Multiple sequence alignment - TraesCS2D01G495700

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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 TraesCS2D01G495700 chr2D 100.000 3126 0 0 1 3126 592409774 592412899 0.000000e+00 5773.0
1 TraesCS2D01G495700 chr2D 80.461 737 69 44 976 1684 619058647 619057958 7.790000e-136 494.0
2 TraesCS2D01G495700 chr2D 77.250 989 114 67 1068 2020 619046810 619045897 7.840000e-131 477.0
3 TraesCS2D01G495700 chr2A 92.210 2041 84 28 64 2063 726984952 726986958 0.000000e+00 2819.0
4 TraesCS2D01G495700 chr2A 90.139 720 58 7 2419 3126 726987494 726988212 0.000000e+00 924.0
5 TraesCS2D01G495700 chr2A 90.446 314 12 8 2072 2385 726987095 726987390 6.280000e-107 398.0
6 TraesCS2D01G495700 chr2A 81.336 509 49 21 1183 1674 749904449 749903970 3.810000e-99 372.0
7 TraesCS2D01G495700 chr2A 79.839 496 47 31 1183 1677 749915308 749914865 2.340000e-81 313.0
8 TraesCS2D01G495700 chr2A 87.838 74 5 4 1068 1140 749904537 749904467 2.000000e-12 84.2
9 TraesCS2D01G495700 chr2B 93.292 805 35 5 1466 2259 718396583 718397379 0.000000e+00 1170.0
10 TraesCS2D01G495700 chr2B 89.692 747 29 13 683 1419 718395876 718396584 0.000000e+00 909.0
11 TraesCS2D01G495700 chr2B 77.137 1041 127 65 935 1940 756571480 756570516 4.650000e-138 501.0
12 TraesCS2D01G495700 chr2B 80.844 616 60 31 1081 1677 756553505 756552929 6.190000e-117 431.0
13 TraesCS2D01G495700 chr4B 92.593 162 11 1 1515 1675 631608690 631608529 6.740000e-57 231.0


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 TraesCS2D01G495700 chr2D 592409774 592412899 3125 False 5773.000000 5773 100.000000 1 3126 1 chr2D.!!$F1 3125
1 TraesCS2D01G495700 chr2D 619057958 619058647 689 True 494.000000 494 80.461000 976 1684 1 chr2D.!!$R2 708
2 TraesCS2D01G495700 chr2D 619045897 619046810 913 True 477.000000 477 77.250000 1068 2020 1 chr2D.!!$R1 952
3 TraesCS2D01G495700 chr2A 726984952 726988212 3260 False 1380.333333 2819 90.931667 64 3126 3 chr2A.!!$F1 3062
4 TraesCS2D01G495700 chr2A 749903970 749904537 567 True 228.100000 372 84.587000 1068 1674 2 chr2A.!!$R2 606
5 TraesCS2D01G495700 chr2B 718395876 718397379 1503 False 1039.500000 1170 91.492000 683 2259 2 chr2B.!!$F1 1576
6 TraesCS2D01G495700 chr2B 756570516 756571480 964 True 501.000000 501 77.137000 935 1940 1 chr2B.!!$R2 1005
7 TraesCS2D01G495700 chr2B 756552929 756553505 576 True 431.000000 431 80.844000 1081 1677 1 chr2B.!!$R1 596

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
41 42 0.030638 GTGTGAGCAAAATGGCACGT 59.969 50.0 0.00 0.00 35.83 4.49 F
966 1007 0.453282 CGGTCGTACGTGTGTACCTG 60.453 60.0 16.05 7.66 46.71 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 1528 0.260230 TGCCTCCGGAGAGAGAGAAT 59.74 55.0 33.39 0.0 43.39 2.40 R
2728 3066 0.100146 GGCCTACTGGACTAACGTCG 59.90 60.0 0.00 0.0 41.16 5.12 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
24 25 7.110179 CATACATCTTCGCAACTATTAGGTG 57.890 40.000 4.27 4.27 35.59 4.00
