AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24208

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24208.t1 MTR_1g023400 72.245 245 56 4 1 242 117 352 1.24e-122 353
MS.gene24208.t1 MTR_1g022200 63.035 257 83 5 3 250 127 380 7.46e-104 306
MS.gene24208.t1 MTR_1g023430 91.447 152 13 0 99 250 29 180 1.09e-102 296
MS.gene24208.t1 MTR_4g080200 47.791 249 115 7 1 242 109 349 1.31e-66 210
MS.gene24208.t1 MTR_1g009110 48.193 249 117 7 1 243 137 379 9.22e-65 206
MS.gene24208.t1 MTR_1g024125 69.492 118 32 2 115 228 38 155 1.20e-53 171
MS.gene24208.t1 MTR_1g037540 45.833 264 110 12 1 242 148 400 1.37e-51 173
MS.gene24208.t1 MTR_1g022105 48.408 157 76 2 68 224 170 321 5.39e-43 148
MS.gene24208.t1 MTR_1g008000 34.400 250 106 14 7 243 65 269 2.07e-24 98.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 56 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCAACATCAATTTGAAAT+TGG 0.185453 1.2:-1563717 None:intergenic
AAATACAACACTCTTGTTAA+TGG 0.207720 1.2:+1563325 MS.gene24208:CDS
CTCCCGTCGTCTTGCACATT+TGG 0.209395 1.2:+1563539 MS.gene24208:CDS
ATAATCTAAGTACTAAATTA+TGG 0.229738 1.2:+1563248 MS.gene24208:CDS
CAACTCCTTGGAGGAAAGTT+TGG 0.295354 1.2:+1563652 MS.gene24208:CDS
GTTTGGTGTCCTAGCTATCT+TGG 0.313901 1.2:-1563794 None:intergenic
ACAAGAGTGTTGTATTTAGA+AGG 0.319163 1.2:-1563319 None:intergenic
TAATTAAATATATCCTAGTT+TGG 0.342785 1.2:-1563811 None:intergenic
TCCCGTCGTCTTGCACATTT+GGG 0.345349 1.2:+1563540 MS.gene24208:CDS
TCTTCTCTCGCAACTTTCAA+TGG 0.354491 1.2:+1563458 MS.gene24208:CDS
TGACGTGTGATGATAGTTAA+AGG 0.366005 1.2:-1563292 None:intergenic
GGCAAAATGAGTTGCCTTGA+TGG 0.369019 1.2:-1563696 None:intergenic
TTGTTAATGGCGTTTATCAT+TGG 0.379442 1.2:+1563338 MS.gene24208:CDS
GACTCATGCATGTATGGTTT+TGG 0.395961 1.2:+1563127 MS.gene24208:CDS
ATGTTTGGCCTTTGGAAGAA+TGG 0.411360 1.2:+1563625 MS.gene24208:CDS
GACAACGACTCATGCATGTA+TGG 0.419933 1.2:+1563121 MS.gene24208:CDS
AAAGGAGGAGGATGTTGAGT+AGG 0.426239 1.2:-1563274 None:intergenic
TGTTTCGTATGTTTGGCCTT+TGG 0.429988 1.2:+1563617 MS.gene24208:CDS
AAGGAGGAGGATGTTGAGTA+GGG 0.432055 1.2:-1563273 None:intergenic
CTTCTCTCGCAACTTTCAAT+GGG 0.434082 1.2:+1563459 MS.gene24208:CDS
GCTTTGAAGTTGATGTTGTC+GGG 0.441312 1.2:-1563160 None:intergenic
GGAAAATGTTGCCGAGATCA+AGG 0.444536 1.2:+1563480 MS.gene24208:CDS
TGAAAGTTGCGAGAGAAGAT+TGG 0.450386 1.2:-1563454 None:intergenic
AGCTTTGAAGTTGATGTTGT+CGG 0.460508 1.2:-1563161 None:intergenic
CGGTGAACCTCTCTAGTTGT+TGG 0.473040 1.2:-1563076 None:intergenic
GGTGAACCTCTCTAGTTGTT+GGG 0.479668 1.2:-1563075 None:intergenic
CGTCTTGCACATTTGGGCAA+TGG 0.493742 1.2:+1563546 MS.gene24208:CDS
