Multiple sequence alignment - TraesCS4D01G270800

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 TraesCS4D01G270800 chr4D 100.000 5644 0 0 1 5644 441640236 441634593 0.000000e+00 10423.0
1 TraesCS4D01G270800 chr4D 84.812 665 85 11 2054 2706 441513609 441512949 0.000000e+00 654.0
2 TraesCS4D01G270800 chr4D 81.679 131 20 3 3047 3177 441512557 441512431 7.730000e-19 106.0
3 TraesCS4D01G270800 chr4D 92.157 51 3 1 2002 2051 139045072 139045022 2.820000e-08 71.3
4 TraesCS4D01G270800 chr4A 93.214 2284 98 16 3400 5644 25806019 25808284 0.000000e+00 3306.0
5 TraesCS4D01G270800 chr4A 92.034 1908 92 28 187 2044 25802101 25803998 0.000000e+00 2627.0
6 TraesCS4D01G270800 chr4A 96.947 1212 29 5 2076 3281 25804104 25805313 0.000000e+00 2026.0
7 TraesCS4D01G270800 chr4A 84.622 1099 155 14 928 2016 26012550 26013644 0.000000e+00 1081.0
8 TraesCS4D01G270800 chr4A 83.988 662 91 11 2056 2706 26013646 26014303 6.210000e-174 621.0
9 TraesCS4D01G270800 chr4A 82.000 600 81 19 2054 2641 26065832 26066416 8.500000e-133 484.0
10 TraesCS4D01G270800 chr4A 83.582 134 18 3 3044 3177 26014692 26014821 7.680000e-24 122.0
11 TraesCS4D01G270800 chr4A 71.254 574 140 23 4953 5515 584384401 584384960 7.680000e-24 122.0
12 TraesCS4D01G270800 chr4A 100.000 52 0 0 3357 3408 25805556 25805607 4.650000e-16 97.1
13 TraesCS4D01G270800 chr4A 84.694 98 12 3 8 104 174146402 174146497 1.670000e-15 95.3
14 TraesCS4D01G270800 chr4A 92.157 51 3 1 2002 2051 246711243 246711293 2.820000e-08 71.3
15 TraesCS4D01G270800 chr4B 90.741 2106 101 46 1 2051 548106682 548104616 0.000000e+00 2723.0
16 TraesCS4D01G270800 chr4B 88.765 2065 186 23 2054 4099 548104571 548102534 0.000000e+00 2486.0
17 TraesCS4D01G270800 chr4B 85.714 1582 128 36 4098 5640 548102410 548100888 0.000000e+00 1580.0
18 TraesCS4D01G270800 chr4B 84.488 1083 156 11 934 2008 547580476 547579398 0.000000e+00 1059.0
19 TraesCS4D01G270800 chr4B 83.433 670 87 16 2054 2706 547579397 547578735 8.090000e-168 601.0
20 TraesCS4D01G270800 chr2B 82.122 1018 153 16 923 1926 676194672 676193670 0.000000e+00 845.0
21 TraesCS4D01G270800 chr2B 84.056 784 102 15 2054 2825 676193590 676192818 0.000000e+00 734.0
22 TraesCS4D01G270800 chr2B 80.357 1008 165 19 937 1926 676680330 676679338 0.000000e+00 734.0
23 TraesCS4D01G270800 chr2B 79.013 1115 190 25 929 2021 676477837 676476745 0.000000e+00 723.0
24 TraesCS4D01G270800 chr2B 82.323 775 101 20 2054 2800 676484897 676484131 1.710000e-179 640.0
25 TraesCS4D01G270800 chr2B 83.309 695 81 17 2054 2722 676589854 676589169 4.840000e-170 608.0
26 TraesCS4D01G270800 chr2B 81.197 702 110 9 929 1622 676590862 676590175 3.850000e-151 545.0
27 TraesCS4D01G270800 chr2B 79.857 561 92 12 929 1484 676485940 676485396 1.910000e-104 390.0
