AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene008094

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene008094.t1 MTR_3g070040 92.857 56 4 0 1 56 1 56 4.96e-33 115
MS.gene008094.t1 MTR_3g070030 88.889 54 6 0 1 54 12 65 1.22e-30 109
MS.gene008094.t1 MTR_7g011130 85.185 54 8 0 1 54 12 65 3.18e-26 97.4
MS.gene008094.t1 MTR_7g011120 81.481 54 10 0 1 54 1 54 8.30e-26 95.9
MS.gene008094.t1 MTR_6g012670 73.077 52 14 0 3 54 15 66 5.15e-21 83.2
MS.gene008094.t1 MTR_4g108760 67.925 53 17 0 2 54 11 63 1.46e-20 82.4
MS.gene008094.t1 MTR_3g435150 66.038 53 18 0 2 54 10 62 8.32e-18 74.3
MS.gene008094.t1 MTR_2g078700 70.213 47 14 0 8 54 23 69 1.16e-17 74.3
MS.gene008094.t1 MTR_6g032770 57.692 52 22 0 3 54 13 64 4.47e-17 72.8
MS.gene008094.t1 MTR_6g084430 63.830 47 17 0 8 54 5 51 2.59e-16 70.5
MS.gene008094.t1 MTR_7g085260 56.604 53 23 0 2 54 11 63 2.60e-16 70.9
MS.gene008094.t1 MTR_1g008740 59.259 54 20 2 2 54 8 60 2.98e-16 70.5
MS.gene008094.t1 MTR_1g008740 59.259 54 20 2 2 54 22 74 3.83e-16 70.1
MS.gene008094.t1 MTR_3g109340 57.447 47 20 0 8 54 22 68 9.52e-15 66.2
MS.gene008094.t1 MTR_3g109340 57.447 47 20 0 8 54 22 68 9.69e-15 66.2
MS.gene008094.t1 MTR_3g116070 57.407 54 21 2 2 54 18 70 7.48e-14 63.9
MS.gene008094.t1 MTR_2g086880 61.702 47 17 1 8 54 19 64 2.54e-13 62.4
MS.gene008094.t1 MTR_2g086880 61.702 47 17 1 8 54 19 64 2.55e-13 62.4
MS.gene008094.t1 MTR_5g076850 55.102 49 22 0 6 54 4 52 3.26e-13 62.0
MS.gene008094.t1 MTR_3g064580 53.061 49 23 0 6 54 4 52 8.09e-13 60.8
MS.gene008094.t1 MTR_2g064090 55.319 47 21 0 8 54 6 52 9.78e-13 60.5
MS.gene008094.t1 MTR_3g096920 52.000 50 24 0 5 54 4 53 1.08e-12 60.5
MS.gene008094.t1 MTR_4g035590 60.000 45 18 0 9 53 9 53 1.51e-12 60.1
MS.gene008094.t1 MTR_3g096920 52.000 50 24 0 5 54 4 53 1.65e-12 59.7
MS.gene008094.t1 MTR_2g079990 52.000 50 24 0 5 54 13 62 5.67e-12 58.5
MS.gene008094.t1 MTR_2g079990 52.000 50 24 0 5 54 13 62 6.03e-12 58.5
MS.gene008094.t1 MTR_1g069805 46.939 49 26 0 8 56 10 58 6.50e-12 58.2
MS.gene008094.t1 MTR_6g477900 52.083 48 23 0 6 53 4 51 1.18e-11 57.0
MS.gene008094.t1 MTR_7g085220 50.000 54 27 0 1 54 1 54 1.29e-11 57.4
MS.gene008094.t1 MTR_7g005280 50.943 53 26 0 2 54 9 61 1.68e-11 57.0
MS.gene008094.t1 MTR_2g080010 48.077 52 27 0 3 54 10 61 1.76e-11 57.0
MS.gene008094.t1 MTR_7g097090 46.939 49 26 0 8 56 10 58 1.84e-11 57.0
MS.gene008094.t1 MTR_3g088110 47.059 51 27 0 6 56 5 55 1.90e-11 57.0
MS.gene008094.t1 MTR_1g090720 62.222 45 16 1 9 53 44 87 2.44e-11 56.6
MS.gene008094.t1 MTR_2g062730 55.556 45 20 0 9 53 11 55 3.34e-11 56.2
MS.gene008094.t1 MTR_2g093810 53.191 47 22 0 8 54 14 60 3.35e-11 56.2
MS.gene008094.t1 MTR_8g059170 50.000 50 25 0 5 54 11 60 3.62e-11 56.2
MS.gene008094.t1 MTR_2g064470 52.941 51 20 2 5 54 8 55 4.53e-11 55.8
MS.gene008094.t1 MTR_8g023840 60.417 48 18 1 9 55 12 59 5.29e-11 55.8
MS.gene008094.t1 MTR_7g100990 46.154 52 28 0 3 54 6 57 5.98e-11 55.5
