AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71409

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71409.t1 MTR_1g075780 90.071 141 14 0 14 154 5 145 8.12e-94 268
MS.gene71409.t1 MTR_4g063510 34.463 177 70 6 17 154 13 182 1.05e-18 78.6
MS.gene71409.t1 MTR_1g075840 42.857 126 56 6 36 154 1 117 7.90e-17 72.0
MS.gene71409.t1 MTR_5g056450 35.333 150 78 6 1 142 1 139 2.97e-14 66.2
MS.gene71409.t1 MTR_1g076050 50.746 67 32 1 89 154 20 86 6.79e-14 63.9
MS.gene71409.t1 MTR_1g041455 30.137 146 89 3 14 149 13 155 4.60e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGACACATCAGTGAATT+TGG 0.236191 1.3:-54305244 MS.gene71409:CDS
TTATCCAACATGTTGATATA+TGG 0.260832 1.3:+54305300 None:intergenic
GTCCCTTGTTGGTGCATTGA+TGG 0.334927 1.3:+54305360 None:intergenic
CCATACCACCAGTCCCTTGT+TGG 0.378244 1.3:+54305349 None:intergenic
AAATTGGATGGCAAAGGGTT+GGG 0.435629 1.3:+54305492 None:intergenic
CAAAGGGTTGGGCATTGATT+CGG 0.452505 1.3:+54305503 None:intergenic
AAAATTGGATGGCAAAGGGT+TGG 0.470006 1.3:+54305491 None:intergenic
CATTGATTCGGCCTGAGGAT+TGG 0.472364 1.3:+54305515 None:intergenic
AAGCCATCTTGAGTCTCATA+TGG 0.473825 1.3:-54305574 MS.gene71409:CDS
CCAACAAGGGACTGGTGGTA+TGG 0.486031 1.3:-54305349 MS.gene71409:CDS
ATTCGGCCTGAGGATTGGTA+TGG 0.511741 1.3:+54305520 None:intergenic
TTGGGCATTGATTCGGCCTG+AGG 0.534860 1.3:+54305510 None:intergenic
CAAAATTATTGATATAGCTA+CGG 0.544419 1.3:+54305643 None:intergenic
TGGGAAAATTGGATGGCAAA+GGG 0.549995 1.3:+54305487 None:intergenic
CCTTGTTGGTGCATTGATGG+TGG 0.554951 1.3:+54305363 None:intergenic
ATTAAACCATACCAATCCTC+AGG 0.560036 1.3:-54305526 MS.gene71409:CDS
ACAACATTAGATTGTTGTTG+TGG 0.560718 1.3:+54305408 None:intergenic
ATGGAAGTCTCTCCGATCGA+TGG 0.567201 1.3:-54305330 MS.gene71409:CDS
TAAGCCATATATCAACATGT+TGG 0.587500 1.3:-54305304 MS.gene71409:CDS
ATGGGAAAATTGGATGGCAA+AGG 0.588129 1.3:+54305486 None:intergenic
TTTGGCATGGGAAAATTGGA+TGG 0.589320 1.3:+54305480 None:intergenic
TCAATGCACCAACAAGGGAC+TGG 0.598187 1.3:-54305357 MS.gene71409:CDS
CCACCATCAATGCACCAACA+AGG 0.600697 1.3:-54305363 MS.gene71409:CDS
ACAATCTAATGTTGTTGATG+TGG 0.605335 1.3:-54305400 MS.gene71409:CDS
GAGCCATATGAGACTCAAGA+TGG 0.605655 1.3:+54305571 None:intergenic
CACCATCAATGCACCAACAA+GGG 0.620275 1.3:-54305362 MS.gene71409:CDS
TATGGCTTAGTTCCATCGAT+CGG 0.625287 1.3:+54305318 None:intergenic
ATGCACCAACAAGGGACTGG+TGG 0.640658 1.3:-54305354 MS.gene71409:CDS
TCACCATCAATCAACATGAG+TGG 0.649434 1.3:-54305687 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATATCAATAATTTTGTATG+TGG - chr1.3:54305266-54305285 MS.gene71409:CDS 15.0%
!! CAAAATTATTGATATAGCTA+CGG + chr1.3:54305262-54305281 None:intergenic 20.0%
!!! TTGTTTTCATGTAATGATTT+TGG + chr1.3:54305443-54305462 None:intergenic 20.0%
! TTATCCAACATGTTGATATA+TGG + chr1.3:54305605-54305624 None:intergenic 25.0%
!! AAATAACATGCTTTTAACGA+AGG + chr1.3:54305468-54305487 None:intergenic 25.0%
ACAATCTAATGTTGTTGATG+TGG - chr1.3:54305502-54305521 MS.gene71409:CDS 30.0%
TAAGCCATATATCAACATGT+TGG - chr1.3:54305598-54305617 MS.gene71409:CDS 30.0%
! AATGAAGACATTTTTCTCGA+TGG + chr1.3:54305630-54305649 None:intergenic 30.0%
! ACAACATTAGATTGTTGTTG+TGG + chr1.3:54305497-54305516 None:intergenic 30.0%
! ATGAAGACATTTTTCTCGAT+GGG + chr1.3:54305629-54305648 None:intergenic 30.0%
!! TCATGTAATGATTTTGGCAT+GGG + chr1.3:54305437-54305456 None:intergenic 30.0%
!! TTCATGTAATGATTTTGGCA+TGG + chr1.3:54305438-54305457 None:intergenic 30.0%
ATTAAACCATACCAATCCTC+AGG - chr1.3:54305376-54305395 MS.gene71409:CDS 35.0%
CAATGACACATCAGTGAATT+TGG - chr1.3:54305658-54305677 MS.gene71409:CDS 35.0%
!! TGATTTTGGCATGGGAAAAT+TGG + chr1.3:54305429-54305448 None:intergenic 35.0%
AAAATTGGATGGCAAAGGGT+TGG + chr1.3:54305414-54305433 None:intergenic 40.0%
AAATTGGATGGCAAAGGGTT+GGG + chr1.3:54305413-54305432 None:intergenic 40.0%
AAGCCATCTTGAGTCTCATA+TGG - chr1.3:54305328-54305347 MS.gene71409:CDS 40.0%
ATGGGAAAATTGGATGGCAA+AGG + chr1.3:54305419-54305438 None:intergenic 40.0%
TATGGCTTAGTTCCATCGAT+CGG + chr1.3:54305587-54305606 None:intergenic 40.0%
TGGGAAAATTGGATGGCAAA+GGG + chr1.3:54305418-54305437 None:intergenic 40.0%
TTTGGCATGGGAAAATTGGA+TGG + chr1.3:54305425-54305444 None:intergenic 40.0%
CACCATCAATGCACCAACAA+GGG - chr1.3:54305540-54305559 MS.gene71409:CDS 45.0%
GAGCCATATGAGACTCAAGA+TGG + chr1.3:54305334-54305353 None:intergenic 45.0%
!! CAAAGGGTTGGGCATTGATT+CGG + chr1.3:54305402-54305421 None:intergenic 45.0%
ATGGAAGTCTCTCCGATCGA+TGG - chr1.3:54305572-54305591 MS.gene71409:CDS 50.0%
CCACCATCAATGCACCAACA+AGG - chr1.3:54305539-54305558 MS.gene71409:CDS 50.0%
GTCCCTTGTTGGTGCATTGA+TGG + chr1.3:54305545-54305564 None:intergenic 50.0%
TCAATGCACCAACAAGGGAC+TGG - chr1.3:54305545-54305564 MS.gene71409:CDS 50.0%
! ATTCGGCCTGAGGATTGGTA+TGG + chr1.3:54305385-54305404 None:intergenic 50.0%
! CCTTGTTGGTGCATTGATGG+TGG + chr1.3:54305542-54305561 None:intergenic 50.0%
!! CATTGATTCGGCCTGAGGAT+TGG + chr1.3:54305390-54305409 None:intergenic 50.0%
ATGCACCAACAAGGGACTGG+TGG - chr1.3:54305548-54305567 MS.gene71409:CDS 55.0%
CCATACCACCAGTCCCTTGT+TGG + chr1.3:54305556-54305575 None:intergenic 55.0%
! CCAACAAGGGACTGGTGGTA+TGG - chr1.3:54305553-54305572 MS.gene71409:CDS 55.0%
!! TTGGGCATTGATTCGGCCTG+AGG + chr1.3:54305395-54305414 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 54305230 54305694 54305230 ID=MS.gene71409
chr1.3 mRNA 54305230 54305694 54305230 ID=MS.gene71409.t1;Parent=MS.gene71409
chr1.3 exon 54305230 54305694 54305230 ID=MS.gene71409.t1.exon1;Parent=MS.gene71409.t1
chr1.3 CDS 54305230 54305694 54305230 ID=cds.MS.gene71409.t1;Parent=MS.gene71409.t1
Gene Sequence

