Multiple sequence alignment - TraesCS5B01G366300

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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 TraesCS5B01G366300 chr5B 100.000 5872 0 0 1 5872 544908729 544914600 0.000000e+00 10844.0
1 TraesCS5B01G366300 chr5B 94.325 793 40 4 3999 4789 544985109 544985898 0.000000e+00 1210.0
2 TraesCS5B01G366300 chr5B 86.428 921 66 26 4854 5728 544989334 544990241 0.000000e+00 953.0
3 TraesCS5B01G366300 chr5B 94.286 35 1 1 3879 3913 544985079 544985112 1.100000e-02 52.8
4 TraesCS5B01G366300 chr5D 93.372 3576 155 33 564 4102 446758953 446762483 0.000000e+00 5216.0
5 TraesCS5B01G366300 chr5D 90.229 1832 82 33 4095 5871 446762699 446764488 0.000000e+00 2302.0
6 TraesCS5B01G366300 chr5D 83.200 125 14 6 29 149 446758300 446758421 2.240000e-19 108.0
7 TraesCS5B01G366300 chr5A 89.848 2305 141 33 3633 5871 564664421 564666698 0.000000e+00 2874.0
8 TraesCS5B01G366300 chr5A 90.347 2134 100 32 3816 5871 564603623 564605728 0.000000e+00 2702.0
9 TraesCS5B01G366300 chr5A 93.783 1705 72 15 564 2253 564600058 564601743 0.000000e+00 2531.0
10 TraesCS5B01G366300 chr5A 93.376 1087 53 11 2736 3818 564602470 564603541 0.000000e+00 1591.0
11 TraesCS5B01G366300 chr5A 93.548 93 6 0 2596 2688 564602376 564602468 7.930000e-29 139.0
12 TraesCS5B01G366300 chr6B 95.617 616 23 3 1 616 655218049 655218660 0.000000e+00 985.0
13 TraesCS5B01G366300 chr6B 96.377 276 6 3 1 276 380971968 380971697 8.970000e-123 451.0
14 TraesCS5B01G366300 chr2B 94.968 616 27 3 1 616 472575995 472575384 0.000000e+00 963.0
15 TraesCS5B01G366300 chr2B 95.290 276 8 3 1 276 103485988 103485718 3.250000e-117 433.0
16 TraesCS5B01G366300 chr3B 95.290 276 8 3 1 276 778613607 778613877 3.250000e-117 433.0
17 TraesCS5B01G366300 chr4B 94.737 190 6 3 87 276 630238176 630237991 5.760000e-75 292.0


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 TraesCS5B01G366300 chr5B 544908729 544914600 5871 False 10844.00 10844 100.000000 1 5872 1 chr5B.!!$F1 5871
1 TraesCS5B01G366300 chr5B 544985079 544990241 5162 False 738.60 1210 91.679667 3879 5728 3 chr5B.!!$F2 1849
2 TraesCS5B01G366300 chr5D 446758300 446764488 6188 False 2542.00 5216 88.933667 29 5871 3 chr5D.!!$F1 5842
3 TraesCS5B01G366300 chr5A 564664421 564666698 2277 False 2874.00 2874 89.848000 3633 5871 1 chr5A.!!$F1 2238
4 TraesCS5B01G366300 chr5A 564600058 564605728 5670 False 1740.75 2702 92.763500 564 5871 4 chr5A.!!$F2 5307
