5D01G294800 chr5B 98.477 2954 17 7 1 2928 472744368 472741417 0.000000e+00 5180.0
12 TraesCS5D01G294800 chr5B 99.386 1792 11 0 2928 4719 472741455 472739664 0.000000e+00 3249.0
13 TraesCS5D01G294800 chr5B 98.203 946 13 2 4720 5665 472739550 472738609 0.000000e+00 1650.0
14 TraesCS5D01G294800 chr5B 90.761 552 29 5 5713 6248 472738393 472737848 0.000000e+00 717.0
15 TraesCS5D01G294800 chr5B 88.764 178 16 4 4552 4727 539314282 539314457 1.360000e-51 215.0
16 TraesCS5D01G294800 chr5B 86.066 122 14 3 5711 5830 316709105 316708985 1.830000e-25 128.0
17 TraesCS5D01G294800 chr5B 73.881 268 56 11 3454 3714 531642830 531643090 1.850000e-15 95.3
18 TraesCS5D01G294800 chr5B 80.159 126 19 4 3598 3720 531705356 531705234 8.630000e-14 89.8
19 TraesCS5D01G294800 chr5A 91.365 2953 175 35 31 2928 495307853 495310780 0.000000e+00 3967.0
20 TraesCS5D01G294800 chr5A 93.195 1396 76 12 3159 4541 495311059 495312448 0.000000e+00 2034.0
21 TraesCS5D01G294800 chr5A 89.606 558 31 11 4720 5265 495312547 495313089 0.000000e+00 684.0
22 TraesCS5D01G294800 chr5A 89.888 267 22 3 2928 3190 495310742 495311007 7.760000e-89 339.0
23 TraesCS5D01G294800 chr5A 80.159 126 19 4 3598 3720 552750004 552749882 8.630000e-14 89.8
24 TraesCS5D01G294800 chr5A 74.884 215 39 11 3598 3802 552676193 552676402 4.010000e-12 84.2
25 TraesCS5D01G294800 chr6A 85.642 794 76 19 1439 2214 98904340 98905113 0.000000e+00 800.0
26 TraesCS5D01G294800 chr6A 91.463 164 11 3 4552 4712 408050921 408051084 8.150000e-54 222.0
27 TraesCS5D01G294800 chr3B 79.198 923 167 13 1236 2148 751109466 751108559 8.900000e-173 617.0
28 TraesCS5D01G294800 chr3B 94.332 247 12 2 6004 6248 67947604 67947850 1.640000e-100 377.0
29 TraesCS5D01G294800 chr2B 95.142 247 9 3 6004 6248 539157670 539157915 2.730000e-103 387.0
30 TraesCS5D01G294800 chr2B 93.421 76 5 0 5884 5959 723434353 723434278 5.120000e-21 113.0
31 TraesCS5D01G294800 chr6B 95.417 240 10 1 6009 6248 304891030 304890792 1.270000e-101 381.0
32 TraesCS5D01G294800 chr6B 90.533 169 12 4 4552 4718 683376074 683376240 2.930000e-53 220.0
33 TraesCS5D01G294800 chr6B 75.000 484 103 13 3589 4062 411104373 411104848 2.280000e-49 207.0
34 TraesCS5D01G294800 chr4B 94.737 247 10 3 6004 6248 34702786 34703031 1.270000e-101 381.0
35 TraesCS5D01G294800 chr4B 85.217 115 15 2 5718 5830 362845720 362845606 3.960000e-22 117.0
36 TraesCS5D01G294800 chr4B 95.833 72 3 0 5888 5959 422217535 422217464 3.960000e-22 117.0
37 TraesCS5D01G294800 chr7B 95.000 240 10 2 6009 6248 21826355 21826118 5.910000e-100 375.0
38 TraesCS5D01G294800 chr1B 94.332 247 11 3 6004 6248 473814736 473814981 5.910000e-100 375.0
