AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47395

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47395.t1 MTR_1g062160 99.507 203 1 0 1 203 1 203 2.81e-154 425
MS.gene47395.t1 MTR_7g102790 78.431 204 41 2 1 202 1 203 9.29e-109 310
MS.gene47395.t1 MTR_5g007230 55.612 196 79 4 7 202 21 208 3.27e-72 218
MS.gene47395.t1 MTR_5g030130 54.680 203 79 4 7 202 35 231 7.68e-72 218
MS.gene47395.t1 MTR_8g066820 55.340 206 73 5 7 202 33 229 3.87e-70 213
MS.gene47395.t1 MTR_4g078170 53.465 202 81 4 7 202 15 209 5.46e-70 212
MS.gene47395.t1 MTR_5g030130 66.667 129 42 1 7 135 35 162 5.20e-59 183
MS.gene47395.t1 MTR_2g084495 38.136 236 100 7 4 201 2 229 4.71e-46 152
MS.gene47395.t1 MTR_2g060500 50.000 146 63 4 1 137 5 149 2.00e-42 140
MS.gene47395.t1 MTR_2g060540 51.408 142 59 4 1 133 5 145 4.36e-42 139
MS.gene47395.t1 MTR_2g084510 37.398 246 101 7 4 201 1 241 2.83e-40 137
MS.gene47395.t1 MTR_2g084525 46.108 167 77 6 4 161 1 163 2.20e-38 132
MS.gene47395.t1 MTR_2g055210 42.308 130 72 3 5 134 100 226 2.24e-33 122
MS.gene47395.t1 MTR_4g094680 32.877 219 119 6 7 201 22 236 3.27e-30 111
MS.gene47395.t1 MTR_4g116300 42.188 128 72 2 7 134 6 131 1.30e-29 110
MS.gene47395.t1 MTR_2g036170 31.250 224 118 6 7 202 37 252 4.41e-28 106
MS.gene47395.t1 MTR_8g105930 36.054 147 70 6 9 134 15 158 3.31e-20 85.5
MS.gene47395.t1 MTR_5g077740 29.744 195 106 6 7 201 23 186 2.05e-19 82.0
MS.gene47395.t1 MTR_8g097310 32.075 159 96 3 46 201 4 153 5.15e-19 80.1
MS.gene47395.t1 MTR_2g083710 49.206 63 30 2 1 62 1 62 8.86e-16 69.3
MS.gene47395.t1 MTR_1g032880 39.535 86 47 3 54 135 27 111 1.34e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47395.t1 AT1G32700 53.769 199 86 3 7 202 12 207 2.58e-71 216
MS.gene47395.t1 AT2G27930 54.327 208 66 3 4 202 1 188 3.64e-68 207
MS.gene47395.t1 AT2G27930 54.327 208 66 3 4 202 1 188 3.64e-68 207
MS.gene47395.t1 AT1G76590 46.957 230 85 4 7 201 18 245 2.26e-65 202
MS.gene47395.t1 AT1G21000 45.923 233 86 6 7 201 13 243 9.13e-65 200
MS.gene47395.t1 AT1G21000 45.923 233 86 6 7 201 16 246 1.04e-64 200
MS.gene47395.t1 AT4G17900 51.471 204 81 7 7 202 20 213 3.53e-64 197
MS.gene47395.t1 AT4G17900 51.471 204 81 7 7 202 34 227 3.95e-64 198
MS.gene47395.t1 AT1G43000 45.581 215 100 5 2 201 11 223 1.64e-60 189
MS.gene47395.t1 AT1G43000 45.581 215 100 5 2 201 4 216 1.91e-60 188
MS.gene47395.t1 AT2G27930 61.290 155 51 1 4 149 1 155 4.33e-59 183
