AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0080048612.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048612.01.T01 MTR_1g072370 69.725 109 11 1 3 111 9 95 5.74e-44 140
MsG0080048612.01.T01 MTR_7g094680 69.725 109 11 1 3 111 9 95 6.25e-44 140
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048612.01.T01 AT4G02840 67.257 113 21 3 3 113 9 107 1.10e-43 139
MsG0080048612.01.T01 AT4G02840 63.964 111 18 1 3 113 9 97 9.18e-42 134
MsG0080048612.01.T01 AT3G07590 63.303 109 18 1 3 111 9 95 2.48e-40 130
MsG0080048612.01.T01 AT3G07590 63.303 109 18 1 3 111 9 95 2.48e-40 130
MsG0080048612.01.T01 AT3G07590 87.692 65 8 0 47 111 5 69 4.58e-37 122

Find 28 sgRNAs with CRISPR-Local

Find 139 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTACCAGCAGTTGGCTTCTT+AGG 0.317812 contig374end:+18895 None:intergenic
CCCCTTTAGAGTTAGCTTAA+CGG 0.355184 contig374end:+19035 None:intergenic
ACCGTTAAGCTAACTCTAAA+GGG 0.355730 contig374end:-19036 MsG0080048612.01.T01:CDS
CCCACTGTAATGGCATGATA+TGG 0.359914 contig374end:+20766 None:intergenic
CTTCAACAAGTAAAGTTTCA+AGG 0.362204 contig374end:+18935 None:intergenic
CTGAGATGATCCAAAGTAAC+TGG 0.363042 contig374end:+19006 None:intergenic
GAAGAATGGTATATTGTTCA+TGG 0.388414 contig374end:-20999 MsG0080048612.01.T01:CDS
GATGGAGTACACGGTGCTAT+TGG 0.413311 contig374end:-20736 MsG0080048612.01.T01:CDS
AACAATCCAACTAGACATAA+TGG 0.413420 contig374end:+18827 None:intergenic
ATTACAGTGGGGTGATTTGA+TGG 0.414952 contig374end:-20754 MsG0080048612.01.T01:CDS
GTTTCAAGGTTCAAGCTGTC+AGG 0.435597 contig374end:+18949 None:intergenic
AACCGTTAAGCTAACTCTAA+AGG 0.451979 contig374end:-19037 MsG0080048612.01.T01:CDS
TACTTGTTGAAGAAGCTCCT+AGG 0.498295 contig374end:-18924 MsG0080048612.01.T01:CDS
ACTTGTTGAAGAAGCTCCTA+GGG 0.502700 contig374end:-18923 MsG0080048612.01.T01:CDS
ATCAAATCACCCCACTGTAA+TGG 0.512593 contig374end:+20756 None:intergenic
CCATATCATGCCATTACAGT+GGG 0.515566 contig374end:-20766 MsG0080048612.01.T01:CDS
ATTGTTCATGGCACTATCAC+AGG 0.523787 contig374end:-20987 MsG0080048612.01.T01:intron
GGCTTCTTAGGCTTGACCCT+AGG 0.525010 contig374end:+18907 None:intergenic
GTCTCAATCGAGTTGAAGAA+TGG 0.529618 contig374end:-21013 MsG0080048612.01.T01:CDS
AAGCCTAAGAAGCCAACTGC+TGG 0.548844 contig374end:-18898 MsG0080048612.01.T01:CDS
ATTCTTCAACTCGATTGAGA+CGG 0.606708 contig374end:+21015 None:intergenic
TTGGATCATCTCAGTGTGAG+AGG 0.610982 contig374end:-18997 MsG0080048612.01.T01:CDS
CAAGGTTCAAGCTGTCAGGA+AGG 0.613711 contig374end:+18953 None:intergenic
TCCATATCATGCCATTACAG+TGG 0.625481 contig374end:-20767 MsG0080048612.01.T01:CDS
CCGTTAAGCTAACTCTAAAG+GGG 0.635466 contig374end:-19035 MsG0080048612.01.T01:CDS
