Multiple sequence alignment - TraesCS3A01G330600

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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 TraesCS3A01G330600 chr3A 100.000 5182 0 0 1 5182 575315340 575310159 0.000000e+00 9570
1 TraesCS3A01G330600 chr3D 96.325 4435 112 18 239 4656 437219049 437214649 0.000000e+00 7239
2 TraesCS3A01G330600 chr3D 89.260 419 28 12 4642 5045 437214632 437214216 4.630000e-140 508
3 TraesCS3A01G330600 chr3D 92.481 133 10 0 5050 5182 437214166 437214034 1.900000e-44 191
4 TraesCS3A01G330600 chr3D 92.727 110 7 1 4 113 437219479 437219371 1.930000e-34 158
5 TraesCS3A01G330600 chr3B 94.967 4331 129 38 180 4466 572489104 572484819 0.000000e+00 6708
6 TraesCS3A01G330600 chr3B 92.821 195 13 1 4463 4656 572484781 572484587 1.100000e-71 281
7 TraesCS3A01G330600 chr1D 87.124 598 72 3 1072 1665 408432322 408432918 0.000000e+00 673
8 TraesCS3A01G330600 chr1B 86.622 598 75 3 1072 1665 549518385 549518981 0.000000e+00 656
9 TraesCS3A01G330600 chr1A 86.455 598 76 3 1072 1665 504313402 504313998 0.000000e+00 651
10 TraesCS3A01G330600 chr6B 88.587 184 17 2 4714 4893 300937499 300937682 2.430000e-53 220
11 TraesCS3A01G330600 chr6B 86.139 202 20 6 4714 4907 550313228 550313027 1.460000e-50 211
12 TraesCS3A01G330600 chr7D 88.108 185 16 4 4714 4893 124605923 124605740 1.130000e-51 215
13 TraesCS3A01G330600 chrUn 87.027 185 19 2 4714 4894 21282931 21282748 2.450000e-48 204
14 TraesCS3A01G330600 chr5D 85.572 201 22 4 4714 4907 324982842 324983042 2.450000e-48 204
15 TraesCS3A01G330600 chr6D 85.075 201 23 5 4714 4907 193573727 193573527 1.140000e-46 198
16 TraesCS3A01G330600 chr4B 84.925 199 20 7 4714 4905 667428865 667428670 5.300000e-45 193
17 TraesCS3A01G330600 chr2B 84.000 200 25 4 4714 4906 410206538 410206737 8.860000e-43 185


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 TraesCS3A01G330600 chr3A 575310159 575315340 5181 True 9570.0 9570 100.00000 1 5182 1 chr3A.!!$R1 5181
1 TraesCS3A01G330600 chr3D 437214034 437219479 5445 True 2024.0 7239 92.69825 4 5182 4 chr3D.!!$R1 5178
2 TraesCS3A01G330600 chr3B 572484587 572489104 4517 True 3494.5 6708 93.89400 180 4656 2 chr3B.!!$R1 4476
3 TraesCS3A01G330600 chr1D 408432322 408432918 596 False 673.0 673 87.12400 1072 1665 1 chr1D.!!$F1 593
4 TraesCS3A01G330600 chr1B 549518385 549518981 596 False 656.0 656 86.62200 1072 1665 1 chr1B.!!$F1 593
5 TraesCS3A01G330600 chr1A 504313402 504313998 596 False 651.0 651 86.45500 1072 1665 1 chr1A.!!$F1 593

