AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073125

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073125.t1 MTR_2g084525 90.647 139 13 0 4 142 1 139 4.63e-93 269
MS.gene073125.t1 MTR_2g084510 86.232 138 19 0 5 142 1 138 3.05e-85 249
MS.gene073125.t1 MTR_2g060540 78.014 141 31 0 3 143 6 146 8.73e-79 229
MS.gene073125.t1 MTR_2g060500 77.857 140 31 0 3 142 6 145 4.77e-78 228
MS.gene073125.t1 MTR_2g084495 66.187 139 47 0 4 142 1 139 2.83e-65 198
MS.gene073125.t1 MTR_1g062160 48.936 141 62 3 3 142 2 133 9.83e-37 125
MS.gene073125.t1 MTR_5g030130 46.667 135 62 3 8 142 36 160 3.00e-36 123
MS.gene073125.t1 MTR_5g030130 46.667 135 62 3 8 142 36 160 9.07e-36 124
MS.gene073125.t1 MTR_4g078170 47.407 135 61 3 8 142 16 140 1.01e-35 122
MS.gene073125.t1 MTR_7g102790 47.222 144 65 3 1 142 1 135 1.84e-35 122
MS.gene073125.t1 MTR_5g007230 45.926 135 63 3 8 142 22 146 2.21e-34 119
MS.gene073125.t1 MTR_8g066820 45.185 135 64 3 8 142 34 158 1.15e-32 115
MS.gene073125.t1 MTR_4g094680 41.176 136 75 4 9 144 24 154 2.39e-26 99.4
MS.gene073125.t1 MTR_2g083710 62.295 61 23 0 3 63 2 62 3.23e-23 86.7
MS.gene073125.t1 MTR_4g116300 37.956 137 75 4 8 144 6 132 3.26e-23 91.7
MS.gene073125.t1 MTR_2g055210 34.559 136 78 4 7 142 101 225 7.89e-21 86.7
MS.gene073125.t1 MTR_2g083720 38.843 121 36 2 3 123 2 84 2.65e-17 72.0
MS.gene073125.t1 MTR_2g036170 33.824 136 73 5 9 144 39 157 7.02e-15 69.3
MS.gene073125.t1 MTR_8g105930 31.973 147 83 5 9 142 15 157 1.41e-14 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073125.t1 AT1G43000 47.857 140 63 3 3 142 12 141 1.39e-37 127
MS.gene073125.t1 AT1G43000 47.857 140 63 3 3 142 5 134 1.44e-37 127
MS.gene073125.t1 AT4G17900 47.794 136 60 4 8 142 21 146 1.17e-34 120
MS.gene073125.t1 AT4G17900 47.794 136 60 4 8 142 35 160 1.42e-34 120
MS.gene073125.t1 AT1G21000 47.143 140 64 4 3 142 9 138 4.78e-33 117
MS.gene073125.t1 AT1G21000 47.143 140 64 4 3 142 12 141 5.07e-33 117
MS.gene073125.t1 AT1G32700 45.522 134 63 3 9 142 14 137 1.43e-31 112
MS.gene073125.t1 AT2G27930 45.926 135 71 2 9 142 6 139 3.59e-31 110
MS.gene073125.t1 AT2G27930 45.926 135 71 2 9 142 6 139 3.59e-31 110
MS.gene073125.t1 AT2G27930 45.000 140 75 2 4 142 1 139 5.91e-31 110
MS.gene073125.t1 AT2G27930 45.000 140 75 2 4 142 1 139 5.91e-31 110
MS.gene073125.t1 AT1G76590 44.444 135 65 4 8 142 19 143 6.49e-30 108
MS.gene073125.t1 AT1G32700 48.113 106 46 2 37 142 2 98 3.11e-26 97.4
MS.gene073125.t1 AT5G46710 43.704 135 65 4 9 142 30 154 4.05e-26 97.1
MS.gene073125.t1 AT5G46710 43.704 135 65 4 9 142 14 138 8.56e-26 97.4
MS.gene073125.t1 AT5G46710 43.704 135 65 4 9 142 30 154 1.57e-25 97.1
MS.gene073125.t1 AT2G12646 40.000 140 73 5 5 144 1 129 1.19e-24 95.5
