AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41305

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41305.t1 MTR_7g062720 40.541 148 80 3 1 146 1 142 5.14e-31 115
MS.gene41305.t1 MTR_4g037355 40.441 136 61 4 155 290 1 116 1.16e-21 89.7
MS.gene41305.t1 MTR_5g061150 35.354 99 64 0 52 150 38 136 4.20e-18 80.1
MS.gene41305.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 1.2:+31511231 MS.gene41305:CDS
AGTCTTATTGCCCTCATTAA+TGG 0.201947 1.2:+31511211 MS.gene41305:CDS
AAAGTTGTGGCGTTTATTTC+AGG 0.203868 1.2:-31511527 None:intergenic
CAAAAGATCCCAAGATCTTA+TGG 0.237847 1.2:+31511153 MS.gene41305:CDS
GATTCTTGAGGGAGAAGATT+TGG 0.253340 1.2:+31511034 MS.gene41305:CDS
GACAAAATTAAGGCAAGATT+TGG 0.257188 1.2:+31511176 MS.gene41305:CDS
CTCAATTAAGTTGTTGTTCC+AGG 0.274617 1.2:-31510985 None:intergenic
CACGACCTCCACCACGAAAA+TGG 0.277262 1.2:-31511643 None:intergenic
GATCTTATGGGACAAAATTA+AGG 0.310971 1.2:+31511166 MS.gene41305:CDS
ATTTACTGAATACTCTGATT+TGG 0.313227 1.2:+31511421 MS.gene41305:CDS
ATTCTTGAGGGAGAAGATTT+GGG 0.333151 1.2:+31511035 MS.gene41305:CDS
AGACAGGTAGTGTCATTCTT+TGG 0.342502 1.2:-31511899 None:intergenic
GGGAGATGTCCCAGAGGAAT+TGG 0.345733 1.2:+31511055 MS.gene41305:CDS
GAAGAGGTTATATGAATTAC+AGG 0.363099 1.2:+31511666 MS.gene41305:CDS
GATTTCTAGAGGGACCTTCC+TGG 0.373636 1.2:-31511742 None:intergenic
CATAGCCACCACGTCCTCTT+TGG 0.374275 1.2:-31511577 None:intergenic
CGTGGTGGCTATGCTCGTTT+TGG 0.395091 1.2:+31511587 MS.gene41305:CDS
ACAAAATTAAGGCAAGATTT+GGG 0.416566 1.2:+31511177 MS.gene41305:CDS
TATAACTGAAAAGGAAAAGT+TGG 0.422757 1.2:+31511334 MS.gene41305:CDS
TGCCCTCATTAATGGATCAA+TGG 0.432677 1.2:+31511219 MS.gene41305:CDS
CGTGGTGGAGGTCGTGGAAG+AGG 0.449888 1.2:+31511650 MS.gene41305:CDS
TCCTGCATGCTTTAGCCCAA+TGG 0.457473 1.2:-31511799 None:intergenic
AAAAGATCCCAAGATCTTAT+GGG 0.458748 1.2:+31511154 MS.gene41305:CDS
AACCATCAGTTGCGTCCTAC+AGG 0.459311 1.2:+31511491 MS.gene41305:CDS
TGGCAAAACTATAACTGAAA+AGG 0.467052 1.2:+31511325 MS.gene41305:CDS
ATCTGTGGATGGAAAGGAAA+GGG 0.491819 1.2:+31511853 MS.gene41305:CDS
ATCAAGCACCACATTGATGA+TGG 0.492315 1.2:+31511107 MS.gene41305:CDS
TGTTATAGATGCGGAAAGAA+AGG 0.495634 1.2:+31511776 MS.gene41305:CDS
CTGGCGACAACTACATAACC+TGG 0.502097 1.2:+31510967 MS.gene41305:CDS
GTTCCATTGATCCATTAATG+AGG 0.509644 1.2:-31511222 None:intergenic
ATGCGGAAAGAAAGGCCATT+GGG 0.516896 1.2:+31511784 MS.gene41305:CDS
TTTGATTGGTCATATTTGAG+AGG 0.522357 1.2:-31511689 None:intergenic
CAAAGAATCTGTGGATGGAA+AGG 0.532926 1.2:+31511847 MS.gene41305:CDS
TTCCATTGATCCATTAATGA+GGG 0.533283 1.2:-31511221 None:intergenic
CGTGGACGAGGTAGAAATCA+TGG 0.535808 1.2:+31511614 MS.gene41305:CDS
