AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene55654

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55654.t1 MTR_8g085590 97.260 146 4 0 1 146 1 146 1.83e-101 288
MS.gene55654.t1 MTR_8g085580 41.406 128 73 2 23 149 22 148 5.32e-31 109
MS.gene55654.t1 MTR_4g081560 41.026 117 67 2 31 146 29 144 2.78e-27 100
MS.gene55654.t1 MTR_7g080280 37.879 132 75 4 18 147 32 158 1.47e-25 95.9
MS.gene55654.t1 MTR_7g053107 35.088 114 72 2 31 143 36 148 2.70e-22 87.8
MS.gene55654.t1 MTR_2g010970 34.188 117 75 2 31 146 28 143 1.21e-21 85.5
MS.gene55654.t1 MTR_4g091980 31.387 137 92 2 12 147 12 147 8.15e-21 83.6
MS.gene55654.t1 MTR_4g091930 28.148 135 95 2 12 145 12 145 3.30e-17 73.9
MS.gene55654.t1 MTR_2g010970 35.227 88 56 1 31 118 28 114 3.53e-17 73.2
MS.gene55654.t1 MTR_4g091970 28.188 149 102 4 1 147 3 148 5.77e-17 73.6
MS.gene55654.t1 MTR_4g064460 29.661 118 81 2 29 145 29 145 8.13e-16 70.5
MS.gene55654.t1 MTR_7g108775 29.008 131 88 3 16 143 14 142 2.47e-14 66.6
MS.gene55654.t1 MTR_7g108775 29.008 131 88 3 16 143 14 142 3.31e-14 66.6
MS.gene55654.t1 MTR_1g088250 35.294 119 71 4 32 147 25 140 4.85e-14 65.9
MS.gene55654.t1 MTR_6g086680 29.688 128 84 3 23 146 27 152 1.04e-13 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55654.t1 AT1G55265 59.322 118 48 0 30 147 53 170 2.95e-47 151
MS.gene55654.t1 AT5G19860 41.379 116 66 2 29 143 34 148 6.23e-27 99.8
MS.gene55654.t1 AT1G61667 38.462 117 69 3 29 143 20 135 1.16e-25 95.9
MS.gene55654.t1 AT1G61667 38.462 117 69 3 29 143 56 171 1.41e-25 96.7
MS.gene55654.t1 AT5G54530 38.261 115 69 2 31 144 29 142 1.51e-24 93.2
MS.gene55654.t1 AT3G07470 31.034 145 97 3 1 143 1 144 1.05e-19 80.5
MS.gene55654.t1 AT3G07470 31.034 145 97 3 1 143 1 144 1.31e-19 80.1
MS.gene55654.t1 AT3G07470 31.034 145 97 3 1 143 1 144 1.51e-19 80.5
MS.gene55654.t1 AT3G07460 32.283 127 83 3 19 143 18 143 6.46e-18 76.3
MS.gene55654.t1 AT5G16380 31.618 136 86 5 13 145 15 146 2.01e-17 75.5
MS.gene55654.t1 AT3G07460 32.283 127 83 3 19 143 18 143 3.66e-17 76.3
MS.gene55654.t1 AT1G02813 28.467 137 95 2 8 143 2 136 7.64e-17 72.8
MS.gene55654.t1 AT4G02360 28.030 132 91 3 13 143 12 140 6.27e-14 65.5
MS.gene55654.t1 AT1G02816 32.031 128 80 5 19 143 21 144 8.28e-14 65.5
MS.gene55654.t1 AT2G03350 35.294 119 71 5 33 148 61 176 1.06e-13 65.5

Find 62 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCACTTACGGTTCCGTTTC+CGG 0.165426 4.3:-15117794 MS.gene55654:CDS
TTCATCTGGCTCCCTGTTAC+TGG 0.204778 4.3:-15117743 MS.gene55654:CDS
TTCCGGTGTTTCCGGGATTC+AGG 0.260942 4.3:-15117777 MS.gene55654:CDS
