AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99883


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99883.t1 MTR_3g072390 98.661 224 3 0 1 224 1 224 5.34e-166 456
MS.gene99883.t1 MTR_5g047050 35.795 176 100 4 61 224 62 236 5.68e-30 111
MS.gene99883.t1 MTR_4g109880 34.545 165 100 3 67 224 59 222 1.50e-26 102
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99883.t1 AT1G44760 58.850 226 73 6 3 224 4 213 8.54e-83 246
MS.gene99883.t1 AT1G44760 58.850 226 73 6 3 224 75 284 1.99e-81 244
MS.gene99883.t1 AT2G03720 38.122 181 99 5 56 224 53 232 1.11e-30 113
MS.gene99883.t1 AT2G03720 39.157 166 90 4 69 224 1 165 1.38e-29 108
MS.gene99883.t1 AT1G69080 32.222 180 101 3 66 224 44 223 1.91e-28 107
MS.gene99883.t1 AT5G17390 36.310 168 97 3 67 224 118 285 2.52e-26 103
MS.gene99883.t1 AT1G69080 34.706 170 96 5 66 224 44 209 5.11e-26 100
MS.gene99883.t1 AT3G03290 34.503 171 96 4 67 224 107 274 1.47e-23 95.5
MS.gene99883.t1 AT4G13450 25.728 206 105 4 66 224 15 219 7.69e-16 73.9

Find 53 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAACTCATGTTGTTAATA+AGG 0.212222 3.2:-65237051 MS.gene99883:CDS
GCAGAAGAACTTCTGGCTTT+TGG 0.227711 3.2:-65235914 MS.gene99883:CDS
ATTCTAAGCATGCAATGATT+TGG 0.290584 3.2:-65237076 MS.gene99883:CDS
CTCATCACTGTGGCCAGTTT+AGG 0.329869 3.2:+65236514 None:intergenic
ACTTACCTTGTTAATCATCT+TGG 0.331349 3.2:-65236966 MS.gene99883:CDS
AGAAAGAAGATGGCTTCTTT+TGG 0.334209 3.2:+65236452 None:intergenic
GATGAGCCAGGTAAAGAAAT+TGG 0.339137 3.2:-65236497 MS.gene99883:CDS
CCAGGTGGCAGAAGAACTTC+TGG 0.346204 3.2:-65235921 MS.gene99883:CDS
CTTACCTTGTTAATCATCTT+GGG 0.346303 3.2:-65236965 MS.gene99883:CDS
TTCTAAGCATGCAATGATTT+GGG 0.371229 3.2:-65237075 MS.gene99883:CDS
ACATACAACAACAATAGTTT+AGG 0.386222 3.2:-65237221 MS.gene99883:CDS
GGGTTTAACATTAACATGTA+TGG 0.388232 3.2:-65237164 MS.gene99883:CDS
CTTGGAAATCAACATCAAAT+AGG 0.391956 3.2:-65237259 MS.gene99883:CDS
AAGAGAAGCCAAGGCAATAA+TGG 0.394438 3.2:-65235958 MS.gene99883:CDS
AGCCATCTTCTTTCTTTAGC+TGG 0.402605 3.2:-65236444 MS.gene99883:intron
AGAGTTATGGTTGTGGTTGA+TGG 0.409544 3.2:-65237107 MS.gene99883:CDS
TGTAATTCAAGGACCTAAAC+TGG 0.413139 3.2:-65236527 MS.gene99883:CDS
CAGCAGCACAGAGGAGTTTG+TGG 0.433556 3.2:-65236025 MS.gene99883:CDS
CTAACTCATGTTGTTAATAA+GGG 0.434772 3.2:-65237050 MS.gene99883:CDS
