Multiple sequence alignment - TraesCS3A01G342300

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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 TraesCS3A01G342300 chr3A 100.000 4517 0 0 1 4517 589392109 589396625 0.000000e+00 8342.0
1 TraesCS3A01G342300 chr3D 97.153 2318 51 5 1 2308 447988562 447990874 0.000000e+00 3901.0
2 TraesCS3A01G342300 chr3D 91.159 2036 94 32 2514 4517 447991218 447993199 0.000000e+00 2684.0
3 TraesCS3A01G342300 chr3D 93.067 952 61 2 930 1876 206467204 206466253 0.000000e+00 1387.0
4 TraesCS3A01G342300 chr3D 94.737 38 2 0 3173 3210 613692586 613692549 4.880000e-05 60.2
5 TraesCS3A01G342300 chr3B 96.729 1804 54 4 688 2488 587565687 587567488 0.000000e+00 3000.0
6 TraesCS3A01G342300 chr3B 87.005 1716 106 54 2825 4480 587567713 587569371 0.000000e+00 1825.0
7 TraesCS3A01G342300 chr3B 92.160 676 36 9 1 667 587564676 587565343 0.000000e+00 939.0
8 TraesCS3A01G342300 chr3B 92.488 213 11 2 2560 2772 587567508 587567715 2.640000e-77 300.0
9 TraesCS3A01G342300 chr3B 92.105 38 3 0 3173 3210 822880155 822880118 2.000000e-03 54.7
10 TraesCS3A01G342300 chr1A 89.173 859 80 4 930 1787 193040815 193041661 0.000000e+00 1059.0
11 TraesCS3A01G342300 chr1A 78.008 1255 252 16 1076 2318 496046234 496044992 0.000000e+00 767.0
12 TraesCS3A01G342300 chr1D 78.140 1258 245 20 1076 2318 399190925 399189683 0.000000e+00 773.0
13 TraesCS3A01G342300 chr1D 84.413 571 83 6 2898 3465 399188907 399188340 1.420000e-154 556.0
14 TraesCS3A01G342300 chr1D 79.891 184 32 5 1511 1692 399044424 399044244 3.670000e-26 130.0
15 TraesCS3A01G342300 chr1B 83.566 572 86 8 2898 3465 535384850 535384283 3.090000e-146 529.0
16 TraesCS3A01G342300 chr4A 80.455 220 36 6 3170 3387 60926384 60926170 1.300000e-35 161.0
17 TraesCS3A01G342300 chr4D 79.452 219 40 5 3170 3387 403396624 403396410 2.810000e-32 150.0
18 TraesCS3A01G342300 chr4B 78.295 129 23 3 3170 3297 500254463 500254339 1.350000e-10 78.7


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 TraesCS3A01G342300 chr3A 589392109 589396625 4516 False 8342.0 8342 100.0000 1 4517 1 chr3A.!!$F1 4516
1 TraesCS3A01G342300 chr3D 447988562 447993199 4637 False 3292.5 3901 94.1560 1 4517 2 chr3D.!!$F1 4516
2 TraesCS3A01G342300 chr3D 206466253 206467204 951 True 1387.0 1387 93.0670 930 1876 1 chr3D.!!$R1 946
3 TraesCS3A01G342300 chr3B 587564676 587569371 4695 False 1516.0 3000 92.0955 1 4480 4 chr3B.!!$F1 4479
4 TraesCS3A01G342300 chr1A 193040815 193041661 846 False 1059.0 1059 89.1730 930 1787 1 chr1A.!!$F1 857
