AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene74252

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene74252.t1 MTR_1g116940 95.633 229 10 0 1 229 30 258 1.90e-149 416
MS.gene74252.t1 MTR_1g053960 55.556 234 92 6 1 229 1 227 6.92e-79 236
MS.gene74252.t1 MTR_1g053960 55.556 234 92 6 1 229 67 293 5.22e-78 236
MS.gene74252.t1 MTR_7g093130 55.230 239 86 8 1 226 1 231 6.21e-78 234
MS.gene74252.t1 MTR_7g093130 55.230 239 86 8 1 226 71 301 7.81e-77 234
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene74252.t1 AT3G12130 43.981 216 98 5 32 229 37 247 9.83e-49 160
MS.gene74252.t1 AT5G06770 43.750 208 102 5 32 229 15 217 2.51e-48 158
MS.gene74252.t1 AT5G06770 43.750 208 102 5 32 229 37 239 5.85e-48 158
MS.gene74252.t1 AT5G06770 43.500 200 98 5 40 229 18 212 4.75e-45 150
MS.gene74252.t1 AT5G06770 43.500 200 98 5 40 229 18 212 4.75e-45 150
MS.gene74252.t1 AT5G06770 43.500 200 98 5 40 229 18 212 4.75e-45 150
MS.gene74252.t1 AT3G12130 51.634 153 63 2 85 229 26 175 2.88e-44 146
MS.gene74252.t1 AT5G06770 51.449 138 66 1 92 229 31 167 9.69e-44 145

Find 77 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGGAGCTGCTGCCGGTTT+TGG 0.155815 1.1:-82195798 MS.gene74252:CDS
ACAGCTGAAGGTCGCAAATT+TGG 0.185089 1.1:-82195954 MS.gene74252:CDS
ACCAAAGGATCCTGCACTTT+TGG 0.214083 1.1:-82195465 MS.gene74252:CDS
CAGCTGAAGGTCGCAAATTT+GGG 0.254177 1.1:-82195953 MS.gene74252:CDS
TTGGTCTTGAAGTTGTTTGC+AGG 0.265962 1.1:+82195504 None:intergenic
CTTCAAGCTCAATATTTCTA+AGG 0.277040 1.1:+82195637 None:intergenic
TAAAATTTCTATCACATTCC+AGG 0.312719 1.1:+82195399 None:intergenic
CAGGTGCTAAACTTTCCATT+AGG 0.322304 1.1:-82195680 MS.gene74252:CDS
GGGAAGGATGGTGGAACATT+TGG 0.327695 1.1:+82196029 None:intergenic
TATTGAACTTGTTGCACAAC+CGG 0.331191 1.1:+82195976 None:intergenic
GCAGCTCCATGAGCTGGAGG+TGG 0.349271 1.1:+82195810 None:intergenic
CCCAAAAGTGCAGGATCCTT+TGG 0.352380 1.1:+82195464 None:intergenic
GCTCCATGAGCTGGAGGTGG+GGG 0.369225 1.1:+82195813 None:intergenic
CTTAGAAATATTGAGCTTGA+AGG 0.380840 1.1:-82195636 MS.gene74252:CDS
AGCTCCATGAGCTGGAGGTG+GGG 0.391671 1.1:+82195812 None:intergenic
CCGAACTCACATTTAGAATA+AGG 0.392968 1.1:+82195571 None:intergenic
AAGCAAATCTATCACATAAC+AGG 0.395520 1.1:-82195699 MS.gene74252:CDS
AGGTGCTAAACTTTCCATTA+GGG 0.399844 1.1:-82195679 MS.gene74252:CDS
