AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0852190


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 42 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTCCATGAGTTTGATTTA+TGG 0.165464 5_4:+43037974 None:intergenic
TTCCCTTTCGCTAATCATTA+AGG 0.243915 5_4:-43038597 Msa0852190:intron
TAGAGCCCAGTTGTTGAAAA+AGG 0.264059 5_4:-43038771 None:intergenic
TGGAGCGGCAGCTGCAGATA+TGG 0.376724 5_4:+43038700 None:intergenic
GCAGCTGCAGATATGGATCT+AGG 0.381091 5_4:+43038707 None:intergenic
GGCACTATATAAAACCAGTT+AGG 0.391939 5_4:+43037995 None:intergenic
GCACTATATAAAACCAGTTA+GGG 0.395114 5_4:+43037996 None:intergenic
AGAGAGAGTGTATGTGTGAA+TGG 0.411788 5_4:+43038680 None:intergenic
GGAGGTTATCATAATCTTTG+TGG 0.432763 5_4:-43038112 Msa0852190:CDS
AGAGACTGTTCCTCGGCCAC+TGG 0.440961 5_4:+43038198 None:intergenic
CATTCGCACAGGCAGTTGTC+GGG 0.443831 5_4:-43038083 Msa0852190:CDS
GAGGTTATCATAATCTTTGT+GGG 0.464601 5_4:-43038111 Msa0852190:CDS
ACATTCGCACAGGCAGTTGT+CGG 0.465169 5_4:-43038084 Msa0852190:CDS
AGAGACTGTTCCTCGGCCAC+AGG 0.487531 5_4:+43038222 None:intergenic
AAAATACCACATAAAAGGTC+AGG 0.488134 5_4:+43038054 None:intergenic
TACCTTAATGATTAGCGAAA+GGG 0.488891 5_4:+43038595 None:intergenic
CTCTCTCTTTGAGAGAGACT+CGG 0.506826 5_4:-43038641 Msa0852190:five_prime_UTR
ACAGTCTCTCCCAGTGGCCG+AGG 0.515343 5_4:-43038208 Msa0852190:CDS
TACTTAGTGAGTCCGTCCTA+TGG 0.519882 5_4:-43038031 Msa0852190:exon
TGTTAACGTCCCTGTGGCCG+AGG 0.525288 5_4:-43038232 Msa0852190:CDS
AGTGCCATAAATCAAACTCA+TGG 0.545857 5_4:-43037978 Msa0852190:three_prime_UTR
GAGACTGTTCCTCGGCCACT+GGG 0.547422 5_4:+43038199 None:intergenic
CAGCTGCAGATATGGATCTA+GGG 0.561068 5_4:+43038708 None:intergenic
AGGGAAGGAAGAAACAATGA+TGG 0.569540 5_4:+43038614 None:intergenic
ATACCTTAATGATTAGCGAA+AGG 0.589059 5_4:+43038594 None:intergenic
CACTGGGAGAGACTGTTCCT+CGG 0.589590 5_4:+43038215 None:intergenic
TGCCGTGGAGATTGTCGAGG+AGG 0.607269 5_4:-43038130 Msa0852190:CDS
GAGACTGTTCCTCGGCCACA+GGG 0.622184 5_4:+43038223 None:intergenic
AACCTCCTCGACAATCTCCA+CGG 0.623848 5_4:+43038128 None:intergenic
GGGAAGGAAGAAACAATGAT+GGG 0.633138 5_4:+43038615 None:intergenic
CCTTGCCGTGGAGATTGTCG+AGG 0.634500 5_4:-43038133 Msa0852190:CDS
CCTCGACAATCTCCACGGCA+AGG 0.648860 5_4:+43038133 None:intergenic
GGCCACAGGGACGTTAACAG+TGG 0.669374 5_4:+43038236 None:intergenic
AACTGGAAGAGACTGTTCCT+CGG 0.670113 5_4:+43038191 None:intergenic
ACTATATAAAACCAGTTAGG+GGG 0.674586 5_4:+43037998 None:intergenic
TGCCACTGTTAACGTCCCTG+TGG 0.677100 5_4:-43038238 Msa0852190:CDS
AAGGAAGAAACAATGATGGG+TGG 0.677187 5_4:+43038618 None:intergenic
CACTATATAAAACCAGTTAG+GGG 0.682263 5_4:+43037997 None:intergenic
GGTTAGATACAACCATAGGA+CGG 0.705181 5_4:+43038019 None:intergenic
CGAGGAACAGTCTCTCCCAG+TGG 0.711633 5_4:-43038214 Msa0852190:CDS
