AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071840.t1 MTR_2g035120 96.203 158 6 0 1 158 1 158 1.81e-109 308
MS.gene071840.t1 MTR_2g035150 86.709 158 21 0 1 158 1 158 2.71e-97 277
MS.gene071840.t1 MTR_2g035100 84.076 157 25 0 1 157 1 157 4.74e-94 269
MS.gene071840.t1 MTR_2g035130 85.350 157 23 0 1 157 1 157 4.90e-94 269
MS.gene071840.t1 MTR_2g035105 82.803 157 27 0 1 157 1 157 1.03e-92 266
MS.gene071840.t1 MTR_6g033450 69.620 158 48 0 1 158 1 158 5.89e-77 226
MS.gene071840.t1 MTR_4g120970 69.620 158 48 0 1 158 1 158 5.89e-77 226
MS.gene071840.t1 MTR_2g035320 59.236 157 64 0 1 157 1 157 2.11e-63 192
MS.gene071840.t1 MTR_2g035190 58.599 157 65 0 1 157 1 157 4.20e-62 188
MS.gene071840.t1 MTR_2g035170 57.325 157 67 0 1 157 1 157 3.58e-59 181
MS.gene071840.t1 MTR_2g035210 56.688 157 68 0 1 157 1 157 6.26e-59 180
MS.gene071840.t1 MTR_2g035220 57.325 157 67 0 1 157 1 157 7.75e-58 177
MS.gene071840.t1 MTR_2g035320 58.586 99 41 0 59 157 24 122 3.72e-36 121
MS.gene071840.t1 MTR_4g120760 38.217 157 96 1 1 156 1 157 1.08e-35 121
MS.gene071840.t1 MTR_4g120760 38.217 157 96 1 1 156 1 157 1.10e-35 121
MS.gene071840.t1 MTR_2g435310 36.943 157 98 1 1 156 1 157 1.80e-35 121
MS.gene071840.t1 MTR_4g120950 45.062 162 82 5 1 158 1 159 1.24e-33 116
MS.gene071840.t1 MTR_4g120940 72.973 74 20 0 85 158 47 120 7.33e-31 108
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 43 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACGAAAGTGAGTTTCTTGA+TGG 0.319436 2.2:+53763498 None:intergenic
TTGATGACATCAACAACCTT+TGG 0.332899 2.2:+53763559 None:intergenic
GGCCCTTGAGGGTTACTGTT+TGG 0.340986 2.2:-53762895 MS.gene071840:CDS
TATATGCTTTAGTTGTAATC+AGG 0.341112 2.2:+53762867 None:intergenic
CACTTTGTGTAAATCATACT+TGG 0.346823 2.2:+53763139 None:intergenic
TGATGACATCAACAACCTTT+GGG 0.365094 2.2:+53763560 None:intergenic
ACTTGGTAGATGATGCTAAC+TGG 0.375253 2.2:-53763115 MS.gene071840:CDS
AGTGAGTTTCTTGATGGTTC+CGG 0.377477 2.2:+53763504 None:intergenic
GAAATCTTCTCTACTGTGTC+TGG 0.378194 2.2:+53763056 None:intergenic
CATCAACAACCTTTGGGATA+AGG 0.380175 2.2:+53763566 None:intergenic
AAGAAACTCACTTTCGTTGA+AGG 0.384811 2.2:-53763493 MS.gene071840:intron
AAAAGTATTGACATTGTTGA+AGG 0.419014 2.2:-53763538 MS.gene071840:CDS
ATTGACATTGTTGAAGGAAA+TGG 0.422286 2.2:-53763532 MS.gene071840:CDS
GCTTTAGTTGTAATCAGGAT+TGG 0.467799 2.2:+53762872 None:intergenic
GCTTACAACTACAGCATAGT+TGG 0.483791 2.2:-53763092 MS.gene071840:CDS
AAAGCTTTGTGAAGTGTAGC+AGG 0.484835 2.2:+53763607 None:intergenic
TTTGAAGCTAAATTGTCTGC+AGG 0.489005 2.2:-53763032 MS.gene071840:CDS
CAAGTATGATTTACACAAAG+TGG 0.491575 2.2:-53763138 MS.gene071840:CDS
