AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene38543

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38543.t1 MTR_3g031100 87.037 216 26 1 1 214 29 244 3.09e-130 366
MS.gene38543.t1 MTR_2g016210 41.176 221 115 3 1 213 29 242 7.42e-49 160
MS.gene38543.t1 MTR_3g031240 48.148 135 70 0 1 135 29 163 1.18e-36 127
MS.gene38543.t1 MTR_3g467080 48.062 129 67 0 1 129 29 157 3.07e-35 122
MS.gene38543.t1 MTR_4g063790 42.553 141 81 0 1 141 29 169 1.18e-32 116
MS.gene38543.t1 MTR_3g465410 42.446 139 80 0 1 139 1 139 1.07e-30 110
MS.gene38543.t1 MTR_3g466980 40.000 160 84 4 1 156 29 180 3.97e-30 111
MS.gene38543.t1 MTR_4g032620 41.270 126 74 0 1 126 29 154 6.41e-27 103
MS.gene38543.t1 MTR_3g065100 33.945 218 125 7 4 211 32 240 1.64e-26 102
MS.gene38543.t1 MTR_4g032290 39.837 123 74 0 6 128 34 156 2.38e-24 96.7
MS.gene38543.t1 MTR_4g031910 37.600 125 78 0 4 128 32 156 4.93e-23 92.8
MS.gene38543.t1 MTR_4g032260 34.959 123 80 0 6 128 34 156 6.58e-21 85.5
MS.gene38543.t1 MTR_8g036130 36.429 140 87 1 1 138 29 168 1.69e-20 86.7
MS.gene38543.t1 MTR_3g466900 32.540 126 84 1 6 131 4 128 2.99e-19 80.5
MS.gene38543.t1 MTR_2g035610 43.182 88 50 0 6 93 34 121 1.79e-18 78.2
MS.gene38543.t1 MTR_5g075380 34.127 126 82 1 1 126 29 153 1.88e-18 79.3
MS.gene38543.t1 MTR_3g466930 31.746 126 85 1 6 131 4 128 4.12e-17 74.7
MS.gene38543.t1 MTR_2g035580 39.231 130 78 1 2 131 30 158 7.04e-17 75.1
MS.gene38543.t1 MTR_3g466830 33.083 133 88 1 1 133 28 159 2.53e-16 73.6
MS.gene38543.t1 MTR_3g466890 30.769 130 89 1 2 131 29 157 1.73e-15 71.2
MS.gene38543.t1 MTR_1g077300 31.746 126 76 3 4 126 32 150 6.88e-14 67.0
MS.gene38543.t1 MTR_1g084950 30.159 126 86 2 4 129 32 155 9.29e-14 66.6
MS.gene38543.t1 MTR_5g047580 28.682 129 90 2 1 129 29 155 6.81e-13 64.3
MS.gene38543.t1 MTR_1g077320 31.200 125 82 3 6 129 34 155 2.64e-12 62.8
MS.gene38543.t1 MTR_1g090710 29.457 129 90 1 1 129 29 156 3.39e-12 62.4
MS.gene38543.t1 MTR_1g090697 29.771 131 86 4 1 129 29 155 1.53e-11 60.5
MS.gene38543.t1 MTR_1g077390 29.851 134 82 4 1 129 29 155 1.71e-11 60.5
MS.gene38543.t1 MTR_1g090783 30.827 133 86 4 1 131 28 156 2.76e-11 60.1
MS.gene38543.t1 MTR_7g011950 30.645 124 84 2 6 129 34 155 5.61e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38543.t1 AT5G48670 35.246 122 78 1 6 127 34 154 1.02e-17 80.5
