AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene055816

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055816.t1 MTR_2g090295 96.761 247 8 0 1 247 1 247 0.0 506
MS.gene055816.t1 MTR_8g465910 57.255 255 90 7 1 247 1 244 4.49e-98 286
MS.gene055816.t1 MTR_2g013550 41.038 212 95 5 37 232 24 221 3.04e-44 149
MS.gene055816.t1 MTR_2g090330 64.545 110 29 2 37 146 30 129 9.54e-44 145
MS.gene055816.t1 MTR_2g090330 64.545 110 29 2 37 146 27 126 1.36e-43 145
MS.gene055816.t1 MTR_2g090325 60.630 127 35 4 29 153 7 120 3.34e-41 140
MS.gene055816.t1 MTR_4g088870 34.979 243 105 10 14 247 1 199 6.32e-33 119
MS.gene055816.t1 MTR_4g088875 39.706 204 98 6 38 232 29 216 1.10e-32 119
MS.gene055816.t1 MTR_1g021895 52.128 94 33 3 37 128 27 110 1.41e-26 103
MS.gene055816.t1 MTR_5g019300 50.562 89 36 2 40 128 35 115 9.18e-26 101
MS.gene055816.t1 MTR_7g093390 41.964 112 51 4 15 126 149 246 4.07e-23 97.4
MS.gene055816.t1 MTR_1g054260 30.921 152 97 4 3 152 55 200 1.55e-21 89.4
MS.gene055816.t1 MTR_4g029440 38.462 130 65 4 8 129 86 208 1.89e-21 92.4
MS.gene055816.t1 MTR_4g029440 38.462 130 65 4 8 129 92 214 2.00e-21 92.4
MS.gene055816.t1 MTR_1g054465 40.449 89 51 2 40 126 55 143 1.02e-20 87.0
MS.gene055816.t1 MTR_1g054280 38.889 108 58 3 19 126 56 155 1.16e-20 88.2
MS.gene055816.t1 MTR_1g054210 43.011 93 44 3 36 126 116 201 8.61e-19 82.4
MS.gene055816.t1 MTR_2g061230 36.667 90 50 1 40 129 107 189 7.40e-16 74.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055816.t1 AT4G03510 46.047 215 108 4 35 247 41 249 2.30e-63 198
MS.gene055816.t1 AT4G03510 46.047 215 108 4 35 247 41 249 2.30e-63 198
MS.gene055816.t1 AT4G03510 46.047 215 108 4 35 247 41 249 2.30e-63 198
MS.gene055816.t1 AT4G03510 46.047 215 108 4 35 247 41 249 2.30e-63 198
MS.gene055816.t1 AT4G28270 40.773 233 88 9 24 247 2 193 8.89e-47 154
MS.gene055816.t1 AT4G27470 42.647 204 89 10 40 232 42 228 1.29e-39 137
MS.gene055816.t1 AT2G23780 36.111 216 113 8 40 245 26 226 3.60e-27 104
MS.gene055816.t1 AT2G23780 36.111 216 113 8 40 245 26 226 3.60e-27 104
MS.gene055816.t1 AT2G23780 36.111 216 113 8 40 245 26 226 3.60e-27 104
MS.gene055816.t1 AT1G74990 44.545 110 49 3 30 137 7 106 1.52e-26 100
MS.gene055816.t1 AT1G19310 44.860 107 49 3 24 128 3 101 3.06e-25 99.8
MS.gene055816.t1 AT3G58030 32.759 232 119 10 27 235 122 339 1.01e-22 96.3
