AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene02256

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene02256.t1 MTR_2g010630 95.333 150 7 0 1 150 16 165 1.02e-108 306
MS.gene02256.t1 MTR_2g010650 88.514 148 15 2 3 150 20 165 3.03e-94 270
MS.gene02256.t1 MTR_2g010700 71.429 154 39 2 1 150 16 168 6.26e-79 231
MS.gene02256.t1 MTR_2g010600 74.497 149 32 3 4 150 18 162 6.74e-79 231
MS.gene02256.t1 MTR_4g050762 73.154 149 34 3 4 150 18 162 3.07e-76 224
MS.gene02256.t1 MTR_2g012370 73.154 149 34 3 4 150 18 162 3.07e-76 224
MS.gene02256.t1 MTR_2g010640 68.667 150 45 2 1 150 16 163 3.46e-72 214
MS.gene02256.t1 MTR_2g010670 68.667 150 46 1 1 150 16 164 3.73e-72 214
MS.gene02256.t1 MTR_2g010690 66.000 150 50 1 1 150 16 164 2.95e-70 209
MS.gene02256.t1 MTR_2g010590 65.541 148 44 3 4 150 18 159 9.12e-70 207
MS.gene02256.t1 MTR_2g010610 62.162 148 28 4 4 150 18 138 6.41e-58 177
MS.gene02256.t1 MTR_2g435490 55.333 150 59 4 3 150 21 164 3.55e-56 174
MS.gene02256.t1 MTR_2g010580 50.676 148 65 4 4 150 24 164 4.07e-49 155
MS.gene02256.t1 MTR_4g092540 46.711 152 72 5 1 150 15 159 2.03e-45 146
MS.gene02256.t1 MTR_4g128750 56.115 139 52 5 15 150 41 173 6.35e-45 145
MS.gene02256.t1 MTR_4g128770 48.936 141 64 5 14 150 70 206 4.54e-44 144
MS.gene02256.t1 MTR_1g067290 38.298 141 76 6 14 149 73 207 8.15e-28 102
MS.gene02256.t1 MTR_8g078770 34.507 142 83 5 14 150 36 172 1.63e-23 90.5
MS.gene02256.t1 MTR_5g018770 31.944 144 86 5 14 150 47 185 5.74e-21 84.3
MS.gene02256.t1 MTR_4g092515 50.633 79 31 4 6 82 24 96 7.24e-17 72.4
MS.gene02256.t1 MTR_5g018755 37.500 88 44 3 67 150 23 103 3.04e-13 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene02256.t1 AT4G33720 61.111 144 49 3 8 150 26 163 7.39e-60 182
MS.gene02256.t1 AT5G26130 59.028 144 54 2 8 150 27 166 4.14e-57 176
MS.gene02256.t1 AT3G19690 58.904 146 51 4 8 150 22 161 1.30e-56 174
MS.gene02256.t1 AT4G33710 58.333 144 55 2 8 150 27 166 5.01e-56 173
MS.gene02256.t1 AT2G14580 59.722 144 49 5 8 150 26 161 2.75e-55 171
MS.gene02256.t1 AT2G14610 58.219 146 52 5 6 150 24 161 1.48e-54 169
MS.gene02256.t1 AT1G50060 55.782 147 57 4 6 150 21 161 5.31e-51 160
MS.gene02256.t1 AT4G33730 51.333 150 64 4 3 150 30 172 5.50e-47 150
MS.gene02256.t1 AT4G25780 51.064 141 61 4 14 150 54 190 5.81e-46 148
MS.gene02256.t1 AT4G25790 49.286 140 62 5 14 150 77 210 2.87e-43 142
MS.gene02256.t1 AT1G50050 52.055 146 63 4 7 150 22 162 3.63e-43 140
MS.gene02256.t1 AT5G57625 50.360 139 60 5 15 150 75 207 5.06e-43 141
MS.gene02256.t1 AT4G30320 50.355 141 64 5 13 150 24 161 9.37e-42 137