ACATTTGGATTTCTACCAAT+TGG 0.402070 1.1:+82196044 None:intergenic
ATGGTGAGTGGGAGCGTGGC+AGG 0.408893 1.1:-82195911 MS.gene74252:CDS
ATCTGAGTCATGTTCCCTAA+TGG 0.413569 1.1:+82195665 None:intergenic
CTAAATGTGAGTTCGGTCTC+TGG 0.419817 1.1:-82195564 MS.gene74252:CDS
CAGCTCCATGAGCTGGAGGT+GGG 0.423034 1.1:+82195811 None:intergenic
CACAACCGGGTCTTAGCAAC+TGG 0.431622 1.1:+82195990 None:intergenic
GCTGCTTTGCATTTGTCCCA+TGG 0.442232 1.1:+82195857 None:intergenic
ATGCAAAGCAGCAGTGTTGA+TGG 0.443234 1.1:-82195846 MS.gene74252:CDS
CTACCAATTGGTGGAATAGC+AGG 0.443500 1.1:+82196056 None:intergenic
CCAGCTCATGGAGCTGCTGC+CGG 0.447956 1.1:-82195804 MS.gene74252:CDS
CCGGCAGCAGCTCCATGAGC+TGG 0.455038 1.1:+82195804 None:intergenic
CCTTATTCTAAATGTGAGTT+CGG 0.456926 1.1:-82195571 MS.gene74252:CDS
AGCTCAATATTTCTAAGGTT+AGG 0.469832 1.1:+82195642 None:intergenic
AGTGGCCGACACTCCAAAAC+CGG 0.472552 1.1:+82195785 None:intergenic
AGTCCTGCTATTCCACCAAT+TGG 0.476108 1.1:-82196059 MS.gene74252:CDS
AGTTCGGTCTCTGGACCTCC+AGG 0.487466 1.1:-82195555 MS.gene74252:CDS
TGGTCTTGAAGTTGTTTGCA+GGG 0.488541 1.1:+82195505 None:intergenic
AAGGTCATGGACCATGGCAC+TGG 0.492421 1.1:+82195590 None:intergenic
GCGCGAGTATCTTCATATGC+AGG 0.492758 1.1:+82195879 None:intergenic
ACCCTTGCTAGAGCTATCAT+TGG 0.494785 1.1:-82195741 MS.gene74252:CDS
ACTGGTGGAGAAGAACCGTC+TGG 0.507265 1.1:+82196008 None:intergenic
CTCCACCAGTTGCTAAGACC+CGG 0.514232 1.1:-82195995 MS.gene74252:CDS
TTTGGATTTCTACCAATTGG+TGG 0.514454 1.1:+82196047 None:intergenic
ACAGATGAATTATGCAAGCC+TGG 0.520202 1.1:-82195417 MS.gene74252:CDS
GCCACGCTCCCACTCACCAT+GGG 0.523824 1.1:+82195914 None:intergenic
TTCCAATGATAGCTCTAGCA+AGG 0.524282 1.1:+82195739 None:intergenic
GCACCTTTCCCCAAAAGTGC+AGG 0.529864 1.1:+82195455 None:intergenic
GAAAGGTGCCACTTCGCGCA+TGG 0.536523 1.1:-82195441 MS.gene74252:CDS
TGCCACGCTCCCACTCACCA+TGG 0.538201 1.1:+82195913 None:intergenic
GTGGGAGCGTGGCAGGCCCA+CGG 0.551387 1.1:-82195904 MS.gene74252:CDS
ATTGAACTTGTTGCACAACC+GGG 0.554392 1.1:+82195977 None:intergenic
TGTTATGTGATAGATTTGCT+TGG 0.557591 1.1:+82195701 None:intergenic
TATGAAGATACTCGCGCCAT+GGG 0.559467 1.1:-82195873 MS.gene74252:CDS
TGCAAAGCAGCAGTGTTGAT+GGG 0.562545 1.1:-82195845 MS.gene74252:CDS
CATCTGTTCCATGCGCGAAG+TGG 0.569090 1.1:+82195433 None:intergenic
CGCGAGTATCTTCATATGCA+GGG 0.573206 1.1:+82195880 None:intergenic
