AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09982


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09982.t1 MTR_7g062720 40.541 148 80 3 1 146 1 142 5.14e-31 115
MS.gene09982.t1 MTR_4g037355 40.441 136 61 4 155 290 1 116 1.16e-21 89.7
MS.gene09982.t1 MTR_5g061150 35.354 99 64 0 52 150 38 136 4.20e-18 80.1
MS.gene09982.t1 MTR_4g112730 57.971 69 28 1 143 211 2 69 7.91e-18 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 61 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGATCAATGGAACAAATTA+AGG 0.196151 1.4:+72185229 MS.gene09982:CDS
AGTCTTATTGCCCTCATTAA+TGG 0.201947 1.4:+72185209 MS.gene09982:CDS
AAAGTTGTGGCGTTTATTTC+AGG 0.203868 1.4:-72185525 None:intergenic
CAAAAGATCCCAAGATCTTA+TGG 0.237847 1.4:+72185151 MS.gene09982:CDS
GATTCTTGAGGGAGAAGATT+TGG 0.253340 1.4:+72185032 MS.gene09982:CDS
GACAAAATTAAGGCAAGATT+TGG 0.257188 1.4:+72185174 MS.gene09982:CDS
CTCAATTAAGTTGTTGTTCC+AGG 0.274617 1.4:-72184983 None:intergenic
CACGACCTCCACCACGAAAA+TGG 0.277262 1.4:-72185641 None:intergenic
GATCTTATGGGACAAAATTA+AGG 0.310971 1.4:+72185164 MS.gene09982:CDS
ATTTACTGAATACTCTGATT+TGG 0.313227 1.4:+72185419 MS.gene09982:CDS
ATTCTTGAGGGAGAAGATTT+GGG 0.333151 1.4:+72185033 MS.gene09982:CDS
AGACAGGTAGTGTCATTCTT+TGG 0.342502 1.4:-72185897 None:intergenic
GGGAGATGTCCCAGAGGAAT+TGG 0.345733 1.4:+72185053 MS.gene09982:CDS
GAAGAGGTTATATGAATTAC+AGG 0.363099 1.4:+72185664 MS.gene09982:CDS
GATTTCTAGAGGGACCTTCC+TGG 0.373636 1.4:-72185740 None:intergenic
CATAGCCACCACGTCCTCTT+TGG 0.374275 1.4:-72185575 None:intergenic
CGTGGTGGCTATGCTCGTTT+TGG 0.395091 1.4:+72185585 MS.gene09982:CDS
ACAAAATTAAGGCAAGATTT+GGG 0.416566 1.4:+72185175 MS.gene09982:CDS
TATAACTGAAAAGGAAAAGT+TGG 0.422757 1.4:+72185332 MS.gene09982:CDS
TGCCCTCATTAATGGATCAA+TGG 0.432677 1.4:+72185217 MS.gene09982:CDS
CGTGGTGGAGGTCGTGGAAG+AGG 0.449888 1.4:+72185648 MS.gene09982:CDS
TCCTGCATGCTTTAGCCCAA+TGG 0.457473 1.4:-72185797 None:intergenic
AAAAGATCCCAAGATCTTAT+GGG 0.458748 1.4:+72185152 MS.gene09982:CDS
AACCATCAGTTGCGTCCTAC+AGG 0.459311 1.4:+72185489 MS.gene09982:CDS
TGGCAAAACTATAACTGAAA+AGG 0.467052 1.4:+72185323 MS.gene09982:CDS
ATCTGTGGATGGAAAGGAAA+GGG 0.491819 1.4:+72185851 MS.gene09982:CDS
ATCAAGCACCACATTGATGA+TGG 0.492315 1.4:+72185105 MS.gene09982:CDS
TGTTATAGATGCGGAAAGAA+AGG 0.495634 1.4:+72185774 MS.gene09982:CDS
CTGGCGACAACTACATAACC+TGG 0.502097 1.4:+72184965 MS.gene09982:CDS
GTTCCATTGATCCATTAATG+AGG 0.509644 1.4:-72185220 None:intergenic
ATGCGGAAAGAAAGGCCATT+GGG 0.516896 1.4:+72185782 MS.gene09982:CDS
TTTGATTGGTCATATTTGAG+AGG 0.522357 1.4:-72185687 None:intergenic
CAAAGAATCTGTGGATGGAA+AGG 0.532926 1.4:+72185845 MS.gene09982:CDS