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
158 187 0.035739 GGGCGGTGAAGACTTACCAA 59.964 55.000 11.81 0.0 36.76 3.67 F
548 773 0.253044 AACCCACCATCATCAGTCCG 59.747 55.000 0.00 0.0 0.00 4.79 F
616 841 1.626825 CCTCCGGTCCTTTTCTTACCA 59.373 52.381 0.00 0.0 32.55 3.25 F
2354 2585 1.224870 TGGACCGCCACAAACTCAA 59.775 52.632 0.00 0.0 39.92 3.02 F
3055 3289 2.076863 GCCACCATAACACACTCAGTC 58.923 52.381 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 1707 1.003580 AGGCCGTTGATGACAATGTCT 59.996 47.619 14.97 0.00 40.28 3.41 R
2101 2331 2.019249 GCATCAACTTCCATAGCAGCA 58.981 47.619 0.00 0.00 0.00 4.41 R
2466 2699 5.012239 AGGAGCATTCATAAGCAACAGAAA 58.988 37.500 0.00 0.00 0.00 2.52 R
4094 4328 1.438651 TCTCAATTCTTTCACGCGGG 58.561 50.000 12.47 6.51 0.00 6.13 R
5049 5372 0.185658 TCGGGTGACGGATATGGGTA 59.814 55.000 0.00 0.00 44.45 3.69 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
64 65 6.345298 TGAATCAAAGATGCCGTATGTAAGA 58.655 36.000 0.00 0.00 0.00 2.10
65 66 6.821160 TGAATCAAAGATGCCGTATGTAAGAA 59.179 34.615 0.00 0.00 0.00 2.52
129 158 8.987890 TGCCTTTTTAAATTTGTCTTCTATTGC 58.012 29.630 0.00 0.00 0.00 3.56
134 163 1.459450 TTTGTCTTCTATTGCCGGGC 58.541 50.000 13.32 13.32 0.00 6.13
158 187 0.035739 GGGCGGTGAAGACTTACCAA 59.964 55.000 11.81 0.00 36.76 3.67
237 395 4.274214 TGTTCTGAACTTGACATGCTCTTG 59.726 41.667 20.18 0.00 0.00 3.02
340 537 7.166691 TCAGTGGTCCAGTAGAAGTTTATAC 57.833 40.000 0.00 0.00 0.00 1.47
341 538 6.722590 TCAGTGGTCCAGTAGAAGTTTATACA 59.277 38.462 0.00 0.00 0.00 2.29
342 539 7.036220 CAGTGGTCCAGTAGAAGTTTATACAG 58.964 42.308 0.00 0.00 0.00 2.74
343 540 6.724905 AGTGGTCCAGTAGAAGTTTATACAGT 59.275 38.462 0.00 0.00 0.00 3.55
344 541 7.892241 AGTGGTCCAGTAGAAGTTTATACAGTA 59.108 37.037 0.00 0.00 0.00 2.74
367 564 9.936329 AGTACATACAATCAAAATTTCCCCTAT 57.064 29.630 0.00 0.00 0.00 2.57
389 592 7.803189 CCTATATAACAATCAAAATCACCGTGC 59.197 37.037 0.00 0.00 0.00 5.34
390 593 2.330231 ACAATCAAAATCACCGTGCG 57.670 45.000 0.00 0.00 0.00 5.34
391 594 1.606668 ACAATCAAAATCACCGTGCGT 59.393 42.857 0.00 0.00 0.00 5.24
392 595 2.034053 ACAATCAAAATCACCGTGCGTT 59.966 40.909 0.00 0.00 0.00 4.84
393 596 2.611974 ATCAAAATCACCGTGCGTTC 57.388 45.000 0.00 0.00 0.00 3.95
394 597 1.588674 TCAAAATCACCGTGCGTTCT 58.411 45.000 0.00 0.00 0.00 3.01
395 598 1.944024 TCAAAATCACCGTGCGTTCTT 59.056 42.857 0.00 0.00 0.00 2.52
396 599 2.356382 TCAAAATCACCGTGCGTTCTTT 59.644 40.909 0.00 0.00 0.00 2.52
