AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071841

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071841.t1 MTR_2g035130 95.541 157 7 0 1 157 1 157 6.42e-106 299
MS.gene071841.t1 MTR_2g035150 84.810 158 24 0 1 158 1 158 6.66e-96 274
MS.gene071841.t1 MTR_2g035100 85.987 157 22 0 1 157 1 157 2.18e-94 270
MS.gene071841.t1 MTR_2g035120 85.443 158 23 0 1 158 1 158 3.69e-94 270
MS.gene071841.t1 MTR_2g035105 84.713 157 24 0 1 157 1 157 5.53e-93 266
MS.gene071841.t1 MTR_6g033450 67.722 158 51 0 1 158 1 158 5.69e-76 223
MS.gene071841.t1 MTR_4g120970 67.722 158 51 0 1 158 1 158 5.69e-76 223
MS.gene071841.t1 MTR_2g035320 59.236 157 64 0 1 157 1 157 8.22e-63 190
MS.gene071841.t1 MTR_2g035190 57.325 157 67 0 1 157 1 157 1.38e-60 184
MS.gene071841.t1 MTR_2g035210 56.051 157 69 0 1 157 1 157 1.64e-58 179
MS.gene071841.t1 MTR_2g035220 56.051 157 69 0 1 157 1 157 1.82e-57 177
MS.gene071841.t1 MTR_2g035170 55.414 157 70 0 1 157 1 157 5.80e-57 175
MS.gene071841.t1 MTR_2g435310 37.179 156 97 1 1 155 1 156 1.20e-35 121
MS.gene071841.t1 MTR_4g120760 38.217 157 96 1 1 156 1 157 2.66e-35 120
MS.gene071841.t1 MTR_4g120760 38.217 157 96 1 1 156 1 157 2.78e-35 120
MS.gene071841.t1 MTR_2g035320 55.556 99 44 0 59 157 24 122 8.83e-34 115
MS.gene071841.t1 MTR_4g120950 43.827 162 84 5 1 158 1 159 2.79e-32 113
MS.gene071841.t1 MTR_4g120940 59.551 89 33 1 70 158 35 120 1.95e-30 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAGCATAGTTGGTGGTTT+TGG 0.149266 2.2:-53749923 MS.gene071841:CDS
TGATGGCATCAATAACCTTT+GGG 0.301288 2.2:+53750825 None:intergenic
TATATACTTTAGTTGTAATC+AGG 0.322045 2.2:+53749707 None:intergenic
AACGATATCAATACTCTTGA+TGG 0.325047 2.2:+53750808 None:intergenic
GAAATCTTCTCCACTGTGTC+TGG 0.343745 2.2:+53749896 None:intergenic
TTGATGGCATCAATAACCTT+TGG 0.345179 2.2:+53750824 None:intergenic
ACTAGGTGCAACATCACTTT+TGG 0.347787 2.2:+53749805 None:intergenic
GGCTCTTGAAGGTTACGTTT+TGG 0.372797 2.2:-53749735 MS.gene071841:CDS
TTTGCAAAGGTTCCTCCATT+TGG 0.376714 2.2:+53749848 None:intergenic
CACTTTGTGCAACACATACT+TGG 0.384404 2.2:+53749979 None:intergenic
CTTAGTAGATGATGTTAACT+TGG 0.391360 2.2:-53749954 MS.gene071841:CDS
CATCAATAACCTTTGGGGTA+AGG 0.433870 2.2:+53750831 None:intergenic
AATGGGTGTTTACAACTTTG+AGG 0.456552 2.2:-53750918 MS.gene071841:CDS
AAGAGTATTGATATCGTTGA+AGG 0.465901 2.2:-53750803 MS.gene071841:CDS
GCTTACCACTACAGCATAGT+TGG 0.468258 2.2:-53749932 MS.gene071841:CDS
AGTGGAGAAGATTTCATTTG+AGG 0.476098 2.2:-53749888 MS.gene071841:CDS
AGAGCTTTGTAAAGTGTAGC+AGG 0.480318 2.2:+53750872 None:intergenic
AAATTGTCTGCAGGTCCAAA+TGG 0.485800 2.2:-53749863 MS.gene071841:CDS
TTTGAGGCTAAATTGTCTGC+AGG 0.495049 2.2:-53749872 MS.gene071841:CDS
AATGGCAAAGCTAGGGGTGA+TGG 0.523022 2.2:-53749767 MS.gene071841:CDS
TTCTTGAGTTCCTCTTCACT+AGG 0.524188 2.2:+53749788 None:intergenic
