Multiple sequence alignment - TraesCS6A01G269400

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 TraesCS6A01G269400 chr6A 100.000 5068 0 0 1 5068 495684844 495689911 0.000000e+00 9359.0
1 TraesCS6A01G269400 chr6A 95.775 71 1 2 907 975 495685716 495685786 4.150000e-21 113.0
2 TraesCS6A01G269400 chr6A 95.775 71 1 2 873 943 495685750 495685818 4.150000e-21 113.0
3 TraesCS6A01G269400 chr6B 95.275 3894 114 24 907 4764 532338461 532342320 0.000000e+00 6107.0
4 TraesCS6A01G269400 chr6B 97.155 949 18 5 1 943 532337585 532338530 0.000000e+00 1594.0
5 TraesCS6A01G269400 chr6B 97.368 38 0 1 873 910 532338494 532338530 4.240000e-06 63.9
6 TraesCS6A01G269400 chr6D 96.648 3640 82 10 907 4513 347687635 347684003 0.000000e+00 6010.0
7 TraesCS6A01G269400 chr6D 95.297 404 13 3 545 943 347687968 347687566 1.990000e-178 636.0
8 TraesCS6A01G269400 chr6D 91.258 469 9 11 1 465 347688409 347687969 1.210000e-170 610.0
9 TraesCS6A01G269400 chr6D 82.402 358 35 9 4539 4879 347684005 347683659 2.310000e-73 287.0
10 TraesCS6A01G269400 chr6D 87.903 124 11 3 4948 5068 347683188 347683066 5.290000e-30 143.0


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 TraesCS6A01G269400 chr6A 495684844 495689911 5067 False 9359.0 9359 100.000000 1 5068 1 chr6A.!!$F1 5067
1 TraesCS6A01G269400 chr6B 532337585 532342320 4735 False 2588.3 6107 96.599333 1 4764 3 chr6B.!!$F1 4763
2 TraesCS6A01G269400 chr6D 347683066 347688409 5343 True 1537.2 6010 90.701600 1 5068 5 chr6D.!!$R1 5067

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
899 910 0.930726 ACCTGGTTGTCCCAAAGGAA 59.069 50.000 0.0 0.0 46.38 3.36 F
2230 2244 1.003003 TGTGCTTGCCTACACATGCTA 59.997 47.619 0.0 0.0 41.67 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2606 2620 1.277273 TGCTGACCTGGAGAATCACAG 59.723 52.381 0.00 0.00 36.25 3.66 R
4210 4257 0.541063 TTCTCTACCGTGGCACCTGA 60.541 55.000 12.86 4.37 0.00 3.86 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
44 49 7.552330 TCGACCACATCATTCTGATTCAAATAA 59.448 33.333 0.00 0.00 34.28 1.40
347 352 7.724061 TCCTTTCTTTTGTTCTATTGGCTAAGT 59.276 33.333 0.00 0.00 0.00 2.24
366 371 9.860898 GGCTAAGTTTTTATCATCTCATTTTGT 57.139 29.630 0.00 0.00 0.00 2.83
523 528 7.446931 TCAAACTGTTCTTTCCTGCATGTATTA 59.553 33.333 0.00 0.00 0.00 0.98
663 674 4.403432 AGTTGCCATTTGCTTGCTGTATAT 59.597 37.500 0.00 0.00 42.00 0.86
760 771 3.383761 CAAATCCAAGACAGCACAAACC 58.616 45.455 0.00 0.00 0.00 3.27
802 813 6.823182 TCAATTGACGGATCATACATCTGTTT 59.177 34.615 3.38 0.00 37.73 2.83
883 894 7.653311 GCTTGTTGTTGATTTTTCTTGATACCT 59.347 33.333 0.00 0.00 0.00 3.08
884 895 8.870160 TTGTTGTTGATTTTTCTTGATACCTG 57.130 30.769 0.00 0.00 0.00 4.00
885 896 7.432869 TGTTGTTGATTTTTCTTGATACCTGG 58.567 34.615 0.00 0.00 0.00 4.45
886 897 7.069331 TGTTGTTGATTTTTCTTGATACCTGGT 59.931 33.333 4.05 4.05 0.00 4.00
887 898 7.595819 TGTTGATTTTTCTTGATACCTGGTT 57.404 32.000 3.84 0.00 0.00 3.67