397 600 2.399396 AAATCACCGTGCGTTCTTTG 57.601 45.000 0.00 0.00 0.00 2.77
398 601 1.588674 AATCACCGTGCGTTCTTTGA 58.411 45.000 0.00 0.00 0.00 2.69
541 766 1.342275 CCATCACCAACCCACCATCAT 60.342 52.381 0.00 0.00 0.00 2.45
542 767 2.026641 CATCACCAACCCACCATCATC 58.973 52.381 0.00 0.00 0.00 2.92
543 768 1.071434 TCACCAACCCACCATCATCA 58.929 50.000 0.00 0.00 0.00 3.07
544 769 1.004628 TCACCAACCCACCATCATCAG 59.995 52.381 0.00 0.00 0.00 2.90
545 770 1.075601 ACCAACCCACCATCATCAGT 58.924 50.000 0.00 0.00 0.00 3.41
546 771 1.004745 ACCAACCCACCATCATCAGTC 59.995 52.381 0.00 0.00 0.00 3.51
547 772 1.683011 CCAACCCACCATCATCAGTCC 60.683 57.143 0.00 0.00 0.00 3.85
548 773 0.253044 AACCCACCATCATCAGTCCG 59.747 55.000 0.00 0.00 0.00 4.79
558 783 2.697761 ATCAGTCCGTCACCGTCCG 61.698 63.158 0.00 0.00 0.00 4.79
616 841 1.626825 CCTCCGGTCCTTTTCTTACCA 59.373 52.381 0.00 0.00 32.55 3.25
1672 1900 6.003950 AGCAAAGCAAGTGAGTTTCCTATAA 58.996 36.000 0.00 0.00 0.00 0.98
1839 2068 5.986004 GTACAAATTTGTAGCTATCGCCT 57.014 39.130 27.29 3.38 43.67 5.52
1841 2070 7.653767 GTACAAATTTGTAGCTATCGCCTAT 57.346 36.000 27.29 2.78 43.67 2.57
1842 2071 6.787085 ACAAATTTGTAGCTATCGCCTATC 57.213 37.500 22.10 0.00 40.16 2.08
1902 2131 6.119536 TGACAGACAGTTATCAAACTTTGGT 58.880 36.000 1.62 0.00 43.60 3.67
1919 2148 7.053316 ACTTTGGTTGAAATGTCATCATGAA 57.947 32.000 0.00 0.00 34.19 2.57
1975 2204 5.220080 GCGTTGCTGACAAAATATTGATGTG 60.220 40.000 10.86 0.82 38.94 3.21
2100 2330 4.439057 CCTTGGCTTGCTAAATACTCGTA 58.561 43.478 0.00 0.00 0.00 3.43
2101 2331 5.057149 CCTTGGCTTGCTAAATACTCGTAT 58.943 41.667 0.00 0.00 0.00 3.06
2173 2404 4.893608 TGCATGACTTGTCTAACTGCTTA 58.106 39.130 0.00 0.00 0.00 3.09
2178 2409 5.479306 TGACTTGTCTAACTGCTTATGTCC 58.521 41.667 2.35 0.00 0.00 4.02
2245 2476 7.491682 TCTACATCAATCGAATCAACTGATCA 58.508 34.615 0.00 0.00 32.75 2.92
2248 2479 7.993101 ACATCAATCGAATCAACTGATCAAAT 58.007 30.769 0.00 0.00 32.75 2.32
2313 2544 4.562789 GGCAATTAATTTCTTGGCGACTTC 59.437 41.667 0.00 0.00 38.03 3.01
2354 2585 1.224870 TGGACCGCCACAAACTCAA 59.775 52.632 0.00 0.00 39.92 3.02
2461 2694 5.181245 TGAACTTGCAGCTAAGTAATTGGTC 59.819 40.000 2.32 0.00 39.86 4.02
2466 2699 5.424757 TGCAGCTAAGTAATTGGTCGTATT 58.575 37.500 0.00 0.00 0.00 1.89
2488 2721 4.970662 TTCTGTTGCTTATGAATGCTCC 57.029 40.909 0.00 0.00 0.00 4.70
2509 2742 9.143155 TGCTCCTAGTCATTATATGTGTTTAGA 57.857 33.333 0.00 0.00 0.00 2.10
2702 2936 3.699538 ACTCTGCATGTGACTTACGGATA 59.300 43.478 0.00 0.00 0.00 2.59