5 TraesCS3A01G342300 chr1A 496044992 496046234 1242 True 767.0 767 78.0080 1076 2318 1 chr1A.!!$R1 1242
6 TraesCS3A01G342300 chr1D 399188340 399190925 2585 True 664.5 773 81.2765 1076 3465 2 chr1D.!!$R2 2389
7 TraesCS3A01G342300 chr1B 535384283 535384850 567 True 529.0 529 83.5660 2898 3465 1 chr1B.!!$R1 567

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
141 150 0.105453 TGGAGCCTATGAGAGGGGAC 60.105 60.000 0.00 0.00 46.81 4.46 F
502 515 1.134220 TGTTATCTGGCCGATGAACCC 60.134 52.381 17.04 2.41 33.48 4.11 F
2433 2810 0.530744 CTGTTGGCACTAGTCGGCTA 59.469 55.000 15.99 0.00 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 2260 1.067295 TCTGTCCTTCCACCTGCAAT 58.933 50.000 0.00 0.0 0.0 3.56 R
2500 2889 1.133482 GCCACCCCCACTAATAGCATT 60.133 52.381 0.00 0.0 0.0 3.56 R
4104 4946 0.038526 GAGGAACGCGGACTGAAGAA 60.039 55.000 12.47 0.0 0.0 2.52 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
141 150 0.105453 TGGAGCCTATGAGAGGGGAC 60.105 60.000 0.00 0.00 46.81 4.46
210 219 2.686915 CTCACCATGGAAGCATTTCTCC 59.313 50.000 21.47 0.00 33.68 3.71
237 246 7.120873 CCTGGATCATTCTATTGGCTTATTCTG 59.879 40.741 0.00 0.00 0.00 3.02
243 252 9.905713 TCATTCTATTGGCTTATTCTGTTACTT 57.094 29.630 0.00 0.00 0.00 2.24
338 347 6.711277 TGGTTATGCCTAATGATAGCTAAGG 58.289 40.000 0.00 0.06 38.35 2.69
403 412 5.869344 TCTCAAGAACATTATCGTGTTGGAG 59.131 40.000 0.00 2.69 42.08 3.86
411 420 4.665833 TTATCGTGTTGGAGGAGGTATG 57.334 45.455 0.00 0.00 0.00 2.39
422 435 6.126863 TGGAGGAGGTATGCTATTATTTGG 57.873 41.667 0.00 0.00 0.00 3.28
438 451 4.954933 GGCCAAATACAGAGCCGA 57.045 55.556 0.00 0.00 35.30 5.54
502 515 1.134220 TGTTATCTGGCCGATGAACCC 60.134 52.381 17.04 2.41 33.48 4.11
525 538 5.506317 CCGTCTTTGGATGATCTAAAATGGC 60.506 44.000 5.49 0.00 0.00 4.40
1831 2185 6.791887 TGTTGCTTCTCTTGATTCTTGTAG 57.208 37.500 0.00 0.00 0.00 2.74
1903 2260 4.280436 TCGTCATCCAAAGGAAAAGCTA 57.720 40.909 0.00 0.00 34.34 3.32
1918 2275 1.289160 AGCTATTGCAGGTGGAAGGA 58.711 50.000 1.12 0.00 42.74 3.36
2318 2675 7.532682 TCTTTGTTTCACCTGTTTTATTTGC 57.467 32.000 0.00 0.00 0.00 3.68
2405 2781 3.247006 TGAAGCGAGGATTGGTAACTC 57.753 47.619 0.00 0.00 37.61 3.01
2407 2783 2.969628 AGCGAGGATTGGTAACTCAG 57.030 50.000 0.00 0.00 37.61 3.35
2433 2810 0.530744 CTGTTGGCACTAGTCGGCTA 59.469 55.000 15.99 0.00 0.00 3.93
2452 2829 4.448732 GGCTACAAGCATTTCCAAAACTTG 59.551 41.667 12.97 12.97 44.75 3.16
2471 2848 7.448748 AACTTGGTTGGAATTCATACTGTAC 57.551 36.000 7.93 0.00 0.00 2.90
