AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0839940

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0839940 MtrunA17_Chr5g0408621 79.508 122 24 1 1 122 938 1058 4.32e-62 204
Msa0839940 MtrunA17_Chr5g0403401 70.866 127 36 1 1 127 892 1017 7.28e-58 192
Msa0839940 MtrunA17_Chr5g0408611 77.869 122 26 1 1 122 891 1011 1.99e-56 188
Msa0839940 MtrunA17_Chr5g0408501 64.800 125 43 1 1 125 1 124 1.39e-53 164
Msa0839940 MtrunA17_Chr5g0408421 63.780 127 45 1 1 127 885 1010 2.99e-52 176
Msa0839940 MtrunA17_Chr5g0407241 66.406 128 42 1 1 128 909 1035 1.53e-51 174
Msa0839940 MtrunA17_Chr5g0408811 68.852 122 34 2 1 122 875 992 1.61e-51 174
Msa0839940 MtrunA17_Chr6g0464161 68.033 122 38 1 1 122 633 753 3.19e-51 172
Msa0839940 MtrunA17_Chr6g0464211 67.213 122 39 1 1 122 903 1023 5.71e-51 173
Msa0839940 MtrunA17_Chr5g0408741 69.106 123 31 2 1 122 808 924 2.39e-50 171
Msa0839940 MtrunA17_Chr2g0300201 67.213 122 39 1 1 122 904 1024 6.93e-50 170
Msa0839940 MtrunA17_Chr5g0408571 65.574 122 41 1 1 122 382 502 7.13e-50 166
Msa0839940 MtrunA17_Chr6g0464171 66.393 122 40 1 1 122 904 1024 9.00e-50 169
Msa0839940 MtrunA17_Chr5g0419221 64.516 124 43 1 1 124 903 1025 9.67e-50 169
Msa0839940 MtrunA17_Chr6g0464141 66.667 123 39 2 1 122 904 1025 8.26e-49 167
Msa0839940 MtrunA17_Chr5g0408581 67.213 122 39 1 1 122 904 1024 1.36e-48 166
Msa0839940 MtrunA17_Chr5g0408511 68.852 122 31 2 1 122 900 1014 1.69e-48 166
Msa0839940 MtrunA17_Chr5g0408801 65.574 122 41 1 1 122 904 1024 1.95e-48 166
Msa0839940 MtrunA17_Chr5g0408431 64.754 122 42 1 1 122 902 1022 1.54e-45 157
Msa0839940 MtrunA17_Chr5g0408821 62.069 116 43 1 1 116 297 411 6.01e-43 145
Msa0839940 MtrunA17_Chr6g0472051 61.765 102 33 1 1 102 108 203 4.41e-40 133
Msa0839940 MtrunA17_Chr5g0408401 54.839 124 54 1 1 124 667 788 2.48e-39 139
Msa0839940 MtrunA17_Chr8g0369631 53.968 126 57 1 1 126 1 125 7.29e-38 125
Msa0839940 MtrunA17_Chr1g0196011 54.167 120 53 2 1 119 730 848 5.71e-36 130
Msa0839940 MtrunA17_Chr1g0196031 50.420 119 59 0 1 119 938 1056 2.26e-34 125
Msa0839940 MtrunA17_Chr3g0113221 52.459 122 54 2 1 122 893 1010 1.60e-33 123
Msa0839940 MtrunA17_Chr8g0367351 49.167 120 59 2 1 119 899 1017 1.17e-32 120
Msa0839940 MtrunA17_Chr8g0366461 52.586 116 46 2 1 116 898 1004 5.82e-32 119
Msa0839940 MtrunA17_Chr6g0464201 59.091 88 30 1 1 88 43 124 1.67e-31 108
Msa0839940 MtrunA17_Chr5g0436851 43.697 119 59 3 2 119 43 154 4.75e-25 93.2
Msa0839940 MtrunA17_Chr2g0314001 44.538 119 58 3 2 119 896 1007 1.16e-23 95.1
