Multiple sequence alignment - TraesCS4A01G416300

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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 TraesCS4A01G416300 chr4A 100.000 3840 0 0 1 3840 685942073 685938234 0.000000e+00 7092
1 TraesCS4A01G416300 chr4A 97.216 1940 53 1 951 2890 685998868 685996930 0.000000e+00 3282
2 TraesCS4A01G416300 chr4A 94.212 1814 92 10 806 2617 686170408 686168606 0.000000e+00 2756
3 TraesCS4A01G416300 chr4A 95.650 1678 52 9 945 2619 686140235 686138576 0.000000e+00 2675
4 TraesCS4A01G416300 chr4A 94.402 661 32 5 3180 3840 584336690 584337345 0.000000e+00 1011
5 TraesCS4A01G416300 chr4A 91.650 491 36 5 3352 3840 486649208 486648721 0.000000e+00 675
6 TraesCS4A01G416300 chr4A 83.378 373 43 13 548 906 686140610 686140243 1.030000e-85 327
7 TraesCS4A01G416300 chr4A 79.255 376 44 19 398 751 686171086 686170723 8.300000e-57 231
8 TraesCS4A01G416300 chr4B 94.524 2721 140 6 47 2760 606819470 606816752 0.000000e+00 4191
9 TraesCS4A01G416300 chr4B 91.327 2087 116 37 548 2617 606909638 606907600 0.000000e+00 2791
10 TraesCS4A01G416300 chr4B 95.114 1760 83 2 858 2617 606828670 606826914 0.000000e+00 2771
11 TraesCS4A01G416300 chr4B 94.323 1779 93 6 844 2617 606867922 606866147 0.000000e+00 2719
12 TraesCS4A01G416300 chr4B 93.276 818 50 3 50 862 606829578 606828761 0.000000e+00 1201
13 TraesCS4A01G416300 chr4B 87.379 309 23 10 548 844 606869258 606868954 1.320000e-89 340
14 TraesCS4A01G416300 chr4B 80.645 155 17 11 396 547 606869429 606869285 1.460000e-19 108
15 TraesCS4A01G416300 chrUn 93.952 2381 100 13 47 2395 61735426 61733058 0.000000e+00 3559
16 TraesCS4A01G416300 chrUn 96.512 1577 55 0 1041 2617 61732955 61731379 0.000000e+00 2608
17 TraesCS4A01G416300 chr4D 92.193 2088 96 40 354 2395 479639494 479637428 0.000000e+00 2891
18 TraesCS4A01G416300 chr4D 96.337 1720 61 1 1041 2760 479637325 479635608 0.000000e+00 2826
19 TraesCS4A01G416300 chr4D 91.567 2087 119 30 548 2617 479676943 479674897 0.000000e+00 2826
20 TraesCS4A01G416300 chr4D 78.286 1400 271 24 1060 2440 479540647 479542032 0.000000e+00 870
21 TraesCS4A01G416300 chr2A 95.111 900 41 3 2943 3840 3504374 3503476 0.000000e+00 1415
22 TraesCS4A01G416300 chr2A 92.405 474 24 9 2933 3400 419484143 419483676 0.000000e+00 665
23 TraesCS4A01G416300 chr5A 94.365 905 47 2 2936 3840 328540520 328541420 0.000000e+00 1386
24 TraesCS4A01G416300 chr1A 93.437 899 57 2 2942 3840 47553476 47554372 0.000000e+00 1332
25 TraesCS4A01G416300 chr1A 93.430 898 53 4 2943 3840 434864675 434865566 0.000000e+00 1327
26 TraesCS4A01G416300 chr1A 93.000 900 58 5 2945 3840 478450127 478449229 0.000000e+00 1308
