AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene050394


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene050394.t1 MTR_7g025100 57.955 88 29 1 136 223 161 240 3.58e-22 92.4
MS.gene050394.t1 MTR_7g025100 44.898 98 38 4 82 172 18 106 2.32e-12 65.5
MS.gene050394.t1 MTR_8g469420 52.381 63 29 1 133 194 26 88 8.63e-15 69.3
MS.gene050394.t1 MTR_5g056700 71.429 42 12 0 133 174 64 105 2.40e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 55 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTACTTTGTCCCTATTCA+TGG 0.213214 2.3:+50299344 None:intergenic
CGAGTGTTATTTACTGCTTC+TGG 0.234323 2.3:+50299390 None:intergenic
GGTAGAGAATTTAAAATTCT+TGG 0.254906 2.3:-50298756 MS.gene050394:CDS
AAACCATCTAAGGGAGAAAA+AGG 0.297995 2.3:-50298489 MS.gene050394:CDS
ATGAGATTCTTGATGTTTGA+TGG 0.301652 2.3:+50298536 None:intergenic
AATAACACTCGATATGGAAT+TGG 0.312098 2.3:-50299378 MS.gene050394:CDS
GTAGAGAATTTAAAATTCTT+GGG 0.338210 2.3:-50298755 MS.gene050394:CDS
GGAAGACTTTGGCCATGAAT+AGG 0.343004 2.3:-50299356 MS.gene050394:CDS
GCAGTAAATAACACTCGATA+TGG 0.343836 2.3:-50299384 MS.gene050394:CDS
CCTTGGGGACTTGATCAAAT+AGG 0.346724 2.3:-50299543 MS.gene050394:CDS
TGACAACTTGGCTCGTCCTC+GGG 0.351832 2.3:+50299483 None:intergenic
TCATGTCCTAGATGATATTC+TGG 0.368983 2.3:+50299516 None:intergenic
GAAGACTTTGGCCATGAATA+GGG 0.384751 2.3:-50299355 MS.gene050394:CDS
CTCATGTAGGCGAATATCCT+TGG 0.392441 2.3:-50299560 MS.gene050394:CDS
TACTGCTTCTGGTTGATTCA+CGG 0.402921 2.3:+50299401 None:intergenic
CGGTCGCATTTGATTCTTGC+GGG 0.407732 2.3:+50299421 None:intergenic
ATCAATTGTCTCTATGCTTA+CGG 0.411301 2.3:-50299456 MS.gene050394:CDS
ATGACAACTTGGCTCGTCCT+CGG 0.433674 2.3:+50299482 None:intergenic
TTTGATTCTTGCGGGTAGTC+TGG 0.439081 2.3:+50299429 None:intergenic
TCATGTAGGCGAATATCCTT+GGG 0.439903 2.3:-50299559 MS.gene050394:CDS
TTCAATACCCTTGACTTTGA+AGG 0.440257 2.3:+50299266 None:intergenic
TCAGTACCTTCATCTTCACT+TGG 0.452527 2.3:+50299315 None:intergenic
AAGATTGTGCTTAGGTCAAA+AGG 0.455133 2.3:-50298638 MS.gene050394:intron
TTCAAAAGTTCGAATCAAGT+TGG 0.472864 2.3:-50298669 MS.gene050394:CDS
ATAACACTCGATATGGAATT+GGG 0.474926 2.3:-50299377 MS.gene050394:CDS
ATATGGAATTGGGAAGACTT+TGG 0.475051 2.3:-50299367 MS.gene050394:CDS
AAAGGTCTGCCTAAGGTCAC+TGG 0.484747 2.3:+50298701 None:intergenic
GCTGAGTGTCCAGTGACCTT+AGG 0.505119 2.3:-50298710 MS.gene050394:CDS
