Multiple sequence alignment - TraesCS1A01G397100

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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 TraesCS1A01G397100 chr1A 100.000 2675 0 0 1 2675 562911927 562914601 0 4940
1 TraesCS1A01G397100 chr1D 90.607 2619 145 39 8 2601 469805505 469808047 0 3380
2 TraesCS1A01G397100 chr1B 87.824 2702 209 59 13 2675 651278215 651280835 0 3057


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 TraesCS1A01G397100 chr1A 562911927 562914601 2674 False 4940 4940 100.000 1 2675 1 chr1A.!!$F1 2674
1 TraesCS1A01G397100 chr1D 469805505 469808047 2542 False 3380 3380 90.607 8 2601 1 chr1D.!!$F1 2593
2 TraesCS1A01G397100 chr1B 651278215 651280835 2620 False 3057 3057 87.824 13 2675 1 chr1B.!!$F1 2662

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
849 868 0.178955 TGTTCACCGAGGGTCCTGTA 60.179 55.0 0.0 0.0 31.02 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 2683 0.250295 ACACATGCCTACGTGCAAGT 60.25 50.0 10.83 10.83 45.84 3.16 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
53 54 5.706833 TCAACACTGCACATAATCAATCTGT 59.293 36.000 0.00 0.00 0.00 3.41
90 91 1.339151 CCCAGTCCTAACAAGAGCACC 60.339 57.143 0.00 0.00 0.00 5.01
134 135 3.446161 AGGATGCCTTGTGATGTTTGATG 59.554 43.478 0.00 0.00 0.00 3.07
156 157 0.931005 CTCGATTCTAACTTGGCGCC 59.069 55.000 22.73 22.73 0.00 6.53
181 182 5.798434 GCCGTTAACATGAATAGGAACAAAC 59.202 40.000 6.39 0.00 0.00 2.93
210 211 5.886960 AGCATTCCTTACTTTAGCAAGTG 57.113 39.130 0.00 0.00 43.54 3.16
214 215 5.917541 TTCCTTACTTTAGCAAGTGTTCG 57.082 39.130 0.00 0.00 43.54 3.95
263 273 3.627395 AGGATCGCACAATTGACCTAA 57.373 42.857 13.59 0.00 0.00 2.69
269 279 2.162208 CGCACAATTGACCTAAGCATGT 59.838 45.455 13.59 0.00 0.00 3.21
295 305 4.106029 AGCGACGAACTGAATAAGCTTA 57.894 40.909 8.99 8.99 0.00 3.09
320 330 1.919918 TGAACAAACAGCGGCAAAAG 58.080 45.000 1.45 0.00 0.00 2.27
730 749 2.807107 CGCCTTGGGATCCATCGGA 61.807 63.158 15.23 0.00 35.55 4.55
731 750 1.072159 GCCTTGGGATCCATCGGAG 59.928 63.158 15.23 3.28 34.05 4.63
753 772 4.035102 GCAGCGGAGGGAGGGTTT 62.035 66.667 0.00 0.00 0.00 3.27
754 773 2.269241 CAGCGGAGGGAGGGTTTC 59.731 66.667 0.00 0.00 0.00 2.78
755 774 3.009714 AGCGGAGGGAGGGTTTCC 61.010 66.667 0.00 0.00 46.00 3.13
764 783 2.034221 AGGGTTTCCGCTGGCTTC 59.966 61.111 0.00 0.00 38.33 3.86
765 784 3.431725 GGGTTTCCGCTGGCTTCG 61.432 66.667 0.00 0.00 0.00 3.79
767 786 4.103103 GTTTCCGCTGGCTTCGGC 62.103 66.667 12.04 0.00 46.05 5.54
774 793 4.988598 CTGGCTTCGGCGGTGTGT 62.989 66.667 7.21 0.00 42.91 3.72
775 794 4.980805 TGGCTTCGGCGGTGTGTC 62.981 66.667 7.21 0.00 42.91 3.67
776 795 4.681978 GGCTTCGGCGGTGTGTCT 62.682 66.667 7.21 0.00 42.91 3.41
777 796 3.112709 GCTTCGGCGGTGTGTCTC 61.113 66.667 7.21 0.00 0.00 3.36
778 797 2.805353 CTTCGGCGGTGTGTCTCG 60.805 66.667 7.21 0.00 0.00 4.04
801 820 2.787473 TGCAGTTCAACCCCTGATAG 57.213 50.000 0.00 0.00 32.78 2.08
807 826 3.195825 AGTTCAACCCCTGATAGTCTTCG 59.804 47.826 0.00 0.00 32.78 3.79
835 854 5.384063 ACAAATGTGTGTTCACTTGTTCA 57.616 34.783 4.59 0.00 44.14 3.18
