AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0193800

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0193800 MtrunA17_Chr2g0284151 76.000 125 26 1 2 122 667 791 1.20e-57 190
Msa0193800 MtrunA17_Chr0c09g0493531 84.259 108 17 0 15 122 739 846 3.48e-57 189
Msa0193800 MtrunA17_Chr2g0284191 83.810 105 17 0 18 122 733 837 1.14e-53 179
Msa0193800 MtrunA17_Chr3g0095201 60.839 143 34 3 2 122 847 989 1.50e-47 162
Msa0193800 MtrunA17_Chr2g0284121 75.676 111 20 1 18 121 1103 1213 2.65e-47 162
Msa0193800 MtrunA17_Chr4g0013491 62.500 112 36 1 18 123 627 738 6.00e-41 143
Msa0193800 MtrunA17_Chr8g0363371 61.739 115 37 1 16 123 716 830 1.79e-40 142
Msa0193800 MtrunA17_Chr8g0362841 61.947 113 36 1 18 123 716 828 2.06e-40 142
Msa0193800 MtrunA17_Chr8g0362431 62.832 113 35 1 18 123 672 784 3.12e-40 141
Msa0193800 MtrunA17_Chr8g0363501 62.832 113 35 1 18 123 410 522 4.70e-40 139
Msa0193800 MtrunA17_Chr8g0363241 61.062 113 37 1 18 123 632 744 4.71e-40 141
Msa0193800 MtrunA17_Chr8g0362391 61.062 113 37 1 18 123 216 328 5.04e-40 135
Msa0193800 MtrunA17_Chr8g0363401 61.062 113 37 1 18 123 679 791 2.93e-39 139
Msa0193800 MtrunA17_Chr8g0363121 61.947 113 36 1 18 123 674 786 3.12e-39 139
Msa0193800 MtrunA17_Chr8g0363601 60.345 116 39 1 15 123 661 776 3.78e-39 138
Msa0193800 MtrunA17_Chr8g0361231 63.717 113 34 1 18 123 966 1078 1.09e-38 137
Msa0193800 MtrunA17_Chr8g0363661 63.717 113 34 1 18 123 727 839 1.27e-38 137
Msa0193800 MtrunA17_Chr1g0176301 62.727 110 34 1 18 120 629 738 3.08e-38 136
Msa0193800 MtrunA17_Chr8g0362911 61.607 112 36 1 15 119 610 721 3.49e-38 135
Msa0193800 MtrunA17_Chr8g0362961 64.220 109 32 1 18 119 1114 1222 3.51e-38 136
Msa0193800 MtrunA17_Chr8g0363281 61.468 109 35 1 18 119 647 755 3.98e-38 135
Msa0193800 MtrunA17_Chr8g0363641 53.333 135 46 3 2 119 115 249 4.52e-38 129
Msa0193800 MtrunA17_Chr8g0363691 61.062 113 37 1 18 123 1138 1250 4.70e-38 135
Msa0193800 MtrunA17_Chr8g0360851 58.929 112 39 1 15 119 895 1006 5.69e-38 135
Msa0193800 MtrunA17_Chr8g0362981 61.207 116 38 1 15 123 627 742 9.08e-38 134
Msa0193800 MtrunA17_Chr8g0362941 59.292 113 39 1 18 123 630 742 1.02e-37 134
Msa0193800 MtrunA17_Chr8g0363061 63.303 109 33 1 18 119 870 978 1.13e-37 134
Msa0193800 MtrunA17_Chr8g0362871 60.177 113 38 1 18 123 664 776 1.22e-37 134
Msa0193800 MtrunA17_Chr8g0363261 58.407 113 40 1 18 123 274 386 1.37e-37 130
Msa0193800 MtrunA17_Chr8g0363221 53.957 139 47 3 2 123 718 856 2.41e-37 133
Msa0193800 MtrunA17_Chr8g0362931 62.385 109 34 1 18 119 1059 1167 4.71e-37 132
Msa0193800 MtrunA17_Chr8g0363191 61.682 107 34 1 20 119 593 699 1.63e-36 131
