AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene045511

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045511.t1 MTR_4g079580 91.034 145 12 1 1 145 1 144 1.10e-89 267
MS.gene045511.t1 MTR_4g079580 96.629 89 3 0 136 224 247 335 2.76e-45 154
MS.gene045511.t1 MTR_2g090960 68.504 127 37 2 1 125 3 128 1.26e-53 175
MS.gene045511.t1 MTR_2g090960 56.627 83 33 3 138 217 239 321 8.92e-21 89.0
MS.gene045511.t1 MTR_8g463380 83.908 87 14 0 3 89 34 120 9.72e-47 160
MS.gene045511.t1 MTR_2g078200 79.762 84 17 0 6 89 3 86 7.94e-45 151
MS.gene045511.t1 MTR_7g015010 59.740 77 31 0 17 93 51 127 2.85e-25 101
MS.gene045511.t1 MTR_6g015350 61.250 80 28 1 17 96 43 119 9.10e-23 94.7
MS.gene045511.t1 MTR_4g109660 58.824 68 28 0 17 84 50 117 1.51e-20 88.2
MS.gene045511.t1 MTR_3g026050 46.392 97 45 2 17 107 51 146 4.53e-20 87.8
MS.gene045511.t1 MTR_6g017055 48.148 81 41 1 3 83 107 186 2.51e-18 83.2
MS.gene045511.t1 MTR_1g103380 55.000 60 27 0 23 82 201 260 5.54e-17 79.3
MS.gene045511.t1 MTR_4g111935 46.250 80 42 1 3 82 113 191 1.24e-15 75.1
MS.gene045511.t1 MTR_7g018500 53.448 58 27 0 25 82 122 179 2.92e-15 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045511.t1 AT3G15030 84.706 85 13 0 5 89 27 111 3.64e-47 160
MS.gene045511.t1 AT3G15030 84.706 85 13 0 5 89 27 111 3.64e-47 160
MS.gene045511.t1 AT3G15030 84.706 85 13 0 5 89 27 111 3.64e-47 160
MS.gene045511.t1 AT3G15030 84.706 85 13 0 5 89 27 111 3.64e-47 160
MS.gene045511.t1 AT1G53230 81.176 85 16 0 5 89 31 115 9.29e-45 154
MS.gene045511.t1 AT1G53230 81.176 85 16 0 5 89 31 115 9.29e-45 154
MS.gene045511.t1 AT2G31070 88.312 77 9 0 5 81 11 87 1.51e-44 152
MS.gene045511.t1 AT4G18390 59.184 98 29 3 17 109 36 127 3.35e-27 107
MS.gene045511.t1 AT4G18390 59.184 98 29 3 17 109 36 127 3.35e-27 107
MS.gene045511.t1 AT1G30210 66.176 68 23 0 17 84 44 111 2.24e-23 96.3
MS.gene045511.t1 AT1G30210 66.176 68 23 0 17 84 44 111 2.24e-23 96.3
MS.gene045511.t1 AT3G02150 63.768 69 25 0 17 85 68 136 1.28e-22 93.2
MS.gene045511.t1 AT3G02150 63.768 69 25 0 17 85 68 136 1.99e-22 94.0
MS.gene045511.t1 AT5G60970 53.012 83 37 1 17 99 57 137 1.10e-20 89.4
MS.gene045511.t1 AT5G08070 51.220 82 37 1 17 95 27 108 1.56e-20 87.0
MS.gene045511.t1 AT5G08070 51.220 82 37 1 17 95 27 108 1.56e-20 87.0
MS.gene045511.t1 AT1G68800 53.846 65 30 0 19 83 108 172 2.28e-19 85.5
MS.gene045511.t1 AT1G68800 53.846 65 30 0 19 83 108 172 2.39e-19 85.5
