Multiple sequence alignment - TraesCS5D01G401100

Loading Multiple Alignment...

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 TraesCS5D01G401100 chr5D 100.000 5970 0 0 1 5970 466224939 466230908 0.000000e+00 11025.0
1 TraesCS5D01G401100 chr5B 93.234 6015 266 55 2 5970 573220701 573226620 0.000000e+00 8722.0
2 TraesCS5D01G401100 chr5A 94.143 5173 194 41 848 5970 586599783 586604896 0.000000e+00 7773.0
3 TraesCS5D01G401100 chr5A 94.423 789 24 9 2 786 586598981 586599753 0.000000e+00 1195.0
4 TraesCS5D01G401100 chr5A 87.850 535 29 16 5087 5602 538233016 538232499 3.980000e-166 595.0
5 TraesCS5D01G401100 chr6A 86.059 538 39 15 5088 5606 218851049 218850529 4.070000e-151 545.0
6 TraesCS5D01G401100 chr3A 85.981 535 37 17 5087 5602 380636011 380636526 6.810000e-149 538.0
7 TraesCS5D01G401100 chr7D 86.885 61 6 2 2046 2105 607448493 607448434 3.860000e-07 67.6


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 TraesCS5D01G401100 chr5D 466224939 466230908 5969 False 11025 11025 100.000 1 5970 1 chr5D.!!$F1 5969
1 TraesCS5D01G401100 chr5B 573220701 573226620 5919 False 8722 8722 93.234 2 5970 1 chr5B.!!$F1 5968
2 TraesCS5D01G401100 chr5A 586598981 586604896 5915 False 4484 7773 94.283 2 5970 2 chr5A.!!$F1 5968
3 TraesCS5D01G401100 chr5A 538232499 538233016 517 True 595 595 87.850 5087 5602 1 chr5A.!!$R1 515
4 TraesCS5D01G401100 chr6A 218850529 218851049 520 True 545 545 86.059 5088 5606 1 chr6A.!!$R1 518
5 TraesCS5D01G401100 chr3A 380636011 380636526 515 False 538 538 85.981 5087 5602 1 chr3A.!!$F1 515

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
619 622 1.988107 TGATGGTTGAGGAGGAGCTTT 59.012 47.619 0.00 0.0 0.00 3.51 F
1308 1339 0.815734 TACCAGAACTACTGCGCCTC 59.184 55.000 4.18 0.0 44.52 4.70 F
1730 1764 0.102481 CCCTCCATGTTCGTAGGTCG 59.898 60.000 0.00 0.0 41.41 4.79 F
2057 2099 0.320374 TGCTACTCCCTGGTTGTTCG 59.680 55.000 0.00 0.0 0.00 3.95 F
2169 2215 0.326264 AATCGCTGGGAGCTGTTTCT 59.674 50.000 0.00 0.0 39.60 2.52 F
2170 2216 0.392193 ATCGCTGGGAGCTGTTTCTG 60.392 55.000 0.00 0.0 39.60 3.02 F
3988 4060 0.976641 TCTTCCGGACTGCTGTCAAT 59.023 50.000 23.12 0.0 44.61 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1636 0.295763 CACATCAACGACGCATCTCG 59.704 55.000 0.0 0.0 45.38 4.04 R
2255 2301 0.463620 GGAACCTGCAAACAGCCAAA 59.536 50.000 0.0 0.0 43.02 3.28 R
2939 2996 2.289444 TGGTCTGTCGAAATCCCACTTC 60.289 50.000 0.0 0.0 0.00 3.01 R
