AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049041

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049041.t1 MTR_7g100010 99.301 143 1 0 1 143 1 143 4.64e-104 293
MS.gene049041.t1 MTR_8g102180 99.301 143 1 0 1 143 1 143 4.64e-104 293
MS.gene049041.t1 MTR_5g098940 42.029 138 80 0 3 140 2 139 9.50e-39 129
MS.gene049041.t1 MTR_1g025190 47.482 139 73 0 3 141 2 140 1.17e-38 128
MS.gene049041.t1 MTR_5g087820 41.791 134 78 0 3 136 26 159 8.53e-35 119
MS.gene049041.t1 MTR_8g077600 37.162 148 80 3 3 141 2 145 1.15e-30 108
MS.gene049041.t1 MTR_8g077600 35.484 93 47 3 3 86 2 90 1.40e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049041.t1 AT2G19790 90.141 142 14 0 1 142 1 142 2.48e-96 274
MS.gene049041.t1 AT1G47830 48.201 139 72 0 3 141 2 140 2.48e-39 129
MS.gene049041.t1 AT2G17380 41.727 139 81 0 3 141 2 140 1.62e-38 128
MS.gene049041.t1 AT4G35410 41.727 139 81 0 3 141 2 140 3.23e-37 125
MS.gene049041.t1 AT3G50860 39.583 144 82 1 3 141 2 145 5.28e-35 119
MS.gene049041.t1 AT3G50860 39.583 144 82 1 3 141 2 145 5.57e-35 119
MS.gene049041.t1 AT4G35410 45.361 97 53 0 3 99 2 98 2.05e-25 93.2

Find 21 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGAATGAGCTTGCTATTT+TGG 0.125124 4.2:-3030280 MS.gene049041:intron
GAAACCATGGATCGACATTT+TGG 0.210891 4.2:-3030237 MS.gene049041:CDS
GGGGATCCGATTCGTGTTAA+TGG 0.262612 4.2:-3031712 MS.gene049041:CDS
GAAGAACGACGAACACTTGA+AGG 0.412781 4.2:-3031636 MS.gene049041:CDS
GCAACTACAAAATTATATAT+AGG 0.415613 4.2:-3030670 MS.gene049041:CDS
TGTTCACCATTAACACGAAT+CGG 0.437301 4.2:+3031706 None:intergenic
TATCATGTTTCATTTAGAAA+AGG 0.473226 4.2:-3030016 MS.gene049041:CDS
TTCATAATACTGAGCAAGAC+GGG 0.525077 4.2:+3031671 None:intergenic
TCTGACTCCTATTCAGCTGA+TGG 0.529053 4.2:-3029929 MS.gene049041:CDS
TTCCTGGTTGGAGTTGATGA+CGG 0.536130 4.2:-3030629 MS.gene049041:CDS
CGCCGTCATCAACTCCAACC+AGG 0.570939 4.2:+3030627 None:intergenic
CCATGGTTTCGACTAAGAGA+TGG 0.572456 4.2:+3030250 None:intergenic
GGTCATGAATGGTTGTATTG+TGG 0.573456 4.2:-3029971 MS.gene049041:CDS
CCTCGCCCGTAATGAAAACC+AGG 0.578527 4.2:-3031595 MS.gene049041:intron
GTTGCCAAAATGTCGATCCA+TGG 0.581731 4.2:+3030233 None:intergenic
GTGTTAATGGTGAACAAACA+AGG 0.589164 4.2:-3031699 MS.gene049041:CDS
TTGGAGGAAATGGTCATGAA+TGG 0.600198 4.2:-3029982 MS.gene049041:CDS
CCATCTCTTAGTCGAAACCA+TGG 0.604583 4.2:-3030250 MS.gene049041:CDS
ATTCATAATACTGAGCAAGA+CGG 0.623435 4.2:+3031670 None:intergenic
TTCGTCGTTCTTCAACAGTG+AGG 0.697820 4.2:+3031646 None:intergenic
GGTTGGAGTTGATGACGGCG+AGG 0.701215 4.2:-3030624 MS.gene049041:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAATAAAATCAATTTGTTT+TGG + chr4.2:3030358-3030377 None:intergenic 10.0%
