AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41516

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41516.t1 MTR_3g466830 95.031 161 8 0 1 161 1 161 2.50e-111 313
MS.gene41516.t1 MTR_3g466890 76.875 160 37 0 1 160 1 160 5.56e-87 251
MS.gene41516.t1 MTR_3g466930 78.125 128 28 0 31 158 2 129 6.00e-72 213
MS.gene41516.t1 MTR_3g466900 74.615 130 33 0 31 160 2 131 3.03e-69 206
MS.gene41516.t1 MTR_3g466980 48.428 159 79 1 2 160 3 158 4.07e-50 160
MS.gene41516.t1 MTR_3g065100 53.896 154 71 0 2 155 3 156 1.83e-49 159
MS.gene41516.t1 MTR_8g036130 48.466 163 81 2 2 161 3 165 4.27e-49 158
MS.gene41516.t1 MTR_4g032620 42.593 162 90 2 2 161 3 163 9.94e-45 147
MS.gene41516.t1 MTR_4g031910 47.205 161 84 1 2 161 3 163 6.99e-42 139
MS.gene41516.t1 MTR_2g035610 54.622 119 54 0 2 120 3 121 5.01e-41 134
MS.gene41516.t1 MTR_1g090697 43.226 155 87 1 2 156 3 156 4.05e-40 133
MS.gene41516.t1 MTR_3g031240 42.500 160 89 2 2 159 3 161 1.70e-39 132
MS.gene41516.t1 MTR_4g032260 49.020 153 77 1 1 152 2 154 1.76e-38 129
MS.gene41516.t1 MTR_1g090783 42.038 157 90 1 1 157 1 156 4.18e-38 127
MS.gene41516.t1 MTR_4g032290 46.914 162 85 1 1 161 2 163 5.58e-38 129
MS.gene41516.t1 MTR_5g075380 43.506 154 87 0 3 156 4 157 8.13e-37 124
MS.gene41516.t1 MTR_5g047580 42.208 154 88 1 2 155 3 155 3.14e-35 120
MS.gene41516.t1 MTR_1g077390 43.421 152 85 1 1 152 2 152 8.86e-34 117
MS.gene41516.t1 MTR_1g090710 39.103 156 93 2 2 156 3 157 1.06e-32 114
MS.gene41516.t1 MTR_2g016210 41.497 147 85 1 3 148 4 150 4.27e-32 115
MS.gene41516.t1 MTR_3g467080 38.158 152 93 1 2 152 3 154 1.28e-30 108
MS.gene41516.t1 MTR_3g031100 37.107 159 99 1 2 159 3 161 3.49e-30 110
MS.gene41516.t1 MTR_7g011950 43.949 157 87 1 2 158 3 158 6.10e-30 107
MS.gene41516.t1 MTR_4g063790 37.419 155 96 1 2 155 3 157 1.40e-29 106
MS.gene41516.t1 MTR_4g028720 42.038 157 90 1 2 158 3 158 7.67e-29 104
MS.gene41516.t1 MTR_1g077320 43.949 157 87 1 2 158 3 158 1.00e-28 103
MS.gene41516.t1 MTR_1g084950 42.857 154 87 1 2 155 3 155 1.13e-28 103
MS.gene41516.t1 MTR_2g035580 40.000 150 90 0 3 152 4 153 1.49e-26 98.6
MS.gene41516.t1 MTR_1g077300 44.025 159 84 3 1 158 2 156 2.60e-26 97.8
MS.gene41516.t1 MTR_4g028800 58.571 70 27 1 3 72 4 71 8.93e-24 89.0
MS.gene41516.t1 MTR_4g019670 33.113 151 100 1 2 152 6 155 7.99e-21 88.2
MS.gene41516.t1 MTR_7g106510 32.237 152 102 1 2 153 6 156 1.53e-19 84.7
MS.gene41516.t1 MTR_3g465410 34.109 129 84 1 28 155 1 129 1.80e-19 79.7
MS.gene41516.t1 MTR_5g047560 36.719 128 64 2 2 129 3 113 2.41e-18 76.6
MS.gene41516.t1 MTR_7g055800 35.043 117 48 2 2 118 3 91 7.29e-17 71.6
