AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66651

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66651.t1 MTR_3g053920 48.971 243 58 3 1 243 103 279 9.23e-62 196
MS.gene66651.t1 MTR_4g103530 86.957 46 6 0 1 46 49 94 1.49e-22 92.0
MS.gene66651.t1 MTR_6g033215 36.458 96 59 1 4 97 199 294 2.56e-12 65.9
MS.gene66651.t1 MTR_0010s0370 44.928 69 34 2 10 75 110 177 9.01e-11 60.1
MS.gene66651.t1 MTR_0010s0350 44.928 69 34 2 10 75 110 177 9.01e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 58 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTAGCTAGCACCGCATTC+TGG 0.141973 4.3:-48931929 None:intergenic
AGAAGCCAGCAGATGTATTT+TGG 0.145079 4.3:-48931976 None:intergenic
CCAAGTCATCCTTTGGGGCT+TGG 0.235303 4.3:+48932032 MS.gene66651:CDS
GTTCCAAACCTTTGCGTAAC+TGG 0.267932 4.3:-48931717 None:intergenic
CCTATGCCTTGACCTACTTT+TGG 0.278124 4.3:-48931417 None:intergenic
CCTGCTTCCAAGTCATCCTT+TGG 0.318496 4.3:+48932025 MS.gene66651:CDS
CTGATGATGGCGTCCGCAAT+TGG 0.330887 4.3:+48931679 MS.gene66651:CDS
CTGCTTCCAAGTCATCCTTT+GGG 0.362390 4.3:+48932026 MS.gene66651:CDS
CAAGGCATAGGAAGCTTCTT+AGG 0.376769 4.3:+48931429 MS.gene66651:CDS
CAACCAACGGTTTGTGGCAG+CGG 0.377733 4.3:-48931739 None:intergenic
CAAGTTCACGGTCTGCCTTT+CGG 0.389727 4.3:+48931384 MS.gene66651:CDS
TGATGATGGCGTCCGCAATT+GGG 0.395960 4.3:+48931680 MS.gene66651:CDS
TTTAGCTAGCACCGCATTCT+GGG 0.402038 4.3:-48931928 None:intergenic
AGCGACTCTGACACACATAT+TGG 0.405483 4.3:-48931493 None:intergenic
AAACCAGTTACGCAAAGGTT+TGG 0.415112 4.3:+48931714 MS.gene66651:CDS
TTCGAATTAGATTCTGATGA+TGG 0.422237 4.3:+48931666 MS.gene66651:CDS
TGTCACAGGTGTGGATTGAT+TGG 0.423731 4.3:+48931615 MS.gene66651:CDS
TGCTTCCAAAATACATCTGC+TGG 0.424718 4.3:+48931971 MS.gene66651:CDS
TGGTTCAGTGGGACAAAGCT+AGG 0.443161 4.3:-48931345 None:intergenic
ATCTTGCAACCAACGGTTTG+TGG 0.450416 4.3:-48931745 None:intergenic
CCAAGCCCCAAAGGATGACT+TGG 0.469128 4.3:-48932032 None:intergenic
ACCATGGATCTTATCGCTCC+TGG 0.475299 4.3:+48931315 None:intergenic
CAAGCAGGTGCTGCTTCTGT+TGG 0.476934 4.3:+48931801 MS.gene66651:CDS
ATCTAATGATGACATACAAT+AGG 0.483060 4.3:+48932082 MS.gene66651:CDS
TGTGACATAGAAGCAGGAAT+AGG 0.487822 4.3:-48931768 None:intergenic
