Multiple sequence alignment - TraesCS5B01G237000

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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 TraesCS5B01G237000 chr5B 100.000 4457 0 0 1 4457 418008365 418012821 0.000000e+00 8231.0
1 TraesCS5B01G237000 chr5D 96.205 3663 105 14 1 3646 353800457 353804102 0.000000e+00 5963.0
2 TraesCS5B01G237000 chr5D 92.522 575 17 15 3897 4457 353804147 353804709 0.000000e+00 800.0
3 TraesCS5B01G237000 chr5A 95.228 2976 115 8 837 3801 454766843 454769802 0.000000e+00 4684.0
4 TraesCS5B01G237000 chr5A 89.577 662 43 16 188 824 454766203 454766863 0.000000e+00 817.0
5 TraesCS5B01G237000 chr5A 87.923 679 30 17 3801 4457 454769768 454770416 0.000000e+00 752.0
6 TraesCS5B01G237000 chr5A 92.347 196 11 2 2 197 454764884 454765075 4.390000e-70 276.0
7 TraesCS5B01G237000 chr3A 89.300 486 21 6 1059 1529 543715934 543716403 8.310000e-162 580.0
8 TraesCS5B01G237000 chr7D 84.043 94 11 3 4118 4209 124165234 124165325 2.210000e-13 87.9
9 TraesCS5B01G237000 chr7B 84.043 94 11 3 4118 4209 85841583 85841674 2.210000e-13 87.9
10 TraesCS5B01G237000 chr7A 86.076 79 7 3 4133 4209 126792759 126792835 1.030000e-11 82.4


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 TraesCS5B01G237000 chr5B 418008365 418012821 4456 False 8231.00 8231 100.00000 1 4457 1 chr5B.!!$F1 4456
1 TraesCS5B01G237000 chr5D 353800457 353804709 4252 False 3381.50 5963 94.36350 1 4457 2 chr5D.!!$F1 4456
2 TraesCS5B01G237000 chr5A 454764884 454770416 5532 False 1632.25 4684 91.26875 2 4457 4 chr5A.!!$F1 4455

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
514 1659 0.400975 GGAGATCAGATGGCCAGCAT 59.599 55.000 25.38 8.92 0.00 3.79 F
541 1686 1.277580 ACCTGGCAGCTTGGCTAGAT 61.278 55.000 9.56 0.00 44.26 1.98 F
1871 3038 1.535028 AGAGCTCGCTGAGATACGATG 59.465 52.381 8.37 0.00 37.72 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 2661 0.463654 TCGGTGCTGCAGTTTCAACT 60.464 50.000 16.64 0.0 40.60 3.16 R
2386 3553 1.002544 CACTTCCTCTCCAACCTCACC 59.997 57.143 0.00 0.0 0.00 4.02 R
3735 4920 0.035439 TTCCACGCCTCTGGAAATCC 60.035 55.000 2.90 0.0 45.61 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
54 55 3.309296 CTGGATAGAGTGGGGCTTTCTA 58.691 50.000 0.00 0.00 0.00 2.10
63 64 1.064463 TGGGGCTTTCTATTGCTGGAG 60.064 52.381 0.00 0.00 0.00 3.86
123 124 4.159377 TCTTGCCTTTTATTTGTCGCTG 57.841 40.909 0.00 0.00 0.00 5.18
134 135 6.926280 TTATTTGTCGCTGTAATTGCTTTG 57.074 33.333 0.00 0.00 0.00 2.77
150 151 6.401955 TTGCTTTGCTTTGTTGTTAACTTC 57.598 33.333 7.22 0.72 0.00 3.01
245 1387 7.250569 ACATTAACATTCTCGGTAGCAATTTG 58.749 34.615 0.00 0.00 0.00 2.32
288 1430 7.002276 TGAAATGATAGATGAGGATTGCACAT 58.998 34.615 0.00 0.00 0.00 3.21
299 1441 7.677454 TGAGGATTGCACATGATATTACATC 57.323 36.000 0.00 0.00 0.00 3.06
