Multiple sequence alignment - TraesCS1D01G192200

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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 TraesCS1D01G192200 chr1D 100.000 4894 0 0 1 4894 267984929 267989822 0.000000e+00 9038.0
1 TraesCS1D01G192200 chr1D 87.531 401 37 7 4216 4611 268461813 268462205 7.470000e-123 451.0
2 TraesCS1D01G192200 chr1D 100.000 32 0 0 4862 4893 267994871 267994840 5.290000e-05 60.2
3 TraesCS1D01G192200 chr1A 94.396 4907 188 40 2 4860 334453558 334448691 0.000000e+00 7457.0
4 TraesCS1D01G192200 chr1A 94.105 475 19 5 4264 4732 334416718 334416247 0.000000e+00 713.0
5 TraesCS1D01G192200 chr1B 93.984 2959 135 20 1826 4769 344841083 344838153 0.000000e+00 4438.0
6 TraesCS1D01G192200 chr1B 95.131 1068 31 11 684 1745 344842247 344841195 0.000000e+00 1664.0
7 TraesCS1D01G192200 chr1B 94.093 237 13 1 440 675 344842518 344842282 4.660000e-95 359.0
8 TraesCS1D01G192200 chr1B 93.750 112 7 0 1 112 344842819 344842708 8.420000e-38 169.0
9 TraesCS1D01G192200 chr1B 89.381 113 10 2 136 246 152450048 152450160 1.840000e-29 141.0
10 TraesCS1D01G192200 chr1B 88.696 115 11 2 136 248 53067462 53067348 6.610000e-29 139.0
11 TraesCS1D01G192200 chr1B 91.463 82 6 1 2427 2507 344840409 344840328 1.440000e-20 111.0
12 TraesCS1D01G192200 chr2A 88.976 127 9 5 127 250 78849741 78849617 8.480000e-33 152.0
13 TraesCS1D01G192200 chr2A 89.256 121 10 3 127 245 367649202 367649321 1.100000e-31 148.0
14 TraesCS1D01G192200 chr2D 88.189 127 9 6 127 250 78567678 78567555 3.950000e-31 147.0
15 TraesCS1D01G192200 chrUn 88.430 121 11 3 127 245 81477680 81477799 5.110000e-30 143.0
16 TraesCS1D01G192200 chr7A 86.822 129 15 2 127 253 522496602 522496730 5.110000e-30 143.0
17 TraesCS1D01G192200 chr7A 100.000 33 0 0 4861 4893 80562771 80562739 1.470000e-05 62.1
18 TraesCS1D01G192200 chr7D 87.603 121 13 2 127 245 110367042 110367162 6.610000e-29 139.0
19 TraesCS1D01G192200 chr7D 100.000 32 0 0 4862 4893 71587012 71587043 5.290000e-05 60.2
20 TraesCS1D01G192200 chr6A 100.000 34 0 0 4860 4893 535278771 535278804 4.090000e-06 63.9
21 TraesCS1D01G192200 chr6A 100.000 32 0 0 4862 4893 535298194 535298163 5.290000e-05 60.2
22 TraesCS1D01G192200 chr6B 100.000 32 0 0 4862 4893 431424143 431424112 5.290000e-05 60.2
23 TraesCS1D01G192200 chr6B 100.000 29 0 0 4862 4890 431404975 431405003 2.000000e-03 54.7
24 TraesCS1D01G192200 chr5D 97.143 35 1 0 4859 4893 306243931 306243965 5.290000e-05 60.2
25 TraesCS1D01G192200 chr3D 100.000 30 0 0 4864 4893 583022146 583022117 6.840000e-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 TraesCS1D01G192200 chr1D 267984929 267989822 4893 False 9038.0 9038 100.0000 1 4894 1 chr1D.!!$F1 4893