3540 3597 4.708726 AGAATCTGCAACATTACAAGGC 57.291 40.909 0.0 0.0 0.00 4.35 R
4075 4147 2.954318 AGCAGGATACATGGCATTTGAC 59.046 45.455 0.0 0.0 41.41 3.18 R
4083 4155 4.529769 TCCTATCTGAAGCAGGATACATGG 59.470 45.833 0.0 0.0 33.48 3.66 R
5504 5598 1.303309 GCTCATATGCACCTGGACAC 58.697 55.000 0.0 0.0 0.00 3.67 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
68 69 3.675698 GTCAGCTTGTAAGTGACAGTAGC 59.324 47.826 15.79 0.00 40.74 3.58
128 129 4.660168 AGATTGCCTGATGAGTTTTCTGT 58.340 39.130 0.00 0.00 0.00 3.41
480 481 4.087182 AGAGTAACTTCTGAATCCCGACA 58.913 43.478 0.00 0.00 0.00 4.35
525 527 2.417257 GCCATTGATTGGGCTGCGA 61.417 57.895 0.00 0.00 46.55 5.10
619 622 1.988107 TGATGGTTGAGGAGGAGCTTT 59.012 47.619 0.00 0.00 0.00 3.51
620 623 2.376518 TGATGGTTGAGGAGGAGCTTTT 59.623 45.455 0.00 0.00 0.00 2.27
694 698 4.842139 ACGAGTGAGCGATGAATAAAAC 57.158 40.909 0.00 0.00 34.83 2.43
700 704 7.955324 CGAGTGAGCGATGAATAAAACTAAAAA 59.045 33.333 0.00 0.00 0.00 1.94
723 727 2.980586 TGTGCTTGTGTTTTTCGATCG 58.019 42.857 9.36 9.36 0.00 3.69
739 743 2.159240 CGATCGATTCTCAGGTGGTTGA 60.159 50.000 10.26 0.00 0.00 3.18
750 754 3.077359 CAGGTGGTTGAGAATTCAGACC 58.923 50.000 8.44 12.20 36.18 3.85
774 778 6.403418 CCTTCAGTCTGATTTGAGATTCTTGC 60.403 42.308 2.68 0.00 0.00 4.01
786 790 6.309712 TGAGATTCTTGCTCTTCTGTTTTG 57.690 37.500 0.00 0.00 33.57 2.44
787 791 6.057533 TGAGATTCTTGCTCTTCTGTTTTGA 58.942 36.000 0.00 0.00 33.57 2.69
788 792 6.204301 TGAGATTCTTGCTCTTCTGTTTTGAG 59.796 38.462 0.00 0.00 33.57 3.02
789 793 5.472820 AGATTCTTGCTCTTCTGTTTTGAGG 59.527 40.000 0.00 0.00 0.00 3.86
790 794 4.422073 TCTTGCTCTTCTGTTTTGAGGA 57.578 40.909 0.00 0.00 0.00 3.71
792 796 5.192927 TCTTGCTCTTCTGTTTTGAGGAAA 58.807 37.500 0.00 0.00 37.62 3.13
793 797 5.829924 TCTTGCTCTTCTGTTTTGAGGAAAT 59.170 36.000 0.00 0.00 37.62 2.17
794 798 6.322201 TCTTGCTCTTCTGTTTTGAGGAAATT 59.678 34.615 0.00 0.00 37.62 1.82
795 799 6.076981 TGCTCTTCTGTTTTGAGGAAATTC 57.923 37.500 0.00 0.00 0.00 2.17
796 800 5.829924 TGCTCTTCTGTTTTGAGGAAATTCT 59.170 36.000 0.00 0.00 0.00 2.40
797 801 6.148264 GCTCTTCTGTTTTGAGGAAATTCTG 58.852 40.000 0.00 0.00 0.00 3.02
798 802 6.238869 GCTCTTCTGTTTTGAGGAAATTCTGT 60.239 38.462 0.00 0.00 0.00 3.41
799 803 7.645058 TCTTCTGTTTTGAGGAAATTCTGTT 57.355 32.000 0.00 0.00 0.00 3.16
801 805 8.531146 TCTTCTGTTTTGAGGAAATTCTGTTTT 58.469 29.630 0.00 0.00 0.00 2.43