345 1487 9.614792 AAACTATAAGCTCTTTACCTGGTATTG 57.385 33.333 7.50 4.00 0.00 1.90
357 1499 7.801716 TTACCTGGTATTGCACAATCTTATC 57.198 36.000 7.50 0.00 32.50 1.75
366 1508 6.985188 TTGCACAATCTTATCTAAGTGGAC 57.015 37.500 0.00 0.00 34.93 4.02
490 1635 4.420168 GAGATGCATAGCTTATCTCGTCC 58.580 47.826 0.00 0.00 37.97 4.79
514 1659 0.400975 GGAGATCAGATGGCCAGCAT 59.599 55.000 25.38 8.92 0.00 3.79
541 1686 1.277580 ACCTGGCAGCTTGGCTAGAT 61.278 55.000 9.56 0.00 44.26 1.98
590 1735 9.986833 GGCCAATTAACAACAAAAATATGAATC 57.013 29.630 0.00 0.00 0.00 2.52
658 1825 9.767684 CTGTTCATGTAAATATTAAAAGTGCGA 57.232 29.630 0.00 0.00 0.00 5.10
740 1907 6.969043 TGGACTTGATATATGGGAAGTGTTT 58.031 36.000 6.24 0.00 0.00 2.83
752 1919 5.009631 TGGGAAGTGTTTGAACTCATATGG 58.990 41.667 2.13 0.00 0.00 2.74
822 1989 5.832539 AGCAATGCTAACCTACCTCATAT 57.167 39.130 5.69 0.00 36.99 1.78
828 1995 8.367911 CAATGCTAACCTACCTCATATAGTTCA 58.632 37.037 0.00 0.00 0.00 3.18
829 1996 7.907841 TGCTAACCTACCTCATATAGTTCAA 57.092 36.000 0.00 0.00 0.00 2.69
869 2036 8.365647 ACCTACCTCATATAATTTTGGTAGTCG 58.634 37.037 13.67 4.69 43.05 4.18
1124 2291 2.675844 CTGTTGTTCCAAACACTGTCGA 59.324 45.455 0.00 0.00 41.97 4.20
1382 2549 4.706962 AGAGGAAAATTGTCATAACCAGCC 59.293 41.667 0.00 0.00 0.00 4.85
1388 2555 3.788227 TTGTCATAACCAGCCTGAAGT 57.212 42.857 0.00 0.00 0.00 3.01
1704 2871 1.675641 CAAGGTGCGGGAAGAAGGG 60.676 63.158 0.00 0.00 0.00 3.95
1871 3038 1.535028 AGAGCTCGCTGAGATACGATG 59.465 52.381 8.37 0.00 37.72 3.84
2386 3553 2.103941 GGGATACTGCCTGAGAAGGAAG 59.896 54.545 0.00 0.00 40.57 3.46
2441 3608 0.723981 GTTCAGATGAAGCTGGCGAC 59.276 55.000 0.00 0.00 36.55 5.19
2796 3963 0.179124 CAGACCGAGCTAAGGCAGAC 60.179 60.000 7.56 0.00 41.70 3.51
2844 4011 4.917906 AGCAGTTTCAAGGGAGATACTT 57.082 40.909 0.00 0.00 29.13 2.24
3039 4206 1.887707 GAAGCGGGTTATGGAGGCG 60.888 63.158 0.00 0.00 0.00 5.52
3103 4270 2.646930 TGGATAAGTTGCATCAGCTGG 58.353 47.619 15.13 0.00 42.74 4.85
3174 4341 5.534207 AATCCATCACAGCACAAGAAAAA 57.466 34.783 0.00 0.00 0.00 1.94
3279 4446 2.027745 TCCTGATGTCTGCCTTCTGAAC 60.028 50.000 0.00 0.00 0.00 3.18
3294 4464 2.810274 TCTGAACAGTGCATGCTCTTTC 59.190 45.455 19.25 21.79 0.00 2.62
3323 4493 1.546476 GGGATCGTCCGCTTCTCATAT 59.454 52.381 0.00 0.00 37.43 1.78
3333 4503 2.502295 GCTTCTCATATGCAAGGAGGG 58.498 52.381 13.28 7.20 0.00 4.30
3336 4506 1.061424 TCTCATATGCAAGGAGGGGGA 60.061 52.381 11.31 0.00 0.00 4.81
3337 4507 1.776667 CTCATATGCAAGGAGGGGGAA 59.223 52.381 0.00 0.00 0.00 3.97
3338 4508 1.494721 TCATATGCAAGGAGGGGGAAC 59.505 52.381 0.00 0.00 0.00 3.62
3341 4511 2.361737 GCAAGGAGGGGGAACAGC 60.362 66.667 0.00 0.00 0.00 4.40
3365 4535 1.000163 AGCTGACACTACCACGACAAG 60.000 52.381 0.00 0.00 0.00 3.16
3442 4612 6.051717 ACGATGTTCATGAATAGGAAGAAGG 58.948 40.000 12.12 0.00 0.00 3.46
