AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1009730

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1009730 MtrunA17_Chr7g0220571 96.875 192 5 1 1 192 1 191 1.61e-136 379
Msa1009730 MtrunA17_Chr6g0456061 66.484 182 56 4 1 178 1 181 1.59e-66 202
Msa1009730 MtrunA17_Chr7g0225661 52.688 186 80 6 9 191 8 188 3.35e-50 160
Msa1009730 MtrunA17_Chr8g0341311 52.151 186 70 8 9 191 8 177 1.03e-45 149
Msa1009730 MtrunA17_Chr4g0035414 52.326 86 38 2 71 156 16 98 1.31e-17 75.9
Msa1009730 MtrunA17_Chr1g0155551 44.330 97 54 0 62 158 4 100 6.62e-17 74.3
Msa1009730 MtrunA17_Chr3g0144941 50.000 80 40 0 77 156 19 98 1.42e-16 73.2
Msa1009730 MtrunA17_Chr4g0054291 35.256 156 83 4 38 175 7 162 7.57e-16 71.6
Msa1009730 MtrunA17_Chr1g0194681 37.405 131 70 4 63 187 7 131 1.09e-13 65.5
Msa1009730 MtrunA17_Chr5g0400901 36.885 122 72 1 57 173 25 146 1.73e-12 62.4
Msa1009730 MtrunA17_Chr5g0410531 37.500 104 60 2 57 155 274 377 4.06e-11 60.8
Msa1009730 MtrunA17_Chr8g0378901 32.292 96 65 0 61 156 8 103 7.22e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1009730 AT3G30530.1 57.143 175 48 8 11 177 12 167 1.31e-48 156
Msa1009730 AT5G38800.1 57.042 142 56 3 40 177 20 160 2.94e-43 142
Msa1009730 AT2G04038.1 64.583 96 34 0 68 163 54 149 2.40e-36 125
Msa1009730 AT5G15830.1 61.616 99 38 0 66 164 52 150 5.63e-35 122
Msa1009730 AT1G13600.1 59.184 98 39 1 69 166 68 164 3.10e-34 120
Msa1009730 AT1G68880.1 45.217 115 58 1 52 166 16 125 1.26e-24 94.0
Msa1009730 AT5G60830.1 51.724 87 41 1 80 165 62 148 4.48e-19 81.3
Msa1009730 AT2G18160.1 50.000 72 36 0 85 156 28 99 2.27e-15 70.9
Msa1009730 AT1G75390.1 46.316 95 50 1 62 156 16 109 2.91e-15 70.5
Msa1009730 AT3G62420.1 46.575 73 39 0 84 156 21 93 4.60e-15 69.3
Msa1009730 AT1G75390.2 45.833 96 51 1 62 157 16 110 1.99e-14 67.0
Msa1009730 AT4G34590.1 45.946 74 40 0 83 156 22 95 2.69e-12 62.4

Find 41 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGGGAGATGGATCTGAATA+TGG 0.215024 7_1:+11670468 None:intergenic
TATAGTTGGTTGGAGAGTTT+TGG 0.282356 7_1:+11670390 None:intergenic
GGAGGATTTGAAAAGGGTTT+TGG 0.298291 7_1:+11670358 None:intergenic
GAAGAATCAGATTTAACATT+TGG 0.320345 7_1:+11669961 None:intergenic
GAGTCCTGAATTAATCTCTT+TGG 0.334240 7_1:+11670503 None:intergenic
AGCTTTGGTCACAGGTGGTT+TGG 0.340519 7_1:-11670173 Msa1009730:CDS