CTTTGTCAACCAAGATAGCT+AGG 0.511992 1.2:+1563785 MS.gene24208:CDS
AAGAATGGCGATCAACTCCT+TGG 0.512877 1.2:+1563640 MS.gene24208:CDS
GCCCAAATGTGCAAGACGAC+GGG 0.513551 1.2:-1563541 None:intergenic
AGCAAGGGAACCCTTGATCT+CGG 0.527450 1.2:-1563491 None:intergenic
GAATATTTGCAGCATAATCA+TGG 0.531645 1.2:-1563387 None:intergenic
GTTGACAAAGGAGCTATGCT+TGG 0.537962 1.2:-1563772 None:intergenic
GTGATGATAGTTAAAGGAGG+AGG 0.543019 1.2:-1563286 None:intergenic
AACAAGTTTCACACACTCAG+AGG 0.544907 1.2:+1563430 MS.gene24208:CDS
GATAGCTAGGACACCAAACT+AGG 0.547828 1.2:+1563798 MS.gene24208:CDS
AATGGCGATCAACTCCTTGG+AGG 0.570585 1.2:+1563643 MS.gene24208:CDS
GTTGATCGCCATTCTTCCAA+AGG 0.574741 1.2:-1563633 None:intergenic
TCAATTATTGTTCTGTGACA+AGG 0.579061 1.2:+1563197 MS.gene24208:CDS
GAAAATGTTGCCGAGATCAA+GGG 0.586335 1.2:+1563481 MS.gene24208:CDS
TGCCCAAATGTGCAAGACGA+CGG 0.589863 1.2:-1563542 None:intergenic
CTAGCTATCTTGGTTGACAA+AGG 0.595687 1.2:-1563784 None:intergenic
ACATGCATGAGTCGTTGTCA+AGG 0.608520 1.2:-1563117 None:intergenic
CTCACATCATATGACCATCA+AGG 0.608996 1.2:+1563682 MS.gene24208:CDS
GGGCAATGGATCAAAGTGGA+TGG 0.609401 1.2:+1563560 MS.gene24208:CDS
CGTGTGATGATAGTTAAAGG+AGG 0.609950 1.2:-1563289 None:intergenic
GATTCTGCACAACATAAGCA+AGG 0.613750 1.2:-1563507 None:intergenic
TCGTTGTCAAGGCAGAGACT+CGG 0.619869 1.2:-1563106 None:intergenic
ACAAGTTTCACACACTCAGA+GGG 0.630363 1.2:+1563431 MS.gene24208:CDS
GGCAGAGACTCGGAGGAACA+CGG 0.631574 1.2:-1563096 None:intergenic
GTGGAACCCAACAACTAGAG+AGG 0.665628 1.2:+1563069 MS.gene24208:CDS
ATTTGGGCAATGGATCAAAG+TGG 0.667392 1.2:+1563556 MS.gene24208:CDS
ATTCTGCACAACATAAGCAA+GGG 0.674457 1.2:-1563506 None:intergenic
TGATGGTCATATGATGTGAG+CGG 0.679098 1.2:-1563679 None:intergenic
TTGTCAAGGCAGAGACTCGG+AGG 0.701974 1.2:-1563103 None:intergenic
AGGAGGAGGATGTTGAGTAG+GGG 0.705269 1.2:-1563272 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATCTAAGTACTAAATTA+TGG + chr1.2:1563248-1563267 MS.gene24208:CDS 15.0%
!!! GAAACATTATATTTCATTTT+CGG + chr1.2:1563219-1563238 MS.gene24208:CDS 15.0%
!!! TTGATGATAATGAATATTTT+TGG + chr1.2:1563734-1563753 MS.gene24208:CDS 15.0%
! AAATACAACACTCTTGTTAA+TGG + chr1.2:1563325-1563344 MS.gene24208:CDS 25.0%
! ATACGAAACATTGAAAAAAC+TGG - chr1.2:1563607-1563626 None:intergenic 25.0%
! TACGAAACATTGAAAAAACT+GGG - chr1.2:1563606-1563625 None:intergenic 25.0%
!! CATCAACATCAATTTGAAAT+TGG - chr1.2:1563720-1563739 None:intergenic 25.0%
!! TTTTCAATGTTTCGTATGTT+TGG + chr1.2:1563610-1563629 MS.gene24208:CDS 25.0%
GAATATTTGCAGCATAATCA+TGG - chr1.2:1563390-1563409 None:intergenic 30.0%