TTCCATTGATCCATTAATGA+GGG 0.533283 1.4:-72185219 None:intergenic
CGTGGACGAGGTAGAAATCA+TGG 0.535808 1.4:+72185612 MS.gene09982:CDS
GGACTCGATAAGATTCTTGA+GGG 0.539399 1.4:+72185021 MS.gene09982:CDS
GCCATTGGGCTAAAGCATGC+AGG 0.539769 1.4:+72185796 MS.gene09982:CDS
CCCTCTAGAAATCATGATGA+TGG 0.541875 1.4:+72185750 MS.gene09982:CDS
TTCCTGTAGGACGCAACTGA+TGG 0.562606 1.4:-72185491 None:intergenic
AAAATCAGCAGCCTCAAGAC+AGG 0.562896 1.4:-72185913 None:intergenic
AATTGAGTATCTTGCATGTG+AGG 0.565013 1.4:+72184999 MS.gene09982:CDS
ATTGAGTATCTTGCATGTGA+GGG 0.575966 1.4:+72185000 MS.gene09982:CDS
TTTGGTTGCAGCCCTTCTAG+TGG 0.582793 1.4:+72185437 MS.gene09982:CDS
GATGCGGAAAGAAAGGCCAT+TGG 0.583841 1.4:+72185781 MS.gene09982:CDS
TTGTGCAATAATTTGATGCA+TGG 0.588693 1.4:-72185289 None:intergenic
TAAAAGATACAAAGAATCTG+TGG 0.594054 1.4:+72185836 MS.gene09982:CDS
AGATACAAAGAATCTGTGGA+TGG 0.602731 1.4:+72185840 MS.gene09982:CDS
GGGACTCGATAAGATTCTTG+AGG 0.606176 1.4:+72185020 MS.gene09982:CDS
ACGCCCTTGATTAAAAGTTG+TGG 0.608515 1.4:-72185538 None:intergenic
GCAATATCACTTGAGATGCA+TGG 0.608661 1.4:-72185374 None:intergenic
TATAATCGCCAAAGAGGACG+TGG 0.608957 1.4:+72185567 MS.gene09982:CDS
ACCATCATCATGATTTCTAG+AGG 0.616492 1.4:-72185751 None:intergenic
GGATACGACATTGTTCCTGT+AGG 0.627452 1.4:-72185504 None:intergenic
GGTGGTTATAATCGCCAAAG+AGG 0.642086 1.4:+72185561 MS.gene09982:CDS
CCATCATCATGATTTCTAGA+GGG 0.647682 1.4:-72185750 None:intergenic
GAATGACACTACCTGTCTTG+AGG 0.649563 1.4:+72185902 MS.gene09982:CDS
AATCTGTGGATGGAAAGGAA+AGG 0.653361 1.4:+72185850 MS.gene09982:CDS
GATGATGGTTGTTATAGATG+CGG 0.696569 1.4:+72185765 MS.gene09982:CDS
AATCGCCAAAGAGGACGTGG+TGG 0.698905 1.4:+72185570 MS.gene09982:CDS
TTTGTAATCCATCATCAATG+TGG 0.715751 1.4:-72185113 None:intergenic
AGATTTGGGAGATGTCCCAG+AGG 0.741186 1.4:+72185047 MS.gene09982:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCAAAATTTTAAGCATAAC+TGG + chr1.4:72184946-72184965 MS.gene09982:CDS 20.0%
! ACAAAATTAAGGCAAGATTT+GGG + chr1.4:72185175-72185194 MS.gene09982:CDS 25.0%
! ATTTACTGAATACTCTGATT+TGG + chr1.4:72185419-72185438 MS.gene09982:CDS 25.0%
! CAATCAAACAAAAATCATCA+GGG + chr1.4:72185702-72185721 MS.gene09982:CDS 25.0%
! TAAAAGATACAAAGAATCTG+TGG + chr1.4:72185836-72185855 MS.gene09982:CDS 25.0%
! TATAACTGAAAAGGAAAAGT+TGG + chr1.4:72185332-72185351 MS.gene09982:CDS 25.0%
!! ATTGCACAATTAGAATTTTG+TGG + chr1.4:72185303-72185322 MS.gene09982:CDS 25.0%
!! TATCTTTTACATAGATACTC+TGG - chr1.4:72185825-72185844 None:intergenic 25.0%
!!! CAACAACAGTTTTATAATCT+TGG - chr1.4:72185257-72185276 None:intergenic 25.0%
!!! TGTTGAAGGAGATTTTAATA+TGG + chr1.4:72185935-72185954 MS.gene09982:CDS 25.0%