802 806 9.154847 CTTCTGTTTTGAGGAAATTCTGTTTTT 57.845 29.630 0.00 0.00 0.00 1.94
855 884 5.376756 TTTTTGTGAGGGGTTACTACACT 57.623 39.130 0.00 0.00 33.41 3.55
856 885 5.376756 TTTTGTGAGGGGTTACTACACTT 57.623 39.130 0.00 0.00 33.41 3.16
857 886 6.497624 TTTTGTGAGGGGTTACTACACTTA 57.502 37.500 0.00 0.00 33.41 2.24
858 887 6.691255 TTTGTGAGGGGTTACTACACTTAT 57.309 37.500 0.00 0.00 33.41 1.73
859 888 7.795534 TTTGTGAGGGGTTACTACACTTATA 57.204 36.000 0.00 0.00 33.41 0.98
860 889 7.983166 TTGTGAGGGGTTACTACACTTATAT 57.017 36.000 0.00 0.00 33.41 0.86
861 890 9.491406 TTTGTGAGGGGTTACTACACTTATATA 57.509 33.333 0.00 0.00 33.41 0.86
862 891 9.664777 TTGTGAGGGGTTACTACACTTATATAT 57.335 33.333 0.00 0.00 33.41 0.86
863 892 9.085645 TGTGAGGGGTTACTACACTTATATATG 57.914 37.037 0.00 0.00 33.41 1.78
864 893 9.305555 GTGAGGGGTTACTACACTTATATATGA 57.694 37.037 2.80 0.00 0.00 2.15
865 894 9.886337 TGAGGGGTTACTACACTTATATATGAA 57.114 33.333 2.80 0.00 0.00 2.57
946 975 2.101917 GCCCATTAGACACTAGCCGTTA 59.898 50.000 0.00 0.00 0.00 3.18
1308 1339 0.815734 TACCAGAACTACTGCGCCTC 59.184 55.000 4.18 0.00 44.52 4.70
1518 1552 3.578456 CGCAAGGAATTCCACGCT 58.422 55.556 26.22 2.40 38.89 5.07
1602 1636 7.312657 TGTTTCTGATCATGCTAATCAGTTC 57.687 36.000 17.73 11.85 46.66 3.01
1604 1638 5.520376 TCTGATCATGCTAATCAGTTCGA 57.480 39.130 17.73 2.15 46.66 3.71
1701 1735 2.971330 CTGCTCCAAGAGGGACATCTAT 59.029 50.000 0.00 0.00 42.15 1.98
1730 1764 0.102481 CCCTCCATGTTCGTAGGTCG 59.898 60.000 0.00 0.00 41.41 4.79
1803 1837 3.627577 TCAGGTGTTCTGTTTCTTTGCTC 59.372 43.478 0.00 0.00 43.76 4.26
1808 1842 4.009675 TGTTCTGTTTCTTTGCTCTGTGT 58.990 39.130 0.00 0.00 0.00 3.72
1947 1981 1.965643 TGCCATCTTTGCAGAAGCTTT 59.034 42.857 0.00 0.00 42.74 3.51
2014 2050 7.667219 CCTCTGGCTGTTATTTGATTATATGGT 59.333 37.037 0.00 0.00 0.00 3.55
2040 2082 3.279116 TGCCACACTGCGACTTGC 61.279 61.111 0.00 0.00 46.70 4.01
2057 2099 0.320374 TGCTACTCCCTGGTTGTTCG 59.680 55.000 0.00 0.00 0.00 3.95
2061 2103 1.374252 CTCCCTGGTTGTTCGTCCG 60.374 63.158 0.00 0.00 0.00 4.79
2143 2189 6.950041 TGATGATTCCTTGAGGTCTTCATTTT 59.050 34.615 10.90 0.00 35.27 1.82
2168 2214 0.729690 GAATCGCTGGGAGCTGTTTC 59.270 55.000 0.00 0.00 39.60 2.78
2169 2215 0.326264 AATCGCTGGGAGCTGTTTCT 59.674 50.000 0.00 0.00 39.60 2.52
2170 2216 0.392193 ATCGCTGGGAGCTGTTTCTG 60.392 55.000 0.00 0.00 39.60 3.02
