AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene042558

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene042558.t1 MTR_6g011450 63.462 156 38 2 44 180 465 620 5.65e-56 187
MS.gene042558.t1 MTR_6g011470 61.538 156 13 3 44 180 28 155 1.84e-55 174
MS.gene042558.t1 MTR_6g011450 63.462 156 38 2 44 180 603 758 2.31e-55 187
MS.gene042558.t1 MTR_4g073340 76.923 104 24 0 43 146 283 386 9.91e-53 176
MS.gene042558.t1 MTR_1g061130 38.596 57 35 0 86 142 838 894 2.35e-11 62.0
MS.gene042558.t1 MTR_1g061130 38.596 57 35 0 86 142 838 894 2.54e-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.gene042558.t1 AT4G04885 55.172 145 46 2 55 180 591 735 5.42e-45 158
MS.gene042558.t1 AT1G66500 42.017 119 42 3 89 180 227 345 1.01e-20 88.6
MS.gene042558.t1 AT5G43620 65.517 58 19 1 89 145 220 277 1.24e-19 85.5

Find 39 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACGAACCTTGAGAATATT+TGG 0.171658 6.3:+21466293 None:intergenic
GTTACAAATGCCATTTCTTT+TGG 0.240735 6.3:-21467374 None:intergenic
GTGACTGCTGTGCTCATCTT+TGG 0.248435 6.3:+21466199 None:intergenic
GGTTGTTGGCTTGACGTATT+AGG 0.261888 6.3:+21466514 None:intergenic
ATCGCATATATAGGTGTCTT+TGG 0.354576 6.3:-21467226 MS.gene042558:CDS
TATGTAATTTGTGATTTATA+TGG 0.358933 6.3:-21466266 MS.gene042558:CDS
TATATAGGTGTCTTTGGAAC+CGG 0.377723 6.3:-21467220 MS.gene042558:CDS
GTCTTTGGAACCGGGCTATT+AGG 0.379584 6.3:-21467211 MS.gene042558:CDS
TGCCCAAGGTGTTATCTCAT+TGG 0.416501 6.3:-21466455 MS.gene042558:CDS
AAATTAGAATATCCAACAAT+TGG 0.418071 6.3:+21466493 None:intergenic
TCAAATGTTAAGACTGCTAC+AGG 0.421125 6.3:-21467340 MS.gene042558:intron
AATATCCAACAATTGGTTGT+TGG 0.433148 6.3:+21466500 None:intergenic
TTTGCAGTAATCGCATATAT+AGG 0.434152 6.3:-21467235 MS.gene042558:intron
ATTCTACCTCATCCGAATCT+TGG 0.451748 6.3:-21466538 MS.gene042558:CDS
GCTCATCTTTGGATTTGAAT+CGG 0.471012 6.3:+21466210 None:intergenic
TCAAGCCAACAACCAATTGT+TGG 0.475162 6.3:-21466505 MS.gene042558:CDS
GCTAAAAGGTGCAGAGACAT+TGG 0.487532 6.3:-21466090 MS.gene042558:intron
GACGTATTAGGACCAAGATT+CGG 0.494335 6.3:+21466526 None:intergenic
ATTGATTTAGTTACCTTCGC+AGG 0.505170 6.3:+21466421 None:intergenic
TTGGGAGTTAAGTCAACTCC+AGG 0.511970 6.3:-21466071 MS.gene042558:CDS
CCACAAGTTGTGCATTGTCT+AGG 0.520332 6.3:+21466236 None:intergenic
CTAAAAGGTGCAGAGACATT+GGG 0.523678 6.3:-21466089 MS.gene042558:intron