Msa0193800 MtrunA17_Chr8g0363111 61.607 112 36 1 15 119 871 982 5.53e-36 129
Msa0193800 MtrunA17_Chr8g0363321 57.778 90 31 1 37 119 1 90 5.74e-28 98.6
Msa0193800 MtrunA17_Chr8g0367351 35.246 122 61 1 18 121 896 1017 5.91e-18 78.6
Msa0193800 MtrunA17_Chr3g0113221 35.593 118 62 2 18 121 890 1007 3.07e-17 76.3
Msa0193800 MtrunA17_Chr5g0408621 35.246 122 62 2 18 122 935 1056 3.20e-17 76.3
Msa0193800 MtrunA17_Chr5g0436851 34.483 116 64 1 18 121 39 154 1.00e-16 71.2
Msa0193800 MtrunA17_Chr5g0408401 36.667 120 60 3 18 121 664 783 1.08e-16 74.7
Msa0193800 MtrunA17_Chr5g0408511 33.621 116 66 2 18 122 897 1012 1.66e-16 74.3
Msa0193800 MtrunA17_Chr8g0369631 32.759 116 60 2 24 121 4 119 1.98e-16 70.1
Msa0193800 MtrunA17_Chr5g0408421 32.520 123 66 1 18 123 882 1004 3.54e-16 73.2
Msa0193800 MtrunA17_Chr6g0464171 32.520 123 66 2 18 123 901 1023 8.82e-16 72.0
Msa0193800 MtrunA17_Chr1g0196011 33.913 115 58 1 18 114 727 841 8.94e-16 72.0
Msa0193800 MtrunA17_Chr6g0464141 32.258 124 66 2 18 123 901 1024 1.11e-15 72.0
Msa0193800 MtrunA17_Chr5g0408571 30.081 123 69 2 18 123 379 501 1.34e-15 71.6
Msa0193800 MtrunA17_Chr5g0436841 37.500 112 63 2 18 122 938 1049 1.76e-15 71.2
Msa0193800 MtrunA17_Chr5g0408741 31.944 144 74 3 3 122 779 922 1.81e-15 71.2
Msa0193800 MtrunA17_Chr5g0408581 32.787 122 65 2 18 122 901 1022 2.47e-15 70.9
Msa0193800 MtrunA17_Chr1g0196031 32.174 115 60 1 18 114 935 1049 9.98e-15 69.3
Msa0193800 MtrunA17_Chr5g0408811 31.667 120 68 2 18 123 872 991 1.16e-14 68.9
Msa0193800 MtrunA17_Chr2g0313911 39.815 108 56 3 18 119 244 348 1.29e-14 68.6
Msa0193800 MtrunA17_Chr5g0403401 30.894 123 68 2 18 123 889 1011 1.37e-14 68.9
Msa0193800 MtrunA17_Chr5g0408611 31.967 122 66 1 18 122 888 1009 1.55e-14 68.6
Msa0193800 MtrunA17_Chr6g0464211 30.081 123 69 2 18 123 900 1022 1.70e-14 68.6
Msa0193800 MtrunA17_Chr5g0436871 32.773 119 68 1 15 121 91 209 2.61e-14 66.2
Msa0193800 MtrunA17_Chr5g0419221 27.848 158 77 3 2 122 864 1021 2.68e-14 67.8
Msa0193800 MtrunA17_Chr8g0366461 36.283 113 63 3 18 121 895 1007 3.58e-14 67.8
Msa0193800 MtrunA17_Chr5g0408801 28.455 123 71 2 18 123 901 1023 3.76e-14 67.4
Msa0193800 MtrunA17_Chr2g0324931 34.615 104 66 2 15 117 864 966 7.62e-14 66.6
Msa0193800 MtrunA17_Chr5g0407241 31.967 122 66 2 18 122 906 1027 8.02e-14 66.6
Msa0193800 MtrunA17_Chr2g0314001 32.759 116 66 1 18 121 892 1007 8.65e-14 66.6
Msa0193800 MtrunA17_Chr5g0436911 32.174 115 66 1 19 121 175 289 1.27e-13 65.5
Msa0193800 MtrunA17_Chr1g0159871 32.759 116 66 1 15 118 816 931 1.44e-13 65.9
Msa0193800 MtrunA17_Chr2g0300201 29.268 123 70 2 17 122 900 1022 1.63e-13 65.9
Msa0193800 MtrunA17_Chr8g0380951 29.167 120 73 1 15 122 855 974 1.86e-13 65.5
