AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051323

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051323.t1 MTR_4g094332 94.643 224 12 0 1 224 1 224 2.75e-136 381
MS.gene051323.t1 MTR_4g094328 93.304 224 15 0 1 224 1 224 1.37e-132 372
MS.gene051323.t1 MTR_4g094330 93.304 224 15 0 1 224 1 224 1.37e-132 372
MS.gene051323.t1 MTR_1g099010 66.169 201 64 1 24 224 21 217 9.89e-90 263
MS.gene051323.t1 MTR_6g034975 65.550 209 69 2 16 224 5 210 9.76e-87 255
MS.gene051323.t1 MTR_4g094325 62.857 210 74 2 15 224 34 239 3.03e-84 250
MS.gene051323.t1 MTR_0119s0010 61.579 190 64 1 30 219 27 207 1.26e-72 220
MS.gene051323.t1 MTR_0119s0020 61.579 190 64 1 30 219 27 207 1.26e-72 220
MS.gene051323.t1 MTR_2g008110 61.579 190 64 1 30 219 27 207 1.60e-72 219
MS.gene051323.t1 MTR_4g094335 57.073 205 79 2 18 219 27 225 1.95e-70 215
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051323.t1 AT3G43660 63.959 197 62 2 29 224 10 198 5.03e-91 266
MS.gene051323.t1 AT3G43630 62.312 199 66 2 24 221 4 194 1.82e-80 239
MS.gene051323.t1 AT1G21140 62.827 191 63 1 34 224 18 200 6.05e-80 238
MS.gene051323.t1 AT1G76800 62.500 200 66 1 25 224 6 196 2.29e-79 236
MS.gene051323.t1 AT3G25190 64.455 211 69 2 18 224 9 217 1.07e-74 225

Find 52 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCTATGGCCATTACTTT+TGG 0.296297 4.1:+19281204 MS.gene051323:CDS
TCTTGTGTTAGAGTGCTTAT+TGG 0.298679 4.1:+19281174 MS.gene051323:CDS
TGTGGTTAGCTTTGCATTGT+TGG 0.307872 4.1:+19281104 MS.gene051323:CDS
TCCAGTAGAACCAATCAATT+TGG 0.330667 4.1:-19281232 None:intergenic
AGCTTTGCATTGTTGGTGTT+TGG 0.347559 4.1:+19281111 MS.gene051323:CDS
TTCAAAGGGCACAGTGGCTT+AGG 0.366043 4.1:+19280707 MS.gene051323:CDS
TGGCTTAGGGCAGCCATGTT+AGG 0.370873 4.1:+19280721 MS.gene051323:CDS
ACCAAATTGATTGGTTCTAC+TGG 0.370878 4.1:+19281231 MS.gene051323:CDS
TTTGGTTTCACCAAATTGAT+TGG 0.383690 4.1:+19281222 MS.gene051323:CDS
ATCTCAACCTCAAAATTGTT+TGG 0.384795 4.1:-19280625 None:intergenic
AGGGCTGCTTGAAATGGATT+TGG 0.388581 4.1:-19280985 None:intergenic
ATCAAAGTAATGCTCCTTGC+TGG 0.393708 4.1:+19280808 MS.gene051323:CDS
GATGCTAGGGCTGCTTGAAA+TGG 0.413748 4.1:-19280991 None:intergenic
ATGCTCCTTGCTGGTTTCGC+TGG 0.425505 4.1:+19280817 MS.gene051323:CDS
GTTTGGAGGAGTGGGAGCAT+TGG 0.437850 4.1:+19281128 MS.gene051323:CDS
TCCTTCATGGCCTCCCACCT+TGG 0.453012 4.1:+19280580 None:intergenic
CAACATTGATTACTTTCAAA+GGG 0.466059 4.1:+19280693 MS.gene051323:CDS
GGTTTCGCTGGTTTAGTAGC+CGG 0.470478 4.1:+19280829 MS.gene051323:CDS
TCAAAGGGCACAGTGGCTTA+GGG 0.472665 4.1:+19280708 MS.gene051323:CDS
AACAGTGATTAGTCCATCAT+TGG 0.482821 4.1:-19280746 None:intergenic
TTAGAGTGCTTATTGGTGGT+TGG 0.485640 4.1:+19281181 MS.gene051323:CDS