39 TraesCS5D01G294800 chr1B 91.411 163 11 3 4552 4712 314565699 314565538 2.930000e-53 220.0
40 TraesCS5D01G294800 chr1B 88.525 122 11 3 5711 5830 151133793 151133673 1.820000e-30 145.0
41 TraesCS5D01G294800 chr1B 87.603 121 13 2 5711 5830 151116915 151116796 8.450000e-29 139.0
42 TraesCS5D01G294800 chr1B 94.521 73 4 0 5887 5959 674894189 674894117 5.120000e-21 113.0
43 TraesCS5D01G294800 chr1B 94.521 73 4 0 5887 5959 675221708 675221780 5.120000e-21 113.0
44 TraesCS5D01G294800 chr1B 93.333 75 5 0 5885 5959 77544283 77544357 1.840000e-20 111.0
45 TraesCS5D01G294800 chr2A 89.714 175 14 4 4543 4715 135473220 135473392 2.930000e-53 220.0
46 TraesCS5D01G294800 chr2A 86.555 119 14 2 5718 5834 102675942 102675824 5.080000e-26 130.0
47 TraesCS5D01G294800 chr2D 90.419 167 14 2 4549 4713 387193692 387193858 1.050000e-52 219.0
48 TraesCS5D01G294800 chr1A 90.058 171 12 5 4549 4717 283855516 283855683 3.790000e-52 217.0
49 TraesCS5D01G294800 chr1A 88.268 179 19 2 4547 4723 58165985 58165807 4.910000e-51 213.0
50 TraesCS5D01G294800 chr1A 84.874 119 12 5 5718 5831 124617177 124617060 1.420000e-21 115.0
51 TraesCS5D01G294800 chr1A 100.000 30 0 0 5643 5672 531984751 531984780 8.750000e-04 56.5
52 TraesCS5D01G294800 chr1A 100.000 29 0 0 5644 5672 48579127 48579099 3.000000e-03 54.7
53 TraesCS5D01G294800 chr1A 96.875 32 1 0 5638 5669 586049226 586049257 3.000000e-03 54.7
54 TraesCS5D01G294800 chr7D 84.444 180 28 0 2561 2740 25344998 25344819 1.790000e-40 178.0
55 TraesCS5D01G294800 chr7D 92.308 78 6 0 5882 5959 321955174 321955097 1.840000e-20 111.0
56 TraesCS5D01G294800 chr4D 86.325 117 14 2 5718 5832 23312171 23312055 6.580000e-25 126.0
57 TraesCS5D01G294800 chr3D 85.217 115 15 2 5718 5830 167554032 167553918 3.960000e-22 117.0
58 TraesCS5D01G294800 chrUn 94.444 72 4 0 5888 5959 87827393 87827464 1.840000e-20 111.0
59 TraesCS5D01G294800 chrUn 94.444 72 4 0 5888 5959 309972438 309972509 1.840000e-20 111.0
60 TraesCS5D01G294800 chr1D 81.159 138 22 4 4283 4418 457936990 457936855 2.380000e-19 108.0
61 TraesCS5D01G294800 chr1D 100.000 31 0 0 5642 5672 462903819 462903849 2.430000e-04 58.4
62 TraesCS5D01G294800 chr1D 100.000 29 0 0 5644 5672 475822720 475822692 3.000000e-03 54.7
63 TraesCS5D01G294800 chr4A 100.000 30 0 0 5643 5672 596481538 596481509 8.750000e-04 56.5


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 TraesCS5D01G294800 chr5D 391975661 391981908 6247 True 11538 11538 100.00000 1 6248 1 chr5D.!!$R3 6247
1 TraesCS5D01G294800 chr5B 472737848 472744368 6520 True 2699 5180 96.70675 1 6248 4 chr5B.!!$R3 6247
2 TraesCS5D01G294800 chr5A 495307853 495313089 5236 False 1756 3967 91.01350 31 5265 4 chr5A.!!$F2 5234
