AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1205440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1205440 MtrunA17_Chr4g0054521 97.101 69 1 1 55 122 862 930 1.69e-38 137
Msa1205440 MtrunA17_Chr5g0400681 95.588 68 2 1 55 121 865 932 1.75e-36 131
Msa1205440 MtrunA17_Chr2g0277081 64.789 71 24 1 55 124 860 930 5.41e-25 98.6
Msa1205440 MtrunA17_Chr5g0442151 69.863 73 19 3 55 124 856 928 5.89e-25 98.6
Msa1205440 MtrunA17_Chr3g0095081 68.116 69 20 2 55 121 900 968 2.21e-24 96.7
Msa1205440 MtrunA17_Chr4g0035464 68.493 73 17 2 55 121 857 929 5.71e-24 95.5
Msa1205440 MtrunA17_Chr7g0262141 58.730 63 25 1 55 116 886 948 1.41e-18 80.1
Msa1205440 MtrunA17_Chr3g0140871 49.367 79 38 2 43 119 848 926 1.16e-17 77.8
Msa1205440 MtrunA17_Chr4g0046511 65.152 66 20 3 55 119 870 933 1.64e-17 77.0
Msa1205440 MtrunA17_Chr4g0058761 53.731 67 30 1 55 120 946 1012 1.51e-16 74.3
Msa1205440 MtrunA17_Chr4g0017251 56.061 66 28 1 55 119 848 913 2.08e-16 73.9
Msa1205440 MtrunA17_Chr2g0280191 60.000 60 23 1 55 113 864 923 2.19e-16 73.9
Msa1205440 MtrunA17_Chr4g0018701 56.667 60 25 1 55 113 894 953 2.26e-16 73.9
Msa1205440 MtrunA17_Chr2g0282831 63.077 65 21 3 55 118 842 904 2.41e-16 73.9
Msa1205440 MtrunA17_Chr1g0183231 53.968 63 27 2 55 116 877 938 2.61e-16 73.9
Msa1205440 MtrunA17_Chr2g0312651 54.839 62 28 0 55 116 982 1043 6.86e-16 72.4
Msa1205440 MtrunA17_Chr1g0190411 55.556 63 26 2 55 116 883 944 1.37e-15 71.6
Msa1205440 MtrunA17_Chr1g0201241 49.275 69 32 1 55 120 895 963 1.45e-15 71.6
Msa1205440 MtrunA17_Chr1g0169841 51.562 64 29 1 55 116 984 1047 6.67e-14 67.0
Msa1205440 MtrunA17_Chr3g0140861 49.231 65 30 2 55 116 834 898 1.41e-13 65.9
Msa1205440 MtrunA17_Chr5g0402071 44.444 72 37 2 55 124 339 409 1.63e-13 65.9
Msa1205440 MtrunA17_Chr5g0419721 50.746 67 27 2 55 120 821 882 2.42e-13 65.1
Msa1205440 MtrunA17_Chr5g0400701 59.184 49 19 1 55 102 880 928 3.58e-13 64.7
Msa1205440 MtrunA17_Chr7g0257621 48.485 66 33 1 55 119 781 846 7.84e-13 63.9
Msa1205440 MtrunA17_Chr7g0258081 50.794 63 29 1 55 115 767 829 1.42e-12 63.2
Msa1205440 MtrunA17_Chr1g0189871 53.030 66 25 3 55 116 974 1037 1.87e-12 62.8
Msa1205440 MtrunA17_Chr2g0324931 50.769 65 29 3 55 118 867 929 2.32e-12 62.4
Msa1205440 MtrunA17_Chr7g0248491 44.118 68 35 2 55 120 333 399 4.03e-12 61.6
Msa1205440 MtrunA17_Chr7g0237821 44.776 67 32 2 55 120 973 1035 7.79e-12 60.8
