AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060207

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060207.t1 MTR_2g076060 91.342 231 12 4 1 229 1 225 1.48e-140 392
MS.gene060207.t1 MTR_5g014400 85.366 41 6 0 52 92 77 117 3.76e-21 89.0
MS.gene060207.t1 MTR_4g021270 67.857 56 10 2 46 101 51 98 5.19e-20 87.0
MS.gene060207.t1 MTR_3g068095 46.067 89 40 3 1 89 9 89 8.55e-20 85.5
MS.gene060207.t1 MTR_5g080660 66.667 48 15 1 45 92 38 84 5.56e-18 80.1
MS.gene060207.t1 MTR_1g070265 81.579 38 7 0 52 89 32 69 7.38e-18 78.6
MS.gene060207.t1 MTR_4g064873 31.333 150 88 3 31 178 2 138 8.45e-16 72.8
MS.gene060207.t1 MTR_7g063220 50.000 58 29 0 33 90 2 59 2.11e-14 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060207.t1 AT3G23130 34.081 223 75 8 30 223 23 202 4.85e-25 98.2
MS.gene060207.t1 AT2G42410 33.482 224 105 8 24 223 9 212 2.75e-24 96.3
MS.gene060207.t1 AT2G42410 33.482 224 105 8 24 223 9 212 2.75e-24 96.3
MS.gene060207.t1 AT2G42410 33.482 224 105 8 24 223 35 238 4.31e-24 96.7
MS.gene060207.t1 AT5G06070 55.263 76 29 1 39 109 37 112 4.99e-22 90.9
MS.gene060207.t1 AT2G37740 92.105 38 3 0 52 89 34 71 2.44e-20 87.8
MS.gene060207.t1 AT4G17810 86.111 36 5 0 52 87 41 76 9.87e-18 78.2
MS.gene060207.t1 AT4G17810 86.111 36 5 0 52 87 41 76 1.80e-17 78.2
MS.gene060207.t1 AT3G09290 50.847 59 27 1 55 111 33 91 7.06e-14 67.8
MS.gene060207.t1 AT3G53820 53.061 49 20 1 44 89 5 53 1.21e-12 63.5

Find 42 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGAATGTGAGAATAAATT+AGG 0.181994 2.3:-20849214 None:intergenic
CAAAGTGATTATAATAATAA+TGG 0.313354 2.3:+20848950 MS.gene060207:CDS
TTAAGGATGGATTTGGAGAT+AGG 0.323598 2.3:+20849460 MS.gene060207:CDS
AAGGGTAATGTGCAAGTAAT+AGG 0.332503 2.3:-20849286 None:intergenic
TTAGGGTTAGTAGTGATAGT+AGG 0.333789 2.3:-20849196 None:intergenic
CTTGGATCTTGAGCTTCGTT+TGG 0.358995 2.3:+20849504 MS.gene060207:CDS
GTCACATGAATGTTCATAGA+AGG 0.359608 2.3:+20849080 MS.gene060207:CDS
TACTACTACTTACTCTAATT+AGG 0.371898 2.3:+20849528 MS.gene060207:CDS
GAGGTCTTTGTGCTCAAAGT+AGG 0.390132 2.3:-20849370 None:intergenic
TTGGATCTTGAGCTTCGTTT+GGG 0.406516 2.3:+20849505 MS.gene060207:CDS
GAAGAACCTTGATCAATTTG+AGG 0.415797 2.3:-20849148 None:intergenic
ATGAATGTGAGAATAAATTA+GGG 0.439290 2.3:-20849213 None:intergenic
