AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0080048690.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048690.01.T01 MTR_6g042220 99.346 153 1 0 1 153 1 153 4.77e-105 298
MsG0080048690.01.T01 MTR_4g006110 99.346 153 1 0 1 153 1 153 4.86e-105 301
MsG0080048690.01.T01 MTR_7g021710 98.693 153 2 0 1 153 1 153 2.96e-104 300
MsG0080048690.01.T01 MTR_5g063410 95.425 153 7 0 1 153 1 153 1.56e-98 285
MsG0080048690.01.T01 MTR_0002s0160 66.019 103 33 1 51 153 160 260 1.02e-40 138
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048690.01.T01 ATCG01080 79.739 153 31 0 1 153 1 153 1.68e-73 218

Find 18 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCATGGTACGGAATTATT+TGG 0.128600 contig404end:+29644 MsG0080048690.01.T01:CDS
AGAAAATCGTGTAGCGTTTC+AGG 0.203741 contig404end:-29301 None:intergenic
CTGGGATCGGGTATTATATT+AGG 0.243721 contig404end:+29334 MsG0080048690.01.T01:CDS
ATTAAAATCTTGGTAATATT+CGG 0.281186 contig404end:-29542 None:intergenic
GTTTGATAAAATATATAATA+AGG 0.323451 contig404end:-29431 None:intergenic
TCTTGCTCAATAATCTGATT+TGG 0.326155 contig404end:-29676 None:intergenic
ATAAGTACTAGTCAACAAAT+TGG 0.328309 contig404end:+29703 MsG0080048690.01.T01:CDS
ATTCCGTACCATGAAGTATC+TGG 0.340621 contig404end:-29637 None:intergenic
CTATTATTCCAGATACTTCA+TGG 0.342688 contig404end:+29629 MsG0080048690.01.T01:CDS
ATTATTGAAATTAGTTCAAA+TGG 0.371871 contig404end:-29753 None:intergenic
CAGTCCAAAGATTAAAATCT+TGG 0.418502 contig404end:-29552 None:intergenic
GCTGTGATGCAGCTACAAAA+TGG 0.434524 contig404end:-29456 None:intergenic
CTGTGATGCAGCTACAAAAT+GGG 0.476099 contig404end:-29455 None:intergenic
GGTATTATATTAGGAAGTCT+AGG 0.532440 contig404end:+29343 MsG0080048690.01.T01:CDS
AATCTTTGGACTGTTGGGGA+TGG 0.537956 contig404end:+29562 MsG0080048690.01.T01:CDS
ATTCCAGATACTTCATGGTA+CGG 0.544710 contig404end:+29634 MsG0080048690.01.T01:CDS
ATCACAGCTACTTATTTACG+TGG 0.622433 contig404end:+29471 MsG0080048690.01.T01:CDS
TCACAGCTACTTATTTACGT+GGG 0.687021 contig404end:+29472 MsG0080048690.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTTGATAAAATATATAATA+AGG - contig404end:29434-29453 None:intergenic 10.0%
!! ATTATTGAAATTAGTTCAAA+TGG - contig404end:29756-29775 None:intergenic 15.0%
!!! ATTAAAATCTTGGTAATATT+CGG - contig404end:29545-29564 None:intergenic 15.0%
!!! ATTACCAAGATTTTAATCTT+TGG + contig404end:29548-29567 MsG0080048690.01.T01:CDS 20.0%
! AACGAAAAAGCAGAAAAAAT+AGG - contig404end:29388-29407 None:intergenic 25.0%
! ACGAAAAAGCAGAAAAAATA+GGG - contig404end:29387-29406 None:intergenic 25.0%
! ATAAGTACTAGTCAACAAAT+TGG + contig404end:29703-29722 MsG0080048690.01.T01:CDS 25.0%
! GTTCAAATGGAAGAAAAAAT+CGG - contig404end:29743-29762 None:intergenic 25.0%
!!! ATTCTTTTAGTTGCTTTGAT+AGG + contig404end:29774-29793 MsG0080048690.01.T02:CDS 25.0%
!!! ATTTTAATCTTTGGACTGTT+GGG + contig404end:29557-29576 MsG0080048690.01.T01:CDS 25.0%
!!! ATTTTTTCTGCTTTTTCGTT+GGG + contig404end:29388-29407 MsG0080048690.01.T01:CDS 25.0%
!!! GATTTTCTTTTAGTCTTTCT+GGG + contig404end:29316-29335 MsG0080048690.01.T01:CDS 25.0%
!!! TATTTTTTCTGCTTTTTCGT+TGG + contig404end:29387-29406 MsG0080048690.01.T01:CDS 25.0%
AAAAGCAGAAAAAATAGGGT+TGG - contig404end:29383-29402 None:intergenic 30.0%
CAGTCCAAAGATTAAAATCT+TGG - contig404end:29555-29574 None:intergenic 30.0%
CTATTATTCCAGATACTTCA+TGG + contig404end:29629-29648 MsG0080048690.01.T01:CDS 30.0%
GGTATTATATTAGGAAGTCT+AGG + contig404end:29343-29362 MsG0080048690.01.T01:CDS 30.0%
TCTTGCTCAATAATCTGATT+TGG - contig404end:29679-29698 None:intergenic 30.0%
! TTTTAATCTTTGGACTGTTG+GGG + contig404end:29558-29577 MsG0080048690.01.T01:CDS 30.0%
!! CGATTTTCTTTTAGTCTTTC+TGG + contig404end:29315-29334 MsG0080048690.01.T01:CDS 30.0%
!! GATTTTAATCTTTGGACTGT+TGG + contig404end:29556-29575 MsG0080048690.01.T01:CDS 30.0%
ATCACAGCTACTTATTTACG+TGG + contig404end:29471-29490 MsG0080048690.01.T01:CDS 35.0%
ATTCCAGATACTTCATGGTA+CGG + contig404end:29634-29653 MsG0080048690.01.T01:CDS 35.0%
CTTCATGGTACGGAATTATT+TGG + contig404end:29644-29663 MsG0080048690.01.T01:CDS 35.0%
TCACAGCTACTTATTTACGT+GGG + contig404end:29472-29491 MsG0080048690.01.T01:CDS 35.0%
!!! TCTTTTAGTCTTTCTGGGAT+CGG + contig404end:29321-29340 MsG0080048690.01.T01:CDS 35.0%
AGAAAATCGTGTAGCGTTTC+AGG - contig404end:29304-29323 None:intergenic 40.0%
CTGGGATCGGGTATTATATT+AGG + contig404end:29334-29353 MsG0080048690.01.T01:CDS 40.0%
CTGTGATGCAGCTACAAAAT+GGG - contig404end:29458-29477 None:intergenic 40.0%
! ATTCCGTACCATGAAGTATC+TGG - contig404end:29640-29659 None:intergenic 40.0%
!!! CTTTTAGTCTTTCTGGGATC+GGG + contig404end:29322-29341 MsG0080048690.01.T01:CDS 40.0%
AATCTTTGGACTGTTGGGGA+TGG + contig404end:29562-29581 MsG0080048690.01.T01:CDS 45.0%
GCTGTGATGCAGCTACAAAA+TGG - contig404end:29459-29478 None:intergenic 45.0%
!!! TTCTGCTTTTTCGTTGGGAC+TGG + contig404end:29393-29412 MsG0080048690.01.T01:CDS 45.0%
Chromosome Type Strat End Strand Name
contig404end gene 29292 29821 29292 ID=MsG0080048690.01;Name=MsG0080048690.01
contig404end mRNA 29292 29765 29292 ID=MsG0080048690.01.T01;Parent=MsG0080048690.01;Name=MsG0080048690.01.T01;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|157
contig404end exon 29292 29765 29292 ID=MsG0080048690.01.T01:exon:5392;Parent=MsG0080048690.01.T01
contig404end CDS 29292 29765 29292 ID=MsG0080048690.01.T01:cds;Parent=MsG0080048690.01.T01
contig404end mRNA 29714 29821 29714 ID=MsG0080048690.01.T02;Parent=MsG0080048690.01;Name=MsG0080048690.01.T02;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|35
contig404end exon 29714 29821 29714 ID=MsG0080048690.01.T02:exon:5393;Parent=MsG0080048690.01.T02
contig404end CDS 29714 29821 29714 ID=MsG0080048690.01.T02:cds;Parent=MsG0080048690.01.T02
contig404end mRNA 29744 29821 29744 ID=MsG0080048690.01.T03;Parent=MsG0080048690.01;Name=MsG0080048690.01.T03;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|25
contig404end exon 29744 29821 29744 ID=MsG0080048690.01.T03:exon:5394;Parent=MsG0080048690.01.T03
contig404end CDS 29744 29821 29744 ID=MsG0080048690.01.T03:cds;Parent=MsG0080048690.01.T03
Gene Sequence