TTAATGATTAGCGAAAGGGA+AGG 0.713195 5_4:+43038599 None:intergenic
GAGTGTATGTGTGAATGGAG+CGG 0.714383 5_4:+43038685 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTAAAAATACCACATAAA+AGG + chr5_4:43038609-43038628 None:intergenic 20.0%
!! AAGTAAAAATACCACATAAA+AGG + chr5_4:43038609-43038628 None:intergenic 20.0%
!! TGAATGTATGATAATGAAGA+AGG + chr5_4:43038100-43038119 None:intergenic 25.0%
! AACTTGCAATAATCAGAAAT+GGG + chr5_4:43038211-43038230 None:intergenic 25.0%
! AAACTTGCAATAATCAGAAA+TGG + chr5_4:43038212-43038231 None:intergenic 25.0%
!! TGAATGTATGATAATGAAGA+AGG + chr5_4:43038100-43038119 None:intergenic 25.0%
! AACTTGCAATAATCAGAAAT+GGG + chr5_4:43038211-43038230 None:intergenic 25.0%
! AAACTTGCAATAATCAGAAA+TGG + chr5_4:43038212-43038231 None:intergenic 25.0%
TACCTTAATGATTAGCGAAA+GGG + chr5_4:43038063-43038082 None:intergenic 30.0%
ATACCTTAATGATTAGCGAA+AGG + chr5_4:43038064-43038083 None:intergenic 30.0%
!! CATTTTAGTGTTCTGTTAGT+TGG - chr5_4:43038235-43038254 Msa0852190:CDS 30.0%
GAGGTTATCATAATCTTTGT+GGG - chr5_4:43038544-43038563 Msa0852190:intron 30.0%
AAAATACCACATAAAAGGTC+AGG + chr5_4:43038604-43038623 None:intergenic 30.0%
ACTATATAAAACCAGTTAGG+GGG + chr5_4:43038660-43038679 None:intergenic 30.0%
CACTATATAAAACCAGTTAG+GGG + chr5_4:43038661-43038680 None:intergenic 30.0%
GCACTATATAAAACCAGTTA+GGG + chr5_4:43038662-43038681 None:intergenic 30.0%
TACCTTAATGATTAGCGAAA+GGG + chr5_4:43038063-43038082 None:intergenic 30.0%
ATACCTTAATGATTAGCGAA+AGG + chr5_4:43038064-43038083 None:intergenic 30.0%
!! CATTTTAGTGTTCTGTTAGT+TGG - chr5_4:43038235-43038254 Msa0852190:CDS 30.0%
GAGGTTATCATAATCTTTGT+GGG - chr5_4:43038544-43038563 Msa0852190:intron 30.0%
AAAATACCACATAAAAGGTC+AGG + chr5_4:43038604-43038623 None:intergenic 30.0%
ACTATATAAAACCAGTTAGG+GGG + chr5_4:43038660-43038679 None:intergenic 30.0%
CACTATATAAAACCAGTTAG+GGG + chr5_4:43038661-43038680 None:intergenic 30.0%
GCACTATATAAAACCAGTTA+GGG + chr5_4:43038662-43038681 None:intergenic 30.0%
TTAATGATTAGCGAAAGGGA+AGG + chr5_4:43038059-43038078 None:intergenic 35.0%
TTCCCTTTCGCTAATCATTA+AGG - chr5_4:43038058-43038077 Msa0852190:CDS 35.0%
TTGCAATAATCAGAAATGGG+TGG + chr5_4:43038208-43038227 None:intergenic 35.0%
!! TTGGATTTGTTGCTGTCTTA+GGG - chr5_4:43038254-43038273 Msa0852190:CDS 35.0%
ATTCAGACATTGCTTCACAT+AGG + chr5_4:43038390-43038409 None:intergenic 35.0%
GGAGGTTATCATAATCTTTG+TGG - chr5_4:43038543-43038562 Msa0852190:intron 35.0%
! CTTTATCCTGACCTTTTATG+TGG - chr5_4:43038595-43038614 Msa0852190:intron 35.0%
GGCACTATATAAAACCAGTT+AGG + chr5_4:43038663-43038682 None:intergenic 35.0%
AGTGCCATAAATCAAACTCA+TGG - chr5_4:43038677-43038696 Msa0852190:five_prime_UTR 35.0%
! CTCTCCATGAGTTTGATTTA+TGG + chr5_4:43038684-43038703 None:intergenic 35.0%