TCGTATACAGTACCAGCAGT+TGG 0.655537 contig374end:+18886 None:intergenic
GGGTGATTTGATGGAGTACA+CGG 0.691050 contig374end:-20745 MsG0080048612.01.T01:CDS
CATATCATGCCATTACAGTG+GGG 0.735357 contig374end:-20765 MsG0080048612.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATAATAATAATAATAATT+AGG + contig374end:18994-19013 None:intergenic 0.0%
!! ATAATAATATAAGAGAAAAT+AGG + contig374end:19205-19224 None:intergenic 10.0%
!! AAGATTACCAAAAATATATA+CGG + contig374end:20177-20196 None:intergenic 15.0%
!! ACAATTAGTATACAAAAATA+TGG + contig374end:20252-20271 None:intergenic 15.0%
!! TATTATTATTACGAGTTTAA+TGG - contig374end:19027-19046 MsG0080048612.01.T01:CDS 15.0%
!! TTTAAATACTTTCTTATTCT+TGG - contig374end:19983-20002 MsG0080048612.01.T01:intron 15.0%
!!! TACAAATTATGTTTTGATTA+TGG - contig374end:20201-20220 MsG0080048612.01.T01:intron 15.0%
!! ATTAAAAAGTGAATGCATAT+CGG - contig374end:20672-20691 MsG0080048612.01.T01:intron 20.0%
!! ATTAGGTTTAACAAAAAATG+TGG + contig374end:18977-18996 None:intergenic 20.0%
!! ATTATTGTACAACATTATCT+AGG - contig374end:19477-19496 MsG0080048612.01.T01:intron 20.0%
!! TCATCAATTGTAAGTTTAAA+AGG - contig374end:20450-20469 MsG0080048612.01.T01:intron 20.0%
!! TTATTGTACAACATTATCTA+GGG - contig374end:19478-19497 MsG0080048612.01.T01:intron 20.0%
!!! CAATAGATCTGTTTTTAAAA+TGG - contig374end:19292-19311 MsG0080048612.01.T01:intron 20.0%
!!! TTTTAAAAACAGATCTATTG+TGG + contig374end:19292-19311 None:intergenic 20.0%
! AAAAAATAAGCCAATCCAAT+TGG - contig374end:19694-19713 MsG0080048612.01.T01:intron 25.0%
! AAAAATAAGCCAATCCAATT+GGG - contig374end:19695-19714 MsG0080048612.01.T01:intron 25.0%
! AAAAATAAGTCAATCCAAAC+GGG + contig374end:19504-19523 None:intergenic 25.0%
! AAATTAGGGTTTAAGAAAAG+CGG + contig374end:18935-18954 None:intergenic 25.0%
! AAGCATGTTTGATAAACTAA+TGG - contig374end:20275-20294 MsG0080048612.01.T01:intron 25.0%
! AATTATTATTTCACACAGTC+AGG - contig374end:19174-19193 MsG0080048612.01.T01:intron 25.0%
! CAAAAATAAGTCAATCCAAA+CGG + contig374end:19505-19524 None:intergenic 25.0%
! CCCACTAAATTAAGAAAAAA+GGG + contig374end:19741-19760 None:intergenic 25.0%
! TGAATCCTTGTATTCTAAAT+TGG - contig374end:20589-20608 MsG0080048612.01.T01:intron 25.0%
! TTTAATACAAGGAAATTCCT+CGG + contig374end:20658-20677 None:intergenic 25.0%
! TTTATTTCATAAGCTTGTCA+AGG + contig374end:19638-19657 None:intergenic 25.0%
!! ATTAGTTTATCAAACATGCT+TGG + contig374end:20276-20295 None:intergenic 25.0%
!! GTGCTTAATTTGATTGTATA+TGG + contig374end:20636-20655 None:intergenic 25.0%
!! TATTGCCAATTTAGAATACA+AGG + contig374end:20597-20616 None:intergenic 25.0%
