AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1444070


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1444070 MtrunA17_Chr3g0087871 96.281 242 7 1 1 240 1 242 2.51e-171 471
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1444070 AT3G63540.1 78.261 138 30 0 102 239 3 140 4.83e-82 242

Find 48 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATATCTAACTTTCCTTTC+TGG 0.121727 tig0030651:+40361 Msa1444070:CDS
TCTTTCTCTGTTCTCTTCTT+TGG 0.152693 tig0030651:-40340 None:intergenic
GGTGGCGGAGGAGGAGAAAA+TGG 0.261123 tig0030651:-39987 None:intergenic
AAACGTTCCTTCCAACCTTC+TGG 0.272048 tig0030651:-40265 None:intergenic
AATATCTAACTTTCCTTTCT+GGG 0.289515 tig0030651:+40362 Msa1444070:CDS
TTAATATCAAAAGTTGAAAA+AGG 0.291067 tig0030651:+40286 Msa1444070:CDS
TTCTGCTGAGTCTTTCTTGT+TGG 0.307382 tig0030651:-40227 None:intergenic
GGTGGTGGTTGTGGTGGTGC+TGG 0.309152 tig0030651:-40008 None:intergenic
GGTGGTTGTGGTGGTGGTTG+TGG 0.314639 tig0030651:-40017 None:intergenic
TATGGTGGTGGTTGTGGTGG+TGG 0.368688 tig0030651:-40023 None:intergenic
TATTATGTTTATGAGATTGA+TGG 0.386671 tig0030651:+40514 Msa1444070:CDS
TATAGCTGCTGCTGCTGTTA+AGG 0.390254 tig0030651:-40092 None:intergenic
GGTGGTGCTGGTGGCGGAGG+AGG 0.407598 tig0030651:-39996 None:intergenic
TGTGGTGGTGCTGGTGGCGG+AGG 0.415764 tig0030651:-39999 None:intergenic
GCTGTTAAGGTGGTGGTTAG+AGG 0.417250 tig0030651:-40079 None:intergenic
TTGTTCAAAACAGCATCTTT+TGG 0.423752 tig0030651:-40400 None:intergenic
GGTTGTGGTGGTGCTGGTGG+CGG 0.427977 tig0030651:-40002 None:intergenic
GGTTGTGGTGGTGGTTGTGG+TGG 0.436083 tig0030651:-40014 None:intergenic
TGATATGGTGGTGGTTGTGG+TGG 0.462996 tig0030651:-40026 None:intergenic
AGGAGATGATTCTGCTGCTA+TGG 0.480110 tig0030651:-40143 None:intergenic
GAAGAAGTGAAAGATGATAA+AGG 0.482410 tig0030651:+40484 Msa1444070:CDS
TCTTTATTCCACTCAGGAGT+AGG 0.485770 tig0030651:-40607 None:intergenic
GTGCCGTAGTAGAGATTGTA+AGG 0.489374 tig0030651:-40163 None:intergenic
GTGGCGGAGGAGGAGAAAAT+GGG 0.492073 tig0030651:-39986 None:intergenic
GCAGCAAACTACGGCGGCTA+CGG 0.501712 tig0030651:+40196 Msa1444070:CDS
AATTTGCAAGATATTATTAG+TGG 0.515902 tig0030651:+40442 Msa1444070:CDS
TGCTGCTGCTGTTAAGGTGG+TGG 0.518372 tig0030651:-40086 None:intergenic
TCCTTATCTTTATTCCACTC+AGG 0.519893 tig0030651:-40613 None:intergenic
TTGTGTTTGAATGAGATAAG+AGG 0.520933 tig0030651:-40052 None:intergenic
GCGGAGGAGGAGAAAATGGG+TGG 0.522990 tig0030651:-39983 None:intergenic
TCCTGAGTGGAATAAAGATA+AGG 0.526998 tig0030651:+40612 Msa1444070:CDS
GGTGGTTGTGGTGGTGCTGG+TGG 0.546258 tig0030651:-40005 None:intergenic
AGGTGGTGATGTTGTCAGAA+TGG 0.556486 tig0030651:-40119 None:intergenic
GCAGCAAGTGCAGCAAACTA+CGG 0.563093 tig0030651:+40187 Msa1444070:CDS
TCTACGACGTTCCAGAAGGT+TGG 0.565732 tig0030651:+40254 Msa1444070:CDS
AGCTGCTGCTGCTGTTAAGG+TGG 0.570466 tig0030651:-40089 None:intergenic
GCAAACTACGGCGGCTACGG+CGG 0.573351 tig0030651:+40199 Msa1444070:CDS
TCTCCTTACAATCTCTACTA+CGG 0.578619 tig0030651:+40160 Msa1444070:CDS
GAGGAGGAGAAAATGGGTGG+TGG 0.579804 tig0030651:-39980 None:intergenic
CGACGTTCCAGAAGGTTGGA+AGG 0.585452 tig0030651:+40258 Msa1444070:CDS
GATGATTCTGCTGCTATGGA+AGG 0.605999 tig0030651:-40139 None:intergenic
GCAAGTGCAGCAAACTACGG+CGG 0.619443 tig0030651:+40190 Msa1444070:CDS
TACATCTACGACGTTCCAGA+AGG 0.628307 tig0030651:+40250 Msa1444070:CDS
CTAACTGACGAAACCCAGAA+AGG 0.634618 tig0030651:-40375 None:intergenic
TTAATGCTCCTACTCCTGAG+TGG 0.644053 tig0030651:+40599 Msa1444070:CDS
GATTCTGCTGCTATGGAAGG+TGG 0.667537 tig0030651:-40136 None:intergenic
TGGTGATGATGAGAAAATTG+TGG 0.687506 tig0030651:-39960 None:intergenic
TGGTGATGTTGTCAGAATGG+TGG 0.721157 tig0030651:-40116 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATATCAAAAGTTGAAAA+AGG + tig0030651:40286-40305 Msa1444070:CDS 15.0%
!! AATTTGCAAGATATTATTAG+TGG + tig0030651:40442-40461 Msa1444070:CDS 20.0%
!! TATTATGTTTATGAGATTGA+TGG + tig0030651:40514-40533 Msa1444070:CDS 20.0%
!! AAAGTTGAAAAAGGTACAAA+TGG + tig0030651:40295-40314 Msa1444070:CDS 25.0%
! AATATCTAACTTTCCTTTCT+GGG + tig0030651:40362-40381 Msa1444070:CDS 25.0%