MS.gene073125.t1 AT2G12646 38.686 137 74 4 8 144 6 132 2.62e-24 94.7
MS.gene073125.t1 AT2G12646 38.686 137 74 4 8 144 6 132 2.62e-24 94.7
MS.gene073125.t1 AT1G31040 36.765 136 74 4 9 144 21 144 6.08e-23 90.9
MS.gene073125.t1 AT3G60670 35.556 135 77 3 8 142 7 131 6.77e-20 82.8
MS.gene073125.t1 AT2G27930 47.561 82 42 1 62 142 61 142 3.18e-17 74.7
MS.gene073125.t1 AT2G27930 47.561 82 42 1 62 142 61 142 3.18e-17 74.7
MS.gene073125.t1 AT2G01818 34.783 138 81 5 9 142 13 145 8.10e-16 71.6

Find 24 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTCATTTCTGAACTTGTT+TGG 0.226434 2.2:-13170055 None:intergenic
TCTATACAAGATTCACATAA+TGG 0.352887 2.2:-13170109 None:intergenic
CATTTCTGAACTTGTTTGGA+TGG 0.368188 2.2:-13170051 None:intergenic
ACCTTGGCTTGTAAACTTGC+TGG 0.395128 2.2:+13169997 MS.gene073125:CDS
CAATGTTGAACCTCTTAAGT+TGG 0.405410 2.2:-13170453 None:intergenic
AATGTTGAACCTCTTAAGTT+GGG 0.440694 2.2:-13170452 None:intergenic
GAGCTCATGCCCAACTTAAG+AGG 0.452892 2.2:+13170443 MS.gene073125:CDS
ATTTCTGAACTTGTTTGGAT+GGG 0.453864 2.2:-13170050 None:intergenic
CACATGTTTGTAAATTTCGT+TGG 0.484536 2.2:-13170359 None:intergenic
GCCAGCAAGTTTACAAGCCA+AGG 0.514131 2.2:-13169998 None:intergenic
AAAAGAGTCCCTATTGTGAC+CGG 0.541668 2.2:-13170482 None:intergenic
TACAAACATGTGGATATCCT+CGG 0.556715 2.2:+13170370 MS.gene073125:CDS
CCAAAGAGCAAAAGTAGGTA+GGG 0.559658 2.2:-13170534 None:intergenic
AGGATATGATGAGTGTACCT+TGG 0.561440 2.2:+13169981 MS.gene073125:intron
CAACTTAAGAGGTTCAACAT+TGG 0.586278 2.2:+13170454 MS.gene073125:CDS
TCACGTAGGTTTGAATTCCG+AGG 0.586677 2.2:-13170387 None:intergenic
GCCAAAGAGCAAAAGTAGGT+AGG 0.587378 2.2:-13170535 None:intergenic
AAGAAGATCATCATATAATG+AGG 0.589252 2.2:+13170327 MS.gene073125:CDS
CAACGAAATTTACAAACATG+TGG 0.600716 2.2:+13170360 MS.gene073125:CDS
GCATGCCAAAGAGCAAAAGT+AGG 0.621061 2.2:-13170539 None:intergenic
TGTATAGAATCTCGTCACAA+AGG 0.636702 2.2:+13170124 MS.gene073125:CDS
AAGATCATCATATAATGAGG+TGG 0.649716 2.2:+13170330 MS.gene073125:CDS
ACTAGAGCTATTAATCACGT+AGG 0.680389 2.2:-13170401 None:intergenic
CAAACAAGTTCAGAAATGAG+CGG 0.722844 2.2:+13170056 MS.gene073125:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTCTTAATGCAATTTTT+GGG + chr2.2:13169947-13169966 MS.gene073125:intron 15.0%
!!! TTTTTTCTTAATGCAATTTT+TGG + chr2.2:13169946-13169965 MS.gene073125:intron 15.0%
!! AGAAAAAACTACAAAGAATT+AGG - chr2.2:13169934-13169953 None:intergenic 20.0%
!! ATTAATAGTAATAAAAGGAG+TGG - chr2.2:13170656-13170675 None:intergenic 20.0%
!! GCTTGACATTATAATTAAAA+TGG - chr2.2:13169912-13169931 None:intergenic 20.0%
!!! ATAATATTTTGCAATGATCT+AGG + chr2.2:13170196-13170215 MS.gene073125:intron 20.0%
!!! ATGTTTTAAACGGTAAAAAA+TGG + chr2.2:13170599-13170618 MS.gene073125:intron 20.0%
