Multiple sequence alignment - TraesCS3B01G168900

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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 TraesCS3B01G168900 chr3B 100.000 3758 0 0 1 3758 169431350 169435107 0.000000e+00 6940.0
1 TraesCS3B01G168900 chr3B 85.152 788 93 16 1032 1804 169424777 169425555 0.000000e+00 785.0
2 TraesCS3B01G168900 chr3B 82.456 855 140 7 1878 2724 169425556 169426408 0.000000e+00 739.0
3 TraesCS3B01G168900 chr3B 88.991 109 12 0 3648 3756 744589467 744589575 6.550000e-28 135.0
4 TraesCS3B01G168900 chr3D 94.440 3615 125 29 103 3653 116021417 116025019 0.000000e+00 5493.0
5 TraesCS3B01G168900 chr3D 85.015 1715 225 21 1032 2724 116011128 116012832 0.000000e+00 1714.0
6 TraesCS3B01G168900 chr3D 94.231 104 6 0 1 104 116021152 116021255 3.890000e-35 159.0
7 TraesCS3B01G168900 chr3A 90.021 2906 151 59 778 3597 112936450 112939302 0.000000e+00 3631.0
8 TraesCS3B01G168900 chr3A 84.781 1715 229 18 1032 2724 112918009 112919713 0.000000e+00 1692.0
9 TraesCS3B01G168900 chr3A 90.798 326 24 5 262 583 112935968 112936291 7.460000e-117 431.0
10 TraesCS3B01G168900 chr3A 88.849 278 23 3 1 272 112933934 112934209 6.010000e-88 335.0
11 TraesCS3B01G168900 chr6D 86.641 262 28 4 4 260 96648784 96648525 2.210000e-72 283.0
12 TraesCS3B01G168900 chr6D 79.501 361 54 15 409 765 93436005 93436349 4.850000e-59 239.0
13 TraesCS3B01G168900 chr5D 95.327 107 5 0 3652 3758 378876270 378876376 1.790000e-38 171.0
14 TraesCS3B01G168900 chr6B 84.277 159 23 2 4 161 179657749 179657592 1.810000e-33 154.0
15 TraesCS3B01G168900 chr1D 92.381 105 8 0 3652 3756 373416121 373416225 2.340000e-32 150.0
16 TraesCS3B01G168900 chr5B 91.589 107 9 0 3652 3758 454270426 454270532 8.410000e-32 148.0
17 TraesCS3B01G168900 chr2D 94.624 93 5 0 3656 3748 626641403 626641495 1.090000e-30 145.0
18 TraesCS3B01G168900 chr7D 92.632 95 7 0 3654 3748 509620526 509620432 1.820000e-28 137.0
19 TraesCS3B01G168900 chr7D 90.385 104 9 1 3646 3748 613463769 613463666 6.550000e-28 135.0
20 TraesCS3B01G168900 chr7D 87.736 106 13 0 3653 3758 227560916 227560811 1.420000e-24 124.0
21 TraesCS3B01G168900 chr1A 91.579 95 8 0 3653 3747 499766555 499766649 8.470000e-27 132.0
22 TraesCS3B01G168900 chr6A 80.435 92 16 2 674 765 115339232 115339143 6.740000e-08 69.4


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 TraesCS3B01G168900 chr3B 169431350 169435107 3757 False 6940.000000 6940 100.000000 1 3758 1 chr3B.!!$F1 3757
1 TraesCS3B01G168900 chr3B 169424777 169426408 1631 False 762.000000 785 83.804000 1032 2724 2 chr3B.!!$F3 1692
2 TraesCS3B01G168900 chr3D 116021152 116025019 3867 False 2826.000000 5493 94.335500 1 3653 2 chr3D.!!$F2 3652
3 TraesCS3B01G168900 chr3D 116011128 116012832 1704 False 1714.000000 1714 85.015000 1032 2724 1 chr3D.!!$F1 1692