MS.gene055816.t1 AT3G58030 32.759 232 119 10 27 235 122 339 1.01e-22 96.3
MS.gene055816.t1 AT3G58030 32.759 232 119 10 27 235 122 339 1.01e-22 96.3
MS.gene055816.t1 AT3G58030 32.759 232 119 10 27 235 122 339 1.01e-22 96.3
MS.gene055816.t1 AT2G42030 33.880 183 91 6 36 213 133 290 2.00e-20 89.7
MS.gene055816.t1 AT2G44410 37.037 108 51 3 25 126 106 202 2.55e-17 80.9

Find 67 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTGTAAGATTGTATGAATT+TGG 0.196085 2.1:-10797562 None:intergenic
TTTCTTCCATGGAATCAATT+TGG 0.249281 2.1:-10796985 None:intergenic
AAAGGCAATGATCACCAATT+AGG 0.249482 2.1:+10797283 MS.gene055816:CDS
GTTGAGAATGATTCGGATAA+TGG 0.278191 2.1:-10797411 None:intergenic
CTTTGGAAGGCGGCGTAGTT+TGG 0.290827 2.1:-10797264 None:intergenic
ATGATATATGCAAGGATCTT+TGG 0.299279 2.1:+10797511 MS.gene055816:CDS
CCAAATTCATACAATCTTAC+AGG 0.303928 2.1:+10797562 MS.gene055816:CDS
GCAAGTGGTGAAGCAATTTC+TGG 0.315559 2.1:+10797034 MS.gene055816:CDS
GAGATTTCTGATTTGCATAC+TGG 0.331060 2.1:-10797208 None:intergenic
TATGGAATAGCATTCAAAAT+AGG 0.331156 2.1:-10797684 None:intergenic
CTGTAAGATTGTATGAATTT+GGG 0.342103 2.1:-10797561 None:intergenic
GATACAAGTTATGGTGTCTT+TGG 0.352630 2.1:+10797484 MS.gene055816:CDS
TTGAGAATGATTCGGATAAT+GGG 0.356464 2.1:-10797410 None:intergenic
CTAGACCGCTTGGTCCTTCA+TGG 0.359817 2.1:+10797320 MS.gene055816:CDS
AAGGCAATGATCACCAATTA+GGG 0.391729 2.1:+10797284 MS.gene055816:CDS
GTGGTATGACACTCCCTAAT+TGG 0.404265 2.1:-10797297 None:intergenic
ATGTTTCACAACATAATTCT+CGG 0.420768 2.1:+10797377 MS.gene055816:CDS
CATGAAGGACCAAGCGGTCT+AGG 0.421483 2.1:-10797319 None:intergenic
TTTGCAGCGTCAAGTGATCT+TGG 0.423758 2.1:-10797355 None:intergenic
ATCAAATGCCTTCTGATCCT+TGG 0.432608 2.1:-10797595 None:intergenic
ATTAAGCCATTTGTAAATGC+AGG 0.444845 2.1:-10797140 None:intergenic
GATCCAGTGGTCACTCTTTG+TGG 0.447780 2.1:+10797100 MS.gene055816:CDS
TAATTGGTGATCATTGCCTT+TGG 0.448612 2.1:-10797281 None:intergenic
GCTGGCCCTGCATTTACAAA+TGG 0.463384 2.1:+10797134 MS.gene055816:CDS
CTCCTCAAAATACTGATTGA+AGG 0.463468 2.1:-10796954 None:intergenic
TATGAACCAAATTGATTCCA+TGG 0.475517 2.1:+10796979 MS.gene055816:CDS
TTTGTGGTCATCTCTACTGC+TGG 0.480977 2.1:+10797116 MS.gene055816:CDS
AATCCATTGGATACAAGTTA+TGG 0.483929 2.1:+10797475 MS.gene055816:CDS
ATAACTTGTATCCAATGGAT+TGG 0.489925 2.1:-10797473 None:intergenic
ATGTATATATGTTTGTCACT+TGG 0.494265 2.1:-10797537 None:intergenic
