Multiple sequence alignment - TraesCS7B01G150800

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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 TraesCS7B01G150800 chr7B 100.000 3134 0 0 1 3134 200021207 200024340 0.000000e+00 5788.0
1 TraesCS7B01G150800 chr7B 80.851 282 20 11 2295 2552 742228452 742228723 1.150000e-44 191.0
2 TraesCS7B01G150800 chr7D 94.439 3093 82 28 62 3134 229768507 229771529 0.000000e+00 4676.0
3 TraesCS7B01G150800 chr7D 100.000 34 0 0 3046 3079 270772179 270772146 2.610000e-06 63.9
4 TraesCS7B01G150800 chr7A 92.282 2436 68 24 62 2439 241366061 241368434 0.000000e+00 3347.0
5 TraesCS7B01G150800 chr7A 92.857 644 29 5 2503 3134 241368433 241369071 0.000000e+00 918.0
6 TraesCS7B01G150800 chr2D 92.806 1682 73 16 643 2295 324016437 324014775 0.000000e+00 2392.0
7 TraesCS7B01G150800 chr2D 93.443 61 1 2 1165 1222 324036972 324037032 1.550000e-13 87.9
8 TraesCS7B01G150800 chr2B 95.455 1320 50 4 860 2179 392530682 392529373 0.000000e+00 2097.0
9 TraesCS7B01G150800 chr2B 89.011 182 13 5 643 824 392537333 392537159 5.260000e-53 219.0
10 TraesCS7B01G150800 chr2B 100.000 32 0 0 832 863 392530723 392530692 3.380000e-05 60.2
11 TraesCS7B01G150800 chr5A 88.835 412 26 10 62 469 106109130 106108735 3.630000e-134 488.0
12 TraesCS7B01G150800 chr5B 90.278 144 7 3 2299 2440 511783600 511783462 6.900000e-42 182.0
13 TraesCS7B01G150800 chr1B 78.049 205 42 3 1159 1360 389980342 389980546 3.280000e-25 126.0
14 TraesCS7B01G150800 chr1B 91.176 68 4 2 1 66 341931970 341931903 1.200000e-14 91.6
15 TraesCS7B01G150800 chr1B 90.000 60 6 0 1 60 4076428 4076487 9.320000e-11 78.7
16 TraesCS7B01G150800 chr1D 77.670 206 41 5 1159 1360 288546048 288546252 1.530000e-23 121.0
17 TraesCS7B01G150800 chr3B 96.296 54 2 0 1 54 635020626 635020679 4.310000e-14 89.8
18 TraesCS7B01G150800 chrUn 88.571 70 8 0 1165 1234 90726739 90726670 5.570000e-13 86.1
19 TraesCS7B01G150800 chr2A 85.542 83 10 2 1156 1237 711510066 711509985 5.570000e-13 86.1


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 TraesCS7B01G150800 chr7B 200021207 200024340 3133 False 5788.0 5788 100.0000 1 3134 1 chr7B.!!$F1 3133
1 TraesCS7B01G150800 chr7D 229768507 229771529 3022 False 4676.0 4676 94.4390 62 3134 1 chr7D.!!$F1 3072
2 TraesCS7B01G150800 chr7A 241366061 241369071 3010 False 2132.5 3347 92.5695 62 3134 2 chr7A.!!$F1 3072