!! TGAGATAAGAGGTTTTGATA+TGG - tig0030651:40044-40063 None:intergenic 30.0%
TTGTGTTTGAATGAGATAAG+AGG - tig0030651:40055-40074 None:intergenic 30.0%
GAATATCTAACTTTCCTTTC+TGG + tig0030651:40361-40380 Msa1444070:CDS 30.0%
! TTGTTCAAAACAGCATCTTT+TGG - tig0030651:40403-40422 None:intergenic 30.0%
GAAGAAGTGAAAGATGATAA+AGG + tig0030651:40484-40503 Msa1444070:CDS 30.0%
! TGGTGATGATGAGAAAATTG+TGG - tig0030651:39963-39982 None:intergenic 35.0%
!! GATAAGAGGTTTTGATATGG+TGG - tig0030651:40041-40060 None:intergenic 35.0%
TCTCCTTACAATCTCTACTA+CGG + tig0030651:40160-40179 Msa1444070:CDS 35.0%
TCTTTCTCTGTTCTCTTCTT+TGG - tig0030651:40343-40362 None:intergenic 35.0%
!!! AGATGCTGTTTTGAACAACT+TGG + tig0030651:40405-40424 Msa1444070:CDS 35.0%
TCCTGAGTGGAATAAAGATA+AGG + tig0030651:40612-40631 Msa1444070:CDS 35.0%
TCCTTATCTTTATTCCACTC+AGG - tig0030651:40616-40635 None:intergenic 35.0%
!!! TTTTGATATGGTGGTGGTTG+TGG - tig0030651:40032-40051 None:intergenic 40.0%
!! AAGAGGTTTTGATATGGTGG+TGG - tig0030651:40038-40057 None:intergenic 40.0%
TTCTGCTGAGTCTTTCTTGT+TGG - tig0030651:40230-40249 None:intergenic 40.0%
TCTTTATTCCACTCAGGAGT+AGG - tig0030651:40610-40629 None:intergenic 40.0%
TATAGCTGCTGCTGCTGTTA+AGG - tig0030651:40095-40114 None:intergenic 45.0%
! TGGTGATGTTGTCAGAATGG+TGG - tig0030651:40119-40138 None:intergenic 45.0%
! AGGTGGTGATGTTGTCAGAA+TGG - tig0030651:40122-40141 None:intergenic 45.0%
GATGATTCTGCTGCTATGGA+AGG - tig0030651:40142-40161 None:intergenic 45.0%
AGGAGATGATTCTGCTGCTA+TGG - tig0030651:40146-40165 None:intergenic 45.0%
GTGCCGTAGTAGAGATTGTA+AGG - tig0030651:40166-40185 None:intergenic 45.0%
TACATCTACGACGTTCCAGA+AGG + tig0030651:40250-40269 Msa1444070:CDS 45.0%
AAACGTTCCTTCCAACCTTC+TGG - tig0030651:40268-40287 None:intergenic 45.0%
CTAACTGACGAAACCCAGAA+AGG - tig0030651:40378-40397 None:intergenic 45.0%
TTAATGCTCCTACTCCTGAG+TGG + tig0030651:40599-40618 Msa1444070:CDS 45.0%
!! TGATATGGTGGTGGTTGTGG+TGG - tig0030651:40029-40048 None:intergenic 50.0%
! GCTGTTAAGGTGGTGGTTAG+AGG - tig0030651:40082-40101 None:intergenic 50.0%
GATTCTGCTGCTATGGAAGG+TGG - tig0030651:40139-40158 None:intergenic 50.0%
GCAGCAAGTGCAGCAAACTA+CGG + tig0030651:40187-40206 Msa1444070:CDS 50.0%
TCTACGACGTTCCAGAAGGT+TGG + tig0030651:40254-40273 Msa1444070:CDS 50.0%
GAGGAGGAGAAAATGGGTGG+TGG - tig0030651:39983-40002 None:intergenic 55.0%
! GTGGCGGAGGAGGAGAAAAT+GGG - tig0030651:39989-40008 None:intergenic 55.0%
!! TATGGTGGTGGTTGTGGTGG+TGG - tig0030651:40026-40045 None:intergenic 55.0%
TGCTGCTGCTGTTAAGGTGG+TGG - tig0030651:40089-40108 None:intergenic 55.0%
AGCTGCTGCTGCTGTTAAGG+TGG - tig0030651:40092-40111 None:intergenic 55.0%
GCAAGTGCAGCAAACTACGG+CGG + tig0030651:40190-40209 Msa1444070:CDS 55.0%
CGACGTTCCAGAAGGTTGGA+AGG + tig0030651:40258-40277 Msa1444070:CDS 55.0%
GCGGAGGAGGAGAAAATGGG+TGG - tig0030651:39986-40005 None:intergenic 60.0%
!! GGTGGCGGAGGAGGAGAAAA+TGG - tig0030651:39990-40009 None:intergenic 60.0%
!! GGTTGTGGTGGTGGTTGTGG+TGG - tig0030651:40017-40036 None:intergenic 60.0%
!! GGTGGTTGTGGTGGTGGTTG+TGG - tig0030651:40020-40039 None:intergenic 60.0%
GCAGCAAACTACGGCGGCTA+CGG + tig0030651:40196-40215 Msa1444070:CDS 60.0%
!! GGTTGTGGTGGTGCTGGTGG+CGG - tig0030651:40005-40024 None:intergenic 65.0%
! GGTGGTTGTGGTGGTGCTGG+TGG - tig0030651:40008-40027 None:intergenic 65.0%
! GGTGGTGGTTGTGGTGGTGC+TGG - tig0030651:40011-40030 None:intergenic 65.0%
GCAAACTACGGCGGCTACGG+CGG + tig0030651:40199-40218 Msa1444070:CDS 65.0%
!! TGTGGTGGTGCTGGTGGCGG+AGG - tig0030651:40002-40021 None:intergenic 70.0%
!! GGTGGTGCTGGTGGCGGAGG+AGG - tig0030651:39999-40018 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
tig0030651 gene 39956 40678 39956 ID=Msa1444070;Name=Msa1444070
tig0030651 mRNA 39956 40678 39956 ID=Msa1444070-mRNA-1;Parent=Msa1444070;Name=Msa1444070-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|240
tig0030651 exon 39956 40678 39956 ID=Msa1444070-mRNA-1:exon:14290;Parent=Msa1444070-mRNA-1
tig0030651 CDS 39956 40678 39956 ID=Msa1444070-mRNA-1:cds;Parent=Msa1444070-mRNA-1
Gene Sequence