2966 3200 6.534475 AAGTTATGTTCGTATGTCCCACTA 57.466 37.500 0.00 0.00 0.00 2.74
3055 3289 2.076863 GCCACCATAACACACTCAGTC 58.923 52.381 0.00 0.00 0.00 3.51
3082 3316 6.875076 ACACAATGTCCTCAATAGGTAGTAC 58.125 40.000 0.00 0.00 44.09 2.73
3083 3317 6.668283 ACACAATGTCCTCAATAGGTAGTACT 59.332 38.462 0.00 0.00 44.09 2.73
3084 3318 7.837689 ACACAATGTCCTCAATAGGTAGTACTA 59.162 37.037 0.00 0.00 44.09 1.82
3101 3335 9.976511 GGTAGTACTAACTTGCATCATGTTATA 57.023 33.333 10.86 1.24 34.88 0.98
3152 3386 5.880887 CCCAAGGAGGAAAAATACACTAGTC 59.119 44.000 0.00 0.00 41.22 2.59
3217 3451 6.957631 TGGACAAGAAAGGCTGAAATATCTA 58.042 36.000 0.00 0.00 0.00 1.98
3599 3833 4.399303 ACCTCAAGGCATACTAAATTGTGC 59.601 41.667 0.00 0.00 39.32 4.57
3906 4140 7.398829 TGTAACTGCCCAGATATAAGAACAAA 58.601 34.615 1.69 0.00 0.00 2.83
4012 4246 4.708726 AGTTTGCAGCCATAATCAACTC 57.291 40.909 0.00 0.00 0.00 3.01
4094 4328 3.773860 AGAGATGAGTCGATGTGTGAC 57.226 47.619 0.00 0.00 36.60 3.67
4198 4432 4.764823 AGCTTAGACAGATTCTCCTATCGG 59.235 45.833 0.00 0.00 35.55 4.18
4260 4494 0.955428 TGTGCTCTTGTCCATTCGGC 60.955 55.000 0.00 0.00 0.00 5.54
4370 4606 4.091509 GTGTTAGTAGCTTGATGTGGTTCG 59.908 45.833 0.00 0.00 0.00 3.95
4393 4629 5.983118 CGCACCATCTTGTGTATATAGAACA 59.017 40.000 0.00 0.00 38.52 3.18
4476 4753 5.482006 TCATGCTTCGAATGATATACCCTG 58.518 41.667 0.00 0.00 0.00 4.45
4595 4873 5.244178 CCAGTGACTAGTCTTCCTACAAAGT 59.756 44.000 23.01 0.32 0.00 2.66
4611 4889 2.403252 AAGTTGGACCCGACATGATC 57.597 50.000 0.00 0.00 32.91 2.92
4651 4929 0.962489 AGTGGACAGAGAGAACGTGG 59.038 55.000 0.00 0.00 0.00 4.94
4670 4980 2.680913 GCAACTACAGCGGTGGCAG 61.681 63.158 20.20 16.99 43.41 4.85
4671 4981 1.301716 CAACTACAGCGGTGGCAGT 60.302 57.895 20.20 17.64 43.41 4.40
4683 4993 1.069227 GGTGGCAGTGTTTGACGATTC 60.069 52.381 0.00 0.00 37.78 2.52
4684 4994 1.873591 GTGGCAGTGTTTGACGATTCT 59.126 47.619 0.00 0.00 37.78 2.40
4685 4995 3.064207 GTGGCAGTGTTTGACGATTCTA 58.936 45.455 0.00 0.00 37.78 2.10
4741 5054 7.727331 TTTTGGCTTGTGAATTTTCCATTAG 57.273 32.000 0.00 0.00 0.00 1.73
4763 5076 8.672823 TTAGTAGATTCGAGCACTGTAATAGA 57.327 34.615 0.00 0.00 0.00 1.98
4826 5143 9.118236 GCTAAATTACAGCTTTGAACTAGTTTG 57.882 33.333 10.02 5.40 36.07 2.93
4829 5146 6.861065 TTACAGCTTTGAACTAGTTTGAGG 57.139 37.500 10.02 3.50 0.00 3.86
4833 5150 4.068599 GCTTTGAACTAGTTTGAGGAGCT 58.931 43.478 10.02 0.00 0.00 4.09
4861 5178 2.027561 TGAAATTGTACCCCTCCTCGTG 60.028 50.000 0.00 0.00 0.00 4.35
