AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85036

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85036.t1 MTR_4g130640 86.928 153 17 2 1 150 1 153 5.53e-92 264
MS.gene85036.t1 MTR_7g069410 45.033 151 41 5 1 150 1 110 6.04e-28 100
MS.gene85036.t1 MTR_6g023775 41.237 97 23 2 80 142 65 161 2.00e-13 64.3
MS.gene85036.t1 MTR_7g031710 70.270 37 11 0 113 149 42 78 4.18e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTTGAAAAGAAATAAAA+TGG 0.207796 4.2:-67844763 MS.gene85036:CDS
GAAATAAAATGGATCGAAAA+AGG 0.213477 4.2:-67844752 MS.gene85036:CDS
CATCATGTTCTGAGAGAAAT+TGG 0.219553 4.2:-67844806 MS.gene85036:CDS
CTAGTAACACTTTCTTCTAT+TGG 0.245408 4.2:+67845026 None:intergenic
TAGTGGTTTACTATCATCTT+GGG 0.287206 4.2:+67844983 None:intergenic
TTTCACTTATTGAAAATTGC+TGG 0.358067 4.2:-67844852 MS.gene85036:CDS
AATTGCTGGTGAAGGAGTTC+AGG 0.416502 4.2:-67844838 MS.gene85036:CDS
TGAGTTATCTTTAGATGAAC+CGG 0.418024 4.2:-67844676 MS.gene85036:CDS
GCTACAATGTTCTTTGATGA+TGG 0.418641 4.2:-67844645 MS.gene85036:CDS
CTGCAGGTGGAAACAAGCTT+TGG 0.435890 4.2:-67844926 MS.gene85036:CDS
TAGAAGAAAGTGTTACTAGT+TGG 0.440821 4.2:-67845022 MS.gene85036:CDS
AACATTGTAGCCTCCAACTC+CGG 0.456994 4.2:+67844657 None:intergenic
ATAGTGGTTTACTATCATCT+TGG 0.457884 4.2:+67844982 None:intergenic
ATCTTTAGATGAACCGGAGT+TGG 0.478188 4.2:-67844670 MS.gene85036:CDS
GTAACACTTTCTTCTATTGG+AGG 0.479958 4.2:+67845029 None:intergenic
AAGATGATAGTAAACCACTA+TGG 0.482539 4.2:-67844980 MS.gene85036:CDS
TTTAGATGAACCGGAGTTGG+AGG 0.500804 4.2:-67844667 MS.gene85036:CDS
ATGTTCTTTGATGATGGAAA+CGG 0.513119 4.2:-67844639 MS.gene85036:CDS
GTGCATACTAATGTTGGAGT+TGG 0.524300 4.2:-67844711 MS.gene85036:CDS
GTTTATGTGCATACTAATGT+TGG 0.532305 4.2:-67844717 MS.gene85036:CDS
TCCTCTGAAGTAGTGAATGT+TGG 0.537803 4.2:-67844588 MS.gene85036:CDS
AGTGGTTTACTATCATCTTG+GGG 0.567164 4.2:+67844984 None:intergenic
AGAGGAAACACGGATTGTAT+CGG 0.567785 4.2:+67844605 None:intergenic
TTATTGAAAATTGCTGGTGA+AGG 0.583272 4.2:-67844846 MS.gene85036:CDS
TTCTTTGATGATGGAAACGG+AGG 0.597380 4.2:-67844636 MS.gene85036:CDS
GTGCAGAATAATGATTCTGC+AGG 0.611185 4.2:-67844942 MS.gene85036:CDS
CAGAATAATGATTCTGCAGG+TGG 0.615421 4.2:-67844939 MS.gene85036:CDS
TGATGATGGAAACGGAGGAG+AGG 0.621097 4.2:-67844631 MS.gene85036:CDS
TCCAACATTCACTACTTCAG+AGG 0.626874 4.2:+67844587 None:intergenic
TCACTACTTCAGAGGAAACA+CGG 0.630269 4.2:+67844595 None:intergenic
ACAGTGACAAATCTCCATAG+TGG 0.653867 4.2:+67844966 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCTTTGAAAAGAAATAAAA+TGG - chr4.2:67844850-67844869 MS.gene85036:CDS 15.0%
!! AAATAAAATGGATCGAAAAA+GGG - chr4.2:67844862-67844881 MS.gene85036:CDS 20.0%
! GAAATAAAATGGATCGAAAA+AGG - chr4.2:67844861-67844880 MS.gene85036:CDS 25.0%
! TTTCACTTATTGAAAATTGC+TGG - chr4.2:67844761-67844780 MS.gene85036:CDS 25.0%
AAGATGATAGTAAACCACTA+TGG - chr4.2:67844633-67844652 MS.gene85036:CDS 30.0%
ATAGTGGTTTACTATCATCT+TGG + chr4.2:67844634-67844653 None:intergenic 30.0%
CTAGTAACACTTTCTTCTAT+TGG + chr4.2:67844590-67844609 None:intergenic 30.0%
GTTTATGTGCATACTAATGT+TGG - chr4.2:67844896-67844915 MS.gene85036:CDS 30.0%
TAGTGGTTTACTATCATCTT+GGG + chr4.2:67844633-67844652 None:intergenic 30.0%
TGAGTTATCTTTAGATGAAC+CGG - chr4.2:67844937-67844956 MS.gene85036:CDS 30.0%
TTATTGAAAATTGCTGGTGA+AGG - chr4.2:67844767-67844786 MS.gene85036:CDS 30.0%
!! ATGTTCTTTGATGATGGAAA+CGG - chr4.2:67844974-67844993 MS.gene85036:CDS 30.0%
!! TAGAAGAAAGTGTTACTAGT+TGG - chr4.2:67844591-67844610 MS.gene85036:CDS 30.0%
AGTGGTTTACTATCATCTTG+GGG + chr4.2:67844632-67844651 None:intergenic 35.0%
GCTACAATGTTCTTTGATGA+TGG - chr4.2:67844968-67844987 MS.gene85036:CDS 35.0%
GTAACACTTTCTTCTATTGG+AGG + chr4.2:67844587-67844606 None:intergenic 35.0%
! ACTTTTGTCAAAAAGAGGTG+AGG - chr4.2:67844717-67844736 MS.gene85036:CDS 35.0%
! GTGCAACTTTTGTCAAAAAG+AGG - chr4.2:67844712-67844731 MS.gene85036:CDS 35.0%
!! CATCATGTTCTGAGAGAAAT+TGG - chr4.2:67844807-67844826 MS.gene85036:CDS 35.0%
ACAGTGACAAATCTCCATAG+TGG + chr4.2:67844650-67844669 None:intergenic 40.0%
ATCTTTAGATGAACCGGAGT+TGG - chr4.2:67844943-67844962 MS.gene85036:CDS 40.0%
CAGAATAATGATTCTGCAGG+TGG - chr4.2:67844674-67844693 MS.gene85036:CDS 40.0%
GTGCAGAATAATGATTCTGC+AGG - chr4.2:67844671-67844690 MS.gene85036:CDS 40.0%
GTGCATACTAATGTTGGAGT+TGG - chr4.2:67844902-67844921 MS.gene85036:CDS 40.0%
TCACTACTTCAGAGGAAACA+CGG + chr4.2:67845021-67845040 None:intergenic 40.0%
TCCAACATTCACTACTTCAG+AGG + chr4.2:67845029-67845048 None:intergenic 40.0%
TCGAAAAAGGGCTGAAGATT+TGG - chr4.2:67844874-67844893 MS.gene85036:CDS 40.0%
! AGAGGAAACACGGATTGTAT+CGG + chr4.2:67845011-67845030 None:intergenic 40.0%
!! TCCTCTGAAGTAGTGAATGT+TGG - chr4.2:67845025-67845044 MS.gene85036:CDS 40.0%
!! TTCTTTGATGATGGAAACGG+AGG - chr4.2:67844977-67844996 MS.gene85036:CDS 40.0%
AACATTGTAGCCTCCAACTC+CGG + chr4.2:67844959-67844978 None:intergenic 45.0%
AATTGCTGGTGAAGGAGTTC+AGG - chr4.2:67844775-67844794 MS.gene85036:CDS 45.0%
TTTAGATGAACCGGAGTTGG+AGG - chr4.2:67844946-67844965 MS.gene85036:CDS 45.0%
CTGCAGGTGGAAACAAGCTT+TGG - chr4.2:67844687-67844706 MS.gene85036:CDS 50.0%
!! TGATGATGGAAACGGAGGAG+AGG - chr4.2:67844982-67845001 MS.gene85036:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 67844581 67845054 67844581 ID=MS.gene85036
chr4.2 mRNA 67844581 67845054 67844581 ID=MS.gene85036.t1;Parent=MS.gene85036
chr4.2 exon 67844581 67845054 67844581 ID=MS.gene85036.t1.exon1;Parent=MS.gene85036.t1
chr4.2 CDS 67844581 67845054 67844581 ID=cds.MS.gene85036.t1;Parent=MS.gene85036.t1
Gene Sequence

