AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0114910

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0114910 MtrunA17_Chr1g0161491 67.005 197 50 2 34 230 9 190 7.91e-78 253
Msa0114910 MtrunA17_Chr1g0161471 65.285 193 51 2 40 230 1 179 9.11e-76 248
Msa0114910 MtrunA17_Chr1g0161511 62.887 194 54 4 40 230 1 179 1.95e-68 227
Msa0114910 MtrunA17_Chr1g0161521 62.887 194 54 4 40 230 1 179 4.49e-68 226
Msa0114910 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
Msa0114910 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:+33258990 Msa0114910:CDS
AGCTTTCATATGAGAATATT+TGG 0.191630 1_3:+33259138 Msa0114910:CDS
ATGGATGCTAGTGCAGATTT+TGG 0.192772 1_3:+33259056 Msa0114910:CDS
CTATTTAAAAGTTACGAAAA+TGG 0.261211 1_3:+33258923 Msa0114910:CDS
TGCAAAGTATCTATTGATTC+AGG 0.268018 1_3:+33259193 Msa0114910:CDS
TAGAAGAATGCCGTTGGCTT+TGG 0.337561 1_3:-33258960 None:intergenic
TGCTGGAAGTTTGTAATTGA+AGG 0.450289 1_3:-33256762 None:intergenic
CTCTGTATTGTGGGGAAAGA+TGG 0.454381 1_3:+33259037 Msa0114910:CDS
AAAAGAGTTGGCATTGAAGA+TGG 0.454789 1_3:+33258629 Msa0114910:CDS
TTGGGATTGGATTGAGAAAG+TGG 0.455481 1_3:+33259075 Msa0114910:CDS
TACCTTGTCTGATCTTGTGC+TGG 0.458868 1_3:-33256779 None:intergenic
ACATTTGTAGAGCAGTATAC+TGG 0.461229 1_3:+33258714 Msa0114910:CDS
GGAAAGATTCTCTGTATTGT+GGG 0.467936 1_3:+33259028 Msa0114910:CDS
TCTACAAATGTCTTTACATC+AGG 0.480962 1_3:-33258702 None:intergenic
AGTAAAACAATTAAGTTGCA+TGG 0.485965 1_3:+33258657 Msa0114910:CDS
AGGAAAGATTCTCTGTATTG+TGG 0.507749 1_3:+33259027 Msa0114910:CDS
AGATCATGCTACATATATGA+TGG 0.530126 1_3:+33258863 Msa0114910:CDS
TATAGGAAAATCAAAAGAGT+TGG 0.542790 1_3:+33258617 Msa0114910:intron
GTTTGAACTTCTTATCGTCA+TGG 0.543349 1_3:-33259112 None:intergenic
GAGATTTGTTCAAATTCGAA+CGG 0.545671 1_3:+33258812 Msa0114910:CDS
TCAGGCACGGTGACATGATG+AGG 0.567959 1_3:-33258684 None:intergenic
AGATTGAACTGCATCAACCA+TGG 0.634369 1_3:+33259162 Msa0114910:CDS
CAGGCACGGTGACATGATGA+GGG 0.635211 1_3:-33258683 None:intergenic
AATCTGTAGAAGAATGCCGT+TGG 0.636903 1_3:-33258966 None:intergenic
AGATATTGATCCAAAGCCAA+CGG 0.640968 1_3:+33258950 Msa0114910:CDS
GAAAGATTCTCTGTATTGTG+GGG 0.645886 1_3:+33259029 Msa0114910:CDS
AAATGTCTTTACATCAGGCA+CGG 0.659012 1_3:-33258697 None:intergenic
TATATGATGGCCTTATGTAG+CGG 0.659739 1_3:+33258876 Msa0114910:CDS
TTCCAGCACAAGATCAGACA+AGG 0.664246 1_3:+33256777 Msa0114910:CDS
ATATGTAGCATGATCTGTAG+TGG 0.696738 1_3:-33258856 None:intergenic
