AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene000242

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000242.t1 MTR_6g073013 97.765 179 4 0 1 179 1 179 4.00e-132 367
MS.gene000242.t1 MTR_7g010300 38.776 196 61 4 19 160 88 278 4.32e-41 141
MS.gene000242.t1 MTR_1g077020 36.723 177 74 6 19 160 9 182 9.02e-34 118
MS.gene000242.t1 MTR_2g076780 31.944 216 87 6 1 160 21 232 2.58e-31 113
MS.gene000242.t1 MTR_5g032600 35.938 192 71 4 19 160 78 267 2.86e-31 114
MS.gene000242.t1 MTR_5g020510 34.010 197 71 7 19 160 99 291 1.35e-29 110
MS.gene000242.t1 MTR_8g069080 31.100 209 87 4 7 160 57 263 3.14e-29 108
MS.gene000242.t1 MTR_3g100650 32.292 192 78 5 19 160 80 269 3.15e-26 101
MS.gene000242.t1 MTR_8g467340 56.338 71 30 1 101 171 271 340 4.22e-22 92.0
MS.gene000242.t1 MTR_8g467340 66.667 51 16 1 19 68 64 114 5.11e-17 77.8
MS.gene000242.t1 MTR_4g134580 56.667 60 25 1 101 160 284 342 6.16e-20 85.9
MS.gene000242.t1 MTR_4g134580 60.000 50 19 1 19 68 113 161 1.12e-14 70.9
MS.gene000242.t1 MTR_6g012280 60.000 60 23 1 101 160 222 280 1.80e-19 84.0
MS.gene000242.t1 MTR_6g012280 57.407 54 16 2 19 68 91 141 4.24e-14 69.3
MS.gene000242.t1 MTR_8g051480 32.800 125 69 3 49 160 2 124 1.84e-17 74.7
MS.gene000242.t1 MTR_5g065440 53.125 64 29 1 97 160 201 263 1.94e-16 75.1
MS.gene000242.t1 MTR_5g065440 56.000 50 21 1 19 68 58 106 1.35e-11 61.6
MS.gene000242.t1 MTR_3g039810 50.000 64 31 1 5 68 6 68 2.54e-15 67.8
MS.gene000242.t1 MTR_8g069380 40.789 76 44 1 86 161 37 111 6.08e-15 67.8
MS.gene000242.t1 MTR_8g442330 33.594 128 67 5 28 139 14 139 1.51e-14 67.4
MS.gene000242.t1 MTR_6g012220 60.000 50 15 1 19 68 21 65 3.16e-14 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000242.t1 AT1G14440 40.741 189 59 6 19 158 90 274 5.06e-40 138
MS.gene000242.t1 AT1G14440 40.741 189 59 6 19 158 90 274 5.06e-40 138
MS.gene000242.t1 AT4G24660 42.012 169 69 3 19 160 49 215 3.07e-39 133
MS.gene000242.t1 AT4G24660 42.012 169 69 3 19 160 49 215 3.98e-39 133
MS.gene000242.t1 AT2G18350 41.243 177 67 5 19 160 82 256 1.13e-38 133
MS.gene000242.t1 AT2G02540 34.579 214 78 5 19 172 87 298 2.86e-38 133
MS.gene000242.t1 AT2G02540 34.579 214 78 5 19 172 87 298 2.86e-38 133
MS.gene000242.t1 AT5G65410 39.227 181 69 5 17 160 73 249 2.91e-38 132
MS.gene000242.t1 AT1G69600 40.741 189 67 7 19 164 31 217 2.30e-35 124
MS.gene000242.t1 AT5G42780 36.224 196 85 4 5 164 50 241 4.73e-35 123
