AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0031020

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0031020 MtrunA17_Chr1g0188911 85.106 188 24 3 1 185 1 187 8.27e-101 290
Msa0031020 MtrunA17_Chr1g0188901 64.356 202 32 4 1 185 1 179 5.11e-67 204
Msa0031020 MtrunA17_Chr1g0197281 46.154 195 58 9 27 198 135 305 5.74e-40 140
Msa0031020 MtrunA17_Chr4g0027991 36.975 119 65 1 43 151 112 230 5.62e-19 83.2
Msa0031020 MtrunA17_Chr2g0320311 37.795 127 55 4 41 155 126 240 6.18e-16 74.7
Msa0031020 MtrunA17_Chr1g0180311 34.646 127 71 3 28 151 104 221 1.64e-15 73.6
Msa0031020 MtrunA17_Chr4g0012791 29.944 177 103 6 1 161 177 348 1.43e-14 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0031020 AT5G04390.1 37.725 167 73 6 39 198 148 290 6.50e-22 92.4
Msa0031020 AT3G10470.1 44.628 121 45 4 39 151 177 283 3.98e-21 90.5
Msa0031020 AT2G28200.1 38.760 129 63 3 37 159 108 226 1.65e-20 87.4
Msa0031020 AT5G03510.1 38.182 110 57 3 42 151 116 214 1.51e-15 73.9
Msa0031020 AT3G46080.1 37.500 112 33 4 42 153 35 109 7.32e-12 62.0
Msa0031020 AT3G46090.1 37.838 111 30 4 42 152 38 109 1.26e-11 61.2
Msa0031020 AT3G49930.1 33.333 111 40 3 44 152 94 172 3.37e-11 60.8

Find 48 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTGATACTATTCAATTTA+AGG 0.113940 1_1:-57591631 None:intergenic
AACAACAAAACCAAGGTTTA+TGG 0.193686 1_1:+57591734 Msa0031020:CDS
AGAAAATGAATGTCTGGATT+TGG 0.301472 1_1:+57591897 Msa0031020:CDS
ATTGATACTATTCAATTTAA+GGG 0.301902 1_1:-57591630 None:intergenic
GGTGGTGTTATTGTTGTTGT+TGG 0.377009 1_1:-57591705 None:intergenic
CATGAACAACAACTCTCTTT+AGG 0.379285 1_1:+57591380 Msa0031020:CDS
CTCGATGAGGTTGCCTCCAC+CGG 0.381070 1_1:-57591827 None:intergenic
GGTTCTTCATCTTCTTCGTC+TGG 0.390134 1_1:-57591866 None:intergenic
TGTGGTTCTAAATTCACATC+TGG 0.409768 1_1:+57591767 Msa0031020:CDS
ATTGAATAGTATCAATGGTA+TGG 0.411197 1_1:+57591637 Msa0031020:CDS
ACAACAAAACCAAGGTTTAT+GGG 0.414502 1_1:+57591735 Msa0031020:CDS
CTACAAAGAAAATGAATGTC+TGG 0.421685 1_1:+57591891 Msa0031020:CDS
GTTATTGTTGTTGTTGGTAG+TGG 0.422125 1_1:-57591699 None:intergenic
CTTTGATCTGCTTAAGCTGC+AGG 0.422484 1_1:-57591931 None:intergenic
GTTTATGGGTGCACCATTTG+TGG 0.429212 1_1:+57591749 Msa0031020:CDS
CTTAAATTGAATAGTATCAA+TGG 0.429294 1_1:+57591632 Msa0031020:CDS
GAATAAGCAATGATGGAGAA+AGG 0.431980 1_1:-57591428 None:intergenic
TTCACTTCATTTCAATCACT+TGG 0.434926 1_1:+57591524 Msa0031020:CDS
GTTGTTGTTGGTAGTGGTGG+TGG 0.454493 1_1:-57591693 None:intergenic