GTATACTGGTGAAGAAAGTG+TGG 0.711055 1_3:+33258728 Msa0114910:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTCTATTTTTTTTCTT+CGG - chr1_3:33258003-33258022 None:intergenic 10.0%
!! CTTTATAATAAAGAAAAAAA+AGG + chr1_3:33258194-33258213 Msa0114910:intron 10.0%
!!! TCATTTCTTTTATTATATAT+TGG + chr1_3:33258390-33258409 Msa0114910:intron 10.0%
!! AATAATTCAAAAAAAGAAAA+TGG - chr1_3:33258581-33258600 None:intergenic 10.0%
!!! TTTAATTTAACCATAATTCA+AGG - chr1_3:33257112-33257131 None:intergenic 15.0%
!!! AATATGTCATTTTTTTTTGA+AGG - chr1_3:33257808-33257827 None:intergenic 15.0%
!! AAATGACATATTTACATAAA+TGG + chr1_3:33257816-33257835 Msa0114910:intron 15.0%
!!! ATTTGAGTTTTTATTTTCCT+CGG + chr1_3:33256935-33256954 Msa0114910:intron 20.0%
!!! GTCAACTTTTTCTTATAATA+AGG - chr1_3:33257151-33257170 None:intergenic 20.0%
!!! TAAGAAAAAGTTGACTTTTT+AGG + chr1_3:33257156-33257175 Msa0114910:intron 20.0%
!!! GTCAATTGTTTCTTATAATA+AGG + chr1_3:33257250-33257269 Msa0114910:intron 20.0%
!!! TCATTACTCTATTGAATTTT+AGG - chr1_3:33257369-33257388 None:intergenic 20.0%
!! TTCTTATTGGTCAAAAATAA+TGG + chr1_3:33257441-33257460 Msa0114910:intron 20.0%
!!! TCAAATTTTGAAAACTTCAT+TGG - chr1_3:33257586-33257605 None:intergenic 20.0%
!!! AATATGTCATTTTGAAACTT+TGG - chr1_3:33257780-33257799 None:intergenic 20.0%
!!! CATTTTCGTAACTTTTAAAT+AGG - chr1_3:33258925-33258944 None:intergenic 20.0%
!! CTATTTAAAAGTTACGAAAA+TGG + chr1_3:33258923-33258942 Msa0114910:CDS 20.0%
!! ACTAAAATTGCGTATGTTTT+TGG + chr1_3:33256716-33256735 Msa0114910:CDS 25.0%
! GAAAATTGACAAGTAAAACA+AGG + chr1_3:33256897-33256916 Msa0114910:intron 25.0%
! TTTAACCATAATTCAAGGTT+TGG - chr1_3:33257107-33257126 None:intergenic 25.0%
! AAATTAAAAAATACTCCCTC+CGG + chr1_3:33257124-33257143 Msa0114910:intron 25.0%
!! CTTTTTCTTATAATAAGGAC+CGG - chr1_3:33257146-33257165 None:intergenic 25.0%
! ACGTTAGTAATTTATACAAG+TGG - chr1_3:33257308-33257327 None:intergenic 25.0%
! AAGCACACAATATTAATACA+AGG + chr1_3:33257342-33257361 Msa0114910:intron 25.0%
! AATAAGAAGTGAGAAAAACA+AGG - chr1_3:33257429-33257448 None:intergenic 25.0%
!!! TTGTTTTTCTCACTTCTTAT+TGG + chr1_3:33257428-33257447 Msa0114910:intron 25.0%
!! TATTTGTCATTTGTCTAGTT+TGG - chr1_3:33257694-33257713 None:intergenic 25.0%
! AGCATTTACAGAAAAAGTAA+AGG + chr1_3:33257894-33257913 Msa0114910:intron 25.0%
!!! TTTCTCTTTTATTTTGTGGT+GGG - chr1_3:33258062-33258081 None:intergenic 25.0%
