AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0132550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0132550 MtrunA17_Chr1g0158131 71.667 60 16 1 16 75 116 174 2.15e-22 88.2
Msa0132550 MtrunA17_Chr1g0158191 66.129 62 20 1 14 75 302 362 3.24e-22 88.2
Msa0132550 MtrunA17_Chr1g0158041 66.667 60 19 1 16 75 304 362 8.71e-21 84.0
Msa0132550 MtrunA17_Chr1g0157811 60.000 60 23 1 16 75 112 170 5.41e-18 76.3
Msa0132550 MtrunA17_Chr1g0157951 53.333 60 25 1 16 75 95 151 7.73e-17 72.8
Msa0132550 MtrunA17_Chr1g0158151 56.452 62 25 2 14 75 297 356 1.89e-16 71.6
Msa0132550 MtrunA17_Chr1g0158091 71.429 42 12 0 34 75 2 43 2.66e-16 71.2
Msa0132550 MtrunA17_Chr1g0157791 56.667 60 25 1 16 75 299 357 1.07e-15 69.7
Msa0132550 MtrunA17_Chr1g0157991 55.000 60 26 1 16 75 306 364 4.83e-15 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 10 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTGTTGGTACAACATTAC+AGG 0.294836 1_3:+63615759 Msa0132550:CDS
GGACTCGTTGAAGTAATAAA+AGG 0.335079 1_3:+63615780 Msa0132550:CDS
TGGCAGTTAGACTTCTGTTT+GGG 0.353241 1_3:+63615883 Msa0132550:CDS
TTGGCAGTTAGACTTCTGTT+TGG 0.364954 1_3:+63615882 Msa0132550:CDS
AGTATCTATATTTATCTTGT+TGG 0.396890 1_3:+63615745 Msa0132550:intron
TTCATTCTATGACGTAGGCT+TGG 0.479652 1_3:+63615830 Msa0132550:CDS
TATGACGTAGGCTTGGCAAT+AGG 0.494487 1_3:+63615837 Msa0132550:CDS
TCGCACTATTGATATACAGA+TGG 0.587433 1_3:+63615919 Msa0132550:CDS
TAAAAGGACAAATTAACTCA+AGG 0.588599 1_3:+63615796 Msa0132550:CDS
GTTTATTCATTCTATGACGT+AGG 0.589542 1_3:+63615825 Msa0132550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTTATTTGTGTTATAA+TGG - chr1_3:63615596-63615615 None:intergenic 10.0%
!!! CTTTTTTTTATGAAATAAAA+AGG - chr1_3:63615656-63615675 None:intergenic 10.0%
!!! TATTTTTATTTGTGTTATAA+TGG - chr1_3:63615596-63615615 None:intergenic 10.0%
!!! CTTTTTTTTATGAAATAAAA+AGG - chr1_3:63615656-63615675 None:intergenic 10.0%
!!! TTATCTTTTCATATTCTTTT+AGG + chr1_3:63614854-63614873 Msa0132550:intron 15.0%
!! AAGAAATATGAAAAAAAACA+TGG + chr1_3:63615353-63615372 Msa0132550:intron 15.0%
!!! AATTTGAACATATTTTATCA+AGG - chr1_3:63615718-63615737 None:intergenic 15.0%
!! TGATAAAATATGTTCAAATT+TGG + chr1_3:63615718-63615737 Msa0132550:intron 15.0%
!!! TTATCTTTTCATATTCTTTT+AGG + chr1_3:63614854-63614873 Msa0132550:intron 15.0%
!! AAGAAATATGAAAAAAAACA+TGG + chr1_3:63615353-63615372 Msa0132550:intron 15.0%
!!! AATTTGAACATATTTTATCA+AGG - chr1_3:63615718-63615737 None:intergenic 15.0%