888 899 7.432869 TGTTGATTTTTCTTGATACCTGGTTG 58.567 34.615 3.84 0.00 0.00 3.77
889 900 7.069331 TGTTGATTTTTCTTGATACCTGGTTGT 59.931 33.333 3.84 0.00 0.00 3.32
890 901 7.214467 TGATTTTTCTTGATACCTGGTTGTC 57.786 36.000 3.84 4.77 0.00 3.18
891 902 6.208599 TGATTTTTCTTGATACCTGGTTGTCC 59.791 38.462 3.84 0.00 0.00 4.02
892 903 3.713826 TTCTTGATACCTGGTTGTCCC 57.286 47.619 3.84 0.00 0.00 4.46
893 904 2.626785 TCTTGATACCTGGTTGTCCCA 58.373 47.619 3.84 0.00 42.51 4.37
894 905 2.983192 TCTTGATACCTGGTTGTCCCAA 59.017 45.455 3.84 2.17 44.65 4.12
895 906 3.396276 TCTTGATACCTGGTTGTCCCAAA 59.604 43.478 3.84 0.00 44.65 3.28
896 907 3.433306 TGATACCTGGTTGTCCCAAAG 57.567 47.619 3.84 0.00 44.65 2.77
897 908 2.041081 TGATACCTGGTTGTCCCAAAGG 59.959 50.000 3.84 0.00 44.65 3.11
898 909 1.822425 TACCTGGTTGTCCCAAAGGA 58.178 50.000 3.84 0.00 44.65 3.36
899 910 0.930726 ACCTGGTTGTCCCAAAGGAA 59.069 50.000 0.00 0.00 46.38 3.36
900 911 1.289530 ACCTGGTTGTCCCAAAGGAAA 59.710 47.619 0.00 0.00 46.38 3.13
901 912 2.292587 ACCTGGTTGTCCCAAAGGAAAA 60.293 45.455 0.00 0.00 46.38 2.29
902 913 2.769095 CCTGGTTGTCCCAAAGGAAAAA 59.231 45.455 0.00 0.00 46.38 1.94
903 914 3.181466 CCTGGTTGTCCCAAAGGAAAAAG 60.181 47.826 0.00 0.00 46.38 2.27
904 915 2.769095 TGGTTGTCCCAAAGGAAAAAGG 59.231 45.455 0.00 0.00 46.38 3.11
905 916 2.484770 GGTTGTCCCAAAGGAAAAAGGC 60.485 50.000 0.00 0.00 46.38 4.35
906 917 2.434336 GTTGTCCCAAAGGAAAAAGGCT 59.566 45.455 0.00 0.00 46.38 4.58
907 918 2.758130 TGTCCCAAAGGAAAAAGGCTT 58.242 42.857 0.00 0.00 46.38 4.35
908 919 2.698274 TGTCCCAAAGGAAAAAGGCTTC 59.302 45.455 0.00 0.00 46.38 3.86
909 920 2.965831 GTCCCAAAGGAAAAAGGCTTCT 59.034 45.455 0.00 0.00 46.38 2.85
910 921 3.388024 GTCCCAAAGGAAAAAGGCTTCTT 59.612 43.478 0.00 0.00 46.38 2.52
911 922 3.387699 TCCCAAAGGAAAAAGGCTTCTTG 59.612 43.478 0.00 0.00 40.08 3.02
912 923 3.387699 CCCAAAGGAAAAAGGCTTCTTGA 59.612 43.478 0.00 0.00 33.47 3.02
913 924 4.040829 CCCAAAGGAAAAAGGCTTCTTGAT 59.959 41.667 0.00 0.00 33.47 2.57
914 925 5.245977 CCCAAAGGAAAAAGGCTTCTTGATA 59.754 40.000 0.00 0.00 33.47 2.15
915 926 6.159293 CCAAAGGAAAAAGGCTTCTTGATAC 58.841 40.000 0.00 0.00 0.00 2.24
916 927 5.984695 AAGGAAAAAGGCTTCTTGATACC 57.015 39.130 0.00 0.00 0.00 2.73
1267 1279 9.221775 GTTGACGTCAATGTTTCATATTAATCC 57.778 33.333 31.81 10.55 38.24 3.01
1636 1649 8.645814 TCTACCAACTTATGAAAGACAGAGTA 57.354 34.615 0.00 0.00 36.50 2.59
1833 1846 8.581578 TCTGACATTAGTGTATTGTGAGTTGTA 58.418 33.333 0.00 0.00 39.09 2.41
1859 1873 3.252554 AGCCTTCTAGCAGCTATAGGT 57.747 47.619 22.70 0.00 34.38 3.08
2066 2080 1.819632 GGTTAGTGCCGCTCCCATG 60.820 63.158 0.00 0.00 0.00 3.66
2230 2244 1.003003 TGTGCTTGCCTACACATGCTA 59.997 47.619 0.00 0.00 41.67 3.49
2231 2245 1.667724 GTGCTTGCCTACACATGCTAG 59.332 52.381 0.00 0.00 40.39 3.42
2447 2461 6.053005 ACCGTCTTTGATCACTTGTTTCTTA 58.947 36.000 0.00 0.00 0.00 2.10
2509 2523 2.491693 CAACGTTATTGGTTGCCCAGAT 59.508 45.455 0.00 0.00 43.15 2.90