TTGTTGGTGTTTGGAGGAGT+GGG 0.488776 4.1:+19281120 MS.gene051323:CDS
TGATGATGAAAGTACTGAAA+AGG 0.488855 4.1:+19280954 MS.gene051323:CDS
ACAACATTGATTACTTTCAA+AGG 0.489039 4.1:+19280692 MS.gene051323:CDS
AAGAATCACAAAATCAGAAT+GGG 0.491528 4.1:+19281069 MS.gene051323:CDS
AAAATGCCAGTGCTGATGCT+AGG 0.492361 4.1:-19281005 None:intergenic
AAAGAATCACAAAATCAGAA+TGG 0.497277 4.1:+19281068 MS.gene051323:CDS
TTTGCATTGTTGGTGTTTGG+AGG 0.499902 4.1:+19281114 MS.gene051323:CDS
GGAGGAGTGGGAGCATTGGT+TGG 0.501548 4.1:+19281132 MS.gene051323:CDS
ATTGTTGGTGTTTGGAGGAG+TGG 0.501761 4.1:+19281119 MS.gene051323:CDS
AGAAAACTATTAGCATGGAT+AGG 0.502706 4.1:-19280649 None:intergenic
TGTGTTAGAGTGCTTATTGG+TGG 0.506211 4.1:+19281177 MS.gene051323:CDS
GCATCGTTGATGATTGGTGT+TGG 0.506584 4.1:+19280769 MS.gene051323:CDS
TATTGGTGGTTGGATGGCTA+TGG 0.515341 4.1:+19281191 MS.gene051323:CDS
ACTGTTGCATCGTTGATGAT+TGG 0.516876 4.1:+19280763 MS.gene051323:CDS
AACCTCAAAATTGTTTGGTG+AGG 0.527938 4.1:-19280620 None:intergenic
GAAAACTATTAGCATGGATA+GGG 0.536330 4.1:-19280648 None:intergenic
AGTGCTTATTGGTGGTTGGA+TGG 0.539553 4.1:+19281185 MS.gene051323:CDS
TTTGGTGAAACCAAAAGTAA+TGG 0.542621 4.1:-19281214 None:intergenic
TCCATCATTGGCTCCTAACA+TGG 0.543290 4.1:-19280734 None:intergenic
CTTTGAGAAAACTATTAGCA+TGG 0.548309 4.1:-19280654 None:intergenic
GGTGCTTGTAGCATGGCAAT+TGG 0.557712 4.1:+19280850 MS.gene051323:CDS
AGCAGCCCTAGCATCAGCAC+TGG 0.559205 4.1:+19280999 MS.gene051323:CDS
ATAAATGCAGCTGCTAGCAA+TGG 0.565330 4.1:-19281045 None:intergenic
AAATGCCAGTGCTGATGCTA+GGG 0.565337 4.1:-19281004 None:intergenic
AATTGCCATGCTACAAGCAC+CGG 0.567135 4.1:-19280848 None:intergenic
AGTAGCCGGTGCTTGTAGCA+TGG 0.572629 4.1:+19280843 MS.gene051323:CDS
GCCATGTTAGGAGCCAATGA+TGG 0.577904 4.1:+19280733 MS.gene051323:CDS
CTAACACAAGACCTCATCAA+AGG 0.611245 4.1:-19281162 None:intergenic
AATGGGAGTTGTAGCTGCTG+TGG 0.646963 4.1:+19281086 MS.gene051323:CDS
CTAAACCAGCGAAACCAGCA+AGG 0.672858 4.1:-19280822 None:intergenic
ATTACTTTCAAAGGGCACAG+TGG 0.699406 4.1:+19280701 MS.gene051323:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGAATCACAAAATCAGAA+TGG + chr4.1:19281068-19281087 MS.gene051323:CDS 25.0%
! AAGAATCACAAAATCAGAAT+GGG + chr4.1:19281069-19281088 MS.gene051323:CDS 25.0%
!! ACAACATTGATTACTTTCAA+AGG + chr4.1:19280692-19280711 MS.gene051323:CDS 25.0%
!! CAACATTGATTACTTTCAAA+GGG + chr4.1:19280693-19280712 MS.gene051323:CDS 25.0%
AGAAAACTATTAGCATGGAT+AGG - chr4.1:19280652-19280671 None:intergenic 30.0%
ATCTCAACCTCAAAATTGTT+TGG - chr4.1:19280628-19280647 None:intergenic 30.0%
GAAAACTATTAGCATGGATA+GGG - chr4.1:19280651-19280670 None:intergenic 30.0%