TCTGCCACCTGGTGCTGATA+AGG 0.435349 3.2:+65235932 None:intergenic
AATGCTGAGTGCTTGACAAT+AGG 0.444116 3.2:-65235988 MS.gene99883:CDS
TGAGACAAATCTGAGTCAAA+TGG 0.450642 3.2:-65237189 MS.gene99883:CDS
TAAGGTAGCCATTATTGCCT+TGG 0.456289 3.2:+65235950 None:intergenic
TAAGACTCAGAAGCACTTTG+AGG 0.458252 3.2:+65236996 None:intergenic
TGGCTTGCAATCTTTGCAAA+GGG 0.487254 3.2:+65236941 None:intergenic
GAAATTGGAGGTCTCTATCC+TGG 0.499739 3.2:-65236482 MS.gene99883:CDS
GTGGAAGCACTTGTAATTCA+AGG 0.506797 3.2:-65236538 MS.gene99883:CDS
AGACCTCCAATTTCTTTACC+TGG 0.507576 3.2:+65236491 None:intergenic
CCAGAAGTTCTTCTGCCACC+TGG 0.508759 3.2:+65235921 None:intergenic
TGGCCTGTCATAGGTGGAAG+TGG 0.514126 3.2:-65236557 MS.gene99883:intron
CTGGCTTGCAATCTTTGCAA+AGG 0.528141 3.2:+65236940 None:intergenic
TGAAGAGAGTTGTGGAATGA+TGG 0.529080 3.2:-65237138 MS.gene99883:CDS
GAGGTCTCTATCCTGGTACT+TGG 0.534821 3.2:-65236475 MS.gene99883:CDS
TACCAGCTAAAGAAAGAAGA+TGG 0.539360 3.2:+65236442 None:intergenic
GATGGTGAGAAAGAGAGTTA+TGG 0.559684 3.2:-65237120 MS.gene99883:CDS
ACTGGCCACAGTGATGAGCC+AGG 0.573013 3.2:-65236509 MS.gene99883:CDS
AGTTAAGTTCAAAAGAGACT+TGG 0.574008 3.2:-65237277 MS.gene99883:CDS
TCAACATCAAATAGGTGGAG+TGG 0.576570 3.2:-65237251 MS.gene99883:CDS
ACAAATCTGAGTCAAATGGA+AGG 0.584700 3.2:-65237185 MS.gene99883:CDS
CTGTTTGTTTACAGTCTCTG+TGG 0.592127 3.2:-65236063 MS.gene99883:intron
GGAGTGAGGAAGAGAAGCCA+AGG 0.601340 3.2:-65235967 MS.gene99883:CDS
CAAATCTGAGTCAAATGGAA+GGG 0.609381 3.2:-65237184 MS.gene99883:CDS
GGAAATCAACATCAAATAGG+TGG 0.613048 3.2:-65237256 MS.gene99883:CDS
CAGCAGCTGCAGCAGCACAG+AGG 0.618197 3.2:-65236034 MS.gene99883:CDS
ATGGCTACCTTATCAGCACC+AGG 0.619844 3.2:-65235939 MS.gene99883:CDS
TATGGAAATGAAGAGAGTTG+TGG 0.622956 3.2:-65237146 MS.gene99883:CDS
GAGCCAGGTAAAGAAATTGG+AGG 0.635543 3.2:-65236494 MS.gene99883:CDS
TTGCAAAGATTGCAAGCCAG+AGG 0.640746 3.2:-65236937 MS.gene99883:intron
GAGAAAGAGAGTTATGGTTG+TGG 0.642404 3.2:-65237114 MS.gene99883:CDS
CTTTACCTGGCTCATCACTG+TGG 0.657425 3.2:+65236504 None:intergenic
GGGACCCAAGATGATTAACA+AGG 0.679967 3.2:+65236961 None:intergenic
AGTGCTTGACAATAGGAGTG+AGG 0.688153 3.2:-65235981 MS.gene99883:CDS
GCTACCTTATCAGCACCAGG+TGG 0.765926 3.2:-65235936 MS.gene99883:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGTAGGAAAATAATTTA+TGG + chr3.2:65236489-65236508 None:intergenic 15.0%
