Multiple sequence alignment - TraesCS4D01G258000

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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 TraesCS4D01G258000 chr4D 100.000 3027 0 0 1 3027 428119900 428116874 0.000000e+00 5590
1 TraesCS4D01G258000 chr4B 92.590 1579 35 22 815 2364 524707964 524706439 0.000000e+00 2193
2 TraesCS4D01G258000 chr4B 95.577 407 11 5 401 804 524708432 524708030 0.000000e+00 645
3 TraesCS4D01G258000 chr4B 85.505 614 45 20 2362 2952 524706411 524705819 4.320000e-168 601
4 TraesCS4D01G258000 chr4B 90.120 415 29 8 1 409 524708916 524708508 2.070000e-146 529
5 TraesCS4D01G258000 chr4A 88.601 1544 101 41 1 1479 38328424 38329957 0.000000e+00 1807
6 TraesCS4D01G258000 chr4A 94.077 574 8 13 1521 2071 38329957 38330527 0.000000e+00 848
7 TraesCS4D01G258000 chr4A 89.831 177 15 3 2853 3027 38330691 38330866 1.090000e-54 224
8 TraesCS4D01G258000 chr4A 90.278 144 9 4 2648 2790 38330532 38330671 1.850000e-42 183


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 TraesCS4D01G258000 chr4D 428116874 428119900 3026 True 5590.0 5590 100.00000 1 3027 1 chr4D.!!$R1 3026
1 TraesCS4D01G258000 chr4B 524705819 524708916 3097 True 992.0 2193 90.94800 1 2952 4 chr4B.!!$R1 2951
2 TraesCS4D01G258000 chr4A 38328424 38330866 2442 False 765.5 1807 90.69675 1 3027 4 chr4A.!!$F1 3026

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
865 1035 0.323542 GAGGGGGAGACAAGACGAGA 60.324 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2343 0.179092 ATACGGGGTAGACTTTGCGC 60.179 55.0 0.0 0.0 0.0 6.09 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
37 38 3.476552 TGGTTGTCTTTCACAGATCCAC 58.523 45.455 0.00 0.00 35.97 4.02
38 39 2.480419 GGTTGTCTTTCACAGATCCACG 59.520 50.000 0.00 0.00 35.97 4.94
41 42 2.102420 TGTCTTTCACAGATCCACGTGT 59.898 45.455 15.65 0.00 32.60 4.49
95 96 2.872245 CGAGTGCAGAAGGAAGACAAAA 59.128 45.455 0.00 0.00 0.00 2.44
103 104 6.599244 TGCAGAAGGAAGACAAAATCGATATT 59.401 34.615 0.00 0.00 0.00 1.28
115 116 8.731275 ACAAAATCGATATTCACAAGGACATA 57.269 30.769 0.00 0.00 0.00 2.29
149 150 9.747898 TTTTCTGCTTTTTATAAGGATGGTCTA 57.252 29.630 0.00 0.00 0.00 2.59
181 188 8.088365 GGTTGGACAATTTTAATATATGGCCTC 58.912 37.037 3.32 0.00 40.01 4.70
407 514 3.715638 ACCCCTGCTAAAAAGTACCTC 57.284 47.619 0.00 0.00 0.00 3.85
537 649 5.593010 CCACTCACCTTAATCTAGTACTGC 58.407 45.833 5.39 0.00 0.00 4.40
597 711 8.029782 TGCCCTATACAGCTAATAAAGAAGAA 57.970 34.615 0.00 0.00 0.00 2.52
862 1032 2.359967 GGGAGGGGGAGACAAGACG 61.360 68.421 0.00 0.00 0.00 4.18
863 1033 1.305046 GGAGGGGGAGACAAGACGA 60.305 63.158 0.00 0.00 0.00 4.20
864 1034 1.324005 GGAGGGGGAGACAAGACGAG 61.324 65.000 0.00 0.00 0.00 4.18
865 1035 0.323542 GAGGGGGAGACAAGACGAGA 60.324 60.000 0.00 0.00 0.00 4.04