MS.gene000242.t1 AT5G15210 38.172 186 67 5 19 160 56 237 3.51e-34 122
MS.gene000242.t1 AT5G60480 38.824 170 73 5 18 158 36 203 2.21e-32 115
MS.gene000242.t1 AT3G50890 38.220 191 76 5 19 169 60 248 5.25e-31 113
MS.gene000242.t1 AT1G14687 37.952 166 73 5 18 159 6 165 6.58e-30 108
MS.gene000242.t1 AT1G75240 60.000 70 23 2 101 170 240 304 1.14e-23 95.1
MS.gene000242.t1 AT1G75240 60.000 50 19 1 19 68 76 124 3.19e-14 69.3
MS.gene000242.t1 AT3G28920 48.148 81 41 1 80 160 171 250 1.14e-19 84.3
MS.gene000242.t1 AT3G28920 50.000 76 33 2 19 89 52 127 4.02e-15 72.0
MS.gene000242.t1 AT5G39760 54.839 62 27 1 99 160 198 258 3.93e-18 80.5
MS.gene000242.t1 AT5G39760 48.649 74 37 1 17 89 54 127 1.38e-15 73.6
MS.gene000242.t1 AT1G74660 58.491 53 21 1 16 68 36 87 2.08e-15 68.6
MS.gene000242.t1 AT1G74660 58.491 53 21 1 16 68 36 87 4.38e-15 67.8
MS.gene000242.t1 AT3G28917 56.000 50 22 0 19 68 33 82 4.14e-14 65.5
MS.gene000242.t1 AT1G18835 54.717 53 20 1 16 68 23 71 2.41e-13 62.8

Find 50 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGGAGGTAGTGGAGGAGA+TGG 0.351040 6.1:+65677334 MS.gene000242:CDS
GAGGAGATGGGAGGAGGAAG+AGG 0.371577 6.1:+65677347 MS.gene000242:CDS
ATGGGATTTGCTGAGAAGTT+AGG 0.383753 6.1:+65677409 MS.gene000242:CDS
AATTCTTCTGATCCTTCAAC+TGG 0.406509 6.1:+65677550 MS.gene000242:CDS
GGCCGCTGCAATGTCGGATC+AGG 0.431193 6.1:+65677294 MS.gene000242:CDS
GAGGAGGTAGTGGAGGAGAT+GGG 0.433503 6.1:+65677335 MS.gene000242:CDS
GAGGTAGTGGAGGAGATGGG+AGG 0.435653 6.1:+65677338 MS.gene000242:CDS
ATCCGACATTGCAGCGGCCG+CGG 0.438358 6.1:-65677290 None:intergenic
GTAGTGGAGGAGATGGGAGG+AGG 0.441484 6.1:+65677341 MS.gene000242:CDS
TGCCGCGGCCGCTGCAATGT+CGG 0.446748 6.1:+65677288 MS.gene000242:CDS
ATCATCTTCTCCTTCTGATC+CGG 0.451236 6.1:-65677388 None:intergenic
TATTCCGGTGGAGGAGGTAG+TGG 0.451652 6.1:+65677325 MS.gene000242:CDS
AGCCGCAGGCTGCACATTGG+AGG 0.456002 6.1:-65677219 None:intergenic
GCAAAATAACCGCGATCACA+AGG 0.458670 6.1:+65677260 MS.gene000242:CDS
AGAAACCATGCAGCAAGCCT+TGG 0.459741 6.1:+65677130 MS.gene000242:CDS
CGTCGGTGGCGTAGCTTCCA+AGG 0.465781 6.1:-65677147 None:intergenic
GAAATTTACGCCGGATCAGA+AGG 0.471585 6.1:+65677378 MS.gene000242:CDS
GATCAGGTGATGGAATATTC+CGG 0.475527 6.1:+65677310 MS.gene000242:CDS
AGCTTCCAAGGCTTGCTGCA+TGG 0.476710 6.1:-65677135 None:intergenic
GAAGTTCCGGTGACAGCCGC+AGG 0.479614 6.1:-65677233 None:intergenic
ATGGGAGGAGGAAGAGGTAC+CGG 0.496163 6.1:+65677353 MS.gene000242:CDS
GAATTAGCATTACCAGTTGA+AGG 0.504250 6.1:-65677562 None:intergenic