3 TraesCS7B01G150800 chr2D 324014775 324016437 1662 True 2392.0 2392 92.8060 643 2295 1 chr2D.!!$R1 1652
4 TraesCS7B01G150800 chr2B 392529373 392530723 1350 True 1078.6 2097 97.7275 832 2179 2 chr2B.!!$R2 1347

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
477 489 0.039888 GCGCGGCAAAGTTCCTAAAA 60.040 50.000 8.83 0.0 0.00 1.52 F
624 636 0.739813 AACGAACAGTATCCAGCGCC 60.740 55.000 2.29 0.0 0.00 6.53 F
921 967 1.269309 CCACGATCGACCAGGATCTTC 60.269 57.143 24.34 0.0 40.52 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1803 0.944311 GCGTCACTCCAATCGTGTGT 60.944 55.000 0.0 0.0 37.28 3.72 R
1849 1927 2.964389 GCTCGCCATCTTCTCCGC 60.964 66.667 0.0 0.0 0.00 5.54 R
2819 2940 0.471211 ACCTCTCTCCCGTGAAACCA 60.471 55.000 0.0 0.0 0.00 3.67 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
17 18 2.669569 TGGGAGCGAGCAAACTGC 60.670 61.111 0.00 0.00 45.46 4.40
18 19 3.435186 GGGAGCGAGCAAACTGCC 61.435 66.667 0.00 0.00 46.52 4.85
19 20 3.793144 GGAGCGAGCAAACTGCCG 61.793 66.667 0.00 0.55 46.52 5.69
32 33 3.774528 TGCCGCTCCGCAGATTCT 61.775 61.111 0.00 0.00 33.92 2.40
33 34 2.417516 GCCGCTCCGCAGATTCTA 59.582 61.111 0.00 0.00 0.00 2.10
34 35 1.663074 GCCGCTCCGCAGATTCTAG 60.663 63.158 0.00 0.00 0.00 2.43
35 36 1.006805 CCGCTCCGCAGATTCTAGG 60.007 63.158 0.00 1.95 0.00 3.02
36 37 1.456196 CCGCTCCGCAGATTCTAGGA 61.456 60.000 9.04 9.04 0.00 2.94
38 39 3.883997 CTCCGCAGATTCTAGGAGC 57.116 57.895 18.62 4.54 42.99 4.70
39 40 1.327303 CTCCGCAGATTCTAGGAGCT 58.673 55.000 18.62 0.00 42.99 4.09
40 41 2.509569 CTCCGCAGATTCTAGGAGCTA 58.490 52.381 18.62 0.00 42.99 3.32
41 42 2.487762 CTCCGCAGATTCTAGGAGCTAG 59.512 54.545 18.62 0.00 42.99 3.42
42 43 2.158593 TCCGCAGATTCTAGGAGCTAGT 60.159 50.000 6.09 0.00 35.72 2.57
43 44 2.030363 CCGCAGATTCTAGGAGCTAGTG 60.030 54.545 0.00 0.00 35.72 2.74
44 45 2.881513 CGCAGATTCTAGGAGCTAGTGA 59.118 50.000 0.00 0.00 35.72 3.41
45 46 3.316588 CGCAGATTCTAGGAGCTAGTGAA 59.683 47.826 0.00 0.00 35.72 3.18
46 47 4.022416 CGCAGATTCTAGGAGCTAGTGAAT 60.022 45.833 0.00 0.00 35.72 2.57
47 48 5.508825 CGCAGATTCTAGGAGCTAGTGAATT 60.509 44.000 0.00 0.00 35.72 2.17
48 49 6.287525 GCAGATTCTAGGAGCTAGTGAATTT 58.712 40.000 0.00 0.00 35.72 1.82
49 50 6.423604 GCAGATTCTAGGAGCTAGTGAATTTC 59.576 42.308 0.00 0.00 35.72 2.17
50 51 6.928492 CAGATTCTAGGAGCTAGTGAATTTCC 59.072 42.308 0.00 0.00 35.72 3.13
51 52 4.920640 TCTAGGAGCTAGTGAATTTCCG 57.079 45.455 0.00 0.00 35.72 4.30