27 TraesCS4A01G416300 chr7A 91.716 676 54 2 2941 3615 69986103 69985429 0.000000e+00 937
28 TraesCS4A01G416300 chr3A 95.474 464 20 1 3378 3840 660861532 660861069 0.000000e+00 739
29 TraesCS4A01G416300 chr3A 93.987 449 20 4 2932 3374 660662087 660661640 0.000000e+00 673
30 TraesCS4A01G416300 chr2D 95.474 464 20 1 3378 3840 542526605 542526142 0.000000e+00 739
31 TraesCS4A01G416300 chr6A 95.692 441 11 7 2940 3374 26629973 26630411 0.000000e+00 702


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 TraesCS4A01G416300 chr4A 685938234 685942073 3839 True 7092.000000 7092 100.0000 1 3840 1 chr4A.!!$R2 3839
1 TraesCS4A01G416300 chr4A 685996930 685998868 1938 True 3282.000000 3282 97.2160 951 2890 1 chr4A.!!$R3 1939
2 TraesCS4A01G416300 chr4A 686138576 686140610 2034 True 1501.000000 2675 89.5140 548 2619 2 chr4A.!!$R4 2071
3 TraesCS4A01G416300 chr4A 686168606 686171086 2480 True 1493.500000 2756 86.7335 398 2617 2 chr4A.!!$R5 2219
4 TraesCS4A01G416300 chr4A 584336690 584337345 655 False 1011.000000 1011 94.4020 3180 3840 1 chr4A.!!$F1 660
5 TraesCS4A01G416300 chr4B 606816752 606819470 2718 True 4191.000000 4191 94.5240 47 2760 1 chr4B.!!$R1 2713
6 TraesCS4A01G416300 chr4B 606907600 606909638 2038 True 2791.000000 2791 91.3270 548 2617 1 chr4B.!!$R2 2069
7 TraesCS4A01G416300 chr4B 606826914 606829578 2664 True 1986.000000 2771 94.1950 50 2617 2 chr4B.!!$R3 2567
8 TraesCS4A01G416300 chr4B 606866147 606869429 3282 True 1055.666667 2719 87.4490 396 2617 3 chr4B.!!$R4 2221
9 TraesCS4A01G416300 chrUn 61731379 61735426 4047 True 3083.500000 3559 95.2320 47 2617 2 chrUn.!!$R1 2570
10 TraesCS4A01G416300 chr4D 479635608 479639494 3886 True 2858.500000 2891 94.2650 354 2760 2 chr4D.!!$R2 2406
11 TraesCS4A01G416300 chr4D 479674897 479676943 2046 True 2826.000000 2826 91.5670 548 2617 1 chr4D.!!$R1 2069
12 TraesCS4A01G416300 chr4D 479540647 479542032 1385 False 870.000000 870 78.2860 1060 2440 1 chr4D.!!$F1 1380
13 TraesCS4A01G416300 chr2A 3503476 3504374 898 True 1415.000000 1415 95.1110 2943 3840 1 chr2A.!!$R1 897
14 TraesCS4A01G416300 chr5A 328540520 328541420 900 False 1386.000000 1386 94.3650 2936 3840 1 chr5A.!!$F1 904
15 TraesCS4A01G416300 chr1A 47553476 47554372 896 False 1332.000000 1332 93.4370 2942 3840 1 chr1A.!!$F1 898
16 TraesCS4A01G416300 chr1A 434864675 434865566 891 False 1327.000000 1327 93.4300 2943 3840 1 chr1A.!!$F2 897
17 TraesCS4A01G416300 chr1A 478449229 478450127 898 True 1308.000000 1308 93.0000 2945 3840 1 chr1A.!!$R1 895
18 TraesCS4A01G416300 chr7A 69985429 69986103 674 True 937.000000 937 91.7160 2941 3615 1 chr7A.!!$R1 674