1 TraesCS1D01G192200 chr1A 334448691 334453558 4867 True 7457.0 7457 94.3960 2 4860 1 chr1A.!!$R2 4858
2 TraesCS1D01G192200 chr1B 344838153 344842819 4666 True 1348.2 4438 93.6842 1 4769 5 chr1B.!!$R2 4768

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
678 765 0.316204 AGGGTGTGTACGAACCGAAG 59.684 55.000 9.89 0.00 37.33 3.79 F
1626 1750 0.171007 TGTACTTGCCGTACCGCTAC 59.829 55.000 7.70 3.12 46.36 3.58 F
2335 2491 0.945265 CATTGCCAGGTTTGTTGCCG 60.945 55.000 0.00 0.00 0.00 5.69 F
3654 3816 1.824852 AGACGCATCACTGGTACATGA 59.175 47.619 0.00 0.00 38.20 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 2468 0.673437 AACAAACCTGGCAATGGTCG 59.327 50.0 0.00 0.00 36.69 4.79 R
2695 2851 2.490903 CCCAAAGTCTGCAATCTTGAGG 59.509 50.0 4.21 8.67 0.00 3.86 R
3715 3877 1.085091 CAGAGCCTCATCAACTGCAC 58.915 55.0 0.00 0.00 0.00 4.57 R
4773 4945 0.523072 GACCATGCGTTCATGCTGTT 59.477 50.0 0.03 0.00 46.69 3.16 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
115 116 6.072008 CCATCACATTCAATTCTTGTACACCA 60.072 38.462 0.00 0.00 0.00 4.17
134 160 5.073144 ACACCATCCGTTCCTAAATATGGAT 59.927 40.000 6.18 0.00 37.80 3.41
157 183 8.150945 GGATTACATACGGATGAATATAGGCAT 58.849 37.037 16.36 0.00 36.48 4.40
189 215 8.180267 AGAATTAGATTCACTCATTTTGCTTCG 58.820 33.333 3.76 0.00 41.71 3.79
193 219 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
198 224 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
215 241 7.994425 ATGTAGTCCATACTGACATCTCTAG 57.006 40.000 0.00 0.00 37.73 2.43
229 255 9.249053 CTGACATCTCTAGAAGGGCTTATATTA 57.751 37.037 0.00 0.00 0.00 0.98
230 256 9.249053 TGACATCTCTAGAAGGGCTTATATTAG 57.751 37.037 0.00 0.00 0.00 1.73
268 296 7.953005 AACATCAACCATGTAATTCACCATA 57.047 32.000 0.00 0.00 45.77 2.74
429 482 8.934507 TCCAAACATTAACGTTTCATTTTTCT 57.065 26.923 5.91 0.00 36.98 2.52
430 483 9.372369 TCCAAACATTAACGTTTCATTTTTCTT 57.628 25.926 5.91 0.00 36.98 2.52
431 484 9.419737 CCAAACATTAACGTTTCATTTTTCTTG 57.580 29.630 5.91 0.00 36.98 3.02
432 485 8.932963 CAAACATTAACGTTTCATTTTTCTTGC 58.067 29.630 5.91 0.00 36.98 4.01
433 486 6.862194 ACATTAACGTTTCATTTTTCTTGCG 58.138 32.000 5.91 0.00 0.00 4.85
434 487 6.693545 ACATTAACGTTTCATTTTTCTTGCGA 59.306 30.769 5.91 0.00 0.00 5.10
435 488 7.221067 ACATTAACGTTTCATTTTTCTTGCGAA 59.779 29.630 5.91 0.00 0.00 4.70
436 489 7.687005 TTAACGTTTCATTTTTCTTGCGAAT 57.313 28.000 5.91 0.00 0.00 3.34
437 490 8.783999 TTAACGTTTCATTTTTCTTGCGAATA 57.216 26.923 5.91 0.00 0.00 1.75
438 491 7.867445 AACGTTTCATTTTTCTTGCGAATAT 57.133 28.000 0.00 0.00 0.00 1.28
