AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040533

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040533.t1 MTR_2g068760 98.851 87 1 0 1 87 73 159 1.92e-59 179
MS.gene040533.t1 MTR_4g083680 63.636 77 21 2 1 70 75 151 3.49e-25 92.4
MS.gene040533.t1 MTR_4g060950 72.917 48 13 0 1 48 85 132 1.01e-18 76.3
MS.gene040533.t1 MTR_1g095850 72.917 48 13 0 1 48 132 179 5.93e-18 75.1
MS.gene040533.t1 MTR_2g093310 40.594 101 44 2 1 85 93 193 3.27e-17 72.4
MS.gene040533.t1 MTR_5g083230 73.913 46 12 0 1 46 66 111 4.48e-17 71.6
MS.gene040533.t1 MTR_3g031660 66.667 51 17 0 1 51 67 117 4.81e-17 71.6
MS.gene040533.t1 MTR_3g071590 71.739 46 13 0 1 46 68 113 1.42e-16 70.1
MS.gene040533.t1 MTR_3g094690 56.250 48 21 0 1 48 107 154 7.34e-14 64.3
MS.gene040533.t1 MTR_3g094690 56.250 48 21 0 1 48 106 153 7.64e-14 64.3
MS.gene040533.t1 MTR_3g077240 47.368 76 40 0 1 76 70 145 2.60e-13 62.0
MS.gene040533.t1 MTR_5g083960 47.761 67 26 1 1 67 99 156 1.63e-12 60.1
MS.gene040533.t1 MTR_4g105170 49.206 63 29 1 1 63 71 130 2.89e-12 59.3
MS.gene040533.t1 MTR_6g005070 52.941 51 23 1 1 51 69 118 4.17e-12 58.2
MS.gene040533.t1 MTR_7g096530 58.140 43 18 0 1 43 75 117 4.61e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040533.t1 AT1G16530 47.368 95 36 4 1 86 75 164 4.77e-20 79.0
MS.gene040533.t1 AT1G31320 85.417 48 7 0 1 48 73 120 2.82e-17 72.0
MS.gene040533.t1 AT2G30130 63.158 57 19 1 1 55 68 124 2.66e-16 70.1
MS.gene040533.t1 AT1G07900 64.583 48 17 0 1 48 93 140 1.64e-15 67.8
MS.gene040533.t1 AT2G28500 62.000 50 19 0 1 50 115 164 1.48e-14 66.2
MS.gene040533.t1 AT5G63090 60.870 46 18 0 1 46 71 116 4.18e-13 61.6
MS.gene040533.t1 AT5G63090 60.870 46 18 0 1 46 71 116 4.18e-13 61.6
MS.gene040533.t1 AT5G63090 60.870 46 18 0 1 46 71 116 4.18e-13 61.6
MS.gene040533.t1 AT5G63090 60.870 46 18 0 1 46 71 116 4.18e-13 61.6
MS.gene040533.t1 AT2G30340 45.098 51 28 0 1 51 112 162 4.20e-12 60.1
MS.gene040533.t1 AT2G30340 45.098 51 28 0 1 51 113 163 4.27e-12 60.1