CCAAAGGATGACTTGGAAGC+AGG 0.490656 4.3:-48932025 None:intergenic
CAACAGAAGCAGCACCTGCT+TGG 0.492986 4.3:-48931800 None:intergenic
TCATTAGATTCACTTGAAAG+TGG 0.496760 4.3:-48932068 None:intergenic
AGTAACAAAAGCACCGTTTG+TGG 0.497986 4.3:-48931559 None:intergenic
CTGCTGGCTTCTTCTTCCAC+AGG 0.507471 4.3:+48931987 MS.gene66651:CDS
GATGATGGCGTCCGCAATTG+GGG 0.507633 4.3:+48931681 MS.gene66651:CDS
TGGCGAGTCCGTGCCACAAA+CGG 0.511841 4.3:+48931546 MS.gene66651:CDS
CACCTTCAGTAGCTGCAGTT+CGG 0.513939 4.3:-48931824 None:intergenic
TGCTTCCAAGTCATCCTTTG+GGG 0.514970 4.3:+48932027 MS.gene66651:CDS
TCACTTGAAAGTGGAGCAGC+AGG 0.515569 4.3:-48932059 None:intergenic
GGATTCATCCAACCAAAAGT+AGG 0.533518 4.3:+48931405 MS.gene66651:CDS
GCAGGTAAGCCAAGCCCCAA+AGG 0.549880 4.3:-48932041 None:intergenic
GTTTGATGTGACATAGAAGC+AGG 0.552176 4.3:-48931774 None:intergenic
TCATGTCAGCTCCCCAATTG+CGG 0.560990 4.3:-48931692 None:intergenic
GAACCGCTGCCACAAACCGT+TGG 0.569652 4.3:+48931736 MS.gene66651:CDS
AACTGCAGCTACTGAAGGTG+TGG 0.577023 4.3:+48931827 MS.gene66651:CDS
AGAATCTAATTCGAACAACT+CGG 0.580030 4.3:-48931658 None:intergenic
CAAAAGCACCGTTTGTGGCA+CGG 0.590707 4.3:-48931554 None:intergenic
GGTTCAGTGGGACAAAGCTA+GGG 0.592996 4.3:-48931344 None:intergenic
TCACATCAAACTCACCAAGC+AGG 0.593385 4.3:+48931786 MS.gene66651:CDS
GTGCTAGCTAAAGAAGGTAA+AGG 0.593767 4.3:+48931939 MS.gene66651:CDS
GAATCTAATTCGAACAACTC+GGG 0.601829 4.3:-48931657 None:intergenic
ACAAAGCTAGGGACGACACC+AGG 0.602101 4.3:-48931333 None:intergenic
AATGCGGTGCTAGCTAAAGA+AGG 0.603825 4.3:+48931933 MS.gene66651:CDS
GGCCGAACTGCAGCTACTGA+AGG 0.610869 4.3:+48931822 MS.gene66651:CDS
ATCCAACCAAAAGTAGGTCA+AGG 0.617189 4.3:+48931411 MS.gene66651:CDS
CCAAAAGTAGGTCAAGGCAT+AGG 0.620618 4.3:+48931417 MS.gene66651:CDS
ACCAGGAGCGATAAGATCCA+TGG 0.622459 4.3:-48931316 None:intergenic
GCTAGTAGCTGAAGTACCTG+TGG 0.624706 4.3:-48932003 None:intergenic
TGTGCTTGCTGCCCAGAATG+CGG 0.637409 4.3:+48931917 MS.gene66651:CDS
ACATGAAACCAGTTACGCAA+AGG 0.638258 4.3:+48931709 MS.gene66651:CDS
GAATAGGATCTTGCAACCAA+CGG 0.654985 4.3:-48931752 None:intergenic
TTTGGTTGGATGAATCCGAA+AGG 0.672828 4.3:-48931399 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTTTAAATATGAAAAATT+GGG + chr4.3:48931585-48931604 MS.gene66651:CDS 10.0%
