AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049536

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049536.t1 MTR_3g466830 95.652 161 7 0 1 161 1 161 3.50e-112 315
MS.gene049536.t1 MTR_3g466890 77.500 160 36 0 1 160 1 160 6.49e-88 254
MS.gene049536.t1 MTR_3g466930 78.906 128 27 0 31 158 2 129 5.04e-73 215
MS.gene049536.t1 MTR_3g466900 75.385 130 32 0 31 160 2 131 2.94e-70 208
MS.gene049536.t1 MTR_3g466980 49.057 159 78 1 2 160 3 158 6.54e-51 162
MS.gene049536.t1 MTR_3g065100 54.545 154 70 0 2 155 3 156 1.59e-50 162
MS.gene049536.t1 MTR_8g036130 49.080 163 80 2 2 161 3 165 2.66e-50 161
MS.gene049536.t1 MTR_4g032620 43.210 162 89 2 2 161 3 163 1.08e-45 149
MS.gene049536.t1 MTR_4g031910 47.826 161 83 1 2 161 3 163 5.66e-43 142
MS.gene049536.t1 MTR_2g035610 54.622 119 54 0 2 120 3 121 4.45e-41 134
MS.gene049536.t1 MTR_1g090697 43.871 155 86 1 2 156 3 156 7.01e-41 135
MS.gene049536.t1 MTR_3g031240 43.125 160 88 2 2 159 3 161 1.98e-40 134
MS.gene049536.t1 MTR_4g032260 49.673 153 76 1 1 152 2 154 1.54e-39 131
MS.gene049536.t1 MTR_4g032290 47.531 162 84 1 1 161 2 163 3.87e-39 132
MS.gene049536.t1 MTR_1g090783 42.675 157 89 1 1 157 1 156 7.25e-39 129
MS.gene049536.t1 MTR_5g075380 44.156 154 86 0 3 156 4 157 7.36e-38 127
MS.gene049536.t1 MTR_5g047580 42.857 154 87 1 2 155 3 155 3.69e-36 122
MS.gene049536.t1 MTR_1g077390 44.079 152 84 1 1 152 2 152 1.48e-34 119
MS.gene049536.t1 MTR_1g090710 39.744 156 92 2 2 156 3 157 1.35e-33 116
MS.gene049536.t1 MTR_2g016210 42.177 147 84 1 3 148 4 150 4.94e-33 117
MS.gene049536.t1 MTR_3g467080 38.158 152 93 1 2 152 3 154 3.35e-31 110
MS.gene049536.t1 MTR_3g031100 37.736 159 98 1 2 159 3 161 4.29e-31 112
MS.gene049536.t1 MTR_7g011950 44.586 157 86 1 2 158 3 158 7.62e-31 109
MS.gene049536.t1 MTR_4g063790 38.065 155 95 1 2 155 3 157 2.00e-30 108
MS.gene049536.t1 MTR_4g028720 42.675 157 89 1 2 158 3 158 9.30e-30 106
MS.gene049536.t1 MTR_1g077320 44.586 157 86 1 2 158 3 158 9.61e-30 106
MS.gene049536.t1 MTR_1g084950 43.506 154 86 1 2 155 3 155 1.34e-29 106
MS.gene049536.t1 MTR_2g035580 40.667 150 89 0 3 152 4 153 2.02e-27 100
MS.gene049536.t1 MTR_1g077300 44.654 159 83 3 1 158 2 156 3.88e-27 100
MS.gene049536.t1 MTR_4g028800 58.571 70 27 1 3 72 4 71 1.07e-23 88.6
MS.gene049536.t1 MTR_4g019670 33.775 151 99 1 2 152 6 155 2.34e-21 89.7
MS.gene049536.t1 MTR_3g465410 34.884 129 83 1 28 155 1 129 2.10e-20 82.0
MS.gene049536.t1 MTR_7g106510 32.895 152 101 1 2 153 6 156 5.41e-20 85.9
MS.gene049536.t1 MTR_5g047560 33.766 154 85 2 2 155 3 139 1.23e-18 77.4
MS.gene049536.t1 MTR_3g093900 28.025 157 113 0 2 158 6 162 5.38e-17 77.4
