AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene80662

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene80662.t1 MTR_5g081990 98.919 185 0 2 1 184 1 184 1.32e-135 376
MS.gene80662.t1 MTR_7g060630 69.841 63 19 0 33 95 8 70 1.05e-27 103
MS.gene80662.t1 MTR_4g084550 61.765 68 26 0 33 100 64 131 9.26e-27 100
MS.gene80662.t1 MTR_8g107210 64.789 71 25 0 25 95 88 158 2.03e-26 103
MS.gene80662.t1 MTR_1g019130 65.152 66 23 0 33 98 90 155 7.54e-26 99.4
MS.gene80662.t1 MTR_1g019130 65.152 66 23 0 33 98 90 155 9.05e-26 99.4
MS.gene80662.t1 MTR_5g021930 59.459 74 26 2 33 105 30 100 1.50e-24 97.4
MS.gene80662.t1 MTR_4g063735 57.576 66 28 0 33 98 25 90 1.27e-23 94.4
MS.gene80662.t1 MTR_8g095580 69.091 55 17 0 44 98 93 147 4.04e-20 82.8
MS.gene80662.t1 MTR_3g088485 67.273 55 18 0 44 98 91 145 9.72e-20 81.6
MS.gene80662.t1 MTR_2g015000 45.312 64 35 0 33 96 55 118 2.60e-15 73.2
MS.gene80662.t1 MTR_7g025010 43.750 64 36 0 33 96 47 110 2.75e-15 73.2
MS.gene80662.t1 MTR_4g088070 40.984 61 36 0 33 93 29 89 3.11e-13 67.4
MS.gene80662.t1 MTR_1g115315 43.333 60 34 0 33 92 85 144 9.96e-12 62.0
MS.gene80662.t1 MTR_1g115315 43.333 60 34 0 33 92 85 144 1.21e-11 62.0
MS.gene80662.t1 MTR_4g088080 39.706 68 39 1 33 100 40 105 4.52e-11 60.8
MS.gene80662.t1 MTR_7g023810 31.193 109 60 2 33 127 68 175 9.45e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene80662.t1 AT3G11260 58.011 181 61 5 14 184 7 182 4.94e-61 187
MS.gene80662.t1 AT5G05770 65.487 113 31 3 4 110 2 112 9.12e-41 134
MS.gene80662.t1 AT3G18010 71.429 63 18 0 33 95 76 138 7.30e-27 104
MS.gene80662.t1 AT2G28610 65.079 63 22 0 33 95 8 70 6.00e-26 100
MS.gene80662.t1 AT5G59340 57.333 75 27 1 21 95 7 76 2.64e-25 98.6
MS.gene80662.t1 AT1G46480 63.492 63 23 0 33 95 90 152 1.16e-24 95.5
MS.gene80662.t1 AT1G46480 63.492 63 23 0 33 95 90 152 6.83e-24 94.7
MS.gene80662.t1 AT2G17950 66.667 63 20 1 33 94 38 100 9.31e-24 95.1
MS.gene80662.t1 AT2G01500 67.273 55 18 0 33 87 61 115 1.09e-21 89.4
MS.gene80662.t1 AT2G33880 45.161 62 34 0 33 94 55 116 5.62e-15 72.0
MS.gene80662.t1 AT2G33880 45.161 62 34 0 33 94 55 116 6.40e-15 72.0
MS.gene80662.t1 AT5G45980 46.774 62 33 0 33 94 55 116 1.68e-14 70.5
MS.gene80662.t1 AT4G35550 42.623 61 35 0 33 93 99 159 5.59e-12 63.2
MS.gene80662.t1 AT1G20700 35.556 90 55 2 19 106 20 108 5.69e-12 60.8
