AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1187290

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGGCGGGGTTGACGATTC+AGG 0.123953 8_1:+26860000 Msa1187290:CDS
GGTGCTTAAAATTTATTATC+TGG 0.297194 8_1:+26860683 Msa1187290:three_prime_UTR
GGAAGCATACGGTCCTTTCT+TGG 0.323111 8_1:+26860346 Msa1187290:CDS
GGAAGTCTTGTTGATTTAGT+TGG 0.335009 8_1:+26860314 Msa1187290:CDS
ATTTGTGTTCCAGATTGTTT+AGG 0.370232 8_1:+26859955 None:intergenic
GGTTTCGTGCGGTTGTTTAG+AGG 0.372941 8_1:+26860713 Msa1187290:three_prime_UTR
AAAATACCTTGAAATCCTTT+GGG 0.373281 8_1:-26860650 None:intergenic
CAGTTAGGACCGAGGCTTCT+TGG 0.380935 8_1:+26859982 Msa1187290:CDS
TTGAATTGTGCTTCTCGCCT+TGG 0.392592 8_1:-26860198 None:intergenic
TTGGCGGGGTTGACGATTCA+GGG 0.399384 8_1:+26860001 Msa1187290:CDS
GATTGTTTAGGCACGCAGTT+AGG 0.416926 8_1:+26859967 None:intergenic
TAGGACCGAGGCTTCTTGGC+GGG 0.423247 8_1:+26859986 Msa1187290:CDS
TGGTATGGAACTTCTTTCTC+CGG 0.445848 8_1:-26860239 None:intergenic
AGTATACTTCACACAGTATC+CGG 0.453436 8_1:+26860142 Msa1187290:CDS
ATTGCAAATGACAATCTTGA+AGG 0.456999 8_1:+26860293 Msa1187290:CDS
AGAGGTAGAGGCAGCGGAAG+AGG 0.457632 8_1:+26860579 Msa1187290:CDS
GTTTCGTGCGGTTGTTTAGA+GGG 0.459047 8_1:+26860714 Msa1187290:three_prime_UTR
AACAAACCCAAAGGATTTCA+AGG 0.473412 8_1:+26860644 Msa1187290:three_prime_UTR
ATTGTGTGATTGATTCATCT+TGG 0.474013 8_1:-26860259 None:intergenic
ATACGGTCCTTTCTTGGATG+AGG 0.503815 8_1:+26860352 Msa1187290:CDS
GTGATTGATTCATCTTGGTA+TGG 0.505565 8_1:-26860254 None:intergenic
AATTTATTATCTGGTAGCAT+AGG 0.515942 8_1:+26860692 Msa1187290:three_prime_UTR
TGATTTAGTTGGAGAAGTTG+AGG 0.526516 8_1:+26860325 Msa1187290:CDS
GTGCGGTTGTTTAGAGGGCG+TGG 0.530935 8_1:+26860719 Msa1187290:three_prime_UTR
CGAATGTTAGGTAGAGGTAG+AGG 0.532296 8_1:+26860567 Msa1187290:intron
TTAGGTAGAGGTAGAGGCAG+CGG 0.532621 8_1:+26860573 Msa1187290:intron
TTAGGACCGAGGCTTCTTGG+CGG 0.539678 8_1:+26859985 Msa1187290:CDS
AACTTTAGAAGATAGTAAGC+CGG 0.555137 8_1:+26860220 Msa1187290:CDS
AAGGTAACCTCATCCAAGAA+AGG 0.563434 8_1:-26860359 None:intergenic
TCAACCCCGCCAAGAAGCCT+CGG 0.565529 8_1:-26859991 None:intergenic
AGGACCGAGGCTTCTTGGCG+GGG 0.566024 8_1:+26859987 Msa1187290:CDS
TGGCGGGGTTGACGATTCAG+GGG 0.574099 8_1:+26860002 Msa1187290:CDS
GTTGGCTGTGATTAAGACCA+AGG 0.613774 8_1:+26860181 Msa1187290:CDS
GGAGAAGTTGAGGAAGCATA+CGG 0.617796 8_1:+26860335 Msa1187290:CDS
CTGGTAGCATAGGTTTCGTG+CGG 0.636336 8_1:+26860702 Msa1187290:three_prime_UTR
TACTTCACACAGTATCCGGA+AGG 0.636948 8_1:+26860146 Msa1187290:CDS
ATCTTCTCAAACAAACCCAA+AGG 0.644202 8_1:+26860635 Msa1187290:three_prime_UTR