MS.gene38543.t1 AT1G65300 30.412 194 122 5 2 183 29 221 1.93e-16 76.3
MS.gene38543.t1 AT5G27810 41.573 89 52 0 1 89 1 89 5.67e-16 71.6
MS.gene38543.t1 AT3G05860 31.288 163 97 4 1 161 29 178 9.53e-16 73.9
MS.gene38543.t1 AT3G05860 31.288 163 97 4 1 161 29 178 1.00e-15 73.2
MS.gene38543.t1 AT3G05860 31.288 163 97 4 1 161 29 178 1.06e-15 73.9
MS.gene38543.t1 AT5G26630 30.159 126 83 2 4 127 32 154 5.95e-13 65.9
MS.gene38543.t1 AT1G65330 38.202 89 55 0 1 89 28 116 6.58e-13 66.6
MS.gene38543.t1 AT5G26650 30.597 134 82 2 1 129 27 154 2.81e-12 65.1
MS.gene38543.t1 AT5G27960 29.016 193 119 7 2 176 28 220 5.67e-12 64.3

Find 48 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCAGACTAACATGAATTA+TGG 0.238809 3.4:+61379066 MS.gene38543:CDS
TGCTTTCTCATACTTCTCTT+TGG 0.254440 3.4:-61378740 None:intergenic
TGGTGGATCTATATAGCTTT+TGG 0.311230 3.4:+61378698 MS.gene38543:CDS
TTACAACCTGCTCATGGGCT+TGG 0.331639 3.4:-61378927 None:intergenic
TAGATAGATCCAAATCCATT+TGG 0.374885 3.4:-61379156 None:intergenic
TACAACCTGCTCATGGGCTT+GGG 0.383623 3.4:-61378926 None:intergenic
AAATGAAGCTGAAGCTATAA+AGG 0.395160 3.4:+61378948 MS.gene38543:CDS
ATCATGGTCAAGCAGAAGTT+TGG 0.397626 3.4:+61378602 MS.gene38543:CDS
TTCAATAGGTATAATGAAGA+AGG 0.408359 3.4:+61378522 None:intergenic
GAAGTATGAGAAAGCAATGA+TGG 0.430824 3.4:+61378747 MS.gene38543:CDS
CAATCAGAGGTTGGATTCAA+TGG 0.439661 3.4:+61378900 MS.gene38543:CDS
AGATAGATCCAAATCCATTT+GGG 0.447437 3.4:-61379155 None:intergenic
CTTCATTTACAACCTGCTCA+TGG 0.458888 3.4:-61378933 None:intergenic
GAGGTAGGTGTAATAATCTA+TGG 0.465342 3.4:+61378574 MS.gene38543:CDS
TATAAAGGATGGAGATTTGT+CGG 0.479871 3.4:+61378963 MS.gene38543:CDS
TCAAAATCAAAATCATCAAA+TGG 0.488359 3.4:-61379132 None:intergenic
AAGTGATGAGCAACTACCTA+TGG 0.489610 3.4:+61379095 MS.gene38543:CDS
AGGAGATATGCGGGATAACA+TGG 0.501537 3.4:+61379020 MS.gene38543:CDS
TTCATTTACAACCTGCTCAT+GGG 0.507437 3.4:-61378932 None:intergenic
ATAATCTATGGTGAAAATCA+TGG 0.511237 3.4:+61378586 MS.gene38543:CDS
ACCTACCTCTACTCCACAAA+GGG 0.515797 3.4:-61378560 None:intergenic
CTTAATTGATGAAAATATGA+AGG 0.521607 3.4:+61378873 MS.gene38543:CDS
AGTGAATTGAGCACCCTTTG+TGG 0.521846 3.4:+61378547 MS.gene38543:CDS
CCTACTCGTAACTATAATGT+TGG 0.540983 3.4:+61378814 MS.gene38543:CDS
GGTAACCCAAGCCCATGAGC+AGG 0.557566 3.4:+61378921 MS.gene38543:CDS
