AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene46082

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46082.t1 MTR_5g097510 83.117 77 9 2 82 158 25 97 1.12e-32 121
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46082.t1 AT3G07790 54.545 77 32 1 82 158 24 97 8.82e-19 82.4

Find 38 sgRNAs with CRISPR-Local

Find 107 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAATGGGAAAATTGAAATT+TGG 0.116656 7.2:-41921786 None:intergenic
AAATGGGAAAATTGAAATTT+GGG 0.220507 7.2:-41921785 None:intergenic
AAAATTGAAATTTGGGGATT+TGG 0.224307 7.2:-41921778 None:intergenic
CCAAGGTTGGATGCAAATTA+AGG 0.251493 7.2:+41920487 None:intergenic
TGAGTGTCATTCAAAGTATC+TGG 0.265393 7.2:+41920514 MS.gene46082:CDS
TCACGAAGCTTTGAGATATT+AGG 0.307878 7.2:-41921959 None:intergenic
CGGGTGATTGAAACATTGTT+AGG 0.319098 7.2:-41921842 None:intergenic
ATTGAAACATTGTTAGGGTT+AGG 0.353649 7.2:-41921836 None:intergenic
TGAAGAGGAGGTTCGTTCAT+TGG 0.355498 7.2:-41921672 None:intergenic
AACCGTATGTAATCTTCAAC+TGG 0.358043 7.2:-41922039 None:intergenic
TTGATGAGATTGAACTGAAA+TGG 0.363866 7.2:-41921802 None:intergenic
TTGGGTGGCGATGATTCTTC+TGG 0.409052 7.2:-41921874 None:intergenic
AGCTTCGTGATCGACTTGAT+TGG 0.434526 7.2:+41921972 MS.gene46082:CDS
TGAAGAAAGTCTTTGATGAT+TGG 0.435183 7.2:-41921750 None:intergenic
TTGAAACATTGTTAGGGTTA+GGG 0.437254 7.2:-41921835 None:intergenic
TGATGAGATTGAACTGAAAT+GGG 0.447265 7.2:-41921801 None:intergenic
TGGGCATCACGAATTTGAAC+AGG 0.498249 7.2:-41922019 None:intergenic
GGGTGATTGAAACATTGTTA+GGG 0.526856 7.2:-41921841 None:intergenic
CTTTGTCAAGAATGTACTCA+TGG 0.541520 7.2:+41921626 MS.gene46082:intron
AGATACATACGCTGAAGCCT+TGG 0.543076 7.2:+41921910 MS.gene46082:CDS
TATCTTCATCAAGAACCGTT+GGG 0.544225 7.2:-41921892 None:intergenic
GATTCTTCTGGTGTTGAACA+CGG 0.545147 7.2:-41921862 None:intergenic
GTATCTTCATCAAGAACCGT+TGG 0.546577 7.2:-41921893 None:intergenic
AATGGGAAAATTGAAATTTG+GGG 0.564215 7.2:-41921784 None:intergenic
GAGTGTCATTCAAAGTATCT+GGG 0.566403 7.2:+41920515 MS.gene46082:CDS
ATTCTTCTGGTGTTGAACAC+GGG 0.567385 7.2:-41921861 None:intergenic
GAAAACCTACCAACAAAAGC+AGG 0.586445 7.2:-41920542 None:intergenic
GCCCAGTTGAAGATTACATA+CGG 0.589563 7.2:+41922037 MS.gene46082:CDS
TGGTGTTGATCTTGAAGAGG+AGG 0.600218 7.2:-41921684 None:intergenic
AAAGTTGATGTTGAAGATCG+TGG 0.616451 7.2:-41921704 None:intergenic
ATTAGGAAAGTTATCACACT+CGG 0.622433 7.2:-41921942 None:intergenic
TGGCTTGAAGTGATAAAGAC+TGG 0.629810 7.2:+41921992 MS.gene46082:CDS
TCGTGGTGTTGATCTTGAAG+AGG 0.635477 7.2:-41921687 None:intergenic
ACACTCGGTTATCTTCTCCA+AGG 0.641969 7.2:-41921927 None:intergenic
ACCGTATGTAATCTTCAACT+GGG 0.649964 7.2:-41922038 None:intergenic
GAAGAATCATCGCCACCCAA+CGG 0.651868 7.2:+41921877 MS.gene46082:CDS