AGAAAATAAAGATGAAGAGT+TGG 0.524053 6.3:-21466024 MS.gene042558:CDS
CCTAGACAATGCACAACTTG+TGG 0.528311 6.3:-21466236 MS.gene042558:CDS
AGCACAGCAGTCACATGGAT+TGG 0.529243 6.3:-21466190 MS.gene042558:CDS
AGCCAATGAGATAACACCTT+GGG 0.530219 6.3:+21466453 None:intergenic
AAAGAAAGCGCCTAATAGCC+CGG 0.541200 6.3:+21467201 None:intergenic
CATCTTTGGATTTGAATCGG+TGG 0.563255 6.3:+21466213 None:intergenic
TTGATTTAGTTACCTTCGCA+GGG 0.565255 6.3:+21466422 None:intergenic
ATTAGTTCACTCATTGCCCA+AGG 0.573674 6.3:-21466469 MS.gene042558:CDS
GAATATTTGGATCAAACTCA+AGG 0.580223 6.3:+21466306 None:intergenic
ATATAGGTGTCTTTGGAACC+GGG 0.582674 6.3:-21467219 MS.gene042558:CDS
AGATGAGCACAGCAGTCACA+TGG 0.587427 6.3:-21466195 MS.gene042558:CDS
GTTTGATCCAAATATTCTCA+AGG 0.588305 6.3:-21466300 MS.gene042558:CDS
GGCTAATCAAGCCCCTGCGA+AGG 0.612023 6.3:-21466434 MS.gene042558:intron
TTAGGACCAAGATTCGGATG+AGG 0.644974 6.3:+21466532 None:intergenic
GTTGGCAGTTCCGTTCGATG+AGG 0.647423 6.3:-21466006 MS.gene042558:CDS
TAGCCAATGAGATAACACCT+TGG 0.659744 6.3:+21466452 None:intergenic
TGATTTAGTTACCTTCGCAG+GGG 0.687811 6.3:+21466423 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAATCATATTAACAACT+TGG + chr6.3:21466257-21466276 None:intergenic 15.0%
!!! ATTAATTCATTTGCAATTTT+TGG - chr6.3:21466678-21466697 MS.gene042558:intron 15.0%
!!! TATGTAATTTGTGATTTATA+TGG - chr6.3:21467102-21467121 MS.gene042558:intron 15.0%
!! AAATTAGAATATCCAACAAT+TGG + chr6.3:21466878-21466897 None:intergenic 20.0%
!! ACAGAATACAATAACAAAAT+TGG + chr6.3:21467025-21467044 None:intergenic 20.0%
!! AGTCTTAACATTTGAAAAAA+AGG + chr6.3:21466023-21466042 None:intergenic 20.0%
!! ATGTTTCTTGAACAAAAAAT+TGG + chr6.3:21466194-21466213 None:intergenic 20.0%
!!! AATATGATTTTAACTATGAC+CGG - chr6.3:21466264-21466283 MS.gene042558:CDS 20.0%
!!! TTTAAGTTGTTCATAATAAC+TGG - chr6.3:21466062-21466081 MS.gene042558:CDS 20.0%
!!! TTTTTTGAAGTAATTTCATG+TGG + chr6.3:21466407-21466426 None:intergenic 20.0%
! AGAAAATAAAGATGAAGAGT+TGG - chr6.3:21467344-21467363 MS.gene042558:CDS 25.0%
! ATAACTTATCCAATCATACT+CGG + chr6.3:21466628-21466647 None:intergenic 25.0%
! ATCATATTAACAACTTGGAA+AGG + chr6.3:21466252-21466271 None:intergenic 25.0%
! CAAAACATTAAAAGGAAAGA+AGG - chr6.3:21466350-21466369 MS.gene042558:intron 25.0%
! TCATTTCGCAAAACATTAAA+AGG - chr6.3:21466342-21466361 MS.gene042558:intron 25.0%
! TGTTATTGTATTCTGTTTGT+AGG - chr6.3:21467029-21467048 MS.gene042558:intron 25.0%