Msa0839940 MtrunA17_Chr1g0159871 46.729 107 51 2 2 108 823 923 2.96e-23 94.0
Msa0839940 MtrunA17_Chr2g0314021 43.697 119 59 3 2 119 896 1007 1.59e-22 92.0
Msa0839940 MtrunA17_Chr5g0436931 40.171 117 64 2 5 121 2 112 1.33e-21 83.2
Msa0839940 MtrunA17_Chr5g0436941 42.500 120 56 3 1 117 889 998 3.71e-21 88.2
Msa0839940 MtrunA17_Chr5g0437331 42.149 121 62 3 2 121 893 1006 9.69e-21 87.0
Msa0839940 MtrunA17_Chr7g0248261 42.017 119 61 3 2 119 847 958 1.22e-20 86.7
Msa0839940 MtrunA17_Chr7g0241921 35.659 129 72 2 1 119 875 1002 2.36e-20 85.9
Msa0839940 MtrunA17_Chr1g0196001 44.944 89 49 0 1 89 898 986 2.58e-20 85.5
Msa0839940 MtrunA17_Chr5g0409241 77.083 48 11 0 1 48 580 627 6.51e-20 84.3
Msa0839940 MtrunA17_Chr5g0436871 41.176 119 62 3 2 119 98 209 9.28e-20 80.9
Msa0839940 MtrunA17_Chr5g0436841 41.803 122 54 2 2 120 942 1049 9.38e-20 84.0
Msa0839940 MtrunA17_Chr5g0436911 41.880 117 60 3 2 117 178 287 1.28e-19 82.0
Msa0839940 MtrunA17_Chr1g0159881 41.818 110 52 2 2 108 364 464 3.87e-19 82.0
Msa0839940 MtrunA17_Chr1g0196051 55.738 61 27 0 1 61 8 68 1.71e-18 73.9
Msa0839940 MtrunA17_Chr5g0436861 37.931 116 66 1 2 117 896 1005 2.68e-17 77.0
Msa0839940 MtrunA17_Chr2g0314031 40.336 119 54 4 2 119 892 994 5.92e-17 76.3
Msa0839940 MtrunA17_Chr8g0360851 33.621 116 66 2 5 120 905 1009 2.32e-16 74.3
Msa0839940 MtrunA17_Chr8g0363061 34.746 118 66 2 5 122 877 983 2.00e-15 71.6
Msa0839940 MtrunA17_Chr8g0363641 32.203 118 69 2 5 122 148 254 4.72e-15 69.3
Msa0839940 MtrunA17_Chr8g0362961 33.898 118 67 2 5 122 1121 1227 5.21e-15 70.5
Msa0839940 MtrunA17_Chr4g0073641 32.203 118 72 2 1 116 856 967 6.34e-15 70.1
Msa0839940 MtrunA17_Chr8g0362911 33.621 116 66 2 5 120 620 724 6.52e-15 70.1
Msa0839940 MtrunA17_Chr8g0362391 30.508 118 71 2 5 122 223 329 6.43e-14 67.0
Msa0839940 MtrunA17_Chr8g0363111 32.759 116 67 3 5 120 881 985 7.12e-14 67.4
Msa0839940 MtrunA17_Chr8g0380951 28.333 120 80 2 1 120 861 974 1.04e-13 66.6
Msa0839940 MtrunA17_Chr8g0363501 32.143 112 65 2 5 116 417 517 1.07e-13 66.6
Msa0839940 MtrunA17_Chr3g0095201 31.034 116 69 1 5 120 885 989 1.72e-13 66.2
Msa0839940 MtrunA17_Chr3g0127671 26.471 136 83 2 1 120 908 1042 1.88e-13 65.9
Msa0839940 MtrunA17_Chr8g0362841 33.654 104 58 2 5 108 723 815 2.26e-13 65.9
Msa0839940 MtrunA17_Chr8g0363191 31.356 118 70 2 5 122 598 704 2.85e-13 65.5
Msa0839940 MtrunA17_Chr8g0362941 31.731 104 60 2 5 108 637 729 3.22e-13 65.5
Msa0839940 MtrunA17_Chr8g0363371 31.731 104 60 2 5 108 725 817 3.36e-13 65.5
Msa0839940 MtrunA17_Chr8g0380941 28.696 115 70 2 1 112 892 997 4.03e-13 65.1