!!! TCCTTTTATTACTATTAATC+CGG + chr2.2:13170657-13170676 MS.gene073125:intron 20.0%
! AAGAAGATCATCATATAATG+AGG + chr2.2:13170327-13170346 MS.gene073125:CDS 25.0%
! CAAATTAAATAACACTCACT+TGG - chr2.2:13170162-13170181 None:intergenic 25.0%
! TCCGGATTAATAGTAATAAA+AGG - chr2.2:13170661-13170680 None:intergenic 25.0%
! TCTATACAAGATTCACATAA+TGG - chr2.2:13170112-13170131 None:intergenic 25.0%
!!! ATTTTTGGGTTTTGTTTCTT+AGG + chr2.2:13169961-13169980 MS.gene073125:intron 25.0%
AAGATCATCATATAATGAGG+TGG + chr2.2:13170330-13170349 MS.gene073125:CDS 30.0%
AATGTTGAACCTCTTAAGTT+GGG - chr2.2:13170455-13170474 None:intergenic 30.0%
ATCAACATGAGTACAATAAC+TGG - chr2.2:13170744-13170763 None:intergenic 30.0%
CAACGAAATTTACAAACATG+TGG + chr2.2:13170360-13170379 MS.gene073125:CDS 30.0%
CACATGTTTGTAAATTTCGT+TGG - chr2.2:13170362-13170381 None:intergenic 30.0%
! ACTTTTCTTTCAACCATTAC+CGG + chr2.2:13170714-13170733 MS.gene073125:intron 30.0%
! ATTTCTGAACTTGTTTGGAT+GGG - chr2.2:13170053-13170072 None:intergenic 30.0%
AATAACTGGTATTCCGGTAA+TGG - chr2.2:13170730-13170749 None:intergenic 35.0%
ACTAGAGCTATTAATCACGT+AGG - chr2.2:13170404-13170423 None:intergenic 35.0%
ACTATTAATCCGGAGATTGA+AGG + chr2.2:13170667-13170686 MS.gene073125:intron 35.0%
AGGTTCAACATTGGAAAAAC+CGG + chr2.2:13170463-13170482 MS.gene073125:CDS 35.0%
CAAACAAGTTCAGAAATGAG+CGG + chr2.2:13170056-13170075 MS.gene073125:CDS 35.0%
CAACTTAAGAGGTTCAACAT+TGG + chr2.2:13170454-13170473 MS.gene073125:CDS 35.0%
CAATGTTGAACCTCTTAAGT+TGG - chr2.2:13170456-13170475 None:intergenic 35.0%
GAGTACAATAACTGGTATTC+CGG - chr2.2:13170736-13170755 None:intergenic 35.0%
TACAAACATGTGGATATCCT+CGG + chr2.2:13170370-13170389 MS.gene073125:CDS 35.0%
TGTATAGAATCTCGTCACAA+AGG + chr2.2:13170124-13170143 MS.gene073125:CDS 35.0%
! CATTTCTGAACTTGTTTGGA+TGG - chr2.2:13170054-13170073 None:intergenic 35.0%
AAAAGAGTCCCTATTGTGAC+CGG - chr2.2:13170485-13170504 None:intergenic 40.0%
AGGATATGATGAGTGTACCT+TGG + chr2.2:13169981-13170000 MS.gene073125:intron 40.0%
CATCATATGCCTTCAATCTC+CGG - chr2.2:13170679-13170698 None:intergenic 40.0%
CCAAAGAGCAAAAGTAGGTA+GGG - chr2.2:13170537-13170556 None:intergenic 40.0%
TGGAAAAACCGGTCACAATA+GGG + chr2.2:13170474-13170493 MS.gene073125:CDS 40.0%
TTGGAAAAACCGGTCACAAT+AGG + chr2.2:13170473-13170492 MS.gene073125:CDS 40.0%
! ATGGATTTTCATTGCAGTCG+AGG - chr2.2:13170093-13170112 None:intergenic 40.0%
! CGCTCATTTCTGAACTTGTT+TGG - chr2.2:13170058-13170077 None:intergenic 40.0%
! TGGCATGCAAGGTGAAATTT+TGG + chr2.2:13170554-13170573 MS.gene073125:intron 40.0%
GCATGCCAAAGAGCAAAAGT+AGG - chr2.2:13170542-13170561 None:intergenic 45.0%
GCCAAAGAGCAAAAGTAGGT+AGG - chr2.2:13170538-13170557 None:intergenic 45.0%
