AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene86569

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86569.t1 MTR_5g023900 74.408 211 24 3 1 201 1 191 6.60e-104 297
MS.gene86569.t1 MTR_5g023880 71.144 201 29 4 1 201 1 172 5.24e-93 269
MS.gene86569.t1 MTR_5g023870 56.604 159 29 4 1 159 1 119 1.07e-50 160
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 68 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTAGTTGGGTTGGTTTCTT+TGG 0.162115 5.1:-14556327 None:intergenic
TTCTCGGAAGGGTTAGGTTT+AGG 0.237072 5.1:-14556248 None:intergenic
TGTTTGCATCTATAACAATT+TGG 0.250606 5.1:-14556533 None:intergenic
GTAGTTGGGTTGGTTTCTTT+GGG 0.266039 5.1:-14556326 None:intergenic
TCTCGGAAGGGTTAGGTTTA+GGG 0.267292 5.1:-14556247 None:intergenic
AACCGCTCTAGAAGTCTTAA+TGG 0.278934 5.1:+14556391 MS.gene86569:CDS
AATGGTTTGTCAGCAGCTTC+TGG 0.287143 5.1:+14556620 MS.gene86569:CDS
TTGAGGGGACTTGTTGTTGG+TGG 0.289994 5.1:-14556279 None:intergenic
TCTGATGAAGGCGAAGGTTT+AGG 0.328241 5.1:+14557203 MS.gene86569:CDS
CCTTCAAAGATCTTTAAGTA+TGG 0.331774 5.1:+14556349 MS.gene86569:CDS
ATACATCACTCTTCTTCATT+AGG 0.332064 5.1:-14557248 None:intergenic
GTCTTGAGGGGACTTGTTGT+TGG 0.343036 5.1:-14556282 None:intergenic
TAGTTGGGTTGGTTTCTTTG+GGG 0.344689 5.1:-14556325 None:intergenic
GTTGAATTCTCGGAAGGGTT+AGG 0.378551 5.1:-14556254 None:intergenic
AAAGATCTTTGAAGGGTAGT+TGG 0.385874 5.1:-14556341 None:intergenic
CTCTTCCTCCTCTTCATAGC+TGG 0.393408 5.1:-14556473 None:intergenic
TGAGGGGACTTGTTGTTGGT+GGG 0.402381 5.1:-14556278 None:intergenic
AGGGGACTTGTTGTTGGTGG+GGG 0.408399 5.1:-14556276 None:intergenic
AGGTGGGGTGGTTGTTGATG+TGG 0.426505 5.1:-14556660 None:intergenic
GAGTTCAGAGCTCGTGAGAA+TGG 0.435144 5.1:+14556413 MS.gene86569:CDS
ACCTCAACCTGATCAATATG+AGG 0.437745 5.1:+14556679 MS.gene86569:CDS
TAACAATTTGGATATATAGA+AGG 0.438362 5.1:-14556521 None:intergenic
AAGATCTTTGAAGGGTAGTT+GGG 0.440116 5.1:-14556340 None:intergenic
CATCAGAGGGAGGGTCTTGA+GGG 0.445658 5.1:-14556295 None:intergenic
CCATACTTAAAGATCTTTGA+AGG 0.449234 5.1:-14556349 None:intergenic
CCCTCATATTGATCAGGTTG+AGG 0.453934 5.1:-14556680 None:intergenic
GAAGCTGCTGACAAACCATT+AGG 0.476282 5.1:-14556617 None:intergenic
TCTTTGAAGGGTAGTTGGGT+TGG 0.478663 5.1:-14556336 None:intergenic
GCAAACATGTGTTTCCCACT+TGG 0.483219 5.1:+14556549 MS.gene86569:CDS
GGTCCTCTATCTCCATTGGC+TGG 0.500299 5.1:-14557136 None:intergenic
CATATTGATCAGGTTGAGGT+GGG 0.500892 5.1:-14556676 None:intergenic
TCATCAGAGGGAGGGTCTTG+AGG 0.508193 5.1:-14556296 None:intergenic
AGTTCAGAGCTCGTGAGAAT+GGG 0.512950 5.1:+14556414 MS.gene86569:CDS
AGCTCGTGAGAATGGGAAGC+TGG 0.512973 5.1:+14556421 MS.gene86569:CDS
AGTTGGGTTGGTTTCTTTGG+GGG 0.515909 5.1:-14556324 None:intergenic
