AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47256

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47256.t1 MTR_6g027320 72.549 51 14 0 5 55 101 151 3.74e-21 80.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATATTAGGAAAATGTTAT+TGG 0.171711 6.3:+18672666 MS.gene47256:intron
CAAACTCTTCCTGGTGGGTT+GGG 0.243881 6.3:-18672801 None:intergenic
ATGTTATTGGATTAAGTATT+GGG 0.250615 6.3:+18672679 MS.gene47256:CDS
GGTAAAGGAAAGGAAGAATT+TGG 0.265021 6.3:+18672734 MS.gene47256:CDS
TTCCTGGTGGGTTGGGGTCA+TGG 0.306424 6.3:-18672794 None:intergenic
GCAAAGCACTTACTTGTTCA+TGG 0.314097 6.3:-18671811 None:intergenic
TTCATTGCTCAAACTCTTCC+TGG 0.317227 6.3:-18672810 None:intergenic
ACTTGTTCATGGATGCTCAT+AGG 0.370607 6.3:-18671800 None:intergenic
TCAAACTCTTCCTGGTGGGT+TGG 0.381881 6.3:-18672802 None:intergenic
AAGGAAGAATTTGGAAATAG+AGG 0.388219 6.3:+18672743 MS.gene47256:CDS
AATGTTATTGGATTAAGTAT+TGG 0.412576 6.3:+18672678 MS.gene47256:CDS
AAACTCTTCCTGGTGGGTTG+GGG 0.418091 6.3:-18672800 None:intergenic
AGTATTGGGGAAGATTCATT+TGG 0.424687 6.3:+18672693 MS.gene47256:CDS
TTGGAAATAGAGGACTATCC+AGG 0.439206 6.3:+18672753 MS.gene47256:CDS
TGGTAAAGGAGAAGAATTCA+TGG 0.444633 6.3:+18672713 MS.gene47256:CDS
TGGTTGTTTGCACCTGTCCC+TGG 0.458930 6.3:-18672771 None:intergenic
GGGGAAGATTCATTTGGTAA+AGG 0.479777 6.3:+18672699 MS.gene47256:CDS
TTGCTCAAACTCTTCCTGGT+GGG 0.496985 6.3:-18672806 None:intergenic
AGGAGAAGAATTCATGGTAA+AGG 0.517055 6.3:+18672719 MS.gene47256:CDS
CACCATGACCCCAACCCACC+AGG 0.517693 6.3:+18672792 MS.gene47256:CDS
ATTGCTCAAACTCTTCCTGG+TGG 0.548775 6.3:-18672807 None:intergenic
AAGAATTCATGGTAAAGGAA+AGG 0.554869 6.3:+18672724 MS.gene47256:CDS
ATAGAGGACTATCCAGGGAC+AGG 0.563265 6.3:+18672759 MS.gene47256:CDS
TGTTATTGGATTAAGTATTG+GGG 0.590218 6.3:+18672680 MS.gene47256:CDS
CTGGTGGGTTGGGGTCATGG+TGG 0.593468 6.3:-18672791 None:intergenic
TGGAAATAGAGGACTATCCA+GGG 0.605163 6.3:+18672754 MS.gene47256:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATTATTTAACCAAATTAA+GGG + chr6.3:18672621-18672640 MS.gene47256:intron 10.0%
!!! AATATTTTTATAAGTTCATA+TGG - chr6.3:18672535-18672554 None:intergenic 10.0%
!!! ATATTTTTATAAGTTCATAT+GGG - chr6.3:18672534-18672553 None:intergenic 10.0%
!! CTAATTATTTAACCAAATTA+AGG + chr6.3:18672620-18672639 MS.gene47256:intron 15.0%
!! AATAAAAAGTAATAAGGAGA+TGG - chr6.3:18672393-18672412 None:intergenic 20.0%
!! AATGTTATTGGATTAAGTAT+TGG + chr6.3:18672678-18672697 MS.gene47256:CDS 20.0%
!! ATGTTATTGGATTAAGTATT+GGG + chr6.3:18672679-18672698 MS.gene47256:CDS 20.0%
!! CAATATTAGGAAAATGTTAT+TGG + chr6.3:18672666-18672685 MS.gene47256:intron 20.0%
!! TGAAATTATGATTAATCATG+TGG + chr6.3:18671920-18671939 MS.gene47256:intron 20.0%
!! TTAAATTGAAGTTGACATAA+AGG + chr6.3:18672099-18672118 MS.gene47256:intron 20.0%
!!! TTATAGCTTTTCTCAATATT+AGG + chr6.3:18672653-18672672 MS.gene47256:intron 20.0%
!!! TTTTCCATTTTATTTTTTGC+AGG + chr6.3:18672440-18672459 MS.gene47256:intron 20.0%
! AACAAATTTCATGTCTTATG+AGG + chr6.3:18672136-18672155 MS.gene47256:intron 25.0%
! TCTTCCTGCAAAAAATAAAA+TGG - chr6.3:18672447-18672466 None:intergenic 25.0%
! TTAAAAGTTGACCATACAAA+TGG + chr6.3:18672019-18672038 MS.gene47256:intron 25.0%
! TTGAAATGATTCCATTTGTA+TGG - chr6.3:18672033-18672052 None:intergenic 25.0%
! TTTCTGTGTGTACAAATATA+TGG - chr6.3:18672067-18672086 None:intergenic 25.0%