2478 2857 7.040686 GGTTGGAATTCATACTGTACACACTTT 60.041 37.037 7.93 0.00 0.00 2.66
2480 2859 6.995686 TGGAATTCATACTGTACACACTTTGT 59.004 34.615 7.93 0.00 42.84 2.83
2488 2867 5.726397 ACTGTACACACTTTGTAAGTCACA 58.274 37.500 0.00 0.00 42.56 3.58
2489 2868 5.810587 ACTGTACACACTTTGTAAGTCACAG 59.189 40.000 0.00 13.23 42.56 3.66
2500 2889 5.545063 TGTAAGTCACAGAGTGATTTGGA 57.455 39.130 15.34 2.48 44.63 3.53
2503 2892 5.954296 AAGTCACAGAGTGATTTGGAATG 57.046 39.130 7.03 0.00 44.63 2.67
2504 2893 3.755378 AGTCACAGAGTGATTTGGAATGC 59.245 43.478 2.90 0.00 44.63 3.56
2507 2896 5.587844 GTCACAGAGTGATTTGGAATGCTAT 59.412 40.000 2.90 0.00 44.63 2.97
2508 2897 6.094603 GTCACAGAGTGATTTGGAATGCTATT 59.905 38.462 2.90 0.00 44.63 1.73
2510 2899 7.496920 TCACAGAGTGATTTGGAATGCTATTAG 59.503 37.037 0.00 0.00 37.67 1.73
2550 3045 6.205464 TGCTAGTTAATATGCTGAATCCTTGC 59.795 38.462 0.00 0.00 0.00 4.01
2606 3101 7.732222 AATTCTGGTCACTCTCTCTTAAGAT 57.268 36.000 5.44 0.00 0.00 2.40
2750 3248 6.756221 TCTTGTTTCTCCTAGTTAGTGTTCC 58.244 40.000 0.00 0.00 0.00 3.62
2756 3254 2.565834 TCCTAGTTAGTGTTCCCTGTGC 59.434 50.000 0.00 0.00 0.00 4.57
2835 3517 3.885297 CGGCAGAAATCCTGGTTGATAAT 59.115 43.478 0.00 0.00 43.13 1.28
2962 3742 5.950758 GAGAGTAAAGATATCTCTCGGCA 57.049 43.478 5.51 0.00 42.65 5.69
2991 3771 0.179150 GACTCGCTCATCTTCACGCT 60.179 55.000 0.00 0.00 0.00 5.07
2997 3777 0.179089 CTCATCTTCACGCTGAGGGG 60.179 60.000 0.51 0.00 33.33 4.79
3024 3804 0.606401 AGTTCATCCACGGCAACCTG 60.606 55.000 0.00 0.00 0.00 4.00
3072 3852 4.803426 CTGGACGGCTGCGTCTCC 62.803 72.222 18.75 11.53 38.76 3.71
3105 3885 0.904649 CACAGCTCATGACCACCCTA 59.095 55.000 0.00 0.00 0.00 3.53
3108 3888 0.043334 AGCTCATGACCACCCTACCT 59.957 55.000 0.00 0.00 0.00 3.08
3530 4310 2.982130 GTGAGGGCGTGTGGAGAT 59.018 61.111 0.00 0.00 0.00 2.75
3563 4345 3.192001 CCATTGTGTTTAGCATGCAGAGT 59.808 43.478 21.98 0.61 0.00 3.24
3564 4346 4.321452 CCATTGTGTTTAGCATGCAGAGTT 60.321 41.667 21.98 0.16 0.00 3.01
3565 4347 5.106197 CCATTGTGTTTAGCATGCAGAGTTA 60.106 40.000 21.98 0.00 0.00 2.24
3566 4348 6.405065 CCATTGTGTTTAGCATGCAGAGTTAT 60.405 38.462 21.98 0.00 0.00 1.89
3602 4384 5.463724 GCTAAGCTAGGTTGCATAGTTACTG 59.536 44.000 17.34 0.00 36.82 2.74
3603 4385 4.408182 AGCTAGGTTGCATAGTTACTGG 57.592 45.455 0.00 0.00 34.99 4.00
3604 4386 3.134804 AGCTAGGTTGCATAGTTACTGGG 59.865 47.826 0.00 0.00 34.99 4.45
3697 4489 6.176183 TCTGTTGATCCCTGATTCTTTCTTC 58.824 40.000 0.00 0.00 0.00 2.87