CAAGTATGTGTTGCACAAAG+TGG 0.538293 2.2:-53749978 MS.gene071841:CDS
AACTCAAGAATGGCAAAGCT+AGG 0.540466 2.2:-53749775 MS.gene071841:CDS
ACTCAAGAATGGCAAAGCTA+GGG 0.556431 2.2:-53749774 MS.gene071841:CDS
GTTGAAGGAGACGGTGGCGC+CGG 0.560015 2.2:-53750788 MS.gene071841:CDS
TGTAGCAGGAGCTACAATAG+AGG 0.565152 2.2:+53750886 None:intergenic
TACCACTACAGCATAGTTGG+TGG 0.567411 2.2:-53749929 MS.gene071841:CDS
TTTCACACTAAGCTTTGCAA+AGG 0.572755 2.2:+53749835 None:intergenic
GATGGCATCAATAACCTTTG+GGG 0.578696 2.2:+53750826 None:intergenic
AGTGAAGAGGAACTCAAGAA+TGG 0.584353 2.2:-53749785 MS.gene071841:CDS
ATTGATATCGTTGAAGGAGA+CGG 0.588878 2.2:-53750797 MS.gene071841:CDS
AACCACCAACTATGCTGTAG+TGG 0.607193 2.2:+53749927 None:intergenic
TGATGTTGCACCTAGTGAAG+AGG 0.613714 2.2:-53749798 MS.gene071841:CDS
TGCTGACAACCTTACCCCAA+AGG 0.621335 2.2:-53750840 MS.gene071841:CDS
TTGTCTGCAGGTCCAAATGG+AGG 0.639420 2.2:-53749860 MS.gene071841:CDS
CTCAAGAATGGCAAAGCTAG+GGG 0.641253 2.2:-53749773 MS.gene071841:CDS
AGCAGGAGCTACAATAGAGG+TGG 0.665165 2.2:+53750889 None:intergenic
GATATCGTTGAAGGAGACGG+TGG 0.715509 2.2:-53750794 MS.gene071841:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTATATATAAAATAAT+AGG - chr2.2:53750595-53750614 MS.gene071841:intron 0.0%
!! ATCATTACTAGTATTATATA+AGG - chr2.2:53750555-53750574 MS.gene071841:intron 15.0%
!! GTGATAAAAAAATTGATAAA+CGG + chr2.2:53750125-53750144 None:intergenic 15.0%
!! ACTCTTATGATTAACATATT+TGG - chr2.2:53750034-53750053 MS.gene071841:intron 20.0%
!!! ATATTTGGTAGCTAATTAAT+TGG - chr2.2:53750049-53750068 MS.gene071841:intron 20.0%
! AACTTACTTTAATACAACCT+TGG + chr2.2:53750245-53750264 None:intergenic 25.0%
! CTTTCAAATATACCGTTAAA+AGG + chr2.2:53750354-53750373 None:intergenic 25.0%
! GACTAAACTATACTTATTTC+CGG + chr2.2:53750430-53750449 None:intergenic 25.0%
! TTAGTCAAAGACAAATTGTT+CGG + chr2.2:53750472-53750491 None:intergenic 25.0%
!! AGAATGCTAGAATATTCTTT+TGG - chr2.2:53750372-53750391 MS.gene071841:intron 25.0%
!!! TGATTTGGTATACTTGAAAA+AGG - chr2.2:53750193-53750212 MS.gene071841:intron 25.0%
AAAAGGTTCTTAGCACAAAA+TGG - chr2.2:53750210-53750229 MS.gene071841:intron 30.0%
AACACAATTGCTTGATTAAC+TGG - chr2.2:53750509-53750528 MS.gene071841:intron 30.0%
AACGATATCAATACTCTTGA+TGG + chr2.2:53749827-53749846 None:intergenic 30.0%
CAAAATGGACAATTTAACCA+AGG - chr2.2:53750225-53750244 MS.gene071841:intron 30.0%
CTTAGTAGATGATGTTAACT+TGG - chr2.2:53750678-53750697 MS.gene071841:intron 30.0%
CTTAGTGATCTCATTCTTTA+TGG - chr2.2:53750318-53750337 MS.gene071841:intron 30.0%
GATCTCATTCTTTATGGAAT+AGG - chr2.2:53750324-53750343 MS.gene071841:intron 30.0%
TAAAGAATGAGATCACTAAG+CGG + chr2.2:53750318-53750337 None:intergenic 30.0%
TAGTCAAAGACAAATTGTTC+GGG + chr2.2:53750471-53750490 None:intergenic 30.0%
TCAAGTATACCAAATCAATG+TGG + chr2.2:53750190-53750209 None:intergenic 30.0%