GGACTCGATAAGATTCTTGA+GGG 0.539399 1.2:+31511023 MS.gene41305:CDS
GCCATTGGGCTAAAGCATGC+AGG 0.539769 1.2:+31511798 MS.gene41305:CDS
CCCTCTAGAAATCATGATGA+TGG 0.541875 1.2:+31511752 MS.gene41305:CDS
TTCCTGTAGGACGCAACTGA+TGG 0.562606 1.2:-31511493 None:intergenic
AAAATCAGCAGCCTCAAGAC+AGG 0.562896 1.2:-31511915 None:intergenic
AATTGAGTATCTTGCATGTG+AGG 0.565013 1.2:+31511001 MS.gene41305:CDS
ATTGAGTATCTTGCATGTGA+GGG 0.575966 1.2:+31511002 MS.gene41305:CDS
TTTGGTTGCAGCCCTTCTAG+TGG 0.582793 1.2:+31511439 MS.gene41305:CDS
GATGCGGAAAGAAAGGCCAT+TGG 0.583841 1.2:+31511783 MS.gene41305:CDS
TTGTGCAATAATTTGATGCA+TGG 0.588693 1.2:-31511291 None:intergenic
TAAAAGATACAAAGAATCTG+TGG 0.594054 1.2:+31511838 MS.gene41305:CDS
AGATACAAAGAATCTGTGGA+TGG 0.602731 1.2:+31511842 MS.gene41305:CDS
GGGACTCGATAAGATTCTTG+AGG 0.606176 1.2:+31511022 MS.gene41305:CDS
ACGCCCTTGATTAAAAGTTG+TGG 0.608515 1.2:-31511540 None:intergenic
GCAATATCACTTGAGATGCA+TGG 0.608661 1.2:-31511376 None:intergenic
TATAATCGCCAAAGAGGACG+TGG 0.608957 1.2:+31511569 MS.gene41305:CDS
ACCATCATCATGATTTCTAG+AGG 0.616492 1.2:-31511753 None:intergenic
GGATACGACATTGTTCCTGT+AGG 0.627452 1.2:-31511506 None:intergenic
GGTGGTTATAATCGCCAAAG+AGG 0.642086 1.2:+31511563 MS.gene41305:CDS
CCATCATCATGATTTCTAGA+GGG 0.647682 1.2:-31511752 None:intergenic
GAATGACACTACCTGTCTTG+AGG 0.649563 1.2:+31511904 MS.gene41305:CDS
AATCTGTGGATGGAAAGGAA+AGG 0.653361 1.2:+31511852 MS.gene41305:CDS
GATGATGGTTGTTATAGATG+CGG 0.696569 1.2:+31511767 MS.gene41305:CDS
AATCGCCAAAGAGGACGTGG+TGG 0.698905 1.2:+31511572 MS.gene41305:CDS
TTTGTAATCCATCATCAATG+TGG 0.715751 1.2:-31511115 None:intergenic
AGATTTGGGAGATGTCCCAG+AGG 0.741186 1.2:+31511049 MS.gene41305:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCAAAATTTTAAGCATAAC+TGG + chr1.2:31510948-31510967 MS.gene41305:CDS 20.0%
! ACAAAATTAAGGCAAGATTT+GGG + chr1.2:31511177-31511196 MS.gene41305:CDS 25.0%
! ATTTACTGAATACTCTGATT+TGG + chr1.2:31511421-31511440 MS.gene41305:CDS 25.0%
! CAATCAAACAAAAATCATCA+GGG + chr1.2:31511704-31511723 MS.gene41305:CDS 25.0%
! TAAAAGATACAAAGAATCTG+TGG + chr1.2:31511838-31511857 MS.gene41305:CDS 25.0%
! TATAACTGAAAAGGAAAAGT+TGG + chr1.2:31511334-31511353 MS.gene41305:CDS 25.0%
!! ATTGCACAATTAGAATTTTG+TGG + chr1.2:31511305-31511324 MS.gene41305:CDS 25.0%
!! TATCTTTTACATAGATACTC+TGG - chr1.2:31511827-31511846 None:intergenic 25.0%
!!! CAACAACAGTTTTATAATCT+TGG - chr1.2:31511259-31511278 None:intergenic 25.0%
!!! TGTTGAAGGAGATTTTAATA+TGG + chr1.2:31511937-31511956 MS.gene41305:CDS 25.0%
AAAAGATCCCAAGATCTTAT+GGG + chr1.2:31511154-31511173 MS.gene41305:CDS 30.0%
