AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0179210

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0179210 MtrunA17_Chr1g0212471 72.487 189 48 2 1 187 1 187 7.99e-95 274
Msa0179210 MtrunA17_Chr4g0022641 55.556 216 81 6 1 205 1 212 7.00e-74 228
Msa0179210 MtrunA17_Chr4g0059631 48.879 223 90 4 1 203 1 219 8.24e-62 193
Msa0179210 MtrunA17_Chr2g0303981 43.299 194 95 4 3 193 5 186 2.77e-47 154
Msa0179210 MtrunA17_Chr6g0457851 35.849 159 99 2 1 157 11 168 2.24e-32 119
Msa0179210 MtrunA17_Chr1g0212151 37.736 159 96 2 1 157 1 158 4.53e-32 119
Msa0179210 MtrunA17_Chr6g0449851 35.465 172 108 2 1 170 1 171 4.06e-31 115
Msa0179210 MtrunA17_Chr6g0449861 31.111 180 121 2 1 178 9 187 2.25e-28 109
Msa0179210 MtrunA17_Chr3g0107381 25.373 201 120 7 1 189 1 183 1.03e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0179210 AT5G55690.1 33.557 149 75 5 1 141 1 133 2.54e-14 70.1
Msa0179210 AT5G55690.2 33.557 149 75 5 1 141 1 133 2.54e-14 70.1

Find 30 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTACAATTGTATGGTCTTC+TGG 0.253429 1_4:+66635885 None:intergenic
TGGTCTTCTGGCCATGTTAT+TGG 0.266179 1_4:+66635897 None:intergenic
TCCAGTCTTGTTAGTGTATT+GGG 0.267250 1_4:+66635980 None:intergenic
TCTTCCATCTTAATTAAATC+TGG 0.297958 1_4:+66635714 None:intergenic
CTCCAGTCTTGTTAGTGTAT+TGG 0.305175 1_4:+66635979 None:intergenic
GTCGTTGACATCAAATATCT+TGG 0.367645 1_4:+66635824 None:intergenic
AGTTCGTTTGTTGAATTATG+AGG 0.398746 1_4:+66635486 None:intergenic
TCCATGTGTTGTTGCATTTG+AGG 0.399480 1_4:+66635552 None:intergenic
GCATCCAGATTTAATTAAGA+TGG 0.417713 1_4:-66635718 Msa0179210:CDS
GCATAGAGTTTACAATTGTA+TGG 0.435000 1_4:+66635877 None:intergenic
TGGAATTTGTAGAATGGGTC+GGG 0.450805 1_4:-66636090 None:intergenic
ATTAAATCTGGATGCCAAGT+TGG 0.464493 1_4:+66635726 None:intergenic
CTTGGGTGTTTCAATCACTT+TGG 0.465321 1_4:+66635842 None:intergenic
GATGATAGCTTTATGCACTT+TGG 0.469421 1_4:+66635761 None:intergenic
TGTTGAATTATGAGGCAAAC+CGG 0.479148 1_4:+66635494 None:intergenic
TTGGAATTTGTAGAATGGGT+CGG 0.500741 1_4:-66636091 None:intergenic
TGAACGACACTAAGTGGGCT+TGG 0.514956 1_4:+66635582 None:intergenic
TCCCAATACACTAACAAGAC+TGG 0.520688 1_4:-66635981 Msa0179210:CDS
TCGTTGACATCAAATATCTT+GGG 0.530959 1_4:+66635825 None:intergenic
ACCTCAAATGCAACAACACA+TGG 0.539597 1_4:-66635553 Msa0179210:CDS
ATGCTATGAACGACACTAAG+TGG 0.542543 1_4:+66635576 None:intergenic
TCGATATCATGTATCCAACT+TGG 0.557370 1_4:-66635740 Msa0179210:CDS
GATTGCTGTTATAAATGCAA+AGG 0.578620 1_4:-66635673 Msa0179210:CDS
GATGATGGTGGTAATAATGC+GGG 0.602556 1_4:-66635921 Msa0179210:CDS
GGATGATATTAGTGAGACGA+TGG 0.621537 1_4:-66635532 Msa0179210:CDS
TAACATGTTGAAAAGTGAGA+TGG 0.625075 1_4:-66635628 Msa0179210:CDS
TGCTATGAACGACACTAAGT+GGG 0.625498 1_4:+66635577 None:intergenic
ATGGATATGACTAATCATGC+CGG 0.642387 1_4:-66635513 Msa0179210:CDS
ATAATGCGGGACCAATAACA+TGG 0.644832 1_4:-66635908 Msa0179210:CDS
TGATGATGGTGGTAATAATG+CGG 0.705229 1_4:-66635922 Msa0179210:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAAATAAGAAAAAAA+TGG - chr1_4:66635748-66635767 Msa0179210:CDS 15.0%
! TCTTCCATCTTAATTAAATC+TGG + chr1_4:66635836-66635855 None:intergenic 25.0%
GCAAAAATACTTTCAAGCAA+AGG - chr1_4:66635519-66635538 Msa0179210:CDS 30.0%
ACTTTCAAGCAAAGGAAAAA+TGG - chr1_4:66635527-66635546 Msa0179210:CDS 30.0%
! TATGATGATGATGATGATGA+TGG - chr1_4:66635611-66635630 Msa0179210:CDS 30.0%
TTTACAATTGTATGGTCTTC+TGG + chr1_4:66635665-66635684 None:intergenic 30.0%
GCATAGAGTTTACAATTGTA+TGG + chr1_4:66635673-66635692 None:intergenic 30.0%
TCGTTGACATCAAATATCTT+GGG + chr1_4:66635725-66635744 None:intergenic 30.0%
GCATCCAGATTTAATTAAGA+TGG - chr1_4:66635829-66635848 Msa0179210:CDS 30.0%
! GATTGCTGTTATAAATGCAA+AGG - chr1_4:66635874-66635893 Msa0179210:CDS 30.0%
TAACATGTTGAAAAGTGAGA+TGG - chr1_4:66635919-66635938 Msa0179210:CDS 30.0%
! AGTTCGTTTGTTGAATTATG+AGG + chr1_4:66636064-66636083 None:intergenic 30.0%
!! TCCAGTCTTGTTAGTGTATT+GGG + chr1_4:66635570-66635589 None:intergenic 35.0%
!! TGATGATGGTGGTAATAATG+CGG - chr1_4:66635625-66635644 Msa0179210:CDS 35.0%
GTCGTTGACATCAAATATCT+TGG + chr1_4:66635726-66635745 None:intergenic 35.0%
!! GATGATAGCTTTATGCACTT+TGG + chr1_4:66635789-66635808 None:intergenic 35.0%
TCGATATCATGTATCCAACT+TGG - chr1_4:66635807-66635826 Msa0179210:CDS 35.0%
ATTAAATCTGGATGCCAAGT+TGG + chr1_4:66635824-66635843 None:intergenic 35.0%
ATGGATATGACTAATCATGC+CGG - chr1_4:66636034-66636053 Msa0179210:CDS 35.0%
TGTTGAATTATGAGGCAAAC+CGG + chr1_4:66636056-66636075 None:intergenic 35.0%
TCCCAATACACTAACAAGAC+TGG - chr1_4:66635566-66635585 Msa0179210:CDS 40.0%
!! CTCCAGTCTTGTTAGTGTAT+TGG + chr1_4:66635571-66635590 None:intergenic 40.0%
!! GATGATGATGATGATGATGG+TGG - chr1_4:66635614-66635633 Msa0179210:CDS 40.0%
!! GATGATGGTGGTAATAATGC+GGG - chr1_4:66635626-66635645 Msa0179210:CDS 40.0%
ATAATGCGGGACCAATAACA+TGG - chr1_4:66635639-66635658 Msa0179210:CDS 40.0%
CTTGGGTGTTTCAATCACTT+TGG + chr1_4:66635708-66635727 None:intergenic 40.0%
TGCTATGAACGACACTAAGT+GGG + chr1_4:66635973-66635992 None:intergenic 40.0%
ATGCTATGAACGACACTAAG+TGG + chr1_4:66635974-66635993 None:intergenic 40.0%
ACCTCAAATGCAACAACACA+TGG - chr1_4:66635994-66636013 Msa0179210:CDS 40.0%
! TCCATGTGTTGTTGCATTTG+AGG + chr1_4:66635998-66636017 None:intergenic 40.0%
GGATGATATTAGTGAGACGA+TGG - chr1_4:66636015-66636034 Msa0179210:CDS 40.0%
TGGTCTTCTGGCCATGTTAT+TGG + chr1_4:66635653-66635672 None:intergenic 45.0%
! TGAACGACACTAAGTGGGCT+TGG + chr1_4:66635968-66635987 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 66635470 66636099 66635470 ID=Msa0179210;Name=Msa0179210
chr1_4 mRNA 66635470 66636099 66635470 ID=Msa0179210-mRNA-1;Parent=Msa0179210;Name=Msa0179210-mRNA-1;_AED=0.26;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|209
chr1_4 exon 66635470 66636099 66635470 ID=Msa0179210-mRNA-1:exon:21895;Parent=Msa0179210-mRNA-1
chr1_4 CDS 66635470 66636099 66635470 ID=Msa0179210-mRNA-1:cds;Parent=Msa0179210-mRNA-1
Gene Sequence