4863 5180 1.486211 ATTGTACCCCTCCTCGTGAG 58.514 55.000 0.00 0.00 41.07 3.51
5009 5332 6.916360 AACTGCATTTATCAAGGAAAAGGA 57.084 33.333 0.00 0.00 0.00 3.36
5013 5336 8.689972 ACTGCATTTATCAAGGAAAAGGATTAG 58.310 33.333 0.00 0.00 0.00 1.73
5022 5345 6.374333 TCAAGGAAAAGGATTAGATTGAACCG 59.626 38.462 0.00 0.00 0.00 4.44
5032 5355 1.561542 AGATTGAACCGGCTGATTCCT 59.438 47.619 0.00 0.00 0.00 3.36
5034 5357 3.199946 AGATTGAACCGGCTGATTCCTAA 59.800 43.478 0.00 0.00 0.00 2.69
5039 5362 1.628846 ACCGGCTGATTCCTAACTGTT 59.371 47.619 0.00 0.00 0.00 3.16
5040 5363 2.009774 CCGGCTGATTCCTAACTGTTG 58.990 52.381 2.69 0.00 0.00 3.33
5041 5364 1.398390 CGGCTGATTCCTAACTGTTGC 59.602 52.381 2.69 0.00 0.00 4.17
5042 5365 2.716217 GGCTGATTCCTAACTGTTGCT 58.284 47.619 2.69 0.00 0.00 3.91
5043 5366 3.678806 CGGCTGATTCCTAACTGTTGCTA 60.679 47.826 2.69 0.00 0.00 3.49
5044 5367 3.873952 GGCTGATTCCTAACTGTTGCTAG 59.126 47.826 2.69 0.00 0.00 3.42
5045 5368 4.508662 GCTGATTCCTAACTGTTGCTAGT 58.491 43.478 2.69 0.00 0.00 2.57
5046 5369 4.331168 GCTGATTCCTAACTGTTGCTAGTG 59.669 45.833 2.69 0.00 0.00 2.74
5047 5370 4.832248 TGATTCCTAACTGTTGCTAGTGG 58.168 43.478 2.69 0.00 0.00 4.00
5048 5371 3.695830 TTCCTAACTGTTGCTAGTGGG 57.304 47.619 2.69 0.00 0.00 4.61
5049 5372 2.616524 TCCTAACTGTTGCTAGTGGGT 58.383 47.619 2.69 0.00 0.00 4.51
5050 5373 3.781808 TCCTAACTGTTGCTAGTGGGTA 58.218 45.455 2.69 0.00 0.00 3.69
5051 5374 3.512724 TCCTAACTGTTGCTAGTGGGTAC 59.487 47.826 2.69 0.00 0.00 3.34
5066 5435 0.683412 GGTACCCATATCCGTCACCC 59.317 60.000 0.00 0.00 0.00 4.61
5072 5441 1.029681 CATATCCGTCACCCGACAGA 58.970 55.000 0.00 0.00 42.74 3.41
5082 5451 0.252197 ACCCGACAGAGTAAATGGGC 59.748 55.000 0.00 0.00 40.41 5.36
5123 5492 6.127111 ACCCATGTTTGCATAGCATCAATTTA 60.127 34.615 0.00 0.00 38.76 1.40
5129 5498 5.099484 TGCATAGCATCAATTTAAGCGAG 57.901 39.130 0.00 0.00 31.71 5.03
5139 5508 7.857389 GCATCAATTTAAGCGAGACATAATCAA 59.143 33.333 0.00 0.00 0.00 2.57
5150 5519 6.088085 GCGAGACATAATCAAAAACAACAAGG 59.912 38.462 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.939802 GTAGTTTTGGAGAATTCTAACCTTAGA 57.060 33.333 8.25 0.00 37.97 2.10
1 2 9.720769 TGTAGTTTTGGAGAATTCTAACCTTAG 57.279 33.333 8.25 0.00 0.00 2.18
20 21 9.300681 TGATTCAAAGGATTTCTCATGTAGTTT 57.699 29.630 0.00 0.00 35.03 2.66
105 106 8.647226 CGGCAATAGAAGACAAATTTAAAAAGG 58.353 33.333 0.00 0.00 0.00 3.11
106 107 8.647226 CCGGCAATAGAAGACAAATTTAAAAAG 58.353 33.333 0.00 0.00 0.00 2.27