!! TGATAAAATATGTTCAAATT+TGG + chr1_3:63615718-63615737 Msa0132550:intron 15.0%
!! CAACGAAAATAATTATTGTT+AGG + chr1_3:63615160-63615179 Msa0132550:intron 20.0%
!! TTCAACAATATCTTTATTGT+TGG - chr1_3:63615200-63615219 None:intergenic 20.0%
!!! ACACAATACCTTTATTTTTA+TGG - chr1_3:63615379-63615398 None:intergenic 20.0%
!!! AAAGTGGAATTTTTTTTAGT+GGG + chr1_3:63615478-63615497 Msa0132550:intron 20.0%
!!! ACATATTTTATCAAGGTTTA+AGG - chr1_3:63615711-63615730 None:intergenic 20.0%
!! AGTATCTATATTTATCTTGT+TGG + chr1_3:63615745-63615764 Msa0132550:intron 20.0%
!! CAACGAAAATAATTATTGTT+AGG + chr1_3:63615160-63615179 Msa0132550:intron 20.0%
!! TTCAACAATATCTTTATTGT+TGG - chr1_3:63615200-63615219 None:intergenic 20.0%
!!! ACACAATACCTTTATTTTTA+TGG - chr1_3:63615379-63615398 None:intergenic 20.0%
!!! AAAGTGGAATTTTTTTTAGT+GGG + chr1_3:63615478-63615497 Msa0132550:intron 20.0%
!!! ACATATTTTATCAAGGTTTA+AGG - chr1_3:63615711-63615730 None:intergenic 20.0%
!! AGTATCTATATTTATCTTGT+TGG + chr1_3:63615745-63615764 Msa0132550:intron 20.0%
! TTAAAGATCACTAAGTAAAG+AGG + chr1_3:63614668-63614687 Msa0132550:intron 25.0%
!! GGAATTATATAAGCTTTTAG+CGG - chr1_3:63615018-63615037 None:intergenic 25.0%
!!! ATCAGCAACAATTAATTTGT+TGG - chr1_3:63615280-63615299 None:intergenic 25.0%
! AAACATGGCCATAAAAATAA+AGG + chr1_3:63615368-63615387 Msa0132550:intron 25.0%
!!! CAAAGTGGAATTTTTTTTAG+TGG + chr1_3:63615477-63615496 Msa0132550:intron 25.0%
! ATAATATGCTAACTAATCCA+CGG - chr1_3:63615509-63615528 None:intergenic 25.0%
!!! TGGATTAGTTAGCATATTAT+TGG + chr1_3:63615509-63615528 Msa0132550:intron 25.0%
! GAAATAAAAAGGATGAAGAA+TGG - chr1_3:63615645-63615664 None:intergenic 25.0%
! TAAAAGGACAAATTAACTCA+AGG + chr1_3:63615796-63615815 Msa0132550:CDS 25.0%
!! TTACATTCTACCATCATTTT+TGG + chr1_3:63615863-63615882 Msa0132550:CDS 25.0%
! TTAAAGATCACTAAGTAAAG+AGG + chr1_3:63614668-63614687 Msa0132550:intron 25.0%
!! GGAATTATATAAGCTTTTAG+CGG - chr1_3:63615018-63615037 None:intergenic 25.0%
!!! ATCAGCAACAATTAATTTGT+TGG - chr1_3:63615280-63615299 None:intergenic 25.0%
! AAACATGGCCATAAAAATAA+AGG + chr1_3:63615368-63615387 Msa0132550:intron 25.0%
!!! CAAAGTGGAATTTTTTTTAG+TGG + chr1_3:63615477-63615496 Msa0132550:intron 25.0%
! ATAATATGCTAACTAATCCA+CGG - chr1_3:63615509-63615528 None:intergenic 25.0%
!!! TGGATTAGTTAGCATATTAT+TGG + chr1_3:63615509-63615528 Msa0132550:intron 25.0%
! GAAATAAAAAGGATGAAGAA+TGG - chr1_3:63615645-63615664 None:intergenic 25.0%