28 TraesCS4D01G270800 chr2B 97.436 39 1 0 2013 2051 571145590 571145628 3.650000e-07 67.6
29 TraesCS4D01G270800 chr2D 80.943 1018 160 18 929 1926 564923593 564922590 0.000000e+00 774.0
30 TraesCS4D01G270800 chr2D 83.526 692 83 15 2054 2722 564922506 564921823 8.030000e-173 617.0
31 TraesCS4D01G270800 chr2D 82.061 262 34 8 4483 4741 564921053 564920802 1.590000e-50 211.0
32 TraesCS4D01G270800 chr2D 81.061 264 33 10 4483 4741 564686620 564686369 1.600000e-45 195.0
33 TraesCS4D01G270800 chr2D 88.889 54 3 2 2001 2051 554308436 554308383 4.720000e-06 63.9
34 TraesCS4D01G270800 chr2A 81.019 1001 159 21 929 1912 705527889 705526903 0.000000e+00 767.0
35 TraesCS4D01G270800 chr2A 83.145 795 101 21 2054 2825 705526800 705526016 0.000000e+00 695.0
36 TraesCS4D01G270800 chr2A 88.889 54 3 2 2001 2051 694471549 694471496 4.720000e-06 63.9
37 TraesCS4D01G270800 chr7D 84.118 170 15 10 718 876 177177726 177177894 2.720000e-33 154.0
38 TraesCS4D01G270800 chr5A 83.621 116 15 4 1 115 637189873 637189985 7.730000e-19 106.0
39 TraesCS4D01G270800 chr1B 83.621 116 12 5 8 122 289526105 289525996 1.000000e-17 102.0
40 TraesCS4D01G270800 chr6D 83.636 110 15 3 8 115 126627709 126627601 3.600000e-17 100.0
41 TraesCS4D01G270800 chr6D 82.692 104 13 5 4047 4146 62432196 62432298 2.800000e-13 87.9
42 TraesCS4D01G270800 chr6D 97.619 42 0 1 3233 3273 14158392 14158433 2.820000e-08 71.3
43 TraesCS4D01G270800 chr5D 91.429 70 5 1 1 70 336456739 336456807 1.670000e-15 95.3
44 TraesCS4D01G270800 chr5D 81.739 115 16 5 8 117 128651018 128650904 2.170000e-14 91.6
45 TraesCS4D01G270800 chr5D 70.191 577 145 22 4950 5515 311470373 311470933 2.800000e-13 87.9
46 TraesCS4D01G270800 chr5D 94.595 37 0 2 3164 3200 260790076 260790110 7.900000e-04 56.5
47 TraesCS4D01G270800 chr1A 81.148 122 15 7 8 122 278230442 278230562 2.170000e-14 91.6
48 TraesCS4D01G270800 chr1A 81.513 119 12 9 4363 4479 428996787 428996677 7.790000e-14 89.8
49 TraesCS4D01G270800 chr7A 80.992 121 16 7 6 122 108840264 108840147 7.790000e-14 89.8
50 TraesCS4D01G270800 chrUn 79.070 129 25 2 5388 5515 81315419 81315546 2.800000e-13 87.9
51 TraesCS4D01G270800 chrUn 95.122 41 2 0 2011 2051 2656053 2656093 1.310000e-06 65.8
52 TraesCS4D01G270800 chrUn 97.297 37 1 0 2015 2051 50304283 50304247 4.720000e-06 63.9
53 TraesCS4D01G270800 chr6A 85.135 74 6 5 4077 4146 79942998 79943070 2.820000e-08 71.3
54 TraesCS4D01G270800 chr3A 100.000 28 0 0 5307 5334 590236625 590236652 1.000000e-02 52.8


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 TraesCS4D01G270800 chr4D 441634593 441640236 5643 True 10423.000 10423 100.000000 1 5644 1 chr4D.!!$R2 5643
1 TraesCS4D01G270800 chr4D 441512431 441513609 1178 True 380.000 654 83.245500 2054 3177 2 chr4D.!!$R3 1123