AACAAAAATCATCAGGGTAA+AGG + chr1.2:31511710-31511729 MS.gene41305:CDS 30.0%
CCAATCAAACAAAAATCATC+AGG + chr1.2:31511703-31511722 MS.gene41305:CDS 30.0%
GAAGAGGTTATATGAATTAC+AGG + chr1.2:31511666-31511685 MS.gene41305:CDS 30.0%
GACAAAATTAAGGCAAGATT+TGG + chr1.2:31511176-31511195 MS.gene41305:CDS 30.0%
GATCTTATGGGACAAAATTA+AGG + chr1.2:31511166-31511185 MS.gene41305:CDS 30.0%
TGGATCAATGGAACAAATTA+AGG + chr1.2:31511231-31511250 MS.gene41305:CDS 30.0%
TGGCAAAACTATAACTGAAA+AGG + chr1.2:31511325-31511344 MS.gene41305:CDS 30.0%
TTCCATTGATCCATTAATGA+GGG - chr1.2:31511224-31511243 None:intergenic 30.0%
TTGTGCAATAATTTGATGCA+TGG - chr1.2:31511294-31511313 None:intergenic 30.0%
TTTGTAATCCATCATCAATG+TGG - chr1.2:31511118-31511137 None:intergenic 30.0%
! AATTTTGTCCCATAAGATCT+TGG - chr1.2:31511165-31511184 None:intergenic 30.0%
! ATTTTGTCCCATAAGATCTT+GGG - chr1.2:31511164-31511183 None:intergenic 30.0%
! TTTGATTGGTCATATTTGAG+AGG - chr1.2:31511692-31511711 None:intergenic 30.0%
!! CCTGATGATTTTTGTTTGAT+TGG - chr1.2:31511706-31511725 None:intergenic 30.0%
AAAGGTAAAAACATCCAGGA+AGG + chr1.2:31511728-31511747 MS.gene41305:CDS 35.0%
AAAGTTGTGGCGTTTATTTC+AGG - chr1.2:31511530-31511549 None:intergenic 35.0%
AATTGAGTATCTTGCATGTG+AGG + chr1.2:31511001-31511020 MS.gene41305:CDS 35.0%
AGATACAAAGAATCTGTGGA+TGG + chr1.2:31511842-31511861 MS.gene41305:CDS 35.0%
ATTCTTGAGGGAGAAGATTT+GGG + chr1.2:31511035-31511054 MS.gene41305:CDS 35.0%
ATTGAGTATCTTGCATGTGA+GGG + chr1.2:31511002-31511021 MS.gene41305:CDS 35.0%
CAAAAGATCCCAAGATCTTA+TGG + chr1.2:31511153-31511172 MS.gene41305:CDS 35.0%
GTTCCATTGATCCATTAATG+AGG - chr1.2:31511225-31511244 None:intergenic 35.0%
TGTTATAGATGCGGAAAGAA+AGG + chr1.2:31511776-31511795 MS.gene41305:CDS 35.0%
! AACGCCACAACTTTTAATCA+AGG + chr1.2:31511536-31511555 MS.gene41305:CDS 35.0%
! ACCATCATCATGATTTCTAG+AGG - chr1.2:31511756-31511775 None:intergenic 35.0%
! ACGCCACAACTTTTAATCAA+GGG + chr1.2:31511537-31511556 MS.gene41305:CDS 35.0%
! ATTTTGTTCAGCCACTAGAA+GGG - chr1.2:31511453-31511472 None:intergenic 35.0%
! CCATCATCATGATTTCTAGA+GGG - chr1.2:31511755-31511774 None:intergenic 35.0%
! CTCAATTAAGTTGTTGTTCC+AGG - chr1.2:31510988-31511007 None:intergenic 35.0%
! GATGATGGTTGTTATAGATG+CGG + chr1.2:31511767-31511786 MS.gene41305:CDS 35.0%
! TATTTTGTTCAGCCACTAGA+AGG - chr1.2:31511454-31511473 None:intergenic 35.0%
! TTTTCTTTGCCAATTCCTCT+GGG - chr1.2:31511067-31511086 None:intergenic 35.0%
! TTTTTCTTTGCCAATTCCTC+TGG - chr1.2:31511068-31511087 None:intergenic 35.0%
!! AGTCTTATTGCCCTCATTAA+TGG + chr1.2:31511211-31511230 MS.gene41305:CDS 35.0%