MS.gene47395.t1 AT2G27930 61.290 155 51 1 4 149 1 155 4.33e-59 183
MS.gene47395.t1 AT5G46710 48.744 199 97 4 7 201 12 209 2.63e-57 180
MS.gene47395.t1 AT5G46710 48.744 199 97 4 7 201 28 225 5.22e-57 180
MS.gene47395.t1 AT1G32700 52.632 171 75 3 35 202 1 168 1.02e-55 175
MS.gene47395.t1 AT5G46710 58.140 129 52 2 7 134 28 155 4.75e-49 157
MS.gene47395.t1 AT2G27930 52.318 151 43 3 61 202 61 191 7.71e-42 140
MS.gene47395.t1 AT2G27930 52.318 151 43 3 61 202 61 191 7.71e-42 140
MS.gene47395.t1 AT1G31040 34.361 227 114 7 7 201 19 242 2.90e-35 124
MS.gene47395.t1 AT3G60670 38.650 163 91 4 1 156 1 161 4.94e-31 114
MS.gene47395.t1 AT2G12646 43.750 128 70 2 7 134 3 128 1.08e-29 110
MS.gene47395.t1 AT2G12646 43.750 128 70 2 7 134 6 131 1.35e-29 110
MS.gene47395.t1 AT2G12646 43.750 128 70 2 7 134 6 131 1.35e-29 110
MS.gene47395.t1 AT2G01818 30.516 213 124 7 9 201 13 221 5.76e-23 92.4

Find 44 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAAGTTCGTTTCTGTTCTT+TGG 0.184177 1.4:+51169464 MS.gene47395:CDS
AGAAGTGGTTTGAGCCATTT+AGG 0.226031 1.4:-51168979 None:intergenic
ATTCCTCACAGGGCTCCTTT+TGG 0.269600 1.4:+51170080 MS.gene47395:CDS
AGAAACGAACTTGGTCTAAA+AGG 0.306972 1.4:-51169455 None:intergenic
ACACAATGTTGGTTCCTAAA+TGG 0.324494 1.4:+51168965 MS.gene47395:CDS
CAAGGATCATCAAGTCATTC+AGG 0.333682 1.4:+51169122 MS.gene47395:CDS
TTTCTTCTCCTTGCGTTTGA+AGG 0.347275 1.4:-51170053 None:intergenic
CAAGTTCGTTTCTGTTCTTT+GGG 0.351554 1.4:+51169465 MS.gene47395:CDS
CTTGTAGGAATAAAGAGAAA+TGG 0.373461 1.4:+51169897 MS.gene47395:CDS
TTTCTGTTCTTTGGGATGTA+AGG 0.374729 1.4:+51169473 MS.gene47395:CDS
CAGAAAATGTTGGACATTAG+TGG 0.376562 1.4:+51169324 MS.gene47395:CDS
GGAGGTGTTGGAGGAGTTGC+TGG 0.378339 1.4:-51170032 None:intergenic
GAGAGGCCTCAACCAAAATC+TGG 0.407501 1.4:+51169393 MS.gene47395:CDS
CAATGATTGAATTAGCTTGT+AGG 0.416656 1.4:+51169882 MS.gene47395:intron
TTGTAGGAATAAAGAGAAAT+GGG 0.420634 1.4:+51169898 MS.gene47395:CDS
TCAAACGCAAGGAGAAGAAA+AGG 0.442491 1.4:+51170056 MS.gene47395:CDS
CCTTACATTTGTGAGATTTG+TGG 0.451494 1.4:+51169426 MS.gene47395:CDS
CTTGCGTTTGAAGGAGGTGT+TGG 0.453994 1.4:-51170044 None:intergenic
GAAGAAAAGGGATTCCTCAC+AGG 0.476374 1.4:+51170069 MS.gene47395:CDS
CCAAAGAACAGAAACGAACT+TGG 0.484387 1.4:-51169464 None:intergenic
CCACAAATCTCACAAATGTA+AGG 0.486176 1.4:-51169426 None:intergenic