4 TraesCS3B01G168900 chr3A 112918009 112919713 1704 False 1692.000000 1692 84.781000 1032 2724 1 chr3A.!!$F1 1692
5 TraesCS3B01G168900 chr3A 112933934 112939302 5368 False 1465.666667 3631 89.889333 1 3597 3 chr3A.!!$F2 3596

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
950 2948 0.596082 GGCGTAGTGTTGGCAATTGT 59.404 50.000 1.92 0.0 0.0 2.71 F
1527 3540 1.080093 CGACAGCACATACACCGGT 60.080 57.895 0.00 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 3846 0.372334 CAATAACCTCCCGAAACGCG 59.628 55.0 3.53 3.53 40.47 6.01 R
3142 5181 0.391597 TTCCCGGTGTCACTCAAGAC 59.608 55.0 0.00 0.00 38.99 3.01 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
34 35 7.065324 GCTACAAACATATTTACAGCACCAGTA 59.935 37.037 0.00 0.00 35.41 2.74
42 43 2.770164 ACAGCACCAGTATTCAGACC 57.230 50.000 0.00 0.00 0.00 3.85
143 307 8.388103 CCTACATTTTATGTTCGTCTAGTTTGG 58.612 37.037 0.00 0.00 41.63 3.28
145 309 5.616488 TTTTATGTTCGTCTAGTTTGGGC 57.384 39.130 0.00 0.00 0.00 5.36
192 362 4.095932 TGTCTACTCTTAGTGGCACATACG 59.904 45.833 21.41 7.25 44.52 3.06
211 381 7.375808 CACATACGCATACATATTTTGTCCAAC 59.624 37.037 0.00 0.00 39.87 3.77
239 409 7.650834 TTTAAATAAACTGCCAGCAATGTTC 57.349 32.000 0.00 0.00 0.00 3.18
274 2213 9.388346 GATTGTCTACTCTACTATTTCATGTCG 57.612 37.037 0.00 0.00 0.00 4.35
276 2215 5.846994 GTCTACTCTACTATTTCATGTCGCG 59.153 44.000 0.00 0.00 0.00 5.87
343 2283 8.347771 GCTGTGATTTTCATAAGATGCAGAATA 58.652 33.333 0.00 0.00 0.00 1.75
368 2308 2.687935 CCAAAGCTGTAGTTGTGTGGTT 59.312 45.455 0.00 0.00 0.00 3.67
393 2333 7.667557 TGGTTAACTCACTGGCAGTATATATC 58.332 38.462 21.59 9.86 0.00 1.63
467 2408 1.945387 CACTACCTGTGGCTGCTATG 58.055 55.000 0.00 0.00 42.68 2.23
566 2507 2.241176 TCCCGGGCATCTTTTCACTAAT 59.759 45.455 18.49 0.00 0.00 1.73
594 2535 5.204833 CGTATTGGCTTTATGTGTATGTGC 58.795 41.667 0.00 0.00 0.00 4.57
649 2591 4.473520 CGGCGAACTGGGCATCCT 62.474 66.667 0.00 0.00 0.00 3.24
739 2686 2.168728 CCAGCCTAGTTGGGTCTTAGAC 59.831 54.545 3.36 3.36 46.24 2.59
741 2688 3.100671 AGCCTAGTTGGGTCTTAGACAG 58.899 50.000 14.72 1.67 44.42 3.51
901 2883 2.044650 CCTGACATGTGGGCCCAG 60.045 66.667 29.55 17.45 0.00 4.45
906 2888 2.436646 CATGTGGGCCCAGTCGTC 60.437 66.667 29.55 14.44 0.00 4.20
934 2929 3.564225 GGGTAGATTGGTAGATTTTGGCG 59.436 47.826 0.00 0.00 0.00 5.69
943 2941 3.126343 GGTAGATTTTGGCGTAGTGTTGG 59.874 47.826 0.00 0.00 0.00 3.77
950 2948 0.596082 GGCGTAGTGTTGGCAATTGT 59.404 50.000 1.92 0.00 0.00 2.71
990 2988 1.538876 CTCCACCCACTCCCTCCAA 60.539 63.158 0.00 0.00 0.00 3.53
1518 3531 1.556591 GCAACATCGTCGACAGCACA 61.557 55.000 17.16 0.00 0.00 4.57
1527 3540 1.080093 CGACAGCACATACACCGGT 60.080 57.895 0.00 0.00 0.00 5.28