3463 4633 1.087501 GCATTCGAAGTGAACCTCCC 58.912 55.000 3.35 0.00 40.00 4.30
3473 4643 2.303311 AGTGAACCTCCCTAGTTTGCTC 59.697 50.000 0.00 0.00 0.00 4.26
3521 4691 7.252708 TGTACATGTATCAAGTAGGTTACACG 58.747 38.462 9.18 0.00 0.00 4.49
3589 4763 1.009389 GGTTTCGTCGGTCTGAGCTG 61.009 60.000 5.23 0.00 0.00 4.24
3590 4764 0.318784 GTTTCGTCGGTCTGAGCTGT 60.319 55.000 5.23 0.00 0.00 4.40
3591 4765 0.039437 TTTCGTCGGTCTGAGCTGTC 60.039 55.000 5.23 0.00 0.00 3.51
3658 4843 3.345508 TCAGAAGCATGCATCTGAACT 57.654 42.857 39.31 17.54 44.44 3.01
3662 4847 3.439476 AGAAGCATGCATCTGAACTTGTC 59.561 43.478 23.73 1.87 0.00 3.18
3674 4859 5.412640 TCTGAACTTGTCGACAGTGTTTTA 58.587 37.500 27.58 21.20 0.00 1.52
3707 4892 8.604035 TCATTTAGCTTGACGATTTGTTATCTC 58.396 33.333 0.00 0.00 0.00 2.75
3723 4908 5.521372 TGTTATCTCTCACATGAGCATTTCG 59.479 40.000 0.00 0.00 41.80 3.46
3725 4910 1.329906 CTCTCACATGAGCATTTCGGC 59.670 52.381 0.00 0.00 41.80 5.54
3729 4914 1.091771 ACATGAGCATTTCGGCCTCG 61.092 55.000 0.00 0.00 37.82 4.63
3730 4915 2.182842 ATGAGCATTTCGGCCTCGC 61.183 57.895 0.00 0.00 36.13 5.03
3731 4916 2.512515 GAGCATTTCGGCCTCGCT 60.513 61.111 0.00 0.41 36.13 4.93
3732 4917 2.817423 GAGCATTTCGGCCTCGCTG 61.817 63.158 0.00 0.00 36.13 5.18
3733 4918 2.819595 GCATTTCGGCCTCGCTGA 60.820 61.111 0.00 0.00 42.66 4.26
3734 4919 2.182842 GCATTTCGGCCTCGCTGAT 61.183 57.895 0.00 0.00 43.86 2.90
3735 4920 1.645455 CATTTCGGCCTCGCTGATG 59.355 57.895 0.00 0.00 43.86 3.07
3736 4921 1.524621 ATTTCGGCCTCGCTGATGG 60.525 57.895 0.00 0.00 43.86 3.51
3737 4922 1.971505 ATTTCGGCCTCGCTGATGGA 61.972 55.000 0.00 0.00 43.86 3.41
3738 4923 1.971505 TTTCGGCCTCGCTGATGGAT 61.972 55.000 0.00 0.00 43.86 3.41
3739 4924 1.971505 TTCGGCCTCGCTGATGGATT 61.972 55.000 0.00 0.00 43.86 3.01
3740 4925 1.524621 CGGCCTCGCTGATGGATTT 60.525 57.895 0.00 0.00 37.02 2.17
3741 4926 1.502163 CGGCCTCGCTGATGGATTTC 61.502 60.000 0.00 0.00 37.02 2.17
3742 4927 1.169034 GGCCTCGCTGATGGATTTCC 61.169 60.000 0.00 0.00 0.00 3.13
3752 4937 1.299648 TGGATTTCCAGAGGCGTGG 59.700 57.895 2.71 2.71 42.01 4.94
3753 4938 1.198094 TGGATTTCCAGAGGCGTGGA 61.198 55.000 7.47 7.47 45.37 4.02
3783 4968 4.284178 ACTGCTCCCAGAATGCAAATTAT 58.716 39.130 0.00 0.00 41.77 1.28
3784 4969 4.713321 ACTGCTCCCAGAATGCAAATTATT 59.287 37.500 0.00 0.00 41.77 1.40
3785 4970 5.893255 ACTGCTCCCAGAATGCAAATTATTA 59.107 36.000 0.00 0.00 41.77 0.98
3786 4971 6.380846 ACTGCTCCCAGAATGCAAATTATTAA 59.619 34.615 0.00 0.00 41.77 1.40
3787 4972 6.808829 TGCTCCCAGAATGCAAATTATTAAG 58.191 36.000 0.00 0.00 33.48 1.85
3788 4973 6.380846 TGCTCCCAGAATGCAAATTATTAAGT 59.619 34.615 0.00 0.00 33.48 2.24
3789 4974 6.920210 GCTCCCAGAATGCAAATTATTAAGTC 59.080 38.462 0.00 0.00 31.97 3.01
3790 4975 7.346751 TCCCAGAATGCAAATTATTAAGTCC 57.653 36.000 0.00 0.00 31.97 3.85
