AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene97040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene97040.t1 MTR_2g049610 79.151 259 33 2 4 262 2 239 3.67e-151 421
MS.gene97040.t1 MTR_2g049630 60.324 247 76 3 1 245 1 227 5.34e-94 281
MS.gene97040.t1 MTR_2g049530 70.115 174 50 1 1 172 1 174 3.32e-83 247
MS.gene97040.t1 MTR_4g107170 46.154 221 104 5 1 214 1 213 3.65e-60 191
MS.gene97040.t1 MTR_4g045977 44.681 235 101 6 4 222 2 223 3.89e-56 185
MS.gene97040.t1 MTR_1g115290 47.159 176 65 5 40 210 2 154 9.39e-41 138
MS.gene97040.t1 MTR_6g018920 38.065 155 89 2 4 152 2 155 5.45e-31 118
MS.gene97040.t1 MTR_1g114730 39.103 156 88 2 4 153 2 156 1.10e-30 117
MS.gene97040.t1 MTR_6g005440 38.065 155 89 3 4 152 2 155 2.15e-29 113
MS.gene97040.t1 MTR_6g005450 34.463 177 109 3 4 174 2 177 1.47e-26 106
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAAATCCATCTATTGTTTC+TGG 0.138351 2.2:+37684026 None:intergenic
GCTTGATAATGTTGCATATT+TGG 0.161075 2.2:-37684111 MS.gene97040:CDS
GGAATGGGAAACTCAATTTA+TGG 0.183833 2.2:-37684063 MS.gene97040:CDS
ATGCAACAAAGTACTGAAAT+TGG 0.240043 2.2:-37684332 MS.gene97040:CDS
GTTGGTCCCCTTCCATGTTC+TGG 0.261192 2.2:+37684426 None:intergenic
TCTTTCACATCAAAGATCTT+TGG 0.287719 2.2:+37684545 None:intergenic
CACAATCTCTTTGTGCACTT+TGG 0.338528 2.2:+37684481 None:intergenic
TCCTGACCAGGTTTAGCAAC+TGG 0.388453 2.2:+37684083 None:intergenic
GTGATTACAAGCTTGAATCT+TGG 0.389216 2.2:+37684376 None:intergenic
CCTTCCATGTTCTGGAAACA+TGG 0.398902 2.2:+37684434 None:intergenic
TCATGGATATGTTGCATTTG+AGG 0.410645 2.2:+37684218 None:intergenic
GCTTTGCCAGAAACAATAGA+TGG 0.415718 2.2:-37684032 MS.gene97040:CDS
ACTTGGTGAAGTTGAAGAAT+TGG 0.421405 2.2:-37684162 MS.gene97040:CDS
CTATTAAACACATTCAAGAT+TGG 0.421571 2.2:-37684766 MS.gene97040:CDS
TGCTAAACCTGGTCAGGAAT+GGG 0.447809 2.2:-37684078 MS.gene97040:CDS
TGTGAGGAGACAACATTATT+CGG 0.449930 2.2:+37684272 None:intergenic
ATGTTGTCTCCTCACATTCA+AGG 0.456551 2.2:-37684265 MS.gene97040:CDS
TCCAGTTGCTAAACCTGGTC+AGG 0.458685 2.2:-37684084 MS.gene97040:CDS
CACTACTCAGACGCAAAATA+CGG 0.473414 2.2:-37684297 MS.gene97040:CDS
GAATCTTGTGGCATAATCAT+TGG 0.478340 2.2:+37684626 None:intergenic
TGAGTTTCCCATTCCTGACC+AGG 0.483105 2.2:+37684071 None:intergenic
TGGAAACATGGGTGCCAAGT+TGG 0.485421 2.2:+37684446 None:intergenic