AATCTGTGGATGGAAAGGAA+AGG + chr1.2:31511852-31511871 MS.gene41305:CDS 40.0%
ACGCCCTTGATTAAAAGTTG+TGG - chr1.2:31511543-31511562 None:intergenic 40.0%
ATCAAGCACCACATTGATGA+TGG + chr1.2:31511107-31511126 MS.gene41305:CDS 40.0%
ATCTGTGGATGGAAAGGAAA+GGG + chr1.2:31511853-31511872 MS.gene41305:CDS 40.0%
CAAAGAATCTGTGGATGGAA+AGG + chr1.2:31511847-31511866 MS.gene41305:CDS 40.0%
GATTCTTGAGGGAGAAGATT+TGG + chr1.2:31511034-31511053 MS.gene41305:CDS 40.0%
GCAATATCACTTGAGATGCA+TGG - chr1.2:31511379-31511398 None:intergenic 40.0%
GGACTCGATAAGATTCTTGA+GGG + chr1.2:31511023-31511042 MS.gene41305:CDS 40.0%
GGGTAAAGGTAAAAACATCC+AGG + chr1.2:31511724-31511743 MS.gene41305:CDS 40.0%
! ACAACTTTTAATCAAGGGCG+TGG + chr1.2:31511542-31511561 MS.gene41305:CDS 40.0%
! AGACAGGTAGTGTCATTCTT+TGG - chr1.2:31511902-31511921 None:intergenic 40.0%
! CCCTCTAGAAATCATGATGA+TGG + chr1.2:31511752-31511771 MS.gene41305:CDS 40.0%
! TGCCCTCATTAATGGATCAA+TGG + chr1.2:31511219-31511238 MS.gene41305:CDS 40.0%
AAAATCAGCAGCCTCAAGAC+AGG - chr1.2:31511918-31511937 None:intergenic 45.0%
ATGCGGAAAGAAAGGCCATT+GGG + chr1.2:31511784-31511803 MS.gene41305:CDS 45.0%
GAATGACACTACCTGTCTTG+AGG + chr1.2:31511904-31511923 MS.gene41305:CDS 45.0%
GGATACGACATTGTTCCTGT+AGG - chr1.2:31511509-31511528 None:intergenic 45.0%
GGGACTCGATAAGATTCTTG+AGG + chr1.2:31511022-31511041 MS.gene41305:CDS 45.0%
GGTGGTTATAATCGCCAAAG+AGG + chr1.2:31511563-31511582 MS.gene41305:CDS 45.0%
TATAATCGCCAAAGAGGACG+TGG + chr1.2:31511569-31511588 MS.gene41305:CDS 45.0%
! CATGGTCGAAACCATTTTCG+TGG + chr1.2:31511632-31511651 MS.gene41305:CDS 45.0%
!! ACTTTTAATCAAGGGCGTGG+TGG + chr1.2:31511545-31511564 MS.gene41305:CDS 45.0%
!!! GAGGCTGCTGATTTTGTTGA+AGG + chr1.2:31511923-31511942 MS.gene41305:CDS 45.0%
AACCATCAGTTGCGTCCTAC+AGG + chr1.2:31511491-31511510 MS.gene41305:CDS 50.0%
AGATTTGGGAGATGTCCCAG+AGG + chr1.2:31511049-31511068 MS.gene41305:CDS 50.0%
CGTGGACGAGGTAGAAATCA+TGG + chr1.2:31511614-31511633 MS.gene41305:CDS 50.0%
CTGGCGACAACTACATAACC+TGG + chr1.2:31510967-31510986 MS.gene41305:CDS 50.0%
GATGCGGAAAGAAAGGCCAT+TGG + chr1.2:31511783-31511802 MS.gene41305:CDS 50.0%
TCCTGCATGCTTTAGCCCAA+TGG - chr1.2:31511802-31511821 None:intergenic 50.0%
TTCCTGTAGGACGCAACTGA+TGG - chr1.2:31511496-31511515 None:intergenic 50.0%
TTTGGTTGCAGCCCTTCTAG+TGG + chr1.2:31511439-31511458 MS.gene41305:CDS 50.0%
! CGAAACCATTTTCGTGGTGG+AGG + chr1.2:31511638-31511657 MS.gene41305:CDS 50.0%
! GATTTCTAGAGGGACCTTCC+TGG - chr1.2:31511745-31511764 None:intergenic 50.0%
! GGTCGAAACCATTTTCGTGG+TGG + chr1.2:31511635-31511654 MS.gene41305:CDS 50.0%