2 TraesCS4D01G270800 chr4A 25802101 25808284 6183 False 2014.025 3306 95.548750 187 5644 4 chr4A.!!$F5 5457
3 TraesCS4D01G270800 chr4A 26012550 26014821 2271 False 608.000 1081 84.064000 928 3177 3 chr4A.!!$F6 2249
4 TraesCS4D01G270800 chr4A 26065832 26066416 584 False 484.000 484 82.000000 2054 2641 1 chr4A.!!$F1 587
5 TraesCS4D01G270800 chr4B 548100888 548106682 5794 True 2263.000 2723 88.406667 1 5640 3 chr4B.!!$R2 5639
6 TraesCS4D01G270800 chr4B 547578735 547580476 1741 True 830.000 1059 83.960500 934 2706 2 chr4B.!!$R1 1772
7 TraesCS4D01G270800 chr2B 676192818 676194672 1854 True 789.500 845 83.089000 923 2825 2 chr2B.!!$R3 1902
8 TraesCS4D01G270800 chr2B 676679338 676680330 992 True 734.000 734 80.357000 937 1926 1 chr2B.!!$R2 989
9 TraesCS4D01G270800 chr2B 676476745 676477837 1092 True 723.000 723 79.013000 929 2021 1 chr2B.!!$R1 1092
10 TraesCS4D01G270800 chr2B 676589169 676590862 1693 True 576.500 608 82.253000 929 2722 2 chr2B.!!$R5 1793
11 TraesCS4D01G270800 chr2B 676484131 676485940 1809 True 515.000 640 81.090000 929 2800 2 chr2B.!!$R4 1871
12 TraesCS4D01G270800 chr2D 564920802 564923593 2791 True 534.000 774 82.176667 929 4741 3 chr2D.!!$R3 3812
13 TraesCS4D01G270800 chr2A 705526016 705527889 1873 True 731.000 767 82.082000 929 2825 2 chr2A.!!$R2 1896

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
55 56 0.671796 CACCGGTTTTGGGAAGGTTC 59.328 55.000 2.97 0.0 32.04 3.62 F
1223 1297 0.809241 CTGCTCCACCTCAGATTCGC 60.809 60.000 0.00 0.0 32.26 4.70 F
1398 1490 2.111999 TTGAGCAGGAACCCTCACCG 62.112 60.000 0.00 0.0 37.03 4.94 F
1523 1615 3.131400 GTGGAACTGAGTATGGAGGTCTC 59.869 52.174 0.00 0.0 0.00 3.36 F
3206 3781 5.129485 TCTCTAGCAGATCCCCTAAACTTTG 59.871 44.000 0.00 0.0 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1490 1.265635 ACGAGACGCAGATCAGATAGC 59.734 52.381 0.00 0.00 0.00 2.97 R
2406 2666 2.226437 GCAACTGACTGTACCAATGGTG 59.774 50.000 16.41 0.25 36.19 4.17 R
3206 3781 2.403561 GCAGGGATAGGATAGGGGATC 58.596 57.143 0.00 0.00 0.00 3.36 R
3328 3914 5.703592 ACCATTGTCTAACTACGCAATGAAA 59.296 36.000 15.09 0.00 46.39 2.69 R
4714 6058 1.358787 ACATCCCCAAATCTGCTCCAA 59.641 47.619 0.00 0.00 0.00 3.53 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
40 41 6.016610 CCCAATATAGTGTTTTATTCCCACCG 60.017 42.308 0.00 0.00 0.00 4.94
46 47 4.052608 GTGTTTTATTCCCACCGGTTTTG 58.947 43.478 2.97 0.00 0.00 2.44
47 48 3.069729 TGTTTTATTCCCACCGGTTTTGG 59.930 43.478 2.97 6.25 0.00 3.28
53 54 1.152631 CCACCGGTTTTGGGAAGGT 60.153 57.895 2.97 0.00 35.24 3.50
55 56 0.671796 CACCGGTTTTGGGAAGGTTC 59.328 55.000 2.97 0.00 32.04 3.62
74 75 5.422214 GTTCTAGAACCTTCCCTGAATCA 57.578 43.478 22.74 0.00 35.36 2.57
75 76 5.805728 GTTCTAGAACCTTCCCTGAATCAA 58.194 41.667 22.74 0.00 35.36 2.57
