AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0862960


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0862960 MtrunA17_Chr5g0444521 90.984 122 8 1 1 122 1 119 1.22e-77 224
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 49 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTTCAGTAAGTTCATTA+AGG 0.284385 5_4:-62706444 Msa0862960:CDS
CCCTTAAGCAATCGTTGTTC+TGG 0.294188 5_4:+62706016 None:intergenic
CTTCTGCATCATCAACCTTC+TGG 0.304356 5_4:+62706107 None:intergenic
ATTGTTTAAGTGTGTGAATT+TGG 0.321935 5_4:-62705985 Msa0862960:three_prime_UTR
CCAGAACAACGATTGCTTAA+GGG 0.353383 5_4:-62706016 Msa0862960:three_prime_UTR
CGCAGCAGCAACATTATCTA+AGG 0.361910 5_4:-62706531 Msa0862960:CDS
GCAGCAACAACAATGATATC+TGG 0.364461 5_4:+62706409 None:intergenic
GCACAACACAAAACTACTTT+GGG 0.366214 5_4:-62706503 Msa0862960:CDS
AGAAAAGAACCGAACCTTAC+TGG 0.375391 5_4:+62706346 None:intergenic
TGTTCACTTGGGATAATGTT+TGG 0.377532 5_4:+62706674 None:intergenic
TCCAGAACAACGATTGCTTA+AGG 0.377860 5_4:-62706017 Msa0862960:three_prime_UTR
GTTCACTTGGGATAATGTTT+GGG 0.382397 5_4:+62706675 None:intergenic
TCTTCAACAAGATATAGTTT+TGG 0.385269 5_4:+62706644 None:intergenic
ATGGATCGGCGGGTTGTGGC+AGG 0.389363 5_4:+62706380 None:intergenic
AAATACTTGCTTATAAAATC+TGG 0.401289 5_4:+62706154 None:intergenic
GAAGCAATGAAGAGGGGAGG+TGG 0.407582 5_4:+62706575 None:intergenic
CTATGTGGCATGGTCTTGCT+TGG 0.417895 5_4:+62706475 None:intergenic
TTTGGTTCACTGTGTTCACT+TGG 0.441499 5_4:+62706662 None:intergenic
AGCACAACACAAAACTACTT+TGG 0.452055 5_4:-62706504 Msa0862960:CDS
AATTTATAATGTATAATGTA+AGG 0.459373 5_4:-62706728 None:intergenic
CAATGATATCTGGAATTGCC+TGG 0.462076 5_4:+62706419 None:intergenic
TGAAGTATACTGATATAAGC+AGG 0.464588 5_4:+62706194 None:intergenic
CTTACTGGGAGAAAAGTAGA+TGG 0.479013 5_4:+62706361 None:intergenic
GTAGATGGATCGGCGGGTTG+TGG 0.490348 5_4:+62706376 None:intergenic
AAGCAATCGTTGTTCTGGAA+TGG 0.491369 5_4:+62706021 None:intergenic
GAAAAGAACCGAACCTTACT+GGG 0.530829 5_4:+62706347 None:intergenic
CTTAGATAATGTTGCTGCTG+CGG 0.540896 5_4:+62706532 None:intergenic
TTGGGATAATGTTTGGGAGG+AGG 0.545339 5_4:+62706681 None:intergenic
TTGGTTCACTGTGTTCACTT+GGG 0.550658 5_4:+62706663 None:intergenic
TTTGGATTTGATAAACTAGA+GGG 0.553590 5_4:-62706133 Msa0862960:CDS
CACTTGGGATAATGTTTGGG+AGG 0.556445 5_4:+62706678 None:intergenic
TGCATGAGAAGCAATGAAGA+GGG 0.563172 5_4:+62706568 None:intergenic
TGGATCGGCGGGTTGTGGCA+GGG 0.568272 5_4:+62706381 None:intergenic
AGAAAAGTAGATGGATCGGC+GGG 0.588206 5_4:+62706370 None:intergenic
AATGATATCTGGAATTGCCT+GGG 0.588413 5_4:+62706420 None:intergenic
GAAGAAAAGTGCTTACTATG+TGG 0.588606 5_4:+62706460 None:intergenic
TGGGAGAAAAGTAGATGGAT+CGG 0.598368 5_4:+62706366 None:intergenic
AAGCTTAGTTAAGTTATGCG+TGG 0.600225 5_4:+62706613 None:intergenic