TAACTTGTATCCAATGGATT+GGG 0.500116 2.1:-10797472 None:intergenic
CTTTGACTGCAACATATGCT+TGG 0.503274 2.1:+10797066 MS.gene055816:CDS
GTTTGGCCGCGGCCGTAGAG+TGG 0.505416 2.1:-10797247 None:intergenic
GAAGCAATTTCTGGTTCTAG+TGG 0.514216 2.1:+10797043 MS.gene055816:CDS
TGGTGATCATTGCCTTTGGA+AGG 0.521075 2.1:-10797277 None:intergenic
TGGTTCACTGCCCAATCCAT+TGG 0.524258 2.1:+10797462 MS.gene055816:CDS
TCATCCCTTGTTCCACTCTA+CGG 0.525770 2.1:+10797235 MS.gene055816:CDS
AAGGCGGCGTAGTTTGGCCG+CGG 0.530973 2.1:-10797258 None:intergenic
GACACAAAACTGTGCAGCAA+AGG 0.541056 2.1:-10797657 None:intergenic
CGCGGCCGTAGAGTGGAACA+AGG 0.543163 2.1:-10797240 None:intergenic
GTGTATCGTTGAGAATGATT+CGG 0.543480 2.1:-10797418 None:intergenic
CAAATTCATACAATCTTACA+GGG 0.556632 2.1:+10797563 MS.gene055816:CDS
GTCATACCACCTAGACCGCT+TGG 0.564556 2.1:+10797310 MS.gene055816:CDS
CAAACTACGCCGCCTTCCAA+AGG 0.572732 2.1:+10797265 MS.gene055816:CDS
GGTAAGTTCGTCATCCATGA+AGG 0.573904 2.1:-10797334 None:intergenic
ACACCATAACTTGTATCCAA+TGG 0.574386 2.1:-10797478 None:intergenic
ACAAAACTGTGCAGCAAAGG+AGG 0.577384 2.1:-10797654 None:intergenic
TGATCATTGCCTTTGGAAGG+CGG 0.577497 2.1:-10797274 None:intergenic
TCAGTAATCCAAGGATCAGA+AGG 0.591994 2.1:+10797587 MS.gene055816:CDS
TGACCACAAAGAGTGACCAC+TGG 0.593140 2.1:-10797103 None:intergenic
TTAAGCCATTTGTAAATGCA+GGG 0.593204 2.1:-10797139 None:intergenic
TCGCCAATGTTTAACACAGG+TGG 0.595550 2.1:+10797442 MS.gene055816:CDS
GATTTGCATACTGGACATTG+TGG 0.605821 2.1:-10797199 None:intergenic
AAATCAAGAGAAGCAGAAGG+AGG 0.609520 2.1:+10797174 MS.gene055816:CDS
GAACCACCTGTGTTAAACAT+TGG 0.613627 2.1:-10797445 None:intergenic
ATGCGAGCTGATAAGTCGCT+CGG 0.619945 2.1:+10797616 MS.gene055816:CDS
TTACAGGGATCAGTAATCCA+AGG 0.633705 2.1:+10797578 MS.gene055816:CDS
CGAAAATCAAGAGAAGCAGA+AGG 0.635468 2.1:+10797171 MS.gene055816:CDS
TGAGAATGATTCGGATAATG+GGG 0.646474 2.1:-10797409 None:intergenic
TTGGTGAGATGATATATGCA+AGG 0.649382 2.1:+10797503 MS.gene055816:CDS
GAAGGACCAAGCGGTCTAGG+TGG 0.660331 2.1:-10797316 None:intergenic
ACTTCGCCAATGTTTAACAC+AGG 0.666429 2.1:+10797439 MS.gene055816:CDS
GGAGTGTGTGCAAGATCCAG+TGG 0.671005 2.1:+10797087 MS.gene055816:CDS
CTTGTTCCACTCTACGGCCG+CGG 0.675004 2.1:+10797241 MS.gene055816:CDS
GTCATCCATGAAGGACCAAG+CGG 0.707584 2.1:-10797325 None:intergenic
GAAGTGTGGAAATGTGCAAG+TGG 0.714630 2.1:+10797019 MS.gene055816:CDS
