AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90898

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90898.t1 MTR_1g116940 95.197 229 11 0 1 229 30 258 2.47e-148 413
MS.gene90898.t1 MTR_1g053960 55.556 234 92 6 1 229 1 227 5.27e-79 237
MS.gene90898.t1 MTR_7g093130 55.230 239 86 8 1 226 1 231 2.62e-78 235
MS.gene90898.t1 MTR_1g053960 55.556 234 92 6 1 229 67 293 3.03e-78 237
MS.gene90898.t1 MTR_7g093130 55.230 239 86 8 1 226 71 301 4.16e-77 234
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90898.t1 AT3G12130 43.981 216 98 5 32 229 37 247 8.18e-49 160
MS.gene90898.t1 AT5G06770 43.750 208 102 5 32 229 15 217 2.35e-48 158
MS.gene90898.t1 AT5G06770 43.750 208 102 5 32 229 37 239 4.87e-48 158
MS.gene90898.t1 AT5G06770 43.500 200 98 5 40 229 18 212 4.04e-45 150
MS.gene90898.t1 AT5G06770 43.500 200 98 5 40 229 18 212 4.04e-45 150
MS.gene90898.t1 AT5G06770 43.500 200 98 5 40 229 18 212 4.04e-45 150
MS.gene90898.t1 AT3G12130 51.634 153 63 2 85 229 26 175 3.21e-44 146
MS.gene90898.t1 AT5G06770 51.449 138 66 1 92 229 31 167 7.64e-44 145

Find 76 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGGAGCTGCTGCCGGTTT+TGG 0.155815 1.2:-86630832 MS.gene90898:CDS
ACAGCTGAAGGTCGCAAATT+TGG 0.185089 1.2:-86630988 MS.gene90898:CDS
ACCAAAGGATCCTGCACTTT+TGG 0.214083 1.2:-86630499 MS.gene90898:CDS
CAGCTGAAGGTCGCAAATTT+GGG 0.254177 1.2:-86630987 MS.gene90898:CDS
TTGGTCTTGAAGTTGTTTGC+AGG 0.265962 1.2:+86630538 None:intergenic
CTTCAAGCTCAATATTTCTA+AGG 0.277040 1.2:+86630671 None:intergenic
TAAAATTTCTATCACATTCC+AGG 0.312719 1.2:+86630433 None:intergenic
CAGGTGCTAAACTTTCCATT+AGG 0.322304 1.2:-86630714 MS.gene90898:CDS
TATTGAACTTGTTGCACAAC+CGG 0.331191 1.2:+86631010 None:intergenic
GCAGCTCCATGAGCTGGAGG+TGG 0.349271 1.2:+86630844 None:intergenic
CCCAAAAGTGCAGGATCCTT+TGG 0.352380 1.2:+86630498 None:intergenic
GCTCCATGAGCTGGAGGTGG+GGG 0.369225 1.2:+86630847 None:intergenic
CTTAGAAATATTGAGCTTGA+AGG 0.380840 1.2:-86630670 MS.gene90898:CDS
ACATTTGAATTTCTACCAAT+TGG 0.391278 1.2:+86631078 None:intergenic
AGCTCCATGAGCTGGAGGTG+GGG 0.391671 1.2:+86630846 None:intergenic
CCGAACTCACATTTAGAATA+AGG 0.392968 1.2:+86630605 None:intergenic
AAGCAAATCTATCACATAAC+AGG 0.395520 1.2:-86630733 MS.gene90898:CDS
AGGTGCTAAACTTTCCATTA+GGG 0.399844 1.2:-86630713 MS.gene90898:CDS