5 TraesCS5B01G366300 chr6B 655218049 655218660 611 False 985.00 985 95.617000 1 616 1 chr6B.!!$F1 615
6 TraesCS5B01G366300 chr2B 472575384 472575995 611 True 963.00 963 94.968000 1 616 1 chr2B.!!$R2 615

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
863 1006 0.396278 CCCCAAGATGCCTCCTTTCC 60.396 60.0 0.00 0.0 0.00 3.13 F
1606 1759 0.030908 GGATGGACCGCGAGAAGTAG 59.969 60.0 8.23 0.0 0.00 2.57 F
1607 1760 0.030908 GATGGACCGCGAGAAGTAGG 59.969 60.0 8.23 0.0 0.00 3.18 F
3572 4080 0.459489 GTTGTTGCTGTGCAGGGAAA 59.541 50.0 1.11 0.0 40.61 3.13 F
4404 5259 1.323271 GCCCTCCTCGTGTCATCTCA 61.323 60.0 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2141 0.034059 AGAGCTGAGGGTGTTTGACG 59.966 55.000 0.0 0.0 0.00 4.35 R
2625 3128 1.004918 CGACGGAACCTGGAAAGCT 60.005 57.895 0.0 0.0 0.00 3.74 R
3591 4099 1.141053 GGCGAATGGAAGGTAGGTGAT 59.859 52.381 0.0 0.0 0.00 3.06 R
4434 5289 0.397941 TCTGTTGCCTGGAGACCAAG 59.602 55.000 0.0 0.0 30.80 3.61 R
5848 10173 1.208614 CGAGGAAGCAGCACAAAGC 59.791 57.895 0.0 0.0 46.19 3.51 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
203 282 6.647212 TCACAATTTACTCTAACAGCATCG 57.353 37.500 0.00 0.00 0.00 3.84
225 304 4.258860 CGCAACTTTGAACAAACGAAACTC 60.259 41.667 0.00 0.00 0.00 3.01
254 333 8.685838 AGCTGGAACATAGTAAACTAACAAAA 57.314 30.769 0.00 0.00 38.20 2.44
272 351 4.218417 ACAAAATTGATGTAGGCACTCACC 59.782 41.667 0.00 0.00 41.75 4.02
356 443 4.747108 ACAATTCTGATAGATTTCGGAGCG 59.253 41.667 0.00 0.00 32.74 5.03
405 492 4.467082 CCAATCCAAATTCACCAAGATCCA 59.533 41.667 0.00 0.00 0.00 3.41
511 628 5.010922 CCAAATCCAACTCCAACTCAATCAA 59.989 40.000 0.00 0.00 0.00 2.57
546 664 2.793933 TCGATTAGTTTTCTCTCCGCG 58.206 47.619 0.00 0.00 0.00 6.46
863 1006 0.396278 CCCCAAGATGCCTCCTTTCC 60.396 60.000 0.00 0.00 0.00 3.13
869 1017 0.990818 GATGCCTCCTTTCCCCCTCT 60.991 60.000 0.00 0.00 0.00 3.69
882 1030 1.045911 CCCCTCTTCCTCCTCCTTCG 61.046 65.000 0.00 0.00 0.00 3.79
895 1043 2.494918 CTTCGGTGCCGGTAGGAG 59.505 66.667 10.94 0.00 41.02 3.69
896 1044 2.036098 TTCGGTGCCGGTAGGAGA 59.964 61.111 10.94 0.00 41.02 3.71
899 1047 2.050350 CGGTGCCGGTAGGAGAGAA 61.050 63.158 1.90 0.00 41.02 2.87
900 1048 1.817209 GGTGCCGGTAGGAGAGAAG 59.183 63.158 1.90 0.00 41.02 2.85
901 1049 0.683504 GGTGCCGGTAGGAGAGAAGA 60.684 60.000 1.90 0.00 41.02 2.87
902 1050 1.183549 GTGCCGGTAGGAGAGAAGAA 58.816 55.000 1.90 0.00 41.02 2.52
938 1087 1.810030 GCTTAACGGGCAGGAGACG 60.810 63.158 0.00 0.00 0.00 4.18
