AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52164

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52164.t1 MTR_7g077620 61.497 374 129 9 1 364 1 369 1.26e-142 410
MS.gene52164.t1 MTR_7g077650 57.662 385 132 12 1 367 1 372 4.49e-133 385
MS.gene52164.t1 MTR_7g077660 57.895 380 128 12 5 367 4 368 3.06e-128 372
MS.gene52164.t1 MTR_7g076110 56.610 295 117 5 82 367 21 313 2.31e-100 300
MS.gene52164.t1 MTR_7g076100 69.099 233 67 4 138 367 70 300 2.80e-100 299
MS.gene52164.t1 MTR_7g076100 77.778 54 12 0 1 54 1 54 1.44e-21 94.0
MS.gene52164.t1 MTR_1g108740 42.547 369 169 15 3 362 2 336 4.48e-72 228
MS.gene52164.t1 MTR_5g038260 41.624 394 182 19 6 367 6 383 1.12e-70 226
MS.gene52164.t1 MTR_5g038230 39.898 391 163 18 6 365 4 353 2.16e-64 209
MS.gene52164.t1 MTR_5g082770 42.951 305 143 9 6 299 4 288 9.60e-62 200
MS.gene52164.t1 MTR_7g076130 75.000 124 28 2 164 284 25 148 2.37e-57 184
MS.gene52164.t1 MTR_1g064570 35.492 417 196 16 5 367 3 400 4.51e-55 186
MS.gene52164.t1 MTR_1g016150 46.829 205 97 7 3 198 2 203 9.35e-45 154
MS.gene52164.t1 MTR_5g082780 40.517 232 96 10 109 322 1 208 2.29e-40 142
MS.gene52164.t1 MTR_1g108750 45.695 151 51 5 6 155 4 124 1.36e-25 100
MS.gene52164.t1 MTR_3g114970 22.951 366 208 13 5 334 3 330 1.35e-13 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 68 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATCATTTGGACTTGTAAT+TGG 0.148563 7.4:+29370714 None:intergenic
TTCGCATAGTAAGTAAAATT+AGG 0.191950 7.4:+29370504 None:intergenic
AAAGAGCAAGCCAACCATTT+TGG 0.203122 7.4:-29370650 MS.gene52164:CDS
ACCATCAAAACAATCAATTT+AGG 0.232527 7.4:-29371016 MS.gene52164:CDS
GATATACTACTACACTTAAA+AGG 0.276632 7.4:+29370792 None:intergenic
AATGAACAAGCTTGAGAGTT+TGG 0.278023 7.4:-29370298 MS.gene52164:CDS
ATTTGGTTGGTTTGCATTAG+TGG 0.297529 7.4:-29370844 MS.gene52164:CDS
AAGATCACCAATGTTGTAAA+TGG 0.306746 7.4:+29370680 None:intergenic
TAGTTTGGTTCTTGACAAAT+TGG 0.317439 7.4:-29371105 MS.gene52164:CDS
TTTCCCGTATGAAAATTATA+AGG 0.318336 7.4:-29370881 MS.gene52164:CDS
GTTGAGATGTGGCAGAATAA+TGG 0.333023 7.4:+29370767 None:intergenic
AGAAGAACTGCCTCTTAGTT+TGG 0.335492 7.4:-29371120 MS.gene52164:CDS
TCGCATAGTAAGTAAAATTA+GGG 0.335896 7.4:+29370505 None:intergenic
AAGATCACATAGAGCATGTT+AGG 0.337175 7.4:-29371082 MS.gene52164:CDS
TGTGACTTAGAATGCTATAC+AGG 0.361873 7.4:+29370925 None:intergenic