GAAGGAAGTCAATCAGAGGT+TGG 0.560602 3.4:+61378891 MS.gene38543:CDS
GAAGTTTGGCCACCCGCGAT+AGG 0.561174 3.4:+61378616 MS.gene38543:CDS
GAAGCTGAAGCTATAAAGGA+TGG 0.563914 3.4:+61378952 MS.gene38543:CDS
GAGCACCCTTTGTGGAGTAG+AGG 0.592281 3.4:+61378555 MS.gene38543:CDS
CATGTTAGTCTGATAACCAT+GGG 0.598401 3.4:-61379058 None:intergenic
TCATGTTAGTCTGATAACCA+TGG 0.598544 3.4:-61379059 None:intergenic
GCTCAAGTGCCGCTGAGTGG+AGG 0.602451 3.4:+61379000 MS.gene38543:CDS
GCTGAGTGGAGGAGATATGC+GGG 0.606989 3.4:+61379011 MS.gene38543:CDS
CGCTGAGTGGAGGAGATATG+CGG 0.609024 3.4:+61379010 MS.gene38543:CDS
TATGCGGGATAACATGGATG+AGG 0.617083 3.4:+61379026 MS.gene38543:CDS
AATCATCAAATGGTGGCATG+AGG 0.619303 3.4:-61379122 None:intergenic
ATTGCTCAAGTGCCGCTGAG+TGG 0.623375 3.4:+61378997 MS.gene38543:CDS
AAATCAAAATCATCAAATGG+TGG 0.629108 3.4:-61379129 None:intergenic
CACACATTCTAGTCCTATCG+CGG 0.630751 3.4:-61378629 None:intergenic
CCAACATTATAGTTACGAGT+AGG 0.633928 3.4:-61378814 None:intergenic
ACACATTCTAGTCCTATCGC+GGG 0.637058 3.4:-61378628 None:intergenic
CACCTACCTCTACTCCACAA+AGG 0.639768 3.4:-61378561 None:intergenic
ACCCTTTGTGGAGTAGAGGT+AGG 0.653228 3.4:+61378559 MS.gene38543:CDS
GGTGGCATGAGGAAGTCCAT+AGG 0.659527 3.4:-61379111 None:intergenic
ATATGAAGGAAGTCAATCAG+AGG 0.667679 3.4:+61378887 MS.gene38543:CDS
CATTCTAGTCCTATCGCGGG+TGG 0.668790 3.4:-61378625 None:intergenic
GATGAGGTTGCTGATACCCA+TGG 0.682185 3.4:+61379042 MS.gene38543:CDS
CGCATATCTCCTCCACTCAG+CGG 0.698486 3.4:-61379009 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTCAAAAGAAACAAAAATA+TGG + chr3.4:61378678-61378697 MS.gene38543:CDS 20.0%
!! CTTAATTGATGAAAATATGA+AGG + chr3.4:61378873-61378892 MS.gene38543:CDS 20.0%
!! TCAAAATCAAAATCATCAAA+TGG - chr3.4:61379135-61379154 None:intergenic 20.0%
!!! CTTCATATTTTCATCAATTA+AGG - chr3.4:61378875-61378894 None:intergenic 20.0%
! AAATCAAAATCATCAAATGG+TGG - chr3.4:61379132-61379151 None:intergenic 25.0%
! ATAATCTATGGTGAAAATCA+TGG + chr3.4:61378586-61378605 MS.gene38543:CDS 25.0%
! CAAAAGAAACAAAAATATGG+TGG + chr3.4:61378681-61378700 MS.gene38543:CDS 25.0%
! TATCAGACTAACATGAATTA+TGG + chr3.4:61379066-61379085 MS.gene38543:CDS 25.0%
AAATGAAGCTGAAGCTATAA+AGG + chr3.4:61378948-61378967 MS.gene38543:CDS 30.0%
AGATAGATCCAAATCCATTT+GGG - chr3.4:61379158-61379177 None:intergenic 30.0%