135 158 4.924305 TCTGCTTTGCAAACATCTTTCT 57.076 36.364 8.05 0.00 38.41 2.52
137 160 6.005583 TCTGCTTTGCAAACATCTTTCTAG 57.994 37.500 8.05 0.00 38.41 2.43
377 403 3.428045 GGGAACATTTTCTGAATCAGCGG 60.428 47.826 5.18 0.00 31.71 5.52
594 627 9.752274 TTTGATTTTCTGAACATTTGTTTTTCG 57.248 25.926 0.00 0.00 38.56 3.46
623 656 7.490962 TCATGAACAGTTTTTCTGAATACGT 57.509 32.000 0.00 0.00 46.27 3.57
627 660 7.925993 TGAACAGTTTTTCTGAATACGTGAAT 58.074 30.769 0.00 0.00 46.27 2.57
666 711 9.679661 TTCTAATCCAGTAAGCATTTTGTGATA 57.320 29.630 0.00 0.00 0.00 2.15
781 844 2.595124 AAGAAAAACAAAGTGGGCGG 57.405 45.000 0.00 0.00 0.00 6.13
812 875 2.852564 GGGCCGGCCTAATAGGGT 60.853 66.667 42.70 0.00 35.37 4.34
882 948 1.067669 CGCTGTATAGGAGCTCAAGCA 59.932 52.381 17.19 5.85 45.16 3.91
1223 1297 0.809241 CTGCTCCACCTCAGATTCGC 60.809 60.000 0.00 0.00 32.26 4.70
1398 1490 2.111999 TTGAGCAGGAACCCTCACCG 62.112 60.000 0.00 0.00 37.03 4.94
1523 1615 3.131400 GTGGAACTGAGTATGGAGGTCTC 59.869 52.174 0.00 0.00 0.00 3.36
2051 2170 6.373216 TCCATAATTCTTGTCGTGGTTTTAGG 59.627 38.462 0.00 0.00 0.00 2.69
2066 2227 6.708949 GTGGTTTTAGGAACTTCACACATAGA 59.291 38.462 0.00 0.00 41.75 1.98
2406 2666 8.995220 TGTAAGTGAAACACAAGGAATATACAC 58.005 33.333 4.75 0.00 41.43 2.90
2415 2675 5.652014 CACAAGGAATATACACACCATTGGT 59.348 40.000 1.37 1.37 35.62 3.67
2567 2827 8.484214 ACATACTAGCAGAATTTCTGGATCTA 57.516 34.615 24.09 16.37 44.43 1.98
2844 3369 6.682423 TGGATTCAACTATGTTGTATGCAG 57.318 37.500 15.72 0.00 0.00 4.41
2900 3472 9.559732 CTGTTCCAAATCTATTATGTATGGTCA 57.440 33.333 0.00 0.00 0.00 4.02
2904 3476 7.936847 TCCAAATCTATTATGTATGGTCACCAC 59.063 37.037 0.00 0.00 35.80 4.16
3206 3781 5.129485 TCTCTAGCAGATCCCCTAAACTTTG 59.871 44.000 0.00 0.00 0.00 2.77
3318 3904 6.183360 GCACACAAACTCATTTCAAACACAAT 60.183 34.615 0.00 0.00 0.00 2.71
3353 3939 5.968254 TCATTGCGTAGTTAGACAATGGTA 58.032 37.500 12.97 0.00 45.93 3.25
3435 4598 6.748132 ACATTGACATCAAACAAGGTTAAGG 58.252 36.000 0.00 0.00 37.67 2.69
3636 4799 1.301165 GTTGTGGTACTTCGGCGGT 60.301 57.895 7.21 0.00 0.00 5.68
3747 4910 2.657237 GGAGGTGACGGTGTCAGG 59.343 66.667 0.00 0.00 43.57 3.86
3759 4922 0.528470 GTGTCAGGGTCGAGGAAGAG 59.472 60.000 0.00 0.00 0.00 2.85
3764 4927 2.047443 GGGTCGAGGAAGAGAGCGT 61.047 63.158 0.00 0.00 35.89 5.07
3816 4979 0.602372 GGAGGCGATGAGGAATCTGC 60.602 60.000 0.00 0.00 35.44 4.26
3896 5059 0.321564 CTGAATCGAGGGTTGTGGCA 60.322 55.000 0.00 0.00 0.00 4.92
3945 5108 3.987954 ATGTTTGGGGGTAGCGGCG 62.988 63.158 0.51 0.51 0.00 6.46
3959 5122 1.089112 GCGGCGTTGGGTTTAATAGT 58.911 50.000 9.37 0.00 0.00 2.12
4303 5641 7.041372 CCCCTCGTATTTAATGTCAAAGTATGG 60.041 40.741 0.00 0.00 0.00 2.74
4481 5824 8.625786 GTCCTAATAAACTTGGACAAAGGTAA 57.374 34.615 6.18 0.00 45.87 2.85
4510 5853 9.944376 TGTTACAAGTGAAGCTCTTATTAGAAT 57.056 29.630 0.00 0.00 0.00 2.40