TTTGCAATGGATCCTCCATT+CGG 0.495837 2.2:+53763008 None:intergenic
ACTAGGAGTAGCATCACCTT+TGG 0.504856 2.2:+53762965 None:intergenic
CTTGGTAGATGATGCTAACT+GGG 0.513123 2.2:-53763114 MS.gene071840:CDS
CTTGAAAAGACCATCACCCT+TGG 0.519688 2.2:+53762917 None:intergenic
TTTCACACTAAGCTTTGCAA+TGG 0.532493 2.2:+53762995 None:intergenic
CTCTCGAGGTCCTCTTCACT+AGG 0.534215 2.2:+53762948 None:intergenic
GTTGAAGGAAATGGTGGCGC+CGG 0.546300 2.2:-53763523 MS.gene071840:CDS
TGATTTACACAAAGTGGACT+TGG 0.556769 2.2:-53763132 MS.gene071840:CDS
AGTGGCAAAGCCAAGGGTGA+TGG 0.558120 2.2:-53762927 MS.gene071840:CDS
CCTCGAGAGTGGCAAAGCCA+AGG 0.566158 2.2:-53762934 MS.gene071840:CDS
AAGTGTAGCAGGAGCTACAA+TGG 0.570662 2.2:+53763618 None:intergenic
CTCGAGAGTGGCAAAGCCAA+GGG 0.586680 2.2:-53762933 MS.gene071840:CDS
CCTTGGCTTTGCCACTCTCG+AGG 0.588424 2.2:+53762934 None:intergenic
AAATTGTCTGCAGGTCCGAA+TGG 0.591580 2.2:-53763023 MS.gene071840:CDS
AGCAGGAGCTACAATGGAGG+TGG 0.593310 2.2:+53763624 None:intergenic
TACAACTACAGCATAGTTGG+AGG 0.598501 2.2:-53763089 MS.gene071840:CDS
AGTGAAGAGGACCTCGAGAG+TGG 0.617170 2.2:-53762945 MS.gene071840:CDS
TGGCCAAACAGTAACCCTCA+AGG 0.618520 2.2:+53762892 None:intergenic
TGCTGACAACCTTATCCCAA+AGG 0.624297 2.2:-53763575 MS.gene071840:CDS
GGCCAAACAGTAACCCTCAA+GGG 0.627034 2.2:+53762893 None:intergenic
TGATGCTACTCCTAGTGAAG+AGG 0.634756 2.2:-53762958 MS.gene071840:CDS
TTGTCTGCAGGTCCGAATGG+AGG 0.646240 2.2:-53763020 MS.gene071840:CDS
AGTGTGAAATACTTCACCAA+AGG 0.651010 2.2:-53762981 MS.gene071840:CDS
GACATTGTTGAAGGAAATGG+TGG 0.661697 2.2:-53763529 MS.gene071840:CDS
TGTAGCAGGAGCTACAATGG+AGG 0.722910 2.2:+53763621 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACCTAAATATATTAAGTAA+TGG - chr2.2:53763315-53763334 MS.gene071840:intron 15.0%
!! AATCTTACTTATTAAGATTT+AGG - chr2.2:53763093-53763112 MS.gene071840:CDS 15.0%
!! ATCTTACTTATTAAGATTTA+GGG - chr2.2:53763094-53763113 MS.gene071840:CDS 15.0%
!!! ATATTTAGGTTTTTAAAAGT+AGG + chr2.2:53763306-53763325 None:intergenic 15.0%
!!! TCATTTTCTCAAAATTTTAT+CGG - chr2.2:53763219-53763238 MS.gene071840:intron 15.0%
!! GACCATTACTTAATATATTT+AGG + chr2.2:53763320-53763339 None:intergenic 20.0%
!!! TTATTAAGATTTAGGGTTTA+GGG - chr2.2:53763101-53763120 MS.gene071840:CDS 20.0%
!! CTTATTAAGATTTAGGGTTT+AGG - chr2.2:53763100-53763119 MS.gene071840:CDS 25.0%
!!! AAAAGTATTGACATTGTTGA+AGG - chr2.2:53762989-53763008 MS.gene071840:CDS 25.0%
ATTGACATTGTTGAAGGAAA+TGG - chr2.2:53762995-53763014 MS.gene071840:CDS 30.0%
CAAGTATGATTTACACAAAG+TGG - chr2.2:53763389-53763408 MS.gene071840:intron 30.0%
CACTTTGTGTAAATCATACT+TGG + chr2.2:53763391-53763410 None:intergenic 30.0%
