AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0880060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0880060 MtrunA17_Chr7g0265731 73.469 196 20 3 22 185 22 217 2.78e-91 265
Msa0880060 MtrunA17_Chr6g0486051 46.610 118 44 2 68 185 48 146 1.11e-28 103
Msa0880060 MtrunA17_Chr2g0287981 39.450 109 63 2 75 182 90 196 6.18e-19 80.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0880060 AT3G52960.1 48.536 239 64 5 1 185 1 234 2.08e-61 191
Msa0880060 AT1G65980.1 58.475 118 46 2 68 185 48 162 2.32e-40 134
Msa0880060 AT1G60740.1 53.390 118 52 2 68 185 48 162 1.58e-37 127
Msa0880060 AT1G65970.1 53.390 118 52 2 68 185 48 162 9.05e-37 125
Msa0880060 AT3G06050.1 39.450 109 63 2 75 182 92 198 1.29e-19 82.4
Msa0880060 AT1G65990.1 43.689 103 51 3 69 171 49 144 1.99e-18 82.4

Find 50 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGATGGTGGCGGAGATTT+TGG 0.162511 6_1:-26126454 None:intergenic
GAGGAGAATCGGAGAGGTTT+TGG 0.170077 6_1:-26126427 None:intergenic
TTTGAGAGGGAGGGTGAATT+TGG 0.195781 6_1:-26126389 None:intergenic
AGGTAGGAGAAGGTGGATTC+AGG 0.275143 6_1:-26126492 None:intergenic
AACCTGTTGGATTGGGTGTT+AGG 0.351123 6_1:+26126823 Msa0880060:CDS
GTCAAGACGTTATGCTTTGT+TGG 0.388577 6_1:+26126845 Msa0880060:CDS
TGCTCACAGAAACACGTTCC+TGG 0.400832 6_1:+26126612 Msa0880060:intron
TGATACAATCGCTTGCATTT+CGG 0.418524 6_1:+26126674 Msa0880060:CDS
GAATTTGGAAGAGAGGGTTT+TGG 0.429478 6_1:-26126374 None:intergenic
GTGATTTCACAAGAGCGATT+GGG 0.431034 6_1:+26126778 Msa0880060:CDS
AGATAAGAGTGAGGTGGTGG+TGG 0.441187 6_1:-26126344 None:intergenic
GGTAGGAGAAGGTGGATTCA+GGG 0.445681 6_1:-26126491 None:intergenic
GACCTAACACCCAATCCAAC+AGG 0.452953 6_1:-26126825 None:intergenic
TTGAAACGGTTGAATTTGAG+AGG 0.455027 6_1:-26126403 None:intergenic
AGCGATAAACCTGTTGGATT+GGG 0.455914 6_1:+26126816 Msa0880060:CDS
AGCGTGGAAGGAGGATTTGA+AGG 0.464799 6_1:+26126719 Msa0880060:CDS
GCTGATTTCTCCACGAATCC+AGG 0.469358 6_1:-26126630 None:intergenic
GGACTTCACCGGCAGGGTCG+AGG 0.473218 6_1:-26126512 None:intergenic
GGTGATTTCACAAGAGCGAT+TGG 0.474269 6_1:+26126777 Msa0880060:CDS
GAGCGATAAACCTGTTGGAT+TGG 0.482422 6_1:+26126815 Msa0880060:CDS
GGAGGGTGAATTTGGAAGAG+AGG 0.482927 6_1:-26126381 None:intergenic
AACGGTTGAATTTGAGAGGG+AGG 0.500645 6_1:-26126399 None:intergenic
GAGTTTGTCGCCGACGGAGA+TGG 0.504087 6_1:-26126469 None:intergenic
