AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0594090

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0594090 MtrunA17_Chr4g0012891 95.161 124 5 1 1 123 1 124 5.65e-81 234
Msa0594090 MtrunA17_Chr7g0244841 45.000 120 60 2 4 123 3 116 5.02e-30 105
Msa0594090 MtrunA17_Chr4g0012951 47.788 113 53 3 9 121 5 111 3.20e-29 103
Msa0594090 MtrunA17_Chr7g0244831 43.333 120 63 2 4 123 3 117 2.77e-28 100
Msa0594090 MtrunA17_Chr4g0012901 39.024 123 71 1 1 123 1 119 8.42e-26 94.7
Msa0594090 MtrunA17_Chr4g0013001 43.363 113 58 3 9 121 5 111 3.28e-25 93.2
Msa0594090 MtrunA17_Chr4g0012961 43.363 113 58 3 9 121 5 111 3.90e-25 92.8
Msa0594090 MtrunA17_Chr7g0244691 42.609 115 61 2 9 123 8 117 1.37e-24 91.7
Msa0594090 MtrunA17_Chr4g0012991 43.363 113 58 3 9 121 60 166 5.46e-24 91.7
Msa0594090 MtrunA17_Chr4g0013251 42.857 119 57 4 5 123 7 114 2.40e-22 85.9
Msa0594090 MtrunA17_Chr2g0309241 39.450 109 60 2 14 122 10 112 3.21e-22 85.5
Msa0594090 MtrunA17_Chr7g0244681 40.833 120 66 2 4 123 3 117 9.68e-22 84.3
Msa0594090 MtrunA17_Chr4g0013261 43.860 114 57 3 10 123 8 114 7.23e-21 82.0
Msa0594090 MtrunA17_Chr4g0013211 38.261 115 65 3 9 123 5 113 7.64e-21 81.6
Msa0594090 MtrunA17_Chr1g0165761 43.802 121 61 3 4 123 3 117 8.77e-21 81.6
Msa0594090 MtrunA17_Chr7g0244741 42.623 122 63 3 4 123 3 119 9.54e-21 81.6
Msa0594090 MtrunA17_Chr7g0244671 38.017 121 69 3 4 123 3 118 2.47e-20 81.6
Msa0594090 MtrunA17_Chr7g0244821 40.164 122 63 3 4 123 3 116 3.89e-20 80.5
Msa0594090 MtrunA17_Chr7g0244641 35.537 121 72 3 4 123 3 118 7.15e-20 79.3
Msa0594090 MtrunA17_Chr7g0244811 37.600 125 70 4 1 123 1 119 3.43e-18 75.1
Msa0594090 MtrunA17_Chr7g0244761 35.833 120 72 2 4 123 28 142 9.02e-18 74.7
Msa0594090 MtrunA17_Chr7g0244721 35.537 121 72 3 4 123 3 118 1.20e-17 73.9
Msa0594090 MtrunA17_Chr7g0244791 35.294 119 72 2 5 123 9 122 3.89e-17 72.4
Msa0594090 MtrunA17_Chr7g0244661 38.843 121 62 4 4 123 3 112 6.66e-17 71.6
Msa0594090 MtrunA17_Chr7g0244751 35.833 120 72 2 4 123 3 117 8.24e-16 68.9
Msa0594090 MtrunA17_Chr7g0244651 36.885 122 71 3 4 123 3 120 7.61e-15 66.6
Msa0594090 MtrunA17_Chr7g0233431 30.108 93 61 1 31 123 41 129 2.44e-13 62.8
Msa0594090 MtrunA17_Chr3g0095991 28.455 123 82 2 2 123 3 120 6.83e-13 61.6
Msa0594090 MtrunA17_Chr3g0095951 28.455 123 82 2 2 123 3 120 2.37e-12 60.1
Msa0594090 MtrunA17_Chr3g0107481 30.645 124 73 5 1 123 1 112 3.24e-12 59.7
Msa0594090 MtrunA17_Chr3g0101431 29.839 124 81 2 1 123 1 119 4.08e-12 59.3
