AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025591

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025591.t1 MTR_4g039380 76.923 117 19 2 1 109 1 117 1.51e-52 160
MS.gene025591.t1 MTR_4g039340 68.702 131 19 3 1 109 1 131 1.38e-47 149
MS.gene025591.t1 MTR_4g039640 67.742 124 18 3 1 109 1 117 8.75e-45 141
MS.gene025591.t1 MTR_4g039400 41.818 110 35 2 1 109 1 82 3.38e-12 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCATTCATCTGGTGTATA+AGG 0.183369 4.4:-65604566 None:intergenic
TCGGGTTCAGGCTGGTTATT+TGG 0.220105 4.4:-65604386 None:intergenic
CTCGATTCTAATATAAAATC+TGG 0.312947 4.4:-65604347 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.358870 4.4:-65604565 None:intergenic
TCAGGCTGGTTATTTGGTGG+TGG 0.474246 4.4:-65604380 None:intergenic
TTGAGGTCGAAAGCTCGAAC+AGG 0.496472 4.4:-65604539 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.506887 4.4:-65604518 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4.4:-65604506 None:intergenic
GGTTCAGGCTGGTTATTTGG+TGG 0.524862 4.4:-65604383 None:intergenic
CGAAAGCTCGAACAGGAGGC+TGG 0.528604 4.4:-65604532 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4.4:-65604500 None:intergenic
TTGTGTCACATTCACTGCAT+AGG 0.586276 4.4:-65604274 None:intergenic
ACTGCTAAAGCTTCTCGAGA+TGG 0.596385 4.4:-65604302 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4.4:-65604556 None:intergenic
ATATTAGAATCGAGTAAACA+AGG 0.624706 4.4:+65604356 MS.gene025591:CDS
AGGTCGAAAGCTCGAACAGG+AGG 0.629084 4.4:-65604536 None:intergenic
TCAAATGGTTGCACATGTGG+AGG 0.671560 4.4:-65604503 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATATTAGAATCGAGTAAACA+AGG + chr4.4:65604356-65604375 MS.gene025591:CDS 25.0%
! CTCGATTCTAATATAAAATC+TGG - chr4.4:65604350-65604369 None:intergenic 25.0%
! TGTTGATGTTCAACATTTTG+TGG - chr4.4:65604449-65604468 None:intergenic 30.0%
! TGATGTTCAACATTTTGTGG+TGG - chr4.4:65604446-65604465 None:intergenic 35.0%
AAGTCAAATGGTTGCACATG+TGG - chr4.4:65604509-65604528 None:intergenic 40.0%
TTGTGTCACATTCACTGCAT+AGG - chr4.4:65604277-65604296 None:intergenic 40.0%
!! TCAACATTTTGTGGTGGAGT+TGG - chr4.4:65604440-65604459 None:intergenic 40.0%
ACTGCTAAAGCTTCTCGAGA+TGG - chr4.4:65604305-65604324 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG - chr4.4:65604559-65604578 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG - chr4.4:65604506-65604525 None:intergenic 45.0%
! GTTGGTGCATTTTGTGGTTG+AGG - chr4.4:65604422-65604441 None:intergenic 45.0%
! TGGTTGAGGCTGAGCATTTT+CGG - chr4.4:65604408-65604427 None:intergenic 45.0%
AATGGTTGCACATGTGGAGG+TGG - chr4.4:65604503-65604522 None:intergenic 50.0%
TTGAGGTCGAAAGCTCGAAC+AGG - chr4.4:65604542-65604561 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG - chr4.4:65604521-65604540 None:intergenic 50.0%
! GGTTCAGGCTGGTTATTTGG+TGG - chr4.4:65604386-65604405 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+GGG - chr4.4:65604407-65604426 None:intergenic 50.0%
! TCAGGCTGGTTATTTGGTGG+TGG - chr4.4:65604383-65604402 None:intergenic 50.0%
! TCGGGTTCAGGCTGGTTATT+TGG - chr4.4:65604389-65604408 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG - chr4.4:65604491-65604510 None:intergenic 50.0%
!!! GGTGGAGTTGGTGCATTTTG+TGG - chr4.4:65604428-65604447 None:intergenic 50.0%
AGGTCGAAAGCTCGAACAGG+AGG - chr4.4:65604539-65604558 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG - chr4.4:65604488-65604507 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG - chr4.4:65604482-65604501 None:intergenic 55.0%
!!! GAGCATTTTCGGGTTCAGGC+TGG - chr4.4:65604397-65604416 None:intergenic 55.0%
!!! GGCTGAGCATTTTCGGGTTC+AGG - chr4.4:65604401-65604420 None:intergenic 55.0%
CGAAAGCTCGAACAGGAGGC+TGG - chr4.4:65604535-65604554 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 65604257 65604586 65604257 ID=MS.gene025591
chr4.4 mRNA 65604257 65604586 65604257 ID=MS.gene025591.t1;Parent=MS.gene025591
chr4.4 exon 65604257 65604586 65604257 ID=MS.gene025591.t1.exon1;Parent=MS.gene025591.t1
chr4.4 CDS 65604257 65604586 65604257 ID=cds.MS.gene025591.t1;Parent=MS.gene025591.t1
Gene Sequence

>MS.gene025591

ATGTCAAAGCTAGAATTCCTATGCAGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCAGATTTTATATTAGAATCGAGTAAACAAGGTCCACCACCAAATAACCAGCCTGAACCCGAAAATGCTCAGCCTCAACCACAAAATGCACCAACTCCACCACAAAATGTTGAACATCAACAACAAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAGCCTCCTGTTCGAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>MS.gene025591.t1

MSKLEFLCSECDTMFPSREALAVHVIEEHHPDFILESSKQGPPPNNQPEPENAQPQPQNAPTPPQNVEHQQQNAPAPPQNAPPPHVQPFDLNQPPVRAFDLNLPYTPDE