Msa0839940 MtrunA17_Chr8g0363401 30.769 104 61 2 5 108 686 778 5.37e-13 64.7
Msa0839940 MtrunA17_Chr8g0363261 31.356 118 70 2 5 122 281 387 6.71e-13 64.3
Msa0839940 MtrunA17_Chr8g0362931 29.808 104 62 2 5 108 1066 1158 1.02e-12 63.9
Msa0839940 MtrunA17_Chr8g0362871 28.814 118 73 2 5 122 671 777 1.20e-12 63.5
Msa0839940 MtrunA17_Chr8g0361231 31.034 116 69 2 5 120 973 1077 1.98e-12 63.2
Msa0839940 MtrunA17_Chr8g0362431 28.846 104 63 1 5 108 679 771 2.14e-12 63.2
Msa0839940 MtrunA17_Chr8g0363601 30.769 104 61 2 5 108 671 763 2.26e-12 62.8
Msa0839940 MtrunA17_Chr1g0176301 31.776 107 56 2 5 108 636 728 2.89e-12 62.8
Msa0839940 MtrunA17_Chr8g0363691 30.769 104 61 2 5 108 1145 1237 3.37e-12 62.4
Msa0839940 MtrunA17_Chr8g0363661 30.769 104 61 2 5 108 734 826 4.23e-12 62.0
Msa0839940 MtrunA17_Chr2g0284121 30.435 115 69 1 5 119 1110 1213 4.32e-12 62.0
Msa0839940 MtrunA17_Chr8g0363241 28.846 104 63 2 5 108 639 731 4.39e-12 62.0
Msa0839940 MtrunA17_Chr8g0363281 28.846 104 63 2 5 108 654 746 1.08e-11 60.8
Msa0839940 MtrunA17_Chr3g0127701 27.407 135 83 2 1 120 863 997 1.09e-11 60.8
Msa0839940 MtrunA17_Chr8g0363121 27.273 121 76 2 5 125 681 789 1.38e-11 60.8
Msa0839940 MtrunA17_Chr4g0013491 29.915 117 68 2 5 120 634 737 1.47e-11 60.5
Msa0839940 MtrunA17_Chr8g0363221 28.846 104 63 2 5 108 751 843 2.85e-11 59.7
Msa0839940 MtrunA17_Chr8g0362981 28.846 104 63 1 5 108 637 729 4.73e-11 59.3
Msa0839940 MtrunA17_Chr2g0284191 27.586 116 66 2 5 120 740 837 5.22e-11 58.9
Msa0839940 MtrunA17_Chr0c09g0493531 26.724 116 67 1 5 120 749 846 6.85e-11 58.5
Msa0839940 MtrunA17_Chr2g0284151 28.448 116 65 2 5 120 694 791 7.35e-11 58.5
Msa0839940 MtrunA17_Chr8g0363321 31.132 106 62 2 17 122 1 95 8.54e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0839940 AT3G47570.1 36.508 126 69 3 1 126 894 1008 1.91e-18 80.9
Msa0839940 AT3G47580.1 37.815 119 63 2 1 119 895 1002 5.75e-18 79.3
Msa0839940 AT2G24130.1 32.258 124 72 2 1 121 848 962 6.14e-18 79.3
Msa0839940 AT2G24130.2 32.258 124 72 2 1 121 863 977 6.45e-18 79.3
Msa0839940 AT3G47110.1 37.815 119 64 3 1 119 911 1019 7.85e-18 79.0
Msa0839940 AT3G47090.1 36.134 119 65 3 1 119 893 1000 1.36e-17 78.2
Msa0839940 AT5G39390.1 36.364 121 55 1 1 121 401 499 2.54e-16 74.7
Msa0839940 AT5G20480.1 35.537 121 56 1 1 121 904 1002 3.21e-16 74.3
Msa0839940 AT5G20480.2 35.537 121 56 1 1 121 904 1002 3.21e-16 74.3

Find 23 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACAATCTTATACATATTT+TGG 0.128114 5_4:-15348156 Msa0839940:CDS