2181 2227 5.047235 GGGAGCTGTTTCTGTTAGTTCTCTA 60.047 44.000 0.00 0.00 0.00 2.43
2182 2228 6.351456 GGGAGCTGTTTCTGTTAGTTCTCTAT 60.351 42.308 0.00 0.00 0.00 1.98
2183 2229 7.147880 GGGAGCTGTTTCTGTTAGTTCTCTATA 60.148 40.741 0.00 0.00 0.00 1.31
2215 2261 9.444600 TTTCTACTGTATTTATTTCACCACCTC 57.555 33.333 0.00 0.00 0.00 3.85
2255 2301 4.307032 ACCACCTACAATTTCTGCTCAT 57.693 40.909 0.00 0.00 0.00 2.90
2263 2309 3.322828 ACAATTTCTGCTCATTTGGCTGT 59.677 39.130 0.00 0.00 0.00 4.40
2429 2476 7.202016 TGTCCTGCTTTACTTAAAACATGAG 57.798 36.000 0.00 0.00 0.00 2.90
2453 2502 1.825090 CTAAACAGTGGGATGCTGCA 58.175 50.000 4.13 4.13 37.47 4.41
2540 2589 4.755266 ACATTTTCCCGCTATGTACTCT 57.245 40.909 0.00 0.00 31.11 3.24
2543 2592 4.811969 TTTTCCCGCTATGTACTCTTCA 57.188 40.909 0.00 0.00 0.00 3.02
2704 2760 6.998074 TGTACTATGCATTAATTTGGCTAGCT 59.002 34.615 15.72 0.00 0.00 3.32
2956 3013 2.770164 AGGAAGTGGGATTTCGACAG 57.230 50.000 0.00 0.00 0.00 3.51
2962 3019 1.002087 GTGGGATTTCGACAGACCACT 59.998 52.381 16.10 0.00 43.70 4.00
2994 3051 4.282950 CAGCATGTGAAAGCGTAATGAT 57.717 40.909 0.00 0.00 35.48 2.45
2999 3056 7.433131 CAGCATGTGAAAGCGTAATGATAATTT 59.567 33.333 0.00 0.00 35.48 1.82
3077 3134 7.228507 CACAAACTATATGGCATAGGTTTGCTA 59.771 37.037 36.03 18.15 41.12 3.49
3524 3581 9.547753 TCTCTTGTATATTAGAACTGAATTGCC 57.452 33.333 0.00 0.00 0.00 4.52
3527 3584 9.888878 CTTGTATATTAGAACTGAATTGCCATG 57.111 33.333 0.00 0.00 0.00 3.66
3685 3757 7.161715 TGGTAGGGCCAAAAATCTATCTAAT 57.838 36.000 6.18 0.00 45.94 1.73
3686 3758 8.282801 TGGTAGGGCCAAAAATCTATCTAATA 57.717 34.615 6.18 0.00 45.94 0.98
3687 3759 8.900802 TGGTAGGGCCAAAAATCTATCTAATAT 58.099 33.333 6.18 0.00 45.94 1.28
3688 3760 9.397280 GGTAGGGCCAAAAATCTATCTAATATC 57.603 37.037 6.18 0.00 37.17 1.63
3821 3893 6.451393 TCGAAATTTAGTCCCATTTTGTTGG 58.549 36.000 0.00 0.00 36.46 3.77
3825 3897 9.719355 GAAATTTAGTCCCATTTTGTTGGTATT 57.281 29.630 0.00 0.00 34.77 1.89
3883 3955 7.895429 TCCCTTGTCCAATTCTCATTCTATTTT 59.105 33.333 0.00 0.00 0.00 1.82
3975 4047 4.822026 ACTTTGAGGAGTATTGTCTTCCG 58.178 43.478 0.00 0.00 0.00 4.30
3988 4060 0.976641 TCTTCCGGACTGCTGTCAAT 59.023 50.000 23.12 0.00 44.61 2.57
3990 4062 2.565391 TCTTCCGGACTGCTGTCAATTA 59.435 45.455 23.12 6.82 44.61 1.40
4083 4155 9.881529 ATTGATTTGTTGTTAAATGTCAAATGC 57.118 25.926 6.23 0.00 38.34 3.56
4200 4272 5.399604 AAGTTGTATTTCCTATTACGCGC 57.600 39.130 5.73 0.00 0.00 6.86