AACGAAAGTGAGTTTCTTGA+TGG + chr2.2:53763032-53763051 None:intergenic 35.0%
AAGAAACTCACTTTCGTTGA+AGG - chr2.2:53763034-53763053 MS.gene071840:CDS 35.0%
AGTGTGAAATACTTCACCAA+AGG - chr2.2:53763546-53763565 MS.gene071840:CDS 35.0%
ATGAATCTATGACATGCAGA+TGG - chr2.2:53763360-53763379 MS.gene071840:intron 35.0%
TGATGACATCAACAACCTTT+GGG + chr2.2:53762970-53762989 None:intergenic 35.0%
TTTCACACTAAGCTTTGCAA+TGG + chr2.2:53763535-53763554 None:intergenic 35.0%
! TGATTTACACAAAGTGGACT+TGG - chr2.2:53763395-53763414 MS.gene071840:intron 35.0%
! TTGATGACATCAACAACCTT+TGG + chr2.2:53762971-53762990 None:intergenic 35.0%
! TTGTCTAAAACTACGAAGCA+CGG + chr2.2:53763274-53763293 None:intergenic 35.0%
! TTTGAAGCTAAATTGTCTGC+AGG - chr2.2:53763495-53763514 MS.gene071840:CDS 35.0%
ACTTGGTAGATGATGCTAAC+TGG - chr2.2:53763412-53763431 MS.gene071840:intron 40.0%
CTTGGTAGATGATGCTAACT+GGG - chr2.2:53763413-53763432 MS.gene071840:intron 40.0%
GAAATCTTCTCTACTGTGTC+TGG + chr2.2:53763474-53763493 None:intergenic 40.0%
GACATTGTTGAAGGAAATGG+TGG - chr2.2:53762998-53763017 MS.gene071840:CDS 40.0%
GCTTACAACTACAGCATAGT+TGG - chr2.2:53763435-53763454 MS.gene071840:intron 40.0%
TACAACTACAGCATAGTTGG+AGG - chr2.2:53763438-53763457 MS.gene071840:intron 40.0%
TTTGCAATGGATCCTCCATT+CGG + chr2.2:53763522-53763541 None:intergenic 40.0%
! AAAGCTTTGTGAAGTGTAGC+AGG + chr2.2:53762923-53762942 None:intergenic 40.0%
! AGTGAGTTTCTTGATGGTTC+CGG + chr2.2:53763026-53763045 None:intergenic 40.0%
!! CATCAACAACCTTTGGGATA+AGG + chr2.2:53762964-53762983 None:intergenic 40.0%
AAATTGTCTGCAGGTCCGAA+TGG - chr2.2:53763504-53763523 MS.gene071840:CDS 45.0%
AAGTGTAGCAGGAGCTACAA+TGG + chr2.2:53762912-53762931 None:intergenic 45.0%
ACTAGGAGTAGCATCACCTT+TGG + chr2.2:53763565-53763584 None:intergenic 45.0%
CTTGAAAAGACCATCACCCT+TGG + chr2.2:53763613-53763632 None:intergenic 45.0%
TGATGCTACTCCTAGTGAAG+AGG - chr2.2:53763569-53763588 MS.gene071840:CDS 45.0%
TGATGTGTCCGTGTTGTGAT+TGG - chr2.2:53763245-53763264 MS.gene071840:intron 45.0%
TGCTGACAACCTTATCCCAA+AGG - chr2.2:53762952-53762971 MS.gene071840:CDS 45.0%
! TCGTGTCGATGTTGAATGTC+AGG + chr2.2:53763175-53763194 None:intergenic 45.0%
!! CAAGGGTGATGGTCTTTTCA+AGG - chr2.2:53763611-53763630 MS.gene071840:CDS 45.0%
!! GAAGTGTCGGTGCAACTTAT+AGG + chr2.2:53763137-53763156 None:intergenic 45.0%
CACGGACACCAATCACAACA+CGG + chr2.2:53763256-53763275 None:intergenic 50.0%
GGCCAAACAGTAACCCTCAA+GGG + chr2.2:53763637-53763656 None:intergenic 50.0%
TGGCCAAACAGTAACCCTCA+AGG + chr2.2:53763638-53763657 None:intergenic 50.0%
TGTAGCAGGAGCTACAATGG+AGG + chr2.2:53762909-53762928 None:intergenic 50.0%
