AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene82560

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82560.t1 MTR_2g105850 94.309 246 11 2 1 243 1 246 1.21e-165 457
MS.gene82560.t1 MTR_2g105850 74.797 246 10 3 1 243 1 197 1.13e-124 352
MS.gene82560.t1 MTR_4g113520 29.900 301 136 8 13 242 15 311 1.87e-38 136
MS.gene82560.t1 MTR_3g087920 47.222 144 73 1 51 191 31 174 1.93e-36 131
MS.gene82560.t1 MTR_3g087920 42.500 80 38 2 171 242 245 324 5.20e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82560.t1 AT1G50440 69.444 252 66 3 1 243 1 250 1.57e-128 363
MS.gene82560.t1 AT1G50440 69.444 252 66 3 1 243 1 250 1.57e-128 363
MS.gene82560.t1 AT1G50440 69.444 252 66 3 1 243 1 250 1.57e-128 363
MS.gene82560.t1 AT1G50440 68.919 222 59 2 1 213 1 221 1.07e-112 322
MS.gene82560.t1 AT1G50440 58.294 211 76 3 1 202 1 208 1.85e-84 251
MS.gene82560.t1 AT1G11020 37.319 276 95 7 38 242 52 320 2.74e-46 157
MS.gene82560.t1 AT2G22120 43.421 152 79 2 24 172 7 154 1.00e-36 132
MS.gene82560.t1 AT2G22120 46.269 67 31 1 181 242 257 323 9.39e-11 61.2
MS.gene82560.t1 AT2G22120 43.421 152 79 2 24 172 7 154 1.20e-36 132
MS.gene82560.t1 AT2G22120 42.683 82 40 2 168 242 242 323 9.66e-11 61.2

Find 57 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAGTTCTCGCCATTATTT+TGG 0.183622 2.4:+110223 MS.gene82560:intron
TGCACAGGTTGTTGCTTTCT+TGG 0.234683 2.4:+110034 MS.gene82560:intron
TTCACAGAGGTGATTCAATA+TGG 0.242810 2.4:-109585 None:intergenic
ATGATCTGTGGACATACTTT+TGG 0.267771 2.4:-109757 None:intergenic
CTCAACCACCATCGATCTTT+AGG 0.272819 2.4:-109869 None:intergenic
GTGCTTATTTATAAATTCTA+TGG 0.292569 2.4:+110059 MS.gene82560:CDS
TTGTCAGACGTGGCAGAAAT+AGG 0.331431 2.4:-109614 None:intergenic
TTGGGTACCTTTGCAATGGC+AGG 0.331526 2.4:-109738 None:intergenic
GACCTTTGTCAATTCTTGTT+TGG 0.347635 2.4:-110321 None:intergenic
ACAGATCATGTCTCGATAAC+TGG 0.347729 2.4:+109771 MS.gene82560:CDS
GCACAGGTTGTTGCTTTCTT+GGG 0.351526 2.4:+110035 MS.gene82560:intron
CATCGATCTTTAGGGACATT+TGG 0.365167 2.4:-109860 None:intergenic
CCTTAGTTCTGTCACATGGC+TGG 0.365929 2.4:-110713 None:intergenic
TCAACCACCATCGATCTTTA+GGG 0.389036 2.4:-109868 None:intergenic
CTTAGTTCTGTCACATGGCT+GGG 0.400790 2.4:-110712 None:intergenic
TTTCTGAAGAAGAAGAATCT+TGG 0.402422 2.4:-109556 None:intergenic
