Multiple sequence alignment - TraesCS3D01G044200

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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 TraesCS3D01G044200 chr3D 100.000 3123 0 0 1 3123 17013095 17009973 0.000000e+00 5768.0
1 TraesCS3D01G044200 chr3B 90.225 1821 65 44 814 2588 24410679 24408926 0.000000e+00 2272.0
2 TraesCS3D01G044200 chr3B 88.084 856 63 12 2 827 24411546 24410700 0.000000e+00 979.0
3 TraesCS3D01G044200 chr3B 83.450 429 33 12 2730 3123 24408886 24408461 6.370000e-97 364.0
4 TraesCS3D01G044200 chr3A 90.402 1594 81 33 738 2309 19862304 19863847 0.000000e+00 2030.0
5 TraesCS3D01G044200 chr3A 90.395 708 38 13 2 685 19861603 19862304 0.000000e+00 904.0
6 TraesCS3D01G044200 chr3A 83.698 411 18 13 2366 2776 19863957 19864318 2.980000e-90 342.0
7 TraesCS3D01G044200 chr3A 85.946 185 21 2 2942 3123 19864456 19864638 3.180000e-45 193.0
8 TraesCS3D01G044200 chr3A 93.182 44 1 1 2791 2834 19864318 19864359 2.600000e-06 63.9
9 TraesCS3D01G044200 chr3A 89.130 46 4 1 384 429 696374381 696374337 4.350000e-04 56.5
10 TraesCS3D01G044200 chr2D 88.579 359 32 3 1420 1778 12874389 12874738 8.000000e-116 427.0
11 TraesCS3D01G044200 chr1B 73.114 1246 243 62 978 2193 55976968 55978151 8.230000e-96 361.0
12 TraesCS3D01G044200 chr1B 74.177 1003 190 39 1217 2193 56140812 56139853 1.380000e-93 353.0
13 TraesCS3D01G044200 chr1B 73.183 1197 221 64 1030 2193 55998281 55999410 1.070000e-89 340.0
14 TraesCS3D01G044200 chr1B 73.679 1022 198 42 1199 2193 56017084 56018061 6.460000e-87 331.0
15 TraesCS3D01G044200 chr1A 73.405 1019 198 41 1203 2193 35536319 35537292 2.340000e-81 313.0
16 TraesCS3D01G044200 chr7D 100.000 28 0 0 385 412 18880319 18880346 6.000000e-03 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 TraesCS3D01G044200 chr3D 17009973 17013095 3122 True 5768.00 5768 100.0000 1 3123 1 chr3D.!!$R1 3122
1 TraesCS3D01G044200 chr3B 24408461 24411546 3085 True 1205.00 2272 87.2530 2 3123 3 chr3B.!!$R1 3121
2 TraesCS3D01G044200 chr3A 19861603 19864638 3035 False 706.58 2030 88.7246 2 3123 5 chr3A.!!$F1 3121
3 TraesCS3D01G044200 chr1B 55976968 55978151 1183 False 361.00 361 73.1140 978 2193 1 chr1B.!!$F1 1215
4 TraesCS3D01G044200 chr1B 56139853 56140812 959 True 353.00 353 74.1770 1217 2193 1 chr1B.!!$R1 976
5 TraesCS3D01G044200 chr1B 55998281 55999410 1129 False 340.00 340 73.1830 1030 2193 1 chr1B.!!$F2 1163
6 TraesCS3D01G044200 chr1B 56017084 56018061 977 False 331.00 331 73.6790 1199 2193 1 chr1B.!!$F3 994
