AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene064028


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene064028.t1 MTR_6g091630 100.000 121 0 0 1 121 1 121 7.55e-85 243
MS.gene064028.t1 MTR_8g101980 97.521 121 3 0 1 121 1 121 8.29e-83 238
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene064028.t1 AT5G56710 84.211 114 18 0 8 121 6 119 3.45e-67 198
MS.gene064028.t1 AT4G26230 83.333 114 19 0 8 121 6 119 1.30e-66 197
MS.gene064028.t1 AT2G19740 81.667 120 21 1 2 121 1 119 4.59e-66 196
MS.gene064028.t1 AT5G56710 58.772 114 13 1 8 121 6 85 6.30e-38 123

Find 36 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGATCTCCTTGATAGCTTT+TGG 0.199036 6.1:+79287088 None:intergenic
ATTCCTAAAGAAGAGTTAAA+AGG 0.277484 6.1:-79286884 MS.gene064028:CDS
TAAAGAAGAGTTAAAAGGTT+TGG 0.305277 6.1:-79286879 MS.gene064028:CDS
TCAAGCTGAACAAGGCTATC+TGG 0.323250 6.1:-79287018 MS.gene064028:CDS
AAAGAAGAGTTAAAAGGTTT+GGG 0.335880 6.1:-79286878 MS.gene064028:CDS
GAAGTGTACCAAGGAGGATC+AGG 0.398880 6.1:-79286982 MS.gene064028:CDS
TTGGTACACTTCTGATTCCC+TGG 0.413987 6.1:+79286993 None:intergenic
AAGATTGAAATTACCATCCA+TGG 0.468912 6.1:+79289027 None:intergenic
GAAGGCACCAAAAGCTATCA+AGG 0.472855 6.1:-79287095 MS.gene064028:CDS
GAACAAGGCTATCTGGAGCC+AGG 0.480113 6.1:-79287011 MS.gene064028:CDS
ATGGTGGAGAAGGGTGCAGC+AGG 0.507040 6.1:-79289104 MS.gene064028:CDS
ATGCGTACCCTGATCCTCCT+TGG 0.524657 6.1:+79286974 None:intergenic
GAGACGCTTGTGGAGATTGA+TGG 0.526766 6.1:+79289049 None:intergenic
AAGGGAGTATAACTCTTCCT+TGG 0.536523 6.1:+79286922 None:intergenic
GAAGCTGAAAATGGTGGAGA+AGG 0.536786 6.1:-79289114 None:intergenic
TCTAACATCGTTAGTGCCCA+TGG 0.538776 6.1:+79287048 None:intergenic
ATCTTCATCATCAATGACCT+TGG 0.551546 6.1:+79286853 None:intergenic
AAACAGCACCTTCAAGAAGA+AGG 0.555549 6.1:-79287113 MS.gene064028:intron
AATCTCCACAAGCGTCTCCA+TGG 0.563199 6.1:-79289044 MS.gene064028:CDS
TCCACAAGCGTCTCCATGGA+TGG 0.567901 6.1:-79289040 MS.gene064028:intron
TGCAGCAGGTAGAAAAGAAG+AGG 0.581022 6.1:-79289090 MS.gene064028:CDS
AAAAGAAGAGGTGGTTACAC+GGG 0.584738 6.1:-79289078 MS.gene064028:CDS
GAAAAGAAGAGGTGGTTACA+CGG 0.586191 6.1:-79289079 MS.gene064028:CDS
ACCATCCATGGAGACGCTTG+TGG 0.589153 6.1:+79289039 None:intergenic
GAATTTCAACGACAGTGACA+AGG 0.604839 6.1:+79286903 None:intergenic