!! AAATTGGAAAGAAAAAAAAA+AGG + chr4.2:3030635-3030654 None:intergenic 15.0%
!! ATGAAAATAAAAGAAAAGAA+TGG + chr4.2:3030067-3030086 None:intergenic 15.0%
!! AAACAATGACAATATGAATT+AGG + chr4.2:3030122-3030141 None:intergenic 20.0%
!! ATATTTATCTACAATGAAAG+TGG + chr4.2:3031270-3031289 None:intergenic 20.0%
!! ATTTAAACATGTGATGAAAT+TGG + chr4.2:3030651-3030670 None:intergenic 20.0%
!! GCAACTACAAAATTATATAT+AGG - chr4.2:3030959-3030978 MS.gene049041:intron 20.0%
!! TATCATGTTTCATTTAGAAA+AGG - chr4.2:3031613-3031632 MS.gene049041:CDS 20.0%
!! TATGAATTAGGTAAAATTGA+AGG + chr4.2:3030110-3030129 None:intergenic 20.0%
!!! ATTCTAGTTGATTTATACAA+AGG - chr4.2:3031052-3031071 MS.gene049041:intron 20.0%
!!! TGAATATTTTTACTATAGAC+AGG - chr4.2:3030496-3030515 MS.gene049041:intron 20.0%
! AGAAACAAAAAATCAGTGTT+TGG + chr4.2:3031551-3031570 None:intergenic 25.0%
! ATTAGGTAAAATTGAAGGTA+AGG + chr4.2:3030105-3030124 None:intergenic 25.0%
! GGAAGAAAACAATAGAATTA+TGG + chr4.2:3031503-3031522 None:intergenic 25.0%
! TAAATAAGACATAGATGTCT+TGG - chr4.2:3030460-3030479 MS.gene049041:intron 25.0%
! TAGATTATATAATCTGTGAG+TGG - chr4.2:3030696-3030715 MS.gene049041:intron 25.0%
! TGTTTATTATTATTCAACCC+TGG - chr4.2:3030137-3030156 MS.gene049041:intron 25.0%
! TTGAATAATAAAGAATGACG+AGG + chr4.2:3030739-3030758 None:intergenic 25.0%
!!! AGAAAAGGTACATTTTATGT+TGG - chr4.2:3031628-3031647 MS.gene049041:CDS 25.0%
!!! CACTGTGTTATATTTTAGTT+GGG - chr4.2:3030607-3030626 MS.gene049041:intron 25.0%
AGAATTATGGAAGTAATGTG+AGG + chr4.2:3031490-3031509 None:intergenic 30.0%
AGTAAGAGAAAGTCAAAAGA+TGG + chr4.2:3030814-3030833 None:intergenic 30.0%
ATTCATAATACTGAGCAAGA+CGG + chr4.2:3029962-3029981 None:intergenic 30.0%
ATTCTTTATTATTCAACCCG+AGG - chr4.2:3030743-3030762 MS.gene049041:intron 30.0%
CCAACTAAAATATAACACAG+TGG + chr4.2:3030609-3030628 None:intergenic 30.0%
GCATATTGTGTTAAATAGTC+TGG - chr4.2:3031095-3031114 MS.gene049041:intron 30.0%
GGTTTATACCAGAAACATAA+GGG - chr4.2:3030848-3030867 MS.gene049041:intron 30.0%
TATAGACAGGAGATAATTGT+TGG - chr4.2:3030509-3030528 MS.gene049041:intron 30.0%
TGAGTGGAATGAAATTGAAA+TGG - chr4.2:3030712-3030731 MS.gene049041:intron 30.0%
TGGTTTATACCAGAAACATA+AGG - chr4.2:3030847-3030866 MS.gene049041:intron 30.0%
TTAACAAGACTAAGAACTTC+AGG + chr4.2:3031216-3031235 None:intergenic 30.0%
TTATTATTATTCAACCCTGG+AGG - chr4.2:3030140-3030159 MS.gene049041:intron 30.0%
TTTCATAATCTATCATGGAG+AGG + chr4.2:3030312-3030331 None:intergenic 30.0%
! ACATTTTATGTTGGAGGAAA+TGG - chr4.2:3031637-3031656 MS.gene049041:CDS 30.0%
