AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000677.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000677.01.T01 MTR_1g010080 96.364 110 3 1 50 158 4 113 1.08e-70 214
MsG0180000677.01.T01 MTR_1g010080 96.364 110 3 1 50 158 36 145 7.73e-70 213
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000677.01.T01 AT4G31115 51.456 103 43 2 59 159 53 150 9.72e-28 105
MsG0180000677.01.T01 AT4G31115 51.456 103 43 2 59 159 77 174 2.09e-27 104

Find 27 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATACCAGTGGGTGAAATTT+TGG 0.136941 1:-9641986 None:intergenic
TTGTAAGGTGTTCCCTTTAC+AGG 0.189342 1:+9643160 MsG0180000677.01.T01:CDS
ATGGATATGGACAACACTTC+TGG 0.311251 1:+9641949 MsG0180000677.01.T01:CDS
AAATTTGTTTGCTACCAAAA+AGG 0.335324 1:+9642251 MsG0180000677.01.T01:CDS
GGTTGAAATGATTTCTTGTA+AGG 0.383448 1:+9643145 MsG0180000677.01.T01:CDS
TGTAACAAATGGTATGGATA+TGG 0.393474 1:+9641936 None:intergenic
ACATATGATGATGATGTTCT+TGG 0.416434 1:+9642291 MsG0180000677.01.T01:CDS
CTCAACAGATGAAGATTGCT+TGG 0.427861 1:+9643124 MsG0180000677.01.T01:CDS
AAGCTGTAAAATCCTGTAAA+GGG 0.436124 1:-9643172 None:intergenic
AACTTCAAAAGTTTAAGTTT+CGG 0.449422 1:-9643068 None:intergenic
AAAGCTGTAAAATCCTGTAA+AGG 0.457307 1:-9643173 None:intergenic
CTCTTGATGCTAACACATAC+AGG 0.460337 1:+9642403 MsG0180000677.01.T01:CDS
CCTTCCAAAATTTCACCCAC+TGG 0.481584 1:+9641982 MsG0180000677.01.T01:CDS
CTGCTGAAATTCCACTAGGC+TGG 0.516337 1:-9642347 None:intergenic
TGGTAGAGCAACAGATGGAA+TGG 0.518315 1:+9643211 MsG0180000677.01.T01:CDS
AGTGAAGGCGGTGACTTCCT+CGG 0.562765 1:+9642209 MsG0180000677.01.T01:CDS
CAAGCAATCTTCATCTGTTG+AGG 0.563145 1:-9643123 None:intergenic
AGAACATCATCATCATATGT+TGG 0.582748 1:-9642288 None:intergenic
GGCTTAGAAATTCACTGATG+TGG 0.588070 1:-9642326 None:intergenic
TATGATGATGATGTTCTTGG+AGG 0.598580 1:+9642294 MsG0180000677.01.T01:CDS
TGATGATGTTCTTGGAGGAA+AGG 0.602689 1:+9642299 MsG0180000677.01.T01:CDS
TTTCTTTGCATTTGAATCCG+AGG 0.616050 1:-9642226 None:intergenic
GAATTTCTAAGCCAGCCTAG+TGG 0.653471 1:+9642336 MsG0180000677.01.T01:CDS
GTAACACGCAGATCTATGAA+AGG 0.668571 1:-9643101 None:intergenic
TTCAGCAGTGCTGAACACAA+AGG 0.692653 1:+9642362 MsG0180000677.01.T01:CDS
AGCACTGCTGAAATTCCACT+AGG 0.696857 1:-9642351 None:intergenic