866 1036 0.323908 AGGGGGAGACAAGACGAGAG 60.324 60.000 0.00 0.00 0.00 3.20
867 1037 0.323542 GGGGGAGACAAGACGAGAGA 60.324 60.000 0.00 0.00 0.00 3.10
868 1038 1.099689 GGGGAGACAAGACGAGAGAG 58.900 60.000 0.00 0.00 0.00 3.20
869 1039 1.340211 GGGGAGACAAGACGAGAGAGA 60.340 57.143 0.00 0.00 0.00 3.10
870 1040 2.014128 GGGAGACAAGACGAGAGAGAG 58.986 57.143 0.00 0.00 0.00 3.20
871 1041 2.355310 GGGAGACAAGACGAGAGAGAGA 60.355 54.545 0.00 0.00 0.00 3.10
872 1042 2.936498 GGAGACAAGACGAGAGAGAGAG 59.064 54.545 0.00 0.00 0.00 3.20
873 1043 3.369052 GGAGACAAGACGAGAGAGAGAGA 60.369 52.174 0.00 0.00 0.00 3.10
874 1044 3.861840 AGACAAGACGAGAGAGAGAGAG 58.138 50.000 0.00 0.00 0.00 3.20
875 1045 3.513912 AGACAAGACGAGAGAGAGAGAGA 59.486 47.826 0.00 0.00 0.00 3.10
876 1046 3.861840 ACAAGACGAGAGAGAGAGAGAG 58.138 50.000 0.00 0.00 0.00 3.20
877 1047 3.513912 ACAAGACGAGAGAGAGAGAGAGA 59.486 47.826 0.00 0.00 0.00 3.10
878 1048 4.115516 CAAGACGAGAGAGAGAGAGAGAG 58.884 52.174 0.00 0.00 0.00 3.20
889 1059 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
951 1129 4.097418 AGCCAGCCAGTAGTATATAAGGG 58.903 47.826 0.00 0.00 0.00 3.95
987 1165 1.694169 ACCCAGCCCTGTATCCCAG 60.694 63.158 0.00 0.00 41.15 4.45
1040 1233 4.798344 CAGCCCCAGCAGGAGCAG 62.798 72.222 4.06 0.00 45.49 4.24
1045 1238 4.834453 CCAGCAGGAGCAGCGGAG 62.834 72.222 0.00 0.00 45.49 4.63
1046 1239 4.834453 CAGCAGGAGCAGCGGAGG 62.834 72.222 0.00 0.00 45.49 4.30
1479 1672 1.380785 CTCGCCTAGGTGGGTGGTA 60.381 63.158 22.11 0.60 37.46 3.25
1480 1673 1.380785 TCGCCTAGGTGGGTGGTAG 60.381 63.158 22.11 0.00 37.46 3.18
1481 1674 1.380785 CGCCTAGGTGGGTGGTAGA 60.381 63.158 15.00 0.00 36.00 2.59
1486 1679 3.924922 CCTAGGTGGGTGGTAGAGTAAT 58.075 50.000 0.00 0.00 0.00 1.89
1499 1692 5.776208 TGGTAGAGTAATTCACAGTACACCA 59.224 40.000 0.00 0.00 29.32 4.17
1579 1780 1.515736 CGAACTAACCGACCGGAGC 60.516 63.158 16.07 0.00 38.96 4.70
1584 1785 0.870307 CTAACCGACCGGAGCAATCG 60.870 60.000 16.07 6.41 38.96 3.34
1908 2132 4.124351 CGTCGCCGCCTACCTCAA 62.124 66.667 0.00 0.00 0.00 3.02
2029 2253 2.815308 CTCGCCCGGTTCTAGCAT 59.185 61.111 0.00 0.00 0.00 3.79
2031 2255 2.658593 CGCCCGGTTCTAGCATCG 60.659 66.667 0.00 0.00 0.00 3.84
2032 2256 2.967615 GCCCGGTTCTAGCATCGC 60.968 66.667 0.00 0.00 0.00 4.58
2033 2257 2.815308 CCCGGTTCTAGCATCGCT 59.185 61.111 0.00 0.00 43.41 4.93
2067 2291 6.371271 GCAAAGAGAGAGAAGAAATTACTGCT 59.629 38.462 0.00 0.00 0.00 4.24
2073 2297 2.751806 AGAAGAAATTACTGCTGCTGCC 59.248 45.455 13.47 0.00 38.71 4.85
2074 2298 2.503895 AGAAATTACTGCTGCTGCCT 57.496 45.000 13.47 0.62 38.71 4.75
2112 2336 3.133464 CGCGTACACGGGGTAGGA 61.133 66.667 13.88 0.00 46.57 2.94
2113 2337 2.803479 GCGTACACGGGGTAGGAG 59.197 66.667 13.88 0.00 39.62 3.69