CAATTGATGCAATGACAACT+TGG 0.506977 2.3:+50299471 None:intergenic
ATCAGTGCCTTCCTCTTCAA+AGG 0.520878 2.3:+50299242 None:intergenic
TACTGAAGCCTTCAAAGTCA+AGG 0.527533 2.3:-50299274 MS.gene050394:CDS
ACCTTGATCTGCTCGTGCTG+TGG 0.528870 2.3:+50299197 None:intergenic
GGAACACCAGAATATCATCT+AGG 0.537774 2.3:-50299522 MS.gene050394:CDS
TAGAGAATTTAAAATTCTTG+GGG 0.542034 2.3:-50298754 MS.gene050394:CDS
CAGTACCTTCATCTTCACTT+GGG 0.544371 2.3:+50299316 None:intergenic
GAAGACCCAAGTGAAGATGA+AGG 0.570364 2.3:-50299321 MS.gene050394:CDS
ATTGAAGCCTTTGAAGAGGA+AGG 0.570514 2.3:-50299249 MS.gene050394:CDS
TCCACAGCACGAGCAGATCA+AGG 0.578845 2.3:-50299198 MS.gene050394:intron
AGCTGGAAAAGGTCTGCCTA+AGG 0.584032 2.3:+50298694 None:intergenic
GGAGTCAACATGAACACAAG+TGG 0.588926 2.3:-50298468 MS.gene050394:CDS
ACTGAAGCTTTCGCAACTGA+AGG 0.593659 2.3:-50299297 MS.gene050394:CDS
GGGTATTGAAGCCTTTGAAG+AGG 0.599355 2.3:-50299253 MS.gene050394:CDS
CCTATTTGATCAAGTCCCCA+AGG 0.609937 2.3:+50299543 None:intergenic
ACTGAAGCCTTCAAAGTCAA+GGG 0.612172 2.3:-50299273 MS.gene050394:CDS
AAAATGGAAGGAGCTATTGG+AGG 0.613804 2.3:-50298444 MS.gene050394:CDS
GACAACTTGGCTCGTCCTCG+GGG 0.614726 2.3:+50299484 None:intergenic
CATGAATAGGGACAAAGTAG+AGG 0.614835 2.3:-50299343 MS.gene050394:CDS
TCAAGAATCTCATAGAGTCA+AGG 0.619546 2.3:-50298526 MS.gene050394:CDS
AGAATATCATCTAGGACATG+AGG 0.626963 2.3:-50299514 MS.gene050394:CDS
ACGGTCGCATTTGATTCTTG+CGG 0.627991 2.3:+50299420 None:intergenic
GAGAACAGTTCATCTCATGT+AGG 0.629071 2.3:-50299573 MS.gene050394:CDS
TAGAGTCAAGGAACCGACAG+AGG 0.651476 2.3:-50298514 MS.gene050394:CDS
AGAGAATTTAAAATTCTTGG+GGG 0.699277 2.3:-50298753 MS.gene050394:CDS
CATGTAGGCGAATATCCTTG+GGG 0.759490 2.3:-50299558 MS.gene050394:CDS
ACATGAGGAGAATGACCCCG+AGG 0.772839 2.3:-50299499 MS.gene050394:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GCAAAAATTGTTAAAATTAA+AGG - chr2.3:50298865-50298884 MS.gene050394:intron 15.0%
!!! GTAGAGAATTTAAAATTCTT+GGG - chr2.3:50299258-50299277 MS.gene050394:CDS 20.0%
!!! TAGAGAATTTAAAATTCTTG+GGG - chr2.3:50299259-50299278 MS.gene050394:CDS 20.0%
! ACATTAAATATCACTCATTC+TGG + chr2.3:50299228-50299247 None:intergenic 25.0%
! ATATCTCACAGTAAAATAAG+AGG - chr2.3:50299420-50299439 MS.gene050394:CDS 25.0%
! ATTGGAATATTGAAACTTCT+AGG + chr2.3:50299054-50299073 None:intergenic 25.0%