MS.gene049536.t1 MTR_7g055800 35.043 117 48 2 2 118 3 91 8.11e-17 71.6
MS.gene049536.t1 MTR_7g055790 42.593 108 44 2 2 109 61 150 1.72e-16 72.4
MS.gene049536.t1 MTR_6g018920 34.545 110 65 3 2 105 3 111 2.51e-13 66.6
MS.gene049536.t1 MTR_6g005440 34.545 110 65 3 2 105 3 111 7.30e-13 65.1
MS.gene049536.t1 MTR_7g055940 33.654 104 41 2 2 105 3 78 1.27e-12 60.1
MS.gene049536.t1 MTR_6g005450 32.727 110 67 3 2 105 3 111 2.00e-12 63.9
MS.gene049536.t1 MTR_1g114730 31.818 110 68 3 2 105 3 111 8.98e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049536.t1 AT5G48670 45.570 158 86 0 2 159 3 160 3.95e-39 135
MS.gene049536.t1 AT1G65300 40.132 152 91 0 1 152 1 152 5.08e-35 123
MS.gene049536.t1 AT1G65330 41.447 152 89 0 1 152 1 152 7.00e-35 123
MS.gene049536.t1 AT3G05860 40.136 147 88 0 2 148 3 149 3.26e-31 112
MS.gene049536.t1 AT3G05860 39.474 152 92 0 2 153 3 154 1.67e-30 111
MS.gene049536.t1 AT3G05860 39.474 152 92 0 2 153 3 154 2.01e-30 111
MS.gene049536.t1 AT5G27810 46.809 94 50 0 28 121 1 94 2.81e-27 99.4
MS.gene049536.t1 AT5G26650 36.000 150 96 0 3 152 2 151 9.57e-27 103
MS.gene049536.t1 AT5G27960 40.678 118 70 0 3 120 2 119 2.22e-26 102
MS.gene049536.t1 AT5G26630 38.411 151 93 0 2 152 3 153 5.14e-26 98.6
MS.gene049536.t1 AT1G31630 31.677 161 109 1 1 161 1 160 2.23e-24 97.1
MS.gene049536.t1 AT2G28700 37.815 119 74 0 2 120 3 121 6.00e-23 92.8
MS.gene049536.t1 AT1G31640 32.450 151 101 1 1 151 1 150 2.03e-22 92.8
MS.gene049536.t1 AT1G22590 29.747 158 108 1 2 159 3 157 6.66e-21 84.0
MS.gene049536.t1 AT5G26580 37.288 118 60 1 3 120 4 107 2.73e-19 83.2
MS.gene049536.t1 AT2G40210 41.414 99 58 0 2 100 3 101 2.77e-16 75.1
MS.gene049536.t1 AT5G55690 31.847 157 85 3 2 151 3 144 1.78e-13 66.6
MS.gene049536.t1 AT5G55690 31.847 157 85 3 2 151 3 144 1.78e-13 66.6
MS.gene049536.t1 AT5G06500 31.356 118 81 0 2 119 3 120 3.41e-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 3.2:+57656822 None:intergenic
CAAAGAGCAATTGATGAAAT+TGG 0.277019 3.2:-57656821 MS.gene049536:CDS
TGGTAATCATAATCTCTAAT+TGG 0.298507 3.2:+57656630 None:intergenic
GAAGGTGAAACTTGCATTCA+TGG 0.348876 3.2:-57657100 MS.gene049536:CDS
TGAAATTGGAGAAGAACAAT+TGG 0.354245 3.2:-57656807 MS.gene049536:CDS
TGAACTTTGTGAGAACCCTT+TGG 0.388392 3.2:+57656920 None:intergenic
CTGAGGTTTGGCCTTCTCCA+TGG 0.412577 3.2:-57656948 MS.gene049536:CDS
TTCATTCAGAGCCTGAGGTT+TGG 0.430822 3.2:-57656960 MS.gene049536:CDS
TCTCCCTCAAATAGCTCTCT+TGG 0.434445 3.2:+57656857 None:intergenic
CTTCTCCATGGGAGGTCCAA+AGG 0.434530 3.2:-57656936 MS.gene049536:CDS
ACCACCCTATGTGGGATTGA+TGG 0.443138 3.2:-57657006 MS.gene049536:CDS
TGAGGTTTGGCCTTCTCCAT+GGG 0.458648 3.2:-57656947 MS.gene049536:CDS