MS.gene008094.t1 MTR_3g093040 48.980 49 25 0 6 54 106 154 8.75e-11 55.1
MS.gene008094.t1 MTR_5g012080 53.333 45 21 0 9 53 8 52 9.33e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene008094.t1 AT3G29035 66.038 53 18 0 2 54 18 70 7.11e-20 80.1
MS.gene008094.t1 AT5G61430 67.925 53 17 0 2 54 10 62 1.36e-19 79.7
MS.gene008094.t1 AT5G53950 70.213 47 14 0 8 54 17 63 6.77e-19 77.8
MS.gene008094.t1 AT5G07680 64.151 53 19 0 2 54 11 63 2.66e-18 75.9
MS.gene008094.t1 AT3G15170 62.264 53 19 1 2 54 15 66 2.23e-17 73.2
MS.gene008094.t1 AT5G07680 67.347 49 16 0 6 54 1 49 4.35e-17 72.4
MS.gene008094.t1 AT3G18400 63.830 47 17 0 8 54 5 51 5.69e-17 72.4
MS.gene008094.t1 AT2G24430 56.604 53 23 0 2 54 10 62 9.89e-17 71.6
MS.gene008094.t1 AT2G24430 56.604 53 23 0 2 54 10 62 9.89e-17 71.6
MS.gene008094.t1 AT5G39610 62.264 53 20 0 2 54 14 66 1.12e-16 71.2
MS.gene008094.t1 AT3G04060 56.364 55 24 0 2 56 14 68 2.67e-16 70.5
MS.gene008094.t1 AT5G18270 58.824 51 21 0 4 54 17 67 7.43e-16 69.3
MS.gene008094.t1 AT5G18270 58.824 51 21 0 4 54 17 67 7.43e-16 69.3
MS.gene008094.t1 AT1G76420 57.692 52 21 1 3 54 18 68 6.08e-15 66.6
MS.gene008094.t1 AT3G03200 57.143 49 21 0 6 54 4 52 1.61e-13 63.2
MS.gene008094.t1 AT5G17260 55.102 49 22 0 6 54 4 52 2.73e-13 62.4
MS.gene008094.t1 AT1G54330 53.061 49 23 0 6 54 4 52 5.06e-13 61.2
MS.gene008094.t1 AT1G65910 51.020 49 24 0 6 54 4 52 7.10e-13 61.2
MS.gene008094.t1 AT3G17730 54.167 48 22 0 6 53 4 51 1.09e-12 60.1
MS.gene008094.t1 AT4G10350 57.778 45 19 0 9 53 10 54 1.54e-12 60.1
MS.gene008094.t1 AT5G04395 51.923 52 25 0 5 56 25 76 1.64e-12 58.9
MS.gene008094.t1 AT4G27410 50.000 50 25 0 5 54 11 60 1.68e-12 59.7
MS.gene008094.t1 AT4G27410 50.000 50 25 0 5 54 11 60 1.85e-12 59.7
MS.gene008094.t1 AT1G33280 57.778 45 19 0 9 53 9 53 3.81e-12 58.9
MS.gene008094.t1 AT2G27300 59.574 47 18 1 8 54 15 60 3.94e-12 58.9
MS.gene008094.t1 AT3G04070 50.943 53 26 0 2 54 4 56 6.28e-12 58.5
MS.gene008094.t1 AT3G04070 50.943 53 26 0 2 54 4 56 6.40e-12 58.5
MS.gene008094.t1 AT1G01720 46.296 54 29 0 3 56 2 55 7.70e-12 58.2
MS.gene008094.t1 AT3G15500 50.000 50 25 0 5 54 11 60 8.91e-12 57.8
MS.gene008094.t1 AT1G61110 53.191 47 22 0 8 54 16 62 9.58e-12 57.8
MS.gene008094.t1 AT1G33060 55.319 47 21 0 8 54 24 70 1.16e-11 57.8
MS.gene008094.t1 AT1G33060 55.319 47 21 0 8 54 24 70 1.20e-11 57.8
MS.gene008094.t1 AT3G12977 40.000 50 30 0 5 54 15 64 1.60e-11 57.0
MS.gene008094.t1 AT1G26870 52.941 51 23 1 4 54 13 62 3.47e-11 56.2
MS.gene008094.t1 AT1G52890 50.000 50 25 0 5 54 11 60 5.31e-11 55.8
MS.gene008094.t1 AT5G08790 48.000 50 26 0 5 54 4 53 6.06e-11 55.5
MS.gene008094.t1 AT5G04410 56.522 46 19 1 9 54 11 55 7.44e-11 55.5
MS.gene008094.t1 AT1G32770 49.020 51 26 0 3 53 11 61 7.47e-11 55.5
MS.gene008094.t1 AT2G46770 47.059 51 27 0 3 53 11 61 7.72e-11 55.5
MS.gene008094.t1 AT2G43000 43.636 55 30 1 2 56 13 66 8.44e-11 55.1