GCACCCATGTTTCCAGAACA+TGG 0.507852 2.2:-37684438 MS.gene97040:CDS
CTTAGTGATATTAATCGACT+TGG 0.509147 2.2:-37684179 MS.gene97040:CDS
CAATCAAAGAAGCAATGGAT+TGG 0.512118 2.2:-37684723 MS.gene97040:CDS
TTGCTAAACCTGGTCAGGAA+TGG 0.512431 2.2:-37684079 MS.gene97040:CDS
TACGAGCAACAAAAGATTGA+GGG 0.530722 2.2:-37684575 MS.gene97040:CDS
CTTCCATGTTCTGGAAACAT+GGG 0.531657 2.2:+37684435 None:intergenic
GTGGCTTCAAATGATCATCA+TGG 0.534306 2.2:+37684201 None:intergenic
GCTTGCTTAATTGTGTATGA+TGG 0.534651 2.2:-37684659 MS.gene97040:CDS
CCATGTTTCCAGAACATGGA+AGG 0.542103 2.2:-37684434 MS.gene97040:CDS
ATACGAGCAACAAAAGATTG+AGG 0.544317 2.2:-37684576 MS.gene97040:CDS
ACATTCAAGATTGGAGAGCT+CGG 0.553672 2.2:-37684757 MS.gene97040:CDS
ACTTTCAATCAAAGAAGCAA+TGG 0.559273 2.2:-37684728 MS.gene97040:CDS
TAGTTAATTTCCCACGAGCA+CGG 0.567005 2.2:+37684786 None:intergenic
TAGAAATGGGCCGTGCTCGT+GGG 0.584542 2.2:-37684796 None:intergenic
GATGATCCAGTTGCTAAACC+TGG 0.589750 2.2:-37684089 MS.gene97040:CDS
ATCAAGCTTCCTTGAATGTG+AGG 0.590592 2.2:+37684256 None:intergenic
CACAAGATTCGACAATTGTA+CGG 0.605972 2.2:-37684613 MS.gene97040:CDS
AGTCGATTAATATCACTAAG+TGG 0.606095 2.2:+37684182 None:intergenic
TTAATTGTGTATGATGGTGA+TGG 0.608708 2.2:-37684653 MS.gene97040:CDS
CGTACAATTGTCGAATCTTG+TGG 0.612214 2.2:+37684614 None:intergenic
ATGTTTCCAGAACATGGAAG+GGG 0.616673 2.2:-37684432 MS.gene97040:CDS
TGATGAAAATGTATCCAACT+TGG 0.619935 2.2:-37684460 MS.gene97040:CDS
CATGTTTCCAGAACATGGAA+GGG 0.620335 2.2:-37684433 MS.gene97040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CTATTAAACACATTCAAGAT+TGG - chr2.2:37684050-37684069 MS.gene97040:CDS 25.0%
! TAAAATCCATCTATTGTTTC+TGG + chr2.2:37684793-37684812 None:intergenic 25.0%
!! AATTGGATGATTTTATGGAT+TGG - chr2.2:37684671-37684690 MS.gene97040:CDS 25.0%
!! ATTGGATGATTTTATGGATT+GGG - chr2.2:37684672-37684691 MS.gene97040:CDS 25.0%
!! TGAAGAATTGGATGATTTTA+TGG - chr2.2:37684666-37684685 MS.gene97040:CDS 25.0%
ACTTTCAATCAAAGAAGCAA+TGG - chr2.2:37684088-37684107 MS.gene97040:CDS 30.0%
AGTCGATTAATATCACTAAG+TGG + chr2.2:37684637-37684656 None:intergenic 30.0%
CTTAGTGATATTAATCGACT+TGG - chr2.2:37684637-37684656 MS.gene97040:CDS 30.0%
TCTTTCACATCAAAGATCTT+TGG + chr2.2:37684274-37684293 None:intergenic 30.0%
