AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1207220


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1207220 MtrunA17_Chr4g0056091 86.025 322 17 6 1 301 1 315 1.46e-178 495
Msa1207220 MtrunA17_Chr7g0231181 37.669 369 148 13 1 301 1 355 5.91e-54 179
Msa1207220 MtrunA17_Chr5g0399261 40.062 322 94 14 1 286 5 263 5.40e-48 161
Msa1207220 MtrunA17_Chr4g0012691 31.793 368 149 9 1 289 2 346 1.59e-34 129
Msa1207220 MtrunA17_Chr4g0018761 28.383 303 140 13 6 288 9 254 9.54e-19 84.0
Msa1207220 MtrunA17_Chr4g0043071 50.000 62 27 1 230 291 441 498 2.62e-11 63.9
Msa1207220 MtrunA17_Chr4g0061301 50.000 64 26 2 231 294 436 493 3.82e-11 63.5
Msa1207220 MtrunA17_Chr1g0207451 31.548 168 75 6 139 291 57 199 6.34e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1207220 AT3G60580.1 36.190 315 155 12 1 298 1 286 1.21e-44 153
Msa1207220 AT1G02030.1 36.943 314 131 11 2 298 3 266 2.66e-40 142
Msa1207220 AT2G45120.1 35.103 339 154 12 1 300 1 312 8.34e-40 142
Msa1207220 AT4G16610.1 38.922 167 70 6 3 152 4 155 3.70e-20 87.0
Msa1207220 AT1G26610.1 48.000 75 34 2 217 291 386 455 2.81e-12 67.4
Msa1207220 AT5G61470.1 42.857 84 38 3 184 257 218 301 2.93e-11 63.5

Find 47 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCTGTTGTAGAAAATTC+TGG 0.230051 8_1:-64672814 None:intergenic
CCAAACACCTTAAAACAAAA+TGG 0.311153 8_1:-64673205 None:intergenic
TCTTTAAATCTAGCAGCAAT+AGG 0.373006 8_1:-64673319 None:intergenic
CACATAGCAACATCTTCTTC+AGG 0.374474 8_1:-64672920 None:intergenic
GGCACCATGAAACTCGGCTT+TGG 0.378686 8_1:-64672839 None:intergenic
GAAACCAAAGCCGAGTTTCA+TGG 0.392923 8_1:+64672835 Msa1207220:CDS
AAGCTTTGTTCAAGGACGTT+TGG 0.415966 8_1:+64672364 Msa1207220:CDS
TCCGATGATGAGAAAGAATC+AGG 0.418255 8_1:-64672463 None:intergenic
TAGATCGTTGTTGACGAGTC+GGG 0.431866 8_1:-64672754 None:intergenic
TGATGCTTTCGCGAGACAAA+TGG 0.443203 8_1:+64672948 Msa1207220:CDS
ACCTGATTCTTTCTCATCAT+CGG 0.450240 8_1:+64672462 Msa1207220:CDS
GTGAATTGTGATGGAGTTGT+TGG 0.452696 8_1:-64672860 None:intergenic
GTTTCGATCTTCAAGAGCAT+TGG 0.459910 8_1:+64673102 Msa1207220:CDS
TTTCGATCTTCAAGAGCATT+GGG 0.469548 8_1:+64673103 Msa1207220:CDS
TTTGGTTCTGGTCAAGCACT+TGG 0.469573 8_1:+64673223 Msa1207220:CDS
TTGTTGTCGTCGTTGTTGTT+TGG 0.479895 8_1:-64672791 None:intergenic
CTCGTCAACAACGATCTAAA+CGG 0.483916 8_1:+64672759 Msa1207220:CDS