MS.gene02256.t1 AT2G19990 46.259 147 71 4 6 150 36 176 7.96e-41 135
MS.gene02256.t1 AT3G09590 47.518 141 64 5 14 150 52 186 7.86e-40 132
MS.gene02256.t1 AT1G50050 51.449 138 60 4 7 142 22 154 7.13e-39 131
MS.gene02256.t1 AT1G01310 46.043 139 67 4 14 150 87 219 4.63e-38 130
MS.gene02256.t1 AT5G02730 47.887 142 64 5 13 150 58 193 8.89e-38 128
MS.gene02256.t1 AT4G07820 43.056 144 75 3 7 150 24 160 3.06e-37 125
MS.gene02256.t1 AT4G31470 42.446 139 72 4 14 150 53 185 6.46e-35 120
MS.gene02256.t1 AT5G66590 39.437 142 75 5 15 150 49 185 5.82e-30 107
MS.gene02256.t1 AT2G19980 41.781 146 63 7 12 150 35 165 9.10e-26 96.3
MS.gene02256.t1 AT2G19970 37.086 151 75 7 12 150 35 177 1.53e-21 85.9

Find 40 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTGTCCCAAACAATATT+TGG 0.192023 2.1:+72919829 None:intergenic
TTAAAATTCCAAATATTGTT+TGG 0.293275 2.1:-72919837 MS.gene02256:CDS
TAAAATTCCAAATATTGTTT+GGG 0.350860 2.1:-72919836 MS.gene02256:CDS
TTGATCCACTCCGGTGGTGG+TGG 0.379754 2.1:-72919757 MS.gene02256:CDS
CGTAGTCTGCTGGTGAGTCT+TGG 0.381814 2.1:+72919902 None:intergenic
ATTACTACTATAATCATAGT+AGG 0.395772 2.1:+72919654 None:intergenic
GCCACTATACTCAGGTGGTT+TGG 0.400142 2.1:-72919606 MS.gene02256:CDS
TCCGGTGGTGGTGGGCGTTA+CGG 0.427305 2.1:-72919748 MS.gene02256:CDS
AGTAGTAATTCATGTACTAA+TGG 0.433484 2.1:-72919640 MS.gene02256:CDS
GTAGTCTGCTGGTGAGTCTT+GGG 0.448748 2.1:+72919903 None:intergenic
TGGAGAAACACACAACGTAT+TGG 0.459583 2.1:-72919586 MS.gene02256:CDS
CTTTCGCCAATATAGTTGCC+AGG 0.474936 2.1:+72919505 None:intergenic
TCCGTAACGCCCACCACCAC+CGG 0.485057 2.1:+72919747 None:intergenic
TGCCGATCTTGCATTGTTGT+GGG 0.491310 2.1:+72919873 None:intergenic
CTGCCGATCTTGCATTGTTG+TGG 0.503037 2.1:+72919872 None:intergenic
TCCAAACCACCTGAGTATAG+TGG 0.511835 2.1:+72919605 None:intergenic
TGCCCACAACAATGCAAGAT+CGG 0.519302 2.1:-72919875 MS.gene02256:CDS
TGATCCACTCCGGTGGTGGT+GGG 0.526774 2.1:-72919756 MS.gene02256:CDS
TCCGTTATCACATTTCACTT+TGG 0.528096 2.1:+72919558 None:intergenic
TGGGCATTCACGTAGTCTGC+TGG 0.533658 2.1:+72919892 None:intergenic
CAATTGATCCACTCCGGTGG+TGG 0.548354 2.1:-72919760 MS.gene02256:CDS
TTTCGCCAATATAGTTGCCA+GGG 0.556325 2.1:+72919506 None:intergenic
TTACTACTATAATCATAGTA+GGG 0.560092 2.1:+72919655 None:intergenic
GCATCGAAGCAGTGAAGTTG+TGG 0.565988 2.1:-72919690 MS.gene02256:CDS
GAGAGCAGCGGCAACATGAG+TGG 0.584608 2.1:-72919712 MS.gene02256:CDS
CATCGAAGCAGTGAAGTTGT+GGG 0.588926 2.1:-72919689 MS.gene02256:CDS
CGCCAATATAGTTGCCAGGG+GGG 0.599696 2.1:+72919509 None:intergenic