GCAGCAACATTATCTAAGGA+TGG 0.606428 5_4:-62706527 Msa0862960:CDS
AGTAAGTTCATTAAGGACCC+AGG 0.609846 5_4:-62706437 Msa0862960:CDS
TAAACTAGAGGGAGACCAGA+AGG 0.616294 5_4:-62706122 Msa0862960:CDS
AAAGTGCTTACTATGTGGCA+TGG 0.619717 5_4:+62706465 None:intergenic
GAAGTATACTGATATAAGCA+GGG 0.632422 5_4:+62706195 None:intergenic
GGGGAGGTGGAGACAAGTCA+TGG 0.642574 5_4:+62706588 None:intergenic
ATGCATGAGAAGCAATGAAG+AGG 0.647708 5_4:+62706567 None:intergenic
TGAGAAGCAATGAAGAGGGG+AGG 0.663602 5_4:+62706572 None:intergenic
GAGAAAAGTAGATGGATCGG+CGG 0.670606 5_4:+62706369 None:intergenic
GCATGAGAAGCAATGAAGAG+GGG 0.705476 5_4:+62706569 None:intergenic
CACAACACAAAACTACTTTG+GGG 0.712340 5_4:-62706502 Msa0862960:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAGTATTTTTTTTTTACACT+AGG - chr5_4:62706340-62706359 Msa0862960:intron 15.0%
!!! TAGTATTTTTTTTTTACACT+AGG - chr5_4:62706340-62706359 Msa0862960:intron 15.0%
!! AAATACTTGCTTATAAAATC+TGG + chr5_4:62706475-62706494 None:intergenic 20.0%
!!! GATTTTATAAGCAAGTATTT+TGG - chr5_4:62706475-62706494 Msa0862960:CDS 20.0%
!! AAATACTTGCTTATAAAATC+TGG + chr5_4:62706475-62706494 None:intergenic 20.0%
!!! GATTTTATAAGCAAGTATTT+TGG - chr5_4:62706475-62706494 Msa0862960:CDS 20.0%
!! TCTTCAACAAGATATAGTTT+TGG + chr5_4:62705985-62706004 None:intergenic 25.0%
! TTTCTTCAGTAAGTTCATTA+AGG - chr5_4:62706182-62706201 Msa0862960:CDS 25.0%
! GTTCATTATGTCATATTTCA+TGG - chr5_4:62706310-62706329 Msa0862960:intron 25.0%
!! TTTTGGATTTGATAAACTAG+AGG - chr5_4:62706492-62706511 Msa0862960:CDS 25.0%
! TTTGGATTTGATAAACTAGA+GGG - chr5_4:62706493-62706512 Msa0862960:CDS 25.0%
!!! TACTTTTTTTCTTCACATCA+GGG + chr5_4:62706561-62706580 None:intergenic 25.0%
!!! ATACTTTTTTTCTTCACATC+AGG + chr5_4:62706562-62706581 None:intergenic 25.0%
! ATTGTTTAAGTGTGTGAATT+TGG - chr5_4:62706641-62706660 Msa0862960:five_prime_UTR 25.0%
!!! CATCTGTATTGTTTTAAACA+TGG - chr5_4:62706701-62706720 Msa0862960:five_prime_UTR 25.0%
!! TCTTCAACAAGATATAGTTT+TGG + chr5_4:62705985-62706004 None:intergenic 25.0%
! TTTCTTCAGTAAGTTCATTA+AGG - chr5_4:62706182-62706201 Msa0862960:CDS 25.0%
! GTTCATTATGTCATATTTCA+TGG - chr5_4:62706310-62706329 Msa0862960:intron 25.0%
!! TTTTGGATTTGATAAACTAG+AGG - chr5_4:62706492-62706511 Msa0862960:CDS 25.0%
! TTTGGATTTGATAAACTAGA+GGG - chr5_4:62706493-62706512 Msa0862960:CDS 25.0%
!!! TACTTTTTTTCTTCACATCA+GGG + chr5_4:62706561-62706580 None:intergenic 25.0%
!!! ATACTTTTTTTCTTCACATC+AGG + chr5_4:62706562-62706581 None:intergenic 25.0%
! ATTGTTTAAGTGTGTGAATT+TGG - chr5_4:62706641-62706660 Msa0862960:five_prime_UTR 25.0%
!!! CATCTGTATTGTTTTAAACA+TGG - chr5_4:62706701-62706720 Msa0862960:five_prime_UTR 25.0%
GAAGTATACTGATATAAGCA+GGG + chr5_4:62706434-62706453 None:intergenic 30.0%
