Multiple sequence alignment - TraesCS3D01G364800

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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 TraesCS3D01G364800 chr3D 100.000 3974 0 0 1 3974 478655894 478651921 0.000000e+00 7339
1 TraesCS3D01G364800 chr3B 89.259 4078 227 83 13 3971 638359799 638355814 0.000000e+00 4909
2 TraesCS3D01G364800 chr3A 92.627 2021 88 25 116 2092 621895909 621893906 0.000000e+00 2850
3 TraesCS3D01G364800 chr3A 88.906 1938 129 42 2094 3971 621893878 621891967 0.000000e+00 2309
4 TraesCS3D01G364800 chr3A 96.875 64 1 1 56 119 621896227 621896165 5.430000e-19 106
5 TraesCS3D01G364800 chr1D 87.793 426 30 5 2531 2935 372360598 372361022 2.780000e-131 479
6 TraesCS3D01G364800 chr1B 87.413 429 33 4 2531 2938 497274561 497274989 1.290000e-129 473
7 TraesCS3D01G364800 chr1A 88.206 407 27 4 2531 2916 471730049 471730455 2.160000e-127 466
8 TraesCS3D01G364800 chr5B 88.889 342 34 4 2531 2870 446996504 446996843 6.140000e-113 418
9 TraesCS3D01G364800 chr5D 88.304 342 36 4 2531 2870 374391715 374392054 1.330000e-109 407
10 TraesCS3D01G364800 chr7B 86.376 367 44 6 2519 2883 193310825 193311187 2.880000e-106 396
11 TraesCS3D01G364800 chr7B 85.195 385 53 4 2532 2914 544481052 544480670 3.720000e-105 392


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 TraesCS3D01G364800 chr3D 478651921 478655894 3973 True 7339 7339 100.000000 1 3974 1 chr3D.!!$R1 3973
1 TraesCS3D01G364800 chr3B 638355814 638359799 3985 True 4909 4909 89.259000 13 3971 1 chr3B.!!$R1 3958
2 TraesCS3D01G364800 chr3A 621891967 621896227 4260 True 1755 2850 92.802667 56 3971 3 chr3A.!!$R1 3915

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
45 46 0.179032 AGTTGGACCGCAATGTGACA 60.179 50.0 0.0 0.0 0.00 3.58 F
839 1129 0.734889 GCGCACATTGACATTAGGCT 59.265 50.0 0.3 0.0 0.00 4.58 F
1125 1415 0.179194 CGTCGACTTTCTCGTCCTCC 60.179 60.0 14.7 0.0 43.45 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1415 0.316278 CAGACGCCATAGACGACGAG 60.316 60.0 0.00 0.00 0.0 4.18 R
2153 2532 0.737019 CAAACACCCGCAATGCCATC 60.737 55.0 0.00 0.00 0.0 3.51 R
2982 3374 0.040781 GATCAGCTAGCTCGGTCGAC 60.041 60.0 16.15 7.13 0.0 4.20 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
45 46 0.179032 AGTTGGACCGCAATGTGACA 60.179 50.000 0.00 0.00 0.00 3.58