AAATGGGCATCAAGTGAAGG+CGG 0.697084 1:+9642197 MsG0180000677.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCAATATAGAAAAAGAATT+AGG - Chr1:9642573-9642592 None:intergenic 15.0%
!!! AAGTTATTTTTTAAATGGTT+TGG + Chr1:9642459-9642478 MsG0180000677.01.T01:intron 15.0%
!!! ACATTTCATATAAGTTATTT+TGG + Chr1:9642773-9642792 MsG0180000677.01.T01:intron 15.0%
!! ATTAAATTAAAGTCAAGTTC+AGG + Chr1:9642521-9642540 MsG0180000677.01.T01:intron 20.0%
!! TATTTACTTATTGTATGTGT+AGG + Chr1:9643036-9643055 MsG0180000677.01.T01:intron 20.0%
!!! AACTTCAAAAGTTTAAGTTT+CGG - Chr1:9643071-9643090 None:intergenic 20.0%
!!! ATTTTCAACCTATTTGTATA+TGG - Chr1:9642629-9642648 None:intergenic 20.0%
!!! GGCTTAAGTTATTTTTTAAA+TGG + Chr1:9642454-9642473 MsG0180000677.01.T01:intron 20.0%
!!! TATTTTTTAAATGGTTTGGA+TGG + Chr1:9642463-9642482 MsG0180000677.01.T01:intron 20.0%
!!! TTTAGACAATTGATTCTATA+GGG - Chr1:9642906-9642925 None:intergenic 20.0%
! ATCCAACAGGAAAAAAAAAA+TGG - Chr1:9642095-9642114 None:intergenic 25.0%
! ATCCTATTCCTTATATTTGA+TGG + Chr1:9642647-9642666 MsG0180000677.01.T01:intron 25.0%
! TAAAAAATAACTTAAGCCAC+TGG - Chr1:9642452-9642471 None:intergenic 25.0%
!! AAATTTGTTTGCTACCAAAA+AGG + Chr1:9642251-9642270 MsG0180000677.01.T01:CDS 25.0%
!! CTTTAGACAATTGATTCTAT+AGG - Chr1:9642907-9642926 None:intergenic 25.0%
!! TAGTTTAACTCTTTCCTTTT+TGG - Chr1:9642268-9642287 None:intergenic 25.0%
!! TATCTATAATTCTTTTCCAG+TGG + Chr1:9642433-9642452 MsG0180000677.01.T01:intron 25.0%
!!! AATCAATTGTCTAAAGCTTT+TGG + Chr1:9642911-9642930 MsG0180000677.01.T01:intron 25.0%
!!! GCTTTTTTTTCTTCTTCTTT+TGG + Chr1:9643191-9643210 MsG0180000677.01.T01:CDS 25.0%
!!! TTCCATTTTTTTTTTCCTGT+TGG + Chr1:9642090-9642109 MsG0180000677.01.T01:intron 25.0%
AAAGCTGTAAAATCCTGTAA+AGG - Chr1:9643176-9643195 None:intergenic 30.0%
AAGCTGTAAAATCCTGTAAA+GGG - Chr1:9643175-9643194 None:intergenic 30.0%
AAGTTAAGTAAACATACCAG+TGG - Chr1:9642001-9642020 None:intergenic 30.0%
AGAACATCATCATCATATGT+TGG - Chr1:9642291-9642310 None:intergenic 30.0%
AGTGAGTAATCAGCTTAATT+AGG + Chr1:9642689-9642708 MsG0180000677.01.T01:intron 30.0%
AGTTAAGTAAACATACCAGT+GGG - Chr1:9642000-9642019 None:intergenic 30.0%
CACCATCAAATATAAGGAAT+AGG - Chr1:9642652-9642671 None:intergenic 30.0%
CAGTTTCACCATATACAAAT+AGG + Chr1:9642618-9642637 MsG0180000677.01.T01:intron 30.0%