439 492 8.958175 AACGTTTCATTTTTCTTGCGAATATA 57.042 26.923 0.00 0.00 0.00 0.86
440 493 8.958175 ACGTTTCATTTTTCTTGCGAATATAA 57.042 26.923 0.00 0.00 0.00 0.98
441 494 9.400638 ACGTTTCATTTTTCTTGCGAATATAAA 57.599 25.926 0.00 0.00 0.00 1.40
442 495 9.656834 CGTTTCATTTTTCTTGCGAATATAAAC 57.343 29.630 0.00 0.00 0.00 2.01
502 588 3.326747 ACTAATCTTCACAACTCACGGC 58.673 45.455 0.00 0.00 0.00 5.68
567 653 9.975218 ATACAATCTTTGTCCCTTAATGTAAGT 57.025 29.630 0.00 0.00 44.12 2.24
652 738 6.842437 ATATAAGGTGTGTATGATCTCGCT 57.158 37.500 0.00 0.00 0.00 4.93
675 762 1.585297 AAAAGGGTGTGTACGAACCG 58.415 50.000 9.89 0.00 37.33 4.44
676 763 0.752054 AAAGGGTGTGTACGAACCGA 59.248 50.000 9.89 0.00 37.33 4.69
677 764 0.752054 AAGGGTGTGTACGAACCGAA 59.248 50.000 9.89 0.00 37.33 4.30
678 765 0.316204 AGGGTGTGTACGAACCGAAG 59.684 55.000 9.89 0.00 37.33 3.79
680 767 1.134226 GGTGTGTACGAACCGAAGTG 58.866 55.000 1.36 0.00 0.00 3.16
681 768 1.536709 GGTGTGTACGAACCGAAGTGT 60.537 52.381 1.36 0.00 0.00 3.55
682 769 2.287547 GGTGTGTACGAACCGAAGTGTA 60.288 50.000 1.36 0.00 0.00 2.90
735 849 7.095774 ACGGAGTATACAGCAATAAATTAAGCG 60.096 37.037 5.50 0.00 41.94 4.68
954 1074 1.002011 GAACCCAACCCTGCTCTCC 60.002 63.158 0.00 0.00 0.00 3.71
955 1075 2.485780 GAACCCAACCCTGCTCTCCC 62.486 65.000 0.00 0.00 0.00 4.30
1182 1305 1.875963 CATTGTCTGGTGCGTTCCC 59.124 57.895 0.00 0.00 0.00 3.97
1586 1710 7.763985 AGACTTGTCTGTTTTAATTTGTTTGGG 59.236 33.333 2.11 0.00 0.00 4.12
1626 1750 0.171007 TGTACTTGCCGTACCGCTAC 59.829 55.000 7.70 3.12 46.36 3.58
1725 1849 3.615496 TGAACGCCGCTCTTATTAGTTTC 59.385 43.478 0.00 0.00 0.00 2.78
1862 2017 1.080722 TACGGCCCTACCCAGGAAA 59.919 57.895 0.00 0.00 45.91 3.13
1863 2018 0.979187 TACGGCCCTACCCAGGAAAG 60.979 60.000 0.00 0.00 45.91 2.62
1867 2022 1.205460 GCCCTACCCAGGAAAGGACA 61.205 60.000 8.34 0.00 45.91 4.02
1875 2030 3.245264 ACCCAGGAAAGGACACTTATTGG 60.245 47.826 0.00 0.00 35.41 3.16
1957 2112 2.687297 AGAAGCATAGGGATCAGCTGA 58.313 47.619 20.79 20.79 37.41 4.26
1979 2134 4.008933 ACAGCCACAGGGTCGAGC 62.009 66.667 5.93 5.93 36.17 5.03
1980 2135 4.007644 CAGCCACAGGGTCGAGCA 62.008 66.667 17.59 0.00 36.17 4.26
2097 2252 9.243637 TGTTTCTTGTCATTACAATTTTACTGC 57.756 29.630 0.00 0.00 44.43 4.40
2127 2283 4.697352 GCTTTGTTGTCCACTCATACTCAT 59.303 41.667 0.00 0.00 0.00 2.90
2174 2330 7.035612 GGGTTTATTCTGATCATGGTTTCAAC 58.964 38.462 0.00 0.00 0.00 3.18
2270 2426 3.649073 TGTTACTGAGTTGATGGACACG 58.351 45.455 0.00 0.00 0.00 4.49
2312 2468 5.026462 CGCTCAAATCAATCATTGACTGAC 58.974 41.667 0.98 3.79 43.48 3.51
2335 2491 0.945265 CATTGCCAGGTTTGTTGCCG 60.945 55.000 0.00 0.00 0.00 5.69
2361 2517 4.082625 TGCTTGTGCCAAGATTCTTATGTG 60.083 41.667 16.28 0.00 38.71 3.21