1677 3690 1.524621 CGCCATCCAGAATTCCGCT 60.525 57.895 0.65 0.00 0.00 5.52
1698 3711 2.551032 TGATGTGCAGTCAAAGAAGCTG 59.449 45.455 0.00 0.00 0.00 4.24
1976 3989 6.402222 GCTCATTCAATCTACCTACCTATGG 58.598 44.000 0.00 0.00 0.00 2.74
2016 4029 2.825836 GGCAAGCTCATGGACGGG 60.826 66.667 0.00 0.00 0.00 5.28
2068 4081 5.125100 CAATGCATTGGATATGTGGTACC 57.875 43.478 28.34 4.43 34.22 3.34
2076 4089 3.716353 TGGATATGTGGTACCTTGATGCT 59.284 43.478 14.36 0.00 0.00 3.79
2288 4304 8.177119 ACTTTCTACCAGAGATTCAGCTATAG 57.823 38.462 0.00 0.00 32.88 1.31
2477 4496 3.793144 CTCGCTGGTTTCGGCTGC 61.793 66.667 0.00 0.00 42.91 5.25
2598 4617 2.604912 AGGGGAATTTGGTGACTTCC 57.395 50.000 0.00 0.00 38.16 3.46
2758 4780 1.141858 CCAGATTCCCCTCCAGTTAGC 59.858 57.143 0.00 0.00 0.00 3.09
2760 4782 2.103941 CAGATTCCCCTCCAGTTAGCTC 59.896 54.545 0.00 0.00 0.00 4.09
2825 4853 4.500887 GCATAGTTTATCCTGTGCCTCGTA 60.501 45.833 0.00 0.00 41.95 3.43
2838 4866 3.004524 GTGCCTCGTATGGTAGGTAGAAG 59.995 52.174 0.00 0.00 35.16 2.85
2841 4869 4.455190 GCCTCGTATGGTAGGTAGAAGTAG 59.545 50.000 0.00 0.00 35.16 2.57
2842 4870 5.744300 GCCTCGTATGGTAGGTAGAAGTAGA 60.744 48.000 0.00 0.00 35.16 2.59
2843 4871 6.294473 CCTCGTATGGTAGGTAGAAGTAGAA 58.706 44.000 0.00 0.00 0.00 2.10
2844 4872 6.769822 CCTCGTATGGTAGGTAGAAGTAGAAA 59.230 42.308 0.00 0.00 0.00 2.52
2845 4873 7.447853 CCTCGTATGGTAGGTAGAAGTAGAAAT 59.552 40.741 0.00 0.00 0.00 2.17
2846 4874 8.388484 TCGTATGGTAGGTAGAAGTAGAAATC 57.612 38.462 0.00 0.00 0.00 2.17
2852 4880 7.123847 TGGTAGGTAGAAGTAGAAATCTTGGAC 59.876 40.741 0.00 0.00 0.00 4.02
2863 4891 9.918630 AGTAGAAATCTTGGACATTTCAATTTG 57.081 29.630 7.66 0.00 41.08 2.32
2994 5027 6.484643 TCAAGCTTCTGGCATTATTACTGATC 59.515 38.462 0.00 0.00 44.79 2.92
3062 5095 2.664851 TTGCCGCGTCTGTTCCAG 60.665 61.111 4.92 0.00 0.00 3.86
3076 5109 4.103153 TCTGTTCCAGTCTCCAACTCAATT 59.897 41.667 0.00 0.00 35.45 2.32
3107 5142 4.054671 CTGGAGAATGGAGCGATTTACTC 58.945 47.826 0.00 0.00 0.00 2.59
3134 5173 0.550147 AAAGAAGCCCTAGCCCCTCA 60.550 55.000 0.00 0.00 41.25 3.86
3142 5181 2.659428 CCCTAGCCCCTCAAAAAGATG 58.341 52.381 0.00 0.00 0.00 2.90
3188 5227 0.391130 GCGTGCTCACAAGATGGGTA 60.391 55.000 0.69 0.00 0.00 3.69
3200 5243 5.010314 CACAAGATGGGTATTGCAATATGCT 59.990 40.000 21.52 11.65 45.31 3.79
3285 5334 3.480133 GCTATGGGTGGAGGCGGT 61.480 66.667 0.00 0.00 0.00 5.68
3326 5376 1.871039 GGAAAACGAAGTGCTACTGCA 59.129 47.619 0.00 0.00 45.00 4.41
3389 5461 3.029074 CAGAACGAAACTTCTGTTTGCG 58.971 45.455 5.56 5.70 45.36 4.85
3414 5486 2.989840 CGTTCTTCGCTGATCTCACTTT 59.010 45.455 0.00 0.00 0.00 2.66
3504 5579 0.036732 TCGAAATTCCAGGCAGCACT 59.963 50.000 0.00 0.00 0.00 4.40
3517 5592 1.445871 CAGCACTAACTCATGCAGCA 58.554 50.000 0.00 0.00 44.59 4.41
