AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480023782.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480023782.01.T01 MTR_7g100010 79.330 179 1 1 1 179 1 143 1.76e-96 276
MsG0480023782.01.T01 MTR_8g102180 79.330 179 1 1 1 179 1 143 1.76e-96 276
MsG0480023782.01.T01 MTR_1g025190 38.286 175 72 1 3 177 2 140 7.99e-32 112
MsG0480023782.01.T01 MTR_5g098940 33.333 174 80 1 3 176 2 139 5.86e-31 110
MsG0480023782.01.T01 MTR_5g087820 32.000 175 83 1 3 177 26 164 5.24e-27 100
MsG0480023782.01.T01 MTR_8g077600 29.891 184 80 4 3 177 2 145 4.59e-23 90.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480023782.01.T01 AT2G19790 71.910 178 14 1 1 178 1 142 8.22e-89 256
MsG0480023782.01.T01 AT1G47830 38.857 175 71 1 3 177 2 140 2.00e-32 113
MsG0480023782.01.T01 AT2G17380 33.143 175 81 1 3 177 2 140 1.20e-30 109
MsG0480023782.01.T01 AT4G35410 33.143 175 81 1 3 177 2 140 2.56e-29 106
MsG0480023782.01.T01 AT3G50860 31.667 180 82 2 3 177 2 145 2.72e-27 100
MsG0480023782.01.T01 AT3G50860 31.667 180 82 2 3 177 2 145 3.80e-27 100
MsG0480023782.01.T01 AT4G35410 33.083 133 53 1 3 135 2 98 1.01e-17 74.7

Find 31 sgRNAs with CRISPR-Local

Find 111 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGAATGAGCTTGCTATTT+TGG 0.125124 4:+89781465 MsG0480023782.01.T01:CDS
GAAACCATGGATCGACATTT+TGG 0.210891 4:+89781508 MsG0480023782.01.T01:CDS
GGGGATCCGATTCGTGTTAA+TGG 0.262612 4:+89780035 MsG0480023782.01.T01:CDS
TACGAACAATTTCGCCTTCA+AGG 0.397557 4:-89780125 None:intergenic
GCAACTACAAAATTATATAT+AGG 0.415613 4:+89781075 MsG0480023782.01.T01:CDS
GAAGAACGACGAACCCTTGA+AGG 0.434936 4:+89780111 MsG0480023782.01.T01:CDS
TGTTCACCATTAACACGAAT+CGG 0.437301 4:-89780041 None:intergenic
TATCATGTTTCATTTAGAAA+AGG 0.473226 4:+89781729 MsG0480023782.01.T01:CDS
TTCATAATACTGAGCAAGAC+GGG 0.525077 4:-89780076 None:intergenic
TCTGACTCCTATTCAGCTGA+TGG 0.529053 4:+89781816 MsG0480023782.01.T01:CDS
ACGAACAATTTCGCCTTCAA+GGG 0.529281 4:-89780124 None:intergenic
TTCCTGGTTGGAGTTGATGA+CGG 0.536130 4:+89781116 MsG0480023782.01.T01:CDS
ATATTTATCTACAATGAAAG+TGG 0.544632 4:-89781383 None:intergenic
TCTACAATGAAAGTGGTACA+TGG 0.545583 4:-89781376 None:intergenic
TTGGTTGCAGAAAGAGAAAG+AGG 0.565774 4:+89780003 MsG0480023782.01.T01:five_prime_UTR
CGCCGTCATCAACTCCAACC+AGG 0.570939 4:-89781118 None:intergenic
CCATGGTTTCGACTAAGAGA+TGG 0.572456 4:-89781495 None:intergenic