TCAATTATTGTTCTGTGACA+AGG + chr1.2:1563197-1563216 MS.gene24208:CDS 30.0%
TGGAGAAAAATGTACAACAT+TGG + chr1.2:1563580-1563599 MS.gene24208:CDS 30.0%
TTGTTAATGGCGTTTATCAT+TGG + chr1.2:1563338-1563357 MS.gene24208:CDS 30.0%
!! ACAAGAGTGTTGTATTTAGA+AGG - chr1.2:1563322-1563341 None:intergenic 30.0%
ATTCTGCACAACATAAGCAA+GGG - chr1.2:1563509-1563528 None:intergenic 35.0%
TGACGTGTGATGATAGTTAA+AGG - chr1.2:1563295-1563314 None:intergenic 35.0%
!! AGCTTTGAAGTTGATGTTGT+CGG - chr1.2:1563164-1563183 None:intergenic 35.0%
AACAAGTTTCACACACTCAG+AGG + chr1.2:1563430-1563449 MS.gene24208:CDS 40.0%
ACAAGTTTCACACACTCAGA+GGG + chr1.2:1563431-1563450 MS.gene24208:CDS 40.0%
ATTTGGGCAATGGATCAAAG+TGG + chr1.2:1563556-1563575 MS.gene24208:CDS 40.0%
CGTGTGATGATAGTTAAAGG+AGG - chr1.2:1563292-1563311 None:intergenic 40.0%
CTAGCTATCTTGGTTGACAA+AGG - chr1.2:1563787-1563806 None:intergenic 40.0%
CTCACATCATATGACCATCA+AGG + chr1.2:1563682-1563701 MS.gene24208:CDS 40.0%
CTTCTCTCGCAACTTTCAAT+GGG + chr1.2:1563459-1563478 MS.gene24208:CDS 40.0%
CTTTGTCAACCAAGATAGCT+AGG + chr1.2:1563785-1563804 MS.gene24208:CDS 40.0%
GAAAATGTTGCCGAGATCAA+GGG + chr1.2:1563481-1563500 MS.gene24208:CDS 40.0%
GATTCTGCACAACATAAGCA+AGG - chr1.2:1563510-1563529 None:intergenic 40.0%
GTGATGATAGTTAAAGGAGG+AGG - chr1.2:1563289-1563308 None:intergenic 40.0%
TCTTCTCTCGCAACTTTCAA+TGG + chr1.2:1563458-1563477 MS.gene24208:CDS 40.0%
TGAAAGTTGCGAGAGAAGAT+TGG - chr1.2:1563457-1563476 None:intergenic 40.0%
TGATGGTCATATGATGTGAG+CGG - chr1.2:1563682-1563701 None:intergenic 40.0%
! ATGTTTGGCCTTTGGAAGAA+TGG + chr1.2:1563625-1563644 MS.gene24208:CDS 40.0%
! GACTCATGCATGTATGGTTT+TGG + chr1.2:1563127-1563146 MS.gene24208:CDS 40.0%
! GTTTTCCAAACTTTCCTCCA+AGG - chr1.2:1563660-1563679 None:intergenic 40.0%
! TGTTTCGTATGTTTGGCCTT+TGG + chr1.2:1563617-1563636 MS.gene24208:CDS 40.0%
!! GCTTTGAAGTTGATGTTGTC+GGG - chr1.2:1563163-1563182 None:intergenic 40.0%
AAAGGAGGAGGATGTTGAGT+AGG - chr1.2:1563277-1563296 None:intergenic 45.0%
AAGAATGGCGATCAACTCCT+TGG + chr1.2:1563640-1563659 MS.gene24208:CDS 45.0%
AAGGAGGAGGATGTTGAGTA+GGG - chr1.2:1563276-1563295 None:intergenic 45.0%
ACATGCATGAGTCGTTGTCA+AGG - chr1.2:1563120-1563139 None:intergenic 45.0%
CAACTCCTTGGAGGAAAGTT+TGG + chr1.2:1563652-1563671 MS.gene24208:CDS 45.0%
GACAACGACTCATGCATGTA+TGG + chr1.2:1563121-1563140 MS.gene24208:CDS 45.0%
GGAAAATGTTGCCGAGATCA+AGG + chr1.2:1563480-1563499 MS.gene24208:CDS 45.0%
GGCAAAATGAGTTGCCTTGA+TGG - chr1.2:1563699-1563718 None:intergenic 45.0%
GGTGAACCTCTCTAGTTGTT+GGG - chr1.2:1563078-1563097 None:intergenic 45.0%
GTTGACAAAGGAGCTATGCT+TGG - chr1.2:1563775-1563794 None:intergenic 45.0%