Msa0594090 MtrunA17_Chr3g0096021 27.642 123 83 2 2 123 3 120 9.31e-12 58.5
Msa0594090 MtrunA17_Chr3g0096031 27.642 123 83 2 2 123 3 120 9.82e-12 58.5
Msa0594090 MtrunA17_Chr3g0105001 29.412 119 78 2 6 123 7 120 2.15e-11 57.4
Msa0594090 MtrunA17_Chr3g0104971 29.412 119 78 2 6 123 7 120 3.54e-11 57.0
Msa0594090 MtrunA17_Chr3g0104981 29.412 119 78 2 6 123 7 120 4.19e-11 56.6
Msa0594090 MtrunA17_Chr3g0105021 29.412 119 78 2 6 123 7 120 4.71e-11 56.6
Msa0594090 MtrunA17_Chr3g0105011 29.412 119 78 2 6 123 7 120 4.71e-11 56.6
Msa0594090 MtrunA17_Chr1g0165751 36.364 121 70 3 4 123 3 117 5.36e-11 57.0
Msa0594090 MtrunA17_Chr3g0104951 34.043 94 56 2 31 123 32 120 6.74e-11 56.2
Msa0594090 MtrunA17_Chr3g0104931 34.043 94 56 2 31 123 32 120 6.74e-11 56.2
Msa0594090 MtrunA17_Chr3g0104941 34.043 94 56 2 31 123 32 120 6.74e-11 56.2
Msa0594090 MtrunA17_Chr3g0104921 34.043 94 56 2 31 123 22 110 7.47e-11 55.8
Msa0594090 MtrunA17_Chr3g0104911 34.043 94 56 2 31 123 22 110 7.47e-11 55.8
Msa0594090 MtrunA17_Chr3g0104991 29.412 119 78 2 6 123 7 120 9.45e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0594090 AT2G15050.3 50.847 118 52 3 9 123 6 120 3.96e-31 108
Msa0594090 AT2G15050.1 50.847 118 52 3 9 123 6 120 5.59e-31 108
Msa0594090 AT2G15050.2 51.351 111 48 3 9 116 6 113 5.51e-29 102
Msa0594090 AT2G38540.1 43.478 115 61 2 9 123 6 116 2.21e-28 101
Msa0594090 AT5G01870.1 45.133 113 56 4 11 123 8 114 1.63e-27 99.4
Msa0594090 AT3G08770.2 49.495 99 46 3 25 123 17 111 7.68e-26 95.1
Msa0594090 AT3G08770.1 49.495 99 46 3 25 123 17 111 8.63e-26 94.7
Msa0594090 AT5G59320.1 48.148 108 50 3 15 122 11 112 9.62e-25 92.0
Msa0594090 AT5G59310.1 48.113 106 43 4 16 121 15 108 1.25e-23 89.4
Msa0594090 AT2G38530.1 42.609 115 62 2 9 123 6 116 8.14e-23 87.4
Msa0594090 AT3G51600.1 42.609 115 62 2 9 123 6 116 5.53e-22 85.1
Msa0594090 AT3G51590.1 40.000 115 63 3 9 123 6 114 1.59e-21 84.0
Msa0594090 AT2G18370.1 35.345 116 68 2 10 123 4 114 3.78e-19 77.8
Msa0594090 AT4G33355.1 35.000 120 71 3 4 123 5 117 1.01e-14 66.6
Msa0594090 AT4G33355.2 34.454 119 71 3 4 122 5 116 3.52e-14 65.1

Find 43 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGTTTGAGCCATAGTATTA+AGG 0.282339 4_2:+21139482 None:intergenic
ATTGTGTTTCTTGTGACTTT+TGG 0.321213 4_2:-21139628 Msa0594090:CDS
AGCAACTAGGCTTGTTTGTT+TGG 0.326931 4_2:-21139653 Msa0594090:CDS
GCCCTAATACCGACTGTAAC+AGG 0.378156 4_2:-21139324 Msa0594090:intron
TACCTGTTACAGTCGGTATT+AGG 0.379758 4_2:+21139322 None:intergenic
