AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0657130


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0657130 MtrunA17_Chr8g0379121 95.595 227 5 2 1 225 205 428 3.51e-157 442
Msa0657130 MtrunA17_Chr2g0283951 39.271 247 79 9 1 225 181 378 4.96e-35 127
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 46 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATCTTCCTTGTGTATTTA+TGG 0.141395 4_3:-66601909 None:intergenic
GATGATTTAAGTACCATTCT+TGG 0.272460 4_3:-66601835 None:intergenic
CTTAAACTCAGTTGCAAATC+AGG 0.297702 4_3:-66602532 None:intergenic
ATGATTGTTCATGATATCTA+AGG 0.331312 4_3:-66602035 None:intergenic
TATAGTTTACCTTGAATTGA+TGG 0.341831 4_3:-66601730 None:intergenic
GAACCAGCAGCTTCAAGTTA+AGG 0.347972 4_3:+66601943 Msa0657130:CDS
GAGTTTCGTGTCGATTTCTT+TGG 0.349363 4_3:-66602602 None:intergenic
TGTGTATTTATGGCTGTTGA+TGG 0.356390 4_3:-66601899 None:intergenic
TCATGAACAATCATCCATAT+TGG 0.374740 4_3:+66602044 Msa0657130:CDS
AAGCTGCTGGTTCAAAGTTA+TGG 0.381198 4_3:-66601933 None:intergenic
AGAAATTGGCTTGGTCTCAT+AGG 0.398094 4_3:-66601992 None:intergenic
GGTACTTAAATCATCAATCT+TGG 0.408196 4_3:+66601843 Msa0657130:CDS
GTGATAAGGATGAGGGATGC+AGG 0.412034 4_3:-66601686 None:intergenic
ATGTTACCTTAATCCGAAAC+GGG 0.413271 4_3:-66602228 None:intergenic
TTCTCTTCAAGAAATTGGCT+TGG 0.425569 4_3:-66602001 None:intergenic
AGACCCGCTGAGGTGAGCTT+TGG 0.428693 4_3:+66602121 Msa0657130:CDS
TTTCCAAAGCTCACCTCAGC+GGG 0.450601 4_3:-66602124 None:intergenic
AATGTTACCTTAATCCGAAA+CGG 0.472630 4_3:-66602229 None:intergenic
CAACATTTCAAGATGGCAAA+TGG 0.480821 4_3:+66601609 None:intergenic
TATCCTTAACTTGAAGCTGC+TGG 0.484791 4_3:-66601946 None:intergenic
ATTCAAAGCCCATCAATTCA+AGG 0.485522 4_3:+66601721 Msa0657130:CDS
ATAGTTTACCTTGAATTGAT+GGG 0.489818 4_3:-66601729 None:intergenic
AATTCATTGCTCATGTAGCT+TGG 0.505208 4_3:-66601869 None:intergenic
AATTTCTTGAAGAGAAAAGA+TGG 0.506639 4_3:+66602008 Msa0657130:CDS
CAAACAAACGGCAACAATGA+TGG 0.520591 4_3:+66602556 Msa0657130:CDS
TTGAACTATTAAAATAGTTG+TGG 0.532058 4_3:-66602189 None:intergenic
TTGGAAACAACACAAGAAGC+AGG 0.535242 4_3:+66602140 Msa0657130:CDS
AACAATGATGGCAAGAGTGA+TGG 0.553546 4_3:+66602568 Msa0657130:CDS
ATGTGAATGTGATAAGGATG+AGG 0.556397 4_3:-66601694 None:intergenic
ATGTGAATGTGAATGTGATA+AGG 0.557968 4_3:-66601700 None:intergenic
TGTGGAAATTATAACTGTGC+TGG 0.573367 4_3:-66601659 None:intergenic