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
510 519 0.369248 GTGCGCTTACCTTCTTACGC 59.631 55.000 9.73 0.00 46.05 4.42 F
623 682 0.746063 CCCAAAGCTTGCTTGTGTCA 59.254 50.000 8.73 0.00 0.00 3.58 F
625 684 1.269413 CCAAAGCTTGCTTGTGTCAGG 60.269 52.381 8.73 1.71 0.00 3.86 F
1471 2973 2.415512 GACGCTATGTTTCTTCCGCTTT 59.584 45.455 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 3117 0.385751 ATGCGGACGAGACGATGATT 59.614 50.000 0.00 0.0 0.00 2.57 R
1863 3365 0.702902 ACCCTGGACGTTCTCCTCTA 59.297 55.000 0.00 0.0 40.26 2.43 R
2660 5625 3.738830 AAGCAAACACTTGTGCATGAT 57.261 38.095 0.00 2.1 43.42 2.45 R
3057 6023 0.601558 ACACACGCGAGTTGTCCTAT 59.398 50.000 15.93 0.0 46.40 2.57 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
29 30 9.915629 AAGTCAAATAACACAAAGTACAAAACA 57.084 25.926 0.00 0.00 0.00 2.83
32 33 9.862371 TCAAATAACACAAAGTACAAAACATGT 57.138 25.926 0.00 0.00 46.36 3.21
38 39 9.477484 AACACAAAGTACAAAACATGTTTAACA 57.523 25.926 23.53 9.09 43.63 2.41
39 40 8.917655 ACACAAAGTACAAAACATGTTTAACAC 58.082 29.630 23.53 18.93 43.63 3.32
40 41 8.916654 CACAAAGTACAAAACATGTTTAACACA 58.083 29.630 23.53 5.71 43.63 3.72
41 42 9.477484 ACAAAGTACAAAACATGTTTAACACAA 57.523 25.926 23.53 4.72 43.63 3.33
44 45 8.865590 AGTACAAAACATGTTTAACACAATCC 57.134 30.769 23.53 5.99 43.63 3.01
45 46 8.470805 AGTACAAAACATGTTTAACACAATCCA 58.529 29.630 23.53 0.00 43.63 3.41
56 57 7.175990 TGTTTAACACAATCCACCTAATCCTTC 59.824 37.037 0.00 0.00 29.87 3.46
95 96 1.021390 CCCTGTGCTAGAACCAAGCG 61.021 60.000 0.00 0.00 43.11 4.68
104 105 5.294552 GTGCTAGAACCAAGCGATTTCTATT 59.705 40.000 0.00 0.00 43.11 1.73
114 115 5.296151 AGCGATTTCTATTCAGATTCCCA 57.704 39.130 0.00 0.00 0.00 4.37
214 215 3.196254 GTGGACCAACGAGACCCTTAATA 59.804 47.826 0.00 0.00 0.00 0.98
298 301 6.384224 TGCTGCATTCTATTTTGTTCTGAAG 58.616 36.000 0.00 0.00 0.00 3.02
331 334 6.670695 ATTCTGAAATTGGGTTTAGCAAGT 57.329 33.333 0.00 0.00 0.00 3.16
487 496 1.630878 CCTCTTGGCCTACTGAAACCT 59.369 52.381 3.32 0.00 0.00 3.50
507 516 3.429043 CGGTGCGCTTACCTTCTTA 57.571 52.632 14.33 0.00 38.62 2.10
509 518 0.997196 GGTGCGCTTACCTTCTTACG 59.003 55.000 9.73 0.00 37.74 3.18
510 519 0.369248 GTGCGCTTACCTTCTTACGC 59.631 55.000 9.73 0.00 46.05 4.42
513 522 1.143969 CGCTTACCTTCTTACGCCCG 61.144 60.000 0.00 0.00 0.00 6.13
623 682 0.746063 CCCAAAGCTTGCTTGTGTCA 59.254 50.000 8.73 0.00 0.00 3.58
625 684 1.269413 CCAAAGCTTGCTTGTGTCAGG 60.269 52.381 8.73 1.71 0.00 3.86
1037 2538 5.227917 AGAGAAGAAAGATAGAAGGGGGA 57.772 43.478 0.00 0.00 0.00 4.81
1471 2973 2.415512 GACGCTATGTTTCTTCCGCTTT 59.584 45.455 0.00 0.00 0.00 3.51