TAGGGTTAGTAGTGATAGTA+GGG 0.449276 2.3:-20849195 None:intergenic
AATATGAACACAAGCTTGAA+AGG 0.476718 2.3:+20848875 MS.gene060207:CDS
AGGTCTTTGTGCTCAAAGTA+GGG 0.478191 2.3:-20849369 None:intergenic
TTTAAATCAGCTCAAGCACT+TGG 0.494247 2.3:+20849055 MS.gene060207:CDS
GTGTATGATCTTGGTGGCCA+TGG 0.499774 2.3:-20849010 None:intergenic
AATAGATATGTTGTTGTGGA+TGG 0.501785 2.3:+20849334 MS.gene060207:CDS
CATGAACCTCAAATTGATCA+AGG 0.507634 2.3:+20849142 MS.gene060207:CDS
GACCTCAGAGAAATCAAAGA+TGG 0.508422 2.3:+20849387 MS.gene060207:CDS
AAGCTACATGTGTATGATCT+TGG 0.515500 2.3:-20849019 None:intergenic
CTTGAGAGTTGTTGCTGAAG+AGG 0.522978 2.3:-20849263 None:intergenic
GCCAGGAGATTATGACAACT+TGG 0.523282 2.3:+20849486 MS.gene060207:CDS
TCAGAAGATTACATGATGAA+TGG 0.523539 2.3:+20848980 MS.gene060207:CDS
AAATCAGCTCAAGCACTTGG+AGG 0.523713 2.3:+20849058 MS.gene060207:CDS
GATTTGGAGATAGGATTGCC+AGG 0.525003 2.3:+20849469 MS.gene060207:CDS
TCCAAGTTGTCATAATCTCC+TGG 0.534174 2.3:-20849487 None:intergenic
TGAGGTTCATGAGTTGGTGG+TGG 0.545714 2.3:-20849130 None:intergenic
TCAATTTGAGGTTCATGAGT+TGG 0.558616 2.3:-20849136 None:intergenic
TGATGAATGGTTGTTATCCA+TGG 0.592785 2.3:+20848993 MS.gene060207:CDS
TTCATAGAAGGGATAGAGCA+AGG 0.597565 2.3:+20849092 MS.gene060207:CDS
ATTTGAGGTTCATGAGTTGG+TGG 0.598442 2.3:-20849133 None:intergenic
TCACATGAATGTTCATAGAA+GGG 0.603355 2.3:+20849081 MS.gene060207:CDS
ATCCATCTTTGATTTCTCTG+AGG 0.605445 2.3:-20849389 None:intergenic
TCAGAGAAATCAAAGATGGA+TGG 0.606828 2.3:+20849391 MS.gene060207:CDS
ACATATCTATTAAACTCAGA+AGG 0.608200 2.3:-20849322 None:intergenic
AGAAGGAGGTGAAACAAACA+AGG 0.612191 2.3:-20849305 None:intergenic
GTTTAATAGATATGTTGTTG+TGG 0.616672 2.3:+20849330 MS.gene060207:CDS
CTACATGTGTATGATCTTGG+TGG 0.625534 2.3:-20849016 None:intergenic
TATCTATTAAACTCAGAAGG+AGG 0.651729 2.3:-20849319 None:intergenic
ATGTGAAGATGATTGTAGCA+TGG 0.675289 2.3:+20849420 MS.gene060207:CDS
GAAGGAGGTGAAACAAACAA+GGG 0.747063 2.3:-20849304 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAAAGTGATTATAATAATAA+TGG + chr2.3:20848950-20848969 MS.gene060207:CDS 15.0%
!! ATGAATGTGAGAATAAATTA+GGG - chr2.3:20849216-20849235 None:intergenic 20.0%
! ACATATCTATTAAACTCAGA+AGG - chr2.3:20849325-20849344 None:intergenic 25.0%
! GATGAATGTGAGAATAAATT+AGG - chr2.3:20849217-20849236 None:intergenic 25.0%