2606 2620 9.765795 ATGTTTCCTTGTCTATAGTACTATTGC 57.234 33.333 20.21 13.92 0.00 3.56
2618 2632 5.939764 AGTACTATTGCTGTGATTCTCCA 57.060 39.130 0.00 0.00 0.00 3.86
2648 2662 6.656693 AGCAATTCTTGTGTAAGCAGTAGAAT 59.343 34.615 0.00 0.00 37.45 2.40
2665 2679 9.665264 GCAGTAGAATTAATACCTGTTATTTGC 57.335 33.333 0.00 0.00 32.31 3.68
2667 2681 9.609346 AGTAGAATTAATACCTGTTATTTGCGT 57.391 29.630 0.00 0.00 32.31 5.24
2717 2731 3.979948 TGTGTTATTTCCTTCGTCGTCA 58.020 40.909 0.00 0.00 0.00 4.35
2817 2831 5.652891 TGTGTAGCCTTCACACCTTTTTAAA 59.347 36.000 0.00 0.00 44.58 1.52
2957 2971 6.635641 CACTATGAATGCACATGAATACTTGC 59.364 38.462 0.00 0.00 35.45 4.01
2991 3027 4.532314 TGTATATGCAGATCAGAGGCAG 57.468 45.455 0.00 0.00 41.40 4.85
3062 3098 8.491958 ACCTTATATCCGTAAGTCCTTCAAATT 58.508 33.333 0.00 0.00 31.24 1.82
3096 3132 2.017049 GACATTCCCGAACTCATTGGG 58.983 52.381 0.00 0.00 44.75 4.12
3170 3206 1.959282 CCTTGCAAGAGACCAAAAGCT 59.041 47.619 28.05 0.00 0.00 3.74
3234 3270 6.487689 TTTTCCGATTGTTTTGTTGCTTTT 57.512 29.167 0.00 0.00 0.00 2.27
3252 3288 4.757149 GCTTTTTCTTTGCTCTGGAGACTA 59.243 41.667 1.35 0.00 0.00 2.59
3270 3306 6.091034 GGAGACTAATCGGTTTTCTTCTTGTC 59.909 42.308 0.00 0.00 0.00 3.18
3305 3341 6.006275 AGGATTGTACATATGTTCCAGCTT 57.994 37.500 21.11 4.33 0.00 3.74
3328 3364 4.729856 CGGCCAAAAGCTGCAGGC 62.730 66.667 17.12 10.05 42.11 4.85
3331 3367 2.602568 CCAAAAGCTGCAGGCCCT 60.603 61.111 17.12 0.44 43.05 5.19
3368 3404 5.240121 CGGGTGGTTAGTATACACACTTTT 58.760 41.667 5.50 0.00 36.41 2.27
3444 3480 2.550180 GTTTCAGTTGGAGCAAGAGGAC 59.450 50.000 0.00 0.00 0.00 3.85
3658 3696 5.388786 GCAAAGAAAACTTCAATTGGATCGC 60.389 40.000 5.42 0.00 32.63 4.58
3677 3715 0.604780 CCAGGCACCACAGAAGAGTG 60.605 60.000 0.00 0.00 39.21 3.51
4210 4257 2.203684 CCCCCTGCTTGCTTGGTT 60.204 61.111 0.00 0.00 0.00 3.67
4237 4284 2.870435 GCCACGGTAGAGAATGTGTTGT 60.870 50.000 0.00 0.00 0.00 3.32
4474 4521 8.766000 TGTACAGTTTGCGAGATTTAATAGAA 57.234 30.769 0.00 0.00 0.00 2.10
4515 4562 7.701445 TGCCTGGTCAAATTTTAAATTTGTTG 58.299 30.769 30.15 21.13 39.36 3.33
4518 4565 7.500559 CCTGGTCAAATTTTAAATTTGTTGGGA 59.499 33.333 30.15 16.09 39.36 4.37
4523 4570 9.114952 TCAAATTTTAAATTTGTTGGGAAGTCC 57.885 29.630 30.15 0.00 39.36 3.85
4524 4571 8.897752 CAAATTTTAAATTTGTTGGGAAGTCCA 58.102 29.630 26.11 0.00 37.42 4.02
4528 4575 5.885449 AAATTTGTTGGGAAGTCCATTCA 57.115 34.783 0.00 0.00 46.52 2.57
4552 4599 0.101399 TTTTGTTGCGCCGTGACAAT 59.899 45.000 4.18 0.00 33.73 2.71
4582 4629 8.576442 TCTCCCTTACATTTTCAAAGCTTTTAG 58.424 33.333 9.53 0.00 0.00 1.85
4659 4708 5.234972 GGTGAGTTTGCCTGAAAATTGAAAG 59.765 40.000 0.00 0.00 0.00 2.62
4723 4772 2.092646 TCGGGGTTCCACTATCAAATGG 60.093 50.000 0.00 0.00 37.32 3.16
4724 4773 2.092646 CGGGGTTCCACTATCAAATGGA 60.093 50.000 0.00 0.00 43.42 3.41
4725 4774 3.435026 CGGGGTTCCACTATCAAATGGAT 60.435 47.826 0.00 0.00 44.49 3.41
