AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene81344

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene81344.t1 MTR_5g095470 98.442 321 5 0 1 321 1 321 0.0 649
MS.gene81344.t1 MTR_3g058410 71.111 315 81 2 17 321 22 336 1.48e-159 449
MS.gene81344.t1 MTR_8g028040 60.839 286 108 1 36 321 17 298 6.02e-125 360
MS.gene81344.t1 MTR_5g023760 48.243 313 151 4 13 320 8 314 1.67e-95 286
MS.gene81344.t1 MTR_5g023760 49.007 302 144 3 13 309 8 304 8.45e-95 284
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene81344.t1 AT3G13110 64.308 325 104 3 5 321 71 391 5.48e-147 419
MS.gene81344.t1 AT1G55920 66.890 299 91 1 23 321 24 314 1.54e-145 412
MS.gene81344.t1 AT5G56760 61.567 268 102 1 55 321 45 312 4.81e-115 335
MS.gene81344.t1 AT4G35640 50.495 303 142 3 18 320 38 332 1.50e-94 285
MS.gene81344.t1 AT2G17640 54.104 268 117 2 53 320 34 295 2.07e-91 275

Find 70 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGCGCGGGAACTTGTATTT+TGG 0.185561 5.2:-80336668 MS.gene81344:CDS
GGAATCTTATCAAGTTTAAT+AGG 0.262166 5.2:+80336526 None:intergenic
GTTGGTGAAACTGCTGTTAT+TGG 0.286982 5.2:-80336784 MS.gene81344:CDS
AGCACCCCGTCACCAATCTT+TGG 0.296687 5.2:+80336694 None:intergenic
ATTGGTGACGGGGTGCTTAT+AGG 0.319174 5.2:-80336688 MS.gene81344:CDS
CAAGGTGTTGATCCCATATC+TGG 0.330087 5.2:+80337323 None:intergenic
CCTATCGCCATGTGCCTTAC+CGG 0.332998 5.2:+80336720 None:intergenic
TTCACACCAAGTTCCAGATA+TGG 0.353879 5.2:-80337336 MS.gene81344:CDS
AATCTTGTCACAGAAATCAT+TGG 0.355787 5.2:-80337172 MS.gene81344:CDS
TAATAGTAACTAGACAAAAT+TGG 0.360866 5.2:+80337201 None:intergenic
TTCTTTGAATTAGCATCAAC+AGG 0.364623 5.2:+80337396 None:intergenic
ATTGGTGATGGTGCTAAAAT+TGG 0.373817 5.2:-80336634 MS.gene81344:CDS
GAAATCATTGGAAACTGCTT+TGG 0.380279 5.2:-80337160 MS.gene81344:CDS
GACTACCGTTGTTGGGAATC+CGG 0.396009 5.2:-80336575 MS.gene81344:CDS
TTTGGGGTTGATATTCATCC+TGG 0.412211 5.2:-80336856 MS.gene81344:CDS
CATTGTTTCTTGAATTTCAA+AGG 0.417026 5.2:-80336976 MS.gene81344:CDS
GGGAATCCGGCTAAATTGAT+TGG 0.417683 5.2:-80336562 MS.gene81344:CDS
GCTCATAATTTGTGGTCAAA+TGG 0.421298 5.2:-80336925 MS.gene81344:CDS
GCACCCCGTCACCAATCTTT+GGG 0.424633 5.2:+80336695 None:intergenic
TATGATTCAGAATCGCGTTT+CGG 0.428319 5.2:-80336884 MS.gene81344:CDS