7 TraesCS3D01G044200 chr1A 35536319 35537292 973 False 313.00 313 73.4050 1203 2193 1 chr1A.!!$F1 990

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
904 970 1.299773 CGGCAAAACACGCACCATT 60.3 52.632 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2592 2816 0.036875 CGGAAAAAGACTCTGCCCCT 59.963 55.0 0.0 0.0 0.0 4.79 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
325 327 4.442052 CCTCTATCCAGATTTGTGAAGCGA 60.442 45.833 0.00 0.00 0.00 4.93
331 333 1.470098 AGATTTGTGAAGCGACCATGC 59.530 47.619 0.00 0.00 0.00 4.06
347 349 5.392919 CGACCATGCCATTTTAGTCATCAAA 60.393 40.000 0.00 0.00 0.00 2.69
365 367 8.646356 GTCATCAAATTGATTTGCGAAACATAA 58.354 29.630 5.63 0.00 45.06 1.90
500 504 6.610075 AACACAAAAGGCAGATTCCAATAT 57.390 33.333 0.00 0.00 0.00 1.28
515 542 8.695456 AGATTCCAATATTATTTGTGTCAACCC 58.305 33.333 0.00 0.00 0.00 4.11
584 612 7.166473 GCAAGTTTTAGTGCTATGACAATATGC 59.834 37.037 0.00 0.00 37.78 3.14
596 624 7.531871 GCTATGACAATATGCATTTACGAACAG 59.468 37.037 3.54 0.00 0.00 3.16
675 703 4.503910 TGACTAGCGAAATGTATGTTGCT 58.496 39.130 2.49 2.49 36.51 3.91
685 713 7.273381 GCGAAATGTATGTTGCTTGTAGAAATT 59.727 33.333 0.00 0.00 0.00 1.82
686 714 8.788813 CGAAATGTATGTTGCTTGTAGAAATTC 58.211 33.333 0.00 0.00 0.00 2.17
688 716 9.630098 AAATGTATGTTGCTTGTAGAAATTCAG 57.370 29.630 0.00 0.00 0.00 3.02
689 717 7.744087 TGTATGTTGCTTGTAGAAATTCAGT 57.256 32.000 0.00 0.00 0.00 3.41
690 718 7.584108 TGTATGTTGCTTGTAGAAATTCAGTG 58.416 34.615 0.00 0.00 0.00 3.66
691 719 6.882610 ATGTTGCTTGTAGAAATTCAGTGA 57.117 33.333 0.00 0.00 0.00 3.41
693 721 7.275888 TGTTGCTTGTAGAAATTCAGTGATT 57.724 32.000 0.00 0.00 0.00 2.57
694 722 7.715657 TGTTGCTTGTAGAAATTCAGTGATTT 58.284 30.769 0.00 0.00 32.16 2.17
695 723 7.648908 TGTTGCTTGTAGAAATTCAGTGATTTG 59.351 33.333 0.00 0.00 29.75 2.32
696 724 6.151691 TGCTTGTAGAAATTCAGTGATTTGC 58.848 36.000 0.00 0.00 29.75 3.68
698 726 6.865205 GCTTGTAGAAATTCAGTGATTTGCTT 59.135 34.615 12.45 0.14 29.75 3.91
699 727 7.148853 GCTTGTAGAAATTCAGTGATTTGCTTG 60.149 37.037 12.45 4.40 29.75 4.01
701 729 7.715657 TGTAGAAATTCAGTGATTTGCTTGTT 58.284 30.769 12.45 0.00 29.75 2.83
706 737 3.951306 TCAGTGATTTGCTTGTTGAACG 58.049 40.909 0.00 0.00 0.00 3.95
731 762 8.873830 CGAAGTTTCTAATGTGTAGATGAACAT 58.126 33.333 0.00 0.00 38.66 2.71
904 970 1.299773 CGGCAAAACACGCACCATT 60.300 52.632 0.00 0.00 0.00 3.16
968 1038 2.605257 GAAAACCCCATAATAGCCCCC 58.395 52.381 0.00 0.00 0.00 5.40
1748 1836 2.746671 TTCTCCGCGACGCTCTCT 60.747 61.111 19.02 0.00 0.00 3.10