3791 4976 6.894654 TCCCAGAATGCAAATTATTAAGTCCA 59.105 34.615 0.00 0.00 31.97 4.02
3792 4977 7.398618 TCCCAGAATGCAAATTATTAAGTCCAA 59.601 33.333 0.00 0.00 31.97 3.53
3793 4978 8.040132 CCCAGAATGCAAATTATTAAGTCCAAA 58.960 33.333 0.00 0.00 31.97 3.28
3794 4979 9.434420 CCAGAATGCAAATTATTAAGTCCAAAA 57.566 29.630 0.00 0.00 31.97 2.44
3804 4989 9.762381 AATTATTAAGTCCAAAATACAGTCCCA 57.238 29.630 0.00 0.00 0.00 4.37
3805 4990 8.801882 TTATTAAGTCCAAAATACAGTCCCAG 57.198 34.615 0.00 0.00 0.00 4.45
3806 4991 4.993705 AAGTCCAAAATACAGTCCCAGA 57.006 40.909 0.00 0.00 0.00 3.86
3807 4992 4.993705 AGTCCAAAATACAGTCCCAGAA 57.006 40.909 0.00 0.00 0.00 3.02
3808 4993 5.520748 AGTCCAAAATACAGTCCCAGAAT 57.479 39.130 0.00 0.00 0.00 2.40
3809 4994 5.256474 AGTCCAAAATACAGTCCCAGAATG 58.744 41.667 0.00 0.00 33.62 2.67
3810 4995 4.016444 TCCAAAATACAGTCCCAGAATGC 58.984 43.478 0.00 0.00 30.24 3.56
3811 4996 3.763360 CCAAAATACAGTCCCAGAATGCA 59.237 43.478 0.00 0.00 30.24 3.96
3812 4997 4.220382 CCAAAATACAGTCCCAGAATGCAA 59.780 41.667 0.00 0.00 30.24 4.08
3813 4998 5.279406 CCAAAATACAGTCCCAGAATGCAAA 60.279 40.000 0.00 0.00 30.24 3.68
3814 4999 6.400568 CAAAATACAGTCCCAGAATGCAAAT 58.599 36.000 0.00 0.00 30.24 2.32
3883 5076 5.999205 ATAAAATGAAATGTGCTGGGTCA 57.001 34.783 0.00 0.00 0.00 4.02
3884 5077 3.665745 AAATGAAATGTGCTGGGTCAC 57.334 42.857 0.00 0.00 37.48 3.67
3890 5083 3.698250 TGTGCTGGGTCACAACTAC 57.302 52.632 0.00 0.00 43.27 2.73
3891 5084 0.833949 TGTGCTGGGTCACAACTACA 59.166 50.000 0.00 0.00 43.27 2.74
3892 5085 1.202639 TGTGCTGGGTCACAACTACAG 60.203 52.381 0.00 0.00 43.27 2.74
3893 5086 1.128200 TGCTGGGTCACAACTACAGT 58.872 50.000 0.00 0.00 34.77 3.55
3894 5087 2.036733 GTGCTGGGTCACAACTACAGTA 59.963 50.000 0.00 0.00 36.97 2.74
3895 5088 2.903784 TGCTGGGTCACAACTACAGTAT 59.096 45.455 0.00 0.00 34.77 2.12
3962 5169 9.730420 ACAGTATTATTCTTGTTTGAACACAAC 57.270 29.630 0.00 0.00 38.92 3.32
3963 5170 9.950680 CAGTATTATTCTTGTTTGAACACAACT 57.049 29.630 0.00 0.00 38.92 3.16
3969 5176 6.417191 TCTTGTTTGAACACAACTACAGAC 57.583 37.500 0.00 0.00 38.92 3.51
4008 5215 2.783135 TGAATCACTCTGCAACCCTTC 58.217 47.619 0.00 0.00 0.00 3.46
4025 5232 4.770531 ACCCTTCCCTGCTTGTAAATTTAC 59.229 41.667 19.44 19.44 0.00 2.01
4030 5237 3.086282 CCTGCTTGTAAATTTACGGGGT 58.914 45.455 20.51 0.00 36.45 4.95
4035 5242 5.099575 GCTTGTAAATTTACGGGGTCATTG 58.900 41.667 20.51 6.46 36.45 2.82
4039 5246 5.416326 TGTAAATTTACGGGGTCATTGGAAG 59.584 40.000 20.51 0.00 36.45 3.46
4040 5247 1.828979 TTTACGGGGTCATTGGAAGC 58.171 50.000 0.00 0.00 0.00 3.86
4041 5248 0.988832 TTACGGGGTCATTGGAAGCT 59.011 50.000 0.00 0.00 0.00 3.74
4043 5250 0.252197 ACGGGGTCATTGGAAGCTAC 59.748 55.000 0.00 0.00 0.00 3.58
4044 5251 0.463833 CGGGGTCATTGGAAGCTACC 60.464 60.000 0.00 0.00 0.00 3.18