TTGAGATGTGGCAGAATAAT+GGG 0.362137 7.4:+29370768 None:intergenic
GTTGAACTTGAAGGATATAA+TGG 0.375803 7.4:+29370548 None:intergenic
AAATTAGGGTTATTTGAGTT+AGG 0.386206 7.4:+29370519 None:intergenic
CGCATCCCCTTGAAGGAAAT+CGG 0.389019 7.4:+29370105 None:intergenic
AATCATTTGGACTTGTAATT+GGG 0.394312 7.4:+29370715 None:intergenic
AAAACCTCGCATCCCCTTGA+AGG 0.402319 7.4:+29370098 None:intergenic
AAAAGGATTGACTAGAGTTA+TGG 0.415743 7.4:+29370809 None:intergenic
TATGAAAATTATAAGGTGTA+TGG 0.418200 7.4:-29370874 MS.gene52164:CDS
CACATAGAGCATGTTAGGTT+TGG 0.419463 7.4:-29371077 MS.gene52164:CDS
AGGTGTATGGACTCTTCATT+TGG 0.419747 7.4:-29370861 MS.gene52164:CDS
GTAGACATCAAGTTTATATG+AGG 0.436334 7.4:+29370359 None:intergenic
GTATGGACTCTTCATTTGGT+TGG 0.436531 7.4:-29370857 MS.gene52164:CDS
GGGATCGACCGCAATTTCAA+TGG 0.438895 7.4:-29370074 MS.gene52164:CDS
TGATGTCTACAAATTAGAAC+TGG 0.443705 7.4:-29370346 MS.gene52164:CDS
TGTGCTATATGAATCCAAAA+TGG 0.443882 7.4:+29370636 None:intergenic
GCTGCAATGACATAATCATT+TGG 0.444853 7.4:+29370702 None:intergenic
ACCAATACCATTCGTCTTCG+AGG 0.449702 7.4:+29370979 None:intergenic
TCCTCGAAGACGAATGGTAT+TGG 0.454535 7.4:-29370980 MS.gene52164:CDS
CAATGAGGAAGGTGGCAGAC+TGG 0.474514 7.4:-29371151 MS.gene52164:CDS
GGATCGACCGCAATTTCAAT+GGG 0.475412 7.4:-29370073 MS.gene52164:CDS
AGGAGGATTGTTGAACTTGA+AGG 0.483112 7.4:+29370539 None:intergenic
TACCATTCGTCTTCGAGGAT+CGG 0.492579 7.4:+29370984 None:intergenic
TGAGAAGATATTTCATCAAT+CGG 0.493569 7.4:-29370392 MS.gene52164:CDS
TTGGTGTCGTGTGCAAGAAT+TGG 0.497007 7.4:-29371058 MS.gene52164:CDS
TTGTCAAGAACCAAACTAAG+AGG 0.512788 7.4:+29371110 None:intergenic
ATTTATGACCATGGTATGCA+TGG 0.513250 7.4:-29370183 MS.gene52164:CDS
AATGAGGAAGGTGGCAGACT+GGG 0.522188 7.4:-29371150 MS.gene52164:CDS
AATCATTGTATGGAGACATA+TGG 0.522661 7.4:-29370419 MS.gene52164:CDS
ATTGCAGCCATTTACAACAT+TGG 0.532590 7.4:-29370687 MS.gene52164:CDS
GCAGACAAGGTAACCTTGTA+GGG 0.532760 7.4:+29370741 None:intergenic
TTGCTATTTGCCGACTGTGA+AGG 0.537297 7.4:-29370576 MS.gene52164:CDS
TTAGGGTTATTTGAGTTAGG+AGG 0.546912 7.4:+29370522 None:intergenic
AGCAGACAAGGTAACCTTGT+AGG 0.548503 7.4:+29370740 None:intergenic
ACATCTCAACTCTCCCTACA+AGG 0.555243 7.4:-29370754 MS.gene52164:CDS
CTCAGGCTTGGCAATGAGGA+AGG 0.555628 7.4:-29371162 None:intergenic
GAGATCTATAATGCGAAGGA+TGG 0.563178 7.4:-29370150 MS.gene52164:CDS