GAAGAACCGTCTGGGAAGGA+TGG 0.574755 1.1:+82196017 None:intergenic
ATATGAAGATACTCGCGCCA+TGG 0.580726 1.1:-82195874 MS.gene74252:CDS
TCTTCATATGCAGGGACCGT+GGG 0.587144 1.1:+82195888 None:intergenic
GAACCGTCTGGGAAGGATGG+TGG 0.589119 1.1:+82196020 None:intergenic
GTCACTTTGCCCATGGTGAG+TGG 0.600587 1.1:-82195923 MS.gene74252:CDS
GCCCATGGTGAGTGGGAGCG+TGG 0.601228 1.1:-82195915 MS.gene74252:CDS
TAGAATAAGGTCATGGACCA+TGG 0.602580 1.1:+82195584 None:intergenic
TCCAATGATAGCTCTAGCAA+GGG 0.603096 1.1:+82195740 None:intergenic
TGGAGAAGAACCGTCTGGGA+AGG 0.604602 1.1:+82196013 None:intergenic
AACAAGTTCAATACAGCTGA+AGG 0.604829 1.1:-82195966 MS.gene74252:CDS
GTCTCTCAGATGATCAATGT+CGG 0.614302 1.1:-82196086 None:intergenic
AACCGGGTCTTAGCAACTGG+TGG 0.615487 1.1:+82195993 None:intergenic
CTGTGTGAAAACTTTACCAA+AGG 0.618887 1.1:-82195480 MS.gene74252:CDS
GGTCTTGAAGTTGTTTGCAG+GGG 0.621193 1.1:+82195506 None:intergenic
TCACTTTGCCCATGGTGAGT+GGG 0.626927 1.1:-82195922 MS.gene74252:CDS
TCACATTTAGAATAAGGTCA+TGG 0.629476 1.1:+82195577 None:intergenic
CTGGTGGAGAAGAACCGTCT+GGG 0.629582 1.1:+82196009 None:intergenic
GATCAAACAAGCCAGTGCCA+TGG 0.633360 1.1:-82195601 MS.gene74252:CDS
ATCTTCATATGCAGGGACCG+TGG 0.634772 1.1:+82195887 None:intergenic
GTTCCACCATCCTTCCCAGA+CGG 0.641586 1.1:-82196023 MS.gene74252:CDS
GCAGCAGCTCCATGAGCTGG+AGG 0.660051 1.1:+82195807 None:intergenic
AGCTGAAGGTCGCAAATTTG+GGG 0.668544 1.1:-82195952 MS.gene74252:CDS
GATAAATGTCACTTTGCCCA+TGG 0.676321 1.1:-82195930 MS.gene74252:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTAATATTAACTTTTGCAG+TGG + chr1.1:82195723-82195742 None:intergenic 20.0%
AAGCAAATCTATCACATAAC+AGG - chr1.1:82195788-82195807 MS.gene74252:CDS 30.0%
ACATTTGGATTTCTACCAAT+TGG + chr1.1:82195446-82195465 None:intergenic 30.0%
AGAGCTATCATTGGAAAAAA+TGG - chr1.1:82195755-82195774 MS.gene74252:CDS 30.0%
CCTTATTCTAAATGTGAGTT+CGG - chr1.1:82195916-82195935 MS.gene74252:CDS 30.0%
CTTAGAAATATTGAGCTTGA+AGG - chr1.1:82195851-82195870 MS.gene74252:CDS 30.0%
! CTTCAAGCTCAATATTTCTA+AGG + chr1.1:82195853-82195872 None:intergenic 30.0%
! TCACATTTAGAATAAGGTCA+TGG + chr1.1:82195913-82195932 None:intergenic 30.0%
! TGTTATGTGATAGATTTGCT+TGG + chr1.1:82195789-82195808 None:intergenic 30.0%
!! AGCTCAATATTTCTAAGGTT+AGG + chr1.1:82195848-82195867 None:intergenic 30.0%
!!! TGTGAAGTAATGTTTTTTCC+TGG + chr1.1:82195953-82195972 None:intergenic 30.0%