25 26 5.086104 ACATCTTCGCAACTATTAGGTGT 57.914 39.130 10.35 0.00 34.77 4.16
26 27 4.870426 ACATCTTCGCAACTATTAGGTGTG 59.130 41.667 14.81 14.81 44.42 3.82
29 30 2.888594 TCGCAACTATTAGGTGTGAGC 58.111 47.619 18.69 0.33 46.42 4.26
30 31 2.232696 TCGCAACTATTAGGTGTGAGCA 59.767 45.455 18.69 0.13 46.42 4.26
31 32 3.000041 CGCAACTATTAGGTGTGAGCAA 59.000 45.455 15.72 0.00 45.85 3.91
32 33 3.435327 CGCAACTATTAGGTGTGAGCAAA 59.565 43.478 15.72 0.00 45.85 3.68
33 34 4.083537 CGCAACTATTAGGTGTGAGCAAAA 60.084 41.667 15.72 0.00 45.85 2.44
34 35 5.391950 CGCAACTATTAGGTGTGAGCAAAAT 60.392 40.000 15.72 0.00 45.85 1.82
35 36 5.801947 GCAACTATTAGGTGTGAGCAAAATG 59.198 40.000 10.35 0.00 34.77 2.32
36 37 6.324819 CAACTATTAGGTGTGAGCAAAATGG 58.675 40.000 0.24 0.00 0.00 3.16
37 38 3.874392 ATTAGGTGTGAGCAAAATGGC 57.126 42.857 0.00 0.00 0.00 4.40
38 39 2.284754 TAGGTGTGAGCAAAATGGCA 57.715 45.000 0.00 0.00 35.83 4.92
39 40 0.675633 AGGTGTGAGCAAAATGGCAC 59.324 50.000 0.00 0.00 35.83 5.01
40 41 0.664166 GGTGTGAGCAAAATGGCACG 60.664 55.000 0.00 0.00 35.83 5.34
41 42 0.030638 GTGTGAGCAAAATGGCACGT 59.969 50.000 0.00 0.00 35.83 4.49
42 43 1.265635 GTGTGAGCAAAATGGCACGTA 59.734 47.619 0.00 0.00 35.83 3.57
43 44 1.265635 TGTGAGCAAAATGGCACGTAC 59.734 47.619 0.00 0.00 35.83 3.67
44 45 1.535462 GTGAGCAAAATGGCACGTACT 59.465 47.619 0.00 0.00 35.83 2.73
45 46 2.739913 GTGAGCAAAATGGCACGTACTA 59.260 45.455 0.00 0.00 35.83 1.82
46 47 3.000041 TGAGCAAAATGGCACGTACTAG 59.000 45.455 0.00 0.00 35.83 2.57
47 48 2.351726 GAGCAAAATGGCACGTACTAGG 59.648 50.000 0.00 0.00 35.83 3.02
48 49 2.081462 GCAAAATGGCACGTACTAGGT 58.919 47.619 0.00 0.00 0.00 3.08
49 50 2.486592 GCAAAATGGCACGTACTAGGTT 59.513 45.455 0.00 0.00 0.00 3.50
50 51 3.425758 GCAAAATGGCACGTACTAGGTTC 60.426 47.826 0.00 0.00 0.00 3.62
51 52 3.975168 AAATGGCACGTACTAGGTTCT 57.025 42.857 0.00 0.00 0.00 3.01
52 53 3.521947 AATGGCACGTACTAGGTTCTC 57.478 47.619 0.00 0.00 0.00 2.87
53 54 1.913778 TGGCACGTACTAGGTTCTCA 58.086 50.000 0.00 0.00 0.00 3.27
54 55 2.241160 TGGCACGTACTAGGTTCTCAA 58.759 47.619 0.00 0.00 0.00 3.02
55 56 2.629137 TGGCACGTACTAGGTTCTCAAA 59.371 45.455 0.00 0.00 0.00 2.69
56 57 3.069872 TGGCACGTACTAGGTTCTCAAAA 59.930 43.478 0.00 0.00 0.00 2.44
57 58 4.060205 GGCACGTACTAGGTTCTCAAAAA 58.940 43.478 0.00 0.00 0.00 1.94
147 149 0.602905 GGCACACGACAAGTTAGGCT 60.603 55.000 0.00 0.00 0.00 4.58
155 157 4.326548 CACGACAAGTTAGGCTAGCTTAAC 59.673 45.833 31.77 31.77 38.33 2.01
171 173 8.560374 GCTAGCTTAACTAAATTAACCAGATGG 58.440 37.037 7.70 0.00 42.17 3.51
184 186 3.872511 CCAGATGGTTATTTTGCTGCA 57.127 42.857 0.00 0.00 0.00 4.41
195 197 4.863152 ATTTTGCTGCAAACAAACTGTC 57.137 36.364 25.99 0.00 36.77 3.51
218 220 5.417266 TCATTGTGACTTGAAAACTGTGGAA 59.583 36.000 0.00 0.00 0.00 3.53
235 237 6.705825 ACTGTGGAAAATCTTTTATTTGTGGC 59.294 34.615 0.00 0.00 0.00 5.01
237 239 5.923684 GTGGAAAATCTTTTATTTGTGGCGA 59.076 36.000 0.00 0.00 0.00 5.54