Msa0193800 MtrunA17_Chr1g0159881 45.312 64 35 0 15 78 357 420 3.00e-13 64.7
Msa0193800 MtrunA17_Chr3g0127701 47.059 68 36 0 15 82 857 924 3.36e-13 64.7
Msa0193800 MtrunA17_Chr5g0408821 27.731 119 69 2 18 119 294 412 3.98e-13 64.3
Msa0193800 MtrunA17_Chr5g0436941 33.036 112 64 1 18 118 886 997 4.54e-13 64.3
Msa0193800 MtrunA17_Chr8g0380941 31.858 113 65 2 15 115 886 998 5.25e-13 64.3
Msa0193800 MtrunA17_Chr2g0314021 31.897 116 67 1 18 121 892 1007 6.13e-13 63.9
Msa0193800 MtrunA17_Chr1g0196001 39.474 76 46 0 18 93 895 970 8.78e-13 63.5
Msa0193800 MtrunA17_Chr7g0237821 34.579 107 65 2 15 118 970 1074 1.22e-12 63.2
Msa0193800 MtrunA17_Chr3g0126181 36.364 110 64 2 15 118 936 1045 1.25e-12 63.2
Msa0193800 MtrunA17_Chr7g0241921 30.597 134 66 2 15 121 869 1002 1.62e-12 62.8
Msa0193800 MtrunA17_Chr3g0127671 44.118 68 38 0 15 82 902 969 1.86e-12 62.8
Msa0193800 MtrunA17_Chr5g0408431 30.894 123 68 2 18 123 899 1021 3.69e-12 62.0
Msa0193800 MtrunA17_Chr1g0196051 42.188 64 37 0 18 81 5 68 3.94e-12 57.4
Msa0193800 MtrunA17_Chr6g0464201 34.524 84 55 0 18 101 40 123 4.18e-12 58.5
Msa0193800 MtrunA17_Chr5g0408501 29.310 116 65 2 25 123 5 120 5.82e-12 58.5
Msa0193800 MtrunA17_Chr6g0464161 30.081 123 69 3 18 123 630 752 6.50e-12 61.2
Msa0193800 MtrunA17_Chr7g0248261 31.304 115 67 1 19 121 844 958 7.03e-12 61.2
Msa0193800 MtrunA17_Chr5g0419721 35.514 107 63 2 15 118 818 921 7.53e-12 60.8
Msa0193800 MtrunA17_Chr5g0436861 31.034 116 68 2 15 118 889 1004 8.48e-12 60.8
Msa0193800 MtrunA17_Chr4g0051961 32.110 109 68 3 18 122 1050 1156 1.21e-11 60.5
Msa0193800 MtrunA17_Chr5g0437331 33.036 112 63 2 23 122 894 1005 1.77e-11 60.1
Msa0193800 MtrunA17_Chr5g0436931 30.909 110 64 2 24 121 1 110 2.07e-11 56.6
Msa0193800 MtrunA17_Chr1g0183231 35.514 107 66 3 15 118 874 980 3.45e-11 58.9
Msa0193800 MtrunA17_Chr4g0060011 35.789 95 59 2 18 110 486 580 3.49e-11 58.9
Msa0193800 MtrunA17_Chr4g0069251 34.000 100 63 3 18 114 351 450 4.17e-11 58.9
Msa0193800 MtrunA17_Chr6g0472051 31.313 99 56 2 18 104 105 203 4.67e-11 57.4
Msa0193800 MtrunA17_Chr5g0409041 33.333 99 64 2 18 114 475 573 4.79e-11 58.5
Msa0193800 MtrunA17_Chr1g0161701 35.185 108 62 4 18 117 753 860 5.52e-11 58.5
Msa0193800 MtrunA17_Chr1g0190411 32.407 108 69 3 15 118 880 987 5.89e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0193800 AT3G47580.1 36.036 111 64 1 18 121 892 1002 4.03e-19 82.0
Msa0193800 AT3G47570.1 36.036 111 64 2 18 121 891 1001 1.09e-17 78.2
Msa0193800 AT3G47090.1 33.929 112 65 2 18 121 890 1000 1.73e-16 74.7
Msa0193800 AT3G47110.1 34.821 112 65 3 18 121 908 1019 2.77e-15 71.2