MS.gene80662.t1 AT1G20700 35.556 90 55 2 19 106 82 170 1.16e-11 61.2
MS.gene80662.t1 AT1G20700 38.667 75 45 1 19 93 82 155 1.20e-11 61.2

Find 24 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTTAACTTGTTCTGTTGT+TGG 0.328649 5.4:+64693487 None:intergenic
AGAGCAAGAATGTGTTCTAT+TGG 0.384217 5.4:-64693372 MS.gene80662:CDS
GATTCACCAAATGAGTTCAA+TGG 0.392997 5.4:+64692917 None:intergenic
AGAGTCTCAATCACTCTATC+AGG 0.404414 5.4:+64692950 None:intergenic
ATGTACAATGGGAGAACAAA+TGG 0.428304 5.4:-64692831 MS.gene80662:CDS
AACACCCACCATTGGACTTA+CGG 0.439714 5.4:-64692808 MS.gene80662:CDS
GGTTTCAGAATCACAAAGCT+AGG 0.453724 5.4:-64693351 MS.gene80662:CDS
TTCTGAATTTGATCAGTGCT+TGG 0.470346 5.4:+64693430 None:intergenic
AGTGGAAGCAGCAGCAGCAC+TGG 0.493876 5.4:-64693532 MS.gene80662:CDS
AATATGGAAGAGAGCATGTC+AGG 0.497698 5.4:-64693595 MS.gene80662:CDS
TTTGCATACACATGTACAAT+GGG 0.499345 5.4:-64692842 MS.gene80662:CDS
AGTAGTTTCCATGGTAAAAG+TGG 0.503916 5.4:-64693550 MS.gene80662:CDS
ACAAATGGAACACCCACCAT+TGG 0.543359 5.4:-64692816 MS.gene80662:CDS
TCATCTGGAAGTAGTTTCCA+TGG 0.556114 5.4:-64693559 MS.gene80662:CDS
GTTTCAGAATCACAAAGCTA+GGG 0.556495 5.4:-64693350 MS.gene80662:CDS
GTATGCATGCAAATGAATGC+AGG 0.569996 5.4:-64692877 MS.gene80662:CDS
AGCAGCACTGGCACAAAGTG+TGG 0.575447 5.4:-64693520 MS.gene80662:CDS
CTCAACCGTAAGTCCAATGG+TGG 0.576156 5.4:+64692803 None:intergenic
GTGAATCAGAATCAGAGAAG+TGG 0.590084 5.4:-64692901 MS.gene80662:CDS
CTGGCACAAAGTGTGGTCGT+TGG 0.591246 5.4:-64693513 MS.gene80662:CDS
AAACTCAACCGTAAGTCCAA+TGG 0.615710 5.4:+64692800 None:intergenic
GTTTGCATACACATGTACAA+TGG 0.618786 5.4:-64692843 MS.gene80662:CDS
TATGCATGCAAATGAATGCA+GGG 0.627141 5.4:-64692876 MS.gene80662:CDS
TCAACCGTAAGTCCAATGGT+GGG 0.711399 5.4:+64692804 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTAAAAAAATTATCTTAAA+AGG - chr5.4:64693291-64693310 MS.gene80662:CDS 10.0%
!!! CTTACTAAATTTTTTACTTT+AGG - chr5.4:64693315-64693334 MS.gene80662:CDS 15.0%
!!! AAATTATTTTTCTAACGAGA+TGG + chr5.4:64693270-64693289 None:intergenic 20.0%
! AATGAATAAATGAGTTGTGT+CGG + chr5.4:64693176-64693195 None:intergenic 25.0%
!!! ACCATAAAAACTAAGTTGAT+TGG + chr5.4:64692986-64693005 None:intergenic 25.0%
!!! TCCAATCAACTTAGTTTTTA+TGG - chr5.4:64692982-64693001 MS.gene80662:intron 25.0%