AAGCTGAAAATGGTGGAGAA+GGG 0.607163 6.1:-79289113 None:intergenic
GAATGACGACGAAGATGCCA+AGG 0.608749 6.1:-79286939 MS.gene064028:CDS
AACAAGGCTATCTGGAGCCA+GGG 0.614836 6.1:-79287010 MS.gene064028:CDS
AAGTGTACCAAGGAGGATCA+GGG 0.622533 6.1:-79286981 MS.gene064028:CDS
AGTTGATGTCAAGCTGAACA+AGG 0.626602 6.1:-79287026 MS.gene064028:CDS
GTTAAAAGGTTTGGGCACCA+AGG 0.626806 6.1:-79286870 MS.gene064028:CDS
AGCAGGTAGAAAAGAAGAGG+TGG 0.632837 6.1:-79289087 MS.gene064028:CDS
AATTTCAACGACAGTGACAA+GGG 0.644182 6.1:+79286904 None:intergenic
GGGTACGCATTGCTCGCAAG+AGG 0.652748 6.1:-79286961 MS.gene064028:CDS
AGGGAATCAGAAGTGTACCA+AGG 0.682823 6.1:-79286991 MS.gene064028:CDS
GAATCAGAAGTGTACCAAGG+AGG 0.739011 6.1:-79286988 MS.gene064028:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTCATGATTTGAAAAAT+CGG - chr6.1:79288633-79288652 MS.gene064028:intron 15.0%
!! AGCACTTATAATATTATAAG+CGG + chr6.1:79288016-79288035 None:intergenic 20.0%
!! ATTAAACTGTTAATCAAAAC+AGG + chr6.1:79287990-79288009 None:intergenic 20.0%
!! TTAAACTGTTAATCAAAACA+GGG + chr6.1:79287989-79288008 None:intergenic 20.0%
!! TTATGACGAGATAAAAATAA+AGG - chr6.1:79287190-79287209 MS.gene064028:intron 20.0%
!! TTATGTAACACAACAATTAT+GGG + chr6.1:79287442-79287461 None:intergenic 20.0%
!! TTGATATTCATATTGTGAAT+TGG + chr6.1:79288663-79288682 None:intergenic 20.0%
!!! AAGCTATTTTTATAAGCTAA+GGG - chr6.1:79287235-79287254 MS.gene064028:intron 20.0%
!!! CTGTGTTTATTAGATAATTT+TGG - chr6.1:79287334-79287353 MS.gene064028:intron 20.0%
!!! TAAGCTATTTTTATAAGCTA+AGG - chr6.1:79287234-79287253 MS.gene064028:intron 20.0%
! AAAAATAAGCCAATCTAAAC+AGG + chr6.1:79287261-79287280 None:intergenic 25.0%
! AAAGAAGAGTTAAAAGGTTT+GGG - chr6.1:79289076-79289095 MS.gene064028:CDS 25.0%
! AAATATGTATGCTGTTCATT+TGG - chr6.1:79288468-79288487 MS.gene064028:intron 25.0%
! AATGAACAGCATACATATTT+AGG + chr6.1:79288468-79288487 None:intergenic 25.0%
! ACTAAGTTATTTATCCATAC+AGG + chr6.1:79287112-79287131 None:intergenic 25.0%
! ATGAACAGCATACATATTTA+GGG + chr6.1:79288467-79288486 None:intergenic 25.0%
! ATGAATTCAAAAACAGCTTA+TGG + chr6.1:79288358-79288377 None:intergenic 25.0%
! ATTCCTAAAGAAGAGTTAAA+AGG - chr6.1:79289070-79289089 MS.gene064028:CDS 25.0%
! CTAAGTTATTTATCCATACA+GGG + chr6.1:79287111-79287130 None:intergenic 25.0%