836 855 5.160641 ACAAATGTGTGTTCACTTGTTCAC 58.839 37.500 4.59 0.00 44.14 3.18
837 856 4.370364 AATGTGTGTTCACTTGTTCACC 57.630 40.909 4.59 0.00 44.14 4.02
838 857 1.735018 TGTGTGTTCACTTGTTCACCG 59.265 47.619 4.59 0.00 44.14 4.94
839 858 2.004017 GTGTGTTCACTTGTTCACCGA 58.996 47.619 4.59 0.00 40.98 4.69
842 861 1.226746 GTTCACTTGTTCACCGAGGG 58.773 55.000 0.00 0.00 0.00 4.30
844 863 0.391597 TCACTTGTTCACCGAGGGTC 59.608 55.000 0.00 0.00 31.02 4.46
847 866 0.320771 CTTGTTCACCGAGGGTCCTG 60.321 60.000 0.00 0.00 31.02 3.86
849 868 0.178955 TGTTCACCGAGGGTCCTGTA 60.179 55.000 0.00 0.00 31.02 2.74
856 875 5.210430 TCACCGAGGGTCCTGTATAAATTA 58.790 41.667 0.00 0.00 31.02 1.40
857 876 5.842328 TCACCGAGGGTCCTGTATAAATTAT 59.158 40.000 0.00 0.00 31.02 1.28
863 882 5.551977 AGGGTCCTGTATAAATTATCAGGGG 59.448 44.000 20.75 8.63 45.07 4.79
864 883 5.312443 GGGTCCTGTATAAATTATCAGGGGT 59.688 44.000 20.75 0.00 45.07 4.95
865 884 6.473758 GGTCCTGTATAAATTATCAGGGGTC 58.526 44.000 20.75 14.89 45.07 4.46
895 914 4.161565 TGATTATACACTTTCACGAGGGCT 59.838 41.667 0.00 0.00 0.00 5.19
896 915 2.674796 ATACACTTTCACGAGGGCTC 57.325 50.000 0.00 0.00 0.00 4.70
913 932 2.920524 GCTCTTAAGCCTTTAGGACCC 58.079 52.381 0.00 0.00 43.10 4.46
914 933 2.238898 GCTCTTAAGCCTTTAGGACCCA 59.761 50.000 0.00 0.00 43.10 4.51
941 960 1.204467 GTTCCTCAGAGGACAGAGCAG 59.796 57.143 19.75 0.00 45.78 4.24
946 965 0.457035 CAGAGGACAGAGCAGAGAGC 59.543 60.000 0.00 0.00 46.19 4.09
956 975 3.957288 GCAGAGAGCCCAGGTAAAA 57.043 52.632 0.00 0.00 37.23 1.52
957 976 1.454201 GCAGAGAGCCCAGGTAAAAC 58.546 55.000 0.00 0.00 37.23 2.43
958 977 1.950954 GCAGAGAGCCCAGGTAAAACC 60.951 57.143 0.00 0.00 36.28 3.27
959 978 0.992695 AGAGAGCCCAGGTAAAACCC 59.007 55.000 0.00 0.00 39.75 4.11
960 979 0.992695 GAGAGCCCAGGTAAAACCCT 59.007 55.000 0.00 0.00 39.75 4.34
961 980 1.354705 GAGAGCCCAGGTAAAACCCTT 59.645 52.381 0.00 0.00 39.75 3.95
1113 1138 1.608717 CGGTCTGGAACTCCTCCCTG 61.609 65.000 0.00 0.00 44.69 4.45
1597 1622 1.605058 CCCCGTGATCGAGAAGGTGT 61.605 60.000 0.00 0.00 39.71 4.16
1635 1660 1.728672 GGAGTACGCCTTCGAGGAG 59.271 63.158 8.60 0.00 41.31 3.69
1648 1673 0.526211 CGAGGAGTCCGATGTGTTCA 59.474 55.000 2.76 0.00 0.00 3.18
1650 1675 2.357952 CGAGGAGTCCGATGTGTTCATA 59.642 50.000 2.76 0.00 34.06 2.15
1680 1706 1.813753 GCCGCGGCAGTGAGATTTA 60.814 57.895 43.55 0.00 41.49 1.40
1693 1719 6.680810 CAGTGAGATTTATTCTTGTTGCCAA 58.319 36.000 0.00 0.00 33.74 4.52
1694 1720 7.147312 CAGTGAGATTTATTCTTGTTGCCAAA 58.853 34.615 0.00 0.00 33.74 3.28
1711 1737 4.233789 GCCAAACATTTGCTCGTCATTTA 58.766 39.130 0.00 0.00 36.86 1.40
1853 1879 7.733402 TTAAGTAACATGTTAAGTTTCGCCT 57.267 32.000 19.63 7.47 0.00 5.52
1857 1883 4.616181 ACATGTTAAGTTTCGCCTATGC 57.384 40.909 0.00 0.00 0.00 3.14
1887 1913 6.072948 CGGTGTAAACATGTCAGGTATTTCAA 60.073 38.462 0.00 0.00 0.00 2.69
1907 1933 4.696877 TCAAGTTCATGATCGCATTTGTCT 59.303 37.500 0.00 0.00 30.68 3.41
1914 1940 2.488937 TGATCGCATTTGTCTGTTGCAT 59.511 40.909 0.00 0.00 36.15 3.96
1915 1941 3.057386 TGATCGCATTTGTCTGTTGCATT 60.057 39.130 0.00 0.00 36.15 3.56