GAGCAAACCCACCAAAATAA+TGG 0.405865 2.4:-110234 None:intergenic
TTCTTTATAGCAATAATATG+TGG 0.428860 2.4:+110263 MS.gene82560:CDS
TGCCGGATATGCCTTGATCT+TGG 0.432553 2.4:+109695 MS.gene82560:CDS
GATGAACTTAGAGAAATGTT+TGG 0.432617 2.4:+110083 MS.gene82560:CDS
ACATGGCTGGGGTCGAGTTC+AGG 0.434273 2.4:-110700 None:intergenic
GAGGTGATTCAATATGGGTT+GGG 0.457987 2.4:-109579 None:intergenic
CTCCAAGATCAAGGCATATC+CGG 0.463345 2.4:-109697 None:intergenic
GGGTACCTTTGCAATGGCAG+GGG 0.470794 2.4:-109736 None:intergenic
TCACAGAGGTGATTCAATAT+GGG 0.474068 2.4:-109584 None:intergenic
GTGACAGAACTAAGGATGTT+GGG 0.491109 2.4:+110721 MS.gene82560:CDS
TGGGTACCTTTGCAATGGCA+GGG 0.492265 2.4:-109737 None:intergenic
GAAAATGAATGCATGATCTC+TGG 0.494455 2.4:-109915 None:intergenic
CGGATATGCCTTGATCTTGG+AGG 0.499840 2.4:+109698 MS.gene82560:CDS
AGAGGTGATTCAATATGGGT+TGG 0.514100 2.4:-109580 None:intergenic
CAAGGCATATCCGGCATTGT+GGG 0.523063 2.4:-109688 None:intergenic
TGTGACAGAACTAAGGATGT+TGG 0.527888 2.4:+110720 MS.gene82560:CDS
AGTCTTCTCCTCCAAGATCA+AGG 0.530295 2.4:-109706 None:intergenic
TCTTTATAGCAATAATATGT+GGG 0.533500 2.4:+110264 MS.gene82560:CDS
AGAAGAAGAATCTTGGTTGT+CGG 0.545346 2.4:-109549 None:intergenic
TTAGTTCTGTCACATGGCTG+GGG 0.552531 2.4:-110711 None:intergenic
ATGCTGATCACCCACAATGC+CGG 0.553024 2.4:+109678 MS.gene82560:CDS
GTTTGGCAAGAACATGGTAG+TGG 0.554746 2.4:-110304 None:intergenic
CCAGCCATGTGACAGAACTA+AGG 0.558116 2.4:+110713 MS.gene82560:CDS
TCAAGGCATATCCGGCATTG+TGG 0.559551 2.4:-109689 None:intergenic
GCCATTGTGTAAAATCCGTA+TGG 0.559880 2.4:-110119 None:intergenic
ATACATATACCAGCTAGTAA+AGG 0.563392 2.4:-110744 None:intergenic
GGTACCTTTGCAATGGCAGG+GGG 0.567201 2.4:-109735 None:intergenic
AACTGGAGGTCTACCAAGGA+GGG 0.573090 2.4:+109788 MS.gene82560:CDS
AGAAGATCGAGAACATGTAA+AGG 0.577463 2.4:+110672 MS.gene82560:CDS
GGTTATGAAGAACATCCATA+CGG 0.581353 2.4:+110104 MS.gene82560:CDS
ATTCTTGTTTGGCAAGAACA+TGG 0.604029 2.4:-110310 None:intergenic
CAAATGTCCCTAAAGATCGA+TGG 0.630129 2.4:+109861 MS.gene82560:CDS
ACATCCTTAGTTCTGTCACA+TGG 0.650556 2.4:-110717 None:intergenic
CGATAACTGGAGGTCTACCA+AGG 0.652909 2.4:+109784 MS.gene82560:CDS
TGCCAAACAAGAATTGACAA+AGG 0.654420 2.4:+110319 MS.gene82560:CDS
AGTTATCGAGACATGATCTG+TGG 0.663655 2.4:-109769 None:intergenic
TAACTGGAGGTCTACCAAGG+AGG 0.663726 2.4:+109787 MS.gene82560:CDS