963 1112 2.671070 GGGCCAGCTTCTGTGCTA 59.329 61.111 4.39 0.00 41.98 3.49
971 1120 3.181485 CCAGCTTCTGTGCTACTACTACC 60.181 52.174 0.00 0.00 41.98 3.18
998 1150 1.117142 TCCTTCCTTCCGTCGGTTGT 61.117 55.000 11.88 0.00 0.00 3.32
1333 1485 3.483869 GGGATCTCCTGCGGGCTT 61.484 66.667 6.73 0.00 35.95 4.35
1563 1715 1.063616 CACATTGCTCGCTCATTCTGG 59.936 52.381 0.00 0.00 0.00 3.86
1592 1745 0.668706 GACGATCAGATGCCGGATGG 60.669 60.000 5.05 0.00 38.77 3.51
1604 1757 2.893398 GGATGGACCGCGAGAAGT 59.107 61.111 8.23 0.00 0.00 3.01
1606 1759 0.030908 GGATGGACCGCGAGAAGTAG 59.969 60.000 8.23 0.00 0.00 2.57
1607 1760 0.030908 GATGGACCGCGAGAAGTAGG 59.969 60.000 8.23 0.00 0.00 3.18
1628 1781 2.222007 TGTGCTGCATTTTGGTTGTC 57.778 45.000 5.27 0.00 0.00 3.18
1778 1931 1.478631 CCTTGGGAAGGGAAGATTGC 58.521 55.000 0.00 0.00 45.27 3.56
1779 1932 1.272648 CCTTGGGAAGGGAAGATTGCA 60.273 52.381 0.00 0.00 45.27 4.08
1806 1959 1.878522 CACGAGTGGAGCGCATACC 60.879 63.158 11.47 10.90 0.00 2.73
1840 1993 6.692681 CACAGAATCAGGTTGTTTGTAACTTG 59.307 38.462 0.00 0.00 38.54 3.16
1849 2002 6.603997 AGGTTGTTTGTAACTTGTTATCCACA 59.396 34.615 0.00 0.00 0.00 4.17
1864 2017 8.279970 TGTTATCCACACTTAATCCAGAAATG 57.720 34.615 0.00 0.00 0.00 2.32
1893 2051 4.454728 TTTTAATCATCAGTTGCTGCCC 57.545 40.909 0.00 0.00 0.00 5.36
1925 2083 8.627208 AATGAATAGTGTGAGAAAGTGAACAT 57.373 30.769 0.00 0.00 0.00 2.71
1926 2084 8.627208 ATGAATAGTGTGAGAAAGTGAACATT 57.373 30.769 0.00 0.00 0.00 2.71
1927 2085 8.450578 TGAATAGTGTGAGAAAGTGAACATTT 57.549 30.769 0.00 0.00 0.00 2.32
1974 2141 7.383102 AGTATTGGACTTGTGATCATCAAAC 57.617 36.000 0.00 3.26 33.13 2.93
1975 2142 4.747540 TTGGACTTGTGATCATCAAACG 57.252 40.909 0.00 0.00 0.00 3.60
1989 2156 2.285083 TCAAACGTCAAACACCCTCAG 58.715 47.619 0.00 0.00 0.00 3.35
2002 2169 1.273495 ACCCTCAGCTCTGATCCTTGA 60.273 52.381 0.00 0.00 39.13 3.02
2177 2344 1.679139 CTTGTGGTGGCTTCTTCACA 58.321 50.000 0.00 0.00 38.21 3.58
2274 2690 3.797256 CAGTACTCTAGTAAACGCCATGC 59.203 47.826 0.00 0.00 31.52 4.06
2276 2692 3.328382 ACTCTAGTAAACGCCATGCAA 57.672 42.857 0.00 0.00 0.00 4.08
2278 2694 4.261801 ACTCTAGTAAACGCCATGCAATT 58.738 39.130 0.00 0.00 0.00 2.32
2279 2695 5.424757 ACTCTAGTAAACGCCATGCAATTA 58.575 37.500 0.00 0.00 0.00 1.40
2280 2696 5.293569 ACTCTAGTAAACGCCATGCAATTAC 59.706 40.000 0.00 0.00 32.85 1.89
2324 2741 6.485648 TGCTCTTCTACAAAACTAGGGAAAAC 59.514 38.462 0.00 0.00 0.00 2.43
