Multiple sequence alignment - TraesCS5A01G080400

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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 TraesCS5A01G080400 chr5A 100.000 3406 0 0 1 3406 100712560 100709155 0.000000e+00 6290.0
1 TraesCS5A01G080400 chr5D 94.665 1912 67 13 1507 3406 100127510 100125622 0.000000e+00 2933.0
2 TraesCS5A01G080400 chr5D 96.724 519 15 2 862 1379 100128031 100127514 0.000000e+00 863.0
3 TraesCS5A01G080400 chr5D 98.026 152 3 0 696 847 100128169 100128018 7.250000e-67 265.0
4 TraesCS5A01G080400 chr5D 83.085 201 32 1 1756 1956 37634695 37634893 7.510000e-42 182.0
5 TraesCS5A01G080400 chr5D 88.312 77 9 0 2666 2742 37638433 37638509 3.620000e-15 93.5
6 TraesCS5A01G080400 chr5B 95.769 1489 49 5 927 2405 108857025 108855541 0.000000e+00 2388.0
7 TraesCS5A01G080400 chr5B 94.074 675 31 6 2465 3132 108855542 108854870 0.000000e+00 1016.0
8 TraesCS5A01G080400 chr5B 86.192 688 85 5 4 684 482992558 482991874 0.000000e+00 736.0
9 TraesCS5A01G080400 chr5B 93.750 128 8 0 2207 2334 28145440 28145567 3.470000e-45 193.0
10 TraesCS5A01G080400 chr5B 97.015 67 2 0 3140 3206 108854836 108854770 2.780000e-21 113.0
11 TraesCS5A01G080400 chr5B 91.803 61 5 0 909 969 27814991 27814931 6.060000e-13 86.1
12 TraesCS5A01G080400 chr6D 88.937 687 67 5 3 684 428446728 428447410 0.000000e+00 839.0
13 TraesCS5A01G080400 chr6D 86.744 694 81 6 1 688 286639409 286638721 0.000000e+00 761.0
14 TraesCS5A01G080400 chr4D 88.423 691 70 7 1 684 504406187 504406874 0.000000e+00 824.0
15 TraesCS5A01G080400 chr4D 88.150 692 71 9 1 684 504350713 504351401 0.000000e+00 813.0
16 TraesCS5A01G080400 chr4D 88.133 691 72 6 1 684 504376813 504377500 0.000000e+00 813.0
17 TraesCS5A01G080400 chr7B 87.915 662 75 3 1 657 333401396 333402057 0.000000e+00 774.0
18 TraesCS5A01G080400 chr2D 87.202 672 75 6 1 666 24527155 24526489 0.000000e+00 754.0
19 TraesCS5A01G080400 chr6B 85.570 693 81 12 1 684 579402766 579403448 0.000000e+00 708.0


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 TraesCS5A01G080400 chr5A 100709155 100712560 3405 True 6290.000000 6290 100.000000 1 3406 1 chr5A.!!$R1 3405
1 TraesCS5A01G080400 chr5D 100125622 100128169 2547 True 1353.666667 2933 96.471667 696 3406 3 chr5D.!!$R1 2710
2 TraesCS5A01G080400 chr5B 108854770 108857025 2255 True 1172.333333 2388 95.619333 927 3206 3 chr5B.!!$R3 2279
3 TraesCS5A01G080400 chr5B 482991874 482992558 684 True 736.000000 736 86.192000 4 684 1 chr5B.!!$R2 680