CTTCATCAAGAACCGTTGGG+TGG 0.673751 7.2:-41921889 None:intergenic
TGTCAAGAATGTACTCATGG+CGG 0.711627 7.2:+41921629 MS.gene46082:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGAAAATAAATTATGAATTT+TGG - chr7.2:41921394-41921413 None:intergenic 10.0%
!!! TTAAAATGATTTTTTAACAA+GGG - chr7.2:41921032-41921051 None:intergenic 10.0%
!!! TTTAAAATGATTTTTTAACA+AGG - chr7.2:41921033-41921052 None:intergenic 10.0%
!!! TTTAGTTTTAATTTTCATTT+TGG + chr7.2:41921198-41921217 MS.gene46082:intron 10.0%
!!! ACAATTTTTAGAATTTAAAC+AGG - chr7.2:41920967-41920986 None:intergenic 15.0%
!!! ATTGAAAGAAATTTTAACAT+AGG - chr7.2:41920796-41920815 None:intergenic 15.0%
!!! CAATTTTTAGAATTTAAACA+GGG - chr7.2:41920966-41920985 None:intergenic 15.0%
!! AAATGGGAAAATTGAAATTT+GGG - chr7.2:41921788-41921807 None:intergenic 20.0%
!! ATTTGCAAAATTCATGAAAA+AGG + chr7.2:41920755-41920774 MS.gene46082:intron 20.0%
!! GACTTTAACAAACTTAAAAA+GGG - chr7.2:41921254-41921273 None:intergenic 20.0%
!! TGACTTTAACAAACTTAAAA+AGG - chr7.2:41921255-41921274 None:intergenic 20.0%
!! TTTGCAAAATTCATGAAAAA+GGG + chr7.2:41920756-41920775 MS.gene46082:intron 20.0%
!!! AATGACTCAAATGATTTTTT+TGG - chr7.2:41920892-41920911 None:intergenic 20.0%
!!! TATTTTTAGGTCCAAAATTA+GGG - chr7.2:41920648-41920667 None:intergenic 20.0%
! AAAAATTTCTATCAACTGCT+GGG + chr7.2:41920611-41920630 MS.gene46082:intron 25.0%
! AAAATTGAAATTTGGGGATT+TGG - chr7.2:41921781-41921800 None:intergenic 25.0%
! AATGGGAAAATTGAAATTTG+GGG - chr7.2:41921787-41921806 None:intergenic 25.0%
! ATTGTTTAAGTCTCTTCAAT+TGG + chr7.2:41920825-41920844 MS.gene46082:intron 25.0%
! GAAATGGGAAAATTGAAATT+TGG - chr7.2:41921789-41921808 None:intergenic 25.0%
! TGACTTATTTATAGATGACA+TGG - chr7.2:41921339-41921358 None:intergenic 25.0%
!! AGAATTGAGCTAGTATTTTT+AGG - chr7.2:41920661-41920680 None:intergenic 25.0%
!! ATGCAAATAACAAAAGTACA+AGG - chr7.2:41921225-41921244 None:intergenic 25.0%
!! TTTCAATTTTGTCCAAGATA+GGG + chr7.2:41920561-41920580 MS.gene46082:intron 25.0%
!! TTTTCAATTTTGTCCAAGAT+AGG + chr7.2:41920560-41920579 MS.gene46082:intron 25.0%
!!! CTCAAATGATTTTTTTGGAA+TGG - chr7.2:41920887-41920906 None:intergenic 25.0%
!!! GTATTTTTAGGTCCAAAATT+AGG - chr7.2:41920649-41920668 None:intergenic 25.0%
ATTAGGAAAGTTATCACACT+CGG - chr7.2:41921945-41921964 None:intergenic 30.0%
ATTGAAACATTGTTAGGGTT+AGG - chr7.2:41921839-41921858 None:intergenic 30.0%
GAAAAATTTCTATCAACTGC+TGG + chr7.2:41920610-41920629 MS.gene46082:intron 30.0%
GACAAAGAAGAGGAATTAAA+GGG - chr7.2:41921613-41921632 None:intergenic 30.0%
TGACAAAGAAGAGGAATTAA+AGG - chr7.2:41921614-41921633 None:intergenic 30.0%
TGATGAGATTGAACTGAAAT+GGG - chr7.2:41921804-41921823 None:intergenic 30.0%
