AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000671.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000671.01.T01 MTR_1g010080 95.172 145 6 1 1 144 1 145 2.85e-99 287
MsG0180000671.01.T01 MTR_1g010080 96.460 113 3 1 33 144 1 113 6.76e-73 219
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000671.01.T01 AT4G31115 51.456 103 43 2 45 145 53 150 6.02e-28 105
MsG0180000671.01.T01 AT4G31115 51.456 103 43 2 45 145 77 174 1.28e-27 104

Find 35 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAACCAGTGGGTGAAATTT+TGG 0.136941 1:+9521759 None:intergenic
TTGTAAGGTGTTCCCTTTAC+AGG 0.189342 1:-9520581 MsG0180000671.01.T01:CDS
ATGGATATGGACAACACTTC+TGG 0.311251 1:-9521796 MsG0180000671.01.T01:CDS
AAATTTGTTTGCTACCAAAA+AGG 0.335324 1:-9521495 MsG0180000671.01.T01:CDS
GGTTGAAATGATTTCTTGTA+AGG 0.383448 1:-9520596 MsG0180000671.01.T01:CDS
TGTAACAAATGGTATGGATA+TGG 0.393474 1:-9521809 MsG0180000671.01.T01:CDS
CAGATTCATTCATTGATTGA+TGG 0.405628 1:-9522011 MsG0180000671.01.T01:exon
ACATATGATGATGATGTTCT+TGG 0.416434 1:-9521455 MsG0180000671.01.T01:CDS
CATACCATTTGTTACACAAA+AGG 0.421304 1:+9521816 None:intergenic
CTCAACAGATGAAGATTGCT+TGG 0.427861 1:-9520617 MsG0180000671.01.T01:CDS
AAGCTGTAAAATCCTGTAAA+GGG 0.436124 1:+9520569 None:intergenic
AACTTCAAAAGTTTAAGTTT+CGG 0.449422 1:+9520673 None:intergenic
AAAGCTGTAAAATCCTGTAA+AGG 0.457307 1:+9520568 None:intergenic
CTCTTGATGCTAACACATAC+AGG 0.460337 1:-9521343 MsG0180000671.01.T01:intron
CCTTCCAAAATTTCACCCAC+TGG 0.462349 1:-9521763 MsG0180000671.01.T01:intron
AGATTCATTCATTGATTGAT+GGG 0.464869 1:-9522010 MsG0180000671.01.T01:intron
TAGTAAGAAAATGGGCATCA+AGG 0.504994 1:-9521558 MsG0180000671.01.T01:CDS
TGAATGAATCTGTGTGGTAA+AGG 0.506154 1:+9522022 None:intergenic
GAATGAATCTGTGTGGTAAA+GGG 0.516149 1:+9522023 None:intergenic
CTGCTGAAATTCCACTAGGC+TGG 0.516337 1:+9521399 None:intergenic
TGGTAGAGCAACAGATGGAA+TGG 0.518315 1:-9520530 MsG0180000671.01.T01:CDS
CAAGCAATCTTCATCTGTTG+AGG 0.563145 1:+9520618 None:intergenic
AGAACATCATCATCATATGT+TGG 0.582748 1:+9521458 None:intergenic
GGCTTAGAAATTCACTGATG+TGG 0.588070 1:+9521420 None:intergenic
GAAAATGGGCATCAAGGTGA+AGG 0.588739 1:-9521552 MsG0180000671.01.T01:CDS
GGTGAAGGCAGTGACTTCCT+CGG 0.589813 1:-9521537 MsG0180000671.01.T01:CDS
TATGATGATGATGTTCTTGG+AGG 0.598580 1:-9521452 MsG0180000671.01.T01:CDS
TGATGATGTTCTTGGAGGAA+AGG 0.602689 1:-9521447 MsG0180000671.01.T01:CDS
TTTCTTTGCATTTGAATCCG+AGG 0.616050 1:+9521520 None:intergenic
GAATTTCTAAGCCAGCCTAG+TGG 0.653471 1:-9521410 MsG0180000671.01.T01:CDS
GTAACACGCAGATCTATGAA+AGG 0.668571 1:+9520640 None:intergenic
TTCAGCAGTGCTGAACACAA+AGG 0.692653 1:-9521384 MsG0180000671.01.T01:CDS
AGCACTGCTGAAATTCCACT+AGG 0.696857 1:+9521395 None:intergenic
AAGTTGTGAGTAACAGACAG+TGG 0.698506 1:-9522090 None:intergenic