TTAATGATTAGCGAAAGGGA+AGG + chr5_4:43038059-43038078 None:intergenic 35.0%
TTCCCTTTCGCTAATCATTA+AGG - chr5_4:43038058-43038077 Msa0852190:CDS 35.0%
TTGCAATAATCAGAAATGGG+TGG + chr5_4:43038208-43038227 None:intergenic 35.0%
!! TTGGATTTGTTGCTGTCTTA+GGG - chr5_4:43038254-43038273 Msa0852190:CDS 35.0%
ATTCAGACATTGCTTCACAT+AGG + chr5_4:43038390-43038409 None:intergenic 35.0%
GGAGGTTATCATAATCTTTG+TGG - chr5_4:43038543-43038562 Msa0852190:intron 35.0%
! CTTTATCCTGACCTTTTATG+TGG - chr5_4:43038595-43038614 Msa0852190:intron 35.0%
GGCACTATATAAAACCAGTT+AGG + chr5_4:43038663-43038682 None:intergenic 35.0%
AGTGCCATAAATCAAACTCA+TGG - chr5_4:43038677-43038696 Msa0852190:five_prime_UTR 35.0%
! CTCTCCATGAGTTTGATTTA+TGG + chr5_4:43038684-43038703 None:intergenic 35.0%
! AGAGAGAGTGTATGTGTGAA+TGG + chr5_4:43037978-43037997 None:intergenic 40.0%
! AAGGAAGAAACAATGATGGG+TGG + chr5_4:43038040-43038059 None:intergenic 40.0%
GGGAAGGAAGAAACAATGAT+GGG + chr5_4:43038043-43038062 None:intergenic 40.0%
AGGGAAGGAAGAAACAATGA+TGG + chr5_4:43038044-43038063 None:intergenic 40.0%
!! GTTGGATTTGTTGCTGTCTT+AGG - chr5_4:43038253-43038272 Msa0852190:CDS 40.0%
TTCACATAGGCAGAAGCAAA+GGG + chr5_4:43038377-43038396 None:intergenic 40.0%
!! TTCGCCTACAAGTTTTTGGA+AGG - chr5_4:43038485-43038504 Msa0852190:intron 40.0%
!! GTTTTTGGAAGGCGTGTTTT+TGG - chr5_4:43038496-43038515 Msa0852190:intron 40.0%
GGTTAGATACAACCATAGGA+CGG + chr5_4:43038639-43038658 None:intergenic 40.0%
! AGAGAGAGTGTATGTGTGAA+TGG + chr5_4:43037978-43037997 None:intergenic 40.0%
! AAGGAAGAAACAATGATGGG+TGG + chr5_4:43038040-43038059 None:intergenic 40.0%
GGGAAGGAAGAAACAATGAT+GGG + chr5_4:43038043-43038062 None:intergenic 40.0%
AGGGAAGGAAGAAACAATGA+TGG + chr5_4:43038044-43038063 None:intergenic 40.0%
!! GTTGGATTTGTTGCTGTCTT+AGG - chr5_4:43038253-43038272 Msa0852190:CDS 40.0%
TTCACATAGGCAGAAGCAAA+GGG + chr5_4:43038377-43038396 None:intergenic 40.0%
!! TTCGCCTACAAGTTTTTGGA+AGG - chr5_4:43038485-43038504 Msa0852190:intron 40.0%
!! GTTTTTGGAAGGCGTGTTTT+TGG - chr5_4:43038496-43038515 Msa0852190:intron 40.0%
GGTTAGATACAACCATAGGA+CGG + chr5_4:43038639-43038658 None:intergenic 40.0%
CAGCTGCAGATATGGATCTA+GGG + chr5_4:43037950-43037969 None:intergenic 45.0%
GAGTGTATGTGTGAATGGAG+CGG + chr5_4:43037973-43037992 None:intergenic 45.0%
! CTCTCTCTTTGAGAGAGACT+CGG - chr5_4:43038014-43038033 Msa0852190:three_prime_UTR 45.0%
TTGCTGTCTTAGGGTCTGTT+TGG - chr5_4:43038263-43038282 Msa0852190:intron 45.0%
CTTCACATAGGCAGAAGCAA+AGG + chr5_4:43038378-43038397 None:intergenic 45.0%
AACTGGAAGAGACTGTTCCT+CGG + chr5_4:43038467-43038486 None:intergenic 45.0%
CCAAAAACTTGTAGGCGAAC+TGG + chr5_4:43038484-43038503 None:intergenic 45.0%