2371 2527 6.127535 CCAAGATTCTTATGTGTTTGCTGGAT 60.128 38.462 0.00 0.00 0.00 3.41
2432 2588 5.582689 ATCGATTGACATGTACTCACAGA 57.417 39.130 0.00 0.00 38.30 3.41
2436 2592 5.578336 CGATTGACATGTACTCACAGATGTT 59.422 40.000 0.00 0.00 38.30 2.71
2526 2682 7.554835 ACATGTTGTGTTCTGTACCTTCTTTAA 59.445 33.333 0.00 0.00 38.01 1.52
2552 2708 9.606631 ATTCTTAGTTTAGGTTTATGAGCTCTG 57.393 33.333 16.19 0.00 37.30 3.35
2905 3061 5.250543 TCCTGGAAGAGATTACATCCAACAA 59.749 40.000 0.00 0.00 41.20 2.83
3010 3166 7.177216 TGTCTATTTGGAAGCTGTCAATCAATT 59.823 33.333 3.30 0.00 0.00 2.32
3163 3319 5.086888 AGAAGTTGTTTACTTTTACGCCG 57.913 39.130 0.00 0.00 47.00 6.46
3294 3455 6.013898 TCTGTGGATGTCTCTTCTCTTCAAAT 60.014 38.462 0.00 0.00 0.00 2.32
3354 3515 7.970061 GTGCAATACATTCTTAGCTTCAAATCA 59.030 33.333 0.00 0.00 0.00 2.57
3372 3534 7.662897 TCAAATCAACCATTTTTAGTACCACC 58.337 34.615 0.00 0.00 31.79 4.61
3603 3765 3.515104 TGTCTGATGGTGCAGTTGATCTA 59.485 43.478 0.00 0.00 37.20 1.98
3654 3816 1.824852 AGACGCATCACTGGTACATGA 59.175 47.619 0.00 0.00 38.20 3.07
3663 3825 2.744202 CACTGGTACATGAGCTTGAACC 59.256 50.000 0.00 0.00 38.20 3.62
3667 3829 2.488153 GGTACATGAGCTTGAACCAACC 59.512 50.000 0.00 0.00 0.00 3.77
3673 3835 3.211045 TGAGCTTGAACCAACCACTTAC 58.789 45.455 0.00 0.00 0.00 2.34
3715 3877 8.909708 TTACTATGGCTCAAAATCATTTTTCG 57.090 30.769 0.00 0.00 32.72 3.46
3912 4074 3.695830 AAGAGCCAAGGTTTGTATCGA 57.304 42.857 0.00 0.00 0.00 3.59
3988 4151 5.784177 ACAATGTGTCAGACGACTAATCTT 58.216 37.500 0.00 0.00 43.06 2.40
4030 4193 6.879458 GGAGGTTCATACAGACTTGTTATTGT 59.121 38.462 0.00 0.00 38.76 2.71
4097 4261 1.677637 TTGTGCCCGTTTGGAAACCC 61.678 55.000 0.00 0.00 37.49 4.11
4099 4263 1.152440 TGCCCGTTTGGAAACCCAT 60.152 52.632 0.00 0.00 37.49 4.00
4138 4302 9.261180 TCAGTAAGACTTTAGTTTGAGAACATG 57.739 33.333 0.00 0.00 38.26 3.21
4220 4385 3.434984 GCCAATTCTCTGTTGTCTCAGTC 59.565 47.826 0.00 0.00 36.85 3.51
4485 4651 4.333649 CGACATTTGTATGAGATGGCTTGT 59.666 41.667 0.00 0.00 35.65 3.16
4520 4689 8.203937 TGTATACCGGTTGATTGAATAAACTG 57.796 34.615 15.04 7.18 30.94 3.16
4543 4712 9.174166 ACTGTTCTTGTGTATCTAAAAACTTGT 57.826 29.630 0.00 0.00 0.00 3.16
4544 4713 9.438291 CTGTTCTTGTGTATCTAAAAACTTGTG 57.562 33.333 0.00 0.00 0.00 3.33
4592 4761 8.713971 ACATCCCATGTATATCTGAGTTAACAA 58.286 33.333 8.61 0.00 42.78 2.83
4632 4801 6.327154 TCTCAAGCATGTAATTTTGCATCTG 58.673 36.000 9.49 5.08 41.35 2.90
4647 4816 1.745320 ATCTGGTGCCCCGTCGTATC 61.745 60.000 0.00 0.00 0.00 2.24
4652 4821 1.750018 TGCCCCGTCGTATCGAAGA 60.750 57.895 6.65 0.00 45.75 2.87