ATGGTGAGTGGGAGCGTGGC+AGG 0.408893 1.2:-86630945 MS.gene90898:CDS
ATCTGAGTCATGTTCCCTAA+TGG 0.413569 1.2:+86630699 None:intergenic
CTAAATGTGAGTTCGGTCTC+TGG 0.419817 1.2:-86630598 MS.gene90898:CDS
CAGCTCCATGAGCTGGAGGT+GGG 0.423034 1.2:+86630845 None:intergenic
CACAACCGGGTCTTAGCAAC+TGG 0.431622 1.2:+86631024 None:intergenic
GCTGCTTTGCATTTGTCCCA+TGG 0.442232 1.2:+86630891 None:intergenic
ATGCAAAGCAGCAGTGTTGA+TGG 0.443234 1.2:-86630880 MS.gene90898:CDS
CTACCAATTGGTGGAATAGC+AGG 0.443500 1.2:+86631090 None:intergenic
CCAGCTCATGGAGCTGCTGC+CGG 0.447956 1.2:-86630838 MS.gene90898:CDS
CCGGCAGCAGCTCCATGAGC+TGG 0.455038 1.2:+86630838 None:intergenic
CCTTATTCTAAATGTGAGTT+CGG 0.456926 1.2:-86630605 MS.gene90898:CDS
AGCTCAATATTTCTAAGGTT+AGG 0.469832 1.2:+86630676 None:intergenic
TTTGAATTTCTACCAATTGG+TGG 0.470976 1.2:+86631081 None:intergenic
AGTGGCCGACACTCCAAAAC+CGG 0.472552 1.2:+86630819 None:intergenic
AGTCCTGCTATTCCACCAAT+TGG 0.476108 1.2:-86631093 MS.gene90898:CDS
AGTTCGGTCTCTGGACCTCC+AGG 0.487466 1.2:-86630589 MS.gene90898:CDS
TGGTCTTGAAGTTGTTTGCA+GGG 0.488541 1.2:+86630539 None:intergenic
AAGGTCATGGACCATGGCAC+TGG 0.492421 1.2:+86630624 None:intergenic
GCGCGAGTATCTTCATATGC+AGG 0.492758 1.2:+86630913 None:intergenic
ACCCTTGCTAGAGCTATCAT+TGG 0.494785 1.2:-86630775 MS.gene90898:CDS
ACTGGTGGAGAAGAACCGTC+TGG 0.507265 1.2:+86631042 None:intergenic
CTCCACCAGTTGCTAAGACC+CGG 0.514232 1.2:-86631029 MS.gene90898:CDS
ACAGATGAATTATGCAAGCC+TGG 0.520202 1.2:-86630451 MS.gene90898:CDS
GCCACGCTCCCACTCACCAT+GGG 0.523824 1.2:+86630948 None:intergenic
TTCCAATGATAGCTCTAGCA+AGG 0.524282 1.2:+86630773 None:intergenic
GCACCTTTCCCCAAAAGTGC+AGG 0.529864 1.2:+86630489 None:intergenic
GAAAGGTGCCACTTCGCGCA+TGG 0.536523 1.2:-86630475 MS.gene90898:CDS
TGCCACGCTCCCACTCACCA+TGG 0.538201 1.2:+86630947 None:intergenic
GTGGGAGCGTGGCAGGCCCA+CGG 0.551387 1.2:-86630938 MS.gene90898:CDS
ATTGAACTTGTTGCACAACC+GGG 0.554392 1.2:+86631011 None:intergenic
TGTTATGTGATAGATTTGCT+TGG 0.557591 1.2:+86630735 None:intergenic
TATGAAGATACTCGCGCCAT+GGG 0.559467 1.2:-86630907 MS.gene90898:CDS
TGCAAAGCAGCAGTGTTGAT+GGG 0.562545 1.2:-86630879 MS.gene90898:CDS
CATCTGTTCCATGCGCGAAG+TGG 0.569090 1.2:+86630467 None:intergenic
CGCGAGTATCTTCATATGCA+GGG 0.573206 1.2:+86630914 None:intergenic
GAAGAACCGTCTGGGAAGGA+TGG 0.574755 1.2:+86631051 None:intergenic