! GTTTAATAGATATGTTGTTG+TGG + chr2.3:20849330-20849349 MS.gene060207:CDS 25.0%
!! TGAAGAAAAGTGAGATTTTA+AGG + chr2.3:20849443-20849462 MS.gene060207:CDS 25.0%
AATAGATATGTTGTTGTGGA+TGG + chr2.3:20849334-20849353 MS.gene060207:CDS 30.0%
AATATGAACACAAGCTTGAA+AGG + chr2.3:20848875-20848894 MS.gene060207:CDS 30.0%
TATCTATTAAACTCAGAAGG+AGG - chr2.3:20849322-20849341 None:intergenic 30.0%
TCACATGAATGTTCATAGAA+GGG + chr2.3:20849081-20849100 MS.gene060207:CDS 30.0%
TCAGAAGATTACATGATGAA+TGG + chr2.3:20848980-20848999 MS.gene060207:CDS 30.0%
!! ACTTTGAGAATGACTTTTGT+TGG - chr2.3:20848936-20848955 None:intergenic 30.0%
!! GAAAAGTGAGATTTTAAGGA+TGG + chr2.3:20849447-20849466 MS.gene060207:CDS 30.0%
!! TGAGATTTTAAGGATGGATT+TGG + chr2.3:20849453-20849472 MS.gene060207:CDS 30.0%
AAGCTACATGTGTATGATCT+TGG - chr2.3:20849022-20849041 None:intergenic 35.0%
AAGGGTAATGTGCAAGTAAT+AGG - chr2.3:20849289-20849308 None:intergenic 35.0%
ATGTGAAGATGATTGTAGCA+TGG + chr2.3:20849420-20849439 MS.gene060207:CDS 35.0%
CATGAACCTCAAATTGATCA+AGG + chr2.3:20849142-20849161 MS.gene060207:CDS 35.0%
GAAGAACCTTGATCAATTTG+AGG - chr2.3:20849151-20849170 None:intergenic 35.0%
GTCACATGAATGTTCATAGA+AGG + chr2.3:20849080-20849099 MS.gene060207:CDS 35.0%
TCAGAGAAATCAAAGATGGA+TGG + chr2.3:20849391-20849410 MS.gene060207:CDS 35.0%
TGATGAATGGTTGTTATCCA+TGG + chr2.3:20848993-20849012 MS.gene060207:CDS 35.0%
TTTAAATCAGCTCAAGCACT+TGG + chr2.3:20849055-20849074 MS.gene060207:CDS 35.0%
! ATCCATCTTTGATTTCTCTG+AGG - chr2.3:20849392-20849411 None:intergenic 35.0%
! TAGGGTTAGTAGTGATAGTA+GGG - chr2.3:20849198-20849217 None:intergenic 35.0%
! TCAATTTGAGGTTCATGAGT+TGG - chr2.3:20849139-20849158 None:intergenic 35.0%
! TTAAGGATGGATTTGGAGAT+AGG + chr2.3:20849460-20849479 MS.gene060207:CDS 35.0%
! TTAGGGTTAGTAGTGATAGT+AGG - chr2.3:20849199-20849218 None:intergenic 35.0%
!!! TGACTTTTGTTGGTGATGAT+TGG - chr2.3:20848926-20848945 None:intergenic 35.0%
AGAAGGAGGTGAAACAAACA+AGG - chr2.3:20849308-20849327 None:intergenic 40.0%
AGGTCTTTGTGCTCAAAGTA+GGG - chr2.3:20849372-20849391 None:intergenic 40.0%
CTACATGTGTATGATCTTGG+TGG - chr2.3:20849019-20849038 None:intergenic 40.0%
GAAGGAGGTGAAACAAACAA+GGG - chr2.3:20849307-20849326 None:intergenic 40.0%
GACCTCAGAGAAATCAAAGA+TGG + chr2.3:20849387-20849406 MS.gene060207:CDS 40.0%