>MS.gene71409

ATGAGTGGCGATTTCACTCAAGAGAACAACCGTAGCTATATCAATAATTTTGTATGTGGATTGTGCAATCATGATTGTACAAACTTCGAATCACTCATAAGCCATCTTGAGTCTCATATGGCTCGAGAAAATCTTGCTATTGCAAGATTAAACCATACCAATCCTCAGGCCGAATCAATGCCCAACCCTTTGCCATCCAATTTTCCCATGCCAAAATCATTACATGAAAACAAAACCTTCGTTAAAAGCATGTTATTTCAGCAACCACAACAACAATCTAATGTTGTTGATGTGGCTTCATTTTCAGCTCCACCATCAATGCACCAACAAGGGACTGGTGGTATGGAAGTCTCTCCGATCGATGGAACTAAGCCATATATCAACATGTTGGATAAACCCATCGAGAAAAATGTCTTCATTAACATCATCAATGACACATCAGTGAATTTGGAGTTAAAGCTCTAG
Protein sequence

>MS.gene71409.t1

MSGDFTQENNRSYINNFVCGLCNHDCTNFESLISHLESHMARENLAIARLNHTNPQAESMPNPLPSNFPMPKSLHENKTFVKSMLFQQPQQQSNVVDVASFSAPPSMHQQGTGGMEVSPIDGTKPYINMLDKPIEKNVFINIINDTSVNLELKL