ATTGCTGAAAGACAAACAAT+GGG 0.582280 4_3:+66602507 Msa0657130:CDS
CATTGCTGAAAGACAAACAA+TGG 0.583238 4_3:+66602506 Msa0657130:CDS
CTGAGTTTAAGTCAAACAAA+CGG 0.584680 4_3:+66602544 Msa0657130:CDS
ATGAGGGATGCAGGAGACTG+TGG 0.594666 4_3:-66601677 None:intergenic
CATTTCAAGATGGCAAATGG+TGG 0.597539 4_3:+66601612 None:intergenic
TGTGAATGTGATAAGGATGA+GGG 0.599304 4_3:-66601693 None:intergenic
TGATTGTTCATGATATCTAA+GGG 0.612865 4_3:-66602034 None:intergenic
TGGTCTCATAGGAGCAAGTG+TGG 0.621257 4_3:-66601981 None:intergenic
GTTTCCAAAGCTCACCTCAG+CGG 0.640457 4_3:-66602125 None:intergenic
TGGAAACAACACAAGAAGCA+GGG 0.655021 4_3:+66602141 Msa0657130:CDS
TGTTACCTTAATCCGAAACG+GGG 0.678201 4_3:-66602227 None:intergenic
AACATCACTTAGACCCGCTG+AGG 0.687013 4_3:+66602111 Msa0657130:CDS
TCAACAGCCATAAATACACA+AGG 0.708092 4_3:+66601902 Msa0657130:CDS
GTTACCTTAATCCGAAACGG+GGG 0.718704 4_3:-66602226 None:intergenic
TTGTTCATGATATCTAAGGG+AGG 0.723510 4_3:-66602031 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAGTTACATTTTTTTACTT+AGG + chr4_3:66601810-66601829 Msa0657130:intron 15.0%
!! ACTATTAAAGAAATTGAAAT+TGG - chr4_3:66602400-66602419 None:intergenic 15.0%
!! TGAGAAAATATATATATGAA+AGG - chr4_3:66602467-66602486 None:intergenic 15.0%
!!! TTTTCATATTATTATTGACA+TGG - chr4_3:66602660-66602679 None:intergenic 15.0%
!!! AAAGTTACATTTTTTTACTT+AGG + chr4_3:66601810-66601829 Msa0657130:intron 15.0%
!! ACTATTAAAGAAATTGAAAT+TGG - chr4_3:66602400-66602419 None:intergenic 15.0%
!! TGAGAAAATATATATATGAA+AGG - chr4_3:66602467-66602486 None:intergenic 15.0%
!!! TTTTCATATTATTATTGACA+TGG - chr4_3:66602660-66602679 None:intergenic 15.0%
!!! TTTATTTTTTTCCATTCAAG+TGG + chr4_3:66601783-66601802 Msa0657130:intron 20.0%
!!! TGTAAATTTTTCTTCCAATA+TGG - chr4_3:66602061-66602080 None:intergenic 20.0%
!! TTGAACTATTAAAATAGTTG+TGG - chr4_3:66602192-66602211 None:intergenic 20.0%
!! TATATATGAAAGGTTAAGAA+AGG - chr4_3:66602457-66602476 None:intergenic 20.0%
!!! TTTATTTTTTTCCATTCAAG+TGG + chr4_3:66601783-66601802 Msa0657130:intron 20.0%
!!! TGTAAATTTTTCTTCCAATA+TGG - chr4_3:66602061-66602080 None:intergenic 20.0%
!! TTGAACTATTAAAATAGTTG+TGG - chr4_3:66602192-66602211 None:intergenic 20.0%
!! TATATATGAAAGGTTAAGAA+AGG - chr4_3:66602457-66602476 None:intergenic 20.0%
! ATAGTTTACCTTGAATTGAT+GGG - chr4_3:66601732-66601751 None:intergenic 25.0%
! TATAGTTTACCTTGAATTGA+TGG - chr4_3:66601733-66601752 None:intergenic 25.0%