2114 2338 2.779033 GCGTACACGGGGTAGGAGG 61.779 68.421 13.88 0.00 39.62 4.30
2115 2339 1.077501 CGTACACGGGGTAGGAGGA 60.078 63.158 4.11 0.00 39.62 3.71
2116 2340 1.379642 CGTACACGGGGTAGGAGGAC 61.380 65.000 4.11 0.00 39.62 3.85
2117 2341 0.323725 GTACACGGGGTAGGAGGACA 60.324 60.000 0.00 0.00 31.13 4.02
2118 2342 0.323725 TACACGGGGTAGGAGGACAC 60.324 60.000 0.00 0.00 0.00 3.67
2119 2343 2.362120 ACGGGGTAGGAGGACACG 60.362 66.667 0.00 0.00 0.00 4.49
2120 2344 3.834799 CGGGGTAGGAGGACACGC 61.835 72.222 0.00 0.00 0.00 5.34
2121 2345 3.834799 GGGGTAGGAGGACACGCG 61.835 72.222 3.53 3.53 0.00 6.01
2122 2346 4.509737 GGGTAGGAGGACACGCGC 62.510 72.222 5.73 0.00 0.00 6.86
2123 2347 3.755628 GGTAGGAGGACACGCGCA 61.756 66.667 5.73 0.00 0.00 6.09
2124 2348 2.260434 GTAGGAGGACACGCGCAA 59.740 61.111 5.73 0.00 0.00 4.85
2125 2349 1.373748 GTAGGAGGACACGCGCAAA 60.374 57.895 5.73 0.00 0.00 3.68
2164 2388 5.518847 TCTTCTCTGTATTTTTACCGCATCG 59.481 40.000 0.00 0.00 0.00 3.84
2169 2399 7.065324 TCTCTGTATTTTTACCGCATCGATTTT 59.935 33.333 0.00 0.00 0.00 1.82
2181 2411 4.671508 CGCATCGATTTTTACTTGCCTCAA 60.672 41.667 0.00 0.00 0.00 3.02
2272 2502 5.388111 CGTACGAGTACTCATCAGTTTTCA 58.612 41.667 22.37 0.00 33.62 2.69
2287 2517 7.295952 TCAGTTTTCATCTCTATCTTTTCGC 57.704 36.000 0.00 0.00 0.00 4.70
2389 2649 2.920227 GCACTGAGAGTTCGAGACTGTG 60.920 54.545 5.20 0.00 39.19 3.66
2390 2650 2.550180 CACTGAGAGTTCGAGACTGTGA 59.450 50.000 5.20 0.00 39.19 3.58
2399 2659 2.727777 TCGAGACTGTGAACGAGTTTG 58.272 47.619 0.00 0.00 0.00 2.93
2400 2660 2.098607 TCGAGACTGTGAACGAGTTTGT 59.901 45.455 0.00 0.00 0.00 2.83
2407 2668 3.194861 TGTGAACGAGTTTGTCTCCTTG 58.805 45.455 0.00 0.00 39.84 3.61
2425 2686 1.376466 GCTCTTCTTGTCCTGCCCA 59.624 57.895 0.00 0.00 0.00 5.36
2438 2706 1.610967 TGCCCACTGTCCATCCGTA 60.611 57.895 0.00 0.00 0.00 4.02
2439 2707 1.144057 GCCCACTGTCCATCCGTAG 59.856 63.158 0.00 0.00 0.00 3.51
2442 2710 0.460284 CCACTGTCCATCCGTAGCAC 60.460 60.000 0.00 0.00 0.00 4.40
2444 2712 0.902984 ACTGTCCATCCGTAGCACCA 60.903 55.000 0.00 0.00 0.00 4.17
2472 2740 3.413861 CGCGCTGCTGCAGTGTTA 61.414 61.111 35.17 0.00 43.09 2.41
2473 2741 2.743752 CGCGCTGCTGCAGTGTTAT 61.744 57.895 35.17 0.00 43.09 1.89
2474 2742 1.503542 GCGCTGCTGCAGTGTTATT 59.496 52.632 35.17 0.00 43.09 1.40
2475 2743 0.522076 GCGCTGCTGCAGTGTTATTC 60.522 55.000 35.17 19.84 43.09 1.75
2476 2744 1.081892 CGCTGCTGCAGTGTTATTCT 58.918 50.000 29.76 0.00 37.23 2.40
2477 2745 1.466167 CGCTGCTGCAGTGTTATTCTT 59.534 47.619 29.76 0.00 37.23 2.52
2478 2746 2.726989 CGCTGCTGCAGTGTTATTCTTG 60.727 50.000 29.76 4.07 37.23 3.02
2484 2752 5.049828 GCTGCAGTGTTATTCTTGGTTTTT 58.950 37.500 16.64 0.00 0.00 1.94
2500 2768 7.496263 TCTTGGTTTTTAGTGGTAAATTTTGCC 59.504 33.333 9.13 9.13 35.79 4.52