4727 4776 5.689031 CGGGGTTCCACTATCAAATGGATAA 60.689 44.000 0.00 0.00 44.49 1.75
4729 4778 6.782494 GGGGTTCCACTATCAAATGGATAATT 59.218 38.462 0.00 0.00 44.49 1.40
4730 4779 7.255942 GGGGTTCCACTATCAAATGGATAATTG 60.256 40.741 0.00 0.00 44.49 2.32
4738 4788 4.757594 TCAAATGGATAATTGGTGCAAGC 58.242 39.130 0.00 0.00 0.00 4.01
4739 4789 4.467082 TCAAATGGATAATTGGTGCAAGCT 59.533 37.500 0.00 0.00 33.76 3.74
4740 4790 4.395959 AATGGATAATTGGTGCAAGCTG 57.604 40.909 0.00 0.00 33.76 4.24
4764 4814 3.400322 AGGATATTGCACCCCTCATTCAT 59.600 43.478 0.00 0.00 0.00 2.57
4781 4845 7.300556 TCATTCATGAAAAATTGGAAGGTGA 57.699 32.000 13.09 4.13 33.08 4.02
4782 4846 7.380536 TCATTCATGAAAAATTGGAAGGTGAG 58.619 34.615 13.09 0.00 33.08 3.51
4783 4847 5.138125 TCATGAAAAATTGGAAGGTGAGC 57.862 39.130 0.00 0.00 0.00 4.26
4788 4852 0.678048 AATTGGAAGGTGAGCGAGGC 60.678 55.000 0.00 0.00 0.00 4.70
4789 4853 2.859273 ATTGGAAGGTGAGCGAGGCG 62.859 60.000 0.00 0.00 0.00 5.52
4800 4864 3.966215 CGAGGCGCTCAAGGAAAA 58.034 55.556 7.64 0.00 0.00 2.29
4801 4865 2.471255 CGAGGCGCTCAAGGAAAAT 58.529 52.632 7.64 0.00 0.00 1.82
4802 4866 0.097674 CGAGGCGCTCAAGGAAAATG 59.902 55.000 7.64 0.00 0.00 2.32
4803 4867 0.179153 GAGGCGCTCAAGGAAAATGC 60.179 55.000 7.64 0.00 0.00 3.56
4818 4882 4.392754 GGAAAATGCGAAAATGCTTGGATT 59.607 37.500 0.00 0.00 35.36 3.01
4853 4917 4.230455 CTCTCCTATGATTTCTCCTGGGT 58.770 47.826 0.00 0.00 0.00 4.51
4857 4921 4.977739 TCCTATGATTTCTCCTGGGTTCAT 59.022 41.667 0.00 0.00 0.00 2.57
4862 4926 4.408921 TGATTTCTCCTGGGTTCATATCGT 59.591 41.667 0.00 0.00 0.00 3.73
4866 4930 3.384789 TCTCCTGGGTTCATATCGTTGAG 59.615 47.826 0.00 0.00 0.00 3.02
4870 4934 4.503910 CTGGGTTCATATCGTTGAGTTCA 58.496 43.478 0.00 0.00 0.00 3.18
4879 4943 6.878923 TCATATCGTTGAGTTCATTGACCTTT 59.121 34.615 0.00 0.00 0.00 3.11
4880 4944 4.811555 TCGTTGAGTTCATTGACCTTTG 57.188 40.909 0.00 0.00 0.00 2.77
4881 4945 3.563808 TCGTTGAGTTCATTGACCTTTGG 59.436 43.478 0.00 0.00 0.00 3.28
4882 4946 3.563808 CGTTGAGTTCATTGACCTTTGGA 59.436 43.478 0.00 0.00 0.00 3.53
4883 4947 4.216257 CGTTGAGTTCATTGACCTTTGGAT 59.784 41.667 0.00 0.00 0.00 3.41
4884 4948 5.464168 GTTGAGTTCATTGACCTTTGGATG 58.536 41.667 0.00 0.00 0.00 3.51
4885 4949 3.507233 TGAGTTCATTGACCTTTGGATGC 59.493 43.478 0.00 0.00 0.00 3.91
4886 4950 3.760684 GAGTTCATTGACCTTTGGATGCT 59.239 43.478 0.00 0.00 0.00 3.79
4887 4951 4.154942 AGTTCATTGACCTTTGGATGCTT 58.845 39.130 0.00 0.00 0.00 3.91
4888 4952 5.324409 AGTTCATTGACCTTTGGATGCTTA 58.676 37.500 0.00 0.00 0.00 3.09
4889 4953 5.954150 AGTTCATTGACCTTTGGATGCTTAT 59.046 36.000 0.00 0.00 0.00 1.73
4890 4954 6.096001 AGTTCATTGACCTTTGGATGCTTATC 59.904 38.462 0.00 0.00 0.00 1.75
4891 4955 4.889409 TCATTGACCTTTGGATGCTTATCC 59.111 41.667 0.00 0.00 41.10 2.59
4902 4966 5.324409 TGGATGCTTATCCATATTTCCACC 58.676 41.667 4.95 0.00 45.19 4.61
4903 4967 5.074929 TGGATGCTTATCCATATTTCCACCT 59.925 40.000 4.95 0.00 45.19 4.00