1916 1942 2.663808 TCGCATTTGTCTGTTGCATTG 58.336 42.857 0.00 0.00 36.15 2.82
1917 1943 2.034432 TCGCATTTGTCTGTTGCATTGT 59.966 40.909 0.00 0.00 36.15 2.71
1918 1944 2.154198 CGCATTTGTCTGTTGCATTGTG 59.846 45.455 0.00 0.00 36.15 3.33
1919 1945 3.125316 GCATTTGTCTGTTGCATTGTGT 58.875 40.909 0.00 0.00 36.40 3.72
1939 1965 4.499040 GTGTTTGTGTGATCGACAAAAAGG 59.501 41.667 19.15 0.00 41.60 3.11
1969 1995 7.387673 TCAATGTGTAGACTTAATGGAGTTGTG 59.612 37.037 0.00 0.00 0.00 3.33
1970 1996 5.547465 TGTGTAGACTTAATGGAGTTGTGG 58.453 41.667 0.00 0.00 0.00 4.17
1971 1997 5.071250 TGTGTAGACTTAATGGAGTTGTGGT 59.929 40.000 0.00 0.00 0.00 4.16
1972 1998 5.638234 GTGTAGACTTAATGGAGTTGTGGTC 59.362 44.000 0.00 0.00 0.00 4.02
1973 1999 4.974645 AGACTTAATGGAGTTGTGGTCA 57.025 40.909 0.00 0.00 0.00 4.02
1974 2000 4.642429 AGACTTAATGGAGTTGTGGTCAC 58.358 43.478 0.00 0.00 0.00 3.67
1975 2001 4.348168 AGACTTAATGGAGTTGTGGTCACT 59.652 41.667 2.66 0.00 0.00 3.41
1983 2009 3.307059 GGAGTTGTGGTCACTAAGCATCT 60.307 47.826 2.66 0.00 37.77 2.90
1990 2016 4.091509 GTGGTCACTAAGCATCTTAACACG 59.908 45.833 0.00 0.00 37.77 4.49
1996 2022 3.813529 AAGCATCTTAACACGCAACTC 57.186 42.857 0.00 0.00 0.00 3.01
2099 2145 9.220767 GGTAAGAGATTAACTGAATGTGACTTT 57.779 33.333 0.00 0.00 0.00 2.66
2145 2197 3.878086 TCTGTGTCGAAATCACTTTGC 57.122 42.857 6.26 0.00 36.83 3.68
2166 2218 3.363378 GCGAGTGACACTCTGTTTTGATG 60.363 47.826 28.34 13.64 42.92 3.07
2188 2240 7.669304 TGATGAACTGATGGAAAACTGGAAATA 59.331 33.333 0.00 0.00 0.00 1.40
2206 2258 2.661176 TATCCCTCCTCCCAACTTGT 57.339 50.000 0.00 0.00 0.00 3.16
2210 2262 0.178992 CCTCCTCCCAACTTGTGCAA 60.179 55.000 0.00 0.00 0.00 4.08
2233 2285 7.466996 GCAAGAGATAATTGAATGTGACTCCTG 60.467 40.741 0.00 0.00 0.00 3.86
2234 2286 6.590068 AGAGATAATTGAATGTGACTCCTGG 58.410 40.000 0.00 0.00 0.00 4.45
2249 2301 2.954318 CTCCTGGGGTATGCAAAATCTG 59.046 50.000 0.00 0.00 0.00 2.90
2271 2323 3.196685 GGCTGAGTACACTGAGAGGATTT 59.803 47.826 0.00 0.00 27.98 2.17
2272 2324 4.429108 GCTGAGTACACTGAGAGGATTTC 58.571 47.826 0.00 0.00 27.98 2.17
2274 2326 3.119459 TGAGTACACTGAGAGGATTTCGC 60.119 47.826 0.00 0.00 0.00 4.70
2285 2337 3.706594 AGAGGATTTCGCCATGTCTTCTA 59.293 43.478 0.00 0.00 0.00 2.10
2286 2338 3.798202 AGGATTTCGCCATGTCTTCTAC 58.202 45.455 0.00 0.00 0.00 2.59
2288 2340 4.649674 AGGATTTCGCCATGTCTTCTACTA 59.350 41.667 0.00 0.00 0.00 1.82
2289 2341 5.305644 AGGATTTCGCCATGTCTTCTACTAT 59.694 40.000 0.00 0.00 0.00 2.12
2290 2342 5.635700 GGATTTCGCCATGTCTTCTACTATC 59.364 44.000 0.00 0.00 0.00 2.08
2325 2381 3.641437 TGTTGCTGCTGTGGTTTTATC 57.359 42.857 0.00 0.00 0.00 1.75
2326 2382 2.031245 TGTTGCTGCTGTGGTTTTATCG 60.031 45.455 0.00 0.00 0.00 2.92
2329 2385 2.483877 TGCTGCTGTGGTTTTATCGAAG 59.516 45.455 0.00 0.00 0.00 3.79
2330 2386 2.742053 GCTGCTGTGGTTTTATCGAAGA 59.258 45.455 0.00 0.00 45.75 2.87
2336 2392 4.710324 TGTGGTTTTATCGAAGAGTGGTT 58.290 39.130 0.00 0.00 43.63 3.67
2348 2404 7.391620 ATCGAAGAGTGGTTAAAACCTGATAA 58.608 34.615 12.87 0.00 45.85 1.75
2372 2428 5.707764 AGATTTTTGAAGGAGCCACTAGTTC 59.292 40.000 0.00 0.00 0.00 3.01
