AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66983


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66983.t1 MTR_6g029250 92.797 236 9 1 1 236 1 228 7.25e-153 424
MS.gene66983.t1 MTR_7g085790 48.077 260 98 9 1 233 1 250 1.33e-65 204
MS.gene66983.t1 MTR_7g085790 44.400 250 83 10 1 233 1 211 5.72e-54 173
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66983.t1 AT3G03870 37.184 277 117 15 1 233 1 264 2.94e-31 116
MS.gene66983.t1 AT5G18130 44.186 172 60 8 91 233 114 278 1.18e-30 115
MS.gene66983.t1 AT3G03870 32.645 242 107 14 1 199 1 229 2.88e-14 70.1
MS.gene66983.t1 AT5G18130 37.857 140 52 7 91 202 114 246 6.31e-14 69.3

Find 36 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAATAGTGGTTTCAATTTA+TGG 0.126095 6.4:+3763241 MS.gene66983:CDS
GTTATGTGAGCTCTTGTTAT+TGG 0.194388 6.4:-3764404 None:intergenic
TCTTTCTCAATAATCATTCT+TGG 0.230298 6.4:-3763174 None:intergenic
AAGATTAAGGAAAATGAAAT+TGG 0.238321 6.4:+3763096 MS.gene66983:CDS
GTTGGTGCTATTTGCACTTT+TGG 0.279828 6.4:+3763282 MS.gene66983:CDS
ATTATTGAGAAAGATGATTT+TGG 0.285258 6.4:+3763183 MS.gene66983:CDS
TTACCAAGTTTGAGGTCTAA+TGG 0.382258 6.4:-3762985 None:intergenic
TAACACCTCAAATGATGTTA+TGG 0.383015 6.4:+3763005 MS.gene66983:CDS
GTGGTTTCAATTTATGGAAG+TGG 0.411257 6.4:+3763247 MS.gene66983:CDS
GAAGCAATTTCTGTTGTAAG+AGG 0.414220 6.4:+3764377 MS.gene66983:CDS
GGTCTAATGGAATTTGTAAA+GGG 0.426783 6.4:-3762972 None:intergenic
TTATGGAAGTGGAGTCTTAG+TGG 0.445021 6.4:+3763258 MS.gene66983:CDS
TTGAGGTGTTACCAAGTTTG+AGG 0.452496 6.4:-3762993 None:intergenic
AGGTCTAATGGAATTTGTAA+AGG 0.463571 6.4:-3762973 None:intergenic
TGGGAAGTAGAGGACAATAG+TGG 0.465059 6.4:+3763228 MS.gene66983:CDS
TTCAGAAGGATCAGAAGAAT+AGG 0.469303 6.4:+3763361 MS.gene66983:CDS
TTGAACCATAACATCATTTG+AGG 0.471724 6.4:-3763010 None:intergenic
TCTTTGCTACTACTTGACTT+TGG 0.472978 6.4:-3763138 None:intergenic
TGGAGATGGATCTTGATGAA+TGG 0.483700 6.4:+3762812 None:intergenic
GAATTTGTAAAGGGACAAGT+TGG 0.486114 6.4:-3762963 None:intergenic
GGAGATGGATCTTGATGAAT+GGG 0.498676 6.4:+3762813 None:intergenic
ATTCCATTAGACCTCAAACT+TGG 0.502699 6.4:+3762982 MS.gene66983:CDS
CAAAGAAGAGGATTCAAGTT+GGG 0.511674 6.4:+3763209 MS.gene66983:CDS