4904 4968 6.012745 GGATGCTTATCCATATTTCCACCTT 58.987 40.000 1.55 0.00 40.43 3.50
4905 4969 6.071728 GGATGCTTATCCATATTTCCACCTTG 60.072 42.308 1.55 0.00 40.43 3.61
4906 4970 6.012337 TGCTTATCCATATTTCCACCTTGA 57.988 37.500 0.00 0.00 0.00 3.02
4907 4971 6.613699 TGCTTATCCATATTTCCACCTTGAT 58.386 36.000 0.00 0.00 0.00 2.57
4916 4980 2.030027 TCCACCTTGATGACCTCACT 57.970 50.000 0.00 0.00 32.17 3.41
4931 4995 2.719739 CTCACTGAGGATGGCATTGTT 58.280 47.619 0.00 0.00 0.00 2.83
4932 4996 2.422479 CTCACTGAGGATGGCATTGTTG 59.578 50.000 0.00 0.00 0.00 3.33
4934 4998 1.108776 CTGAGGATGGCATTGTTGGG 58.891 55.000 0.00 0.00 0.00 4.12
4961 5456 9.908152 AAGCATACAAATGATGATCATTACATG 57.092 29.630 19.93 20.42 45.57 3.21
4962 5457 9.292195 AGCATACAAATGATGATCATTACATGA 57.708 29.630 25.09 12.29 45.57 3.07
4964 5459 9.537848 CATACAAATGATGATCATTACATGACG 57.462 33.333 19.93 6.56 45.57 4.35
4974 5469 3.056179 TCATTACATGACGACCTCTGCAA 60.056 43.478 0.00 0.00 33.59 4.08
4981 5476 4.002906 TGACGACCTCTGCAAATAAAGT 57.997 40.909 0.00 0.00 0.00 2.66
4982 5477 3.745975 TGACGACCTCTGCAAATAAAGTG 59.254 43.478 0.00 0.00 0.00 3.16
4983 5478 2.484264 ACGACCTCTGCAAATAAAGTGC 59.516 45.455 0.00 0.00 42.55 4.40
4994 5489 5.919196 GCAAATAAAGTGCAATTCTTGGTG 58.081 37.500 0.00 0.00 41.80 4.17
4996 5491 6.369615 GCAAATAAAGTGCAATTCTTGGTGAT 59.630 34.615 0.00 0.00 41.80 3.06
5058 5555 3.295973 CCTCCCAAGGTCAAGTTTTTCA 58.704 45.455 0.00 0.00 37.94 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 49 2.029649 GCTGGTGCAATCTGACACAATT 60.030 45.455 0.00 0.00 38.57 2.32
75 80 5.473504 TCTTTGATGAACACTTTAAGCTCCC 59.526 40.000 0.00 0.00 0.00 4.30
376 381 3.133691 TGGAGATGATGCGCTGATAAAC 58.866 45.455 9.73 0.00 0.00 2.01
523 528 6.403866 TGGTTGATTTAGTTTTCACATGCT 57.596 33.333 0.00 0.00 0.00 3.79
663 674 1.942776 TGAGCCTTGACCTCAGATGA 58.057 50.000 0.00 0.00 34.59 2.92
802 813 3.934457 TCTTGTCTATCAGTTCGCACA 57.066 42.857 0.00 0.00 0.00 4.57
887 898 2.470057 AGCCTTTTTCCTTTGGGACA 57.530 45.000 0.00 0.00 42.05 4.02
888 899 2.965831 AGAAGCCTTTTTCCTTTGGGAC 59.034 45.455 0.00 0.00 42.05 4.46
889 900 3.328535 AGAAGCCTTTTTCCTTTGGGA 57.671 42.857 0.00 0.00 40.36 4.37
890 901 3.387699 TCAAGAAGCCTTTTTCCTTTGGG 59.612 43.478 0.00 0.00 0.00 4.12
891 902 4.670896 TCAAGAAGCCTTTTTCCTTTGG 57.329 40.909 0.00 0.00 0.00 3.28
892 903 6.015095 AGGTATCAAGAAGCCTTTTTCCTTTG 60.015 38.462 0.00 0.00 0.00 2.77
893 904 6.015095 CAGGTATCAAGAAGCCTTTTTCCTTT 60.015 38.462 0.00 0.00 0.00 3.11
894 905 5.478332 CAGGTATCAAGAAGCCTTTTTCCTT 59.522 40.000 0.00 0.00 0.00 3.36
895 906 5.012893 CAGGTATCAAGAAGCCTTTTTCCT 58.987 41.667 0.00 0.00 0.00 3.36
896 907 4.158579 CCAGGTATCAAGAAGCCTTTTTCC 59.841 45.833 0.00 0.00 0.00 3.13
897 908 4.767409 ACCAGGTATCAAGAAGCCTTTTTC 59.233 41.667 0.00 0.00 0.00 2.29
898 909 4.740902 ACCAGGTATCAAGAAGCCTTTTT 58.259 39.130 0.00 0.00 0.00 1.94
