AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84836

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84836.t1 MTR_8g026960 97.510 241 5 1 1 240 1 241 2.17e-173 476
MS.gene84836.t1 MTR_3g092150 43.541 209 112 3 35 240 40 245 2.22e-48 160
MS.gene84836.t1 MTR_6g007647 53.125 96 45 0 35 130 35 130 4.31e-30 112
MS.gene84836.t1 MTR_6g007647 53.125 96 45 0 35 130 69 164 1.08e-29 112
MS.gene84836.t1 MTR_8g089895 48.148 108 56 0 35 142 56 163 3.47e-29 111
MS.gene84836.t1 MTR_3g086790 38.547 179 97 6 13 187 44 213 1.03e-26 105
MS.gene84836.t1 MTR_6g011610 50.000 112 47 2 14 125 86 188 1.24e-26 104
MS.gene84836.t1 MTR_6g011610 50.000 112 47 2 14 125 67 169 1.28e-26 103
MS.gene84836.t1 MTR_8g468210 40.945 127 70 1 1 127 50 171 4.43e-26 102
MS.gene84836.t1 MTR_5g038280 48.571 105 53 1 35 138 89 193 7.52e-26 103
MS.gene84836.t1 MTR_8g469430 37.222 180 90 6 35 197 91 264 8.80e-26 102
MS.gene84836.t1 MTR_1g061660 39.583 144 66 4 26 160 52 183 2.60e-25 99.8
MS.gene84836.t1 MTR_5g039000 40.984 122 72 0 6 127 50 171 6.39e-25 99.8
MS.gene84836.t1 MTR_4g107650 42.478 113 62 1 35 147 97 206 6.84e-25 100
MS.gene84836.t1 MTR_3g080100 33.668 199 100 6 24 202 15 201 7.39e-24 95.5
MS.gene84836.t1 MTR_3g080100 33.511 188 97 5 35 202 61 240 1.06e-23 95.9
MS.gene84836.t1 MTR_7g103340 48.352 91 40 1 35 125 65 148 5.72e-22 90.9
MS.gene84836.t1 MTR_7g010020 40.800 125 62 2 1 125 53 165 2.78e-21 90.1
MS.gene84836.t1 MTR_5g019680 51.852 81 34 1 21 101 46 121 2.93e-18 80.5
MS.gene84836.t1 MTR_5g019650 51.852 81 34 1 21 101 46 121 9.93e-18 79.3
MS.gene84836.t1 MTR_4g100550 44.578 83 46 0 36 118 123 205 2.77e-14 70.9
MS.gene84836.t1 MTR_7g093430 40.741 108 59 1 11 118 143 245 5.19e-14 70.1
MS.gene84836.t1 MTR_4g126900 42.169 83 48 0 36 118 91 173 1.06e-13 68.2
MS.gene84836.t1 MTR_7g027265 43.243 74 39 1 16 89 6 76 2.93e-12 62.8
MS.gene84836.t1 MTR_5g014890 43.373 83 47 0 36 118 126 208 3.12e-12 65.1
MS.gene84836.t1 MTR_1g054285 43.373 83 47 0 36 118 157 239 3.65e-12 65.1
MS.gene84836.t1 MTR_5g013010 42.169 83 48 0 36 118 139 221 8.36e-12 63.9
MS.gene84836.t1 MTR_2g061030 41.111 90 50 1 32 118 196 285 1.13e-11 63.9
MS.gene84836.t1 MTR_3g103590 31.200 125 82 2 36 157 148 271 2.01e-11 62.8
MS.gene84836.t1 MTR_4g097600 42.169 83 48 0 36 118 130 212 2.18e-11 62.4
MS.gene84836.t1 MTR_8g006705 42.169 83 48 0 36 118 149 231 3.69e-11 62.0