4 TraesCS5A01G080400 chr6D 428446728 428447410 682 False 839.000000 839 88.937000 3 684 1 chr6D.!!$F1 681
5 TraesCS5A01G080400 chr6D 286638721 286639409 688 True 761.000000 761 86.744000 1 688 1 chr6D.!!$R1 687
6 TraesCS5A01G080400 chr4D 504406187 504406874 687 False 824.000000 824 88.423000 1 684 1 chr4D.!!$F3 683
7 TraesCS5A01G080400 chr4D 504350713 504351401 688 False 813.000000 813 88.150000 1 684 1 chr4D.!!$F1 683
8 TraesCS5A01G080400 chr4D 504376813 504377500 687 False 813.000000 813 88.133000 1 684 1 chr4D.!!$F2 683
9 TraesCS5A01G080400 chr7B 333401396 333402057 661 False 774.000000 774 87.915000 1 657 1 chr7B.!!$F1 656
10 TraesCS5A01G080400 chr2D 24526489 24527155 666 True 754.000000 754 87.202000 1 666 1 chr2D.!!$R1 665
11 TraesCS5A01G080400 chr6B 579402766 579403448 682 False 708.000000 708 85.570000 1 684 1 chr6B.!!$F1 683

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
489 505 0.031585 CCTAACGTAGCTGCGCCATA 59.968 55.0 24.6 13.48 34.88 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 2470 0.698818 AGCTTCCGTTGGAAATCCCT 59.301 50.0 0.0 0.0 41.54 4.2 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
26 27 1.291877 GCTGTGTGGGCGAACTAGTG 61.292 60.000 0.00 0.00 0.00 2.74
52 53 1.133915 CCACACAACCACCACCTAGTT 60.134 52.381 0.00 0.00 0.00 2.24
99 100 0.596577 GCTCACACGACACTCCTACA 59.403 55.000 0.00 0.00 0.00 2.74
115 117 3.521531 TCCTACATTGTGGATGGCAACTA 59.478 43.478 1.15 0.00 40.21 2.24
144 147 2.406130 CGAACGTGGCAACTAGGTAAA 58.594 47.619 0.00 0.00 37.61 2.01
185 189 1.371183 TTGCTAGACGGCAACTGCT 59.629 52.632 1.06 0.00 45.64 4.24
236 240 3.888323 ACACATGGCAACTGTGATTAACA 59.112 39.130 23.92 0.00 45.44 2.41
281 285 3.071479 CACACGTGGCAACTAGGTAAAT 58.929 45.455 21.57 0.00 37.61 1.40
289 293 4.638421 TGGCAACTAGGTAAATACACATGC 59.362 41.667 0.00 0.00 37.61 4.06
302 306 7.753309 AAATACACATGCCAACTACTGTTTA 57.247 32.000 0.00 0.00 33.52 2.01
305 309 5.130350 ACACATGCCAACTACTGTTTAACT 58.870 37.500 0.00 0.00 33.52 2.24
343 349 2.760634 ATCACACACGGCAACTATGA 57.239 45.000 0.00 0.00 0.00 2.15
368 374 0.668096 TTACACGCGGCAACTACCAG 60.668 55.000 12.47 0.00 0.00 4.00
414 420 8.154649 AGTTAACCAAAACAGATAGAGTTGTG 57.845 34.615 0.88 0.00 34.66 3.33
462 477 6.667414 AGGATGGCAACTAAATTGTTATTCCA 59.333 34.615 0.00 0.00 40.77 3.53
464 479 5.704888 TGGCAACTAAATTGTTATTCCACG 58.295 37.500 0.00 0.00 40.77 4.94
488 504 1.227263 CCTAACGTAGCTGCGCCAT 60.227 57.895 24.60 13.04 34.88 4.40
489 505 0.031585 CCTAACGTAGCTGCGCCATA 59.968 55.000 24.60 13.48 34.88 2.74