253 255 1.502231 GCGAAGTGTGAGTGTGACAT 58.498 50.000 0.00 0.00 0.00 3.06
458 462 1.525197 TGACACGCGAGCTACAAAAAG 59.475 47.619 15.93 0.00 0.00 2.27
462 466 3.064271 ACACGCGAGCTACAAAAAGAAAA 59.936 39.130 15.93 0.00 0.00 2.29
532 536 6.074569 ACTGTTTTCAAAACCGCAATTTATCG 60.075 34.615 10.56 0.00 0.00 2.92
552 556 2.584791 GTTTTTGTGTAGCTCGCATGG 58.415 47.619 0.00 0.00 36.40 3.66
597 601 9.990360 ATAATTCACACATATAATACACGTCCA 57.010 29.630 0.00 0.00 0.00 4.02
598 602 8.902540 AATTCACACATATAATACACGTCCAT 57.097 30.769 0.00 0.00 0.00 3.41
599 603 9.990360 AATTCACACATATAATACACGTCCATA 57.010 29.630 0.00 0.00 0.00 2.74
677 706 2.180017 GCTGCACTCGCCAAATGG 59.820 61.111 0.00 0.00 37.32 3.16
679 708 1.798735 CTGCACTCGCCAAATGGAG 59.201 57.895 2.98 0.00 37.32 3.86
693 722 5.753921 GCCAAATGGAGTACATACTAGTGTC 59.246 44.000 5.39 0.00 39.40 3.67
697 726 7.676683 AATGGAGTACATACTAGTGTCCAAT 57.323 36.000 5.39 0.00 39.40 3.16
710 739 5.920193 AGTGTCCAATTGTGGGATTTATG 57.080 39.130 4.43 0.00 46.01 1.90
711 740 5.332743 AGTGTCCAATTGTGGGATTTATGT 58.667 37.500 4.43 0.00 46.01 2.29
712 741 6.489603 AGTGTCCAATTGTGGGATTTATGTA 58.510 36.000 4.43 0.00 46.01 2.29
732 762 1.052617 TATAGCCGGCCATTGCACTA 58.947 50.000 26.15 6.51 40.13 2.74
795 832 3.057547 CTGGCTAGCTCGCTGTCGT 62.058 63.158 15.72 0.00 36.96 4.34
964 1005 1.574428 ACGGTCGTACGTGTGTACC 59.426 57.895 16.05 13.68 46.71 3.34
965 1006 0.884704 ACGGTCGTACGTGTGTACCT 60.885 55.000 16.05 2.68 46.71 3.08
966 1007 0.453282 CGGTCGTACGTGTGTACCTG 60.453 60.000 16.05 7.66 46.71 4.00
1447 1528 1.052124 ACGACCCTGTCCACTTTGGA 61.052 55.000 0.00 0.00 45.98 3.53
1484 1565 2.613223 GGCAACAACAGTAGGAGGAGAC 60.613 54.545 0.00 0.00 0.00 3.36
1634 1721 1.153549 CAGCTGCGTAGGGAGAACC 60.154 63.158 8.24 0.00 40.67 3.62
1716 1813 5.636121 TGTCGTTGCCATTTAGTTACTGTAG 59.364 40.000 0.00 0.00 0.00 2.74
1719 1816 6.707161 TCGTTGCCATTTAGTTACTGTAGTTT 59.293 34.615 0.00 0.00 0.00 2.66
1720 1817 6.795114 CGTTGCCATTTAGTTACTGTAGTTTG 59.205 38.462 0.00 0.00 0.00 2.93
1721 1818 7.307514 CGTTGCCATTTAGTTACTGTAGTTTGA 60.308 37.037 0.00 0.00 0.00 2.69
1723 1820 8.630054 TGCCATTTAGTTACTGTAGTTTGATT 57.370 30.769 0.00 0.00 0.00 2.57
1764 1861 3.194062 TCGAAGCATTACGATGATTGCA 58.806 40.909 0.00 0.00 41.64 4.08
1879 1979 2.691771 CCAGCAGAAGCAGCAGCAG 61.692 63.158 3.17 0.00 45.49 4.24
2116 2374 8.364142 ACTTGCTTAGAGTAATATGATGAGTCC 58.636 37.037 0.00 0.00 0.00 3.85
2139 2397 6.670902 TCCCTCTCCGTAATAATATTAAGGGG 59.329 42.308 19.77 17.86 40.15 4.79
2206 2464 2.517959 TCTTTCCATCACAAGGCCTTG 58.482 47.619 38.30 38.30 45.58 3.61
2246 2504 3.010420 GCAAGAAGATAGGGGTGTGTTC 58.990 50.000 0.00 0.00 0.00 3.18
2278 2536 0.038744 ACCATGTAGCTTGCTTGCCT 59.961 50.000 0.00 0.00 0.00 4.75
2279 2537 0.454600 CCATGTAGCTTGCTTGCCTG 59.545 55.000 0.00 0.00 0.00 4.85
2280 2538 0.179145 CATGTAGCTTGCTTGCCTGC 60.179 55.000 0.00 0.00 0.00 4.85
2281 2539 0.609957 ATGTAGCTTGCTTGCCTGCA 60.610 50.000 0.00 0.00 41.65 4.41