Msa1205440 MtrunA17_Chr3g0123141 42.683 82 38 4 42 116 762 841 1.30e-11 60.5
Msa1205440 MtrunA17_Chr4g0018801 46.667 60 31 1 55 113 665 724 1.76e-11 60.1
Msa1205440 MtrunA17_Chr2g0296591 48.611 72 32 4 55 122 1127 1197 2.32e-11 59.7
Msa1205440 MtrunA17_Chr6g0485721 43.182 88 43 3 36 116 245 332 4.01e-11 58.9
Msa1205440 MtrunA17_Chr8g0342071 45.070 71 36 2 55 122 623 693 6.54e-11 58.2
Msa1205440 MtrunA17_Chr1g0204461 38.462 104 53 4 25 124 815 911 9.22e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1205440 AT5G65700.1 91.176 68 5 1 55 121 867 934 8.88e-35 127
Msa1205440 AT5G65700.2 91.176 68 5 1 55 121 867 934 8.88e-35 127
Msa1205440 AT3G49670.1 85.294 68 9 1 55 121 863 930 7.51e-32 118
Msa1205440 AT1G75820.1 67.123 73 18 2 55 121 864 936 2.44e-24 97.1
Msa1205440 AT4G20270.1 65.217 69 22 2 55 121 884 952 1.98e-23 94.4
Msa1205440 AT4G28650.1 56.061 66 28 1 55 119 876 941 2.49e-18 80.1
Msa1205440 AT1G08590.1 53.333 60 27 1 55 113 899 958 2.72e-16 73.9
Msa1205440 AT1G09970.1 52.381 63 29 1 55 116 853 915 6.95e-16 72.8
Msa1205440 AT1G09970.2 52.381 63 29 1 55 116 854 916 7.02e-16 72.8
Msa1205440 AT1G34110.1 50.746 67 32 1 55 120 948 1014 2.05e-15 71.6
Msa1205440 AT1G34110.2 50.746 67 32 1 55 120 948 1014 2.09e-15 71.6
Msa1205440 AT5G49660.1 52.381 63 29 1 55 116 835 897 2.89e-15 71.2
Msa1205440 AT5G61480.1 52.381 63 29 1 55 116 896 958 3.08e-15 71.2
Msa1205440 AT1G28440.1 54.545 66 27 3 55 119 863 926 1.63e-14 68.9
Msa1205440 AT3G19700.1 71.111 45 12 1 55 98 863 907 2.15e-14 68.6
Msa1205440 AT1G17230.2 51.613 62 30 0 55 116 972 1033 2.37e-14 68.6
Msa1205440 AT2G33170.2 47.826 69 36 0 55 123 998 1066 2.42e-14 68.6
Msa1205440 AT2G33170.1 47.826 69 36 0 55 123 998 1066 2.42e-14 68.6
Msa1205440 AT5G63930.1 54.839 62 28 0 55 116 978 1039 2.44e-14 68.6
Msa1205440 AT5G63930.2 54.839 62 28 0 55 116 914 975 2.65e-14 68.6
Msa1205440 AT1G17230.1 51.613 62 30 0 55 116 972 1033 2.74e-14 68.6
Msa1205440 AT4G28490.1 55.556 63 25 3 55 116 868 928 1.09e-13 66.6
Msa1205440 AT2G41820.1 46.970 66 34 1 55 119 782 847 2.98e-13 65.5
Msa1205440 AT5G48940.1 44.776 67 31 2 55 120 967 1028 1.49e-12 63.5
Msa1205440 AT3G24240.1 47.692 65 29 2 55 118 966 1026 1.88e-12 63.2
Msa1205440 AT1G55610.1 42.188 64 34 2 55 116 1034 1096 5.96e-12 61.6
Msa1205440 AT1G55610.2 42.188 64 34 2 55 116 1034 1096 5.96e-12 61.6
