AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0670860

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0670860 MtrunA17_Chr4g0009901 87.931 116 14 0 1 116 1 116 2.02e-72 216
Msa0670860 MtrunA17_Chr4g0009851 79.487 117 23 1 1 116 1 117 1.24e-63 195
Msa0670860 MtrunA17_Chr4g0010001 83.146 89 15 0 1 89 1 89 1.24e-52 160
Msa0670860 MtrunA17_Chr5g0423031 85.393 89 13 0 1 89 1 89 1.71e-52 163
Msa0670860 MtrunA17_Chr4g0009981 84.375 64 10 0 53 116 1 64 1.66e-34 119
Msa0670860 MtrunA17_Chr1g0161431 50.926 108 52 1 10 116 11 118 3.60e-33 121
Msa0670860 MtrunA17_Chr8g0391911 47.664 107 55 1 10 115 9 115 6.12e-31 110
Msa0670860 MtrunA17_Chr6g0456631 45.455 110 58 1 9 116 8 117 1.55e-29 104
Msa0670860 MtrunA17_Chr8g0383961 47.107 121 59 2 1 116 1 121 2.50e-29 106
Msa0670860 MtrunA17_Chr4g0011071 77.966 59 13 0 58 116 38 96 2.08e-28 101
Msa0670860 MtrunA17_Chr3g0123131 45.370 108 58 1 10 116 13 120 3.58e-28 107
Msa0670860 MtrunA17_Chr4g0067981 45.370 108 58 1 10 116 31 138 4.69e-28 106
Msa0670860 MtrunA17_Chr2g0294911 44.444 108 59 1 10 116 29 136 2.17e-26 102
Msa0670860 MtrunA17_Chr6g0471041 47.222 108 56 1 10 116 14 121 2.49e-25 98.2
Msa0670860 MtrunA17_Chr8g0376881 42.202 109 62 1 9 116 24 132 3.03e-25 98.6
Msa0670860 MtrunA17_Chr1g0149841 40.541 111 65 1 7 116 2 112 4.85e-23 92.4
Msa0670860 MtrunA17_Chr7g0275891 39.286 112 66 1 7 116 2 113 8.47e-22 87.8
Msa0670860 MtrunA17_Chr3g0137101 40.741 108 63 1 10 116 8 115 2.07e-21 87.8
Msa0670860 MtrunA17_Chr1g0149851 40.541 111 65 1 7 116 2 112 2.23e-21 87.8
Msa0670860 MtrunA17_Chr4g0074401 37.037 108 67 1 10 116 17 124 2.17e-19 82.0
Msa0670860 MtrunA17_Chr4g0074411 35.398 113 72 1 5 116 13 125 2.61e-19 82.0
Msa0670860 MtrunA17_Chr7g0275401 36.036 111 70 1 7 116 2 112 1.78e-17 75.5
Msa0670860 MtrunA17_Chr2g0304841 34.259 108 70 1 10 116 18 125 2.03e-17 76.6
Msa0670860 MtrunA17_Chr3g0134481 37.037 108 67 1 10 116 8 115 2.61e-17 73.6
Msa0670860 MtrunA17_Chr3g0134461 34.862 109 69 2 10 116 8 116 1.15e-14 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0670860 AT2G01760.1 45.536 112 59 2 7 116 4 115 3.87e-28 105
Msa0670860 AT1G67710.1 44.860 107 58 1 11 116 8 114 7.23e-28 106
Msa0670860 AT3G16857.1 42.593 108 61 1 10 116 33 140 8.44e-25 97.8
Msa0670860 AT3G16857.2 42.593 108 61 1 10 116 33 140 8.48e-25 97.8
Msa0670860 AT2G01760.2 36.429 140 59 3 7 116 4 143 2.23e-22 90.5
Msa0670860 AT4G31920.1 38.889 108 65 1 10 116 13 120 3.55e-21 87.4
Msa0670860 AT2G25180.1 38.889 108 65 1 10 116 13 120 6.50e-21 86.7
Msa0670860 AT5G58080.1 37.963 108 65 2 10 116 14 120 4.60e-15 70.1
Msa0670860 AT5G49240.1 31.193 109 74 1 9 116 37 145 8.21e-15 68.6
Msa0670860 AT1G49190.1 31.818 110 70 2 10 116 30 137 4.32e-14 67.4
Msa0670860 AT1G49190.2 31.818 110 70 2 10 116 30 137 8.53e-14 66.6
Msa0670860 AT3G16857.3 40.580 69 40 1 49 116 2 70 9.03e-13 63.5
Msa0670860 AT3G62670.1 30.000 90 62 1 28 116 53 142 1.32e-12 63.2