!!! ATTTTTTAAAACAAGACAAT+TGG + chr3.2:65237047-65237066 None:intergenic 15.0%
!!! TTTTTTAAAACAAGACAATT+GGG + chr3.2:65237046-65237065 None:intergenic 15.0%
!! AATTAGTTGAAAAGAGAAAA+AGG + chr3.2:65236457-65236476 None:intergenic 20.0%
!! AATTTACTATTGTCAATTAG+AGG + chr3.2:65236987-65237006 None:intergenic 20.0%
!! ATTAGTTGAAAAGAGAAAAA+GGG + chr3.2:65236456-65236475 None:intergenic 20.0%
!!! TTGTTCAATTGATAGTTAAT+TGG - chr3.2:65236401-65236420 MS.gene99883:intron 20.0%
!!! TTTTTAAAACAAGACAATTG+GGG + chr3.2:65237045-65237064 None:intergenic 20.0%
! AAAGGTTACTGATATTGTTA+TGG - chr3.2:65236637-65236656 MS.gene99883:intron 25.0%
! ACATACAACAACAATAGTTT+AGG - chr3.2:65235993-65236012 MS.gene99883:CDS 25.0%
! ACTAACTCATGTTGTTAATA+AGG - chr3.2:65236163-65236182 MS.gene99883:intron 25.0%
! CATCTAAAGAATAGAAAAGT+AGG + chr3.2:65236503-65236522 None:intergenic 25.0%
! CTAACTCATGTTGTTAATAA+GGG - chr3.2:65236164-65236183 MS.gene99883:intron 25.0%
! GAAAAGCTGAAAATAAAACA+AGG + chr3.2:65236562-65236581 None:intergenic 25.0%
! GATAGTTAATTGGAGTAATT+AGG - chr3.2:65236411-65236430 MS.gene99883:intron 25.0%
! TATCCTCAATACAAAGAAAA+AGG - chr3.2:65236619-65236638 MS.gene99883:intron 25.0%
! TTTCTTTGTATTGAGGATAA+GGG + chr3.2:65236618-65236637 None:intergenic 25.0%
!! CAATTTACAATTTTCAACAG+AGG + chr3.2:65236891-65236910 None:intergenic 25.0%
!! TAACCTTTTTCTTTGTATTG+AGG + chr3.2:65236625-65236644 None:intergenic 25.0%
!! TTTTCTTTGTATTGAGGATA+AGG + chr3.2:65236619-65236638 None:intergenic 25.0%
!!! ATACGTTTTTCTTGTTACTT+GGG - chr3.2:65237085-65237104 MS.gene99883:CDS 25.0%
!!! CTACTTTTCTATTCTTTAGA+TGG - chr3.2:65236501-65236520 MS.gene99883:CDS 25.0%
ACTTACCTTGTTAATCATCT+TGG - chr3.2:65236248-65236267 MS.gene99883:intron 30.0%
AGTTAAGTTCAAAAGAGACT+TGG - chr3.2:65235937-65235956 MS.gene99883:CDS 30.0%
ATTCTAAGCATGCAATGATT+TGG - chr3.2:65236138-65236157 MS.gene99883:intron 30.0%
CTTACCTTGTTAATCATCTT+GGG - chr3.2:65236249-65236268 MS.gene99883:intron 30.0%
CTTGGAAATCAACATCAAAT+AGG - chr3.2:65235955-65235974 MS.gene99883:CDS 30.0%
GAAAAACGTATGACATCAAA+AGG + chr3.2:65237076-65237095 None:intergenic 30.0%
GGGTTTAACATTAACATGTA+TGG - chr3.2:65236050-65236069 MS.gene99883:CDS 30.0%
TGTTGTAAATTGCTTGTGTT+TGG + chr3.2:65236811-65236830 None:intergenic 30.0%
TTCTAAGCATGCAATGATTT+GGG - chr3.2:65236139-65236158 MS.gene99883:intron 30.0%