!!! CCCTTTTTTCTTAATTTAGT+GGG - contig374end:19738-19757 MsG0080048612.01.T01:intron 25.0%
!!! TCCCTTTTTTCTTAATTTAG+TGG - contig374end:19737-19756 MsG0080048612.01.T01:intron 25.0%
!!! TGCATTCACTTTTTAATACA+AGG + contig374end:20669-20688 None:intergenic 25.0%
!!! TTATTTTTCCTTGCTTTTCT+TGG - contig374end:19904-19923 MsG0080048612.01.T01:intron 25.0%
!!! TTTTGATCTTGCTTTAGAAT+AGG - contig374end:19880-19899 MsG0080048612.01.T01:intron 25.0%
AAGGGAATCCATATTCTATT+AGG + contig374end:19723-19742 None:intergenic 30.0%
AATATCACATTTACCATGCA+AGG + contig374end:20013-20032 None:intergenic 30.0%
ACATTTGAATGAGCTGTAAT+TGG - contig374end:19353-19372 MsG0080048612.01.T01:intron 30.0%
ACCAAAAATATATACGGCAA+AGG + contig374end:20171-20190 None:intergenic 30.0%
ACTTACTAATCCTAACTTTC+CGG - contig374end:20383-20402 MsG0080048612.01.T01:intron 30.0%
AGGGAATCCATATTCTATTA+GGG + contig374end:19722-19741 None:intergenic 30.0%
CTTCAACAAGTAAAGTTTCA+AGG + contig374end:20942-20961 None:intergenic 30.0%
GAAGAATGGTATATTGTTCA+TGG - contig374end:18875-18894 MsG0080048612.01.T01:CDS 30.0%
GCCCACTAAATTAAGAAAAA+AGG + contig374end:19742-19761 None:intergenic 30.0%
TCATTCAAATGTCAAATCTG+CGG + contig374end:19345-19364 None:intergenic 30.0%
! AATTGATGACCACATAATTC+TGG + contig374end:20439-20458 None:intergenic 30.0%
! AGTACCTGTTCTTTTCTATA+TGG - contig374end:19442-19461 MsG0080048612.01.T01:intron 30.0%
! ATTGATGACCACATAATTCT+GGG + contig374end:20438-20457 None:intergenic 30.0%
! GAAAGTTAGGATTAGTAAGT+TGG + contig374end:20383-20402 None:intergenic 30.0%
! GCTTTTCTTAAACCCTAATT+TGG - contig374end:18934-18953 MsG0080048612.01.T01:CDS 30.0%
! TCCTTTGCCGTATATATTTT+TGG - contig374end:20167-20186 MsG0080048612.01.T01:intron 30.0%
!! TCTTGCCTTTTATTTGTGAT+GGG - contig374end:20724-20743 MsG0080048612.01.T01:intron 30.0%
!! TTCTTGCCTTTTATTTGTGA+TGG - contig374end:20723-20742 MsG0080048612.01.T01:intron 30.0%
!!! TACATACGAAGCATTGTTTT+GGG - contig374end:19262-19281 MsG0080048612.01.T01:intron 30.0%
!!! TTACATACGAAGCATTGTTT+TGG - contig374end:19261-19280 MsG0080048612.01.T01:intron 30.0%
AAAATTTACCAGTAGACCCT+AGG - contig374end:19835-19854 MsG0080048612.01.T01:intron 35.0%
AACCGTTAAGCTAACTCTAA+AGG - contig374end:20837-20856 MsG0080048612.01.T01:intron 35.0%
AAGTTGGAAAGCTACACTAA+TGG + contig374end:20367-20386 None:intergenic 35.0%
AATCTAACAAGAAGCTACCT+AGG + contig374end:19855-19874 None:intergenic 35.0%
ACCGTTAAGCTAACTCTAAA+GGG - contig374end:20838-20857 MsG0080048612.01.T01:intron 35.0%
AGAAAACAATGAGCTGACAA+CGG + contig374end:20142-20161 None:intergenic 35.0%
ATCTAACAAGAAGCTACCTA+GGG + contig374end:19854-19873 None:intergenic 35.0%
