AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76206

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76206.t1 MTR_1g112340 100.000 108 0 0 1 108 1 108 3.45e-79 228
MS.gene76206.t1 MTR_2g025480 36.634 101 64 0 4 104 6 106 1.26e-18 74.7
MS.gene76206.t1 MTR_2g025470 35.227 88 57 0 2 89 4 91 2.14e-15 66.6
MS.gene76206.t1 MTR_2g025470 35.227 88 57 0 2 89 4 91 2.61e-15 65.9
MS.gene76206.t1 MTR_7g031440 49.231 65 31 2 44 106 13 77 1.22e-13 62.4
MS.gene76206.t1 MTR_2g025470 35.211 71 46 0 2 72 4 74 5.37e-12 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76206.t1 AT5G20090 82.857 105 18 0 4 108 6 110 2.63e-66 195
MS.gene76206.t1 AT5G20090 82.857 105 18 0 4 108 6 110 2.63e-66 195
MS.gene76206.t1 AT5G20090 82.857 105 18 0 4 108 6 110 2.63e-66 195
MS.gene76206.t1 AT5G20090 85.870 92 13 0 4 95 6 97 7.79e-60 178
MS.gene76206.t1 AT4G14695 36.190 105 63 2 4 108 6 106 5.92e-17 70.5
MS.gene76206.t1 AT4G14695 36.190 105 63 2 4 108 6 106 5.92e-17 70.5
MS.gene76206.t1 AT4G22310 34.884 86 56 0 4 89 6 91 3.69e-16 68.6
MS.gene76206.t1 AT4G05590 34.091 88 58 0 2 89 4 91 9.46e-16 67.4
MS.gene76206.t1 AT4G05590 36.364 66 42 0 2 67 4 69 1.04e-11 56.2
MS.gene76206.t1 AT4G05590 51.163 43 21 0 2 44 4 46 3.11e-11 56.6

Find 23 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGCTGCCTTCAAAGCATTT+TGG 0.198269 1.1:+79450930 MS.gene76206:CDS
TTTGGGGACCTGTTGCTAAC+TGG 0.209422 1.1:+79450984 MS.gene76206:CDS
GTCCTAAAACAACTCACTTT+TGG 0.228614 1.1:+79450966 MS.gene76206:CDS
CCCTTCTGCCCTTGCCCATC+TGG 0.254260 1.1:-79451430 None:intergenic
ATGTTGCCAGAGATCATTTC+TGG 0.312321 1.1:-79451195 None:intergenic
TTGGGGACCTGTTGCTAACT+GGG 0.366196 1.1:+79450985 MS.gene76206:CDS
ACTATTCCAAAATGCTTTGA+AGG 0.425288 1.1:-79450936 None:intergenic
ACAAATCCCCAGTTAGCAAC+AGG 0.476332 1.1:-79450992 None:intergenic
ACCAGATGGGCAAGGGCAGA+AGG 0.477199 1.1:+79451429 MS.gene76206:CDS
AAACCTCCAGAAATGATCTC+TGG 0.493647 1.1:+79451189 MS.gene76206:CDS
TAGGTATCTCTCGGGGAAGA+AGG 0.506852 1.1:+79451979 MS.gene76206:intron
ATGATCTCTGGCAACATGAC+AGG 0.524581 1.1:+79451201 MS.gene76206:CDS
CATTGTTCATGAGATTTGCA+TGG 0.542535 1.1:+79451334 MS.gene76206:CDS
AGCTCTATCAACATACCAGA+TGG 0.550987 1.1:+79451415 MS.gene76206:CDS
GTTCATGAGATTTGCATGGA+TGG 0.554530 1.1:+79451338 MS.gene76206:CDS