3600 5680 5.946377 CCCTTGACTGCTAGGATTAAGTTTT 59.054 40.000 0.00 0.00 39.07 2.43
3665 5745 3.246064 TTTTTGGGCGACGCTACG 58.754 55.556 20.77 0.00 0.00 3.51
3683 5763 4.789075 CGTCCGCCGGTCGATGTT 62.789 66.667 17.69 0.00 41.67 2.71
3684 5764 2.433664 GTCCGCCGGTCGATGTTT 60.434 61.111 17.96 0.00 41.67 2.83
3685 5765 1.153784 GTCCGCCGGTCGATGTTTA 60.154 57.895 17.96 0.00 41.67 2.01
3686 5766 1.140161 TCCGCCGGTCGATGTTTAG 59.860 57.895 17.96 1.91 41.67 1.85
3687 5767 1.140161 CCGCCGGTCGATGTTTAGA 59.860 57.895 17.96 0.00 41.67 2.10
3688 5768 0.249322 CCGCCGGTCGATGTTTAGAT 60.249 55.000 17.96 0.00 41.67 1.98
3689 5769 1.567504 CGCCGGTCGATGTTTAGATT 58.432 50.000 12.11 0.00 41.67 2.40
3690 5770 1.931172 CGCCGGTCGATGTTTAGATTT 59.069 47.619 12.11 0.00 41.67 2.17
3691 5771 2.350498 CGCCGGTCGATGTTTAGATTTT 59.650 45.455 12.11 0.00 41.67 1.82
3692 5772 3.552699 CGCCGGTCGATGTTTAGATTTTA 59.447 43.478 12.11 0.00 41.67 1.52
3693 5773 4.210537 CGCCGGTCGATGTTTAGATTTTAT 59.789 41.667 12.11 0.00 41.67 1.40
3694 5774 5.611844 CGCCGGTCGATGTTTAGATTTTATC 60.612 44.000 12.11 0.00 41.67 1.75
3695 5775 5.333875 GCCGGTCGATGTTTAGATTTTATCC 60.334 44.000 1.90 0.00 0.00 2.59
3696 5776 5.107607 CCGGTCGATGTTTAGATTTTATCCG 60.108 44.000 0.00 0.00 0.00 4.18
3697 5777 5.461078 CGGTCGATGTTTAGATTTTATCCGT 59.539 40.000 0.00 0.00 0.00 4.69
3698 5778 6.345565 CGGTCGATGTTTAGATTTTATCCGTC 60.346 42.308 0.00 0.00 0.00 4.79
3699 5779 6.345565 GGTCGATGTTTAGATTTTATCCGTCG 60.346 42.308 0.00 0.00 31.76 5.12
3700 5780 5.174398 TCGATGTTTAGATTTTATCCGTCGC 59.826 40.000 0.00 0.00 31.09 5.19
3701 5781 5.611844 CGATGTTTAGATTTTATCCGTCGCC 60.612 44.000 0.00 0.00 0.00 5.54
3702 5782 4.761975 TGTTTAGATTTTATCCGTCGCCT 58.238 39.130 0.00 0.00 0.00 5.52
3703 5783 4.807304 TGTTTAGATTTTATCCGTCGCCTC 59.193 41.667 0.00 0.00 0.00 4.70
3704 5784 2.135664 AGATTTTATCCGTCGCCTCG 57.864 50.000 0.00 0.00 0.00 4.63
3705 5785 1.679680 AGATTTTATCCGTCGCCTCGA 59.320 47.619 0.00 0.00 0.00 4.04
3717 5797 4.143333 CCTCGACGGCCGTTGGAT 62.143 66.667 38.47 15.69 39.75 3.41
3718 5798 2.885644 CTCGACGGCCGTTGGATG 60.886 66.667 38.47 26.19 39.75 3.51
3725 5805 3.810896 GCCGTTGGATGCCCGAAC 61.811 66.667 0.00 0.00 34.29 3.95
3726 5806 2.046314 CCGTTGGATGCCCGAACT 60.046 61.111 0.00 0.00 34.29 3.01
3727 5807 2.398554 CCGTTGGATGCCCGAACTG 61.399 63.158 0.00 0.00 34.29 3.16
3728 5808 1.375396 CGTTGGATGCCCGAACTGA 60.375 57.895 0.00 0.00 34.29 3.41
3729 5809 0.744414 CGTTGGATGCCCGAACTGAT 60.744 55.000 0.00 0.00 34.29 2.90
3730 5810 1.472552 CGTTGGATGCCCGAACTGATA 60.473 52.381 0.00 0.00 34.29 2.15
3731 5811 2.213499 GTTGGATGCCCGAACTGATAG 58.787 52.381 0.00 0.00 34.29 2.08
3732 5812 0.106708 TGGATGCCCGAACTGATAGC 59.893 55.000 0.00 0.00 34.29 2.97
3733 5813 0.603975 GGATGCCCGAACTGATAGCC 60.604 60.000 0.00 0.00 0.00 3.93