TGAAGTATACTGATATAAGC+AGG + chr5_4:62706435-62706454 None:intergenic 30.0%
GAAGTATACTGATATAAGCA+GGG + chr5_4:62706434-62706453 None:intergenic 30.0%
TGAAGTATACTGATATAAGC+AGG + chr5_4:62706435-62706454 None:intergenic 30.0%
GTTCACTTGGGATAATGTTT+GGG + chr5_4:62705954-62705973 None:intergenic 35.0%
TGTTCACTTGGGATAATGTT+TGG + chr5_4:62705955-62705974 None:intergenic 35.0%
AAGCTTAGTTAAGTTATGCG+TGG + chr5_4:62706016-62706035 None:intergenic 35.0%
AGCACAACACAAAACTACTT+TGG - chr5_4:62706122-62706141 Msa0862960:CDS 35.0%
GCACAACACAAAACTACTTT+GGG - chr5_4:62706123-62706142 Msa0862960:CDS 35.0%
CACAACACAAAACTACTTTG+GGG - chr5_4:62706124-62706143 Msa0862960:CDS 35.0%
!! GAAGAAAAGTGCTTACTATG+TGG + chr5_4:62706169-62706188 None:intergenic 35.0%
! AATGATATCTGGAATTGCCT+GGG + chr5_4:62706209-62706228 None:intergenic 35.0%
CAAGCTGCAAACTTAAAACA+AGG - chr5_4:62706371-62706390 Msa0862960:CDS 35.0%
GTTCACTTGGGATAATGTTT+GGG + chr5_4:62705954-62705973 None:intergenic 35.0%
TGTTCACTTGGGATAATGTT+TGG + chr5_4:62705955-62705974 None:intergenic 35.0%
AAGCTTAGTTAAGTTATGCG+TGG + chr5_4:62706016-62706035 None:intergenic 35.0%
AGCACAACACAAAACTACTT+TGG - chr5_4:62706122-62706141 Msa0862960:CDS 35.0%
GCACAACACAAAACTACTTT+GGG - chr5_4:62706123-62706142 Msa0862960:CDS 35.0%
CACAACACAAAACTACTTTG+GGG - chr5_4:62706124-62706143 Msa0862960:CDS 35.0%
!! GAAGAAAAGTGCTTACTATG+TGG + chr5_4:62706169-62706188 None:intergenic 35.0%
! AATGATATCTGGAATTGCCT+GGG + chr5_4:62706209-62706228 None:intergenic 35.0%
CAAGCTGCAAACTTAAAACA+AGG - chr5_4:62706371-62706390 Msa0862960:CDS 35.0%
TTGGTTCACTGTGTTCACTT+GGG + chr5_4:62705966-62705985 None:intergenic 40.0%
! TTTGGTTCACTGTGTTCACT+TGG + chr5_4:62705967-62705986 None:intergenic 40.0%
TGCATGAGAAGCAATGAAGA+GGG + chr5_4:62706061-62706080 None:intergenic 40.0%
ATGCATGAGAAGCAATGAAG+AGG + chr5_4:62706062-62706081 None:intergenic 40.0%
CTTAGATAATGTTGCTGCTG+CGG + chr5_4:62706097-62706116 None:intergenic 40.0%
GCAGCAACATTATCTAAGGA+TGG - chr5_4:62706099-62706118 Msa0862960:CDS 40.0%
! AAAGTGCTTACTATGTGGCA+TGG + chr5_4:62706164-62706183 None:intergenic 40.0%
AGTAAGTTCATTAAGGACCC+AGG - chr5_4:62706189-62706208 Msa0862960:CDS 40.0%
! CAATGATATCTGGAATTGCC+TGG + chr5_4:62706210-62706229 None:intergenic 40.0%
GCAGCAACAACAATGATATC+TGG + chr5_4:62706220-62706239 None:intergenic 40.0%
TGGGAGAAAAGTAGATGGAT+CGG + chr5_4:62706263-62706282 None:intergenic 40.0%
CTTACTGGGAGAAAAGTAGA+TGG + chr5_4:62706268-62706287 None:intergenic 40.0%
!! CATCTACTTTTCTCCCAGTA+AGG - chr5_4:62706266-62706285 Msa0862960:intron 40.0%
! ACTTTTCTCCCAGTAAGGTT+CGG - chr5_4:62706271-62706290 Msa0862960:intron 40.0%
GAAAAGAACCGAACCTTACT+GGG + chr5_4:62706282-62706301 None:intergenic 40.0%
AGAAAAGAACCGAACCTTAC+TGG + chr5_4:62706283-62706302 None:intergenic 40.0%