2363 2780 4.801891 ACTGCTAATGTGAAATGCAACAG 58.198 39.130 0.00 0.00 33.07 3.16
2428 2845 4.754618 TCTCGCTAATGTGAAATGTTGTGT 59.245 37.500 0.00 0.00 31.75 3.72
2497 2920 6.846988 TCATCCATTGGGCATAAGTTACATA 58.153 36.000 2.09 0.00 0.00 2.29
2508 2931 9.953565 GGGCATAAGTTACATAGGTTATGATAA 57.046 33.333 3.26 0.00 39.45 1.75
2692 3195 9.529325 AATTTCAAATGCATCTCATCTATTGTG 57.471 29.630 0.00 0.00 33.40 3.33
2693 3196 7.634671 TTCAAATGCATCTCATCTATTGTGT 57.365 32.000 0.00 0.00 33.40 3.72
2694 3197 8.735692 TTCAAATGCATCTCATCTATTGTGTA 57.264 30.769 0.00 0.00 33.40 2.90
2696 3199 8.615211 TCAAATGCATCTCATCTATTGTGTAAC 58.385 33.333 0.00 0.00 33.40 2.50
2728 3235 7.243604 TCATTTGACTTTCCAATGCCTATTT 57.756 32.000 0.00 0.00 0.00 1.40
2734 3241 2.937469 TCCAATGCCTATTTGCAACG 57.063 45.000 0.00 0.00 45.84 4.10
2756 3263 9.314321 CAACGTATGGATTTACTGAGTTTCTAT 57.686 33.333 0.00 0.00 0.00 1.98
2796 3303 4.394920 TCAGCAAACTCAAACTTCGAACTT 59.605 37.500 0.00 0.00 0.00 2.66
2877 3384 5.126067 GTCCATGTAATCCAAGTAGCATGT 58.874 41.667 0.00 0.00 0.00 3.21
3088 3596 7.067494 GGAATATACATTTGCCTTTGTCTCACT 59.933 37.037 0.00 0.00 0.00 3.41
3572 4080 0.459489 GTTGTTGCTGTGCAGGGAAA 59.541 50.000 1.11 0.00 40.61 3.13
3582 4090 4.264253 CTGTGCAGGGAAATCTTGACATA 58.736 43.478 0.00 0.00 0.00 2.29
3616 4124 3.023832 CCTACCTTCCATTCGCCATTTT 58.976 45.455 0.00 0.00 0.00 1.82
3744 4258 2.101750 GACGTTGAAAACCATTTGGGGT 59.898 45.455 0.96 0.00 46.28 4.95
3762 4277 8.570068 TTTGGGGTGTGAAAGTATTACTAATC 57.430 34.615 0.00 0.32 0.00 1.75
4110 4939 5.100259 TGTAAGAGCCTCTTATTCGTTTCG 58.900 41.667 16.78 0.00 40.64 3.46
4189 5044 4.627611 AGTTCTACATCACATTGCATGC 57.372 40.909 11.82 11.82 0.00 4.06
4221 5076 4.808364 TGCAAGCAACTAAAATTTCACACC 59.192 37.500 0.00 0.00 0.00 4.16
4404 5259 1.323271 GCCCTCCTCGTGTCATCTCA 61.323 60.000 0.00 0.00 0.00 3.27
4434 5289 2.497770 GCTTCCCATGCCATGTGC 59.502 61.111 3.63 0.00 41.77 4.57
4568 5423 1.834263 CTACTGGTTAGAGCCTGCCTT 59.166 52.381 0.00 0.00 0.00 4.35
4705 5560 7.371875 GCGATAGATTTGTTTCTTGATTTCTCG 59.628 37.037 0.00 0.00 39.76 4.04
4736 5591 2.556534 ACGAGAGATAAAACCGACCG 57.443 50.000 0.00 0.00 0.00 4.79
4747 5602 1.043022 AACCGACCGTGTACCTTCTT 58.957 50.000 0.00 0.00 0.00 2.52
4754 5609 4.312443 GACCGTGTACCTTCTTGATTTCA 58.688 43.478 0.00 0.00 0.00 2.69
4782 5637 6.349300 TCATAGATCCTTTTCTGTAGTTGGC 58.651 40.000 0.00 0.00 0.00 4.52
4798 9046 6.922957 TGTAGTTGGCAAGATGAACAAAATTC 59.077 34.615 0.00 0.00 0.00 2.17