52 53 4.533815 TCTAGGAGCTAGTGAATTTCCGA 58.466 43.478 0.00 0.00 35.72 4.55
53 54 4.954202 TCTAGGAGCTAGTGAATTTCCGAA 59.046 41.667 0.00 0.00 35.72 4.30
54 55 3.863041 AGGAGCTAGTGAATTTCCGAAC 58.137 45.455 0.00 0.00 33.16 3.95
55 56 2.603560 GGAGCTAGTGAATTTCCGAACG 59.396 50.000 0.00 0.00 0.00 3.95
56 57 2.603560 GAGCTAGTGAATTTCCGAACGG 59.396 50.000 6.94 6.94 0.00 4.44
57 58 1.664151 GCTAGTGAATTTCCGAACGGG 59.336 52.381 13.29 0.00 35.59 5.28
58 59 2.277084 CTAGTGAATTTCCGAACGGGG 58.723 52.381 13.29 0.00 36.01 5.73
59 60 0.958876 AGTGAATTTCCGAACGGGGC 60.959 55.000 13.29 0.21 36.01 5.80
60 61 0.958876 GTGAATTTCCGAACGGGGCT 60.959 55.000 13.29 0.00 36.01 5.19
69 70 0.174845 CGAACGGGGCTTCATAGTCA 59.825 55.000 0.00 0.00 0.00 3.41
82 83 6.858478 GGCTTCATAGTCAAACTTCTGTTTTC 59.142 38.462 0.00 0.00 43.13 2.29
112 113 7.221450 TGTCTTTTAAAGGTGTATAGCTGTGT 58.779 34.615 4.77 0.00 34.27 3.72
113 114 7.386848 TGTCTTTTAAAGGTGTATAGCTGTGTC 59.613 37.037 4.77 0.00 34.27 3.67
114 115 7.603024 GTCTTTTAAAGGTGTATAGCTGTGTCT 59.397 37.037 4.77 0.00 34.27 3.41
115 116 7.602644 TCTTTTAAAGGTGTATAGCTGTGTCTG 59.397 37.037 4.77 0.00 34.27 3.51
116 117 6.599356 TTAAAGGTGTATAGCTGTGTCTGA 57.401 37.500 0.00 0.00 34.27 3.27
117 118 5.683876 AAAGGTGTATAGCTGTGTCTGAT 57.316 39.130 0.00 0.00 34.27 2.90
118 119 6.791867 AAAGGTGTATAGCTGTGTCTGATA 57.208 37.500 0.00 0.00 34.27 2.15
119 120 5.776173 AGGTGTATAGCTGTGTCTGATAC 57.224 43.478 0.00 0.00 32.40 2.24
373 376 4.564372 CCATTATATCAGCGGACAGATTCG 59.436 45.833 0.00 0.00 0.00 3.34
376 379 4.848562 ATATCAGCGGACAGATTCGTAA 57.151 40.909 0.00 0.00 0.00 3.18
458 470 4.443034 GCTATTAGCCTGGTATTATCGGGG 60.443 50.000 4.21 0.00 34.48 5.73
474 486 2.744709 GGCGCGGCAAAGTTCCTA 60.745 61.111 29.32 0.00 0.00 2.94
475 487 2.329614 GGCGCGGCAAAGTTCCTAA 61.330 57.895 29.32 0.00 0.00 2.69
477 489 0.039888 GCGCGGCAAAGTTCCTAAAA 60.040 50.000 8.83 0.00 0.00 1.52
481 493 2.860971 GCGGCAAAGTTCCTAAAACCAC 60.861 50.000 0.00 0.00 0.00 4.16
483 495 2.619646 GGCAAAGTTCCTAAAACCACGA 59.380 45.455 0.00 0.00 0.00 4.35
484 496 3.254903 GGCAAAGTTCCTAAAACCACGAT 59.745 43.478 0.00 0.00 0.00 3.73
485 497 4.226761 GCAAAGTTCCTAAAACCACGATG 58.773 43.478 0.00 0.00 0.00 3.84
486 498 4.023536 GCAAAGTTCCTAAAACCACGATGA 60.024 41.667 0.00 0.00 0.00 2.92
487 499 5.689819 CAAAGTTCCTAAAACCACGATGAG 58.310 41.667 0.00 0.00 0.00 2.90