MS.gene045511.t1 AT1G67260 50.000 66 33 0 18 83 82 147 9.62e-18 80.9
MS.gene045511.t1 AT1G67260 50.000 66 33 0 18 83 82 147 9.62e-18 80.9
MS.gene045511.t1 AT1G67260 50.000 66 33 0 18 83 82 147 1.05e-17 80.9
MS.gene045511.t1 AT3G18550 50.769 65 32 0 18 82 143 207 3.28e-15 74.3
MS.gene045511.t1 AT3G18550 50.769 65 32 0 18 82 143 207 3.28e-15 74.3
MS.gene045511.t1 AT3G18550 54.098 61 28 0 22 82 147 207 3.35e-15 74.3
MS.gene045511.t1 AT3G18550 50.769 65 32 0 18 82 143 207 3.51e-15 73.9

Find 50 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCATCAAGCTTCAATCTT+TGG 0.193207 4.2:+30557106 MS.gene045511:CDS
TGTCCACCTTGAACTGTATC+AGG 0.337666 4.2:-30557169 None:intergenic
TTCGACTGAAGGGCCTCATT+TGG 0.352467 4.2:-30557004 None:intergenic
AGGAGAAGAAGAAGGTCTAT+TGG 0.357996 4.2:-30557212 None:intergenic
GAAGTAGGGATGAGGAGTAC+TGG 0.386702 4.2:+30556227 None:intergenic
TGCATTCCTGATACAGTTCA+AGG 0.398078 4.2:+30557163 MS.gene045511:CDS
AGCCAATCCACTGCTTTGCT+TGG 0.398100 4.2:-30556422 None:intergenic
GGAGAGATAGTTCAGGTAGA+AGG 0.398765 4.2:+30556254 MS.gene045511:CDS
TAGAAGGAGGACACATAGTT+CGG 0.402620 4.2:+30556270 MS.gene045511:CDS
GGAAGCAGGTTTGTTTCTGA+TGG 0.414475 4.2:+30557127 MS.gene045511:CDS
TTTGTTTCTGATGGATTAGC+AGG 0.421645 4.2:+30557136 MS.gene045511:CDS
AACTTTGCTCAGTTGTGGTT+AGG 0.425546 4.2:-30557232 None:intergenic
AAGCTTCAATCTTTGGAAGC+AGG 0.461093 4.2:+30557113 MS.gene045511:CDS
TGGAGGAGGAGAGATAGTTC+AGG 0.462988 4.2:+30556247 MS.gene045511:CDS
CAAAAGGTCCTCGTGATCGC+AGG 0.468784 4.2:+30556333 MS.gene045511:CDS
GGAGAAACATCAGAATCTAA+TGG 0.478617 4.2:+30556578 MS.gene045511:CDS
AGAAGGAGGACACATAGTTC+GGG 0.484476 4.2:+30556271 MS.gene045511:CDS
TTTCGCATTCTGTTAGTACA+TGG 0.488530 4.2:+30557029 MS.gene045511:CDS
AGCAAGGTTTACACATCAAA+AGG 0.489089 4.2:+30556317 MS.gene045511:CDS
AACTCAAGTGGAATGGTTGT+TGG 0.490485 4.2:+30556557 MS.gene045511:CDS
CTTCAGAGGTTCATCATCAC+AGG 0.503181 4.2:+30557074 MS.gene045511:CDS
AAGCTCCGCGAGCTTGTCAA+TGG 0.510986 4.2:-30556465 None:intergenic
GGGATGAGGAGTACTGGAGG+AGG 0.516880 4.2:+30556233 None:intergenic
TCCTATGGATTCTTCTTCAG+AGG 0.520790 4.2:+30557060 MS.gene045511:CDS
GACCAAGCAAAGCAGTGGAT+TGG 0.524360 4.2:+30556420 MS.gene045511:CDS
CTTCCTCCATGGCATCCAAT+CGG 0.535397 4.2:+30556485 MS.gene045511:CDS
TAGAAAACTTTGCTCAGTTG+TGG 0.537314 4.2:-30557237 None:intergenic
TACATGGAATGAGATTCCTA+TGG 0.537407 4.2:+30557045 MS.gene045511:CDS