AACAAGTTCAATACAGCTGA+AGG - chr1.1:82195521-82195540 MS.gene74252:CDS 35.0%
AGGTGCTAAACTTTCCATTA+GGG - chr1.1:82195808-82195827 MS.gene74252:CDS 35.0%
CTGTGTGAAAACTTTACCAA+AGG - chr1.1:82196007-82196026 MS.gene74252:CDS 35.0%
TTTGGATTTCTACCAATTGG+TGG + chr1.1:82195443-82195462 None:intergenic 35.0%
! CCGAACTCACATTTAGAATA+AGG + chr1.1:82195919-82195938 None:intergenic 35.0%
!! TATTGAACTTGTTGCACAAC+CGG + chr1.1:82195514-82195533 None:intergenic 35.0%
!!! GAAGTAATGTTTTTTCCTGG+AGG + chr1.1:82195950-82195969 None:intergenic 35.0%
ACAGATGAATTATGCAAGCC+TGG - chr1.1:82196070-82196089 MS.gene74252:CDS 40.0%
ATCTGAGTCATGTTCCCTAA+TGG + chr1.1:82195825-82195844 None:intergenic 40.0%
CAGGTGCTAAACTTTCCATT+AGG - chr1.1:82195807-82195826 MS.gene74252:CDS 40.0%
TAGAATAAGGTCATGGACCA+TGG + chr1.1:82195906-82195925 None:intergenic 40.0%
! GGTAAAGTTTTCACACAGCT+TGG + chr1.1:82196005-82196024 None:intergenic 40.0%
! TGGTCTTGAAGTTGTTTGCA+GGG + chr1.1:82195985-82196004 None:intergenic 40.0%
!! ATTGAACTTGTTGCACAACC+GGG + chr1.1:82195513-82195532 None:intergenic 40.0%
!! GATAAATGTCACTTTGCCCA+TGG - chr1.1:82195557-82195576 MS.gene74252:CDS 40.0%
!! TCCAATGATAGCTCTAGCAA+GGG + chr1.1:82195750-82195769 None:intergenic 40.0%
!! TTCCAATGATAGCTCTAGCA+AGG + chr1.1:82195751-82195770 None:intergenic 40.0%
!! TTGGTCTTGAAGTTGTTTGC+AGG + chr1.1:82195986-82196005 None:intergenic 40.0%
ACAGCTGAAGGTCGCAAATT+TGG - chr1.1:82195533-82195552 MS.gene74252:CDS 45.0%
ACCCTTGCTAGAGCTATCAT+TGG - chr1.1:82195746-82195765 MS.gene74252:CDS 45.0%
AGCTGAAGGTCGCAAATTTG+GGG - chr1.1:82195535-82195554 MS.gene74252:CDS 45.0%
AGTCCTGCTATTCCACCAAT+TGG - chr1.1:82195428-82195447 MS.gene74252:CDS 45.0%
ATATGAAGATACTCGCGCCA+TGG - chr1.1:82195613-82195632 MS.gene74252:CDS 45.0%
CAGCTGAAGGTCGCAAATTT+GGG - chr1.1:82195534-82195553 MS.gene74252:CDS 45.0%
CGCGAGTATCTTCATATGCA+GGG + chr1.1:82195610-82195629 None:intergenic 45.0%
CTAAATGTGAGTTCGGTCTC+TGG - chr1.1:82195923-82195942 MS.gene74252:CDS 45.0%
CTACCAATTGGTGGAATAGC+AGG + chr1.1:82195434-82195453 None:intergenic 45.0%
GGTCTTGAAGTTGTTTGCAG+GGG + chr1.1:82195984-82196003 None:intergenic 45.0%
TATGAAGATACTCGCGCCAT+GGG - chr1.1:82195614-82195633 MS.gene74252:CDS 45.0%
! ACCAAAGGATCCTGCACTTT+TGG - chr1.1:82196022-82196041 MS.gene74252:CDS 45.0%