488 500 4.618920 AGTTCCTAAAACCACGATGAGT 57.381 40.909 0.00 0.00 0.00 3.41
489 501 5.733620 AGTTCCTAAAACCACGATGAGTA 57.266 39.130 0.00 0.00 0.00 2.59
490 502 6.105397 AGTTCCTAAAACCACGATGAGTAA 57.895 37.500 0.00 0.00 0.00 2.24
491 503 6.708285 AGTTCCTAAAACCACGATGAGTAAT 58.292 36.000 0.00 0.00 0.00 1.89
492 504 7.166167 AGTTCCTAAAACCACGATGAGTAATT 58.834 34.615 0.00 0.00 0.00 1.40
493 505 7.664318 AGTTCCTAAAACCACGATGAGTAATTT 59.336 33.333 0.00 0.00 0.00 1.82
494 506 8.938906 GTTCCTAAAACCACGATGAGTAATTTA 58.061 33.333 0.00 0.00 0.00 1.40
495 507 9.504708 TTCCTAAAACCACGATGAGTAATTTAA 57.495 29.630 0.00 0.00 0.00 1.52
496 508 9.504708 TCCTAAAACCACGATGAGTAATTTAAA 57.495 29.630 0.00 0.00 0.00 1.52
500 512 8.980143 AAACCACGATGAGTAATTTAAAATGG 57.020 30.769 0.00 0.00 0.00 3.16
501 513 7.931578 ACCACGATGAGTAATTTAAAATGGA 57.068 32.000 0.00 0.00 0.00 3.41
502 514 8.343168 ACCACGATGAGTAATTTAAAATGGAA 57.657 30.769 0.00 0.00 0.00 3.53
503 515 8.458843 ACCACGATGAGTAATTTAAAATGGAAG 58.541 33.333 0.00 0.00 0.00 3.46
504 516 7.915397 CCACGATGAGTAATTTAAAATGGAAGG 59.085 37.037 0.00 0.00 0.00 3.46
618 630 4.720530 ACAAACGAAACGAACAGTATCC 57.279 40.909 0.00 0.00 0.00 2.59
619 631 4.121317 ACAAACGAAACGAACAGTATCCA 58.879 39.130 0.00 0.00 0.00 3.41
620 632 4.210537 ACAAACGAAACGAACAGTATCCAG 59.789 41.667 0.00 0.00 0.00 3.86
621 633 2.334838 ACGAAACGAACAGTATCCAGC 58.665 47.619 0.00 0.00 0.00 4.85
622 634 1.320555 CGAAACGAACAGTATCCAGCG 59.679 52.381 0.00 0.00 0.00 5.18
623 635 1.060698 GAAACGAACAGTATCCAGCGC 59.939 52.381 0.00 0.00 0.00 5.92
624 636 0.739813 AACGAACAGTATCCAGCGCC 60.740 55.000 2.29 0.00 0.00 6.53
625 637 2.230940 CGAACAGTATCCAGCGCCG 61.231 63.158 2.29 0.00 0.00 6.46
626 638 2.511600 AACAGTATCCAGCGCCGC 60.512 61.111 2.29 0.00 0.00 6.53
627 639 4.873129 ACAGTATCCAGCGCCGCG 62.873 66.667 8.83 8.83 0.00 6.46
628 640 4.569023 CAGTATCCAGCGCCGCGA 62.569 66.667 18.91 0.00 0.00 5.87
629 641 3.833645 AGTATCCAGCGCCGCGAA 61.834 61.111 18.91 0.00 0.00 4.70
630 642 3.330853 GTATCCAGCGCCGCGAAG 61.331 66.667 18.91 7.47 0.00 3.79
751 768 9.845214 AGCTCGAATATATTCCCCCTATAATAT 57.155 33.333 17.83 0.00 33.82 1.28
863 880 1.534595 GCTCTGCAAGGTCAACTCAAG 59.465 52.381 0.00 0.00 0.00 3.02
921 967 1.269309 CCACGATCGACCAGGATCTTC 60.269 57.143 24.34 0.00 40.52 2.87
922 968 1.405463 CACGATCGACCAGGATCTTCA 59.595 52.381 24.34 0.00 40.52 3.02
923 969 2.035193 CACGATCGACCAGGATCTTCAT 59.965 50.000 24.34 0.00 40.52 2.57