3 TraesCS5D01G294800 chr6A 98904340 98905113 773 False 800 800 85.64200 1439 2214 1 chr6A.!!$F1 775
4 TraesCS5D01G294800 chr3B 751108559 751109466 907 True 617 617 79.19800 1236 2148 1 chr3B.!!$R1 912

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
1126 1152 3.290710 GGGAGATGCTGAAATTTAGGCA 58.709 45.455 16.37 16.37 39.06 4.75 F
2930 3035 3.769739 TGCACCTTATCATATTCCGCT 57.230 42.857 0.00 0.00 0.00 5.52 F
4000 4198 1.068194 GTCAGTGACTGGAGGACGAAG 60.068 57.143 16.26 0.00 31.51 3.79 F
4115 4316 2.213499 GTTGCATCAGGATAAGGACCG 58.787 52.381 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2945 3050 6.604171 ACTTGGAATATGATAAGGTGCATCA 58.396 36.000 0.00 0.0 36.86 3.07 R
4012 4210 4.156477 AGTGGAGAACTTAAGCTCTCTGT 58.844 43.478 26.95 14.2 37.41 3.41 R
5160 5487 0.107703 GGATCGGCCAACTGTCATCA 60.108 55.000 2.24 0.0 36.34 3.07 R
5443 5770 0.239879 TTTGTCCGGCGCAATTCTTC 59.760 50.000 10.83 0.0 0.00 2.87 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
1126 1152 3.290710 GGGAGATGCTGAAATTTAGGCA 58.709 45.455 16.37 16.37 39.06 4.75
2927 3032 8.798859 AACTATGATGCACCTTATCATATTCC 57.201 34.615 7.27 0.00 43.07 3.01
2928 3033 7.044181 ACTATGATGCACCTTATCATATTCCG 58.956 38.462 7.27 0.43 43.07 4.30
2929 3034 4.002982 TGATGCACCTTATCATATTCCGC 58.997 43.478 0.00 0.00 30.03 5.54
2930 3035 3.769739 TGCACCTTATCATATTCCGCT 57.230 42.857 0.00 0.00 0.00 5.52
2931 3036 4.085357 TGCACCTTATCATATTCCGCTT 57.915 40.909 0.00 0.00 0.00 4.68
2932 3037 5.222079 TGCACCTTATCATATTCCGCTTA 57.778 39.130 0.00 0.00 0.00 3.09
2933 3038 5.804639 TGCACCTTATCATATTCCGCTTAT 58.195 37.500 0.00 0.00 0.00 1.73
2934 3039 6.237901 TGCACCTTATCATATTCCGCTTATT 58.762 36.000 0.00 0.00 0.00 1.40
2935 3040 7.390823 TGCACCTTATCATATTCCGCTTATTA 58.609 34.615 0.00 0.00 0.00 0.98
2936 3041 8.046708 TGCACCTTATCATATTCCGCTTATTAT 58.953 33.333 0.00 0.00 0.00 1.28
2937 3042 8.338259 GCACCTTATCATATTCCGCTTATTATG 58.662 37.037 0.00 0.00 0.00 1.90
2938 3043 9.383519 CACCTTATCATATTCCGCTTATTATGT 57.616 33.333 0.00 0.00 0.00 2.29
2939 3044 9.959721 ACCTTATCATATTCCGCTTATTATGTT 57.040 29.630 0.00 0.00 0.00 2.71
2950 3055 8.251750 TCCGCTTATTATGTTAACTATGATGC 57.748 34.615 7.22 3.09 0.00 3.91
2951 3056 7.875554 TCCGCTTATTATGTTAACTATGATGCA 59.124 33.333 7.22 0.00 0.00 3.96
2952 3057 7.957484 CCGCTTATTATGTTAACTATGATGCAC 59.043 37.037 7.22 0.00 0.00 4.57
2953 3058 7.957484 CGCTTATTATGTTAACTATGATGCACC 59.043 37.037 7.22 0.00 0.00 5.01
2954 3059 9.003658 GCTTATTATGTTAACTATGATGCACCT 57.996 33.333 7.22 0.00 0.00 4.00
3355 3552 6.604795 ACTGCTTTATTCTGCCACTCATTTAT 59.395 34.615 0.00 0.00 0.00 1.40
