AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene86911

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86911.t1 MTR_1g106730 54.152 277 29 9 3 208 2 251 2.31e-79 238
MS.gene86911.t1 MTR_3g102980 51.562 128 44 6 4 130 1 111 3.18e-26 101
MS.gene86911.t1 MTR_1g018420 50.588 85 20 3 54 131 38 107 1.96e-17 77.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86911.t1 AT3G49930 49.485 97 34 3 36 129 34 118 4.62e-21 87.4
MS.gene86911.t1 AT5G67450 37.681 138 57 6 4 129 1 121 2.09e-19 83.6
MS.gene86911.t1 AT1G27730 39.716 141 57 5 4 141 1 116 9.39e-19 81.3
MS.gene86911.t1 AT3G19580 44.444 99 44 2 54 152 66 153 7.80e-18 79.7
MS.gene86911.t1 AT3G19580 44.444 99 44 2 54 152 66 153 7.80e-18 79.7
MS.gene86911.t1 AT5G04340 41.905 105 49 3 40 141 30 125 1.38e-15 73.2
MS.gene86911.t1 AT5G43170 35.593 118 49 4 41 152 28 124 3.16e-13 65.9

Find 51 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACATTAATCTTGGTCTTCT+TGG 0.185197 1.2:+79285625 None:intergenic
TACCTCTTGTTCATTGATTC+CGG 0.301905 1.2:+79285595 None:intergenic
GATTCATGAACGTGAGTCTT+TGG 0.319967 1.2:-79286254 MS.gene86911:CDS
GGCGAGATTAACATTAATCT+TGG 0.353029 1.2:+79285616 None:intergenic
CGTTGCCGGTAACCGCTAAA+AGG 0.357837 1.2:-79285565 MS.gene86911:CDS
TTCTGGTCTCCGGTTGGATT+CGG 0.364389 1.2:-79285659 MS.gene86911:CDS
CAGCGCCTCTCACTGAATTC+TGG 0.379619 1.2:-79285676 MS.gene86911:CDS
CGATCAAAACGGCCGCGTAT+TGG 0.396652 1.2:-79286220 MS.gene86911:CDS
AGAGGTAGAAAGTCCGTTGC+CGG 0.419568 1.2:-79285579 MS.gene86911:CDS
TGATGAAGATTTACGGTGGC+TGG 0.425019 1.2:+79285973 None:intergenic
GACTGTCTCGTTGACGGCGG+TGG 0.426617 1.2:+79285940 None:intergenic
TCTCGTTGACGGCGGTGGAT+TGG 0.428167 1.2:+79285945 None:intergenic
CCACCAAGTGCTTGATAAGA+TGG 0.436761 1.2:+79286004 None:intergenic
GCTTTGAATTCTTCTCCAAC+AGG 0.439849 1.2:-79286325 MS.gene86911:CDS
TGATTCAGCTTCACCGGTGA+TGG 0.483480 1.2:+79286055 None:intergenic
CTTGTTGTTGTTTGAAGCGT+GGG 0.484440 1.2:+79286287 None:intergenic
TGTTGTTTGAAGCGTGGGAA+TGG 0.492509 1.2:+79286292 None:intergenic
CCATCTTATCAAGCACTTGG+TGG 0.494016 1.2:-79286004 MS.gene86911:CDS
TTCCCATCTTATCAAGCACT+TGG 0.496098 1.2:-79286007 MS.gene86911:CDS
TCTCCACCACCGAATCCAAC+CGG 0.506094 1.2:+79285650 None:intergenic
ACTGAATTCTGGTCTCCGGT+TGG 0.515567 1.2:-79285665 MS.gene86911:CDS
TCTCACTGAATTCTGGTCTC+CGG 0.517672 1.2:-79285669 MS.gene86911:CDS
GATATTCTTCTTCAGTGGGT+GGG 0.517674 1.2:+79286194 None:intergenic