TTCTAACTTGGAGAAACGAG+AGG 0.573200 7.4:+29370224 None:intergenic
AACCGATCCTCGAAGACGAA+TGG 0.576438 7.4:-29370986 MS.gene52164:CDS
TGTAATTGGGTCAGCAGACA+AGG 0.582291 7.4:+29370728 None:intergenic
GTGCAAGAATTGGCAATCAG+TGG 0.594179 7.4:-29371048 MS.gene52164:CDS
TATCAATCCCATTGAAATTG+CGG 0.600714 7.4:+29370066 None:intergenic
ATTTCCTTCAAGGGGATGCG+AGG 0.607717 7.4:-29370102 MS.gene52164:CDS
CTATATGAATCCAAAATGGT+TGG 0.609689 7.4:+29370640 None:intergenic
GTTAGAGATCTATAATGCGA+AGG 0.619212 7.4:-29370154 MS.gene52164:CDS
AATGGTGTGTCCTTCACAGT+CGG 0.630964 7.4:+29370566 None:intergenic
GTGACTTAGAATGCTATACA+GGG 0.641264 7.4:+29370926 None:intergenic
ACTCTAAACCATGCATACCA+TGG 0.661226 7.4:+29370175 None:intergenic
AGGCTTGGCAATGAGGAAGG+TGG 0.663381 7.4:-29371159 None:intergenic
TTGTAGGGAGAGTTGAGATG+TGG 0.664401 7.4:+29370756 None:intergenic
ACACAGAAACTGAATAACCA+TGG 0.677256 7.4:+29370250 None:intergenic
ATGCGAAGATAGCTAGCACA+AGG 0.689632 7.4:-29370488 MS.gene52164:CDS
TTAGAACTGGATGCCCAGAG+TGG 0.702949 7.4:-29370333 MS.gene52164:CDS
ATTGTATGGAGACATATGGA+TGG 0.705109 7.4:-29370415 MS.gene52164:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATAATGTTGTATTTTATAA+AGG - chr7.4:29370617-29370636 MS.gene52164:CDS 10.0%
!!! ATTTATTTTATTTATGACCA+TGG - chr7.4:29371025-29371044 MS.gene52164:CDS 15.0%
!! TATGAAAATTATAAGGTGTA+TGG - chr7.4:29370343-29370362 MS.gene52164:CDS 20.0%
!!! AAATCTTTTCATAATAGCAT+TGG + chr7.4:29370769-29370788 None:intergenic 20.0%
!!! AATCTTTTCATAATAGCATT+GGG + chr7.4:29370768-29370787 None:intergenic 20.0%
!!! TACACCTTATAATTTTCATA+CGG + chr7.4:29370343-29370362 None:intergenic 20.0%
!!! TATTTTGTGAAATCATTGTA+TGG - chr7.4:29370788-29370807 MS.gene52164:CDS 20.0%
! AATCATTTGGACTTGTAATT+GGG + chr7.4:29370505-29370524 None:intergenic 25.0%
! ACCATCAAAACAATCAATTT+AGG - chr7.4:29370201-29370220 MS.gene52164:CDS 25.0%
! GATATACTACTACACTTAAA+AGG + chr7.4:29370428-29370447 None:intergenic 25.0%
! TAATCATTTGGACTTGTAAT+TGG + chr7.4:29370506-29370525 None:intergenic 25.0%
! TCGCATAGTAAGTAAAATTA+GGG + chr7.4:29370715-29370734 None:intergenic 25.0%
! TGAGAAGATATTTCATCAAT+CGG - chr7.4:29370825-29370844 MS.gene52164:CDS 25.0%
! TTCGCATAGTAAGTAAAATT+AGG + chr7.4:29370716-29370735 None:intergenic 25.0%
! TTTCCCGTATGAAAATTATA+AGG - chr7.4:29370336-29370355 MS.gene52164:CDS 25.0%