MS.gene41516.t1 MTR_7g055790 42.593 108 44 2 2 109 61 150 1.51e-16 72.4
MS.gene41516.t1 MTR_3g093900 27.389 157 114 0 2 158 6 162 3.70e-16 75.1
MS.gene41516.t1 MTR_6g018920 34.545 110 65 3 2 105 3 111 2.03e-13 66.6
MS.gene41516.t1 MTR_6g005440 34.545 110 65 3 2 105 3 111 6.88e-13 65.1
MS.gene41516.t1 MTR_7g055940 33.654 104 41 2 2 105 3 78 1.25e-12 60.5
MS.gene41516.t1 MTR_6g005450 32.727 110 67 3 2 105 3 111 1.56e-12 64.3
MS.gene41516.t1 MTR_1g114730 31.818 110 68 3 2 105 3 111 7.76e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41516.t1 AT5G48670 44.937 158 87 0 2 159 3 160 5.17e-38 132
MS.gene41516.t1 AT1G65300 40.132 152 91 0 1 152 1 152 1.13e-34 122
MS.gene41516.t1 AT1G65330 41.447 152 89 0 1 152 1 152 1.39e-34 122
MS.gene41516.t1 AT3G05860 44.538 119 66 0 2 120 3 121 8.32e-31 110
MS.gene41516.t1 AT3G05860 44.538 119 66 0 2 120 3 121 3.17e-30 110
MS.gene41516.t1 AT3G05860 44.538 119 66 0 2 120 3 121 4.53e-30 110
MS.gene41516.t1 AT5G27810 46.809 94 50 0 28 121 1 94 2.75e-27 99.4
MS.gene41516.t1 AT5G26650 41.525 118 69 0 3 120 2 119 1.20e-26 103
MS.gene41516.t1 AT5G27960 40.678 118 70 0 3 120 2 119 2.00e-26 102
MS.gene41516.t1 AT5G26630 37.748 151 94 0 2 152 3 153 4.12e-25 96.3
MS.gene41516.t1 AT1G31630 31.677 161 109 1 1 161 1 160 4.90e-24 95.9
MS.gene41516.t1 AT2G28700 37.815 119 74 0 2 120 3 121 4.45e-23 93.2
MS.gene41516.t1 AT1G31640 38.333 120 73 1 1 120 1 119 2.22e-22 92.8
MS.gene41516.t1 AT1G22590 29.114 158 109 1 2 159 3 157 5.08e-20 81.6
MS.gene41516.t1 AT5G26580 37.288 118 60 1 3 120 4 107 2.65e-19 83.2
MS.gene41516.t1 AT2G40210 41.414 99 58 0 2 100 3 101 2.64e-16 75.1
MS.gene41516.t1 AT5G55690 31.847 157 85 3 2 151 3 144 2.88e-13 65.9
MS.gene41516.t1 AT5G55690 31.847 157 85 3 2 151 3 144 2.88e-13 65.9
MS.gene41516.t1 AT5G06500 31.356 118 81 0 2 119 3 120 3.08e-13 65.5

Find 34 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATTTCATCAATTGCTCTT+TGG 0.234493 3.1:+51281863 None:intergenic
CAAAGAGCAATTGATGAAAT+TGG 0.277019 3.1:-51281862 MS.gene41516:CDS
TGGTAATCATAATCTCTAAT+TGG 0.298507 3.1:+51281671 None:intergenic
GAAGGTGAAACTTGCATTCA+TGG 0.348876 3.1:-51282141 MS.gene41516:CDS
TGAAATTGGAGAAGAACAAT+TGG 0.354245 3.1:-51281848 MS.gene41516:CDS
TGAACTTTGTGAGAACCCTT+TGG 0.388392 3.1:+51281961 None:intergenic
CTGAGGTTTGGCCTTCTCCA+TGG 0.412577 3.1:-51281989 MS.gene41516:CDS
TTCATTCAGAGCCTGAGGTT+TGG 0.430822 3.1:-51282001 MS.gene41516:CDS
TCTCCCTCAAATAGCTCTCT+TGG 0.434445 3.1:+51281898 None:intergenic
CTTCTCCATGGGAGGTCCAA+AGG 0.434530 3.1:-51281977 MS.gene41516:CDS
ACCACCCTATGTGGGATTGA+TGG 0.443138 3.1:-51282047 MS.gene41516:CDS
TGAGGTTTGGCCTTCTCCAT+GGG 0.458648 3.1:-51281988 MS.gene41516:CDS