924 970 2.294791 ACGATCGACCAGGATCTTCATC 59.705 50.000 24.34 0.00 40.52 2.92
1126 1172 2.203195 AGAAGCTTGTGCGCACCA 60.203 55.556 35.72 25.43 45.42 4.17
1430 1493 9.817809 TTGATGTTACTAGTACTCCATTGATTC 57.182 33.333 0.91 0.00 0.00 2.52
1849 1927 1.669115 CTGACGACCAAGTGCCCAG 60.669 63.158 0.00 0.00 0.00 4.45
2172 2276 8.937634 ATCAAAATTCAATCTGACTATTTGGC 57.062 30.769 0.00 0.00 30.68 4.52
2396 2505 4.569943 ACGATAATGTGCCCAGATGATAC 58.430 43.478 0.00 0.00 0.00 2.24
2398 2507 2.260844 AATGTGCCCAGATGATACGG 57.739 50.000 0.00 0.00 0.00 4.02
2453 2562 1.203287 GCCCTTGATCAAAAGTGAGGC 59.797 52.381 9.88 10.72 37.14 4.70
2483 2592 3.877508 GCTATTGACCGGTCATTTAGCTT 59.122 43.478 40.09 24.54 42.35 3.74
2494 2603 3.699038 GTCATTTAGCTTGCCCAACCATA 59.301 43.478 0.00 0.00 0.00 2.74
2495 2604 4.342092 GTCATTTAGCTTGCCCAACCATAT 59.658 41.667 0.00 0.00 0.00 1.78
2507 2616 5.777732 TGCCCAACCATATTTAACTTTCACT 59.222 36.000 0.00 0.00 0.00 3.41
2509 2618 7.158697 GCCCAACCATATTTAACTTTCACTTT 58.841 34.615 0.00 0.00 0.00 2.66
2664 2779 2.317609 GCACGTCGGCTGTGACAAT 61.318 57.895 14.54 0.00 39.73 2.71
2669 2784 4.505217 CGGCTGTGACAATCGCGC 62.505 66.667 0.00 0.00 0.00 6.86
2806 2922 5.916320 CCAGGGTACGTATTTTGTTTTGTTC 59.084 40.000 0.00 0.00 0.00 3.18
2826 2947 7.353414 TGTTCCATTGTTTTATCTGGTTTCA 57.647 32.000 0.00 0.00 0.00 2.69
2943 3065 1.491668 AGACACGTACCATGGCCATA 58.508 50.000 20.30 0.00 0.00 2.74
3098 3220 4.373116 GGGTGCAGCGTCGAGGAA 62.373 66.667 9.75 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.669569 GCAGTTTGCTCGCTCCCA 60.670 61.111 0.00 0.00 40.96 4.37
1 2 3.435186 GGCAGTTTGCTCGCTCCC 61.435 66.667 0.67 0.00 44.28 4.30
2 3 3.793144 CGGCAGTTTGCTCGCTCC 61.793 66.667 0.67 0.00 44.28 4.70
20 21 1.327303 AGCTCCTAGAATCTGCGGAG 58.673 55.000 19.64 19.64 44.58 4.63
21 22 2.158593 ACTAGCTCCTAGAATCTGCGGA 60.159 50.000 0.00 0.00 37.49 5.54
22 23 2.030363 CACTAGCTCCTAGAATCTGCGG 60.030 54.545 6.29 0.00 37.49 5.69
23 24 2.881513 TCACTAGCTCCTAGAATCTGCG 59.118 50.000 6.29 0.00 37.49 5.18
24 25 4.927978 TTCACTAGCTCCTAGAATCTGC 57.072 45.455 6.29 0.00 37.49 4.26
25 26 6.928492 GGAAATTCACTAGCTCCTAGAATCTG 59.072 42.308 6.29 0.00 37.49 2.90
26 27 6.239176 CGGAAATTCACTAGCTCCTAGAATCT 60.239 42.308 6.29 0.00 37.49 2.40
27 28 5.923684 CGGAAATTCACTAGCTCCTAGAATC 59.076 44.000 6.29 0.00 37.49 2.52