!! ATCTTTTCTCTTCAAGAAAT+TGG - chr4_3:66602009-66602028 None:intergenic 25.0%
! AATTTCTTGAAGAGAAAAGA+TGG + chr4_3:66602008-66602027 Msa0657130:CDS 25.0%
! TGATTGTTCATGATATCTAA+GGG - chr4_3:66602037-66602056 None:intergenic 25.0%
! ATGATTGTTCATGATATCTA+AGG - chr4_3:66602038-66602057 None:intergenic 25.0%
! CATTAATAACTATATGCTAC+TGG + chr4_3:66602248-66602267 Msa0657130:intron 25.0%
! ATAGTTTACCTTGAATTGAT+GGG - chr4_3:66601732-66601751 None:intergenic 25.0%
! TATAGTTTACCTTGAATTGA+TGG - chr4_3:66601733-66601752 None:intergenic 25.0%
!! ATCTTTTCTCTTCAAGAAAT+TGG - chr4_3:66602009-66602028 None:intergenic 25.0%
! AATTTCTTGAAGAGAAAAGA+TGG + chr4_3:66602008-66602027 Msa0657130:CDS 25.0%
! TGATTGTTCATGATATCTAA+GGG - chr4_3:66602037-66602056 None:intergenic 25.0%
! ATGATTGTTCATGATATCTA+AGG - chr4_3:66602038-66602057 None:intergenic 25.0%
! CATTAATAACTATATGCTAC+TGG + chr4_3:66602248-66602267 Msa0657130:intron 25.0%
ATGTGAATGTGAATGTGATA+AGG - chr4_3:66601703-66601722 None:intergenic 30.0%
! TAACTTTAATGCCACTTGAA+TGG - chr4_3:66601797-66601816 None:intergenic 30.0%
GATGATTTAAGTACCATTCT+TGG - chr4_3:66601838-66601857 None:intergenic 30.0%
GGTACTTAAATCATCAATCT+TGG + chr4_3:66601843-66601862 Msa0657130:CDS 30.0%
TGATCTTCCTTGTGTATTTA+TGG - chr4_3:66601912-66601931 None:intergenic 30.0%
TCATGAACAATCATCCATAT+TGG + chr4_3:66602044-66602063 Msa0657130:CDS 30.0%
AATGTTACCTTAATCCGAAA+CGG - chr4_3:66602232-66602251 None:intergenic 30.0%
TGGAACAAATAGTATAGTGA+CGG + chr4_3:66602268-66602287 Msa0657130:intron 30.0%
ATTGCTGAAAGACAAACAAT+GGG + chr4_3:66602507-66602526 Msa0657130:CDS 30.0%
CTGAGTTTAAGTCAAACAAA+CGG + chr4_3:66602544-66602563 Msa0657130:CDS 30.0%
ATGTGAATGTGAATGTGATA+AGG - chr4_3:66601703-66601722 None:intergenic 30.0%
! TAACTTTAATGCCACTTGAA+TGG - chr4_3:66601797-66601816 None:intergenic 30.0%
GATGATTTAAGTACCATTCT+TGG - chr4_3:66601838-66601857 None:intergenic 30.0%
GGTACTTAAATCATCAATCT+TGG + chr4_3:66601843-66601862 Msa0657130:CDS 30.0%
TGATCTTCCTTGTGTATTTA+TGG - chr4_3:66601912-66601931 None:intergenic 30.0%
TCATGAACAATCATCCATAT+TGG + chr4_3:66602044-66602063 Msa0657130:CDS 30.0%
AATGTTACCTTAATCCGAAA+CGG - chr4_3:66602232-66602251 None:intergenic 30.0%
TGGAACAAATAGTATAGTGA+CGG + chr4_3:66602268-66602287 Msa0657130:intron 30.0%
ATTGCTGAAAGACAAACAAT+GGG + chr4_3:66602507-66602526 Msa0657130:CDS 30.0%
CTGAGTTTAAGTCAAACAAA+CGG + chr4_3:66602544-66602563 Msa0657130:CDS 30.0%