TTCTCCATGGGAGGTCCAAA+GGG 0.475139 3.1:-51281976 MS.gene41516:CDS
GAAATTGGAGAAGAACAATT+GGG 0.477120 3.1:-51281847 MS.gene41516:CDS
AAGAGAGCTATTTGAGGGAG+AGG 0.486973 3.1:-51281896 MS.gene41516:CDS
GGAAATTAATGAGAAGATGA+TGG 0.489612 3.1:-51281733 MS.gene41516:CDS
AAGTTTCACCTTCTTTCTCA+TGG 0.490030 3.1:+51282151 None:intergenic
CATGGAGAAGGCCAAACCTC+AGG 0.496084 3.1:+51281990 None:intergenic
AATGAACTCACCACCCTATG+TGG 0.505218 3.1:-51282056 MS.gene41516:CDS
GATGATGGAGATTACTTCAA+AGG 0.514408 3.1:-51281718 MS.gene41516:CDS
GCATCCATCAATCCCACATA+GGG 0.545713 3.1:+51282043 None:intergenic
GAACCAAGAGAGCTATTTGA+GGG 0.547706 3.1:-51281901 MS.gene41516:CDS
AGAACCCTTTGGACCTCCCA+TGG 0.549154 3.1:+51281972 None:intergenic
AAGACATTGAAACAAGATCA+AGG 0.553196 3.1:+51281812 None:intergenic
TGAACCAAGAGAGCTATTTG+AGG 0.555069 3.1:-51281902 MS.gene41516:CDS
CTTTGGACCTCCCATGGAGA+AGG 0.564387 3.1:+51281978 None:intergenic
CGAATTTCATTCAGAGCCTG+AGG 0.566026 3.1:-51282006 MS.gene41516:CDS
CACACTGACCATGAGAAAGA+AGG 0.576636 3.1:-51282159 None:intergenic
CGCATCCATCAATCCCACAT+AGG 0.580138 3.1:+51282042 None:intergenic
AGTTATTCAGAATTCGAGCA+AGG 0.604546 3.1:-51281936 MS.gene41516:CDS
GGTTTGGCCTTCTCCATGGG+AGG 0.605628 3.1:-51281985 MS.gene41516:CDS
TCCATCAATCCCACATAGGG+TGG 0.620094 3.1:+51282046 None:intergenic
ATGAACTCACCACCCTATGT+GGG 0.624743 3.1:-51282055 MS.gene41516:CDS
TCATGGTCAGTGATTCCGCA+AGG 0.658742 3.1:-51282124 MS.gene41516:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAAAAGAGTTTGATCAAGA+AGG - chr3.1:51281754-51281773 MS.gene41516:CDS 25.0%
AAGACATTGAAACAAGATCA+AGG + chr3.1:51282026-51282045 None:intergenic 30.0%
CAAAGAGCAATTGATGAAAT+TGG - chr3.1:51281973-51281992 MS.gene41516:CDS 30.0%
CAATTTCATCAATTGCTCTT+TGG + chr3.1:51281975-51281994 None:intergenic 30.0%
GAAATTGGAGAAGAACAATT+GGG - chr3.1:51281988-51282007 MS.gene41516:CDS 30.0%
GGAAATTAATGAGAAGATGA+TGG - chr3.1:51282102-51282121 MS.gene41516:CDS 30.0%
TGAAATTGGAGAAGAACAAT+TGG - chr3.1:51281987-51282006 MS.gene41516:CDS 30.0%
!! GTTGTAAGTTATTTTCCTTG+CGG + chr3.1:51281729-51281748 None:intergenic 30.0%
AGTTATTCAGAATTCGAGCA+AGG - chr3.1:51281899-51281918 MS.gene41516:CDS 35.0%
!! ATGTTTTGAATGATCTCGCA+TGG - chr3.1:51282080-51282099 MS.gene41516:CDS 35.0%
!! GATGATGGAGATTACTTCAA+AGG - chr3.1:51282117-51282136 MS.gene41516:CDS 35.0%
!! TGTTTTGAATGATCTCGCAT+GGG - chr3.1:51282081-51282100 MS.gene41516:CDS 35.0%
GAACCAAGAGAGCTATTTGA+GGG - chr3.1:51281934-51281953 MS.gene41516:CDS 40.0%
GAAGGTGAAACTTGCATTCA+TGG - chr3.1:51281694-51281713 MS.gene41516:CDS 40.0%