ATGTCCCTAAAGATCGATGG+TGG 0.685209 2.4:+109864 MS.gene82560:CDS
GATCATGTCTCGATAACTGG+AGG 0.685887 2.4:+109774 MS.gene82560:CDS
TATATCATGATTGTCAGACG+TGG 0.692189 2.4:-109624 None:intergenic
AAATAGGAATAATTTCACAG+AGG 0.778628 2.4:-109598 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACCTTAAATTTTTATAAAAA+AGG - chr2.4:110601-110620 None:intergenic 10.0%
!!! TCCTTTTTTATAAAAATTTA+AGG + chr2.4:110597-110616 MS.gene82560:intron 10.0%
!! AATGAAATACATAAAATCGT+AGG - chr2.4:109976-109995 None:intergenic 20.0%
!! ATGAAATACATAAAATCGTA+GGG - chr2.4:109975-109994 None:intergenic 20.0%
!! GTGCTTATTTATAAATTCTA+TGG + chr2.4:110059-110078 MS.gene82560:CDS 20.0%
!! TAAACAATACAATACAAGAA+CGG - chr2.4:110539-110558 None:intergenic 20.0%
!! TCTTTATAGCAATAATATGT+GGG + chr2.4:110264-110283 MS.gene82560:CDS 20.0%
!! TTCTTGTATTGTATTGTTTA+AGG + chr2.4:110539-110558 MS.gene82560:intron 20.0%
!! TTCTTTATAGCAATAATATG+TGG + chr2.4:110263-110282 MS.gene82560:CDS 20.0%
! AAACAATACAATACAAGAAC+GGG - chr2.4:110538-110557 None:intergenic 25.0%
! AAATAGGAATAATTTCACAG+AGG - chr2.4:109601-109620 None:intergenic 25.0%
! TGAAATACATAAAATCGTAG+GGG - chr2.4:109974-109993 None:intergenic 25.0%
!! AATTGATTCTGAGTCATATA+AGG + chr2.4:110567-110586 MS.gene82560:intron 25.0%
AAAACAAAGTCAGAAATGAG+TGG - chr2.4:110204-110223 None:intergenic 30.0%
AAAAGCTGCAAACAAACATT+GGG - chr2.4:110181-110200 None:intergenic 30.0%
ATTTGAGAGTGGTGAATAAA+TGG - chr2.4:110153-110172 None:intergenic 30.0%
GATGAACTTAGAGAAATGTT+TGG + chr2.4:110083-110102 MS.gene82560:CDS 30.0%
GGTCATAAGATATGCAATTT+CGG + chr2.4:110493-110512 MS.gene82560:intron 30.0%
GTCATAAGATATGCAATTTC+GGG + chr2.4:110494-110513 MS.gene82560:intron 30.0%
TTTGAGAGTGGTGAATAAAT+GGG - chr2.4:110152-110171 None:intergenic 30.0%
! TTTCTGAAGAAGAAGAATCT+TGG - chr2.4:109559-109578 None:intergenic 30.0%
! TTTTCCTTTTCTAATTGCAC+AGG + chr2.4:110019-110038 MS.gene82560:intron 30.0%
!! TAACATGCTTCACTTTTATG+TGG - chr2.4:110399-110418 None:intergenic 30.0%
ACAACCTGTGCAATTAGAAA+AGG - chr2.4:110026-110045 None:intergenic 35.0%
AGAAGAAGAATCTTGGTTGT+CGG - chr2.4:109552-109571 None:intergenic 35.0%
AGAAGATCGAGAACATGTAA+AGG + chr2.4:110672-110691 MS.gene82560:CDS 35.0%
ATACATAAAATCGTAGGGGA+TGG - chr2.4:109970-109989 None:intergenic 35.0%
GAAAAGCTGCAAACAAACAT+TGG - chr2.4:110182-110201 None:intergenic 35.0%