AAAAGATCCCAAGATCTTAT+GGG + chr1.4:72185152-72185171 MS.gene09982:CDS 30.0%
AACAAAAATCATCAGGGTAA+AGG + chr1.4:72185708-72185727 MS.gene09982:CDS 30.0%
CCAATCAAACAAAAATCATC+AGG + chr1.4:72185701-72185720 MS.gene09982:CDS 30.0%
GAAGAGGTTATATGAATTAC+AGG + chr1.4:72185664-72185683 MS.gene09982:CDS 30.0%
GACAAAATTAAGGCAAGATT+TGG + chr1.4:72185174-72185193 MS.gene09982:CDS 30.0%
GATCTTATGGGACAAAATTA+AGG + chr1.4:72185164-72185183 MS.gene09982:CDS 30.0%
TGGATCAATGGAACAAATTA+AGG + chr1.4:72185229-72185248 MS.gene09982:CDS 30.0%
TGGCAAAACTATAACTGAAA+AGG + chr1.4:72185323-72185342 MS.gene09982:CDS 30.0%
TTCCATTGATCCATTAATGA+GGG - chr1.4:72185222-72185241 None:intergenic 30.0%
TTGTGCAATAATTTGATGCA+TGG - chr1.4:72185292-72185311 None:intergenic 30.0%
TTTGTAATCCATCATCAATG+TGG - chr1.4:72185116-72185135 None:intergenic 30.0%
! AATTTTGTCCCATAAGATCT+TGG - chr1.4:72185163-72185182 None:intergenic 30.0%
! ATTTTGTCCCATAAGATCTT+GGG - chr1.4:72185162-72185181 None:intergenic 30.0%
! TTTGATTGGTCATATTTGAG+AGG - chr1.4:72185690-72185709 None:intergenic 30.0%
!! CCTGATGATTTTTGTTTGAT+TGG - chr1.4:72185704-72185723 None:intergenic 30.0%
AAAGGTAAAAACATCCAGGA+AGG + chr1.4:72185726-72185745 MS.gene09982:CDS 35.0%
AAAGTTGTGGCGTTTATTTC+AGG - chr1.4:72185528-72185547 None:intergenic 35.0%
AATTGAGTATCTTGCATGTG+AGG + chr1.4:72184999-72185018 MS.gene09982:CDS 35.0%
AGATACAAAGAATCTGTGGA+TGG + chr1.4:72185840-72185859 MS.gene09982:CDS 35.0%
ATTCTTGAGGGAGAAGATTT+GGG + chr1.4:72185033-72185052 MS.gene09982:CDS 35.0%
ATTGAGTATCTTGCATGTGA+GGG + chr1.4:72185000-72185019 MS.gene09982:CDS 35.0%
CAAAAGATCCCAAGATCTTA+TGG + chr1.4:72185151-72185170 MS.gene09982:CDS 35.0%
GTTCCATTGATCCATTAATG+AGG - chr1.4:72185223-72185242 None:intergenic 35.0%
TGTTATAGATGCGGAAAGAA+AGG + chr1.4:72185774-72185793 MS.gene09982:CDS 35.0%
! AACGCCACAACTTTTAATCA+AGG + chr1.4:72185534-72185553 MS.gene09982:CDS 35.0%
! ACCATCATCATGATTTCTAG+AGG - chr1.4:72185754-72185773 None:intergenic 35.0%
! ACGCCACAACTTTTAATCAA+GGG + chr1.4:72185535-72185554 MS.gene09982:CDS 35.0%
! ATTTTGTTCAGCCACTAGAA+GGG - chr1.4:72185451-72185470 None:intergenic 35.0%
! CCATCATCATGATTTCTAGA+GGG - chr1.4:72185753-72185772 None:intergenic 35.0%
! CTCAATTAAGTTGTTGTTCC+AGG - chr1.4:72184986-72185005 None:intergenic 35.0%
! GATGATGGTTGTTATAGATG+CGG + chr1.4:72185765-72185784 MS.gene09982:CDS 35.0%
! TATTTTGTTCAGCCACTAGA+AGG - chr1.4:72185452-72185471 None:intergenic 35.0%
! TTTTCTTTGCCAATTCCTCT+GGG - chr1.4:72185065-72185084 None:intergenic 35.0%
! TTTTTCTTTGCCAATTCCTC+TGG - chr1.4:72185066-72185085 None:intergenic 35.0%