! CATAAACACTTCTGAGAATA+TGG - chr4.2:3030238-3030257 MS.gene049041:CDS 30.0%
! CTAGTTGATTTATACAAAGG+CGG - chr4.2:3031055-3031074 MS.gene049041:intron 30.0%
! GCTGATTTCATAATCTATCA+TGG + chr4.2:3030317-3030336 None:intergenic 30.0%
!! AAAGGTACATTTTATGTTGG+AGG - chr4.2:3031631-3031650 MS.gene049041:CDS 30.0%
!! AACATACCTGGTTTTCATTA+CGG + chr4.2:3030043-3030062 None:intergenic 30.0%
!!! CCACTGTGTTATATTTTAGT+TGG - chr4.2:3030606-3030625 MS.gene049041:intron 30.0%
AAGTCAATCCCTTATGTTTC+TGG + chr4.2:3030859-3030878 None:intergenic 35.0%
AATCTATCATGGAGAGGTTA+TGG + chr4.2:3030306-3030325 None:intergenic 35.0%
AGCAAACTTGAATCCAAAGA+TGG + chr4.2:3030776-3030795 None:intergenic 35.0%
AGGTAAAATTGAAGGTAAGG+AGG + chr4.2:3030102-3030121 None:intergenic 35.0%
GAAAAGAATGGAAACATACC+TGG + chr4.2:3030055-3030074 None:intergenic 35.0%
GTGTTAATGGTGAACAAACA+AGG - chr4.2:3029930-3029949 MS.gene049041:CDS 35.0%
TCTACAATGAAAGTGGTACA+TGG + chr4.2:3031263-3031282 None:intergenic 35.0%
TCTTACTCATATTGATGCGT+TGG - chr4.2:3030827-3030846 MS.gene049041:intron 35.0%
TGTTCACCATTAACACGAAT+CGG + chr4.2:3029926-3029945 None:intergenic 35.0%
TTCATAATACTGAGCAAGAC+GGG + chr4.2:3029961-3029980 None:intergenic 35.0%
TTGAAGCTAAGTTCAGAAGA+TGG + chr4.2:3031528-3031547 None:intergenic 35.0%
! ATTATTCAACCCGAGGTTTT+AGG - chr4.2:3030750-3030769 MS.gene049041:intron 35.0%
! GTTTTATCCATCAGCTGAAT+AGG + chr4.2:3031710-3031729 None:intergenic 35.0%
! TGGCTGATACATTTTTGTCA+TGG - chr4.2:3030913-3030932 MS.gene049041:intron 35.0%
!! ACATACCTGGTTTTCATTAC+GGG + chr4.2:3030042-3030061 None:intergenic 35.0%
!!! CTATGCATCTTTGTTTTTCC+TGG - chr4.2:3030984-3031003 MS.gene049041:intron 35.0%
AAAAGATGGCCTAAAACCTC+GGG + chr4.2:3030800-3030819 None:intergenic 40.0%
AACTTTCTCTTCCCCAATTC+TGG + chr4.2:3030548-3030567 None:intergenic 40.0%
ACTTTCTCTTCCCCAATTCT+GGG + chr4.2:3030547-3030566 None:intergenic 40.0%
AGCTAAGTTCAGAAGATGGA+AGG + chr4.2:3031524-3031543 None:intergenic 40.0%
AGTGGTCATCACTATGTGAT+CGG - chr4.2:3031135-3031154 MS.gene049041:intron 40.0%
CAAAAGATGGCCTAAAACCT+CGG + chr4.2:3030801-3030820 None:intergenic 40.0%
CAATCTAATTGCTACCTCCA+GGG + chr4.2:3030157-3030176 None:intergenic 40.0%
CCAGTTTCTTTAGACAAGCA+AGG + chr4.2:3031166-3031185 None:intergenic 40.0%
CCTTGCTTGTCTAAAGAAAC+TGG - chr4.2:3031163-3031182 MS.gene049041:intron 40.0%
GGTCATGAATGGTTGTATTG+TGG - chr4.2:3031658-3031677 MS.gene049041:CDS 40.0%
TCAATCTAATTGCTACCTCC+AGG + chr4.2:3030158-3030177 None:intergenic 40.0%
TCTGCAAAATTGTCGACAGA+AGG + chr4.2:3031334-3031353 None:intergenic 40.0%
TGTATCAGCCAGATGAATCA+TGG + chr4.2:3030904-3030923 None:intergenic 40.0%