2501 2769 6.890293 TGGTTTTTAGTGGTAAATTTTGCCT 58.110 32.000 15.94 1.32 36.27 4.75
2502 2770 6.763610 TGGTTTTTAGTGGTAAATTTTGCCTG 59.236 34.615 15.94 0.00 36.27 4.85
2503 2771 6.764085 GGTTTTTAGTGGTAAATTTTGCCTGT 59.236 34.615 15.94 6.91 36.27 4.00
2504 2772 7.254624 GGTTTTTAGTGGTAAATTTTGCCTGTG 60.255 37.037 15.94 0.00 36.27 3.66
2505 2773 3.385193 AGTGGTAAATTTTGCCTGTGC 57.615 42.857 15.94 5.56 36.27 4.57
2517 2785 3.201353 TGCCTGTGCAAACACTAGTAA 57.799 42.857 0.00 0.00 46.66 2.24
2518 2786 3.138304 TGCCTGTGCAAACACTAGTAAG 58.862 45.455 0.00 0.00 46.66 2.34
2519 2787 3.433031 TGCCTGTGCAAACACTAGTAAGT 60.433 43.478 0.00 0.00 46.66 2.24
2520 2788 4.202274 TGCCTGTGCAAACACTAGTAAGTA 60.202 41.667 0.00 0.00 46.66 2.24
2521 2789 6.252014 TGCCTGTGCAAACACTAGTAAGTAC 61.252 44.000 0.00 0.00 46.66 2.73
2525 2793 5.780984 GTGCAAACACTAGTAAGTACTCCT 58.219 41.667 0.00 0.00 43.85 3.69
2526 2794 6.917533 GTGCAAACACTAGTAAGTACTCCTA 58.082 40.000 0.00 0.00 43.85 2.94
2527 2795 7.545489 GTGCAAACACTAGTAAGTACTCCTAT 58.455 38.462 0.00 0.00 43.85 2.57
2528 2796 7.488471 GTGCAAACACTAGTAAGTACTCCTATG 59.512 40.741 0.00 3.86 43.85 2.23
2529 2797 6.979238 GCAAACACTAGTAAGTACTCCTATGG 59.021 42.308 0.00 0.00 37.73 2.74
2530 2798 6.712179 AACACTAGTAAGTACTCCTATGGC 57.288 41.667 0.00 0.00 37.73 4.40
2537 2805 6.318913 AGTAAGTACTCCTATGGCTCATCAT 58.681 40.000 0.00 0.00 0.00 2.45
2543 2811 3.254089 TCCTATGGCTCATCATCCATGT 58.746 45.455 4.17 0.00 42.62 3.21
2552 2820 5.708697 GGCTCATCATCCATGTCATCATTTA 59.291 40.000 0.00 0.00 33.66 1.40
2556 2824 8.331730 TCATCATCCATGTCATCATTTATGTC 57.668 34.615 0.00 0.00 36.89 3.06
2562 2833 7.225725 TCCATGTCATCATTTATGTCTGCATA 58.774 34.615 0.00 0.00 36.89 3.14
2595 2868 4.949856 ACATTTGGATAAGTGATCACACCC 59.050 41.667 27.02 19.93 46.99 4.61
2597 2870 1.484653 TGGATAAGTGATCACACCCCG 59.515 52.381 27.02 0.00 46.99 5.73
2608 2881 4.037446 TGATCACACCCCGAAAAGAAAAAG 59.963 41.667 0.00 0.00 0.00 2.27
2611 2892 4.037446 TCACACCCCGAAAAGAAAAAGATG 59.963 41.667 0.00 0.00 0.00 2.90
2614 2895 2.595386 CCCGAAAAGAAAAAGATGGCG 58.405 47.619 0.00 0.00 0.00 5.69
2616 2897 3.234386 CCGAAAAGAAAAAGATGGCGTC 58.766 45.455 0.00 0.00 0.00 5.19
2748 3029 2.291465 AGTATCGTGTAGCGCGGATAAA 59.709 45.455 8.83 0.00 41.07 1.40
2761 3042 4.369182 CGCGGATAAAGAAGTTGACCTAT 58.631 43.478 0.00 0.00 0.00 2.57
2762 3043 5.526115 CGCGGATAAAGAAGTTGACCTATA 58.474 41.667 0.00 0.00 0.00 1.31
2813 3094 2.171840 GAGGAAAAAGAAGAAGGCCCC 58.828 52.381 0.00 0.00 0.00 5.80
2815 3096 0.888619 GAAAAAGAAGAAGGCCCCGG 59.111 55.000 0.00 0.00 0.00 5.73
2816 3097 0.541998 AAAAAGAAGAAGGCCCCGGG 60.542 55.000 15.80 15.80 0.00 5.73
2871 3153 2.559840 CGGCTGTGACTCGTACGT 59.440 61.111 16.05 0.00 0.00 3.57