TGTGGAAATTATAACTGTGC+TGG - chr4_3:66601662-66601681 None:intergenic 35.0%
TGTGAATGTGATAAGGATGA+GGG - chr4_3:66601696-66601715 None:intergenic 35.0%
ATGTGAATGTGATAAGGATG+AGG - chr4_3:66601697-66601716 None:intergenic 35.0%
ATTCAAAGCCCATCAATTCA+AGG + chr4_3:66601721-66601740 Msa0657130:CDS 35.0%
! TTTTACTTAGGCACCAAGAA+TGG + chr4_3:66601822-66601841 Msa0657130:intron 35.0%
AATTCATTGCTCATGTAGCT+TGG - chr4_3:66601872-66601891 None:intergenic 35.0%
TGTGTATTTATGGCTGTTGA+TGG - chr4_3:66601902-66601921 None:intergenic 35.0%
TCAACAGCCATAAATACACA+AGG + chr4_3:66601902-66601921 Msa0657130:CDS 35.0%
TTCTCTTCAAGAAATTGGCT+TGG - chr4_3:66602004-66602023 None:intergenic 35.0%
TTGTTCATGATATCTAAGGG+AGG - chr4_3:66602034-66602053 None:intergenic 35.0%
ATGTTACCTTAATCCGAAAC+GGG - chr4_3:66602231-66602250 None:intergenic 35.0%
TAGTGACAAGAGAATTAGAG+AGG - chr4_3:66602320-66602339 None:intergenic 35.0%
ATTGGCAAAAGAAACGTAGA+AGG - chr4_3:66602382-66602401 None:intergenic 35.0%
CATTGCTGAAAGACAAACAA+TGG + chr4_3:66602506-66602525 Msa0657130:CDS 35.0%
CTTAAACTCAGTTGCAAATC+AGG - chr4_3:66602535-66602554 None:intergenic 35.0%
TGTGGAAATTATAACTGTGC+TGG - chr4_3:66601662-66601681 None:intergenic 35.0%
TGTGAATGTGATAAGGATGA+GGG - chr4_3:66601696-66601715 None:intergenic 35.0%
ATGTGAATGTGATAAGGATG+AGG - chr4_3:66601697-66601716 None:intergenic 35.0%
ATTCAAAGCCCATCAATTCA+AGG + chr4_3:66601721-66601740 Msa0657130:CDS 35.0%
! TTTTACTTAGGCACCAAGAA+TGG + chr4_3:66601822-66601841 Msa0657130:intron 35.0%
AATTCATTGCTCATGTAGCT+TGG - chr4_3:66601872-66601891 None:intergenic 35.0%
TGTGTATTTATGGCTGTTGA+TGG - chr4_3:66601902-66601921 None:intergenic 35.0%
TCAACAGCCATAAATACACA+AGG + chr4_3:66601902-66601921 Msa0657130:CDS 35.0%
TTCTCTTCAAGAAATTGGCT+TGG - chr4_3:66602004-66602023 None:intergenic 35.0%
TTGTTCATGATATCTAAGGG+AGG - chr4_3:66602034-66602053 None:intergenic 35.0%
ATGTTACCTTAATCCGAAAC+GGG - chr4_3:66602231-66602250 None:intergenic 35.0%
TAGTGACAAGAGAATTAGAG+AGG - chr4_3:66602320-66602339 None:intergenic 35.0%
ATTGGCAAAAGAAACGTAGA+AGG - chr4_3:66602382-66602401 None:intergenic 35.0%
CATTGCTGAAAGACAAACAA+TGG + chr4_3:66602506-66602525 Msa0657130:CDS 35.0%
CTTAAACTCAGTTGCAAATC+AGG - chr4_3:66602535-66602554 None:intergenic 35.0%
!! AAGCTGCTGGTTCAAAGTTA+TGG - chr4_3:66601936-66601955 None:intergenic 40.0%
! TATCCTTAACTTGAAGCTGC+TGG - chr4_3:66601949-66601968 None:intergenic 40.0%