CATAGTCACCATCAAATATA+AGG - Chr1:9642658-9642677 None:intergenic 30.0%
GGTTGAAATGATTTCTTGTA+AGG + Chr1:9643145-9643164 MsG0180000677.01.T01:CDS 30.0%
! ACATATGATGATGATGTTCT+TGG + Chr1:9642291-9642310 MsG0180000677.01.T01:CDS 30.0%
!! CTTATATTTGATGGTGACTA+TGG + Chr1:9642656-9642675 MsG0180000677.01.T01:intron 30.0%
!!! GTTATTTTGGTAAGCAATCT+TGG + Chr1:9642786-9642805 MsG0180000677.01.T01:intron 30.0%
!!! TTTTTTTCCTGTTGGATTGT+AGG + Chr1:9642098-9642117 MsG0180000677.01.T01:intron 30.0%
CTGATTACTCACTCATACAA+CGG - Chr1:9642682-9642701 None:intergenic 35.0%
GCTTATATAAGCTTCTGTAC+TGG - Chr1:9642870-9642889 None:intergenic 35.0%
TAAAAATGGGCATCAAGTGA+AGG + Chr1:9642194-9642213 MsG0180000677.01.T01:CDS 35.0%
TTTCTTTGCATTTGAATCCG+AGG - Chr1:9642229-9642248 None:intergenic 35.0%
! TATGATGATGATGTTCTTGG+AGG + Chr1:9642294-9642313 MsG0180000677.01.T01:CDS 35.0%
! TTGATTCTATAGGGCTTGTT+TGG - Chr1:9642897-9642916 None:intergenic 35.0%
!! GAAATTTTGGAAGGAATGTG+TGG - Chr1:9641976-9641995 None:intergenic 35.0%
ATGGATATGGACAACACTTC+TGG + Chr1:9641949-9641968 MsG0180000677.01.T01:CDS 40.0%
CAAGCAATCTTCATCTGTTG+AGG - Chr1:9643126-9643145 None:intergenic 40.0%
CTCAACAGATGAAGATTGCT+TGG + Chr1:9643124-9643143 MsG0180000677.01.T01:CDS 40.0%
CTCTTGATGCTAACACATAC+AGG + Chr1:9642403-9642422 MsG0180000677.01.T01:CDS 40.0%
GGCTTAGAAATTCACTGATG+TGG - Chr1:9642329-9642348 None:intergenic 40.0%
GTAACACGCAGATCTATGAA+AGG - Chr1:9643104-9643123 None:intergenic 40.0%
GTCAGATAGAGCAGAAACAA+AGG - Chr1:9642042-9642061 None:intergenic 40.0%
! CATACCAGTGGGTGAAATTT+TGG - Chr1:9641989-9642008 None:intergenic 40.0%
! TCTATAGGGCTTGTTTGGAT+TGG - Chr1:9642892-9642911 None:intergenic 40.0%
! TCTTTTGGTAGAGCAACAGA+TGG + Chr1:9643206-9643225 MsG0180000677.01.T01:CDS 40.0%
! TGATGATGTTCTTGGAGGAA+AGG + Chr1:9642299-9642318 MsG0180000677.01.T01:CDS 40.0%
! TTGTAAGGTGTTCCCTTTAC+AGG + Chr1:9643160-9643179 MsG0180000677.01.T01:CDS 40.0%
! TTTGAGACCTACAATCCAAC+AGG - Chr1:9642108-9642127 None:intergenic 40.0%
AAATGGGCATCAAGTGAAGG+CGG + Chr1:9642197-9642216 MsG0180000677.01.T01:CDS 45.0%
AGCACTGCTGAAATTCCACT+AGG - Chr1:9642354-9642373 None:intergenic 45.0%
CCTTCCAAAATTTCACCCAC+TGG + Chr1:9641982-9642001 MsG0180000677.01.T01:CDS 45.0%
GAATTTCTAAGCCAGCCTAG+TGG + Chr1:9642336-9642355 MsG0180000677.01.T01:CDS 45.0%