2282 2540 1.211190 GTAGCTTGCTTGCCTGCAC 59.789 57.895 0.00 0.00 43.20 4.57
2283 2541 2.327343 TAGCTTGCTTGCCTGCACG 61.327 57.895 0.00 0.63 43.20 5.34
2284 2542 3.969802 GCTTGCTTGCCTGCACGT 61.970 61.111 0.00 0.00 43.20 4.49
2336 2594 3.591835 CGTTTGGTGGCCTGCGTT 61.592 61.111 3.32 0.00 0.00 4.84
2337 2595 2.255172 CGTTTGGTGGCCTGCGTTA 61.255 57.895 3.32 0.00 0.00 3.18
2338 2596 1.579429 GTTTGGTGGCCTGCGTTAG 59.421 57.895 3.32 0.00 0.00 2.34
2339 2597 2.265182 TTTGGTGGCCTGCGTTAGC 61.265 57.895 3.32 0.00 45.41 3.09
2345 2603 4.110493 GCCTGCGTTAGCCACTAG 57.890 61.111 0.00 0.00 44.33 2.57
2346 2604 1.515954 GCCTGCGTTAGCCACTAGA 59.484 57.895 0.00 0.00 44.33 2.43
2347 2605 0.105039 GCCTGCGTTAGCCACTAGAT 59.895 55.000 0.00 0.00 44.33 1.98
2348 2606 1.858091 CCTGCGTTAGCCACTAGATG 58.142 55.000 0.00 0.00 44.33 2.90
2374 2632 2.584492 TCTCGCATACACTGGACATG 57.416 50.000 0.00 0.00 0.00 3.21
2385 2643 5.772393 ACACTGGACATGATTAAGGGTTA 57.228 39.130 0.00 0.00 0.00 2.85
2386 2644 6.134535 ACACTGGACATGATTAAGGGTTAA 57.865 37.500 0.00 0.00 0.00 2.01
2387 2645 5.944007 ACACTGGACATGATTAAGGGTTAAC 59.056 40.000 0.00 0.00 0.00 2.01
2388 2646 5.943416 CACTGGACATGATTAAGGGTTAACA 59.057 40.000 8.10 0.00 0.00 2.41
2394 2683 7.444487 GGACATGATTAAGGGTTAACATCTACC 59.556 40.741 8.10 0.00 0.00 3.18
2404 2693 6.442564 AGGGTTAACATCTACCTATGACACAA 59.557 38.462 8.10 0.00 34.75 3.33
2420 2709 3.011119 ACACAAAAAGTACTCGGCAACA 58.989 40.909 0.00 0.00 0.00 3.33
2421 2710 3.440872 ACACAAAAAGTACTCGGCAACAA 59.559 39.130 0.00 0.00 0.00 2.83
2423 2712 3.042887 CAAAAAGTACTCGGCAACAAGC 58.957 45.455 0.00 0.00 44.65 4.01
2447 2775 4.344474 CCGTAGGCGAGCGATCCC 62.344 72.222 0.00 0.00 46.14 3.85
2476 2804 2.054458 TGGCGAACCAGTTGCTAGA 58.946 52.632 0.00 0.00 42.67 2.43
2478 2806 0.037232 GGCGAACCAGTTGCTAGAGT 60.037 55.000 0.00 0.00 35.26 3.24
2480 2808 1.461127 GCGAACCAGTTGCTAGAGTTG 59.539 52.381 0.00 0.00 0.00 3.16
2484 2812 1.160137 CCAGTTGCTAGAGTTGTGGC 58.840 55.000 0.00 0.00 0.00 5.01
2486 2814 0.320771 AGTTGCTAGAGTTGTGGCCG 60.321 55.000 0.00 0.00 0.00 6.13
2489 2817 2.103042 GCTAGAGTTGTGGCCGCAG 61.103 63.158 20.15 7.88 0.00 5.18
2510 2838 3.595108 GAAGTGCGCGCAAAGGGAC 62.595 63.158 38.24 22.45 34.27 4.46
2529 2860 3.302347 GAGGAGGGTGTCGTGGCAG 62.302 68.421 0.00 0.00 0.00 4.85
2536 2867 1.373497 GTGTCGTGGCAGAGGACTG 60.373 63.158 12.63 0.00 45.91 3.51
2566 2898 2.766239 CAGTATGCGTGTGATGGCA 58.234 52.632 0.00 0.00 44.29 4.92
2568 2900 1.086696 AGTATGCGTGTGATGGCAAC 58.913 50.000 0.00 0.00 43.26 4.17
2586 2918 3.872240 GCAACATTAGTCCAGTAGGCCAA 60.872 47.826 5.01 0.00 33.74 4.52
2587 2919 4.331968 CAACATTAGTCCAGTAGGCCAAA 58.668 43.478 5.01 0.00 33.74 3.28
2588 2920 4.222124 ACATTAGTCCAGTAGGCCAAAG 57.778 45.455 5.01 0.00 33.74 2.77
2644 2982 2.561373 GTTGCTAGCGTTGTGGCC 59.439 61.111 10.77 0.00 0.00 5.36
2698 3036 1.214062 GTGTCGAGGCAGAGGACTG 59.786 63.158 0.00 0.00 45.91 3.51