3698 4490 4.937620 TGTTGATCCCTGATTCTTTCTTCG 59.062 41.667 0.00 0.00 0.00 3.79
3699 4491 3.535561 TGATCCCTGATTCTTTCTTCGC 58.464 45.455 0.00 0.00 0.00 4.70
3789 4597 1.751924 GGTGTTTGTGTTGCCCTGTAA 59.248 47.619 0.00 0.00 0.00 2.41
3804 4614 3.934579 CCCTGTAATTTGGCATGCTTTTC 59.065 43.478 18.92 0.53 0.00 2.29
3806 4616 5.240121 CCTGTAATTTGGCATGCTTTTCTT 58.760 37.500 18.92 7.83 0.00 2.52
3813 4623 1.895131 GGCATGCTTTTCTTCCCAGAA 59.105 47.619 18.92 0.00 37.24 3.02
3842 4652 9.865152 TGATTAATGGGATTCATTGAGTTGATA 57.135 29.630 0.00 0.00 45.00 2.15
3888 4699 3.432252 AGATTTCTAGTTTGGCGTTCGTG 59.568 43.478 0.00 0.00 0.00 4.35
3919 4734 4.332637 GTGTGCCGCAGTTGCTGG 62.333 66.667 0.00 6.59 39.32 4.85
3927 4742 3.371063 CAGTTGCTGGCTGCCCTG 61.371 66.667 17.53 11.71 42.00 4.45
3928 4743 4.673375 AGTTGCTGGCTGCCCTGG 62.673 66.667 17.53 7.61 42.00 4.45
3930 4745 4.223125 TTGCTGGCTGCCCTGGTT 62.223 61.111 17.53 0.00 42.00 3.67
3931 4746 2.839609 TTGCTGGCTGCCCTGGTTA 61.840 57.895 17.53 0.00 42.00 2.85
3932 4747 2.751837 GCTGGCTGCCCTGGTTAC 60.752 66.667 17.53 0.00 35.15 2.50
3933 4748 2.436646 CTGGCTGCCCTGGTTACG 60.437 66.667 17.53 0.00 0.00 3.18
3934 4749 2.925706 TGGCTGCCCTGGTTACGA 60.926 61.111 17.53 0.00 0.00 3.43
3935 4750 2.125106 GGCTGCCCTGGTTACGAG 60.125 66.667 7.66 0.00 0.00 4.18
4086 4926 4.193334 TCTGGAGCACGCCGATCG 62.193 66.667 8.51 8.51 45.38 3.69
4115 4957 2.049433 ACCGCGTTCTTCAGTCCG 60.049 61.111 4.92 0.00 0.00 4.79
4174 5016 3.488090 GGCACGTGTTAGGAGCGC 61.488 66.667 18.38 0.00 0.00 5.92
4175 5017 3.838795 GCACGTGTTAGGAGCGCG 61.839 66.667 18.38 0.00 44.28 6.86
4176 5018 3.179265 CACGTGTTAGGAGCGCGG 61.179 66.667 8.83 0.00 43.19 6.46
4213 5055 1.986575 GCGAATGCCAGCCACTCTTC 61.987 60.000 0.00 0.00 33.98 2.87
4269 5124 4.458642 GGCAATCAAAGCTCTTCTCTTCTT 59.541 41.667 0.00 0.00 0.00 2.52
4273 5128 3.008485 TCAAAGCTCTTCTCTTCTTCCCC 59.992 47.826 0.00 0.00 0.00 4.81
4289 5147 2.893398 CCAGAGTACGGGACCAGC 59.107 66.667 0.00 0.00 33.26 4.85
4290 5148 1.682684 CCAGAGTACGGGACCAGCT 60.683 63.158 0.00 0.00 33.26 4.24
4291 5149 0.395311 CCAGAGTACGGGACCAGCTA 60.395 60.000 0.00 0.00 33.26 3.32
4292 5150 1.025812 CAGAGTACGGGACCAGCTAG 58.974 60.000 0.00 0.00 0.00 3.42
4293 5151 0.106619 AGAGTACGGGACCAGCTAGG 60.107 60.000 0.00 0.00 45.67 3.02
4331 5190 2.903547 CGGGTCCACGGTTTGCAAG 61.904 63.158 0.00 0.00 0.00 4.01
4346 5205 4.096003 AAGTGCGACGGGGATGGG 62.096 66.667 0.00 0.00 0.00 4.00
4364 5223 4.803426 CTCCGCTCCGCTGTCCAC 62.803 72.222 0.00 0.00 0.00 4.02