GGTCATGAATGGTTGTATTG+TGG 0.573456 4:+89781774 MsG0480023782.01.T01:CDS
ACACATAAAGCAGCAGTGAC+AGG 0.577419 4:-89781904 None:intergenic
CCTCGCCCGTAATGAAAACC+AGG 0.578527 4:+89780152 MsG0480023782.01.T01:CDS
GTTGCCAAAATGTCGATCCA+TGG 0.581731 4:-89781512 None:intergenic
AAACATCATAAGAGATACAA+AGG 0.582694 4:+89781842 MsG0480023782.01.T01:exon
GTGTTAATGGTGAACAAACA+AGG 0.589164 4:+89780048 MsG0480023782.01.T01:CDS
TCTGCAAAATTGTCGACAGA+AGG 0.592031 4:-89781447 None:intergenic
AATTGTAACATAGAAATACA+TGG 0.596701 4:-89781880 None:intergenic
TTGGAGGAAATGGTCATGAA+TGG 0.600198 4:+89781763 MsG0480023782.01.T01:CDS
CCATCTCTTAGTCGAAACCA+TGG 0.604583 4:+89781495 MsG0480023782.01.T01:CDS
ATTCATAATACTGAGCAAGA+CGG 0.623435 4:-89780077 None:intergenic
TATTTCAGTTGTGTGAGCGT+TGG 0.633020 4:+89779984 MsG0480023782.01.T01:five_prime_UTR
TTCGTCGTTCTTCAACAGTG+AGG 0.697820 4:-89780101 None:intergenic
GGTTGGAGTTGATGACGGCG+AGG 0.701215 4:+89781121 MsG0480023782.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAATAAAATCAATTTGTTT+TGG - Chr4:89780474-89780493 None:intergenic 10.0%
!! AAATTGGAAAGAAAAAAAAA+AGG - Chr4:89780751-89780770 None:intergenic 15.0%
!!! GTTTTATTCATAAAGAAAAT+TGG - Chr4:89781965-89781984 None:intergenic 15.0%
!! AATTGTAACATAGAAATACA+TGG - Chr4:89781883-89781902 None:intergenic 20.0%
!! ATATTTATCTACAATGAAAG+TGG - Chr4:89781386-89781405 None:intergenic 20.0%
!! ATTTAAACATGTGATGAAAT+TGG - Chr4:89780767-89780786 None:intergenic 20.0%
!! GATGAAAAAAAAGAAAAGAA+TGG - Chr4:89780185-89780204 None:intergenic 20.0%
!! GCAACTACAAAATTATATAT+AGG + Chr4:89781075-89781094 MsG0480023782.01.T01:CDS 20.0%
!! TATCATGTTTCATTTAGAAA+AGG + Chr4:89781729-89781748 MsG0480023782.01.T01:CDS 20.0%
!!! AAATAGTGTTTTCAATACAA+AGG - Chr4:89779969-89779988 None:intergenic 20.0%
!!! ATTCTAGTTGATTTATACAA+AGG + Chr4:89781168-89781187 MsG0480023782.01.T01:intron 20.0%
!!! TGAATATTTTTACTATAGAC+AGG + Chr4:89780612-89780631 MsG0480023782.01.T01:intron 20.0%
! AAACAATGACAATGTGAATT+AGG - Chr4:89780239-89780258 None:intergenic 25.0%
! AAACATCATAAGAGATACAA+AGG + Chr4:89781842-89781861 MsG0480023782.01.T01:exon 25.0%
! AAGAGAAAGAGGAATAAAAA+TGG + Chr4:89780014-89780033 MsG0480023782.01.T01:exon 25.0%
! AGAAACAAAAAATCAGTGTT+TGG - Chr4:89781667-89781686 None:intergenic 25.0%
! AGAGAAAGAGGAATAAAAAT+GGG + Chr4:89780015-89780034 MsG0480023782.01.T01:exon 25.0%