>MsG0080048690.01.T03

TTTTTTCTTCCATTTGAACTAATTTCAATAATTCTTTTAGTTGCTTTGATAGGTGCAATTGTCGTAGCTCGCCAGTAA

>MsG0080048690.01.T02

TCAACAAATTGGAATTCATTTATCAACCGATTTTTTCTTCCATTTGAACTAATTTCAATAATTCTTTTAGTTGCTTTGATAGGTGCAATTGTCGTAGCTCGCCAGTAA

>MsG0080048690.01.T01

ATGGATTTGCCTGAAACGCTACACGATTTTCTTTTAGTCTTTCTGGGATCGGGTATTATATTAGGAAGTCTAGGAGTAGTATTACTTACCAACCCTATTTTTTCTGCTTTTTCGTTGGGACTGGTTCTTGTTTGTATATCCTTATTATATATTTTATCAAACTCCCATTTTGTAGCTGCATCACAGCTACTTATTTACGTGGGAGCTATTAACATTTTAATCATATTTGCTGTGATGTTCATGAATAGTTCCGAATATTACCAAGATTTTAATCTTTGGACTGTTGGGGATGGAATTACTTTGATAGTTTGTACAAGTATTTTTGTTTCACTAATAACTATTATTCCAGATACTTCATGGTACGGAATTATTTGGACTACAAGACCAAATCAGATTATTGAGCAAGATTTGATAAGTACTAGTCAACAAATTGGAATTCATTTATCAACCGATTTTTTCTTCCATTTGAACTAA

Protein sequence

>MsG0080048690.01.T03

FFLPFELISIILLVALIGAIVVARQ*

>MsG0080048690.01.T02

STNWNSFINRFFLPFELISIILLVALIGAIVVARQ*

>MsG0080048690.01.T01

MDLPETLHDFLLVFLGSGIILGSLGVVLLTNPIFSAFSLGLVLVCISLLYILSNSHFVAASQLLIYVGAINILIIFAVMFMNSSEYYQDFNLWTVGDGITLIVCTSIFVSLITIIPDTSWYGIIWTTRPNQIIEQDLISTSQQIGIHLSTDFFFHLN*