AGATATTCTTCTTCAGTGGG+TGG 0.522083 1.2:+79286193 None:intergenic
TGTTTCATCATTGTCTTCAC+CGG 0.523785 1.2:+79285529 None:intergenic
TCTCCGGTTGGATTCGGTGG+TGG 0.527155 1.2:-79285653 MS.gene86911:CDS
CACCGGTGATTCAGCTTCAC+CGG 0.531534 1.2:+79286049 None:intergenic
AAGATTAATGTTAATCTCGC+CGG 0.533608 1.2:-79285614 MS.gene86911:CDS
AACAGAGACTGTCTCGTTGA+CGG 0.534230 1.2:+79285934 None:intergenic
GTTGCAGTCGCCGCCATCAC+CGG 0.540954 1.2:-79286068 MS.gene86911:CDS
CACCGGTGAAGCTGAATCAC+CGG 0.548157 1.2:-79286051 MS.gene86911:CDS
AGCGAGATATTCTTCTTCAG+TGG 0.552258 1.2:+79286189 None:intergenic
GCGAGATATTCTTCTTCAGT+GGG 0.560158 1.2:+79286190 None:intergenic
TGGTCTCCGGTTGGATTCGG+TGG 0.560623 1.2:-79285656 MS.gene86911:CDS
GGTGATGGCGGCGACTGCAA+CGG 0.560799 1.2:+79286070 None:intergenic
GTTTCCGTGTCAACGGTCAC+CGG 0.569344 1.2:-79285914 MS.gene86911:intron
CACCAAGTGCTTGATAAGAT+GGG 0.573814 1.2:+79286005 None:intergenic
AGTCTCTGTTTCCGTGTCAA+CGG 0.584449 1.2:-79285921 MS.gene86911:CDS
TTCAGCTTCACCGGTGATGG+CGG 0.589012 1.2:+79286058 None:intergenic
CTTTGTTACAAACACTGCAC+CGG 0.591435 1.2:+79286032 None:intergenic
CGCCGGAATCAATGAACAAG+AGG 0.596526 1.2:-79285597 MS.gene86911:CDS
AATGGAATAGTAGCTCCTGT+TGG 0.598789 1.2:+79286310 None:intergenic
CAAAGCTTGTAACTCTAAAG+CGG 0.606121 1.2:+79286342 None:intergenic
CTTACCGGTGACCGTTGACA+CGG 0.608002 1.2:+79285910 None:intergenic
TCTTGTTGTTGTTTGAAGCG+TGG 0.615448 1.2:+79286286 None:intergenic
GGAGACCAGAATTCAGTGAG+AGG 0.681730 1.2:+79285671 None:intergenic
TGCTTTGAGAGAGCATGATG+AGG 0.697077 1.2:+79286161 None:intergenic
GTGGGTGGGTTACCAATACG+CGG 0.720792 1.2:+79286208 None:intergenic
TTTCTGATGAAGATTTACGG+TGG 0.727105 1.2:+79285969 None:intergenic
AGAGACTGTCTCGTTGACGG+CGG 0.729919 1.2:+79285937 None:intergenic
TCTTCACCGGAAAACAAACG+CGG 0.774869 1.2:+79285542 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCAAAAAGAAACGATCAAAA+CGG - chr1.2:79285638-79285657 MS.gene86911:CDS 25.0%
AAGATTAATGTTAATCTCGC+CGG - chr1.2:79286255-79286274 MS.gene86911:CDS 30.0%
TGTTACTGTTGTTATGATTG+TGG + chr1.2:79286083-79286102 None:intergenic 30.0%
! AACATTAATCTTGGTCTTCT+TGG + chr1.2:79286247-79286266 None:intergenic 30.0%
! GGTTTTCTGATGAAGATTTA+CGG + chr1.2:79285906-79285925 None:intergenic 30.0%
AGGAAAACTCTTGTGACAAA+TGG + chr1.2:79285998-79286017 None:intergenic 35.0%
GGCGAGATTAACATTAATCT+TGG + chr1.2:79286256-79286275 None:intergenic 35.0%