TTCCTTTCACACCCAGAATT+GGG - chr4.2:3030533-3030552 MS.gene049041:intron 40.0%
TTGGAGGAAATGGTCATGAA+TGG - chr4.2:3031647-3031666 MS.gene049041:CDS 40.0%
TTTCCTTTCACACCCAGAAT+TGG - chr4.2:3030532-3030551 MS.gene049041:intron 40.0%
! GAAACCATGGATCGACATTT+TGG - chr4.2:3031392-3031411 MS.gene049041:intron 40.0%
!!! GCAGAATGAGCTTGCTATTT+TGG - chr4.2:3031349-3031368 MS.gene049041:intron 40.0%
!!! GCATCTTTGTTTTTCCTGGT+TGG - chr4.2:3030988-3031007 MS.gene049041:intron 40.0%
CAAAGATGGCCTAAAACCTC+GGG + chr4.2:3030762-3030781 None:intergenic 45.0%
CCAAAGATGGCCTAAAACCT+CGG + chr4.2:3030763-3030782 None:intergenic 45.0%
CCATCTCTTAGTCGAAACCA+TGG - chr4.2:3031379-3031398 MS.gene049041:intron 45.0%
CCATGGTTTCGACTAAGAGA+TGG + chr4.2:3031382-3031401 None:intergenic 45.0%
GAAGAACGACGAACACTTGA+AGG - chr4.2:3029993-3030012 MS.gene049041:CDS 45.0%
GATCACATAGTGATGACCAC+TGG + chr4.2:3031136-3031155 None:intergenic 45.0%
GCTTTGATCTTACTGACCAG+TGG - chr4.2:3031117-3031136 MS.gene049041:intron 45.0%
GTTGCCAAAATGTCGATCCA+TGG + chr4.2:3031399-3031418 None:intergenic 45.0%
TCCTTTCACACCCAGAATTG+GGG - chr4.2:3030534-3030553 MS.gene049041:intron 45.0%
TCTGACTCCTATTCAGCTGA+TGG - chr4.2:3031700-3031719 MS.gene049041:CDS 45.0%
TCTGCTCACCATGATTCATC+TGG - chr4.2:3030893-3030912 MS.gene049041:intron 45.0%
TTCGTCGTTCTTCAACAGTG+AGG + chr4.2:3029986-3030005 None:intergenic 45.0%
!! TTCCTGGTTGGAGTTGATGA+CGG - chr4.2:3031000-3031019 MS.gene049041:intron 45.0%
!!! AGTTTGCTACCCGAGGTTTT+AGG - chr4.2:3030788-3030807 MS.gene049041:intron 45.0%
ACAGAGACTCTAGTCACAGC+AGG + chr4.2:3031431-3031450 None:intergenic 50.0%
TCCCCAATTCTGGGTGTGAA+AGG + chr4.2:3030538-3030557 None:intergenic 50.0%
! GGGGATCCGATTCGTGTTAA+TGG - chr4.2:3029917-3029936 MS.gene049041:CDS 50.0%
!! GGATCGACATTTTGGCAACG+TGG - chr4.2:3031400-3031419 MS.gene049041:intron 50.0%
!! GGATTCAAGTTTGCTACCCG+AGG - chr4.2:3030781-3030800 MS.gene049041:intron 50.0%
!!! CCGAGGTTTTAGGCCATCTT+TGG - chr4.2:3030760-3030779 MS.gene049041:intron 50.0%
CCTCGCCCGTAATGAAAACC+AGG - chr4.2:3030034-3030053 MS.gene049041:intron 55.0%
!! CCTGGTTTTCATTACGGGCG+AGG + chr4.2:3030037-3030056 None:intergenic 55.0%
CGCCGTCATCAACTCCAACC+AGG + chr4.2:3031005-3031024 None:intergenic 60.0%
!! GGTTGGAGTTGATGACGGCG+AGG - chr4.2:3031005-3031024 MS.gene049041:intron 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 3029915 3031736 3029915 ID=MS.gene049041
chr4.2 mRNA 3029915 3031736 3029915 ID=MS.gene049041.t1;Parent=MS.gene049041
chr4.2 exon 3031596 3031736 3031596 ID=MS.gene049041.t1.exon1;Parent=MS.gene049041.t1