1615 3117 6.737622 GCATCCTATTTGGTACTATCGTCACA 60.738 42.308 0.00 0.00 37.07 3.58
1863 3365 2.641815 AGGTGCTCAACAAGGAGATCTT 59.358 45.455 0.00 0.00 37.05 2.40
2660 5625 1.338107 ACATCTCCGGTGACACAGAA 58.662 50.000 8.68 0.00 0.00 3.02
2798 5763 5.581874 CCCTAAACCTAGCATTGCATTTTTG 59.418 40.000 11.91 5.38 0.00 2.44
2804 5769 1.874872 AGCATTGCATTTTTGTGGTGC 59.125 42.857 11.91 0.00 39.26 5.01
2805 5770 1.398705 GCATTGCATTTTTGTGGTGCG 60.399 47.619 3.15 0.00 41.61 5.34
2854 5819 8.577048 TTGTCAATAAAATACCCCGTTCATTA 57.423 30.769 0.00 0.00 0.00 1.90
2864 5829 8.533569 AATACCCCGTTCATTAGATTTGATTT 57.466 30.769 0.00 0.00 0.00 2.17
2890 5855 3.177228 AGATCACCTCTTGCCTGTAGTT 58.823 45.455 0.00 0.00 0.00 2.24
2891 5856 3.584848 AGATCACCTCTTGCCTGTAGTTT 59.415 43.478 0.00 0.00 0.00 2.66
2892 5857 4.777896 AGATCACCTCTTGCCTGTAGTTTA 59.222 41.667 0.00 0.00 0.00 2.01
2893 5858 5.426833 AGATCACCTCTTGCCTGTAGTTTAT 59.573 40.000 0.00 0.00 0.00 1.40
2894 5859 5.499004 TCACCTCTTGCCTGTAGTTTATT 57.501 39.130 0.00 0.00 0.00 1.40
2895 5860 5.876357 TCACCTCTTGCCTGTAGTTTATTT 58.124 37.500 0.00 0.00 0.00 1.40
2896 5861 6.303839 TCACCTCTTGCCTGTAGTTTATTTT 58.696 36.000 0.00 0.00 0.00 1.82
2897 5862 6.775629 TCACCTCTTGCCTGTAGTTTATTTTT 59.224 34.615 0.00 0.00 0.00 1.94
2922 5887 7.749539 TTTTAAAACGAAGGCTCAAGAAAAG 57.250 32.000 0.00 0.00 0.00 2.27
2923 5888 3.355626 AAACGAAGGCTCAAGAAAAGC 57.644 42.857 0.00 0.00 39.09 3.51
2924 5889 2.262423 ACGAAGGCTCAAGAAAAGCT 57.738 45.000 0.00 0.00 39.75 3.74
2925 5890 2.147150 ACGAAGGCTCAAGAAAAGCTC 58.853 47.619 0.00 0.00 39.75 4.09
2926 5891 1.127582 CGAAGGCTCAAGAAAAGCTCG 59.872 52.381 0.00 0.00 39.75 5.03
2927 5892 1.466558 GAAGGCTCAAGAAAAGCTCGG 59.533 52.381 0.00 0.00 39.75 4.63
2928 5893 0.957888 AGGCTCAAGAAAAGCTCGGC 60.958 55.000 0.00 0.00 39.75 5.54
2929 5894 0.957888 GGCTCAAGAAAAGCTCGGCT 60.958 55.000 0.00 0.00 42.56 5.52
2996 5962 2.201022 AACTCGTCCACACGCCTCT 61.201 57.895 0.00 0.00 46.28 3.69
3002 5968 0.818296 GTCCACACGCCTCTATCACT 59.182 55.000 0.00 0.00 0.00 3.41
3057 6023 6.152492 TGAATTAGCTGATTTTGTATGCCACA 59.848 34.615 5.07 0.00 34.51 4.17
3085 6051 3.935872 CGCGTGTGTGGTGTGTGG 61.936 66.667 0.00 0.00 0.00 4.17
3195 6161 3.103213 AAGGGCTGGTGTGTGGGT 61.103 61.111 0.00 0.00 0.00 4.51
3233 6199 4.095400 ACCCGCCTCCTCTCCCAT 62.095 66.667 0.00 0.00 0.00 4.00
3237 6203 2.565645 CGCCTCCTCTCCCATACCG 61.566 68.421 0.00 0.00 0.00 4.02
3385 6356 3.761897 ACTGCCCTAGTATGTTTTGCAA 58.238 40.909 0.00 0.00 38.04 4.08
3516 6490 1.351430 GCGTGCACGTAAGCAGATGA 61.351 55.000 36.80 0.00 46.69 2.92