TAAGATTCCTAGCCACACTA+TGG 0.429403 5.2:-80336512 MS.gene81344:CDS
CTCCAAGGACTACCGTTGTT+GGG 0.430566 5.2:-80336582 MS.gene81344:CDS
TCACACCAAGTTCCAGATAT+GGG 0.433106 5.2:-80337335 MS.gene81344:CDS
CCTCCAAGGACTACCGTTGT+TGG 0.444028 5.2:-80336583 MS.gene81344:CDS
GGCGATAGGCACCCAAAGAT+TGG 0.446766 5.2:-80336706 MS.gene81344:CDS
TTCCCTCCAATCAATTTAGC+CGG 0.459568 5.2:+80336556 None:intergenic
TTCCCAACAACGGTAGTCCT+TGG 0.463382 5.2:+80336580 None:intergenic
AGTTGTGGAACAATCTGAAA+AGG 0.473399 5.2:-80337289 MS.gene81344:CDS
ATTCATCCTGGAGCTAAGAT+TGG 0.476533 5.2:-80336844 MS.gene81344:CDS
TGCTGGTTCAGTTGTGATCA+AGG 0.485621 5.2:-80336611 MS.gene81344:CDS
AGATCAGAAAGTGTTGTACT+AGG 0.509118 5.2:+80337099 None:intergenic
ATAGGGTAGCTCATAATTTG+TGG 0.510040 5.2:-80336933 MS.gene81344:CDS
CCACTTCCAATCTTAGCTCC+AGG 0.510730 5.2:+80336838 None:intergenic
CCTGGAGCTAAGATTGGAAG+TGG 0.517686 5.2:-80336838 MS.gene81344:CDS
TTGCACGGTGTGACGTTGGG+AGG 0.518697 5.2:-80336745 MS.gene81344:CDS
TTTAGCATGTCAAGCTCATA+GGG 0.523451 5.2:-80336950 MS.gene81344:CDS
GGTGTGACGTTGGGAGGGAC+CGG 0.524462 5.2:-80336739 MS.gene81344:CDS
GGGAATATTAAGATTGGTGA+TGG 0.534999 5.2:-80336646 MS.gene81344:CDS
TGAACATGACTTATACAAGC+AGG 0.543036 5.2:+80336997 None:intergenic
GATGGTGCTAAAATTGGTGC+TGG 0.548397 5.2:-80336628 MS.gene81344:CDS
GGCACCCAAAGATTGGTGAC+GGG 0.548991 5.2:-80336699 MS.gene81344:CDS
TGATCATGCAACTGGGATTG+TGG 0.549413 5.2:-80336806 MS.gene81344:CDS
CACTGCTTAATTTAACAGCA+AGG 0.553156 5.2:+80337130 None:intergenic
ATAATTTGTGGTCAAATGGA+AGG 0.554078 5.2:-80336921 MS.gene81344:CDS
TTGATCCCATATCTGGAACT+TGG 0.557376 5.2:+80337330 None:intergenic
CACAACTGAACTTGTATGCA+AGG 0.562621 5.2:+80337305 None:intergenic
GGAGGGACCGGTAAGGCACA+TGG 0.563182 5.2:-80336727 MS.gene81344:CDS
TGCACGGTGTGACGTTGGGA+GGG 0.567057 5.2:-80336744 MS.gene81344:CDS
GACGGGGTGCTTATAGGCGC+GGG 0.567274 5.2:-80336682 MS.gene81344:CDS
CCGGTAAGGCACATGGCGAT+AGG 0.568492 5.2:-80336720 MS.gene81344:CDS
CCAACAACGGTAGTCCTTGG+AGG 0.574914 5.2:+80336583 None:intergenic
CTTGCATACAAGTTCAGTTG+TGG 0.582578 5.2:-80337304 MS.gene81344:CDS
AATCCGGCTAAATTGATTGG+AGG 0.584845 5.2:-80336559 MS.gene81344:CDS
AGGCACCCAAAGATTGGTGA+CGG 0.586567 5.2:-80336700 MS.gene81344:CDS
TTATGTGTGGATGAAGATGC+AGG 0.590043 5.2:-80337253 MS.gene81344:CDS