28 29 5.598830 TCGGAAATTCACTAGCTCCTAGAAT 59.401 40.000 6.29 0.00 37.49 2.40
29 30 4.954202 TCGGAAATTCACTAGCTCCTAGAA 59.046 41.667 6.29 0.00 37.49 2.10
30 31 4.533815 TCGGAAATTCACTAGCTCCTAGA 58.466 43.478 6.29 0.00 37.49 2.43
31 32 4.920640 TCGGAAATTCACTAGCTCCTAG 57.079 45.455 0.00 0.00 39.72 3.02
32 33 4.439700 CGTTCGGAAATTCACTAGCTCCTA 60.440 45.833 0.00 0.00 0.00 2.94
33 34 3.676324 CGTTCGGAAATTCACTAGCTCCT 60.676 47.826 0.00 0.00 0.00 3.69
34 35 2.603560 CGTTCGGAAATTCACTAGCTCC 59.396 50.000 0.00 0.00 0.00 4.70
35 36 2.603560 CCGTTCGGAAATTCACTAGCTC 59.396 50.000 5.19 0.00 0.00 4.09
36 37 2.618053 CCGTTCGGAAATTCACTAGCT 58.382 47.619 5.19 0.00 0.00 3.32
37 38 1.664151 CCCGTTCGGAAATTCACTAGC 59.336 52.381 13.08 0.00 0.00 3.42
38 39 2.277084 CCCCGTTCGGAAATTCACTAG 58.723 52.381 13.08 0.00 0.00 2.57
39 40 1.676615 GCCCCGTTCGGAAATTCACTA 60.677 52.381 13.08 0.00 0.00 2.74
40 41 0.958876 GCCCCGTTCGGAAATTCACT 60.959 55.000 13.08 0.00 0.00 3.41
41 42 0.958876 AGCCCCGTTCGGAAATTCAC 60.959 55.000 13.08 0.00 0.00 3.18
42 43 0.250989 AAGCCCCGTTCGGAAATTCA 60.251 50.000 13.08 0.00 0.00 2.57
43 44 0.450583 GAAGCCCCGTTCGGAAATTC 59.549 55.000 13.08 9.10 0.00 2.17
44 45 0.250989 TGAAGCCCCGTTCGGAAATT 60.251 50.000 13.08 3.95 0.00 1.82
45 46 0.034477 ATGAAGCCCCGTTCGGAAAT 60.034 50.000 13.08 0.00 0.00 2.17
46 47 0.614294 TATGAAGCCCCGTTCGGAAA 59.386 50.000 13.08 0.00 0.00 3.13
47 48 0.177141 CTATGAAGCCCCGTTCGGAA 59.823 55.000 13.08 0.00 0.00 4.30
48 49 0.974010 ACTATGAAGCCCCGTTCGGA 60.974 55.000 13.08 0.00 0.00 4.55
49 50 0.529992 GACTATGAAGCCCCGTTCGG 60.530 60.000 4.08 4.08 0.00 4.30
50 51 0.174845 TGACTATGAAGCCCCGTTCG 59.825 55.000 0.00 0.00 0.00 3.95
51 52 2.396590 TTGACTATGAAGCCCCGTTC 57.603 50.000 0.00 0.00 0.00 3.95
52 53 2.039879 AGTTTGACTATGAAGCCCCGTT 59.960 45.455 0.00 0.00 0.00 4.44
53 54 1.628846 AGTTTGACTATGAAGCCCCGT 59.371 47.619 0.00 0.00 0.00 5.28
54 55 2.403252 AGTTTGACTATGAAGCCCCG 57.597 50.000 0.00 0.00 0.00 5.73
55 56 3.691609 CAGAAGTTTGACTATGAAGCCCC 59.308 47.826 0.00 0.00 0.00 5.80
56 57 4.327680 ACAGAAGTTTGACTATGAAGCCC 58.672 43.478 1.63 0.00 0.00 5.19
57 58 5.948992 AACAGAAGTTTGACTATGAAGCC 57.051 39.130 1.63 0.00 33.11 4.35
58 59 7.643579 AGAAAACAGAAGTTTGACTATGAAGC 58.356 34.615 0.00 0.00 46.79 3.86
95 96 5.683876 ATCAGACACAGCTATACACCTTT 57.316 39.130 0.00 0.00 0.00 3.11
258 261 7.531716 TCCAGCGGTGTAAATAAAATAAGTTG 58.468 34.615 14.40 0.00 0.00 3.16
