AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0818030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0818030 MtrunA17_Chr5g0436931 87.273 110 14 0 9 118 1 110 2.15e-68 201
Msa0818030 MtrunA17_Chr5g0436861 85.593 118 17 0 3 120 892 1009 4.55e-65 212
Msa0818030 MtrunA17_Chr7g0248261 75.424 118 29 0 3 120 843 960 4.68e-57 189
Msa0818030 MtrunA17_Chr5g0436911 72.034 118 33 0 3 120 174 291 8.20e-57 177
Msa0818030 MtrunA17_Chr5g0437331 79.825 114 23 0 7 120 893 1006 3.32e-56 187
Msa0818030 MtrunA17_Chr5g0436851 71.053 114 33 0 3 116 39 152 7.92e-55 168
Msa0818030 MtrunA17_Chr1g0159871 72.881 118 32 0 3 120 819 936 6.30e-53 177
Msa0818030 MtrunA17_Chr5g0436841 75.424 118 24 1 3 120 938 1050 2.53e-52 176
Msa0818030 MtrunA17_Chr1g0159881 75.455 110 27 0 3 112 360 469 3.61e-52 170
Msa0818030 MtrunA17_Chr5g0436871 67.797 118 38 0 3 120 94 211 1.15e-51 162
Msa0818030 MtrunA17_Chr2g0314001 66.949 118 39 0 3 120 892 1009 1.37e-50 171
Msa0818030 MtrunA17_Chr2g0314021 66.949 118 39 0 3 120 892 1009 5.36e-50 169
Msa0818030 MtrunA17_Chr3g0078621 73.684 95 25 0 26 120 1 95 5.71e-47 146
Msa0818030 MtrunA17_Chr5g0436941 62.069 116 43 1 3 118 886 1000 6.73e-42 146
Msa0818030 MtrunA17_Chr2g0314031 58.475 118 40 1 3 120 888 996 8.16e-39 137
Msa0818030 MtrunA17_Chr8g0366461 43.103 116 63 1 3 118 895 1007 1.91e-25 99.8
Msa0818030 MtrunA17_Chr5g0408811 40.833 120 69 1 3 120 872 991 1.77e-22 91.3
Msa0818030 MtrunA17_Chr5g0408401 39.831 118 67 1 3 116 664 781 4.59e-22 90.1
Msa0818030 MtrunA17_Chr8g0367351 44.262 122 62 2 3 118 896 1017 2.56e-21 87.8
Msa0818030 MtrunA17_Chr3g0113221 39.655 116 68 1 3 116 890 1005 3.56e-21 87.4
Msa0818030 MtrunA17_Chr8g0369631 39.655 116 64 2 7 116 2 117 1.12e-20 80.5
Msa0818030 MtrunA17_Chr5g0408581 39.024 123 70 1 3 120 901 1023 2.19e-20 85.1
Msa0818030 MtrunA17_Chr5g0408621 38.889 126 66 2 3 120 935 1057 3.59e-20 84.7
Msa0818030 MtrunA17_Chr1g0196011 36.800 125 67 2 3 118 727 848 5.06e-20 84.3
Msa0818030 MtrunA17_Chr5g0408741 38.843 121 69 2 3 120 805 923 8.69e-20 83.6
Msa0818030 MtrunA17_Chr2g0300201 38.525 122 70 1 3 119 901 1022 9.74e-20 83.2
Msa0818030 MtrunA17_Chr5g0408511 40.367 109 64 1 3 111 897 1004 1.04e-19 83.2
Msa0818030 MtrunA17_Chr5g0408501 38.333 120 65 2 7 119 2 119 1.28e-19 78.2
Msa0818030 MtrunA17_Chr5g0408801 36.585 123 73 1 3 120 901 1023 1.78e-19 82.8
Msa0818030 MtrunA17_Chr6g0464211 37.398 123 72 1 3 120 900 1022 2.12e-19 82.4
Msa0818030 MtrunA17_Chr6g0464141 37.903 124 71 1 3 120 901 1024 2.47e-19 82.0
Msa0818030 MtrunA17_Chr6g0472051 40.404 99 59 0 3 101 105 203 2.52e-19 79.3
Msa0818030 MtrunA17_Chr8g0352041 56.452 62 27 0 15 76 48 109 2.93e-19 76.6
Msa0818030 MtrunA17_Chr5g0419221 33.333 123 77 1 3 120 900 1022 7.55e-19 80.9
Msa0818030 MtrunA17_Chr8g0362391 35.897 117 70 1 3 119 216 327 8.71e-19 79.7