ATCAGGAAGGCCTTTCTTTC+TGG 0.133261 5_4:-15347954 Msa0839940:intron
AGAAAGTTTCAAGGTCATTT+AGG 0.199604 5_4:-15347755 None:intergenic
ATTATATTCATTCTTTCTTT+TGG 0.265564 5_4:+15348002 None:intergenic
AAAAGAAAGAATGAATATAA+TGG 0.369108 5_4:-15348000 Msa0839940:CDS
ACCAAGCATTTATCTACAAT+TGG 0.379453 5_4:+15348065 None:intergenic
ATGGTGATATGTATAGCTTC+GGG 0.402332 5_4:-15348274 Msa0839940:CDS
TATGGTGATATGTATAGCTT+CGG 0.415997 5_4:-15348275 Msa0839940:CDS
TAAGATTGGACTTGCTTGTT+CGG 0.416004 5_4:-15348033 Msa0839940:CDS
AAAATATGTATAAGATTGTC+AGG 0.436658 5_4:+15348158 None:intergenic
ATAGAGAGTTGAGCATAATC+AGG 0.451744 5_4:-15347971 Msa0839940:CDS
TCCAATTGTAGATAAATGCT+TGG 0.465185 5_4:-15348066 Msa0839940:CDS
GGTTCAGAAATATCCACATA+TGG 0.485598 5_4:-15348293 Msa0839940:CDS
GCTATACATATCACCATATG+TGG 0.520089 5_4:+15348280 None:intergenic
ACGTATAAAATGTTTGAAGA+TGG 0.536177 5_4:-15348215 Msa0839940:CDS
TGAGGTGAAAGAAAGTTTCA+AGG 0.540953 5_4:-15347764 Msa0839940:CDS
GATTGGACTTGCTTGTTCGG+TGG 0.544774 5_4:-15348030 Msa0839940:CDS
CTTATGCTAGAAATGCTGAC+AGG 0.602775 5_4:-15348248 Msa0839940:CDS
AATTGGAGTGAAATTACCAC+TGG 0.618962 5_4:+15348082 None:intergenic
AGAGTTGAGCATAATCAGGA+AGG 0.632385 5_4:-15347967 Msa0839940:CDS
TTCAGGTGTTCACAGTAGTG+AGG 0.641060 5_4:-15347782 Msa0839940:intron
ATAGAAGATGGAGTCACCAG+TGG 0.684678 5_4:-15348098 Msa0839940:CDS
TGGTGATATGTATAGCTTCG+GGG 0.688856 5_4:-15348273 Msa0839940:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTATATTCATTCTTTCTTT+TGG + chr5_4:15348053-15348072 None:intergenic 15.0%
!! AAAAGAAAGAATGAATATAA+TGG - chr5_4:15348052-15348071 Msa0839940:CDS 15.0%
!! AAAATATGTATAAGATTGTC+AGG + chr5_4:15347897-15347916 None:intergenic 20.0%
!!! TGACAATCTTATACATATTT+TGG - chr5_4:15347896-15347915 Msa0839940:intron 20.0%
!!! ATTTTTGCTTCTTCATTTTT+TGG + chr5_4:15347936-15347955 None:intergenic 20.0%
!! TCTTCAAACATTTTATACGT+CGG + chr5_4:15347837-15347856 None:intergenic 25.0%
! ACGTATAAAATGTTTGAAGA+TGG - chr5_4:15347837-15347856 Msa0839940:intron 25.0%
!! TTTTCAATTGCATAACAAGA+TGG + chr5_4:15348207-15348226 None:intergenic 25.0%
!! ATCTTTGTATTTTGTAGTTG+AGG + chr5_4:15348232-15348251 None:intergenic 25.0%
!!! ATAGTTTTCTTATCGATTTC+AGG - chr5_4:15348253-15348272 Msa0839940:CDS 25.0%
TATGGTGATATGTATAGCTT+CGG - chr5_4:15347777-15347796 Msa0839940:CDS 30.0%
GAAGAAGCAAAAATAGAAGA+TGG - chr5_4:15347942-15347961 Msa0839940:intron 30.0%
TCCAATTGTAGATAAATGCT+TGG - chr5_4:15347986-15348005 Msa0839940:CDS 30.0%
ACCAAGCATTTATCTACAAT+TGG + chr5_4:15347990-15348009 None:intergenic 30.0%