CTTTCAATTGAACATTCTCT+TGG 0.350205 7_1:+11670082 None:intergenic
AAACTCTCCAACCAACTATA+TGG 0.354645 7_1:-11670387 Msa1009730:CDS
CAAACCAAAGAGATTAATTC+AGG 0.365256 7_1:-11670507 Msa1009730:CDS
GAGGTGTTTGGATGGTGTTT+TGG 0.378558 7_1:+11670418 None:intergenic
AAGTCTTGGAGGATTTGAAA+AGG 0.435873 7_1:+11670351 None:intergenic
GCTTGATGAGCTTTGGTCAC+AGG 0.439356 7_1:-11670181 Msa1009730:CDS
TTTGGTTAAAACCATATAGT+TGG 0.439584 7_1:+11670376 None:intergenic
ACATTTGGTGAAGTGATACT+AGG 0.443961 7_1:+11669976 None:intergenic
AGGGAGATGGATCTGAATAT+GGG 0.460373 7_1:+11670469 None:intergenic
ATTAATCTCTTTGGTTTGCA+TGG 0.465724 7_1:+11670512 None:intergenic
TGGATGTTGAGGTGTTTGGA+TGG 0.476729 7_1:+11670410 None:intergenic
ATGTTATAGTTACATGATGA+TGG 0.477265 7_1:+11670444 None:intergenic
ATAGTTACATGATGATGGAT+AGG 0.478143 7_1:+11670449 None:intergenic
AGCTTCAGAACTTAGACAAA+TGG 0.487701 7_1:-11670055 Msa1009730:CDS
TTTGTTTCCTCATTCGTGAC+CGG 0.488943 7_1:+11670208 None:intergenic
GGTCACAGGTGGTTTGGCTA+AGG 0.490458 7_1:-11670167 Msa1009730:CDS
AGGATGGAGGACTGAAGTCT+TGG 0.496834 7_1:+11670337 None:intergenic
GTGACCGGCGTGCTGACTCT+CGG 0.498415 7_1:+11670223 None:intergenic
ATGGAGGACTGAAGTCTTGG+AGG 0.500414 7_1:+11670340 None:intergenic
AGTCTTGGAGGATTTGAAAA+GGG 0.502731 7_1:+11670352 None:intergenic
GTTAAAACCATATAGTTGGT+TGG 0.514391 7_1:+11670380 None:intergenic
CGAAAGAAAACATCGAAGAA+TGG 0.528388 7_1:-11670253 Msa1009730:CDS
TGATGAGCTTTGGTCACAGG+TGG 0.534117 7_1:-11670178 Msa1009730:CDS
CATGATGATGGATAGGGAGA+TGG 0.535502 7_1:+11670456 None:intergenic
TAGTTACATGATGATGGATA+GGG 0.553972 7_1:+11670450 None:intergenic
TTCTTTCGTTGATTAGACCT+AGG 0.573011 7_1:+11670268 None:intergenic
ACATCTTCAAGAGGACTCAA+AGG 0.584334 7_1:+11670000 None:intergenic
CATAAGCAGCAACTCAACTT+CGG 0.598589 7_1:-11670310 Msa1009730:CDS
TTGCTGCTTATGCATGAGGA+TGG 0.607001 7_1:+11670321 None:intergenic
CAACTCAACTTCGGACGAAG+CGG 0.624164 7_1:-11670301 Msa1009730:CDS
ATACTAGGAACATCTTCAAG+AGG 0.631208 7_1:+11669991 None:intergenic
CTGCTTATGCATGAGGATGG+AGG 0.633472 7_1:+11670324 None:intergenic
TGAGTTGCTGCTTATGCATG+AGG 0.648721 7_1:+11670317 None:intergenic
GAAGCGGACGAACAAAACCT+AGG 0.674445 7_1:-11670285 Msa1009730:CDS
CGAACCGAGAGTCAGCACGC+CGG 0.752861 7_1:-11670227 Msa1009730:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATGTTATAGTTACATGATGA+TGG + chr7_1:11670023-11670042 None:intergenic 25.0%