ATATGAAGATACTCGCGCCA+TGG 0.580726 1.2:-86630908 MS.gene90898:CDS
TCTTCATATGCAGGGACCGT+GGG 0.587144 1.2:+86630922 None:intergenic
GAACCGTCTGGGAAGGATGG+TGG 0.589119 1.2:+86631054 None:intergenic
GTCACTTTGCCCATGGTGAG+TGG 0.600587 1.2:-86630957 MS.gene90898:CDS
GCCCATGGTGAGTGGGAGCG+TGG 0.601228 1.2:-86630949 MS.gene90898:CDS
TAGAATAAGGTCATGGACCA+TGG 0.602580 1.2:+86630618 None:intergenic
TCCAATGATAGCTCTAGCAA+GGG 0.603096 1.2:+86630774 None:intergenic
TGGAGAAGAACCGTCTGGGA+AGG 0.604602 1.2:+86631047 None:intergenic
AACAAGTTCAATACAGCTGA+AGG 0.604829 1.2:-86631000 MS.gene90898:CDS
GTCTCTCAGATGATCAATGT+CGG 0.614302 1.2:-86631120 None:intergenic
AACCGGGTCTTAGCAACTGG+TGG 0.615487 1.2:+86631027 None:intergenic
CTGTGTGAAAACTTTACCAA+AGG 0.618887 1.2:-86630514 MS.gene90898:CDS
GGTCTTGAAGTTGTTTGCAG+GGG 0.621193 1.2:+86630540 None:intergenic
TCACTTTGCCCATGGTGAGT+GGG 0.626927 1.2:-86630956 MS.gene90898:CDS
TCACATTTAGAATAAGGTCA+TGG 0.629476 1.2:+86630611 None:intergenic
CTGGTGGAGAAGAACCGTCT+GGG 0.629582 1.2:+86631043 None:intergenic
GATCAAACAAGCCAGTGCCA+TGG 0.633360 1.2:-86630635 MS.gene90898:CDS
ATCTTCATATGCAGGGACCG+TGG 0.634772 1.2:+86630921 None:intergenic
GTTCCACCATCCTTCCCAGA+CGG 0.641586 1.2:-86631057 MS.gene90898:CDS
GCAGCAGCTCCATGAGCTGG+AGG 0.660051 1.2:+86630841 None:intergenic
AGCTGAAGGTCGCAAATTTG+GGG 0.668544 1.2:-86630986 MS.gene90898:CDS
GATAAATGTCACTTTGCCCA+TGG 0.676321 1.2:-86630964 MS.gene90898:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTAATATTAACTTTTGCAG+TGG + chr1.2:86630757-86630776 None:intergenic 20.0%
! ACATTTGAATTTCTACCAAT+TGG + chr1.2:86630480-86630499 None:intergenic 25.0%
AAGCAAATCTATCACATAAC+AGG - chr1.2:86630822-86630841 MS.gene90898:CDS 30.0%
AGAGCTATCATTGGAAAAAA+TGG - chr1.2:86630789-86630808 MS.gene90898:CDS 30.0%
CCTTATTCTAAATGTGAGTT+CGG - chr1.2:86630950-86630969 MS.gene90898:CDS 30.0%
CTTAGAAATATTGAGCTTGA+AGG - chr1.2:86630885-86630904 MS.gene90898:CDS 30.0%
TTTGAATTTCTACCAATTGG+TGG + chr1.2:86630477-86630496 None:intergenic 30.0%
! CTTCAAGCTCAATATTTCTA+AGG + chr1.2:86630887-86630906 None:intergenic 30.0%
! TCACATTTAGAATAAGGTCA+TGG + chr1.2:86630947-86630966 None:intergenic 30.0%
! TGTTATGTGATAGATTTGCT+TGG + chr1.2:86630823-86630842 None:intergenic 30.0%
!! AGCTCAATATTTCTAAGGTT+AGG + chr1.2:86630882-86630901 None:intergenic 30.0%