TCAACTTCCATTCCAGTAAC+AGG 0.329362 4.3:+15117731 None:intergenic
GGTTCCGTTTCCGGTGTTTC+CGG 0.329438 4.3:-15117785 MS.gene55654:CDS
ATGGAAGTTGATTCCCGTTC+TGG 0.333675 4.3:-15117719 MS.gene55654:CDS
GTTCCGTTTCCGGTGTTTCC+GGG 0.340302 4.3:-15117784 MS.gene55654:CDS
ACCGGAGAAGCGAACGTAAC+AGG 0.340745 4.3:+15117853 None:intergenic
GGTATGCTTCAATTCTTTGT+TGG 0.346268 4.3:-15117698 MS.gene55654:CDS
GTGTAGGAGGCGATGTTGTT+AGG 0.359883 4.3:+15117917 None:intergenic
CCCTGTTACGTTCGCTTCTC+CGG 0.394931 4.3:-15117854 MS.gene55654:CDS
TGTTAGGAAGGATGCCCTTT+GGG 0.399077 4.3:+15117933 None:intergenic
GCCCTTTGGGAAACCGTAAT+CGG 0.407957 4.3:+15117946 None:intergenic
AGCTTTGTCTAAGAAATTAC+CGG 0.420637 4.3:-15117675 MS.gene55654:CDS
CCCTTTGGGAAACCGTAATC+GGG 0.430500 4.3:+15117947 None:intergenic
CACGACCTCCTCCCCGATTA+CGG 0.436117 4.3:-15117959 MS.gene55654:CDS
TCCTACACCCTCTCCTCATC+CGG 0.443813 4.3:-15117902 MS.gene55654:CDS
AGGCCAAGATGCTCTTCATC+TGG 0.445884 4.3:-15117757 MS.gene55654:CDS
GAAGGGTTGTGGCTGTTGCA+TGG 0.449955 4.3:+15117993 None:intergenic
GAATTGAAGCATACCAGAAC+GGG 0.452831 4.3:+15117706 None:intergenic
CCCGATTACGGTTTCCCAAA+GGG 0.457567 4.3:-15117947 MS.gene55654:CDS
TTGTTAGGAAGGATGCCCTT+TGG 0.469698 4.3:+15117932 None:intergenic
CGTAATCGGGGAGGAGGTCG+TGG 0.480861 4.3:+15117960 None:intergenic
TACTACGACACCCTCGTCAC+CGG 0.484561 4.3:-15117821 MS.gene55654:CDS
AATCCCGGAAACACCGGAAA+CGG 0.488780 4.3:+15117781 None:intergenic
CTGGCTCCCTGTTACTGGAA+TGG 0.520106 4.3:-15117738 MS.gene55654:CDS
CTGTTGCATGGGATATGAAT+AGG 0.520381 4.3:+15118005 None:intergenic
GAGATGGAGGGTGAAGTAAC+CGG 0.520551 4.3:+15117883 None:intergenic
CCGGAGAAGCGAACGTAACA+GGG 0.524118 4.3:+15117854 None:intergenic
AGGAGGCGATGTTGTTAGGA+AGG 0.525908 4.3:+15117921 None:intergenic
AGGAGGTCGTGGATGTCCGA+TGG 0.528432 4.3:+15117971 None:intergenic
GAGCATCTTGGCCTGAATCC+CGG 0.529909 4.3:+15117766 None:intergenic
GAGGGTGAAGTAACCGGATG+AGG 0.538161 4.3:+15117889 None:intergenic
GGAAACCGTAATCGGGGAGG+AGG 0.542068 4.3:+15117954 None:intergenic
GGTCGTGGATGTCCGATGGA+AGG 0.542935 4.3:+15117975 None:intergenic
GAGCCAGATGAAGAGCATCT+TGG 0.544202 4.3:+15117754 None:intergenic
AAGGGTTGTGGCTGTTGCAT+GGG 0.549396 4.3:+15117994 None:intergenic
CCCCGATTACGGTTTCCCAA+AGG 0.549824 4.3:-15117948 MS.gene55654:CDS
AATCAGTTTCAAGATGTGCC+TGG 0.550036 4.3:-15117650 MS.gene55654:CDS
AAGTGAGGGTTCCGGTGACG+AGG 0.556293 4.3:+15117810 None:intergenic
GTCGTGGATGTCCGATGGAA+GGG 0.557395 4.3:+15117976 None:intergenic
GGCCTGAATCCCGGAAACAC+CGG 0.568473 4.3:+15117775 None:intergenic