TGGGGACCTGTTGCTAACTG+GGG 0.569942 1.1:+79450986 MS.gene76206:CDS
CCAGATGGGCAAGGGCAGAA+GGG 0.596928 1.1:+79451430 MS.gene76206:CDS
TCAACATACCAGATGGGCAA+GGG 0.612119 1.1:+79451422 MS.gene76206:CDS
ATCAACATACCAGATGGGCA+AGG 0.629052 1.1:+79451421 MS.gene76206:CDS
TTGCCAGAGATCATTTCTGG+AGG 0.633949 1.1:-79451192 None:intergenic
ATCTCTGGCAACATGACAGG+AGG 0.639198 1.1:+79451204 MS.gene76206:CDS
GCTCTATCAACATACCAGAT+GGG 0.640411 1.1:+79451416 MS.gene76206:CDS
GCAAGAAGTAGATAGTTACG+TGG 0.764982 1.1:-79451366 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTATTTTATATGGAAA+GGG + chr1.1:79451150-79451169 MS.gene76206:intron 10.0%
!!! TTATTTTATTTTATATGGAA+AGG + chr1.1:79451149-79451168 MS.gene76206:intron 10.0%
!! AAATACTAACATTACATTTA+AGG - chr1.1:79451747-79451766 None:intergenic 15.0%
!! AATAATAAATAGATGATCAT+AGG - chr1.1:79451036-79451055 None:intergenic 15.0%
!! ATAATAAATAGATGATCATA+GGG - chr1.1:79451035-79451054 None:intergenic 15.0%
!! TACTTTATTAGTGTTAAAAA+TGG + chr1.1:79451091-79451110 MS.gene76206:intron 15.0%
!!! ATTTTATTTTATATGGAAAG+GGG + chr1.1:79451151-79451170 MS.gene76206:intron 15.0%
!!! AGTATTTTATTTTGACTGAA+TGG + chr1.1:79451903-79451922 MS.gene76206:intron 20.0%
! ATATGTCGGATTACTAATAA+AGG + chr1.1:79451932-79451951 MS.gene76206:intron 25.0%
!! AATGCATTGATATATGTAGT+GGG - chr1.1:79451847-79451866 None:intergenic 25.0%
!! ATCTTTGCAATTTCTTTTGT+AGG + chr1.1:79451960-79451979 MS.gene76206:intron 25.0%
!! GCATATTAGTTTAAAACCAA+AGG - chr1.1:79451123-79451142 None:intergenic 25.0%
!! TTAAAAATGGTCTTAACCTT+TGG + chr1.1:79451104-79451123 MS.gene76206:intron 25.0%
ACTATTCCAAAATGCTTTGA+AGG - chr1.1:79450939-79450958 None:intergenic 30.0%
TGAAAAGTTGACATTCTTCT+TGG + chr1.1:79451246-79451265 MS.gene76206:intron 30.0%
TTGTACATATATCGTTGTCA+TGG + chr1.1:79451707-79451726 MS.gene76206:intron 30.0%
! ATGCATTGATATATGTAGTG+GGG - chr1.1:79451846-79451865 None:intergenic 30.0%
! CAATGCATTGATATATGTAG+TGG - chr1.1:79451848-79451867 None:intergenic 30.0%
! TTTCTTTTGTAGGTATCTCT+CGG + chr1.1:79451970-79451989 MS.gene76206:intron 30.0%
!! TCCTAAAACAACTCACTTTT+GGG + chr1.1:79450967-79450986 MS.gene76206:CDS 30.0%
!!! ACCTTTTAAGGTGAATAAGT+GGG + chr1.1:79451804-79451823 MS.gene76206:intron 30.0%
AAAGTAGCAGCAAATAGAAC+AGG - chr1.1:79451496-79451515 None:intergenic 35.0%