!! ATTTGTATGGTCAACTTTTA+AGG - chr6.3:18672020-18672039 None:intergenic 25.0%
!! TCTTATCTACGTTTTCTTTT+TGG + chr6.3:18672221-18672240 MS.gene47256:intron 25.0%
!! TGTTATTGGATTAAGTATTG+GGG + chr6.3:18672680-18672699 MS.gene47256:CDS 25.0%
!! TTTAGTACAATCTCAAGTTT+TGG - chr6.3:18671872-18671891 None:intergenic 25.0%
AACAAGTTAGACCCTTAATT+TGG - chr6.3:18672635-18672654 None:intergenic 30.0%
AAGAATTCATGGTAAAGGAA+AGG + chr6.3:18672724-18672743 MS.gene47256:CDS 30.0%
AAGGAAGAATTTGGAAATAG+AGG + chr6.3:18672743-18672762 MS.gene47256:CDS 30.0%
AATGCAAACTTCACTAGTTA+AGG + chr6.3:18672496-18672515 MS.gene47256:intron 30.0%
TATGATTAATCATGTGGAGA+AGG + chr6.3:18671926-18671945 MS.gene47256:intron 30.0%
TTAACTAGTGAAGTTTGCAT+TGG - chr6.3:18672497-18672516 None:intergenic 30.0%
TTCTATACATACTCGTTGTT+TGG - chr6.3:18672330-18672349 None:intergenic 30.0%
!! CAAAATATAAAGCTTGCTAG+AGG - chr6.3:18672597-18672616 None:intergenic 30.0%
AAAGAATAAGAGACAGTGCA+GGG - chr6.3:18672269-18672288 None:intergenic 35.0%
AGGAGAAGAATTCATGGTAA+AGG + chr6.3:18672719-18672738 MS.gene47256:CDS 35.0%
GCACTGTCTCTTATTCTTTA+TGG + chr6.3:18672270-18672289 MS.gene47256:intron 35.0%
GGTAAAGGAAAGGAAGAATT+TGG + chr6.3:18672734-18672753 MS.gene47256:CDS 35.0%
TAAAGAATAAGAGACAGTGC+AGG - chr6.3:18672270-18672289 None:intergenic 35.0%
TGGTAAAGGAGAAGAATTCA+TGG + chr6.3:18672713-18672732 MS.gene47256:CDS 35.0%
TGTCAAAGGATGAAAAATCC+AGG + chr6.3:18672471-18672490 MS.gene47256:intron 35.0%
! AGTATTGGGGAAGATTCATT+TGG + chr6.3:18672693-18672712 MS.gene47256:CDS 35.0%
! TGCAGGAAGATTTTTGTCAA+AGG + chr6.3:18672457-18672476 MS.gene47256:intron 35.0%
GGGGAAGATTCATTTGGTAA+AGG + chr6.3:18672699-18672718 MS.gene47256:CDS 40.0%
TGGAAATAGAGGACTATCCA+GGG + chr6.3:18672754-18672773 MS.gene47256:CDS 40.0%
TTGGAAATAGAGGACTATCC+AGG + chr6.3:18672753-18672772 MS.gene47256:CDS 40.0%
! GCAAAGCACTTACTTGTTCA+TGG - chr6.3:18671814-18671833 None:intergenic 40.0%
! TAGTGAAGTTTGCATTGGCC+TGG - chr6.3:18672492-18672511 None:intergenic 45.0%
!! TATAATTATTTATTTGTATA+TGG + chr6.3:18672360-18672379 MS.gene47256:intron 5.0%
!! TTAATTAATAAAAAGTAATA+AGG - chr6.3:18672399-18672418 None:intergenic 5.0%
ATAGAGGACTATCCAGGGAC+AGG + chr6.3:18672759-18672778 MS.gene47256:CDS 50.0%
! TCAAACTCTTCCTGGTGGGT+TGG - chr6.3:18672805-18672824 None:intergenic 50.0%
!! AAACTCTTCCTGGTGGGTTG+GGG - chr6.3:18672803-18672822 None:intergenic 50.0%
!! CAAACTCTTCCTGGTGGGTT+GGG - chr6.3:18672804-18672823 None:intergenic 50.0%
TGGTTGTTTGCACCTGTCCC+TGG - chr6.3:18672774-18672793 None:intergenic 55.0%
!! TTCCTGGTGGGTTGGGGTCA+TGG - chr6.3:18672797-18672816 None:intergenic 60.0%
CACCATGACCCCAACCCACC+AGG + chr6.3:18672792-18672811 MS.gene47256:CDS 65.0%
!! CTGGTGGGTTGGGGTCATGG+TGG - chr6.3:18672794-18672813 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 18671803 18672824 18671803 ID=MS.gene47256
chr6.3 mRNA 18671803 18672824 18671803 ID=MS.gene47256.t1;Parent=MS.gene47256
chr6.3 exon 18671803 18671820 18671803 ID=MS.gene47256.t1.exon1;Parent=MS.gene47256.t1
chr6.3 CDS 18671803 18671820 18671803 ID=cds.MS.gene47256.t1;Parent=MS.gene47256.t1
chr6.3 exon 18672675 18672824 18672675 ID=MS.gene47256.t1.exon2;Parent=MS.gene47256.t1
chr6.3 CDS 18672675 18672824 18672675 ID=cds.MS.gene47256.t1;Parent=MS.gene47256.t1
Gene Sequence