499 515 2.744709 GCGCCATAACGTGTGGGT 60.745 61.111 18.67 0.00 37.22 4.51
558 576 2.882927 AGTACTTGTTGAGCGTGTGA 57.117 45.000 0.00 0.00 0.00 3.58
585 603 2.085042 TAGTTGCGCCCACACGTGTA 62.085 55.000 22.90 0.76 34.88 2.90
666 687 1.709760 GATGTGTGGACGCATGTCG 59.290 57.895 10.48 7.79 46.01 4.35
676 697 3.181474 TGGACGCATGTCGAATATACCAA 60.181 43.478 14.88 0.98 46.49 3.67
679 700 4.185394 ACGCATGTCGAATATACCAAACA 58.815 39.130 14.88 0.00 41.67 2.83
685 706 6.656314 TGTCGAATATACCAAACATGTGAC 57.344 37.500 0.00 0.00 0.00 3.67
688 709 4.025229 CGAATATACCAAACATGTGACCGG 60.025 45.833 0.00 0.00 0.00 5.28
689 710 4.764050 ATATACCAAACATGTGACCGGA 57.236 40.909 9.46 0.00 0.00 5.14
690 711 2.172851 TACCAAACATGTGACCGGAC 57.827 50.000 9.46 1.07 0.00 4.79
691 712 0.882927 ACCAAACATGTGACCGGACG 60.883 55.000 9.46 0.00 0.00 4.79
692 713 0.882927 CCAAACATGTGACCGGACGT 60.883 55.000 9.46 0.00 0.00 4.34
693 714 0.511221 CAAACATGTGACCGGACGTC 59.489 55.000 9.46 7.13 42.33 4.34
694 715 0.601841 AAACATGTGACCGGACGTCC 60.602 55.000 25.28 25.28 41.18 4.79
700 721 1.411977 TGTGACCGGACGTCCTTTTTA 59.588 47.619 30.92 11.64 41.18 1.52
820 841 3.917760 CTCGGATCCGGAGTGGCC 61.918 72.222 32.79 7.83 40.25 5.36
830 851 2.262915 GAGTGGCCTGTGTCCTCG 59.737 66.667 3.32 0.00 0.00 4.63
837 858 2.158957 TGGCCTGTGTCCTCGATAAATC 60.159 50.000 3.32 0.00 0.00 2.17
838 859 2.158957 GGCCTGTGTCCTCGATAAATCA 60.159 50.000 0.00 0.00 0.00 2.57
839 860 3.495100 GGCCTGTGTCCTCGATAAATCAT 60.495 47.826 0.00 0.00 0.00 2.45
840 861 3.743396 GCCTGTGTCCTCGATAAATCATC 59.257 47.826 0.00 0.00 0.00 2.92
841 862 4.310769 CCTGTGTCCTCGATAAATCATCC 58.689 47.826 0.00 0.00 0.00 3.51
842 863 4.310769 CTGTGTCCTCGATAAATCATCCC 58.689 47.826 0.00 0.00 0.00 3.85
843 864 3.967326 TGTGTCCTCGATAAATCATCCCT 59.033 43.478 0.00 0.00 0.00 4.20
844 865 4.202253 TGTGTCCTCGATAAATCATCCCTG 60.202 45.833 0.00 0.00 0.00 4.45
845 866 3.967326 TGTCCTCGATAAATCATCCCTGT 59.033 43.478 0.00 0.00 0.00 4.00
846 867 4.202253 TGTCCTCGATAAATCATCCCTGTG 60.202 45.833 0.00 0.00 0.00 3.66
847 868 3.967326 TCCTCGATAAATCATCCCTGTGT 59.033 43.478 0.00 0.00 0.00 3.72
848 869 4.408921 TCCTCGATAAATCATCCCTGTGTT 59.591 41.667 0.00 0.00 0.00 3.32
849 870 5.104527 TCCTCGATAAATCATCCCTGTGTTT 60.105 40.000 0.00 0.00 0.00 2.83
850 871 5.008019 CCTCGATAAATCATCCCTGTGTTTG 59.992 44.000 0.00 0.00 0.00 2.93
851 872 5.496556 TCGATAAATCATCCCTGTGTTTGT 58.503 37.500 0.00 0.00 0.00 2.83
852 873 5.584649 TCGATAAATCATCCCTGTGTTTGTC 59.415 40.000 0.00 0.00 0.00 3.18