TAAAATGACTAGGGTCCAAA+AGG 0.492758 1.4:-51170095 None:intergenic
GCGTTTGAAGGAGGTGTTGG+AGG 0.501278 1.4:-51170041 None:intergenic
CTTCTCCTTGCGTTTGAAGG+AGG 0.504177 1.4:-51170050 None:intergenic
GAGGTATCAACAATGGAAGA+AGG 0.508623 1.4:+51169954 MS.gene47395:CDS
GGCTGAAATTCAGAAAATGT+TGG 0.529817 1.4:+51169314 MS.gene47395:CDS
ATTTGTGAGATTTGTGGAAG+AGG 0.530195 1.4:+51169432 MS.gene47395:CDS
ACATTCACTCCTTGCGGCGT+CGG 0.535957 1.4:-51169037 None:intergenic
CAAACGCAAGGAGAAGAAAA+GGG 0.546728 1.4:+51170057 MS.gene47395:CDS
AGAACGACAATAGAAGCAAA+AGG 0.552138 1.4:-51169091 None:intergenic
AGATTCACGCCGACGCCGCA+AGG 0.561083 1.4:+51169028 MS.gene47395:CDS
AGGTATCAACAATGGAAGAA+GGG 0.569523 1.4:+51169955 MS.gene47395:CDS
TTTAGATGCAAATAACAATG+AGG 0.589036 1.4:+51169935 MS.gene47395:CDS
CTTCATATCATGATGTAGTG+AGG 0.591334 1.4:+51169289 MS.gene47395:CDS
TAACAATGAGGTATCAACAA+TGG 0.597297 1.4:+51169947 MS.gene47395:CDS
TTCATATCATGATGTAGTGA+GGG 0.599632 1.4:+51169290 MS.gene47395:CDS
TTGTCGTTCTTCAAAACACA+AGG 0.606276 1.4:+51169104 MS.gene47395:CDS
CAACACCTCCTTCAAACGCA+AGG 0.609547 1.4:+51170045 MS.gene47395:CDS
TTGCGTGAAGGCTCACAACA+AGG 0.621390 1.4:+51170002 MS.gene47395:CDS
AAGAAAAGGGATTCCTCACA+GGG 0.635472 1.4:+51170070 MS.gene47395:CDS
CATGTTACATTCACTCCTTG+CGG 0.659509 1.4:-51169043 None:intergenic
CAAGAAGAAGAATTGCGTGA+AGG 0.666815 1.4:+51169990 MS.gene47395:CDS
ATATCATGATGTAGTGAGGG+TGG 0.676670 1.4:+51169293 MS.gene47395:CDS
GGTCCAAAAGGAGCCCTGTG+AGG 0.707085 1.4:-51170083 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAAAAAATATATACTTT+AGG - chr1.4:51169247-51169266 None:intergenic 10.0%
!!! AAAGTATATATTTTTTTTGT+TGG + chr1.4:51169247-51169266 MS.gene47395:intron 10.0%
!! ATAATTATTGAATAGTAGAT+AGG + chr1.4:51169776-51169795 MS.gene47395:intron 15.0%
!!! TATGCACATTTTTTTATAAT+GGG + chr1.4:51169173-51169192 MS.gene47395:intron 15.0%
!!! TTATGCACATTTTTTTATAA+TGG + chr1.4:51169172-51169191 MS.gene47395:intron 15.0%
!! TAAGAAAATAATTTAGGAAC+CGG - chr1.4:51169155-51169174 None:intergenic 20.0%
!! TATATGAAGCATATAACTAT+AGG + chr1.4:51169666-51169685 MS.gene47395:intron 20.0%
!! TGTGCATAAGAAAATAATTT+AGG - chr1.4:51169161-51169180 None:intergenic 20.0%
!!! ATGCACATTTTTTTATAATG+GGG + chr1.4:51169174-51169193 MS.gene47395:intron 20.0%
!!! TTTAAAATTATGATGTGAAG+AGG - chr1.4:51169571-51169590 None:intergenic 20.0%
! ATACACATGATGATTAATGA+TGG - chr1.4:51169649-51169668 None:intergenic 25.0%
