AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0080048951.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048951.01.T01 MTR_4g123470 88.679 106 12 0 1 106 120 225 1.03e-68 205
MsG0080048951.01.T01 MTR_7g113060 86.842 38 5 0 68 105 3 40 4.91e-18 75.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGTTCCCATCGCTGGATA+TGG 0.269011 contig561end:-1391 MsG0080048951.01.T01:CDS
TAGGAACTACCTGATGCTTT+TGG 0.332739 contig561end:-1256 MsG0080048951.01.T01:CDS
AATCGTGATGCTTAACTCTA+AGG 0.346259 contig561end:+1227 None:intergenic
ACCTTTGAAGTTCCCATCGC+TGG 0.405354 contig561end:-1397 MsG0080048951.01.T01:CDS
TCCGAACATCACATCTGGTA+TGG 0.430547 contig561end:+1141 None:intergenic
AGGAATTTGCCAAAAGCATC+AGG 0.443467 contig561end:+1247 None:intergenic
CCGAACATCACATCTGGTAT+GGG 0.460591 contig561end:+1142 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 contig561end:-1101 MsG0080048951.01.T01:CDS
CCAGATGTGATGTTCGGAAA+AGG 0.491103 contig561end:-1136 MsG0080048951.01.T01:CDS
ACATGATGTTGCCGCACTCA+TGG 0.495582 contig561end:+1426 None:intergenic
CCCATACCAGATGTGATGTT+CGG 0.499659 contig561end:-1142 MsG0080048951.01.T01:CDS
TGTGCTGCCAATGGTATTGA+GGG 0.501205 contig561end:-1100 MsG0080048951.01.T01:CDS
ACAGAAATGATATTGTCATA+AGG 0.528831 contig561end:+1187 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 contig561end:-1062 MsG0080048951.01.T01:CDS
GTCGATCCATATCCAGCGAT+GGG 0.570762 contig561end:+1385 None:intergenic
TCCAGCGATGGGAACTTCAA+AGG 0.575653 contig561end:+1396 None:intergenic
CGTCGATCCATATCCAGCGA+TGG 0.575921 contig561end:+1384 None:intergenic
CATAAGGTCCGCACAACATG+AGG 0.581838 contig561end:+1203 None:intergenic
GTCTCCGCCCTCAATACCAT+TGG 0.581950 contig561end:+1093 None:intergenic
CACGATTACCTCATGTTGTG+CGG 0.605525 contig561end:-1211 MsG0080048951.01.T01:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.616871 contig561end:-1132 MsG0080048951.01.T01:CDS
ACCGTATCATTCCATGAGTG+CGG 0.643748 contig561end:-1437 None:intergenic
CGAACATCACATCTGGTATG+GGG 0.646248 contig561end:+1143 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 contig561end:-1371 MsG0080048951.01.T01:intron
GCTGCCAATGGTATTGAGGG+CGG 0.739556 contig561end:-1097 MsG0080048951.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCTGATTTTATTTTTTTT+AGG - contig561end:1179-1198 MsG0080048951.01.T01:CDS 10.0%
!! AAAAAACAATAAACAACCTT+CGG + contig561end:1102-1121 None:intergenic 20.0%
!!! TTTTAAAGTTGTTCAATTAG+AGG - contig561end:1119-1138 MsG0080048951.01.T01:CDS 20.0%
! ACAGAAATGATATTGTCATA+AGG + contig561end:1270-1289 None:intergenic 25.0%
AATCGTGATGCTTAACTCTA+AGG + contig561end:1230-1249 None:intergenic 35.0%
ATGTGATGTTCGGAAAAGGT+TGG - contig561end:1322-1341 MsG0080048951.01.T01:intron 40.0%
! TAGGAACTACCTGATGCTTT+TGG - contig561end:1198-1217 MsG0080048951.01.T01:CDS 40.0%