3734 5814 0.946221 GATGCCCGAACTGATAGCCG 60.946 60.000 0.00 0.00 0.00 5.52
3735 5815 1.686325 ATGCCCGAACTGATAGCCGT 61.686 55.000 0.00 0.00 0.00 5.68
3736 5816 1.591863 GCCCGAACTGATAGCCGTC 60.592 63.158 0.00 0.00 0.00 4.79
3737 5817 2.017559 GCCCGAACTGATAGCCGTCT 62.018 60.000 0.00 0.00 0.00 4.18
3738 5818 0.249073 CCCGAACTGATAGCCGTCTG 60.249 60.000 0.00 0.00 0.00 3.51
3739 5819 0.738975 CCGAACTGATAGCCGTCTGA 59.261 55.000 0.00 0.00 0.00 3.27
3740 5820 1.338337 CCGAACTGATAGCCGTCTGAT 59.662 52.381 0.00 0.00 0.00 2.90
3741 5821 2.605823 CCGAACTGATAGCCGTCTGATC 60.606 54.545 0.00 0.00 0.00 2.92
3742 5822 2.292016 CGAACTGATAGCCGTCTGATCT 59.708 50.000 0.00 0.00 0.00 2.75
3743 5823 3.498777 CGAACTGATAGCCGTCTGATCTA 59.501 47.826 0.00 0.00 0.00 1.98
3744 5824 4.377943 CGAACTGATAGCCGTCTGATCTAG 60.378 50.000 0.00 0.00 0.00 2.43
3745 5825 4.093472 ACTGATAGCCGTCTGATCTAGT 57.907 45.455 0.00 0.00 0.00 2.57
3746 5826 3.818210 ACTGATAGCCGTCTGATCTAGTG 59.182 47.826 0.00 0.00 0.00 2.74
3747 5827 3.818210 CTGATAGCCGTCTGATCTAGTGT 59.182 47.826 0.00 0.00 0.00 3.55
3748 5828 4.207955 TGATAGCCGTCTGATCTAGTGTT 58.792 43.478 0.00 0.00 0.00 3.32
3749 5829 4.276183 TGATAGCCGTCTGATCTAGTGTTC 59.724 45.833 0.00 0.00 0.00 3.18
3750 5830 2.447443 AGCCGTCTGATCTAGTGTTCA 58.553 47.619 0.00 0.00 0.00 3.18
3751 5831 2.164624 AGCCGTCTGATCTAGTGTTCAC 59.835 50.000 0.00 0.00 0.00 3.18
3752 5832 2.786854 CCGTCTGATCTAGTGTTCACG 58.213 52.381 0.00 0.00 0.00 4.35
3753 5833 2.177977 CGTCTGATCTAGTGTTCACGC 58.822 52.381 0.00 0.00 0.00 5.34
3754 5834 2.531206 GTCTGATCTAGTGTTCACGCC 58.469 52.381 0.00 0.00 0.00 5.68
3755 5835 1.476891 TCTGATCTAGTGTTCACGCCC 59.523 52.381 0.00 0.00 0.00 6.13
3756 5836 0.535335 TGATCTAGTGTTCACGCCCC 59.465 55.000 0.00 0.00 0.00 5.80
3757 5837 0.527817 GATCTAGTGTTCACGCCCCG 60.528 60.000 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.568620 AAGTAAACTGGACAGGTCTGAAT 57.431 39.130 4.84 0.00 0.00 2.57
42 43 3.632145 AGCCACAAAAGTAAACTGGACAG 59.368 43.478 0.00 0.00 0.00 3.51
192 362 7.985634 AATTCGTTGGACAAAATATGTATGC 57.014 32.000 0.00 0.00 44.12 3.14
211 381 6.942886 TTGCTGGCAGTTTATTTAAATTCG 57.057 33.333 17.16 0.00 0.00 3.34
274 2213 6.645003 TGATATGTCATTACCAATCTACACGC 59.355 38.462 0.00 0.00 0.00 5.34
276 2215 9.764363 TCTTGATATGTCATTACCAATCTACAC 57.236 33.333 0.00 0.00 33.56 2.90
343 2283 3.565482 CACACAACTACAGCTTTGGACAT 59.435 43.478 1.22 0.00 0.00 3.06
345 2285 2.290641 CCACACAACTACAGCTTTGGAC 59.709 50.000 1.22 0.00 0.00 4.02
368 2308 5.950544 ATATACTGCCAGTGAGTTAACCA 57.049 39.130 7.83 0.00 0.00 3.67
393 2333 4.645535 TCAGATCTTCACTCAAACCCAAG 58.354 43.478 0.00 0.00 0.00 3.61
643 2585 2.446435 TGGTGAAAGCCTAAAGGATGC 58.554 47.619 0.00 0.00 37.39 3.91