ACATCTTGAAACTGATTCGC+CGG 0.569152 4.3:+15117656 None:intergenic
GTCACCGGAACCCTCACTTA+CGG 0.574574 4.3:-15117806 MS.gene55654:CDS
TGTTGAAAAGAATTGAAACA+AGG 0.578826 4.3:+15118030 None:intergenic
ACCGGATGAGGAGAGGGTGT+AGG 0.581276 4.3:+15117901 None:intergenic
GTCGTAGTAGACTAATTGAC+CGG 0.588836 4.3:+15117835 None:intergenic
GAAGTAACCGGATGAGGAGA+GGG 0.591167 4.3:+15117895 None:intergenic
CGGAAACGGAACCGTAAGTG+AGG 0.593119 4.3:+15117795 None:intergenic
GGATGAGGAGAGGGTGTAGG+AGG 0.593846 4.3:+15117904 None:intergenic
GGAACCGTAAGTGAGGGTTC+CGG 0.598341 4.3:+15117802 None:intergenic
AACAGCCACAACCCTTCCAT+CGG 0.601184 4.3:-15117987 MS.gene55654:CDS
AGAATTGAAGCATACCAGAA+CGG 0.613753 4.3:+15117705 None:intergenic
TGAAGTAACCGGATGAGGAG+AGG 0.621652 4.3:+15117894 None:intergenic
CAACTTCCATTCCAGTAACA+GGG 0.628240 4.3:+15117732 None:intergenic
AGTGAGGGTTCCGGTGACGA+GGG 0.629622 4.3:+15117811 None:intergenic
GATGTCCGATGGAAGGGTTG+TGG 0.630291 4.3:+15117982 None:intergenic
TTGGGAAACCGTAATCGGGG+AGG 0.667430 4.3:+15117951 None:intergenic
CCTTTGGGAAACCGTAATCG+GGG 0.689281 4.3:+15117948 None:intergenic
CGGAGAAGCGAACGTAACAG+GGG 0.693110 4.3:+15117855 None:intergenic
GGAAACGGAACCGTAAGTGA+GGG 0.696303 4.3:+15117796 None:intergenic
GGAGAAGCGAACGTAACAGG+GGG 0.736155 4.3:+15117856 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGTTGAAAAGAATTGAAACA+AGG + chr4.3:15117653-15117672 None:intergenic 25.0%
! AGCTTTGTCTAAGAAATTAC+CGG - chr4.3:15118005-15118024 MS.gene55654:CDS 30.0%
! GAATTGAAACAAGGTTTTCA+AGG + chr4.3:15117644-15117663 None:intergenic 30.0%
AGAATTGAAGCATACCAGAA+CGG + chr4.3:15117978-15117997 None:intergenic 35.0%
GGTATGCTTCAATTCTTTGT+TGG - chr4.3:15117982-15118001 MS.gene55654:CDS 35.0%
!! AAACAAGGTTTTCAAGGTTC+TGG + chr4.3:15117638-15117657 None:intergenic 35.0%
!!! AGAAGTTTTGAAGAACATCC+AGG + chr4.3:15118051-15118070 None:intergenic 35.0%
AATCAGTTTCAAGATGTGCC+TGG - chr4.3:15118030-15118049 MS.gene55654:CDS 40.0%
CAACTTCCATTCCAGTAACA+GGG + chr4.3:15117951-15117970 None:intergenic 40.0%
CTGTTGCATGGGATATGAAT+AGG + chr4.3:15117678-15117697 None:intergenic 40.0%
GAATTGAAGCATACCAGAAC+GGG + chr4.3:15117977-15117996 None:intergenic 40.0%
GTCGTAGTAGACTAATTGAC+CGG + chr4.3:15117848-15117867 None:intergenic 40.0%
TCAACTTCCATTCCAGTAAC+AGG + chr4.3:15117952-15117971 None:intergenic 40.0%
!! ACATCTTGAAACTGATTCGC+CGG + chr4.3:15118027-15118046 None:intergenic 40.0%
TGTTAGGAAGGATGCCCTTT+GGG + chr4.3:15117750-15117769 None:intergenic 45.0%
TTGTTAGGAAGGATGCCCTT+TGG + chr4.3:15117751-15117770 None:intergenic 45.0%