4897 9149 2.760385 CCTCGGTCACTCCCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
5056 9337 5.413499 CATTTGTTGGGTGGATCAAATCTC 58.587 41.667 0.00 0.00 38.08 2.75
5228 9518 6.322456 TGGAACATGTTTGTTTCATCTGGTTA 59.678 34.615 13.36 0.00 44.68 2.85
5237 9527 8.928733 GTTTGTTTCATCTGGTTATACTCGTTA 58.071 33.333 0.00 0.00 0.00 3.18
5243 9533 9.661563 TTCATCTGGTTATACTCGTTAATGTTT 57.338 29.630 0.00 0.00 0.00 2.83
5359 9666 2.419324 GAGCTGCTCAGTGGAAATTCTG 59.581 50.000 24.02 0.00 0.00 3.02
5360 9667 2.157738 GCTGCTCAGTGGAAATTCTGT 58.842 47.619 0.00 0.00 33.89 3.41
5361 9668 2.161211 GCTGCTCAGTGGAAATTCTGTC 59.839 50.000 0.00 0.00 33.89 3.51
5362 9669 3.405831 CTGCTCAGTGGAAATTCTGTCA 58.594 45.455 0.00 0.00 33.89 3.58
5364 9671 4.005650 TGCTCAGTGGAAATTCTGTCATC 58.994 43.478 0.00 0.00 33.89 2.92
5373 9685 4.331168 GGAAATTCTGTCATCAGGTCGAAG 59.669 45.833 0.00 0.00 41.59 3.79
5374 9686 4.808414 AATTCTGTCATCAGGTCGAAGA 57.192 40.909 0.00 0.00 41.59 2.87
5420 9732 5.358922 ACTATCTGAGCTGCTTTCTCAATC 58.641 41.667 2.53 0.00 39.77 2.67
5491 9807 6.160576 TGCATAATTTTGGCCTATCCTTTC 57.839 37.500 3.32 0.00 35.26 2.62
5492 9808 5.660417 TGCATAATTTTGGCCTATCCTTTCA 59.340 36.000 3.32 0.00 35.26 2.69
5518 9834 5.464722 CAGGATGACAGTACATATCAACAGC 59.535 44.000 0.00 0.00 39.69 4.40
5704 10020 9.901172 AGTATGTTTTTACCTAGTTGGGATTAG 57.099 33.333 0.00 0.00 41.11 1.73
5718 10034 8.090788 AGTTGGGATTAGAAGCTGTTTATCTA 57.909 34.615 0.00 0.00 0.00 1.98
5871 10196 0.321346 TGTGCTGCTTCCTCGATCAA 59.679 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.006110 CAGATCTTTTGTGCCATGTTGGT 59.994 43.478 0.00 0.00 40.46 3.67
136 140 1.145759 TTCGAGCGATAAAGGCTGCG 61.146 55.000 0.00 0.00 41.72 5.18
149 153 6.538021 AGCATCCAGATAATTATCATTCGAGC 59.462 38.462 24.00 18.96 35.17 5.03
203 282 4.857037 AGAGTTTCGTTTGTTCAAAGTTGC 59.143 37.500 0.00 0.00 0.00 4.17
225 304 7.602644 TGTTAGTTTACTATGTTCCAGCTTGAG 59.397 37.037 0.00 0.00 0.00 3.02
254 333 2.681976 GCTGGTGAGTGCCTACATCAAT 60.682 50.000 0.00 0.00 0.00 2.57
356 443 1.876664 GAACAGCCGAGCCCTTTTC 59.123 57.895 0.00 0.00 0.00 2.29
420 508 7.319646 CGATTTCTTGGGTAAATGAAATTGGA 58.680 34.615 0.00 0.00 38.67 3.53
421 509 6.534793 CCGATTTCTTGGGTAAATGAAATTGG 59.465 38.462 15.06 15.06 45.80 3.16
482 587 2.760650 GTTGGAGTTGGATTTGGGGATC 59.239 50.000 0.00 0.00 0.00 3.36
511 628 5.090139 ACTAATCGATCTTGGGAGGATGAT 58.910 41.667 0.00 0.00 0.00 2.45
546 664 3.400054 CTTCGACTCCCCCACCCC 61.400 72.222 0.00 0.00 0.00 4.95