4000 4198 1.068194 GTCAGTGACTGGAGGACGAAG 60.068 57.143 16.26 0.00 31.51 3.79
4012 4210 5.007034 TGGAGGACGAAGCAAATTTGATTA 58.993 37.500 20.80 1.00 36.85 1.75
4115 4316 2.213499 GTTGCATCAGGATAAGGACCG 58.787 52.381 0.00 0.00 0.00 4.79
4152 4353 5.901552 ACACTTTTTCTGTGTAACCATTGG 58.098 37.500 0.00 0.00 45.49 3.16
4412 4613 7.849804 TCTATTGAGGAGTTTTTATGCAGAC 57.150 36.000 0.00 0.00 0.00 3.51
4683 4886 9.582431 TGTAGTCCGTATTGAAATCTCTAAAAG 57.418 33.333 0.00 0.00 0.00 2.27
5176 5503 1.234821 GTTTGATGACAGTTGGCCGA 58.765 50.000 0.00 0.00 0.00 5.54
5295 5622 4.637276 ACGTGATAATGGTGTTCAGTCAA 58.363 39.130 0.00 0.00 0.00 3.18
5318 5645 4.589216 ATTGTCTTGGAAATGTGGTGTG 57.411 40.909 0.00 0.00 0.00 3.82
5397 5724 8.291191 TGATGTTATAAATGTCAATGCTTGGA 57.709 30.769 0.00 0.00 0.00 3.53
5430 5757 9.838339 AAACGTTTAGGATGATTTGATCTCTAT 57.162 29.630 12.83 0.00 0.00 1.98
5431 5758 9.838339 AACGTTTAGGATGATTTGATCTCTATT 57.162 29.630 0.00 0.00 0.00 1.73
5432 5759 9.838339 ACGTTTAGGATGATTTGATCTCTATTT 57.162 29.630 0.00 0.00 0.00 1.40
5515 5842 1.377333 GCACCAGGCCTCTTGGTAC 60.377 63.158 14.45 6.00 36.11 3.34
5580 5907 4.572389 CAGGCTACAGCGAAGTATGAAAAT 59.428 41.667 0.00 0.00 43.26 1.82
5649 5976 3.528532 CAACCCATTTACGGACTACTCC 58.471 50.000 0.00 0.00 0.00 3.85
5652 5979 2.364647 CCCATTTACGGACTACTCCCTC 59.635 54.545 0.00 0.00 31.93 4.30
5700 6113 9.700831 ATATAAAGCAAAATAAGTGAACTCCCT 57.299 29.630 0.00 0.00 0.00 4.20
5703 6116 5.006386 AGCAAAATAAGTGAACTCCCTCTG 58.994 41.667 0.00 0.00 0.00 3.35
5705 6118 5.241728 GCAAAATAAGTGAACTCCCTCTGTT 59.758 40.000 0.00 0.00 0.00 3.16
5706 6119 6.239036 GCAAAATAAGTGAACTCCCTCTGTTT 60.239 38.462 0.00 0.00 0.00 2.83
5707 6120 7.363431 CAAAATAAGTGAACTCCCTCTGTTTC 58.637 38.462 0.00 0.00 0.00 2.78
5710 6123 5.888982 AAGTGAACTCCCTCTGTTTCTAA 57.111 39.130 0.00 0.00 0.00 2.10
5711 6124 5.888982 AGTGAACTCCCTCTGTTTCTAAA 57.111 39.130 0.00 0.00 0.00 1.85
5895 6405 1.538419 CCGCGGATTTTCTACTCCCTC 60.538 57.143 24.07 0.00 0.00 4.30
5911 6421 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
5917 6427 2.597305 CGTCCGGAAATACTTGTCGAAG 59.403 50.000 5.23 0.00 35.07 3.79
5921 6431 5.350640 GTCCGGAAATACTTGTCGAAGAAAT 59.649 40.000 5.23 0.00 39.69 2.17
5981 6492 3.803555 CAAAGAACTCTTGCATCGTGTC 58.196 45.455 0.00 0.00 36.12 3.67
5994 6505 2.273370 TCGTGTCGGTCTTAAGCATC 57.727 50.000 0.00 0.00 0.00 3.91
6006 6517 4.331168 GTCTTAAGCATCTCCATGTGACAC 59.669 45.833 0.00 0.00 31.86 3.67
6007 6518 2.865119 AAGCATCTCCATGTGACACA 57.135 45.000 11.41 11.41 31.86 3.72
6021 6532 3.563808 TGTGACACACAAGCAAAGGATAC 59.436 43.478 3.56 0.00 41.69 2.24
6025 6536 3.003275 ACACACAAGCAAAGGATACAACG 59.997 43.478 0.00 0.00 41.41 4.10
