AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene022312

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene022312.t1 MTR_3g077560 97.638 127 3 0 1 127 1 127 2.14e-91 260
MS.gene022312.t1 MTR_3g077570 81.667 120 19 1 1 120 1 117 2.16e-70 207
MS.gene022312.t1 MTR_7g035245 59.048 105 43 0 21 125 3 107 4.95e-44 139
MS.gene022312.t1 MTR_1g069255 48.000 100 49 2 25 123 87 184 9.13e-26 95.9
MS.gene022312.t1 MTR_2g038560 42.000 100 51 1 15 114 29 121 6.23e-23 87.0
MS.gene022312.t1 MTR_2g038560 42.000 100 51 1 15 114 70 162 8.08e-23 88.2
MS.gene022312.t1 MTR_2g038560 42.000 100 51 1 15 114 73 165 8.86e-23 87.8
MS.gene022312.t1 MTR_5g021090 42.353 85 49 0 30 114 42 126 1.91e-19 78.2
MS.gene022312.t1 MTR_2g019900 38.000 100 62 0 21 120 1 100 2.00e-18 74.7
MS.gene022312.t1 MTR_7g022690 39.423 104 62 1 18 120 27 130 7.89e-18 73.9
MS.gene022312.t1 MTR_1g088905 34.000 100 66 0 21 120 1 100 8.74e-18 73.2
MS.gene022312.t1 MTR_7g022710 40.385 104 61 1 18 120 27 130 9.08e-18 73.9
MS.gene022312.t1 MTR_7g022550 39.423 104 62 1 18 120 27 130 1.56e-17 73.2
MS.gene022312.t1 MTR_7g108250 34.000 100 66 0 21 120 1 100 1.40e-16 70.1
MS.gene022312.t1 MTR_4g119050 35.644 101 64 1 21 120 1 101 1.10e-15 67.8
MS.gene022312.t1 MTR_4g119030 35.644 101 64 1 21 120 1 101 1.10e-15 67.8
MS.gene022312.t1 MTR_4g119040 35.644 101 64 1 21 120 1 101 1.10e-15 67.8
MS.gene022312.t1 MTR_7g108220 36.634 101 63 1 21 120 1 101 1.17e-15 67.8
MS.gene022312.t1 MTR_7g026770 37.615 109 67 1 13 120 14 122 2.13e-15 70.9
MS.gene022312.t1 MTR_1g088925 34.043 94 62 0 21 114 1 94 2.35e-15 67.0
MS.gene022312.t1 MTR_1g088920 34.043 94 62 0 21 114 1 94 2.59e-15 66.6
MS.gene022312.t1 MTR_2g048970 35.354 99 60 1 26 120 33 131 5.77e-15 66.6
MS.gene022312.t1 MTR_7g108210 35.644 101 64 1 21 120 1 101 5.95e-15 65.9
MS.gene022312.t1 MTR_1g088910 35.000 100 65 0 21 120 1 100 1.07e-14 65.1
MS.gene022312.t1 MTR_2g019950 32.000 100 68 0 21 120 1 100 1.86e-14 64.7
MS.gene022312.t1 MTR_7g108260 35.106 94 61 0 27 120 7 100 3.27e-14 63.9
MS.gene022312.t1 MTR_1g088895 35.106 94 61 0 27 120 7 100 1.45e-13 62.4
MS.gene022312.t1 MTR_5g077550 40.476 84 48 1 39 120 38 121 1.74e-13 62.8
MS.gene022312.t1 MTR_7g108200 31.915 94 64 0 21 114 1 94 2.26e-12 59.3
MS.gene022312.t1 MTR_2g014760 35.000 100 62 3 22 120 28 125 3.20e-12 59.3
MS.gene022312.t1 MTR_2g090755 35.135 111 63 3 13 120 34 138 4.23e-11 57.0