2876 3158 1.799181 CTGTGACTCGTACGTGATCG 58.201 55.000 22.86 6.97 43.34 3.69
2891 3173 4.602006 CGTGATCGTCTCTTGTCATGTAT 58.398 43.478 0.00 0.00 0.00 2.29
2954 3236 1.407258 GCTCCACTGCACCTACTAGAG 59.593 57.143 0.00 0.00 0.00 2.43
2989 3271 5.012561 GGTTTATCATCCAGCCACTATCTCT 59.987 44.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.061411 CAATGCTCGATGCCACACG 59.939 57.895 4.73 0.00 42.00 4.49
38 39 1.226491 GCAATGCTCGATGCCACAC 60.226 57.895 0.00 0.00 42.00 3.82
41 42 3.817787 GAGCAATGCTCGATGCCA 58.182 55.556 20.11 0.00 45.85 4.92
95 96 7.445121 ACACATATGTCCTTGTGAATATCGAT 58.555 34.615 5.07 2.16 44.74 3.59
103 104 8.729756 CAGAAAATAACACATATGTCCTTGTGA 58.270 33.333 5.07 0.00 44.74 3.58
266 283 5.163561 ACCATGATAACTGCCAAAAATACCG 60.164 40.000 0.00 0.00 0.00 4.02
407 514 9.135189 TCTTCTCCAATTATAATTGTGGAATGG 57.865 33.333 28.10 20.24 43.24 3.16
862 1032 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
863 1033 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
864 1034 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
865 1035 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
866 1036 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
867 1037 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
868 1038 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
869 1039 3.312890 CCCTCTCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
870 1040 2.370189 CCCCTCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
871 1041 2.293856 ACCCCTCTCTCTCTCTCTCTCT 60.294 54.545 0.00 0.00 0.00 3.10
872 1042 2.127708 ACCCCTCTCTCTCTCTCTCTC 58.872 57.143 0.00 0.00 0.00 3.20
873 1043 2.286935 ACCCCTCTCTCTCTCTCTCT 57.713 55.000 0.00 0.00 0.00 3.10
874 1044 2.224548 GCTACCCCTCTCTCTCTCTCTC 60.225 59.091 0.00 0.00 0.00 3.20
875 1045 1.774856 GCTACCCCTCTCTCTCTCTCT 59.225 57.143 0.00 0.00 0.00 3.10
876 1046 1.202891 GGCTACCCCTCTCTCTCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
877 1047 0.850784 GGCTACCCCTCTCTCTCTCT 59.149 60.000 0.00 0.00 0.00 3.10
878 1048 0.553819 TGGCTACCCCTCTCTCTCTC 59.446 60.000 0.00 0.00 0.00 3.20
889 1059 1.077716 ATGGCGTTCTTGGCTACCC 60.078 57.895 0.00 0.00 35.06 3.69
964 1142 2.650813 GATACAGGGCTGGGTCGCAG 62.651 65.000 12.42 12.42 34.19 5.18
978 1156 1.000521 ACGACGGACCTGGGATACA 60.001 57.895 0.00 0.00 39.74 2.29
987 1165 1.226717 GAGCATGAGACGACGGACC 60.227 63.158 0.00 0.00 0.00 4.46
991 1169 2.278206 CCGGAGCATGAGACGACG 60.278 66.667 0.00 0.00 0.00 5.12
1035 1213 2.415426 GAGCTACCTCCGCTGCTC 59.585 66.667 0.00 0.00 43.75 4.26
1039 1232 4.824515 AGCCGAGCTACCTCCGCT 62.825 66.667 0.00 1.62 44.32 5.52
1040 1233 4.273257 GAGCCGAGCTACCTCCGC 62.273 72.222 0.00 0.00 39.88 5.54
1041 1234 3.597728 GGAGCCGAGCTACCTCCG 61.598 72.222 10.09 0.00 39.88 4.63