3583 6557 3.005155 GCACATGGCAACTCTCTCTTTTT 59.995 43.478 0.00 0.00 43.97 1.94
3594 6568 3.074412 TCTCTCTTTTTCCCGAACATGC 58.926 45.455 0.00 0.00 0.00 4.06
3601 6575 2.810439 TTCCCGAACATGCTTTTTGG 57.190 45.000 0.00 0.00 0.00 3.28
3634 6608 1.338674 TGTAGCGCTACATGGCAACTT 60.339 47.619 39.24 4.05 40.77 2.66
3785 6761 1.933500 GCAGTTGAGCAAACATGGCAG 60.934 52.381 0.00 0.00 41.61 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.915629 TGTTTTGTACTTTGTGTTATTTGACTT 57.084 25.926 0.00 0.00 0.00 3.01
6 7 9.862371 ACATGTTTTGTACTTTGTGTTATTTGA 57.138 25.926 0.00 0.00 36.57 2.69
12 13 9.477484 TGTTAAACATGTTTTGTACTTTGTGTT 57.523 25.926 27.66 2.12 37.68 3.32
13 14 8.917655 GTGTTAAACATGTTTTGTACTTTGTGT 58.082 29.630 27.66 2.57 37.68 3.72
14 15 8.916654 TGTGTTAAACATGTTTTGTACTTTGTG 58.083 29.630 27.66 0.00 37.68 3.33
15 16 9.477484 TTGTGTTAAACATGTTTTGTACTTTGT 57.523 25.926 27.66 3.30 38.99 2.83
18 19 9.308318 GGATTGTGTTAAACATGTTTTGTACTT 57.692 29.630 27.66 14.72 38.99 2.24
19 20 8.470805 TGGATTGTGTTAAACATGTTTTGTACT 58.529 29.630 27.66 6.29 38.99 2.73
20 21 8.536407 GTGGATTGTGTTAAACATGTTTTGTAC 58.464 33.333 27.66 21.49 38.99 2.90
21 22 7.707035 GGTGGATTGTGTTAAACATGTTTTGTA 59.293 33.333 27.66 8.62 38.99 2.41
22 23 6.536941 GGTGGATTGTGTTAAACATGTTTTGT 59.463 34.615 27.66 7.81 38.99 2.83
23 24 6.760770 AGGTGGATTGTGTTAAACATGTTTTG 59.239 34.615 27.66 0.00 38.99 2.44
24 25 6.883744 AGGTGGATTGTGTTAAACATGTTTT 58.116 32.000 27.66 9.06 38.99 2.43
25 26 6.478512 AGGTGGATTGTGTTAAACATGTTT 57.521 33.333 25.99 25.99 38.99 2.83
26 27 7.589958 TTAGGTGGATTGTGTTAAACATGTT 57.410 32.000 4.92 4.92 38.99 2.71
27 28 7.093945 GGATTAGGTGGATTGTGTTAAACATGT 60.094 37.037 0.00 0.00 38.99 3.21
28 29 7.122650 AGGATTAGGTGGATTGTGTTAAACATG 59.877 37.037 0.00 0.00 38.99 3.21
29 30 7.182060 AGGATTAGGTGGATTGTGTTAAACAT 58.818 34.615 0.00 0.00 38.99 2.71
30 31 6.548321 AGGATTAGGTGGATTGTGTTAAACA 58.452 36.000 0.00 0.00 36.85 2.83
31 32 7.175990 TGAAGGATTAGGTGGATTGTGTTAAAC 59.824 37.037 0.00 0.00 0.00 2.01
32 33 7.235079 TGAAGGATTAGGTGGATTGTGTTAAA 58.765 34.615 0.00 0.00 0.00 1.52
33 34 6.785076 TGAAGGATTAGGTGGATTGTGTTAA 58.215 36.000 0.00 0.00 0.00 2.01
34 35 6.381498 TGAAGGATTAGGTGGATTGTGTTA 57.619 37.500 0.00 0.00 0.00 2.41
35 36 5.255397 TGAAGGATTAGGTGGATTGTGTT 57.745 39.130 0.00 0.00 0.00 3.32
36 37 4.927267 TGAAGGATTAGGTGGATTGTGT 57.073 40.909 0.00 0.00 0.00 3.72
37 38 5.500234 TCTTGAAGGATTAGGTGGATTGTG 58.500 41.667 0.00 0.00 0.00 3.33
38 39 5.779241 TCTTGAAGGATTAGGTGGATTGT 57.221 39.130 0.00 0.00 0.00 2.71
39 40 7.466746 TTTTCTTGAAGGATTAGGTGGATTG 57.533 36.000 0.00 0.00 0.00 2.67
40 41 8.670521 AATTTTCTTGAAGGATTAGGTGGATT 57.329 30.769 0.00 0.00 0.00 3.01