! TAAAAGGACAAATTAACTCA+AGG + chr1_3:63615796-63615815 Msa0132550:CDS 25.0%
!! TTACATTCTACCATCATTTT+TGG + chr1_3:63615863-63615882 Msa0132550:CDS 25.0%
! TAACTAACTTGCAAGTTTGT+AGG - chr1_3:63614726-63614745 None:intergenic 30.0%
ACAATATCAACTTTGCTAGT+AGG + chr1_3:63614800-63614819 Msa0132550:intron 30.0%
CAATATCAACTTTGCTAGTA+GGG + chr1_3:63614801-63614820 Msa0132550:intron 30.0%
ATCAACGTAACTTATTGTTG+GGG - chr1_3:63615119-63615138 None:intergenic 30.0%
CATCAACGTAACTTATTGTT+GGG - chr1_3:63615120-63615139 None:intergenic 30.0%
TATTTCTTGTAGTGTCACAT+CGG + chr1_3:63615322-63615341 Msa0132550:intron 30.0%
GAATTTCTTGCACAAATAGT+AGG + chr1_3:63615403-63615422 Msa0132550:intron 30.0%
CAATGATTACAGAAACTGAA+TGG - chr1_3:63615455-63615474 None:intergenic 30.0%
TCTGTAATCATTGATCAAAG+TGG + chr1_3:63615462-63615481 Msa0132550:intron 30.0%
AAACGATACAAGATTTAACG+TGG - chr1_3:63615538-63615557 None:intergenic 30.0%
GTTTATTCATTCTATGACGT+AGG + chr1_3:63615825-63615844 Msa0132550:CDS 30.0%
! TAACTAACTTGCAAGTTTGT+AGG - chr1_3:63614726-63614745 None:intergenic 30.0%
ACAATATCAACTTTGCTAGT+AGG + chr1_3:63614800-63614819 Msa0132550:intron 30.0%
CAATATCAACTTTGCTAGTA+GGG + chr1_3:63614801-63614820 Msa0132550:intron 30.0%
ATCAACGTAACTTATTGTTG+GGG - chr1_3:63615119-63615138 None:intergenic 30.0%
CATCAACGTAACTTATTGTT+GGG - chr1_3:63615120-63615139 None:intergenic 30.0%
TATTTCTTGTAGTGTCACAT+CGG + chr1_3:63615322-63615341 Msa0132550:intron 30.0%
GAATTTCTTGCACAAATAGT+AGG + chr1_3:63615403-63615422 Msa0132550:intron 30.0%
CAATGATTACAGAAACTGAA+TGG - chr1_3:63615455-63615474 None:intergenic 30.0%
TCTGTAATCATTGATCAAAG+TGG + chr1_3:63615462-63615481 Msa0132550:intron 30.0%
AAACGATACAAGATTTAACG+TGG - chr1_3:63615538-63615557 None:intergenic 30.0%
GTTTATTCATTCTATGACGT+AGG + chr1_3:63615825-63615844 Msa0132550:CDS 30.0%
! ACTCAGGATATCAAGTTGTA+AGG - chr1_3:63614752-63614771 None:intergenic 35.0%
GCAACAACATAACATCTGAT+GGG - chr1_3:63615039-63615058 None:intergenic 35.0%
TGCAACAACATAACATCTGA+TGG - chr1_3:63615040-63615059 None:intergenic 35.0%
ATTATTCCCGACGAAAAATG+AGG + chr1_3:63615070-63615089 Msa0132550:intron 35.0%
! TTGGGGATACTATGTTCTTT+TGG - chr1_3:63615102-63615121 None:intergenic 35.0%
GCATCAACGTAACTTATTGT+TGG - chr1_3:63615121-63615140 None:intergenic 35.0%
CAACAATTTATTGAAGTCGC+TGG - chr1_3:63615240-63615259 None:intergenic 35.0%
ATTTCTTGTAGTGTCACATC+GGG + chr1_3:63615323-63615342 Msa0132550:intron 35.0%
!! ATAGTAGGTTTTGCTATAGC+TGG + chr1_3:63615418-63615437 Msa0132550:intron 35.0%