!! TTCTGTTTGTAGGATTTTAT+TGG - chr6.3:21467039-21467058 MS.gene042558:intron 25.0%
!!! ATATGATTTTAACTATGACC+GGG - chr6.3:21466265-21466284 MS.gene042558:CDS 25.0%
!!! CTCTTCATCTTTATTTTCTT+CGG + chr6.3:21467343-21467362 None:intergenic 25.0%
AAAAAGGAAGCCAAAAGAAA+TGG + chr6.3:21466007-21466026 None:intergenic 30.0%
AAATGAAGACTTAGGATACT+TGG + chr6.3:21466328-21466347 None:intergenic 30.0%
AAGTGAAGATGAAACTGATT+CGG + chr6.3:21466547-21466566 None:intergenic 30.0%
AATATCCAACAATTGGTTGT+TGG + chr6.3:21466871-21466890 None:intergenic 30.0%
ATCTATTCTGATGTTTCATG+TGG + chr6.3:21466475-21466494 None:intergenic 30.0%
GAATATTTGGATCAAACTCA+AGG + chr6.3:21467065-21467084 None:intergenic 30.0%
GTTTGATCCAAATATTCTCA+AGG - chr6.3:21467068-21467087 MS.gene042558:intron 30.0%
TAGTAATGAGATCTGAGAAA+AGG + chr6.3:21466101-21466120 None:intergenic 30.0%
TATAATCCATGGGAAAATTC+AGG + chr6.3:21466522-21466541 None:intergenic 30.0%
TTTGCAGTAATCGCATATAT+AGG - chr6.3:21466133-21466152 MS.gene042558:intron 30.0%
! TGATTCGGATTATAATCCAT+GGG + chr6.3:21466532-21466551 None:intergenic 30.0%
!! GCTTACAGTTTTTAGACATA+CGG + chr6.3:21467218-21467237 None:intergenic 30.0%
!! TGTTGATGATGCCAATTAAT+GGG - chr6.3:21466294-21466313 MS.gene042558:CDS 30.0%
!! TTGTTGATGATGCCAATTAA+TGG - chr6.3:21466293-21466312 MS.gene042558:CDS 30.0%
!!! TTCATCTTTATTTTCTTCGG+TGG + chr6.3:21467340-21467359 None:intergenic 30.0%
AAGGAAAGAAGGAAATCTAG+AGG - chr6.3:21466361-21466380 MS.gene042558:intron 35.0%
ACGCAATCAAGTAAAATGGA+AGG + chr6.3:21467001-21467020 None:intergenic 35.0%
ATCGCATATATAGGTGTCTT+TGG - chr6.3:21466142-21466161 MS.gene042558:intron 35.0%
CCTATTCCATACCAAAGAAT+CGG - chr6.3:21466755-21466774 MS.gene042558:intron 35.0%
CTTCAGTCACATAACTTACT+TGG + chr6.3:21466222-21466241 None:intergenic 35.0%
GCTCATCTTTGGATTTGAAT+CGG + chr6.3:21467161-21467180 None:intergenic 35.0%
TATTTGACAGTCGAGATTAG+AGG - chr6.3:21466597-21466616 MS.gene042558:intron 35.0%
TCAAATGTTAAGACTGCTAC+AGG - chr6.3:21466028-21466047 MS.gene042558:CDS 35.0%
TGACGAACCTTGAGAATATT+TGG + chr6.3:21467078-21467097 None:intergenic 35.0%
TGGAAATGAACCCCATTAAT+TGG + chr6.3:21466308-21466327 None:intergenic 35.0%
TGGTACGCAATCAAGTAAAA+TGG + chr6.3:21467005-21467024 None:intergenic 35.0%
TGGTGATCTTTGCAATAGTT+TGG - chr6.3:21466698-21466717 MS.gene042558:intron 35.0%