MS.gene022312.t1 MTR_1g015890 31.132 106 69 2 18 120 43 147 8.22e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene022312.t1 AT5G63030 65.354 127 42 1 1 127 1 125 5.05e-59 178
MS.gene022312.t1 AT5G40370 62.857 105 39 0 21 125 3 107 4.80e-47 147
MS.gene022312.t1 AT5G40370 64.835 91 32 0 35 125 42 132 4.17e-41 133
MS.gene022312.t1 AT2G20270 48.000 100 50 2 20 117 73 172 2.33e-24 92.0
MS.gene022312.t1 AT5G20500 42.105 95 55 0 24 118 35 129 3.18e-23 88.2
MS.gene022312.t1 AT1G77370 46.512 86 46 0 30 115 43 128 2.75e-22 85.5
MS.gene022312.t1 AT4G28730 41.748 103 56 2 16 117 68 167 2.86e-21 84.0
MS.gene022312.t1 AT5G14070 38.532 109 59 1 20 120 30 138 1.63e-19 78.6
MS.gene022312.t1 AT2G20270 37.795 127 50 2 20 117 73 199 3.29e-19 79.7
MS.gene022312.t1 AT5G18600 38.000 100 62 0 21 120 1 100 1.83e-17 72.4
MS.gene022312.t1 AT1G77370 36.036 111 45 1 30 114 43 153 6.82e-17 72.4
MS.gene022312.t1 AT1G03020 39.000 100 61 0 21 120 1 100 1.26e-16 70.1
MS.gene022312.t1 AT3G02000 36.697 109 63 1 18 120 26 134 5.36e-16 69.7
MS.gene022312.t1 AT4G15700 39.394 99 59 1 22 120 3 100 9.70e-16 67.8
MS.gene022312.t1 AT4G33040 32.203 118 76 1 7 120 25 142 1.58e-15 68.6
MS.gene022312.t1 AT3G62930 35.000 100 65 0 21 120 1 100 1.61e-15 67.4
MS.gene022312.t1 AT4G15670 34.000 100 66 0 21 120 1 100 5.01e-15 66.2
MS.gene022312.t1 AT4G15680 33.000 100 67 0 21 120 1 100 9.57e-15 65.5
MS.gene022312.t1 AT4G15690 37.374 99 61 1 22 120 3 100 1.40e-14 65.1
MS.gene022312.t1 AT4G15660 34.000 100 66 0 21 120 1 100 2.39e-14 64.3
MS.gene022312.t1 AT3G62950 30.693 101 69 1 21 120 1 101 3.01e-14 64.3
MS.gene022312.t1 AT1G28480 32.773 119 67 3 7 120 25 135 3.40e-14 65.1
MS.gene022312.t1 AT3G21460 33.000 100 67 0 21 120 1 100 1.19e-13 62.8
MS.gene022312.t1 AT2G47880 31.000 100 69 0 21 120 1 100 1.27e-13 62.4
MS.gene022312.t1 AT1G06830 31.915 94 64 0 21 114 1 94 3.33e-13 61.2
MS.gene022312.t1 AT3G62960 30.851 94 65 0 21 114 1 94 4.44e-13 61.2
MS.gene022312.t1 AT5G11930 33.645 107 61 3 15 120 49 146 6.08e-13 62.0
MS.gene022312.t1 AT2G47870 29.703 101 70 1 21 120 1 101 7.13e-13 60.5
MS.gene022312.t1 AT4G28730 40.789 76 41 2 16 90 68 140 1.42e-12 60.8
MS.gene022312.t1 AT2G30540 32.979 94 63 0 21 114 1 94 1.45e-12 59.7

Find 34 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTGTTTCCATCTCTTCTT+TGG 0.212250 3.4:-74482228 None:intergenic
ACAGTACCTAATGTGTTTAT+TGG 0.265313 3.4:+74483086 MS.gene022312:CDS