154 414 3.764237 TCTACGGCCTCAGTTTTTCTT 57.236 42.857 0.00 0.00 0.00 2.52
155 415 4.081322 TCTACGGCCTCAGTTTTTCTTT 57.919 40.909 0.00 0.00 0.00 2.52
237 497 0.830648 CCGGTACATCCACATCCACT 59.169 55.000 0.00 0.00 35.57 4.00
632 918 4.715523 ATTCACACGCCCCCACGG 62.716 66.667 0.00 0.00 37.37 4.94
755 1045 3.051479 AAACGTAAAGGCGCCCGG 61.051 61.111 26.15 10.65 34.88 5.73
839 1129 0.734889 GCGCACATTGACATTAGGCT 59.265 50.000 0.30 0.00 0.00 4.58
853 1143 3.834799 GGCTGCTGCTGCCATTCC 61.835 66.667 36.06 15.41 45.75 3.01
984 1274 7.680113 GCGAGGCCTCTATTACTTACTGATATC 60.680 44.444 29.73 0.00 0.00 1.63
1125 1415 0.179194 CGTCGACTTTCTCGTCCTCC 60.179 60.000 14.70 0.00 43.45 4.30
1243 1557 0.465097 CCATGATCACCCTGCACCTC 60.465 60.000 0.00 0.00 0.00 3.85
1360 1674 2.854736 TGACATCATGGAGGAGGAGA 57.145 50.000 0.00 0.00 0.00 3.71
1437 1754 2.092323 GAGTTGGAACCTAACCATGGC 58.908 52.381 13.04 0.00 37.26 4.40
1468 1785 1.077828 TGGAGGCAGAGGAGAAAGAGA 59.922 52.381 0.00 0.00 0.00 3.10
1713 2034 6.037098 GCTCTTATATATTACCACTCGCCTG 58.963 44.000 0.00 0.00 0.00 4.85
1791 2112 4.647424 ATTGGACACGCAAAAGAAAGAA 57.353 36.364 0.00 0.00 0.00 2.52
1820 2146 9.547753 GATCTAGAAATTTAATCAGCTGGTACA 57.452 33.333 15.13 0.20 0.00 2.90
1864 2198 4.892934 AGAGAACCGAGATCATCTAAGCTT 59.107 41.667 3.48 3.48 0.00 3.74
1868 2202 3.133721 ACCGAGATCATCTAAGCTTGCTT 59.866 43.478 9.86 12.65 0.00 3.91
1940 2282 2.497273 CCTGCCCCAAATCTTAACCAAG 59.503 50.000 0.00 0.00 0.00 3.61
2100 2479 0.311790 CTTGCATGCAGAACACCGTT 59.688 50.000 21.50 0.00 0.00 4.44
2153 2532 4.636435 ACACCGGCCACTTTCCCG 62.636 66.667 0.00 0.00 43.97 5.14
2250 2629 6.808704 GTGTCAATTTATTCCAAAGAGAAGGC 59.191 38.462 0.00 0.00 0.00 4.35
2256 2635 2.795231 TCCAAAGAGAAGGCCTGATG 57.205 50.000 5.69 0.00 0.00 3.07
2338 2722 3.128589 CCCAAACATGTATATATGCCCGC 59.871 47.826 9.21 0.00 0.00 6.13
2420 2804 6.077197 TCAATCATGACGAACAACGAAAATC 58.923 36.000 0.00 0.00 45.77 2.17
2458 2842 3.343941 AAACGCCTATCAAGTGGCTTA 57.656 42.857 0.00 0.00 46.42 3.09
2530 2922 4.948621 TGCATAACATGTGTTGATGGATGA 59.051 37.500 0.00 0.00 38.90 2.92
2531 2923 5.595133 TGCATAACATGTGTTGATGGATGAT 59.405 36.000 0.00 0.00 38.90 2.45
2532 2924 5.918576 GCATAACATGTGTTGATGGATGATG 59.081 40.000 0.00 3.34 38.90 3.07
2980 3372 1.135199 GCTTCCAACGGTGAGATCGTA 60.135 52.381 0.00 0.00 40.18 3.43