MS.gene84836.t1 MTR_1g017090 40.964 83 49 0 36 118 133 215 7.11e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84836.t1 AT2G46680 49.603 252 108 6 8 240 7 258 3.28e-65 203
MS.gene84836.t1 AT3G61890 54.545 209 85 5 36 240 33 235 3.11e-63 197
MS.gene84836.t1 AT2G46680 48.810 252 108 7 8 240 7 256 1.07e-61 194
MS.gene84836.t1 AT3G01470 44.531 128 70 1 35 161 70 197 4.68e-31 115
MS.gene84836.t1 AT2G22430 52.747 91 43 0 35 125 64 154 1.19e-28 110
MS.gene84836.t1 AT4G40060 50.549 91 45 0 35 125 61 151 2.32e-28 109
MS.gene84836.t1 AT5G65310 48.113 106 49 1 20 125 47 146 1.21e-27 107
MS.gene84836.t1 AT5G65310 48.113 106 49 1 20 125 65 164 1.42e-27 107
MS.gene84836.t1 AT5G15150 39.865 148 78 3 11 157 96 233 3.20e-27 106
MS.gene84836.t1 AT1G69780 45.946 111 55 2 15 125 72 177 3.54e-25 100
MS.gene84836.t1 AT3G01220 45.536 112 51 2 14 125 71 172 1.05e-24 99.4
MS.gene84836.t1 AT4G36740 57.746 71 30 0 35 105 57 127 1.69e-22 92.0
MS.gene84836.t1 AT4G36740 57.746 71 30 0 35 105 58 128 1.82e-22 92.0
MS.gene84836.t1 AT1G26960 47.788 113 46 3 13 125 57 156 1.20e-21 90.5
MS.gene84836.t1 AT2G18550 42.500 120 61 2 35 146 63 182 2.29e-21 89.0
MS.gene84836.t1 AT5G03790 38.760 129 58 3 35 163 79 186 3.11e-21 89.0
MS.gene84836.t1 AT1G27045 45.098 102 56 0 35 136 70 171 1.28e-20 87.8
MS.gene84836.t1 AT5G03790 45.263 95 52 0 35 129 79 173 1.49e-20 86.3
MS.gene84836.t1 AT5G66700 53.521 71 33 0 35 105 73 143 2.58e-20 86.7
MS.gene84836.t1 AT1G27045 48.810 84 43 0 35 118 19 102 2.49e-19 82.8
MS.gene84836.t1 AT1G27045 48.810 84 43 0 35 118 27 110 2.57e-19 82.8
MS.gene84836.t1 AT1G27045 48.810 84 43 0 35 118 27 110 2.57e-19 82.8
MS.gene84836.t1 AT1G27045 48.810 84 43 0 35 118 70 153 3.03e-19 83.6
MS.gene84836.t1 AT2G36610 41.176 102 48 2 32 125 70 167 4.10e-18 79.7
MS.gene84836.t1 AT5G53980 41.071 112 58 2 24 135 3 106 1.01e-16 75.1
MS.gene84836.t1 AT4G37790 40.964 83 49 0 36 118 129 211 1.24e-11 63.5
MS.gene84836.t1 AT2G22800 42.169 83 48 0 36 118 116 198 1.32e-11 63.2
MS.gene84836.t1 AT2G44910 41.772 79 46 0 36 114 166 244 1.67e-11 63.2
MS.gene84836.t1 AT3G60390 41.772 79 46 0 36 114 165 243 1.79e-11 63.2
MS.gene84836.t1 AT5G06710 39.759 83 50 0 36 118 193 275 2.34e-11 63.2
MS.gene84836.t1 AT2G01430 35.455 110 67 1 9 118 119 224 3.50e-11 62.0
MS.gene84836.t1 AT4G17460 41.772 79 46 0 36 114 138 216 4.38e-11 62.0
MS.gene84836.t1 AT4G16780 41.772 79 46 0 36 114 132 210 5.44e-11 61.6