2782 3122 4.814294 AGGAACGACGCCGATGGC 62.814 66.667 0.00 0.00 46.75 4.40
2800 3140 4.910585 GATGGCGACGGCGGGAAT 62.911 66.667 15.06 4.20 41.24 3.01
2822 3162 1.892338 ATGGTTTCCATGCGGCAAG 59.108 52.632 6.82 1.43 43.39 4.01
2898 3238 8.999431 CCATAACATGAACACTTTAGTACAGTT 58.001 33.333 0.00 0.00 0.00 3.16
2923 3263 6.576662 AACAGGGAGATACACATATACTCG 57.423 41.667 0.00 0.00 0.00 4.18
2941 3281 1.333308 TCGTCTACGACCGTTGAAACA 59.667 47.619 8.11 0.00 44.22 2.83
2990 3330 3.887621 AACAGCGAGATAAAGCTACCA 57.112 42.857 0.00 0.00 42.52 3.25
2992 3332 2.131183 CAGCGAGATAAAGCTACCAGC 58.869 52.381 0.00 0.00 42.52 4.85
2996 3336 2.362397 CGAGATAAAGCTACCAGCCAGA 59.638 50.000 0.00 0.00 43.77 3.86
3011 3351 2.159382 GCCAGAGGAAATTCCAAACGA 58.841 47.619 15.21 0.00 39.61 3.85
3031 3371 2.779755 TCCACCATGTGCGACTAATT 57.220 45.000 0.00 0.00 31.34 1.40
3045 3385 5.931146 TGCGACTAATTTGGCAAAATTCATT 59.069 32.000 17.70 8.76 43.41 2.57
3071 3411 9.081997 TCAAAATAGTTTCAAACATGAACACAC 57.918 29.630 2.41 0.00 0.00 3.82
3087 3427 8.815189 CATGAACACACAATTGAACATTTACAA 58.185 29.630 13.59 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.701841 ACACCTAATAGTTGCGAAGATGTATG 59.298 38.462 0.00 0.00 0.00 2.39
1 2 6.701841 CACACCTAATAGTTGCGAAGATGTAT 59.298 38.462 0.00 0.00 0.00 2.29
2 3 6.040247 CACACCTAATAGTTGCGAAGATGTA 58.960 40.000 0.00 0.00 0.00 2.29
3 4 4.870426 CACACCTAATAGTTGCGAAGATGT 59.130 41.667 0.00 0.00 0.00 3.06
4 5 5.109210 TCACACCTAATAGTTGCGAAGATG 58.891 41.667 0.00 0.00 0.00 2.90
5 6 5.339008 TCACACCTAATAGTTGCGAAGAT 57.661 39.130 0.00 0.00 0.00 2.40
6 7 4.744570 CTCACACCTAATAGTTGCGAAGA 58.255 43.478 0.00 0.00 0.00 2.87
7 8 3.307242 GCTCACACCTAATAGTTGCGAAG 59.693 47.826 0.00 0.00 0.00 3.79
9 10 2.232696 TGCTCACACCTAATAGTTGCGA 59.767 45.455 0.00 0.00 0.00 5.10
10 11 2.616960 TGCTCACACCTAATAGTTGCG 58.383 47.619 0.00 0.00 0.00 4.85
11 12 5.371115 TTTTGCTCACACCTAATAGTTGC 57.629 39.130 0.00 0.00 0.00 4.17
12 13 6.324819 CCATTTTGCTCACACCTAATAGTTG 58.675 40.000 0.00 0.00 0.00 3.16
13 14 5.105756 GCCATTTTGCTCACACCTAATAGTT 60.106 40.000 0.00 0.00 0.00 2.24
14 15 4.399303 GCCATTTTGCTCACACCTAATAGT 59.601 41.667 0.00 0.00 0.00 2.12
15 16 4.398988 TGCCATTTTGCTCACACCTAATAG 59.601 41.667 0.00 0.00 0.00 1.73
16 17 4.157656 GTGCCATTTTGCTCACACCTAATA 59.842 41.667 0.00 0.00 0.00 0.98
17 18 3.056607 GTGCCATTTTGCTCACACCTAAT 60.057 43.478 0.00 0.00 0.00 1.73
18 19 2.295909 GTGCCATTTTGCTCACACCTAA 59.704 45.455 0.00 0.00 0.00 2.69
19 20 1.885887 GTGCCATTTTGCTCACACCTA 59.114 47.619 0.00 0.00 0.00 3.08
20 21 0.675633 GTGCCATTTTGCTCACACCT 59.324 50.000 0.00 0.00 0.00 4.00
21 22 0.664166 CGTGCCATTTTGCTCACACC 60.664 55.000 0.00 0.00 0.00 4.16
22 23 0.030638 ACGTGCCATTTTGCTCACAC 59.969 50.000 0.00 0.00 0.00 3.82
23 24 1.265635 GTACGTGCCATTTTGCTCACA 59.734 47.619 0.00 0.00 0.00 3.58
24 25 1.535462 AGTACGTGCCATTTTGCTCAC 59.465 47.619 0.00 0.00 0.00 3.51
25 26 1.890876 AGTACGTGCCATTTTGCTCA 58.109 45.000 0.00 0.00 0.00 4.26