GGGAGATAAGAGTGAGGTGG+TGG 0.509192 6_1:-26126347 None:intergenic
GAGGGTGAATTTGGAAGAGA+GGG 0.514701 6_1:-26126380 None:intergenic
TATGCTTTGTTGGCTGAAGA+TGG 0.518833 6_1:+26126855 Msa0880060:CDS
TTCTCCTACCTCGACCCTGC+CGG 0.521198 6_1:+26126504 Msa0880060:CDS
TTCAGGGAGTTTGTCGCCGA+CGG 0.523891 6_1:-26126475 None:intergenic
ACGGTTGAATTTGAGAGGGA+GGG 0.537771 6_1:-26126398 None:intergenic
GATTTGAGCGATAAACCTGT+TGG 0.550461 6_1:+26126810 Msa0880060:CDS
GGCAGGGTCGAGGTAGGAGA+AGG 0.551945 6_1:-26126502 None:intergenic
GTCGCCGACGGAGATGGTGG+CGG 0.556756 6_1:-26126463 None:intergenic
ATCAGCGGAGCTAAAAGCGA+AGG 0.573209 6_1:+26126647 Msa0880060:CDS
TGATTTCACAAGAGCGATTG+GGG 0.578015 6_1:+26126779 Msa0880060:CDS
TTTGTCGCCGACGGAGATGG+TGG 0.580050 6_1:-26126466 None:intergenic
TGGTTTGGACTTCACCGGCA+GGG 0.580205 6_1:-26126518 None:intergenic
GAAACACGTTCCTGGATTCG+TGG 0.581971 6_1:+26126620 Msa0880060:intron
GGGGAAGAGGAGAATCGGAG+AGG 0.599413 6_1:-26126433 None:intergenic
ATCTCCGCCACCATCTCCGT+CGG 0.611751 6_1:+26126459 Msa0880060:CDS
AGGTGGTGGTGGAAGATGAG+AGG 0.612703 6_1:-26126333 None:intergenic
TGAAACGGTTGAATTTGAGA+GGG 0.618873 6_1:-26126402 None:intergenic
AGGGTCGAGGTAGGAGAAGG+TGG 0.620333 6_1:-26126499 None:intergenic
TTTGGGAGATAAGAGTGAGG+TGG 0.623641 6_1:-26126350 None:intergenic
TTCACCGGCAGGGTCGAGGT+AGG 0.624603 6_1:-26126508 None:intergenic
TGTGATGAAAGCGTGGAAGG+AGG 0.635880 6_1:+26126710 Msa0880060:CDS
GTTTGTGATGAAAGCGTGGA+AGG 0.651012 6_1:+26126707 Msa0880060:CDS
TCAGCGGAGCTAAAAGCGAA+GGG 0.675110 6_1:+26126648 Msa0880060:CDS
TTTGAAGGTGAACGATGAAG+TGG 0.684338 6_1:+26126734 Msa0880060:CDS
ATGCGTTTGTGATGAAAGCG+TGG 0.693181 6_1:+26126703 Msa0880060:CDS
TGGATTCGTGGAGAAATCAG+CGG 0.698367 6_1:+26126632 Msa0880060:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTGTTAAGCTTTTCAATT+TGG + chr6_1:26126878-26126897 Msa0880060:CDS 25.0%
! TGTTAAGCTTTTCAATTTGG+AGG + chr6_1:26126881-26126900 Msa0880060:CDS 30.0%
TGAAACGGTTGAATTTGAGA+GGG - chr6_1:26126405-26126424 None:intergenic 35.0%
TTGAAACGGTTGAATTTGAG+AGG - chr6_1:26126406-26126425 None:intergenic 35.0%
!!! CTGCTTTTTTGCCTTTTGTT+AGG - chr6_1:26126557-26126576 None:intergenic 35.0%
TGATACAATCGCTTGCATTT+CGG + chr6_1:26126674-26126693 Msa0880060:CDS 35.0%
! AAGCTTTTCAATTTGGAGGA+AGG + chr6_1:26126885-26126904 Msa0880060:CDS 35.0%