TGACGGGGTGCTTATAGGCG+CGG 0.592802 5.2:-80336683 MS.gene81344:CDS
ACATGATCCATAGTGTGGCT+AGG 0.594971 5.2:+80336505 None:intergenic
GGAACAATCTGAAAAGGTTG+AGG 0.607641 5.2:-80337283 MS.gene81344:CDS
CATGCAACTGGGATTGTGGT+TGG 0.611902 5.2:-80336802 MS.gene81344:CDS
GACGTTGGGAGGGACCGGTA+AGG 0.614643 5.2:-80336734 MS.gene81344:CDS
ATCCGGCTAAATTGATTGGA+GGG 0.620898 5.2:-80336558 MS.gene81344:CDS
TCACATGAATGATCATCATG+TGG 0.621543 5.2:+80337366 None:intergenic
GAACATGACTTATACAAGCA+GGG 0.643802 5.2:+80336998 None:intergenic
GATAACATAATCATAAAACT+CGG 0.645462 5.2:+80336471 None:intergenic
TGATCAAGGAAGTTCCTCCA+AGG 0.647904 5.2:-80336597 MS.gene81344:CDS
TTGAGGATGAAGATTATGTG+TGG 0.651581 5.2:-80337266 MS.gene81344:CDS
GCACCCAAAGATTGGTGACG+GGG 0.678109 5.2:-80336698 MS.gene81344:CDS
CTGGAGCTAAGATTGGAAGT+GGG 0.679499 5.2:-80336837 MS.gene81344:CDS
GTGCAACATGATCCATAGTG+TGG 0.717179 5.2:+80336500 None:intergenic
TTTAGCCGGATTCCCAACAA+CGG 0.717753 5.2:+80336570 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATAACATAATCATAAAACT+CGG + chr5.2:80337411-80337430 None:intergenic 20.0%
!! TAATAGTAACTAGACAAAAT+TGG + chr5.2:80336681-80336700 None:intergenic 20.0%
!!! TGATCTTTTTGTTAGAATTT+TGG - chr5.2:80336797-80336816 MS.gene81344:CDS 20.0%
! GGAATCTTATCAAGTTTAAT+AGG + chr5.2:80337356-80337375 None:intergenic 25.0%
!! CATTGTTTCTTGAATTTCAA+AGG - chr5.2:80336903-80336922 MS.gene81344:CDS 25.0%
!!! ATTTTGGGGAATATTAAGAT+TGG - chr5.2:80337227-80337246 MS.gene81344:CDS 25.0%
AATCTTGTCACAGAAATCAT+TGG - chr5.2:80336707-80336726 MS.gene81344:CDS 30.0%
TTCTTTGAATTAGCATCAAC+AGG + chr5.2:80336486-80336505 None:intergenic 30.0%
! AATGATGTGTCTATTTTGCA+CGG - chr5.2:80337119-80337138 MS.gene81344:CDS 30.0%
! ATAATTTGTGGTCAAATGGA+AGG - chr5.2:80336958-80336977 MS.gene81344:CDS 30.0%
AGTTGTGGAACAATCTGAAA+AGG - chr5.2:80336590-80336609 MS.gene81344:CDS 35.0%
ATAGGGTAGCTCATAATTTG+TGG - chr5.2:80336946-80336965 MS.gene81344:CDS 35.0%
CACTGCTTAATTTAACAGCA+AGG + chr5.2:80336752-80336771 None:intergenic 35.0%
GAAATCATTGGAAACTGCTT+TGG - chr5.2:80336719-80336738 MS.gene81344:CDS 35.0%
GAACATGACTTATACAAGCA+GGG + chr5.2:80336884-80336903 None:intergenic 35.0%
GGGAATATTAAGATTGGTGA+TGG - chr5.2:80337233-80337252 MS.gene81344:CDS 35.0%