! CCAGTTCGCCTACAAGTTTT+TGG - chr5_4:43038481-43038500 Msa0852190:intron 45.0%
CACGCCTTCCAAAAACTTGT+AGG + chr5_4:43038492-43038511 None:intergenic 45.0%
! TGTGGGTTTTACATTCGCAC+AGG - chr5_4:43038561-43038580 Msa0852190:intron 45.0%
TACTTAGTGAGTCCGTCCTA+TGG - chr5_4:43038624-43038643 Msa0852190:five_prime_UTR 45.0%
AGGGGGTTAGATACAACCAT+AGG + chr5_4:43038643-43038662 None:intergenic 45.0%
GTTGTATCTAACCCCCTAAC+TGG - chr5_4:43038646-43038665 Msa0852190:five_prime_UTR 45.0%
CAGCTGCAGATATGGATCTA+GGG + chr5_4:43037950-43037969 None:intergenic 45.0%
GAGTGTATGTGTGAATGGAG+CGG + chr5_4:43037973-43037992 None:intergenic 45.0%
! CTCTCTCTTTGAGAGAGACT+CGG - chr5_4:43038014-43038033 Msa0852190:three_prime_UTR 45.0%
TTGCTGTCTTAGGGTCTGTT+TGG - chr5_4:43038263-43038282 Msa0852190:intron 45.0%
CTTCACATAGGCAGAAGCAA+AGG + chr5_4:43038378-43038397 None:intergenic 45.0%
AACTGGAAGAGACTGTTCCT+CGG + chr5_4:43038467-43038486 None:intergenic 45.0%
CCAAAAACTTGTAGGCGAAC+TGG + chr5_4:43038484-43038503 None:intergenic 45.0%
! CCAGTTCGCCTACAAGTTTT+TGG - chr5_4:43038481-43038500 Msa0852190:intron 45.0%
CACGCCTTCCAAAAACTTGT+AGG + chr5_4:43038492-43038511 None:intergenic 45.0%
! TGTGGGTTTTACATTCGCAC+AGG - chr5_4:43038561-43038580 Msa0852190:intron 45.0%
TACTTAGTGAGTCCGTCCTA+TGG - chr5_4:43038624-43038643 Msa0852190:five_prime_UTR 45.0%
AGGGGGTTAGATACAACCAT+AGG + chr5_4:43038643-43038662 None:intergenic 45.0%
GTTGTATCTAACCCCCTAAC+TGG - chr5_4:43038646-43038665 Msa0852190:five_prime_UTR 45.0%
GCAGCTGCAGATATGGATCT+AGG + chr5_4:43037951-43037970 None:intergenic 50.0%
!!! TGTTTTTGGTTGCCTTGCCG+TGG - chr5_4:43038510-43038529 Msa0852190:intron 50.0%
AACCTCCTCGACAATCTCCA+CGG + chr5_4:43038530-43038549 None:intergenic 50.0%
ACATTCGCACAGGCAGTTGT+CGG - chr5_4:43038571-43038590 Msa0852190:intron 50.0%
GCAGCTGCAGATATGGATCT+AGG + chr5_4:43037951-43037970 None:intergenic 50.0%
!!! TGTTTTTGGTTGCCTTGCCG+TGG - chr5_4:43038510-43038529 Msa0852190:intron 50.0%
AACCTCCTCGACAATCTCCA+CGG + chr5_4:43038530-43038549 None:intergenic 50.0%
ACATTCGCACAGGCAGTTGT+CGG - chr5_4:43038571-43038590 Msa0852190:intron 50.0%
TGCCACTGTTAACGTCCCTG+TGG - chr5_4:43038417-43038436 Msa0852190:intron 55.0%
CACTGGGAGAGACTGTTCCT+CGG + chr5_4:43038443-43038462 None:intergenic 55.0%
CATTCGCACAGGCAGTTGTC+GGG - chr5_4:43038572-43038591 Msa0852190:intron 55.0%
TGCCACTGTTAACGTCCCTG+TGG - chr5_4:43038417-43038436 Msa0852190:intron 55.0%
CACTGGGAGAGACTGTTCCT+CGG + chr5_4:43038443-43038462 None:intergenic 55.0%
CATTCGCACAGGCAGTTGTC+GGG - chr5_4:43038572-43038591 Msa0852190:intron 55.0%
TGGAGCGGCAGCTGCAGATA+TGG + chr5_4:43037958-43037977 None:intergenic 60.0%
GGCCACAGGGACGTTAACAG+TGG + chr5_4:43038422-43038441 None:intergenic 60.0%
TGTTAACGTCCCTGTGGCCG+AGG - chr5_4:43038423-43038442 Msa0852190:intron 60.0%