!!! TGTGAAGTAATGTTTTTTCC+TGG + chr1.2:86630987-86631006 None:intergenic 30.0%
AACAAGTTCAATACAGCTGA+AGG - chr1.2:86630555-86630574 MS.gene90898:CDS 35.0%
AGGTGCTAAACTTTCCATTA+GGG - chr1.2:86630842-86630861 MS.gene90898:CDS 35.0%
CTGTGTGAAAACTTTACCAA+AGG - chr1.2:86631041-86631060 MS.gene90898:CDS 35.0%
! CCGAACTCACATTTAGAATA+AGG + chr1.2:86630953-86630972 None:intergenic 35.0%
!! TATTGAACTTGTTGCACAAC+CGG + chr1.2:86630548-86630567 None:intergenic 35.0%
!!! GAAGTAATGTTTTTTCCTGG+AGG + chr1.2:86630984-86631003 None:intergenic 35.0%
ACAGATGAATTATGCAAGCC+TGG - chr1.2:86631104-86631123 MS.gene90898:CDS 40.0%
ATCTGAGTCATGTTCCCTAA+TGG + chr1.2:86630859-86630878 None:intergenic 40.0%
CAGGTGCTAAACTTTCCATT+AGG - chr1.2:86630841-86630860 MS.gene90898:CDS 40.0%
TAGAATAAGGTCATGGACCA+TGG + chr1.2:86630940-86630959 None:intergenic 40.0%
! GGTAAAGTTTTCACACAGCT+TGG + chr1.2:86631039-86631058 None:intergenic 40.0%
! TGGTCTTGAAGTTGTTTGCA+GGG + chr1.2:86631019-86631038 None:intergenic 40.0%
!! ATTGAACTTGTTGCACAACC+GGG + chr1.2:86630547-86630566 None:intergenic 40.0%
!! GATAAATGTCACTTTGCCCA+TGG - chr1.2:86630591-86630610 MS.gene90898:CDS 40.0%
!! TCCAATGATAGCTCTAGCAA+GGG + chr1.2:86630784-86630803 None:intergenic 40.0%
!! TTCCAATGATAGCTCTAGCA+AGG + chr1.2:86630785-86630804 None:intergenic 40.0%
!! TTGGTCTTGAAGTTGTTTGC+AGG + chr1.2:86631020-86631039 None:intergenic 40.0%
ACAGCTGAAGGTCGCAAATT+TGG - chr1.2:86630567-86630586 MS.gene90898:CDS 45.0%
ACCCTTGCTAGAGCTATCAT+TGG - chr1.2:86630780-86630799 MS.gene90898:CDS 45.0%
AGCTGAAGGTCGCAAATTTG+GGG - chr1.2:86630569-86630588 MS.gene90898:CDS 45.0%
AGTCCTGCTATTCCACCAAT+TGG - chr1.2:86630462-86630481 MS.gene90898:CDS 45.0%
ATATGAAGATACTCGCGCCA+TGG - chr1.2:86630647-86630666 MS.gene90898:CDS 45.0%
CAGCTGAAGGTCGCAAATTT+GGG - chr1.2:86630568-86630587 MS.gene90898:CDS 45.0%
CGCGAGTATCTTCATATGCA+GGG + chr1.2:86630644-86630663 None:intergenic 45.0%
CTAAATGTGAGTTCGGTCTC+TGG - chr1.2:86630957-86630976 MS.gene90898:CDS 45.0%
CTACCAATTGGTGGAATAGC+AGG + chr1.2:86630468-86630487 None:intergenic 45.0%
GGTCTTGAAGTTGTTTGCAG+GGG + chr1.2:86631018-86631037 None:intergenic 45.0%
TATGAAGATACTCGCGCCAT+GGG - chr1.2:86630648-86630667 MS.gene90898:CDS 45.0%
! ACCAAAGGATCCTGCACTTT+TGG - chr1.2:86631056-86631075 MS.gene90898:CDS 45.0%
