AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene024857

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene024857.t1 MTR_5g006470 93.085 188 13 0 1 188 1 188 5.86e-131 365
MS.gene024857.t1 MTR_5g006450 78.421 190 39 1 1 188 1 190 5.65e-104 297
MS.gene024857.t1 MTR_5g006460 77.436 195 35 6 1 188 1 193 2.27e-99 285
MS.gene024857.t1 MTR_5g006520 76.316 190 43 1 1 188 1719 1908 4.24e-96 305
MS.gene024857.t1 MTR_5g006510 72.778 180 44 3 12 188 14 191 5.60e-90 261
MS.gene024857.t1 MTR_1g103110 64.737 190 65 1 1 188 1 190 4.44e-86 251
MS.gene024857.t1 MTR_1g103150 63.158 190 68 1 1 188 1 190 1.38e-84 248
MS.gene024857.t1 MTR_7g114410 44.970 169 92 1 17 185 4 171 1.00e-46 151
MS.gene024857.t1 MTR_7g024780 42.941 170 95 2 16 185 3 170 6.21e-42 139
MS.gene024857.t1 MTR_7g114410 44.156 154 85 1 17 170 4 156 2.74e-41 137
MS.gene024857.t1 MTR_3g463610 42.442 172 95 2 17 185 3 173 5.60e-41 138
MS.gene024857.t1 MTR_7g024760 41.566 166 94 2 20 185 7 169 2.33e-39 132
MS.gene024857.t1 MTR_7g024765 41.566 166 94 2 20 185 7 169 2.28e-38 130
MS.gene024857.t1 MTR_1g103320 49.367 79 40 0 51 129 11 89 5.45e-20 81.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene024857.t1 AT2G32020 54.491 167 71 3 20 185 18 180 3.78e-57 178
MS.gene024857.t1 AT2G32030 51.381 181 75 4 6 185 17 185 1.79e-56 176
MS.gene024857.t1 AT3G22560 39.535 172 101 2 16 185 2 172 7.81e-37 126