AATCAATGAATGAATCTGTG+TGG 0.749340 1:+9522016 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTATTTTAGTAAGAAAAT+GGG - Chr1:9521013-9521032 MsG0180000671.01.T01:intron 10.0%
!!! TATTTATTTTAGTAAGAAAA+TGG - Chr1:9521012-9521031 MsG0180000671.01.T01:intron 10.0%
!! AAAATACTATTCCTTATATT+TGG - Chr1:9521478-9521497 MsG0180000671.01.T01:CDS 15.0%
!! AGTAAATGAAAAAAAAACAT+TGG + Chr1:9520606-9520625 None:intergenic 15.0%
!! TTCAATATAGAAAAAGAATT+AGG + Chr1:9521406-9521425 None:intergenic 15.0%
!!! AAGTTATTTTTTAAATGGTT+TGG - Chr1:9521292-9521311 MsG0180000671.01.T01:intron 15.0%
!!! ACATTTCATATAAGTTATTT+TGG - Chr1:9521611-9521630 MsG0180000671.01.T01:intron 15.0%
!! ACTATGAAATCTTGAAATTA+TGG + Chr1:9520680-9520699 None:intergenic 20.0%
!! ATTAAATTAAAGTCAAGTTC+AGG - Chr1:9521355-9521374 MsG0180000671.01.T01:CDS 20.0%
!! TATTTACTTATTGTATGTGT+AGG - Chr1:9521874-9521893 MsG0180000671.01.T01:intron 20.0%
!! TTTCAAGATTTCATAGTTAT+TGG - Chr1:9520683-9520702 MsG0180000671.01.T01:CDS 20.0%
!!! AACTTCAAAAGTTTAAGTTT+CGG + Chr1:9521909-9521928 None:intergenic 20.0%
!!! ATTTTTTAAATGGTTTGGAT+TGG - Chr1:9521297-9521316 MsG0180000671.01.T01:intron 20.0%
!!! GGCTTAAGTTATTTTTTAAA+TGG - Chr1:9521287-9521306 MsG0180000671.01.T01:intron 20.0%
!!! TTTAGACAATTGATTCTATA+GGG + Chr1:9521744-9521763 None:intergenic 20.0%
!!! TTTTCAACCTATTTTGTATA+TGG + Chr1:9521462-9521481 None:intergenic 20.0%
! ACTATTCCTTATATTTGGAA+TGG - Chr1:9521483-9521502 MsG0180000671.01.T01:CDS 25.0%
! AGTTTCACCATATACAAAAT+AGG - Chr1:9521452-9521471 MsG0180000671.01.T01:CDS 25.0%
! TAAAAAATAACTTAAGCCAC+TGG + Chr1:9521285-9521304 None:intergenic 25.0%
!! AAATTTGTTTGCTACCAAAA+AGG - Chr1:9521084-9521103 MsG0180000671.01.T01:intron 25.0%
!! AGATTCATTCATTGATTGAT+GGG - Chr1:9520569-9520588 MsG0180000671.01.T01:CDS 25.0%
!! CTTTAGACAATTGATTCTAT+AGG + Chr1:9521745-9521764 None:intergenic 25.0%
!! TAGTTTAACTCTTTCCTTTT+TGG + Chr1:9521101-9521120 None:intergenic 25.0%
!! TATCTTTAATTCTTTTCCAG+TGG - Chr1:9521266-9521285 MsG0180000671.01.T01:intron 25.0%
!! TTTATGTTCCATTGATAGTT+TGG - Chr1:9520714-9520733 MsG0180000671.01.T01:intron 25.0%
!!! AATCAATTGTCTAAAGCTTT+TGG - Chr1:9521749-9521768 MsG0180000671.01.T01:intron 25.0%
!!! GCTTTTTTTTCTTCTTCTTT+TGG - Chr1:9522029-9522048 MsG0180000671.01.T01:five_prime_UTR 25.0%
!!! TGCTTTCATTTTTTACCTAT+TGG - Chr1:9520919-9520938 MsG0180000671.01.T01:intron 25.0%
!!! TTTTTTACCTATTGGATTGT+AGG - Chr1:9520927-9520946 MsG0180000671.01.T01:intron 25.0%
AAAGCTGTAAAATCCTGTAA+AGG + Chr1:9522014-9522033 None:intergenic 30.0%
AAGCTGTAAAATCCTGTAAA+GGG + Chr1:9522013-9522032 None:intergenic 30.0%
AAGTTAAGTAAACAAACCAG+TGG + Chr1:9520835-9520854 None:intergenic 30.0%
AATCAATGAATGAATCTGTG+TGG + Chr1:9520566-9520585 None:intergenic 30.0%