!!! GAAGAGAGGGTTTTGGTTTT+GGG - chr6_1:26126370-26126389 None:intergenic 40.0%
! GAATTTGGAAGAGAGGGTTT+TGG - chr6_1:26126377-26126396 None:intergenic 40.0%
!! ATTTTGGGGAAGAGGAGAAT+CGG - chr6_1:26126441-26126460 None:intergenic 40.0%
TTTGAAGGTGAACGATGAAG+TGG + chr6_1:26126734-26126753 Msa0880060:CDS 40.0%
! AAGTGGTGCTTTTGTCTGAT+GGG + chr6_1:26126751-26126770 Msa0880060:CDS 40.0%
GTGATTTCACAAGAGCGATT+GGG + chr6_1:26126778-26126797 Msa0880060:CDS 40.0%
TGATTTCACAAGAGCGATTG+GGG + chr6_1:26126779-26126798 Msa0880060:CDS 40.0%
GATTTGAGCGATAAACCTGT+TGG + chr6_1:26126810-26126829 Msa0880060:CDS 40.0%
AGCGATAAACCTGTTGGATT+GGG + chr6_1:26126816-26126835 Msa0880060:CDS 40.0%
GTCAAGACGTTATGCTTTGT+TGG + chr6_1:26126845-26126864 Msa0880060:CDS 40.0%
! TATGCTTTGTTGGCTGAAGA+TGG + chr6_1:26126855-26126874 Msa0880060:CDS 40.0%
! CTTTTCAATTTGGAGGAAGG+TGG + chr6_1:26126888-26126907 Msa0880060:CDS 40.0%
TTTGGGAGATAAGAGTGAGG+TGG - chr6_1:26126353-26126372 None:intergenic 45.0%
!!! GGTTTTGGGAGATAAGAGTG+AGG - chr6_1:26126356-26126375 None:intergenic 45.0%
!!! GGAAGAGAGGGTTTTGGTTT+TGG - chr6_1:26126371-26126390 None:intergenic 45.0%
GAGGGTGAATTTGGAAGAGA+GGG - chr6_1:26126383-26126402 None:intergenic 45.0%
TTTGAGAGGGAGGGTGAATT+TGG - chr6_1:26126392-26126411 None:intergenic 45.0%
ACGGTTGAATTTGAGAGGGA+GGG - chr6_1:26126401-26126420 None:intergenic 45.0%
AACGGTTGAATTTGAGAGGG+AGG - chr6_1:26126402-26126421 None:intergenic 45.0%
!!! GGAGAGGTTTTGGGTTGAAA+CGG - chr6_1:26126420-26126439 None:intergenic 45.0%
! AGGAGAATCGGAGAGGTTTT+GGG - chr6_1:26126429-26126448 None:intergenic 45.0%
! GGTTATGGTTTGGACTTCAC+CGG - chr6_1:26126526-26126545 None:intergenic 45.0%
TGTTAGGTCAGAGACGGTTA+TGG - chr6_1:26126541-26126560 None:intergenic 45.0%
ACCGTCTCTGACCTAACAAA+AGG + chr6_1:26126543-26126562 Msa0880060:intron 45.0%
! GCCTTTTGTTAGGTCAGAGA+CGG - chr6_1:26126547-26126566 None:intergenic 45.0%
! ACGTGTTTCTGTGAGCATGT+TGG - chr6_1:26126609-26126628 None:intergenic 45.0%
TGGATTCGTGGAGAAATCAG+CGG + chr6_1:26126632-26126651 Msa0880060:CDS 45.0%
ATGCGTTTGTGATGAAAGCG+TGG + chr6_1:26126703-26126722 Msa0880060:CDS 45.0%
! GTTTGTGATGAAAGCGTGGA+AGG + chr6_1:26126707-26126726 Msa0880060:CDS 45.0%
! GAAGTGGTGCTTTTGTCTGA+TGG + chr6_1:26126750-26126769 Msa0880060:CDS 45.0%