1042 1235 3.597728 CGGAGCCGAGCTACCTCC 61.598 72.222 13.98 13.98 39.88 4.30
1043 1236 3.597728 CCGGAGCCGAGCTACCTC 61.598 72.222 11.05 0.00 39.88 3.85
1479 1672 4.321750 CGGTGGTGTACTGTGAATTACTCT 60.322 45.833 0.00 0.00 0.00 3.24
1480 1673 3.924686 CGGTGGTGTACTGTGAATTACTC 59.075 47.826 0.00 0.00 0.00 2.59
1481 1674 3.575256 TCGGTGGTGTACTGTGAATTACT 59.425 43.478 0.00 0.00 36.98 2.24
1486 1679 1.068125 CGATCGGTGGTGTACTGTGAA 60.068 52.381 7.38 0.00 36.98 3.18
1527 1720 5.175859 CGTGCAAGGAAAGGAAAGACTATA 58.824 41.667 0.00 0.00 0.00 1.31
1528 1721 4.003648 CGTGCAAGGAAAGGAAAGACTAT 58.996 43.478 0.00 0.00 0.00 2.12
1579 1780 3.686241 TCAAGAACCTGCTTGATCGATTG 59.314 43.478 0.00 0.00 46.73 2.67
2029 2253 4.218635 TCTCTCTTTGCTTTTCTCTAGCGA 59.781 41.667 0.00 0.00 41.54 4.93
2031 2255 5.719173 TCTCTCTCTTTGCTTTTCTCTAGC 58.281 41.667 0.00 0.00 39.10 3.42
2032 2256 7.601856 TCTTCTCTCTCTTTGCTTTTCTCTAG 58.398 38.462 0.00 0.00 0.00 2.43
2033 2257 7.531857 TCTTCTCTCTCTTTGCTTTTCTCTA 57.468 36.000 0.00 0.00 0.00 2.43
2035 2259 7.489574 TTTCTTCTCTCTCTTTGCTTTTCTC 57.510 36.000 0.00 0.00 0.00 2.87
2037 2261 9.605955 GTAATTTCTTCTCTCTCTTTGCTTTTC 57.394 33.333 0.00 0.00 0.00 2.29
2039 2263 8.782144 CAGTAATTTCTTCTCTCTCTTTGCTTT 58.218 33.333 0.00 0.00 0.00 3.51
2040 2264 7.094848 GCAGTAATTTCTTCTCTCTCTTTGCTT 60.095 37.037 0.00 0.00 0.00 3.91
2042 2266 6.371271 AGCAGTAATTTCTTCTCTCTCTTTGC 59.629 38.462 0.00 0.00 0.00 3.68
2043 2267 7.623925 GCAGCAGTAATTTCTTCTCTCTCTTTG 60.624 40.741 0.00 0.00 0.00 2.77
2067 2291 1.601759 GAAACCAGCAGAGGCAGCA 60.602 57.895 0.00 0.00 44.61 4.41
2102 2326 2.362120 CGTGTCCTCCTACCCCGT 60.362 66.667 0.00 0.00 0.00 5.28
2103 2327 3.834799 GCGTGTCCTCCTACCCCG 61.835 72.222 0.00 0.00 0.00 5.73
2104 2328 3.834799 CGCGTGTCCTCCTACCCC 61.835 72.222 0.00 0.00 0.00 4.95
2105 2329 4.509737 GCGCGTGTCCTCCTACCC 62.510 72.222 8.43 0.00 0.00 3.69
2108 2332 1.080093 CTTTGCGCGTGTCCTCCTA 60.080 57.895 8.43 0.00 0.00 2.94
2109 2333 2.357517 CTTTGCGCGTGTCCTCCT 60.358 61.111 8.43 0.00 0.00 3.69
2110 2334 2.665185 ACTTTGCGCGTGTCCTCC 60.665 61.111 8.43 0.00 0.00 4.30
2111 2335 0.388134 TAGACTTTGCGCGTGTCCTC 60.388 55.000 18.88 0.00 0.00 3.71
2112 2336 0.666577 GTAGACTTTGCGCGTGTCCT 60.667 55.000 18.88 9.41 0.00 3.85
2113 2337 1.623973 GGTAGACTTTGCGCGTGTCC 61.624 60.000 18.88 8.52 0.00 4.02
2114 2338 1.623973 GGGTAGACTTTGCGCGTGTC 61.624 60.000 8.43 16.07 0.00 3.67
2115 2339 1.666872 GGGTAGACTTTGCGCGTGT 60.667 57.895 8.43 0.28 0.00 4.49
2116 2340 2.388232 GGGGTAGACTTTGCGCGTG 61.388 63.158 8.43 0.00 0.00 5.34
2117 2341 2.047560 GGGGTAGACTTTGCGCGT 60.048 61.111 8.43 0.00 0.00 6.01
2118 2342 2.546645 TACGGGGTAGACTTTGCGCG 62.547 60.000 0.00 0.00 0.00 6.86