! ATGGAAGTTGATTCCCGTTC+TGG - chr4.3:15117961-15117980 MS.gene55654:CDS 45.0%
!! CAAGGTTTTCAAGGTTCTGG+TGG + chr4.3:15117635-15117654 None:intergenic 45.0%
AACAGCCACAACCCTTCCAT+CGG - chr4.3:15117693-15117712 MS.gene55654:CDS 50.0%
AAGGGTTGTGGCTGTTGCAT+GGG + chr4.3:15117689-15117708 None:intergenic 50.0%
AATCCCGGAAACACCGGAAA+CGG + chr4.3:15117902-15117921 None:intergenic 50.0%
AGGAGGCGATGTTGTTAGGA+AGG + chr4.3:15117762-15117781 None:intergenic 50.0%
AGGCCAAGATGCTCTTCATC+TGG - chr4.3:15117923-15117942 MS.gene55654:CDS 50.0%
CCCGATTACGGTTTCCCAAA+GGG - chr4.3:15117733-15117752 MS.gene55654:CDS 50.0%
CTCACTTACGGTTCCGTTTC+CGG - chr4.3:15117886-15117905 MS.gene55654:CDS 50.0%
GAAGTAACCGGATGAGGAGA+GGG + chr4.3:15117788-15117807 None:intergenic 50.0%
GAGATGGAGGGTGAAGTAAC+CGG + chr4.3:15117800-15117819 None:intergenic 50.0%
GGAAACGGAACCGTAAGTGA+GGG + chr4.3:15117887-15117906 None:intergenic 50.0%
GTGTAGGAGGCGATGTTGTT+AGG + chr4.3:15117766-15117785 None:intergenic 50.0%
TGAAGTAACCGGATGAGGAG+AGG + chr4.3:15117789-15117808 None:intergenic 50.0%
! CCCTTTGGGAAACCGTAATC+GGG + chr4.3:15117736-15117755 None:intergenic 50.0%
! CCTTTGGGAAACCGTAATCG+GGG + chr4.3:15117735-15117754 None:intergenic 50.0%
! GCCCTTTGGGAAACCGTAAT+CGG + chr4.3:15117737-15117756 None:intergenic 50.0%
! TTCATCTGGCTCCCTGTTAC+TGG - chr4.3:15117937-15117956 MS.gene55654:CDS 50.0%
!! GAGCCAGATGAAGAGCATCT+TGG + chr4.3:15117929-15117948 None:intergenic 50.0%
AACAGGGGGATTGGAGATGG+AGG + chr4.3:15117813-15117832 None:intergenic 55.0%
ACAGGGGGATTGGAGATGGA+GGG + chr4.3:15117812-15117831 None:intergenic 55.0%
ACCGGAGAAGCGAACGTAAC+AGG + chr4.3:15117830-15117849 None:intergenic 55.0%
AGCGAACGTAACAGGGGGAT+TGG + chr4.3:15117822-15117841 None:intergenic 55.0%
CCCCGATTACGGTTTCCCAA+AGG - chr4.3:15117732-15117751 MS.gene55654:CDS 55.0%
CCCTGTTACGTTCGCTTCTC+CGG - chr4.3:15117826-15117845 MS.gene55654:CDS 55.0%
CCGGAGAAGCGAACGTAACA+GGG + chr4.3:15117829-15117848 None:intergenic 55.0%
CGGAAACGGAACCGTAAGTG+AGG + chr4.3:15117888-15117907 None:intergenic 55.0%
CGGAGAAGCGAACGTAACAG+GGG + chr4.3:15117828-15117847 None:intergenic 55.0%
CGTAACAGGGGGATTGGAGA+TGG + chr4.3:15117816-15117835 None:intergenic 55.0%
CTGGCTCCCTGTTACTGGAA+TGG - chr4.3:15117942-15117961 MS.gene55654:CDS 55.0%
GAAGGGTTGTGGCTGTTGCA+TGG + chr4.3:15117690-15117709 None:intergenic 55.0%
GAGCATCTTGGCCTGAATCC+CGG + chr4.3:15117917-15117936 None:intergenic 55.0%
GAGGGTGAAGTAACCGGATG+AGG + chr4.3:15117794-15117813 None:intergenic 55.0%