CATTGTTCATGAGATTTGCA+TGG + chr1.1:79451334-79451353 MS.gene76206:CDS 35.0%
TACATATATCGTTGTCATGG+TGG + chr1.1:79451710-79451729 MS.gene76206:intron 35.0%
! GTCCTAAAACAACTCACTTT+TGG + chr1.1:79450966-79450985 MS.gene76206:CDS 35.0%
! TATTTTATATGGAAAGGGGC+TGG + chr1.1:79451155-79451174 MS.gene76206:intron 35.0%
! TCAACTTTTCATGAAAGCAG+AGG - chr1.1:79451237-79451256 None:intergenic 35.0%
! TGGCTAGAATTCACCTTTTA+AGG + chr1.1:79451792-79451811 MS.gene76206:intron 35.0%
! TTCTTTTGTAGGTATCTCTC+GGG + chr1.1:79451971-79451990 MS.gene76206:intron 35.0%
!! CCTAAAACAACTCACTTTTG+GGG + chr1.1:79450968-79450987 MS.gene76206:CDS 35.0%
!! CTGAATGGTGCTATATATGT+CGG + chr1.1:79451918-79451937 MS.gene76206:intron 35.0%
!!! CACCTTTTAAGGTGAATAAG+TGG + chr1.1:79451803-79451822 MS.gene76206:intron 35.0%
!!! CCTTTTAAGGTGAATAAGTG+GGG + chr1.1:79451805-79451824 MS.gene76206:intron 35.0%
!!! TTTTTTGTCAAGTAGCCTAG+TGG + chr1.1:79451772-79451791 MS.gene76206:intron 35.0%
AAACCTCCAGAAATGATCTC+TGG + chr1.1:79451189-79451208 MS.gene76206:CDS 40.0%
AAAGGTGAATTCTAGCCACT+AGG - chr1.1:79451790-79451809 None:intergenic 40.0%
AGCTCTATCAACATACCAGA+TGG + chr1.1:79451415-79451434 MS.gene76206:CDS 40.0%
ATGTTGCCAGAGATCATTTC+TGG - chr1.1:79451198-79451217 None:intergenic 40.0%
CCCCACTTATTCACCTTAAA+AGG - chr1.1:79451808-79451827 None:intergenic 40.0%
GCAAGAAGTAGATAGTTACG+TGG - chr1.1:79451369-79451388 None:intergenic 40.0%
GCTCTATCAACATACCAGAT+GGG + chr1.1:79451416-79451435 MS.gene76206:CDS 40.0%
GTTCATGAGATTTGCATGGA+TGG + chr1.1:79451338-79451357 MS.gene76206:CDS 40.0%
TTGACATTCTTCTTGGCGTA+TGG + chr1.1:79451253-79451272 MS.gene76206:intron 40.0%
! TCTTTTGTAGGTATCTCTCG+GGG + chr1.1:79451972-79451991 MS.gene76206:intron 40.0%
!! CCCCAAAAGTGAGTTGTTTT+AGG - chr1.1:79450971-79450990 None:intergenic 40.0%
!!! GCATTTTGGAATAGTCCAGT+TGG + chr1.1:79450944-79450963 MS.gene76206:CDS 40.0%
!!! TGAGTTGTTTTAGGACCAAC+TGG - chr1.1:79450962-79450981 None:intergenic 40.0%
ACAAATCCCCAGTTAGCAAC+AGG - chr1.1:79450995-79451014 None:intergenic 45.0%
ATCAACATACCAGATGGGCA+AGG + chr1.1:79451421-79451440 MS.gene76206:CDS 45.0%
ATGATCTCTGGCAACATGAC+AGG + chr1.1:79451201-79451220 MS.gene76206:CDS 45.0%
CACTAGTACTCTCTCTGTTC+TGG + chr1.1:79451607-79451626 MS.gene76206:intron 45.0%