! ATTAGGTAAAATTGAAGGTA+AGG - Chr4:89780222-89780241 None:intergenic 25.0%
! GGAAGAAAACAATAGAATTA+TGG - Chr4:89781619-89781638 None:intergenic 25.0%
! TAAATAAGACATAGATGTCT+TGG + Chr4:89780576-89780595 MsG0480023782.01.T01:intron 25.0%
! TAGATTATATAATCTGTGAG+TGG + Chr4:89780812-89780831 MsG0480023782.01.T01:intron 25.0%
! TGTGAATTAGGTAAAATTGA+AGG - Chr4:89780227-89780246 None:intergenic 25.0%
! TGTTTATTATTATTCAACCC+TGG + Chr4:89780254-89780273 MsG0480023782.01.T01:intron 25.0%
! TTGAATAATAAAGAATGACG+AGG - Chr4:89780855-89780874 None:intergenic 25.0%
!!! AGAAAAGGTACATTTTATGT+TGG + Chr4:89781744-89781763 MsG0480023782.01.T01:CDS 25.0%
!!! CACTGTGTTATATTTTAGTT+GGG + Chr4:89780723-89780742 MsG0480023782.01.T01:intron 25.0%
AGAATTATGGAAGTAATGTG+AGG - Chr4:89781606-89781625 None:intergenic 30.0%
AGTAAGAGAAAGTCAAAAGA+TGG - Chr4:89780930-89780949 None:intergenic 30.0%
ATTCATAATACTGAGCAAGA+CGG - Chr4:89780080-89780099 None:intergenic 30.0%
ATTCTTTATTATTCAACCCG+AGG + Chr4:89780859-89780878 MsG0480023782.01.T01:intron 30.0%
CCAACTAAAATATAACACAG+TGG - Chr4:89780725-89780744 None:intergenic 30.0%
GAGAAAGAGGAATAAAAATG+GGG + Chr4:89780016-89780035 MsG0480023782.01.T01:exon 30.0%
GCATATTGTGTTAAATAGTC+TGG + Chr4:89781211-89781230 MsG0480023782.01.T01:intron 30.0%
GGTTTATACCAGAAACATAA+GGG + Chr4:89780964-89780983 MsG0480023782.01.T01:intron 30.0%
TATAGACAGGAGATAATTGT+TGG + Chr4:89780625-89780644 MsG0480023782.01.T01:intron 30.0%
TCTTACTCATATTGATGTGT+TGG + Chr4:89780943-89780962 MsG0480023782.01.T01:intron 30.0%
TGAGTGGAATGAAATTGAAA+TGG + Chr4:89780828-89780847 MsG0480023782.01.T01:intron 30.0%
TGGTTTATACCAGAAACATA+AGG + Chr4:89780963-89780982 MsG0480023782.01.T01:intron 30.0%
TTAACAAGACTAAGAACTTC+AGG - Chr4:89781332-89781351 None:intergenic 30.0%
TTATTATTATTCAACCCTGG+AGG + Chr4:89780257-89780276 MsG0480023782.01.T01:intron 30.0%
TTTCATAATCTATCATGGAG+AGG - Chr4:89780428-89780447 None:intergenic 30.0%
! ACATTTTATGTTGGAGGAAA+TGG + Chr4:89781753-89781772 MsG0480023782.01.T01:CDS 30.0%
! CATAAACACTTCTGAGAATA+TGG + Chr4:89780354-89780373 MsG0480023782.01.T01:intron 30.0%
! CTAGTTGATTTATACAAAGG+CGG + Chr4:89781171-89781190 MsG0480023782.01.T01:intron 30.0%
! GCTGATTTCATAATCTATCA+TGG - Chr4:89780433-89780452 None:intergenic 30.0%
!! AAAGGTACATTTTATGTTGG+AGG + Chr4:89781747-89781766 MsG0480023782.01.T01:CDS 30.0%
!! AACATACCTGGTTTTCATTA+CGG - Chr4:89780161-89780180 None:intergenic 30.0%