TAGATAGATCCAAATCCATT+TGG - chr3.4:61379159-61379178 None:intergenic 30.0%
TATAAAGGATGGAGATTTGT+CGG + chr3.4:61378963-61378982 MS.gene38543:CDS 30.0%
! TATATAGCTTTTGGATGCAA+AGG + chr3.4:61378707-61378726 MS.gene38543:CDS 30.0%
!!! GATTTTGATTTTGACCCAAA+TGG + chr3.4:61379141-61379160 MS.gene38543:CDS 30.0%
ATATGAAGGAAGTCAATCAG+AGG + chr3.4:61378887-61378906 MS.gene38543:CDS 35.0%
CCAACATTATAGTTACGAGT+AGG - chr3.4:61378817-61378836 None:intergenic 35.0%
CCTACTCGTAACTATAATGT+TGG + chr3.4:61378814-61378833 MS.gene38543:CDS 35.0%
GAAGTATGAGAAAGCAATGA+TGG + chr3.4:61378747-61378766 MS.gene38543:CDS 35.0%
GAGGTAGGTGTAATAATCTA+TGG + chr3.4:61378574-61378593 MS.gene38543:CDS 35.0%
TGCTTTCTCATACTTCTCTT+TGG - chr3.4:61378743-61378762 None:intergenic 35.0%
TTCATTTACAACCTGCTCAT+GGG - chr3.4:61378935-61378954 None:intergenic 35.0%
! CATGTTAGTCTGATAACCAT+GGG - chr3.4:61379061-61379080 None:intergenic 35.0%
! TCATGTTAGTCTGATAACCA+TGG - chr3.4:61379062-61379081 None:intergenic 35.0%
!! GATTTTGACCCAAATGGATT+TGG + chr3.4:61379147-61379166 MS.gene38543:CDS 35.0%
!! TGGTGGATCTATATAGCTTT+TGG + chr3.4:61378698-61378717 MS.gene38543:CDS 35.0%
AAGTGATGAGCAACTACCTA+TGG + chr3.4:61379095-61379114 MS.gene38543:CDS 40.0%
AATCATCAAATGGTGGCATG+AGG - chr3.4:61379125-61379144 None:intergenic 40.0%
ATCATGGTCAAGCAGAAGTT+TGG + chr3.4:61378602-61378621 MS.gene38543:CDS 40.0%
CAATCAGAGGTTGGATTCAA+TGG + chr3.4:61378900-61378919 MS.gene38543:CDS 40.0%
CTTCATTTACAACCTGCTCA+TGG - chr3.4:61378936-61378955 None:intergenic 40.0%
GAAGCTGAAGCTATAAAGGA+TGG + chr3.4:61378952-61378971 MS.gene38543:CDS 40.0%
! AGCTTTTGGATGCAAAGGAT+TGG + chr3.4:61378712-61378731 MS.gene38543:CDS 40.0%
ACACATTCTAGTCCTATCGC+GGG - chr3.4:61378631-61378650 None:intergenic 45.0%
ACCTACCTCTACTCCACAAA+GGG - chr3.4:61378563-61378582 None:intergenic 45.0%
AGGAGATATGCGGGATAACA+TGG + chr3.4:61379020-61379039 MS.gene38543:CDS 45.0%
AGTGAATTGAGCACCCTTTG+TGG + chr3.4:61378547-61378566 MS.gene38543:CDS 45.0%
CACACATTCTAGTCCTATCG+CGG - chr3.4:61378632-61378651 None:intergenic 45.0%
GAAGGAAGTCAATCAGAGGT+TGG + chr3.4:61378891-61378910 MS.gene38543:CDS 45.0%
TATGCGGGATAACATGGATG+AGG + chr3.4:61379026-61379045 MS.gene38543:CDS 45.0%
ACCCTTTGTGGAGTAGAGGT+AGG + chr3.4:61378559-61378578 MS.gene38543:CDS 50.0%