!!! TTGGTTTCGCTTTTTAAGAT+TGG - chr5_4:15348005-15348024 Msa0839940:CDS 30.0%
AAAAATCTCACCAGAAAGAA+AGG + chr5_4:15348111-15348130 None:intergenic 30.0%
GGTTCAGAAATATCCACATA+TGG - chr5_4:15347759-15347778 Msa0839940:CDS 35.0%
GCTATACATATCACCATATG+TGG + chr5_4:15347775-15347794 None:intergenic 35.0%
ATGGTGATATGTATAGCTTC+GGG - chr5_4:15347778-15347797 Msa0839940:CDS 35.0%
AATTGGAGTGAAATTACCAC+TGG + chr5_4:15347973-15347992 None:intergenic 35.0%
! TAAGATTGGACTTGCTTGTT+CGG - chr5_4:15348019-15348038 Msa0839940:CDS 35.0%
ATAGAGAGTTGAGCATAATC+AGG - chr5_4:15348081-15348100 Msa0839940:CDS 35.0%
TAAGAGCTAAGCAATGACTT+AGG + chr5_4:15348147-15348166 None:intergenic 35.0%
TGAGGTGAAAGAAAGTTTCA+AGG - chr5_4:15348288-15348307 Msa0839940:CDS 35.0%
TGGTGATATGTATAGCTTCG+GGG - chr5_4:15347779-15347798 Msa0839940:CDS 40.0%
CTTATGCTAGAAATGCTGAC+AGG - chr5_4:15347804-15347823 Msa0839940:intron 40.0%
AGAGTTGAGCATAATCAGGA+AGG - chr5_4:15348085-15348104 Msa0839940:CDS 40.0%
ATAGAAGATGGAGTCACCAG+TGG - chr5_4:15347954-15347973 Msa0839940:intron 45.0%
ATCAGGAAGGCCTTTCTTTC+TGG - chr5_4:15348098-15348117 Msa0839940:CDS 45.0%
TTCAGGTGTTCACAGTAGTG+AGG - chr5_4:15348270-15348289 Msa0839940:CDS 45.0%
! GATTGGACTTGCTTGTTCGG+TGG - chr5_4:15348022-15348041 Msa0839940:CDS 50.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 15347756 15348318 15347756 ID=Msa0839940;Name=Msa0839940
chr5_4 mRNA 15347756 15348318 15347756 ID=Msa0839940-mRNA-1;Parent=Msa0839940;Name=Msa0839940-mRNA-1;_AED=0.72;_eAED=0.72;_QI=0|0|0|0.5|1|1|2|0|135
chr5_4 exon 15347955 15348318 15347955 ID=Msa0839940-mRNA-1:exon:6604;Parent=Msa0839940-mRNA-1
chr5_4 exon 15347756 15347799 15347756 ID=Msa0839940-mRNA-1:exon:6603;Parent=Msa0839940-mRNA-1
chr5_4 CDS 15347955 15348318 15347955 ID=Msa0839940-mRNA-1:cds;Parent=Msa0839940-mRNA-1
chr5_4 CDS 15347756 15347799 15347756 ID=Msa0839940-mRNA-1:cds;Parent=Msa0839940-mRNA-1
Gene Sequence

>Msa0839940

ATGGGTTCAGAAATATCCACATATGGTGATATGTATAGCTTCGGGGTGCTTATGCTAGAAATGCTGACAGGAAAAAGACCGACGTATAAAATGTTTGAAGATGGTCAAAACTTGCATATGTTTGTAAAAAGTTCATTTCCTGACAATCTTATACATATTTTGGACTCACATCTTGTTCCAAAAAATGAAGAAGCAAAAATAGAAGATGGAGTCACCAGTGGTAATTTCACTCCAATTGTAGATAAATGCTTGGTTTCGCTTTTTAAGATTGGACTTGCTTGTTCGGTGGAATCACCAAAAGAAAGAATGAATATAATGGATGTTAATAGAGAGTTGAGCATAATCAGGAAGGCCTTTCTTTCTGGTGTTCACAGTAGTGAGGTGAAAGAAAGTTTCAAGGTCATTTAG
Protein sequence

>Msa0839940

MGSEISTYGDMYSFGVLMLEMLTGKRPTYKMFEDGQNLHMFVKSSFPDNLIHILDSHLVPKNEEAKIEDGVTSGNFTPIVDKCLVSLFKIGLACSVESPKERMNIMDVNRELSIIRKAFLSGVHSSEVKESFKVI*