! GCACCGACACTTCTGATTGA+CGG - chr2.2:53763144-53763163 MS.gene071840:CDS 50.0%
! GCACCGTCAATCAGAAGTGT+CGG + chr2.2:53763150-53763169 None:intergenic 50.0%
!! GGTCTTTTCAAGGCCCTTGA+GGG - chr2.2:53763621-53763640 MS.gene071840:CDS 50.0%
!! TGGTCTTTTCAAGGCCCTTG+AGG - chr2.2:53763620-53763639 MS.gene071840:CDS 50.0%
AGCAGGAGCTACAATGGAGG+TGG + chr2.2:53762906-53762925 None:intergenic 55.0%
AGTGAAGAGGACCTCGAGAG+TGG - chr2.2:53763582-53763601 MS.gene071840:CDS 55.0%
AGTGGCAAAGCCAAGGGTGA+TGG - chr2.2:53763600-53763619 MS.gene071840:CDS 55.0%
CTCGAGAGTGGCAAAGCCAA+GGG - chr2.2:53763594-53763613 MS.gene071840:CDS 55.0%
CTCTCGAGGTCCTCTTCACT+AGG + chr2.2:53763582-53763601 None:intergenic 55.0%
GGCCCTTGAGGGTTACTGTT+TGG - chr2.2:53763632-53763651 MS.gene071840:CDS 55.0%
TTGTCTGCAGGTCCGAATGG+AGG - chr2.2:53763507-53763526 MS.gene071840:CDS 55.0%
! GTTGAAGGAAATGGTGGCGC+CGG - chr2.2:53763004-53763023 MS.gene071840:CDS 55.0%
CCTCGAGAGTGGCAAAGCCA+AGG - chr2.2:53763593-53763612 MS.gene071840:CDS 60.0%
!! CCTTGGCTTTGCCACTCTCG+AGG + chr2.2:53763596-53763615 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 53762875 53763674 53762875 ID=MS.gene071840
chr2.2 mRNA 53762875 53763674 53762875 ID=MS.gene071840.t1;Parent=MS.gene071840
chr2.2 exon 53763494 53763674 53763494 ID=MS.gene071840.t1.exon1;Parent=MS.gene071840.t1
chr2.2 CDS 53763494 53763674 53763494 ID=cds.MS.gene071840.t1;Parent=MS.gene071840.t1
chr2.2 exon 53762875 53763170 53762875 ID=MS.gene071840.t1.exon2;Parent=MS.gene071840.t1
chr2.2 CDS 53762875 53763170 53762875 ID=cds.MS.gene071840.t1;Parent=MS.gene071840.t1
Gene Sequence

>MS.gene071840

ATGGGTGTCATCAATTTTGAGGAAGAAACCACCTCCATTGTAGCTCCTGCTACACTTCACAAAGCTTTTGTTACAGATGCTGACAACCTTATCCCAAAGGTTGTTGATGTCATCAAAAGTATTGACATTGTTGAAGGAAATGGTGGCGCCGGAACCATCAAGAAACTCACTTTCGTTGAAGGTCAGTATCAATATATTTGTTATATTTCTTATAAGCAAATCTTACTTATTAAGATTTAGGGTTTAGGGTTATTTTAGACCTATAAGTTGCACCGACACTTCTGATTGACGGTGCGTCCTGACATTCAACATCGACACGACACTTGTGATTACATTGAATTATGTCATTTTCTCAAAATTTTATCGGCGTTGATGTGTCCGTGTTGTGATTGGTGTCCGTGCTTCGTAGTTTTAGACAAATTCTTGTACCTACTTTTAAAAACCTAAATATATTAAGTAATGGTCATGATATTTATGATTGTGAAATGAATCTATGACATGCAGATGGTGAAACCAAGTATGATTTACACAAAGTGGACTTGGTAGATGATGCTAACTGGGCTTACAACTACAGCATAGTTGGAGGTGATAGTCTTCCAGACACAGTAGAGAAGATTTCATTTGAAGCTAAATTGTCTGCAGGTCCGAATGGAGGATCCATTGCAAAGCTTAGTGTGAAATACTTCACCAAAGGTGATGCTACTCCTAGTGAAGAGGACCTCGAGAGTGGCAAAGCCAAGGGTGATGGTCTTTTCAAGGCCCTTGAGGGTTACTGTTTGGCCAATCCTGATTACAACTAA
Protein sequence

>MS.gene071840.t1

MGVINFEEETTSIVAPATLHKAFVTDADNLIPKVVDVIKSIDIVEGNGGAGTIKKLTFVEDGETKYDLHKVDLVDDANWAYNYSIVGGDSLPDTVEKISFEAKLSAGPNGGSIAKLSVKYFTKGDATPSEEDLESGKAKGDGLFKALEGYCLANPDYN