TTGAAACATTGTTAGGGTTA+GGG - chr7.2:41921838-41921857 None:intergenic 30.0%
TTGATGAGATTGAACTGAAA+TGG - chr7.2:41921805-41921824 None:intergenic 30.0%
! ATAGATGACATGGTAAGTTT+TGG - chr7.2:41921329-41921348 None:intergenic 30.0%
! TAGATGACATGGTAAGTTTT+GGG - chr7.2:41921328-41921347 None:intergenic 30.0%
! TGAAGAAAGTCTTTGATGAT+TGG - chr7.2:41921753-41921772 None:intergenic 30.0%
!! AGAGTGTTATACCCTAATTT+TGG + chr7.2:41920634-41920653 MS.gene46082:intron 30.0%
AAAAGACTAAAATGCCCCTA+GGG - chr7.2:41920931-41920950 None:intergenic 35.0%
AACCGTATGTAATCTTCAAC+TGG - chr7.2:41922042-41922061 None:intergenic 35.0%
ACCGTATGTAATCTTCAACT+GGG - chr7.2:41922041-41922060 None:intergenic 35.0%
AGAGAAAGTTGTTAGAAGAG+AGG - chr7.2:41921427-41921446 None:intergenic 35.0%
CTTTGTCAAGAATGTACTCA+TGG + chr7.2:41921626-41921645 MS.gene46082:intron 35.0%
GAAATGAAATGAAGAGAGTG+TGG - chr7.2:41921561-41921580 None:intergenic 35.0%
GAGAAAGTTGTTAGAAGAGA+GGG - chr7.2:41921426-41921445 None:intergenic 35.0%
GGGTGATTGAAACATTGTTA+GGG - chr7.2:41921844-41921863 None:intergenic 35.0%
GTACATTCTTGACAAAGAAG+AGG - chr7.2:41921623-41921642 None:intergenic 35.0%
TATCTTCATCAAGAACCGTT+GGG - chr7.2:41921895-41921914 None:intergenic 35.0%
! GAGTGTCATTCAAAGTATCT+GGG + chr7.2:41920515-41920534 MS.gene46082:CDS 35.0%
! TGAGTGTCATTCAAAGTATC+TGG + chr7.2:41920514-41920533 MS.gene46082:CDS 35.0%
!! AAAGTTGATGTTGAAGATCG+TGG - chr7.2:41921707-41921726 None:intergenic 35.0%
!! TCACGAAGCTTTGAGATATT+AGG - chr7.2:41921962-41921981 None:intergenic 35.0%
!! TTGTTATGGTGGTTTGTTAG+AGG - chr7.2:41921494-41921513 None:intergenic 35.0%
AAAGACTAAAATGCCCCTAG+GGG - chr7.2:41920930-41920949 None:intergenic 40.0%
AAATGACCAAAATGCCCCTA+GGG - chr7.2:41921088-41921107 None:intergenic 40.0%
CGGGTGATTGAAACATTGTT+AGG - chr7.2:41921845-41921864 None:intergenic 40.0%
GAAAACCTACCAACAAAAGC+AGG - chr7.2:41920545-41920564 None:intergenic 40.0%
GAAAAGACTAAAATGCCCCT+AGG - chr7.2:41920932-41920951 None:intergenic 40.0%
GAAGTTGTTGTGGTGGTTAA+AGG - chr7.2:41921530-41921549 None:intergenic 40.0%
GCCCAGTTGAAGATTACATA+CGG + chr7.2:41922037-41922056 MS.gene46082:CDS 40.0%
GTATCTTCATCAAGAACCGT+TGG - chr7.2:41921896-41921915 None:intergenic 40.0%
TGGCTTGAAGTGATAAAGAC+TGG + chr7.2:41921992-41922011 MS.gene46082:CDS 40.0%
TGTCAAGAATGTACTCATGG+CGG + chr7.2:41921629-41921648 MS.gene46082:intron 40.0%
! ATGAAATGAAGAGAGTGTGG+TGG - chr7.2:41921558-41921577 None:intergenic 40.0%
! ATTCTTCTGGTGTTGAACAC+GGG - chr7.2:41921864-41921883 None:intergenic 40.0%
! ATTTTGTCCAAGATAGGGTG+TGG + chr7.2:41920566-41920585 MS.gene46082:intron 40.0%
! CTATGGTGGAAGTTAGTTAG+AGG - chr7.2:41921452-41921471 None:intergenic 40.0%