ATTCTTCAACTCGATTGAGA+CGG + contig374end:18862-18881 None:intergenic 35.0%
CTGTCCATATAGAAAAGAAC+AGG + contig374end:19449-19468 None:intergenic 35.0%
GGGAATCCATATTCTATTAG+GGG + contig374end:19721-19740 None:intergenic 35.0%
GTTTAAAAGGTCCAATGTGT+AGG - contig374end:20463-20482 MsG0080048612.01.T01:intron 35.0%
TATTCTTGGTTATCCTTGCA+TGG - contig374end:19997-20016 MsG0080048612.01.T01:intron 35.0%
! ACTAATTAGCTCTTCAACCT+TGG + contig374end:19416-19435 None:intergenic 35.0%
! ATAATTCTGGGGGATTCAAT+TGG + contig374end:20426-20445 None:intergenic 35.0%
! GGAATTCCAAGTAAGTTGAA+GGG + contig374end:19324-19343 None:intergenic 35.0%
! GTGAACATGATTTGTGAGTA+TGG - contig374end:20566-20585 MsG0080048612.01.T01:intron 35.0%
! TACAATCAAATTAAGCACCG+AGG - contig374end:20638-20657 MsG0080048612.01.T01:intron 35.0%
! TTGATGACCACATAATTCTG+GGG + contig374end:20437-20456 None:intergenic 35.0%
!! AGTTCTTGATTTGTCGTTTC+TGG - contig374end:19947-19966 MsG0080048612.01.T01:intron 35.0%
!! CTTGCCTTTTATTTGTGATG+GGG - contig374end:20725-20744 MsG0080048612.01.T01:intron 35.0%
AATGGAACAGGCATTAGAGA+TGG + contig374end:20349-20368 None:intergenic 40.0%
ACTGTCCGATTGTACAGATA+AGG + contig374end:20081-20100 None:intergenic 40.0%
ATCAAATCACCCCACTGTAA+TGG + contig374end:19121-19140 None:intergenic 40.0%
ATGGAACAGGCATTAGAGAT+GGG + contig374end:20348-20367 None:intergenic 40.0%
ATTACAGTGGGGTGATTTGA+TGG - contig374end:19120-19139 MsG0080048612.01.T01:intron 40.0%
ATTGGGCCCCTAATAGAATA+TGG - contig374end:19712-19731 MsG0080048612.01.T01:intron 40.0%
ATTGTTCATGGCACTATCAC+AGG - contig374end:18887-18906 MsG0080048612.01.T01:CDS 40.0%
CAAAGCACAGAGCCAAATTA+GGG + contig374end:18949-18968 None:intergenic 40.0%
CATATCATGCCATTACAGTG+GGG - contig374end:19109-19128 MsG0080048612.01.T01:intron 40.0%
CCAAATGTTGATGTTCTGTC+TGG - contig374end:19761-19780 MsG0080048612.01.T01:intron 40.0%
CCAGACAGAACATCAACATT+TGG + contig374end:19764-19783 None:intergenic 40.0%
CCATATCATGCCATTACAGT+GGG - contig374end:19108-19127 MsG0080048612.01.T01:intron 40.0%
CTCACCCCATCACAAATAAA+AGG + contig374end:20732-20751 None:intergenic 40.0%
CTGAGATGATCCAAAGTAAC+TGG + contig374end:20871-20890 None:intergenic 40.0%
CTGTCCGATTGTACAGATAA+GGG + contig374end:20080-20099 None:intergenic 40.0%
GAAAGCTACACTAATGGAAC+AGG + contig374end:20361-20380 None:intergenic 40.0%
GCTGATGATATTGCAGCATA+TGG + contig374end:20230-20249 None:intergenic 40.0%
GGGGAAAAATCCAGTTACTT+TGG - contig374end:20858-20877 MsG0080048612.01.T01:intron 40.0%
GTAACAAAGCAACAAGTCCA+AGG + contig374end:20784-20803 None:intergenic 40.0%