1850 1938 3.352447 GCAGAAGCAGCTCGATGTA 57.648 52.632 0.00 0.00 41.58 2.29
1854 1942 3.257393 CAGAAGCAGCTCGATGTAAGTT 58.743 45.455 0.00 0.00 0.00 2.66
1855 1943 3.305629 CAGAAGCAGCTCGATGTAAGTTC 59.694 47.826 0.00 0.00 0.00 3.01
1856 1944 1.914634 AGCAGCTCGATGTAAGTTCG 58.085 50.000 0.00 0.00 37.94 3.95
1857 1945 1.202582 AGCAGCTCGATGTAAGTTCGT 59.797 47.619 0.00 0.00 37.82 3.85
1858 1946 1.584308 GCAGCTCGATGTAAGTTCGTC 59.416 52.381 0.00 0.00 37.82 4.20
1859 1947 2.186076 CAGCTCGATGTAAGTTCGTCC 58.814 52.381 0.00 0.00 37.82 4.79
1860 1948 1.134560 AGCTCGATGTAAGTTCGTCCC 59.865 52.381 0.00 0.00 37.82 4.46
1861 1949 1.134560 GCTCGATGTAAGTTCGTCCCT 59.865 52.381 0.00 0.00 37.82 4.20
1862 1950 2.416972 GCTCGATGTAAGTTCGTCCCTT 60.417 50.000 0.00 0.00 37.82 3.95
1863 1951 3.436496 CTCGATGTAAGTTCGTCCCTTC 58.564 50.000 0.00 0.00 37.82 3.46
1864 1952 2.165030 TCGATGTAAGTTCGTCCCTTCC 59.835 50.000 0.00 0.00 37.82 3.46
1865 1953 2.737679 CGATGTAAGTTCGTCCCTTCCC 60.738 54.545 0.00 0.00 32.08 3.97
1970 2083 4.181010 CCCCGTCCCCAGATGCTG 62.181 72.222 0.00 0.00 0.00 4.41
2072 2196 3.446799 CAACAGTAAGCAAAGCAAAGCA 58.553 40.909 0.00 0.00 0.00 3.91
2073 2197 3.360249 ACAGTAAGCAAAGCAAAGCAG 57.640 42.857 0.00 0.00 0.00 4.24
2074 2198 2.951642 ACAGTAAGCAAAGCAAAGCAGA 59.048 40.909 0.00 0.00 0.00 4.26
2075 2199 3.004106 ACAGTAAGCAAAGCAAAGCAGAG 59.996 43.478 0.00 0.00 0.00 3.35
2076 2200 3.004106 CAGTAAGCAAAGCAAAGCAGAGT 59.996 43.478 0.00 0.00 0.00 3.24
2098 2222 3.627123 TGAATTCGCCGATCACAATTCAT 59.373 39.130 6.98 0.00 39.30 2.57
2099 2223 4.096231 TGAATTCGCCGATCACAATTCATT 59.904 37.500 6.98 0.00 39.30 2.57
2100 2224 3.673746 TTCGCCGATCACAATTCATTC 57.326 42.857 0.00 0.00 0.00 2.67
2101 2225 2.626840 TCGCCGATCACAATTCATTCA 58.373 42.857 0.00 0.00 0.00 2.57
2102 2226 2.351418 TCGCCGATCACAATTCATTCAC 59.649 45.455 0.00 0.00 0.00 3.18
2172 2301 0.608640 GGTCATATAGGGTCGGGCTG 59.391 60.000 0.00 0.00 0.00 4.85
2173 2302 1.629043 GTCATATAGGGTCGGGCTGA 58.371 55.000 0.00 0.00 0.00 4.26
2174 2303 2.180276 GTCATATAGGGTCGGGCTGAT 58.820 52.381 0.00 0.00 0.00 2.90
2199 2329 2.219080 TGAATCCCAGCAGCATTCAA 57.781 45.000 3.89 0.00 34.35 2.69
2208 2338 4.256920 CCAGCAGCATTCAACTAGTAGTT 58.743 43.478 9.85 9.85 39.39 2.24
2221 2367 5.952033 AACTAGTAGTTGTAGCAGTAGTGC 58.048 41.667 14.82 15.00 42.89 4.40
2223 2369 6.127952 AACTAGTAGTTGTAGCAGTAGTGCTC 60.128 42.308 27.99 18.84 46.65 4.26
2224 2370 8.229461 AACTAGTAGTTGTAGCAGTAGTGCTCT 61.229 40.741 27.99 20.01 46.65 4.09