Find 17 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCTTGTGCTTGAGCTAAT+TGG 0.150837 2.3:-27239713 None:intergenic
TGCTTGTGCTTGAGCTAATT+GGG 0.350545 2.3:-27239712 None:intergenic
AAGAAAAGAACCTGCTTGAT+TGG 0.406684 2.3:-27239821 None:intergenic
ATGAAGCAAATGCAAGAGTA+AGG 0.428990 2.3:+27239625 MS.gene040533:CDS
GATGATGATCAGATGAGAAT+TGG 0.476334 2.3:-27239758 None:intergenic
AGAGTAAGGGATCCTGTGTA+TGG 0.521523 2.3:+27239639 MS.gene040533:CDS
TGAAGCAAATGCAAGAGTAA+GGG 0.570272 2.3:+27239626 MS.gene040533:CDS
AAAATGTGTACCAATCAAGC+AGG 0.584103 2.3:+27239811 MS.gene040533:CDS
GGATCCTGTGTATGGATGTG+TGG 0.591101 2.3:+27239647 MS.gene040533:CDS
AGCTAGCTAGTAAGACCACA+AGG 0.627089 2.3:-27239865 None:intergenic
GATCCTGTGTATGGATGTGT+GGG 0.634230 2.3:+27239648 MS.gene040533:CDS
ATTAGCTCAAGCACAAGCAG+AGG 0.647477 2.3:+27239716 MS.gene040533:CDS
GATGGTGGTGACGAATTCGA+TGG 0.671990 2.3:-27239786 None:intergenic
ATCTACTTGTTGCTGCAGAG+AGG 0.672706 2.3:-27239679 None:intergenic
ACAAAATGGGACAATCCTTG+TGG 0.674959 2.3:+27239850 MS.gene040533:CDS
GGTGGTGACGAATTCGATGG+TGG 0.676502 2.3:-27239783 None:intergenic
GCTCCCACACATCCATACAC+AGG 0.680929 2.3:-27239651 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTTCTTCACCAAACAAAAT+GGG + chr2.3:27239837-27239856 MS.gene040533:CDS 25.0%
! CTTTTCTTCACCAAACAAAA+TGG + chr2.3:27239836-27239855 MS.gene040533:CDS 30.0%
AAAATGTGTACCAATCAAGC+AGG + chr2.3:27239811-27239830 MS.gene040533:CDS 35.0%
AAGAAAAGAACCTGCTTGAT+TGG - chr2.3:27239824-27239843 None:intergenic 35.0%
ATGAAGCAAATGCAAGAGTA+AGG + chr2.3:27239625-27239644 MS.gene040533:CDS 35.0%
GATGATGATCAGATGAGAAT+TGG - chr2.3:27239761-27239780 None:intergenic 35.0%
TGAAGCAAATGCAAGAGTAA+GGG + chr2.3:27239626-27239645 MS.gene040533:CDS 35.0%
! AAGGATTGTCCCATTTTGTT+TGG - chr2.3:27239849-27239868 None:intergenic 35.0%
! GATTGGTACACATTTTCTGA+TGG - chr2.3:27239807-27239826 None:intergenic 35.0%
ACAAAATGGGACAATCCTTG+TGG + chr2.3:27239850-27239869 MS.gene040533:CDS 40.0%
TGCTTGTGCTTGAGCTAATT+GGG - chr2.3:27239715-27239734 None:intergenic 40.0%
! TGGTACACATTTTCTGATGG+TGG - chr2.3:27239804-27239823 None:intergenic 40.0%
AGAGTAAGGGATCCTGTGTA+TGG + chr2.3:27239639-27239658 MS.gene040533:CDS 45.0%
ATTAGCTCAAGCACAAGCAG+AGG + chr2.3:27239716-27239735 MS.gene040533:CDS 45.0%
CTGCTTGTGCTTGAGCTAAT+TGG - chr2.3:27239716-27239735 None:intergenic 45.0%
GATCCTGTGTATGGATGTGT+GGG + chr2.3:27239648-27239667 MS.gene040533:CDS 45.0%
! ATCTACTTGTTGCTGCAGAG+AGG - chr2.3:27239682-27239701 None:intergenic 45.0%
GGATCCTGTGTATGGATGTG+TGG + chr2.3:27239647-27239666 MS.gene040533:CDS 50.0%
! GATGGTGGTGACGAATTCGA+TGG - chr2.3:27239789-27239808 None:intergenic 50.0%
GCTCCCACACATCCATACAC+AGG - chr2.3:27239654-27239673 None:intergenic 55.0%
! GGTGGTGACGAATTCGATGG+TGG - chr2.3:27239786-27239805 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 27239618 27239881 27239618 ID=MS.gene040533
chr2.3 mRNA 27239618 27239881 27239618 ID=MS.gene040533.t1;Parent=MS.gene040533
chr2.3 exon 27239618 27239881 27239618 ID=MS.gene040533.t1.exon1;Parent=MS.gene040533.t1
chr2.3 CDS 27239618 27239881 27239618 ID=cds.MS.gene040533.t1;Parent=MS.gene040533.t1
Gene Sequence

>MS.gene040533

ATGGTATATGAAGCAAATGCAAGAGTAAGGGATCCTGTGTATGGATGTGTGGGAGCTATATCCTCTCTGCAGCAACAAGTAGATGTGCTACAAACCCAATTAGCTCAAGCACAAGCAGAGGTTGTGCATATGAAGATGCACCAATTCTCATCTGATCATCATCAACCACCATCGAATTCGTCACCACCATCAGAAAATGTGTACCAATCAAGCAGGTTCTTTTCTTCACCAAACAAAATGGGACAATCCTTGTGGTCTTACTAG
Protein sequence

>MS.gene040533.t1

MVYEANARVRDPVYGCVGAISSLQQQVDVLQTQLAQAQAEVVHMKMHQFSSDHHQPPSNSSPPSENVYQSSRFFSSPNKMGQSLWSY