853 874 5.353956 CGATAAATCATCCCTGTGTTTGTCA 59.646 40.000 0.00 0.00 0.00 3.58
854 875 6.128035 CGATAAATCATCCCTGTGTTTGTCAA 60.128 38.462 0.00 0.00 0.00 3.18
855 876 5.867903 AAATCATCCCTGTGTTTGTCAAA 57.132 34.783 0.00 0.00 0.00 2.69
856 877 5.867903 AATCATCCCTGTGTTTGTCAAAA 57.132 34.783 0.00 0.00 0.00 2.44
857 878 5.867903 ATCATCCCTGTGTTTGTCAAAAA 57.132 34.783 0.00 0.00 0.00 1.94
905 926 2.096713 GCGAGCGACAATATCCAACATC 60.097 50.000 0.00 0.00 0.00 3.06
988 1009 0.760567 ATCCAGATCCAGCAGCGGTA 60.761 55.000 3.62 0.00 0.00 4.02
1228 1256 4.115199 ACCCCTCAGCAATCCGCC 62.115 66.667 0.00 0.00 44.04 6.13
1390 1418 4.528206 CCTTGGGGTTTGAGCTCTTTTATT 59.472 41.667 16.19 0.00 0.00 1.40
1485 1513 4.082523 CGTGGGCGTGGACTGGAT 62.083 66.667 0.00 0.00 0.00 3.41
1493 1521 0.459237 CGTGGACTGGATGCAGAGAC 60.459 60.000 22.24 12.19 0.00 3.36
1622 1650 0.447801 CTTGCCGACATGTTACTGCC 59.552 55.000 0.00 0.00 0.00 4.85
1624 1652 0.391130 TGCCGACATGTTACTGCCTC 60.391 55.000 0.00 0.00 0.00 4.70
1625 1653 1.090052 GCCGACATGTTACTGCCTCC 61.090 60.000 0.00 0.00 0.00 4.30
1677 1705 5.126067 GTGTACTGGCATGGTGAAATCTAT 58.874 41.667 0.00 0.00 0.00 1.98
1739 1767 2.237392 ACTGACTTCCTAAGCACCATCC 59.763 50.000 0.00 0.00 0.00 3.51
1765 1793 9.760660 CTTTCTTCTTACAATGTTATTTCCTCG 57.239 33.333 0.00 0.00 0.00 4.63
1947 1978 3.161866 GAGAAGGGGGTGTATTTTGCAA 58.838 45.455 0.00 0.00 0.00 4.08
1993 2024 6.037786 TCGAGTTTGGATACTCACTGAATT 57.962 37.500 0.00 0.00 43.79 2.17
1994 2025 7.165460 TCGAGTTTGGATACTCACTGAATTA 57.835 36.000 0.00 0.00 43.79 1.40
1995 2026 7.033791 TCGAGTTTGGATACTCACTGAATTAC 58.966 38.462 0.00 0.00 43.79 1.89
1996 2027 6.255887 CGAGTTTGGATACTCACTGAATTACC 59.744 42.308 0.00 0.00 43.79 2.85
2138 2169 8.870879 CCAGCTATTTACAGTACAGTAAAAGAC 58.129 37.037 22.49 15.61 44.41 3.01
2164 2195 3.689347 TGGAGTTGAATTCAGACCATGG 58.311 45.455 11.19 11.19 0.00 3.66
2168 2199 4.530875 AGTTGAATTCAGACCATGGGATC 58.469 43.478 18.09 5.36 0.00 3.36
2340 2371 1.617850 ACATGCGCCCAAAAAGATTGA 59.382 42.857 4.18 0.00 0.00 2.57
2402 2433 2.131067 ACCTTGTTTGTTGGGCCCG 61.131 57.895 19.37 0.00 0.00 6.13
2412 2443 1.847737 TGTTGGGCCCGTAATAAGGAT 59.152 47.619 19.37 0.00 0.00 3.24
2463 2494 1.459450 TTTCCAACGGAAGCTATGCC 58.541 50.000 0.00 0.00 43.06 4.40
2492 2523 1.557099 TGCATACGTCTCTGTCCCTT 58.443 50.000 0.00 0.00 0.00 3.95
2510 2541 0.603707 TTGAGCTGCTTCACTTCCCG 60.604 55.000 2.53 0.00 0.00 5.14
2597 2628 5.644206 TGCTCAGTTATAGCTAGATCTACCG 59.356 44.000 0.00 0.00 40.73 4.02