2981 3373 2.527100 CTTCCAACGGTGAGATCGTAC 58.473 52.381 0.00 0.00 40.18 3.67
2982 3374 0.448990 TCCAACGGTGAGATCGTACG 59.551 55.000 9.53 9.53 40.18 3.67
2983 3375 0.169672 CCAACGGTGAGATCGTACGT 59.830 55.000 16.05 2.33 40.18 3.57
3054 3479 3.506108 CAGTGCATGCTAGGGTGC 58.494 61.111 20.33 0.59 41.61 5.01
3309 3751 8.575565 ACATAGCAATTTATGAGTACGTACAG 57.424 34.615 26.55 6.63 35.48 2.74
3325 3768 5.122328 CGTACAGAACGTTTATTGCCTAC 57.878 43.478 0.46 1.62 46.72 3.18
3333 3776 5.961395 ACGTTTATTGCCTACTGTAATCG 57.039 39.130 0.00 0.00 31.27 3.34
3334 3777 4.269363 ACGTTTATTGCCTACTGTAATCGC 59.731 41.667 0.00 0.00 31.27 4.58
3348 3791 6.791303 ACTGTAATCGCTGAAGTTTTTGAAA 58.209 32.000 0.00 0.00 0.00 2.69
3351 3794 8.641499 TGTAATCGCTGAAGTTTTTGAAATTT 57.359 26.923 0.00 0.00 0.00 1.82
3364 3807 9.341078 AGTTTTTGAAATTTTCATTACTGCCAT 57.659 25.926 12.39 0.00 39.84 4.40
3365 3808 9.597999 GTTTTTGAAATTTTCATTACTGCCATC 57.402 29.630 12.39 0.00 39.84 3.51
3369 3812 3.756082 TTTTCATTACTGCCATCCCCT 57.244 42.857 0.00 0.00 0.00 4.79
3370 3813 2.734755 TTCATTACTGCCATCCCCTG 57.265 50.000 0.00 0.00 0.00 4.45
3371 3814 1.595311 TCATTACTGCCATCCCCTGT 58.405 50.000 0.00 0.00 0.00 4.00
3372 3815 1.490490 TCATTACTGCCATCCCCTGTC 59.510 52.381 0.00 0.00 0.00 3.51
3373 3816 1.492176 CATTACTGCCATCCCCTGTCT 59.508 52.381 0.00 0.00 0.00 3.41
3374 3817 0.911769 TTACTGCCATCCCCTGTCTG 59.088 55.000 0.00 0.00 0.00 3.51
3375 3818 0.252696 TACTGCCATCCCCTGTCTGT 60.253 55.000 0.00 0.00 0.00 3.41
3376 3819 1.136329 ACTGCCATCCCCTGTCTGTT 61.136 55.000 0.00 0.00 0.00 3.16
3377 3820 0.911769 CTGCCATCCCCTGTCTGTTA 59.088 55.000 0.00 0.00 0.00 2.41
3378 3821 1.281867 CTGCCATCCCCTGTCTGTTAA 59.718 52.381 0.00 0.00 0.00 2.01
3430 3873 7.804614 TCGTTTTGATTGGTATAACATTTGC 57.195 32.000 0.00 0.00 0.00 3.68
3435 3878 5.900425 TGATTGGTATAACATTTGCGCAAT 58.100 33.333 25.64 11.73 0.00 3.56
3445 3888 6.869421 AACATTTGCGCAATCAATAACTAC 57.131 33.333 25.64 0.00 0.00 2.73
3453 3897 7.186128 TGCGCAATCAATAACTACAACAATAG 58.814 34.615 8.16 0.00 0.00 1.73
3507 3951 7.817418 GGTAACTCTGGCATCCAAATATAAA 57.183 36.000 0.00 0.00 30.80 1.40
3508 3952 8.409358 GGTAACTCTGGCATCCAAATATAAAT 57.591 34.615 0.00 0.00 30.80 1.40
3509 3953 8.299570 GGTAACTCTGGCATCCAAATATAAATG 58.700 37.037 0.00 0.00 30.80 2.32