Msa1205440 AT4G20140.1 45.070 71 36 3 55 122 1133 1203 6.79e-12 61.6
Msa1205440 AT1G72180.1 50.746 67 31 2 55 119 858 924 1.98e-11 60.1
Msa1205440 AT5G65710.1 62.222 45 16 1 55 98 868 912 1.98e-11 60.1
Msa1205440 AT2G42960.3 45.588 68 34 2 55 120 355 421 2.25e-11 60.1
Msa1205440 AT2G42960.5 45.588 68 34 2 55 120 355 421 2.25e-11 60.1
Msa1205440 AT2G42960.4 45.588 68 34 2 55 120 355 421 2.25e-11 60.1
Msa1205440 AT2G42960.1 45.588 68 34 2 55 120 355 421 2.25e-11 60.1
Msa1205440 AT5G62230.1 38.710 93 49 3 36 124 796 884 7.31e-11 58.5
Msa1205440 AT4G01330.2 40.278 72 32 3 55 120 334 400 7.44e-11 58.5
Msa1205440 AT1G67720.1 42.857 84 39 4 42 118 760 841 7.50e-11 58.5
Msa1205440 AT4G01330.1 40.278 72 32 3 55 120 334 400 7.73e-11 58.5
Msa1205440 AT5G02290.2 47.059 68 26 2 55 116 250 313 7.75e-11 58.5
Msa1205440 AT5G02290.1 47.059 68 26 2 55 116 250 313 7.75e-11 58.5
Msa1205440 AT5G62230.2 38.710 93 49 3 36 124 748 836 8.18e-11 58.5
Msa1205440 AT5G44700.1 44.928 69 34 2 55 119 1128 1196 9.84e-11 58.2

Find 45 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAAACCAGTTGGAGAATT+TGG 0.201190 8_1:-61740249 Msa1205440:CDS
TCCTTCAGTTCCACTTGATT+TGG 0.289005 8_1:-61740145 Msa1205440:CDS
TTTCTTCGCCATTTGCATCT+TGG 0.302672 8_1:-61740533 Msa1205440:CDS
CTTCAAATCCTCTCCTGTTT+CGG 0.326008 8_1:-61740570 Msa1205440:CDS
GGAAGAGGATGAGTTGTAGA+AGG 0.328957 8_1:+61740660 None:intergenic
GAAACTATATCGCAATTATA+AGG 0.347253 8_1:-61740716 Msa1205440:five_prime_UTR
GGTTGAATGAGAGGAGGAAG+AGG 0.371326 8_1:+61740645 None:intergenic
GAGAGATGGGTGACCGAAAC+AGG 0.379925 8_1:+61740557 None:intergenic
TGTGGGGTGTGGAAAGTACT+TGG 0.421647 8_1:+61740618 None:intergenic
CCATCACCAAATTCTCCAAC+TGG 0.439622 8_1:+61740243 None:intergenic
AAAAGCGACGTCTACAGCTT+TGG 0.457382 8_1:-61740300 Msa1205440:CDS
AAGAGGATGAGTTGTAGAAG+GGG 0.479924 8_1:+61740662 None:intergenic
CTTCGCCATTTGCATCTTGG+TGG 0.481603 8_1:-61740530 Msa1205440:intron
GAAGAGGATGAGTTGTAGAA+GGG 0.483107 8_1:+61740661 None:intergenic
CGAAACAGGAGAGGATTTGA+AGG 0.488102 8_1:+61740571 None:intergenic
TGAGTGGTATTCAGAGATGT+GGG 0.503238 8_1:+61740601 None:intergenic
ATTTGAAGGAGAGGAGTGAG+TGG 0.514237 8_1:+61740585 None:intergenic
GTGAGTGGTATTCAGAGATG+TGG 0.523967 8_1:+61740600 None:intergenic
CAGGAGAGGATTTGAAGGAG+AGG 0.528888 8_1:+61740576 None:intergenic
GTACTTCTAGAGCTTGTAGC+AGG 0.534823 8_1:-61740273 Msa1205440:CDS