6030 6541 4.457603 ACAAGCAAAGGATACAACGCAATA 59.542 37.500 0.00 0.00 41.41 1.90
6031 6542 5.125417 ACAAGCAAAGGATACAACGCAATAT 59.875 36.000 0.00 0.00 41.41 1.28
6032 6543 5.173774 AGCAAAGGATACAACGCAATATG 57.826 39.130 0.00 0.00 41.41 1.78
6038 6549 5.853936 AGGATACAACGCAATATGAGCTTA 58.146 37.500 0.00 0.00 41.41 3.09
6068 6579 5.966742 AAAGGTGAGAGATAACCAAAAGC 57.033 39.130 0.00 0.00 0.00 3.51
6070 6581 2.678336 GGTGAGAGATAACCAAAAGCGG 59.322 50.000 0.00 0.00 0.00 5.52
6096 6607 3.707793 GATGGAGACGAGGATGTGTTAC 58.292 50.000 0.00 0.00 0.00 2.50
6108 6619 3.683340 GGATGTGTTACCGAAGTTCCTTC 59.317 47.826 0.00 0.00 37.16 3.46
6170 6681 0.613012 ACAATGCTCCCCAAGAAGCC 60.613 55.000 0.00 0.00 0.00 4.35
6211 6722 2.112928 ACGCCCTCACACAATGCA 59.887 55.556 0.00 0.00 0.00 3.96
6218 6729 1.816835 CCTCACACAATGCAAGATGCT 59.183 47.619 3.78 0.00 45.31 3.79
6237 6748 3.244875 TGCTGTGATTCCACTATTGGTGT 60.245 43.478 0.00 0.00 44.35 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.275936 ACAACAATTTTCCAGACTTCTCCG 59.724 41.667 0.00 0.00 0.00 4.63
1126 1152 6.409524 TTCCATTTGAGCTTCTTGACATTT 57.590 33.333 0.00 0.00 0.00 2.32
1220 1246 4.346418 AGTTCTTGAGTGATGTTCTCCACT 59.654 41.667 0.00 0.00 45.37 4.00
2837 2942 8.768397 TGGTCATGGTTACAGTAAGATTATTCT 58.232 33.333 0.00 0.00 0.00 2.40
2924 3029 8.717821 GCATCATAGTTAACATAATAAGCGGAA 58.282 33.333 8.61 0.00 0.00 4.30
2925 3030 7.875554 TGCATCATAGTTAACATAATAAGCGGA 59.124 33.333 8.61 0.00 0.00 5.54
2926 3031 7.957484 GTGCATCATAGTTAACATAATAAGCGG 59.043 37.037 8.61 0.00 0.00 5.52
2927 3032 7.957484 GGTGCATCATAGTTAACATAATAAGCG 59.043 37.037 8.61 0.00 0.00 4.68
2928 3033 9.003658 AGGTGCATCATAGTTAACATAATAAGC 57.996 33.333 8.61 4.37 0.00 3.09
2939 3044 9.890629 GGAATATGATAAGGTGCATCATAGTTA 57.109 33.333 11.48 0.00 44.47 2.24
2940 3045 8.385491 TGGAATATGATAAGGTGCATCATAGTT 58.615 33.333 11.48 7.12 44.47 2.24
2941 3046 7.921304 TGGAATATGATAAGGTGCATCATAGT 58.079 34.615 11.48 9.28 44.47 2.12
2942 3047 8.797350 TTGGAATATGATAAGGTGCATCATAG 57.203 34.615 11.48 0.00 44.47 2.23
2943 3048 8.385491 ACTTGGAATATGATAAGGTGCATCATA 58.615 33.333 8.91 8.91 45.03 2.15
2944 3049 7.236529 ACTTGGAATATGATAAGGTGCATCAT 58.763 34.615 0.00 1.98 43.72 2.45
2945 3050 6.604171 ACTTGGAATATGATAAGGTGCATCA 58.396 36.000 0.00 0.00 36.86 3.07
2946 3051 7.516198 AACTTGGAATATGATAAGGTGCATC 57.484 36.000 0.00 0.00 0.00 3.91
2947 3052 8.995027 TTAACTTGGAATATGATAAGGTGCAT 57.005 30.769 0.00 0.00 0.00 3.96
2948 3053 8.995027 ATTAACTTGGAATATGATAAGGTGCA 57.005 30.769 0.00 0.00 0.00 4.57
4000 4198 8.239998 ACTTAAGCTCTCTGTAATCAAATTTGC 58.760 33.333 13.54 0.04 0.00 3.68