AAAGTAGTTGCAAACTCAAG+TGG 0.543287 4.2:+30556545 MS.gene045511:CDS
AGACAATTGAGTGAGAATCA+AGG 0.556151 4.2:+30556620 MS.gene045511:CDS
GTAGGGATGAGGAGTACTGG+AGG 0.556752 4.2:+30556230 None:intergenic
AGCTCGCGGAGCTTCCTCCA+TGG 0.559593 4.2:+30556474 MS.gene045511:CDS
AGTTGCAAACTCAAGTGGAA+TGG 0.583308 4.2:+30556550 MS.gene045511:CDS
ACTTTCTGAACTTCTTCTAG+AGG 0.585901 4.2:-30556527 None:intergenic
TTCAGAATACTCTCCAAATG+AGG 0.589921 4.2:+30556991 MS.gene045511:CDS
ACAGTTCAAGGTGGACAAGA+GGG 0.596091 4.2:+30557175 MS.gene045511:CDS
AAAAGGTCCTCGTGATCGCA+GGG 0.597089 4.2:+30556334 MS.gene045511:CDS
TACAGTTCAAGGTGGACAAG+AGG 0.610010 4.2:+30557174 MS.gene045511:CDS
TGCTTGGTCTGTCATAGCCG+AGG 0.612632 4.2:-30556406 None:intergenic
TACGATGTTCAAGATCGCCT+CGG 0.620277 4.2:+30556389 MS.gene045511:CDS
AGTCGAACCCTGCGATCACG+AGG 0.621133 4.2:-30556341 None:intergenic
AGTATTCTGAACCTGAACCT+TGG 0.621967 4.2:-30556979 None:intergenic
GAGATAGTTCAGGTAGAAGG+AGG 0.622890 4.2:+30556257 MS.gene045511:CDS
TTGAACATCGTAGAATTCGA+TGG 0.627660 4.2:-30556378 None:intergenic
TGACAGACCAAGCAAAGCAG+TGG 0.629311 4.2:+30556415 MS.gene045511:CDS
TTGTGGTTAGGAGAAGAAGA+AGG 0.640804 4.2:-30557220 None:intergenic
TCGCCGATTGGATGCCATGG+AGG 0.652394 4.2:-30556488 None:intergenic
ACCTCTGAAGAAGAATCCAT+AGG 0.653923 4.2:-30557061 None:intergenic
GTCTTCCATTGACAAGCTCG+CGG 0.658985 4.2:+30556460 MS.gene045511:CDS
ATTCCTGATACAGTTCAAGG+TGG 0.774068 4.2:+30557166 MS.gene045511:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTTTCTTTATATAATCAT+TGG - chr4.2:30556927-30556946 None:intergenic 15.0%
!! AATGATTATATAAAGAAAGT+TGG + chr4.2:30556926-30556945 MS.gene045511:intron 15.0%
!! AATATCATAGAATTGAGAAT+TGG + chr4.2:30556888-30556907 MS.gene045511:intron 20.0%
!! AATTCTCAATTCTATGATAT+TGG - chr4.2:30556889-30556908 None:intergenic 20.0%
! GTGAAATGAAAGTTGAATTA+TGG - chr4.2:30556649-30556668 None:intergenic 25.0%
! TATAAAGAAAGTTGGATTCA+TGG + chr4.2:30556934-30556953 MS.gene045511:intron 25.0%
!! ATTGGTTCTCAAAAAAAGTT+TGG - chr4.2:30556871-30556890 None:intergenic 25.0%
!!! AAAAAGTTTGGTTTTGGTTT+TGG - chr4.2:30556859-30556878 None:intergenic 25.0%
!!! TCTCAAAAAAAGTTTGGTTT+TGG - chr4.2:30556865-30556884 None:intergenic 25.0%
!! GGTTTTCATTTGAAGTTTCA+TGG - chr4.2:30556838-30556857 None:intergenic 30.0%
AAAGTAGTTGCAAACTCAAG+TGG + chr4.2:30556545-30556564 MS.gene045511:CDS 35.0%
AATGCGAAAAATTCGACTGA+AGG - chr4.2:30557018-30557037 None:intergenic 35.0%