GGTTCTGGTCAAGCACTTGG+TGG 0.484093 8_1:+64673226 Msa1207220:CDS
TGAAGAAGAAGAGGGATCGG+TGG 0.488736 8_1:+64673009 Msa1207220:CDS
TCATCTTCTTCAAGTGGAGC+TGG 0.500458 8_1:-64673364 None:intergenic
ACAAATGCAAGCTTTGTTCA+AGG 0.502681 8_1:+64672356 Msa1207220:CDS
GCGAAGAATGGTAATGGTAA+TGG 0.505680 8_1:+64673157 Msa1207220:CDS
ACATAGCAACATCTTCTTCA+GGG 0.525812 8_1:-64672919 None:intergenic
AAGTTATTGAAACGAGTTCG+TGG 0.531632 8_1:+64673049 Msa1207220:CDS
GCAGTGGAAGTTGATGAAGA+AGG 0.533864 8_1:-64673274 None:intergenic
TGTCGCGATGAAGCGAAGAA+TGG 0.548591 8_1:+64673145 Msa1207220:CDS
TCTTGTTCAGTGAATTGTGA+TGG 0.549593 8_1:-64672869 None:intergenic
CAGTGGAAGTTGATGAAGAA+GGG 0.550853 8_1:-64673273 None:intergenic
TTTGGCAATGGAAGAGCACT+TGG 0.550999 8_1:+64672382 Msa1207220:CDS
GTTGTTGGCACCATGAAACT+CGG 0.554243 8_1:-64672845 None:intergenic
TTAGATCGTTGTTGACGAGT+CGG 0.558622 8_1:-64672755 None:intergenic
GGAACAAGATGAAGAAGAAG+AGG 0.558902 8_1:+64673000 Msa1207220:CDS
AGATCATCATCTTCTTCAAG+TGG 0.559232 8_1:-64673370 None:intergenic
GGCAATGGAAGAGCACTTGG+TGG 0.563472 8_1:+64672385 Msa1207220:CDS
TGTTCAAGGACGTTTGGCAA+TGG 0.572618 8_1:+64672370 Msa1207220:CDS
GATGAAGCGAAGAATGGTAA+TGG 0.574456 8_1:+64673151 Msa1207220:CDS
AGCACTTGGTGGACACATGA+AGG 0.581864 8_1:+64672396 Msa1207220:CDS
ATTAACATTAACATTAGCAG+TGG 0.584695 8_1:-64673290 None:intergenic
AGATGAAGAAGAAGAGGGAT+CGG 0.594748 8_1:+64673006 Msa1207220:CDS
AGTTATTGAAACGAGTTCGT+GGG 0.596995 8_1:+64673050 Msa1207220:CDS
GTATCAGAAACTGAACTCAC+AGG 0.612015 8_1:-64672893 None:intergenic
CATAGCAACATCTTCTTCAG+GGG 0.618873 8_1:-64672918 None:intergenic
GAACAAGATGAAGAAGAAGA+GGG 0.633530 8_1:+64673001 Msa1207220:CDS
AGCATTTGTGTGAAAACTGT+GGG 0.639279 8_1:+64673074 Msa1207220:CDS
ATCGGTGGAGAAAATATCGA+AGG 0.639870 8_1:+64673024 Msa1207220:CDS
GATGAACAACATCAACAATG+TGG 0.658258 8_1:+64672979 Msa1207220:CDS
AAGCATTTGTGTGAAAACTG+TGG 0.714401 8_1:+64673073 Msa1207220:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATGTCCATTTTGTTTTA+AGG + chr8_1:64673198-64673217 Msa1207220:CDS 25.0%
! ATTAACATTAACATTAGCAG+TGG - chr8_1:64673293-64673312 None:intergenic 25.0%
!!! TGAATGTCCATTTTGTTTTA+AGG + chr8_1:64673198-64673217 Msa1207220:CDS 25.0%
! ATTAACATTAACATTAGCAG+TGG - chr8_1:64673293-64673312 None:intergenic 25.0%
TCTTCTGTTGTAGAAAATTC+TGG - chr8_1:64672817-64672836 None:intergenic 30.0%