GTAAATTGAGGTCAAATCCA+CGG + chr1.2:79286173-79286192 None:intergenic 35.0%
TGTTTCATCATTGTCTTCAC+CGG + chr1.2:79286343-79286362 None:intergenic 35.0%
TTTCTGATGAAGATTTACGG+TGG + chr1.2:79285903-79285922 None:intergenic 35.0%
! CAAAGCTTGTAACTCTAAAG+CGG + chr1.2:79285530-79285549 None:intergenic 35.0%
!! TACCTCTTGTTCATTGATTC+CGG + chr1.2:79286277-79286296 None:intergenic 35.0%
AATGGAATAGTAGCTCCTGT+TGG + chr1.2:79285562-79285581 None:intergenic 40.0%
AGATATTCTTCTTCAGTGGG+TGG + chr1.2:79285679-79285698 None:intergenic 40.0%
AGCGAGATATTCTTCTTCAG+TGG + chr1.2:79285683-79285702 None:intergenic 40.0%
CACAAACGATGTCACTATGA+AGG - chr1.2:79286039-79286058 MS.gene86911:CDS 40.0%
CACCAAGTGCTTGATAAGAT+GGG + chr1.2:79285867-79285886 None:intergenic 40.0%
CTTTGTTACAAACACTGCAC+CGG + chr1.2:79285840-79285859 None:intergenic 40.0%
GATATTCTTCTTCAGTGGGT+GGG + chr1.2:79285678-79285697 None:intergenic 40.0%
GATTCATGAACGTGAGTCTT+TGG - chr1.2:79285615-79285634 MS.gene86911:CDS 40.0%
GCGAGATATTCTTCTTCAGT+GGG + chr1.2:79285682-79285701 None:intergenic 40.0%
TTCCCATCTTATCAAGCACT+TGG - chr1.2:79285862-79285881 MS.gene86911:intron 40.0%
! GCTTTGAATTCTTCTCCAAC+AGG - chr1.2:79285544-79285563 MS.gene86911:CDS 40.0%
! TGTCACAAGAGTTTTCCTAC+CGG - chr1.2:79286000-79286019 MS.gene86911:CDS 40.0%
!! CTTGTTGTTGTTTGAAGCGT+GGG + chr1.2:79285585-79285604 None:intergenic 40.0%
!! TCTTGTTGTTGTTTGAAGCG+TGG + chr1.2:79285586-79285605 None:intergenic 40.0%
AACAGAGACTGTCTCGTTGA+CGG + chr1.2:79285938-79285957 None:intergenic 45.0%
AATTGAGGTCAAATCCACGG+TGG + chr1.2:79286170-79286189 None:intergenic 45.0%
AGCAACGTCAATAACAGCAG+TGG - chr1.2:79286102-79286121 MS.gene86911:CDS 45.0%
AGTCTCTGTTTCCGTGTCAA+CGG - chr1.2:79285948-79285967 MS.gene86911:CDS 45.0%
CCACCAAGTGCTTGATAAGA+TGG + chr1.2:79285868-79285887 None:intergenic 45.0%
CCATCTTATCAAGCACTTGG+TGG - chr1.2:79285865-79285884 MS.gene86911:intron 45.0%
TCTCACTGAATTCTGGTCTC+CGG - chr1.2:79286200-79286219 MS.gene86911:CDS 45.0%
TCTTCACCGGAAAACAAACG+CGG + chr1.2:79286330-79286349 None:intergenic 45.0%
TGATGAAGATTTACGGTGGC+TGG + chr1.2:79285899-79285918 None:intergenic 45.0%
! AAACAAACGCGGCCTTTTAG+CGG + chr1.2:79286319-79286338 None:intergenic 45.0%
! TGTTGTTTGAAGCGTGGGAA+TGG + chr1.2:79285580-79285599 None:intergenic 45.0%
!! AAAAGGCCGCGTTTGTTTTC+CGG - chr1.2:79286321-79286340 MS.gene86911:CDS 45.0%