26 27 2.351726 CCTAGTACGTGCCATTTTGCTC 59.648 50.000 0.00 0.00 0.00 4.26
27 28 2.290071 ACCTAGTACGTGCCATTTTGCT 60.290 45.455 0.00 0.00 0.00 3.91
28 29 2.081462 ACCTAGTACGTGCCATTTTGC 58.919 47.619 0.00 0.00 0.00 3.68
29 30 4.000988 AGAACCTAGTACGTGCCATTTTG 58.999 43.478 0.00 0.00 0.00 2.44
30 31 4.251268 GAGAACCTAGTACGTGCCATTTT 58.749 43.478 0.00 0.00 0.00 1.82
31 32 3.259876 TGAGAACCTAGTACGTGCCATTT 59.740 43.478 0.00 0.00 0.00 2.32
32 33 2.829720 TGAGAACCTAGTACGTGCCATT 59.170 45.455 0.00 0.00 0.00 3.16
33 34 2.453521 TGAGAACCTAGTACGTGCCAT 58.546 47.619 0.00 0.00 0.00 4.40
34 35 1.913778 TGAGAACCTAGTACGTGCCA 58.086 50.000 0.00 0.00 0.00 4.92
35 36 3.308438 TTTGAGAACCTAGTACGTGCC 57.692 47.619 0.00 0.00 0.00 5.01
62 63 2.691011 AGTTGTGGTACGTGCCATTTTT 59.309 40.909 28.46 12.14 41.08 1.94
77 79 4.876107 ACCAGACACAAACTAGAAGTTGTG 59.124 41.667 24.24 24.24 38.66 3.33
78 80 5.099042 ACCAGACACAAACTAGAAGTTGT 57.901 39.130 0.00 0.96 38.66 3.32
135 137 8.719560 ATTTAGTTAAGCTAGCCTAACTTGTC 57.280 34.615 32.98 11.83 34.89 3.18
171 173 6.105657 ACAGTTTGTTTGCAGCAAAATAAC 57.894 33.333 22.26 24.10 37.54 1.89
175 177 3.657634 TGACAGTTTGTTTGCAGCAAAA 58.342 36.364 22.26 9.97 37.54 2.44
176 178 3.309961 TGACAGTTTGTTTGCAGCAAA 57.690 38.095 16.93 16.93 33.96 3.68
177 179 3.523606 ATGACAGTTTGTTTGCAGCAA 57.476 38.095 2.83 2.83 0.00 3.91
178 180 3.188492 CAATGACAGTTTGTTTGCAGCA 58.812 40.909 0.00 0.00 0.00 4.41
179 181 3.000523 CACAATGACAGTTTGTTTGCAGC 59.999 43.478 0.00 0.00 35.18 5.25
180 182 4.266029 GTCACAATGACAGTTTGTTTGCAG 59.734 41.667 4.08 0.00 46.22 4.41
181 183 4.172505 GTCACAATGACAGTTTGTTTGCA 58.827 39.130 4.08 0.00 46.22 4.08
195 197 5.247507 TCCACAGTTTTCAAGTCACAATG 57.752 39.130 0.00 0.00 0.00 2.82
218 220 6.420604 CACACTTCGCCACAAATAAAAGATTT 59.579 34.615 0.00 0.00 0.00 2.17
235 237 5.845985 ATTTATGTCACACTCACACTTCG 57.154 39.130 0.00 0.00 0.00 3.79
237 239 7.995289 TCAAAATTTATGTCACACTCACACTT 58.005 30.769 0.00 0.00 0.00 3.16
289 291 8.049117 TCTGCCATTTGATAGACTTTTAGACAT 58.951 33.333 0.00 0.00 0.00 3.06
290 292 7.394016 TCTGCCATTTGATAGACTTTTAGACA 58.606 34.615 0.00 0.00 0.00 3.41
293 295 9.346725 GTTTTCTGCCATTTGATAGACTTTTAG 57.653 33.333 0.00 0.00 0.00 1.85
434 438 0.038618 TGTAGCTCGCGTGTCAATGT 60.039 50.000 5.77 0.00 0.00 2.71
438 442 1.525197 CTTTTTGTAGCTCGCGTGTCA 59.475 47.619 5.77 2.43 0.00 3.58
479 483 9.073475 ACCAGTGCATATACTGTTTTCTAAAAA 57.927 29.630 5.19 0.00 45.12 1.94
532 536 2.584791 CCATGCGAGCTACACAAAAAC 58.415 47.619 0.00 0.00 0.00 2.43
669 679 5.671493 ACACTAGTATGTACTCCATTTGGC 58.329 41.667 0.00 0.00 37.73 4.52
674 684 7.125811 ACAATTGGACACTAGTATGTACTCCAT 59.874 37.037 10.83 0.00 37.73 3.41
677 706 7.757097 CACAATTGGACACTAGTATGTACTC 57.243 40.000 10.83 0.00 37.73 2.59
693 722 8.686334 GGCTATATACATAAATCCCACAATTGG 58.314 37.037 10.83 0.00 43.50 3.16
697 726 6.411376 CCGGCTATATACATAAATCCCACAA 58.589 40.000 0.00 0.00 0.00 3.33
