AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene48173

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene48173.t1 MTR_6g034975 99.048 210 2 0 1 210 1 210 2.89e-151 418
MS.gene48173.t1 MTR_1g099010 80.000 215 34 3 2 210 6 217 6.25e-114 324
MS.gene48173.t1 MTR_4g094332 64.593 209 71 2 5 210 16 224 2.96e-85 251
MS.gene48173.t1 MTR_4g094328 64.115 209 72 2 5 210 16 224 1.04e-83 248
MS.gene48173.t1 MTR_4g094330 64.115 209 72 2 5 210 16 224 1.04e-83 248
MS.gene48173.t1 MTR_4g094325 62.673 217 70 4 1 210 27 239 1.94e-81 243
MS.gene48173.t1 MTR_2g008110 67.179 195 54 2 11 205 23 207 5.46e-78 233
MS.gene48173.t1 MTR_0119s0010 67.179 195 54 2 11 205 23 207 5.64e-78 233
MS.gene48173.t1 MTR_0119s0020 67.179 195 54 2 11 205 23 207 5.64e-78 233
MS.gene48173.t1 MTR_4g094335 57.674 215 84 3 3 210 17 231 2.15e-67 207
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene48173.t1 AT3G43660 68.095 210 55 2 1 210 1 198 2.33e-101 291
MS.gene48173.t1 AT1G21140 74.372 199 42 3 15 210 8 200 6.73e-95 275
MS.gene48173.t1 AT3G43630 74.747 198 38 3 11 208 10 195 1.96e-93 271
MS.gene48173.t1 AT1G76800 72.059 204 43 2 7 210 7 196 4.63e-90 263
MS.gene48173.t1 AT3G25190 57.143 217 86 2 1 210 1 217 6.63e-68 207