TTGATTTAGTTACCTTCGCA+GGG + chr6.3:21466949-21466968 None:intergenic 35.0%
TTGTTTCCGATTCTTTGGTA+TGG + chr6.3:21466764-21466783 None:intergenic 35.0%
! AAGAGTTGTTTCCGATTCTT+TGG + chr6.3:21466769-21466788 None:intergenic 35.0%
! ATTGATTTAGTTACCTTCGC+AGG + chr6.3:21466950-21466969 None:intergenic 35.0%
! GTTTTGCGAAATGAAGACTT+AGG + chr6.3:21466336-21466355 None:intergenic 35.0%
! TGATTACCTGAATTTTCCCA+TGG - chr6.3:21466513-21466532 MS.gene042558:CDS 35.0%
!! CTGATTCGGATTATAATCCA+TGG + chr6.3:21466533-21466552 None:intergenic 35.0%
!! GTTGATGATGCCAATTAATG+GGG - chr6.3:21466295-21466314 MS.gene042558:CDS 35.0%
!! TATATAGGTGTCTTTGGAAC+CGG - chr6.3:21466148-21466167 MS.gene042558:intron 35.0%
!! TTTATTTTCTTCGGTGGTCT+CGG + chr6.3:21467334-21467353 None:intergenic 35.0%
AGCCAATGAGATAACACCTT+GGG + chr6.3:21466918-21466937 None:intergenic 40.0%
ATTAGTTCACTCATTGCCCA+AGG - chr6.3:21466899-21466918 MS.gene042558:intron 40.0%
ATTCTACCTCATCCGAATCT+TGG - chr6.3:21466830-21466849 MS.gene042558:intron 40.0%
CATCTTTGGATTTGAATCGG+TGG + chr6.3:21467158-21467177 None:intergenic 40.0%
CCGATTCTTTGGTATGGAAT+AGG + chr6.3:21466758-21466777 None:intergenic 40.0%
CTTTGGTATGGAATAGGAAG+TGG + chr6.3:21466752-21466771 None:intergenic 40.0%
GACGTATTAGGACCAAGATT+CGG + chr6.3:21466845-21466864 None:intergenic 40.0%
GCATCATCAACAATGTTACC+CGG + chr6.3:21466286-21466305 None:intergenic 40.0%
TAGCCAATGAGATAACACCT+TGG + chr6.3:21466919-21466938 None:intergenic 40.0%
TCAAGCCAACAACCAATTGT+TGG - chr6.3:21466863-21466882 MS.gene042558:intron 40.0%
TGATTTAGTTACCTTCGCAG+GGG + chr6.3:21466948-21466967 None:intergenic 40.0%
! CTAAAAGGTGCAGAGACATT+GGG - chr6.3:21467279-21467298 MS.gene042558:intron 40.0%
!! ATATAGGTGTCTTTGGAACC+GGG - chr6.3:21466149-21466168 MS.gene042558:intron 40.0%
ACTCACAAACTACTTGCGAG+AGG + chr6.3:21467247-21467266 None:intergenic 45.0%
AGTGAGACGATGTGGCTAAA+AGG - chr6.3:21467264-21467283 MS.gene042558:intron 45.0%
AGTTTGTGAGTGAGACGATG+TGG - chr6.3:21467256-21467275 MS.gene042558:intron 45.0%
CCACAAGTTGTGCATTGTCT+AGG + chr6.3:21467135-21467154 None:intergenic 45.0%
CCTAGACAATGCACAACTTG+TGG - chr6.3:21467132-21467151 MS.gene042558:intron 45.0%
GATTCGGATGAGGTAGAATC+TGG + chr6.3:21466829-21466848 None:intergenic 45.0%
GGAATAGGAAGTGGCATAAC+AGG + chr6.3:21466743-21466762 None:intergenic 45.0%
TTAGGACCAAGATTCGGATG+AGG + chr6.3:21466839-21466858 None:intergenic 45.0%
