AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54736

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54736.t1 MTR_6g008860 98.675 151 2 0 1 151 1 151 1.99e-110 310
MS.gene54736.t1 MTR_4g071650 98.675 151 2 0 1 151 1 151 1.99e-110 310
MS.gene54736.t1 MTR_7g089310 83.721 43 7 0 102 144 1 43 7.47e-19 76.3
MS.gene54736.t1 MTR_7g099500 34.211 114 75 0 33 146 11 124 2.18e-18 76.3
MS.gene54736.t1 MTR_7g098910 34.513 113 73 1 25 137 14 125 9.46e-18 75.1
MS.gene54736.t1 MTR_8g063580 35.185 108 68 1 33 138 12 119 1.71e-15 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54736.t1 AT5G26594 32.143 112 76 0 33 144 18 129 1.01e-17 74.7

Find 27 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACCTCAGGTCCATTGATTA+TGG 0.203630 6.2:-4457160 None:intergenic
CTCTCTCGGGTCAAAGGTTT+TGG 0.227586 6.2:-4457901 None:intergenic
AGCAATGCATTCATTGGATA+TGG 0.328332 6.2:-4456985 None:intergenic
GCTTCTTGAGCACTATTTGC+AGG 0.339727 6.2:-4457078 None:intergenic
CACTATTTGCAGGCTCTGTT+CGG 0.378455 6.2:-4457068 None:intergenic
CATCATATGCTTGAATCAAT+AGG 0.390164 6.2:+4457042 MS.gene54736:CDS
TTTGATTTGCCCATAATCAA+TGG 0.409566 6.2:+4457150 MS.gene54736:CDS
GATCAAAATGTGCAAATGTT+TGG 0.412226 6.2:+4457853 MS.gene54736:CDS
ACCTCAGGTCCATTGATTAT+GGG 0.435172 6.2:-4457159 None:intergenic
TCTACTAGCAATGCATTCAT+TGG 0.442738 6.2:-4456991 None:intergenic
GTGAGGCAAATGCGTGCAAT+GGG 0.477196 6.2:+4457790 MS.gene54736:CDS
CATATGATGCTCTAAGCGTC+TGG 0.510351 6.2:-4457028 None:intergenic
TGATGAACACAAAACTCTCT+CGG 0.519844 6.2:-4457915 None:intergenic
ACAAAACTCTCTCGGGTCAA+AGG 0.520328 6.2:-4457907 None:intergenic
ATGAATGCATTGCTAGTAGA+TGG 0.520529 6.2:+4456994 MS.gene54736:CDS
GATGAACACAAAACTCTCTC+GGG 0.532140 6.2:-4457914 None:intergenic
AAGTTGCAATCAACAATGGA+TGG 0.566106 6.2:+4456883 None:intergenic
GGGATACAGAGCAAGGTGGT+TGG 0.588650 6.2:+4457811 MS.gene54736:CDS
GGTGAGGCAAATGCGTGCAA+TGG 0.603553 6.2:+4457789 MS.gene54736:CDS
ACAATGGATGGAGGAACCAC+AGG 0.607474 6.2:+4456895 None:intergenic
TGCAATGGGGATACAGAGCA+AGG 0.629234 6.2:+4457804 MS.gene54736:CDS
GCCCATAATCAATGGACCTG+AGG 0.632543 6.2:+4457158 MS.gene54736:CDS
ATATGCATTAGTTTCACATG+CGG 0.660237 6.2:-4457951 None:intergenic
TTGCAATCAACAATGGATGG+AGG 0.668830 6.2:+4456886 None:intergenic
GAGGAACCACAGGATATAAG+CGG 0.671047 6.2:+4456905 MS.gene54736:CDS
AATGGGGATACAGAGCAAGG+TGG 0.782718 6.2:+4457807 MS.gene54736:CDS
TGAGGCAAATGCGTGCAATG+GGG 0.798344 6.2:+4457791 MS.gene54736:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATATATAAGTAATTTTGTT+CGG - chr6.2:4457354-4457373 None:intergenic 10.0%
!!! ATATATAAGTAATTTTGTTC+GGG - chr6.2:4457353-4457372 None:intergenic 15.0%
!! AAAATTGACAACTCATTTAT+GGG - chr6.2:4457689-4457708 None:intergenic 20.0%
!! ATTACTTATATATTAACCAC+TGG + chr6.2:4457360-4457379 MS.gene54736:intron 20.0%
!! TAAAATTGACAACTCATTTA+TGG - chr6.2:4457690-4457709 None:intergenic 20.0%
!!! AAATAAATTTTTGATACCTC+AGG - chr6.2:4457177-4457196 None:intergenic 20.0%
! CAGTTAATCTCATATTTAGA+CGG + chr6.2:4457281-4457300 MS.gene54736:intron 25.0%
!! CAACTAGTTAGTTTAAAATG+TGG - chr6.2:4457235-4457254 None:intergenic 25.0%
!!! GGATCTATTTTGATCATATA+TGG - chr6.2:4457490-4457509 None:intergenic 25.0%
!!! TTCCTAATTACTTTTGTAGT+TGG + chr6.2:4457768-4457787 MS.gene54736:intron 25.0%
ACTTATATATTAACCACTGG+CGG + chr6.2:4457363-4457382 MS.gene54736:intron 30.0%
ATCCTTTGTCATCAACTTTA+TGG + chr6.2:4457506-4457525 MS.gene54736:intron 30.0%
CACCAACTACAAAAGTAATT+AGG - chr6.2:4457773-4457792 None:intergenic 30.0%
CATCATATGCTTGAATCAAT+AGG + chr6.2:4457042-4457061 MS.gene54736:CDS 30.0%
GATCAAAATGTGCAAATGTT+TGG + chr6.2:4457853-4457872 MS.gene54736:CDS 30.0%
TAATCTCATATTTAGACGGT+GGG + chr6.2:4457285-4457304 MS.gene54736:intron 30.0%
TGAGATGAATTCTTATCAAC+TGG + chr6.2:4457433-4457452 MS.gene54736:intron 30.0%
TTAATCTCATATTTAGACGG+TGG + chr6.2:4457284-4457303 MS.gene54736:intron 30.0%