CATCACTCTTCTTCATTAGG+AGG 0.517441 5.1:-14557245 None:intergenic
GAGGGGTCCTCTATCTCCAT+TGG 0.519182 5.1:-14557140 None:intergenic
AAGCCAGCCAATGGAGATAG+AGG 0.520626 5.1:+14557133 MS.gene86569:CDS
GACTGCATTGATGAACCATA+TGG 0.524295 5.1:+14556571 MS.gene86569:CDS
TTGATCAGGTTGAGGTGGGG+TGG 0.536734 5.1:-14556672 None:intergenic
GAGGGGACTTGTTGTTGGTG+GGG 0.544991 5.1:-14556277 None:intergenic
AATGGGAAGCTGGCAGCTGA+TGG 0.545369 5.1:+14556431 MS.gene86569:CDS
TCAAAGATCTTTAAGTATGG+AGG 0.548782 5.1:+14556352 MS.gene86569:CDS
TCATATTGATCAGGTTGAGG+TGG 0.558741 5.1:-14556677 None:intergenic
TGATGATGAAAGCCAGCCAA+TGG 0.578386 5.1:+14557124 MS.gene86569:CDS
GAGTAATATTCGTGAAGTGA+AGG 0.580783 5.1:+14556493 MS.gene86569:CDS
CTGGCAGCTGATGGAGAAGG+TGG 0.580844 5.1:+14556440 MS.gene86569:CDS
GGGGTGGTTGTTGATGTGGA+AGG 0.586960 5.1:-14556656 None:intergenic
CATACTTAAAGATCTTTGAA+GGG 0.591140 5.1:-14556348 None:intergenic
CTCCATTAAGACTTCTAGAG+CGG 0.592315 5.1:-14556393 None:intergenic
ATATTGATCAGGTTGAGGTG+GGG 0.595131 5.1:-14556675 None:intergenic
ATGGTCCAGCTATGAAGAGG+AGG 0.603822 5.1:+14556468 MS.gene86569:CDS
CTCGGATGCAACATCATCAG+AGG 0.604023 5.1:-14557159 None:intergenic
GGGGATTCATCATCAGAGGG+AGG 0.610326 5.1:-14556305 None:intergenic
TCGGATGCAACATCATCAGA+GGG 0.613962 5.1:-14557158 None:intergenic
GATGGAGAAGGTGGAAGTGA+TGG 0.614959 5.1:+14556449 MS.gene86569:CDS
ACTGCATCTGAGTCTGATGA+AGG 0.623088 5.1:+14557191 MS.gene86569:CDS
AATTTGGATATATAGAAGGA+TGG 0.631395 5.1:-14556517 None:intergenic
TCTGAGTCTGATGAAGGCGA+AGG 0.633192 5.1:+14557197 MS.gene86569:CDS
TTCATCAATGCAGTCCAAGT+GGG 0.634799 5.1:-14556563 None:intergenic
GTGATGGTCCAGCTATGAAG+AGG 0.637063 5.1:+14556465 MS.gene86569:CDS
AAGCTGGCAGCTGATGGAGA+AGG 0.643145 5.1:+14556437 MS.gene86569:CDS
GTTCATCAATGCAGTCCAAG+TGG 0.645025 5.1:-14556564 None:intergenic
AGATGCAGTATCATCAGACT+CGG 0.649465 5.1:-14557177 None:intergenic
CCTCAACCTGATCAATATGA+GGG 0.650750 5.1:+14556680 MS.gene86569:CDS
ATCAGAGGGAGGGTCTTGAG+GGG 0.650850 5.1:-14556294 None:intergenic
GGGATTCATCATCAGAGGGA+GGG 0.659890 5.1:-14556304 None:intergenic
CGGATGCAACATCATCAGAG+GGG 0.768604 5.1:-14557157 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTTGAATTAGAAAATT+AGG - chr5.1:14556717-14556736 None:intergenic 15.0%
!! TTATAATTATAATTGCTTCA+TGG - chr5.1:14557076-14557095 None:intergenic 15.0%
!! AACATTACATAATTGAATCT+TGG - chr5.1:14556823-14556842 None:intergenic 20.0%
!! TAACAATTTGGATATATAGA+AGG - chr5.1:14556524-14556543 None:intergenic 20.0%
!!! AATGTTTTTCTTTTGTTACT+AGG + chr5.1:14557101-14557120 MS.gene86569:intron 20.0%
!!! TTTTTCGCACTATAATTTTT+AGG + chr5.1:14556753-14556772 MS.gene86569:intron 20.0%
! AATTTGGATATATAGAAGGA+TGG - chr5.1:14556520-14556539 None:intergenic 25.0%