TTCTTTGTATTGAGGATAAG+GGG + chr3.2:65236617-65236636 None:intergenic 30.0%
! CATACGTTTTTCTTGTTACT+TGG - chr3.2:65237084-65237103 MS.gene99883:CDS 30.0%
ACAAATCTGAGTCAAATGGA+AGG - chr3.2:65236029-65236048 MS.gene99883:CDS 35.0%
ATATTGTTATGGCCTGTCAT+AGG - chr3.2:65236648-65236667 MS.gene99883:intron 35.0%
CAAATCTGAGTCAAATGGAA+GGG - chr3.2:65236030-65236049 MS.gene99883:CDS 35.0%
CTCAAAAATGAAGCTGAACT+TGG + chr3.2:65235915-65235934 None:intergenic 35.0%
GGAAATCAACATCAAATAGG+TGG - chr3.2:65235958-65235977 MS.gene99883:CDS 35.0%
TACACTTAGCTGACATATCA+TGG + chr3.2:65236933-65236952 None:intergenic 35.0%
TACCAGCTAAAGAAAGAAGA+TGG + chr3.2:65236775-65236794 None:intergenic 35.0%
TATGGAAATGAAGAGAGTTG+TGG - chr3.2:65236068-65236087 MS.gene99883:intron 35.0%
TCCATGATATGTCAGTTAAG+TGG - chr3.2:65236832-65236851 MS.gene99883:intron 35.0%
TCTTTGTATTGAGGATAAGG+GGG + chr3.2:65236616-65236635 None:intergenic 35.0%
TGAGACAAATCTGAGTCAAA+TGG - chr3.2:65236025-65236044 MS.gene99883:CDS 35.0%
TGTAATTCAAGGACCTAAAC+TGG - chr3.2:65236687-65236706 MS.gene99883:intron 35.0%
! AGAAAGAAGATGGCTTCTTT+TGG + chr3.2:65236765-65236784 None:intergenic 35.0%
!! CAAGTTCAGCTTCATTTTTG+AGG - chr3.2:65235913-65235932 MS.gene99883:CDS 35.0%
AAACAAGACAATTGGGGTGA+TGG + chr3.2:65237039-65237058 None:intergenic 40.0%
AAGAGAAGCCAAGGCAATAA+TGG - chr3.2:65237256-65237275 MS.gene99883:CDS 40.0%
AATGCTGAGTGCTTGACAAT+AGG - chr3.2:65237226-65237245 MS.gene99883:CDS 40.0%
AGACCTCCAATTTCTTTACC+TGG + chr3.2:65236726-65236745 None:intergenic 40.0%
AGAGTTATGGTTGTGGTTGA+TGG - chr3.2:65236107-65236126 MS.gene99883:intron 40.0%
AGCCATCTTCTTTCTTTAGC+TGG - chr3.2:65236770-65236789 MS.gene99883:intron 40.0%
CTGTTTGTTTACAGTCTCTG+TGG - chr3.2:65237151-65237170 MS.gene99883:CDS 40.0%
GAGAAAGAGAGTTATGGTTG+TGG - chr3.2:65236100-65236119 MS.gene99883:intron 40.0%
GATGAGCCAGGTAAAGAAAT+TGG - chr3.2:65236717-65236736 MS.gene99883:intron 40.0%
GATGGTGAGAAAGAGAGTTA+TGG - chr3.2:65236094-65236113 MS.gene99883:intron 40.0%
GCCACTTAACTGACATATCA+TGG + chr3.2:65236836-65236855 None:intergenic 40.0%
TAAGGTAGCCATTATTGCCT+TGG + chr3.2:65237267-65237286 None:intergenic 40.0%
TCAACATCAAATAGGTGGAG+TGG - chr3.2:65235963-65235982 MS.gene99883:CDS 40.0%
TGAAGAGAGTTGTGGAATGA+TGG - chr3.2:65236076-65236095 MS.gene99883:intron 40.0%