TAGGCACGCAGTTAGGACCG+AGG 0.679710 8_1:+26859974 Msa1187290:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAAGGTATTTTTATGATATA+AGG + chr8_1:26860662-26860681 Msa1187290:three_prime_UTR 20.0%
!!! CAAGGTATTTTTATGATATA+AGG + chr8_1:26860662-26860681 Msa1187290:three_prime_UTR 20.0%
! ACCATTAATGTAAAAATCCA+GGG - chr8_1:26860080-26860099 None:intergenic 25.0%
! AATATCTTTATCCCATTCAA+AGG - chr8_1:26860381-26860400 None:intergenic 25.0%
! AAAATACCTTGAAATCCTTT+GGG - chr8_1:26860653-26860672 None:intergenic 25.0%
! AAAAATACCTTGAAATCCTT+TGG - chr8_1:26860654-26860673 None:intergenic 25.0%
! GGTGCTTAAAATTTATTATC+TGG + chr8_1:26860683-26860702 Msa1187290:three_prime_UTR 25.0%
! AATTTATTATCTGGTAGCAT+AGG + chr8_1:26860692-26860711 Msa1187290:three_prime_UTR 25.0%
! ACCATTAATGTAAAAATCCA+GGG - chr8_1:26860080-26860099 None:intergenic 25.0%
! AATATCTTTATCCCATTCAA+AGG - chr8_1:26860381-26860400 None:intergenic 25.0%
! AAAATACCTTGAAATCCTTT+GGG - chr8_1:26860653-26860672 None:intergenic 25.0%
! AAAAATACCTTGAAATCCTT+TGG - chr8_1:26860654-26860673 None:intergenic 25.0%
! GGTGCTTAAAATTTATTATC+TGG + chr8_1:26860683-26860702 Msa1187290:three_prime_UTR 25.0%
! AATTTATTATCTGGTAGCAT+AGG + chr8_1:26860692-26860711 Msa1187290:three_prime_UTR 25.0%
TTAATGTAAAAATCCAGGGT+TGG - chr8_1:26860076-26860095 None:intergenic 30.0%
! ACCCTGGATTTTTACATTAA+TGG + chr8_1:26860076-26860095 Msa1187290:intron 30.0%
CACCATTAATGTAAAAATCC+AGG - chr8_1:26860081-26860100 None:intergenic 30.0%
!! GTGTGAAGTATACTTGTTTT+TGG - chr8_1:26860136-26860155 None:intergenic 30.0%
!!! AACCAATCTTTTTTTCCTTC+CGG - chr8_1:26860164-26860183 None:intergenic 30.0%
! AACTTTAGAAGATAGTAAGC+CGG + chr8_1:26860220-26860239 Msa1187290:CDS 30.0%
! ATTGTGTGATTGATTCATCT+TGG - chr8_1:26860262-26860281 None:intergenic 30.0%
ATTGCAAATGACAATCTTGA+AGG + chr8_1:26860293-26860312 Msa1187290:CDS 30.0%
ATCATCATCATCATCTTCTT+CGG - chr8_1:26860426-26860445 None:intergenic 30.0%
TGATGAAACATATTCTGACT+AGG + chr8_1:26860448-26860467 Msa1187290:intron 30.0%
TAAGTCATGCAAGAATAAGA+GGG - chr8_1:26860493-26860512 None:intergenic 30.0%
ATAAGTCATGCAAGAATAAG+AGG - chr8_1:26860494-26860513 None:intergenic 30.0%
TTGTATTGTTCACGAATGTT+AGG + chr8_1:26860555-26860574 Msa1187290:intron 30.0%
TTAATGTAAAAATCCAGGGT+TGG - chr8_1:26860076-26860095 None:intergenic 30.0%
! ACCCTGGATTTTTACATTAA+TGG + chr8_1:26860076-26860095 Msa1187290:intron 30.0%
CACCATTAATGTAAAAATCC+AGG - chr8_1:26860081-26860100 None:intergenic 30.0%
!! GTGTGAAGTATACTTGTTTT+TGG - chr8_1:26860136-26860155 None:intergenic 30.0%
!!! AACCAATCTTTTTTTCCTTC+CGG - chr8_1:26860164-26860183 None:intergenic 30.0%