2119 2343 0.179092 ATACGGGGTAGACTTTGCGC 60.179 55.000 0.00 0.00 0.00 6.09
2120 2344 2.304751 AATACGGGGTAGACTTTGCG 57.695 50.000 0.00 0.00 0.00 4.85
2121 2345 3.870274 AGAAATACGGGGTAGACTTTGC 58.130 45.455 0.00 0.00 0.00 3.68
2122 2346 5.731591 AGAAGAAATACGGGGTAGACTTTG 58.268 41.667 0.00 0.00 0.00 2.77
2123 2347 5.720520 AGAGAAGAAATACGGGGTAGACTTT 59.279 40.000 0.00 0.00 0.00 2.66
2124 2348 5.127356 CAGAGAAGAAATACGGGGTAGACTT 59.873 44.000 0.00 0.00 0.00 3.01
2125 2349 4.645588 CAGAGAAGAAATACGGGGTAGACT 59.354 45.833 0.00 0.00 0.00 3.24
2164 2388 6.080406 CGAGTCTTTGAGGCAAGTAAAAATC 58.920 40.000 0.00 0.00 0.00 2.17
2169 2399 2.631062 TCCGAGTCTTTGAGGCAAGTAA 59.369 45.455 0.00 0.00 0.00 2.24
2181 2411 3.077359 CTGGCATTTTCTTCCGAGTCTT 58.923 45.455 0.00 0.00 0.00 3.01
2272 2502 6.707440 TCTTCTCAGCGAAAAGATAGAGAT 57.293 37.500 0.00 0.00 32.76 2.75
2300 2530 3.366422 GCAAACGCAGTGAAAAGACAAAA 59.634 39.130 0.00 0.00 45.00 2.44
2372 2632 2.031944 CGTTCACAGTCTCGAACTCTCA 60.032 50.000 9.09 0.00 39.49 3.27
2389 2649 2.476997 GAGCAAGGAGACAAACTCGTTC 59.523 50.000 0.00 0.00 46.42 3.95
2399 2659 2.301583 AGGACAAGAAGAGCAAGGAGAC 59.698 50.000 0.00 0.00 0.00 3.36
2400 2660 2.301296 CAGGACAAGAAGAGCAAGGAGA 59.699 50.000 0.00 0.00 0.00 3.71
2407 2668 0.957888 GTGGGCAGGACAAGAAGAGC 60.958 60.000 0.00 0.00 0.00 4.09
2425 2686 0.902984 TGGTGCTACGGATGGACAGT 60.903 55.000 0.00 0.00 0.00 3.55
2463 2731 7.199766 CACTAAAAACCAAGAATAACACTGCA 58.800 34.615 0.00 0.00 0.00 4.41
2473 2741 8.884726 GCAAAATTTACCACTAAAAACCAAGAA 58.115 29.630 0.00 0.00 0.00 2.52
2474 2742 7.496263 GGCAAAATTTACCACTAAAAACCAAGA 59.504 33.333 5.50 0.00 0.00 3.02
2475 2743 7.497579 AGGCAAAATTTACCACTAAAAACCAAG 59.502 33.333 11.60 0.00 0.00 3.61
2476 2744 7.281100 CAGGCAAAATTTACCACTAAAAACCAA 59.719 33.333 11.60 0.00 0.00 3.67
2477 2745 6.763610 CAGGCAAAATTTACCACTAAAAACCA 59.236 34.615 11.60 0.00 0.00 3.67
2478 2746 6.764085 ACAGGCAAAATTTACCACTAAAAACC 59.236 34.615 11.60 0.00 0.00 3.27
2484 2752 4.513198 GCACAGGCAAAATTTACCACTA 57.487 40.909 11.60 0.00 40.72 2.74
2498 2766 7.768059 GAGTACTTACTAGTGTTTGCACAGGC 61.768 46.154 5.39 0.00 41.33 4.85
2500 2768 5.634020 GGAGTACTTACTAGTGTTTGCACAG 59.366 44.000 5.39 0.00 41.33 3.66
2501 2769 5.303589 AGGAGTACTTACTAGTGTTTGCACA 59.696 40.000 5.39 0.00 41.33 4.57
2502 2770 5.780984 AGGAGTACTTACTAGTGTTTGCAC 58.219 41.667 5.39 0.00 40.18 4.57
2503 2771 7.363530 CCATAGGAGTACTTACTAGTGTTTGCA 60.364 40.741 5.39 0.00 36.50 4.08
2504 2772 6.979238 CCATAGGAGTACTTACTAGTGTTTGC 59.021 42.308 5.39 0.00 36.50 3.68
2505 2773 6.979238 GCCATAGGAGTACTTACTAGTGTTTG 59.021 42.308 5.39 6.71 36.50 2.93
2517 2785 4.093011 GGATGATGAGCCATAGGAGTACT 58.907 47.826 0.00 0.00 0.00 2.73
2518 2786 3.834813 TGGATGATGAGCCATAGGAGTAC 59.165 47.826 0.00 0.00 30.61 2.73