Find 28 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAAATAGTTACAATAATT+TGG 0.124744 8.4:-69963063 MS.gene84836:CDS
CTACTCTGACTTTGCTCTAT+TGG 0.221851 8.4:+69962621 None:intergenic
GCTAATTGCAACTTCTTTCT+TGG 0.222692 8.4:+69963185 None:intergenic
ATTATCAATGGTGGGACTTT+TGG 0.297638 8.4:-69962320 MS.gene84836:CDS
TTTGAATCAAATGATTTGTT+AGG 0.319546 8.4:-69962357 MS.gene84836:CDS
AGCCAAGACAAGTTGCTATA+TGG 0.331941 8.4:-69963145 MS.gene84836:CDS
TCAAAAGCACTCCAATCTTC+TGG 0.368233 8.4:+69962375 None:intergenic
TGTTCTGATCTTTCCATTGA+AGG 0.384421 8.4:+69962513 None:intergenic
CTTTAACATCACCAGAAGAT+TGG 0.390865 8.4:-69962386 MS.gene84836:CDS
ATGGAAAGTGCATCAGAAAA+TGG 0.406512 8.4:-69962573 MS.gene84836:CDS
TGATGAACAAATCAAATCAT+TGG 0.409448 8.4:-69963240 MS.gene84836:CDS
TTTGGTTTAGAAGATGAAAC+TGG 0.409611 8.4:-69962441 MS.gene84836:CDS
AGCATAAAAGTTGAATACTT+TGG 0.419671 8.4:-69962459 MS.gene84836:CDS
GATCTTTCCATTGAAGGACT+TGG 0.420894 8.4:+69962519 None:intergenic
TTCAAAACAAAAGAGCTAGA+TGG 0.440130 8.4:-69963121 MS.gene84836:CDS
TTGCAATTAGCTAGAGAGCT+TGG 0.453561 8.4:-69963173 MS.gene84836:CDS
AAAGTTTGAATCTATGAAGA+AGG 0.456244 8.4:-69963036 MS.gene84836:CDS
AAGACAAACATTACTAATAC+AGG 0.463639 8.4:-69963012 MS.gene84836:intron
AACCATATAGCAACTTGTCT+TGG 0.480304 8.4:+69963143 None:intergenic
GGTGAAACCAAGTCCTTCAA+TGG 0.505148 8.4:-69962526 MS.gene84836:CDS
TATAGTTATTCAGCAGAAGC+AGG 0.509566 8.4:-69963338 MS.gene84836:CDS
AATCAAGTTGTGATTATCAA+TGG 0.520398 8.4:-69962332 MS.gene84836:CDS
AACAATCAAATGTGAGGCTG+AGG 0.535331 8.4:-69962547 MS.gene84836:CDS
CAAGTTGTGATTATCAATGG+TGG 0.557189 8.4:-69962329 MS.gene84836:CDS
AAGTTGTGATTATCAATGGT+GGG 0.604345 8.4:-69962328 MS.gene84836:CDS
AGTTAAAGAAGCAAACAGCA+TGG 0.635070 8.4:-69962592 MS.gene84836:CDS
TGGAGGAACAATCAAATGTG+AGG 0.637358 8.4:-69962553 MS.gene84836:CDS
GAAAGTGCATCAGAAAATGG+AGG 0.672573 8.4:-69962570 MS.gene84836:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAAATAGTTACAATAATT+TGG - chr8.4:69962604-69962623 MS.gene84836:CDS 15.0%
!! TGCGAAATTATTATTAATAA+CGG - chr8.4:69962804-69962823 MS.gene84836:intron 15.0%
!! GAAATTATTATTAATAACGG+TGG - chr8.4:69962807-69962826 MS.gene84836:intron 20.0%
!! TATTCATATAGTAATTTGAC+TGG - chr8.4:69962979-69962998 MS.gene84836:intron 20.0%
!!! ATAAATTTGTTTGCTTAGAA+TGG - chr8.4:69962712-69962731 MS.gene84836:intron 20.0%