TATGATTCAGAATCGCGTTT+CGG - chr5.2:80336995-80337014 MS.gene81344:CDS 35.0%
TCACATGAATGATCATCATG+TGG + chr5.2:80336516-80336535 None:intergenic 35.0%
TGAACATGACTTATACAAGC+AGG + chr5.2:80336885-80336904 None:intergenic 35.0%
TTGAGGATGAAGATTATGTG+TGG - chr5.2:80336613-80336632 MS.gene81344:CDS 35.0%
TTTAGCATGTCAAGCTCATA+GGG - chr5.2:80336929-80336948 MS.gene81344:CDS 35.0%
! ATTTTGCTTGATCATGCAAC+TGG - chr5.2:80337065-80337084 MS.gene81344:CDS 35.0%
! GCTCATAATTTGTGGTCAAA+TGG - chr5.2:80336954-80336973 MS.gene81344:CDS 35.0%
! TTTTAGCATGTCAAGCTCAT+AGG - chr5.2:80336928-80336947 MS.gene81344:CDS 35.0%
! TTTTGCTTGATCATGCAACT+GGG - chr5.2:80337066-80337085 MS.gene81344:CDS 35.0%
!! AGATCAGAAAGTGTTGTACT+AGG + chr5.2:80336783-80336802 None:intergenic 35.0%
!! ATTGGTGATGGTGCTAAAAT+TGG - chr5.2:80337245-80337264 MS.gene81344:CDS 35.0%
AATCCGGCTAAATTGATTGG+AGG - chr5.2:80337320-80337339 MS.gene81344:CDS 40.0%
ATCCGGCTAAATTGATTGGA+GGG - chr5.2:80337321-80337340 MS.gene81344:CDS 40.0%
ATTCATCCTGGAGCTAAGAT+TGG - chr5.2:80337035-80337054 MS.gene81344:CDS 40.0%
CACAACTGAACTTGTATGCA+AGG + chr5.2:80336577-80336596 None:intergenic 40.0%
CTTGCATACAAGTTCAGTTG+TGG - chr5.2:80336575-80336594 MS.gene81344:CDS 40.0%
GGAACAATCTGAAAAGGTTG+AGG - chr5.2:80336596-80336615 MS.gene81344:CDS 40.0%
TAAGATTCCTAGCCACACTA+TGG - chr5.2:80337367-80337386 MS.gene81344:CDS 40.0%
TCACACCAAGTTCCAGATAT+GGG - chr5.2:80336544-80336563 MS.gene81344:CDS 40.0%
TTATGTGTGGATGAAGATGC+AGG - chr5.2:80336626-80336645 MS.gene81344:CDS 40.0%
TTCACACCAAGTTCCAGATA+TGG - chr5.2:80336543-80336562 MS.gene81344:CDS 40.0%
TTCCCTCCAATCAATTTAGC+CGG + chr5.2:80337326-80337345 None:intergenic 40.0%
! AATCGCGTTTCGGAAGTTTT+TGG - chr5.2:80337005-80337024 MS.gene81344:CDS 40.0%
! ATCGCGTTTCGGAAGTTTTT+GGG - chr5.2:80337006-80337025 MS.gene81344:CDS 40.0%
! GTTGGTGAAACTGCTGTTAT+TGG - chr5.2:80337095-80337114 MS.gene81344:CDS 40.0%
! TTGATCCCATATCTGGAACT+TGG + chr5.2:80336552-80336571 None:intergenic 40.0%
!! TTTGGGGTTGATATTCATCC+TGG - chr5.2:80337023-80337042 MS.gene81344:CDS 40.0%
ACATGATCCATAGTGTGGCT+AGG + chr5.2:80337377-80337396 None:intergenic 45.0%
CTGGAGCTAAGATTGGAAGT+GGG - chr5.2:80337042-80337061 MS.gene81344:CDS 45.0%
GGGAATCCGGCTAAATTGAT+TGG - chr5.2:80337317-80337336 MS.gene81344:CDS 45.0%