TTTATTTGTTGCAGCTGTTT+TGG 0.272729 3.4:+74483247 MS.gene022312:intron
TCAGAGCTGAGCAGAGTTCT+TGG 0.303817 3.4:-74483324 None:intergenic
CACTTTCTATATCCATTTCA+AGG 0.388516 3.4:-74482851 None:intergenic
ATCCATTTCAAGGACCTTGT+AGG 0.400003 3.4:-74482841 None:intergenic
CTTATTGTGGTTACTGCAAA+CGG 0.407824 3.4:+74482787 MS.gene022312:CDS
CAAATAATGGGTTCTATGCT+TGG 0.415863 3.4:+74482185 None:intergenic
ATTCCCCTTCTCACTGATGC+TGG 0.424957 3.4:+74483293 MS.gene022312:CDS
AACCTACAAGGTCCTTGAAA+TGG 0.451012 3.4:+74482839 MS.gene022312:CDS
TTGCCTCCAATAAACACATT+AGG 0.466203 3.4:-74483092 None:intergenic
CGCTCCAGCATCAGTGAGAA+GGG 0.479868 3.4:-74483297 None:intergenic
TTATTGTGGTTACTGCAAAC+GGG 0.502636 3.4:+74482788 MS.gene022312:CDS
AATAACCTGAAGACAAAGAC+GGG 0.504868 3.4:-74482284 None:intergenic
TGGTTACTGCAAACGGGTCA+AGG 0.522187 3.4:+74482794 MS.gene022312:CDS
GTACCTAATGTGTTTATTGG+AGG 0.525018 3.4:+74483089 MS.gene022312:CDS
GCAGCATTAACTGAGTGGAC+AGG 0.525614 3.4:+74483056 MS.gene022312:CDS
ATTGGAGGCAAGCACATTGG+TGG 0.528449 3.4:+74483104 MS.gene022312:CDS
TATGACAGTAAGACTTATTG+TGG 0.543804 3.4:+74482774 MS.gene022312:intron
TCAAGGGACCAAAGAAGAGA+TGG 0.547018 3.4:+74482220 MS.gene022312:CDS
TCGCTCCAGCATCAGTGAGA+AGG 0.547446 3.4:-74483298 None:intergenic
CTTGGTTCTCAGAAGACTCA+AGG 0.550504 3.4:+74482203 MS.gene022312:CDS
CAGCATTAACTGAGTGGACA+GGG 0.563697 3.4:+74483057 MS.gene022312:CDS
TAACTGAGTGGACAGGGCAA+AGG 0.599599 3.4:+74483063 MS.gene022312:CDS
AAGGATCTACTCAAACAGCT+AGG 0.624288 3.4:+74482813 MS.gene022312:CDS
AAATAACCTGAAGACAAAGA+CGG 0.625074 3.4:-74482285 None:intergenic
TTGGTTCTCAGAAGACTCAA+GGG 0.625272 3.4:+74482204 MS.gene022312:CDS
ACAGCTAGGAGCAACCTACA+AGG 0.634355 3.4:+74482827 MS.gene022312:CDS
TTTATTGGAGGCAAGCACAT+TGG 0.645273 3.4:+74483101 MS.gene022312:CDS
GGGGAATCAATTGACCTGCA+CGG 0.659613 3.4:-74483277 None:intergenic
GCTCCAGCATCAGTGAGAAG+GGG 0.673549 3.4:-74483296 None:intergenic
TTCATGCAGCATTAACTGAG+TGG 0.679113 3.4:+74483051 MS.gene022312:CDS
ATAACCTGAAGACAAAGACG+GGG 0.734989 3.4:-74482283 None:intergenic
TAACCTGAAGACAAAGACGG+GGG 0.745087 3.4:-74482282 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATATTTTTTTAGGTAATAG+GGG + chr3.4:74482370-74482389 MS.gene022312:intron 15.0%
!!! CAATATTTTTTTAGGTAATA+GGG + chr3.4:74482369-74482388 MS.gene022312:intron 15.0%
!!! TCAATATTTTTTTAGGTAAT+AGG + chr3.4:74482368-74482387 MS.gene022312:intron 15.0%