GGGTATAAGCTTGTCACAAC+TGG 0.381388 4_2:+21139571 None:intergenic
GAAGACCAGCAGCAAGGTTA+AGG 0.386841 4_2:+21139383 None:intergenic
ACCTGTTACAGTCGGTATTA+GGG 0.395247 4_2:+21139323 None:intergenic
GTAACAGCTGCTTCAGCCTT+AGG 0.410392 4_2:+21139604 None:intergenic
AGTAAGGAACCTTAATACTA+TGG 0.425103 4_2:-21139491 Msa0594090:CDS
AACAGCTCTACGATCATTTG+TGG 0.431202 4_2:+21139462 None:intergenic
AATGAGTTGGGCCAATCTGC+AGG 0.439780 4_2:+21139183 None:intergenic
GTATCATGTATGATCGAGAT+TGG 0.440193 4_2:-21139153 Msa0594090:CDS
CAACTACATTAGCCTCATCA+TGG 0.440554 4_2:-21139689 Msa0594090:exon
AGTCGGTATTAGGGCTGATC+TGG 0.443403 4_2:+21139332 None:intergenic
TTAAACCTTAACCTTGCTGC+TGG 0.450896 4_2:-21139388 Msa0594090:CDS
TGTGTTTCTTACATTATGAC+TGG 0.454062 4_2:-21139547 Msa0594090:CDS
CACAGTGTTGTAATGGAGTA+AGG 0.461553 4_2:-21139507 Msa0594090:CDS
AAAGTATCTATGTTAGCAAA+TGG 0.481009 4_2:+21139719 None:intergenic
GTTAACAGCATTCTTAATGC+AGG 0.496302 4_2:+21139435 None:intergenic
GATACGATCGAGAATGAGTT+GGG 0.498736 4_2:+21139171 None:intergenic
AAGAATGCTGTTAACCAAAG+TGG 0.504107 4_2:-21139427 Msa0594090:CDS
ATGTTAACACCACATTTCCT+TGG 0.522311 4_2:+21139361 None:intergenic
GTATTAGGGCTGATCTGGTA+AGG 0.526182 4_2:+21139337 None:intergenic
TATCATGTATGATCGAGATT+GGG 0.526852 4_2:-21139152 Msa0594090:CDS
AACTACATTAGCCTCATCAT+GGG 0.529171 4_2:-21139688 Msa0594090:exon
TAGTGTAACTGAAACCACTT+TGG 0.541012 4_2:+21139413 None:intergenic
GCTTGTCACAACTGGACCAC+AGG 0.541996 4_2:+21139579 None:intergenic
TCATATGTAGCCCTGCAGAT+TGG 0.543843 4_2:-21139194 Msa0594090:intron
GTTCCTGCACAGTGTTGTAA+TGG 0.544737 4_2:-21139514 Msa0594090:CDS
ACCTTGCTGCTGGTCTTCCA+AGG 0.551966 4_2:-21139378 Msa0594090:CDS
TGATACGATCGAGAATGAGT+TGG 0.568077 4_2:+21139170 None:intergenic
GTTACTCAACTGTAGCAACT+AGG 0.578078 4_2:-21139666 Msa0594090:CDS
GTTTCTTACATTATGACTGG+TGG 0.579604 4_2:-21139544 Msa0594090:CDS
GCTGGTCTTCCAAGGAAATG+TGG 0.584199 4_2:-21139370 Msa0594090:CDS
ACTCCATTACAACACTGTGC+AGG 0.590449 4_2:+21139511 None:intergenic
GAAGCAGCTGTTACATCCTG+TGG 0.593294 4_2:-21139595 Msa0594090:CDS
TCCTTGGAAGACCAGCAGCA+AGG 0.622205 4_2:+21139377 None:intergenic
ATGAGTTGGGCCAATCTGCA+GGG 0.638852 4_2:+21139184 None:intergenic
GTCATAATGTAAGAAACACA+AGG 0.653065 4_2:+21139550 None:intergenic
CAGTTGAGTAACCCATGATG+AGG 0.658849 4_2:+21139677 None:intergenic
TAAGTGGTACCTGTTACAGT+CGG 0.691959 4_2:+21139315 None:intergenic
TCATAATGTAAGAAACACAA+GGG 0.708823 4_2:+21139551 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACATATATATACTAAA+GGG + chr4_2:21139589-21139608 None:intergenic 10.0%