CTTGGGTAAGGTTGAATGAG+AGG 0.535384 8_1:+61740636 None:intergenic
TCGCAATTATAAGGCTAAGC+TGG 0.538745 8_1:-61740707 Msa1205440:five_prime_UTR
TGGAGTAGACATTGTGCAAT+GGG 0.549400 8_1:-61740223 Msa1205440:CDS
CTGGCGGCAAAGCGGCGATG+AGG 0.549532 8_1:-61740688 Msa1205440:exon
AGTTACCACCAAGATGCAAA+TGG 0.549678 8_1:+61740525 None:intergenic
AGTGGAACTGAAGGAAGTCT+AGG 0.552601 8_1:+61740153 None:intergenic
GCCAAATCAAGTGGAACTGA+AGG 0.557383 8_1:+61740144 None:intergenic
CCAGTTGGAGAATTTGGTGA+TGG 0.564487 8_1:-61740243 Msa1205440:CDS
GTATTCAGAGATGTGGGGTG+TGG 0.567728 8_1:+61740607 None:intergenic
GTGTGGAAAGTACTTGGGTA+AGG 0.576259 8_1:+61740624 None:intergenic
ACGTATTAGGCCAAATCAAG+TGG 0.578291 8_1:+61740135 None:intergenic
GACTATCGATAGTTTCACAT+TGG 0.588550 8_1:-61740794 Msa1205440:five_prime_UTR
ATGGCGAAGAAAAGAGAGAT+GGG 0.595466 8_1:+61740544 None:intergenic
GTGGGGTGTGGAAAGTACTT+GGG 0.597175 8_1:+61740619 None:intergenic
AATGGCGAAGAAAAGAGAGA+TGG 0.599455 8_1:+61740543 None:intergenic
AAAATGACAGACTCAAACAA+AGG 0.599944 8_1:-61740195 Msa1205440:CDS
GGGTAAGGTTGAATGAGAGG+AGG 0.606338 8_1:+61740639 None:intergenic
ATGGAGTAGACATTGTGCAA+TGG 0.636956 8_1:-61740224 Msa1205440:CDS
CAATTATAAGGCTAAGCTGG+CGG 0.638574 8_1:-61740704 Msa1205440:five_prime_UTR
ATGGGTGACCGAAACAGGAG+AGG 0.645390 8_1:+61740562 None:intergenic
AGGCTAAGCTGGCGGCAAAG+CGG 0.651684 8_1:-61740696 Msa1205440:five_prime_UTR
TAGTTTCGCGACGAAGACGA+TGG 0.658492 8_1:+61740732 None:intergenic
GTAGCAGGAAGAAAACCAGT+TGG 0.667156 8_1:-61740258 Msa1205440:CDS
CGACGTCTACAGCTTTGGTG+TGG 0.688691 8_1:-61740295 Msa1205440:CDS
GAGTGGTATTCAGAGATGTG+GGG 0.694116 8_1:+61740602 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATTCAAAAAAAATAAAAT+TGG + chr8_1:61740510-61740529 None:intergenic 10.0%
!! ATCAAGATTCAAACTATTAA+GGG + chr8_1:61740467-61740486 None:intergenic 20.0%
!! TTAATAGTTTGAATCTTGAT+CGG - chr8_1:61740467-61740486 Msa1205440:intron 20.0%
! GAAACTATATCGCAATTATA+AGG - chr8_1:61740226-61740245 Msa1205440:CDS 25.0%
! GATCAAGATTCAAACTATTA+AGG + chr8_1:61740468-61740487 None:intergenic 25.0%
! CTAAAATACCTAGTTTGAAA+TGG - chr8_1:61740528-61740547 Msa1205440:intron 25.0%
AAAATGACAGACTCAAACAA+AGG - chr8_1:61740747-61740766 Msa1205440:five_prime_UTR 30.0%
GACTATCGATAGTTTCACAT+TGG - chr8_1:61740148-61740167 Msa1205440:CDS 35.0%