TATATTGATTTCAATGAAGA+TGG 0.511704 6.4:+3762856 MS.gene66983:CDS
TGTTCTTTGGAAGCCAACAT+AGG 0.514724 6.4:+3763331 MS.gene66983:CDS
AAGCAATTTCTGTTGTAAGA+GGG 0.518875 6.4:+3764378 MS.gene66983:CDS
GGATTCAAGTTGGGAAGTAG+AGG 0.539605 6.4:+3763218 MS.gene66983:CDS
AGCAATTTCTGTTGTAAGAG+GGG 0.561387 6.4:+3764379 MS.gene66983:CDS
ATTTCAGAGGATTAAGCAAG+TGG 0.575069 6.4:+3764331 MS.gene66983:intron
AAGTGGAGTCTTAGTGGTGT+TGG 0.575334 6.4:+3763264 MS.gene66983:CDS
ACAAGAGCTCACATAACAGT+TGG 0.586253 6.4:+3764410 MS.gene66983:CDS
ACAAAGAAGAGGATTCAAGT+TGG 0.588072 6.4:+3763208 MS.gene66983:CDS
AGAGCTCACATAACAGTTGG+TGG 0.589518 6.4:+3764413 MS.gene66983:CDS
TGGGAATCAATCTCTAGTGA+TGG 0.593054 6.4:+3762832 MS.gene66983:CDS
ATCAGAAAGTGCTTTAGACA+TGG 0.600275 6.4:+3762906 MS.gene66983:CDS
TCAAATCTATGCTGATGACA+AGG 0.621211 6.4:+3763386 MS.gene66983:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCAAATCATATATATTTTTT+TGG + chr6.4:3763427-3763446 MS.gene66983:intron 10.0%
!!! TTTTAGTCATTATATTGTTA+AGG + chr6.4:3763676-3763695 MS.gene66983:intron 15.0%
!!! TTTTGATTCGAAAAATAAAT+TGG - chr6.4:3763945-3763964 None:intergenic 15.0%
!! AAGATTAAGGAAAATGAAAT+TGG + chr6.4:3763096-3763115 MS.gene66983:CDS 20.0%
!! ATCATTTATTCAAGAAATAC+CGG + chr6.4:3764044-3764063 MS.gene66983:intron 20.0%
!! TTCATAAAGTCAATTATAAG+TGG - chr6.4:3764014-3764033 None:intergenic 20.0%
!!! AAATAAATTGGAGTATCAAT+TGG - chr6.4:3763933-3763952 None:intergenic 20.0%
!!! ACAAGTTTTCTTTAAGATTA+AGG + chr6.4:3763083-3763102 MS.gene66983:CDS 20.0%
!!! ATTATTGAGAAAGATGATTT+TGG + chr6.4:3763183-3763202 MS.gene66983:CDS 20.0%
!!! GGATGGAATTTTATTATATT+TGG + chr6.4:3764254-3764273 MS.gene66983:intron 20.0%
!!! TATATTGATTTCAATGAAGA+TGG + chr6.4:3762856-3762875 MS.gene66983:CDS 20.0%
!!! TTTTACTCTATAGTATTTCA+GGG - chr6.4:3764214-3764233 None:intergenic 20.0%
!!! TTTTTACTCTATAGTATTTC+AGG - chr6.4:3764215-3764234 None:intergenic 20.0%
! AAAAAAAGTTTCCTAGGAAA+AGG + chr6.4:3762883-3762902 MS.gene66983:CDS 25.0%
! ACAATAGTGGTTTCAATTTA+TGG + chr6.4:3763241-3763260 MS.gene66983:CDS 25.0%
! CGAATGTCATCAATATTTAT+CGG - chr6.4:3763808-3763827 None:intergenic 25.0%
! TCATTTATTCAAGAAATACC+GGG + chr6.4:3764045-3764064 MS.gene66983:intron 25.0%
! TCTTTCTCAATAATCATTCT+TGG - chr6.4:3763177-3763196 None:intergenic 25.0%