! ATGCAAAGCAGCAGTGTTGA+TGG - chr1.1:82195641-82195660 MS.gene74252:CDS 45.0%
! CAAAGGATCCTGCACTTTTG+GGG - chr1.1:82196024-82196043 MS.gene74252:CDS 45.0%
! CCAAAGGATCCTGCACTTTT+GGG - chr1.1:82196023-82196042 MS.gene74252:CDS 45.0%
!! TGCAAAGCAGCAGTGTTGAT+GGG - chr1.1:82195642-82195661 MS.gene74252:CDS 45.0%
ATCTTCATATGCAGGGACCG+TGG + chr1.1:82195603-82195622 None:intergenic 50.0%
GATCAAACAAGCCAGTGCCA+TGG - chr1.1:82195886-82195905 MS.gene74252:CDS 50.0%
GCGCGAGTATCTTCATATGC+AGG + chr1.1:82195611-82195630 None:intergenic 50.0%
TCACTTTGCCCATGGTGAGT+GGG - chr1.1:82195565-82195584 MS.gene74252:CDS 50.0%
TCTTCATATGCAGGGACCGT+GGG + chr1.1:82195602-82195621 None:intergenic 50.0%
! CCCAAAAGTGCAGGATCCTT+TGG + chr1.1:82196026-82196045 None:intergenic 50.0%
! GCTGCTTTGCATTTGTCCCA+TGG + chr1.1:82195633-82195652 None:intergenic 50.0%
!! GATCCTGCACTTTTGGGGAA+AGG - chr1.1:82196029-82196048 MS.gene74252:CDS 50.0%
!! GGGAAGGATGGTGGAACATT+TGG + chr1.1:82195461-82195480 None:intergenic 50.0%
AACCGGGTCTTAGCAACTGG+TGG + chr1.1:82195497-82195516 None:intergenic 55.0%
AAGGTCATGGACCATGGCAC+TGG + chr1.1:82195900-82195919 None:intergenic 55.0%
ACTGGTGGAGAAGAACCGTC+TGG + chr1.1:82195482-82195501 None:intergenic 55.0%
AGTGGCCGACACTCCAAAAC+CGG + chr1.1:82195705-82195724 None:intergenic 55.0%
CACAACCGGGTCTTAGCAAC+TGG + chr1.1:82195500-82195519 None:intergenic 55.0%
CATCTGTTCCATGCGCGAAG+TGG + chr1.1:82196057-82196076 None:intergenic 55.0%
CTCCACCAGTTGCTAAGACC+CGG - chr1.1:82195492-82195511 MS.gene74252:CDS 55.0%
CTGGTGGAGAAGAACCGTCT+GGG + chr1.1:82195481-82195500 None:intergenic 55.0%
GAAGAACCGTCTGGGAAGGA+TGG + chr1.1:82195473-82195492 None:intergenic 55.0%
GTTCCACCATCCTTCCCAGA+CGG - chr1.1:82195464-82195483 MS.gene74252:CDS 55.0%
TGGAGAAGAACCGTCTGGGA+AGG + chr1.1:82195477-82195496 None:intergenic 55.0%
! GCACCTTTCCCCAAAAGTGC+AGG + chr1.1:82196035-82196054 None:intergenic 55.0%
! GTCACTTTGCCCATGGTGAG+TGG - chr1.1:82195564-82195583 MS.gene74252:CDS 55.0%
!!! TGCTGCCGGTTTTGGAGTGT+CGG - chr1.1:82195697-82195716 MS.gene74252:CDS 55.0%
AGCTCCATGAGCTGGAGGTG+GGG + chr1.1:82195678-82195697 None:intergenic 60.0%
AGTTCGGTCTCTGGACCTCC+AGG - chr1.1:82195932-82195951 MS.gene74252:CDS 60.0%
CAGCTCCATGAGCTGGAGGT+GGG + chr1.1:82195679-82195698 None:intergenic 60.0%
GAACCGTCTGGGAAGGATGG+TGG + chr1.1:82195470-82195489 None:intergenic 60.0%