TTTGGTGAAACCAAAAGTAA+TGG - chr4.1:19281217-19281236 None:intergenic 30.0%
! CTTTGAGAAAACTATTAGCA+TGG - chr4.1:19280657-19280676 None:intergenic 30.0%
! TTTGGTTTCACCAAATTGAT+TGG + chr4.1:19281222-19281241 MS.gene051323:CDS 30.0%
!! TGATGATGAAAGTACTGAAA+AGG + chr4.1:19280954-19280973 MS.gene051323:CDS 30.0%
CACCTTGGAGAAAAAACTAA+CGG + chr4.1:19280595-19280614 MS.gene051323:CDS 35.0%
TCCAGTAGAACCAATCAATT+TGG - chr4.1:19281235-19281254 None:intergenic 35.0%
TTGGAAAAACTCCTTTGATG+AGG + chr4.1:19281151-19281170 MS.gene051323:CDS 35.0%
! AACAGTGATTAGTCCATCAT+TGG - chr4.1:19280749-19280768 None:intergenic 35.0%
! AACCTCAAAATTGTTTGGTG+AGG - chr4.1:19280623-19280642 None:intergenic 35.0%
! AACCTCACCAAACAATTTTG+AGG + chr4.1:19280618-19280637 MS.gene051323:CDS 35.0%
! TCTTGTGTTAGAGTGCTTAT+TGG + chr4.1:19281174-19281193 MS.gene051323:CDS 35.0%
!! ACCAAATTGATTGGTTCTAC+TGG + chr4.1:19281231-19281250 MS.gene051323:CDS 35.0%
!!! GTTAGTTTTTTCTCCAAGGT+GGG - chr4.1:19280596-19280615 None:intergenic 35.0%
!!! TTCCGTTAGTTTTTTCTCCA+AGG - chr4.1:19280600-19280619 None:intergenic 35.0%
ATAAATGCAGCTGCTAGCAA+TGG - chr4.1:19281048-19281067 None:intergenic 40.0%
ATCAAAGTAATGCTCCTTGC+TGG + chr4.1:19280808-19280827 MS.gene051323:CDS 40.0%
CTAACACAAGACCTCATCAA+AGG - chr4.1:19281165-19281184 None:intergenic 40.0%
! AGCTTTGCATTGTTGGTGTT+TGG + chr4.1:19281111-19281130 MS.gene051323:CDS 40.0%
! ATGGCTATGGCCATTACTTT+TGG + chr4.1:19281204-19281223 MS.gene051323:CDS 40.0%
! ATTACTTTCAAAGGGCACAG+TGG + chr4.1:19280701-19280720 MS.gene051323:CDS 40.0%
! TGTGTTAGAGTGCTTATTGG+TGG + chr4.1:19281177-19281196 MS.gene051323:CDS 40.0%
! TTAGAGTGCTTATTGGTGGT+TGG + chr4.1:19281181-19281200 MS.gene051323:CDS 40.0%
! TTTGCATTGTTGGTGTTTGG+AGG + chr4.1:19281114-19281133 MS.gene051323:CDS 40.0%
!! ACTGTTGCATCGTTGATGAT+TGG + chr4.1:19280763-19280782 MS.gene051323:CDS 40.0%
!! TGTGGTTAGCTTTGCATTGT+TGG + chr4.1:19281104-19281123 MS.gene051323:CDS 40.0%
!!! CGTTAGTTTTTTCTCCAAGG+TGG - chr4.1:19280597-19280616 None:intergenic 40.0%
AATTGCCATGCTACAAGCAC+CGG - chr4.1:19280851-19280870 None:intergenic 45.0%
! AGGGCTGCTTGAAATGGATT+TGG - chr4.1:19280988-19281007 None:intergenic 45.0%
! AGTGCTTATTGGTGGTTGGA+TGG + chr4.1:19281185-19281204 MS.gene051323:CDS 45.0%
! ATTGTTGGTGTTTGGAGGAG+TGG + chr4.1:19281119-19281138 MS.gene051323:CDS 45.0%
! TATTGGTGGTTGGATGGCTA+TGG + chr4.1:19281191-19281210 MS.gene051323:CDS 45.0%
! TTGTTGGTGTTTGGAGGAGT+GGG + chr4.1:19281120-19281139 MS.gene051323:CDS 45.0%
!! AAAATGCCAGTGCTGATGCT+AGG - chr4.1:19281008-19281027 None:intergenic 45.0%
!! AAATGCCAGTGCTGATGCTA+GGG - chr4.1:19281007-19281026 None:intergenic 45.0%
!! GCATCGTTGATGATTGGTGT+TGG + chr4.1:19280769-19280788 MS.gene051323:CDS 45.0%