! CTTATGTAACACAACAATTA+TGG + chr6.1:79287443-79287462 None:intergenic 25.0%
! GTGAGTAAATTAATAGTTTG+TGG - chr6.1:79288490-79288509 MS.gene064028:intron 25.0%
! TAAAGAAGAGTTAAAAGGTT+TGG - chr6.1:79289075-79289094 MS.gene064028:CDS 25.0%
! TATGAAAATAAGCTGAATAC+AGG + chr6.1:79287847-79287866 None:intergenic 25.0%
! TATGTAACACAACAATTATG+GGG + chr6.1:79287441-79287460 None:intergenic 25.0%
! TGCTAATTTCTGTTTATGTT+TGG - chr6.1:79288799-79288818 MS.gene064028:intron 25.0%
! TTTCATGATCTAACTACATT+AGG - chr6.1:79287963-79287982 MS.gene064028:intron 25.0%
!! AGTGATGAAATTGATGATTA+TGG + chr6.1:79287932-79287951 None:intergenic 25.0%
!! ATACATATTTAGGGTTTGTT+TGG + chr6.1:79288458-79288477 None:intergenic 25.0%
!! CTCAAATAAGCTATTTCAAA+AGG - chr6.1:79288201-79288220 MS.gene064028:intron 25.0%
!! TCAATTTTGTAGATCTACTA+GGG - chr6.1:79287716-79287735 MS.gene064028:intron 25.0%
!! TTCAATTTTGTAGATCTACT+AGG - chr6.1:79287715-79287734 MS.gene064028:intron 25.0%
!!! AAACCTTTTAACTCTTCTTT+AGG + chr6.1:79289076-79289095 None:intergenic 25.0%
!!! GCTGTTTTAAAAAAACATCA+TGG + chr6.1:79287876-79287895 None:intergenic 25.0%
!!! TAATATGAATTGAGTTGAGT+TGG - chr6.1:79288516-79288535 MS.gene064028:intron 25.0%
!!! TCCTGTAATATTGTTTTAGT+TGG - chr6.1:79287689-79287708 MS.gene064028:intron 25.0%
AAGATTGAAATTACCATCCA+TGG + chr6.1:79286930-79286949 None:intergenic 30.0%
ATGTAACACAACAATTATGG+GGG + chr6.1:79287440-79287459 None:intergenic 30.0%
ATTCTCTAATGGCATAACAT+TGG + chr6.1:79288181-79288200 None:intergenic 30.0%
GCCAACTAAAACAATATTAC+AGG + chr6.1:79287693-79287712 None:intergenic 30.0%
GCTATGTGTAATTGCATAAT+TGG - chr6.1:79288737-79288756 MS.gene064028:intron 30.0%
TAGGATCTGTTTGGATAAAT+AGG - chr6.1:79287482-79287501 MS.gene064028:intron 30.0%
TGTCATCAACTGTTTCAATA+AGG + chr6.1:79287815-79287834 None:intergenic 30.0%
! AAAATTTGCTCAAAAAGCCA+TGG - chr6.1:79288889-79288908 MS.gene064028:intron 30.0%
! AAATTTGCTCAAAAAGCCAT+GGG - chr6.1:79288890-79288909 MS.gene064028:intron 30.0%
! GCTTATTTGAGATTCTCTAA+TGG + chr6.1:79288192-79288211 None:intergenic 30.0%
! TATTTAGGGTTTGTTTGGAT+AGG + chr6.1:79288453-79288472 None:intergenic 30.0%
! TCAGTTTTCTGTGTTTACAT+TGG - chr6.1:79287635-79287654 MS.gene064028:intron 30.0%
!! CGTTTCAAATTTGTTGATCT+AGG - chr6.1:79287463-79287482 MS.gene064028:intron 30.0%