649 2591 3.244044 GCATTGGTTGGTGAAAGCCTAAA 60.244 43.478 0.00 0.00 35.29 1.85
901 2883 2.159085 CCAATCTACCCCTTCTGACGAC 60.159 54.545 0.00 0.00 0.00 4.34
906 2888 5.896073 AATCTACCAATCTACCCCTTCTG 57.104 43.478 0.00 0.00 0.00 3.02
934 2929 6.535508 TGGTTTAAAACAATTGCCAACACTAC 59.464 34.615 2.71 0.00 0.00 2.73
943 2941 4.211164 GTGGAGCTGGTTTAAAACAATTGC 59.789 41.667 7.47 7.57 0.00 3.56
950 2948 2.175931 TGGGAGTGGAGCTGGTTTAAAA 59.824 45.455 0.00 0.00 0.00 1.52
990 2988 2.195139 GATGCCATGGCTGGAGCT 59.805 61.111 35.53 14.21 46.37 4.09
1487 3500 1.880221 CGATGTTGCCAAGGTACACCA 60.880 52.381 0.38 0.00 38.89 4.17
1527 3540 1.116536 TGAGGTTGGCGTGGTAGACA 61.117 55.000 0.00 0.00 0.00 3.41
1602 3615 2.268920 GGCAGGATCAAGTCGGCA 59.731 61.111 0.00 0.00 31.60 5.69
1608 3621 0.755079 TCGAGATGGGCAGGATCAAG 59.245 55.000 0.00 0.00 0.00 3.02
1677 3690 2.551032 CAGCTTCTTTGACTGCACATCA 59.449 45.455 0.00 0.00 0.00 3.07
1698 3711 2.396157 GGTGTTCGACGGAATGGCC 61.396 63.158 0.00 0.00 34.05 5.36
1731 3744 0.863799 GGAACGAAACGAACACCTCC 59.136 55.000 0.00 0.00 0.00 4.30
1833 3846 0.372334 CAATAACCTCCCGAAACGCG 59.628 55.000 3.53 3.53 40.47 6.01
1976 3989 4.224433 CAAGAATGGCGTGATATCAATGC 58.776 43.478 18.40 18.40 0.00 3.56
2016 4029 3.751479 AACCCAAAATTGTGCTCCTTC 57.249 42.857 0.00 0.00 0.00 3.46
2068 4081 7.325660 ACCACAGATGTAAATTAGCATCAAG 57.674 36.000 18.44 14.12 42.72 3.02
2076 4089 7.171653 TGTGATCCAACCACAGATGTAAATTA 58.828 34.615 0.00 0.00 39.36 1.40
2288 4304 6.182039 TCTTGCTATACACATTGCTGTTTC 57.818 37.500 0.00 0.00 34.46 2.78
2477 4496 1.153107 TCATTGATGCCCAGCTCGG 60.153 57.895 0.00 0.00 0.00 4.63
2479 4498 1.948145 CTTCTCATTGATGCCCAGCTC 59.052 52.381 0.00 0.00 0.00 4.09
2696 4715 2.568696 TAAGCACGAGTCATCAGAGC 57.431 50.000 0.00 0.00 0.00 4.09
2758 4780 0.811915 ACAGTTCCGGATCGTCTGAG 59.188 55.000 23.43 8.91 0.00 3.35
2760 4782 1.743958 AGTACAGTTCCGGATCGTCTG 59.256 52.381 4.15 14.11 0.00 3.51
2825 4853 7.844779 TCCAAGATTTCTACTTCTACCTACCAT 59.155 37.037 0.00 0.00 0.00 3.55
2838 4866 9.912634 TCAAATTGAAATGTCCAAGATTTCTAC 57.087 29.630 9.92 0.00 39.55 2.59
2841 4869 9.264719 AGTTCAAATTGAAATGTCCAAGATTTC 57.735 29.630 10.27 0.00 38.22 2.17
2842 4870 9.264719 GAGTTCAAATTGAAATGTCCAAGATTT 57.735 29.630 13.58 0.00 38.22 2.17
2843 4871 8.423349 TGAGTTCAAATTGAAATGTCCAAGATT 58.577 29.630 13.58 0.00 38.22 2.40
2844 4872 7.869429 GTGAGTTCAAATTGAAATGTCCAAGAT 59.131 33.333 13.58 0.00 38.22 2.40
2845 4873 7.068593 AGTGAGTTCAAATTGAAATGTCCAAGA 59.931 33.333 13.58 0.00 38.22 3.02
2846 4874 7.168637 CAGTGAGTTCAAATTGAAATGTCCAAG 59.831 37.037 13.58 0.00 38.22 3.61
2852 4880 8.051909 CGAAAACAGTGAGTTCAAATTGAAATG 58.948 33.333 13.58 8.51 40.26 2.32
2863 4891 7.095607 ACTGATACATTCGAAAACAGTGAGTTC 60.096 37.037 17.95 0.00 40.26 3.01