! GTGCTTTTGTCTGATGGGAA+TGG + chr6_1:26126756-26126775 Msa0880060:CDS 45.0%
GGTGATTTCACAAGAGCGAT+TGG + chr6_1:26126777-26126796 Msa0880060:CDS 45.0%
GAGCGATAAACCTGTTGGAT+TGG + chr6_1:26126815-26126834 Msa0880060:CDS 45.0%
! AACCTGTTGGATTGGGTGTT+AGG + chr6_1:26126823-26126842 Msa0880060:CDS 45.0%
! GGTGGTGCTTTTACTTTCAG+TGG + chr6_1:26126906-26126925 Msa0880060:CDS 45.0%
! AGATAAGAGTGAGGTGGTGG+TGG - chr6_1:26126347-26126366 None:intergenic 50.0%
GGAGGGTGAATTTGGAAGAG+AGG - chr6_1:26126384-26126403 None:intergenic 50.0%
! GAGGAGAATCGGAGAGGTTT+TGG - chr6_1:26126430-26126449 None:intergenic 50.0%
!!! AGATGGTGGCGGAGATTTTG+GGG - chr6_1:26126455-26126474 None:intergenic 50.0%
!!! GAGATGGTGGCGGAGATTTT+GGG - chr6_1:26126456-26126475 None:intergenic 50.0%
! GGTAGGAGAAGGTGGATTCA+GGG - chr6_1:26126494-26126513 None:intergenic 50.0%
! AGGTAGGAGAAGGTGGATTC+AGG - chr6_1:26126495-26126514 None:intergenic 50.0%
GGTCAGAGACGGTTATGGTT+TGG - chr6_1:26126536-26126555 None:intergenic 50.0%
TGGTGTGAAAGCTCCTGGAA+CGG - chr6_1:26126589-26126608 None:intergenic 50.0%
CATGTTGGTGTGAAAGCTCC+TGG - chr6_1:26126594-26126613 None:intergenic 50.0%
TGCTCACAGAAACACGTTCC+TGG + chr6_1:26126612-26126631 Msa0880060:intron 50.0%
GAAACACGTTCCTGGATTCG+TGG + chr6_1:26126620-26126639 Msa0880060:intron 50.0%
! GCTGATTTCTCCACGAATCC+AGG - chr6_1:26126633-26126652 None:intergenic 50.0%
ATCAGCGGAGCTAAAAGCGA+AGG + chr6_1:26126647-26126666 Msa0880060:CDS 50.0%
TCAGCGGAGCTAAAAGCGAA+GGG + chr6_1:26126648-26126667 Msa0880060:CDS 50.0%
! TGTGATGAAAGCGTGGAAGG+AGG + chr6_1:26126710-26126729 Msa0880060:CDS 50.0%
AGCGTGGAAGGAGGATTTGA+AGG + chr6_1:26126719-26126738 Msa0880060:CDS 50.0%
GACCTAACACCCAATCCAAC+AGG - chr6_1:26126828-26126847 None:intergenic 50.0%
!! AGGTGGTGGTGGAAGATGAG+AGG - chr6_1:26126336-26126355 None:intergenic 55.0%
GGGAGATAAGAGTGAGGTGG+TGG - chr6_1:26126350-26126369 None:intergenic 55.0%
!! TGGCGGAGATTTTGGGGAAG+AGG - chr6_1:26126449-26126468 None:intergenic 55.0%
!!! GGAGATGGTGGCGGAGATTT+TGG - chr6_1:26126457-26126476 None:intergenic 55.0%
TTCAGGGAGTTTGTCGCCGA+CGG - chr6_1:26126478-26126497 None:intergenic 55.0%
! TGGTTTGGACTTCACCGGCA+GGG - chr6_1:26126521-26126540 None:intergenic 55.0%
! ATGGTTTGGACTTCACCGGC+AGG - chr6_1:26126522-26126541 None:intergenic 55.0%