4045 5252 0.919710 GGGGTCATTGGAAGCTACCT 59.080 55.000 0.00 0.00 0.00 3.08
4046 5253 1.408822 GGGGTCATTGGAAGCTACCTG 60.409 57.143 0.00 0.00 0.00 4.00
4047 5254 1.408822 GGGTCATTGGAAGCTACCTGG 60.409 57.143 0.00 0.00 0.00 4.45
4048 5255 1.383523 GTCATTGGAAGCTACCTGGC 58.616 55.000 0.00 0.00 0.00 4.85
4049 5256 0.255890 TCATTGGAAGCTACCTGGCC 59.744 55.000 0.00 0.00 0.00 5.36
4060 5267 2.009774 CTACCTGGCCAAAATCAGTCG 58.990 52.381 7.01 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.832912 CCCCACTCTATCCAGGTGC 59.167 63.158 0.00 0.00 0.00 5.01
54 55 4.147321 ACAATTTGACAGTCTCCAGCAAT 58.853 39.130 2.79 0.00 0.00 3.56
63 64 4.044426 GGTCTTGCAACAATTTGACAGTC 58.956 43.478 14.06 0.00 34.24 3.51
95 96 7.201350 GCGACAAATAAAAGGCAAGATTGTTAG 60.201 37.037 0.00 0.00 30.37 2.34
123 124 7.905126 AGTTAACAACAAAGCAAAGCAATTAC 58.095 30.769 8.61 0.00 0.00 1.89
134 135 2.390938 GGCCGAAGTTAACAACAAAGC 58.609 47.619 8.61 2.87 0.00 3.51
221 1359 7.471721 TCAAATTGCTACCGAGAATGTTAATG 58.528 34.615 0.00 0.00 0.00 1.90
229 1371 3.188460 GCACTTCAAATTGCTACCGAGAA 59.812 43.478 0.00 0.00 35.74 2.87
245 1387 4.836125 TTCACATTCTTCCTTGCACTTC 57.164 40.909 0.00 0.00 0.00 3.01
251 1393 9.117183 TCATCTATCATTTCACATTCTTCCTTG 57.883 33.333 0.00 0.00 0.00 3.61
288 1430 6.645003 GCATCAACCTGTACGATGTAATATCA 59.355 38.462 8.77 0.00 39.00 2.15
299 1441 4.481930 TTGAAAAGCATCAACCTGTACG 57.518 40.909 0.00 0.00 34.50 3.67
345 1487 4.025647 GCGTCCACTTAGATAAGATTGTGC 60.026 45.833 6.61 1.99 37.08 4.57
357 1499 2.094700 TCTAGCTTGTGCGTCCACTTAG 60.095 50.000 0.00 0.00 45.42 2.18
366 1508 0.527600 TGGCGTATCTAGCTTGTGCG 60.528 55.000 0.00 0.00 45.42 5.34
444 1587 6.272324 TCCATGAACTCGGGATAAGGAATATT 59.728 38.462 0.00 0.00 0.00 1.28
449 1592 2.965831 CTCCATGAACTCGGGATAAGGA 59.034 50.000 0.00 0.00 0.00 3.36
490 1635 0.883814 GGCCATCTGATCTCCAAGCG 60.884 60.000 0.00 0.00 0.00 4.68
514 1659 2.595463 GCTGCCAGGTCAACTGCA 60.595 61.111 0.00 0.00 46.14 4.41
541 1686 3.808466 TTGTGCTGGCAAAAATACACA 57.192 38.095 0.00 0.00 36.33 3.72
637 1804 9.729023 TCCATTCGCACTTTTAATATTTACATG 57.271 29.630 0.00 0.00 0.00 3.21
647 1814 6.205784 CAGAAAACTCCATTCGCACTTTTAA 58.794 36.000 0.00 0.00 32.04 1.52
658 1825 4.534103 AGAGCTCTACCAGAAAACTCCATT 59.466 41.667 16.50 0.00 0.00 3.16
869 2036 7.696872 GCATGCTGATATATGTTCATGAATCAC 59.303 37.037 12.12 0.00 34.79 3.06
1124 2291 4.487714 TCAGTCAAGTTTTCCAGTGAGT 57.512 40.909 0.00 0.00 0.00 3.41
1382 2549 4.963276 TGTTGTTGTTCCTTCACTTCAG 57.037 40.909 0.00 0.00 0.00 3.02
1388 2555 6.491394 CGACTAATTTGTTGTTGTTCCTTCA 58.509 36.000 0.00 0.00 0.00 3.02
1494 2661 0.463654 TCGGTGCTGCAGTTTCAACT 60.464 50.000 16.64 0.00 40.60 3.16
1704 2871 1.404843 ATCTTCTCTGGTACTCGGGC 58.595 55.000 0.00 0.00 0.00 6.13