GTGCAGCCTGCGGCTGTCAC+CGG 0.504708 6.1:+65677227 MS.gene000242:CDS
TGGAGGCTGTTTACCGCGGA+TGG 0.511123 6.1:-65677202 None:intergenic
GGATCAGAAGGAGAAGATGA+TGG 0.523708 6.1:+65677390 MS.gene000242:CDS
TCCTCCACTACCTCCTCCAC+CGG 0.526819 6.1:-65677329 None:intergenic
GATCCGGCGTAAATTTCGTC+CGG 0.537660 6.1:-65677372 None:intergenic
ATGGAATATTCCGGTGGAGG+AGG 0.538823 6.1:+65677319 MS.gene000242:CDS
AGCTACGCCACCGACGGCTG+TGG 0.543017 6.1:+65677154 MS.gene000242:CDS
AACTTGATGAAGAAATTGAA+AGG 0.558617 6.1:+65677452 MS.gene000242:CDS
GACAGCCGCAGGCTGCACAT+TGG 0.578845 6.1:-65677222 None:intergenic
GGCACTCTCCCTTGTGATCG+CGG 0.582002 6.1:-65677269 None:intergenic
TGCAATGTCGGATCAGGTGA+TGG 0.582441 6.1:+65677300 MS.gene000242:CDS
GATCAGAAGGAGAAGATGAT+GGG 0.588034 6.1:+65677391 MS.gene000242:CDS
TCCGGTGGAGGAGGTAGTGG+AGG 0.589804 6.1:+65677328 MS.gene000242:CDS
GATTTGCTGAGAAGTTAGGA+TGG 0.591144 6.1:+65677413 MS.gene000242:CDS
GTGATGGAATATTCCGGTGG+AGG 0.592071 6.1:+65677316 MS.gene000242:CDS
CAAAATAACCGCGATCACAA+GGG 0.605300 6.1:+65677261 MS.gene000242:CDS
GAATTCACCACAGCCGTCGG+TGG 0.607731 6.1:-65677161 None:intergenic
GGATGGCGATGAGTCGTCGA+TGG 0.613786 6.1:-65677185 None:intergenic
CACACACTACTGAGTAAGAG+AGG 0.616345 6.1:-65677584 None:intergenic
AGCCTCCAATGTGCAGCCTG+CGG 0.622915 6.1:+65677217 MS.gene000242:CDS
GATCACAAGGGAGAGTGCCG+CGG 0.625206 6.1:+65677273 MS.gene000242:CDS
CGACGACTCATCGCCATCCG+CGG 0.627176 6.1:+65677189 MS.gene000242:CDS
CTTGGAAGCTACGCCACCGA+CGG 0.637476 6.1:+65677148 MS.gene000242:CDS
CACCTGATCCGACATTGCAG+CGG 0.660435 6.1:-65677296 None:intergenic
GGTGAATTCACCACAGCCGT+CGG 0.668848 6.1:-65677164 None:intergenic
ACATTGGAGGCTGTTTACCG+CGG 0.690521 6.1:-65677206 None:intergenic
CAGGTGATGGAATATTCCGG+TGG 0.696299 6.1:+65677313 MS.gene000242:CDS
GTACCGGACGAAATTTACGC+CGG 0.738784 6.1:+65677369 MS.gene000242:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AACTTGATGAAGAAATTGAA+AGG + chr6.1:65677452-65677471 MS.gene000242:CDS 25.0%
! TGTGAGTAGACAAGTTTTTA+AGG + chr6.1:65677492-65677511 MS.gene000242:CDS 30.0%
!!! GTAGACAAGTTTTTAAGGTT+TGG + chr6.1:65677497-65677516 MS.gene000242:CDS 30.0%
AATTCTTCTGATCCTTCAAC+TGG + chr6.1:65677550-65677569 MS.gene000242:CDS 35.0%
GAATTAGCATTACCAGTTGA+AGG - chr6.1:65677565-65677584 None:intergenic 35.0%
!! GAAAGGTTTTGTGAAAGTGT+TGG + chr6.1:65677469-65677488 MS.gene000242:CDS 35.0%
ATCATCTTCTCCTTCTGATC+CGG - chr6.1:65677391-65677410 None:intergenic 40.0%