GGGGAAGAGGAGAATCGGAG+AGG - chr6_1:26126436-26126455 None:intergenic 60.0%
ATCTCCGCCACCATCTCCGT+CGG + chr6_1:26126459-26126478 Msa0880060:CDS 60.0%
TTTGTCGCCGACGGAGATGG+TGG - chr6_1:26126469-26126488 None:intergenic 60.0%
GAGTTTGTCGCCGACGGAGA+TGG - chr6_1:26126472-26126491 None:intergenic 60.0%
AGGGTCGAGGTAGGAGAAGG+TGG - chr6_1:26126502-26126521 None:intergenic 60.0%
TTCTCCTACCTCGACCCTGC+CGG + chr6_1:26126504-26126523 Msa0880060:CDS 60.0%
AAGCTCCTGGAACGGCGAAG+AGG - chr6_1:26126581-26126600 None:intergenic 60.0%
GGCAGGGTCGAGGTAGGAGA+AGG - chr6_1:26126505-26126524 None:intergenic 65.0%
TTCACCGGCAGGGTCGAGGT+AGG - chr6_1:26126511-26126530 None:intergenic 65.0%
GCAGTCCTCTTCGCCGTTCC+AGG + chr6_1:26126573-26126592 Msa0880060:intron 65.0%
! GTCGCCGACGGAGATGGTGG+CGG - chr6_1:26126466-26126485 None:intergenic 70.0%
GGACTTCACCGGCAGGGTCG+AGG - chr6_1:26126515-26126534 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 26126304 26126956 26126304 ID=Msa0880060;Name=Msa0880060
chr6_1 mRNA 26126304 26126956 26126304 ID=Msa0880060-mRNA-1;Parent=Msa0880060;Name=Msa0880060-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0|0|1|1|1|2|0|185
chr6_1 exon 26126304 26126525 26126304 ID=Msa0880060-mRNA-1:exon:6355;Parent=Msa0880060-mRNA-1
chr6_1 exon 26126621 26126956 26126621 ID=Msa0880060-mRNA-1:exon:6356;Parent=Msa0880060-mRNA-1
chr6_1 CDS 26126304 26126525 26126304 ID=Msa0880060-mRNA-1:cds;Parent=Msa0880060-mRNA-1
chr6_1 CDS 26126621 26126956 26126621 ID=Msa0880060-mRNA-1:cds;Parent=Msa0880060-mRNA-1
Gene Sequence

>Msa0880060

ATGGCAACATCACTCTCTTTCTCTAGACTCCTCTCATCTTCCACCACCACCTCACTCTTATCTCCCAAAACCAAAACCCTCTCTTCCAAATTCACCCTCCCTCTCAAATTCAACCGTTTCAACCCAAAACCTCTCCGATTCTCCTCTTCCCCAAAATCTCCGCCACCATCTCCGTCGGCGACAAACTCCCTGAATCCACCTTCTCCTACCTCGACCCTGCCGAAACACGTTCCTGGATTCGTGGAGAAATCAGCGGAGCTAAAAGCGAAGGGAGTTGATACAATCGCTTGCATTTCGGTGAACGATGCGTTTGTGATGAAAGCGTGGAAGGAGGATTTGAAGGTGAACGATGAAGTGGTGCTTTTGTCTGATGGGAATGGTGATTTCACAAGAGCGATTGGGGTTGAGCTTGATTTGAGCGATAAACCTGTTGGATTGGGTGTTAGGTCAAGACGTTATGCTTTGTTGGCTGAAGATGGTGTTGTTAAGCTTTTCAATTTGGAGGAAGGTGGTGCTTTTACTTTCAGTGGTGCTGATGATATTCTCAAAGTTCTTTGA
Protein sequence

>Msa0880060

MATSLSFSRLLSSSTTTSLLSPKTKTLSSKFTLPLKFNRFNPKPLRFSSSPKSPPPSPSATNSLNPPSPTSTLPKHVPGFVEKSAELKAKGVDTIACISVNDAFVMKAWKEDLKVNDEVVLLSDGNGDFTRAIGVELDLSDKPVGLGVRSRRYALLAEDGVVKLFNLEEGGAFTFSGADDILKVL*