TGAACCAAGAGAGCTATTTG+AGG - chr3.1:51281933-51281952 MS.gene41516:CDS 40.0%
TGAACTTTGTGAGAACCCTT+TGG + chr3.1:51281877-51281896 None:intergenic 40.0%
AAGAGAGCTATTTGAGGGAG+AGG - chr3.1:51281939-51281958 MS.gene41516:CDS 45.0%
AATGAACTCACCACCCTATG+TGG - chr3.1:51281779-51281798 MS.gene41516:CDS 45.0%
ATGAACTCACCACCCTATGT+GGG - chr3.1:51281780-51281799 MS.gene41516:CDS 45.0%
CGAATTTCATTCAGAGCCTG+AGG - chr3.1:51281829-51281848 MS.gene41516:CDS 45.0%
GCATCCATCAATCCCACATA+GGG + chr3.1:51281795-51281814 None:intergenic 45.0%
TCTCCCTCAAATAGCTCTCT+TGG + chr3.1:51281940-51281959 None:intergenic 45.0%
TTCATTCAGAGCCTGAGGTT+TGG - chr3.1:51281834-51281853 MS.gene41516:CDS 45.0%
ACCACCCTATGTGGGATTGA+TGG - chr3.1:51281788-51281807 MS.gene41516:CDS 50.0%
CGCATCCATCAATCCCACAT+AGG + chr3.1:51281796-51281815 None:intergenic 50.0%
TCATGGTCAGTGATTCCGCA+AGG - chr3.1:51281711-51281730 MS.gene41516:CDS 50.0%
TCCATCAATCCCACATAGGG+TGG + chr3.1:51281792-51281811 None:intergenic 50.0%
TTCTCCATGGGAGGTCCAAA+GGG - chr3.1:51281859-51281878 MS.gene41516:CDS 50.0%
! TGAGGTTTGGCCTTCTCCAT+GGG - chr3.1:51281847-51281866 MS.gene41516:CDS 50.0%
AGAACCCTTTGGACCTCCCA+TGG + chr3.1:51281866-51281885 None:intergenic 55.0%
CATGGAGAAGGCCAAACCTC+AGG + chr3.1:51281848-51281867 None:intergenic 55.0%
CTTCTCCATGGGAGGTCCAA+AGG - chr3.1:51281858-51281877 MS.gene41516:CDS 55.0%
CTTTGGACCTCCCATGGAGA+AGG + chr3.1:51281860-51281879 None:intergenic 55.0%
! CTGAGGTTTGGCCTTCTCCA+TGG - chr3.1:51281846-51281865 MS.gene41516:CDS 55.0%
! GGTTTGGCCTTCTCCATGGG+AGG - chr3.1:51281850-51281869 MS.gene41516:CDS 60.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 51281686 51282171 51281686 ID=MS.gene41516
chr3.1 mRNA 51281686 51282171 51281686 ID=MS.gene41516.t1;Parent=MS.gene41516
chr3.1 exon 51281686 51282171 51281686 ID=MS.gene41516.t1.exon1;Parent=MS.gene41516.t1
chr3.1 CDS 51281686 51282171 51281686 ID=cds.MS.gene41516.t1;Parent=MS.gene41516.t1
Gene Sequence

>MS.gene41516

ATGAGAAAGAAGGTGAAACTTGCATTCATGGTCAGTGATTCCGCAAGGAAAATAACTTACAACAAAAGAAAAAAGAGTTTGATCAAGAAGGTTAATGAACTCACCACCCTATGTGGGATTGATGGATGCGCTATAGTTTATAGCGAATTTCATTCAGAGCCTGAGGTTTGGCCTTCTCCATGGGAGGTCCAAAGGGTTCTCACAAAGTTCAAAAGTTATTCAGAATTCGAGCAAGGAAAGAAGAAGCTGAACCAAGAGAGCTATTTGAGGGAGAGGATTATGAAGTCCAAAGAGCAATTGATGAAATTGGAGAAGAACAATTGGGAGACAGAGAAGTCCTTGATCTTGTTTCAATGTCTTGTCAAAGAAAATTTTGTTGACACTTTGAACACAAATGTTTTGAATGATCTCGCATGGGAAATTAATGAGAAGATGATGGAGATTACTTCAAAGGTCAATGAATTAGACACAAGTGCAGCCAATTAG
Protein sequence

>MS.gene41516.t1

MRKKVKLAFMVSDSARKITYNKRKKSLIKKVNELTTLCGIDGCAIVYSEFHSEPEVWPSPWEVQRVLTKFKSYSEFEQGKKKLNQESYLRERIMKSKEQLMKLEKNNWETEKSLILFQCLVKENFVDTLNTNVLNDLAWEINEKMMEITSKVNELDTSAAN