!! AGTCTTATTGCCCTCATTAA+TGG + chr1.4:72185209-72185228 MS.gene09982:CDS 35.0%
AATCTGTGGATGGAAAGGAA+AGG + chr1.4:72185850-72185869 MS.gene09982:CDS 40.0%
ACGCCCTTGATTAAAAGTTG+TGG - chr1.4:72185541-72185560 None:intergenic 40.0%
ATCAAGCACCACATTGATGA+TGG + chr1.4:72185105-72185124 MS.gene09982:CDS 40.0%
ATCTGTGGATGGAAAGGAAA+GGG + chr1.4:72185851-72185870 MS.gene09982:CDS 40.0%
CAAAGAATCTGTGGATGGAA+AGG + chr1.4:72185845-72185864 MS.gene09982:CDS 40.0%
GATTCTTGAGGGAGAAGATT+TGG + chr1.4:72185032-72185051 MS.gene09982:CDS 40.0%
GCAATATCACTTGAGATGCA+TGG - chr1.4:72185377-72185396 None:intergenic 40.0%
GGACTCGATAAGATTCTTGA+GGG + chr1.4:72185021-72185040 MS.gene09982:CDS 40.0%
GGGTAAAGGTAAAAACATCC+AGG + chr1.4:72185722-72185741 MS.gene09982:CDS 40.0%
! ACAACTTTTAATCAAGGGCG+TGG + chr1.4:72185540-72185559 MS.gene09982:CDS 40.0%
! AGACAGGTAGTGTCATTCTT+TGG - chr1.4:72185900-72185919 None:intergenic 40.0%
! CCCTCTAGAAATCATGATGA+TGG + chr1.4:72185750-72185769 MS.gene09982:CDS 40.0%
! TGCCCTCATTAATGGATCAA+TGG + chr1.4:72185217-72185236 MS.gene09982:CDS 40.0%
AAAATCAGCAGCCTCAAGAC+AGG - chr1.4:72185916-72185935 None:intergenic 45.0%
ATGCGGAAAGAAAGGCCATT+GGG + chr1.4:72185782-72185801 MS.gene09982:CDS 45.0%
GAATGACACTACCTGTCTTG+AGG + chr1.4:72185902-72185921 MS.gene09982:CDS 45.0%
GGATACGACATTGTTCCTGT+AGG - chr1.4:72185507-72185526 None:intergenic 45.0%
GGGACTCGATAAGATTCTTG+AGG + chr1.4:72185020-72185039 MS.gene09982:CDS 45.0%
GGTGGTTATAATCGCCAAAG+AGG + chr1.4:72185561-72185580 MS.gene09982:CDS 45.0%
TATAATCGCCAAAGAGGACG+TGG + chr1.4:72185567-72185586 MS.gene09982:CDS 45.0%
! CATGGTCGAAACCATTTTCG+TGG + chr1.4:72185630-72185649 MS.gene09982:CDS 45.0%
!! ACTTTTAATCAAGGGCGTGG+TGG + chr1.4:72185543-72185562 MS.gene09982:CDS 45.0%
!!! GAGGCTGCTGATTTTGTTGA+AGG + chr1.4:72185921-72185940 MS.gene09982:CDS 45.0%
AACCATCAGTTGCGTCCTAC+AGG + chr1.4:72185489-72185508 MS.gene09982:CDS 50.0%
AGATTTGGGAGATGTCCCAG+AGG + chr1.4:72185047-72185066 MS.gene09982:CDS 50.0%
CGTGGACGAGGTAGAAATCA+TGG + chr1.4:72185612-72185631 MS.gene09982:CDS 50.0%
CTGGCGACAACTACATAACC+TGG + chr1.4:72184965-72184984 MS.gene09982:CDS 50.0%
GATGCGGAAAGAAAGGCCAT+TGG + chr1.4:72185781-72185800 MS.gene09982:CDS 50.0%
TCCTGCATGCTTTAGCCCAA+TGG - chr1.4:72185800-72185819 None:intergenic 50.0%
TTCCTGTAGGACGCAACTGA+TGG - chr1.4:72185494-72185513 None:intergenic 50.0%
TTTGGTTGCAGCCCTTCTAG+TGG + chr1.4:72185437-72185456 MS.gene09982:CDS 50.0%
! CGAAACCATTTTCGTGGTGG+AGG + chr1.4:72185636-72185655 MS.gene09982:CDS 50.0%
! GATTTCTAGAGGGACCTTCC+TGG - chr1.4:72185743-72185762 None:intergenic 50.0%
! GGTCGAAACCATTTTCGTGG+TGG + chr1.4:72185633-72185652 MS.gene09982:CDS 50.0%