GTGCAACATGATCCATAGTG+TGG + chr5.2:80337382-80337401 None:intergenic 45.0%
TGATCAAGGAAGTTCCTCCA+AGG - chr5.2:80337282-80337301 MS.gene81344:CDS 45.0%
TGATCATGCAACTGGGATTG+TGG - chr5.2:80337073-80337092 MS.gene81344:CDS 45.0%
TTTAGCCGGATTCCCAACAA+CGG + chr5.2:80337312-80337331 None:intergenic 45.0%
! ATTTTGCACGGTGTGACGTT+GGG - chr5.2:80337131-80337150 MS.gene81344:CDS 45.0%
! GATGGTGCTAAAATTGGTGC+TGG - chr5.2:80337251-80337270 MS.gene81344:CDS 45.0%
! TATTTTGCACGGTGTGACGT+TGG - chr5.2:80337130-80337149 MS.gene81344:CDS 45.0%
! TCGCGTTTCGGAAGTTTTTG+GGG - chr5.2:80337007-80337026 MS.gene81344:CDS 45.0%
!! CAAGGTGTTGATCCCATATC+TGG + chr5.2:80336559-80336578 None:intergenic 45.0%
!! TGCTGGTTCAGTTGTGATCA+AGG - chr5.2:80337268-80337287 MS.gene81344:CDS 45.0%
AGGCACCCAAAGATTGGTGA+CGG - chr5.2:80337179-80337198 MS.gene81344:CDS 50.0%
CATGCAACTGGGATTGTGGT+TGG - chr5.2:80337077-80337096 MS.gene81344:CDS 50.0%
CCACTTCCAATCTTAGCTCC+AGG + chr5.2:80337044-80337063 None:intergenic 50.0%
CCTGGAGCTAAGATTGGAAG+TGG - chr5.2:80337041-80337060 MS.gene81344:CDS 50.0%
CTCCAAGGACTACCGTTGTT+GGG - chr5.2:80337297-80337316 MS.gene81344:CDS 50.0%
GACTACCGTTGTTGGGAATC+CGG - chr5.2:80337304-80337323 MS.gene81344:CDS 50.0%
TTCCCAACAACGGTAGTCCT+TGG + chr5.2:80337302-80337321 None:intergenic 50.0%
! AGGCGCGGGAACTTGTATTT+TGG - chr5.2:80337211-80337230 MS.gene81344:CDS 50.0%
! GCGCGGGAACTTGTATTTTG+GGG - chr5.2:80337213-80337232 MS.gene81344:CDS 50.0%
! GGCGCGGGAACTTGTATTTT+GGG - chr5.2:80337212-80337231 MS.gene81344:CDS 50.0%
!! ATTGGTGACGGGGTGCTTAT+AGG - chr5.2:80337191-80337210 MS.gene81344:CDS 50.0%
AGCACCCCGTCACCAATCTT+TGG + chr5.2:80337188-80337207 None:intergenic 55.0%
CCAACAACGGTAGTCCTTGG+AGG + chr5.2:80337299-80337318 None:intergenic 55.0%
CCTATCGCCATGTGCCTTAC+CGG + chr5.2:80337162-80337181 None:intergenic 55.0%
CCTCCAAGGACTACCGTTGT+TGG - chr5.2:80337296-80337315 MS.gene81344:CDS 55.0%
GCACCCCGTCACCAATCTTT+GGG + chr5.2:80337187-80337206 None:intergenic 55.0%
GGCGATAGGCACCCAAAGAT+TGG - chr5.2:80337173-80337192 MS.gene81344:CDS 55.0%
! GGCACCCAAAGATTGGTGAC+GGG - chr5.2:80337180-80337199 MS.gene81344:CDS 55.0%
!! GCACCCAAAGATTGGTGACG+GGG - chr5.2:80337181-80337200 MS.gene81344:CDS 55.0%
CCGGTAAGGCACATGGCGAT+AGG - chr5.2:80337159-80337178 MS.gene81344:CDS 60.0%