!! ATTTCTCAATAAATACAAAG+TGG + chr3.4:74482959-74482978 MS.gene022312:intron 20.0%
!! TCATAACATAAATTACAGAT+GGG - chr3.4:74482759-74482778 None:intergenic 20.0%
!! TTTCTCAATAAATACAAAGT+GGG + chr3.4:74482960-74482979 MS.gene022312:intron 20.0%
!!! GAAATATGTCTTTTGATTTA+TGG + chr3.4:74482447-74482466 MS.gene022312:intron 20.0%
!!! TGAGTTGAAAAATAAATTCA+AGG + chr3.4:74482557-74482576 MS.gene022312:intron 20.0%
! ATGCTTTATGAAAATGAACA+AGG - chr3.4:74482712-74482731 None:intergenic 25.0%
! ATTTGTCTTTACCTATTTGA+AGG + chr3.4:74483014-74483033 MS.gene022312:intron 25.0%
! CAACATGTATTGTATTGAAT+TGG + chr3.4:74482647-74482666 MS.gene022312:intron 25.0%
! GTCATAACATAAATTACAGA+TGG - chr3.4:74482760-74482779 None:intergenic 25.0%
! GTTGATCAAAATACTAGTTA+AGG + chr3.4:74482340-74482359 MS.gene022312:intron 25.0%
! TTGTATTGAATTGGTTGTTA+AGG + chr3.4:74482656-74482675 MS.gene022312:intron 25.0%
! TTTATGAAAATGAACAAGGA+GGG - chr3.4:74482708-74482727 None:intergenic 25.0%
!!! GGAGATGTCAATATTTTTTT+AGG + chr3.4:74482361-74482380 MS.gene022312:intron 25.0%
!!! TTATTTCTATATACTGTGCA+TGG + chr3.4:74482417-74482436 MS.gene022312:intron 25.0%
AAATAACCTGAAGACAAAGA+CGG - chr3.4:74482288-74482307 None:intergenic 30.0%
AATTACAGATGGGATTATCA+AGG - chr3.4:74482749-74482768 None:intergenic 30.0%
ACAGTACCTAATGTGTTTAT+TGG + chr3.4:74483086-74483105 MS.gene022312:CDS 30.0%
CACTTTCTATATCCATTTCA+AGG - chr3.4:74482854-74482873 None:intergenic 30.0%
CTTTATGAAAATGAACAAGG+AGG - chr3.4:74482709-74482728 None:intergenic 30.0%
TATGACAGTAAGACTTATTG+TGG + chr3.4:74482774-74482793 MS.gene022312:intron 30.0%
TTGGTTGTTAAGGTATAGTT+TGG + chr3.4:74482666-74482685 MS.gene022312:intron 30.0%
! TCTAGCTTCAAATTAGAATG+AGG + chr3.4:74482610-74482629 MS.gene022312:intron 30.0%
!! TTTATTTGTTGCAGCTGTTT+TGG + chr3.4:74483247-74483266 MS.gene022312:intron 30.0%
AATAACCTGAAGACAAAGAC+GGG - chr3.4:74482287-74482306 None:intergenic 35.0%
AATCTCAACCCAGATAGAAA+AGG - chr3.4:74482903-74482922 None:intergenic 35.0%
CACATGAAAAAAGAAGCAAC+AGG - chr3.4:74483153-74483172 None:intergenic 35.0%
CTTATTGTGGTTACTGCAAA+CGG + chr3.4:74482787-74482806 MS.gene022312:CDS 35.0%
CTTTACCTATTTGAAGGTGA+TGG + chr3.4:74483020-74483039 MS.gene022312:intron 35.0%
GTACCTAATGTGTTTATTGG+AGG + chr3.4:74483089-74483108 MS.gene022312:CDS 35.0%
TGACACTACAAAACCAAACA+CGG - chr3.4:74482479-74482498 None:intergenic 35.0%
TTATTGTGGTTACTGCAAAC+GGG + chr3.4:74482788-74482807 MS.gene022312:CDS 35.0%
