AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0114970

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0114970 MtrunA17_Chr1g0161491 67.005 197 50 2 34 230 9 190 7.91e-78 253
Msa0114970 MtrunA17_Chr1g0161471 65.285 193 51 2 40 230 1 179 9.11e-76 248
Msa0114970 MtrunA17_Chr1g0161511 62.887 194 54 4 40 230 1 179 1.95e-68 227
Msa0114970 MtrunA17_Chr1g0161521 62.887 194 54 4 40 230 1 179 4.49e-68 226
Msa0114970 MtrunA17_Chr1g0161451 33.871 186 108 3 44 229 3 173 2.12e-26 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0114970 AT1G14790.1 40.426 188 97 3 43 230 2 174 4.29e-41 150

Find 31 sgRNAs with CRISPR-Local

Find 135 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACGATGTTAAATTGTATTT+TGG 0.150856 1_3:+33445121 Msa0114970:CDS
AGCTTTCATATGAGAATATT+TGG 0.191630 1_3:+33445269 Msa0114970:CDS
ATGGATGCTAGTGCAGATTT+TGG 0.192772 1_3:+33445187 Msa0114970:CDS
CTATTTAAAAGTTACGAAAA+TGG 0.261211 1_3:+33445054 Msa0114970:CDS
TGCAAAGTATCTATTGATTC+AGG 0.268018 1_3:+33445324 Msa0114970:CDS
TAGAAGAATGCCGTTGGCTT+TGG 0.337561 1_3:-33445091 None:intergenic
TGCTGGAAGTTTGTAATTGA+AGG 0.450289 1_3:-33442893 None:intergenic
CTCTGTATTGTGGGGAAAGA+TGG 0.454381 1_3:+33445168 Msa0114970:CDS
AAAAGAGTTGGCATTGAAGA+TGG 0.454789 1_3:+33444760 Msa0114970:CDS
TTGGGATTGGATTGAGAAAG+TGG 0.455481 1_3:+33445206 Msa0114970:CDS
TACCTTGTCTGATCTTGTGC+TGG 0.458868 1_3:-33442910 None:intergenic
ACATTTGTAGAGCAGTATAC+TGG 0.461229 1_3:+33444845 Msa0114970:CDS
GGAAAGATTCTCTGTATTGT+GGG 0.467936 1_3:+33445159 Msa0114970:CDS
TCTACAAATGTCTTTACATC+AGG 0.480962 1_3:-33444833 None:intergenic
AGTAAAACAATTAAGTTGCA+TGG 0.485965 1_3:+33444788 Msa0114970:CDS
AGGAAAGATTCTCTGTATTG+TGG 0.507749 1_3:+33445158 Msa0114970:CDS
AGATCATGCTACATATATGA+TGG 0.530126 1_3:+33444994 Msa0114970:CDS
TATAGGAAAATCAAAAGAGT+TGG 0.542790 1_3:+33444748 Msa0114970:intron
GTTTGAACTTCTTATCGTCA+TGG 0.543349 1_3:-33445243 None:intergenic
GAGATTTGTTCAAATTCGAA+CGG 0.545671 1_3:+33444943 Msa0114970:CDS
TCAGGCACGGTGACATGATG+AGG 0.567959 1_3:-33444815 None:intergenic
AGATTGAACTGCATCAACCA+TGG 0.634369 1_3:+33445293 Msa0114970:CDS
CAGGCACGGTGACATGATGA+GGG 0.635211 1_3:-33444814 None:intergenic
AATCTGTAGAAGAATGCCGT+TGG 0.636903 1_3:-33445097 None:intergenic
AGATATTGATCCAAAGCCAA+CGG 0.640968 1_3:+33445081 Msa0114970:CDS
GAAAGATTCTCTGTATTGTG+GGG 0.645886 1_3:+33445160 Msa0114970:CDS
AAATGTCTTTACATCAGGCA+CGG 0.659012 1_3:-33444828 None:intergenic