TCAACATACCAGATGGGCAA+GGG + chr1.1:79451422-79451441 MS.gene76206:CDS 45.0%
TGAGCATAACTCAGTTGGCA+GGG - chr1.1:79451872-79451891 None:intergenic 45.0%
TGCCAACTGAGTTATGCTCA+CGG + chr1.1:79451872-79451891 MS.gene76206:intron 45.0%
! AGGTGAATAAGTGGGGTGTT+CGG + chr1.1:79451812-79451831 MS.gene76206:intron 45.0%
! TACTCTCTCTGTTCTGGATC+TGG + chr1.1:79451613-79451632 MS.gene76206:intron 45.0%
! TTGCCAGAGATCATTTCTGG+AGG - chr1.1:79451195-79451214 None:intergenic 45.0%
!! AACAGAGAGAGTACTAGTGG+TGG - chr1.1:79451606-79451625 None:intergenic 45.0%
!! CAGAACAGAGAGAGTACTAG+TGG - chr1.1:79451609-79451628 None:intergenic 45.0%
!! TGGCTGCCTTCAAAGCATTT+TGG + chr1.1:79450930-79450949 MS.gene76206:CDS 45.0%
!! ATATAAAATAAAATAAAAGT+TGG - chr1.1:79451145-79451164 None:intergenic 5.0%
!!! AACTTTTATTTTATTTTATA+TGG + chr1.1:79451144-79451163 MS.gene76206:intron 5.0%
ATCTCTGGCAACATGACAGG+AGG + chr1.1:79451204-79451223 MS.gene76206:CDS 50.0%
CCAACTGAGTTATGCTCACG+GGG + chr1.1:79451874-79451893 MS.gene76206:intron 50.0%
GCCAACTGAGTTATGCTCAC+GGG + chr1.1:79451873-79451892 MS.gene76206:intron 50.0%
GTGAGCATAACTCAGTTGGC+AGG - chr1.1:79451873-79451892 None:intergenic 50.0%
TAGGTATCTCTCGGGGAAGA+AGG + chr1.1:79451979-79451998 MS.gene76206:intron 50.0%
TCTTCTTGGCGTATGGTCTG+TGG + chr1.1:79451260-79451279 MS.gene76206:intron 50.0%
TGGCAACATGACAGGAGGTT+TGG + chr1.1:79451209-79451228 MS.gene76206:intron 50.0%
TTGGGGACCTGTTGCTAACT+GGG + chr1.1:79450985-79451004 MS.gene76206:CDS 50.0%
TTTGGGGACCTGTTGCTAAC+TGG + chr1.1:79450984-79451003 MS.gene76206:CDS 50.0%
! CTCTGTTCTGGATCTGGTGT+TGG + chr1.1:79451619-79451638 MS.gene76206:intron 50.0%
! GGTGAATAAGTGGGGTGTTC+GGG + chr1.1:79451813-79451832 MS.gene76206:intron 50.0%
! GTGAATAAGTGGGGTGTTCG+GGG + chr1.1:79451814-79451833 MS.gene76206:intron 50.0%
!! TCTGGATCTGGTGTTGGTGT+GGG + chr1.1:79451625-79451644 MS.gene76206:intron 50.0%
!! TTCTGGATCTGGTGTTGGTG+TGG + chr1.1:79451624-79451643 MS.gene76206:intron 50.0%
CCCCGTGAGCATAACTCAGT+TGG - chr1.1:79451877-79451896 None:intergenic 55.0%
TGGGGACCTGTTGCTAACTG+GGG + chr1.1:79450986-79451005 MS.gene76206:CDS 55.0%
ACCAGATGGGCAAGGGCAGA+AGG + chr1.1:79451429-79451448 MS.gene76206:CDS 60.0%
CCAGATGGGCAAGGGCAGAA+GGG + chr1.1:79451430-79451449 MS.gene76206:CDS 60.0%