!!! TGTTTTTTATAAGCGACTCT+TGG - chr6.1:79288081-79288100 MS.gene064028:intron 30.0%
AATTTCAACGACAGTGACAA+GGG + chr6.1:79289053-79289072 None:intergenic 35.0%
ATCTTCATCATCAATGACCT+TGG + chr6.1:79289104-79289123 None:intergenic 35.0%
TGTCATTGTTCATAAGTTGC+TGG + chr6.1:79288399-79288418 None:intergenic 35.0%
! TTGTTGATCTAGGATCTGTT+TGG - chr6.1:79287473-79287492 MS.gene064028:intron 35.0%
AAAAGAAGAGGTGGTTACAC+GGG - chr6.1:79286876-79286895 MS.gene064028:CDS 40.0%
AAACAGCACCTTCAAGAAGA+AGG - chr6.1:79288841-79288860 MS.gene064028:intron 40.0%
AACACAACAATTATGGGGGA+AGG + chr6.1:79287436-79287455 None:intergenic 40.0%
CTATAGATCTAGACCCTGTA+TGG - chr6.1:79287095-79287114 MS.gene064028:CDS 40.0%
CTATTTGCATAAGCTCCTGT+TGG - chr6.1:79287776-79287795 MS.gene064028:intron 40.0%
GAAAAGAAGAGGTGGTTACA+CGG - chr6.1:79286875-79286894 MS.gene064028:CDS 40.0%
GAATTTCAACGACAGTGACA+AGG + chr6.1:79289054-79289073 None:intergenic 40.0%
! AAGGGAGTATAACTCTTCCT+TGG + chr6.1:79289035-79289054 None:intergenic 40.0%
! AGTTGATGTCAAGCTGAACA+AGG - chr6.1:79288928-79288947 MS.gene064028:intron 40.0%
! ATCTACTAGGGTGTTAGGAT+CGG - chr6.1:79287728-79287747 MS.gene064028:intron 40.0%
! TGTAGATCTACTAGGGTGTT+AGG - chr6.1:79287723-79287742 MS.gene064028:intron 40.0%
! TTCATAAGTTGCTGGCTGTT+TGG + chr6.1:79288391-79288410 None:intergenic 40.0%
!! CTGATCTCCTTGATAGCTTT+TGG + chr6.1:79288869-79288888 None:intergenic 40.0%
!!! TTTTGGTGCCTTCTTCTTGA+AGG + chr6.1:79288852-79288871 None:intergenic 40.0%
AAGCTCCTGTTGGACTGTTT+GGG - chr6.1:79287786-79287805 MS.gene064028:intron 45.0%
AAGTGTACCAAGGAGGATCA+GGG - chr6.1:79288973-79288992 MS.gene064028:intron 45.0%
AGCAGGTAGAAAAGAAGAGG+TGG - chr6.1:79286867-79286886 MS.gene064028:CDS 45.0%
AGCTAAGGGCCTGTTTAGAT+TGG - chr6.1:79287249-79287268 MS.gene064028:intron 45.0%
GTTAAAAGGTTTGGGCACCA+AGG - chr6.1:79289084-79289103 MS.gene064028:CDS 45.0%
TAAGCTCCTGTTGGACTGTT+TGG - chr6.1:79287785-79287804 MS.gene064028:intron 45.0%
TCAAGCTGAACAAGGCTATC+TGG - chr6.1:79288936-79288955 MS.gene064028:intron 45.0%
TCTAACATCGTTAGTGCCCA+TGG + chr6.1:79288909-79288928 None:intergenic 45.0%
TGCAGCAGGTAGAAAAGAAG+AGG - chr6.1:79286864-79286883 MS.gene064028:CDS 45.0%
TTGGTACACTTCTGATTCCC+TGG + chr6.1:79288964-79288983 None:intergenic 45.0%