AACGCCCACCACCACCGGAG+TGG 0.599839 2.1:+72919752 None:intergenic
GAAAATATCGCAGAGAGCAG+CGG 0.617856 2.1:-72919724 MS.gene02256:CDS
TTCGCCAATATAGTTGCCAG+GGG 0.619900 2.1:+72919507 None:intergenic
GCCAAAGTGAAATGTGATAA+CGG 0.620952 2.1:-72919559 MS.gene02256:CDS
AAGCTATGCTAATCAACGCA+AGG 0.634047 2.1:-72919788 MS.gene02256:CDS
GATTGTCAATTGATCCACTC+CGG 0.636911 2.1:-72919766 MS.gene02256:CDS
CGAAGCAGTGAAGTTGTGGG+TGG 0.656466 2.1:-72919686 MS.gene02256:CDS
TCGCCAATATAGTTGCCAGG+GGG 0.658113 2.1:+72919508 None:intergenic
TGTCAATTGATCCACTCCGG+TGG 0.661722 2.1:-72919763 MS.gene02256:CDS
GTGTGGCCACTATACTCAGG+TGG 0.688606 2.1:-72919611 MS.gene02256:CDS
TGTACTAATGGTGAAATGTG+TGG 0.714246 2.1:-72919628 MS.gene02256:CDS
AATGTGTGGCCACTATACTC+AGG 0.735120 2.1:-72919614 MS.gene02256:CDS
AAAGTGAAATGTGATAACGG+AGG 0.789855 2.1:-72919556 MS.gene02256:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATTCCAAATATTGTTT+GGG - chr2.1:72919584-72919603 MS.gene02256:CDS 15.0%
!! TTAAAATTCCAAATATTGTT+TGG - chr2.1:72919583-72919602 MS.gene02256:CDS 15.0%
!! ATTACTACTATAATCATAGT+AGG + chr2.1:72919769-72919788 None:intergenic 20.0%
!! TTACTACTATAATCATAGTA+GGG + chr2.1:72919768-72919787 None:intergenic 20.0%
! AGTAGTAATTCATGTACTAA+TGG - chr2.1:72919780-72919799 MS.gene02256:CDS 25.0%
TTGTTGTCCCAAACAATATT+TGG + chr2.1:72919594-72919613 None:intergenic 30.0%
GCCAAAGTGAAATGTGATAA+CGG - chr2.1:72919861-72919880 MS.gene02256:CDS 35.0%
TCCGTTATCACATTTCACTT+TGG + chr2.1:72919865-72919884 None:intergenic 35.0%
TGTACTAATGGTGAAATGTG+TGG - chr2.1:72919792-72919811 MS.gene02256:CDS 35.0%
!! AAAGTGAAATGTGATAACGG+AGG - chr2.1:72919864-72919883 MS.gene02256:CDS 35.0%
AAGCTATGCTAATCAACGCA+AGG - chr2.1:72919632-72919651 MS.gene02256:CDS 40.0%
GATTGTCAATTGATCCACTC+CGG - chr2.1:72919654-72919673 MS.gene02256:CDS 40.0%
TGGAGAAACACACAACGTAT+TGG - chr2.1:72919834-72919853 MS.gene02256:CDS 40.0%
TTTCGCCAATATAGTTGCCA+GGG + chr2.1:72919917-72919936 None:intergenic 40.0%
AATGTGTGGCCACTATACTC+AGG - chr2.1:72919806-72919825 MS.gene02256:CDS 45.0%
CATCGAAGCAGTGAAGTTGT+GGG - chr2.1:72919731-72919750 MS.gene02256:CDS 45.0%
CTTTCGCCAATATAGTTGCC+AGG + chr2.1:72919918-72919937 None:intergenic 45.0%
GAAAATATCGCAGAGAGCAG+CGG - chr2.1:72919696-72919715 MS.gene02256:CDS 45.0%
TCCAAACCACCTGAGTATAG+TGG + chr2.1:72919818-72919837 None:intergenic 45.0%
TGCCCACAACAATGCAAGAT+CGG - chr2.1:72919545-72919564 MS.gene02256:CDS 45.0%
TGCCGATCTTGCATTGTTGT+GGG + chr2.1:72919550-72919569 None:intergenic 45.0%
TTCGCCAATATAGTTGCCAG+GGG + chr2.1:72919916-72919935 None:intergenic 45.0%
