AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene074049

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene074049.t1 MTR_4g123470 86.735 98 13 0 8 105 128 225 5.14e-61 186
MS.gene074049.t1 MTR_7g113060 81.081 37 7 0 67 103 3 39 1.04e-16 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGTTCATATCGCTGGATA+TGG 0.323519 6.1:+7677099 MS.gene074049:intron
CACAGTGCATGTACAAAATC+AGG 0.330296 6.1:+7676687 MS.gene074049:CDS
AATCGTGATGTTTCACTCTA+AGG 0.341127 6.1:-7677261 None:intergenic
AGGAATTTGCCAAAAGTATC+AGG 0.344083 6.1:-7677241 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 6.1:+7677232 MS.gene074049:intron
TGCAAACATCACATTTGGTA+TGG 0.417128 6.1:-7677347 None:intergenic
TACCTTGAAGTTCATATCGC+TGG 0.426647 6.1:+7677093 MS.gene074049:intron
TTGTGCTGCCAATGGTATTG+AGG 0.463000 6.1:+7677387 MS.gene074049:CDS
TTCATGTGTTTATCAACGCT+TGG 0.469883 6.1:-7677470 None:intergenic
GCAAACATCACATTTGGTAT+GGG 0.477791 6.1:-7677346 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 6.1:+7677388 MS.gene074049:CDS
CCAAATGTGATGTTTGCAAA+AGG 0.525477 6.1:+7677352 MS.gene074049:CDS
ACAAGAATGATATTGTCATA+AGG 0.528831 6.1:-7677301 None:intergenic
TTTCAAGTGCAAGTGCATCA+TGG 0.533968 6.1:+7677426 MS.gene074049:CDS
CAAACATCACATTTGGTATG+GGG 0.561110 6.1:-7677345 None:intergenic
ATGTGATGTTTGCAAAAGGT+TGG 0.562809 6.1:+7677356 MS.gene074049:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 6.1:-7677395 None:intergenic
CACGATTACGTCATGTTGTG+CGG 0.590860 6.1:+7677277 MS.gene074049:CDS
TGGATCGACGAAATCACCGA+AGG 0.700849 6.1:+7677119 MS.gene074049:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 6.1:+7677391 MS.gene074049:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTATTTAAATAAAATGAA+CGG + chr6.1:7676737-7676756 MS.gene074049:intron 10.0%
!!! AGTTTTTTTTTCTTTTTTTT+AGG + chr6.1:7677213-7677232 MS.gene074049:intron 10.0%
!! AAAAAAAAATAAACAACCTT+CGG - chr6.1:7677138-7677157 None:intergenic 15.0%
!! TTAGATATATGCTATAATAA+AGG + chr6.1:7677171-7677190 MS.gene074049:intron 15.0%
! AAATATTTAGCAACGAAGAA+TGG - chr6.1:7676812-7676831 None:intergenic 25.0%
! ACAAGAATGATATTGTCATA+AGG - chr6.1:7677304-7677323 None:intergenic 25.0%
AGTTAGGCAGAAAAAGTTTA+CGG - chr6.1:7676766-7676785 None:intergenic 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr6.1:7676891-7676910 MS.gene074049:intron 30.0%
! TAAATATTTCTACGAGCTAC+CGG + chr6.1:7676823-7676842 MS.gene074049:intron 30.0%
! TGGATACGATGACATATTTT+TGG - chr6.1:7677453-7677472 None:intergenic 30.0%
AATCGTGATGTTTCACTCTA+AGG - chr6.1:7677264-7677283 None:intergenic 35.0%
ATGTGATGTTTGCAAAAGGT+TGG + chr6.1:7677356-7677375 MS.gene074049:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr6.1:7676974-7676993 MS.gene074049:intron 35.0%
CAAACATCACATTTGGTATG+GGG - chr6.1:7677348-7677367 None:intergenic 35.0%
CCAAATGTGATGTTTGCAAA+AGG + chr6.1:7677352-7677371 MS.gene074049:CDS 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr6.1:7676944-7676963 MS.gene074049:intron 35.0%
GAACTTCAAGGTACAATAAC+AGG - chr6.1:7677086-7677105 None:intergenic 35.0%
GCAAACATCACATTTGGTAT+GGG - chr6.1:7677349-7677368 None:intergenic 35.0%
TGCAAACATCACATTTGGTA+TGG - chr6.1:7677350-7677369 None:intergenic 35.0%
! CCTTTTGCAAACATCACATT+TGG - chr6.1:7677355-7677374 None:intergenic 35.0%
! TAGGAACTACCTGATACTTT+TGG + chr6.1:7677232-7677251 MS.gene074049:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr6.1:7676994-7677013 None:intergenic 35.0%
!! ACTTTTTCTGCCTAACTTCT+AGG + chr6.1:7676769-7676788 MS.gene074049:intron 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG - chr6.1:7677244-7677263 None:intergenic 35.0%
ATCCAGCGATATGAACTTCA+AGG - chr6.1:7677098-7677117 None:intergenic 40.0%
CACAGTGCATGTACAAAATC+AGG + chr6.1:7676687-7676706 MS.gene074049:CDS 40.0%
GAAGTTCATATCGCTGGATA+TGG + chr6.1:7677099-7677118 MS.gene074049:intron 40.0%
TACCTTGAAGTTCATATCGC+TGG + chr6.1:7677093-7677112 MS.gene074049:intron 40.0%
! TTTCAAGTGCAAGTGCATCA+TGG + chr6.1:7677426-7677445 MS.gene074049:CDS 40.0%
ACCCTATCATTCCATGAGTG+CGG + chr6.1:7677054-7677073 MS.gene074049:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr6.1:7676988-7677007 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr6.1:7676977-7676996 MS.gene074049:intron 45.0%
CACGATTACGTCATGTTGTG+CGG + chr6.1:7677277-7677296 MS.gene074049:CDS 45.0%
TCTCCGACATCCTAGAAGTT+AGG - chr6.1:7676782-7676801 None:intergenic 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr6.1:7677387-7677406 MS.gene074049:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr6.1:7677379-7677398 MS.gene074049:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr6.1:7677388-7677407 MS.gene074049:CDS 45.0%
!! CTGCCTAACTTCTAGGATGT+CGG + chr6.1:7676776-7676795 MS.gene074049:intron 45.0%
AGTTAGTCGGCCGTTGTTGA+CGG + chr6.1:7676904-7676923 MS.gene074049:intron 50.0%
CTCCAACCATCCGTCAACAA+CGG - chr6.1:7676917-7676936 None:intergenic 50.0%
GCACTCATGGAATGATAGGG+TGG - chr6.1:7677055-7677074 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr6.1:7677058-7677077 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr6.1:7677059-7677078 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG + chr6.1:7677119-7677138 MS.gene074049:CDS 50.0%
! GAGCAATGGCACTTGCTAGA+TGG + chr6.1:7676845-7676864 MS.gene074049:intron 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr6.1:7676852-7676871 MS.gene074049:intron 50.0%
! TCTAGCAAGTGCCATTGCTC+CGG - chr6.1:7676845-7676864 None:intergenic 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr6.1:7676851-7676870 MS.gene074049:intron 50.0%
GTCTCCGCCCTCAATACCAT+TGG - chr6.1:7677398-7677417 None:intergenic 55.0%
TCTACGAGCTACCGGAGCAA+TGG + chr6.1:7676831-7676850 MS.gene074049:intron 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr6.1:7677391-7677410 MS.gene074049:CDS 55.0%
ACAGGATGCTGCCGCACTCA+TGG - chr6.1:7677068-7677087 None:intergenic 60.0%
AGTCGGCCGTTGTTGACGGA+TGG + chr6.1:7676908-7676927 MS.gene074049:intron 60.0%
! GGCCGTTGTTGACGGATGGT+TGG + chr6.1:7676912-7676931 MS.gene074049:intron 60.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 7676675 7677480 7676675 ID=MS.gene074049
chr6.1 mRNA 7676675 7677480 7676675 ID=MS.gene074049.t1;Parent=MS.gene074049
chr6.1 exon 7676675 7676708 7676675 ID=MS.gene074049.t1.exon1;Parent=MS.gene074049.t1
chr6.1 CDS 7676675 7676708 7676675 ID=cds.MS.gene074049.t1;Parent=MS.gene074049.t1
chr6.1 exon 7677103 7677140 7677103 ID=MS.gene074049.t1.exon2;Parent=MS.gene074049.t1
chr6.1 CDS 7677103 7677140 7677103 ID=cds.MS.gene074049.t1;Parent=MS.gene074049.t1
chr6.1 exon 7677235 7677480 7677235 ID=MS.gene074049.t1.exon3;Parent=MS.gene074049.t1
chr6.1 CDS 7677235 7677480 7677235 ID=cds.MS.gene074049.t1;Parent=MS.gene074049.t1
Gene Sequence