Find 22 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGAATTTGTTGGAAAGAA+TGG 0.358508 4_4:+13717253 Msa0670860:CDS
TTCTGATGCCTTGAATTTGT+TGG 0.373586 4_4:+13717244 Msa0670860:CDS
AAAGTGACTAACCTTGATAA+TGG 0.378712 4_4:-13717087 None:intergenic
ATCAGAAGCTGTGTTACATT+TGG 0.412873 4_4:-13717228 None:intergenic
CATTCTTTCCAACAAATTCA+AGG 0.419108 4_4:-13717252 None:intergenic
TGTAATCGATTCCATTATCA+AGG 0.450836 4_4:+13717076 Msa0670860:CDS
AATAAATTCTTACTAATGAC+AGG 0.461511 4_4:-13717365 None:intergenic
TTGAGACCAGCAGGGAATGA+TGG 0.467536 4_4:-13717001 None:intergenic
AAGTCATAAGCATCCATGTT+TGG 0.471983 4_4:-13717311 None:intergenic
AATGTGGGGCGTGTACATAT+TGG 0.479655 4_4:+13717508 Msa0670860:CDS
CACTTTCCTCAACTCTATTG+AGG 0.492388 4_4:+13717048 Msa0670860:CDS
GCAATAACCTTGAGACCAGC+AGG 0.494358 4_4:-13717010 None:intergenic
ATCATTCCCTGCTGGTCTCA+AGG 0.520371 4_4:+13717003 Msa0670860:CDS
GACAACCCATCATTCCCTGC+TGG 0.539365 4_4:+13716995 Msa0670860:CDS
TGAGACCAGCAGGGAATGAT+GGG 0.539790 4_4:-13717000 None:intergenic
TTATGAAGTCTATTCAATGT+GGG 0.540178 4_4:+13717493 Msa0670860:CDS
ATTATGAAGTCTATTCAATG+TGG 0.558796 4_4:+13717492 Msa0670860:CDS
GAAAGTGATGTCATGATCAA+TGG 0.586165 4_4:-13717032 None:intergenic
TGATGCTCATATGCCAAACA+TGG 0.604750 4_4:+13717298 Msa0670860:CDS
ACATCTCCTCAATAGAGTTG+AGG 0.625514 4_4:-13717054 None:intergenic
TATGAAGTCTATTCAATGTG+GGG 0.656343 4_4:+13717494 Msa0670860:CDS
CAATAACCTTGAGACCAGCA+GGG 0.699486 4_4:-13717009 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAATTCTTACTAATGAC+AGG - chr4_4:13717368-13717387 None:intergenic 20.0%
!!! TTATTTCTTTTTTGTAGTGA+TGG + chr4_4:13717446-13717465 Msa0670860:intron 20.0%
! ATTATGAAGTCTATTCAATG+TGG + chr4_4:13717492-13717511 Msa0670860:CDS 25.0%
! TTATGAAGTCTATTCAATGT+GGG + chr4_4:13717493-13717512 Msa0670860:CDS 25.0%
! TGTAATCGATTCCATTATCA+AGG + chr4_4:13717076-13717095 Msa0670860:CDS 30.0%
AAAGTGACTAACCTTGATAA+TGG - chr4_4:13717090-13717109 None:intergenic 30.0%
CATTCTTTCCAACAAATTCA+AGG - chr4_4:13717255-13717274 None:intergenic 30.0%
!! CTTGAATTTGTTGGAAAGAA+TGG + chr4_4:13717253-13717272 Msa0670860:CDS 30.0%
!!! TGAGTTTTAGGGTAACATTT+TGG - chr4_4:13717340-13717359 None:intergenic 30.0%
TATGAAGTCTATTCAATGTG+GGG + chr4_4:13717494-13717513 Msa0670860:CDS 30.0%
GAAAGTGATGTCATGATCAA+TGG - chr4_4:13717035-13717054 None:intergenic 35.0%
ATCAGAAGCTGTGTTACATT+TGG - chr4_4:13717231-13717250 None:intergenic 35.0%
