AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001097

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001097 MtrunA17_Chr1g0159291 80.220 91 17 1 42 132 1 90 1.75e-46 146
MsaG001097 MtrunA17_Chr1g0195851 35.484 124 78 1 9 132 3 124 1.15e-20 83.6
MsaG001097 MtrunA17_Chr4g0076381 38.202 89 55 0 44 132 58 146 6.72e-20 82.8
MsaG001097 MtrunA17_Chr3g0102351 37.500 104 64 1 44 147 27 129 7.26e-20 81.6
MsaG001097 MtrunA17_Chr1g0185911 38.947 95 58 0 38 132 23 117 9.63e-20 80.9
MsaG001097 MtrunA17_Chr7g0263601 35.714 112 69 1 44 152 26 137 3.72e-19 79.3
MsaG001097 MtrunA17_Chr8g0382931 37.736 106 65 1 44 149 28 132 5.43e-19 79.3
MsaG001097 MtrunA17_Chr4g0076321 40.698 86 51 0 47 132 22 107 5.51e-19 77.8
MsaG001097 MtrunA17_Chr1g0165041 40.449 89 53 0 44 132 6 94 6.21e-19 79.0
MsaG001097 MtrunA17_Chr2g0290491 39.362 94 56 1 44 137 17 109 6.60e-19 78.6
MsaG001097 MtrunA17_Chr5g0446491 40.449 89 53 0 44 132 23 111 9.42e-19 78.6
MsaG001097 MtrunA17_Chr2g0296321 33.929 112 63 1 21 132 54 154 1.16e-17 77.0
MsaG001097 MtrunA17_Chr8g0384451 40.000 90 54 0 44 133 40 129 1.51e-17 75.9
MsaG001097 MtrunA17_Chr4g0067091 34.579 107 70 0 26 132 4 110 2.49e-17 75.5
MsaG001097 MtrunA17_Chr1g0191981 35.714 84 54 0 49 132 9 92 3.63e-17 72.8
MsaG001097 MtrunA17_Chr1g0159271 41.935 93 53 1 58 149 1 93 2.05e-15 67.8
MsaG001097 MtrunA17_Chr1g0158951 39.535 86 38 1 80 151 25 110 1.15e-14 65.9
MsaG001097 MtrunA17_Chr5g0446601 32.941 85 57 0 49 133 29 113 1.09e-13 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001097 AT2G38880.7 39.623 106 63 1 44 148 21 126 3.83e-21 84.0
MsaG001097 AT3G53340.5 39.640 111 64 1 44 151 29 139 8.38e-21 84.0
MsaG001097 AT3G53340.1 39.640 111 64 1 44 151 29 139 8.38e-21 84.0
MsaG001097 AT2G38880.3 38.889 108 63 1 44 148 21 128 9.19e-21 82.8
MsaG001097 AT2G38880.2 38.889 108 63 1 44 148 21 128 9.73e-21 82.8
MsaG001097 AT2G38880.1 38.889 108 63 1 44 148 21 128 9.73e-21 82.8
MsaG001097 AT2G38880.5 38.889 108 63 1 44 148 21 128 9.73e-21 82.8
MsaG001097 AT2G37060.2 38.739 111 65 1 44 151 30 140 2.54e-20 82.4
MsaG001097 AT2G37060.3 38.739 111 65 1 44 151 30 140 2.54e-20 82.4
MsaG001097 AT2G37060.1 38.739 111 65 1 44 151 30 140 2.54e-20 82.4
MsaG001097 AT2G47810.1 37.374 99 62 0 34 132 41 139 2.23e-19 79.7
MsaG001097 AT4G14540.1 40.449 89 53 0 44 132 21 109 2.25e-19 79.7
MsaG001097 AT2G38880.4 40.449 89 53 0 44 132 21 109 2.66e-19 78.2
MsaG001097 AT5G47640.1 41.573 89 52 0 44 132 27 115 5.97e-19 79.3
MsaG001097 AT2G38880.11 40.449 89 53 0 44 132 21 109 6.32e-19 78.6
MsaG001097 AT2G38880.8 40.449 89 53 0 44 132 21 109 6.32e-19 78.6
MsaG001097 AT1G21970.1 32.432 148 83 2 1 132 1 147 1.69e-18 79.3
MsaG001097 AT2G38880.9 40.449 89 53 0 44 132 21 109 2.08e-18 77.0
MsaG001097 AT2G38880.10 40.449 89 53 0 44 132 21 109 2.08e-18 77.0
MsaG001097 AT2G38880.6 40.449 89 53 0 44 132 21 109 2.08e-18 77.0
MsaG001097 AT3G53340.4 41.573 89 52 0 44 132 29 117 4.16e-18 75.5
MsaG001097 AT5G47670.2 35.000 100 65 0 44 143 29 128 5.67e-18 77.0
MsaG001097 AT5G47670.1 35.000 100 65 0 44 143 58 157 1.15e-17 77.0
MsaG001097 AT5G47670.3 35.000 100 65 0 44 143 58 157 1.15e-17 77.0
MsaG001097 AT3G53340.3 41.573 89 52 0 44 132 29 117 8.80e-17 72.8
MsaG001097 AT3G53340.2 41.573 89 52 0 44 132 29 117 8.80e-17 72.8
MsaG001097 AT2G13570.1 40.000 90 54 0 44 133 36 125 1.74e-16 73.6
MsaG001097 AT1G09030.1 31.481 108 67 1 42 142 1 108 4.77e-16 70.5