!! GAAAGGTGCCACTTCGCGCA+TGG - chr1.1:82196046-82196065 MS.gene74252:CDS 60.0%
!!! CATGGAGCTGCTGCCGGTTT+TGG - chr1.1:82195689-82195708 MS.gene74252:CDS 60.0%
CCAGCTCATGGAGCTGCTGC+CGG - chr1.1:82195683-82195702 MS.gene74252:CDS 65.0%
GCAGCAGCTCCATGAGCTGG+AGG + chr1.1:82195683-82195702 None:intergenic 65.0%
GCAGCTCCATGAGCTGGAGG+TGG + chr1.1:82195680-82195699 None:intergenic 65.0%
GCCACGCTCCCACTCACCAT+GGG + chr1.1:82195576-82195595 None:intergenic 65.0%
GCTCCATGAGCTGGAGGTGG+GGG + chr1.1:82195677-82195696 None:intergenic 65.0%
TGCCACGCTCCCACTCACCA+TGG + chr1.1:82195577-82195596 None:intergenic 65.0%
! ATGGTGAGTGGGAGCGTGGC+AGG - chr1.1:82195576-82195595 MS.gene74252:CDS 65.0%
CCGGCAGCAGCTCCATGAGC+TGG + chr1.1:82195686-82195705 None:intergenic 70.0%
GAGCCCCCACCTCCAGCTCA+TGG - chr1.1:82195671-82195690 MS.gene74252:CDS 70.0%
GCCCATGGTGAGTGGGAGCG+TGG - chr1.1:82195572-82195591 MS.gene74252:CDS 70.0%
! GTGGGAGCGTGGCAGGCCCA+CGG - chr1.1:82195583-82195602 MS.gene74252:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 82195410 82196099 82195410 ID=MS.gene74252
chr1.1 mRNA 82195410 82196099 82195410 ID=MS.gene74252.t1;Parent=MS.gene74252
chr1.1 exon 82195410 82196099 82195410 ID=MS.gene74252.t1.exon1;Parent=MS.gene74252.t1
chr1.1 CDS 82195410 82196099 82195410 ID=cds.MS.gene74252.t1;Parent=MS.gene74252.t1
Gene Sequence

>MS.gene74252

ATGATCAATGTCGGTAGCAGTCCTGCTATTCCACCAATTGGTAGAAATCCAAATGTTCCACCATCCTTCCCAGACGGTTCTTCTCCACCAGTTGCTAAGACCCGGTTGTGCAACAAGTTCAATACAGCTGAAGGTCGCAAATTTGGGGATAAATGTCACTTTGCCCATGGTGAGTGGGAGCGTGGCAGGCCCACGGTCCCTGCATATGAAGATACTCGCGCCATGGGACAAATGCAAAGCAGCAGTGTTGATGGGAGAATTGAGCCCCCACCTCCAGCTCATGGAGCTGCTGCCGGTTTTGGAGTGTCGGCCACTGCAAAAGTTAATATTAATGCTACCCTTGCTAGAGCTATCATTGGAAAAAATGGTGTTAACTCCAAGCAAATCTATCACATAACAGGTGCTAAACTTTCCATTAGGGAACATGACTCAGATCCTAACCTTAGAAATATTGAGCTTGAAGGCAGTTTTGATCAGATCAAACAAGCCAGTGCCATGGTCCATGACCTTATTCTAAATGTGAGTTCGGTCTCTGGACCTCCAGGAAAAAACATTACTTCACAGACTTCTGCCCCTGCAAACAACTTCAAGACCAAGCTGTGTGAAAACTTTACCAAAGGATCCTGCACTTTTGGGGAAAGGTGCCACTTCGCGCATGGAACAGATGAATTATGCAAGCCTGGAATGTGA
Protein sequence

>MS.gene74252.t1

MINVGSSPAIPPIGRNPNVPPSFPDGSSPPVAKTRLCNKFNTAEGRKFGDKCHFAHGEWERGRPTVPAYEDTRAMGQMQSSSVDGRIEPPPPAHGAAAGFGVSATAKVNINATLARAIIGKNGVNSKQIYHITGAKLSIREHDSDPNLRNIELEGSFDQIKQASAMVHDLILNVSSVSGPPGKNITSQTSAPANNFKTKLCENFTKGSCTFGERCHFAHGTDELCKPGM