!! TAACTTTAAATATGAAAAAT+TGG + chr4.3:48931584-48931603 MS.gene66651:CDS 10.0%
! AAAAATCAATATGGTTCAGT+GGG - chr4.3:48931359-48931378 None:intergenic 25.0%
!!! ACTGAACCATATTGATTTTT+GGG + chr4.3:48931359-48931378 MS.gene66651:CDS 25.0%
AGAATCTAATTCGAACAACT+CGG - chr4.3:48931661-48931680 None:intergenic 30.0%
CAAAAATCAATATGGTTCAG+TGG - chr4.3:48931360-48931379 None:intergenic 30.0%
CTTGAACCCAAAAATCAATA+TGG - chr4.3:48931368-48931387 None:intergenic 30.0%
TCATTAGATTCACTTGAAAG+TGG - chr4.3:48932071-48932090 None:intergenic 30.0%
TTCGAATTAGATTCTGATGA+TGG + chr4.3:48931666-48931685 MS.gene66651:CDS 30.0%
!!! CACTGAACCATATTGATTTT+TGG + chr4.3:48931358-48931377 MS.gene66651:CDS 30.0%
GAATCTAATTCGAACAACTC+GGG - chr4.3:48931660-48931679 None:intergenic 35.0%
!!! GATTTTTGGGTTCAAGTTCA+CGG + chr4.3:48931372-48931391 MS.gene66651:CDS 35.0%
AAACCAGTTACGCAAAGGTT+TGG + chr4.3:48931714-48931733 MS.gene66651:CDS 40.0%
ACATGAAACCAGTTACGCAA+AGG + chr4.3:48931709-48931728 MS.gene66651:CDS 40.0%
ATCCAACCAAAAGTAGGTCA+AGG + chr4.3:48931411-48931430 MS.gene66651:CDS 40.0%
GAATAGGATCTTGCAACCAA+CGG - chr4.3:48931755-48931774 None:intergenic 40.0%
GGATTCATCCAACCAAAAGT+AGG + chr4.3:48931405-48931424 MS.gene66651:CDS 40.0%
GTGCTAGCTAAAGAAGGTAA+AGG + chr4.3:48931939-48931958 MS.gene66651:CDS 40.0%
GTTTGATGTGACATAGAAGC+AGG - chr4.3:48931777-48931796 None:intergenic 40.0%
TGCTTCCAAAATACATCTGC+TGG + chr4.3:48931971-48931990 MS.gene66651:CDS 40.0%
TGTGACATAGAAGCAGGAAT+AGG - chr4.3:48931771-48931790 None:intergenic 40.0%
TTTGGTTGGATGAATCCGAA+AGG - chr4.3:48931402-48931421 None:intergenic 40.0%
! AATTGGGTGTGTTTTGTCAC+AGG + chr4.3:48931601-48931620 MS.gene66651:CDS 40.0%
! AGAAGCCAGCAGATGTATTT+TGG - chr4.3:48931979-48931998 None:intergenic 40.0%
!! AGTAACAAAAGCACCGTTTG+TGG - chr4.3:48931562-48931581 None:intergenic 40.0%
AGCGACTCTGACACACATAT+TGG - chr4.3:48931496-48931515 None:intergenic 45.0%
ATCTTGCAACCAACGGTTTG+TGG - chr4.3:48931748-48931767 None:intergenic 45.0%
CAAGGCATAGGAAGCTTCTT+AGG + chr4.3:48931429-48931448 MS.gene66651:CDS 45.0%
CCAAAAGTAGGTCAAGGCAT+AGG + chr4.3:48931417-48931436 MS.gene66651:CDS 45.0%
CTGCTTCCAAGTCATCCTTT+GGG + chr4.3:48932026-48932045 MS.gene66651:CDS 45.0%