! GAAACATTCAAAAAGATCAA+AGG - chr2.3:50299144-50299163 MS.gene050394:intron 25.0%
!! AGAGAATTTAAAATTCTTGG+GGG - chr2.3:50299260-50299279 MS.gene050394:CDS 25.0%
!! GGTAGAGAATTTAAAATTCT+TGG - chr2.3:50299257-50299276 MS.gene050394:CDS 25.0%
AATAACACTCGATATGGAAT+TGG - chr2.3:50298635-50298654 MS.gene050394:intron 30.0%
AGTCTAAAAAGATTGTGCTT+AGG - chr2.3:50299367-50299386 MS.gene050394:CDS 30.0%
ATAACACTCGATATGGAATT+GGG - chr2.3:50298636-50298655 MS.gene050394:intron 30.0%
ATCAATTGTCTCTATGCTTA+CGG - chr2.3:50298557-50298576 MS.gene050394:intron 30.0%
ATGAGATTCTTGATGTTTGA+TGG + chr2.3:50299480-50299499 None:intergenic 30.0%
TCAAAAAGATCAAAGGTCTA+TGG - chr2.3:50299151-50299170 MS.gene050394:intron 30.0%
TTCAAAAGTTCGAATCAAGT+TGG - chr2.3:50299344-50299363 MS.gene050394:CDS 30.0%
!!! CTGTGGAATTCATTTTTTCT+AGG + chr2.3:50298802-50298821 None:intergenic 30.0%
AAACCATCTAAGGGAGAAAA+AGG - chr2.3:50299524-50299543 MS.gene050394:CDS 35.0%
AACACAAGTGGAAAAATGGA+AGG - chr2.3:50299557-50299576 MS.gene050394:CDS 35.0%
AACACATCGTTGCTAGAAAT+TGG + chr2.3:50299072-50299091 None:intergenic 35.0%
AAGATTGTGCTTAGGTCAAA+AGG - chr2.3:50299375-50299394 MS.gene050394:CDS 35.0%
ACAGAGGAAAAACCATCTAA+GGG - chr2.3:50299515-50299534 MS.gene050394:CDS 35.0%
ATATGGAATTGGGAAGACTT+TGG - chr2.3:50298646-50298665 MS.gene050394:CDS 35.0%
CAATTGATGCAATGACAACT+TGG + chr2.3:50298545-50298564 None:intergenic 35.0%
CATGAACACAAGTGGAAAAA+TGG - chr2.3:50299553-50299572 MS.gene050394:CDS 35.0%
GATATCCATTCTGATGTTGT+TGG + chr2.3:50298974-50298993 None:intergenic 35.0%
GATATTTAATGTGCAAGTCG+AGG - chr2.3:50299236-50299255 MS.gene050394:CDS 35.0%
GCAGTAAATAACACTCGATA+TGG - chr2.3:50298629-50298648 MS.gene050394:intron 35.0%
TAAAATAAGAGGCAAGATGC+AGG - chr2.3:50299431-50299450 MS.gene050394:CDS 35.0%
TCAAGAATCTCATAGAGTCA+AGG - chr2.3:50299487-50299506 MS.gene050394:CDS 35.0%
TCATGTCCTAGATGATATTC+TGG + chr2.3:50298500-50298519 None:intergenic 35.0%
TGAATGTTTCCAATGACATC+AGG + chr2.3:50299134-50299153 None:intergenic 35.0%
TGTAACATTTGCATGCAACA+AGG + chr2.3:50298926-50298945 None:intergenic 35.0%
TTCAATACCCTTGACTTTGA+AGG + chr2.3:50298750-50298769 None:intergenic 35.0%
! AGAATATCATCTAGGACATG+AGG - chr2.3:50298499-50298518 MS.gene050394:CDS 35.0%
! GTTTGATGGTTTCAACTACA+TGG + chr2.3:50299466-50299485 None:intergenic 35.0%