AGTATCAGATCAAAGTTTCA+AGG + chr5.4:64693216-64693235 None:intergenic 30.0%
TTTGCATACACATGTACAAT+GGG - chr5.4:64693543-64693562 MS.gene80662:CDS 30.0%
! CTTTTTCCATTGAACTCATT+TGG - chr5.4:64693462-64693481 MS.gene80662:CDS 30.0%
! TCTTTTCCTCATATATTGCA+GGG - chr5.4:64693391-64693410 MS.gene80662:CDS 30.0%
! TTCTTTTCCTCATATATTGC+AGG - chr5.4:64693390-64693409 MS.gene80662:CDS 30.0%
!! AGTTTAACTTGTTCTGTTGT+TGG + chr5.4:64692901-64692920 None:intergenic 30.0%
AGAGCAAGAATGTGTTCTAT+TGG - chr5.4:64693013-64693032 MS.gene80662:intron 35.0%
AGTAGTTTCCATGGTAAAAG+TGG - chr5.4:64692835-64692854 MS.gene80662:CDS 35.0%
ATACATGTTACATCATCGTC+AGG + chr5.4:64693363-64693382 None:intergenic 35.0%
ATGTACAATGGGAGAACAAA+TGG - chr5.4:64693554-64693573 MS.gene80662:CDS 35.0%
GATTCACCAAATGAGTTCAA+TGG + chr5.4:64693471-64693490 None:intergenic 35.0%
GTTTCAGAATCACAAAGCTA+GGG - chr5.4:64693035-64693054 MS.gene80662:intron 35.0%
GTTTGCATACACATGTACAA+TGG - chr5.4:64693542-64693561 MS.gene80662:CDS 35.0%
TACATGTTACATCATCGTCA+GGG + chr5.4:64693362-64693381 None:intergenic 35.0%
TATGCATGCAAATGAATGCA+GGG - chr5.4:64693509-64693528 MS.gene80662:CDS 35.0%
TTCTGAATTTGATCAGTGCT+TGG + chr5.4:64692958-64692977 None:intergenic 35.0%
!!! GGTTTCTTTTGATGATGACA+AGG - chr5.4:64693077-64693096 MS.gene80662:intron 35.0%
AAACTCAACCGTAAGTCCAA+TGG + chr5.4:64693588-64693607 None:intergenic 40.0%
AGAGTCTCAATCACTCTATC+AGG + chr5.4:64693438-64693457 None:intergenic 40.0%
AGCAAACCCTGCAATATATG+AGG + chr5.4:64693400-64693419 None:intergenic 40.0%
CTTTAGGCCTCTTAATGCAT+TGG - chr5.4:64693331-64693350 MS.gene80662:CDS 40.0%
GGAAAGACAAAAACGTCGTA+AGG - chr5.4:64693056-64693075 MS.gene80662:intron 40.0%
GGTTTCAGAATCACAAAGCT+AGG - chr5.4:64693034-64693053 MS.gene80662:intron 40.0%
GTATGCATGCAAATGAATGC+AGG - chr5.4:64693508-64693527 MS.gene80662:CDS 40.0%
GTGAATCAGAATCAGAGAAG+TGG - chr5.4:64693484-64693503 MS.gene80662:CDS 40.0%
TCATCTGGAAGTAGTTTCCA+TGG - chr5.4:64692826-64692845 MS.gene80662:CDS 40.0%
! GGCTTTTGCATGAAATCATC+TGG - chr5.4:64692811-64692830 MS.gene80662:CDS 40.0%
! TGACTGAACTTTTCAGAGCA+GGG - chr5.4:64692923-64692942 MS.gene80662:CDS 40.0%
AACACCCACCATTGGACTTA+CGG - chr5.4:64693577-64693596 MS.gene80662:CDS 45.0%
ACAAATGGAACACCCACCAT+TGG - chr5.4:64693569-64693588 MS.gene80662:CDS 45.0%
TCAACCGTAAGTCCAATGGT+GGG + chr5.4:64693584-64693603 None:intergenic 45.0%