>MS.gene47256

ATGAGCATCCATGAACAAGTAAGTGCTTTGCATTTGATTTTATAACTCTTCTATCTAAGCAAGAATCCAAAACTTGAGATTGTACTAAACATGCATTAATATTTTGTTAAATACAAATGAAATTATGATTAATCATGTGGAGACATGCATTAATATTTTGTTAAATACAAATGAAATTATGATTAATCATGTGGAGAAGGTACATCTAGAAAAACCTTAAAAGTTGACCATACAAATGGAATCATTTCAACAATTGAACAACCATATATTTGTACACACAGAAATTACAAAAATGTTTAAATTGAAGTTGACATAAAGGACATTTCATATACAAACAAATTTCATGTCTTATGAGGATTCTATATATGCATTGTATTCACATAGTTTCTCTTATCATCACTATATTTCTTTGCTCTTATCTTATCTACGTTTTCTTTTTGGTTCAACATGTTCAACAAATTTGCCCTGCACTGTCTCTTATTCTTTATGGTTTTCGCATGTCTTCTTCTTTCATCTTCTTCTCTCCAAACAACGAGTATGTATAGAAAATTTTTAAATATAATTATTTATTTGTATATGGAATTTGTCCATCTCCTTATTACTTTTTATTAATTAAGTTCACTAATAAACATATCTATTTTCCATTTTATTTTTTGCAGGAAGATTTTTGTCAAAGGATGAAAAATCCAGGCCAATGCAAACTTCACTAGTTAAGGTTGTAAGTATGACCCATATGAACTTATAAAAATATTTTAATTCTTGAACTCTTTAATATTCTTAATTTCAAATTTCCTCTAGCAAGCTTTATATTTTGCTTCTAATTATTTAACCAAATTAAGGGTCTAACTTGTTATAGCTTTTCTCAATATTAGGAAAATGTTATTGGATTAAGTATTGGGGAAGATTCATTTGGTAAAGGAGAAGAATTCATGGTAAAGGAAAGGAAGAATTTGGAAATAGAGGACTATCCAGGGACAGGTGCAAACAACCACCATGACCCCAACCCACCAGGAAGAGTTTGA
Protein sequence

>MS.gene47256.t1

MSIHEQENVIGLSIGEDSFGKGEEFMVKERKNLEIEDYPGTGANNHHDPNPPGRV