CCAAACACCTTAAAACAAAA+TGG - chr8_1:64673208-64673227 None:intergenic 30.0%
!!! CCATTTTGTTTTAAGGTGTT+TGG + chr8_1:64673205-64673224 Msa1207220:CDS 30.0%
TCTTTAAATCTAGCAGCAAT+AGG - chr8_1:64673322-64673341 None:intergenic 30.0%
TCTTCTGTTGTAGAAAATTC+TGG - chr8_1:64672817-64672836 None:intergenic 30.0%
CCAAACACCTTAAAACAAAA+TGG - chr8_1:64673208-64673227 None:intergenic 30.0%
!!! CCATTTTGTTTTAAGGTGTT+TGG + chr8_1:64673205-64673224 Msa1207220:CDS 30.0%
TCTTTAAATCTAGCAGCAAT+AGG - chr8_1:64673322-64673341 None:intergenic 30.0%
!! ACAAATGCAAGCTTTGTTCA+AGG + chr8_1:64672356-64672375 Msa1207220:CDS 35.0%
ACCTGATTCTTTCTCATCAT+CGG + chr8_1:64672462-64672481 Msa1207220:CDS 35.0%
!!! GCAACTTTGAGACTTTTCTT+GGG - chr8_1:64672553-64672572 None:intergenic 35.0%
!!! TGCAACTTTGAGACTTTTCT+TGG - chr8_1:64672554-64672573 None:intergenic 35.0%
TCTTGTTCAGTGAATTGTGA+TGG - chr8_1:64672872-64672891 None:intergenic 35.0%
ACATAGCAACATCTTCTTCA+GGG - chr8_1:64672922-64672941 None:intergenic 35.0%
GATGAACAACATCAACAATG+TGG + chr8_1:64672979-64672998 Msa1207220:CDS 35.0%
GAACAAGATGAAGAAGAAGA+GGG + chr8_1:64673001-64673020 Msa1207220:CDS 35.0%
AAGTTATTGAAACGAGTTCG+TGG + chr8_1:64673049-64673068 Msa1207220:CDS 35.0%
AGTTATTGAAACGAGTTCGT+GGG + chr8_1:64673050-64673069 Msa1207220:CDS 35.0%
AAGCATTTGTGTGAAAACTG+TGG + chr8_1:64673073-64673092 Msa1207220:CDS 35.0%
AGCATTTGTGTGAAAACTGT+GGG + chr8_1:64673074-64673093 Msa1207220:CDS 35.0%
!! TTTCGATCTTCAAGAGCATT+GGG + chr8_1:64673103-64673122 Msa1207220:CDS 35.0%
!!! TGTTTTAAGGTGTTTGGTTC+TGG + chr8_1:64673211-64673230 Msa1207220:CDS 35.0%
AGATCATCATCTTCTTCAAG+TGG - chr8_1:64673373-64673392 None:intergenic 35.0%
!! ACAAATGCAAGCTTTGTTCA+AGG + chr8_1:64672356-64672375 Msa1207220:CDS 35.0%
ACCTGATTCTTTCTCATCAT+CGG + chr8_1:64672462-64672481 Msa1207220:CDS 35.0%
!!! GCAACTTTGAGACTTTTCTT+GGG - chr8_1:64672553-64672572 None:intergenic 35.0%
!!! TGCAACTTTGAGACTTTTCT+TGG - chr8_1:64672554-64672573 None:intergenic 35.0%
TCTTGTTCAGTGAATTGTGA+TGG - chr8_1:64672872-64672891 None:intergenic 35.0%
ACATAGCAACATCTTCTTCA+GGG - chr8_1:64672922-64672941 None:intergenic 35.0%
GATGAACAACATCAACAATG+TGG + chr8_1:64672979-64672998 Msa1207220:CDS 35.0%
GAACAAGATGAAGAAGAAGA+GGG + chr8_1:64673001-64673020 Msa1207220:CDS 35.0%
AAGTTATTGAAACGAGTTCG+TGG + chr8_1:64673049-64673068 Msa1207220:CDS 35.0%
AGTTATTGAAACGAGTTCGT+GGG + chr8_1:64673050-64673069 Msa1207220:CDS 35.0%
AAGCATTTGTGTGAAAACTG+TGG + chr8_1:64673073-64673092 Msa1207220:CDS 35.0%
AGCATTTGTGTGAAAACTGT+GGG + chr8_1:64673074-64673093 Msa1207220:CDS 35.0%
!! TTTCGATCTTCAAGAGCATT+GGG + chr8_1:64673103-64673122 Msa1207220:CDS 35.0%
!!! TGTTTTAAGGTGTTTGGTTC+TGG + chr8_1:64673211-64673230 Msa1207220:CDS 35.0%
AGATCATCATCTTCTTCAAG+TGG - chr8_1:64673373-64673392 None:intergenic 35.0%
!! AAGCTTTGTTCAAGGACGTT+TGG + chr8_1:64672364-64672383 Msa1207220:CDS 40.0%
TCCGATGATGAGAAAGAATC+AGG - chr8_1:64672466-64672485 None:intergenic 40.0%
TTAGATCGTTGTTGACGAGT+CGG - chr8_1:64672758-64672777 None:intergenic 40.0%
CTCGTCAACAACGATCTAAA+CGG + chr8_1:64672759-64672778 Msa1207220:CDS 40.0%
! TTGTTGTCGTCGTTGTTGTT+TGG - chr8_1:64672794-64672813 None:intergenic 40.0%
! GTGAATTGTGATGGAGTTGT+TGG - chr8_1:64672863-64672882 None:intergenic 40.0%
GTATCAGAAACTGAACTCAC+AGG - chr8_1:64672896-64672915 None:intergenic 40.0%
CATAGCAACATCTTCTTCAG+GGG - chr8_1:64672921-64672940 None:intergenic 40.0%
CACATAGCAACATCTTCTTC+AGG - chr8_1:64672923-64672942 None:intergenic 40.0%
GGAACAAGATGAAGAAGAAG+AGG + chr8_1:64673000-64673019 Msa1207220:CDS 40.0%
AGATGAAGAAGAAGAGGGAT+CGG + chr8_1:64673006-64673025 Msa1207220:CDS 40.0%
ATCGGTGGAGAAAATATCGA+AGG + chr8_1:64673024-64673043 Msa1207220:CDS 40.0%
! GTTTCGATCTTCAAGAGCAT+TGG + chr8_1:64673102-64673121 Msa1207220:CDS 40.0%
GATGAAGCGAAGAATGGTAA+TGG + chr8_1:64673151-64673170 Msa1207220:CDS 40.0%
!! GCGAAGAATGGTAATGGTAA+TGG + chr8_1:64673157-64673176 Msa1207220:CDS 40.0%
!! CAGTGGAAGTTGATGAAGAA+GGG - chr8_1:64673276-64673295 None:intergenic 40.0%
!! AAGCTTTGTTCAAGGACGTT+TGG + chr8_1:64672364-64672383 Msa1207220:CDS 40.0%
TCCGATGATGAGAAAGAATC+AGG - chr8_1:64672466-64672485 None:intergenic 40.0%
TTAGATCGTTGTTGACGAGT+CGG - chr8_1:64672758-64672777 None:intergenic 40.0%
CTCGTCAACAACGATCTAAA+CGG + chr8_1:64672759-64672778 Msa1207220:CDS 40.0%
! TTGTTGTCGTCGTTGTTGTT+TGG - chr8_1:64672794-64672813 None:intergenic 40.0%
! GTGAATTGTGATGGAGTTGT+TGG - chr8_1:64672863-64672882 None:intergenic 40.0%
GTATCAGAAACTGAACTCAC+AGG - chr8_1:64672896-64672915 None:intergenic 40.0%
CATAGCAACATCTTCTTCAG+GGG - chr8_1:64672921-64672940 None:intergenic 40.0%
CACATAGCAACATCTTCTTC+AGG - chr8_1:64672923-64672942 None:intergenic 40.0%
GGAACAAGATGAAGAAGAAG+AGG + chr8_1:64673000-64673019 Msa1207220:CDS 40.0%
AGATGAAGAAGAAGAGGGAT+CGG + chr8_1:64673006-64673025 Msa1207220:CDS 40.0%
ATCGGTGGAGAAAATATCGA+AGG + chr8_1:64673024-64673043 Msa1207220:CDS 40.0%
! GTTTCGATCTTCAAGAGCAT+TGG + chr8_1:64673102-64673121 Msa1207220:CDS 40.0%
GATGAAGCGAAGAATGGTAA+TGG + chr8_1:64673151-64673170 Msa1207220:CDS 40.0%
!! GCGAAGAATGGTAATGGTAA+TGG + chr8_1:64673157-64673176 Msa1207220:CDS 40.0%
!! CAGTGGAAGTTGATGAAGAA+GGG - chr8_1:64673276-64673295 None:intergenic 40.0%
TGTTCAAGGACGTTTGGCAA+TGG + chr8_1:64672370-64672389 Msa1207220:CDS 45.0%
!! TTTGGCAATGGAAGAGCACT+TGG + chr8_1:64672382-64672401 Msa1207220:CDS 45.0%
TAGATCGTTGTTGACGAGTC+GGG - chr8_1:64672757-64672776 None:intergenic 45.0%
GAAACCAAAGCCGAGTTTCA+TGG + chr8_1:64672835-64672854 Msa1207220:CDS 45.0%
GTTGTTGGCACCATGAAACT+CGG - chr8_1:64672848-64672867 None:intergenic 45.0%
TGATGCTTTCGCGAGACAAA+TGG + chr8_1:64672948-64672967 Msa1207220:CDS 45.0%
!! TTTGGTTCTGGTCAAGCACT+TGG + chr8_1:64673223-64673242 Msa1207220:CDS 45.0%
!! GCAGTGGAAGTTGATGAAGA+AGG - chr8_1:64673277-64673296 None:intergenic 45.0%
TCATCTTCTTCAAGTGGAGC+TGG - chr8_1:64673367-64673386 None:intergenic 45.0%
TGTTCAAGGACGTTTGGCAA+TGG + chr8_1:64672370-64672389 Msa1207220:CDS 45.0%
!! TTTGGCAATGGAAGAGCACT+TGG + chr8_1:64672382-64672401 Msa1207220:CDS 45.0%
TAGATCGTTGTTGACGAGTC+GGG - chr8_1:64672757-64672776 None:intergenic 45.0%
GAAACCAAAGCCGAGTTTCA+TGG + chr8_1:64672835-64672854 Msa1207220:CDS 45.0%
GTTGTTGGCACCATGAAACT+CGG - chr8_1:64672848-64672867 None:intergenic 45.0%
TGATGCTTTCGCGAGACAAA+TGG + chr8_1:64672948-64672967 Msa1207220:CDS 45.0%
!! TTTGGTTCTGGTCAAGCACT+TGG + chr8_1:64673223-64673242 Msa1207220:CDS 45.0%
!! GCAGTGGAAGTTGATGAAGA+AGG - chr8_1:64673277-64673296 None:intergenic 45.0%
TCATCTTCTTCAAGTGGAGC+TGG - chr8_1:64673367-64673386 None:intergenic 45.0%
! AGCACTTGGTGGACACATGA+AGG + chr8_1:64672396-64672415 Msa1207220:CDS 50.0%
TGAAGAAGAAGAGGGATCGG+TGG + chr8_1:64673009-64673028 Msa1207220:CDS 50.0%
TGTCGCGATGAAGCGAAGAA+TGG + chr8_1:64673145-64673164 Msa1207220:CDS 50.0%
! AGCACTTGGTGGACACATGA+AGG + chr8_1:64672396-64672415 Msa1207220:CDS 50.0%
TGAAGAAGAAGAGGGATCGG+TGG + chr8_1:64673009-64673028 Msa1207220:CDS 50.0%
TGTCGCGATGAAGCGAAGAA+TGG + chr8_1:64673145-64673164 Msa1207220:CDS 50.0%