2609 2640 3.567397 AGATCTACCGTTACCATGAGCT 58.433 45.455 0.00 0.00 0.00 4.09
2663 2700 7.757624 TCCAAATTAAGACTTGTGTTTGACAAC 59.242 33.333 16.70 0.00 39.78 3.32
2664 2701 7.253618 CCAAATTAAGACTTGTGTTTGACAACG 60.254 37.037 16.70 0.00 39.78 4.10
2709 2746 5.544176 TCTCCCATTCTAAGGCATAACTAGG 59.456 44.000 0.00 0.00 0.00 3.02
2721 2758 6.011481 AGGCATAACTAGGTAGTCCTATGTC 58.989 44.000 8.46 5.73 44.30 3.06
2734 2771 1.405821 CCTATGTCCTCGGTGTCAGAC 59.594 57.143 0.00 0.00 0.00 3.51
2822 2859 4.890088 AGAATGCAAGCATGTGTTGAATT 58.110 34.783 8.50 13.26 36.09 2.17
2848 2885 4.269363 ACAGTTTAACGTTTCAGAGAACCG 59.731 41.667 5.91 0.00 0.00 4.44
2912 2949 9.944663 GTTTCTATGTTCGGATAAATATGCAAA 57.055 29.630 0.00 0.00 0.00 3.68
3080 3126 4.084589 CGGCATTTTGCTTCAGGTAAAAAC 60.085 41.667 0.00 0.00 44.28 2.43
3138 3213 7.141100 ACAGTCAAAGACCAAAATATAACGG 57.859 36.000 0.00 0.00 32.18 4.44
3139 3214 6.027749 CAGTCAAAGACCAAAATATAACGGC 58.972 40.000 0.00 0.00 32.18 5.68
3165 3240 2.090658 GTGAGATTGTGTGCTTCGTACG 59.909 50.000 9.53 9.53 0.00 3.67
3213 3289 2.472695 TTGGATGTGAGACTTTCCCG 57.527 50.000 0.00 0.00 0.00 5.14
3229 3305 6.007703 ACTTTCCCGAAGATAAATTGGTGAA 58.992 36.000 0.00 0.00 38.77 3.18
3268 3346 1.160137 GACAAGTCACATGACCCAGC 58.840 55.000 8.41 0.00 45.85 4.85
3319 3397 4.120946 AGACTACTGTTCCAGTTCTCCT 57.879 45.455 1.74 0.00 42.59 3.69
3374 3452 2.032894 CGAGCGACACTTTGTGTTGATT 60.033 45.455 18.90 8.24 45.05 2.57
3382 3460 4.821805 ACACTTTGTGTTGATTGGTAGAGG 59.178 41.667 0.00 0.00 45.08 3.69
3396 3474 3.181417 TGGTAGAGGTAGATCCATCCTGG 60.181 52.174 5.80 0.00 39.43 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.193536 GGTGGTTGTGTGGGCAGAC 61.194 63.158 0.00 0.00 0.00 3.51
82 83 2.626266 ACAATGTAGGAGTGTCGTGTGA 59.374 45.455 0.00 0.00 0.00 3.58
99 100 3.439857 ACTGTAGTTGCCATCCACAAT 57.560 42.857 0.00 0.00 0.00 2.71
144 147 1.985473 ATCACAGTTGCCATGTGTGT 58.015 45.000 11.76 0.06 46.49 3.72
185 189 1.814169 TTGCCACGTACGCACAACA 60.814 52.632 16.72 4.02 35.56 3.33
236 240 5.536161 GGTCCAATCATAGTTGCCATGTATT 59.464 40.000 0.00 0.00 0.00 1.89
281 285 6.292923 AGTTAAACAGTAGTTGGCATGTGTA 58.707 36.000 0.00 0.00 38.17 2.90
289 293 7.551262 TGCCACATATAGTTAAACAGTAGTTGG 59.449 37.037 0.00 0.00 38.17 3.77
302 306 9.326413 GTGATTAACTACTTGCCACATATAGTT 57.674 33.333 0.00 0.00 39.02 2.24
305 309 8.261522 TGTGTGATTAACTACTTGCCACATATA 58.738 33.333 0.00 0.00 35.83 0.86
343 349 1.810151 AGTTGCCGCGTGTAATCAAAT 59.190 42.857 4.92 0.00 0.00 2.32