TTCTAATCTGAGTATCATTC+CGG - chr2.2:53750408-53750427 MS.gene071841:intron 30.0%
! GAAGAATAACCACATTGATT+TGG - chr2.2:53750178-53750197 MS.gene071841:intron 30.0%
! GACAAAAGTGATTTTCTTGA+TGG + chr2.2:53749872-53749891 None:intergenic 30.0%
!! AAGAAAATCACTTTTGTCGA+AGG - chr2.2:53749874-53749893 MS.gene071841:CDS 30.0%
!! AAGAGTATTGATATCGTTGA+AGG - chr2.2:53749829-53749848 MS.gene071841:CDS 30.0%
AGTGGAGAAGATTTCATTTG+AGG - chr2.2:53750744-53750763 MS.gene071841:intron 35.0%
ATCTAACTGCGAAATTCACA+CGG - chr2.2:53749940-53749959 MS.gene071841:CDS 35.0%
ATTGATATCGTTGAAGGAGA+CGG - chr2.2:53749835-53749854 MS.gene071841:CDS 35.0%
TGATGGCATCAATAACCTTT+GGG + chr2.2:53749810-53749829 None:intergenic 35.0%
TTTAACCAATGATGTGCAGA+TGG - chr2.2:53750625-53750644 MS.gene071841:intron 35.0%
TTTCACACTAAGCTTTGCAA+AGG + chr2.2:53750800-53750819 None:intergenic 35.0%
! GGAATAGGTCATCCTTTTAA+CGG - chr2.2:53750339-53750358 MS.gene071841:intron 35.0%
! TTGATGGCATCAATAACCTT+TGG + chr2.2:53749811-53749830 None:intergenic 35.0%
!! AGTGATTTTCTTGATGGTTC+CGG + chr2.2:53749866-53749885 None:intergenic 35.0%
AAATTGTCTGCAGGTCCAAA+TGG - chr2.2:53750769-53750788 MS.gene071841:CDS 40.0%
AACTCAAGAATGGCAAAGCT+AGG - chr2.2:53750857-53750876 MS.gene071841:CDS 40.0%
ACTCAAGAATGGCAAAGCTA+GGG - chr2.2:53750858-53750877 MS.gene071841:CDS 40.0%
AGTGAAGAGGAACTCAAGAA+TGG - chr2.2:53750847-53750866 MS.gene071841:CDS 40.0%
CAAGTATGTGTTGCACAAAG+TGG - chr2.2:53750654-53750673 MS.gene071841:intron 40.0%
CACTTTGTGCAACACATACT+TGG + chr2.2:53750656-53750675 None:intergenic 40.0%
GATGGCATCAATAACCTTTG+GGG + chr2.2:53749809-53749828 None:intergenic 40.0%
TTCTTGAGTTCCTCTTCACT+AGG + chr2.2:53750847-53750866 None:intergenic 40.0%
TTTCACCATCTGCACATCAT+TGG + chr2.2:53750633-53750652 None:intergenic 40.0%
TTTGCAAAGGTTCCTCCATT+TGG + chr2.2:53750787-53750806 None:intergenic 40.0%
! ACTAGGTGCAACATCACTTT+TGG + chr2.2:53750830-53750849 None:intergenic 40.0%
! AGAGCTTTGTAAAGTGTAGC+AGG + chr2.2:53749763-53749782 None:intergenic 40.0%
! TTTGAGGCTAAATTGTCTGC+AGG - chr2.2:53750760-53750779 MS.gene071841:CDS 40.0%
!! CATCAATAACCTTTGGGGTA+AGG + chr2.2:53749804-53749823 None:intergenic 40.0%
!! TAGGGGTGATGGTCTTTTTA+AGG - chr2.2:53750876-53750895 MS.gene071841:CDS 40.0%
!!! ACAGCATAGTTGGTGGTTTT+GGG - chr2.2:53750710-53750729 MS.gene071841:intron 40.0%
!!! GGTCTTTTTAAGGCTCTTGA+AGG - chr2.2:53750886-53750905 MS.gene071841:CDS 40.0%
!!! TACAGCATAGTTGGTGGTTT+TGG - chr2.2:53750709-53750728 MS.gene071841:intron 40.0%
AACCACCAACTATGCTGTAG+TGG + chr2.2:53750708-53750727 None:intergenic 45.0%
CTCAAGAATGGCAAAGCTAG+GGG - chr2.2:53750859-53750878 MS.gene071841:CDS 45.0%
GAAATCTTCTCCACTGTGTC+TGG + chr2.2:53750739-53750758 None:intergenic 45.0%
GCTTACCACTACAGCATAGT+TGG - chr2.2:53750700-53750719 MS.gene071841:intron 45.0%