GCGGCCGTAGAGTGGAACAA+GGG 0.719279 2.1:-10797239 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATGTATATATGTTTGTCACT+TGG - chr2.1:10797540-10797559 None:intergenic 25.0%
! ATGTTTCACAACATAATTCT+CGG + chr2.1:10797377-10797396 MS.gene055816:CDS 25.0%
! CAAATTCATACAATCTTACA+GGG + chr2.1:10797563-10797582 MS.gene055816:CDS 25.0%
! CTGTAAGATTGTATGAATTT+GGG - chr2.1:10797564-10797583 None:intergenic 25.0%
AAAAATCATCTCAAGAAGTG+TGG + chr2.1:10797005-10797024 MS.gene055816:CDS 30.0%
AATCCATTGGATACAAGTTA+TGG + chr2.1:10797475-10797494 MS.gene055816:CDS 30.0%
ATGATATATGCAAGGATCTT+TGG + chr2.1:10797511-10797530 MS.gene055816:CDS 30.0%
ATTAAGCCATTTGTAAATGC+AGG - chr2.1:10797143-10797162 None:intergenic 30.0%
CCAAATTCATACAATCTTAC+AGG + chr2.1:10797562-10797581 MS.gene055816:CDS 30.0%
CCTGTAAGATTGTATGAATT+TGG - chr2.1:10797565-10797584 None:intergenic 30.0%
TTAAGCCATTTGTAAATGCA+GGG - chr2.1:10797142-10797161 None:intergenic 30.0%
TTTCTTCCATGGAATCAATT+TGG - chr2.1:10796988-10797007 None:intergenic 30.0%
! ATAACTTGTATCCAATGGAT+TGG - chr2.1:10797476-10797495 None:intergenic 30.0%
! TAACTTGTATCCAATGGATT+GGG - chr2.1:10797475-10797494 None:intergenic 30.0%
! TATGAACCAAATTGATTCCA+TGG + chr2.1:10796979-10796998 MS.gene055816:CDS 30.0%
! TTGAGAATGATTCGGATAAT+GGG - chr2.1:10797413-10797432 None:intergenic 30.0%
! TTGAGATGATTTTTCTTCCA+TGG - chr2.1:10796999-10797018 None:intergenic 30.0%
!! TTCAATCAGTATTTTGAGGA+GGG + chr2.1:10796956-10796975 MS.gene055816:CDS 30.0%
AAAGGCAATGATCACCAATT+AGG + chr2.1:10797283-10797302 MS.gene055816:CDS 35.0%
AAGGCAATGATCACCAATTA+GGG + chr2.1:10797284-10797303 MS.gene055816:CDS 35.0%
GATACAAGTTATGGTGTCTT+TGG + chr2.1:10797484-10797503 MS.gene055816:CDS 35.0%
GTGTATCGTTGAGAATGATT+CGG - chr2.1:10797421-10797440 None:intergenic 35.0%
TTGGTGAGATGATATATGCA+AGG + chr2.1:10797503-10797522 MS.gene055816:CDS 35.0%
! ACACCATAACTTGTATCCAA+TGG - chr2.1:10797481-10797500 None:intergenic 35.0%
! CTCCTCAAAATACTGATTGA+AGG - chr2.1:10796957-10796976 None:intergenic 35.0%
! CTTCTGCTTCTCTTGATTTT+CGG - chr2.1:10797173-10797192 None:intergenic 35.0%
! GAGATTTCTGATTTGCATAC+TGG - chr2.1:10797211-10797230 None:intergenic 35.0%
! GTTGAGAATGATTCGGATAA+TGG - chr2.1:10797414-10797433 None:intergenic 35.0%
! TAATTGGTGATCATTGCCTT+TGG - chr2.1:10797284-10797303 None:intergenic 35.0%