TTCTCCATGGGAGGTCCAAA+GGG 0.475139 3.2:-57656935 MS.gene049536:CDS
GAAATTGGAGAAGAACAATT+GGG 0.477120 3.2:-57656806 MS.gene049536:CDS
AAGAGAGCTATTTGAGGGAG+AGG 0.486973 3.2:-57656855 MS.gene049536:CDS
AAGTTTCACCTTCTTTCTCA+TGG 0.490030 3.2:+57657110 None:intergenic
CATGGAGAAGGCCAAACCTC+AGG 0.496084 3.2:+57656949 None:intergenic
AATGAACTCACCACCCTATG+TGG 0.505218 3.2:-57657015 MS.gene049536:CDS
GATGAAGGAGATTACTTCAA+AGG 0.505350 3.2:-57656677 MS.gene049536:CDS
GGAAATTAATGAGAAGATGA+AGG 0.515316 3.2:-57656692 MS.gene049536:CDS
GCATCCATCAATCCCACATA+GGG 0.545713 3.2:+57657002 None:intergenic
GAACCAAGAGAGCTATTTGA+GGG 0.547706 3.2:-57656860 MS.gene049536:CDS
AGAACCCTTTGGACCTCCCA+TGG 0.549154 3.2:+57656931 None:intergenic
AAGACATTGAAACAAGATCA+AGG 0.553196 3.2:+57656771 None:intergenic
TGAACCAAGAGAGCTATTTG+AGG 0.555069 3.2:-57656861 MS.gene049536:CDS
CTTTGGACCTCCCATGGAGA+AGG 0.564387 3.2:+57656937 None:intergenic
CGAATTTCATTCAGAGCCTG+AGG 0.566026 3.2:-57656965 MS.gene049536:CDS
CACACTGACCATGAGAAAGA+AGG 0.576636 3.2:-57657118 None:intergenic
CGCATCCATCAATCCCACAT+AGG 0.580138 3.2:+57657001 None:intergenic
AGTTATTCAGAATTCGAGCA+AGG 0.604546 3.2:-57656895 MS.gene049536:CDS
GGTTTGGCCTTCTCCATGGG+AGG 0.605628 3.2:-57656944 MS.gene049536:CDS
TCCATCAATCCCACATAGGG+TGG 0.620094 3.2:+57657005 None:intergenic
ATGAACTCACCACCCTATGT+GGG 0.624743 3.2:-57657014 MS.gene049536:CDS
TCATGGTCAGTGATTCCGCA+AGG 0.658742 3.2:-57657083 MS.gene049536:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAAAAGAGTTTGATCAAGA+AGG - chr3.2:57656713-57656732 MS.gene049536:CDS 25.0%
AAGACATTGAAACAAGATCA+AGG + chr3.2:57656985-57657004 None:intergenic 30.0%
CAAAGAGCAATTGATGAAAT+TGG - chr3.2:57656932-57656951 MS.gene049536:CDS 30.0%
CAATTTCATCAATTGCTCTT+TGG + chr3.2:57656934-57656953 None:intergenic 30.0%
GAAATTGGAGAAGAACAATT+GGG - chr3.2:57656947-57656966 MS.gene049536:CDS 30.0%
GGAAATTAATGAGAAGATGA+AGG - chr3.2:57657061-57657080 MS.gene049536:CDS 30.0%
TGAAATTGGAGAAGAACAAT+TGG - chr3.2:57656946-57656965 MS.gene049536:CDS 30.0%
!! GTTGTAAGTTATTTTCCTTG+CGG + chr3.2:57656688-57656707 None:intergenic 30.0%
AGTTATTCAGAATTCGAGCA+AGG - chr3.2:57656858-57656877 MS.gene049536:CDS 35.0%
GATGAAGGAGATTACTTCAA+AGG - chr3.2:57657076-57657095 MS.gene049536:CDS 35.0%
!! ATGTTTTGAATGATCTCGCA+TGG - chr3.2:57657039-57657058 MS.gene049536:CDS 35.0%
!! TGTTTTGAATGATCTCGCAT+GGG - chr3.2:57657040-57657059 MS.gene049536:CDS 35.0%
GAACCAAGAGAGCTATTTGA+GGG - chr3.2:57656893-57656912 MS.gene049536:CDS 40.0%
GAAGGTGAAACTTGCATTCA+TGG - chr3.2:57656653-57656672 MS.gene049536:CDS 40.0%
TGAACCAAGAGAGCTATTTG+AGG - chr3.2:57656892-57656911 MS.gene049536:CDS 40.0%