4666 4835 7.537649 GTCGTATCGAAGATGCTGATACAATTA 59.462 37.037 10.97 0.00 45.12 1.40
4670 4839 5.119125 TCGAAGATGCTGATACAATTATGCG 59.881 40.000 0.00 0.00 0.00 4.73
4681 4850 3.694734 ACAATTATGCGCTGAAATTCCG 58.305 40.909 9.73 4.10 0.00 4.30
4688 4857 1.069227 GCGCTGAAATTCCGTTCACTT 60.069 47.619 0.00 0.00 33.92 3.16
4705 4874 3.904965 TCACTTGTAGGTGTATCCCACAA 59.095 43.478 0.00 0.00 46.44 3.33
4716 4885 5.329493 GTGTATCCCACAATAAAAGTTCGC 58.671 41.667 0.00 0.00 43.92 4.70
4751 4920 7.697691 TCTACGCACTAGTACTTGGTTATTAC 58.302 38.462 0.00 0.00 0.00 1.89
4752 4921 6.521151 ACGCACTAGTACTTGGTTATTACT 57.479 37.500 0.00 0.00 0.00 2.24
4753 4922 6.558909 ACGCACTAGTACTTGGTTATTACTC 58.441 40.000 0.00 0.00 0.00 2.59
4797 4969 0.740868 CATGAACGCATGGTCGAGGT 60.741 55.000 0.00 0.00 46.45 3.85
4798 4970 0.460284 ATGAACGCATGGTCGAGGTC 60.460 55.000 0.00 0.00 32.31 3.85
4808 4980 4.142227 GCATGGTCGAGGTCTAGAAAGTTA 60.142 45.833 0.00 0.00 0.00 2.24
4813 4985 5.532032 GGTCGAGGTCTAGAAAGTTATAGCT 59.468 44.000 0.00 0.00 0.00 3.32
4816 4988 6.262720 TCGAGGTCTAGAAAGTTATAGCTTCC 59.737 42.308 1.99 0.00 0.00 3.46
4843 5015 4.677673 ATTTGGCAAAAGCTCTTCAAGT 57.322 36.364 17.70 0.00 0.00 3.16
4860 5032 1.981256 AGTTCAAGCCATTCACCGTT 58.019 45.000 0.00 0.00 0.00 4.44
4861 5033 1.608590 AGTTCAAGCCATTCACCGTTG 59.391 47.619 0.00 0.00 0.00 4.10
4862 5034 0.958091 TTCAAGCCATTCACCGTTGG 59.042 50.000 0.00 0.00 36.03 3.77
4863 5035 0.893270 TCAAGCCATTCACCGTTGGG 60.893 55.000 0.00 0.00 40.11 4.12
4874 5046 3.396951 CCGTTGGGTGAAGTCTGTT 57.603 52.632 0.00 0.00 0.00 3.16
4875 5047 1.675552 CCGTTGGGTGAAGTCTGTTT 58.324 50.000 0.00 0.00 0.00 2.83
4876 5048 2.021457 CCGTTGGGTGAAGTCTGTTTT 58.979 47.619 0.00 0.00 0.00 2.43
4877 5049 3.207778 CCGTTGGGTGAAGTCTGTTTTA 58.792 45.455 0.00 0.00 0.00 1.52
4878 5050 3.628487 CCGTTGGGTGAAGTCTGTTTTAA 59.372 43.478 0.00 0.00 0.00 1.52
4879 5051 4.096682 CCGTTGGGTGAAGTCTGTTTTAAA 59.903 41.667 0.00 0.00 0.00 1.52
4880 5052 5.032220 CGTTGGGTGAAGTCTGTTTTAAAC 58.968 41.667 0.20 0.20 0.00 2.01
4881 5053 5.345702 GTTGGGTGAAGTCTGTTTTAAACC 58.654 41.667 5.32 0.00 0.00 3.27
4882 5054 3.955551 TGGGTGAAGTCTGTTTTAAACCC 59.044 43.478 5.32 0.00 45.21 4.11
4883 5055 4.212716 GGGTGAAGTCTGTTTTAAACCCT 58.787 43.478 5.32 0.00 42.32 4.34
4884 5056 4.037565 GGGTGAAGTCTGTTTTAAACCCTG 59.962 45.833 5.32 0.00 42.32 4.45
4885 5057 4.885325 GGTGAAGTCTGTTTTAAACCCTGA 59.115 41.667 5.32 0.00 0.00 3.86
4886 5058 5.358725 GGTGAAGTCTGTTTTAAACCCTGAA 59.641 40.000 5.32 0.00 0.00 3.02
4887 5059 6.263344 GTGAAGTCTGTTTTAAACCCTGAAC 58.737 40.000 5.32 0.00 0.00 3.18
4888 5060 6.095021 GTGAAGTCTGTTTTAAACCCTGAACT 59.905 38.462 5.32 0.00 0.00 3.01