TTGCCTCCAATAAACACATT+AGG - chr3.4:74483095-74483114 None:intergenic 35.0%
! GCTTTGTACCTTTTCTATCT+GGG + chr3.4:74482892-74482911 MS.gene022312:intron 35.0%
! TGCTTTGTACCTTTTCTATC+TGG + chr3.4:74482891-74482910 MS.gene022312:intron 35.0%
!!! CTGTTGCTTCTTTTTTCATG+TGG + chr3.4:74483151-74483170 MS.gene022312:intron 35.0%
AACCTACAAGGTCCTTGAAA+TGG + chr3.4:74482839-74482858 MS.gene022312:CDS 40.0%
AAGGATCTACTCAAACAGCT+AGG + chr3.4:74482813-74482832 MS.gene022312:CDS 40.0%
ATAACCTGAAGACAAAGACG+GGG - chr3.4:74482286-74482305 None:intergenic 40.0%
ATCCATTTCAAGGACCTTGT+AGG - chr3.4:74482844-74482863 None:intergenic 40.0%
CATCTCCATCACCTTCAAAT+AGG - chr3.4:74483028-74483047 None:intergenic 40.0%
GACACTACAAAACCAAACAC+GGG - chr3.4:74482478-74482497 None:intergenic 40.0%
TTCATGCAGCATTAACTGAG+TGG + chr3.4:74483051-74483070 MS.gene022312:CDS 40.0%
TTTATTGGAGGCAAGCACAT+TGG + chr3.4:74483101-74483120 MS.gene022312:CDS 40.0%
! CGTTGTTTCCATCTCTTCTT+TGG - chr3.4:74482231-74482250 None:intergenic 40.0%
! TTGGTTCTCAGAAGACTCAA+GGG + chr3.4:74482204-74482223 MS.gene022312:CDS 40.0%
CAGCATTAACTGAGTGGACA+GGG + chr3.4:74483057-74483076 MS.gene022312:CDS 45.0%
TAACCTGAAGACAAAGACGG+GGG - chr3.4:74482285-74482304 None:intergenic 45.0%
TCAAGGGACCAAAGAAGAGA+TGG + chr3.4:74482220-74482239 MS.gene022312:CDS 45.0%
TTTATGGTCAAGCCCGTGTT+TGG + chr3.4:74482463-74482482 MS.gene022312:intron 45.0%
! CATTGGTGGTTGTGACTGTA+AGG + chr3.4:74483118-74483137 MS.gene022312:intron 45.0%
! CTTGGTTCTCAGAAGACTCA+AGG + chr3.4:74482203-74482222 MS.gene022312:CDS 45.0%
ACAGCTAGGAGCAACCTACA+AGG + chr3.4:74482827-74482846 MS.gene022312:CDS 50.0%
ATTCCCCTTCTCACTGATGC+TGG + chr3.4:74483293-74483312 MS.gene022312:CDS 50.0%
ATTGGAGGCAAGCACATTGG+TGG + chr3.4:74483104-74483123 MS.gene022312:CDS 50.0%
GCAGCATTAACTGAGTGGAC+AGG + chr3.4:74483056-74483075 MS.gene022312:CDS 50.0%
GGGGAATCAATTGACCTGCA+CGG - chr3.4:74483280-74483299 None:intergenic 50.0%
TAACTGAGTGGACAGGGCAA+AGG + chr3.4:74483063-74483082 MS.gene022312:CDS 50.0%
TCAGAGCTGAGCAGAGTTCT+TGG - chr3.4:74483327-74483346 None:intergenic 50.0%
TGGTTACTGCAAACGGGTCA+AGG + chr3.4:74482794-74482813 MS.gene022312:CDS 50.0%
!!! GTTTTGGAGAAACACCGTGC+AGG + chr3.4:74483263-74483282 MS.gene022312:CDS 50.0%
CGCTCCAGCATCAGTGAGAA+GGG - chr3.4:74483300-74483319 None:intergenic 55.0%
CTTCCCCCGTCTTTGTCTTC+AGG + chr3.4:74482279-74482298 MS.gene022312:CDS 55.0%