Msa0818030 MtrunA17_Chr5g0403401 36.585 123 73 1 3 120 889 1011 8.72e-19 80.5
Msa0818030 MtrunA17_Chr5g0408821 35.833 120 72 1 3 117 294 413 9.52e-19 80.1
Msa0818030 MtrunA17_Chr5g0408571 37.097 124 71 2 3 120 379 501 1.33e-18 80.1
Msa0818030 MtrunA17_Chr6g0464161 37.398 123 72 1 3 120 630 752 1.38e-18 80.1
Msa0818030 MtrunA17_Chr6g0464171 36.585 123 73 1 3 120 901 1023 1.52e-18 80.1
Msa0818030 MtrunA17_Chr5g0408611 37.795 127 66 2 3 120 888 1010 1.77e-18 79.7
Msa0818030 MtrunA17_Chr5g0408421 34.959 123 75 1 3 120 882 1004 6.63e-18 78.2
Msa0818030 MtrunA17_Chr1g0196031 36.885 122 71 2 3 118 935 1056 7.33e-18 78.2
Msa0818030 MtrunA17_Chr8g0363261 35.043 117 71 2 3 119 274 385 5.01e-17 75.5
Msa0818030 MtrunA17_Chr8g0363111 34.167 120 68 2 3 119 874 985 5.88e-17 75.5
Msa0818030 MtrunA17_Chr2g0284121 34.513 113 69 2 3 115 1103 1210 7.30e-17 75.1
Msa0818030 MtrunA17_Chr8g0360851 33.333 117 73 1 3 119 898 1009 7.58e-17 75.1
Msa0818030 MtrunA17_Chr3g0127701 30.435 138 75 1 3 119 860 997 7.94e-17 75.1
Msa0818030 MtrunA17_Chr5g0408431 36.585 123 73 1 3 120 899 1021 1.32e-16 74.3
Msa0818030 MtrunA17_Chr8g0363371 34.483 116 65 2 3 115 718 825 1.77e-16 73.9
Msa0818030 MtrunA17_Chr8g0362431 32.743 113 71 1 3 115 672 779 1.85e-16 73.9
Msa0818030 MtrunA17_Chr6g0464201 42.683 82 47 0 3 84 40 121 1.91e-16 69.7
Msa0818030 MtrunA17_Chr5g0407241 34.426 122 75 1 3 119 906 1027 1.98e-16 73.9
Msa0818030 MtrunA17_Chr7g0241921 32.824 131 73 2 3 118 872 1002 2.81e-16 73.6
Msa0818030 MtrunA17_Chr8g0363601 34.513 113 69 2 3 115 664 771 3.09e-16 73.2
Msa0818030 MtrunA17_Chr8g0362871 33.333 117 73 1 3 119 664 775 3.24e-16 73.2
Msa0818030 MtrunA17_Chr8g0363401 33.628 113 70 1 3 115 679 786 3.28e-16 73.2
Msa0818030 MtrunA17_Chr8g0363691 34.513 113 69 2 3 115 1138 1245 3.63e-16 73.2
Msa0818030 MtrunA17_Chr3g0095201 31.858 113 72 2 3 115 878 985 3.64e-16 73.2
Msa0818030 MtrunA17_Chr8g0363061 35.537 121 67 3 3 120 870 982 3.97e-16 73.2
Msa0818030 MtrunA17_Chr4g0013491 33.333 117 72 1 3 119 627 737 5.00e-16 72.8
Msa0818030 MtrunA17_Chr8g0362911 32.479 117 74 2 3 119 613 724 5.24e-16 72.8
Msa0818030 MtrunA17_Chr8g0362941 33.333 117 65 3 3 115 630 737 7.52e-16 72.4
Msa0818030 MtrunA17_Chr8g0363281 32.743 113 71 2 3 115 647 754 7.76e-16 72.0
Msa0818030 MtrunA17_Chr8g0362961 33.884 121 69 3 3 120 1114 1226 7.80e-16 72.4
Msa0818030 MtrunA17_Chr8g0363501 34.483 116 65 2 3 115 410 517 8.18e-16 72.0
Msa0818030 MtrunA17_Chr8g0363121 31.858 113 72 1 3 115 674 781 8.49e-16 72.0
Msa0818030 MtrunA17_Chr8g0363661 34.513 113 69 2 3 115 727 834 9.97e-16 72.0
Msa0818030 MtrunA17_Chr8g0362841 34.483 116 65 3 3 115 716 823 1.36e-15 71.6
Msa0818030 MtrunA17_Chr8g0363191 35.593 118 65 3 5 119 593 702 1.39e-15 71.6
Msa0818030 MtrunA17_Chr1g0176301 34.167 120 68 3 3 119 629 740 1.87e-15 71.2
Msa0818030 MtrunA17_Chr3g0127671 28.986 138 77 1 3 119 905 1042 2.81e-15 70.5