4203 4275 5.176958 AGTTGTATTTCCTATTACGCGCATC 59.823 40.000 5.73 0.00 0.00 3.91
4242 4314 4.989279 ATGATGTGGGTTGCAAGAATAC 57.011 40.909 0.00 0.00 0.00 1.89
4371 4444 9.458727 AGCACAATGATCAATCCTATATTTAGG 57.541 33.333 0.00 2.94 45.68 2.69
4427 4500 7.476667 TGTGGGTTGCAAATAATAATAGTTCG 58.523 34.615 0.00 0.00 0.00 3.95
4559 4632 7.986320 CACTGATATGAGTGAAATCTTCTTCCT 59.014 37.037 16.44 0.00 45.39 3.36
4595 4668 8.479689 TCAGTCTTATGATTTTATCCCGTGTAA 58.520 33.333 0.00 0.00 0.00 2.41
4635 4708 5.801350 TCAGCATCAATTCCTTAGTTTCG 57.199 39.130 0.00 0.00 0.00 3.46
4659 4732 2.945456 ACTCCATATCTGCGTCACCTA 58.055 47.619 0.00 0.00 0.00 3.08
4669 4742 0.803740 GCGTCACCTAGTCGACTCTT 59.196 55.000 23.89 4.34 0.00 2.85
4683 4756 2.679837 CGACTCTTAACGGCAGTAGGTA 59.320 50.000 0.00 0.00 0.00 3.08
4708 4781 6.107901 TCCATTGTTCCAAAAGGTTTATGG 57.892 37.500 0.00 0.00 35.49 2.74
4879 4952 2.079170 TGCTGGAAATGGGTGTCAAA 57.921 45.000 0.00 0.00 0.00 2.69
5325 5417 4.934001 CACTTGCCGAGCATCATTAGATAT 59.066 41.667 0.00 0.00 38.76 1.63
5434 5528 9.309516 CTGGAAATATTTCATGACTGGAAAATG 57.690 33.333 25.55 0.00 37.74 2.32
5504 5598 7.416154 TCACCAAATACTTCTTTCTTACACG 57.584 36.000 0.00 0.00 0.00 4.49
5566 5674 4.957296 ACAAGGTCGTATCTTTTGACACT 58.043 39.130 0.00 0.00 34.32 3.55
5628 5741 6.687604 ACCATTCAACCATTTAAGCTGTAAC 58.312 36.000 0.00 0.00 0.00 2.50
5712 5825 2.047274 CGTGCCGGACTGGTCAAT 60.047 61.111 5.05 0.00 41.21 2.57
5836 5949 9.467258 CACTTATCAAAGTTCACAAATCAACAT 57.533 29.630 0.00 0.00 43.60 2.71
5837 5950 9.683069 ACTTATCAAAGTTCACAAATCAACATC 57.317 29.630 0.00 0.00 43.60 3.06
5838 5951 9.681692 CTTATCAAAGTTCACAAATCAACATCA 57.318 29.630 0.00 0.00 0.00 3.07
5839 5952 9.681692 TTATCAAAGTTCACAAATCAACATCAG 57.318 29.630 0.00 0.00 0.00 2.90
5840 5953 7.099266 TCAAAGTTCACAAATCAACATCAGT 57.901 32.000 0.00 0.00 0.00 3.41
5841 5954 6.974048 TCAAAGTTCACAAATCAACATCAGTG 59.026 34.615 0.00 0.00 0.00 3.66
5870 5985 4.273318 ACCTGCAAAATCTCAAGGGATAC 58.727 43.478 0.00 0.00 0.00 2.24
5898 6013 3.751698 AGGGAAGAATACTGAAAACGCAC 59.248 43.478 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.462047 GGATGGTACCGGTCTTGCAG 60.462 60.000 12.40 0.00 0.00 4.41
12 13 2.039787 TGAGTGGCCGGGATGGTA 59.960 61.111 2.18 0.00 41.21 3.25
13 14 3.402681 CTGAGTGGCCGGGATGGT 61.403 66.667 2.18 0.00 41.21 3.55
128 129 6.631971 TTTCAGTTAAGTGACATTGCATCA 57.368 33.333 12.62 0.00 0.00 3.07