TATATGATGGCCTTATGTAG+CGG 0.659739 1_3:+33445007 Msa0114970:CDS
TTCCAGCACAAGATCAGACA+AGG 0.664246 1_3:+33442908 Msa0114970:CDS
ATATGTAGCATGATCTGTAG+TGG 0.696738 1_3:-33444987 None:intergenic
GTATACTGGTGAAGAAAGTG+TGG 0.711055 1_3:+33444859 Msa0114970:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTCTATTTTTTTTCTT+CGG - chr1_3:33444134-33444153 None:intergenic 10.0%
!! CTTTATAATAAAGAAAAAAA+AGG + chr1_3:33444325-33444344 Msa0114970:intron 10.0%
!!! TCATTTCTTTTATTATATAT+TGG + chr1_3:33444521-33444540 Msa0114970:intron 10.0%
!! AATAATTCAAAAAAAGAAAA+TGG - chr1_3:33444712-33444731 None:intergenic 10.0%
!!! TTTAATTTAACCATAATTCA+AGG - chr1_3:33443243-33443262 None:intergenic 15.0%
!!! AATATGTCATTTTTTTTTGA+AGG - chr1_3:33443939-33443958 None:intergenic 15.0%
!! AAATGACATATTTACATAAA+TGG + chr1_3:33443947-33443966 Msa0114970:intron 15.0%
!!! ATTTGAGTTTTTATTTTCCT+CGG + chr1_3:33443066-33443085 Msa0114970:intron 20.0%
!!! GTCAACTTTTTCTTATAATA+AGG - chr1_3:33443282-33443301 None:intergenic 20.0%
!!! TAAGAAAAAGTTGACTTTTT+AGG + chr1_3:33443287-33443306 Msa0114970:intron 20.0%
!!! GTCAATTGTTTCTTATAATA+AGG + chr1_3:33443381-33443400 Msa0114970:intron 20.0%
!!! TCATTACTCTATTGAATTTT+AGG - chr1_3:33443500-33443519 None:intergenic 20.0%
!! TTCTTATTGGTCAAAAATAA+TGG + chr1_3:33443572-33443591 Msa0114970:intron 20.0%
!!! TCAAATTTTGAAAACTTCAT+TGG - chr1_3:33443717-33443736 None:intergenic 20.0%
!!! AATATGTCATTTTGAAACTT+TGG - chr1_3:33443911-33443930 None:intergenic 20.0%
!!! CATTTTCGTAACTTTTAAAT+AGG - chr1_3:33445056-33445075 None:intergenic 20.0%
!! CTATTTAAAAGTTACGAAAA+TGG + chr1_3:33445054-33445073 Msa0114970:CDS 20.0%
!! ACTAAAATTGCGTATGTTTT+TGG + chr1_3:33442847-33442866 Msa0114970:CDS 25.0%
! GAAAATTGACAAGTAAAACA+AGG + chr1_3:33443028-33443047 Msa0114970:intron 25.0%
! TTTAACCATAATTCAAGGTT+TGG - chr1_3:33443238-33443257 None:intergenic 25.0%
! AAATTAAAAAATACTCCCTC+CGG + chr1_3:33443255-33443274 Msa0114970:intron 25.0%
!! CTTTTTCTTATAATAAGGAC+CGG - chr1_3:33443277-33443296 None:intergenic 25.0%
! ACGTTAGTAATTTATACAAG+TGG - chr1_3:33443439-33443458 None:intergenic 25.0%
! AAGCACACAATATTAATACA+AGG + chr1_3:33443473-33443492 Msa0114970:intron 25.0%
! AATAAGAAGTGAGAAAAACA+AGG - chr1_3:33443560-33443579 None:intergenic 25.0%
!!! TTGTTTTTCTCACTTCTTAT+TGG + chr1_3:33443559-33443578 Msa0114970:intron 25.0%
!! TATTTGTCATTTGTCTAGTT+TGG - chr1_3:33443825-33443844 None:intergenic 25.0%
! AGCATTTACAGAAAAAGTAA+AGG + chr1_3:33444025-33444044 Msa0114970:intron 25.0%