ACTTTCTGAACTTCTTCTAG+AGG - chr4.2:30556530-30556549 None:intergenic 35.0%
AGACAATTGAGTGAGAATCA+AGG + chr4.2:30556620-30556639 MS.gene045511:CDS 35.0%
AGCAAGGTTTACACATCAAA+AGG + chr4.2:30556317-30556336 MS.gene045511:CDS 35.0%
ATCACAATGGTTTCATTCCA+TGG + chr4.2:30556789-30556808 MS.gene045511:intron 35.0%
ATGCGAAAAATTCGACTGAA+GGG - chr4.2:30557017-30557036 None:intergenic 35.0%
GAATGAAACCATTGTGATCT+TGG - chr4.2:30556787-30556806 None:intergenic 35.0%
GGAGAAACATCAGAATCTAA+TGG + chr4.2:30556578-30556597 MS.gene045511:CDS 35.0%
GGATCAGTTTCAACATTATG+TGG - chr4.2:30556671-30556690 None:intergenic 35.0%
GTTCATCAAGCTTCAATCTT+TGG + chr4.2:30557106-30557125 MS.gene045511:CDS 35.0%
TAAAAAAGATCGTCACAGCA+AGG + chr4.2:30556301-30556320 MS.gene045511:CDS 35.0%
TACATGGAATGAGATTCCTA+TGG + chr4.2:30557045-30557064 MS.gene045511:CDS 35.0%
TTCAGAATACTCTCCAAATG+AGG + chr4.2:30556991-30557010 MS.gene045511:CDS 35.0%
TTGAACATCGTAGAATTCGA+TGG - chr4.2:30556381-30556400 None:intergenic 35.0%
TTTCGCATTCTGTTAGTACA+TGG + chr4.2:30557029-30557048 MS.gene045511:CDS 35.0%
! GTAGTTGGAAAGAAAGGTAT+AGG - chr4.2:30556692-30556711 None:intergenic 35.0%
!! AGGGTAGTTCTGAAAATTGA+TGG - chr4.2:30556732-30556751 None:intergenic 35.0%
!! TTTGTTTCTGATGGATTAGC+AGG + chr4.2:30557136-30557155 MS.gene045511:CDS 35.0%
!!! GTAAACTCACAGCCATTTTT+AGG + chr4.2:30556956-30556975 MS.gene045511:intron 35.0%
AACTCAAGTGGAATGGTTGT+TGG + chr4.2:30556557-30556576 MS.gene045511:CDS 40.0%
AGGAGAAGAAGAAGGTCTAT+TGG - chr4.2:30557215-30557234 None:intergenic 40.0%
AGTATTCTGAACCTGAACCT+TGG - chr4.2:30556982-30557001 None:intergenic 40.0%
AGTTGCAAACTCAAGTGGAA+TGG + chr4.2:30556550-30556569 MS.gene045511:CDS 40.0%
ATTCCTGATACAGTTCAAGG+TGG + chr4.2:30557166-30557185 MS.gene045511:CDS 40.0%
CATTCCTTCCAAGATCACAA+TGG + chr4.2:30556776-30556795 MS.gene045511:intron 40.0%
GAAACCATTGTGATCTTGGA+AGG - chr4.2:30556783-30556802 None:intergenic 40.0%
GAAGAAGTAGAAGAGGTAGT+TGG - chr4.2:30556707-30556726 None:intergenic 40.0%
GAAGAGGTAGTTGGAAAGAA+AGG - chr4.2:30556698-30556717 None:intergenic 40.0%
GATGGATGAAGAAGTAGAAG+AGG - chr4.2:30556714-30556733 None:intergenic 40.0%
TAGAAGGAGGACACATAGTT+CGG + chr4.2:30556270-30556289 MS.gene045511:CDS 40.0%
TCCTATGGATTCTTCTTCAG+AGG + chr4.2:30557060-30557079 MS.gene045511:CDS 40.0%
TGCATTCCTGATACAGTTCA+AGG + chr4.2:30557163-30557182 MS.gene045511:CDS 40.0%