! AACTTTAGAAGATAGTAAGC+CGG + chr8_1:26860220-26860239 Msa1187290:CDS 30.0%
! ATTGTGTGATTGATTCATCT+TGG - chr8_1:26860262-26860281 None:intergenic 30.0%
ATTGCAAATGACAATCTTGA+AGG + chr8_1:26860293-26860312 Msa1187290:CDS 30.0%
ATCATCATCATCATCTTCTT+CGG - chr8_1:26860426-26860445 None:intergenic 30.0%
TGATGAAACATATTCTGACT+AGG + chr8_1:26860448-26860467 Msa1187290:intron 30.0%
TAAGTCATGCAAGAATAAGA+GGG - chr8_1:26860493-26860512 None:intergenic 30.0%
ATAAGTCATGCAAGAATAAG+AGG - chr8_1:26860494-26860513 None:intergenic 30.0%
TTGTATTGTTCACGAATGTT+AGG + chr8_1:26860555-26860574 Msa1187290:intron 30.0%
!!! GTTTTATTTTAGACCAACCC+TGG + chr8_1:26860060-26860079 Msa1187290:intron 35.0%
!! ATTAATGGTGCTGCAAAGTT+TGG + chr8_1:26860091-26860110 Msa1187290:intron 35.0%
AGTATACTTCACACAGTATC+CGG + chr8_1:26860142-26860161 Msa1187290:CDS 35.0%
ATCCGGAAGGAAAAAAAGAT+TGG + chr8_1:26860159-26860178 Msa1187290:CDS 35.0%
GGAAGGAAAAAAAGATTGGT+TGG + chr8_1:26860163-26860182 Msa1187290:CDS 35.0%
! GTGATTGATTCATCTTGGTA+TGG - chr8_1:26860257-26860276 None:intergenic 35.0%
!! GGAAGTCTTGTTGATTTAGT+TGG + chr8_1:26860314-26860333 Msa1187290:CDS 35.0%
TGATTTAGTTGGAGAAGTTG+AGG + chr8_1:26860325-26860344 Msa1187290:CDS 35.0%
ATCTTCTCAAACAAACCCAA+AGG + chr8_1:26860635-26860654 Msa1187290:three_prime_UTR 35.0%
AACAAACCCAAAGGATTTCA+AGG + chr8_1:26860644-26860663 Msa1187290:three_prime_UTR 35.0%
!!! GTTTTATTTTAGACCAACCC+TGG + chr8_1:26860060-26860079 Msa1187290:intron 35.0%
!! ATTAATGGTGCTGCAAAGTT+TGG + chr8_1:26860091-26860110 Msa1187290:intron 35.0%
AGTATACTTCACACAGTATC+CGG + chr8_1:26860142-26860161 Msa1187290:CDS 35.0%
ATCCGGAAGGAAAAAAAGAT+TGG + chr8_1:26860159-26860178 Msa1187290:CDS 35.0%
GGAAGGAAAAAAAGATTGGT+TGG + chr8_1:26860163-26860182 Msa1187290:CDS 35.0%
! GTGATTGATTCATCTTGGTA+TGG - chr8_1:26860257-26860276 None:intergenic 35.0%
!! GGAAGTCTTGTTGATTTAGT+TGG + chr8_1:26860314-26860333 Msa1187290:CDS 35.0%
TGATTTAGTTGGAGAAGTTG+AGG + chr8_1:26860325-26860344 Msa1187290:CDS 35.0%
ATCTTCTCAAACAAACCCAA+AGG + chr8_1:26860635-26860654 Msa1187290:three_prime_UTR 35.0%
AACAAACCCAAAGGATTTCA+AGG + chr8_1:26860644-26860663 Msa1187290:three_prime_UTR 35.0%
TGGTATGGAACTTCTTTCTC+CGG - chr8_1:26860242-26860261 None:intergenic 40.0%
AAGGTAACCTCATCCAAGAA+AGG - chr8_1:26860362-26860381 None:intergenic 40.0%
TGGATGAGGTTACCTTTGAA+TGG + chr8_1:26860366-26860385 Msa1187290:intron 40.0%
GGATGAGGTTACCTTTGAAT+GGG + chr8_1:26860367-26860386 Msa1187290:intron 40.0%
TGTTCACGAATGTTAGGTAG+AGG + chr8_1:26860561-26860580 Msa1187290:intron 40.0%