899 910 4.388577 ACCAGGTATCAAGAAGCCTTTT 57.611 40.909 0.00 0.00 0.00 2.27
900 911 4.082125 CAACCAGGTATCAAGAAGCCTTT 58.918 43.478 0.00 0.00 0.00 3.11
901 912 3.074538 ACAACCAGGTATCAAGAAGCCTT 59.925 43.478 0.00 0.00 0.00 4.35
902 913 2.644798 ACAACCAGGTATCAAGAAGCCT 59.355 45.455 0.00 0.00 0.00 4.58
903 914 3.010420 GACAACCAGGTATCAAGAAGCC 58.990 50.000 0.00 0.00 0.00 4.35
904 915 3.010420 GGACAACCAGGTATCAAGAAGC 58.990 50.000 0.00 0.00 35.97 3.86
905 916 3.009033 TGGGACAACCAGGTATCAAGAAG 59.991 47.826 0.00 0.00 46.80 2.85
906 917 2.983192 TGGGACAACCAGGTATCAAGAA 59.017 45.455 0.00 0.00 46.80 2.52
907 918 2.626785 TGGGACAACCAGGTATCAAGA 58.373 47.619 0.00 0.00 46.80 3.02
1029 1041 6.723298 ATACAACTGTTATCCAGAGGAGAG 57.277 41.667 0.00 0.00 44.49 3.20
1267 1279 2.980568 TCTTAACGGCCACCTACATTG 58.019 47.619 2.24 0.00 0.00 2.82
1412 1424 6.080406 CCGCAAAGACTTCAATAAAGAAGAC 58.920 40.000 10.37 4.64 46.18 3.01
1636 1649 0.951040 CTGACTCCGCGAAAGGCTTT 60.951 55.000 13.25 13.25 40.44 3.51
1696 1709 4.357325 AGTATCCCCTCTGGTGCATATAG 58.643 47.826 0.00 0.00 34.77 1.31
1833 1846 3.990959 AGCTGCTAGAAGGCTTTAACT 57.009 42.857 0.00 0.00 31.81 2.24
1859 1873 5.068855 TCAGTTGATCTGCAAAATTGGAACA 59.931 36.000 0.00 0.00 43.32 3.18
2066 2080 2.829384 TTCTCTGTGTGGTGGGGCC 61.829 63.158 0.00 0.00 37.90 5.80
2230 2244 7.175104 TGAAGAAGGTCCATTTATTAGTTGCT 58.825 34.615 0.00 0.00 0.00 3.91
2231 2245 7.391148 TGAAGAAGGTCCATTTATTAGTTGC 57.609 36.000 0.00 0.00 0.00 4.17
2467 2481 6.183360 CGTTGCAAATCTTGAGAATCTCATCT 60.183 38.462 14.31 0.00 40.39 2.90
2509 2523 1.607178 CTGGGGCCATGTTTGCTCA 60.607 57.895 4.39 0.00 0.00 4.26
2602 2616 2.306805 TGACCTGGAGAATCACAGCAAT 59.693 45.455 0.00 0.00 36.25 3.56
2606 2620 1.277273 TGCTGACCTGGAGAATCACAG 59.723 52.381 0.00 0.00 36.25 3.66
2648 2662 9.386010 ACAGATAACGCAAATAACAGGTATTAA 57.614 29.630 0.00 0.00 31.82 1.40
2665 2679 8.129840 ACAGATGCTAGTAACTTACAGATAACG 58.870 37.037 1.79 0.00 0.00 3.18
2667 2681 9.185680 TCACAGATGCTAGTAACTTACAGATAA 57.814 33.333 1.79 0.00 0.00 1.75
2743 2757 5.576563 TCTCAAGAAAACAGGACCCATAA 57.423 39.130 0.00 0.00 0.00 1.90
2817 2831 5.221303 GCACTCCATAAACCATGCATAACAT 60.221 40.000 0.00 0.00 40.66 2.71
2836 2850 3.059352 ACCTAACATGGAGTTGCACTC 57.941 47.619 0.00 7.52 44.32 3.51
2847 2861 5.681105 CGTGTCTTGTTTCAAACCTAACATG 59.319 40.000 0.00 1.46 34.52 3.21
2848 2862 5.587043 TCGTGTCTTGTTTCAAACCTAACAT 59.413 36.000 0.00 0.00 34.52 2.71
2957 2971 6.108687 TCTGCATATACAAAGAACCACTGAG 58.891 40.000 0.00 0.00 0.00 3.35
2991 3027 3.587797 TCATTACCTCCGACAGTTGAC 57.412 47.619 0.00 0.00 0.00 3.18
3096 3132 9.909644 GTAGAAGGAAAAGGAAAATTAGGAAAC 57.090 33.333 0.00 0.00 0.00 2.78
3212 3248 6.370166 AGAAAAAGCAACAAAACAATCGGAAA 59.630 30.769 0.00 0.00 0.00 3.13
3222 3258 5.122082 CCAGAGCAAAGAAAAAGCAACAAAA 59.878 36.000 0.00 0.00 0.00 2.44
3224 3260 4.081752 TCCAGAGCAAAGAAAAAGCAACAA 60.082 37.500 0.00 0.00 0.00 2.83