! TTTGGTTAAAACCATATAGT+TGG + chr7_1:11670091-11670110 None:intergenic 25.0%
! GAAGAATCAGATTTAACATT+TGG + chr7_1:11670506-11670525 None:intergenic 25.0%
CAAACCAAAGAGATTAATTC+AGG - chr7_1:11669957-11669976 Msa1009730:CDS 30.0%
!! TAGTTACATGATGATGGATA+GGG + chr7_1:11670017-11670036 None:intergenic 30.0%
!! ATAGTTACATGATGATGGAT+AGG + chr7_1:11670018-11670037 None:intergenic 30.0%
GTTAAAACCATATAGTTGGT+TGG + chr7_1:11670087-11670106 None:intergenic 30.0%
CTTTCAATTGAACATTCTCT+TGG + chr7_1:11670385-11670404 None:intergenic 30.0%
GAGTCCTGAATTAATCTCTT+TGG + chr7_1:11669964-11669983 None:intergenic 35.0%
! TATAGTTGGTTGGAGAGTTT+TGG + chr7_1:11670077-11670096 None:intergenic 35.0%
AAACTCTCCAACCAACTATA+TGG - chr7_1:11670077-11670096 Msa1009730:CDS 35.0%
AGTCTTGGAGGATTTGAAAA+GGG + chr7_1:11670115-11670134 None:intergenic 35.0%
AAGTCTTGGAGGATTTGAAA+AGG + chr7_1:11670116-11670135 None:intergenic 35.0%
! TTCTTTCGTTGATTAGACCT+AGG + chr7_1:11670199-11670218 None:intergenic 35.0%
CGAAAGAAAACATCGAAGAA+TGG - chr7_1:11670211-11670230 Msa1009730:CDS 35.0%
AAAAACAGCTTGATGAGCTT+TGG - chr7_1:11670276-11670295 Msa1009730:CDS 35.0%
AGCTTCAGAACTTAGACAAA+TGG - chr7_1:11670409-11670428 Msa1009730:CDS 35.0%
ATACTAGGAACATCTTCAAG+AGG + chr7_1:11670476-11670495 None:intergenic 35.0%
! ACATTTGGTGAAGTGATACT+AGG + chr7_1:11670491-11670510 None:intergenic 35.0%
AGGGAGATGGATCTGAATAT+GGG + chr7_1:11669998-11670017 None:intergenic 40.0%
TAGGGAGATGGATCTGAATA+TGG + chr7_1:11669999-11670018 None:intergenic 40.0%
!! GTTTTGGATGTTGAGGTGTT+TGG + chr7_1:11670061-11670080 None:intergenic 40.0%
!!! TTGGAGAGTTTTGGATGTTG+AGG + chr7_1:11670068-11670087 None:intergenic 40.0%
! GGAGGATTTGAAAAGGGTTT+TGG + chr7_1:11670109-11670128 None:intergenic 40.0%
CATAAGCAGCAACTCAACTT+CGG - chr7_1:11670154-11670173 Msa1009730:CDS 40.0%
TTTGTTTCCTCATTCGTGAC+CGG + chr7_1:11670259-11670278 None:intergenic 40.0%
ACATCTTCAAGAGGACTCAA+AGG + chr7_1:11670467-11670486 None:intergenic 40.0%
!! CATGATGATGGATAGGGAGA+TGG + chr7_1:11670011-11670030 None:intergenic 45.0%
!! GAGGTGTTTGGATGGTGTTT+TGG + chr7_1:11670049-11670068 None:intergenic 45.0%
! TGGATGTTGAGGTGTTTGGA+TGG + chr7_1:11670057-11670076 None:intergenic 45.0%