4407 5278 2.499685 GCGTCTCGGCCAGGTAAT 59.500 61.111 2.24 0.00 0.00 1.89
4408 5279 1.737816 GCGTCTCGGCCAGGTAATA 59.262 57.895 2.24 0.00 0.00 0.98
4409 5280 0.596859 GCGTCTCGGCCAGGTAATAC 60.597 60.000 2.24 0.00 0.00 1.89
4410 5281 0.742505 CGTCTCGGCCAGGTAATACA 59.257 55.000 2.24 0.00 0.00 2.29
4411 5282 1.269102 CGTCTCGGCCAGGTAATACAG 60.269 57.143 2.24 0.00 0.00 2.74
4436 5307 1.078115 TGGGGGATGATGATGGATGG 58.922 55.000 0.00 0.00 0.00 3.51
4437 5308 1.375610 GGGGGATGATGATGGATGGA 58.624 55.000 0.00 0.00 0.00 3.41
4438 5309 1.928077 GGGGGATGATGATGGATGGAT 59.072 52.381 0.00 0.00 0.00 3.41
4439 5310 2.357881 GGGGGATGATGATGGATGGATG 60.358 54.545 0.00 0.00 0.00 3.51
4446 5317 0.325933 TGATGGATGGATGATCGCCC 59.674 55.000 2.33 0.00 30.87 6.13
4498 5369 0.949105 GATTTCACGTGGCGGTGTCT 60.949 55.000 17.00 0.00 39.00 3.41
4513 5384 1.822186 GTCTGTTGCGGTTGGGTGT 60.822 57.895 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
210 219 3.803186 AGCCAATAGAATGATCCAGGG 57.197 47.619 0.00 0.00 0.00 4.45
303 312 4.701956 AGGCATAACCAGAAATTGTTCG 57.298 40.909 0.00 0.00 43.14 3.95
338 347 5.725325 AGAACTCTCCTGTTTGTACCTAC 57.275 43.478 0.00 0.00 0.00 3.18
403 412 4.662278 TGGCCAAATAATAGCATACCTCC 58.338 43.478 0.61 0.00 0.00 4.30
411 420 6.152379 GCTCTGTATTTGGCCAAATAATAGC 58.848 40.000 39.70 37.23 42.75 2.97
422 435 2.160417 GCATATCGGCTCTGTATTTGGC 59.840 50.000 0.00 0.00 0.00 4.52
438 451 5.565439 GCTTTGACAGACCAAACTTGCATAT 60.565 40.000 0.00 0.00 33.07 1.78
502 515 5.066375 TGCCATTTTAGATCATCCAAAGACG 59.934 40.000 0.00 0.00 0.00 4.18
525 538 7.148390 TGCATGTTCATGGCTTTAAAATCAATG 60.148 33.333 13.55 0.00 0.00 2.82
1903 2260 1.067295 TCTGTCCTTCCACCTGCAAT 58.933 50.000 0.00 0.00 0.00 3.56
1918 2275 2.158143 AGTCTTCCTTAGGGGTGTCTGT 60.158 50.000 0.00 0.00 36.25 3.41
2405 2781 4.632153 ACTAGTGCCAACAGTTAAGTCTG 58.368 43.478 0.00 0.00 40.80 3.51
2407 2783 3.673809 CGACTAGTGCCAACAGTTAAGTC 59.326 47.826 0.00 0.00 33.90 3.01
2452 2829 5.938125 AGTGTGTACAGTATGAATTCCAACC 59.062 40.000 2.27 0.00 39.69 3.77
2462 2839 7.436970 TGTGACTTACAAAGTGTGTACAGTATG 59.563 37.037 0.00 0.00 42.56 2.39
2478 2857 5.545063 TCCAAATCACTCTGTGACTTACA 57.455 39.130 2.31 0.00 45.65 2.41
2480 2859 5.412594 GCATTCCAAATCACTCTGTGACTTA 59.587 40.000 2.31 0.00 45.65 2.24
2488 2867 6.769822 CCACTAATAGCATTCCAAATCACTCT 59.230 38.462 0.00 0.00 0.00 3.24
2489 2868 6.016777 CCCACTAATAGCATTCCAAATCACTC 60.017 42.308 0.00 0.00 0.00 3.51