! TGGCTTGCAATCTTTGCAAA+GGG + chr3.2:65236276-65236295 None:intergenic 40.0%
!! GTGGAAGCACTTGTAATTCA+AGG - chr3.2:65236676-65236695 MS.gene99883:intron 40.0%
!! TAAGACTCAGAAGCACTTTG+AGG + chr3.2:65236221-65236240 None:intergenic 40.0%
AAACCACACCAAGTTACCTC+TGG + chr3.2:65236296-65236315 None:intergenic 45.0%
AGTGCTTGACAATAGGAGTG+AGG - chr3.2:65237233-65237252 MS.gene99883:CDS 45.0%
ATTGCAAGCCAGAGGTAACT+TGG - chr3.2:65236285-65236304 MS.gene99883:intron 45.0%
GAAATTGGAGGTCTCTATCC+TGG - chr3.2:65236732-65236751 MS.gene99883:intron 45.0%
GAGCCAGGTAAAGAAATTGG+AGG - chr3.2:65236720-65236739 MS.gene99883:intron 45.0%
GGGACCCAAGATGATTAACA+AGG + chr3.2:65236256-65236275 None:intergenic 45.0%
TTGCAAAGATTGCAAGCCAG+AGG - chr3.2:65236277-65236296 MS.gene99883:intron 45.0%
TTGTTATGGCCTGTCATAGG+TGG - chr3.2:65236651-65236670 MS.gene99883:intron 45.0%
! CTGGCTTGCAATCTTTGCAA+AGG + chr3.2:65236277-65236296 None:intergenic 45.0%
!!! GCAGAAGAACTTCTGGCTTT+TGG - chr3.2:65237300-65237319 MS.gene99883:CDS 45.0%
ATGGCTACCTTATCAGCACC+AGG - chr3.2:65237275-65237294 MS.gene99883:CDS 50.0%
CTCATCACTGTGGCCAGTTT+AGG + chr3.2:65236703-65236722 None:intergenic 50.0%
CTTCCACTTCCACCTATGAC+AGG + chr3.2:65236663-65236682 None:intergenic 50.0%
CTTTACCTGGCTCATCACTG+TGG + chr3.2:65236713-65236732 None:intergenic 50.0%
GAGGTCTCTATCCTGGTACT+TGG - chr3.2:65236739-65236758 MS.gene99883:intron 50.0%
! AAGCCAGAGGTAACTTGGTG+TGG - chr3.2:65236290-65236309 MS.gene99883:intron 50.0%
! GCTTCTTTTGGCCAAGTACC+AGG + chr3.2:65236753-65236772 None:intergenic 50.0%
CAGCAGCACAGAGGAGTTTG+TGG - chr3.2:65237189-65237208 MS.gene99883:CDS 55.0%
CCAGAAGTTCTTCTGCCACC+TGG + chr3.2:65237296-65237315 None:intergenic 55.0%
CCAGGTGGCAGAAGAACTTC+TGG - chr3.2:65237293-65237312 MS.gene99883:CDS 55.0%
GCTACCTTATCAGCACCAGG+TGG - chr3.2:65237278-65237297 MS.gene99883:CDS 55.0%
GGAGTGAGGAAGAGAAGCCA+AGG - chr3.2:65237247-65237266 MS.gene99883:CDS 55.0%
TGGCCTGTCATAGGTGGAAG+TGG - chr3.2:65236657-65236676 MS.gene99883:intron 55.0%
!! TCTGCCACCTGGTGCTGATA+AGG + chr3.2:65237285-65237304 None:intergenic 55.0%
ACTGGCCACAGTGATGAGCC+AGG - chr3.2:65236705-65236724 MS.gene99883:intron 60.0%
CAGCAGCTGCAGCAGCACAG+AGG - chr3.2:65237180-65237199 MS.gene99883:CDS 65.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 65235909 65237327 65235909 ID=MS.gene99883