!!! CCACTGTGTTATATTTTAGT+TGG + Chr4:89780722-89780741 MsG0480023782.01.T01:intron 30.0%
AAGTCAATCCCTTATGTTTC+TGG - Chr4:89780975-89780994 None:intergenic 35.0%
AATCTATCATGGAGAGGTTA+TGG - Chr4:89780422-89780441 None:intergenic 35.0%
AGCAAACTTGAATCCAAAGA+TGG - Chr4:89780892-89780911 None:intergenic 35.0%
AGGTAAAATTGAAGGTAAGG+AGG - Chr4:89780219-89780238 None:intergenic 35.0%
GAAAAGAATGGAAACATACC+TGG - Chr4:89780173-89780192 None:intergenic 35.0%
GTGTTAATGGTGAACAAACA+AGG + Chr4:89780048-89780067 MsG0480023782.01.T01:CDS 35.0%
TCTACAATGAAAGTGGTACA+TGG - Chr4:89781379-89781398 None:intergenic 35.0%
TGTTCACCATTAACACGAAT+CGG - Chr4:89780044-89780063 None:intergenic 35.0%
TTCATAATACTGAGCAAGAC+GGG - Chr4:89780079-89780098 None:intergenic 35.0%
TTGAAGCTAAGTTCAGAAGA+TGG - Chr4:89781644-89781663 None:intergenic 35.0%
! ATTATTCAACCCGAGGTTTT+AGG + Chr4:89780866-89780885 MsG0480023782.01.T01:intron 35.0%
! GTTTTATCCATCAGCTGAAT+AGG - Chr4:89781826-89781845 None:intergenic 35.0%
! TGGCTGATACATTTTTGTCA+TGG + Chr4:89781029-89781048 MsG0480023782.01.T01:intron 35.0%
!! ACATACCTGGTTTTCATTAC+GGG - Chr4:89780160-89780179 None:intergenic 35.0%
!!! CTATGCATCTTTGTTTTTCC+TGG + Chr4:89781100-89781119 MsG0480023782.01.T01:CDS 35.0%
AAAAGATGGCCTAAAACCTC+GGG - Chr4:89780916-89780935 None:intergenic 40.0%
AACTTTCTCTTCCCCAATTC+TGG - Chr4:89780664-89780683 None:intergenic 40.0%
ACGAACAATTTCGCCTTCAA+GGG - Chr4:89780127-89780146 None:intergenic 40.0%
ACTTTCTCTTCCCCAATTCT+GGG - Chr4:89780663-89780682 None:intergenic 40.0%
AGCTAAGTTCAGAAGATGGA+AGG - Chr4:89781640-89781659 None:intergenic 40.0%
AGTGGTCATCACTATGTGAT+CGG + Chr4:89781251-89781270 MsG0480023782.01.T01:intron 40.0%
CAAAAGATGGCCTAAAACCT+CGG - Chr4:89780917-89780936 None:intergenic 40.0%
CAATCTAATTGCTACCTCCA+GGG - Chr4:89780274-89780293 None:intergenic 40.0%
CCAGTTTCTTTAGACAAGCA+AGG - Chr4:89781282-89781301 None:intergenic 40.0%
CCTTGCTTGTCTAAAGAAAC+TGG + Chr4:89781279-89781298 MsG0480023782.01.T01:intron 40.0%
GGTCATGAATGGTTGTATTG+TGG + Chr4:89781774-89781793 MsG0480023782.01.T01:CDS 40.0%
TACGAACAATTTCGCCTTCA+AGG - Chr4:89780128-89780147 None:intergenic 40.0%
TATTTCAGTTGTGTGAGCGT+TGG + Chr4:89779984-89780003 MsG0480023782.01.T01:five_prime_UTR 40.0%
TCAATCTAATTGCTACCTCC+AGG - Chr4:89780275-89780294 None:intergenic 40.0%
TCTGCAAAATTGTCGACAGA+AGG - Chr4:89781450-89781469 None:intergenic 40.0%