! ATGCAAAGCAGCAGTGTTGA+TGG - chr1.2:86630675-86630694 MS.gene90898:CDS 45.0%
! CAAAGGATCCTGCACTTTTG+GGG - chr1.2:86631058-86631077 MS.gene90898:CDS 45.0%
! CCAAAGGATCCTGCACTTTT+GGG - chr1.2:86631057-86631076 MS.gene90898:CDS 45.0%
!! TGCAAAGCAGCAGTGTTGAT+GGG - chr1.2:86630676-86630695 MS.gene90898:CDS 45.0%
ATCTTCATATGCAGGGACCG+TGG + chr1.2:86630637-86630656 None:intergenic 50.0%
GATCAAACAAGCCAGTGCCA+TGG - chr1.2:86630920-86630939 MS.gene90898:CDS 50.0%
GCGCGAGTATCTTCATATGC+AGG + chr1.2:86630645-86630664 None:intergenic 50.0%
TCACTTTGCCCATGGTGAGT+GGG - chr1.2:86630599-86630618 MS.gene90898:CDS 50.0%
TCTTCATATGCAGGGACCGT+GGG + chr1.2:86630636-86630655 None:intergenic 50.0%
! CCCAAAAGTGCAGGATCCTT+TGG + chr1.2:86631060-86631079 None:intergenic 50.0%
! GCTGCTTTGCATTTGTCCCA+TGG + chr1.2:86630667-86630686 None:intergenic 50.0%
!! GATCCTGCACTTTTGGGGAA+AGG - chr1.2:86631063-86631082 MS.gene90898:CDS 50.0%
AACCGGGTCTTAGCAACTGG+TGG + chr1.2:86630531-86630550 None:intergenic 55.0%
AAGGTCATGGACCATGGCAC+TGG + chr1.2:86630934-86630953 None:intergenic 55.0%
ACTGGTGGAGAAGAACCGTC+TGG + chr1.2:86630516-86630535 None:intergenic 55.0%
AGTGGCCGACACTCCAAAAC+CGG + chr1.2:86630739-86630758 None:intergenic 55.0%
CACAACCGGGTCTTAGCAAC+TGG + chr1.2:86630534-86630553 None:intergenic 55.0%
CATCTGTTCCATGCGCGAAG+TGG + chr1.2:86631091-86631110 None:intergenic 55.0%
CTCCACCAGTTGCTAAGACC+CGG - chr1.2:86630526-86630545 MS.gene90898:CDS 55.0%
CTGGTGGAGAAGAACCGTCT+GGG + chr1.2:86630515-86630534 None:intergenic 55.0%
GAAGAACCGTCTGGGAAGGA+TGG + chr1.2:86630507-86630526 None:intergenic 55.0%
GTTCCACCATCCTTCCCAGA+CGG - chr1.2:86630498-86630517 MS.gene90898:CDS 55.0%
TGGAGAAGAACCGTCTGGGA+AGG + chr1.2:86630511-86630530 None:intergenic 55.0%
! GCACCTTTCCCCAAAAGTGC+AGG + chr1.2:86631069-86631088 None:intergenic 55.0%
! GTCACTTTGCCCATGGTGAG+TGG - chr1.2:86630598-86630617 MS.gene90898:CDS 55.0%
!!! TGCTGCCGGTTTTGGAGTGT+CGG - chr1.2:86630731-86630750 MS.gene90898:CDS 55.0%
AGCTCCATGAGCTGGAGGTG+GGG + chr1.2:86630712-86630731 None:intergenic 60.0%
AGTTCGGTCTCTGGACCTCC+AGG - chr1.2:86630966-86630985 MS.gene90898:CDS 60.0%
CAGCTCCATGAGCTGGAGGT+GGG + chr1.2:86630713-86630732 None:intergenic 60.0%
GAACCGTCTGGGAAGGATGG+TGG + chr1.2:86630504-86630523 None:intergenic 60.0%