! ATACTAATTAATTGTTGTGC+TGG + chr1.4:51169859-51169878 MS.gene47395:intron 25.0%
! TAAATGTGATGAAATGTCAA+TGG - chr1.4:51169701-51169720 None:intergenic 25.0%
! TGATGGAAGGAATATAATTA+TGG - chr1.4:51169632-51169651 None:intergenic 25.0%
! TTGTAGGAATAAAGAGAAAT+GGG + chr1.4:51169898-51169917 MS.gene47395:CDS 25.0%
! TTTAGATGCAAATAACAATG+AGG + chr1.4:51169935-51169954 MS.gene47395:CDS 25.0%
!!! ACATTTTTTTATAATGGGGT+TGG + chr1.4:51169178-51169197 MS.gene47395:intron 25.0%
!!! TTTGATTTTGATTTTTGAGC+AGG + chr1.4:51168942-51168961 MS.gene47395:intron 25.0%
AAAAATGGTGTACTAAGAAG+TGG - chr1.4:51168997-51169016 None:intergenic 30.0%
AAGTCATTCAGGTAAATTAC+CGG + chr1.4:51169133-51169152 MS.gene47395:intron 30.0%
ATGAGCTTTCCAAATAATGT+AGG - chr1.4:51169605-51169624 None:intergenic 30.0%
CTTGTAGGAATAAAGAGAAA+TGG + chr1.4:51169897-51169916 MS.gene47395:CDS 30.0%
TTCATATCATGATGTAGTGA+GGG + chr1.4:51169290-51169309 MS.gene47395:CDS 30.0%
TTGAATAGTAGATAGGAACA+TGG + chr1.4:51169783-51169802 MS.gene47395:intron 30.0%
! ACATGATGATTAATGATGGA+AGG - chr1.4:51169645-51169664 None:intergenic 30.0%
! TAACAATGAGGTATCAACAA+TGG + chr1.4:51169947-51169966 MS.gene47395:CDS 30.0%
!! CAATGATTGAATTAGCTTGT+AGG + chr1.4:51169882-51169901 MS.gene47395:intron 30.0%
!!! GAGTTTTATTTCTGAATGAG+AGG + chr1.4:51169376-51169395 MS.gene47395:CDS 30.0%
AGAAACGAACTTGGTCTAAA+AGG - chr1.4:51169458-51169477 None:intergenic 35.0%
AGAACGACAATAGAAGCAAA+AGG - chr1.4:51169094-51169113 None:intergenic 35.0%
AGCTTTCCAAATAATGTAGG+TGG - chr1.4:51169602-51169621 None:intergenic 35.0%
AGGTATCAACAATGGAAGAA+GGG + chr1.4:51169955-51169974 MS.gene47395:CDS 35.0%
ATCTGACACTCGTTGAAAAA+TGG - chr1.4:51169012-51169031 None:intergenic 35.0%
ATTTGTGAGATTTGTGGAAG+AGG + chr1.4:51169432-51169451 MS.gene47395:CDS 35.0%
CAAGTTCGTTTCTGTTCTTT+GGG + chr1.4:51169465-51169484 MS.gene47395:CDS 35.0%
CAGAAAATGTTGGACATTAG+TGG + chr1.4:51169324-51169343 MS.gene47395:CDS 35.0%
CCACAAATCTCACAAATGTA+AGG - chr1.4:51169429-51169448 None:intergenic 35.0%
CCTTACATTTGTGAGATTTG+TGG + chr1.4:51169426-51169445 MS.gene47395:CDS 35.0%
CTTCATATCATGATGTAGTG+AGG + chr1.4:51169289-51169308 MS.gene47395:CDS 35.0%
GGCTGAAATTCAGAAAATGT+TGG + chr1.4:51169314-51169333 MS.gene47395:CDS 35.0%
TTCCAAATAATGTAGGTGGT+GGG - chr1.4:51169598-51169617 None:intergenic 35.0%
TTGTCGTTCTTCAAAACACA+AGG + chr1.4:51169104-51169123 MS.gene47395:CDS 35.0%