chr3.2 mRNA 65235909 65237327 65235909 ID=MS.gene99883.t1;Parent=MS.gene99883
chr3.2 exon 65236938 65237327 65236938 ID=MS.gene99883.t1.exon1;Parent=MS.gene99883.t1
chr3.2 CDS 65236938 65237327 65236938 ID=cds.MS.gene99883.t1;Parent=MS.gene99883.t1
chr3.2 exon 65236445 65236566 65236445 ID=MS.gene99883.t1.exon2;Parent=MS.gene99883.t1
chr3.2 CDS 65236445 65236566 65236445 ID=cds.MS.gene99883.t1;Parent=MS.gene99883.t1
chr3.2 exon 65235909 65236071 65235909 ID=MS.gene99883.t1.exon3;Parent=MS.gene99883.t1
chr3.2 CDS 65235909 65236071 65235909 ID=cds.MS.gene99883.t1;Parent=MS.gene99883.t1
Gene Sequence

>MS.gene99883

ATGCCAAGTTCAGCTTCATTTTTGAGGCAGTTAAGTTCAAAAGAGACTTGGAAATCAACATCAAATAGGTGGAGTGGAAAAAACACATACAACAACAATAGTTTAGGAGTTACTTGTGAGACAAATCTGAGTCAAATGGAAGGGTTTAACATTAACATGTATGGAAATGAAGAGAGTTGTGGAATGATGGTGAGAAAGAGAGTTATGGTTGTGGTTGATGGTACTTCACATTCTAAGCATGCAATGATTTGGGCACTAACTCATGTTGTTAATAAGGGTGATTTGTTGACTTTGCTTTACATTGTTTCTCCTCAAAGTGCTTCTGAGTCTTATTCTTCTACTTACCTTGTTAATCATCTTGGGTCCCTTTGCAAAGATTGCAAGCCAGAGGTAACTTGGTGTGGTTTTTTAGTTCAATTAGATTTTGTTCTTTTCTCAATTTTCATAGTGCTTTGTAGATCTTTACTCAGAAAATTATGTGAATTTTCAATGTTGTTCAATTGATAGTTAATTGGAGTAATTAGGAATTATTATGATACTCACTCCCTTTTTCTCTTTTCAACTAATTTTTCTTTTGCCATAAATTATTTTCCTACTTTTCTATTCTTTAGATGGTATAGTGTCTGAACTTTGAGCTGCATGCACTAGTTCCTTGTTTTATTTTCAGCTTTTCTTTTAAGTTTCAACATCTCTCGCTTTTATGTCCCCCTTATCCTCAATACAAAGAAAAAGGTTACTGATATTGTTATGGCCTGTCATAGGTGGAAGTGGAAGCACTTGTAATTCAAGGACCTAAACTGGCCACAGTGATGAGCCAGGTAAAGAAATTGGAGGTCTCTATCCTGGTACTTGGCCAAAAGAAGCCATCTTCTTTCTTTAGCTGGTAAGAGTCTTATCATCCAAACACAAGCAATTTACAACAGTCCATGATATGTCAGTTAAGTGGCATAGAGCTTGAACTTGTAAACAGAGTTCAAATCCTCTGTTGAAAATTGTAAATTGATATTAATTTTGCAACAGTCCATGATATGTCAGCTAAGTGTACAGAGCTTGAACTTGTAAACAGAGTTCAAATCCTCTAATTGACAATAGTAAATTGAATTAATCTCTTTAATTAATGATAGTTTCCATCACCCCAATTGTCTTGTTTTAAAAAATTTGCATCCTTTTGATGTCATACGTTTTTCTTGTTACTTGGGTATTTTGAATTTTTTAAAATTCAGTGTTTGTAATTAATCATTACTGTTTGTTTACAGTCTCTGTGGAAGTAGCAGCAGCTGCAGCAGCACAGAGGAGTTTGTGGAGTACTGTATCAACAATGCTGAGTGCTTGACAATAGGAGTGAGGAAGAGAAGCCAAGGCAATAATGGCTACCTTATCAGCACCAGGTGGCAGAAGAACTTCTGGCTTTTGGCTTAG

Protein sequence

>MS.gene99883.t1

MPSSASFLRQLSSKETWKSTSNRWSGKNTYNNNSLGVTCETNLSQMEGFNINMYGNEESCGMMVRKRVMVVVDGTSHSKHAMIWALTHVVNKGDLLTLLYIVSPQSASESYSSTYLVNHLGSLCKDCKPEVEVEALVIQGPKLATVMSQVKKLEVSILVLGQKKPSSFFSCLCGSSSSCSSTEEFVEYCINNAECLTIGVRKRSQGNNGYLISTRWQKNFWLLA