!! AAGCAATCGTTGTTCTGGAA+TGG + chr5_4:62706608-62706627 None:intergenic 40.0%
TCCAGAACAACGATTGCTTA+AGG - chr5_4:62706609-62706628 Msa0862960:five_prime_UTR 40.0%
CCAGAACAACGATTGCTTAA+GGG - chr5_4:62706610-62706629 Msa0862960:five_prime_UTR 40.0%
TTGGTTCACTGTGTTCACTT+GGG + chr5_4:62705966-62705985 None:intergenic 40.0%
! TTTGGTTCACTGTGTTCACT+TGG + chr5_4:62705967-62705986 None:intergenic 40.0%
TGCATGAGAAGCAATGAAGA+GGG + chr5_4:62706061-62706080 None:intergenic 40.0%
ATGCATGAGAAGCAATGAAG+AGG + chr5_4:62706062-62706081 None:intergenic 40.0%
CTTAGATAATGTTGCTGCTG+CGG + chr5_4:62706097-62706116 None:intergenic 40.0%
GCAGCAACATTATCTAAGGA+TGG - chr5_4:62706099-62706118 Msa0862960:CDS 40.0%
! AAAGTGCTTACTATGTGGCA+TGG + chr5_4:62706164-62706183 None:intergenic 40.0%
AGTAAGTTCATTAAGGACCC+AGG - chr5_4:62706189-62706208 Msa0862960:CDS 40.0%
! CAATGATATCTGGAATTGCC+TGG + chr5_4:62706210-62706229 None:intergenic 40.0%
GCAGCAACAACAATGATATC+TGG + chr5_4:62706220-62706239 None:intergenic 40.0%
TGGGAGAAAAGTAGATGGAT+CGG + chr5_4:62706263-62706282 None:intergenic 40.0%
CTTACTGGGAGAAAAGTAGA+TGG + chr5_4:62706268-62706287 None:intergenic 40.0%
!! CATCTACTTTTCTCCCAGTA+AGG - chr5_4:62706266-62706285 Msa0862960:intron 40.0%
! ACTTTTCTCCCAGTAAGGTT+CGG - chr5_4:62706271-62706290 Msa0862960:intron 40.0%
GAAAAGAACCGAACCTTACT+GGG + chr5_4:62706282-62706301 None:intergenic 40.0%
AGAAAAGAACCGAACCTTAC+TGG + chr5_4:62706283-62706302 None:intergenic 40.0%
!! AAGCAATCGTTGTTCTGGAA+TGG + chr5_4:62706608-62706627 None:intergenic 40.0%
TCCAGAACAACGATTGCTTA+AGG - chr5_4:62706609-62706628 Msa0862960:five_prime_UTR 40.0%
CCAGAACAACGATTGCTTAA+GGG - chr5_4:62706610-62706629 Msa0862960:five_prime_UTR 40.0%
TTGGGATAATGTTTGGGAGG+AGG + chr5_4:62705948-62705967 None:intergenic 45.0%
CACTTGGGATAATGTTTGGG+AGG + chr5_4:62705951-62705970 None:intergenic 45.0%
GCATGAGAAGCAATGAAGAG+GGG + chr5_4:62706060-62706079 None:intergenic 45.0%
CGCAGCAGCAACATTATCTA+AGG - chr5_4:62706095-62706114 Msa0862960:exon 45.0%
AGAAAAGTAGATGGATCGGC+GGG + chr5_4:62706259-62706278 None:intergenic 45.0%
GAGAAAAGTAGATGGATCGG+CGG + chr5_4:62706260-62706279 None:intergenic 45.0%
TAAACTAGAGGGAGACCAGA+AGG - chr5_4:62706504-62706523 Msa0862960:CDS 45.0%
CTTCTGCATCATCAACCTTC+TGG + chr5_4:62706522-62706541 None:intergenic 45.0%
CCCTTAAGCAATCGTTGTTC+TGG + chr5_4:62706613-62706632 None:intergenic 45.0%
TTGGGATAATGTTTGGGAGG+AGG + chr5_4:62705948-62705967 None:intergenic 45.0%
CACTTGGGATAATGTTTGGG+AGG + chr5_4:62705951-62705970 None:intergenic 45.0%
GCATGAGAAGCAATGAAGAG+GGG + chr5_4:62706060-62706079 None:intergenic 45.0%
CGCAGCAGCAACATTATCTA+AGG - chr5_4:62706095-62706114 Msa0862960:exon 45.0%
AGAAAAGTAGATGGATCGGC+GGG + chr5_4:62706259-62706278 None:intergenic 45.0%