2388 2444 1.217942 AGTTCTGGCCTTTTGGGAAGT 59.782 47.619 3.32 0.00 40.82 3.01
2401 2457 1.279558 TGGGAAGTGCGGTGCTTATAA 59.720 47.619 0.00 0.00 0.00 0.98
2402 2458 2.092646 TGGGAAGTGCGGTGCTTATAAT 60.093 45.455 0.00 0.00 0.00 1.28
2426 2482 9.777297 AATGGCTTGAACTTAAAAATACAATGT 57.223 25.926 0.00 0.00 0.00 2.71
2438 2494 6.763303 AAAATACAATGTTTCTGTTTCCGC 57.237 33.333 0.00 0.00 0.00 5.54
2481 2537 1.295357 TGAAACCGTGCTGTATGCCG 61.295 55.000 0.00 0.00 42.00 5.69
2497 2553 2.717485 CGATTGCGCCCTTGATGG 59.283 61.111 4.18 0.00 0.00 3.51
2520 2576 1.940613 CGAATCGAGTTCCATTTCCCC 59.059 52.381 0.00 0.00 33.04 4.81
2528 2584 4.765339 CGAGTTCCATTTCCCCTTTTTACT 59.235 41.667 0.00 0.00 0.00 2.24
2529 2585 5.335661 CGAGTTCCATTTCCCCTTTTTACTG 60.336 44.000 0.00 0.00 0.00 2.74
2542 2598 5.579119 CCCTTTTTACTGTTTGGTGTTGAAC 59.421 40.000 0.00 0.00 0.00 3.18
2549 2605 4.082245 ACTGTTTGGTGTTGAACTTGAAGG 60.082 41.667 0.00 0.00 0.00 3.46
2550 2606 3.194542 TGTTTGGTGTTGAACTTGAAGGG 59.805 43.478 0.00 0.00 0.00 3.95
2567 2624 0.991920 GGGTGACTGGATTCAAGGGA 59.008 55.000 0.00 0.00 0.00 4.20
2579 2636 3.874383 TTCAAGGGAGTGAATTGTCCA 57.126 42.857 0.00 0.00 32.56 4.02
2601 2658 1.131126 CATGGATGTGTCGTTGAAGCC 59.869 52.381 0.00 0.00 0.00 4.35
2604 2661 0.798776 GATGTGTCGTTGAAGCCTGG 59.201 55.000 0.00 0.00 0.00 4.45
2605 2662 0.396435 ATGTGTCGTTGAAGCCTGGA 59.604 50.000 0.00 0.00 0.00 3.86
2607 2664 0.586802 GTGTCGTTGAAGCCTGGAAC 59.413 55.000 0.00 0.00 0.00 3.62
2608 2665 0.179234 TGTCGTTGAAGCCTGGAACA 59.821 50.000 0.00 0.00 0.00 3.18
2609 2666 1.305201 GTCGTTGAAGCCTGGAACAA 58.695 50.000 0.00 0.00 38.70 2.83
2610 2667 1.673920 GTCGTTGAAGCCTGGAACAAA 59.326 47.619 0.00 0.00 38.70 2.83
2611 2668 1.673920 TCGTTGAAGCCTGGAACAAAC 59.326 47.619 0.00 0.00 38.70 2.93
2612 2669 1.269051 CGTTGAAGCCTGGAACAAACC 60.269 52.381 0.00 0.00 38.70 3.27
2613 2670 1.754226 GTTGAAGCCTGGAACAAACCA 59.246 47.619 0.00 0.00 38.70 3.67
2618 2675 2.173519 AGCCTGGAACAAACCATGATG 58.826 47.619 0.00 0.00 38.70 3.07
2619 2676 1.404583 GCCTGGAACAAACCATGATGC 60.405 52.381 0.00 0.00 38.70 3.91
2620 2677 1.205417 CCTGGAACAAACCATGATGCC 59.795 52.381 0.00 0.00 38.70 4.40
2621 2678 0.887247 TGGAACAAACCATGATGCCG 59.113 50.000 0.00 0.00 34.77 5.69
2622 2679 0.887933 GGAACAAACCATGATGCCGT 59.112 50.000 0.00 0.00 0.00 5.68
2623 2680 1.402720 GGAACAAACCATGATGCCGTG 60.403 52.381 0.00 0.00 0.00 4.94
2628 2685 2.591753 CCATGATGCCGTGGGACT 59.408 61.111 0.00 0.00 44.07 3.85
2629 2686 1.077501 CCATGATGCCGTGGGACTT 60.078 57.895 0.00 0.00 44.07 3.01
2630 2687 1.378882 CCATGATGCCGTGGGACTTG 61.379 60.000 0.00 0.00 44.07 3.16
2631 2688 1.750399 ATGATGCCGTGGGACTTGC 60.750 57.895 0.00 0.00 0.00 4.01
2632 2689 2.359850 GATGCCGTGGGACTTGCA 60.360 61.111 0.00 0.00 38.23 4.08
2633 2690 2.672996 ATGCCGTGGGACTTGCAC 60.673 61.111 0.00 0.00 36.41 4.57
2636 2693 2.340809 CCGTGGGACTTGCACGTA 59.659 61.111 0.00 0.00 40.29 3.57
2640 2697 2.345991 GGGACTTGCACGTAGGCA 59.654 61.111 0.00 0.00 43.19 4.75
2649 2706 1.361668 GCACGTAGGCATGTGTCCAG 61.362 60.000 0.00 0.00 42.66 3.86
2658 2715 1.339055 GCATGTGTCCAGCCTGAAGTA 60.339 52.381 0.00 0.00 0.00 2.24