! TGAGAATGATTCGGATAATG+GGG - chr2.1:10797412-10797431 None:intergenic 35.0%
!! CTTCAATCAGTATTTTGAGG+AGG + chr2.1:10796955-10796974 MS.gene055816:CDS 35.0%
AAATCAAGAGAAGCAGAAGG+AGG + chr2.1:10797174-10797193 MS.gene055816:CDS 40.0%
ACTTCGCCAATGTTTAACAC+AGG + chr2.1:10797439-10797458 MS.gene055816:CDS 40.0%
ATCAAATGCCTTCTGATCCT+TGG - chr2.1:10797598-10797617 None:intergenic 40.0%
CGAAAATCAAGAGAAGCAGA+AGG + chr2.1:10797171-10797190 MS.gene055816:CDS 40.0%
CTTTGACTGCAACATATGCT+TGG + chr2.1:10797066-10797085 MS.gene055816:CDS 40.0%
GAACCACCTGTGTTAAACAT+TGG - chr2.1:10797448-10797467 None:intergenic 40.0%
GATTTGCATACTGGACATTG+TGG - chr2.1:10797202-10797221 None:intergenic 40.0%
TCAGTAATCCAAGGATCAGA+AGG + chr2.1:10797587-10797606 MS.gene055816:CDS 40.0%
TTACAGGGATCAGTAATCCA+AGG + chr2.1:10797578-10797597 MS.gene055816:CDS 40.0%
! GGCCTTCAATCAGTATTTTG+AGG + chr2.1:10796952-10796971 MS.gene055816:CDS 40.0%
!! GAAGCAATTTCTGGTTCTAG+TGG + chr2.1:10797043-10797062 MS.gene055816:CDS 40.0%
ACAAAACTGTGCAGCAAAGG+AGG - chr2.1:10797657-10797676 None:intergenic 45.0%
GAAGTGTGGAAATGTGCAAG+TGG + chr2.1:10797019-10797038 MS.gene055816:CDS 45.0%
GACACAAAACTGTGCAGCAA+AGG - chr2.1:10797660-10797679 None:intergenic 45.0%
GCAAGTGGTGAAGCAATTTC+TGG + chr2.1:10797034-10797053 MS.gene055816:CDS 45.0%
GGTAAGTTCGTCATCCATGA+AGG - chr2.1:10797337-10797356 None:intergenic 45.0%
GTGGTATGACACTCCCTAAT+TGG - chr2.1:10797300-10797319 None:intergenic 45.0%
TCATCCCTTGTTCCACTCTA+CGG + chr2.1:10797235-10797254 MS.gene055816:CDS 45.0%
TCGCCAATGTTTAACACAGG+TGG + chr2.1:10797442-10797461 MS.gene055816:CDS 45.0%
TGGTGATCATTGCCTTTGGA+AGG - chr2.1:10797280-10797299 None:intergenic 45.0%
TTTGCAGCGTCAAGTGATCT+TGG - chr2.1:10797358-10797377 None:intergenic 45.0%
TTTGTGGTCATCTCTACTGC+TGG + chr2.1:10797116-10797135 MS.gene055816:CDS 45.0%
! GCTTCTCTTGATTTTCGGCA+TGG - chr2.1:10797168-10797187 None:intergenic 45.0%
! TGATCATTGCCTTTGGAAGG+CGG - chr2.1:10797277-10797296 None:intergenic 45.0%
ATGCGAGCTGATAAGTCGCT+CGG + chr2.1:10797616-10797635 MS.gene055816:CDS 50.0%
GATCCAGTGGTCACTCTTTG+TGG + chr2.1:10797100-10797119 MS.gene055816:CDS 50.0%
GCTGGCCCTGCATTTACAAA+TGG + chr2.1:10797134-10797153 MS.gene055816:CDS 50.0%
GTCATCCATGAAGGACCAAG+CGG - chr2.1:10797328-10797347 None:intergenic 50.0%
TGACCACAAAGAGTGACCAC+TGG - chr2.1:10797106-10797125 None:intergenic 50.0%