TTACAGAAACTGAATGGTAG+AGG - chr1_3:63615449-63615468 None:intergenic 35.0%
TCTTGTTGGTACAACATTAC+AGG + chr1_3:63615759-63615778 Msa0132550:CDS 35.0%
GGACTCGTTGAAGTAATAAA+AGG + chr1_3:63615780-63615799 Msa0132550:CDS 35.0%
AGTCTAACTGCCAAAAATGA+TGG - chr1_3:63615876-63615895 None:intergenic 35.0%
TCGCACTATTGATATACAGA+TGG + chr1_3:63615919-63615938 Msa0132550:CDS 35.0%
! ACTCAGGATATCAAGTTGTA+AGG - chr1_3:63614752-63614771 None:intergenic 35.0%
GCAACAACATAACATCTGAT+GGG - chr1_3:63615039-63615058 None:intergenic 35.0%
TGCAACAACATAACATCTGA+TGG - chr1_3:63615040-63615059 None:intergenic 35.0%
ATTATTCCCGACGAAAAATG+AGG + chr1_3:63615070-63615089 Msa0132550:intron 35.0%
! TTGGGGATACTATGTTCTTT+TGG - chr1_3:63615102-63615121 None:intergenic 35.0%
GCATCAACGTAACTTATTGT+TGG - chr1_3:63615121-63615140 None:intergenic 35.0%
CAACAATTTATTGAAGTCGC+TGG - chr1_3:63615240-63615259 None:intergenic 35.0%
ATTTCTTGTAGTGTCACATC+GGG + chr1_3:63615323-63615342 Msa0132550:intron 35.0%
!! ATAGTAGGTTTTGCTATAGC+TGG + chr1_3:63615418-63615437 Msa0132550:intron 35.0%
TTACAGAAACTGAATGGTAG+AGG - chr1_3:63615449-63615468 None:intergenic 35.0%
TCTTGTTGGTACAACATTAC+AGG + chr1_3:63615759-63615778 Msa0132550:CDS 35.0%
GGACTCGTTGAAGTAATAAA+AGG + chr1_3:63615780-63615799 Msa0132550:CDS 35.0%
AGTCTAACTGCCAAAAATGA+TGG - chr1_3:63615876-63615895 None:intergenic 35.0%
TCGCACTATTGATATACAGA+TGG + chr1_3:63615919-63615938 Msa0132550:CDS 35.0%
ACTTGCAAGTTTGTAGGACT+AGG - chr1_3:63614720-63614739 None:intergenic 40.0%
CTTCGTCTAGATTCAAACTC+AGG - chr1_3:63614768-63614787 None:intergenic 40.0%
CTGAGTTTGAATCTAGACGA+AGG + chr1_3:63614766-63614785 Msa0132550:intron 40.0%
TCAACTTTGCTAGTAGGGTT+AGG + chr1_3:63614806-63614825 Msa0132550:intron 40.0%
!!! TTTTTTAGTGGGTATGTCCG+TGG + chr1_3:63615489-63615508 Msa0132550:intron 40.0%
TTCATTCTATGACGTAGGCT+TGG + chr1_3:63615830-63615849 Msa0132550:CDS 40.0%
TTGGCAGTTAGACTTCTGTT+TGG + chr1_3:63615882-63615901 Msa0132550:CDS 40.0%
TGGCAGTTAGACTTCTGTTT+GGG + chr1_3:63615883-63615902 Msa0132550:CDS 40.0%
ACAGATGGCGAAAAAGACAT+TGG + chr1_3:63615934-63615953 Msa0132550:CDS 40.0%
ACTTGCAAGTTTGTAGGACT+AGG - chr1_3:63614720-63614739 None:intergenic 40.0%
CTTCGTCTAGATTCAAACTC+AGG - chr1_3:63614768-63614787 None:intergenic 40.0%
CTGAGTTTGAATCTAGACGA+AGG + chr1_3:63614766-63614785 Msa0132550:intron 40.0%
TCAACTTTGCTAGTAGGGTT+AGG + chr1_3:63614806-63614825 Msa0132550:intron 40.0%