!! GGCAATGGAAGAGCACTTGG+TGG + chr8_1:64672385-64672404 Msa1207220:CDS 55.0%
GGCACCATGAAACTCGGCTT+TGG - chr8_1:64672842-64672861 None:intergenic 55.0%
! GGTTCTGGTCAAGCACTTGG+TGG + chr8_1:64673226-64673245 Msa1207220:CDS 55.0%
!! GGCAATGGAAGAGCACTTGG+TGG + chr8_1:64672385-64672404 Msa1207220:CDS 55.0%
GGCACCATGAAACTCGGCTT+TGG - chr8_1:64672842-64672861 None:intergenic 55.0%
! GGTTCTGGTCAAGCACTTGG+TGG + chr8_1:64673226-64673245 Msa1207220:CDS 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 64672346 64673414 64672346 ID=Msa1207220;Name=Msa1207220
chr8_1 mRNA 64672346 64673414 64672346 ID=Msa1207220-mRNA-1;Parent=Msa1207220;Name=Msa1207220-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|1|1|1|2|0|301
chr8_1 exon 64672346 64672559 64672346 ID=Msa1207220-mRNA-1:exon:21085;Parent=Msa1207220-mRNA-1
chr8_1 exon 64672723 64673414 64672723 ID=Msa1207220-mRNA-1:exon:21086;Parent=Msa1207220-mRNA-1
chr8_1 CDS 64672346 64672559 64672346 ID=Msa1207220-mRNA-1:cds;Parent=Msa1207220-mRNA-1
chr8_1 CDS 64672723 64673414 64672723 ID=Msa1207220-mRNA-1:cds;Parent=Msa1207220-mRNA-1
Gene Sequence

>Msa1207220

ATGGAAAGACACAAATGCAAGCTTTGTTCAAGGACGTTTGGCAATGGAAGAGCACTTGGTGGACACATGAAGGCTCATCTTGCTATTGCTAAGTCTCAACAGAAACAATTCACTCAACCTGATTCTTTCTCATCATCGGAATCAGAACAAGAAGAAGAAGAAGAAGAAGAAAAAACTTTGATTAATTATGTTTTGAGAGAGAATCCCAAGAAAAATAGAGAAAGTGAGACTGAGTCAAAGAACAACCCGACTCGTCAACAACGATCTAAACGGAACAGAAAACCAAACAACAACGACGACAACAACCAGAATTTTCTACAACAGAAGAAACCAAAGCCGAGTTTCATGGTGCCAACAACTCCATCACAATTCACTGAACAAGAACCTGTGAGTTCAGTTTCTGATACTTCCCCTGAAGAAGATGTTGCTATGTGTCTCATGATGCTTTCGCGAGACAAATGGAGTAGAAAGATGAACAACATCAACAATGTGGAACAAGATGAAGAAGAAGAGGGATCGGTGGAGAAAATATCGAAGGTGAAGTTATTGAAACGAGTTCGTGGGAAGCATTTGTGTGAAAACTGTGGGAAGACGTTTCGATCTTCAAGAGCATTGGGAAGTCATAGAAGTATTTGTTGTCGCGATGAAGCGAAGAATGGTAATGGTAATGGTAAAGATGATAAGATTTTTGAATGTCCATTTTGTTTTAAGGTGTTTGGTTCTGGTCAAGCACTTGGTGGTCACAAGAGATCTCATCTCATGATCCCTTCTTCATCAACTTCCACTGCTAATGTTAATGTTAATGTTAATCCTATTGCTGCTAGATTTAAAGAGAGTTTCATAGATCTCAATATGCCAGCTCCACTTGAAGAAGATGATGATCTTAGTGTTGTTTCTGATGCCTAA

Protein sequence

>Msa1207220

MERHKCKLCSRTFGNGRALGGHMKAHLAIAKSQQKQFTQPDSFSSSESEQEEEEEEEKTLINYVLRENPKKNRESETESKNNPTRQQRSKRNRKPNNNDDNNQNFLQQKKPKPSFMVPTTPSQFTEQEPVSSVSDTSPEEDVAMCLMMLSRDKWSRKMNNINNVEQDEEEEGSVEKISKVKLLKRVRGKHLCENCGKTFRSSRALGSHRSICCRDEAKNGNGNGKDDKIFECPFCFKVFGSGQALGGHKRSHLMIPSSSTSTANVNVNVNPIAARFKESFIDLNMPAPLEEDDDLSVVSDA*