! ACTTAATTACTCATGTTCAT+GGG - chr1_3:33258087-33258106 None:intergenic 25.0%
! AACTTAATTACTCATGTTCA+TGG - chr1_3:33258088-33258107 None:intergenic 25.0%
! ATGAAAGTAACTAGTGATAA+AGG + chr1_3:33258242-33258261 Msa0114910:intron 25.0%
!!! GCATTCTATTATTTTTACAG+TGG + chr1_3:33258333-33258352 Msa0114910:intron 25.0%
! AATGGTATATCTAAGAAAGA+AGG - chr1_3:33258563-33258582 None:intergenic 25.0%
!! TTGATTTTCCTATATAGGAT+TGG - chr1_3:33258611-33258630 None:intergenic 25.0%
!!! CTCTTTTGATTTTCCTATAT+AGG - chr1_3:33258616-33258635 None:intergenic 25.0%
! TATAGGAAAATCAAAAGAGT+TGG + chr1_3:33258617-33258636 Msa0114910:intron 25.0%
!! AGTAAAACAATTAAGTTGCA+TGG + chr1_3:33258657-33258676 Msa0114910:CDS 25.0%
!! GACGATGTTAAATTGTATTT+TGG + chr1_3:33258990-33259009 Msa0114910:CDS 25.0%
! AGCTTTCATATGAGAATATT+TGG + chr1_3:33259138-33259157 Msa0114910:CDS 25.0%
!!! TTGTTTTTAGCACAGGATAA+TGG + chr1_3:33256831-33256850 Msa0114910:intron 30.0%
TTTCTTATAATAAGGACCGA+AGG + chr1_3:33257258-33257277 Msa0114910:intron 30.0%
TTCTTATAATAAGGACCGAA+GGG + chr1_3:33257259-33257278 Msa0114910:intron 30.0%
TACTAACGTGAACTTATTCT+TGG + chr1_3:33257319-33257338 Msa0114910:intron 30.0%
TCAACAAAGTTGTCATCAAA+TGG - chr1_3:33257403-33257422 None:intergenic 30.0%
!!! AACCACTTTTTGACAACTTT+TGG - chr1_3:33257526-33257545 None:intergenic 30.0%
!!! TCATTTTGAAACTTTGGATG+AGG - chr1_3:33257774-33257793 None:intergenic 30.0%
!!! GTTTCTCTTTTATTTTGTGG+TGG - chr1_3:33258063-33258082 None:intergenic 30.0%
!!! GGTGTTTCTCTTTTATTTTG+TGG - chr1_3:33258066-33258085 None:intergenic 30.0%
TAGTGATAAAGGACATATGT+GGG + chr1_3:33258253-33258272 Msa0114910:intron 30.0%
GGTGATATATCAACAATCAT+TGG + chr1_3:33258354-33258373 Msa0114910:intron 30.0%
TTTCTTCTCCAATCCTATAT+AGG + chr1_3:33258600-33258619 Msa0114910:intron 30.0%
TCTACAAATGTCTTTACATC+AGG - chr1_3:33258705-33258724 None:intergenic 30.0%
GTGTGGTTGCTATAAAAATA+AGG + chr1_3:33258745-33258764 Msa0114910:CDS 30.0%
! GAGATTTGTTCAAATTCGAA+CGG + chr1_3:33258812-33258831 Msa0114910:CDS 30.0%
AGATCATGCTACATATATGA+TGG + chr1_3:33258863-33258882 Msa0114910:CDS 30.0%
!!! CAATTTTTTTCCGCTACATA+AGG - chr1_3:33258889-33258908 None:intergenic 30.0%
!!! TACTTTGCAGTTTTAAACCA+TGG - chr1_3:33259182-33259201 None:intergenic 30.0%
!! TGCAAAGTATCTATTGATTC+AGG + chr1_3:33259193-33259212 Msa0114910:CDS 30.0%
TGCTGGAAGTTTGTAATTGA+AGG - chr1_3:33256765-33256784 None:intergenic 35.0%
!! TTTTTAGCACAGGATAATGG+CGG + chr1_3:33256834-33256853 Msa0114910:intron 35.0%