2956 4984 9.494271 TGCCAGAAGCTTGATTATATTAAGTAG 57.506 33.333 2.10 0.00 44.23 2.57
2994 5027 7.620600 GCTTGTGAACATGCAGAAAATAATGTG 60.621 37.037 14.44 0.00 43.80 3.21
3062 5095 3.063180 CGATGAGCAATTGAGTTGGAGAC 59.937 47.826 10.34 0.00 38.29 3.36
3142 5181 0.391597 TTCCCGGTGTCACTCAAGAC 59.608 55.000 0.00 0.00 38.99 3.01
3200 5243 1.699083 TGGAAGAACATCTCCAGCACA 59.301 47.619 0.00 0.00 0.00 4.57
3326 5376 6.186234 AGGCTCAGAAAGAAAGAAGCAATAT 58.814 36.000 0.00 0.00 0.00 1.28
3327 5377 5.564550 AGGCTCAGAAAGAAAGAAGCAATA 58.435 37.500 0.00 0.00 0.00 1.90
3328 5378 4.405548 AGGCTCAGAAAGAAAGAAGCAAT 58.594 39.130 0.00 0.00 0.00 3.56
3329 5379 3.825328 AGGCTCAGAAAGAAAGAAGCAA 58.175 40.909 0.00 0.00 0.00 3.91
3389 5461 0.737715 AGATCAGCGAAGAACGTGCC 60.738 55.000 0.00 0.00 44.60 5.01
3425 5497 2.810439 AGACAACAGTGAGCTCAGTC 57.190 50.000 21.41 20.58 0.00 3.51
3504 5579 3.018856 CCATCCTTTGCTGCATGAGTTA 58.981 45.455 1.84 0.00 0.00 2.24
3577 5657 7.454260 AAAAACTTAATCCTAGCAGTCAAGG 57.546 36.000 0.00 0.00 0.00 3.61
3666 5746 2.870667 TAAACATCGACCGGCGGACG 62.871 60.000 37.52 37.52 41.67 4.79
3667 5747 1.143969 CTAAACATCGACCGGCGGAC 61.144 60.000 35.78 26.64 41.33 4.79
3668 5748 1.140161 CTAAACATCGACCGGCGGA 59.860 57.895 35.78 11.41 41.33 5.54
3669 5749 0.249322 ATCTAAACATCGACCGGCGG 60.249 55.000 27.06 27.06 41.33 6.13
3670 5750 1.567504 AATCTAAACATCGACCGGCG 58.432 50.000 0.00 6.66 42.69 6.46
3671 5751 5.333875 GGATAAAATCTAAACATCGACCGGC 60.334 44.000 0.00 0.00 0.00 6.13
3672 5752 5.107607 CGGATAAAATCTAAACATCGACCGG 60.108 44.000 0.00 0.00 0.00 5.28
3673 5753 5.461078 ACGGATAAAATCTAAACATCGACCG 59.539 40.000 0.00 0.00 39.90 4.79
3674 5754 6.345565 CGACGGATAAAATCTAAACATCGACC 60.346 42.308 0.00 0.00 0.00 4.79
3675 5755 6.569821 CGACGGATAAAATCTAAACATCGAC 58.430 40.000 0.00 0.00 0.00 4.20
3676 5756 5.174398 GCGACGGATAAAATCTAAACATCGA 59.826 40.000 0.00 0.00 0.00 3.59
3677 5757 5.363517 GCGACGGATAAAATCTAAACATCG 58.636 41.667 0.00 0.00 0.00 3.84
3678 5758 5.465724 AGGCGACGGATAAAATCTAAACATC 59.534 40.000 0.00 0.00 0.00 3.06
3679 5759 5.365619 AGGCGACGGATAAAATCTAAACAT 58.634 37.500 0.00 0.00 0.00 2.71
3680 5760 4.761975 AGGCGACGGATAAAATCTAAACA 58.238 39.130 0.00 0.00 0.00 2.83
3681 5761 4.085210 CGAGGCGACGGATAAAATCTAAAC 60.085 45.833 0.00 0.00 0.00 2.01
3682 5762 4.046462 CGAGGCGACGGATAAAATCTAAA 58.954 43.478 0.00 0.00 0.00 1.85
3683 5763 3.316029 TCGAGGCGACGGATAAAATCTAA 59.684 43.478 0.00 0.00 0.00 2.10
3684 5764 2.880268 TCGAGGCGACGGATAAAATCTA 59.120 45.455 0.00 0.00 0.00 1.98
3685 5765 1.679680 TCGAGGCGACGGATAAAATCT 59.320 47.619 0.00 0.00 0.00 2.40
3686 5766 1.785430 GTCGAGGCGACGGATAAAATC 59.215 52.381 4.11 0.00 46.56 2.17
3687 5767 1.849097 GTCGAGGCGACGGATAAAAT 58.151 50.000 4.11 0.00 46.56 1.82