360 361 1.226717 CGCTTCTCGGAGGTACTGC 60.227 63.158 4.96 2.49 45.89 4.40
480 481 0.243907 CACATCTCGAGGACACCGTT 59.756 55.000 13.56 0.00 0.00 4.44
520 522 1.211190 GGGCTTGCTCTTTTCGCAG 59.789 57.895 0.00 0.00 38.80 5.18
525 527 1.051008 CCCAAAGGGCTTGCTCTTTT 58.949 50.000 16.79 1.63 35.35 2.27
596 598 1.407989 GCTCCTCCTCAACCATCAAGG 60.408 57.143 0.00 0.00 45.67 3.61
694 698 8.963130 TCGAAAAACACAAGCACATATTTTTAG 58.037 29.630 0.00 0.00 31.33 1.85
700 704 5.121611 TCGATCGAAAAACACAAGCACATAT 59.878 36.000 16.99 0.00 0.00 1.78
750 754 6.372103 AGCAAGAATCTCAAATCAGACTGAAG 59.628 38.462 9.70 2.28 0.00 3.02
774 778 7.269477 ACAGAATTTCCTCAAAACAGAAGAG 57.731 36.000 0.00 0.00 0.00 2.85
833 862 5.376756 AGTGTAGTAACCCCTCACAAAAA 57.623 39.130 0.00 0.00 0.00 1.94
834 863 5.376756 AAGTGTAGTAACCCCTCACAAAA 57.623 39.130 0.00 0.00 0.00 2.44
835 864 6.691255 ATAAGTGTAGTAACCCCTCACAAA 57.309 37.500 0.00 0.00 0.00 2.83
836 865 7.983166 ATATAAGTGTAGTAACCCCTCACAA 57.017 36.000 0.00 0.00 0.00 3.33
837 866 9.085645 CATATATAAGTGTAGTAACCCCTCACA 57.914 37.037 0.00 0.00 0.00 3.58
838 867 9.305555 TCATATATAAGTGTAGTAACCCCTCAC 57.694 37.037 0.00 0.00 0.00 3.51
839 868 9.886337 TTCATATATAAGTGTAGTAACCCCTCA 57.114 33.333 0.00 0.00 0.00 3.86
860 889 9.352784 CGCATGGTTTATTTTCTTTTCTTCATA 57.647 29.630 0.00 0.00 0.00 2.15
861 890 7.872483 ACGCATGGTTTATTTTCTTTTCTTCAT 59.128 29.630 0.00 0.00 0.00 2.57
862 891 7.206687 ACGCATGGTTTATTTTCTTTTCTTCA 58.793 30.769 0.00 0.00 0.00 3.02
863 892 7.637709 ACGCATGGTTTATTTTCTTTTCTTC 57.362 32.000 0.00 0.00 0.00 2.87
864 893 8.432110 AAACGCATGGTTTATTTTCTTTTCTT 57.568 26.923 9.66 0.00 46.76 2.52
1602 1636 0.295763 CACATCAACGACGCATCTCG 59.704 55.000 0.00 0.00 45.38 4.04
1604 1638 0.670239 TGCACATCAACGACGCATCT 60.670 50.000 0.00 0.00 0.00 2.90
1674 1708 0.959372 CCCTCTTGGAGCAGTGCTTG 60.959 60.000 20.80 10.21 39.88 4.01
1701 1735 3.118555 CGAACATGGAGGGGTACATGTAA 60.119 47.826 7.25 0.00 37.29 2.41
1730 1764 3.357079 CAACCGCAGACCAGCACC 61.357 66.667 0.00 0.00 0.00 5.01
1803 1837 5.523552 TGAGACTTGTAATTGTCACACACAG 59.476 40.000 0.00 0.00 35.97 3.66
1808 1842 4.511454 GCAGTGAGACTTGTAATTGTCACA 59.489 41.667 12.47 0.00 37.39 3.58
2014 2050 0.950836 GCAGTGTGGCACATTGTACA 59.049 50.000 34.00 6.32 44.52 2.90
2040 2082 1.067071 GGACGAACAACCAGGGAGTAG 60.067 57.143 0.00 0.00 0.00 2.57
2143 2189 1.382522 GCTCCCAGCGATTCATGAAA 58.617 50.000 13.09 0.00 0.00 2.69