CTGCCGATCTTGCATTGTTG+TGG + chr2.1:72919551-72919570 None:intergenic 50.0%
GCATCGAAGCAGTGAAGTTG+TGG - chr2.1:72919730-72919749 MS.gene02256:CDS 50.0%
GCCACTATACTCAGGTGGTT+TGG - chr2.1:72919814-72919833 MS.gene02256:CDS 50.0%
GTAGTCTGCTGGTGAGTCTT+GGG + chr2.1:72919520-72919539 None:intergenic 50.0%
TCGCCAATATAGTTGCCAGG+GGG + chr2.1:72919915-72919934 None:intergenic 50.0%
TGTCAATTGATCCACTCCGG+TGG - chr2.1:72919657-72919676 MS.gene02256:CDS 50.0%
ACTTGCAATTACGACCCCCC+TGG - chr2.1:72919897-72919916 MS.gene02256:CDS 55.0%
CAATTGATCCACTCCGGTGG+TGG - chr2.1:72919660-72919679 MS.gene02256:CDS 55.0%
CGAAGCAGTGAAGTTGTGGG+TGG - chr2.1:72919734-72919753 MS.gene02256:CDS 55.0%
CGCCAATATAGTTGCCAGGG+GGG + chr2.1:72919914-72919933 None:intergenic 55.0%
CGTAGTCTGCTGGTGAGTCT+TGG + chr2.1:72919521-72919540 None:intergenic 55.0%
GACCCCCCTGGCAACTATAT+TGG - chr2.1:72919909-72919928 MS.gene02256:CDS 55.0%
GTGTGGCCACTATACTCAGG+TGG - chr2.1:72919809-72919828 MS.gene02256:CDS 55.0%
TGGGCATTCACGTAGTCTGC+TGG + chr2.1:72919531-72919550 None:intergenic 55.0%
GAGAGCAGCGGCAACATGAG+TGG - chr2.1:72919708-72919727 MS.gene02256:CDS 60.0%
! TGATCCACTCCGGTGGTGGT+GGG - chr2.1:72919664-72919683 MS.gene02256:CDS 60.0%
! TTGATCCACTCCGGTGGTGG+TGG - chr2.1:72919663-72919682 MS.gene02256:CDS 60.0%
TCCGTAACGCCCACCACCAC+CGG + chr2.1:72919676-72919695 None:intergenic 65.0%
!! TCCGGTGGTGGTGGGCGTTA+CGG - chr2.1:72919672-72919691 MS.gene02256:CDS 65.0%
AACGCCCACCACCACCGGAG+TGG + chr2.1:72919671-72919690 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 72919495 72919947 72919495 ID=MS.gene02256
chr2.1 mRNA 72919495 72919947 72919495 ID=MS.gene02256.t1;Parent=MS.gene02256
chr2.1 exon 72919495 72919947 72919495 ID=MS.gene02256.t1.exon1;Parent=MS.gene02256.t1
chr2.1 CDS 72919495 72919947 72919495 ID=cds.MS.gene02256.t1;Parent=MS.gene02256.t1
Gene Sequence

>MS.gene02256

ATGGGTAGTCACGTTGCACATGCCCAAGACTCACCAGCAGACTACGTGAATGCCCACAACAATGCAAGATCGGCAGTTCATACAAACGTTAAAATTCCAAATATTGTTTGGGACAACAAAGTTGCTGCTTTTGCACAAAGCTATGCTAATCAACGCAAGGATTGTCAATTGATCCACTCCGGTGGTGGTGGGCGTTACGGAGAAAATATCGCAGAGAGCAGCGGCAACATGAGTGGCATCGAAGCAGTGAAGTTGTGGGTGGATGAAAAACCCTACTATGATTATAGTAGTAATTCATGTACTAATGGTGAAATGTGTGGCCACTATACTCAGGTGGTTTGGAGAAACACACAACGTATTGGATGTGCCAAAGTGAAATGTGATAACGGAGGCACATTCATTACTTGCAATTACGACCCCCCTGGCAACTATATTGGCGAAAGACCTTACTAA
Protein sequence

>MS.gene02256.t1

MGSHVAHAQDSPADYVNAHNNARSAVHTNVKIPNIVWDNKVAAFAQSYANQRKDCQLIHSGGGGRYGENIAESSGNMSGIEAVKLWVDEKPYYDYSSNSCTNGEMCGHYTQVVWRNTQRIGCAKVKCDNGGTFITCNYDPPGNYIGERPY