TAGTTTGAATCTTGATCGGA+TGG - chr8_1:61740471-61740490 Msa1205440:intron 35.0%
AGAAAACCAGTTGGAGAATT+TGG - chr8_1:61740693-61740712 Msa1205440:exon 35.0%
TCGCAATTATAAGGCTAAGC+TGG - chr8_1:61740235-61740254 Msa1205440:CDS 40.0%
CAATTATAAGGCTAAGCTGG+CGG - chr8_1:61740238-61740257 Msa1205440:CDS 40.0%
AAGAGGATGAGTTGTAGAAG+GGG + chr8_1:61740283-61740302 None:intergenic 40.0%
GAAGAGGATGAGTTGTAGAA+GGG + chr8_1:61740284-61740303 None:intergenic 40.0%
TGAGTGGTATTCAGAGATGT+GGG + chr8_1:61740344-61740363 None:intergenic 40.0%
CTTCAAATCCTCTCCTGTTT+CGG - chr8_1:61740372-61740391 Msa1205440:intron 40.0%
ATGGCGAAGAAAAGAGAGAT+GGG + chr8_1:61740401-61740420 None:intergenic 40.0%
AATGGCGAAGAAAAGAGAGA+TGG + chr8_1:61740402-61740421 None:intergenic 40.0%
TTTCTTCGCCATTTGCATCT+TGG - chr8_1:61740409-61740428 Msa1205440:intron 40.0%
AGTTACCACCAAGATGCAAA+TGG + chr8_1:61740420-61740439 None:intergenic 40.0%
CATCTGGACCATTTCAAACT+AGG + chr8_1:61740539-61740558 None:intergenic 40.0%
! AGTTTGAAATGGTCCAGATG+TGG - chr8_1:61740539-61740558 Msa1205440:CDS 40.0%
ATGGAGTAGACATTGTGCAA+TGG - chr8_1:61740718-61740737 Msa1205440:five_prime_UTR 40.0%
TGGAGTAGACATTGTGCAAT+GGG - chr8_1:61740719-61740738 Msa1205440:five_prime_UTR 40.0%
TCCTTCAGTTCCACTTGATT+TGG - chr8_1:61740797-61740816 Msa1205440:five_prime_UTR 40.0%
GGAAGAGGATGAGTTGTAGA+AGG + chr8_1:61740285-61740304 None:intergenic 45.0%
CTTGGGTAAGGTTGAATGAG+AGG + chr8_1:61740309-61740328 None:intergenic 45.0%
!! GTGTGGAAAGTACTTGGGTA+AGG + chr8_1:61740321-61740340 None:intergenic 45.0%
GAGTGGTATTCAGAGATGTG+GGG + chr8_1:61740343-61740362 None:intergenic 45.0%
GTGAGTGGTATTCAGAGATG+TGG + chr8_1:61740345-61740364 None:intergenic 45.0%
ATTTGAAGGAGAGGAGTGAG+TGG + chr8_1:61740360-61740379 None:intergenic 45.0%
CGAAACAGGAGAGGATTTGA+AGG + chr8_1:61740374-61740393 None:intergenic 45.0%
CAAAGAGAATCAGCCACATC+TGG + chr8_1:61740555-61740574 None:intergenic 45.0%
AAAAGCGACGTCTACAGCTT+TGG - chr8_1:61740642-61740661 Msa1205440:CDS 45.0%
!! GTACTTCTAGAGCTTGTAGC+AGG - chr8_1:61740669-61740688 Msa1205440:CDS 45.0%
GTAGCAGGAAGAAAACCAGT+TGG - chr8_1:61740684-61740703 Msa1205440:exon 45.0%
CCATCACCAAATTCTCCAAC+TGG + chr8_1:61740702-61740721 None:intergenic 45.0%
! CCAGTTGGAGAATTTGGTGA+TGG - chr8_1:61740699-61740718 Msa1205440:five_prime_UTR 45.0%
AGTGGAACTGAAGGAAGTCT+AGG + chr8_1:61740792-61740811 None:intergenic 45.0%