!!! TTTCTCTTTTATTTTGTGGT+GGG - chr1_3:33444193-33444212 None:intergenic 25.0%
! ACTTAATTACTCATGTTCAT+GGG - chr1_3:33444218-33444237 None:intergenic 25.0%
! AACTTAATTACTCATGTTCA+TGG - chr1_3:33444219-33444238 None:intergenic 25.0%
! ATGAAAGTAACTAGTGATAA+AGG + chr1_3:33444373-33444392 Msa0114970:intron 25.0%
!!! GCATTCTATTATTTTTACAG+TGG + chr1_3:33444464-33444483 Msa0114970:intron 25.0%
! AATGGTATATCTAAGAAAGA+AGG - chr1_3:33444694-33444713 None:intergenic 25.0%
!! TTGATTTTCCTATATAGGAT+TGG - chr1_3:33444742-33444761 None:intergenic 25.0%
!!! CTCTTTTGATTTTCCTATAT+AGG - chr1_3:33444747-33444766 None:intergenic 25.0%
! TATAGGAAAATCAAAAGAGT+TGG + chr1_3:33444748-33444767 Msa0114970:intron 25.0%
!! AGTAAAACAATTAAGTTGCA+TGG + chr1_3:33444788-33444807 Msa0114970:CDS 25.0%
!! GACGATGTTAAATTGTATTT+TGG + chr1_3:33445121-33445140 Msa0114970:CDS 25.0%
! AGCTTTCATATGAGAATATT+TGG + chr1_3:33445269-33445288 Msa0114970:CDS 25.0%
!!! TTGTTTTTAGCACAGGATAA+TGG + chr1_3:33442962-33442981 Msa0114970:intron 30.0%
TTTCTTATAATAAGGACCGA+AGG + chr1_3:33443389-33443408 Msa0114970:intron 30.0%
TTCTTATAATAAGGACCGAA+GGG + chr1_3:33443390-33443409 Msa0114970:intron 30.0%
TACTAACGTGAACTTATTCT+TGG + chr1_3:33443450-33443469 Msa0114970:intron 30.0%
TCAACAAAGTTGTCATCAAA+TGG - chr1_3:33443534-33443553 None:intergenic 30.0%
!!! AACCACTTTTTGACAACTTT+TGG - chr1_3:33443657-33443676 None:intergenic 30.0%
!!! TCATTTTGAAACTTTGGATG+AGG - chr1_3:33443905-33443924 None:intergenic 30.0%
!!! GTTTCTCTTTTATTTTGTGG+TGG - chr1_3:33444194-33444213 None:intergenic 30.0%
!!! GGTGTTTCTCTTTTATTTTG+TGG - chr1_3:33444197-33444216 None:intergenic 30.0%
TAGTGATAAAGGACATATGT+GGG + chr1_3:33444384-33444403 Msa0114970:intron 30.0%
GGTGATATATCAACAATCAT+TGG + chr1_3:33444485-33444504 Msa0114970:intron 30.0%
TTTCTTCTCCAATCCTATAT+AGG + chr1_3:33444731-33444750 Msa0114970:intron 30.0%
TCTACAAATGTCTTTACATC+AGG - chr1_3:33444836-33444855 None:intergenic 30.0%
GTGTGGTTGCTATAAAAATA+AGG + chr1_3:33444876-33444895 Msa0114970:CDS 30.0%
! GAGATTTGTTCAAATTCGAA+CGG + chr1_3:33444943-33444962 Msa0114970:CDS 30.0%
AGATCATGCTACATATATGA+TGG + chr1_3:33444994-33445013 Msa0114970:CDS 30.0%
!!! CAATTTTTTTCCGCTACATA+AGG - chr1_3:33445020-33445039 None:intergenic 30.0%
!!! TACTTTGCAGTTTTAAACCA+TGG - chr1_3:33445313-33445332 None:intergenic 30.0%
!! TGCAAAGTATCTATTGATTC+AGG + chr1_3:33445324-33445343 Msa0114970:CDS 30.0%
TGCTGGAAGTTTGTAATTGA+AGG - chr1_3:33442896-33442915 None:intergenic 35.0%