CAAAATAACCGCGATCACAA+GGG + chr6.1:65677261-65677280 MS.gene000242:CDS 40.0%
GATCAGAAGGAGAAGATGAT+GGG + chr6.1:65677391-65677410 MS.gene000242:CDS 40.0%
!! ATGGGATTTGCTGAGAAGTT+AGG + chr6.1:65677409-65677428 MS.gene000242:CDS 40.0%
!! GATCAGGTGATGGAATATTC+CGG + chr6.1:65677310-65677329 MS.gene000242:CDS 40.0%
!! GATTTGCTGAGAAGTTAGGA+TGG + chr6.1:65677413-65677432 MS.gene000242:CDS 40.0%
!! TTATTTTGCGGTGGAAGTTC+CGG - chr6.1:65677249-65677268 None:intergenic 40.0%
!! TTGTGATCGCGGTTATTTTG+CGG - chr6.1:65677261-65677280 None:intergenic 40.0%
GAAATTTACGCCGGATCAGA+AGG + chr6.1:65677378-65677397 MS.gene000242:CDS 45.0%
GCAAAATAACCGCGATCACA+AGG + chr6.1:65677260-65677279 MS.gene000242:CDS 45.0%
GGATCAGAAGGAGAAGATGA+TGG + chr6.1:65677390-65677409 MS.gene000242:CDS 45.0%
ACATTGGAGGCTGTTTACCG+CGG - chr6.1:65677209-65677228 None:intergenic 50.0%
AGAAACCATGCAGCAAGCCT+TGG + chr6.1:65677130-65677149 MS.gene000242:CDS 50.0%
ATGGAATATTCCGGTGGAGG+AGG + chr6.1:65677319-65677338 MS.gene000242:CDS 50.0%
GATCCGGCGTAAATTTCGTC+CGG - chr6.1:65677375-65677394 None:intergenic 50.0%
GTACCGGACGAAATTTACGC+CGG + chr6.1:65677369-65677388 MS.gene000242:CDS 50.0%
TGCAATGTCGGATCAGGTGA+TGG + chr6.1:65677300-65677319 MS.gene000242:CDS 50.0%
! GTGATGGAATATTCCGGTGG+AGG + chr6.1:65677316-65677335 MS.gene000242:CDS 50.0%
!! CAGGTGATGGAATATTCCGG+TGG + chr6.1:65677313-65677332 MS.gene000242:CDS 50.0%
!! TGATCGCGGTTATTTTGCGG+TGG - chr6.1:65677258-65677277 None:intergenic 50.0%
CACCTGATCCGACATTGCAG+CGG - chr6.1:65677299-65677318 None:intergenic 55.0%
GGTGAATTCACCACAGCCGT+CGG - chr6.1:65677167-65677186 None:intergenic 55.0%
TATTCCGGTGGAGGAGGTAG+TGG + chr6.1:65677325-65677344 MS.gene000242:CDS 55.0%
! ATGGGAGGAGGAAGAGGTAC+CGG + chr6.1:65677353-65677372 MS.gene000242:CDS 55.0%
!! AGCTTCCAAGGCTTGCTGCA+TGG - chr6.1:65677138-65677157 None:intergenic 55.0%
!! GAGGAGGTAGTGGAGGAGAT+GGG + chr6.1:65677335-65677354 MS.gene000242:CDS 55.0%
AGCCTCCAATGTGCAGCCTG+CGG + chr6.1:65677217-65677236 MS.gene000242:CDS 60.0%
CTTGGAAGCTACGCCACCGA+CGG + chr6.1:65677148-65677167 MS.gene000242:CDS 60.0%
GAATTCACCACAGCCGTCGG+TGG - chr6.1:65677164-65677183 None:intergenic 60.0%
GAGGAGATGGGAGGAGGAAG+AGG + chr6.1:65677347-65677366 MS.gene000242:CDS 60.0%
GGATGGCGATGAGTCGTCGA+TGG - chr6.1:65677188-65677207 None:intergenic 60.0%
GGCACTCTCCCTTGTGATCG+CGG - chr6.1:65677272-65677291 None:intergenic 60.0%