3234 3270 4.382040 CCGATTAGTCTCCAGAGCAAAGAA 60.382 45.833 0.00 0.00 0.00 2.52
3252 3288 5.070001 TGGATGACAAGAAGAAAACCGATT 58.930 37.500 0.00 0.00 0.00 3.34
3270 3306 8.733458 CATATGTACAATCCTAATGGTTGGATG 58.267 37.037 0.00 0.00 41.76 3.51
3305 3341 1.600636 CAGCTTTTGGCCGGACAGA 60.601 57.895 11.51 1.65 43.05 3.41
3368 3404 1.847798 AACGAACAGGCTATGGGGCA 61.848 55.000 0.00 0.00 43.56 5.36
3444 3480 1.466167 CCGAGCAATGTGTCCTGAAAG 59.534 52.381 0.00 0.00 0.00 2.62
3506 3542 6.425114 AGCTGCTCGGTTTTATAGATATGTTG 59.575 38.462 0.00 0.00 0.00 3.33
3658 3696 0.604780 CACTCTTCTGTGGTGCCTGG 60.605 60.000 0.00 0.00 34.56 4.45
3677 3715 2.167398 TTACTCTCAGTGGGCCGTGC 62.167 60.000 0.00 0.00 0.00 5.34
3956 4003 4.410400 GGGACAGGGGGCTTCACG 62.410 72.222 0.00 0.00 0.00 4.35
4210 4257 0.541063 TTCTCTACCGTGGCACCTGA 60.541 55.000 12.86 4.37 0.00 3.86
4237 4284 1.742880 GCAGGCTCGAGCACATTCA 60.743 57.895 36.27 0.00 44.36 2.57
4536 4583 2.011540 TATATTGTCACGGCGCAACA 57.988 45.000 10.83 9.07 0.00 3.33
4542 4589 3.963428 AGGGAGATATATTGTCACGGC 57.037 47.619 0.00 0.00 0.00 5.68
4552 4599 9.920946 AAGCTTTGAAAATGTAAGGGAGATATA 57.079 29.630 0.00 0.00 0.00 0.86
4582 4629 5.339008 AAAACTTCAAACCAAAGAGACCC 57.661 39.130 0.00 0.00 0.00 4.46
4661 4710 6.575162 AATGGACTAAAAGTTGGCTTACAG 57.425 37.500 0.00 0.00 33.95 2.74
4668 4717 4.034048 CGGATCGAATGGACTAAAAGTTGG 59.966 45.833 0.00 0.00 0.00 3.77
4672 4721 6.417191 TTTTCGGATCGAATGGACTAAAAG 57.583 37.500 3.56 0.00 45.28 2.27
4723 4772 3.696051 TCCTTCAGCTTGCACCAATTATC 59.304 43.478 0.00 0.00 0.00 1.75
4724 4773 3.700538 TCCTTCAGCTTGCACCAATTAT 58.299 40.909 0.00 0.00 0.00 1.28
4725 4774 3.153369 TCCTTCAGCTTGCACCAATTA 57.847 42.857 0.00 0.00 0.00 1.40
4727 4776 2.226962 ATCCTTCAGCTTGCACCAAT 57.773 45.000 0.00 0.00 0.00 3.16
4729 4778 3.018856 CAATATCCTTCAGCTTGCACCA 58.981 45.455 0.00 0.00 0.00 4.17
4730 4779 2.223665 GCAATATCCTTCAGCTTGCACC 60.224 50.000 0.00 0.00 41.33 5.01
4738 4788 2.173356 TGAGGGGTGCAATATCCTTCAG 59.827 50.000 7.16 0.00 32.78 3.02
4739 4789 2.204463 TGAGGGGTGCAATATCCTTCA 58.796 47.619 7.16 7.16 34.87 3.02
4740 4790 3.515602 ATGAGGGGTGCAATATCCTTC 57.484 47.619 0.00 0.00 0.00 3.46
4764 4814 3.218453 TCGCTCACCTTCCAATTTTTCA 58.782 40.909 0.00 0.00 0.00 2.69
4783 4847 0.097674 CATTTTCCTTGAGCGCCTCG 59.902 55.000 2.29 0.00 32.35 4.63
4789 4853 3.181527 GCATTTTCGCATTTTCCTTGAGC 60.182 43.478 0.00 0.00 0.00 4.26
4790 4854 4.240096 AGCATTTTCGCATTTTCCTTGAG 58.760 39.130 0.00 0.00 0.00 3.02
4796 4860 5.535043 AATCCAAGCATTTTCGCATTTTC 57.465 34.783 0.00 0.00 0.00 2.29
4797 4861 5.945466 AAATCCAAGCATTTTCGCATTTT 57.055 30.435 0.00 0.00 0.00 1.82
4798 4862 8.715191 TTATAAATCCAAGCATTTTCGCATTT 57.285 26.923 0.00 0.00 0.00 2.32
4799 4863 8.715191 TTTATAAATCCAAGCATTTTCGCATT 57.285 26.923 0.00 0.00 0.00 3.56
4800 4864 8.715191 TTTTATAAATCCAAGCATTTTCGCAT 57.285 26.923 0.00 0.00 0.00 4.73
4801 4865 8.715191 ATTTTATAAATCCAAGCATTTTCGCA 57.285 26.923 0.00 0.00 0.00 5.10