Find 23 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCTATGTCCATTACTTT+TGG 0.207489 6.4:+7542652 MS.gene48173:CDS
CAAGATCATATTTGGTTTGT+TGG 0.270531 6.4:-7542090 None:intergenic
TTTGGGCTTACTAAGTTGAT+TGG 0.343858 6.4:+7542670 MS.gene48173:CDS
GGCTACCAACCCGGCAAAAC+CGG 0.371040 6.4:-7542281 None:intergenic
GGTTGGTTAGGGGCTGTGTT+GGG 0.375737 6.4:+7542580 MS.gene48173:CDS
TGGTTGGTTAGGGGCTGTGT+TGG 0.391725 6.4:+7542579 MS.gene48173:CDS
GTTAGGGGCTGTGTTGGGTA+AGG 0.394809 6.4:+7542585 MS.gene48173:CDS
CTCCACAGCTTCGCTAATGA+TGG 0.415096 6.4:+7542216 MS.gene48173:CDS
ATCAAAGCAATGATCTTAAC+CGG 0.418707 6.4:+7542262 MS.gene48173:CDS
GGTGCATGCAGCATGGCAAT+AGG 0.426664 6.4:+7542304 MS.gene48173:CDS
TTGGGCTTACTAAGTTGATT+GGG 0.437883 6.4:+7542671 MS.gene48173:CDS
ATGAAAAGAGAGAAAGAAAG+AGG 0.469828 6.4:+7542373 MS.gene48173:CDS
CTTAGTAAGCCCAAAAGTAA+TGG 0.481590 6.4:-7542662 None:intergenic
GCTGCAGCTTGTAGAGGATT+AGG 0.482303 6.4:-7542433 None:intergenic
GCATGCACCGGCTACCAACC+CGG 0.522518 6.4:-7542290 None:intergenic
TATTGCCATGCTGCATGCAC+CGG 0.557551 6.4:-7542302 None:intergenic
AGGGATTATAAGGTGAGAGT+TGG 0.562126 6.4:+7542517 MS.gene48173:CDS
GGTAGCCGGTGCATGCAGCA+TGG 0.575221 6.4:+7542297 MS.gene48173:CDS
ACCCATCATTAGCGAAGCTG+TGG 0.580136 6.4:-7542218 None:intergenic
TCCACAGCTTCGCTAATGAT+GGG 0.583720 6.4:+7542217 MS.gene48173:CDS
GAAGCTGCTGCAGCTTGTAG+AGG 0.586901 6.4:-7542439 None:intergenic
ACTAAGTTGATTGGGACAAG+TGG 0.608678 6.4:+7542679 MS.gene48173:CDS
GCTTCGCTAATGATGGGTGT+CGG 0.616336 6.4:+7542223 MS.gene48173:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTTAGGTCTGTTTTAA+GGG + chr6.4:7542612-7542631 MS.gene48173:CDS 20.0%
!!! ATTTTTCTCAAGATCATATT+TGG - chr6.4:7542101-7542120 None:intergenic 20.0%
!!! TTTTTTCATAAGGGATTATA+AGG + chr6.4:7542507-7542526 MS.gene48173:CDS 20.0%
! ATAATCCCTTATGAAAAAAG+CGG - chr6.4:7542506-7542525 None:intergenic 25.0%
! CTTAAAACAGACCTAAAAAT+TGG - chr6.4:7542613-7542632 None:intergenic 25.0%
!!! AATCTTTTGTTTCAACTTCT+AGG - chr6.4:7542132-7542151 None:intergenic 25.0%
!!! ATCTTTTGTTTCAACTTCTA+GGG - chr6.4:7542131-7542150 None:intergenic 25.0%
!!! CAATTTTTAGGTCTGTTTTA+AGG + chr6.4:7542611-7542630 MS.gene48173:CDS 25.0%
ACTACTCAAAAAGATCACAA+TGG + chr6.4:7542155-7542174 MS.gene48173:CDS 30.0%
ATCAAAGCAATGATCTTAAC+CGG + chr6.4:7542262-7542281 MS.gene48173:CDS 30.0%
ATGAAAAGAGAGAAAGAAAG+AGG + chr6.4:7542373-7542392 MS.gene48173:CDS 30.0%
!! AGTTTTGCTTTGCTTGTTTT+TGG + chr6.4:7542559-7542578 MS.gene48173:CDS 30.0%
!! CAAGATCATATTTGGTTTGT+TGG - chr6.4:7542093-7542112 None:intergenic 30.0%
!!! TCAGCTTTAGCTTTTTCTAT+TGG + chr6.4:7542460-7542479 MS.gene48173:CDS 30.0%
!!! TCTGTTTTAAGGGTTTTGTT+TGG + chr6.4:7542622-7542641 MS.gene48173:CDS 30.0%
ATGAAAAAAGCGGCAAGTAA+TGG - chr6.4:7542496-7542515 None:intergenic 35.0%
CTTAGTAAGCCCAAAAGTAA+TGG - chr6.4:7542665-7542684 None:intergenic 35.0%
! ATGGCTATGTCCATTACTTT+TGG + chr6.4:7542652-7542671 MS.gene48173:CDS 35.0%
!! AGCTTTTTCTATTGGTGCAA+TGG + chr6.4:7542468-7542487 MS.gene48173:CDS 35.0%
!! TGGCTATGTCCATTACTTTT+GGG + chr6.4:7542653-7542672 MS.gene48173:CDS 35.0%
!! TTGGGCTTACTAAGTTGATT+GGG + chr6.4:7542671-7542690 MS.gene48173:CDS 35.0%
!! TTTGGGCTTACTAAGTTGAT+TGG + chr6.4:7542670-7542689 MS.gene48173:CDS 35.0%
!!! ACTTGCCGCTTTTTTCATAA+GGG + chr6.4:7542498-7542517 MS.gene48173:CDS 35.0%
!!! GTTTTAAGGGTTTTGTTTGG+TGG + chr6.4:7542625-7542644 MS.gene48173:CDS 35.0%
!!! TACTTGCCGCTTTTTTCATA+AGG + chr6.4:7542497-7542516 MS.gene48173:CDS 35.0%
!!! TGCTTGTTTTTGGTTGGTTA+GGG + chr6.4:7542569-7542588 MS.gene48173:CDS 35.0%
!!! TTGCTTGTTTTTGGTTGGTT+AGG + chr6.4:7542568-7542587 MS.gene48173:CDS 35.0%
!!! TTGCTTTGCTTGTTTTTGGT+TGG + chr6.4:7542563-7542582 MS.gene48173:CDS 35.0%
AGGGATTATAAGGTGAGAGT+TGG + chr6.4:7542517-7542536 MS.gene48173:CDS 40.0%
! TGGGTAAGGCTCCAATTTTT+AGG + chr6.4:7542599-7542618 MS.gene48173:CDS 40.0%
!! ACTAAGTTGATTGGGACAAG+TGG + chr6.4:7542679-7542698 MS.gene48173:CDS 40.0%
!! ATGATCTTAACCGGTTTTGC+CGG + chr6.4:7542271-7542290 MS.gene48173:CDS 40.0%
!!! GCTTGTTTTTGGTTGGTTAG+GGG + chr6.4:7542570-7542589 MS.gene48173:CDS 40.0%
!!! TAAGGGTTTTGTTTGGTGGT+TGG + chr6.4:7542629-7542648 MS.gene48173:CDS 40.0%
TCCACAGCTTCGCTAATGAT+GGG + chr6.4:7542217-7542236 MS.gene48173:CDS 45.0%
! TGGCTAAGAGCAGCAGTTTT+AGG + chr6.4:7542175-7542194 MS.gene48173:CDS 45.0%
!! TGATCTTAACCGGTTTTGCC+GGG + chr6.4:7542272-7542291 MS.gene48173:CDS 45.0%
!!! GCAGTTTTAGGAGCTAACGA+CGG + chr6.4:7542187-7542206 MS.gene48173:CDS 45.0%
!!! GGTTTTGTTTGGTGGTTGGA+TGG + chr6.4:7542633-7542652 MS.gene48173:CDS 45.0%
ACCCATCATTAGCGAAGCTG+TGG - chr6.4:7542221-7542240 None:intergenic 50.0%
CTCCACAGCTTCGCTAATGA+TGG + chr6.4:7542216-7542235 MS.gene48173:CDS 50.0%
GCTGCAGCTTGTAGAGGATT+AGG - chr6.4:7542436-7542455 None:intergenic 50.0%
TATTGCCATGCTGCATGCAC+CGG - chr6.4:7542305-7542324 None:intergenic 50.0%
!! GCTTCGCTAATGATGGGTGT+CGG + chr6.4:7542223-7542242 MS.gene48173:CDS 50.0%
GAAGCTGCTGCAGCTTGTAG+AGG - chr6.4:7542442-7542461 None:intergenic 55.0%
GGTGCATGCAGCATGGCAAT+AGG + chr6.4:7542304-7542323 MS.gene48173:CDS 55.0%
GTTAGGGGCTGTGTTGGGTA+AGG + chr6.4:7542585-7542604 MS.gene48173:CDS 55.0%
! GGTTGGTTAGGGGCTGTGTT+GGG + chr6.4:7542580-7542599 MS.gene48173:CDS 55.0%
! TGGTTGGTTAGGGGCTGTGT+TGG + chr6.4:7542579-7542598 MS.gene48173:CDS 55.0%
!! CTTAACCGGTTTTGCCGGGT+TGG + chr6.4:7542276-7542295 MS.gene48173:CDS 55.0%
GGCTACCAACCCGGCAAAAC+CGG - chr6.4:7542284-7542303 None:intergenic 60.0%
!!! GGTTTTGCCGGGTTGGTAGC+CGG + chr6.4:7542283-7542302 MS.gene48173:CDS 60.0%
GGTAGCCGGTGCATGCAGCA+TGG + chr6.4:7542297-7542316 MS.gene48173:CDS 65.0%
!! GCATGCACCGGCTACCAACC+CGG - chr6.4:7542293-7542312 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 7542076 7542708 7542076 ID=MS.gene48173
chr6.4 mRNA 7542076 7542708 7542076 ID=MS.gene48173.t1;Parent=MS.gene48173
chr6.4 exon 7542076 7542708 7542076 ID=MS.gene48173.t1.exon1;Parent=MS.gene48173.t1
chr6.4 CDS 7542076 7542708 7542076 ID=cds.MS.gene48173.t1;Parent=MS.gene48173.t1
Gene Sequence

