AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1355890

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1355890 MtrunA17_Chr3g0135901 100.000 110 0 0 1 110 1 110 1.29e-74 216
Msa1355890 MtrunA17_Chr4g0071001 55.906 127 35 5 1 110 1 123 6.70e-35 116
Msa1355890 MtrunA17_Chr1g0151181 67.241 116 30 5 1 108 1 116 5.05e-32 108
Msa1355890 MtrunA17_Chr2g0329951 49.541 109 44 4 6 109 4 106 3.69e-26 93.6
Msa1355890 MtrunA17_Chr8g0342841 50.495 101 49 1 6 106 4 103 5.42e-22 83.2
Msa1355890 MtrunA17_Chr8g0342831 50.495 101 49 1 6 106 4 103 5.42e-22 83.2
Msa1355890 MtrunA17_Chr7g0269811 46.667 60 32 0 51 110 32 91 4.15e-14 62.4
Msa1355890 MtrunA17_Chr1g0195031 42.373 59 34 0 52 110 48 106 7.54e-13 59.7
Msa1355890 MtrunA17_Chr1g0201581 54.386 57 21 2 56 110 35 88 3.34e-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
Msa1355890 AT5G11970.1 59.091 110 39 3 1 110 1 104 1.86e-35 117
Msa1355890 AT2G19460.1 45.455 121 46 5 1 107 1 115 4.28e-21 81.6
Msa1355890 AT2G19460.2 45.455 121 46 5 1 107 53 167 2.02e-20 81.3
Msa1355890 AT2G47480.1 51.613 62 27 1 50 108 47 108 5.95e-15 65.5
Msa1355890 AT3G13910.1 58.621 58 23 1 45 101 40 97 2.57e-14 63.9
Msa1355890 AT3G13910.2 58.621 58 23 1 45 101 40 97 5.56e-14 63.2
Msa1355890 AT1G72720.1 62.222 45 17 0 65 109 81 125 6.50e-14 63.5
Msa1355890 AT3G62640.1 51.111 45 22 0 65 109 66 110 6.38e-13 60.5
Msa1355890 AT3G05725.1 35.115 131 55 7 1 109 1 123 1.66e-12 59.7
Msa1355890 AT4G09890.1 53.846 39 18 0 66 104 39 77 5.75e-11 54.7