TGGTATGGAACTTCTTTCTC+CGG - chr8_1:26860242-26860261 None:intergenic 40.0%
AAGGTAACCTCATCCAAGAA+AGG - chr8_1:26860362-26860381 None:intergenic 40.0%
TGGATGAGGTTACCTTTGAA+TGG + chr8_1:26860366-26860385 Msa1187290:intron 40.0%
GGATGAGGTTACCTTTGAAT+GGG + chr8_1:26860367-26860386 Msa1187290:intron 40.0%
TGTTCACGAATGTTAGGTAG+AGG + chr8_1:26860561-26860580 Msa1187290:intron 40.0%
TACTTCACACAGTATCCGGA+AGG + chr8_1:26860146-26860165 Msa1187290:CDS 45.0%
GTTGGCTGTGATTAAGACCA+AGG + chr8_1:26860181-26860200 Msa1187290:CDS 45.0%
TTGAATTGTGCTTCTCGCCT+TGG - chr8_1:26860201-26860220 None:intergenic 45.0%
! GGAGAAGTTGAGGAAGCATA+CGG + chr8_1:26860335-26860354 Msa1187290:CDS 45.0%
ATACGGTCCTTTCTTGGATG+AGG + chr8_1:26860352-26860371 Msa1187290:CDS 45.0%
CGAATGTTAGGTAGAGGTAG+AGG + chr8_1:26860567-26860586 Msa1187290:intron 45.0%
GTTTCGTGCGGTTGTTTAGA+GGG + chr8_1:26860714-26860733 Msa1187290:three_prime_UTR 45.0%
TACTTCACACAGTATCCGGA+AGG + chr8_1:26860146-26860165 Msa1187290:CDS 45.0%
GTTGGCTGTGATTAAGACCA+AGG + chr8_1:26860181-26860200 Msa1187290:CDS 45.0%
TTGAATTGTGCTTCTCGCCT+TGG - chr8_1:26860201-26860220 None:intergenic 45.0%
! GGAGAAGTTGAGGAAGCATA+CGG + chr8_1:26860335-26860354 Msa1187290:CDS 45.0%
ATACGGTCCTTTCTTGGATG+AGG + chr8_1:26860352-26860371 Msa1187290:CDS 45.0%
CGAATGTTAGGTAGAGGTAG+AGG + chr8_1:26860567-26860586 Msa1187290:intron 45.0%
GTTTCGTGCGGTTGTTTAGA+GGG + chr8_1:26860714-26860733 Msa1187290:three_prime_UTR 45.0%
! GGAAGCATACGGTCCTTTCT+TGG + chr8_1:26860346-26860365 Msa1187290:CDS 50.0%
TTAGGTAGAGGTAGAGGCAG+CGG + chr8_1:26860573-26860592 Msa1187290:intron 50.0%
CTGGTAGCATAGGTTTCGTG+CGG + chr8_1:26860702-26860721 Msa1187290:three_prime_UTR 50.0%
GGTTTCGTGCGGTTGTTTAG+AGG + chr8_1:26860713-26860732 Msa1187290:three_prime_UTR 50.0%
! GGAAGCATACGGTCCTTTCT+TGG + chr8_1:26860346-26860365 Msa1187290:CDS 50.0%
TTAGGTAGAGGTAGAGGCAG+CGG + chr8_1:26860573-26860592 Msa1187290:intron 50.0%
CTGGTAGCATAGGTTTCGTG+CGG + chr8_1:26860702-26860721 Msa1187290:three_prime_UTR 50.0%
GGTTTCGTGCGGTTGTTTAG+AGG + chr8_1:26860713-26860732 Msa1187290:three_prime_UTR 50.0%
CAGTTAGGACCGAGGCTTCT+TGG + chr8_1:26859982-26860001 Msa1187290:CDS 55.0%
TTAGGACCGAGGCTTCTTGG+CGG + chr8_1:26859985-26860004 Msa1187290:CDS 55.0%
TTGGCGGGGTTGACGATTCA+GGG + chr8_1:26860001-26860020 Msa1187290:CDS 55.0%
CAGTTAGGACCGAGGCTTCT+TGG + chr8_1:26859982-26860001 Msa1187290:CDS 55.0%
TTAGGACCGAGGCTTCTTGG+CGG + chr8_1:26859985-26860004 Msa1187290:CDS 55.0%
TTGGCGGGGTTGACGATTCA+GGG + chr8_1:26860001-26860020 Msa1187290:CDS 55.0%
TAGGCACGCAGTTAGGACCG+AGG + chr8_1:26859974-26859993 Msa1187290:CDS 60.0%