>MS.gene48173

ATGGCATCACTAAACCAACAAACCAAATATGATCTTGAGAAAAATTCAACAACCCTAGAAGTTGAAACAAAAGATTTTGACTACTCAAAAAGATCACAATGGCTAAGAGCAGCAGTTTTAGGAGCTAACGACGGATTAGTCTCCACAGCTTCGCTAATGATGGGTGTCGGTGCAGTCAAGCAAGACATCAAAGCAATGATCTTAACCGGTTTTGCCGGGTTGGTAGCCGGTGCATGCAGCATGGCAATAGGTGAATTTGTCTCTGTATACTCACAATTAGACATTGAAGTTGCTCAAATGAAAAGAGAGAAAGAAAGAGGAAGAGAAATCAATGATGATGAAGAGAAAGAAAGTTTGCCTAATCCTCTACAAGCTGCAGCAGCTTCAGCTTTAGCTTTTTCTATTGGTGCAATGGTGCCATTACTTGCCGCTTTTTTCATAAGGGATTATAAGGTGAGAGTTGGTGTTGTTGTAGCTGCAGTTAGTTTTGCTTTGCTTGTTTTTGGTTGGTTAGGGGCTGTGTTGGGTAAGGCTCCAATTTTTAGGTCTGTTTTAAGGGTTTTGTTTGGTGGTTGGATGGCTATGTCCATTACTTTTGGGCTTACTAAGTTGATTGGGACAAGTGGACTTTAG
Protein sequence

>MS.gene48173.t1

MASLNQQTKYDLEKNSTTLEVETKDFDYSKRSQWLRAAVLGANDGLVSTASLMMGVGAVKQDIKAMILTGFAGLVAGACSMAIGEFVSVYSQLDIEVAQMKREKERGREINDDEEKESLPNPLQAAAASALAFSIGAMVPLLAAFFIRDYKVRVGVVVAAVSFALLVFGWLGAVLGKAPIFRSVLRVLFGGWMAMSITFGLTKLIGTSGL