!! AGGAATTTGCCAAAAGCATC+AGG + contig561end:1210-1229 None:intergenic 40.0%
CACGATTACCTCATGTTGTG+CGG - contig561end:1243-1262 MsG0080048951.01.T01:CDS 45.0%
CCAGATGTGATGTTCGGAAA+AGG - contig561end:1318-1337 MsG0080048951.01.T01:intron 45.0%
CCCATACCAGATGTGATGTT+CGG - contig561end:1312-1331 MsG0080048951.01.T01:intron 45.0%
CCGAACATCACATCTGGTAT+GGG + contig561end:1315-1334 None:intergenic 45.0%
CGAACATCACATCTGGTATG+GGG + contig561end:1314-1333 None:intergenic 45.0%
TCCGAACATCACATCTGGTA+TGG + contig561end:1316-1335 None:intergenic 45.0%
TTGTGCTGCCAATGGTATTG+AGG - contig561end:1353-1372 MsG0080048951.01.T01:intron 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - contig561end:1345-1364 MsG0080048951.01.T01:intron 45.0%
! CCTTTTCCGAACATCACATC+TGG + contig561end:1321-1340 None:intergenic 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - contig561end:1354-1373 MsG0080048951.01.T01:intron 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG - contig561end:1392-1411 MsG0080048951.01.T01:CDS 45.0%
CATAAGGTCCGCACAACATG+AGG + contig561end:1254-1273 None:intergenic 50.0%
GAAGTTCCCATCGCTGGATA+TGG - contig561end:1063-1082 MsG0080048951.01.T01:CDS 50.0%
GTCGATCCATATCCAGCGAT+GGG + contig561end:1072-1091 None:intergenic 50.0%
TCCAGCGATGGGAACTTCAA+AGG + contig561end:1061-1080 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - contig561end:1083-1102 MsG0080048951.01.T01:CDS 50.0%
!! ACCTTTGAAGTTCCCATCGC+TGG - contig561end:1057-1076 MsG0080048951.01.T01:CDS 50.0%
CGTCGATCCATATCCAGCGA+TGG + contig561end:1073-1092 None:intergenic 55.0%
GTCTCCGCCCTCAATACCAT+TGG + contig561end:1364-1383 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - contig561end:1357-1376 MsG0080048951.01.T01:intron 55.0%
Chromosome Type Strat End Strand Name
contig561end gene 1030 1446 1030 ID=MsG0080048951.01;Name=MsG0080048951.01
contig561end mRNA 1030 1446 1030 ID=MsG0080048951.01.T01;Parent=MsG0080048951.01;Name=MsG0080048951.01.T01;_AED=0.50;_eAED=0.50;_QI=0|0|0|1|0|0.5|2|0|106
contig561end exon 1372 1446 1372 ID=MsG0080048951.01.T01:exon:19998;Parent=MsG0080048951.01.T01
contig561end exon 1030 1275 1030 ID=MsG0080048951.01.T01:exon:19999;Parent=MsG0080048951.01.T01
contig561end CDS 1372 1446 1372 ID=MsG0080048951.01.T01:cds;Parent=MsG0080048951.01.T01
contig561end CDS 1030 1275 1030 ID=MsG0080048951.01.T01:cds;Parent=MsG0080048951.01.T01
Gene Sequence

>MsG0080048951.01.T01

ATGAGTGCGGCAACATCATGTTATTGTACCTTTGAAGTTCCCATCGCTGGATATGGATCGACGAAATCACCGAAGGAACTACCTGATGCTTTTGGCAAATTCCTTAGAGTTAAGCATCACGATTACCTCATGTTGTGCGGACCTTATGACAATATCATTTCTGTGAGACTCAAATATACAGACGACCCCATACCAGATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCTAAGCGTTGA
Protein sequence

>MsG0080048951.01.T01

MSAATSCYCTFEVPIAGYGSTKSPKELPDAFGKFLRVKHHDYLMLCGPYDNIISVRLKYTDDPIPDVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKR*