AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580026709.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580026709.01.T01 MTR_8g072680 69.524 105 32 0 1 105 1 105 2.55e-46 149
MsG0580026709.01.T01 MTR_8g072680 69.524 105 32 0 1 105 1 105 3.10e-46 148
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580026709.01.T01 AT1G06790 51.429 105 51 0 1 105 1 105 1.24e-32 114
MsG0580026709.01.T01 AT1G06790 51.429 105 51 0 1 105 1 105 1.30e-32 114

Find 25 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAATAACCTCCACCGTAAA+TGG 0.246586 5:+42694566 None:intergenic
GAAGATAGAGCCGTCTTTAA+TGG 0.275944 5:+42695127 None:intergenic
CTTATTTCATCTGATGCTAA+TGG 0.347694 5:-42694536 MsG0580026709.01.T01:CDS
GATCATGTTTCGTCCATTTA+CGG 0.382904 5:-42694579 MsG0580026709.01.T01:CDS
ATGTTAGGTTATTGCAAACT+TGG 0.384232 5:-42695180 MsG0580026709.01.T01:intron
TTCTGTATGGCTTCTCGAAT+GGG 0.396840 5:+42695354 None:intergenic
CCTCTCAAGCTCTTTCTGTA+TGG 0.417659 5:+42695341 None:intergenic
TTTCTGTATGGCTTCTCGAA+TGG 0.442706 5:+42695353 None:intergenic
TAATTATCTCTTGTCATATG+TGG 0.476081 5:-42694471 MsG0580026709.01.T01:intron
GTTTCGTCCATTTACGGTGG+AGG 0.497836 5:-42694573 MsG0580026709.01.T01:CDS
ACAAGAGATAATTACAATCA+AGG 0.511680 5:+42694480 None:intergenic
TAAGTCGGAGCACCTTTGCT+AGG 0.527142 5:+42695104 None:intergenic
TGTTAGGTTATTGCAAACTT+GGG 0.534817 5:-42695179 MsG0580026709.01.T01:intron
GCAAGAAGAGAAGGAGGCAA+AGG 0.546432 5:+42695381 None:intergenic
TATGCTCAATCTTACTGAGA+TGG 0.560969 5:+42695409 None:intergenic
CCATACAGAAAGAGCTTGAG+AGG 0.566325 5:-42695341 MsG0580026709.01.T01:CDS
GGCTCTATCTTCCCTAGCAA+AGG 0.570353 5:-42695116 MsG0580026709.01.T01:CDS
AAGTCGGAGCACCTTTGCTA+GGG 0.579836 5:+42695105 None:intergenic
CATGTTTCGTCCATTTACGG+TGG 0.587034 5:-42694576 MsG0580026709.01.T01:CDS
CTCAACGAACCAAACACACC+CGG 0.588644 5:+42694021 None:intergenic
ATGGGAAGAGCAAGAAGAGA+AGG 0.589387 5:+42695372 None:intergenic
GGAAGAGCAAGAAGAGAAGG+AGG 0.589523 5:+42695375 None:intergenic
TAAACTCATACTAGGTAAGT+CGG 0.600321 5:+42695089 None:intergenic
GATATCATATCCATTAAAGA+CGG 0.615158 5:-42695137 MsG0580026709.01.T01:CDS
TATCATAAATAGATATGCAA+AGG 0.616023 5:+42695156 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTCTTTCATACTAATAATT+AGG - Chr5:42695078-42695097 MsG0580026709.01.T01:intron 15.0%
!! ATCAGAAACTAACTTAAAAA+TGG + Chr5:42695107-42695126 None:intergenic 20.0%
!! ATTATGGTTTATGAACTTAA+TGG - Chr5:42694560-42694579 MsG0580026709.01.T01:CDS 20.0%
!! GTCAAATAAATTACATATAG+TGG + Chr5:42694159-42694178 None:intergenic 20.0%
!! TATCATAAATAGATATGCAA+AGG + Chr5:42694242-42694261 None:intergenic 20.0%
!!! AGTCCTTAAATTTTGATTTA+CGG - Chr5:42694499-42694518 MsG0580026709.01.T01:CDS 20.0%
!!! ATTTTTTGTTTCAACAAGAT+GGG + Chr5:42695054-42695073 None:intergenic 20.0%
!!! TATTTTTTGTTTCAACAAGA+TGG + Chr5:42695055-42695074 None:intergenic 20.0%
!!! TGCTAACATTTTTTTTTTGA+AGG - Chr5:42694101-42694120 MsG0580026709.01.T01:intron 20.0%
!!! TTGCGTTTTAAAAAACATTA+TGG - Chr5:42694544-42694563 MsG0580026709.01.T01:CDS 20.0%
! AATGATGAACATAGATTTGT+AGG + Chr5:42694682-42694701 None:intergenic 25.0%
! ACAAGAGATAATTACAATCA+AGG + Chr5:42694918-42694937 None:intergenic 25.0%
! GATATCATATCCATTAAAGA+CGG - Chr5:42694258-42694277 MsG0580026709.01.T01:intron 25.0%
! TAATTATCTCTTGTCATATG+TGG - Chr5:42694924-42694943 MsG0580026709.01.T01:intron 25.0%
! TTTAAGGACTAAATTTCAAG+TGG + Chr5:42694489-42694508 None:intergenic 25.0%
!! CATGTTTCTATAATCATGTT+AGG - Chr5:42694200-42694219 MsG0580026709.01.T01:intron 25.0%
!! TTAACTTTTGTTCAGATCAT+TGG - Chr5:42694341-42694360 MsG0580026709.01.T01:intron 25.0%
!! TTAAGGACTAAATTTCAAGT+GGG + Chr5:42694488-42694507 None:intergenic 25.0%
!!! ATTACATATAGTGGATCATA+AGG + Chr5:42694150-42694169 None:intergenic 25.0%
!!! TTACATATAGTGGATCATAA+GGG + Chr5:42694149-42694168 None:intergenic 25.0%
ACTATGCAATATCTGTATTC+TGG - Chr5:42694767-42694786 MsG0580026709.01.T01:intron 30.0%
ACTTACCTAGTATGAGTTTA+TGG - Chr5:42694309-42694328 MsG0580026709.01.T01:intron 30.0%
ATAGCACGACATAAAATTTG+TGG + Chr5:42694525-42694544 None:intergenic 30.0%
ATGTTAGGTTATTGCAAACT+TGG - Chr5:42694215-42694234 MsG0580026709.01.T01:intron 30.0%
CTTATTTCATCTGATGCTAA+TGG - Chr5:42694859-42694878 MsG0580026709.01.T01:intron 30.0%
GATGAGCAGAATAAAATTTG+TGG - Chr5:42695124-42695143 MsG0580026709.01.T01:CDS 30.0%
TAAACTCATACTAGGTAAGT+CGG + Chr5:42694309-42694328 None:intergenic 30.0%
TCTTGTACCTATCTTGTATA+TGG + Chr5:42695008-42695027 None:intergenic 30.0%
TGGCCGTAAATCAAAATTTA+AGG + Chr5:42694505-42694524 None:intergenic 30.0%
TGTTAGGTTATTGCAAACTT+GGG - Chr5:42694216-42694235 MsG0580026709.01.T01:intron 30.0%
TGTTGTAAAGTGATATTTGC+TGG - Chr5:42694646-42694665 MsG0580026709.01.T01:intron 30.0%
! TTTTGCTCCATATACAAGAT+AGG - Chr5:42694998-42695017 MsG0580026709.01.T01:intron 30.0%
!! GTGATATTTGCTGGAATTTT+CGG - Chr5:42694655-42694674 MsG0580026709.01.T01:intron 30.0%
!! TATCTGTATTCTGGAATTTC+TGG - Chr5:42694776-42694795 MsG0580026709.01.T01:intron 30.0%
!!! TATTGTTCGGTTGTTTTTTC+CGG - Chr5:42695355-42695374 MsG0580026709.01.T01:CDS 30.0%
CCAATCCATAAACTCATACT+AGG + Chr5:42694317-42694336 None:intergenic 35.0%
CCTAGTATGAGTTTATGGAT+TGG - Chr5:42694314-42694333 MsG0580026709.01.T01:intron 35.0%
GACACGAGATAATTGCAATA+AGG + Chr5:42694970-42694989 None:intergenic 35.0%
GATCATGTTTCGTCCATTTA+CGG - Chr5:42694816-42694835 MsG0580026709.01.T01:intron 35.0%
GGAAAAAACAACCGAACAAT+AGG + Chr5:42695356-42695375 None:intergenic 35.0%
GGACTTGGATTCTACATAAA+GGG - Chr5:42694362-42694381 MsG0580026709.01.T01:intron 35.0%
TATGCTCAATCTTACTGAGA+TGG + Chr5:42693989-42694008 None:intergenic 35.0%
TGGACTTGGATTCTACATAA+AGG - Chr5:42694361-42694380 MsG0580026709.01.T01:intron 35.0%
TTCTACATAAAGGGACTATG+AGG - Chr5:42694371-42694390 MsG0580026709.01.T01:intron 35.0%
TTTGTTCAGATCATTGGACT+TGG - Chr5:42694347-42694366 MsG0580026709.01.T01:intron 35.0%
! TGAGAGGCTTTTCTTAGATA+AGG - Chr5:42694070-42694089 MsG0580026709.01.T01:intron 35.0%
! TTGCAATTTTCTGTTGCACT+TGG - Chr5:42694700-42694719 MsG0580026709.01.T01:intron 35.0%
!! AAGTTTTATCCCACTGAATG+GGG + Chr5:42694609-42694628 None:intergenic 35.0%
!! CAAGTTTTATCCCACTGAAT+GGG + Chr5:42694610-42694629 None:intergenic 35.0%
!!! ATTGTTCGGTTGTTTTTTCC+GGG - Chr5:42695356-42695375 MsG0580026709.01.T01:CDS 35.0%
AATACCACACAGCAGTACTA+TGG + Chr5:42695162-42695181 None:intergenic 40.0%
ATACCACACAGCAGTACTAT+GGG + Chr5:42695161-42695180 None:intergenic 40.0%
CCATTCAGTGGGATAAAACT+TGG - Chr5:42694608-42694627 MsG0580026709.01.T01:intron 40.0%
GAAGATAGAGCCGTCTTTAA+TGG + Chr5:42694271-42694290 None:intergenic 40.0%
GTAATAACCTCCACCGTAAA+TGG + Chr5:42694832-42694851 None:intergenic 40.0%
TTCTGTATGGCTTCTCGAAT+GGG + Chr5:42694044-42694063 None:intergenic 40.0%
TTTCTGTATGGCTTCTCGAA+TGG + Chr5:42694045-42694064 None:intergenic 40.0%
! AGTACTGCTGTGTGGTATTT+TGG - Chr5:42695163-42695182 MsG0580026709.01.T01:CDS 40.0%
!! CCAAGTTTTATCCCACTGAA+TGG + Chr5:42694611-42694630 None:intergenic 40.0%
!! TGTATTCTGGAATTTCTGGC+AGG - Chr5:42694780-42694799 MsG0580026709.01.T01:intron 40.0%
!!! GGTATTTTGGTGTTGATAGC+AGG - Chr5:42695176-42695195 MsG0580026709.01.T01:CDS 40.0%
!!! TTGTTTTTTCCGGGTGTGTT+TGG - Chr5:42695365-42695384 MsG0580026709.01.T01:CDS 40.0%
ACTGAATGGGGTCGACTATA+TGG + Chr5:42694597-42694616 None:intergenic 45.0%
AGGGGGTCATTCCTATTGTT+CGG - Chr5:42695342-42695361 MsG0580026709.01.T01:CDS 45.0%
ATATAGTCGACCCCATTCAG+TGG - Chr5:42694596-42694615 MsG0580026709.01.T01:CDS 45.0%
ATGGGAAGAGCAAGAAGAGA+AGG + Chr5:42694026-42694045 None:intergenic 45.0%
CATGTTTCGTCCATTTACGG+TGG - Chr5:42694819-42694838 MsG0580026709.01.T01:intron 45.0%
CCATACAGAAAGAGCTTGAG+AGG - Chr5:42694054-42694073 MsG0580026709.01.T01:CDS 45.0%
CCTCTCAAGCTCTTTCTGTA+TGG + Chr5:42694057-42694076 None:intergenic 45.0%
TATAGTCGACCCCATTCAGT+GGG - Chr5:42694597-42694616 MsG0580026709.01.T01:intron 45.0%
!! ATTCTGGAATTTCTGGCAGG+TGG - Chr5:42694783-42694802 MsG0580026709.01.T01:intron 45.0%
CAACCCATAGTACTGCTGTG+TGG - Chr5:42695155-42695174 MsG0580026709.01.T01:CDS 50.0%
CTCAACGAACCAAACACACC+CGG + Chr5:42695377-42695396 None:intergenic 50.0%
CTGTGGTGTGGTATGCATAG+GGG - Chr5:42695324-42695343 MsG0580026709.01.T01:intron 50.0%
GCAAGAAGAGAAGGAGGCAA+AGG + Chr5:42694017-42694036 None:intergenic 50.0%
GCTGTGGTGTGGTATGCATA+GGG - Chr5:42695323-42695342 MsG0580026709.01.T01:intron 50.0%
GGAAGAGCAAGAAGAGAAGG+AGG + Chr5:42694023-42694042 None:intergenic 50.0%
GGACTATGAGGTCGAATGCT+GGG - Chr5:42694383-42694402 MsG0580026709.01.T01:intron 50.0%
GGCTCTATCTTCCCTAGCAA+AGG - Chr5:42694279-42694298 MsG0580026709.01.T01:intron 50.0%
GTTTCGTCCATTTACGGTGG+AGG - Chr5:42694822-42694841 MsG0580026709.01.T01:intron 50.0%
TGCTGTGGTGTGGTATGCAT+AGG - Chr5:42695322-42695341 MsG0580026709.01.T01:intron 50.0%
TGTGGTGTGGTATGCATAGG+GGG - Chr5:42695325-42695344 MsG0580026709.01.T01:intron 50.0%
! AAGTCGGAGCACCTTTGCTA+GGG + Chr5:42694293-42694312 None:intergenic 50.0%
! TAAGTCGGAGCACCTTTGCT+AGG + Chr5:42694294-42694313 None:intergenic 50.0%
!! TCTGTTTGAGTTGCTGCTGC+TGG - Chr5:42695209-42695228 MsG0580026709.01.T01:intron 50.0%
CTGGGTTTGATGCTGTGGTG+TGG - Chr5:42695312-42695331 MsG0580026709.01.T01:intron 55.0%
GGGACTATGAGGTCGAATGC+TGG - Chr5:42694382-42694401 MsG0580026709.01.T01:intron 55.0%
! CGTTGGAGTGTTTGAGGGCT+GGG - Chr5:42695294-42695313 MsG0580026709.01.T01:intron 55.0%
CTGCTGGCAGCAGCAACAAC+TGG + Chr5:42695251-42695270 None:intergenic 60.0%
GAGGGCTGGGTTTGATGCTG+TGG - Chr5:42695307-42695326 MsG0580026709.01.T01:intron 60.0%
! GCGCGCGTTGGAGTGTTTGA+GGG - Chr5:42695289-42695308 MsG0580026709.01.T01:intron 60.0%
! GCGTTGGAGTGTTTGAGGGC+TGG - Chr5:42695293-42695312 MsG0580026709.01.T01:intron 60.0%
! TGCGCGCGTTGGAGTGTTTG+AGG - Chr5:42695288-42695307 MsG0580026709.01.T01:intron 60.0%
TCCTGCACCACAGCAGCTGC+TGG + Chr5:42695267-42695286 None:intergenic 65.0%
TGGTGCAGGATTGCGCGCGT+TGG - Chr5:42695277-42695296 MsG0580026709.01.T01:intron 65.0%
GCCAGCAGCTGCTGTGGTGC+AGG - Chr5:42695263-42695282 MsG0580026709.01.T01:intron 70.0%
GCTGCTGCCAGCAGCTGCTG+TGG - Chr5:42695257-42695276 MsG0580026709.01.T01:intron 70.0%
Chromosome Type Strat End Strand Name
Chr5 gene 42693981 42695436 42693981 ID=MsG0580026709.01;Name=MsG0580026709.01
Chr5 mRNA 42693981 42695436 42693981 ID=MsG0580026709.01.T01;Parent=MsG0580026709.01;Name=MsG0580026709.01.T01;_AED=0.22;_eAED=0.22;_QI=0|0|0|0.75|0.33|0.25|4|0|147
Chr5 exon 42695326 42695436 42695326 ID=MsG0580026709.01.T01:exon:13457;Parent=MsG0580026709.01.T01
Chr5 exon 42695100 42695195 42695100 ID=MsG0580026709.01.T01:exon:13456;Parent=MsG0580026709.01.T01
Chr5 exon 42694472 42694615 42694472 ID=MsG0580026709.01.T01:exon:13455;Parent=MsG0580026709.01.T01
Chr5 exon 42693981 42694073 42693981 ID=MsG0580026709.01.T01:exon:13454;Parent=MsG0580026709.01.T01
Chr5 CDS 42695326 42695436 42695326 ID=MsG0580026709.01.T01:cds;Parent=MsG0580026709.01.T01
Chr5 CDS 42695100 42695195 42695100 ID=MsG0580026709.01.T01:cds;Parent=MsG0580026709.01.T01
Chr5 CDS 42694472 42694615 42694472 ID=MsG0580026709.01.T01:cds;Parent=MsG0580026709.01.T01
Chr5 CDS 42693981 42694073 42693981 ID=MsG0580026709.01.T01:cds;Parent=MsG0580026709.01.T01
Gene Sequence

>MsG0580026709.01.T01

ATGTTCCATCTCAGTAAGATTGAGCATACATTGCCTTTGCCTCCTTCTCTTCTTGCTCTTCCCATTCGAGAAGCCATACAGAAAGAGCTTGAGAGGCTTTTCTTAGATAAGGTTATTGCAAACTTGGGCCTTTGCATATCTATTTATGATATCATATCCATTAAAGACGGCTCTATCTTCCCTAGCAAAGGTGCTCCGACTTACCTAGTGGTATTTAATTTGATCATGTTTCGTCCATTTACGGTGGAGGTTATTACTGCAAAACTTATTTCATCTGATGCTAATGGCATACACTGTATGTATTCAATTTTTAGTTTGTTCCTTGATTGTAATTATCTCTTGTCATATGTGGGGGTCATTCCTATTGTTCGGTTGTTTTTTCCGGGTGTGTTTGGTTCGTTGAGAATTTCTTGTCTTAATTATGTGTATGTACAAACGTTGTAG
Protein sequence

>MsG0580026709.01.T01

MFHLSKIEHTLPLPPSLLALPIREAIQKELERLFLDKVIANLGLCISIYDIISIKDGSIFPSKGAPTYLVVFNLIMFRPFTVEVITAKLISSDANGIHCMYSIFSLFLDCNYLLSYVGVIPIVRLFFPGVFGSLRISCLNYVYVQTL*