TAGGACCGAGGCTTCTTGGC+GGG + chr8_1:26859986-26860005 Msa1187290:CDS 60.0%
TCAACCCCGCCAAGAAGCCT+CGG - chr8_1:26859994-26860013 None:intergenic 60.0%
CTTGGCGGGGTTGACGATTC+AGG + chr8_1:26860000-26860019 Msa1187290:CDS 60.0%
TGGCGGGGTTGACGATTCAG+GGG + chr8_1:26860002-26860021 Msa1187290:CDS 60.0%
AGAGGTAGAGGCAGCGGAAG+AGG + chr8_1:26860579-26860598 Msa1187290:CDS 60.0%
GTGCGGTTGTTTAGAGGGCG+TGG + chr8_1:26860719-26860738 Msa1187290:three_prime_UTR 60.0%
TAGGCACGCAGTTAGGACCG+AGG + chr8_1:26859974-26859993 Msa1187290:CDS 60.0%
TAGGACCGAGGCTTCTTGGC+GGG + chr8_1:26859986-26860005 Msa1187290:CDS 60.0%
TCAACCCCGCCAAGAAGCCT+CGG - chr8_1:26859994-26860013 None:intergenic 60.0%
CTTGGCGGGGTTGACGATTC+AGG + chr8_1:26860000-26860019 Msa1187290:CDS 60.0%
TGGCGGGGTTGACGATTCAG+GGG + chr8_1:26860002-26860021 Msa1187290:CDS 60.0%
AGAGGTAGAGGCAGCGGAAG+AGG + chr8_1:26860579-26860598 Msa1187290:CDS 60.0%
GTGCGGTTGTTTAGAGGGCG+TGG + chr8_1:26860719-26860738 Msa1187290:three_prime_UTR 60.0%
AGGACCGAGGCTTCTTGGCG+GGG + chr8_1:26859987-26860006 Msa1187290:CDS 65.0%
AGGACCGAGGCTTCTTGGCG+GGG + chr8_1:26859987-26860006 Msa1187290:CDS 65.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 26859970 26860758 26859970 ID=Msa1187290;Name=Msa1187290
chr8_1 mRNA 26859970 26860758 26859970 ID=Msa1187290-mRNA-1;Parent=Msa1187290;Name=Msa1187290-mRNA-1;_AED=0.25;_eAED=0.60;_QI=0|0|0.33|0.66|0|0|3|146|110
chr8_1 exon 26859970 26860023 26859970 ID=Msa1187290-mRNA-1:exon:9443;Parent=Msa1187290-mRNA-1
chr8_1 exon 26860131 26860373 26860131 ID=Msa1187290-mRNA-1:exon:9444;Parent=Msa1187290-mRNA-1
chr8_1 exon 26860577 26860758 26860577 ID=Msa1187290-mRNA-1:exon:9445;Parent=Msa1187290-mRNA-1
chr8_1 CDS 26859970 26860023 26859970 ID=Msa1187290-mRNA-1:cds;Parent=Msa1187290-mRNA-1
chr8_1 CDS 26860131 26860373 26860131 ID=Msa1187290-mRNA-1:cds;Parent=Msa1187290-mRNA-1
chr8_1 CDS 26860577 26860612 26860577 ID=Msa1187290-mRNA-1:cds;Parent=Msa1187290-mRNA-1
chr8_1 three_prime_UTR 26860613 26860758 26860613 ID=Msa1187290-mRNA-1:three_prime_utr;Parent=Msa1187290-mRNA-1
Gene Sequence

>Msa1187290

TGTTTAGGCACGCAGTTAGGACCGAGGCTTCTTGGCGGGGTTGACGATTCAGGGATCCAAAAACAAGTATACTTCACACAGTATCCGGAAGGAAAAAAAGATTGGTTGGCTGTGATTAAGACCAAGGCGAGAAGCACAATTCAAACTTTAGAAGATAGTAAGCCGGAGAAAGAAGTTCCATACCAAGATGAATCAATCACACAATCACACGTGACAATTGCAAATGACAATCTTGAAGGAAGTCTTGTTGATTTAGTTGGAGAAGTTGAGGAAGCATACGGTCCTTTCTTGGATGAGGTAGAGGTAGAGGCAGCGGAAGAGGTAAAAGAATAA
Protein sequence

>Msa1187290

CLGTQLGPRLLGGVDDSGIQKQVYFTQYPEGKKDWLAVIKTKARSTIQTLEDSKPEKEVPYQDESITQSHVTIANDNLEGSLVDLVGEVEEAYGPFLDEVEVEAAEEVKE*