! TGCTGCATCATTTCTTTTGT+AGG + chr2.3:50298899-50298918 None:intergenic 35.0%
! TTAGATGGTTTTTCCTCTGT+CGG + chr2.3:50299515-50299534 None:intergenic 35.0%
!!! ACTTTTGAAGTAGCTGGAAA+AGG + chr2.3:50299333-50299352 None:intergenic 35.0%
!!! ATTCGAACTTTTGAAGTAGC+TGG + chr2.3:50299339-50299358 None:intergenic 35.0%
AAAATGGAAGGAGCTATTGG+AGG - chr2.3:50299569-50299588 MS.gene050394:CDS 40.0%
ACTGAAGCCTTCAAAGTCAA+GGG - chr2.3:50298740-50298759 MS.gene050394:CDS 40.0%
CAAAGGTCTATGGATGATAC+CGG - chr2.3:50299161-50299180 MS.gene050394:intron 40.0%
CAGTACCTTCATCTTCACTT+GGG + chr2.3:50298700-50298719 None:intergenic 40.0%
CATGAATAGGGACAAAGTAG+AGG - chr2.3:50298670-50298689 MS.gene050394:CDS 40.0%
CTAGCAACGATGTGTTTCTT+GGG - chr2.3:50299076-50299095 MS.gene050394:intron 40.0%
CTCTACTTTGTCCCTATTCA+TGG + chr2.3:50298672-50298691 None:intergenic 40.0%
GAAGACTTTGGCCATGAATA+GGG - chr2.3:50298658-50298677 MS.gene050394:CDS 40.0%
GACAGAGGAAAAACCATCTA+AGG - chr2.3:50299514-50299533 MS.gene050394:CDS 40.0%
GAGAACAGTTCATCTCATGT+AGG - chr2.3:50298440-50298459 MS.gene050394:CDS 40.0%
GCTGCTTCTTAAGTTTCACA+AGG + chr2.3:50298952-50298971 None:intergenic 40.0%
GGAAAAATGGAAGGAGCTAT+TGG - chr2.3:50299566-50299585 MS.gene050394:CDS 40.0%
GGAACACCAGAATATCATCT+AGG - chr2.3:50298491-50298510 MS.gene050394:CDS 40.0%
GGACGCTTTATGTGATTTAG+GGG - chr2.3:50299098-50299117 MS.gene050394:intron 40.0%
GGGACGCTTTATGTGATTTA+GGG - chr2.3:50299097-50299116 MS.gene050394:intron 40.0%
TACTGAAGCCTTCAAAGTCA+AGG - chr2.3:50298739-50298758 MS.gene050394:CDS 40.0%
TAGCAACGATGTGTTTCTTG+GGG - chr2.3:50299077-50299096 MS.gene050394:intron 40.0%
TAGCATCAACCTGATGTCAT+TGG - chr2.3:50299122-50299141 MS.gene050394:intron 40.0%
TCAGTACCTTCATCTTCACT+TGG + chr2.3:50298701-50298720 None:intergenic 40.0%
TCATCTACTTCATGTTAGCG+TGG + chr2.3:50299012-50299031 None:intergenic 40.0%
TCATGTAGGCGAATATCCTT+GGG - chr2.3:50298454-50298473 MS.gene050394:CDS 40.0%
TCTAGCAACGATGTGTTTCT+TGG - chr2.3:50299075-50299094 MS.gene050394:intron 40.0%
! ACTCCTTTTTCTCCCTTAGA+TGG + chr2.3:50299530-50299549 None:intergenic 40.0%
! ATTGAAGCCTTTGAAGAGGA+AGG - chr2.3:50298764-50298783 MS.gene050394:intron 40.0%
! TACTGCTTCTGGTTGATTCA+CGG + chr2.3:50298615-50298634 None:intergenic 40.0%
!! CGAGTGTTATTTACTGCTTC+TGG + chr2.3:50298626-50298645 None:intergenic 40.0%