4012 4210 4.156477 AGTGGAGAACTTAAGCTCTCTGT 58.844 43.478 26.95 14.20 37.41 3.41
4115 4316 7.642586 ACAGAAAAAGTGTTACTCGCAAATAAC 59.357 33.333 0.00 0.00 32.85 1.89
4152 4353 4.666402 GCAAAAACATAAAGCGCCATTGAC 60.666 41.667 2.29 0.00 0.00 3.18
4412 4613 8.617290 ATTTATACATAAAGAAGGCTTACCGG 57.383 34.615 0.00 0.00 37.03 5.28
4683 4886 5.541484 TCCCTCCGTTCCTAAATATAAGTCC 59.459 44.000 0.00 0.00 0.00 3.85
5160 5487 0.107703 GGATCGGCCAACTGTCATCA 60.108 55.000 2.24 0.00 36.34 3.07
5176 5503 7.420214 CGGATAATACCAATATGGCTTAGGGAT 60.420 40.741 7.59 0.00 42.67 3.85
5295 5622 5.358922 CACACCACATTTCCAAGACAATTT 58.641 37.500 0.00 0.00 0.00 1.82
5397 5724 7.876068 TCAAATCATCCTAAACGTTTGTCTACT 59.124 33.333 23.46 0.00 0.00 2.57
5443 5770 0.239879 TTTGTCCGGCGCAATTCTTC 59.760 50.000 10.83 0.00 0.00 2.87
5446 5773 0.729140 CTGTTTGTCCGGCGCAATTC 60.729 55.000 10.83 8.78 0.00 2.17
5504 5831 0.741221 CTCGCAAGGTACCAAGAGGC 60.741 60.000 15.94 8.78 36.56 4.70
5580 5907 1.227527 CCAGGTTGACGTGTGCTCA 60.228 57.895 0.00 0.00 0.00 4.26
5673 6086 9.736023 GGGAGTTCACTTATTTTGCTTTATATG 57.264 33.333 0.00 0.00 0.00 1.78
5835 6330 2.916269 TGGACTGGGTTGGATTGACATA 59.084 45.455 0.00 0.00 0.00 2.29
5848 6343 6.542821 TCTGCCTAATTAATTATGGACTGGG 58.457 40.000 19.57 12.50 0.00 4.45
5849 6344 7.040409 GGTTCTGCCTAATTAATTATGGACTGG 60.040 40.741 19.57 13.02 0.00 4.00
5895 6405 1.135315 TCGACAAGTATTTCCGGACGG 60.135 52.381 1.83 3.96 0.00 4.79
5940 6451 8.997621 TCTTTGCAGACGTATTTTAGTTCTAT 57.002 30.769 0.00 0.00 0.00 1.98
5981 6492 2.868583 CACATGGAGATGCTTAAGACCG 59.131 50.000 6.67 0.00 32.14 4.79
5994 6505 1.596603 TGCTTGTGTGTCACATGGAG 58.403 50.000 9.31 8.60 44.16 3.86
6006 6517 2.031245 TGCGTTGTATCCTTTGCTTGTG 60.031 45.455 0.00 0.00 0.00 3.33
6007 6518 2.226330 TGCGTTGTATCCTTTGCTTGT 58.774 42.857 0.00 0.00 0.00 3.16
6021 6532 4.598406 TGTGTAAGCTCATATTGCGTTG 57.402 40.909 0.00 0.00 35.28 4.10
6025 6536 7.148239 ACCTTTACTTGTGTAAGCTCATATTGC 60.148 37.037 0.00 0.00 39.49 3.56
6030 6541 5.865085 TCACCTTTACTTGTGTAAGCTCAT 58.135 37.500 0.00 0.00 39.49 2.90
6031 6542 5.069914 TCTCACCTTTACTTGTGTAAGCTCA 59.930 40.000 0.00 0.00 39.49 4.26
6032 6543 5.539048 TCTCACCTTTACTTGTGTAAGCTC 58.461 41.667 0.00 0.00 39.49 4.09
6038 6549 6.042781 TGGTTATCTCTCACCTTTACTTGTGT 59.957 38.462 0.00 0.00 33.76 3.72
6068 6579 1.064296 CTCGTCTCCATCGGTTCCG 59.936 63.158 4.74 4.74 0.00 4.30
6070 6581 1.033574 ATCCTCGTCTCCATCGGTTC 58.966 55.000 0.00 0.00 0.00 3.62
6152 6663 0.612732 TGGCTTCTTGGGGAGCATTG 60.613 55.000 0.00 0.00 0.00 2.82
6170 6681 1.068741 GAGAATACGGTGGCCCTAGTG 59.931 57.143 0.00 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.