2492 2871 5.139727 CCCCACTAATAGCATTCCAAATCA 58.860 41.667 0.00 0.00 0.00 2.57
2500 2889 1.133482 GCCACCCCCACTAATAGCATT 60.133 52.381 0.00 0.00 0.00 3.56
2503 2892 0.478507 ATGCCACCCCCACTAATAGC 59.521 55.000 0.00 0.00 0.00 2.97
2504 2893 4.335416 CATTATGCCACCCCCACTAATAG 58.665 47.826 0.00 0.00 0.00 1.73
2507 2896 1.410932 GCATTATGCCACCCCCACTAA 60.411 52.381 5.80 0.00 37.42 2.24
2508 2897 0.184933 GCATTATGCCACCCCCACTA 59.815 55.000 5.80 0.00 37.42 2.74
2510 2899 0.184933 TAGCATTATGCCACCCCCAC 59.815 55.000 14.10 0.00 46.52 4.61
2550 3045 7.862873 AGAAATTTTAGAGAAAAGGACAAAGCG 59.137 33.333 0.00 0.00 37.94 4.68
2593 3088 6.975196 TGGAGGATTCATCTTAAGAGAGAG 57.025 41.667 11.53 1.44 34.85 3.20
2594 3089 7.927683 ATTGGAGGATTCATCTTAAGAGAGA 57.072 36.000 11.53 8.64 34.85 3.10
2750 3248 0.947244 GTTGAGTTCAGTGGCACAGG 59.053 55.000 21.41 11.68 41.80 4.00
2756 3254 7.678947 ATTAAATCTCAGTTGAGTTCAGTGG 57.321 36.000 8.85 0.00 42.60 4.00
2823 3384 8.786898 CATGGACACTAAATATTATCAACCAGG 58.213 37.037 0.00 0.00 0.00 4.45
2824 3385 8.786898 CCATGGACACTAAATATTATCAACCAG 58.213 37.037 5.56 0.00 0.00 4.00
2835 3517 5.755409 ACAGACACCATGGACACTAAATA 57.245 39.130 21.47 0.00 0.00 1.40
2946 3726 2.636893 AGCCATGCCGAGAGATATCTTT 59.363 45.455 6.70 0.01 0.00 2.52
2962 3742 3.069980 GAGCGAGTCCACGAGCCAT 62.070 63.158 0.00 0.00 35.09 4.40
2991 3771 2.203938 AACTTCCCGCTCCCCTCA 60.204 61.111 0.00 0.00 0.00 3.86
2997 3777 1.084370 CGTGGATGAACTTCCCGCTC 61.084 60.000 4.67 0.00 34.67 5.03
3024 3804 3.927142 ACAGAAGGATGTTCGACGATTTC 59.073 43.478 0.00 0.00 0.00 2.17
3072 3852 2.745884 TGTGCCAGGCCGAATTCG 60.746 61.111 20.92 20.92 39.44 3.34
3075 3855 3.984193 GAGCTGTGCCAGGCCGAAT 62.984 63.158 9.64 0.00 31.21 3.34
3087 3867 0.905357 GTAGGGTGGTCATGAGCTGT 59.095 55.000 24.30 9.66 0.00 4.40
3156 3936 0.321996 ACTTCTGGGTCGGCTTCTTC 59.678 55.000 0.00 0.00 0.00 2.87
3524 4304 5.945784 CACAATGGGACTCTTTTTATCTCCA 59.054 40.000 0.00 0.00 0.00 3.86
3525 4305 5.946377 ACACAATGGGACTCTTTTTATCTCC 59.054 40.000 0.00 0.00 0.00 3.71
3530 4310 6.547880 TGCTAAACACAATGGGACTCTTTTTA 59.452 34.615 0.00 0.00 0.00 1.52
3602 4384 7.334671 GCTCAAAGCTATCTATATAACCAACCC 59.665 40.741 0.00 0.00 38.45 4.11
3603 4385 7.063544 CGCTCAAAGCTATCTATATAACCAACC 59.936 40.741 0.00 0.00 39.60 3.77
3604 4386 7.813148 TCGCTCAAAGCTATCTATATAACCAAC 59.187 37.037 0.00 0.00 39.60 3.77
3697 4489 3.488489 CACAGAAAAATTACCCGAAGCG 58.512 45.455 0.00 0.00 0.00 4.68
3698 4490 3.242518 GCACAGAAAAATTACCCGAAGC 58.757 45.455 0.00 0.00 0.00 3.86