Msa0193800 AT1G78530.1 36.134 119 71 3 7 120 232 350 1.25e-14 68.9
Msa0193800 AT5G20480.1 31.731 104 67 1 18 121 901 1000 6.12e-14 67.4
Msa0193800 AT5G20480.2 31.731 104 67 1 18 121 901 1000 6.12e-14 67.4
Msa0193800 AT3G24240.1 36.449 107 63 2 15 118 963 1067 1.95e-13 65.9
Msa0193800 AT3G19700.1 32.432 111 71 1 15 121 860 970 2.11e-13 65.9
Msa0193800 AT5G39390.1 33.333 108 60 2 18 121 398 497 7.93e-13 63.9
Msa0193800 AT5G49660.1 33.000 100 65 1 18 115 835 934 8.81e-12 61.2
Msa0193800 AT1G09970.1 33.673 98 63 1 15 110 850 947 1.93e-11 60.1
Msa0193800 AT1G27190.1 36.275 102 60 3 18 114 475 576 2.42e-11 59.7
Msa0193800 AT2G35620.3 31.313 99 66 2 18 114 473 571 2.51e-11 59.7
Msa0193800 AT2G35620.1 31.313 99 66 2 18 114 473 571 2.51e-11 59.7
Msa0193800 AT2G35620.2 31.313 99 66 2 18 114 473 571 2.51e-11 59.7
Msa0193800 AT2G35620.4 31.313 99 66 2 18 114 473 571 2.51e-11 59.7
Msa0193800 AT1G17750.1 29.688 128 79 1 3 119 951 1078 3.19e-11 59.7
Msa0193800 AT1G09970.2 33.333 96 62 1 17 110 853 948 4.76e-11 58.9
Msa0193800 AT2G01950.1 34.167 120 62 3 18 120 1013 1132 5.78e-11 58.9
Msa0193800 AT1G31420.2 32.323 99 65 2 18 114 475 573 8.19e-11 58.2
Msa0193800 AT1G31420.1 32.323 99 65 2 18 114 476 574 8.35e-11 58.2
Msa0193800 AT1G31420.3 32.323 99 65 2 18 114 476 574 8.35e-11 58.2
Msa0193800 AT1G69990.1 36.538 104 57 4 18 114 462 563 8.85e-11 58.2
Msa0193800 AT5G62710.2 33.333 99 64 2 18 114 450 548 9.24e-11 58.2

Find 20 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGGGAGTGATTTCAGTTAA+AGG 0.316584 2_1:+9650905 Msa0193800:CDS
AAAGGAGATGTGTACAGCTT+TGG 0.347263 2_1:+9650923 Msa0193800:CDS
ACATACAGAGTATGGATCTA+AGG 0.361988 2_1:+9650886 Msa0193800:CDS
CACAACTTCCATACTGGAAT+TGG 0.365939 2_1:-9651041 None:intergenic
AAGGAGATGTGTACAGCTTT+GGG 0.368651 2_1:+9650924 Msa0193800:CDS
AAGAATTAACCTTGAAAACT+TGG 0.377924 2_1:+9651002 Msa0193800:CDS
ACATGTATACATACAGAGTA+TGG 0.393941 2_1:+9650878 Msa0193800:CDS
CAGCTTTGGGATAATGCTAA+TGG 0.394665 2_1:+9650937 Msa0193800:CDS
TCTGAAAACATTTCATCTGT+TGG 0.418545 2_1:-9650980 None:intergenic
GTAATCCACAACTTCCATAC+TGG 0.452542 2_1:-9651047 None:intergenic
GTCATATTAATGCGTGCCTC+AGG 0.456398 2_1:-9651142 None:intergenic
ATCAATGGCCAATTCCAGTA+TGG 0.472821 2_1:+9651033 Msa0193800:CDS
AACTTGGATTAGTGAATCAA+TGG 0.481330 2_1:+9651018 Msa0193800:CDS
AGATCAAGACCTCATTCATC+GGG 0.512947 2_1:+9651188 Msa0193800:CDS
CATACAGAGTATGGATCTAA+GGG 0.518547 2_1:+9650887 Msa0193800:CDS
AAGATCAAGACCTCATTCAT+CGG 0.543601 2_1:+9651187 Msa0193800:CDS
TACAATTTAGACTCAAAACA+TGG 0.552869 2_1:+9651067 Msa0193800:CDS
CAATTCCAGTATGGAAGTTG+TGG 0.560878 2_1:+9651042 Msa0193800:CDS
ACAATTTAGACTCAAAACAT+GGG 0.636017 2_1:+9651068 Msa0193800:CDS