4889 5061 6.317893 TGAAGTCTGTTTTAAACCCTGAACTC 59.682 38.462 5.32 3.10 0.00 3.01
4890 5062 4.814771 AGTCTGTTTTAAACCCTGAACTCG 59.185 41.667 5.32 0.00 0.00 4.18
4891 5063 4.573607 GTCTGTTTTAAACCCTGAACTCGT 59.426 41.667 5.32 0.00 0.00 4.18
4892 5064 5.754890 GTCTGTTTTAAACCCTGAACTCGTA 59.245 40.000 5.32 0.00 0.00 3.43
4893 5065 6.426025 GTCTGTTTTAAACCCTGAACTCGTAT 59.574 38.462 5.32 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 5.122554 TGGGTTAACATAGTTGCATGTTACG 59.877 40.000 9.57 0.00 46.10 3.18
115 116 9.886132 GTATGTAATCCATATTTAGGAACGGAT 57.114 33.333 0.00 0.00 38.29 4.18
166 192 7.383102 ACGAAGCAAAATGAGTGAATCTAAT 57.617 32.000 0.00 0.00 0.00 1.73
193 219 7.174253 CCTTCTAGAGATGTCAGTATGGACTAC 59.826 44.444 0.00 0.00 38.61 2.73
198 224 4.021544 GCCCTTCTAGAGATGTCAGTATGG 60.022 50.000 0.00 0.00 36.16 2.74
215 241 6.887002 CCCTCCATTTCTAATATAAGCCCTTC 59.113 42.308 0.00 0.00 0.00 3.46
229 255 5.501156 GTTGATGTTACTCCCTCCATTTCT 58.499 41.667 0.00 0.00 0.00 2.52
230 256 4.640647 GGTTGATGTTACTCCCTCCATTTC 59.359 45.833 0.00 0.00 0.00 2.17
234 261 2.626785 TGGTTGATGTTACTCCCTCCA 58.373 47.619 0.00 0.00 0.00 3.86
235 262 3.054361 ACATGGTTGATGTTACTCCCTCC 60.054 47.826 0.00 0.00 43.20 4.30
268 296 2.814023 TTTTTCCATGCACGGTGGT 58.186 47.368 10.60 0.00 37.96 4.16
428 481 9.729023 TGAACCATTAATGTTTATATTCGCAAG 57.271 29.630 14.25 0.00 0.00 4.01
439 492 9.369904 GATTGCTTGTATGAACCATTAATGTTT 57.630 29.630 14.25 6.31 0.00 2.83
440 493 8.530311 TGATTGCTTGTATGAACCATTAATGTT 58.470 29.630 14.25 8.51 0.00 2.71
441 494 8.065473 TGATTGCTTGTATGAACCATTAATGT 57.935 30.769 14.25 0.00 0.00 2.71
442 495 9.537192 AATGATTGCTTGTATGAACCATTAATG 57.463 29.630 8.58 8.58 0.00 1.90
446 499 9.941325 TTTAAATGATTGCTTGTATGAACCATT 57.059 25.926 0.00 0.00 0.00 3.16
568 654 8.352942 CCTTTATTGTAAGAAACTGCAAAGACT 58.647 33.333 0.00 0.00 0.00 3.24
660 747 0.032540 ACTTCGGTTCGTACACACCC 59.967 55.000 5.12 0.00 0.00 4.61
706 819 7.958053 AATTTATTGCTGTATACTCCGTACC 57.042 36.000 4.17 0.00 0.00 3.34
719 833 5.890334 TCCCTTTCGCTTAATTTATTGCTG 58.110 37.500 0.00 0.00 0.00 4.41
826 945 1.355718 GGGGAATGAGGATGGGAGCA 61.356 60.000 0.00 0.00 0.00 4.26
1586 1710 3.185188 CACCGAGCAATCACTATACATGC 59.815 47.826 0.00 0.00 37.28 4.06
1626 1750 4.920340 TGTAAAACACACAGCAAACACTTG 59.080 37.500 0.00 0.00 31.60 3.16
1758 1882 6.262496 TCTCTATAACCAGAAGTACATGACCG 59.738 42.308 0.00 0.00 0.00 4.79
1829 1984 3.445857 GGCCGTACTCTGAGATTTACAC 58.554 50.000 12.44 0.00 0.00 2.90
1862 2017 8.325787 TGTACATAATCAACCAATAAGTGTCCT 58.674 33.333 0.00 0.00 0.00 3.85
1863 2018 8.500753 TGTACATAATCAACCAATAAGTGTCC 57.499 34.615 0.00 0.00 0.00 4.02