2157 2203 3.997681 GAGAACTAACAGAAACAGCTCCC 59.002 47.826 0.00 0.00 0.00 4.30
2194 2240 7.390718 GTGAAGAGGTGGTGAAATAAATACAGT 59.609 37.037 0.00 0.00 0.00 3.55
2211 2257 8.437575 TGGTTATTAAAAGAGAAGTGAAGAGGT 58.562 33.333 0.00 0.00 0.00 3.85
2215 2261 8.622948 AGGTGGTTATTAAAAGAGAAGTGAAG 57.377 34.615 0.00 0.00 0.00 3.02
2255 2301 0.463620 GGAACCTGCAAACAGCCAAA 59.536 50.000 0.00 0.00 43.02 3.28
2429 2476 1.098050 CATCCCACTGTTTAGCCAGC 58.902 55.000 0.00 0.00 35.83 4.85
2453 2502 6.881065 TGATGCTCTAAATGTCTGCTAAAAGT 59.119 34.615 0.00 0.00 0.00 2.66
2540 2589 7.925483 CCAAACTGGAACAATAAAGACATTGAA 59.075 33.333 3.01 0.00 40.96 2.69
2543 2592 7.069331 TCACCAAACTGGAACAATAAAGACATT 59.931 33.333 0.00 0.00 40.96 2.71
2866 2922 8.539770 TGCTAAGAGATATAAGCTAATTGTGC 57.460 34.615 0.00 0.00 35.95 4.57
2939 2996 2.289444 TGGTCTGTCGAAATCCCACTTC 60.289 50.000 0.00 0.00 0.00 3.01
2956 3013 4.846779 TGCTGTCCAAAATTTAGTGGTC 57.153 40.909 8.44 4.48 36.23 4.02
2962 3019 5.695816 GCTTTCACATGCTGTCCAAAATTTA 59.304 36.000 0.00 0.00 0.00 1.40
3111 3168 9.956720 GTTTACTGCATAGCAATTGAGAATATT 57.043 29.630 10.34 0.00 38.41 1.28
3112 3169 9.347240 AGTTTACTGCATAGCAATTGAGAATAT 57.653 29.630 10.34 0.00 38.41 1.28
3113 3170 8.737168 AGTTTACTGCATAGCAATTGAGAATA 57.263 30.769 10.34 0.00 38.41 1.75
3114 3171 7.636150 AGTTTACTGCATAGCAATTGAGAAT 57.364 32.000 10.34 0.00 38.41 2.40
3124 3181 5.582665 AGACAGCTTAAGTTTACTGCATAGC 59.417 40.000 4.02 0.00 33.35 2.97
3527 3584 4.735662 TTACAAGGCATGTACGTTTCAC 57.264 40.909 1.44 0.00 44.11 3.18
3540 3597 4.708726 AGAATCTGCAACATTACAAGGC 57.291 40.909 0.00 0.00 0.00 4.35
3620 3677 5.539955 GGTGGCCAGAATATCAAAACCATAT 59.460 40.000 5.11 0.00 0.00 1.78
3697 3769 9.342308 CCTTTGATGCTATTAGGACTTCAAATA 57.658 33.333 11.85 0.00 37.06 1.40
3698 3770 7.201857 GCCTTTGATGCTATTAGGACTTCAAAT 60.202 37.037 11.85 0.00 37.06 2.32
3699 3771 6.095440 GCCTTTGATGCTATTAGGACTTCAAA 59.905 38.462 11.25 11.25 36.01 2.69
3794 3866 9.632807 CAACAAAATGGGACTAAATTTCGAATA 57.367 29.630 0.00 0.00 0.00 1.75
3799 3871 9.719355 AATACCAACAAAATGGGACTAAATTTC 57.281 29.630 0.00 0.00 45.18 2.17
3821 3893 9.874215 GTTGGTCAGTTAACACTAGAAAAATAC 57.126 33.333 8.61 0.00 0.00 1.89
3825 3897 7.562135 AGAGTTGGTCAGTTAACACTAGAAAA 58.438 34.615 8.61 0.00 0.00 2.29
3975 4047 5.048782 TGACAATTGTAATTGACAGCAGTCC 60.049 40.000 20.68 0.00 46.72 3.85