Msa0818030 MtrunA17_Chr8g0361231 33.913 115 67 2 3 115 966 1073 3.07e-15 70.5
Msa0818030 MtrunA17_Chr8g0363641 31.897 116 74 2 4 119 142 252 4.44e-15 68.9
Msa0818030 MtrunA17_Chr8g0363241 32.759 116 67 2 3 115 632 739 5.14e-15 69.7
Msa0818030 MtrunA17_Chr8g0362931 33.621 116 66 2 3 115 1059 1166 6.26e-15 69.7
Msa0818030 MtrunA17_Chr8g0362981 31.858 113 72 1 3 115 630 737 1.11e-14 68.9
Msa0818030 MtrunA17_Chr2g0284191 33.333 117 66 3 3 119 733 837 1.51e-14 68.6
Msa0818030 MtrunA17_Chr1g0196051 47.541 61 32 0 3 63 5 65 2.42e-14 62.8
Msa0818030 MtrunA17_Chr2g0284151 34.188 117 65 3 3 119 687 791 2.44e-14 67.8
Msa0818030 MtrunA17_Chr0c09g0493531 33.333 117 66 3 3 119 742 846 2.55e-14 67.8
Msa0818030 MtrunA17_Chr1g0196001 46.774 62 33 0 3 64 895 956 8.44e-14 66.2
Msa0818030 MtrunA17_Chr8g0363221 30.435 115 69 2 4 115 745 851 5.17e-13 64.3
Msa0818030 MtrunA17_Chr4g0073641 33.898 118 76 2 3 118 853 970 9.43e-13 63.5
Msa0818030 MtrunA17_Chr7g0262141 33.043 115 69 3 3 117 886 992 3.15e-12 62.0
Msa0818030 MtrunA17_Chr8g0380951 26.496 117 86 0 3 119 858 974 2.68e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0818030 AT3G47580.1 39.167 120 62 2 3 119 892 1003 2.54e-25 99.8
Msa0818030 AT3G47110.1 39.831 118 65 2 3 119 908 1020 3.41e-23 93.6
Msa0818030 AT3G47570.1 40.833 120 60 2 3 119 891 1002 4.98e-23 93.2
Msa0818030 AT3G47090.1 36.752 117 69 1 3 119 890 1001 3.84e-20 85.1
Msa0818030 AT5G20480.1 36.752 117 58 2 3 119 901 1001 4.03e-19 82.0
Msa0818030 AT5G20480.2 36.752 117 58 2 3 119 901 1001 4.03e-19 82.0
Msa0818030 AT5G39390.1 35.897 117 59 2 3 119 398 498 2.17e-16 73.9
Msa0818030 AT2G24130.1 29.661 118 83 0 3 120 845 962 6.37e-14 67.0
Msa0818030 AT2G24130.2 29.661 118 83 0 3 120 860 977 6.82e-14 67.0

Find 17 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTGTTAGAGATGCTTAC+TGG 0.311174 5_3:+53477666 Msa0818030:CDS
AGAAGGAATTCTTGATATAG+TGG 0.358148 5_3:+53477758 Msa0818030:CDS
CTAGTGATGTTTGCTAAAAT+AGG 0.420102 5_3:+53477849 Msa0818030:CDS
TGTTGTGGAAAACAACATAA+AGG 0.479381 5_3:+53477821 Msa0818030:CDS
TTGTGAGCATTCGATGAGTA+GGG 0.501770 5_3:-53477893 None:intergenic
TTTGTGAGCATTCGATGAGT+AGG 0.504715 5_3:-53477894 None:intergenic
AGGTGGTATGGTATCACCAC+AGG 0.524921 5_3:+53477620 Msa0818030:CDS
TGTAAGATGAAAATTCAAGA+AGG 0.533141 5_3:+53477741 Msa0818030:CDS
AGAGTATGGATCAGGTGGTA+TGG 0.541407 5_3:+53477608 Msa0818030:intron
GTTTGAATAGAGTATGGATC+AGG 0.543606 5_3:+53477600 Msa0818030:intron
TAAGCAGAAGTTGCTCTGCT+AGG 0.556440 5_3:+53477944 Msa0818030:CDS
TCACAAAAGATGTTATCTGT+TGG 0.563725 5_3:-53477696 None:intergenic
TCGATGAGTAGGGAATTCTT+CGG 0.594088 5_3:-53477883 None:intergenic
TGAATAGAGTATGGATCAGG+TGG 0.614600 5_3:+53477603 Msa0818030:intron
TGACAATCAAACACATGTTG+TGG 0.662742 5_3:+53477806 Msa0818030:CDS