2238 2390 2.367844 GCTCTAAGCAGCGTCAGTG 58.632 57.895 0.00 0.00 41.89 3.66
2309 2464 0.036765 GGAGGACGCAATGTGGTGTA 60.037 55.000 0.00 0.00 0.00 2.90
2311 2466 0.394938 AGGACGCAATGTGGTGTACA 59.605 50.000 0.00 0.00 44.87 2.90
2358 2527 5.034797 TCGTTAACATCTATCTCTGTTGCG 58.965 41.667 6.39 0.00 36.34 4.85
2359 2528 4.207224 CGTTAACATCTATCTCTGTTGCGG 59.793 45.833 6.39 0.00 36.34 5.69
2360 2529 3.895232 AACATCTATCTCTGTTGCGGT 57.105 42.857 0.00 0.00 34.43 5.68
2361 2530 3.170791 ACATCTATCTCTGTTGCGGTG 57.829 47.619 0.00 0.00 0.00 4.94
2362 2531 1.863454 CATCTATCTCTGTTGCGGTGC 59.137 52.381 0.00 0.00 0.00 5.01
2363 2532 0.179137 TCTATCTCTGTTGCGGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
2364 2533 1.148157 CTATCTCTGTTGCGGTGCGG 61.148 60.000 0.00 0.00 0.00 5.69
2431 2641 4.320608 TTCTGGAAGATGTTTTGTTGGC 57.679 40.909 0.00 0.00 46.36 4.52
2432 2642 3.295093 TCTGGAAGATGTTTTGTTGGCA 58.705 40.909 0.00 0.00 38.67 4.92
2448 2658 2.395360 GCACTAATTGCCGTGGCGA 61.395 57.895 2.68 2.68 46.63 5.54
2449 2659 1.715585 CACTAATTGCCGTGGCGAG 59.284 57.895 6.98 3.98 45.51 5.03
2450 2660 2.106683 ACTAATTGCCGTGGCGAGC 61.107 57.895 6.98 0.00 45.51 5.03
2451 2661 2.046796 TAATTGCCGTGGCGAGCA 60.047 55.556 6.98 0.99 45.51 4.26
2452 2662 2.040213 CTAATTGCCGTGGCGAGCAG 62.040 60.000 6.98 2.55 45.51 4.24
2453 2663 2.796483 TAATTGCCGTGGCGAGCAGT 62.796 55.000 6.98 0.00 45.51 4.40
2454 2664 2.796483 AATTGCCGTGGCGAGCAGTA 62.796 55.000 6.98 0.00 45.51 2.74
2455 2665 4.735132 TGCCGTGGCGAGCAGTAC 62.735 66.667 6.37 0.00 45.51 2.73
2460 2670 1.738099 GTGGCGAGCAGTACCAGTG 60.738 63.158 0.00 0.00 33.12 3.66
2545 2755 2.346365 GGACGGCTTCGAAACCCT 59.654 61.111 11.91 0.20 37.63 4.34
2546 2756 2.033194 GGACGGCTTCGAAACCCTG 61.033 63.158 11.91 1.73 37.63 4.45
2547 2757 2.032071 ACGGCTTCGAAACCCTGG 59.968 61.111 11.91 1.03 37.63 4.45
2548 2758 3.431725 CGGCTTCGAAACCCTGGC 61.432 66.667 11.91 4.20 35.61 4.85
2549 2759 2.282180 GGCTTCGAAACCCTGGCA 60.282 61.111 6.30 0.00 0.00 4.92
2616 2840 0.435008 CAGAGTCTTTTTCCGTCGCG 59.565 55.000 0.00 0.00 0.00 5.87
2670 2894 2.118513 AGTGAGGGCCGAGTGAGT 59.881 61.111 0.00 0.00 0.00 3.41
2834 3065 1.343821 CGTCCACGCACGCTTTATC 59.656 57.895 0.00 0.00 31.96 1.75
2839 3070 2.321060 CGCACGCTTTATCGCCTG 59.679 61.111 0.00 0.00 0.00 4.85
2840 3071 2.023320 GCACGCTTTATCGCCTGC 59.977 61.111 0.00 0.00 35.45 4.85
2841 3072 2.749865 GCACGCTTTATCGCCTGCA 61.750 57.895 0.00 0.00 40.24 4.41
2844 3075 2.463620 CGCTTTATCGCCTGCAGCA 61.464 57.895 8.66 0.00 44.04 4.41