TTGGGAGTTAAGTCAACTCC+AGG - chr6.3:21467297-21467316 MS.gene042558:intron 45.0%
! AGAATCTGGAGTAGAGCATG+TGG + chr6.3:21466815-21466834 None:intergenic 45.0%
! GAATCTGGAGTAGAGCATGT+GGG + chr6.3:21466814-21466833 None:intergenic 45.0%
! GCTAAAAGGTGCAGAGACAT+TGG - chr6.3:21467278-21467297 MS.gene042558:intron 45.0%
! TGCCCAAGGTGTTATCTCAT+TGG - chr6.3:21466913-21466932 MS.gene042558:intron 45.0%
!! AAAGAAAGCGCCTAATAGCC+CGG + chr6.3:21466170-21466189 None:intergenic 45.0%
!! GAGGAGTATCCGAGTATGAT+TGG - chr6.3:21466616-21466635 MS.gene042558:intron 45.0%
!! GGTTGTTGGCTTGACGTATT+AGG + chr6.3:21466857-21466876 None:intergenic 45.0%
AACAGGTCGTGCATTTGGCA+GGG + chr6.3:21466726-21466745 None:intergenic 50.0%
AGATGAGCACAGCAGTCACA+TGG - chr6.3:21467173-21467192 MS.gene042558:CDS 50.0%
AGCACAGCAGTCACATGGAT+TGG - chr6.3:21467178-21467197 MS.gene042558:CDS 50.0%
GGCATAACAGGTCGTGCATT+TGG + chr6.3:21466731-21466750 None:intergenic 50.0%
GTCTCGGTTGGCAAAAAACC+TGG + chr6.3:21467318-21467337 None:intergenic 50.0%
GTGACTGCTGTGCTCATCTT+TGG + chr6.3:21467172-21467191 None:intergenic 50.0%
TAACAGGTCGTGCATTTGGC+AGG + chr6.3:21466727-21466746 None:intergenic 50.0%
! TTTTCTTCGGTGGTCTCGGT+TGG + chr6.3:21467330-21467349 None:intergenic 50.0%
!! GTCTTTGGAACCGGGCTATT+AGG - chr6.3:21466157-21466176 MS.gene042558:intron 50.0%
ACAGGTCGTGCATTTGGCAG+GGG + chr6.3:21466725-21466744 None:intergenic 55.0%
GTTGGCAGTTCCGTTCGATG+AGG - chr6.3:21467362-21467381 MS.gene042558:CDS 55.0%
TTCCGACCTTTACCTCCAGC+TGG - chr6.3:21466788-21466807 MS.gene042558:intron 55.0%
AGTAGAGCATGTGGGCCAGC+TGG + chr6.3:21466806-21466825 None:intergenic 60.0%
CAGGTCGTGCATTTGGCAGG+GGG + chr6.3:21466724-21466743 None:intergenic 60.0%
GGCCAGCTGGAGGTAAAGGT+CGG + chr6.3:21466793-21466812 None:intergenic 60.0%
GGCTAATCAAGCCCCTGCGA+AGG - chr6.3:21466934-21466953 MS.gene042558:intron 60.0%
TGTGGGCCAGCTGGAGGTAA+AGG + chr6.3:21466797-21466816 None:intergenic 60.0%
AGAGCATGTGGGCCAGCTGG+AGG + chr6.3:21466803-21466822 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 21466001 21467389 21466001 ID=MS.gene042558
chr6.3 mRNA 21466001 21467389 21466001 ID=MS.gene042558.t1;Parent=MS.gene042558
chr6.3 exon 21467341 21467389 21467341 ID=MS.gene042558.t1.exon1;Parent=MS.gene042558.t1
chr6.3 CDS 21467341 21467389 21467341 ID=cds.MS.gene042558.t1;Parent=MS.gene042558.t1