TACTCTCCCTTCAACTTACT+TGG - contig374end:19315-19334 MsG0080048612.01.T01:intron 40.0%
TAGTAGACACACCTACACAT+TGG + contig374end:20477-20496 None:intergenic 40.0%
TATCTGTACAATCGGACAGT+AGG - contig374end:20081-20100 MsG0080048612.01.T01:intron 40.0%
TATTCTATTAGGGGCCCAAT+TGG + contig374end:19712-19731 None:intergenic 40.0%
TCCATATCATGCCATTACAG+TGG - contig374end:19107-19126 MsG0080048612.01.T01:intron 40.0%
TCTCCCCTTATCTGTACAAT+CGG - contig374end:20073-20092 MsG0080048612.01.T01:intron 40.0%
TGACAACGGTTGAAGAGAAT+TGG + contig374end:20128-20147 None:intergenic 40.0%
TGATGACCACATAATTCTGG+GGG + contig374end:20436-20455 None:intergenic 40.0%
TGTCCGATTGTACAGATAAG+GGG + contig374end:20079-20098 None:intergenic 40.0%
TTGAATCCCCCAGAATTATG+TGG - contig374end:20427-20446 MsG0080048612.01.T01:intron 40.0%
! ACTTGTTGAAGAAGCTCCTA+GGG - contig374end:20951-20970 MsG0080048612.01.T01:intron 40.0%
! CCGTTAAGCTAACTCTAAAG+GGG - contig374end:20839-20858 MsG0080048612.01.T01:intron 40.0%
! CGGAATTCCAAGTAAGTTGA+AGG + contig374end:19325-19344 None:intergenic 40.0%
! GAGAAACAGCTGACTTCAAT+TGG + contig374end:19089-19108 None:intergenic 40.0%
! GCATTAGTTGTACTGATCCT+TGG - contig374end:20764-20783 MsG0080048612.01.T01:CDS 40.0%
! TACTTGTTGAAGAAGCTCCT+AGG - contig374end:20950-20969 MsG0080048612.01.T01:intron 40.0%
!! CCCCTTTAGAGTTAGCTTAA+CGG + contig374end:20842-20861 None:intergenic 40.0%
!! GTCTCAATCGAGTTGAAGAA+TGG - contig374end:18861-18880 MsG0080048612.01.T01:CDS 40.0%
!! TGGACTTGTTGCTTTGTTAC+AGG - contig374end:20784-20803 MsG0080048612.01.T01:intron 40.0%
!!! TTTTCTTGGTGTTCTGCTCT+GGG - contig374end:19918-19937 MsG0080048612.01.T01:intron 40.0%
CCCACTGTAATGGCATGATA+TGG + contig374end:19111-19130 None:intergenic 45.0%
GAAAACTTCCTGTCTTGCCA+AGG - contig374end:19396-19415 MsG0080048612.01.T01:intron 45.0%
GCAAAGCACAGAGCCAAATT+AGG + contig374end:18950-18969 None:intergenic 45.0%
GCAGAACACCAAGAAAAGCA+AGG + contig374end:19915-19934 None:intergenic 45.0%
GGGATTCAATTGGAGGAGAA+TGG + contig374end:20416-20435 None:intergenic 45.0%
GGGTGATTTGATGGAGTACA+CGG - contig374end:19129-19148 MsG0080048612.01.T01:intron 45.0%
GTTTCAAGGTTCAAGCTGTC+AGG + contig374end:20928-20947 None:intergenic 45.0%
TATTAGGGGCCCAATTGGAT+TGG + contig374end:19707-19726 None:intergenic 45.0%
TCGTATACAGTACCAGCAGT+TGG + contig374end:20991-21010 None:intergenic 45.0%
TGGTGTGTTTCCGGAAAGTT+AGG + contig374end:20396-20415 None:intergenic 45.0%
TTGGATCATCTCAGTGTGAG+AGG - contig374end:20877-20896 MsG0080048612.01.T01:intron 45.0%
! AACATTATCTAGGGCCCGTT+TGG - contig374end:19487-19506 MsG0080048612.01.T01:intron 45.0%
! ATTCTGGGGGATTCAATTGG+AGG + contig374end:20423-20442 None:intergenic 45.0%