GAAAATGAATGCATGATCTC+TGG - chr2.4:109918-109937 None:intergenic 35.0%
GACCTTTGTCAATTCTTGTT+TGG - chr2.4:110324-110343 None:intergenic 35.0%
GGTTATGAAGAACATCCATA+CGG + chr2.4:110104-110123 MS.gene82560:CDS 35.0%
TATATCATGATTGTCAGACG+TGG - chr2.4:109627-109646 None:intergenic 35.0%
TCACAGAGGTGATTCAATAT+GGG - chr2.4:109587-109606 None:intergenic 35.0%
TGCCAAACAAGAATTGACAA+AGG + chr2.4:110319-110338 MS.gene82560:CDS 35.0%
TTCACAGAGGTGATTCAATA+TGG - chr2.4:109588-109607 None:intergenic 35.0%
! ATGATCTGTGGACATACTTT+TGG - chr2.4:109760-109779 None:intergenic 35.0%
! ATTCTTGTTTGGCAAGAACA+TGG - chr2.4:110313-110332 None:intergenic 35.0%
! TCCATACGGATTTTACACAA+TGG + chr2.4:110118-110137 MS.gene82560:CDS 35.0%
! TGATCTGTGGACATACTTTT+GGG - chr2.4:109759-109778 None:intergenic 35.0%
!! TGCTTCACTTTTATGTGGAT+TGG - chr2.4:110394-110413 None:intergenic 35.0%
!!! CTGTTTACTTTTTTGACGTC+AGG + chr2.4:110639-110658 MS.gene82560:intron 35.0%
ACAGATCATGTCTCGATAAC+TGG + chr2.4:109771-109790 MS.gene82560:CDS 40.0%
AGAGGTGATTCAATATGGGT+TGG - chr2.4:109583-109602 None:intergenic 40.0%
AGTTATCGAGACATGATCTG+TGG - chr2.4:109772-109791 None:intergenic 40.0%
ATTGGGCATGAATTTGAGAG+TGG - chr2.4:110164-110183 None:intergenic 40.0%
CAAATGTCCCTAAAGATCGA+TGG + chr2.4:109861-109880 MS.gene82560:CDS 40.0%
CTTGCTGCAAAACACATCTT+TGG + chr2.4:110472-110491 MS.gene82560:intron 40.0%
GAGCAAACCCACCAAAATAA+TGG - chr2.4:110237-110256 None:intergenic 40.0%
GAGGTGATTCAATATGGGTT+GGG - chr2.4:109582-109601 None:intergenic 40.0%
GCCATTGTGTAAAATCCGTA+TGG - chr2.4:110122-110141 None:intergenic 40.0%
GTGACAGAACTAAGGATGTT+GGG + chr2.4:110721-110740 MS.gene82560:CDS 40.0%
TCAACCACCATCGATCTTTA+GGG - chr2.4:109871-109890 None:intergenic 40.0%
TGTGACAGAACTAAGGATGT+TGG + chr2.4:110720-110739 MS.gene82560:CDS 40.0%
! CATCGATCTTTAGGGACATT+TGG - chr2.4:109863-109882 None:intergenic 40.0%
! TACGGATTTTACACAATGGC+TGG + chr2.4:110122-110141 MS.gene82560:CDS 40.0%
! TGCAGTTCTCGCCATTATTT+TGG + chr2.4:110223-110242 MS.gene82560:intron 40.0%
!! ACATCCTTAGTTCTGTCACA+TGG - chr2.4:110720-110739 None:intergenic 40.0%
!! ACTTTTGGGTACCTTTGCAA+TGG - chr2.4:109745-109764 None:intergenic 40.0%
!! TTTTTGACGTCAGGAGTATG+TGG + chr2.4:110648-110667 MS.gene82560:intron 40.0%