chr6.3 exon 21467168 21467250 21467168 ID=MS.gene042558.t1.exon2;Parent=MS.gene042558.t1
chr6.3 CDS 21467168 21467250 21467168 ID=cds.MS.gene042558.t1;Parent=MS.gene042558.t1
chr6.3 exon 21466435 21466560 21466435 ID=MS.gene042558.t1.exon3;Parent=MS.gene042558.t1
chr6.3 CDS 21466435 21466560 21466435 ID=cds.MS.gene042558.t1;Parent=MS.gene042558.t1
chr6.3 exon 21466159 21466339 21466159 ID=MS.gene042558.t1.exon4;Parent=MS.gene042558.t1
chr6.3 CDS 21466159 21466339 21466159 ID=cds.MS.gene042558.t1;Parent=MS.gene042558.t1
chr6.3 exon 21466001 21466104 21466001 ID=MS.gene042558.t1.exon5;Parent=MS.gene042558.t1
chr6.3 CDS 21466001 21466104 21466001 ID=cds.MS.gene042558.t1;Parent=MS.gene042558.t1
Gene Sequence

>MS.gene042558

ATGCCATTTCTTTTGGCTTCCTTTTTTTCAAATGTTAAGACTGCTACAGGTTTGTTTCTACTTTAAGTTGTTCATAATAACTGGTGTGTTAATATTGCCTTTTCTCAGATCTCATTACTAATGTTTTTGATATTTGCAGTAATCGCATATATAGGTGTCTTTGGAACCGGGCTATTAGGCGCTTTCTTTTCCAATTTTTTGTTCAAGAAACATCATTTCCAAGTAAGTTATGTGACTGAAGAATGATACCTTTCCAAGTTGTTAATATGATTTTAACTATGACCGGGTAACATTGTTGATGATGCCAATTAATGGGGTTCATTTCCAAGTATCCTAAGTCTTCATTTCGCAAAACATTAAAAGGAAAGAAGGAAATCTAGAGGAACAATGATCTTCACATAAACCACATGAAATTACTTCAAAAAATTTCAACACAACGAAGAAAAGATAAATTTTTTAATTGTCAATAAGCCACATGAAACATCAGAATAGATTTTATTAATTGATGAATTTGATTACCTGAATTTTCCCATGGATTATAATCCGAATCAGTTTCATCTTCACTTTCAAAGTCATTATTTATAGCTTATAAAGTTTATTTGACAGTCGAGATTAGAGGAGTATCCGAGTATGATTGGATAAGTTATCATATTCATATACAATCACTTATTCGATGAATTAATTCATTTGCAATTTTTGGTGATCTTTGCAATAGTTTGGCCCCCTGCCAAATGCACGACCTGTTATGCCACTTCCTATTCCATACCAAAGAATCGGAAACAACTCTTTCCGACCTTTACCTCCAGCTGGCCCACATGCTCTACTCCAGATTCTACCTCATCCGAATCTTGGTCCTAATACGTCAAGCCAACAACCAATTGTTGGATATTCTAATTTGATTAGTTCACTCATTGCCCAAGGTGTTATCTCATTGGCTAATCAAGCCCCTGCGAAGGTAACTAAATCAATCGTTAGTTCAGTTTTTATATCACATTTTCCTTCCATTTTACTTGATTGCGTACCAATTTTGTTATTGTATTCTGTTTGTAGGATTTTATTGGCCTTGAGTTTGATCCAAATATTCTCAAGGTTCGTCATGAATATGTAATTTGTGATTTATATGGTGATTTTCCTAGACAATGCACAACTTGTGGCCACCGATTCAAATCCAAAGATGAGCACAGCAGTCACATGGATTGGCATGTGACAAAGAACCGTATGTCTAAAAACTGTAAGCAAAAGTCCTCTCGCAAGTAGTTTGTGAGTGAGACGATGTGGCTAAAAGGTGCAGAGACATTGGGAGTTAAGTCAACTCCAGGTTTTTTGCCAACCGAGACCACCGAAGAAAATAAAGATGAAGAGTTGGCAGTTCCGTTCGATGAGGATTAA
Protein sequence

>MS.gene042558.t1

MPFLLASFFSNVKTATVIAYIGVFGTGLLGAFFSNFLFKKHHFQILPHPNLGPNTSSQQPIVGYSNLISSLIAQGVISLANQAPAKDFIGLEFDPNILKVRHEYVICDLYGDFPRQCTTCGHRFKSKDEHSSHMDWHVTKNRMSKNCAETLGVKSTPGFLPTETTEENKDEELAVPFDED