!! TTTTTAGCACAGGATAATGG+CGG + chr1_3:33442965-33442984 Msa0114970:intron 35.0%
!!! GGGGTATTTTGGTATTTTAC+TGG + chr1_3:33443137-33443156 Msa0114970:intron 35.0%
TGCTGTTCACACATGTTAAA+GGG - chr1_3:33443174-33443193 None:intergenic 35.0%
! TTGCTGTTCACACATGTTAA+AGG - chr1_3:33443175-33443194 None:intergenic 35.0%
CAAGTCCAAACCTTGAATTA+TGG + chr1_3:33443230-33443249 Msa0114970:intron 35.0%
TTCTTATAATAAGGACCGGA+GGG - chr1_3:33443273-33443292 None:intergenic 35.0%
TTTCTTATAATAAGGACCGG+AGG - chr1_3:33443274-33443293 None:intergenic 35.0%
GTGGTTTAGATGAGATGATA+TGG - chr1_3:33443420-33443439 None:intergenic 35.0%
AGAGAGAAAAAGAAAGAGAG+AGG + chr1_3:33443595-33443614 Msa0114970:intron 35.0%
GTCCAAAAGTTGTCAAAAAG+TGG + chr1_3:33443652-33443671 Msa0114970:intron 35.0%
ACTAGATGCATATGTTTGTG+CGG - chr1_3:33443786-33443805 None:intergenic 35.0%
! ATTTGTCTAGTTTGGTCGTT+AGG - chr1_3:33443817-33443836 None:intergenic 35.0%
AAAAGTAAAGGCAACCATCA+AGG + chr1_3:33444037-33444056 Msa0114970:intron 35.0%
CTAGTGATAAAGGACATATG+TGG + chr1_3:33444383-33444402 Msa0114970:intron 35.0%
!! CACTGACTTCAAATAGTTTG+AGG + chr1_3:33444565-33444584 Msa0114970:intron 35.0%
! AAAAGAGTTGGCATTGAAGA+TGG + chr1_3:33444760-33444779 Msa0114970:CDS 35.0%
AAATGTCTTTACATCAGGCA+CGG - chr1_3:33444831-33444850 None:intergenic 35.0%
ACATTTGTAGAGCAGTATAC+TGG + chr1_3:33444845-33444864 Msa0114970:CDS 35.0%
ATATGTAGCATGATCTGTAG+TGG - chr1_3:33444990-33445009 None:intergenic 35.0%
!! TATATGATGGCCTTATGTAG+CGG + chr1_3:33445007-33445026 Msa0114970:CDS 35.0%
AGATATTGATCCAAAGCCAA+CGG + chr1_3:33445081-33445100 Msa0114970:CDS 35.0%
AGGAAAGATTCTCTGTATTG+TGG + chr1_3:33445158-33445177 Msa0114970:CDS 35.0%
GGAAAGATTCTCTGTATTGT+GGG + chr1_3:33445159-33445178 Msa0114970:CDS 35.0%
GAAAGATTCTCTGTATTGTG+GGG + chr1_3:33445160-33445179 Msa0114970:CDS 35.0%
GTTTGAACTTCTTATCGTCA+TGG - chr1_3:33445246-33445265 None:intergenic 35.0%
CACAAGATCAGACAAGGTAA+TGG + chr1_3:33442914-33442933 Msa0114970:intron 40.0%
CTAAAAACAACAACGCGAAC+AGG - chr1_3:33442952-33442971 None:intergenic 40.0%
! TAATGGCGGAAATAGATCAG+AGG + chr1_3:33442979-33442998 Msa0114970:intron 40.0%
AGATGATATGGTACTCCCTT+CGG - chr1_3:33443408-33443427 None:intergenic 40.0%
AGTCAAGTCCTTACTTGTCA+CGG + chr1_3:33443737-33443756 Msa0114970:intron 40.0%
! GTGGTCACGATTTGTTTGTT+TGG - chr1_3:33443764-33443783 None:intergenic 40.0%
!!! AACGGTGTCATTCTTTTGGT+AGG - chr1_3:33444066-33444085 None:intergenic 40.0%