!! TATGCTCGTTTTGGTGGTCG+TGG + chr1.2:31511596-31511615 MS.gene41305:CDS 50.0%
AATCGCCAAAGAGGACGTGG+TGG + chr1.2:31511572-31511591 MS.gene41305:CDS 55.0%
CACGACCTCCACCACGAAAA+TGG - chr1.2:31511646-31511665 None:intergenic 55.0%
CATAGCCACCACGTCCTCTT+TGG - chr1.2:31511580-31511599 None:intergenic 55.0%
GCCATTGGGCTAAAGCATGC+AGG + chr1.2:31511798-31511817 MS.gene41305:CDS 55.0%
GGGAGATGTCCCAGAGGAAT+TGG + chr1.2:31511055-31511074 MS.gene41305:CDS 55.0%
! CGTGGTGGCTATGCTCGTTT+TGG + chr1.2:31511587-31511606 MS.gene41305:CDS 55.0%
! GGTGGCTATGCTCGTTTTGG+TGG + chr1.2:31511590-31511609 MS.gene41305:CDS 55.0%
!! CATTTTCGTGGTGGAGGTCG+TGG + chr1.2:31511644-31511663 MS.gene41305:CDS 55.0%
!! CGTTTTGGTGGTCGTGGACG+AGG + chr1.2:31511602-31511621 MS.gene41305:CDS 60.0%
! CGTGGTGGAGGTCGTGGAAG+AGG + chr1.2:31511650-31511669 MS.gene41305:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 31510927 31511964 31510927 ID=MS.gene41305
chr1.2 mRNA 31510927 31511964 31510927 ID=MS.gene41305.t1;Parent=MS.gene41305
chr1.2 exon 31510927 31511964 31510927 ID=MS.gene41305.t1.exon1;Parent=MS.gene41305.t1
chr1.2 CDS 31510927 31511964 31510927 ID=cds.MS.gene41305.t1;Parent=MS.gene41305.t1
Gene Sequence

>MS.gene41305

ATGTCAAATGTTAAGCATCAATTCAAAATTTTAAGCATAACTGGCGACAACTACATAACCTGGAACAACAACTTAATTGAGTATCTTGCATGTGAGGGACTCGATAAGATTCTTGAGGGAGAAGATTTGGGAGATGTCCCAGAGGAATTGGCAAAGAAAAAATCAAAAGTAAATCGTATAATCAAGCACCACATTGATGATGGATTACAAACAGAGTATTCAAATGCAAAAGATCCCAAGATCTTATGGGACAAAATTAAGGCAAGATTTGGGCATCAGAAGAAAGTCTTATTGCCCTCATTAATGGATCAATGGAACAAATTAAGGTTCCAAGATTATAAAACTGTTGTTGCATATAACTCTGCCATGCATCAAATTATTGCACAATTAGAATTTTGTGGCAAAACTATAACTGAAAAGGAAAAGTTGGAGAAAACATTCTCAACTTTCCATGCATCTCAAGTGATATTGCAACAACAATATAGAATGAGAGAATTTACTGAATACTCTGATTTGGTTGCAGCCCTTCTAGTGGCTGAACAAAATAACGAGCTGCTCATTAAAAACCATCAGTTGCGTCCTACAGGAACAATGTCGTATCCTGAAATAAACGCCACAACTTTTAATCAAGGGCGTGGTGGTTATAATCGCCAAAGAGGACGTGGTGGCTATGCTCGTTTTGGTGGTCGTGGACGAGGTAGAAATCATGGTCGAAACCATTTTCGTGGTGGAGGTCGTGGAAGAGGTTATATGAATTACAGGCCTCTCAAATATGACCAATCAAACAAAAATCATCAGGGTAAAGGTAAAAACATCCAGGAAGGTCCCTCTAGAAATCATGATGATGGTTGTTATAGATGCGGAAAGAAAGGCCATTGGGCTAAAGCATGCAGGACACCAGAGTATCTATGTAAAAGATACAAAGAATCTGTGGATGGAAAGGAAAGGGAAGTTAATTTTAATGAAATTGAACCAAAGAATGACACTACCTGTCTTGAGGCTGCTGATTTTGTTGAAGGAGATTTTAATATGGATTAA
Protein sequence

>MS.gene41305.t1

MSNVKHQFKILSITGDNYITWNNNLIEYLACEGLDKILEGEDLGDVPEELAKKKSKVNRIIKHHIDDGLQTEYSNAKDPKILWDKIKARFGHQKKVLLPSLMDQWNKLRFQDYKTVVAYNSAMHQIIAQLEFCGKTITEKEKLEKTFSTFHASQVILQQQYRMREFTEYSDLVAALLVAEQNNELLIKNHQLRPTGTMSYPEINATTFNQGRGGYNRQRGRGGYARFGGRGRGRNHGRNHFRGGGRGRGYMNYRPLKYDQSNKNHQGKGKNIQEGPSRNHDDGCYRCGKKGHWAKACRTPEYLCKRYKESVDGKEREVNFNEIEPKNDTTCLEAADFVEGDFNMD