TGATGAAAATGTATCCAACT+TGG - chr2.2:37684356-37684375 MS.gene97040:CDS 30.0%
! TTAATTGTGTATGATGGTGA+TGG - chr2.2:37684163-37684182 MS.gene97040:CDS 30.0%
!! ATGCAACAAAGTACTGAAAT+TGG - chr2.2:37684484-37684503 MS.gene97040:CDS 30.0%
!! GCTTGATAATGTTGCATATT+TGG - chr2.2:37684705-37684724 MS.gene97040:CDS 30.0%
!! TCTGAATTTTCTAGCAAGTT+TGG - chr2.2:37684127-37684146 MS.gene97040:CDS 30.0%
!!! TCGCAATAAAAGTTTTGAGT+TGG + chr2.2:37684411-37684430 None:intergenic 30.0%
ATACGAGCAACAAAAGATTG+AGG - chr2.2:37684240-37684259 MS.gene97040:CDS 35.0%
CAATCAAAGAAGCAATGGAT+TGG - chr2.2:37684093-37684112 MS.gene97040:CDS 35.0%
CACAAGATTCGACAATTGTA+CGG - chr2.2:37684203-37684222 MS.gene97040:CDS 35.0%
GAATCTTGTGGCATAATCAT+TGG + chr2.2:37684193-37684212 None:intergenic 35.0%
GCTTGCTTAATTGTGTATGA+TGG - chr2.2:37684157-37684176 MS.gene97040:CDS 35.0%
GGAATGGGAAACTCAATTTA+TGG - chr2.2:37684753-37684772 MS.gene97040:CDS 35.0%
GTGATTACAAGCTTGAATCT+TGG + chr2.2:37684443-37684462 None:intergenic 35.0%
TACGAGCAACAAAAGATTGA+GGG - chr2.2:37684241-37684260 MS.gene97040:CDS 35.0%
TCATGGATATGTTGCATTTG+AGG + chr2.2:37684601-37684620 None:intergenic 35.0%
TGTGAGGAGACAACATTATT+CGG + chr2.2:37684547-37684566 None:intergenic 35.0%
! ACTTGGTGAAGTTGAAGAAT+TGG - chr2.2:37684654-37684673 MS.gene97040:CDS 35.0%
!!! TTGCTCGTATTTTTCAAGCA+TGG + chr2.2:37684230-37684249 None:intergenic 35.0%
ACATTCAAGATTGGAGAGCT+CGG - chr2.2:37684059-37684078 MS.gene97040:CDS 40.0%
ATCAAGCTTCCTTGAATGTG+AGG + chr2.2:37684563-37684582 None:intergenic 40.0%
ATGTTGTCTCCTCACATTCA+AGG - chr2.2:37684551-37684570 MS.gene97040:CDS 40.0%
ATGTTTCCAGAACATGGAAG+GGG - chr2.2:37684384-37684403 MS.gene97040:CDS 40.0%
CACAATCTCTTTGTGCACTT+TGG + chr2.2:37684338-37684357 None:intergenic 40.0%
CACTACTCAGACGCAAAATA+CGG - chr2.2:37684519-37684538 MS.gene97040:CDS 40.0%
CATGTTTCCAGAACATGGAA+GGG - chr2.2:37684383-37684402 MS.gene97040:CDS 40.0%
CGTACAATTGTCGAATCTTG+TGG + chr2.2:37684205-37684224 None:intergenic 40.0%
GCTTTGCCAGAAACAATAGA+TGG - chr2.2:37684784-37684803 MS.gene97040:CDS 40.0%
GTGGCTTCAAATGATCATCA+TGG + chr2.2:37684618-37684637 None:intergenic 40.0%
TAGTTAATTTCCCACGAGCA+CGG + chr2.2:37684033-37684052 None:intergenic 40.0%
!! CTTCCATGTTCTGGAAACAT+GGG + chr2.2:37684384-37684403 None:intergenic 40.0%