GGTGGTATGGTATCACCACA+GGG 0.719298 5_3:+53477621 Msa0818030:CDS
TAGCTATAGATATCTCCCTG+TGG 0.746367 5_3:-53477636 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAGACAAAAAAAAGAAGA+AGG - chr5_3:53477569-53477588 None:intergenic 20.0%
! ACAAAAAAAAGAAGAAGGAA+TGG - chr5_3:53477564-53477583 None:intergenic 25.0%
! TGTAAGATGAAAATTCAAGA+AGG + chr5_3:53477741-53477760 Msa0818030:CDS 25.0%
! CACACATTTTTGACAACATA+CGG - chr5_3:53477512-53477531 None:intergenic 30.0%
!! GTTGTTGTTTGAATAGAGTA+TGG + chr5_3:53477594-53477613 Msa0818030:intron 30.0%
TCACAAAAGATGTTATCTGT+TGG - chr5_3:53477699-53477718 None:intergenic 30.0%
AGAAGGAATTCTTGATATAG+TGG + chr5_3:53477758-53477777 Msa0818030:CDS 30.0%
TGTTGTGGAAAACAACATAA+AGG + chr5_3:53477821-53477840 Msa0818030:CDS 30.0%
! CTAGTGATGTTTGCTAAAAT+AGG + chr5_3:53477849-53477868 Msa0818030:CDS 30.0%
GTTTGAATAGAGTATGGATC+AGG + chr5_3:53477600-53477619 Msa0818030:intron 35.0%
TGACAATCAAACACATGTTG+TGG + chr5_3:53477806-53477825 Msa0818030:CDS 35.0%
TGAATAGAGTATGGATCAGG+TGG + chr5_3:53477603-53477622 Msa0818030:intron 40.0%
TAGCTATAGATATCTCCCTG+TGG - chr5_3:53477639-53477658 None:intergenic 40.0%
CTTCTGTTAGAGATGCTTAC+TGG + chr5_3:53477666-53477685 Msa0818030:CDS 40.0%
TCGATGAGTAGGGAATTCTT+CGG - chr5_3:53477886-53477905 None:intergenic 40.0%
TTGTGAGCATTCGATGAGTA+GGG - chr5_3:53477896-53477915 None:intergenic 40.0%
TTTGTGAGCATTCGATGAGT+AGG - chr5_3:53477897-53477916 None:intergenic 40.0%
AGAGTATGGATCAGGTGGTA+TGG + chr5_3:53477608-53477627 Msa0818030:intron 45.0%
AGGTGGTATGGTATCACCAC+AGG + chr5_3:53477620-53477639 Msa0818030:CDS 50.0%
GGTGGTATGGTATCACCACA+GGG + chr5_3:53477621-53477640 Msa0818030:CDS 50.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 53477504 53477965 53477504 ID=Msa0818030;Name=Msa0818030
chr5_3 mRNA 53477504 53477965 53477504 ID=Msa0818030-mRNA-1;Parent=Msa0818030;Name=Msa0818030-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|0|0|0.5|1|1|2|0|120
chr5_3 exon 53477504 53477510 53477504 ID=Msa0818030-mRNA-1:exon:16134;Parent=Msa0818030-mRNA-1
chr5_3 exon 53477610 53477965 53477610 ID=Msa0818030-mRNA-1:exon:16135;Parent=Msa0818030-mRNA-1
chr5_3 CDS 53477504 53477510 53477504 ID=Msa0818030-mRNA-1:cds;Parent=Msa0818030-mRNA-1
chr5_3 CDS 53477610 53477965 53477610 ID=Msa0818030-mRNA-1:cds;Parent=Msa0818030-mRNA-1
Gene Sequence

>Msa0818030

ATGCACCAGTATGGATCAGGTGGTATGGTATCACCACAGGGAGATATCTATAGCTATGAAATTCTTCTGTTAGAGATGCTTACTGGAAAGAGACCAACAGATAACATCTTTTGTGAGAATCTAAGCTTACACAAATTTTGTAAGATGAAAATTCAAGAAGGAATTCTTGATATAGTGGATTCATGCTTGCTTATGTCATTTGCTGACAATCAAACACATGTTGTGGAAAACAACATAAAGGAGTGTCTAGTGATGTTTGCTAAAATAGGAGTTGCATGTTCCGAAGAATTCCCTACTCATCGAATGCTCACAAAAGATGTTATAGTGAAGTTGCTTGAAATTAAGCAGAAGTTGCTCTGCTAG
Protein sequence

>Msa0818030

MHQYGSGGMVSPQGDIYSYEILLLEMLTGKRPTDNIFCENLSLHKFCKMKIQEGILDIVDSCLLMSFADNQTHVVENNIKECLVMFAKIGVACSEEFPTHRMLTKDVIVKLLEIKQKLLC*