TTCTGATGCCTTGAATTTGT+TGG + chr4_4:13717244-13717263 Msa0670860:CDS 35.0%
AAGTCATAAGCATCCATGTT+TGG - chr4_4:13717314-13717333 None:intergenic 35.0%
! GACAGGAATGTTGAGTTTTA+GGG - chr4_4:13717351-13717370 None:intergenic 35.0%
! TGACAGGAATGTTGAGTTTT+AGG - chr4_4:13717352-13717371 None:intergenic 35.0%
CACTTTCCTCAACTCTATTG+AGG + chr4_4:13717048-13717067 Msa0670860:CDS 40.0%
ACATCTCCTCAATAGAGTTG+AGG - chr4_4:13717057-13717076 None:intergenic 40.0%
TGATGCTCATATGCCAAACA+TGG + chr4_4:13717298-13717317 Msa0670860:CDS 40.0%
CAATAACCTTGAGACCAGCA+GGG - chr4_4:13717012-13717031 None:intergenic 45.0%
AATGTGGGGCGTGTACATAT+TGG + chr4_4:13717508-13717527 Msa0670860:CDS 45.0%
TGAGACCAGCAGGGAATGAT+GGG - chr4_4:13717003-13717022 None:intergenic 50.0%
TTGAGACCAGCAGGGAATGA+TGG - chr4_4:13717004-13717023 None:intergenic 50.0%
! ATCATTCCCTGCTGGTCTCA+AGG + chr4_4:13717003-13717022 Msa0670860:CDS 50.0%
GCAATAACCTTGAGACCAGC+AGG - chr4_4:13717013-13717032 None:intergenic 50.0%
GACAACCCATCATTCCCTGC+TGG + chr4_4:13716995-13717014 Msa0670860:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 13716980 13717542 13716980 ID=Msa0670860;Name=Msa0670860
chr4_4 mRNA 13716980 13717542 13716980 ID=Msa0670860-mRNA-1;Parent=Msa0670860;Name=Msa0670860-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0|0|1|0.5|0.66|3|0|116
chr4_4 exon 13716980 13717097 13716980 ID=Msa0670860-mRNA-1:exon:4174;Parent=Msa0670860-mRNA-1
chr4_4 exon 13717225 13717374 13717225 ID=Msa0670860-mRNA-1:exon:4175;Parent=Msa0670860-mRNA-1
chr4_4 exon 13717463 13717542 13717463 ID=Msa0670860-mRNA-1:exon:4176;Parent=Msa0670860-mRNA-1
chr4_4 CDS 13716980 13717097 13716980 ID=Msa0670860-mRNA-1:cds;Parent=Msa0670860-mRNA-1
chr4_4 CDS 13717225 13717374 13717225 ID=Msa0670860-mRNA-1:cds;Parent=Msa0670860-mRNA-1
chr4_4 CDS 13717463 13717542 13717463 ID=Msa0670860-mRNA-1:cds;Parent=Msa0670860-mRNA-1
Gene Sequence

>Msa0670860

ATGGCTGTTTTCGTTGACAACCCATCATTCCCTGCTGGTCTCAAGGTTATTGCCATTGATCATGACATCACTTTCCTCAACTCTATTGAGGAGATGTGTAATCGATTCCATTATCAAGTTACCAAATGTAACACAGCTTCTGATGCCTTGAATTTGTTGGAAAGAATGGACTGTTTCGATTTAATGTTGATTGATGCTCATATGCCAAACATGGATGCTTATGACTTTGTCCAAAATGTTACCCTAAAACTCAACATTCCTGTCATTATGATGGCTGTTGATTTCGCAAAAAGTTCTATTATGAAGTCTATTCAATGTGGGGCGTGTACATATTGGACTAAGCCTTTG
Protein sequence

>Msa0670860

MAVFVDNPSFPAGLKVIAIDHDITFLNSIEEMCNRFHYQVTKCNTASDALNLLERMDCFDLMLIDAHMPNMDAYDFVQNVTLKLNIPVIMMAVDFAKSSIMKSIQCGACTYWTKPL