!! AAATTAGGGTTATTTGAGTT+AGG + chr7.4:29370701-29370720 None:intergenic 25.0%
!! AATCGAATCTTTTTCTAACT+TGG + chr7.4:29371008-29371027 None:intergenic 25.0%
!! ACACCTTATAATTTTCATAC+GGG + chr7.4:29370342-29370361 None:intergenic 25.0%
!!! GAAGACAACATTTTATTTGT+CGG - chr7.4:29370941-29370960 MS.gene52164:CDS 25.0%
!!! TCCTAAATTGATTGTTTTGA+TGG + chr7.4:29370205-29370224 None:intergenic 25.0%
AAAAGGATTGACTAGAGTTA+TGG + chr7.4:29370411-29370430 None:intergenic 30.0%
AAGATCACCAATGTTGTAAA+TGG + chr7.4:29370540-29370559 None:intergenic 30.0%
AATCATTGTATGGAGACATA+TGG - chr7.4:29370798-29370817 MS.gene52164:CDS 30.0%
ATACGGGAAAAAAATGTAAC+AGG + chr7.4:29370326-29370345 None:intergenic 30.0%
CTATATGAATCCAAAATGGT+TGG + chr7.4:29370580-29370599 None:intergenic 30.0%
GTAGACATCAAGTTTATATG+AGG + chr7.4:29370861-29370880 None:intergenic 30.0%
GTTGAACTTGAAGGATATAA+TGG + chr7.4:29370672-29370691 None:intergenic 30.0%
TGATGTCTACAAATTAGAAC+TGG - chr7.4:29370871-29370890 MS.gene52164:CDS 30.0%
TGTGCTATATGAATCCAAAA+TGG + chr7.4:29370584-29370603 None:intergenic 30.0%
!! ATTTTATTTGTCGGAAACCA+TGG - chr7.4:29370950-29370969 MS.gene52164:CDS 30.0%
!! TAGTTTGGTTCTTGACAAAT+TGG - chr7.4:29370112-29370131 MS.gene52164:CDS 30.0%
!! TTTTCATAATAGCATTGGGA+TGG + chr7.4:29370764-29370783 None:intergenic 30.0%
!!! ATTTTTACCGATTTCCTTCA+AGG - chr7.4:29371105-29371124 MS.gene52164:CDS 30.0%
!!! TTTTTACCGATTTCCTTCAA+GGG - chr7.4:29371106-29371125 MS.gene52164:CDS 30.0%
AAGATCACATAGAGCATGTT+AGG - chr7.4:29370135-29370154 MS.gene52164:CDS 35.0%
AATGAACAAGCTTGAGAGTT+TGG - chr7.4:29370919-29370938 MS.gene52164:CDS 35.0%
ACACAGAAACTGAATAACCA+TGG + chr7.4:29370970-29370989 None:intergenic 35.0%
ATTGCAGCCATTTACAACAT+TGG - chr7.4:29370530-29370549 MS.gene52164:CDS 35.0%
ATTGTATGGAGACATATGGA+TGG - chr7.4:29370802-29370821 MS.gene52164:CDS 35.0%
ATTTATGACCATGGTATGCA+TGG - chr7.4:29371034-29371053 MS.gene52164:CDS 35.0%
GCTGCAATGACATAATCATT+TGG + chr7.4:29370518-29370537 None:intergenic 35.0%
GTGACTTAGAATGCTATACA+GGG + chr7.4:29370294-29370313 None:intergenic 35.0%
GTTAGAGATCTATAATGCGA+AGG - chr7.4:29371063-29371082 MS.gene52164:CDS 35.0%
TGTGACTTAGAATGCTATAC+AGG + chr7.4:29370295-29370314 None:intergenic 35.0%
TTGAGATGTGGCAGAATAAT+GGG + chr7.4:29370452-29370471 None:intergenic 35.0%
TTGTCAAGAACCAAACTAAG+AGG + chr7.4:29370110-29370129 None:intergenic 35.0%