TACCACTACAGCATAGTTGG+TGG - chr2.2:53750703-53750722 MS.gene071841:intron 45.0%
TGATGTTGCACCTAGTGAAG+AGG - chr2.2:53750834-53750853 MS.gene071841:CDS 45.0%
TGTAGCAGGAGCTACAATAG+AGG + chr2.2:53749749-53749768 None:intergenic 45.0%
! GGCTCTTGAAGGTTACGTTT+TGG - chr2.2:53750897-53750916 MS.gene071841:CDS 45.0%
AATGGCAAAGCTAGGGGTGA+TGG - chr2.2:53750865-53750884 MS.gene071841:CDS 50.0%
AGCAGGAGCTACAATAGAGG+TGG + chr2.2:53749746-53749765 None:intergenic 50.0%
GATATCGTTGAAGGAGACGG+TGG - chr2.2:53749838-53749857 MS.gene071841:CDS 50.0%
TGCTGACAACCTTACCCCAA+AGG - chr2.2:53749792-53749811 MS.gene071841:CDS 50.0%
TTGTCTGCAGGTCCAAATGG+AGG - chr2.2:53750772-53750791 MS.gene071841:CDS 50.0%
! TTTTGGGCTTCCAGACACAG+TGG - chr2.2:53750726-53750745 MS.gene071841:intron 50.0%
GTTGAAGGAGACGGTGGCGC+CGG - chr2.2:53749844-53749863 MS.gene071841:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 53749715 53750939 53749715 ID=MS.gene071841
chr2.2 mRNA 53749715 53750939 53749715 ID=MS.gene071841.t1;Parent=MS.gene071841
chr2.2 exon 53750759 53750939 53750759 ID=MS.gene071841.t1.exon1;Parent=MS.gene071841.t1
chr2.2 CDS 53750759 53750939 53750759 ID=cds.MS.gene071841.t1;Parent=MS.gene071841.t1
chr2.2 exon 53749715 53750010 53749715 ID=MS.gene071841.t1.exon2;Parent=MS.gene071841.t1
chr2.2 CDS 53749715 53750010 53749715 ID=cds.MS.gene071841.t1;Parent=MS.gene071841.t1
Gene Sequence

>MS.gene071841

ATGGGTGTTTACAACTTTGAGGATGAAACCACCTCTATTGTAGCTCCTGCTACACTTTACAAAGCTCTTGTTACAGATGCTGACAACCTTACCCCAAAGGTTATTGATGCCATCAAGAGTATTGATATCGTTGAAGGAGACGGTGGCGCCGGAACCATCAAGAAAATCACTTTTGTCGAAGGTCAGTATAAATATATGTGTGTATTTTTTTTATTATTATAAAGAATCTAACTGCGAAATTCACACGGATTAAGAGAAAAATTGATTCACTATACAGATAAAATACAATTTATAAAATATATGAGAGTGTTTAGTAGACACTCTTATGATTAACATATTTGGTAGCTAATTAATTGGTTTGAGAAAATATTTTCTATTTTTACTTTAATTATAGAATTACTACTTTACCGTTTATCAATTTTTTTATCACTTTACTAGTAATTGTGACACTTTGATGTTAGTAGAAGAATAACCACATTGATTTGGTATACTTGAAAAAGGTTCTTAGCACAAAATGGACAATTTAACCAAGGTTGTATTAAAGTAAGTTTATACTTAAAAAGATAAAATAAAATGAAGTTCTTATAAGAAAGTAAATTTCCGCTTAGTGATCTCATTCTTTATGGAATAGGTCATCCTTTTAACGGTATATTTGAAAGAATGCTAGAATATTCTTTTGGTGATATTATTTTGTTCTAATCTGAGTATCATTCCGGAAATAAGTATAGTTTAGTCAAAATTATCTCAAATTCTCCCGAACAATTTGTCTTTGACTAAAATCAATTAACTATTTAAACACAATTGCTTGATTAACTGGAACTTGATTATTTTATTGATGATATCATTACTAGTATTATATAAGGATTGTTCATTAGCTTGTTTTTTTATATATAAAATAATAGGTCATCATTTTAACCAATGATGTGCAGATGGTGAAACCAAGTATGTGTTGCACAAAGTGGACTTAGTAGATGATGTTAACTTGGCTTACCACTACAGCATAGTTGGTGGTTTTGGGCTTCCAGACACAGTGGAGAAGATTTCATTTGAGGCTAAATTGTCTGCAGGTCCAAATGGAGGAACCTTTGCAAAGCTTAGTGTGAAATACTTCACCAAAAGTGATGTTGCACCTAGTGAAGAGGAACTCAAGAATGGCAAAGCTAGGGGTGATGGTCTTTTTAAGGCTCTTGAAGGTTACGTTTTGGCAAATCCTGATTACAACTAA
Protein sequence

>MS.gene071841.t1

MGVYNFEDETTSIVAPATLYKALVTDADNLTPKVIDAIKSIDIVEGDGGAGTIKKITFVEDGETKYVLHKVDLVDDVNLAYHYSIVGGFGLPDTVEKISFEAKLSAGPNGGTFAKLSVKYFTKSDVAPSEEELKNGKARGDGLFKALEGYVLANPDYN