!! TGCTTTGAGAGAGCATGATG+AGG + chr1.2:79285711-79285730 None:intergenic 45.0%
ACTGAATTCTGGTCTCCGGT+TGG - chr1.2:79286204-79286223 MS.gene86911:CDS 50.0%
AGAGGTAGAAAGTCCGTTGC+CGG - chr1.2:79286290-79286309 MS.gene86911:CDS 50.0%
AGTGGAATCACAGTCTCCGA+CGG - chr1.2:79286120-79286139 MS.gene86911:CDS 50.0%
CGCCGGAATCAATGAACAAG+AGG - chr1.2:79286272-79286291 MS.gene86911:CDS 50.0%
GGAACACTCGTGCATCTTAC+CGG + chr1.2:79285977-79285996 None:intergenic 50.0%
GGAGACCAGAATTCAGTGAG+AGG + chr1.2:79286201-79286220 None:intergenic 50.0%
TGATTCAGCTTCACCGGTGA+TGG + chr1.2:79285817-79285836 None:intergenic 50.0%
TTCTGGTCTCCGGTTGGATT+CGG - chr1.2:79286210-79286229 MS.gene86911:CDS 50.0%
TTTCCTACCGGTCAAGCTCT+TGG - chr1.2:79286012-79286031 MS.gene86911:CDS 50.0%
! CTTTTAGCGGTTACCGGCAA+CGG + chr1.2:79286306-79286325 None:intergenic 50.0%
!! TGAGAGGCGCTGGTAAATTG+AGG + chr1.2:79286185-79286204 None:intergenic 50.0%
AAATCCACGGTGGCTGATGG+AGG + chr1.2:79286160-79286179 None:intergenic 55.0%
AGAGACTGTCTCGTTGACGG+CGG + chr1.2:79285935-79285954 None:intergenic 55.0%
CACCGGTGAAGCTGAATCAC+CGG - chr1.2:79285818-79285837 MS.gene86911:intron 55.0%
CACCGGTGATTCAGCTTCAC+CGG + chr1.2:79285823-79285842 None:intergenic 55.0%
CAGCGCCTCTCACTGAATTC+TGG - chr1.2:79286193-79286212 MS.gene86911:CDS 55.0%
CGATCAAAACGGCCGCGTAT+TGG - chr1.2:79285649-79285668 MS.gene86911:CDS 55.0%
CGTTGCCGGTAACCGCTAAA+AGG - chr1.2:79286304-79286323 MS.gene86911:CDS 55.0%
CTTACCGGTGACCGTTGACA+CGG + chr1.2:79285962-79285981 None:intergenic 55.0%
GTCAAATCCACGGTGGCTGA+TGG + chr1.2:79286163-79286182 None:intergenic 55.0%
GTGTCCACCAAGAGCTTGAC+CGG + chr1.2:79286022-79286041 None:intergenic 55.0%
GTTTCCGTGTCAACGGTCAC+CGG - chr1.2:79285955-79285974 MS.gene86911:CDS 55.0%
TCTCCACCACCGAATCCAAC+CGG + chr1.2:79286222-79286241 None:intergenic 55.0%
! CAGAATTCAGTGAGAGGCGC+TGG + chr1.2:79286195-79286214 None:intergenic 55.0%
! TTCAGCTTCACCGGTGATGG+CGG + chr1.2:79285814-79285833 None:intergenic 55.0%
!! GTGGGTGGGTTACCAATACG+CGG + chr1.2:79285664-79285683 None:intergenic 55.0%
CCACCAAGAGCTTGACCGGT+AGG + chr1.2:79286018-79286037 None:intergenic 60.0%
CCTACCGGTCAAGCTCTTGG+TGG - chr1.2:79286015-79286034 MS.gene86911:CDS 60.0%
GGAATCACAGTCTCCGACGG+CGG - chr1.2:79286123-79286142 MS.gene86911:CDS 60.0%
TCTCGTTGACGGCGGTGGAT+TGG + chr1.2:79285927-79285946 None:intergenic 60.0%