Find 39 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAATCAATGATCTCTTCTT+TGG 0.196407 5.3:+1585580 None:intergenic
GGGAGTTCTTAGGAAGTATT+TGG 0.241791 5.3:-1585135 MS.gene024857:CDS
CTCTTCTTTGGCACATGGTT+TGG 0.246122 5.3:+1585592 None:intergenic
ATAATCTAAGCTCTATATAT+TGG 0.258828 5.3:-1585304 MS.gene024857:CDS
TCCTAAGAACTCCCTCCTTT+TGG 0.260104 5.3:+1585144 None:intergenic
ATCAAGGTCAGAAAGATTAA+AGG 0.290557 5.3:+1585538 None:intergenic
TAATCTAAGCTCTATATATT+GGG 0.291812 5.3:-1585303 MS.gene024857:CDS
GTTGATGCCATCTTCTTTGC+TGG 0.294680 5.3:+1585454 None:intergenic
AGGTTCCCATGAGCAGAATT+TGG 0.303996 5.3:+1585481 None:intergenic
TGCTGTGAAACAAATTATTA+AGG 0.312252 5.3:-1585261 MS.gene024857:CDS
CCATCTTCTTTGCTGGTGTA+AGG 0.323803 5.3:+1585461 None:intergenic
AAAATGAAACTTATTAAAGT+TGG 0.351635 5.3:+1585057 None:intergenic
TCTCCAAGTATGAAAATTCA+TGG 0.373432 5.3:+1585231 None:intergenic
TCCAAAAGGAGGGAGTTCTT+AGG 0.394554 5.3:-1585145 MS.gene024857:CDS
TAAAGGGTCGGAGTGTGATT+TGG 0.396804 5.3:+1585555 None:intergenic
TGCATTGATGATCGTGCTAT+TGG 0.407515 5.3:-1585386 MS.gene024857:CDS
AGGAAACAATCTGCAGAACT+TGG 0.436712 5.3:-1585329 MS.gene024857:CDS
TTCTGACCTTGATGATGTAA+TGG 0.440976 5.3:-1585528 MS.gene024857:CDS
TCAAGGTCAGAAAGATTAAA+GGG 0.477441 5.3:+1585539 None:intergenic
CTTGTCGATGTTGAAAATGT+TGG 0.484592 5.3:-1585197 MS.gene024857:CDS
GCTCTATATATTGGGGCAAA+GGG 0.493310 5.3:-1585295 MS.gene024857:CDS
CAAAGAGTGTTGGAGAAAGC+TGG 0.499760 5.3:-1585170 MS.gene024857:CDS
AGCTCTATATATTGGGGCAA+AGG 0.501996 5.3:-1585296 MS.gene024857:CDS
TTGTCGATGTTGAAAATGTT+GGG 0.503194 5.3:-1585196 MS.gene024857:CDS
AAGTGGCCAAATTCTGCTCA+TGG 0.511724 5.3:-1585487 MS.gene024857:CDS
AGGAAGTATTTGGTCATGAA+AGG 0.520639 5.3:-1585125 MS.gene024857:CDS
ATGATCTCTTCTTTGGCACA+TGG 0.535452 5.3:+1585587 None:intergenic
GGAGAAAGCTGGTTTCCAAA+AGG 0.547990 5.3:-1585159 MS.gene024857:CDS
CCTTACACCAGCAAAGAAGA+TGG 0.560893 5.3:-1585461 MS.gene024857:CDS
GAAAGCTGGTTTCCAAAAGG+AGG 0.562242 5.3:-1585156 MS.gene024857:CDS
TGTTGGGTCACAAAGAGTGT+TGG 0.566749 5.3:-1585180 MS.gene024857:CDS
AGTGGCCAAATTCTGCTCAT+GGG 0.587986 5.3:-1585486 MS.gene024857:CDS
AATCTAAGCTCTATATATTG+GGG 0.593409 5.3:-1585302 MS.gene024857:CDS
GCCACACCATTACATCATCA+AGG 0.594693 5.3:+1585522 None:intergenic
GGTCAGAAAGATTAAAGGGT+CGG 0.596865 5.3:+1585543 None:intergenic
TCACACCTGAAGATAAAAGC+AGG 0.598275 5.3:-1585349 MS.gene024857:CDS
GTGGCATACTGATGATAAAG+TGG 0.623600 5.3:-1585504 MS.gene024857:CDS
AAAGCTGGTTTCCAAAAGGA+GGG 0.657724 5.3:-1585155 MS.gene024857:CDS
ACCTTGATGATGTAATGGTG+TGG 0.686805 5.3:-1585523 MS.gene024857:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATCTAAGCTCTATATAT+TGG - chr5.3:1585380-1585399 MS.gene024857:CDS 20.0%
!! TAATCTAAGCTCTATATATT+GGG - chr5.3:1585381-1585400 MS.gene024857:CDS 20.0%
! AATCTAAGCTCTATATATTG+GGG - chr5.3:1585382-1585401 MS.gene024857:CDS 25.0%
! TGCTGTGAAACAAATTATTA+AGG - chr5.3:1585423-1585442 MS.gene024857:CDS 25.0%
!! ATTCCATGAATTTTCATACT+TGG - chr5.3:1585450-1585469 MS.gene024857:CDS 25.0%
ATCAAGGTCAGAAAGATTAA+AGG + chr5.3:1585149-1585168 None:intergenic 30.0%
CAAATCAATGATCTCTTCTT+TGG + chr5.3:1585107-1585126 None:intergenic 30.0%
TCAAGGTCAGAAAGATTAAA+GGG + chr5.3:1585148-1585167 None:intergenic 30.0%
TCTCCAAGTATGAAAATTCA+TGG + chr5.3:1585456-1585475 None:intergenic 30.0%
TTGTCGATGTTGAAAATGTT+GGG - chr5.3:1585488-1585507 MS.gene024857:CDS 30.0%
! ATGAATTTTCATACTTGGAG+AGG - chr5.3:1585455-1585474 MS.gene024857:CDS 30.0%
CTTGTCGATGTTGAAAATGT+TGG - chr5.3:1585487-1585506 MS.gene024857:CDS 35.0%
!! AGGAAGTATTTGGTCATGAA+AGG - chr5.3:1585559-1585578 MS.gene024857:CDS 35.0%
!! TGTTTCCTGCTTTTATCTTC+AGG + chr5.3:1585343-1585362 None:intergenic 35.0%
!! TTCTGACCTTGATGATGTAA+TGG - chr5.3:1585156-1585175 MS.gene024857:CDS 35.0%
AGCTCTATATATTGGGGCAA+AGG - chr5.3:1585388-1585407 MS.gene024857:CDS 40.0%
AGGAAACAATCTGCAGAACT+TGG - chr5.3:1585355-1585374 MS.gene024857:CDS 40.0%
ATGATCTCTTCTTTGGCACA+TGG + chr5.3:1585100-1585119 None:intergenic 40.0%
GCTCTATATATTGGGGCAAA+GGG - chr5.3:1585389-1585408 MS.gene024857:CDS 40.0%
GGTCAGAAAGATTAAAGGGT+CGG + chr5.3:1585144-1585163 None:intergenic 40.0%
GTGGCATACTGATGATAAAG+TGG - chr5.3:1585180-1585199 MS.gene024857:CDS 40.0%
TCACACCTGAAGATAAAAGC+AGG - chr5.3:1585335-1585354 MS.gene024857:CDS 40.0%
! AAAGCTGGTTTCCAAAAGGA+GGG - chr5.3:1585529-1585548 MS.gene024857:CDS 40.0%
! TGCATTGATGATCGTGCTAT+TGG - chr5.3:1585298-1585317 MS.gene024857:CDS 40.0%
!! ACCTTGATGATGTAATGGTG+TGG - chr5.3:1585161-1585180 MS.gene024857:CDS 40.0%
!! GGGAGTTCTTAGGAAGTATT+TGG - chr5.3:1585549-1585568 MS.gene024857:CDS 40.0%
AAGTGGCCAAATTCTGCTCA+TGG - chr5.3:1585197-1585216 MS.gene024857:CDS 45.0%
AGGTTCCCATGAGCAGAATT+TGG + chr5.3:1585206-1585225 None:intergenic 45.0%
AGTGGCCAAATTCTGCTCAT+GGG - chr5.3:1585198-1585217 MS.gene024857:CDS 45.0%
CCATCTTCTTTGCTGGTGTA+AGG + chr5.3:1585226-1585245 None:intergenic 45.0%
CCTTACACCAGCAAAGAAGA+TGG - chr5.3:1585223-1585242 MS.gene024857:CDS 45.0%
CTCTTCTTTGGCACATGGTT+TGG + chr5.3:1585095-1585114 None:intergenic 45.0%
GCCACACCATTACATCATCA+AGG + chr5.3:1585165-1585184 None:intergenic 45.0%
GTTGATGCCATCTTCTTTGC+TGG + chr5.3:1585233-1585252 None:intergenic 45.0%
TAAAGGGTCGGAGTGTGATT+TGG + chr5.3:1585132-1585151 None:intergenic 45.0%
TCCAAAAGGAGGGAGTTCTT+AGG - chr5.3:1585539-1585558 MS.gene024857:CDS 45.0%
! GAAAGCTGGTTTCCAAAAGG+AGG - chr5.3:1585528-1585547 MS.gene024857:CDS 45.0%
! GGAGAAAGCTGGTTTCCAAA+AGG - chr5.3:1585525-1585544 MS.gene024857:CDS 45.0%
! TCCTAAGAACTCCCTCCTTT+TGG + chr5.3:1585543-1585562 None:intergenic 45.0%
! TGTTGGGTCACAAAGAGTGT+TGG - chr5.3:1585504-1585523 MS.gene024857:CDS 45.0%
!! CAAAGAGTGTTGGAGAAAGC+TGG - chr5.3:1585514-1585533 MS.gene024857:CDS 45.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 1585070 1585636 1585070 ID=MS.gene024857
chr5.3 mRNA 1585070 1585636 1585070 ID=MS.gene024857.t1;Parent=MS.gene024857
chr5.3 exon 1585070 1585636 1585070 ID=MS.gene024857.t1.exon1;Parent=MS.gene024857.t1
chr5.3 CDS 1585070 1585636 1585070 ID=cds.MS.gene024857.t1;Parent=MS.gene024857.t1
Gene Sequence