TGGTTCACTGCCCAATCCAT+TGG + chr2.1:10797462-10797481 MS.gene055816:CDS 50.0%
CAAACTACGCCGCCTTCCAA+AGG + chr2.1:10797265-10797284 MS.gene055816:CDS 55.0%
CATGAAGGACCAAGCGGTCT+AGG - chr2.1:10797322-10797341 None:intergenic 55.0%
CTAGACCGCTTGGTCCTTCA+TGG + chr2.1:10797320-10797339 MS.gene055816:CDS 55.0%
GGAGTGTGTGCAAGATCCAG+TGG + chr2.1:10797087-10797106 MS.gene055816:CDS 55.0%
GTCATACCACCTAGACCGCT+TGG + chr2.1:10797310-10797329 MS.gene055816:CDS 55.0%
! CTTTGGAAGGCGGCGTAGTT+TGG - chr2.1:10797267-10797286 None:intergenic 55.0%
CTTGTTCCACTCTACGGCCG+CGG + chr2.1:10797241-10797260 MS.gene055816:CDS 60.0%
GAAGGACCAAGCGGTCTAGG+TGG - chr2.1:10797319-10797338 None:intergenic 60.0%
GCGGCCGTAGAGTGGAACAA+GGG - chr2.1:10797242-10797261 None:intergenic 60.0%
AAGGCGGCGTAGTTTGGCCG+CGG - chr2.1:10797261-10797280 None:intergenic 65.0%
CGCGGCCGTAGAGTGGAACA+AGG - chr2.1:10797243-10797262 None:intergenic 65.0%
GTTTGGCCGCGGCCGTAGAG+TGG - chr2.1:10797250-10797269 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 10796950 10797693 10796950 ID=MS.gene055816
chr2.1 mRNA 10796950 10797693 10796950 ID=MS.gene055816.t1;Parent=MS.gene055816
chr2.1 exon 10796950 10797693 10796950 ID=MS.gene055816.t1.exon1;Parent=MS.gene055816.t1
chr2.1 CDS 10796950 10797693 10796950 ID=cds.MS.gene055816.t1;Parent=MS.gene055816.t1
Gene Sequence

>MS.gene055816

ATGGCCTTCAATCAGTATTTTGAGGAGGGTATGAACCAAATTGATTCCATGGAAGAAAAATCATCTCAAGAAGTGTGGAAATGTGCAAGTGGTGAAGCAATTTCTGGTTCTAGTGGCTTTGACTGCAACATATGCTTGGAGTGTGTGCAAGATCCAGTGGTCACTCTTTGTGGTCATCTCTACTGCTGGCCCTGCATTTACAAATGGCTTAATTTCCATGCCGAAAATCAAGAGAAGCAGAAGGAGGAGCCACAATGTCCAGTATGCAAATCAGAAATCTCAAAATCATCCCTTGTTCCACTCTACGGCCGCGGCCAAACTACGCCGCCTTCCAAAGGCAATGATCACCAATTAGGGAGTGTCATACCACCTAGACCGCTTGGTCCTTCATGGATGACGAACTTACCAAGATCACTTGACGCTGCAAATGTTTCACAACATAATTCTCGGTCTTATCATCCCCATTATCCGAATCATTCTCAACGATACACTTCGCCAATGTTTAACACAGGTGGTTCACTGCCCAATCCATTGGATACAAGTTATGGTGTCTTTGGTGAGATGATATATGCAAGGATCTTTGGAAACCAAGTGACAAACATATATACATACCCAAATTCATACAATCTTACAGGGATCAGTAATCCAAGGATCAGAAGGCATTTGATGCGAGCTGATAAGTCGCTCGGTAGAATCTGTTTCTTCCTCCTTTGCTGCACAGTTTTGTGTCTTCTCCTATTTTGA
Protein sequence

>MS.gene055816.t1

MAFNQYFEEGMNQIDSMEEKSSQEVWKCASGEAISGSSGFDCNICLECVQDPVVTLCGHLYCWPCIYKWLNFHAENQEKQKEEPQCPVCKSEISKSSLVPLYGRGQTTPPSKGNDHQLGSVIPPRPLGPSWMTNLPRSLDAANVSQHNSRSYHPHYPNHSQRYTSPMFNTGGSLPNPLDTSYGVFGEMIYARIFGNQVTNIYTYPNSYNLTGISNPRIRRHLMRADKSLGRICFFLLCCTVLCLLLF