!!! AGTTCTCGCCATTATTTTGG+TGG + chr2.4:110226-110245 MS.gene82560:intron 40.0%
!!! ATTTTGGTGGGTTTGCTCTA+TGG + chr2.4:110239-110258 MS.gene82560:CDS 40.0%
!!! GTTCTCGCCATTATTTTGGT+GGG + chr2.4:110227-110246 MS.gene82560:intron 40.0%
AGAAAAAGCAAAGCCCTCCT+TGG - chr2.4:109804-109823 None:intergenic 45.0%
AGTCTTCTCCTCCAAGATCA+AGG - chr2.4:109709-109728 None:intergenic 45.0%
ATGTCCCTAAAGATCGATGG+TGG + chr2.4:109864-109883 MS.gene82560:CDS 45.0%
CTCAACCACCATCGATCTTT+AGG - chr2.4:109872-109891 None:intergenic 45.0%
CTCCAAGATCAAGGCATATC+CGG - chr2.4:109700-109719 None:intergenic 45.0%
CTTGCTGCAAAACACGTCTT+TGG + chr2.4:110437-110456 MS.gene82560:intron 45.0%
GATCATGTCTCGATAACTGG+AGG + chr2.4:109774-109793 MS.gene82560:CDS 45.0%
GTTTGGCAAGAACATGGTAG+TGG - chr2.4:110307-110326 None:intergenic 45.0%
TTGTCAGACGTGGCAGAAAT+AGG - chr2.4:109617-109636 None:intergenic 45.0%
!! CTTAGTTCTGTCACATGGCT+GGG - chr2.4:110715-110734 None:intergenic 45.0%
!! GCACAGGTTGTTGCTTTCTT+GGG + chr2.4:110035-110054 MS.gene82560:intron 45.0%
!! TGCACAGGTTGTTGCTTTCT+TGG + chr2.4:110034-110053 MS.gene82560:intron 45.0%
!! TTAGTTCTGTCACATGGCTG+GGG - chr2.4:110714-110733 None:intergenic 45.0%
AACTGGAGGTCTACCAAGGA+GGG + chr2.4:109788-109807 MS.gene82560:CDS 50.0%
ATGCTGATCACCCACAATGC+CGG + chr2.4:109678-109697 MS.gene82560:CDS 50.0%
CAAGGCATATCCGGCATTGT+GGG - chr2.4:109691-109710 None:intergenic 50.0%
CCAGCCATGTGACAGAACTA+AGG + chr2.4:110713-110732 MS.gene82560:CDS 50.0%
CGATAACTGGAGGTCTACCA+AGG + chr2.4:109784-109803 MS.gene82560:CDS 50.0%
CGGATATGCCTTGATCTTGG+AGG + chr2.4:109698-109717 MS.gene82560:CDS 50.0%
TAACTGGAGGTCTACCAAGG+AGG + chr2.4:109787-109806 MS.gene82560:CDS 50.0%
TCAAGGCATATCCGGCATTG+TGG - chr2.4:109692-109711 None:intergenic 50.0%
TGCCGGATATGCCTTGATCT+TGG + chr2.4:109695-109714 MS.gene82560:CDS 50.0%
TGGGTACCTTTGCAATGGCA+GGG - chr2.4:109740-109759 None:intergenic 50.0%
TTGGGTACCTTTGCAATGGC+AGG - chr2.4:109741-109760 None:intergenic 50.0%
!! CCTTAGTTCTGTCACATGGC+TGG - chr2.4:110716-110735 None:intergenic 50.0%
ATTGCCCCCTGCCATTGCAA+AGG + chr2.4:109731-109750 MS.gene82560:CDS 55.0%
GGGTACCTTTGCAATGGCAG+GGG - chr2.4:109739-109758 None:intergenic 55.0%
GGTACCTTTGCAATGGCAGG+GGG - chr2.4:109738-109757 None:intergenic 55.0%
ACATGGCTGGGGTCGAGTTC+AGG - chr2.4:110703-110722 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 109530 110753 109530 ID=MS.gene82560