!!! GGGGTATTTTGGTATTTTAC+TGG + chr1_3:33257006-33257025 Msa0114910:intron 35.0%
TGCTGTTCACACATGTTAAA+GGG - chr1_3:33257043-33257062 None:intergenic 35.0%
! TTGCTGTTCACACATGTTAA+AGG - chr1_3:33257044-33257063 None:intergenic 35.0%
CAAGTCCAAACCTTGAATTA+TGG + chr1_3:33257099-33257118 Msa0114910:intron 35.0%
TTCTTATAATAAGGACCGGA+GGG - chr1_3:33257142-33257161 None:intergenic 35.0%
TTTCTTATAATAAGGACCGG+AGG - chr1_3:33257143-33257162 None:intergenic 35.0%
GTGGTTTAGATGAGATGATA+TGG - chr1_3:33257289-33257308 None:intergenic 35.0%
AGAGAGAAAAAGAAAGAGAG+AGG + chr1_3:33257464-33257483 Msa0114910:intron 35.0%
GTCCAAAAGTTGTCAAAAAG+TGG + chr1_3:33257521-33257540 Msa0114910:intron 35.0%
ACTAGATGCATATGTTTGTG+CGG - chr1_3:33257655-33257674 None:intergenic 35.0%
! ATTTGTCTAGTTTGGTCGTT+AGG - chr1_3:33257686-33257705 None:intergenic 35.0%
AAAAGTAAAGGCAACCATCA+AGG + chr1_3:33257906-33257925 Msa0114910:intron 35.0%
CTAGTGATAAAGGACATATG+TGG + chr1_3:33258252-33258271 Msa0114910:intron 35.0%
!! CACTGACTTCAAATAGTTTG+AGG + chr1_3:33258434-33258453 Msa0114910:intron 35.0%
! AAAAGAGTTGGCATTGAAGA+TGG + chr1_3:33258629-33258648 Msa0114910:CDS 35.0%
AAATGTCTTTACATCAGGCA+CGG - chr1_3:33258700-33258719 None:intergenic 35.0%
ACATTTGTAGAGCAGTATAC+TGG + chr1_3:33258714-33258733 Msa0114910:CDS 35.0%
ATATGTAGCATGATCTGTAG+TGG - chr1_3:33258859-33258878 None:intergenic 35.0%
!! TATATGATGGCCTTATGTAG+CGG + chr1_3:33258876-33258895 Msa0114910:CDS 35.0%
AGATATTGATCCAAAGCCAA+CGG + chr1_3:33258950-33258969 Msa0114910:CDS 35.0%
AGGAAAGATTCTCTGTATTG+TGG + chr1_3:33259027-33259046 Msa0114910:CDS 35.0%
GGAAAGATTCTCTGTATTGT+GGG + chr1_3:33259028-33259047 Msa0114910:CDS 35.0%
GAAAGATTCTCTGTATTGTG+GGG + chr1_3:33259029-33259048 Msa0114910:CDS 35.0%
GTTTGAACTTCTTATCGTCA+TGG - chr1_3:33259115-33259134 None:intergenic 35.0%
CACAAGATCAGACAAGGTAA+TGG + chr1_3:33256783-33256802 Msa0114910:intron 40.0%
CTAAAAACAACAACGCGAAC+AGG - chr1_3:33256821-33256840 None:intergenic 40.0%
! TAATGGCGGAAATAGATCAG+AGG + chr1_3:33256848-33256867 Msa0114910:intron 40.0%
AGATGATATGGTACTCCCTT+CGG - chr1_3:33257277-33257296 None:intergenic 40.0%
AGTCAAGTCCTTACTTGTCA+CGG + chr1_3:33257606-33257625 Msa0114910:intron 40.0%
! GTGGTCACGATTTGTTTGTT+TGG - chr1_3:33257633-33257652 None:intergenic 40.0%
!!! AACGGTGTCATTCTTTTGGT+AGG - chr1_3:33257935-33257954 None:intergenic 40.0%
!!! GTTCAACGGTGTCATTCTTT+TGG - chr1_3:33257939-33257958 None:intergenic 40.0%