! TTGTATATTGAACTAAACCT+TGG + chr6.4:3764303-3764322 MS.gene66983:intron 25.0%
!! AGAATCTGGTTTAGTATAAA+TGG + chr6.4:3763525-3763544 MS.gene66983:intron 25.0%
!! TCAAGATTTTAAATTGCTCT+TGG + chr6.4:3763590-3763609 MS.gene66983:intron 25.0%
!! TTTTCGAATCAAAACAATCA+GGG + chr6.4:3763951-3763970 MS.gene66983:intron 25.0%
!!! ATTGATGATTCTTTAGAGTT+GGG + chr6.4:3763746-3763765 MS.gene66983:intron 25.0%
!!! GTAAAAAAGTGTTAACTTTG+TGG + chr6.4:3764228-3764247 MS.gene66983:intron 25.0%
!!! TCTATTTGTGTTTTGTTCTT+TGG + chr6.4:3763318-3763337 MS.gene66983:CDS 25.0%
!!! TTTTTCGAATCAAAACAATC+AGG + chr6.4:3763950-3763969 MS.gene66983:intron 25.0%
AAAGTCAATTATAAGTGGCA+TGG - chr6.4:3764009-3764028 None:intergenic 30.0%
AAGCAATTTCTGTTGTAAGA+GGG + chr6.4:3764378-3764397 MS.gene66983:CDS 30.0%
ACATAGGAAAAAACTTCAGA+AGG + chr6.4:3763347-3763366 MS.gene66983:CDS 30.0%
AGGTCTAATGGAATTTGTAA+AGG - chr6.4:3762976-3762995 None:intergenic 30.0%
CTTAGTCATTTGATCTTGAT+CGG + chr6.4:3763845-3763864 MS.gene66983:intron 30.0%
GAATCATCAATCAACTAACA+AGG - chr6.4:3763737-3763756 None:intergenic 30.0%
GACAAGGTTAGTAAATTTCT+TGG + chr6.4:3763402-3763421 MS.gene66983:intron 30.0%
GGTCTAATGGAATTTGTAAA+GGG - chr6.4:3762975-3762994 None:intergenic 30.0%
TAACACCTCAAATGATGTTA+TGG + chr6.4:3763005-3763024 MS.gene66983:CDS 30.0%
TTGAACCATAACATCATTTG+AGG - chr6.4:3763013-3763032 None:intergenic 30.0%
!! GATTGATGATTCTTTAGAGT+TGG + chr6.4:3763745-3763764 MS.gene66983:intron 30.0%
!! TTGATGATTCTTTAGAGTTG+GGG + chr6.4:3763747-3763766 MS.gene66983:intron 30.0%
!!! ACAAGTTGGTTTTGTTTTCT+TGG - chr6.4:3762952-3762971 None:intergenic 30.0%
!!! TCTGAAGTTTTTTCCTATGT+TGG - chr6.4:3763347-3763366 None:intergenic 30.0%
AAGAAATACCGGGAAATACT+TGG + chr6.4:3764055-3764074 MS.gene66983:intron 35.0%
ACAAAGAAGAGGATTCAAGT+TGG + chr6.4:3763208-3763227 MS.gene66983:CDS 35.0%
AGAAATACCGGGAAATACTT+GGG + chr6.4:3764056-3764075 MS.gene66983:intron 35.0%
AGCAATTTCTGTTGTAAGAG+GGG + chr6.4:3764379-3764398 MS.gene66983:CDS 35.0%
ATTCCATTAGACCTCAAACT+TGG + chr6.4:3762982-3763001 MS.gene66983:CDS 35.0%
ATTTCAGAGGATTAAGCAAG+TGG + chr6.4:3764331-3764350 MS.gene66983:intron 35.0%
GAAGCAATTTCTGTTGTAAG+AGG + chr6.4:3764377-3764396 MS.gene66983:CDS 35.0%