41 42 8.670521 AAATTTTCTTGAAGGATTAGGTGGAT 57.329 30.769 0.00 0.00 0.00 3.41
42 43 7.950124 AGAAATTTTCTTGAAGGATTAGGTGGA 59.050 33.333 5.82 0.00 36.36 4.02
43 44 8.127150 AGAAATTTTCTTGAAGGATTAGGTGG 57.873 34.615 5.82 0.00 36.36 4.61
56 57 8.981647 CACAGGGAAAACATAGAAATTTTCTTG 58.018 33.333 16.39 15.19 42.13 3.02
70 71 2.173782 TGGTTCTAGCACAGGGAAAACA 59.826 45.455 0.00 0.00 0.00 2.83
76 77 1.021390 CGCTTGGTTCTAGCACAGGG 61.021 60.000 0.00 0.00 38.55 4.45
95 96 8.688747 AGAACATGGGAATCTGAATAGAAATC 57.311 34.615 0.00 0.00 36.32 2.17
104 105 6.813293 TGAATAGAGAACATGGGAATCTGA 57.187 37.500 0.00 0.00 0.00 3.27
149 150 6.996509 AGCCAAAAATGTAGAATTGTGATGT 58.003 32.000 0.00 0.00 0.00 3.06
240 241 7.496529 TTCAGAACATTTAGAGTCCTGTTTG 57.503 36.000 0.00 0.00 32.28 2.93
242 243 7.054124 TGTTTCAGAACATTTAGAGTCCTGTT 58.946 34.615 0.00 0.00 40.71 3.16
273 276 5.946298 TCAGAACAAAATAGAATGCAGCAG 58.054 37.500 0.00 0.00 0.00 4.24
298 301 5.066505 ACCCAATTTCAGAATTCAGATACGC 59.933 40.000 8.44 0.00 33.25 4.42
331 334 8.545229 ACAATGTTTGAAATTGTTCTTCAACA 57.455 26.923 0.00 0.00 43.94 3.33
507 516 3.213264 CCTACATGGTACGGGCGT 58.787 61.111 0.00 0.00 0.00 5.68
781 1134 2.028567 GTCTTGCCTTGAGAGCTACAGT 60.029 50.000 0.00 0.00 0.00 3.55
912 2398 9.726438 GTAAGGAGATATTGTAGTATGCCAATT 57.274 33.333 0.00 0.00 33.54 2.32
984 2485 2.099098 GCTTGTGTGCTTTGTTAGGTGT 59.901 45.455 0.00 0.00 0.00 4.16
1016 2517 5.663556 TCTTCCCCCTTCTATCTTTCTTCTC 59.336 44.000 0.00 0.00 0.00 2.87
1037 2538 3.181480 GGCGATCTCTCAGCTAAACTCTT 60.181 47.826 0.00 0.00 0.00 2.85
1498 3000 0.975556 TGGTGGCGCTGAGAGGATAA 60.976 55.000 7.64 0.00 0.00 1.75
1615 3117 0.385751 ATGCGGACGAGACGATGATT 59.614 50.000 0.00 0.00 0.00 2.57
1863 3365 0.702902 ACCCTGGACGTTCTCCTCTA 59.297 55.000 0.00 0.00 40.26 2.43
2660 5625 3.738830 AAGCAAACACTTGTGCATGAT 57.261 38.095 0.00 2.10 43.42 2.45
2798 5763 1.421410 CGAATACAGAGCCGCACCAC 61.421 60.000 0.00 0.00 0.00 4.16
2804 5769 2.333926 TCACAAACGAATACAGAGCCG 58.666 47.619 0.00 0.00 0.00 5.52
2805 5770 3.994392 TCTTCACAAACGAATACAGAGCC 59.006 43.478 0.00 0.00 0.00 4.70
2854 5819 7.862512 GAGGTGATCTCTTGAAATCAAATCT 57.137 36.000 0.00 0.00 39.38 2.40
2897 5862 7.201487 GCTTTTCTTGAGCCTTCGTTTTAAAAA 60.201 33.333 1.31 0.00 34.06 1.94
2898 5863 6.254804 GCTTTTCTTGAGCCTTCGTTTTAAAA 59.745 34.615 0.00 0.00 34.06 1.52
2899 5864 5.746721 GCTTTTCTTGAGCCTTCGTTTTAAA 59.253 36.000 0.00 0.00 34.06 1.52
2900 5865 5.067283 AGCTTTTCTTGAGCCTTCGTTTTAA 59.933 36.000 0.00 0.00 41.03 1.52
2901 5866 4.578928 AGCTTTTCTTGAGCCTTCGTTTTA 59.421 37.500 0.00 0.00 41.03 1.52