!!! TTTGAATCAAATGATTTGTT+AGG - chr8.4:69963310-69963329 MS.gene84836:CDS 20.0%
! AAAGTTTGAATCTATGAAGA+AGG - chr8.4:69962631-69962650 MS.gene84836:CDS 25.0%
! AAGACAAACATTACTAATAC+AGG - chr8.4:69962655-69962674 MS.gene84836:intron 25.0%
! AGAAAAACAAGAATACAAAG+AGG - chr8.4:69962399-69962418 MS.gene84836:CDS 25.0%
! AGCATAAAAGTTGAATACTT+TGG - chr8.4:69963208-69963227 MS.gene84836:CDS 25.0%
! ATCTTGTCAACATTTCAAAA+TGG + chr8.4:69962780-69962799 None:intergenic 25.0%
! TGATGAACAAATCAAATCAT+TGG - chr8.4:69962427-69962446 MS.gene84836:CDS 25.0%
!! AATCAAGTTGTGATTATCAA+TGG - chr8.4:69963335-69963354 MS.gene84836:CDS 25.0%
AAGTTGTGATTATCAATGGT+GGG - chr8.4:69963339-69963358 MS.gene84836:CDS 30.0%
TTCAAAACAAAAGAGCTAGA+TGG - chr8.4:69962546-69962565 MS.gene84836:CDS 30.0%
! GATTGACTTTGTATCTTAAG+TGG + chr8.4:69962864-69962883 None:intergenic 30.0%
! TTTGGTTTAGAAGATGAAAC+TGG - chr8.4:69963226-69963245 MS.gene84836:CDS 30.0%
!! CTTGTTTTTCTTCTTTCTCA+TGG + chr8.4:69962390-69962409 None:intergenic 30.0%
AACCATATAGCAACTTGTCT+TGG + chr8.4:69962527-69962546 None:intergenic 35.0%
AGTTAAAGAAGCAAACAGCA+TGG - chr8.4:69963075-69963094 MS.gene84836:CDS 35.0%
CAAGTTGTGATTATCAATGG+TGG - chr8.4:69963338-69963357 MS.gene84836:CDS 35.0%
CTAATAACCATCGTGTTCAT+CGG + chr8.4:69962906-69962925 None:intergenic 35.0%
CTTTAACATCACCAGAAGAT+TGG - chr8.4:69963281-69963300 MS.gene84836:CDS 35.0%
GATGAACACGATGGTTATTA+GGG - chr8.4:69962905-69962924 MS.gene84836:intron 35.0%
GCTAATTGCAACTTCTTTCT+TGG + chr8.4:69962485-69962504 None:intergenic 35.0%
TATAGTTATTCAGCAGAAGC+AGG - chr8.4:69962329-69962348 MS.gene84836:CDS 35.0%
TGTTCTGATCTTTCCATTGA+AGG + chr8.4:69963157-69963176 None:intergenic 35.0%
! AATTTTGCTGAACATGCTGA+TGG - chr8.4:69963256-69963275 MS.gene84836:CDS 35.0%
! ATGGAAAGTGCATCAGAAAA+TGG - chr8.4:69963094-69963113 MS.gene84836:CDS 35.0%
!! ATTATCAATGGTGGGACTTT+TGG - chr8.4:69963347-69963366 MS.gene84836:CDS 35.0%
AACAATCAAATGTGAGGCTG+AGG - chr8.4:69963120-69963139 MS.gene84836:CDS 40.0%
AGCCAAGACAAGTTGCTATA+TGG - chr8.4:69962522-69962541 MS.gene84836:CDS 40.0%
CGATGAACACGATGGTTATT+AGG - chr8.4:69962904-69962923 MS.gene84836:intron 40.0%
CTACTCTGACTTTGCTCTAT+TGG + chr8.4:69963049-69963068 None:intergenic 40.0%
GATCTTTCCATTGAAGGACT+TGG + chr8.4:69963151-69963170 None:intergenic 40.0%
TGGAGGAACAATCAAATGTG+AGG - chr8.4:69963114-69963133 MS.gene84836:CDS 40.0%
TTGCAATTAGCTAGAGAGCT+TGG - chr8.4:69962494-69962513 MS.gene84836:CDS 40.0%