chr2.4 mRNA 109530 110753 109530 ID=MS.gene82560.t1;Parent=MS.gene82560
chr2.4 exon 109530 109952 109530 ID=MS.gene82560.t1.exon1;Parent=MS.gene82560.t1
chr2.4 CDS 109530 109952 109530 ID=cds.MS.gene82560.t1;Parent=MS.gene82560.t1
chr2.4 exon 110041 110143 110041 ID=MS.gene82560.t1.exon2;Parent=MS.gene82560.t1
chr2.4 CDS 110041 110143 110041 ID=cds.MS.gene82560.t1;Parent=MS.gene82560.t1
chr2.4 exon 110228 110340 110228 ID=MS.gene82560.t1.exon3;Parent=MS.gene82560.t1
chr2.4 CDS 110228 110340 110228 ID=cds.MS.gene82560.t1;Parent=MS.gene82560.t1
chr2.4 exon 110661 110753 110661 ID=MS.gene82560.t1.exon4;Parent=MS.gene82560.t1
chr2.4 CDS 110661 110753 110661 ID=cds.MS.gene82560.t1;Parent=MS.gene82560.t1
Gene Sequence

>MS.gene82560

ATGCAATTAGCTTCAAACACCGACAACCAAGATTCTTCTTCTTCAGAAACCCAACCCATATTGAATCACCTCTGTGAAATTATTCCTATTTCTGCCACGTCTGACAATCATGATATAGAGAATGAGTCTTCTCGTCTTGTTGTTGTAAATGCTGATCACCCACAATGCCGGATATGCCTTGATCTTGGAGGAGAAGACTTAATTGCCCCCTGCCATTGCAAAGGTACCCAAAAGTATGTCCACAGATCATGTCTCGATAACTGGAGGTCTACCAAGGAGGGCTTTGCTTTTTCTCACTGTACAGAATGCAGAGCTGTCTTCATAATTCGACCAAATGTCCCTAAAGATCGATGGTGGTTGAGATTGAAATTTCAGTTTCTTGTTGCCAGAGATCATGCATTCATTTTCATCATTGTTCAACTCGTATGTATATGTATCCATCCCCTACGATTTTATGTATTTCATTCAGAGAATATGTCTGTTCATTTCTTTTCCTTTTCTAATTGCACAGGTTGTTGCTTTCTTGGGAGTGCTTATTTATAAATTCTATGGAGATGAACTTAGAGAAATGTTTGGTTATGAAGAACATCCATACGGATTTTACACAATGGCTGGTATTCCCATTTATTCACCACTCTCAAATTCATGCCCAATGTTTGTTTGCAGCTTTTCCACTCATTTCTGACTTTGTTTTGCAGTTCTCGCCATTATTTTGGTGGGTTTGCTCTATGGCTTCTTTATAGCAATAATATGTGGGCAAAGAATCAATGAACGCCACTACCATGTTCTTGCCAAACAAGAATTGACAAAGGTCTGCTATGTAATAGTAATAAATGCTTTCAAATTACTTTGACTTACAATCCAATCCACATAAAAGTGAAGCATGTTACTCAAAACTAGTAATATGCTTGCTGCAAAACACGTCTTTGGTCATAAGATATACTTGCTGCAAAACACATCTTTGGTCATAAGATATGCAATTTCGGGAAAACAATCATTTAACTACCCGTTCTTGTATTGTATTGTTTAAGGATTATAATTGATTCTGAGTCATATAAGGACTATATTCCTTTTTTATAAAAATTTAAGGTATTCAACTCTTCACTCTGCTGTTTACTTTTTTGACGTCAGGAGTATGTGGTAGAAGATCGAGAACATGTAAAGGATGTGCCTGAACTCGACCCCAGCCATGTGACAGAACTAAGGATGTTGGGCCTTTACTAG
Protein sequence

>MS.gene82560.t1

MQLASNTDNQDSSSSETQPILNHLCEIIPISATSDNHDIENESSRLVVVNADHPQCRICLDLGGEDLIAPCHCKGTQKYVHRSCLDNWRSTKEGFAFSHCTECRAVFIIRPNVPKDRWWLRLKFQFLVARDHAFIFIIVQLVVAFLGVLIYKFYGDELREMFGYEEHPYGFYTMAVLAIILVGLLYGFFIAIICGQRINERHYHVLAKQELTKEYVVEDREHVKDVPELDPSHVTELRMLGLY