TGTATCAGCCAGATGAATCA+TGG - Chr4:89781020-89781039 None:intergenic 40.0%
TTCCTTTCACACCCAGAATT+GGG + Chr4:89780649-89780668 MsG0480023782.01.T01:intron 40.0%
TTGGAGGAAATGGTCATGAA+TGG + Chr4:89781763-89781782 MsG0480023782.01.T01:CDS 40.0%
TTGGTTGCAGAAAGAGAAAG+AGG + Chr4:89780003-89780022 MsG0480023782.01.T01:five_prime_UTR 40.0%
TTTCCTTTCACACCCAGAAT+TGG + Chr4:89780648-89780667 MsG0480023782.01.T01:intron 40.0%
! GAAACCATGGATCGACATTT+TGG + Chr4:89781508-89781527 MsG0480023782.01.T01:CDS 40.0%
!!! GCAGAATGAGCTTGCTATTT+TGG + Chr4:89781465-89781484 MsG0480023782.01.T01:CDS 40.0%
!!! GCATCTTTGTTTTTCCTGGT+TGG + Chr4:89781104-89781123 MsG0480023782.01.T01:CDS 40.0%
ACACATAAAGCAGCAGTGAC+AGG - Chr4:89781907-89781926 None:intergenic 45.0%
CAAAGATGGCCTAAAACCTC+GGG - Chr4:89780878-89780897 None:intergenic 45.0%
CCAAAGATGGCCTAAAACCT+CGG - Chr4:89780879-89780898 None:intergenic 45.0%
CCATCTCTTAGTCGAAACCA+TGG + Chr4:89781495-89781514 MsG0480023782.01.T01:CDS 45.0%
CCATGGTTTCGACTAAGAGA+TGG - Chr4:89781498-89781517 None:intergenic 45.0%
GATCACATAGTGATGACCAC+TGG - Chr4:89781252-89781271 None:intergenic 45.0%
GCTTTGATCTTACTGACCAG+TGG + Chr4:89781233-89781252 MsG0480023782.01.T01:intron 45.0%
GTTGCCAAAATGTCGATCCA+TGG - Chr4:89781515-89781534 None:intergenic 45.0%
TCCTTTCACACCCAGAATTG+GGG + Chr4:89780650-89780669 MsG0480023782.01.T01:intron 45.0%
TCTGACTCCTATTCAGCTGA+TGG + Chr4:89781816-89781835 MsG0480023782.01.T01:CDS 45.0%
TCTGCTCACCATGATTCATC+TGG + Chr4:89781009-89781028 MsG0480023782.01.T01:intron 45.0%
TTCGTCGTTCTTCAACAGTG+AGG - Chr4:89780104-89780123 None:intergenic 45.0%
!! TTCCTGGTTGGAGTTGATGA+CGG + Chr4:89781116-89781135 MsG0480023782.01.T01:CDS 45.0%
!!! AGTTTGCTACCCGAGGTTTT+AGG + Chr4:89780904-89780923 MsG0480023782.01.T01:intron 45.0%
ACAGAGACTCTAGTCACAGC+AGG - Chr4:89781547-89781566 None:intergenic 50.0%
GAAGAACGACGAACCCTTGA+AGG + Chr4:89780111-89780130 MsG0480023782.01.T01:CDS 50.0%
TCCCCAATTCTGGGTGTGAA+AGG - Chr4:89780654-89780673 None:intergenic 50.0%
! GGGGATCCGATTCGTGTTAA+TGG + Chr4:89780035-89780054 MsG0480023782.01.T01:CDS 50.0%
!! GGATCGACATTTTGGCAACG+TGG + Chr4:89781516-89781535 MsG0480023782.01.T01:CDS 50.0%
!! GGATTCAAGTTTGCTACCCG+AGG + Chr4:89780897-89780916 MsG0480023782.01.T01:intron 50.0%
!!! CCGAGGTTTTAGGCCATCTT+TGG + Chr4:89780876-89780895 MsG0480023782.01.T01:intron 50.0%