GAGACTGTTCCTCGGCCACA+GGG + chr5_4:43038435-43038454 None:intergenic 60.0%
AGAGACTGTTCCTCGGCCAC+AGG + chr5_4:43038436-43038455 None:intergenic 60.0%
CGAGGAACAGTCTCTCCCAG+TGG - chr5_4:43038441-43038460 Msa0852190:intron 60.0%
GAGACTGTTCCTCGGCCACT+GGG + chr5_4:43038459-43038478 None:intergenic 60.0%
AGAGACTGTTCCTCGGCCAC+TGG + chr5_4:43038436-43038455 None:intergenic 60.0%
CCTCGACAATCTCCACGGCA+AGG + chr5_4:43038525-43038544 None:intergenic 60.0%
CCTTGCCGTGGAGATTGTCG+AGG - chr5_4:43038522-43038541 Msa0852190:intron 60.0%
TGCCGTGGAGATTGTCGAGG+AGG - chr5_4:43038525-43038544 Msa0852190:intron 60.0%
TGGAGCGGCAGCTGCAGATA+TGG + chr5_4:43037958-43037977 None:intergenic 60.0%
GGCCACAGGGACGTTAACAG+TGG + chr5_4:43038422-43038441 None:intergenic 60.0%
TGTTAACGTCCCTGTGGCCG+AGG - chr5_4:43038423-43038442 Msa0852190:intron 60.0%
GAGACTGTTCCTCGGCCACA+GGG + chr5_4:43038435-43038454 None:intergenic 60.0%
AGAGACTGTTCCTCGGCCAC+AGG + chr5_4:43038436-43038455 None:intergenic 60.0%
CGAGGAACAGTCTCTCCCAG+TGG - chr5_4:43038441-43038460 Msa0852190:intron 60.0%
GAGACTGTTCCTCGGCCACT+GGG + chr5_4:43038459-43038478 None:intergenic 60.0%
AGAGACTGTTCCTCGGCCAC+TGG + chr5_4:43038436-43038455 None:intergenic 60.0%
CCTCGACAATCTCCACGGCA+AGG + chr5_4:43038525-43038544 None:intergenic 60.0%
CCTTGCCGTGGAGATTGTCG+AGG - chr5_4:43038522-43038541 Msa0852190:intron 60.0%
TGCCGTGGAGATTGTCGAGG+AGG - chr5_4:43038525-43038544 Msa0852190:intron 60.0%
ACAGTCTCTCCCAGTGGCCG+AGG - chr5_4:43038447-43038466 Msa0852190:intron 65.0%
ACAGTCTCTCCCAGTGGCCG+AGG - chr5_4:43038447-43038466 Msa0852190:intron 65.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 43037899 43038778 43037899 ID=Msa0852190;Name=Msa0852190
chr5_4 mRNA 43037899 43038778 43037899 ID=Msa0852190-mRNA-1;Parent=Msa0852190;Name=Msa0852190-mRNA-1;_AED=0.00;_eAED=0.00;_QI=181|0|0.5|1|0|0.5|2|148|76
chr5_4 exon 43037899 43038277 43037899 ID=Msa0852190-mRNA-1:exon:13616;Parent=Msa0852190-mRNA-1
chr5_4 exon 43038598 43038778 43038598 ID=Msa0852190-mRNA-1:exon:13615;Parent=Msa0852190-mRNA-1
chr5_4 five_prime_UTR 43038598 43038778 43038598 ID=Msa0852190-mRNA-1:five_prime_utr;Parent=Msa0852190-mRNA-1
chr5_4 CDS 43038047 43038277 43038047 ID=Msa0852190-mRNA-1:cds;Parent=Msa0852190-mRNA-1
chr5_4 three_prime_UTR 43037899 43038046 43037899 ID=Msa0852190-mRNA-1:three_prime_utr;Parent=Msa0852190-mRNA-1
Gene Sequence

>Msa0852190

ATGTCTGAATCTGAAGCTGCCACTGTTAACGTCCCTGTGGCCGAGGAACAGTCTCTCCCAGTGGCCGAGGAACAGTCTCTTCCAGTTCGCCTACAAGTTTTTGGAAGGCGTGTTTTTGGTTGCCTTGCCGTGGAGATTGTCGAGGAGGTTATCATAATCTTTGTGGGTTTTACATTCGCACAGGCAGTTGTCGGGCTTTATCCTGACCTTTTATGTGGTATTTTTACTTAG

Protein sequence

>Msa0852190

MSESEAATVNVPVAEEQSLPVAEEQSLPVRLQVFGRRVFGCLAVEIVEEVIIIFVGFTFAQAVVGLYPDLLCGIFT*