1871 3038 2.436417 TGCCCTGTTGTATCTCTTTGC 58.564 47.619 0.00 0.00 0.00 3.68
1972 3139 5.105513 GCTCTAGCTCCTCTTTAACTGACTT 60.106 44.000 0.00 0.00 38.21 3.01
2349 3516 6.169094 CAGTATCCCTTCCATATAAGCAGTG 58.831 44.000 0.00 0.00 0.00 3.66
2386 3553 1.002544 CACTTCCTCTCCAACCTCACC 59.997 57.143 0.00 0.00 0.00 4.02
2441 3608 1.674221 CCTCAAGCTCTTTCCTGGTCG 60.674 57.143 0.00 0.00 0.00 4.79
2844 4011 3.002791 CTCTTCTGATGCTTTAACCGCA 58.997 45.455 1.52 1.52 42.25 5.69
2889 4056 3.376546 CCTCCTCTTTGTATTCTTGCAGC 59.623 47.826 0.00 0.00 0.00 5.25
3039 4206 2.637947 GCCTCCTTGATCTTCTCAACC 58.362 52.381 0.00 0.00 38.97 3.77
3103 4270 4.381292 CCTCCTTTCATCAATCTGTTTGGC 60.381 45.833 0.00 0.00 35.92 4.52
3174 4341 3.437049 GCTCGCTCTCCATTGTTAACTTT 59.563 43.478 7.22 0.00 0.00 2.66
3191 4358 1.999024 CTCTTCTTTTCCTCAGCTCGC 59.001 52.381 0.00 0.00 0.00 5.03
3279 4446 4.072903 TGCATCGAAAGAGCATGCACTG 62.073 50.000 21.98 7.53 45.53 3.66
3294 4464 3.032609 GACGATCCCGCTGCATCG 61.033 66.667 16.29 16.29 46.03 3.84
3323 4493 3.170362 CTGTTCCCCCTCCTTGCA 58.830 61.111 0.00 0.00 0.00 4.08
3341 4511 2.096174 GTCGTGGTAGTGTCAGCTCTAG 59.904 54.545 0.00 0.00 0.00 2.43
3356 4526 1.009675 GTTGCTGCACTTGTCGTGG 60.010 57.895 0.00 0.00 43.97 4.94
3358 4528 0.461870 TCTGTTGCTGCACTTGTCGT 60.462 50.000 0.00 0.00 0.00 4.34
3365 4535 0.318445 CTTTGGCTCTGTTGCTGCAC 60.318 55.000 0.00 0.00 0.00 4.57
3442 4612 0.095417 GAGGTTCACTTCGAATGCGC 59.905 55.000 0.00 0.00 35.63 6.09
3550 4724 9.410556 CGAAACCAGATTTAATTTCTGAACAAT 57.589 29.630 14.45 0.00 42.63 2.71
3563 4737 3.256383 TCAGACCGACGAAACCAGATTTA 59.744 43.478 0.00 0.00 0.00 1.40
3589 4763 5.444663 AAGAGAAAAGATTGCAAGGTGAC 57.555 39.130 4.94 0.00 0.00 3.67
3590 4764 5.360714 ACAAAGAGAAAAGATTGCAAGGTGA 59.639 36.000 4.94 0.00 0.00 4.02
3591 4765 5.594926 ACAAAGAGAAAAGATTGCAAGGTG 58.405 37.500 4.94 0.00 0.00 4.00
3633 4815 4.524053 TCAGATGCATGCTTCTGATTCTT 58.476 39.130 40.95 18.56 45.82 2.52
3648 4833 2.156504 CACTGTCGACAAGTTCAGATGC 59.843 50.000 20.49 0.00 0.00 3.91
3650 4835 3.735237 ACACTGTCGACAAGTTCAGAT 57.265 42.857 20.49 0.00 0.00 2.90
3658 4843 6.109320 ACGAAAATAAAACACTGTCGACAA 57.891 33.333 20.49 2.65 0.00 3.18
3662 4847 7.603297 AAATGACGAAAATAAAACACTGTCG 57.397 32.000 0.00 0.00 0.00 4.35
3707 4892 0.379669 GGCCGAAATGCTCATGTGAG 59.620 55.000 5.66 5.66 44.75 3.51
3723 4908 1.169034 GGAAATCCATCAGCGAGGCC 61.169 60.000 0.00 0.00 35.64 5.19
3725 4910 1.139654 TCTGGAAATCCATCAGCGAGG 59.860 52.381 1.93 0.00 46.46 4.63
3729 4914 1.316651 GCCTCTGGAAATCCATCAGC 58.683 55.000 1.93 2.61 46.46 4.26
3730 4915 1.134280 ACGCCTCTGGAAATCCATCAG 60.134 52.381 1.93 2.45 46.46 2.90
3731 4916 0.911769 ACGCCTCTGGAAATCCATCA 59.088 50.000 1.93 0.00 46.46 3.07
3732 4917 1.303309 CACGCCTCTGGAAATCCATC 58.697 55.000 1.93 0.00 46.46 3.51