! CTGACTGAACTTTTCAGAGC+AGG - chr5.4:64692922-64692941 MS.gene80662:CDS 45.0%
!! TGCTGCTTCCACTTTTACCA+TGG + chr5.4:64692846-64692865 None:intergenic 45.0%
CTCAACCGTAAGTCCAATGG+TGG + chr5.4:64693585-64693604 None:intergenic 50.0%
GGCCTCTTAATGCATTGGAC+CGG - chr5.4:64693336-64693355 MS.gene80662:CDS 50.0%
TGTTACATCATCGTCAGGGC+CGG + chr5.4:64693358-64693377 None:intergenic 50.0%
CTGGCACAAAGTGTGGTCGT+TGG - chr5.4:64692872-64692891 MS.gene80662:CDS 55.0%
GGCCGGTCCAATGCATTAAG+AGG + chr5.4:64693341-64693360 None:intergenic 55.0%
!! AGCAGCACTGGCACAAAGTG+TGG - chr5.4:64692865-64692884 MS.gene80662:CDS 55.0%
AGTGGAAGCAGCAGCAGCAC+TGG - chr5.4:64692853-64692872 MS.gene80662:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 64692793 64693614 64692793 ID=MS.gene80662
chr5.4 mRNA 64692793 64693614 64692793 ID=MS.gene80662.t1;Parent=MS.gene80662
chr5.4 exon 64693263 64693614 64693263 ID=MS.gene80662.t1.exon1;Parent=MS.gene80662.t1
chr5.4 CDS 64693263 64693614 64693263 ID=cds.MS.gene80662.t1;Parent=MS.gene80662.t1
chr5.4 exon 64692793 64692995 64692793 ID=MS.gene80662.t1.exon2;Parent=MS.gene80662.t1
chr5.4 CDS 64692793 64692995 64692793 ID=cds.MS.gene80662.t1;Parent=MS.gene80662.t1
Gene Sequence

>MS.gene80662

ATGGAAGAGAGCATGTCAGGCTTTTGCATGAAATCATCTGGAAGTAGTTTCCATGGTAAAAGTGGAAGCAGCAGCAGCACTGGCACAAAGTGTGGTCGTTGGAATCCAACAACAGAACAAGTTAAACTTCTGACTGAACTTTTCAGAGCAGGGCTCAGAACTCCAAGCACTGATCAAATTCAGAAAATATCCAATCAACTTAGTTTTTATGGTAAGATAGAGAGCAAGAATGTGTTCTATTGGTTTCAGAATCACAAAGCTAGGGAAAGACAAAAACGTCGTAAGGTTTCTTTTGATGATGACAAGGATGTCATAGTTCATAGAGACAACTCTATGAATGCTTCAACACAAAGTAAGTCAAAAATCACTTACTCTATTTACCGACACAACTCATTTATTCATTTACTTTCGTATCAATTTCCTTGAAACTTTGATCTGATACTATGTTAATCACAAGATCTAAGAGATAAAGATCCATCTCGTTAGAAAAATAATTTTGTTAAAAAAATTATCTTAAAAGGTCTTACTAAATTTTTTACTTTAGGCCTCTTAATGCATTGGACCGGCCCTGACGATGATGTAACATGTATTTGACACTTCTTTTCCTCATATATTGCAGGGTTTGCTGAGATGTACTCAGAACCTGATAGAGTGATTGAGACTCTCGAACTTTTTCCATTGAACTCATTTGGTGAATCAGAATCAGAGAAGTGGAGTATGCATGCAAATGAATGCAGGGAAAATACAATGTTTGCATACACATGTACAATGGGAGAACAAATGGAACACCCACCATTGGACTTACGGTTGAGTTTTGTGTAA
Protein sequence

>MS.gene80662.t1

MEESMSGFCMKSSGSSFHGKSGSSSSTGTKCGRWNPTTEQVKLLTELFRAGLRTPSTDQIQKISNQLSFYGKIESKNVFYWFQNHKARERQKRRKVSFDDDKDVIVHRDNSMNASTQRFAEMYSEPDRVIETLELFPLNSFGESESEKWSMHANECRENTMFAYTCTMGEQMEHPPLDLRLSFV