TCCTCCACTACCTCCTCCAC+CGG - chr6.1:65677332-65677351 None:intergenic 60.0%
TGGAGGCTGTTTACCGCGGA+TGG - chr6.1:65677205-65677224 None:intergenic 60.0%
! GTAGTGGAGGAGATGGGAGG+AGG + chr6.1:65677341-65677360 MS.gene000242:CDS 60.0%
!! GAGGTAGTGGAGGAGATGGG+AGG + chr6.1:65677338-65677357 MS.gene000242:CDS 60.0%
!! GATCACAAGGGAGAGTGCCG+CGG + chr6.1:65677273-65677292 MS.gene000242:CDS 60.0%
!! GGAGGAGGTAGTGGAGGAGA+TGG + chr6.1:65677334-65677353 MS.gene000242:CDS 60.0%
AGCCGCAGGCTGCACATTGG+AGG - chr6.1:65677222-65677241 None:intergenic 65.0%
ATCCGACATTGCAGCGGCCG+CGG - chr6.1:65677293-65677312 None:intergenic 65.0%
CGACGACTCATCGCCATCCG+CGG + chr6.1:65677189-65677208 MS.gene000242:CDS 65.0%
CGTCGGTGGCGTAGCTTCCA+AGG - chr6.1:65677150-65677169 None:intergenic 65.0%
GAAGTTCCGGTGACAGCCGC+AGG - chr6.1:65677236-65677255 None:intergenic 65.0%
GACAGCCGCAGGCTGCACAT+TGG - chr6.1:65677225-65677244 None:intergenic 65.0%
GGCCGCTGCAATGTCGGATC+AGG + chr6.1:65677294-65677313 MS.gene000242:CDS 65.0%
! TCCGGTGGAGGAGGTAGTGG+AGG + chr6.1:65677328-65677347 MS.gene000242:CDS 65.0%
AGCTACGCCACCGACGGCTG+TGG + chr6.1:65677154-65677173 MS.gene000242:CDS 70.0%
GTGCAGCCTGCGGCTGTCAC+CGG + chr6.1:65677227-65677246 MS.gene000242:CDS 70.0%
TGCCGCGGCCGCTGCAATGT+CGG + chr6.1:65677288-65677307 MS.gene000242:CDS 70.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 65677061 65677600 65677061 ID=MS.gene000242
chr6.1 mRNA 65677061 65677600 65677061 ID=MS.gene000242.t1;Parent=MS.gene000242
chr6.1 exon 65677061 65677600 65677061 ID=MS.gene000242.t1.exon1;Parent=MS.gene000242.t1
chr6.1 CDS 65677061 65677600 65677061 ID=cds.MS.gene000242.t1;Parent=MS.gene000242.t1
Gene Sequence

>MS.gene000242

ATGGAAGGAGGAGCAATGTTATCATCTTCATCATCACATTCACAAAACTATATCTACAGAGAGTGTTTAAGAAACCATGCAGCAAGCCTTGGAAGCTACGCCACCGACGGCTGTGGTGAATTCACCATCGACGACTCATCGCCATCCGCGGTAAACAGCCTCCAATGTGCAGCCTGCGGCTGTCACCGGAACTTCCACCGCAAAATAACCGCGATCACAAGGGAGAGTGCCGCGGCCGCTGCAATGTCGGATCAGGTGATGGAATATTCCGGTGGAGGAGGTAGTGGAGGAGATGGGAGGAGGAAGAGGTACCGGACGAAATTTACGCCGGATCAGAAGGAGAAGATGATGGGATTTGCTGAGAAGTTAGGATGGAAATTGCAGAGAAAAGAACTTGATGAAGAAATTGAAAGGTTTTGTGAAAGTGTTGGTGTGAGTAGACAAGTTTTTAAGGTTTGGATGCATAATCATAAGAATTCTTGTTTCTTAAATTCTTCTGATCCTTCAACTGGTAATGCTAATTCCTCTCTTACTCAGTAG
Protein sequence

>MS.gene000242.t1

MEGGAMLSSSSSHSQNYIYRECLRNHAASLGSYATDGCGEFTIDDSSPSAVNSLQCAACGCHRNFHRKITAITRESAAAAAMSDQVMEYSGGGGSGGDGRRKRYRTKFTPDQKEKMMGFAEKLGWKLQRKELDEEIERFCESVGVSRQVFKVWMHNHKNSCFLNSSDPSTGNANSSLTQ