863 1006 1.045911 CGAAGGAGGAGGAAGAGGGG 61.046 65.000 0.00 0.00 0.00 4.79
882 1030 0.683504 TCTTCTCTCCTACCGGCACC 60.684 60.000 0.00 0.00 0.00 5.01
895 1043 1.202940 AGCCCAACCCAACTTCTTCTC 60.203 52.381 0.00 0.00 0.00 2.87
896 1044 0.853530 AGCCCAACCCAACTTCTTCT 59.146 50.000 0.00 0.00 0.00 2.85
899 1047 1.153756 CCAGCCCAACCCAACTTCT 59.846 57.895 0.00 0.00 0.00 2.85
900 1048 1.908299 CCCAGCCCAACCCAACTTC 60.908 63.158 0.00 0.00 0.00 3.01
901 1049 2.201210 CCCAGCCCAACCCAACTT 59.799 61.111 0.00 0.00 0.00 2.66
902 1050 4.621087 GCCCAGCCCAACCCAACT 62.621 66.667 0.00 0.00 0.00 3.16
940 1089 1.450312 CAGAAGCTGGCCCGTTAGG 60.450 63.158 0.00 0.00 39.47 2.69
963 1112 3.261137 GGAAGGAAGCAACTGGTAGTAGT 59.739 47.826 0.00 0.00 0.00 2.73
971 1120 1.160137 CGGAAGGAAGGAAGCAACTG 58.840 55.000 0.00 0.00 0.00 3.16
1333 1485 3.296709 GAGGAGCGCGGAGTGGAAA 62.297 63.158 8.83 0.00 39.19 3.13
1438 1590 4.653888 CCGGCGAGGTTGGGGTTT 62.654 66.667 9.30 0.00 34.51 3.27
1563 1715 4.260538 GGCATCTGATCGTCAGTGAAATTC 60.261 45.833 12.62 0.00 44.58 2.17
1592 1745 0.739561 ACATCCTACTTCTCGCGGTC 59.260 55.000 6.13 0.00 0.00 4.79
1604 1757 2.806434 ACCAAAATGCAGCACATCCTA 58.194 42.857 0.00 0.00 38.34 2.94
1606 1759 2.070783 CAACCAAAATGCAGCACATCC 58.929 47.619 0.00 0.00 38.34 3.51
1607 1760 2.733026 GACAACCAAAATGCAGCACATC 59.267 45.455 0.00 0.00 38.34 3.06
1628 1781 1.067425 CAGCCACAACCATCAACCATG 60.067 52.381 0.00 0.00 0.00 3.66
1778 1931 1.575922 CCACTCGTGGCAATGTGTG 59.424 57.895 8.30 8.30 44.73 3.82
1779 1932 4.063529 CCACTCGTGGCAATGTGT 57.936 55.556 2.72 3.28 44.73 3.72
1806 1959 1.815212 CTGATTCTGTGATCGCCGCG 61.815 60.000 6.39 6.39 0.00 6.46
1840 1993 7.148086 TGCATTTCTGGATTAAGTGTGGATAAC 60.148 37.037 0.00 0.00 0.00 1.89
1876 2029 1.272313 ACAGGGCAGCAACTGATGATT 60.272 47.619 19.82 0.00 38.09 2.57
1893 2051 5.868043 TCTCACACTATTCATTTGCACAG 57.132 39.130 0.00 0.00 0.00 3.66
1951 2118 6.128282 ACGTTTGATGATCACAAGTCCAATAC 60.128 38.462 0.00 0.00 0.00 1.89
1958 2125 5.065859 TGTTTGACGTTTGATGATCACAAGT 59.934 36.000 0.00 0.00 0.00 3.16
1972 2139 0.180406 AGCTGAGGGTGTTTGACGTT 59.820 50.000 0.00 0.00 0.00 3.99
1973 2140 0.249911 GAGCTGAGGGTGTTTGACGT 60.250 55.000 0.00 0.00 0.00 4.34
1974 2141 0.034059 AGAGCTGAGGGTGTTTGACG 59.966 55.000 0.00 0.00 0.00 4.35
1975 2142 1.070758 TCAGAGCTGAGGGTGTTTGAC 59.929 52.381 0.00 0.00 34.14 3.18
1989 2156 4.437930 CCGTCAAAATTCAAGGATCAGAGC 60.438 45.833 0.00 0.00 0.00 4.09