! CATACTTAAAGATCTTTGAA+GGG - chr5.1:14556351-14556370 None:intergenic 25.0%
! CATATATATGTTTGTGTGTA+TGG - chr5.1:14556925-14556944 None:intergenic 25.0%
! TGTTTGCATCTATAACAATT+TGG - chr5.1:14556536-14556555 None:intergenic 25.0%
! TTATGAGATCAAATTCATGT+AGG + chr5.1:14556968-14556987 MS.gene86569:intron 25.0%
AAAAATGGTGTTCTTCCATA+TGG - chr5.1:14556589-14556608 None:intergenic 30.0%
CATTAGGATCACAACAAAAA+TGG - chr5.1:14556604-14556623 None:intergenic 30.0%
CCATACTTAAAGATCTTTGA+AGG - chr5.1:14556352-14556371 None:intergenic 30.0%
CCTTCAAAGATCTTTAAGTA+TGG + chr5.1:14556349-14556368 MS.gene86569:CDS 30.0%
TATATAGCCAATAAAACCCT+AGG - chr5.1:14556794-14556813 None:intergenic 30.0%
TCAAAGATCTTTAAGTATGG+AGG + chr5.1:14556352-14556371 MS.gene86569:CDS 30.0%
!! CATTTTTGTTGTGATCCTAA+TGG + chr5.1:14556602-14556621 MS.gene86569:CDS 30.0%
GAGTAATATTCGTGAAGTGA+AGG + chr5.1:14556493-14556512 MS.gene86569:CDS 35.0%
! AAAGATCTTTGAAGGGTAGT+TGG - chr5.1:14556344-14556363 None:intergenic 35.0%
! AAGATCTTTGAAGGGTAGTT+GGG - chr5.1:14556343-14556362 None:intergenic 35.0%
! GTTTTACCCTCATATTGATC+AGG - chr5.1:14556689-14556708 None:intergenic 35.0%
ACCTCAACCTGATCAATATG+AGG + chr5.1:14556679-14556698 MS.gene86569:CDS 40.0%
AGATGCAGTATCATCAGACT+CGG - chr5.1:14557180-14557199 None:intergenic 40.0%
CCAATAAAACCCTAGGTCAT+TGG - chr5.1:14556787-14556806 None:intergenic 40.0%
CCTCAACCTGATCAATATGA+GGG + chr5.1:14556680-14556699 MS.gene86569:CDS 40.0%
TTCATCAATGCAGTCCAAGT+GGG - chr5.1:14556566-14556585 None:intergenic 40.0%
! CTCCATTAAGACTTCTAGAG+CGG - chr5.1:14556396-14556415 None:intergenic 40.0%
! GACTGCATTGATGAACCATA+TGG + chr5.1:14556571-14556590 MS.gene86569:CDS 40.0%
!! AACCGCTCTAGAAGTCTTAA+TGG + chr5.1:14556391-14556410 MS.gene86569:CDS 40.0%
!! ATATTGATCAGGTTGAGGTG+GGG - chr5.1:14556678-14556697 None:intergenic 40.0%
!! CATATTGATCAGGTTGAGGT+GGG - chr5.1:14556679-14556698 None:intergenic 40.0%
!! CCAATGACCTAGGGTTTTAT+TGG + chr5.1:14556784-14556803 MS.gene86569:intron 40.0%
!! GTAGTTGGGTTGGTTTCTTT+GGG - chr5.1:14556329-14556348 None:intergenic 40.0%
!! TAGTTGGGTTGGTTTCTTTG+GGG - chr5.1:14556328-14556347 None:intergenic 40.0%
!! TCATATTGATCAGGTTGAGG+TGG - chr5.1:14556680-14556699 None:intergenic 40.0%
ACTGCATCTGAGTCTGATGA+AGG + chr5.1:14557191-14557210 MS.gene86569:CDS 45.0%
AGTTCAGAGCTCGTGAGAAT+GGG + chr5.1:14556414-14556433 MS.gene86569:CDS 45.0%
GAAGCTGCTGACAAACCATT+AGG - chr5.1:14556620-14556639 None:intergenic 45.0%
GCAAACATGTGTTTCCCACT+TGG + chr5.1:14556549-14556568 MS.gene86569:CDS 45.0%
GTCAACACTCCAATGACCTA+GGG + chr5.1:14556775-14556794 MS.gene86569:intron 45.0%
GTTCATCAATGCAGTCCAAG+TGG - chr5.1:14556567-14556586 None:intergenic 45.0%