4714 6058 8.697507 AGGTCTCTGTGATTTTTAAGAAATGT 57.302 30.769 1.86 0.00 0.00 2.71
4823 6175 2.216898 AGTGCTTTTGTGTCTCAGCTC 58.783 47.619 0.00 0.00 0.00 4.09
5045 6401 2.431454 CCCTTCTCCTTTCACTTCTGC 58.569 52.381 0.00 0.00 0.00 4.26
5054 6410 5.620206 TCCTTTCACTTCTGCTATTGACAA 58.380 37.500 0.00 0.00 0.00 3.18
5135 6497 9.733556 TTTATAGGTTGCTATGAAGAAGAAACA 57.266 29.630 0.00 0.00 0.00 2.83
5136 6498 9.733556 TTATAGGTTGCTATGAAGAAGAAACAA 57.266 29.630 0.00 0.00 0.00 2.83
5144 6506 9.896645 TGCTATGAAGAAGAAACAAAGATCTAT 57.103 29.630 0.00 0.00 0.00 1.98
5263 6628 4.821805 TGAGTGACATTTGGAAGAAGGAAC 59.178 41.667 0.00 0.00 0.00 3.62
5333 6698 8.353423 AGGTGACAAGAATACTGCATATTTTT 57.647 30.769 0.00 0.00 33.37 1.94
5447 6813 6.092533 GGATGTTGCCACCAATTTTATGAAAG 59.907 38.462 0.00 0.00 32.75 2.62
5458 6824 8.040727 ACCAATTTTATGAAAGCCTATTTGGAC 58.959 33.333 14.31 0.00 38.35 4.02
5613 7015 3.134458 GTCCTGATGGCCTATCTTTTCG 58.866 50.000 3.32 0.00 36.71 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.048294 GGGAATAAAACACTATATTGGGCCG 60.048 44.000 0.00 0.00 0.00 6.13
53 54 6.642733 ATTGATTCAGGGAAGGTTCTAGAA 57.357 37.500 0.00 0.00 0.00 2.10
55 56 7.709149 AAAATTGATTCAGGGAAGGTTCTAG 57.291 36.000 0.00 0.00 0.00 2.43
99 115 6.127952 TGCAAAGCAGAAAAAGAAAGCAAAAT 60.128 30.769 0.00 0.00 33.32 1.82
100 116 5.180868 TGCAAAGCAGAAAAAGAAAGCAAAA 59.819 32.000 0.00 0.00 33.32 2.44
109 125 5.978934 AGATGTTTGCAAAGCAGAAAAAG 57.021 34.783 13.26 0.00 41.39 2.27
354 380 3.441572 CGCTGATTCAGAAAATGTTCCCT 59.558 43.478 17.87 0.00 33.92 4.20
578 611 9.091784 TCATGATTTTCGAAAAACAAATGTTCA 57.908 25.926 29.49 22.99 37.25 3.18
582 615 9.360514 CTGTTCATGATTTTCGAAAAACAAATG 57.639 29.630 29.49 24.39 34.94 2.32
586 619 8.472683 AAACTGTTCATGATTTTCGAAAAACA 57.527 26.923 28.44 28.44 35.59 2.83
592 625 7.702386 TCAGAAAAACTGTTCATGATTTTCGA 58.298 30.769 18.73 16.53 45.86 3.71
749 812 6.561737 TTGTTTTTCTTTTTCCGCCTTTTT 57.438 29.167 0.00 0.00 0.00 1.94
901 967 5.183014 AGGATTTCAGACAAAACGGAAAC 57.817 39.130 0.00 0.00 36.97 2.78
1398 1490 1.265635 ACGAGACGCAGATCAGATAGC 59.734 52.381 0.00 0.00 0.00 2.97
2051 2170 5.409520 TGCAATCTGTCTATGTGTGAAGTTC 59.590 40.000 0.00 0.00 0.00 3.01
2066 2227 7.439056 CCTTTGAAATACAAAAGTGCAATCTGT 59.561 33.333 6.99 6.99 45.97 3.41
2307 2538 5.360144 GGTCACTTCAATAGCTACTGACCTA 59.640 44.000 3.98 0.00 40.55 3.08
2406 2666 2.226437 GCAACTGACTGTACCAATGGTG 59.774 50.000 16.41 0.25 36.19 4.17
2415 2675 3.769739 AGTTGGATGCAACTGACTGTA 57.230 42.857 29.14 0.00 43.08 2.74
2684 2955 9.482627 TCCACATACATCCAAATTTGTAAAAAC 57.517 29.630 16.73 0.00 32.46 2.43
2844 3369 9.807386 GATGTGTAACTGTTACTTACAAATGTC 57.193 33.333 25.91 15.19 33.79 3.06
2900 3472 5.525454 TGATATATACCGAGGGTAGTGGT 57.475 43.478 0.62 0.00 41.83 4.16