!! AGAAATTGGCTTGGTCTCAT+AGG - chr4_3:66601995-66602014 None:intergenic 40.0%
TTGGAAACAACACAAGAAGC+AGG + chr4_3:66602140-66602159 Msa0657130:CDS 40.0%
TGGAAACAACACAAGAAGCA+GGG + chr4_3:66602141-66602160 Msa0657130:CDS 40.0%
TTGAATTTGATCCCCCGTTT+CGG + chr4_3:66602215-66602234 Msa0657130:CDS 40.0%
TGTTACCTTAATCCGAAACG+GGG - chr4_3:66602230-66602249 None:intergenic 40.0%
CAAACAAACGGCAACAATGA+TGG + chr4_3:66602556-66602575 Msa0657130:CDS 40.0%
AACAATGATGGCAAGAGTGA+TGG + chr4_3:66602568-66602587 Msa0657130:CDS 40.0%
!! GAGTTTCGTGTCGATTTCTT+TGG - chr4_3:66602605-66602624 None:intergenic 40.0%
!! AAGCTGCTGGTTCAAAGTTA+TGG - chr4_3:66601936-66601955 None:intergenic 40.0%
! TATCCTTAACTTGAAGCTGC+TGG - chr4_3:66601949-66601968 None:intergenic 40.0%
!! AGAAATTGGCTTGGTCTCAT+AGG - chr4_3:66601995-66602014 None:intergenic 40.0%
TTGGAAACAACACAAGAAGC+AGG + chr4_3:66602140-66602159 Msa0657130:CDS 40.0%
TGGAAACAACACAAGAAGCA+GGG + chr4_3:66602141-66602160 Msa0657130:CDS 40.0%
TTGAATTTGATCCCCCGTTT+CGG + chr4_3:66602215-66602234 Msa0657130:CDS 40.0%
TGTTACCTTAATCCGAAACG+GGG - chr4_3:66602230-66602249 None:intergenic 40.0%
CAAACAAACGGCAACAATGA+TGG + chr4_3:66602556-66602575 Msa0657130:CDS 40.0%
AACAATGATGGCAAGAGTGA+TGG + chr4_3:66602568-66602587 Msa0657130:CDS 40.0%
!! GAGTTTCGTGTCGATTTCTT+TGG - chr4_3:66602605-66602624 None:intergenic 40.0%
! GAACCAGCAGCTTCAAGTTA+AGG + chr4_3:66601943-66601962 Msa0657130:CDS 45.0%
GTTACCTTAATCCGAAACGG+GGG - chr4_3:66602229-66602248 None:intergenic 45.0%
! GAACCAGCAGCTTCAAGTTA+AGG + chr4_3:66601943-66601962 Msa0657130:CDS 45.0%
GTTACCTTAATCCGAAACGG+GGG - chr4_3:66602229-66602248 None:intergenic 45.0%
GTGATAAGGATGAGGGATGC+AGG - chr4_3:66601689-66601708 None:intergenic 50.0%
TGGTCTCATAGGAGCAAGTG+TGG - chr4_3:66601984-66602003 None:intergenic 50.0%
AACATCACTTAGACCCGCTG+AGG + chr4_3:66602111-66602130 Msa0657130:CDS 50.0%
TTTCCAAAGCTCACCTCAGC+GGG - chr4_3:66602127-66602146 None:intergenic 50.0%
GTTTCCAAAGCTCACCTCAG+CGG - chr4_3:66602128-66602147 None:intergenic 50.0%
TGATCCCCCGTTTCGGATTA+AGG + chr4_3:66602222-66602241 Msa0657130:CDS 50.0%
GTGATAAGGATGAGGGATGC+AGG - chr4_3:66601689-66601708 None:intergenic 50.0%
TGGTCTCATAGGAGCAAGTG+TGG - chr4_3:66601984-66602003 None:intergenic 50.0%
AACATCACTTAGACCCGCTG+AGG + chr4_3:66602111-66602130 Msa0657130:CDS 50.0%