GAATTTGTAAAGGGACAAGT+TGG - chr6.4:3762966-3762985 None:intergenic 35.0%
GGTGAGAAAAAAAGTTTCCT+AGG + chr6.4:3762877-3762896 MS.gene66983:CDS 35.0%
GTGGTTTCAATTTATGGAAG+TGG + chr6.4:3763247-3763266 MS.gene66983:CDS 35.0%
TACTCTATAGTATTTCAGGG+TGG - chr6.4:3764211-3764230 None:intergenic 35.0%
TCAAATCTATGCTGATGACA+AGG + chr6.4:3763386-3763405 MS.gene66983:CDS 35.0%
TCTTTGCTACTACTTGACTT+TGG - chr6.4:3763141-3763160 None:intergenic 35.0%
TGTCAATGACTGATGTTTGT+CGG + chr6.4:3763502-3763521 MS.gene66983:intron 35.0%
TTCAGAAGGATCAGAAGAAT+AGG + chr6.4:3763361-3763380 MS.gene66983:CDS 35.0%
! AAAGTGTTAACTTTGTGGCA+AGG + chr6.4:3764233-3764252 MS.gene66983:intron 35.0%
! CAAAGAAGAGGATTCAAGTT+GGG + chr6.4:3763209-3763228 MS.gene66983:CDS 35.0%
! GTTATGTGAGCTCTTGTTAT+TGG - chr6.4:3764407-3764426 None:intergenic 35.0%
! TTACCAAGTTTGAGGTCTAA+TGG - chr6.4:3762988-3763007 None:intergenic 35.0%
!! AAATACTTGGGTGCCATTAA+TGG + chr6.4:3764068-3764087 MS.gene66983:intron 35.0%
!! ATCAGAAAGTGCTTTAGACA+TGG + chr6.4:3762906-3762925 MS.gene66983:CDS 35.0%
!! ATCCTCTGAAATCAAAACCA+AGG - chr6.4:3764323-3764342 None:intergenic 35.0%
!! TGATTTTGGTGACAAAGAAG+AGG + chr6.4:3763197-3763216 MS.gene66983:CDS 35.0%
!!! AACCTTGGTTTTGATTTCAG+AGG + chr6.4:3764318-3764337 MS.gene66983:intron 35.0%
!!! AGTTGGTTTTGTTTTCTTGG+TGG - chr6.4:3762949-3762968 None:intergenic 35.0%
!!! TTTTGTTTTCTTGGTGGTGA+AGG - chr6.4:3762943-3762962 None:intergenic 35.0%
ACAAGAGCTCACATAACAGT+TGG + chr6.4:3764410-3764429 MS.gene66983:CDS 40.0%
ACACACACATCCACAATGTT+TGG - chr6.4:3764128-3764147 None:intergenic 40.0%
CACACACATCCACAATGTTT+GGG - chr6.4:3764127-3764146 None:intergenic 40.0%
TGGGAATCAATCTCTAGTGA+TGG + chr6.4:3762832-3762851 MS.gene66983:CDS 40.0%
TGTTAACTTTGTGGCAAGGA+TGG + chr6.4:3764237-3764256 MS.gene66983:intron 40.0%
TTATGGAAGTGGAGTCTTAG+TGG + chr6.4:3763258-3763277 MS.gene66983:CDS 40.0%
TTGTTAAGGCTGCAATCACA+TGG + chr6.4:3763690-3763709 MS.gene66983:intron 40.0%
! CACTTTCTGATCCTTTTCCT+AGG - chr6.4:3762897-3762916 None:intergenic 40.0%
! TGTTCTTTGGAAGCCAACAT+AGG + chr6.4:3763331-3763350 MS.gene66983:CDS 40.0%
! TTGAGGTGTTACCAAGTTTG+AGG - chr6.4:3762996-3763015 None:intergenic 40.0%