!! AAAATACATATATATACTAA+AGG + chr4_2:21139590-21139609 None:intergenic 10.0%
!! ACATATGTGAATATTATAAG+TGG + chr4_2:21139558-21139577 None:intergenic 20.0%
!! AAAGTATCTATGTTAGCAAA+TGG + chr4_2:21139138-21139157 None:intergenic 25.0%
! TCATAATGTAAGAAACACAA+GGG + chr4_2:21139306-21139325 None:intergenic 25.0%
! ATTGTGTTTCTTGTGACTTT+TGG - chr4_2:21139226-21139245 Msa0594090:intron 30.0%
GTCATAATGTAAGAAACACA+AGG + chr4_2:21139307-21139326 None:intergenic 30.0%
TGTGTTTCTTACATTATGAC+TGG - chr4_2:21139307-21139326 Msa0594090:intron 30.0%
AGTAAGGAACCTTAATACTA+TGG - chr4_2:21139363-21139382 Msa0594090:CDS 30.0%
TATCATGTATGATCGAGATT+GGG - chr4_2:21139702-21139721 Msa0594090:five_prime_UTR 30.0%
! AACTACATTAGCCTCATCAT+GGG - chr4_2:21139166-21139185 Msa0594090:CDS 35.0%
GTTTCTTACATTATGACTGG+TGG - chr4_2:21139310-21139329 Msa0594090:intron 35.0%
TGGTTTGAGCCATAGTATTA+AGG + chr4_2:21139375-21139394 None:intergenic 35.0%
GTTAACAGCATTCTTAATGC+AGG + chr4_2:21139422-21139441 None:intergenic 35.0%
AAGAATGCTGTTAACCAAAG+TGG - chr4_2:21139427-21139446 Msa0594090:CDS 35.0%
TAGTGTAACTGAAACCACTT+TGG + chr4_2:21139444-21139463 None:intergenic 35.0%
ATGTTAACACCACATTTCCT+TGG + chr4_2:21139496-21139515 None:intergenic 35.0%
GTATCATGTATGATCGAGAT+TGG - chr4_2:21139701-21139720 Msa0594090:five_prime_UTR 35.0%
! CAACTACATTAGCCTCATCA+TGG - chr4_2:21139165-21139184 Msa0594090:CDS 40.0%
GTTACTCAACTGTAGCAACT+AGG - chr4_2:21139188-21139207 Msa0594090:intron 40.0%
! AGCAACTAGGCTTGTTTGTT+TGG - chr4_2:21139201-21139220 Msa0594090:intron 40.0%
! TCTTGTGACTTTTGGTCCTA+AGG - chr4_2:21139234-21139253 Msa0594090:intron 40.0%
! CACAGTGTTGTAATGGAGTA+AGG - chr4_2:21139347-21139366 Msa0594090:CDS 40.0%
AACAGCTCTACGATCATTTG+TGG + chr4_2:21139395-21139414 None:intergenic 40.0%
TTAAACCTTAACCTTGCTGC+TGG - chr4_2:21139466-21139485 Msa0594090:CDS 40.0%
ACCTGTTACAGTCGGTATTA+GGG + chr4_2:21139534-21139553 None:intergenic 40.0%
TACCTGTTACAGTCGGTATT+AGG + chr4_2:21139535-21139554 None:intergenic 40.0%
TAAGTGGTACCTGTTACAGT+CGG + chr4_2:21139542-21139561 None:intergenic 40.0%
GATACGATCGAGAATGAGTT+GGG + chr4_2:21139686-21139705 None:intergenic 40.0%
TGATACGATCGAGAATGAGT+TGG + chr4_2:21139687-21139706 None:intergenic 40.0%
CAGTTGAGTAACCCATGATG+AGG + chr4_2:21139180-21139199 None:intergenic 45.0%
GGGTATAAGCTTGTCACAAC+TGG + chr4_2:21139286-21139305 None:intergenic 45.0%
GTTCCTGCACAGTGTTGTAA+TGG - chr4_2:21139340-21139359 Msa0594090:CDS 45.0%