GAAGACAAAGACGGGGGAAG+AGG - chr3.4:74482279-74482298 None:intergenic 55.0%
GCTCCAGCATCAGTGAGAAG+GGG - chr3.4:74483299-74483318 None:intergenic 55.0%
TCGCTCCAGCATCAGTGAGA+AGG - chr3.4:74483301-74483320 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 74482191 74483346 74482191 ID=MS.gene022312
chr3.4 mRNA 74482191 74483346 74482191 ID=MS.gene022312.t1;Parent=MS.gene022312
chr3.4 exon 74482191 74482300 74482191 ID=MS.gene022312.t1.exon1;Parent=MS.gene022312.t1
chr3.4 CDS 74482191 74482300 74482191 ID=cds.MS.gene022312.t1;Parent=MS.gene022312.t1
chr3.4 exon 74482782 74482870 74482782 ID=MS.gene022312.t1.exon2;Parent=MS.gene022312.t1
chr3.4 CDS 74482782 74482870 74482782 ID=cds.MS.gene022312.t1;Parent=MS.gene022312.t1
chr3.4 exon 74483036 74483134 74483036 ID=MS.gene022312.t1.exon3;Parent=MS.gene022312.t1
chr3.4 CDS 74483036 74483134 74483036 ID=cds.MS.gene022312.t1;Parent=MS.gene022312.t1
chr3.4 exon 74483261 74483346 74483261 ID=MS.gene022312.t1.exon4;Parent=MS.gene022312.t1
chr3.4 CDS 74483261 74483346 74483261 ID=cds.MS.gene022312.t1;Parent=MS.gene022312.t1
Gene Sequence

>MS.gene022312

ATGGGTTCTATGCTTGGTTCTCAGAAGACTCAAGGGACCAAAGAAGAGATGGAAACAACGTTGAATAAAACTAAACAGATTGCTGCCTCTTCCCCCGTCTTTGTCTTCAGGTTATTTTTATTTCTATCTAATCTTAGTAACATGTTTTTGTTGATCAAAATACTAGTTAAGGAGATGTCAATATTTTTTTAGGTAATAGGGGAATCTCGAAATAGAGAGACTATATTTATTTCTATATACTGTGCATGGAAGTTTAGAAATATGTCTTTTGATTTATGGTCAAGCCCGTGTTTGGTTTTGTAGTGTCACAAATTAATTTTGAATGAATTGATTATAGCTAAGAATGAATTGAATGTAAAAAGAAAATGAGTTGAAAAATAAATTCAAGGCTAAAAAAATAATTCTATAAAACTACATATTCTAGCTTCAAATTAGAATGAGGTAAAATTAGTTCTGCAACATGTATTGTATTGAATTGGTTGTTAAGGTATAGTTTGGTGTTTTTCACATGTAGCCCTCCTTGTTCATTTTCATAAAGCATTTTTTTGTTTTTAACCTTGATAATCCCATCTGTAATTTATGTTATGACAGTAAGACTTATTGTGGTTACTGCAAACGGGTCAAGGATCTACTCAAACAGCTAGGAGCAACCTACAAGGTCCTTGAAATGGATATAGAAAGTGAGTTTACTTATTTCTCATGCTTTGTACCTTTTCTATCTGGGTTGAGATTGTATGTGAATGTGCAAAATGCAAAAATGAGAGTCTTATTTCTCAATAAATACAAAGTGGGTCTATCTATTATTATTATCTTCTGTTCTTGAATTTGTCTTTACCTATTTGAAGGTGATGGAGATGAGATTCATGCAGCATTAACTGAGTGGACAGGGCAAAGGACAGTACCTAATGTGTTTATTGGAGGCAAGCACATTGGTGGTTGTGACTGTAAGGCTACACACTCCTGTTGCTTCTTTTTTCATGTGGCAAAGACAAAATTAGAGTTGTTTTTTTCTTTCTCTGTTTTCATTATTTGTGTGTGTAATATTTTTATCACATGTTTATTTGTTGCAGCTGTTTTGGAGAAACACCGTGCAGGTCAATTGATTCCCCTTCTCACTGATGCTGGAGCGATCGCCAAGAACTCTGCTCAGCTCTGA
Protein sequence

>MS.gene022312.t1

MGSMLGSQKTQGTKEEMETTLNKTKQIAASSPVFVFSKTYCGYCKRVKDLLKQLGATYKVLEMDIESDGDEIHAALTEWTGQRTVPNVFIGGKHIGGCDSVLEKHRAGQLIPLLTDAGAIAKNSAQL