!!! GTTCAACGGTGTCATTCTTT+TGG - chr1_3:33444070-33444089 None:intergenic 40.0%
CTAGTAGATTCGACGTTCAA+CGG - chr1_3:33444084-33444103 None:intergenic 40.0%
! TCGAATTGATTCACATGCGA+CGG + chr1_3:33444348-33444367 Msa0114970:intron 40.0%
AAGCAAGAAGAAGTTGTCGT+GGG - chr1_3:33444442-33444461 None:intergenic 40.0%
TAAGCAAGAAGAAGTTGTCG+TGG - chr1_3:33444443-33444462 None:intergenic 40.0%
GTATACTGGTGAAGAAAGTG+TGG + chr1_3:33444859-33444878 Msa0114970:CDS 40.0%
GCGGAAAAAAATTGCAGTTC+TGG + chr1_3:33445026-33445045 Msa0114970:CDS 40.0%
AATCTGTAGAAGAATGCCGT+TGG - chr1_3:33445100-33445119 None:intergenic 40.0%
!! TTTTGGCTGTCAGATCTCAA+AGG + chr1_3:33445138-33445157 Msa0114970:CDS 40.0%
! ATGGATGCTAGTGCAGATTT+TGG + chr1_3:33445187-33445206 Msa0114970:CDS 40.0%
! TGGATGCTAGTGCAGATTTT+GGG + chr1_3:33445188-33445207 Msa0114970:CDS 40.0%
TTGGGATTGGATTGAGAAAG+TGG + chr1_3:33445206-33445225 Msa0114970:CDS 40.0%
AGATTGAACTGCATCAACCA+TGG + chr1_3:33445293-33445312 Msa0114970:CDS 40.0%
TTCCAGCACAAGATCAGACA+AGG + chr1_3:33442908-33442927 Msa0114970:CDS 45.0%
TACCTTGTCTGATCTTGTGC+TGG - chr1_3:33442913-33442932 None:intergenic 45.0%
!!! CGCGTTGTTGTTTTTAGCAC+AGG + chr1_3:33442955-33442974 Msa0114970:intron 45.0%
!! CAGCCGGGTTTATTTTTCCT+CGG + chr1_3:33443099-33443118 Msa0114970:intron 45.0%
CTGCCGAGGAAAAATAAACC+CGG - chr1_3:33443105-33443124 None:intergenic 45.0%
!!! TAACTGCAGAGGGGGTATTT+TGG + chr1_3:33443126-33443145 Msa0114970:intron 45.0%
TGTTTGGTCCGTGACAAGTA+AGG - chr1_3:33443748-33443767 None:intergenic 45.0%
AGATGCATATGTTTGTGCGG+TGG - chr1_3:33443783-33443802 None:intergenic 45.0%
AGTTTGGTCGTTAGGCTTGT+CGG - chr1_3:33443809-33443828 None:intergenic 45.0%
! CTTTTGGTAGGCTTCCTTGA+TGG - chr1_3:33444054-33444073 None:intergenic 45.0%
! CGAATTGATTCACATGCGAC+GGG + chr1_3:33444349-33444368 Msa0114970:intron 45.0%
AAGAAGAAGTTGTCGTGGGT+TGG - chr1_3:33444438-33444457 None:intergenic 45.0%
TTGTCGTCAATGTCAACGTC+AGG - chr1_3:33444606-33444625 None:intergenic 45.0%
GACATTCTTGCTCTCTTTCC+AGG + chr1_3:33444628-33444647 Msa0114970:intron 45.0%
TCTCTTTCCAGGATTCCTCA+AGG + chr1_3:33444639-33444658 Msa0114970:intron 45.0%
!! TAGAAGAATGCCGTTGGCTT+TGG - chr1_3:33445094-33445113 None:intergenic 45.0%
CTCTGTATTGTGGGGAAAGA+TGG + chr1_3:33445168-33445187 Msa0114970:CDS 45.0%
!!! GCTAGTGCAGATTTTGGGAT+TGG + chr1_3:33445193-33445212 Msa0114970:CDS 45.0%
!! ATCAGCATCGACAGACCTTG+AGG - chr1_3:33444657-33444676 None:intergenic 50.0%