!! GAAAGGTGCCACTTCGCGCA+TGG - chr1.2:86631080-86631099 MS.gene90898:CDS 60.0%
!!! CATGGAGCTGCTGCCGGTTT+TGG - chr1.2:86630723-86630742 MS.gene90898:CDS 60.0%
CCAGCTCATGGAGCTGCTGC+CGG - chr1.2:86630717-86630736 MS.gene90898:CDS 65.0%
GCAGCAGCTCCATGAGCTGG+AGG + chr1.2:86630717-86630736 None:intergenic 65.0%
GCAGCTCCATGAGCTGGAGG+TGG + chr1.2:86630714-86630733 None:intergenic 65.0%
GCCACGCTCCCACTCACCAT+GGG + chr1.2:86630610-86630629 None:intergenic 65.0%
GCTCCATGAGCTGGAGGTGG+GGG + chr1.2:86630711-86630730 None:intergenic 65.0%
TGCCACGCTCCCACTCACCA+TGG + chr1.2:86630611-86630630 None:intergenic 65.0%
! ATGGTGAGTGGGAGCGTGGC+AGG - chr1.2:86630610-86630629 MS.gene90898:CDS 65.0%
CCGGCAGCAGCTCCATGAGC+TGG + chr1.2:86630720-86630739 None:intergenic 70.0%
GAGCCCCCACCTCCAGCTCA+TGG - chr1.2:86630705-86630724 MS.gene90898:CDS 70.0%
GCCCATGGTGAGTGGGAGCG+TGG - chr1.2:86630606-86630625 MS.gene90898:CDS 70.0%
! GTGGGAGCGTGGCAGGCCCA+CGG - chr1.2:86630617-86630636 MS.gene90898:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 86630444 86631133 86630444 ID=MS.gene90898
chr1.2 mRNA 86630444 86631133 86630444 ID=MS.gene90898.t1;Parent=MS.gene90898
chr1.2 exon 86630444 86631133 86630444 ID=MS.gene90898.t1.exon1;Parent=MS.gene90898.t1
chr1.2 CDS 86630444 86631133 86630444 ID=cds.MS.gene90898.t1;Parent=MS.gene90898.t1
Gene Sequence

>MS.gene90898

ATGATCAATGTCGGTAGCAGTCCTGCTATTCCACCAATTGGTAGAAATTCAAATGTTCCACCATCCTTCCCAGACGGTTCTTCTCCACCAGTTGCTAAGACCCGGTTGTGCAACAAGTTCAATACAGCTGAAGGTCGCAAATTTGGGGATAAATGTCACTTTGCCCATGGTGAGTGGGAGCGTGGCAGGCCCACGGTCCCTGCATATGAAGATACTCGCGCCATGGGACAAATGCAAAGCAGCAGTGTTGATGGGAGAATTGAGCCCCCACCTCCAGCTCATGGAGCTGCTGCCGGTTTTGGAGTGTCGGCCACTGCAAAAGTTAATATTAATGCTACCCTTGCTAGAGCTATCATTGGAAAAAATGGTGTTAACTCCAAGCAAATCTATCACATAACAGGTGCTAAACTTTCCATTAGGGAACATGACTCAGATCCTAACCTTAGAAATATTGAGCTTGAAGGCAGTTTTGATCAGATCAAACAAGCCAGTGCCATGGTCCATGACCTTATTCTAAATGTGAGTTCGGTCTCTGGACCTCCAGGAAAAAACATTACTTCACAGACTTCTGCCCCTGCAAACAACTTCAAGACCAAGCTGTGTGAAAACTTTACCAAAGGATCCTGCACTTTTGGGGAAAGGTGCCACTTCGCGCATGGAACAGATGAATTATGCAAGCCTGGAATGTGA
Protein sequence

>MS.gene90898.t1

MINVGSSPAIPPIGRNSNVPPSFPDGSSPPVAKTRLCNKFNTAEGRKFGDKCHFAHGEWERGRPTVPAYEDTRAMGQMQSSSVDGRIEPPPPAHGAAAGFGVSATAKVNINATLARAIIGKNGVNSKQIYHITGAKLSIREHDSDPNLRNIELEGSFDQIKQASAMVHDLILNVSSVSGPPGKNITSQTSAPANNFKTKLCENFTKGSCTFGERCHFAHGTDELCKPGM