Find 21 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGTACTCACAGGTGGTTTA+TGG 0.228498 tig0015247:-36078 Msa1355890:CDS
CTCTTCTTCCTCTGAAGTTC+AGG 0.289847 tig0015247:+36180 None:intergenic
AGCTTTCTATCTGCATCATT+TGG 0.373432 tig0015247:+36343 None:intergenic
TATAAAATGTATTCTGTTGA+AGG 0.385236 tig0015247:-36147 Msa1355890:CDS
CTAAGATCATAAGGCTTAGA+TGG 0.404348 tig0015247:+36312 None:intergenic
ATGCAGATAGAAAGCTACTA+TGG 0.407129 tig0015247:-36336 Msa1355890:CDS
TATCTGCATCATTTGGCCAT+TGG 0.440208 tig0015247:+36350 None:intergenic
CTATAGCTTCTAAGATCATA+AGG 0.444134 tig0015247:+36303 None:intergenic
CTGAACTTCAGAGGAAGAAG+AGG 0.478478 tig0015247:-36179 Msa1355890:CDS
TTCTTCAACTTCAAATCCTT+AGG 0.481282 tig0015247:+36258 None:intergenic
AAGGATTTGAAGTTGAAGAA+AGG 0.511800 tig0015247:-36255 Msa1355890:CDS
CTTAGGAGTTTGTTGTACAT+AGG 0.522202 tig0015247:+36275 None:intergenic
CTATGTACAACAAACTCCTA+AGG 0.555597 tig0015247:-36274 Msa1355890:CDS
TCTGTTGAAGGCAAAGTCAA+AGG 0.571369 tig0015247:-36135 Msa1355890:CDS
CTTTCAGAAAGAGTTTCAGA+TGG 0.576426 tig0015247:-36110 Msa1355890:CDS
ACTCACAGGTGGTTTATGGT+TGG 0.580184 tig0015247:-36074 Msa1355890:CDS
TGTCTGATCCTGAACTTCAG+AGG 0.591643 tig0015247:-36188 Msa1355890:CDS
AGATCAAAATCTTATGCCAA+TGG 0.604385 tig0015247:-36366 Msa1355890:CDS
GCTTAAGAACAAGTACTCAC+AGG 0.640169 tig0015247:-36088 Msa1355890:CDS
TGAACTTCAGAGGAAGAAGA+GGG 0.657165 tig0015247:-36178 Msa1355890:CDS
TAAGAACAAGTACTCACAGG+TGG 0.685797 tig0015247:-36085 Msa1355890:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAAAATGTATTCTGTTGA+AGG - tig0015247:36305-36324 Msa1355890:CDS 20.0%
AGATCAAAATCTTATGCCAA+TGG - tig0015247:36086-36105 Msa1355890:CDS 30.0%
!! CTATAGCTTCTAAGATCATA+AGG + tig0015247:36152-36171 None:intergenic 30.0%
TTCTTCAACTTCAAATCCTT+AGG + tig0015247:36197-36216 None:intergenic 30.0%
! AAGGATTTGAAGTTGAAGAA+AGG - tig0015247:36197-36216 Msa1355890:CDS 30.0%
! AAAGGTAAAAGCTTTTCATC+TGG - tig0015247:36215-36234 Msa1355890:CDS 30.0%
AGCTTTCTATCTGCATCATT+TGG + tig0015247:36112-36131 None:intergenic 35.0%
ATGCAGATAGAAAGCTACTA+TGG - tig0015247:36116-36135 Msa1355890:CDS 35.0%
CTAAGATCATAAGGCTTAGA+TGG + tig0015247:36143-36162 None:intergenic 35.0%
!! CTTAGGAGTTTGTTGTACAT+AGG + tig0015247:36180-36199 None:intergenic 35.0%
CTATGTACAACAAACTCCTA+AGG - tig0015247:36178-36197 Msa1355890:CDS 35.0%
CTTTCAGAAAGAGTTTCAGA+TGG - tig0015247:36342-36361 Msa1355890:CDS 35.0%
TATCTGCATCATTTGGCCAT+TGG + tig0015247:36105-36124 None:intergenic 40.0%
TGAACTTCAGAGGAAGAAGA+GGG - tig0015247:36274-36293 Msa1355890:CDS 40.0%
TCTGTTGAAGGCAAAGTCAA+AGG - tig0015247:36317-36336 Msa1355890:CDS 40.0%
GCTTAAGAACAAGTACTCAC+AGG - tig0015247:36364-36383 Msa1355890:CDS 40.0%
TAAGAACAAGTACTCACAGG+TGG - tig0015247:36367-36386 Msa1355890:CDS 40.0%
AAGTACTCACAGGTGGTTTA+TGG - tig0015247:36374-36393 Msa1355890:CDS 40.0%
TGTCTGATCCTGAACTTCAG+AGG - tig0015247:36264-36283 Msa1355890:CDS 45.0%
!! CTCTTCTTCCTCTGAAGTTC+AGG + tig0015247:36275-36294 None:intergenic 45.0%
CTGAACTTCAGAGGAAGAAG+AGG - tig0015247:36273-36292 Msa1355890:CDS 45.0%
ACTCACAGGTGGTTTATGGT+TGG - tig0015247:36378-36397 Msa1355890:CDS 45.0%
Chromosome Type Strat End Strand Name
tig0015247 gene 36071 36403 36071 ID=Msa1355890;Name=Msa1355890
tig0015247 mRNA 36071 36403 36071 ID=Msa1355890-mRNA-1;Parent=Msa1355890;Name=Msa1355890-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|110
tig0015247 exon 36071 36403 36071 ID=Msa1355890-mRNA-1:exon:9647;Parent=Msa1355890-mRNA-1
tig0015247 CDS 36071 36403 36071 ID=Msa1355890-mRNA-1:cds;Parent=Msa1355890-mRNA-1
Gene Sequence

>Msa1355890

ATGGAAGATTTTCAGAGATCAAAATCTTATGCCAATGGCCAAATGATGCAGATAGAAAGCTACTATGGACCATCTAAGCCTTATGATCTTAGAAGCTATAGTTCTTCCTATGTACAACAAACTCCTAAGGATTTGAAGTTGAAGAAAGGTAAAAGCTTTTCATCTGGTTCTTCTTTTTCGAAGTCTTTGAGTTTGTCTGATCCTGAACTTCAGAGGAAGAAGAGGGTTGCTAGCTATAAAATGTATTCTGTTGAAGGCAAAGTCAAAGGATCTTTCAGAAAGAGTTTCAGATGGCTTAAGAACAAGTACTCACAGGTGGTTTATGGTTGGTAG
Protein sequence

>Msa1355890

MEDFQRSKSYANGQMMQIESYYGPSKPYDLRSYSSSYVQQTPKDLKLKKGKSFSSGSSFSKSLSLSDPELQRKKRVASYKMYSVEGKVKGSFRKSFRWLKNKYSQVVYGW*