2904 3476 7.942894 TGTATGGATGATATATACCGAGGGTAG 59.057 40.741 0.62 0.00 41.83 3.18
3206 3781 2.403561 GCAGGGATAGGATAGGGGATC 58.596 57.143 0.00 0.00 0.00 3.36
3325 3911 7.850982 CCATTGTCTAACTACGCAATGAAATAC 59.149 37.037 15.09 0.00 46.39 1.89
3328 3914 5.703592 ACCATTGTCTAACTACGCAATGAAA 59.296 36.000 15.09 0.00 46.39 2.69
3337 3923 8.876790 GTTAATGTGGTACCATTGTCTAACTAC 58.123 37.037 19.72 0.47 35.85 2.73
3346 3932 8.219546 TGTATGATGTTAATGTGGTACCATTG 57.780 34.615 19.72 0.00 35.85 2.82
3353 3939 8.518430 TTTGCTATGTATGATGTTAATGTGGT 57.482 30.769 0.00 0.00 0.00 4.16
3577 4740 2.567615 ACAAGTTTGCGGTAGAGATCCT 59.432 45.455 0.00 0.00 0.00 3.24
3617 4780 2.377310 CCGCCGAAGTACCACAACG 61.377 63.158 0.00 0.00 0.00 4.10
3636 4799 3.075005 GCTCTGTCCCCGCTACCA 61.075 66.667 0.00 0.00 0.00 3.25
3645 4808 0.678366 TGTCTCCTCGAGCTCTGTCC 60.678 60.000 12.85 0.00 0.00 4.02
3647 4810 0.885196 GTTGTCTCCTCGAGCTCTGT 59.115 55.000 12.85 0.00 0.00 3.41
3679 4842 3.365265 CACCTCCCAAACGCAGCC 61.365 66.667 0.00 0.00 0.00 4.85
3688 4851 2.447572 TGTCACTGCCACCTCCCA 60.448 61.111 0.00 0.00 0.00 4.37
3747 4910 1.137825 CACGCTCTCTTCCTCGACC 59.862 63.158 0.00 0.00 0.00 4.79
3764 4927 2.347114 CACTCCGTGCATGGACCA 59.653 61.111 24.15 3.95 33.48 4.02
3805 4968 1.910722 GCCTCCTGCAGATTCCTCA 59.089 57.895 17.39 0.00 40.77 3.86
3816 4979 0.318441 TCGAGTTTCACTGCCTCCTG 59.682 55.000 0.00 0.00 0.00 3.86
3824 4987 1.523758 GCCACCAATCGAGTTTCACT 58.476 50.000 0.00 0.00 0.00 3.41
3896 5059 0.392461 ACCGCACATCCATTTACGCT 60.392 50.000 0.00 0.00 0.00 5.07
3927 5090 2.044352 GCCGCTACCCCCAAACAT 60.044 61.111 0.00 0.00 0.00 2.71
3945 5108 5.650543 CCTGCATTCACTATTAAACCCAAC 58.349 41.667 0.00 0.00 0.00 3.77
3959 5122 3.923013 CCGATTGGCCTGCATTCA 58.077 55.556 3.32 0.00 0.00 2.57
4049 5212 1.672881 CTAGCCCATTTTTGCTCTCGG 59.327 52.381 0.00 0.00 39.00 4.63
4051 5214 3.876320 CTCTCTAGCCCATTTTTGCTCTC 59.124 47.826 0.00 0.00 39.00 3.20
4127 5416 4.388577 GGGATTAAACCCCATCTAGCAT 57.611 45.455 9.69 0.00 43.81 3.79
4230 5566 9.134504 AGGGGTACCATTTATATCCAAATATGA 57.865 33.333 15.35 0.00 44.85 2.15
4554 5898 2.420022 AGAACATACCGCAGACAAATGC 59.580 45.455 0.00 0.00 42.95 3.56
4714 6058 1.358787 ACATCCCCAAATCTGCTCCAA 59.641 47.619 0.00 0.00 0.00 3.53
5045 6401 8.816640 AAGTTTAAATTGCCAGTTGTCAATAG 57.183 30.769 0.00 0.00 33.05 1.73
5144 6506 8.827832 ACATCAAGAATATCAAATTCCTGGAA 57.172 30.769 12.26 12.26 0.00 3.53
5447 6813 5.163550 GGTTTAGGTTCATGTCCAAATAGGC 60.164 44.000 11.03 0.00 37.29 3.93
5458 6824 7.013274 CAGGTGTATATTGGGTTTAGGTTCATG 59.987 40.741 0.00 0.00 0.00 3.07
5570 6972 0.825010 GGAGCCCCACTTGCATATGG 60.825 60.000 4.56 9.36 35.59 2.74


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

AutoCloner maintained by Alex Coulton.