3688 5768 3.334078 GTCGAGGCGACGGATAAAA 57.666 52.632 4.11 0.00 46.56 1.52
3700 5780 4.143333 ATCCAACGGCCGTCGAGG 62.143 66.667 34.29 30.81 42.43 4.63
3701 5781 2.885644 CATCCAACGGCCGTCGAG 60.886 66.667 34.29 23.48 42.43 4.04
3708 5788 3.810896 GTTCGGGCATCCAACGGC 61.811 66.667 0.00 0.00 0.00 5.68
3709 5789 2.046314 AGTTCGGGCATCCAACGG 60.046 61.111 0.00 0.00 32.83 4.44
3710 5790 0.744414 ATCAGTTCGGGCATCCAACG 60.744 55.000 0.00 0.00 32.83 4.10
3711 5791 2.213499 CTATCAGTTCGGGCATCCAAC 58.787 52.381 0.00 0.00 0.00 3.77
3712 5792 1.475034 GCTATCAGTTCGGGCATCCAA 60.475 52.381 0.00 0.00 0.00 3.53
3713 5793 0.106708 GCTATCAGTTCGGGCATCCA 59.893 55.000 0.00 0.00 0.00 3.41
3714 5794 0.603975 GGCTATCAGTTCGGGCATCC 60.604 60.000 0.00 0.00 0.00 3.51
3715 5795 0.946221 CGGCTATCAGTTCGGGCATC 60.946 60.000 0.00 0.00 0.00 3.91
3716 5796 1.069765 CGGCTATCAGTTCGGGCAT 59.930 57.895 0.00 0.00 0.00 4.40
3717 5797 2.292794 GACGGCTATCAGTTCGGGCA 62.293 60.000 0.00 0.00 0.00 5.36
3718 5798 1.591863 GACGGCTATCAGTTCGGGC 60.592 63.158 0.00 0.00 0.00 6.13
3719 5799 0.249073 CAGACGGCTATCAGTTCGGG 60.249 60.000 0.00 0.00 0.00 5.14
3720 5800 0.738975 TCAGACGGCTATCAGTTCGG 59.261 55.000 0.00 0.00 0.00 4.30
3721 5801 2.292016 AGATCAGACGGCTATCAGTTCG 59.708 50.000 0.00 0.00 0.00 3.95
3722 5802 4.517453 ACTAGATCAGACGGCTATCAGTTC 59.483 45.833 0.00 0.00 0.00 3.01
3723 5803 4.277174 CACTAGATCAGACGGCTATCAGTT 59.723 45.833 0.00 0.00 0.00 3.16
3724 5804 3.818210 CACTAGATCAGACGGCTATCAGT 59.182 47.826 0.00 0.00 0.00 3.41
3725 5805 3.818210 ACACTAGATCAGACGGCTATCAG 59.182 47.826 0.00 0.00 0.00 2.90
3726 5806 3.821748 ACACTAGATCAGACGGCTATCA 58.178 45.455 0.00 0.00 0.00 2.15
3727 5807 4.276183 TGAACACTAGATCAGACGGCTATC 59.724 45.833 0.00 0.00 0.00 2.08
3728 5808 4.036971 GTGAACACTAGATCAGACGGCTAT 59.963 45.833 0.00 0.00 0.00 2.97
3729 5809 3.377485 GTGAACACTAGATCAGACGGCTA 59.623 47.826 0.00 0.00 0.00 3.93
3730 5810 2.164624 GTGAACACTAGATCAGACGGCT 59.835 50.000 0.00 0.00 0.00 5.52
3731 5811 2.531206 GTGAACACTAGATCAGACGGC 58.469 52.381 0.00 0.00 0.00 5.68
3732 5812 2.786854 CGTGAACACTAGATCAGACGG 58.213 52.381 0.00 0.00 0.00 4.79
3733 5813 2.177977 GCGTGAACACTAGATCAGACG 58.822 52.381 0.00 0.34 0.00 4.18
3734 5814 2.531206 GGCGTGAACACTAGATCAGAC 58.469 52.381 0.00 0.00 0.00 3.51
3735 5815 1.476891 GGGCGTGAACACTAGATCAGA 59.523 52.381 0.00 0.00 0.00 3.27
3736 5816 1.471676 GGGGCGTGAACACTAGATCAG 60.472 57.143 0.00 0.00 0.00 2.90
3737 5817 0.535335 GGGGCGTGAACACTAGATCA 59.465 55.000 0.00 0.00 0.00 2.92
3738 5818 0.527817 CGGGGCGTGAACACTAGATC 60.528 60.000 0.00 0.00 0.00 2.75
3739 5819 1.515954 CGGGGCGTGAACACTAGAT 59.484 57.895 0.00 0.00 0.00 1.98
3740 5820 2.967397 CGGGGCGTGAACACTAGA 59.033 61.111 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.