!! TAATGGCATGGTGCCATTAA+TGG + chr6.4:3764175-3764194 MS.gene66983:intron 40.0%
!!! GTTGGTGCTATTTGCACTTT+TGG + chr6.4:3763282-3763301 MS.gene66983:CDS 40.0%
AAGTGGAGTCTTAGTGGTGT+TGG + chr6.4:3763264-3763283 MS.gene66983:CDS 45.0%
AATGGCACCCAAGTATTTCC+CGG - chr6.4:3764066-3764085 None:intergenic 45.0%
AGAGCTCACATAACAGTTGG+TGG + chr6.4:3764413-3764432 MS.gene66983:CDS 45.0%
AGTATTTCAGGGTGGCACTT+TGG - chr6.4:3764203-3764222 None:intergenic 45.0%
CATCAATGGCCAGGATGTAA+TGG - chr6.4:3764101-3764120 None:intergenic 45.0%
CATTACATCCTGGCCATTGA+TGG + chr6.4:3764099-3764118 MS.gene66983:intron 45.0%
CTGATGTTTGTCGGAGAATC+TGG + chr6.4:3763511-3763530 MS.gene66983:intron 45.0%
GTTGAATCTCAGTCGATCGT+GGG + chr6.4:3763973-3763992 MS.gene66983:intron 45.0%
TGGGAAGTAGAGGACAATAG+TGG + chr6.4:3763228-3763247 MS.gene66983:CDS 45.0%
! CAATGTTTGGGTGCCATCAA+TGG - chr6.4:3764115-3764134 None:intergenic 45.0%
! CTGCAATCACATGGCAGTTT+TGG + chr6.4:3763699-3763718 MS.gene66983:intron 45.0%
! TGTGTGTGGTGGAGATCTAA+TGG + chr6.4:3764158-3764177 MS.gene66983:intron 45.0%
! TTGATGGCACCCAAACATTG+TGG + chr6.4:3764115-3764134 MS.gene66983:intron 45.0%
!! CTTTAGAGTTGGGGAGTTTG+TGG + chr6.4:3763756-3763775 MS.gene66983:intron 45.0%
!! GGATTCAAGTTGGGAAGTAG+AGG + chr6.4:3763218-3763237 MS.gene66983:CDS 45.0%
!! TAATGGCACGGTGCCATTAA+TGG - chr6.4:3764084-3764103 None:intergenic 45.0%
!! TGGCACTTTGGTGCCATTAA+TGG - chr6.4:3764191-3764210 None:intergenic 45.0%
ATGGCCAGGATGTAATGGCA+CGG - chr6.4:3764096-3764115 None:intergenic 50.0%
GGTTGAATCTCAGTCGATCG+TGG + chr6.4:3763972-3763991 MS.gene66983:intron 50.0%
GTGTGTGATGTGTGTGTGTG+TGG + chr6.4:3764144-3764163 MS.gene66983:intron 50.0%
TGTGATGTGTGTGTGTGTGG+TGG + chr6.4:3764147-3764166 MS.gene66983:intron 50.0%
! GTGGTGGAGATCTAATGGCA+TGG + chr6.4:3764163-3764182 MS.gene66983:intron 50.0%
! TTTGGGTGCCATCAATGGCC+AGG - chr6.4:3764110-3764129 None:intergenic 55.0%
! GGCACCGTGCCATTACATCC+TGG + chr6.4:3764089-3764108 MS.gene66983:intron 60.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 3762817 3764457 3762817 ID=MS.gene66983
chr6.4 mRNA 3762817 3764457 3762817 ID=MS.gene66983.t1;Parent=MS.gene66983
chr6.4 exon 3762817 3763407 3762817 ID=MS.gene66983.t1.exon1;Parent=MS.gene66983.t1