GAGAAAAGTAGATGGATCGG+CGG + chr5_4:62706260-62706279 None:intergenic 45.0%
TAAACTAGAGGGAGACCAGA+AGG - chr5_4:62706504-62706523 Msa0862960:CDS 45.0%
CTTCTGCATCATCAACCTTC+TGG + chr5_4:62706522-62706541 None:intergenic 45.0%
CCCTTAAGCAATCGTTGTTC+TGG + chr5_4:62706613-62706632 None:intergenic 45.0%
TGAGAAGCAATGAAGAGGGG+AGG + chr5_4:62706057-62706076 None:intergenic 50.0%
! CTATGTGGCATGGTCTTGCT+TGG + chr5_4:62706154-62706173 None:intergenic 50.0%
TGAGAAGCAATGAAGAGGGG+AGG + chr5_4:62706057-62706076 None:intergenic 50.0%
! CTATGTGGCATGGTCTTGCT+TGG + chr5_4:62706154-62706173 None:intergenic 50.0%
GAAGCAATGAAGAGGGGAGG+TGG + chr5_4:62706054-62706073 None:intergenic 55.0%
GAAGCAATGAAGAGGGGAGG+TGG + chr5_4:62706054-62706073 None:intergenic 55.0%
GGGGAGGTGGAGACAAGTCA+TGG + chr5_4:62706041-62706060 None:intergenic 60.0%
!! GTAGATGGATCGGCGGGTTG+TGG + chr5_4:62706253-62706272 None:intergenic 60.0%
GGGGAGGTGGAGACAAGTCA+TGG + chr5_4:62706041-62706060 None:intergenic 60.0%
!! GTAGATGGATCGGCGGGTTG+TGG + chr5_4:62706253-62706272 None:intergenic 60.0%
!! TGGATCGGCGGGTTGTGGCA+GGG + chr5_4:62706248-62706267 None:intergenic 65.0%
!! ATGGATCGGCGGGTTGTGGC+AGG + chr5_4:62706249-62706268 None:intergenic 65.0%
!! TGGATCGGCGGGTTGTGGCA+GGG + chr5_4:62706248-62706267 None:intergenic 65.0%
!! ATGGATCGGCGGGTTGTGGC+AGG + chr5_4:62706249-62706268 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 62705905 62706743 62705905 ID=Msa0862960;Name=Msa0862960
chr5_4 mRNA 62705905 62706743 62705905 ID=Msa0862960-mRNA-1;Parent=Msa0862960;Name=Msa0862960-mRNA-1;_AED=0.08;_eAED=0.08;_QI=135|1|1|1|1|1|2|194|122
chr5_4 exon 62705905 62706219 62705905 ID=Msa0862960-mRNA-1:exon:19637;Parent=Msa0862960-mRNA-1
chr5_4 exon 62706361 62706743 62706361 ID=Msa0862960-mRNA-1:exon:19636;Parent=Msa0862960-mRNA-1
chr5_4 five_prime_UTR 62706609 62706743 62706609 ID=Msa0862960-mRNA-1:five_prime_utr;Parent=Msa0862960-mRNA-1
chr5_4 CDS 62706361 62706608 62706361 ID=Msa0862960-mRNA-1:cds;Parent=Msa0862960-mRNA-1
chr5_4 CDS 62706099 62706219 62706099 ID=Msa0862960-mRNA-1:cds;Parent=Msa0862960-mRNA-1
chr5_4 three_prime_UTR 62705905 62706098 62705905 ID=Msa0862960-mRNA-1:three_prime_utr;Parent=Msa0862960-mRNA-1
Gene Sequence

>Msa0862960

ATGACTTGTCTCCACCTCCCCTCTTCATTGCTTCTCATGCATACAAAACTCAAACCGCAGCAGCAACATTATCTAAGGATGGAGCACAACACAAAACTACTTTGGGGAGAACCAAGCAAGACCATGCCACATAGTAAGCACTTTTCTTCAGTAAGTTCATTAAGGACCCAGGCAATTCCAGATATCATTGTTGTTGCTGCTACTTCCCTGCCACAACCCGCCGATCCATCTACTTTTCTCCCAGTAAGTGCCCTGCTTATATCAGTATACTTCATAGCAAATTTCGTCGTGCCAGATTTTATAAGCAAGTATTTTGGATTTGATAAACTAGAGGGAGACCAGAAGGTTGATGATGCAGAAGATAAATAG

Protein sequence

>Msa0862960

MTCLHLPSSLLLMHTKLKPQQQHYLRMEHNTKLLWGEPSKTMPHSKHFSSVSSLRTQAIPDIIVVAATSLPQPADPSTFLPVSALLISVYFIANFVVPDFISKYFGFDKLEGDQKVDDAEDK*