CTGTCCCACTGAAAAAAGAG+TGG + chr4.3:48931526-48931545 MS.gene66651:CDS 45.0%
GTTCCAAACCTTTGCGTAAC+TGG - chr4.3:48931720-48931739 None:intergenic 45.0%
TCACATCAAACTCACCAAGC+AGG + chr4.3:48931786-48931805 MS.gene66651:CDS 45.0%
TGCTTCCAAGTCATCCTTTG+GGG + chr4.3:48932027-48932046 MS.gene66651:CDS 45.0%
TTTAGCTAGCACCGCATTCT+GGG - chr4.3:48931931-48931950 None:intergenic 45.0%
! AATGCGGTGCTAGCTAAAGA+AGG + chr4.3:48931933-48931952 MS.gene66651:CDS 45.0%
! CCTATGCCTTGACCTACTTT+TGG - chr4.3:48931420-48931439 None:intergenic 45.0%
! TGTCACAGGTGTGGATTGAT+TGG + chr4.3:48931615-48931634 MS.gene66651:CDS 45.0%
!! TGCCTTGACCTACTTTTGGT+TGG - chr4.3:48931416-48931435 None:intergenic 45.0%
!!! ACTCGCCACTCTTTTTTCAG+TGG - chr4.3:48931534-48931553 None:intergenic 45.0%
!!! CTCGCCACTCTTTTTTCAGT+GGG - chr4.3:48931533-48931552 None:intergenic 45.0%
AACTGCAGCTACTGAAGGTG+TGG + chr4.3:48931827-48931846 MS.gene66651:CDS 50.0%
CAAGTTCACGGTCTGCCTTT+CGG + chr4.3:48931384-48931403 MS.gene66651:CDS 50.0%
CACCTTCAGTAGCTGCAGTT+CGG - chr4.3:48931827-48931846 None:intergenic 50.0%
CCTGCTTCCAAGTCATCCTT+TGG + chr4.3:48932025-48932044 MS.gene66651:CDS 50.0%
CTTTAGCTAGCACCGCATTC+TGG - chr4.3:48931932-48931951 None:intergenic 50.0%
GGTTCAGTGGGACAAAGCTA+GGG - chr4.3:48931347-48931366 None:intergenic 50.0%
TCACTTGAAAGTGGAGCAGC+AGG - chr4.3:48932062-48932081 None:intergenic 50.0%
TCATGTCAGCTCCCCAATTG+CGG - chr4.3:48931695-48931714 None:intergenic 50.0%
TGGTTCAGTGGGACAAAGCT+AGG - chr4.3:48931348-48931367 None:intergenic 50.0%
! CCAAAGGATGACTTGGAAGC+AGG - chr4.3:48932028-48932047 None:intergenic 50.0%
! GCTAGTAGCTGAAGTACCTG+TGG - chr4.3:48932006-48932025 None:intergenic 50.0%
! GGTGTGTTTTGTCACAGGTG+TGG + chr4.3:48931606-48931625 MS.gene66651:CDS 50.0%
!! CAAAAGCACCGTTTGTGGCA+CGG - chr4.3:48931557-48931576 None:intergenic 50.0%
!! TGATGATGGCGTCCGCAATT+GGG + chr4.3:48931680-48931699 MS.gene66651:CDS 50.0%
ACAAAGCTAGGGACGACACC+AGG - chr4.3:48931336-48931355 None:intergenic 55.0%
CAACAGAAGCAGCACCTGCT+TGG - chr4.3:48931803-48931822 None:intergenic 55.0%
CAACCAACGGTTTGTGGCAG+CGG - chr4.3:48931742-48931761 None:intergenic 55.0%
CCAAGCCCCAAAGGATGACT+TGG - chr4.3:48932035-48932054 None:intergenic 55.0%