3988 4060 6.533730 AGTGACCTTCAGATGACAATTGTAA 58.466 36.000 11.95 4.13 0.00 2.41
3990 4062 4.978099 AGTGACCTTCAGATGACAATTGT 58.022 39.130 11.78 11.78 0.00 2.71
4057 4129 9.881529 GCATTTGACATTTAACAACAAATCAAT 57.118 25.926 0.00 0.00 38.52 2.57
4075 4147 2.954318 AGCAGGATACATGGCATTTGAC 59.046 45.455 0.00 0.00 41.41 3.18
4083 4155 4.529769 TCCTATCTGAAGCAGGATACATGG 59.470 45.833 0.00 0.00 33.48 3.66
4200 4272 8.464404 CATCATAGCCATAAAGTTATTGGGATG 58.536 37.037 6.23 6.44 0.00 3.51
4203 4275 7.309377 CCACATCATAGCCATAAAGTTATTGGG 60.309 40.741 6.23 0.00 0.00 4.12
4371 4444 1.745653 GAAGTGCTTGGAATACAGGGC 59.254 52.381 0.00 0.00 0.00 5.19
4427 4500 5.948992 AACAAATTCTAGCAGTTGGACTC 57.051 39.130 7.45 0.00 0.00 3.36
4499 4572 7.904094 TGTTGCATTTGACATTTTGTAAGAAC 58.096 30.769 0.00 0.00 0.00 3.01
4513 4586 5.348179 CAGTGAGTTTTGTTGTTGCATTTGA 59.652 36.000 0.00 0.00 0.00 2.69
4622 4695 9.110502 GATATGGAGTTTTCGAAACTAAGGAAT 57.889 33.333 10.79 0.29 0.00 3.01
4635 4708 3.309954 GGTGACGCAGATATGGAGTTTTC 59.690 47.826 0.00 0.00 0.00 2.29
4659 4732 1.245732 ACTGCCGTTAAGAGTCGACT 58.754 50.000 20.18 20.18 0.00 4.18
4669 4742 2.512692 TGGAGTACCTACTGCCGTTA 57.487 50.000 1.93 0.00 43.07 3.18
4708 4781 0.536006 ACTGACCAGGTGAAAGCAGC 60.536 55.000 0.00 0.00 42.72 5.25
4879 4952 5.047590 TGCTGACAATGCTTCAATCTCAAAT 60.048 36.000 0.00 0.00 0.00 2.32
5434 5528 6.067263 TGTGTACATGAAGTTTGTTAAGCC 57.933 37.500 0.00 0.00 0.00 4.35
5504 5598 1.303309 GCTCATATGCACCTGGACAC 58.697 55.000 0.00 0.00 0.00 3.67
5602 5710 6.909550 ACAGCTTAAATGGTTGAATGGTTA 57.090 33.333 0.00 0.00 0.00 2.85
5628 5741 6.260050 ACGAACATATGGGCTTGTACTTAATG 59.740 38.462 7.80 0.00 0.00 1.90
5813 5926 9.681692 CTGATGTTGATTTGTGAACTTTGATAA 57.318 29.630 0.00 0.00 0.00 1.75
5836 5949 5.769662 AGATTTTGCAGGTAATGAACACTGA 59.230 36.000 0.00 0.00 31.61 3.41
5837 5950 6.017400 AGATTTTGCAGGTAATGAACACTG 57.983 37.500 0.00 0.00 32.55 3.66
5838 5951 5.769662 TGAGATTTTGCAGGTAATGAACACT 59.230 36.000 0.00 0.00 0.00 3.55
5839 5952 6.012658 TGAGATTTTGCAGGTAATGAACAC 57.987 37.500 0.00 0.00 0.00 3.32
5840 5953 6.294675 CCTTGAGATTTTGCAGGTAATGAACA 60.295 38.462 0.00 0.00 0.00 3.18
5841 5954 6.095377 CCTTGAGATTTTGCAGGTAATGAAC 58.905 40.000 0.00 0.00 0.00 3.18
5870 5985 4.672587 TTCAGTATTCTTCCCTCCATCG 57.327 45.455 0.00 0.00 0.00 3.84
5898 6013 3.279434 GGAAAGTGGGGTAAGCACATAG 58.721 50.000 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.