GTTGAATTCTCGGAAGGGTT+AGG - chr5.1:14556257-14556276 None:intergenic 45.0%
TCGGATGCAACATCATCAGA+GGG - chr5.1:14557161-14557180 None:intergenic 45.0%
TCTCGGAAGGGTTAGGTTTA+GGG - chr5.1:14556250-14556269 None:intergenic 45.0%
TCTGATGAAGGCGAAGGTTT+AGG + chr5.1:14557203-14557222 MS.gene86569:CDS 45.0%
TTCTCGGAAGGGTTAGGTTT+AGG - chr5.1:14556251-14556270 None:intergenic 45.0%
TTGGGGGATTCATCATCAGA+GGG - chr5.1:14556311-14556330 None:intergenic 45.0%
TTTGGGGGATTCATCATCAG+AGG - chr5.1:14556312-14556331 None:intergenic 45.0%
! AATGGTTTGTCAGCAGCTTC+TGG + chr5.1:14556620-14556639 MS.gene86569:CDS 45.0%
! CCCTCATATTGATCAGGTTG+AGG - chr5.1:14556683-14556702 None:intergenic 45.0%
! TCTTTGAAGGGTAGTTGGGT+TGG - chr5.1:14556339-14556358 None:intergenic 45.0%
! TGATGATGAAAGCCAGCCAA+TGG + chr5.1:14557124-14557143 MS.gene86569:CDS 45.0%
!! AGTTGGGTTGGTTTCTTTGG+GGG - chr5.1:14556327-14556346 None:intergenic 45.0%
!! GGTAGTTGGGTTGGTTTCTT+TGG - chr5.1:14556330-14556349 None:intergenic 45.0%
!!! AGACTTCTAGAGCGGTTTTC+AGG - chr5.1:14556388-14556407 None:intergenic 45.0%
!!! TAATTTTTTTTTTAACTAAT+CGG + chr5.1:14557006-14557025 MS.gene86569:intron 5.0%
AAGCCAGCCAATGGAGATAG+AGG + chr5.1:14557133-14557152 MS.gene86569:CDS 50.0%
ATGGTCCAGCTATGAAGAGG+AGG + chr5.1:14556468-14556487 MS.gene86569:CDS 50.0%
CGGATGCAACATCATCAGAG+GGG - chr5.1:14557160-14557179 None:intergenic 50.0%
CTCGGATGCAACATCATCAG+AGG - chr5.1:14557162-14557181 None:intergenic 50.0%
CTCTTCCTCCTCTTCATAGC+TGG - chr5.1:14556476-14556495 None:intergenic 50.0%
GAGTTCAGAGCTCGTGAGAA+TGG + chr5.1:14556413-14556432 MS.gene86569:CDS 50.0%
GATGGAGAAGGTGGAAGTGA+TGG + chr5.1:14556449-14556468 MS.gene86569:CDS 50.0%
GGGATTCATCATCAGAGGGA+GGG - chr5.1:14556307-14556326 None:intergenic 50.0%
GGTCAACACTCCAATGACCT+AGG + chr5.1:14556774-14556793 MS.gene86569:intron 50.0%
GTGATGGTCCAGCTATGAAG+AGG + chr5.1:14556465-14556484 MS.gene86569:CDS 50.0%
TCTGAGTCTGATGAAGGCGA+AGG + chr5.1:14557197-14557216 MS.gene86569:CDS 50.0%
TGGGGGTTGAATTCTCGGAA+GGG - chr5.1:14556262-14556281 None:intergenic 50.0%
! GTTGGTGGGGGTTGAATTCT+CGG - chr5.1:14556267-14556286 None:intergenic 50.0%
!! GTCTTGAGGGGACTTGTTGT+TGG - chr5.1:14556285-14556304 None:intergenic 50.0%
!! TGAGGGGACTTGTTGTTGGT+GGG - chr5.1:14556281-14556300 None:intergenic 50.0%
!! TTGAGGGGACTTGTTGTTGG+TGG - chr5.1:14556282-14556301 None:intergenic 50.0%
AAGCTGGCAGCTGATGGAGA+AGG + chr5.1:14556437-14556456 MS.gene86569:CDS 55.0%
AATGGGAAGCTGGCAGCTGA+TGG + chr5.1:14556431-14556450 MS.gene86569:CDS 55.0%
AGCTCGTGAGAATGGGAAGC+TGG + chr5.1:14556421-14556440 MS.gene86569:CDS 55.0%
AGGTGGGGTGGTTGTTGATG+TGG - chr5.1:14556663-14556682 None:intergenic 55.0%