Find 41 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGGAATCTGTTCGGTTTCT+TGG 0.253943 1:+15067522 MsaT001097.1:CDS
TGCACTTCCTCGCCCATTGC+TGG 0.310496 1:-15067288 None:intergenic
ATTTACCATGGACGATGAAT+AGG 0.379799 1:+15067490 MsaT001097.1:CDS
AGGAATCTGTTCGGTTTCTT+GGG 0.395690 1:+15067523 MsaT001097.1:CDS
GATGCTCTACATTGGCTTGT+TGG 0.407680 1:-15067446 None:intergenic
GATGAATAGGTTGGGCTTTG+AGG 0.427694 1:+15067503 MsaT001097.1:CDS
ACCAACAACAACACTGGCAT+TGG 0.458777 1:+15067243 MsaT001097.1:CDS
CCATGGACGATGAATAGGTT+GGG 0.462368 1:+15067495 MsaT001097.1:CDS
TCCAATGCCAGTGTTGTTGT+TGG 0.470529 1:-15067244 None:intergenic
TCAACGTTGGTCATCATCAT+TGG 0.472149 1:-15067607 None:intergenic
GACTCTTGTCACGTGACTGA+TGG 0.479441 1:-15067319 None:intergenic
CGCAACCACATGGATGGGTC+AGG 0.482696 1:+15067564 MsaT001097.1:CDS
AACTATCGCAACCACATGGA+TGG 0.490022 1:+15067558 MsaT001097.1:CDS
CAACATTCAACTCCAGCAAT+GGG 0.504417 1:+15067276 MsaT001097.1:CDS
CCATTGCTGGAGTTGAATGT+TGG 0.510977 1:-15067275 None:intergenic
GCCAGTGTTGTTGTTGGTGG+CGG 0.514598 1:-15067238 None:intergenic
AATGCCAGTGTTGTTGTTGG+TGG 0.520685 1:-15067241 None:intergenic
CGTTCGACACAATCAAGATC+TGG 0.523771 1:+15066142 MsaT001097.1:CDS
TCATCAGTGATTATTGTGTC+TGG 0.528332 1:-15067360 None:intergenic
TGGGCTTTGAGGAATCTGTT+CGG 0.532618 1:+15067514 MsaT001097.1:CDS
ATGGATGGGTCAGGTGCTAG+TGG 0.541112 1:+15067573 MsaT001097.1:CDS
ACCATGGACGATGAATAGGT+TGG 0.547202 1:+15067494 MsaT001097.1:CDS
CCAACATTCAACTCCAGCAA+TGG 0.549683 1:+15067275 MsaT001097.1:CDS
ATTCTCTTGATGCTCTACAT+TGG 0.555958 1:-15067454 None:intergenic
CGAACGGTTGTTGTTAGATG+AGG 0.556426 1:-15066125 None:intergenic
AATAATCACTGATGATGCTA+AGG 0.558102 1:+15067368 MsaT001097.1:CDS
TTCAACTCCAGCAATGGGCG+AGG 0.564498 1:+15067281 MsaT001097.1:CDS
ACTCTTGTCACGTGACTGAT+GGG 0.569137 1:-15067318 None:intergenic
CCCAACCTATTCATCGTCCA+TGG 0.569851 1:-15067495 None:intergenic
TGTTAATTTCATATCAACGT+TGG 0.572546 1:-15067620 None:intergenic
TGTGTCTAAATTTATGAACA+AGG 0.573477 1:+15067407 MsaT001097.1:CDS
GAACGGTTGTTGTTAGATGA+GGG 0.584819 1:-15066124 None:intergenic
CAGATCTTGATTGTGTCGAA+CGG 0.594407 1:-15066141 None:intergenic
ACCGCCACCAACAACAACAC+TGG 0.598342 1:+15067237 MsaT001097.1:CDS
TCCTGAAGTAATATGGAGCG+TGG 0.600798 1:+15066097 None:intergenic
ACTATCGCAACCACATGGAT+GGG 0.604393 1:+15067559 MsaT001097.1:CDS
TATGAACAAGGTCACAAGTG+AGG 0.614031 1:+15067419 MsaT001097.1:CDS
TTTCCGCTGATGATTTACCA+TGG 0.630530 1:+15067478 MsaT001097.1:CDS
TCAGTGATTATTGTGTCTGG+TGG 0.634070 1:-15067357 None:intergenic
CGTCCATGGTAAATCATCAG+CGG 0.677500 1:-15067481 None:intergenic
TAGCACCTGACCCATCCATG+TGG 0.736156 1:-15067569 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 15066109 15067629 15066109 ID=MsaG001097
Chr1 mRNA 15066109 15067629 15066109 ID=MsaT001097.1;Parent=MsaG001097
Chr1 exon 15066109 15066163 15066109 ID=MsaT001097.1.exon1;Parent=MsaT001097.1
Chr1 CDS 15066109 15066163 15066109 ID=cds.MsaT001097.1;Parent=MsaT001097.1
Chr1 exon 15067226 15067629 15067226 ID=MsaT001097.1.exon2;Parent=MsaT001097.1
Chr1 CDS 15067226 15067629 15067226 ID=cds.MsaT001097.1;Parent=MsaT001097.1
Gene Sequence