>MS.gene024857

ATGGAAGAAACTTTTATTTCTTCCAAACCATGTGCCAAAGAAGAGATCATTGATTTGAACCAAATCACACTCCGACCCTTTAATCTTTCTGACCTTGATGATGTAATGGTGTGGCATACTGATGATAAAGTGGCCAAATTCTGCTCATGGGAACCTTACACCAGCAAAGAAGATGGCATCAACTTCATTGAAAATATAGAAAGCAAGTTTCTATGTTGCAAAGCAATATGCATTGATGATCGTGCTATTGGTTGTATTCTTTTGTTCACACCTGAAGATAAAAGCAGGAAACAATCTGCAGAACTTGGCTATAATCTAAGCTCTATATATTGGGGCAAAGGGATTGTCACGTGTGCTGTGAAACAAATTATTAAGGTTGCATTCCATGAATTTTCATACTTGGAGAGGCTTGAAGCACTTGTCGATGTTGAAAATGTTGGGTCACAAAGAGTGTTGGAGAAAGCTGGTTTCCAAAAGGAGGGAGTTCTTAGGAAGTATTTGGTCATGAAAGGAAAAAGCAGAGATATGATCATGTTTAGTGTTCTTTCTACTGATCTCCAACTTTAA
Protein sequence

>MS.gene024857.t1

MEETFISSKPCAKEEIIDLNQITLRPFNLSDLDDVMVWHTDDKVAKFCSWEPYTSKEDGINFIENIESKFLCCKAICIDDRAIGCILLFTPEDKSRKQSAELGYNLSSIYWGKGIVTCAVKQIIKVAFHEFSYLERLEALVDVENVGSQRVLEKAGFQKEGVLRKYLVMKGKSRDMIMFSVLSTDLQL