TGCACGGTGTGACGTTGGGA+GGG - chr5.2:80337135-80337154 MS.gene81344:CDS 60.0%
TTGCACGGTGTGACGTTGGG+AGG - chr5.2:80337134-80337153 MS.gene81344:CDS 60.0%
! TGACGGGGTGCTTATAGGCG+CGG - chr5.2:80337196-80337215 MS.gene81344:CDS 60.0%
GACGTTGGGAGGGACCGGTA+AGG - chr5.2:80337145-80337164 MS.gene81344:CDS 65.0%
GGAGGGACCGGTAAGGCACA+TGG - chr5.2:80337152-80337171 MS.gene81344:CDS 65.0%
GGTGTGACGTTGGGAGGGAC+CGG - chr5.2:80337140-80337159 MS.gene81344:CDS 65.0%
! GACGGGGTGCTTATAGGCGC+GGG - chr5.2:80337197-80337216 MS.gene81344:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 80336468 80337433 80336468 ID=MS.gene81344
chr5.2 mRNA 80336468 80337433 80336468 ID=MS.gene81344.t1;Parent=MS.gene81344
chr5.2 exon 80336468 80337433 80336468 ID=MS.gene81344.t1.exon1;Parent=MS.gene81344.t1
chr5.2 CDS 80336468 80337433 80336468 ID=cds.MS.gene81344.t1;Parent=MS.gene81344.t1
Gene Sequence

>MS.gene81344

ATGTCTGTTTCTTCTCCTGTTGATGCTAATTCAAAGAATCTTTTACCACATGATGATCATTCATGTGAAAAATTCTTCACACCAAGTTCCAGATATGGGATCAACACCTTGCATACAAGTTCAGTTGTGGAACAATCTGAAAAGGTTGAGGATGAAGATTATGTGTGGATGAAGATGCAGGAAGAAGCTAAAGTTGATGTCACTGCTGAACCAATTTTGTCTAGTTACTATTATGTTTCAATCTTGTCACAGAAATCATTGGAAACTGCTTTGGCTAATCACCTTGCTGTTAAATTAAGCAGTGTAAGTCTTCCTAGTACAACACTTTCTGATCTTTTTGTTAGAATTTTGGAATCTGATAAAGAAATTATGTATGCTATGAAAAATGATCTAAAAGCAGTTAATGAAAGAGACCCTGCTTGTATAAGTCATGTTCATTGTTTCTTGAATTTCAAAGGCTTTTTAGCATGTCAAGCTCATAGGGTAGCTCATAATTTGTGGTCAAATGGAAGGAAAATTTTAGCAGTTATGATTCAGAATCGCGTTTCGGAAGTTTTTGGGGTTGATATTCATCCTGGAGCTAAGATTGGAAGTGGGATTTTGCTTGATCATGCAACTGGGATTGTGGTTGGTGAAACTGCTGTTATTGGAAATGATGTGTCTATTTTGCACGGTGTGACGTTGGGAGGGACCGGTAAGGCACATGGCGATAGGCACCCAAAGATTGGTGACGGGGTGCTTATAGGCGCGGGAACTTGTATTTTGGGGAATATTAAGATTGGTGATGGTGCTAAAATTGGTGCTGGTTCAGTTGTGATCAAGGAAGTTCCTCCAAGGACTACCGTTGTTGGGAATCCGGCTAAATTGATTGGAGGGAAGAATAATCCTATTAAACTTGATAAGATTCCTAGCCACACTATGGATCATGTTGCACATATTTCCGAGTTTTATGATTATGTTATCTAG
Protein sequence

>MS.gene81344.t1

MSVSSPVDANSKNLLPHDDHSCEKFFTPSSRYGINTLHTSSVVEQSEKVEDEDYVWMKMQEEAKVDVTAEPILSSYYYVSILSQKSLETALANHLAVKLSSVSLPSTTLSDLFVRILESDKEIMYAMKNDLKAVNERDPACISHVHCFLNFKGFLACQAHRVAHNLWSNGRKILAVMIQNRVSEVFGVDIHPGAKIGSGILLDHATGIVVGETAVIGNDVSILHGVTLGGTGKAHGDRHPKIGDGVLIGAGTCILGNIKIGDGAKIGAGSVVIKEVPPRTTVVGNPAKLIGGKNNPIKLDKIPSHTMDHVAHISEFYDYVI