Find 10 sgRNAs with CRISPR-Local

Find 14 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATGAAAAGGTCGAATTTC+CGG 0.216715 3.3:-61294715 MS.gene008094:CDS
AAATCATTACCTTGTCAAAA+AGG 0.228485 3.3:-61294655 MS.gene008094:CDS
AATGAAAAGGTCGAATTTCC+GGG 0.351715 3.3:-61294714 MS.gene008094:CDS
ATGATTTATAAGCTCTTCAT+CGG 0.528076 3.3:+61294671 None:intergenic
TTTATAAGCTCTTCATCGGT+CGG 0.530344 3.3:+61294675 None:intergenic
AATTTACCTGGCAAATCCCA+TGG 0.560572 3.3:+61294573 None:intergenic
TGTGAACCATGGGATTTGCC+AGG 0.562377 3.3:-61294579 MS.gene008094:intron
TATGAATAAGTGTGAACCAT+GGG 0.641317 3.3:-61294589 MS.gene008094:CDS
ATATGAATAAGTGTGAACCA+TGG 0.681966 3.3:-61294590 MS.gene008094:CDS
GGATAGAATCGAAAACAACC+CGG 0.686902 3.3:+61294696 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAACATTAAATTTACC+TGG + chr3.3:61294650-61294669 None:intergenic 15.0%
!! CCAAAAAAAAAATAGTAATA+TGG - chr3.3:61294714-61294733 MS.gene008094:CDS 15.0%
!!! CCATATTACTATTTTTTTTT+TGG + chr3.3:61294717-61294736 None:intergenic 15.0%
! AAATCATTACCTTGTCAAAA+AGG - chr3.3:61294553-61294572 MS.gene008094:intron 25.0%
! ATGATTTATAAGCTCTTCAT+CGG + chr3.3:61294540-61294559 None:intergenic 25.0%
AAATGAAAAGGTCGAATTTC+CGG - chr3.3:61294493-61294512 MS.gene008094:intron 30.0%
ATATGAATAAGTGTGAACCA+TGG - chr3.3:61294618-61294637 MS.gene008094:CDS 30.0%
TATGAATAAGTGTGAACCAT+GGG - chr3.3:61294619-61294638 MS.gene008094:CDS 30.0%
AATGAAAAGGTCGAATTTCC+GGG - chr3.3:61294494-61294513 MS.gene008094:intron 35.0%
TTTATAAGCTCTTCATCGGT+CGG + chr3.3:61294536-61294555 None:intergenic 35.0%
! TGTCATCAACCTTTTTGACA+AGG + chr3.3:61294565-61294584 None:intergenic 35.0%
AATTTACCTGGCAAATCCCA+TGG + chr3.3:61294638-61294657 None:intergenic 40.0%
GGATAGAATCGAAAACAACC+CGG + chr3.3:61294515-61294534 None:intergenic 40.0%
TGTGAACCATGGGATTTGCC+AGG - chr3.3:61294629-61294648 MS.gene008094:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 61294488 61294742 61294488 ID=MS.gene008094
chr3.3 mRNA 61294488 61294742 61294488 ID=MS.gene008094.t1;Parent=MS.gene008094
chr3.3 exon 61294580 61294742 61294580 ID=MS.gene008094.t1.exon1;Parent=MS.gene008094.t1
chr3.3 CDS 61294580 61294742 61294580 ID=cds.MS.gene008094.t1;Parent=MS.gene008094.t1
chr3.3 exon 61294488 61294501 61294488 ID=MS.gene008094.t1.exon2;Parent=MS.gene008094.t1
chr3.3 CDS 61294488 61294501 61294488 ID=cds.MS.gene008094.t1;Parent=MS.gene008094.t1
Gene Sequence

>MS.gene008094

ATGGAAAATGAAAAGGTCGAATTTCCGGGTTGTTTTCGATTCTATCCGACCGATGAAGAGCTTATAAATCATTACCTTGTCAAAAAGGTTGATGACAATAGCTTCTCTGCTATAGCTATTGCTGAAGTTGATATGAATAAGTGTGAACCATGGGATTTGCCAGGTAAATTTAATGTTTTTTTATAAGTAAATACTAGTTGTTATTATATTATATTAGTATGTCTAACCAAAAAAAAAATAGTAATATGGATATGA
Protein sequence

>MS.gene008094.t1

MENEKVEFPGCFRFYPTDEELINHYLVKKVDDNSFSAIAIAEVDMNKCEPWDLPVIWI