! TTAGGGTTATTTGAGTTAGG+AGG + chr7.4:29370698-29370717 None:intergenic 35.0%
!! ATTTGGTTGGTTTGCATTAG+TGG - chr7.4:29370373-29370392 MS.gene52164:CDS 35.0%
!! TTGTTCAAGTTTTCCACTCT+GGG + chr7.4:29370900-29370919 None:intergenic 35.0%
!! TTTGTTCAAGTTTTCCACTC+TGG + chr7.4:29370901-29370920 None:intergenic 35.0%
!!! TTTTACCGATTTCCTTCAAG+GGG - chr7.4:29371107-29371126 MS.gene52164:CDS 35.0%
ACTCTAAACCATGCATACCA+TGG + chr7.4:29371045-29371064 None:intergenic 40.0%
AGAAGAACTGCCTCTTAGTT+TGG - chr7.4:29370097-29370116 MS.gene52164:CDS 40.0%
AGGAGGATTGTTGAACTTGA+AGG + chr7.4:29370681-29370700 None:intergenic 40.0%
AGGTGTATGGACTCTTCATT+TGG - chr7.4:29370356-29370375 MS.gene52164:CDS 40.0%
CACATAGAGCATGTTAGGTT+TGG - chr7.4:29370140-29370159 MS.gene52164:CDS 40.0%
GAGATCTATAATGCGAAGGA+TGG - chr7.4:29371067-29371086 MS.gene52164:CDS 40.0%
GTATGGACTCTTCATTTGGT+TGG - chr7.4:29370360-29370379 MS.gene52164:CDS 40.0%
GTTGAGATGTGGCAGAATAA+TGG + chr7.4:29370453-29370472 None:intergenic 40.0%
TTCTAACTTGGAGAAACGAG+AGG + chr7.4:29370996-29371015 None:intergenic 40.0%
! AAAGAGCAAGCCAACCATTT+TGG - chr7.4:29370567-29370586 MS.gene52164:CDS 40.0%
AATGGTGTGTCCTTCACAGT+CGG + chr7.4:29370654-29370673 None:intergenic 45.0%
ACATCTCAACTCTCCCTACA+AGG - chr7.4:29370463-29370482 MS.gene52164:CDS 45.0%
ACCAATACCATTCGTCTTCG+AGG + chr7.4:29370241-29370260 None:intergenic 45.0%
AGCAGACAAGGTAACCTTGT+AGG + chr7.4:29370480-29370499 None:intergenic 45.0%
ATGCGAAGATAGCTAGCACA+AGG - chr7.4:29370729-29370748 MS.gene52164:CDS 45.0%
GCAGACAAGGTAACCTTGTA+GGG + chr7.4:29370479-29370498 None:intergenic 45.0%
GGATCGACCGCAATTTCAAT+GGG - chr7.4:29371144-29371163 MS.gene52164:CDS 45.0%
GTGCAAGAATTGGCAATCAG+TGG - chr7.4:29370169-29370188 MS.gene52164:CDS 45.0%
TACCATTCGTCTTCGAGGAT+CGG + chr7.4:29370236-29370255 None:intergenic 45.0%
TCCTCGAAGACGAATGGTAT+TGG - chr7.4:29370237-29370256 MS.gene52164:CDS 45.0%
TGTAATTGGGTCAGCAGACA+AGG + chr7.4:29370492-29370511 None:intergenic 45.0%
TTGTAGGGAGAGTTGAGATG+TGG + chr7.4:29370464-29370483 None:intergenic 45.0%
!! TTGCTATTTGCCGACTGTGA+AGG - chr7.4:29370641-29370660 MS.gene52164:CDS 45.0%
!! TTGGTGTCGTGTGCAAGAAT+TGG - chr7.4:29370159-29370178 MS.gene52164:CDS 45.0%
AAAACCTCGCATCCCCTTGA+AGG + chr7.4:29371122-29371141 None:intergenic 50.0%
AACCGATCCTCGAAGACGAA+TGG - chr7.4:29370231-29370250 MS.gene52164:CDS 50.0%