chr6.4 CDS 3762817 3763407 3762817 ID=cds.MS.gene66983.t1;Parent=MS.gene66983.t1
chr6.4 exon 3764338 3764457 3764338 ID=MS.gene66983.t1.exon2;Parent=MS.gene66983.t1
chr6.4 CDS 3764338 3764457 3764338 ID=cds.MS.gene66983.t1;Parent=MS.gene66983.t1
Gene Sequence

>MS.gene66983

ATGGATCTTGATGAATGGGAATCAATCTCTAGTGATGGCTATATTGATTTCAATGAAGATGGTGAGAAAAAAAGTTTCCTAGGAAAAGGATCAGAAAGTGCTTTAGACATGGAATATTTGTATCCTTCACCACCAAGAAAACAAAACCAACTTGTCCCTTTACAAATTCCATTAGACCTCAAACTTGGTAACACCTCAAATGATGTTATGGTTCAAGACATCACAAAGAATCAATCTCTTGAAGCTGATCAAGAAGAAAATGTGTCACAAGTTTTCTTTAAGATTAAGGAAAATGAAATTGGTGACATGAAAATTGAATCACCAAAGTCAAGTAGTAGCAAAGAGTTTATTACTTCTCCAAGAATGATTATTGAGAAAGATGATTTTGGTGACAAAGAAGAGGATTCAAGTTGGGAAGTAGAGGACAATAGTGGTTTCAATTTATGGAAGTGGAGTCTTAGTGGTGTTGGTGCTATTTGCACTTTTGGTGTTGTTGCTGCTTCTATTTGTGTTTTGTTCTTTGGAAGCCAACATAGGAAAAAACTTCAGAAGGATCAGAAGAATAGGTTTCAAATCTATGCTGATGACAAGGTTAGTAAATTTCTTGGTTTCAAATCATATATATTTTTTTGGTTTGCTTATAAATTAATTTGTTTGATTAATAGTACGAAGTATCTATCAACTTTGTCAATGACTGATGTTTGTCGGAGAATCTGGTTTAGTATAAATGGTTTAAATTATAGAAATTTATATTGATTTAGTATAGAATTTAGTCAAGATTTTAAATTGCTCTTGGTGTTACACTAATACACTTGAAAATAAGAAAAATTATAGACAAACAAAGTTTATGTAGCAATGATTTTAGTCATTATATTGTTAAGGCTGCAATCACATGGCAGTTTTGGAGACTTATGAAACCTTGTTAGTTGATTGATGATTCTTTAGAGTTGGGGAGTTTGTGGAGTCATAGTTAGCATGTATCGATCATCCGATAAATATTGATGACATTCGTTTATCAAATTTAAAATCTTAGTCATTTGATCTTGATCGGATATATTTGACTAATTGACTATGTGACTGTATAGATTCTCTAACTTTATGAAATTTGAATCTCCAATTGATACTCCAATTTATTTTTCGAATCAAAACAATCAGGGTTGAATCTCAGTCGATCGTGGGAGCAAAATCACCATGCCACTTATAATTGACTTTATGAAACACAACTGTATCATTTATTCAAGAAATACCGGGAAATACTTGGGTGCCATTAATGGCACCGTGCCATTACATCCTGGCCATTGATGGCACCCAAACATTGTGGATGTGTGTGTGTGATGTGTGTGTGTGTGGTGGAGATCTAATGGCATGGTGCCATTAATGGCACCAAAGTGCCACCCTGAAATACTATAGAGTAAAAAAGTGTTAACTTTGTGGCAAGGATGGAATTTTATTATATTTGGTTAAATATTCAATTGATTATGAGTTATTGTATATTGAACTAAACCTTGGTTTTGATTTCAGAGGATTAAGCAAGTGGTGCAGCATGCAACAAAATTGAATGAAGCAATTTCTGTTGTAAGAGGGGTTCCAATAACAAGAGCTCACATAACAGTTGGTGGCAACTATGATTTCTTTGATTGA

Protein sequence

>MS.gene66983.t1

MDLDEWESISSDGYIDFNEDGEKKSFLGKGSESALDMEYLYPSPPRKQNQLVPLQIPLDLKLGNTSNDVMVQDITKNQSLEADQEENVSQVFFKIKENEIGDMKIESPKSSSSKEFITSPRMIIEKDDFGDKEEDSSWEVEDNSGFNLWKWSLSGVGAICTFGVVAASICVLFFGSQHRKKLQKDQKNRFQIYADDKRIKQVVQHATKLNEAISVVRGVPITRAHITVGGNYDFFD