2661 2718 1.339055 TGTGTCCAGCCTGAAGTATGC 60.339 52.381 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.449068 CCAACAATATCGTGCCTGATACTC 59.551 45.833 0.00 0.00 33.86 2.59
1 2 4.100963 TCCAACAATATCGTGCCTGATACT 59.899 41.667 0.00 0.00 33.86 2.12
2 3 4.377021 TCCAACAATATCGTGCCTGATAC 58.623 43.478 0.00 0.00 33.86 2.24
3 4 4.681074 TCCAACAATATCGTGCCTGATA 57.319 40.909 0.00 0.00 35.43 2.15
4 5 3.558931 TCCAACAATATCGTGCCTGAT 57.441 42.857 0.00 0.00 0.00 2.90
5 6 3.342377 TTCCAACAATATCGTGCCTGA 57.658 42.857 0.00 0.00 0.00 3.86
6 7 4.637483 AATTCCAACAATATCGTGCCTG 57.363 40.909 0.00 0.00 0.00 4.85
53 54 2.104792 CTGGGATTAAGAAGATGCCCGA 59.895 50.000 0.00 0.00 38.42 5.14
90 91 6.978659 TCCTCTGCATTTCAGTAGTAATTACG 59.021 38.462 9.91 0.00 43.32 3.18
134 135 2.534757 GCGCCAAGTTAGAATCGAGTAC 59.465 50.000 0.00 0.00 0.00 2.73
156 157 3.619483 TGTTCCTATTCATGTTAACGGCG 59.381 43.478 4.80 4.80 0.00 6.46
181 182 7.816640 TGCTAAAGTAAGGAATGCTTTGTTAG 58.183 34.615 0.00 0.50 42.88 2.34
210 211 2.281762 CGCCTAGATTTGTAGTGCGAAC 59.718 50.000 10.11 0.00 39.79 3.95
214 215 5.986004 AAATACGCCTAGATTTGTAGTGC 57.014 39.130 0.00 0.00 0.00 4.40
263 273 1.069906 GTTCGTCGCTTCAAACATGCT 60.070 47.619 0.00 0.00 0.00 3.79
269 279 4.377022 GCTTATTCAGTTCGTCGCTTCAAA 60.377 41.667 0.00 0.00 0.00 2.69
295 305 1.001378 GCCGCTGTTTGTTCATTGAGT 60.001 47.619 0.00 0.00 0.00 3.41
320 330 6.474751 GCCACTTCTGATTTATTTTCAGCATC 59.525 38.462 0.00 0.00 40.35 3.91
327 337 4.380867 CGGCTGCCACTTCTGATTTATTTT 60.381 41.667 20.29 0.00 0.00 1.82
328 338 3.129287 CGGCTGCCACTTCTGATTTATTT 59.871 43.478 20.29 0.00 0.00 1.40
329 339 2.684881 CGGCTGCCACTTCTGATTTATT 59.315 45.455 20.29 0.00 0.00 1.40
330 340 2.092968 TCGGCTGCCACTTCTGATTTAT 60.093 45.455 20.29 0.00 0.00 1.40
331 341 1.277842 TCGGCTGCCACTTCTGATTTA 59.722 47.619 20.29 0.00 0.00 1.40
360 370 1.372087 CCCATTTGGTGAGCTCTCGC 61.372 60.000 16.19 6.32 39.26 5.03
745 764 3.569200 AAGCCAGCGGAAACCCTCC 62.569 63.158 0.00 0.00 41.40 4.30
746 765 2.034221 AAGCCAGCGGAAACCCTC 59.966 61.111 0.00 0.00 0.00 4.30
747 766 2.034221 GAAGCCAGCGGAAACCCT 59.966 61.111 0.00 0.00 0.00 4.34
748 767 3.431725 CGAAGCCAGCGGAAACCC 61.432 66.667 0.00 0.00 0.00 4.11
757 776 4.988598 ACACACCGCCGAAGCCAG 62.989 66.667 0.00 0.00 34.57 4.85
759 778 4.681978 AGACACACCGCCGAAGCC 62.682 66.667 0.00 0.00 34.57 4.35
761 780 2.543687 ATCGAGACACACCGCCGAAG 62.544 60.000 0.00 0.00 32.84 3.79
764 783 1.736645 AAATCGAGACACACCGCCG 60.737 57.895 0.00 0.00 0.00 6.46
765 784 1.787847 CAAATCGAGACACACCGCC 59.212 57.895 0.00 0.00 0.00 6.13
766 785 1.132640 GCAAATCGAGACACACCGC 59.867 57.895 0.00 0.00 0.00 5.68
767 786 0.439985 CTGCAAATCGAGACACACCG 59.560 55.000 0.00 0.00 0.00 4.94
768 787 1.512926 ACTGCAAATCGAGACACACC 58.487 50.000 0.00 0.00 0.00 4.16
769 788 2.543848 TGAACTGCAAATCGAGACACAC 59.456 45.455 0.00 0.00 0.00 3.82
770 789 2.832563 TGAACTGCAAATCGAGACACA 58.167 42.857 0.00 0.00 0.00 3.72
771 790 3.545633 GTTGAACTGCAAATCGAGACAC 58.454 45.455 0.00 0.00 38.44 3.67
772 791 2.548057 GGTTGAACTGCAAATCGAGACA 59.452 45.455 0.00 0.00 38.44 3.41