TTTCCAAAGCTCACCTCAGC+GGG - chr4_3:66602127-66602146 None:intergenic 50.0%
GTTTCCAAAGCTCACCTCAG+CGG - chr4_3:66602128-66602147 None:intergenic 50.0%
TGATCCCCCGTTTCGGATTA+AGG + chr4_3:66602222-66602241 Msa0657130:CDS 50.0%
ATGAGGGATGCAGGAGACTG+TGG - chr4_3:66601680-66601699 None:intergenic 55.0%
ATGAGGGATGCAGGAGACTG+TGG - chr4_3:66601680-66601699 None:intergenic 55.0%
AGACCCGCTGAGGTGAGCTT+TGG + chr4_3:66602121-66602140 Msa0657130:CDS 60.0%
AGACCCGCTGAGGTGAGCTT+TGG + chr4_3:66602121-66602140 Msa0657130:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 66601621 66602683 66601621 ID=Msa0657130;Name=Msa0657130
chr4_3 mRNA 66601621 66602683 66601621 ID=Msa0657130-mRNA-1;Parent=Msa0657130;Name=Msa0657130-mRNA-1;_AED=0.11;_eAED=0.11;_QI=0|0.5|0.33|1|1|1|3|47|225
chr4_3 exon 66601621 66601742 66601621 ID=Msa0657130-mRNA-1:exon:19184;Parent=Msa0657130-mRNA-1
chr4_3 exon 66601832 66602243 66601832 ID=Msa0657130-mRNA-1:exon:19185;Parent=Msa0657130-mRNA-1
chr4_3 exon 66602493 66602683 66602493 ID=Msa0657130-mRNA-1:exon:19186;Parent=Msa0657130-mRNA-1
chr4_3 CDS 66601621 66601742 66601621 ID=Msa0657130-mRNA-1:cds;Parent=Msa0657130-mRNA-1
chr4_3 CDS 66601832 66602243 66601832 ID=Msa0657130-mRNA-1:cds;Parent=Msa0657130-mRNA-1
chr4_3 CDS 66602493 66602636 66602493 ID=Msa0657130-mRNA-1:cds;Parent=Msa0657130-mRNA-1
chr4_3 three_prime_UTR 66602637 66602683 66602637 ID=Msa0657130-mRNA-1:three_prime_utr;Parent=Msa0657130-mRNA-1
Gene Sequence

>Msa0657130

ATGGCAAATGGTGGAATTGTTCTAGAAACTAATTACAACCAGCACAGTTATAATTTCCACAGTCTCCTGCATCCCTCATCCTTATCACATTCACATTCACATTCAAAGCCCATCAATTCAAGGCACCAAGAATGGTACTTAAATCATCAATCTTGGAGACCAAGCTACATGAGCAATGAATTAGTTATGCCATCAACAGCCATAAATACACAAGGAAGATCATCCATAACTTTGAACCAGCAGCTTCAAGTTAAGGATACTACAGTCACTACCACACTTGCTCCTATGAGACCAAGCCAATTTCTTGAAGAGAAAAGATGGCCTCCCTTAGATATCATGAACAATCATCCATATTGGAAGAAAAATTTACATGATAATTTTTCTAATAATACTTGTGATAGAACATCACTTAGACCCGCTGAGGTGAGCTTTGGAAACAACACAAGAAGCAGGGAAAACATATCAAACATCAATAATGACCACAACTATTTTAATAGTTCAAAGATTGAATTTGATCCCCCGTTTCGGATTAAGTTGAATCAAGAGACATTGCTGAAAGACAAACAATGGGTGCCTGATTTGCAACTGAGTTTAAGTCAAACAAACGGCAACAATGATGGCAAGAGTGATGGTTTGAGAGAAACCAAAGAAATCGACACGAAACTCTCACTTTCTTAG

Protein sequence

>Msa0657130

MANGGIVLETNYNQHSYNFHSLLHPSSLSHSHSHSKPINSRHQEWYLNHQSWRPSYMSNELVMPSTAINTQGRSSITLNQQLQVKDTTVTTTLAPMRPSQFLEEKRWPPLDIMNNHPYWKKNLHDNFSNNTCDRTSLRPAEVSFGNNTRSRENISNINNDHNYFNSSKIEFDPPFRIKLNQETLLKDKQWVPDLQLSLSQTNGNNDGKSDGLRETKEIDTKLSLS*