ATTTCCTTCAAGGGGATGCG+AGG - chr7.4:29371115-29371134 MS.gene52164:CDS 50.0%
CGCATCCCCTTGAAGGAAAT+CGG + chr7.4:29371115-29371134 None:intergenic 50.0%
GGGATCGACCGCAATTTCAA+TGG - chr7.4:29371143-29371162 MS.gene52164:CDS 50.0%
TTAGAACTGGATGCCCAGAG+TGG - chr7.4:29370884-29370903 MS.gene52164:CDS 50.0%
! CAAGGGGATGCGAGGTTTTT+GGG - chr7.4:29371123-29371142 MS.gene52164:CDS 50.0%
! TCAAGGGGATGCGAGGTTTT+TGG - chr7.4:29371122-29371141 MS.gene52164:CDS 50.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 29370068 29371171 29370068 ID=MS.gene52164
chr7.4 mRNA 29370068 29371171 29370068 ID=MS.gene52164.t1;Parent=MS.gene52164
chr7.4 exon 29370068 29371171 29370068 ID=MS.gene52164.t1.exon1;Parent=MS.gene52164.t1
chr7.4 CDS 29370068 29371171 29370068 ID=cds.MS.gene52164.t1;Parent=MS.gene52164.t1
Gene Sequence

>MS.gene52164

ATGAGGAAGGTGGCAGACTGGGCTAACTTAGAAGAACTGCCTCTTAGTTTGGTTCTTGACAAATTGGAAGATCACATAGAGCATGTTAGGTTTGGTGTCGTGTGCAAGAATTGGCAATCAGTGGAAAAGCTTAACCATCAAAACAATCAATTTAGGATTAATAAACCGATCCTCGAAGACGAATGGTATTGGTCTTATACGCATACAAAAAACGAGAAGAGATCCCTGTATAGCATTCTAAGTCACAAAGAGTATCCTGTTACATTTTTTTCCCGTATGAAAATTATAAGGTGTATGGACTCTTCATTTGGTTGGTTTGCATTAGTGGACAATAACAATGCCATAACTCTAGTCAATCCTTTTAAGTGTAGTAGTATATCTCCCATTATTCTGCCACATCTCAACTCTCCCTACAAGGTTACCTTGTCTGCTGACCCAATTACAAGTCCAAATGATTATGTCATTGCAGCCATTTACAACATTGGTGATCTTGCTTTCAAAAGAGCAAGCCAACCATTTTGGATTCATATAGCACATGAATTTGCTATCAATAATGTTGTATTTTATAAAGGCTTGCTATTTGCCGACTGTGAAGGACACACCATTATATCCTTCAAGTTCAACAATCCTCCTAACTCAAATAACCCTAATTTTACTTACTATGCGAAGATAGCTAGCACAAGGTATAGTGTTCCATCCCAATGCTATTATGAAAAGATTTATTTTGTGAAATCATTGTATGGAGACATATGGATGGTGAGAAGATATTTCATCAATCGGTATGACAAGTCCTCATATAAACTTGATGTCTACAAATTAGAACTGGATGCCCAGAGTGGAAAACTTGAACAAATGAACAAGCTTGAGAGTTTGGAAGACAACATTTTATTTGTCGGAAACCATGGTTATTCAGTTTCTGTGTCAGCCTCTCGTTTCTCCAAGTTAGAAAAAGATTCGATTTATTTTATTTATGACCATGGTATGCATGGTTTAGAGTTAGAGATCTATAATGCGAAGGATGGAAGCTGTCAGAGACAATTTTTACCGATTTCCTTCAAGGGGATGCGAGGTTTTTGGGATCGACCGCAATTTCAATGGGATTGA
Protein sequence

>MS.gene52164.t1

MRKVADWANLEELPLSLVLDKLEDHIEHVRFGVVCKNWQSVEKLNHQNNQFRINKPILEDEWYWSYTHTKNEKRSLYSILSHKEYPVTFFSRMKIIRCMDSSFGWFALVDNNNAITLVNPFKCSSISPIILPHLNSPYKVTLSADPITSPNDYVIAAIYNIGDLAFKRASQPFWIHIAHEFAINNVVFYKGLLFADCEGHTIISFKFNNPPNSNNPNFTYYAKIASTRYSVPSQCYYEKIYFVKSLYGDIWMVRRYFINRYDKSSYKLDVYKLELDAQSGKLEQMNKLESLEDNILFVGNHGYSVSVSASRFSKLEKDSIYFIYDHGMHGLELEIYNAKDGSCQRQFLPISFKGMRGFWDRPQFQWD