!! AATTACTTTTGTAGTTGGTG+AGG + chr6.2:4457773-4457792 MS.gene54736:intron 30.0%
!! TACCATAAAGTTGATGACAA+AGG - chr6.2:4457511-4457530 None:intergenic 30.0%
!! TTTGATTTGCCCATAATCAA+TGG + chr6.2:4457150-4457169 MS.gene54736:CDS 30.0%
!!! TCAACTGGACTATTTTTTGT+TGG + chr6.2:4457448-4457467 MS.gene54736:intron 30.0%
AGCAATGCATTCATTGGATA+TGG - chr6.2:4456988-4457007 None:intergenic 35.0%
ATGAATGCATTGCTAGTAGA+TGG + chr6.2:4456994-4457013 MS.gene54736:CDS 35.0%
ATTTATGGGCTTGGATTTGA+CGG - chr6.2:4457675-4457694 None:intergenic 35.0%
GGTATCTTTATACTGACGAT+GGG + chr6.2:4457384-4457403 MS.gene54736:intron 35.0%
TCTACTAGCAATGCATTCAT+TGG - chr6.2:4456994-4457013 None:intergenic 35.0%
TCTCACGTATTTCTTTGTTC+TGG - chr6.2:4457323-4457342 None:intergenic 35.0%
TGATGAACACAAAACTCTCT+CGG - chr6.2:4457918-4457937 None:intergenic 35.0%
!! AGAGTTTTGTGTTCATCACT+GGG + chr6.2:4457920-4457939 MS.gene54736:CDS 35.0%
!!! ATCCACATTTTTTTCTCCTC+GGG - chr6.2:4456940-4456959 None:intergenic 35.0%
!!! GATCCACATTTTTTTCTCCT+CGG - chr6.2:4456941-4456960 None:intergenic 35.0%
AATCAAACAACCCCACTTGA+TGG + chr6.2:4457619-4457638 MS.gene54736:intron 40.0%
ATATTTAGACGGTGGGTCTT+TGG + chr6.2:4457292-4457311 MS.gene54736:intron 40.0%
CGGTATCTTTATACTGACGA+TGG + chr6.2:4457383-4457402 MS.gene54736:intron 40.0%
GATGAACACAAAACTCTCTC+GGG - chr6.2:4457917-4457936 None:intergenic 40.0%
TATTTAGACGGTGGGTCTTT+GGG + chr6.2:4457293-4457312 MS.gene54736:intron 40.0%
TGACAACTCATTTATGGGCT+TGG - chr6.2:4457684-4457703 None:intergenic 40.0%
! ACCTCAGGTCCATTGATTAT+GGG - chr6.2:4457162-4457181 None:intergenic 40.0%
! GCGATGCAAATTTTGTTGAC+TGG + chr6.2:4457099-4457118 MS.gene54736:CDS 40.0%
! TACCTCAGGTCCATTGATTA+TGG - chr6.2:4457163-4457182 None:intergenic 40.0%
!! GAGAGTTTTGTGTTCATCAC+TGG + chr6.2:4457919-4457938 MS.gene54736:CDS 40.0%
!! TCAAGTTGACTCCATCAAGT+GGG - chr6.2:4457633-4457652 None:intergenic 40.0%
!! TTTTTGCCGCTTATATCCTG+TGG - chr6.2:4456914-4456933 None:intergenic 40.0%
ACAAAACTCTCTCGGGTCAA+AGG - chr6.2:4457910-4457929 None:intergenic 45.0%
AGCCCGAGGAGAAAAAAATG+TGG + chr6.2:4456935-4456954 MS.gene54736:CDS 45.0%
CACTATTTGCAGGCTCTGTT+CGG - chr6.2:4457071-4457090 None:intergenic 45.0%
CAGTATAAAGATACCGCCAG+TGG - chr6.2:4457379-4457398 None:intergenic 45.0%
GAGGAACCACAGGATATAAG+CGG + chr6.2:4456905-4456924 MS.gene54736:CDS 45.0%
GCTTCTTGAGCACTATTTGC+AGG - chr6.2:4457081-4457100 None:intergenic 45.0%
! CAAGTTGACTCCATCAAGTG+GGG - chr6.2:4457632-4457651 None:intergenic 45.0%
! CATATGATGCTCTAAGCGTC+TGG - chr6.2:4457031-4457050 None:intergenic 45.0%
!! GTCAAGTTGACTCCATCAAG+TGG - chr6.2:4457634-4457653 None:intergenic 45.0%
AATGGGGATACAGAGCAAGG+TGG + chr6.2:4457807-4457826 MS.gene54736:CDS 50.0%
GCCCATAATCAATGGACCTG+AGG + chr6.2:4457158-4457177 MS.gene54736:CDS 50.0%
GTGAGGCAAATGCGTGCAAT+GGG + chr6.2:4457790-4457809 MS.gene54736:CDS 50.0%
TAAGCGGCAAAAAAAGCCCG+AGG + chr6.2:4456921-4456940 MS.gene54736:CDS 50.0%
TGAGGCAAATGCGTGCAATG+GGG + chr6.2:4457791-4457810 MS.gene54736:CDS 50.0%
TGCAATGGGGATACAGAGCA+AGG + chr6.2:4457804-4457823 MS.gene54736:CDS 50.0%
! CTCTCTCGGGTCAAAGGTTT+TGG - chr6.2:4457904-4457923 None:intergenic 50.0%
!!! GGTCAAAGGTTTTGGAGTGC+TGG - chr6.2:4457896-4457915 None:intergenic 50.0%
GGGATACAGAGCAAGGTGGT+TGG + chr6.2:4457811-4457830 MS.gene54736:CDS 55.0%
GGTGAGGCAAATGCGTGCAA+TGG + chr6.2:4457789-4457808 MS.gene54736:CDS 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 4456898 4457960 4456898 ID=MS.gene54736
chr6.2 mRNA 4456898 4457960 4456898 ID=MS.gene54736.t1;Parent=MS.gene54736
chr6.2 exon 4456898 4457179 4456898 ID=MS.gene54736.t1.exon1;Parent=MS.gene54736.t1
chr6.2 CDS 4456898 4457179 4456898 ID=cds.MS.gene54736.t1;Parent=MS.gene54736.t1
chr6.2 exon 4457787 4457960 4457787 ID=MS.gene54736.t1.exon2;Parent=MS.gene54736.t1
chr6.2 CDS 4457787 4457960 4457787 ID=cds.MS.gene54736.t1;Parent=MS.gene54736.t1
Gene Sequence