CCATGTTTCCAGAACATGGA+AGG - chr2.2:37684382-37684401 MS.gene97040:CDS 45.0%
GATGATCCAGTTGCTAAACC+TGG - chr2.2:37684727-37684746 MS.gene97040:CDS 45.0%
TGCTAAACCTGGTCAGGAAT+GGG - chr2.2:37684738-37684757 MS.gene97040:CDS 45.0%
TTGCTAAACCTGGTCAGGAA+TGG - chr2.2:37684737-37684756 MS.gene97040:CDS 45.0%
!! CCTTCCATGTTCTGGAAACA+TGG + chr2.2:37684385-37684404 None:intergenic 45.0%
GCACCCATGTTTCCAGAACA+TGG - chr2.2:37684378-37684397 MS.gene97040:CDS 50.0%
TCCAGTTGCTAAACCTGGTC+AGG - chr2.2:37684732-37684751 MS.gene97040:CDS 50.0%
TCCTGACCAGGTTTAGCAAC+TGG + chr2.2:37684736-37684755 None:intergenic 50.0%
TGAGTTTCCCATTCCTGACC+AGG + chr2.2:37684748-37684767 None:intergenic 50.0%
TGGAAACATGGGTGCCAAGT+TGG + chr2.2:37684373-37684392 None:intergenic 50.0%
GTTGGTCCCCTTCCATGTTC+TGG + chr2.2:37684393-37684412 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 37684025 37684813 37684025 ID=MS.gene97040
chr2.2 mRNA 37684025 37684813 37684025 ID=MS.gene97040.t1;Parent=MS.gene97040
chr2.2 exon 37684025 37684813 37684025 ID=MS.gene97040.t1.exon1;Parent=MS.gene97040.t1
chr2.2 CDS 37684025 37684813 37684025 ID=cds.MS.gene97040.t1;Parent=MS.gene97040.t1
Gene Sequence

>MS.gene97040

ATGGGCCGTGCTCGTGGGAAATTAACTATTAAACACATTCAAGATTGGAGAGCTCGGAAATCAACTTTCAATCAAAGAAGCAATGGATTGGCAAAAAAAGTTTCTGAATTTTCTAGCAAGTTTGGAGTTGAAGCTTGCTTAATTGTGTATGATGGTGATGGTAGACCAATGATTATGCCACAAGATTCGACAATTGTACGGTCCATGCTTGAAAAATACGAGCAACAAAAGATTGAGGGTACAACTCCAAAGATCTTTGATGTGAAAGACTATTTTGCAAATAAGAAGAATAAGATTGAAGCTGATATTTCCAAAGTGCACAAAGAGATTGTGATGAAAATGTATCCAACTTGGCACCCATGTTTCCAGAACATGGAAGGGGACCAACTCAAAACTTTTATTGCGATTGTAGATGCCAAGATTCAAGCTTGTAATCACAAAATTAACATGCTAAAGAAAATGCAACAAAGTACTGAAATTGGTTTCATGCTAAACACTACTCAGACGCAAAATACGGCTCCGAATAATGTTGTCTCCTCACATTCAAGGAAGCTTGATGTCACTGATAGATTTCCTCAAATGCAACATATCCATGATGATCATTTGAAGCCACTTAGTGATATTAATCGACTTGGTGAAGTTGAAGAATTGGATGATTTTATGGATTGGGCTAATCAAGTGCTTGATAATGTTGCATATTTGGATGATCCAGTTGCTAAACCTGGTCAGGAATGGGAAACTCAATTTATGGATTTTGATGCTTTGCCAGAAACAATAGATGGATTTTAA
Protein sequence

>MS.gene97040.t1

MGRARGKLTIKHIQDWRARKSTFNQRSNGLAKKVSEFSSKFGVEACLIVYDGDGRPMIMPQDSTIVRSMLEKYEQQKIEGTTPKIFDVKDYFANKKNKIEADISKVHKEIVMKMYPTWHPCFQNMEGDQLKTFIAIVDAKIQACNHKINMLKKMQQSTEIGFMLNTTQTQNTAPNNVVSSHSRKLDVTDRFPQMQHIHDDHLKPLSDINRLGEVEELDDFMDWANQVLDNVAYLDDPVAKPGQEWETQFMDFDALPETIDGF