ACTCCATTACAACACTGTGC+AGG + chr4_2:21139346-21139365 None:intergenic 45.0%
GTATTAGGGCTGATCTGGTA+AGG + chr4_2:21139520-21139539 None:intergenic 45.0%
TCATATGTAGCCCTGCAGAT+TGG - chr4_2:21139660-21139679 Msa0594090:CDS 45.0%
GTAACAGCTGCTTCAGCCTT+AGG + chr4_2:21139253-21139272 None:intergenic 50.0%
GAAGCAGCTGTTACATCCTG+TGG - chr4_2:21139259-21139278 Msa0594090:intron 50.0%
GAAGACCAGCAGCAAGGTTA+AGG + chr4_2:21139474-21139493 None:intergenic 50.0%
!! GCTGGTCTTCCAAGGAAATG+TGG - chr4_2:21139484-21139503 Msa0594090:CDS 50.0%
AGTCGGTATTAGGGCTGATC+TGG + chr4_2:21139525-21139544 None:intergenic 50.0%
! GCCCTAATACCGACTGTAAC+AGG - chr4_2:21139530-21139549 Msa0594090:CDS 50.0%
! ATGAGTTGGGCCAATCTGCA+GGG + chr4_2:21139673-21139692 None:intergenic 50.0%
! AATGAGTTGGGCCAATCTGC+AGG + chr4_2:21139674-21139693 None:intergenic 50.0%
GCTTGTCACAACTGGACCAC+AGG + chr4_2:21139278-21139297 None:intergenic 55.0%
!! ACCTTGCTGCTGGTCTTCCA+AGG - chr4_2:21139476-21139495 Msa0594090:CDS 55.0%
TCCTTGGAAGACCAGCAGCA+AGG + chr4_2:21139480-21139499 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 21139128 21139748 21139128 ID=Msa0594090;Name=Msa0594090
chr4_2 mRNA 21139128 21139748 21139128 ID=Msa0594090-mRNA-1;Parent=Msa0594090;Name=Msa0594090-mRNA-1;_AED=0.47;_eAED=0.47;_QI=56|0|0.5|0.5|1|1|2|0|148
chr4_2 exon 21139128 21139206 21139128 ID=Msa0594090-mRNA-1:exon:5933;Parent=Msa0594090-mRNA-1
chr4_2 exon 21139325 21139748 21139325 ID=Msa0594090-mRNA-1:exon:5932;Parent=Msa0594090-mRNA-1
chr4_2 five_prime_UTR 21139693 21139748 21139693 ID=Msa0594090-mRNA-1:five_prime_utr;Parent=Msa0594090-mRNA-1
chr4_2 CDS 21139325 21139692 21139325 ID=Msa0594090-mRNA-1:cds;Parent=Msa0594090-mRNA-1
chr4_2 CDS 21139128 21139206 21139128 ID=Msa0594090-mRNA-1:cds;Parent=Msa0594090-mRNA-1
Gene Sequence

>Msa0594090

ATGGGTTACTCAACTGTAGCAACTAGGCTTGTTTGTTTGGCAATTGTGTTTCTTGTGACTTTTGGTCCTAAGGCTGAAGCAGCTGTTACATCCTGTGGTCCAGTTGTGACAAGCTTATACCCTTGTGTTTCTTACATTATGACTGGTGGAAACACTGTTCCTGCACAGTGTTGTAATGGAGTAAGGAACCTTAATACTATGGCTCAAACCACAAATGATCGTAGAGCTGTTTGTACCTGCATTAAGAATGCTGTTAACCAAAGTGGTTTCAGTTACACTAATTTAAACCTTAACCTTGCTGCTGGTCTTCCAAGGAAATGTGGTGTTAACATTCCTTACCAGATCAGCCCTAATACCGACTGTAACAGCCCTGCAGATTGGCCCAACTCATTCTCGATCGTATCATGTATGATCGAGATTGGGCTAGATCGAGATGTAGAGCTGTAG
Protein sequence

>Msa0594090

MGYSTVATRLVCLAIVFLVTFGPKAEAAVTSCGPVVTSLYPCVSYIMTGGNTVPAQCCNGVRNLNTMAQTTNDRRAVCTCIKNAVNQSGFSYTNLNLNLAAGLPRKCGVNIPYQISPNTDCNSPADWPNSFSIVSCMIEIGLDRDVEL*