! TTGCTGCTTATGCATGAGGA+TGG + chr7_1:11670146-11670165 None:intergenic 45.0%
! TGAGTTGCTGCTTATGCATG+AGG + chr7_1:11670150-11670169 None:intergenic 45.0%
ATGGAGGACTGAAGTCTTGG+AGG + chr7_1:11670127-11670146 None:intergenic 50.0%
AGGATGGAGGACTGAAGTCT+TGG + chr7_1:11670130-11670149 None:intergenic 50.0%
CTGCTTATGCATGAGGATGG+AGG + chr7_1:11670143-11670162 None:intergenic 50.0%
CAACTCAACTTCGGACGAAG+CGG - chr7_1:11670163-11670182 Msa1009730:CDS 50.0%
GAAGCGGACGAACAAAACCT+AGG - chr7_1:11670179-11670198 Msa1009730:CDS 50.0%
! GCTTGATGAGCTTTGGTCAC+AGG - chr7_1:11670283-11670302 Msa1009730:CDS 50.0%
! TGATGAGCTTTGGTCACAGG+TGG - chr7_1:11670286-11670305 Msa1009730:CDS 50.0%
! AGCTTTGGTCACAGGTGGTT+TGG - chr7_1:11670291-11670310 Msa1009730:CDS 50.0%
! GGTCACAGGTGGTTTGGCTA+AGG - chr7_1:11670297-11670316 Msa1009730:CDS 55.0%
CGAACCGAGAGTCAGCACGC+CGG - chr7_1:11670237-11670256 Msa1009730:CDS 65.0%
!! GTGACCGGCGTGCTGACTCT+CGG + chr7_1:11670244-11670263 None:intergenic 65.0%
CAGCACGCCGGTCACGAATG+AGG - chr7_1:11670249-11670268 Msa1009730:CDS 65.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 11669954 11670532 11669954 ID=Msa1009730;Name=Msa1009730
chr7_1 mRNA 11669954 11670532 11669954 ID=Msa1009730-mRNA-1;Parent=Msa1009730;Name=Msa1009730-mRNA-1;_AED=0.36;_eAED=0.36;_QI=0|-1|0|1|-1|1|1|0|192
chr7_1 exon 11669954 11670532 11669954 ID=Msa1009730-mRNA-1:exon:3092;Parent=Msa1009730-mRNA-1
chr7_1 CDS 11669954 11670532 11669954 ID=Msa1009730-mRNA-1:cds;Parent=Msa1009730-mRNA-1
Gene Sequence

>Msa1009730

ATGCAAACCAAAGAGATTAATTCAGGACTCAATTATTTACTCCCATATTCAGATCCATCTCCCTATCCATCATCATGTAACTATAACATGATCCAAAACACCATCCAAACACCTCAACATCCAAAACTCTCCAACCAACTATATGGTTTTAACCAAAACCCTTTTCAAATCCTCCAAGACTTCAGTCCTCCATCCTCATGCATAAGCAGCAACTCAACTTCGGACGAAGCGGACGAACAAAACCTAGGTCTAATCAACGAAAGAAAACATCGAAGAATGGTATCGAACCGAGAGTCAGCACGCCGGTCACGAATGAGGAAACAAAAACAGCTTGATGAGCTTTGGTCACAGGTGGTTTGGCTAAGGAATGAGAATCATCAATTACTAGATAAGCTCAACAATTTCTGTGAGACTCATGATAAAGTTGTCCAAGAGAATGTTCAATTGAAAGAACAAGCTTCAGAACTTAGACAAATGGTGTGTGATATGCAGTTACATAGTACTTGTCTTCCTTTGAGTCCTCTTGAAGATGTTCCTAGTATCACTTCACCAAATGTTAAATCTGATTCTTCAAACTAA
Protein sequence

>Msa1009730

MQTKEINSGLNYLLPYSDPSPYPSSCNYNMIQNTIQTPQHPKLSNQLYGFNQNPFQILQDFSPPSSCISSNSTSDEADEQNLGLINERKHRRMVSNRESARRSRMRKQKQLDELWSQVVWLRNENHQLLDKLNNFCETHDKVVQENVQLKEQASELRQMVCDMQLHSTCLPLSPLEDVPSITSPNVKSDSSN*