ATGTTGTGTAGATTCACCTG+AGG 0.709814 2_1:+9651126 Msa0193800:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGAATTAACCTTGAAAACT+TGG + chr2_1:9651002-9651021 Msa0193800:CDS 25.0%
! TACAATTTAGACTCAAAACA+TGG + chr2_1:9651067-9651086 Msa0193800:CDS 25.0%
! ACAATTTAGACTCAAAACAT+GGG + chr2_1:9651068-9651087 Msa0193800:CDS 25.0%
ACATGTATACATACAGAGTA+TGG + chr2_1:9650878-9650897 Msa0193800:CDS 30.0%
TCTGAAAACATTTCATCTGT+TGG - chr2_1:9650983-9651002 None:intergenic 30.0%
! TTCACTAATCCAAGTTTTCA+AGG - chr2_1:9651014-9651033 None:intergenic 30.0%
!! AACTTGGATTAGTGAATCAA+TGG + chr2_1:9651018-9651037 Msa0193800:CDS 30.0%
ACATACAGAGTATGGATCTA+AGG + chr2_1:9650886-9650905 Msa0193800:CDS 35.0%
CATACAGAGTATGGATCTAA+GGG + chr2_1:9650887-9650906 Msa0193800:CDS 35.0%
AAGGGAGTGATTTCAGTTAA+AGG + chr2_1:9650905-9650924 Msa0193800:CDS 35.0%
AAGATCAAGACCTCATTCAT+CGG + chr2_1:9651187-9651206 Msa0193800:CDS 35.0%
AAAGGAGATGTGTACAGCTT+TGG + chr2_1:9650923-9650942 Msa0193800:CDS 40.0%
AAGGAGATGTGTACAGCTTT+GGG + chr2_1:9650924-9650943 Msa0193800:CDS 40.0%
!! CAGCTTTGGGATAATGCTAA+TGG + chr2_1:9650937-9650956 Msa0193800:CDS 40.0%
ATCAATGGCCAATTCCAGTA+TGG + chr2_1:9651033-9651052 Msa0193800:CDS 40.0%
CACAACTTCCATACTGGAAT+TGG - chr2_1:9651044-9651063 None:intergenic 40.0%
CAATTCCAGTATGGAAGTTG+TGG + chr2_1:9651042-9651061 Msa0193800:CDS 40.0%
GTAATCCACAACTTCCATAC+TGG - chr2_1:9651050-9651069 None:intergenic 40.0%
ATGTTGTGTAGATTCACCTG+AGG + chr2_1:9651126-9651145 Msa0193800:CDS 40.0%
AGATCAAGACCTCATTCATC+GGG + chr2_1:9651188-9651207 Msa0193800:CDS 40.0%
GTCATATTAATGCGTGCCTC+AGG - chr2_1:9651145-9651164 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 9650842 9651213 9650842 ID=Msa0193800;Name=Msa0193800
chr2_1 mRNA 9650842 9651213 9650842 ID=Msa0193800-mRNA-1;Parent=Msa0193800;Name=Msa0193800-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|123
chr2_1 exon 9650842 9651213 9650842 ID=Msa0193800-mRNA-1:exon:4416;Parent=Msa0193800-mRNA-1
chr2_1 CDS 9650842 9651213 9650842 ID=Msa0193800-mRNA-1:cds;Parent=Msa0193800-mRNA-1
Gene Sequence

>Msa0193800

ATGTATGTTTCAGATTTTTTTATAACTAGTGATAATACATGTATACATACAGAGTATGGATCTAAGGGAGTGATTTCAGTTAAAGGAGATGTGTACAGCTTTGGGATAATGCTAATGGAAATGTTCACTGCAAAGACGCCAACAGATGAAATGTTTTCAGAAGAATTAACCTTGAAAACTTGGATTAGTGAATCAATGGCCAATTCCAGTATGGAAGTTGTGGATTACAATTTAGACTCAAAACATGGGAAAGAAATTAATGTTATCTTAGCTTTAGCATTAAGATGTTGTGTAGATTCACCTGAGGCACGCATTAATATGACAAATGTAACTGCGTCGTTAATCAAGATCAAGACCTCATTCATCGGGTGA
Protein sequence

>Msa0193800

MYVSDFFITSDNTCIHTEYGSKGVISVKGDVYSFGIMLMEMFTAKTPTDEMFSEELTLKTWISESMANSSMEVVDYNLDSKHGKEINVILALALRCCVDSPEARINMTNVTASLIKIKTSFIG*