AAGCTTGTAGGAGTAGCTGA+TGG - chr2.3:50299189-50299208 MS.gene050394:intron 45.0%
ACGGTCGCATTTGATTCTTG+CGG + chr2.3:50298596-50298615 None:intergenic 45.0%
ACTGAAGCTTTCGCAACTGA+AGG - chr2.3:50298716-50298735 MS.gene050394:CDS 45.0%
AGCAGCCAACAACATCAGAA+TGG - chr2.3:50298966-50298985 MS.gene050394:intron 45.0%
ATCAGTGCCTTCCTCTTCAA+AGG + chr2.3:50298774-50298793 None:intergenic 45.0%
CATGTAGGCGAATATCCTTG+GGG - chr2.3:50298455-50298474 MS.gene050394:CDS 45.0%
CATGTTAGCGTGGTAATCTC+TGG + chr2.3:50299002-50299021 None:intergenic 45.0%
CCTATTTGATCAAGTCCCCA+AGG + chr2.3:50298473-50298492 None:intergenic 45.0%
CCTTGGGGACTTGATCAAAT+AGG - chr2.3:50298470-50298489 MS.gene050394:CDS 45.0%
CTCATGTAGGCGAATATCCT+TGG - chr2.3:50298453-50298472 MS.gene050394:CDS 45.0%
CTTGGGGGACATAGTAATGA+TGG - chr2.3:50299275-50299294 MS.gene050394:CDS 45.0%
GAAGACCCAAGTGAAGATGA+AGG - chr2.3:50298692-50298711 MS.gene050394:CDS 45.0%
GGAAGACTTTGGCCATGAAT+AGG - chr2.3:50298657-50298676 MS.gene050394:CDS 45.0%
GGAGTCAACATGAACACAAG+TGG - chr2.3:50299545-50299564 MS.gene050394:CDS 45.0%
GGGGACGCTTTATGTGATTT+AGG - chr2.3:50299096-50299115 MS.gene050394:intron 45.0%
TTTGATTCTTGCGGGTAGTC+TGG + chr2.3:50298587-50298606 None:intergenic 45.0%
!! GGGTATTGAAGCCTTTGAAG+AGG - chr2.3:50298760-50298779 MS.gene050394:CDS 45.0%
AAAGGTCTGCCTAAGGTCAC+TGG + chr2.3:50299315-50299334 None:intergenic 50.0%
ACTCCTACAAGCTTCTCAGC+CGG + chr2.3:50299183-50299202 None:intergenic 50.0%
AGCGTGGTAATCTCTGGCTA+AGG + chr2.3:50298996-50299015 None:intergenic 50.0%
AGCTGGAAAAGGTCTGCCTA+AGG + chr2.3:50299322-50299341 None:intergenic 50.0%
CGGTCGCATTTGATTCTTGC+GGG + chr2.3:50298595-50298614 None:intergenic 50.0%
TAGAGTCAAGGAACCGACAG+AGG - chr2.3:50299499-50299518 MS.gene050394:CDS 50.0%
! ATACCGGCTGAGAAGCTTGT+AGG - chr2.3:50299177-50299196 MS.gene050394:intron 50.0%
! ATGACAACTTGGCTCGTCCT+CGG + chr2.3:50298534-50298553 None:intergenic 50.0%
ACATGAGGAGAATGACCCCG+AGG - chr2.3:50298514-50298533 MS.gene050394:CDS 55.0%
ACCTTGATCTGCTCGTGCTG+TGG + chr2.3:50298819-50298838 None:intergenic 55.0%
CGAGCAGATCAAGGTCAAGG+TGG - chr2.3:50298824-50298843 MS.gene050394:intron 55.0%
GCACGAGCAGATCAAGGTCA+AGG - chr2.3:50298821-50298840 MS.gene050394:intron 55.0%
GCTGAGTGTCCAGTGACCTT+AGG - chr2.3:50299303-50299322 MS.gene050394:CDS 55.0%
TCCACAGCACGAGCAGATCA+AGG - chr2.3:50298815-50298834 MS.gene050394:intron 55.0%