111 112 4.097286 GCCCGGCAATAGAAGACAAATTTA 59.903 41.667 3.91 0.00 0.00 1.40
112 113 3.119137 GCCCGGCAATAGAAGACAAATTT 60.119 43.478 3.91 0.00 0.00 1.82
113 114 2.427095 GCCCGGCAATAGAAGACAAATT 59.573 45.455 3.91 0.00 0.00 1.82
114 115 2.024414 GCCCGGCAATAGAAGACAAAT 58.976 47.619 3.91 0.00 0.00 2.32
115 116 1.271652 TGCCCGGCAATAGAAGACAAA 60.272 47.619 10.50 0.00 34.76 2.83
118 119 0.107654 AGTGCCCGGCAATAGAAGAC 60.108 55.000 15.39 0.00 41.47 3.01
119 120 1.491668 TAGTGCCCGGCAATAGAAGA 58.508 50.000 15.39 0.00 41.47 2.87
134 163 0.608640 AAGTCTTCACCGCCCTAGTG 59.391 55.000 0.00 0.00 36.54 2.74
158 187 7.972301 AGAGTTTATGCAAGAGATAGCCTTAT 58.028 34.615 0.00 0.00 0.00 1.73
340 537 8.066612 AGGGGAAATTTTGATTGTATGTACTG 57.933 34.615 0.00 0.00 0.00 2.74
341 538 9.936329 ATAGGGGAAATTTTGATTGTATGTACT 57.064 29.630 0.00 0.00 0.00 2.73
361 558 7.447238 ACGGTGATTTTGATTGTTATATAGGGG 59.553 37.037 0.00 0.00 0.00 4.79
367 564 5.122554 ACGCACGGTGATTTTGATTGTTATA 59.877 36.000 13.29 0.00 0.00 0.98
369 566 3.251245 ACGCACGGTGATTTTGATTGTTA 59.749 39.130 13.29 0.00 0.00 2.41
389 592 0.859232 CCACGTCCAGTCAAAGAACG 59.141 55.000 0.00 0.00 0.00 3.95
390 593 1.865340 GACCACGTCCAGTCAAAGAAC 59.135 52.381 5.29 0.00 33.08 3.01
391 594 1.537348 CGACCACGTCCAGTCAAAGAA 60.537 52.381 9.76 0.00 33.08 2.52
392 595 0.031585 CGACCACGTCCAGTCAAAGA 59.968 55.000 9.76 0.00 33.08 2.52
393 596 1.557443 GCGACCACGTCCAGTCAAAG 61.557 60.000 9.76 0.00 41.98 2.77
394 597 1.593209 GCGACCACGTCCAGTCAAA 60.593 57.895 9.76 0.00 41.98 2.69
395 598 2.028484 GCGACCACGTCCAGTCAA 59.972 61.111 9.76 0.00 41.98 3.18
396 599 3.986006 GGCGACCACGTCCAGTCA 61.986 66.667 9.76 0.00 41.98 3.41
397 600 3.986006 TGGCGACCACGTCCAGTC 61.986 66.667 0.00 0.00 43.97 3.51
398 601 4.295119 GTGGCGACCACGTCCAGT 62.295 66.667 12.22 0.00 44.95 4.00
601 826 1.162698 GGCGTGGTAAGAAAAGGACC 58.837 55.000 0.00 0.00 0.00 4.46
1263 1491 2.035442 GTTGAAGAGGTGCTCGGCC 61.035 63.158 0.00 0.00 35.36 6.13
1479 1707 1.003580 AGGCCGTTGATGACAATGTCT 59.996 47.619 14.97 0.00 40.28 3.41
1836 2065 4.889995 ACCAGATTAAAAAGGCTGATAGGC 59.110 41.667 0.00 0.00 41.73 3.93
1837 2066 6.712547 CCTACCAGATTAAAAAGGCTGATAGG 59.287 42.308 0.00 0.00 38.06 2.57
1838 2067 7.509546 TCCTACCAGATTAAAAAGGCTGATAG 58.490 38.462 0.00 0.00 0.00 2.08
1839 2068 7.127339 ACTCCTACCAGATTAAAAAGGCTGATA 59.873 37.037 0.00 0.00 0.00 2.15
1840 2069 6.069381 ACTCCTACCAGATTAAAAAGGCTGAT 60.069 38.462 0.00 0.00 0.00 2.90