GATGTCCGATGGAAGGGTTG+TGG + chr4.3:15117701-15117720 None:intergenic 55.0%
GGAACCGTAAGTGAGGGTTC+CGG + chr4.3:15117881-15117900 None:intergenic 55.0%
GGAGAAGCGAACGTAACAGG+GGG + chr4.3:15117827-15117846 None:intergenic 55.0%
GGTTCCGTTTCCGGTGTTTC+CGG - chr4.3:15117895-15117914 MS.gene55654:CDS 55.0%
GTCACCGGAACCCTCACTTA+CGG - chr4.3:15117874-15117893 MS.gene55654:CDS 55.0%
GTCGTGGATGTCCGATGGAA+GGG + chr4.3:15117707-15117726 None:intergenic 55.0%
GTTCCGTTTCCGGTGTTTCC+GGG - chr4.3:15117896-15117915 MS.gene55654:CDS 55.0%
TACTACGACACCCTCGTCAC+CGG - chr4.3:15117859-15117878 MS.gene55654:CDS 55.0%
TCCTACACCCTCTCCTCATC+CGG - chr4.3:15117778-15117797 MS.gene55654:CDS 55.0%
TTCCGGTGTTTCCGGGATTC+AGG - chr4.3:15117903-15117922 MS.gene55654:CDS 55.0%
TTGGGAAACCGTAATCGGGG+AGG + chr4.3:15117732-15117751 None:intergenic 55.0%
AAGTGAGGGTTCCGGTGACG+AGG + chr4.3:15117873-15117892 None:intergenic 60.0%
AGGAGGTCGTGGATGTCCGA+TGG + chr4.3:15117712-15117731 None:intergenic 60.0%
AGTGAGGGTTCCGGTGACGA+GGG + chr4.3:15117872-15117891 None:intergenic 60.0%
CACGACCTCCTCCCCGATTA+CGG - chr4.3:15117721-15117740 MS.gene55654:CDS 60.0%
GGAAACCGTAATCGGGGAGG+AGG + chr4.3:15117729-15117748 None:intergenic 60.0%
GGCCTGAATCCCGGAAACAC+CGG + chr4.3:15117908-15117927 None:intergenic 60.0%
GGTCGTGGATGTCCGATGGA+AGG + chr4.3:15117708-15117727 None:intergenic 60.0%
! ACCGGATGAGGAGAGGGTGT+AGG + chr4.3:15117782-15117801 None:intergenic 60.0%
! GGATGAGGAGAGGGTGTAGG+AGG + chr4.3:15117779-15117798 None:intergenic 60.0%
CGTAATCGGGGAGGAGGTCG+TGG + chr4.3:15117723-15117742 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 15117628 15118074 15117628 ID=MS.gene55654
chr4.3 mRNA 15117628 15118074 15117628 ID=MS.gene55654.t1;Parent=MS.gene55654
chr4.3 exon 15117628 15118074 15117628 ID=MS.gene55654.t1.exon1;Parent=MS.gene55654.t1
chr4.3 CDS 15117628 15118074 15117628 ID=cds.MS.gene55654.t1;Parent=MS.gene55654.t1
Gene Sequence

>MS.gene55654

ATGTCCACCAGAACCTTGAAAACCTTGTTTCAATTCTTTTCAACATTCCTATTCATATCCCATGCAACAGCCACAACCCTTCCATCGGACATCCACGACCTCCTCCCCGATTACGGTTTCCCAAAGGGCATCCTTCCTAACAACATCGCCTCCTACACCCTCTCCTCATCCGGTTACTTCACCCTCCATCTCCAATCCCCCTGTTACGTTCGCTTCTCCGGTCAATTAGTCTACTACGACACCCTCGTCACCGGAACCCTCACTTACGGTTCCGTTTCCGGTGTTTCCGGGATTCAGGCCAAGATGCTCTTCATCTGGCTCCCTGTTACTGGAATGGAAGTTGATTCCCGTTCTGGTATGCTTCAATTCTTTGTTGGAGCTTTGTCTAAGAAATTACCGGCGAATCAGTTTCAAGATGTGCCTGGATGTTCTTCAAAACTTCTGCAA
Protein sequence

>MS.gene55654.t1

MSTRTLKTLFQFFSTFLFISHATATTLPSDIHDLLPDYGFPKGILPNNIASYTLSSSGYFTLHLQSPCYVRFSGQLVYYDTLVTGTLTYGSVSGVSGIQAKMLFIWLPVTGMEVDSRSGMLQFFVGALSKKLPANQFQDVPGCSSKLLQ