!! TCCATCATTGGCTCCTAACA+TGG - chr4.1:19280737-19280756 None:intergenic 45.0%
!!! AGTTTTTTCTCCAAGGTGGG+AGG - chr4.1:19280593-19280612 None:intergenic 45.0%
!!! TCAGCACTGGCATTTTCTGT+TGG + chr4.1:19281012-19281031 MS.gene051323:CDS 45.0%
AATGGGAGTTGTAGCTGCTG+TGG + chr4.1:19281086-19281105 MS.gene051323:CDS 50.0%
CTAAACCAGCGAAACCAGCA+AGG - chr4.1:19280825-19280844 None:intergenic 50.0%
GATGCTAGGGCTGCTTGAAA+TGG - chr4.1:19280994-19281013 None:intergenic 50.0%
GCCATGTTAGGAGCCAATGA+TGG + chr4.1:19280733-19280752 MS.gene051323:CDS 50.0%
GGTGCTTGTAGCATGGCAAT+TGG + chr4.1:19280850-19280869 MS.gene051323:CDS 50.0%
! TCAAAGGGCACAGTGGCTTA+GGG + chr4.1:19280708-19280727 MS.gene051323:CDS 50.0%
! TTCAAAGGGCACAGTGGCTT+AGG + chr4.1:19280707-19280726 MS.gene051323:CDS 50.0%
!! GGTTTCGCTGGTTTAGTAGC+CGG + chr4.1:19280829-19280848 MS.gene051323:CDS 50.0%
AGTAGCCGGTGCTTGTAGCA+TGG + chr4.1:19280843-19280862 MS.gene051323:CDS 55.0%
TGGCTTAGGGCAGCCATGTT+AGG + chr4.1:19280721-19280740 MS.gene051323:CDS 55.0%
! GTTTGGAGGAGTGGGAGCAT+TGG + chr4.1:19281128-19281147 MS.gene051323:CDS 55.0%
!! ATGCTCCTTGCTGGTTTCGC+TGG + chr4.1:19280817-19280836 MS.gene051323:CDS 55.0%
AGCAGCCCTAGCATCAGCAC+TGG + chr4.1:19280999-19281018 MS.gene051323:CDS 60.0%
!! GGAGGAGTGGGAGCATTGGT+TGG + chr4.1:19281132-19281151 MS.gene051323:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 19280586 19281260 19280586 ID=MS.gene051323
chr4.1 mRNA 19280586 19281260 19280586 ID=MS.gene051323.t1;Parent=MS.gene051323
chr4.1 exon 19280586 19281260 19280586 ID=MS.gene051323.t1.exon1;Parent=MS.gene051323.t1
chr4.1 CDS 19280586 19281260 19280586 ID=cds.MS.gene051323.t1;Parent=MS.gene051323.t1
Gene Sequence

>MS.gene051323

ATGGCCTCCCACCTTGGAGAAAAAACTAACGGAACCTCACCAAACAATTTTGAGGTTGAGATCCCTATCCATGCTAATAGTTTTCTCAAAGTTGAAAAAGAGAGCAACAACATTGATTACTTTCAAAGGGCACAGTGGCTTAGGGCAGCCATGTTAGGAGCCAATGATGGACTAATCACTGTTGCATCGTTGATGATTGGTGTTGGAGCTATAAAAGAAGACATCAAAGTAATGCTCCTTGCTGGTTTCGCTGGTTTAGTAGCCGGTGCTTGTAGCATGGCAATTGGTGAGTTTGTTTCTGTTTATACTCAATATGACATTGAGATAGCTCAGATAAATAGAGAAAGAGAAGCTAATAATAATGACAATGATGATGAAAGTACTGAAAAGGAGAAATTGCCAAATCCATTTCAAGCAGCCCTAGCATCAGCACTGGCATTTTCTGTTGGTGCAGTGATGCCATTGCTAGCAGCTGCATTTATAAAGAATCACAAAATCAGAATGGGAGTTGTAGCTGCTGTGGTTAGCTTTGCATTGTTGGTGTTTGGAGGAGTGGGAGCATTGGTTGGAAAAACTCCTTTGATGAGGTCTTGTGTTAGAGTGCTTATTGGTGGTTGGATGGCTATGGCCATTACTTTTGGTTTCACCAAATTGATTGGTTCTACTGGACTTTGA
Protein sequence

>MS.gene051323.t1

MASHLGEKTNGTSPNNFEVEIPIHANSFLKVEKESNNIDYFQRAQWLRAAMLGANDGLITVASLMIGVGAIKEDIKVMLLAGFAGLVAGACSMAIGEFVSVYTQYDIEIAQINREREANNNDNDDESTEKEKLPNPFQAALASALAFSVGAVMPLLAAAFIKNHKIRMGVVAAVVSFALLVFGGVGALVGKTPLMRSCVRVLIGGWMAMAITFGFTKLIGSTGL