1875 2030 9.507280 CAAAACCTCATCATGTACATAATCAAC 57.493 33.333 8.32 0.00 0.00 3.18
1895 2050 8.107399 AGAAGCTTAAGTATTACCACAAAACC 57.893 34.615 0.00 0.00 0.00 3.27
1957 2112 1.376466 GACCCTGTGGCTGTGATGT 59.624 57.895 0.00 0.00 33.59 3.06
1966 2121 2.821366 GCATGCTCGACCCTGTGG 60.821 66.667 11.37 0.00 37.80 4.17
1979 2134 3.120095 TCAGAGAAAATTGTCAGCGCATG 60.120 43.478 11.47 5.22 0.00 4.06
1980 2135 3.076621 TCAGAGAAAATTGTCAGCGCAT 58.923 40.909 11.47 0.00 0.00 4.73
2097 2252 1.270550 GTGGACAACAAAGCCCATCAG 59.729 52.381 0.00 0.00 0.00 2.90
2127 2283 5.305386 CCCATCATAGGAATGACTGACAGTA 59.695 44.000 8.41 0.00 44.79 2.74
2174 2330 3.697542 TGGCAAGAATCTGTGATCCAATG 59.302 43.478 0.00 0.00 0.00 2.82
2312 2468 0.673437 AACAAACCTGGCAATGGTCG 59.327 50.000 0.00 0.00 36.69 4.79
2361 2517 6.039616 TGTTTCAACTACAAATCCAGCAAAC 58.960 36.000 0.00 0.00 0.00 2.93
2432 2588 6.547510 AGAACTAAAGAAGGCACAGAAAACAT 59.452 34.615 0.00 0.00 0.00 2.71
2436 2592 6.204882 GCTAAGAACTAAAGAAGGCACAGAAA 59.795 38.462 0.00 0.00 0.00 2.52
2526 2682 9.606631 CAGAGCTCATAAACCTAAACTAAGAAT 57.393 33.333 17.77 0.00 0.00 2.40
2552 2708 8.028938 ACATGTAACTTATGATTGCTGGAAAAC 58.971 33.333 0.00 0.00 0.00 2.43
2695 2851 2.490903 CCCAAAGTCTGCAATCTTGAGG 59.509 50.000 4.21 8.67 0.00 3.86
2905 3061 9.533831 AAACCTACCTCAGTGATCAATTTTAAT 57.466 29.630 0.00 0.00 0.00 1.40
3010 3166 5.991933 AGCTCAGAAACAGACTCATCTTA 57.008 39.130 0.00 0.00 30.42 2.10
3310 3471 4.069304 TGCACAGAAACCAACCAGTATAC 58.931 43.478 0.00 0.00 0.00 1.47
3354 3515 5.336134 GCATTCGGTGGTACTAAAAATGGTT 60.336 40.000 9.82 0.00 0.00 3.67
3603 3765 5.645497 GTCAAACACCAGCATTCTCTCTAAT 59.355 40.000 0.00 0.00 0.00 1.73
3654 3816 2.218603 CGTAAGTGGTTGGTTCAAGCT 58.781 47.619 10.50 0.00 41.66 3.74
3673 3835 7.149031 GCCATAGTAAAGCAAACAAAACTAACG 60.149 37.037 0.00 0.00 0.00 3.18
3715 3877 1.085091 CAGAGCCTCATCAACTGCAC 58.915 55.000 0.00 0.00 0.00 4.57
3912 4074 8.036273 ACGAAATATTTTCAACCAGACGTATT 57.964 30.769 1.43 0.00 0.00 1.89
3988 4151 2.687297 CTCCTCAGGATTCCAGGATCA 58.313 52.381 11.25 0.00 35.70 2.92
4138 4302 8.251026 ACTTACAAATAGAATTTTAAGCAGGGC 58.749 33.333 0.00 0.00 0.00 5.19
4169 4334 4.326009 CACAAGAAACGTGGAAAAACAAGG 59.674 41.667 0.00 0.00 0.00 3.61
4220 4385 9.968870 AACCAAATGAAATGAAATTCAAAATGG 57.031 25.926 0.00 13.15 42.22 3.16
4247 4412 4.281941 GCTTGAATCCCTGGAAAAAGTCTT 59.718 41.667 0.00 0.00 0.00 3.01
4249 4414 3.829026 AGCTTGAATCCCTGGAAAAAGTC 59.171 43.478 0.00 0.00 0.00 3.01
4250 4415 3.849527 AGCTTGAATCCCTGGAAAAAGT 58.150 40.909 0.00 0.00 0.00 2.66
4251 4416 5.982890 TTAGCTTGAATCCCTGGAAAAAG 57.017 39.130 0.00 0.00 0.00 2.27