!!! TTTTTTAGTGGGTATGTCCG+TGG + chr1_3:63615489-63615508 Msa0132550:intron 40.0%
TTCATTCTATGACGTAGGCT+TGG + chr1_3:63615830-63615849 Msa0132550:CDS 40.0%
TTGGCAGTTAGACTTCTGTT+TGG + chr1_3:63615882-63615901 Msa0132550:CDS 40.0%
TGGCAGTTAGACTTCTGTTT+GGG + chr1_3:63615883-63615902 Msa0132550:CDS 40.0%
ACAGATGGCGAAAAAGACAT+TGG + chr1_3:63615934-63615953 Msa0132550:CDS 40.0%
GCAGCGACAAGTTATGTTGT+TGG + chr1_3:63614956-63614975 Msa0132550:intron 45.0%
CGGCAATATTGTGAAATCGC+TGG - chr1_3:63614998-63615017 None:intergenic 45.0%
!! CAGCAACCTCATTTTTCGTC+GGG - chr1_3:63615079-63615098 None:intergenic 45.0%
!! GCAGCAACCTCATTTTTCGT+CGG - chr1_3:63615080-63615099 None:intergenic 45.0%
TATGACGTAGGCTTGGCAAT+AGG + chr1_3:63615837-63615856 Msa0132550:CDS 45.0%
GCAGCGACAAGTTATGTTGT+TGG + chr1_3:63614956-63614975 Msa0132550:intron 45.0%
CGGCAATATTGTGAAATCGC+TGG - chr1_3:63614998-63615017 None:intergenic 45.0%
!! CAGCAACCTCATTTTTCGTC+GGG - chr1_3:63615079-63615098 None:intergenic 45.0%
!! GCAGCAACCTCATTTTTCGT+CGG - chr1_3:63615080-63615099 None:intergenic 45.0%
TATGACGTAGGCTTGGCAAT+AGG + chr1_3:63615837-63615856 Msa0132550:CDS 45.0%
!!! TTTATATTATTTTTTTTGAA+AGG - chr1_3:63614933-63614952 None:intergenic 5.0%
!!! TTTATATTATTTTTTTTGAA+AGG - chr1_3:63614933-63614952 None:intergenic 5.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 63614660 63615959 63614660 ID=Msa0132550;Name=Msa0132550
chr1_3 mRNA 63614660 63615959 63614660 ID=Msa0132550-mRNA-1;Parent=Msa0132550;Name=Msa0132550-mRNA-1;_AED=0.50;_eAED=0.54;_QI=0|0|0|0.33|0|0|3|0|75
chr1_3 exon 63614660 63614665 63614660 ID=Msa0132550-mRNA-1:exon:21325;Parent=Msa0132550-mRNA-1
chr1_3 exon 63614960 63614965 63614960 ID=Msa0132550-mRNA-1:exon:21326;Parent=Msa0132550-mRNA-1
chr1_3 exon 63615747 63615959 63615747 ID=Msa0132550-mRNA-1:exon:21327;Parent=Msa0132550-mRNA-1
chr1_3 CDS 63614660 63614665 63614660 ID=Msa0132550-mRNA-1:cds;Parent=Msa0132550-mRNA-1
chr1_3 CDS 63614960 63614965 63614960 ID=Msa0132550-mRNA-1:cds;Parent=Msa0132550-mRNA-1
chr1_3 CDS 63615747 63615959 63615747 ID=Msa0132550-mRNA-1:cds;Parent=Msa0132550-mRNA-1
Gene Sequence

>Msa0132550

ATGGATCGACAATATCTATATTTATCTTGTTGGTACAACATTACAGGACTCGTTGAAGTAATAAAAGGACAAATTAACTCAAGGAAAGACGTTTATTCATTCTATGACGTAGGCTTGGCAATAGGACATTACATTCTACCATCATTTTTGGCAGTTAGACTTCTGTTTGGGATAACATTTTTTATCGCACTATTGATATACAGATGGCGAAAAAGACATTGGTCA

Protein sequence

>Msa0132550

MDRQYLYLSCWYNITGLVEVIKGQINSRKDVYSFYDVGLAIGHYILPSFLAVRLLFGITFFIALLIYRWRKRHWS