342 345 6.014925 TGTCCGCTGATATAATGGTAAAGCTA 60.015 38.462 0.00 0.00 0.00 3.32
355 358 4.799678 CTTACGAATCTGTCCGCTGATAT 58.200 43.478 0.00 0.00 33.71 1.63
373 376 3.434299 TGCTACTTTAACGGCAAGCTTAC 59.566 43.478 0.00 0.00 0.00 2.34
376 379 1.804748 GTGCTACTTTAACGGCAAGCT 59.195 47.619 0.00 0.00 36.43 3.74
458 470 0.039888 TTTTAGGAACTTTGCCGCGC 60.040 50.000 0.00 0.00 41.75 6.86
469 481 7.989416 AAATTACTCATCGTGGTTTTAGGAA 57.011 32.000 0.00 0.00 0.00 3.36
470 482 9.504708 TTTAAATTACTCATCGTGGTTTTAGGA 57.495 29.630 0.00 0.00 0.00 2.94
474 486 9.418045 CCATTTTAAATTACTCATCGTGGTTTT 57.582 29.630 0.00 0.00 0.00 2.43
475 487 8.798402 TCCATTTTAAATTACTCATCGTGGTTT 58.202 29.630 0.00 0.00 0.00 3.27
477 489 7.931578 TCCATTTTAAATTACTCATCGTGGT 57.068 32.000 0.00 0.00 0.00 4.16
481 493 8.893727 ACTCCTTCCATTTTAAATTACTCATCG 58.106 33.333 0.00 0.00 0.00 3.84
523 535 0.391130 CAGCCCGACGAATTCCTTGA 60.391 55.000 0.00 0.00 0.00 3.02
535 547 2.614983 GTTTTGACACTAAACAGCCCGA 59.385 45.455 0.00 0.00 35.94 5.14
621 633 1.692148 TAATTCTGTGCTTCGCGGCG 61.692 55.000 17.70 17.70 34.52 6.46
622 634 0.026803 CTAATTCTGTGCTTCGCGGC 59.973 55.000 6.13 2.62 0.00 6.53
623 635 0.026803 GCTAATTCTGTGCTTCGCGG 59.973 55.000 6.13 0.00 0.00 6.46
624 636 0.721154 TGCTAATTCTGTGCTTCGCG 59.279 50.000 0.00 0.00 0.00 5.87
625 637 1.530646 GCTGCTAATTCTGTGCTTCGC 60.531 52.381 0.00 0.00 0.00 4.70
626 638 1.267235 CGCTGCTAATTCTGTGCTTCG 60.267 52.381 0.00 0.00 0.00 3.79
627 639 1.530646 GCGCTGCTAATTCTGTGCTTC 60.531 52.381 0.00 0.00 38.07 3.86
628 640 0.449388 GCGCTGCTAATTCTGTGCTT 59.551 50.000 0.00 0.00 38.07 3.91
629 641 1.372087 GGCGCTGCTAATTCTGTGCT 61.372 55.000 7.64 0.00 40.02 4.40
630 642 1.063166 GGCGCTGCTAATTCTGTGC 59.937 57.895 7.64 2.22 39.61 4.57
631 643 1.349627 CGGCGCTGCTAATTCTGTG 59.650 57.895 7.64 0.00 0.00 3.66
632 644 2.464459 GCGGCGCTGCTAATTCTGT 61.464 57.895 33.43 0.00 0.00 3.41
633 645 1.980951 TTGCGGCGCTGCTAATTCTG 61.981 55.000 38.42 0.00 35.36 3.02
634 646 1.305219 TTTGCGGCGCTGCTAATTCT 61.305 50.000 38.42 0.00 35.36 2.40
635 647 0.863119 CTTTGCGGCGCTGCTAATTC 60.863 55.000 38.42 12.44 35.36 2.17
636 648 1.137404 CTTTGCGGCGCTGCTAATT 59.863 52.632 38.42 0.00 35.36 1.40
637 649 2.793946 CTTTGCGGCGCTGCTAAT 59.206 55.556 38.42 0.00 35.36 1.73
638 650 4.101790 GCTTTGCGGCGCTGCTAA 62.102 61.111 38.42 34.40 35.36 3.09