! ATTTGTGATGGGGTGAGAAG+TGG - contig374end:20735-20754 MsG0080048612.01.T01:CDS 45.0%
! GTTGATGTTCTGTCTGGAGT+TGG - contig374end:19767-19786 MsG0080048612.01.T01:intron 45.0%
!!! CTTTTCTTGGTGTTCTGCTC+TGG - contig374end:19917-19936 MsG0080048612.01.T01:intron 45.0%
AAGCCTAAGAAGCCAACTGC+TGG - contig374end:20976-20995 MsG0080048612.01.T01:intron 50.0%
AGAAGCTACCTAGGGTCTAC+TGG + contig374end:19846-19865 None:intergenic 50.0%
CAAGGTTCAAGCTGTCAGGA+AGG + contig374end:20924-20943 None:intergenic 50.0%
CTCTTCAACCTTGGCAAGAC+AGG + contig374end:19407-19426 None:intergenic 50.0%
CTGTACAATCGGACAGTAGG+AGG - contig374end:20084-20103 MsG0080048612.01.T01:intron 50.0%
GGAGGAGAATGGTGTGTTTC+CGG + contig374end:20405-20424 None:intergenic 50.0%
TGATGGGGTGAGAAGTGGTT+TGG - contig374end:20740-20759 MsG0080048612.01.T01:CDS 50.0%
! CAGATGCACTGACGCTGTAT+AGG + contig374end:20312-20331 None:intergenic 50.0%
! GTACCAGCAGTTGGCTTCTT+AGG + contig374end:20982-21001 None:intergenic 50.0%
!! GATGGAGTACACGGTGCTAT+TGG - contig374end:19138-19157 MsG0080048612.01.T01:intron 50.0%
GGCTTCTTAGGCTTGACCCT+AGG + contig374end:20970-20989 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
contig374end gene 18837 21059 18837 ID=MsG0080048612.01;Name=MsG0080048612.01
contig374end mRNA 18837 21059 18837 ID=MsG0080048612.01.T01;Parent=MsG0080048612.01;Name=MsG0080048612.01.T01;_AED=0.50;_eAED=0.66;_QI=0|0|0|1|0|0|3|0|130
contig374end exon 20988 21059 20988 ID=MsG0080048612.01.T01:exon:37913;Parent=MsG0080048612.01.T01
contig374end exon 20730 20796 20730 ID=MsG0080048612.01.T01:exon:37914;Parent=MsG0080048612.01.T01
contig374end exon 18837 19090 18837 ID=MsG0080048612.01.T01:exon:37915;Parent=MsG0080048612.01.T01
contig374end CDS 20988 21059 20988 ID=MsG0080048612.01.T01:cds;Parent=MsG0080048612.01.T01
contig374end CDS 20730 20796 20730 ID=MsG0080048612.01.T01:cds;Parent=MsG0080048612.01.T01
contig374end CDS 18837 19090 18837 ID=MsG0080048612.01.T01:cds;Parent=MsG0080048612.01.T01
Gene Sequence

>MsG0080048612.01.T01

TCTCATGAAGTGAACAACGAAACCGTCTCAATCGAGTTGAAGAATGGTATATTGTTCATGGCACTATCACAGCTGTTTCTCCATATCATGCCATTACAGTGGGGTGATTTGATGGAGTACACGGTGCTATTGGATGACAGTGTTGACATCAGTATGAATACACATTTGAAAACCGTTAAGCTAACTCTAAAGGGGAAAAATCCAGTTACTTTGGATCATCTCAGTGTGAGAGGCAACAACATTCGTTATTATATCCTTCCTGACAGCTTGAACCTTGAAACTTTACTTGTTGAAGAAGCTCCTAGGGTCAAGCCTAAGAAGCCAACTGCTGGTACTGTATACGACTATTTGATAGTAACTATGATGCTTTTCAATCAGAGCCATTATGTCTAG
Protein sequence

>MsG0080048612.01.T01

SHEVNNETVSIELKNGILFMALSQLFLHIMPLQWGDLMEYTVLLDDSVDISMNTHLKTVKLTLKGKNPVTLDHLSVRGNNIRYYILPDSLNLETLLVEEAPRVKPKKPTAGTVYDYLIVTMMLFNQSHYV*