2002 2169 3.634910 ACCTGTTACAAGCCGTCAAAATT 59.365 39.130 0.00 0.00 0.00 1.82
2141 2308 3.595758 GCAACCGCAGCAACTGGT 61.596 61.111 0.00 0.00 38.36 4.00
2177 2344 2.650116 ATCCGAGGTCAGCGCAAGT 61.650 57.895 11.47 0.00 41.68 3.16
2253 2420 3.446161 TGCATGGCGTTTACTAGAGTACT 59.554 43.478 0.00 0.00 0.00 2.73
2254 2421 3.777478 TGCATGGCGTTTACTAGAGTAC 58.223 45.455 0.00 0.00 0.00 2.73
2255 2422 4.459390 TTGCATGGCGTTTACTAGAGTA 57.541 40.909 0.00 0.00 0.00 2.59
2256 2423 3.328382 TTGCATGGCGTTTACTAGAGT 57.672 42.857 0.00 0.00 0.00 3.24
2257 2424 4.882671 AATTGCATGGCGTTTACTAGAG 57.117 40.909 0.00 0.00 0.00 2.43
2258 2425 5.424757 AGTAATTGCATGGCGTTTACTAGA 58.575 37.500 11.50 0.00 37.20 2.43
2260 2427 6.819649 AGTTAGTAATTGCATGGCGTTTACTA 59.180 34.615 13.93 13.93 38.65 1.82
2261 2428 5.646360 AGTTAGTAATTGCATGGCGTTTACT 59.354 36.000 15.30 15.30 39.90 2.24
2268 2684 6.198966 GCACAATAAGTTAGTAATTGCATGGC 59.801 38.462 0.00 0.00 34.63 4.40
2274 2690 9.494479 CATCAGTGCACAATAAGTTAGTAATTG 57.506 33.333 21.04 2.32 36.80 2.32
2402 2819 5.238432 ACAACATTTCACATTAGCGAGAACA 59.762 36.000 0.00 0.00 0.00 3.18
2428 2845 5.774690 AGTTGGAGGAAAAATATTGTGCTGA 59.225 36.000 0.00 0.00 0.00 4.26
2529 2952 9.237187 TGCCAAATACTGTTAAGATGTTGATTA 57.763 29.630 0.00 0.00 0.00 1.75
2530 2953 8.121305 TGCCAAATACTGTTAAGATGTTGATT 57.879 30.769 0.00 0.00 0.00 2.57
2548 2976 9.474313 TTGAATACTAGGAAAGTAATGCCAAAT 57.526 29.630 0.00 0.00 43.87 2.32
2625 3128 1.004918 CGACGGAACCTGGAAAGCT 60.005 57.895 0.00 0.00 0.00 3.74
2671 3174 8.618677 AGTTACACAATAGATGAGATGCATTTG 58.381 33.333 0.00 0.94 37.34 2.32
2706 3213 5.876460 GCAAATAGGCATTGGAAAGTCAAAT 59.124 36.000 0.00 0.00 0.00 2.32
2709 3216 3.831333 TGCAAATAGGCATTGGAAAGTCA 59.169 39.130 0.00 0.00 39.25 3.41
2710 3217 4.454728 TGCAAATAGGCATTGGAAAGTC 57.545 40.909 0.00 0.00 39.25 3.01
2728 3235 4.827692 ACTCAGTAAATCCATACGTTGCA 58.172 39.130 0.00 0.00 0.00 4.08
2756 3263 8.097038 AGTTTGCTGAAGATCATAGACAAGTTA 58.903 33.333 0.00 0.00 0.00 2.24
2796 3303 3.271250 GGAATTGCTTCCTCTGCCA 57.729 52.632 0.00 0.00 46.44 4.92
2993 3500 7.918562 TGCAAGTTCTAATTTTTCCAGTGTAAC 59.081 33.333 0.00 0.00 0.00 2.50
2999 3506 9.912634 TTAGATTGCAAGTTCTAATTTTTCCAG 57.087 29.630 15.41 0.00 31.26 3.86
3059 3567 8.000780 AGACAAAGGCAAATGTATATTCCTTC 57.999 34.615 5.88 0.00 32.32 3.46
3088 3596 7.562454 GCAGTAGGCATAATTAACCAACTTA 57.438 36.000 9.80 0.00 43.97 2.24
3201 3709 8.417106 ACATCTCTATGAATACAGTGGTGTTAG 58.583 37.037 0.00 0.00 35.98 2.34