TCGTCTGGTTTCAAAGCCAT+TGG 0.468001 1_1:-57591851 None:intergenic
GTGCATGGTGGAAGGTCATA+TGG 0.468572 1_1:-57591805 None:intergenic
TTCACATCTGGCCAGGCACT+TGG 0.470440 1_1:+57591779 Msa0031020:CDS
AAGACTTGTTTGTTGTTGCT+TGG 0.471818 1_1:-57591977 None:intergenic
TGTAGAAGAATAAGCAATGA+TGG 0.477070 1_1:-57591435 None:intergenic
TATTCTTCTACAAGAGAAGA+AGG 0.493297 1_1:+57591446 Msa0031020:CDS
TCATATGGCCACCAAGTGCC+TGG 0.495422 1_1:-57591790 None:intergenic
AATAAGCAATGATGGAGAAA+GGG 0.498901 1_1:-57591427 None:intergenic
TGTGAATTTAGAACCACAAA+TGG 0.504130 1_1:-57591762 None:intergenic
CTTCCACCATGCACCGGTGG+AGG 0.506143 1_1:+57591814 Msa0031020:CDS
TTGAATAGTATCAATGGTAT+GGG 0.515059 1_1:+57591638 Msa0031020:CDS
ACTTCATTTCAATCACTTGG+AGG 0.515461 1_1:+57591527 Msa0031020:CDS
GAAGCCTAGAGATGATTGTC+AGG 0.519135 1_1:+57591568 Msa0031020:CDS
ATTGTTGTTGTTGGTAGTGG+TGG 0.519273 1_1:-57591696 None:intergenic
GCAATGATGGAGAAAGGGAT+AGG 0.524368 1_1:-57591422 None:intergenic
ACATCTGGCCAGGCACTTGG+TGG 0.529943 1_1:+57591782 Msa0031020:CDS
GTTGTTGGTAGTGGTGGTGG+TGG 0.530069 1_1:-57591690 None:intergenic
TTCTAAATTCACATCTGGCC+AGG 0.531142 1_1:+57591772 Msa0031020:CDS
CTCCACCGGTGCATGGTGGA+AGG 0.537215 1_1:-57591813 None:intergenic
TGAACCTGACAATCATCTCT+AGG 0.556365 1_1:-57591572 None:intergenic
AGGTTGCCTCCACCGGTGCA+TGG 0.568155 1_1:-57591820 None:intergenic
AATGGTGCACCCATAAACCT+TGG 0.579571 1_1:-57591744 None:intergenic
TATGACCTTCCACCATGCAC+CGG 0.585865 1_1:+57591808 Msa0031020:CDS
CAAAGCCATTGGTCTCGATG+AGG 0.605389 1_1:-57591840 None:intergenic
GGCAACCTCATCGAGACCAA+TGG 0.607582 1_1:+57591835 Msa0031020:CDS
GACCTTCCACCATGCACCGG+TGG 0.615351 1_1:+57591811 Msa0031020:CDS
GATCTGCTTAAGCTGCAGGA+AGG 0.638172 1_1:-57591927 None:intergenic
TTGCCTCCACCGGTGCATGG+TGG 0.647313 1_1:-57591817 None:intergenic
CAGTATTGACAATTCATCCG+AGG 0.653167 1_1:-57592012 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTGATACTATTCAATTTAA+GGG - chr1_1:57591633-57591652 None:intergenic 15.0%
!! CATTGATACTATTCAATTTA+AGG - chr1_1:57591634-57591653 None:intergenic 20.0%
!! CTTAAATTGAATAGTATCAA+TGG + chr1_1:57591632-57591651 Msa0031020:CDS 20.0%
! ATTGAATAGTATCAATGGTA+TGG + chr1_1:57591637-57591656 Msa0031020:CDS 25.0%
! TTGAATAGTATCAATGGTAT+GGG + chr1_1:57591638-57591657 Msa0031020:CDS 25.0%
! AATAAGCAATGATGGAGAAA+GGG - chr1_1:57591430-57591449 None:intergenic 30.0%
TGTAGAAGAATAAGCAATGA+TGG - chr1_1:57591438-57591457 None:intergenic 30.0%