TTGTGGTTAGGAGAAGAAGA+AGG - chr4.2:30557223-30557242 None:intergenic 40.0%
! AACTACCCTTCTGAAAACCT+TGG + chr4.2:30556743-30556762 MS.gene045511:intron 40.0%
! AAGCTTCAATCTTTGGAAGC+AGG + chr4.2:30557113-30557132 MS.gene045511:CDS 40.0%
! ACCTCTGAAGAAGAATCCAT+AGG - chr4.2:30557064-30557083 None:intergenic 40.0%
!! AGAGTTTGATTTTCGCCGAT+TGG - chr4.2:30556503-30556522 None:intergenic 40.0%
!! CATACTTGTTGTGATTGCCA+TGG - chr4.2:30556809-30556828 None:intergenic 40.0%
!!! GCTGTGACGATCTTTTTTAC+TGG - chr4.2:30556300-30556319 None:intergenic 40.0%
!!! GTGACGATCTTTTTTACTGG+TGG - chr4.2:30556297-30556316 None:intergenic 40.0%
ACAGTTCAAGGTGGACAAGA+GGG + chr4.2:30557175-30557194 MS.gene045511:CDS 45.0%
AGAAGGAGGACACATAGTTC+GGG + chr4.2:30556271-30556290 MS.gene045511:CDS 45.0%
CCTGAACCTTGGCCTAAAAA+TGG - chr4.2:30556971-30556990 None:intergenic 45.0%
CTTCAGAGGTTCATCATCAC+AGG + chr4.2:30557074-30557093 MS.gene045511:CDS 45.0%
CTTGGAAGGAATGAAGAGAG+AGG - chr4.2:30556769-30556788 None:intergenic 45.0%
GAGATAGTTCAGGTAGAAGG+AGG + chr4.2:30556257-30556276 MS.gene045511:CDS 45.0%
GGAGAGATAGTTCAGGTAGA+AGG + chr4.2:30556254-30556273 MS.gene045511:CDS 45.0%
TACAGTTCAAGGTGGACAAG+AGG + chr4.2:30557174-30557193 MS.gene045511:CDS 45.0%
TACGATGTTCAAGATCGCCT+CGG + chr4.2:30556389-30556408 MS.gene045511:CDS 45.0%
TGTCCACCTTGAACTGTATC+AGG - chr4.2:30557172-30557191 None:intergenic 45.0%
! AGAGGCCAAGGTTTTCAGAA+GGG - chr4.2:30556751-30556770 None:intergenic 45.0%
!! CCATTTTTAGGCCAAGGTTC+AGG + chr4.2:30556968-30556987 MS.gene045511:intron 45.0%
!! GGAAGCAGGTTTGTTTCTGA+TGG + chr4.2:30557127-30557146 MS.gene045511:CDS 45.0%
!!! TCACAGCCATTTTTAGGCCA+AGG + chr4.2:30556962-30556981 MS.gene045511:intron 45.0%
AAAAGGTCCTCGTGATCGCA+GGG + chr4.2:30556334-30556353 MS.gene045511:CDS 50.0%
AGCCAATCCACTGCTTTGCT+TGG - chr4.2:30556425-30556444 None:intergenic 50.0%
AGGAATGAAGAGAGAGGCCA+AGG - chr4.2:30556763-30556782 None:intergenic 50.0%
CTTCCTCCATGGCATCCAAT+CGG + chr4.2:30556485-30556504 MS.gene045511:CDS 50.0%
GACCAAGCAAAGCAGTGGAT+TGG + chr4.2:30556420-30556439 MS.gene045511:CDS 50.0%
GTCTTCCATTGACAAGCTCG+CGG + chr4.2:30556460-30556479 MS.gene045511:CDS 50.0%
TGACAGACCAAGCAAAGCAG+TGG + chr4.2:30556415-30556434 MS.gene045511:CDS 50.0%
TGGAGGAGGAGAGATAGTTC+AGG + chr4.2:30556247-30556266 MS.gene045511:CDS 50.0%
TTCGACTGAAGGGCCTCATT+TGG - chr4.2:30557007-30557026 None:intergenic 50.0%
! GAGAGGCCAAGGTTTTCAGA+AGG - chr4.2:30556752-30556771 None:intergenic 50.0%