CTAGTAGATTCGACGTTCAA+CGG - chr1_3:33257953-33257972 None:intergenic 40.0%
! TCGAATTGATTCACATGCGA+CGG + chr1_3:33258217-33258236 Msa0114910:intron 40.0%
AAGCAAGAAGAAGTTGTCGT+GGG - chr1_3:33258311-33258330 None:intergenic 40.0%
TAAGCAAGAAGAAGTTGTCG+TGG - chr1_3:33258312-33258331 None:intergenic 40.0%
GTATACTGGTGAAGAAAGTG+TGG + chr1_3:33258728-33258747 Msa0114910:CDS 40.0%
GCGGAAAAAAATTGCAGTTC+TGG + chr1_3:33258895-33258914 Msa0114910:CDS 40.0%
AATCTGTAGAAGAATGCCGT+TGG - chr1_3:33258969-33258988 None:intergenic 40.0%
!! TTTTGGCTGTCAGATCTCAA+AGG + chr1_3:33259007-33259026 Msa0114910:CDS 40.0%
! ATGGATGCTAGTGCAGATTT+TGG + chr1_3:33259056-33259075 Msa0114910:CDS 40.0%
! TGGATGCTAGTGCAGATTTT+GGG + chr1_3:33259057-33259076 Msa0114910:CDS 40.0%
TTGGGATTGGATTGAGAAAG+TGG + chr1_3:33259075-33259094 Msa0114910:CDS 40.0%
AGATTGAACTGCATCAACCA+TGG + chr1_3:33259162-33259181 Msa0114910:CDS 40.0%
TTCCAGCACAAGATCAGACA+AGG + chr1_3:33256777-33256796 Msa0114910:CDS 45.0%
TACCTTGTCTGATCTTGTGC+TGG - chr1_3:33256782-33256801 None:intergenic 45.0%
!!! CGCGTTGTTGTTTTTAGCAC+AGG + chr1_3:33256824-33256843 Msa0114910:intron 45.0%
!! CAGCCGGGTTTATTTTTCCT+CGG + chr1_3:33256968-33256987 Msa0114910:intron 45.0%
CTGCCGAGGAAAAATAAACC+CGG - chr1_3:33256974-33256993 None:intergenic 45.0%
!!! TAACTGCAGAGGGGGTATTT+TGG + chr1_3:33256995-33257014 Msa0114910:intron 45.0%
TGTTTGGTCCGTGACAAGTA+AGG - chr1_3:33257617-33257636 None:intergenic 45.0%
AGATGCATATGTTTGTGCGG+TGG - chr1_3:33257652-33257671 None:intergenic 45.0%
AGTTTGGTCGTTAGGCTTGT+CGG - chr1_3:33257678-33257697 None:intergenic 45.0%
! CTTTTGGTAGGCTTCCTTGA+TGG - chr1_3:33257923-33257942 None:intergenic 45.0%
! CGAATTGATTCACATGCGAC+GGG + chr1_3:33258218-33258237 Msa0114910:intron 45.0%
AAGAAGAAGTTGTCGTGGGT+TGG - chr1_3:33258307-33258326 None:intergenic 45.0%
TTGTCGTCAATGTCAACGTC+AGG - chr1_3:33258475-33258494 None:intergenic 45.0%
GACATTCTTGCTCTCTTTCC+AGG + chr1_3:33258497-33258516 Msa0114910:intron 45.0%
TCTCTTTCCAGGATTCCTCA+AGG + chr1_3:33258508-33258527 Msa0114910:intron 45.0%
!! TAGAAGAATGCCGTTGGCTT+TGG - chr1_3:33258963-33258982 None:intergenic 45.0%
CTCTGTATTGTGGGGAAAGA+TGG + chr1_3:33259037-33259056 Msa0114910:CDS 45.0%
!!! GCTAGTGCAGATTTTGGGAT+TGG + chr1_3:33259062-33259081 Msa0114910:CDS 45.0%
!! ATCAGCATCGACAGACCTTG+AGG - chr1_3:33258526-33258545 None:intergenic 50.0%
CCTCGGTAGTTAACTGCAGC+CGG + chr1_3:33256952-33256971 Msa0114910:intron 55.0%