2902 5867 3.381590 AGCTTTTCTTGAGCCTTCGTTTT 59.618 39.130 0.00 0.00 41.03 2.43
2903 5868 2.952310 AGCTTTTCTTGAGCCTTCGTTT 59.048 40.909 0.00 0.00 41.03 3.60
2904 5869 2.550180 GAGCTTTTCTTGAGCCTTCGTT 59.450 45.455 0.00 0.00 41.03 3.85
2905 5870 2.147150 GAGCTTTTCTTGAGCCTTCGT 58.853 47.619 0.00 0.00 41.03 3.85
2906 5871 1.127582 CGAGCTTTTCTTGAGCCTTCG 59.872 52.381 0.00 0.00 41.03 3.79
2907 5872 1.466558 CCGAGCTTTTCTTGAGCCTTC 59.533 52.381 0.00 0.00 41.03 3.46
2908 5873 1.528129 CCGAGCTTTTCTTGAGCCTT 58.472 50.000 0.00 0.00 41.03 4.35
2909 5874 0.957888 GCCGAGCTTTTCTTGAGCCT 60.958 55.000 0.00 0.00 41.03 4.58
2910 5875 0.957888 AGCCGAGCTTTTCTTGAGCC 60.958 55.000 0.00 0.00 41.03 4.70
2911 5876 2.549332 AGCCGAGCTTTTCTTGAGC 58.451 52.632 0.00 0.00 33.89 4.26
2921 5886 4.453136 TCGTTGTTAATTTAAAGCCGAGCT 59.547 37.500 0.00 0.00 42.56 4.09
2922 5887 4.714851 TCGTTGTTAATTTAAAGCCGAGC 58.285 39.130 0.00 0.00 0.00 5.03
2923 5888 7.611821 TTTTCGTTGTTAATTTAAAGCCGAG 57.388 32.000 0.00 0.00 0.00 4.63
2924 5889 7.648510 ACATTTTCGTTGTTAATTTAAAGCCGA 59.351 29.630 0.00 0.00 0.00 5.54
2925 5890 7.779349 ACATTTTCGTTGTTAATTTAAAGCCG 58.221 30.769 0.00 0.00 0.00 5.52
2931 5896 8.689069 GGCGTTAACATTTTCGTTGTTAATTTA 58.311 29.630 6.39 0.00 45.87 1.40
2932 5897 7.306690 GGGCGTTAACATTTTCGTTGTTAATTT 60.307 33.333 6.39 0.00 45.87 1.82
2933 5898 6.144241 GGGCGTTAACATTTTCGTTGTTAATT 59.856 34.615 6.39 0.00 45.87 1.40
2934 5899 5.630264 GGGCGTTAACATTTTCGTTGTTAAT 59.370 36.000 6.39 0.00 45.87 1.40
2938 5903 2.358267 TGGGCGTTAACATTTTCGTTGT 59.642 40.909 6.39 0.00 0.00 3.32
2996 5962 4.526650 TGCAGAAGTTACTGGACAGTGATA 59.473 41.667 14.86 0.00 42.52 2.15
3057 6023 0.601558 ACACACGCGAGTTGTCCTAT 59.398 50.000 15.93 0.00 46.40 2.57
3233 6199 1.671054 GCAACTGGCAGCTTCGGTA 60.671 57.895 15.89 0.00 43.97 4.02
3444 6417 6.003326 ACATATGACAACTGACATGTTTGGA 58.997 36.000 10.38 0.92 33.00 3.53
3447 6420 7.169645 GCAAAACATATGACAACTGACATGTTT 59.830 33.333 10.38 5.01 32.45 2.83
3461 6434 5.451659 GCCATGTACCATGCAAAACATATGA 60.452 40.000 10.38 0.00 36.64 2.15
3516 6490 8.040727 AGTTGCCATTTAAAAAGAAAGAGTTGT 58.959 29.630 0.00 0.00 0.00 3.32
3583 6557 0.316841 GCCAAAAAGCATGTTCGGGA 59.683 50.000 0.00 0.00 0.00 5.14
3634 6608 3.461378 TGCCACCTACTAACACTAGGA 57.539 47.619 0.00 0.00 35.23 2.94
3684 6658 3.706594 CCATGTGTGGTCTGGTCTACTAT 59.293 47.826 0.00 0.00 40.83 2.12
3685 6659 3.096852 CCATGTGTGGTCTGGTCTACTA 58.903 50.000 0.00 0.00 40.83 1.82
3785 6761 1.359848 CCATGTCGGACAACTACAGC 58.640 55.000 15.72 0.00 36.56 4.40


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

AutoCloner maintained by Alex Coulton.