CACCTACCTCTACTCCACAA+AGG - chr3.4:61378564-61378583 None:intergenic 50.0%
GATGAGGTTGCTGATACCCA+TGG + chr3.4:61379042-61379061 MS.gene38543:CDS 50.0%
TACAACCTGCTCATGGGCTT+GGG - chr3.4:61378929-61378948 None:intergenic 50.0%
TTACAACCTGCTCATGGGCT+TGG - chr3.4:61378930-61378949 None:intergenic 50.0%
CATTCTAGTCCTATCGCGGG+TGG - chr3.4:61378628-61378647 None:intergenic 55.0%
CGCATATCTCCTCCACTCAG+CGG - chr3.4:61379012-61379031 None:intergenic 55.0%
CGCTGAGTGGAGGAGATATG+CGG + chr3.4:61379010-61379029 MS.gene38543:CDS 55.0%
GAGCACCCTTTGTGGAGTAG+AGG + chr3.4:61378555-61378574 MS.gene38543:CDS 55.0%
GCTGAGTGGAGGAGATATGC+GGG + chr3.4:61379011-61379030 MS.gene38543:CDS 55.0%
GGTGGCATGAGGAAGTCCAT+AGG - chr3.4:61379114-61379133 None:intergenic 55.0%
! ATTGCTCAAGTGCCGCTGAG+TGG + chr3.4:61378997-61379016 MS.gene38543:CDS 55.0%
GAAGTTTGGCCACCCGCGAT+AGG + chr3.4:61378616-61378635 MS.gene38543:CDS 60.0%
GGTAACCCAAGCCCATGAGC+AGG + chr3.4:61378921-61378940 MS.gene38543:CDS 60.0%
! GCTCAAGTGCCGCTGAGTGG+AGG + chr3.4:61379000-61379019 MS.gene38543:CDS 65.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 61378535 61379179 61378535 ID=MS.gene38543
chr3.4 mRNA 61378535 61379179 61378535 ID=MS.gene38543.t1;Parent=MS.gene38543
chr3.4 exon 61378535 61379179 61378535 ID=MS.gene38543.t1.exon1;Parent=MS.gene38543.t1
chr3.4 CDS 61378535 61379179 61378535 ID=cds.MS.gene38543.t1;Parent=MS.gene38543.t1
Gene Sequence

>MS.gene38543

ATGAAGAAGGCTAGTGAATTGAGCACCCTTTGTGGAGTAGAGGTAGGTGTAATAATCTATGGTGAAAATCATGGTCAAGCAGAAGTTTGGCCACCCGCGATAGGACTAGAATGTGTGTTGCACAAGTTTGAGAGTTTGTCTGAACTCAAAAGAAACAAAAATATGGTGGATCTATATAGCTTTTGGATGCAAAGGATTGGAAAAGCCAAAGAGAAGTATGAGAAAGCAATGATGGAAAACAAGAAGAAAGAAATGACTAATTTTATACGTCAATTTATTCCTACTCGTAACTATAATGTTGGTGATATGAGCTTAAATGATATCAATTATCTGACGACCTTAATTGATGAAAATATGAAGGAAGTCAATCAGAGGTTGGATTCAATGGTAACCCAAGCCCATGAGCAGGTTGTAAATGAAGCTGAAGCTATAAAGGATGGAGATTTGTCGGCTAGTACAAACATTGCTCAAGTGCCGCTGAGTGGAGGAGATATGCGGGATAACATGGATGAGGTTGCTGATACCCATGGTTATCAGACTAACATGAATTATGGTTTGCAAAGTGATGAGCAACTACCTATGGACTTCCTCATGCCACCATTTGATGATTTTGATTTTGACCCAAATGGATTTGGATCTATCTAG
Protein sequence

>MS.gene38543.t1

MKKASELSTLCGVEVGVIIYGENHGQAEVWPPAIGLECVLHKFESLSELKRNKNMVDLYSFWMQRIGKAKEKYEKAMMENKKKEMTNFIRQFIPTRNYNVGDMSLNDINYLTTLIDENMKEVNQRLDSMVTQAHEQVVNEAEAIKDGDLSASTNIAQVPLSGGDMRDNMDEVADTHGYQTNMNYGLQSDEQLPMDFLMPPFDDFDFDPNGFGSI