4485 4651 1.524961 CGGTATACAAGCCCAGGCA 59.475 57.895 12.03 0.00 44.88 4.75
4592 4761 9.321562 CATGCTTGAGATAATAAAAGGCAAATT 57.678 29.630 0.00 0.00 0.00 1.82
4594 4763 7.839907 ACATGCTTGAGATAATAAAAGGCAAA 58.160 30.769 6.60 0.00 0.00 3.68
4632 4801 2.948840 CTTCGATACGACGGGGCACC 62.949 65.000 0.00 0.00 42.25 5.01
4636 4805 0.663568 GCATCTTCGATACGACGGGG 60.664 60.000 0.00 0.00 34.89 5.73
4639 4808 2.384899 TCAGCATCTTCGATACGACG 57.615 50.000 0.00 0.00 34.89 5.12
4647 4816 5.311271 CGCATAATTGTATCAGCATCTTCG 58.689 41.667 0.00 0.00 0.00 3.79
4652 4821 4.067192 TCAGCGCATAATTGTATCAGCAT 58.933 39.130 11.47 0.00 0.00 3.79
4666 4835 1.135689 GTGAACGGAATTTCAGCGCAT 60.136 47.619 11.47 0.00 36.15 4.73
4670 4839 3.626028 ACAAGTGAACGGAATTTCAGC 57.374 42.857 0.00 0.00 36.15 4.26
4681 4850 4.546829 TGGGATACACCTACAAGTGAAC 57.453 45.455 0.00 0.00 40.34 3.18
4716 4885 4.611943 ACTAGTGCGTAGAATAGCATGTG 58.388 43.478 0.00 0.00 45.69 3.21
4752 4921 9.326413 GCTGTTTGTTAAGCTTAAGGATATAGA 57.674 33.333 19.16 0.00 36.47 1.98
4753 4922 9.109393 TGCTGTTTGTTAAGCTTAAGGATATAG 57.891 33.333 19.16 13.48 40.21 1.31
4771 4943 1.336148 ACCATGCGTTCATGCTGTTTG 60.336 47.619 0.03 0.00 46.69 2.93
4773 4945 0.523072 GACCATGCGTTCATGCTGTT 59.477 50.000 0.03 0.00 46.69 3.16
4797 4969 4.587684 CCCGGGAAGCTATAACTTTCTAGA 59.412 45.833 18.48 0.00 0.00 2.43
4798 4970 4.587684 TCCCGGGAAGCTATAACTTTCTAG 59.412 45.833 24.50 0.00 0.00 2.43
4808 4980 1.754201 GCCAAATTCCCGGGAAGCTAT 60.754 52.381 37.49 20.96 37.56 2.97
4813 4985 1.346068 CTTTTGCCAAATTCCCGGGAA 59.654 47.619 37.24 37.24 38.59 3.97
4816 4988 2.839629 GCTTTTGCCAAATTCCCGG 58.160 52.632 0.00 0.00 40.15 5.73
4843 5015 0.958091 CCAACGGTGAATGGCTTGAA 59.042 50.000 0.00 0.00 0.00 2.69
4860 5032 3.955551 GGGTTTAAAACAGACTTCACCCA 59.044 43.478 5.45 0.00 42.09 4.51
4861 5033 4.037565 CAGGGTTTAAAACAGACTTCACCC 59.962 45.833 5.45 1.04 42.74 4.61
4862 5034 4.885325 TCAGGGTTTAAAACAGACTTCACC 59.115 41.667 5.45 0.00 0.00 4.02
4863 5035 6.095021 AGTTCAGGGTTTAAAACAGACTTCAC 59.905 38.462 5.45 0.00 0.00 3.18
4864 5036 6.184789 AGTTCAGGGTTTAAAACAGACTTCA 58.815 36.000 5.45 0.00 0.00 3.02
4865 5037 6.511282 CGAGTTCAGGGTTTAAAACAGACTTC 60.511 42.308 5.45 2.67 0.00 3.01
4866 5038 5.296035 CGAGTTCAGGGTTTAAAACAGACTT 59.704 40.000 5.45 0.00 0.00 3.01
4867 5039 4.814771 CGAGTTCAGGGTTTAAAACAGACT 59.185 41.667 5.45 3.00 0.00 3.24
4868 5040 4.573607 ACGAGTTCAGGGTTTAAAACAGAC 59.426 41.667 5.45 0.00 0.00 3.51
4869 5041 4.773013 ACGAGTTCAGGGTTTAAAACAGA 58.227 39.130 5.45 0.00 0.00 3.41
4870 5042 6.796705 ATACGAGTTCAGGGTTTAAAACAG 57.203 37.500 5.45 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.