AGAACATCATCATCATATGT+TGG + Chr1:9521124-9521143 None:intergenic 30.0%
AGTGAGTAATCAGCTTAATT+AGG - Chr1:9521526-9521545 MsG0180000671.01.T01:CDS 30.0%
AGTTAAGTAAACAAACCAGT+GGG + Chr1:9520834-9520853 None:intergenic 30.0%
GGTTGAAATGATTTCTTGTA+AGG - Chr1:9521983-9522002 MsG0180000671.01.T01:intron 30.0%
TGTAACAAATGGTATGGATA+TGG - Chr1:9520770-9520789 MsG0180000671.01.T01:intron 30.0%
! ACATATGATGATGATGTTCT+TGG - Chr1:9521124-9521143 MsG0180000671.01.T01:intron 30.0%
! CAATCCTTTTGTGTAACAAA+TGG - Chr1:9520759-9520778 MsG0180000671.01.T01:intron 30.0%
! CAGATTCATTCATTGATTGA+TGG - Chr1:9520568-9520587 MsG0180000671.01.T01:CDS 30.0%
! CATACCATTTGTTACACAAA+AGG + Chr1:9520766-9520785 None:intergenic 30.0%
! CTTTTGTGTAACAAATGGTA+TGG - Chr1:9520764-9520783 MsG0180000671.01.T01:intron 30.0%
!!! GTTATTTTGGTAAGCAATCT+TGG - Chr1:9521624-9521643 MsG0180000671.01.T01:intron 30.0%
GAATGAATCTGTGTGGTAAA+GGG + Chr1:9520559-9520578 None:intergenic 35.0%
GCTTATATAAGCTTCTGTAC+TGG + Chr1:9521708-9521727 None:intergenic 35.0%
GTCACACCATTCCAAATATA+AGG + Chr1:9521492-9521511 None:intergenic 35.0%
TAATTTGATTGCAGTGCTAG+TGG + Chr1:9520632-9520651 None:intergenic 35.0%
TAGTAAGAAAATGGGCATCA+AGG - Chr1:9521021-9521040 MsG0180000671.01.T01:intron 35.0%
TGAATGAATCTGTGTGGTAA+AGG + Chr1:9520560-9520579 None:intergenic 35.0%
TTCAGATAGAGCAGAAACAA+AGG + Chr1:9520873-9520892 None:intergenic 35.0%
TTTCTTTGCATTTGAATCCG+AGG + Chr1:9521062-9521081 None:intergenic 35.0%
! TATGATGATGATGTTCTTGG+AGG - Chr1:9521127-9521146 MsG0180000671.01.T01:intron 35.0%
! TATTTGGAATGGTGTGACTA+TGG - Chr1:9521494-9521513 MsG0180000671.01.T01:CDS 35.0%
! TTGATTCTATAGGGCTTGTT+TGG + Chr1:9521735-9521754 None:intergenic 35.0%
! TTTGAGACCTACAATCCAAT+AGG + Chr1:9520937-9520956 None:intergenic 35.0%
!! AGAAAGCACCAAACTATCAA+TGG + Chr1:9520725-9520744 None:intergenic 35.0%
!! GAAATTTTGGAAGGAATGTG+TGG + Chr1:9520810-9520829 None:intergenic 35.0%
ATGGATATGGACAACACTTC+TGG - Chr1:9520783-9520802 MsG0180000671.01.T01:intron 40.0%
CAAGCAATCTTCATCTGTTG+AGG + Chr1:9521964-9521983 None:intergenic 40.0%
CTCAACAGATGAAGATTGCT+TGG - Chr1:9521962-9521981 MsG0180000671.01.T01:intron 40.0%
CTCTTGATGCTAACACATAC+AGG - Chr1:9521236-9521255 MsG0180000671.01.T01:intron 40.0%
GCTGATTACTCACTCATACA+AGG + Chr1:9521520-9521539 None:intergenic 40.0%
GGCTTAGAAATTCACTGATG+TGG + Chr1:9521162-9521181 None:intergenic 40.0%
GTAACACGCAGATCTATGAA+AGG + Chr1:9521942-9521961 None:intergenic 40.0%
! CAAACCAGTGGGTGAAATTT+TGG + Chr1:9520823-9520842 None:intergenic 40.0%
! TCTATAGGGCTTGTTTGGAT+TGG + Chr1:9521730-9521749 None:intergenic 40.0%
! TCTTTTGGTAGAGCAACAGA+TGG - Chr1:9522044-9522063 MsG0180000671.01.T01:five_prime_UTR 40.0%
! TGATGATGTTCTTGGAGGAA+AGG - Chr1:9521132-9521151 MsG0180000671.01.T01:intron 40.0%