3521 3965 7.648142 TCCAAATATAAATGGAGATTTGCGAC 58.352 34.615 5.90 0.00 40.74 5.19
3525 3969 8.627208 AATATAAATGGAGATTTGCGACATCT 57.373 30.769 0.00 0.00 33.63 2.90
3546 3990 6.432607 TCTGATGAAAGACTTTGATCATGC 57.567 37.500 24.41 9.38 41.31 4.06
3547 3991 5.356190 TCTGATGAAAGACTTTGATCATGCC 59.644 40.000 24.41 3.92 41.31 4.40
3622 4070 4.717877 TGATTCCAGAGTTCAAGCTTTGA 58.282 39.130 0.00 0.00 38.04 2.69
3625 4073 3.884895 TCCAGAGTTCAAGCTTTGACAA 58.115 40.909 0.00 0.00 39.87 3.18
3638 4086 8.149647 TCAAGCTTTGACAATATTTGGTTCATT 58.850 29.630 0.00 0.00 34.08 2.57
3641 4089 7.933033 AGCTTTGACAATATTTGGTTCATTGTT 59.067 29.630 1.17 0.00 41.65 2.83
3711 4159 6.047511 ACCATTTTTATGTTGCATAAGCCA 57.952 33.333 0.00 0.00 41.13 4.75
3732 4180 7.373493 AGCCACATATTATCAAGCAATTAAGC 58.627 34.615 0.00 0.00 0.00 3.09
3744 4192 5.126396 AGCAATTAAGCTTGGACAAAGAC 57.874 39.130 9.86 0.00 43.70 3.01
3752 4201 2.287009 GCTTGGACAAAGACGGTCAAAG 60.287 50.000 11.27 5.51 45.21 2.77
3756 4205 3.118702 TGGACAAAGACGGTCAAAGTACA 60.119 43.478 11.27 9.01 37.00 2.90
3757 4206 3.246936 GGACAAAGACGGTCAAAGTACAC 59.753 47.826 11.27 0.00 37.00 2.90
3773 4222 8.434661 TCAAAGTACACCGTATATTTTTCGAAC 58.565 33.333 0.00 0.00 0.00 3.95
3774 4223 6.559042 AGTACACCGTATATTTTTCGAACG 57.441 37.500 0.00 0.00 0.00 3.95
3871 4320 7.175293 ACGTTAAGTGACCTTTAAAATATGGCA 59.825 33.333 0.00 0.00 31.89 4.92
3872 4321 8.188139 CGTTAAGTGACCTTTAAAATATGGCAT 58.812 33.333 4.88 4.88 31.89 4.40
3881 4330 8.860088 ACCTTTAAAATATGGCATAGTGGATTC 58.140 33.333 13.39 0.00 0.00 2.52
3904 4353 1.815003 CATTCCCTCAGCCACAAGTTC 59.185 52.381 0.00 0.00 0.00 3.01
3909 4358 2.544685 CCTCAGCCACAAGTTCTATCG 58.455 52.381 0.00 0.00 0.00 2.92
3915 4364 5.580691 TCAGCCACAAGTTCTATCGTATTTG 59.419 40.000 0.00 0.00 0.00 2.32
3938 4387 6.696411 TGGTGATGGAAAAATAAATGTGTCC 58.304 36.000 0.00 0.00 0.00 4.02
3951 4400 5.649782 AAATGTGTCCTCTATTTTGGCAG 57.350 39.130 0.00 0.00 0.00 4.85
3957 4406 6.599244 TGTGTCCTCTATTTTGGCAGATTTAG 59.401 38.462 0.00 0.00 0.00 1.85
3965 4414 9.200817 TCTATTTTGGCAGATTTAGGCTATTTT 57.799 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.827835 GGGTTGGCTACTTCTTCTCTTTTT 59.172 41.667 0.00 0.00 0.00 1.94
2 3 4.141251 TGGGTTGGCTACTTCTTCTCTTTT 60.141 41.667 0.00 0.00 0.00 2.27