710 739 1.737793 GTGCAATGGCCGGCTATATAC 59.262 52.381 26.87 19.67 40.13 1.47
711 740 1.628340 AGTGCAATGGCCGGCTATATA 59.372 47.619 26.87 12.30 40.13 0.86
712 741 0.401738 AGTGCAATGGCCGGCTATAT 59.598 50.000 26.87 15.16 40.13 0.86
732 762 3.309265 CCTTCCTCTACTACCCACAGTCT 60.309 52.174 0.00 0.00 0.00 3.24
795 832 5.387788 TGGTACTCTTACTACACTGTTCCA 58.612 41.667 0.00 0.00 0.00 3.53
879 917 9.833182 GCAAGGAAAAGAGAGAATACTTTTAAG 57.167 33.333 0.00 0.00 43.36 1.85
1447 1528 0.260230 TGCCTCCGGAGAGAGAGAAT 59.740 55.000 33.39 0.00 43.39 2.40
1723 1820 9.499585 GCTTCGAATATCTAGCACGTAATAATA 57.500 33.333 0.00 0.00 33.88 0.98
1739 1836 6.147656 TGCAATCATCGTAATGCTTCGAATAT 59.852 34.615 0.00 0.00 39.45 1.28
1764 1861 4.671377 CAAGCCAACAATGCAATACGTAT 58.329 39.130 1.14 1.14 0.00 3.06
1879 1979 3.426568 GAGCGGCACCTCTGTTGC 61.427 66.667 1.45 0.00 0.00 4.17
2116 2374 6.885922 CCCCCTTAATATTATTACGGAGAGG 58.114 44.000 16.66 10.63 0.00 3.69
2139 2397 5.535406 AGCTCAATTGATTCATTCATCTCCC 59.465 40.000 8.96 0.00 33.34 4.30
2206 2464 1.739562 CACCTCGCTCACTCAAGCC 60.740 63.158 0.00 0.00 39.17 4.35
2246 2504 1.102809 ACATGGTATGCATGCACCCG 61.103 55.000 25.37 16.06 33.61 5.28
2280 2538 1.378882 ATAATGCAGCCAGCCACGTG 61.379 55.000 9.08 9.08 44.83 4.49
2281 2539 0.680921 AATAATGCAGCCAGCCACGT 60.681 50.000 0.00 0.00 44.83 4.49
2282 2540 0.248743 CAATAATGCAGCCAGCCACG 60.249 55.000 0.00 0.00 44.83 4.94
2283 2541 1.105457 TCAATAATGCAGCCAGCCAC 58.895 50.000 0.00 0.00 44.83 5.01
2284 2542 1.752498 CTTCAATAATGCAGCCAGCCA 59.248 47.619 0.00 0.00 44.83 4.75
2307 2565 3.489416 GCCACCAAACGTCAAAGAAAATC 59.511 43.478 0.00 0.00 0.00 2.17
2354 2612 2.495669 TCATGTCCAGTGTATGCGAGAA 59.504 45.455 0.00 0.00 0.00 2.87
2374 2632 9.708092 GTCATAGGTAGATGTTAACCCTTAATC 57.292 37.037 2.48 0.00 36.34 1.75
2385 2643 9.216117 GTACTTTTTGTGTCATAGGTAGATGTT 57.784 33.333 0.00 0.00 0.00 2.71
2386 2644 8.594550 AGTACTTTTTGTGTCATAGGTAGATGT 58.405 33.333 0.00 0.00 0.00 3.06
2387 2645 9.088512 GAGTACTTTTTGTGTCATAGGTAGATG 57.911 37.037 0.00 0.00 0.00 2.90
2388 2646 7.974501 CGAGTACTTTTTGTGTCATAGGTAGAT 59.025 37.037 0.00 0.00 0.00 1.98
2394 2683 4.688879 TGCCGAGTACTTTTTGTGTCATAG 59.311 41.667 0.00 0.00 0.00 2.23
2404 2693 2.294074 TGCTTGTTGCCGAGTACTTTT 58.706 42.857 0.00 0.00 42.00 2.27
2420 2709 2.825836 GCCTACGGCTGCATGCTT 60.826 61.111 20.33 0.48 46.69 3.91
2430 2719 4.344474 GGGATCGCTCGCCTACGG 62.344 72.222 1.84 0.00 40.63 4.02
2473 2801 2.662596 CCTGCGGCCACAACTCTA 59.337 61.111 2.24 0.00 0.00 2.43
2478 2806 4.659172 CTTCCCCTGCGGCCACAA 62.659 66.667 2.24 0.00 0.00 3.33
2489 2817 4.404654 CTTTGCGCGCACTTCCCC 62.405 66.667 36.72 0.01 0.00 4.81
2499 2827 2.815647 CTCCTCGTCCCTTTGCGC 60.816 66.667 0.00 0.00 0.00 6.09
2503 2831 1.152096 ACACCCTCCTCGTCCCTTT 60.152 57.895 0.00 0.00 0.00 3.11
2510 2838 4.436998 GCCACGACACCCTCCTCG 62.437 72.222 0.00 0.00 35.96 4.63
2524 2855 1.305633 CTCTCCCAGTCCTCTGCCA 60.306 63.158 0.00 0.00 40.09 4.92