! GAGGTTGAAGATGAAGCTTT+TGG - chr7.2:41921475-41921494 None:intergenic 40.0%
! GATTCTTCTGGTGTTGAACA+CGG - chr7.2:41921865-41921884 None:intergenic 40.0%
!! GAAGATGAAGCTTTTGGCTA+TGG - chr7.2:41921469-41921488 None:intergenic 40.0%
!! TCGAGTCATTTTAGTCCCTA+GGG + chr7.2:41921070-41921089 MS.gene46082:intron 40.0%
!! TTCGAGTCATTTTAGTCCCT+AGG + chr7.2:41921069-41921088 MS.gene46082:intron 40.0%
!!! ATGGTAAGTTTTGGGCCAAT+TGG - chr7.2:41921320-41921339 None:intergenic 40.0%
ACACTCGGTTATCTTCTCCA+AGG - chr7.2:41921930-41921949 None:intergenic 45.0%
AGATACATACGCTGAAGCCT+TGG + chr7.2:41921910-41921929 MS.gene46082:CDS 45.0%
GAAATGACCAAAATGCCCCT+AGG - chr7.2:41921089-41921108 None:intergenic 45.0%
GGTGGTTATGGAAGTTGTTG+TGG - chr7.2:41921540-41921559 None:intergenic 45.0%
GGTTATGGAAGTTGTTGTGG+TGG - chr7.2:41921537-41921556 None:intergenic 45.0%
GTTGTTGTGGTGGTTAAAGG+TGG - chr7.2:41921527-41921546 None:intergenic 45.0%
TGAAGAGGAGGTTCGTTCAT+TGG - chr7.2:41921675-41921694 None:intergenic 45.0%
TGGGCATCACGAATTTGAAC+AGG - chr7.2:41922022-41922041 None:intergenic 45.0%
TTGAGTCAGTTTAGCCCCTA+GGG + chr7.2:41920913-41920932 MS.gene46082:intron 45.0%
TTTGAGTCAGTTTAGCCCCT+AGG + chr7.2:41920912-41920931 MS.gene46082:intron 45.0%
! TGAAGAGAGTGTGGTGGTTA+TGG - chr7.2:41921552-41921571 None:intergenic 45.0%
!! AGCTTCGTGATCGACTTGAT+TGG + chr7.2:41921972-41921991 MS.gene46082:CDS 45.0%
!! CGAGTCATTTTAGTCCCTAG+GGG + chr7.2:41921071-41921090 MS.gene46082:intron 45.0%
!! GATGAAGCTTTTGGCTATGG+TGG - chr7.2:41921466-41921485 None:intergenic 45.0%
!! TCGTGGTGTTGATCTTGAAG+AGG - chr7.2:41921690-41921709 None:intergenic 45.0%
!! TGGTGTTGATCTTGAAGAGG+AGG - chr7.2:41921687-41921706 None:intergenic 45.0%
!!! AAGTTTTGGGCCAATTGGAG+TGG - chr7.2:41921315-41921334 None:intergenic 45.0%
!!! AGTTTTGGGCCAATTGGAGT+GGG - chr7.2:41921314-41921333 None:intergenic 45.0%
!!! TTTAGTCCCTAGGGGCATTT+TGG + chr7.2:41921079-41921098 MS.gene46082:intron 45.0%
AGGGTGTGGAAGAAGCTGAA+AGG + chr7.2:41920580-41920599 MS.gene46082:intron 50.0%
CTTCATCAAGAACCGTTGGG+TGG - chr7.2:41921892-41921911 None:intergenic 50.0%
GAAGAATCATCGCCACCCAA+CGG + chr7.2:41921877-41921896 MS.gene46082:CDS 50.0%
GCTTCTTCCACACCCTATCT+TGG - chr7.2:41920576-41920595 None:intergenic 50.0%
GTGGAGGGAAGTTGTTATGG+TGG - chr7.2:41921505-41921524 None:intergenic 50.0%
GTTGTGGTGGTTAAAGGTGG+TGG - chr7.2:41921524-41921543 None:intergenic 50.0%
TGAGTCAGTTTAGCCCCTAG+GGG + chr7.2:41920914-41920933 MS.gene46082:intron 50.0%
TTGGGTGGCGATGATTCTTC+TGG - chr7.2:41921877-41921896 None:intergenic 50.0%
! GTGGTGGAGGGAAGTTGTTA+TGG - chr7.2:41921508-41921527 None:intergenic 50.0%
!! GACTGCCTGCTTTTGTTGGT+AGG + chr7.2:41920537-41920556 MS.gene46082:intron 50.0%