GGCAAGGGCAGAAGGGTAAG+TGG + chr1.1:79451437-79451456 MS.gene76206:intron 60.0%
CCCTTCTGCCCTTGCCCATC+TGG - chr1.1:79451433-79451452 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 79450929 79452024 79450929 ID=MS.gene76206
chr1.1 mRNA 79450929 79452024 79450929 ID=MS.gene76206.t1;Parent=MS.gene76206
chr1.1 exon 79450929 79451021 79450929 ID=MS.gene76206.t1.exon1;Parent=MS.gene76206.t1
chr1.1 CDS 79450929 79451021 79450929 ID=cds.MS.gene76206.t1;Parent=MS.gene76206.t1
chr1.1 exon 79451171 79451225 79451171 ID=MS.gene76206.t1.exon2;Parent=MS.gene76206.t1
chr1.1 CDS 79451171 79451225 79451171 ID=cds.MS.gene76206.t1;Parent=MS.gene76206.t1
chr1.1 exon 79451316 79451451 79451316 ID=MS.gene76206.t1.exon3;Parent=MS.gene76206.t1
chr1.1 CDS 79451316 79451451 79451316 ID=cds.MS.gene76206.t1;Parent=MS.gene76206.t1
chr1.1 exon 79451982 79452024 79451982 ID=MS.gene76206.t1.exon4;Parent=MS.gene76206.t1
chr1.1 CDS 79451982 79452024 79451982 ID=cds.MS.gene76206.t1;Parent=MS.gene76206.t1
Gene Sequence

>MS.gene76206

ATGGCTGCCTTCAAAGCATTTTGGAATAGTCCAGTTGGTCCTAAAACAACTCACTTTTGGGGACCTGTTGCTAACTGGGGATTTGTCGCAGCTGTGAGTTTCACCCTATGATCATCTATTTATTATTATTATTATTATTATTAACAAAGTCGTGCATTTATTTACTTTATTAGTGTTAAAAATGGTCTTAACCTTTGGTTTTAAACTAATATGCCAACTTTTATTTTATTTTATATGGAAAGGGGCTGGCTGACATCAATAAACCTCCAGAAATGATCTCTGGCAACATGACAGGAGGTTTGGCACCTCTGCTTTCATGAAAAGTTGACATTCTTCTTGGCGTATGGTCTGTGGATTAATCATTTTATCTCATTTTTATTGCTGCAGCAATGTGTATATATTCAGCATTGTTCATGAGATTTGCATGGATGGTACAGCCACGTAACTATCTACTTCTTGCATGTCATGCTTCAAATGAGACTGTTCAGCTCTATCAACATACCAGATGGGCAAGGGCAGAAGGGTAAGTGGCTAACATGCAAGCAAAACAAAACATTTTTTCAACCTGTTCTATTTGCTGCTACTTTACGAGACAACAATGTTTCATGTTTTATAAATGCTATTTTAACTTGTAACATGTTTATAATATTAATTGCAATATACTTTTAACTTGACCACCACTAGTACTCTCTCTGTTCTGGATCTGGTGTTGGTGTGGGAAAAGTTTTCTTCAAGTTACAATAAACAACAATACTTTGTGTATTCTCGTTTATTCAAATTGTACATATATCGTTGTCATGGTGGTGTGCACTTGTCCTTAAATGTAATGTTAGTATTTTTTTTTTTTTTGTCAAGTAGCCTAGTGGCTAGAATTCACCTTTTAAGGTGAATAAGTGGGGTGTTCGGGGTTCGAACCCCACTACATATATCAATGCATTGTCCCTGCCAACTGAGTTATGCTCACGGGGACTGTTAGTATTTTATTTTGACTGAATGGTGCTATATATGTCGGATTACTAATAAAGGTTTGTATCTTTGCAATTTCTTTTGTAGGTATCTCTCGGGGAAGAAGGAGAAAGAAGCTTCATCAGAGTGA
Protein sequence

>MS.gene76206.t1

MAAFKAFWNSPVGPKTTHFWGPVANWGFVAAGLADINKPPEMISGNMTGAMCIYSALFMRFAWMVQPRNYLLLACHASNETVQLYQHTRWARAEGYLSGKKEKEASSE