! AGGGAATCAGAAGTGTACCA+AGG - chr6.1:79288963-79288982 MS.gene064028:intron 45.0%
! GAATCAGAAGTGTACCAAGG+AGG - chr6.1:79288966-79288985 MS.gene064028:intron 45.0%
! TCGCACTGTTTTGTGTGTTG+TGG - chr6.1:79288551-79288570 MS.gene064028:intron 45.0%
!! GAAGGCACCAAAAGCTATCA+AGG - chr6.1:79288859-79288878 MS.gene064028:intron 45.0%
!! TTAATTAAAATTAAAATCAT+GGG + chr6.1:79287065-79287084 None:intergenic 5.0%
!! TTTAATTAAAATTAAAATCA+TGG + chr6.1:79287066-79287085 None:intergenic 5.0%
AATCTCCACAAGCGTCTCCA+TGG - chr6.1:79286910-79286929 MS.gene064028:CDS 50.0%
AGCGACTCTTGGAGAGCTTA+TGG - chr6.1:79288092-79288111 MS.gene064028:intron 50.0%
GAAGTGTACCAAGGAGGATC+AGG - chr6.1:79288972-79288991 MS.gene064028:intron 50.0%
GAATGACGACGAAGATGCCA+AGG - chr6.1:79289015-79289034 MS.gene064028:intron 50.0%
GAGACGCTTGTGGAGATTGA+TGG + chr6.1:79286908-79286927 None:intergenic 50.0%
! AACAAGGCTATCTGGAGCCA+GGG - chr6.1:79288944-79288963 MS.gene064028:intron 50.0%
! CTAGGGTGTTAGGATCGGTT+TGG - chr6.1:79287733-79287752 MS.gene064028:intron 50.0%
ACCATCCATGGAGACGCTTG+TGG + chr6.1:79286918-79286937 None:intergenic 55.0%
ATGCGTACCCTGATCCTCCT+TGG + chr6.1:79288983-79289002 None:intergenic 55.0%
GGTCTCCCAAACAGTCCAAC+AGG + chr6.1:79287794-79287813 None:intergenic 55.0%
TCCACAAGCGTCTCCATGGA+TGG - chr6.1:79286914-79286933 MS.gene064028:CDS 55.0%
! GAACAAGGCTATCTGGAGCC+AGG - chr6.1:79288943-79288962 MS.gene064028:intron 55.0%
GGGTACGCATTGCTCGCAAG+AGG - chr6.1:79288993-79289012 MS.gene064028:intron 60.0%
! ATGGTGGAGAAGGGTGCAGC+AGG - chr6.1:79286850-79286869 MS.gene064028:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 79286850 79289126 79286850 ID=MS.gene064028
chr6.1 mRNA 79286850 79289126 79286850 ID=MS.gene064028.t1;Parent=MS.gene064028
chr6.1 exon 79289041 79289126 79289041 ID=MS.gene064028.t1.exon1;Parent=MS.gene064028.t1
chr6.1 CDS 79289041 79289126 79289041 ID=cds.MS.gene064028.t1;Parent=MS.gene064028.t1
chr6.1 exon 79286850 79287129 79286850 ID=MS.gene064028.t1.exon2;Parent=MS.gene064028.t1
chr6.1 CDS 79286850 79287129 79286850 ID=cds.MS.gene064028.t1;Parent=MS.gene064028.t1
Gene Sequence

>MS.gene064028