3699 4491 3.669557 CGGCACAGAAAAATTACCCGAAG 60.670 47.826 0.00 0.00 36.79 3.79
3789 4597 2.638855 TGGGAAGAAAAGCATGCCAAAT 59.361 40.909 15.66 0.00 32.50 2.32
3804 4614 5.448654 TCCCATTAATCACATTCTGGGAAG 58.551 41.667 13.45 0.00 44.71 3.46
3813 4623 8.418662 CAACTCAATGAATCCCATTAATCACAT 58.581 33.333 0.00 0.00 43.27 3.21
3888 4699 3.136808 GGCACACGAATCAAATCTTCC 57.863 47.619 0.00 0.00 0.00 3.46
3919 4734 2.820037 GCTCGTAACCAGGGCAGC 60.820 66.667 0.00 0.00 0.00 5.25
3922 4737 2.125106 CCTGCTCGTAACCAGGGC 60.125 66.667 0.00 0.00 43.87 5.19
3925 4740 2.103042 GCTGCCTGCTCGTAACCAG 61.103 63.158 0.00 0.00 38.95 4.00
3927 4742 1.671054 TTGCTGCCTGCTCGTAACC 60.671 57.895 0.00 0.00 43.37 2.85
3928 4743 1.227999 TGTTGCTGCCTGCTCGTAAC 61.228 55.000 0.00 6.21 43.37 2.50
3930 4745 1.070615 TTGTTGCTGCCTGCTCGTA 59.929 52.632 0.00 0.00 43.37 3.43
3931 4746 2.203195 TTGTTGCTGCCTGCTCGT 60.203 55.556 0.00 0.00 43.37 4.18
3932 4747 2.253452 GTTGTTGCTGCCTGCTCG 59.747 61.111 0.00 0.00 43.37 5.03
3933 4748 2.253452 CGTTGTTGCTGCCTGCTC 59.747 61.111 0.00 0.00 43.37 4.26
3934 4749 2.516930 ACGTTGTTGCTGCCTGCT 60.517 55.556 0.00 0.00 43.37 4.24
3935 4750 2.050985 GACGTTGTTGCTGCCTGC 60.051 61.111 0.00 0.00 43.25 4.85
4052 4892 3.595108 GACTGGAAAAGGCGCGTGC 62.595 63.158 13.78 13.78 41.71 5.34
4104 4946 0.038526 GAGGAACGCGGACTGAAGAA 60.039 55.000 12.47 0.00 0.00 2.52
4255 5110 2.187100 CTGGGGAAGAAGAGAAGAGCT 58.813 52.381 0.00 0.00 0.00 4.09
4273 5128 1.025812 CTAGCTGGTCCCGTACTCTG 58.974 60.000 0.00 0.00 0.00 3.35
4317 5176 2.829206 CGCACTTGCAAACCGTGGA 61.829 57.895 16.37 0.00 42.21 4.02
4324 5183 3.283684 CCCCGTCGCACTTGCAAA 61.284 61.111 0.00 0.00 42.21 3.68
4403 5274 6.182507 TCATCCCCCATGTTACTGTATTAC 57.817 41.667 0.00 0.00 33.66 1.89
4407 5278 4.302930 TCATCATCCCCCATGTTACTGTA 58.697 43.478 0.00 0.00 33.66 2.74
4408 5279 3.122480 TCATCATCCCCCATGTTACTGT 58.878 45.455 0.00 0.00 33.66 3.55
4409 5280 3.862877 TCATCATCCCCCATGTTACTG 57.137 47.619 0.00 0.00 33.66 2.74
4410 5281 3.074985 CCATCATCATCCCCCATGTTACT 59.925 47.826 0.00 0.00 33.66 2.24
4411 5282 3.074390 TCCATCATCATCCCCCATGTTAC 59.926 47.826 0.00 0.00 33.66 2.50
4436 5307 1.294659 GGCGAATGAGGGCGATCATC 61.295 60.000 4.54 0.00 39.00 2.92
4437 5308 1.302033 GGCGAATGAGGGCGATCAT 60.302 57.895 0.00 0.00 41.72 2.45
4438 5309 2.108976 GGCGAATGAGGGCGATCA 59.891 61.111 0.00 0.00 0.00 2.92
4498 5369 2.830827 CCACACCCAACCGCAACA 60.831 61.111 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.