TGGTAGAGCAACAGATGGAA+TGG + Chr1:9643211-9643230 MsG0180000677.01.T01:CDS 45.0%
! CCAGTGGGTGAAATTTTGGA+AGG - Chr1:9641985-9642004 None:intergenic 45.0%
! TTCAGCAGTGCTGAACACAA+AGG + Chr1:9642362-9642381 MsG0180000677.01.T01:CDS 45.0%
!! ATTTATTTATTTAGTAAAAA+TGG + Chr1:9642180-9642199 MsG0180000677.01.T01:CDS 5.0%
!! TTTATTTATTTAGTAAAAAT+GGG + Chr1:9642181-9642200 MsG0180000677.01.T01:CDS 5.0%
CTGCTGAAATTCCACTAGGC+TGG - Chr1:9642350-9642369 None:intergenic 50.0%
GATTGCACTAGCTAGTGCTG+TGG + Chr1:9642994-9643013 MsG0180000677.01.T01:intron 50.0%
AGTGAAGGCGGTGACTTCCT+CGG + Chr1:9642209-9642228 MsG0180000677.01.T01:CDS 55.0%
Chromosome Type Strat End Strand Name
Chr1 gene 9641944 9643259 9641944 ID=MsG0180000677.01;Name=MsG0180000677.01
Chr1 mRNA 9641944 9643259 9641944 ID=MsG0180000677.01.T01;Parent=MsG0180000677.01;Name=MsG0180000677.01.T01;_AED=0.50;_eAED=0.56;_QI=0|0|0|1|0.5|0.66|3|0|188
Chr1 exon 9641944 9642003 9641944 ID=MsG0180000677.01.T01:exon:1821;Parent=MsG0180000677.01.T01
Chr1 exon 9642120 9642424 9642120 ID=MsG0180000677.01.T01:exon:1820;Parent=MsG0180000677.01.T01
Chr1 exon 9643058 9643259 9643058 ID=MsG0180000677.01.T01:exon:1819;Parent=MsG0180000677.01.T01
Chr1 CDS 9641944 9642003 9641944 ID=MsG0180000677.01.T01:cds;Parent=MsG0180000677.01.T01
Chr1 CDS 9642120 9642424 9642120 ID=MsG0180000677.01.T01:cds;Parent=MsG0180000677.01.T01
Chr1 CDS 9643058 9643259 9643058 ID=MsG0180000677.01.T01:cds;Parent=MsG0180000677.01.T01
Gene Sequence

>MsG0180000677.01.T01

ATGGTATGGATATGGACAACACTTCTGGACCACACATTCCTTCCAAAATTTCACCCACTGGTCTCAAATCTTGTGAACTTTGATCTTTTCTATGAGTTGTTACTTTTGTTCATAAATTTGATTTATTTATTTAGTAAAAATGGGCATCAAGTGAAGGCGGTGACTTCCTCGGATTCAAATGCAAAGAAAGCAAATTTGTTTGCTACCAAAAAGGAAAGAGTTAAACTACCAACATATGATGATGATGTTCTTGGAGGAAAGGAATACCACATCAGTGAATTTCTAAGCCAGCCTAGTGGAATTTCAGCAGTGCTGAACACAAAGGTCTTGCAATCATTTCAATCTCTTGATGCTAACACATACAGGTGTGAACTACCGAAACTTAAACTTTTGAAGTTTGAAGTTTCTCCTTTCATAGATCTGCGTGTTACCTCAACAGATGAAGATTGCTTGGTTGAAATGATTTCTTGTAAGGTGTTCCCTTTACAGGATTTTACAGCTTTTTTTTCTTCTTCTTTTGGTAGAGCAACAGATGGAATGGAACACACATACGCACACGCACGATGA

Protein sequence

>MsG0180000677.01.T01

MVWIWTTLLDHTFLPKFHPLVSNLVNFDLFYELLLLFINLIYLFSKNGHQVKAVTSSDSNAKKANLFATKKERVKLPTYDDDVLGGKEYHISEFLSQPSGISAVLNTKVLQSFQSLDANTYRCELPKLKLLKFEVSPFIDLRVTSTDEDCLVEMISCKVFPLQDFTAFFSSSFGRATDGMEHTYAHAR*