2529 2860 0.534873 GCACTTCTCTCCCAGTCCTC 59.465 60.000 0.00 0.00 0.00 3.71
2536 2867 1.804372 CGCATACTGCACTTCTCTCCC 60.804 57.143 0.00 0.00 45.36 4.30
2555 2887 2.095853 GGACTAATGTTGCCATCACACG 59.904 50.000 0.00 0.00 0.00 4.49
2566 2898 4.567747 CCTTTGGCCTACTGGACTAATGTT 60.568 45.833 3.32 0.00 43.49 2.71
2568 2900 3.545703 CCTTTGGCCTACTGGACTAATG 58.454 50.000 3.32 0.00 43.49 1.90
2569 2901 2.092375 GCCTTTGGCCTACTGGACTAAT 60.092 50.000 3.32 0.00 44.06 1.73
2596 2928 2.493501 GCGTCGTTCCTCCTACCC 59.506 66.667 0.00 0.00 0.00 3.69
2597 2929 2.493501 GGCGTCGTTCCTCCTACC 59.506 66.667 0.00 0.00 0.00 3.18
2599 2931 1.452651 ATCGGCGTCGTTCCTCCTA 60.453 57.895 10.18 0.00 37.69 2.94
2600 2932 2.754658 ATCGGCGTCGTTCCTCCT 60.755 61.111 10.18 0.00 37.69 3.69
2624 2962 2.173382 CACAACGCTAGCAACGCC 59.827 61.111 16.45 0.00 0.00 5.68
2625 2963 2.173382 CCACAACGCTAGCAACGC 59.827 61.111 16.45 0.00 0.00 4.84
2644 2982 4.389576 GCGTGCACTTCCCTTGCG 62.390 66.667 16.19 0.00 43.34 4.85
2658 2996 3.441290 CTCCTCGTCCCTTCGCGT 61.441 66.667 5.77 0.00 0.00 6.01
2659 2997 4.194720 CCTCCTCGTCCCTTCGCG 62.195 72.222 0.00 0.00 0.00 5.87
2698 3036 1.474143 GCATACTGCACTTCTCCTCCC 60.474 57.143 0.00 0.00 44.26 4.30
2728 3066 0.100146 GGCCTACTGGACTAACGTCG 59.900 60.000 0.00 0.00 41.16 5.12
2763 3103 2.490217 CATCGGCGTCGTTCCTCT 59.510 61.111 10.18 0.00 37.69 3.69
2792 3132 0.455815 GAAACCATGTCATTCCCGCC 59.544 55.000 0.00 0.00 0.00 6.13
2822 3162 5.227908 TGTTCTCACTCTTATTCGTCAACC 58.772 41.667 0.00 0.00 0.00 3.77
2860 3200 9.906660 GTGTTCATGTTATGGTTTAGAAATTCA 57.093 29.630 0.00 0.00 0.00 2.57
2887 3227 9.092338 TGTATCTCCCTGTTAAACTGTACTAAA 57.908 33.333 0.00 0.00 0.00 1.85
2898 3238 7.722728 ACGAGTATATGTGTATCTCCCTGTTAA 59.277 37.037 0.00 0.00 0.00 2.01
2899 3239 7.229308 ACGAGTATATGTGTATCTCCCTGTTA 58.771 38.462 0.00 0.00 0.00 2.41
2902 3242 5.941058 AGACGAGTATATGTGTATCTCCCTG 59.059 44.000 0.00 0.00 0.00 4.45
2956 3296 1.653679 CGCTGTTTCACACGACTTTCG 60.654 52.381 0.00 0.00 46.93 3.46
2964 3304 3.433615 AGCTTTATCTCGCTGTTTCACAC 59.566 43.478 0.00 0.00 34.69 3.82
2966 3306 4.033014 GGTAGCTTTATCTCGCTGTTTCAC 59.967 45.833 0.00 0.00 37.05 3.18
2990 3330 2.162681 CGTTTGGAATTTCCTCTGGCT 58.837 47.619 16.25 0.00 37.46 4.75
2992 3332 3.378427 GGATCGTTTGGAATTTCCTCTGG 59.622 47.826 16.25 4.31 37.46 3.86
2996 3336 3.089284 GGTGGATCGTTTGGAATTTCCT 58.911 45.455 16.25 0.00 37.46 3.36
3011 3351 3.281727 AATTAGTCGCACATGGTGGAT 57.718 42.857 0.00 0.00 33.64 3.41
3045 3385 9.081997 GTGTGTTCATGTTTGAAACTATTTTGA 57.918 29.630 9.69 2.66 43.29 2.69
3054 3394 7.386025 TGTTCAATTGTGTGTTCATGTTTGAAA 59.614 29.630 5.13 0.00 43.29 2.69
3087 3427 9.981460 AATTTCCTTTGACCAGTAGATTTATCT 57.019 29.630 0.00 0.00 40.86 1.98
3094 3434 5.576563 TGGAATTTCCTTTGACCAGTAGA 57.423 39.130 16.25 0.00 37.46 2.59


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

AutoCloner maintained by Alex Coulton.