chr4.2 CDS 3031596 3031736 3031596 ID=cds.MS.gene049041.t1;Parent=MS.gene049041.t1
chr4.2 exon 3030625 3030711 3030625 ID=MS.gene049041.t1.exon2;Parent=MS.gene049041.t1
chr4.2 CDS 3030625 3030711 3030625 ID=cds.MS.gene049041.t1;Parent=MS.gene049041.t1
chr4.2 exon 3030230 3030298 3030230 ID=MS.gene049041.t1.exon3;Parent=MS.gene049041.t1
chr4.2 CDS 3030230 3030298 3030230 ID=cds.MS.gene049041.t1;Parent=MS.gene049041.t1
chr4.2 exon 3029915 3030049 3029915 ID=MS.gene049041.t1.exon4;Parent=MS.gene049041.t1
chr4.2 CDS 3029915 3030049 3029915 ID=cds.MS.gene049041.t1;Parent=MS.gene049041.t1
Gene Sequence

>MS.gene049041

ATGGGGATCCGATTCGTGTTAATGGTGAACAAACAAGGACAGACCCGTCTTGCTCAGTATTATGAATACCTCACTGTTGAAGAACGACGAACACTTGAAGGCGAAATTGTTCGTAAATGCCTCGCCCGTAATGAAAACCAGGTATGTTTCCATTCTTTTCTTTTATTTTCATCAGATCTTCATACCTCCTTACCTTCAATTTTACCTAATTCATATTGTCATTGTTTATTATTATTCAACCCTGGAGGTAGCAATTAGATTGAGAGCTTAATTCAAAATTTAAGACAATCTTAGTTTACAATTTGACTCAACTGAATATCAAACATAAACACTTCTGAGAATATGGAAACAGCTTACAACATGTTCATAAGTTACTTGCAGATTATTTCCATAACCTCTCCATGATAGATTATGAAATCAGCTTATAGTTATAGCTTATTCCAAAACAAATTGATTTTATTTTGTCTTTTGTTTCAGAAATAGCTTATGCATAAGTACTCATATGATAAATGTTATGTTGTAAGCACTTAATTAATTTGTTTATCTAAATAAGACATAGATGTCTTGGAAAGTTATTTATTTGAATATTTTTACTATAGACAGGAGATAATTGTTGGTTTCCTTTCACACCCAGAATTGGGGAAGAGAAAGTTGTTAGTGAGATATTGAATGCAATAGAATAGAATGCATTCCACTGTGTTATATTTTAGTTGGGAACCTTTTTTTTTTCTTTCCAATTTCATCACATGTTTAAATCTTAGCTTAGATTTTGTGTTATTATTAGATTATATAATCTGTGAGTGGAATGAAATTGAAATGGACCTCGTCATTCTTTATTATTCAACCCGAGGTTTTAGGCCATCTTTGGATTCAAGTTTGCTACCCGAGGTTTTAGGCCATCTTTTGACTTTCTCTTACTCATATTGATGCGTTGGTTTATACCAGAAACATAAGGGATTGACTTGTCTTATTGTTGTTTCTGCTCACCATGATTCATCTGGCTGATACATTTTTGTCATGGACAGTGTTCATTTGTTGAGCATCGCAACTACAAAATTATATATAGGCGCTATGCATCTTTGTTTTTCCTGGTTGGAGTTGATGACGGCGAGGTAATTCATTGTTTCTATATTTCTCATTCTAGTTGATTTATACAAAGGCGGTGAATAATTTGAAATGAGCATATTGTGTTAAATAGTCTGGCTTTGATCTTACTGACCAGTGGTCATCACTATGTGATCGGCTTAGCCTTGCTTGTCTAAAGAAACTGGAAGAATTATCTGTTGTAAACTCAGAAACCTGAAGTTCTTAGTCTTGTTAAACACTTCAGCTTCAGCAAAATTTTCCATGTACCACTTTCATTGTAGATAAATATGATATCATTTCAATTCTGCTTCTACTTGATTGTTCATTCTACCTTCTGTCGACAATTTTGCAGAATGAGCTTGCTATTTTGGAATTTATCCATCTCTTAGTCGAAACCATGGATCGACATTTTGGCAACGTGGTAAGTCCTGCTGTGACTAGAGTCTCTGTAGTTTTGTGTTTGTTGAAATTGAAAGTAATGTGTCTCCTCACATTACTTCCATAATTCTATTGTTTTCTTCCTTCCATCTTCTGAACTTAGCTTCAACCAAACACTGATTTTTTGTTTCTCAAATTTCTTCTTGTCTGCTTAAATTTGCAGTGTGAGCTAGATATCATGTTTCATTTAGAAAAGGTACATTTTATGTTGGAGGAAATGGTCATGAATGGTTGTATTGTGGAGACAAGCAAATCAAATATTCTGACTCCTATTCAGCTGATGGATAAAACATCATAA
Protein sequence

>MS.gene049041.t1

MGIRFVLMVNKQGQTRLAQYYEYLTVEERRTLEGEIVRKCLARNENQCSFVEHRNYKIIYRRYASLFFLVGVDDGENELAILEFIHLLVETMDRHFGNVCELDIMFHLEKVHFMLEEMVMNGCIVETSKSNILTPIQLMDKTS