>Msa1444070

ATGGCCACAATTTTCTCATCATCACCACCACCCATTTTCTCCTCCTCCGCCACCAGCACCACCACAACCACCACCACAACCACCACCATATCAAAACCTCTTATCTCATTCAAACACAAACAACCTCTAACCACCACCTTAACAGCAGCAGCAGCTATAGCCACCATTCTGACAACATCACCACCTTCCATAGCAGCAGAATCATCTCCTTACAATCTCTACTACGGCACAGCAGCAAGTGCAGCAAACTACGGCGGCTACGGCGGAAACTCCAACAAGAAAGACTCAGCAGAATACATCTACGACGTTCCAGAAGGTTGGAAGGAACGTTTAATATCAAAAGTTGAAAAAGGTACAAATGGAACAGACAGTGAATTCTACAATCCAAAGAAGAGAACAGAGAAAGAATATCTAACTTTCCTTTCTGGGTTTCGTCAGTTAGCACCAAAAGATGCTGTTTTGAACAACTTGGCACTTTCTGATGTGAATTTGCAAGATATTATTAGTGGTGCTGATAATGTGAGTTCTGAAGAAGTGAAAGATGATAAAGGTCAAGTTTATTATGTTTATGAGATTGATGGCGTTGCTTATCATAGCTTGATTTCTGTTACTTGTGCTAATAATAAGCTTTATGCTCATTTTGTTAATGCTCCTACTCCTGAGTGGAATAAAGATAAGGATCTTCTCACTCATGTTCATAAGTCTTTTAAGACTATTGTATAA

Protein sequence

>Msa1444070

MATIFSSSPPPIFSSSATSTTTTTTTTTTISKPLISFKHKQPLTTTLTAAAAIATILTTSPPSIAAESSPYNLYYGTAASAANYGGYGGNSNKKDSAEYIYDVPEGWKERLISKVEKGTNGTDSEFYNPKKRTEKEYLTFLSGFRQLAPKDAVLNNLALSDVNLQDIISGADNVSSEEVKDDKGQVYYVYEIDGVAYHSLISVTCANNKLYAHFVNAPTPEWNKDKDLLTHVHKSFKTIV*