413 419 4.191544 GTTGGCAGATGTAGTTAGCATCA 58.808 43.478 7.83 0.00 43.66 3.07
414 420 3.561725 GGTTGGCAGATGTAGTTAGCATC 59.438 47.826 0.00 0.00 42.08 3.91
456 471 2.031120 CGTTAGGTACCCCGTGGAATA 58.969 52.381 8.74 0.00 35.12 1.75
459 474 0.329931 TACGTTAGGTACCCCGTGGA 59.670 55.000 24.20 9.10 34.95 4.02
462 477 0.034089 AGCTACGTTAGGTACCCCGT 60.034 55.000 21.04 21.04 34.21 5.28
464 479 0.103755 GCAGCTACGTTAGGTACCCC 59.896 60.000 8.74 0.00 34.67 4.95
488 504 4.319622 CGAAGCAAAAATACCCACACGTTA 60.320 41.667 0.00 0.00 0.00 3.18
489 505 3.549221 CGAAGCAAAAATACCCACACGTT 60.549 43.478 0.00 0.00 0.00 3.99
524 541 4.021368 ACAAGTACTACGCATCTTCACCTT 60.021 41.667 0.00 0.00 0.00 3.50
536 553 2.404029 CACACGCTCAACAAGTACTACG 59.596 50.000 0.00 0.00 0.00 3.51
558 576 1.666872 GGGCGCAACTACTTCGTGT 60.667 57.895 10.83 0.00 0.00 4.49
666 687 5.007332 GTCCGGTCACATGTTTGGTATATTC 59.993 44.000 0.00 0.00 0.00 1.75
676 697 4.667420 GACGTCCGGTCACATGTT 57.333 55.556 3.51 0.00 45.36 2.71
685 706 3.754850 AGGAAAATAAAAAGGACGTCCGG 59.245 43.478 28.26 0.00 42.08 5.14
688 709 9.518906 TTTACAAAGGAAAATAAAAAGGACGTC 57.481 29.630 7.13 7.13 0.00 4.34
689 710 9.304731 GTTTACAAAGGAAAATAAAAAGGACGT 57.695 29.630 0.00 0.00 0.00 4.34
690 711 9.303537 TGTTTACAAAGGAAAATAAAAAGGACG 57.696 29.630 0.00 0.00 0.00 4.79
820 841 4.039730 AGGGATGATTTATCGAGGACACAG 59.960 45.833 0.00 0.00 36.62 3.66
830 851 6.757897 TGACAAACACAGGGATGATTTATC 57.242 37.500 0.00 0.00 34.93 1.75
859 880 2.094675 CCGCTCACAGGGATGATTTTT 58.905 47.619 0.00 0.00 0.00 1.94
860 881 1.004745 ACCGCTCACAGGGATGATTTT 59.995 47.619 0.00 0.00 0.00 1.82
861 882 0.620556 ACCGCTCACAGGGATGATTT 59.379 50.000 0.00 0.00 0.00 2.17
862 883 0.179000 GACCGCTCACAGGGATGATT 59.821 55.000 0.00 0.00 0.00 2.57
863 884 0.977627 TGACCGCTCACAGGGATGAT 60.978 55.000 0.00 0.00 0.00 2.45
864 885 1.191489 TTGACCGCTCACAGGGATGA 61.191 55.000 0.00 0.00 0.00 2.92
905 926 5.334879 CGTCCAACAAGAAAACCATCCTAAG 60.335 44.000 0.00 0.00 0.00 2.18
988 1009 4.158764 CGTCTGGTCCATCTCTCTACTTTT 59.841 45.833 0.00 0.00 0.00 2.27
1228 1256 2.279517 GTGGAGGTCGGCATAGCG 60.280 66.667 0.00 0.00 0.00 4.26
1350 1378 3.083997 GGAGGAGATGGGCGTGGT 61.084 66.667 0.00 0.00 0.00 4.16
1390 1418 6.641723 TCAAACACGATGTAGTTTCGTTCATA 59.358 34.615 0.00 0.00 46.96 2.15
1485 1513 1.224069 GCTGTTGCTTCGTCTCTGCA 61.224 55.000 0.00 0.00 36.03 4.41
1493 1521 1.444895 GGCCATTGCTGTTGCTTCG 60.445 57.895 0.00 0.00 40.48 3.79
1677 1705 5.278414 CCTCATAACAAAATGACAGTGCACA 60.278 40.000 21.04 0.00 32.51 4.57