3 4 3.394606 TGGGTTGGCTACTTCTTCTCTTT 59.605 43.478 0.00 0.00 0.00 2.52
4 5 2.979678 TGGGTTGGCTACTTCTTCTCTT 59.020 45.455 0.00 0.00 0.00 2.85
5 6 2.621070 TGGGTTGGCTACTTCTTCTCT 58.379 47.619 0.00 0.00 0.00 3.10
6 7 3.244596 ACTTGGGTTGGCTACTTCTTCTC 60.245 47.826 0.00 0.00 0.00 2.87
7 8 2.711547 ACTTGGGTTGGCTACTTCTTCT 59.288 45.455 0.00 0.00 0.00 2.85
8 9 3.141767 ACTTGGGTTGGCTACTTCTTC 57.858 47.619 0.00 0.00 0.00 2.87
9 10 3.222603 CAACTTGGGTTGGCTACTTCTT 58.777 45.455 0.00 0.00 46.37 2.52
10 11 2.863809 CAACTTGGGTTGGCTACTTCT 58.136 47.619 0.00 0.00 46.37 2.85
45 46 2.086610 AGGCAAACCCAGTGTTGATT 57.913 45.000 0.00 0.00 37.23 2.57
69 70 0.736053 GAACGCACCACAAGAAACCA 59.264 50.000 0.00 0.00 0.00 3.67
154 414 4.806330 TGAAAAGTGTTGCGGTGTAAAAA 58.194 34.783 0.00 0.00 0.00 1.94
155 415 4.416620 CTGAAAAGTGTTGCGGTGTAAAA 58.583 39.130 0.00 0.00 0.00 1.52
237 497 8.734386 CATACACATGCATAGTGAGAGTAGATA 58.266 37.037 25.89 12.17 40.16 1.98
509 782 0.955919 GAGCCCGGTTTGGAGACTTG 60.956 60.000 0.00 0.00 42.00 3.16
511 784 2.593956 GGAGCCCGGTTTGGAGACT 61.594 63.158 0.00 0.00 42.00 3.24
513 786 3.327404 GGGAGCCCGGTTTGGAGA 61.327 66.667 0.00 0.00 42.00 3.71
663 953 1.884464 CACACTCGATCCATGGGCG 60.884 63.158 13.02 16.16 0.00 6.13
731 1021 1.261089 GCGCCTTTACGTTTGTGTGTA 59.739 47.619 0.00 0.00 34.88 2.90
839 1129 1.679977 GGAAGGAATGGCAGCAGCA 60.680 57.895 2.65 0.00 44.61 4.41
853 1143 1.562008 GGAAGGAGGGGAAAGAGGAAG 59.438 57.143 0.00 0.00 0.00 3.46
984 1274 1.447317 CCATCTTGATTTCGGCGGGG 61.447 60.000 7.21 0.00 0.00 5.73
1032 1322 3.470567 GAGGCGACAACGTGCTCG 61.471 66.667 6.63 6.63 41.98 5.03
1125 1415 0.316278 CAGACGCCATAGACGACGAG 60.316 60.000 0.00 0.00 0.00 4.18
1243 1557 3.433314 CCCATGATCTCTTCCTTGACTGG 60.433 52.174 0.00 0.00 0.00 4.00
1360 1674 1.767681 GTCATCATCTTCCTCCTGGCT 59.232 52.381 0.00 0.00 0.00 4.75
1437 1754 3.365265 GCCTCCACCTTGCAACCG 61.365 66.667 0.00 0.00 0.00 4.44
1534 1851 4.567385 GCCGCTCTCTGCTCCGAG 62.567 72.222 0.00 0.00 40.11 4.63
1561 1878 2.435693 GGATCCAGTACCCGCAGCT 61.436 63.158 6.95 0.00 0.00 4.24
1568 1885 2.416260 GCGTCGGGATCCAGTACC 59.584 66.667 15.23 1.75 0.00 3.34
1737 2058 7.489113 ACAAAATCAATCGAATCATGGCTTAAC 59.511 33.333 0.00 0.00 0.00 2.01
1791 2112 9.638176 ACCAGCTGATTAAATTTCTAGATCATT 57.362 29.630 17.39 0.00 0.00 2.57