!! TTTTCGCCGATTGGATGCCA+TGG - chr4.2:30556494-30556513 None:intergenic 50.0%
AAGCTCCGCGAGCTTGTCAA+TGG - chr4.2:30556468-30556487 None:intergenic 55.0%
CAAAAGGTCCTCGTGATCGC+AGG + chr4.2:30556333-30556352 MS.gene045511:CDS 55.0%
TGCTTGGTCTGTCATAGCCG+AGG - chr4.2:30556409-30556428 None:intergenic 55.0%
AGTCGAACCCTGCGATCACG+AGG - chr4.2:30556344-30556363 None:intergenic 60.0%
! TCGCCGATTGGATGCCATGG+AGG - chr4.2:30556491-30556510 None:intergenic 60.0%
AGCTCGCGGAGCTTCCTCCA+TGG + chr4.2:30556474-30556493 MS.gene045511:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 30556236 30557246 30556236 ID=MS.gene045511
chr4.2 mRNA 30556236 30557246 30556236 ID=MS.gene045511.t1;Parent=MS.gene045511
chr4.2 exon 30556236 30556641 30556236 ID=MS.gene045511.t1.exon1;Parent=MS.gene045511.t1
chr4.2 CDS 30556236 30556641 30556236 ID=cds.MS.gene045511.t1;Parent=MS.gene045511.t1
chr4.2 exon 30556978 30557246 30556978 ID=MS.gene045511.t1.exon2;Parent=MS.gene045511.t1
chr4.2 CDS 30556978 30557246 30556978 ID=cds.MS.gene045511.t1;Parent=MS.gene045511.t1
Gene Sequence

>MS.gene045511

ATGAGGAGTACTGGAGGAGGAGAGATAGTTCAGGTAGAAGGAGGACACATAGTTCGGGCCACCAGTAAAAAAGATCGTCACAGCAAGGTTTACACATCAAAAGGTCCTCGTGATCGCAGGGTTCGACTCTCAGCACACACAGCCATCGAATTCTACGATGTTCAAGATCGCCTCGGCTATGACAGACCAAGCAAAGCAGTGGATTGGCTCATCAAGAAAGCAAAGTCTTCCATTGACAAGCTCGCGGAGCTTCCTCCATGGCATCCAATCGGCGAAAATCAAACTCTGAAACCTCTAGAAGAAGTTCAGAAAGTAGTTGCAAACTCAAGTGGAATGGTTGTTGGAGAAACATCAGAATCTAATGGTTACAATTTTCATTTTTTAAGACAATTGAGTGAGAATCAAGGTAACCATAATTCAACTTTCATTTCACCACATAATGTTGAAACTGATCCTATACCTTTCTTTCCAACTACCTCTTCTACTTCTTCATCCATCAATTTTCAGAACTACCCTTCTGAAAACCTTGGCCTCTCTCTTCATTCCTTCCAAGATCACAATGGTTTCATTCCATGGCAATCACAACAAGTATGTGAAAACCATGAAACTTCAAATGAAAACCAAAACCAAAACCAAACTTTTTTTGAGAACCAATATCATAGAATTGAGAATTGGAACAATGAAACAACCAATGATTATATAAAGAAAGTTGGATTCATGGTAAACTCACAGCCATTTTTAGGCCAAGGTTCAGGTTCAGAATACTCTCCAAATGAGGCCCTTCAGTCGAATTTTTCGCATTCTGTTAGTACATGGAATGAGATTCCTATGGATTCTTCTTCAGAGGTTCATCATCACAGGTCTCAACAAGTTCATCAAGCTTCAATCTTTGGAAGCAGGTTTGTTTCTGATGGATTAGCAGGTTTCTGCATTCCTGATACAGTTCAAGGTGGACAAGAGGGTCATAGAGTTTCTTCCAATAGACCTTCTTCTTCTCCTAACCACAACTGA
Protein sequence

>MS.gene045511.t1

MRSTGGGEIVQVEGGHIVRATSKKDRHSKVYTSKGPRDRRVRLSAHTAIEFYDVQDRLGYDRPSKAVDWLIKKAKSSIDKLAELPPWHPIGENQTLKPLEEVQKVVANSSGMVVGETSESNGYNFHFLRQLSENQGQGSGSEYSPNEALQSNFSHSVSTWNEIPMDSSSEVHHHRSQQVHQASIFGSRFVSDGLAGFCIPDTVQGGQEGHRVSSNRPSSSPNHN