773 792 2.095718 GGGTTGAACTGCAAATCGAGAC 60.096 50.000 0.00 0.00 38.44 3.36
774 793 2.151202 GGGTTGAACTGCAAATCGAGA 58.849 47.619 0.00 0.00 38.44 4.04
775 794 1.200020 GGGGTTGAACTGCAAATCGAG 59.800 52.381 0.00 0.00 38.44 4.04
776 795 1.202879 AGGGGTTGAACTGCAAATCGA 60.203 47.619 0.00 0.00 38.44 3.59
777 796 1.068333 CAGGGGTTGAACTGCAAATCG 60.068 52.381 0.00 0.00 38.44 3.34
778 797 2.238521 TCAGGGGTTGAACTGCAAATC 58.761 47.619 0.00 0.00 38.44 2.17
801 820 6.044512 ACACACATTTGTTCTTACGAAGAC 57.955 37.500 0.00 0.00 37.23 3.01
824 843 0.834612 ACCCTCGGTGAACAAGTGAA 59.165 50.000 0.00 0.00 32.98 3.18
827 846 0.763223 AGGACCCTCGGTGAACAAGT 60.763 55.000 0.00 0.00 35.25 3.16
829 848 1.052124 ACAGGACCCTCGGTGAACAA 61.052 55.000 0.00 0.00 35.25 2.83
830 849 0.178955 TACAGGACCCTCGGTGAACA 60.179 55.000 0.00 0.00 35.25 3.18
831 850 1.192428 ATACAGGACCCTCGGTGAAC 58.808 55.000 0.00 0.00 35.25 3.18
832 851 2.832643 TATACAGGACCCTCGGTGAA 57.167 50.000 0.00 0.00 35.25 3.18
833 852 2.832643 TTATACAGGACCCTCGGTGA 57.167 50.000 0.00 0.00 35.25 4.02
834 853 4.417426 AATTTATACAGGACCCTCGGTG 57.583 45.455 0.00 0.00 35.25 4.94
835 854 5.842328 TGATAATTTATACAGGACCCTCGGT 59.158 40.000 0.00 0.00 39.44 4.69
836 855 6.354794 TGATAATTTATACAGGACCCTCGG 57.645 41.667 0.00 0.00 0.00 4.63
857 876 9.615660 AGTGTATAATCATAAATAGACCCCTGA 57.384 33.333 0.00 0.00 0.00 3.86
895 914 3.265995 CCTTGGGTCCTAAAGGCTTAAGA 59.734 47.826 6.67 0.00 36.78 2.10
896 915 3.265995 TCCTTGGGTCCTAAAGGCTTAAG 59.734 47.826 15.47 0.00 42.35 1.85
903 922 3.559384 GGAACTGTCCTTGGGTCCTAAAG 60.559 52.174 0.00 0.00 41.24 1.85
905 924 1.982958 GGAACTGTCCTTGGGTCCTAA 59.017 52.381 0.00 0.00 41.24 2.69
926 945 1.954733 GCTCTCTGCTCTGTCCTCTGA 60.955 57.143 0.00 0.00 38.95 3.27
932 951 1.516892 CTGGGCTCTCTGCTCTGTC 59.483 63.158 0.00 0.00 44.09 3.51
934 953 0.685785 TACCTGGGCTCTCTGCTCTG 60.686 60.000 0.00 0.00 44.09 3.35
941 960 0.992695 AGGGTTTTACCTGGGCTCTC 59.007 55.000 0.00 0.00 40.04 3.20
946 965 1.081481 AGGGAAGGGTTTTACCTGGG 58.919 55.000 0.00 0.00 40.87 4.45
948 967 2.803956 GGAAGGGAAGGGTTTTACCTG 58.196 52.381 0.00 0.00 40.87 4.00
950 969 1.074405 ACGGAAGGGAAGGGTTTTACC 59.926 52.381 0.00 0.00 37.60 2.85
951 970 2.156917 CACGGAAGGGAAGGGTTTTAC 58.843 52.381 0.00 0.00 35.60 2.01
952 971 1.074244 CCACGGAAGGGAAGGGTTTTA 59.926 52.381 0.00 0.00 35.60 1.52
953 972 0.178973 CCACGGAAGGGAAGGGTTTT 60.179 55.000 0.00 0.00 35.60 2.43
954 973 1.458927 CCACGGAAGGGAAGGGTTT 59.541 57.895 0.00 0.00 35.60 3.27
955 974 3.167414 CCACGGAAGGGAAGGGTT 58.833 61.111 0.00 0.00 35.60 4.11
956 975 3.647771 GCCACGGAAGGGAAGGGT 61.648 66.667 0.00 0.00 35.60 4.34
957 976 3.330720 AGCCACGGAAGGGAAGGG 61.331 66.667 0.00 0.00 35.60 3.95
958 977 2.045926 CAGCCACGGAAGGGAAGG 60.046 66.667 0.00 0.00 35.60 3.46
959 978 2.045926 CCAGCCACGGAAGGGAAG 60.046 66.667 0.00 0.00 35.60 3.46
960 979 4.344865 GCCAGCCACGGAAGGGAA 62.345 66.667 0.00 0.00 35.60 3.97
1113 1138 1.737008 GGCGAACTTGACGAGGACC 60.737 63.158 0.00 0.00 0.00 4.46
1551 1576 2.741211 GGAACGGCGTCCCAGAAC 60.741 66.667 11.54 0.00 0.00 3.01