TATTCTTCTACAAGAGAAGA+AGG + chr1_1:57591446-57591465 Msa0031020:CDS 30.0%
TTCACTTCATTTCAATCACT+TGG + chr1_1:57591524-57591543 Msa0031020:CDS 30.0%
AACAACAAAACCAAGGTTTA+TGG + chr1_1:57591734-57591753 Msa0031020:CDS 30.0%
ACAACAAAACCAAGGTTTAT+GGG + chr1_1:57591735-57591754 Msa0031020:CDS 30.0%
! TGTGAATTTAGAACCACAAA+TGG - chr1_1:57591765-57591784 None:intergenic 30.0%
! ACATTCATTTTCTTTGTAGG+TGG - chr1_1:57591890-57591909 None:intergenic 30.0%
! CAGACATTCATTTTCTTTGT+AGG - chr1_1:57591893-57591912 None:intergenic 30.0%
CTACAAAGAAAATGAATGTC+TGG + chr1_1:57591891-57591910 Msa0031020:CDS 30.0%
AGAAAATGAATGTCTGGATT+TGG + chr1_1:57591897-57591916 Msa0031020:CDS 30.0%
CATGAACAACAACTCTCTTT+AGG + chr1_1:57591380-57591399 Msa0031020:CDS 35.0%
! GAATAAGCAATGATGGAGAA+AGG - chr1_1:57591431-57591450 None:intergenic 35.0%
ACTTCATTTCAATCACTTGG+AGG + chr1_1:57591527-57591546 Msa0031020:CDS 35.0%
! GCTTCTTGTGAACTTTTCTA+TGG - chr1_1:57591553-57591572 None:intergenic 35.0%
! GTTATTGTTGTTGTTGGTAG+TGG - chr1_1:57591702-57591721 None:intergenic 35.0%
!!! CTTGGTTTTGTTGTTGTTGT+TGG - chr1_1:57591729-57591748 None:intergenic 35.0%
CAACAACAACAACAAAACCA+AGG + chr1_1:57591727-57591746 Msa0031020:CDS 35.0%
!! TGTGGTTCTAAATTCACATC+TGG + chr1_1:57591767-57591786 Msa0031020:CDS 35.0%
!! AAGACTTGTTTGTTGTTGCT+TGG - chr1_1:57591980-57591999 None:intergenic 35.0%
TGAACCTGACAATCATCTCT+AGG - chr1_1:57591575-57591594 None:intergenic 40.0%
!! ATTGTTGTTGTTGGTAGTGG+TGG - chr1_1:57591699-57591718 None:intergenic 40.0%
!! GGTGGTGTTATTGTTGTTGT+TGG - chr1_1:57591708-57591727 None:intergenic 40.0%
!!! GGTTTTGTTGTTGTTGTTGG+TGG - chr1_1:57591726-57591745 None:intergenic 40.0%
TTCTAAATTCACATCTGGCC+AGG + chr1_1:57591772-57591791 Msa0031020:CDS 40.0%
! GCAATGATGGAGAAAGGGAT+AGG - chr1_1:57591425-57591444 None:intergenic 45.0%
GAAGCCTAGAGATGATTGTC+AGG + chr1_1:57591568-57591587 Msa0031020:CDS 45.0%
AATGGTGCACCCATAAACCT+TGG - chr1_1:57591747-57591766 None:intergenic 45.0%
GTTTATGGGTGCACCATTTG+TGG + chr1_1:57591749-57591768 Msa0031020:CDS 45.0%
! TCGTCTGGTTTCAAAGCCAT+TGG - chr1_1:57591854-57591873 None:intergenic 45.0%
GGTTCTTCATCTTCTTCGTC+TGG - chr1_1:57591869-57591888 None:intergenic 45.0%
CTTTGATCTGCTTAAGCTGC+AGG - chr1_1:57591934-57591953 None:intergenic 45.0%
!!! GTCTTGTTTTCAGTGCACCT+CGG + chr1_1:57591995-57592014 Msa0031020:CDS 45.0%
!! GTTGTTGTTGGTAGTGGTGG+TGG - chr1_1:57591696-57591715 None:intergenic 50.0%
! GTGCATGGTGGAAGGTCATA+TGG - chr1_1:57591808-57591827 None:intergenic 50.0%