CCTCGGTAGTTAACTGCAGC+CGG + chr1_3:33443083-33443102 Msa0114970:intron 55.0%
CTCGGTAGTTAACTGCAGCC+GGG + chr1_3:33443084-33443103 Msa0114970:intron 55.0%
TCCTCGGCAGTTAACTGCAG+AGG + chr1_3:33443115-33443134 Msa0114970:intron 55.0%
CCTCGGCAGTTAACTGCAGA+GGG + chr1_3:33443116-33443135 Msa0114970:intron 55.0%
CTCGGCAGTTAACTGCAGAG+GGG + chr1_3:33443117-33443136 Msa0114970:intron 55.0%
TCGGCAGTTAACTGCAGAGG+GGG + chr1_3:33443118-33443137 Msa0114970:intron 55.0%
CGACAGACCTTGAGGAATCC+TGG - chr1_3:33444649-33444668 None:intergenic 55.0%
CAGGCACGGTGACATGATGA+GGG - chr1_3:33444817-33444836 None:intergenic 55.0%
TCAGGCACGGTGACATGATG+AGG - chr1_3:33444818-33444837 None:intergenic 55.0%
CCGGCTGCAGTTAACTACCG+AGG - chr1_3:33443086-33443105 None:intergenic 60.0%
CCCTCTGCAGTTAACTGCCG+AGG - chr1_3:33443119-33443138 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 33442839 33445375 33442839 ID=Msa0114970;Name=Msa0114970
chr1_3 mRNA 33442839 33445375 33442839 ID=Msa0114970-mRNA-1;Parent=Msa0114970;Name=Msa0114970-mRNA-1;_AED=0.17;_eAED=0.17;_QI=0|0|0|0.5|0|0.5|2|0|237
chr1_3 exon 33442839 33442929 33442839 ID=Msa0114970-mRNA-1:exon:10497;Parent=Msa0114970-mRNA-1
chr1_3 exon 33444753 33445375 33444753 ID=Msa0114970-mRNA-1:exon:10498;Parent=Msa0114970-mRNA-1
chr1_3 CDS 33442839 33442929 33442839 ID=Msa0114970-mRNA-1:cds;Parent=Msa0114970-mRNA-1
chr1_3 CDS 33444753 33445375 33444753 ID=Msa0114970-mRNA-1:cds;Parent=Msa0114970-mRNA-1
Gene Sequence

>Msa0114970

ATGTTCAAACTAAAATTGCGTATGTTTTTGGAATTACAAAATGAAGCTGTGTCACCTTCAATTACAAACTTCCAGCACAAGATCAGACAAGGAAAATCAAAAGAGTTGGCATTGAAGATGGTTAAAAGTAAAACAATTAAGTTGCATGGATTCCCTCATCATGTCACCGTGCCTGATGTAAAGACATTTGTAGAGCAGTATACTGGTGAAGAAAGTGTGGTTGCTATAAAAATAAGGAAGTGTAGTTGCTATAAAAATAAGTGTTGTTGCTATAAAAAGAAGAGATTTGTTCAAATTCGAACGGCATTTGCAATTATTCAATTCACCACTACAGATCATGCTACATATATGATGGCCTTATGTAGCGGAAAAAAATTGCAGTTCTGGAAATCCTATTTAAAAGTTACGAAAATGGAAAGAGATATTGATCCAAAGCCAACGGCATTCTTCTACAGATTAGACGATGTTAAATTGTATTTTGGCTGTCAGATCTCAAAGGAAAGATTCTCTGTATTGTGGGGAAAGATGGATGCTAGTGCAGATTTTGGGATTGGATTGAGAAAGTGGCGATTCTCTATGTGCCATGACGATAAGAAGTTCAAACTTGAGCTTTCATATGAGAATATTTGGAAGATTGAACTGCATCAACCATGGTTTAAAACTGCAAAGTATCTATTGATTCAGGTTGTTAAATTCAACTTTTCATTATTTTAA
Protein sequence

>Msa0114970

MFKLKLRMFLELQNEAVSPSITNFQHKIRQGKSKELALKMVKSKTIKLHGFPHHVTVPDVKTFVEQYTGEESVVAIKIRKCSCYKNKCCCYKKKRFVQIRTAFAIIQFTTTDHATYMMALCSGKKLQFWKSYLKVTKMERDIDPKPTAFFYRLDDVKLYFGCQISKERFSVLWGKMDASADFGIGLRKWRFSMCHDDKKFKLELSYENIWKIELHQPWFKTAKYLLIQVVKFNFSLF*