658 670 9.455847 CAAACTTATAAATGAGCTGCTAATTCC 57.544 33.333 12.58 0.00 0.00 3.01
750 767 3.818210 AGCTCGATCGTCTCTGTCATTAT 59.182 43.478 15.94 0.00 0.00 1.28
751 768 3.002759 CAGCTCGATCGTCTCTGTCATTA 59.997 47.826 15.94 0.00 0.00 1.90
752 769 2.020720 AGCTCGATCGTCTCTGTCATT 58.979 47.619 15.94 0.00 0.00 2.57
753 770 1.333308 CAGCTCGATCGTCTCTGTCAT 59.667 52.381 15.94 0.00 0.00 3.06
754 771 0.729690 CAGCTCGATCGTCTCTGTCA 59.270 55.000 15.94 0.00 0.00 3.58
863 880 5.276584 GCGATCGAAGATGTAATATGGATGC 60.277 44.000 21.57 0.00 45.12 3.91
921 967 2.310647 TGGATGGATGGATGGATGGATG 59.689 50.000 0.00 0.00 0.00 3.51
922 968 2.651190 TGGATGGATGGATGGATGGAT 58.349 47.619 0.00 0.00 0.00 3.41
923 969 2.136974 TGGATGGATGGATGGATGGA 57.863 50.000 0.00 0.00 0.00 3.41
924 970 3.362706 GAATGGATGGATGGATGGATGG 58.637 50.000 0.00 0.00 0.00 3.51
1111 1157 2.723746 CTTGGTGCGCACAAGCTT 59.276 55.556 38.60 0.00 38.89 3.74
1126 1172 1.028868 GCGAAGATGGCCTCAAGCTT 61.029 55.000 3.32 0.00 43.05 3.74
1312 1358 1.457346 CATGCTTTCTCCACCACCTC 58.543 55.000 0.00 0.00 0.00 3.85
1430 1493 4.902443 ATGATGAGCAGAGCAATTTCAG 57.098 40.909 0.00 0.00 0.00 3.02
1583 1646 1.984297 GTTCTTGTCGGCGAAGTACTC 59.016 52.381 12.92 0.00 0.00 2.59
1596 1659 2.711009 TCCTTCATGGTGAGGTTCTTGT 59.289 45.455 9.53 0.00 37.07 3.16
1725 1803 0.944311 GCGTCACTCCAATCGTGTGT 60.944 55.000 0.00 0.00 37.28 3.72
1849 1927 2.964389 GCTCGCCATCTTCTCCGC 60.964 66.667 0.00 0.00 0.00 5.54
2258 2363 5.587043 ACTTCACGAGAAAATGTTACAACCA 59.413 36.000 0.00 0.00 32.35 3.67
2274 2379 7.061673 CACAATGAACTTTTCAAAACTTCACGA 59.938 33.333 6.99 0.00 43.95 4.35
2396 2505 7.532546 CCATGCGTTAAAAATGTATGTATACCG 59.467 37.037 0.00 0.00 38.39 4.02
2398 2507 9.594038 CTCCATGCGTTAAAAATGTATGTATAC 57.406 33.333 0.00 0.00 38.39 1.47
2453 2562 3.139077 GACCGGTCAATAGCCCATTAAG 58.861 50.000 29.75 0.00 0.00 1.85
2483 2592 5.777732 AGTGAAAGTTAAATATGGTTGGGCA 59.222 36.000 0.00 0.00 0.00 5.36
2669 2784 1.601171 CTGCTTGAGGTCAGAGGGG 59.399 63.158 0.00 0.00 32.26 4.79
2680 2796 1.207811 TCGATGATTGCTCCTGCTTGA 59.792 47.619 0.00 0.00 40.48 3.02
2767 2883 1.552792 CCCTGGGAACAAGAGAGAGAC 59.447 57.143 7.01 0.00 42.06 3.36
2806 2922 5.160641 CCGTGAAACCAGATAAAACAATGG 58.839 41.667 0.00 0.00 38.83 3.16
2819 2940 0.471211 ACCTCTCTCCCGTGAAACCA 60.471 55.000 0.00 0.00 0.00 3.67
2826 2947 1.076923 ATGCGTACCTCTCTCCCGT 60.077 57.895 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.