! TGACAACTTGGCTCGTCCTC+GGG + chr2.3:50298533-50298552 None:intergenic 55.0%
! GACAACTTGGCTCGTCCTCG+GGG + chr2.3:50298532-50298551 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 50298437 50299598 50298437 ID=MS.gene050394
chr2.3 mRNA 50298437 50299598 50298437 ID=MS.gene050394.t1;Parent=MS.gene050394
chr2.3 exon 50299199 50299598 50299199 ID=MS.gene050394.t1.exon1;Parent=MS.gene050394.t1
chr2.3 CDS 50299199 50299598 50299199 ID=cds.MS.gene050394.t1;Parent=MS.gene050394.t1
chr2.3 exon 50298639 50298782 50298639 ID=MS.gene050394.t1.exon2;Parent=MS.gene050394.t1
chr2.3 CDS 50298639 50298782 50298639 ID=cds.MS.gene050394.t1;Parent=MS.gene050394.t1
chr2.3 exon 50298437 50298564 50298437 ID=MS.gene050394.t1.exon3;Parent=MS.gene050394.t1
chr2.3 CDS 50298437 50298564 50298437 ID=cds.MS.gene050394.t1;Parent=MS.gene050394.t1
Gene Sequence

>MS.gene050394

ATGGAGAACAGTTCATCTCATGTAGGCGAATATCCTTGGGGACTTGATCAAATAGGAACACCAGAATATCATCTAGGACATGAGGAGAATGACCCCGAGGACGAGCCAAGTTGTCATTGCATCAATTGTCTCTATGCTTACGGACTACCAGACTACCCGCAAGAATCAAATGCGACCGTGAATCAACCAGAAGCAGTAAATAACACTCGATATGGAATTGGGAAGACTTTGGCCATGAATAGGGACAAAGTAGAGGAAGACCCAAGTGAAGATGAAGGTACTGAAGCTTTCGCAACTGAAGGTACTGAAGCCTTCAAAGTCAAGGGTATTGAAGCCTTTGAAGAGGAAGGCACTGATGCTTTCCTAGAAAAAATGAATTCCACAGCACGAGCAGATCAAGGTCAAGGTGGAAGTTTCGAGCAATTCTTGCAAAAATTGTTAAAATTAAAGGTGTAAATGCCTACAAAAGAAATGATGCAGCAGAATCCTTGTTGCATGCAAATGTTACAAAACCTTGTGAAACTTAAGAAGCAGCCAACAACATCAGAATGGATATCCTTAGCCAGAGATTACCACGCTAACATGAAGTAGATGATCGCATCAAAATTAAAGATCCTAGAAGTTTCAATATTCCAATTTCTAGCAACGATGTGTTTCTTGGGGACGCTTTATGTGATTTAGGGGCTAGCATCAACCTGATGTCATTGGAAACATTCAAAAAGATCAAAGGTCTATGGATGATACCGGCTGAGAAGCTTGTAGGAGTAGCTGATGGAACATTACATGAACCAGAATGAGTGATATTTAATGTGCAAGTCGAGGTAGAGAATTTAAAATTCTTGGGGGACATAGTAATGATGGATATAGCTGAGTGTCCAGTGACCTTAGGCAGACCTTTTCCAGCTACTTCAAAAGTTCGAATCAAGTTGGAGTCTAAAAAGATTGTGCTTAGGTCAAAAGGTGAATACTTGATATGATACATCATATCTCACAGTAAAATAAGAGGCAAGATGCAGGTACTGAATGCCATGTAGTTGAAACCATCAAACATCAAGAATCTCATAGAGTCAAGGAACCGACAGAGGAAAAACCATCTAAGGGAGAAAAAGGAGTCAACATGAACACAAGTGGAAAAATGGAAGGAGCTATTGGAGGCTCCTAG

Protein sequence

>MS.gene050394.t1

MENSSSHVGEYPWGLDQIGTPEYHLGHEENDPEDEPSCHCINCLYAYGLPDYPQESNATVNQPEAVNNTRYGIGKTLAMNRDKVEEDPSEDEGTEAFATEGTEAFKVKGIEAFEEEGTDAFLEKMNSTARADQVEVENLKFLGDIVMMDIAECPVTLGRPFPATSKVRIKLESKKIVLRSKVETIKHQESHRVKEPTEEKPSKGEKGVNMNTSGKMEGAIGGS