1739 1767 9.760660 CGAGGAAATAACATTGTAAGAAGAAAG 57.239 33.333 0.00 0.00 0.00 2.62
1765 1793 5.064441 ACCAATGCAAGCTCTTTATTGAC 57.936 39.130 13.55 0.00 31.50 3.18
1947 1978 2.816087 GCTGACATTGACCATCAAGTGT 59.184 45.455 0.00 2.77 40.05 3.55
2105 2136 7.712639 ACTGTACTGTAAATAGCTGGATTGATG 59.287 37.037 3.21 0.00 0.00 3.07
2138 2169 4.580167 TGGTCTGAATTCAACTCCAACTTG 59.420 41.667 17.74 1.81 0.00 3.16
2144 2175 3.019564 CCCATGGTCTGAATTCAACTCC 58.980 50.000 11.73 11.90 0.00 3.85
2164 2195 8.553459 TTCAAGTCTAGTTTCAAAGATGATCC 57.447 34.615 0.00 0.00 34.96 3.36
2168 2199 6.348868 GCCCTTCAAGTCTAGTTTCAAAGATG 60.349 42.308 0.00 0.00 0.00 2.90
2412 2443 8.565896 ACAAGCTTGTCAATCAATTATCTACA 57.434 30.769 26.36 0.00 36.50 2.74
2439 2470 0.698818 AGCTTCCGTTGGAAATCCCT 59.301 50.000 0.00 0.00 41.54 4.20
2463 2494 4.678742 CAGAGACGTATGCATCATGTGTAG 59.321 45.833 0.19 0.00 0.00 2.74
2492 2523 1.004560 CGGGAAGTGAAGCAGCTCA 60.005 57.895 0.00 0.00 0.00 4.26
2510 2541 6.578023 ACTGAACTCTTTCATAGACTATGCC 58.422 40.000 16.38 1.15 41.05 4.40
2609 2640 2.513753 CTTACAACTGAACCCATGGCA 58.486 47.619 6.09 0.00 0.00 4.92
2663 2700 3.641648 ACCACAACATTTCTTGCATTCG 58.358 40.909 0.00 0.00 0.00 3.34
2664 2701 5.291971 AGAACCACAACATTTCTTGCATTC 58.708 37.500 0.00 0.00 0.00 2.67
2709 2746 2.617774 GACACCGAGGACATAGGACTAC 59.382 54.545 0.00 0.00 0.00 2.73
2822 2859 6.698766 GGTTCTCTGAAACGTTAAACTGTCTA 59.301 38.462 0.00 0.00 0.00 2.59
2848 2885 1.198637 GTGTCTGCATTTGAGACTGCC 59.801 52.381 4.86 0.00 40.54 4.85
2912 2949 4.465660 TGCTCTGCTCTACTTGAAGAAGAT 59.534 41.667 0.00 0.00 32.98 2.40
2988 3034 5.555966 TGTGTTGGAGAATGTAGTGCATAA 58.444 37.500 0.00 0.00 36.67 1.90
3080 3126 4.379499 GCTAATTTTCTTCACCCAGTTCGG 60.379 45.833 0.00 0.00 0.00 4.30
3137 3212 0.110056 CACACAATCTCACAAGCGCC 60.110 55.000 2.29 0.00 0.00 6.53
3138 3213 0.727122 GCACACAATCTCACAAGCGC 60.727 55.000 0.00 0.00 0.00 5.92
3139 3214 0.870393 AGCACACAATCTCACAAGCG 59.130 50.000 0.00 0.00 0.00 4.68
3213 3289 5.476945 ACCCTGTGTTCACCAATTTATCTTC 59.523 40.000 0.37 0.00 0.00 2.87
3229 3305 3.008049 GTCCATCTTCTTGTACCCTGTGT 59.992 47.826 0.00 0.00 0.00 3.72
3281 3359 0.474184 TCTAGGGCTTGCCTATTGCC 59.526 55.000 11.71 0.00 45.42 4.52
3319 3397 8.611257 TCCTCTCCCATAAGTCAGAAAATTAAA 58.389 33.333 0.00 0.00 0.00 1.52
3374 3452 4.119556 CAGGATGGATCTACCTCTACCA 57.880 50.000 0.00 0.00 39.86 3.25


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

AutoCloner maintained by Alex Coulton.