2519 2787 4.132122 TGGATGATGAGCCATAGGAGTA 57.868 45.455 0.00 0.00 30.61 2.59
2520 2788 2.981921 TGGATGATGAGCCATAGGAGT 58.018 47.619 0.00 0.00 30.61 3.85
2527 2795 2.440253 TGATGACATGGATGATGAGCCA 59.560 45.455 0.00 0.00 43.43 4.75
2528 2796 3.136009 TGATGACATGGATGATGAGCC 57.864 47.619 0.00 0.00 35.80 4.70
2529 2797 5.707242 AAATGATGACATGGATGATGAGC 57.293 39.130 0.00 0.00 36.79 4.26
2530 2798 8.336801 ACATAAATGATGACATGGATGATGAG 57.663 34.615 0.00 0.00 39.06 2.90
2537 2805 5.438833 TGCAGACATAAATGATGACATGGA 58.561 37.500 0.00 0.00 39.06 3.41
2552 2820 9.687210 CAAATGTAATTATGCTTATGCAGACAT 57.313 29.630 9.36 9.67 44.91 3.06
2571 2842 6.119536 GGGTGTGATCACTTATCCAAATGTA 58.880 40.000 25.55 0.00 43.41 2.29
2572 2843 4.949856 GGGTGTGATCACTTATCCAAATGT 59.050 41.667 25.55 0.00 43.41 2.71
2574 2845 4.536765 GGGGTGTGATCACTTATCCAAAT 58.463 43.478 25.55 0.00 43.41 2.32
2583 2854 1.697432 TCTTTTCGGGGTGTGATCACT 59.303 47.619 25.55 0.00 43.41 3.41
2587 2858 4.211920 TCTTTTTCTTTTCGGGGTGTGAT 58.788 39.130 0.00 0.00 0.00 3.06
2588 2859 3.622630 TCTTTTTCTTTTCGGGGTGTGA 58.377 40.909 0.00 0.00 0.00 3.58
2589 2860 4.298332 CATCTTTTTCTTTTCGGGGTGTG 58.702 43.478 0.00 0.00 0.00 3.82
2590 2861 3.320826 CCATCTTTTTCTTTTCGGGGTGT 59.679 43.478 0.00 0.00 0.00 4.16
2595 2868 3.058224 AGACGCCATCTTTTTCTTTTCGG 60.058 43.478 0.00 0.00 31.62 4.30
2597 2870 4.023193 TCCAGACGCCATCTTTTTCTTTTC 60.023 41.667 0.00 0.00 34.41 2.29
2608 2881 2.156343 GGACTTATCCAGACGCCATC 57.844 55.000 0.00 0.00 45.47 3.51
2638 2919 4.847512 AGCCATAGGAGTAGAGTAGCTCTA 59.152 45.833 0.00 2.07 41.50 2.43
2639 2920 3.655777 AGCCATAGGAGTAGAGTAGCTCT 59.344 47.826 0.00 4.02 43.83 4.09
2645 2926 3.963476 ACTCAGCCATAGGAGTAGAGT 57.037 47.619 0.00 0.00 42.30 3.24
2748 3029 3.519510 TGGCAAGCTATAGGTCAACTTCT 59.480 43.478 4.63 0.00 0.00 2.85
2761 3042 2.042464 CCTACTCCAGATGGCAAGCTA 58.958 52.381 0.00 0.00 34.44 3.32
2762 3043 0.835941 CCTACTCCAGATGGCAAGCT 59.164 55.000 0.00 0.00 34.44 3.74
2857 3139 1.799181 CGATCACGTACGAGTCACAG 58.201 55.000 24.41 3.02 34.56 3.66
2858 3140 3.961570 CGATCACGTACGAGTCACA 57.038 52.632 24.41 0.00 34.56 3.58
2871 3153 6.207691 TGAATACATGACAAGAGACGATCA 57.792 37.500 0.00 0.00 0.00 2.92
2876 3158 3.553511 CGCCTGAATACATGACAAGAGAC 59.446 47.826 0.00 0.00 0.00 3.36
2877 3159 3.195610 ACGCCTGAATACATGACAAGAGA 59.804 43.478 0.00 0.00 0.00 3.10
2878 3160 3.308053 CACGCCTGAATACATGACAAGAG 59.692 47.826 0.00 0.00 0.00 2.85
2891 3173 0.464036 ACTGTCTTGTCACGCCTGAA 59.536 50.000 0.00 0.00 0.00 3.02
2954 3236 6.260271 GCTGGATGATAAACCCAGTAAAGTAC 59.740 42.308 0.00 0.00 46.86 2.73
2972 3254 3.229293 TCTCAGAGATAGTGGCTGGATG 58.771 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.