4837 4901 6.270000 ACGATATGAACCCAGGAGAAATCATA 59.730 38.462 0.00 0.00 35.11 2.15
4839 4903 4.408921 ACGATATGAACCCAGGAGAAATCA 59.591 41.667 0.00 0.00 0.00 2.57
4853 4917 6.406370 AGGTCAATGAACTCAACGATATGAA 58.594 36.000 0.00 0.00 0.00 2.57
4857 4921 5.411361 CCAAAGGTCAATGAACTCAACGATA 59.589 40.000 0.00 0.00 0.00 2.92
4862 4926 4.022068 GCATCCAAAGGTCAATGAACTCAA 60.022 41.667 0.00 0.00 0.00 3.02
4866 4930 4.525912 AAGCATCCAAAGGTCAATGAAC 57.474 40.909 0.00 0.00 0.00 3.18
4881 4945 6.716628 TCAAGGTGGAAATATGGATAAGCATC 59.283 38.462 0.00 0.00 0.00 3.91
4882 4946 6.613699 TCAAGGTGGAAATATGGATAAGCAT 58.386 36.000 0.00 0.00 0.00 3.79
4883 4947 6.012337 TCAAGGTGGAAATATGGATAAGCA 57.988 37.500 0.00 0.00 0.00 3.91
4884 4948 6.716628 TCATCAAGGTGGAAATATGGATAAGC 59.283 38.462 0.00 0.00 0.00 3.09
4885 4949 7.175641 GGTCATCAAGGTGGAAATATGGATAAG 59.824 40.741 0.00 0.00 0.00 1.73
4886 4950 7.004086 GGTCATCAAGGTGGAAATATGGATAA 58.996 38.462 0.00 0.00 0.00 1.75
4887 4951 6.332635 AGGTCATCAAGGTGGAAATATGGATA 59.667 38.462 0.00 0.00 0.00 2.59
4888 4952 5.135020 AGGTCATCAAGGTGGAAATATGGAT 59.865 40.000 0.00 0.00 0.00 3.41
4889 4953 4.478317 AGGTCATCAAGGTGGAAATATGGA 59.522 41.667 0.00 0.00 0.00 3.41
4890 4954 4.796606 AGGTCATCAAGGTGGAAATATGG 58.203 43.478 0.00 0.00 0.00 2.74
4891 4955 5.297776 GTGAGGTCATCAAGGTGGAAATATG 59.702 44.000 0.00 0.00 40.43 1.78
4892 4956 5.192522 AGTGAGGTCATCAAGGTGGAAATAT 59.807 40.000 0.00 0.00 40.43 1.28
4893 4957 4.536090 AGTGAGGTCATCAAGGTGGAAATA 59.464 41.667 0.00 0.00 40.43 1.40
4894 4958 3.331889 AGTGAGGTCATCAAGGTGGAAAT 59.668 43.478 0.00 0.00 40.43 2.17
4895 4959 2.711009 AGTGAGGTCATCAAGGTGGAAA 59.289 45.455 0.00 0.00 40.43 3.13
4896 4960 2.038952 CAGTGAGGTCATCAAGGTGGAA 59.961 50.000 0.00 0.00 40.43 3.53
4897 4961 1.625315 CAGTGAGGTCATCAAGGTGGA 59.375 52.381 0.00 0.00 40.43 4.02
4898 4962 1.625315 TCAGTGAGGTCATCAAGGTGG 59.375 52.381 0.00 0.00 40.43 4.61
4899 4963 2.354503 CCTCAGTGAGGTCATCAAGGTG 60.355 54.545 28.38 0.86 44.25 4.00
4900 4964 1.905215 CCTCAGTGAGGTCATCAAGGT 59.095 52.381 28.38 0.00 44.25 3.50
4901 4965 2.687700 CCTCAGTGAGGTCATCAAGG 57.312 55.000 28.38 2.96 44.25 3.61
4916 4980 0.703488 TCCCAACAATGCCATCCTCA 59.297 50.000 0.00 0.00 0.00 3.86
4924 4988 3.591196 TTGTATGCTTCCCAACAATGC 57.409 42.857 0.00 0.00 0.00 3.56
4931 4995 5.447757 TGATCATCATTTGTATGCTTCCCA 58.552 37.500 0.00 0.00 0.00 4.37
4932 4996 6.585695 ATGATCATCATTTGTATGCTTCCC 57.414 37.500 1.18 0.00 32.13 3.97
4960 5455 3.745975 CACTTTATTTGCAGAGGTCGTCA 59.254 43.478 0.00 0.00 0.00 4.35
4961 5456 3.424962 GCACTTTATTTGCAGAGGTCGTC 60.425 47.826 0.00 0.00 39.93 4.20
4962 5457 2.484264 GCACTTTATTTGCAGAGGTCGT 59.516 45.455 0.00 0.00 39.93 4.34
4990 5485 6.565036 TCCATAGAGGATAAGATGATCACCA 58.435 40.000 0.00 0.00 43.07 4.17


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

AutoCloner maintained by Alex Coulton.