2845 3076 1.779025 CGCTTTATCGCCTGCAGCAT 61.779 55.000 8.66 2.12 44.04 3.79
2878 3148 3.688475 TACGTTACGCGCTGAGGCC 62.688 63.158 5.73 0.00 46.11 5.19
2880 3150 4.452733 GTTACGCGCTGAGGCCCT 62.453 66.667 5.73 0.00 34.44 5.19
2886 3156 2.182842 GCGCTGAGGCCCTGTTATG 61.183 63.158 0.00 0.00 34.44 1.90
2889 3159 1.379642 GCTGAGGCCCTGTTATGTGC 61.380 60.000 0.00 0.00 0.00 4.57
2890 3160 0.254178 CTGAGGCCCTGTTATGTGCT 59.746 55.000 0.00 0.00 0.00 4.40
2940 3217 3.243636 CCATTTTGCACAGCTCTGTTCTT 60.244 43.478 0.00 0.00 42.83 2.52
2973 3253 4.138817 CGAAAATCGTACTGTTTGGAACG 58.861 43.478 0.00 0.00 34.72 3.95
3017 3300 9.403110 GTTATTAGTCCAATGATGATGAATTGC 57.597 33.333 0.00 0.00 33.34 3.56
3027 3310 2.204463 TGATGAATTGCCCTGGTCCTA 58.796 47.619 0.00 0.00 0.00 2.94
3029 3312 3.181440 TGATGAATTGCCCTGGTCCTATC 60.181 47.826 0.00 0.00 0.00 2.08
3038 3321 1.546773 CCTGGTCCTATCCTCTCCGAG 60.547 61.905 0.00 0.00 0.00 4.63
3093 3376 0.313357 GCTCGTACGGATAACCCCTC 59.687 60.000 16.52 0.00 0.00 4.30
3094 3377 0.590195 CTCGTACGGATAACCCCTCG 59.410 60.000 16.52 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 148 8.779354 ATTTTGTGTTTGCTAACCAACTTTTA 57.221 26.923 8.56 0.00 33.15 1.52
295 297 6.265649 TCACAAATCTGGATAGAGGTAGTAGC 59.734 42.308 0.00 0.00 36.14 3.58
325 327 5.999205 TTTGATGACTAAAATGGCATGGT 57.001 34.783 0.00 0.00 0.00 3.55
347 349 5.750067 GGCATCTTATGTTTCGCAAATCAAT 59.250 36.000 0.00 0.00 0.00 2.57
474 478 5.860941 TGGAATCTGCCTTTTGTGTTTTA 57.139 34.783 0.00 0.00 0.00 1.52
486 490 7.715657 TGACACAAATAATATTGGAATCTGCC 58.284 34.615 0.00 0.00 34.56 4.85
500 504 2.279935 AGCGGGGTTGACACAAATAA 57.720 45.000 0.00 0.00 0.00 1.40
515 542 7.867445 AACATTTAAAACAATTCAGTAGCGG 57.133 32.000 0.00 0.00 0.00 5.52
584 612 3.617263 GGCAGTACCTCTGTTCGTAAATG 59.383 47.826 0.00 0.00 45.23 2.32
610 638 1.546099 GCCCTCTTTACAAACCCGGAA 60.546 52.381 0.73 0.00 0.00 4.30
651 679 5.063944 AGCAACATACATTTCGCTAGTCAAG 59.936 40.000 0.00 0.00 0.00 3.02
675 703 7.715657 ACAAGCAAATCACTGAATTTCTACAA 58.284 30.769 0.00 0.00 0.00 2.41
685 713 3.625313 TCGTTCAACAAGCAAATCACTGA 59.375 39.130 0.00 0.00 0.00 3.41
686 714 3.951306 TCGTTCAACAAGCAAATCACTG 58.049 40.909 0.00 0.00 0.00 3.66
688 716 4.351192 ACTTCGTTCAACAAGCAAATCAC 58.649 39.130 0.00 0.00 0.00 3.06
689 717 4.630894 ACTTCGTTCAACAAGCAAATCA 57.369 36.364 0.00 0.00 0.00 2.57
690 718 5.743872 AGAAACTTCGTTCAACAAGCAAATC 59.256 36.000 0.00 0.00 0.00 2.17
691 719 5.650543 AGAAACTTCGTTCAACAAGCAAAT 58.349 33.333 0.00 0.00 0.00 2.32
693 721 4.695217 AGAAACTTCGTTCAACAAGCAA 57.305 36.364 0.00 0.00 0.00 3.91