ATCAGAGGGAGGGTCTTGAG+GGG - chr5.1:14556297-14556316 None:intergenic 55.0%
CATCAGAGGGAGGGTCTTGA+GGG - chr5.1:14556298-14556317 None:intergenic 55.0%
GAGGGGTCCTCTATCTCCAT+TGG - chr5.1:14557143-14557162 None:intergenic 55.0%
GGGGATTCATCATCAGAGGG+AGG - chr5.1:14556308-14556327 None:intergenic 55.0%
GGGGTGGTTGTTGATGTGGA+AGG - chr5.1:14556659-14556678 None:intergenic 55.0%
GGTCCTCTATCTCCATTGGC+TGG - chr5.1:14557139-14557158 None:intergenic 55.0%
GTGGGGGTTGAATTCTCGGA+AGG - chr5.1:14556263-14556282 None:intergenic 55.0%
TCATCAGAGGGAGGGTCTTG+AGG - chr5.1:14556299-14556318 None:intergenic 55.0%
!! AGGGGACTTGTTGTTGGTGG+GGG - chr5.1:14556279-14556298 None:intergenic 55.0%
!! GAGGGGACTTGTTGTTGGTG+GGG - chr5.1:14556280-14556299 None:intergenic 55.0%
!! TTGATCAGGTTGAGGTGGGG+TGG - chr5.1:14556675-14556694 None:intergenic 55.0%
CTGGCAGCTGATGGAGAAGG+TGG + chr5.1:14556440-14556459 MS.gene86569:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 14556239 14557265 14556239 ID=MS.gene86569
chr5.1 mRNA 14556239 14557265 14556239 ID=MS.gene86569.t1;Parent=MS.gene86569
chr5.1 exon 14556239 14556701 14556239 ID=MS.gene86569.t1.exon1;Parent=MS.gene86569.t1
chr5.1 CDS 14556239 14556701 14556239 ID=cds.MS.gene86569.t1;Parent=MS.gene86569.t1
chr5.1 exon 14557123 14557265 14557123 ID=MS.gene86569.t1.exon2;Parent=MS.gene86569.t1
chr5.1 CDS 14557123 14557265 14557123 ID=cds.MS.gene86569.t1;Parent=MS.gene86569.t1
Gene Sequence

>MS.gene86569

ATGCAGAACCCTAAACCTAACCCTTCCGAGAATTCAACCCCCACCAACAACAAGTCCCCTCAAGACCCTCCCTCTGATGATGAATCCCCCAAAGAAACCAACCCAACTACCCTTCAAAGATCTTTAAGTATGGAGGAAGAAGATGTCCTGAAAACCGCTCTAGAAGTCTTAATGGAGTTCAGAGCTCGTGAGAATGGGAAGCTGGCAGCTGATGGAGAAGGTGGAAGTGATGGTCCAGCTATGAAGAGGAGGAAGAGTAATATTCGTGAAGTGAAGGACCATCCTTCTATATATCCAAATTGTTATAGATGCAAACATGTGTTTCCCACTTGGACTGCATTGATGAACCATATGGAAGAACACCATTTTTGTTGTGATCCTAATGGTTTGTCAGCAGCTTCTGGTTTTTCTGCACTTCCTTCCACATCAACAACCACCCCACCTCAACCTGATCAATATGAGGGTAAAACTAAAACCTAATTTTCTAATTCAAACTATTTATTGTCATGTTTTTTTTTTCGCACTATAATTTTTAGGTCAACACTCCAATGACCTAGGGTTTTATTGGCTATATATCATGTCCAAGATTCAATTATGTAATGTTATGTCATTTTTTTTTTTTTTTACATTTAATTATTTTGATTTCAAAGTACTTGTGTATAGAACATTCATAAAAGATTGTACCATACACACAAACATATATATGTTCACTTTGAGTGTTGCTTAAGTTTATGAGATCAAATTCATGTAGGCATCTAGATATATCTTAATTTTTTTTTTAACTAATCGGTTTTTAATTTGACGATTTGCTTTTTCTTCAAACTAATGTTTTTACCATGAAGCAATTATAATTATAATTTTGAATGTTTTTCTTTTGTTACTAGGTGATGATGAAAGCCAGCCAATGGAGATAGAGGACCCCTCTGATGATGTTGCATCCGAGTCTGATGATACTGCATCTGAGTCTGATGAAGGCGAAGGTTTAGGATTCGACTTGAACGAGTTGCCTCCTAATGAAGAAGAGTGA
Protein sequence

>MS.gene86569.t1

MQNPKPNPSENSTPTNNKSPQDPPSDDESPKETNPTTLQRSLSMEEEDVLKTALEVLMEFRARENGKLAADGEGGSDGPAMKRRKSNIREVKDHPSIYPNCYRCKHVFPTWTALMNHMEEHHFCCDPNGLSAASGFSALPSTSTTTPPQPDQYEGDDESQPMEIEDPSDDVASESDDTASESDEGEGLGFDLNELPPNEEE