1810 2136 6.325919 TGGACTTAAATTTTGTACCAGCTG 57.674 37.500 6.78 6.78 0.00 4.24
1820 2146 6.655003 TCTCTCATTCGCTGGACTTAAATTTT 59.345 34.615 0.00 0.00 0.00 1.82
1824 2158 4.801330 TCTCTCATTCGCTGGACTTAAA 57.199 40.909 0.00 0.00 0.00 1.52
1864 2198 5.530543 TGATTCATGGCGAATTATGTAAGCA 59.469 36.000 0.00 0.00 44.65 3.91
1868 2202 7.742556 TTGATGATTCATGGCGAATTATGTA 57.257 32.000 3.32 0.00 44.65 2.29
1940 2282 3.188159 TGTAACCAAGTGTGTGGAGAC 57.812 47.619 0.00 0.00 41.65 3.36
1990 2339 2.415512 GTGTGGCCTTTGTAGAACGATC 59.584 50.000 3.32 0.00 0.00 3.69
2100 2479 2.119484 AACTTCGACGGGGCCATTCA 62.119 55.000 4.39 0.00 0.00 2.57
2153 2532 0.737019 CAAACACCCGCAATGCCATC 60.737 55.000 0.00 0.00 0.00 3.51
2396 2780 5.411083 TTTTCGTTGTTCGTCATGATTGA 57.589 34.783 0.00 0.00 40.80 2.57
2404 2788 3.001939 AGTGTGGATTTTCGTTGTTCGTC 59.998 43.478 0.00 0.00 40.80 4.20
2420 2804 4.637968 CGTTTTCATGATCGTTAGTGTGG 58.362 43.478 0.00 0.00 0.00 4.17
2488 2880 4.268359 TGCATGCACACACTGGATTATTA 58.732 39.130 18.46 0.00 0.00 0.98
2489 2881 3.090790 TGCATGCACACACTGGATTATT 58.909 40.909 18.46 0.00 0.00 1.40
2490 2882 2.725637 TGCATGCACACACTGGATTAT 58.274 42.857 18.46 0.00 0.00 1.28
2532 2924 3.072486 GCCCCACATGTGCATCTGC 62.072 63.158 20.81 12.84 42.50 4.26
2610 3002 2.103042 GTAGCACGGCAGCTTCAGG 61.103 63.158 6.76 0.00 43.70 3.86
2980 3372 2.436292 AGCTAGCTCGGTCGACGT 60.436 61.111 12.68 0.00 44.69 4.34
2981 3373 1.777030 ATCAGCTAGCTCGGTCGACG 61.777 60.000 16.15 0.57 46.11 5.12
2982 3374 0.040781 GATCAGCTAGCTCGGTCGAC 60.041 60.000 16.15 7.13 0.00 4.20
2983 3375 1.499688 CGATCAGCTAGCTCGGTCGA 61.500 60.000 29.86 19.58 32.50 4.20
2986 3378 0.945813 GTACGATCAGCTAGCTCGGT 59.054 55.000 23.57 16.88 40.02 4.69
2987 3379 1.231221 AGTACGATCAGCTAGCTCGG 58.769 55.000 23.57 11.88 40.02 4.63
2989 3381 5.870433 TCTATGTAGTACGATCAGCTAGCTC 59.130 44.000 16.15 2.95 0.00 4.09
2990 3382 5.795972 TCTATGTAGTACGATCAGCTAGCT 58.204 41.667 12.68 12.68 0.00 3.32
2991 3383 6.314152 TGATCTATGTAGTACGATCAGCTAGC 59.686 42.308 6.62 6.62 37.82 3.42
3037 3462 1.377594 TGCACCCTAGCATGCACTG 60.378 57.895 21.98 8.99 46.63 3.66
3038 3463 3.080641 TGCACCCTAGCATGCACT 58.919 55.556 21.98 1.90 46.63 4.40
3045 3470 1.525535 CTCCTGCATGCACCCTAGC 60.526 63.158 18.46 0.00 0.00 3.42
3046 3471 1.147824 CCTCCTGCATGCACCCTAG 59.852 63.158 18.46 11.16 0.00 3.02