>Msa0179210

ATGGGTCGGGCGAAAATAACTATGAAATACATCAAAAATAAGAAAAATCGCAAAAATACTTTCAAGCAAAGGAAAAATGGACTCATAAAGAAAATTTCCCAATACACTAACAAGACTGGAGCAAAAGCTTGCTTGATTGTGTATGATGATGATGATGATGATGGTGGTAATAATGCGGGACCAATAACATGGCCAGAAGACCATACAATTGTAAACTCTATGCTTCAAGAGTTTACCAAAGTGATTGAAACACCCAAGATATTTGATGTCAACGACTACTTTGAAAATAAGAAAAAAATGGTTGAAACTGAGATTACCAAAGTGCATAAAGCTATCATCGATATCATGTATCCAACTTGGCATCCAGATTTAATTAAGATGGAAGAGAGTGAACTCAAAGACTTGATTGCTGTTATAAATGCAAAGGTAGATGCTTGTAATCTCAAAATTAACATGTTGAAAAGTGAGATGGTGAAAGAGAATGTTGTTTTGAATCCAAGCCCACTTAGTGTCGTTCATAGCATACCTCAAATGCAACAACACATGGATGATATTAGTGAGACGATGGATATGACTAATCATGCCGGTTTGCCTCATAATTCAACAAACGAACTTGATTTAAACACATGA
Protein sequence

>Msa0179210

MGRAKITMKYIKNKKNRKNTFKQRKNGLIKKISQYTNKTGAKACLIVYDDDDDDGGNNAGPITWPEDHTIVNSMLQEFTKVIETPKIFDVNDYFENKKKMVETEITKVHKAIIDIMYPTWHPDLIKMEESELKDLIAVINAKVDACNLKINMLKSEMVKENVVLNPSPLSVVHSIPQMQQHMDDISETMDMTNHAGLPHNSTNELDLNT*