TCCAAGTTGTCATAATCTCC+TGG - chr2.3:20849490-20849509 None:intergenic 40.0%
TTCATAGAAGGGATAGAGCA+AGG + chr2.3:20849092-20849111 MS.gene060207:CDS 40.0%
TTGGATCTTGAGCTTCGTTT+GGG + chr2.3:20849505-20849524 MS.gene060207:CDS 40.0%
! ATTTGAGGTTCATGAGTTGG+TGG - chr2.3:20849136-20849155 None:intergenic 40.0%
AAATCAGCTCAAGCACTTGG+AGG + chr2.3:20849058-20849077 MS.gene060207:CDS 45.0%
CTTGAGAGTTGTTGCTGAAG+AGG - chr2.3:20849266-20849285 None:intergenic 45.0%
CTTGGATCTTGAGCTTCGTT+TGG + chr2.3:20849504-20849523 MS.gene060207:CDS 45.0%
GAGGTCTTTGTGCTCAAAGT+AGG - chr2.3:20849373-20849392 None:intergenic 45.0%
GATTTGGAGATAGGATTGCC+AGG + chr2.3:20849469-20849488 MS.gene060207:CDS 45.0%
GCCAGGAGATTATGACAACT+TGG + chr2.3:20849486-20849505 MS.gene060207:CDS 45.0%
! GTGTATGATCTTGGTGGCCA+TGG - chr2.3:20849013-20849032 None:intergenic 50.0%
!! TGAGGTTCATGAGTTGGTGG+TGG - chr2.3:20849133-20849152 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 20848860 20849549 20848860 ID=MS.gene060207
chr2.3 mRNA 20848860 20849549 20848860 ID=MS.gene060207.t1;Parent=MS.gene060207
chr2.3 exon 20848860 20849549 20848860 ID=MS.gene060207.t1.exon1;Parent=MS.gene060207.t1
chr2.3 CDS 20848860 20849549 20848860 ID=cds.MS.gene060207.t1;Parent=MS.gene060207.t1
Gene Sequence

>MS.gene060207

ATGATGAAGAGGAACAATATGAACACAAGCTTGAAAGGCTATAATCACACTTATTACAACAGTCCAATCATCACCAACAAAAGTCATTCTCAAAGTGATTATAATAATAATGGATCATCATCAGAAGATTACATGATGAATGGTTGTTATCCATGGCCACCAAGATCATACACATGTAGCTTTTGCAGAAAAGAGTTTAAATCAGCTCAAGCACTTGGAGGTCACATGAATGTTCATAGAAGGGATAGAGCAAGGCTTAGACAATCATCACCACCACCAACTCATGAACCTCAAATTGATCAAGGTTCTTCTATGCTTAATCTTAATCTTAATAACCCTACTATCACTACTAACCCTAATTTATTCTCACATTCATCTTCATCTTCTTCATCATTATCATCAACCTCTTCAGCAACAACTCTCAAGCCTATTACTTGCACATTACCCTTGTTTGTTTCACCTCCTTCTGAGTTTAATAGATATGTTGTTGTGGATGGTATTTTGTTGAACCCTACTTTGAGCACAAAGACCTCAGAGAAATCAAAGATGGATGGTTTTGAATGTGAAGATGATTGTAGCATGGTGAAGAAAAGTGAGATTTTAAGGATGGATTTGGAGATAGGATTGCCAGGAGATTATGACAACTTGGATCTTGAGCTTCGTTTGGGTACTACTACTTACTCTAATTAG
Protein sequence

>MS.gene060207.t1

MMKRNNMNTSLKGYNHTYYNSPIITNKSHSQSDYNNNGSSSEDYMMNGCYPWPPRSYTCSFCRKEFKSAQALGGHMNVHRRDRARLRQSSPPPTHEPQIDQGSSMLNLNLNNPTITTNPNLFSHSSSSSSSLSSTSSATTLKPITCTLPLFVSPPSEFNRYVVVDGILLNPTLSTKTSEKSKMDGFECEDDCSMVKKSEILRMDLEIGLPGDYDNLDLELRLGTTTYSN