TTTCCAAATAATGTAGGTGG+TGG - chr1.4:51169599-51169618 None:intergenic 35.0%
!! ACACAATGTTGGTTCCTAAA+TGG + chr1.4:51168965-51168984 MS.gene47395:CDS 35.0%
!! TTTCTGTTCTTTGGGATGTA+AGG + chr1.4:51169473-51169492 MS.gene47395:CDS 35.0%
AAGAAAAGGGATTCCTCACA+GGG + chr1.4:51170070-51170089 MS.gene47395:CDS 40.0%
AGAAGTGGTTTGAGCCATTT+AGG - chr1.4:51168982-51169001 None:intergenic 40.0%
ATATCATGATGTAGTGAGGG+TGG + chr1.4:51169293-51169312 MS.gene47395:CDS 40.0%
CAAACGCAAGGAGAAGAAAA+GGG + chr1.4:51170057-51170076 MS.gene47395:CDS 40.0%
CAAGAAGAAGAATTGCGTGA+AGG + chr1.4:51169990-51170009 MS.gene47395:CDS 40.0%
CAAGGATCATCAAGTCATTC+AGG + chr1.4:51169122-51169141 MS.gene47395:CDS 40.0%
CATGTTACATTCACTCCTTG+CGG - chr1.4:51169046-51169065 None:intergenic 40.0%
CCAAAGAACAGAAACGAACT+TGG - chr1.4:51169467-51169486 None:intergenic 40.0%
CCAAGTTCGTTTCTGTTCTT+TGG + chr1.4:51169464-51169483 MS.gene47395:CDS 40.0%
TCAAACGCAAGGAGAAGAAA+AGG + chr1.4:51170056-51170075 MS.gene47395:CDS 40.0%
TTTCTTCTCCTTGCGTTTGA+AGG - chr1.4:51170056-51170075 None:intergenic 40.0%
! GAGGTATCAACAATGGAAGA+AGG + chr1.4:51169954-51169973 MS.gene47395:CDS 40.0%
! TTTTGAGCAGGACACAATGT+TGG + chr1.4:51168954-51168973 MS.gene47395:intron 40.0%
!! GGAACTGCTTTTCCAGATTT+TGG - chr1.4:51169408-51169427 None:intergenic 40.0%
!!! GCTTTTCCAGATTTTGGTTG+AGG - chr1.4:51169402-51169421 None:intergenic 40.0%
CACCCACCACCTACATTATT+TGG + chr1.4:51169593-51169612 MS.gene47395:intron 45.0%
GAAGAAAAGGGATTCCTCAC+AGG + chr1.4:51170069-51170088 MS.gene47395:CDS 45.0%
CAACACCTCCTTCAAACGCA+AGG + chr1.4:51170045-51170064 MS.gene47395:CDS 50.0%
CTTCTCCTTGCGTTTGAAGG+AGG - chr1.4:51170053-51170072 None:intergenic 50.0%
GAGAGGCCTCAACCAAAATC+TGG + chr1.4:51169393-51169412 MS.gene47395:CDS 50.0%
TTGCGTGAAGGCTCACAACA+AGG + chr1.4:51170002-51170021 MS.gene47395:CDS 50.0%
! ATTCCTCACAGGGCTCCTTT+TGG + chr1.4:51170080-51170099 MS.gene47395:CDS 50.0%
! CTTGCGTTTGAAGGAGGTGT+TGG - chr1.4:51170047-51170066 None:intergenic 50.0%
ACATTCACTCCTTGCGGCGT+CGG - chr1.4:51169040-51169059 None:intergenic 55.0%
!! GCGTTTGAAGGAGGTGTTGG+AGG - chr1.4:51170044-51170063 None:intergenic 55.0%
GGTCCAAAAGGAGCCCTGTG+AGG - chr1.4:51170086-51170105 None:intergenic 60.0%
!! GGAGGTGTTGGAGGAGTTGC+TGG - chr1.4:51170035-51170054 None:intergenic 60.0%