!! TATGCTCGTTTTGGTGGTCG+TGG + chr1.4:72185594-72185613 MS.gene09982:CDS 50.0%
AATCGCCAAAGAGGACGTGG+TGG + chr1.4:72185570-72185589 MS.gene09982:CDS 55.0%
CACGACCTCCACCACGAAAA+TGG - chr1.4:72185644-72185663 None:intergenic 55.0%
CATAGCCACCACGTCCTCTT+TGG - chr1.4:72185578-72185597 None:intergenic 55.0%
GCCATTGGGCTAAAGCATGC+AGG + chr1.4:72185796-72185815 MS.gene09982:CDS 55.0%
GGGAGATGTCCCAGAGGAAT+TGG + chr1.4:72185053-72185072 MS.gene09982:CDS 55.0%
! CGTGGTGGCTATGCTCGTTT+TGG + chr1.4:72185585-72185604 MS.gene09982:CDS 55.0%
! GGTGGCTATGCTCGTTTTGG+TGG + chr1.4:72185588-72185607 MS.gene09982:CDS 55.0%
!! CATTTTCGTGGTGGAGGTCG+TGG + chr1.4:72185642-72185661 MS.gene09982:CDS 55.0%
!! CGTTTTGGTGGTCGTGGACG+AGG + chr1.4:72185600-72185619 MS.gene09982:CDS 60.0%
! CGTGGTGGAGGTCGTGGAAG+AGG + chr1.4:72185648-72185667 MS.gene09982:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 72184925 72185962 72184925 ID=MS.gene09982
chr1.4 mRNA 72184925 72185962 72184925 ID=MS.gene09982.t1;Parent=MS.gene09982
chr1.4 exon 72184925 72185962 72184925 ID=MS.gene09982.t1.exon1;Parent=MS.gene09982.t1
chr1.4 CDS 72184925 72185962 72184925 ID=cds.MS.gene09982.t1;Parent=MS.gene09982.t1
Gene Sequence

>MS.gene09982

ATGTCAAATGTTAAGCATCAATTCAAAATTTTAAGCATAACTGGCGACAACTACATAACCTGGAACAACAACTTAATTGAGTATCTTGCATGTGAGGGACTCGATAAGATTCTTGAGGGAGAAGATTTGGGAGATGTCCCAGAGGAATTGGCAAAGAAAAAATCAAAAGTAAATCGTATAATCAAGCACCACATTGATGATGGATTACAAACAGAGTATTCAAATGCAAAAGATCCCAAGATCTTATGGGACAAAATTAAGGCAAGATTTGGGCATCAGAAGAAAGTCTTATTGCCCTCATTAATGGATCAATGGAACAAATTAAGGTTCCAAGATTATAAAACTGTTGTTGCATATAACTCTGCCATGCATCAAATTATTGCACAATTAGAATTTTGTGGCAAAACTATAACTGAAAAGGAAAAGTTGGAGAAAACATTCTCAACTTTCCATGCATCTCAAGTGATATTGCAACAACAATATAGAATGAGAGAATTTACTGAATACTCTGATTTGGTTGCAGCCCTTCTAGTGGCTGAACAAAATAACGAGCTGCTCATTAAAAACCATCAGTTGCGTCCTACAGGAACAATGTCGTATCCTGAAATAAACGCCACAACTTTTAATCAAGGGCGTGGTGGTTATAATCGCCAAAGAGGACGTGGTGGCTATGCTCGTTTTGGTGGTCGTGGACGAGGTAGAAATCATGGTCGAAACCATTTTCGTGGTGGAGGTCGTGGAAGAGGTTATATGAATTACAGGCCTCTCAAATATGACCAATCAAACAAAAATCATCAGGGTAAAGGTAAAAACATCCAGGAAGGTCCCTCTAGAAATCATGATGATGGTTGTTATAGATGCGGAAAGAAAGGCCATTGGGCTAAAGCATGCAGGACACCAGAGTATCTATGTAAAAGATACAAAGAATCTGTGGATGGAAAGGAAAGGGAAGTTAATTTTAATGAAATTGAACCAAAGAATGACACTACCTGTCTTGAGGCTGCTGATTTTGTTGAAGGAGATTTTAATATGGATTAA

Protein sequence

>MS.gene09982.t1

MSNVKHQFKILSITGDNYITWNNNLIEYLACEGLDKILEGEDLGDVPEELAKKKSKVNRIIKHHIDDGLQTEYSNAKDPKILWDKIKARFGHQKKVLLPSLMDQWNKLRFQDYKTVVAYNSAMHQIIAQLEFCGKTITEKEKLEKTFSTFHASQVILQQQYRMREFTEYSDLVAALLVAEQNNELLIKNHQLRPTGTMSYPEINATTFNQGRGGYNRQRGRGGYARFGGRGRGRNHGRNHFRGGGRGRGYMNYRPLKYDQSNKNHQGKGKNIQEGPSRNHDDGCYRCGKKGHWAKACRTPEYLCKRYKESVDGKEREVNFNEIEPKNDTTCLEAADFVEGDFNMD