TCACGTAGGTTTGAATTCCG+AGG - chr2.2:13170390-13170409 None:intergenic 45.0%
! CGGAGATTGAAGGCATATGA+TGG + chr2.2:13170677-13170696 MS.gene073125:intron 45.0%
! CTTTTGCTCTTTGGCATGCA+AGG + chr2.2:13170543-13170562 MS.gene073125:CDS 45.0%
!! ACCTTGGCTTGTAAACTTGC+TGG + chr2.2:13169997-13170016 MS.gene073125:CDS 45.0%
!! CCCTACCTACTTTTGCTCTT+TGG + chr2.2:13170534-13170553 MS.gene073125:CDS 45.0%
!! ACATAATATAAAAATATAAT+AGG - chr2.2:13170583-13170602 None:intergenic 5.0%
!!! TTTTTATATTATGTTTTAAA+CGG + chr2.2:13170589-13170608 MS.gene073125:intron 5.0%
GAGCTCATGCCCAACTTAAG+AGG + chr2.2:13170443-13170462 MS.gene073125:CDS 50.0%
GCCAGCAAGTTTACAAGCCA+AGG - chr2.2:13170001-13170020 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 13169890 13170791 13169890 ID=MS.gene073125
chr2.2 mRNA 13169890 13170791 13169890 ID=MS.gene073125.t1;Parent=MS.gene073125
chr2.2 exon 13169890 13169895 13169890 ID=MS.gene073125.t1.exon1;Parent=MS.gene073125.t1
chr2.2 CDS 13169890 13169895 13169890 ID=cds.MS.gene073125.t1;Parent=MS.gene073125.t1
chr2.2 exon 13169983 13170162 13169983 ID=MS.gene073125.t1.exon2;Parent=MS.gene073125.t1
chr2.2 CDS 13169983 13170162 13169983 ID=cds.MS.gene073125.t1;Parent=MS.gene073125.t1
chr2.2 exon 13170325 13170564 13170325 ID=MS.gene073125.t1.exon3;Parent=MS.gene073125.t1
chr2.2 CDS 13170325 13170564 13170325 ID=cds.MS.gene073125.t1;Parent=MS.gene073125.t1
chr2.2 exon 13170783 13170791 13170783 ID=MS.gene073125.t1.exon4;Parent=MS.gene073125.t1
chr2.2 CDS 13170783 13170791 13170783 ID=cds.MS.gene073125.t1;Parent=MS.gene073125.t1
Gene Sequence

>MS.gene073125

ATGACGGTAATGTGTCTATCCATTTTAATTATAATGTCAAGCCTAATTCTTTGTAGTTTTTTCTTAATGCAATTTTTGGGTTTTGTTTCTTAGGATATGATGAGTGTACCTTGGCTTGTAAACTTGCTGGCAATCACTTCGTTTTTCACAACATGTGAAGCCCATCCAAACAAGTTCAGAAATGAGCGGAACAAGTTCTGCCTCGACTGCAATGAAAATCCATTATGTGAATCTTGTATAGAATCTCGTCACAAAGGTCATAGAGTTATCCAAGTGAGTGTTATTTAATTTGATTACTAGATCTGTATAATATTTTGCAATGATCTAGGTATCTGTGTCATATCTATTTCTCTTCGCTTTGTTTTTGTTACACTTAAGCAATTTTAATTGATTTTTTTTAACTATGTTATGTAAATATTTGCAATGATAAATCAGATAAGAAGATCATCATATAATGAGGTGGTTAAGACCAACGAAATTTACAAACATGTGGATATCCTCGGAATTCAAACCTACGTGATTAATAGCTCTAGTGTTGTATTCTTAAGCAAGAGAGCTCATGCCCAACTTAAGAGGTTCAACATTGGAAAAACCGGTCACAATAGGGACTCTTTTTGTAAGAGATGTGATAGAAATCTTGCAGACCCTACCTACTTTTGCTCTTTGGCATGCAAGGTGAAATTTTGGTTTCCTATTATATTTTTATATTATGTTTTAAACGGTAAAAAATGGTTCAATATATGAAAAACTAGTATATTTTATTCCACTCCTTTTATTACTATTAATCCGGAGATTGAAGGCATATGATGGAGATTATAACTTAAACTTTTCTTTCAACCATTACCGGAATACCAGTTATTGTACTCATGTTGATTTTGTTTTCTTTTTGAAAGAATGATTAA
Protein sequence

>MS.gene073125.t1

MTDMMSVPWLVNLLAITSFFTTCEAHPNKFRNERNKFCLDCNENPLCESCIESRHKGHRVIQIRRSSYNEVVKTNEIYKHVDILGIQTYVINSSSVVFLSKRAHAQLKRFNIGKTGHNRDSFCKRCDRNLADPTYFCSLACKND