TGGTCTCCGGTTGGATTCGG+TGG - chr1.2:79286213-79286232 MS.gene86911:CDS 60.0%
! CGCGGCCTTTTAGCGGTTAC+CGG + chr1.2:79286312-79286331 None:intergenic 60.0%
!! TCTCCGGTTGGATTCGGTGG+TGG - chr1.2:79286216-79286235 MS.gene86911:CDS 60.0%
ATCACAGTCTCCGACGGCGG+CGG - chr1.2:79286126-79286145 MS.gene86911:CDS 65.0%
GACTGTCTCGTTGACGGCGG+TGG + chr1.2:79285932-79285951 None:intergenic 65.0%
GTTGCAGTCGCCGCCATCAC+CGG - chr1.2:79285801-79285820 MS.gene86911:intron 65.0%
TCCACGGTGGCTGATGGAGG+AGG + chr1.2:79286157-79286176 None:intergenic 65.0%
TCCTCCTCCATCAGCCACCG+TGG - chr1.2:79286153-79286172 MS.gene86911:CDS 65.0%
!! GGTGATGGCGGCGACTGCAA+CGG + chr1.2:79285802-79285821 None:intergenic 65.0%
! GGAGGACGCGCCGCCGCCGT+CGG + chr1.2:79286139-79286158 None:intergenic 85.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 79285523 79286368 79285523 ID=MS.gene86911
chr1.2 mRNA 79285523 79286368 79285523 ID=MS.gene86911.t1;Parent=MS.gene86911
chr1.2 exon 79285915 79286368 79285915 ID=MS.gene86911.t1.exon1;Parent=MS.gene86911.t1
chr1.2 CDS 79285915 79286368 79285915 ID=cds.MS.gene86911.t1;Parent=MS.gene86911.t1
chr1.2 exon 79285523 79285695 79285523 ID=MS.gene86911.t1.exon2;Parent=MS.gene86911.t1
chr1.2 CDS 79285523 79285695 79285523 ID=cds.MS.gene86911.t1;Parent=MS.gene86911.t1
Gene Sequence

>MS.gene86911

ATGGCCGCTTTAGAGTTACAAGCTTTGAATTCTTCTCCAACAGGAGCTACTATTCCATTCCCACGCTTCAAACAACAACAAGAAAATCAAGAGATTCATGAACGTGAGTCTTTGGTCAAAAAGAAACGATCAAAACGGCCGCGTATTGGTAACCCACCCACTGAAGAAGAATATCTCGCTCTCTGCCTCATCATGCTCTCTCAAAGCAACAACAACGAAAAAATCAACATCTCTGAATCTCATCATCAAATTGAATCATCATCTTCACAACAACAACCGTTGCAGTCGCCGCCATCACCGGTGAAGCTGAATCACCGGTGCAGTGTTTGTAACAAAGCTTTCCCATCTTATCAAGCACTTGGTGGTCACAAAGCCAGCCACCGTAAATCTTCATCAGAAAACCAATCCACCGCCGTCAACGAGACAGTCTCTGTTTCCGTGTCAACGGTCACCGGTAAGATGCACGAGTGTTCCATTTGTCACAAGAGTTTTCCTACCGGTCAAGCTCTTGGTGGACACAAACGATGTCACTATGAAGGAGTCATCAACAACAACAACCACAATCATAACAACAGTAACAGCAACGTCAATAACAGCAGTGGAATCACAGTCTCCGACGGCGGCGGCGCGTCCTCCTCCATCAGCCACCGTGGATTTGACCTCAATTTACCAGCGCCTCTCACTGAATTCTGGTCTCCGGTTGGATTCGGTGGTGGAGATTCCAAGAAGACCAAGATTAATGTTAATCTCGCCGGAATCAATGAACAAGAGGTAGAAAGTCCGTTGCCGGTAACCGCTAAAAGGCCGCGTTTGTTTTCCGGTGAAGACAATGATGAAACAGTGTAG
Protein sequence

>MS.gene86911.t1

MAALELQALNSSPTGATIPFPRFKQQQENQEIHERESLVKKKRSKRPRIGNPPTEEEYLALCLIMLSQSNNNEKINISESHHQIESSSSQQQPLQSPPSPVKLNHRCSVCNKAFPSYQALGGHKASHRKSSSENQSTAVNETVSVSVSTVTAPLTEFWSPVGFGGGDSKKTKINVNLAGINEQEVESPLPVTAKRPRLFSGEDNDETV