1841 2070 5.250774 ACTCCTACCAGATTAAAAAGGCTGA 59.749 40.000 0.00 0.00 0.00 4.26
1842 2071 5.501156 ACTCCTACCAGATTAAAAAGGCTG 58.499 41.667 0.00 0.00 0.00 4.85
1975 2204 8.882415 TGTACGGATTTATCTTCTACAATTCC 57.118 34.615 0.00 0.00 0.00 3.01
2100 2330 2.621998 GCATCAACTTCCATAGCAGCAT 59.378 45.455 0.00 0.00 0.00 3.79
2101 2331 2.019249 GCATCAACTTCCATAGCAGCA 58.981 47.619 0.00 0.00 0.00 4.41
2158 2389 5.971763 AGAGGACATAAGCAGTTAGACAAG 58.028 41.667 0.00 0.00 0.00 3.16
2178 2409 6.431234 ATTTGCACAAAGTTAGGGACTAAGAG 59.569 38.462 1.92 0.00 40.85 2.85
2313 2544 5.614324 TTCACCCACAGATATTACCTCTG 57.386 43.478 0.00 0.00 44.60 3.35
2461 2694 6.968904 AGCATTCATAAGCAACAGAAAATACG 59.031 34.615 0.00 0.00 0.00 3.06
2466 2699 5.012239 AGGAGCATTCATAAGCAACAGAAA 58.988 37.500 0.00 0.00 0.00 2.52
2702 2936 7.765819 GGAACCTTAGCTGCAATAAAATCAATT 59.234 33.333 1.02 0.00 0.00 2.32
2966 3200 4.079253 AGTGGTCGAAATATGGCAAAAGT 58.921 39.130 0.00 0.00 0.00 2.66
3101 3335 5.883661 CTGATTCGTTGGAATTAGTGCATT 58.116 37.500 0.00 0.00 42.86 3.56
3152 3386 7.928167 TGGATGTTGACAGCTAAGATATAACTG 59.072 37.037 0.00 0.00 31.98 3.16
3350 3584 4.474651 AGGTGGGTGATGTAGATCATTTCA 59.525 41.667 5.77 2.80 40.78 2.69
3431 3665 4.217754 TGCATTACGACCTTTCAACAAC 57.782 40.909 0.00 0.00 0.00 3.32
3599 3833 6.656693 AGAGACACCCTGAAATGAATTGTTAG 59.343 38.462 0.00 0.00 0.00 2.34
4012 4246 6.142798 GTGCACATGAGTAAACAAATCAACAG 59.857 38.462 13.17 0.00 0.00 3.16
4094 4328 1.438651 TCTCAATTCTTTCACGCGGG 58.561 50.000 12.47 6.51 0.00 6.13
4198 4432 8.189460 TCTAGCGACTAATAGAAAGAAGGAAAC 58.811 37.037 0.00 0.00 0.00 2.78
4260 4494 3.800863 CAGCAGAAGCAGCAGCCG 61.801 66.667 0.00 0.00 45.49 5.52
4370 4606 7.786178 TTGTTCTATATACACAAGATGGTGC 57.214 36.000 0.00 0.00 42.55 5.01
4452 4688 6.111382 CAGGGTATATCATTCGAAGCATGAT 58.889 40.000 15.10 15.10 42.77 2.45
4494 4772 3.935203 CACATCTGTTCGAGCAGGTAATT 59.065 43.478 26.28 7.00 37.12 1.40
4595 4873 1.567357 TGAGATCATGTCGGGTCCAA 58.433 50.000 0.00 0.00 0.00 3.53
4611 4889 5.632764 CACTTACATCTATTCGCCTGATGAG 59.367 44.000 8.86 0.69 39.72 2.90
4651 4929 3.431725 GCCACCGCTGTAGTTGCC 61.432 66.667 0.00 0.00 0.00 4.52
4665 4975 2.254546 AGAATCGTCAAACACTGCCA 57.745 45.000 0.00 0.00 0.00 4.92
4730 5043 7.225538 CAGTGCTCGAATCTACTAATGGAAAAT 59.774 37.037 0.00 0.00 0.00 1.82
4741 5054 7.192148 TCTCTATTACAGTGCTCGAATCTAC 57.808 40.000 0.00 0.00 0.00 2.59
4804 5117 7.719633 TCCTCAAACTAGTTCAAAGCTGTAATT 59.280 33.333 8.95 0.00 0.00 1.40