>MS.gene54736

ATGGATGGAGGAACCACAGGATATAAGCGGCAAAAAAAGCCCGAGGAGAAAAAAATGTGGATCAAAAAGCGTGAATTGTATGACACTCCATATCCAATGAATGCATTGCTAGTAGATGGTGTGACTGCAACCAGACGCTTAGAGCATCATATGCTTGAATCAATAGGCATCCGAACAGAGCCTGCAAATAGTGCTCAAGAAGCGATGCAAATTTTGTTGACTGGTGTCAAATTTGACTTCATATTTGTTGATTTTGATTTGCCCATAATCAATGGACCTGAGGTATCAAAAATTTATTTATTTATCATTTTGCTTATTTTTTTTATTTCATTTGCCACATTTTAAACTAACTAGTTGATAGCTTATATAAACATCAAATAAAACAGTTAATCTCATATTTAGACGGTGGGTCTTTGGGTTTACCAGAACAAAGAAATACGTGAGACTCAGATCCCGAACAAAATTACTTATATATTAACCACTGGCGGTATCTTTATACTGACGATGGGTTTCATACTCACATATTCTCTAGATCTGAGATGAATTCTTATCAACTGGACTATTTTTTGTTGGTAATATTCGTCTATAGCCATATATGATCAAAATAGATCCTTTGTCATCAACTTTATGGTACATTCGACTCAAGATAGTTCAGCTATGAGATATATATATATATATATATATATATATATATATATATATATATATGTTTATATATTTTAATCAAACAACCCCACTTGATGGAGTCAACTTGACAACATCGTAAAGTTGACTCCGTCAAATCCAAGCCCATAAATGAGTTGTCAATTTTAAAAAAAATTGAGATTTAATATCGATTGTTTAGTTAGAAATAATTCATCTCATGCAATGTTCCTAATTACTTTTGTAGTTGGTGAGGCAAATGCGTGCAATGGGGATACAGAGCAAGGTGGTTGGTATGTTAACAAACTTCAATGATCAAAATGTGCAAATGTTTGGAGAAGCAAGAGCTAATGCCAGCACTCCAAAACCTTTGACCCGAGAGAGTTTTGTGTTCATCACTGGGATCTTGCGCCGCATGTGA
Protein sequence

>MS.gene54736.t1

MDGGTTGYKRQKKPEEKKMWIKKRELYDTPYPMNALLVDGVTATRRLEHHMLESIGIRTEPANSAQEAMQILLTGVKFDFIFVDFDLPIINGPELVRQMRAMGIQSKVVGMLTNFNDQNVQMFGEARANASTPKPLTRESFVFITGILRRM