694 722 5.804692 TTAGAAACTTCGTTCAACAAGCA 57.195 34.783 0.00 0.00 0.00 3.91
695 723 6.140737 CACATTAGAAACTTCGTTCAACAAGC 59.859 38.462 0.00 0.00 0.00 4.01
696 724 7.186804 ACACATTAGAAACTTCGTTCAACAAG 58.813 34.615 0.00 0.00 0.00 3.16
698 726 6.671614 ACACATTAGAAACTTCGTTCAACA 57.328 33.333 0.00 0.00 0.00 3.33
699 727 8.068893 TCTACACATTAGAAACTTCGTTCAAC 57.931 34.615 0.00 0.00 0.00 3.18
701 729 8.085909 TCATCTACACATTAGAAACTTCGTTCA 58.914 33.333 0.00 0.00 0.00 3.18
769 801 8.066000 CCATTTTTCTTTGAGAAATGTTTCAGC 58.934 33.333 16.72 0.99 43.06 4.26
927 993 6.710597 TTCGCCTCTGATTTAGTACTATGT 57.289 37.500 2.79 0.00 0.00 2.29
928 994 7.042658 GGTTTTCGCCTCTGATTTAGTACTATG 60.043 40.741 2.79 0.00 0.00 2.23
929 995 6.985059 GGTTTTCGCCTCTGATTTAGTACTAT 59.015 38.462 2.79 0.00 0.00 2.12
1012 1082 0.825010 GGAATAGTAGGCGTCGGGGA 60.825 60.000 0.00 0.00 0.00 4.81
1850 1938 1.199425 GGGAGGGAAGGGACGAACTT 61.199 60.000 0.00 0.00 0.00 2.66
1854 1942 3.988678 ACGGGAGGGAAGGGACGA 61.989 66.667 0.00 0.00 0.00 4.20
1855 1943 3.771160 CACGGGAGGGAAGGGACG 61.771 72.222 0.00 0.00 32.31 4.79
1856 1944 4.097361 GCACGGGAGGGAAGGGAC 62.097 72.222 0.00 0.00 32.31 4.46
1859 1947 3.787001 GAGGCACGGGAGGGAAGG 61.787 72.222 0.00 0.00 32.31 3.46
1860 1948 3.787001 GGAGGCACGGGAGGGAAG 61.787 72.222 0.00 0.00 32.31 3.46
1861 1949 4.332543 AGGAGGCACGGGAGGGAA 62.333 66.667 0.00 0.00 32.31 3.97
1862 1950 4.779733 GAGGAGGCACGGGAGGGA 62.780 72.222 0.00 0.00 32.31 4.20
1863 1951 4.787280 AGAGGAGGCACGGGAGGG 62.787 72.222 0.00 0.00 0.00 4.30
1864 1952 3.465403 CAGAGGAGGCACGGGAGG 61.465 72.222 0.00 0.00 0.00 4.30
1865 1953 4.154347 GCAGAGGAGGCACGGGAG 62.154 72.222 0.00 0.00 0.00 4.30
2072 2196 1.204704 TGTGATCGGCGAATTCACTCT 59.795 47.619 31.61 9.76 40.29 3.24
2073 2197 1.640428 TGTGATCGGCGAATTCACTC 58.360 50.000 31.61 18.60 40.29 3.51
2074 2198 2.093306 TTGTGATCGGCGAATTCACT 57.907 45.000 31.61 11.15 40.29 3.41
2075 2199 3.181511 TGAATTGTGATCGGCGAATTCAC 60.182 43.478 27.85 27.85 39.00 3.18
2076 2200 3.006247 TGAATTGTGATCGGCGAATTCA 58.994 40.909 22.88 22.88 40.69 2.57
2098 2222 2.865670 GCGGCAACCAATTGATTGTGAA 60.866 45.455 14.09 0.00 38.15 3.18
2099 2223 1.336702 GCGGCAACCAATTGATTGTGA 60.337 47.619 14.09 0.00 38.15 3.58
2100 2224 1.070038 GCGGCAACCAATTGATTGTG 58.930 50.000 14.09 8.25 38.15 3.33
2101 2225 0.037419 GGCGGCAACCAATTGATTGT 60.037 50.000 14.09 0.00 38.15 2.71
2102 2226 0.037512 TGGCGGCAACCAATTGATTG 60.038 50.000 10.22 8.29 38.15 2.67