! TTGTAAGGTGTTCCCTTTAC+AGG - Chr1:9521998-9522017 MsG0180000671.01.T01:intron 40.0%
AGCACTGCTGAAATTCCACT+AGG + Chr1:9521187-9521206 None:intergenic 45.0%
CCTTCCAAAATTTCACCCAC+TGG - Chr1:9520816-9520835 MsG0180000671.01.T01:intron 45.0%
GAAAATGGGCATCAAGGTGA+AGG - Chr1:9521027-9521046 MsG0180000671.01.T01:intron 45.0%
GAATTTCTAAGCCAGCCTAG+TGG - Chr1:9521169-9521188 MsG0180000671.01.T01:intron 45.0%
TGGTAGAGCAACAGATGGAA+TGG - Chr1:9522049-9522068 MsG0180000671.01.T01:five_prime_UTR 45.0%
! CCAGTGGGTGAAATTTTGGA+AGG + Chr1:9520819-9520838 None:intergenic 45.0%
! TTCAGCAGTGCTGAACACAA+AGG - Chr1:9521195-9521214 MsG0180000671.01.T01:intron 45.0%
CTGCTGAAATTCCACTAGGC+TGG + Chr1:9521183-9521202 None:intergenic 50.0%
GATTGCACTAGCTAGTGCTG+TGG - Chr1:9521832-9521851 MsG0180000671.01.T01:intron 50.0%
GGTGAAGGCAGTGACTTCCT+CGG - Chr1:9521042-9521061 MsG0180000671.01.T01:intron 55.0%
Chromosome Type Strat End Strand Name
Chr1 gene 9520504 9522097 9520504 ID=MsG0180000671.01;Name=MsG0180000671.01
Chr1 mRNA 9520504 9522097 9520504 ID=MsG0180000671.01.T01;Parent=MsG0180000671.01;Name=MsG0180000671.01.T01;_AED=0.50;_eAED=0.52;_QI=83|1|0.75|1|0.33|0.5|4|0|174
Chr1 exon 9522011 9522097 9522011 ID=MsG0180000671.01.T01:exon:1687;Parent=MsG0180000671.01.T01
Chr1 exon 9521764 9521848 9521764 ID=MsG0180000671.01.T01:exon:1688;Parent=MsG0180000671.01.T01
Chr1 exon 9521344 9521577 9521344 ID=MsG0180000671.01.T01:exon:1689;Parent=MsG0180000671.01.T01
Chr1 exon 9520504 9520705 9520504 ID=MsG0180000671.01.T01:exon:1690;Parent=MsG0180000671.01.T01
Chr1 five_prime_UTR 9522015 9522097 9522015 ID=MsG0180000671.01.T01:five_prime_utr;Parent=MsG0180000671.01.T01
Chr1 CDS 9522011 9522014 9522011 ID=MsG0180000671.01.T01:cds;Parent=MsG0180000671.01.T01
Chr1 CDS 9521764 9521848 9521764 ID=MsG0180000671.01.T01:cds;Parent=MsG0180000671.01.T01
Chr1 CDS 9521344 9521577 9521344 ID=MsG0180000671.01.T01:cds;Parent=MsG0180000671.01.T01
Chr1 CDS 9520504 9520705 9520504 ID=MsG0180000671.01.T01:cds;Parent=MsG0180000671.01.T01
Gene Sequence

>MsG0180000671.01.T01

ATGGCAAAAGCAATCCTTTTGTGTAACAAATGGTATGGATATGGACAACACTTCTGGACCACACATTCCTTCCAAAATTTCACCCACTGTAAGAAAATGGGCATCAAGGTGAAGGCAGTGACTTCCTCGGATTCAAATGCAAAGAAAGCAAATTTGTTTGCTACCAAAAAGGAAAGAGTTAAACTACCAACATATGATGATGATGTTCTTGGAGGAAAGGAATACCACATCAGTGAATTTCTAAGCCAGCCTAGTGGAATTTCAGCAGTGCTGAACACAAAGGTCTTGCAATCATTTCAATCTCTTGATGCTAACACATACAGGTGTGAACTACCGAAACTTAAACTTTTGAAGTTTGAAGTTTCTCCTTTCATAGATCTGCGTGTTACCTCAACAGATGAAGATTGCTTGGTTGAAATGATTTCTTGTAAGGTGTTCCCTTTACAGGATTTTACAGCTTTTTTTTCTTCTTCTTTTGGTAGAGCAACAGATGGAATGGAACACACATACGCACACGCACGATGA

Protein sequence

>MsG0180000671.01.T01

MAKAILLCNKWYGYGQHFWTTHSFQNFTHCKKMGIKVKAVTSSDSNAKKANLFATKKERVKLPTYDDDVLGGKEYHISEFLSQPSGISAVLNTKVLQSFQSLDANTYRCELPKLKLLKFEVSPFIDLRVTSTDEDCLVEMISCKVFPLQDFTAFFSSSFGRATDGMEHTYAHAR*