! GATGATGGCGTCCGCAATTG+GGG + chr4.3:48931681-48931700 MS.gene66651:CDS 55.0%
! TGTGCTTGCTGCCCAGAATG+CGG + chr4.3:48931917-48931936 MS.gene66651:CDS 55.0%
!! CAAGCAGGTGCTGCTTCTGT+TGG + chr4.3:48931801-48931820 MS.gene66651:CDS 55.0%
!! CCAAGTCATCCTTTGGGGCT+TGG + chr4.3:48932032-48932051 MS.gene66651:CDS 55.0%
!! CTGATGATGGCGTCCGCAAT+TGG + chr4.3:48931679-48931698 MS.gene66651:CDS 55.0%
!! CTGCTGGCTTCTTCTTCCAC+AGG + chr4.3:48931987-48932006 MS.gene66651:CDS 55.0%
GAACCGCTGCCACAAACCGT+TGG + chr4.3:48931736-48931755 MS.gene66651:CDS 60.0%
GCAGGTAAGCCAAGCCCCAA+AGG - chr4.3:48932044-48932063 None:intergenic 60.0%
GGCCGAACTGCAGCTACTGA+AGG + chr4.3:48931822-48931841 MS.gene66651:CDS 60.0%
TGGCGAGTCCGTGCCACAAA+CGG + chr4.3:48931546-48931565 MS.gene66651:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 48931318 48932103 48931318 ID=MS.gene66651
chr4.3 mRNA 48931318 48932103 48931318 ID=MS.gene66651.t1;Parent=MS.gene66651
chr4.3 exon 48931318 48932103 48931318 ID=MS.gene66651.t1.exon1;Parent=MS.gene66651.t1
chr4.3 CDS 48931318 48932103 48931318 ID=cds.MS.gene66651.t1;Parent=MS.gene66651.t1
Gene Sequence

>MS.gene66651

ATGGATCTTATCGCTCCTGGTGTCGTCCCTAGCTTTGTCCCACTGAACCATATTGATTTTTGGGTTCAAGTTCACGGTCTGCCTTTCGGATTCATCCAACCAAAAGTAGGTCAAGGCATAGGAAGCTTCTTAGGCACTTTCAAAGCATATGATAATCGCAACTCAATTCATAGTTCCAATATGTGTGTCAGAGTCGCTATTGTTGTCACTGTCCCACTGAAAAAAGAGTGGCGAGTCCGTGCCACAAACGGTGCTTTTGTTACTGTTAACTTTAAATATGAAAAATTGGGTGTGTTTTGTCACAGGTGTGGATTGATTGGTCATACTGACAAAGTGTGTCCCGAGTTGTTCGAATTAGATTCTGATGATGGCGTCCGCAATTGGGGAGCTGACATGAAACCAGTTACGCAAAGGTTTGGAACCGCTGCCACAAACCGTTGGTTGCAAGATCCTATTCCTGCTTCTATGTCACATCAAACTCACCAAGCAGGTGCTGCTTCTGTTGGCCGAACTGCAGCTACTGAAGGTGTGGAAAATTCTGCAACTTTCAATGATCGTATGCTCACTCTTCAGATGCAACTTACTGCTATGCAACAAGATGTGCTTGCTGCCCAGAATGCGGTGCTAGCTAAAGAAGGTAAAGGTGCAAGTTCTGCTTCCAAAATACATCTGCTGGCTTCTTCTTCCACAGGTACTTCAGCTACTAGCCTGCTTCCAAGTCATCCTTTGGGGCTTGGCTTACCTGCTGCTCCACTTTCAAGTGAATCTAATGATGACATACAATAG
Protein sequence

>MS.gene66651.t1

MDLIAPGVVPSFVPLNHIDFWVQVHGLPFGFIQPKVGQGIGSFLGTFKAYDNRNSIHSSNMCVRVAIVVTVPLKKEWRVRATNGAFVTVNFKYEKLGVFCHRCGLIGHTDKVCPELFELDSDDGVRNWGADMKPVTQRFGTAATNRWLQDPIPASMSHQTHQAGAASVGRTAATEGVENSATFNDRMLTLQMQLTAMQQDVLAAQNAVLAKEGKGASSASKIHLLASSSTGTSATSLLPSHPLGLGLPAAPLSSESNDDIQ