>MsaT001097.1

ATGGAGCGTGGAAGTCCCTCATCTAACAACAACCGTTCGACACAATCAAGATCTGCTGAAGGAAACACCGCCACCAACAACAACACTGGCATTGGAACTGAGAACCAACATTCAACTCCAGCAATGGGCGAGGAAGTGCATGTGATTCCCATCAGTCACGTGACAAGAGTCATGCAGAATGTTCTTCCACCAGACACAATAATCACTGATGATGCTAAGGAGTTAATGCAATTGTTTGTGTCTAAATTTATGAACAAGGTCACAAGTGAGGCTTTCCAACAAGCCAATGTAGAGCATCAAGAGAATGTTTCCGCTGATGATTTACCATGGACGATGAATAGGTTGGGCTTTGAGGAATCTGTTCGGTTTCTTGGGAAATACCTCAAAAACTATCGCAACCACATGGATGGGTCAGGTGCTAGTGGCTCAAACAATGCCAATGATGATGACCAACGTTGA
Protein sequence

>MsaT001097.1

MERGSPSSNNNRSTQSRSAEGNTATNNNTGIGTENQHSTPAMGEEVHVIPISHVTRVMQNVLPPDTIITDDAKELMQLFVSKFMNKVTSEAFQQANVEHQENVSADDLPWTMNRLGFEESVRFLGKYLKNYRNHMDGSGASGSNNANDDDQR*