1635 1660 2.460918 CGGAGTATGAACACATCGGAC 58.539 52.381 0.00 0.00 0.00 4.79
1693 1719 6.128035 TGCTATGTAAATGACGAGCAAATGTT 60.128 34.615 0.00 0.00 43.18 2.71
1694 1720 5.353956 TGCTATGTAAATGACGAGCAAATGT 59.646 36.000 0.00 0.00 43.18 2.71
1853 1879 3.504134 ACATGTTTACACCGCAAAGCATA 59.496 39.130 0.00 0.00 0.00 3.14
1857 1883 3.554524 CTGACATGTTTACACCGCAAAG 58.445 45.455 0.00 0.00 0.00 2.77
1887 1913 4.005650 ACAGACAAATGCGATCATGAACT 58.994 39.130 0.00 0.00 32.23 3.01
1907 1933 3.582714 TCACACAAACACAATGCAACA 57.417 38.095 0.00 0.00 0.00 3.33
1914 1940 4.686839 TTTGTCGATCACACAAACACAA 57.313 36.364 13.49 0.00 38.53 3.33
1915 1941 4.686839 TTTTGTCGATCACACAAACACA 57.313 36.364 16.06 3.73 42.17 3.72
1916 1942 4.499040 CCTTTTTGTCGATCACACAAACAC 59.501 41.667 16.06 0.00 42.17 3.32
1917 1943 4.396478 TCCTTTTTGTCGATCACACAAACA 59.604 37.500 16.06 10.94 42.17 2.83
1918 1944 4.915704 TCCTTTTTGTCGATCACACAAAC 58.084 39.130 16.06 0.00 42.17 2.93
1919 1945 5.568685 TTCCTTTTTGTCGATCACACAAA 57.431 34.783 13.49 13.49 41.05 2.83
1939 1965 9.167311 ACTCCATTAAGTCTACACATTGAATTC 57.833 33.333 0.00 0.00 0.00 2.17
1969 1995 3.062234 GCGTGTTAAGATGCTTAGTGACC 59.938 47.826 9.46 0.00 0.00 4.02
1970 1996 3.678072 TGCGTGTTAAGATGCTTAGTGAC 59.322 43.478 16.82 0.00 0.00 3.67
1971 1997 3.920446 TGCGTGTTAAGATGCTTAGTGA 58.080 40.909 16.82 0.00 0.00 3.41
1972 1998 4.152402 AGTTGCGTGTTAAGATGCTTAGTG 59.848 41.667 16.82 0.00 0.00 2.74
1973 1999 4.315803 AGTTGCGTGTTAAGATGCTTAGT 58.684 39.130 16.82 6.27 0.00 2.24
1974 2000 4.201724 GGAGTTGCGTGTTAAGATGCTTAG 60.202 45.833 16.82 0.00 0.00 2.18
1975 2001 3.682858 GGAGTTGCGTGTTAAGATGCTTA 59.317 43.478 16.82 3.70 0.00 3.09
1983 2009 2.206750 GACACAGGAGTTGCGTGTTAA 58.793 47.619 0.00 0.00 43.65 2.01
1990 2016 3.988379 TGATTTTGACACAGGAGTTGC 57.012 42.857 0.00 0.00 0.00 4.17
1996 2022 7.168637 CACAAGAAGATTTGATTTTGACACAGG 59.831 37.037 0.00 0.00 0.00 4.00
2035 2081 4.441079 GGGCATTTCATCAGTTCATCAAGG 60.441 45.833 0.00 0.00 0.00 3.61
2105 2151 9.429359 ACACAGAAGTTGAGTTAATTATCTCTG 57.571 33.333 19.49 12.77 0.00 3.35
2116 2162 5.006746 GTGATTTCGACACAGAAGTTGAGTT 59.993 40.000 0.13 0.00 38.05 3.01
2166 2218 7.416777 GGGATATTTCCAGTTTTCCATCAGTTC 60.417 40.741 4.48 0.00 44.60 3.01
2188 2240 0.995024 CACAAGTTGGGAGGAGGGAT 59.005 55.000 7.96 0.00 0.00 3.85
2206 2258 6.317140 GGAGTCACATTCAATTATCTCTTGCA 59.683 38.462 0.00 0.00 0.00 4.08
2210 2262 6.409005 CCCAGGAGTCACATTCAATTATCTCT 60.409 42.308 0.00 0.00 0.00 3.10
2233 2285 1.410153 CAGCCAGATTTTGCATACCCC 59.590 52.381 0.00 0.00 0.00 4.95
2234 2286 2.360165 CTCAGCCAGATTTTGCATACCC 59.640 50.000 0.00 0.00 0.00 3.69
2249 2301 1.840737 TCCTCTCAGTGTACTCAGCC 58.159 55.000 0.00 0.00 0.00 4.85
2271 2323 3.898517 CGATAGTAGAAGACATGGCGA 57.101 47.619 0.00 0.00 0.00 5.54
2348 2404 5.248380 ACTAGTGGCTCCTTCAAAAATCT 57.752 39.130 0.00 0.00 0.00 2.40
2354 2410 2.303022 CCAGAACTAGTGGCTCCTTCAA 59.697 50.000 0.00 0.00 0.00 2.69
2372 2428 1.667722 GCACTTCCCAAAAGGCCAG 59.332 57.895 5.01 0.00 34.51 4.85
2388 2444 1.675483 CAAGCCATTATAAGCACCGCA 59.325 47.619 0.18 0.00 0.00 5.69