>MS.gene074049

ATGTTTGTTCTTCACAGTGCATGTACAAAATCAGGTTTGTTTCATTTGATGATTTAATCTTTTTCTATTTAAATAAAATGAACGGATTCCGTAAACTTTTTCTGCCTAACTTCTAGGATGTCGGAGAACTGCAACCATTCTTCGTTGCTAAATATTTCTACGAGCTACCGGAGCAATGGCACTTGCTAGATGGTGATGGGAATACTCATAACGTCATGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACGGATGGTTGGAGTGCATTGCGATTATTCTACGAGTTTAGTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACATTACTCTAGCTGATTATCCACCCTATCATTCCATGAGTGCGGCAGCATCCTGTTATTGTACCTTGAAGTTCATATCGCTGGATATGGATCGACGAAATCACCGAAGGTTGTTTATTTTTTTTTTGATGCTATTCAATTAGATATATGCTATAATAAAGGATTTTTGTCTGTCATTAACAGTTTTTTTTTCTTTTTTTTAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTGCGGACCTTATGACAATATCATTCTTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTTGCAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCATCATGGACCAAAAATATGTCATCGTATCCAAGCGTTGA
Protein sequence

>MS.gene074049.t1

MFVLHSACTKSVHIAGYGSTKSPKELPDTFGKFLRVKHHDYVMLCGPYDNIILVRLKYTDDPIPNVMFAKGWTSFCAANGIEGGDVLIFKCKCIMDQKYVIVSKR