>MS.gene85036

ATGCCTCCAATAGAAGAAAGTGTTACTAGTTGGTTTGCTTCAAAAGAACCCCAAGATGATAGTAAACCACTATGGAGATTTGTCACTGTTGTGCAGAATAATGATTCTGCAGGTGGAAACAAGCTTTGGAAGTGCAACTTTTGTCAAAAAGAGGTGAGGAGTTCATACTCTATAGCGAGATTTCACTTATTGAAAATTGCTGGTGAAGGAGTTCAGGTATGTTCTTCATCATGTTCTGAGAGAAATTGGAGTACTTACTCTTTTATTCAATCTTTGAAAAGAAATAAAATGGATCGAAAAAGGGCTGAAGATTTGGTTTATGTGCATACTAATGTTGGAGTTGGAATTGAATTAGCTGAGTTATCTTTAGATGAACCGGAGTTGGAGGCTACAATGTTCTTTGATGATGGAAACGGAGGAGAGGAGACCGATACAATCCGTGTTTCCTCTGAAGTAGTGAATGTTGGACTATGA
Protein sequence

>MS.gene85036.t1

MPPIEESVTSWFASKEPQDDSKPLWRFVTVVQNNDSAGGNKLWKCNFCQKEVRSSYSIARFHLLKIAGEGVQVCSSSCSERNWSTYSFIQSLKRNKMDRKRAEDLVYVHTNVGVGIELAELSLDEPELEATMFFDDGNGGEETDTIRVSSEVVNVGL