ATGGTGGAGAAGGGTGCAGCAGGTAGAAAAGAAGAGGTGGTTACACGGGAGTATACCATCAATCTCCACAAGCGTCTCCATGGATGGTAATTTCAATCTTTCGATTATTTGCTTCTCATGATTCAACTCTCTGTTTTTCATTGCAAATATTGATTCATCATTTTTGTTGTTAATTTCATGATTTAACTGCTAATCAGTAATTTTCTCACTTGCCCATGATTTTAATTTTAATTAAAGTTCAATTTCTATAGATCTAGACCCTGTATGGATAAATAACTTAGTTTGCAGCTTATATTGTAAAGTTAAATTGTTCTTATAAGCGCTTAGTTGTAAGCTATTTTTATGACGAGATAAAAATAAAGGTTAATTGTTTTTTGTTAGTTATAAGCTATTTTTATAAGCTAAGGGCCTGTTTAGATTGGCTTATTTTTGAGCTTATGAATGCTAATAAGTAAGCTTTTATGTTAATTTAATAAGCTATACACTGTGTTTATTAGATAATTTTGGAGAGTTTATGAAAAATAGTTGAAAACAACTTGTGCAATAGATGCTCAAATAAGCTTGTTATTCAGTAATTTTCTCACCTTCCCCCATAATTGTTGTGTTACATAAGCGTTTCAAATTTGTTGATCTAGGATCTGTTTGGATAAATAGGCTAATTTGCAGTGTTTACTGTAAGTACTTATCATGATAAATGCTACTTTTGTTAAACTATGTTAGATAACATATGAAAAGAAGCTGATAACACGTAATAACATGTCACGAGTAATTTTGACTTTTGTGATTCAGTTTTCTGTGTTTACATTGGAAATTACAACTTATCAGTAATTTTCTCACTTTCCTGTAATATTGTTTTAGTTGGCATTTCAATTTTGTAGATCTACTAGGGTGTTAGGATCGGTTTGGATCGACTTATTTATGCTTATCTATTTGCATAAGCTCCTGTTGGACTGTTTGGGAGACCTTATTGAAACAGTTGATGACATTTTCATAACCTGTATTCAGCTTATTTTCATAATCTCTCCATGATGTTTTTTTAAAACAGCTTATAACTACTAATCAGTAATTTTCTCACTTTTCCATAATCATCAATTTCATCACTTTAATTGTTAATTTCATGATCTAACTACATTAGGCCCTGTTTTGATTAACAGTTTAATTTGCCGCTTATAATATTATAAGTGCTTAGTTATAAGCTATTTTTATAACAAAAGATAAAATAAATTTAAATTGTTTTTTATAAGCGACTCTTGGAGAGCTTATGGAAATAAGCTGAAACAACTTATGCACAAAGTCATAAGCTGTTTTAATAAGCTCTTACAGTCATTCCAATGTTATGCCATTAGAGAATCTCAAATAAGCTATTTCAAAAGGCTCTAAGTATTTATGCTGTTCATTTGATGTTAATGAGTAAATTATTATAGTTTGTGAACAATGTCATTAGCTGTTTGTGTATGTTATCTGCGAGAACTTATAAAATAGCTGAAAGCAGCTTATGAACAATGCCATAAGCTGTTTTTGAATTCATATATGTTTTTCCAAACAGCCAGCAACTTATGAACAATGACAAAATTTATGTGAGTAAATAAGCTCAAATAAGCCTATCCAAACAAACCCTAAATATGTATGCTGTTCATTTGGTGAGTAAATTAATAGTTTGTGGTTTTAATATGAATTGAGTTGAGTTGGAATGCATCTGAATCGCACTGTTTTGTGTGTTGTGGACTCTCAGTTTTTTAGTCATATTGATTTTTGACTTGTTTCTTTTTTACTGTGTATCTTATTATTCATGATTTGAAAAATCGGTATGCCAATTCACAATATGAATATCAATATAAGCTCTGTTTCGTTGCTTTGAGATCAAGTTATTTTTTGTAGATGATTCATGCTATGTGTAATTGCATAATTGGATCTGTTTATAGTTTCTGTAATTGTATAACTAGATCTCTTGCTAATTTCTGTTTATGTTTGGTATTTTTTTGTATGTAAAAAAACAGCACCTTCAAGAAGAAGGCACCAAAAGCTATCAAGGAGATCAGAAAATTTGCTCAAAAAGCCATGGGCACTAACGATGTTAGAGTTGATGTCAAGCTGAACAAGGCTATCTGGAGCCAGGGAATCAGAAGTGTACCAAGGAGGATCAGGGTACGCATTGCTCGCAAGAGGAATGACGACGAAGATGCCAAGGAAGAGTTATACTCCCTTGTCACTGTCGTTGAAATTCCTAAAGAAGAGTTAAAAGGTTTGGGCACCAAGGTCATTGATGATGAAGATTGA

Protein sequence

>MS.gene064028.t1

MVEKGAAGRKEEVVTREYTINLHKRLHGCTFKKKAPKAIKEIRKFAQKAMGTNDVRVDVKLNKAIWSQGIRSVPRRIRVRIARKRNDDEDAKEELYSLVTVVEIPKEELKGLGTKVIDDED