3527 4035 7.770433 CCACCATGAATGACTATCTTTAAGACA 59.230 37.037 0.00 0.00 0.00 3.41
3582 4090 8.568617 AATGGAAGGTAGGTGATACTAAGAAT 57.431 34.615 0.00 0.00 34.56 2.40
3591 4099 1.141053 GGCGAATGGAAGGTAGGTGAT 59.859 52.381 0.00 0.00 0.00 3.06
3723 4237 2.101750 ACCCCAAATGGTTTTCAACGTC 59.898 45.455 0.00 0.00 33.91 4.34
3762 4277 6.472887 TCCCAGTATTTTCTTGGACTTACTG 58.527 40.000 0.00 0.00 37.40 2.74
3838 4438 5.763204 TGCCTGACTGGTTAACTTTAAGAAG 59.237 40.000 5.42 3.27 38.35 2.85
4021 4627 6.707599 AACTGAAGCTTAGTTACGACAATC 57.292 37.500 15.35 0.00 36.66 2.67
4110 4939 7.816995 ACAAGAATGTTGAGAGAGACATCTTAC 59.183 37.037 0.00 0.00 35.91 2.34
4189 5044 4.439305 TTAGTTGCTTGCATTTAGCTGG 57.561 40.909 10.10 0.00 45.94 4.85
4221 5076 8.723942 AAGTAAATTCAGGTAAGCTACTCATG 57.276 34.615 0.00 0.00 0.00 3.07
4404 5259 1.032114 GGGAAGCGCCTATTGCAACT 61.032 55.000 2.29 0.00 41.33 3.16
4434 5289 0.397941 TCTGTTGCCTGGAGACCAAG 59.602 55.000 0.00 0.00 30.80 3.61
4568 5423 1.416401 AGGAGTTTTCGCCAACTGAGA 59.584 47.619 4.00 0.00 42.33 3.27
4611 5466 9.185192 GCATGCCTGTAATATTATTGTTTCTTC 57.815 33.333 6.36 0.00 0.00 2.87
4705 5560 7.412020 GGTTTTATCTCTCGTTTCACATCACTC 60.412 40.741 0.00 0.00 0.00 3.51
4736 5591 7.672983 TGAATCTGAAATCAAGAAGGTACAC 57.327 36.000 0.00 0.00 0.00 2.90
4754 5609 9.829507 CAACTACAGAAAAGGATCTATGAATCT 57.170 33.333 0.00 0.00 0.00 2.40
4782 5637 7.201410 GCATGCTACAGAATTTTGTTCATCTTG 60.201 37.037 11.37 3.72 32.56 3.02
4798 9046 5.685954 CAGCAATAAAATCAGCATGCTACAG 59.314 40.000 22.19 8.71 41.82 2.74
5056 9337 3.074412 ACATGAGGTAAAAGAAGTGCGG 58.926 45.455 0.00 0.00 0.00 5.69
5176 9466 3.182152 ACCTAGGCTTGAACTATGTGGT 58.818 45.455 9.30 0.00 0.00 4.16
5237 9527 6.472887 TCCGGACTTCTCTTATTCAAACATT 58.527 36.000 0.00 0.00 0.00 2.71
5243 9533 4.601084 ACTCTCCGGACTTCTCTTATTCA 58.399 43.478 0.00 0.00 0.00 2.57
5355 9662 4.808414 AATCTTCGACCTGATGACAGAA 57.192 40.909 0.00 0.00 46.03 3.02
5391 9703 2.370349 AGCAGCTCAGATAGTACGTGT 58.630 47.619 0.00 0.00 0.00 4.49
5475 9790 3.430453 CTGGTGAAAGGATAGGCCAAAA 58.570 45.455 5.01 0.00 40.02 2.44
5491 9807 5.535753 TGATATGTACTGTCATCCTGGTG 57.464 43.478 0.00 0.00 0.00 4.17
5492 9808 5.425217 TGTTGATATGTACTGTCATCCTGGT 59.575 40.000 0.00 0.00 0.00 4.00
5848 10173 1.208614 CGAGGAAGCAGCACAAAGC 59.791 57.895 0.00 0.00 46.19 3.51


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

AutoCloner maintained by Alex Coulton.