GCCAAATCAAGTGGAACTGA+AGG + chr8_1:61740801-61740820 None:intergenic 45.0%
TAGTTTCGCGACGAAGACGA+TGG + chr8_1:61740213-61740232 None:intergenic 50.0%
GGTTGAATGAGAGGAGGAAG+AGG + chr8_1:61740300-61740319 None:intergenic 50.0%
GGGTAAGGTTGAATGAGAGG+AGG + chr8_1:61740306-61740325 None:intergenic 50.0%
!! GTGGGGTGTGGAAAGTACTT+GGG + chr8_1:61740326-61740345 None:intergenic 50.0%
!! TGTGGGGTGTGGAAAGTACT+TGG + chr8_1:61740327-61740346 None:intergenic 50.0%
GTATTCAGAGATGTGGGGTG+TGG + chr8_1:61740338-61740357 None:intergenic 50.0%
CAGGAGAGGATTTGAAGGAG+AGG + chr8_1:61740369-61740388 None:intergenic 50.0%
CTTCGCCATTTGCATCTTGG+TGG - chr8_1:61740412-61740431 Msa1205440:intron 50.0%
ATGGGTGACCGAAACAGGAG+AGG + chr8_1:61740383-61740402 None:intergenic 55.0%
GAGAGATGGGTGACCGAAAC+AGG + chr8_1:61740388-61740407 None:intergenic 55.0%
! CGACGTCTACAGCTTTGGTG+TGG - chr8_1:61740647-61740666 Msa1205440:CDS 55.0%
AGGCTAAGCTGGCGGCAAAG+CGG - chr8_1:61740246-61740265 Msa1205440:CDS 60.0%
CTGGCGGCAAAGCGGCGATG+AGG - chr8_1:61740254-61740273 Msa1205440:CDS 70.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 61740140 61740824 61740140 ID=Msa1205440;Name=Msa1205440
chr8_1 mRNA 61740140 61740824 61740140 ID=Msa1205440-mRNA-1;Parent=Msa1205440;Name=Msa1205440-mRNA-1;_AED=0.19;_eAED=0.19;_QI=131|1|0.5|1|1|1|2|0|124
chr8_1 exon 61740140 61740351 61740140 ID=Msa1205440-mRNA-1:exon:20025;Parent=Msa1205440-mRNA-1
chr8_1 exon 61740531 61740824 61740531 ID=Msa1205440-mRNA-1:exon:20024;Parent=Msa1205440-mRNA-1
chr8_1 five_prime_UTR 61740694 61740824 61740694 ID=Msa1205440-mRNA-1:five_prime_utr;Parent=Msa1205440-mRNA-1
chr8_1 CDS 61740531 61740693 61740531 ID=Msa1205440-mRNA-1:cds;Parent=Msa1205440-mRNA-1
chr8_1 CDS 61740140 61740351 61740140 ID=Msa1205440-mRNA-1:cds;Parent=Msa1205440-mRNA-1
Gene Sequence

>Msa1205440

ATGAGGCTTCCCCTTCTACAACTCATCCTCTTCCTCCTCTCATTCAACCTTACCCAAGTACTTTCCACACCCCACATCTCTGAATACCACTCACTCCTCTCCTTCAAATCCTCTCCTGTTTCGGTCACCCATCTCTCTTTTCTTCGCCATTTGCATCTTGGTGAGTATGCATACACATTGAAAGTCGATGAAAAAAGCGACGTCTACAGCTTTGGTGTGGTACTTCTAGAGCTTGTAGCAGGAAGAAAACCAGTTGGAGAATTTGGTGATGGAGTAGACATTGTGCAATGGGTGAGAAAAATGACAGACTCAAACAAAGGTGTTCTAAAAGTACTTGATCCTAGACTTCCTTCAGTTCCACTTGATTTGGCCTAA
Protein sequence

>Msa1205440

MRLPLLQLILFLLSFNLTQVLSTPHISEYHSLLSFKSSPVSVTHLSFLRHLHLGEYAYTLKVDEKSDVYSFGVVLLELVAGRKPVGEFGDGVDIVQWVRKMTDSNKGVLKVLDPRLPSVPLDLA*