CTCGGTAGTTAACTGCAGCC+GGG + chr1_3:33256953-33256972 Msa0114910:intron 55.0%
TCCTCGGCAGTTAACTGCAG+AGG + chr1_3:33256984-33257003 Msa0114910:intron 55.0%
CCTCGGCAGTTAACTGCAGA+GGG + chr1_3:33256985-33257004 Msa0114910:intron 55.0%
CTCGGCAGTTAACTGCAGAG+GGG + chr1_3:33256986-33257005 Msa0114910:intron 55.0%
TCGGCAGTTAACTGCAGAGG+GGG + chr1_3:33256987-33257006 Msa0114910:intron 55.0%
CGACAGACCTTGAGGAATCC+TGG - chr1_3:33258518-33258537 None:intergenic 55.0%
CAGGCACGGTGACATGATGA+GGG - chr1_3:33258686-33258705 None:intergenic 55.0%
TCAGGCACGGTGACATGATG+AGG - chr1_3:33258687-33258706 None:intergenic 55.0%
CCGGCTGCAGTTAACTACCG+AGG - chr1_3:33256955-33256974 None:intergenic 60.0%
CCCTCTGCAGTTAACTGCCG+AGG - chr1_3:33256988-33257007 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 33256708 33259244 33256708 ID=Msa0114910;Name=Msa0114910
chr1_3 mRNA 33256708 33259244 33256708 ID=Msa0114910-mRNA-1;Parent=Msa0114910;Name=Msa0114910-mRNA-1;_AED=0.17;_eAED=0.17;_QI=0|0|0|0.5|0|0.5|2|0|237
chr1_3 exon 33256708 33256798 33256708 ID=Msa0114910-mRNA-1:exon:10464;Parent=Msa0114910-mRNA-1
chr1_3 exon 33258622 33259244 33258622 ID=Msa0114910-mRNA-1:exon:10465;Parent=Msa0114910-mRNA-1
chr1_3 CDS 33256708 33256798 33256708 ID=Msa0114910-mRNA-1:cds;Parent=Msa0114910-mRNA-1
chr1_3 CDS 33258622 33259244 33258622 ID=Msa0114910-mRNA-1:cds;Parent=Msa0114910-mRNA-1
Gene Sequence

>Msa0114910

ATGTTCAAACTAAAATTGCGTATGTTTTTGGAATTACAAAATGAAGCTGTGTCACCTTCAATTACAAACTTCCAGCACAAGATCAGACAAGGAAAATCAAAAGAGTTGGCATTGAAGATGGTTAAAAGTAAAACAATTAAGTTGCATGGATTCCCTCATCATGTCACCGTGCCTGATGTAAAGACATTTGTAGAGCAGTATACTGGTGAAGAAAGTGTGGTTGCTATAAAAATAAGGAAGTGTAGTTGCTATAAAAATAAGTGTTGTTGCTATAAAAAGAAGAGATTTGTTCAAATTCGAACGGCATTTGCAATTATTCAATTCACCACTACAGATCATGCTACATATATGATGGCCTTATGTAGCGGAAAAAAATTGCAGTTCTGGAAATCCTATTTAAAAGTTACGAAAATGGAAAGAGATATTGATCCAAAGCCAACGGCATTCTTCTACAGATTAGACGATGTTAAATTGTATTTTGGCTGTCAGATCTCAAAGGAAAGATTCTCTGTATTGTGGGGAAAGATGGATGCTAGTGCAGATTTTGGGATTGGATTGAGAAAGTGGCGATTCTCTATGTGCCATGACGATAAGAAGTTCAAACTTGAGCTTTCATATGAGAATATTTGGAAGATTGAACTGCATCAACCATGGTTTAAAACTGCAAAGTATCTATTGATTCAGGTTGTTAAATTCAACTTTTCATTATTTTAA
Protein sequence

>Msa0114910

MFKLKLRMFLELQNEAVSPSITNFQHKIRQGKSKELALKMVKSKTIKLHGFPHHVTVPDVKTFVEQYTGEESVVAIKIRKCSCYKNKCCCYKKKRFVQIRTAFAIIQFTTTDHATYMMALCSGKKLQFWKSYLKVTKMERDIDPKPTAFFYRLDDVKLYFGCQISKERFSVLWGKMDASADFGIGLRKWRFSMCHDDKKFKLELSYENIWKIELHQPWFKTAKYLLIQVVKFNFSLF*