3047 3472 1.306911 TCCTCCTGCATGCACCCTA 60.307 57.895 18.46 1.16 0.00 3.53
3048 3473 2.611800 TCCTCCTGCATGCACCCT 60.612 61.111 18.46 0.00 0.00 4.34
3049 3474 2.124403 CTCCTCCTGCATGCACCC 60.124 66.667 18.46 0.00 0.00 4.61
3050 3475 2.827642 GCTCCTCCTGCATGCACC 60.828 66.667 18.46 0.00 0.00 5.01
3052 3477 1.676635 GTTGCTCCTCCTGCATGCA 60.677 57.895 21.29 21.29 40.34 3.96
3053 3478 2.758089 CGTTGCTCCTCCTGCATGC 61.758 63.158 11.82 11.82 40.34 4.06
3054 3479 1.078918 TCGTTGCTCCTCCTGCATG 60.079 57.895 0.00 0.00 40.34 4.06
3060 3494 0.896226 ACTTACCTCGTTGCTCCTCC 59.104 55.000 0.00 0.00 0.00 4.30
3309 3751 6.408428 CGATTACAGTAGGCAATAAACGTTC 58.592 40.000 0.00 0.00 0.00 3.95
3321 3764 6.147164 TCAAAAACTTCAGCGATTACAGTAGG 59.853 38.462 0.00 0.00 0.00 3.18
3324 3767 6.371809 TTCAAAAACTTCAGCGATTACAGT 57.628 33.333 0.00 0.00 0.00 3.55
3325 3768 7.858052 ATTTCAAAAACTTCAGCGATTACAG 57.142 32.000 0.00 0.00 0.00 2.74
3348 3791 3.962718 CAGGGGATGGCAGTAATGAAAAT 59.037 43.478 0.00 0.00 0.00 1.82
3351 3794 1.922447 ACAGGGGATGGCAGTAATGAA 59.078 47.619 0.00 0.00 0.00 2.57
3364 3807 7.027874 ACAATAGAAATTAACAGACAGGGGA 57.972 36.000 0.00 0.00 0.00 4.81
3365 3808 7.112779 AGACAATAGAAATTAACAGACAGGGG 58.887 38.462 0.00 0.00 0.00 4.79
3399 3842 9.400638 TGTTATACCAATCAAAACGAATTCAAC 57.599 29.630 6.22 0.00 0.00 3.18
3478 3922 2.375174 TGGATGCCAGAGTTACCTGTTT 59.625 45.455 0.00 0.00 32.43 2.83
3488 3932 6.944290 TCTCCATTTATATTTGGATGCCAGAG 59.056 38.462 4.99 0.00 41.09 3.35
3492 3936 7.332678 GCAAATCTCCATTTATATTTGGATGCC 59.667 37.037 12.49 0.00 41.09 4.40
3495 3939 8.299570 GTCGCAAATCTCCATTTATATTTGGAT 58.700 33.333 0.00 0.00 41.09 3.41
3507 3951 3.548745 TCAGATGTCGCAAATCTCCAT 57.451 42.857 0.00 0.00 31.92 3.41
3508 3952 3.118665 TCATCAGATGTCGCAAATCTCCA 60.119 43.478 10.34 0.00 31.92 3.86
3509 3953 3.461061 TCATCAGATGTCGCAAATCTCC 58.539 45.455 10.34 0.00 31.92 3.71
3521 3965 6.913132 GCATGATCAAAGTCTTTCATCAGATG 59.087 38.462 15.84 11.62 0.00 2.90
3525 3969 5.258841 AGGCATGATCAAAGTCTTTCATCA 58.741 37.500 13.48 13.48 0.00 3.07
3592 4040 9.466497 AGCTTGAACTCTGGAATCAAATAAATA 57.534 29.630 0.00 0.00 33.08 1.40
3598 4046 5.593909 TCAAAGCTTGAACTCTGGAATCAAA 59.406 36.000 0.00 0.00 36.59 2.69
3607 4055 7.014615 ACCAAATATTGTCAAAGCTTGAACTCT 59.985 33.333 0.00 0.00 42.15 3.24