CCTCGCCCGTAATGAAAACC+AGG + Chr4:89780152-89780171 MsG0480023782.01.T01:CDS 55.0%
!! CCTGGTTTTCATTACGGGCG+AGG - Chr4:89780155-89780174 None:intergenic 55.0%
CGCCGTCATCAACTCCAACC+AGG - Chr4:89781121-89781140 None:intergenic 60.0%
!! GGTTGGAGTTGATGACGGCG+AGG + Chr4:89781121-89781140 MsG0480023782.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr4 gene 89779961 89781997 89779961 ID=MsG0480023782.01;Name=MsG0480023782.01
Chr4 mRNA 89779961 89781997 89779961 ID=MsG0480023782.01.T01;Parent=MsG0480023782.01;Name=MsG0480023782.01.T01;_AED=0.33;_eAED=0.40;_QI=72|0.66|0.75|1|0.33|0.5|4|145|179
Chr4 exon 89779961 89780173 89779961 ID=MsG0480023782.01.T01:exon:12497;Parent=MsG0480023782.01.T01
Chr4 exon 89781056 89781142 89781056 ID=MsG0480023782.01.T01:exon:12498;Parent=MsG0480023782.01.T01
Chr4 exon 89781361 89781537 89781361 ID=MsG0480023782.01.T01:exon:12499;Parent=MsG0480023782.01.T01
Chr4 exon 89781718 89781997 89781718 ID=MsG0480023782.01.T01:exon:12500;Parent=MsG0480023782.01.T01
Chr4 five_prime_UTR 89779961 89780032 89779961 ID=MsG0480023782.01.T01:five_prime_utr;Parent=MsG0480023782.01.T01
Chr4 CDS 89780033 89780173 89780033 ID=MsG0480023782.01.T01:cds;Parent=MsG0480023782.01.T01
Chr4 CDS 89781056 89781142 89781056 ID=MsG0480023782.01.T01:cds;Parent=MsG0480023782.01.T01
Chr4 CDS 89781361 89781537 89781361 ID=MsG0480023782.01.T01:cds;Parent=MsG0480023782.01.T01
Chr4 CDS 89781718 89781852 89781718 ID=MsG0480023782.01.T01:cds;Parent=MsG0480023782.01.T01
Chr4 three_prime_UTR 89781853 89781997 89781853 ID=MsG0480023782.01.T01:three_prime_utr;Parent=MsG0480023782.01.T01
Gene Sequence

>MsG0480023782.01.T01

ATGGGGATCCGATTCGTGTTAATGGTGAACAAACAAGGACAGACCCGTCTTGCTCAGTATTATGAATACCTCACTGTTGAAGAACGACGAACCCTTGAAGGCGAAATTGTTCGTAAATGCCTCGCCCGTAATGAAAACCAGTGTTCATTTGTTGAGCATCGCAACTACAAAATTATATATAGGCGCTATGCATCTTTGTTTTTCCTGGTTGGAGTTGATGACGGCGAGCTTCAGCAAAATTTTCCATGTACCACTTTCATTGTAGATAAATATGATATCATTTCAATTCTGCTTCTACTTGATTGTTCATTCTACCTTCTGTCGACAATTTTGCAGAATGAGCTTGCTATTTTGGAATTTATCCATCTCTTAGTCGAAACCATGGATCGACATTTTGGCAACGTGTGTGAGCTAGATATCATGTTTCATTTAGAAAAGGTACATTTTATGTTGGAGGAAATGGTCATGAATGGTTGTATTGTGGAGACAAGCAAATCAAATATTCTGACTCCTATTCAGCTGATGGATAAAACATCATAA
Protein sequence

>MsG0480023782.01.T01

MGIRFVLMVNKQGQTRLAQYYEYLTVEERRTLEGEIVRKCLARNENQCSFVEHRNYKIIYRRYASLFFLVGVDDGELQQNFPCTTFIVDKYDIISILLLLDCSFYLLSTILQNELAILEFIHLLVETMDRHFGNVCELDIMFHLEKVHFMLEEMVMNGCIVETSKSNILTPIQLMDKTS*