3733 4918 0.107017 CCACGCCTCTGGAAATCCAT 60.107 55.000 1.93 0.00 46.46 3.41
3734 4919 1.198094 TCCACGCCTCTGGAAATCCA 61.198 55.000 1.53 1.53 45.30 3.41
3735 4920 0.035439 TTCCACGCCTCTGGAAATCC 60.035 55.000 2.90 0.00 45.61 3.01
3736 4921 3.551259 TTCCACGCCTCTGGAAATC 57.449 52.632 2.90 0.00 45.61 2.17
3739 4924 3.068881 CCTTCCACGCCTCTGGAA 58.931 61.111 5.24 5.24 46.27 3.53
3740 4925 3.706373 GCCTTCCACGCCTCTGGA 61.706 66.667 0.00 0.00 38.66 3.86
3741 4926 3.672295 GAGCCTTCCACGCCTCTGG 62.672 68.421 0.00 0.00 0.00 3.86
3742 4927 1.323271 TAGAGCCTTCCACGCCTCTG 61.323 60.000 0.00 0.00 0.00 3.35
3743 4928 1.000486 TAGAGCCTTCCACGCCTCT 60.000 57.895 0.00 0.00 0.00 3.69
3744 4929 1.142097 GTAGAGCCTTCCACGCCTC 59.858 63.158 0.00 0.00 0.00 4.70
3745 4930 1.305381 AGTAGAGCCTTCCACGCCT 60.305 57.895 0.00 0.00 0.00 5.52
3746 4931 1.153549 CAGTAGAGCCTTCCACGCC 60.154 63.158 0.00 0.00 0.00 5.68
3747 4932 1.811679 GCAGTAGAGCCTTCCACGC 60.812 63.158 0.00 0.00 0.00 5.34
3748 4933 0.179124 GAGCAGTAGAGCCTTCCACG 60.179 60.000 0.00 0.00 34.23 4.94
3749 4934 0.176910 GGAGCAGTAGAGCCTTCCAC 59.823 60.000 0.00 0.00 31.23 4.02
3750 4935 0.978146 GGGAGCAGTAGAGCCTTCCA 60.978 60.000 0.00 0.00 32.19 3.53
3751 4936 0.978146 TGGGAGCAGTAGAGCCTTCC 60.978 60.000 0.00 0.00 34.23 3.46
3752 4937 0.463620 CTGGGAGCAGTAGAGCCTTC 59.536 60.000 0.00 0.00 34.23 3.46
3753 4938 0.041833 TCTGGGAGCAGTAGAGCCTT 59.958 55.000 0.00 0.00 34.23 4.35
3783 4968 6.442541 TCTGGGACTGTATTTTGGACTTAA 57.557 37.500 0.00 0.00 0.00 1.85
3784 4969 6.442541 TTCTGGGACTGTATTTTGGACTTA 57.557 37.500 0.00 0.00 0.00 2.24
3785 4970 4.993705 TCTGGGACTGTATTTTGGACTT 57.006 40.909 0.00 0.00 0.00 3.01
3786 4971 4.993705 TTCTGGGACTGTATTTTGGACT 57.006 40.909 0.00 0.00 0.00 3.85
3787 4972 4.142381 GCATTCTGGGACTGTATTTTGGAC 60.142 45.833 0.00 0.00 0.00 4.02
3788 4973 4.016444 GCATTCTGGGACTGTATTTTGGA 58.984 43.478 0.00 0.00 0.00 3.53
3789 4974 3.763360 TGCATTCTGGGACTGTATTTTGG 59.237 43.478 0.00 0.00 0.00 3.28
3790 4975 5.389859 TTGCATTCTGGGACTGTATTTTG 57.610 39.130 0.00 0.00 0.00 2.44
3791 4976 6.610075 ATTTGCATTCTGGGACTGTATTTT 57.390 33.333 0.00 0.00 0.00 1.82
3792 4977 6.610075 AATTTGCATTCTGGGACTGTATTT 57.390 33.333 0.00 0.00 0.00 1.40
3793 4978 7.397192 ACTTAATTTGCATTCTGGGACTGTATT 59.603 33.333 0.00 0.00 0.00 1.89
3794 4979 6.891908 ACTTAATTTGCATTCTGGGACTGTAT 59.108 34.615 0.00 0.00 0.00 2.29
3795 4980 6.245408 ACTTAATTTGCATTCTGGGACTGTA 58.755 36.000 0.00 0.00 0.00 2.74
3796 4981 5.079643 ACTTAATTTGCATTCTGGGACTGT 58.920 37.500 0.00 0.00 0.00 3.55
3797 4982 5.393461 GGACTTAATTTGCATTCTGGGACTG 60.393 44.000 0.00 0.00 0.00 3.51
3798 4983 4.706962 GGACTTAATTTGCATTCTGGGACT 59.293 41.667 0.00 0.00 0.00 3.85
3799 4984 4.462483 TGGACTTAATTTGCATTCTGGGAC 59.538 41.667 0.00 0.00 0.00 4.46