2401 2457 9.777297 AACATTGTATTTTTAAGTTCAAGCCAT 57.223 25.926 0.00 0.00 0.00 4.40
2402 2458 9.606631 AAACATTGTATTTTTAAGTTCAAGCCA 57.393 25.926 0.00 0.00 0.00 4.75
2426 2482 2.224670 ACTACATGGGCGGAAACAGAAA 60.225 45.455 0.00 0.00 0.00 2.52
2438 2494 2.231235 GTGCCAAAAGGAACTACATGGG 59.769 50.000 0.00 0.00 38.49 4.00
2497 2553 1.330829 GAAATGGAACTCGATTCGCCC 59.669 52.381 0.00 0.94 38.31 6.13
2520 2576 7.596995 TCAAGTTCAACACCAAACAGTAAAAAG 59.403 33.333 0.00 0.00 0.00 2.27
2528 2584 3.194542 CCCTTCAAGTTCAACACCAAACA 59.805 43.478 0.00 0.00 0.00 2.83
2529 2585 3.194755 ACCCTTCAAGTTCAACACCAAAC 59.805 43.478 0.00 0.00 0.00 2.93
2542 2598 3.423539 TGAATCCAGTCACCCTTCAAG 57.576 47.619 0.00 0.00 0.00 3.02
2549 2605 1.630878 ACTCCCTTGAATCCAGTCACC 59.369 52.381 0.00 0.00 0.00 4.02
2550 2606 2.303022 TCACTCCCTTGAATCCAGTCAC 59.697 50.000 0.00 0.00 0.00 3.67
2579 2636 2.679837 GCTTCAACGACACATCCATGAT 59.320 45.455 0.00 0.00 0.00 2.45
2591 2648 1.673920 GTTTGTTCCAGGCTTCAACGA 59.326 47.619 0.00 0.00 0.00 3.85
2601 2658 1.135315 CGGCATCATGGTTTGTTCCAG 60.135 52.381 0.00 0.00 41.05 3.86
2604 2661 1.402720 CCACGGCATCATGGTTTGTTC 60.403 52.381 0.00 0.00 0.00 3.18
2605 2662 0.602562 CCACGGCATCATGGTTTGTT 59.397 50.000 0.00 0.00 0.00 2.83
2607 2664 0.964860 TCCCACGGCATCATGGTTTG 60.965 55.000 0.00 0.00 33.80 2.93
2608 2665 0.965363 GTCCCACGGCATCATGGTTT 60.965 55.000 0.00 0.00 33.80 3.27
2609 2666 1.378514 GTCCCACGGCATCATGGTT 60.379 57.895 0.00 0.00 33.80 3.67
2610 2667 1.852157 AAGTCCCACGGCATCATGGT 61.852 55.000 0.00 0.00 33.80 3.55
2611 2668 1.077501 AAGTCCCACGGCATCATGG 60.078 57.895 0.00 0.00 35.59 3.66
2612 2669 1.996786 GCAAGTCCCACGGCATCATG 61.997 60.000 0.00 0.00 0.00 3.07
2613 2670 1.750399 GCAAGTCCCACGGCATCAT 60.750 57.895 0.00 0.00 0.00 2.45
2621 2678 2.033194 GCCTACGTGCAAGTCCCAC 61.033 63.158 9.05 0.00 0.00 4.61
2622 2679 1.836999 ATGCCTACGTGCAAGTCCCA 61.837 55.000 9.05 5.52 45.84 4.37
2623 2680 1.078426 ATGCCTACGTGCAAGTCCC 60.078 57.895 9.05 0.00 45.84 4.46
2624 2681 0.673644 ACATGCCTACGTGCAAGTCC 60.674 55.000 9.05 0.00 45.84 3.85
2625 2682 0.443869 CACATGCCTACGTGCAAGTC 59.556 55.000 9.05 0.00 45.84 3.01
2626 2683 0.250295 ACACATGCCTACGTGCAAGT 60.250 50.000 10.83 10.83 45.84 3.16
2627 2684 0.443869 GACACATGCCTACGTGCAAG 59.556 55.000 4.54 3.18 45.84 4.01
2628 2685 0.953471 GGACACATGCCTACGTGCAA 60.953 55.000 4.54 0.00 45.84 4.08
2629 2686 1.375396 GGACACATGCCTACGTGCA 60.375 57.895 2.77 2.77 46.94 4.57
2630 2687 1.361668 CTGGACACATGCCTACGTGC 61.362 60.000 0.00 0.00 36.57 5.34
2631 2688 1.361668 GCTGGACACATGCCTACGTG 61.362 60.000 0.00 0.00 39.10 4.49
2632 2689 1.079127 GCTGGACACATGCCTACGT 60.079 57.895 0.00 0.00 0.00 3.57
2633 2690 1.815421 GGCTGGACACATGCCTACG 60.815 63.158 0.00 0.00 43.05 3.51
2634 2691 4.225497 GGCTGGACACATGCCTAC 57.775 61.111 0.00 0.00 43.05 3.18
2640 2697 2.681976 GCATACTTCAGGCTGGACACAT 60.682 50.000 15.73 0.00 0.00 3.21
2649 2706 1.020437 GCAAGAGGCATACTTCAGGC 58.980 55.000 0.00 0.00 43.97 4.85


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

AutoCloner maintained by Alex Coulton.