2172 2301 4.077108 TGCTGCTGGGATTCATATCAATC 58.923 43.478 0.00 0.00 32.09 2.67
2173 2302 4.108501 TGCTGCTGGGATTCATATCAAT 57.891 40.909 0.00 0.00 32.09 2.57
2174 2303 3.581265 TGCTGCTGGGATTCATATCAA 57.419 42.857 0.00 0.00 32.09 2.57
2199 2329 5.564048 GCACTACTGCTACAACTACTAGT 57.436 43.478 0.00 0.00 40.63 2.57
2220 2366 0.109086 TCACTGACGCTGCTTAGAGC 60.109 55.000 0.00 0.00 42.82 4.09
2221 2367 1.201181 ACTCACTGACGCTGCTTAGAG 59.799 52.381 0.00 0.00 0.00 2.43
2222 2368 1.068264 CACTCACTGACGCTGCTTAGA 60.068 52.381 0.00 0.00 0.00 2.10
2223 2369 1.068264 TCACTCACTGACGCTGCTTAG 60.068 52.381 0.00 0.00 0.00 2.18
2224 2370 0.958822 TCACTCACTGACGCTGCTTA 59.041 50.000 0.00 0.00 0.00 3.09
2225 2371 0.319728 ATCACTCACTGACGCTGCTT 59.680 50.000 0.00 0.00 0.00 3.91
2226 2372 0.319728 AATCACTCACTGACGCTGCT 59.680 50.000 0.00 0.00 0.00 4.24
2228 2374 2.257894 GAGAATCACTCACTGACGCTG 58.742 52.381 0.00 0.00 44.36 5.18
2229 2375 1.203523 GGAGAATCACTCACTGACGCT 59.796 52.381 0.00 0.00 46.54 5.07
2231 2377 2.873609 CTGGAGAATCACTCACTGACG 58.126 52.381 0.00 0.00 46.54 4.35
2232 2378 2.028658 TGCTGGAGAATCACTCACTGAC 60.029 50.000 0.00 0.00 46.54 3.51
2238 2390 1.277557 ACCACTGCTGGAGAATCACTC 59.722 52.381 2.24 0.00 40.55 3.51
2325 2494 9.171701 GAGATAGATGTTAACGATTGTACTGAC 57.828 37.037 0.26 0.00 0.00 3.51
2358 2527 0.674895 AGAAGCATTGAGACCGCACC 60.675 55.000 0.00 0.00 0.00 5.01
2359 2528 1.129437 GAAGAAGCATTGAGACCGCAC 59.871 52.381 0.00 0.00 0.00 5.34
2360 2529 1.002430 AGAAGAAGCATTGAGACCGCA 59.998 47.619 0.00 0.00 0.00 5.69
2361 2530 1.396301 CAGAAGAAGCATTGAGACCGC 59.604 52.381 0.00 0.00 0.00 5.68
2362 2531 2.414481 CACAGAAGAAGCATTGAGACCG 59.586 50.000 0.00 0.00 0.00 4.79
2363 2532 2.161211 GCACAGAAGAAGCATTGAGACC 59.839 50.000 0.00 0.00 0.00 3.85
2364 2533 2.810274 TGCACAGAAGAAGCATTGAGAC 59.190 45.455 0.00 0.00 32.55 3.36
2431 2641 1.715585 CTCGCCACGGCAATTAGTG 59.284 57.895 9.11 2.09 42.06 2.74
2432 2642 2.106683 GCTCGCCACGGCAATTAGT 61.107 57.895 9.11 0.00 42.06 2.24
2446 2656 0.109086 CTCACCACTGGTACTGCTCG 60.109 60.000 0.00 0.00 32.11 5.03
2448 2658 1.674057 GCTCACCACTGGTACTGCT 59.326 57.895 0.00 0.00 32.11 4.24
2449 2659 1.738099 CGCTCACCACTGGTACTGC 60.738 63.158 0.00 4.95 32.11 4.40
2450 2660 1.738099 GCGCTCACCACTGGTACTG 60.738 63.158 0.00 0.00 32.11 2.74
2451 2661 2.657237 GCGCTCACCACTGGTACT 59.343 61.111 0.00 0.00 32.11 2.73
2452 2662 2.809601 CGCGCTCACCACTGGTAC 60.810 66.667 5.56 0.00 32.11 3.34
2453 2663 2.986979 TCGCGCTCACCACTGGTA 60.987 61.111 5.56 0.00 32.11 3.25