TATGACCTTCCACCATGCAC+CGG + chr1_1:57591808-57591827 Msa0031020:CDS 50.0%
! CAAAGCCATTGGTCTCGATG+AGG - chr1_1:57591843-57591862 None:intergenic 50.0%
GATCTGCTTAAGCTGCAGGA+AGG - chr1_1:57591930-57591949 None:intergenic 50.0%
!! GTTGTTGGTAGTGGTGGTGG+TGG - chr1_1:57591693-57591712 None:intergenic 55.0%
TTCACATCTGGCCAGGCACT+TGG + chr1_1:57591779-57591798 Msa0031020:CDS 55.0%
TCATATGGCCACCAAGTGCC+TGG - chr1_1:57591793-57591812 None:intergenic 55.0%
GGCAACCTCATCGAGACCAA+TGG + chr1_1:57591835-57591854 Msa0031020:CDS 55.0%
ACATCTGGCCAGGCACTTGG+TGG + chr1_1:57591782-57591801 Msa0031020:CDS 60.0%
CTCGATGAGGTTGCCTCCAC+CGG - chr1_1:57591830-57591849 None:intergenic 60.0%
GACCTTCCACCATGCACCGG+TGG + chr1_1:57591811-57591830 Msa0031020:CDS 65.0%
! CTCCACCGGTGCATGGTGGA+AGG - chr1_1:57591816-57591835 None:intergenic 65.0%
! CTTCCACCATGCACCGGTGG+AGG + chr1_1:57591814-57591833 Msa0031020:CDS 65.0%
TTGCCTCCACCGGTGCATGG+TGG - chr1_1:57591820-57591839 None:intergenic 65.0%
AGGTTGCCTCCACCGGTGCA+TGG - chr1_1:57591823-57591842 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 57591368 57592021 57591368 ID=Msa0031020;Name=Msa0031020
chr1_1 mRNA 57591368 57592021 57591368 ID=Msa0031020-mRNA-1;Parent=Msa0031020;Name=Msa0031020-mRNA-1;_AED=0.36;_eAED=0.36;_QI=0|-1|0|1|-1|1|1|0|217
chr1_1 exon 57591368 57592021 57591368 ID=Msa0031020-mRNA-1:exon:17431;Parent=Msa0031020-mRNA-1
chr1_1 CDS 57591368 57592021 57591368 ID=Msa0031020-mRNA-1:cds;Parent=Msa0031020-mRNA-1
Gene Sequence

>Msa0031020

ATGGAAGCATCTCATGAACAACAACTCTCTTTAGGCTCTATAGAACAACAATCTCCTATCCCTTTCTCCATCATTGCTTATTCTTCTACAAGAGAAGAAGGAACAAGAGAAAGTGCACGTTACAATGTGTATGCATGCAAAACATGCAAGAAAACTTTCACTTCATTTCAATCACTTGGAGGCCATAGAAAAGTTCACAAGAAGCCTAGAGATGATTGTCAGGTTCAAGAGTTTCAATTCAAAATCAATAATAAATCAATTTCCCTTAAATTGAATAGTATCAATGGTATGGGAAATATATATGCTAGTAGCAACAACAACACCACCACCACCACTACCAACAACAACAATAACACCACCAACAACAACAACAAAACCAAGGTTTATGGGTGCACCATTTGTGGTTCTAAATTCACATCTGGCCAGGCACTTGGTGGCCATATGACCTTCCACCATGCACCGGTGGAGGCAACCTCATCGAGACCAATGGCTTTGAAACCAGACGAAGAAGATGAAGAACCACCTACAAAGAAAATGAATGTCTGGATTTGGATCTCAACCTTCCTGCAGCTTAAGCAGATCAAAGATAATCATGCTTTGTCTTATAATCCAAGCAACAACAAACAAGTCTTGTTTTCAGTGCACCTCGGATGA
Protein sequence

>Msa0031020

MEASHEQQLSLGSIEQQSPIPFSIIAYSSTREEGTRESARYNVYACKTCKKTFTSFQSLGGHRKVHKKPRDDCQVQEFQFKINNKSISLKLNSINGMGNIYASSNNNTTTTTTNNNNNTTNNNNKTKVYGCTICGSKFTSGQALGGHMTFHHAPVEATSSRPMALKPDEEDEEPPTKKMNVWIWISTFLQLKQIKDNHALSYNPSNNKQVLFSVHLG*