3800 4985 4.671831 TGGACTTAATTTGCATTCTGGGA 58.328 39.130 0.00 0.00 0.00 4.37
3801 4986 5.404466 TTGGACTTAATTTGCATTCTGGG 57.596 39.130 0.00 0.00 0.00 4.45
3802 4987 7.727331 TTTTTGGACTTAATTTGCATTCTGG 57.273 32.000 0.00 0.00 0.00 3.86
3854 5039 8.872845 CCCAGCACATTTCATTTTATTCTAAAC 58.127 33.333 0.00 0.00 0.00 2.01
3859 5044 6.311200 GTGACCCAGCACATTTCATTTTATTC 59.689 38.462 0.00 0.00 38.63 1.75
3876 5069 6.761714 GGAATAATACTGTAGTTGTGACCCAG 59.238 42.308 0.00 0.00 33.65 4.45
3883 5076 8.863872 AGCAAAAGGAATAATACTGTAGTTGT 57.136 30.769 0.00 0.00 0.00 3.32
3886 5079 9.953565 TGTAAGCAAAAGGAATAATACTGTAGT 57.046 29.630 0.00 0.00 0.00 2.73
3888 5081 9.953565 ACTGTAAGCAAAAGGAATAATACTGTA 57.046 29.630 0.00 0.00 37.60 2.74
3889 5082 8.863872 ACTGTAAGCAAAAGGAATAATACTGT 57.136 30.769 0.00 0.00 37.60 3.55
3895 5088 9.781633 TGTACTTACTGTAAGCAAAAGGAATAA 57.218 29.630 23.74 0.00 39.39 1.40
3911 5104 9.807386 GTAGTTGTTTTGCTAATGTACTTACTG 57.193 33.333 0.00 0.00 0.00 2.74
3947 5152 6.176975 TGTCTGTAGTTGTGTTCAAACAAG 57.823 37.500 0.00 0.00 40.60 3.16
3959 5166 5.121611 TGTTGTGTGAACTTGTCTGTAGTTG 59.878 40.000 0.00 0.00 36.04 3.16
3960 5167 5.121768 GTGTTGTGTGAACTTGTCTGTAGTT 59.878 40.000 0.00 0.00 38.49 2.24
3961 5168 4.630069 GTGTTGTGTGAACTTGTCTGTAGT 59.370 41.667 0.00 0.00 0.00 2.73
3962 5169 4.034048 GGTGTTGTGTGAACTTGTCTGTAG 59.966 45.833 0.00 0.00 0.00 2.74
3963 5170 3.936453 GGTGTTGTGTGAACTTGTCTGTA 59.064 43.478 0.00 0.00 0.00 2.74
3964 5171 2.747446 GGTGTTGTGTGAACTTGTCTGT 59.253 45.455 0.00 0.00 0.00 3.41
3965 5172 2.746904 TGGTGTTGTGTGAACTTGTCTG 59.253 45.455 0.00 0.00 0.00 3.51
3969 5176 4.368874 TCAATGGTGTTGTGTGAACTTG 57.631 40.909 0.00 0.00 0.00 3.16
4008 5215 2.425668 CCCCGTAAATTTACAAGCAGGG 59.574 50.000 24.27 23.10 33.28 4.45
4025 5232 0.463833 GGTAGCTTCCAATGACCCCG 60.464 60.000 4.19 0.00 0.00 5.73
4030 5237 0.255890 GGCCAGGTAGCTTCCAATGA 59.744 55.000 12.41 0.00 0.00 2.57
4035 5242 1.751351 GATTTTGGCCAGGTAGCTTCC 59.249 52.381 5.11 0.07 0.00 3.46
4039 5246 1.745653 GACTGATTTTGGCCAGGTAGC 59.254 52.381 5.11 0.00 34.85 3.58
4040 5247 2.009774 CGACTGATTTTGGCCAGGTAG 58.990 52.381 5.11 4.29 34.85 3.18
4041 5248 1.626321 TCGACTGATTTTGGCCAGGTA 59.374 47.619 5.11 0.00 34.85 3.08
4043 5250 1.533625 TTCGACTGATTTTGGCCAGG 58.466 50.000 5.11 0.00 34.85 4.45
4044 5251 3.941483 ACTATTCGACTGATTTTGGCCAG 59.059 43.478 5.11 0.00 36.53 4.85
4045 5252 3.950397 ACTATTCGACTGATTTTGGCCA 58.050 40.909 0.00 0.00 0.00 5.36
4046 5253 4.965119 AACTATTCGACTGATTTTGGCC 57.035 40.909 0.00 0.00 0.00 5.36
4047 5254 5.938322 TCAAACTATTCGACTGATTTTGGC 58.062 37.500 0.00 0.00 0.00 4.52
4048 5255 6.546395 CCTCAAACTATTCGACTGATTTTGG 58.454 40.000 0.00 0.00 0.00 3.28
4049 5256 6.024049 GCCTCAAACTATTCGACTGATTTTG 58.976 40.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.