TGAACTTTGTGAGAACCCTT+TGG + chr3.2:57656836-57656855 None:intergenic 40.0%
AAGAGAGCTATTTGAGGGAG+AGG - chr3.2:57656898-57656917 MS.gene049536:CDS 45.0%
AATGAACTCACCACCCTATG+TGG - chr3.2:57656738-57656757 MS.gene049536:CDS 45.0%
ATGAACTCACCACCCTATGT+GGG - chr3.2:57656739-57656758 MS.gene049536:CDS 45.0%
CGAATTTCATTCAGAGCCTG+AGG - chr3.2:57656788-57656807 MS.gene049536:CDS 45.0%
GCATCCATCAATCCCACATA+GGG + chr3.2:57656754-57656773 None:intergenic 45.0%
TCTCCCTCAAATAGCTCTCT+TGG + chr3.2:57656899-57656918 None:intergenic 45.0%
TTCATTCAGAGCCTGAGGTT+TGG - chr3.2:57656793-57656812 MS.gene049536:CDS 45.0%
ACCACCCTATGTGGGATTGA+TGG - chr3.2:57656747-57656766 MS.gene049536:CDS 50.0%
CGCATCCATCAATCCCACAT+AGG + chr3.2:57656755-57656774 None:intergenic 50.0%
TCATGGTCAGTGATTCCGCA+AGG - chr3.2:57656670-57656689 MS.gene049536:CDS 50.0%
TCCATCAATCCCACATAGGG+TGG + chr3.2:57656751-57656770 None:intergenic 50.0%
TTCTCCATGGGAGGTCCAAA+GGG - chr3.2:57656818-57656837 MS.gene049536:CDS 50.0%
! TGAGGTTTGGCCTTCTCCAT+GGG - chr3.2:57656806-57656825 MS.gene049536:CDS 50.0%
AGAACCCTTTGGACCTCCCA+TGG + chr3.2:57656825-57656844 None:intergenic 55.0%
CATGGAGAAGGCCAAACCTC+AGG + chr3.2:57656807-57656826 None:intergenic 55.0%
CTTCTCCATGGGAGGTCCAA+AGG - chr3.2:57656817-57656836 MS.gene049536:CDS 55.0%
CTTTGGACCTCCCATGGAGA+AGG + chr3.2:57656819-57656838 None:intergenic 55.0%
! CTGAGGTTTGGCCTTCTCCA+TGG - chr3.2:57656805-57656824 MS.gene049536:CDS 55.0%
! GGTTTGGCCTTCTCCATGGG+AGG - chr3.2:57656809-57656828 MS.gene049536:CDS 60.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 57656645 57657130 57656645 ID=MS.gene049536
chr3.2 mRNA 57656645 57657130 57656645 ID=MS.gene049536.t1;Parent=MS.gene049536
chr3.2 exon 57656645 57657130 57656645 ID=MS.gene049536.t1.exon1;Parent=MS.gene049536.t1
chr3.2 CDS 57656645 57657130 57656645 ID=cds.MS.gene049536.t1;Parent=MS.gene049536.t1
Gene Sequence

>MS.gene049536

ATGAGAAAGAAGGTGAAACTTGCATTCATGGTCAGTGATTCCGCAAGGAAAATAACTTACAACAAAAGAAAAAAGAGTTTGATCAAGAAGGTTAATGAACTCACCACCCTATGTGGGATTGATGGATGCGCTATAGTTTATAGCGAATTTCATTCAGAGCCTGAGGTTTGGCCTTCTCCATGGGAGGTCCAAAGGGTTCTCACAAAGTTCAAAAGTTATTCAGAATTCGAGCAAGGAAAGAAGAAGCTGAACCAAGAGAGCTATTTGAGGGAGAGGATTATGAAGTCCAAAGAGCAATTGATGAAATTGGAGAAGAACAATTGGGAGACAGAGAAGTCCTTGATCTTGTTTCAATGTCTTGTCAAAGAAAATTTTGTTGACACTTTGAACACAAATGTTTTGAATGATCTCGCATGGGAAATTAATGAGAAGATGAAGGAGATTACTTCAAAGGTCAATGAATTAGACACAAGTGCAGCCAATTAG
Protein sequence

>MS.gene049536.t1

MRKKVKLAFMVSDSARKITYNKRKKSLIKKVNELTTLCGIDGCAIVYSEFHSEPEVWPSPWEVQRVLTKFKSYSEFEQGKKKLNQESYLRERIMKSKEQLMKLEKNNWETEKSLILFQCLVKENFVDTLNTNVLNDLAWEINEKMKEITSKVNELDTSAAN