!! TGGTGGTTAAAGGTGGTGGA+GGG - chr7.2:41921520-41921539 None:intergenic 50.0%
GCCAATTGGAGTGGGACATG+TGG - chr7.2:41921306-41921325 None:intergenic 55.0%
GCCACATGTCCCACTCCAAT+TGG + chr7.2:41921302-41921321 MS.gene46082:intron 55.0%
! GTGGTGGTTAAAGGTGGTGG+AGG - chr7.2:41921521-41921540 None:intergenic 55.0%
!! CTGGGACTGCCTGCTTTTGT+TGG + chr7.2:41920533-41920552 MS.gene46082:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 41920497 41922063 41920497 ID=MS.gene46082
chr7.2 mRNA 41920497 41922063 41920497 ID=MS.gene46082.t1;Parent=MS.gene46082
chr7.2 exon 41920497 41920554 41920497 ID=MS.gene46082.t1.exon1;Parent=MS.gene46082.t1
chr7.2 CDS 41920497 41920554 41920497 ID=cds.MS.gene46082.t1;Parent=MS.gene46082.t1
chr7.2 exon 41921636 41922063 41921636 ID=MS.gene46082.t1.exon2;Parent=MS.gene46082.t1
chr7.2 CDS 41921636 41922063 41921636 ID=cds.MS.gene46082.t1;Parent=MS.gene46082.t1
Gene Sequence

>MS.gene46082

ATGCAAATTAAGGTTGTTGAGTGTCATTCAAAGTATCTGGGACTGCCTGCTTTTGTTGGTAGGTTTTCAATTTTGTCCAAGATAGGGTGTGGAAGAAGCTGAAAGGTTCGAAAGAAAAATTTCTATCAACTGCTGGGAGAGTGTTATACCCTAATTTTGGACCTAAAAATACTAGCTCAATTCTTCTTTTCTTGCATTTCAAGTCATTTGATATGTCTCTGATCAGTTGCATTTTTCTCTGCATTTTATTTCAATATTATTTGCAAAATTCATGAAAAAGGGCATTTTAGTCATTTCCTATGTTAAAATTTCTTTCAATCTTTTAAAAATTGTTTAAGTCTCTTCAATTGGTTTATATAAGTCTTTGTTTCAATCTCATGTCAAAATCCATTCCAAAAAAATCATTTGAGTCATTTTTGAGTCAGTTTAGCCCCTAGGGGCATTTTAGTCTTTTCATGTGTTAAAACCCTGTTTAAATTCTAAAAATTGTCTCTGAGTCTTTTAATTCGCTTGTATAAACTCTTGCTTTGATCCCTTGTTAAAAAATCATTTTAAAATTGCATTTGAGTCGTTTCGAGTCATTTTAGTCCCTAGGGGCATTTTGGTCATTTCACATAAAATCTCTGTTTCATTTTAATTTGTTTTGTTGTTTTTAATCGTCTCGCTTTACGTTAATTTTCAATTTACTTTTTCAATTCAATTTTAGTTTTAATTTTCATTTTGGTCCTTGTACTTTTGTTATTTGCATTTTAATCCCTTTTTAAGTTTGTTAAAGTCAAAGTCAAGAGTTTGTTACAAGTCAAGTGCCACATGTCCCACTCCAATTGGCCCAAAACTTACCATGTCATCTATAAATAAGTCAAAGTCACACACTAATCATTTTCACAAAAATCACCAAAATTCATAATTTATTTTCTCTCTATTTTCCCTCTCTTCTAACAACTTTCTCTCTCCTCTAACTAACTTCCACCATAGCCAAAAGCTTCATCTTCAACCTCTAACAAACCACCATAACAACTTCCCTCCACCACCTTTAACCACCACAACAACTTCCATAACCACCACACTCTCTTCATTTCATTTCATTTCTAATAACAGTAACAACATACAAATCCCTTTAATTCCTCTTCTTTGTCAAGAATGTACTCATGGCGGCATCATCATTTTCATCTTCTCCAATGAACGAACCTCCTCTTCAAGATCAACACCACGATCTTCAACATCAACTTTAACAAGAACGACAGCAATCTTCACCAATCATCAAAGACTTTCTTCACAAAACCAAATCCCCAAATTTCAATTTTCCCATTTCAGTTCAATCTCATCAATTCAATCGAACCCTAACCCTAACAATGTTTCAATCACCCGTGTTCAACACCAGAAGAATCATCGCCACCCAACGGTTCTTGATGAAGATACATACGCTGAAGCCTTGGAGAAGATAACCGAGTGTGATAACTTTCCTAATATCTCAAAGCTTCGTGATCGACTTGATTGGCTTGAAGTGATAAAGACTGGTGATCCTGTTCAAATTCGTGATGCCCAGTTGAAGATTACATACGGTTGA
Protein sequence

>MS.gene46082.t1

MQIKVVECHSKYLGLPAFVECTHGGIIIFIFSNERTSSSRSTPRSSTSTLTRTTAIFTNHQRLSSQNQIPKFQFSHFSSISSIQSNPNPNNVSITRVQHQKNHRHPTVLDEDTYAEALEKITECDNFPNISKLRDRLDWLEVIKTGDPVQIRDAQLKITYG