AGATTCACGCCGACGCCGCA+AGG + chr1.4:51169028-51169047 MS.gene47395:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 51168875 51170109 51168875 ID=MS.gene47395
chr1.4 mRNA 51168875 51170109 51168875 ID=MS.gene47395.t1;Parent=MS.gene47395
chr1.4 exon 51168875 51168877 51168875 ID=MS.gene47395.t1.exon1;Parent=MS.gene47395.t1
chr1.4 CDS 51168875 51168877 51168875 ID=cds.MS.gene47395.t1;Parent=MS.gene47395.t1
chr1.4 exon 51168964 51169143 51168964 ID=MS.gene47395.t1.exon2;Parent=MS.gene47395.t1
chr1.4 CDS 51168964 51169143 51168964 ID=cds.MS.gene47395.t1;Parent=MS.gene47395.t1
chr1.4 exon 51169279 51169494 51169279 ID=MS.gene47395.t1.exon3;Parent=MS.gene47395.t1
chr1.4 CDS 51169279 51169494 51169279 ID=cds.MS.gene47395.t1;Parent=MS.gene47395.t1
chr1.4 exon 51169897 51170109 51169897 ID=MS.gene47395.t1.exon4;Parent=MS.gene47395.t1
chr1.4 CDS 51169897 51170109 51169897 ID=cds.MS.gene47395.t1;Parent=MS.gene47395.t1
Gene Sequence

>MS.gene47395

ATGGTATGTATATACACATATAACTTATGTTTTGAATTTAATATGTTCATATGATTTTGATTTTGATTTTGATTTTGATTTTTGAGCAGGACACAATGTTGGTTCCTAAATGGCTCAAACCACTTCTTAGTACACCATTTTTCAACGAGTGTCAGATTCACGCCGACGCCGCAAGGAGTGAATGTAACATGTTTTGTCTAGATTGCAATGTTGATGCCTTTTGCTTCTATTGTCGTTCTTCAAAACACAAGGATCATCAAGTCATTCAGGTAAATTACCGGTTCCTAAATTATTTTCTTATGCACATTTTTTTATAATGGGGTTGGTTAAATTTTGTGATTTTTTAATATGATCTTCATTTTTCTTTATCCTAAAGTATATATTTTTTTTGTTGGTTTAATTAGATAAGACGATCTTCATATCATGATGTAGTGAGGGTGGCTGAAATTCAGAAAATGTTGGACATTAGTGGAGTACAAACTTATGTGATCAATAGTGCTAGAGTTTTATTTCTGAATGAGAGGCCTCAACCAAAATCTGGAAAAGCAGTTCCTTACATTTGTGAGATTTGTGGAAGAGGCCTTTTAGACCAAGTTCGTTTCTGTTCTTTGGGATGTAAGGTGAGATTTTGTTTCATAAACATTTTTCATATCATCAAAATGTACATATAATTCACAAATCAAATAGCTTAGTCCTCTTCACATCATAATTTTAAAAACACCCACCACCTACATTATTTGGAAAGCTCATCACACCATAATTATATTCCTTCCATCATTAATCATCATGTGTATATGAAGCATATAACTATAGGCGCAGTACTCCATTGACATTTCATCACATTTATAAAAATAATCATATTATTATCTAGTTAATATTATTGATATATTTTTTTATAAAGATAATTATTGAATAGTAGATAGGAACATGGTATAATAATGTGTATAAAATAATAATGAATCAATATATGATTTGTTTAATTTGATACTAATTAATTGTTGTGCTGGCAATGATTGAATTAGCTTGTAGGAATAAAGAGAAATGGGAATGCAAGCTTTGTTTTAGATGCAAATAACAATGAGGTATCAACAATGGAAGAAGGGATGTCAAGACAACAAGAAGAAGAATTGCGTGAAGGCTCACAACAAGGCATGTATCCAGCAACTCCTCCAACACCTCCTTCAAACGCAAGGAGAAGAAAAGGGATTCCTCACAGGGCTCCTTTTGGACCCTAG
Protein sequence

>MS.gene47395.t1

MDTMLVPKWLKPLLSTPFFNECQIHADAARSECNMFCLDCNVDAFCFYCRSSKHKDHQVIQIRRSSYHDVVRVAEIQKMLDISGVQTYVINSARVLFLNERPQPKSGKAVPYICEICGRGLLDQVRFCSLGCKLVGIKRNGNASFVLDANNNEVSTMEEGMSRQQEEELREGSQQGMYPATPPTPPSNARRRKGIPHRAPFGP