4808 5121 5.036117 TCCTCAAACTAGTTCAAAGCTGT 57.964 39.130 8.95 0.00 0.00 4.40
4809 5122 4.083590 GCTCCTCAAACTAGTTCAAAGCTG 60.084 45.833 8.95 2.40 0.00 4.24
4818 5135 5.059833 CACTCAAAAGCTCCTCAAACTAGT 58.940 41.667 0.00 0.00 0.00 2.57
4821 5138 4.156455 TCACTCAAAAGCTCCTCAAACT 57.844 40.909 0.00 0.00 0.00 2.66
4826 5143 5.444663 ACAATTTCACTCAAAAGCTCCTC 57.555 39.130 0.00 0.00 0.00 3.71
4829 5146 5.461526 GGGTACAATTTCACTCAAAAGCTC 58.538 41.667 0.00 0.00 0.00 4.09
4833 5150 4.830600 GGAGGGGTACAATTTCACTCAAAA 59.169 41.667 0.00 0.00 0.00 2.44
4861 5178 8.236586 TCATTTGCAATAACAAGTACATCACTC 58.763 33.333 0.00 0.00 36.04 3.51
4863 5180 8.741101 TTCATTTGCAATAACAAGTACATCAC 57.259 30.769 0.00 0.00 0.00 3.06
4904 5221 5.403246 TGCTTTGTTTCATTACACACGTTT 58.597 33.333 0.00 0.00 0.00 3.60
4905 5222 4.987832 TGCTTTGTTTCATTACACACGTT 58.012 34.783 0.00 0.00 0.00 3.99
4906 5223 4.334203 TCTGCTTTGTTTCATTACACACGT 59.666 37.500 0.00 0.00 0.00 4.49
4908 5225 5.821204 ACTCTGCTTTGTTTCATTACACAC 58.179 37.500 0.00 0.00 0.00 3.82
4909 5226 6.989759 TCTACTCTGCTTTGTTTCATTACACA 59.010 34.615 0.00 0.00 0.00 3.72
4910 5227 7.421530 TCTACTCTGCTTTGTTTCATTACAC 57.578 36.000 0.00 0.00 0.00 2.90
4911 5228 8.621532 AATCTACTCTGCTTTGTTTCATTACA 57.378 30.769 0.00 0.00 0.00 2.41
4912 5229 9.899226 AAAATCTACTCTGCTTTGTTTCATTAC 57.101 29.630 0.00 0.00 0.00 1.89
5009 5332 4.137543 GGAATCAGCCGGTTCAATCTAAT 58.862 43.478 1.90 0.00 0.00 1.73
5013 5336 2.044123 AGGAATCAGCCGGTTCAATC 57.956 50.000 1.90 0.00 0.00 2.67
5017 5340 2.280628 CAGTTAGGAATCAGCCGGTTC 58.719 52.381 1.90 0.00 0.00 3.62
5022 5345 2.716217 AGCAACAGTTAGGAATCAGCC 58.284 47.619 0.00 0.00 0.00 4.85
5032 5355 3.967332 GGTACCCACTAGCAACAGTTA 57.033 47.619 0.00 0.00 0.00 2.24
5047 5370 3.033035 CGGGTGACGGATATGGGTACC 62.033 61.905 2.17 2.17 45.35 3.34
5048 5371 0.316204 CGGGTGACGGATATGGGTAC 59.684 60.000 0.00 0.00 39.42 3.34
5049 5372 0.185658 TCGGGTGACGGATATGGGTA 59.814 55.000 0.00 0.00 44.45 3.69
5050 5373 1.075822 TCGGGTGACGGATATGGGT 60.076 57.895 0.00 0.00 44.45 4.51
5051 5374 1.366366 GTCGGGTGACGGATATGGG 59.634 63.158 0.00 0.00 44.45 4.00
5066 5435 1.338674 TGGTGCCCATTTACTCTGTCG 60.339 52.381 0.00 0.00 0.00 4.35
5072 5441 1.001393 CCCGTGGTGCCCATTTACT 60.001 57.895 0.00 0.00 35.28 2.24
5123 5492 6.734137 TGTTGTTTTTGATTATGTCTCGCTT 58.266 32.000 0.00 0.00 0.00 4.68
5129 5498 9.522804 TTGTACCTTGTTGTTTTTGATTATGTC 57.477 29.630 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.