3680 4128 8.845413 ATGCAACATAAAAATGGTATTGTGTT 57.155 26.923 0.00 0.00 40.17 3.32
3686 4134 7.710475 GTGGCTTATGCAACATAAAAATGGTAT 59.290 33.333 3.29 0.00 42.54 2.73
3689 4137 6.348621 GTGGCTTATGCAACATAAAAATGG 57.651 37.500 3.29 0.00 42.54 3.16
3701 4149 5.769162 TGCTTGATAATATGTGGCTTATGCA 59.231 36.000 2.72 0.00 41.91 3.96
3702 4150 6.258230 TGCTTGATAATATGTGGCTTATGC 57.742 37.500 0.00 0.00 38.76 3.14
3708 4156 7.373493 AGCTTAATTGCTTGATAATATGTGGC 58.627 34.615 0.00 0.00 40.93 5.01
3731 4179 1.305201 TTGACCGTCTTTGTCCAAGC 58.695 50.000 0.00 0.00 31.70 4.01
3732 4180 2.943033 ACTTTGACCGTCTTTGTCCAAG 59.057 45.455 0.00 0.00 39.86 3.61
3733 4181 2.993937 ACTTTGACCGTCTTTGTCCAA 58.006 42.857 0.00 0.00 31.60 3.53
3734 4182 2.702592 ACTTTGACCGTCTTTGTCCA 57.297 45.000 0.00 0.00 31.60 4.02
3735 4183 3.246936 GTGTACTTTGACCGTCTTTGTCC 59.753 47.826 0.00 0.00 31.60 4.02
3736 4184 3.246936 GGTGTACTTTGACCGTCTTTGTC 59.753 47.826 0.00 0.00 0.00 3.18
3737 4185 3.200483 GGTGTACTTTGACCGTCTTTGT 58.800 45.455 0.00 0.00 0.00 2.83
3752 4201 5.717251 CCGTTCGAAAAATATACGGTGTAC 58.283 41.667 13.15 0.00 44.90 2.90
3769 4218 3.302935 TCGAAAGATACTCGATCCGTTCG 60.303 47.826 11.73 11.73 45.38 3.95
3773 4222 4.469625 TTCTCGAAAGATACTCGATCCG 57.530 45.455 0.00 0.00 43.85 4.18
3774 4223 7.435488 TCATTTTTCTCGAAAGATACTCGATCC 59.565 37.037 0.00 0.00 43.85 3.36
3777 4226 7.313646 AGTCATTTTTCTCGAAAGATACTCGA 58.686 34.615 0.00 0.00 42.75 4.04
3809 4258 9.584008 ACGTTTCCTATATCTATAAAGGAGTCA 57.416 33.333 0.00 0.00 0.00 3.41
3834 4283 9.720667 AAAGGTCACTTAACGTTTATAAACAAC 57.279 29.630 24.27 8.21 35.96 3.32
3845 4294 7.175293 TGCCATATTTTAAAGGTCACTTAACGT 59.825 33.333 0.00 0.00 35.41 3.99
3846 4295 7.531716 TGCCATATTTTAAAGGTCACTTAACG 58.468 34.615 0.00 0.00 35.41 3.18
3861 4310 6.655078 GTGGAATCCACTATGCCATATTTT 57.345 37.500 24.21 0.00 45.77 1.82
3881 4330 0.251297 TTGTGGCTGAGGGAATGTGG 60.251 55.000 0.00 0.00 0.00 4.17
3893 4342 4.876107 CCAAATACGATAGAACTTGTGGCT 59.124 41.667 0.00 0.00 41.38 4.75
3894 4343 4.634443 ACCAAATACGATAGAACTTGTGGC 59.366 41.667 0.00 0.00 41.38 5.01
3915 4364 6.935167 AGGACACATTTATTTTTCCATCACC 58.065 36.000 0.00 0.00 0.00 4.02
3938 4387 7.992754 ATAGCCTAAATCTGCCAAAATAGAG 57.007 36.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.