2454 2664 4.363990 CTCGCGCTCACCACTGGT 62.364 66.667 5.56 0.00 35.62 4.00
2484 2694 3.741476 CCAGCCAGAAACGCAGCC 61.741 66.667 0.00 0.00 0.00 4.85
2485 2695 4.410743 GCCAGCCAGAAACGCAGC 62.411 66.667 0.00 0.00 0.00 5.25
2486 2696 2.670934 AGCCAGCCAGAAACGCAG 60.671 61.111 0.00 0.00 0.00 5.18
2487 2697 2.979676 CAGCCAGCCAGAAACGCA 60.980 61.111 0.00 0.00 0.00 5.24
2490 2700 1.239968 CCAGACAGCCAGCCAGAAAC 61.240 60.000 0.00 0.00 0.00 2.78
2492 2702 2.752358 CCAGACAGCCAGCCAGAA 59.248 61.111 0.00 0.00 0.00 3.02
2493 2703 4.025858 GCCAGACAGCCAGCCAGA 62.026 66.667 0.00 0.00 0.00 3.86
2592 2816 0.036875 CGGAAAAAGACTCTGCCCCT 59.963 55.000 0.00 0.00 0.00 4.79
2594 2818 1.157585 GACGGAAAAAGACTCTGCCC 58.842 55.000 0.00 0.00 0.00 5.36
2616 2840 2.794631 CGAGCAACCAGGAAACAAACAC 60.795 50.000 0.00 0.00 0.00 3.32
2670 2894 0.257328 TGCCTGTCAACCAACTCCAA 59.743 50.000 0.00 0.00 0.00 3.53
2711 2935 3.300765 ACGACCACGACAGGGACC 61.301 66.667 0.00 0.00 42.66 4.46
2712 2936 2.049433 CACGACCACGACAGGGAC 60.049 66.667 0.00 0.00 42.66 4.46
2713 2937 3.299977 CCACGACCACGACAGGGA 61.300 66.667 0.00 0.00 42.66 4.20
2740 2964 1.589779 GTCACCGAACGAACGAACTTT 59.410 47.619 0.14 0.00 35.09 2.66
2839 3070 1.424493 CCTCCTTTCGACGATGCTGC 61.424 60.000 0.00 0.00 0.00 5.25
2840 3071 0.108615 ACCTCCTTTCGACGATGCTG 60.109 55.000 0.00 0.00 0.00 4.41
2841 3072 0.608640 AACCTCCTTTCGACGATGCT 59.391 50.000 0.00 0.00 0.00 3.79
2844 3075 1.815003 ACGTAACCTCCTTTCGACGAT 59.185 47.619 0.00 0.00 34.54 3.73
2845 3076 1.238439 ACGTAACCTCCTTTCGACGA 58.762 50.000 0.00 0.00 34.54 4.20
2850 3081 1.650645 CGCGTAACGTAACCTCCTTTC 59.349 52.381 0.00 0.00 36.87 2.62
2910 3187 4.764172 AGCTGTGCAAAATGGTGTTAAAA 58.236 34.783 0.00 0.00 0.00 1.52
2913 3190 3.004629 CAGAGCTGTGCAAAATGGTGTTA 59.995 43.478 0.00 0.00 0.00 2.41
2920 3197 5.336213 CCATAAGAACAGAGCTGTGCAAAAT 60.336 40.000 11.42 0.00 44.13 1.82
2926 3203 3.875727 CCATCCATAAGAACAGAGCTGTG 59.124 47.826 9.74 9.74 44.13 3.66
2928 3205 3.875727 CACCATCCATAAGAACAGAGCTG 59.124 47.826 0.00 0.00 0.00 4.24
2940 3217 2.912771 ACGATTTTCGCACCATCCATA 58.087 42.857 0.00 0.00 45.12 2.74
3017 3300 0.540830 CGGAGAGGATAGGACCAGGG 60.541 65.000 0.00 0.00 0.00 4.45
3038 3321 1.154225 CGTTGCCAAATCAGACGGC 60.154 57.895 0.00 0.00 46.43 5.68
3093 3376 1.516386 CTACGGTAGGTGCACTGCG 60.516 63.158 17.98 5.91 31.84 5.18
3094 3377 0.037605 AACTACGGTAGGTGCACTGC 60.038 55.000 17.98 6.33 0.00 4.40


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

AutoCloner maintained by Alex Coulton.