! GAAAGTGCATCAGAAAATGG+AGG - chr8.4:69963097-69963116 MS.gene84836:CDS 40.0%
!! TCAAAAGCACTCCAATCTTC+TGG + chr8.4:69963295-69963314 None:intergenic 40.0%
GGTGAAACCAAGTCCTTCAA+TGG - chr8.4:69963141-69963160 MS.gene84836:CDS 45.0%
GTTCATCGGTATCAACTCAG+TGG + chr8.4:69962892-69962911 None:intergenic 45.0%
GTTGATACCGATGAACACGA+TGG - chr8.4:69962896-69962915 MS.gene84836:intron 45.0%
!! ATTAAAAATTAAAATTGAAT+TGG + chr8.4:69962757-69962776 None:intergenic 5.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 69962314 69963375 69962314 ID=MS.gene84836
chr8.4 mRNA 69962314 69963375 69962314 ID=MS.gene84836.t1;Parent=MS.gene84836
chr8.4 exon 69963013 69963375 69963013 ID=MS.gene84836.t1.exon1;Parent=MS.gene84836.t1
chr8.4 CDS 69963013 69963375 69963013 ID=cds.MS.gene84836.t1;Parent=MS.gene84836.t1
chr8.4 exon 69962314 69962673 69962314 ID=MS.gene84836.t1.exon2;Parent=MS.gene84836.t1
chr8.4 CDS 69962314 69962673 69962314 ID=cds.MS.gene84836.t1;Parent=MS.gene84836.t1
Gene Sequence

>MS.gene84836

ATGGAATATAGTCAATATAGTTATTCAGCAGAAGCAGGAGAAGAAGAAACATACACAACTAGTAGCACATCTTCCATGAGAAAGAAGAAAAACAAGAATACAAAGAGGTTTAGTGATGAACAAATCAAATCATTGGAAACTATGTTTGAGACTGAGACAAGACTTGAACCAAGAAAGAAGTTGCAATTAGCTAGAGAGCTTGGATTGCAGCCAAGACAAGTTGCTATATGGTTTCAAAACAAAAGAGCTAGATGGAAATCAAAGCAACTTGAAAGAGAATACAACAAACTTCAAAATAGTTACAATAATTTGGCTTCAAAGTTTGAATCTATGAAGAAGGAAAGACAAACATTACTAATACAGGTACTTAGTAGTTGCTAATTAGTAATAATTTTCATATAAATTTGTTTGCTTAGAATGGACTAACATATGTCATATATCCAATTCAATTTTAATTTTTAATCCATTTTGAAATGTTGACAAGATATCGTGCGAAATTATTATTAATAACGGTGGCACTAATAGTTATTTTACAATTGTCACATGTCCACTTAAGATACAAAGTCAATCTCTTACCACTGAGTTGATACCGATGAACACGATGGTTATTAGGGTCACTTAAATTACTAATATATTACATTTTGTATTGATTATTATCATATAGTTATTCATATAGTAATTTGACTGGTTTTCATTCAACAGTTGCAGAAGCTGAATGATCTAATACAAAAGCCAATAGAGCAAAGTCAGAGTAGTTCACAAGTTAAAGAAGCAAACAGCATGGAAAGTGCATCAGAAAATGGAGGAACAATCAAATGTGAGGCTGAGGTGAAACCAAGTCCTTCAATGGAAAGATCAGAACATGTACTTGATGTTCTATCAGATGATGACACAAGCATAAAAGTTGAATACTTTGGTTTAGAAGATGAAACTGGTCTAATGAATTTTGCTGAACATGCTGATGGTTCTTTAACATCACCAGAAGATTGGAGTGCTTTTGAATCAAATGATTTGTTAGGTCAATCAAGTTGTGATTATCAATGGTGGGACTTTTGGTCTTGA
Protein sequence

>MS.gene84836.t1

MEYSQYSYSAEAGEEETYTTSSTSSMRKKKNKNTKRFSDEQIKSLETMFETETRLEPRKKLQLARELGLQPRQVAIWFQNKRARWKSKQLEREYNKLQNSYNNLASKFESMKKERQTLLIQLQKLNDLIQKPIEQSQSSSQVKEANSMESASENGGTIKCEAEVKPSPSMERSEHVLDVLSDDDTSIKVEYFGLEDETGLMNFAEHADGSLTSPEDWSAFESNDLLGQSSCDYQWWDFWS