GTTGATCGCCATTCTTCCAA+AGG - chr1.2:1563636-1563655 None:intergenic 45.0%
!! GTTTGGTGTCCTAGCTATCT+TGG - chr1.2:1563797-1563816 None:intergenic 45.0%
AATGGCGATCAACTCCTTGG+AGG + chr1.2:1563643-1563662 MS.gene24208:CDS 50.0%
AGCAAGGGAACCCTTGATCT+CGG - chr1.2:1563494-1563513 None:intergenic 50.0%
AGGAGGAGGATGTTGAGTAG+GGG - chr1.2:1563275-1563294 None:intergenic 50.0%
CGGTGAACCTCTCTAGTTGT+TGG - chr1.2:1563079-1563098 None:intergenic 50.0%
CGTCTTGCACATTTGGGCAA+TGG + chr1.2:1563546-1563565 MS.gene24208:CDS 50.0%
GGGCAATGGATCAAAGTGGA+TGG + chr1.2:1563560-1563579 MS.gene24208:CDS 50.0%
GTGGAACCCAACAACTAGAG+AGG + chr1.2:1563069-1563088 MS.gene24208:CDS 50.0%
TCCCGTCGTCTTGCACATTT+GGG + chr1.2:1563540-1563559 MS.gene24208:CDS 50.0%
TCGTTGTCAAGGCAGAGACT+CGG - chr1.2:1563109-1563128 None:intergenic 50.0%
TGCCCAAATGTGCAAGACGA+CGG - chr1.2:1563545-1563564 None:intergenic 50.0%
CTCCCGTCGTCTTGCACATT+TGG + chr1.2:1563539-1563558 MS.gene24208:CDS 55.0%
GCCCAAATGTGCAAGACGAC+GGG - chr1.2:1563544-1563563 None:intergenic 55.0%
TTGTCAAGGCAGAGACTCGG+AGG - chr1.2:1563106-1563125 None:intergenic 55.0%
GGCAGAGACTCGGAGGAACA+CGG - chr1.2:1563099-1563118 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 1563067 1563819 1563067 ID=MS.gene24208
chr1.2 mRNA 1563067 1563819 1563067 ID=MS.gene24208.t1;Parent=MS.gene24208
chr1.2 exon 1563067 1563819 1563067 ID=MS.gene24208.t1.exon1;Parent=MS.gene24208.t1
chr1.2 CDS 1563067 1563819 1563067 ID=cds.MS.gene24208.t1;Parent=MS.gene24208.t1
Gene Sequence

>MS.gene24208

ATGTGGAACCCAACAACTAGAGAGGTTCACCGTGTTCCTCCGAGTCTCTGCCTTGACAACGACTCATGCATGTATGGTTTTGGTGCTGATGATCCCGACAACATCAACTTCAAAGCTGTGAAACTTCATATCAATTATTGTTCTGTGACAAGGAAACATTATATTTCATTTTCGGAAGTTTATAATCTAAGTACTAAATTATGGACCCCTACTCAACATCCTCCTCCTTTAACTATCATCACACGTCAATGTCCTTCTAAATACAACACTCTTGTTAATGGCGTTTATCATTGGATTACAGAGAATACATACTACTATCACCATGATTATGCTGCAAATATTCTATGTTTTGACTTTCACAGCAACAAGTTTCACACACTCAGAGGGCCAATCTTCTCTCGCAACTTTCAATGGGAAAATGTTGCCGAGATCAAGGGTTCCCTTGCTTATGTTGTGCAGAATCACTTCAATGCTCCCGTCGTCTTGCACATTTGGGCAATGGATCAAAGTGGATGGAGAAAAATGTACAACATTGGCCCAGTTTTTTCAATGTTTCGTATGTTTGGCCTTTGGAAGAATGGCGATCAACTCCTTGGAGGAAAGTTTGGAAAACCGCTCACATCATATGACCATCAAGGCAACTCATTTTGCCAATTTCAAATTGATGTTGATGATAATGAATATTTTTGGATTCATGAGTATGTGCCAAGCATAGCTCCTTTGTCAACCAAGATAGCTAGGACACCAAACTAG
Protein sequence

>MS.gene24208.t1

MWNPTTREVHRVPPSLCLDNDSCMYGFGADDPDNINFKAVKLHINYCSVTRKHYISFSEVYNLSTKLWTPTQHPPPLTIITRQCPSKYNTLVNGVYHWITENTYYYHHDYAANILCFDFHSNKFHTLRGPIFSRNFQWENVAEIKGSLAYVVQNHFNAPVVLHIWAMDQSGWRKMYNIGPVFSMFRMFGLWKNGDQLLGGKFGKPLTSYDHQGNSFCQFQIDVDDNEYFWIHEYVPSIAPLSTKIARTPN